Multiple sequence alignment - TraesCS2B01G307100

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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 TraesCS2B01G307100 chr2B 100.000 3015 0 0 1 3015 439368219 439365205 0.000000e+00 5568
1 TraesCS2B01G307100 chr2D 92.867 1444 75 8 833 2259 369762982 369761550 0.000000e+00 2071
2 TraesCS2B01G307100 chr2D 91.052 637 36 10 197 830 369763879 369763261 0.000000e+00 841
3 TraesCS2B01G307100 chr2D 93.005 386 24 3 1640 2024 534524895 534525278 7.300000e-156 560
4 TraesCS2B01G307100 chr2D 90.741 378 28 4 2373 2748 369761433 369761061 5.800000e-137 497
5 TraesCS2B01G307100 chr2D 94.762 210 11 0 1 210 369764107 369763898 8.060000e-86 327
6 TraesCS2B01G307100 chr2A 90.476 1344 96 19 1423 2748 500771566 500770237 0.000000e+00 1744
7 TraesCS2B01G307100 chr2A 92.835 656 34 10 1 653 500773234 500772589 0.000000e+00 939
8 TraesCS2B01G307100 chr2A 86.176 774 45 25 641 1370 500772327 500771572 0.000000e+00 780
9 TraesCS2B01G307100 chr2A 91.755 376 29 1 1640 2015 765923585 765923212 3.440000e-144 521
10 TraesCS2B01G307100 chr2A 94.937 237 7 4 2781 3015 422919403 422919636 1.710000e-97 366
11 TraesCS2B01G307100 chr4D 90.164 610 37 10 1423 2012 20901808 20902414 0.000000e+00 773
12 TraesCS2B01G307100 chr4D 92.287 376 29 0 1640 2015 210835325 210834950 4.420000e-148 534
13 TraesCS2B01G307100 chr1B 93.085 376 26 0 1640 2015 676162738 676162363 4.390000e-153 551
14 TraesCS2B01G307100 chr5D 92.553 376 28 0 1640 2015 465680391 465680016 9.510000e-150 540
15 TraesCS2B01G307100 chr6D 92.493 373 28 0 1640 2012 51405265 51405637 4.420000e-148 534
16 TraesCS2B01G307100 chrUn 97.458 236 5 1 2781 3015 79565323 79565088 4.680000e-108 401
17 TraesCS2B01G307100 chr7B 97.826 230 4 1 2787 3015 707650461 707650690 2.180000e-106 396
18 TraesCS2B01G307100 chr7B 95.745 235 6 3 2783 3015 648394852 648395084 2.840000e-100 375
19 TraesCS2B01G307100 chr7B 95.359 237 7 3 2781 3015 75063472 75063238 1.020000e-99 374
20 TraesCS2B01G307100 chr5A 96.186 236 8 1 2781 3015 10722135 10721900 4.720000e-103 385
21 TraesCS2B01G307100 chr5A 96.943 229 6 1 2788 3015 601167137 601167365 1.700000e-102 383
22 TraesCS2B01G307100 chr5B 96.170 235 5 3 2783 3015 344304842 344305074 6.100000e-102 381
23 TraesCS2B01G307100 chr7A 93.802 242 13 2 2775 3015 726138711 726138951 2.210000e-96 363
24 TraesCS2B01G307100 chr1A 84.528 265 21 6 1423 1670 16029281 16029542 8.350000e-61 244


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 TraesCS2B01G307100 chr2B 439365205 439368219 3014 True 5568.000000 5568 100.0000 1 3015 1 chr2B.!!$R1 3014
1 TraesCS2B01G307100 chr2D 369761061 369764107 3046 True 934.000000 2071 92.3555 1 2748 4 chr2D.!!$R1 2747
2 TraesCS2B01G307100 chr2A 500770237 500773234 2997 True 1154.333333 1744 89.8290 1 2748 3 chr2A.!!$R2 2747
3 TraesCS2B01G307100 chr4D 20901808 20902414 606 False 773.000000 773 90.1640 1423 2012 1 chr4D.!!$F1 589

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
533 567 0.538977 TGTCGGACTCTCGGTTCCTT 60.539 55.0 9.88 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2702 0.466555 CCAACAAAAGACGGGGTGGA 60.467 55.0 0.0 0.0 0.0 4.02 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
28 29 8.723777 TCGAAATTCGATGTACATAGATACAC 57.276 34.615 17.87 10.19 44.82 2.90
52 53 7.376866 CACTTTAGTGTGTTTGCTACTCATTTG 59.623 37.037 1.69 0.00 40.96 2.32
220 253 4.243793 AGTCTAGTACTGAGTCTGGCAT 57.756 45.455 5.39 0.00 36.93 4.40
340 373 4.386245 CGGTGCGCTAGAGAAGTC 57.614 61.111 9.73 0.00 0.00 3.01
341 374 1.583967 CGGTGCGCTAGAGAAGTCG 60.584 63.158 9.73 0.00 0.00 4.18
374 407 2.978010 CCACCACCACGCAAGGAC 60.978 66.667 0.00 0.00 46.39 3.85
533 567 0.538977 TGTCGGACTCTCGGTTCCTT 60.539 55.000 9.88 0.00 0.00 3.36
534 568 0.602060 GTCGGACTCTCGGTTCCTTT 59.398 55.000 0.00 0.00 0.00 3.11
535 569 1.000618 GTCGGACTCTCGGTTCCTTTT 59.999 52.381 0.00 0.00 0.00 2.27
536 570 1.271656 TCGGACTCTCGGTTCCTTTTC 59.728 52.381 0.00 0.00 0.00 2.29
553 587 8.604035 GTTCCTTTTCTTTGTTTTGATCCTTTC 58.396 33.333 0.00 0.00 0.00 2.62
607 641 2.841389 CCGTTTCGTGTTCCGTCG 59.159 61.111 0.00 0.00 37.94 5.12
653 963 1.471676 CCAGACTCCTAACGTGGCATC 60.472 57.143 0.00 0.00 0.00 3.91
760 1070 1.595109 GCGATGACCGATGGATGCA 60.595 57.895 0.00 0.00 41.76 3.96
782 1094 1.837439 CCATGCTGGGTCTGTAGGTAA 59.163 52.381 0.00 0.00 32.67 2.85
786 1098 2.176889 GCTGGGTCTGTAGGTAAGACA 58.823 52.381 5.97 0.00 44.86 3.41
1031 1628 0.177141 GTTCCCATCCGAATCCGACA 59.823 55.000 0.00 0.00 38.22 4.35
1105 1702 4.570874 GGAGGAATCCCGGGCAGC 62.571 72.222 18.49 6.69 37.58 5.25
1106 1703 4.918201 GAGGAATCCCGGGCAGCG 62.918 72.222 18.49 0.00 37.58 5.18
1162 1759 3.533720 CGAGGGGTATTCGCTGGA 58.466 61.111 0.00 0.00 38.88 3.86
1300 1917 7.434307 GCTTAGCACTGAATATCGTAGTGTTAA 59.566 37.037 15.61 15.61 42.10 2.01
1314 1931 4.568152 AGTGTTAATTTCACCTGTGTGC 57.432 40.909 8.99 0.00 42.46 4.57
1321 1938 0.599991 TTCACCTGTGTGCGCACTAG 60.600 55.000 37.59 31.80 45.44 2.57
1353 1970 0.901580 TACCACCAACCGTCCTCCTC 60.902 60.000 0.00 0.00 0.00 3.71
1405 2022 3.547468 CGGCAAAACTTGTTCTGTCTTTG 59.453 43.478 0.00 0.00 0.00 2.77
1417 2034 6.255215 TGTTCTGTCTTTGTCGATTTGTTTC 58.745 36.000 0.00 0.00 0.00 2.78
1421 2038 4.975502 TGTCTTTGTCGATTTGTTTCATGC 59.024 37.500 0.00 0.00 0.00 4.06
1448 2065 5.755375 TGATGAACGCTCAATCTAATTCTCC 59.245 40.000 0.00 0.00 34.49 3.71
1457 2074 7.384115 CGCTCAATCTAATTCTCCGGTTATTAA 59.616 37.037 0.00 0.00 0.00 1.40
1463 2080 9.726438 ATCTAATTCTCCGGTTATTAATTGGAG 57.274 33.333 15.59 15.59 46.06 3.86
1502 2119 5.509272 TGTATTTACTCGCTCGTTAAAGTCG 59.491 40.000 0.00 0.00 0.00 4.18
1826 2469 2.920912 TTCGCCTCCTTCACCGGT 60.921 61.111 0.00 0.00 0.00 5.28
1903 2546 2.029073 CGACCCAGTGACGCAACT 59.971 61.111 0.00 0.00 0.00 3.16
1944 2587 3.127589 TCAAGAACGCTCGACAATGAAA 58.872 40.909 0.00 0.00 0.00 2.69
2048 2701 5.476945 ACTCTTGTTTTCTCTCTCTCTCTCC 59.523 44.000 0.00 0.00 0.00 3.71
2049 2702 5.640147 TCTTGTTTTCTCTCTCTCTCTCCT 58.360 41.667 0.00 0.00 0.00 3.69
2131 2784 1.688772 ATTATCCTGCTTGCCTGCTG 58.311 50.000 0.00 0.00 0.00 4.41
2143 2796 4.106925 CTGCTGCTCCCCACCCTC 62.107 72.222 0.00 0.00 0.00 4.30
2173 2826 7.069344 TGAGATGGAGTTATATTGGTCAGAGA 58.931 38.462 0.00 0.00 0.00 3.10
2174 2827 7.014711 TGAGATGGAGTTATATTGGTCAGAGAC 59.985 40.741 0.00 0.00 0.00 3.36
2194 2850 3.815401 GACTATGAGCTTGTGTGGTGTTT 59.185 43.478 0.00 0.00 0.00 2.83
2200 2856 1.926510 GCTTGTGTGGTGTTTTCTTGC 59.073 47.619 0.00 0.00 0.00 4.01
2309 3006 2.030628 GGAGGAGCATCTCTTAGTACGC 60.031 54.545 6.34 0.00 34.39 4.42
2384 3087 4.178540 CGTTGAAACGTATGACAGGGTAT 58.821 43.478 7.41 0.00 46.63 2.73
2387 3090 6.347888 CGTTGAAACGTATGACAGGGTATTTT 60.348 38.462 7.41 0.00 46.63 1.82
2428 3131 4.630111 AGATCTCAGATTTCTTGGATCGC 58.370 43.478 0.00 0.00 36.93 4.58
2434 3137 4.454161 TCAGATTTCTTGGATCGCGAAAAA 59.546 37.500 15.24 7.12 31.30 1.94
2438 3141 5.873179 TTTCTTGGATCGCGAAAAATAGT 57.127 34.783 15.24 0.00 0.00 2.12
2439 3142 6.971527 TTTCTTGGATCGCGAAAAATAGTA 57.028 33.333 15.24 0.00 0.00 1.82
2491 3194 2.125512 ATGGTGCTTCCGCGTCTC 60.126 61.111 4.92 0.00 39.65 3.36
2515 3218 2.206750 GTGGTTGCGTTCACTTCACTA 58.793 47.619 0.00 0.00 0.00 2.74
2557 3260 7.201266 GCTGTCTTGATTAAGCGTTTGTTTATG 60.201 37.037 0.00 0.00 33.82 1.90
2568 3271 5.799936 AGCGTTTGTTTATGTTATCATGTGC 59.200 36.000 0.00 0.00 35.70 4.57
2691 3394 6.868864 GCTATTTCGTAGGCAATCAAGATCTA 59.131 38.462 0.00 0.00 0.00 1.98
2755 3458 9.851686 AATTACTGCTAATCCTTACATGAATGA 57.148 29.630 0.00 0.00 0.00 2.57
2756 3459 9.851686 ATTACTGCTAATCCTTACATGAATGAA 57.148 29.630 0.00 0.00 0.00 2.57
2757 3460 7.798596 ACTGCTAATCCTTACATGAATGAAG 57.201 36.000 0.00 0.00 0.00 3.02
2758 3461 6.769822 ACTGCTAATCCTTACATGAATGAAGG 59.230 38.462 0.00 6.90 36.89 3.46
2759 3462 5.532406 TGCTAATCCTTACATGAATGAAGGC 59.468 40.000 0.00 0.00 36.20 4.35
2760 3463 5.767168 GCTAATCCTTACATGAATGAAGGCT 59.233 40.000 0.00 0.00 36.20 4.58
2761 3464 6.072783 GCTAATCCTTACATGAATGAAGGCTC 60.073 42.308 0.00 0.00 36.20 4.70
2762 3465 4.842531 TCCTTACATGAATGAAGGCTCA 57.157 40.909 0.00 0.00 36.20 4.26
2763 3466 4.774124 TCCTTACATGAATGAAGGCTCAG 58.226 43.478 0.00 0.00 36.20 3.35
2764 3467 4.471025 TCCTTACATGAATGAAGGCTCAGA 59.529 41.667 0.00 0.00 36.20 3.27
2765 3468 4.574013 CCTTACATGAATGAAGGCTCAGAC 59.426 45.833 0.00 0.00 34.23 3.51
2766 3469 3.996921 ACATGAATGAAGGCTCAGACT 57.003 42.857 0.00 0.00 34.23 3.24
2767 3470 4.298103 ACATGAATGAAGGCTCAGACTT 57.702 40.909 0.00 0.00 34.23 3.01
2768 3471 5.426689 ACATGAATGAAGGCTCAGACTTA 57.573 39.130 0.00 0.00 34.23 2.24
2769 3472 5.426504 ACATGAATGAAGGCTCAGACTTAG 58.573 41.667 0.00 0.00 34.23 2.18
2770 3473 5.188555 ACATGAATGAAGGCTCAGACTTAGA 59.811 40.000 0.00 0.00 34.23 2.10
2771 3474 5.336150 TGAATGAAGGCTCAGACTTAGAG 57.664 43.478 0.00 0.00 34.23 2.43
2777 3480 1.064946 CTCAGACTTAGAGCGCCCG 59.935 63.158 2.29 0.00 0.00 6.13
2778 3481 2.583593 CAGACTTAGAGCGCCCGC 60.584 66.667 2.29 4.20 42.33 6.13
2842 3545 4.191015 GGTGATTCCCCTCCCGCC 62.191 72.222 0.00 0.00 0.00 6.13
2843 3546 4.547367 GTGATTCCCCTCCCGCCG 62.547 72.222 0.00 0.00 0.00 6.46
2857 3560 4.525949 GCCGGCGTAACCTCCCTC 62.526 72.222 12.58 0.00 35.61 4.30
2858 3561 2.758737 CCGGCGTAACCTCCCTCT 60.759 66.667 6.01 0.00 35.61 3.69
2859 3562 2.783288 CCGGCGTAACCTCCCTCTC 61.783 68.421 6.01 0.00 35.61 3.20
2860 3563 1.753463 CGGCGTAACCTCCCTCTCT 60.753 63.158 0.00 0.00 35.61 3.10
2861 3564 1.726533 CGGCGTAACCTCCCTCTCTC 61.727 65.000 0.00 0.00 35.61 3.20
2862 3565 0.396001 GGCGTAACCTCCCTCTCTCT 60.396 60.000 0.00 0.00 34.51 3.10
2863 3566 1.476477 GCGTAACCTCCCTCTCTCTT 58.524 55.000 0.00 0.00 0.00 2.85
2864 3567 1.406180 GCGTAACCTCCCTCTCTCTTC 59.594 57.143 0.00 0.00 0.00 2.87
2865 3568 2.724454 CGTAACCTCCCTCTCTCTTCA 58.276 52.381 0.00 0.00 0.00 3.02
2866 3569 3.292460 CGTAACCTCCCTCTCTCTTCAT 58.708 50.000 0.00 0.00 0.00 2.57
2867 3570 3.316868 CGTAACCTCCCTCTCTCTTCATC 59.683 52.174 0.00 0.00 0.00 2.92
2868 3571 3.774842 AACCTCCCTCTCTCTTCATCT 57.225 47.619 0.00 0.00 0.00 2.90
2869 3572 3.312736 ACCTCCCTCTCTCTTCATCTC 57.687 52.381 0.00 0.00 0.00 2.75
2870 3573 2.858768 ACCTCCCTCTCTCTTCATCTCT 59.141 50.000 0.00 0.00 0.00 3.10
2871 3574 3.117512 ACCTCCCTCTCTCTTCATCTCTC 60.118 52.174 0.00 0.00 0.00 3.20
2872 3575 3.490348 CTCCCTCTCTCTTCATCTCTCC 58.510 54.545 0.00 0.00 0.00 3.71
2873 3576 3.130450 TCCCTCTCTCTTCATCTCTCCT 58.870 50.000 0.00 0.00 0.00 3.69
2874 3577 3.138283 TCCCTCTCTCTTCATCTCTCCTC 59.862 52.174 0.00 0.00 0.00 3.71
2875 3578 3.141398 CCTCTCTCTTCATCTCTCCTCG 58.859 54.545 0.00 0.00 0.00 4.63
2876 3579 2.549754 CTCTCTCTTCATCTCTCCTCGC 59.450 54.545 0.00 0.00 0.00 5.03
2877 3580 1.608590 CTCTCTTCATCTCTCCTCGCC 59.391 57.143 0.00 0.00 0.00 5.54
2878 3581 0.310543 CTCTTCATCTCTCCTCGCCG 59.689 60.000 0.00 0.00 0.00 6.46
2879 3582 1.299773 CTTCATCTCTCCTCGCCGC 60.300 63.158 0.00 0.00 0.00 6.53
2880 3583 2.691674 CTTCATCTCTCCTCGCCGCC 62.692 65.000 0.00 0.00 0.00 6.13
2881 3584 4.637489 CATCTCTCCTCGCCGCCG 62.637 72.222 0.00 0.00 0.00 6.46
2957 3660 4.959596 GGCTCCGCTCCGATCTGC 62.960 72.222 0.00 0.00 0.00 4.26
2958 3661 4.212913 GCTCCGCTCCGATCTGCA 62.213 66.667 0.00 0.00 0.00 4.41
2959 3662 2.733301 CTCCGCTCCGATCTGCAT 59.267 61.111 0.00 0.00 0.00 3.96
2960 3663 1.372748 CTCCGCTCCGATCTGCATC 60.373 63.158 0.00 0.00 0.00 3.91
2969 3672 2.435418 GATCTGCATCGGAGGGTCT 58.565 57.895 0.00 0.00 0.00 3.85
2970 3673 0.316841 GATCTGCATCGGAGGGTCTC 59.683 60.000 0.00 0.00 0.00 3.36
2971 3674 1.459455 ATCTGCATCGGAGGGTCTCG 61.459 60.000 0.00 0.00 0.00 4.04
2972 3675 3.144120 CTGCATCGGAGGGTCTCGG 62.144 68.421 0.00 0.00 33.08 4.63
2973 3676 2.833582 GCATCGGAGGGTCTCGGA 60.834 66.667 7.46 7.46 42.37 4.55
2974 3677 2.203771 GCATCGGAGGGTCTCGGAT 61.204 63.158 10.78 10.78 46.47 4.18
2975 3678 1.960612 CATCGGAGGGTCTCGGATC 59.039 63.158 12.87 0.00 44.71 3.36
2976 3679 1.228613 ATCGGAGGGTCTCGGATCC 60.229 63.158 0.00 0.00 43.68 3.36
2978 3681 2.913060 GGAGGGTCTCGGATCCGG 60.913 72.222 32.79 22.83 38.00 5.14
2979 3682 2.913060 GAGGGTCTCGGATCCGGG 60.913 72.222 32.79 30.92 38.00 5.73
3005 3708 4.154347 CTGGCGAGGCTCCCTGTC 62.154 72.222 18.79 4.84 31.76 3.51
3006 3709 4.704103 TGGCGAGGCTCCCTGTCT 62.704 66.667 18.79 0.00 31.76 3.41
3007 3710 3.844090 GGCGAGGCTCCCTGTCTC 61.844 72.222 9.32 0.00 43.60 3.36
3008 3711 3.844090 GCGAGGCTCCCTGTCTCC 61.844 72.222 9.32 0.00 44.14 3.71
3009 3712 2.043450 CGAGGCTCCCTGTCTCCT 60.043 66.667 9.32 0.00 44.14 3.69
3010 3713 2.422231 CGAGGCTCCCTGTCTCCTG 61.422 68.421 9.32 0.00 44.14 3.86
3011 3714 2.686835 AGGCTCCCTGTCTCCTGC 60.687 66.667 0.00 0.00 29.57 4.85
3012 3715 4.154347 GGCTCCCTGTCTCCTGCG 62.154 72.222 0.00 0.00 0.00 5.18
3013 3716 4.154347 GCTCCCTGTCTCCTGCGG 62.154 72.222 0.00 0.00 0.00 5.69
3014 3717 4.154347 CTCCCTGTCTCCTGCGGC 62.154 72.222 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.639039 TCAAATGAGTAGCAAACACACTAAAG 58.361 34.615 0.00 0.00 31.11 1.85
140 141 2.938798 AGGTTGAATCCCCGGCCA 60.939 61.111 2.24 0.00 0.00 5.36
220 253 0.885879 ACGCTACGGAATCTGACACA 59.114 50.000 0.00 0.00 0.00 3.72
328 361 0.384974 GATCGGCGACTTCTCTAGCG 60.385 60.000 13.76 0.00 0.00 4.26
340 373 0.249868 TGGCTCCAATTAGATCGGCG 60.250 55.000 0.00 0.00 0.00 6.46
341 374 1.230324 GTGGCTCCAATTAGATCGGC 58.770 55.000 0.00 0.00 0.00 5.54
460 493 2.359975 CCAGTTTCTCACCGGGCC 60.360 66.667 6.32 0.00 0.00 5.80
533 567 5.047188 GGCGAAAGGATCAAAACAAAGAAA 58.953 37.500 0.00 0.00 0.00 2.52
534 568 4.340950 AGGCGAAAGGATCAAAACAAAGAA 59.659 37.500 0.00 0.00 0.00 2.52
535 569 3.888930 AGGCGAAAGGATCAAAACAAAGA 59.111 39.130 0.00 0.00 0.00 2.52
536 570 4.229876 GAGGCGAAAGGATCAAAACAAAG 58.770 43.478 0.00 0.00 0.00 2.77
631 665 0.824759 GCCACGTTAGGAGTCTGGAT 59.175 55.000 0.00 0.00 0.00 3.41
639 673 0.320858 TTTGCGATGCCACGTTAGGA 60.321 50.000 0.00 0.00 35.59 2.94
773 1083 4.966965 ACTCGTGATGTCTTACCTACAG 57.033 45.455 0.00 0.00 0.00 2.74
995 1592 2.202479 CGAGATCTCGCACGCACA 60.202 61.111 30.41 0.00 46.50 4.57
1068 1665 3.944945 GACCCCGAAACCGTGGGT 61.945 66.667 13.94 13.94 46.28 4.51
1314 1931 4.209288 GGTAATCAGTTGTATGCTAGTGCG 59.791 45.833 0.00 0.00 43.34 5.34
1321 1938 4.142469 GGTTGGTGGTAATCAGTTGTATGC 60.142 45.833 0.00 0.00 0.00 3.14
1353 1970 2.416547 CCGTGTAATCAACAGCTCAAGG 59.583 50.000 0.00 0.00 39.29 3.61
1405 2022 2.487762 TCAGGGCATGAAACAAATCGAC 59.512 45.455 0.00 0.00 34.02 4.20
1417 2034 0.745486 TGAGCGTTCATCAGGGCATG 60.745 55.000 0.00 0.00 0.00 4.06
1421 2038 2.322355 AGATTGAGCGTTCATCAGGG 57.678 50.000 1.75 0.00 32.27 4.45
1448 2065 5.107607 CGTTCCGATCTCCAATTAATAACCG 60.108 44.000 0.00 0.00 0.00 4.44
1457 2074 3.819564 TGATTCGTTCCGATCTCCAAT 57.180 42.857 0.00 0.00 35.23 3.16
1463 2080 7.409449 CGAGTAAATACATGATTCGTTCCGATC 60.409 40.741 0.00 0.00 35.23 3.69
1526 2143 1.425428 GAAGCCATTTCTGTCGCGG 59.575 57.895 6.13 0.00 32.83 6.46
1528 2145 0.881118 TTGGAAGCCATTTCTGTCGC 59.119 50.000 0.00 0.00 36.03 5.19
1638 2272 2.159085 CCACCTCCTCCGTGTATTCTTC 60.159 54.545 0.00 0.00 0.00 2.87
1734 2371 2.429930 CACTTGAAGGACCCGGCA 59.570 61.111 0.00 0.00 0.00 5.69
1915 2558 2.251040 CGAGCGTTCTTGATTCTCGAA 58.749 47.619 4.17 0.00 46.59 3.71
1994 2637 2.416836 CGACACAATACATCGTGGGAGT 60.417 50.000 0.00 0.00 37.45 3.85
2000 2643 4.112634 CTCCAATCGACACAATACATCGT 58.887 43.478 0.00 0.00 37.16 3.73
2048 2701 0.951558 CAACAAAAGACGGGGTGGAG 59.048 55.000 0.00 0.00 0.00 3.86
2049 2702 0.466555 CCAACAAAAGACGGGGTGGA 60.467 55.000 0.00 0.00 0.00 4.02
2131 2784 1.380380 CAAATGGAGGGTGGGGAGC 60.380 63.158 0.00 0.00 0.00 4.70
2143 2796 7.720957 TGACCAATATAACTCCATCTCAAATGG 59.279 37.037 0.00 0.00 40.48 3.16
2159 2812 7.507277 ACAAGCTCATAGTCTCTGACCAATATA 59.493 37.037 0.00 0.00 32.18 0.86
2173 2826 3.492102 AACACCACACAAGCTCATAGT 57.508 42.857 0.00 0.00 0.00 2.12
2174 2827 4.516698 AGAAAACACCACACAAGCTCATAG 59.483 41.667 0.00 0.00 0.00 2.23
2200 2856 9.121517 GCATGGATTTAACTGAAATGATAATCG 57.878 33.333 0.00 0.00 37.90 3.34
2363 3062 6.490566 AAATACCCTGTCATACGTTTCAAC 57.509 37.500 0.00 0.00 0.00 3.18
2384 3087 3.911260 TCAGGGGTGATGTACTACCAAAA 59.089 43.478 13.82 0.00 38.74 2.44
2387 3090 2.313643 TCTCAGGGGTGATGTACTACCA 59.686 50.000 13.82 0.00 38.74 3.25
2428 3131 7.359264 CCTGTGTCTGTGACTTACTATTTTTCG 60.359 40.741 0.00 0.00 33.15 3.46
2434 3137 5.646577 GACCTGTGTCTGTGACTTACTAT 57.353 43.478 0.00 0.00 38.53 2.12
2462 3165 4.510340 CGGAAGCACCATGGTAAATAGTAC 59.490 45.833 19.28 2.64 38.90 2.73
2463 3166 4.699637 CGGAAGCACCATGGTAAATAGTA 58.300 43.478 19.28 0.00 38.90 1.82
2464 3167 3.541632 CGGAAGCACCATGGTAAATAGT 58.458 45.455 19.28 0.00 38.90 2.12
2491 3194 0.738389 AAGTGAACGCAACCACCAAG 59.262 50.000 0.00 0.00 34.00 3.61
2568 3271 6.367969 TGATCATACAGCGATGAGAAATCATG 59.632 38.462 8.12 0.00 39.18 3.07
2576 3279 3.678548 CCACATGATCATACAGCGATGAG 59.321 47.826 8.12 0.00 39.18 2.90
2612 3315 1.156736 CTTTGCAAGGTTCGTCCGAT 58.843 50.000 0.00 0.00 41.99 4.18
2743 3446 5.426504 AGTCTGAGCCTTCATTCATGTAAG 58.573 41.667 0.00 0.00 31.68 2.34
2748 3451 5.916318 CTCTAAGTCTGAGCCTTCATTCAT 58.084 41.667 0.00 0.00 31.68 2.57
2749 3452 5.336150 CTCTAAGTCTGAGCCTTCATTCA 57.664 43.478 0.00 0.00 31.68 2.57
2759 3462 1.064946 CGGGCGCTCTAAGTCTGAG 59.935 63.158 5.36 0.00 34.87 3.35
2760 3463 3.064987 GCGGGCGCTCTAAGTCTGA 62.065 63.158 5.36 0.00 38.26 3.27
2761 3464 2.583593 GCGGGCGCTCTAAGTCTG 60.584 66.667 5.36 0.00 38.26 3.51
2762 3465 4.194720 CGCGGGCGCTCTAAGTCT 62.195 66.667 5.36 0.00 39.32 3.24
2825 3528 4.191015 GGCGGGAGGGGAATCACC 62.191 72.222 0.00 0.00 38.08 4.02
2826 3529 4.547367 CGGCGGGAGGGGAATCAC 62.547 72.222 0.00 0.00 0.00 3.06
2840 3543 4.525949 GAGGGAGGTTACGCCGGC 62.526 72.222 19.07 19.07 43.70 6.13
2841 3544 2.758737 AGAGGGAGGTTACGCCGG 60.759 66.667 0.00 0.00 43.70 6.13
2842 3545 1.726533 GAGAGAGGGAGGTTACGCCG 61.727 65.000 0.00 0.00 43.70 6.46
2843 3546 0.396001 AGAGAGAGGGAGGTTACGCC 60.396 60.000 0.00 0.00 35.57 5.68
2844 3547 1.406180 GAAGAGAGAGGGAGGTTACGC 59.594 57.143 0.00 0.00 0.00 4.42
2845 3548 2.724454 TGAAGAGAGAGGGAGGTTACG 58.276 52.381 0.00 0.00 0.00 3.18
2846 3549 4.542697 AGATGAAGAGAGAGGGAGGTTAC 58.457 47.826 0.00 0.00 0.00 2.50
2847 3550 4.480537 AGAGATGAAGAGAGAGGGAGGTTA 59.519 45.833 0.00 0.00 0.00 2.85
2848 3551 3.272020 AGAGATGAAGAGAGAGGGAGGTT 59.728 47.826 0.00 0.00 0.00 3.50
2849 3552 2.858768 AGAGATGAAGAGAGAGGGAGGT 59.141 50.000 0.00 0.00 0.00 3.85
2850 3553 3.490348 GAGAGATGAAGAGAGAGGGAGG 58.510 54.545 0.00 0.00 0.00 4.30
2851 3554 3.139025 AGGAGAGATGAAGAGAGAGGGAG 59.861 52.174 0.00 0.00 0.00 4.30
2852 3555 3.130450 AGGAGAGATGAAGAGAGAGGGA 58.870 50.000 0.00 0.00 0.00 4.20
2853 3556 3.490348 GAGGAGAGATGAAGAGAGAGGG 58.510 54.545 0.00 0.00 0.00 4.30
2854 3557 3.141398 CGAGGAGAGATGAAGAGAGAGG 58.859 54.545 0.00 0.00 0.00 3.69
2855 3558 2.549754 GCGAGGAGAGATGAAGAGAGAG 59.450 54.545 0.00 0.00 0.00 3.20
2856 3559 2.571212 GCGAGGAGAGATGAAGAGAGA 58.429 52.381 0.00 0.00 0.00 3.10
2857 3560 1.608590 GGCGAGGAGAGATGAAGAGAG 59.391 57.143 0.00 0.00 0.00 3.20
2858 3561 1.686355 GGCGAGGAGAGATGAAGAGA 58.314 55.000 0.00 0.00 0.00 3.10
2859 3562 0.310543 CGGCGAGGAGAGATGAAGAG 59.689 60.000 0.00 0.00 0.00 2.85
2860 3563 1.729470 GCGGCGAGGAGAGATGAAGA 61.729 60.000 12.98 0.00 0.00 2.87
2861 3564 1.299773 GCGGCGAGGAGAGATGAAG 60.300 63.158 12.98 0.00 0.00 3.02
2862 3565 2.786495 GGCGGCGAGGAGAGATGAA 61.786 63.158 12.98 0.00 0.00 2.57
2863 3566 3.219928 GGCGGCGAGGAGAGATGA 61.220 66.667 12.98 0.00 0.00 2.92
2864 3567 4.637489 CGGCGGCGAGGAGAGATG 62.637 72.222 29.19 0.00 0.00 2.90
2942 3645 1.372748 GATGCAGATCGGAGCGGAG 60.373 63.158 0.00 0.00 0.00 4.63
2943 3646 2.730733 GATGCAGATCGGAGCGGA 59.269 61.111 0.00 0.00 0.00 5.54
2944 3647 2.732468 CGATGCAGATCGGAGCGG 60.732 66.667 1.69 0.00 46.51 5.52
2951 3654 0.316841 GAGACCCTCCGATGCAGATC 59.683 60.000 0.00 0.00 0.00 2.75
2952 3655 1.459455 CGAGACCCTCCGATGCAGAT 61.459 60.000 0.00 0.00 0.00 2.90
2953 3656 2.121538 CGAGACCCTCCGATGCAGA 61.122 63.158 0.00 0.00 0.00 4.26
2954 3657 2.415010 CGAGACCCTCCGATGCAG 59.585 66.667 0.00 0.00 0.00 4.41
2955 3658 2.928988 ATCCGAGACCCTCCGATGCA 62.929 60.000 0.00 0.00 29.97 3.96
2956 3659 2.148558 GATCCGAGACCCTCCGATGC 62.149 65.000 3.27 0.00 30.94 3.91
2957 3660 1.528292 GGATCCGAGACCCTCCGATG 61.528 65.000 0.00 0.00 30.94 3.84
2958 3661 1.228613 GGATCCGAGACCCTCCGAT 60.229 63.158 0.00 0.00 32.80 4.18
2959 3662 2.195139 GGATCCGAGACCCTCCGA 59.805 66.667 0.00 0.00 0.00 4.55
2960 3663 3.288290 CGGATCCGAGACCCTCCG 61.288 72.222 30.62 0.00 43.98 4.63
2961 3664 2.913060 CCGGATCCGAGACCCTCC 60.913 72.222 35.42 0.00 42.83 4.30
2962 3665 2.913060 CCCGGATCCGAGACCCTC 60.913 72.222 35.42 0.00 42.83 4.30
2988 3691 4.154347 GACAGGGAGCCTCGCCAG 62.154 72.222 4.99 1.32 0.00 4.85
2989 3692 4.704103 AGACAGGGAGCCTCGCCA 62.704 66.667 4.99 0.00 0.00 5.69
2990 3693 3.844090 GAGACAGGGAGCCTCGCC 61.844 72.222 4.99 0.00 0.00 5.54
2991 3694 3.844090 GGAGACAGGGAGCCTCGC 61.844 72.222 0.00 0.00 0.00 5.03
2992 3695 2.043450 AGGAGACAGGGAGCCTCG 60.043 66.667 0.00 0.00 0.00 4.63
2993 3696 2.730524 GCAGGAGACAGGGAGCCTC 61.731 68.421 0.00 0.00 0.00 4.70
2994 3697 2.686835 GCAGGAGACAGGGAGCCT 60.687 66.667 0.00 0.00 0.00 4.58
2995 3698 4.154347 CGCAGGAGACAGGGAGCC 62.154 72.222 0.00 0.00 30.95 4.70


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

AutoCloner maintained by Alex Coulton.