Multiple sequence alignment - TraesCS4B01G223600

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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 TraesCS4B01G223600 chr4B 100.000 2396 0 0 1 2396 468000311 468002706 0.000000e+00 4425.0
1 TraesCS4B01G223600 chr4D 88.848 1354 54 35 482 1797 380531420 380532714 0.000000e+00 1574.0
2 TraesCS4B01G223600 chr4D 90.407 615 26 16 1796 2386 380532750 380533355 0.000000e+00 778.0
3 TraesCS4B01G223600 chr4A 90.646 1208 67 24 496 1686 83312977 83311799 0.000000e+00 1563.0
4 TraesCS4B01G223600 chr4A 91.115 619 34 9 1794 2396 83311613 83311000 0.000000e+00 819.0
5 TraesCS4B01G223600 chr4A 82.093 497 73 13 3 498 83313706 83313225 6.160000e-111 411.0
6 TraesCS4B01G223600 chr4A 96.429 56 2 0 1742 1797 83311702 83311647 2.540000e-15 93.5


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 TraesCS4B01G223600 chr4B 468000311 468002706 2395 False 4425.000 4425 100.00000 1 2396 1 chr4B.!!$F1 2395
1 TraesCS4B01G223600 chr4D 380531420 380533355 1935 False 1176.000 1574 89.62750 482 2386 2 chr4D.!!$F1 1904
2 TraesCS4B01G223600 chr4A 83311000 83313706 2706 True 721.625 1563 90.07075 3 2396 4 chr4A.!!$R1 2393

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
129 130 0.038526 CGAGGTTGTGAGCGGTAGTT 60.039 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1679 0.891373 CGAGGTATGGATCGGAGCAT 59.109 55.0 0.0 0.0 35.33 3.79 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
22 23 0.935898 CTACATGCAGCTGCTAGTGC 59.064 55.000 36.61 13.42 42.66 4.40
31 32 3.729965 CTGCTAGTGCTGCGAGGGG 62.730 68.421 0.00 0.00 40.48 4.79
49 50 1.816224 GGGCGGAACACATGTTACAAT 59.184 47.619 7.72 0.00 38.79 2.71
50 51 3.011119 GGGCGGAACACATGTTACAATA 58.989 45.455 7.72 0.00 38.79 1.90
53 54 4.095782 GGCGGAACACATGTTACAATATGT 59.904 41.667 7.72 0.00 40.72 2.29
60 61 4.513442 ACATGTTACAATATGTGAGGCGT 58.487 39.130 3.84 0.00 38.97 5.68
62 63 3.183754 TGTTACAATATGTGAGGCGTCG 58.816 45.455 1.39 0.00 0.00 5.12
75 76 2.876645 CGTCGACGCTTGGAGCTC 60.877 66.667 26.59 4.71 39.60 4.09
78 79 4.421479 CGACGCTTGGAGCTCGGT 62.421 66.667 7.83 0.08 39.60 4.69
93 94 2.029288 CGGTGCTGCAAGTCGATGT 61.029 57.895 2.77 0.00 35.30 3.06
105 106 1.002366 GTCGATGTTGCAAGAGCGAT 58.998 50.000 34.26 3.48 46.23 4.58
106 107 1.001624 TCGATGTTGCAAGAGCGATG 58.998 50.000 29.70 5.89 46.23 3.84
109 110 2.348311 CGATGTTGCAAGAGCGATGATC 60.348 50.000 27.69 4.76 46.23 2.92
110 111 1.372582 TGTTGCAAGAGCGATGATCC 58.627 50.000 0.00 0.00 46.23 3.36
111 112 0.302890 GTTGCAAGAGCGATGATCCG 59.697 55.000 0.00 0.00 46.23 4.18
112 113 0.175531 TTGCAAGAGCGATGATCCGA 59.824 50.000 0.00 0.00 46.23 4.55
120 121 0.179111 GCGATGATCCGAGGTTGTGA 60.179 55.000 0.00 0.00 0.00 3.58
125 126 2.227089 GATCCGAGGTTGTGAGCGGT 62.227 60.000 0.00 0.00 43.92 5.68
127 128 1.153823 CCGAGGTTGTGAGCGGTAG 60.154 63.158 0.00 0.00 38.99 3.18
129 130 0.038526 CGAGGTTGTGAGCGGTAGTT 60.039 55.000 0.00 0.00 0.00 2.24
130 131 1.429463 GAGGTTGTGAGCGGTAGTTG 58.571 55.000 0.00 0.00 0.00 3.16
132 133 0.865769 GGTTGTGAGCGGTAGTTGTG 59.134 55.000 0.00 0.00 0.00 3.33
164 165 1.398041 CATGGCTATGTTGTGACGGTG 59.602 52.381 1.12 0.00 0.00 4.94
166 167 0.953471 GGCTATGTTGTGACGGTGCA 60.953 55.000 0.00 0.00 0.00 4.57
169 170 1.460743 CTATGTTGTGACGGTGCAGTG 59.539 52.381 0.00 0.00 0.00 3.66
172 173 1.887242 TTGTGACGGTGCAGTGAGC 60.887 57.895 0.00 0.00 45.96 4.26
183 184 1.227639 GCAGTGAGCATAGCTGATGG 58.772 55.000 0.00 0.00 44.79 3.51
190 191 3.137446 AGCATAGCTGATGGTCCATTC 57.863 47.619 5.65 0.24 42.79 2.67
191 192 1.802960 GCATAGCTGATGGTCCATTCG 59.197 52.381 5.65 1.46 35.91 3.34
192 193 2.420642 CATAGCTGATGGTCCATTCGG 58.579 52.381 5.65 5.87 31.20 4.30
193 194 1.496060 TAGCTGATGGTCCATTCGGT 58.504 50.000 5.65 8.34 0.00 4.69
194 195 0.620556 AGCTGATGGTCCATTCGGTT 59.379 50.000 5.65 0.21 0.00 4.44
195 196 1.017387 GCTGATGGTCCATTCGGTTC 58.983 55.000 5.65 0.00 0.00 3.62
196 197 1.407437 GCTGATGGTCCATTCGGTTCT 60.407 52.381 5.65 0.00 0.00 3.01
197 198 2.158957 GCTGATGGTCCATTCGGTTCTA 60.159 50.000 5.65 0.00 0.00 2.10
198 199 3.458189 CTGATGGTCCATTCGGTTCTAC 58.542 50.000 5.65 0.00 0.00 2.59
199 200 2.159156 TGATGGTCCATTCGGTTCTACG 60.159 50.000 5.65 0.00 0.00 3.51
204 205 3.518590 GTCCATTCGGTTCTACGACAAT 58.481 45.455 0.00 0.00 43.37 2.71
206 207 2.030457 CCATTCGGTTCTACGACAATGC 59.970 50.000 0.00 0.00 43.37 3.56
207 208 2.736144 TTCGGTTCTACGACAATGCT 57.264 45.000 0.00 0.00 43.37 3.79
209 210 3.141002 TCGGTTCTACGACAATGCTAC 57.859 47.619 0.00 0.00 38.06 3.58
211 212 2.190981 GGTTCTACGACAATGCTACGG 58.809 52.381 0.00 0.00 0.00 4.02
213 214 3.181497 GGTTCTACGACAATGCTACGGTA 60.181 47.826 0.00 0.00 0.00 4.02
220 221 3.381949 GACAATGCTACGGTATGGAGAC 58.618 50.000 0.00 0.00 0.00 3.36
239 240 5.007724 GGAGACACAAAGGAAAACTACACAG 59.992 44.000 0.00 0.00 0.00 3.66
240 241 4.335594 AGACACAAAGGAAAACTACACAGC 59.664 41.667 0.00 0.00 0.00 4.40
241 242 4.270008 ACACAAAGGAAAACTACACAGCT 58.730 39.130 0.00 0.00 0.00 4.24
242 243 4.705023 ACACAAAGGAAAACTACACAGCTT 59.295 37.500 0.00 0.00 0.00 3.74
243 244 5.036737 CACAAAGGAAAACTACACAGCTTG 58.963 41.667 0.00 0.00 0.00 4.01
244 245 4.097892 ACAAAGGAAAACTACACAGCTTGG 59.902 41.667 0.00 0.00 0.00 3.61
245 246 3.857157 AGGAAAACTACACAGCTTGGA 57.143 42.857 0.00 0.00 0.00 3.53
249 250 3.788227 AAACTACACAGCTTGGATGGA 57.212 42.857 0.00 0.00 0.00 3.41
257 258 2.371841 ACAGCTTGGATGGACTACAACA 59.628 45.455 0.00 0.00 0.00 3.33
259 260 1.740025 GCTTGGATGGACTACAACAGC 59.260 52.381 0.00 0.00 0.00 4.40
280 281 2.356135 GTTGCTTTAGAAGATCCGGCA 58.644 47.619 0.00 0.00 0.00 5.69
281 282 2.945668 GTTGCTTTAGAAGATCCGGCAT 59.054 45.455 0.00 0.00 0.00 4.40
302 303 2.301870 TGGCGGTCAGTCTAATCACTTT 59.698 45.455 0.00 0.00 0.00 2.66
355 356 4.021981 GCCTTATGTCTGAATTATTGGCCC 60.022 45.833 0.00 0.00 0.00 5.80
356 357 4.216257 CCTTATGTCTGAATTATTGGCCCG 59.784 45.833 0.00 0.00 0.00 6.13
357 358 2.799126 TGTCTGAATTATTGGCCCGT 57.201 45.000 0.00 0.00 0.00 5.28
359 360 1.676006 GTCTGAATTATTGGCCCGTGG 59.324 52.381 0.00 0.00 0.00 4.94
361 362 2.025793 TCTGAATTATTGGCCCGTGGAA 60.026 45.455 0.00 0.00 0.00 3.53
362 363 2.958355 CTGAATTATTGGCCCGTGGAAT 59.042 45.455 0.00 0.00 0.00 3.01
364 365 4.537751 TGAATTATTGGCCCGTGGAATAA 58.462 39.130 0.00 3.82 0.00 1.40
365 366 5.144100 TGAATTATTGGCCCGTGGAATAAT 58.856 37.500 10.68 10.68 34.97 1.28
366 367 6.307776 TGAATTATTGGCCCGTGGAATAATA 58.692 36.000 14.93 2.09 33.23 0.98
367 368 6.951198 TGAATTATTGGCCCGTGGAATAATAT 59.049 34.615 14.93 8.25 33.23 1.28
424 425 8.675504 TCCACTTTTAGATTTCGACTAGACTAG 58.324 37.037 8.00 8.00 0.00 2.57
440 441 4.200874 AGACTAGAGTATTGGACAGACCG 58.799 47.826 0.00 0.00 42.61 4.79
446 447 4.398673 AGAGTATTGGACAGACCGTTCTAC 59.601 45.833 0.00 0.00 42.61 2.59
451 452 2.079925 GGACAGACCGTTCTACGTACT 58.920 52.381 0.00 0.00 40.58 2.73
460 461 3.231965 CGTTCTACGTACTGTCACCTTG 58.768 50.000 0.00 0.00 36.74 3.61
463 464 2.816087 TCTACGTACTGTCACCTTGTCC 59.184 50.000 0.00 0.00 0.00 4.02
466 467 1.067776 CGTACTGTCACCTTGTCCCTC 60.068 57.143 0.00 0.00 0.00 4.30
472 473 1.073199 CACCTTGTCCCTCCACCAC 59.927 63.158 0.00 0.00 0.00 4.16
475 476 1.004918 CTTGTCCCTCCACCACGTC 60.005 63.158 0.00 0.00 0.00 4.34
494 495 1.277273 TCTGTGGCTTCACCTCATCAG 59.723 52.381 0.00 0.00 41.03 2.90
556 808 4.035558 TGCCAAGAAAGAATATCATCGTGC 59.964 41.667 0.00 0.00 0.00 5.34
575 827 3.067180 GTGCTCCCAAACATACATCATGG 59.933 47.826 0.00 0.00 39.13 3.66
600 852 9.136952 GGTACACGTAAAGCTAATGATAATAGG 57.863 37.037 0.00 0.00 0.00 2.57
605 857 8.639761 ACGTAAAGCTAATGATAATAGGTCTGT 58.360 33.333 0.00 0.00 31.12 3.41
619 871 3.582164 AGGTCTGTTTCTGAACCTCTCT 58.418 45.455 0.00 0.00 34.80 3.10
679 932 0.469705 TGGGGTGCTGTTTTGCTGAT 60.470 50.000 0.00 0.00 0.00 2.90
742 995 2.378028 GCAGACAGCGTCAATCCTC 58.622 57.895 10.52 0.00 34.60 3.71
743 996 1.086634 GCAGACAGCGTCAATCCTCC 61.087 60.000 10.52 0.00 34.60 4.30
744 997 0.247460 CAGACAGCGTCAATCCTCCA 59.753 55.000 10.52 0.00 34.60 3.86
746 999 2.101415 CAGACAGCGTCAATCCTCCATA 59.899 50.000 10.52 0.00 34.60 2.74
747 1000 2.766263 AGACAGCGTCAATCCTCCATAA 59.234 45.455 10.52 0.00 34.60 1.90
749 1002 3.733337 ACAGCGTCAATCCTCCATAATC 58.267 45.455 0.00 0.00 0.00 1.75
750 1003 3.389329 ACAGCGTCAATCCTCCATAATCT 59.611 43.478 0.00 0.00 0.00 2.40
751 1004 3.993081 CAGCGTCAATCCTCCATAATCTC 59.007 47.826 0.00 0.00 0.00 2.75
752 1005 2.989840 GCGTCAATCCTCCATAATCTCG 59.010 50.000 0.00 0.00 0.00 4.04
753 1006 3.553096 GCGTCAATCCTCCATAATCTCGT 60.553 47.826 0.00 0.00 0.00 4.18
754 1007 3.983988 CGTCAATCCTCCATAATCTCGTG 59.016 47.826 0.00 0.00 0.00 4.35
755 1008 4.310769 GTCAATCCTCCATAATCTCGTGG 58.689 47.826 0.00 0.00 36.82 4.94
756 1009 3.070018 CAATCCTCCATAATCTCGTGGC 58.930 50.000 0.00 0.00 35.43 5.01
757 1010 1.788229 TCCTCCATAATCTCGTGGCA 58.212 50.000 0.00 0.00 35.43 4.92
758 1011 1.412710 TCCTCCATAATCTCGTGGCAC 59.587 52.381 7.79 7.79 35.43 5.01
787 1040 8.778358 GTCTAGGTGAATGAATAATTTAGCCAG 58.222 37.037 0.00 0.00 33.84 4.85
805 1059 0.825010 AGCAAAGTCCACAAGCCCAG 60.825 55.000 0.00 0.00 0.00 4.45
811 1065 0.398318 GTCCACAAGCCCAGAGACTT 59.602 55.000 0.00 0.00 0.00 3.01
818 1072 0.116143 AGCCCAGAGACTTCACTCCT 59.884 55.000 0.00 0.00 37.60 3.69
830 1084 0.387929 TCACTCCTCGCACGAACTTT 59.612 50.000 0.00 0.00 0.00 2.66
836 1090 2.069273 CCTCGCACGAACTTTCAATCT 58.931 47.619 0.00 0.00 0.00 2.40
849 1105 0.591659 TCAATCTATCCGTCCTCGCG 59.408 55.000 0.00 0.00 35.54 5.87
900 1163 2.955751 CTAGCAGTTACGCGCCCCTC 62.956 65.000 5.73 0.00 36.85 4.30
902 1165 3.771160 CAGTTACGCGCCCCTCCT 61.771 66.667 5.73 0.00 0.00 3.69
903 1166 2.043652 AGTTACGCGCCCCTCCTA 60.044 61.111 5.73 0.00 0.00 2.94
904 1167 2.105729 GTTACGCGCCCCTCCTAC 59.894 66.667 5.73 0.00 0.00 3.18
905 1168 3.149648 TTACGCGCCCCTCCTACC 61.150 66.667 5.73 0.00 0.00 3.18
944 1207 1.068121 CTTCCACTTTCCCCACCTCT 58.932 55.000 0.00 0.00 0.00 3.69
963 1226 2.832661 AGGCCAAGCAAACGCACA 60.833 55.556 5.01 0.00 0.00 4.57
990 1253 1.372128 GGCAACGCAAAGAAGCAGG 60.372 57.895 0.00 0.00 0.00 4.85
1128 1400 2.087009 GGCGTCGTGGTTCTTCTCG 61.087 63.158 0.00 0.00 0.00 4.04
1137 1409 1.808945 TGGTTCTTCTCGTACGAGGAC 59.191 52.381 37.27 28.57 42.20 3.85
1344 1616 1.139734 CATGGTCGTCGTCCTCCTG 59.860 63.158 9.90 1.89 0.00 3.86
1348 1620 2.750637 TCGTCGTCCTCCTGCTCC 60.751 66.667 0.00 0.00 0.00 4.70
1390 1662 3.650647 TTCCAGGACATGTGGAAGC 57.349 52.632 1.15 0.00 46.96 3.86
1407 1679 3.470709 GAAGCCTTGATGGAATGATCGA 58.529 45.455 0.00 0.00 38.35 3.59
1485 1761 5.923114 TCGTATCGATCTGTAGTACACCTAC 59.077 44.000 0.00 0.00 45.36 3.18
1497 1773 7.218145 GTAGTACACCTACGAATGATTGTTG 57.782 40.000 0.00 0.00 36.94 3.33
1498 1774 4.630069 AGTACACCTACGAATGATTGTTGC 59.370 41.667 0.00 0.00 0.00 4.17
1501 1777 4.154195 ACACCTACGAATGATTGTTGCTTC 59.846 41.667 0.00 0.00 0.00 3.86
1502 1778 3.689649 ACCTACGAATGATTGTTGCTTCC 59.310 43.478 0.00 0.00 0.00 3.46
1503 1779 3.689161 CCTACGAATGATTGTTGCTTCCA 59.311 43.478 0.00 0.00 0.00 3.53
1504 1780 3.559238 ACGAATGATTGTTGCTTCCAC 57.441 42.857 0.00 0.00 0.00 4.02
1805 2194 4.363999 CACAAAGGAAGATAGTAGGAGCG 58.636 47.826 0.00 0.00 0.00 5.03
1870 2260 5.687166 TCGTTCTGGTATTATCCCTTTGT 57.313 39.130 0.00 0.00 0.00 2.83
1887 2277 3.592814 TGAGCGTATCTCGGCCCG 61.593 66.667 0.00 0.00 44.86 6.13
2000 2403 2.715763 TAGGGAGAGGTTGTTGGTCT 57.284 50.000 0.00 0.00 0.00 3.85
2059 2463 6.422333 TGCATGATCCACAGAAACCTTATTA 58.578 36.000 0.00 0.00 0.00 0.98
2132 2536 2.708051 GGGTAGTGCCTACTTTTCCAC 58.292 52.381 10.83 0.00 37.16 4.02
2145 2549 1.153353 TTTCCACCATCTTCGAACGC 58.847 50.000 0.00 0.00 0.00 4.84
2201 2617 2.801111 GGGGAGAAAATTACTCGATCGC 59.199 50.000 11.09 0.00 35.49 4.58
2204 2620 4.360563 GGAGAAAATTACTCGATCGCTGA 58.639 43.478 11.09 0.00 35.49 4.26
2346 2769 1.599047 CTGGATGCCTTCTCGTGGT 59.401 57.895 0.00 0.00 0.00 4.16
2391 2814 4.185394 TGCGAGTCTTGTTCAAAGTGTTA 58.815 39.130 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.202851 CCCTCGCAGCACTAGCAG 60.203 66.667 0.00 0.00 45.49 4.24
26 27 0.035820 TAACATGTGTTCCGCCCCTC 60.036 55.000 0.00 0.00 39.31 4.30
28 29 0.606944 TGTAACATGTGTTCCGCCCC 60.607 55.000 0.00 0.00 39.31 5.80
31 32 5.027737 CACATATTGTAACATGTGTTCCGC 58.972 41.667 0.00 0.00 44.50 5.54
38 39 4.513442 ACGCCTCACATATTGTAACATGT 58.487 39.130 0.00 0.00 35.79 3.21
39 40 4.318050 CGACGCCTCACATATTGTAACATG 60.318 45.833 0.00 0.00 0.00 3.21
75 76 1.568612 AACATCGACTTGCAGCACCG 61.569 55.000 0.00 0.00 0.00 4.94
78 79 1.575922 GCAACATCGACTTGCAGCA 59.424 52.632 19.86 0.00 43.04 4.41
93 94 0.175531 TCGGATCATCGCTCTTGCAA 59.824 50.000 0.00 0.00 39.64 4.08
105 106 1.215382 CGCTCACAACCTCGGATCA 59.785 57.895 0.00 0.00 0.00 2.92
106 107 1.519455 CCGCTCACAACCTCGGATC 60.519 63.158 0.00 0.00 44.23 3.36
109 110 1.153823 CTACCGCTCACAACCTCGG 60.154 63.158 0.00 0.00 46.61 4.63
110 111 0.038526 AACTACCGCTCACAACCTCG 60.039 55.000 0.00 0.00 0.00 4.63
111 112 1.270147 ACAACTACCGCTCACAACCTC 60.270 52.381 0.00 0.00 0.00 3.85
112 113 0.756903 ACAACTACCGCTCACAACCT 59.243 50.000 0.00 0.00 0.00 3.50
120 121 2.007049 GCAGCATACACAACTACCGCT 61.007 52.381 0.00 0.00 0.00 5.52
125 126 1.349357 TGGTGGCAGCATACACAACTA 59.651 47.619 16.56 0.00 39.31 2.24
127 128 1.135315 CATGGTGGCAGCATACACAAC 60.135 52.381 29.56 0.00 39.31 3.32
129 130 0.680601 CCATGGTGGCAGCATACACA 60.681 55.000 29.56 3.02 39.31 3.72
130 131 2.109431 CCATGGTGGCAGCATACAC 58.891 57.895 29.56 0.00 34.09 2.90
149 150 1.460743 CACTGCACCGTCACAACATAG 59.539 52.381 0.00 0.00 0.00 2.23
150 151 1.069358 TCACTGCACCGTCACAACATA 59.931 47.619 0.00 0.00 0.00 2.29
164 165 1.227639 CCATCAGCTATGCTCACTGC 58.772 55.000 0.00 0.00 36.40 4.40
166 167 1.415659 GGACCATCAGCTATGCTCACT 59.584 52.381 0.00 0.00 36.40 3.41
169 170 2.855209 ATGGACCATCAGCTATGCTC 57.145 50.000 0.00 0.00 36.40 4.26
172 173 2.224378 ACCGAATGGACCATCAGCTATG 60.224 50.000 7.63 0.00 39.21 2.23
173 174 2.050144 ACCGAATGGACCATCAGCTAT 58.950 47.619 7.63 0.00 39.21 2.97
176 177 1.017387 GAACCGAATGGACCATCAGC 58.983 55.000 7.63 0.00 39.21 4.26
177 178 2.698855 AGAACCGAATGGACCATCAG 57.301 50.000 7.63 4.83 39.21 2.90
180 181 2.104967 TCGTAGAACCGAATGGACCAT 58.895 47.619 0.00 0.00 39.21 3.55
181 182 1.203052 GTCGTAGAACCGAATGGACCA 59.797 52.381 0.00 0.00 39.69 4.02
182 183 1.203052 TGTCGTAGAACCGAATGGACC 59.797 52.381 0.00 0.00 39.69 4.46
183 184 2.642139 TGTCGTAGAACCGAATGGAC 57.358 50.000 0.00 0.00 39.69 4.02
184 185 3.517602 CATTGTCGTAGAACCGAATGGA 58.482 45.455 0.00 0.00 39.69 3.41
185 186 2.030457 GCATTGTCGTAGAACCGAATGG 59.970 50.000 0.00 0.00 39.69 3.16
186 187 2.930040 AGCATTGTCGTAGAACCGAATG 59.070 45.455 0.00 0.00 39.69 2.67
187 188 3.247006 AGCATTGTCGTAGAACCGAAT 57.753 42.857 0.00 0.00 39.69 3.34
188 189 2.736144 AGCATTGTCGTAGAACCGAA 57.264 45.000 0.00 0.00 39.69 4.30
189 190 2.476686 CGTAGCATTGTCGTAGAACCGA 60.477 50.000 0.00 0.00 39.69 4.69
190 191 1.844357 CGTAGCATTGTCGTAGAACCG 59.156 52.381 0.00 0.00 39.69 4.44
191 192 2.190981 CCGTAGCATTGTCGTAGAACC 58.809 52.381 0.00 0.00 39.69 3.62
192 193 2.872370 ACCGTAGCATTGTCGTAGAAC 58.128 47.619 0.00 0.00 39.69 3.01
193 194 4.498513 CCATACCGTAGCATTGTCGTAGAA 60.499 45.833 0.00 0.00 39.69 2.10
194 195 3.004002 CCATACCGTAGCATTGTCGTAGA 59.996 47.826 0.00 0.00 0.00 2.59
195 196 3.004002 TCCATACCGTAGCATTGTCGTAG 59.996 47.826 0.00 0.00 0.00 3.51
196 197 2.950975 TCCATACCGTAGCATTGTCGTA 59.049 45.455 0.00 0.00 0.00 3.43
197 198 1.752498 TCCATACCGTAGCATTGTCGT 59.248 47.619 0.00 0.00 0.00 4.34
198 199 2.034179 TCTCCATACCGTAGCATTGTCG 59.966 50.000 0.00 0.00 0.00 4.35
199 200 3.181479 TGTCTCCATACCGTAGCATTGTC 60.181 47.826 0.00 0.00 0.00 3.18
204 205 1.842052 TGTGTCTCCATACCGTAGCA 58.158 50.000 0.00 0.00 0.00 3.49
206 207 3.446161 TCCTTTGTGTCTCCATACCGTAG 59.554 47.826 0.00 0.00 0.00 3.51
207 208 3.433343 TCCTTTGTGTCTCCATACCGTA 58.567 45.455 0.00 0.00 0.00 4.02
209 210 3.328382 TTCCTTTGTGTCTCCATACCG 57.672 47.619 0.00 0.00 0.00 4.02
211 212 6.708949 TGTAGTTTTCCTTTGTGTCTCCATAC 59.291 38.462 0.00 0.00 0.00 2.39
213 214 5.531287 GTGTAGTTTTCCTTTGTGTCTCCAT 59.469 40.000 0.00 0.00 0.00 3.41
220 221 4.900635 AGCTGTGTAGTTTTCCTTTGTG 57.099 40.909 0.00 0.00 0.00 3.33
227 228 4.072131 TCCATCCAAGCTGTGTAGTTTTC 58.928 43.478 0.00 0.00 0.00 2.29
230 231 2.639839 AGTCCATCCAAGCTGTGTAGTT 59.360 45.455 0.00 0.00 0.00 2.24
232 233 3.195610 TGTAGTCCATCCAAGCTGTGTAG 59.804 47.826 0.00 0.00 0.00 2.74
239 240 1.740025 GCTGTTGTAGTCCATCCAAGC 59.260 52.381 0.00 0.00 0.00 4.01
240 241 2.002586 CGCTGTTGTAGTCCATCCAAG 58.997 52.381 0.00 0.00 0.00 3.61
241 242 1.346395 ACGCTGTTGTAGTCCATCCAA 59.654 47.619 0.00 0.00 0.00 3.53
242 243 0.973632 ACGCTGTTGTAGTCCATCCA 59.026 50.000 0.00 0.00 0.00 3.41
243 244 1.732259 CAACGCTGTTGTAGTCCATCC 59.268 52.381 11.62 0.00 0.00 3.51
244 245 1.128692 GCAACGCTGTTGTAGTCCATC 59.871 52.381 18.15 1.46 0.00 3.51
245 246 1.156736 GCAACGCTGTTGTAGTCCAT 58.843 50.000 18.15 0.00 0.00 3.41
249 250 3.724374 TCTAAAGCAACGCTGTTGTAGT 58.276 40.909 18.15 9.27 39.62 2.73
257 258 2.271800 CGGATCTTCTAAAGCAACGCT 58.728 47.619 0.00 0.00 42.56 5.07
259 260 1.327764 GCCGGATCTTCTAAAGCAACG 59.672 52.381 5.05 0.00 0.00 4.10
280 281 2.111384 AGTGATTAGACTGACCGCCAT 58.889 47.619 0.00 0.00 0.00 4.40
281 282 1.557099 AGTGATTAGACTGACCGCCA 58.443 50.000 0.00 0.00 0.00 5.69
302 303 4.108570 TGATTTAGGCCTAAAGTGAGGGA 58.891 43.478 34.75 16.21 38.30 4.20
338 339 2.364632 CACGGGCCAATAATTCAGACA 58.635 47.619 4.39 0.00 0.00 3.41
340 341 1.562008 TCCACGGGCCAATAATTCAGA 59.438 47.619 4.39 0.00 0.00 3.27
355 356 7.229228 TCAAGTCGACAAATATTATTCCACG 57.771 36.000 19.50 0.00 0.00 4.94
356 357 9.438291 CATTCAAGTCGACAAATATTATTCCAC 57.562 33.333 19.50 0.00 0.00 4.02
357 358 8.620416 CCATTCAAGTCGACAAATATTATTCCA 58.380 33.333 19.50 0.00 0.00 3.53
359 360 9.651718 GTCCATTCAAGTCGACAAATATTATTC 57.348 33.333 19.50 0.00 0.00 1.75
361 362 8.731275 TGTCCATTCAAGTCGACAAATATTAT 57.269 30.769 19.50 0.00 32.51 1.28
362 363 7.822334 ACTGTCCATTCAAGTCGACAAATATTA 59.178 33.333 19.50 0.00 34.98 0.98
364 365 6.173339 ACTGTCCATTCAAGTCGACAAATAT 58.827 36.000 19.50 2.91 34.98 1.28
365 366 5.547465 ACTGTCCATTCAAGTCGACAAATA 58.453 37.500 19.50 0.31 34.98 1.40
366 367 4.389374 ACTGTCCATTCAAGTCGACAAAT 58.611 39.130 19.50 11.26 34.98 2.32
367 368 3.804036 ACTGTCCATTCAAGTCGACAAA 58.196 40.909 19.50 9.33 34.98 2.83
399 400 8.675504 TCTAGTCTAGTCGAAATCTAAAAGTGG 58.324 37.037 6.77 0.00 0.00 4.00
412 413 6.097981 TCTGTCCAATACTCTAGTCTAGTCGA 59.902 42.308 6.77 0.00 0.00 4.20
424 425 3.870633 AGAACGGTCTGTCCAATACTC 57.129 47.619 0.00 0.00 35.57 2.59
440 441 4.225208 GACAAGGTGACAGTACGTAGAAC 58.775 47.826 0.00 0.00 0.00 3.01
446 447 0.966920 AGGGACAAGGTGACAGTACG 59.033 55.000 0.00 0.00 0.00 3.67
451 452 1.415672 GGTGGAGGGACAAGGTGACA 61.416 60.000 0.00 0.00 0.00 3.58
460 461 2.207924 ACAGACGTGGTGGAGGGAC 61.208 63.158 0.00 0.00 0.00 4.46
472 473 0.036952 ATGAGGTGAAGCCACAGACG 60.037 55.000 0.00 0.00 44.93 4.18
475 476 1.002888 ACTGATGAGGTGAAGCCACAG 59.997 52.381 0.00 0.00 44.93 3.66
494 495 5.592054 TGCTGATATGTGCAGAGTAGTAAC 58.408 41.667 0.00 0.00 35.39 2.50
556 808 5.296780 GTGTACCATGATGTATGTTTGGGAG 59.703 44.000 0.00 0.00 34.87 4.30
575 827 9.688592 ACCTATTATCATTAGCTTTACGTGTAC 57.311 33.333 0.00 0.00 0.00 2.90
595 847 5.782845 AGAGAGGTTCAGAAACAGACCTATT 59.217 40.000 0.00 0.00 37.10 1.73
600 852 3.612955 CGGAGAGAGGTTCAGAAACAGAC 60.613 52.174 0.00 0.00 37.10 3.51
605 857 0.608640 GGCGGAGAGAGGTTCAGAAA 59.391 55.000 0.00 0.00 0.00 2.52
609 861 2.636412 CGTGGCGGAGAGAGGTTCA 61.636 63.158 0.00 0.00 0.00 3.18
679 932 4.242586 TCCCAGTGGACGTCCCCA 62.243 66.667 31.19 12.39 35.03 4.96
734 987 3.244215 GCCACGAGATTATGGAGGATTGA 60.244 47.826 0.00 0.00 38.34 2.57
742 995 0.880278 CCCGTGCCACGAGATTATGG 60.880 60.000 20.57 5.36 46.05 2.74
743 996 0.179084 ACCCGTGCCACGAGATTATG 60.179 55.000 20.57 0.00 46.05 1.90
744 997 0.104304 GACCCGTGCCACGAGATTAT 59.896 55.000 20.57 0.00 46.05 1.28
746 999 0.968901 TAGACCCGTGCCACGAGATT 60.969 55.000 20.57 4.22 46.05 2.40
747 1000 1.379443 TAGACCCGTGCCACGAGAT 60.379 57.895 20.57 2.88 46.05 2.75
749 1002 2.490217 CTAGACCCGTGCCACGAG 59.510 66.667 20.57 8.31 46.05 4.18
750 1003 3.066190 CCTAGACCCGTGCCACGA 61.066 66.667 20.57 0.00 46.05 4.35
751 1004 3.379445 ACCTAGACCCGTGCCACG 61.379 66.667 10.95 10.95 42.11 4.94
752 1005 1.823169 TTCACCTAGACCCGTGCCAC 61.823 60.000 0.00 0.00 0.00 5.01
753 1006 0.907704 ATTCACCTAGACCCGTGCCA 60.908 55.000 0.00 0.00 0.00 4.92
754 1007 0.462047 CATTCACCTAGACCCGTGCC 60.462 60.000 0.00 0.00 0.00 5.01
755 1008 0.535335 TCATTCACCTAGACCCGTGC 59.465 55.000 0.00 0.00 0.00 5.34
756 1009 3.543680 ATTCATTCACCTAGACCCGTG 57.456 47.619 0.00 0.00 0.00 4.94
757 1010 5.888982 ATTATTCATTCACCTAGACCCGT 57.111 39.130 0.00 0.00 0.00 5.28
758 1011 7.095187 GCTAAATTATTCATTCACCTAGACCCG 60.095 40.741 0.00 0.00 0.00 5.28
787 1040 0.823356 TCTGGGCTTGTGGACTTTGC 60.823 55.000 0.00 0.00 0.00 3.68
805 1059 0.455295 CGTGCGAGGAGTGAAGTCTC 60.455 60.000 0.00 0.00 0.00 3.36
811 1065 0.387929 AAAGTTCGTGCGAGGAGTGA 59.612 50.000 0.00 0.00 0.00 3.41
818 1072 3.863424 GGATAGATTGAAAGTTCGTGCGA 59.137 43.478 0.00 0.00 0.00 5.10
830 1084 0.591659 CGCGAGGACGGATAGATTGA 59.408 55.000 0.00 0.00 40.15 2.57
922 1185 0.251209 GGTGGGGAAAGTGGAAGGAC 60.251 60.000 0.00 0.00 0.00 3.85
944 1207 2.518112 TGCGTTTGCTTGGCCTGA 60.518 55.556 3.32 0.00 43.34 3.86
990 1253 2.125147 TACGACATGGCTGCCTGC 60.125 61.111 21.03 10.32 41.94 4.85
1128 1400 2.359531 CTCCTCCATGAAGTCCTCGTAC 59.640 54.545 0.00 0.00 0.00 3.67
1137 1409 1.227089 CGACGCCTCCTCCATGAAG 60.227 63.158 0.00 0.00 0.00 3.02
1344 1616 3.731653 GAAGCTGGCGAGGAGGAGC 62.732 68.421 0.00 0.00 0.00 4.70
1348 1620 2.125350 GTGGAAGCTGGCGAGGAG 60.125 66.667 0.00 0.00 0.00 3.69
1390 1662 3.409570 AGCATCGATCATTCCATCAAGG 58.590 45.455 0.00 0.00 39.47 3.61
1407 1679 0.891373 CGAGGTATGGATCGGAGCAT 59.109 55.000 0.00 0.00 35.33 3.79
1485 1761 2.489329 AGGTGGAAGCAACAATCATTCG 59.511 45.455 0.00 0.00 36.26 3.34
1745 2078 1.379044 CTCCCACCAACTGCCATCC 60.379 63.158 0.00 0.00 0.00 3.51
1746 2079 2.048603 GCTCCCACCAACTGCCATC 61.049 63.158 0.00 0.00 0.00 3.51
1747 2080 2.036256 GCTCCCACCAACTGCCAT 59.964 61.111 0.00 0.00 0.00 4.40
1748 2081 2.370459 ATTGCTCCCACCAACTGCCA 62.370 55.000 0.00 0.00 0.00 4.92
1749 2082 1.598701 GATTGCTCCCACCAACTGCC 61.599 60.000 0.00 0.00 0.00 4.85
1805 2194 2.756207 GTCCCAGAACTCTCCAGTCTAC 59.244 54.545 0.00 0.00 29.93 2.59
1870 2260 2.946172 TACGGGCCGAGATACGCTCA 62.946 60.000 35.78 0.77 44.15 4.26
1887 2277 3.490078 CGAGAGGACAAGATTCTGGCTAC 60.490 52.174 0.00 0.00 0.00 3.58
2000 2403 5.972935 ACGTACAAGTGATATCCATTGACA 58.027 37.500 18.74 7.53 0.00 3.58
2059 2463 2.534042 TCGGGATCTTTCTCCTGTCT 57.466 50.000 0.00 0.00 41.67 3.41
2116 2520 2.644798 AGATGGTGGAAAAGTAGGCACT 59.355 45.455 0.00 0.00 46.37 4.40
2132 2536 2.509336 AGCGGCGTTCGAAGATGG 60.509 61.111 9.37 0.00 42.43 3.51
2145 2549 3.568538 GCCTTAATTAATGATGCAGCGG 58.431 45.455 0.00 0.00 0.00 5.52
2201 2617 1.711060 AACAACAACCGCACCGTCAG 61.711 55.000 0.00 0.00 0.00 3.51
2204 2620 2.474612 GGAACAACAACCGCACCGT 61.475 57.895 0.00 0.00 0.00 4.83
2248 2666 6.811253 TCGCCACATACTTTAATTTCTTGT 57.189 33.333 0.00 0.00 0.00 3.16
2264 2684 1.686325 GGGGCTAGAGATTCGCCACA 61.686 60.000 0.00 0.00 46.40 4.17
2265 2685 1.069935 GGGGCTAGAGATTCGCCAC 59.930 63.158 0.00 0.00 45.53 5.01
2266 2686 2.498941 CGGGGCTAGAGATTCGCCA 61.499 63.158 0.00 0.00 45.53 5.69
2267 2687 2.340443 CGGGGCTAGAGATTCGCC 59.660 66.667 0.00 0.00 43.03 5.54
2346 2769 1.846124 ACTCCCCGGCTTCAGGAAA 60.846 57.895 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.