Multiple sequence alignment - TraesCS2B01G067000

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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 TraesCS2B01G067000 chr2B 100.000 4451 0 0 1 4451 33842985 33838535 0.000000e+00 8220
1 TraesCS2B01G067000 chr2D 91.912 3771 218 34 1 3714 20771893 20768153 0.000000e+00 5193
2 TraesCS2B01G067000 chr2D 91.565 2632 208 6 736 3358 20634440 20631814 0.000000e+00 3618
3 TraesCS2B01G067000 chr2D 88.427 2696 289 14 807 3487 20608081 20605394 0.000000e+00 3229
4 TraesCS2B01G067000 chr2D 84.952 3110 360 42 354 3452 20427797 20424785 0.000000e+00 3051
5 TraesCS2B01G067000 chr2D 78.520 419 73 13 3215 3623 20615957 20615546 4.420000e-65 259
6 TraesCS2B01G067000 chr2D 95.876 97 3 1 124 219 20616340 20616244 5.960000e-34 156
7 TraesCS2B01G067000 chr2D 81.457 151 23 5 3920 4070 20424447 20424302 7.820000e-23 119
8 TraesCS2B01G067000 chr2D 89.247 93 9 1 127 219 20635303 20635212 1.010000e-21 115
9 TraesCS2B01G067000 chr2A 89.359 3665 323 26 745 4378 21255172 21251544 0.000000e+00 4545
10 TraesCS2B01G067000 chr2A 86.119 3069 369 29 807 3838 21231358 21228310 0.000000e+00 3254
11 TraesCS2B01G067000 chr2A 89.392 707 45 18 1 690 21255854 21255161 0.000000e+00 863
12 TraesCS2B01G067000 chr2A 86.822 387 40 8 761 1144 21236578 21236200 5.320000e-114 422
13 TraesCS2B01G067000 chr2A 88.506 87 7 2 133 219 21231782 21231699 7.880000e-18 102


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 TraesCS2B01G067000 chr2B 33838535 33842985 4450 True 8220.0 8220 100.0000 1 4451 1 chr2B.!!$R1 4450
1 TraesCS2B01G067000 chr2D 20768153 20771893 3740 True 5193.0 5193 91.9120 1 3714 1 chr2D.!!$R2 3713
2 TraesCS2B01G067000 chr2D 20605394 20608081 2687 True 3229.0 3229 88.4270 807 3487 1 chr2D.!!$R1 2680
3 TraesCS2B01G067000 chr2D 20631814 20635303 3489 True 1866.5 3618 90.4060 127 3358 2 chr2D.!!$R5 3231
4 TraesCS2B01G067000 chr2D 20424302 20427797 3495 True 1585.0 3051 83.2045 354 4070 2 chr2D.!!$R3 3716
5 TraesCS2B01G067000 chr2D 20615546 20616340 794 True 207.5 259 87.1980 124 3623 2 chr2D.!!$R4 3499
6 TraesCS2B01G067000 chr2A 21251544 21255854 4310 True 2704.0 4545 89.3755 1 4378 2 chr2A.!!$R3 4377
7 TraesCS2B01G067000 chr2A 21228310 21231782 3472 True 1678.0 3254 87.3125 133 3838 2 chr2A.!!$R2 3705

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
885 1344 0.035739 ATTTTCCACCGTGCCGTACT 59.964 50.0 0.00 0.0 0.00 2.73 F
1360 1861 0.101399 CGATGAAGTCTGGAGTCCCG 59.899 60.0 6.74 0.0 34.29 5.14 F
1473 1974 0.399949 TCCCGGCTGATACCATCCTT 60.400 55.0 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 2287 0.319083 TGCCGAAATACACCGTCTGT 59.681 50.000 0.00 0.0 36.82 3.41 R
3264 3768 1.888436 TTGCCTCATCGTCGCCTTCT 61.888 55.000 0.00 0.0 0.00 2.85 R
3515 4334 5.227908 TGAAGCTTCGGTAGAAAACAGTAG 58.772 41.667 21.11 0.0 35.71 2.57 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 7.839680 AAAAAGGTGAAATCTGACTAACCAT 57.160 32.000 0.00 0.00 0.00 3.55
64 65 8.494016 ACTAGAAATTAAATCCGTTCTTCAGG 57.506 34.615 0.00 0.00 32.69 3.86
76 77 2.099141 TCTTCAGGAATTCAGGCGTG 57.901 50.000 7.93 0.00 0.00 5.34
238 243 6.655425 ACCAATTACAGCTTAGAAAAGGACTC 59.345 38.462 0.00 0.00 32.98 3.36
300 305 3.778075 TCCCCGTCATAGAAAAGGAATCA 59.222 43.478 0.00 0.00 0.00 2.57
308 313 6.489361 GTCATAGAAAAGGAATCAGATGCCAT 59.511 38.462 10.43 0.00 0.00 4.40
360 632 4.281898 ACCTGTTGGTGGTAGACATTAC 57.718 45.455 0.00 0.00 46.51 1.89
396 668 2.422597 CTCATTACAGTGTTTGGCCGA 58.577 47.619 0.00 0.00 0.00 5.54
439 716 6.239120 CCAAGTCAAGTCAAGTCAATGGAAAT 60.239 38.462 0.00 0.00 0.00 2.17
440 717 6.566197 AGTCAAGTCAAGTCAATGGAAATC 57.434 37.500 0.00 0.00 0.00 2.17
513 962 9.807921 TGGAACTTTTATCAGGATTTAGAGTTT 57.192 29.630 0.00 0.00 0.00 2.66
544 993 3.119101 GGAAGACGCCTTCTGTATCAAGA 60.119 47.826 11.41 0.00 46.16 3.02
559 1008 9.230122 TCTGTATCAAGAGACAAATAAATTGCA 57.770 29.630 0.00 0.00 43.13 4.08
560 1009 9.499585 CTGTATCAAGAGACAAATAAATTGCAG 57.500 33.333 0.00 0.00 43.13 4.41
616 1065 1.239347 GGAACCAGACTGGCACTTTC 58.761 55.000 21.95 16.27 42.67 2.62
621 1070 1.815003 CCAGACTGGCACTTTCCATTC 59.185 52.381 8.99 0.00 36.41 2.67
629 1078 2.307049 GCACTTTCCATTCGAAACGTG 58.693 47.619 0.00 0.66 39.74 4.49
630 1079 2.307049 CACTTTCCATTCGAAACGTGC 58.693 47.619 0.00 0.00 35.49 5.34
639 1088 1.792057 CGAAACGTGCGTTGATGGC 60.792 57.895 10.81 0.00 38.47 4.40
730 1188 6.323739 TCAGGAATACCTTTTTCTGCTTTGTT 59.676 34.615 0.00 0.00 45.36 2.83
757 1215 4.415881 TCAAGTTTAACAGTCAGCAGGA 57.584 40.909 0.00 0.00 0.00 3.86
759 1217 5.376625 TCAAGTTTAACAGTCAGCAGGAAT 58.623 37.500 0.00 0.00 0.00 3.01
780 1238 2.653726 ACCTTTCTGTGCATGACAACA 58.346 42.857 0.00 0.00 32.80 3.33
878 1337 4.397730 TCATGGACATTATTTTCCACCGTG 59.602 41.667 0.00 0.00 44.80 4.94
879 1338 2.490115 TGGACATTATTTTCCACCGTGC 59.510 45.455 0.00 0.00 36.96 5.34
880 1339 2.159296 GGACATTATTTTCCACCGTGCC 60.159 50.000 0.00 0.00 0.00 5.01
881 1340 1.470890 ACATTATTTTCCACCGTGCCG 59.529 47.619 0.00 0.00 0.00 5.69
882 1341 1.470890 CATTATTTTCCACCGTGCCGT 59.529 47.619 0.00 0.00 0.00 5.68
883 1342 2.469274 TTATTTTCCACCGTGCCGTA 57.531 45.000 0.00 0.00 0.00 4.02
884 1343 1.724429 TATTTTCCACCGTGCCGTAC 58.276 50.000 0.00 0.00 0.00 3.67
885 1344 0.035739 ATTTTCCACCGTGCCGTACT 59.964 50.000 0.00 0.00 0.00 2.73
886 1345 0.881159 TTTTCCACCGTGCCGTACTG 60.881 55.000 0.00 0.00 0.00 2.74
887 1346 1.746322 TTTCCACCGTGCCGTACTGA 61.746 55.000 0.00 0.00 0.00 3.41
888 1347 2.424705 TTCCACCGTGCCGTACTGAC 62.425 60.000 0.00 0.00 0.00 3.51
970 1448 1.020437 GGGCATAAGCTTGCTCTCAC 58.980 55.000 9.86 0.00 40.09 3.51
1013 1491 0.469705 AAAGCAATGGCACCTCACCA 60.470 50.000 0.00 0.00 44.61 4.17
1069 1550 1.318158 GGGGGTTTCATCTGCTGCTG 61.318 60.000 0.00 0.00 0.00 4.41
1070 1551 1.318158 GGGGTTTCATCTGCTGCTGG 61.318 60.000 6.69 0.00 0.00 4.85
1269 1770 1.123077 AGAGCAGTCAAGACACACCA 58.877 50.000 2.72 0.00 0.00 4.17
1322 1823 2.282745 GGCTGCTGGGTTGCTCTT 60.283 61.111 0.00 0.00 0.00 2.85
1338 1839 1.135315 CTTGCTTCGCAACCCATCG 59.865 57.895 0.00 0.00 43.99 3.84
1360 1861 0.101399 CGATGAAGTCTGGAGTCCCG 59.899 60.000 6.74 0.00 34.29 5.14
1473 1974 0.399949 TCCCGGCTGATACCATCCTT 60.400 55.000 0.00 0.00 0.00 3.36
1535 2036 2.160721 AGAAGCCGTCTCATCCCTAA 57.839 50.000 0.00 0.00 0.00 2.69
1689 2190 4.097741 CAGTTGGTGTTCAATGAAACTGGA 59.902 41.667 13.92 0.00 37.73 3.86
1779 2280 3.058293 GTGATTTCTTCAATCGTGCCACA 60.058 43.478 0.00 0.00 44.07 4.17
1786 2287 0.943673 CAATCGTGCCACACTTGACA 59.056 50.000 0.00 0.00 31.34 3.58
1830 2331 2.906389 TGTCTACCCAAAGAGCAGACAT 59.094 45.455 0.00 0.00 40.38 3.06
1852 2353 2.038033 GCCGTAATAGTATGGGGCTTGA 59.962 50.000 10.34 0.00 36.94 3.02
1859 2360 3.303351 AGTATGGGGCTTGAAATGGAG 57.697 47.619 0.00 0.00 0.00 3.86
1901 2402 3.875727 CAGAACATCTGCCAGGTGATAAG 59.124 47.826 12.92 0.00 37.72 1.73
1932 2433 4.684134 GGCAGTGGGGCATGTGGT 62.684 66.667 0.00 0.00 42.77 4.16
1971 2472 0.617935 TCGATGGCACCCAGAATCAA 59.382 50.000 0.00 0.00 36.75 2.57
2044 2545 2.008242 ATACAAAGGTTGCAGGCCAA 57.992 45.000 5.01 0.00 0.00 4.52
2153 2657 3.014304 AGCCGACTATGAGGAGTACAA 57.986 47.619 0.00 0.00 0.00 2.41
2223 2727 3.050275 GCCACAGCCGTCTTCCAC 61.050 66.667 0.00 0.00 0.00 4.02
2224 2728 2.425592 CCACAGCCGTCTTCCACA 59.574 61.111 0.00 0.00 0.00 4.17
2790 3294 1.271543 TGCAATGAGGGAACTGACAGG 60.272 52.381 7.51 0.00 44.43 4.00
2817 3321 7.210174 TGCTAGTATATGAGTTCATGACCAAC 58.790 38.462 0.00 0.00 37.15 3.77
2849 3353 1.732259 CGAGTTCCTTTTCGGTGATGG 59.268 52.381 0.00 0.00 33.39 3.51
2970 3474 5.390885 CGACATAAAACCACAGAACATCCTG 60.391 44.000 0.00 0.00 39.93 3.86
2984 3488 1.132453 CATCCTGCTCGACGACAACTA 59.868 52.381 0.00 0.00 0.00 2.24
3192 3696 1.697284 ATGTGGAGCTAGAGATCGCA 58.303 50.000 0.00 0.00 0.00 5.10
3204 3708 1.520590 GAGATCGCAGATGAAGAACGC 59.479 52.381 0.00 0.00 45.12 4.84
3264 3768 1.112113 GGAGGATCGACTTGCTGGTA 58.888 55.000 0.00 0.00 34.37 3.25
3461 3969 0.535335 CTTCCGTAGTGGCCTGCTTA 59.465 55.000 3.32 0.00 37.80 3.09
3515 4334 9.587772 AGATTATGTAATACACGGATAATCTGC 57.412 33.333 18.64 2.16 39.29 4.26
3528 4347 6.979238 ACGGATAATCTGCTACTGTTTTCTAC 59.021 38.462 0.00 0.00 0.00 2.59
3529 4348 6.421202 CGGATAATCTGCTACTGTTTTCTACC 59.579 42.308 0.00 0.00 0.00 3.18
3554 4373 7.645340 CCGAAGCTTCAGAATTAATGGTAAATG 59.355 37.037 25.47 3.14 0.00 2.32
3555 4374 7.166473 CGAAGCTTCAGAATTAATGGTAAATGC 59.834 37.037 25.47 0.00 0.00 3.56
3572 4398 4.445452 AATGCAGTATTTCAGGCACTTG 57.555 40.909 0.00 0.00 39.34 3.16
3596 4423 5.734498 GTGTTTAGCTGAACAAATAGCATCG 59.266 40.000 23.94 0.00 40.86 3.84
3660 4489 8.902540 TGTATCTTCTTTCCGTAATGCATATT 57.097 30.769 0.00 0.00 0.00 1.28
3719 4559 9.601810 TGTCATACATTCTATACAATACTCCCT 57.398 33.333 0.00 0.00 0.00 4.20
3751 4591 8.712228 ACAAAAAGAAATCATTCTCTACCCTT 57.288 30.769 0.00 0.00 45.19 3.95
3847 4687 2.660189 CCACTGGCATGAAACAATCC 57.340 50.000 0.00 0.00 0.00 3.01
3857 4697 4.092383 GCATGAAACAATCCTTCAATGTGC 59.908 41.667 0.00 0.00 36.43 4.57
3860 4700 4.341806 TGAAACAATCCTTCAATGTGCTGT 59.658 37.500 0.00 0.00 29.93 4.40
3866 4706 5.824904 ATCCTTCAATGTGCTGTTGATAC 57.175 39.130 1.01 0.00 35.68 2.24
3871 4711 5.778161 TCAATGTGCTGTTGATACGTAAG 57.222 39.130 0.00 0.00 35.34 2.34
3874 4714 2.993220 TGTGCTGTTGATACGTAAGCAG 59.007 45.455 16.97 11.77 44.03 4.24
3886 4726 7.041721 TGATACGTAAGCAGTGAATCAAGAAT 58.958 34.615 0.00 0.00 45.62 2.40
3887 4727 7.549134 TGATACGTAAGCAGTGAATCAAGAATT 59.451 33.333 0.00 0.00 45.62 2.17
3888 4728 6.560253 ACGTAAGCAGTGAATCAAGAATTT 57.440 33.333 0.00 0.00 45.62 1.82
3939 4779 2.683362 GGCTACCTTGTATTTCAGGCAC 59.317 50.000 0.00 0.00 0.00 5.01
3954 4794 0.108804 GGCACTTACGTCTAGCTGCA 60.109 55.000 17.89 0.00 0.00 4.41
3957 4797 1.649171 CACTTACGTCTAGCTGCAACG 59.351 52.381 16.86 16.86 41.93 4.10
3964 4804 2.540515 GTCTAGCTGCAACGAATAGCA 58.459 47.619 1.02 0.00 39.84 3.49
3967 4807 1.060937 GCTGCAACGAATAGCACCG 59.939 57.895 0.00 0.00 37.40 4.94
3974 4814 4.684242 TGCAACGAATAGCACCGATAATAG 59.316 41.667 0.00 0.00 35.51 1.73
3977 4817 6.581370 CAACGAATAGCACCGATAATAGTTG 58.419 40.000 0.00 0.00 0.00 3.16
3979 4819 6.278363 ACGAATAGCACCGATAATAGTTGTT 58.722 36.000 0.00 0.00 0.00 2.83
3986 4826 8.732746 AGCACCGATAATAGTTGTTTATCTTT 57.267 30.769 0.00 0.00 35.05 2.52
4071 4912 7.738437 ATCCATTTTAGTCAAACATTCCCAT 57.262 32.000 0.00 0.00 0.00 4.00
4075 4916 7.331687 CCATTTTAGTCAAACATTCCCATCAAC 59.668 37.037 0.00 0.00 0.00 3.18
4077 4918 6.573664 TTAGTCAAACATTCCCATCAACTG 57.426 37.500 0.00 0.00 0.00 3.16
4082 4923 7.121759 AGTCAAACATTCCCATCAACTGAATAG 59.878 37.037 0.00 0.00 0.00 1.73
4111 4952 2.172505 TGAATAGGTATGGGCTGGTGTG 59.827 50.000 0.00 0.00 0.00 3.82
4115 4956 0.039035 GGTATGGGCTGGTGTGGAAA 59.961 55.000 0.00 0.00 0.00 3.13
4122 4963 1.560505 GCTGGTGTGGAAAATCCCAT 58.439 50.000 0.00 0.00 38.66 4.00
4125 4966 3.513515 GCTGGTGTGGAAAATCCCATAAA 59.486 43.478 0.00 0.00 38.66 1.40
4134 4975 5.046663 TGGAAAATCCCATAAAACCTTGCTC 60.047 40.000 0.00 0.00 35.03 4.26
4139 4980 6.906157 ATCCCATAAAACCTTGCTCATATG 57.094 37.500 0.00 0.00 0.00 1.78
4149 4990 1.232119 TGCTCATATGCAAGCGATGG 58.768 50.000 10.77 0.00 41.51 3.51
4165 5006 6.029346 AGCGATGGATCAAGAAAAATGTTT 57.971 33.333 0.00 0.00 0.00 2.83
4170 5011 9.190858 CGATGGATCAAGAAAAATGTTTTTACA 57.809 29.630 3.64 0.00 40.21 2.41
4197 5038 8.507249 AGCATAGTTTGACTAATTTCAGAACAC 58.493 33.333 0.00 0.00 33.89 3.32
4200 5041 7.027778 AGTTTGACTAATTTCAGAACACCAC 57.972 36.000 0.00 0.00 0.00 4.16
4202 5043 6.861065 TTGACTAATTTCAGAACACCACTC 57.139 37.500 0.00 0.00 0.00 3.51
4203 5044 6.174720 TGACTAATTTCAGAACACCACTCT 57.825 37.500 0.00 0.00 0.00 3.24
4206 5047 8.375506 TGACTAATTTCAGAACACCACTCTATT 58.624 33.333 0.00 0.00 0.00 1.73
4212 5053 9.965902 ATTTCAGAACACCACTCTATTTATTCT 57.034 29.630 0.00 0.00 0.00 2.40
4213 5054 9.436957 TTTCAGAACACCACTCTATTTATTCTC 57.563 33.333 0.00 0.00 0.00 2.87
4214 5055 8.367660 TCAGAACACCACTCTATTTATTCTCT 57.632 34.615 0.00 0.00 0.00 3.10
4250 5091 6.611381 TGCAAAATAAATACTCTGCACTGTC 58.389 36.000 0.00 0.00 35.02 3.51
4259 5100 4.558538 ACTCTGCACTGTCAAAATTCAC 57.441 40.909 0.00 0.00 0.00 3.18
4262 5103 3.316029 TCTGCACTGTCAAAATTCACAGG 59.684 43.478 13.76 6.66 43.78 4.00
4265 5106 3.568007 GCACTGTCAAAATTCACAGGGTA 59.432 43.478 13.24 0.00 44.64 3.69
4266 5107 4.037446 GCACTGTCAAAATTCACAGGGTAA 59.963 41.667 13.24 0.00 44.64 2.85
4267 5108 5.278957 GCACTGTCAAAATTCACAGGGTAAT 60.279 40.000 13.24 0.00 44.64 1.89
4269 5110 7.362920 GCACTGTCAAAATTCACAGGGTAATAT 60.363 37.037 13.24 0.00 44.64 1.28
4272 5119 9.573133 CTGTCAAAATTCACAGGGTAATATTTC 57.427 33.333 0.00 0.00 37.04 2.17
4279 5126 6.001449 TCACAGGGTAATATTTCTGAAGGG 57.999 41.667 15.44 6.45 0.00 3.95
4281 5128 5.590259 CACAGGGTAATATTTCTGAAGGGTG 59.410 44.000 15.44 0.00 0.00 4.61
4296 5143 5.734720 TGAAGGGTGATTCAGACAGTAATC 58.265 41.667 0.00 0.00 34.31 1.75
4297 5144 4.392921 AGGGTGATTCAGACAGTAATCG 57.607 45.455 0.00 0.00 35.32 3.34
4300 5147 3.430929 GGTGATTCAGACAGTAATCGGCT 60.431 47.826 0.00 0.00 35.32 5.52
4301 5148 4.202121 GGTGATTCAGACAGTAATCGGCTA 60.202 45.833 0.00 0.00 35.32 3.93
4309 5156 3.531538 ACAGTAATCGGCTACATTGGTG 58.468 45.455 0.00 0.00 0.00 4.17
4345 5192 6.846786 AGTAAAACAAACAAACAAACAAACGC 59.153 30.769 0.00 0.00 0.00 4.84
4357 5204 0.942252 ACAAACGCCTTCTTTCCGAC 59.058 50.000 0.00 0.00 0.00 4.79
4387 5234 3.782889 GCAACCAGCAGTAAATTAGGG 57.217 47.619 0.00 0.00 44.79 3.53
4388 5235 2.427095 GCAACCAGCAGTAAATTAGGGG 59.573 50.000 0.00 0.00 44.79 4.79
4389 5236 3.023832 CAACCAGCAGTAAATTAGGGGG 58.976 50.000 0.00 0.00 0.00 5.40
4440 5287 9.423061 CACTGAATTTCACTAAAATTTTAGGGG 57.577 33.333 30.67 24.22 45.47 4.79
4441 5288 8.593679 ACTGAATTTCACTAAAATTTTAGGGGG 58.406 33.333 30.67 22.33 45.47 5.40
4442 5289 8.499288 TGAATTTCACTAAAATTTTAGGGGGT 57.501 30.769 30.67 18.42 45.47 4.95
4443 5290 9.603189 TGAATTTCACTAAAATTTTAGGGGGTA 57.397 29.630 30.67 19.94 45.47 3.69
4450 5297 8.941977 CACTAAAATTTTAGGGGGTAAAAATGC 58.058 33.333 31.51 0.00 42.58 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.290483 GAATTCCTGAAGAACGGATTTAATTTC 57.710 33.333 0.00 0.00 37.29 2.17
55 56 2.160417 CACGCCTGAATTCCTGAAGAAC 59.840 50.000 2.27 0.00 37.29 3.01
64 65 0.804989 CCTTGTCCACGCCTGAATTC 59.195 55.000 0.00 0.00 0.00 2.17
76 77 1.075536 ACCACTCAATTCCCCTTGTCC 59.924 52.381 0.00 0.00 0.00 4.02
109 110 0.107848 GGCACATGGCTACGGTTAGT 60.108 55.000 0.00 0.00 44.01 2.24
238 243 1.987770 GTGTTGCATCTTTTGGCATCG 59.012 47.619 0.00 0.00 40.17 3.84
300 305 0.330604 AGCTGTGACCAATGGCATCT 59.669 50.000 0.00 0.00 0.00 2.90
308 313 0.181114 AACTGCTCAGCTGTGACCAA 59.819 50.000 19.61 0.00 40.40 3.67
360 632 1.938585 TGAGGACAGGAACAGTAGGG 58.061 55.000 0.00 0.00 0.00 3.53
439 716 2.356695 CGCATCTCATGGCATTCAAAGA 59.643 45.455 0.00 0.00 0.00 2.52
440 717 2.098607 ACGCATCTCATGGCATTCAAAG 59.901 45.455 0.00 0.00 0.00 2.77
477 926 9.919416 TCCTGATAAAAGTTCCATCAATTATGA 57.081 29.630 2.14 0.00 37.86 2.15
513 962 0.322277 AGGCGTCTTCCGTCAGTCTA 60.322 55.000 0.00 0.00 45.80 2.59
544 993 6.639632 ACACTGTCTGCAATTTATTTGTCT 57.360 33.333 0.00 0.00 37.65 3.41
558 1007 4.446371 AGGAACTGAGAAAACACTGTCTG 58.554 43.478 0.00 0.00 37.18 3.51
559 1008 4.407296 AGAGGAACTGAGAAAACACTGTCT 59.593 41.667 0.00 0.00 41.55 3.41
560 1009 4.698575 AGAGGAACTGAGAAAACACTGTC 58.301 43.478 0.00 0.00 41.55 3.51
616 1065 0.233590 TCAACGCACGTTTCGAATGG 59.766 50.000 13.12 0.00 36.00 3.16
621 1070 1.792057 GCCATCAACGCACGTTTCG 60.792 57.895 5.55 5.53 36.00 3.46
629 1078 2.645730 TACCAAATTGCCATCAACGC 57.354 45.000 0.00 0.00 34.60 4.84
630 1079 4.621034 GTCTTTACCAAATTGCCATCAACG 59.379 41.667 0.00 0.00 34.60 4.10
730 1188 5.105957 TGCTGACTGTTAAACTTGAAGCAAA 60.106 36.000 0.00 0.00 35.37 3.68
757 1215 4.826733 TGTTGTCATGCACAGAAAGGTATT 59.173 37.500 0.00 0.00 35.97 1.89
759 1217 3.814625 TGTTGTCATGCACAGAAAGGTA 58.185 40.909 0.00 0.00 35.97 3.08
780 1238 5.488919 TCCTCTCCCTATCAGTGACATTTTT 59.511 40.000 0.00 0.00 0.00 1.94
881 1340 3.370061 GTGGAATAGTTTGGCGTCAGTAC 59.630 47.826 0.00 0.00 0.00 2.73
882 1341 3.592059 GTGGAATAGTTTGGCGTCAGTA 58.408 45.455 0.00 0.00 0.00 2.74
883 1342 2.423577 GTGGAATAGTTTGGCGTCAGT 58.576 47.619 0.00 0.00 0.00 3.41
884 1343 1.393539 CGTGGAATAGTTTGGCGTCAG 59.606 52.381 0.00 0.00 0.00 3.51
885 1344 1.001068 TCGTGGAATAGTTTGGCGTCA 59.999 47.619 0.00 0.00 0.00 4.35
886 1345 1.717194 TCGTGGAATAGTTTGGCGTC 58.283 50.000 0.00 0.00 0.00 5.19
887 1346 2.073816 CTTCGTGGAATAGTTTGGCGT 58.926 47.619 0.00 0.00 0.00 5.68
888 1347 2.343101 TCTTCGTGGAATAGTTTGGCG 58.657 47.619 0.00 0.00 0.00 5.69
897 1366 0.038526 ACGCGTCTTCTTCGTGGAAT 60.039 50.000 5.58 0.00 42.04 3.01
943 1415 1.002857 AAGCTTATGCCCCTTGGAGT 58.997 50.000 0.00 0.00 40.80 3.85
970 1448 2.075355 TTGGTTGGTGCCCCTACTGG 62.075 60.000 0.00 0.00 36.78 4.00
1013 1491 4.115199 GGAGGAAGCGCCATGGGT 62.115 66.667 15.13 0.00 40.02 4.51
1069 1550 1.160137 GTGATGTTCACCTGTGCTCC 58.840 55.000 0.00 0.00 41.37 4.70
1269 1770 1.975407 GCTGGATGGCACTTGCACT 60.975 57.895 3.15 0.00 44.36 4.40
1310 1811 1.871772 CGAAGCAAGAGCAACCCAG 59.128 57.895 0.00 0.00 45.49 4.45
1338 1839 1.135333 GGACTCCAGACTTCATCGTCC 59.865 57.143 0.00 0.00 34.46 4.79
1387 1888 0.463654 AAGTTGCCTGTGTCGAGCAA 60.464 50.000 5.04 5.04 43.83 3.91
1473 1974 0.179020 CAGGAAGCACTTGTGTGGGA 60.179 55.000 2.61 0.00 43.97 4.37
1506 2007 3.830755 TGAGACGGCTTCTAAGTACCTTT 59.169 43.478 0.00 0.00 33.22 3.11
1689 2190 7.065803 CCATTTGTCGTTGTGAAGTATATCCTT 59.934 37.037 0.00 0.00 0.00 3.36
1786 2287 0.319083 TGCCGAAATACACCGTCTGT 59.681 50.000 0.00 0.00 36.82 3.41
1830 2331 1.724545 AGCCCCATACTATTACGGCA 58.275 50.000 0.00 0.00 38.90 5.69
1835 2336 6.467194 CCTCCATTTCAAGCCCCATACTATTA 60.467 42.308 0.00 0.00 0.00 0.98
1838 2339 3.138283 CCTCCATTTCAAGCCCCATACTA 59.862 47.826 0.00 0.00 0.00 1.82
1852 2353 0.329596 GAGCTCACCACCCTCCATTT 59.670 55.000 9.40 0.00 0.00 2.32
1859 2360 0.681243 GGGAATTGAGCTCACCACCC 60.681 60.000 25.41 25.41 0.00 4.61
1901 2402 0.681175 ACTGCCAGCATTTGTTTCCC 59.319 50.000 0.00 0.00 0.00 3.97
1932 2433 3.002246 CGAAGCTGCAGTAACTGTTGAAA 59.998 43.478 16.64 0.00 33.43 2.69
1971 2472 2.570752 TGGGCATTGGCATATTGTTGTT 59.429 40.909 12.70 0.00 43.71 2.83
2080 2581 4.947147 AAACTTGGCCGCCGCTGA 62.947 61.111 4.58 0.00 34.44 4.26
2153 2657 3.072184 GCATTCAGTCTCATCTATGGGGT 59.928 47.826 0.00 0.00 0.00 4.95
2790 3294 5.866633 GGTCATGAACTCATATACTAGCAGC 59.133 44.000 2.64 0.00 34.26 5.25
2838 3342 2.046700 GGCCGACCATCACCGAAA 60.047 61.111 0.00 0.00 35.26 3.46
2849 3353 3.134127 GGCTCCAATGTGGCCGAC 61.134 66.667 0.00 0.00 37.47 4.79
2970 3474 2.052157 GCCATATAGTTGTCGTCGAGC 58.948 52.381 0.00 0.00 0.00 5.03
2984 3488 3.482156 AGTCTGCAATCTTCGCCATAT 57.518 42.857 0.00 0.00 0.00 1.78
3120 3624 2.231235 CACCCCAAAGCTGTAAACATCC 59.769 50.000 0.00 0.00 0.00 3.51
3192 3696 5.105554 AGTCAGTATTGAGCGTTCTTCATCT 60.106 40.000 0.00 0.00 32.98 2.90
3204 3708 4.471904 TGCCCAGTAAGTCAGTATTGAG 57.528 45.455 0.00 0.00 32.98 3.02
3264 3768 1.888436 TTGCCTCATCGTCGCCTTCT 61.888 55.000 0.00 0.00 0.00 2.85
3515 4334 5.227908 TGAAGCTTCGGTAGAAAACAGTAG 58.772 41.667 21.11 0.00 35.71 2.57
3528 4347 6.677781 TTACCATTAATTCTGAAGCTTCGG 57.322 37.500 26.56 26.56 34.85 4.30
3529 4348 7.166473 GCATTTACCATTAATTCTGAAGCTTCG 59.834 37.037 21.11 15.42 0.00 3.79
3554 4373 2.554032 ACACAAGTGCCTGAAATACTGC 59.446 45.455 0.00 0.00 0.00 4.40
3555 4374 4.836125 AACACAAGTGCCTGAAATACTG 57.164 40.909 0.00 0.00 0.00 2.74
3572 4398 5.734498 CGATGCTATTTGTTCAGCTAAACAC 59.266 40.000 0.59 0.00 38.80 3.32
3596 4423 6.374565 AAGAAAAGATACAGATGCATCAGC 57.625 37.500 27.81 10.89 42.57 4.26
3634 4463 9.507329 AATATGCATTACGGAAAGAAGATACAT 57.493 29.630 3.54 0.00 0.00 2.29
3679 4518 8.517878 AGAATGTATGACAAAAACAGATTCAGG 58.482 33.333 0.00 0.00 0.00 3.86
3715 4555 7.889873 TGATTTCTTTTTGTTTACAGAGGGA 57.110 32.000 0.00 0.00 0.00 4.20
3716 4556 9.196552 GAATGATTTCTTTTTGTTTACAGAGGG 57.803 33.333 0.00 0.00 0.00 4.30
3748 4588 1.834263 CACCTCTACCCCTCTTCAAGG 59.166 57.143 0.00 0.00 45.77 3.61
3751 4591 3.491766 ATTCACCTCTACCCCTCTTCA 57.508 47.619 0.00 0.00 0.00 3.02
3802 4642 7.689313 GCCCAGACCATGTAGATATAGAAAACA 60.689 40.741 0.00 0.00 0.00 2.83
3838 4678 4.874970 ACAGCACATTGAAGGATTGTTTC 58.125 39.130 0.00 0.00 0.00 2.78
3847 4687 4.668576 ACGTATCAACAGCACATTGAAG 57.331 40.909 0.00 0.97 39.43 3.02
3857 4697 5.576774 TGATTCACTGCTTACGTATCAACAG 59.423 40.000 0.00 4.74 0.00 3.16
3860 4700 6.394809 TCTTGATTCACTGCTTACGTATCAA 58.605 36.000 0.00 0.20 0.00 2.57
3866 4706 7.858052 AAAAATTCTTGATTCACTGCTTACG 57.142 32.000 0.00 0.00 0.00 3.18
3898 4738 9.555727 GGTAGCCATTGTTCTTCAAACTATATA 57.444 33.333 0.00 0.00 39.62 0.86
3900 4740 7.630082 AGGTAGCCATTGTTCTTCAAACTATA 58.370 34.615 0.00 0.00 39.62 1.31
3901 4741 6.485171 AGGTAGCCATTGTTCTTCAAACTAT 58.515 36.000 0.00 0.00 39.62 2.12
3902 4742 5.876357 AGGTAGCCATTGTTCTTCAAACTA 58.124 37.500 0.00 0.00 39.62 2.24
3903 4743 4.729868 AGGTAGCCATTGTTCTTCAAACT 58.270 39.130 0.00 0.00 39.62 2.66
3904 4744 5.221244 ACAAGGTAGCCATTGTTCTTCAAAC 60.221 40.000 0.00 0.00 36.23 2.93
3914 4754 4.202050 GCCTGAAATACAAGGTAGCCATTG 60.202 45.833 0.00 0.00 0.00 2.82
3919 4759 3.610911 AGTGCCTGAAATACAAGGTAGC 58.389 45.455 0.00 0.00 0.00 3.58
3939 4779 7.002969 GCTATTCGTTGCAGCTAGACGTAAG 62.003 48.000 7.67 5.50 37.95 2.34
3954 4794 6.278363 ACAACTATTATCGGTGCTATTCGTT 58.722 36.000 0.00 0.00 0.00 3.85
4038 4879 9.474920 TGTTTGACTAAAATGGATTCATCAAAC 57.525 29.630 16.64 16.64 39.02 2.93
4043 4884 8.260114 GGGAATGTTTGACTAAAATGGATTCAT 58.740 33.333 0.00 0.00 34.56 2.57
4077 4918 8.474025 CCCATACCTATTCAGATCTGACTATTC 58.526 40.741 25.07 0.00 39.66 1.75
4082 4923 4.530161 AGCCCATACCTATTCAGATCTGAC 59.470 45.833 25.07 8.97 39.66 3.51
4087 4928 3.328931 CACCAGCCCATACCTATTCAGAT 59.671 47.826 0.00 0.00 0.00 2.90
4088 4929 2.705658 CACCAGCCCATACCTATTCAGA 59.294 50.000 0.00 0.00 0.00 3.27
4089 4930 2.439507 ACACCAGCCCATACCTATTCAG 59.560 50.000 0.00 0.00 0.00 3.02
4096 4937 0.039035 TTTCCACACCAGCCCATACC 59.961 55.000 0.00 0.00 0.00 2.73
4111 4952 5.046663 TGAGCAAGGTTTTATGGGATTTTCC 60.047 40.000 0.00 0.00 35.23 3.13
4115 4956 6.239402 GCATATGAGCAAGGTTTTATGGGATT 60.239 38.462 6.97 0.00 0.00 3.01
4134 4975 3.749609 TCTTGATCCATCGCTTGCATATG 59.250 43.478 0.00 0.00 0.00 1.78
4139 4980 3.492421 TTTTCTTGATCCATCGCTTGC 57.508 42.857 0.00 0.00 0.00 4.01
4170 5011 9.066892 TGTTCTGAAATTAGTCAAACTATGCTT 57.933 29.630 0.00 0.00 29.64 3.91
4177 5018 7.012421 AGAGTGGTGTTCTGAAATTAGTCAAAC 59.988 37.037 0.00 0.00 0.00 2.93
4186 5027 9.965902 AGAATAAATAGAGTGGTGTTCTGAAAT 57.034 29.630 0.00 0.00 0.00 2.17
4219 5060 8.415553 TGCAGAGTATTTATTTTGCATATGCTT 58.584 29.630 27.13 12.53 42.66 3.91
4221 5062 7.864379 AGTGCAGAGTATTTATTTTGCATATGC 59.136 33.333 21.09 21.09 42.64 3.14
4222 5063 9.177304 CAGTGCAGAGTATTTATTTTGCATATG 57.823 33.333 0.00 0.00 42.64 1.78
4223 5064 8.906867 ACAGTGCAGAGTATTTATTTTGCATAT 58.093 29.630 0.03 0.00 42.64 1.78
4224 5065 8.279970 ACAGTGCAGAGTATTTATTTTGCATA 57.720 30.769 0.03 0.00 42.64 3.14
4225 5066 7.094248 TGACAGTGCAGAGTATTTATTTTGCAT 60.094 33.333 0.03 0.00 42.64 3.96
4226 5067 6.206438 TGACAGTGCAGAGTATTTATTTTGCA 59.794 34.615 0.00 0.00 39.03 4.08
4227 5068 6.611381 TGACAGTGCAGAGTATTTATTTTGC 58.389 36.000 0.00 0.00 0.00 3.68
4243 5084 2.362077 ACCCTGTGAATTTTGACAGTGC 59.638 45.455 8.70 0.00 40.20 4.40
4259 5100 6.001449 TCACCCTTCAGAAATATTACCCTG 57.999 41.667 0.00 0.00 0.00 4.45
4279 5126 3.786635 AGCCGATTACTGTCTGAATCAC 58.213 45.455 3.49 0.00 32.58 3.06
4281 5128 4.933330 TGTAGCCGATTACTGTCTGAATC 58.067 43.478 0.00 0.00 0.00 2.52
4289 5136 2.287915 GCACCAATGTAGCCGATTACTG 59.712 50.000 0.00 0.00 0.00 2.74
4291 5138 2.285083 TGCACCAATGTAGCCGATTAC 58.715 47.619 0.00 0.00 0.00 1.89
4296 5143 2.755836 GTAATGCACCAATGTAGCCG 57.244 50.000 0.00 0.00 0.00 5.52
4320 5167 6.846786 GCGTTTGTTTGTTTGTTTGTTTTACT 59.153 30.769 0.00 0.00 0.00 2.24
4327 5174 4.151512 AGAAGGCGTTTGTTTGTTTGTTTG 59.848 37.500 0.00 0.00 0.00 2.93
4338 5185 0.942252 GTCGGAAAGAAGGCGTTTGT 59.058 50.000 0.00 0.00 0.00 2.83
4339 5186 1.069906 CAGTCGGAAAGAAGGCGTTTG 60.070 52.381 0.00 0.00 0.00 2.93
4340 5187 1.202604 TCAGTCGGAAAGAAGGCGTTT 60.203 47.619 0.00 0.00 0.00 3.60
4341 5188 0.391597 TCAGTCGGAAAGAAGGCGTT 59.608 50.000 0.00 0.00 0.00 4.84
4342 5189 0.608640 ATCAGTCGGAAAGAAGGCGT 59.391 50.000 0.00 0.00 0.00 5.68
4343 5190 1.394917 CAATCAGTCGGAAAGAAGGCG 59.605 52.381 0.00 0.00 0.00 5.52
4344 5191 1.131315 GCAATCAGTCGGAAAGAAGGC 59.869 52.381 0.00 0.00 0.00 4.35
4345 5192 1.740025 GGCAATCAGTCGGAAAGAAGG 59.260 52.381 0.00 0.00 0.00 3.46
4414 5261 9.423061 CCCCTAAAATTTTAGTGAAATTCAGTG 57.577 33.333 27.93 13.34 44.98 3.66
4415 5262 8.593679 CCCCCTAAAATTTTAGTGAAATTCAGT 58.406 33.333 27.93 8.50 44.98 3.41
4416 5263 8.593679 ACCCCCTAAAATTTTAGTGAAATTCAG 58.406 33.333 27.93 14.28 44.98 3.02
4417 5264 8.499288 ACCCCCTAAAATTTTAGTGAAATTCA 57.501 30.769 27.93 0.00 44.98 2.57
4424 5271 8.941977 GCATTTTTACCCCCTAAAATTTTAGTG 58.058 33.333 27.93 20.53 38.73 2.74


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

AutoCloner maintained by Alex Coulton.