Multiple sequence alignment - TraesCS5B01G197900

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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 TraesCS5B01G197900 chr5B 100.000 4067 0 0 2679 6745 357106827 357102761 0.000000e+00 7511
1 TraesCS5B01G197900 chr5B 100.000 2283 0 0 1 2283 357109505 357107223 0.000000e+00 4217
2 TraesCS5B01G197900 chr5B 77.925 530 92 18 4773 5300 356722009 356721503 2.360000e-79 307
3 TraesCS5B01G197900 chr5B 89.954 219 22 0 2679 2897 357106770 357106552 3.980000e-72 283
4 TraesCS5B01G197900 chr5B 89.954 219 22 0 2736 2954 357106827 357106609 3.980000e-72 283
5 TraesCS5B01G197900 chr5B 75.052 485 86 25 5260 5732 356721501 356721040 6.900000e-45 193
6 TraesCS5B01G197900 chr5B 85.143 175 13 7 2059 2227 357107390 357107223 4.180000e-37 167
7 TraesCS5B01G197900 chr5B 85.143 175 13 7 2116 2283 357107447 357107279 4.180000e-37 167
8 TraesCS5B01G197900 chr5A 94.481 2881 94 33 3886 6708 404312938 404310065 0.000000e+00 4379
9 TraesCS5B01G197900 chr5A 96.167 2270 75 9 2 2259 404316770 404314501 0.000000e+00 3699
10 TraesCS5B01G197900 chr5A 97.099 1172 34 0 2679 3850 404314176 404313005 0.000000e+00 1977
11 TraesCS5B01G197900 chr5A 88.584 219 25 0 2679 2897 404314119 404313901 4.010000e-67 267
12 TraesCS5B01G197900 chr5A 87.838 222 27 0 2733 2954 404314179 404313958 1.870000e-65 261
13 TraesCS5B01G197900 chr5A 85.143 175 13 7 2116 2283 404314701 404314533 4.180000e-37 167
14 TraesCS5B01G197900 chr5A 74.074 486 88 28 5260 5732 404232944 404232484 1.500000e-36 165
15 TraesCS5B01G197900 chr5A 90.756 119 10 1 1501 1619 440988307 440988424 2.520000e-34 158
16 TraesCS5B01G197900 chr5A 84.667 150 11 6 2059 2202 404314644 404314501 9.120000e-29 139
17 TraesCS5B01G197900 chr5A 90.698 86 8 0 2179 2264 404314701 404314616 1.540000e-21 115
18 TraesCS5B01G197900 chr5D 94.989 2634 82 26 3886 6478 311309480 311306856 0.000000e+00 4087
19 TraesCS5B01G197900 chr5D 95.254 2128 56 12 188 2283 311313253 311311139 0.000000e+00 3328
20 TraesCS5B01G197900 chr5D 97.275 1211 31 2 2679 3889 311310734 311309526 0.000000e+00 2052
21 TraesCS5B01G197900 chr5D 79.920 498 93 6 4806 5300 310703469 310702976 6.430000e-95 359
22 TraesCS5B01G197900 chr5D 89.427 227 24 0 2728 2954 311310742 311310516 3.080000e-73 287
23 TraesCS5B01G197900 chr5D 86.531 245 15 9 6481 6708 311306820 311306577 3.120000e-63 254
24 TraesCS5B01G197900 chr5D 85.222 203 18 6 2059 2255 311311306 311311110 1.480000e-46 198
25 TraesCS5B01G197900 chr5D 74.167 480 93 24 5260 5732 310702974 310702519 3.230000e-38 171
26 TraesCS5B01G197900 chr5D 85.143 175 13 6 2116 2283 311311363 311311195 4.180000e-37 167
27 TraesCS5B01G197900 chr5D 90.678 118 11 0 1500 1617 308353468 308353351 2.520000e-34 158
28 TraesCS5B01G197900 chr5D 87.050 139 12 3 2059 2197 311311243 311311111 1.170000e-32 152
29 TraesCS5B01G197900 chr5D 94.737 76 4 0 2059 2134 311311186 311311111 1.190000e-22 119
30 TraesCS5B01G197900 chr5D 88.372 86 10 0 2179 2264 311311363 311311278 3.330000e-18 104
31 TraesCS5B01G197900 chr1B 91.667 120 10 0 1500 1619 48266477 48266358 4.180000e-37 167
32 TraesCS5B01G197900 chr2D 90.756 119 10 1 1501 1618 607675742 607675860 2.520000e-34 158
33 TraesCS5B01G197900 chrUn 89.831 118 12 0 1501 1618 61037037 61037154 1.170000e-32 152
34 TraesCS5B01G197900 chr6B 88.800 125 13 1 1500 1623 500829703 500829827 1.170000e-32 152
35 TraesCS5B01G197900 chr3D 89.831 118 12 0 1500 1617 613777480 613777597 1.170000e-32 152


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 TraesCS5B01G197900 chr5B 357102761 357109505 6744 True 2104.666667 7511 91.699000 1 6745 6 chr5B.!!$R2 6744
1 TraesCS5B01G197900 chr5B 356721040 356722009 969 True 250.000000 307 76.488500 4773 5732 2 chr5B.!!$R1 959
2 TraesCS5B01G197900 chr5A 404310065 404316770 6705 True 1375.500000 4379 90.584625 2 6708 8 chr5A.!!$R2 6706
3 TraesCS5B01G197900 chr5D 311306577 311313253 6676 True 1074.800000 4087 90.400000 188 6708 10 chr5D.!!$R3 6520
4 TraesCS5B01G197900 chr5D 310702519 310703469 950 True 265.000000 359 77.043500 4806 5732 2 chr5D.!!$R2 926

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
379 385 0.105760 TCTCCTCCAGATCTGCCCTC 60.106 60.000 17.76 0.00 0.00 4.30 F
1514 1544 0.324460 CAAGGTACTCCCTCCGTCCT 60.324 60.000 0.00 0.00 45.47 3.85 F
2074 2111 0.555769 AACTTTTGGTCCTGGAGCCA 59.444 50.000 22.16 16.74 0.00 4.75 F
2764 2810 0.750546 ACTAGACCACCTATCGCGCA 60.751 55.000 8.75 0.00 0.00 6.09 F
4076 4171 1.338674 TGAAACTAGTGGCATCGGTGG 60.339 52.381 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2245 0.378257 CGGGAGGAACAAATGCGATG 59.622 55.000 0.0 0.0 0.00 3.84 R
2764 2810 3.418684 AAACGTTAGCTGGAGGAACAT 57.581 42.857 0.0 0.0 0.00 2.71 R
3794 3840 2.602676 GCTACCCAGGCTTGACCCA 61.603 63.158 0.0 0.0 40.58 4.51 R
4729 4837 1.806542 CAGACTGAATTGGTGAACCCG 59.193 52.381 0.0 0.0 35.15 5.28 R
6007 6173 0.687354 ACTCACCGACCTTGAGCAAT 59.313 50.000 0.0 0.0 43.79 3.56 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
53 54 3.844359 GTGACGACGCGAAAATACC 57.156 52.632 15.93 0.00 0.00 2.73
78 79 1.300963 GGGCACATGAGGCAGAAGA 59.699 57.895 17.96 0.00 35.46 2.87
119 120 2.504032 GGATCGCCGATGGGTTGA 59.496 61.111 3.34 0.00 34.97 3.18
131 132 1.068943 TGGGTTGAAAGGGGCCAGTA 61.069 55.000 4.39 0.00 0.00 2.74
154 155 1.644786 GAAATCGCGGTGGGGTTGAG 61.645 60.000 6.13 0.00 0.00 3.02
186 187 0.602638 GATGGCGGCATTCATCGGTA 60.603 55.000 26.52 0.00 31.83 4.02
199 200 4.229304 TCATCGGTACATTGGTTTGGAT 57.771 40.909 0.00 0.00 0.00 3.41
204 205 2.291930 GGTACATTGGTTTGGATGGGGA 60.292 50.000 0.00 0.00 0.00 4.81
205 206 2.946791 ACATTGGTTTGGATGGGGAT 57.053 45.000 0.00 0.00 0.00 3.85
379 385 0.105760 TCTCCTCCAGATCTGCCCTC 60.106 60.000 17.76 0.00 0.00 4.30
669 699 2.111251 GAATACCAGCCTCCGCCC 59.889 66.667 0.00 0.00 34.57 6.13
701 731 4.778143 ATTCCGTCCGCACCCAGC 62.778 66.667 0.00 0.00 40.87 4.85
772 802 0.798776 ATCGCTTTTGCCGAACTCAG 59.201 50.000 0.00 0.00 43.93 3.35
836 866 8.715191 ACTGATTCAGATTCTAGTGATTTGTC 57.285 34.615 20.33 0.00 35.18 3.18
1514 1544 0.324460 CAAGGTACTCCCTCCGTCCT 60.324 60.000 0.00 0.00 45.47 3.85
1515 1545 0.324460 AAGGTACTCCCTCCGTCCTG 60.324 60.000 0.00 0.00 45.47 3.86
1703 1734 9.403110 CTCTGAATTTTGTGAAGAAAACCTATG 57.597 33.333 0.00 0.00 0.00 2.23
1781 1818 9.176460 TGTCTATGCTGAATGATGTTTTCATAA 57.824 29.630 0.00 0.00 44.51 1.90
1916 1953 4.215109 AGTAATATGGCAGGCGGATTTTT 58.785 39.130 0.00 0.00 0.00 1.94
2056 2093 1.388547 GCCAGCGGTAATTGATGGAA 58.611 50.000 0.79 0.00 45.67 3.53
2074 2111 0.555769 AACTTTTGGTCCTGGAGCCA 59.444 50.000 22.16 16.74 0.00 4.75
2208 2245 1.946475 GAGCCGTGACTAGACCACCC 61.946 65.000 0.00 0.00 0.00 4.61
2764 2810 0.750546 ACTAGACCACCTATCGCGCA 60.751 55.000 8.75 0.00 0.00 6.09
3066 3112 6.631016 TGCCTCTTGTGAACTTATAGTACTG 58.369 40.000 5.39 0.00 0.00 2.74
3084 3130 5.952947 AGTACTGACAACCTAGCTCATAAGT 59.047 40.000 0.00 0.00 0.00 2.24
3434 3480 4.350245 AGCTGTTGGTATGTACTGGTCTA 58.650 43.478 0.00 0.00 0.00 2.59
3505 3551 6.545298 AGATGTATGATTTCTTGGAAAGGAGC 59.455 38.462 0.00 0.00 46.24 4.70
3794 3840 5.105997 GCATGTCTTTTCAATAGAGGCTTGT 60.106 40.000 0.00 0.00 0.00 3.16
4076 4171 1.338674 TGAAACTAGTGGCATCGGTGG 60.339 52.381 0.00 0.00 0.00 4.61
4165 4260 9.814899 CTAATAATGATCTCTATTCTTCCGCAT 57.185 33.333 0.00 0.00 0.00 4.73
4310 4410 4.946784 AGTTGCTTCCGTTGATGTTATC 57.053 40.909 0.00 0.00 0.00 1.75
4633 4741 5.393135 CGAGACAGCACCTTCAGAAATACTA 60.393 44.000 0.00 0.00 0.00 1.82
4729 4837 7.607991 TGAAGAGAGAATGAGGTGTAAATTTCC 59.392 37.037 0.00 0.00 0.00 3.13
4769 4877 3.011818 TGTTCAGGCATCTACAAGCATG 58.988 45.455 0.00 0.00 43.27 4.06
5154 5266 4.719773 AGGTAAGGGCATTGTATCTGTACA 59.280 41.667 0.00 0.00 39.00 2.90
5202 5314 1.304464 GTGCCCCAGGAGAAAAGGG 60.304 63.158 0.00 0.00 42.94 3.95
5232 5344 4.523943 TGAATTGCAAGCTACATCCAAGTT 59.476 37.500 4.94 0.00 0.00 2.66
5588 5745 3.437049 GCGAGGAAATAGCAGAGTTTGTT 59.563 43.478 0.00 0.00 0.00 2.83
5591 5748 5.163913 CGAGGAAATAGCAGAGTTTGTTGAG 60.164 44.000 0.00 0.00 0.00 3.02
5598 5755 9.502091 AAATAGCAGAGTTTGTTGAGTATGTTA 57.498 29.630 0.00 0.00 0.00 2.41
5685 5842 7.014134 TGGATGATTCTGCAGAAAAGTTTGTTA 59.986 33.333 31.55 11.62 37.61 2.41
5693 5850 6.791303 TGCAGAAAAGTTTGTTATCTCGTTT 58.209 32.000 0.00 0.00 0.00 3.60
5749 5906 5.809001 TGAAACTGGATTAGCATGAAGACT 58.191 37.500 0.00 0.00 0.00 3.24
5832 5995 7.889873 TTTTGATTGTCTTCTTCCCACTTTA 57.110 32.000 0.00 0.00 0.00 1.85
5836 5999 7.287061 TGATTGTCTTCTTCCCACTTTAAAGA 58.713 34.615 21.92 0.00 0.00 2.52
5890 6053 6.017400 AGTCGATGCAATTTGAATTTGAGT 57.983 33.333 0.00 0.00 0.00 3.41
5942 6108 1.290009 GAATGTGCTGCCGCCTTTT 59.710 52.632 0.00 0.00 34.43 2.27
5951 6117 2.255252 CCGCCTTTTTCAGTGCCG 59.745 61.111 0.00 0.00 0.00 5.69
5952 6118 2.429069 CGCCTTTTTCAGTGCCGC 60.429 61.111 0.00 0.00 0.00 6.53
5992 6158 3.612423 GCGGGTAATCACAAAGAAATTGC 59.388 43.478 0.00 0.00 43.13 3.56
6007 6173 3.795688 AATTGCCTCAGTTCCTTCTCA 57.204 42.857 0.00 0.00 0.00 3.27
6117 6283 2.502142 ATGAAGCAGTCATTCTGGCA 57.498 45.000 0.00 0.00 45.13 4.92
6118 6284 1.527034 TGAAGCAGTCATTCTGGCAC 58.473 50.000 0.00 0.00 43.78 5.01
6119 6285 1.072806 TGAAGCAGTCATTCTGGCACT 59.927 47.619 0.00 0.00 43.78 4.40
6120 6286 1.467734 GAAGCAGTCATTCTGGCACTG 59.532 52.381 0.00 0.00 43.78 3.66
6121 6287 0.399454 AGCAGTCATTCTGGCACTGT 59.601 50.000 3.00 0.00 43.78 3.55
6122 6288 0.520404 GCAGTCATTCTGGCACTGTG 59.480 55.000 2.76 2.76 43.78 3.66
6123 6289 1.888215 CAGTCATTCTGGCACTGTGT 58.112 50.000 9.86 0.00 40.23 3.72
6176 6346 5.576447 TGTAGATAGACTTCGCATGTTGA 57.424 39.130 0.00 0.00 0.00 3.18
6188 6358 3.469899 GCATGTTGACATTAACAGCGA 57.530 42.857 0.00 0.00 43.14 4.93
6251 6425 0.468226 TGGGACTCTTTCAGCGTGTT 59.532 50.000 0.00 0.00 0.00 3.32
6255 6429 0.759346 ACTCTTTCAGCGTGTTCCCT 59.241 50.000 0.00 0.00 0.00 4.20
6260 6434 0.739462 TTCAGCGTGTTCCCTATGCG 60.739 55.000 0.00 0.00 35.28 4.73
6276 6450 1.310933 TGCGGGGAGTCTCTTCGTAC 61.311 60.000 13.74 0.00 0.00 3.67
6282 6456 4.758674 CGGGGAGTCTCTTCGTACATATAA 59.241 45.833 0.00 0.00 0.00 0.98
6365 6571 8.325046 AGCTGAGTTTTTCTTATATCTTCACCT 58.675 33.333 0.00 0.00 0.00 4.00
6373 6579 5.446860 TCTTATATCTTCACCTCCACGACT 58.553 41.667 0.00 0.00 0.00 4.18
6472 6679 6.796705 ACGTGAGGGTCATTTACTAAAAAG 57.203 37.500 0.00 0.00 0.00 2.27
6498 6738 6.377780 ACTTGCGTTTTCATTTTTGCTTTTT 58.622 28.000 0.00 0.00 0.00 1.94
6527 6767 9.030301 ACACCGTTTCTATTTTTCTTTTCATTG 57.970 29.630 0.00 0.00 0.00 2.82
6605 6862 8.490355 GTTCTTTTTCCATGCATTGTTTCTTAG 58.510 33.333 0.00 0.00 0.00 2.18
6708 6965 9.624697 CAGCAATTAAGCTTACATAGTCAAAAA 57.375 29.630 5.45 0.00 43.70 1.94
6730 6987 7.637631 AAAAATTATGTGGCCAAAGTGTTTT 57.362 28.000 7.24 10.17 0.00 2.43
6731 6988 7.637631 AAAATTATGTGGCCAAAGTGTTTTT 57.362 28.000 7.24 7.35 0.00 1.94
6732 6989 6.859420 AATTATGTGGCCAAAGTGTTTTTC 57.141 33.333 7.24 0.00 0.00 2.29
6733 6990 3.902881 ATGTGGCCAAAGTGTTTTTCA 57.097 38.095 7.24 0.00 0.00 2.69
6734 6991 3.685139 TGTGGCCAAAGTGTTTTTCAA 57.315 38.095 7.24 0.00 0.00 2.69
6735 6992 3.594134 TGTGGCCAAAGTGTTTTTCAAG 58.406 40.909 7.24 0.00 0.00 3.02
6736 6993 3.007398 TGTGGCCAAAGTGTTTTTCAAGT 59.993 39.130 7.24 0.00 0.00 3.16
6737 6994 3.616821 GTGGCCAAAGTGTTTTTCAAGTC 59.383 43.478 7.24 0.00 0.00 3.01
6738 6995 2.857748 GGCCAAAGTGTTTTTCAAGTCG 59.142 45.455 0.00 0.00 0.00 4.18
6739 6996 3.507786 GCCAAAGTGTTTTTCAAGTCGT 58.492 40.909 0.00 0.00 0.00 4.34
6740 6997 4.439016 GGCCAAAGTGTTTTTCAAGTCGTA 60.439 41.667 0.00 0.00 0.00 3.43
6741 6998 5.096849 GCCAAAGTGTTTTTCAAGTCGTAA 58.903 37.500 0.00 0.00 0.00 3.18
6742 6999 5.004061 GCCAAAGTGTTTTTCAAGTCGTAAC 59.996 40.000 0.00 0.00 0.00 2.50
6743 7000 6.319399 CCAAAGTGTTTTTCAAGTCGTAACT 58.681 36.000 0.00 0.00 37.32 2.24
6744 7001 6.250527 CCAAAGTGTTTTTCAAGTCGTAACTG 59.749 38.462 0.00 0.00 35.36 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.743928 CCTGGACCTCGCTTGTGC 60.744 66.667 0.00 0.00 0.00 4.57
44 45 1.885850 CCCCGCCTCGGTATTTTCG 60.886 63.158 4.47 0.00 46.80 3.46
62 63 1.703438 CGCTCTTCTGCCTCATGTGC 61.703 60.000 0.00 0.00 0.00 4.57
72 73 2.202756 GTACCCGGCGCTCTTCTG 60.203 66.667 7.64 0.00 0.00 3.02
105 106 1.376683 CCTTTCAACCCATCGGCGA 60.377 57.895 13.87 13.87 0.00 5.54
115 116 1.268625 CGTTTACTGGCCCCTTTCAAC 59.731 52.381 0.00 0.00 0.00 3.18
119 120 2.368311 TTTCGTTTACTGGCCCCTTT 57.632 45.000 0.00 0.00 0.00 3.11
131 132 2.329614 CCCCACCGCGATTTCGTTT 61.330 57.895 8.23 0.00 42.22 3.60
165 166 2.620112 CGATGAATGCCGCCATCCC 61.620 63.158 0.00 0.00 36.67 3.85
168 169 0.884704 GTACCGATGAATGCCGCCAT 60.885 55.000 0.00 0.00 0.00 4.40
173 174 2.297701 ACCAATGTACCGATGAATGCC 58.702 47.619 0.00 0.00 0.00 4.40
186 187 2.469952 CATCCCCATCCAAACCAATGT 58.530 47.619 0.00 0.00 0.00 2.71
258 262 5.239087 CACGGTATTCTCTTCTAGGTCTACC 59.761 48.000 0.00 0.00 0.00 3.18
259 263 5.277925 GCACGGTATTCTCTTCTAGGTCTAC 60.278 48.000 0.00 0.00 0.00 2.59
379 385 2.429069 GCGGGCAACAAGAAAGCG 60.429 61.111 0.00 0.00 39.74 4.68
772 802 6.588348 AATTGCTAAGTCAGTTGCAAAAAC 57.412 33.333 0.00 0.00 46.31 2.43
836 866 4.832823 ACCAAATCTCCACCTGTAAAAAGG 59.167 41.667 0.00 0.00 43.57 3.11
1391 1421 7.547370 TCCAAATTTGAACCTAAACAAACACAG 59.453 33.333 19.86 0.00 38.50 3.66
1575 1606 2.813754 ACTTGTCACGGAAATGGATGTG 59.186 45.455 0.00 0.00 0.00 3.21
1703 1734 7.329717 CCCGAGATAAAACATTATACTGCTCTC 59.670 40.741 0.00 0.00 0.00 3.20
1999 2036 6.711277 ACACACTAACAGGATGATATGTGTT 58.289 36.000 0.00 0.00 39.95 3.32
2035 2072 0.751277 CCATCAATTACCGCTGGCCA 60.751 55.000 4.71 4.71 0.00 5.36
2056 2093 0.779997 ATGGCTCCAGGACCAAAAGT 59.220 50.000 13.07 0.00 39.96 2.66
2074 2111 3.961408 GGTGTGATAGGTGGTCTAGTCAT 59.039 47.826 0.00 0.00 0.00 3.06
2208 2245 0.378257 CGGGAGGAACAAATGCGATG 59.622 55.000 0.00 0.00 0.00 3.84
2259 2296 0.727398 GAACAAGTGCGATAGGTGGC 59.273 55.000 0.00 0.00 0.00 5.01
2764 2810 3.418684 AAACGTTAGCTGGAGGAACAT 57.581 42.857 0.00 0.00 0.00 2.71
3066 3112 6.836577 GATCAACTTATGAGCTAGGTTGTC 57.163 41.667 9.11 4.34 43.98 3.18
3084 3130 8.239038 AGGTCGATACAATCTTAAGAGATCAA 57.761 34.615 11.53 0.00 41.78 2.57
3434 3480 5.136816 TGTTGCAAGCATAAATGACATGT 57.863 34.783 0.00 0.00 0.00 3.21
3484 3530 5.067023 CCAGCTCCTTTCCAAGAAATCATAC 59.933 44.000 0.00 0.00 0.00 2.39
3794 3840 2.602676 GCTACCCAGGCTTGACCCA 61.603 63.158 0.00 0.00 40.58 4.51
4161 4256 8.324567 ACTACAAATGTTTTAAACAACAATGCG 58.675 29.630 14.70 8.47 45.86 4.73
4310 4410 4.449068 AGTCACAGTTGATTTCTAAGCACG 59.551 41.667 0.00 0.00 33.11 5.34
4481 4582 9.877178 TTTACTTTTCTAATGTTCAGGCAAAAA 57.123 25.926 0.00 0.00 0.00 1.94
4633 4741 6.041523 GGCCTTCTCTTCTGTAGTATTCTCAT 59.958 42.308 0.00 0.00 0.00 2.90
4729 4837 1.806542 CAGACTGAATTGGTGAACCCG 59.193 52.381 0.00 0.00 35.15 5.28
4769 4877 2.208431 CCATCGCCTTTCTCATCACTC 58.792 52.381 0.00 0.00 0.00 3.51
5154 5266 4.952957 TCAGCTTATCTGAGACTAGCACTT 59.047 41.667 16.76 0.00 46.34 3.16
5202 5314 5.314923 TGTAGCTTGCAATTCAGAATTCC 57.685 39.130 5.32 0.00 0.00 3.01
5232 5344 4.799715 TCCAAAGTTTCCTTGTTCCCTA 57.200 40.909 0.00 0.00 0.00 3.53
5393 5547 6.092670 TCTCATTTCGAGTTTGCCTAATTCAG 59.907 38.462 0.00 0.00 42.88 3.02
5588 5745 7.392953 TCTTTGGTTGATGCAATAACATACTCA 59.607 33.333 15.54 0.00 0.00 3.41
5591 5748 6.473455 GCTCTTTGGTTGATGCAATAACATAC 59.527 38.462 15.54 2.82 0.00 2.39
5598 5755 3.259876 ACATGCTCTTTGGTTGATGCAAT 59.740 39.130 0.00 0.00 34.07 3.56
5732 5889 3.135348 CCCTCAGTCTTCATGCTAATCCA 59.865 47.826 0.00 0.00 0.00 3.41
5749 5906 3.452264 CCTGACATAGTGACATTCCCTCA 59.548 47.826 0.00 0.00 0.00 3.86
5817 5974 6.659824 AGTGTTCTTTAAAGTGGGAAGAAGA 58.340 36.000 14.74 0.00 39.34 2.87
5832 5995 7.624360 TCAGTAATGTCACAAAGTGTTCTTT 57.376 32.000 0.00 0.00 43.66 2.52
5836 5999 5.356751 TGCTTCAGTAATGTCACAAAGTGTT 59.643 36.000 0.00 0.00 34.79 3.32
5901 6067 7.294676 TCAGAATGTCAGTGATTCAATTACG 57.705 36.000 8.75 0.00 37.40 3.18
5942 6108 2.844451 GCAACAAGGCGGCACTGAA 61.844 57.895 13.08 0.00 0.00 3.02
5992 6158 3.269178 GAGCAATGAGAAGGAACTGAGG 58.731 50.000 0.00 0.00 40.86 3.86
6007 6173 0.687354 ACTCACCGACCTTGAGCAAT 59.313 50.000 0.00 0.00 43.79 3.56
6116 6282 2.234661 TCAGGATAGCCAGAACACAGTG 59.765 50.000 0.00 0.00 36.29 3.66
6117 6283 2.540383 TCAGGATAGCCAGAACACAGT 58.460 47.619 0.00 0.00 36.29 3.55
6118 6284 3.616956 TTCAGGATAGCCAGAACACAG 57.383 47.619 0.00 0.00 35.08 3.66
6119 6285 3.776969 AGATTCAGGATAGCCAGAACACA 59.223 43.478 7.04 0.00 41.72 3.72
6120 6286 4.414337 AGATTCAGGATAGCCAGAACAC 57.586 45.455 7.04 5.22 41.72 3.32
6121 6287 5.431765 GAAAGATTCAGGATAGCCAGAACA 58.568 41.667 7.04 0.00 41.72 3.18
6122 6288 4.509600 CGAAAGATTCAGGATAGCCAGAAC 59.490 45.833 7.04 2.35 41.72 3.01
6123 6289 4.697514 CGAAAGATTCAGGATAGCCAGAA 58.302 43.478 7.35 7.35 42.88 3.02
6188 6358 0.322975 AACTGATCTCGCCAACAGCT 59.677 50.000 0.00 0.00 40.39 4.24
6255 6429 0.395311 ACGAAGAGACTCCCCGCATA 60.395 55.000 12.33 0.00 0.00 3.14
6260 6434 6.002704 TCTTATATGTACGAAGAGACTCCCC 58.997 44.000 0.00 0.00 0.00 4.81
6365 6571 5.619309 CGAGAGAAACAGATAAAGTCGTGGA 60.619 44.000 0.00 0.00 0.00 4.02
6426 6633 7.066525 ACGTAGAAACAACCAGATCAAAAGAAA 59.933 33.333 0.00 0.00 0.00 2.52
6498 6738 6.702716 AAAGAAAAATAGAAACGGTGTGGA 57.297 33.333 0.00 0.00 0.00 4.02
6708 6965 6.825721 TGAAAAACACTTTGGCCACATAATTT 59.174 30.769 3.88 0.64 0.00 1.82
6709 6966 6.352516 TGAAAAACACTTTGGCCACATAATT 58.647 32.000 3.88 0.00 0.00 1.40
6710 6967 5.923204 TGAAAAACACTTTGGCCACATAAT 58.077 33.333 3.88 0.00 0.00 1.28
6711 6968 5.344743 TGAAAAACACTTTGGCCACATAA 57.655 34.783 3.88 0.00 0.00 1.90
6712 6969 5.105146 ACTTGAAAAACACTTTGGCCACATA 60.105 36.000 3.88 0.00 0.00 2.29
6713 6970 3.902881 TGAAAAACACTTTGGCCACAT 57.097 38.095 3.88 0.00 0.00 3.21
6714 6971 3.007398 ACTTGAAAAACACTTTGGCCACA 59.993 39.130 3.88 0.00 0.00 4.17
6715 6972 3.595173 ACTTGAAAAACACTTTGGCCAC 58.405 40.909 3.88 0.00 0.00 5.01
6716 6973 3.674682 CGACTTGAAAAACACTTTGGCCA 60.675 43.478 0.00 0.00 0.00 5.36
6717 6974 2.857748 CGACTTGAAAAACACTTTGGCC 59.142 45.455 0.00 0.00 0.00 5.36
6718 6975 3.507786 ACGACTTGAAAAACACTTTGGC 58.492 40.909 0.00 0.00 0.00 4.52
6719 6976 6.250527 CAGTTACGACTTGAAAAACACTTTGG 59.749 38.462 0.00 0.00 32.54 3.28
6720 6977 7.192676 CAGTTACGACTTGAAAAACACTTTG 57.807 36.000 0.00 0.00 32.54 2.77


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

AutoCloner maintained by Alex Coulton.