Multiple sequence alignment - TraesCS5B01G439200

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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 TraesCS5B01G439200 chr5B 100.000 3543 0 0 1 3543 611482567 611479025 0.000000e+00 6543
1 TraesCS5B01G439200 chr5D 92.325 3127 144 57 485 3543 495032749 495029651 0.000000e+00 4357
2 TraesCS5B01G439200 chr5D 89.885 435 20 7 75 502 495034839 495034422 4.020000e-149 538
3 TraesCS5B01G439200 chr5A 91.002 2945 134 54 655 3543 619099747 619096878 0.000000e+00 3849
4 TraesCS5B01G439200 chr5A 83.258 663 32 19 26 655 619100408 619099792 1.450000e-148 536
5 TraesCS5B01G439200 chr1D 77.353 340 58 16 1413 1743 119010744 119010415 2.170000e-42 183
6 TraesCS5B01G439200 chr1A 77.126 341 57 18 1413 1743 131521532 131521203 1.010000e-40 178
7 TraesCS5B01G439200 chr1B 76.106 339 64 14 1413 1743 181218219 181217890 1.020000e-35 161
8 TraesCS5B01G439200 chr7D 76.157 281 46 17 1490 1758 525774364 525774093 1.030000e-25 128
9 TraesCS5B01G439200 chr7B 75.986 279 50 15 1490 1758 562409238 562408967 1.030000e-25 128
10 TraesCS5B01G439200 chr7A 76.071 280 48 15 1490 1758 606330896 606330625 1.030000e-25 128
11 TraesCS5B01G439200 chr6B 75.899 278 52 12 1490 1758 134000202 133999931 1.030000e-25 128


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 TraesCS5B01G439200 chr5B 611479025 611482567 3542 True 6543.0 6543 100.000 1 3543 1 chr5B.!!$R1 3542
1 TraesCS5B01G439200 chr5D 495029651 495034839 5188 True 2447.5 4357 91.105 75 3543 2 chr5D.!!$R1 3468
2 TraesCS5B01G439200 chr5A 619096878 619100408 3530 True 2192.5 3849 87.130 26 3543 2 chr5A.!!$R1 3517

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
200 211 0.304705 GCCACCGAATAGTGAATGCG 59.695 55.0 0.00 0.0 40.34 4.73 F
1171 3007 0.114560 AACAAGAGAGGTCCCGGAGA 59.885 55.0 0.73 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 3129 0.035152 GCCCCATCATCATCGCCATA 60.035 55.0 0.0 0.0 0.0 2.74 R
2919 4800 0.250513 GCAGTGGTCCCAAGTCCTAG 59.749 60.0 0.0 0.0 0.0 3.02 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
38 39 1.769733 TACGTTTTCAGACGAACCCG 58.230 50.000 0.00 0.00 45.47 5.28
55 56 3.606687 ACCCGTATGTCAATGGAAGAAC 58.393 45.455 0.00 0.00 0.00 3.01
60 61 5.980116 CCGTATGTCAATGGAAGAACTAGAG 59.020 44.000 0.00 0.00 0.00 2.43
86 87 0.919710 GTCCTGGCTAGGGTGGAATT 59.080 55.000 17.16 0.00 44.70 2.17
91 92 3.555966 CTGGCTAGGGTGGAATTAAAGG 58.444 50.000 0.00 0.00 0.00 3.11
95 96 2.231716 AGGGTGGAATTAAAGGTGCC 57.768 50.000 0.00 0.00 0.00 5.01
200 211 0.304705 GCCACCGAATAGTGAATGCG 59.695 55.000 0.00 0.00 40.34 4.73
214 226 0.798776 AATGCGAGACGAAAAGGCTG 59.201 50.000 0.00 0.00 39.26 4.85
239 251 2.108514 TTGCGCCTCTGCACTATGC 61.109 57.895 4.18 0.00 46.25 3.14
240 252 3.275338 GCGCCTCTGCACTATGCC 61.275 66.667 0.00 0.00 44.23 4.40
241 253 2.187685 CGCCTCTGCACTATGCCA 59.812 61.111 0.00 0.00 44.23 4.92
242 254 1.450134 CGCCTCTGCACTATGCCAA 60.450 57.895 0.00 0.00 44.23 4.52
243 255 1.026182 CGCCTCTGCACTATGCCAAA 61.026 55.000 0.00 0.00 44.23 3.28
244 256 0.737219 GCCTCTGCACTATGCCAAAG 59.263 55.000 0.00 0.00 44.23 2.77
270 282 2.503356 ACAGGAAGAATCGATGAAGCCT 59.497 45.455 0.00 1.25 0.00 4.58
340 352 0.960364 GCTGATTGGGTGGCGAAAGA 60.960 55.000 0.00 0.00 0.00 2.52
341 353 1.533625 CTGATTGGGTGGCGAAAGAA 58.466 50.000 0.00 0.00 0.00 2.52
342 354 1.470098 CTGATTGGGTGGCGAAAGAAG 59.530 52.381 0.00 0.00 0.00 2.85
343 355 1.073125 TGATTGGGTGGCGAAAGAAGA 59.927 47.619 0.00 0.00 0.00 2.87
344 356 2.290896 TGATTGGGTGGCGAAAGAAGAT 60.291 45.455 0.00 0.00 0.00 2.40
345 357 2.286365 TTGGGTGGCGAAAGAAGATT 57.714 45.000 0.00 0.00 0.00 2.40
346 358 1.821216 TGGGTGGCGAAAGAAGATTC 58.179 50.000 0.00 0.00 0.00 2.52
347 359 1.073125 TGGGTGGCGAAAGAAGATTCA 59.927 47.619 0.00 0.00 0.00 2.57
348 360 2.159382 GGGTGGCGAAAGAAGATTCAA 58.841 47.619 0.00 0.00 0.00 2.69
349 361 2.556622 GGGTGGCGAAAGAAGATTCAAA 59.443 45.455 0.00 0.00 0.00 2.69
350 362 3.366374 GGGTGGCGAAAGAAGATTCAAAG 60.366 47.826 0.00 0.00 0.00 2.77
560 2269 8.621532 TTCAGCACTAAAAGAACATGATTAGT 57.378 30.769 0.00 3.59 38.71 2.24
665 2394 1.095228 AACACGATGGGCCATAAGCG 61.095 55.000 21.26 20.89 45.17 4.68
688 2462 6.656945 CGAGAGGAATTAATGAATGAAGCTG 58.343 40.000 0.00 0.00 0.00 4.24
737 2511 3.437049 AGCAATAAGGAAACGCAGAACTC 59.563 43.478 0.00 0.00 0.00 3.01
792 2572 7.814264 TTCCACCAATAACAAATGCAAAATT 57.186 28.000 0.00 0.00 0.00 1.82
793 2573 8.908786 TTCCACCAATAACAAATGCAAAATTA 57.091 26.923 0.00 0.00 0.00 1.40
794 2574 8.908786 TCCACCAATAACAAATGCAAAATTAA 57.091 26.923 0.00 0.00 0.00 1.40
795 2575 9.512588 TCCACCAATAACAAATGCAAAATTAAT 57.487 25.926 0.00 0.00 0.00 1.40
851 2631 1.487142 TGAAGAAAACGGTCAGTGGGA 59.513 47.619 0.00 0.00 0.00 4.37
852 2632 2.105821 TGAAGAAAACGGTCAGTGGGAT 59.894 45.455 0.00 0.00 0.00 3.85
903 2691 4.087892 CCGTGTCCTCAGGGCCAG 62.088 72.222 6.18 0.00 41.63 4.85
927 2715 3.977244 GGGCACAAAGGCACACGG 61.977 66.667 0.00 0.00 46.44 4.94
976 2765 0.320421 AAACACGGACGATCACCCAG 60.320 55.000 0.00 0.00 0.00 4.45
1065 2869 3.119531 CGAAGCTTTGGTTTGCATGGATA 60.120 43.478 5.72 0.00 0.00 2.59
1091 2895 2.494059 CAATGATACCCCGGACATCAC 58.506 52.381 0.73 0.00 31.83 3.06
1112 2948 8.517878 CATCACCATTAAACAAAGAGAGAACAT 58.482 33.333 0.00 0.00 0.00 2.71
1121 2957 4.627467 ACAAAGAGAGAACATACGATGCAC 59.373 41.667 0.00 0.00 0.00 4.57
1122 2958 4.727507 AAGAGAGAACATACGATGCACT 57.272 40.909 0.00 0.00 0.00 4.40
1123 2959 4.727507 AGAGAGAACATACGATGCACTT 57.272 40.909 0.00 0.00 0.00 3.16
1124 2960 4.428209 AGAGAGAACATACGATGCACTTG 58.572 43.478 0.00 0.00 0.00 3.16
1128 2964 2.385013 ACATACGATGCACTTGCTCA 57.615 45.000 2.33 0.00 42.66 4.26
1147 2983 0.323542 ACCACCAACGAACACCCAAA 60.324 50.000 0.00 0.00 0.00 3.28
1160 2996 5.468746 CGAACACCCAAAGAATAACAAGAGA 59.531 40.000 0.00 0.00 0.00 3.10
1161 2997 6.347725 CGAACACCCAAAGAATAACAAGAGAG 60.348 42.308 0.00 0.00 0.00 3.20
1162 2998 5.316987 ACACCCAAAGAATAACAAGAGAGG 58.683 41.667 0.00 0.00 0.00 3.69
1163 2999 5.163088 ACACCCAAAGAATAACAAGAGAGGT 60.163 40.000 0.00 0.00 0.00 3.85
1164 3000 5.412904 CACCCAAAGAATAACAAGAGAGGTC 59.587 44.000 0.00 0.00 0.00 3.85
1165 3001 4.944317 CCCAAAGAATAACAAGAGAGGTCC 59.056 45.833 0.00 0.00 0.00 4.46
1166 3002 4.944317 CCAAAGAATAACAAGAGAGGTCCC 59.056 45.833 0.00 0.00 0.00 4.46
1167 3003 4.473477 AAGAATAACAAGAGAGGTCCCG 57.527 45.455 0.00 0.00 0.00 5.14
1168 3004 2.766828 AGAATAACAAGAGAGGTCCCGG 59.233 50.000 0.00 0.00 0.00 5.73
1169 3005 2.544844 ATAACAAGAGAGGTCCCGGA 57.455 50.000 0.73 0.00 0.00 5.14
1170 3006 1.848652 TAACAAGAGAGGTCCCGGAG 58.151 55.000 0.73 0.00 0.00 4.63
1171 3007 0.114560 AACAAGAGAGGTCCCGGAGA 59.885 55.000 0.73 0.00 0.00 3.71
1172 3008 0.323908 ACAAGAGAGGTCCCGGAGAG 60.324 60.000 0.73 0.00 0.00 3.20
1178 3014 0.753848 GAGGTCCCGGAGAGGAGAAG 60.754 65.000 0.73 0.00 45.00 2.85
1179 3015 1.215679 AGGTCCCGGAGAGGAGAAGA 61.216 60.000 0.73 0.00 45.00 2.87
1233 3069 3.366476 GCACGGCAGGACATATACTAGAG 60.366 52.174 0.00 0.00 0.00 2.43
1240 3076 6.049149 GCAGGACATATACTAGAGCACAAAA 58.951 40.000 0.00 0.00 0.00 2.44
1242 3078 7.041721 CAGGACATATACTAGAGCACAAAACA 58.958 38.462 0.00 0.00 0.00 2.83
1247 3083 7.334421 ACATATACTAGAGCACAAAACACAAGG 59.666 37.037 0.00 0.00 0.00 3.61
1252 3088 2.860136 GAGCACAAAACACAAGGAAAGC 59.140 45.455 0.00 0.00 0.00 3.51
1254 3090 2.999355 GCACAAAACACAAGGAAAGCAA 59.001 40.909 0.00 0.00 0.00 3.91
1255 3091 3.062504 GCACAAAACACAAGGAAAGCAAG 59.937 43.478 0.00 0.00 0.00 4.01
1256 3092 3.062504 CACAAAACACAAGGAAAGCAAGC 59.937 43.478 0.00 0.00 0.00 4.01
1257 3093 3.260740 CAAAACACAAGGAAAGCAAGCA 58.739 40.909 0.00 0.00 0.00 3.91
1258 3094 3.608316 AAACACAAGGAAAGCAAGCAA 57.392 38.095 0.00 0.00 0.00 3.91
1259 3095 2.584492 ACACAAGGAAAGCAAGCAAC 57.416 45.000 0.00 0.00 0.00 4.17
1260 3096 1.824230 ACACAAGGAAAGCAAGCAACA 59.176 42.857 0.00 0.00 0.00 3.33
1261 3097 2.431782 ACACAAGGAAAGCAAGCAACAT 59.568 40.909 0.00 0.00 0.00 2.71
1262 3098 3.118665 ACACAAGGAAAGCAAGCAACATT 60.119 39.130 0.00 0.00 0.00 2.71
1263 3099 3.492011 CACAAGGAAAGCAAGCAACATTC 59.508 43.478 0.00 0.00 0.00 2.67
1277 3113 4.403432 AGCAACATTCCATTCCATTACCTG 59.597 41.667 0.00 0.00 0.00 4.00
1278 3114 4.685924 CAACATTCCATTCCATTACCTGC 58.314 43.478 0.00 0.00 0.00 4.85
1279 3115 3.299503 ACATTCCATTCCATTACCTGCC 58.700 45.455 0.00 0.00 0.00 4.85
1280 3116 2.051334 TTCCATTCCATTACCTGCCG 57.949 50.000 0.00 0.00 0.00 5.69
1281 3117 1.208706 TCCATTCCATTACCTGCCGA 58.791 50.000 0.00 0.00 0.00 5.54
1282 3118 1.140852 TCCATTCCATTACCTGCCGAG 59.859 52.381 0.00 0.00 0.00 4.63
1283 3119 1.597742 CATTCCATTACCTGCCGAGG 58.402 55.000 0.00 0.00 46.21 4.63
1291 3127 2.124570 CCTGCCGAGGTCCCATTG 60.125 66.667 0.00 0.00 34.16 2.82
1292 3128 2.671070 CTGCCGAGGTCCCATTGT 59.329 61.111 0.00 0.00 0.00 2.71
1293 3129 1.002134 CTGCCGAGGTCCCATTGTT 60.002 57.895 0.00 0.00 0.00 2.83
1309 3145 4.380128 CCATTGTTATGGCGATGATGATGG 60.380 45.833 0.00 0.00 44.64 3.51
1310 3146 2.781923 TGTTATGGCGATGATGATGGG 58.218 47.619 0.00 0.00 0.00 4.00
1312 3148 0.035152 TATGGCGATGATGATGGGGC 60.035 55.000 0.00 0.00 0.00 5.80
1313 3149 3.052082 GGCGATGATGATGGGGCG 61.052 66.667 0.00 0.00 0.00 6.13
1314 3150 3.052082 GCGATGATGATGGGGCGG 61.052 66.667 0.00 0.00 0.00 6.13
1315 3151 2.427320 CGATGATGATGGGGCGGT 59.573 61.111 0.00 0.00 0.00 5.68
1316 3152 1.669115 CGATGATGATGGGGCGGTC 60.669 63.158 0.00 0.00 0.00 4.79
1317 3153 1.669115 GATGATGATGGGGCGGTCG 60.669 63.158 0.00 0.00 0.00 4.79
1318 3154 2.099652 GATGATGATGGGGCGGTCGA 62.100 60.000 0.00 0.00 0.00 4.20
1319 3155 2.280186 GATGATGGGGCGGTCGAC 60.280 66.667 7.13 7.13 0.00 4.20
1480 3343 2.135581 ACGGACGACCCCAAGAACA 61.136 57.895 0.00 0.00 0.00 3.18
1641 3504 3.394836 GGCCTGCTCTCCGACCTT 61.395 66.667 0.00 0.00 0.00 3.50
1761 3624 4.016706 ACCGGCAACTTCCCCTCG 62.017 66.667 0.00 0.00 0.00 4.63
1843 3715 4.529769 TCATCATCATCATCTGTACCTCCC 59.470 45.833 0.00 0.00 0.00 4.30
1889 3761 2.543777 TAACAACTGGCTGTCTGTCC 57.456 50.000 0.00 0.00 0.00 4.02
2221 4093 3.567797 GGCATCGTCGGCAAGCTC 61.568 66.667 0.00 0.00 0.00 4.09
2419 4291 3.197790 CAGAACTGCATCGCCGGG 61.198 66.667 2.18 0.00 0.00 5.73
2518 4390 2.867855 ATCGCCACCGCCGATGTAT 61.868 57.895 0.00 0.00 43.14 2.29
2674 4547 9.632807 CGGAAACAAAGAAATAACAATGGATTA 57.367 29.630 0.00 0.00 0.00 1.75
2749 4622 5.805728 TCTTTACCTGTTCCTTCCTCATTC 58.194 41.667 0.00 0.00 0.00 2.67
2794 4675 8.833231 AGTCCTACATAATCATACGAAAATGG 57.167 34.615 0.00 0.00 0.00 3.16
2795 4676 8.647796 AGTCCTACATAATCATACGAAAATGGA 58.352 33.333 0.00 0.00 0.00 3.41
2919 4800 7.748241 GTCAGAATTCAGTTCAGAATTAGTTGC 59.252 37.037 8.44 0.00 45.51 4.17
2928 4809 6.876257 AGTTCAGAATTAGTTGCTAGGACTTG 59.124 38.462 0.00 0.00 0.00 3.16
3021 4902 6.470278 ACTGTTCGGCTAAATTAGTTAACCT 58.530 36.000 0.88 0.00 0.00 3.50
3047 4928 6.134535 AGTGTTAAACATATGAACCCTGGA 57.865 37.500 10.38 0.00 0.00 3.86
3173 5054 3.746045 AGCTACAAAAACAGAGGACGA 57.254 42.857 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.454585 AAAACGTATATCGATAACTGAATTCGA 57.545 29.630 9.61 0.00 44.93 3.71
1 2 9.709701 GAAAACGTATATCGATAACTGAATTCG 57.290 33.333 9.61 5.26 42.86 3.34
4 5 9.961265 TCTGAAAACGTATATCGATAACTGAAT 57.039 29.630 9.61 0.00 42.86 2.57
5 6 9.229784 GTCTGAAAACGTATATCGATAACTGAA 57.770 33.333 9.61 0.00 42.86 3.02
6 7 7.585210 CGTCTGAAAACGTATATCGATAACTGA 59.415 37.037 9.61 0.00 42.86 3.41
7 8 7.585210 TCGTCTGAAAACGTATATCGATAACTG 59.415 37.037 9.61 4.55 43.08 3.16
8 9 7.633621 TCGTCTGAAAACGTATATCGATAACT 58.366 34.615 9.61 0.00 43.08 2.24
9 10 7.827156 TCGTCTGAAAACGTATATCGATAAC 57.173 36.000 9.61 8.19 43.08 1.89
10 11 7.376866 GGTTCGTCTGAAAACGTATATCGATAA 59.623 37.037 9.61 0.00 43.08 1.75
11 12 6.852853 GGTTCGTCTGAAAACGTATATCGATA 59.147 38.462 7.75 7.75 43.08 2.92
12 13 5.684626 GGTTCGTCTGAAAACGTATATCGAT 59.315 40.000 2.16 2.16 43.08 3.59
13 14 5.030295 GGTTCGTCTGAAAACGTATATCGA 58.970 41.667 0.00 0.00 43.08 3.59
14 15 4.205792 GGGTTCGTCTGAAAACGTATATCG 59.794 45.833 0.00 0.00 43.08 2.92
15 16 4.205792 CGGGTTCGTCTGAAAACGTATATC 59.794 45.833 0.00 0.00 43.08 1.63
16 17 4.107622 CGGGTTCGTCTGAAAACGTATAT 58.892 43.478 0.00 0.00 43.08 0.86
17 18 3.500982 CGGGTTCGTCTGAAAACGTATA 58.499 45.455 0.00 0.00 43.08 1.47
18 19 2.331194 CGGGTTCGTCTGAAAACGTAT 58.669 47.619 0.00 0.00 43.08 3.06
19 20 1.769733 CGGGTTCGTCTGAAAACGTA 58.230 50.000 0.00 0.00 43.08 3.57
20 21 2.596875 CGGGTTCGTCTGAAAACGT 58.403 52.632 0.00 0.00 43.08 3.99
38 39 7.113658 TCCTCTAGTTCTTCCATTGACATAC 57.886 40.000 0.00 0.00 0.00 2.39
39 40 7.733773 TTCCTCTAGTTCTTCCATTGACATA 57.266 36.000 0.00 0.00 0.00 2.29
60 61 1.285078 ACCCTAGCCAGGACAAATTCC 59.715 52.381 0.00 0.00 45.91 3.01
72 73 3.288092 CACCTTTAATTCCACCCTAGCC 58.712 50.000 0.00 0.00 0.00 3.93
200 211 1.801178 CTTGTCCAGCCTTTTCGTCTC 59.199 52.381 0.00 0.00 0.00 3.36
214 226 2.970974 GCAGAGGCGCAACTTGTCC 61.971 63.158 10.83 0.00 0.00 4.02
239 251 3.612479 CGATTCTTCCTGTTTGGCTTTGG 60.612 47.826 0.00 0.00 35.26 3.28
240 252 3.253188 TCGATTCTTCCTGTTTGGCTTTG 59.747 43.478 0.00 0.00 35.26 2.77
241 253 3.486383 TCGATTCTTCCTGTTTGGCTTT 58.514 40.909 0.00 0.00 35.26 3.51
242 254 3.140325 TCGATTCTTCCTGTTTGGCTT 57.860 42.857 0.00 0.00 35.26 4.35
243 255 2.859165 TCGATTCTTCCTGTTTGGCT 57.141 45.000 0.00 0.00 35.26 4.75
244 256 3.009723 TCATCGATTCTTCCTGTTTGGC 58.990 45.455 0.00 0.00 35.26 4.52
270 282 1.075542 GCACGAATGTTGACGATGGA 58.924 50.000 0.00 0.00 0.00 3.41
348 360 8.725148 GCTCTTGTGCTTATGTATAATATGCTT 58.275 33.333 5.25 0.00 0.00 3.91
349 361 7.335422 GGCTCTTGTGCTTATGTATAATATGCT 59.665 37.037 5.25 0.00 0.00 3.79
350 362 7.119699 TGGCTCTTGTGCTTATGTATAATATGC 59.880 37.037 0.00 0.00 0.00 3.14
447 459 4.499183 ACTTAACATGCGAGAAAGAGAGG 58.501 43.478 0.00 0.00 0.00 3.69
503 516 0.815615 CTGCCCAGGGAAAGTATCGC 60.816 60.000 10.89 0.00 41.15 4.58
505 518 3.808984 CCTGCCCAGGGAAAGTATC 57.191 57.895 10.89 0.00 44.87 2.24
560 2269 4.763279 TCTCGCCGGTCTTGATTATATGTA 59.237 41.667 1.90 0.00 0.00 2.29
665 2394 7.520292 GCTCAGCTTCATTCATTAATTCCTCTC 60.520 40.741 0.00 0.00 0.00 3.20
688 2462 5.619625 AAACTCTTTGTCTGCTATTGCTC 57.380 39.130 0.00 0.00 40.48 4.26
737 2511 5.684704 TGGTAAGATGCCTTCTCTTTATGG 58.315 41.667 0.00 0.00 34.81 2.74
793 2573 8.571336 GCCAACAGAGCATACAGATAAATTATT 58.429 33.333 0.00 0.00 0.00 1.40
794 2574 7.095060 CGCCAACAGAGCATACAGATAAATTAT 60.095 37.037 0.00 0.00 0.00 1.28
795 2575 6.202762 CGCCAACAGAGCATACAGATAAATTA 59.797 38.462 0.00 0.00 0.00 1.40
796 2576 5.008019 CGCCAACAGAGCATACAGATAAATT 59.992 40.000 0.00 0.00 0.00 1.82
797 2577 4.512944 CGCCAACAGAGCATACAGATAAAT 59.487 41.667 0.00 0.00 0.00 1.40
851 2631 3.441572 GCCTGCACTCAGTGACAAAATAT 59.558 43.478 9.70 0.00 38.66 1.28
852 2632 2.813754 GCCTGCACTCAGTGACAAAATA 59.186 45.455 9.70 0.00 38.66 1.40
903 2691 2.359975 CCTTTGTGCCCGACTCCC 60.360 66.667 0.00 0.00 0.00 4.30
927 2715 2.159327 AGCAAATTGACTTTGGCTGC 57.841 45.000 0.00 0.00 43.73 5.25
976 2765 1.595093 CGGATTTTGGGAGTGGGTGC 61.595 60.000 0.00 0.00 0.00 5.01
1052 2843 1.298339 GCGCGTATCCATGCAAACC 60.298 57.895 8.43 0.00 36.39 3.27
1065 2869 2.203153 GGGGTATCATTGGCGCGT 60.203 61.111 8.43 0.00 0.00 6.01
1091 2895 8.251750 TCGTATGTTCTCTCTTTGTTTAATGG 57.748 34.615 0.00 0.00 0.00 3.16
1112 2948 0.320050 TGGTGAGCAAGTGCATCGTA 59.680 50.000 6.00 0.00 45.16 3.43
1121 2957 0.307760 GTTCGTTGGTGGTGAGCAAG 59.692 55.000 0.00 0.00 40.21 4.01
1122 2958 0.393132 TGTTCGTTGGTGGTGAGCAA 60.393 50.000 0.00 0.00 37.24 3.91
1123 2959 1.092921 GTGTTCGTTGGTGGTGAGCA 61.093 55.000 0.00 0.00 0.00 4.26
1124 2960 1.647084 GTGTTCGTTGGTGGTGAGC 59.353 57.895 0.00 0.00 0.00 4.26
1128 2964 0.323542 TTTGGGTGTTCGTTGGTGGT 60.324 50.000 0.00 0.00 0.00 4.16
1147 2983 2.766828 CCGGGACCTCTCTTGTTATTCT 59.233 50.000 0.00 0.00 0.00 2.40
1160 2996 1.215679 TCTTCTCCTCTCCGGGACCT 61.216 60.000 0.00 0.00 0.00 3.85
1161 2997 0.753848 CTCTTCTCCTCTCCGGGACC 60.754 65.000 0.00 0.00 0.00 4.46
1162 2998 1.388837 GCTCTTCTCCTCTCCGGGAC 61.389 65.000 0.00 0.00 0.00 4.46
1163 2999 1.076632 GCTCTTCTCCTCTCCGGGA 60.077 63.158 0.00 0.00 0.00 5.14
1164 3000 2.485795 CGCTCTTCTCCTCTCCGGG 61.486 68.421 0.00 0.00 0.00 5.73
1165 3001 3.115556 CGCTCTTCTCCTCTCCGG 58.884 66.667 0.00 0.00 0.00 5.14
1166 3002 2.411290 GCGCTCTTCTCCTCTCCG 59.589 66.667 0.00 0.00 0.00 4.63
1167 3003 2.811799 GGCGCTCTTCTCCTCTCC 59.188 66.667 7.64 0.00 0.00 3.71
1168 3004 2.411290 CGGCGCTCTTCTCCTCTC 59.589 66.667 7.64 0.00 0.00 3.20
1169 3005 3.144193 CCGGCGCTCTTCTCCTCT 61.144 66.667 7.64 0.00 0.00 3.69
1170 3006 4.882396 GCCGGCGCTCTTCTCCTC 62.882 72.222 12.58 0.00 0.00 3.71
1199 3035 2.392974 GCCGTGCGTTTAATCCGGT 61.393 57.895 0.00 0.00 40.70 5.28
1203 3039 0.096454 GTCCTGCCGTGCGTTTAATC 59.904 55.000 0.00 0.00 0.00 1.75
1207 3043 0.392461 ATATGTCCTGCCGTGCGTTT 60.392 50.000 0.00 0.00 0.00 3.60
1233 3069 2.615869 TGCTTTCCTTGTGTTTTGTGC 58.384 42.857 0.00 0.00 0.00 4.57
1240 3076 1.824230 TGTTGCTTGCTTTCCTTGTGT 59.176 42.857 0.00 0.00 0.00 3.72
1242 3078 3.493176 GGAATGTTGCTTGCTTTCCTTGT 60.493 43.478 10.68 0.00 37.26 3.16
1247 3083 3.681417 GGAATGGAATGTTGCTTGCTTTC 59.319 43.478 0.00 0.00 33.03 2.62
1252 3088 5.105228 AGGTAATGGAATGGAATGTTGCTTG 60.105 40.000 0.00 0.00 0.00 4.01
1254 3090 4.403432 CAGGTAATGGAATGGAATGTTGCT 59.597 41.667 0.00 0.00 0.00 3.91
1255 3091 4.685924 CAGGTAATGGAATGGAATGTTGC 58.314 43.478 0.00 0.00 0.00 4.17
1256 3092 4.441913 GGCAGGTAATGGAATGGAATGTTG 60.442 45.833 0.00 0.00 0.00 3.33
1257 3093 3.706086 GGCAGGTAATGGAATGGAATGTT 59.294 43.478 0.00 0.00 0.00 2.71
1258 3094 3.299503 GGCAGGTAATGGAATGGAATGT 58.700 45.455 0.00 0.00 0.00 2.71
1259 3095 2.294233 CGGCAGGTAATGGAATGGAATG 59.706 50.000 0.00 0.00 0.00 2.67
1260 3096 2.174639 TCGGCAGGTAATGGAATGGAAT 59.825 45.455 0.00 0.00 0.00 3.01
1261 3097 1.562008 TCGGCAGGTAATGGAATGGAA 59.438 47.619 0.00 0.00 0.00 3.53
1262 3098 1.140852 CTCGGCAGGTAATGGAATGGA 59.859 52.381 0.00 0.00 0.00 3.41
1263 3099 1.597742 CTCGGCAGGTAATGGAATGG 58.402 55.000 0.00 0.00 0.00 3.16
1277 3113 1.308998 CATAACAATGGGACCTCGGC 58.691 55.000 0.00 0.00 0.00 5.54
1278 3114 1.967319 CCATAACAATGGGACCTCGG 58.033 55.000 0.00 0.00 38.04 4.63
1279 3115 1.308998 GCCATAACAATGGGACCTCG 58.691 55.000 6.54 0.00 41.94 4.63
1280 3116 1.134220 TCGCCATAACAATGGGACCTC 60.134 52.381 6.54 0.00 41.94 3.85
1281 3117 0.916086 TCGCCATAACAATGGGACCT 59.084 50.000 6.54 0.00 41.94 3.85
1282 3118 1.608590 CATCGCCATAACAATGGGACC 59.391 52.381 6.54 0.00 41.94 4.46
1283 3119 2.571212 TCATCGCCATAACAATGGGAC 58.429 47.619 6.54 0.00 41.94 4.46
1284 3120 3.148412 CATCATCGCCATAACAATGGGA 58.852 45.455 6.54 3.00 41.94 4.37
1285 3121 3.148412 TCATCATCGCCATAACAATGGG 58.852 45.455 6.54 0.00 41.94 4.00
1286 3122 4.380128 CCATCATCATCGCCATAACAATGG 60.380 45.833 0.00 0.00 44.44 3.16
1287 3123 4.380128 CCCATCATCATCGCCATAACAATG 60.380 45.833 0.00 0.00 0.00 2.82
1288 3124 3.760151 CCCATCATCATCGCCATAACAAT 59.240 43.478 0.00 0.00 0.00 2.71
1289 3125 3.148412 CCCATCATCATCGCCATAACAA 58.852 45.455 0.00 0.00 0.00 2.83
1290 3126 2.552809 CCCCATCATCATCGCCATAACA 60.553 50.000 0.00 0.00 0.00 2.41
1291 3127 2.086869 CCCCATCATCATCGCCATAAC 58.913 52.381 0.00 0.00 0.00 1.89
1292 3128 1.614051 GCCCCATCATCATCGCCATAA 60.614 52.381 0.00 0.00 0.00 1.90
1293 3129 0.035152 GCCCCATCATCATCGCCATA 60.035 55.000 0.00 0.00 0.00 2.74
1516 3379 2.809601 GCAGTAGACGCCGTGGTG 60.810 66.667 0.00 0.00 0.00 4.17
1641 3504 1.070786 GTTGAGGTGGAAGACGGCA 59.929 57.895 0.00 0.00 0.00 5.69
1889 3761 0.803768 CTTGAGAGACGCCATGGACG 60.804 60.000 18.40 20.56 0.00 4.79
2032 3904 2.741985 TTGGCCAGCACGATCACG 60.742 61.111 5.11 0.00 45.75 4.35
2155 4027 1.880340 GTCCAGCTTGCCGATCTCG 60.880 63.158 0.00 0.00 39.44 4.04
2221 4093 4.402528 TTGCCGATGGTGTCCGGG 62.403 66.667 0.00 0.00 45.42 5.73
2689 4562 5.680619 TCTTTGCCTTTCAGTTGAGTTCTA 58.319 37.500 0.00 0.00 0.00 2.10
2749 4622 8.166422 AGGACTAGTAAACAATTGTTTCTTGG 57.834 34.615 33.71 25.77 44.15 3.61
2790 4671 5.466393 GCCAAATTAGCGCATTATTTCCATT 59.534 36.000 11.47 0.00 0.00 3.16
2791 4672 4.990426 GCCAAATTAGCGCATTATTTCCAT 59.010 37.500 11.47 0.00 0.00 3.41
2792 4673 4.367450 GCCAAATTAGCGCATTATTTCCA 58.633 39.130 11.47 0.00 0.00 3.53
2793 4674 4.972286 GCCAAATTAGCGCATTATTTCC 57.028 40.909 11.47 2.37 0.00 3.13
2919 4800 0.250513 GCAGTGGTCCCAAGTCCTAG 59.749 60.000 0.00 0.00 0.00 3.02
3021 4902 8.164733 TCCAGGGTTCATATGTTTAACACTTTA 58.835 33.333 7.60 0.00 34.69 1.85
3214 5097 2.743553 TGGTGGTACCCTAGCTAGAAC 58.256 52.381 22.70 15.56 37.50 3.01
3268 5151 3.319137 TTCCTCTCTGACCAATCGTTG 57.681 47.619 0.00 0.00 0.00 4.10
3471 5355 3.676646 GGTCAAGCTGCAAAATTCACATC 59.323 43.478 1.02 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.