Multiple sequence alignment - TraesCS6D01G162500

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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 TraesCS6D01G162500 chr6D 100.000 3980 0 0 1 3980 141134273 141138252 0.000000e+00 7350
1 TraesCS6D01G162500 chr6D 83.212 137 21 1 565 701 378032357 378032491 1.500000e-24 124
2 TraesCS6D01G162500 chr6A 91.431 2089 103 24 1953 3980 185319880 185321953 0.000000e+00 2796
3 TraesCS6D01G162500 chr6A 93.586 1185 53 9 766 1937 185318723 185319897 0.000000e+00 1746
4 TraesCS6D01G162500 chr6A 90.639 673 39 7 90 750 185318076 185318736 0.000000e+00 872
5 TraesCS6D01G162500 chr6A 94.186 86 5 0 1 86 185317958 185318043 8.970000e-27 132
6 TraesCS6D01G162500 chr6B 96.082 1174 44 2 766 1937 240400426 240401599 0.000000e+00 1912
7 TraesCS6D01G162500 chr6B 92.586 1214 39 14 1952 3128 240401582 240402781 0.000000e+00 1696
8 TraesCS6D01G162500 chr6B 89.770 870 48 17 3130 3980 240402821 240403668 0.000000e+00 1075
9 TraesCS6D01G162500 chr6B 89.894 663 49 11 89 750 240399794 240400439 0.000000e+00 837
10 TraesCS6D01G162500 chr6B 93.182 88 6 0 1 88 240399677 240399764 3.230000e-26 130
11 TraesCS6D01G162500 chr7D 80.311 193 28 5 565 753 120308017 120308203 1.930000e-28 137
12 TraesCS6D01G162500 chr2B 79.894 189 29 5 565 750 539337196 539337378 3.230000e-26 130
13 TraesCS6D01G162500 chr2B 83.212 137 21 1 565 701 335806327 335806461 1.500000e-24 124
14 TraesCS6D01G162500 chr1D 83.942 137 20 1 565 701 101104177 101104311 3.230000e-26 130
15 TraesCS6D01G162500 chr1D 83.942 137 20 1 565 701 438205895 438205761 3.230000e-26 130
16 TraesCS6D01G162500 chr5B 79.474 190 29 5 565 750 395705876 395706059 4.180000e-25 126


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 TraesCS6D01G162500 chr6D 141134273 141138252 3979 False 7350.0 7350 100.0000 1 3980 1 chr6D.!!$F1 3979
1 TraesCS6D01G162500 chr6A 185317958 185321953 3995 False 1386.5 2796 92.4605 1 3980 4 chr6A.!!$F1 3979
2 TraesCS6D01G162500 chr6B 240399677 240403668 3991 False 1130.0 1912 92.3028 1 3980 5 chr6B.!!$F1 3979

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
162 192 0.756442 TTGCAGCTGCCCTGACTTTT 60.756 50.000 34.64 0.0 44.64 2.27 F
232 262 1.008693 TCGGGGGTCCTACCTTTACAT 59.991 52.381 0.00 0.0 38.64 2.29 F
1944 2023 0.106708 GATGCCCCTATTCAGTCGCA 59.893 55.000 0.00 0.0 0.00 5.10 F
1946 2025 0.326595 TGCCCCTATTCAGTCGCAAA 59.673 50.000 0.00 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1325 0.323629 TCTAGGGCAGAACCAAACCG 59.676 55.000 0.00 0.00 42.05 4.44 R
1955 2034 1.065126 GCCTAACAACAGGGCATCTCT 60.065 52.381 0.00 0.00 44.69 3.10 R
2831 2963 0.250124 TGAGAACCAACCGCGAACAT 60.250 50.000 8.23 0.00 0.00 2.71 R
3310 3488 0.461548 TGCTCATGATCACGGAGGAC 59.538 55.000 21.46 10.73 0.00 3.85 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
162 192 0.756442 TTGCAGCTGCCCTGACTTTT 60.756 50.000 34.64 0.00 44.64 2.27
232 262 1.008693 TCGGGGGTCCTACCTTTACAT 59.991 52.381 0.00 0.00 38.64 2.29
285 315 1.451207 CCCCAATCGGCATCAACGA 60.451 57.895 0.00 0.00 45.19 3.85
379 409 3.829886 AACAAATACATGAGTGTGGCG 57.170 42.857 0.00 0.00 39.39 5.69
380 410 3.052455 ACAAATACATGAGTGTGGCGA 57.948 42.857 0.00 0.00 39.39 5.54
451 481 5.173131 GTGGAATGATGTTTTTGTCGACAAC 59.827 40.000 29.74 19.87 35.28 3.32
525 555 1.174078 TGTGTGCTTGTGCCTCCATG 61.174 55.000 0.00 0.00 38.71 3.66
657 699 4.884164 GGCATCTTCTTGTAAGCTTGGTAT 59.116 41.667 9.86 0.00 0.00 2.73
658 700 6.055588 GGCATCTTCTTGTAAGCTTGGTATA 58.944 40.000 9.86 0.00 0.00 1.47
692 734 2.875296 ACCAAGCAATCACTAGCCAAA 58.125 42.857 0.00 0.00 0.00 3.28
721 763 5.185828 GGCAACTTGTTTCTAGGAAATCCAT 59.814 40.000 1.67 0.00 38.89 3.41
741 783 2.408271 TTTTTGGCATGTGCAAACCA 57.592 40.000 7.36 0.00 44.36 3.67
742 784 2.408271 TTTTGGCATGTGCAAACCAA 57.592 40.000 7.36 6.84 44.36 3.67
743 785 2.634815 TTTGGCATGTGCAAACCAAT 57.365 40.000 7.36 0.00 41.59 3.16
744 786 2.166821 TTGGCATGTGCAAACCAATC 57.833 45.000 7.36 0.00 44.36 2.67
745 787 1.046204 TGGCATGTGCAAACCAATCA 58.954 45.000 7.36 0.00 44.36 2.57
746 788 1.624312 TGGCATGTGCAAACCAATCAT 59.376 42.857 7.36 0.00 44.36 2.45
747 789 2.004017 GGCATGTGCAAACCAATCATG 58.996 47.619 7.36 6.80 44.36 3.07
749 791 2.967362 CATGTGCAAACCAATCATGCT 58.033 42.857 0.00 0.00 40.66 3.79
750 792 3.331150 CATGTGCAAACCAATCATGCTT 58.669 40.909 0.00 0.00 40.66 3.91
751 793 3.472283 TGTGCAAACCAATCATGCTTT 57.528 38.095 0.00 0.00 40.66 3.51
752 794 3.806380 TGTGCAAACCAATCATGCTTTT 58.194 36.364 0.00 0.00 40.66 2.27
753 795 4.197750 TGTGCAAACCAATCATGCTTTTT 58.802 34.783 0.00 0.00 40.66 1.94
813 855 1.383799 CCCAATTCTGGCCCACTCA 59.616 57.895 0.00 0.00 41.99 3.41
930 991 1.686325 GCCGAGATAAGGGGAGCACA 61.686 60.000 0.00 0.00 0.00 4.57
1038 1114 4.246206 TCGTCGTCTATGGGCGCG 62.246 66.667 0.00 0.00 0.00 6.86
1072 1148 3.862402 CCCTCGACCTCGACGACG 61.862 72.222 0.00 0.00 44.22 5.12
1282 1358 1.417890 CCCTAGATTGATTCCTGCCGT 59.582 52.381 0.00 0.00 0.00 5.68
1473 1549 4.143986 AGGGATCTGTAGTTTAGCAAGC 57.856 45.455 0.00 0.00 0.00 4.01
1492 1569 1.126662 GCTGTTTGCTTTAATTGCGCC 59.873 47.619 4.18 0.00 38.95 6.53
1496 1573 0.246086 TTGCTTTAATTGCGCCTGGG 59.754 50.000 4.18 0.00 0.00 4.45
1608 1687 8.868916 ACTGTCATTGTTTGTTTGAATTAACAC 58.131 29.630 0.00 0.00 37.72 3.32
1935 2014 6.501805 TGTTCATACAATAGAGATGCCCCTAT 59.498 38.462 0.00 0.00 0.00 2.57
1936 2015 7.017551 TGTTCATACAATAGAGATGCCCCTATT 59.982 37.037 0.00 0.00 36.36 1.73
1937 2016 7.187824 TCATACAATAGAGATGCCCCTATTC 57.812 40.000 0.00 0.00 34.40 1.75
1938 2017 6.730507 TCATACAATAGAGATGCCCCTATTCA 59.269 38.462 0.00 0.00 34.40 2.57
1939 2018 5.495926 ACAATAGAGATGCCCCTATTCAG 57.504 43.478 0.00 0.00 34.40 3.02
1940 2019 4.910304 ACAATAGAGATGCCCCTATTCAGT 59.090 41.667 0.00 0.00 34.40 3.41
1941 2020 5.012561 ACAATAGAGATGCCCCTATTCAGTC 59.987 44.000 0.00 0.00 34.40 3.51
1942 2021 1.967066 AGAGATGCCCCTATTCAGTCG 59.033 52.381 0.00 0.00 0.00 4.18
1943 2022 0.394565 AGATGCCCCTATTCAGTCGC 59.605 55.000 0.00 0.00 0.00 5.19
1944 2023 0.106708 GATGCCCCTATTCAGTCGCA 59.893 55.000 0.00 0.00 0.00 5.10
1945 2024 0.546122 ATGCCCCTATTCAGTCGCAA 59.454 50.000 0.00 0.00 30.35 4.85
1946 2025 0.326595 TGCCCCTATTCAGTCGCAAA 59.673 50.000 0.00 0.00 0.00 3.68
1947 2026 1.271652 TGCCCCTATTCAGTCGCAAAA 60.272 47.619 0.00 0.00 0.00 2.44
1948 2027 1.816224 GCCCCTATTCAGTCGCAAAAA 59.184 47.619 0.00 0.00 0.00 1.94
2056 2135 5.982516 GTCTTATTCTCCTGTGTGAGCATAG 59.017 44.000 0.00 0.00 34.18 2.23
2090 2169 4.525912 ACCCTTGATTTTGCTTGACATC 57.474 40.909 0.00 0.00 0.00 3.06
2094 2173 6.267471 ACCCTTGATTTTGCTTGACATCTTAA 59.733 34.615 0.00 0.00 0.00 1.85
2103 2182 4.576053 TGCTTGACATCTTAATTCCGATGG 59.424 41.667 16.64 4.99 40.93 3.51
2137 2232 5.880332 TGATCCTCTTGTACCAAATGCTTAC 59.120 40.000 0.00 0.00 0.00 2.34
2159 2254 9.286170 CTTACTGTAGATAGCTCAGTAATGGTA 57.714 37.037 22.04 9.33 46.38 3.25
2166 2261 7.751646 AGATAGCTCAGTAATGGTACTAGAGT 58.248 38.462 0.00 0.00 38.58 3.24
2363 2494 7.676572 GCGGAAGTAAGTGTCAAATCCTATTTC 60.677 40.741 0.00 0.00 0.00 2.17
2365 2496 8.451748 GGAAGTAAGTGTCAAATCCTATTTCAC 58.548 37.037 0.00 0.00 0.00 3.18
2529 2661 4.256920 GCAACATCTCACAGAAGGTATGT 58.743 43.478 0.00 0.00 0.00 2.29
2552 2684 7.013220 TGTGAGATCCTAATGCCTCTATAAGT 58.987 38.462 0.00 0.00 0.00 2.24
2559 2691 7.310634 TCCTAATGCCTCTATAAGTCCCTTTA 58.689 38.462 0.00 0.00 0.00 1.85
2583 2715 4.125703 CCACTTGATCTGCATCTTCCTAC 58.874 47.826 0.00 0.00 0.00 3.18
2588 2720 4.763073 TGATCTGCATCTTCCTACAACTG 58.237 43.478 0.00 0.00 0.00 3.16
2590 2722 3.930336 TCTGCATCTTCCTACAACTGTG 58.070 45.455 0.00 0.00 0.00 3.66
2610 2742 6.648310 ACTGTGATGGATTTTCTATATGCTCG 59.352 38.462 0.00 0.00 0.00 5.03
2643 2775 6.150307 TGACGTTGCAAGTAATTTCATATGGT 59.850 34.615 0.00 0.00 0.00 3.55
2656 2788 7.931015 ATTTCATATGGTAGGTCAAGGACTA 57.069 36.000 2.13 0.00 32.47 2.59
2666 2798 2.897969 GGTCAAGGACTACAGTGGAAGA 59.102 50.000 0.00 0.00 32.47 2.87
2669 2801 4.932200 GTCAAGGACTACAGTGGAAGATTG 59.068 45.833 0.00 1.54 0.00 2.67
2683 2815 4.346709 TGGAAGATTGTAGTGTCAGACCAA 59.653 41.667 0.00 0.00 0.00 3.67
2700 2832 3.690460 ACCAAGGAGTTTGATGGATGAC 58.310 45.455 0.00 0.00 39.21 3.06
2706 2838 4.229123 AGGAGTTTGATGGATGACCTGATT 59.771 41.667 0.00 0.00 37.04 2.57
2988 3120 3.118186 CCCGGAGTAAATGATACCCAACA 60.118 47.826 0.73 0.00 0.00 3.33
3198 3369 7.660617 AGTGCAATCAGATATTTATCCTCTGTG 59.339 37.037 0.00 0.00 38.05 3.66
3201 3372 9.494271 GCAATCAGATATTTATCCTCTGTGTTA 57.506 33.333 0.00 0.00 38.05 2.41
3214 3392 4.757149 CCTCTGTGTTAACTCCTTCCAAAG 59.243 45.833 7.22 0.00 0.00 2.77
3221 3399 6.262273 GTGTTAACTCCTTCCAAAGTTGATGA 59.738 38.462 7.22 0.00 36.44 2.92
3302 3480 4.003788 CCAGCCGACCGACAACCT 62.004 66.667 0.00 0.00 0.00 3.50
3305 3483 1.301479 AGCCGACCGACAACCTTTC 60.301 57.895 0.00 0.00 0.00 2.62
3306 3484 1.595929 GCCGACCGACAACCTTTCA 60.596 57.895 0.00 0.00 0.00 2.69
3307 3485 0.953960 GCCGACCGACAACCTTTCAT 60.954 55.000 0.00 0.00 0.00 2.57
3308 3486 1.519408 CCGACCGACAACCTTTCATT 58.481 50.000 0.00 0.00 0.00 2.57
3310 3488 2.350388 CCGACCGACAACCTTTCATTTG 60.350 50.000 0.00 0.00 0.00 2.32
3311 3489 2.289547 CGACCGACAACCTTTCATTTGT 59.710 45.455 0.00 0.00 38.67 2.83
3312 3490 3.606153 CGACCGACAACCTTTCATTTGTC 60.606 47.826 4.69 4.69 45.45 3.18
3313 3491 2.621526 ACCGACAACCTTTCATTTGTCC 59.378 45.455 8.48 0.00 45.93 4.02
3314 3492 2.884639 CCGACAACCTTTCATTTGTCCT 59.115 45.455 8.48 0.00 45.93 3.85
3315 3493 3.058224 CCGACAACCTTTCATTTGTCCTC 60.058 47.826 8.48 0.00 45.93 3.71
3316 3494 3.058224 CGACAACCTTTCATTTGTCCTCC 60.058 47.826 8.48 0.00 45.93 4.30
3397 3590 0.915872 ACTCCATCTGCACATCCCCA 60.916 55.000 0.00 0.00 0.00 4.96
3398 3591 0.465097 CTCCATCTGCACATCCCCAC 60.465 60.000 0.00 0.00 0.00 4.61
3399 3592 1.206811 TCCATCTGCACATCCCCACA 61.207 55.000 0.00 0.00 0.00 4.17
3402 3595 1.203052 CATCTGCACATCCCCACAAAC 59.797 52.381 0.00 0.00 0.00 2.93
3440 3634 5.464069 ACACCTTTTTAGGGGAAAGTTCAT 58.536 37.500 0.00 0.00 35.49 2.57
3607 3802 3.886123 ACCTATCGGGAAGAACAAATGG 58.114 45.455 0.00 0.00 38.76 3.16
3669 3864 4.762765 AGAGAGACCGGTGATATGATACAC 59.237 45.833 14.63 0.00 36.44 2.90
3707 3902 0.459078 GAACCCGCTACTAGTGACCC 59.541 60.000 5.39 0.00 0.00 4.46
3758 3953 0.316689 CGACAAACACCGGCAAGTTC 60.317 55.000 0.00 0.00 0.00 3.01
3884 4079 0.872021 CACGTAAGCTCGCCATCCTC 60.872 60.000 0.00 0.00 45.62 3.71
3885 4080 1.038130 ACGTAAGCTCGCCATCCTCT 61.038 55.000 0.00 0.00 45.62 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.982295 TCATGCGAAGAGAATGGTATTACG 59.018 41.667 0.00 0.00 0.00 3.18
162 192 6.753913 ATGGTCTAGCTATTCATCTTTGGA 57.246 37.500 0.00 0.00 0.00 3.53
232 262 2.028484 GACAGTTGTGGCGACGGA 59.972 61.111 0.00 0.00 0.00 4.69
285 315 1.903183 GTCTAGCTGAACCCCTCAACT 59.097 52.381 0.00 0.00 34.75 3.16
379 409 7.758528 ACAAGACATATAGAGTACCAAACGTTC 59.241 37.037 0.00 0.00 0.00 3.95
380 410 7.609056 ACAAGACATATAGAGTACCAAACGTT 58.391 34.615 0.00 0.00 0.00 3.99
419 449 7.551585 ACAAAAACATCATTCCACACTTAACA 58.448 30.769 0.00 0.00 0.00 2.41
420 450 7.096640 CGACAAAAACATCATTCCACACTTAAC 60.097 37.037 0.00 0.00 0.00 2.01
433 463 3.866327 TCTCGTTGTCGACAAAAACATCA 59.134 39.130 31.20 5.30 41.35 3.07
525 555 5.065235 TGCAGGTACCCTAAAAACAACTAC 58.935 41.667 8.74 0.00 29.64 2.73
626 668 6.647895 AGCTTACAAGAAGATGCCAAATTTTG 59.352 34.615 1.99 1.99 0.00 2.44
657 699 6.777213 TTGCTTGGTTACCAACTTTTCTTA 57.223 33.333 13.44 0.00 38.75 2.10
658 700 5.669164 TTGCTTGGTTACCAACTTTTCTT 57.331 34.783 13.44 0.00 38.75 2.52
692 734 6.478512 TTCCTAGAAACAAGTTGCCAAAAT 57.521 33.333 1.81 0.00 0.00 1.82
754 796 6.523840 AGCATGATTGGTTTAGCTTCAAAAA 58.476 32.000 0.00 0.00 0.00 1.94
755 797 6.100404 AGCATGATTGGTTTAGCTTCAAAA 57.900 33.333 0.00 0.00 0.00 2.44
756 798 5.243507 TGAGCATGATTGGTTTAGCTTCAAA 59.756 36.000 0.00 0.00 32.62 2.69
757 799 4.766373 TGAGCATGATTGGTTTAGCTTCAA 59.234 37.500 0.00 0.00 32.62 2.69
758 800 4.334552 TGAGCATGATTGGTTTAGCTTCA 58.665 39.130 0.00 0.00 32.62 3.02
759 801 4.970662 TGAGCATGATTGGTTTAGCTTC 57.029 40.909 0.00 0.00 32.62 3.86
760 802 5.927281 ATTGAGCATGATTGGTTTAGCTT 57.073 34.783 0.00 0.00 32.62 3.74
761 803 5.887598 TGTATTGAGCATGATTGGTTTAGCT 59.112 36.000 0.00 0.00 32.62 3.32
762 804 5.973565 GTGTATTGAGCATGATTGGTTTAGC 59.026 40.000 0.00 0.00 32.62 3.09
763 805 7.087409 TGTGTATTGAGCATGATTGGTTTAG 57.913 36.000 0.00 0.00 32.62 1.85
764 806 6.404623 GCTGTGTATTGAGCATGATTGGTTTA 60.405 38.462 0.00 0.00 35.15 2.01
813 855 1.743995 GTTGGGCCGTGATTAGCGT 60.744 57.895 0.00 0.00 0.00 5.07
960 1021 3.920093 GAGGGGTTTGCCAGGGTCG 62.920 68.421 0.00 0.00 36.17 4.79
961 1022 2.035783 GAGGGGTTTGCCAGGGTC 59.964 66.667 0.00 0.00 36.17 4.46
962 1023 3.966543 CGAGGGGTTTGCCAGGGT 61.967 66.667 0.00 0.00 36.17 4.34
969 1030 4.778143 CGGAGGGCGAGGGGTTTG 62.778 72.222 0.00 0.00 0.00 2.93
1038 1114 2.785258 GCGAACTCAATGTCGCCC 59.215 61.111 6.78 0.00 44.62 6.13
1249 1325 0.323629 TCTAGGGCAGAACCAAACCG 59.676 55.000 0.00 0.00 42.05 4.44
1292 1368 1.128692 GCAAGGTCACATACTCGCAAC 59.871 52.381 0.00 0.00 0.00 4.17
1473 1549 2.409378 CAGGCGCAATTAAAGCAAACAG 59.591 45.455 10.83 0.00 0.00 3.16
1492 1569 2.369983 ATTATCCACATGGCACCCAG 57.630 50.000 0.00 0.00 36.75 4.45
1496 1573 8.891671 ATTATTTTGAATTATCCACATGGCAC 57.108 30.769 0.00 0.00 34.44 5.01
1551 1630 9.985730 TTCAATCTAAATTGCCCATTATTCATC 57.014 29.630 0.00 0.00 41.76 2.92
1608 1687 5.482163 AATGTTAAATTCCCACCACCAAG 57.518 39.130 0.00 0.00 0.00 3.61
1949 2028 6.378280 CCTAACAACAGGGCATCTCTATTTTT 59.622 38.462 0.00 0.00 31.47 1.94
1950 2029 5.888161 CCTAACAACAGGGCATCTCTATTTT 59.112 40.000 0.00 0.00 31.47 1.82
1951 2030 5.440610 CCTAACAACAGGGCATCTCTATTT 58.559 41.667 0.00 0.00 31.47 1.40
1952 2031 4.687219 GCCTAACAACAGGGCATCTCTATT 60.687 45.833 0.00 0.00 44.69 1.73
1953 2032 3.181450 GCCTAACAACAGGGCATCTCTAT 60.181 47.826 0.00 0.00 44.69 1.98
1954 2033 2.170607 GCCTAACAACAGGGCATCTCTA 59.829 50.000 0.00 0.00 44.69 2.43
1955 2034 1.065126 GCCTAACAACAGGGCATCTCT 60.065 52.381 0.00 0.00 44.69 3.10
1956 2035 1.383523 GCCTAACAACAGGGCATCTC 58.616 55.000 0.00 0.00 44.69 2.75
1957 2036 3.577389 GCCTAACAACAGGGCATCT 57.423 52.632 0.00 0.00 44.69 2.90
1961 2040 3.257127 TGTAAATTGCCTAACAACAGGGC 59.743 43.478 0.00 0.00 42.27 5.19
1962 2041 4.522789 ACTGTAAATTGCCTAACAACAGGG 59.477 41.667 0.00 0.00 42.27 4.45
1963 2042 5.705609 ACTGTAAATTGCCTAACAACAGG 57.294 39.130 0.00 0.00 42.27 4.00
1964 2043 8.349983 ACTTAACTGTAAATTGCCTAACAACAG 58.650 33.333 0.00 0.00 42.27 3.16
1965 2044 8.228035 ACTTAACTGTAAATTGCCTAACAACA 57.772 30.769 0.00 0.00 42.27 3.33
2011 2090 4.890088 ACGTTGTCTGATAGGCAAAAGTA 58.110 39.130 0.00 0.00 42.02 2.24
2090 2169 4.695455 ACAAGTGACACCATCGGAATTAAG 59.305 41.667 0.84 0.00 0.00 1.85
2094 2173 2.038426 TCACAAGTGACACCATCGGAAT 59.962 45.455 0.84 0.00 34.14 3.01
2103 2182 3.733337 ACAAGAGGATCACAAGTGACAC 58.267 45.455 4.84 0.00 43.11 3.67
2137 2232 7.753309 AGTACCATTACTGAGCTATCTACAG 57.247 40.000 0.00 0.00 37.15 2.74
2159 2254 7.095187 GCTGTGTTGCAATTTAGTAACTCTAGT 60.095 37.037 0.59 0.00 35.50 2.57
2166 2261 5.010516 ACATGGCTGTGTTGCAATTTAGTAA 59.989 36.000 0.59 0.00 33.22 2.24
2176 2278 2.699954 AGTAGTACATGGCTGTGTTGC 58.300 47.619 2.52 0.00 36.79 4.17
2259 2361 7.350467 CAGCATGCATTTACTATACTCACTTG 58.650 38.462 21.98 0.00 0.00 3.16
2529 2661 6.665680 GGACTTATAGAGGCATTAGGATCTCA 59.334 42.308 0.00 0.00 33.80 3.27
2552 2684 3.523157 TGCAGATCAAGTGGATAAAGGGA 59.477 43.478 0.00 0.00 36.00 4.20
2559 2691 3.458857 AGGAAGATGCAGATCAAGTGGAT 59.541 43.478 0.00 0.00 39.53 3.41
2583 2715 8.162878 AGCATATAGAAAATCCATCACAGTTG 57.837 34.615 0.00 0.00 0.00 3.16
2588 2720 5.409520 TGCGAGCATATAGAAAATCCATCAC 59.590 40.000 0.00 0.00 0.00 3.06
2590 2722 6.486253 TTGCGAGCATATAGAAAATCCATC 57.514 37.500 0.00 0.00 0.00 3.51
2610 2742 1.135972 ACTTGCAACGTCATCGATTGC 60.136 47.619 12.60 12.60 45.00 3.56
2643 2775 3.820195 TCCACTGTAGTCCTTGACCTA 57.180 47.619 0.00 0.00 32.18 3.08
2656 2788 4.588951 TCTGACACTACAATCTTCCACTGT 59.411 41.667 0.00 0.00 0.00 3.55
2666 2798 3.904339 ACTCCTTGGTCTGACACTACAAT 59.096 43.478 10.38 0.00 0.00 2.71
2669 2801 4.058817 CAAACTCCTTGGTCTGACACTAC 58.941 47.826 10.38 0.00 0.00 2.73
2683 2815 3.184628 TCAGGTCATCCATCAAACTCCT 58.815 45.455 0.00 0.00 35.89 3.69
2700 2832 3.212685 GCCCTCATCTTCTTCAATCAGG 58.787 50.000 0.00 0.00 0.00 3.86
2706 2838 1.852633 TCTCGCCCTCATCTTCTTCA 58.147 50.000 0.00 0.00 0.00 3.02
2831 2963 0.250124 TGAGAACCAACCGCGAACAT 60.250 50.000 8.23 0.00 0.00 2.71
2988 3120 3.443329 CAGCAGATGTCCGATAGATAGCT 59.557 47.826 0.00 0.00 31.76 3.32
3139 3310 7.781324 AGACCATCAAATTTGTAAGGAACAT 57.219 32.000 23.32 6.23 38.10 2.71
3198 3369 6.877611 TCATCAACTTTGGAAGGAGTTAAC 57.122 37.500 0.00 0.00 34.52 2.01
3201 3372 5.885465 AGATCATCAACTTTGGAAGGAGTT 58.115 37.500 0.00 0.00 36.58 3.01
3240 3418 9.696917 AGACCACAAAATGTTTTCTGAAATATC 57.303 29.630 3.31 0.00 0.00 1.63
3302 3480 4.014569 TGATCACGGAGGACAAATGAAA 57.985 40.909 0.00 0.00 0.00 2.69
3305 3483 3.534554 TCATGATCACGGAGGACAAATG 58.465 45.455 0.00 0.00 0.00 2.32
3306 3484 3.801698 CTCATGATCACGGAGGACAAAT 58.198 45.455 15.32 0.00 0.00 2.32
3307 3485 2.677902 GCTCATGATCACGGAGGACAAA 60.678 50.000 21.46 0.00 0.00 2.83
3308 3486 1.134699 GCTCATGATCACGGAGGACAA 60.135 52.381 21.46 0.00 0.00 3.18
3310 3488 0.461548 TGCTCATGATCACGGAGGAC 59.538 55.000 21.46 10.73 0.00 3.85
3311 3489 1.417288 ATGCTCATGATCACGGAGGA 58.583 50.000 21.46 20.05 33.48 3.71
3312 3490 2.251409 AATGCTCATGATCACGGAGG 57.749 50.000 21.46 8.80 0.00 4.30
3313 3491 4.024556 GGTTTAATGCTCATGATCACGGAG 60.025 45.833 17.75 17.75 0.00 4.63
3314 3492 3.876914 GGTTTAATGCTCATGATCACGGA 59.123 43.478 0.42 0.00 0.00 4.69
3315 3493 3.879295 AGGTTTAATGCTCATGATCACGG 59.121 43.478 0.42 0.00 0.00 4.94
3316 3494 4.260907 CCAGGTTTAATGCTCATGATCACG 60.261 45.833 0.42 0.00 0.00 4.35
3367 3560 3.253188 TGCAGATGGAGTTTAACAGCAAC 59.747 43.478 0.00 0.00 0.00 4.17
3397 3590 8.161699 AGGTGTTATGTTATCTTTTCGTTTGT 57.838 30.769 0.00 0.00 0.00 2.83
3398 3591 9.458374 AAAGGTGTTATGTTATCTTTTCGTTTG 57.542 29.630 0.00 0.00 0.00 2.93
3440 3634 6.987992 GGGTTCGATTACATGTAAGATGGTAA 59.012 38.462 22.03 8.81 0.00 2.85
3475 3670 4.082125 CAACCTAGCCCTCTTTTTCACAT 58.918 43.478 0.00 0.00 0.00 3.21
3574 3769 2.563471 CGATAGGTATAGGCTTCGGC 57.437 55.000 0.00 0.00 40.88 5.54
3607 3802 1.237285 ATGTTGTGCTCCGGCTGTTC 61.237 55.000 0.00 0.00 39.59 3.18
3616 3811 3.709987 AGTTTTTGCTGATGTTGTGCTC 58.290 40.909 0.00 0.00 0.00 4.26
3619 3814 5.820131 TCAGTAGTTTTTGCTGATGTTGTG 58.180 37.500 0.00 0.00 42.63 3.33
3669 3864 6.090898 CGGGTTCTCTATGTAAAGTTGTGAAG 59.909 42.308 0.00 0.00 0.00 3.02
3866 4061 1.038130 AGAGGATGGCGAGCTTACGT 61.038 55.000 0.00 0.00 35.59 3.57
3940 4136 1.748493 ACTCTCTCTTGCTGATCGACC 59.252 52.381 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.