Multiple sequence alignment - TraesCS4A01G031100

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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 TraesCS4A01G031100 chr4A 100.000 5748 0 0 1 5748 24222946 24228693 0.000000e+00 10615.0
1 TraesCS4A01G031100 chr4B 92.772 5811 290 50 1 5735 552834488 552828732 0.000000e+00 8285.0
2 TraesCS4A01G031100 chr4D 93.517 5383 231 44 406 5735 443514564 443509247 0.000000e+00 7899.0
3 TraesCS4A01G031100 chr4D 90.000 200 19 1 1 199 443515770 443515571 2.050000e-64 257.0
4 TraesCS4A01G031100 chr6B 91.489 47 3 1 2654 2699 184363823 184363777 4.810000e-06 63.9


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 TraesCS4A01G031100 chr4A 24222946 24228693 5747 False 10615 10615 100.0000 1 5748 1 chr4A.!!$F1 5747
1 TraesCS4A01G031100 chr4B 552828732 552834488 5756 True 8285 8285 92.7720 1 5735 1 chr4B.!!$R1 5734
2 TraesCS4A01G031100 chr4D 443509247 443515770 6523 True 4078 7899 91.7585 1 5735 2 chr4D.!!$R1 5734

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
203 205 0.320421 GCACGCAGTCCTTAAGTGGA 60.320 55.000 0.97 0.0 41.61 4.02 F
1220 2031 0.179004 TGGGCCACAACAACGATCTT 60.179 50.000 0.00 0.0 0.00 2.40 F
1240 2051 0.962489 AGTCCTTCTCTGACCACACG 59.038 55.000 0.00 0.0 33.09 4.49 F
1914 2735 1.065491 TGACAAGGAACCCCATGATCG 60.065 52.381 0.00 0.0 34.88 3.69 F
3629 4451 0.322098 CAATCAACCACCTACCGCCA 60.322 55.000 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 2033 0.038159 CCGTGTGGTCAGAGAAGGAC 60.038 60.0 0.00 0.0 34.52 3.85 R
2125 2946 1.123077 TATAGGACAGTGCAGCAGGG 58.877 55.0 0.00 0.0 0.00 4.45 R
3146 3967 1.454572 GCATGCACCACAGTCCACAA 61.455 55.0 14.21 0.0 0.00 3.33 R
3838 4660 0.109086 AAGCTCAGGTGATCGTGTCG 60.109 55.0 0.00 0.0 0.00 4.35 R
4948 5785 0.592637 TCAAACGTTGAGCCTGCATG 59.407 50.0 0.00 0.0 34.08 4.06 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
53 54 5.359576 TGCTTAAGAACAAGTGGTTGAATGT 59.640 36.000 6.67 0.00 40.63 2.71
55 56 6.856426 GCTTAAGAACAAGTGGTTGAATGTAC 59.144 38.462 6.67 0.00 40.63 2.90
56 57 7.468084 GCTTAAGAACAAGTGGTTGAATGTACA 60.468 37.037 6.67 0.00 40.63 2.90
75 76 0.541863 ATAAAGTGGAGCGTGAGGGG 59.458 55.000 0.00 0.00 0.00 4.79
203 205 0.320421 GCACGCAGTCCTTAAGTGGA 60.320 55.000 0.97 0.00 41.61 4.02
225 227 5.278957 GGAAACATGTGCAGTAAACTCCAAT 60.279 40.000 0.00 0.00 0.00 3.16
261 263 8.920665 CACTATGTTTATCATTTTTCGGCAAAA 58.079 29.630 0.00 0.00 38.76 2.44
331 378 4.649088 AAAGGTTTCTGGTTTTTCCTCG 57.351 40.909 0.00 0.00 37.07 4.63
334 381 1.679153 GTTTCTGGTTTTTCCTCGGCA 59.321 47.619 0.00 0.00 37.07 5.69
335 382 2.060050 TTCTGGTTTTTCCTCGGCAA 57.940 45.000 0.00 0.00 37.07 4.52
498 1300 3.860754 GCACTTGCCTATTTGGTTGAACC 60.861 47.826 7.57 7.57 38.35 3.62
516 1318 8.537858 GGTTGAACCCTAGAACTTAGATCTTAA 58.462 37.037 2.08 0.00 30.04 1.85
603 1405 5.693814 GCATGTTAAATATGCCTGTAGCTC 58.306 41.667 12.62 0.00 43.88 4.09
636 1438 3.306088 CGTTGCCTCTTCTGTCTAGGAAA 60.306 47.826 0.00 0.00 31.64 3.13
640 1442 5.978814 TGCCTCTTCTGTCTAGGAAATAAC 58.021 41.667 0.00 0.00 31.64 1.89
651 1456 8.319143 TGTCTAGGAAATAACAAAACACTAGC 57.681 34.615 0.00 0.00 0.00 3.42
663 1468 7.369803 ACAAAACACTAGCACAGATGATTAG 57.630 36.000 0.00 0.00 0.00 1.73
664 1469 7.161404 ACAAAACACTAGCACAGATGATTAGA 58.839 34.615 0.00 0.00 0.00 2.10
675 1480 2.128035 GATGATTAGAACACGAGGGCG 58.872 52.381 0.00 0.00 44.79 6.13
681 1486 3.358076 GAACACGAGGGCGAGAGGG 62.358 68.421 0.00 0.00 41.64 4.30
735 1540 2.451490 TCCTGTACTCTCTTCAGCAGG 58.549 52.381 0.00 0.00 43.37 4.85
741 1546 2.452505 ACTCTCTTCAGCAGGTAGACC 58.547 52.381 0.00 0.00 0.00 3.85
762 1567 3.005578 CCCTGTACTTAACTCGATAGGCC 59.994 52.174 0.00 0.00 0.00 5.19
815 1620 4.623932 TCACTAGATGAACAAGGCAAGT 57.376 40.909 0.00 0.00 33.02 3.16
839 1644 1.358051 ATGATGCAGCCATGGAGGGA 61.358 55.000 18.40 7.96 38.09 4.20
857 1662 1.490490 GGATGTCCTGGCCATTGTAGA 59.510 52.381 5.51 0.00 0.00 2.59
861 1666 2.575735 TGTCCTGGCCATTGTAGATTCA 59.424 45.455 5.51 0.00 0.00 2.57
865 1670 3.763360 CCTGGCCATTGTAGATTCACAAA 59.237 43.478 5.51 0.00 41.50 2.83
875 1680 6.545504 TGTAGATTCACAAAGCTTGTCTTC 57.454 37.500 0.00 0.00 43.23 2.87
887 1692 3.140325 CTTGTCTTCCAAGCACCCTAA 57.860 47.619 0.00 0.00 43.84 2.69
949 1754 3.437049 GTGTCCTTTTGTCTGTCTATGGC 59.563 47.826 0.00 0.00 0.00 4.40
962 1773 9.274206 TGTCTGTCTATGGCGTCTATATATATC 57.726 37.037 0.00 0.00 0.00 1.63
965 1776 8.850007 TGTCTATGGCGTCTATATATATCTCC 57.150 38.462 0.00 0.00 0.00 3.71
1024 1835 0.870393 TGCTTTTCTGCTTCTGCTCG 59.130 50.000 0.00 0.00 40.48 5.03
1035 1846 1.801178 CTTCTGCTCGTTGTTTCCTCC 59.199 52.381 0.00 0.00 0.00 4.30
1071 1882 1.896220 TTGATCCTGTTCAGTGCACC 58.104 50.000 14.63 0.00 0.00 5.01
1072 1883 0.764271 TGATCCTGTTCAGTGCACCA 59.236 50.000 14.63 3.00 0.00 4.17
1077 1888 0.816825 CTGTTCAGTGCACCACAGCT 60.817 55.000 21.85 0.00 36.74 4.24
1080 1891 0.181114 TTCAGTGCACCACAGCTTCT 59.819 50.000 14.63 0.00 36.74 2.85
1108 1919 3.068024 ACATGTAGTGGTTTTTGTGCAGG 59.932 43.478 0.00 0.00 0.00 4.85
1114 1925 3.260632 AGTGGTTTTTGTGCAGGTTTTCT 59.739 39.130 0.00 0.00 0.00 2.52
1115 1926 4.000325 GTGGTTTTTGTGCAGGTTTTCTT 59.000 39.130 0.00 0.00 0.00 2.52
1121 1932 5.596836 TTTGTGCAGGTTTTCTTTCATCT 57.403 34.783 0.00 0.00 0.00 2.90
1127 1938 8.203485 TGTGCAGGTTTTCTTTCATCTTTTTAT 58.797 29.630 0.00 0.00 0.00 1.40
1152 1963 4.756642 TGTTTGTCAGATCAGATGTTCACC 59.243 41.667 0.00 0.00 0.00 4.02
1216 2027 0.180642 TACTTGGGCCACAACAACGA 59.819 50.000 5.23 0.00 34.76 3.85
1220 2031 0.179004 TGGGCCACAACAACGATCTT 60.179 50.000 0.00 0.00 0.00 2.40
1222 2033 1.737793 GGGCCACAACAACGATCTTAG 59.262 52.381 4.39 0.00 0.00 2.18
1229 2040 5.230942 CACAACAACGATCTTAGTCCTTCT 58.769 41.667 0.00 0.00 0.00 2.85
1240 2051 0.962489 AGTCCTTCTCTGACCACACG 59.038 55.000 0.00 0.00 33.09 4.49
1264 2075 5.278022 GGTTTCATCTCCAACTTCTGTCAAC 60.278 44.000 0.00 0.00 0.00 3.18
1265 2076 4.963318 TCATCTCCAACTTCTGTCAACT 57.037 40.909 0.00 0.00 0.00 3.16
1386 2200 1.930908 GCAGAAGCACAGCACCATCC 61.931 60.000 0.00 0.00 41.58 3.51
1410 2224 8.789762 TCCAATGCATCTATAACATGAATTCAG 58.210 33.333 14.54 8.57 28.22 3.02
1571 2385 5.864418 ATCCAATCTGTATTGCATGCTTT 57.136 34.783 20.33 8.70 41.06 3.51
1599 2413 4.525912 AGCAATCCAACCATTTTGTCTC 57.474 40.909 0.00 0.00 0.00 3.36
1601 2415 4.590222 AGCAATCCAACCATTTTGTCTCTT 59.410 37.500 0.00 0.00 0.00 2.85
1622 2436 7.707035 TCTCTTAAAGATAAAACCTCGCATCTC 59.293 37.037 0.00 0.00 0.00 2.75
1687 2506 5.593909 TGTGGCTAAAAGGATACATGAATGG 59.406 40.000 0.00 0.00 41.41 3.16
1729 2548 4.512484 AGGAAGCAAGACAAGCTATTCTC 58.488 43.478 0.00 0.00 42.53 2.87
1732 2551 5.522097 GGAAGCAAGACAAGCTATTCTCTAC 59.478 44.000 0.00 0.00 42.53 2.59
1820 2639 5.477984 TCGGGTAACAGTTATACTCAACACT 59.522 40.000 0.00 0.00 39.74 3.55
1841 2662 2.765689 TGGTCCCTGTTGTCCAAAAT 57.234 45.000 0.00 0.00 0.00 1.82
1914 2735 1.065491 TGACAAGGAACCCCATGATCG 60.065 52.381 0.00 0.00 34.88 3.69
1934 2755 8.131455 TGATCGTTATATTCAGAAACAGAAGC 57.869 34.615 0.00 0.00 0.00 3.86
2119 2940 5.964477 TGTCCTCTAACTATTTCACATCCCT 59.036 40.000 0.00 0.00 0.00 4.20
2125 2946 5.391312 AACTATTTCACATCCCTGCAAAC 57.609 39.130 0.00 0.00 0.00 2.93
2142 2963 1.127567 AACCCTGCTGCACTGTCCTA 61.128 55.000 0.00 0.00 0.00 2.94
2286 3107 8.324163 ACAACCATGAAAGTGAAAGATACTAC 57.676 34.615 0.00 0.00 0.00 2.73
2418 3239 1.267806 CATTTCAGTGTGTGTCTGCCC 59.732 52.381 0.00 0.00 33.48 5.36
2562 3383 1.959085 CAACCGCAAGCTCATTGGT 59.041 52.632 0.00 0.00 39.47 3.67
2718 3539 1.443872 CAACGCGAGCTACTTCGGT 60.444 57.895 15.93 0.00 40.79 4.69
2856 3677 3.753539 GACGACGCACTGCACGAC 61.754 66.667 19.62 12.30 33.81 4.34
2964 3785 4.101448 ATGCAGCTCGGGGTGTCC 62.101 66.667 17.10 0.20 42.33 4.02
2976 3797 1.663702 GGTGTCCACGGTGTTCTCG 60.664 63.158 7.45 0.00 0.00 4.04
3089 3910 4.933064 GGTGATCGCGCTCGGGAG 62.933 72.222 5.56 0.00 40.35 4.30
3146 3967 0.466007 TGGCCGACTATGCATGCATT 60.466 50.000 36.23 21.15 37.82 3.56
3174 3995 1.755959 TGTGGTGCATGCAAGAAACTT 59.244 42.857 24.58 0.00 0.00 2.66
3175 3996 2.168106 TGTGGTGCATGCAAGAAACTTT 59.832 40.909 24.58 0.00 0.00 2.66
3252 4073 4.933505 TTGTGAAGGACATGAAAATGCA 57.066 36.364 0.00 0.00 33.40 3.96
3324 4145 5.304614 ACACAATGCCTACCGAGTATCTATT 59.695 40.000 0.00 0.00 0.00 1.73
3414 4236 1.668101 GGCGTCTGGGAAGATCGTCT 61.668 60.000 8.59 0.00 0.00 4.18
3443 4265 1.626356 CCACGATGGGGATGGTGTCT 61.626 60.000 0.00 0.00 32.67 3.41
3629 4451 0.322098 CAATCAACCACCTACCGCCA 60.322 55.000 0.00 0.00 0.00 5.69
3642 4464 2.356793 CGCCATCGGATCTGAGCC 60.357 66.667 10.61 0.82 0.00 4.70
3648 4470 2.892640 CGGATCTGAGCCGTCCAA 59.107 61.111 25.03 0.00 43.66 3.53
3649 4471 1.443407 CGGATCTGAGCCGTCCAAT 59.557 57.895 25.03 0.00 43.66 3.16
3688 4510 1.803519 CACGCGCTCTTCTCTGACC 60.804 63.158 5.73 0.00 0.00 4.02
3740 4562 3.545481 CGACCGTGCACATCTCGC 61.545 66.667 18.64 0.00 0.00 5.03
3838 4660 5.794894 TCTCCAAACATTCTCAAGGTAGAC 58.205 41.667 0.00 0.00 0.00 2.59
3841 4663 4.389077 CCAAACATTCTCAAGGTAGACGAC 59.611 45.833 0.00 0.00 0.00 4.34
3865 4687 1.303888 CACCTGAGCTTGGCATGGT 60.304 57.895 4.63 4.63 0.00 3.55
3906 4728 1.998315 CTGAACCGATCTGTTGCTGAG 59.002 52.381 7.29 0.00 0.00 3.35
4000 4822 2.125350 CCTCTGGACAAGCGCTCC 60.125 66.667 12.06 9.16 0.00 4.70
4093 4915 3.936203 GTGCACCCGACCTGGTCA 61.936 66.667 25.42 3.58 36.12 4.02
4585 5407 0.792640 AGTACTACGTCACCGTCACG 59.207 55.000 0.00 0.00 46.28 4.35
4754 5580 3.053842 TACTACTGAGTACTGACCCCCAG 60.054 52.174 0.00 2.49 41.72 4.45
4779 5605 7.443879 AGAAGCTACCTAGTTACGGTTATCTAC 59.556 40.741 0.00 0.00 35.98 2.59
4783 5609 6.456795 ACCTAGTTACGGTTATCTACAACC 57.543 41.667 0.00 0.00 43.88 3.77
4812 5638 2.592308 GGCTTCCGGGCTTCAGAT 59.408 61.111 0.00 0.00 37.53 2.90
4824 5657 1.485895 GCTTCAGATCAGGGCTTCTCT 59.514 52.381 0.00 0.00 0.00 3.10
4825 5658 2.093021 GCTTCAGATCAGGGCTTCTCTT 60.093 50.000 0.00 0.00 0.00 2.85
4826 5659 3.133721 GCTTCAGATCAGGGCTTCTCTTA 59.866 47.826 0.00 0.00 0.00 2.10
4833 5666 1.065854 CAGGGCTTCTCTTAGTGTGGG 60.066 57.143 0.00 0.00 0.00 4.61
4840 5673 2.846193 TCTCTTAGTGTGGGTTTGTGC 58.154 47.619 0.00 0.00 0.00 4.57
4843 5676 3.561143 TCTTAGTGTGGGTTTGTGCAAT 58.439 40.909 0.00 0.00 0.00 3.56
4920 5757 0.035534 AGCATACATTGTGGGTGCGA 60.036 50.000 14.02 0.00 37.09 5.10
4928 5765 2.500509 TTGTGGGTGCGACAAATTTC 57.499 45.000 0.00 0.00 29.80 2.17
4930 5767 1.751351 TGTGGGTGCGACAAATTTCAA 59.249 42.857 0.00 0.00 0.00 2.69
4939 5776 5.342259 GTGCGACAAATTTCAAAGTGATACC 59.658 40.000 0.00 0.00 0.00 2.73
4941 5778 5.918011 GCGACAAATTTCAAAGTGATACCAA 59.082 36.000 0.00 0.00 0.00 3.67
4942 5779 6.088085 GCGACAAATTTCAAAGTGATACCAAG 59.912 38.462 0.00 0.00 0.00 3.61
4943 5780 6.088085 CGACAAATTTCAAAGTGATACCAAGC 59.912 38.462 0.00 0.00 0.00 4.01
4944 5781 6.815089 ACAAATTTCAAAGTGATACCAAGCA 58.185 32.000 0.00 0.00 0.00 3.91
4948 5785 2.813754 TCAAAGTGATACCAAGCAGCAC 59.186 45.455 0.00 0.00 0.00 4.40
4960 5797 3.676216 CAGCACATGCAGGCTCAA 58.324 55.556 6.64 0.00 45.16 3.02
4961 5798 1.211969 CAGCACATGCAGGCTCAAC 59.788 57.895 6.64 0.00 45.16 3.18
4986 5825 6.862608 CGTTTGATGATTCATTTCACCTTCAA 59.137 34.615 0.00 0.00 0.00 2.69
4991 5830 6.564709 TGATTCATTTCACCTTCAACTCTG 57.435 37.500 0.00 0.00 0.00 3.35
4992 5831 5.474532 TGATTCATTTCACCTTCAACTCTGG 59.525 40.000 0.00 0.00 0.00 3.86
5005 5844 4.389374 TCAACTCTGGGAACATTTGAGAC 58.611 43.478 0.00 0.00 41.51 3.36
5011 5857 1.468914 GGGAACATTTGAGACGCCTTC 59.531 52.381 0.00 0.00 0.00 3.46
5045 5891 2.401766 CGATGCTGGGCAGTGGAAC 61.402 63.158 0.00 0.00 43.65 3.62
5227 6093 5.290493 TGAAATCCGTTCCAGCTATATGT 57.710 39.130 0.00 0.00 35.12 2.29
5231 6097 1.419374 CGTTCCAGCTATATGTCGGC 58.581 55.000 0.00 0.00 0.00 5.54
5295 6161 2.438434 GTGCCCTCGGGACCAATG 60.438 66.667 6.08 0.00 38.12 2.82
5382 6248 4.103311 AGACAGCCAAATATAGGAGGGAAC 59.897 45.833 0.00 0.00 0.00 3.62
5405 6271 9.477484 GAACATCGTTCTATATAAATGTGTCCT 57.523 33.333 0.00 0.00 0.00 3.85
5520 6387 2.135933 GTTCTCCTGGTGTTTCTCGTG 58.864 52.381 0.00 0.00 0.00 4.35
5523 6390 1.068588 CTCCTGGTGTTTCTCGTGTCA 59.931 52.381 0.00 0.00 0.00 3.58
5676 6552 8.092068 CCACATATATAACATGACGGGTCTTTA 58.908 37.037 0.00 0.00 0.00 1.85
5720 6596 1.066929 TCACACTCATGCATGCGTAGT 60.067 47.619 21.17 16.53 0.00 2.73
5735 6611 7.709182 TGCATGCGTAGTTAATAGTTCTTGTAT 59.291 33.333 14.09 0.00 0.00 2.29
5736 6612 9.188588 GCATGCGTAGTTAATAGTTCTTGTATA 57.811 33.333 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.167693 CCCTCACGCTCCACTTTATGTA 59.832 50.000 0.00 0.00 0.00 2.29
55 56 1.656652 CCCTCACGCTCCACTTTATG 58.343 55.000 0.00 0.00 0.00 1.90
56 57 0.541863 CCCCTCACGCTCCACTTTAT 59.458 55.000 0.00 0.00 0.00 1.40
75 76 9.869757 ACCATGCCTAATTAAATAAGTTTTCAC 57.130 29.630 0.00 0.00 0.00 3.18
203 205 5.789643 ATTGGAGTTTACTGCACATGTTT 57.210 34.783 3.42 0.00 44.04 2.83
278 325 5.591877 CCTGCAACCTTCTATAGCAAAATCT 59.408 40.000 0.00 0.00 34.45 2.40
498 1300 9.384764 CCAAAAGGTTAAGATCTAAGTTCTAGG 57.615 37.037 0.00 0.00 0.00 3.02
516 1318 5.538433 TCAGCTTAAATAAGTGCCAAAAGGT 59.462 36.000 2.42 0.00 35.75 3.50
603 1405 1.135915 AGAGGCAACGAGACAGCTATG 59.864 52.381 0.00 0.00 46.39 2.23
636 1438 7.928307 ATCATCTGTGCTAGTGTTTTGTTAT 57.072 32.000 0.00 0.00 0.00 1.89
640 1442 7.601073 TCTAATCATCTGTGCTAGTGTTTTG 57.399 36.000 0.00 0.00 0.00 2.44
651 1456 4.115516 CCCTCGTGTTCTAATCATCTGTG 58.884 47.826 0.00 0.00 0.00 3.66
663 1468 2.182030 CCTCTCGCCCTCGTGTTC 59.818 66.667 0.00 0.00 36.96 3.18
664 1469 3.382832 CCCTCTCGCCCTCGTGTT 61.383 66.667 0.00 0.00 36.96 3.32
675 1480 4.285260 TGTTAACTCCAACCTAACCCTCTC 59.715 45.833 7.22 0.00 0.00 3.20
681 1486 8.347771 CCTAAAGTTTGTTAACTCCAACCTAAC 58.652 37.037 7.22 0.00 43.74 2.34
735 1540 6.204495 CCTATCGAGTTAAGTACAGGGTCTAC 59.796 46.154 0.00 0.00 0.00 2.59
741 1546 3.890147 AGGCCTATCGAGTTAAGTACAGG 59.110 47.826 1.29 0.00 0.00 4.00
762 1567 2.301296 AGATGGCGGGTGAGATGATTAG 59.699 50.000 0.00 0.00 0.00 1.73
815 1620 1.116308 CCATGGCTGCATCATTCCAA 58.884 50.000 0.00 0.00 31.66 3.53
839 1644 3.202818 TGAATCTACAATGGCCAGGACAT 59.797 43.478 13.05 0.00 29.26 3.06
845 1650 3.193267 GCTTTGTGAATCTACAATGGCCA 59.807 43.478 8.56 8.56 40.00 5.36
875 1680 1.039233 CCATGCCTTAGGGTGCTTGG 61.039 60.000 0.00 0.09 43.56 3.61
949 1754 6.065374 AGTGGCAGGGAGATATATATAGACG 58.935 44.000 0.00 0.00 0.00 4.18
962 1773 2.930019 TGGTGGAGTGGCAGGGAG 60.930 66.667 0.00 0.00 0.00 4.30
1024 1835 3.057245 GCAAATGAGAGGGAGGAAACAAC 60.057 47.826 0.00 0.00 0.00 3.32
1035 1846 2.097036 TCAATGGCAGCAAATGAGAGG 58.903 47.619 0.00 0.00 0.00 3.69
1071 1882 4.934001 ACTACATGTGAATGAGAAGCTGTG 59.066 41.667 9.11 0.00 0.00 3.66
1072 1883 5.157940 ACTACATGTGAATGAGAAGCTGT 57.842 39.130 9.11 0.00 0.00 4.40
1096 1907 5.854431 TGAAAGAAAACCTGCACAAAAAC 57.146 34.783 0.00 0.00 0.00 2.43
1152 1963 3.444742 ACAGAAGAGAGAGCAGACATGAG 59.555 47.826 0.00 0.00 0.00 2.90
1216 2027 4.464597 GTGTGGTCAGAGAAGGACTAAGAT 59.535 45.833 0.00 0.00 35.61 2.40
1220 2031 2.160205 CGTGTGGTCAGAGAAGGACTA 58.840 52.381 0.00 0.00 35.61 2.59
1222 2033 0.038159 CCGTGTGGTCAGAGAAGGAC 60.038 60.000 0.00 0.00 34.52 3.85
1240 2051 4.389374 TGACAGAAGTTGGAGATGAAACC 58.611 43.478 0.00 0.00 0.00 3.27
1386 2200 8.297426 AGCTGAATTCATGTTATAGATGCATTG 58.703 33.333 8.96 0.00 0.00 2.82
1410 2224 8.180267 TCGTAGTACTACTTGAAATAACTCAGC 58.820 37.037 26.36 0.00 34.04 4.26
1490 2304 7.675962 ATGGCATAAGTAGTACAAACGAAAA 57.324 32.000 0.00 0.00 0.00 2.29
1536 2350 6.727824 ACAGATTGGATAAACTGAGAAACG 57.272 37.500 0.00 0.00 38.55 3.60
1571 2385 6.183360 ACAAAATGGTTGGATTGCTTCAAGTA 60.183 34.615 0.00 0.00 0.00 2.24
1599 2413 7.492669 TCTGAGATGCGAGGTTTTATCTTTAAG 59.507 37.037 0.00 0.00 30.49 1.85
1601 2415 6.873997 TCTGAGATGCGAGGTTTTATCTTTA 58.126 36.000 0.00 0.00 30.49 1.85
1614 2428 3.448660 TCTCCAAATTCTCTGAGATGCGA 59.551 43.478 8.42 3.67 0.00 5.10
1622 2436 7.040892 TGAGAACAAACATCTCCAAATTCTCTG 60.041 37.037 10.89 0.00 42.14 3.35
1687 2506 0.381801 CCGGCCTGCAATATTGTGAC 59.618 55.000 16.61 7.31 0.00 3.67
1820 2639 3.885976 TTTTGGACAACAGGGACCATA 57.114 42.857 0.00 0.00 32.31 2.74
1914 2735 6.312918 TGACCGCTTCTGTTTCTGAATATAAC 59.687 38.462 0.00 0.00 0.00 1.89
1934 2755 4.021981 TGCTCCTGAATACTGATATGACCG 60.022 45.833 0.00 0.00 0.00 4.79
2125 2946 1.123077 TATAGGACAGTGCAGCAGGG 58.877 55.000 0.00 0.00 0.00 4.45
2142 2963 4.764172 CCAGAGAAGCTACAAGCAAGTAT 58.236 43.478 1.22 0.00 45.56 2.12
2511 3332 4.069232 TCGAACTGCTGGCCTCCG 62.069 66.667 3.32 0.00 0.00 4.63
2559 3380 3.060020 GAGGTAGTAGCGCGCACCA 62.060 63.158 31.95 17.00 33.27 4.17
2856 3677 3.545481 GAGATGACGTGCACGCCG 61.545 66.667 37.35 16.64 44.43 6.46
3089 3910 1.675641 ACCACGAAGGAGGCATTGC 60.676 57.895 0.00 0.00 41.22 3.56
3146 3967 1.454572 GCATGCACCACAGTCCACAA 61.455 55.000 14.21 0.00 0.00 3.33
3174 3995 4.558226 ATGAGAAGTGCACTGTATCCAA 57.442 40.909 22.49 5.95 0.00 3.53
3175 3996 4.558226 AATGAGAAGTGCACTGTATCCA 57.442 40.909 22.49 14.03 0.00 3.41
3249 4070 4.498177 CGCTAGTGCTCTCTACTAAATGCA 60.498 45.833 0.00 0.00 36.97 3.96
3252 4073 5.127491 AGACGCTAGTGCTCTCTACTAAAT 58.873 41.667 2.40 0.00 36.97 1.40
3324 4145 3.701241 GCAAATCGGTCAGTCAAAACAA 58.299 40.909 0.00 0.00 0.00 2.83
3401 4223 0.976641 AGCACAAGACGATCTTCCCA 59.023 50.000 0.00 0.00 33.78 4.37
3414 4236 0.321564 CCCATCGTGGAGAAGCACAA 60.322 55.000 5.71 0.00 40.96 3.33
3575 4397 3.244044 GGCTCTGGATGTAGTTGAGGATC 60.244 52.174 0.00 0.00 0.00 3.36
3643 4465 4.759096 GTGCGTGCGCCATTGGAC 62.759 66.667 14.16 0.00 41.09 4.02
3662 4484 1.478622 GAAGAGCGCGTGATCTCAGC 61.479 60.000 18.18 6.58 40.73 4.26
3688 4510 3.993234 GCAGACGATGGATGCGCG 61.993 66.667 0.00 0.00 0.00 6.86
3734 4556 3.532155 GGTCCTGCTCGGCGAGAT 61.532 66.667 38.56 0.00 0.00 2.75
3740 4562 4.477975 GACGACGGTCCTGCTCGG 62.478 72.222 1.91 0.00 37.19 4.63
3838 4660 0.109086 AAGCTCAGGTGATCGTGTCG 60.109 55.000 0.00 0.00 0.00 4.35
3841 4663 1.364626 GCCAAGCTCAGGTGATCGTG 61.365 60.000 6.98 0.00 0.00 4.35
3865 4687 5.363580 TCAGTCCATACATATGTGCTCTTCA 59.636 40.000 18.81 0.00 31.82 3.02
3879 4701 3.802948 ACAGATCGGTTCAGTCCATAC 57.197 47.619 0.00 0.00 0.00 2.39
3906 4728 4.724602 TGACGTCAGGCTGCGAGC 62.725 66.667 28.77 21.39 41.46 5.03
3982 4804 2.125350 GAGCGCTTGTCCAGAGGG 60.125 66.667 13.26 0.00 0.00 4.30
4000 4822 0.031585 TGTCGAAGTTCCACTCCGTG 59.968 55.000 2.25 0.00 0.00 4.94
4093 4915 4.681978 GACTTGACTGCGGCCGGT 62.682 66.667 29.38 17.94 0.00 5.28
4606 5428 2.741985 TCGCCGAAGTCGTACCGA 60.742 61.111 0.00 2.62 37.74 4.69
4754 5580 6.631971 AGATAACCGTAACTAGGTAGCTTC 57.368 41.667 0.00 0.00 41.95 3.86
4812 5638 1.902508 CCACACTAAGAGAAGCCCTGA 59.097 52.381 0.00 0.00 0.00 3.86
4824 5657 3.027412 ACATTGCACAAACCCACACTAA 58.973 40.909 0.00 0.00 0.00 2.24
4825 5658 2.660572 ACATTGCACAAACCCACACTA 58.339 42.857 0.00 0.00 0.00 2.74
4826 5659 1.484038 ACATTGCACAAACCCACACT 58.516 45.000 0.00 0.00 0.00 3.55
4833 5666 5.895889 GTGAAATCGAAAACATTGCACAAAC 59.104 36.000 2.54 0.00 39.00 2.93
4840 5673 5.115472 CCAACGAGTGAAATCGAAAACATTG 59.885 40.000 7.20 0.27 45.56 2.82
4843 5676 3.002862 CCCAACGAGTGAAATCGAAAACA 59.997 43.478 7.20 0.00 45.56 2.83
4884 5717 3.410631 TGCTCCTTTAACATGACCGAA 57.589 42.857 0.00 0.00 0.00 4.30
4886 5719 4.188462 TGTATGCTCCTTTAACATGACCG 58.812 43.478 0.00 0.00 0.00 4.79
4920 5757 6.815089 TGCTTGGTATCACTTTGAAATTTGT 58.185 32.000 0.00 0.00 0.00 2.83
4928 5765 2.553602 TGTGCTGCTTGGTATCACTTTG 59.446 45.455 0.00 0.00 0.00 2.77
4930 5767 2.566833 TGTGCTGCTTGGTATCACTT 57.433 45.000 0.00 0.00 0.00 3.16
4943 5780 1.211969 GTTGAGCCTGCATGTGCTG 59.788 57.895 9.91 5.75 42.66 4.41
4944 5781 2.330372 CGTTGAGCCTGCATGTGCT 61.330 57.895 6.55 5.33 42.66 4.40
4948 5785 0.592637 TCAAACGTTGAGCCTGCATG 59.407 50.000 0.00 0.00 34.08 4.06
4960 5797 5.964958 AGGTGAAATGAATCATCAAACGT 57.035 34.783 0.00 0.00 39.49 3.99
4961 5798 6.380995 TGAAGGTGAAATGAATCATCAAACG 58.619 36.000 0.00 0.00 39.49 3.60
4986 5825 2.872038 GCGTCTCAAATGTTCCCAGAGT 60.872 50.000 0.00 0.00 0.00 3.24
4991 5830 1.468914 GAAGGCGTCTCAAATGTTCCC 59.531 52.381 0.00 0.00 0.00 3.97
4992 5831 2.427506 AGAAGGCGTCTCAAATGTTCC 58.572 47.619 0.00 0.00 0.00 3.62
5005 5844 2.125350 GCTGGTCAGGAGAAGGCG 60.125 66.667 0.00 0.00 0.00 5.52
5011 5857 4.463879 CGCCCAGCTGGTCAGGAG 62.464 72.222 30.63 15.52 36.04 3.69
5206 6072 4.386049 CGACATATAGCTGGAACGGATTTC 59.614 45.833 0.00 0.00 36.31 2.17
5227 6093 1.544691 GAGTGGAGTAGAAAGTGCCGA 59.455 52.381 0.00 0.00 0.00 5.54
5231 6097 4.950050 ACTTGTGAGTGGAGTAGAAAGTG 58.050 43.478 0.00 0.00 33.99 3.16
5277 6143 2.610859 ATTGGTCCCGAGGGCACT 60.611 61.111 2.58 0.00 34.68 4.40
5295 6161 5.825151 ACTAGAGTGATACCCGGTTAACTAC 59.175 44.000 5.42 0.00 0.00 2.73
5362 6228 4.437682 TGTTCCCTCCTATATTTGGCTG 57.562 45.455 0.00 0.00 0.00 4.85
5405 6271 4.202749 TGGAGGGTTCACTCTAGGACTTTA 60.203 45.833 2.05 0.00 37.63 1.85
5408 6274 1.717077 TGGAGGGTTCACTCTAGGACT 59.283 52.381 2.05 0.00 37.63 3.85
5557 6424 1.047002 CCTCCTCCATCCTGTAGCTG 58.953 60.000 0.00 0.00 0.00 4.24
5558 6425 0.762461 GCCTCCTCCATCCTGTAGCT 60.762 60.000 0.00 0.00 0.00 3.32
5562 6429 2.765807 CCGCCTCCTCCATCCTGT 60.766 66.667 0.00 0.00 0.00 4.00
5563 6430 2.946988 TACCCGCCTCCTCCATCCTG 62.947 65.000 0.00 0.00 0.00 3.86
5661 6528 8.974060 AAACATTATATAAAGACCCGTCATGT 57.026 30.769 4.77 0.00 0.00 3.21
5666 6533 7.986889 ACGGTTAAACATTATATAAAGACCCGT 59.013 33.333 4.77 10.14 0.00 5.28
5676 6552 7.830201 TGAAAGGGTGACGGTTAAACATTATAT 59.170 33.333 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.