Multiple sequence alignment - TraesCS7B01G421100

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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 TraesCS7B01G421100 chr7B 100.000 3532 0 0 1 3532 690241703 690238172 0.000000e+00 6523
1 TraesCS7B01G421100 chr7D 89.742 1394 78 25 2161 3531 606315060 606313709 0.000000e+00 1722
2 TraesCS7B01G421100 chr7D 83.882 1154 121 34 981 2116 606316168 606315062 0.000000e+00 1040
3 TraesCS7B01G421100 chr7D 90.972 288 24 1 675 960 606316559 606316272 1.540000e-103 387
4 TraesCS7B01G421100 chrUn 90.632 886 45 10 987 1859 83313875 83313015 0.000000e+00 1142
5 TraesCS7B01G421100 chrUn 88.514 888 69 22 1905 2775 83313019 83312148 0.000000e+00 1044
6 TraesCS7B01G421100 chrUn 90.083 484 37 4 2946 3426 83311968 83311493 5.010000e-173 617
7 TraesCS7B01G421100 chrUn 92.000 175 11 2 2774 2947 83312180 83312008 3.520000e-60 243
8 TraesCS7B01G421100 chr6B 96.889 675 20 1 1 675 603151901 603151228 0.000000e+00 1129
9 TraesCS7B01G421100 chr2A 92.931 679 43 4 2 676 744921470 744922147 0.000000e+00 983
10 TraesCS7B01G421100 chr3A 92.751 676 44 5 5 677 727540108 727539435 0.000000e+00 972
11 TraesCS7B01G421100 chr7A 92.024 677 49 4 2 675 404501247 404501921 0.000000e+00 946
12 TraesCS7B01G421100 chr7A 91.298 655 53 4 26 676 544265436 544264782 0.000000e+00 891
13 TraesCS7B01G421100 chr5A 88.856 682 69 6 1 681 692049588 692048913 0.000000e+00 832
14 TraesCS7B01G421100 chr4A 88.279 674 74 5 1 674 627807748 627807080 0.000000e+00 802
15 TraesCS7B01G421100 chr1B 87.592 677 72 10 4 676 632211114 632210446 0.000000e+00 774
16 TraesCS7B01G421100 chr1B 91.880 234 11 4 1572 1797 155123338 155123571 1.580000e-83 320
17 TraesCS7B01G421100 chr2B 86.344 681 81 11 1 675 704126449 704127123 0.000000e+00 732


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 TraesCS7B01G421100 chr7B 690238172 690241703 3531 True 6523.000000 6523 100.000000 1 3532 1 chr7B.!!$R1 3531
1 TraesCS7B01G421100 chr7D 606313709 606316559 2850 True 1049.666667 1722 88.198667 675 3531 3 chr7D.!!$R1 2856
2 TraesCS7B01G421100 chrUn 83311493 83313875 2382 True 761.500000 1142 90.307250 987 3426 4 chrUn.!!$R1 2439
3 TraesCS7B01G421100 chr6B 603151228 603151901 673 True 1129.000000 1129 96.889000 1 675 1 chr6B.!!$R1 674
4 TraesCS7B01G421100 chr2A 744921470 744922147 677 False 983.000000 983 92.931000 2 676 1 chr2A.!!$F1 674
5 TraesCS7B01G421100 chr3A 727539435 727540108 673 True 972.000000 972 92.751000 5 677 1 chr3A.!!$R1 672
6 TraesCS7B01G421100 chr7A 404501247 404501921 674 False 946.000000 946 92.024000 2 675 1 chr7A.!!$F1 673
7 TraesCS7B01G421100 chr7A 544264782 544265436 654 True 891.000000 891 91.298000 26 676 1 chr7A.!!$R1 650
8 TraesCS7B01G421100 chr5A 692048913 692049588 675 True 832.000000 832 88.856000 1 681 1 chr5A.!!$R1 680
9 TraesCS7B01G421100 chr4A 627807080 627807748 668 True 802.000000 802 88.279000 1 674 1 chr4A.!!$R1 673
10 TraesCS7B01G421100 chr1B 632210446 632211114 668 True 774.000000 774 87.592000 4 676 1 chr1B.!!$R1 672
11 TraesCS7B01G421100 chr2B 704126449 704127123 674 False 732.000000 732 86.344000 1 675 1 chr2B.!!$F1 674

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
735 749 0.183492 AAGCAAGCACAAGGTCTCCA 59.817 50.0 0.0 0.0 0.00 3.86 F
1073 1172 0.174162 GGCCCATGCAATGTGAACTC 59.826 55.0 0.0 0.0 44.81 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1874 0.531090 CAAAACCGTCTGACCGTGGA 60.531 55.0 7.14 0.0 0.00 4.02 R
3011 3212 0.750911 CTCCATCTTCCTTGGCCTGC 60.751 60.0 3.32 0.0 34.06 4.85 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
158 160 2.045045 CTGGCTGGCCCGAAATCA 60.045 61.111 9.28 0.00 35.87 2.57
330 332 1.742880 GATGAAGCTGTGCGAGGCA 60.743 57.895 0.00 0.00 35.60 4.75
473 481 4.821805 CCCAGCAGATCGGTTTTGTAATAT 59.178 41.667 0.00 0.00 0.00 1.28
577 588 2.325484 TCCTGGTAGTGCTTGAACTCA 58.675 47.619 0.00 0.00 0.00 3.41
630 644 5.222027 TGTTTCTGGGACTGATGTATTTCCA 60.222 40.000 0.00 0.00 35.89 3.53
705 719 7.607991 ACTGAATAATCCTGTCGAAACTGAAAT 59.392 33.333 0.00 0.00 0.00 2.17
719 733 8.124823 TCGAAACTGAAATTATCATCATCAAGC 58.875 33.333 0.00 0.00 37.44 4.01
735 749 0.183492 AAGCAAGCACAAGGTCTCCA 59.817 50.000 0.00 0.00 0.00 3.86
738 752 1.073897 AAGCACAAGGTCTCCAGCC 59.926 57.895 0.00 0.00 0.00 4.85
744 758 1.081092 AAGGTCTCCAGCCTAGGCA 59.919 57.895 34.70 14.36 44.88 4.75
745 759 0.327000 AAGGTCTCCAGCCTAGGCAT 60.327 55.000 34.70 17.45 44.88 4.40
746 760 1.053264 AGGTCTCCAGCCTAGGCATG 61.053 60.000 34.70 26.40 44.88 4.06
747 761 1.449353 GTCTCCAGCCTAGGCATGG 59.551 63.158 34.70 32.60 44.88 3.66
784 798 1.753649 CAGGCCATCGGATAGATCGAT 59.246 52.381 5.01 0.00 46.64 3.59
798 812 3.220110 AGATCGATACGGAACAGCCTTA 58.780 45.455 0.00 0.00 0.00 2.69
799 813 3.635373 AGATCGATACGGAACAGCCTTAA 59.365 43.478 0.00 0.00 0.00 1.85
804 818 2.745515 ACGGAACAGCCTTAAGAGAC 57.254 50.000 3.36 0.00 0.00 3.36
816 830 3.308402 CCTTAAGAGACAAGGGGCATTCA 60.308 47.826 3.36 0.00 39.16 2.57
850 866 3.003173 CTTGGTGAGGAGGCGGGA 61.003 66.667 0.00 0.00 0.00 5.14
854 870 2.680352 GTGAGGAGGCGGGAGACA 60.680 66.667 0.00 0.00 44.00 3.41
889 905 2.447379 ATCGGGGAGCTGGCTGAT 60.447 61.111 0.00 0.00 0.00 2.90
895 911 2.437359 GAGCTGGCTGATGCGGTT 60.437 61.111 0.00 0.00 40.82 4.44
917 933 3.703127 ACGCCCCCTTCGTCTTCC 61.703 66.667 0.00 0.00 34.84 3.46
918 934 4.468689 CGCCCCCTTCGTCTTCCC 62.469 72.222 0.00 0.00 0.00 3.97
920 936 2.609610 CCCCCTTCGTCTTCCCCA 60.610 66.667 0.00 0.00 0.00 4.96
960 976 2.498726 CAGCTCCCTCTTCCTCGC 59.501 66.667 0.00 0.00 0.00 5.03
962 978 3.141488 GCTCCCTCTTCCTCGCGA 61.141 66.667 9.26 9.26 0.00 5.87
965 981 3.441290 CCCTCTTCCTCGCGACGT 61.441 66.667 3.71 0.00 0.00 4.34
966 982 2.567049 CCTCTTCCTCGCGACGTT 59.433 61.111 3.71 0.00 0.00 3.99
967 983 1.080705 CCTCTTCCTCGCGACGTTT 60.081 57.895 3.71 0.00 0.00 3.60
968 984 0.666577 CCTCTTCCTCGCGACGTTTT 60.667 55.000 3.71 0.00 0.00 2.43
969 985 1.137513 CTCTTCCTCGCGACGTTTTT 58.862 50.000 3.71 0.00 0.00 1.94
989 1088 1.730451 TTCAGTGTGTCGACTCCGCA 61.730 55.000 17.92 7.76 35.37 5.69
1021 1120 1.847890 GCTGTACGCGGCCTTTTTCA 61.848 55.000 12.47 0.00 41.02 2.69
1065 1164 2.045438 TTCGACGGCCCATGCAAT 60.045 55.556 0.00 0.00 40.13 3.56
1073 1172 0.174162 GGCCCATGCAATGTGAACTC 59.826 55.000 0.00 0.00 44.81 3.01
1085 1184 5.116074 GCAATGTGAACTCTTGTGAATTTCG 59.884 40.000 0.00 0.00 0.00 3.46
1145 1244 1.627297 AATCCCCTTCGGCTCACTCC 61.627 60.000 0.00 0.00 0.00 3.85
1188 1291 2.051345 CCAACAAGAACCACGCGC 60.051 61.111 5.73 0.00 0.00 6.86
1439 1543 1.947456 GAAGACGCACAAGGTTTCCTT 59.053 47.619 0.00 0.00 45.88 3.36
1468 1572 1.676529 CTTCTCTGGGCTCGTTATCGA 59.323 52.381 0.00 0.00 44.12 3.59
1480 1584 3.845178 TCGTTATCGAGAAGTGCACATT 58.155 40.909 21.04 10.39 41.35 2.71
1482 1586 4.091365 TCGTTATCGAGAAGTGCACATTTG 59.909 41.667 21.04 7.82 41.35 2.32
1483 1587 4.143115 CGTTATCGAGAAGTGCACATTTGT 60.143 41.667 21.04 3.62 39.71 2.83
1485 1589 1.792367 TCGAGAAGTGCACATTTGTCG 59.208 47.619 23.85 23.85 42.32 4.35
1487 1591 1.264020 GAGAAGTGCACATTTGTCGCA 59.736 47.619 21.04 4.45 32.57 5.10
1488 1592 1.881973 AGAAGTGCACATTTGTCGCAT 59.118 42.857 21.04 0.00 35.64 4.73
1530 1634 1.441729 CTCCGGTCTGTGTGTGTGT 59.558 57.895 0.00 0.00 0.00 3.72
1532 1636 1.153449 CCGGTCTGTGTGTGTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
1534 1638 0.739462 CGGTCTGTGTGTGTGTGTGT 60.739 55.000 0.00 0.00 0.00 3.72
1535 1639 0.726827 GGTCTGTGTGTGTGTGTGTG 59.273 55.000 0.00 0.00 0.00 3.82
1536 1640 1.438651 GTCTGTGTGTGTGTGTGTGT 58.561 50.000 0.00 0.00 0.00 3.72
1537 1641 1.128507 GTCTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1538 1642 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
1539 1643 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1540 1644 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1576 1680 4.388499 CGGTTCAGGGTGACGGGG 62.388 72.222 0.00 0.00 0.00 5.73
1750 1863 6.292061 CGAGAGCTAAATGTGAATTCAGTAGC 60.292 42.308 21.59 21.59 36.24 3.58
1760 1873 1.453155 ATTCAGTAGCGCCCAAACTG 58.547 50.000 18.47 18.47 41.58 3.16
1761 1874 0.107831 TTCAGTAGCGCCCAAACTGT 59.892 50.000 21.68 0.00 41.12 3.55
1762 1875 0.320421 TCAGTAGCGCCCAAACTGTC 60.320 55.000 21.68 0.00 41.12 3.51
1768 1881 2.203294 GCCCAAACTGTCCACGGT 60.203 61.111 0.00 0.00 36.96 4.83
1779 1892 0.531311 GTCCACGGTCAGACGGTTTT 60.531 55.000 10.95 0.00 38.39 2.43
1828 1941 4.347453 GGCTGTGCCCAAACTGCG 62.347 66.667 0.00 0.00 44.06 5.18
1867 1997 2.811317 GAGCTGTGAGGTTCGGCG 60.811 66.667 0.00 0.00 41.47 6.46
1868 1998 3.575351 GAGCTGTGAGGTTCGGCGT 62.575 63.158 6.85 0.00 41.47 5.68
1871 2001 0.947180 GCTGTGAGGTTCGGCGTAAA 60.947 55.000 6.85 0.00 0.00 2.01
1875 2005 3.191669 TGTGAGGTTCGGCGTAAATATG 58.808 45.455 6.85 0.00 0.00 1.78
1876 2006 2.542595 GTGAGGTTCGGCGTAAATATGG 59.457 50.000 6.85 0.00 0.00 2.74
1878 2008 1.140252 AGGTTCGGCGTAAATATGGCT 59.860 47.619 6.85 0.00 35.80 4.75
1881 2011 0.882927 TCGGCGTAAATATGGCTGGC 60.883 55.000 6.85 0.00 35.80 4.85
1892 2022 0.622136 ATGGCTGGCTGAATCTGTCA 59.378 50.000 2.00 0.00 34.17 3.58
1917 2047 9.848172 CAGTTTCTTAATTTGTAACAACAATGC 57.152 29.630 0.00 0.00 0.00 3.56
1928 2066 6.893759 TGTAACAACAATGCACATAGTGTAC 58.106 36.000 0.00 0.00 35.75 2.90
1929 2067 6.483640 TGTAACAACAATGCACATAGTGTACA 59.516 34.615 0.00 0.00 35.75 2.90
1930 2068 5.611796 ACAACAATGCACATAGTGTACAG 57.388 39.130 0.00 0.00 35.75 2.74
1934 2072 4.690748 ACAATGCACATAGTGTACAGTGTC 59.309 41.667 13.66 6.89 46.13 3.67
1941 2079 2.751166 AGTGTACAGTGTCTGGCATC 57.249 50.000 1.37 0.00 35.51 3.91
1954 2092 1.203441 TGGCATCCAGAAGCTCCTGT 61.203 55.000 0.00 0.00 32.43 4.00
1958 2096 2.877300 GCATCCAGAAGCTCCTGTTTGA 60.877 50.000 0.00 0.00 32.43 2.69
1960 2098 3.340814 TCCAGAAGCTCCTGTTTGATC 57.659 47.619 0.00 0.00 32.43 2.92
1963 2101 3.055240 CCAGAAGCTCCTGTTTGATCTCT 60.055 47.826 0.00 0.00 32.43 3.10
2008 2146 7.942341 AGGTAATTTCAACTCATTCCACAGTTA 59.058 33.333 0.00 0.00 31.41 2.24
2020 2158 8.821686 TCATTCCACAGTTAATGAACCATAAT 57.178 30.769 5.84 0.00 38.74 1.28
2102 2242 5.647658 TGTGCTATTACTGCAAACTGCTAAT 59.352 36.000 0.00 0.26 45.31 1.73
2104 2244 6.688813 GTGCTATTACTGCAAACTGCTAATTC 59.311 38.462 0.00 0.00 45.31 2.17
2117 2257 9.897744 CAAACTGCTAATTCTTGAATAGTGAAA 57.102 29.630 0.00 0.00 0.00 2.69
2133 2273 4.952460 AGTGAAATTTGATATGCCATGCC 58.048 39.130 0.00 0.00 0.00 4.40
2134 2274 3.737266 GTGAAATTTGATATGCCATGCCG 59.263 43.478 0.00 0.00 0.00 5.69
2136 2276 3.374220 AATTTGATATGCCATGCCGTG 57.626 42.857 0.00 0.00 0.00 4.94
2240 2380 6.425210 ACAGATTAGCAACCATGAGCTATA 57.575 37.500 12.96 7.01 42.39 1.31
2245 2385 4.065321 AGCAACCATGAGCTATAGTGTC 57.935 45.455 0.84 0.00 39.78 3.67
2249 2389 6.013898 AGCAACCATGAGCTATAGTGTCATAT 60.014 38.462 15.42 7.78 39.78 1.78
2252 2392 9.881649 CAACCATGAGCTATAGTGTCATATTAT 57.118 33.333 15.42 4.80 29.64 1.28
2253 2393 9.881649 AACCATGAGCTATAGTGTCATATTATG 57.118 33.333 15.42 0.00 29.64 1.90
2273 2420 5.913137 ATGAAACACAACTGTCTGGAAAA 57.087 34.783 0.00 0.00 0.00 2.29
2288 2435 3.831911 CTGGAAAATTAAGCCACTGGGAA 59.168 43.478 0.00 0.00 35.59 3.97
2308 2455 6.775629 TGGGAAAGTAACAGTAATTTGCTCTT 59.224 34.615 0.00 0.00 36.31 2.85
2309 2456 7.084486 GGGAAAGTAACAGTAATTTGCTCTTG 58.916 38.462 0.00 0.00 36.31 3.02
2333 2481 7.957002 TGGAATTTCAATTTTGGTGTAGCTTA 58.043 30.769 0.00 0.00 0.00 3.09
2417 2569 2.647875 CCGCGGTGCCAATTTTCA 59.352 55.556 19.50 0.00 0.00 2.69
2423 2576 1.736696 CGGTGCCAATTTTCATGCCTC 60.737 52.381 0.00 0.00 0.00 4.70
2424 2577 1.551883 GGTGCCAATTTTCATGCCTCT 59.448 47.619 0.00 0.00 0.00 3.69
2425 2578 2.613691 GTGCCAATTTTCATGCCTCTG 58.386 47.619 0.00 0.00 0.00 3.35
2426 2579 2.231964 GTGCCAATTTTCATGCCTCTGA 59.768 45.455 0.00 0.00 0.00 3.27
2427 2580 2.494471 TGCCAATTTTCATGCCTCTGAG 59.506 45.455 0.00 0.00 0.00 3.35
2428 2581 2.756760 GCCAATTTTCATGCCTCTGAGA 59.243 45.455 6.17 0.00 0.00 3.27
2602 2756 6.701400 ACCACTTGTAATTTTGTGCATCTTTC 59.299 34.615 0.00 0.00 0.00 2.62
2662 2820 4.778534 ACTTCACATTCCAAGCAATCAG 57.221 40.909 0.00 0.00 0.00 2.90
2686 2844 9.396022 CAGAAACAACTATTCATATGGGTAGTT 57.604 33.333 19.36 19.36 37.75 2.24
2692 2850 7.067496 ACTATTCATATGGGTAGTTCAGTGG 57.933 40.000 2.13 0.00 0.00 4.00
2737 2895 3.005050 CACTTGGTTGAGATGTGTGCATT 59.995 43.478 0.00 0.00 35.07 3.56
2785 2943 1.344438 TGTGCCAAGACTCGATTCACT 59.656 47.619 5.50 0.00 0.00 3.41
2786 2944 1.728971 GTGCCAAGACTCGATTCACTG 59.271 52.381 5.50 2.24 0.00 3.66
2829 2988 3.627395 TGACACCAGAAACAAGACACT 57.373 42.857 0.00 0.00 0.00 3.55
2869 3028 3.997021 AGGTTCTTTGAGTAGTCATTGCG 59.003 43.478 0.00 0.00 30.85 4.85
2914 3074 0.179018 GCCAGGGCTTCATACCGAAT 60.179 55.000 2.30 0.00 38.26 3.34
2918 3078 2.366916 CAGGGCTTCATACCGAATCTCT 59.633 50.000 0.00 0.00 30.41 3.10
3099 3300 9.499369 AATGTATATTAGGATCCAGTGAGCTAT 57.501 33.333 15.82 3.78 0.00 2.97
3100 3301 8.901472 TGTATATTAGGATCCAGTGAGCTATT 57.099 34.615 15.82 0.00 0.00 1.73
3157 3359 1.471119 AGACGCAAGATCCGACCTTA 58.529 50.000 0.00 0.00 43.62 2.69
3204 3408 5.932303 TCCAACAACACTTCTATACTTGCTC 59.068 40.000 0.00 0.00 0.00 4.26
3338 3544 0.038343 GCTCATCATCTCGCCTCCTC 60.038 60.000 0.00 0.00 0.00 3.71
3348 3554 2.636412 CGCCTCCTCACCTCAACGA 61.636 63.158 0.00 0.00 0.00 3.85
3354 3560 1.697432 TCCTCACCTCAACGACCAAAT 59.303 47.619 0.00 0.00 0.00 2.32
3355 3561 2.105821 TCCTCACCTCAACGACCAAATT 59.894 45.455 0.00 0.00 0.00 1.82
3356 3562 2.884639 CCTCACCTCAACGACCAAATTT 59.115 45.455 0.00 0.00 0.00 1.82
3357 3563 3.317993 CCTCACCTCAACGACCAAATTTT 59.682 43.478 0.00 0.00 0.00 1.82
3417 3625 4.098055 TGAGATCGTCTAGAAGTGTTGC 57.902 45.455 5.55 0.00 0.00 4.17
3523 3734 6.075762 TGCATGGTAGATAATTTGATGTGC 57.924 37.500 0.00 0.00 0.00 4.57
3524 3735 5.593502 TGCATGGTAGATAATTTGATGTGCA 59.406 36.000 0.00 0.00 35.60 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 141 2.044946 ATTTCGGGCCAGCCAGAC 60.045 61.111 11.23 0.00 39.88 3.51
158 160 4.834496 TCATTTTCTTCTCAAAGGTGGCAT 59.166 37.500 0.00 0.00 33.03 4.40
330 332 2.362120 GTGATTGGCTGCCTGGCT 60.362 61.111 21.03 0.00 42.34 4.75
577 588 5.363868 CAGAAAGAAGGGAAAGGGAAAAAGT 59.636 40.000 0.00 0.00 0.00 2.66
630 644 4.218312 GACCCCTTTCCATTGCATAGAAT 58.782 43.478 0.00 0.00 0.00 2.40
677 691 7.608153 TCAGTTTCGACAGGATTATTCAGTTA 58.392 34.615 0.00 0.00 0.00 2.24
705 719 5.163591 CCTTGTGCTTGCTTGATGATGATAA 60.164 40.000 0.00 0.00 0.00 1.75
719 733 1.239968 GGCTGGAGACCTTGTGCTTG 61.240 60.000 0.00 0.00 0.00 4.01
735 749 1.055040 GTGATCTCCATGCCTAGGCT 58.945 55.000 33.07 16.79 42.51 4.58
738 752 1.332195 TCGGTGATCTCCATGCCTAG 58.668 55.000 13.99 0.00 0.00 3.02
784 798 3.159472 TGTCTCTTAAGGCTGTTCCGTA 58.841 45.455 1.85 0.00 40.77 4.02
798 812 1.611673 CGTGAATGCCCCTTGTCTCTT 60.612 52.381 0.00 0.00 0.00 2.85
799 813 0.036010 CGTGAATGCCCCTTGTCTCT 60.036 55.000 0.00 0.00 0.00 3.10
804 818 0.734889 GTCATCGTGAATGCCCCTTG 59.265 55.000 0.00 0.00 35.17 3.61
850 866 1.901085 GTCCTGGGCGAGATTGTCT 59.099 57.895 0.00 0.00 0.00 3.41
854 870 4.162690 GGCGTCCTGGGCGAGATT 62.163 66.667 26.96 0.00 0.00 2.40
872 888 2.447379 ATCAGCCAGCTCCCCGAT 60.447 61.111 0.00 0.00 0.00 4.18
918 934 3.775654 GAGTCACCCCGGAGCTGG 61.776 72.222 0.73 0.00 0.00 4.85
948 964 2.488087 AAACGTCGCGAGGAAGAGGG 62.488 60.000 32.99 7.23 0.00 4.30
967 983 2.198406 CGGAGTCGACACACTGAAAAA 58.802 47.619 19.50 0.00 39.00 1.94
968 984 1.847818 CGGAGTCGACACACTGAAAA 58.152 50.000 19.50 0.00 39.00 2.29
969 985 0.596600 GCGGAGTCGACACACTGAAA 60.597 55.000 19.50 0.00 39.00 2.69
970 986 1.007734 GCGGAGTCGACACACTGAA 60.008 57.895 19.50 0.00 39.00 3.02
971 987 2.130073 CTGCGGAGTCGACACACTGA 62.130 60.000 19.50 3.96 39.00 3.41
973 989 2.645567 CTGCGGAGTCGACACACT 59.354 61.111 19.50 0.00 39.00 3.55
974 990 3.106407 GCTGCGGAGTCGACACAC 61.106 66.667 19.50 8.25 39.00 3.82
1021 1120 1.070127 ACATATGGGGCTGGCCTGAT 61.070 55.000 20.47 14.19 36.10 2.90
1062 1161 5.116074 GCGAAATTCACAAGAGTTCACATTG 59.884 40.000 0.00 0.00 0.00 2.82
1063 1162 5.215160 GCGAAATTCACAAGAGTTCACATT 58.785 37.500 0.00 0.00 0.00 2.71
1065 1164 3.003275 GGCGAAATTCACAAGAGTTCACA 59.997 43.478 0.00 0.00 0.00 3.58
1073 1172 1.201877 CGTACGGGCGAAATTCACAAG 60.202 52.381 7.57 0.00 0.00 3.16
1145 1244 1.355066 GCGTCTTCTTCCTCTTGCGG 61.355 60.000 0.00 0.00 0.00 5.69
1188 1291 0.388659 CCATGGCTTCCTCTCTCTCG 59.611 60.000 0.00 0.00 0.00 4.04
1439 1543 1.608717 GCCCAGAGAAGAAGGCGAGA 61.609 60.000 0.00 0.00 35.30 4.04
1468 1572 1.308047 TGCGACAAATGTGCACTTCT 58.692 45.000 19.41 0.00 32.86 2.85
1470 1574 2.396601 CAATGCGACAAATGTGCACTT 58.603 42.857 19.41 9.21 42.11 3.16
1472 1576 1.062258 CCAATGCGACAAATGTGCAC 58.938 50.000 10.75 10.75 42.11 4.57
1485 1589 2.368655 AATCAAGAAACGCCCAATGC 57.631 45.000 0.00 0.00 0.00 3.56
1487 1591 3.165071 AGGAAATCAAGAAACGCCCAAT 58.835 40.909 0.00 0.00 0.00 3.16
1488 1592 2.556622 GAGGAAATCAAGAAACGCCCAA 59.443 45.455 0.00 0.00 0.00 4.12
1530 1634 2.405805 GCCTGCACACACACACACA 61.406 57.895 0.00 0.00 0.00 3.72
1532 1636 3.201297 CGCCTGCACACACACACA 61.201 61.111 0.00 0.00 0.00 3.72
1534 1638 2.894879 GACGCCTGCACACACACA 60.895 61.111 0.00 0.00 0.00 3.72
1535 1639 4.000557 CGACGCCTGCACACACAC 62.001 66.667 0.00 0.00 0.00 3.82
1576 1680 2.582498 CGCACGATCTTCCCGGTC 60.582 66.667 0.00 0.00 0.00 4.79
1750 1863 3.353836 CCGTGGACAGTTTGGGCG 61.354 66.667 0.00 0.00 0.00 6.13
1760 1873 0.531311 AAAACCGTCTGACCGTGGAC 60.531 55.000 7.14 0.00 0.00 4.02
1761 1874 0.531090 CAAAACCGTCTGACCGTGGA 60.531 55.000 7.14 0.00 0.00 4.02
1762 1875 0.812412 ACAAAACCGTCTGACCGTGG 60.812 55.000 1.55 0.38 0.00 4.94
1768 1881 2.011222 GACACCAACAAAACCGTCTGA 58.989 47.619 0.00 0.00 0.00 3.27
1796 1909 1.187974 CAGCCCTGGAAATGCATTCA 58.812 50.000 13.38 6.52 39.98 2.57
1828 1941 2.149973 ATGAAGCCCAGGAATTCACC 57.850 50.000 7.93 0.00 35.89 4.02
1867 1997 4.823989 ACAGATTCAGCCAGCCATATTTAC 59.176 41.667 0.00 0.00 0.00 2.01
1868 1998 5.052693 ACAGATTCAGCCAGCCATATTTA 57.947 39.130 0.00 0.00 0.00 1.40
1871 2001 2.440627 TGACAGATTCAGCCAGCCATAT 59.559 45.455 0.00 0.00 0.00 1.78
1875 2005 2.777969 CTGACAGATTCAGCCAGCC 58.222 57.895 0.00 0.00 45.51 4.85
1892 2022 9.593134 TGCATTGTTGTTACAAATTAAGAAACT 57.407 25.926 0.00 0.00 46.62 2.66
1893 2023 9.631639 GTGCATTGTTGTTACAAATTAAGAAAC 57.368 29.630 0.00 0.00 46.62 2.78
1898 2028 9.973450 ACTATGTGCATTGTTGTTACAAATTAA 57.027 25.926 0.00 0.00 46.62 1.40
1901 2031 7.432869 ACACTATGTGCATTGTTGTTACAAAT 58.567 30.769 0.00 0.00 41.25 2.32
1905 2035 6.893759 TGTACACTATGTGCATTGTTGTTAC 58.106 36.000 0.00 1.67 38.04 2.50
1906 2036 6.708502 ACTGTACACTATGTGCATTGTTGTTA 59.291 34.615 0.09 0.00 41.89 2.41
1907 2037 5.530915 ACTGTACACTATGTGCATTGTTGTT 59.469 36.000 0.09 0.00 41.89 2.83
1908 2038 5.049474 CACTGTACACTATGTGCATTGTTGT 60.049 40.000 8.54 0.00 41.89 3.32
1917 2047 3.254060 GCCAGACACTGTACACTATGTG 58.746 50.000 10.50 10.50 39.75 3.21
1941 2079 3.055240 AGAGATCAAACAGGAGCTTCTGG 60.055 47.826 25.98 8.65 38.98 3.86
1954 2092 7.869937 CAGAGAACTAGTCACAAAGAGATCAAA 59.130 37.037 0.00 0.00 0.00 2.69
1958 2096 6.909550 ACAGAGAACTAGTCACAAAGAGAT 57.090 37.500 0.00 0.00 0.00 2.75
1960 2098 6.207810 ACCTACAGAGAACTAGTCACAAAGAG 59.792 42.308 0.00 0.00 0.00 2.85
1963 2101 7.828508 TTACCTACAGAGAACTAGTCACAAA 57.171 36.000 0.00 0.00 0.00 2.83
2020 2158 7.428020 GGCAACTGATTTGATATTAGCATCAA 58.572 34.615 0.00 0.00 41.90 2.57
2036 2174 1.677217 GCCTTCTTCTCGGCAACTGAT 60.677 52.381 0.00 0.00 45.59 2.90
2039 2177 1.374758 CGCCTTCTTCTCGGCAACT 60.375 57.895 0.00 0.00 46.62 3.16
2056 2194 6.194508 CACAAATACATATGAAAGAAACGCCG 59.805 38.462 10.38 0.00 0.00 6.46
2104 2244 9.976511 ATGGCATATCAAATTTCACTATTCAAG 57.023 29.630 0.00 0.00 0.00 3.02
2117 2257 2.555325 CTCACGGCATGGCATATCAAAT 59.445 45.455 20.37 0.00 0.00 2.32
2119 2259 1.596603 CTCACGGCATGGCATATCAA 58.403 50.000 20.37 0.00 0.00 2.57
2175 2315 8.950007 TCTCAAGGGACCAAATAATACTTTTT 57.050 30.769 0.00 0.00 0.00 1.94
2176 2316 8.803235 GTTCTCAAGGGACCAAATAATACTTTT 58.197 33.333 0.00 0.00 0.00 2.27
2240 2380 8.621532 ACAGTTGTGTTTCATAATATGACACT 57.378 30.769 19.31 7.32 39.91 3.55
2245 2385 8.267620 TCCAGACAGTTGTGTTTCATAATATG 57.732 34.615 0.00 0.00 36.88 1.78
2249 2389 7.397892 TTTTCCAGACAGTTGTGTTTCATAA 57.602 32.000 0.00 0.00 36.88 1.90
2252 2392 5.913137 ATTTTCCAGACAGTTGTGTTTCA 57.087 34.783 0.00 0.00 36.88 2.69
2253 2393 7.043391 GCTTAATTTTCCAGACAGTTGTGTTTC 60.043 37.037 0.00 0.00 36.88 2.78
2262 2402 4.082571 CCAGTGGCTTAATTTTCCAGACAG 60.083 45.833 0.00 0.00 0.00 3.51
2273 2420 4.993028 TGTTACTTTCCCAGTGGCTTAAT 58.007 39.130 2.61 0.00 35.97 1.40
2288 2435 7.817418 TTCCAAGAGCAAATTACTGTTACTT 57.183 32.000 0.00 0.00 0.00 2.24
2308 2455 6.418057 AGCTACACCAAAATTGAAATTCCA 57.582 33.333 0.00 0.00 0.00 3.53
2309 2456 9.435688 AATAAGCTACACCAAAATTGAAATTCC 57.564 29.630 0.00 0.00 0.00 3.01
2333 2481 9.122779 GGAGTCATAGTACTACAGTCTGTAAAT 57.877 37.037 13.63 7.71 31.67 1.40
2338 2486 6.768381 TCATGGAGTCATAGTACTACAGTCTG 59.232 42.308 4.31 0.00 43.52 3.51
2406 2558 2.494471 CTCAGAGGCATGAAAATTGGCA 59.506 45.455 0.00 0.00 41.77 4.92
2417 2569 2.101783 CAGTCTCAGTCTCAGAGGCAT 58.898 52.381 4.46 0.00 40.12 4.40
2423 2576 4.036734 GGAAGATAGCAGTCTCAGTCTCAG 59.963 50.000 0.00 0.00 0.00 3.35
2424 2577 3.951037 GGAAGATAGCAGTCTCAGTCTCA 59.049 47.826 0.00 0.00 0.00 3.27
2425 2578 3.003275 CGGAAGATAGCAGTCTCAGTCTC 59.997 52.174 0.00 0.00 0.00 3.36
2426 2579 2.948979 CGGAAGATAGCAGTCTCAGTCT 59.051 50.000 0.00 0.00 0.00 3.24
2427 2580 2.542824 GCGGAAGATAGCAGTCTCAGTC 60.543 54.545 0.00 0.00 0.00 3.51
2428 2581 1.407258 GCGGAAGATAGCAGTCTCAGT 59.593 52.381 0.00 0.00 0.00 3.41
2626 2784 5.394224 TGTGAAGTATGACAATGGTACGA 57.606 39.130 0.00 0.00 0.00 3.43
2628 2786 6.597672 TGGAATGTGAAGTATGACAATGGTAC 59.402 38.462 0.00 0.00 0.00 3.34
2634 2792 5.069318 TGCTTGGAATGTGAAGTATGACAA 58.931 37.500 0.00 0.00 0.00 3.18
2637 2795 5.945191 TGATTGCTTGGAATGTGAAGTATGA 59.055 36.000 0.00 0.00 0.00 2.15
2640 2798 5.559770 TCTGATTGCTTGGAATGTGAAGTA 58.440 37.500 0.00 0.00 0.00 2.24
2662 2820 9.391006 TGAACTACCCATATGAATAGTTGTTTC 57.609 33.333 24.68 16.01 37.85 2.78
2737 2895 2.095212 CGGTCAGTGAATCGAGTCTTCA 60.095 50.000 14.66 5.10 0.00 3.02
2803 2962 6.204688 GTGTCTTGTTTCTGGTGTCATAATCA 59.795 38.462 0.00 0.00 0.00 2.57
2829 2988 5.373812 AACCTGAAGTTCCTCAAGAAAGA 57.626 39.130 0.00 0.00 35.85 2.52
2869 3028 8.853345 CAATGTTACAACAGAGATAATTTGTGC 58.147 33.333 0.84 0.00 43.04 4.57
2914 3074 5.954752 ACAATGTCTAGATCCAACTCAGAGA 59.045 40.000 3.79 0.00 0.00 3.10
2918 3078 4.937620 GCAACAATGTCTAGATCCAACTCA 59.062 41.667 0.00 0.00 0.00 3.41
2965 3166 2.096069 CAGGTTGCTCAGATGACAAACG 60.096 50.000 7.22 0.00 36.13 3.60
3006 3207 1.605738 CTTCCTTGGCCTGCTGCTT 60.606 57.895 3.32 0.00 40.92 3.91
3007 3208 1.860944 ATCTTCCTTGGCCTGCTGCT 61.861 55.000 3.32 0.00 40.92 4.24
3008 3209 1.379576 ATCTTCCTTGGCCTGCTGC 60.380 57.895 3.32 0.00 40.16 5.25
3009 3210 1.035932 CCATCTTCCTTGGCCTGCTG 61.036 60.000 3.32 0.00 0.00 4.41
3010 3211 1.210204 TCCATCTTCCTTGGCCTGCT 61.210 55.000 3.32 0.00 34.06 4.24
3011 3212 0.750911 CTCCATCTTCCTTGGCCTGC 60.751 60.000 3.32 0.00 34.06 4.85
3012 3213 0.914644 TCTCCATCTTCCTTGGCCTG 59.085 55.000 3.32 0.00 34.06 4.85
3014 3215 0.915364 AGTCTCCATCTTCCTTGGCC 59.085 55.000 0.00 0.00 34.06 5.36
3015 3216 2.797177 AAGTCTCCATCTTCCTTGGC 57.203 50.000 0.00 0.00 34.06 4.52
3071 3272 9.326489 AGCTCACTGGATCCTAATATACATTAA 57.674 33.333 14.23 0.00 0.00 1.40
3074 3275 9.499369 AATAGCTCACTGGATCCTAATATACAT 57.501 33.333 14.23 0.00 0.00 2.29
3075 3276 8.901472 AATAGCTCACTGGATCCTAATATACA 57.099 34.615 14.23 0.00 0.00 2.29
3079 3280 9.647918 CCTATAATAGCTCACTGGATCCTAATA 57.352 37.037 14.23 0.00 0.00 0.98
3080 3281 8.125733 ACCTATAATAGCTCACTGGATCCTAAT 58.874 37.037 14.23 0.00 0.00 1.73
3204 3408 1.466167 CCTTCGAATGCCACAGACTTG 59.534 52.381 0.00 0.00 0.00 3.16
3211 3415 1.087501 GGAGAACCTTCGAATGCCAC 58.912 55.000 0.00 0.00 0.00 5.01
3212 3416 0.984230 AGGAGAACCTTCGAATGCCA 59.016 50.000 0.00 0.00 45.36 4.92
3355 3561 8.980481 TTAAAGATTTGGGGTATTTGCAAAAA 57.020 26.923 17.19 4.25 0.00 1.94
3356 3562 7.663493 CCTTAAAGATTTGGGGTATTTGCAAAA 59.337 33.333 17.19 2.96 0.00 2.44
3357 3563 7.016661 TCCTTAAAGATTTGGGGTATTTGCAAA 59.983 33.333 15.44 15.44 0.00 3.68
3374 3582 8.701895 TCTCAGTTCTAACTTTGTCCTTAAAGA 58.298 33.333 5.36 0.00 39.46 2.52
3417 3625 2.355197 TGTAATGGGTTCATGCTGTCG 58.645 47.619 0.00 0.00 33.18 4.35
3499 3710 6.096564 TGCACATCAAATTATCTACCATGCAA 59.903 34.615 0.00 0.00 35.42 4.08
3500 3711 5.593502 TGCACATCAAATTATCTACCATGCA 59.406 36.000 0.00 0.00 35.94 3.96


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

AutoCloner maintained by Alex Coulton.