Multiple sequence alignment - TraesCS1A01G202600

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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 TraesCS1A01G202600 chr1A 100.000 4110 0 0 1 4110 363656882 363652773 0.000000e+00 7590
1 TraesCS1A01G202600 chr1A 83.407 2260 257 73 697 2872 363420008 363422233 0.000000e+00 1988
2 TraesCS1A01G202600 chr1A 87.132 272 23 7 3119 3380 363422524 363422793 8.640000e-77 298
3 TraesCS1A01G202600 chr1A 98.230 113 2 0 2984 3096 363422231 363422343 9.010000e-47 198
4 TraesCS1A01G202600 chr1D 91.369 1958 118 17 3 1941 291589253 291587328 0.000000e+00 2632
5 TraesCS1A01G202600 chr1D 88.039 2065 135 54 1935 3943 291587248 291585240 0.000000e+00 2342
6 TraesCS1A01G202600 chr1D 89.689 708 57 7 841 1535 291083123 291083827 0.000000e+00 889
7 TraesCS1A01G202600 chr1D 78.934 788 122 28 1938 2703 291084323 291085088 2.850000e-136 496
8 TraesCS1A01G202600 chr1D 92.241 348 25 1 1564 1911 291083908 291084253 3.690000e-135 492
9 TraesCS1A01G202600 chr1D 79.680 625 77 23 2984 3574 291085271 291085879 4.950000e-109 405
10 TraesCS1A01G202600 chr1D 88.800 125 14 0 3986 4110 291581330 291581206 1.980000e-33 154
11 TraesCS1A01G202600 chr1B 89.879 1492 103 31 633 2097 392530524 392529054 0.000000e+00 1875
12 TraesCS1A01G202600 chr1B 85.832 1694 166 49 692 2359 392150314 392151959 0.000000e+00 1731
13 TraesCS1A01G202600 chr1B 85.366 1722 106 69 2154 3811 392528963 392527324 0.000000e+00 1650
14 TraesCS1A01G202600 chr1B 93.643 582 36 1 1 582 392531336 392530756 0.000000e+00 869
15 TraesCS1A01G202600 chr1B 88.530 279 15 8 3838 4110 392527326 392527059 5.130000e-84 322


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 TraesCS1A01G202600 chr1A 363652773 363656882 4109 True 7590.000000 7590 100.000000 1 4110 1 chr1A.!!$R1 4109
1 TraesCS1A01G202600 chr1A 363420008 363422793 2785 False 828.000000 1988 89.589667 697 3380 3 chr1A.!!$F1 2683
2 TraesCS1A01G202600 chr1D 291581206 291589253 8047 True 1709.333333 2632 89.402667 3 4110 3 chr1D.!!$R1 4107
3 TraesCS1A01G202600 chr1D 291083123 291085879 2756 False 570.500000 889 85.136000 841 3574 4 chr1D.!!$F1 2733
4 TraesCS1A01G202600 chr1B 392150314 392151959 1645 False 1731.000000 1731 85.832000 692 2359 1 chr1B.!!$F1 1667
5 TraesCS1A01G202600 chr1B 392527059 392531336 4277 True 1179.000000 1875 89.354500 1 4110 4 chr1B.!!$R1 4109

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
703 885 0.317160 ACAACGATCACAGCCTTCGA 59.683 50.0 0.0 0.0 36.73 3.71 F
1886 2154 0.749649 CGGAGAGAGCTATGCAGGTT 59.250 55.0 0.0 0.0 30.99 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 2897 0.467804 TGGCTGAAACTTTTTGGGCC 59.532 50.0 0.0 0.0 38.67 5.80 R
3628 4348 0.036388 TCAGAGCGTTGGATGGGTTC 60.036 55.0 0.0 0.0 0.00 3.62 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
106 107 9.893634 TTTTTATATGAACCATTTCTACGGAGA 57.106 29.630 0.00 0.00 32.36 3.71
315 316 7.433131 TCATGTATTACGTTTCTTCCGTGTATC 59.567 37.037 0.00 0.00 39.22 2.24
319 320 7.689953 ATTACGTTTCTTCCGTGTATCATAC 57.310 36.000 0.00 0.00 39.22 2.39
366 367 2.747177 TCCAGTGAACGATACCCTGAT 58.253 47.619 0.00 0.00 0.00 2.90
421 422 3.728718 GGTGATACTTGTTTGTTTGCGTG 59.271 43.478 0.00 0.00 0.00 5.34
422 423 4.347813 GTGATACTTGTTTGTTTGCGTGT 58.652 39.130 0.00 0.00 0.00 4.49
450 451 3.915575 GCCCCAGCTCAGTCATTG 58.084 61.111 0.00 0.00 35.50 2.82
458 459 4.460382 CCCAGCTCAGTCATTGTAATTGTT 59.540 41.667 0.00 0.00 0.00 2.83
460 461 5.413833 CCAGCTCAGTCATTGTAATTGTTCT 59.586 40.000 0.00 0.00 0.00 3.01
480 481 9.698309 TTGTTCTTAACTCACAATTGTTTTTCA 57.302 25.926 8.77 0.00 0.00 2.69
499 500 7.527183 GTTTTTCAAAACGATATGCTTTTCAGC 59.473 33.333 0.00 0.00 41.40 4.26
620 785 2.305927 CTGAAAGCCCCTACCTTCTTGA 59.694 50.000 0.00 0.00 0.00 3.02
627 792 6.092346 AGCCCCTACCTTCTTGAAAATATT 57.908 37.500 0.00 0.00 0.00 1.28
631 796 6.098266 CCCCTACCTTCTTGAAAATATTTGGG 59.902 42.308 0.39 3.45 0.00 4.12
685 867 4.376717 CCGCTAAAGTCGTGGTAAGAAAAC 60.377 45.833 0.00 0.00 0.00 2.43
703 885 0.317160 ACAACGATCACAGCCTTCGA 59.683 50.000 0.00 0.00 36.73 3.71
908 1090 4.101942 GACTTGATCTACTTGTCTCTGCG 58.898 47.826 0.00 0.00 0.00 5.18
911 1093 2.159324 TGATCTACTTGTCTCTGCGCTG 60.159 50.000 9.73 8.88 0.00 5.18
936 1131 6.310711 GCAGACACAGGTTCTGTACTATAAAC 59.689 42.308 0.00 0.00 43.43 2.01
953 1148 3.683365 AAACACTTCATTCCAATGCCC 57.317 42.857 0.00 0.00 36.36 5.36
1038 1233 1.160137 CCTGCTTGCTACTTGTGTCC 58.840 55.000 0.00 0.00 0.00 4.02
1090 1297 1.968017 CGGCCTGACAGTGCAACAT 60.968 57.895 15.09 0.00 41.43 2.71
1266 1473 1.537135 GCTATGGAGAAGCCTGACGAC 60.537 57.143 0.00 0.00 37.63 4.34
1310 1521 5.649782 AATGGAGGTTGCTAACTGATTTG 57.350 39.130 0.00 0.00 0.00 2.32
1395 1610 5.473931 TGTACACTGTGTGTTTTTGCAAAT 58.526 33.333 22.97 0.00 45.08 2.32
1458 1673 1.524849 GGAGCTCGGGCCATTTCTC 60.525 63.158 2.00 5.39 39.73 2.87
1482 1697 2.110901 AGAAAGATGTGCCTGAGCTG 57.889 50.000 0.00 0.00 40.80 4.24
1539 1784 8.807948 AGTGCAAACCAAGACTAACATATTAT 57.192 30.769 0.00 0.00 0.00 1.28
1570 1837 7.933033 ACAAACAATTTTCATAGCAATGGAAGT 59.067 29.630 0.00 0.00 32.04 3.01
1598 1865 3.733337 AGCTTACTGTCTGGTGAACTTG 58.267 45.455 0.00 0.00 0.00 3.16
1728 1995 7.254932 GCAACACAGATATATGTTTCCTCTTCC 60.255 40.741 0.00 0.00 0.00 3.46
1867 2135 7.965107 CACAAAATGAAAGAGTTCTACATAGCC 59.035 37.037 0.00 0.00 34.60 3.93
1886 2154 0.749649 CGGAGAGAGCTATGCAGGTT 59.250 55.000 0.00 0.00 30.99 3.50
1914 2182 7.925483 GCCACCTTATTCATAGATAGCTAGATG 59.075 40.741 0.00 3.33 0.00 2.90
1974 2327 4.604843 TGCTCATTGTAATTCTCTTGCG 57.395 40.909 0.00 0.00 0.00 4.85
2058 2411 4.479786 AGCCTCCAGAGAAAACTACATC 57.520 45.455 0.00 0.00 0.00 3.06
2101 2460 6.706270 GGTACACACATGCAGCTATAATAAGT 59.294 38.462 0.00 0.00 0.00 2.24
2103 2462 6.586344 ACACACATGCAGCTATAATAAGTCT 58.414 36.000 0.00 0.00 0.00 3.24
2122 2510 7.897575 AAGTCTCAAGAATGTTAGCACTTAG 57.102 36.000 0.00 0.00 0.00 2.18
2282 2712 3.793144 GCAACTTCAGCGCGGAGG 61.793 66.667 17.58 17.58 0.00 4.30
2461 2897 2.788191 AAGCGTCCTCCTTGGCTTCG 62.788 60.000 0.00 0.00 41.57 3.79
2516 2985 3.713288 TCGATCGGTCCATGTGATTAAC 58.287 45.455 16.41 0.00 0.00 2.01
2684 3156 2.418334 CCCTACTCTCTTTGCCGGTAAC 60.418 54.545 3.74 0.00 0.00 2.50
2727 3204 1.482182 CTTGGACTCGGGATCATGTCA 59.518 52.381 0.00 0.00 0.00 3.58
2741 3223 1.811965 CATGTCATTTCGGTGGCTGAA 59.188 47.619 0.00 0.00 0.00 3.02
2744 3226 1.197721 GTCATTTCGGTGGCTGAACTG 59.802 52.381 2.79 2.79 32.86 3.16
2745 3227 1.071542 TCATTTCGGTGGCTGAACTGA 59.928 47.619 6.64 6.64 36.53 3.41
2746 3228 1.879380 CATTTCGGTGGCTGAACTGAA 59.121 47.619 5.30 5.30 42.37 3.02
2747 3229 3.790691 TTCGGTGGCTGAACTGAAA 57.209 47.368 6.54 0.00 41.39 2.69
2748 3230 2.270352 TTCGGTGGCTGAACTGAAAT 57.730 45.000 6.54 0.00 41.39 2.17
2749 3231 3.410631 TTCGGTGGCTGAACTGAAATA 57.589 42.857 6.54 0.00 41.39 1.40
2750 3232 2.695359 TCGGTGGCTGAACTGAAATAC 58.305 47.619 0.00 0.00 32.46 1.89
2751 3233 2.301870 TCGGTGGCTGAACTGAAATACT 59.698 45.455 0.00 0.00 32.46 2.12
2763 3245 9.994432 CTGAACTGAAATACTGAATATTGTTCC 57.006 33.333 0.00 0.00 35.14 3.62
2792 3289 1.584308 GCAGCGACTCTATCAACGTTC 59.416 52.381 0.00 0.00 0.00 3.95
2806 3303 1.282248 ACGTTCTGTGGCACGATTCG 61.282 55.000 13.77 19.11 39.76 3.34
2842 3339 0.798389 CGATCGTCAAGAAGCTCGCA 60.798 55.000 7.03 0.00 0.00 5.10
2851 3348 4.400961 AAGCTCGCACAGGAGGGC 62.401 66.667 0.00 0.00 41.13 5.19
2874 3371 3.213506 TCCGCATATGGATTTTCAGGTG 58.786 45.455 4.56 0.00 31.53 4.00
2879 3376 1.755179 ATGGATTTTCAGGTGGAGCG 58.245 50.000 0.00 0.00 0.00 5.03
2881 3378 0.804989 GGATTTTCAGGTGGAGCGTG 59.195 55.000 0.00 0.00 0.00 5.34
2894 3391 3.684788 GTGGAGCGTGTGAGATGTATTTT 59.315 43.478 0.00 0.00 0.00 1.82
2895 3392 4.154195 GTGGAGCGTGTGAGATGTATTTTT 59.846 41.667 0.00 0.00 0.00 1.94
2916 3413 2.292292 TGCCTTTAGGTTTTGTCTTCGC 59.708 45.455 0.00 0.00 37.57 4.70
2922 3419 6.258068 CCTTTAGGTTTTGTCTTCGCCTATAG 59.742 42.308 0.00 0.00 33.56 1.31
2946 3443 8.567285 AGAAGTTCAGGTGGAAATAAATACAG 57.433 34.615 5.50 0.00 37.23 2.74
2947 3444 8.164070 AGAAGTTCAGGTGGAAATAAATACAGT 58.836 33.333 5.50 0.00 37.23 3.55
2949 3446 8.788325 AGTTCAGGTGGAAATAAATACAGTAC 57.212 34.615 0.00 0.00 37.23 2.73
2950 3447 7.827729 AGTTCAGGTGGAAATAAATACAGTACC 59.172 37.037 0.00 0.00 37.23 3.34
2951 3448 7.504926 TCAGGTGGAAATAAATACAGTACCT 57.495 36.000 0.00 0.00 36.51 3.08
2952 3449 7.553881 CAGGTGGAAATAAATACAGTACCTG 57.446 40.000 0.00 0.00 44.37 4.00
2969 3466 1.953686 CCTGGTGTCATTTTCCGTTGT 59.046 47.619 0.00 0.00 0.00 3.32
3025 3522 1.807165 CCCTACGACGTCGACGAGA 60.807 63.158 41.52 21.92 43.02 4.04
3073 3570 3.382832 AAGGAGGACTGGTCGCCG 61.383 66.667 5.90 0.00 32.27 6.46
3156 3837 4.100808 AGTTGCTTCCAATTGGTTGCTAAA 59.899 37.500 29.58 20.32 36.24 1.85
3160 3841 9.513793 GTTGCTTCCAATTGGTTGCTAAACAAC 62.514 40.741 29.58 24.19 44.27 3.32
3208 3889 5.463286 TGTCGTTATCTCACACGTTACATT 58.537 37.500 0.00 0.00 37.66 2.71
3427 4135 3.933332 CGTTTCCTGAATAAGACCTGGAC 59.067 47.826 0.00 0.00 31.46 4.02
3466 4178 4.451629 TGGTTGTGTTACTAGCTAGCTC 57.548 45.455 23.26 7.00 0.00 4.09
3467 4179 4.087182 TGGTTGTGTTACTAGCTAGCTCT 58.913 43.478 23.26 10.38 0.00 4.09
3502 4214 3.181474 ACGCTGCCTCTAGTTTCTAATCC 60.181 47.826 0.00 0.00 0.00 3.01
3506 4218 3.181475 TGCCTCTAGTTTCTAATCCAGCG 60.181 47.826 0.00 0.00 0.00 5.18
3548 4260 7.264221 TCATTGCAAAACACAACTTGTAGAAT 58.736 30.769 1.71 0.00 37.51 2.40
3590 4302 1.697432 TCAGAGGATGGACGGTGTTTT 59.303 47.619 0.00 0.00 0.00 2.43
3591 4303 2.901192 TCAGAGGATGGACGGTGTTTTA 59.099 45.455 0.00 0.00 0.00 1.52
3628 4348 2.852143 GCATGCGAAACCGAGATCAATG 60.852 50.000 0.00 0.00 0.00 2.82
3642 4373 1.173043 TCAATGAACCCATCCAACGC 58.827 50.000 0.00 0.00 31.40 4.84
3646 4377 0.321564 TGAACCCATCCAACGCTCTG 60.322 55.000 0.00 0.00 0.00 3.35
3696 4432 0.171455 GGCTAGGATAGGATCGTGCG 59.829 60.000 0.00 0.00 39.70 5.34
3706 4442 1.693083 GGATCGTGCGGTACAAGTGC 61.693 60.000 0.00 0.00 0.00 4.40
3780 4521 0.539669 AAGGGGGAGGCAAAAGAACG 60.540 55.000 0.00 0.00 0.00 3.95
3795 4536 0.237498 GAACGGCCGAAAAGTTCCAG 59.763 55.000 35.90 0.00 38.53 3.86
3800 4541 1.966451 CCGAAAAGTTCCAGGCGCT 60.966 57.895 7.64 0.00 0.00 5.92
3820 4561 2.689083 CAGCATGCCATTTGCCATG 58.311 52.632 15.66 0.00 41.06 3.66
3821 4562 0.813610 CAGCATGCCATTTGCCATGG 60.814 55.000 15.66 7.63 41.06 3.66
3822 4563 0.978667 AGCATGCCATTTGCCATGGA 60.979 50.000 18.40 0.00 41.64 3.41
3823 4564 0.531974 GCATGCCATTTGCCATGGAG 60.532 55.000 18.40 0.00 41.64 3.86
3824 4565 0.828022 CATGCCATTTGCCATGGAGT 59.172 50.000 18.40 0.00 41.64 3.85
3840 4581 4.541482 GTCGCCATGCATGCACCG 62.541 66.667 25.37 24.13 0.00 4.94
3841 4582 4.774503 TCGCCATGCATGCACCGA 62.775 61.111 25.37 25.92 0.00 4.69
3843 4584 2.333938 GCCATGCATGCACCGATC 59.666 61.111 25.37 7.01 0.00 3.69
3879 4621 4.200283 GGGCGACGGCAGAGAGAG 62.200 72.222 23.66 0.00 42.47 3.20
3880 4622 3.134792 GGCGACGGCAGAGAGAGA 61.135 66.667 17.49 0.00 42.47 3.10
3902 4644 2.586245 CAGAGCGCAGGGGATTGA 59.414 61.111 11.47 0.00 0.00 2.57
3934 4680 2.241722 CGATGCCATGTGAAACGAAAC 58.758 47.619 0.00 0.00 42.39 2.78
3935 4681 2.241722 GATGCCATGTGAAACGAAACG 58.758 47.619 0.00 0.00 42.39 3.60
3936 4682 1.300481 TGCCATGTGAAACGAAACGA 58.700 45.000 0.00 0.00 42.39 3.85
3937 4683 1.671328 TGCCATGTGAAACGAAACGAA 59.329 42.857 0.00 0.00 42.39 3.85
3938 4684 2.097629 TGCCATGTGAAACGAAACGAAA 59.902 40.909 0.00 0.00 42.39 3.46
3939 4685 2.466205 GCCATGTGAAACGAAACGAAAC 59.534 45.455 0.00 0.00 42.39 2.78
4007 8626 2.972713 ACCATATCAATCTACCGTGGCT 59.027 45.455 0.00 0.00 0.00 4.75
4014 8633 1.330655 ATCTACCGTGGCTGAGGTGG 61.331 60.000 8.87 6.52 41.51 4.61
4035 8654 1.303615 GACGGAGGGGAGAGAGACA 59.696 63.158 0.00 0.00 0.00 3.41
4041 8660 1.216710 GGGGAGAGAGACAAGCGTG 59.783 63.158 0.00 0.00 0.00 5.34
4100 8720 3.645268 AATGAGCCCCTGTTCCGGC 62.645 63.158 0.00 0.00 46.09 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 8.549548 TGTTCTTTTATTACAAACGAATCACGA 58.450 29.630 0.00 0.00 45.77 4.35
84 85 8.014070 TGTTCTCCGTAGAAATGGTTCATATA 57.986 34.615 0.00 0.00 43.30 0.86
92 93 3.065371 GGCAATGTTCTCCGTAGAAATGG 59.935 47.826 0.00 0.00 43.30 3.16
106 107 9.853177 ACTAGCTTAATAAGAATAGGCAATGTT 57.147 29.630 3.88 0.00 0.00 2.71
366 367 5.417170 AAGGGGGCATATTTTCCTTCATA 57.583 39.130 0.00 0.00 32.94 2.15
421 422 1.725641 GCTGGGGCTATTGCAAAAAC 58.274 50.000 1.71 0.00 41.91 2.43
460 461 9.193133 TCGTTTTGAAAAACAATTGTGAGTTAA 57.807 25.926 12.82 3.00 46.52 2.01
479 480 7.188834 TCATAGCTGAAAAGCATATCGTTTTG 58.811 34.615 0.00 0.00 37.25 2.44
480 481 7.320443 TCATAGCTGAAAAGCATATCGTTTT 57.680 32.000 0.00 0.00 37.25 2.43
499 500 7.495279 AGCAAGAGCATTCTAGTTTCTTCATAG 59.505 37.037 0.00 0.00 45.49 2.23
557 558 1.823295 GGTGCGGGCTAGATGAGAA 59.177 57.895 0.00 0.00 0.00 2.87
620 785 9.435688 GAGCATTTCTTACAACCCAAATATTTT 57.564 29.630 0.00 0.00 0.00 1.82
627 792 3.826157 CCTGAGCATTTCTTACAACCCAA 59.174 43.478 0.00 0.00 0.00 4.12
685 867 1.325640 CATCGAAGGCTGTGATCGTTG 59.674 52.381 6.25 4.92 37.79 4.10
825 1007 4.044317 TCCCCTCTTCAGAACTACAGTACT 59.956 45.833 0.00 0.00 0.00 2.73
908 1090 0.533755 ACAGAACCTGTGTCTGCAGC 60.534 55.000 9.47 4.92 43.63 5.25
911 1093 2.821991 AGTACAGAACCTGTGTCTGC 57.178 50.000 9.64 0.00 45.01 4.26
936 1131 2.564062 AGTTGGGCATTGGAATGAAGTG 59.436 45.455 3.47 0.00 38.70 3.16
953 1148 2.296190 GCTTGGGGTTGTAGGAAAGTTG 59.704 50.000 0.00 0.00 0.00 3.16
1090 1297 1.153066 TGGCTGCGTCAAGGTTTGA 60.153 52.632 0.00 0.00 37.33 2.69
1266 1473 0.620556 ACCATAGGACCAGTGGCTTG 59.379 55.000 9.78 0.00 36.47 4.01
1395 1610 0.396974 AACAGCCAGGTCCTGCAAAA 60.397 50.000 13.99 0.00 33.65 2.44
1458 1673 2.414481 CTCAGGCACATCTTTCTTCACG 59.586 50.000 0.00 0.00 0.00 4.35
1482 1697 0.394565 AGGCATACGGATTGAGCTCC 59.605 55.000 12.15 0.00 0.00 4.70
1570 1837 4.649218 TCACCAGACAGTAAGCTATGCATA 59.351 41.667 6.20 6.20 0.00 3.14
1734 2001 4.202357 GGCAAGAAATCCCTTCCTTGTTTT 60.202 41.667 0.00 0.00 34.21 2.43
1755 2022 7.315142 TGAAAGAAATGTCATGTTATCTTGGC 58.685 34.615 0.00 0.00 0.00 4.52
1867 2135 0.749649 AACCTGCATAGCTCTCTCCG 59.250 55.000 0.00 0.00 0.00 4.63
1886 2154 6.439636 AGCTATCTATGAATAAGGTGGCAA 57.560 37.500 0.00 0.00 34.27 4.52
1949 2302 6.363088 CGCAAGAGAATTACAATGAGCAAAAA 59.637 34.615 0.00 0.00 43.02 1.94
1974 2327 3.250280 TGTAATGTCCTAGCGATCGAGTC 59.750 47.826 21.57 0.32 0.00 3.36
2058 2411 2.242043 ACCAGGATGCCTTTGAAGTTG 58.758 47.619 0.00 0.00 31.97 3.16
2101 2460 5.793817 TGCTAAGTGCTAACATTCTTGAGA 58.206 37.500 0.00 0.00 43.37 3.27
2103 2462 5.551233 ACTGCTAAGTGCTAACATTCTTGA 58.449 37.500 0.00 0.00 43.37 3.02
2140 2528 2.749076 CCCGATCTGCACTTCATTTTGA 59.251 45.455 0.00 0.00 0.00 2.69
2282 2712 2.505118 GCACTCGCGAGACAGGAC 60.505 66.667 40.58 18.71 35.39 3.85
2315 2745 2.517598 CGTGGAGGACGTTGAACTG 58.482 57.895 0.00 0.00 43.50 3.16
2461 2897 0.467804 TGGCTGAAACTTTTTGGGCC 59.532 50.000 0.00 0.00 38.67 5.80
2464 2900 4.570369 ACGAAAATGGCTGAAACTTTTTGG 59.430 37.500 0.00 0.00 31.66 3.28
2465 2901 5.519927 AGACGAAAATGGCTGAAACTTTTTG 59.480 36.000 0.00 0.00 0.00 2.44
2657 3129 2.626149 GGCAAAGAGAGTAGGGGTAGGA 60.626 54.545 0.00 0.00 0.00 2.94
2684 3156 4.335037 GCATTTCAGCTAGGAGGAGAAAAG 59.665 45.833 0.00 0.00 32.65 2.27
2727 3204 2.270352 TTCAGTTCAGCCACCGAAAT 57.730 45.000 0.00 0.00 0.00 2.17
2741 3223 6.823689 AGCGGAACAATATTCAGTATTTCAGT 59.176 34.615 0.00 0.00 30.53 3.41
2744 3226 7.472543 ACAAGCGGAACAATATTCAGTATTTC 58.527 34.615 0.00 0.00 30.53 2.17
2745 3227 7.391148 ACAAGCGGAACAATATTCAGTATTT 57.609 32.000 0.00 0.00 30.53 1.40
2746 3228 7.391148 AACAAGCGGAACAATATTCAGTATT 57.609 32.000 0.00 0.00 33.23 1.89
2747 3229 7.250569 CAAACAAGCGGAACAATATTCAGTAT 58.749 34.615 0.00 0.00 0.00 2.12
2748 3230 6.607689 CAAACAAGCGGAACAATATTCAGTA 58.392 36.000 0.00 0.00 0.00 2.74
2749 3231 5.460646 CAAACAAGCGGAACAATATTCAGT 58.539 37.500 0.00 0.00 0.00 3.41
2750 3232 4.324402 GCAAACAAGCGGAACAATATTCAG 59.676 41.667 0.00 0.00 0.00 3.02
2751 3233 4.233789 GCAAACAAGCGGAACAATATTCA 58.766 39.130 0.00 0.00 0.00 2.57
2792 3289 0.948623 TTGTCCGAATCGTGCCACAG 60.949 55.000 0.82 0.00 0.00 3.66
2806 3303 3.967715 GGAAGCACCGTCTTGTCC 58.032 61.111 0.00 0.00 0.00 4.02
2851 3348 2.816087 CCTGAAAATCCATATGCGGAGG 59.184 50.000 0.00 0.00 38.83 4.30
2874 3371 4.651994 CAAAAATACATCTCACACGCTCC 58.348 43.478 0.00 0.00 0.00 4.70
2879 3376 7.029563 CCTAAAGGCAAAAATACATCTCACAC 58.970 38.462 0.00 0.00 0.00 3.82
2881 3378 7.158099 ACCTAAAGGCAAAAATACATCTCAC 57.842 36.000 0.00 0.00 39.32 3.51
2894 3391 3.243267 GCGAAGACAAAACCTAAAGGCAA 60.243 43.478 0.00 0.00 39.32 4.52
2895 3392 2.292292 GCGAAGACAAAACCTAAAGGCA 59.708 45.455 0.00 0.00 39.32 4.75
2916 3413 9.853177 ATTTATTTCCACCTGAACTTCTATAGG 57.147 33.333 0.00 0.00 36.39 2.57
2922 3419 8.336801 ACTGTATTTATTTCCACCTGAACTTC 57.663 34.615 0.00 0.00 31.05 3.01
2945 3442 2.370849 ACGGAAAATGACACCAGGTACT 59.629 45.455 0.00 0.00 43.88 2.73
2946 3443 2.774687 ACGGAAAATGACACCAGGTAC 58.225 47.619 0.00 0.00 0.00 3.34
2947 3444 3.142951 CAACGGAAAATGACACCAGGTA 58.857 45.455 0.00 0.00 0.00 3.08
2949 3446 1.953686 ACAACGGAAAATGACACCAGG 59.046 47.619 0.00 0.00 0.00 4.45
2950 3447 3.315191 AGAACAACGGAAAATGACACCAG 59.685 43.478 0.00 0.00 0.00 4.00
2951 3448 3.283751 AGAACAACGGAAAATGACACCA 58.716 40.909 0.00 0.00 0.00 4.17
2952 3449 3.982576 AGAACAACGGAAAATGACACC 57.017 42.857 0.00 0.00 0.00 4.16
3073 3570 0.947244 CCTGCTTGTGAGTGAACCAC 59.053 55.000 0.00 0.00 35.23 4.16
3100 3597 6.811665 GGGATTGTCCAATTAGTTAAAACAGC 59.188 38.462 0.00 0.00 38.64 4.40
3180 3861 6.426980 AACGTGTGAGATAACGACATACTA 57.573 37.500 1.80 0.00 42.32 1.82
3189 3870 6.884187 ACACAAATGTAACGTGTGAGATAAC 58.116 36.000 9.81 0.00 44.35 1.89
3427 4135 1.130373 CCATGAAATCAACCACGTCCG 59.870 52.381 0.00 0.00 0.00 4.79
3466 4178 0.248580 CAGCGTAGAGAGCAGAGCAG 60.249 60.000 0.00 0.00 37.01 4.24
3467 4179 1.805910 CAGCGTAGAGAGCAGAGCA 59.194 57.895 0.00 0.00 37.01 4.26
3502 4214 1.566211 ATCCATCCTAGATCCCGCTG 58.434 55.000 0.00 0.00 0.00 5.18
3506 4218 4.704057 GCAATGAAATCCATCCTAGATCCC 59.296 45.833 0.00 0.00 33.53 3.85
3509 4221 7.124599 TGTTTTGCAATGAAATCCATCCTAGAT 59.875 33.333 0.00 0.00 33.53 1.98
3590 4302 1.371183 GCCCGCATCATAGCCAGTA 59.629 57.895 0.00 0.00 0.00 2.74
3591 4303 2.060567 ATGCCCGCATCATAGCCAGT 62.061 55.000 0.00 0.00 29.42 4.00
3628 4348 0.036388 TCAGAGCGTTGGATGGGTTC 60.036 55.000 0.00 0.00 0.00 3.62
3642 4373 4.935205 TCACGTTGGAATTAATGGTCAGAG 59.065 41.667 0.00 0.00 0.00 3.35
3677 4413 0.171455 CGCACGATCCTATCCTAGCC 59.829 60.000 0.00 0.00 0.00 3.93
3757 4498 1.062505 TCTTTTGCCTCCCCCTTGTTT 60.063 47.619 0.00 0.00 0.00 2.83
3758 4499 0.560688 TCTTTTGCCTCCCCCTTGTT 59.439 50.000 0.00 0.00 0.00 2.83
3759 4500 0.560688 TTCTTTTGCCTCCCCCTTGT 59.439 50.000 0.00 0.00 0.00 3.16
3780 4521 2.962569 GCCTGGAACTTTTCGGCC 59.037 61.111 0.00 0.00 32.16 6.13
3820 4561 2.825387 TGCATGCATGGCGACTCC 60.825 61.111 27.34 9.80 0.00 3.85
3821 4562 2.406401 GTGCATGCATGGCGACTC 59.594 61.111 25.64 10.52 0.00 3.36
3822 4563 3.136123 GGTGCATGCATGGCGACT 61.136 61.111 25.64 0.00 0.00 4.18
3823 4564 4.541482 CGGTGCATGCATGGCGAC 62.541 66.667 25.64 17.41 0.00 5.19
3824 4565 4.774503 TCGGTGCATGCATGGCGA 62.775 61.111 25.64 9.97 0.00 5.54
3877 4619 2.508887 CTGCGCTCTGCCTGTCTC 60.509 66.667 9.73 0.00 45.60 3.36
3878 4620 4.079850 CCTGCGCTCTGCCTGTCT 62.080 66.667 9.73 0.00 45.60 3.41
3902 4644 1.738099 GGCATCGTGTTCGTGAGCT 60.738 57.895 0.00 0.00 38.33 4.09
3934 4680 6.136071 ACAAGTCAGAATTCATTTCGTTTCG 58.864 36.000 8.44 0.00 39.46 3.46
3935 4681 7.914537 AACAAGTCAGAATTCATTTCGTTTC 57.085 32.000 8.44 0.00 39.46 2.78
3936 4682 8.190784 AGAAACAAGTCAGAATTCATTTCGTTT 58.809 29.630 8.44 9.41 39.46 3.60
3937 4683 7.645340 CAGAAACAAGTCAGAATTCATTTCGTT 59.355 33.333 8.44 1.21 39.46 3.85
3938 4684 7.134815 CAGAAACAAGTCAGAATTCATTTCGT 58.865 34.615 8.44 0.00 39.46 3.85
3939 4685 6.580041 CCAGAAACAAGTCAGAATTCATTTCG 59.420 38.462 8.44 6.53 39.46 3.46
4014 8633 4.816984 TCTCTCCCCTCCGTCGCC 62.817 72.222 0.00 0.00 0.00 5.54
4019 8638 1.671901 GCTTGTCTCTCTCCCCTCCG 61.672 65.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.