Multiple sequence alignment - TraesCS2A01G580700

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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 TraesCS2A01G580700 chr2A 100.000 3255 0 0 1 3255 772968565 772965311 0.000000e+00 6011.0
1 TraesCS2A01G580700 chr2D 97.894 2469 15 4 800 3255 647509492 647511936 0.000000e+00 4237.0
2 TraesCS2A01G580700 chr2D 99.516 413 2 0 204 616 647508540 647508952 0.000000e+00 752.0
3 TraesCS2A01G580700 chr2B 87.398 976 68 22 253 1189 788539402 788538443 0.000000e+00 1070.0
4 TraesCS2A01G580700 chr2B 88.889 648 66 3 1640 2286 788535170 788534528 0.000000e+00 793.0
5 TraesCS2A01G580700 chr2B 87.838 666 43 20 2612 3253 788525365 788524714 0.000000e+00 747.0
6 TraesCS2A01G580700 chr2B 91.417 501 30 10 2760 3254 788534112 788533619 0.000000e+00 675.0
7 TraesCS2A01G580700 chr2B 93.556 419 25 2 1231 1647 788537558 788537140 9.920000e-175 623.0
8 TraesCS2A01G580700 chr2B 92.414 145 11 0 2386 2530 788525527 788525383 1.180000e-49 207.0
9 TraesCS2A01G580700 chr2B 84.536 97 4 1 2434 2530 788534333 788534248 5.790000e-13 86.1
10 TraesCS2A01G580700 chr2B 95.122 41 2 0 2356 2396 788531196 788531156 7.540000e-07 65.8
11 TraesCS2A01G580700 chrUn 97.143 175 5 0 1 175 290195170 290194996 2.460000e-76 296.0
12 TraesCS2A01G580700 chrUn 97.143 175 5 0 1 175 326178377 326178203 2.460000e-76 296.0
13 TraesCS2A01G580700 chrUn 97.143 175 5 0 1 175 327556423 327556249 2.460000e-76 296.0
14 TraesCS2A01G580700 chrUn 97.143 175 5 0 1 175 369433521 369433347 2.460000e-76 296.0
15 TraesCS2A01G580700 chrUn 95.906 171 7 0 4 174 90450261 90450431 8.890000e-71 278.0
16 TraesCS2A01G580700 chr6B 97.143 175 5 0 1 175 20187088 20187262 2.460000e-76 296.0
17 TraesCS2A01G580700 chr4A 97.126 174 5 0 1 174 717820334 717820507 8.830000e-76 294.0
18 TraesCS2A01G580700 chr1B 95.402 174 8 0 1 174 202680510 202680683 8.890000e-71 278.0
19 TraesCS2A01G580700 chr3A 94.798 173 9 0 2 174 42047943 42048115 1.490000e-68 270.0


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 TraesCS2A01G580700 chr2A 772965311 772968565 3254 True 6011.00 6011 100.000 1 3255 1 chr2A.!!$R1 3254
1 TraesCS2A01G580700 chr2D 647508540 647511936 3396 False 2494.50 4237 98.705 204 3255 2 chr2D.!!$F1 3051
2 TraesCS2A01G580700 chr2B 788531156 788539402 8246 True 552.15 1070 90.153 253 3254 6 chr2B.!!$R2 3001
3 TraesCS2A01G580700 chr2B 788524714 788525527 813 True 477.00 747 90.126 2386 3253 2 chr2B.!!$R1 867

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
81 82 0.247736 ACCGGTGAAGATGCAGTCTC 59.752 55.0 6.12 0.0 35.67 3.36 F
198 199 0.322187 TTCCAGCCGAGCCTAAAACC 60.322 55.0 0.00 0.0 0.00 3.27 F
200 201 0.394352 CCAGCCGAGCCTAAAACCAT 60.394 55.0 0.00 0.0 0.00 3.55 F
774 806 0.396435 TCGTCAAGGACCACTGCAAT 59.604 50.0 0.00 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1103 1491 1.154225 GCGCGTCTTTGGTTCATGG 60.154 57.895 8.43 0.0 0.0 3.66 R
1353 2605 2.610219 CGACATGACAATTTTCGCCA 57.390 45.000 0.00 0.0 0.0 5.69 R
1356 2608 2.914861 TGTGCGACATGACAATTTTCG 58.085 42.857 0.00 0.0 0.0 3.46 R
2550 5867 2.928801 TGCTGAGCTAAAAGGTGACA 57.071 45.000 5.83 0.0 0.0 3.58 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 4.237724 GACCTTTGGATAGCAAAAACAGC 58.762 43.478 0.00 0.00 0.00 4.40
23 24 3.640967 ACCTTTGGATAGCAAAAACAGCA 59.359 39.130 0.00 0.00 0.00 4.41
24 25 4.100808 ACCTTTGGATAGCAAAAACAGCAA 59.899 37.500 0.00 0.00 0.00 3.91
25 26 5.055812 CCTTTGGATAGCAAAAACAGCAAA 58.944 37.500 0.00 0.00 0.00 3.68
26 27 5.702209 CCTTTGGATAGCAAAAACAGCAAAT 59.298 36.000 0.00 0.00 0.00 2.32
27 28 6.873076 CCTTTGGATAGCAAAAACAGCAAATA 59.127 34.615 0.00 0.00 0.00 1.40
28 29 7.550196 CCTTTGGATAGCAAAAACAGCAAATAT 59.450 33.333 0.00 0.00 0.00 1.28
29 30 9.585099 CTTTGGATAGCAAAAACAGCAAATATA 57.415 29.630 0.00 0.00 0.00 0.86
31 32 9.531942 TTGGATAGCAAAAACAGCAAATATATG 57.468 29.630 0.00 0.00 0.00 1.78
32 33 8.911965 TGGATAGCAAAAACAGCAAATATATGA 58.088 29.630 0.00 0.00 0.00 2.15
33 34 9.403110 GGATAGCAAAAACAGCAAATATATGAG 57.597 33.333 0.00 0.00 0.00 2.90
34 35 8.807667 ATAGCAAAAACAGCAAATATATGAGC 57.192 30.769 2.29 2.29 0.00 4.26
35 36 6.870769 AGCAAAAACAGCAAATATATGAGCT 58.129 32.000 6.39 6.39 37.95 4.09
36 37 7.325694 AGCAAAAACAGCAAATATATGAGCTT 58.674 30.769 8.92 1.03 34.61 3.74
37 38 7.277098 AGCAAAAACAGCAAATATATGAGCTTG 59.723 33.333 8.92 6.66 34.61 4.01
38 39 7.464977 GCAAAAACAGCAAATATATGAGCTTGG 60.465 37.037 8.92 3.48 34.61 3.61
39 40 7.408756 AAAACAGCAAATATATGAGCTTGGA 57.591 32.000 8.92 0.00 34.61 3.53
40 41 6.382869 AACAGCAAATATATGAGCTTGGAC 57.617 37.500 8.92 0.00 34.61 4.02
41 42 5.439721 ACAGCAAATATATGAGCTTGGACA 58.560 37.500 8.92 0.00 34.61 4.02
42 43 5.297776 ACAGCAAATATATGAGCTTGGACAC 59.702 40.000 8.92 0.00 34.61 3.67
43 44 4.512944 AGCAAATATATGAGCTTGGACACG 59.487 41.667 6.39 0.00 32.52 4.49
44 45 4.776743 CAAATATATGAGCTTGGACACGC 58.223 43.478 0.00 0.00 0.00 5.34
45 46 3.751479 ATATATGAGCTTGGACACGCA 57.249 42.857 3.61 0.00 0.00 5.24
46 47 2.627515 ATATGAGCTTGGACACGCAT 57.372 45.000 3.61 0.00 0.00 4.73
47 48 3.751479 ATATGAGCTTGGACACGCATA 57.249 42.857 3.61 0.00 33.92 3.14
48 49 2.627515 ATGAGCTTGGACACGCATAT 57.372 45.000 3.61 0.00 0.00 1.78
49 50 2.401583 TGAGCTTGGACACGCATATT 57.598 45.000 3.61 0.00 0.00 1.28
50 51 2.710377 TGAGCTTGGACACGCATATTT 58.290 42.857 3.61 0.00 0.00 1.40
51 52 2.419673 TGAGCTTGGACACGCATATTTG 59.580 45.455 3.61 0.00 0.00 2.32
52 53 1.745087 AGCTTGGACACGCATATTTGG 59.255 47.619 3.61 0.00 0.00 3.28
53 54 1.798813 GCTTGGACACGCATATTTGGC 60.799 52.381 0.00 0.00 0.00 4.52
54 55 1.472082 CTTGGACACGCATATTTGGCA 59.528 47.619 0.00 0.00 0.00 4.92
55 56 0.808125 TGGACACGCATATTTGGCAC 59.192 50.000 0.00 0.00 0.00 5.01
56 57 0.808125 GGACACGCATATTTGGCACA 59.192 50.000 0.00 0.00 0.00 4.57
76 77 3.778619 CCATACCGGTGAAGATGCA 57.221 52.632 19.93 0.00 0.00 3.96
77 78 1.586422 CCATACCGGTGAAGATGCAG 58.414 55.000 19.93 0.00 0.00 4.41
78 79 1.134401 CCATACCGGTGAAGATGCAGT 60.134 52.381 19.93 0.00 0.00 4.40
79 80 2.205074 CATACCGGTGAAGATGCAGTC 58.795 52.381 19.93 0.00 0.00 3.51
80 81 1.557099 TACCGGTGAAGATGCAGTCT 58.443 50.000 19.93 0.00 39.43 3.24
81 82 0.247736 ACCGGTGAAGATGCAGTCTC 59.752 55.000 6.12 0.00 35.67 3.36
82 83 0.460987 CCGGTGAAGATGCAGTCTCC 60.461 60.000 0.00 0.00 35.67 3.71
83 84 0.460987 CGGTGAAGATGCAGTCTCCC 60.461 60.000 0.00 0.00 35.67 4.30
84 85 0.908198 GGTGAAGATGCAGTCTCCCT 59.092 55.000 0.00 0.00 35.67 4.20
85 86 1.134551 GGTGAAGATGCAGTCTCCCTC 60.135 57.143 0.00 0.00 35.67 4.30
86 87 1.830477 GTGAAGATGCAGTCTCCCTCT 59.170 52.381 0.00 0.00 35.67 3.69
87 88 2.106566 TGAAGATGCAGTCTCCCTCTC 58.893 52.381 0.00 0.00 35.67 3.20
88 89 1.066908 GAAGATGCAGTCTCCCTCTCG 59.933 57.143 0.00 0.00 35.67 4.04
89 90 0.754957 AGATGCAGTCTCCCTCTCGG 60.755 60.000 0.00 0.00 28.45 4.63
90 91 0.753479 GATGCAGTCTCCCTCTCGGA 60.753 60.000 0.00 0.00 38.83 4.55
97 98 4.837085 TCCCTCTCGGAGTCGTTT 57.163 55.556 4.69 0.00 34.86 3.60
98 99 2.264124 TCCCTCTCGGAGTCGTTTG 58.736 57.895 4.69 0.00 34.86 2.93
99 100 1.446272 CCCTCTCGGAGTCGTTTGC 60.446 63.158 4.69 0.00 37.69 3.68
100 101 1.801913 CCTCTCGGAGTCGTTTGCG 60.802 63.158 4.69 0.00 37.69 4.85
101 102 1.209383 CTCTCGGAGTCGTTTGCGA 59.791 57.895 4.69 5.60 45.79 5.10
123 124 4.778143 GTTGGCAGGGGCGATCGT 62.778 66.667 17.81 0.00 42.47 3.73
124 125 4.776322 TTGGCAGGGGCGATCGTG 62.776 66.667 17.81 8.05 42.47 4.35
165 166 4.154613 GTCAGCGAGACGTCAAGG 57.845 61.111 19.50 7.24 37.53 3.61
166 167 2.089349 GTCAGCGAGACGTCAAGGC 61.089 63.158 19.50 16.91 37.53 4.35
167 168 3.175240 CAGCGAGACGTCAAGGCG 61.175 66.667 19.50 15.80 37.94 5.52
168 169 4.421479 AGCGAGACGTCAAGGCGG 62.421 66.667 19.50 0.90 35.98 6.13
169 170 4.719369 GCGAGACGTCAAGGCGGT 62.719 66.667 19.50 0.00 35.98 5.68
170 171 2.805353 CGAGACGTCAAGGCGGTG 60.805 66.667 19.50 0.00 35.98 4.94
171 172 2.432628 GAGACGTCAAGGCGGTGG 60.433 66.667 19.50 0.00 35.98 4.61
172 173 2.915659 AGACGTCAAGGCGGTGGA 60.916 61.111 19.50 0.00 35.98 4.02
173 174 2.432628 GACGTCAAGGCGGTGGAG 60.433 66.667 11.55 0.00 35.98 3.86
174 175 4.681978 ACGTCAAGGCGGTGGAGC 62.682 66.667 0.00 0.00 35.98 4.70
176 177 4.373116 GTCAAGGCGGTGGAGCGA 62.373 66.667 1.74 0.00 38.18 4.93
177 178 4.069232 TCAAGGCGGTGGAGCGAG 62.069 66.667 1.74 0.00 38.18 5.03
183 184 4.069232 CGGTGGAGCGAGCTTCCA 62.069 66.667 1.25 1.25 0.00 3.53
184 185 2.125350 GGTGGAGCGAGCTTCCAG 60.125 66.667 5.84 0.00 33.74 3.86
185 186 2.817396 GTGGAGCGAGCTTCCAGC 60.817 66.667 5.84 1.31 42.84 4.85
186 187 4.087892 TGGAGCGAGCTTCCAGCC 62.088 66.667 1.25 3.26 43.77 4.85
188 189 4.135153 GAGCGAGCTTCCAGCCGA 62.135 66.667 0.00 0.00 43.77 5.54
189 190 4.140599 AGCGAGCTTCCAGCCGAG 62.141 66.667 9.80 0.00 43.77 4.63
192 193 3.780173 GAGCTTCCAGCCGAGCCT 61.780 66.667 0.00 0.00 43.77 4.58
193 194 2.364317 AGCTTCCAGCCGAGCCTA 60.364 61.111 0.00 0.00 43.77 3.93
194 195 1.961180 GAGCTTCCAGCCGAGCCTAA 61.961 60.000 0.00 0.00 43.77 2.69
195 196 1.078426 GCTTCCAGCCGAGCCTAAA 60.078 57.895 0.00 0.00 34.48 1.85
196 197 0.676782 GCTTCCAGCCGAGCCTAAAA 60.677 55.000 0.00 0.00 34.48 1.52
197 198 1.087501 CTTCCAGCCGAGCCTAAAAC 58.912 55.000 0.00 0.00 0.00 2.43
198 199 0.322187 TTCCAGCCGAGCCTAAAACC 60.322 55.000 0.00 0.00 0.00 3.27
199 200 1.002624 CCAGCCGAGCCTAAAACCA 60.003 57.895 0.00 0.00 0.00 3.67
200 201 0.394352 CCAGCCGAGCCTAAAACCAT 60.394 55.000 0.00 0.00 0.00 3.55
201 202 0.734889 CAGCCGAGCCTAAAACCATG 59.265 55.000 0.00 0.00 0.00 3.66
202 203 1.032114 AGCCGAGCCTAAAACCATGC 61.032 55.000 0.00 0.00 0.00 4.06
646 672 1.153086 GCCGGCATCCTCATCAACT 60.153 57.895 24.80 0.00 0.00 3.16
652 678 2.686915 GGCATCCTCATCAACTTCCAAG 59.313 50.000 0.00 0.00 0.00 3.61
653 679 2.686915 GCATCCTCATCAACTTCCAAGG 59.313 50.000 0.00 0.00 0.00 3.61
656 682 1.089920 CTCATCAACTTCCAAGGCCG 58.910 55.000 0.00 0.00 0.00 6.13
755 781 4.320456 CTGGGGCTGTGACGTGCT 62.320 66.667 0.00 0.00 0.00 4.40
774 806 0.396435 TCGTCAAGGACCACTGCAAT 59.604 50.000 0.00 0.00 0.00 3.56
775 807 0.518636 CGTCAAGGACCACTGCAATG 59.481 55.000 0.00 0.00 0.00 2.82
787 819 2.194326 GCAATGGCCTCCTCCTCC 59.806 66.667 3.32 0.00 0.00 4.30
1103 1491 2.432628 CGACGTGCCTTGGTCTCC 60.433 66.667 0.00 0.00 0.00 3.71
1342 2594 7.655236 TGCCATGTGAAATTTACAGAAATTG 57.345 32.000 0.00 0.00 43.10 2.32
1343 2595 7.215789 TGCCATGTGAAATTTACAGAAATTGT 58.784 30.769 0.00 0.00 43.10 2.71
1344 2596 7.384660 TGCCATGTGAAATTTACAGAAATTGTC 59.615 33.333 0.00 0.00 43.10 3.18
1345 2597 7.384660 GCCATGTGAAATTTACAGAAATTGTCA 59.615 33.333 0.00 1.86 43.10 3.58
1346 2598 9.426837 CCATGTGAAATTTACAGAAATTGTCAT 57.573 29.630 0.00 1.28 43.10 3.06
1351 2603 9.558648 TGAAATTTACAGAAATTGTCATGATCG 57.441 29.630 0.00 0.00 43.10 3.69
1352 2604 9.773328 GAAATTTACAGAAATTGTCATGATCGA 57.227 29.630 0.00 0.00 43.10 3.59
1354 2606 9.726232 AATTTACAGAAATTGTCATGATCGATG 57.274 29.630 0.54 0.00 42.46 3.84
1355 2607 5.746307 ACAGAAATTGTCATGATCGATGG 57.254 39.130 0.54 0.00 33.87 3.51
1356 2608 4.036027 ACAGAAATTGTCATGATCGATGGC 59.964 41.667 0.54 0.00 33.87 4.40
1357 2609 3.249320 AGAAATTGTCATGATCGATGGCG 59.751 43.478 0.54 0.00 39.81 5.69
1358 2610 9.970702 TACAGAAATTGTCATGATCGATGGCGA 62.971 40.741 0.54 0.00 45.16 5.54
1895 5126 0.036010 AGATCTTGTCCTTGGCCGTG 60.036 55.000 0.00 0.00 0.00 4.94
1977 5208 2.824341 ACGATAATCCCCCTCGTGATAC 59.176 50.000 0.00 0.00 43.40 2.24
2231 5462 0.035534 ATACACGCCATGCTTGACCA 60.036 50.000 0.22 0.00 32.11 4.02
2244 5475 2.613223 GCTTGACCACAGAGTTCCCTAC 60.613 54.545 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.237724 GCTGTTTTTGCTATCCAAAGGTC 58.762 43.478 0.00 0.00 43.77 3.85
1 2 3.640967 TGCTGTTTTTGCTATCCAAAGGT 59.359 39.130 0.00 0.00 43.77 3.50
2 3 4.255833 TGCTGTTTTTGCTATCCAAAGG 57.744 40.909 0.00 0.00 43.77 3.11
3 4 6.790285 ATTTGCTGTTTTTGCTATCCAAAG 57.210 33.333 0.00 0.00 43.77 2.77
5 6 9.531942 CATATATTTGCTGTTTTTGCTATCCAA 57.468 29.630 0.00 0.00 0.00 3.53
6 7 8.911965 TCATATATTTGCTGTTTTTGCTATCCA 58.088 29.630 0.00 0.00 0.00 3.41
7 8 9.403110 CTCATATATTTGCTGTTTTTGCTATCC 57.597 33.333 0.00 0.00 0.00 2.59
8 9 8.909671 GCTCATATATTTGCTGTTTTTGCTATC 58.090 33.333 0.00 0.00 0.00 2.08
9 10 8.636213 AGCTCATATATTTGCTGTTTTTGCTAT 58.364 29.630 8.05 0.00 34.19 2.97
10 11 7.999679 AGCTCATATATTTGCTGTTTTTGCTA 58.000 30.769 8.05 0.00 34.19 3.49
11 12 6.870769 AGCTCATATATTTGCTGTTTTTGCT 58.129 32.000 8.05 0.00 34.19 3.91
12 13 7.396419 CAAGCTCATATATTTGCTGTTTTTGC 58.604 34.615 9.26 0.00 35.79 3.68
13 14 7.760794 TCCAAGCTCATATATTTGCTGTTTTTG 59.239 33.333 9.26 4.90 35.79 2.44
14 15 7.761249 GTCCAAGCTCATATATTTGCTGTTTTT 59.239 33.333 9.26 0.00 35.79 1.94
15 16 7.093814 TGTCCAAGCTCATATATTTGCTGTTTT 60.094 33.333 9.26 0.00 35.79 2.43
16 17 6.377996 TGTCCAAGCTCATATATTTGCTGTTT 59.622 34.615 9.26 0.00 35.79 2.83
17 18 5.887598 TGTCCAAGCTCATATATTTGCTGTT 59.112 36.000 9.26 0.00 35.79 3.16
18 19 5.297776 GTGTCCAAGCTCATATATTTGCTGT 59.702 40.000 9.26 0.31 35.79 4.40
19 20 5.559608 CGTGTCCAAGCTCATATATTTGCTG 60.560 44.000 9.26 5.25 35.79 4.41
20 21 4.512944 CGTGTCCAAGCTCATATATTTGCT 59.487 41.667 3.99 3.99 37.37 3.91
21 22 4.776743 CGTGTCCAAGCTCATATATTTGC 58.223 43.478 0.00 0.00 0.00 3.68
22 23 4.273235 TGCGTGTCCAAGCTCATATATTTG 59.727 41.667 6.75 0.00 36.75 2.32
23 24 4.450976 TGCGTGTCCAAGCTCATATATTT 58.549 39.130 6.75 0.00 36.75 1.40
24 25 4.071961 TGCGTGTCCAAGCTCATATATT 57.928 40.909 6.75 0.00 36.75 1.28
25 26 3.751479 TGCGTGTCCAAGCTCATATAT 57.249 42.857 6.75 0.00 36.75 0.86
26 27 3.751479 ATGCGTGTCCAAGCTCATATA 57.249 42.857 6.75 0.00 36.75 0.86
27 28 2.627515 ATGCGTGTCCAAGCTCATAT 57.372 45.000 6.75 0.00 36.75 1.78
28 29 3.751479 ATATGCGTGTCCAAGCTCATA 57.249 42.857 6.75 0.00 36.75 2.15
29 30 2.627515 ATATGCGTGTCCAAGCTCAT 57.372 45.000 6.75 0.00 36.75 2.90
30 31 2.401583 AATATGCGTGTCCAAGCTCA 57.598 45.000 6.75 0.00 36.75 4.26
31 32 2.223340 CCAAATATGCGTGTCCAAGCTC 60.223 50.000 6.75 0.00 36.75 4.09
32 33 1.745087 CCAAATATGCGTGTCCAAGCT 59.255 47.619 6.75 0.00 36.75 3.74
33 34 1.798813 GCCAAATATGCGTGTCCAAGC 60.799 52.381 0.00 0.00 36.35 4.01
34 35 1.472082 TGCCAAATATGCGTGTCCAAG 59.528 47.619 0.00 0.00 0.00 3.61
35 36 1.201181 GTGCCAAATATGCGTGTCCAA 59.799 47.619 0.00 0.00 0.00 3.53
36 37 0.808125 GTGCCAAATATGCGTGTCCA 59.192 50.000 0.00 0.00 0.00 4.02
37 38 0.808125 TGTGCCAAATATGCGTGTCC 59.192 50.000 0.00 0.00 0.00 4.02
38 39 2.250188 GTTGTGCCAAATATGCGTGTC 58.750 47.619 0.00 0.00 0.00 3.67
39 40 1.067915 GGTTGTGCCAAATATGCGTGT 60.068 47.619 0.00 0.00 37.17 4.49
40 41 1.067985 TGGTTGTGCCAAATATGCGTG 60.068 47.619 0.00 0.00 45.94 5.34
41 42 1.252175 TGGTTGTGCCAAATATGCGT 58.748 45.000 0.00 0.00 45.94 5.24
58 59 1.134401 ACTGCATCTTCACCGGTATGG 60.134 52.381 6.87 0.00 46.41 2.74
59 60 2.159043 AGACTGCATCTTCACCGGTATG 60.159 50.000 6.87 8.99 31.62 2.39
60 61 2.101582 GAGACTGCATCTTCACCGGTAT 59.898 50.000 6.87 0.00 38.00 2.73
61 62 1.476891 GAGACTGCATCTTCACCGGTA 59.523 52.381 6.87 0.00 38.00 4.02
62 63 0.247736 GAGACTGCATCTTCACCGGT 59.752 55.000 0.00 0.00 38.00 5.28
63 64 0.460987 GGAGACTGCATCTTCACCGG 60.461 60.000 0.00 0.00 38.00 5.28
64 65 0.460987 GGGAGACTGCATCTTCACCG 60.461 60.000 0.00 0.00 38.00 4.94
65 66 0.908198 AGGGAGACTGCATCTTCACC 59.092 55.000 0.00 3.37 38.00 4.02
66 67 1.830477 AGAGGGAGACTGCATCTTCAC 59.170 52.381 5.21 0.00 38.00 3.18
67 68 2.106566 GAGAGGGAGACTGCATCTTCA 58.893 52.381 12.58 0.00 38.00 3.02
68 69 1.066908 CGAGAGGGAGACTGCATCTTC 59.933 57.143 12.58 5.52 38.00 2.87
69 70 1.110442 CGAGAGGGAGACTGCATCTT 58.890 55.000 12.58 0.00 38.00 2.40
70 71 2.805897 CGAGAGGGAGACTGCATCT 58.194 57.895 11.16 11.16 41.91 2.90
83 84 1.209383 TCGCAAACGACTCCGAGAG 59.791 57.895 1.33 0.00 45.12 3.20
84 85 3.347168 TCGCAAACGACTCCGAGA 58.653 55.556 1.33 0.00 45.12 4.04
93 94 2.426752 CCAACGGCTTCGCAAACG 60.427 61.111 0.00 0.00 42.01 3.60
94 95 2.729491 GCCAACGGCTTCGCAAAC 60.729 61.111 0.00 0.00 46.69 2.93
106 107 4.778143 ACGATCGCCCCTGCCAAC 62.778 66.667 16.60 0.00 0.00 3.77
107 108 4.776322 CACGATCGCCCCTGCCAA 62.776 66.667 16.60 0.00 0.00 4.52
144 145 4.477975 GACGTCTCGCTGACCCCG 62.478 72.222 8.70 0.00 42.49 5.73
145 146 2.820767 CTTGACGTCTCGCTGACCCC 62.821 65.000 17.92 0.00 42.49 4.95
146 147 1.444553 CTTGACGTCTCGCTGACCC 60.445 63.158 17.92 0.00 42.49 4.46
147 148 1.444553 CCTTGACGTCTCGCTGACC 60.445 63.158 17.92 0.00 42.49 4.02
148 149 2.089349 GCCTTGACGTCTCGCTGAC 61.089 63.158 17.92 0.00 42.06 3.51
149 150 2.258591 GCCTTGACGTCTCGCTGA 59.741 61.111 17.92 0.00 0.00 4.26
150 151 3.175240 CGCCTTGACGTCTCGCTG 61.175 66.667 17.92 7.99 0.00 5.18
151 152 4.421479 CCGCCTTGACGTCTCGCT 62.421 66.667 17.92 0.00 0.00 4.93
152 153 4.719369 ACCGCCTTGACGTCTCGC 62.719 66.667 17.92 13.72 0.00 5.03
153 154 2.805353 CACCGCCTTGACGTCTCG 60.805 66.667 17.92 13.84 0.00 4.04
154 155 2.432628 CCACCGCCTTGACGTCTC 60.433 66.667 17.92 2.59 0.00 3.36
155 156 2.915659 TCCACCGCCTTGACGTCT 60.916 61.111 17.92 0.00 0.00 4.18
156 157 2.432628 CTCCACCGCCTTGACGTC 60.433 66.667 9.11 9.11 0.00 4.34
157 158 4.681978 GCTCCACCGCCTTGACGT 62.682 66.667 0.00 0.00 0.00 4.34
159 160 4.373116 TCGCTCCACCGCCTTGAC 62.373 66.667 0.00 0.00 0.00 3.18
160 161 4.069232 CTCGCTCCACCGCCTTGA 62.069 66.667 0.00 0.00 0.00 3.02
166 167 3.997064 CTGGAAGCTCGCTCCACCG 62.997 68.421 1.25 0.00 0.00 4.94
167 168 2.125350 CTGGAAGCTCGCTCCACC 60.125 66.667 1.25 4.97 0.00 4.61
178 179 1.087501 GTTTTAGGCTCGGCTGGAAG 58.912 55.000 2.95 0.00 0.00 3.46
179 180 0.322187 GGTTTTAGGCTCGGCTGGAA 60.322 55.000 2.95 0.00 0.00 3.53
180 181 1.298667 GGTTTTAGGCTCGGCTGGA 59.701 57.895 2.95 0.00 0.00 3.86
181 182 0.394352 ATGGTTTTAGGCTCGGCTGG 60.394 55.000 2.95 0.00 0.00 4.85
182 183 0.734889 CATGGTTTTAGGCTCGGCTG 59.265 55.000 2.95 0.00 0.00 4.85
183 184 1.032114 GCATGGTTTTAGGCTCGGCT 61.032 55.000 0.00 0.00 0.00 5.52
184 185 1.312371 TGCATGGTTTTAGGCTCGGC 61.312 55.000 0.00 0.00 0.00 5.54
185 186 0.451783 GTGCATGGTTTTAGGCTCGG 59.548 55.000 0.00 0.00 0.00 4.63
186 187 1.135689 GTGTGCATGGTTTTAGGCTCG 60.136 52.381 0.00 0.00 0.00 5.03
187 188 1.885887 TGTGTGCATGGTTTTAGGCTC 59.114 47.619 0.00 0.00 0.00 4.70
188 189 1.888512 CTGTGTGCATGGTTTTAGGCT 59.111 47.619 0.00 0.00 0.00 4.58
189 190 1.613437 ACTGTGTGCATGGTTTTAGGC 59.387 47.619 0.00 0.00 0.00 3.93
190 191 3.149196 AGACTGTGTGCATGGTTTTAGG 58.851 45.455 0.00 0.00 0.00 2.69
191 192 4.275689 TCAAGACTGTGTGCATGGTTTTAG 59.724 41.667 0.00 0.00 0.00 1.85
192 193 4.203226 TCAAGACTGTGTGCATGGTTTTA 58.797 39.130 0.00 0.00 0.00 1.52
193 194 3.023119 TCAAGACTGTGTGCATGGTTTT 58.977 40.909 0.00 0.00 0.00 2.43
194 195 2.653726 TCAAGACTGTGTGCATGGTTT 58.346 42.857 0.00 0.00 0.00 3.27
195 196 2.346766 TCAAGACTGTGTGCATGGTT 57.653 45.000 0.00 0.00 0.00 3.67
196 197 1.949525 GTTCAAGACTGTGTGCATGGT 59.050 47.619 0.00 0.00 0.00 3.55
197 198 2.224606 AGTTCAAGACTGTGTGCATGG 58.775 47.619 0.00 0.00 37.17 3.66
198 199 3.136763 AGAGTTCAAGACTGTGTGCATG 58.863 45.455 0.00 0.00 39.19 4.06
199 200 3.482156 AGAGTTCAAGACTGTGTGCAT 57.518 42.857 0.00 0.00 39.19 3.96
200 201 2.938451 CAAGAGTTCAAGACTGTGTGCA 59.062 45.455 0.00 0.00 39.19 4.57
201 202 3.198068 TCAAGAGTTCAAGACTGTGTGC 58.802 45.455 0.00 0.00 39.19 4.57
202 203 4.149571 CGATCAAGAGTTCAAGACTGTGTG 59.850 45.833 0.00 0.00 39.19 3.82
627 653 2.203056 TTGATGAGGATGCCGGCG 60.203 61.111 23.90 0.00 0.00 6.46
628 654 0.749454 AAGTTGATGAGGATGCCGGC 60.749 55.000 22.73 22.73 0.00 6.13
646 672 2.358247 GAACTCGCGGCCTTGGAA 60.358 61.111 6.13 0.00 0.00 3.53
739 765 4.314440 GAGCACGTCACAGCCCCA 62.314 66.667 0.00 0.00 0.00 4.96
755 781 0.396435 ATTGCAGTGGTCCTTGACGA 59.604 50.000 0.00 0.00 32.65 4.20
774 806 4.016790 AGCAGGAGGAGGAGGCCA 62.017 66.667 5.01 0.00 0.00 5.36
775 807 3.478274 CAGCAGGAGGAGGAGGCC 61.478 72.222 0.00 0.00 0.00 5.19
1103 1491 1.154225 GCGCGTCTTTGGTTCATGG 60.154 57.895 8.43 0.00 0.00 3.66
1342 2594 3.885484 ATTTTCGCCATCGATCATGAC 57.115 42.857 0.00 0.00 45.04 3.06
1343 2595 3.627123 ACAATTTTCGCCATCGATCATGA 59.373 39.130 0.00 0.00 45.04 3.07
1344 2596 3.956233 ACAATTTTCGCCATCGATCATG 58.044 40.909 0.00 0.00 45.04 3.07
1345 2597 3.627123 TGACAATTTTCGCCATCGATCAT 59.373 39.130 0.00 0.00 45.04 2.45
1346 2598 3.006247 TGACAATTTTCGCCATCGATCA 58.994 40.909 0.00 0.00 45.04 2.92
1347 2599 3.673746 TGACAATTTTCGCCATCGATC 57.326 42.857 0.00 0.00 45.04 3.69
1348 2600 3.378112 ACATGACAATTTTCGCCATCGAT 59.622 39.130 0.00 0.00 45.04 3.59
1349 2601 2.746904 ACATGACAATTTTCGCCATCGA 59.253 40.909 0.00 0.00 43.89 3.59
1350 2602 3.100817 GACATGACAATTTTCGCCATCG 58.899 45.455 0.00 0.00 0.00 3.84
1351 2603 3.100817 CGACATGACAATTTTCGCCATC 58.899 45.455 0.00 0.00 0.00 3.51
1352 2604 3.135414 CGACATGACAATTTTCGCCAT 57.865 42.857 0.00 0.00 0.00 4.40
1353 2605 2.610219 CGACATGACAATTTTCGCCA 57.390 45.000 0.00 0.00 0.00 5.69
1356 2608 2.914861 TGTGCGACATGACAATTTTCG 58.085 42.857 0.00 0.00 0.00 3.46
1357 2609 5.633996 TTTTGTGCGACATGACAATTTTC 57.366 34.783 0.00 0.00 32.27 2.29
1895 5126 3.790091 TGTATCTCAGATCTGCTTGCAC 58.210 45.455 18.36 11.55 0.00 4.57
1977 5208 6.373774 AGCTTGTTCTTTGTAATCTGGAGATG 59.626 38.462 0.00 0.00 34.49 2.90
2244 5475 4.635223 TGAGCTCCTGAATCAATTATCCG 58.365 43.478 12.15 0.00 0.00 4.18
2537 5854 7.494298 GCTAAAAGGTGACAAAAATCCTTTCAA 59.506 33.333 7.32 0.66 45.69 2.69
2539 5856 7.210174 AGCTAAAAGGTGACAAAAATCCTTTC 58.790 34.615 7.32 0.00 45.69 2.62
2550 5867 2.928801 TGCTGAGCTAAAAGGTGACA 57.071 45.000 5.83 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.