Multiple sequence alignment - TraesCS2A01G462600

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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 TraesCS2A01G462600 chr2A 100.000 3350 0 0 1 3350 708183730 708187079 0.000000e+00 6187.0
1 TraesCS2A01G462600 chr2B 92.278 3354 161 41 1 3303 681538132 681541438 0.000000e+00 4669.0
2 TraesCS2A01G462600 chr2B 96.970 33 1 0 3127 3159 681541178 681541210 4.670000e-04 56.5
3 TraesCS2A01G462600 chr2D 92.241 3338 161 39 1 3303 568939222 568942496 0.000000e+00 4639.0
4 TraesCS2A01G462600 chr5A 92.766 235 14 1 485 719 131829769 131830000 1.490000e-88 337.0
5 TraesCS2A01G462600 chr4A 92.766 235 14 1 485 719 352466067 352466298 1.490000e-88 337.0
6 TraesCS2A01G462600 chr4A 96.970 33 1 0 1868 1900 740940556 740940588 4.670000e-04 56.5
7 TraesCS2A01G462600 chr1B 92.766 235 14 1 485 719 615956004 615956235 1.490000e-88 337.0
8 TraesCS2A01G462600 chrUn 92.340 235 15 1 485 719 50158745 50158976 6.930000e-87 331.0
9 TraesCS2A01G462600 chr6B 92.340 235 15 1 485 719 23538819 23539050 6.930000e-87 331.0
10 TraesCS2A01G462600 chr6A 92.340 235 15 1 485 719 558112422 558112191 6.930000e-87 331.0
11 TraesCS2A01G462600 chr3B 92.340 235 15 1 485 719 454140558 454140789 6.930000e-87 331.0


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 TraesCS2A01G462600 chr2A 708183730 708187079 3349 False 6187.00 6187 100.000 1 3350 1 chr2A.!!$F1 3349
1 TraesCS2A01G462600 chr2B 681538132 681541438 3306 False 2362.75 4669 94.624 1 3303 2 chr2B.!!$F1 3302
2 TraesCS2A01G462600 chr2D 568939222 568942496 3274 False 4639.00 4639 92.241 1 3303 1 chr2D.!!$F1 3302

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
600 607 0.321564 TTGGTCGATTGGCTGTCCAG 60.322 55.0 0.0 0.0 44.53 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 2428 0.173481 TACGAAGTGGCAGCAGCTAG 59.827 55.0 0.0 0.0 45.73 3.42 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
62 63 1.691434 TGCTGAATTGGTTGGGGAAAC 59.309 47.619 0.00 0.00 38.12 2.78
93 94 3.189287 CACCTTTCCTGTTAGTGATGTGC 59.811 47.826 0.00 0.00 0.00 4.57
104 105 3.186047 GATGTGCGACGGTTCCGG 61.186 66.667 15.66 0.00 0.00 5.14
144 145 3.531538 TCTACATCGTTTTCATGGCTCC 58.468 45.455 0.00 0.00 0.00 4.70
167 168 2.420043 CCACCGGACGTGTGTTCT 59.580 61.111 9.46 0.00 41.26 3.01
168 169 1.663702 CCACCGGACGTGTGTTCTC 60.664 63.158 9.46 0.00 41.26 2.87
181 182 1.136336 GTGTTCTCTTTTACTGGCGCG 60.136 52.381 0.00 0.00 0.00 6.86
232 233 3.376234 GTGTTTTAGCCGGGTTTATCCTC 59.624 47.826 13.43 0.00 36.25 3.71
248 249 9.674068 GGTTTATCCTCTAAATCTGGGATTATC 57.326 37.037 0.00 0.00 39.11 1.75
262 263 8.603898 TCTGGGATTATCTTGTAGTTTCAGTA 57.396 34.615 0.00 0.00 0.00 2.74
364 365 7.138736 CGTTAATTTTGGACTGTTTCTCATGT 58.861 34.615 0.00 0.00 0.00 3.21
365 366 7.647715 CGTTAATTTTGGACTGTTTCTCATGTT 59.352 33.333 0.00 0.00 0.00 2.71
415 416 3.684788 GTCTAATGTGCTACCAGGTTGTG 59.315 47.826 0.00 0.00 0.00 3.33
483 484 1.666888 GGCCTTTGTCTTCGTGCATTG 60.667 52.381 0.00 0.00 0.00 2.82
600 607 0.321564 TTGGTCGATTGGCTGTCCAG 60.322 55.000 0.00 0.00 44.53 3.86
644 651 4.510038 AGCCATTGTCTTGTTGATTGAC 57.490 40.909 0.00 0.00 0.00 3.18
694 701 6.560253 TGTTTAGTTCCTTGCTTGATTCTC 57.440 37.500 0.00 0.00 0.00 2.87
770 777 5.972107 ATTTTCTGTGCAAATAGTCAGCT 57.028 34.783 0.00 0.00 0.00 4.24
817 824 6.014242 TGAATCTGATGTTGAACTCTGTACCT 60.014 38.462 0.00 0.00 0.00 3.08
969 976 2.932261 ACCTCTGAACTTTTGTGTCCC 58.068 47.619 0.00 0.00 0.00 4.46
992 999 1.471676 GGTCTGCGGTGATAAGTCAGG 60.472 57.143 0.00 0.00 34.36 3.86
1056 1063 2.703536 TGTTGCTGTTCCTGGTTCTCTA 59.296 45.455 0.00 0.00 0.00 2.43
1221 1228 3.629398 GCTGTGATAGTTCAGATTTGGGG 59.371 47.826 0.00 0.00 34.02 4.96
1374 1381 3.430098 CCTGGACAAGCAGATCAGACTAC 60.430 52.174 0.00 0.00 0.00 2.73
1377 1384 2.763448 GACAAGCAGATCAGACTACCCT 59.237 50.000 0.00 0.00 0.00 4.34
1527 1534 3.252484 GATCCGTCGCGAAACCGG 61.252 66.667 25.60 25.60 43.03 5.28
1542 1549 4.227134 CGGTGGATGAGGCTCCCG 62.227 72.222 12.86 13.18 34.12 5.14
1657 1664 5.507985 GGCCTTGCTATTTGGATGTACAATC 60.508 44.000 0.00 0.00 0.00 2.67
1696 1703 0.528466 TCGCTGCACTCCGATGAATC 60.528 55.000 0.00 0.00 0.00 2.52
1707 1714 0.857935 CGATGAATCTTCCTCGCTGC 59.142 55.000 5.00 0.00 38.20 5.25
1719 1726 4.093952 CGCTGCCTGTTTGCCTCG 62.094 66.667 0.00 0.00 0.00 4.63
1725 1732 2.335712 CCTGTTTGCCTCGGGAAGC 61.336 63.158 0.00 0.00 33.49 3.86
1765 1772 1.224592 GCTGGTGGGTGTGATAGGG 59.775 63.158 0.00 0.00 0.00 3.53
1812 1819 2.636830 CTGTACAATTCAGAGGCTGGG 58.363 52.381 0.00 0.00 35.20 4.45
1845 1852 1.236616 TGCCAGACATGAACTTGCCG 61.237 55.000 0.00 0.00 0.00 5.69
1846 1853 1.503542 CCAGACATGAACTTGCCGC 59.496 57.895 0.00 0.00 0.00 6.53
1992 1999 2.570302 ACATAATATGTACCCCGGAGGC 59.430 50.000 0.73 0.00 45.38 4.70
2178 2185 1.982073 CTTTCAAGGGATGCGGCGAC 61.982 60.000 12.98 2.02 0.00 5.19
2181 2188 4.473520 AAGGGATGCGGCGACAGG 62.474 66.667 12.98 0.00 0.00 4.00
2398 2405 2.815478 CCGCCACTTGTTTAGCAAAAA 58.185 42.857 0.00 0.00 36.53 1.94
2421 2428 0.248215 CCGATTCGTTGCTGCCATTC 60.248 55.000 5.20 0.00 0.00 2.67
2438 2445 0.390340 TTCTAGCTGCTGCCACTTCG 60.390 55.000 13.43 0.00 40.80 3.79
2475 2482 4.503714 TTCAGATATGACACCCCCTTTC 57.496 45.455 0.00 0.00 0.00 2.62
2533 2540 5.006552 GCATAGAGAGCATTCAGTTCAGTTC 59.993 44.000 0.00 0.00 0.00 3.01
2589 2597 7.930217 TCAAAAGTCCTTATTCTTGTTGTCTG 58.070 34.615 0.00 0.00 0.00 3.51
2625 2634 3.496884 TCCACGCAGTATTCTTTGTTCAC 59.503 43.478 0.00 0.00 41.61 3.18
2626 2635 3.498397 CCACGCAGTATTCTTTGTTCACT 59.502 43.478 0.00 0.00 41.61 3.41
2627 2636 4.377431 CCACGCAGTATTCTTTGTTCACTC 60.377 45.833 0.00 0.00 41.61 3.51
2654 2683 2.107141 CTGGGCCGAGTCGAATCC 59.893 66.667 15.64 12.42 0.00 3.01
2700 2729 5.063691 GTCTCTGTCCCATACGTATAGATCG 59.936 48.000 7.96 4.36 0.00 3.69
2715 2744 8.093307 ACGTATAGATCGGTAGATTCTGTTCTA 58.907 37.037 0.00 0.00 37.19 2.10
2718 2747 5.124645 AGATCGGTAGATTCTGTTCTACGT 58.875 41.667 0.00 0.00 45.96 3.57
2719 2748 6.286758 AGATCGGTAGATTCTGTTCTACGTA 58.713 40.000 0.00 0.00 45.96 3.57
2720 2749 5.725110 TCGGTAGATTCTGTTCTACGTAC 57.275 43.478 0.00 0.00 45.96 3.67
2721 2750 5.178061 TCGGTAGATTCTGTTCTACGTACA 58.822 41.667 0.00 0.00 45.96 2.90
2751 2780 2.935849 AGTATGTGTGTGTGTGTGTGTG 59.064 45.455 0.00 0.00 0.00 3.82
2755 2784 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
2786 2822 4.693566 CAGAGTCGGGCAGTAAACATTTTA 59.306 41.667 0.00 0.00 0.00 1.52
2835 2876 1.448013 GTACGCAGGCTCAAGGGAC 60.448 63.158 0.00 0.00 0.00 4.46
2934 2985 2.677875 CCTGCTCCAACTTGCCCC 60.678 66.667 0.00 0.00 0.00 5.80
2976 3029 1.682451 TACCCGCCAATTCCCTCTCG 61.682 60.000 0.00 0.00 0.00 4.04
2978 3031 2.897350 CGCCAATTCCCTCTCGGC 60.897 66.667 0.00 0.00 39.45 5.54
2982 3035 1.626356 CCAATTCCCTCTCGGCCTCA 61.626 60.000 0.00 0.00 0.00 3.86
2983 3036 0.462759 CAATTCCCTCTCGGCCTCAC 60.463 60.000 0.00 0.00 0.00 3.51
3005 3058 1.084289 ATTTCTTTCGCGGTACAGCC 58.916 50.000 12.54 0.00 0.00 4.85
3016 3069 1.268589 CGGTACAGCCTGACAGATACG 60.269 57.143 3.32 0.00 34.25 3.06
3087 3160 3.969287 TGATCACTTTCTGAGGTGAGG 57.031 47.619 16.37 0.00 44.13 3.86
3088 3161 3.242867 TGATCACTTTCTGAGGTGAGGT 58.757 45.455 16.37 5.62 44.13 3.85
3089 3162 3.007290 TGATCACTTTCTGAGGTGAGGTG 59.993 47.826 16.37 3.30 44.13 4.00
3090 3163 2.677914 TCACTTTCTGAGGTGAGGTGA 58.322 47.619 10.14 0.96 37.52 4.02
3091 3164 2.630098 TCACTTTCTGAGGTGAGGTGAG 59.370 50.000 10.14 0.00 37.52 3.51
3092 3165 1.974236 ACTTTCTGAGGTGAGGTGAGG 59.026 52.381 0.00 0.00 0.00 3.86
3093 3166 2.251818 CTTTCTGAGGTGAGGTGAGGA 58.748 52.381 0.00 0.00 0.00 3.71
3094 3167 2.630889 TTCTGAGGTGAGGTGAGGAT 57.369 50.000 0.00 0.00 0.00 3.24
3095 3168 2.151502 TCTGAGGTGAGGTGAGGATC 57.848 55.000 0.00 0.00 0.00 3.36
3096 3169 1.118838 CTGAGGTGAGGTGAGGATCC 58.881 60.000 2.48 2.48 0.00 3.36
3097 3170 0.712979 TGAGGTGAGGTGAGGATCCT 59.287 55.000 16.13 16.13 38.09 3.24
3098 3171 1.118838 GAGGTGAGGTGAGGATCCTG 58.881 60.000 22.02 0.00 35.20 3.86
3206 3279 1.468520 CGGGTTTCATTTGTCAGCGAT 59.531 47.619 0.00 0.00 0.00 4.58
3215 3288 4.154015 TCATTTGTCAGCGATACAGTTTGG 59.846 41.667 0.00 0.00 0.00 3.28
3238 3312 3.443925 GGCCTTTTCTGCCTCGCC 61.444 66.667 0.00 0.00 45.70 5.54
3271 3352 3.068024 TGAATTTTCTGCCTCGCTTTTGT 59.932 39.130 0.00 0.00 0.00 2.83
3279 3360 3.407698 TGCCTCGCTTTTGTTGATTCTA 58.592 40.909 0.00 0.00 0.00 2.10
3280 3361 3.818210 TGCCTCGCTTTTGTTGATTCTAA 59.182 39.130 0.00 0.00 0.00 2.10
3289 3373 3.247006 TGTTGATTCTAAGGCTCGGTC 57.753 47.619 0.00 0.00 0.00 4.79
3290 3374 2.093658 TGTTGATTCTAAGGCTCGGTCC 60.094 50.000 0.00 0.00 0.00 4.46
3303 3387 2.346365 GGTCCTGTCAACCGGGTC 59.654 66.667 6.32 0.00 40.86 4.46
3304 3388 2.513259 GGTCCTGTCAACCGGGTCA 61.513 63.158 6.32 0.00 40.86 4.02
3305 3389 1.448497 GTCCTGTCAACCGGGTCAA 59.552 57.895 6.32 0.00 40.86 3.18
3306 3390 0.179040 GTCCTGTCAACCGGGTCAAA 60.179 55.000 6.32 0.00 40.86 2.69
3307 3391 0.547075 TCCTGTCAACCGGGTCAAAA 59.453 50.000 6.32 0.00 40.86 2.44
3308 3392 1.144093 TCCTGTCAACCGGGTCAAAAT 59.856 47.619 6.32 0.00 40.86 1.82
3309 3393 1.269448 CCTGTCAACCGGGTCAAAATG 59.731 52.381 6.32 0.00 34.56 2.32
3310 3394 1.269448 CTGTCAACCGGGTCAAAATGG 59.731 52.381 6.32 0.00 0.00 3.16
3311 3395 1.133761 TGTCAACCGGGTCAAAATGGA 60.134 47.619 6.32 0.00 0.00 3.41
3312 3396 1.268625 GTCAACCGGGTCAAAATGGAC 59.731 52.381 6.32 0.00 37.06 4.02
3313 3397 0.239879 CAACCGGGTCAAAATGGACG 59.760 55.000 6.32 0.00 38.70 4.79
3314 3398 0.891904 AACCGGGTCAAAATGGACGG 60.892 55.000 6.32 0.00 46.16 4.79
3315 3399 1.003112 CCGGGTCAAAATGGACGGA 60.003 57.895 0.00 0.00 43.69 4.69
3316 3400 0.606944 CCGGGTCAAAATGGACGGAA 60.607 55.000 0.00 0.00 43.69 4.30
3317 3401 0.519961 CGGGTCAAAATGGACGGAAC 59.480 55.000 0.00 0.00 38.70 3.62
3318 3402 1.880646 CGGGTCAAAATGGACGGAACT 60.881 52.381 0.00 0.00 38.70 3.01
3319 3403 2.235891 GGGTCAAAATGGACGGAACTT 58.764 47.619 0.00 0.00 38.70 2.66
3320 3404 2.228103 GGGTCAAAATGGACGGAACTTC 59.772 50.000 0.00 0.00 38.70 3.01
3321 3405 2.882137 GGTCAAAATGGACGGAACTTCA 59.118 45.455 0.00 0.00 38.70 3.02
3322 3406 3.316868 GGTCAAAATGGACGGAACTTCAA 59.683 43.478 0.00 0.00 38.70 2.69
3323 3407 4.287720 GTCAAAATGGACGGAACTTCAAC 58.712 43.478 0.00 0.00 0.00 3.18
3324 3408 3.948473 TCAAAATGGACGGAACTTCAACA 59.052 39.130 0.00 0.00 0.00 3.33
3325 3409 3.982576 AAATGGACGGAACTTCAACAC 57.017 42.857 0.00 0.00 0.00 3.32
3326 3410 2.631160 ATGGACGGAACTTCAACACA 57.369 45.000 0.00 0.00 0.00 3.72
3327 3411 2.404923 TGGACGGAACTTCAACACAA 57.595 45.000 0.00 0.00 0.00 3.33
3328 3412 2.712709 TGGACGGAACTTCAACACAAA 58.287 42.857 0.00 0.00 0.00 2.83
3329 3413 3.082548 TGGACGGAACTTCAACACAAAA 58.917 40.909 0.00 0.00 0.00 2.44
3330 3414 3.697045 TGGACGGAACTTCAACACAAAAT 59.303 39.130 0.00 0.00 0.00 1.82
3331 3415 4.158764 TGGACGGAACTTCAACACAAAATT 59.841 37.500 0.00 0.00 0.00 1.82
3332 3416 5.357314 TGGACGGAACTTCAACACAAAATTA 59.643 36.000 0.00 0.00 0.00 1.40
3333 3417 5.684184 GGACGGAACTTCAACACAAAATTAC 59.316 40.000 0.00 0.00 0.00 1.89
3334 3418 5.584442 ACGGAACTTCAACACAAAATTACC 58.416 37.500 0.00 0.00 0.00 2.85
3335 3419 5.358725 ACGGAACTTCAACACAAAATTACCT 59.641 36.000 0.00 0.00 0.00 3.08
3336 3420 5.912955 CGGAACTTCAACACAAAATTACCTC 59.087 40.000 0.00 0.00 0.00 3.85
3337 3421 6.459024 CGGAACTTCAACACAAAATTACCTCA 60.459 38.462 0.00 0.00 0.00 3.86
3338 3422 7.262048 GGAACTTCAACACAAAATTACCTCAA 58.738 34.615 0.00 0.00 0.00 3.02
3339 3423 7.926018 GGAACTTCAACACAAAATTACCTCAAT 59.074 33.333 0.00 0.00 0.00 2.57
3340 3424 9.959749 GAACTTCAACACAAAATTACCTCAATA 57.040 29.630 0.00 0.00 0.00 1.90
3341 3425 9.965824 AACTTCAACACAAAATTACCTCAATAG 57.034 29.630 0.00 0.00 0.00 1.73
3342 3426 9.349713 ACTTCAACACAAAATTACCTCAATAGA 57.650 29.630 0.00 0.00 0.00 1.98
3343 3427 9.831737 CTTCAACACAAAATTACCTCAATAGAG 57.168 33.333 0.00 0.00 41.72 2.43
3344 3428 8.918202 TCAACACAAAATTACCTCAATAGAGT 57.082 30.769 0.00 0.00 40.40 3.24
3345 3429 8.783093 TCAACACAAAATTACCTCAATAGAGTG 58.217 33.333 0.00 0.00 40.40 3.51
3346 3430 7.145932 ACACAAAATTACCTCAATAGAGTGC 57.854 36.000 0.00 0.00 40.40 4.40
3347 3431 6.128282 ACACAAAATTACCTCAATAGAGTGCG 60.128 38.462 0.00 0.00 40.40 5.34
3348 3432 6.092122 CACAAAATTACCTCAATAGAGTGCGA 59.908 38.462 0.00 0.00 40.40 5.10
3349 3433 6.823689 ACAAAATTACCTCAATAGAGTGCGAT 59.176 34.615 0.00 0.00 40.40 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 2.561569 ACAGGAAAGGTGACAAAGACG 58.438 47.619 0.00 0.00 0.00 4.18
104 105 0.951558 AAACCACACATTCTGTCGCC 59.048 50.000 0.00 0.00 0.00 5.54
164 165 1.425412 GACGCGCCAGTAAAAGAGAA 58.575 50.000 5.73 0.00 0.00 2.87
167 168 0.108992 ATCGACGCGCCAGTAAAAGA 60.109 50.000 5.73 0.00 0.00 2.52
168 169 0.719465 AATCGACGCGCCAGTAAAAG 59.281 50.000 5.73 0.00 0.00 2.27
181 182 1.209127 CCACCGCAAACCAATCGAC 59.791 57.895 0.00 0.00 0.00 4.20
262 263 4.274950 TCGCCGAAAGAACAAGAAGAAAAT 59.725 37.500 0.00 0.00 0.00 1.82
271 272 0.586319 CAGCTTCGCCGAAAGAACAA 59.414 50.000 0.00 0.00 0.00 2.83
290 291 5.697633 TGGAACACGTAAACTGGATTCTTAC 59.302 40.000 0.00 0.00 0.00 2.34
291 292 5.856156 TGGAACACGTAAACTGGATTCTTA 58.144 37.500 0.00 0.00 0.00 2.10
292 293 4.710324 TGGAACACGTAAACTGGATTCTT 58.290 39.130 0.00 0.00 0.00 2.52
364 365 4.341487 TCCGTCAGTTCTAGATCCAAGAA 58.659 43.478 0.00 4.41 0.00 2.52
365 366 3.964411 TCCGTCAGTTCTAGATCCAAGA 58.036 45.455 0.00 0.00 0.00 3.02
415 416 3.215244 CACAACAAAATCGTCGTAGCAC 58.785 45.455 0.00 0.00 0.00 4.40
483 484 7.675637 GCCGTAAACATTGTACTAACATCCTTC 60.676 40.741 0.00 0.00 34.97 3.46
622 629 4.154015 CGTCAATCAACAAGACAATGGCTA 59.846 41.667 0.00 0.00 32.68 3.93
644 651 2.119457 GCAAAAAGGTGAGAAACTGCG 58.881 47.619 0.00 0.00 0.00 5.18
770 777 5.242171 TCATACAGGAACGTTCACTCTTGTA 59.758 40.000 28.24 23.48 38.17 2.41
842 849 6.075205 CGATCAAAAAGAAAAACAGCAGACAG 60.075 38.462 0.00 0.00 0.00 3.51
969 976 0.537188 ACTTATCACCGCAGACCCAG 59.463 55.000 0.00 0.00 0.00 4.45
992 999 9.710900 AATCTTGTAAATCTTCCATTGTTTTCC 57.289 29.630 0.00 0.00 0.00 3.13
1056 1063 0.036022 GCCTGAAGAGGTGCAGAACT 59.964 55.000 0.00 0.00 42.15 3.01
1221 1228 5.407407 TCTCCACTTCCAGTTCATTACTC 57.593 43.478 0.00 0.00 33.85 2.59
1260 1267 1.556911 TCACCTCCTGATTGGCTCTTC 59.443 52.381 0.00 0.00 35.26 2.87
1374 1381 3.070159 TGTTCAGACAAGAGAGTGAAGGG 59.930 47.826 0.00 0.00 31.49 3.95
1527 1534 1.330655 TTCTCGGGAGCCTCATCCAC 61.331 60.000 0.00 0.00 41.52 4.02
1542 1549 2.033049 GCAGTCATCACATGGCATTCTC 59.967 50.000 0.00 0.00 37.34 2.87
1657 1664 1.066858 AGACCAATGGCGTGTCAGTAG 60.067 52.381 0.00 0.00 0.00 2.57
1696 1703 1.871772 CAAACAGGCAGCGAGGAAG 59.128 57.895 0.00 0.00 0.00 3.46
1707 1714 2.335712 GCTTCCCGAGGCAAACAGG 61.336 63.158 0.00 0.00 33.19 4.00
1719 1726 2.016096 GCAATCTCACCAGAGCTTCCC 61.016 57.143 0.00 0.00 41.81 3.97
1725 1732 2.719739 ACAATGGCAATCTCACCAGAG 58.280 47.619 0.00 0.00 39.88 3.35
1765 1772 2.914777 GATCTCAGCACCTGCCCGTC 62.915 65.000 0.00 0.00 43.38 4.79
1812 1819 2.360475 GGCAAGGTCTCCCACTGC 60.360 66.667 0.00 0.00 39.76 4.40
1975 1982 3.250816 TGCCTCCGGGGTACATATT 57.749 52.632 0.00 0.00 37.43 1.28
1992 1999 4.767255 GACTGGGAGGCGCTGGTG 62.767 72.222 7.64 0.00 0.00 4.17
2178 2185 2.513204 CCGATGACCAGCAGCCTG 60.513 66.667 0.00 0.00 38.85 4.85
2275 2282 4.459089 GAGCACCTCCCAGTCGGC 62.459 72.222 0.00 0.00 0.00 5.54
2421 2428 0.173481 TACGAAGTGGCAGCAGCTAG 59.827 55.000 0.00 0.00 45.73 3.42
2460 2467 1.605453 GCGGAAAGGGGGTGTCATA 59.395 57.895 0.00 0.00 0.00 2.15
2475 2482 0.804544 TTTAATCGACAGCTCCGCGG 60.805 55.000 22.12 22.12 0.00 6.46
2533 2540 5.823045 AGTGTTAAAAGAGAAGTTCCAGGTG 59.177 40.000 0.00 0.00 0.00 4.00
2625 2634 1.154205 CGGCCCAGCAGAATAACGAG 61.154 60.000 0.00 0.00 0.00 4.18
2626 2635 1.153449 CGGCCCAGCAGAATAACGA 60.153 57.895 0.00 0.00 0.00 3.85
2627 2636 1.153449 TCGGCCCAGCAGAATAACG 60.153 57.895 0.00 0.00 28.67 3.18
2654 2683 8.162878 AGACAATATATGCAACTGAAAGATGG 57.837 34.615 0.00 0.00 37.20 3.51
2700 2729 8.152309 AGTATGTACGTAGAACAGAATCTACC 57.848 38.462 0.00 0.00 45.87 3.18
2755 2784 0.249868 TGCCCGACTCTGAACAACAG 60.250 55.000 0.00 0.00 46.97 3.16
2771 2806 5.983118 AGCAAAGTGTAAAATGTTTACTGCC 59.017 36.000 14.30 4.57 0.00 4.85
2786 2822 0.467844 TGCATGGACCAGCAAAGTGT 60.468 50.000 14.01 0.00 37.90 3.55
2835 2876 2.143876 ATTGATTTGGTCCCTTCCCG 57.856 50.000 0.00 0.00 0.00 5.14
2934 2985 2.949106 CAGGGAAACACAGCAGCG 59.051 61.111 0.00 0.00 0.00 5.18
2976 3029 1.401539 GCGAAAGAAATGTGTGAGGCC 60.402 52.381 0.00 0.00 0.00 5.19
2978 3031 1.135972 CCGCGAAAGAAATGTGTGAGG 60.136 52.381 8.23 0.00 0.00 3.86
2982 3035 2.478894 CTGTACCGCGAAAGAAATGTGT 59.521 45.455 8.23 0.00 0.00 3.72
2983 3036 2.724839 GCTGTACCGCGAAAGAAATGTG 60.725 50.000 8.23 0.00 0.00 3.21
3005 3058 0.175760 CCACCACCCGTATCTGTCAG 59.824 60.000 0.00 0.00 0.00 3.51
3032 3085 1.000938 CAGACAGACAGCCTTTTTGCC 60.001 52.381 0.00 0.00 0.00 4.52
3033 3086 1.601412 GCAGACAGACAGCCTTTTTGC 60.601 52.381 0.00 0.00 0.00 3.68
3034 3087 1.000938 GGCAGACAGACAGCCTTTTTG 60.001 52.381 0.00 0.00 45.80 2.44
3035 3088 1.322442 GGCAGACAGACAGCCTTTTT 58.678 50.000 0.00 0.00 45.80 1.94
3087 3160 0.999712 TTTTCCCCCAGGATCCTCAC 59.000 55.000 12.69 0.00 43.54 3.51
3088 3161 2.000290 ATTTTCCCCCAGGATCCTCA 58.000 50.000 12.69 0.00 43.54 3.86
3089 3162 3.815757 GCATATTTTCCCCCAGGATCCTC 60.816 52.174 12.69 0.00 43.54 3.71
3090 3163 2.110721 GCATATTTTCCCCCAGGATCCT 59.889 50.000 9.02 9.02 43.54 3.24
3091 3164 2.529632 GCATATTTTCCCCCAGGATCC 58.470 52.381 2.48 2.48 43.54 3.36
3092 3165 2.162681 CGCATATTTTCCCCCAGGATC 58.837 52.381 0.00 0.00 43.54 3.36
3093 3166 1.203050 CCGCATATTTTCCCCCAGGAT 60.203 52.381 0.00 0.00 43.54 3.24
3094 3167 0.184933 CCGCATATTTTCCCCCAGGA 59.815 55.000 0.00 0.00 41.88 3.86
3095 3168 1.463553 GCCGCATATTTTCCCCCAGG 61.464 60.000 0.00 0.00 0.00 4.45
3096 3169 1.795170 CGCCGCATATTTTCCCCCAG 61.795 60.000 0.00 0.00 0.00 4.45
3097 3170 1.826054 CGCCGCATATTTTCCCCCA 60.826 57.895 0.00 0.00 0.00 4.96
3098 3171 2.561037 CCGCCGCATATTTTCCCCC 61.561 63.158 0.00 0.00 0.00 5.40
3184 3257 0.243636 GCTGACAAATGAAACCCGGG 59.756 55.000 22.25 22.25 0.00 5.73
3206 3279 4.354162 GCCCCGGGCCAAACTGTA 62.354 66.667 18.83 0.00 44.06 2.74
3246 3327 3.288809 AGCGAGGCAGAAAATTCAAAC 57.711 42.857 0.00 0.00 0.00 2.93
3271 3352 2.168521 CAGGACCGAGCCTTAGAATCAA 59.831 50.000 0.00 0.00 35.66 2.57
3279 3360 1.371558 GTTGACAGGACCGAGCCTT 59.628 57.895 0.00 0.00 35.66 4.35
3280 3361 2.584391 GGTTGACAGGACCGAGCCT 61.584 63.158 0.00 0.00 39.37 4.58
3289 3373 1.269448 CATTTTGACCCGGTTGACAGG 59.731 52.381 0.00 0.00 0.00 4.00
3290 3374 1.269448 CCATTTTGACCCGGTTGACAG 59.731 52.381 0.00 0.00 0.00 3.51
3303 3387 4.041723 GTGTTGAAGTTCCGTCCATTTTG 58.958 43.478 0.00 0.00 0.00 2.44
3304 3388 3.697045 TGTGTTGAAGTTCCGTCCATTTT 59.303 39.130 0.00 0.00 0.00 1.82
3305 3389 3.283751 TGTGTTGAAGTTCCGTCCATTT 58.716 40.909 0.00 0.00 0.00 2.32
3306 3390 2.925724 TGTGTTGAAGTTCCGTCCATT 58.074 42.857 0.00 0.00 0.00 3.16
3307 3391 2.631160 TGTGTTGAAGTTCCGTCCAT 57.369 45.000 0.00 0.00 0.00 3.41
3308 3392 2.404923 TTGTGTTGAAGTTCCGTCCA 57.595 45.000 0.00 0.00 0.00 4.02
3309 3393 3.768468 TTTTGTGTTGAAGTTCCGTCC 57.232 42.857 0.00 0.00 0.00 4.79
3310 3394 5.684184 GGTAATTTTGTGTTGAAGTTCCGTC 59.316 40.000 0.00 0.00 0.00 4.79
3311 3395 5.358725 AGGTAATTTTGTGTTGAAGTTCCGT 59.641 36.000 0.00 0.00 0.00 4.69
3312 3396 5.827666 AGGTAATTTTGTGTTGAAGTTCCG 58.172 37.500 0.00 0.00 0.00 4.30
3313 3397 6.801575 TGAGGTAATTTTGTGTTGAAGTTCC 58.198 36.000 0.00 0.00 0.00 3.62
3314 3398 8.871686 ATTGAGGTAATTTTGTGTTGAAGTTC 57.128 30.769 0.00 0.00 0.00 3.01
3315 3399 9.965824 CTATTGAGGTAATTTTGTGTTGAAGTT 57.034 29.630 0.00 0.00 0.00 2.66
3316 3400 9.349713 TCTATTGAGGTAATTTTGTGTTGAAGT 57.650 29.630 0.00 0.00 0.00 3.01
3317 3401 9.831737 CTCTATTGAGGTAATTTTGTGTTGAAG 57.168 33.333 0.00 0.00 36.70 3.02
3318 3402 9.349713 ACTCTATTGAGGTAATTTTGTGTTGAA 57.650 29.630 9.03 0.00 44.29 2.69
3319 3403 8.783093 CACTCTATTGAGGTAATTTTGTGTTGA 58.217 33.333 9.03 0.00 44.29 3.18
3320 3404 7.538678 GCACTCTATTGAGGTAATTTTGTGTTG 59.461 37.037 9.03 0.00 44.29 3.33
3321 3405 7.573096 CGCACTCTATTGAGGTAATTTTGTGTT 60.573 37.037 9.03 0.00 44.29 3.32
3322 3406 6.128282 CGCACTCTATTGAGGTAATTTTGTGT 60.128 38.462 9.03 0.00 44.29 3.72
3323 3407 6.092122 TCGCACTCTATTGAGGTAATTTTGTG 59.908 38.462 9.03 3.17 44.29 3.33
3324 3408 6.170506 TCGCACTCTATTGAGGTAATTTTGT 58.829 36.000 9.03 0.00 44.29 2.83
3325 3409 6.662414 TCGCACTCTATTGAGGTAATTTTG 57.338 37.500 9.03 0.00 44.29 2.44


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

AutoCloner maintained by Alex Coulton.