Multiple sequence alignment - TraesCS3A01G274900

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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 TraesCS3A01G274900 chr3A 100.000 3661 0 0 1 3661 504022581 504026241 0.000000e+00 6761
1 TraesCS3A01G274900 chr3D 91.976 3290 126 58 427 3661 380813267 380816473 0.000000e+00 4486
2 TraesCS3A01G274900 chr3D 90.000 430 22 5 11 427 380812810 380813231 1.500000e-148 536
3 TraesCS3A01G274900 chr3B 91.497 3293 142 53 427 3661 496613267 496616479 0.000000e+00 4403
4 TraesCS3A01G274900 chr3B 88.511 235 10 3 200 417 496612602 496612836 6.030000e-68 268
5 TraesCS3A01G274900 chr6A 86.860 449 50 3 1797 2245 438036587 438036148 9.130000e-136 494
6 TraesCS3A01G274900 chr1A 81.560 423 50 19 2247 2661 530781635 530782037 1.270000e-84 324
7 TraesCS3A01G274900 chr1A 80.309 259 29 15 1048 1298 530780395 530780639 3.760000e-40 176
8 TraesCS3A01G274900 chr1A 87.288 118 8 5 1782 1899 530781185 530781295 1.070000e-25 128
9 TraesCS3A01G274900 chr1D 87.755 245 27 2 2247 2491 432319747 432319988 2.150000e-72 283
10 TraesCS3A01G274900 chr1D 93.805 113 4 1 1189 1298 432318830 432318942 2.260000e-37 167
11 TraesCS3A01G274900 chr1D 87.288 118 8 5 1782 1899 432319300 432319410 1.070000e-25 128
12 TraesCS3A01G274900 chr1B 88.889 225 25 0 2247 2471 583760654 583760878 1.000000e-70 278
13 TraesCS3A01G274900 chr1B 80.859 256 30 13 1048 1298 583759616 583759857 2.250000e-42 183
14 TraesCS3A01G274900 chr1B 86.508 126 10 5 1782 1907 583760213 583760331 8.250000e-27 132
15 TraesCS3A01G274900 chr4B 89.372 207 21 1 2262 2467 658212378 658212584 3.630000e-65 259
16 TraesCS3A01G274900 chr5A 87.111 225 28 1 2262 2485 696925397 696925173 1.690000e-63 254
17 TraesCS3A01G274900 chr4D 89.048 210 16 5 2262 2467 509057230 509057024 1.690000e-63 254
18 TraesCS3A01G274900 chr2A 82.564 195 22 11 2266 2454 635512088 635512276 1.050000e-35 161


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 TraesCS3A01G274900 chr3A 504022581 504026241 3660 False 6761.000000 6761 100.000000 1 3661 1 chr3A.!!$F1 3660
1 TraesCS3A01G274900 chr3D 380812810 380816473 3663 False 2511.000000 4486 90.988000 11 3661 2 chr3D.!!$F1 3650
2 TraesCS3A01G274900 chr3B 496612602 496616479 3877 False 2335.500000 4403 90.004000 200 3661 2 chr3B.!!$F1 3461
3 TraesCS3A01G274900 chr1A 530780395 530782037 1642 False 209.333333 324 83.052333 1048 2661 3 chr1A.!!$F1 1613

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
623 1070 0.039527 CGTAAAACAGGTTGCTGGGC 60.040 55.0 0.00 0.0 0.00 5.36 F
625 1072 0.187361 TAAAACAGGTTGCTGGGCCT 59.813 50.0 4.53 0.0 35.04 5.19 F
973 1454 0.233332 GCCGCAGATAGAATCGTTGC 59.767 55.0 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1994 0.098200 GGAGCGGTTTAATTGCGGAC 59.902 55.0 0.00 0.0 0.00 4.79 R
1853 2486 0.391793 GCAGCTTGTGTAGGTCCTCC 60.392 60.0 0.00 0.0 30.51 4.30 R
2799 3495 0.521735 GGCTAACCAAACGGAAGCAG 59.478 55.0 10.99 0.0 37.63 4.24 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
47 48 1.135333 TGCATAAGCGGTATGTCGTCA 59.865 47.619 10.85 0.00 46.23 4.35
78 79 4.568592 CCAAAAGCCCTAGAAAGTGGAGAT 60.569 45.833 0.00 0.00 0.00 2.75
89 90 5.196695 AGAAAGTGGAGATGCCCTTAATTC 58.803 41.667 0.00 0.00 34.97 2.17
93 94 0.868406 GAGATGCCCTTAATTCGCCG 59.132 55.000 0.00 0.00 0.00 6.46
110 111 1.748493 GCCGAATTACCTGCATTCCAA 59.252 47.619 0.00 0.00 0.00 3.53
111 112 2.165437 GCCGAATTACCTGCATTCCAAA 59.835 45.455 0.00 0.00 0.00 3.28
170 171 4.039366 CACCTAGCCTCCTATAACAACCTC 59.961 50.000 0.00 0.00 0.00 3.85
171 172 3.579151 CCTAGCCTCCTATAACAACCTCC 59.421 52.174 0.00 0.00 0.00 4.30
182 184 0.704664 ACAACCTCCCCTTTCCATCC 59.295 55.000 0.00 0.00 0.00 3.51
197 199 7.147689 CCCTTTCCATCCATTCATTTCATAACA 60.148 37.037 0.00 0.00 0.00 2.41
203 205 4.098349 TCCATTCATTTCATAACAGCCTGC 59.902 41.667 0.00 0.00 0.00 4.85
206 208 5.818136 TTCATTTCATAACAGCCTGCTAC 57.182 39.130 0.00 0.00 0.00 3.58
240 242 2.425668 ACCGTTTCCCAAAGTTCAGTTG 59.574 45.455 0.00 0.00 0.00 3.16
270 277 0.321021 TAAAACCGCCGCTGGTCTAA 59.679 50.000 7.25 0.00 42.89 2.10
307 319 1.508808 CGAGTACCCTCCGAGCTAGC 61.509 65.000 6.62 6.62 33.93 3.42
335 347 3.386768 TTGAACTCCTCTTTCTGGACG 57.613 47.619 0.00 0.00 0.00 4.79
417 436 3.841870 GGCAATCCCGATCAACCC 58.158 61.111 0.00 0.00 0.00 4.11
418 437 1.227383 GGCAATCCCGATCAACCCT 59.773 57.895 0.00 0.00 0.00 4.34
419 438 1.103398 GGCAATCCCGATCAACCCTG 61.103 60.000 0.00 0.00 0.00 4.45
421 440 1.681780 GCAATCCCGATCAACCCTGAA 60.682 52.381 0.00 0.00 34.49 3.02
422 441 2.292267 CAATCCCGATCAACCCTGAAG 58.708 52.381 0.00 0.00 34.49 3.02
423 442 0.181350 ATCCCGATCAACCCTGAAGC 59.819 55.000 0.00 0.00 34.49 3.86
435 875 2.975489 ACCCTGAAGCAAAGAGAGAGAA 59.025 45.455 0.00 0.00 0.00 2.87
441 881 5.491982 TGAAGCAAAGAGAGAGAATTACCC 58.508 41.667 0.00 0.00 0.00 3.69
512 957 0.951040 CGTGAAACTCCAGTCCAGCC 60.951 60.000 0.00 0.00 31.75 4.85
538 985 2.680913 GCGGTTGTAGCCAGCAGTG 61.681 63.158 0.00 0.00 0.00 3.66
581 1028 1.862815 GCGCAGGCAGCAAAGAATATG 60.863 52.381 0.30 0.00 46.13 1.78
623 1070 0.039527 CGTAAAACAGGTTGCTGGGC 60.040 55.000 0.00 0.00 0.00 5.36
624 1071 0.317160 GTAAAACAGGTTGCTGGGCC 59.683 55.000 0.00 0.00 0.00 5.80
625 1072 0.187361 TAAAACAGGTTGCTGGGCCT 59.813 50.000 4.53 0.00 35.04 5.19
630 1077 4.066139 GGTTGCTGGGCCTGGGAT 62.066 66.667 12.70 0.00 0.00 3.85
631 1078 2.037847 GTTGCTGGGCCTGGGATT 59.962 61.111 12.70 0.00 0.00 3.01
632 1079 1.306296 GTTGCTGGGCCTGGGATTA 59.694 57.895 12.70 0.00 0.00 1.75
633 1080 1.037579 GTTGCTGGGCCTGGGATTAC 61.038 60.000 12.70 0.00 0.00 1.89
671 1118 4.331992 GGAACCCGATAAGTTTTACTGCTC 59.668 45.833 0.00 0.00 0.00 4.26
672 1119 3.518590 ACCCGATAAGTTTTACTGCTCG 58.481 45.455 0.00 0.00 34.62 5.03
673 1120 2.864343 CCCGATAAGTTTTACTGCTCGG 59.136 50.000 17.00 17.00 45.28 4.63
679 1126 7.902032 CGATAAGTTTTACTGCTCGGATAAAA 58.098 34.615 0.00 0.00 32.59 1.52
681 1128 9.704098 GATAAGTTTTACTGCTCGGATAAAAAG 57.296 33.333 0.00 0.00 31.47 2.27
682 1129 6.496338 AGTTTTACTGCTCGGATAAAAAGG 57.504 37.500 0.00 0.00 31.47 3.11
683 1130 5.414765 AGTTTTACTGCTCGGATAAAAAGGG 59.585 40.000 0.00 0.00 31.47 3.95
693 1156 2.952310 GGATAAAAAGGGTGCTGGCTAG 59.048 50.000 0.00 0.00 0.00 3.42
694 1157 2.507407 TAAAAAGGGTGCTGGCTAGG 57.493 50.000 0.00 0.00 0.00 3.02
695 1158 0.900182 AAAAAGGGTGCTGGCTAGGC 60.900 55.000 9.85 9.85 0.00 3.93
755 1221 1.604593 GTTGGTGGTGCATGCCTCT 60.605 57.895 16.68 0.00 0.00 3.69
853 1321 4.569564 CACGCCAATTAAACCCTACTACTC 59.430 45.833 0.00 0.00 0.00 2.59
878 1346 2.493973 CAGCACTCCTCCTCTCGC 59.506 66.667 0.00 0.00 0.00 5.03
879 1347 2.757917 AGCACTCCTCCTCTCGCC 60.758 66.667 0.00 0.00 0.00 5.54
963 1444 4.812476 AACGCAGCGCCGCAGATA 62.812 61.111 16.61 0.00 0.00 1.98
965 1446 4.931188 CGCAGCGCCGCAGATAGA 62.931 66.667 17.04 0.00 0.00 1.98
966 1447 2.586079 GCAGCGCCGCAGATAGAA 60.586 61.111 13.36 0.00 0.00 2.10
968 1449 1.895280 GCAGCGCCGCAGATAGAATC 61.895 60.000 13.36 0.00 0.00 2.52
969 1450 1.372251 AGCGCCGCAGATAGAATCG 60.372 57.895 13.36 0.00 0.00 3.34
970 1451 1.661821 GCGCCGCAGATAGAATCGT 60.662 57.895 3.15 0.00 0.00 3.73
971 1452 1.215655 GCGCCGCAGATAGAATCGTT 61.216 55.000 3.15 0.00 0.00 3.85
972 1453 0.504384 CGCCGCAGATAGAATCGTTG 59.496 55.000 0.00 0.00 0.00 4.10
973 1454 0.233332 GCCGCAGATAGAATCGTTGC 59.767 55.000 0.00 0.00 0.00 4.17
974 1455 0.504384 CCGCAGATAGAATCGTTGCG 59.496 55.000 13.49 13.49 46.82 4.85
975 1456 1.200483 CGCAGATAGAATCGTTGCGT 58.800 50.000 12.65 0.00 44.14 5.24
976 1457 1.071894 CGCAGATAGAATCGTTGCGTG 60.072 52.381 12.65 0.00 44.14 5.34
977 1458 1.332377 GCAGATAGAATCGTTGCGTGC 60.332 52.381 0.00 0.00 0.00 5.34
978 1459 1.071894 CAGATAGAATCGTTGCGTGCG 60.072 52.381 0.00 0.00 0.00 5.34
979 1460 0.921347 GATAGAATCGTTGCGTGCGT 59.079 50.000 0.00 0.00 0.00 5.24
1122 1603 4.097361 GAGGAAGGGGTGGGCGAC 62.097 72.222 0.00 0.00 0.00 5.19
1433 1935 3.247006 TCTCTTCCATTTACACGAGGC 57.753 47.619 0.00 0.00 0.00 4.70
1436 1938 3.745799 TCTTCCATTTACACGAGGCAAA 58.254 40.909 0.00 0.00 0.00 3.68
1458 1960 8.005466 GCAAATTCATGGAAAAATGCATATACG 58.995 33.333 0.00 0.00 32.64 3.06
1459 1961 8.489559 CAAATTCATGGAAAAATGCATATACGG 58.510 33.333 0.00 0.00 0.00 4.02
1503 2009 6.068931 CGATAAATAGTCCGCAATTAAACCG 58.931 40.000 0.00 0.00 0.00 4.44
1594 2227 2.113131 AACAGCTGCCACGCGTAAAC 62.113 55.000 13.44 4.69 34.40 2.01
1727 2360 3.186613 GGAGTTCTCGAAACGAAGCAAAT 59.813 43.478 0.00 0.00 34.74 2.32
1729 2362 5.107220 GGAGTTCTCGAAACGAAGCAAATTA 60.107 40.000 0.00 0.00 34.74 1.40
1731 2364 5.465724 AGTTCTCGAAACGAAGCAAATTACT 59.534 36.000 0.00 0.00 34.74 2.24
1732 2365 5.264060 TCTCGAAACGAAGCAAATTACTG 57.736 39.130 0.00 0.00 34.74 2.74
1733 2366 4.986034 TCTCGAAACGAAGCAAATTACTGA 59.014 37.500 0.00 0.00 34.74 3.41
1853 2486 2.202676 GAGGAGAGCTTCGCCACG 60.203 66.667 8.23 0.00 38.94 4.94
2205 2889 4.383861 CGCAGGCACAGGCTCAGA 62.384 66.667 0.00 0.00 40.87 3.27
2799 3495 8.894731 GGAGTTATATTTTCCCAGTTTTCTCTC 58.105 37.037 0.00 0.00 0.00 3.20
2800 3496 9.674068 GAGTTATATTTTCCCAGTTTTCTCTCT 57.326 33.333 0.00 0.00 0.00 3.10
2801 3497 9.454859 AGTTATATTTTCCCAGTTTTCTCTCTG 57.545 33.333 0.00 0.00 0.00 3.35
2802 3498 6.765915 ATATTTTCCCAGTTTTCTCTCTGC 57.234 37.500 0.00 0.00 0.00 4.26
2803 3499 3.864789 TTTCCCAGTTTTCTCTCTGCT 57.135 42.857 0.00 0.00 0.00 4.24
2804 3500 3.864789 TTCCCAGTTTTCTCTCTGCTT 57.135 42.857 0.00 0.00 0.00 3.91
2819 3515 0.891904 TGCTTCCGTTTGGTTAGCCC 60.892 55.000 0.00 0.00 40.76 5.19
2931 3627 4.445019 CCCCTCAGAAACTAATTCTAGGGC 60.445 50.000 17.94 0.00 46.80 5.19
3027 3725 6.073003 GCGCCTAGCTAGAATATGAAAACAAT 60.073 38.462 22.70 0.00 44.04 2.71
3045 3743 4.057432 ACAATCTTTTCGGCCAATTGTTG 58.943 39.130 2.24 1.11 37.28 3.33
3072 3770 4.576053 CGAGATAACTCCCATTCATGCAAA 59.424 41.667 0.00 0.00 39.76 3.68
3073 3771 5.240183 CGAGATAACTCCCATTCATGCAAAT 59.760 40.000 0.00 0.00 39.76 2.32
3074 3772 6.567321 CGAGATAACTCCCATTCATGCAAATC 60.567 42.308 0.00 0.00 39.76 2.17
3075 3773 6.371278 AGATAACTCCCATTCATGCAAATCT 58.629 36.000 0.00 0.00 0.00 2.40
3076 3774 4.996788 AACTCCCATTCATGCAAATCTC 57.003 40.909 0.00 0.00 0.00 2.75
3077 3775 3.294214 ACTCCCATTCATGCAAATCTCC 58.706 45.455 0.00 0.00 0.00 3.71
3085 3783 1.404391 CATGCAAATCTCCAGTCCAGC 59.596 52.381 0.00 0.00 0.00 4.85
3141 3839 2.293677 GCAAGGATGAATCTCATGGCTG 59.706 50.000 0.00 0.00 37.20 4.85
3200 3921 3.441808 TTGTGTGCGCAACCGAACG 62.442 57.895 14.00 0.00 46.26 3.95
3214 3935 1.459592 CCGAACGAGCAAAGTTACCTG 59.540 52.381 0.00 0.00 31.14 4.00
3216 3937 2.408704 CGAACGAGCAAAGTTACCTGAG 59.591 50.000 0.00 0.00 31.14 3.35
3287 4012 2.430244 CCGTCGGAACTCACACGG 60.430 66.667 4.91 4.79 45.38 4.94
3291 4016 0.736325 GTCGGAACTCACACGGGATG 60.736 60.000 0.00 0.00 0.00 3.51
3297 4022 3.458189 GAACTCACACGGGATGATTAGG 58.542 50.000 0.00 0.00 0.00 2.69
3298 4023 2.467880 ACTCACACGGGATGATTAGGT 58.532 47.619 0.00 0.00 0.00 3.08
3303 4028 4.341235 TCACACGGGATGATTAGGTTAGAG 59.659 45.833 0.00 0.00 0.00 2.43
3397 4125 3.605664 GTTGCCTGGTGGTGGTGC 61.606 66.667 0.00 0.00 35.27 5.01
3476 4209 3.414486 CACCTTTCCGTGGGTTTCT 57.586 52.632 0.00 0.00 32.95 2.52
3484 4217 1.065709 TCCGTGGGTTTCTGGATAAGC 60.066 52.381 0.00 0.00 0.00 3.09
3487 4220 1.745653 GTGGGTTTCTGGATAAGCAGC 59.254 52.381 0.00 0.00 0.00 5.25
3498 4231 2.030946 GGATAAGCAGCGTCATTCACAC 59.969 50.000 0.00 0.00 0.00 3.82
3499 4232 2.162319 TAAGCAGCGTCATTCACACA 57.838 45.000 0.00 0.00 0.00 3.72
3500 4233 0.588252 AAGCAGCGTCATTCACACAC 59.412 50.000 0.00 0.00 0.00 3.82
3501 4234 0.532640 AGCAGCGTCATTCACACACA 60.533 50.000 0.00 0.00 0.00 3.72
3502 4235 0.384725 GCAGCGTCATTCACACACAC 60.385 55.000 0.00 0.00 0.00 3.82
3503 4236 0.936600 CAGCGTCATTCACACACACA 59.063 50.000 0.00 0.00 0.00 3.72
3522 4255 3.123620 CCTCGCTGCTGCAACCTC 61.124 66.667 16.29 0.00 39.64 3.85
3538 4272 1.731433 CCTCGCCTGGATTGCCATTG 61.731 60.000 0.00 0.00 44.91 2.82
3558 4292 2.281761 AAGTGGCCTGGTGAAGCG 60.282 61.111 3.32 0.00 0.00 4.68
3589 4324 0.599204 CGCCGTAACCAACACTGACT 60.599 55.000 0.00 0.00 0.00 3.41
3591 4326 0.865769 CCGTAACCAACACTGACTGC 59.134 55.000 0.00 0.00 0.00 4.40
3606 4341 0.827925 ACTGCCGTCAGAGGTCAGAA 60.828 55.000 8.12 0.00 42.95 3.02
3607 4342 0.389166 CTGCCGTCAGAGGTCAGAAC 60.389 60.000 0.00 0.00 42.95 3.01
3608 4343 0.827925 TGCCGTCAGAGGTCAGAACT 60.828 55.000 0.00 0.00 0.00 3.01
3609 4344 0.109039 GCCGTCAGAGGTCAGAACTC 60.109 60.000 7.48 7.48 35.20 3.01
3610 4345 1.248486 CCGTCAGAGGTCAGAACTCA 58.752 55.000 18.14 0.00 37.43 3.41
3611 4346 1.201181 CCGTCAGAGGTCAGAACTCAG 59.799 57.143 18.14 9.95 37.43 3.35
3612 4347 2.155279 CGTCAGAGGTCAGAACTCAGA 58.845 52.381 18.14 12.34 37.43 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.828520 GGTCTTGACTCTCACCTGATGA 59.171 50.000 0.61 0.00 35.45 2.92
2 3 2.564504 TGGTCTTGACTCTCACCTGATG 59.435 50.000 0.61 0.00 0.00 3.07
3 4 2.894731 TGGTCTTGACTCTCACCTGAT 58.105 47.619 0.61 0.00 0.00 2.90
4 5 2.365617 GTTGGTCTTGACTCTCACCTGA 59.634 50.000 0.61 0.00 0.00 3.86
5 6 2.366916 AGTTGGTCTTGACTCTCACCTG 59.633 50.000 0.61 0.00 0.00 4.00
6 7 2.683768 AGTTGGTCTTGACTCTCACCT 58.316 47.619 0.61 0.00 0.00 4.00
7 8 3.477210 AAGTTGGTCTTGACTCTCACC 57.523 47.619 0.61 0.00 34.77 4.02
31 32 3.581024 ACTTTGACGACATACCGCTTA 57.419 42.857 0.00 0.00 0.00 3.09
35 36 2.533266 GGGTACTTTGACGACATACCG 58.467 52.381 9.13 0.00 36.87 4.02
47 48 2.990998 TCTAGGGCTTTTGGGGTACTTT 59.009 45.455 0.00 0.00 0.00 2.66
78 79 1.757682 AATTCGGCGAATTAAGGGCA 58.242 45.000 37.98 10.32 40.00 5.36
89 90 0.307760 GGAATGCAGGTAATTCGGCG 59.692 55.000 0.00 0.00 35.31 6.46
93 94 6.455360 TCATCTTTGGAATGCAGGTAATTC 57.545 37.500 0.00 0.00 34.00 2.17
110 111 3.233507 TCTTGCAAGGCCTTTTCATCTT 58.766 40.909 25.73 0.00 0.00 2.40
111 112 2.824341 CTCTTGCAAGGCCTTTTCATCT 59.176 45.455 25.73 0.00 0.00 2.90
170 171 4.032310 TGAAATGAATGGATGGAAAGGGG 58.968 43.478 0.00 0.00 0.00 4.79
171 172 5.881923 ATGAAATGAATGGATGGAAAGGG 57.118 39.130 0.00 0.00 0.00 3.95
182 184 5.258456 AGCAGGCTGTTATGAAATGAATG 57.742 39.130 17.16 0.00 0.00 2.67
197 199 0.251634 GCAAGAGGAAGTAGCAGGCT 59.748 55.000 0.00 0.00 0.00 4.58
203 205 1.546476 ACGGTGAGCAAGAGGAAGTAG 59.454 52.381 0.00 0.00 0.00 2.57
206 208 1.801178 GAAACGGTGAGCAAGAGGAAG 59.199 52.381 0.00 0.00 0.00 3.46
240 242 1.335597 GGCGGTTTTACTTGCCAACTC 60.336 52.381 0.00 0.00 46.76 3.01
270 277 3.036084 CGTCGCAAACTGCTCCGT 61.036 61.111 0.00 0.00 42.25 4.69
291 298 1.608109 GTAAGCTAGCTCGGAGGGTAC 59.392 57.143 19.65 11.06 0.00 3.34
307 319 6.091441 CCAGAAAGAGGAGTTCAAATCGTAAG 59.909 42.308 0.00 0.00 0.00 2.34
335 347 2.036571 CGTACGGGGAAGGTTTGCC 61.037 63.158 7.57 0.00 40.98 4.52
417 436 5.584251 GGGTAATTCTCTCTCTTTGCTTCAG 59.416 44.000 0.00 0.00 0.00 3.02
418 437 5.491982 GGGTAATTCTCTCTCTTTGCTTCA 58.508 41.667 0.00 0.00 0.00 3.02
419 438 4.878971 GGGGTAATTCTCTCTCTTTGCTTC 59.121 45.833 0.00 0.00 0.00 3.86
421 440 3.201045 GGGGGTAATTCTCTCTCTTTGCT 59.799 47.826 0.00 0.00 0.00 3.91
422 441 3.054361 TGGGGGTAATTCTCTCTCTTTGC 60.054 47.826 0.00 0.00 0.00 3.68
423 442 4.518249 GTGGGGGTAATTCTCTCTCTTTG 58.482 47.826 0.00 0.00 0.00 2.77
435 875 0.545787 TCAGGTCACGTGGGGGTAAT 60.546 55.000 17.00 0.00 0.00 1.89
560 1007 1.656818 TATTCTTTGCTGCCTGCGCC 61.657 55.000 4.18 0.00 46.63 6.53
592 1039 3.619929 CCTGTTTTACGGTTTATCCTCGG 59.380 47.826 0.00 0.00 0.00 4.63
623 1070 5.952347 AGTTACTTGGTAGTAATCCCAGG 57.048 43.478 0.00 0.00 45.80 4.45
624 1071 6.598064 CCAAAGTTACTTGGTAGTAATCCCAG 59.402 42.308 0.00 0.00 45.80 4.45
625 1072 6.272792 TCCAAAGTTACTTGGTAGTAATCCCA 59.727 38.462 0.00 0.00 45.80 4.37
626 1073 6.714278 TCCAAAGTTACTTGGTAGTAATCCC 58.286 40.000 0.00 0.00 45.80 3.85
627 1074 7.120285 GGTTCCAAAGTTACTTGGTAGTAATCC 59.880 40.741 0.00 0.00 45.80 3.01
628 1075 7.120285 GGGTTCCAAAGTTACTTGGTAGTAATC 59.880 40.741 0.00 0.00 45.80 1.75
629 1076 6.944290 GGGTTCCAAAGTTACTTGGTAGTAAT 59.056 38.462 0.00 0.00 45.80 1.89
630 1077 6.298361 GGGTTCCAAAGTTACTTGGTAGTAA 58.702 40.000 0.00 0.00 45.29 2.24
631 1078 5.511202 CGGGTTCCAAAGTTACTTGGTAGTA 60.511 44.000 0.00 0.00 45.29 1.82
632 1079 4.722220 GGGTTCCAAAGTTACTTGGTAGT 58.278 43.478 0.00 0.00 45.29 2.73
633 1080 3.749609 CGGGTTCCAAAGTTACTTGGTAG 59.250 47.826 0.00 0.00 45.29 3.18
645 1092 5.048573 GCAGTAAAACTTATCGGGTTCCAAA 60.049 40.000 0.00 0.00 0.00 3.28
648 1095 4.259356 AGCAGTAAAACTTATCGGGTTCC 58.741 43.478 0.00 0.00 0.00 3.62
652 1099 2.864343 CCGAGCAGTAAAACTTATCGGG 59.136 50.000 16.51 4.46 44.12 5.14
671 1118 0.455815 GCCAGCACCCTTTTTATCCG 59.544 55.000 0.00 0.00 0.00 4.18
672 1119 1.852633 AGCCAGCACCCTTTTTATCC 58.147 50.000 0.00 0.00 0.00 2.59
673 1120 2.952310 CCTAGCCAGCACCCTTTTTATC 59.048 50.000 0.00 0.00 0.00 1.75
674 1121 2.950418 GCCTAGCCAGCACCCTTTTTAT 60.950 50.000 0.00 0.00 0.00 1.40
675 1122 1.615919 GCCTAGCCAGCACCCTTTTTA 60.616 52.381 0.00 0.00 0.00 1.52
676 1123 0.900182 GCCTAGCCAGCACCCTTTTT 60.900 55.000 0.00 0.00 0.00 1.94
879 1347 2.735237 GGAGATAACGCGAGGGGG 59.265 66.667 15.93 0.00 0.00 5.40
953 1434 0.504384 CAACGATTCTATCTGCGGCG 59.496 55.000 0.51 0.51 0.00 6.46
954 1435 0.233332 GCAACGATTCTATCTGCGGC 59.767 55.000 0.00 0.00 0.00 6.53
955 1436 0.504384 CGCAACGATTCTATCTGCGG 59.496 55.000 12.65 0.00 44.89 5.69
956 1437 3.985805 CGCAACGATTCTATCTGCG 57.014 52.632 8.30 8.30 43.89 5.18
957 1438 1.332377 GCACGCAACGATTCTATCTGC 60.332 52.381 0.00 0.00 0.00 4.26
958 1439 1.071894 CGCACGCAACGATTCTATCTG 60.072 52.381 0.00 0.00 0.00 2.90
960 1441 0.921347 ACGCACGCAACGATTCTATC 59.079 50.000 0.00 0.00 0.00 2.08
961 1442 0.921347 GACGCACGCAACGATTCTAT 59.079 50.000 0.00 0.00 0.00 1.98
963 1444 2.380410 GGACGCACGCAACGATTCT 61.380 57.895 0.00 0.00 0.00 2.40
964 1445 2.095843 GGACGCACGCAACGATTC 59.904 61.111 0.00 0.00 0.00 2.52
965 1446 2.663520 TGGACGCACGCAACGATT 60.664 55.556 0.00 0.00 0.00 3.34
966 1447 3.411351 GTGGACGCACGCAACGAT 61.411 61.111 0.00 0.00 0.00 3.73
1028 1509 4.394712 AGCCCTTCTTGTCGCGGG 62.395 66.667 6.13 0.00 39.76 6.13
1156 1655 3.470567 CTTGACGACGACTGCGGC 61.471 66.667 0.00 0.00 43.80 6.53
1157 1656 3.470567 GCTTGACGACGACTGCGG 61.471 66.667 0.00 0.00 43.17 5.69
1158 1657 2.710971 CTGCTTGACGACGACTGCG 61.711 63.158 0.00 0.00 44.79 5.18
1159 1658 2.375766 CCTGCTTGACGACGACTGC 61.376 63.158 0.00 5.43 0.00 4.40
1160 1659 0.730834 CTCCTGCTTGACGACGACTG 60.731 60.000 0.00 0.00 0.00 3.51
1161 1660 1.581954 CTCCTGCTTGACGACGACT 59.418 57.895 0.00 0.00 0.00 4.18
1162 1661 1.444553 CCTCCTGCTTGACGACGAC 60.445 63.158 0.00 0.00 0.00 4.34
1416 1918 4.701956 ATTTGCCTCGTGTAAATGGAAG 57.298 40.909 3.82 0.00 37.79 3.46
1433 1935 8.489559 CCGTATATGCATTTTTCCATGAATTTG 58.510 33.333 3.54 0.00 0.00 2.32
1436 1938 7.523293 TCCGTATATGCATTTTTCCATGAAT 57.477 32.000 3.54 0.00 0.00 2.57
1480 1986 5.849604 GCGGTTTAATTGCGGACTATTTATC 59.150 40.000 0.00 0.00 0.00 1.75
1484 1990 3.275999 AGCGGTTTAATTGCGGACTATT 58.724 40.909 0.00 0.00 0.00 1.73
1488 1994 0.098200 GGAGCGGTTTAATTGCGGAC 59.902 55.000 0.00 0.00 0.00 4.79
1594 2227 1.163420 TTTGGTAGTGTGCAGTGCCG 61.163 55.000 13.72 0.00 39.09 5.69
1653 2286 2.348666 ACTCGAATTCTTGTGCGCATAC 59.651 45.455 15.91 1.03 0.00 2.39
1705 2338 1.779569 TGCTTCGTTTCGAGAACTCC 58.220 50.000 8.24 0.00 37.14 3.85
1727 2360 2.416202 CTCATGCATGCGTGTTCAGTAA 59.584 45.455 33.08 15.60 34.75 2.24
1729 2362 0.800631 CTCATGCATGCGTGTTCAGT 59.199 50.000 33.08 1.85 34.75 3.41
1731 2364 0.956902 AGCTCATGCATGCGTGTTCA 60.957 50.000 33.08 17.58 42.74 3.18
1732 2365 0.522705 CAGCTCATGCATGCGTGTTC 60.523 55.000 33.08 25.49 42.74 3.18
1733 2366 1.239296 ACAGCTCATGCATGCGTGTT 61.239 50.000 33.08 20.00 42.74 3.32
1853 2486 0.391793 GCAGCTTGTGTAGGTCCTCC 60.392 60.000 0.00 0.00 30.51 4.30
2634 3327 2.510238 CTGCTGCCGGTAGTCTGC 60.510 66.667 21.31 11.17 0.00 4.26
2636 3329 2.681778 AGCTGCTGCCGGTAGTCT 60.682 61.111 21.31 12.52 40.80 3.24
2799 3495 0.521735 GGCTAACCAAACGGAAGCAG 59.478 55.000 10.99 0.00 37.63 4.24
2800 3496 0.891904 GGGCTAACCAAACGGAAGCA 60.892 55.000 10.99 0.00 37.63 3.91
2801 3497 1.880894 GGGCTAACCAAACGGAAGC 59.119 57.895 0.00 0.00 39.85 3.86
2802 3498 0.604511 ACGGGCTAACCAAACGGAAG 60.605 55.000 0.00 0.00 40.22 3.46
2803 3499 0.885596 CACGGGCTAACCAAACGGAA 60.886 55.000 0.00 0.00 40.22 4.30
2804 3500 1.301874 CACGGGCTAACCAAACGGA 60.302 57.895 0.00 0.00 40.22 4.69
2819 3515 2.111756 GAGCTCAACAAAAAGCACACG 58.888 47.619 9.40 0.00 41.06 4.49
2854 3550 5.052693 TGGGGAGGATCATGAACTAAATG 57.947 43.478 0.00 0.00 36.25 2.32
2931 3627 7.129109 TGCTAAGAAATAAAAGGACTCAACG 57.871 36.000 0.00 0.00 0.00 4.10
2978 3676 6.624917 GCAGAAAAAGAAGCAAAAATCGAAAC 59.375 34.615 0.00 0.00 0.00 2.78
2985 3683 2.607180 GGCGCAGAAAAAGAAGCAAAAA 59.393 40.909 10.83 0.00 0.00 1.94
3027 3725 2.810439 CCAACAATTGGCCGAAAAGA 57.190 45.000 10.83 0.00 45.17 2.52
3045 3743 4.873746 TGAATGGGAGTTATCTCGATCC 57.126 45.455 0.00 0.00 41.26 3.36
3072 3770 1.969923 GCTATCTGCTGGACTGGAGAT 59.030 52.381 15.22 15.22 45.03 2.75
3073 3771 1.407936 GCTATCTGCTGGACTGGAGA 58.592 55.000 3.19 3.19 38.70 3.71
3074 3772 3.984838 GCTATCTGCTGGACTGGAG 57.015 57.895 0.00 0.00 38.95 3.86
3085 3783 4.392047 TCATACCATGCCAAAGCTATCTG 58.608 43.478 0.00 0.00 40.80 2.90
3287 4012 4.614078 CGCGAGACTCTAACCTAATCATCC 60.614 50.000 0.00 0.00 0.00 3.51
3291 4016 3.311871 TCACGCGAGACTCTAACCTAATC 59.688 47.826 15.93 0.00 0.00 1.75
3331 4056 2.208431 CTCTGATTGGATCCAACGAGC 58.792 52.381 29.32 18.08 38.88 5.03
3379 4104 3.286751 CACCACCACCAGGCAACG 61.287 66.667 0.00 0.00 46.39 4.10
3397 4125 1.665137 ACCCTAGTTACCCCCAACAG 58.335 55.000 0.00 0.00 0.00 3.16
3449 4177 2.586293 CGGAAAGGTGGTACCCCGT 61.586 63.158 10.07 5.74 39.75 5.28
3463 4191 2.617021 GCTTATCCAGAAACCCACGGAA 60.617 50.000 0.00 0.00 0.00 4.30
3476 4209 2.279741 GTGAATGACGCTGCTTATCCA 58.720 47.619 0.00 0.00 0.00 3.41
3484 4217 0.936600 TGTGTGTGTGAATGACGCTG 59.063 50.000 0.00 0.00 35.94 5.18
3487 4220 0.586319 GGGTGTGTGTGTGAATGACG 59.414 55.000 0.00 0.00 0.00 4.35
3498 4231 3.046087 CAGCAGCGAGGGTGTGTG 61.046 66.667 0.00 0.00 33.19 3.82
3499 4232 4.996434 GCAGCAGCGAGGGTGTGT 62.996 66.667 7.59 0.00 38.49 3.72
3500 4233 4.994471 TGCAGCAGCGAGGGTGTG 62.994 66.667 0.00 0.00 46.23 3.82
3501 4234 4.254709 TTGCAGCAGCGAGGGTGT 62.255 61.111 0.00 0.00 46.23 4.16
3502 4235 3.730761 GTTGCAGCAGCGAGGGTG 61.731 66.667 0.00 2.08 46.23 4.61
3549 4283 1.202557 AGGTAAAACGACGCTTCACCA 60.203 47.619 6.11 0.00 0.00 4.17
3550 4284 1.458445 GAGGTAAAACGACGCTTCACC 59.542 52.381 0.00 0.00 0.00 4.02
3558 4292 1.386748 GTTACGGCGAGGTAAAACGAC 59.613 52.381 16.62 0.00 34.41 4.34
3589 4324 0.827925 AGTTCTGACCTCTGACGGCA 60.828 55.000 0.00 0.00 0.00 5.69
3591 4326 1.201181 CTGAGTTCTGACCTCTGACGG 59.799 57.143 3.83 0.00 0.00 4.79
3606 4341 0.403271 ATTGTGCTGCCCTTCTGAGT 59.597 50.000 0.00 0.00 0.00 3.41
3607 4342 0.809385 CATTGTGCTGCCCTTCTGAG 59.191 55.000 0.00 0.00 0.00 3.35
3608 4343 1.246056 GCATTGTGCTGCCCTTCTGA 61.246 55.000 0.00 0.00 40.96 3.27
3609 4344 1.214589 GCATTGTGCTGCCCTTCTG 59.785 57.895 0.00 0.00 40.96 3.02
3610 4345 3.690745 GCATTGTGCTGCCCTTCT 58.309 55.556 0.00 0.00 40.96 2.85


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

AutoCloner maintained by Alex Coulton.