Multiple sequence alignment - TraesCS2A01G052000

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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 TraesCS2A01G052000 chr2A 100.000 2459 0 0 1 2459 20555535 20553077 0.000000e+00 4542.0
1 TraesCS2A01G052000 chr2A 79.699 133 22 5 298 427 3441059 3440929 9.360000e-15 91.6
2 TraesCS2A01G052000 chr2D 91.343 2137 134 17 1 2116 19651723 19653829 0.000000e+00 2874.0
3 TraesCS2A01G052000 chr2D 91.525 354 17 7 2108 2456 19654081 19654426 2.210000e-130 475.0
4 TraesCS2A01G052000 chrUn 88.176 1700 115 38 1 1672 16703869 16702228 0.000000e+00 1947.0
5 TraesCS2A01G052000 chrUn 88.125 1701 115 39 1 1672 16714408 16712766 0.000000e+00 1941.0
6 TraesCS2A01G052000 chrUn 88.118 1700 117 37 1 1672 141678251 141676609 0.000000e+00 1941.0
7 TraesCS2A01G052000 chrUn 88.582 797 80 9 1152 1946 301128685 301127898 0.000000e+00 957.0
8 TraesCS2A01G052000 chrUn 88.457 797 81 9 1152 1946 301124052 301123265 0.000000e+00 952.0
9 TraesCS2A01G052000 chrUn 87.955 797 85 9 1152 1946 273040865 273040078 0.000000e+00 929.0
10 TraesCS2A01G052000 chrUn 87.781 802 87 9 1144 1943 227513930 227514722 0.000000e+00 928.0
11 TraesCS2A01G052000 chrUn 87.781 802 87 9 1144 1943 282694975 282695767 0.000000e+00 928.0
12 TraesCS2A01G052000 chrUn 87.500 360 29 8 2108 2459 16690239 16689888 3.810000e-108 401.0
13 TraesCS2A01G052000 chrUn 87.069 348 35 7 1758 2100 16496704 16497046 3.840000e-103 385.0
14 TraesCS2A01G052000 chrUn 86.455 347 39 5 1758 2100 351929821 351930163 8.300000e-100 374.0
15 TraesCS2A01G052000 chrUn 93.750 96 5 1 2364 2459 301122884 301122790 2.550000e-30 143.0
16 TraesCS2A01G052000 chrUn 93.750 96 5 1 2364 2459 301127517 301127423 2.550000e-30 143.0
17 TraesCS2A01G052000 chrUn 92.929 99 6 1 2361 2459 325151441 325151538 2.550000e-30 143.0
18 TraesCS2A01G052000 chrUn 96.429 84 3 0 2376 2459 141670689 141670606 3.300000e-29 139.0
19 TraesCS2A01G052000 chrUn 91.919 99 7 1 2361 2459 16497504 16497601 1.190000e-28 137.0
20 TraesCS2A01G052000 chrUn 91.919 99 7 1 2361 2459 351930618 351930715 1.190000e-28 137.0
21 TraesCS2A01G052000 chrUn 93.333 60 4 0 1934 1993 16695228 16695169 3.370000e-14 89.8
22 TraesCS2A01G052000 chr3D 83.459 133 19 3 296 427 470876401 470876271 1.190000e-23 121.0
23 TraesCS2A01G052000 chr2B 81.890 127 14 8 305 429 613067489 613067608 5.600000e-17 99.0
24 TraesCS2A01G052000 chr6A 83.178 107 14 4 324 427 482610609 482610504 7.240000e-16 95.3
25 TraesCS2A01G052000 chr4D 78.519 135 29 0 293 427 410409709 410409843 3.370000e-14 89.8


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 TraesCS2A01G052000 chr2A 20553077 20555535 2458 True 4542.00 4542 100.00000 1 2459 1 chr2A.!!$R2 2458
1 TraesCS2A01G052000 chr2D 19651723 19654426 2703 False 1674.50 2874 91.43400 1 2456 2 chr2D.!!$F1 2455
2 TraesCS2A01G052000 chrUn 16702228 16703869 1641 True 1947.00 1947 88.17600 1 1672 1 chrUn.!!$R3 1671
3 TraesCS2A01G052000 chrUn 16712766 16714408 1642 True 1941.00 1941 88.12500 1 1672 1 chrUn.!!$R4 1671
4 TraesCS2A01G052000 chrUn 141676609 141678251 1642 True 1941.00 1941 88.11800 1 1672 1 chrUn.!!$R6 1671
5 TraesCS2A01G052000 chrUn 273040078 273040865 787 True 929.00 929 87.95500 1152 1946 1 chrUn.!!$R7 794
6 TraesCS2A01G052000 chrUn 227513930 227514722 792 False 928.00 928 87.78100 1144 1943 1 chrUn.!!$F1 799
7 TraesCS2A01G052000 chrUn 282694975 282695767 792 False 928.00 928 87.78100 1144 1943 1 chrUn.!!$F2 799
8 TraesCS2A01G052000 chrUn 301122790 301128685 5895 True 548.75 957 91.13475 1152 2459 4 chrUn.!!$R8 1307
9 TraesCS2A01G052000 chrUn 16496704 16497601 897 False 261.00 385 89.49400 1758 2459 2 chrUn.!!$F4 701
10 TraesCS2A01G052000 chrUn 351929821 351930715 894 False 255.50 374 89.18700 1758 2459 2 chrUn.!!$F5 701

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
950 980 0.035458 GTGGCCGGATTGCTAGCTAT 59.965 55.0 17.23 14.36 0.0 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 6688 0.250295 GTACACTGGCCTCAAGTGCA 60.25 55.0 18.99 6.12 37.08 4.57 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
97 98 2.026641 CATGTTCATTACCTGGCAGGG 58.973 52.381 35.34 18.83 40.58 4.45
98 99 1.072266 TGTTCATTACCTGGCAGGGT 58.928 50.000 35.34 22.95 40.58 4.34
153 154 2.554124 GGGCAGAGAAGAAAAGAAGGCT 60.554 50.000 0.00 0.00 0.00 4.58
187 188 1.527380 GTGAAGGGTTGTTCGGGCA 60.527 57.895 0.00 0.00 0.00 5.36
205 206 1.690352 GCATGGGCATAAGGATTTGCT 59.310 47.619 0.00 0.00 40.72 3.91
287 288 6.382859 TCCTGATAGTTAGTTGTTAGATGCCA 59.617 38.462 0.00 0.00 0.00 4.92
302 303 1.909700 TGCCATTGTCTTGTCTTCCC 58.090 50.000 0.00 0.00 0.00 3.97
328 330 4.556699 GCAGGATACAAACACCAAACAGAC 60.557 45.833 0.00 0.00 41.41 3.51
329 331 4.578516 CAGGATACAAACACCAAACAGACA 59.421 41.667 0.00 0.00 41.41 3.41
388 392 1.913419 GACAAAGGGTAGGATCCACCA 59.087 52.381 25.45 6.23 42.04 4.17
427 431 1.214062 CACAGGAGACGAGGCAGAC 59.786 63.158 0.00 0.00 0.00 3.51
451 455 1.871080 CTATAGCGAGGCCAAAGTGG 58.129 55.000 5.01 0.00 41.55 4.00
519 523 1.003580 TCCAAGTGGCTGGATGAAGTC 59.996 52.381 0.00 0.00 40.71 3.01
549 553 7.278646 GCAACTTGACTTGAAAGAATTCCTTTT 59.721 33.333 0.65 0.00 44.63 2.27
567 584 4.319901 CCTTTTAAAATAACAGCGCACGAC 59.680 41.667 11.47 0.00 0.00 4.34
573 590 2.630592 TAACAGCGCACGACCACACA 62.631 55.000 11.47 0.00 0.00 3.72
574 591 3.705638 CAGCGCACGACCACACAG 61.706 66.667 11.47 0.00 0.00 3.66
631 648 3.189910 TGTCCACACATCAGACGTACTAC 59.810 47.826 0.00 0.00 33.09 2.73
632 649 3.439476 GTCCACACATCAGACGTACTACT 59.561 47.826 0.00 0.00 0.00 2.57
633 650 4.633126 GTCCACACATCAGACGTACTACTA 59.367 45.833 0.00 0.00 0.00 1.82
645 662 5.072058 AGACGTACTACTACTCATCATCCCT 59.928 44.000 0.00 0.00 0.00 4.20
707 735 3.745480 CGGTCATGGAATTGTCATAGCCT 60.745 47.826 0.00 0.00 0.00 4.58
735 764 4.142160 GGGGCACATTTCAGAGTATTTTCC 60.142 45.833 0.00 0.00 0.00 3.13
804 833 7.041635 CATGGAAATCATGTGCCACTTATTA 57.958 36.000 0.00 0.00 46.11 0.98
808 837 7.341512 TGGAAATCATGTGCCACTTATTATTGA 59.658 33.333 0.00 0.00 0.00 2.57
809 838 8.362639 GGAAATCATGTGCCACTTATTATTGAT 58.637 33.333 0.00 0.00 0.00 2.57
814 843 8.432013 TCATGTGCCACTTATTATTGATAGTCT 58.568 33.333 0.00 0.00 0.00 3.24
832 861 8.462811 TGATAGTCTAGCTAATAATAGTGCTGC 58.537 37.037 0.00 0.00 37.02 5.25
837 866 8.254508 GTCTAGCTAATAATAGTGCTGCCTAAT 58.745 37.037 0.00 0.00 37.02 1.73
864 893 6.767524 TTTCATTGCTAATAAATCGTGGGT 57.232 33.333 0.00 0.00 0.00 4.51
867 896 6.350103 TCATTGCTAATAAATCGTGGGTACA 58.650 36.000 0.00 0.00 0.00 2.90
869 898 7.500892 TCATTGCTAATAAATCGTGGGTACAAT 59.499 33.333 0.00 0.00 0.00 2.71
882 911 5.238583 GTGGGTACAATCATATACAGGAGC 58.761 45.833 0.00 0.00 0.00 4.70
930 960 3.636231 CTTGCCCCTCGTCCACCA 61.636 66.667 0.00 0.00 0.00 4.17
946 976 1.524621 CCAGTGGCCGGATTGCTAG 60.525 63.158 5.05 0.00 0.00 3.42
947 977 2.182842 CAGTGGCCGGATTGCTAGC 61.183 63.158 5.05 8.10 0.00 3.42
948 978 2.190578 GTGGCCGGATTGCTAGCT 59.809 61.111 17.23 0.00 0.00 3.32
949 979 1.048724 AGTGGCCGGATTGCTAGCTA 61.049 55.000 17.23 9.14 0.00 3.32
950 980 0.035458 GTGGCCGGATTGCTAGCTAT 59.965 55.000 17.23 14.36 0.00 2.97
951 981 1.275291 GTGGCCGGATTGCTAGCTATA 59.725 52.381 17.23 1.55 0.00 1.31
952 982 1.550524 TGGCCGGATTGCTAGCTATAG 59.449 52.381 17.23 11.07 0.00 1.31
953 983 1.134670 GGCCGGATTGCTAGCTATAGG 60.135 57.143 17.23 19.49 0.00 2.57
954 984 1.825474 GCCGGATTGCTAGCTATAGGA 59.175 52.381 25.86 2.24 0.00 2.94
955 985 2.159170 GCCGGATTGCTAGCTATAGGAG 60.159 54.545 25.86 12.63 30.25 3.69
956 986 2.428890 CCGGATTGCTAGCTATAGGAGG 59.571 54.545 20.62 13.83 30.25 4.30
957 987 3.357203 CGGATTGCTAGCTATAGGAGGA 58.643 50.000 17.23 0.00 30.25 3.71
958 988 3.764434 CGGATTGCTAGCTATAGGAGGAA 59.236 47.826 17.23 0.00 30.25 3.36
959 989 4.381079 CGGATTGCTAGCTATAGGAGGAAC 60.381 50.000 17.23 0.00 30.25 3.62
978 1008 1.376812 GGAACGGGTTCATTCGGCT 60.377 57.895 13.08 0.00 41.20 5.52
1065 1095 3.175240 CTGTTCGACTGCGCCGAG 61.175 66.667 4.18 0.00 37.35 4.63
1068 1098 3.449227 TTCGACTGCGCCGAGGAT 61.449 61.111 4.18 0.00 37.35 3.24
1071 1101 2.279120 GACTGCGCCGAGGATCAG 60.279 66.667 4.18 0.00 33.17 2.90
1084 1114 1.219124 GATCAGGGCGTCTGCTTGA 59.781 57.895 3.54 0.00 43.06 3.02
1189 1219 1.745489 CTCTACTTTGCGGTGGGGC 60.745 63.158 0.00 0.00 0.00 5.80
1230 5893 2.298610 CAGTGGATCTACTCCTGCGTA 58.701 52.381 9.05 0.00 45.21 4.42
1272 5935 2.439701 TACGGGCTCCAGGAGACG 60.440 66.667 21.89 23.51 38.87 4.18
1474 6137 1.996292 ATGACAGACACGTTCATCGG 58.004 50.000 0.00 0.00 44.69 4.18
1475 6138 0.955905 TGACAGACACGTTCATCGGA 59.044 50.000 0.00 0.00 44.69 4.55
1478 6141 0.458543 CAGACACGTTCATCGGAGGG 60.459 60.000 0.00 0.00 44.69 4.30
1480 6143 2.885644 CACGTTCATCGGAGGGCG 60.886 66.667 0.00 6.14 44.69 6.13
1481 6144 4.143333 ACGTTCATCGGAGGGCGG 62.143 66.667 10.82 0.00 44.69 6.13
1483 6146 2.777972 CGTTCATCGGAGGGCGGTA 61.778 63.158 0.00 0.00 35.71 4.02
1490 6153 4.795469 TCATCGGAGGGCGGTATATATAA 58.205 43.478 0.00 0.00 0.00 0.98
1493 6156 6.325545 TCATCGGAGGGCGGTATATATAAATT 59.674 38.462 0.00 0.00 0.00 1.82
1712 6379 3.763360 CCTTTTGTGTGGCATCCATCTTA 59.237 43.478 0.00 0.00 35.28 2.10
1713 6380 4.220382 CCTTTTGTGTGGCATCCATCTTAA 59.780 41.667 0.00 0.00 35.28 1.85
1714 6381 5.105228 CCTTTTGTGTGGCATCCATCTTAAT 60.105 40.000 0.00 0.00 35.28 1.40
1715 6382 5.999205 TTTGTGTGGCATCCATCTTAATT 57.001 34.783 0.00 0.00 35.28 1.40
1725 6392 8.713971 TGGCATCCATCTTAATTTAGTTCTCTA 58.286 33.333 0.00 0.00 0.00 2.43
1768 6435 4.725556 TGTTTCTCACGATGTTACTTGC 57.274 40.909 0.00 0.00 0.00 4.01
1803 6470 4.888239 TGAGAGTCCGTATTTAAGAGGGAG 59.112 45.833 0.98 0.00 31.69 4.30
1854 6524 2.158943 GCCTAGTCGGAGCCTAATTGTT 60.159 50.000 0.00 0.00 33.16 2.83
1925 6595 4.973168 ACAAGAAATTGGCAGAGTACTCA 58.027 39.130 24.44 3.92 0.00 3.41
2018 6688 0.537188 GGTCGACCATGATGGAGTGT 59.463 55.000 29.75 0.00 40.96 3.55
2021 6691 0.391528 CGACCATGATGGAGTGTGCA 60.392 55.000 20.11 0.00 40.96 4.57
2039 6709 1.543429 GCACTTGAGGCCAGTGTACTT 60.543 52.381 19.69 0.00 36.09 2.24
2049 6719 1.202879 CCAGTGTACTTTGGGAAGCCA 60.203 52.381 7.98 0.00 36.29 4.75
2102 6772 0.329596 GTGCCTTGGATCCTGGACTT 59.670 55.000 22.88 0.00 0.00 3.01
2111 6781 2.305927 GGATCCTGGACTTGAGGTTTGA 59.694 50.000 3.84 0.00 31.85 2.69
2135 7065 1.291877 GCGTTGTCTCACAAGCCGAT 61.292 55.000 4.19 0.00 39.00 4.18
2138 7068 2.671351 CGTTGTCTCACAAGCCGATAGT 60.671 50.000 0.00 0.00 39.00 2.12
2155 7085 6.430451 CCGATAGTATTTTGCACCATCTTTC 58.570 40.000 0.00 0.00 0.00 2.62
2156 7086 6.038161 CCGATAGTATTTTGCACCATCTTTCA 59.962 38.462 0.00 0.00 0.00 2.69
2157 7087 7.415095 CCGATAGTATTTTGCACCATCTTTCAA 60.415 37.037 0.00 0.00 0.00 2.69
2158 7088 7.429340 CGATAGTATTTTGCACCATCTTTCAAC 59.571 37.037 0.00 0.00 0.00 3.18
2159 7089 6.655078 AGTATTTTGCACCATCTTTCAACT 57.345 33.333 0.00 0.00 0.00 3.16
2160 7090 7.054491 AGTATTTTGCACCATCTTTCAACTT 57.946 32.000 0.00 0.00 0.00 2.66
2161 7091 6.925165 AGTATTTTGCACCATCTTTCAACTTG 59.075 34.615 0.00 0.00 0.00 3.16
2162 7092 3.731652 TTGCACCATCTTTCAACTTGG 57.268 42.857 0.00 0.00 35.31 3.61
2163 7093 2.942804 TGCACCATCTTTCAACTTGGA 58.057 42.857 0.00 0.00 33.36 3.53
2164 7094 3.499338 TGCACCATCTTTCAACTTGGAT 58.501 40.909 0.00 0.00 33.36 3.41
2165 7095 3.507233 TGCACCATCTTTCAACTTGGATC 59.493 43.478 0.00 0.00 33.36 3.36
2182 7112 1.876156 GATCCATTAAGAAGCGCCCAG 59.124 52.381 2.29 0.00 0.00 4.45
2196 7126 1.818674 CGCCCAGCTTATTTTTGACCT 59.181 47.619 0.00 0.00 0.00 3.85
2220 7150 7.042051 CCTTCGTCTCTTTCAACAACATTCTTA 60.042 37.037 0.00 0.00 0.00 2.10
2276 7210 9.250624 CTTACTACATTGATGGCTAACTCTAAC 57.749 37.037 0.00 0.00 0.00 2.34
2318 7252 5.099575 GGGCCTGTACGAATGTAATTTTTG 58.900 41.667 0.84 0.00 36.07 2.44
2331 7265 6.971527 TGTAATTTTTGATCGTACGTGGAT 57.028 33.333 16.05 0.74 0.00 3.41
2362 7296 4.884744 TGCAACTAAGCAAAGTAGGTGAAA 59.115 37.500 0.73 0.00 42.46 2.69
2423 7357 2.328473 CACTACACAGTGTGATCACCG 58.672 52.381 29.58 13.50 46.03 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.303021 ACATGCAACCAAATGATTCAAAAC 57.697 33.333 0.00 0.00 0.00 2.43
97 98 0.668535 GTTTCAGGTGGTTGCCTCAC 59.331 55.000 0.00 0.00 36.58 3.51
98 99 0.550914 AGTTTCAGGTGGTTGCCTCA 59.449 50.000 0.00 0.00 36.58 3.86
111 112 6.384015 TGCCCTAATTCTCTATCAGAGTTTCA 59.616 38.462 3.26 0.00 42.83 2.69
153 154 1.595109 CACGTGTTGGAGCTCTGCA 60.595 57.895 14.64 7.46 0.00 4.41
182 183 0.540365 AATCCTTATGCCCATGCCCG 60.540 55.000 0.00 0.00 36.33 6.13
187 188 3.317455 TGAGCAAATCCTTATGCCCAT 57.683 42.857 0.00 0.00 43.57 4.00
205 206 4.814234 GGTGATGTCAACACACTACTTTGA 59.186 41.667 14.40 0.00 39.65 2.69
302 303 4.202101 TGTTTGGTGTTTGTATCCTGCTTG 60.202 41.667 0.00 0.00 0.00 4.01
337 341 4.340381 GGGCTCATGCTTCATTTTAGATGT 59.660 41.667 0.00 0.00 39.59 3.06
338 342 4.583489 AGGGCTCATGCTTCATTTTAGATG 59.417 41.667 0.00 0.00 39.59 2.90
339 343 4.801164 AGGGCTCATGCTTCATTTTAGAT 58.199 39.130 0.00 0.00 39.59 1.98
340 344 4.080129 AGAGGGCTCATGCTTCATTTTAGA 60.080 41.667 0.00 0.00 39.59 2.10
388 392 0.466189 CCTTAGGGCCATTGATGCGT 60.466 55.000 6.18 0.00 0.00 5.24
413 417 3.462678 GGGGTCTGCCTCGTCTCC 61.463 72.222 0.00 0.00 34.45 3.71
451 455 2.113243 AAATAGCGGCGGATCCCTCC 62.113 60.000 9.78 6.90 38.29 4.30
482 486 6.240002 CCACTTGGACTAGGGATTTGCTATAT 60.240 42.308 0.00 0.00 37.39 0.86
519 523 6.566197 ATTCTTTCAAGTCAAGTTGCCTAG 57.434 37.500 0.00 0.00 0.00 3.02
548 552 2.806818 TGGTCGTGCGCTGTTATTTTAA 59.193 40.909 9.73 0.00 0.00 1.52
549 553 2.158058 GTGGTCGTGCGCTGTTATTTTA 59.842 45.455 9.73 0.00 0.00 1.52
567 584 1.089920 GCCTTCATACAGCTGTGTGG 58.910 55.000 34.41 23.70 37.52 4.17
573 590 5.008019 CGTTATTTCATGCCTTCATACAGCT 59.992 40.000 0.00 0.00 0.00 4.24
574 591 5.007626 TCGTTATTTCATGCCTTCATACAGC 59.992 40.000 0.00 0.00 0.00 4.40
575 592 6.258727 AGTCGTTATTTCATGCCTTCATACAG 59.741 38.462 0.00 0.00 0.00 2.74
631 648 4.573900 GCCACATTAGGGATGATGAGTAG 58.426 47.826 0.00 0.00 39.15 2.57
632 649 3.006859 CGCCACATTAGGGATGATGAGTA 59.993 47.826 0.00 0.00 39.15 2.59
633 650 2.224378 CGCCACATTAGGGATGATGAGT 60.224 50.000 0.00 0.00 39.15 3.41
645 662 2.884997 ATTGGAGCGGCGCCACATTA 62.885 55.000 30.40 11.18 32.04 1.90
707 735 3.393687 ACTCTGAAATGTGCCCCCTATA 58.606 45.455 0.00 0.00 0.00 1.31
749 778 7.945134 TCTCCCGATAAAAATAGTACAGTACC 58.055 38.462 7.13 0.00 0.00 3.34
753 782 7.667557 TCCATCTCCCGATAAAAATAGTACAG 58.332 38.462 0.00 0.00 0.00 2.74
754 783 7.606135 TCCATCTCCCGATAAAAATAGTACA 57.394 36.000 0.00 0.00 0.00 2.90
808 837 7.617723 AGGCAGCACTATTATTAGCTAGACTAT 59.382 37.037 0.00 0.00 35.19 2.12
809 838 6.948886 AGGCAGCACTATTATTAGCTAGACTA 59.051 38.462 0.00 0.00 35.19 2.59
814 843 9.793259 AAAATTAGGCAGCACTATTATTAGCTA 57.207 29.630 0.00 0.00 35.19 3.32
844 873 6.612247 TGTACCCACGATTTATTAGCAATG 57.388 37.500 0.00 0.00 0.00 2.82
846 875 6.824196 TGATTGTACCCACGATTTATTAGCAA 59.176 34.615 0.00 0.00 0.00 3.91
864 893 5.513094 GCCAAGGCTCCTGTATATGATTGTA 60.513 44.000 3.29 0.00 38.26 2.41
867 896 3.245052 GGCCAAGGCTCCTGTATATGATT 60.245 47.826 11.40 0.00 41.60 2.57
869 898 1.699634 GGCCAAGGCTCCTGTATATGA 59.300 52.381 11.40 0.00 41.60 2.15
882 911 2.914289 CTAGCAGGAGGGCCAAGG 59.086 66.667 6.18 0.00 36.29 3.61
930 960 1.048724 TAGCTAGCAATCCGGCCACT 61.049 55.000 18.83 0.00 0.00 4.00
941 971 2.107726 TCCGTTCCTCCTATAGCTAGCA 59.892 50.000 18.83 3.19 0.00 3.49
946 976 1.000496 CCGTTCCGTTCCTCCTATAGC 60.000 57.143 0.00 0.00 0.00 2.97
947 977 1.612463 CCCGTTCCGTTCCTCCTATAG 59.388 57.143 0.00 0.00 0.00 1.31
948 978 1.063717 ACCCGTTCCGTTCCTCCTATA 60.064 52.381 0.00 0.00 0.00 1.31
949 979 0.325016 ACCCGTTCCGTTCCTCCTAT 60.325 55.000 0.00 0.00 0.00 2.57
950 980 0.542702 AACCCGTTCCGTTCCTCCTA 60.543 55.000 0.00 0.00 0.00 2.94
951 981 1.824224 GAACCCGTTCCGTTCCTCCT 61.824 60.000 0.00 0.00 34.75 3.69
952 982 1.375140 GAACCCGTTCCGTTCCTCC 60.375 63.158 0.00 0.00 34.75 4.30
953 983 0.036671 ATGAACCCGTTCCGTTCCTC 60.037 55.000 5.17 0.00 39.10 3.71
954 984 0.399075 AATGAACCCGTTCCGTTCCT 59.601 50.000 5.17 0.00 39.10 3.36
955 985 0.800631 GAATGAACCCGTTCCGTTCC 59.199 55.000 5.17 0.00 39.10 3.62
956 986 0.441145 CGAATGAACCCGTTCCGTTC 59.559 55.000 5.17 8.38 40.06 3.95
957 987 0.952010 CCGAATGAACCCGTTCCGTT 60.952 55.000 5.17 0.89 38.77 4.44
958 988 1.375013 CCGAATGAACCCGTTCCGT 60.375 57.895 5.17 0.00 38.77 4.69
959 989 2.746803 GCCGAATGAACCCGTTCCG 61.747 63.158 5.17 2.15 38.77 4.30
965 995 2.710902 GGGCAAGCCGAATGAACCC 61.711 63.158 4.80 0.00 36.85 4.11
993 1023 2.512286 GCTGCTGGCATGCTCGTA 60.512 61.111 18.92 7.47 41.35 3.43
1065 1095 1.817099 CAAGCAGACGCCCTGATCC 60.817 63.158 9.31 0.00 45.78 3.36
1068 1098 1.078918 CATCAAGCAGACGCCCTGA 60.079 57.895 9.31 0.00 45.78 3.86
1071 1101 2.825836 CCCATCAAGCAGACGCCC 60.826 66.667 0.00 0.00 39.83 6.13
1122 1152 2.206635 CTTGTCCAGGATCTCCGCT 58.793 57.895 0.00 0.00 42.08 5.52
1173 1203 2.040544 CAGCCCCACCGCAAAGTAG 61.041 63.158 0.00 0.00 0.00 2.57
1474 6137 5.820947 CCACCAATTTATATATACCGCCCTC 59.179 44.000 0.00 0.00 0.00 4.30
1475 6138 5.252164 ACCACCAATTTATATATACCGCCCT 59.748 40.000 0.00 0.00 0.00 5.19
1478 6141 5.646360 AGCACCACCAATTTATATATACCGC 59.354 40.000 0.00 0.00 0.00 5.68
1480 6143 8.047310 AGCTAGCACCACCAATTTATATATACC 58.953 37.037 18.83 0.00 0.00 2.73
1712 6379 5.297029 GGGCAGCGAAATAGAGAACTAAATT 59.703 40.000 0.00 0.00 32.04 1.82
1713 6380 4.816925 GGGCAGCGAAATAGAGAACTAAAT 59.183 41.667 0.00 0.00 32.04 1.40
1714 6381 4.189231 GGGCAGCGAAATAGAGAACTAAA 58.811 43.478 0.00 0.00 32.04 1.85
1715 6382 3.737047 CGGGCAGCGAAATAGAGAACTAA 60.737 47.826 0.00 0.00 32.04 2.24
1725 6392 1.598130 GATAGCCGGGCAGCGAAAT 60.598 57.895 23.09 0.13 38.01 2.17
1733 6400 0.733150 GAAACAAGTGATAGCCGGGC 59.267 55.000 12.11 12.11 0.00 6.13
1768 6435 2.488545 CGGACTCTCATATTCCTACCCG 59.511 54.545 0.00 0.00 0.00 5.28
1803 6470 1.153429 CTCGTCCCGAATCCCCAAC 60.153 63.158 0.00 0.00 34.74 3.77
1832 6502 1.412710 CAATTAGGCTCCGACTAGGCA 59.587 52.381 0.00 0.00 44.19 4.75
1925 6595 2.514803 ACAATTTCTTTAGCCGCACCT 58.485 42.857 0.00 0.00 0.00 4.00
2018 6688 0.250295 GTACACTGGCCTCAAGTGCA 60.250 55.000 18.99 6.12 37.08 4.57
2021 6691 2.487265 CCAAAGTACACTGGCCTCAAGT 60.487 50.000 3.32 0.00 0.00 3.16
2039 6709 1.694150 CTAGGATCGATGGCTTCCCAA 59.306 52.381 0.54 0.00 46.14 4.12
2049 6719 4.927267 ACTCATCTCCTCTAGGATCGAT 57.073 45.455 0.00 0.00 44.46 3.59
2102 6772 1.227031 AACGCGACGTCAAACCTCA 60.227 52.632 15.93 0.00 39.99 3.86
2111 6781 1.206745 CTTGTGAGACAACGCGACGT 61.207 55.000 15.93 9.40 43.97 4.34
2135 7065 7.759489 AGTTGAAAGATGGTGCAAAATACTA 57.241 32.000 0.00 0.00 0.00 1.82
2138 7068 6.041409 TCCAAGTTGAAAGATGGTGCAAAATA 59.959 34.615 3.87 0.00 34.50 1.40
2155 7085 4.731773 GCGCTTCTTAATGGATCCAAGTTG 60.732 45.833 20.67 9.98 0.00 3.16
2156 7086 3.378427 GCGCTTCTTAATGGATCCAAGTT 59.622 43.478 20.67 12.31 0.00 2.66
2157 7087 2.945668 GCGCTTCTTAATGGATCCAAGT 59.054 45.455 20.67 12.55 0.00 3.16
2158 7088 2.291741 GGCGCTTCTTAATGGATCCAAG 59.708 50.000 20.67 12.26 0.00 3.61
2159 7089 2.297701 GGCGCTTCTTAATGGATCCAA 58.702 47.619 20.67 0.00 0.00 3.53
2160 7090 1.476833 GGGCGCTTCTTAATGGATCCA 60.477 52.381 18.88 18.88 0.00 3.41
2161 7091 1.239347 GGGCGCTTCTTAATGGATCC 58.761 55.000 7.64 4.20 0.00 3.36
2162 7092 1.876156 CTGGGCGCTTCTTAATGGATC 59.124 52.381 7.64 0.00 0.00 3.36
2163 7093 1.972872 CTGGGCGCTTCTTAATGGAT 58.027 50.000 7.64 0.00 0.00 3.41
2164 7094 0.748005 GCTGGGCGCTTCTTAATGGA 60.748 55.000 7.64 0.00 35.14 3.41
2165 7095 1.729881 GCTGGGCGCTTCTTAATGG 59.270 57.895 7.64 0.00 35.14 3.16
2182 7112 5.864628 AGAGACGAAGGTCAAAAATAAGC 57.135 39.130 0.00 0.00 45.92 3.09
2192 7122 3.869246 TGTTGTTGAAAGAGACGAAGGTC 59.131 43.478 0.00 0.00 43.76 3.85
2196 7126 6.677781 AAGAATGTTGTTGAAAGAGACGAA 57.322 33.333 0.00 0.00 0.00 3.85
2240 7174 7.689313 GCCATCAATGTAGTAAGGGATTGTCTA 60.689 40.741 0.00 0.00 0.00 2.59
2276 7210 3.306710 GCCCCAAGAATTGTTTTACCCAG 60.307 47.826 0.00 0.00 46.99 4.45
2318 7252 4.148348 GCATCTTGTTATCCACGTACGATC 59.852 45.833 24.41 0.00 0.00 3.69
2331 7265 6.633500 ACTTTGCTTAGTTGCATCTTGTTA 57.367 33.333 1.93 0.00 42.96 2.41
2362 7296 2.229784 GGTTAGCTGCATGTGCTTTTCT 59.770 45.455 17.73 1.32 41.46 2.52
2418 7352 3.325425 TCCATCTAACAAAGTTCCGGTGA 59.675 43.478 0.00 0.00 0.00 4.02
2423 7357 6.731164 TCGTTTTTCCATCTAACAAAGTTCC 58.269 36.000 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.