Multiple sequence alignment - TraesCS1A01G398600

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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 TraesCS1A01G398600 chr1A 100.000 3347 0 0 1 3347 563689144 563692490 0.000000e+00 6181.0
1 TraesCS1A01G398600 chr1A 87.636 1561 156 21 982 2520 563765300 563766845 0.000000e+00 1779.0
2 TraesCS1A01G398600 chr1A 80.868 1406 224 35 1145 2520 563783631 563785021 0.000000e+00 1064.0
3 TraesCS1A01G398600 chr1D 92.206 2271 113 33 833 3068 470080757 470082998 0.000000e+00 3155.0
4 TraesCS1A01G398600 chr1D 87.128 1546 165 19 995 2520 470124043 470125574 0.000000e+00 1722.0
5 TraesCS1A01G398600 chr1D 83.032 1550 208 34 1097 2612 470077534 470079062 0.000000e+00 1354.0
6 TraesCS1A01G398600 chr1D 81.893 1215 192 24 1102 2302 470190083 470191283 0.000000e+00 1000.0
7 TraesCS1A01G398600 chr1D 91.504 718 45 11 2 708 470079996 470080708 0.000000e+00 974.0
8 TraesCS1A01G398600 chr1D 82.911 749 118 9 1132 1878 470180537 470181277 0.000000e+00 665.0
9 TraesCS1A01G398600 chr1D 78.226 868 146 29 1682 2522 470191312 470192163 1.780000e-142 516.0
10 TraesCS1A01G398600 chr1D 93.676 253 13 3 3096 3347 470083093 470083343 3.150000e-100 375.0
11 TraesCS1A01G398600 chr1B 90.185 2435 164 51 2 2396 652462169 652464568 0.000000e+00 3103.0
12 TraesCS1A01G398600 chr1B 86.906 1558 159 24 995 2520 652485789 652487333 0.000000e+00 1705.0
13 TraesCS1A01G398600 chr1B 83.182 1540 199 35 1131 2635 652459744 652461258 0.000000e+00 1354.0
14 TraesCS1A01G398600 chr1B 79.322 1446 247 39 1101 2520 652569922 652571341 0.000000e+00 966.0
15 TraesCS1A01G398600 chr1B 82.487 788 126 11 1096 1880 652467679 652468457 0.000000e+00 680.0
16 TraesCS1A01G398600 chr1B 89.247 558 37 9 2514 3066 652464925 652465464 0.000000e+00 676.0
17 TraesCS1A01G398600 chr1B 96.296 162 4 2 2354 2515 652464607 652464766 7.120000e-67 265.0
18 TraesCS1A01G398600 chr1B 81.148 122 6 4 3096 3217 652465552 652465656 7.700000e-12 82.4
19 TraesCS1A01G398600 chr1B 93.617 47 3 0 2294 2340 652577097 652577143 1.670000e-08 71.3
20 TraesCS1A01G398600 chr1B 92.500 40 3 0 2405 2444 652464597 652464636 1.300000e-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 TraesCS1A01G398600 chr1A 563689144 563692490 3346 False 6181.0 6181 100.000000 1 3347 1 chr1A.!!$F1 3346
1 TraesCS1A01G398600 chr1A 563765300 563766845 1545 False 1779.0 1779 87.636000 982 2520 1 chr1A.!!$F2 1538
2 TraesCS1A01G398600 chr1A 563783631 563785021 1390 False 1064.0 1064 80.868000 1145 2520 1 chr1A.!!$F3 1375
3 TraesCS1A01G398600 chr1D 470124043 470125574 1531 False 1722.0 1722 87.128000 995 2520 1 chr1D.!!$F1 1525
4 TraesCS1A01G398600 chr1D 470077534 470083343 5809 False 1464.5 3155 90.104500 2 3347 4 chr1D.!!$F3 3345
5 TraesCS1A01G398600 chr1D 470190083 470192163 2080 False 758.0 1000 80.059500 1102 2522 2 chr1D.!!$F4 1420
6 TraesCS1A01G398600 chr1D 470180537 470181277 740 False 665.0 665 82.911000 1132 1878 1 chr1D.!!$F2 746
7 TraesCS1A01G398600 chr1B 652485789 652487333 1544 False 1705.0 1705 86.906000 995 2520 1 chr1B.!!$F1 1525
8 TraesCS1A01G398600 chr1B 652569922 652571341 1419 False 966.0 966 79.322000 1101 2520 1 chr1B.!!$F2 1419
9 TraesCS1A01G398600 chr1B 652459744 652468457 8713 False 888.4 3103 87.863571 2 3217 7 chr1B.!!$F4 3215

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
489 3012 0.034574 ACACCCACACACACACACAT 60.035 50.0 0.0 0.0 0.0 3.21 F
490 3013 0.381445 CACCCACACACACACACATG 59.619 55.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 4146 0.475044 TAAGGGTCGGCCAGTTTTGT 59.525 50.000 9.07 0.0 36.17 2.83 R
2464 5828 1.064017 ACTGAACACCACACCAACCAT 60.064 47.619 0.00 0.0 0.00 3.55 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
68 2578 6.249192 TCTCCATCTTCTCTCAGTCTGTTTA 58.751 40.000 0.00 0.00 0.00 2.01
72 2582 9.206690 TCCATCTTCTCTCAGTCTGTTTATTAT 57.793 33.333 0.00 0.00 0.00 1.28
161 2677 5.060427 TGGCCTTTGCATATACATAAGGT 57.940 39.130 3.32 0.00 38.08 3.50
201 2717 7.717436 TCACAAAATGTTCAGGTGATAGTTGTA 59.283 33.333 0.00 0.00 33.88 2.41
228 2744 7.422399 GCTGGTCGGCTTCAAAAATAATAATA 58.578 34.615 0.00 0.00 0.00 0.98
278 2794 4.427096 TTGAACTGCAAAAACGTCTGAA 57.573 36.364 0.00 0.00 32.46 3.02
279 2795 4.630894 TGAACTGCAAAAACGTCTGAAT 57.369 36.364 0.00 0.00 0.00 2.57
297 2813 4.086457 TGAATTTTTGGTAAGGAGGGAGC 58.914 43.478 0.00 0.00 0.00 4.70
350 2866 5.593968 ACATATTTCGTAGACGGCATAACA 58.406 37.500 1.67 0.00 40.29 2.41
357 2873 3.060363 CGTAGACGGCATAACACTTCAAC 59.940 47.826 0.00 0.00 35.37 3.18
359 2875 3.067106 AGACGGCATAACACTTCAACAG 58.933 45.455 0.00 0.00 0.00 3.16
394 2911 3.603770 CGAACATGAAAATTCGCTGGAAC 59.396 43.478 0.00 0.00 41.00 3.62
438 2961 3.256631 CCCTGGGCATATTAGAAACATGC 59.743 47.826 0.00 0.00 43.43 4.06
459 2982 9.598517 ACATGCTTTAGAATTTCTTTTGAACAA 57.401 25.926 3.86 0.00 38.30 2.83
476 2999 8.792830 TTTGAACAATTTATTTTTCACACCCA 57.207 26.923 4.09 0.00 0.00 4.51
489 3012 0.034574 ACACCCACACACACACACAT 60.035 50.000 0.00 0.00 0.00 3.21
490 3013 0.381445 CACCCACACACACACACATG 59.619 55.000 0.00 0.00 0.00 3.21
492 3015 0.662619 CCCACACACACACACATGTC 59.337 55.000 0.00 0.00 36.72 3.06
502 3028 5.633182 ACACACACACATGTCTTTTTCAAAC 59.367 36.000 0.00 0.00 36.72 2.93
511 3037 6.417635 ACATGTCTTTTTCAAACAGTATTGCG 59.582 34.615 0.00 0.00 0.00 4.85
574 3100 2.350772 CCAAGTGCCAACTGAAATCGAC 60.351 50.000 0.00 0.00 36.51 4.20
622 3149 3.489229 GCGGGAACTCATTTTCTTATGCC 60.489 47.826 0.00 0.00 0.00 4.40
627 3154 3.596214 ACTCATTTTCTTATGCCGACGT 58.404 40.909 0.00 0.00 0.00 4.34
645 3174 2.812011 ACGTGGGCTTTTATTCAGTGAC 59.188 45.455 0.00 0.00 0.00 3.67
657 3186 4.363990 AGTGACTGAGCGTGCGGG 62.364 66.667 0.00 0.00 0.00 6.13
769 3314 4.529377 ACTGATACTTTAGTTGGTTCGGGA 59.471 41.667 0.00 0.00 0.00 5.14
800 3355 0.542938 CCACTCTCCACTCCACTCCA 60.543 60.000 0.00 0.00 0.00 3.86
802 3357 0.485099 ACTCTCCACTCCACTCCACT 59.515 55.000 0.00 0.00 0.00 4.00
805 3360 1.599606 CTCCACTCCACTCCACTCCG 61.600 65.000 0.00 0.00 0.00 4.63
810 3365 4.007644 CCACTCCACTCCGCAGCA 62.008 66.667 0.00 0.00 0.00 4.41
811 3366 2.433838 CACTCCACTCCGCAGCAG 60.434 66.667 0.00 0.00 0.00 4.24
812 3367 2.919856 ACTCCACTCCGCAGCAGT 60.920 61.111 0.00 0.00 0.00 4.40
813 3368 2.125753 CTCCACTCCGCAGCAGTC 60.126 66.667 0.00 0.00 0.00 3.51
814 3369 2.917227 TCCACTCCGCAGCAGTCA 60.917 61.111 0.00 0.00 0.00 3.41
815 3370 2.740055 CCACTCCGCAGCAGTCAC 60.740 66.667 0.00 0.00 0.00 3.67
816 3371 2.029518 CACTCCGCAGCAGTCACA 59.970 61.111 0.00 0.00 0.00 3.58
817 3372 2.029666 ACTCCGCAGCAGTCACAC 59.970 61.111 0.00 0.00 0.00 3.82
818 3373 2.029518 CTCCGCAGCAGTCACACA 59.970 61.111 0.00 0.00 0.00 3.72
819 3374 2.280119 TCCGCAGCAGTCACACAC 60.280 61.111 0.00 0.00 0.00 3.82
820 3375 2.280389 CCGCAGCAGTCACACACT 60.280 61.111 0.00 0.00 34.67 3.55
821 3376 2.313172 CCGCAGCAGTCACACACTC 61.313 63.158 0.00 0.00 30.26 3.51
822 3377 2.313172 CGCAGCAGTCACACACTCC 61.313 63.158 0.00 0.00 30.26 3.85
823 3378 1.963338 GCAGCAGTCACACACTCCC 60.963 63.158 0.00 0.00 30.26 4.30
824 3379 1.302033 CAGCAGTCACACACTCCCC 60.302 63.158 0.00 0.00 30.26 4.81
825 3380 1.460305 AGCAGTCACACACTCCCCT 60.460 57.895 0.00 0.00 30.26 4.79
826 3381 1.004440 GCAGTCACACACTCCCCTC 60.004 63.158 0.00 0.00 30.26 4.30
827 3382 1.674057 CAGTCACACACTCCCCTCC 59.326 63.158 0.00 0.00 30.26 4.30
828 3383 1.121407 CAGTCACACACTCCCCTCCA 61.121 60.000 0.00 0.00 30.26 3.86
829 3384 1.122019 AGTCACACACTCCCCTCCAC 61.122 60.000 0.00 0.00 0.00 4.02
830 3385 1.122019 GTCACACACTCCCCTCCACT 61.122 60.000 0.00 0.00 0.00 4.00
831 3386 0.832135 TCACACACTCCCCTCCACTC 60.832 60.000 0.00 0.00 0.00 3.51
904 3483 4.477119 GGTACCCGCCTCCCTCCT 62.477 72.222 0.00 0.00 0.00 3.69
909 3488 2.272471 CCGCCTCCCTCCTTTTCC 59.728 66.667 0.00 0.00 0.00 3.13
946 3527 3.764466 CTCCCTTGCTCGCTCGGT 61.764 66.667 0.00 0.00 0.00 4.69
958 3539 2.440247 CTCGGTGATTTGGGCCCC 60.440 66.667 22.27 3.54 0.00 5.80
1052 3634 1.269166 CTTCCGTTCCGTGATTCTCG 58.731 55.000 1.25 1.25 0.00 4.04
1072 3654 2.034001 CGTTGGTGTTTTCTGTCTCGTC 60.034 50.000 0.00 0.00 0.00 4.20
1074 3656 1.135527 TGGTGTTTTCTGTCTCGTCGT 59.864 47.619 0.00 0.00 0.00 4.34
1086 3668 1.063616 TCTCGTCGTGATGTCGGAATC 59.936 52.381 0.00 0.00 0.00 2.52
1088 3670 0.870307 CGTCGTGATGTCGGAATCCC 60.870 60.000 0.00 0.00 0.00 3.85
1127 3718 2.001872 GTTGCTTGCTTGTTTTGCAGT 58.998 42.857 0.00 0.00 41.71 4.40
1227 3818 3.200593 GTGCTCAGCATGCTCCCG 61.201 66.667 19.68 7.28 41.91 5.14
1647 4238 1.400846 GTCCTGTGCTCGACGAATCTA 59.599 52.381 0.00 0.00 0.00 1.98
1652 4243 2.228103 TGTGCTCGACGAATCTAGTTGT 59.772 45.455 0.00 0.00 0.00 3.32
1797 4388 1.275291 CTCTACGCCCTCACCAAAGAA 59.725 52.381 0.00 0.00 0.00 2.52
1902 5151 4.341806 GGTGATCCATGGTATTCAATTGCA 59.658 41.667 12.58 0.00 0.00 4.08
1999 5248 1.095600 GATTTTCTGCCGGGTTCCTC 58.904 55.000 2.18 0.00 0.00 3.71
2147 5405 0.539051 AGGTCATTGCCCTTCTCTCG 59.461 55.000 0.00 0.00 0.00 4.04
2464 5828 5.627135 TCTATCTGACCGTGGTATGTATGA 58.373 41.667 0.00 0.00 0.00 2.15
2555 6088 5.570320 AGGTTATTCTGTTAGTTGCCATGT 58.430 37.500 0.00 0.00 0.00 3.21
2556 6089 5.415701 AGGTTATTCTGTTAGTTGCCATGTG 59.584 40.000 0.00 0.00 0.00 3.21
2558 6091 6.373216 GGTTATTCTGTTAGTTGCCATGTGTA 59.627 38.462 0.00 0.00 0.00 2.90
2559 6092 5.880054 ATTCTGTTAGTTGCCATGTGTAC 57.120 39.130 0.00 0.00 0.00 2.90
2560 6093 4.344359 TCTGTTAGTTGCCATGTGTACA 57.656 40.909 0.00 0.00 0.00 2.90
2561 6094 4.314961 TCTGTTAGTTGCCATGTGTACAG 58.685 43.478 0.00 0.00 34.55 2.74
2562 6095 4.065088 CTGTTAGTTGCCATGTGTACAGT 58.935 43.478 0.00 0.00 0.00 3.55
2563 6096 5.011227 TCTGTTAGTTGCCATGTGTACAGTA 59.989 40.000 0.00 0.00 34.78 2.74
2564 6097 5.800296 TGTTAGTTGCCATGTGTACAGTAT 58.200 37.500 0.00 0.00 0.00 2.12
2565 6098 6.234920 TGTTAGTTGCCATGTGTACAGTATT 58.765 36.000 0.00 0.00 0.00 1.89
2613 6146 9.573166 TGATGGTTACTATGCAAGCTATTAATT 57.427 29.630 0.00 0.00 0.00 1.40
2631 6164 3.660111 GCGCCGGCTTTCAACTGT 61.660 61.111 26.68 0.00 35.83 3.55
2708 6241 1.941975 GCAATAATTTGGCATGGTGGC 59.058 47.619 0.00 0.00 44.03 5.01
2716 6249 2.673523 GCATGGTGGCCTCTGACT 59.326 61.111 3.32 0.00 0.00 3.41
2717 6250 1.451028 GCATGGTGGCCTCTGACTC 60.451 63.158 3.32 0.00 0.00 3.36
2718 6251 1.908340 GCATGGTGGCCTCTGACTCT 61.908 60.000 3.32 0.00 0.00 3.24
2719 6252 0.177604 CATGGTGGCCTCTGACTCTC 59.822 60.000 3.32 0.00 0.00 3.20
2720 6253 0.042431 ATGGTGGCCTCTGACTCTCT 59.958 55.000 3.32 0.00 0.00 3.10
2721 6254 0.902048 TGGTGGCCTCTGACTCTCTG 60.902 60.000 3.32 0.00 0.00 3.35
2722 6255 0.613292 GGTGGCCTCTGACTCTCTGA 60.613 60.000 3.32 0.00 0.00 3.27
2723 6256 0.530288 GTGGCCTCTGACTCTCTGAC 59.470 60.000 3.32 0.00 0.00 3.51
2724 6257 0.613292 TGGCCTCTGACTCTCTGACC 60.613 60.000 3.32 0.00 0.00 4.02
2725 6258 1.326951 GGCCTCTGACTCTCTGACCC 61.327 65.000 0.00 0.00 0.00 4.46
2726 6259 0.613292 GCCTCTGACTCTCTGACCCA 60.613 60.000 0.00 0.00 0.00 4.51
2757 6290 3.930634 AGATTTCCTTTGTGCTCAAGC 57.069 42.857 0.98 0.00 42.50 4.01
2811 6344 5.441500 TGTGGTCTGAACACCTATTTCAAA 58.558 37.500 22.15 0.00 38.05 2.69
3085 6621 8.995027 ATTTATTTATCATGTAAGTGGGCTGA 57.005 30.769 0.00 0.00 0.00 4.26
3086 6622 8.815565 TTTATTTATCATGTAAGTGGGCTGAA 57.184 30.769 0.00 0.00 0.00 3.02
3088 6624 6.509418 TTTATCATGTAAGTGGGCTGAAAC 57.491 37.500 0.00 0.00 0.00 2.78
3089 6625 3.500448 TCATGTAAGTGGGCTGAAACA 57.500 42.857 0.00 0.00 0.00 2.83
3090 6626 4.032960 TCATGTAAGTGGGCTGAAACAT 57.967 40.909 0.00 0.00 0.00 2.71
3091 6627 5.172687 TCATGTAAGTGGGCTGAAACATA 57.827 39.130 0.00 0.00 0.00 2.29
3092 6628 5.754782 TCATGTAAGTGGGCTGAAACATAT 58.245 37.500 0.00 0.00 0.00 1.78
3093 6629 6.186957 TCATGTAAGTGGGCTGAAACATATT 58.813 36.000 0.00 0.00 0.00 1.28
3094 6630 6.663093 TCATGTAAGTGGGCTGAAACATATTT 59.337 34.615 0.00 0.00 0.00 1.40
3123 6726 1.136695 TGCAAAGTGGACTTTTGGCTG 59.863 47.619 12.95 1.54 43.07 4.85
3187 6790 9.420551 ACGGAAACAAACAGTACAAAAATAAAA 57.579 25.926 0.00 0.00 0.00 1.52
3269 7023 7.858052 GTATGCATGAAAAATGTATACTGCC 57.142 36.000 10.16 0.00 41.34 4.85
3281 7035 5.551305 TGTATACTGCCAATGAGCTACAT 57.449 39.130 4.17 0.00 41.45 2.29
3283 7037 7.061566 TGTATACTGCCAATGAGCTACATTA 57.938 36.000 4.17 0.00 46.01 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 2554 4.314522 ACAGACTGAGAGAAGATGGAGA 57.685 45.455 10.08 0.00 0.00 3.71
201 2717 0.467290 TTTTTGAAGCCGACCAGCCT 60.467 50.000 0.00 0.00 0.00 4.58
228 2744 4.706842 ACAGACCAATCACCAGTAAACT 57.293 40.909 0.00 0.00 0.00 2.66
253 2769 5.514914 TCAGACGTTTTTGCAGTTCAATTTC 59.485 36.000 0.00 0.00 34.12 2.17
278 2794 3.825908 TGCTCCCTCCTTACCAAAAAT 57.174 42.857 0.00 0.00 0.00 1.82
279 2795 3.227614 GTTGCTCCCTCCTTACCAAAAA 58.772 45.455 0.00 0.00 0.00 1.94
297 2813 8.173775 TGCATTTAAGAAACACACAAATTGTTG 58.826 29.630 0.00 1.58 37.26 3.33
450 2973 9.231297 TGGGTGTGAAAAATAAATTGTTCAAAA 57.769 25.926 9.37 0.57 43.48 2.44
451 2974 8.669243 GTGGGTGTGAAAAATAAATTGTTCAAA 58.331 29.630 9.37 2.69 43.48 2.69
459 2982 6.045955 GTGTGTGTGGGTGTGAAAAATAAAT 58.954 36.000 0.00 0.00 0.00 1.40
474 2997 1.667236 AGACATGTGTGTGTGTGTGG 58.333 50.000 1.15 0.00 39.09 4.17
476 2999 4.217334 TGAAAAAGACATGTGTGTGTGTGT 59.783 37.500 1.15 0.00 39.09 3.72
489 3012 5.885881 ACGCAATACTGTTTGAAAAAGACA 58.114 33.333 1.38 0.00 0.00 3.41
490 3013 7.901874 TTACGCAATACTGTTTGAAAAAGAC 57.098 32.000 1.38 0.00 0.00 3.01
502 3028 6.627395 TTCCCCAATATTTACGCAATACTG 57.373 37.500 0.00 0.00 29.65 2.74
574 3100 6.639632 TCTCCTTTTCAAAGAGGAACAATG 57.360 37.500 3.86 0.00 41.33 2.82
622 3149 2.073816 ACTGAATAAAAGCCCACGTCG 58.926 47.619 0.00 0.00 0.00 5.12
627 3154 4.326826 CTCAGTCACTGAATAAAAGCCCA 58.673 43.478 9.30 0.00 40.18 5.36
638 3167 2.050077 CGCACGCTCAGTCACTGA 60.050 61.111 7.44 7.44 38.25 3.41
645 3174 4.529219 TATGGCCCGCACGCTCAG 62.529 66.667 0.00 0.00 0.00 3.35
697 3232 3.705051 AGGGTAAGTATCAGTCCAACGA 58.295 45.455 0.00 0.00 0.00 3.85
741 3286 6.128634 CGAACCAACTAAAGTATCAGTCCAAC 60.129 42.308 0.00 0.00 0.00 3.77
755 3300 0.766131 TGGCTTCCCGAACCAACTAA 59.234 50.000 0.00 0.00 0.00 2.24
756 3301 0.035739 GTGGCTTCCCGAACCAACTA 59.964 55.000 0.00 0.00 34.63 2.24
757 3302 1.228154 GTGGCTTCCCGAACCAACT 60.228 57.895 0.00 0.00 34.63 3.16
758 3303 1.527380 TGTGGCTTCCCGAACCAAC 60.527 57.895 0.00 0.00 34.63 3.77
759 3304 1.527380 GTGTGGCTTCCCGAACCAA 60.527 57.895 0.00 0.00 34.63 3.67
760 3305 2.112297 GTGTGGCTTCCCGAACCA 59.888 61.111 0.00 0.00 0.00 3.67
769 3314 0.394565 GAGAGTGGAGTGTGTGGCTT 59.605 55.000 0.00 0.00 0.00 4.35
800 3355 2.029666 GTGTGACTGCTGCGGAGT 59.970 61.111 16.72 3.54 0.00 3.85
802 3357 2.280119 GTGTGTGACTGCTGCGGA 60.280 61.111 16.72 0.00 0.00 5.54
805 3360 1.963338 GGGAGTGTGTGACTGCTGC 60.963 63.158 0.00 0.00 42.57 5.25
810 3365 1.122019 GTGGAGGGGAGTGTGTGACT 61.122 60.000 0.00 0.00 37.76 3.41
811 3366 1.122019 AGTGGAGGGGAGTGTGTGAC 61.122 60.000 0.00 0.00 0.00 3.67
812 3367 0.832135 GAGTGGAGGGGAGTGTGTGA 60.832 60.000 0.00 0.00 0.00 3.58
813 3368 1.674057 GAGTGGAGGGGAGTGTGTG 59.326 63.158 0.00 0.00 0.00 3.82
814 3369 1.536662 GGAGTGGAGGGGAGTGTGT 60.537 63.158 0.00 0.00 0.00 3.72
815 3370 1.536418 TGGAGTGGAGGGGAGTGTG 60.536 63.158 0.00 0.00 0.00 3.82
816 3371 1.536662 GTGGAGTGGAGGGGAGTGT 60.537 63.158 0.00 0.00 0.00 3.55
817 3372 1.229336 AGTGGAGTGGAGGGGAGTG 60.229 63.158 0.00 0.00 0.00 3.51
818 3373 1.079438 GAGTGGAGTGGAGGGGAGT 59.921 63.158 0.00 0.00 0.00 3.85
819 3374 1.687493 GGAGTGGAGTGGAGGGGAG 60.687 68.421 0.00 0.00 0.00 4.30
820 3375 2.450243 GGAGTGGAGTGGAGGGGA 59.550 66.667 0.00 0.00 0.00 4.81
821 3376 2.122729 TGGAGTGGAGTGGAGGGG 59.877 66.667 0.00 0.00 0.00 4.79
822 3377 1.536418 TGTGGAGTGGAGTGGAGGG 60.536 63.158 0.00 0.00 0.00 4.30
823 3378 0.833834 AGTGTGGAGTGGAGTGGAGG 60.834 60.000 0.00 0.00 0.00 4.30
824 3379 0.605589 GAGTGTGGAGTGGAGTGGAG 59.394 60.000 0.00 0.00 0.00 3.86
825 3380 0.832135 GGAGTGTGGAGTGGAGTGGA 60.832 60.000 0.00 0.00 0.00 4.02
826 3381 1.121407 TGGAGTGTGGAGTGGAGTGG 61.121 60.000 0.00 0.00 0.00 4.00
827 3382 0.319728 CTGGAGTGTGGAGTGGAGTG 59.680 60.000 0.00 0.00 0.00 3.51
828 3383 1.476007 GCTGGAGTGTGGAGTGGAGT 61.476 60.000 0.00 0.00 0.00 3.85
829 3384 1.190833 AGCTGGAGTGTGGAGTGGAG 61.191 60.000 0.00 0.00 0.00 3.86
830 3385 1.152247 AGCTGGAGTGTGGAGTGGA 60.152 57.895 0.00 0.00 0.00 4.02
831 3386 1.294780 GAGCTGGAGTGTGGAGTGG 59.705 63.158 0.00 0.00 0.00 4.00
889 3449 1.229723 AAAAGGAGGGAGGCGGGTA 60.230 57.895 0.00 0.00 0.00 3.69
965 3546 2.954868 CGGAAGCGACGGGATTCG 60.955 66.667 0.00 0.00 41.96 3.34
988 3569 1.083806 TCGAACATCTGGCGTGCATC 61.084 55.000 0.00 0.00 0.00 3.91
1052 3634 2.034001 CGACGAGACAGAAAACACCAAC 60.034 50.000 0.00 0.00 0.00 3.77
1127 3718 3.247056 TTCTCCGCCGCCATCAACA 62.247 57.895 0.00 0.00 0.00 3.33
1555 4146 0.475044 TAAGGGTCGGCCAGTTTTGT 59.525 50.000 9.07 0.00 36.17 2.83
1647 4238 2.113139 CCGACCAGGGCAACAACT 59.887 61.111 0.00 0.00 39.74 3.16
1797 4388 3.199946 TGTTCACCACAAGAAGGTTCTCT 59.800 43.478 0.00 0.00 37.23 3.10
1902 5151 2.420022 GAGCATAGCGTTGTTGGTGAAT 59.580 45.455 0.00 0.00 0.00 2.57
1999 5248 1.915614 GCAACAGCTCCACCGTCATG 61.916 60.000 0.00 0.00 0.00 3.07
2147 5405 3.485745 CACCCGGGACCCCATACC 61.486 72.222 32.02 0.00 35.37 2.73
2464 5828 1.064017 ACTGAACACCACACCAACCAT 60.064 47.619 0.00 0.00 0.00 3.55
2528 6059 6.775708 TGGCAACTAACAGAATAACCTAGTT 58.224 36.000 0.00 0.00 34.03 2.24
2589 6122 8.299570 GCAATTAATAGCTTGCATAGTAACCAT 58.700 33.333 6.63 0.00 45.50 3.55
2607 6140 0.814457 TGAAAGCCGGCGCAATTAAT 59.186 45.000 23.20 0.00 37.52 1.40
2613 6146 3.659092 CAGTTGAAAGCCGGCGCA 61.659 61.111 23.20 18.06 37.52 6.09
2615 6148 0.110373 GTAACAGTTGAAAGCCGGCG 60.110 55.000 23.20 6.46 0.00 6.46
2682 6215 6.318144 CCACCATGCCAAATTATTGCAAAATA 59.682 34.615 1.71 0.00 35.10 1.40
2688 6221 1.941975 GCCACCATGCCAAATTATTGC 59.058 47.619 0.00 0.00 35.10 3.56
2708 6241 1.181786 GTGGGTCAGAGAGTCAGAGG 58.818 60.000 0.00 0.00 0.00 3.69
2725 6258 6.147821 CACAAAGGAAATCTACCACTACAGTG 59.852 42.308 2.23 2.23 45.23 3.66
2726 6259 6.231211 CACAAAGGAAATCTACCACTACAGT 58.769 40.000 0.00 0.00 0.00 3.55
2757 6290 1.142465 AGGCCCATCACAAGATAGCTG 59.858 52.381 0.00 0.00 34.67 4.24
2760 6293 2.947652 CACAAGGCCCATCACAAGATAG 59.052 50.000 0.00 0.00 31.88 2.08
2811 6344 2.494073 TGTCCCGTGCTTGAAAAAGTTT 59.506 40.909 0.00 0.00 0.00 2.66
2996 6532 9.638239 TCATAAAATTTCCAGAAAAGATTTCGG 57.362 29.630 0.00 7.12 33.56 4.30
3068 6604 4.032960 TGTTTCAGCCCACTTACATGAT 57.967 40.909 0.00 0.00 0.00 2.45
3070 6606 6.455360 AATATGTTTCAGCCCACTTACATG 57.545 37.500 0.00 0.00 0.00 3.21
3071 6607 8.766994 ATAAATATGTTTCAGCCCACTTACAT 57.233 30.769 0.00 0.00 0.00 2.29
3072 6608 8.588290 AATAAATATGTTTCAGCCCACTTACA 57.412 30.769 0.00 0.00 0.00 2.41
3073 6609 8.135529 GGAATAAATATGTTTCAGCCCACTTAC 58.864 37.037 0.00 0.00 0.00 2.34
3074 6610 8.058847 AGGAATAAATATGTTTCAGCCCACTTA 58.941 33.333 0.00 0.00 0.00 2.24
3076 6612 6.435164 AGGAATAAATATGTTTCAGCCCACT 58.565 36.000 0.00 0.00 0.00 4.00
3077 6613 6.715347 AGGAATAAATATGTTTCAGCCCAC 57.285 37.500 0.00 0.00 0.00 4.61
3078 6614 8.859090 CATTAGGAATAAATATGTTTCAGCCCA 58.141 33.333 0.00 0.00 0.00 5.36
3079 6615 7.814587 GCATTAGGAATAAATATGTTTCAGCCC 59.185 37.037 0.00 0.00 0.00 5.19
3080 6616 8.359642 TGCATTAGGAATAAATATGTTTCAGCC 58.640 33.333 0.00 0.00 0.00 4.85
3081 6617 9.748708 TTGCATTAGGAATAAATATGTTTCAGC 57.251 29.630 0.00 0.00 0.00 4.26
3088 6624 9.683069 GTCCACTTTGCATTAGGAATAAATATG 57.317 33.333 0.00 0.00 0.00 1.78
3089 6625 9.646522 AGTCCACTTTGCATTAGGAATAAATAT 57.353 29.630 0.00 0.00 0.00 1.28
3090 6626 9.474313 AAGTCCACTTTGCATTAGGAATAAATA 57.526 29.630 0.00 0.00 30.82 1.40
3091 6627 7.961326 AGTCCACTTTGCATTAGGAATAAAT 57.039 32.000 0.00 0.00 0.00 1.40
3092 6628 7.775053 AAGTCCACTTTGCATTAGGAATAAA 57.225 32.000 0.00 0.00 30.82 1.40
3093 6629 7.775053 AAAGTCCACTTTGCATTAGGAATAA 57.225 32.000 3.84 0.00 43.87 1.40
3094 6630 7.309744 CCAAAAGTCCACTTTGCATTAGGAATA 60.310 37.037 5.46 0.00 44.69 1.75
3187 6790 4.774726 ACTGGTACATGACTCACTCTCATT 59.225 41.667 0.00 0.00 38.20 2.57


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

AutoCloner maintained by Alex Coulton.