Multiple sequence alignment - TraesCS5B01G358100

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 TraesCS5B01G358100 chr5B 100.000 3749 0 0 1 3749 537786294 537782546 0.000000e+00 6924.0
1 TraesCS5B01G358100 chr5D 91.927 3233 158 32 583 3749 441406411 441403216 0.000000e+00 4429.0
2 TraesCS5B01G358100 chr5A 93.327 2218 103 18 783 2982 558176957 558174767 0.000000e+00 3234.0
3 TraesCS5B01G358100 chr5A 82.682 716 61 21 3074 3749 558174323 558173631 9.030000e-161 577.0
4 TraesCS5B01G358100 chr5A 86.395 147 3 7 578 719 558177111 558176977 1.090000e-30 145.0
5 TraesCS5B01G358100 chr1D 87.777 1399 113 22 1526 2919 239622538 239621193 0.000000e+00 1583.0
6 TraesCS5B01G358100 chr1D 86.970 660 56 12 2263 2919 212525835 212526467 0.000000e+00 715.0
7 TraesCS5B01G358100 chr1D 82.692 104 16 2 1360 1462 416627321 416627219 1.430000e-14 91.6
8 TraesCS5B01G358100 chr4B 87.707 1391 118 22 1534 2919 339264340 339262998 0.000000e+00 1572.0
9 TraesCS5B01G358100 chr2D 87.420 1399 113 20 1526 2919 118533048 118534388 0.000000e+00 1550.0
10 TraesCS5B01G358100 chr4D 87.134 1399 123 21 1526 2919 93450124 93448778 0.000000e+00 1533.0
11 TraesCS5B01G358100 chr3B 88.785 1070 86 12 1534 2601 809806232 809807269 0.000000e+00 1280.0
12 TraesCS5B01G358100 chr3B 89.094 541 33 8 16 553 498329412 498329929 0.000000e+00 649.0
13 TraesCS5B01G358100 chr3B 88.930 542 34 10 16 554 498323255 498322737 0.000000e+00 645.0
14 TraesCS5B01G358100 chr3B 88.540 541 36 16 16 553 498296447 498296964 1.900000e-177 632.0
15 TraesCS5B01G358100 chr3B 88.192 542 38 9 16 554 498330529 498331047 1.140000e-174 623.0
16 TraesCS5B01G358100 chr3B 88.170 541 38 9 16 553 498333917 498333400 4.110000e-174 621.0
17 TraesCS5B01G358100 chr3B 87.723 505 36 4 16 517 498295355 498295836 1.950000e-157 566.0
18 TraesCS5B01G358100 chr3A 88.197 1076 95 9 1597 2672 431134968 431136011 0.000000e+00 1254.0
19 TraesCS5B01G358100 chr3A 82.569 218 21 9 2706 2920 431136012 431136215 3.850000e-40 176.0
20 TraesCS5B01G358100 chr7B 84.000 275 27 9 2648 2919 375392208 375392468 8.040000e-62 248.0


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 TraesCS5B01G358100 chr5B 537782546 537786294 3748 True 6924.000000 6924 100.0000 1 3749 1 chr5B.!!$R1 3748
1 TraesCS5B01G358100 chr5D 441403216 441406411 3195 True 4429.000000 4429 91.9270 583 3749 1 chr5D.!!$R1 3166
2 TraesCS5B01G358100 chr5A 558173631 558177111 3480 True 1318.666667 3234 87.4680 578 3749 3 chr5A.!!$R1 3171
3 TraesCS5B01G358100 chr1D 239621193 239622538 1345 True 1583.000000 1583 87.7770 1526 2919 1 chr1D.!!$R1 1393
4 TraesCS5B01G358100 chr1D 212525835 212526467 632 False 715.000000 715 86.9700 2263 2919 1 chr1D.!!$F1 656
5 TraesCS5B01G358100 chr4B 339262998 339264340 1342 True 1572.000000 1572 87.7070 1534 2919 1 chr4B.!!$R1 1385
6 TraesCS5B01G358100 chr2D 118533048 118534388 1340 False 1550.000000 1550 87.4200 1526 2919 1 chr2D.!!$F1 1393
7 TraesCS5B01G358100 chr4D 93448778 93450124 1346 True 1533.000000 1533 87.1340 1526 2919 1 chr4D.!!$R1 1393
8 TraesCS5B01G358100 chr3B 809806232 809807269 1037 False 1280.000000 1280 88.7850 1534 2601 1 chr3B.!!$F1 1067
9 TraesCS5B01G358100 chr3B 498322737 498323255 518 True 645.000000 645 88.9300 16 554 1 chr3B.!!$R1 538
10 TraesCS5B01G358100 chr3B 498329412 498331047 1635 False 636.000000 649 88.6430 16 554 2 chr3B.!!$F3 538
11 TraesCS5B01G358100 chr3B 498333400 498333917 517 True 621.000000 621 88.1700 16 553 1 chr3B.!!$R2 537
12 TraesCS5B01G358100 chr3B 498295355 498296964 1609 False 599.000000 632 88.1315 16 553 2 chr3B.!!$F2 537
13 TraesCS5B01G358100 chr3A 431134968 431136215 1247 False 715.000000 1254 85.3830 1597 2920 2 chr3A.!!$F1 1323

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
790 798 0.036671 CAACTAACCGTCCCCACTCC 60.037 60.0 0.0 0.0 0.0 3.85 F
2214 2293 0.537188 ACAAATGGGTCGAGATCGCT 59.463 50.0 0.0 0.0 39.6 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 2375 1.009900 CGAGATGGTAGGCGACGAC 60.010 63.158 0.00 0.0 34.90 4.34 R
3238 3882 0.883153 TCATGGCACTTGCACATCAC 59.117 50.000 3.15 0.0 44.36 3.06 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
34 35 4.838486 GACGCTCCCTGCTCGACG 62.838 72.222 0.00 0.00 40.11 5.12
54 55 4.147449 CTCGACATGGCGGCCTCA 62.147 66.667 23.19 0.00 0.00 3.86
93 94 2.394563 GCGTTCTCTGCTTGGAGCC 61.395 63.158 0.00 0.00 41.51 4.70
115 116 4.845580 CATGGCGGCCTCGAGCTT 62.846 66.667 21.46 0.00 43.05 3.74
121 122 3.706373 GGCCTCGAGCTTGACCCA 61.706 66.667 6.99 0.00 43.05 4.51
135 136 3.473647 CCCATCCCAGCTCGCTGA 61.474 66.667 19.78 1.62 46.30 4.26
188 189 0.532573 TCCTGCATCTCCTCGAACAC 59.467 55.000 0.00 0.00 0.00 3.32
199 200 0.597637 CTCGAACACGGCAGAACAGT 60.598 55.000 0.00 0.00 0.00 3.55
207 208 1.961394 ACGGCAGAACAGTAGAGAACA 59.039 47.619 0.00 0.00 0.00 3.18
209 210 2.689646 GGCAGAACAGTAGAGAACACC 58.310 52.381 0.00 0.00 0.00 4.16
254 255 4.628715 GCTGATTTAGTTGAGGGATTGGGA 60.629 45.833 0.00 0.00 0.00 4.37
262 263 0.679960 GAGGGATTGGGAAACACCGG 60.680 60.000 0.00 0.00 40.11 5.28
284 285 2.620562 CACTGTGTGCTAGCTTGCA 58.379 52.632 19.10 19.10 41.05 4.08
285 286 0.516001 CACTGTGTGCTAGCTTGCAG 59.484 55.000 23.27 20.36 44.20 4.41
286 287 1.233285 ACTGTGTGCTAGCTTGCAGC 61.233 55.000 23.27 18.14 44.20 5.25
295 296 3.755434 GCTTGCAGCTCCTTGTGT 58.245 55.556 0.00 0.00 38.45 3.72
296 297 1.285023 GCTTGCAGCTCCTTGTGTG 59.715 57.895 0.00 0.00 38.45 3.82
297 298 1.285023 CTTGCAGCTCCTTGTGTGC 59.715 57.895 0.00 0.00 36.42 4.57
298 299 1.152902 TTGCAGCTCCTTGTGTGCT 60.153 52.632 0.00 0.00 44.35 4.40
299 300 0.108396 TTGCAGCTCCTTGTGTGCTA 59.892 50.000 0.00 0.00 41.70 3.49
300 301 0.321034 TGCAGCTCCTTGTGTGCTAG 60.321 55.000 0.00 0.00 41.70 3.42
316 317 6.030228 GTGTGCTAGCTTGACCATTTAATTC 58.970 40.000 17.23 0.00 0.00 2.17
325 326 9.118300 AGCTTGACCATTTAATTCAGAGATTAG 57.882 33.333 0.00 0.00 0.00 1.73
359 363 1.889829 CAGAGGAGGACGGATATGACC 59.110 57.143 0.00 0.00 0.00 4.02
398 402 5.648526 GTCAGTGAGACTAGACTGTAATCCA 59.351 44.000 0.00 0.00 44.09 3.41
399 403 6.320164 GTCAGTGAGACTAGACTGTAATCCAT 59.680 42.308 0.00 0.00 44.09 3.41
450 454 5.279406 CCAAACAGATGCAGGGTTCAAAATA 60.279 40.000 0.00 0.00 0.00 1.40
452 456 4.019174 ACAGATGCAGGGTTCAAAATAGG 58.981 43.478 0.00 0.00 0.00 2.57
476 480 3.222603 GGGATTCCAAAGTTGAGTGTGT 58.777 45.455 4.80 0.00 0.00 3.72
478 482 4.499696 GGGATTCCAAAGTTGAGTGTGTTG 60.500 45.833 4.80 0.00 0.00 3.33
483 487 6.279513 TCCAAAGTTGAGTGTGTTGATTTT 57.720 33.333 0.00 0.00 0.00 1.82
495 499 6.725834 AGTGTGTTGATTTTAGGGATTGGAAT 59.274 34.615 0.00 0.00 0.00 3.01
505 509 3.608067 AGGGATTGGAATTTTGGGGTTT 58.392 40.909 0.00 0.00 0.00 3.27
517 521 7.549134 GGAATTTTGGGGTTTGATTTAGCTAAG 59.451 37.037 6.24 0.00 0.00 2.18
520 524 3.245443 TGGGGTTTGATTTAGCTAAGCCA 60.245 43.478 13.38 9.66 41.02 4.75
538 542 4.019174 AGCCATATGAGTTCAAGGTTTGG 58.981 43.478 3.65 0.00 0.00 3.28
553 557 4.101114 AGGTTTGGTTTGGACTTTTTCCT 58.899 39.130 0.00 0.00 46.10 3.36
554 558 4.161565 AGGTTTGGTTTGGACTTTTTCCTC 59.838 41.667 0.00 0.00 46.10 3.71
555 559 4.109766 GTTTGGTTTGGACTTTTTCCTCG 58.890 43.478 0.00 0.00 46.10 4.63
557 561 2.946990 TGGTTTGGACTTTTTCCTCGAC 59.053 45.455 0.00 0.00 46.10 4.20
558 562 2.032290 GGTTTGGACTTTTTCCTCGACG 60.032 50.000 0.00 0.00 46.10 5.12
564 568 2.867975 GACTTTTTCCTCGACGAAACCA 59.132 45.455 8.80 0.02 31.57 3.67
566 570 3.497262 ACTTTTTCCTCGACGAAACCATC 59.503 43.478 8.80 0.00 31.57 3.51
574 578 3.470267 CGAAACCATCGTCACCCG 58.530 61.111 0.00 0.00 46.52 5.28
576 580 1.004200 GAAACCATCGTCACCCGGT 60.004 57.895 0.00 0.00 37.11 5.28
577 581 1.004200 AAACCATCGTCACCCGGTC 60.004 57.895 0.00 0.00 37.11 4.79
578 582 1.760479 AAACCATCGTCACCCGGTCA 61.760 55.000 0.00 0.00 37.11 4.02
579 583 2.125673 CCATCGTCACCCGGTCAC 60.126 66.667 0.00 0.00 37.11 3.67
580 584 2.125673 CATCGTCACCCGGTCACC 60.126 66.667 0.00 0.00 37.11 4.02
724 731 2.976356 GGTAACCGAGCCGTTCCT 59.024 61.111 0.00 0.00 0.00 3.36
725 732 1.447314 GGTAACCGAGCCGTTCCTG 60.447 63.158 0.00 0.00 0.00 3.86
726 733 2.098831 GTAACCGAGCCGTTCCTGC 61.099 63.158 0.00 0.00 0.00 4.85
735 742 4.077184 CGTTCCTGCCCCTGCGTA 62.077 66.667 0.00 0.00 41.78 4.42
736 743 2.349755 GTTCCTGCCCCTGCGTAA 59.650 61.111 0.00 0.00 41.78 3.18
737 744 2.038837 GTTCCTGCCCCTGCGTAAC 61.039 63.158 0.00 0.00 41.78 2.50
738 745 3.262448 TTCCTGCCCCTGCGTAACC 62.262 63.158 0.00 0.00 41.78 2.85
740 747 4.077184 CTGCCCCTGCGTAACCGA 62.077 66.667 0.00 0.00 41.78 4.69
741 748 4.077184 TGCCCCTGCGTAACCGAG 62.077 66.667 0.00 0.00 41.78 4.63
743 750 4.832608 CCCCTGCGTAACCGAGCC 62.833 72.222 0.00 0.00 35.63 4.70
749 756 4.807039 CGTAACCGAGCCCCACCG 62.807 72.222 0.00 0.00 35.63 4.94
779 787 0.775542 AACCCCCACTCCAACTAACC 59.224 55.000 0.00 0.00 0.00 2.85
781 789 1.486145 CCCCCACTCCAACTAACCGT 61.486 60.000 0.00 0.00 0.00 4.83
790 798 0.036671 CAACTAACCGTCCCCACTCC 60.037 60.000 0.00 0.00 0.00 3.85
791 799 1.196766 AACTAACCGTCCCCACTCCC 61.197 60.000 0.00 0.00 0.00 4.30
792 800 2.284847 TAACCGTCCCCACTCCCC 60.285 66.667 0.00 0.00 0.00 4.81
995 1007 3.532232 TCTTCTGATCCACCTACCTACCT 59.468 47.826 0.00 0.00 0.00 3.08
1437 1456 1.812922 CGTGCTGGAGATGGTGCTC 60.813 63.158 0.00 0.00 0.00 4.26
1503 1522 3.760035 CGGTGGAGGGACCTCACG 61.760 72.222 19.30 15.50 44.40 4.35
1880 1937 4.265056 GGTGCTGGGGGTGTTCGT 62.265 66.667 0.00 0.00 0.00 3.85
1935 2013 2.125512 GAGAAGCATGTCCGGCGT 60.126 61.111 6.01 0.00 36.08 5.68
2083 2161 4.250305 ACGGTCACGGCAAGGCTT 62.250 61.111 0.00 0.00 46.48 4.35
2124 2202 1.002868 TCAGGCAAGGCAAGCTCTC 60.003 57.895 0.00 0.00 0.00 3.20
2214 2293 0.537188 ACAAATGGGTCGAGATCGCT 59.463 50.000 0.00 0.00 39.60 4.93
2244 2323 2.742372 GACGTCGGCTTGGCATGT 60.742 61.111 0.00 0.00 0.00 3.21
2250 2329 2.676471 GGCTTGGCATGTTCCGGT 60.676 61.111 0.00 0.00 0.00 5.28
2320 2399 2.491022 GCCTACCATCTCGACGCCT 61.491 63.158 0.00 0.00 0.00 5.52
2505 2584 4.357947 TCGACACCGCTGCTCCAC 62.358 66.667 0.00 0.00 35.37 4.02
2511 2590 3.699894 CCGCTGCTCCACTGGACT 61.700 66.667 0.00 0.00 0.00 3.85
2619 2698 3.071580 GATCTTCGGCAAGGTCCTG 57.928 57.895 0.00 0.00 34.03 3.86
2751 2929 1.447489 CGTGCTGCTCCTCTGAAGG 60.447 63.158 0.00 0.00 44.89 3.46
2761 2939 4.373116 TCTGAAGGTCGCCGGTGC 62.373 66.667 11.05 5.44 0.00 5.01
2909 3187 3.607422 TGTTCATGCTGAGTTTGTTCG 57.393 42.857 0.00 0.00 0.00 3.95
2982 3266 5.300752 ACCACAATCAGACTCACTTTGTAG 58.699 41.667 0.00 0.00 31.08 2.74
2983 3267 4.153117 CCACAATCAGACTCACTTTGTAGC 59.847 45.833 0.00 0.00 31.08 3.58
2984 3268 4.751600 CACAATCAGACTCACTTTGTAGCA 59.248 41.667 0.00 0.00 31.08 3.49
3043 3361 2.906389 AGAGAAAGGGCATGTGACTGTA 59.094 45.455 0.00 0.00 0.00 2.74
3095 3736 8.980143 ATGTAATGTTAATGTAAGTTGGTTGC 57.020 30.769 0.00 0.00 0.00 4.17
3105 3746 3.733443 AAGTTGGTTGCCAAATCACTC 57.267 42.857 1.79 0.00 45.73 3.51
3108 3749 2.622942 GTTGGTTGCCAAATCACTCTCA 59.377 45.455 1.79 0.00 45.73 3.27
3117 3758 4.264253 CCAAATCACTCTCAATGGCAGTA 58.736 43.478 0.00 0.00 0.00 2.74
3238 3882 3.250040 CGTGGGTCTCTTTTAAACTGTGG 59.750 47.826 0.00 0.00 0.00 4.17
3265 3910 2.367894 TGCAAGTGCCATGATCCAAAAA 59.632 40.909 0.00 0.00 41.18 1.94
3328 3980 0.824759 AGGACAGATCTGTAACCCGC 59.175 55.000 27.95 14.17 45.05 6.13
3385 4037 9.352191 AGTACTAGTCTACCCAATTGTATAGTG 57.648 37.037 0.00 2.26 0.00 2.74
3417 4069 1.159285 TGTTCTGAAGAGCCATTGCG 58.841 50.000 0.00 0.00 44.33 4.85
3441 4093 6.342111 GTTAGTTTACCTCTGAGAAGGGATG 58.658 44.000 6.17 0.00 41.04 3.51
3473 4125 9.050601 GGAATCTTTATCATTCTAGTTGGTGAG 57.949 37.037 0.00 0.00 31.82 3.51
3575 5019 6.806751 TGAGAATTAAGACCAGTTCTATCCG 58.193 40.000 0.00 0.00 32.51 4.18
3697 5210 5.957798 TCATGAACCAGAGCATCATTTTTC 58.042 37.500 0.00 0.00 37.82 2.29
3698 5211 4.424061 TGAACCAGAGCATCATTTTTCG 57.576 40.909 0.00 0.00 37.82 3.46
3700 5213 1.474077 ACCAGAGCATCATTTTTCGCC 59.526 47.619 0.00 0.00 37.82 5.54
3701 5214 1.532505 CCAGAGCATCATTTTTCGCCG 60.533 52.381 0.00 0.00 37.82 6.46
3702 5215 1.398041 CAGAGCATCATTTTTCGCCGA 59.602 47.619 0.00 0.00 37.82 5.54
3703 5216 2.083774 AGAGCATCATTTTTCGCCGAA 58.916 42.857 0.00 0.00 37.82 4.30
3704 5217 2.487762 AGAGCATCATTTTTCGCCGAAA 59.512 40.909 8.43 8.43 37.82 3.46
3728 5246 6.560003 AAGAAAAGAAACCCAATCCAAAGT 57.440 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.984193 GAGCTTGAGGCCGCCATGT 62.984 63.158 13.15 0.00 43.05 3.21
115 116 3.785859 GCGAGCTGGGATGGGTCA 61.786 66.667 0.00 0.00 0.00 4.02
121 122 0.106335 CAAGATCAGCGAGCTGGGAT 59.894 55.000 22.93 11.49 43.75 3.85
155 156 4.357279 AGGAGCACAAGGGCAGCC 62.357 66.667 1.26 1.26 35.83 4.85
176 177 1.176619 TTCTGCCGTGTTCGAGGAGA 61.177 55.000 0.00 0.00 39.71 3.71
188 189 2.329379 GTGTTCTCTACTGTTCTGCCG 58.671 52.381 0.00 0.00 0.00 5.69
199 200 0.322816 AGTACGGCCGGTGTTCTCTA 60.323 55.000 31.76 6.95 0.00 2.43
207 208 0.752743 TAGCACATAGTACGGCCGGT 60.753 55.000 31.76 17.55 0.00 5.28
209 210 0.663568 GCTAGCACATAGTACGGCCG 60.664 60.000 26.86 26.86 33.65 6.13
240 241 1.893137 GGTGTTTCCCAATCCCTCAAC 59.107 52.381 0.00 0.00 0.00 3.18
254 255 4.868116 ACAGTGCGGCCGGTGTTT 62.868 61.111 29.38 0.00 0.00 2.83
279 280 1.170919 AGCACACAAGGAGCTGCAAG 61.171 55.000 8.35 1.17 37.20 4.01
280 281 0.108396 TAGCACACAAGGAGCTGCAA 59.892 50.000 8.35 0.00 39.30 4.08
281 282 0.321034 CTAGCACACAAGGAGCTGCA 60.321 55.000 8.35 0.00 39.30 4.41
282 283 1.642952 GCTAGCACACAAGGAGCTGC 61.643 60.000 10.63 0.00 39.30 5.25
283 284 0.036577 AGCTAGCACACAAGGAGCTG 60.037 55.000 18.83 0.00 41.82 4.24
284 285 0.689623 AAGCTAGCACACAAGGAGCT 59.310 50.000 18.83 0.00 45.23 4.09
285 286 0.801251 CAAGCTAGCACACAAGGAGC 59.199 55.000 18.83 0.00 0.00 4.70
286 287 2.072298 GTCAAGCTAGCACACAAGGAG 58.928 52.381 18.83 0.00 0.00 3.69
287 288 1.270839 GGTCAAGCTAGCACACAAGGA 60.271 52.381 18.83 0.31 0.00 3.36
288 289 1.160137 GGTCAAGCTAGCACACAAGG 58.840 55.000 18.83 0.00 0.00 3.61
289 290 1.882912 TGGTCAAGCTAGCACACAAG 58.117 50.000 18.83 0.00 0.00 3.16
290 291 2.566833 ATGGTCAAGCTAGCACACAA 57.433 45.000 18.83 3.80 0.00 3.33
291 292 2.566833 AATGGTCAAGCTAGCACACA 57.433 45.000 18.83 8.67 0.00 3.72
292 293 5.567138 ATTAAATGGTCAAGCTAGCACAC 57.433 39.130 18.83 9.72 0.00 3.82
293 294 5.709631 TGAATTAAATGGTCAAGCTAGCACA 59.290 36.000 18.83 7.94 0.00 4.57
294 295 6.094048 TCTGAATTAAATGGTCAAGCTAGCAC 59.906 38.462 18.83 6.29 0.00 4.40
295 296 6.179756 TCTGAATTAAATGGTCAAGCTAGCA 58.820 36.000 18.83 0.00 0.00 3.49
296 297 6.540189 TCTCTGAATTAAATGGTCAAGCTAGC 59.460 38.462 6.62 6.62 0.00 3.42
297 298 8.674263 ATCTCTGAATTAAATGGTCAAGCTAG 57.326 34.615 0.00 0.00 0.00 3.42
299 300 7.951347 AATCTCTGAATTAAATGGTCAAGCT 57.049 32.000 0.00 0.00 0.00 3.74
300 301 8.348507 CCTAATCTCTGAATTAAATGGTCAAGC 58.651 37.037 0.00 0.00 0.00 4.01
316 317 6.882656 TGTCTCTCAAATTCCCTAATCTCTG 58.117 40.000 0.00 0.00 0.00 3.35
325 326 3.118445 CCTCCTCTGTCTCTCAAATTCCC 60.118 52.174 0.00 0.00 0.00 3.97
359 363 0.243907 CTGACAGTGTGACCCTACCG 59.756 60.000 0.00 0.00 0.00 4.02
369 373 3.818210 CAGTCTAGTCTCACTGACAGTGT 59.182 47.826 29.87 16.48 46.03 3.55
398 402 4.676109 TGGGAAATCAACAATCCTGACAT 58.324 39.130 0.00 0.00 33.61 3.06
399 403 4.081406 CTGGGAAATCAACAATCCTGACA 58.919 43.478 0.00 0.00 33.61 3.58
450 454 0.611896 CAACTTTGGAATCCCGGCCT 60.612 55.000 0.00 0.00 34.29 5.19
452 456 0.811281 CTCAACTTTGGAATCCCGGC 59.189 55.000 0.00 0.00 34.29 6.13
476 480 7.401246 CCCAAAATTCCAATCCCTAAAATCAA 58.599 34.615 0.00 0.00 0.00 2.57
478 482 6.069673 ACCCCAAAATTCCAATCCCTAAAATC 60.070 38.462 0.00 0.00 0.00 2.17
483 487 4.427956 AACCCCAAAATTCCAATCCCTA 57.572 40.909 0.00 0.00 0.00 3.53
495 499 5.279758 GGCTTAGCTAAATCAAACCCCAAAA 60.280 40.000 7.74 0.00 0.00 2.44
505 509 7.508687 TGAACTCATATGGCTTAGCTAAATCA 58.491 34.615 7.74 8.98 0.00 2.57
517 521 3.763897 ACCAAACCTTGAACTCATATGGC 59.236 43.478 2.13 0.00 0.00 4.40
520 524 6.015434 GTCCAAACCAAACCTTGAACTCATAT 60.015 38.462 0.00 0.00 0.00 1.78
567 571 3.608662 TCGTGGTGACCGGGTGAC 61.609 66.667 3.30 6.24 0.00 3.67
568 572 3.608662 GTCGTGGTGACCGGGTGA 61.609 66.667 3.30 0.00 42.04 4.02
576 580 3.371063 GGGAGCGAGTCGTGGTGA 61.371 66.667 15.08 0.00 0.00 4.02
577 581 4.778415 CGGGAGCGAGTCGTGGTG 62.778 72.222 15.08 0.00 0.00 4.17
580 584 4.477975 GTCCGGGAGCGAGTCGTG 62.478 72.222 15.08 0.00 0.00 4.35
724 731 4.077184 CTCGGTTACGCAGGGGCA 62.077 66.667 0.00 0.00 41.24 5.36
726 733 4.832608 GGCTCGGTTACGCAGGGG 62.833 72.222 0.00 0.00 40.69 4.79
728 735 4.832608 GGGGCTCGGTTACGCAGG 62.833 72.222 0.00 0.00 40.69 4.85
730 737 4.382320 GTGGGGCTCGGTTACGCA 62.382 66.667 0.00 0.00 40.69 5.24
739 746 3.056328 GAAAGTGCGGTGGGGCTC 61.056 66.667 0.00 0.00 0.00 4.70
740 747 4.660938 GGAAAGTGCGGTGGGGCT 62.661 66.667 0.00 0.00 0.00 5.19
743 750 3.801068 TTGGGGAAAGTGCGGTGGG 62.801 63.158 0.00 0.00 0.00 4.61
749 756 2.603473 GGGGGTTGGGGAAAGTGC 60.603 66.667 0.00 0.00 0.00 4.40
779 787 2.760385 GAGAGGGGAGTGGGGACG 60.760 72.222 0.00 0.00 0.00 4.79
781 789 3.273654 ACGAGAGGGGAGTGGGGA 61.274 66.667 0.00 0.00 0.00 4.81
790 798 2.829458 GTCGGGGAGACGAGAGGG 60.829 72.222 0.00 0.00 44.42 4.30
1363 1382 2.969238 CGCCACCGCATCATCCTC 60.969 66.667 0.00 0.00 34.03 3.71
1560 1579 1.524008 CCCCGAACAGGAAAAGCCAC 61.524 60.000 0.00 0.00 45.00 5.01
1566 1585 1.669440 CTCGACCCCGAACAGGAAA 59.331 57.895 0.00 0.00 45.04 3.13
1758 1814 2.343758 GTCTTGACGGAGCCAGCA 59.656 61.111 0.00 0.00 0.00 4.41
1794 1851 1.555075 GTGAGAGGGCTGAACACCATA 59.445 52.381 0.00 0.00 0.00 2.74
1949 2027 2.045926 CTCCCAGCCGGAACTTGG 60.046 66.667 5.05 6.70 41.40 3.61
2083 2161 1.601759 GCTGCTTCTGTTGCCTGGA 60.602 57.895 0.00 0.00 0.00 3.86
2267 2346 2.414481 GACTCGCAGTAGACGTAGAACA 59.586 50.000 0.00 0.00 0.00 3.18
2296 2375 1.009900 CGAGATGGTAGGCGACGAC 60.010 63.158 0.00 0.00 34.90 4.34
2320 2399 2.571757 GACGACGGACCATGAGCA 59.428 61.111 0.00 0.00 0.00 4.26
2529 2608 3.640000 GAATCCATGGGCGCGTCG 61.640 66.667 13.02 0.00 0.00 5.12
2751 2929 4.509737 GGAGTAGGCACCGGCGAC 62.510 72.222 9.30 0.00 42.47 5.19
2761 2939 3.501062 GTGGAAAAGGAAAACGGAGTAGG 59.499 47.826 0.00 0.00 45.00 3.18
2982 3266 5.528690 TCATATGTAGATTGACCAAGCTTGC 59.471 40.000 21.43 9.00 38.17 4.01
2983 3267 7.741027 ATCATATGTAGATTGACCAAGCTTG 57.259 36.000 19.93 19.93 38.17 4.01
3043 3361 6.467677 AGAAAAGTGTAGAGTGTATGCATGT 58.532 36.000 10.16 0.00 0.00 3.21
3077 3718 6.926272 TGATTTGGCAACCAACTTACATTAAC 59.074 34.615 0.00 0.00 43.82 2.01
3078 3719 6.926272 GTGATTTGGCAACCAACTTACATTAA 59.074 34.615 0.00 0.00 43.82 1.40
3079 3720 6.266558 AGTGATTTGGCAACCAACTTACATTA 59.733 34.615 0.00 0.00 43.82 1.90
3080 3721 5.070313 AGTGATTTGGCAACCAACTTACATT 59.930 36.000 0.00 1.18 43.82 2.71
3081 3722 4.588528 AGTGATTTGGCAACCAACTTACAT 59.411 37.500 0.00 0.00 43.82 2.29
3082 3723 3.957497 AGTGATTTGGCAACCAACTTACA 59.043 39.130 0.00 3.36 43.82 2.41
3083 3724 4.278419 AGAGTGATTTGGCAACCAACTTAC 59.722 41.667 0.00 1.27 43.82 2.34
3084 3725 4.469657 AGAGTGATTTGGCAACCAACTTA 58.530 39.130 0.00 0.00 43.82 2.24
3085 3726 3.299503 AGAGTGATTTGGCAACCAACTT 58.700 40.909 0.00 0.00 43.82 2.66
3086 3727 2.887152 GAGAGTGATTTGGCAACCAACT 59.113 45.455 0.00 3.32 43.82 3.16
3090 3731 3.367703 CCATTGAGAGTGATTTGGCAACC 60.368 47.826 0.00 0.00 0.00 3.77
3095 3736 3.087031 ACTGCCATTGAGAGTGATTTGG 58.913 45.455 0.00 0.00 0.00 3.28
3105 3746 4.100035 TGTGATAGTCCTACTGCCATTGAG 59.900 45.833 0.00 0.00 0.00 3.02
3108 3749 4.225042 TGTTGTGATAGTCCTACTGCCATT 59.775 41.667 0.00 0.00 0.00 3.16
3117 3758 3.679917 CGCAGGATTGTTGTGATAGTCCT 60.680 47.826 0.00 0.00 34.16 3.85
3212 3856 1.061546 TTAAAAGAGACCCACGGCCT 58.938 50.000 0.00 0.00 0.00 5.19
3238 3882 0.883153 TCATGGCACTTGCACATCAC 59.117 50.000 3.15 0.00 44.36 3.06
3292 3944 5.103301 TCTGTCCTCATCTCTCTCCCTTTAT 60.103 44.000 0.00 0.00 0.00 1.40
3293 3945 4.230733 TCTGTCCTCATCTCTCTCCCTTTA 59.769 45.833 0.00 0.00 0.00 1.85
3328 3980 6.647212 TCTGTGATAGAGTACAATTTTGCG 57.353 37.500 0.00 0.00 0.00 4.85
3385 4037 7.009265 GGCTCTTCAGAACAAAAGTACAAAAAC 59.991 37.037 0.00 0.00 0.00 2.43
3398 4050 1.159285 CGCAATGGCTCTTCAGAACA 58.841 50.000 0.00 0.00 38.10 3.18
3417 4069 5.997384 TCCCTTCTCAGAGGTAAACTAAC 57.003 43.478 0.00 0.00 34.88 2.34
3627 5125 7.460071 TGGTCCTACTAGTGATTACTATCTCC 58.540 42.308 5.39 0.00 38.65 3.71
3644 5142 3.265791 CAACAGATGCTCTTGGTCCTAC 58.734 50.000 0.00 0.00 0.00 3.18
3647 5145 2.191128 ACAACAGATGCTCTTGGTCC 57.809 50.000 0.00 0.00 0.00 4.46
3648 5146 3.437049 GGTAACAACAGATGCTCTTGGTC 59.563 47.826 0.00 0.00 0.00 4.02
3697 5210 2.792674 GGGTTTCTTTTCTTTTTCGGCG 59.207 45.455 0.00 0.00 0.00 6.46
3698 5211 3.787785 TGGGTTTCTTTTCTTTTTCGGC 58.212 40.909 0.00 0.00 0.00 5.54
3700 5213 6.045955 TGGATTGGGTTTCTTTTCTTTTTCG 58.954 36.000 0.00 0.00 0.00 3.46
3701 5214 7.857734 TTGGATTGGGTTTCTTTTCTTTTTC 57.142 32.000 0.00 0.00 0.00 2.29
3702 5215 7.888021 ACTTTGGATTGGGTTTCTTTTCTTTTT 59.112 29.630 0.00 0.00 0.00 1.94
3703 5216 7.402054 ACTTTGGATTGGGTTTCTTTTCTTTT 58.598 30.769 0.00 0.00 0.00 2.27
3704 5217 6.957631 ACTTTGGATTGGGTTTCTTTTCTTT 58.042 32.000 0.00 0.00 0.00 2.52
3706 5219 7.508977 TGATACTTTGGATTGGGTTTCTTTTCT 59.491 33.333 0.00 0.00 0.00 2.52
3707 5220 7.666623 TGATACTTTGGATTGGGTTTCTTTTC 58.333 34.615 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.