Multiple sequence alignment - TraesCS4A01G087300

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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 TraesCS4A01G087300 chr4A 100.000 3092 0 0 1 3092 91755613 91752522 0.000000e+00 5710.0
1 TraesCS4A01G087300 chr4A 90.476 63 6 0 2671 2733 43717726 43717664 1.980000e-12 84.2
2 TraesCS4A01G087300 chr4D 93.494 2152 94 24 971 3092 372513385 372515520 0.000000e+00 3157.0
3 TraesCS4A01G087300 chr4D 86.676 683 27 21 282 950 372512670 372513302 0.000000e+00 699.0
4 TraesCS4A01G087300 chr4D 91.473 129 8 2 1 129 372509712 372509837 1.140000e-39 174.0
5 TraesCS4A01G087300 chr4D 90.566 53 5 0 2671 2723 19875655 19875603 1.540000e-08 71.3
6 TraesCS4A01G087300 chr4B 93.467 1592 45 23 971 2542 457770291 457771843 0.000000e+00 2309.0
7 TraesCS4A01G087300 chr4B 89.706 544 50 4 2551 3092 457772136 457772675 0.000000e+00 689.0
8 TraesCS4A01G087300 chr4B 87.603 484 29 10 1 461 457768842 457769317 1.630000e-147 532.0
9 TraesCS4A01G087300 chr4B 83.399 506 30 24 458 950 457769744 457770208 1.330000e-113 420.0
10 TraesCS4A01G087300 chr1A 94.667 75 4 0 335 409 526431736 526431810 1.950000e-22 117.0
11 TraesCS4A01G087300 chr6D 92.063 63 5 0 2671 2733 437599939 437600001 4.250000e-14 89.8
12 TraesCS4A01G087300 chr5D 92.063 63 5 0 2671 2733 329160778 329160840 4.250000e-14 89.8
13 TraesCS4A01G087300 chr5B 92.063 63 5 0 2671 2733 694375730 694375792 4.250000e-14 89.8
14 TraesCS4A01G087300 chr1D 92.063 63 5 0 2671 2733 51864855 51864917 4.250000e-14 89.8
15 TraesCS4A01G087300 chr1D 92.063 63 5 0 2671 2733 461632212 461632274 4.250000e-14 89.8


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 TraesCS4A01G087300 chr4A 91752522 91755613 3091 True 5710.000000 5710 100.000000 1 3092 1 chr4A.!!$R2 3091
1 TraesCS4A01G087300 chr4D 372509712 372515520 5808 False 1343.333333 3157 90.547667 1 3092 3 chr4D.!!$F1 3091
2 TraesCS4A01G087300 chr4B 457768842 457772675 3833 False 987.500000 2309 88.543750 1 3092 4 chr4B.!!$F1 3091

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
733 3871 0.037512 CCTGTCAGTCAGCCAGTCAG 60.038 60.0 0.0 0.0 42.38 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2707 6244 0.330267 TTACCTAAACCCTGCAGCCC 59.67 55.0 8.66 0.0 0.0 5.19 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
79 80 9.878737 AAGGGTGTCATATAGTAGTACATAACT 57.121 33.333 2.52 0.00 42.62 2.24
110 111 2.311542 TGGTTGGGCTATTTCTCATGGT 59.688 45.455 0.00 0.00 0.00 3.55
125 126 2.354510 TCATGGTGCCGATTTCGAAATC 59.645 45.455 31.95 31.95 43.02 2.17
134 261 2.536928 CGATTTCGAAATCAAGTCCGGC 60.537 50.000 36.88 17.27 43.85 6.13
142 269 3.726517 CAAGTCCGGCCACGCTTG 61.727 66.667 2.24 9.60 39.22 4.01
186 335 1.654023 GACATGGCTTGGTAACCGGC 61.654 60.000 0.00 0.00 0.00 6.13
241 392 2.051334 TGAATATTGTCCCCGCCAAG 57.949 50.000 0.00 0.00 0.00 3.61
249 400 0.960861 GTCCCCGCCAAGAAAGAAGG 60.961 60.000 0.00 0.00 0.00 3.46
257 408 5.454755 CCCGCCAAGAAAGAAGGAGATAATA 60.455 44.000 0.00 0.00 0.00 0.98
320 3016 5.630264 TGAAAGATGCAAACATGTTCATTCG 59.370 36.000 12.39 0.00 38.74 3.34
325 3021 3.255395 TGCAAACATGTTCATTCGGTGAT 59.745 39.130 12.39 0.00 36.54 3.06
335 3031 3.653344 TCATTCGGTGATATAGCAGTGC 58.347 45.455 7.13 7.13 0.00 4.40
383 3079 0.652592 GTGGAGTGCGCATATGTCAC 59.347 55.000 15.91 14.23 0.00 3.67
424 3120 2.100197 GGCAAAAGTATCTGTTCCCCC 58.900 52.381 0.00 0.00 0.00 5.40
516 3642 1.463528 GGTTTCTTATCGTGTGTGCGC 60.464 52.381 0.00 0.00 0.00 6.09
574 3700 3.773154 GAGCCCCTCTCCCTCCCT 61.773 72.222 0.00 0.00 35.77 4.20
575 3701 3.767044 GAGCCCCTCTCCCTCCCTC 62.767 73.684 0.00 0.00 35.77 4.30
582 3720 2.015726 TCTCCCTCCCTCCCTCTCC 61.016 68.421 0.00 0.00 0.00 3.71
584 3722 4.179599 CCCTCCCTCCCTCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
615 3753 1.488527 AACGACGAGTCAGAAACAGC 58.511 50.000 0.00 0.00 0.00 4.40
624 3762 1.082104 CAGAAACAGCGCGAAACCC 60.082 57.895 12.10 0.00 0.00 4.11
642 3780 1.154282 CAGACGCGCGTTAGAGTCA 60.154 57.895 38.03 0.00 42.21 3.41
643 3781 1.128724 CAGACGCGCGTTAGAGTCAG 61.129 60.000 38.03 15.88 42.21 3.51
644 3782 1.154263 GACGCGCGTTAGAGTCAGT 60.154 57.895 38.03 9.86 40.04 3.41
645 3783 1.126996 GACGCGCGTTAGAGTCAGTC 61.127 60.000 38.03 16.20 40.04 3.51
671 3809 1.833049 CTTATCCCTCCGCCGTCCT 60.833 63.158 0.00 0.00 0.00 3.85
686 3824 3.213402 CCTCCTCCGCCTCTCGTC 61.213 72.222 0.00 0.00 36.19 4.20
708 3846 2.027653 TCCTTCACAGTTCACACACACA 60.028 45.455 0.00 0.00 0.00 3.72
710 3848 2.464157 TCACAGTTCACACACACACA 57.536 45.000 0.00 0.00 0.00 3.72
711 3849 2.073056 TCACAGTTCACACACACACAC 58.927 47.619 0.00 0.00 0.00 3.82
712 3850 1.075542 ACAGTTCACACACACACACG 58.924 50.000 0.00 0.00 0.00 4.49
714 3852 1.061887 GTTCACACACACACACGCC 59.938 57.895 0.00 0.00 0.00 5.68
716 3854 2.513666 CACACACACACACGCCCT 60.514 61.111 0.00 0.00 0.00 5.19
717 3855 2.513666 ACACACACACACGCCCTG 60.514 61.111 0.00 0.00 0.00 4.45
718 3856 2.513666 CACACACACACGCCCTGT 60.514 61.111 0.00 0.00 0.00 4.00
719 3857 2.203015 ACACACACACGCCCTGTC 60.203 61.111 0.00 0.00 0.00 3.51
720 3858 2.203001 CACACACACGCCCTGTCA 60.203 61.111 0.00 0.00 0.00 3.58
721 3859 2.108976 ACACACACGCCCTGTCAG 59.891 61.111 0.00 0.00 0.00 3.51
722 3860 2.108976 CACACACGCCCTGTCAGT 59.891 61.111 0.00 0.00 0.00 3.41
723 3861 1.956170 CACACACGCCCTGTCAGTC 60.956 63.158 0.00 0.00 0.00 3.51
724 3862 2.421314 CACACGCCCTGTCAGTCA 59.579 61.111 0.00 0.00 0.00 3.41
725 3863 1.665916 CACACGCCCTGTCAGTCAG 60.666 63.158 0.00 0.00 43.27 3.51
726 3864 2.740055 CACGCCCTGTCAGTCAGC 60.740 66.667 0.00 0.00 42.38 4.26
727 3865 4.008933 ACGCCCTGTCAGTCAGCC 62.009 66.667 0.00 0.00 42.38 4.85
728 3866 4.007644 CGCCCTGTCAGTCAGCCA 62.008 66.667 0.00 0.00 42.38 4.75
729 3867 2.046507 GCCCTGTCAGTCAGCCAG 60.047 66.667 0.00 0.00 42.38 4.85
730 3868 2.888447 GCCCTGTCAGTCAGCCAGT 61.888 63.158 0.00 0.00 42.38 4.00
731 3869 1.294780 CCCTGTCAGTCAGCCAGTC 59.705 63.158 0.00 0.00 42.38 3.51
732 3870 1.475169 CCCTGTCAGTCAGCCAGTCA 61.475 60.000 0.00 0.00 42.38 3.41
733 3871 0.037512 CCTGTCAGTCAGCCAGTCAG 60.038 60.000 0.00 0.00 42.38 3.51
734 3872 0.669932 CTGTCAGTCAGCCAGTCAGC 60.670 60.000 0.00 0.00 37.36 4.26
735 3873 1.375268 GTCAGTCAGCCAGTCAGCC 60.375 63.158 0.00 0.00 0.00 4.85
736 3874 1.838396 TCAGTCAGCCAGTCAGCCA 60.838 57.895 0.00 0.00 0.00 4.75
737 3875 1.375652 CAGTCAGCCAGTCAGCCAG 60.376 63.158 0.00 0.00 0.00 4.85
738 3876 1.840650 AGTCAGCCAGTCAGCCAGT 60.841 57.895 0.00 0.00 0.00 4.00
784 3922 2.340443 CCCGCCTCCGCTTCTATC 59.660 66.667 0.00 0.00 0.00 2.08
937 4088 4.378030 CGATATAAACGCACGTACTCTTCC 59.622 45.833 0.00 0.00 0.00 3.46
950 4102 2.192608 CTCTTCCCGCAAAGCAGCAC 62.193 60.000 0.00 0.00 0.00 4.40
951 4103 2.203337 TTCCCGCAAAGCAGCACT 60.203 55.556 0.00 0.00 0.00 4.40
952 4104 2.467946 CTTCCCGCAAAGCAGCACTG 62.468 60.000 0.00 0.00 0.00 3.66
953 4105 3.289834 CCCGCAAAGCAGCACTGT 61.290 61.111 0.00 0.00 0.00 3.55
954 4106 1.965930 CCCGCAAAGCAGCACTGTA 60.966 57.895 0.00 0.00 0.00 2.74
955 4107 1.207593 CCGCAAAGCAGCACTGTAC 59.792 57.895 0.00 0.00 0.00 2.90
956 4108 1.207593 CGCAAAGCAGCACTGTACC 59.792 57.895 0.00 0.00 0.00 3.34
958 4110 0.890996 GCAAAGCAGCACTGTACCCT 60.891 55.000 0.00 0.00 0.00 4.34
959 4111 1.610624 GCAAAGCAGCACTGTACCCTA 60.611 52.381 0.00 0.00 0.00 3.53
960 4112 2.350522 CAAAGCAGCACTGTACCCTAG 58.649 52.381 0.00 0.00 0.00 3.02
964 4116 1.067821 GCAGCACTGTACCCTAGCTAG 59.932 57.143 14.20 14.20 33.59 3.42
965 4117 2.379972 CAGCACTGTACCCTAGCTAGT 58.620 52.381 19.31 5.46 33.59 2.57
967 4119 3.952323 CAGCACTGTACCCTAGCTAGTAA 59.048 47.826 19.31 1.61 33.59 2.24
968 4120 4.036971 CAGCACTGTACCCTAGCTAGTAAG 59.963 50.000 19.31 10.09 33.59 2.34
971 4123 5.008514 GCACTGTACCCTAGCTAGTAAGTAC 59.991 48.000 24.95 24.95 0.00 2.73
974 4126 5.688807 TGTACCCTAGCTAGTAAGTACCTG 58.311 45.833 26.77 10.48 31.28 4.00
975 4127 4.877436 ACCCTAGCTAGTAAGTACCTGT 57.123 45.455 19.31 0.31 0.00 4.00
976 4128 4.534797 ACCCTAGCTAGTAAGTACCTGTG 58.465 47.826 19.31 0.00 0.00 3.66
977 4129 4.229123 ACCCTAGCTAGTAAGTACCTGTGA 59.771 45.833 19.31 0.00 0.00 3.58
1281 4496 0.616964 AGAGCCTGGAGATCTGCACA 60.617 55.000 13.58 2.06 0.00 4.57
1575 4799 2.057408 CCTGCTCCTCTCCTTCGCT 61.057 63.158 0.00 0.00 0.00 4.93
1613 4843 1.946475 GAGGACGAGGGGAAGAACCG 61.946 65.000 0.00 0.00 40.11 4.44
1671 4904 2.904866 CGCGAGGAGGAGGAGGAG 60.905 72.222 0.00 0.00 0.00 3.69
1734 4967 0.536687 TCGTCGAGGTCAAGGTCAGT 60.537 55.000 4.85 0.00 0.00 3.41
1938 5171 4.785453 CTGCCTGGCCCGGAAGAC 62.785 72.222 16.37 0.00 30.51 3.01
2542 5794 1.002773 TCCTTCTAAACCGGCCTGAAC 59.997 52.381 0.00 0.00 0.00 3.18
2574 6111 4.884668 AGACCAAAAGGACGATAAGACA 57.115 40.909 0.00 0.00 0.00 3.41
2586 6123 5.687730 GGACGATAAGACACACATGTAGATG 59.312 44.000 0.00 0.00 39.95 2.90
2602 6139 2.573609 GATGGGGAACACGACTCGGG 62.574 65.000 0.00 0.00 35.82 5.14
2638 6175 1.006102 CGGAGGTCGTCAAGCAGTT 60.006 57.895 0.00 0.00 0.00 3.16
2707 6244 8.899427 TTCTTTCATAGAATGATAGGAAGCAG 57.101 34.615 7.28 0.00 37.96 4.24
2710 6247 2.947127 AGAATGATAGGAAGCAGGGC 57.053 50.000 0.00 0.00 0.00 5.19
2733 6270 5.297029 GCTGCAGGGTTTAGGTAAGAAATAG 59.703 44.000 17.12 0.00 0.00 1.73
2737 6274 6.592870 CAGGGTTTAGGTAAGAAATAGAGGG 58.407 44.000 0.00 0.00 0.00 4.30
2766 6303 1.681264 AGGCGGAAAAAGAACAAGGTG 59.319 47.619 0.00 0.00 0.00 4.00
2824 6361 1.065926 TGCTGCCTAATCACCTGTCAG 60.066 52.381 0.00 0.00 0.00 3.51
2853 6390 5.528690 GCATGAACTCTTGCACTAATCCATA 59.471 40.000 11.53 0.00 43.80 2.74
2886 6423 9.408648 TCTTCCTTGTTTGTTCTTAGATCTTTT 57.591 29.630 0.00 0.00 0.00 2.27
2914 6451 1.217244 GGTTGGGTATGCTCGTCGT 59.783 57.895 0.00 0.00 0.00 4.34
2940 6477 4.255510 AGACCAAAGGCAATGATGGTAT 57.744 40.909 0.00 0.00 45.85 2.73
2941 6478 5.387113 AGACCAAAGGCAATGATGGTATA 57.613 39.130 0.00 0.00 45.85 1.47
2942 6479 5.765510 AGACCAAAGGCAATGATGGTATAA 58.234 37.500 0.00 0.00 45.85 0.98
2944 6481 4.649218 ACCAAAGGCAATGATGGTATAACC 59.351 41.667 0.00 0.00 44.11 2.85
2974 6511 5.163343 TGTTCACAAGGCTAACAAGTCTAGT 60.163 40.000 0.00 0.00 30.54 2.57
2976 6513 4.587262 TCACAAGGCTAACAAGTCTAGTCA 59.413 41.667 0.00 0.00 0.00 3.41
2988 6525 8.880991 AACAAGTCTAGTCAGGAATAGAGTTA 57.119 34.615 20.21 0.00 44.78 2.24
2996 6533 4.811557 GTCAGGAATAGAGTTAAAGCGCAT 59.188 41.667 11.47 0.00 0.00 4.73
3002 6539 3.887621 AGAGTTAAAGCGCATCACCTA 57.112 42.857 11.47 0.00 0.00 3.08
3017 6554 5.885912 GCATCACCTAAATTTTCTAGGGTCA 59.114 40.000 9.73 0.00 40.37 4.02
3025 6563 2.038863 TTTCTAGGGTCAGAGGGCAA 57.961 50.000 0.00 0.00 0.00 4.52
3040 6578 0.034089 GGCAACCTCCAAGGCTACAT 60.034 55.000 0.00 0.00 39.63 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 6.071391 AGCCCAACCATTTCTGTTTAGTTATG 60.071 38.462 0.00 0.00 0.00 1.90
74 75 6.016555 AGCCCAACCATTTCTGTTTAGTTAT 58.983 36.000 0.00 0.00 0.00 1.89
75 76 5.390387 AGCCCAACCATTTCTGTTTAGTTA 58.610 37.500 0.00 0.00 0.00 2.24
76 77 4.223144 AGCCCAACCATTTCTGTTTAGTT 58.777 39.130 0.00 0.00 0.00 2.24
78 79 6.530019 AATAGCCCAACCATTTCTGTTTAG 57.470 37.500 0.00 0.00 0.00 1.85
79 80 6.723977 AGAAATAGCCCAACCATTTCTGTTTA 59.276 34.615 7.74 0.00 43.76 2.01
81 82 5.086621 AGAAATAGCCCAACCATTTCTGTT 58.913 37.500 7.74 0.00 43.76 3.16
82 83 4.677182 AGAAATAGCCCAACCATTTCTGT 58.323 39.130 7.74 0.00 43.76 3.41
83 84 4.706476 TGAGAAATAGCCCAACCATTTCTG 59.294 41.667 12.19 0.00 44.82 3.02
84 85 4.934356 TGAGAAATAGCCCAACCATTTCT 58.066 39.130 8.17 8.17 46.50 2.52
85 86 5.452356 CCATGAGAAATAGCCCAACCATTTC 60.452 44.000 0.00 0.00 38.42 2.17
110 111 2.418628 GGACTTGATTTCGAAATCGGCA 59.581 45.455 33.97 23.57 46.01 5.69
125 126 3.726517 CAAGCGTGGCCGGACTTG 61.727 66.667 9.82 14.67 34.16 3.16
142 269 5.338365 AGATTTTCTCATCATTTTGCGCTC 58.662 37.500 9.73 0.00 0.00 5.03
186 335 4.218417 ACTCTTCCAATCCAATTGAAACGG 59.782 41.667 7.12 2.36 42.83 4.44
241 392 8.470805 TCGGCATCTATATTATCTCCTTCTTTC 58.529 37.037 0.00 0.00 0.00 2.62
320 3016 0.597637 ACGCGCACTGCTATATCACC 60.598 55.000 5.73 0.00 43.27 4.02
325 3021 1.518352 CCACACGCGCACTGCTATA 60.518 57.895 5.73 0.00 43.27 1.31
335 3031 4.973360 CGGGCAAAACCACACGCG 62.973 66.667 3.53 3.53 42.05 6.01
361 3057 1.091771 ACATATGCGCACTCCACTGC 61.092 55.000 14.90 0.00 0.00 4.40
568 3694 4.179599 GGGGGAGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
569 3695 4.548513 CGGGGGAGAGGGAGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
624 3762 1.128724 CTGACTCTAACGCGCGTCTG 61.129 60.000 37.77 29.21 0.00 3.51
642 3780 2.489437 GGAGGGATAAGCTCGGTAGACT 60.489 54.545 0.00 0.00 0.00 3.24
643 3781 1.887854 GGAGGGATAAGCTCGGTAGAC 59.112 57.143 0.00 0.00 0.00 2.59
644 3782 1.544982 CGGAGGGATAAGCTCGGTAGA 60.545 57.143 0.00 0.00 0.00 2.59
645 3783 0.882474 CGGAGGGATAAGCTCGGTAG 59.118 60.000 0.00 0.00 0.00 3.18
686 3824 2.609459 GTGTGTGTGAACTGTGAAGGAG 59.391 50.000 0.00 0.00 0.00 3.69
708 3846 2.737180 CTGACTGACAGGGCGTGT 59.263 61.111 13.36 13.36 44.49 4.49
710 3848 4.008933 GGCTGACTGACAGGGCGT 62.009 66.667 7.51 0.00 45.82 5.68
711 3849 4.007644 TGGCTGACTGACAGGGCG 62.008 66.667 7.51 0.00 45.82 6.13
716 3854 1.368950 GCTGACTGGCTGACTGACA 59.631 57.895 0.00 0.00 0.00 3.58
717 3855 1.375268 GGCTGACTGGCTGACTGAC 60.375 63.158 0.00 0.00 38.32 3.51
718 3856 1.824224 CTGGCTGACTGGCTGACTGA 61.824 60.000 7.41 0.00 41.53 3.41
719 3857 1.375652 CTGGCTGACTGGCTGACTG 60.376 63.158 7.41 0.00 41.53 3.51
720 3858 1.825281 GACTGGCTGACTGGCTGACT 61.825 60.000 17.05 0.00 41.53 3.41
721 3859 1.375268 GACTGGCTGACTGGCTGAC 60.375 63.158 17.05 9.02 41.53 3.51
722 3860 1.824224 CTGACTGGCTGACTGGCTGA 61.824 60.000 17.05 0.00 41.53 4.26
723 3861 1.375652 CTGACTGGCTGACTGGCTG 60.376 63.158 10.37 10.37 43.88 4.85
724 3862 1.825281 GACTGACTGGCTGACTGGCT 61.825 60.000 7.41 0.00 42.34 4.75
725 3863 1.375268 GACTGACTGGCTGACTGGC 60.375 63.158 0.00 0.00 42.18 4.85
726 3864 0.037512 CTGACTGACTGGCTGACTGG 60.038 60.000 0.00 0.00 0.00 4.00
727 3865 0.678395 ACTGACTGACTGGCTGACTG 59.322 55.000 0.00 0.00 0.00 3.51
728 3866 0.965439 GACTGACTGACTGGCTGACT 59.035 55.000 0.00 0.00 0.00 3.41
729 3867 0.387878 CGACTGACTGACTGGCTGAC 60.388 60.000 0.00 0.00 0.00 3.51
730 3868 1.527433 CCGACTGACTGACTGGCTGA 61.527 60.000 0.00 0.00 0.00 4.26
731 3869 1.080230 CCGACTGACTGACTGGCTG 60.080 63.158 0.00 0.00 0.00 4.85
732 3870 2.936912 GCCGACTGACTGACTGGCT 61.937 63.158 0.00 0.00 39.38 4.75
733 3871 2.433318 GCCGACTGACTGACTGGC 60.433 66.667 0.00 0.00 35.04 4.85
734 3872 2.262915 GGCCGACTGACTGACTGG 59.737 66.667 0.00 0.00 0.00 4.00
735 3873 2.126307 CGGCCGACTGACTGACTG 60.126 66.667 24.07 0.00 0.00 3.51
736 3874 3.374402 CCGGCCGACTGACTGACT 61.374 66.667 30.73 0.00 0.00 3.41
737 3875 3.628280 GACCGGCCGACTGACTGAC 62.628 68.421 30.73 4.13 0.00 3.51
738 3876 3.371063 GACCGGCCGACTGACTGA 61.371 66.667 30.73 0.00 0.00 3.41
769 3907 1.081774 CGAGATAGAAGCGGAGGCG 60.082 63.158 0.00 0.00 46.35 5.52
819 3957 1.492176 AGAGAGAGAGAGAGGGAGCAG 59.508 57.143 0.00 0.00 0.00 4.24
820 3958 1.212688 CAGAGAGAGAGAGAGGGAGCA 59.787 57.143 0.00 0.00 0.00 4.26
821 3959 1.212935 ACAGAGAGAGAGAGAGGGAGC 59.787 57.143 0.00 0.00 0.00 4.70
825 3976 2.677836 CACGAACAGAGAGAGAGAGAGG 59.322 54.545 0.00 0.00 0.00 3.69
891 4042 2.674380 CTGGTGCTGGGCTGGTTC 60.674 66.667 0.00 0.00 0.00 3.62
915 4066 4.678742 GGGAAGAGTACGTGCGTTTATATC 59.321 45.833 1.66 0.00 0.00 1.63
937 4088 1.207593 GTACAGTGCTGCTTTGCGG 59.792 57.895 0.00 0.00 38.08 5.69
950 4102 5.764192 CAGGTACTTACTAGCTAGGGTACAG 59.236 48.000 31.18 24.80 34.60 2.74
951 4103 5.192522 ACAGGTACTTACTAGCTAGGGTACA 59.807 44.000 31.18 14.90 34.60 2.90
952 4104 5.530543 CACAGGTACTTACTAGCTAGGGTAC 59.469 48.000 27.22 27.22 34.60 3.34
953 4105 5.429762 TCACAGGTACTTACTAGCTAGGGTA 59.570 44.000 24.35 18.82 34.60 3.69
954 4106 4.229123 TCACAGGTACTTACTAGCTAGGGT 59.771 45.833 24.35 19.71 34.60 4.34
955 4107 4.789807 TCACAGGTACTTACTAGCTAGGG 58.210 47.826 24.35 15.48 34.60 3.53
956 4108 4.276431 GCTCACAGGTACTTACTAGCTAGG 59.724 50.000 24.35 9.60 34.60 3.02
958 4110 4.205587 GGCTCACAGGTACTTACTAGCTA 58.794 47.826 0.00 0.00 34.60 3.32
959 4111 3.025262 GGCTCACAGGTACTTACTAGCT 58.975 50.000 0.00 0.00 34.60 3.32
960 4112 2.758979 TGGCTCACAGGTACTTACTAGC 59.241 50.000 0.00 0.00 34.60 3.42
964 4116 1.900486 AGGTGGCTCACAGGTACTTAC 59.100 52.381 7.49 0.00 34.60 2.34
965 4117 1.899814 CAGGTGGCTCACAGGTACTTA 59.100 52.381 7.49 0.00 34.60 2.24
967 4119 1.831652 GCAGGTGGCTCACAGGTACT 61.832 60.000 7.49 0.00 38.71 2.73
968 4120 1.376037 GCAGGTGGCTCACAGGTAC 60.376 63.158 7.49 0.00 40.25 3.34
971 4123 4.007644 TCGCAGGTGGCTCACAGG 62.008 66.667 7.49 0.91 41.67 4.00
1302 4517 4.856607 GAGAAGCCGTCGGAGCCG 62.857 72.222 17.49 1.74 41.35 5.52
1452 4676 2.584418 CTCATCTGCAGCGACCCG 60.584 66.667 9.47 0.00 0.00 5.28
1671 4904 2.833582 TCCTCCTCGCCGTCATCC 60.834 66.667 0.00 0.00 0.00 3.51
2142 5376 1.526917 GTGGAGGCATGGAATCGGG 60.527 63.158 0.00 0.00 0.00 5.14
2427 5679 9.010366 GTTTAACAGATGAAGTTTGTTCAACTC 57.990 33.333 7.49 0.00 45.77 3.01
2429 5681 8.682128 TGTTTAACAGATGAAGTTTGTTCAAC 57.318 30.769 0.00 7.70 38.46 3.18
2430 5682 9.698309 TTTGTTTAACAGATGAAGTTTGTTCAA 57.302 25.926 0.00 0.00 36.52 2.69
2506 5758 1.616159 AGGAACCGGACAAAATGGTG 58.384 50.000 9.46 0.00 35.79 4.17
2542 5794 1.463444 CTTTTGGTCTTAGTTCGCCGG 59.537 52.381 0.00 0.00 0.00 6.13
2574 6111 2.354704 CGTGTTCCCCATCTACATGTGT 60.355 50.000 9.11 0.00 0.00 3.72
2586 6123 4.078516 CCCCGAGTCGTGTTCCCC 62.079 72.222 12.31 0.00 0.00 4.81
2602 6139 1.384222 CGGCCCAAGCTATTCCAACC 61.384 60.000 0.00 0.00 39.73 3.77
2638 6175 2.041485 TCACTGATTGATGGAGCCCAAA 59.959 45.455 0.00 0.00 36.95 3.28
2707 6244 0.330267 TTACCTAAACCCTGCAGCCC 59.670 55.000 8.66 0.00 0.00 5.19
2710 6247 6.650120 TCTATTTCTTACCTAAACCCTGCAG 58.350 40.000 6.78 6.78 0.00 4.41
2766 6303 5.159209 CACTTCTTTGGCATCAACTCAATC 58.841 41.667 0.00 0.00 31.78 2.67
2846 6383 9.401058 CAAACAAGGAAGAGTAGAATATGGATT 57.599 33.333 0.00 0.00 0.00 3.01
2853 6390 9.495572 CTAAGAACAAACAAGGAAGAGTAGAAT 57.504 33.333 0.00 0.00 0.00 2.40
2914 6451 4.706476 CCATCATTGCCTTTGGTCTTCTTA 59.294 41.667 0.00 0.00 0.00 2.10
2940 6477 2.925724 CCTTGTGAACACACCTGGTTA 58.074 47.619 7.16 0.00 41.67 2.85
2941 6478 1.762708 CCTTGTGAACACACCTGGTT 58.237 50.000 7.16 0.00 41.67 3.67
2942 6479 0.751643 GCCTTGTGAACACACCTGGT 60.752 55.000 7.16 0.00 41.67 4.00
2944 6481 2.254546 TAGCCTTGTGAACACACCTG 57.745 50.000 7.16 1.00 41.67 4.00
2946 6483 2.294074 TGTTAGCCTTGTGAACACACC 58.706 47.619 7.16 0.16 41.67 4.16
2974 6511 4.465632 TGCGCTTTAACTCTATTCCTGA 57.534 40.909 9.73 0.00 0.00 3.86
2976 6513 4.811557 GTGATGCGCTTTAACTCTATTCCT 59.188 41.667 9.73 0.00 0.00 3.36
2988 6525 5.391312 AGAAAATTTAGGTGATGCGCTTT 57.609 34.783 9.73 0.00 0.00 3.51
2996 6533 6.070194 CCTCTGACCCTAGAAAATTTAGGTGA 60.070 42.308 5.05 0.00 36.71 4.02
3002 6539 3.333680 TGCCCTCTGACCCTAGAAAATTT 59.666 43.478 0.00 0.00 0.00 1.82
3025 6563 1.898863 ATCCATGTAGCCTTGGAGGT 58.101 50.000 4.37 0.00 45.19 3.85
3037 6575 3.760684 GACTCAAAGGCTTGAATCCATGT 59.239 43.478 0.00 0.00 41.05 3.21
3040 6578 3.072915 TCAGACTCAAAGGCTTGAATCCA 59.927 43.478 0.00 0.00 38.33 3.41


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

AutoCloner maintained by Alex Coulton.