Multiple sequence alignment - TraesCS7D01G239400

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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 TraesCS7D01G239400 chr7D 100.000 2928 0 0 1 2928 204088877 204085950 0.000000e+00 5408.0
1 TraesCS7D01G239400 chr7D 75.936 374 68 17 1565 1922 34337289 34337656 3.880000e-39 172.0
2 TraesCS7D01G239400 chr7A 87.966 2734 176 76 283 2928 215881180 215878512 0.000000e+00 3085.0
3 TraesCS7D01G239400 chr7A 85.957 235 26 4 58 288 215881722 215881491 8.110000e-61 244.0
4 TraesCS7D01G239400 chr7A 75.785 446 87 17 1492 1922 34722065 34722504 3.820000e-49 206.0
5 TraesCS7D01G239400 chr7B 89.507 1868 81 41 287 2064 167688500 167686658 0.000000e+00 2257.0
6 TraesCS7D01G239400 chr7B 88.712 877 90 9 2057 2928 167685833 167684961 0.000000e+00 1062.0
7 TraesCS7D01G239400 chr7B 95.699 93 4 0 70 162 167714068 167713976 1.820000e-32 150.0
8 TraesCS7D01G239400 chr4D 76.910 576 111 17 1364 1922 508807751 508807181 1.020000e-79 307.0
9 TraesCS7D01G239400 chr3A 95.556 45 2 0 2290 2334 413993304 413993348 4.050000e-09 73.1


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 TraesCS7D01G239400 chr7D 204085950 204088877 2927 True 5408.0 5408 100.0000 1 2928 1 chr7D.!!$R1 2927
1 TraesCS7D01G239400 chr7A 215878512 215881722 3210 True 1664.5 3085 86.9615 58 2928 2 chr7A.!!$R1 2870
2 TraesCS7D01G239400 chr7B 167684961 167688500 3539 True 1659.5 2257 89.1095 287 2928 2 chr7B.!!$R2 2641
3 TraesCS7D01G239400 chr4D 508807181 508807751 570 True 307.0 307 76.9100 1364 1922 1 chr4D.!!$R1 558

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
583 914 0.185901 AGCAAGCACCAGAAAGGGAA 59.814 50.0 0.0 0.0 43.89 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 3411 0.181587 TGCGGTGTTCTTTGGGAGAA 59.818 50.0 0.0 0.0 42.03 2.87 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
66 67 2.524302 CGTAATTAAAACATGTGCGGCG 59.476 45.455 0.51 0.51 0.00 6.46
69 70 0.386605 TTAAAACATGTGCGGCGCAG 60.387 50.000 37.27 25.89 40.08 5.18
88 89 2.328099 CGGCAGCTTGGTGAAGTCC 61.328 63.158 3.84 0.00 0.00 3.85
91 92 0.957888 GCAGCTTGGTGAAGTCCCTC 60.958 60.000 3.84 0.00 0.00 4.30
146 147 7.115663 GTGTGAGACACTTGAATCTTAGACTTC 59.884 40.741 0.00 0.00 45.27 3.01
162 163 3.746492 AGACTTCGTGGTCTTGCATAAAC 59.254 43.478 7.10 0.00 43.14 2.01
163 164 3.740115 ACTTCGTGGTCTTGCATAAACT 58.260 40.909 0.00 0.00 0.00 2.66
164 165 4.134563 ACTTCGTGGTCTTGCATAAACTT 58.865 39.130 0.00 0.00 0.00 2.66
180 181 7.136772 GCATAAACTTTTGAACCGTAGAAAGT 58.863 34.615 0.00 0.00 42.36 2.66
183 184 9.768662 ATAAACTTTTGAACCGTAGAAAGTCTA 57.231 29.630 0.00 0.00 40.38 2.59
192 193 9.961265 TGAACCGTAGAAAGTCTATGTATAATG 57.039 33.333 4.29 0.00 34.87 1.90
196 197 9.114965 CCGTAGAAAGTCTATGTATAATGAACG 57.885 37.037 4.29 0.00 34.87 3.95
198 199 9.680315 GTAGAAAGTCTATGTATAATGAACGCT 57.320 33.333 0.00 0.00 30.76 5.07
200 201 9.035607 AGAAAGTCTATGTATAATGAACGCTTG 57.964 33.333 0.00 0.00 0.00 4.01
201 202 8.718102 AAAGTCTATGTATAATGAACGCTTGT 57.282 30.769 0.00 0.00 0.00 3.16
202 203 9.811995 AAAGTCTATGTATAATGAACGCTTGTA 57.188 29.630 0.00 0.00 0.00 2.41
203 204 8.798748 AGTCTATGTATAATGAACGCTTGTAC 57.201 34.615 0.00 0.00 0.00 2.90
204 205 8.630917 AGTCTATGTATAATGAACGCTTGTACT 58.369 33.333 0.00 0.00 0.00 2.73
205 206 9.888878 GTCTATGTATAATGAACGCTTGTACTA 57.111 33.333 0.00 0.00 0.00 1.82
234 235 5.597182 AGTTTCTTAGCCATATACTCCACGA 59.403 40.000 0.00 0.00 0.00 4.35
237 238 4.277672 TCTTAGCCATATACTCCACGACAC 59.722 45.833 0.00 0.00 0.00 3.67
241 242 4.833380 AGCCATATACTCCACGACACTTAT 59.167 41.667 0.00 0.00 0.00 1.73
246 247 7.042051 CCATATACTCCACGACACTTATTTTGG 60.042 40.741 0.00 0.00 0.00 3.28
249 250 4.069304 CTCCACGACACTTATTTTGGGAA 58.931 43.478 0.00 0.00 0.00 3.97
251 252 3.818773 CCACGACACTTATTTTGGGAAGT 59.181 43.478 0.00 0.00 36.31 3.01
254 255 5.929992 CACGACACTTATTTTGGGAAGTAGA 59.070 40.000 0.00 0.00 34.13 2.59
255 256 6.425721 CACGACACTTATTTTGGGAAGTAGAA 59.574 38.462 0.00 0.00 34.13 2.10
259 260 9.498176 GACACTTATTTTGGGAAGTAGAAAGTA 57.502 33.333 0.00 0.00 34.13 2.24
312 640 5.246203 ACACTGTTATTTACTCTCCAGCTGA 59.754 40.000 17.39 0.00 0.00 4.26
388 716 2.126502 GTTGTTGCGCCCGATTGG 60.127 61.111 4.18 0.00 37.09 3.16
399 727 1.001378 GCCCGATTGGAATTTGGATCG 60.001 52.381 0.00 9.81 40.62 3.69
400 728 1.001378 CCCGATTGGAATTTGGATCGC 60.001 52.381 0.00 0.00 39.86 4.58
401 729 1.001378 CCGATTGGAATTTGGATCGCC 60.001 52.381 0.00 0.00 39.86 5.54
402 730 1.001378 CGATTGGAATTTGGATCGCCC 60.001 52.381 5.68 0.00 35.57 6.13
403 731 1.341209 GATTGGAATTTGGATCGCCCC 59.659 52.381 0.00 0.00 0.00 5.80
404 732 0.686112 TTGGAATTTGGATCGCCCCC 60.686 55.000 0.00 0.00 0.00 5.40
446 774 5.801380 CAGCTACTTTTGGTAAACCTCCTA 58.199 41.667 0.02 0.00 36.82 2.94
447 775 6.235664 CAGCTACTTTTGGTAAACCTCCTAA 58.764 40.000 0.02 0.00 36.82 2.69
533 864 5.201713 TCCGAACTCCATTATTAGAGCAG 57.798 43.478 0.00 0.00 33.18 4.24
583 914 0.185901 AGCAAGCACCAGAAAGGGAA 59.814 50.000 0.00 0.00 43.89 3.97
719 1081 4.866088 AATGCAATTGTCCGCACG 57.134 50.000 7.40 0.00 41.79 5.34
723 1085 2.126888 CAATTGTCCGCACGCACC 60.127 61.111 0.00 0.00 0.00 5.01
724 1086 2.593148 AATTGTCCGCACGCACCA 60.593 55.556 0.00 0.00 0.00 4.17
725 1087 2.616330 AATTGTCCGCACGCACCAG 61.616 57.895 0.00 0.00 0.00 4.00
762 1145 2.880879 CCAGTCGATGACGCCACG 60.881 66.667 0.00 0.00 37.67 4.94
1075 1467 0.979665 CAAGACCCTCCTCAAGAGCA 59.020 55.000 0.00 0.00 41.74 4.26
1089 1481 1.752683 AGAGCAACGACCTCTACGAT 58.247 50.000 0.00 0.00 37.88 3.73
1093 1485 2.950309 AGCAACGACCTCTACGATGTAT 59.050 45.455 0.00 0.00 36.29 2.29
1096 1488 2.294979 ACGACCTCTACGATGTATGCA 58.705 47.619 0.00 0.00 34.70 3.96
1097 1489 2.290916 ACGACCTCTACGATGTATGCAG 59.709 50.000 0.00 0.00 34.70 4.41
1100 1492 3.556999 ACCTCTACGATGTATGCAGACT 58.443 45.455 13.44 0.00 0.00 3.24
1104 1496 2.586258 ACGATGTATGCAGACTGTCC 57.414 50.000 13.44 0.00 0.00 4.02
1105 1497 2.103373 ACGATGTATGCAGACTGTCCT 58.897 47.619 13.44 0.00 0.00 3.85
1106 1498 2.159184 ACGATGTATGCAGACTGTCCTG 60.159 50.000 13.44 3.77 37.23 3.86
1135 1542 3.806521 CGTCCCTGAATTTATCTGCTGAG 59.193 47.826 0.00 0.00 0.00 3.35
1136 1543 4.442052 CGTCCCTGAATTTATCTGCTGAGA 60.442 45.833 0.00 0.00 0.00 3.27
1137 1544 5.431765 GTCCCTGAATTTATCTGCTGAGAA 58.568 41.667 0.00 0.00 0.00 2.87
1138 1545 6.060788 GTCCCTGAATTTATCTGCTGAGAAT 58.939 40.000 1.28 1.05 0.00 2.40
1139 1546 6.545298 GTCCCTGAATTTATCTGCTGAGAATT 59.455 38.462 13.79 13.79 0.00 2.17
1140 1547 7.716998 GTCCCTGAATTTATCTGCTGAGAATTA 59.283 37.037 13.85 0.00 0.00 1.40
1141 1548 8.274322 TCCCTGAATTTATCTGCTGAGAATTAA 58.726 33.333 13.85 8.75 0.00 1.40
1144 1551 9.894783 CTGAATTTATCTGCTGAGAATTAATGG 57.105 33.333 13.85 5.53 0.00 3.16
1145 1552 8.355169 TGAATTTATCTGCTGAGAATTAATGGC 58.645 33.333 13.85 6.11 0.00 4.40
1147 1554 1.942657 TCTGCTGAGAATTAATGGCGC 59.057 47.619 0.00 0.00 0.00 6.53
1149 1556 0.937304 GCTGAGAATTAATGGCGCGA 59.063 50.000 12.10 0.00 0.00 5.87
1150 1557 1.070309 GCTGAGAATTAATGGCGCGAG 60.070 52.381 12.10 0.00 0.00 5.03
1152 1559 1.933181 TGAGAATTAATGGCGCGAGTG 59.067 47.619 12.10 0.00 0.00 3.51
1154 1561 2.351726 GAGAATTAATGGCGCGAGTGTT 59.648 45.455 12.10 0.40 0.00 3.32
1155 1562 2.095853 AGAATTAATGGCGCGAGTGTTG 59.904 45.455 12.10 0.00 0.00 3.33
1157 1564 1.231221 TTAATGGCGCGAGTGTTGTT 58.769 45.000 12.10 0.00 0.00 2.83
1158 1565 1.231221 TAATGGCGCGAGTGTTGTTT 58.769 45.000 12.10 0.00 0.00 2.83
1159 1566 0.317770 AATGGCGCGAGTGTTGTTTG 60.318 50.000 12.10 0.00 0.00 2.93
1160 1567 1.163420 ATGGCGCGAGTGTTGTTTGA 61.163 50.000 12.10 0.00 0.00 2.69
1174 1581 5.748152 GTGTTGTTTGATTTGCAGTACATGT 59.252 36.000 2.69 2.69 0.00 3.21
1235 1642 0.532573 GAGCTCCGACAGATCACCAA 59.467 55.000 0.87 0.00 37.49 3.67
1274 1685 1.977293 ATTCCGCTCCCTTCTCCTGC 61.977 60.000 0.00 0.00 0.00 4.85
1279 1690 1.617839 CTCCCTTCTCCTGCCCCTT 60.618 63.158 0.00 0.00 0.00 3.95
1289 1700 0.324091 CCTGCCCCTTGAGAATTGCT 60.324 55.000 0.00 0.00 0.00 3.91
1298 1709 3.243434 CCTTGAGAATTGCTGATCATGGC 60.243 47.826 0.00 0.00 32.35 4.40
1308 1721 3.955551 TGCTGATCATGGCATGTGTATTT 59.044 39.130 25.62 6.46 33.23 1.40
2052 2496 7.342026 ACCCGCTCCTCTTTCAAATAAATTATT 59.658 33.333 0.00 0.00 0.00 1.40
2123 3399 3.814625 TGGATAAAATATGCGCACTCCA 58.185 40.909 14.90 13.43 0.00 3.86
2125 3401 4.826733 TGGATAAAATATGCGCACTCCAAT 59.173 37.500 14.90 1.88 0.00 3.16
2131 3407 5.424121 AATATGCGCACTCCAATAACTTC 57.576 39.130 14.90 0.00 0.00 3.01
2133 3409 2.346803 TGCGCACTCCAATAACTTCTC 58.653 47.619 5.66 0.00 0.00 2.87
2135 3411 3.003480 GCGCACTCCAATAACTTCTCTT 58.997 45.455 0.30 0.00 0.00 2.85
2173 3449 4.115199 CCCCCTTTCCCGCCTCTG 62.115 72.222 0.00 0.00 0.00 3.35
2193 3470 1.351012 CGACTACTAGCCGTCACCG 59.649 63.158 11.25 0.00 0.00 4.94
2194 3471 1.364626 CGACTACTAGCCGTCACCGT 61.365 60.000 11.25 0.00 0.00 4.83
2206 3483 0.739813 GTCACCGTAGCCATGACACC 60.740 60.000 0.00 0.00 41.94 4.16
2296 3573 0.455464 CATGTCACTTACGGACGCGA 60.455 55.000 15.93 0.00 38.10 5.87
2311 3588 2.567049 CGACTCCCCTGACGTGTC 59.433 66.667 0.00 0.00 0.00 3.67
2390 3667 2.348888 CCGCTCCGTCACTTACCCT 61.349 63.158 0.00 0.00 0.00 4.34
2393 3670 1.972198 CTCCGTCACTTACCCTGCA 59.028 57.895 0.00 0.00 0.00 4.41
2401 3678 1.004745 CACTTACCCTGCATCAACCCT 59.995 52.381 0.00 0.00 0.00 4.34
2410 3687 0.527565 GCATCAACCCTTCGCACAAT 59.472 50.000 0.00 0.00 0.00 2.71
2413 3690 0.608035 TCAACCCTTCGCACAATCCC 60.608 55.000 0.00 0.00 0.00 3.85
2478 3755 0.436531 GTTTCTTCGCTCGAGCACAG 59.563 55.000 34.69 27.62 42.21 3.66
2520 3798 2.813908 GCCACCTTCTACGCCACG 60.814 66.667 0.00 0.00 0.00 4.94
2566 3844 0.324943 AAGCTACCTCAACATGCCGT 59.675 50.000 0.00 0.00 0.00 5.68
2571 3849 0.889186 ACCTCAACATGCCGTCCAAC 60.889 55.000 0.00 0.00 0.00 3.77
2683 3981 0.179006 GGGATCAGCAACATCTCCCC 60.179 60.000 0.00 0.00 39.80 4.81
2755 4054 1.547675 CCGGGGATGGATTATTGGTGG 60.548 57.143 0.00 0.00 0.00 4.61
2785 4085 4.447054 GGAGATGCTCTAAACACGATGATG 59.553 45.833 0.00 0.00 0.00 3.07
2838 4138 5.580691 CCATCTTAAAGTCATGCTTCGTGTA 59.419 40.000 3.38 0.00 36.17 2.90
2868 4168 0.669318 TCTGGTGGTTCGACGATTGC 60.669 55.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 9.005180 CGCACATGTTTTAATTACGTGAATATT 57.995 29.630 14.13 0.00 36.31 1.28
38 39 7.642194 CCGCACATGTTTTAATTACGTGAATAT 59.358 33.333 14.13 0.00 36.31 1.28
39 40 6.962116 CCGCACATGTTTTAATTACGTGAATA 59.038 34.615 14.13 0.00 36.31 1.75
40 41 5.797934 CCGCACATGTTTTAATTACGTGAAT 59.202 36.000 14.13 0.00 36.31 2.57
41 42 5.147865 CCGCACATGTTTTAATTACGTGAA 58.852 37.500 14.13 0.00 36.31 3.18
42 43 4.713806 CCGCACATGTTTTAATTACGTGA 58.286 39.130 14.13 0.00 36.31 4.35
43 44 3.299542 GCCGCACATGTTTTAATTACGTG 59.700 43.478 0.00 8.24 38.26 4.49
44 45 3.494232 GCCGCACATGTTTTAATTACGT 58.506 40.909 0.00 0.00 0.00 3.57
45 46 2.524302 CGCCGCACATGTTTTAATTACG 59.476 45.455 0.00 0.00 0.00 3.18
46 47 2.277834 GCGCCGCACATGTTTTAATTAC 59.722 45.455 3.15 0.00 0.00 1.89
47 48 2.095212 TGCGCCGCACATGTTTTAATTA 60.095 40.909 8.16 0.00 31.71 1.40
48 49 1.336332 TGCGCCGCACATGTTTTAATT 60.336 42.857 8.16 0.00 31.71 1.40
49 50 0.242286 TGCGCCGCACATGTTTTAAT 59.758 45.000 8.16 0.00 31.71 1.40
50 51 0.386605 CTGCGCCGCACATGTTTTAA 60.387 50.000 8.16 0.00 33.79 1.52
51 52 1.208870 CTGCGCCGCACATGTTTTA 59.791 52.632 8.16 0.00 33.79 1.52
52 53 2.050168 CTGCGCCGCACATGTTTT 60.050 55.556 8.16 0.00 33.79 2.43
53 54 4.705519 GCTGCGCCGCACATGTTT 62.706 61.111 19.50 0.00 33.79 2.83
69 70 2.970974 GACTTCACCAAGCTGCCGC 61.971 63.158 0.00 0.00 32.09 6.53
74 75 1.674057 CGAGGGACTTCACCAAGCT 59.326 57.895 0.00 0.00 41.55 3.74
146 147 4.854399 TCAAAAGTTTATGCAAGACCACG 58.146 39.130 0.00 0.00 0.00 4.94
162 163 7.653767 ACATAGACTTTCTACGGTTCAAAAG 57.346 36.000 7.57 7.57 30.79 2.27
190 191 7.441458 AGAAACTCTTTTAGTACAAGCGTTCAT 59.559 33.333 5.20 0.00 37.50 2.57
192 193 7.175073 AGAAACTCTTTTAGTACAAGCGTTC 57.825 36.000 5.20 2.94 37.50 3.95
196 197 7.172703 TGGCTAAGAAACTCTTTTAGTACAAGC 59.827 37.037 0.00 0.00 37.50 4.01
205 206 8.548877 TGGAGTATATGGCTAAGAAACTCTTTT 58.451 33.333 0.00 0.00 37.89 2.27
206 207 7.988028 GTGGAGTATATGGCTAAGAAACTCTTT 59.012 37.037 0.00 0.00 37.89 2.52
207 208 7.501844 GTGGAGTATATGGCTAAGAAACTCTT 58.498 38.462 0.00 0.00 40.35 2.85
234 235 9.856162 TTACTTTCTACTTCCCAAAATAAGTGT 57.144 29.630 0.00 0.00 36.62 3.55
259 260 8.050316 ACTGGGAGTTGAAAGGATATATCATT 57.950 34.615 14.60 10.80 31.34 2.57
264 269 8.607713 TGTAAAACTGGGAGTTGAAAGGATATA 58.392 33.333 0.00 0.00 38.66 0.86
312 640 1.102978 GGTTCGGTGGCAATTGCTAT 58.897 50.000 28.42 0.00 41.70 2.97
411 739 2.512286 TAGCTGCTCGCATGTGGC 60.512 61.111 4.91 9.39 42.61 5.01
426 754 5.942236 GGGTTAGGAGGTTTACCAAAAGTAG 59.058 44.000 1.13 0.00 38.89 2.57
427 755 5.372066 TGGGTTAGGAGGTTTACCAAAAGTA 59.628 40.000 1.13 0.00 38.89 2.24
446 774 2.351706 TGAACGGCTAACTTTGGGTT 57.648 45.000 0.00 0.00 41.54 4.11
447 775 2.227194 CTTGAACGGCTAACTTTGGGT 58.773 47.619 0.00 0.00 0.00 4.51
462 793 3.216800 AGATGACTGTTGCTTGCTTGAA 58.783 40.909 0.00 0.00 0.00 2.69
506 837 7.039011 TGCTCTAATAATGGAGTTCGGATACAT 60.039 37.037 0.00 0.00 36.59 2.29
719 1081 2.027460 CCAACGTTTGGCTGGTGC 59.973 61.111 0.00 0.00 45.17 5.01
727 1089 0.659123 GGCTACGCAACCAACGTTTG 60.659 55.000 0.00 0.00 41.93 2.93
728 1090 1.096386 TGGCTACGCAACCAACGTTT 61.096 50.000 0.00 0.00 41.93 3.60
729 1091 1.503818 CTGGCTACGCAACCAACGTT 61.504 55.000 0.00 0.00 41.93 3.99
746 1129 3.545481 GCGTGGCGTCATCGACTG 61.545 66.667 14.54 0.00 46.49 3.51
762 1145 4.602696 GCGATGCGATGCAGTGGC 62.603 66.667 0.00 0.00 43.65 5.01
885 1277 2.294233 AGCACGGCCATTATTTATGCTG 59.706 45.455 2.24 0.00 40.29 4.41
913 1305 3.869272 GGAGATGCTGCGGCGTTG 61.869 66.667 14.76 2.49 42.25 4.10
1035 1427 2.340078 GTCTCGCTGCTGTGGACA 59.660 61.111 15.66 0.00 0.00 4.02
1096 1488 2.653702 GAGCGTGCAGGACAGTCT 59.346 61.111 11.29 0.00 0.00 3.24
1097 1489 2.807045 CGAGCGTGCAGGACAGTC 60.807 66.667 11.29 0.00 0.00 3.51
1100 1492 4.357947 GGACGAGCGTGCAGGACA 62.358 66.667 11.29 0.00 36.45 4.02
1104 1496 2.842394 ATTCAGGGACGAGCGTGCAG 62.842 60.000 15.96 8.12 38.24 4.41
1105 1497 2.449031 AATTCAGGGACGAGCGTGCA 62.449 55.000 15.96 0.00 38.24 4.57
1106 1498 1.298859 AAATTCAGGGACGAGCGTGC 61.299 55.000 5.95 5.95 35.66 5.34
1135 1542 2.159572 ACAACACTCGCGCCATTAATTC 60.160 45.455 0.00 0.00 0.00 2.17
1136 1543 1.810151 ACAACACTCGCGCCATTAATT 59.190 42.857 0.00 0.00 0.00 1.40
1137 1544 1.448985 ACAACACTCGCGCCATTAAT 58.551 45.000 0.00 0.00 0.00 1.40
1138 1545 1.231221 AACAACACTCGCGCCATTAA 58.769 45.000 0.00 0.00 0.00 1.40
1139 1546 1.069568 CAAACAACACTCGCGCCATTA 60.070 47.619 0.00 0.00 0.00 1.90
1140 1547 0.317770 CAAACAACACTCGCGCCATT 60.318 50.000 0.00 0.00 0.00 3.16
1141 1548 1.163420 TCAAACAACACTCGCGCCAT 61.163 50.000 0.00 0.00 0.00 4.40
1144 1551 1.447938 CAAATCAAACAACACTCGCGC 59.552 47.619 0.00 0.00 0.00 6.86
1145 1552 1.447938 GCAAATCAAACAACACTCGCG 59.552 47.619 0.00 0.00 0.00 5.87
1147 1554 3.694734 ACTGCAAATCAAACAACACTCG 58.305 40.909 0.00 0.00 0.00 4.18
1149 1556 5.574891 TGTACTGCAAATCAAACAACACT 57.425 34.783 0.00 0.00 0.00 3.55
1150 1557 5.748152 ACATGTACTGCAAATCAAACAACAC 59.252 36.000 0.00 0.00 0.00 3.32
1152 1559 6.475076 TCAACATGTACTGCAAATCAAACAAC 59.525 34.615 0.00 0.00 0.00 3.32
1154 1561 6.141560 TCAACATGTACTGCAAATCAAACA 57.858 33.333 0.00 0.00 0.00 2.83
1155 1562 6.917477 TCTTCAACATGTACTGCAAATCAAAC 59.083 34.615 0.00 0.00 0.00 2.93
1157 1564 6.437928 GTCTTCAACATGTACTGCAAATCAA 58.562 36.000 0.00 0.00 0.00 2.57
1158 1565 5.334028 CGTCTTCAACATGTACTGCAAATCA 60.334 40.000 0.00 0.00 0.00 2.57
1159 1566 5.082059 CGTCTTCAACATGTACTGCAAATC 58.918 41.667 0.00 0.00 0.00 2.17
1160 1567 4.754618 TCGTCTTCAACATGTACTGCAAAT 59.245 37.500 0.00 0.00 0.00 2.32
1174 1581 1.067425 CGGGTACACCATCGTCTTCAA 60.067 52.381 0.00 0.00 40.22 2.69
1235 1642 0.038618 TGCGTACAAGATGTGCTCGT 60.039 50.000 0.00 0.00 30.49 4.18
1274 1685 3.008835 TGATCAGCAATTCTCAAGGGG 57.991 47.619 0.00 0.00 0.00 4.79
1279 1690 3.007473 TGCCATGATCAGCAATTCTCA 57.993 42.857 7.14 0.00 35.69 3.27
1289 1700 7.774625 TCTTCTAAAATACACATGCCATGATCA 59.225 33.333 12.53 0.00 0.00 2.92
1308 1721 8.896744 CCATTAACTCATCTGCAATTCTTCTAA 58.103 33.333 0.00 0.00 0.00 2.10
1331 1744 5.341169 ACCAGAACAAATAAACATCCCCAT 58.659 37.500 0.00 0.00 0.00 4.00
1923 2355 2.036733 CTCCGCCGGTCCTATAATCAAA 59.963 50.000 1.63 0.00 0.00 2.69
1982 2425 0.376852 TCGCGAATAAACATGCCAGC 59.623 50.000 6.20 0.00 0.00 4.85
2114 3390 2.622436 AGAGAAGTTATTGGAGTGCGC 58.378 47.619 0.00 0.00 0.00 6.09
2123 3399 7.998964 TGTTCTTTGGGAGAAAGAGAAGTTATT 59.001 33.333 0.00 0.00 45.59 1.40
2125 3401 6.766467 GTGTTCTTTGGGAGAAAGAGAAGTTA 59.234 38.462 0.00 0.00 45.59 2.24
2131 3407 2.808543 CGGTGTTCTTTGGGAGAAAGAG 59.191 50.000 0.00 0.00 45.59 2.85
2133 3409 1.266989 GCGGTGTTCTTTGGGAGAAAG 59.733 52.381 0.00 0.00 45.59 2.62
2135 3411 0.181587 TGCGGTGTTCTTTGGGAGAA 59.818 50.000 0.00 0.00 42.03 2.87
2193 3470 2.189521 CCGGGGTGTCATGGCTAC 59.810 66.667 0.00 0.00 0.00 3.58
2194 3471 3.792736 GCCGGGGTGTCATGGCTA 61.793 66.667 2.18 0.00 44.16 3.93
2206 3483 4.478371 GGTAAACGGGGAGCCGGG 62.478 72.222 2.18 0.00 37.53 5.73
2273 3550 2.668250 CGTCCGTAAGTGACATGACAA 58.332 47.619 0.00 0.00 37.38 3.18
2274 3551 1.667756 GCGTCCGTAAGTGACATGACA 60.668 52.381 0.00 0.00 37.38 3.58
2296 3573 1.831286 AACGACACGTCAGGGGAGT 60.831 57.895 0.00 0.00 39.99 3.85
2311 3588 2.256158 CATGCCAGTGTGCCAACG 59.744 61.111 1.78 0.00 0.00 4.10
2343 3620 4.169264 TCTGACATACTACCCCCTGACATA 59.831 45.833 0.00 0.00 0.00 2.29
2355 3632 1.878088 GCGGGATCGTCTGACATACTA 59.122 52.381 8.73 0.00 38.89 1.82
2390 3667 0.821301 TTGTGCGAAGGGTTGATGCA 60.821 50.000 0.00 0.00 0.00 3.96
2393 3670 1.463674 GGATTGTGCGAAGGGTTGAT 58.536 50.000 0.00 0.00 0.00 2.57
2401 3678 1.445410 CGAGACGGGATTGTGCGAA 60.445 57.895 0.00 0.00 0.00 4.70
2410 3687 1.153208 GAGGTAGCTCGAGACGGGA 60.153 63.158 18.75 0.00 0.00 5.14
2462 3739 2.126307 GCTGTGCTCGAGCGAAGA 60.126 61.111 31.95 16.55 45.83 2.87
2478 3755 1.968540 GGCACAGTGGACTTGAGGC 60.969 63.158 1.84 0.00 0.00 4.70
2536 3814 2.490217 GTAGCTTCAGAGGCGCGA 59.510 61.111 12.10 0.00 34.52 5.87
2546 3824 1.009829 CGGCATGTTGAGGTAGCTTC 58.990 55.000 0.00 0.00 0.00 3.86
2571 3849 0.610232 CCTTCTTTCACCTGCCAGGG 60.610 60.000 16.70 4.22 40.58 4.45
2606 3885 3.165685 GGCATGCATTGGGCCCAT 61.166 61.111 29.23 13.49 43.89 4.00
2648 3946 2.818751 TCCCCAATACATTCACCACC 57.181 50.000 0.00 0.00 0.00 4.61
2650 3948 3.688126 GCTGATCCCCAATACATTCACCA 60.688 47.826 0.00 0.00 0.00 4.17
2740 4039 6.068010 TCCAACATACCACCAATAATCCATC 58.932 40.000 0.00 0.00 0.00 3.51
2785 4085 4.575885 TGCCACCTCACTATAAACAAGTC 58.424 43.478 0.00 0.00 0.00 3.01
2838 4138 5.014858 TCGAACCACCAGATCTTTAGTAGT 58.985 41.667 0.00 0.00 0.00 2.73
2868 4168 3.006967 CCGGAGATAATCCCCTACAAGTG 59.993 52.174 0.00 0.00 46.50 3.16


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

AutoCloner maintained by Alex Coulton.