Multiple sequence alignment - TraesCS2D01G127200

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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 TraesCS2D01G127200 chr2D 100.000 2235 0 0 1471 3705 73861519 73863753 0.000000e+00 4128.0
1 TraesCS2D01G127200 chr2D 100.000 1275 0 0 1 1275 73860049 73861323 0.000000e+00 2355.0
2 TraesCS2D01G127200 chr2D 86.275 204 25 3 3416 3616 73862875 73863078 6.230000e-53 219.0
3 TraesCS2D01G127200 chr2D 86.275 204 25 3 2827 3030 73863464 73863664 6.230000e-53 219.0
4 TraesCS2D01G127200 chr2A 95.261 2068 56 13 1471 3527 73283310 73285346 0.000000e+00 3238.0
5 TraesCS2D01G127200 chr2A 91.932 818 55 3 1 813 73274201 73275012 0.000000e+00 1134.0
6 TraesCS2D01G127200 chr2A 97.260 365 4 1 917 1275 73282871 73283235 6.800000e-172 614.0
7 TraesCS2D01G127200 chr2A 93.088 217 13 2 3490 3705 73285339 73285554 2.150000e-82 316.0
8 TraesCS2D01G127200 chr2A 81.620 321 31 18 3405 3702 73376461 73376776 1.330000e-59 241.0
9 TraesCS2D01G127200 chr2B 96.385 1217 39 2 1471 2683 112201447 112202662 0.000000e+00 1999.0
10 TraesCS2D01G127200 chr2B 96.947 393 11 1 884 1275 112200980 112201372 0.000000e+00 658.0
11 TraesCS2D01G127200 chr2B 82.769 325 28 15 3405 3705 112641938 112642258 7.890000e-67 265.0
12 TraesCS2D01G127200 chr2B 81.957 327 28 16 3405 3705 112461405 112461726 7.950000e-62 248.0
13 TraesCS2D01G127200 chr2B 81.790 324 28 21 3405 3703 113162815 113163132 3.700000e-60 243.0
14 TraesCS2D01G127200 chr2B 82.946 258 19 17 3405 3639 113028470 113028725 3.750000e-50 209.0
15 TraesCS2D01G127200 chr2B 85.057 174 15 3 720 882 112200773 112200946 2.290000e-37 167.0
16 TraesCS2D01G127200 chr2B 80.347 173 26 4 2606 2776 113028294 113028460 1.400000e-24 124.0
17 TraesCS2D01G127200 chr2B 80.899 89 5 5 2479 2567 113162496 113162572 4.000000e-05 60.2


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 TraesCS2D01G127200 chr2D 73860049 73863753 3704 False 1730.250000 4128 93.137500 1 3705 4 chr2D.!!$F1 3704
1 TraesCS2D01G127200 chr2A 73282871 73285554 2683 False 1389.333333 3238 95.203000 917 3705 3 chr2A.!!$F3 2788
2 TraesCS2D01G127200 chr2A 73274201 73275012 811 False 1134.000000 1134 91.932000 1 813 1 chr2A.!!$F1 812
3 TraesCS2D01G127200 chr2B 112200773 112202662 1889 False 941.333333 1999 92.796333 720 2683 3 chr2B.!!$F3 1963

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
620 621 0.383124 GATGCGGCGATTTAAGCGAC 60.383 55.000 12.98 1.43 35.00 5.19 F
746 751 0.603569 GTGAAGTCAAGCGAGGGAGA 59.396 55.000 0.00 0.00 0.00 3.71 F
747 752 1.000955 GTGAAGTCAAGCGAGGGAGAA 59.999 52.381 0.00 0.00 0.00 2.87 F
2604 2663 1.208052 TGCCTCAAGCCATACTCTGAC 59.792 52.381 0.00 0.00 42.71 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 2382 2.473760 CCTCCGCTCGATCTCACGT 61.474 63.158 0.0 0.0 34.70 4.49 R
2632 2691 3.896272 AGTCGTCTAAAACCTCTGTTCCT 59.104 43.478 0.0 0.0 32.15 3.36 R
2634 2693 4.868067 TCAGTCGTCTAAAACCTCTGTTC 58.132 43.478 0.0 0.0 32.15 3.18 R
3503 3573 0.669318 GATGTGACGAACGCCTCCAA 60.669 55.000 0.0 0.0 0.00 3.53 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
17 18 2.285368 AGAGACCGCCCCCATTGA 60.285 61.111 0.00 0.00 0.00 2.57
94 95 3.904339 GGAGGGCTTGACCAATATCTAGA 59.096 47.826 0.00 0.00 42.05 2.43
132 133 0.458025 CCTTAGACTCGAACCACGCC 60.458 60.000 0.00 0.00 42.26 5.68
188 189 2.037772 CGAGCTCAACCATATAGGCCTT 59.962 50.000 12.58 0.81 43.14 4.35
234 235 0.785378 CGACGACCATACGTTTTGCA 59.215 50.000 0.00 0.00 46.52 4.08
265 266 1.561542 ACAGGGAGGCCATTCTAACAG 59.438 52.381 5.01 0.00 0.00 3.16
299 300 4.218578 CAGAGAGCGCCTGCCGAT 62.219 66.667 2.29 0.00 44.31 4.18
300 301 4.218578 AGAGAGCGCCTGCCGATG 62.219 66.667 2.29 0.00 44.31 3.84
341 342 2.298163 GGTTCTCGAAGTAGTGGACCAA 59.702 50.000 0.00 0.00 0.00 3.67
396 397 1.806542 GTGACGAATGTGTTGAGCCAT 59.193 47.619 0.00 0.00 0.00 4.40
430 431 7.818446 CCAGTGTATCCATATTTCAGATCTCTG 59.182 40.741 0.00 0.56 45.08 3.35
514 515 4.785453 CCTGAAGGAGGCGGTGGC 62.785 72.222 0.00 0.00 34.01 5.01
550 551 4.728102 CTGCGCGGACCCGTTACA 62.728 66.667 11.90 5.36 42.09 2.41
566 567 3.625938 GTTACAGACGAAACACGACTCT 58.374 45.455 0.00 0.00 43.88 3.24
590 591 2.434359 GCCTTCCCCGTCGACAAG 60.434 66.667 17.16 11.09 0.00 3.16
591 592 2.434359 CCTTCCCCGTCGACAAGC 60.434 66.667 17.16 0.00 0.00 4.01
615 616 2.390938 CGACTAGATGCGGCGATTTAA 58.609 47.619 12.98 0.00 0.00 1.52
620 621 0.383124 GATGCGGCGATTTAAGCGAC 60.383 55.000 12.98 1.43 35.00 5.19
624 625 3.710233 GGCGATTTAAGCGACGATG 57.290 52.632 6.84 0.00 35.00 3.84
679 680 3.775654 CGGAGGCAGAGGGGTGTC 61.776 72.222 0.00 0.00 0.00 3.67
690 691 2.690778 GGGGTGTCGTTGAGCATGC 61.691 63.158 10.51 10.51 0.00 4.06
717 718 2.518587 GGCGGGGGCAAGGATAAC 60.519 66.667 0.00 0.00 0.00 1.89
746 751 0.603569 GTGAAGTCAAGCGAGGGAGA 59.396 55.000 0.00 0.00 0.00 3.71
747 752 1.000955 GTGAAGTCAAGCGAGGGAGAA 59.999 52.381 0.00 0.00 0.00 2.87
810 815 5.336150 TGTTTCCACTGCTCAAAATTGAA 57.664 34.783 0.00 0.00 36.64 2.69
815 831 3.374745 CACTGCTCAAAATTGAAGCGTT 58.625 40.909 0.00 0.00 36.64 4.84
839 855 7.979444 TTCCTAACACTTTTGAGAATTCGAT 57.021 32.000 0.00 0.00 0.00 3.59
890 938 8.975439 CGAATCTTGTAAGTAGTTTAACACAGT 58.025 33.333 0.00 0.00 0.00 3.55
906 954 4.067896 ACACAGTTCACTCAATCACCATC 58.932 43.478 0.00 0.00 0.00 3.51
1102 1151 2.359975 CGCCCCTGTTTCCACTCC 60.360 66.667 0.00 0.00 0.00 3.85
2327 2382 3.797353 GGCGGGCAGAAGATCCCA 61.797 66.667 0.00 0.00 42.75 4.37
2396 2451 2.885135 TGGTCAGCATGTTCCTCATT 57.115 45.000 0.00 0.00 37.40 2.57
2471 2526 2.069273 AGTCCGAGAGAACATTTTGCG 58.931 47.619 0.00 0.00 0.00 4.85
2508 2563 1.438651 TGTAAGACGAAGCCATGCAC 58.561 50.000 0.00 0.00 0.00 4.57
2603 2662 1.483827 CTGCCTCAAGCCATACTCTGA 59.516 52.381 0.00 0.00 42.71 3.27
2604 2663 1.208052 TGCCTCAAGCCATACTCTGAC 59.792 52.381 0.00 0.00 42.71 3.51
2629 2688 7.175816 ACTCTAGTCACATTGCGTATCTGATAT 59.824 37.037 0.00 0.00 0.00 1.63
2630 2689 7.308435 TCTAGTCACATTGCGTATCTGATATG 58.692 38.462 11.68 11.68 0.00 1.78
2632 2691 6.515832 AGTCACATTGCGTATCTGATATGAA 58.484 36.000 18.67 7.23 0.00 2.57
2634 2693 5.928264 TCACATTGCGTATCTGATATGAAGG 59.072 40.000 18.67 13.44 0.00 3.46
2636 2695 6.424812 CACATTGCGTATCTGATATGAAGGAA 59.575 38.462 18.67 10.15 0.00 3.36
2639 2698 5.532557 TGCGTATCTGATATGAAGGAACAG 58.467 41.667 18.67 0.00 0.00 3.16
2707 2766 7.484641 GCGAAACAAATTTGCTAGATTATCACA 59.515 33.333 18.12 0.00 43.90 3.58
2753 2818 4.374702 GCACCGAGCTGCACAACG 62.375 66.667 1.02 2.09 41.15 4.10
2763 2828 4.374702 GCACAACGCTCAGCACCG 62.375 66.667 0.00 0.00 37.77 4.94
2814 2883 3.382865 TCTCCACAGATGTCTGATACTGC 59.617 47.826 16.41 0.00 46.59 4.40
2822 2891 6.551227 ACAGATGTCTGATACTGCTAATACCA 59.449 38.462 16.41 0.00 46.59 3.25
2844 2913 4.161189 CAGAACCTGATGACTCCAGTACAT 59.839 45.833 0.00 0.00 32.44 2.29
2865 2934 1.612676 ATGCTTCAAGTTGCTGCTCA 58.387 45.000 16.72 4.33 0.00 4.26
2873 2942 4.388485 TCAAGTTGCTGCTCAATAACTCA 58.612 39.130 0.00 0.00 36.99 3.41
2881 2951 4.237724 CTGCTCAATAACTCAGACGTCAA 58.762 43.478 19.50 4.29 0.00 3.18
2904 2974 2.649245 TTCATCTCCCAGCGGCATCG 62.649 60.000 1.45 0.00 39.81 3.84
2922 2992 1.964223 TCGATATCAGAACTGGAGGCC 59.036 52.381 3.12 0.00 0.00 5.19
2930 3000 3.591254 AACTGGAGGCCTTCGTCGC 62.591 63.158 6.77 0.00 0.00 5.19
2956 3026 9.512435 CATCTGAGCCAACATTAAGAAAAATAG 57.488 33.333 0.00 0.00 0.00 1.73
3028 3098 3.537580 CAATCAATTGGGAAGGGCAATG 58.462 45.455 5.42 0.00 34.22 2.82
3039 3109 5.545723 TGGGAAGGGCAATGAAATAGAAAAA 59.454 36.000 0.00 0.00 0.00 1.94
3100 3170 3.484229 CGCAAGTTGCTGCTCTATGTTAC 60.484 47.826 24.61 0.00 42.25 2.50
3101 3171 3.686726 GCAAGTTGCTGCTCTATGTTACT 59.313 43.478 20.71 0.00 40.96 2.24
3102 3172 4.870426 GCAAGTTGCTGCTCTATGTTACTA 59.130 41.667 20.71 0.00 40.96 1.82
3107 3177 8.012957 AGTTGCTGCTCTATGTTACTATTACT 57.987 34.615 0.00 0.00 0.00 2.24
3109 3179 8.543774 GTTGCTGCTCTATGTTACTATTACTTG 58.456 37.037 0.00 0.00 0.00 3.16
3161 3231 2.131183 GCTGCTCTATAACTCGCAAGG 58.869 52.381 0.00 0.00 38.47 3.61
3174 3244 2.228822 CTCGCAAGGTACAAGGCAAAAT 59.771 45.455 0.00 0.00 38.47 1.82
3178 3248 3.917985 GCAAGGTACAAGGCAAAATAACG 59.082 43.478 0.00 0.00 0.00 3.18
3179 3249 3.842732 AGGTACAAGGCAAAATAACGC 57.157 42.857 0.00 0.00 0.00 4.84
3180 3250 3.150767 AGGTACAAGGCAAAATAACGCA 58.849 40.909 0.00 0.00 0.00 5.24
3181 3251 3.570550 AGGTACAAGGCAAAATAACGCAA 59.429 39.130 0.00 0.00 0.00 4.85
3182 3252 4.038162 AGGTACAAGGCAAAATAACGCAAA 59.962 37.500 0.00 0.00 0.00 3.68
3183 3253 4.745620 GGTACAAGGCAAAATAACGCAAAA 59.254 37.500 0.00 0.00 0.00 2.44
3184 3254 5.407084 GGTACAAGGCAAAATAACGCAAAAT 59.593 36.000 0.00 0.00 0.00 1.82
3185 3255 6.586844 GGTACAAGGCAAAATAACGCAAAATA 59.413 34.615 0.00 0.00 0.00 1.40
3186 3256 7.116519 GGTACAAGGCAAAATAACGCAAAATAA 59.883 33.333 0.00 0.00 0.00 1.40
3187 3257 6.883129 ACAAGGCAAAATAACGCAAAATAAC 58.117 32.000 0.00 0.00 0.00 1.89
3198 3268 5.888412 ACGCAAAATAACTTCAAAGCAAG 57.112 34.783 0.00 0.00 0.00 4.01
3231 3301 5.716228 ACAAACCAAAATCCAGCATGATAGA 59.284 36.000 0.00 0.00 39.69 1.98
3232 3302 6.211184 ACAAACCAAAATCCAGCATGATAGAA 59.789 34.615 0.00 0.00 39.69 2.10
3233 3303 5.841957 ACCAAAATCCAGCATGATAGAAC 57.158 39.130 0.00 0.00 39.69 3.01
3234 3304 5.263599 ACCAAAATCCAGCATGATAGAACA 58.736 37.500 0.00 0.00 39.69 3.18
3235 3305 5.895534 ACCAAAATCCAGCATGATAGAACAT 59.104 36.000 0.00 0.00 39.69 2.71
3236 3306 6.381994 ACCAAAATCCAGCATGATAGAACATT 59.618 34.615 0.00 0.00 39.69 2.71
3237 3307 6.921857 CCAAAATCCAGCATGATAGAACATTC 59.078 38.462 0.00 0.00 39.69 2.67
3238 3308 7.201884 CCAAAATCCAGCATGATAGAACATTCT 60.202 37.037 0.00 0.00 39.69 2.40
3239 3309 6.879276 AATCCAGCATGATAGAACATTCTG 57.121 37.500 4.34 0.00 39.69 3.02
3242 3312 5.419760 CAGCATGATAGAACATTCTGGTG 57.580 43.478 4.34 0.80 39.69 4.17
3243 3313 3.881688 AGCATGATAGAACATTCTGGTGC 59.118 43.478 4.34 8.69 38.19 5.01
3244 3314 3.881688 GCATGATAGAACATTCTGGTGCT 59.118 43.478 4.34 0.00 38.19 4.40
3245 3315 4.261072 GCATGATAGAACATTCTGGTGCTG 60.261 45.833 4.34 0.00 38.19 4.41
3251 3321 1.696063 ACATTCTGGTGCTGCTTTGT 58.304 45.000 0.00 0.00 0.00 2.83
3253 3323 2.035066 ACATTCTGGTGCTGCTTTGTTC 59.965 45.455 0.00 0.00 0.00 3.18
3286 3356 7.916128 CGATAGTCTCAAAATAATGACGAGT 57.084 36.000 0.00 0.00 34.92 4.18
3332 3402 4.917906 ACTTCTTTATCTCCCAAGTGCT 57.082 40.909 0.00 0.00 0.00 4.40
3342 3412 2.554032 CTCCCAAGTGCTACAGGTTTTG 59.446 50.000 0.00 0.00 0.00 2.44
3447 3517 5.185454 TCCAGTACATAATGCTCCAAGTTG 58.815 41.667 0.00 0.00 0.00 3.16
3458 3528 2.869192 GCTCCAAGTTGCTGCTCTATAC 59.131 50.000 0.00 0.00 0.00 1.47
3465 3535 4.026744 AGTTGCTGCTCTATACCTCAGAA 58.973 43.478 0.00 0.00 0.00 3.02
3466 3536 4.467795 AGTTGCTGCTCTATACCTCAGAAA 59.532 41.667 0.00 0.00 0.00 2.52
3476 3546 7.225734 GCTCTATACCTCAGAAATCAAGGTTTC 59.774 40.741 11.33 0.00 40.53 2.78
3493 3563 2.649245 TTCATCTCCCAGCGGCATCG 62.649 60.000 1.45 0.00 39.81 3.84
3503 3573 2.614779 CAGCGGCATCGATATCAGAAT 58.385 47.619 1.45 0.00 39.00 2.40
3534 3634 3.738982 TCGTCACATCTGAACCAACATT 58.261 40.909 0.00 0.00 0.00 2.71
3553 3653 8.147704 CCAACATTAAGAAAAATACTGGGTGTT 58.852 33.333 0.00 0.00 0.00 3.32
3556 3656 9.758651 ACATTAAGAAAAATACTGGGTGTTTTC 57.241 29.630 5.81 8.53 36.21 2.29
3680 3780 6.598064 TCAAAGAAAGTAGCTAATACAAGCCC 59.402 38.462 0.00 0.00 43.86 5.19
3694 3794 2.497273 ACAAGCCCAAATCCAGCATAAC 59.503 45.455 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.361771 CAATGAGGCTGGCCCCTT 59.638 61.111 8.11 0.00 34.69 3.95
26 27 5.186198 ACCTACTAACAATGACAATGAGGC 58.814 41.667 0.00 0.00 0.00 4.70
81 82 7.038659 GCATGATGTAGGTCTAGATATTGGTC 58.961 42.308 0.00 0.00 0.00 4.02
94 95 3.051581 AGGAGAATGGCATGATGTAGGT 58.948 45.455 0.00 0.00 0.00 3.08
132 133 5.351458 TCACATATCATCGTCAAGAACCAG 58.649 41.667 0.00 0.00 0.00 4.00
167 168 1.620819 AGGCCTATATGGTTGAGCTCG 59.379 52.381 1.29 0.00 38.35 5.03
188 189 4.927782 AGGCCAAGCGCAACGACA 62.928 61.111 11.47 0.00 40.31 4.35
227 228 1.340889 TGTGCCAAGGAGATGCAAAAC 59.659 47.619 0.00 0.00 36.65 2.43
234 235 4.587520 TCCCTGTGCCAAGGAGAT 57.412 55.556 3.36 0.00 40.02 2.75
253 254 1.808133 CGAGCCTCCTGTTAGAATGGC 60.808 57.143 0.00 0.00 40.54 4.40
265 266 2.272918 CTGGACTTCGTCGAGCCTCC 62.273 65.000 10.80 9.22 32.29 4.30
297 298 4.870991 CGGGAGAAACTTAACTTCCTCATC 59.129 45.833 0.00 0.00 30.07 2.92
299 300 3.007614 CCGGGAGAAACTTAACTTCCTCA 59.992 47.826 0.00 0.00 30.07 3.86
300 301 3.007723 ACCGGGAGAAACTTAACTTCCTC 59.992 47.826 6.32 0.00 30.07 3.71
341 342 2.044135 CGCGCGCGTATGATATGATAT 58.956 47.619 42.49 0.00 34.35 1.63
371 372 0.234625 CAACACATTCGTCACCACGG 59.765 55.000 0.00 0.00 46.70 4.94
379 380 1.078709 CGATGGCTCAACACATTCGT 58.921 50.000 0.00 0.00 0.00 3.85
459 460 3.599792 CTTTGAAGCACTGCGGCGG 62.600 63.158 9.78 7.39 39.27 6.13
460 461 2.127118 CTTTGAAGCACTGCGGCG 60.127 61.111 0.51 0.51 39.27 6.46
550 551 1.269102 CCACAGAGTCGTGTTTCGTCT 60.269 52.381 12.11 0.00 40.19 4.18
559 560 2.100879 GAAGGCCACCACAGAGTCGT 62.101 60.000 5.01 0.00 0.00 4.34
562 563 2.529744 GGGAAGGCCACCACAGAGT 61.530 63.158 18.41 0.00 35.15 3.24
565 566 4.722700 CGGGGAAGGCCACCACAG 62.723 72.222 18.93 9.49 32.22 3.66
606 607 0.232303 CCATCGTCGCTTAAATCGCC 59.768 55.000 0.00 0.00 0.00 5.54
607 608 0.383124 GCCATCGTCGCTTAAATCGC 60.383 55.000 0.00 0.00 0.00 4.58
633 634 1.867233 CGCCCCACTAAGATTCAATCG 59.133 52.381 0.00 0.00 0.00 3.34
670 671 1.021390 CATGCTCAACGACACCCCTC 61.021 60.000 0.00 0.00 0.00 4.30
679 680 2.174107 CACCACGCATGCTCAACG 59.826 61.111 17.13 1.61 0.00 4.10
705 706 0.035820 TGACACCGTTATCCTTGCCC 60.036 55.000 0.00 0.00 0.00 5.36
714 715 0.386476 ACTTCACGCTGACACCGTTA 59.614 50.000 0.00 0.00 36.69 3.18
717 718 0.874175 TTGACTTCACGCTGACACCG 60.874 55.000 0.00 0.00 0.00 4.94
815 831 7.979444 ATCGAATTCTCAAAAGTGTTAGGAA 57.021 32.000 3.52 0.00 0.00 3.36
869 885 9.095065 AGTGAACTGTGTTAAACTACTTACAAG 57.905 33.333 0.00 0.00 0.00 3.16
872 888 8.638685 TGAGTGAACTGTGTTAAACTACTTAC 57.361 34.615 0.00 0.00 0.00 2.34
877 893 7.225931 GGTGATTGAGTGAACTGTGTTAAACTA 59.774 37.037 0.00 0.00 0.00 2.24
882 898 5.029807 TGGTGATTGAGTGAACTGTGTTA 57.970 39.130 0.00 0.00 0.00 2.41
890 938 5.863965 TGTGTTAGATGGTGATTGAGTGAA 58.136 37.500 0.00 0.00 0.00 3.18
906 954 3.041874 CTCAGCGAGCCTGTGTTAG 57.958 57.895 0.00 0.00 42.38 2.34
1092 1141 1.541620 AGGGAGGGGGAGTGGAAAC 60.542 63.158 0.00 0.00 0.00 2.78
2327 2382 2.473760 CCTCCGCTCGATCTCACGT 61.474 63.158 0.00 0.00 34.70 4.49
2414 2469 8.954950 ACATATTCTGTTTGATGAAGTCTAGG 57.045 34.615 0.00 0.00 32.90 3.02
2471 2526 7.570691 CGTCTTACAAACAGGAACAGATTTACC 60.571 40.741 0.00 0.00 0.00 2.85
2508 2563 7.239166 AGAATTTGTGCAAGAGATACATACG 57.761 36.000 0.00 0.00 0.00 3.06
2603 2662 4.640647 TCAGATACGCAATGTGACTAGAGT 59.359 41.667 0.00 0.00 33.16 3.24
2604 2663 5.175090 TCAGATACGCAATGTGACTAGAG 57.825 43.478 0.00 0.00 33.16 2.43
2619 2678 7.296628 ACCTCTGTTCCTTCATATCAGATAC 57.703 40.000 0.00 0.00 35.17 2.24
2629 2688 4.342951 TCGTCTAAAACCTCTGTTCCTTCA 59.657 41.667 0.00 0.00 32.15 3.02
2630 2689 4.685165 GTCGTCTAAAACCTCTGTTCCTTC 59.315 45.833 0.00 0.00 32.15 3.46
2632 2691 3.896272 AGTCGTCTAAAACCTCTGTTCCT 59.104 43.478 0.00 0.00 32.15 3.36
2634 2693 4.868067 TCAGTCGTCTAAAACCTCTGTTC 58.132 43.478 0.00 0.00 32.15 3.18
2636 2695 4.931661 TTCAGTCGTCTAAAACCTCTGT 57.068 40.909 0.00 0.00 0.00 3.41
2639 2698 5.383130 GCAATTTCAGTCGTCTAAAACCTC 58.617 41.667 0.00 0.00 0.00 3.85
2753 2818 1.370900 CTTGTTTGCGGTGCTGAGC 60.371 57.895 0.00 0.00 0.00 4.26
2763 2828 4.494690 GCTTTTCTTTTCAGGCTTGTTTGC 60.495 41.667 0.00 0.00 0.00 3.68
2804 2873 6.040955 CAGGTTCTGGTATTAGCAGTATCAGA 59.959 42.308 19.42 2.89 43.70 3.27
2814 2883 5.363868 TGGAGTCATCAGGTTCTGGTATTAG 59.636 44.000 0.00 0.00 31.51 1.73
2822 2891 3.779444 TGTACTGGAGTCATCAGGTTCT 58.221 45.455 0.00 0.00 36.62 3.01
2844 2913 3.148412 TGAGCAGCAACTTGAAGCATTA 58.852 40.909 0.00 0.00 0.00 1.90
2865 2934 8.190888 GATGAAATCTTGACGTCTGAGTTATT 57.809 34.615 17.92 10.51 41.17 1.40
2904 2974 3.553922 CGAAGGCCTCCAGTTCTGATATC 60.554 52.174 5.23 0.00 0.00 1.63
2922 2992 0.737367 TTGGCTCAGATGCGACGAAG 60.737 55.000 0.00 0.00 0.00 3.79
2930 3000 9.512435 CTATTTTTCTTAATGTTGGCTCAGATG 57.488 33.333 0.00 0.00 0.00 2.90
2991 3061 7.169308 CCAATTGATTGCATTTCTTAGCATCTC 59.831 37.037 7.12 0.00 40.94 2.75
2998 3068 6.352051 CCCTTCCCAATTGATTGCATTTCTTA 60.352 38.462 7.12 0.00 36.48 2.10
3028 3098 6.096673 TGAACCCCTTGCTTTTTCTATTTC 57.903 37.500 0.00 0.00 0.00 2.17
3039 3109 3.532641 AATTCTCTTGAACCCCTTGCT 57.467 42.857 0.00 0.00 34.71 3.91
3100 3170 5.005203 CAGCAACTTCGAGCTCAAGTAATAG 59.995 44.000 23.13 16.70 39.50 1.73
3101 3171 4.864806 CAGCAACTTCGAGCTCAAGTAATA 59.135 41.667 23.13 0.00 39.50 0.98
3102 3172 3.681897 CAGCAACTTCGAGCTCAAGTAAT 59.318 43.478 23.13 12.03 39.50 1.89
3107 3177 0.250038 AGCAGCAACTTCGAGCTCAA 60.250 50.000 15.40 6.48 39.50 3.02
3109 3179 2.077403 GAGCAGCAACTTCGAGCTC 58.923 57.895 2.73 2.73 43.95 4.09
3161 3231 5.891810 TTTTGCGTTATTTTGCCTTGTAC 57.108 34.783 0.00 0.00 0.00 2.90
3174 3244 6.975772 ACTTGCTTTGAAGTTATTTTGCGTTA 59.024 30.769 0.00 0.00 31.92 3.18
3178 3248 6.811299 GCTACTTGCTTTGAAGTTATTTTGC 58.189 36.000 0.00 0.00 37.38 3.68
3198 3268 6.972901 GCTGGATTTTGGTTTGTATTAGCTAC 59.027 38.462 0.00 0.00 0.00 3.58
3211 3281 5.263599 TGTTCTATCATGCTGGATTTTGGT 58.736 37.500 0.00 0.00 0.00 3.67
3231 3301 2.034124 ACAAAGCAGCACCAGAATGTT 58.966 42.857 0.00 0.00 0.00 2.71
3232 3302 1.696063 ACAAAGCAGCACCAGAATGT 58.304 45.000 0.00 0.00 0.00 2.71
3233 3303 2.295349 AGAACAAAGCAGCACCAGAATG 59.705 45.455 0.00 0.00 0.00 2.67
3234 3304 2.590821 AGAACAAAGCAGCACCAGAAT 58.409 42.857 0.00 0.00 0.00 2.40
3235 3305 2.057137 AGAACAAAGCAGCACCAGAA 57.943 45.000 0.00 0.00 0.00 3.02
3236 3306 2.928801 TAGAACAAAGCAGCACCAGA 57.071 45.000 0.00 0.00 0.00 3.86
3237 3307 3.755378 AGAATAGAACAAAGCAGCACCAG 59.245 43.478 0.00 0.00 0.00 4.00
3238 3308 3.754965 AGAATAGAACAAAGCAGCACCA 58.245 40.909 0.00 0.00 0.00 4.17
3239 3309 4.773323 AAGAATAGAACAAAGCAGCACC 57.227 40.909 0.00 0.00 0.00 5.01
3240 3310 5.316770 CGTAAGAATAGAACAAAGCAGCAC 58.683 41.667 0.00 0.00 43.02 4.40
3241 3311 5.530519 CGTAAGAATAGAACAAAGCAGCA 57.469 39.130 0.00 0.00 43.02 4.41
3318 3388 3.116096 ACCTGTAGCACTTGGGAGATA 57.884 47.619 0.00 0.00 0.00 1.98
3332 3402 3.826524 TCCATGCAGTTCAAAACCTGTA 58.173 40.909 0.00 0.00 0.00 2.74
3342 3412 3.733077 GCAAGCTGTTATCCATGCAGTTC 60.733 47.826 0.00 0.00 34.10 3.01
3380 3450 5.921408 GCAGGTATTAGTAGTGTGCTATGTC 59.079 44.000 0.00 0.00 0.00 3.06
3422 3492 5.186198 ACTTGGAGCATTATGTACTGGAAC 58.814 41.667 0.00 0.00 0.00 3.62
3447 3517 5.207110 TGATTTCTGAGGTATAGAGCAGC 57.793 43.478 0.00 0.00 0.00 5.25
3458 3528 5.356470 GGAGATGAAACCTTGATTTCTGAGG 59.644 44.000 0.00 0.00 39.02 3.86
3465 3535 3.359950 GCTGGGAGATGAAACCTTGATT 58.640 45.455 0.00 0.00 0.00 2.57
3466 3536 2.681976 CGCTGGGAGATGAAACCTTGAT 60.682 50.000 0.00 0.00 0.00 2.57
3476 3546 2.446142 ATCGATGCCGCTGGGAGATG 62.446 60.000 0.00 0.00 34.06 2.90
3493 3563 3.430218 CGAACGCCTCCAATTCTGATATC 59.570 47.826 0.00 0.00 0.00 1.63
3503 3573 0.669318 GATGTGACGAACGCCTCCAA 60.669 55.000 0.00 0.00 0.00 3.53
3534 3634 8.754991 TCTGAAAACACCCAGTATTTTTCTTA 57.245 30.769 11.80 2.59 38.32 2.10
3575 3675 9.722056 AATTGATTGCATTTCGTAGTATCTTTC 57.278 29.630 0.00 0.00 0.00 2.62
3586 3686 5.005971 GTCATTCCCAATTGATTGCATTTCG 59.994 40.000 7.12 0.00 36.48 3.46


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

AutoCloner maintained by Alex Coulton.