Multiple sequence alignment - TraesCS4A01G331000

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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 TraesCS4A01G331000 chr4A 100.000 4074 0 0 1 4074 615458337 615454264 0.000000e+00 7524.0
1 TraesCS4A01G331000 chr4A 80.190 2206 306 66 1 2144 616699819 616701955 0.000000e+00 1531.0
2 TraesCS4A01G331000 chr4A 80.491 1548 180 52 2605 4074 615374354 615372851 0.000000e+00 1074.0
3 TraesCS4A01G331000 chr4A 82.271 1286 165 36 998 2242 615376102 615374839 0.000000e+00 1053.0
4 TraesCS4A01G331000 chr4A 81.604 723 83 24 1 704 616687949 616688640 1.650000e-153 553.0
5 TraesCS4A01G331000 chr4A 87.786 262 18 8 2331 2592 615374781 615374534 1.110000e-75 294.0
6 TraesCS4A01G331000 chr5B 91.713 4115 251 42 2 4074 697870119 697866053 0.000000e+00 5627.0
7 TraesCS4A01G331000 chr5B 84.615 1261 170 13 990 2247 697832246 697831007 0.000000e+00 1232.0
8 TraesCS4A01G331000 chr5B 79.625 1600 243 51 599 2157 699282960 699281403 0.000000e+00 1072.0
9 TraesCS4A01G331000 chr5B 78.813 1331 219 37 845 2150 703805047 703803755 0.000000e+00 837.0
10 TraesCS4A01G331000 chr5B 85.921 483 59 6 2605 3084 697830521 697830045 1.310000e-139 507.0
11 TraesCS4A01G331000 chr5B 76.673 553 110 16 2520 3065 699790222 699789682 5.150000e-74 289.0
12 TraesCS4A01G331000 chr5B 85.556 270 23 7 3820 4074 697865369 697865101 6.710000e-68 268.0
13 TraesCS4A01G331000 chr5B 87.895 190 18 3 1978 2167 697820163 697820347 6.860000e-53 219.0
14 TraesCS4A01G331000 chr5B 77.778 369 55 17 1832 2176 703893995 703893630 6.900000e-48 202.0
15 TraesCS4A01G331000 chr5D 91.543 4127 241 54 1 4074 552682733 552686804 0.000000e+00 5589.0
16 TraesCS4A01G331000 chr5D 84.652 1264 167 16 990 2248 552728996 552730237 0.000000e+00 1234.0
17 TraesCS4A01G331000 chr5D 85.348 546 69 9 2602 3144 552730714 552731251 4.600000e-154 555.0
18 TraesCS4A01G331000 chr5D 75.215 1279 245 50 936 2176 552407625 552408869 1.290000e-149 540.0
19 TraesCS4A01G331000 chr5D 75.185 1213 235 46 980 2159 542411225 542410046 2.810000e-141 512.0
20 TraesCS4A01G331000 chr5D 75.467 1178 215 46 1003 2153 552129717 552128587 1.310000e-139 507.0
21 TraesCS4A01G331000 chr5D 89.394 264 22 1 999 1262 551409722 551409465 1.090000e-85 327.0
22 TraesCS4A01G331000 chr5D 76.630 552 112 15 2520 3065 551544400 551543860 5.150000e-74 289.0
23 TraesCS4A01G331000 chr5D 78.397 287 53 8 2685 2968 552069237 552069517 1.160000e-40 178.0
24 TraesCS4A01G331000 chr5D 94.118 51 3 0 690 740 552500292 552500342 1.210000e-10 78.7
25 TraesCS4A01G331000 chr2D 76.291 1181 223 39 999 2149 651431730 651432883 9.820000e-161 577.0
26 TraesCS4A01G331000 chr2B 76.254 1196 215 46 999 2157 781149700 781150863 4.570000e-159 571.0
27 TraesCS4A01G331000 chr2A 76.046 956 192 26 999 1943 776170804 776169875 2.870000e-126 462.0
28 TraesCS4A01G331000 chr6D 79.431 457 83 8 2642 3092 25613964 25613513 3.060000e-81 313.0
29 TraesCS4A01G331000 chr6B 78.431 459 87 8 2643 3093 41434192 41433738 5.150000e-74 289.0
30 TraesCS4A01G331000 chr4D 80.511 313 47 9 999 1307 280248945 280248643 1.140000e-55 228.0
31 TraesCS4A01G331000 chrUn 76.804 194 35 10 122 313 23399715 23399900 2.590000e-17 100.0


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 TraesCS4A01G331000 chr4A 615454264 615458337 4073 True 7524.0 7524 100.0000 1 4074 1 chr4A.!!$R1 4073
1 TraesCS4A01G331000 chr4A 616699819 616701955 2136 False 1531.0 1531 80.1900 1 2144 1 chr4A.!!$F2 2143
2 TraesCS4A01G331000 chr4A 615372851 615376102 3251 True 807.0 1074 83.5160 998 4074 3 chr4A.!!$R2 3076
3 TraesCS4A01G331000 chr4A 616687949 616688640 691 False 553.0 553 81.6040 1 704 1 chr4A.!!$F1 703
4 TraesCS4A01G331000 chr5B 697865101 697870119 5018 True 2947.5 5627 88.6345 2 4074 2 chr5B.!!$R6 4072
5 TraesCS4A01G331000 chr5B 699281403 699282960 1557 True 1072.0 1072 79.6250 599 2157 1 chr5B.!!$R1 1558
6 TraesCS4A01G331000 chr5B 697830045 697832246 2201 True 869.5 1232 85.2680 990 3084 2 chr5B.!!$R5 2094
7 TraesCS4A01G331000 chr5B 703803755 703805047 1292 True 837.0 837 78.8130 845 2150 1 chr5B.!!$R3 1305
8 TraesCS4A01G331000 chr5B 699789682 699790222 540 True 289.0 289 76.6730 2520 3065 1 chr5B.!!$R2 545
9 TraesCS4A01G331000 chr5D 552682733 552686804 4071 False 5589.0 5589 91.5430 1 4074 1 chr5D.!!$F4 4073
10 TraesCS4A01G331000 chr5D 552728996 552731251 2255 False 894.5 1234 85.0000 990 3144 2 chr5D.!!$F5 2154
11 TraesCS4A01G331000 chr5D 552407625 552408869 1244 False 540.0 540 75.2150 936 2176 1 chr5D.!!$F2 1240
12 TraesCS4A01G331000 chr5D 542410046 542411225 1179 True 512.0 512 75.1850 980 2159 1 chr5D.!!$R1 1179
13 TraesCS4A01G331000 chr5D 552128587 552129717 1130 True 507.0 507 75.4670 1003 2153 1 chr5D.!!$R4 1150
14 TraesCS4A01G331000 chr5D 551543860 551544400 540 True 289.0 289 76.6300 2520 3065 1 chr5D.!!$R3 545
15 TraesCS4A01G331000 chr2D 651431730 651432883 1153 False 577.0 577 76.2910 999 2149 1 chr2D.!!$F1 1150
16 TraesCS4A01G331000 chr2B 781149700 781150863 1163 False 571.0 571 76.2540 999 2157 1 chr2B.!!$F1 1158
17 TraesCS4A01G331000 chr2A 776169875 776170804 929 True 462.0 462 76.0460 999 1943 1 chr2A.!!$R1 944


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
186 187 0.253044 TCTCCTCCAGATTTTGCGGG 59.747 55.000 0.0 0.0 0.00 6.13 F
230 251 0.689623 CCTTTCTCTGCCACTCCAGT 59.310 55.000 0.0 0.0 34.47 4.00 F
422 444 0.968901 ACGAAGCTCCGACATGGGTA 60.969 55.000 0.0 0.0 38.76 3.69 F
1406 1507 0.737715 GTGAGCTACGGCAAGACTGG 60.738 60.000 0.0 0.0 41.70 4.00 F
1961 2117 2.166829 TGTGCATTTACACATCACCCC 58.833 47.619 0.0 0.0 45.36 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1431 1.182667 GGGGGTGACATGTAAAAGCC 58.817 55.000 13.05 13.05 0.00 4.35 R
1406 1507 4.322567 GGATATGGAGAACTCAAGGCATC 58.677 47.826 4.23 0.00 0.00 3.91 R
2296 2478 2.535012 TGCACGGACATTGTCTTACA 57.465 45.000 16.02 7.34 32.47 2.41 R
2673 3085 0.543277 TTGCCACCAACCAAATGCAA 59.457 45.000 0.00 0.00 36.46 4.08 R
3926 4411 0.740737 CGGCCAGCCAAGATAAAAGG 59.259 55.000 9.78 0.00 35.37 3.11 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
32 33 1.046472 CATGGGCATGCCAATCCAGT 61.046 55.000 36.56 8.91 37.98 4.00
40 41 3.555586 GCATGCCAATCCAGTTTTGTTCT 60.556 43.478 6.36 0.00 0.00 3.01
59 60 6.895782 TGTTCTAATTTTATCGGATGTCCCT 58.104 36.000 0.00 0.00 0.00 4.20
63 64 9.908747 TTCTAATTTTATCGGATGTCCCTAAAA 57.091 29.630 0.00 12.71 35.71 1.52
67 68 6.509523 TTTATCGGATGTCCCTAAAAGGAT 57.490 37.500 0.00 0.00 37.67 3.24
102 103 5.012046 TCCAGTTGAAGATGCTCTTAGACAA 59.988 40.000 0.00 0.00 36.73 3.18
106 107 7.547019 CAGTTGAAGATGCTCTTAGACAATACA 59.453 37.037 0.00 0.00 36.73 2.29
112 113 4.363138 TGCTCTTAGACAATACATGAGCG 58.637 43.478 0.00 0.00 45.61 5.03
115 116 4.363138 TCTTAGACAATACATGAGCGCAG 58.637 43.478 11.47 0.00 0.00 5.18
127 128 5.061853 ACATGAGCGCAGATTAATCTTCAT 58.938 37.500 18.51 18.51 33.31 2.57
147 148 1.373536 GAGTTTTCTCCCCTTCCCCT 58.626 55.000 0.00 0.00 40.79 4.79
148 149 1.282447 GAGTTTTCTCCCCTTCCCCTC 59.718 57.143 0.00 0.00 40.79 4.30
166 167 1.227176 CGGCGGCTAGGGTAAACTC 60.227 63.158 7.61 0.00 0.00 3.01
173 174 2.960384 GGCTAGGGTAAACTCTCTCCTC 59.040 54.545 0.00 0.00 0.00 3.71
178 179 3.273618 AGGGTAAACTCTCTCCTCCAGAT 59.726 47.826 0.00 0.00 0.00 2.90
181 182 5.045505 GGGTAAACTCTCTCCTCCAGATTTT 60.046 44.000 0.00 0.00 30.39 1.82
184 185 2.093764 ACTCTCTCCTCCAGATTTTGCG 60.094 50.000 0.00 0.00 0.00 4.85
185 186 1.208052 TCTCTCCTCCAGATTTTGCGG 59.792 52.381 0.00 0.00 0.00 5.69
186 187 0.253044 TCTCCTCCAGATTTTGCGGG 59.747 55.000 0.00 0.00 0.00 6.13
187 188 1.378514 TCCTCCAGATTTTGCGGGC 60.379 57.895 0.00 0.00 0.00 6.13
188 189 2.764314 CCTCCAGATTTTGCGGGCG 61.764 63.158 0.00 0.00 0.00 6.13
189 190 1.745115 CTCCAGATTTTGCGGGCGA 60.745 57.895 0.00 0.00 0.00 5.54
190 191 1.709147 CTCCAGATTTTGCGGGCGAG 61.709 60.000 0.00 0.00 0.00 5.03
191 192 2.100991 CAGATTTTGCGGGCGAGC 59.899 61.111 0.00 0.00 37.71 5.03
192 193 3.134127 AGATTTTGCGGGCGAGCC 61.134 61.111 5.37 5.37 36.02 4.70
202 203 2.280186 GGCGAGCCCGTGGATTAG 60.280 66.667 1.97 0.00 38.24 1.73
203 204 2.967615 GCGAGCCCGTGGATTAGC 60.968 66.667 0.00 0.00 38.24 3.09
204 205 2.815308 CGAGCCCGTGGATTAGCT 59.185 61.111 0.00 0.00 38.56 3.32
205 206 2.038690 CGAGCCCGTGGATTAGCTA 58.961 57.895 0.00 0.00 35.23 3.32
226 247 1.301293 CCCCCTTTCTCTGCCACTC 59.699 63.158 0.00 0.00 0.00 3.51
230 251 0.689623 CCTTTCTCTGCCACTCCAGT 59.310 55.000 0.00 0.00 34.47 4.00
239 260 2.281761 CACTCCAGTGGTGGTGGC 60.282 66.667 21.69 0.00 45.28 5.01
240 261 3.941188 ACTCCAGTGGTGGTGGCG 61.941 66.667 15.44 0.00 45.28 5.69
241 262 4.704833 CTCCAGTGGTGGTGGCGG 62.705 72.222 9.54 0.00 45.28 6.13
284 305 3.512680 CTTCACTCGGGCTAGTAGTTTG 58.487 50.000 0.00 0.00 0.00 2.93
292 314 2.172082 GGGCTAGTAGTTTGGGTTAGGG 59.828 54.545 0.00 0.00 0.00 3.53
293 315 2.172082 GGCTAGTAGTTTGGGTTAGGGG 59.828 54.545 0.00 0.00 0.00 4.79
302 324 5.531198 AGTTTGGGTTAGGGGTTTTTAGTT 58.469 37.500 0.00 0.00 0.00 2.24
307 329 3.438087 GGTTAGGGGTTTTTAGTTCTCGC 59.562 47.826 0.00 0.00 0.00 5.03
310 332 1.810755 GGGGTTTTTAGTTCTCGCAGG 59.189 52.381 0.00 0.00 0.00 4.85
313 335 2.350484 GGTTTTTAGTTCTCGCAGGTGC 60.350 50.000 0.00 0.00 37.78 5.01
340 362 1.664965 GGCAGTTGACGACGCTTCT 60.665 57.895 0.00 0.00 0.00 2.85
364 386 2.650322 TCGAGTTTGTTTTCTGGGCTT 58.350 42.857 0.00 0.00 0.00 4.35
414 436 3.911989 GTATTCGACGAAGCTCCGA 57.088 52.632 16.40 0.00 0.00 4.55
416 438 1.089112 TATTCGACGAAGCTCCGACA 58.911 50.000 16.40 0.00 31.60 4.35
420 442 1.519455 GACGAAGCTCCGACATGGG 60.519 63.158 0.00 0.00 38.76 4.00
422 444 0.968901 ACGAAGCTCCGACATGGGTA 60.969 55.000 0.00 0.00 38.76 3.69
446 468 4.079827 CTCTCCTTGAGGGGGCAT 57.920 61.111 0.00 0.00 39.08 4.40
460 482 1.567175 GGGGCATGGTTAGGGTTTCTA 59.433 52.381 0.00 0.00 0.00 2.10
463 486 3.542648 GGCATGGTTAGGGTTTCTAGTC 58.457 50.000 0.00 0.00 0.00 2.59
464 487 3.054655 GGCATGGTTAGGGTTTCTAGTCA 60.055 47.826 0.00 0.00 0.00 3.41
466 489 4.576463 GCATGGTTAGGGTTTCTAGTCATG 59.424 45.833 0.00 0.00 39.87 3.07
473 496 1.068474 GTTTCTAGTCATGCGTGCGT 58.932 50.000 0.00 0.00 0.00 5.24
474 497 1.067693 TTTCTAGTCATGCGTGCGTG 58.932 50.000 7.74 7.74 0.00 5.34
495 518 8.272866 TGCGTGACGATAAATATTTGATGTTAG 58.727 33.333 10.10 3.78 0.00 2.34
516 539 8.692710 TGTTAGTTTGATCTACGATGAACCTAT 58.307 33.333 0.00 0.00 0.00 2.57
578 609 2.145225 GTGACAGCACTAGCACACG 58.855 57.895 0.00 0.00 45.49 4.49
596 627 2.428491 ACGAGAGTGTGAGTACTCCAG 58.572 52.381 20.11 7.88 46.48 3.86
674 715 1.827681 TCTTCTCCTCCGTCTCTGTG 58.172 55.000 0.00 0.00 0.00 3.66
757 798 4.209538 CCATCTAATCAGCCACCAAATCA 58.790 43.478 0.00 0.00 0.00 2.57
758 799 4.831155 CCATCTAATCAGCCACCAAATCAT 59.169 41.667 0.00 0.00 0.00 2.45
761 815 2.832643 ATCAGCCACCAAATCATCCA 57.167 45.000 0.00 0.00 0.00 3.41
762 816 2.601240 TCAGCCACCAAATCATCCAA 57.399 45.000 0.00 0.00 0.00 3.53
778 832 1.824852 TCCAAATCGACTAGCAGCAGA 59.175 47.619 0.00 0.00 0.00 4.26
984 1058 1.892209 GTTCCAACCAACAGATCGGT 58.108 50.000 0.00 0.00 36.98 4.69
1079 1156 3.878519 CGACGACCTCCTCCTCGC 61.879 72.222 0.00 0.00 32.98 5.03
1083 1160 1.258445 ACGACCTCCTCCTCGCAATT 61.258 55.000 0.00 0.00 32.98 2.32
1330 1431 1.590932 CATCAAAGCCCTCATCCTCG 58.409 55.000 0.00 0.00 0.00 4.63
1406 1507 0.737715 GTGAGCTACGGCAAGACTGG 60.738 60.000 0.00 0.00 41.70 4.00
1571 1700 2.431942 ACATTCCGACGTCACCGC 60.432 61.111 17.16 0.00 37.70 5.68
1961 2117 2.166829 TGTGCATTTACACATCACCCC 58.833 47.619 0.00 0.00 45.36 4.95
2211 2374 6.376978 GCATGTTACTGGAATATTCAGCATC 58.623 40.000 17.07 0.13 35.78 3.91
2291 2473 7.907214 AGTGTGTACAGTCCTCATTTTAATC 57.093 36.000 0.00 0.00 0.00 1.75
2296 2478 7.119846 GTGTACAGTCCTCATTTTAATCTTGCT 59.880 37.037 0.00 0.00 0.00 3.91
2429 2614 9.598517 GATGCACATATCCCTTTTCATTAAAAA 57.401 29.630 0.00 0.00 34.26 1.94
2466 2651 9.673454 AAAGTATGTTGGTCGAAAGAAATAAAC 57.327 29.630 0.00 0.00 45.01 2.01
2562 2754 8.922058 TTACTTTACGTAGGATTCAGTTCATC 57.078 34.615 0.00 0.00 0.00 2.92
2586 2787 8.243961 TCCAAATTCATCCAAAAACTCTACAA 57.756 30.769 0.00 0.00 0.00 2.41
2636 3048 5.527214 AGTGCTTTTCAAATTTTTAGGTGGC 59.473 36.000 0.00 0.00 0.00 5.01
2660 3072 8.296000 GGCCAAAATATTTAATTGCAGTTGTTT 58.704 29.630 4.47 0.00 0.00 2.83
2661 3073 9.676195 GCCAAAATATTTAATTGCAGTTGTTTT 57.324 25.926 4.47 2.37 0.00 2.43
2715 3130 9.329913 GCAAGTTTAGTTAACATGTGTTATCTG 57.670 33.333 19.39 9.06 39.51 2.90
2977 3392 2.154567 AGGAGTGCAATGCCATTGAT 57.845 45.000 21.24 5.81 42.83 2.57
3136 3551 4.690082 GCTCATGGCTTCTGCTAGAGCA 62.690 54.545 17.42 3.80 46.06 4.26
3197 3638 5.758296 CGACTTTACATTACAGCATGGGTAT 59.242 40.000 0.00 0.00 43.62 2.73
3305 3755 6.051717 CAGAATGTGACTTTGGGATAGTAGG 58.948 44.000 0.00 0.00 0.00 3.18
3442 3907 6.133356 TGGTGTTCCATTTTCCTTCTAGTTT 58.867 36.000 0.00 0.00 39.03 2.66
3498 3963 3.716601 AGAAAAGGAAATTTGTGCGTGG 58.283 40.909 0.00 0.00 0.00 4.94
3508 3973 0.593518 TTGTGCGTGGCAAATTGACG 60.594 50.000 0.00 0.00 41.47 4.35
3578 4043 1.532868 CCACAAGCTTTCGTTCTCCTG 59.467 52.381 0.00 0.00 0.00 3.86
3668 4147 0.909610 TGGAGGCGGAAGGTGATTCT 60.910 55.000 0.00 0.00 38.07 2.40
3687 4166 6.529829 TGATTCTTTGTTTGAACCGAAGTTTG 59.470 34.615 0.00 0.00 35.94 2.93
3701 4180 3.281727 AAGTTTGGCACTTCTCTGTCA 57.718 42.857 0.00 0.00 42.62 3.58
3717 4196 4.960938 TCTGTCAATGTGCACTCTTACTT 58.039 39.130 19.41 0.00 0.00 2.24
3813 4298 7.449086 TGTTAACTATAAACTGGTTGGGAAAGG 59.551 37.037 7.22 0.00 30.31 3.11
3868 4353 4.177165 TGTGCATAAACTGGCTGATTTG 57.823 40.909 0.00 0.00 0.00 2.32
3874 4359 6.208402 TGCATAAACTGGCTGATTTGTCTTTA 59.792 34.615 0.00 0.00 0.00 1.85
4054 4552 1.446907 GGTCTGTGAGACAAGCATGG 58.553 55.000 6.10 0.00 46.79 3.66
4057 4555 0.803117 CTGTGAGACAAGCATGGCAG 59.197 55.000 0.00 0.00 36.86 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.614812 AAAACTGGATTGGCATGCCC 59.385 50.000 33.44 18.47 34.56 5.36
32 33 8.463607 GGGACATCCGATAAAATTAGAACAAAA 58.536 33.333 0.00 0.00 36.71 2.44
40 41 8.496088 TCCTTTTAGGGACATCCGATAAAATTA 58.504 33.333 14.95 7.86 37.29 1.40
59 60 6.484288 ACTGGATTGACATGTCATCCTTTTA 58.516 36.000 33.39 22.78 39.64 1.52
63 64 4.019051 TCAACTGGATTGACATGTCATCCT 60.019 41.667 33.39 22.75 42.62 3.24
102 103 6.226052 TGAAGATTAATCTGCGCTCATGTAT 58.774 36.000 18.61 0.00 35.06 2.29
106 107 5.303165 TCATGAAGATTAATCTGCGCTCAT 58.697 37.500 18.61 18.55 35.06 2.90
112 113 8.127954 GGAGAAAACTCATGAAGATTAATCTGC 58.872 37.037 18.61 17.10 37.19 4.26
115 116 7.777440 AGGGGAGAAAACTCATGAAGATTAATC 59.223 37.037 7.41 7.41 0.00 1.75
127 128 1.073098 GGGGAAGGGGAGAAAACTCA 58.927 55.000 0.00 0.00 0.00 3.41
147 148 1.669999 GAGTTTACCCTAGCCGCCGA 61.670 60.000 0.00 0.00 0.00 5.54
148 149 1.227176 GAGTTTACCCTAGCCGCCG 60.227 63.158 0.00 0.00 0.00 6.46
166 167 1.661341 CCGCAAAATCTGGAGGAGAG 58.339 55.000 0.00 0.00 32.80 3.20
173 174 2.793946 CTCGCCCGCAAAATCTGG 59.206 61.111 0.00 0.00 0.00 3.86
185 186 2.280186 CTAATCCACGGGCTCGCC 60.280 66.667 5.51 0.00 40.63 5.54
186 187 2.083835 TAGCTAATCCACGGGCTCGC 62.084 60.000 5.51 0.00 40.63 5.03
187 188 0.318784 GTAGCTAATCCACGGGCTCG 60.319 60.000 3.27 3.27 43.02 5.03
188 189 0.033642 GGTAGCTAATCCACGGGCTC 59.966 60.000 0.00 0.00 36.40 4.70
189 190 1.408453 GGGTAGCTAATCCACGGGCT 61.408 60.000 0.00 0.00 38.62 5.19
190 191 1.070957 GGGTAGCTAATCCACGGGC 59.929 63.158 0.00 0.00 0.00 6.13
191 192 1.752833 GGGGTAGCTAATCCACGGG 59.247 63.158 14.19 0.00 0.00 5.28
192 193 1.752833 GGGGGTAGCTAATCCACGG 59.247 63.158 14.19 0.00 0.00 4.94
223 244 3.941188 CGCCACCACCACTGGAGT 61.941 66.667 0.71 0.00 40.55 3.85
237 258 3.716204 GATTTCCCTCCCCACCGCC 62.716 68.421 0.00 0.00 0.00 6.13
239 260 0.693092 TAGGATTTCCCTCCCCACCG 60.693 60.000 0.00 0.00 43.31 4.94
240 261 1.141185 CTAGGATTTCCCTCCCCACC 58.859 60.000 0.00 0.00 43.31 4.61
241 262 0.474614 GCTAGGATTTCCCTCCCCAC 59.525 60.000 0.00 0.00 43.31 4.61
242 263 1.054406 CGCTAGGATTTCCCTCCCCA 61.054 60.000 0.00 0.00 43.31 4.96
284 305 4.005650 CGAGAACTAAAAACCCCTAACCC 58.994 47.826 0.00 0.00 0.00 4.11
292 314 2.350484 GCACCTGCGAGAACTAAAAACC 60.350 50.000 0.00 0.00 0.00 3.27
293 315 2.917363 GCACCTGCGAGAACTAAAAAC 58.083 47.619 0.00 0.00 0.00 2.43
319 341 4.681978 GCGTCGTCAACTGCCCCT 62.682 66.667 0.00 0.00 0.00 4.79
330 352 0.592148 ACTCGAAGAAGAAGCGTCGT 59.408 50.000 0.00 0.00 40.00 4.34
340 362 3.066203 GCCCAGAAAACAAACTCGAAGAA 59.934 43.478 0.00 0.00 34.09 2.52
379 401 2.083167 TACGTCCCAATCGACAAACC 57.917 50.000 0.00 0.00 32.74 3.27
420 442 0.827368 CTCAAGGAGAGGGCAGGTAC 59.173 60.000 0.00 0.00 40.84 3.34
422 444 4.143740 CTCAAGGAGAGGGCAGGT 57.856 61.111 0.00 0.00 40.84 4.00
429 451 1.530771 CATGCCCCCTCAAGGAGAG 59.469 63.158 0.00 0.00 44.31 3.20
441 463 2.241430 ACTAGAAACCCTAACCATGCCC 59.759 50.000 0.00 0.00 0.00 5.36
442 464 3.054655 TGACTAGAAACCCTAACCATGCC 60.055 47.826 0.00 0.00 0.00 4.40
445 467 4.683400 CGCATGACTAGAAACCCTAACCAT 60.683 45.833 0.00 0.00 0.00 3.55
446 468 3.369052 CGCATGACTAGAAACCCTAACCA 60.369 47.826 0.00 0.00 0.00 3.67
460 482 3.105782 CGTCACGCACGCATGACT 61.106 61.111 15.30 0.00 42.87 3.41
484 507 9.599866 TCATCGTAGATCAAACTAACATCAAAT 57.400 29.630 0.00 0.00 45.12 2.32
488 511 7.707035 AGGTTCATCGTAGATCAAACTAACATC 59.293 37.037 0.00 0.00 45.12 3.06
489 512 7.556844 AGGTTCATCGTAGATCAAACTAACAT 58.443 34.615 0.00 0.00 45.12 2.71
519 542 6.621931 TCCCACCCAAATACTCCTATATGAAA 59.378 38.462 0.00 0.00 0.00 2.69
577 608 2.417239 GTCTGGAGTACTCACACTCTCG 59.583 54.545 23.91 7.88 43.73 4.04
578 609 3.681593 AGTCTGGAGTACTCACACTCTC 58.318 50.000 23.91 5.72 43.73 3.20
674 715 1.703411 CTCTCAGAGAGTGGGGATCC 58.297 60.000 18.33 1.92 37.57 3.36
688 729 1.552337 GTGAGTGGATTGGAGCTCTCA 59.448 52.381 14.64 7.25 0.00 3.27
757 798 2.432146 TCTGCTGCTAGTCGATTTGGAT 59.568 45.455 0.00 0.00 0.00 3.41
758 799 1.824852 TCTGCTGCTAGTCGATTTGGA 59.175 47.619 0.00 0.00 0.00 3.53
761 815 2.263077 CGTTCTGCTGCTAGTCGATTT 58.737 47.619 0.00 0.00 0.00 2.17
762 816 1.914634 CGTTCTGCTGCTAGTCGATT 58.085 50.000 0.00 0.00 0.00 3.34
880 942 3.610669 CATCCTCCCTCCGGCGAG 61.611 72.222 9.30 3.68 35.72 5.03
881 943 4.137615 TCATCCTCCCTCCGGCGA 62.138 66.667 9.30 0.00 0.00 5.54
991 1065 2.609299 TGACTCCATGGCCGGGAA 60.609 61.111 16.04 0.19 33.11 3.97
1330 1431 1.182667 GGGGGTGACATGTAAAAGCC 58.817 55.000 13.05 13.05 0.00 4.35
1406 1507 4.322567 GGATATGGAGAACTCAAGGCATC 58.677 47.826 4.23 0.00 0.00 3.91
1571 1700 6.482451 GCTTATTGCAAGCGTTAATAAGTG 57.518 37.500 18.59 5.35 42.30 3.16
1961 2117 7.756722 CAGCTGAAATTGGTAAAATAGAACAGG 59.243 37.037 8.42 0.00 0.00 4.00
2211 2374 6.750501 CAGATCAATTTCCTGCTATGTTGTTG 59.249 38.462 0.00 0.00 0.00 3.33
2291 2473 3.067106 ACGGACATTGTCTTACAGCAAG 58.933 45.455 16.02 1.09 35.38 4.01
2296 2478 2.535012 TGCACGGACATTGTCTTACA 57.465 45.000 16.02 7.34 32.47 2.41
2328 2510 4.286032 ACAAGGTACTACAATCCAGCAGAA 59.714 41.667 0.00 0.00 38.49 3.02
2453 2638 6.142320 GCTCACCTGTTTGTTTATTTCTTTCG 59.858 38.462 0.00 0.00 0.00 3.46
2466 2651 1.741706 CCTATGCTGCTCACCTGTTTG 59.258 52.381 0.00 0.00 0.00 2.93
2562 2754 7.599998 CCTTGTAGAGTTTTTGGATGAATTTGG 59.400 37.037 0.00 0.00 0.00 3.28
2620 2879 9.579932 AAATATTTTGGCCACCTAAAAATTTGA 57.420 25.926 15.64 1.48 35.64 2.69
2631 3040 5.879777 ACTGCAATTAAATATTTTGGCCACC 59.120 36.000 3.88 0.00 0.00 4.61
2660 3072 7.201679 CCAACCAAATGCAAGACAATGTAAAAA 60.202 33.333 0.00 0.00 0.00 1.94
2661 3073 6.259608 CCAACCAAATGCAAGACAATGTAAAA 59.740 34.615 0.00 0.00 0.00 1.52
2673 3085 0.543277 TTGCCACCAACCAAATGCAA 59.457 45.000 0.00 0.00 36.46 4.08
2679 3091 2.741145 ACTAAACTTGCCACCAACCAA 58.259 42.857 0.00 0.00 0.00 3.67
2715 3130 6.199937 ACTTCATGCATGGACATAGAAAAC 57.800 37.500 25.97 0.00 0.00 2.43
2977 3392 1.075970 CACCTGGGATCTCCTCGGA 60.076 63.158 0.00 0.00 36.20 4.55
3197 3638 8.654230 TTTGAAAAGCAGTGCACAAATAATAA 57.346 26.923 21.04 2.35 0.00 1.40
3305 3755 5.068591 ACTGTTTTTCACCTGGTACCATTTC 59.931 40.000 16.75 0.01 0.00 2.17
3357 3822 2.835027 TGCTATGCAGAAGAGATGCTG 58.165 47.619 3.11 0.00 44.17 4.41
3465 3930 6.806668 ATTTCCTTTTCTTTTTGACCCTCA 57.193 33.333 0.00 0.00 0.00 3.86
3498 3963 7.618442 TCGACTTTCTATATTCGTCAATTTGC 58.382 34.615 0.00 0.00 33.20 3.68
3578 4043 0.924090 CAAGCTTCGACCATCGCTAC 59.076 55.000 0.00 0.00 40.21 3.58
3668 4147 3.254892 GCCAAACTTCGGTTCAAACAAA 58.745 40.909 0.00 0.00 37.14 2.83
3687 4166 1.198637 GCACATTGACAGAGAAGTGCC 59.801 52.381 0.00 0.00 44.68 5.01
3701 4180 3.743521 TGCTGAAGTAAGAGTGCACATT 58.256 40.909 21.04 15.53 0.00 2.71
3717 4196 4.381612 CGATAGTTTGTTCTACCCTGCTGA 60.382 45.833 0.00 0.00 0.00 4.26
3793 4278 4.157840 GCACCTTTCCCAACCAGTTTATAG 59.842 45.833 0.00 0.00 0.00 1.31
3813 4298 6.873076 CAGATAATGGAATAGGAAGAGAGCAC 59.127 42.308 0.00 0.00 0.00 4.40
3868 4353 6.434340 AGATCCCAGTCCAATTTTGTAAAGAC 59.566 38.462 0.00 0.00 0.00 3.01
3874 4359 4.082125 GACAGATCCCAGTCCAATTTTGT 58.918 43.478 0.00 0.00 0.00 2.83
3926 4411 0.740737 CGGCCAGCCAAGATAAAAGG 59.259 55.000 9.78 0.00 35.37 3.11



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

AutoCloner maintained by Alex Coulton.