Multiple sequence alignment - TraesCS4A01G362600

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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 TraesCS4A01G362600 chr4A 100.000 2315 0 0 1 2315 636217508 636215194 0.000000e+00 4276.0
1 TraesCS4A01G362600 chr4A 85.714 273 37 2 179 449 586022141 586021869 1.050000e-73 287.0
2 TraesCS4A01G362600 chr7A 93.502 1385 85 5 179 1559 348724630 348726013 0.000000e+00 2054.0
3 TraesCS4A01G362600 chr7A 95.389 759 32 3 1559 2315 160029749 160028992 0.000000e+00 1205.0
4 TraesCS4A01G362600 chr7A 88.618 615 59 7 179 783 595409010 595408397 0.000000e+00 737.0
5 TraesCS4A01G362600 chr4B 89.405 1076 75 19 179 1215 654696408 654695333 0.000000e+00 1319.0
6 TraesCS4A01G362600 chr4B 87.600 871 65 19 179 1007 654803326 654802457 0.000000e+00 970.0
7 TraesCS4A01G362600 chr4B 84.700 634 84 8 178 800 574294699 574294068 2.530000e-174 621.0
8 TraesCS4A01G362600 chr4B 95.122 287 13 1 1274 1559 574293352 574293066 3.510000e-123 451.0
9 TraesCS4A01G362600 chr3A 96.706 759 23 2 1559 2315 596694112 596694870 0.000000e+00 1262.0
10 TraesCS4A01G362600 chr3A 95.767 756 29 3 1559 2312 542320757 542321511 0.000000e+00 1216.0
11 TraesCS4A01G362600 chr3A 95.383 758 34 1 1559 2315 62004392 62003635 0.000000e+00 1205.0
12 TraesCS4A01G362600 chr5A 95.910 758 27 2 1559 2315 602543267 602542513 0.000000e+00 1225.0
13 TraesCS4A01G362600 chr5A 95.282 763 26 5 1563 2315 690028960 690029722 0.000000e+00 1201.0
14 TraesCS4A01G362600 chr6A 95.526 760 28 3 1559 2315 164463447 164464203 0.000000e+00 1210.0
15 TraesCS4A01G362600 chr6A 95.163 765 27 5 1559 2315 4659453 4658691 0.000000e+00 1199.0
16 TraesCS4A01G362600 chr6A 95.263 760 30 3 1559 2315 67090803 67090047 0.000000e+00 1199.0
17 TraesCS4A01G362600 chr5B 86.660 982 87 21 179 1116 488978330 488979311 0.000000e+00 1048.0
18 TraesCS4A01G362600 chr3D 90.762 617 46 4 178 784 41134795 41135410 0.000000e+00 813.0
19 TraesCS4A01G362600 chr3D 96.646 328 10 1 1232 1559 41135422 41135748 5.630000e-151 544.0
20 TraesCS4A01G362600 chr3D 87.967 241 18 8 532 761 218735515 218735755 8.150000e-70 274.0
21 TraesCS4A01G362600 chr1B 85.229 589 62 9 177 756 50257070 50257642 1.190000e-162 582.0
22 TraesCS4A01G362600 chr1B 91.623 191 14 2 821 1010 562378229 562378040 1.760000e-66 263.0
23 TraesCS4A01G362600 chr1B 86.243 189 14 1 1051 1227 562378041 562377853 6.530000e-46 195.0
24 TraesCS4A01G362600 chr1A 88.184 457 37 10 787 1227 513626756 513626301 1.580000e-146 529.0
25 TraesCS4A01G362600 chr6B 95.819 287 11 1 1274 1559 653200374 653200088 1.620000e-126 462.0
26 TraesCS4A01G362600 chr1D 86.232 414 33 11 829 1227 416102062 416101658 5.910000e-116 427.0
27 TraesCS4A01G362600 chr1D 86.313 358 37 7 179 526 299566292 299566647 1.680000e-101 379.0
28 TraesCS4A01G362600 chr6D 93.357 286 19 0 1274 1559 46496571 46496286 7.650000e-115 424.0
29 TraesCS4A01G362600 chr2A 92.542 295 19 2 1265 1559 674139241 674139532 9.890000e-114 420.0
30 TraesCS4A01G362600 chr2A 86.447 273 35 2 179 449 196081573 196081301 4.840000e-77 298.0
31 TraesCS4A01G362600 chr2A 85.766 274 37 2 178 449 514663501 514663774 2.910000e-74 289.0
32 TraesCS4A01G362600 chr5D 85.824 261 35 2 179 437 79715959 79716219 2.270000e-70 276.0
33 TraesCS4A01G362600 chr2D 82.437 279 39 6 1274 1550 341666853 341667123 3.850000e-58 235.0
34 TraesCS4A01G362600 chr2D 86.420 81 11 0 1279 1359 260032999 260033079 3.170000e-14 89.8


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 TraesCS4A01G362600 chr4A 636215194 636217508 2314 True 4276.0 4276 100.000 1 2315 1 chr4A.!!$R2 2314
1 TraesCS4A01G362600 chr7A 348724630 348726013 1383 False 2054.0 2054 93.502 179 1559 1 chr7A.!!$F1 1380
2 TraesCS4A01G362600 chr7A 160028992 160029749 757 True 1205.0 1205 95.389 1559 2315 1 chr7A.!!$R1 756
3 TraesCS4A01G362600 chr7A 595408397 595409010 613 True 737.0 737 88.618 179 783 1 chr7A.!!$R2 604
4 TraesCS4A01G362600 chr4B 654695333 654696408 1075 True 1319.0 1319 89.405 179 1215 1 chr4B.!!$R1 1036
5 TraesCS4A01G362600 chr4B 654802457 654803326 869 True 970.0 970 87.600 179 1007 1 chr4B.!!$R2 828
6 TraesCS4A01G362600 chr4B 574293066 574294699 1633 True 536.0 621 89.911 178 1559 2 chr4B.!!$R3 1381
7 TraesCS4A01G362600 chr3A 596694112 596694870 758 False 1262.0 1262 96.706 1559 2315 1 chr3A.!!$F2 756
8 TraesCS4A01G362600 chr3A 542320757 542321511 754 False 1216.0 1216 95.767 1559 2312 1 chr3A.!!$F1 753
9 TraesCS4A01G362600 chr3A 62003635 62004392 757 True 1205.0 1205 95.383 1559 2315 1 chr3A.!!$R1 756
10 TraesCS4A01G362600 chr5A 602542513 602543267 754 True 1225.0 1225 95.910 1559 2315 1 chr5A.!!$R1 756
11 TraesCS4A01G362600 chr5A 690028960 690029722 762 False 1201.0 1201 95.282 1563 2315 1 chr5A.!!$F1 752
12 TraesCS4A01G362600 chr6A 164463447 164464203 756 False 1210.0 1210 95.526 1559 2315 1 chr6A.!!$F1 756
13 TraesCS4A01G362600 chr6A 4658691 4659453 762 True 1199.0 1199 95.163 1559 2315 1 chr6A.!!$R1 756
14 TraesCS4A01G362600 chr6A 67090047 67090803 756 True 1199.0 1199 95.263 1559 2315 1 chr6A.!!$R2 756
15 TraesCS4A01G362600 chr5B 488978330 488979311 981 False 1048.0 1048 86.660 179 1116 1 chr5B.!!$F1 937
16 TraesCS4A01G362600 chr3D 41134795 41135748 953 False 678.5 813 93.704 178 1559 2 chr3D.!!$F2 1381
17 TraesCS4A01G362600 chr1B 50257070 50257642 572 False 582.0 582 85.229 177 756 1 chr1B.!!$F1 579

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
159 160 0.040425 GTTGACAATGACCCACACGC 60.04 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 2083 0.462047 CGAATCGGCACTAAAGGGCT 60.462 55.0 3.89 0.0 0.0 5.19 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
30 31 1.683943 GCAGCAGGCTTATCCATTGA 58.316 50.000 0.00 0.00 40.25 2.57
31 32 1.336125 GCAGCAGGCTTATCCATTGAC 59.664 52.381 0.00 0.00 40.25 3.18
32 33 1.600957 CAGCAGGCTTATCCATTGACG 59.399 52.381 0.00 0.00 37.29 4.35
33 34 0.308993 GCAGGCTTATCCATTGACGC 59.691 55.000 0.00 0.00 37.29 5.19
34 35 0.583438 CAGGCTTATCCATTGACGCG 59.417 55.000 3.53 3.53 37.29 6.01
35 36 0.532862 AGGCTTATCCATTGACGCGG 60.533 55.000 12.47 0.00 37.29 6.46
36 37 1.279840 GCTTATCCATTGACGCGGC 59.720 57.895 12.47 8.67 0.00 6.53
37 38 1.564622 CTTATCCATTGACGCGGCG 59.435 57.895 22.36 22.36 0.00 6.46
38 39 1.151777 CTTATCCATTGACGCGGCGT 61.152 55.000 29.85 29.85 45.10 5.68
51 52 4.070552 GGCGTCTGGAAGCGACCT 62.071 66.667 2.85 0.00 35.86 3.85
52 53 2.811317 GCGTCTGGAAGCGACCTG 60.811 66.667 0.00 3.80 35.93 4.00
53 54 2.125912 CGTCTGGAAGCGACCTGG 60.126 66.667 0.00 0.00 35.93 4.45
54 55 2.932234 CGTCTGGAAGCGACCTGGT 61.932 63.158 0.00 0.00 35.93 4.00
55 56 1.371558 GTCTGGAAGCGACCTGGTT 59.628 57.895 0.00 0.00 42.02 3.67
56 57 0.606604 GTCTGGAAGCGACCTGGTTA 59.393 55.000 0.00 0.00 38.70 2.85
57 58 0.895530 TCTGGAAGCGACCTGGTTAG 59.104 55.000 0.00 0.00 38.70 2.34
68 69 1.176527 CCTGGTTAGGTGCACATTGG 58.823 55.000 20.43 6.53 39.39 3.16
69 70 0.527565 CTGGTTAGGTGCACATTGGC 59.472 55.000 20.43 5.18 0.00 4.52
70 71 1.240641 TGGTTAGGTGCACATTGGCG 61.241 55.000 20.43 0.00 36.28 5.69
71 72 1.154035 GTTAGGTGCACATTGGCGC 60.154 57.895 20.43 0.00 43.38 6.53
77 78 3.814268 GCACATTGGCGCCGTGAT 61.814 61.111 29.78 18.22 32.23 3.06
78 79 2.404789 CACATTGGCGCCGTGATC 59.595 61.111 30.97 5.41 32.23 2.92
79 80 3.195002 ACATTGGCGCCGTGATCG 61.195 61.111 30.97 15.64 0.00 3.69
80 81 3.195002 CATTGGCGCCGTGATCGT 61.195 61.111 23.90 0.00 35.01 3.73
81 82 1.880796 CATTGGCGCCGTGATCGTA 60.881 57.895 23.90 0.00 35.01 3.43
82 83 1.153529 ATTGGCGCCGTGATCGTAA 60.154 52.632 23.90 8.13 35.01 3.18
83 84 0.741574 ATTGGCGCCGTGATCGTAAA 60.742 50.000 23.90 7.29 35.01 2.01
84 85 1.355796 TTGGCGCCGTGATCGTAAAG 61.356 55.000 23.90 0.00 35.01 1.85
85 86 2.320044 GCGCCGTGATCGTAAAGC 59.680 61.111 0.00 0.00 35.01 3.51
86 87 2.613486 CGCCGTGATCGTAAAGCG 59.387 61.111 0.00 0.00 43.01 4.68
87 88 2.320044 GCCGTGATCGTAAAGCGC 59.680 61.111 0.00 0.00 41.07 5.92
88 89 2.449525 GCCGTGATCGTAAAGCGCA 61.450 57.895 11.47 0.00 41.07 6.09
89 90 1.631072 CCGTGATCGTAAAGCGCAG 59.369 57.895 11.47 0.00 41.07 5.18
90 91 2.348140 CCGTGATCGTAAAGCGCAGC 62.348 60.000 11.47 0.00 45.65 5.25
112 113 4.688419 CAGCGGCGCAACAGTTGG 62.688 66.667 35.02 8.43 0.00 3.77
119 120 4.645921 GCAACAGTTGGGGCGCAC 62.646 66.667 15.28 4.83 0.00 5.34
120 121 4.326766 CAACAGTTGGGGCGCACG 62.327 66.667 10.83 0.00 0.00 5.34
133 134 2.742372 GCACGGCTGGACGATGTT 60.742 61.111 1.84 0.00 37.61 2.71
134 135 2.740714 GCACGGCTGGACGATGTTC 61.741 63.158 1.84 0.00 37.61 3.18
135 136 1.374125 CACGGCTGGACGATGTTCA 60.374 57.895 1.84 0.00 37.61 3.18
136 137 0.948623 CACGGCTGGACGATGTTCAA 60.949 55.000 1.84 0.00 37.61 2.69
137 138 0.670546 ACGGCTGGACGATGTTCAAG 60.671 55.000 1.84 0.00 37.61 3.02
138 139 0.670546 CGGCTGGACGATGTTCAAGT 60.671 55.000 0.00 0.00 35.47 3.16
139 140 1.079503 GGCTGGACGATGTTCAAGTC 58.920 55.000 0.00 4.18 0.00 3.01
140 141 0.716108 GCTGGACGATGTTCAAGTCG 59.284 55.000 0.00 0.00 43.13 4.18
147 148 3.852471 CGATGTTCAAGTCGTTGACAA 57.148 42.857 0.00 0.00 42.60 3.18
148 149 4.389664 CGATGTTCAAGTCGTTGACAAT 57.610 40.909 0.00 0.00 42.60 2.71
149 150 4.143835 CGATGTTCAAGTCGTTGACAATG 58.856 43.478 0.59 0.59 42.60 2.82
150 151 4.084589 CGATGTTCAAGTCGTTGACAATGA 60.085 41.667 5.98 5.98 42.60 2.57
151 152 4.530094 TGTTCAAGTCGTTGACAATGAC 57.470 40.909 26.41 26.41 42.60 3.06
152 153 3.311322 TGTTCAAGTCGTTGACAATGACC 59.689 43.478 28.79 17.50 46.27 4.02
153 154 2.489971 TCAAGTCGTTGACAATGACCC 58.510 47.619 28.79 12.05 46.27 4.46
154 155 2.158885 TCAAGTCGTTGACAATGACCCA 60.159 45.455 28.79 15.19 46.27 4.51
155 156 1.878953 AGTCGTTGACAATGACCCAC 58.121 50.000 28.79 11.61 46.27 4.61
156 157 1.140052 AGTCGTTGACAATGACCCACA 59.860 47.619 28.79 0.00 46.27 4.17
157 158 1.263217 GTCGTTGACAATGACCCACAC 59.737 52.381 24.29 4.46 40.70 3.82
158 159 0.234625 CGTTGACAATGACCCACACG 59.765 55.000 0.75 0.00 0.00 4.49
159 160 0.040425 GTTGACAATGACCCACACGC 60.040 55.000 0.00 0.00 0.00 5.34
160 161 1.502990 TTGACAATGACCCACACGCG 61.503 55.000 3.53 3.53 0.00 6.01
161 162 3.308878 GACAATGACCCACACGCGC 62.309 63.158 5.73 0.00 0.00 6.86
162 163 4.444024 CAATGACCCACACGCGCG 62.444 66.667 30.96 30.96 0.00 6.86
163 164 4.980805 AATGACCCACACGCGCGT 62.981 61.111 32.73 32.73 0.00 6.01
173 174 2.738521 ACGCGCGTGATTTCTGCT 60.739 55.556 37.37 5.31 0.00 4.24
174 175 2.317609 ACGCGCGTGATTTCTGCTT 61.318 52.632 37.37 4.65 0.00 3.91
175 176 1.154413 CGCGCGTGATTTCTGCTTT 60.154 52.632 24.19 0.00 0.00 3.51
283 284 1.003851 GGTACAAAGCGCGCTATTGA 58.996 50.000 38.15 26.88 0.00 2.57
292 293 2.674852 AGCGCGCTATTGATATGGATTG 59.325 45.455 35.79 0.00 0.00 2.67
293 294 2.789092 GCGCGCTATTGATATGGATTGC 60.789 50.000 26.67 0.00 0.00 3.56
294 295 2.416202 CGCGCTATTGATATGGATTGCA 59.584 45.455 5.56 0.00 0.00 4.08
295 296 3.484721 CGCGCTATTGATATGGATTGCAG 60.485 47.826 5.56 0.00 0.00 4.41
296 297 3.730061 GCGCTATTGATATGGATTGCAGC 60.730 47.826 0.00 0.00 0.00 5.25
297 298 3.437741 CGCTATTGATATGGATTGCAGCA 59.562 43.478 0.00 0.00 0.00 4.41
315 318 4.583871 CAGCAGGTTGGTTTCTCTTAGAT 58.416 43.478 0.00 0.00 0.00 1.98
317 320 6.352516 CAGCAGGTTGGTTTCTCTTAGATAT 58.647 40.000 0.00 0.00 0.00 1.63
319 322 6.069963 AGCAGGTTGGTTTCTCTTAGATATGT 60.070 38.462 0.00 0.00 0.00 2.29
347 355 3.153024 GTGTGATACACCGCACCAT 57.847 52.632 0.71 0.00 43.05 3.55
350 358 1.002544 TGTGATACACCGCACCATCAA 59.997 47.619 0.00 0.00 34.19 2.57
384 392 3.226346 AGTAGCGCGAGTTGTAAATCA 57.774 42.857 12.10 0.00 0.00 2.57
395 403 5.402568 CGAGTTGTAAATCATGCGCTACTAT 59.597 40.000 9.73 0.00 0.00 2.12
399 407 9.104965 AGTTGTAAATCATGCGCTACTATTAAA 57.895 29.630 9.73 0.00 0.00 1.52
474 490 1.306296 CACCATCCACCCCCGATTT 59.694 57.895 0.00 0.00 0.00 2.17
508 524 2.285368 TCCGCCCCCACAATCTCT 60.285 61.111 0.00 0.00 0.00 3.10
572 590 2.440147 CCCTGTTCCACCATGGCA 59.560 61.111 13.04 0.00 37.47 4.92
747 766 3.962421 GCTGCTCATGGGCATCGC 61.962 66.667 23.11 18.65 41.63 4.58
994 1142 1.240641 ATTGTGCGCGGACCAAATCA 61.241 50.000 28.22 5.14 0.00 2.57
1000 1148 1.368641 CGCGGACCAAATCATGAAGA 58.631 50.000 0.00 0.00 0.00 2.87
1012 1160 0.698886 CATGAAGATGGGGGAGGGGA 60.699 60.000 0.00 0.00 0.00 4.81
1291 1795 1.143684 CAACCATAGTCATCCCCAGGG 59.856 57.143 0.00 0.00 0.00 4.45
1376 1881 9.906660 CAGTTTTATGCTCTTTTATGGTTACAA 57.093 29.630 0.00 0.00 0.00 2.41
1467 1972 6.016192 AGCTTGATCAGAATTATGATGCTTGG 60.016 38.462 19.83 6.93 40.02 3.61
1506 2011 6.705863 ATTCTGTCATTTAAGGCAGATTCC 57.294 37.500 0.00 0.00 37.74 3.01
1517 2022 3.802866 AGGCAGATTCCGAAGATTCTTC 58.197 45.455 15.17 15.17 31.78 2.87
1561 2066 6.350612 GGAGATAGAGTATAACCATCCAGCAC 60.351 46.154 0.00 0.00 0.00 4.40
1568 2073 0.987294 AACCATCCAGCACTAGCACT 59.013 50.000 0.00 0.00 45.49 4.40
1578 2083 4.002982 CAGCACTAGCACTGGTTCATAAA 58.997 43.478 4.96 0.00 45.49 1.40
1593 2098 2.237643 TCATAAAGCCCTTTAGTGCCGA 59.762 45.455 6.63 0.00 38.30 5.54
1773 2286 7.881232 TGTTTGGGTGTGTTTTGGTTTTATTTA 59.119 29.630 0.00 0.00 0.00 1.40
1878 2392 7.602644 TGAAAGTATCGCAGATTAGTTTGACTT 59.397 33.333 0.00 0.00 45.12 3.01
1891 2405 3.890756 AGTTTGACTTGATGCATGTGGAA 59.109 39.130 2.46 0.00 0.00 3.53
2027 2541 2.742053 TCCAGTTGAAACTAATCTGCGC 59.258 45.455 0.00 0.00 37.08 6.09
2288 2812 8.141835 TCGAGTTCAACATGGTAATGATATTG 57.858 34.615 0.00 0.00 37.24 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.937391 CCTGCTGCTTGCGCTATAC 59.063 57.895 9.73 0.00 46.63 1.47
1 2 1.889105 GCCTGCTGCTTGCGCTATA 60.889 57.895 9.73 0.00 46.63 1.31
2 3 3.207669 GCCTGCTGCTTGCGCTAT 61.208 61.111 9.73 0.00 46.63 2.97
11 12 1.336125 GTCAATGGATAAGCCTGCTGC 59.664 52.381 0.00 0.00 41.71 5.25
12 13 1.600957 CGTCAATGGATAAGCCTGCTG 59.399 52.381 0.00 0.00 37.63 4.41
13 14 1.959042 CGTCAATGGATAAGCCTGCT 58.041 50.000 0.00 0.00 37.63 4.24
14 15 0.308993 GCGTCAATGGATAAGCCTGC 59.691 55.000 0.00 0.00 37.63 4.85
15 16 0.583438 CGCGTCAATGGATAAGCCTG 59.417 55.000 0.00 0.00 37.63 4.85
16 17 0.532862 CCGCGTCAATGGATAAGCCT 60.533 55.000 4.92 0.00 37.63 4.58
17 18 1.941812 CCGCGTCAATGGATAAGCC 59.058 57.895 4.92 0.00 37.10 4.35
18 19 1.279840 GCCGCGTCAATGGATAAGC 59.720 57.895 4.92 0.00 0.00 3.09
19 20 1.151777 ACGCCGCGTCAATGGATAAG 61.152 55.000 13.85 0.00 33.69 1.73
20 21 1.153529 ACGCCGCGTCAATGGATAA 60.154 52.632 13.85 0.00 33.69 1.75
21 22 2.497293 ACGCCGCGTCAATGGATA 59.503 55.556 13.85 0.00 33.69 2.59
34 35 4.070552 AGGTCGCTTCCAGACGCC 62.071 66.667 0.00 0.00 39.38 5.68
35 36 2.811317 CAGGTCGCTTCCAGACGC 60.811 66.667 0.00 0.00 39.38 5.19
36 37 2.125912 CCAGGTCGCTTCCAGACG 60.126 66.667 0.00 0.00 39.38 4.18
37 38 0.606604 TAACCAGGTCGCTTCCAGAC 59.393 55.000 0.00 0.00 37.86 3.51
38 39 0.895530 CTAACCAGGTCGCTTCCAGA 59.104 55.000 0.00 0.00 0.00 3.86
39 40 0.108138 CCTAACCAGGTCGCTTCCAG 60.108 60.000 0.00 0.00 37.15 3.86
40 41 1.980052 CCTAACCAGGTCGCTTCCA 59.020 57.895 0.00 0.00 37.15 3.53
41 42 4.934989 CCTAACCAGGTCGCTTCC 57.065 61.111 0.00 0.00 37.15 3.46
50 51 0.527565 GCCAATGTGCACCTAACCAG 59.472 55.000 15.69 0.00 0.00 4.00
51 52 1.240641 CGCCAATGTGCACCTAACCA 61.241 55.000 15.69 0.00 0.00 3.67
52 53 1.506262 CGCCAATGTGCACCTAACC 59.494 57.895 15.69 0.00 0.00 2.85
61 62 2.404789 GATCACGGCGCCAATGTG 59.595 61.111 28.98 25.24 34.96 3.21
62 63 2.566057 TACGATCACGGCGCCAATGT 62.566 55.000 28.98 14.07 44.46 2.71
63 64 1.425267 TTACGATCACGGCGCCAATG 61.425 55.000 28.98 23.63 44.46 2.82
64 65 0.741574 TTTACGATCACGGCGCCAAT 60.742 50.000 28.98 16.62 44.46 3.16
65 66 1.355796 CTTTACGATCACGGCGCCAA 61.356 55.000 28.98 11.85 44.46 4.52
66 67 1.807981 CTTTACGATCACGGCGCCA 60.808 57.895 28.98 7.49 44.46 5.69
67 68 3.003478 CTTTACGATCACGGCGCC 58.997 61.111 19.07 19.07 44.46 6.53
68 69 2.320044 GCTTTACGATCACGGCGC 59.680 61.111 6.90 0.00 44.46 6.53
79 80 1.423056 CTGCTCAGCTGCGCTTTAC 59.577 57.895 27.46 0.84 36.40 2.01
80 81 3.880591 CTGCTCAGCTGCGCTTTA 58.119 55.556 27.46 8.53 36.40 1.85
95 96 4.688419 CCAACTGTTGCGCCGCTG 62.688 66.667 11.67 4.20 0.00 5.18
102 103 4.645921 GTGCGCCCCAACTGTTGC 62.646 66.667 14.94 4.03 0.00 4.17
103 104 4.326766 CGTGCGCCCCAACTGTTG 62.327 66.667 13.50 13.50 0.00 3.33
116 117 2.740714 GAACATCGTCCAGCCGTGC 61.741 63.158 0.00 0.00 0.00 5.34
117 118 0.948623 TTGAACATCGTCCAGCCGTG 60.949 55.000 0.00 0.00 0.00 4.94
118 119 0.670546 CTTGAACATCGTCCAGCCGT 60.671 55.000 0.00 0.00 0.00 5.68
119 120 0.670546 ACTTGAACATCGTCCAGCCG 60.671 55.000 0.00 0.00 0.00 5.52
120 121 1.079503 GACTTGAACATCGTCCAGCC 58.920 55.000 0.00 0.00 0.00 4.85
121 122 0.716108 CGACTTGAACATCGTCCAGC 59.284 55.000 0.00 0.00 33.63 4.85
127 128 3.852471 TTGTCAACGACTTGAACATCG 57.148 42.857 0.00 0.00 43.97 3.84
128 129 5.140177 GTCATTGTCAACGACTTGAACATC 58.860 41.667 4.55 0.00 38.17 3.06
129 130 4.024048 GGTCATTGTCAACGACTTGAACAT 60.024 41.667 11.26 0.00 38.17 2.71
130 131 3.311322 GGTCATTGTCAACGACTTGAACA 59.689 43.478 11.26 0.00 38.17 3.18
131 132 3.303791 GGGTCATTGTCAACGACTTGAAC 60.304 47.826 11.26 2.59 38.17 3.18
132 133 2.875933 GGGTCATTGTCAACGACTTGAA 59.124 45.455 11.26 0.00 38.17 2.69
133 134 2.158885 TGGGTCATTGTCAACGACTTGA 60.159 45.455 11.26 0.00 33.76 3.02
134 135 2.032030 GTGGGTCATTGTCAACGACTTG 60.032 50.000 11.26 0.00 33.15 3.16
135 136 2.218603 GTGGGTCATTGTCAACGACTT 58.781 47.619 11.26 0.00 33.15 3.01
136 137 1.140052 TGTGGGTCATTGTCAACGACT 59.860 47.619 11.26 0.00 33.15 4.18
137 138 1.263217 GTGTGGGTCATTGTCAACGAC 59.737 52.381 3.15 3.15 0.00 4.34
138 139 1.588674 GTGTGGGTCATTGTCAACGA 58.411 50.000 0.00 0.00 0.00 3.85
139 140 0.234625 CGTGTGGGTCATTGTCAACG 59.765 55.000 0.00 0.00 0.00 4.10
140 141 0.040425 GCGTGTGGGTCATTGTCAAC 60.040 55.000 0.00 0.00 0.00 3.18
141 142 1.502990 CGCGTGTGGGTCATTGTCAA 61.503 55.000 0.00 0.00 0.00 3.18
142 143 1.958715 CGCGTGTGGGTCATTGTCA 60.959 57.895 0.00 0.00 0.00 3.58
143 144 2.860293 CGCGTGTGGGTCATTGTC 59.140 61.111 0.00 0.00 0.00 3.18
144 145 3.353836 GCGCGTGTGGGTCATTGT 61.354 61.111 8.43 0.00 0.00 2.71
145 146 4.444024 CGCGCGTGTGGGTCATTG 62.444 66.667 24.19 0.00 0.00 2.82
146 147 4.980805 ACGCGCGTGTGGGTCATT 62.981 61.111 37.37 5.31 0.00 2.57
156 157 1.841663 AAAGCAGAAATCACGCGCGT 61.842 50.000 32.73 32.73 0.00 6.01
157 158 1.122419 GAAAGCAGAAATCACGCGCG 61.122 55.000 30.96 30.96 0.00 6.86
158 159 0.110238 TGAAAGCAGAAATCACGCGC 60.110 50.000 5.73 0.00 0.00 6.86
159 160 1.069973 TGTGAAAGCAGAAATCACGCG 60.070 47.619 3.53 3.53 44.95 6.01
160 161 2.310577 GTGTGAAAGCAGAAATCACGC 58.689 47.619 3.33 3.33 44.95 5.34
161 162 3.885484 AGTGTGAAAGCAGAAATCACG 57.115 42.857 0.00 0.00 44.95 4.35
162 163 7.334421 TCCTAATAGTGTGAAAGCAGAAATCAC 59.666 37.037 0.00 0.00 42.90 3.06
163 164 7.394016 TCCTAATAGTGTGAAAGCAGAAATCA 58.606 34.615 0.00 0.00 0.00 2.57
164 165 7.849804 TCCTAATAGTGTGAAAGCAGAAATC 57.150 36.000 0.00 0.00 0.00 2.17
165 166 8.635765 TTTCCTAATAGTGTGAAAGCAGAAAT 57.364 30.769 0.00 0.00 0.00 2.17
166 167 8.458573 TTTTCCTAATAGTGTGAAAGCAGAAA 57.541 30.769 0.00 0.00 0.00 2.52
167 168 8.514594 CATTTTCCTAATAGTGTGAAAGCAGAA 58.485 33.333 0.00 0.00 0.00 3.02
168 169 7.362056 GCATTTTCCTAATAGTGTGAAAGCAGA 60.362 37.037 0.00 0.00 0.00 4.26
169 170 6.749118 GCATTTTCCTAATAGTGTGAAAGCAG 59.251 38.462 0.00 0.00 0.00 4.24
170 171 6.434028 AGCATTTTCCTAATAGTGTGAAAGCA 59.566 34.615 0.00 0.00 0.00 3.91
171 172 6.856895 AGCATTTTCCTAATAGTGTGAAAGC 58.143 36.000 0.00 0.00 0.00 3.51
174 175 8.405531 GCATAAGCATTTTCCTAATAGTGTGAA 58.594 33.333 0.00 0.00 41.58 3.18
175 176 7.930217 GCATAAGCATTTTCCTAATAGTGTGA 58.070 34.615 0.00 0.00 41.58 3.58
199 200 9.893305 ACAAACACTACTGATAAACTTTTATGC 57.107 29.630 0.00 0.00 33.72 3.14
204 205 9.567848 CACAAACAAACACTACTGATAAACTTT 57.432 29.630 0.00 0.00 0.00 2.66
212 213 3.942748 GGGACACAAACAAACACTACTGA 59.057 43.478 0.00 0.00 0.00 3.41
261 262 0.391927 ATAGCGCGCTTTGTACCCAA 60.392 50.000 41.04 18.75 0.00 4.12
283 284 2.313317 CCAACCTGCTGCAATCCATAT 58.687 47.619 3.02 0.00 0.00 1.78
292 293 1.322442 AAGAGAAACCAACCTGCTGC 58.678 50.000 0.00 0.00 0.00 5.25
293 294 4.008074 TCTAAGAGAAACCAACCTGCTG 57.992 45.455 0.00 0.00 0.00 4.41
294 295 4.917906 ATCTAAGAGAAACCAACCTGCT 57.082 40.909 0.00 0.00 0.00 4.24
295 296 6.116126 ACATATCTAAGAGAAACCAACCTGC 58.884 40.000 0.00 0.00 0.00 4.85
296 297 9.099454 GTAACATATCTAAGAGAAACCAACCTG 57.901 37.037 0.00 0.00 0.00 4.00
297 298 9.047947 AGTAACATATCTAAGAGAAACCAACCT 57.952 33.333 0.00 0.00 0.00 3.50
335 338 5.707242 TTTTTATTTGATGGTGCGGTGTA 57.293 34.783 0.00 0.00 0.00 2.90
373 381 8.657074 TTAATAGTAGCGCATGATTTACAACT 57.343 30.769 11.47 0.00 0.00 3.16
384 392 9.823647 ATAGCTATTCATTTAATAGTAGCGCAT 57.176 29.630 11.47 0.00 46.08 4.73
395 403 6.180472 GCCTGGGCTATAGCTATTCATTTAA 58.820 40.000 23.53 0.00 41.70 1.52
399 407 2.169352 CGCCTGGGCTATAGCTATTCAT 59.831 50.000 23.53 0.00 41.70 2.57
414 422 2.202878 CGTGGGTGTATCGCCTGG 60.203 66.667 0.00 0.00 33.98 4.45
474 490 1.591280 GGAGGAGAGGGGTGGGAGTA 61.591 65.000 0.00 0.00 0.00 2.59
572 590 3.386237 GAGCCCAGGACGAGCTGT 61.386 66.667 0.00 0.00 36.87 4.40
691 709 1.456518 CCTCTCCTCATCGGCCTCA 60.457 63.158 0.00 0.00 0.00 3.86
994 1142 0.047802 TTCCCCTCCCCCATCTTCAT 59.952 55.000 0.00 0.00 0.00 2.57
1000 1148 2.044620 GACCTTCCCCTCCCCCAT 59.955 66.667 0.00 0.00 0.00 4.00
1012 1160 2.352032 CCTTCTCCTCCGCGACCTT 61.352 63.158 8.23 0.00 0.00 3.50
1074 1222 1.219393 GGCCTCCTTCTTGACCTCG 59.781 63.158 0.00 0.00 0.00 4.63
1291 1795 1.632589 ATGGAAGGAAAAGTGGCACC 58.367 50.000 15.27 0.00 0.00 5.01
1561 2066 2.945668 GGGCTTTATGAACCAGTGCTAG 59.054 50.000 0.00 0.00 0.00 3.42
1568 2073 3.761752 GCACTAAAGGGCTTTATGAACCA 59.238 43.478 0.00 0.00 34.86 3.67
1578 2083 0.462047 CGAATCGGCACTAAAGGGCT 60.462 55.000 3.89 0.00 0.00 5.19
1593 2098 4.233010 CACATTAGTGCCGGTTACCGAAT 61.233 47.826 26.59 13.31 43.90 3.34
1701 2214 1.331756 CGGTACTAATGTCCTACGCGT 59.668 52.381 19.17 19.17 0.00 6.01
1878 2392 1.561076 AGCTAGGTTCCACATGCATCA 59.439 47.619 0.00 0.00 0.00 3.07
1891 2405 7.310113 GGCATATACTTGATGACTTAGCTAGGT 60.310 40.741 8.45 8.45 28.94 3.08
2288 2812 4.735662 TTGTGGTGTTATGAACGCTTAC 57.264 40.909 3.19 4.15 41.52 2.34


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

AutoCloner maintained by Alex Coulton.