Multiple sequence alignment - TraesCS2A01G559300

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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 TraesCS2A01G559300 chr2A 100.000 4014 0 0 1 4014 762294398 762290385 0.000000e+00 7413
1 TraesCS2A01G559300 chr2A 92.893 197 13 1 395 590 762298775 762298971 6.570000e-73 285
2 TraesCS2A01G559300 chr2D 93.320 2425 134 16 1601 4014 637650592 637652999 0.000000e+00 3555
3 TraesCS2A01G559300 chr2D 89.041 730 46 21 887 1601 637649854 637650564 0.000000e+00 874
4 TraesCS2A01G559300 chr2D 85.606 264 8 7 590 837 637649162 637649411 2.400000e-62 250
5 TraesCS2A01G559300 chr2D 81.111 180 28 4 1906 2084 641895648 641895822 5.410000e-29 139
6 TraesCS2A01G559300 chr2D 93.976 83 5 0 2837 2919 598020597 598020679 4.210000e-25 126
7 TraesCS2A01G559300 chr2D 92.771 83 6 0 2837 2919 598048788 598048870 1.960000e-23 121
8 TraesCS2A01G559300 chr2B 92.204 2437 161 17 1601 4014 795063468 795065898 0.000000e+00 3421
9 TraesCS2A01G559300 chr2B 82.833 1066 64 38 602 1597 795062404 795063420 0.000000e+00 845
10 TraesCS2A01G559300 chr3B 93.160 307 14 4 1 303 52929421 52929724 1.020000e-120 444
11 TraesCS2A01G559300 chr3B 92.258 310 16 5 1 306 160145676 160145981 2.220000e-117 433
12 TraesCS2A01G559300 chr3B 95.652 253 11 0 339 591 52929833 52930085 1.340000e-109 407
13 TraesCS2A01G559300 chr3B 93.651 252 11 3 339 590 160146091 160146337 4.900000e-99 372
14 TraesCS2A01G559300 chr3B 91.960 199 14 2 395 591 52924917 52924719 1.100000e-70 278
15 TraesCS2A01G559300 chr3B 91.667 192 14 2 400 590 160141659 160141469 8.550000e-67 265
16 TraesCS2A01G559300 chr3B 92.929 99 6 1 258 355 160145983 160146081 4.180000e-30 143
17 TraesCS2A01G559300 chr3B 90.909 99 5 2 258 355 52929728 52929823 3.260000e-26 130
18 TraesCS2A01G559300 chr3A 93.878 294 12 3 1 293 174282517 174282805 4.760000e-119 438
19 TraesCS2A01G559300 chr3A 93.676 253 16 0 339 591 174283126 174283378 2.930000e-101 379
20 TraesCS2A01G559300 chr3A 91.837 98 4 1 262 355 174283019 174283116 2.520000e-27 134
21 TraesCS2A01G559300 chr7B 79.439 428 59 13 186 586 571595833 571596258 3.950000e-70 276
22 TraesCS2A01G559300 chr7B 74.956 567 108 23 2467 3016 425716931 425717480 3.120000e-56 230
23 TraesCS2A01G559300 chr7B 85.047 214 32 0 2041 2254 425716448 425716661 6.750000e-53 219
24 TraesCS2A01G559300 chr7B 80.288 208 38 1 3798 4005 426113933 426114137 1.930000e-33 154
25 TraesCS2A01G559300 chr7B 94.805 77 4 0 1037 1113 425714133 425714209 1.960000e-23 121
26 TraesCS2A01G559300 chr4A 79.439 428 59 13 189 589 690101963 690101538 3.950000e-70 276
27 TraesCS2A01G559300 chr6A 79.661 413 55 14 186 571 584922998 584923408 1.840000e-68 270
28 TraesCS2A01G559300 chr7A 75.089 562 103 26 2473 3016 472196569 472197111 1.120000e-55 228
29 TraesCS2A01G559300 chr7A 84.112 214 34 0 2041 2254 472196078 472196291 1.460000e-49 207
30 TraesCS2A01G559300 chr7A 79.327 208 40 1 3798 4005 472571744 472571948 4.180000e-30 143
31 TraesCS2A01G559300 chr7A 94.805 77 4 0 1037 1113 472195029 472195105 1.960000e-23 121
32 TraesCS2A01G559300 chr7D 84.579 214 33 0 2041 2254 411307678 411307891 3.140000e-51 213
33 TraesCS2A01G559300 chr7D 74.517 569 107 27 2467 3016 411308159 411308708 3.140000e-51 213
34 TraesCS2A01G559300 chr7D 79.327 208 40 1 3798 4005 411609591 411609795 4.180000e-30 143
35 TraesCS2A01G559300 chr7D 94.805 77 4 0 1037 1113 411306648 411306724 1.960000e-23 121


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 TraesCS2A01G559300 chr2A 762290385 762294398 4013 True 7413.000000 7413 100.000000 1 4014 1 chr2A.!!$R1 4013
1 TraesCS2A01G559300 chr2D 637649162 637652999 3837 False 1559.666667 3555 89.322333 590 4014 3 chr2D.!!$F4 3424
2 TraesCS2A01G559300 chr2B 795062404 795065898 3494 False 2133.000000 3421 87.518500 602 4014 2 chr2B.!!$F1 3412
3 TraesCS2A01G559300 chr3B 52929421 52930085 664 False 327.000000 444 93.240333 1 591 3 chr3B.!!$F1 590
4 TraesCS2A01G559300 chr3B 160145676 160146337 661 False 316.000000 433 92.946000 1 590 3 chr3B.!!$F2 589
5 TraesCS2A01G559300 chr3A 174282517 174283378 861 False 317.000000 438 93.130333 1 591 3 chr3A.!!$F1 590

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
393 670 0.983378 AGTATCCAAAGAGGCCCGCT 60.983 55.0 0.00 0.0 37.29 5.52 F
1284 1992 0.545646 AGGAGCAGGAGGAGCAATTC 59.454 55.0 0.00 0.0 0.00 2.17 F
1539 2280 0.183014 TTTTGCACCTGTAACCGGGA 59.817 50.0 6.32 0.0 39.78 5.14 F
1859 2645 0.249120 TGAACATCGTGCTCGGGAAT 59.751 50.0 8.49 0.0 37.69 3.01 F
2956 3745 0.034896 GGAGCCAAGGAACGAACTCA 59.965 55.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1380 2102 0.178944 TCCCAGTCCAACGAAGAGGA 60.179 55.000 0.0 0.0 33.50 3.71 R
2777 3566 0.040067 GCAACAGCAACCTACAGCAC 60.040 55.000 0.0 0.0 0.00 4.40 R
2779 3568 0.239347 CTGCAACAGCAACCTACAGC 59.761 55.000 0.0 0.0 37.91 4.40 R
2959 3748 0.250513 GCATCTCCACCCGACTTCTT 59.749 55.000 0.0 0.0 0.00 2.52 R
3900 4717 1.614903 TGGGCGAAAACTTCTCTCGTA 59.385 47.619 0.0 0.0 35.06 3.43 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
42 43 1.764723 CAGGGATCACTATGCCACTGA 59.235 52.381 0.00 0.00 45.78 3.41
43 44 2.171237 CAGGGATCACTATGCCACTGAA 59.829 50.000 0.00 0.00 45.78 3.02
71 72 1.081892 CACAACCAGCCTCTGATTCG 58.918 55.000 0.00 0.00 32.44 3.34
86 87 5.592054 TCTGATTCGAGTGTTCATACCATC 58.408 41.667 0.00 0.00 0.00 3.51
240 241 2.202690 CCGCCTGATTACGACGCA 60.203 61.111 0.00 0.00 0.00 5.24
266 295 3.255379 GGAAGACATCGCCGTCGC 61.255 66.667 0.00 0.00 40.98 5.19
267 296 3.255379 GAAGACATCGCCGTCGCC 61.255 66.667 0.00 0.00 40.98 5.54
355 632 2.551938 GCTGAAGCTCTGTTCTTTCCCT 60.552 50.000 0.00 0.00 38.21 4.20
393 670 0.983378 AGTATCCAAAGAGGCCCGCT 60.983 55.000 0.00 0.00 37.29 5.52
400 677 2.456287 AAAGAGGCCCGCTGTCAGTC 62.456 60.000 0.00 0.00 0.00 3.51
429 706 2.744166 GCGTCCAGTTAACCCTAATCCC 60.744 54.545 0.88 0.00 0.00 3.85
437 714 1.921869 AACCCTAATCCCAGCCACGG 61.922 60.000 0.00 0.00 0.00 4.94
486 763 1.819753 AGCACTAATGGGCTGGGATA 58.180 50.000 0.00 0.00 39.30 2.59
491 768 2.856231 ACTAATGGGCTGGGATAAACCA 59.144 45.455 0.00 0.00 41.20 3.67
536 813 5.494724 TGATTTCAGGGATTCTCAGTTCAG 58.505 41.667 0.00 0.00 0.00 3.02
554 831 3.754965 TCAGGGTTTGATTCAGACTTGG 58.245 45.455 7.22 0.00 0.00 3.61
600 877 9.642327 TTTTAGACTTTTCCCTAACAAAAACAC 57.358 29.630 0.00 0.00 0.00 3.32
601 878 6.216801 AGACTTTTCCCTAACAAAAACACC 57.783 37.500 0.00 0.00 0.00 4.16
678 962 9.513727 GTAAAGGTAGTAGGAGAAAAGTATTCG 57.486 37.037 0.00 0.00 0.00 3.34
789 1091 4.416738 GCGGCAGCTTCCTCCCTT 62.417 66.667 0.00 0.00 41.01 3.95
792 1094 2.273776 GCAGCTTCCTCCCTTCCC 59.726 66.667 0.00 0.00 0.00 3.97
794 1096 1.617839 CAGCTTCCTCCCTTCCCCT 60.618 63.158 0.00 0.00 0.00 4.79
795 1097 1.164541 AGCTTCCTCCCTTCCCCTT 59.835 57.895 0.00 0.00 0.00 3.95
851 1162 1.668151 GACGCGGCCTTCTTCTTGT 60.668 57.895 12.47 0.00 0.00 3.16
864 1175 2.112691 TCTTCTTGTCTTCCTCTCCCCT 59.887 50.000 0.00 0.00 0.00 4.79
865 1176 2.723530 TCTTGTCTTCCTCTCCCCTT 57.276 50.000 0.00 0.00 0.00 3.95
925 1620 4.203076 AGCTACTAACCGCGGCCG 62.203 66.667 28.58 24.05 0.00 6.13
1250 1957 2.679837 CTGATTTGGTGCTAATGCGAGT 59.320 45.455 0.00 0.00 43.34 4.18
1284 1992 0.545646 AGGAGCAGGAGGAGCAATTC 59.454 55.000 0.00 0.00 0.00 2.17
1366 2074 6.586844 GCGGTTTCCATAGATTCATACTACTC 59.413 42.308 0.00 0.00 0.00 2.59
1374 2096 7.816995 CCATAGATTCATACTACTCCAAGAAGC 59.183 40.741 0.00 0.00 0.00 3.86
1380 2102 1.276421 ACTACTCCAAGAAGCGCACAT 59.724 47.619 11.47 0.00 0.00 3.21
1381 2103 1.929836 CTACTCCAAGAAGCGCACATC 59.070 52.381 11.47 4.78 0.00 3.06
1382 2104 0.674895 ACTCCAAGAAGCGCACATCC 60.675 55.000 11.47 0.00 0.00 3.51
1383 2105 0.392193 CTCCAAGAAGCGCACATCCT 60.392 55.000 11.47 0.00 0.00 3.24
1384 2106 0.391661 TCCAAGAAGCGCACATCCTC 60.392 55.000 11.47 0.00 0.00 3.71
1393 2115 0.389817 CGCACATCCTCTTCGTTGGA 60.390 55.000 0.00 0.00 36.72 3.53
1419 2141 4.039092 TGCCTCCTTCAGCAGCCC 62.039 66.667 0.00 0.00 33.08 5.19
1420 2142 4.039092 GCCTCCTTCAGCAGCCCA 62.039 66.667 0.00 0.00 0.00 5.36
1451 2173 3.820195 TGGACCTAGTGGTTCAGTCTA 57.180 47.619 0.00 0.00 46.50 2.59
1492 2215 0.533531 CAGCACTTCAGCTCACCACA 60.534 55.000 0.00 0.00 44.54 4.17
1539 2280 0.183014 TTTTGCACCTGTAACCGGGA 59.817 50.000 6.32 0.00 39.78 5.14
1547 2288 1.206371 CCTGTAACCGGGACTCGATTT 59.794 52.381 6.32 0.00 39.78 2.17
1576 2317 0.587768 TTACAGCGTCGTGTTCTCGA 59.412 50.000 5.92 0.00 37.51 4.04
1618 2403 8.567285 ACTATTAAGAACAATGACCTCCTTTG 57.433 34.615 0.00 0.00 36.37 2.77
1619 2404 8.164070 ACTATTAAGAACAATGACCTCCTTTGT 58.836 33.333 0.00 0.00 42.68 2.83
1641 2426 2.796593 GGAGAGCAATGTGTTTGTTTGC 59.203 45.455 0.00 0.00 44.67 3.68
1649 2434 5.163933 GCAATGTGTTTGTTTGCTGATATGG 60.164 40.000 0.00 0.00 41.86 2.74
1659 2444 3.882102 TGCTGATATGGCATTAACCCT 57.118 42.857 4.78 0.00 34.56 4.34
1660 2445 4.183223 TGCTGATATGGCATTAACCCTT 57.817 40.909 4.78 0.00 34.56 3.95
1663 2448 5.711506 TGCTGATATGGCATTAACCCTTATG 59.288 40.000 4.78 0.00 34.56 1.90
1736 2522 4.218635 GTCCACTTCATATGCTCCTCGATA 59.781 45.833 0.00 0.00 0.00 2.92
1859 2645 0.249120 TGAACATCGTGCTCGGGAAT 59.751 50.000 8.49 0.00 37.69 3.01
1977 2763 2.223340 GCCTGCATTATTCCTGTTCACG 60.223 50.000 0.00 0.00 0.00 4.35
2024 2811 4.458989 TGCTGCCTATAACAACTTTTCTGG 59.541 41.667 0.00 0.00 0.00 3.86
2113 2900 0.460311 CTTCGCTGGTCCCGATAGTT 59.540 55.000 0.00 0.00 34.35 2.24
2122 2909 2.799282 TCCCGATAGTTGGGGGAATA 57.201 50.000 2.45 0.00 46.81 1.75
2125 2912 2.709397 CCCGATAGTTGGGGGAATACTT 59.291 50.000 0.00 0.00 44.10 2.24
2146 2933 2.902486 TCTGACCTCAATGACAGAGCTT 59.098 45.455 0.00 0.00 35.01 3.74
2149 2936 3.834813 TGACCTCAATGACAGAGCTTAGT 59.165 43.478 0.00 0.00 0.00 2.24
2156 2943 5.177511 TCAATGACAGAGCTTAGTTTCAACG 59.822 40.000 0.00 0.00 0.00 4.10
2161 2948 5.807344 ACAGAGCTTAGTTTCAACGTTTTC 58.193 37.500 0.00 0.00 0.00 2.29
2273 3060 2.071540 ACATGCTCATCTCGTTGTGTG 58.928 47.619 0.00 0.00 0.00 3.82
2310 3097 2.153645 CAACTGCTGTTGTCTGGCATA 58.846 47.619 23.89 0.00 46.08 3.14
2316 3103 2.936498 GCTGTTGTCTGGCATACGTAAT 59.064 45.455 0.00 0.00 0.00 1.89
2321 3108 7.067532 TGTTGTCTGGCATACGTAATTTTAG 57.932 36.000 0.00 0.00 0.00 1.85
2364 3151 9.458374 TCTTCCGAAAATGATTAGTTGTTTTTC 57.542 29.630 0.00 0.00 34.51 2.29
2365 3152 9.243637 CTTCCGAAAATGATTAGTTGTTTTTCA 57.756 29.630 0.00 0.00 36.54 2.69
2379 3167 7.931275 AGTTGTTTTTCAAGTTAGAGGATCAC 58.069 34.615 0.00 0.00 36.41 3.06
2412 3201 7.221450 AGTTCTTAATGTAGTGTTACTGCCAA 58.779 34.615 0.00 0.00 29.18 4.52
2421 3210 3.118408 AGTGTTACTGCCAAGTTCAGTCA 60.118 43.478 0.74 0.00 43.13 3.41
2438 3227 4.040339 TCAGTCATGTAAGTTCTTGCCTCA 59.960 41.667 0.00 0.00 0.00 3.86
2442 3231 4.284490 TCATGTAAGTTCTTGCCTCAGTCT 59.716 41.667 0.00 0.00 0.00 3.24
2586 3375 3.490419 GGTTCTACACACACGACTCTGTT 60.490 47.826 0.00 0.00 0.00 3.16
2655 3444 4.718774 TGCCTCAACTTCTCCATCTTCTAT 59.281 41.667 0.00 0.00 0.00 1.98
2714 3503 3.818773 GCTGGCAACCTTAAAGTAAGACA 59.181 43.478 0.00 0.00 38.02 3.41
2718 3507 6.744112 TGGCAACCTTAAAGTAAGACAATTG 58.256 36.000 3.24 3.24 38.02 2.32
2732 3521 8.982723 AGTAAGACAATTGTGGACTATCTATGT 58.017 33.333 17.58 0.00 0.00 2.29
2753 3542 5.755849 TGTTTTCTTCCCTCAAGTTTCTCT 58.244 37.500 0.00 0.00 33.27 3.10
2758 3547 4.040952 TCTTCCCTCAAGTTTCTCTTCTGG 59.959 45.833 0.00 0.00 33.63 3.86
2764 3553 6.464465 CCCTCAAGTTTCTCTTCTGGTTCTAA 60.464 42.308 0.00 0.00 33.63 2.10
2768 3557 7.282450 TCAAGTTTCTCTTCTGGTTCTAAAACC 59.718 37.037 0.29 0.29 43.70 3.27
2851 3640 3.057736 CGATCTCCCCAATGAATGCAATC 60.058 47.826 0.00 0.00 0.00 2.67
2956 3745 0.034896 GGAGCCAAGGAACGAACTCA 59.965 55.000 0.00 0.00 0.00 3.41
2959 3748 0.534203 GCCAAGGAACGAACTCACCA 60.534 55.000 0.00 0.00 0.00 4.17
3078 3867 3.666274 TGACGGTACATTACAGTTTGGG 58.334 45.455 0.00 0.00 37.22 4.12
3141 3930 2.427095 GGGCAACACTTTCTTGTGAAGT 59.573 45.455 1.47 0.00 40.12 3.01
3192 3983 5.364446 TGAGGGTTTGTTCAGTCACTAGTTA 59.636 40.000 0.00 0.00 0.00 2.24
3225 4016 9.556030 GGTTGCTAGTTATCAACTTAATCAAAC 57.444 33.333 9.79 0.00 42.81 2.93
3379 4192 1.338960 TGGCGCATTGTCTCTGATTGA 60.339 47.619 10.83 0.00 0.00 2.57
3434 4247 5.288472 GCCACTTCCAAAATTTAGTTATGCG 59.712 40.000 0.00 0.00 0.00 4.73
3544 4359 6.433093 GGTACATGTATTTTGGACCTCACTTT 59.567 38.462 9.18 0.00 43.64 2.66
3600 4416 9.431887 TCTGGATAACTTTACAAGTGAATACAC 57.568 33.333 0.00 0.00 41.91 2.90
3611 4427 2.365582 GTGAATACACACACCCATCCC 58.634 52.381 0.00 0.00 45.32 3.85
3632 4448 4.082300 CCCATGTACACTGCTTGCAAAATA 60.082 41.667 0.00 0.00 0.00 1.40
3640 4456 5.922544 ACACTGCTTGCAAAATAGCTAAAAG 59.077 36.000 9.40 1.46 38.22 2.27
3758 4575 0.249741 AAGTTACAGTTGCCGCGAGT 60.250 50.000 8.23 0.00 0.00 4.18
3900 4717 0.737715 GCGACTCATTCTTCGGCACT 60.738 55.000 0.00 0.00 35.73 4.40
3948 4765 3.084039 CAGTTGCTTGTCCCATGTGTAT 58.916 45.455 0.00 0.00 0.00 2.29
4008 4825 3.139077 GTTTTGTTCATCGACTCCCACT 58.861 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.268869 TAGTGATCCCTGCTCCCCAT 59.731 55.000 0.00 0.00 0.00 4.00
56 57 0.534412 CACTCGAATCAGAGGCTGGT 59.466 55.000 0.00 0.00 42.31 4.00
71 72 6.115446 TCCATTTCTGATGGTATGAACACTC 58.885 40.000 5.07 0.00 40.06 3.51
86 87 3.686726 CCTCGTCCTTCTTTCCATTTCTG 59.313 47.826 0.00 0.00 0.00 3.02
178 179 4.090057 GTCGCCCGTGCAAGAAGC 62.090 66.667 0.00 2.80 45.96 3.86
240 241 1.038130 CGATGTCTTCCTCCTCCCGT 61.038 60.000 0.00 0.00 0.00 5.28
378 655 3.249189 ACAGCGGGCCTCTTTGGA 61.249 61.111 0.84 0.00 38.35 3.53
393 670 2.178273 CGCGACGATGGACTGACA 59.822 61.111 0.00 0.00 0.00 3.58
400 677 0.457166 TTAACTGGACGCGACGATGG 60.457 55.000 15.93 0.00 0.00 3.51
429 706 3.818787 GGATTGCTGCCGTGGCTG 61.819 66.667 12.84 12.86 42.51 4.85
437 714 4.133796 GGGCGTTGGGATTGCTGC 62.134 66.667 0.00 0.00 0.00 5.25
486 763 4.343814 CCCTGTGTTTGTTAATCCTGGTTT 59.656 41.667 0.00 0.00 0.00 3.27
491 768 4.447138 TCACCCTGTGTTTGTTAATCCT 57.553 40.909 0.00 0.00 34.79 3.24
536 813 4.021102 TCTCCAAGTCTGAATCAAACCC 57.979 45.455 0.00 0.00 0.00 4.11
678 962 6.093633 GGGTTGATTGAAAGATACAGTACCAC 59.906 42.308 0.00 0.00 0.00 4.16
789 1091 2.003247 AGGAGAGAGTAGGAAGGGGA 57.997 55.000 0.00 0.00 0.00 4.81
792 1094 3.720002 AGGAGTAGGAGAGAGTAGGAAGG 59.280 52.174 0.00 0.00 0.00 3.46
794 1096 4.166531 GGAAGGAGTAGGAGAGAGTAGGAA 59.833 50.000 0.00 0.00 0.00 3.36
795 1097 3.717913 GGAAGGAGTAGGAGAGAGTAGGA 59.282 52.174 0.00 0.00 0.00 2.94
851 1162 1.396594 GGGGAAGGGGAGAGGAAGA 59.603 63.158 0.00 0.00 0.00 2.87
996 1694 3.532155 GCGGCCGACTCCATCTCT 61.532 66.667 33.48 0.00 0.00 3.10
997 1695 4.593864 GGCGGCCGACTCCATCTC 62.594 72.222 33.48 7.28 0.00 2.75
1038 1736 3.984193 GAGGATGGCAAGCACGGCT 62.984 63.158 0.00 0.00 42.56 5.52
1047 1745 2.605607 CCACCACTGGAGGATGGCA 61.606 63.158 5.62 0.00 40.55 4.92
1250 1957 4.263572 CCTTGTGGGTGTGGCCGA 62.264 66.667 0.00 0.00 38.44 5.54
1329 2037 0.889186 GAAACCGCAGAAAGGGAGCA 60.889 55.000 0.00 0.00 0.00 4.26
1330 2038 1.587043 GGAAACCGCAGAAAGGGAGC 61.587 60.000 0.00 0.00 0.00 4.70
1366 2074 0.392193 AGAGGATGTGCGCTTCTTGG 60.392 55.000 9.73 0.00 0.00 3.61
1374 2096 0.389817 TCCAACGAAGAGGATGTGCG 60.390 55.000 0.00 0.00 31.30 5.34
1380 2102 0.178944 TCCCAGTCCAACGAAGAGGA 60.179 55.000 0.00 0.00 33.50 3.71
1381 2103 0.247736 CTCCCAGTCCAACGAAGAGG 59.752 60.000 0.00 0.00 0.00 3.69
1382 2104 0.390472 GCTCCCAGTCCAACGAAGAG 60.390 60.000 0.00 0.00 0.00 2.85
1383 2105 0.832135 AGCTCCCAGTCCAACGAAGA 60.832 55.000 0.00 0.00 0.00 2.87
1384 2106 0.671781 CAGCTCCCAGTCCAACGAAG 60.672 60.000 0.00 0.00 0.00 3.79
1393 2115 2.204059 AAGGAGGCAGCTCCCAGT 60.204 61.111 0.00 0.00 44.37 4.00
1408 2130 0.680280 AATGAGCTGGGCTGCTGAAG 60.680 55.000 9.95 0.00 44.17 3.02
1409 2131 0.679002 GAATGAGCTGGGCTGCTGAA 60.679 55.000 9.95 0.14 44.17 3.02
1410 2132 1.077930 GAATGAGCTGGGCTGCTGA 60.078 57.895 9.95 2.77 44.17 4.26
1411 2133 1.378119 TGAATGAGCTGGGCTGCTG 60.378 57.895 9.95 0.00 44.17 4.41
1413 2135 1.378250 AGTGAATGAGCTGGGCTGC 60.378 57.895 0.00 0.00 39.88 5.25
1414 2136 1.030488 CCAGTGAATGAGCTGGGCTG 61.030 60.000 0.00 0.00 46.27 4.85
1415 2137 1.302285 CCAGTGAATGAGCTGGGCT 59.698 57.895 0.00 0.00 46.27 5.19
1416 2138 3.915575 CCAGTGAATGAGCTGGGC 58.084 61.111 0.00 0.00 46.27 5.36
1419 2141 2.499289 ACTAGGTCCAGTGAATGAGCTG 59.501 50.000 9.12 0.00 39.49 4.24
1420 2142 2.826488 ACTAGGTCCAGTGAATGAGCT 58.174 47.619 5.19 5.19 41.76 4.09
1451 2173 5.147032 TGAAGGGGACAACATCTCAAAATT 58.853 37.500 0.00 0.00 0.00 1.82
1492 2215 8.492415 TTGCTACTAAGGATTACATACAGGAT 57.508 34.615 0.00 0.00 0.00 3.24
1515 2249 3.049206 CGGTTACAGGTGCAAAACATTG 58.951 45.455 0.00 0.00 0.00 2.82
1539 2280 4.385825 TGTAAACCAAGAGCAAATCGAGT 58.614 39.130 0.00 0.00 0.00 4.18
1547 2288 1.508632 GACGCTGTAAACCAAGAGCA 58.491 50.000 0.00 0.00 35.57 4.26
1576 2317 5.560966 AATAGTTCATTCCATTTTCGCGT 57.439 34.783 5.77 0.00 0.00 6.01
1618 2403 3.715628 AACAAACACATTGCTCTCCAC 57.284 42.857 0.00 0.00 43.13 4.02
1619 2404 3.737663 GCAAACAAACACATTGCTCTCCA 60.738 43.478 2.69 0.00 44.54 3.86
1641 2426 7.765695 AACATAAGGGTTAATGCCATATCAG 57.234 36.000 0.00 0.00 0.00 2.90
1649 2434 6.531594 GCAGAAGAAAACATAAGGGTTAATGC 59.468 38.462 0.00 0.00 0.00 3.56
1736 2522 3.135056 GATCGCGACGTAAGCCCCT 62.135 63.158 12.93 0.00 45.62 4.79
1930 2716 0.973632 AGCACAGAATGACGGTACCA 59.026 50.000 13.54 0.00 39.69 3.25
1931 2717 1.204941 AGAGCACAGAATGACGGTACC 59.795 52.381 0.16 0.16 39.69 3.34
1977 2763 3.743396 CACCACAACTCTACTGCTTCTTC 59.257 47.826 0.00 0.00 0.00 2.87
2024 2811 1.349627 CTGCATCACACGGAATCGC 59.650 57.895 0.00 0.00 40.63 4.58
2119 2906 6.611613 TCTGTCATTGAGGTCAGAAGTATT 57.388 37.500 3.65 0.00 34.61 1.89
2122 2909 3.306641 GCTCTGTCATTGAGGTCAGAAGT 60.307 47.826 6.84 0.00 36.67 3.01
2125 2912 2.533916 AGCTCTGTCATTGAGGTCAGA 58.466 47.619 5.61 5.61 37.70 3.27
2146 2933 5.122082 ACAGAAACCGAAAACGTTGAAACTA 59.878 36.000 0.00 0.00 0.00 2.24
2149 2936 4.159857 CACAGAAACCGAAAACGTTGAAA 58.840 39.130 0.00 0.00 0.00 2.69
2156 2943 1.477105 GCAGCACAGAAACCGAAAAC 58.523 50.000 0.00 0.00 0.00 2.43
2161 2948 1.210931 CATGGCAGCACAGAAACCG 59.789 57.895 0.00 0.00 0.00 4.44
2191 2978 1.593209 GGTCTTTGTCGACGTGGCA 60.593 57.895 11.62 0.00 34.75 4.92
2200 2987 2.746362 CTCTGCCAAGATGGTCTTTGTC 59.254 50.000 0.00 0.00 40.46 3.18
2296 3083 5.545658 AAATTACGTATGCCAGACAACAG 57.454 39.130 0.00 0.00 0.00 3.16
2353 3140 9.052759 GTGATCCTCTAACTTGAAAAACAACTA 57.947 33.333 0.00 0.00 34.56 2.24
2364 3151 9.442047 AACTAAATCTTGTGATCCTCTAACTTG 57.558 33.333 0.00 0.00 31.51 3.16
2365 3152 9.660180 GAACTAAATCTTGTGATCCTCTAACTT 57.340 33.333 0.00 0.00 31.51 2.66
2395 3183 4.968259 TGAACTTGGCAGTAACACTACAT 58.032 39.130 0.00 0.00 30.68 2.29
2403 3191 4.085357 ACATGACTGAACTTGGCAGTAA 57.915 40.909 0.00 0.00 45.94 2.24
2407 3195 4.085357 ACTTACATGACTGAACTTGGCA 57.915 40.909 0.00 0.00 0.00 4.92
2409 3198 6.662616 CAAGAACTTACATGACTGAACTTGG 58.337 40.000 0.00 0.00 0.00 3.61
2412 3201 4.757149 GGCAAGAACTTACATGACTGAACT 59.243 41.667 0.00 0.00 0.00 3.01
2421 3210 4.284490 TCAGACTGAGGCAAGAACTTACAT 59.716 41.667 0.00 0.00 0.00 2.29
2468 3257 5.479306 AGTACACTGTGTTAATGCTGTAGG 58.521 41.667 19.73 0.00 0.00 3.18
2544 3333 1.227176 GTCGATTACGCCACCTCCC 60.227 63.158 0.00 0.00 39.58 4.30
2586 3375 9.109393 CCTAGGATGATAATCAACGAAGAAAAA 57.891 33.333 1.05 0.00 0.00 1.94
2596 3385 4.533707 CCCTGAGCCTAGGATGATAATCAA 59.466 45.833 14.75 0.00 40.42 2.57
2655 3444 1.819928 CGGTGGTTGAATGGATCACA 58.180 50.000 0.00 0.00 37.92 3.58
2714 3503 9.178758 GGAAGAAAACATAGATAGTCCACAATT 57.821 33.333 0.00 0.00 0.00 2.32
2718 3507 6.890293 AGGGAAGAAAACATAGATAGTCCAC 58.110 40.000 0.00 0.00 0.00 4.02
2732 3521 6.543831 CAGAAGAGAAACTTGAGGGAAGAAAA 59.456 38.462 0.00 0.00 39.13 2.29
2771 3560 1.881973 AGCAACCTACAGCACAATGTG 59.118 47.619 9.36 9.36 34.56 3.21
2777 3566 0.040067 GCAACAGCAACCTACAGCAC 60.040 55.000 0.00 0.00 0.00 4.40
2778 3567 0.465278 TGCAACAGCAACCTACAGCA 60.465 50.000 0.00 0.00 34.85 4.41
2779 3568 0.239347 CTGCAACAGCAACCTACAGC 59.761 55.000 0.00 0.00 37.91 4.40
2800 3589 3.434739 GGAAGATCAGCCATGAGACCAAT 60.435 47.826 0.00 0.00 39.29 3.16
2935 3724 1.674651 GTTCGTTCCTTGGCTCCCC 60.675 63.158 0.00 0.00 0.00 4.81
2956 3745 0.471211 TCTCCACCCGACTTCTTGGT 60.471 55.000 0.00 0.00 0.00 3.67
2959 3748 0.250513 GCATCTCCACCCGACTTCTT 59.749 55.000 0.00 0.00 0.00 2.52
3078 3867 2.344950 CCTCAACTCAGCATCTGTGTC 58.655 52.381 2.58 0.00 37.24 3.67
3141 3930 3.949132 TGCCTGAGTACAACATATGCAA 58.051 40.909 1.58 0.00 0.00 4.08
3242 4033 2.105477 AGAAGCACCATCCTAATCGCAT 59.895 45.455 0.00 0.00 0.00 4.73
3333 4128 1.859383 TTCGATGCAAACACGACTCA 58.141 45.000 0.00 0.00 35.82 3.41
3386 4199 7.110810 GCTTAACCTTTATGTTCCTAAGTCCT 58.889 38.462 0.00 0.00 0.00 3.85
3544 4359 4.290942 TCTTTTAGGCAAACTTTTGGGGA 58.709 39.130 3.95 0.00 38.57 4.81
3600 4416 1.281867 AGTGTACATGGGATGGGTGTG 59.718 52.381 0.00 0.00 33.60 3.82
3611 4427 4.560035 GCTATTTTGCAAGCAGTGTACATG 59.440 41.667 0.00 0.00 38.63 3.21
3649 4466 2.128035 CGCCGTTATGGAGTTCATCTC 58.872 52.381 0.00 0.00 42.00 2.75
3758 4575 4.853468 TCAGGGACCTGTAAATATTGCA 57.147 40.909 17.34 0.00 43.96 4.08
3900 4717 1.614903 TGGGCGAAAACTTCTCTCGTA 59.385 47.619 0.00 0.00 35.06 3.43
3948 4765 3.732212 CATCATCGATTACCTGAGGCAA 58.268 45.455 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.