Multiple sequence alignment - TraesCS5B01G517300

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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 TraesCS5B01G517300 chr5B 100.000 2489 0 0 1 2489 680823445 680820957 0.000000e+00 4597
1 TraesCS5B01G517300 chr4A 98.052 924 12 1 1566 2489 603073610 603074527 0.000000e+00 1602
2 TraesCS5B01G517300 chr4A 94.864 701 32 1 808 1504 629391686 629392386 0.000000e+00 1092
3 TraesCS5B01G517300 chr4A 90.311 805 59 9 1 799 629387767 629388558 0.000000e+00 1037
4 TraesCS5B01G517300 chr4A 86.217 653 54 17 1845 2488 105235878 105236503 0.000000e+00 675
5 TraesCS5B01G517300 chr4A 87.452 518 29 7 1973 2470 209502248 209501747 4.650000e-157 564
6 TraesCS5B01G517300 chr4A 91.443 409 34 1 1577 1985 209502610 209502203 6.010000e-156 560
7 TraesCS5B01G517300 chr4A 87.451 255 19 12 1566 1814 105229084 105229331 5.240000e-72 281
8 TraesCS5B01G517300 chr4B 96.861 924 21 1 1566 2489 165021479 165022394 0.000000e+00 1539
9 TraesCS5B01G517300 chr2D 89.089 944 52 15 1572 2489 218774105 218773187 0.000000e+00 1125
10 TraesCS5B01G517300 chr2D 93.564 404 22 3 1585 1985 627184950 627185352 1.270000e-167 599
11 TraesCS5B01G517300 chr2D 90.157 447 19 5 2067 2489 343110685 343110240 2.160000e-155 558
12 TraesCS5B01G517300 chr2D 86.245 538 22 12 1973 2489 627185307 627185813 1.010000e-148 536
13 TraesCS5B01G517300 chr7A 85.597 729 43 15 1577 2282 734041531 734040842 0.000000e+00 708
14 TraesCS5B01G517300 chr7A 84.911 729 48 15 1577 2282 734047762 734047073 0.000000e+00 680
15 TraesCS5B01G517300 chr5A 86.983 653 52 17 1845 2489 643238971 643239598 0.000000e+00 704
16 TraesCS5B01G517300 chr2A 86.544 654 50 17 1845 2489 161594587 161593963 0.000000e+00 686
17 TraesCS5B01G517300 chr1A 86.239 654 50 17 1845 2489 545922782 545922160 0.000000e+00 673
18 TraesCS5B01G517300 chr1D 81.404 812 81 25 1717 2487 163405325 163404543 1.270000e-167 599
19 TraesCS5B01G517300 chr7D 92.548 416 29 1 1572 1985 161545960 161546375 1.650000e-166 595
20 TraesCS5B01G517300 chr7D 86.989 538 32 11 1973 2489 161546330 161546850 2.780000e-159 571
21 TraesCS5B01G517300 chr3A 88.652 141 14 2 1566 1706 452374102 452373964 1.180000e-38 171


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 TraesCS5B01G517300 chr5B 680820957 680823445 2488 True 4597.0 4597 100.0000 1 2489 1 chr5B.!!$R1 2488
1 TraesCS5B01G517300 chr4A 603073610 603074527 917 False 1602.0 1602 98.0520 1566 2489 1 chr4A.!!$F3 923
2 TraesCS5B01G517300 chr4A 629387767 629392386 4619 False 1064.5 1092 92.5875 1 1504 2 chr4A.!!$F4 1503
3 TraesCS5B01G517300 chr4A 105235878 105236503 625 False 675.0 675 86.2170 1845 2488 1 chr4A.!!$F2 643
4 TraesCS5B01G517300 chr4A 209501747 209502610 863 True 562.0 564 89.4475 1577 2470 2 chr4A.!!$R1 893
5 TraesCS5B01G517300 chr4B 165021479 165022394 915 False 1539.0 1539 96.8610 1566 2489 1 chr4B.!!$F1 923
6 TraesCS5B01G517300 chr2D 218773187 218774105 918 True 1125.0 1125 89.0890 1572 2489 1 chr2D.!!$R1 917
7 TraesCS5B01G517300 chr2D 627184950 627185813 863 False 567.5 599 89.9045 1585 2489 2 chr2D.!!$F1 904
8 TraesCS5B01G517300 chr7A 734040842 734041531 689 True 708.0 708 85.5970 1577 2282 1 chr7A.!!$R1 705
9 TraesCS5B01G517300 chr7A 734047073 734047762 689 True 680.0 680 84.9110 1577 2282 1 chr7A.!!$R2 705
10 TraesCS5B01G517300 chr5A 643238971 643239598 627 False 704.0 704 86.9830 1845 2489 1 chr5A.!!$F1 644
11 TraesCS5B01G517300 chr2A 161593963 161594587 624 True 686.0 686 86.5440 1845 2489 1 chr2A.!!$R1 644
12 TraesCS5B01G517300 chr1A 545922160 545922782 622 True 673.0 673 86.2390 1845 2489 1 chr1A.!!$R1 644
13 TraesCS5B01G517300 chr1D 163404543 163405325 782 True 599.0 599 81.4040 1717 2487 1 chr1D.!!$R1 770
14 TraesCS5B01G517300 chr7D 161545960 161546850 890 False 583.0 595 89.7685 1572 2489 2 chr7D.!!$F1 917

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
271 274 0.536006 AGTGCTCTTTGCCTCACACC 60.536 55.0 0.0 0.0 42.0 4.16 F
989 4115 0.600255 CACTCCACCACGACAGGAAC 60.600 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 4588 0.902531 CGTCCTCCTTGTGGGTATGT 59.097 55.0 0.0 0.0 36.25 2.29 R
2295 5594 0.871057 CACACACACACACACACACA 59.129 50.0 0.0 0.0 0.00 3.72 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
26 27 4.920640 TTAAACCCGACATTTGCTCAAA 57.079 36.364 0.00 0.00 34.46 2.69
29 30 1.608590 ACCCGACATTTGCTCAAACTG 59.391 47.619 0.00 1.41 32.51 3.16
40 41 4.551702 TGCTCAAACTGGTATAGAAGCA 57.448 40.909 0.00 0.00 0.00 3.91
57 58 6.516739 AGAAGCAGTTTTAAATTCCTAGCC 57.483 37.500 0.00 0.00 0.00 3.93
58 59 6.249192 AGAAGCAGTTTTAAATTCCTAGCCT 58.751 36.000 0.00 0.00 0.00 4.58
148 151 8.827832 TCAATCAGATGAGGATTTAAACCAAT 57.172 30.769 8.80 3.51 32.86 3.16
178 181 9.823647 TTTAGAGCATTTAAACCAACAATTTGA 57.176 25.926 2.79 0.00 34.24 2.69
181 184 5.465056 AGCATTTAAACCAACAATTTGACCG 59.535 36.000 2.79 0.00 34.24 4.79
192 195 3.181487 ACAATTTGACCGCCATTATGAGC 60.181 43.478 2.79 0.00 0.00 4.26
208 211 3.678056 TGAGCGTGTTGAACTATCCTT 57.322 42.857 0.00 0.00 0.00 3.36
209 212 4.002906 TGAGCGTGTTGAACTATCCTTT 57.997 40.909 0.00 0.00 0.00 3.11
235 238 7.381948 TGCAAACAGTTAGCATCAATGTTAAAG 59.618 33.333 1.51 1.47 35.69 1.85
237 240 9.462174 CAAACAGTTAGCATCAATGTTAAAGAA 57.538 29.630 1.51 0.00 35.69 2.52
271 274 0.536006 AGTGCTCTTTGCCTCACACC 60.536 55.000 0.00 0.00 42.00 4.16
314 317 9.778741 TTTCTCTCAACTACATCATTAACTTGT 57.221 29.630 0.00 0.00 0.00 3.16
316 319 9.856488 TCTCTCAACTACATCATTAACTTGTAC 57.144 33.333 0.00 0.00 0.00 2.90
317 320 9.862371 CTCTCAACTACATCATTAACTTGTACT 57.138 33.333 0.00 0.00 0.00 2.73
342 345 1.232119 CGGTGCCCGTTTTTACTCTT 58.768 50.000 5.56 0.00 42.73 2.85
344 347 1.335597 GGTGCCCGTTTTTACTCTTGC 60.336 52.381 0.00 0.00 0.00 4.01
352 355 1.808411 TTTTACTCTTGCTGGGCTCG 58.192 50.000 0.00 0.00 0.00 5.03
353 356 0.673644 TTTACTCTTGCTGGGCTCGC 60.674 55.000 0.00 0.00 0.00 5.03
377 380 3.312421 CAGGGGCACATAAATTACAGACG 59.688 47.826 0.00 0.00 0.00 4.18
381 384 4.034048 GGGCACATAAATTACAGACGTGAG 59.966 45.833 0.00 0.00 0.00 3.51
390 393 1.179814 ACAGACGTGAGAGGGGTGTC 61.180 60.000 0.00 0.00 0.00 3.67
404 408 3.913163 AGGGGTGTCTCTGAAAATCTCTT 59.087 43.478 0.00 0.00 0.00 2.85
432 436 3.443045 GCCGTGCCTGATTGGGTG 61.443 66.667 0.00 0.00 36.00 4.61
472 477 3.600388 CAAGTTAGTGGATGGTGGAGTC 58.400 50.000 0.00 0.00 0.00 3.36
476 481 1.734655 AGTGGATGGTGGAGTCAACT 58.265 50.000 0.00 0.00 0.00 3.16
479 484 2.039084 GTGGATGGTGGAGTCAACTTCT 59.961 50.000 0.00 0.00 35.72 2.85
579 584 3.197333 GTCCTTCCCTTAACCACTACCTC 59.803 52.174 0.00 0.00 0.00 3.85
610 615 6.159398 AGTTCATCCAGGTCTCATTAAATCCT 59.841 38.462 0.00 0.00 0.00 3.24
613 618 7.056635 TCATCCAGGTCTCATTAAATCCTTTC 58.943 38.462 0.00 0.00 0.00 2.62
617 622 7.950124 TCCAGGTCTCATTAAATCCTTTCTTTT 59.050 33.333 0.00 0.00 0.00 2.27
645 650 8.953665 AGAATATATGGAAAAGAGAATCCCAGT 58.046 33.333 0.00 0.00 34.68 4.00
649 654 4.398319 TGGAAAAGAGAATCCCAGTTCAC 58.602 43.478 0.00 0.00 34.68 3.18
670 675 6.738114 TCACTTTGTCATAAGCCTTTTCAAG 58.262 36.000 0.00 0.00 0.00 3.02
710 717 9.167311 AGTTGATCTTTGTAATTCAGATGGTAC 57.833 33.333 0.00 0.00 0.00 3.34
747 754 9.136952 ACTTGAGTAATAGTACAAGTTTTAGCG 57.863 33.333 2.81 0.00 46.69 4.26
756 763 2.031683 ACAAGTTTTAGCGTGCACAGAC 59.968 45.455 18.64 5.48 0.00 3.51
758 765 2.494059 AGTTTTAGCGTGCACAGACAT 58.506 42.857 18.64 0.00 0.00 3.06
759 766 2.224079 AGTTTTAGCGTGCACAGACATG 59.776 45.455 18.64 0.00 0.00 3.21
766 773 2.474526 GCGTGCACAGACATGAATACAC 60.475 50.000 18.64 0.00 0.00 2.90
768 775 3.423515 CGTGCACAGACATGAATACACAC 60.424 47.826 18.64 0.14 0.00 3.82
773 780 4.756642 CACAGACATGAATACACACCAAGT 59.243 41.667 0.00 0.00 0.00 3.16
799 806 0.828022 TGTATAGGCCGTGTCCAAGG 59.172 55.000 0.00 0.00 0.00 3.61
805 812 3.052082 CCGTGTCCAAGGCTGCTG 61.052 66.667 0.00 0.00 0.00 4.41
806 813 3.730761 CGTGTCCAAGGCTGCTGC 61.731 66.667 7.10 7.10 38.76 5.25
845 3971 2.233654 CGCCGATGAAGCTTCTCCG 61.234 63.158 26.09 24.98 0.00 4.63
846 3972 2.529619 GCCGATGAAGCTTCTCCGC 61.530 63.158 26.09 20.38 0.00 5.54
847 3973 1.884926 CCGATGAAGCTTCTCCGCC 60.885 63.158 26.09 10.19 0.00 6.13
874 4000 3.521937 TCCGGATCCTAACAGAAACCATT 59.478 43.478 10.75 0.00 0.00 3.16
889 4015 6.007703 AGAAACCATTGGATCCTAACGAAAA 58.992 36.000 14.23 0.00 0.00 2.29
897 4023 3.822167 GGATCCTAACGAAAACAACCCAA 59.178 43.478 3.84 0.00 0.00 4.12
902 4028 1.842052 ACGAAAACAACCCAACACCT 58.158 45.000 0.00 0.00 0.00 4.00
978 4104 4.351054 CCCACAGCCCACTCCACC 62.351 72.222 0.00 0.00 0.00 4.61
989 4115 0.600255 CACTCCACCACGACAGGAAC 60.600 60.000 0.00 0.00 0.00 3.62
1108 4238 2.708255 GCCGTCCGTCGTCTCTAG 59.292 66.667 0.00 0.00 37.94 2.43
1164 4294 1.000496 CCGAGCGTCCTTATTAGGTCC 60.000 57.143 0.00 0.00 42.60 4.46
1188 4318 1.739562 CTGCAAGCTGGACGTCTCC 60.740 63.158 16.46 0.00 37.04 3.71
1207 4337 4.508128 CGGCGGCCGTCTACATGT 62.508 66.667 32.14 2.69 42.73 3.21
1245 4375 3.902086 GGGCGGGAGTACGAGCTC 61.902 72.222 2.73 2.73 35.47 4.09
1458 4588 1.663379 CCAGGTCCGACTGCGTCATA 61.663 60.000 8.91 0.00 37.16 2.15
1476 4606 3.709653 TCATACATACCCACAAGGAGGAC 59.290 47.826 0.00 0.00 39.89 3.85
1491 4621 0.393077 AGGACGACCTTTGGTGACAG 59.607 55.000 0.00 0.00 45.36 3.51
1494 4624 1.227823 CGACCTTTGGTGACAGCCA 60.228 57.895 1.47 0.00 44.54 4.75
1509 4639 3.386543 GCCACTGGCGATAGATTGT 57.613 52.632 3.73 0.00 39.62 2.71
1510 4640 1.668419 GCCACTGGCGATAGATTGTT 58.332 50.000 3.73 0.00 39.62 2.83
1511 4641 2.833794 GCCACTGGCGATAGATTGTTA 58.166 47.619 3.73 0.00 39.62 2.41
1512 4642 2.802816 GCCACTGGCGATAGATTGTTAG 59.197 50.000 3.73 0.00 39.62 2.34
1513 4643 3.393800 CCACTGGCGATAGATTGTTAGG 58.606 50.000 0.00 0.00 39.76 2.69
1514 4644 2.802816 CACTGGCGATAGATTGTTAGGC 59.197 50.000 0.00 0.00 39.76 3.93
1515 4645 2.700897 ACTGGCGATAGATTGTTAGGCT 59.299 45.455 0.00 0.00 39.76 4.58
1516 4646 3.243907 ACTGGCGATAGATTGTTAGGCTC 60.244 47.826 0.00 0.00 39.76 4.70
1517 4647 2.037251 TGGCGATAGATTGTTAGGCTCC 59.963 50.000 0.00 0.00 39.76 4.70
1518 4648 2.037251 GGCGATAGATTGTTAGGCTCCA 59.963 50.000 0.00 0.00 39.76 3.86
1519 4649 3.307059 GGCGATAGATTGTTAGGCTCCAT 60.307 47.826 0.00 0.00 39.76 3.41
1520 4650 3.929610 GCGATAGATTGTTAGGCTCCATC 59.070 47.826 0.00 0.00 39.76 3.51
1521 4651 4.322349 GCGATAGATTGTTAGGCTCCATCT 60.322 45.833 0.00 0.00 39.76 2.90
1522 4652 5.788450 CGATAGATTGTTAGGCTCCATCTT 58.212 41.667 0.00 0.00 39.76 2.40
1523 4653 6.226787 CGATAGATTGTTAGGCTCCATCTTT 58.773 40.000 0.00 0.00 39.76 2.52
1524 4654 6.146837 CGATAGATTGTTAGGCTCCATCTTTG 59.853 42.308 0.00 0.00 39.76 2.77
1525 4655 4.530875 AGATTGTTAGGCTCCATCTTTGG 58.469 43.478 0.00 0.00 45.15 3.28
1526 4656 3.806949 TTGTTAGGCTCCATCTTTGGT 57.193 42.857 0.00 0.00 44.06 3.67
1527 4657 3.071874 TGTTAGGCTCCATCTTTGGTG 57.928 47.619 0.00 0.00 44.06 4.17
1534 4664 3.565905 CTCCATCTTTGGTGCTTGAAC 57.434 47.619 0.00 0.00 44.06 3.18
1535 4665 2.229784 CTCCATCTTTGGTGCTTGAACC 59.770 50.000 0.00 0.00 44.06 3.62
1552 4682 8.707938 GCTTGAACCAGCAAAATAAATCTAAT 57.292 30.769 0.00 0.00 39.83 1.73
1553 4683 8.811378 GCTTGAACCAGCAAAATAAATCTAATC 58.189 33.333 0.00 0.00 39.83 1.75
1608 4740 0.670546 ATTGCTTCTGGTCGTCCGTG 60.671 55.000 0.00 0.00 36.30 4.94
1992 5169 2.432456 TGCTCGTCGGACATGCAC 60.432 61.111 17.25 0.19 0.00 4.57
2295 5594 7.637631 TGCATATATGTTAATTGGTGTGTGT 57.362 32.000 14.14 0.00 0.00 3.72
2296 5595 7.479150 TGCATATATGTTAATTGGTGTGTGTG 58.521 34.615 14.14 0.00 0.00 3.82
2297 5596 7.121907 TGCATATATGTTAATTGGTGTGTGTGT 59.878 33.333 14.14 0.00 0.00 3.72
2298 5597 7.431960 GCATATATGTTAATTGGTGTGTGTGTG 59.568 37.037 14.14 0.00 0.00 3.82
2299 5598 6.892658 ATATGTTAATTGGTGTGTGTGTGT 57.107 33.333 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.957466 GGAATTTAAAACTGCTTCTATACCAGT 58.043 33.333 0.00 0.00 41.26 4.00
107 110 2.818751 TTGATAAAGGGATGGCCGTT 57.181 45.000 0.00 0.00 43.76 4.44
108 111 2.174639 TGATTGATAAAGGGATGGCCGT 59.825 45.455 0.00 0.00 33.83 5.68
109 112 2.816087 CTGATTGATAAAGGGATGGCCG 59.184 50.000 0.00 0.00 33.83 6.13
115 118 7.398289 AATCCTCATCTGATTGATAAAGGGA 57.602 36.000 0.00 0.00 37.64 4.20
158 161 5.674989 CGGTCAAATTGTTGGTTTAAATGC 58.325 37.500 0.00 0.00 35.29 3.56
181 184 2.420022 AGTTCAACACGCTCATAATGGC 59.580 45.455 0.00 0.00 0.00 4.40
192 195 4.481930 TTGCAAAGGATAGTTCAACACG 57.518 40.909 0.00 0.00 0.00 4.49
193 196 5.587289 TGTTTGCAAAGGATAGTTCAACAC 58.413 37.500 13.26 0.00 0.00 3.32
198 201 6.086871 GCTAACTGTTTGCAAAGGATAGTTC 58.913 40.000 23.18 13.28 0.00 3.01
208 211 5.199024 ACATTGATGCTAACTGTTTGCAA 57.801 34.783 27.79 15.64 40.24 4.08
209 212 4.852134 ACATTGATGCTAACTGTTTGCA 57.148 36.364 26.67 26.67 41.13 4.08
235 238 2.093394 GCACTACTCTCCCCTTTCCTTC 60.093 54.545 0.00 0.00 0.00 3.46
237 240 1.079658 AGCACTACTCTCCCCTTTCCT 59.920 52.381 0.00 0.00 0.00 3.36
271 274 7.491682 TGAGAGAAAATTTGGGAGTTTCAAAG 58.508 34.615 0.00 0.00 43.03 2.77
331 334 2.095718 CGAGCCCAGCAAGAGTAAAAAC 60.096 50.000 0.00 0.00 0.00 2.43
336 339 2.579201 GCGAGCCCAGCAAGAGTA 59.421 61.111 0.00 0.00 34.19 2.59
353 356 2.020720 TGTAATTTATGTGCCCCTGCG 58.979 47.619 0.00 0.00 41.78 5.18
356 359 3.054655 ACGTCTGTAATTTATGTGCCCCT 60.055 43.478 0.00 0.00 0.00 4.79
358 361 3.936453 TCACGTCTGTAATTTATGTGCCC 59.064 43.478 0.00 0.00 31.59 5.36
359 362 4.868171 TCTCACGTCTGTAATTTATGTGCC 59.132 41.667 0.00 0.00 31.59 5.01
377 380 1.633774 TTCAGAGACACCCCTCTCAC 58.366 55.000 0.00 0.00 41.29 3.51
381 384 3.517500 AGAGATTTTCAGAGACACCCCTC 59.482 47.826 0.00 0.00 0.00 4.30
444 449 2.012673 CATCCACTAACTTGCAGCTCC 58.987 52.381 0.00 0.00 0.00 4.70
448 453 2.086869 CCACCATCCACTAACTTGCAG 58.913 52.381 0.00 0.00 0.00 4.41
472 477 6.867662 AGTCCATGAACTTGTAAGAAGTTG 57.132 37.500 6.68 0.00 40.27 3.16
476 481 9.739276 ATGATTTAGTCCATGAACTTGTAAGAA 57.261 29.630 0.00 0.00 0.00 2.52
479 484 8.946085 GTGATGATTTAGTCCATGAACTTGTAA 58.054 33.333 0.00 0.00 0.00 2.41
514 519 0.622136 ACCGGGGGTCCATAAACTTC 59.378 55.000 6.32 0.00 0.00 3.01
579 584 3.077359 GAGACCTGGATGAACTGGTTTG 58.923 50.000 0.00 0.00 41.96 2.93
626 631 5.012893 GTGAACTGGGATTCTCTTTTCCAT 58.987 41.667 0.00 0.00 33.43 3.41
627 632 4.104738 AGTGAACTGGGATTCTCTTTTCCA 59.895 41.667 0.00 0.00 30.17 3.53
642 647 5.695851 AAGGCTTATGACAAAGTGAACTG 57.304 39.130 0.00 0.00 0.00 3.16
645 650 6.707440 TGAAAAGGCTTATGACAAAGTGAA 57.293 33.333 0.00 0.00 0.00 3.18
670 675 9.606631 ACAAAGATCAACTATCTCTGTATTTCC 57.393 33.333 0.00 0.00 42.85 3.13
684 691 9.167311 GTACCATCTGAATTACAAAGATCAACT 57.833 33.333 0.00 0.00 0.00 3.16
747 754 3.120199 GGTGTGTATTCATGTCTGTGCAC 60.120 47.826 10.75 10.75 0.00 4.57
756 763 3.367292 GGCCAACTTGGTGTGTATTCATG 60.367 47.826 9.63 0.00 40.46 3.07
758 765 2.235016 GGCCAACTTGGTGTGTATTCA 58.765 47.619 9.63 0.00 40.46 2.57
759 766 1.199097 CGGCCAACTTGGTGTGTATTC 59.801 52.381 9.63 0.00 40.46 1.75
766 773 2.006888 CTATACACGGCCAACTTGGTG 58.993 52.381 9.63 3.82 40.46 4.17
768 775 1.663695 CCTATACACGGCCAACTTGG 58.336 55.000 2.24 3.10 41.55 3.61
821 3947 2.579684 AAGCTTCATCGGCGACCTCC 62.580 60.000 13.76 0.00 34.52 4.30
822 3948 1.148759 GAAGCTTCATCGGCGACCTC 61.149 60.000 21.67 0.00 34.52 3.85
845 3971 0.967662 GTTAGGATCCGGACCTAGGC 59.032 60.000 23.37 18.60 40.46 3.93
846 3972 2.158505 TCTGTTAGGATCCGGACCTAGG 60.159 54.545 23.37 7.41 40.46 3.02
847 3973 3.225177 TCTGTTAGGATCCGGACCTAG 57.775 52.381 23.37 17.65 40.46 3.02
874 4000 3.181442 TGGGTTGTTTTCGTTAGGATCCA 60.181 43.478 15.82 0.00 0.00 3.41
960 4086 3.570212 GTGGAGTGGGCTGTGGGT 61.570 66.667 0.00 0.00 0.00 4.51
962 4088 3.569210 TGGTGGAGTGGGCTGTGG 61.569 66.667 0.00 0.00 0.00 4.17
978 4104 2.317609 CCTTGCGGTTCCTGTCGTG 61.318 63.158 0.00 0.00 0.00 4.35
989 4115 0.243636 GGTTGACATTTCCCTTGCGG 59.756 55.000 0.00 0.00 0.00 5.69
1196 4326 2.002586 CCAGCTTCAACATGTAGACGG 58.997 52.381 0.00 0.00 0.00 4.79
1205 4335 1.150536 GGGGTCACCAGCTTCAACA 59.849 57.895 0.00 0.00 39.85 3.33
1207 4337 2.429930 CGGGGTCACCAGCTTCAA 59.570 61.111 0.00 0.00 40.22 2.69
1380 4510 4.504916 CTGCCGTGGAGGAGCGAG 62.505 72.222 0.00 0.00 45.00 5.03
1458 4588 0.902531 CGTCCTCCTTGTGGGTATGT 59.097 55.000 0.00 0.00 36.25 2.29
1476 4606 1.227823 TGGCTGTCACCAAAGGTCG 60.228 57.895 0.00 0.00 36.55 4.79
1491 4621 1.668419 AACAATCTATCGCCAGTGGC 58.332 50.000 25.07 25.07 46.75 5.01
1494 4624 2.700897 AGCCTAACAATCTATCGCCAGT 59.299 45.455 0.00 0.00 0.00 4.00
1516 4646 5.713282 GCTGGTTCAAGCACCAAAGATGG 62.713 52.174 0.00 0.00 46.60 3.51
1517 4647 2.608752 GCTGGTTCAAGCACCAAAGATG 60.609 50.000 0.00 0.00 46.60 2.90
1518 4648 1.615392 GCTGGTTCAAGCACCAAAGAT 59.385 47.619 0.00 0.00 46.60 2.40
1519 4649 1.032014 GCTGGTTCAAGCACCAAAGA 58.968 50.000 0.00 0.00 46.60 2.52
1520 4650 3.575399 GCTGGTTCAAGCACCAAAG 57.425 52.632 0.00 0.00 46.60 2.77
1527 4657 8.707938 ATTAGATTTATTTTGCTGGTTCAAGC 57.292 30.769 0.00 0.00 43.82 4.01
1547 4677 9.624037 AGGTAGAGAGGTAGAGATTAGATTAGA 57.376 37.037 0.00 0.00 0.00 2.10
1550 4680 9.401496 AGTAGGTAGAGAGGTAGAGATTAGATT 57.599 37.037 0.00 0.00 0.00 2.40
1551 4681 8.984112 AGTAGGTAGAGAGGTAGAGATTAGAT 57.016 38.462 0.00 0.00 0.00 1.98
1552 4682 9.895507 TTAGTAGGTAGAGAGGTAGAGATTAGA 57.104 37.037 0.00 0.00 0.00 2.10
1558 4688 9.506018 GGTTTATTAGTAGGTAGAGAGGTAGAG 57.494 40.741 0.00 0.00 0.00 2.43
1559 4689 9.007494 TGGTTTATTAGTAGGTAGAGAGGTAGA 57.993 37.037 0.00 0.00 0.00 2.59
1560 4690 9.287373 CTGGTTTATTAGTAGGTAGAGAGGTAG 57.713 40.741 0.00 0.00 0.00 3.18
1561 4691 7.723172 GCTGGTTTATTAGTAGGTAGAGAGGTA 59.277 40.741 0.00 0.00 0.00 3.08
1562 4692 6.550481 GCTGGTTTATTAGTAGGTAGAGAGGT 59.450 42.308 0.00 0.00 0.00 3.85
1563 4693 6.294065 CGCTGGTTTATTAGTAGGTAGAGAGG 60.294 46.154 0.00 0.00 0.00 3.69
1564 4694 6.485984 TCGCTGGTTTATTAGTAGGTAGAGAG 59.514 42.308 0.00 0.00 0.00 3.20
2295 5594 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2296 5595 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2297 5596 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2298 5597 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2299 5598 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.