Multiple sequence alignment - TraesCS6A01G139600

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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 TraesCS6A01G139600 chr6A 100.000 3284 0 0 1 3284 114267394 114270677 0.000000e+00 6065
1 TraesCS6A01G139600 chr6D 91.162 2874 189 33 1 2850 95250646 95247814 0.000000e+00 3840
2 TraesCS6A01G139600 chr6D 93.548 310 5 3 2951 3245 95247672 95247363 6.460000e-122 448
3 TraesCS6A01G139600 chr6B 89.971 2742 173 35 563 3245 177792974 177795672 0.000000e+00 3446
4 TraesCS6A01G139600 chr6B 88.583 508 55 2 4 509 177787331 177787837 6.020000e-172 614
5 TraesCS6A01G139600 chr6B 95.161 62 3 0 511 572 177787992 177788053 7.500000e-17 99
6 TraesCS6A01G139600 chr2D 87.536 1035 77 24 1651 2682 118403637 118404622 0.000000e+00 1149
7 TraesCS6A01G139600 chr2D 88.056 854 68 11 920 1757 118386209 118387044 0.000000e+00 981
8 TraesCS6A01G139600 chr2D 90.086 464 33 10 1572 2033 118402535 118402987 1.010000e-164 590
9 TraesCS6A01G139600 chr2D 89.871 464 34 7 1572 2033 118400953 118401405 4.720000e-163 584
10 TraesCS6A01G139600 chr2D 89.655 464 35 10 1572 2033 118389940 118390392 2.200000e-161 579
11 TraesCS6A01G139600 chr2D 89.009 464 35 12 1572 2033 118388611 118389060 7.960000e-156 560
12 TraesCS6A01G139600 chr2D 88.793 464 39 10 1572 2033 118389496 118389948 1.030000e-154 556
13 TraesCS6A01G139600 chr2D 88.578 464 40 10 1572 2033 118389052 118389504 4.790000e-153 551
14 TraesCS6A01G139600 chr2D 88.647 414 34 7 1616 2027 118388211 118388613 2.940000e-135 492
15 TraesCS6A01G139600 chr2D 89.974 379 25 10 1651 2027 118402170 118402537 8.240000e-131 477
16 TraesCS6A01G139600 chr2D 86.345 249 23 7 1785 2033 118400724 118400961 9.040000e-66 261


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 TraesCS6A01G139600 chr6A 114267394 114270677 3283 False 6065.000000 6065 100.000000 1 3284 1 chr6A.!!$F1 3283
1 TraesCS6A01G139600 chr6D 95247363 95250646 3283 True 2144.000000 3840 92.355000 1 3245 2 chr6D.!!$R1 3244
2 TraesCS6A01G139600 chr6B 177792974 177795672 2698 False 3446.000000 3446 89.971000 563 3245 1 chr6B.!!$F1 2682
3 TraesCS6A01G139600 chr6B 177787331 177788053 722 False 356.500000 614 91.872000 4 572 2 chr6B.!!$F2 568
4 TraesCS6A01G139600 chr2D 118386209 118390392 4183 False 619.833333 981 88.789667 920 2033 6 chr2D.!!$F1 1113
5 TraesCS6A01G139600 chr2D 118400724 118404622 3898 False 612.200000 1149 88.762400 1572 2682 5 chr2D.!!$F2 1110

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
57 59 0.391597 ACAAACTCCATGTCGTCGGT 59.608 50.0 0.00 0.00 0.00 4.69 F
964 1133 0.393077 ACAGTGACCAGTGTACTGCC 59.607 55.0 15.34 1.87 44.22 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1537 0.169009 GTTTTCACCATCTCAGGCGC 59.831 55.0 0.00 0.0 0.0 6.53 R
2810 7806 0.110678 TGGCACCGTGATTAAACCCA 59.889 50.0 1.65 0.0 0.0 4.51 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
57 59 0.391597 ACAAACTCCATGTCGTCGGT 59.608 50.000 0.00 0.00 0.00 4.69
67 69 0.820482 TGTCGTCGGTGTCCTTCTCA 60.820 55.000 0.00 0.00 0.00 3.27
217 219 4.603535 GGCAGTGCAGGGGGTGTT 62.604 66.667 18.61 0.00 0.00 3.32
232 236 1.064017 GGTGTTGATGGCTAATGGGGA 60.064 52.381 0.00 0.00 0.00 4.81
276 280 2.032071 CAAAGGGGGAGCGAACGT 59.968 61.111 0.00 0.00 0.00 3.99
288 292 0.458025 GCGAACGTGGGTAAGAGAGG 60.458 60.000 0.00 0.00 0.00 3.69
308 312 2.802106 GGACGCGGGAGAGAGAAG 59.198 66.667 12.47 0.00 0.00 2.85
352 356 3.963374 AGGATTTGAGATGGATCGAGACA 59.037 43.478 0.00 0.00 0.00 3.41
387 391 5.182950 ACATGACAAATAAGTTCAATCGGCA 59.817 36.000 0.00 0.00 0.00 5.69
397 401 1.725641 TCAATCGGCATCATATCCGC 58.274 50.000 0.00 0.00 44.91 5.54
400 404 0.615331 ATCGGCATCATATCCGCCTT 59.385 50.000 0.00 0.00 44.91 4.35
402 406 1.204704 TCGGCATCATATCCGCCTTAG 59.795 52.381 0.00 0.00 44.91 2.18
406 410 4.372656 GGCATCATATCCGCCTTAGATAC 58.627 47.826 0.00 0.00 42.78 2.24
422 426 7.259161 CCTTAGATACGAGCTGAGTTTAAAGT 58.741 38.462 0.00 0.00 0.00 2.66
585 742 2.423892 TGGCGTTTGCTTGTCTGTTAAA 59.576 40.909 0.00 0.00 42.25 1.52
605 762 2.953821 CAACACGCGGCTCCAAAT 59.046 55.556 12.47 0.00 0.00 2.32
636 793 4.841443 AACAACACCGATTTCCCTTTAC 57.159 40.909 0.00 0.00 0.00 2.01
673 830 6.183361 ACAAAGATTGAGAGAGGTGTACTGTT 60.183 38.462 0.00 0.00 0.00 3.16
676 833 2.526432 TGAGAGAGGTGTACTGTTCCC 58.474 52.381 0.00 0.00 0.00 3.97
801 965 4.344865 TCGGCCCCTCAAACAGCC 62.345 66.667 0.00 0.00 42.18 4.85
842 1006 2.415491 GGCCTGTCAGAAAAATTACCGC 60.415 50.000 0.00 0.00 0.00 5.68
850 1014 0.963225 AAAAATTACCGCGCCAGGTT 59.037 45.000 12.38 0.00 43.00 3.50
851 1015 1.823797 AAAATTACCGCGCCAGGTTA 58.176 45.000 12.38 3.94 43.00 2.85
857 1021 2.380084 ACCGCGCCAGGTTATATATG 57.620 50.000 0.00 0.00 43.00 1.78
964 1133 0.393077 ACAGTGACCAGTGTACTGCC 59.607 55.000 15.34 1.87 44.22 4.85
970 1139 2.507102 CAGTGTACTGCCCGCTCG 60.507 66.667 0.00 0.00 37.15 5.03
1146 1327 2.508887 CTGTCGCTGGAGAGCAGC 60.509 66.667 0.00 0.00 46.62 5.25
1383 1566 3.299977 GTGAAAACCCACCGGCCC 61.300 66.667 0.00 0.00 0.00 5.80
1734 4367 2.125229 TCGTCGTCCTCCTCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
1986 5940 3.376935 CTCCCCGCGCATGAACTCT 62.377 63.158 8.75 0.00 0.00 3.24
2064 7041 2.997315 CACTCCAGCCTCCGGTCA 60.997 66.667 0.00 0.00 0.00 4.02
2264 7244 2.433838 CAGCGTGAGTGGCAGAGG 60.434 66.667 0.00 0.00 0.00 3.69
2275 7255 2.743928 GCAGAGGTCTTGGCACCG 60.744 66.667 0.00 0.00 41.90 4.94
2376 7366 3.921257 GCAGCATTTCCTTTGCCTT 57.079 47.368 0.00 0.00 41.06 4.35
2377 7367 2.174363 GCAGCATTTCCTTTGCCTTT 57.826 45.000 0.00 0.00 41.06 3.11
2378 7368 3.317603 GCAGCATTTCCTTTGCCTTTA 57.682 42.857 0.00 0.00 41.06 1.85
2379 7369 3.256558 GCAGCATTTCCTTTGCCTTTAG 58.743 45.455 0.00 0.00 41.06 1.85
2380 7370 3.256558 CAGCATTTCCTTTGCCTTTAGC 58.743 45.455 0.00 0.00 41.06 3.09
2508 7498 3.449018 TGTCTTTAGGAGAAGCTGGCTAG 59.551 47.826 0.00 0.00 35.79 3.42
2528 7518 1.602311 GCTAGAGCCCCATGTTCATG 58.398 55.000 5.88 5.88 34.31 3.07
2529 7519 1.602311 CTAGAGCCCCATGTTCATGC 58.398 55.000 7.21 0.00 0.00 4.06
2530 7520 1.142465 CTAGAGCCCCATGTTCATGCT 59.858 52.381 7.21 2.12 34.40 3.79
2531 7521 0.395311 AGAGCCCCATGTTCATGCTG 60.395 55.000 7.21 2.32 31.23 4.41
2571 7562 6.534793 CCCCATGTAAATTTTGTCTAATGTGC 59.465 38.462 0.00 0.00 0.00 4.57
2592 7583 3.829026 GCTTCACCATCCTTTTTCCTCTT 59.171 43.478 0.00 0.00 0.00 2.85
2593 7584 4.082517 GCTTCACCATCCTTTTTCCTCTTC 60.083 45.833 0.00 0.00 0.00 2.87
2627 7619 3.189080 TGTTTCTCCAAGCACATTCGATG 59.811 43.478 0.00 0.00 0.00 3.84
2631 7623 0.527113 CCAAGCACATTCGATGGCAA 59.473 50.000 0.00 0.00 33.60 4.52
2635 7627 1.470098 AGCACATTCGATGGCAAGTTC 59.530 47.619 0.00 0.00 33.60 3.01
2639 7631 2.095768 ACATTCGATGGCAAGTTCGTTG 60.096 45.455 8.63 9.85 39.41 4.10
2682 7674 9.625747 AGGAGAAAAGATATGAAAGAGATTTCC 57.374 33.333 0.00 0.00 0.00 3.13
2683 7675 8.555361 GGAGAAAAGATATGAAAGAGATTTCCG 58.445 37.037 0.00 0.00 0.00 4.30
2693 7685 7.834068 TGAAAGAGATTTCCGAACTATTCTG 57.166 36.000 0.00 0.00 0.00 3.02
2696 7688 5.665459 AGAGATTTCCGAACTATTCTGGTG 58.335 41.667 0.00 0.00 0.00 4.17
2697 7689 4.770795 AGATTTCCGAACTATTCTGGTGG 58.229 43.478 0.00 0.00 0.00 4.61
2698 7690 2.396590 TTCCGAACTATTCTGGTGGC 57.603 50.000 0.00 0.00 0.00 5.01
2699 7691 0.539986 TCCGAACTATTCTGGTGGCC 59.460 55.000 0.00 0.00 0.00 5.36
2700 7692 0.541863 CCGAACTATTCTGGTGGCCT 59.458 55.000 3.32 0.00 0.00 5.19
2701 7693 1.656652 CGAACTATTCTGGTGGCCTG 58.343 55.000 3.32 0.00 0.00 4.85
2702 7694 1.207089 CGAACTATTCTGGTGGCCTGA 59.793 52.381 3.32 0.00 0.00 3.86
2703 7695 2.633488 GAACTATTCTGGTGGCCTGAC 58.367 52.381 3.32 0.00 31.34 3.51
2723 7715 2.222445 ACGGCGTTATTGTTGTCTGTTC 59.778 45.455 6.77 0.00 0.00 3.18
2729 7721 4.670621 CGTTATTGTTGTCTGTTCTTGCAC 59.329 41.667 0.00 0.00 0.00 4.57
2737 7729 2.098614 TCTGTTCTTGCACTGCCAAAA 58.901 42.857 0.00 0.00 0.00 2.44
2738 7730 2.694628 TCTGTTCTTGCACTGCCAAAAT 59.305 40.909 0.00 0.00 0.00 1.82
2739 7731 3.054878 CTGTTCTTGCACTGCCAAAATC 58.945 45.455 0.00 0.00 0.00 2.17
2740 7732 2.224018 TGTTCTTGCACTGCCAAAATCC 60.224 45.455 0.00 0.00 0.00 3.01
2741 7733 1.702182 TCTTGCACTGCCAAAATCCA 58.298 45.000 0.00 0.00 0.00 3.41
2742 7734 2.250031 TCTTGCACTGCCAAAATCCAT 58.750 42.857 0.00 0.00 0.00 3.41
2743 7735 2.028839 TCTTGCACTGCCAAAATCCATG 60.029 45.455 0.00 0.00 0.00 3.66
2745 7737 2.523245 TGCACTGCCAAAATCCATGTA 58.477 42.857 0.00 0.00 0.00 2.29
2746 7738 2.230992 TGCACTGCCAAAATCCATGTAC 59.769 45.455 0.00 0.00 0.00 2.90
2748 7740 1.472480 ACTGCCAAAATCCATGTACGC 59.528 47.619 0.00 0.00 0.00 4.42
2749 7741 1.745087 CTGCCAAAATCCATGTACGCT 59.255 47.619 0.00 0.00 0.00 5.07
2750 7742 1.472082 TGCCAAAATCCATGTACGCTG 59.528 47.619 0.00 0.00 0.00 5.18
2766 7761 4.382345 ACGCTGTAGTTACCCTATTGTC 57.618 45.455 0.00 0.00 0.00 3.18
2779 7774 9.408069 GTTACCCTATTGTCAGTATCTTAATCG 57.592 37.037 0.00 0.00 0.00 3.34
2782 7777 6.809196 CCCTATTGTCAGTATCTTAATCGCTC 59.191 42.308 0.00 0.00 0.00 5.03
2783 7778 6.809196 CCTATTGTCAGTATCTTAATCGCTCC 59.191 42.308 0.00 0.00 0.00 4.70
2784 7779 4.585955 TGTCAGTATCTTAATCGCTCCC 57.414 45.455 0.00 0.00 0.00 4.30
2795 7790 5.873164 TCTTAATCGCTCCCTGTAAAAAGTC 59.127 40.000 0.00 0.00 0.00 3.01
2798 7793 1.337447 CGCTCCCTGTAAAAAGTCGGA 60.337 52.381 0.00 0.00 0.00 4.55
2799 7794 2.347731 GCTCCCTGTAAAAAGTCGGAG 58.652 52.381 0.00 0.00 39.94 4.63
2801 7796 2.565834 CTCCCTGTAAAAAGTCGGAGGA 59.434 50.000 0.00 0.00 34.49 3.71
2810 7806 1.137697 AAGTCGGAGGAAAAGGGTGT 58.862 50.000 0.00 0.00 0.00 4.16
2847 7843 2.315176 CCATGTGGACCTGGTGAAAAA 58.685 47.619 2.82 0.00 37.39 1.94
2852 7848 3.053991 TGTGGACCTGGTGAAAAAGAAGA 60.054 43.478 2.82 0.00 0.00 2.87
2854 7850 3.202151 TGGACCTGGTGAAAAAGAAGAGT 59.798 43.478 2.82 0.00 0.00 3.24
2864 7874 5.232838 GTGAAAAAGAAGAGTTGCACAATGG 59.767 40.000 0.00 0.00 0.00 3.16
2867 7877 2.233271 AGAAGAGTTGCACAATGGTGG 58.767 47.619 1.53 0.00 45.38 4.61
2873 7883 2.093021 AGTTGCACAATGGTGGCTTTTT 60.093 40.909 1.53 0.00 45.38 1.94
2876 7886 1.881591 CACAATGGTGGCTTTTTGGG 58.118 50.000 0.00 0.00 41.45 4.12
2878 7888 0.036590 CAATGGTGGCTTTTTGGGGG 59.963 55.000 0.00 0.00 0.00 5.40
2893 7903 2.273179 GGGGGAACTTTTCGTGGCC 61.273 63.158 0.00 0.00 0.00 5.36
2899 7909 0.536460 AACTTTTCGTGGCCGGTGAT 60.536 50.000 1.90 0.00 33.95 3.06
2900 7910 1.234615 ACTTTTCGTGGCCGGTGATG 61.235 55.000 1.90 0.00 33.95 3.07
2901 7911 0.953471 CTTTTCGTGGCCGGTGATGA 60.953 55.000 1.90 0.00 33.95 2.92
2902 7912 0.953471 TTTTCGTGGCCGGTGATGAG 60.953 55.000 1.90 0.00 33.95 2.90
2903 7913 2.107041 TTTCGTGGCCGGTGATGAGT 62.107 55.000 1.90 0.00 33.95 3.41
2904 7914 2.779951 TTCGTGGCCGGTGATGAGTG 62.780 60.000 1.90 0.00 33.95 3.51
2905 7915 2.662596 GTGGCCGGTGATGAGTGA 59.337 61.111 1.90 0.00 0.00 3.41
2906 7916 1.741770 GTGGCCGGTGATGAGTGAC 60.742 63.158 1.90 0.00 0.00 3.67
2907 7917 1.913262 TGGCCGGTGATGAGTGACT 60.913 57.895 1.90 0.00 0.00 3.41
2908 7918 1.448540 GGCCGGTGATGAGTGACTG 60.449 63.158 1.90 0.00 0.00 3.51
2909 7919 2.103042 GCCGGTGATGAGTGACTGC 61.103 63.158 1.90 0.00 0.00 4.40
2910 7920 1.593787 CCGGTGATGAGTGACTGCT 59.406 57.895 0.00 0.00 0.00 4.24
2911 7921 0.738762 CCGGTGATGAGTGACTGCTG 60.739 60.000 0.00 0.00 0.00 4.41
2912 7922 0.738762 CGGTGATGAGTGACTGCTGG 60.739 60.000 0.00 0.00 0.00 4.85
2913 7923 0.322975 GGTGATGAGTGACTGCTGGT 59.677 55.000 0.00 0.00 0.00 4.00
2914 7924 1.550524 GGTGATGAGTGACTGCTGGTA 59.449 52.381 0.00 0.00 0.00 3.25
2927 7937 1.476891 TGCTGGTAACTCGATGGAGAC 59.523 52.381 12.14 0.00 43.27 3.36
2930 7940 0.739561 GGTAACTCGATGGAGACGCT 59.260 55.000 12.14 0.00 43.27 5.07
3267 8344 2.750237 CCCCCGCTGCTGGTTTAC 60.750 66.667 9.31 0.00 0.00 2.01
3268 8345 2.351276 CCCCGCTGCTGGTTTACT 59.649 61.111 9.31 0.00 0.00 2.24
3269 8346 2.040544 CCCCGCTGCTGGTTTACTG 61.041 63.158 9.31 0.00 0.00 2.74
3270 8347 1.003839 CCCGCTGCTGGTTTACTGA 60.004 57.895 1.46 0.00 0.00 3.41
3271 8348 0.392998 CCCGCTGCTGGTTTACTGAT 60.393 55.000 1.46 0.00 0.00 2.90
3272 8349 1.453155 CCGCTGCTGGTTTACTGATT 58.547 50.000 0.00 0.00 0.00 2.57
3273 8350 1.812571 CCGCTGCTGGTTTACTGATTT 59.187 47.619 0.00 0.00 0.00 2.17
3274 8351 3.006940 CCGCTGCTGGTTTACTGATTTA 58.993 45.455 0.00 0.00 0.00 1.40
3275 8352 3.627577 CCGCTGCTGGTTTACTGATTTAT 59.372 43.478 0.00 0.00 0.00 1.40
3276 8353 4.260784 CCGCTGCTGGTTTACTGATTTATC 60.261 45.833 0.00 0.00 0.00 1.75
3277 8354 4.572389 CGCTGCTGGTTTACTGATTTATCT 59.428 41.667 0.00 0.00 0.00 1.98
3278 8355 5.277058 CGCTGCTGGTTTACTGATTTATCTC 60.277 44.000 0.00 0.00 0.00 2.75
3279 8356 5.008118 GCTGCTGGTTTACTGATTTATCTCC 59.992 44.000 0.00 0.00 0.00 3.71
3280 8357 5.116180 TGCTGGTTTACTGATTTATCTCCG 58.884 41.667 0.00 0.00 0.00 4.63
3281 8358 4.024809 GCTGGTTTACTGATTTATCTCCGC 60.025 45.833 0.00 0.00 0.00 5.54
3282 8359 4.448210 TGGTTTACTGATTTATCTCCGCC 58.552 43.478 0.00 0.00 0.00 6.13
3283 8360 4.163458 TGGTTTACTGATTTATCTCCGCCT 59.837 41.667 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 59 6.042093 AGAGAATGTAGTTGTTGAGAAGGACA 59.958 38.462 0.00 0.00 0.00 4.02
67 69 4.327680 GGAAGGCAGAGAATGTAGTTGTT 58.672 43.478 0.00 0.00 0.00 2.83
203 205 1.075482 CATCAACACCCCCTGCACT 59.925 57.895 0.00 0.00 0.00 4.40
207 209 0.331278 TTAGCCATCAACACCCCCTG 59.669 55.000 0.00 0.00 0.00 4.45
217 219 1.776667 CTCCTTCCCCATTAGCCATCA 59.223 52.381 0.00 0.00 0.00 3.07
232 236 2.571216 CCACGTCACCGACCTCCTT 61.571 63.158 0.00 0.00 37.88 3.36
276 280 0.679002 CGTCCGTCCTCTCTTACCCA 60.679 60.000 0.00 0.00 0.00 4.51
288 292 3.878519 CTCTCTCCCGCGTCCGTC 61.879 72.222 4.92 0.00 0.00 4.79
308 312 3.371102 TCAAATCGATCTGACCGATCC 57.629 47.619 7.49 0.00 44.85 3.36
330 334 3.963374 TGTCTCGATCCATCTCAAATCCT 59.037 43.478 0.00 0.00 0.00 3.24
352 356 8.561738 ACTTATTTGTCATGTTATTTCCGACT 57.438 30.769 0.00 0.00 0.00 4.18
363 367 5.182950 TGCCGATTGAACTTATTTGTCATGT 59.817 36.000 0.00 0.00 0.00 3.21
365 369 5.895636 TGCCGATTGAACTTATTTGTCAT 57.104 34.783 0.00 0.00 0.00 3.06
387 391 4.036971 GCTCGTATCTAAGGCGGATATGAT 59.963 45.833 15.08 0.00 39.46 2.45
397 401 7.221067 CACTTTAAACTCAGCTCGTATCTAAGG 59.779 40.741 0.00 0.00 0.00 2.69
400 404 7.154435 ACACTTTAAACTCAGCTCGTATCTA 57.846 36.000 0.00 0.00 0.00 1.98
402 406 5.288952 GGACACTTTAAACTCAGCTCGTATC 59.711 44.000 0.00 0.00 0.00 2.24
406 410 2.737252 GGGACACTTTAAACTCAGCTCG 59.263 50.000 0.00 0.00 0.00 5.03
422 426 3.055819 GCATCTCTAACAGAACTGGGACA 60.056 47.826 6.76 0.00 33.62 4.02
509 513 5.784177 CGGCAGTGATAATAATGTACTCCT 58.216 41.667 0.00 0.00 0.00 3.69
559 716 0.657368 GACAAGCAAACGCCAAGACG 60.657 55.000 0.00 0.00 39.50 4.18
605 762 1.813178 TCGGTGTTGTTTTTGTCTGCA 59.187 42.857 0.00 0.00 0.00 4.41
636 793 5.936372 TCTCAATCTTTGTGTCTGAATCTGG 59.064 40.000 0.00 0.00 0.00 3.86
673 830 3.884693 TCGACTAATTGTATAGTGCGGGA 59.115 43.478 0.00 0.00 36.28 5.14
676 833 5.564504 GCTACTCGACTAATTGTATAGTGCG 59.435 44.000 0.00 0.00 36.28 5.34
831 995 0.963225 AACCTGGCGCGGTAATTTTT 59.037 45.000 8.83 0.00 35.89 1.94
842 1006 2.850060 CGCGTACATATATAACCTGGCG 59.150 50.000 0.00 6.50 0.00 5.69
850 1014 2.925578 AAGGCGCGCGTACATATATA 57.074 45.000 32.35 0.00 0.00 0.86
851 1015 2.074547 AAAGGCGCGCGTACATATAT 57.925 45.000 32.35 6.38 0.00 0.86
857 1021 3.557479 GGGTAAAGGCGCGCGTAC 61.557 66.667 32.35 24.70 0.00 3.67
877 1041 3.665675 AATGCCGAGACAGGGACGC 62.666 63.158 0.00 0.00 33.38 5.19
878 1042 1.079127 AAATGCCGAGACAGGGACG 60.079 57.895 0.00 0.00 33.38 4.79
933 1102 1.005037 TCACTGTACTTGGCTGCGG 60.005 57.895 0.00 0.00 0.00 5.69
934 1103 1.291877 GGTCACTGTACTTGGCTGCG 61.292 60.000 0.00 0.00 0.00 5.18
935 1104 0.250295 TGGTCACTGTACTTGGCTGC 60.250 55.000 0.00 0.00 0.00 5.25
1179 1360 1.084370 CGATGAACTCCTTGGACGCC 61.084 60.000 0.00 0.00 0.00 5.68
1354 1537 0.169009 GTTTTCACCATCTCAGGCGC 59.831 55.000 0.00 0.00 0.00 6.53
1397 1580 0.883833 GAACACGTAGGGGTCGAAGA 59.116 55.000 0.00 0.00 0.00 2.87
1398 1581 0.886563 AGAACACGTAGGGGTCGAAG 59.113 55.000 0.00 0.00 0.00 3.79
1461 1644 3.672295 CTGGACCTTCCTGAGCCGC 62.672 68.421 0.00 0.00 37.65 6.53
1462 1645 1.984570 TCTGGACCTTCCTGAGCCG 60.985 63.158 0.00 0.00 39.21 5.52
1734 4367 3.434319 TCGTGGTCGTAGGCGGAC 61.434 66.667 0.00 0.00 38.89 4.79
1986 5940 0.672401 GGAACACGATCTTGCCGGAA 60.672 55.000 5.05 0.00 0.00 4.30
2264 7244 1.080569 CATTTGCCGGTGCCAAGAC 60.081 57.895 1.90 0.00 36.33 3.01
2275 7255 6.038050 TCAAAACAAGGTCAATTTCATTTGCC 59.962 34.615 0.00 0.00 0.00 4.52
2352 7332 2.416431 GCAAAGGAAATGCTGCCTAGTG 60.416 50.000 0.00 0.00 40.64 2.74
2375 7365 5.838531 TTTTCGTTCCCTTTTCTGCTAAA 57.161 34.783 0.00 0.00 0.00 1.85
2376 7366 5.591067 TCTTTTTCGTTCCCTTTTCTGCTAA 59.409 36.000 0.00 0.00 0.00 3.09
2377 7367 5.127491 TCTTTTTCGTTCCCTTTTCTGCTA 58.873 37.500 0.00 0.00 0.00 3.49
2378 7368 3.951680 TCTTTTTCGTTCCCTTTTCTGCT 59.048 39.130 0.00 0.00 0.00 4.24
2379 7369 4.301637 TCTTTTTCGTTCCCTTTTCTGC 57.698 40.909 0.00 0.00 0.00 4.26
2380 7370 6.503524 TCAATCTTTTTCGTTCCCTTTTCTG 58.496 36.000 0.00 0.00 0.00 3.02
2571 7562 5.048434 GTGAAGAGGAAAAAGGATGGTGAAG 60.048 44.000 0.00 0.00 0.00 3.02
2592 7583 4.584874 TGGAGAAACAGAACACAAAGTGA 58.415 39.130 3.88 0.00 36.96 3.41
2593 7584 4.963276 TGGAGAAACAGAACACAAAGTG 57.037 40.909 0.00 0.00 39.75 3.16
2635 7627 5.637810 TCCTATTGCTTAAGAGTTCACAACG 59.362 40.000 6.67 0.00 36.23 4.10
2639 7631 7.907214 TTTCTCCTATTGCTTAAGAGTTCAC 57.093 36.000 6.67 0.00 0.00 3.18
2649 7641 9.911788 TCTTTCATATCTTTTCTCCTATTGCTT 57.088 29.630 0.00 0.00 0.00 3.91
2682 7674 1.207089 TCAGGCCACCAGAATAGTTCG 59.793 52.381 5.01 0.00 34.02 3.95
2683 7675 2.633488 GTCAGGCCACCAGAATAGTTC 58.367 52.381 5.01 0.00 0.00 3.01
2688 7680 2.671070 CCGTCAGGCCACCAGAAT 59.329 61.111 5.01 0.00 0.00 2.40
2698 7690 1.127951 GACAACAATAACGCCGTCAGG 59.872 52.381 0.00 0.00 41.62 3.86
2699 7691 2.066262 AGACAACAATAACGCCGTCAG 58.934 47.619 0.00 0.00 0.00 3.51
2700 7692 1.795872 CAGACAACAATAACGCCGTCA 59.204 47.619 0.00 0.00 0.00 4.35
2701 7693 1.796459 ACAGACAACAATAACGCCGTC 59.204 47.619 0.00 0.00 0.00 4.79
2702 7694 1.873698 ACAGACAACAATAACGCCGT 58.126 45.000 0.00 0.00 0.00 5.68
2703 7695 2.478894 AGAACAGACAACAATAACGCCG 59.521 45.455 0.00 0.00 0.00 6.46
2723 7715 2.289195 ACATGGATTTTGGCAGTGCAAG 60.289 45.455 18.61 0.00 0.00 4.01
2729 7721 1.745087 AGCGTACATGGATTTTGGCAG 59.255 47.619 0.00 0.00 0.00 4.85
2737 7729 3.069158 GGGTAACTACAGCGTACATGGAT 59.931 47.826 0.00 0.00 0.00 3.41
2738 7730 2.428171 GGGTAACTACAGCGTACATGGA 59.572 50.000 0.00 0.00 0.00 3.41
2739 7731 2.429610 AGGGTAACTACAGCGTACATGG 59.570 50.000 0.00 0.00 0.00 3.66
2740 7732 3.795623 AGGGTAACTACAGCGTACATG 57.204 47.619 0.00 0.00 0.00 3.21
2741 7733 5.361857 ACAATAGGGTAACTACAGCGTACAT 59.638 40.000 0.00 0.00 33.70 2.29
2742 7734 4.706476 ACAATAGGGTAACTACAGCGTACA 59.294 41.667 0.00 0.00 33.70 2.90
2743 7735 5.163622 TGACAATAGGGTAACTACAGCGTAC 60.164 44.000 0.00 0.00 33.70 3.67
2745 7737 3.765511 TGACAATAGGGTAACTACAGCGT 59.234 43.478 0.00 0.00 33.70 5.07
2746 7738 4.142227 ACTGACAATAGGGTAACTACAGCG 60.142 45.833 0.00 0.00 33.70 5.18
2748 7740 8.466617 AGATACTGACAATAGGGTAACTACAG 57.533 38.462 0.00 0.00 33.70 2.74
2749 7741 8.834004 AAGATACTGACAATAGGGTAACTACA 57.166 34.615 0.00 0.00 33.70 2.74
2766 7761 4.592485 ACAGGGAGCGATTAAGATACTG 57.408 45.455 0.00 0.00 0.00 2.74
2779 7774 2.347731 CTCCGACTTTTTACAGGGAGC 58.652 52.381 0.00 0.00 35.16 4.70
2782 7777 3.412237 TTCCTCCGACTTTTTACAGGG 57.588 47.619 0.00 0.00 0.00 4.45
2783 7778 4.215613 CCTTTTCCTCCGACTTTTTACAGG 59.784 45.833 0.00 0.00 0.00 4.00
2784 7779 4.215613 CCCTTTTCCTCCGACTTTTTACAG 59.784 45.833 0.00 0.00 0.00 2.74
2795 7790 1.303317 CCCACACCCTTTTCCTCCG 60.303 63.158 0.00 0.00 0.00 4.63
2798 7793 3.691698 TTAAACCCACACCCTTTTCCT 57.308 42.857 0.00 0.00 0.00 3.36
2799 7794 3.898741 TGATTAAACCCACACCCTTTTCC 59.101 43.478 0.00 0.00 0.00 3.13
2801 7796 3.319689 CGTGATTAAACCCACACCCTTTT 59.680 43.478 0.00 0.00 33.13 2.27
2810 7806 0.110678 TGGCACCGTGATTAAACCCA 59.889 50.000 1.65 0.00 0.00 4.51
2847 7843 2.233271 CCACCATTGTGCAACTCTTCT 58.767 47.619 0.00 0.00 41.35 2.85
2852 7848 1.122227 AAAGCCACCATTGTGCAACT 58.878 45.000 0.00 0.00 41.35 3.16
2854 7850 2.286872 CAAAAAGCCACCATTGTGCAA 58.713 42.857 0.00 0.00 41.35 4.08
2876 7886 2.622962 CGGCCACGAAAAGTTCCCC 61.623 63.158 2.24 0.00 44.60 4.81
2878 7888 1.895231 ACCGGCCACGAAAAGTTCC 60.895 57.895 0.00 0.00 44.60 3.62
2879 7889 1.161563 TCACCGGCCACGAAAAGTTC 61.162 55.000 0.00 0.00 44.60 3.01
2888 7898 1.741770 GTCACTCATCACCGGCCAC 60.742 63.158 0.00 0.00 0.00 5.01
2893 7903 0.738762 CCAGCAGTCACTCATCACCG 60.739 60.000 0.00 0.00 0.00 4.94
2899 7909 1.269723 CGAGTTACCAGCAGTCACTCA 59.730 52.381 16.70 0.00 46.05 3.41
2900 7910 1.540267 TCGAGTTACCAGCAGTCACTC 59.460 52.381 9.89 9.89 43.48 3.51
2901 7911 1.617322 TCGAGTTACCAGCAGTCACT 58.383 50.000 0.00 0.00 35.58 3.41
2902 7912 2.263077 CATCGAGTTACCAGCAGTCAC 58.737 52.381 0.00 0.00 0.00 3.67
2903 7913 1.204704 CCATCGAGTTACCAGCAGTCA 59.795 52.381 0.00 0.00 0.00 3.41
2904 7914 1.476891 TCCATCGAGTTACCAGCAGTC 59.523 52.381 0.00 0.00 0.00 3.51
2905 7915 1.478510 CTCCATCGAGTTACCAGCAGT 59.521 52.381 0.00 0.00 0.00 4.40
2906 7916 1.751351 TCTCCATCGAGTTACCAGCAG 59.249 52.381 0.00 0.00 37.40 4.24
2907 7917 1.476891 GTCTCCATCGAGTTACCAGCA 59.523 52.381 0.00 0.00 37.40 4.41
2908 7918 1.534175 CGTCTCCATCGAGTTACCAGC 60.534 57.143 0.00 0.00 37.40 4.85
2909 7919 1.534175 GCGTCTCCATCGAGTTACCAG 60.534 57.143 0.00 0.00 37.40 4.00
2910 7920 0.454600 GCGTCTCCATCGAGTTACCA 59.545 55.000 0.00 0.00 37.40 3.25
2911 7921 0.739561 AGCGTCTCCATCGAGTTACC 59.260 55.000 0.00 0.00 37.40 2.85
2912 7922 1.534175 CCAGCGTCTCCATCGAGTTAC 60.534 57.143 0.00 0.00 37.40 2.50
2913 7923 0.738975 CCAGCGTCTCCATCGAGTTA 59.261 55.000 0.00 0.00 37.40 2.24
2914 7924 1.513158 CCAGCGTCTCCATCGAGTT 59.487 57.895 0.00 0.00 37.40 3.01
2927 7937 1.061887 CCGATTTAAACGGCCAGCG 59.938 57.895 2.24 0.00 43.74 5.18
3250 8327 2.750237 GTAAACCAGCAGCGGGGG 60.750 66.667 16.74 7.85 0.00 5.40
3251 8328 2.040544 CAGTAAACCAGCAGCGGGG 61.041 63.158 16.74 10.49 0.00 5.73
3252 8329 0.392998 ATCAGTAAACCAGCAGCGGG 60.393 55.000 10.48 10.48 0.00 6.13
3253 8330 1.453155 AATCAGTAAACCAGCAGCGG 58.547 50.000 2.15 2.15 0.00 5.52
3254 8331 4.572389 AGATAAATCAGTAAACCAGCAGCG 59.428 41.667 0.00 0.00 0.00 5.18
3255 8332 5.008118 GGAGATAAATCAGTAAACCAGCAGC 59.992 44.000 0.00 0.00 0.00 5.25
3256 8333 5.235186 CGGAGATAAATCAGTAAACCAGCAG 59.765 44.000 0.00 0.00 0.00 4.24
3257 8334 5.116180 CGGAGATAAATCAGTAAACCAGCA 58.884 41.667 0.00 0.00 0.00 4.41
3258 8335 4.024809 GCGGAGATAAATCAGTAAACCAGC 60.025 45.833 0.00 0.00 0.00 4.85
3259 8336 4.511826 GGCGGAGATAAATCAGTAAACCAG 59.488 45.833 0.00 0.00 0.00 4.00
3260 8337 4.163458 AGGCGGAGATAAATCAGTAAACCA 59.837 41.667 0.00 0.00 0.00 3.67
3261 8338 4.704965 AGGCGGAGATAAATCAGTAAACC 58.295 43.478 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.