Multiple sequence alignment - TraesCS6D01G298900

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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 TraesCS6D01G298900 chr6D 100.000 3092 0 0 1 3092 409523831 409526922 0.000000e+00 5710.0
1 TraesCS6D01G298900 chr6B 94.596 2998 148 12 1 2995 615255344 615258330 0.000000e+00 4626.0
2 TraesCS6D01G298900 chr6B 94.285 2432 126 7 1 2430 615181430 615183850 0.000000e+00 3709.0
3 TraesCS6D01G298900 chr6B 86.483 2752 315 36 272 2978 615365766 615368505 0.000000e+00 2968.0
4 TraesCS6D01G298900 chr6B 91.328 542 35 7 2428 2959 615184233 615184772 0.000000e+00 730.0
5 TraesCS6D01G298900 chr3A 81.765 170 26 5 2685 2851 669963983 669964150 1.500000e-28 137.0
6 TraesCS6D01G298900 chr3A 81.765 170 26 5 2685 2851 669991760 669991593 1.500000e-28 137.0
7 TraesCS6D01G298900 chr3D 79.429 175 26 8 2685 2851 534682539 534682367 7.010000e-22 115.0
8 TraesCS6D01G298900 chr7B 79.290 169 30 4 2685 2851 149341657 149341492 2.520000e-21 113.0
9 TraesCS6D01G298900 chrUn 78.788 132 25 3 2685 2814 65135201 65135331 5.490000e-13 86.1
10 TraesCS6D01G298900 chr5D 89.091 55 6 0 2685 2739 553766696 553766750 5.530000e-08 69.4


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 TraesCS6D01G298900 chr6D 409523831 409526922 3091 False 5710.0 5710 100.0000 1 3092 1 chr6D.!!$F1 3091
1 TraesCS6D01G298900 chr6B 615255344 615258330 2986 False 4626.0 4626 94.5960 1 2995 1 chr6B.!!$F1 2994
2 TraesCS6D01G298900 chr6B 615365766 615368505 2739 False 2968.0 2968 86.4830 272 2978 1 chr6B.!!$F2 2706
3 TraesCS6D01G298900 chr6B 615181430 615184772 3342 False 2219.5 3709 92.8065 1 2959 2 chr6B.!!$F3 2958

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
438 439 0.178981 ACACCTTGCTGCCACTCAAT 60.179 50.0 0.0 0.0 0.00 2.57 F
1362 1367 0.692756 TATGGGAGCCATTCACGGGA 60.693 55.0 0.0 0.0 42.23 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1383 1.056125 TGATGGATGATCCCGGCTGT 61.056 55.0 9.36 0.0 35.03 4.40 R
3066 3509 0.385390 CCCTTGCACTTTGGTGTCAC 59.615 55.0 0.00 0.0 44.65 3.67 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
121 122 3.636231 CGACCCCTGGTGGAAGCA 61.636 66.667 8.04 0.00 45.41 3.91
188 189 5.923204 TCTCAGCTTGTCTTCTTTCTCTTT 58.077 37.500 0.00 0.00 0.00 2.52
264 265 0.688487 CCCCAAACCGTTCTCTGGTA 59.312 55.000 0.84 0.00 39.29 3.25
307 308 4.645588 CCTCTAACCCGTTGACTTCTCTAT 59.354 45.833 0.00 0.00 0.00 1.98
312 313 3.896272 ACCCGTTGACTTCTCTATATCCC 59.104 47.826 0.00 0.00 0.00 3.85
371 372 1.406614 GCTGAGAATCACCTCCACCAG 60.407 57.143 0.00 0.00 42.56 4.00
394 395 0.462047 CGTTGTATCCACCCAGGCTC 60.462 60.000 0.00 0.00 37.29 4.70
419 420 3.325870 CTCGGTCTTATCAGCAACACAA 58.674 45.455 0.00 0.00 0.00 3.33
421 422 2.805671 CGGTCTTATCAGCAACACAACA 59.194 45.455 0.00 0.00 0.00 3.33
437 438 0.395586 AACACCTTGCTGCCACTCAA 60.396 50.000 0.00 0.00 0.00 3.02
438 439 0.178981 ACACCTTGCTGCCACTCAAT 60.179 50.000 0.00 0.00 0.00 2.57
473 474 2.964209 TCCGCCTTGGATCTATCTCTT 58.036 47.619 0.00 0.00 43.74 2.85
685 688 5.354767 TGTTGTATGCAAAATTTGTGCTCA 58.645 33.333 12.62 6.79 42.69 4.26
692 695 9.299963 GTATGCAAAATTTGTGCTCACATATAA 57.700 29.630 12.62 0.00 42.69 0.98
714 717 4.847198 ACATCATCAAACACCAGCTATCA 58.153 39.130 0.00 0.00 0.00 2.15
765 768 5.616270 TGCTAGGTTTCGAATATGCCATAA 58.384 37.500 0.00 0.00 0.00 1.90
817 821 6.203338 ACTCAATTTTTCATGATTTGGTGCAC 59.797 34.615 8.80 8.80 0.00 4.57
1050 1054 8.462016 GCTGATATTATTTGTGATATTGGGGAC 58.538 37.037 0.00 0.00 0.00 4.46
1069 1073 6.011981 TGGGGACAGTCTTTTGGATAGTAATT 60.012 38.462 0.00 0.00 35.01 1.40
1080 1084 5.372343 TGGATAGTAATTGCCATGACAGT 57.628 39.130 0.00 0.00 0.00 3.55
1147 1151 7.919621 CCATCTCATCTTATCAAAGGCTTTTTC 59.080 37.037 10.36 0.00 33.22 2.29
1192 1196 6.314648 TGTTCTTGAGGAGATCAATGAATTCG 59.685 38.462 0.04 0.00 46.71 3.34
1218 1222 3.620427 TGCACTGTACATCGGGTATTT 57.380 42.857 0.00 0.00 33.76 1.40
1236 1240 7.320399 GGGTATTTGTTAATCTTTCAACTGGG 58.680 38.462 0.00 0.00 0.00 4.45
1362 1367 0.692756 TATGGGAGCCATTCACGGGA 60.693 55.000 0.00 0.00 42.23 5.14
1378 1383 5.432645 TCACGGGATATCTTGTGCAATTTA 58.567 37.500 17.62 3.23 32.48 1.40
1619 1624 2.640826 AGTTGTTCAAGATAACCGGGGA 59.359 45.455 6.32 0.00 0.00 4.81
1650 1655 6.834107 TGAGATGCATGGAGAATTCATTCTA 58.166 36.000 2.46 0.00 46.47 2.10
1729 1734 5.192522 TCTGGAGGAGGCAATCTTCTTATTT 59.807 40.000 1.25 0.00 34.50 1.40
1846 1853 7.549147 TTCCTTAGTAACACAAGGTGTATCT 57.451 36.000 2.00 6.94 46.79 1.98
1862 1869 5.006746 GGTGTATCTCTGTTAATGCCGAAAG 59.993 44.000 0.00 0.00 0.00 2.62
1884 1891 5.449553 AGTTTCCCAACTGTCAGAGAAAAT 58.550 37.500 6.91 6.68 42.05 1.82
1931 1938 3.412386 GATATAGTGGGCCATGTGGAAC 58.588 50.000 10.70 0.00 37.39 3.62
2034 2041 0.457443 GAAGGCCCTTAAGCATGTGC 59.543 55.000 0.00 0.00 42.49 4.57
2036 2043 2.426406 GGCCCTTAAGCATGTGCCC 61.426 63.158 0.57 0.00 43.38 5.36
2164 2171 6.586463 GGGCAACTTTCTTTTTACTTATCTGC 59.414 38.462 0.00 0.00 0.00 4.26
2307 2314 7.944729 AACTCATGCTTTTGGTACATAGATT 57.055 32.000 0.00 0.00 39.30 2.40
2370 2407 8.417106 AGATAAGTTGACAGTACATACCTCATG 58.583 37.037 0.00 0.00 40.78 3.07
2397 2434 8.557450 ACAACCATTCTGGACCTTACTATTAAT 58.443 33.333 0.00 0.00 40.96 1.40
2510 2942 7.839200 AGTATATGGTTTCTATTTGGCAAAGGT 59.161 33.333 18.61 5.06 0.00 3.50
2517 2949 0.105246 ATTTGGCAAAGGTGGTGGGA 60.105 50.000 18.61 0.00 0.00 4.37
2520 2952 1.045911 TGGCAAAGGTGGTGGGAAAC 61.046 55.000 0.00 0.00 0.00 2.78
2752 3194 1.072648 CAACCCTGAACCCCGAAACTA 59.927 52.381 0.00 0.00 0.00 2.24
2766 3208 3.302870 CCGAAACTAGTCAAAACACACCG 60.303 47.826 0.00 0.00 0.00 4.94
2861 3304 7.936584 TCAATGTTGACTGGGTAGTTAAAAAG 58.063 34.615 0.00 0.00 37.25 2.27
2862 3305 6.894339 ATGTTGACTGGGTAGTTAAAAAGG 57.106 37.500 0.00 0.00 37.25 3.11
2863 3306 5.757988 TGTTGACTGGGTAGTTAAAAAGGT 58.242 37.500 0.00 0.00 37.25 3.50
2865 3308 5.633655 TGACTGGGTAGTTAAAAAGGTGA 57.366 39.130 0.00 0.00 37.25 4.02
2962 3405 4.811908 TCGAATGAAACTCATACCACGAA 58.188 39.130 0.00 0.00 35.76 3.85
2990 3433 7.923888 TCGTATTGTACATCTACTAACTCACC 58.076 38.462 0.00 0.00 0.00 4.02
2995 3438 4.473477 ACATCTACTAACTCACCAAGCC 57.527 45.455 0.00 0.00 0.00 4.35
2996 3439 3.838317 ACATCTACTAACTCACCAAGCCA 59.162 43.478 0.00 0.00 0.00 4.75
2997 3440 4.286032 ACATCTACTAACTCACCAAGCCAA 59.714 41.667 0.00 0.00 0.00 4.52
2998 3441 5.045578 ACATCTACTAACTCACCAAGCCAAT 60.046 40.000 0.00 0.00 0.00 3.16
2999 3442 4.832248 TCTACTAACTCACCAAGCCAATG 58.168 43.478 0.00 0.00 0.00 2.82
3000 3443 2.795329 ACTAACTCACCAAGCCAATGG 58.205 47.619 0.00 0.00 46.38 3.16
3015 3458 4.831107 GCCAATGGCTAAATTCTTTTGGA 58.169 39.130 18.47 0.00 46.69 3.53
3016 3459 4.872124 GCCAATGGCTAAATTCTTTTGGAG 59.128 41.667 18.47 0.00 46.69 3.86
3017 3460 5.569428 GCCAATGGCTAAATTCTTTTGGAGT 60.569 40.000 18.47 0.00 46.69 3.85
3018 3461 6.350949 GCCAATGGCTAAATTCTTTTGGAGTA 60.351 38.462 18.47 0.00 46.69 2.59
3019 3462 7.260603 CCAATGGCTAAATTCTTTTGGAGTAG 58.739 38.462 0.00 0.00 0.00 2.57
3020 3463 7.093771 CCAATGGCTAAATTCTTTTGGAGTAGT 60.094 37.037 0.00 0.00 0.00 2.73
3021 3464 8.306761 CAATGGCTAAATTCTTTTGGAGTAGTT 58.693 33.333 0.00 0.00 0.00 2.24
3022 3465 9.528489 AATGGCTAAATTCTTTTGGAGTAGTTA 57.472 29.630 0.00 0.00 0.00 2.24
3023 3466 9.700831 ATGGCTAAATTCTTTTGGAGTAGTTAT 57.299 29.630 0.00 0.00 0.00 1.89
3024 3467 9.174166 TGGCTAAATTCTTTTGGAGTAGTTATC 57.826 33.333 0.00 0.00 0.00 1.75
3025 3468 9.397280 GGCTAAATTCTTTTGGAGTAGTTATCT 57.603 33.333 0.00 0.00 0.00 1.98
3030 3473 9.793259 AATTCTTTTGGAGTAGTTATCTTGACA 57.207 29.630 0.00 0.00 0.00 3.58
3031 3474 9.793259 ATTCTTTTGGAGTAGTTATCTTGACAA 57.207 29.630 0.00 0.00 0.00 3.18
3032 3475 8.833231 TCTTTTGGAGTAGTTATCTTGACAAG 57.167 34.615 9.03 9.03 0.00 3.16
3033 3476 8.647796 TCTTTTGGAGTAGTTATCTTGACAAGA 58.352 33.333 19.85 19.85 42.69 3.02
3034 3477 9.273016 CTTTTGGAGTAGTTATCTTGACAAGAA 57.727 33.333 21.29 8.65 41.63 2.52
3035 3478 8.833231 TTTGGAGTAGTTATCTTGACAAGAAG 57.167 34.615 21.29 0.00 41.63 2.85
3036 3479 6.936279 TGGAGTAGTTATCTTGACAAGAAGG 58.064 40.000 21.29 0.00 41.63 3.46
3037 3480 5.813157 GGAGTAGTTATCTTGACAAGAAGGC 59.187 44.000 21.29 13.39 41.63 4.35
3038 3481 6.360370 AGTAGTTATCTTGACAAGAAGGCA 57.640 37.500 21.29 5.22 41.63 4.75
3039 3482 6.769512 AGTAGTTATCTTGACAAGAAGGCAA 58.230 36.000 21.29 10.48 44.95 4.52
3040 3483 7.398024 AGTAGTTATCTTGACAAGAAGGCAAT 58.602 34.615 21.29 6.94 46.24 3.56
3041 3484 6.506500 AGTTATCTTGACAAGAAGGCAATG 57.493 37.500 21.29 0.00 46.24 2.82
3042 3485 3.863142 ATCTTGACAAGAAGGCAATGC 57.137 42.857 21.29 0.00 46.24 3.56
3043 3486 2.585330 TCTTGACAAGAAGGCAATGCA 58.415 42.857 15.58 0.00 46.24 3.96
3044 3487 3.159472 TCTTGACAAGAAGGCAATGCAT 58.841 40.909 15.58 0.00 46.24 3.96
3045 3488 3.575256 TCTTGACAAGAAGGCAATGCATT 59.425 39.130 15.58 4.30 46.24 3.56
3046 3489 4.766373 TCTTGACAAGAAGGCAATGCATTA 59.234 37.500 15.58 0.00 46.24 1.90
3047 3490 4.707030 TGACAAGAAGGCAATGCATTAG 57.293 40.909 12.53 7.98 31.02 1.73
3048 3491 3.444742 TGACAAGAAGGCAATGCATTAGG 59.555 43.478 12.53 1.62 31.02 2.69
3049 3492 3.434309 ACAAGAAGGCAATGCATTAGGT 58.566 40.909 12.53 1.27 31.02 3.08
3050 3493 3.445096 ACAAGAAGGCAATGCATTAGGTC 59.555 43.478 12.53 2.05 31.02 3.85
3051 3494 3.659183 AGAAGGCAATGCATTAGGTCT 57.341 42.857 12.53 4.72 31.02 3.85
3052 3495 3.549794 AGAAGGCAATGCATTAGGTCTC 58.450 45.455 12.53 5.70 31.02 3.36
3053 3496 3.201708 AGAAGGCAATGCATTAGGTCTCT 59.798 43.478 12.53 7.85 31.02 3.10
3054 3497 3.659183 AGGCAATGCATTAGGTCTCTT 57.341 42.857 12.53 0.00 0.00 2.85
3055 3498 3.285484 AGGCAATGCATTAGGTCTCTTG 58.715 45.455 12.53 0.00 0.00 3.02
3056 3499 2.360165 GGCAATGCATTAGGTCTCTTGG 59.640 50.000 12.53 0.00 0.00 3.61
3057 3500 2.360165 GCAATGCATTAGGTCTCTTGGG 59.640 50.000 12.53 0.00 0.00 4.12
3058 3501 3.889815 CAATGCATTAGGTCTCTTGGGA 58.110 45.455 12.53 0.00 0.00 4.37
3059 3502 4.467769 CAATGCATTAGGTCTCTTGGGAT 58.532 43.478 12.53 0.00 0.00 3.85
3060 3503 5.624159 CAATGCATTAGGTCTCTTGGGATA 58.376 41.667 12.53 0.00 0.00 2.59
3061 3504 5.912149 ATGCATTAGGTCTCTTGGGATAA 57.088 39.130 0.00 0.00 0.00 1.75
3062 3505 5.036117 TGCATTAGGTCTCTTGGGATAAC 57.964 43.478 0.00 0.00 0.00 1.89
3063 3506 4.141482 TGCATTAGGTCTCTTGGGATAACC 60.141 45.833 0.00 0.00 40.81 2.85
3064 3507 4.103311 GCATTAGGTCTCTTGGGATAACCT 59.897 45.833 0.00 0.00 39.39 3.50
3065 3508 5.307196 GCATTAGGTCTCTTGGGATAACCTA 59.693 44.000 0.00 0.00 38.06 3.08
3066 3509 6.519213 GCATTAGGTCTCTTGGGATAACCTAG 60.519 46.154 0.00 0.00 42.62 3.02
3067 3510 4.628661 AGGTCTCTTGGGATAACCTAGT 57.371 45.455 0.00 0.00 42.02 2.57
3068 3511 4.290942 AGGTCTCTTGGGATAACCTAGTG 58.709 47.826 0.00 0.00 42.02 2.74
3069 3512 4.016479 AGGTCTCTTGGGATAACCTAGTGA 60.016 45.833 0.00 0.00 42.02 3.41
3071 3514 4.942944 TCTCTTGGGATAACCTAGTGACA 58.057 43.478 0.00 0.00 42.02 3.58
3072 3515 4.710375 TCTCTTGGGATAACCTAGTGACAC 59.290 45.833 0.00 0.00 42.02 3.67
3073 3516 3.773119 TCTTGGGATAACCTAGTGACACC 59.227 47.826 0.84 0.00 42.02 4.16
3074 3517 3.193395 TGGGATAACCTAGTGACACCA 57.807 47.619 0.84 0.00 41.11 4.17
3075 3518 3.522759 TGGGATAACCTAGTGACACCAA 58.477 45.455 0.84 0.00 41.11 3.67
3076 3519 3.911260 TGGGATAACCTAGTGACACCAAA 59.089 43.478 0.84 0.00 41.11 3.28
3077 3520 4.019681 TGGGATAACCTAGTGACACCAAAG 60.020 45.833 0.84 0.00 41.11 2.77
3078 3521 4.019591 GGGATAACCTAGTGACACCAAAGT 60.020 45.833 0.84 0.00 35.85 2.66
3079 3522 6.087632 GGGATAACCTAGTGACACCAAAGTG 61.088 48.000 0.84 0.00 42.56 3.16
3087 3530 3.458653 CACCAAAGTGCAAGGGGG 58.541 61.111 0.00 0.00 37.14 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.168496 AGAGCGCTACTAAGGTCACAA 58.832 47.619 11.50 0.00 37.34 3.33
188 189 0.756294 TGTCAGCGTTGGAGGAAGAA 59.244 50.000 0.00 0.00 0.00 2.52
214 215 0.109723 GTGAGGTGCACCCTACCAAA 59.890 55.000 32.29 7.41 46.51 3.28
307 308 2.771943 GGGATCGGATGCTAATGGGATA 59.228 50.000 9.42 0.00 0.00 2.59
312 313 2.146342 GTGTGGGATCGGATGCTAATG 58.854 52.381 9.42 0.00 0.00 1.90
361 362 1.125633 ACAACGTTACTGGTGGAGGT 58.874 50.000 0.00 0.00 0.00 3.85
394 395 0.461548 TGCTGATAAGACCGAGCTGG 59.538 55.000 0.00 0.00 46.41 4.85
419 420 0.178981 ATTGAGTGGCAGCAAGGTGT 60.179 50.000 8.44 0.00 0.00 4.16
421 422 2.814805 ATATTGAGTGGCAGCAAGGT 57.185 45.000 8.44 0.00 0.00 3.50
437 438 2.638363 GGCGGAGAAGGGGAAACTATAT 59.362 50.000 0.00 0.00 0.00 0.86
438 439 2.044758 GGCGGAGAAGGGGAAACTATA 58.955 52.381 0.00 0.00 0.00 1.31
473 474 9.442047 GTCATTCAATTTAAGGAGAGAAGAAGA 57.558 33.333 0.00 0.00 0.00 2.87
685 688 6.830324 AGCTGGTGTTTGATGATGTTATATGT 59.170 34.615 0.00 0.00 0.00 2.29
692 695 4.847198 TGATAGCTGGTGTTTGATGATGT 58.153 39.130 0.00 0.00 0.00 3.06
714 717 5.181748 GCATCATGGAGAACTAAACTCACT 58.818 41.667 0.00 0.00 36.26 3.41
817 821 7.494625 ACAGAAATGTATCCACAACCTATAACG 59.505 37.037 0.00 0.00 38.42 3.18
908 912 5.424757 TGGTACATTCTAAGTACATGCACC 58.575 41.667 5.84 5.84 42.73 5.01
1050 1054 6.757897 TGGCAATTACTATCCAAAAGACTG 57.242 37.500 0.00 0.00 0.00 3.51
1080 1084 9.788960 GAACATACATATCTCATAGCGACATAA 57.211 33.333 0.00 0.00 0.00 1.90
1115 1119 5.883685 TTGATAAGATGAGATGGCTGACT 57.116 39.130 0.00 0.00 0.00 3.41
1192 1196 1.665679 CCGATGTACAGTGCAATCACC 59.334 52.381 0.33 0.00 44.16 4.02
1218 1222 2.817258 CCGCCCAGTTGAAAGATTAACA 59.183 45.455 0.00 0.00 0.00 2.41
1236 1240 3.554692 CGACGCTTGACCATCCGC 61.555 66.667 0.00 0.00 0.00 5.54
1362 1367 4.036734 CCGGCTGTAAATTGCACAAGATAT 59.963 41.667 0.00 0.00 0.00 1.63
1378 1383 1.056125 TGATGGATGATCCCGGCTGT 61.056 55.000 9.36 0.00 35.03 4.40
1650 1655 2.293318 TGCTGGAGCCTCGTGGATT 61.293 57.895 7.92 0.00 41.18 3.01
1729 1734 1.546923 CTCTGCAATGCCAATGACCAA 59.453 47.619 1.53 0.00 0.00 3.67
1846 1853 3.504520 GGGAAACTTTCGGCATTAACAGA 59.495 43.478 0.00 0.00 0.00 3.41
1862 1869 5.774498 ATTTTCTCTGACAGTTGGGAAAC 57.226 39.130 1.59 0.00 0.00 2.78
1884 1891 6.204108 CAGAGATGCATGCTTGATATACACAA 59.796 38.462 20.33 0.00 0.00 3.33
1931 1938 5.065731 GGCCTCATCAAACTGAACTCATAAG 59.934 44.000 0.00 0.00 0.00 1.73
1949 1956 1.945354 CTTACGCTTCCGAGGCCTCA 61.945 60.000 31.67 11.42 38.29 3.86
2034 2041 3.294214 ACAGTAGTGTATAAGGACCGGG 58.706 50.000 6.32 0.00 34.05 5.73
2036 2043 8.192774 TGAATAAACAGTAGTGTATAAGGACCG 58.807 37.037 3.00 0.00 35.08 4.79
2164 2171 3.032017 ACATGTTCACTTCACTCCTCG 57.968 47.619 0.00 0.00 0.00 4.63
2307 2314 6.262944 GCCATACAGTCATCATTAAATGGTCA 59.737 38.462 0.00 0.00 35.99 4.02
2485 2917 7.920682 CACCTTTGCCAAATAGAAACCATATAC 59.079 37.037 0.00 0.00 0.00 1.47
2510 2942 2.164624 CGAAAAACAGTGTTTCCCACCA 59.835 45.455 21.10 0.00 45.74 4.17
2517 2949 7.586747 TGAAAAGAGTACGAAAAACAGTGTTT 58.413 30.769 15.58 15.58 0.00 2.83
2520 2952 7.000575 TCTGAAAAGAGTACGAAAAACAGTG 57.999 36.000 0.00 0.00 0.00 3.66
2683 3117 4.537015 GGTTGAAATGTGGACTTTTCTCG 58.463 43.478 15.31 0.00 39.39 4.04
2752 3194 2.413310 AGTTCCGGTGTGTTTTGACT 57.587 45.000 0.00 0.00 0.00 3.41
2766 3208 5.932883 AGTTTTGAATCTCGAGGTTAGTTCC 59.067 40.000 11.76 0.00 0.00 3.62
2857 3300 9.045223 GCTTTGTTGAGATTAATTTCACCTTTT 57.955 29.630 8.13 0.00 0.00 2.27
2859 3302 7.725251 TGCTTTGTTGAGATTAATTTCACCTT 58.275 30.769 8.13 0.00 0.00 3.50
2861 3304 9.294030 CTATGCTTTGTTGAGATTAATTTCACC 57.706 33.333 8.13 2.62 0.00 4.02
2862 3305 8.801913 GCTATGCTTTGTTGAGATTAATTTCAC 58.198 33.333 8.13 5.26 0.00 3.18
2863 3306 8.742777 AGCTATGCTTTGTTGAGATTAATTTCA 58.257 29.630 4.62 4.62 33.89 2.69
2942 3385 4.935808 AGGTTCGTGGTATGAGTTTCATTC 59.064 41.667 0.00 0.00 38.26 2.67
2962 3405 7.772292 TGAGTTAGTAGATGTACAATACGAGGT 59.228 37.037 0.00 0.00 0.00 3.85
2995 3438 7.830739 ACTACTCCAAAAGAATTTAGCCATTG 58.169 34.615 0.00 0.00 37.28 2.82
2996 3439 8.422577 AACTACTCCAAAAGAATTTAGCCATT 57.577 30.769 0.00 0.00 37.28 3.16
2997 3440 9.700831 ATAACTACTCCAAAAGAATTTAGCCAT 57.299 29.630 0.00 0.00 37.28 4.40
2998 3441 9.174166 GATAACTACTCCAAAAGAATTTAGCCA 57.826 33.333 0.00 0.00 37.28 4.75
2999 3442 9.397280 AGATAACTACTCCAAAAGAATTTAGCC 57.603 33.333 0.00 0.00 37.28 3.93
3004 3447 9.793259 TGTCAAGATAACTACTCCAAAAGAATT 57.207 29.630 0.00 0.00 0.00 2.17
3005 3448 9.793259 TTGTCAAGATAACTACTCCAAAAGAAT 57.207 29.630 0.00 0.00 0.00 2.40
3006 3449 9.273016 CTTGTCAAGATAACTACTCCAAAAGAA 57.727 33.333 6.76 0.00 0.00 2.52
3007 3450 8.647796 TCTTGTCAAGATAACTACTCCAAAAGA 58.352 33.333 11.36 0.00 31.20 2.52
3008 3451 8.833231 TCTTGTCAAGATAACTACTCCAAAAG 57.167 34.615 11.36 0.00 31.20 2.27
3009 3452 9.273016 CTTCTTGTCAAGATAACTACTCCAAAA 57.727 33.333 15.95 0.00 37.38 2.44
3010 3453 7.878127 CCTTCTTGTCAAGATAACTACTCCAAA 59.122 37.037 15.95 0.00 37.38 3.28
3011 3454 7.386851 CCTTCTTGTCAAGATAACTACTCCAA 58.613 38.462 15.95 0.00 37.38 3.53
3012 3455 6.574465 GCCTTCTTGTCAAGATAACTACTCCA 60.574 42.308 15.95 0.00 37.38 3.86
3013 3456 5.813157 GCCTTCTTGTCAAGATAACTACTCC 59.187 44.000 15.95 0.00 37.38 3.85
3014 3457 6.398918 TGCCTTCTTGTCAAGATAACTACTC 58.601 40.000 15.95 1.84 37.38 2.59
3015 3458 6.360370 TGCCTTCTTGTCAAGATAACTACT 57.640 37.500 15.95 0.00 37.38 2.57
3016 3459 7.467623 CATTGCCTTCTTGTCAAGATAACTAC 58.532 38.462 15.95 4.35 37.38 2.73
3017 3460 6.094048 GCATTGCCTTCTTGTCAAGATAACTA 59.906 38.462 15.95 6.09 37.38 2.24
3018 3461 5.105997 GCATTGCCTTCTTGTCAAGATAACT 60.106 40.000 15.95 0.00 37.38 2.24
3019 3462 5.098211 GCATTGCCTTCTTGTCAAGATAAC 58.902 41.667 15.95 8.78 37.38 1.89
3020 3463 4.766373 TGCATTGCCTTCTTGTCAAGATAA 59.234 37.500 15.95 9.56 37.38 1.75
3021 3464 4.334552 TGCATTGCCTTCTTGTCAAGATA 58.665 39.130 15.95 6.69 37.38 1.98
3022 3465 3.159472 TGCATTGCCTTCTTGTCAAGAT 58.841 40.909 15.95 0.00 37.38 2.40
3023 3466 2.585330 TGCATTGCCTTCTTGTCAAGA 58.415 42.857 11.36 11.36 35.26 3.02
3024 3467 3.587797 ATGCATTGCCTTCTTGTCAAG 57.412 42.857 6.21 6.21 0.00 3.02
3025 3468 4.082081 CCTAATGCATTGCCTTCTTGTCAA 60.082 41.667 22.27 0.00 0.00 3.18
3026 3469 3.444742 CCTAATGCATTGCCTTCTTGTCA 59.555 43.478 22.27 0.00 0.00 3.58
3027 3470 3.445096 ACCTAATGCATTGCCTTCTTGTC 59.555 43.478 22.27 0.00 0.00 3.18
3028 3471 3.434309 ACCTAATGCATTGCCTTCTTGT 58.566 40.909 22.27 4.52 0.00 3.16
3029 3472 3.698040 AGACCTAATGCATTGCCTTCTTG 59.302 43.478 22.27 3.94 0.00 3.02
3030 3473 3.950395 GAGACCTAATGCATTGCCTTCTT 59.050 43.478 22.27 1.62 0.00 2.52
3031 3474 3.201708 AGAGACCTAATGCATTGCCTTCT 59.798 43.478 22.27 16.24 0.00 2.85
3032 3475 3.549794 AGAGACCTAATGCATTGCCTTC 58.450 45.455 22.27 12.10 0.00 3.46
3033 3476 3.659183 AGAGACCTAATGCATTGCCTT 57.341 42.857 22.27 5.25 0.00 4.35
3034 3477 3.285484 CAAGAGACCTAATGCATTGCCT 58.715 45.455 22.27 12.34 0.00 4.75
3035 3478 2.360165 CCAAGAGACCTAATGCATTGCC 59.640 50.000 22.27 7.95 0.00 4.52
3036 3479 2.360165 CCCAAGAGACCTAATGCATTGC 59.640 50.000 22.27 0.46 0.00 3.56
3037 3480 3.889815 TCCCAAGAGACCTAATGCATTG 58.110 45.455 22.27 8.68 0.00 2.82
3038 3481 4.803329 ATCCCAAGAGACCTAATGCATT 57.197 40.909 17.56 17.56 0.00 3.56
3039 3482 5.456763 GGTTATCCCAAGAGACCTAATGCAT 60.457 44.000 0.00 0.00 32.18 3.96
3040 3483 4.141482 GGTTATCCCAAGAGACCTAATGCA 60.141 45.833 0.00 0.00 32.18 3.96
3041 3484 4.103311 AGGTTATCCCAAGAGACCTAATGC 59.897 45.833 0.00 0.00 39.48 3.56
3042 3485 5.896073 AGGTTATCCCAAGAGACCTAATG 57.104 43.478 0.00 0.00 39.48 1.90
3043 3486 6.555360 CACTAGGTTATCCCAAGAGACCTAAT 59.445 42.308 0.00 0.00 41.01 1.73
3044 3487 5.897824 CACTAGGTTATCCCAAGAGACCTAA 59.102 44.000 0.00 0.00 41.01 2.69
3045 3488 5.195146 TCACTAGGTTATCCCAAGAGACCTA 59.805 44.000 0.00 0.00 40.83 3.08
3046 3489 4.016479 TCACTAGGTTATCCCAAGAGACCT 60.016 45.833 0.00 0.00 42.27 3.85
3047 3490 4.099727 GTCACTAGGTTATCCCAAGAGACC 59.900 50.000 0.00 0.00 34.72 3.85
3048 3491 4.710375 TGTCACTAGGTTATCCCAAGAGAC 59.290 45.833 10.78 10.78 37.82 3.36
3049 3492 4.710375 GTGTCACTAGGTTATCCCAAGAGA 59.290 45.833 0.00 0.00 34.66 3.10
3050 3493 4.141914 GGTGTCACTAGGTTATCCCAAGAG 60.142 50.000 2.35 0.00 34.66 2.85
3051 3494 3.773119 GGTGTCACTAGGTTATCCCAAGA 59.227 47.826 2.35 0.00 34.66 3.02
3052 3495 3.517901 TGGTGTCACTAGGTTATCCCAAG 59.482 47.826 2.35 0.00 34.66 3.61
3053 3496 3.522759 TGGTGTCACTAGGTTATCCCAA 58.477 45.455 2.35 0.00 34.66 4.12
3054 3497 3.193395 TGGTGTCACTAGGTTATCCCA 57.807 47.619 2.35 0.00 34.66 4.37
3055 3498 4.019591 ACTTTGGTGTCACTAGGTTATCCC 60.020 45.833 2.35 0.00 0.00 3.85
3056 3499 4.935808 CACTTTGGTGTCACTAGGTTATCC 59.064 45.833 2.35 0.00 38.54 2.59
3057 3500 4.392138 GCACTTTGGTGTCACTAGGTTATC 59.608 45.833 2.35 0.00 44.65 1.75
3058 3501 4.202419 TGCACTTTGGTGTCACTAGGTTAT 60.202 41.667 2.35 0.00 44.65 1.89
3059 3502 3.134985 TGCACTTTGGTGTCACTAGGTTA 59.865 43.478 2.35 0.00 44.65 2.85
3060 3503 2.092646 TGCACTTTGGTGTCACTAGGTT 60.093 45.455 2.35 0.00 44.65 3.50
3061 3504 1.488812 TGCACTTTGGTGTCACTAGGT 59.511 47.619 2.35 0.00 44.65 3.08
3062 3505 2.254546 TGCACTTTGGTGTCACTAGG 57.745 50.000 2.35 0.00 44.65 3.02
3063 3506 2.549754 CCTTGCACTTTGGTGTCACTAG 59.450 50.000 2.35 1.35 44.65 2.57
3064 3507 2.571212 CCTTGCACTTTGGTGTCACTA 58.429 47.619 2.35 0.00 44.65 2.74
3065 3508 1.392589 CCTTGCACTTTGGTGTCACT 58.607 50.000 2.35 0.00 44.65 3.41
3066 3509 0.385390 CCCTTGCACTTTGGTGTCAC 59.615 55.000 0.00 0.00 44.65 3.67
3067 3510 0.754957 CCCCTTGCACTTTGGTGTCA 60.755 55.000 0.00 0.00 44.65 3.58
3068 3511 1.463553 CCCCCTTGCACTTTGGTGTC 61.464 60.000 0.00 0.00 44.65 3.67
3069 3512 1.457455 CCCCCTTGCACTTTGGTGT 60.457 57.895 0.00 0.00 44.65 4.16
3070 3513 3.458653 CCCCCTTGCACTTTGGTG 58.541 61.111 0.00 0.00 45.53 4.17


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

AutoCloner maintained by Alex Coulton.