Multiple sequence alignment - TraesCS2D01G476100

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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 TraesCS2D01G476100 chr2D 100.000 4055 0 0 1 4055 578696057 578700111 0.000000e+00 7489
1 TraesCS2D01G476100 chr2A 90.521 4125 255 64 1 4022 716226954 716231045 0.000000e+00 5326
2 TraesCS2D01G476100 chr2B 91.709 3377 181 55 733 4027 695587630 695590989 0.000000e+00 4593
3 TraesCS2D01G476100 chr2B 83.900 677 64 22 1 642 695586915 695587581 4.480000e-169 604


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 TraesCS2D01G476100 chr2D 578696057 578700111 4054 False 7489.0 7489 100.0000 1 4055 1 chr2D.!!$F1 4054
1 TraesCS2D01G476100 chr2A 716226954 716231045 4091 False 5326.0 5326 90.5210 1 4022 1 chr2A.!!$F1 4021
2 TraesCS2D01G476100 chr2B 695586915 695590989 4074 False 2598.5 4593 87.8045 1 4027 2 chr2B.!!$F1 4026

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
985 1079 0.687757 CCACATCTCGGAGGGGAAGA 60.688 60.0 4.96 0.0 0.0 2.87 F
2436 2562 0.256752 TGGGAGATGTGGCATTGGAG 59.743 55.0 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 2725 0.038166 GGCTTCACACCATCCTCCAA 59.962 55.0 0.0 0.0 0.0 3.53 R
3869 4010 0.888736 TCAACAGCACATGGGTTCGG 60.889 55.0 0.0 0.0 0.0 4.30 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
120 130 9.250624 TGTATTATGTTTTTCGGTTTCCTTTTG 57.749 29.630 0.00 0.00 0.00 2.44
121 131 9.251792 GTATTATGTTTTTCGGTTTCCTTTTGT 57.748 29.630 0.00 0.00 0.00 2.83
125 136 6.889494 TGTTTTTCGGTTTCCTTTTGTTTTC 58.111 32.000 0.00 0.00 0.00 2.29
133 144 8.852135 TCGGTTTCCTTTTGTTTTCTATTATGT 58.148 29.630 0.00 0.00 0.00 2.29
278 311 4.450082 AGCCGTTCACTTTTTGTTTTCT 57.550 36.364 0.00 0.00 0.00 2.52
279 312 5.570234 AGCCGTTCACTTTTTGTTTTCTA 57.430 34.783 0.00 0.00 0.00 2.10
522 563 8.294954 AGCTACAGTAATCATACAGTAACACT 57.705 34.615 0.00 0.00 34.72 3.55
537 579 6.611381 CAGTAACACTGGGACAACAATAATG 58.389 40.000 0.00 0.00 42.35 1.90
549 591 4.156556 ACAACAATAATGGCTACAGTGCTG 59.843 41.667 0.00 0.00 0.00 4.41
563 605 1.957695 TGCTGTCGCTGCACTGAAG 60.958 57.895 0.00 0.00 33.63 3.02
658 700 0.890090 AGCGTCGTATAGGAGCTCCC 60.890 60.000 29.54 12.87 36.42 4.30
670 712 1.756561 AGCTCCCCTCGCTCTTCTC 60.757 63.158 0.00 0.00 30.49 2.87
671 713 2.055042 GCTCCCCTCGCTCTTCTCA 61.055 63.158 0.00 0.00 0.00 3.27
672 714 1.608717 GCTCCCCTCGCTCTTCTCAA 61.609 60.000 0.00 0.00 0.00 3.02
673 715 0.898320 CTCCCCTCGCTCTTCTCAAA 59.102 55.000 0.00 0.00 0.00 2.69
674 716 1.276421 CTCCCCTCGCTCTTCTCAAAA 59.724 52.381 0.00 0.00 0.00 2.44
675 717 1.276421 TCCCCTCGCTCTTCTCAAAAG 59.724 52.381 0.00 0.00 0.00 2.27
676 718 1.276421 CCCCTCGCTCTTCTCAAAAGA 59.724 52.381 0.00 0.00 0.00 2.52
731 773 3.062466 CCTCGTCCTGGCGACTGA 61.062 66.667 8.74 0.00 39.56 3.41
787 849 1.115930 ATCTCGATTAGCCCTGCCGT 61.116 55.000 0.00 0.00 0.00 5.68
813 875 2.816087 CGCCTTAATGCTAGCCATCATT 59.184 45.455 13.29 7.74 36.87 2.57
814 876 3.365666 CGCCTTAATGCTAGCCATCATTG 60.366 47.826 13.29 0.00 34.95 2.82
843 905 2.684843 CGCAACCTGAGAGCTTGGC 61.685 63.158 0.00 0.00 0.00 4.52
844 906 1.303155 GCAACCTGAGAGCTTGGCT 60.303 57.895 0.00 0.00 43.88 4.75
845 907 1.584380 GCAACCTGAGAGCTTGGCTG 61.584 60.000 0.00 0.00 39.88 4.85
846 908 1.303155 AACCTGAGAGCTTGGCTGC 60.303 57.895 0.00 0.00 39.88 5.25
933 1027 2.757314 CACATGCTCTGGTAGACTGAGA 59.243 50.000 5.58 0.00 45.14 3.27
985 1079 0.687757 CCACATCTCGGAGGGGAAGA 60.688 60.000 4.96 0.00 0.00 2.87
1326 1420 0.685097 ACCAGTTCACGTATGGCAGT 59.315 50.000 7.87 0.00 37.64 4.40
1455 1549 2.024176 TGGACATGTACCTGAGGTGT 57.976 50.000 15.83 2.78 36.19 4.16
1468 1562 2.920912 GGTGTGGGTCGGTGGAGA 60.921 66.667 0.00 0.00 0.00 3.71
1509 1603 1.964223 GCGATGGAGAGGAAGGATGTA 59.036 52.381 0.00 0.00 0.00 2.29
1611 1705 1.065854 AGAGAAGGTATGTGCTGGCAC 60.066 52.381 17.55 17.55 46.33 5.01
1613 1707 1.369091 GAAGGTATGTGCTGGCACCG 61.369 60.000 20.80 0.00 45.63 4.94
1619 1713 0.608856 ATGTGCTGGCACCGAAATCA 60.609 50.000 20.80 3.14 45.63 2.57
1624 1718 1.959042 CTGGCACCGAAATCAGCTAT 58.041 50.000 0.00 0.00 0.00 2.97
1629 1723 3.058639 GGCACCGAAATCAGCTATTCATC 60.059 47.826 0.00 0.00 0.00 2.92
1630 1724 3.812053 GCACCGAAATCAGCTATTCATCT 59.188 43.478 0.00 0.00 0.00 2.90
1631 1725 4.274459 GCACCGAAATCAGCTATTCATCTT 59.726 41.667 0.00 0.00 0.00 2.40
1632 1726 5.745514 CACCGAAATCAGCTATTCATCTTG 58.254 41.667 0.00 0.00 0.00 3.02
1633 1727 4.274459 ACCGAAATCAGCTATTCATCTTGC 59.726 41.667 0.00 0.00 0.00 4.01
1634 1728 4.514441 CCGAAATCAGCTATTCATCTTGCT 59.486 41.667 0.00 0.00 36.04 3.91
1635 1729 5.698089 CCGAAATCAGCTATTCATCTTGCTA 59.302 40.000 0.00 0.00 34.10 3.49
1661 1755 1.244019 GCCTTGAAATGTGCGGTCCT 61.244 55.000 0.00 0.00 0.00 3.85
1678 1772 3.388308 GTCCTGCTCACATACTGCTATG 58.612 50.000 0.00 0.00 36.54 2.23
1680 1774 3.320256 TCCTGCTCACATACTGCTATGAG 59.680 47.826 0.29 0.00 41.29 2.90
1701 1795 2.181975 CACCTCAAATCCATGCCCTTT 58.818 47.619 0.00 0.00 0.00 3.11
1710 1804 7.725251 TCAAATCCATGCCCTTTATTGTAATC 58.275 34.615 0.00 0.00 0.00 1.75
1728 1830 3.525268 ATCGTAGTGTGTCATGCATGA 57.475 42.857 25.42 25.42 0.00 3.07
1729 1831 3.525268 TCGTAGTGTGTCATGCATGAT 57.475 42.857 30.89 17.64 39.30 2.45
1734 1836 7.029563 TCGTAGTGTGTCATGCATGATATATC 58.970 38.462 30.89 18.34 39.30 1.63
1789 1892 5.972107 AAATTTGGGACTCTCTGAATGTG 57.028 39.130 0.00 0.00 0.00 3.21
1792 1895 5.762179 TTTGGGACTCTCTGAATGTGTAT 57.238 39.130 0.00 0.00 0.00 2.29
1820 1923 8.554835 TTTTATCATCGAAATGTACCAGACAA 57.445 30.769 0.00 0.00 42.78 3.18
1821 1924 8.554835 TTTATCATCGAAATGTACCAGACAAA 57.445 30.769 0.00 0.00 42.78 2.83
1823 1926 5.789521 TCATCGAAATGTACCAGACAAAGA 58.210 37.500 0.00 0.00 42.78 2.52
1845 1948 9.840427 AAAGATAACCAAAATTGTTACTCATCG 57.160 29.630 0.00 0.00 0.00 3.84
1849 1952 4.518970 ACCAAAATTGTTACTCATCGCTGT 59.481 37.500 0.00 0.00 0.00 4.40
1850 1953 5.009610 ACCAAAATTGTTACTCATCGCTGTT 59.990 36.000 0.00 0.00 0.00 3.16
1881 1984 9.128107 CGTTGACATAAAATTAGCACTTTCAAT 57.872 29.630 0.00 0.00 0.00 2.57
1914 2037 4.505191 CCACTGTTCAATTTCTGCTTGTTG 59.495 41.667 0.00 0.00 0.00 3.33
1925 2048 9.786105 CAATTTCTGCTTGTTGGTTTAAATTTT 57.214 25.926 0.00 0.00 0.00 1.82
1926 2049 9.786105 AATTTCTGCTTGTTGGTTTAAATTTTG 57.214 25.926 0.00 0.00 0.00 2.44
2016 2142 0.524862 CAGAAATGCTGCCTGACCAC 59.475 55.000 0.00 0.00 37.90 4.16
2077 2203 1.269621 GTGTGCTCACTAACACGGAGT 60.270 52.381 11.58 0.00 41.11 3.85
2088 2214 1.878953 ACACGGAGTTGATTCACACC 58.121 50.000 0.00 0.00 41.61 4.16
2091 2217 1.416401 ACGGAGTTGATTCACACCTGT 59.584 47.619 0.00 0.00 37.78 4.00
2205 2331 8.628280 CGAGTGATATATGACTCCATATGTGAT 58.372 37.037 21.96 0.00 43.70 3.06
2263 2389 6.777091 TGGGTACTCCATGGATAAAAATCATG 59.223 38.462 16.63 1.50 41.46 3.07
2274 2400 5.628193 GGATAAAAATCATGCTGAAGATGCG 59.372 40.000 0.00 0.00 0.00 4.73
2424 2550 2.235402 CAAAAAGCAGCCAATGGGAGAT 59.765 45.455 0.00 0.00 35.59 2.75
2436 2562 0.256752 TGGGAGATGTGGCATTGGAG 59.743 55.000 0.00 0.00 0.00 3.86
2463 2589 6.761242 ACGCTCTAGTTGATATGTATGCAAAA 59.239 34.615 0.00 0.00 0.00 2.44
2469 2595 5.887598 AGTTGATATGTATGCAAAAGCAGGA 59.112 36.000 0.00 0.00 0.00 3.86
2599 2725 3.181440 TGTGAGCCTTTTTGAGAGGATGT 60.181 43.478 0.00 0.00 36.33 3.06
2625 2751 0.951558 ATGGTGTGAAGCCAAACGAC 59.048 50.000 0.00 0.00 39.72 4.34
2672 2798 2.839486 TGTGGTCATTCTGGTCTGAC 57.161 50.000 0.00 0.00 40.82 3.51
2673 2799 2.046292 TGTGGTCATTCTGGTCTGACA 58.954 47.619 10.38 0.00 42.83 3.58
2741 2867 4.492494 TTGATCCAAGAGCTGAGCATTA 57.508 40.909 7.39 0.00 0.00 1.90
2772 2898 2.747686 GACCTTCTTGGCCGTGGA 59.252 61.111 0.00 0.00 40.22 4.02
2803 2929 1.432270 GGATGCGTGGAAGCTAGTGC 61.432 60.000 0.00 0.00 38.13 4.40
2908 3034 3.893813 AGAAACTGCAGCCAAGAATCTTT 59.106 39.130 15.27 3.03 0.00 2.52
3018 3144 6.670695 ACAAGGAAATTAATGGCTGAAACT 57.329 33.333 0.00 0.00 0.00 2.66
3048 3174 0.536006 AGGAAGCTGGTTGCAGTGTC 60.536 55.000 13.45 0.00 45.94 3.67
3059 3185 2.999355 GTTGCAGTGTCCTCTGAAGATC 59.001 50.000 0.78 0.00 37.61 2.75
3061 3187 2.634453 TGCAGTGTCCTCTGAAGATCAA 59.366 45.455 0.00 0.00 37.61 2.57
3123 3249 3.548745 TTGTCCTGATAGATGCACCAG 57.451 47.619 0.00 0.00 0.00 4.00
3192 3319 1.555075 TCCAACATGTAGAGCCTCCAC 59.445 52.381 0.00 0.00 0.00 4.02
3203 3330 3.944087 AGAGCCTCCACATCTTTGTAAC 58.056 45.455 0.00 0.00 33.76 2.50
3219 3346 5.733620 TTGTAACCTCTAACCGACTTCAT 57.266 39.130 0.00 0.00 0.00 2.57
3226 3353 6.807789 ACCTCTAACCGACTTCATAATCTTC 58.192 40.000 0.00 0.00 0.00 2.87
3230 3357 3.112263 ACCGACTTCATAATCTTCCCCA 58.888 45.455 0.00 0.00 0.00 4.96
3249 3376 4.337555 CCCCATTTGATTAAGCAGTGAGAG 59.662 45.833 9.05 0.39 0.00 3.20
3279 3406 3.630769 ACTTATCAGCAGCCATCATGTTG 59.369 43.478 0.00 0.00 0.00 3.33
3340 3475 9.744468 AACTTTTGTATAGTTGTTCATTTGGAC 57.256 29.630 0.00 0.00 34.68 4.02
3342 3477 9.180678 CTTTTGTATAGTTGTTCATTTGGACAC 57.819 33.333 0.00 0.00 0.00 3.67
3353 3488 1.327303 TTTGGACACATCTGTTGGGC 58.673 50.000 0.00 0.00 28.72 5.36
3358 3493 2.076863 GACACATCTGTTGGGCTACAC 58.923 52.381 0.00 0.00 28.72 2.90
3428 3563 3.251729 GCGGATGCATGTTTGACTCATAT 59.748 43.478 2.46 0.00 42.15 1.78
3457 3592 6.358974 TGTCAGTATTCTCAATTCTGTCCA 57.641 37.500 3.64 0.86 37.50 4.02
3458 3593 6.768483 TGTCAGTATTCTCAATTCTGTCCAA 58.232 36.000 3.64 0.00 37.50 3.53
3460 3595 7.884877 TGTCAGTATTCTCAATTCTGTCCAATT 59.115 33.333 3.64 0.00 37.50 2.32
3494 3629 6.592994 GGACAGTTACAGGTTTATGGTCTTAC 59.407 42.308 0.00 0.00 0.00 2.34
3524 3662 2.936919 ACTCCAACTTGTCTGCATCA 57.063 45.000 0.00 0.00 0.00 3.07
3525 3663 3.213206 ACTCCAACTTGTCTGCATCAA 57.787 42.857 0.00 0.00 0.00 2.57
3526 3664 3.759581 ACTCCAACTTGTCTGCATCAAT 58.240 40.909 5.21 0.00 0.00 2.57
3602 3741 7.914427 TTCCCTTCTGTACATGACTATATGT 57.086 36.000 0.00 0.00 43.34 2.29
3622 3761 3.181453 TGTCGATACCCTGTTTTTCCACA 60.181 43.478 0.00 0.00 0.00 4.17
3631 3770 3.432252 CCTGTTTTTCCACACTACGCTAG 59.568 47.826 0.00 0.00 0.00 3.42
3655 3794 5.127682 GCCATTTCTCTTTTGATGTGGGTAT 59.872 40.000 0.00 0.00 0.00 2.73
3746 3886 4.455533 TGTTGAATCTGACAGTGCCAATAC 59.544 41.667 1.59 0.00 0.00 1.89
3777 3917 5.372343 TGATCTATTGCATACCCTGTGTT 57.628 39.130 0.00 0.00 0.00 3.32
3840 3980 0.249280 CCAAAAGCCACCACGTTTCC 60.249 55.000 0.00 0.00 0.00 3.13
3912 4053 7.596995 TGACTTAAGTTTTGTTTGTTGAGTTGG 59.403 33.333 10.02 0.00 0.00 3.77
3926 4067 8.441312 TTGTTGAGTTGGTTTACCTAGTAAAG 57.559 34.615 0.30 0.00 38.44 1.85
4042 4183 7.997107 TTTTCAGTACTGTAGCATAATACGG 57.003 36.000 21.99 0.00 37.92 4.02
4043 4184 6.704289 TTCAGTACTGTAGCATAATACGGT 57.296 37.500 21.99 4.01 45.18 4.83
4044 4185 6.704289 TCAGTACTGTAGCATAATACGGTT 57.296 37.500 21.99 0.00 41.46 4.44
4045 4186 7.806409 TCAGTACTGTAGCATAATACGGTTA 57.194 36.000 21.99 0.00 41.46 2.85
4046 4187 8.400184 TCAGTACTGTAGCATAATACGGTTAT 57.600 34.615 21.99 0.00 41.46 1.89
4047 4188 8.853126 TCAGTACTGTAGCATAATACGGTTATT 58.147 33.333 21.99 0.00 41.46 1.40
4048 4189 9.125906 CAGTACTGTAGCATAATACGGTTATTC 57.874 37.037 15.06 0.00 41.46 1.75
4049 4190 9.075678 AGTACTGTAGCATAATACGGTTATTCT 57.924 33.333 0.00 0.00 41.46 2.40
4050 4191 9.688592 GTACTGTAGCATAATACGGTTATTCTT 57.311 33.333 3.87 0.00 41.46 2.52
4051 4192 8.813643 ACTGTAGCATAATACGGTTATTCTTC 57.186 34.615 0.00 0.00 41.46 2.87
4052 4193 8.639761 ACTGTAGCATAATACGGTTATTCTTCT 58.360 33.333 0.00 0.00 41.46 2.85
4053 4194 9.477484 CTGTAGCATAATACGGTTATTCTTCTT 57.523 33.333 0.00 0.00 0.00 2.52
4054 4195 9.826574 TGTAGCATAATACGGTTATTCTTCTTT 57.173 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 105 9.251792 ACAAAAGGAAACCGAAAAACATAATAC 57.748 29.630 0.00 0.00 0.00 1.89
101 111 6.706716 AGAAAACAAAAGGAAACCGAAAAACA 59.293 30.769 0.00 0.00 0.00 2.83
455 493 8.558973 TTCAAGTTTGTGAACATTTTTGGAAT 57.441 26.923 0.00 0.00 38.26 3.01
490 531 8.260818 ACTGTATGATTACTGTAGCTTCACAAT 58.739 33.333 0.00 0.00 38.34 2.71
494 535 8.745590 TGTTACTGTATGATTACTGTAGCTTCA 58.254 33.333 0.00 0.00 41.14 3.02
522 563 4.263727 ACTGTAGCCATTATTGTTGTCCCA 60.264 41.667 0.00 0.00 0.00 4.37
549 591 0.734253 ACGATCTTCAGTGCAGCGAC 60.734 55.000 0.00 0.00 0.00 5.19
563 605 6.145534 TCAAACAATCACTGACTGTAACGATC 59.854 38.462 0.00 0.00 0.00 3.69
624 666 3.111038 GCTTATTGCGTCCAGGGC 58.889 61.111 0.00 0.00 0.00 5.19
645 687 0.251430 AGCGAGGGGAGCTCCTATAC 60.251 60.000 31.36 18.72 41.83 1.47
658 700 5.424121 TTTTTCTTTTGAGAAGAGCGAGG 57.576 39.130 0.00 0.00 0.00 4.63
762 824 0.037232 GGGCTAATCGAGATTCCGGG 60.037 60.000 0.00 0.00 32.50 5.73
787 849 1.270839 GGCTAGCATTAAGGCGATGGA 60.271 52.381 18.24 0.00 39.27 3.41
813 875 2.115911 GGTTGCGGTGTTGGTGTCA 61.116 57.895 0.00 0.00 0.00 3.58
814 876 1.822186 AGGTTGCGGTGTTGGTGTC 60.822 57.895 0.00 0.00 0.00 3.67
845 907 2.908940 CCGATCCCATGCCCAAGC 60.909 66.667 0.00 0.00 40.48 4.01
846 908 1.228063 CTCCGATCCCATGCCCAAG 60.228 63.158 0.00 0.00 0.00 3.61
847 909 2.918248 CTCCGATCCCATGCCCAA 59.082 61.111 0.00 0.00 0.00 4.12
933 1027 0.261991 TGCCTCCGGACTAGGAAGAT 59.738 55.000 12.29 0.00 40.25 2.40
1304 1398 1.070914 TGCCATACGTGAACTGGTTCA 59.929 47.619 11.53 11.53 46.27 3.18
1455 1549 2.668632 GCATTCTCCACCGACCCA 59.331 61.111 0.00 0.00 0.00 4.51
1468 1562 1.802636 CAAACATCCGCCTCGCATT 59.197 52.632 0.00 0.00 0.00 3.56
1509 1603 0.598065 GCAAGGCATTCCACGAAACT 59.402 50.000 0.00 0.00 33.74 2.66
1611 1705 4.514441 AGCAAGATGAATAGCTGATTTCGG 59.486 41.667 0.00 0.00 35.72 4.30
1613 1707 7.022384 GCATAGCAAGATGAATAGCTGATTTC 58.978 38.462 0.00 0.00 37.94 2.17
1619 1713 4.755629 CAGTGCATAGCAAGATGAATAGCT 59.244 41.667 0.00 0.00 41.47 3.32
1624 1718 2.019249 GGCAGTGCATAGCAAGATGAA 58.981 47.619 18.61 0.00 41.47 2.57
1629 1723 1.456296 TCAAGGCAGTGCATAGCAAG 58.544 50.000 18.61 0.00 41.47 4.01
1630 1724 1.908344 TTCAAGGCAGTGCATAGCAA 58.092 45.000 18.61 0.48 41.47 3.91
1631 1725 1.908344 TTTCAAGGCAGTGCATAGCA 58.092 45.000 18.61 0.00 35.60 3.49
1632 1726 2.165030 ACATTTCAAGGCAGTGCATAGC 59.835 45.455 18.61 4.89 0.00 2.97
1633 1727 3.766151 CACATTTCAAGGCAGTGCATAG 58.234 45.455 18.61 5.50 0.00 2.23
1634 1728 3.853831 CACATTTCAAGGCAGTGCATA 57.146 42.857 18.61 0.00 0.00 3.14
1635 1729 2.736144 CACATTTCAAGGCAGTGCAT 57.264 45.000 18.61 7.05 0.00 3.96
1678 1772 0.743097 GGCATGGATTTGAGGTGCTC 59.257 55.000 0.00 0.00 36.15 4.26
1680 1774 0.685458 AGGGCATGGATTTGAGGTGC 60.685 55.000 0.00 0.00 35.17 5.01
1701 1795 6.334202 TGCATGACACACTACGATTACAATA 58.666 36.000 0.00 0.00 0.00 1.90
1710 1804 7.008992 CAGATATATCATGCATGACACACTACG 59.991 40.741 30.92 12.75 40.03 3.51
1766 1869 6.542821 ACACATTCAGAGAGTCCCAAATTTA 58.457 36.000 0.00 0.00 0.00 1.40
1799 1902 6.406370 TCTTTGTCTGGTACATTTCGATGAT 58.594 36.000 0.00 0.00 38.10 2.45
1804 1907 6.370442 TGGTTATCTTTGTCTGGTACATTTCG 59.630 38.462 0.00 0.00 38.10 3.46
1820 1923 7.968405 GCGATGAGTAACAATTTTGGTTATCTT 59.032 33.333 0.00 0.00 33.68 2.40
1821 1924 7.336931 AGCGATGAGTAACAATTTTGGTTATCT 59.663 33.333 0.00 0.00 33.68 1.98
1823 1926 7.094377 ACAGCGATGAGTAACAATTTTGGTTAT 60.094 33.333 8.12 0.00 33.68 1.89
1845 1948 7.617533 AATTTTATGTCAACGTTACAACAGC 57.382 32.000 0.00 0.00 0.00 4.40
1849 1952 8.561212 AGTGCTAATTTTATGTCAACGTTACAA 58.439 29.630 0.00 0.00 0.00 2.41
1850 1953 8.090250 AGTGCTAATTTTATGTCAACGTTACA 57.910 30.769 0.00 6.76 0.00 2.41
1881 1984 7.973388 CAGAAATTGAACAGTGGACAAAAGTTA 59.027 33.333 7.99 0.00 0.00 2.24
1882 1985 6.813152 CAGAAATTGAACAGTGGACAAAAGTT 59.187 34.615 7.99 0.00 0.00 2.66
1884 1987 5.232838 GCAGAAATTGAACAGTGGACAAAAG 59.767 40.000 7.99 0.75 0.00 2.27
1886 1989 4.402155 AGCAGAAATTGAACAGTGGACAAA 59.598 37.500 7.99 0.00 0.00 2.83
1887 1990 3.953612 AGCAGAAATTGAACAGTGGACAA 59.046 39.130 6.69 6.69 0.00 3.18
1888 1991 3.554934 AGCAGAAATTGAACAGTGGACA 58.445 40.909 0.00 0.00 0.00 4.02
1889 1992 4.202050 ACAAGCAGAAATTGAACAGTGGAC 60.202 41.667 0.00 0.00 0.00 4.02
2016 2142 5.947228 TTAGAGCACTTCCAAATGTGAAG 57.053 39.130 0.00 8.94 43.82 3.02
2088 2214 6.710744 CCCAGTAGCCCAACTTTATTATACAG 59.289 42.308 0.00 0.00 0.00 2.74
2091 2217 5.673113 ACCCCAGTAGCCCAACTTTATTATA 59.327 40.000 0.00 0.00 0.00 0.98
2220 2346 1.068281 CCACTGATCAGCGCAGTAGAT 59.932 52.381 22.83 7.31 44.28 1.98
2263 2389 0.532417 AGCTCCATCGCATCTTCAGC 60.532 55.000 0.00 0.00 0.00 4.26
2274 2400 2.687700 TCTTGCAGAAGAGCTCCATC 57.312 50.000 10.93 9.61 32.98 3.51
2424 2550 0.955428 GAGCGTTCTCCAATGCCACA 60.955 55.000 0.00 0.00 44.59 4.17
2436 2562 5.920840 TGCATACATATCAACTAGAGCGTTC 59.079 40.000 0.00 0.00 0.00 3.95
2463 2589 3.022406 GGCATCTGAAAATTCTCCTGCT 58.978 45.455 11.35 0.00 0.00 4.24
2469 2595 1.747355 CGCCTGGCATCTGAAAATTCT 59.253 47.619 20.29 0.00 0.00 2.40
2599 2725 0.038166 GGCTTCACACCATCCTCCAA 59.962 55.000 0.00 0.00 0.00 3.53
2625 2751 4.310769 ACAGAAGAGAAAGGAATGTCACG 58.689 43.478 0.00 0.00 0.00 4.35
2672 2798 4.706476 TGAAATACTCCATCCCTTTGCTTG 59.294 41.667 0.00 0.00 0.00 4.01
2673 2799 4.706962 GTGAAATACTCCATCCCTTTGCTT 59.293 41.667 0.00 0.00 0.00 3.91
2741 2867 3.093057 AGAAGGTCGATAGCAGAACTGT 58.907 45.455 3.77 0.00 35.56 3.55
2772 2898 1.478510 CACGCATCCTCTAACTGACCT 59.521 52.381 0.00 0.00 0.00 3.85
2803 2929 4.220693 TGGGTTCAGTATCCACATTCTG 57.779 45.455 0.00 0.00 0.00 3.02
2880 3006 0.183492 TGGCTGCAGTTTCTCCAAGT 59.817 50.000 16.64 0.00 0.00 3.16
2908 3034 4.345257 AGAACTCTCAGCACCTTTACTGAA 59.655 41.667 0.00 0.00 42.12 3.02
3018 3144 0.538057 CAGCTTCCTTGCCACCAGAA 60.538 55.000 0.00 0.00 0.00 3.02
3123 3249 5.163612 GGTCTGAGGGTAATTCAAAAGCATC 60.164 44.000 0.00 0.00 0.00 3.91
3128 3254 6.133356 ACAAAGGTCTGAGGGTAATTCAAAA 58.867 36.000 0.00 0.00 0.00 2.44
3130 3256 5.313712 GACAAAGGTCTGAGGGTAATTCAA 58.686 41.667 0.00 0.00 40.99 2.69
3133 3259 3.655777 TGGACAAAGGTCTGAGGGTAATT 59.344 43.478 0.00 0.00 43.77 1.40
3192 3319 5.721232 AGTCGGTTAGAGGTTACAAAGATG 58.279 41.667 0.00 0.00 0.00 2.90
3203 3330 6.217294 GGAAGATTATGAAGTCGGTTAGAGG 58.783 44.000 0.00 0.00 0.00 3.69
3219 3346 7.068593 CACTGCTTAATCAAATGGGGAAGATTA 59.931 37.037 0.00 0.00 33.22 1.75
3226 3353 4.272489 TCTCACTGCTTAATCAAATGGGG 58.728 43.478 0.00 0.00 0.00 4.96
3230 3357 9.107177 CATTAGACTCTCACTGCTTAATCAAAT 57.893 33.333 0.00 0.00 0.00 2.32
3249 3376 4.697514 TGGCTGCTGATAAGTCATTAGAC 58.302 43.478 0.00 0.00 45.31 2.59
3279 3406 2.200373 ATGTGCACTTACCCTGAACC 57.800 50.000 19.41 0.00 0.00 3.62
3340 3475 2.350522 GAGTGTAGCCCAACAGATGTG 58.649 52.381 0.00 0.00 0.00 3.21
3342 3477 1.407437 GGGAGTGTAGCCCAACAGATG 60.407 57.143 0.00 0.00 45.31 2.90
3390 3525 4.085107 GCATCCGCAAAACTTTTACAGTTG 60.085 41.667 0.00 0.00 40.78 3.16
3428 3563 8.807118 ACAGAATTGAGAATACTGACAAGACTA 58.193 33.333 0.00 0.00 33.53 2.59
3457 3592 8.650143 ACCTGTAACTGTCCAATCAATAAATT 57.350 30.769 0.00 0.00 0.00 1.82
3458 3593 8.650143 AACCTGTAACTGTCCAATCAATAAAT 57.350 30.769 0.00 0.00 0.00 1.40
3460 3595 9.747898 ATAAACCTGTAACTGTCCAATCAATAA 57.252 29.630 0.00 0.00 0.00 1.40
3476 3611 7.563724 AAAGGAGTAAGACCATAAACCTGTA 57.436 36.000 0.00 0.00 0.00 2.74
3505 3640 2.936919 TGATGCAGACAAGTTGGAGT 57.063 45.000 7.96 0.00 0.00 3.85
3506 3641 4.216902 TCAATTGATGCAGACAAGTTGGAG 59.783 41.667 3.38 0.00 0.00 3.86
3512 3650 7.741027 ATAGGTATCAATTGATGCAGACAAG 57.259 36.000 29.86 3.37 38.64 3.16
3550 3688 6.323739 ACAAACTGGTTTATCCACTGATGTTT 59.676 34.615 0.00 0.00 41.93 2.83
3602 3741 3.071892 AGTGTGGAAAAACAGGGTATCGA 59.928 43.478 0.00 0.00 0.00 3.59
3622 3761 4.473477 AAAGAGAAATGGCTAGCGTAGT 57.527 40.909 9.00 0.00 0.00 2.73
3631 3770 3.259123 ACCCACATCAAAAGAGAAATGGC 59.741 43.478 0.00 0.00 0.00 4.40
3746 3886 2.589720 TGCAATAGATCAAGGCCATGG 58.410 47.619 7.63 7.63 0.00 3.66
3777 3917 0.969149 ATCTGCTTCACTCGACACCA 59.031 50.000 0.00 0.00 0.00 4.17
3840 3980 8.982685 ACATATTCAATTATTCACTGAGTAGCG 58.017 33.333 0.00 0.00 0.00 4.26
3869 4010 0.888736 TCAACAGCACATGGGTTCGG 60.889 55.000 0.00 0.00 0.00 4.30
4027 4168 9.477484 AAGAAGAATAACCGTATTATGCTACAG 57.523 33.333 0.00 0.00 27.16 2.74
4028 4169 9.826574 AAAGAAGAATAACCGTATTATGCTACA 57.173 29.630 0.00 0.00 27.16 2.74


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

AutoCloner maintained by Alex Coulton.