Multiple sequence alignment - TraesCS2D01G340100

Loading Multiple Alignment...

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 TraesCS2D01G340100 chr2D 100.000 4656 0 0 1 4656 434360874 434356219 0.000000e+00 8599.0
1 TraesCS2D01G340100 chr2D 84.461 547 53 17 2716 3240 434676616 434676080 1.160000e-140 510.0
2 TraesCS2D01G340100 chr2D 95.604 91 3 1 2154 2243 133265670 133265760 1.350000e-30 145.0
3 TraesCS2D01G340100 chr2D 96.552 87 3 0 2157 2243 387188243 387188157 1.350000e-30 145.0
4 TraesCS2D01G340100 chr2B 93.899 2344 88 23 1886 4190 513283811 513281484 0.000000e+00 3485.0
5 TraesCS2D01G340100 chr2B 94.106 1001 35 10 900 1886 513286076 513285086 0.000000e+00 1500.0
6 TraesCS2D01G340100 chr2B 89.638 801 66 10 1 798 513287115 513286329 0.000000e+00 1003.0
7 TraesCS2D01G340100 chr2B 84.954 545 50 17 2717 3240 513289029 513288496 1.480000e-144 523.0
8 TraesCS2D01G340100 chr2B 87.405 262 15 8 4405 4656 513281119 513280866 7.630000e-73 285.0
9 TraesCS2D01G340100 chr2B 86.207 87 10 1 4280 4366 513281283 513281199 4.960000e-15 93.5
10 TraesCS2D01G340100 chr2A 93.737 1485 46 7 2669 4121 552492947 552494416 0.000000e+00 2183.0
11 TraesCS2D01G340100 chr2A 93.906 1001 34 11 902 1886 552489670 552490659 0.000000e+00 1485.0
12 TraesCS2D01G340100 chr2A 93.696 920 42 13 1 913 552488733 552489643 0.000000e+00 1363.0
13 TraesCS2D01G340100 chr2A 87.125 567 33 6 2073 2638 552492420 552492947 1.430000e-169 606.0
14 TraesCS2D01G340100 chr2A 84.288 541 53 16 2716 3234 552486725 552487255 2.500000e-137 499.0
15 TraesCS2D01G340100 chr2A 93.870 261 11 4 4397 4656 552494849 552495105 5.650000e-104 388.0
16 TraesCS2D01G340100 chr2A 92.075 265 16 4 4393 4656 711105493 711105753 7.360000e-98 368.0
17 TraesCS2D01G340100 chr2A 78.947 513 77 21 946 1456 552471457 552471940 2.090000e-83 320.0
18 TraesCS2D01G340100 chr2A 95.395 152 7 0 1883 2034 552492267 552492418 4.650000e-60 243.0
19 TraesCS2D01G340100 chr2A 89.474 57 4 2 2677 2732 179291330 179291275 2.320000e-08 71.3
20 TraesCS2D01G340100 chr2A 92.157 51 2 2 2678 2728 423207509 423207461 2.320000e-08 71.3
21 TraesCS2D01G340100 chr5A 93.208 265 13 4 4393 4656 671469167 671469427 7.310000e-103 385.0
22 TraesCS2D01G340100 chr5A 91.698 265 17 4 4393 4656 34037554 34037814 3.420000e-96 363.0
23 TraesCS2D01G340100 chr7A 92.453 265 15 4 4393 4656 394230974 394231234 1.580000e-99 374.0
24 TraesCS2D01G340100 chr7A 96.552 87 3 0 2157 2243 271735240 271735154 1.350000e-30 145.0
25 TraesCS2D01G340100 chr7A 91.228 57 4 1 4280 4335 394230897 394230953 5.000000e-10 76.8
26 TraesCS2D01G340100 chr1A 92.453 265 15 4 4393 4656 74487951 74488211 1.580000e-99 374.0
27 TraesCS2D01G340100 chr4A 91.985 262 16 4 4396 4656 129128931 129128674 3.420000e-96 363.0
28 TraesCS2D01G340100 chr4A 93.023 172 7 4 4484 4654 40100068 40099901 3.600000e-61 246.0
29 TraesCS2D01G340100 chr4A 81.203 133 13 9 1745 1871 11579675 11579801 3.830000e-16 97.1
30 TraesCS2D01G340100 chr4A 89.655 58 3 1 2659 2716 56270079 56270133 2.320000e-08 71.3
31 TraesCS2D01G340100 chr1B 94.737 95 5 0 2159 2253 424541356 424541262 1.040000e-31 148.0
32 TraesCS2D01G340100 chr7D 96.512 86 3 0 2159 2244 334858078 334858163 4.860000e-30 143.0
33 TraesCS2D01G340100 chr7D 97.531 81 2 0 2158 2238 567711964 567712044 6.280000e-29 139.0
34 TraesCS2D01G340100 chr7B 96.512 86 3 0 2158 2243 622247079 622247164 4.860000e-30 143.0
35 TraesCS2D01G340100 chr5B 96.512 86 3 0 2158 2243 381187397 381187482 4.860000e-30 143.0
36 TraesCS2D01G340100 chr4D 94.643 56 2 1 2662 2716 50885700 50885755 8.300000e-13 86.1
37 TraesCS2D01G340100 chr4D 91.228 57 4 1 2660 2716 1643573 1643628 5.000000e-10 76.8
38 TraesCS2D01G340100 chr4B 87.719 57 6 1 2660 2716 2211710 2211765 1.080000e-06 65.8
39 TraesCS2D01G340100 chr4B 87.719 57 6 1 2660 2716 2241683 2241738 1.080000e-06 65.8


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 TraesCS2D01G340100 chr2D 434356219 434360874 4655 True 8599.000000 8599 100.000000 1 4656 1 chr2D.!!$R2 4655
1 TraesCS2D01G340100 chr2D 434676080 434676616 536 True 510.000000 510 84.461000 2716 3240 1 chr2D.!!$R3 524
2 TraesCS2D01G340100 chr2B 513280866 513289029 8163 True 1148.250000 3485 89.368167 1 4656 6 chr2B.!!$R1 4655
3 TraesCS2D01G340100 chr2A 552486725 552495105 8380 False 966.714286 2183 91.716714 1 4656 7 chr2A.!!$F3 4655

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
822 2981 2.125106 GCCAACGCCTCCCTACAG 60.125 66.667 0.0 0.0 0.0 2.74 F
2071 6050 0.107831 AACCTGGCTTTAGTGCGACA 59.892 50.000 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 6412 0.037232 AAGAAGGACGAAGAAGCGGG 60.037 55.0 0.0 0.0 35.12 6.13 R
3702 7709 0.843309 TCCCACAGGCTTGAACTTCA 59.157 50.0 1.4 0.0 0.00 3.02 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
31 2184 6.541641 ACATAGCTTTCTTCTTGGATGTCATC 59.458 38.462 4.06 4.06 0.00 2.92
36 2189 3.371034 TCTTCTTGGATGTCATCGGGTA 58.629 45.455 6.74 0.00 0.00 3.69
169 2324 7.601856 CCTTTTGGTGTGTCATATTATTGTGT 58.398 34.615 0.00 0.00 34.07 3.72
170 2325 7.754924 CCTTTTGGTGTGTCATATTATTGTGTC 59.245 37.037 0.00 0.00 34.07 3.67
171 2326 7.751768 TTTGGTGTGTCATATTATTGTGTCA 57.248 32.000 0.00 0.00 0.00 3.58
210 2365 6.481954 AGCTAGGTGATGTTTAAGTTTTCG 57.518 37.500 0.00 0.00 0.00 3.46
231 2386 3.493503 CGCTCGGTATTCCTCAATAAACC 59.506 47.826 0.00 0.00 0.00 3.27
354 2510 2.355108 GCAGGTCTCCAGCTAACATTCA 60.355 50.000 0.00 0.00 33.11 2.57
460 2616 2.202557 TGTAGATGTCCGCACGCG 60.203 61.111 3.53 3.53 39.44 6.01
547 2704 5.525378 CGAAAATGAGGAAGGTGAATAGGAG 59.475 44.000 0.00 0.00 0.00 3.69
822 2981 2.125106 GCCAACGCCTCCCTACAG 60.125 66.667 0.00 0.00 0.00 2.74
862 3023 3.730215 TCTTGCTTAGCCCAATTACCA 57.270 42.857 0.29 0.00 0.00 3.25
864 3025 5.381184 TCTTGCTTAGCCCAATTACCATA 57.619 39.130 0.29 0.00 0.00 2.74
874 3035 2.159382 CAATTACCATACGGCCCATCC 58.841 52.381 0.00 0.00 34.57 3.51
926 3274 5.596845 GCTAGAGATCCGAACTTTCTGAAT 58.403 41.667 0.00 0.00 0.00 2.57
1008 3356 0.731174 GGTACAAAACAATGGCGGCG 60.731 55.000 0.51 0.51 0.00 6.46
1074 3422 2.586792 GCACCTTCCGCCTCTGAT 59.413 61.111 0.00 0.00 0.00 2.90
1075 3423 1.817099 GCACCTTCCGCCTCTGATG 60.817 63.158 0.00 0.00 0.00 3.07
1076 3424 1.599047 CACCTTCCGCCTCTGATGT 59.401 57.895 0.00 0.00 0.00 3.06
1218 3566 2.755650 GACGTGTCTGTGAACTCCATT 58.244 47.619 0.00 0.00 0.00 3.16
1222 3570 2.054021 TGTCTGTGAACTCCATTCCCA 58.946 47.619 0.00 0.00 36.36 4.37
1225 3574 2.162681 CTGTGAACTCCATTCCCAACC 58.837 52.381 0.00 0.00 36.36 3.77
1287 3636 1.045350 TGAGGGAGCGGATGGAGAAG 61.045 60.000 0.00 0.00 0.00 2.85
1431 3782 2.949177 TGGTTGGCACTCACTTACAT 57.051 45.000 0.00 0.00 0.00 2.29
1451 3802 2.170166 TGGGTTCATGTTGGCAATCTC 58.830 47.619 1.92 0.00 0.00 2.75
1533 3884 1.675483 ACAATTCGTGCAAACTGAGCA 59.325 42.857 0.00 0.00 40.19 4.26
1628 3979 6.947733 ACCAGGATATTGTTTCATTGTCAAGA 59.052 34.615 0.00 0.00 0.00 3.02
1730 4081 4.466370 TCAGGTGTTAGTATCTCCAACAGG 59.534 45.833 2.92 0.00 33.10 4.00
1733 4084 4.020485 GGTGTTAGTATCTCCAACAGGTGT 60.020 45.833 0.00 0.00 33.10 4.16
1784 4148 1.398692 TGGACCCAAAAACAGTGCTC 58.601 50.000 0.00 0.00 0.00 4.26
1846 4210 0.390492 GGCAGCTCCATATTTTGGCC 59.610 55.000 0.00 0.00 46.01 5.36
2009 5986 5.983118 TGTATGTTGTAGCGTATTGGATCAG 59.017 40.000 0.00 0.00 0.00 2.90
2012 5989 3.452755 TGTAGCGTATTGGATCAGTGG 57.547 47.619 0.00 0.00 0.00 4.00
2070 6049 0.796927 GAACCTGGCTTTAGTGCGAC 59.203 55.000 0.00 0.00 0.00 5.19
2071 6050 0.107831 AACCTGGCTTTAGTGCGACA 59.892 50.000 0.00 0.00 0.00 4.35
2136 6115 0.988832 ATGCCCTCTTGGTCCGTTTA 59.011 50.000 0.00 0.00 36.04 2.01
2215 6194 3.363341 TCAGTTCGGAATTTTGGTTGC 57.637 42.857 0.00 0.00 0.00 4.17
2216 6195 2.690497 TCAGTTCGGAATTTTGGTTGCA 59.310 40.909 0.00 0.00 0.00 4.08
2336 6315 2.117423 TCTGCTGTCTGTCCCCGA 59.883 61.111 0.00 0.00 0.00 5.14
2504 6483 2.326222 CCACGCTGTAAGGCACAAA 58.674 52.632 0.00 0.00 36.48 2.83
2528 6507 2.542597 TGTTCGCGCGGTATATTTTCT 58.457 42.857 31.69 0.00 0.00 2.52
2536 6515 5.022021 GCGCGGTATATTTTCTCATTATGC 58.978 41.667 8.83 0.00 0.00 3.14
2716 6695 6.642733 ACAATTAATATGGATCGGAGGGAT 57.357 37.500 0.00 0.00 38.35 3.85
2985 6964 5.434408 TGCTCTGAGGTATCGAAGTACTTA 58.566 41.667 8.42 0.00 0.00 2.24
3044 7048 9.586732 TGAGCTATTGGTAATTAATTGGCTTAT 57.413 29.630 11.05 1.48 30.99 1.73
3216 7220 5.794687 TTTGTTATTGAGCTCATACCACG 57.205 39.130 19.04 0.00 0.00 4.94
3267 7272 4.396478 CGAATCCTGTCTTCTCTAGTGTCA 59.604 45.833 0.00 0.00 0.00 3.58
3276 7281 1.543358 TCTCTAGTGTCACTGCAGCTG 59.457 52.381 15.27 10.11 0.00 4.24
3326 7331 6.941857 TGTGTACAGCCTATTCAGTTCAATA 58.058 36.000 0.00 0.00 0.00 1.90
3360 7366 7.834068 TTAGCAAGCTACAGACTTTGAATAG 57.166 36.000 0.40 0.00 0.00 1.73
3589 7596 2.216046 TGTTCAGAGACAGCTGCAAAG 58.784 47.619 15.27 0.10 35.86 2.77
3753 7760 0.178998 CCTTGAGATGGGCTCCATGG 60.179 60.000 4.97 4.97 45.26 3.66
3767 7774 2.766263 CTCCATGGAGTACAAGCCTGTA 59.234 50.000 30.55 0.00 37.47 2.74
3809 7816 3.259123 TCAGATTGTACTTCAGCAGAGCA 59.741 43.478 0.00 0.00 0.00 4.26
3811 7818 4.270566 CAGATTGTACTTCAGCAGAGCATC 59.729 45.833 0.00 0.00 0.00 3.91
3812 7819 3.683365 TTGTACTTCAGCAGAGCATCA 57.317 42.857 0.00 0.00 37.82 3.07
3909 7919 4.696402 TCCATGCAATTGAATTCTTTTGCC 59.304 37.500 27.79 17.57 42.87 4.52
3947 7957 6.767902 ACAGAGTTCACTGAGCTCAAAATAAA 59.232 34.615 18.85 5.33 41.31 1.40
4002 8015 6.775629 GGTAAATATTGCTTGAGGTATTCCCA 59.224 38.462 0.00 0.00 34.66 4.37
4088 8104 9.144298 CCCCAGTCAGAGTTATTCTACTAATAA 57.856 37.037 0.00 0.00 33.83 1.40
4121 8137 1.961793 TTCAACCTCCAACCAACTCG 58.038 50.000 0.00 0.00 0.00 4.18
4132 8308 6.017934 CCTCCAACCAACTCGATAATACATTG 60.018 42.308 0.00 0.00 0.00 2.82
4142 8318 4.511454 TCGATAATACATTGAAGCCACTGC 59.489 41.667 0.00 0.00 37.95 4.40
4151 8327 1.709147 GAAGCCACTGCCGTGCTATG 61.709 60.000 2.22 0.00 39.86 2.23
4168 8344 9.594038 CCGTGCTATGTTCACAATATTAATAAC 57.406 33.333 0.00 0.00 34.27 1.89
4196 8380 6.183360 GGTCCCAAACTACCATGTATTGAATG 60.183 42.308 0.00 0.00 35.73 2.67
4215 8399 8.958175 TTGAATGGTCAAAATTATGTTACGAC 57.042 30.769 0.00 0.00 40.87 4.34
4235 8469 4.377431 CGACACAGTAACTCAAAATCTGCC 60.377 45.833 0.00 0.00 0.00 4.85
4253 8520 1.434555 CCGCCGTCACTAAATGTCAA 58.565 50.000 0.00 0.00 0.00 3.18
4254 8521 2.006888 CCGCCGTCACTAAATGTCAAT 58.993 47.619 0.00 0.00 0.00 2.57
4260 8527 6.745450 CGCCGTCACTAAATGTCAATATTTTT 59.255 34.615 0.00 0.00 32.79 1.94
4262 8529 7.753132 GCCGTCACTAAATGTCAATATTTTTCA 59.247 33.333 0.00 0.00 32.79 2.69
4316 8613 4.025360 TGTTCTATAAACAGGGCTACGGA 58.975 43.478 0.00 0.00 0.00 4.69
4366 8663 6.430925 TGTTGGGCATGCTATGATAATTACTC 59.569 38.462 18.92 0.00 0.00 2.59
4367 8664 6.378661 TGGGCATGCTATGATAATTACTCT 57.621 37.500 18.92 0.00 0.00 3.24
4368 8665 7.494922 TGGGCATGCTATGATAATTACTCTA 57.505 36.000 18.92 0.00 0.00 2.43
4369 8666 7.917003 TGGGCATGCTATGATAATTACTCTAA 58.083 34.615 18.92 0.00 0.00 2.10
4370 8667 8.382405 TGGGCATGCTATGATAATTACTCTAAA 58.618 33.333 18.92 0.00 0.00 1.85
4371 8668 9.231297 GGGCATGCTATGATAATTACTCTAAAA 57.769 33.333 18.92 0.00 0.00 1.52
4384 8681 8.691661 AATTACTCTAAAACCATGACAAGTGT 57.308 30.769 0.00 0.00 0.00 3.55
4386 8683 8.514330 TTACTCTAAAACCATGACAAGTGTTT 57.486 30.769 0.00 0.00 32.62 2.83
4387 8684 7.404671 ACTCTAAAACCATGACAAGTGTTTT 57.595 32.000 13.90 13.90 41.99 2.43
4390 8687 7.831753 TCTAAAACCATGACAAGTGTTTTGAA 58.168 30.769 16.83 7.43 40.16 2.69
4391 8688 8.307483 TCTAAAACCATGACAAGTGTTTTGAAA 58.693 29.630 16.83 5.83 40.16 2.69
4394 8691 8.647143 AAACCATGACAAGTGTTTTGAAATAG 57.353 30.769 0.00 0.00 0.00 1.73
4476 8817 1.379044 CCACTCAGCCAATCCCCAC 60.379 63.158 0.00 0.00 0.00 4.61
4495 8836 1.165270 CCACGAACCCATTTCACTCC 58.835 55.000 0.00 0.00 33.24 3.85
4614 8962 5.539048 ACAATACACGAAGCTACAAAGAGT 58.461 37.500 0.00 0.00 0.00 3.24
4615 8963 6.684686 ACAATACACGAAGCTACAAAGAGTA 58.315 36.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.272018 CCAAGAAGAAAGCTATGTCCGATG 59.728 45.833 0.00 0.00 0.00 3.84
1 2 4.162320 TCCAAGAAGAAAGCTATGTCCGAT 59.838 41.667 0.00 0.00 0.00 4.18
3 4 3.861840 TCCAAGAAGAAAGCTATGTCCG 58.138 45.455 0.00 0.00 0.00 4.79
4 5 5.189180 ACATCCAAGAAGAAAGCTATGTCC 58.811 41.667 0.00 0.00 0.00 4.02
31 2184 3.935203 GACAAGCATATCCATGATACCCG 59.065 47.826 0.00 0.00 33.67 5.28
59 2212 6.089283 CACACCAAAAATGTTGTATCAATCCG 59.911 38.462 0.00 0.00 0.00 4.18
152 2306 9.636879 CCAAAAATGACACAATAATATGACACA 57.363 29.630 0.00 0.00 0.00 3.72
169 2324 3.766545 AGCTTGACTAGGCCAAAAATGA 58.233 40.909 5.01 0.00 0.00 2.57
170 2325 5.240713 CTAGCTTGACTAGGCCAAAAATG 57.759 43.478 5.01 0.00 44.14 2.32
210 2365 3.493503 CGGTTTATTGAGGAATACCGAGC 59.506 47.826 5.61 0.00 36.48 5.03
231 2386 8.634475 AAAAAGAAGAAAAGAAAGGTTGATCG 57.366 30.769 0.00 0.00 0.00 3.69
279 2434 1.416243 ACAACCTGGTACGAGGAACA 58.584 50.000 28.59 0.00 36.51 3.18
363 2519 3.639094 AGTGAACTGTACTCTGTTGAGCT 59.361 43.478 0.00 0.00 43.85 4.09
453 2609 3.015293 AAAGCTCATGACGCGTGCG 62.015 57.895 20.70 13.39 46.03 5.34
460 2616 3.122613 CAGTTCGAGACAAAGCTCATGAC 59.877 47.826 6.48 0.78 34.56 3.06
579 2736 6.691255 ACCTATTTTATCGGTATTGGCCTA 57.309 37.500 3.32 0.00 0.00 3.93
688 2846 4.637276 TGATTTTTCTAGGTGCAAGTCGA 58.363 39.130 0.00 0.00 0.00 4.20
689 2847 4.142816 CCTGATTTTTCTAGGTGCAAGTCG 60.143 45.833 0.00 0.00 0.00 4.18
780 2939 5.510520 CCTCCTTGCTAGCGATTTATCTCTT 60.511 44.000 10.77 0.00 0.00 2.85
822 2981 2.803479 GCTAATGCTGGGCTGCAC 59.197 61.111 0.50 0.00 46.33 4.57
862 3023 1.762708 CAAAACTGGATGGGCCGTAT 58.237 50.000 0.00 0.00 40.66 3.06
864 3025 2.275380 GCAAAACTGGATGGGCCGT 61.275 57.895 0.00 0.00 40.66 5.68
939 3287 1.813192 GGAGGCCGAGAAGACAGAG 59.187 63.158 0.00 0.00 0.00 3.35
982 3330 2.095263 CCATTGTTTTGTACCTCTGCCG 60.095 50.000 0.00 0.00 0.00 5.69
984 3332 2.668279 CGCCATTGTTTTGTACCTCTGC 60.668 50.000 0.00 0.00 0.00 4.26
985 3333 2.095263 CCGCCATTGTTTTGTACCTCTG 60.095 50.000 0.00 0.00 0.00 3.35
986 3334 2.159382 CCGCCATTGTTTTGTACCTCT 58.841 47.619 0.00 0.00 0.00 3.69
987 3335 1.402325 GCCGCCATTGTTTTGTACCTC 60.402 52.381 0.00 0.00 0.00 3.85
990 3338 0.731174 CCGCCGCCATTGTTTTGTAC 60.731 55.000 0.00 0.00 0.00 2.90
991 3339 1.581954 CCGCCGCCATTGTTTTGTA 59.418 52.632 0.00 0.00 0.00 2.41
992 3340 2.338257 CCGCCGCCATTGTTTTGT 59.662 55.556 0.00 0.00 0.00 2.83
993 3341 3.111442 GCCGCCGCCATTGTTTTG 61.111 61.111 0.00 0.00 0.00 2.44
1037 3385 2.232298 CTCCGCTCTGGTGGTCTTCC 62.232 65.000 0.00 0.00 43.20 3.46
1218 3566 4.323477 CGACAAGGCGGGTTGGGA 62.323 66.667 0.00 0.00 0.00 4.37
1222 3570 0.596082 CAAAATCGACAAGGCGGGTT 59.404 50.000 0.00 0.00 0.00 4.11
1225 3574 0.109781 CACCAAAATCGACAAGGCGG 60.110 55.000 0.00 0.00 0.00 6.13
1431 3782 2.170166 GAGATTGCCAACATGAACCCA 58.830 47.619 0.00 0.00 0.00 4.51
1451 3802 4.300803 ACATAGCGGCAATGCAAATTATG 58.699 39.130 7.79 11.25 37.31 1.90
1605 3956 9.865321 AAATCTTGACAATGAAACAATATCCTG 57.135 29.630 0.00 0.00 0.00 3.86
1619 3970 5.634118 TCTCCTCAACCAAATCTTGACAAT 58.366 37.500 0.00 0.00 0.00 2.71
1628 3979 7.890127 TCAAGACAATTATCTCCTCAACCAAAT 59.110 33.333 0.00 0.00 0.00 2.32
1752 4116 2.534990 TGGGTCCAAATGGCCTAAAAG 58.465 47.619 3.32 0.00 33.64 2.27
1821 4185 4.186159 CAAAATATGGAGCTGCCCAAAAG 58.814 43.478 12.73 0.00 40.04 2.27
2009 5986 5.449177 GCTGCCAATATAACTGAAGTTCCAC 60.449 44.000 0.00 0.00 39.31 4.02
2012 5989 5.818136 TGCTGCCAATATAACTGAAGTTC 57.182 39.130 0.00 0.00 39.31 3.01
2070 6049 6.183360 ACGTGTTTAAGGTGATAGCATGAATG 60.183 38.462 0.00 0.00 0.00 2.67
2071 6050 5.880332 ACGTGTTTAAGGTGATAGCATGAAT 59.120 36.000 0.00 0.00 0.00 2.57
2215 6194 2.022195 AGCTTCATGCACTAGCCAATG 58.978 47.619 11.63 0.00 45.94 2.82
2216 6195 2.431954 AGCTTCATGCACTAGCCAAT 57.568 45.000 11.63 0.00 45.94 3.16
2249 6228 2.548547 GGCAAGGGGGAAGGGAAGT 61.549 63.158 0.00 0.00 0.00 3.01
2431 6410 2.854187 GAAGGACGAAGAAGCGGGGG 62.854 65.000 0.00 0.00 35.12 5.40
2432 6411 1.448013 GAAGGACGAAGAAGCGGGG 60.448 63.158 0.00 0.00 35.12 5.73
2433 6412 0.037232 AAGAAGGACGAAGAAGCGGG 60.037 55.000 0.00 0.00 35.12 6.13
2434 6413 1.336887 TGAAGAAGGACGAAGAAGCGG 60.337 52.381 0.00 0.00 35.12 5.52
2504 6483 3.955771 AATATACCGCGCGAACATTTT 57.044 38.095 34.63 17.83 0.00 1.82
2528 6507 7.469343 AGGGATAACCATACAATGCATAATGA 58.531 34.615 14.85 0.00 43.89 2.57
2725 6704 5.098211 GCCAATCGAAGAATTTTGAGGAAG 58.902 41.667 0.00 0.00 43.58 3.46
3044 7048 8.085909 TCGAATCTAAGAATGAACAACACAGTA 58.914 33.333 0.00 0.00 0.00 2.74
3106 7110 2.751806 CAGGAAGCCTTTCATCAGTTCC 59.248 50.000 0.00 0.00 34.90 3.62
3222 7227 6.515832 TCGCATAGCAAAGAGAGAATCAATA 58.484 36.000 0.00 0.00 37.82 1.90
3267 7272 1.900498 GGAACTTGGCAGCTGCAGT 60.900 57.895 37.63 29.61 44.36 4.40
3276 7281 3.554934 TGATGGATGTATGGAACTTGGC 58.445 45.455 0.00 0.00 0.00 4.52
3326 7331 7.123547 AGTCTGTAGCTTGCTAATAGAAGTTCT 59.876 37.037 10.87 10.87 0.00 3.01
3589 7596 1.135199 CACACAGCCTCAATTGCATCC 60.135 52.381 0.00 0.00 0.00 3.51
3701 7708 0.954452 CCCACAGGCTTGAACTTCAC 59.046 55.000 1.40 0.00 0.00 3.18
3702 7709 0.843309 TCCCACAGGCTTGAACTTCA 59.157 50.000 1.40 0.00 0.00 3.02
3753 7760 2.176889 TGTCCCTACAGGCTTGTACTC 58.823 52.381 4.29 0.00 38.76 2.59
3767 7774 3.767673 TGAAGCGATACTAAACTGTCCCT 59.232 43.478 0.00 0.00 0.00 4.20
3781 7788 3.868077 GCTGAAGTACAATCTGAAGCGAT 59.132 43.478 0.00 0.00 0.00 4.58
3809 7816 5.700373 CCAAATTTCCGGATTTTGTTGTGAT 59.300 36.000 26.29 1.23 30.36 3.06
3811 7818 4.319405 GCCAAATTTCCGGATTTTGTTGTG 60.319 41.667 26.29 17.48 30.36 3.33
3812 7819 3.812609 GCCAAATTTCCGGATTTTGTTGT 59.187 39.130 26.29 2.64 30.36 3.32
3909 7919 1.888215 ACTCTGTCACAATGTGCCAG 58.112 50.000 17.27 17.27 40.33 4.85
3947 7957 5.497474 AGAATTAATCAGTTACGCCCAGTT 58.503 37.500 0.00 0.00 0.00 3.16
4088 8104 3.233507 AGGTTGAAATGCAGGACAATGT 58.766 40.909 0.00 0.00 0.00 2.71
4095 8111 1.273327 GGTTGGAGGTTGAAATGCAGG 59.727 52.381 0.00 0.00 0.00 4.85
4121 8137 4.319766 CGGCAGTGGCTTCAATGTATTATC 60.320 45.833 15.48 0.00 38.57 1.75
4142 8318 9.594038 GTTATTAATATTGTGAACATAGCACGG 57.406 33.333 0.00 0.00 39.07 4.94
4151 8327 7.558444 TGGGACCTGGTTATTAATATTGTGAAC 59.442 37.037 0.00 0.00 0.00 3.18
4168 8344 1.354368 ACATGGTAGTTTGGGACCTGG 59.646 52.381 0.00 0.00 36.62 4.45
4196 8380 6.894828 ACTGTGTCGTAACATAATTTTGACC 58.105 36.000 2.69 0.00 37.81 4.02
4212 8396 4.377431 GGCAGATTTTGAGTTACTGTGTCG 60.377 45.833 0.00 0.00 0.00 4.35
4214 8398 3.498397 CGGCAGATTTTGAGTTACTGTGT 59.502 43.478 0.00 0.00 0.00 3.72
4215 8399 3.667960 GCGGCAGATTTTGAGTTACTGTG 60.668 47.826 0.00 0.00 0.00 3.66
4235 8469 5.403897 AATATTGACATTTAGTGACGGCG 57.596 39.130 4.80 4.80 0.00 6.46
4316 8613 4.335416 GGCTGCATGTACATTATGGGTAT 58.665 43.478 5.37 0.00 0.00 2.73
4366 8663 8.472683 TTTCAAAACACTTGTCATGGTTTTAG 57.527 30.769 7.60 4.51 40.38 1.85
4368 8665 7.920160 ATTTCAAAACACTTGTCATGGTTTT 57.080 28.000 0.00 0.00 42.36 2.43
4369 8666 8.257306 ACTATTTCAAAACACTTGTCATGGTTT 58.743 29.630 0.00 0.00 37.45 3.27
4370 8667 7.781056 ACTATTTCAAAACACTTGTCATGGTT 58.219 30.769 0.00 0.00 0.00 3.67
4371 8668 7.346751 ACTATTTCAAAACACTTGTCATGGT 57.653 32.000 0.00 0.00 0.00 3.55
4374 8671 9.120538 ACTGTACTATTTCAAAACACTTGTCAT 57.879 29.630 0.00 0.00 0.00 3.06
4376 8673 9.859692 GTACTGTACTATTTCAAAACACTTGTC 57.140 33.333 10.64 0.00 0.00 3.18
4377 8674 9.609346 AGTACTGTACTATTTCAAAACACTTGT 57.391 29.630 18.42 0.00 37.23 3.16
4393 8690 9.772973 CTTGAGATCATCTACTAGTACTGTACT 57.227 37.037 22.72 22.72 42.68 2.73
4394 8691 9.767228 TCTTGAGATCATCTACTAGTACTGTAC 57.233 37.037 9.93 9.93 0.00 2.90
4453 8794 2.912956 GGGGATTGGCTGAGTGGATATA 59.087 50.000 0.00 0.00 0.00 0.86
4476 8817 1.165270 GGAGTGAAATGGGTTCGTGG 58.835 55.000 0.00 0.00 39.30 4.94
4495 8836 2.562298 TGCCCTCATACTTTGCAAAAGG 59.438 45.455 16.72 16.72 0.00 3.11
4526 8867 3.369471 GGTAGAGTTGTTGCTGCCTATGA 60.369 47.826 0.00 0.00 34.52 2.15
4614 8962 2.029020 CGCATCATTGGGTAGCTAGCTA 60.029 50.000 20.67 20.67 0.00 3.32
4615 8963 1.270518 CGCATCATTGGGTAGCTAGCT 60.271 52.381 23.12 23.12 0.00 3.32
4616 8964 1.151668 CGCATCATTGGGTAGCTAGC 58.848 55.000 14.67 14.67 0.00 3.42
4617 8965 1.800805 CCGCATCATTGGGTAGCTAG 58.199 55.000 0.00 0.00 34.12 3.42


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

AutoCloner maintained by Alex Coulton.