Multiple sequence alignment - TraesCS2A01G413800

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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 TraesCS2A01G413800 chr2A 100.000 2905 0 0 1 2905 670880074 670882978 0.000000e+00 5365.0
1 TraesCS2A01G413800 chr2D 92.584 2562 124 41 82 2605 525700261 525697728 0.000000e+00 3618.0
2 TraesCS2A01G413800 chr2D 91.586 309 9 6 2605 2905 525697667 525697368 7.490000e-111 411.0
3 TraesCS2A01G413800 chr2D 80.000 80 13 2 199 276 126756139 126756217 4.040000e-04 56.5
4 TraesCS2A01G413800 chr2B 94.305 1668 52 15 1256 2905 621775400 621777042 0.000000e+00 2514.0
5 TraesCS2A01G413800 chr2B 86.525 1321 80 52 1 1277 621774105 621775371 0.000000e+00 1363.0
6 TraesCS2A01G413800 chr6D 86.905 84 11 0 1380 1463 325600195 325600278 8.570000e-16 95.3
7 TraesCS2A01G413800 chr6A 87.059 85 9 2 1380 1463 464249996 464250079 8.570000e-16 95.3
8 TraesCS2A01G413800 chr6B 86.420 81 11 0 1383 1463 497434159 497434079 3.990000e-14 89.8
9 TraesCS2A01G413800 chr7B 83.562 73 10 2 111 182 641335145 641335074 1.870000e-07 67.6
10 TraesCS2A01G413800 chr7A 92.683 41 3 0 111 151 193687121 193687161 3.130000e-05 60.2
11 TraesCS2A01G413800 chr5B 90.476 42 4 0 123 164 531397711 531397670 4.040000e-04 56.5


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 TraesCS2A01G413800 chr2A 670880074 670882978 2904 False 5365.0 5365 100.000 1 2905 1 chr2A.!!$F1 2904
1 TraesCS2A01G413800 chr2D 525697368 525700261 2893 True 2014.5 3618 92.085 82 2905 2 chr2D.!!$R1 2823
2 TraesCS2A01G413800 chr2B 621774105 621777042 2937 False 1938.5 2514 90.415 1 2905 2 chr2B.!!$F1 2904

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
194 205 0.030369 GTCGACACAGACACCTTCGT 59.970 55.000 11.55 0.0 40.65 3.85 F
696 736 1.068333 CACCCAGCATCCGTTTCTTTG 60.068 52.381 0.00 0.0 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1270 0.179073 GAGATGGACGGATGGTGTGG 60.179 60.0 0.00 0.00 0.00 4.17 R
2041 2172 0.722469 GCACGATGCACGAGTGTTTG 60.722 55.0 16.16 5.54 44.26 2.93 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
36 37 7.147976 GCATTGTGGTTTCTTCTAACAGAAAT 58.852 34.615 0.00 0.00 43.17 2.17
38 39 6.539649 TGTGGTTTCTTCTAACAGAAATCG 57.460 37.500 0.00 0.00 44.05 3.34
42 43 7.170998 GTGGTTTCTTCTAACAGAAATCGAAGA 59.829 37.037 0.00 0.00 44.05 2.87
43 44 7.385205 TGGTTTCTTCTAACAGAAATCGAAGAG 59.615 37.037 0.00 0.00 44.05 2.85
44 45 7.599245 GGTTTCTTCTAACAGAAATCGAAGAGA 59.401 37.037 0.00 0.00 43.17 3.10
48 49 8.361139 TCTTCTAACAGAAATCGAAGAGAAAGT 58.639 33.333 0.00 0.00 36.22 2.66
118 129 9.574516 AGACACATACACTCATATATACACTCA 57.425 33.333 0.00 0.00 0.00 3.41
137 148 5.563751 CACTCACATTTATAAACGCACACAC 59.436 40.000 0.00 0.00 0.00 3.82
151 162 1.822990 CACACACGTACACCCTATCCT 59.177 52.381 0.00 0.00 0.00 3.24
152 163 2.097825 ACACACGTACACCCTATCCTC 58.902 52.381 0.00 0.00 0.00 3.71
171 182 1.092921 CGTGAGGACCTCCGAGAGAG 61.093 65.000 19.11 0.00 42.83 3.20
174 185 0.253610 GAGGACCTCCGAGAGAGTGA 59.746 60.000 10.74 0.00 41.47 3.41
176 187 0.034863 GGACCTCCGAGAGAGTGAGT 60.035 60.000 0.00 0.00 41.47 3.41
177 188 1.375551 GACCTCCGAGAGAGTGAGTC 58.624 60.000 0.00 0.00 41.47 3.36
184 195 1.127766 CGAGAGAGTGAGTCGACACAG 59.872 57.143 19.50 0.00 42.45 3.66
185 196 2.418692 GAGAGAGTGAGTCGACACAGA 58.581 52.381 19.50 0.00 42.45 3.41
186 197 2.147958 AGAGAGTGAGTCGACACAGAC 58.852 52.381 19.50 13.68 42.45 3.51
187 198 1.874231 GAGAGTGAGTCGACACAGACA 59.126 52.381 19.50 6.80 43.24 3.41
189 200 0.669077 AGTGAGTCGACACAGACACC 59.331 55.000 19.50 5.40 43.24 4.16
191 202 1.067212 GTGAGTCGACACAGACACCTT 59.933 52.381 19.50 0.00 43.24 3.50
192 203 1.337071 TGAGTCGACACAGACACCTTC 59.663 52.381 19.50 2.69 43.24 3.46
194 205 0.030369 GTCGACACAGACACCTTCGT 59.970 55.000 11.55 0.00 40.65 3.85
195 206 1.265095 GTCGACACAGACACCTTCGTA 59.735 52.381 11.55 0.00 40.65 3.43
196 207 1.534163 TCGACACAGACACCTTCGTAG 59.466 52.381 0.00 0.00 0.00 3.51
198 209 2.664971 CGACACAGACACCTTCGTAGAC 60.665 54.545 0.00 0.00 34.32 2.59
206 238 2.079158 CACCTTCGTAGACCGTAGTCA 58.921 52.381 0.00 0.00 46.15 3.41
235 267 1.081892 CTCTTCCCACTGAATGCACG 58.918 55.000 0.00 0.00 31.06 5.34
260 292 6.096001 GTCACCTGAATGCCTGAAATAAATCT 59.904 38.462 0.00 0.00 0.00 2.40
277 309 5.984233 AAATCTAATAAATGCGAGCACGA 57.016 34.783 8.01 0.00 42.66 4.35
279 311 2.794910 TCTAATAAATGCGAGCACGAGC 59.205 45.455 8.01 0.00 42.66 5.03
377 409 6.098409 AGCAAGTAGGAGCTAGTAGCAAATAA 59.902 38.462 23.77 2.80 45.56 1.40
515 547 1.865865 ACAACAACACGGACTAGCTG 58.134 50.000 0.00 0.00 0.00 4.24
530 562 1.732308 GCTGGCAGCTTAGGCAATC 59.268 57.895 31.37 0.00 43.93 2.67
638 671 6.264088 CGCCTACTAGTAGTAAAACTGGAAG 58.736 44.000 24.84 8.99 32.27 3.46
696 736 1.068333 CACCCAGCATCCGTTTCTTTG 60.068 52.381 0.00 0.00 0.00 2.77
705 745 2.582052 TCCGTTTCTTTGCAACTGGAT 58.418 42.857 0.00 0.00 0.00 3.41
739 779 2.279582 TTCTCGGCGTCTTGAATCTC 57.720 50.000 6.85 0.00 0.00 2.75
777 818 3.424300 CACTGGTGCCCGCATATG 58.576 61.111 0.00 0.00 0.00 1.78
778 819 2.516930 ACTGGTGCCCGCATATGC 60.517 61.111 18.08 18.08 37.78 3.14
835 885 5.516339 CCAATTCACCGTGCAATAAGATTTC 59.484 40.000 0.00 0.00 0.00 2.17
844 894 9.950680 ACCGTGCAATAAGATTTCTTTTATATG 57.049 29.630 0.00 0.00 37.40 1.78
1039 1091 1.225704 GCCCATCTTCTGTCCCTGG 59.774 63.158 0.00 0.00 0.00 4.45
1207 1259 3.522553 GCTTCCAGCACTCGTAAGTATT 58.477 45.455 0.00 0.00 41.89 1.89
1208 1260 3.552294 GCTTCCAGCACTCGTAAGTATTC 59.448 47.826 0.00 0.00 41.89 1.75
1209 1261 3.795623 TCCAGCACTCGTAAGTATTCC 57.204 47.619 0.00 0.00 33.25 3.01
1210 1262 3.362706 TCCAGCACTCGTAAGTATTCCT 58.637 45.455 0.00 0.00 33.25 3.36
1211 1263 3.380637 TCCAGCACTCGTAAGTATTCCTC 59.619 47.826 0.00 0.00 33.25 3.71
1212 1264 3.491104 CCAGCACTCGTAAGTATTCCTCC 60.491 52.174 0.00 0.00 33.25 4.30
1213 1265 3.130516 CAGCACTCGTAAGTATTCCTCCA 59.869 47.826 0.00 0.00 33.25 3.86
1214 1266 3.130693 AGCACTCGTAAGTATTCCTCCAC 59.869 47.826 0.00 0.00 33.25 4.02
1215 1267 3.130693 GCACTCGTAAGTATTCCTCCACT 59.869 47.826 0.00 0.00 33.25 4.00
1216 1268 4.673441 CACTCGTAAGTATTCCTCCACTG 58.327 47.826 0.00 0.00 33.25 3.66
1217 1269 3.130693 ACTCGTAAGTATTCCTCCACTGC 59.869 47.826 0.00 0.00 32.59 4.40
1218 1270 2.429610 TCGTAAGTATTCCTCCACTGCC 59.570 50.000 0.00 0.00 39.48 4.85
1219 1271 2.483188 CGTAAGTATTCCTCCACTGCCC 60.483 54.545 0.00 0.00 0.00 5.36
1220 1272 1.668826 AAGTATTCCTCCACTGCCCA 58.331 50.000 0.00 0.00 0.00 5.36
1221 1273 0.912486 AGTATTCCTCCACTGCCCAC 59.088 55.000 0.00 0.00 0.00 4.61
1222 1274 0.618458 GTATTCCTCCACTGCCCACA 59.382 55.000 0.00 0.00 0.00 4.17
1223 1275 0.618458 TATTCCTCCACTGCCCACAC 59.382 55.000 0.00 0.00 0.00 3.82
1224 1276 2.142292 ATTCCTCCACTGCCCACACC 62.142 60.000 0.00 0.00 0.00 4.16
1225 1277 3.569210 CCTCCACTGCCCACACCA 61.569 66.667 0.00 0.00 0.00 4.17
1226 1278 2.759114 CTCCACTGCCCACACCAT 59.241 61.111 0.00 0.00 0.00 3.55
1227 1279 1.377725 CTCCACTGCCCACACCATC 60.378 63.158 0.00 0.00 0.00 3.51
1228 1280 2.361610 CCACTGCCCACACCATCC 60.362 66.667 0.00 0.00 0.00 3.51
1229 1281 2.747460 CACTGCCCACACCATCCG 60.747 66.667 0.00 0.00 0.00 4.18
1230 1282 3.249189 ACTGCCCACACCATCCGT 61.249 61.111 0.00 0.00 0.00 4.69
1231 1283 2.436646 CTGCCCACACCATCCGTC 60.437 66.667 0.00 0.00 0.00 4.79
1232 1284 3.976701 CTGCCCACACCATCCGTCC 62.977 68.421 0.00 0.00 0.00 4.79
1233 1285 4.028490 GCCCACACCATCCGTCCA 62.028 66.667 0.00 0.00 0.00 4.02
1234 1286 2.998097 CCCACACCATCCGTCCAT 59.002 61.111 0.00 0.00 0.00 3.41
1254 1322 0.176910 CTCTTCTTCTTCCTCCGCCC 59.823 60.000 0.00 0.00 0.00 6.13
1319 1441 7.985752 GGGAACAAACACTAGCTAGTATATGTT 59.014 37.037 30.53 30.53 37.17 2.71
1352 1474 9.491675 CTAGCTAATCTTGCAGTAGTAGTAGTA 57.508 37.037 0.00 0.00 0.00 1.82
1456 1578 3.939837 ATGTGCGACTGGTGCCTCG 62.940 63.158 0.00 0.00 0.00 4.63
1702 1827 1.953138 GCCTGATCGAGCATGACCG 60.953 63.158 10.25 0.00 0.00 4.79
1863 1990 4.674281 ATAGTAAGTACTCTGGCTTGGC 57.326 45.455 0.00 0.00 37.73 4.52
1942 2073 3.596214 TCTCTTGTGCCGGTAATCTTTC 58.404 45.455 1.90 0.00 0.00 2.62
1952 2083 4.460505 CCGGTAATCTTTCGTTTGTTCAC 58.539 43.478 0.00 0.00 0.00 3.18
1978 2109 4.592778 TGGATGCATGCTTACATACTCCTA 59.407 41.667 20.33 0.00 33.67 2.94
1988 2119 8.276252 TGCTTACATACTCCTAATTGGTTTTC 57.724 34.615 0.00 0.00 37.07 2.29
1994 2125 8.265764 ACATACTCCTAATTGGTTTTCTCTACC 58.734 37.037 0.00 0.00 37.07 3.18
2033 2164 3.393089 TTGCTGTCCTCTTCTCAACTC 57.607 47.619 0.00 0.00 0.00 3.01
2041 2172 5.221342 TGTCCTCTTCTCAACTCTGTTCTTC 60.221 44.000 0.00 0.00 0.00 2.87
2131 2262 3.726859 TGGGGAATTAAGGATGCCATAGT 59.273 43.478 0.00 0.00 34.72 2.12
2132 2263 4.202567 TGGGGAATTAAGGATGCCATAGTC 60.203 45.833 0.00 0.00 34.72 2.59
2133 2264 4.336280 GGGAATTAAGGATGCCATAGTCC 58.664 47.826 0.00 0.00 34.72 3.85
2165 2296 4.661240 TGCATCTCTAGGAGTCTAGGTACT 59.339 45.833 0.00 0.00 42.42 2.73
2375 2518 1.063951 GCAGTCAACGAGTCGTACCG 61.064 60.000 20.23 10.80 39.99 4.02
2557 2704 4.463539 AGAGATAGAGATATGCAGTGGCTG 59.536 45.833 0.00 0.00 41.91 4.85
2559 2706 2.906691 AGAGATATGCAGTGGCTGAC 57.093 50.000 0.00 0.00 41.91 3.51
2575 2722 2.616510 GCTGACAGGTTTCTATGCCACT 60.617 50.000 4.26 0.00 0.00 4.00
2580 2727 3.055530 ACAGGTTTCTATGCCACTCTCAG 60.056 47.826 0.00 0.00 0.00 3.35
2691 2902 7.473735 AGATTCAGATCTCTTCACACAGTAA 57.526 36.000 0.00 0.00 38.21 2.24
2692 2903 7.901029 AGATTCAGATCTCTTCACACAGTAAA 58.099 34.615 0.00 0.00 38.21 2.01
2694 2905 7.715265 TTCAGATCTCTTCACACAGTAAAAC 57.285 36.000 0.00 0.00 0.00 2.43
2746 2962 7.256083 CCATCTTCAGGAAAAGGTGATTCTTTT 60.256 37.037 2.70 2.70 46.07 2.27
2747 2963 7.660030 TCTTCAGGAAAAGGTGATTCTTTTT 57.340 32.000 4.41 0.00 44.21 1.94
2748 2964 7.716612 TCTTCAGGAAAAGGTGATTCTTTTTC 58.283 34.615 4.41 6.62 44.21 2.29
2766 2982 1.450312 CCAGTTAAGCCGGCCTCAG 60.450 63.158 26.15 8.61 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.079643 AGAAGAAACCACAATGCCTTACAT 58.920 37.500 0.00 0.00 42.30 2.29
5 6 4.469657 AGAAGAAACCACAATGCCTTACA 58.530 39.130 0.00 0.00 0.00 2.41
87 90 9.613957 GTATATATGAGTGTATGTGTCTGTGTC 57.386 37.037 0.00 0.00 0.00 3.67
93 96 9.613957 GTGAGTGTATATATGAGTGTATGTGTC 57.386 37.037 0.00 0.00 0.00 3.67
118 129 4.735662 ACGTGTGTGCGTTTATAAATGT 57.264 36.364 16.79 0.00 43.04 2.71
122 133 3.428198 GGTGTACGTGTGTGCGTTTATAA 59.572 43.478 0.00 0.00 43.04 0.98
126 137 1.430707 GGGTGTACGTGTGTGCGTTT 61.431 55.000 0.00 0.00 43.04 3.60
137 148 1.602851 CTCACGAGGATAGGGTGTACG 59.397 57.143 0.00 0.00 33.51 3.67
151 162 1.078356 CTCTCGGAGGTCCTCACGA 60.078 63.158 22.99 22.99 34.21 4.35
152 163 1.078356 TCTCTCGGAGGTCCTCACG 60.078 63.158 20.72 19.44 31.08 4.35
171 182 0.669077 AGGTGTCTGTGTCGACTCAC 59.331 55.000 17.92 15.81 38.63 3.51
174 185 0.311165 CGAAGGTGTCTGTGTCGACT 59.689 55.000 17.92 0.00 35.00 4.18
176 187 1.534163 CTACGAAGGTGTCTGTGTCGA 59.466 52.381 0.00 0.00 35.71 4.20
177 188 1.534163 TCTACGAAGGTGTCTGTGTCG 59.466 52.381 0.00 0.00 37.71 4.35
213 245 1.003580 TGCATTCAGTGGGAAGAGACC 59.996 52.381 0.00 0.00 39.30 3.85
218 250 0.798776 GACGTGCATTCAGTGGGAAG 59.201 55.000 0.00 0.00 39.30 3.46
235 267 5.643379 TTTATTTCAGGCATTCAGGTGAC 57.357 39.130 0.00 0.00 0.00 3.67
260 292 1.521006 CGCTCGTGCTCGCATTTATTA 59.479 47.619 7.97 0.00 36.97 0.98
277 309 0.896226 GGGTTCAACTCCTAGACGCT 59.104 55.000 0.00 0.00 0.00 5.07
279 311 2.168496 TCAGGGTTCAACTCCTAGACG 58.832 52.381 0.00 0.00 0.00 4.18
326 358 1.595093 GCAAGGTTCGGTTGGATGGG 61.595 60.000 0.00 0.00 0.00 4.00
358 390 7.455641 CTAGCTTATTTGCTACTAGCTCCTA 57.544 40.000 9.49 0.00 42.97 2.94
359 391 6.339587 CTAGCTTATTTGCTACTAGCTCCT 57.660 41.667 9.49 0.00 42.97 3.69
377 409 4.092968 CGACCGAAACAAATTTAGCTAGCT 59.907 41.667 23.12 23.12 0.00 3.32
515 547 1.307097 CTCTGATTGCCTAAGCTGCC 58.693 55.000 0.00 0.00 40.80 4.85
530 562 4.218766 AGTGGACACTGCGTGTACTCTG 62.219 54.545 20.24 0.00 45.63 3.35
557 589 4.036852 TGGCATGTGAAATGAAACGTACAA 59.963 37.500 0.00 0.00 0.00 2.41
638 671 3.808656 GTCTCCGGGTCGACGTCC 61.809 72.222 10.58 5.06 0.00 4.79
696 736 3.084786 ACTTCTAGCCAAATCCAGTTGC 58.915 45.455 0.00 0.00 0.00 4.17
705 745 3.252458 GCCGAGAAAAACTTCTAGCCAAA 59.748 43.478 0.00 0.00 0.00 3.28
739 779 4.899239 GCCACCGCTCCAGGATCG 62.899 72.222 5.66 5.66 34.73 3.69
778 819 2.705220 CGAGTCGGTGCATGCATG 59.295 61.111 25.64 22.70 0.00 4.06
835 885 2.719798 GCACGGCAGCACATATAAAAG 58.280 47.619 0.00 0.00 0.00 2.27
844 894 3.749735 AAACAACGCACGGCAGCAC 62.750 57.895 0.00 0.00 0.00 4.40
1021 1073 1.225704 CCAGGGACAGAAGATGGGC 59.774 63.158 0.00 0.00 0.00 5.36
1039 1091 4.813697 GCAAGATCAGGAAGGAATGTCTAC 59.186 45.833 0.00 0.00 0.00 2.59
1207 1259 3.249189 GGTGTGGGCAGTGGAGGA 61.249 66.667 0.00 0.00 0.00 3.71
1208 1260 2.826777 GATGGTGTGGGCAGTGGAGG 62.827 65.000 0.00 0.00 0.00 4.30
1209 1261 1.377725 GATGGTGTGGGCAGTGGAG 60.378 63.158 0.00 0.00 0.00 3.86
1210 1262 2.756400 GATGGTGTGGGCAGTGGA 59.244 61.111 0.00 0.00 0.00 4.02
1211 1263 2.361610 GGATGGTGTGGGCAGTGG 60.362 66.667 0.00 0.00 0.00 4.00
1212 1264 2.747460 CGGATGGTGTGGGCAGTG 60.747 66.667 0.00 0.00 0.00 3.66
1213 1265 3.249189 ACGGATGGTGTGGGCAGT 61.249 61.111 0.00 0.00 0.00 4.40
1214 1266 2.436646 GACGGATGGTGTGGGCAG 60.437 66.667 0.00 0.00 0.00 4.85
1215 1267 4.028490 GGACGGATGGTGTGGGCA 62.028 66.667 0.00 0.00 0.00 5.36
1216 1268 3.344137 ATGGACGGATGGTGTGGGC 62.344 63.158 0.00 0.00 0.00 5.36
1217 1269 1.153168 GATGGACGGATGGTGTGGG 60.153 63.158 0.00 0.00 0.00 4.61
1218 1270 0.179073 GAGATGGACGGATGGTGTGG 60.179 60.000 0.00 0.00 0.00 4.17
1219 1271 0.826715 AGAGATGGACGGATGGTGTG 59.173 55.000 0.00 0.00 0.00 3.82
1220 1272 1.482593 GAAGAGATGGACGGATGGTGT 59.517 52.381 0.00 0.00 0.00 4.16
1221 1273 1.759445 AGAAGAGATGGACGGATGGTG 59.241 52.381 0.00 0.00 0.00 4.17
1222 1274 2.166907 AGAAGAGATGGACGGATGGT 57.833 50.000 0.00 0.00 0.00 3.55
1223 1275 2.697751 AGAAGAAGAGATGGACGGATGG 59.302 50.000 0.00 0.00 0.00 3.51
1224 1276 4.367450 GAAGAAGAAGAGATGGACGGATG 58.633 47.826 0.00 0.00 0.00 3.51
1225 1277 3.386402 GGAAGAAGAAGAGATGGACGGAT 59.614 47.826 0.00 0.00 0.00 4.18
1226 1278 2.761208 GGAAGAAGAAGAGATGGACGGA 59.239 50.000 0.00 0.00 0.00 4.69
1227 1279 2.763448 AGGAAGAAGAAGAGATGGACGG 59.237 50.000 0.00 0.00 0.00 4.79
1228 1280 3.181480 GGAGGAAGAAGAAGAGATGGACG 60.181 52.174 0.00 0.00 0.00 4.79
1229 1281 3.181480 CGGAGGAAGAAGAAGAGATGGAC 60.181 52.174 0.00 0.00 0.00 4.02
1230 1282 3.027412 CGGAGGAAGAAGAAGAGATGGA 58.973 50.000 0.00 0.00 0.00 3.41
1231 1283 2.482839 GCGGAGGAAGAAGAAGAGATGG 60.483 54.545 0.00 0.00 0.00 3.51
1232 1284 2.482839 GGCGGAGGAAGAAGAAGAGATG 60.483 54.545 0.00 0.00 0.00 2.90
1233 1285 1.760029 GGCGGAGGAAGAAGAAGAGAT 59.240 52.381 0.00 0.00 0.00 2.75
1234 1286 1.187087 GGCGGAGGAAGAAGAAGAGA 58.813 55.000 0.00 0.00 0.00 3.10
1254 1322 6.776744 TCCTCATCCATTCATATCAAGAAGG 58.223 40.000 0.00 0.00 0.00 3.46
1319 1441 7.878127 ACTACTGCAAGATTAGCTAGAAAACAA 59.122 33.333 0.00 0.00 37.43 2.83
1352 1474 4.692625 GCACCGCATATATGAGAAAGATGT 59.307 41.667 17.10 2.77 0.00 3.06
1650 1772 5.390251 GGCGCCTAAAACTAGTTTCTAACAC 60.390 44.000 22.15 9.85 31.45 3.32
1702 1827 8.301002 CCTCATAACTAGCTGGTCTTACTTATC 58.699 40.741 2.06 0.00 0.00 1.75
1863 1990 7.326789 CACACAAACAGCATAAGATAAGGTTTG 59.673 37.037 11.47 11.47 45.34 2.93
1942 2073 3.010624 TGCATCCAATGTGAACAAACG 57.989 42.857 0.00 0.00 0.00 3.60
1952 2083 5.335426 GGAGTATGTAAGCATGCATCCAATG 60.335 44.000 21.98 0.00 39.68 2.82
1978 2109 4.079253 ACATGCGGTAGAGAAAACCAATT 58.921 39.130 0.00 0.00 36.78 2.32
1988 2119 2.554806 TCACGTAACATGCGGTAGAG 57.445 50.000 0.00 0.00 0.00 2.43
1994 2125 3.778718 GCAAAGTAATCACGTAACATGCG 59.221 43.478 0.00 0.00 0.00 4.73
2033 2164 2.351418 TGCACGAGTGTTTGAAGAACAG 59.649 45.455 5.07 0.00 0.00 3.16
2041 2172 0.722469 GCACGATGCACGAGTGTTTG 60.722 55.000 16.16 5.54 44.26 2.93
2102 2233 7.582719 TGGCATCCTTAATTCCCCATATATAC 58.417 38.462 0.00 0.00 0.00 1.47
2105 2236 6.672946 ATGGCATCCTTAATTCCCCATATA 57.327 37.500 0.00 0.00 30.35 0.86
2131 2262 3.648067 CCTAGAGATGCAAGGTATTGGGA 59.352 47.826 0.00 0.00 36.88 4.37
2132 2263 3.648067 TCCTAGAGATGCAAGGTATTGGG 59.352 47.826 1.39 0.00 36.88 4.12
2133 2264 4.346418 ACTCCTAGAGATGCAAGGTATTGG 59.654 45.833 1.39 0.00 33.78 3.16
2197 2333 2.359169 CGGGAACAGCAGCTAGGGA 61.359 63.158 0.00 0.00 0.00 4.20
2198 2334 2.187946 CGGGAACAGCAGCTAGGG 59.812 66.667 0.00 0.00 0.00 3.53
2199 2335 2.187946 CCGGGAACAGCAGCTAGG 59.812 66.667 0.00 0.00 0.00 3.02
2273 2409 1.904378 CTACCTAGCTCCGGCCTCC 60.904 68.421 0.00 0.00 39.73 4.30
2274 2410 2.566570 GCTACCTAGCTCCGGCCTC 61.567 68.421 0.00 0.00 45.62 4.70
2275 2411 2.522193 GCTACCTAGCTCCGGCCT 60.522 66.667 0.00 0.00 45.62 5.19
2336 2479 2.324014 TACATGCATCGACCCTGGCC 62.324 60.000 0.00 0.00 0.00 5.36
2557 2704 3.055819 TGAGAGTGGCATAGAAACCTGTC 60.056 47.826 0.00 0.00 0.00 3.51
2559 2706 3.055530 ACTGAGAGTGGCATAGAAACCTG 60.056 47.826 0.00 0.00 0.00 4.00
2575 2722 6.319152 CGTATAAAAGGAGGAGAAGACTGAGA 59.681 42.308 0.00 0.00 0.00 3.27
2580 2727 7.332213 AGTACGTATAAAAGGAGGAGAAGAC 57.668 40.000 0.00 0.00 0.00 3.01
2661 2872 8.131731 TGTGTGAAGAGATCTGAATCTTATACG 58.868 37.037 0.00 0.00 42.46 3.06
2691 2902 9.431887 CATGCCATATATAGGTACGTTTAGTTT 57.568 33.333 0.00 0.00 0.00 2.66
2692 2903 8.038944 CCATGCCATATATAGGTACGTTTAGTT 58.961 37.037 0.00 0.00 0.00 2.24
2694 2905 6.479001 GCCATGCCATATATAGGTACGTTTAG 59.521 42.308 0.00 0.00 0.00 1.85
2713 2929 0.396139 TTCCTGAAGATGGGCCATGC 60.396 55.000 26.77 15.35 0.00 4.06
2714 2930 2.148446 TTTCCTGAAGATGGGCCATG 57.852 50.000 26.77 8.95 0.00 3.66
2715 2931 2.625087 CCTTTTCCTGAAGATGGGCCAT 60.625 50.000 21.39 21.39 0.00 4.40
2749 2965 2.109126 GCTGAGGCCGGCTTAACTG 61.109 63.158 28.56 18.12 41.43 3.16
2766 2982 6.018180 CACTATTAATTCCCGGTCTTAACAGC 60.018 42.308 0.00 0.00 0.00 4.40
2843 3059 2.297895 TAGGGTCGGCAGCATTGGT 61.298 57.895 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.