Multiple sequence alignment - TraesCS2A01G189600

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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 TraesCS2A01G189600 chr2A 100.000 3995 0 0 1 3995 156363785 156367779 0 7378
1 TraesCS2A01G189600 chr2D 93.270 3180 137 42 846 3995 145895874 145892742 0 4615
2 TraesCS2A01G189600 chr2D 85.229 853 64 36 1 820 145896690 145895867 0 821
3 TraesCS2A01G189600 chr2B 90.264 3184 203 52 1 3149 206121967 206118856 0 4063
4 TraesCS2A01G189600 chr2B 89.739 614 44 16 3397 3995 206117663 206117054 0 767


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 TraesCS2A01G189600 chr2A 156363785 156367779 3994 False 7378 7378 100.0000 1 3995 1 chr2A.!!$F1 3994
1 TraesCS2A01G189600 chr2D 145892742 145896690 3948 True 2718 4615 89.2495 1 3995 2 chr2D.!!$R1 3994
2 TraesCS2A01G189600 chr2B 206117054 206121967 4913 True 2415 4063 90.0015 1 3995 2 chr2B.!!$R1 3994

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
269 285 0.374758 CATTGACCCGTGCGATCTTG 59.625 55.0 0.0 0.0 0.0 3.02 F
1695 1747 0.103937 CGGAGCTGAGGAAGATGGTC 59.896 60.0 0.0 0.0 0.0 4.02 F
1792 1844 0.181350 CCACTCCATCTACAAGGCCC 59.819 60.0 0.0 0.0 0.0 5.80 F
2389 2441 0.576328 GGAGACGCTCGACTACTACG 59.424 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 1987 0.387929 GGGCGATGTGGAAGTCGATA 59.612 55.0 0.0 0.0 40.11 2.92 R
2730 2782 0.235926 GCGAGGTCACAAAAGCAGTC 59.764 55.0 0.0 0.0 0.00 3.51 R
2848 2900 0.248949 GCCTAGACCTAAGTTCGGCG 60.249 60.0 0.0 0.0 0.00 6.46 R
3517 4580 2.291540 CCCTACTCCAAAAAGGGCATGA 60.292 50.0 0.0 0.0 43.47 3.07 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
76 89 4.285851 GCTTGCAAGCCTAGTCGT 57.714 55.556 36.21 0.00 46.20 4.34
79 92 1.687494 CTTGCAAGCCTAGTCGTCGC 61.687 60.000 14.65 0.00 0.00 5.19
82 95 2.161486 CAAGCCTAGTCGTCGCAGC 61.161 63.158 0.00 0.00 0.00 5.25
86 99 4.476410 CTAGTCGTCGCAGCCGCA 62.476 66.667 0.00 0.00 38.40 5.69
87 100 4.771356 TAGTCGTCGCAGCCGCAC 62.771 66.667 0.00 0.00 38.40 5.34
119 134 1.526917 TACGGCCTCGGTACTAGCC 60.527 63.158 0.00 0.00 42.18 3.93
120 135 2.269520 TACGGCCTCGGTACTAGCCA 62.270 60.000 0.00 0.00 46.08 4.75
121 136 2.846652 CGGCCTCGGTACTAGCCAG 61.847 68.421 0.00 5.62 46.08 4.85
122 137 2.417936 GCCTCGGTACTAGCCAGC 59.582 66.667 0.00 0.00 0.00 4.85
183 199 0.389817 CTCAGACCGCGTCAAATGGA 60.390 55.000 4.92 0.00 34.60 3.41
184 200 0.389817 TCAGACCGCGTCAAATGGAG 60.390 55.000 4.92 0.00 34.60 3.86
185 201 1.079127 AGACCGCGTCAAATGGAGG 60.079 57.895 4.92 0.00 34.60 4.30
192 208 1.890876 CGTCAAATGGAGGTTGGTGA 58.109 50.000 0.00 0.00 0.00 4.02
206 222 5.782925 AGGTTGGTGATAGATTAGACCTCT 58.217 41.667 0.00 0.00 30.85 3.69
214 230 6.584563 GTGATAGATTAGACCTCTCGATTTGC 59.415 42.308 0.00 0.00 0.00 3.68
218 234 2.125106 ACCTCTCGATTTGCGCCC 60.125 61.111 4.18 0.00 40.61 6.13
268 284 0.744414 CCATTGACCCGTGCGATCTT 60.744 55.000 0.00 0.00 0.00 2.40
269 285 0.374758 CATTGACCCGTGCGATCTTG 59.625 55.000 0.00 0.00 0.00 3.02
315 331 3.629398 CAGTTGATTAATCCTGTCCCTGC 59.371 47.826 12.90 0.00 0.00 4.85
352 368 0.899019 GGTGTGGTTGGTTTGGTTGT 59.101 50.000 0.00 0.00 0.00 3.32
379 395 3.726517 CGGGTCAAACTGCTGCCG 61.727 66.667 0.00 0.00 0.00 5.69
382 398 2.193536 GGTCAAACTGCTGCCGGTT 61.194 57.895 1.90 0.00 42.26 4.44
386 402 1.756561 AAACTGCTGCCGGTTTGGT 60.757 52.632 16.14 0.00 46.13 3.67
387 403 2.015227 AAACTGCTGCCGGTTTGGTG 62.015 55.000 16.14 0.00 46.13 4.17
388 404 4.347453 CTGCTGCCGGTTTGGTGC 62.347 66.667 1.90 0.00 41.21 5.01
390 406 4.645921 GCTGCCGGTTTGGTGCAC 62.646 66.667 8.80 8.80 41.21 4.57
397 421 1.827789 GGTTTGGTGCACTGCAGGA 60.828 57.895 19.93 0.00 40.08 3.86
486 513 1.068250 GCGCTCAGGTCATACTCCC 59.932 63.158 0.00 0.00 0.00 4.30
491 518 2.237392 GCTCAGGTCATACTCCCACTTT 59.763 50.000 0.00 0.00 0.00 2.66
492 519 3.451178 GCTCAGGTCATACTCCCACTTTA 59.549 47.826 0.00 0.00 0.00 1.85
493 520 4.442192 GCTCAGGTCATACTCCCACTTTAG 60.442 50.000 0.00 0.00 0.00 1.85
499 526 6.832900 AGGTCATACTCCCACTTTAGTAGTAC 59.167 42.308 0.00 0.00 34.56 2.73
602 640 4.787551 TCCCTTCACTTGCTTCTTGTTAA 58.212 39.130 0.00 0.00 0.00 2.01
627 665 2.795329 AGGATGCCTACTGGTTGTTTG 58.205 47.619 0.00 0.00 35.27 2.93
630 668 2.428544 TGCCTACTGGTTGTTTGTGT 57.571 45.000 0.00 0.00 35.27 3.72
632 670 2.425312 TGCCTACTGGTTGTTTGTGTTG 59.575 45.455 0.00 0.00 35.27 3.33
633 671 2.223711 GCCTACTGGTTGTTTGTGTTGG 60.224 50.000 0.00 0.00 35.27 3.77
635 673 3.445805 CCTACTGGTTGTTTGTGTTGGTT 59.554 43.478 0.00 0.00 0.00 3.67
636 674 3.586100 ACTGGTTGTTTGTGTTGGTTC 57.414 42.857 0.00 0.00 0.00 3.62
637 675 3.161866 ACTGGTTGTTTGTGTTGGTTCT 58.838 40.909 0.00 0.00 0.00 3.01
638 676 3.056891 ACTGGTTGTTTGTGTTGGTTCTG 60.057 43.478 0.00 0.00 0.00 3.02
706 752 8.510243 TTATATATGCCTTGTATGCCATCTTG 57.490 34.615 0.00 0.00 0.00 3.02
709 755 3.544684 TGCCTTGTATGCCATCTTGTAG 58.455 45.455 0.00 0.00 0.00 2.74
718 764 4.386867 TGCCATCTTGTAGTGCTAGTAC 57.613 45.455 2.24 2.24 0.00 2.73
780 826 7.934665 TGTGATTGTTAGGCTCTTGTACTTTTA 59.065 33.333 0.00 0.00 0.00 1.52
825 871 8.830580 CAGTATGTTATTATTTCCTGTGTCTGG 58.169 37.037 0.00 0.00 0.00 3.86
829 875 7.410174 TGTTATTATTTCCTGTGTCTGGGATT 58.590 34.615 0.00 0.00 0.00 3.01
836 882 2.421107 CCTGTGTCTGGGATTGAGATGG 60.421 54.545 0.00 0.00 0.00 3.51
840 886 2.644299 TGTCTGGGATTGAGATGGTGTT 59.356 45.455 0.00 0.00 0.00 3.32
841 887 3.074390 TGTCTGGGATTGAGATGGTGTTT 59.926 43.478 0.00 0.00 0.00 2.83
842 888 3.691609 GTCTGGGATTGAGATGGTGTTTC 59.308 47.826 0.00 0.00 0.00 2.78
843 889 3.019564 CTGGGATTGAGATGGTGTTTCC 58.980 50.000 0.00 0.00 0.00 3.13
907 956 3.104512 AGTGTATGCTTGGCTACCAGTA 58.895 45.455 0.00 0.00 33.81 2.74
977 1026 9.877178 TCTTATTACTCTCCTGTTTCAGATTTC 57.123 33.333 0.00 0.00 32.44 2.17
1009 1058 5.467738 TCTGGATTTCTGGGCTAGAAGATA 58.532 41.667 13.21 0.00 45.66 1.98
1010 1059 5.541868 TCTGGATTTCTGGGCTAGAAGATAG 59.458 44.000 13.21 10.52 45.66 2.08
1011 1060 5.467738 TGGATTTCTGGGCTAGAAGATAGA 58.532 41.667 13.21 0.00 45.66 1.98
1012 1061 6.087456 TGGATTTCTGGGCTAGAAGATAGAT 58.913 40.000 13.21 4.07 45.66 1.98
1024 1073 5.883685 AGAAGATAGATCCATGCAGTGAA 57.116 39.130 0.00 0.00 0.00 3.18
1038 1087 2.537625 GCAGTGAATAGTGCGTCAGATC 59.462 50.000 0.00 0.00 42.84 2.75
1045 1094 0.969149 AGTGCGTCAGATCCTTCACA 59.031 50.000 0.00 0.00 0.00 3.58
1071 1120 1.692519 AGTATGGCCGATACTCCAACC 59.307 52.381 17.24 0.00 43.36 3.77
1140 1189 2.927014 GCAGTTCCAGTTCCAGTACTCG 60.927 54.545 0.00 0.00 0.00 4.18
1224 1273 1.135257 CACCTCTACAGCCTCAAGTCG 60.135 57.143 0.00 0.00 0.00 4.18
1254 1306 2.287909 CGCTAGCTATGAGAACCAGGTC 60.288 54.545 13.93 0.00 0.00 3.85
1452 1504 2.005960 CTGTGACGACCGAGGATCCC 62.006 65.000 8.55 0.00 0.00 3.85
1497 1549 1.742268 GACCTTGAGGCTGAAATGCTC 59.258 52.381 0.00 0.00 39.32 4.26
1539 1591 2.826738 AGCCTCGAGAGCTCCGTC 60.827 66.667 15.71 8.38 34.91 4.79
1580 1632 2.125350 GGAGAAGTGGGCGCAGAG 60.125 66.667 10.83 0.00 0.00 3.35
1590 1642 1.522580 GGCGCAGAGGATGGACTTC 60.523 63.158 10.83 0.00 0.00 3.01
1695 1747 0.103937 CGGAGCTGAGGAAGATGGTC 59.896 60.000 0.00 0.00 0.00 4.02
1792 1844 0.181350 CCACTCCATCTACAAGGCCC 59.819 60.000 0.00 0.00 0.00 5.80
1924 1976 3.400054 CCGTCAAGGGGGAGGACC 61.400 72.222 0.00 0.00 35.97 4.46
1953 2005 2.218953 TTATCGACTTCCACATCGCC 57.781 50.000 0.00 0.00 38.24 5.54
2037 2089 1.300233 GAGGATCACCGGCATCGAC 60.300 63.158 0.00 0.00 41.83 4.20
2103 2155 1.520342 GAGGAGGCTGTCGCACATC 60.520 63.158 0.00 0.00 38.10 3.06
2127 2179 1.377856 GCTCTGCAAGGTCCCCTTC 60.378 63.158 0.00 0.00 42.67 3.46
2171 2223 3.151022 CGAGGAGGTGGAGGAGGC 61.151 72.222 0.00 0.00 0.00 4.70
2389 2441 0.576328 GGAGACGCTCGACTACTACG 59.424 60.000 0.00 0.00 0.00 3.51
2736 2788 1.524621 GTGCTGTGGTGTGACTGCT 60.525 57.895 0.00 0.00 40.44 4.24
2759 2811 2.407428 TGACCTCGCTGCTCGTAGG 61.407 63.158 0.00 2.02 39.63 3.18
2793 2845 3.869912 GCATGCTTTGTTGGACTCTAGGA 60.870 47.826 11.37 0.00 0.00 2.94
2796 2848 2.680339 GCTTTGTTGGACTCTAGGATGC 59.320 50.000 0.00 0.00 0.00 3.91
2797 2849 3.620966 GCTTTGTTGGACTCTAGGATGCT 60.621 47.826 0.00 0.00 0.00 3.79
2798 2850 3.616956 TTGTTGGACTCTAGGATGCTG 57.383 47.619 0.00 0.00 0.00 4.41
2799 2851 1.208052 TGTTGGACTCTAGGATGCTGC 59.792 52.381 0.00 0.00 0.00 5.25
2871 2924 1.409427 CGAACTTAGGTCTAGGCCTGG 59.591 57.143 26.65 19.46 39.60 4.45
2875 2928 4.554553 ACTTAGGTCTAGGCCTGGATAA 57.445 45.455 26.65 15.82 39.60 1.75
2876 2929 4.484912 ACTTAGGTCTAGGCCTGGATAAG 58.515 47.826 26.65 26.20 39.60 1.73
2892 2945 5.397360 TGGATAAGAGGCTGATGAGATGTA 58.603 41.667 0.00 0.00 0.00 2.29
2893 2946 5.479724 TGGATAAGAGGCTGATGAGATGTAG 59.520 44.000 0.00 0.00 0.00 2.74
2894 2947 5.480073 GGATAAGAGGCTGATGAGATGTAGT 59.520 44.000 0.00 0.00 0.00 2.73
2963 3016 9.586150 GACGTCTAATCTTAATGTAATTGCATG 57.414 33.333 9.95 0.00 36.99 4.06
2989 3042 0.689055 AGTCTCAATCAGCACTGCCA 59.311 50.000 0.00 0.00 0.00 4.92
2990 3043 1.072806 AGTCTCAATCAGCACTGCCAA 59.927 47.619 0.00 0.00 0.00 4.52
3019 3073 8.004087 ACTAAAATGATTTGAGATGATGGGTG 57.996 34.615 9.24 0.00 0.00 4.61
3037 3091 1.541588 GTGTTGGTGCCTTTGGAGATC 59.458 52.381 0.00 0.00 0.00 2.75
3071 3127 0.036388 GAGGGAAAGCCATCACGACA 60.036 55.000 0.00 0.00 44.29 4.35
3126 3182 5.925509 TCCACCAGGCTAGATATACAAAAC 58.074 41.667 0.00 0.00 33.74 2.43
3204 3333 2.908688 AAATTGCCGAAGCTTTGGTT 57.091 40.000 29.66 16.17 40.80 3.67
3230 3359 4.041938 TGAATAGCCACCATCATGCATAGA 59.958 41.667 0.00 0.00 0.00 1.98
3249 3378 6.480320 GCATAGACTAAACCACTTCCATACAG 59.520 42.308 0.00 0.00 0.00 2.74
3250 3379 7.556844 CATAGACTAAACCACTTCCATACAGT 58.443 38.462 0.00 0.00 0.00 3.55
3252 3381 5.046520 AGACTAAACCACTTCCATACAGTCC 60.047 44.000 0.00 0.00 32.25 3.85
3255 3384 1.825474 ACCACTTCCATACAGTCCGAG 59.175 52.381 0.00 0.00 0.00 4.63
3287 3416 0.036388 TTCTCGCATCCAACCTGTCC 60.036 55.000 0.00 0.00 0.00 4.02
3307 3436 3.565764 CTGCAAGGATTAGACCATCCA 57.434 47.619 2.62 0.00 44.93 3.41
3389 3518 1.576356 GCAAAACAAAATGCCCACGA 58.424 45.000 0.00 0.00 36.56 4.35
3437 4500 1.140652 CCAATCTCCTCCTGAAGGCTC 59.859 57.143 0.00 0.00 45.78 4.70
3517 4580 3.554934 TCTTGATGCACTTCTGGTTGTT 58.445 40.909 0.00 0.00 0.00 2.83
3552 4615 4.600111 TGGAGTAGGGTTGGAACTTGTAAT 59.400 41.667 0.00 0.00 0.00 1.89
3553 4616 5.073965 TGGAGTAGGGTTGGAACTTGTAATT 59.926 40.000 0.00 0.00 0.00 1.40
3560 4623 5.106277 GGGTTGGAACTTGTAATTGAGTAGC 60.106 44.000 0.00 0.00 0.00 3.58
3567 4630 7.255139 GGAACTTGTAATTGAGTAGCACAAAGT 60.255 37.037 0.00 0.00 0.00 2.66
3568 4631 8.671384 AACTTGTAATTGAGTAGCACAAAGTA 57.329 30.769 0.00 0.00 0.00 2.24
3569 4632 8.671384 ACTTGTAATTGAGTAGCACAAAGTAA 57.329 30.769 0.00 0.00 0.00 2.24
3570 4633 9.116067 ACTTGTAATTGAGTAGCACAAAGTAAA 57.884 29.630 0.00 0.00 0.00 2.01
3571 4634 9.382244 CTTGTAATTGAGTAGCACAAAGTAAAC 57.618 33.333 0.00 0.00 0.00 2.01
3572 4635 7.867752 TGTAATTGAGTAGCACAAAGTAAACC 58.132 34.615 0.00 0.00 0.00 3.27
3632 4724 7.879160 TCCATAAATAACAGTTGTCTTAACGGT 59.121 33.333 0.00 0.00 0.00 4.83
3637 4730 9.940166 AAATAACAGTTGTCTTAACGGTAAAAG 57.060 29.630 0.00 0.00 0.00 2.27
3641 4734 8.042944 ACAGTTGTCTTAACGGTAAAAGAAAA 57.957 30.769 7.26 6.18 33.70 2.29
3643 4736 9.511144 CAGTTGTCTTAACGGTAAAAGAAAATT 57.489 29.630 10.33 5.61 32.87 1.82
3646 4739 9.649024 TTGTCTTAACGGTAAAAGAAAATTACG 57.351 29.630 7.26 0.00 34.74 3.18
3647 4740 9.039870 TGTCTTAACGGTAAAAGAAAATTACGA 57.960 29.630 7.26 0.00 34.74 3.43
3987 5081 2.568509 TGCAGACACTCTCATCATTCCA 59.431 45.455 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.536558 CAAAAAGTACTAGCCAAAAACAAAAAC 57.463 29.630 0.00 0.00 0.00 2.43
85 98 1.595929 GTACGGGTGGTGTGGTGTG 60.596 63.158 0.00 0.00 0.00 3.82
86 99 2.823829 GTACGGGTGGTGTGGTGT 59.176 61.111 0.00 0.00 0.00 4.16
87 100 2.356553 CGTACGGGTGGTGTGGTG 60.357 66.667 7.57 0.00 0.00 4.17
88 101 3.618750 CCGTACGGGTGGTGTGGT 61.619 66.667 27.00 0.00 0.00 4.16
122 137 1.202698 GCTTGGTCATGGCCTAGTAGG 60.203 57.143 25.41 12.27 38.80 3.18
183 199 5.782925 AGAGGTCTAATCTATCACCAACCT 58.217 41.667 0.00 0.00 38.55 3.50
184 200 5.278561 CGAGAGGTCTAATCTATCACCAACC 60.279 48.000 0.00 0.00 0.00 3.77
185 201 5.531659 TCGAGAGGTCTAATCTATCACCAAC 59.468 44.000 0.00 0.00 0.00 3.77
192 208 5.704888 CGCAAATCGAGAGGTCTAATCTAT 58.295 41.667 0.00 0.00 41.67 1.98
214 230 4.277593 TGCTTGTTTTGGCGGGCG 62.278 61.111 0.00 0.00 0.00 6.13
218 234 0.597568 TGGATCTGCTTGTTTTGGCG 59.402 50.000 0.00 0.00 0.00 5.69
257 273 6.706055 ATAAATATACACAAGATCGCACGG 57.294 37.500 0.00 0.00 0.00 4.94
268 284 9.898152 TGACATCCACTGAAATAAATATACACA 57.102 29.630 0.00 0.00 0.00 3.72
298 314 1.230324 GCGCAGGGACAGGATTAATC 58.770 55.000 0.30 6.93 0.00 1.75
333 349 0.899019 ACAACCAAACCAACCACACC 59.101 50.000 0.00 0.00 0.00 4.16
379 395 1.391157 TTCCTGCAGTGCACCAAACC 61.391 55.000 15.37 0.00 33.79 3.27
382 398 1.412079 ATTTTCCTGCAGTGCACCAA 58.588 45.000 15.37 6.80 33.79 3.67
383 399 1.412079 AATTTTCCTGCAGTGCACCA 58.588 45.000 15.37 4.23 33.79 4.17
384 400 3.193267 TCATAATTTTCCTGCAGTGCACC 59.807 43.478 15.37 0.00 33.79 5.01
386 402 4.705991 TCATCATAATTTTCCTGCAGTGCA 59.294 37.500 18.58 18.58 36.92 4.57
387 403 5.252969 TCATCATAATTTTCCTGCAGTGC 57.747 39.130 13.81 8.58 0.00 4.40
388 404 5.359009 ACCTCATCATAATTTTCCTGCAGTG 59.641 40.000 13.81 4.33 0.00 3.66
389 405 5.359009 CACCTCATCATAATTTTCCTGCAGT 59.641 40.000 13.81 0.00 0.00 4.40
390 406 5.221185 CCACCTCATCATAATTTTCCTGCAG 60.221 44.000 6.78 6.78 0.00 4.41
397 421 7.595488 AGTAATCCCCACCTCATCATAATTTT 58.405 34.615 0.00 0.00 0.00 1.82
452 479 2.356796 CGCGCGCAAACAAAAGAGG 61.357 57.895 32.61 5.79 0.00 3.69
486 513 5.557891 ACAGCCGTAGTACTACTAAAGTG 57.442 43.478 26.36 18.51 39.39 3.16
520 547 2.982130 CCAAGACTCCCAGTCCGG 59.018 66.667 0.00 0.00 46.18 5.14
521 548 2.266055 GCCAAGACTCCCAGTCCG 59.734 66.667 0.00 0.00 46.18 4.79
619 657 3.586100 ACAGAACCAACACAAACAACC 57.414 42.857 0.00 0.00 0.00 3.77
622 660 5.736813 AGTAGTACAGAACCAACACAAACA 58.263 37.500 2.52 0.00 0.00 2.83
623 661 5.813672 TGAGTAGTACAGAACCAACACAAAC 59.186 40.000 2.52 0.00 0.00 2.93
625 663 5.601583 TGAGTAGTACAGAACCAACACAA 57.398 39.130 2.52 0.00 0.00 3.33
626 664 5.601583 TTGAGTAGTACAGAACCAACACA 57.398 39.130 2.52 0.00 0.00 3.72
627 665 6.018994 CACTTTGAGTAGTACAGAACCAACAC 60.019 42.308 2.52 0.00 0.00 3.32
630 668 6.229936 ACACTTTGAGTAGTACAGAACCAA 57.770 37.500 2.52 0.00 0.00 3.67
632 670 7.494952 AGAAAACACTTTGAGTAGTACAGAACC 59.505 37.037 2.52 0.00 0.00 3.62
633 671 8.421673 AGAAAACACTTTGAGTAGTACAGAAC 57.578 34.615 2.52 0.00 0.00 3.01
635 673 8.255206 TGAAGAAAACACTTTGAGTAGTACAGA 58.745 33.333 2.52 0.00 0.00 3.41
636 674 8.420374 TGAAGAAAACACTTTGAGTAGTACAG 57.580 34.615 2.52 0.00 0.00 2.74
637 675 8.255206 TCTGAAGAAAACACTTTGAGTAGTACA 58.745 33.333 2.52 0.00 0.00 2.90
638 676 8.541312 GTCTGAAGAAAACACTTTGAGTAGTAC 58.459 37.037 0.00 0.00 0.00 2.73
699 745 9.069082 AGTAATAGTACTAGCACTACAAGATGG 57.931 37.037 14.50 0.00 38.87 3.51
709 755 9.804758 AGTGATGAAAAGTAATAGTACTAGCAC 57.195 33.333 8.85 7.14 39.79 4.40
820 866 3.356529 AACACCATCTCAATCCCAGAC 57.643 47.619 0.00 0.00 0.00 3.51
844 890 9.866655 AGAATTGGTGTATTGTATACATGGAAT 57.133 29.630 6.36 0.00 0.00 3.01
961 1010 5.466728 TGAAACGAGAAATCTGAAACAGGAG 59.533 40.000 0.00 0.00 31.51 3.69
964 1013 7.014115 CAGATGAAACGAGAAATCTGAAACAG 58.986 38.462 13.79 0.00 45.81 3.16
977 1026 3.624861 CCCAGAAATCCAGATGAAACGAG 59.375 47.826 0.00 0.00 0.00 4.18
1009 1058 3.474600 GCACTATTCACTGCATGGATCT 58.525 45.455 0.00 0.00 33.31 2.75
1010 1059 2.222678 CGCACTATTCACTGCATGGATC 59.777 50.000 0.00 0.00 32.57 3.36
1011 1060 2.216046 CGCACTATTCACTGCATGGAT 58.784 47.619 0.00 0.00 32.57 3.41
1012 1061 1.066215 ACGCACTATTCACTGCATGGA 60.066 47.619 0.00 0.00 32.57 3.41
1024 1073 2.760650 TGTGAAGGATCTGACGCACTAT 59.239 45.455 0.00 0.00 0.00 2.12
1030 1079 3.303881 TGTTCTGTGAAGGATCTGACG 57.696 47.619 0.00 0.00 0.00 4.35
1038 1087 2.749621 GGCCATACTTGTTCTGTGAAGG 59.250 50.000 0.00 0.00 0.00 3.46
1045 1094 3.069729 GGAGTATCGGCCATACTTGTTCT 59.930 47.826 21.41 6.02 46.76 3.01
1071 1120 2.520536 GGGGTGGATCATCCGGGAG 61.521 68.421 0.00 0.00 40.17 4.30
1140 1189 1.678970 GGGATGCTGTGGGTTGTCC 60.679 63.158 0.00 0.00 0.00 4.02
1206 1255 1.133407 GACGACTTGAGGCTGTAGAGG 59.867 57.143 0.00 0.00 0.00 3.69
1208 1257 1.905637 TGACGACTTGAGGCTGTAGA 58.094 50.000 0.00 0.00 0.00 2.59
1224 1273 3.500299 TCTCATAGCTAGCGTCTGATGAC 59.500 47.826 9.55 0.00 39.70 3.06
1254 1306 0.997932 GAGTGTGCTTCATCTGAGCG 59.002 55.000 0.00 0.00 0.00 5.03
1388 1440 2.432628 CGTTGGTGGAGTCGGAGC 60.433 66.667 0.00 0.00 0.00 4.70
1413 1465 0.950555 TGACGCATGAAGCACTCACC 60.951 55.000 0.00 0.00 46.13 4.02
1452 1504 2.802556 GCTTCTGCTTCAGATCGTTG 57.197 50.000 0.00 0.00 40.39 4.10
1509 1561 1.671328 TCGAGGCTGTTCACTATCTCG 59.329 52.381 0.00 0.00 43.46 4.04
1518 1570 1.140804 GGAGCTCTCGAGGCTGTTC 59.859 63.158 26.44 17.06 40.40 3.18
1551 1603 3.708220 CTTCTCCGGCTCCAGCGAC 62.708 68.421 0.00 0.00 43.26 5.19
1580 1632 3.335711 CCCTGGGGAAGTCCATCC 58.664 66.667 4.27 0.00 36.05 3.51
1792 1844 2.045536 GGGCTCCTTGCACCTCAG 60.046 66.667 0.00 0.00 45.15 3.35
1924 1976 3.243737 TGGAAGTCGATAATGTGGATCCG 60.244 47.826 7.39 0.00 0.00 4.18
1935 1987 0.387929 GGGCGATGTGGAAGTCGATA 59.612 55.000 0.00 0.00 40.11 2.92
1953 2005 3.746949 GATCCACTGCGCTCCCTGG 62.747 68.421 9.73 7.91 0.00 4.45
1962 2014 1.406860 GGAGGAGGGAGATCCACTGC 61.407 65.000 0.47 1.47 42.26 4.40
2199 2251 2.946762 GTGAAGTTCACCGCCAGC 59.053 61.111 23.03 0.00 41.37 4.85
2217 2269 2.360852 ATGTGGTGCAGCTCCAGC 60.361 61.111 16.74 11.75 42.49 4.85
2379 2431 1.370172 GATGGCCGCGTAGTAGTCG 60.370 63.158 4.92 0.00 0.00 4.18
2382 2434 0.660595 CGAAGATGGCCGCGTAGTAG 60.661 60.000 4.92 0.00 0.00 2.57
2389 2441 2.586357 GGACTCGAAGATGGCCGC 60.586 66.667 0.00 0.00 33.89 6.53
2661 2713 4.914420 CAGCCGAGGTAGAGCGCG 62.914 72.222 0.00 0.00 0.00 6.86
2721 2773 1.745087 ACAAAAGCAGTCACACCACAG 59.255 47.619 0.00 0.00 0.00 3.66
2730 2782 0.235926 GCGAGGTCACAAAAGCAGTC 59.764 55.000 0.00 0.00 0.00 3.51
2736 2788 1.221466 CGAGCAGCGAGGTCACAAAA 61.221 55.000 11.05 0.00 44.97 2.44
2759 2811 3.003068 ACAAAGCATGCATCTAGATTCGC 59.997 43.478 21.98 5.27 0.00 4.70
2796 2848 3.738246 CCACAGCAGCAGCAGCAG 61.738 66.667 12.92 6.60 45.49 4.24
2797 2849 4.259131 TCCACAGCAGCAGCAGCA 62.259 61.111 12.92 0.00 45.49 4.41
2798 2850 3.432588 CTCCACAGCAGCAGCAGC 61.433 66.667 3.17 0.46 45.49 5.25
2799 2851 1.299562 CTTCTCCACAGCAGCAGCAG 61.300 60.000 3.17 0.00 45.49 4.24
2830 2882 1.196127 GCGTTACAACAGCAGGTTACC 59.804 52.381 0.00 0.00 37.72 2.85
2848 2900 0.248949 GCCTAGACCTAAGTTCGGCG 60.249 60.000 0.00 0.00 0.00 6.46
2871 2924 6.588719 ACTACATCTCATCAGCCTCTTATC 57.411 41.667 0.00 0.00 0.00 1.75
2875 2928 4.826733 CACTACTACATCTCATCAGCCTCT 59.173 45.833 0.00 0.00 0.00 3.69
2876 2929 4.022416 CCACTACTACATCTCATCAGCCTC 60.022 50.000 0.00 0.00 0.00 4.70
2892 2945 2.824341 CCCTCGAACTTGTACCACTACT 59.176 50.000 0.00 0.00 0.00 2.57
2893 2946 2.673326 GCCCTCGAACTTGTACCACTAC 60.673 54.545 0.00 0.00 0.00 2.73
2894 2947 1.547372 GCCCTCGAACTTGTACCACTA 59.453 52.381 0.00 0.00 0.00 2.74
2963 3016 5.062809 GCAGTGCTGATTGAGACTTACTTAC 59.937 44.000 8.18 0.00 0.00 2.34
2967 3020 2.675348 GGCAGTGCTGATTGAGACTTAC 59.325 50.000 16.11 0.00 0.00 2.34
2970 3023 0.689055 TGGCAGTGCTGATTGAGACT 59.311 50.000 16.11 0.00 0.00 3.24
3019 3073 2.206576 AGATCTCCAAAGGCACCAAC 57.793 50.000 0.00 0.00 0.00 3.77
3204 3333 2.689471 GCATGATGGTGGCTATTCAACA 59.311 45.455 0.00 0.00 38.85 3.33
3230 3359 4.322499 CGGACTGTATGGAAGTGGTTTAGT 60.322 45.833 0.00 0.00 0.00 2.24
3249 3378 7.541091 TGCGAGAATATCATAATTAACTCGGAC 59.459 37.037 0.00 0.00 43.60 4.79
3250 3379 7.599171 TGCGAGAATATCATAATTAACTCGGA 58.401 34.615 0.00 0.00 43.60 4.55
3252 3381 8.535592 GGATGCGAGAATATCATAATTAACTCG 58.464 37.037 0.00 0.00 45.29 4.18
3255 3384 9.760660 GTTGGATGCGAGAATATCATAATTAAC 57.239 33.333 0.00 0.00 0.00 2.01
3287 3416 3.565764 TGGATGGTCTAATCCTTGCAG 57.434 47.619 4.93 0.00 45.57 4.41
3307 3436 6.150140 CCTACTGCAAAAGCTAGAACTTTCAT 59.850 38.462 0.00 0.00 38.92 2.57
3389 3518 5.704354 ACTGGAGTACTGATCAGAGATGAT 58.296 41.667 29.27 8.10 0.00 2.45
3437 4500 6.730960 AAATTGAATATTGTTGCTGCCTTG 57.269 33.333 0.00 0.00 0.00 3.61
3517 4580 2.291540 CCCTACTCCAAAAAGGGCATGA 60.292 50.000 0.00 0.00 43.47 3.07
3552 4615 7.012610 GGTTTAGGTTTACTTTGTGCTACTCAA 59.987 37.037 0.00 0.00 0.00 3.02
3553 4616 6.484308 GGTTTAGGTTTACTTTGTGCTACTCA 59.516 38.462 0.00 0.00 0.00 3.41
3560 4623 7.045126 TGATTGGGTTTAGGTTTACTTTGTG 57.955 36.000 0.00 0.00 0.00 3.33
3568 4631 9.065798 CAATCATTTTTGATTGGGTTTAGGTTT 57.934 29.630 17.06 0.00 46.75 3.27
3569 4632 8.620116 CAATCATTTTTGATTGGGTTTAGGTT 57.380 30.769 17.06 0.00 46.75 3.50
3601 4693 7.944729 AGACAACTGTTATTTATGGATGCTT 57.055 32.000 0.00 0.00 0.00 3.91
3725 4818 8.700644 GTTGTACAGCGAACCTAATATGATTAG 58.299 37.037 0.00 0.09 0.00 1.73
3866 4960 5.224888 TGTGTATCGGTTACAAGTCAGTTC 58.775 41.667 0.71 0.00 42.37 3.01


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

AutoCloner maintained by Alex Coulton.