Multiple sequence alignment - TraesCS5A01G459100

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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 TraesCS5A01G459100 chr5A 100.000 3251 0 0 1 3251 639302651 639299401 0.000000e+00 6004
1 TraesCS5A01G459100 chr5A 81.609 1131 200 7 1109 2235 639293243 639292117 0.000000e+00 929
2 TraesCS5A01G459100 chr5D 91.047 2703 166 35 560 3251 510967200 510964563 0.000000e+00 3581
3 TraesCS5A01G459100 chr5D 82.083 1133 194 8 1109 2235 510959330 510958201 0.000000e+00 959
4 TraesCS5A01G459100 chr5D 95.370 432 12 3 80 507 510967644 510967217 0.000000e+00 680
5 TraesCS5A01G459100 chr5D 93.056 72 5 0 1 72 510968044 510967973 4.440000e-19 106
6 TraesCS5A01G459100 chr5B 89.937 2524 174 41 72 2577 642280922 642283383 0.000000e+00 3181
7 TraesCS5A01G459100 chr5B 82.099 1134 192 9 1109 2235 642142272 642141143 0.000000e+00 959
8 TraesCS5A01G459100 chr5B 80.813 1131 194 15 1109 2232 642306726 642307840 0.000000e+00 865
9 TraesCS5A01G459100 chr5B 92.771 581 31 4 2615 3194 642290591 642291161 0.000000e+00 830


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 TraesCS5A01G459100 chr5A 639299401 639302651 3250 True 6004.000000 6004 100.000000 1 3251 1 chr5A.!!$R2 3250
1 TraesCS5A01G459100 chr5A 639292117 639293243 1126 True 929.000000 929 81.609000 1109 2235 1 chr5A.!!$R1 1126
2 TraesCS5A01G459100 chr5D 510964563 510968044 3481 True 1455.666667 3581 93.157667 1 3251 3 chr5D.!!$R2 3250
3 TraesCS5A01G459100 chr5D 510958201 510959330 1129 True 959.000000 959 82.083000 1109 2235 1 chr5D.!!$R1 1126
4 TraesCS5A01G459100 chr5B 642280922 642283383 2461 False 3181.000000 3181 89.937000 72 2577 1 chr5B.!!$F1 2505
5 TraesCS5A01G459100 chr5B 642141143 642142272 1129 True 959.000000 959 82.099000 1109 2235 1 chr5B.!!$R1 1126
6 TraesCS5A01G459100 chr5B 642306726 642307840 1114 False 865.000000 865 80.813000 1109 2232 1 chr5B.!!$F3 1123
7 TraesCS5A01G459100 chr5B 642290591 642291161 570 False 830.000000 830 92.771000 2615 3194 1 chr5B.!!$F2 579

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
716 1043 0.109781 ATGCAATGCGTTCGGTTCAC 60.11 50.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2712 3060 0.183971 TTCCACTTTCCCGCTTCCAA 59.816 50.0 0.0 0.0 0.0 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
28 29 2.014554 CGTTGTGACCGGTGAGACG 61.015 63.158 14.63 14.06 0.00 4.18
31 32 1.385756 TTGTGACCGGTGAGACGACA 61.386 55.000 14.63 0.00 35.47 4.35
89 411 0.389948 GAGCACGTTGAACTCCCGAT 60.390 55.000 0.00 0.00 0.00 4.18
96 418 3.244112 ACGTTGAACTCCCGATTTTCTCT 60.244 43.478 0.00 0.00 0.00 3.10
192 515 2.964464 TGGTACCAGTCGTCCAAGTAAA 59.036 45.455 11.60 0.00 0.00 2.01
239 562 5.068198 ACGGCTTCGATGAGTTATTAGGTAA 59.932 40.000 1.89 0.00 37.63 2.85
451 778 4.058817 GTGTTCTCGAAGGAGTCATGTTT 58.941 43.478 0.00 0.00 41.26 2.83
472 799 7.995289 TGTTTAATTTAGTGCCGATCATCAAT 58.005 30.769 0.00 0.00 0.00 2.57
473 800 8.128582 TGTTTAATTTAGTGCCGATCATCAATC 58.871 33.333 0.00 0.00 0.00 2.67
474 801 7.800155 TTAATTTAGTGCCGATCATCAATCA 57.200 32.000 0.00 0.00 33.65 2.57
475 802 6.698008 AATTTAGTGCCGATCATCAATCAA 57.302 33.333 0.00 0.00 33.65 2.57
510 837 0.956633 ATGATGATTGCGGTGCCATC 59.043 50.000 0.00 0.00 36.77 3.51
523 850 1.815003 GTGCCATCTGAAGAACCAAGG 59.185 52.381 0.00 0.00 0.00 3.61
547 874 3.057736 CCGTGCACTACTACACACTAAGT 60.058 47.826 16.19 0.00 36.57 2.24
548 875 4.154737 CCGTGCACTACTACACACTAAGTA 59.845 45.833 16.19 0.00 36.57 2.24
549 876 5.084722 CGTGCACTACTACACACTAAGTAC 58.915 45.833 16.19 0.00 36.57 2.73
550 877 5.084722 GTGCACTACTACACACTAAGTACG 58.915 45.833 10.32 0.00 36.77 3.67
551 878 4.756642 TGCACTACTACACACTAAGTACGT 59.243 41.667 0.00 0.00 0.00 3.57
552 879 5.931724 TGCACTACTACACACTAAGTACGTA 59.068 40.000 0.00 0.00 0.00 3.57
553 880 6.128553 TGCACTACTACACACTAAGTACGTAC 60.129 42.308 18.10 18.10 0.00 3.67
555 882 7.275779 GCACTACTACACACTAAGTACGTACTA 59.724 40.741 27.59 14.82 34.99 1.82
556 883 8.587950 CACTACTACACACTAAGTACGTACTAC 58.412 40.741 27.59 3.43 34.99 2.73
557 884 8.524487 ACTACTACACACTAAGTACGTACTACT 58.476 37.037 27.59 16.03 37.28 2.57
609 936 3.328505 GGCATGGAGTTGGATTTTTGTG 58.671 45.455 0.00 0.00 0.00 3.33
660 987 0.741221 GCCTACTCTCGCACCCTTTG 60.741 60.000 0.00 0.00 0.00 2.77
700 1027 2.400399 GCATGGTGATGTATGCAATGC 58.600 47.619 0.00 0.00 46.72 3.56
702 1029 3.738590 GCATGGTGATGTATGCAATGCAA 60.739 43.478 13.45 0.00 43.73 4.08
703 1030 4.627058 CATGGTGATGTATGCAATGCAAT 58.373 39.130 13.45 0.26 43.73 3.56
704 1031 4.048241 TGGTGATGTATGCAATGCAATG 57.952 40.909 13.45 0.00 43.73 2.82
716 1043 0.109781 ATGCAATGCGTTCGGTTCAC 60.110 50.000 0.00 0.00 0.00 3.18
742 1069 1.975837 GCTAGCTAGCTATGTCGCTG 58.024 55.000 33.71 12.09 45.62 5.18
743 1070 1.975837 CTAGCTAGCTATGTCGCTGC 58.024 55.000 24.36 3.48 41.12 5.25
744 1071 1.268079 CTAGCTAGCTATGTCGCTGCA 59.732 52.381 24.36 0.44 41.12 4.41
745 1072 0.678395 AGCTAGCTATGTCGCTGCAT 59.322 50.000 17.69 0.00 41.12 3.96
746 1073 0.788995 GCTAGCTATGTCGCTGCATG 59.211 55.000 7.70 0.00 41.12 4.06
747 1074 0.788995 CTAGCTATGTCGCTGCATGC 59.211 55.000 11.82 11.82 41.12 4.06
766 1093 2.415426 GCACCCAACCAAACCACG 59.585 61.111 0.00 0.00 0.00 4.94
779 1110 4.012895 CCACGCACCGAACTGCAC 62.013 66.667 0.00 0.00 36.94 4.57
788 1119 2.946762 GAACTGCACGCCCAACTC 59.053 61.111 0.00 0.00 0.00 3.01
801 1134 1.524482 CAACTCCAGAGCCTAGCCC 59.476 63.158 0.00 0.00 0.00 5.19
804 1137 1.382420 CTCCAGAGCCTAGCCCTGT 60.382 63.158 0.00 0.00 0.00 4.00
815 1148 2.676748 CTAGCCCTGTCTCTCTCCATT 58.323 52.381 0.00 0.00 0.00 3.16
816 1149 1.202330 AGCCCTGTCTCTCTCCATTG 58.798 55.000 0.00 0.00 0.00 2.82
817 1150 1.198713 GCCCTGTCTCTCTCCATTGA 58.801 55.000 0.00 0.00 0.00 2.57
818 1151 1.767681 GCCCTGTCTCTCTCCATTGAT 59.232 52.381 0.00 0.00 0.00 2.57
819 1152 2.224257 GCCCTGTCTCTCTCCATTGATC 60.224 54.545 0.00 0.00 0.00 2.92
820 1153 3.036819 CCCTGTCTCTCTCCATTGATCA 58.963 50.000 0.00 0.00 0.00 2.92
822 1155 3.450096 CCTGTCTCTCTCCATTGATCACA 59.550 47.826 0.00 0.00 0.00 3.58
824 1157 4.825422 TGTCTCTCTCCATTGATCACAAC 58.175 43.478 0.00 0.00 38.90 3.32
827 1160 4.081254 TCTCTCTCCATTGATCACAACCAG 60.081 45.833 0.00 0.00 38.90 4.00
830 1163 0.179156 CCATTGATCACAACCAGCGC 60.179 55.000 0.00 0.00 38.90 5.92
831 1164 0.179156 CATTGATCACAACCAGCGCC 60.179 55.000 2.29 0.00 38.90 6.53
832 1165 0.608856 ATTGATCACAACCAGCGCCA 60.609 50.000 2.29 0.00 38.90 5.69
835 1168 2.187599 GATCACAACCAGCGCCACAC 62.188 60.000 2.29 0.00 0.00 3.82
855 1188 2.366266 ACCTATAAATACGCCTCGCCAA 59.634 45.455 0.00 0.00 0.00 4.52
887 1220 4.113354 GTCTTCATCCATCCGTTACTCAC 58.887 47.826 0.00 0.00 0.00 3.51
916 1249 6.013379 ACTCTTCTTCTCCCATCAAACACATA 60.013 38.462 0.00 0.00 0.00 2.29
917 1250 6.409704 TCTTCTTCTCCCATCAAACACATAG 58.590 40.000 0.00 0.00 0.00 2.23
918 1251 4.517285 TCTTCTCCCATCAAACACATAGC 58.483 43.478 0.00 0.00 0.00 2.97
919 1252 4.225942 TCTTCTCCCATCAAACACATAGCT 59.774 41.667 0.00 0.00 0.00 3.32
920 1253 5.425217 TCTTCTCCCATCAAACACATAGCTA 59.575 40.000 0.00 0.00 0.00 3.32
921 1254 5.282055 TCTCCCATCAAACACATAGCTAG 57.718 43.478 0.00 0.00 0.00 3.42
922 1255 4.962362 TCTCCCATCAAACACATAGCTAGA 59.038 41.667 0.00 0.00 0.00 2.43
923 1256 5.425217 TCTCCCATCAAACACATAGCTAGAA 59.575 40.000 0.00 0.00 0.00 2.10
924 1257 6.061022 TCCCATCAAACACATAGCTAGAAA 57.939 37.500 0.00 0.00 0.00 2.52
925 1258 5.880332 TCCCATCAAACACATAGCTAGAAAC 59.120 40.000 0.00 0.00 0.00 2.78
926 1259 5.882557 CCCATCAAACACATAGCTAGAAACT 59.117 40.000 0.00 0.00 0.00 2.66
953 1286 1.550065 CGTCACTACGCCTTCATCTG 58.450 55.000 0.00 0.00 43.12 2.90
962 1295 1.407299 CGCCTTCATCTGTCCATCCAA 60.407 52.381 0.00 0.00 0.00 3.53
963 1296 2.726821 GCCTTCATCTGTCCATCCAAA 58.273 47.619 0.00 0.00 0.00 3.28
984 1319 7.447238 TCCAAAACTCATACTTCGATTCCTTTT 59.553 33.333 0.00 0.00 0.00 2.27
1017 1352 3.894547 AATGGCGTCGACCACCACC 62.895 63.158 23.21 11.93 44.17 4.61
1026 1361 3.883744 GACCACCACCAGGCTCGTG 62.884 68.421 5.17 5.17 39.06 4.35
1032 1367 3.860605 ACCAGGCTCGTGTGTGCA 61.861 61.111 0.00 0.00 36.33 4.57
1035 1370 4.626081 AGGCTCGTGTGTGCACCC 62.626 66.667 15.69 2.52 42.39 4.61
1038 1373 2.666190 CTCGTGTGTGCACCCCTG 60.666 66.667 15.69 1.93 42.39 4.45
1039 1374 3.460672 CTCGTGTGTGCACCCCTGT 62.461 63.158 15.69 0.00 42.39 4.00
1048 1386 2.900106 GCACCCCTGTTCCTGCTCT 61.900 63.158 0.00 0.00 0.00 4.09
1056 1394 0.322975 TGTTCCTGCTCTTGCTCTCC 59.677 55.000 0.00 0.00 40.48 3.71
1057 1395 0.322975 GTTCCTGCTCTTGCTCTCCA 59.677 55.000 0.00 0.00 40.48 3.86
1064 1402 1.339438 GCTCTTGCTCTCCATGTCCAA 60.339 52.381 0.00 0.00 36.03 3.53
1065 1403 2.683152 GCTCTTGCTCTCCATGTCCAAT 60.683 50.000 0.00 0.00 36.03 3.16
1095 1433 2.125350 CAAGAGACCGGCAGCTCC 60.125 66.667 0.00 0.00 0.00 4.70
1248 1586 1.302993 GCTCGTACCCAAGGGCAAA 60.303 57.895 4.70 0.00 39.32 3.68
1254 1592 2.619590 CGTACCCAAGGGCAAAACCTAT 60.620 50.000 4.70 0.00 40.87 2.57
1264 1602 2.424956 GGCAAAACCTATCTGCTCAAGG 59.575 50.000 0.00 0.00 36.32 3.61
1450 1788 1.021390 CAACGGTGAGATCTGGTGGC 61.021 60.000 0.00 0.00 0.00 5.01
1539 1877 5.086104 TCTGCACTAATCTAAAGGTGGAC 57.914 43.478 0.00 0.00 0.00 4.02
1563 1901 4.020543 ACCTGAAACTTGTAAACAGCCAA 58.979 39.130 0.00 0.00 0.00 4.52
1734 2072 3.982475 TGACTGCATATCCATCGAGAAC 58.018 45.455 0.00 0.00 0.00 3.01
1951 2289 7.983484 TCGTATTCCAGAATATGATCATGGATG 59.017 37.037 18.72 10.90 41.69 3.51
1952 2290 7.254692 CGTATTCCAGAATATGATCATGGATGC 60.255 40.741 18.72 3.39 40.83 3.91
2022 2363 1.065102 CCATGCAAGAGCCAGAATTCG 59.935 52.381 0.00 0.00 41.13 3.34
2277 2618 7.495934 GCTGTAATGGAAATGAGCTAGTTTAGA 59.504 37.037 0.00 0.00 0.00 2.10
2365 2707 3.302161 GTTGTAGTTCCTTTTGGGGGTT 58.698 45.455 0.00 0.00 40.87 4.11
2367 2709 3.568443 TGTAGTTCCTTTTGGGGGTTTC 58.432 45.455 0.00 0.00 40.87 2.78
2369 2711 4.416179 TGTAGTTCCTTTTGGGGGTTTCTA 59.584 41.667 0.00 0.00 40.87 2.10
2371 2713 2.895404 GTTCCTTTTGGGGGTTTCTACC 59.105 50.000 0.00 0.00 40.19 3.18
2374 2716 3.143168 TCCTTTTGGGGGTTTCTACCAAT 59.857 43.478 0.00 0.00 43.22 3.16
2396 2738 9.058174 CCAATAATATGAAATGTGTTACCGGTA 57.942 33.333 11.16 11.16 0.00 4.02
2420 2762 6.696411 AGGTGTTTTCTTGTTGAAATGAACA 58.304 32.000 0.00 0.00 43.34 3.18
2421 2763 7.158021 AGGTGTTTTCTTGTTGAAATGAACAA 58.842 30.769 0.00 0.00 43.34 2.83
2422 2764 7.823799 AGGTGTTTTCTTGTTGAAATGAACAAT 59.176 29.630 0.00 0.00 43.22 2.71
2445 2791 9.774742 CAATAATGTTTAACACTCTTAGCTTCC 57.225 33.333 0.00 0.00 0.00 3.46
2508 2854 9.927081 AAGTCAATTCTTCCTATAATTCATGGT 57.073 29.630 0.00 0.00 0.00 3.55
2509 2855 9.927081 AGTCAATTCTTCCTATAATTCATGGTT 57.073 29.630 0.00 0.00 0.00 3.67
2542 2890 9.939802 TTACATCTAGGAAGAGTAAAGGTTTTC 57.060 33.333 0.00 0.00 34.49 2.29
2552 2900 7.454260 AGAGTAAAGGTTTTCCAAAGCTATG 57.546 36.000 1.55 0.00 43.73 2.23
2553 2901 6.025749 AGTAAAGGTTTTCCAAAGCTATGC 57.974 37.500 1.55 0.00 43.73 3.14
2562 2910 4.970662 TCCAAAGCTATGCTGATGTTTC 57.029 40.909 0.00 0.00 39.62 2.78
2563 2911 4.334552 TCCAAAGCTATGCTGATGTTTCA 58.665 39.130 0.00 0.00 39.62 2.69
2610 2958 8.918202 AATAGAACACCATCACTACAAGAAAA 57.082 30.769 0.00 0.00 0.00 2.29
2654 3002 6.803366 TTACTTACTAGTCCTTGGGGATTC 57.197 41.667 0.00 0.00 44.33 2.52
2712 3060 1.549203 GATGTTGCCACCACTGGAAT 58.451 50.000 0.71 0.00 40.55 3.01
2714 3062 1.039068 TGTTGCCACCACTGGAATTG 58.961 50.000 0.71 0.00 40.55 2.32
2720 3068 0.523072 CACCACTGGAATTGGAAGCG 59.477 55.000 0.71 0.00 37.58 4.68
2726 3074 1.474077 CTGGAATTGGAAGCGGGAAAG 59.526 52.381 0.00 0.00 0.00 2.62
2745 3093 6.404403 GGGAAAGTGGAAATTTAACGATCTCC 60.404 42.308 0.00 0.51 32.38 3.71
2746 3094 6.150474 GGAAAGTGGAAATTTAACGATCTCCA 59.850 38.462 0.00 0.00 32.38 3.86
2749 3097 6.108097 GTGGAAATTTAACGATCTCCACTC 57.892 41.667 15.62 0.00 46.09 3.51
2771 3123 9.243637 CACTCTACTAGCAAGAATCAAATCTAC 57.756 37.037 0.00 0.00 0.00 2.59
2783 3135 7.339482 AGAATCAAATCTACTAAACCCAGACC 58.661 38.462 0.00 0.00 0.00 3.85
2831 3183 8.594881 TCTCAAACTTAGAGATTGTCTCAAAC 57.405 34.615 9.42 0.00 45.73 2.93
2934 3289 4.216257 CCATCAAGAACGGAACTCACAATT 59.784 41.667 0.00 0.00 0.00 2.32
2958 3313 4.742417 TCATGACACCAAAGTTGTTTGTG 58.258 39.130 0.00 0.00 41.44 3.33
2991 3346 3.831333 TGGCATCAACATTGGAAGCTTAA 59.169 39.130 0.00 0.00 0.00 1.85
2992 3347 4.467082 TGGCATCAACATTGGAAGCTTAAT 59.533 37.500 0.00 0.00 0.00 1.40
2993 3348 5.046448 TGGCATCAACATTGGAAGCTTAATT 60.046 36.000 0.00 0.00 0.00 1.40
2994 3349 6.154192 TGGCATCAACATTGGAAGCTTAATTA 59.846 34.615 0.00 0.00 0.00 1.40
3013 3368 8.757307 TTAATTAGGGGATGATAACTCCAGAT 57.243 34.615 0.00 0.00 34.24 2.90
3015 3370 7.654287 ATTAGGGGATGATAACTCCAGATTT 57.346 36.000 0.00 0.00 34.24 2.17
3019 3374 5.397899 GGGGATGATAACTCCAGATTTGACA 60.398 44.000 0.00 0.00 34.24 3.58
3073 3428 3.134127 GCATGACCAACGGAGCCC 61.134 66.667 0.00 0.00 0.00 5.19
3094 3449 2.939103 CGGATCAAGAAATGTCAGGGAC 59.061 50.000 0.00 0.00 0.00 4.46
3208 3564 1.419387 AGAGCCAGGAATCAGCCATAC 59.581 52.381 0.00 0.00 0.00 2.39
3214 3570 2.092753 CAGGAATCAGCCATACAGGTGT 60.093 50.000 0.00 0.00 40.61 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.926527 TGTTGATTGTAGCATGTCGTCTC 59.073 43.478 0.00 0.00 0.00 3.36
24 25 3.925379 TGTTGATTGTAGCATGTCGTCT 58.075 40.909 0.00 0.00 0.00 4.18
28 29 3.129287 CCCCTTGTTGATTGTAGCATGTC 59.871 47.826 0.00 0.00 0.00 3.06
31 32 2.102578 GCCCCTTGTTGATTGTAGCAT 58.897 47.619 0.00 0.00 0.00 3.79
89 411 4.265904 TGTGTAATCGCCTCAGAGAAAA 57.734 40.909 0.00 0.00 0.00 2.29
96 418 4.155826 CCTTGAAATTGTGTAATCGCCTCA 59.844 41.667 0.00 0.00 0.00 3.86
192 515 0.181114 ATCCGTGCATGCATGTACCT 59.819 50.000 33.25 19.90 39.77 3.08
256 579 2.093973 GCTTTTCTCGATCTGGACCTGA 60.094 50.000 3.23 3.23 0.00 3.86
387 710 1.530323 AATGGAAAAGTAGCGCCGTT 58.470 45.000 2.29 0.00 0.00 4.44
451 778 7.800155 TTGATTGATGATCGGCACTAAATTA 57.200 32.000 0.00 0.00 37.60 1.40
472 799 6.493115 TCATCATTGGCCTTCTTTAGTTTTGA 59.507 34.615 3.32 0.00 0.00 2.69
473 800 6.690530 TCATCATTGGCCTTCTTTAGTTTTG 58.309 36.000 3.32 0.00 0.00 2.44
474 801 6.916360 TCATCATTGGCCTTCTTTAGTTTT 57.084 33.333 3.32 0.00 0.00 2.43
475 802 7.325694 CAATCATCATTGGCCTTCTTTAGTTT 58.674 34.615 3.32 0.00 36.48 2.66
510 837 1.073199 ACGGGCCTTGGTTCTTCAG 59.927 57.895 0.84 0.00 0.00 3.02
523 850 1.012486 GTGTGTAGTAGTGCACGGGC 61.012 60.000 12.01 0.34 41.91 6.13
547 874 8.841300 TCTTCGTCTCTTCTATAGTAGTACGTA 58.159 37.037 22.74 17.40 31.20 3.57
548 875 7.711846 TCTTCGTCTCTTCTATAGTAGTACGT 58.288 38.462 22.74 0.00 31.20 3.57
549 876 8.572828 TTCTTCGTCTCTTCTATAGTAGTACG 57.427 38.462 20.23 20.23 0.00 3.67
551 878 9.881649 TGTTTCTTCGTCTCTTCTATAGTAGTA 57.118 33.333 6.31 0.00 0.00 1.82
552 879 8.667463 GTGTTTCTTCGTCTCTTCTATAGTAGT 58.333 37.037 6.31 0.00 0.00 2.73
553 880 7.847078 CGTGTTTCTTCGTCTCTTCTATAGTAG 59.153 40.741 0.00 0.00 0.00 2.57
555 882 6.544622 CGTGTTTCTTCGTCTCTTCTATAGT 58.455 40.000 0.00 0.00 0.00 2.12
556 883 5.452944 GCGTGTTTCTTCGTCTCTTCTATAG 59.547 44.000 0.00 0.00 0.00 1.31
557 884 5.330295 GCGTGTTTCTTCGTCTCTTCTATA 58.670 41.667 0.00 0.00 0.00 1.31
558 885 4.167268 GCGTGTTTCTTCGTCTCTTCTAT 58.833 43.478 0.00 0.00 0.00 1.98
609 936 0.458889 ATGCATGCATGTTTCGCACC 60.459 50.000 31.74 8.94 43.35 5.01
700 1027 0.179250 CTCGTGAACCGAACGCATTG 60.179 55.000 0.00 0.00 46.75 2.82
702 1029 2.380410 GCTCGTGAACCGAACGCAT 61.380 57.895 0.00 0.00 46.75 4.73
703 1030 2.132517 TAGCTCGTGAACCGAACGCA 62.133 55.000 0.00 0.00 46.75 5.24
704 1031 1.403972 CTAGCTCGTGAACCGAACGC 61.404 60.000 0.00 0.00 46.75 4.84
743 1070 2.865598 TTTGGTTGGGTGCGGCATG 61.866 57.895 5.72 0.00 0.00 4.06
744 1071 2.522923 TTTGGTTGGGTGCGGCAT 60.523 55.556 5.72 0.00 0.00 4.40
745 1072 3.532155 GTTTGGTTGGGTGCGGCA 61.532 61.111 0.00 0.00 0.00 5.69
746 1073 4.293648 GGTTTGGTTGGGTGCGGC 62.294 66.667 0.00 0.00 0.00 6.53
747 1074 2.835431 TGGTTTGGTTGGGTGCGG 60.835 61.111 0.00 0.00 0.00 5.69
753 1080 2.415426 GGTGCGTGGTTTGGTTGG 59.585 61.111 0.00 0.00 0.00 3.77
779 1110 2.303549 CTAGGCTCTGGAGTTGGGCG 62.304 65.000 0.00 0.00 0.00 6.13
801 1134 4.732672 TGTGATCAATGGAGAGAGACAG 57.267 45.455 0.00 0.00 0.00 3.51
804 1137 3.840078 TGGTTGTGATCAATGGAGAGAGA 59.160 43.478 0.00 0.00 35.92 3.10
815 1148 1.965930 GTGGCGCTGGTTGTGATCA 60.966 57.895 7.64 0.00 0.00 2.92
816 1149 1.965930 TGTGGCGCTGGTTGTGATC 60.966 57.895 7.64 0.00 0.00 2.92
817 1150 2.112928 TGTGGCGCTGGTTGTGAT 59.887 55.556 7.64 0.00 0.00 3.06
818 1151 2.899838 GTGTGGCGCTGGTTGTGA 60.900 61.111 7.64 0.00 0.00 3.58
819 1152 3.964875 GGTGTGGCGCTGGTTGTG 61.965 66.667 7.64 0.00 0.00 3.33
820 1153 2.124507 ATAGGTGTGGCGCTGGTTGT 62.125 55.000 7.64 0.00 0.00 3.32
822 1155 0.616371 TTATAGGTGTGGCGCTGGTT 59.384 50.000 7.64 0.00 0.00 3.67
824 1157 1.967319 ATTTATAGGTGTGGCGCTGG 58.033 50.000 7.64 0.00 0.00 4.85
827 1160 1.193874 GCGTATTTATAGGTGTGGCGC 59.806 52.381 0.00 0.00 35.77 6.53
830 1163 3.314553 CGAGGCGTATTTATAGGTGTGG 58.685 50.000 0.00 0.00 0.00 4.17
831 1164 2.729882 GCGAGGCGTATTTATAGGTGTG 59.270 50.000 0.00 0.00 0.00 3.82
832 1165 2.288640 GGCGAGGCGTATTTATAGGTGT 60.289 50.000 0.00 0.00 0.00 4.16
835 1168 2.735134 GTTGGCGAGGCGTATTTATAGG 59.265 50.000 0.00 0.00 0.00 2.57
887 1220 4.277515 TGATGGGAGAAGAAGAGTTGTG 57.722 45.455 0.00 0.00 0.00 3.33
916 1249 5.474189 AGTGACGACTTTCTAGTTTCTAGCT 59.526 40.000 0.00 0.00 33.84 3.32
917 1250 5.701855 AGTGACGACTTTCTAGTTTCTAGC 58.298 41.667 0.00 0.00 33.84 3.42
953 1286 5.175859 TCGAAGTATGAGTTTTGGATGGAC 58.824 41.667 0.00 0.00 0.00 4.02
962 1295 7.878127 TCTCAAAAGGAATCGAAGTATGAGTTT 59.122 33.333 0.00 0.00 34.77 2.66
963 1296 7.386851 TCTCAAAAGGAATCGAAGTATGAGTT 58.613 34.615 0.00 0.00 34.77 3.01
984 1319 2.420547 CGCCATTTTGGGAGAGATCTCA 60.421 50.000 24.39 1.30 44.60 3.27
1026 1361 1.898574 CAGGAACAGGGGTGCACAC 60.899 63.158 20.43 16.45 0.00 3.82
1032 1367 1.763770 CAAGAGCAGGAACAGGGGT 59.236 57.895 0.00 0.00 0.00 4.95
1035 1370 0.324285 AGAGCAAGAGCAGGAACAGG 59.676 55.000 0.00 0.00 45.49 4.00
1038 1373 0.322975 TGGAGAGCAAGAGCAGGAAC 59.677 55.000 0.00 0.00 45.49 3.62
1039 1374 1.065636 CATGGAGAGCAAGAGCAGGAA 60.066 52.381 0.00 0.00 45.49 3.36
1048 1386 1.466856 GCATTGGACATGGAGAGCAA 58.533 50.000 0.00 0.00 0.00 3.91
1056 1394 2.163010 GACTGAGTTGGCATTGGACATG 59.837 50.000 0.00 0.00 0.00 3.21
1057 1395 2.440409 GACTGAGTTGGCATTGGACAT 58.560 47.619 0.00 0.00 0.00 3.06
1064 1402 1.980765 TCTCTTGGACTGAGTTGGCAT 59.019 47.619 0.00 0.00 33.59 4.40
1065 1403 1.070758 GTCTCTTGGACTGAGTTGGCA 59.929 52.381 0.00 0.00 41.46 4.92
1095 1433 2.847327 TCTGAGTGGAGCTTTTGAGG 57.153 50.000 0.00 0.00 0.00 3.86
1179 1517 4.659172 TTCCACGCCTTGGCCAGG 62.659 66.667 8.15 8.15 46.47 4.45
1236 1574 1.716503 AGATAGGTTTTGCCCTTGGGT 59.283 47.619 7.61 0.00 38.26 4.51
1248 1586 1.289160 TGGCCTTGAGCAGATAGGTT 58.711 50.000 3.32 0.00 46.50 3.50
1254 1592 1.300963 GGTGATGGCCTTGAGCAGA 59.699 57.895 3.32 0.00 46.50 4.26
1320 1658 3.834726 CTCGGAGGAGCGATGAGT 58.165 61.111 0.00 0.00 32.61 3.41
1360 1698 1.557269 AAGATCCAGCGCCTCCTGTT 61.557 55.000 2.29 0.00 0.00 3.16
1450 1788 1.261619 GTTGGTCTTGCACGAGTTCTG 59.738 52.381 0.00 0.00 0.00 3.02
1539 1877 4.142271 TGGCTGTTTACAAGTTTCAGGTTG 60.142 41.667 0.00 0.00 0.00 3.77
1563 1901 2.813754 CTGAACCGACACATGGATTTGT 59.186 45.455 0.00 0.00 0.00 2.83
1734 2072 2.854777 GACATGAAGATCGTGAGTTCCG 59.145 50.000 0.00 0.00 36.89 4.30
1918 2256 9.906660 GATCATATTCTGGAATACGATATCCTC 57.093 37.037 10.54 0.00 36.63 3.71
1951 2289 3.779759 TGATAATTGGATTTTGCACGGC 58.220 40.909 0.00 0.00 0.00 5.68
1952 2290 6.019640 GTCAATGATAATTGGATTTTGCACGG 60.020 38.462 2.80 0.00 32.65 4.94
2022 2363 1.530183 ATCCCGTACCTCTACCGCC 60.530 63.158 0.00 0.00 0.00 6.13
2067 2408 3.053019 TGATGGCATCCTTGGAAATGGTA 60.053 43.478 23.92 0.00 0.00 3.25
2246 2587 7.995488 ACTAGCTCATTTCCATTACAGCTTAAT 59.005 33.333 0.00 0.00 38.22 1.40
2252 2593 8.821894 GTCTAAACTAGCTCATTTCCATTACAG 58.178 37.037 0.00 0.00 0.00 2.74
2257 2598 7.341805 ACATGTCTAAACTAGCTCATTTCCAT 58.658 34.615 0.00 0.00 0.00 3.41
2322 2664 7.094377 ACAACGATGTATGCAAAAGTAGGATTT 60.094 33.333 0.00 0.00 38.24 2.17
2369 2711 7.558444 ACCGGTAACACATTTCATATTATTGGT 59.442 33.333 4.49 0.00 0.00 3.67
2374 2716 7.711772 CACCTACCGGTAACACATTTCATATTA 59.288 37.037 16.65 0.00 43.24 0.98
2420 2762 9.515226 TGGAAGCTAAGAGTGTTAAACATTATT 57.485 29.630 0.00 0.00 0.00 1.40
2421 2763 9.515226 TTGGAAGCTAAGAGTGTTAAACATTAT 57.485 29.630 0.00 0.00 0.00 1.28
2422 2764 8.911918 TTGGAAGCTAAGAGTGTTAAACATTA 57.088 30.769 0.00 0.00 0.00 1.90
2427 2773 6.003950 AGCATTGGAAGCTAAGAGTGTTAAA 58.996 36.000 0.00 0.00 41.32 1.52
2536 2884 4.082026 ACATCAGCATAGCTTTGGAAAACC 60.082 41.667 6.29 0.00 36.40 3.27
2542 2890 4.707030 TGAAACATCAGCATAGCTTTGG 57.293 40.909 6.29 0.00 36.40 3.28
2552 2900 3.581024 TGCCTCATTTGAAACATCAGC 57.419 42.857 0.00 0.00 0.00 4.26
2553 2901 5.475719 ACAATGCCTCATTTGAAACATCAG 58.524 37.500 0.00 0.00 31.05 2.90
2654 3002 1.869767 GCAGGATGAACAAGATAGCGG 59.130 52.381 0.00 0.00 39.69 5.52
2712 3060 0.183971 TTCCACTTTCCCGCTTCCAA 59.816 50.000 0.00 0.00 0.00 3.53
2714 3062 1.545841 ATTTCCACTTTCCCGCTTCC 58.454 50.000 0.00 0.00 0.00 3.46
2720 3068 6.404403 GGAGATCGTTAAATTTCCACTTTCCC 60.404 42.308 0.00 0.00 31.70 3.97
2745 3093 9.243637 GTAGATTTGATTCTTGCTAGTAGAGTG 57.756 37.037 0.00 0.00 0.00 3.51
2746 3094 9.196139 AGTAGATTTGATTCTTGCTAGTAGAGT 57.804 33.333 0.00 0.00 0.00 3.24
2771 3123 2.228822 GCACATGTTGGTCTGGGTTTAG 59.771 50.000 0.00 0.00 0.00 1.85
2783 3135 7.365741 AGAAAATCTCTAACTTGCACATGTTG 58.634 34.615 11.06 0.00 30.22 3.33
2831 3183 0.391528 TGATGTGGATGCCGTCAGTG 60.392 55.000 0.00 0.00 0.00 3.66
2934 3289 5.636965 CACAAACAACTTTGGTGTCATGAAA 59.363 36.000 0.00 0.00 41.12 2.69
2958 3313 2.203209 GATGCCATGTCCCGGACC 60.203 66.667 15.24 0.00 0.00 4.46
2991 3346 7.295672 TCAAATCTGGAGTTATCATCCCCTAAT 59.704 37.037 0.00 0.00 35.86 1.73
2992 3347 6.619437 TCAAATCTGGAGTTATCATCCCCTAA 59.381 38.462 0.00 0.00 35.86 2.69
2993 3348 6.043243 GTCAAATCTGGAGTTATCATCCCCTA 59.957 42.308 0.00 0.00 35.86 3.53
2994 3349 4.977739 TCAAATCTGGAGTTATCATCCCCT 59.022 41.667 0.00 0.00 35.86 4.79
3073 3428 2.939103 GTCCCTGACATTTCTTGATCCG 59.061 50.000 0.00 0.00 32.09 4.18
3094 3449 5.860941 ATATCCTTAGCATATCCACTCCG 57.139 43.478 0.00 0.00 0.00 4.63
3174 3530 3.407046 GCTCTTGCATGGCTTCGCC 62.407 63.158 0.00 0.00 43.67 5.54
3185 3541 1.382692 GGCTGATTCCTGGCTCTTGC 61.383 60.000 0.00 0.00 38.76 4.01
3208 3564 2.687425 TGAACACCACATTCAACACCTG 59.313 45.455 0.00 0.00 33.16 4.00
3214 3570 9.513906 TCTAATATTCTTGAACACCACATTCAA 57.486 29.630 0.00 0.68 42.37 2.69


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

AutoCloner maintained by Alex Coulton.