Multiple sequence alignment - TraesCS6B01G082800

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 TraesCS6B01G082800 chr6B 100.000 2587 0 0 1 2587 59589379 59586793 0.000000e+00 4778.0
1 TraesCS6B01G082800 chr6B 92.222 900 53 9 654 1552 58807991 58807108 0.000000e+00 1258.0
2 TraesCS6B01G082800 chr6B 95.506 623 24 2 1968 2587 58318917 58318296 0.000000e+00 992.0
3 TraesCS6B01G082800 chr6B 84.283 948 93 25 853 1767 61490295 61491219 0.000000e+00 874.0
4 TraesCS6B01G082800 chr6B 89.088 559 39 13 850 1397 58057889 58057342 0.000000e+00 675.0
5 TraesCS6B01G082800 chr6B 83.534 747 76 27 850 1584 78151496 78150785 0.000000e+00 654.0
6 TraesCS6B01G082800 chr6B 89.633 463 38 9 1076 1532 60928425 60928883 4.800000e-162 580.0
7 TraesCS6B01G082800 chr6B 94.675 338 17 1 1 338 58809856 58809520 8.200000e-145 523.0
8 TraesCS6B01G082800 chr6B 84.881 463 51 12 1488 1936 58319372 58318915 1.410000e-122 449.0
9 TraesCS6B01G082800 chr6B 93.772 289 15 3 372 657 58809518 58809230 5.110000e-117 431.0
10 TraesCS6B01G082800 chr6B 95.000 200 8 2 1 200 59098038 59097841 1.930000e-81 313.0
11 TraesCS6B01G082800 chr6B 81.338 284 38 14 240 516 59787094 59786819 1.560000e-52 217.0
12 TraesCS6B01G082800 chr6A 83.225 1693 173 65 444 2106 33009210 33007599 0.000000e+00 1450.0
13 TraesCS6B01G082800 chr6A 83.406 922 75 24 853 1768 33949074 33949923 0.000000e+00 784.0
14 TraesCS6B01G082800 chr6A 93.506 462 25 3 1076 1532 33548105 33548566 0.000000e+00 682.0
15 TraesCS6B01G082800 chr6A 94.005 367 17 3 2225 2587 33007471 33007106 3.760000e-153 551.0
16 TraesCS6B01G082800 chr6A 76.868 281 26 16 1834 2079 33950110 33950386 3.500000e-24 122.0
17 TraesCS6B01G082800 chr6D 86.597 1149 84 33 426 1546 29384177 29385283 0.000000e+00 1205.0
18 TraesCS6B01G082800 chr6D 87.601 863 70 22 853 1711 28708278 28707449 0.000000e+00 966.0
19 TraesCS6B01G082800 chr6D 85.303 973 60 34 1579 2506 29385288 29386222 0.000000e+00 928.0
20 TraesCS6B01G082800 chr6D 88.849 556 41 14 850 1395 29756780 29757324 0.000000e+00 664.0
21 TraesCS6B01G082800 chr6D 84.034 357 51 6 6 358 29382339 29382693 3.190000e-89 339.0
22 TraesCS6B01G082800 chr6D 83.754 357 52 6 6 358 29383330 29383684 1.480000e-87 333.0
23 TraesCS6B01G082800 chr6D 95.082 61 3 0 2525 2585 29386205 29386265 2.120000e-16 97.1


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 TraesCS6B01G082800 chr6B 59586793 59589379 2586 True 4778.000000 4778 100.000000 1 2587 1 chr6B.!!$R3 2586
1 TraesCS6B01G082800 chr6B 61490295 61491219 924 False 874.000000 874 84.283000 853 1767 1 chr6B.!!$F2 914
2 TraesCS6B01G082800 chr6B 58807108 58809856 2748 True 737.333333 1258 93.556333 1 1552 3 chr6B.!!$R7 1551
3 TraesCS6B01G082800 chr6B 58318296 58319372 1076 True 720.500000 992 90.193500 1488 2587 2 chr6B.!!$R6 1099
4 TraesCS6B01G082800 chr6B 58057342 58057889 547 True 675.000000 675 89.088000 850 1397 1 chr6B.!!$R1 547
5 TraesCS6B01G082800 chr6B 78150785 78151496 711 True 654.000000 654 83.534000 850 1584 1 chr6B.!!$R5 734
6 TraesCS6B01G082800 chr6A 33007106 33009210 2104 True 1000.500000 1450 88.615000 444 2587 2 chr6A.!!$R1 2143
7 TraesCS6B01G082800 chr6A 33949074 33950386 1312 False 453.000000 784 80.137000 853 2079 2 chr6A.!!$F2 1226
8 TraesCS6B01G082800 chr6D 28707449 28708278 829 True 966.000000 966 87.601000 853 1711 1 chr6D.!!$R1 858
9 TraesCS6B01G082800 chr6D 29756780 29757324 544 False 664.000000 664 88.849000 850 1395 1 chr6D.!!$F1 545
10 TraesCS6B01G082800 chr6D 29382339 29386265 3926 False 580.420000 1205 86.954000 6 2585 5 chr6D.!!$F2 2579

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
874 3566 0.179004 ATTTTGGAGCCACGTCACCA 60.179 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2526 5604 0.026803 GCATTCAGACGGTCGATTGC 59.973 55.0 21.57 21.57 33.09 3.56 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
120 123 2.045326 TGAGGGGGTAGGATGTACAAGT 59.955 50.000 0.00 0.00 0.00 3.16
234 238 2.105128 GTGCGTCAGAGGATCCGG 59.895 66.667 5.98 0.00 33.66 5.14
237 241 3.082579 GCGTCAGAGGATCCGGCTT 62.083 63.158 5.98 0.00 33.66 4.35
312 316 4.836175 TCTGAACCAACAGTAGGACATACA 59.164 41.667 0.00 0.00 38.79 2.29
358 362 2.203437 GCCCGTGGGTCCACTTTT 60.203 61.111 16.93 0.00 44.16 2.27
360 364 2.037871 CCCGTGGGTCCACTTTTTG 58.962 57.895 16.93 2.40 44.16 2.44
364 368 1.265905 CGTGGGTCCACTTTTTGTAGC 59.734 52.381 16.93 0.00 44.16 3.58
367 694 1.203013 GGGTCCACTTTTTGTAGCCCT 60.203 52.381 0.00 0.00 33.29 5.19
375 702 1.212250 TTTTGTAGCCCTCCTCCCCC 61.212 60.000 0.00 0.00 0.00 5.40
410 1809 3.605634 TGTGGTGAGGCACATATTACAC 58.394 45.455 0.00 0.00 35.86 2.90
558 1981 8.532977 TCTACATTAAAAATTTTCTGCTTGCC 57.467 30.769 3.41 0.00 0.00 4.52
562 1985 2.549064 AAATTTTCTGCTTGCCCACC 57.451 45.000 0.00 0.00 0.00 4.61
573 1996 2.497273 GCTTGCCCACCAATGAATAGTT 59.503 45.455 0.00 0.00 31.91 2.24
612 2035 3.696051 AGTGATGAACGGATTGAATTGGG 59.304 43.478 0.00 0.00 0.00 4.12
623 2046 6.607198 ACGGATTGAATTGGGTTAGATGATTT 59.393 34.615 0.00 0.00 0.00 2.17
667 3333 7.856145 AAGCTCACTCCTAATACATGAAAAG 57.144 36.000 0.00 0.00 0.00 2.27
711 3382 0.732571 AAATAAGCGGGCACGACATG 59.267 50.000 15.48 0.00 44.60 3.21
768 3442 6.483640 GGTAATTTGTCTGGTAGCTGGATAAG 59.516 42.308 0.00 0.00 0.00 1.73
796 3470 5.163663 ACGAATTTGTTGCAAGAAACAGAGA 60.164 36.000 22.45 1.27 40.93 3.10
874 3566 0.179004 ATTTTGGAGCCACGTCACCA 60.179 50.000 0.00 0.00 0.00 4.17
1047 3745 2.092753 TCCTCCTCCATTTGCATCTCAC 60.093 50.000 0.00 0.00 0.00 3.51
1418 4125 1.519455 CTGCCCAATCGAGTCGACC 60.519 63.158 19.16 2.76 39.18 4.79
1457 4168 1.355971 TTCTCGTGCTATGGTTTCGC 58.644 50.000 0.00 0.00 0.00 4.70
1464 4175 2.742053 GTGCTATGGTTTCGCTTCTGAA 59.258 45.455 0.00 0.00 0.00 3.02
1465 4176 3.375299 GTGCTATGGTTTCGCTTCTGAAT 59.625 43.478 0.00 0.00 0.00 2.57
1466 4177 4.009675 TGCTATGGTTTCGCTTCTGAATT 58.990 39.130 0.00 0.00 0.00 2.17
1467 4178 4.094887 TGCTATGGTTTCGCTTCTGAATTC 59.905 41.667 0.00 0.00 0.00 2.17
1468 4179 4.094887 GCTATGGTTTCGCTTCTGAATTCA 59.905 41.667 8.12 8.12 0.00 2.57
1469 4180 4.691860 ATGGTTTCGCTTCTGAATTCAG 57.308 40.909 26.56 26.56 45.08 3.02
1486 4201 2.279741 TCAGAGTGTGTGAGTTGTTGC 58.720 47.619 0.00 0.00 0.00 4.17
1500 4215 1.174078 TGTTGCTCCGTCGGTCTGTA 61.174 55.000 11.88 0.00 0.00 2.74
1516 4240 4.404715 GGTCTGTATAGTTAGTGGAAGGCA 59.595 45.833 0.00 0.00 0.00 4.75
1548 4281 5.757320 TGAATGCAATCGAAATTGTTGGTTT 59.243 32.000 0.00 0.00 43.54 3.27
1631 4404 2.749621 CTGGCTTGTTCCTGTACATTCC 59.250 50.000 0.00 0.00 0.00 3.01
1659 4432 1.418373 TCAGCAAGAACGTCGATGTG 58.582 50.000 11.82 0.00 0.00 3.21
1701 4478 5.049749 TCGTTTCGATTTTCTTGCTGAATGA 60.050 36.000 0.00 0.00 34.24 2.57
1788 4668 1.855213 CGTTGGTCGTACAGTCGGGA 61.855 60.000 0.00 0.00 34.52 5.14
1792 4672 2.019249 TGGTCGTACAGTCGGGAATAG 58.981 52.381 0.00 0.00 0.00 1.73
1826 4721 0.682209 CAGGCCAATCTCAACCCCAG 60.682 60.000 5.01 0.00 0.00 4.45
1882 4796 0.453950 CGTTGCAATCTGCTGCTGTC 60.454 55.000 0.59 0.00 45.31 3.51
1931 4858 6.996282 TGATGTATCATGATTCTGTTCTGCAT 59.004 34.615 14.65 2.68 0.00 3.96
1933 4860 7.634671 TGTATCATGATTCTGTTCTGCATTT 57.365 32.000 14.65 0.00 0.00 2.32
1938 4873 8.339344 TCATGATTCTGTTCTGCATTTCTTTA 57.661 30.769 0.00 0.00 0.00 1.85
1945 4880 7.224297 TCTGTTCTGCATTTCTTTAAGTACCT 58.776 34.615 0.00 0.00 0.00 3.08
1948 4883 7.719633 TGTTCTGCATTTCTTTAAGTACCTCTT 59.280 33.333 0.00 0.00 39.89 2.85
1951 4886 8.784043 TCTGCATTTCTTTAAGTACCTCTTTTC 58.216 33.333 0.00 0.00 37.56 2.29
1953 4888 7.227910 TGCATTTCTTTAAGTACCTCTTTTCGT 59.772 33.333 0.00 0.00 37.56 3.85
1954 4889 7.534239 GCATTTCTTTAAGTACCTCTTTTCGTG 59.466 37.037 0.00 0.00 37.56 4.35
1955 4890 8.557029 CATTTCTTTAAGTACCTCTTTTCGTGT 58.443 33.333 0.00 0.00 37.56 4.49
1956 4891 9.768662 ATTTCTTTAAGTACCTCTTTTCGTGTA 57.231 29.630 0.00 0.00 37.56 2.90
1963 4907 6.675987 AGTACCTCTTTTCGTGTACTACTTG 58.324 40.000 0.00 0.00 41.43 3.16
1993 4937 6.808829 TGATCATGGGCTTCATAATGAAAAC 58.191 36.000 0.00 0.00 35.73 2.43
2000 4944 3.128589 GCTTCATAATGAAAACGGAGCCA 59.871 43.478 0.00 0.00 35.73 4.75
2239 5237 4.701651 CCATGAGTTGGCTAACATCTGAAA 59.298 41.667 15.86 0.00 39.09 2.69
2309 5307 1.410517 TCCTCCTCGCATTGATCACTC 59.589 52.381 0.00 0.00 0.00 3.51
2320 5318 5.791974 CGCATTGATCACTCACTTTACTTTG 59.208 40.000 0.00 0.00 0.00 2.77
2403 5407 6.260870 TGCCGAAGCAGAACATAATTTTTA 57.739 33.333 0.00 0.00 46.52 1.52
2413 5417 7.276438 GCAGAACATAATTTTTAAGGGAAGCAG 59.724 37.037 0.00 0.00 0.00 4.24
2506 5584 3.062234 GGAAAATCAATCGACCGTCTGAC 59.938 47.826 0.00 0.00 0.00 3.51
2507 5585 3.594603 AAATCAATCGACCGTCTGACT 57.405 42.857 6.21 0.00 0.00 3.41
2508 5586 2.568696 ATCAATCGACCGTCTGACTG 57.431 50.000 6.21 1.64 0.00 3.51
2509 5587 1.530323 TCAATCGACCGTCTGACTGA 58.470 50.000 6.22 0.00 0.00 3.41
2510 5588 2.092323 TCAATCGACCGTCTGACTGAT 58.908 47.619 6.22 1.78 0.00 2.90
2511 5589 2.492088 TCAATCGACCGTCTGACTGATT 59.508 45.455 6.22 7.26 0.00 2.57
2512 5590 2.853731 ATCGACCGTCTGACTGATTC 57.146 50.000 6.22 0.00 0.00 2.52
2513 5591 1.530323 TCGACCGTCTGACTGATTCA 58.470 50.000 6.22 0.00 0.00 2.57
2514 5592 2.092323 TCGACCGTCTGACTGATTCAT 58.908 47.619 6.22 0.00 32.17 2.57
2515 5593 2.097629 TCGACCGTCTGACTGATTCATC 59.902 50.000 6.22 0.00 32.17 2.92
2516 5594 2.159379 CGACCGTCTGACTGATTCATCA 60.159 50.000 6.22 0.00 32.17 3.07
2517 5595 3.673323 CGACCGTCTGACTGATTCATCAA 60.673 47.826 6.22 0.00 36.18 2.57
2518 5596 3.854666 ACCGTCTGACTGATTCATCAAG 58.145 45.455 6.22 0.00 36.18 3.02
2519 5597 3.511540 ACCGTCTGACTGATTCATCAAGA 59.488 43.478 6.22 0.00 36.18 3.02
2520 5598 4.021104 ACCGTCTGACTGATTCATCAAGAA 60.021 41.667 6.22 0.00 41.28 2.52
2521 5599 4.328440 CCGTCTGACTGATTCATCAAGAAC 59.672 45.833 6.21 0.00 39.49 3.01
2522 5600 4.925646 CGTCTGACTGATTCATCAAGAACA 59.074 41.667 6.21 0.00 39.49 3.18
2523 5601 5.164012 CGTCTGACTGATTCATCAAGAACAC 60.164 44.000 6.21 0.00 39.49 3.32
2524 5602 5.698089 GTCTGACTGATTCATCAAGAACACA 59.302 40.000 0.00 0.00 39.49 3.72
2525 5603 6.203530 GTCTGACTGATTCATCAAGAACACAA 59.796 38.462 0.00 0.00 39.49 3.33
2526 5604 6.426025 TCTGACTGATTCATCAAGAACACAAG 59.574 38.462 0.00 0.00 39.49 3.16
2527 5605 5.049198 TGACTGATTCATCAAGAACACAAGC 60.049 40.000 0.00 0.00 39.49 4.01
2528 5606 4.823442 ACTGATTCATCAAGAACACAAGCA 59.177 37.500 0.00 0.00 39.49 3.91
2529 5607 5.300034 ACTGATTCATCAAGAACACAAGCAA 59.700 36.000 0.00 0.00 39.49 3.91
2530 5608 6.015688 ACTGATTCATCAAGAACACAAGCAAT 60.016 34.615 0.00 0.00 39.49 3.56
2531 5609 6.384224 TGATTCATCAAGAACACAAGCAATC 58.616 36.000 0.00 0.00 39.49 2.67
2532 5610 4.408993 TCATCAAGAACACAAGCAATCG 57.591 40.909 0.00 0.00 0.00 3.34
2533 5611 4.064388 TCATCAAGAACACAAGCAATCGA 58.936 39.130 0.00 0.00 0.00 3.59
2534 5612 3.878086 TCAAGAACACAAGCAATCGAC 57.122 42.857 0.00 0.00 0.00 4.20
2535 5613 2.548057 TCAAGAACACAAGCAATCGACC 59.452 45.455 0.00 0.00 0.00 4.79
2536 5614 1.148310 AGAACACAAGCAATCGACCG 58.852 50.000 0.00 0.00 0.00 4.79
2537 5615 0.865769 GAACACAAGCAATCGACCGT 59.134 50.000 0.00 0.00 0.00 4.83
2538 5616 0.865769 AACACAAGCAATCGACCGTC 59.134 50.000 0.00 0.00 0.00 4.79
2539 5617 0.033504 ACACAAGCAATCGACCGTCT 59.966 50.000 0.00 0.00 0.00 4.18
2540 5618 0.439985 CACAAGCAATCGACCGTCTG 59.560 55.000 0.00 0.00 0.00 3.51
2541 5619 0.317160 ACAAGCAATCGACCGTCTGA 59.683 50.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.187958 CCCCACTGATAGTTGACTCCA 58.812 52.381 0.00 0.00 0.00 3.86
9 10 2.832129 TCACCCCACTGATAGTTGACTC 59.168 50.000 0.00 0.00 0.00 3.36
106 109 7.034397 GGTAGTTCTTCACTTGTACATCCTAC 58.966 42.308 0.00 0.00 36.88 3.18
120 123 3.056821 CACATCTCCACGGTAGTTCTTCA 60.057 47.826 0.00 0.00 0.00 3.02
237 241 4.994201 GTGTGCTCCACGCGACGA 62.994 66.667 15.93 6.39 43.27 4.20
312 316 1.675310 CACGTGTGCCCCATCATGT 60.675 57.895 7.58 0.00 34.66 3.21
358 362 2.042261 GGGGGAGGAGGGCTACAA 59.958 66.667 0.00 0.00 0.00 2.41
375 702 0.036952 ACCACAGCGATGACTTGAGG 60.037 55.000 8.12 1.59 0.00 3.86
410 1809 1.297967 CCTCGCAGTCGTCTGATCG 60.298 63.158 14.02 8.41 43.76 3.69
541 1962 3.213506 GGTGGGCAAGCAGAAAATTTTT 58.786 40.909 4.63 0.00 0.00 1.94
552 1974 2.102578 ACTATTCATTGGTGGGCAAGC 58.897 47.619 0.00 0.00 0.00 4.01
556 1979 6.040842 ACATATTCAACTATTCATTGGTGGGC 59.959 38.462 0.00 0.00 0.00 5.36
558 1981 8.685427 TCAACATATTCAACTATTCATTGGTGG 58.315 33.333 0.00 0.00 0.00 4.61
562 1985 9.941664 GTCCTCAACATATTCAACTATTCATTG 57.058 33.333 0.00 0.00 0.00 2.82
573 1996 5.189539 TCATCACTGGTCCTCAACATATTCA 59.810 40.000 0.00 0.00 0.00 2.57
612 2035 9.945904 CCTCCCCTACTATTTAAATCATCTAAC 57.054 37.037 3.39 0.00 0.00 2.34
623 2046 4.385977 GCTTTTGCCCTCCCCTACTATTTA 60.386 45.833 0.00 0.00 40.15 1.40
667 3333 3.848272 TTGGATTTCGCCTTGTCATTC 57.152 42.857 0.00 0.00 0.00 2.67
695 3364 1.153647 CTCATGTCGTGCCCGCTTA 60.154 57.895 0.00 0.00 0.00 3.09
768 3442 3.347958 TCTTGCAACAAATTCGTCCAC 57.652 42.857 0.00 0.00 0.00 4.02
796 3470 1.740380 CGAGGCGAGACATCATTGGTT 60.740 52.381 0.00 0.00 0.00 3.67
874 3566 2.443016 AGAGAGAGGGCGCGGATT 60.443 61.111 8.83 0.00 0.00 3.01
1047 3745 1.678425 GGCTTCTTCCTTGGAGCTGAG 60.678 57.143 0.00 0.00 0.00 3.35
1287 3993 2.506438 GCGTGCTCGGTGTAGGTC 60.506 66.667 10.52 0.00 37.56 3.85
1406 4113 1.025812 CTAGCAGGGTCGACTCGATT 58.974 55.000 16.46 4.70 38.42 3.34
1437 4147 1.933853 GCGAAACCATAGCACGAGAAT 59.066 47.619 0.00 0.00 0.00 2.40
1464 4175 3.313526 GCAACAACTCACACACTCTGAAT 59.686 43.478 0.00 0.00 0.00 2.57
1465 4176 2.677836 GCAACAACTCACACACTCTGAA 59.322 45.455 0.00 0.00 0.00 3.02
1466 4177 2.093500 AGCAACAACTCACACACTCTGA 60.093 45.455 0.00 0.00 0.00 3.27
1467 4178 2.283298 AGCAACAACTCACACACTCTG 58.717 47.619 0.00 0.00 0.00 3.35
1468 4179 2.555199 GAGCAACAACTCACACACTCT 58.445 47.619 0.00 0.00 36.65 3.24
1469 4180 1.599542 GGAGCAACAACTCACACACTC 59.400 52.381 0.00 0.00 38.50 3.51
1470 4181 1.668419 GGAGCAACAACTCACACACT 58.332 50.000 0.00 0.00 38.50 3.55
1474 4185 0.874175 CGACGGAGCAACAACTCACA 60.874 55.000 0.00 0.00 38.50 3.58
1486 4201 4.025061 CACTAACTATACAGACCGACGGAG 60.025 50.000 23.38 12.34 0.00 4.63
1500 4215 5.370880 AGATCCATTGCCTTCCACTAACTAT 59.629 40.000 0.00 0.00 0.00 2.12
1516 4240 5.840243 TTTCGATTGCATTCAGATCCATT 57.160 34.783 9.14 0.00 0.00 3.16
1548 4281 8.890124 TTTCATTCAGATTCATTTCTTGCAAA 57.110 26.923 0.00 0.00 0.00 3.68
1631 4404 6.077197 TCGACGTTCTTGCTGATAAATTTTG 58.923 36.000 0.00 0.00 0.00 2.44
1659 4432 6.790825 CGAAACGAAAATTACTGAAAGAGTCC 59.209 38.462 0.00 0.00 37.43 3.85
1788 4668 3.055530 CCTGCAGGAGCGATATTCCTATT 60.056 47.826 29.88 0.00 43.17 1.73
1792 4672 0.952984 GCCTGCAGGAGCGATATTCC 60.953 60.000 37.21 10.52 46.23 3.01
1826 4721 4.819761 TGGCACAGATCGCGCTCC 62.820 66.667 5.56 0.00 0.00 4.70
1882 4796 5.263599 AGGCATCAGACATCTAGGATCTAG 58.736 45.833 0.00 0.00 0.00 2.43
1931 4858 9.034544 GTACACGAAAAGAGGTACTTAAAGAAA 57.965 33.333 0.00 0.00 41.55 2.52
1933 4860 7.945134 AGTACACGAAAAGAGGTACTTAAAGA 58.055 34.615 0.00 0.00 41.55 2.52
1938 4873 6.890979 AGTAGTACACGAAAAGAGGTACTT 57.109 37.500 8.40 0.00 41.55 2.24
1945 4880 5.068198 AGACACCAAGTAGTACACGAAAAGA 59.932 40.000 2.52 0.00 0.00 2.52
1948 4883 4.338964 TCAGACACCAAGTAGTACACGAAA 59.661 41.667 2.52 0.00 0.00 3.46
1951 4886 3.909776 TCAGACACCAAGTAGTACACG 57.090 47.619 2.52 0.00 0.00 4.49
1953 4888 5.105351 CCATGATCAGACACCAAGTAGTACA 60.105 44.000 0.09 0.00 0.00 2.90
1954 4889 5.352284 CCATGATCAGACACCAAGTAGTAC 58.648 45.833 0.09 0.00 0.00 2.73
1955 4890 4.405680 CCCATGATCAGACACCAAGTAGTA 59.594 45.833 0.09 0.00 0.00 1.82
1956 4891 3.198635 CCCATGATCAGACACCAAGTAGT 59.801 47.826 0.09 0.00 0.00 2.73
1963 4907 1.065199 TGAAGCCCATGATCAGACACC 60.065 52.381 0.09 0.00 0.00 4.16
1993 4937 4.864334 GGCTCACCCATGGCTCCG 62.864 72.222 6.09 0.00 0.00 4.63
2000 4944 1.898863 ATAACAGGAGGCTCACCCAT 58.101 50.000 17.69 0.63 36.11 4.00
2309 5307 6.963796 AGCTTGTGAATCTCAAAGTAAAGTG 58.036 36.000 0.00 0.00 0.00 3.16
2320 5318 5.210715 CAGTGTGAAAAGCTTGTGAATCTC 58.789 41.667 0.00 0.00 0.00 2.75
2364 5368 1.662876 CGGCACATCACCTTTTGTTCG 60.663 52.381 0.00 0.00 0.00 3.95
2403 5407 3.565307 TCAAATGTGTTCTGCTTCCCTT 58.435 40.909 0.00 0.00 0.00 3.95
2413 5417 4.927425 AGCAGCAATCAATCAAATGTGTTC 59.073 37.500 0.00 0.00 0.00 3.18
2464 5469 2.423373 CCTCCCATCGAATGTTCCCAAT 60.423 50.000 0.00 0.00 0.00 3.16
2465 5470 1.064758 CCTCCCATCGAATGTTCCCAA 60.065 52.381 0.00 0.00 0.00 4.12
2466 5471 0.546122 CCTCCCATCGAATGTTCCCA 59.454 55.000 0.00 0.00 0.00 4.37
2506 5584 5.366829 TGCTTGTGTTCTTGATGAATCAG 57.633 39.130 0.00 0.00 38.19 2.90
2507 5585 5.771153 TTGCTTGTGTTCTTGATGAATCA 57.229 34.783 0.00 0.00 36.99 2.57
2508 5586 5.510674 CGATTGCTTGTGTTCTTGATGAATC 59.489 40.000 0.00 0.00 36.99 2.52
2509 5587 5.181811 TCGATTGCTTGTGTTCTTGATGAAT 59.818 36.000 0.00 0.00 36.99 2.57
2510 5588 4.514816 TCGATTGCTTGTGTTCTTGATGAA 59.485 37.500 0.00 0.00 0.00 2.57
2511 5589 4.064388 TCGATTGCTTGTGTTCTTGATGA 58.936 39.130 0.00 0.00 0.00 2.92
2512 5590 4.153986 GTCGATTGCTTGTGTTCTTGATG 58.846 43.478 0.00 0.00 0.00 3.07
2513 5591 3.189287 GGTCGATTGCTTGTGTTCTTGAT 59.811 43.478 0.00 0.00 0.00 2.57
2514 5592 2.548057 GGTCGATTGCTTGTGTTCTTGA 59.452 45.455 0.00 0.00 0.00 3.02
2515 5593 2.662791 CGGTCGATTGCTTGTGTTCTTG 60.663 50.000 0.00 0.00 0.00 3.02
2516 5594 1.531149 CGGTCGATTGCTTGTGTTCTT 59.469 47.619 0.00 0.00 0.00 2.52
2517 5595 1.148310 CGGTCGATTGCTTGTGTTCT 58.852 50.000 0.00 0.00 0.00 3.01
2518 5596 0.865769 ACGGTCGATTGCTTGTGTTC 59.134 50.000 0.00 0.00 0.00 3.18
2519 5597 0.865769 GACGGTCGATTGCTTGTGTT 59.134 50.000 0.00 0.00 0.00 3.32
2520 5598 0.033504 AGACGGTCGATTGCTTGTGT 59.966 50.000 1.89 0.00 0.00 3.72
2521 5599 0.439985 CAGACGGTCGATTGCTTGTG 59.560 55.000 1.89 0.00 0.00 3.33
2522 5600 0.317160 TCAGACGGTCGATTGCTTGT 59.683 50.000 1.89 0.00 0.00 3.16
2523 5601 1.428448 TTCAGACGGTCGATTGCTTG 58.572 50.000 1.89 0.00 0.00 4.01
2524 5602 2.002586 CATTCAGACGGTCGATTGCTT 58.997 47.619 1.89 0.00 0.00 3.91
2525 5603 1.645034 CATTCAGACGGTCGATTGCT 58.355 50.000 1.89 0.00 0.00 3.91
2526 5604 0.026803 GCATTCAGACGGTCGATTGC 59.973 55.000 21.57 21.57 33.09 3.56
2527 5605 1.590238 GAGCATTCAGACGGTCGATTG 59.410 52.381 1.89 10.35 0.00 2.67
2528 5606 1.927895 GAGCATTCAGACGGTCGATT 58.072 50.000 1.89 0.00 0.00 3.34
2529 5607 3.650409 GAGCATTCAGACGGTCGAT 57.350 52.632 1.89 0.00 0.00 3.59
2531 5609 3.680525 CGAGCATTCAGACGGTCG 58.319 61.111 1.89 6.30 45.25 4.79
2532 5610 0.388649 ACACGAGCATTCAGACGGTC 60.389 55.000 0.00 0.00 0.00 4.79
2533 5611 0.033504 AACACGAGCATTCAGACGGT 59.966 50.000 0.00 0.00 0.00 4.83
2534 5612 0.439985 CAACACGAGCATTCAGACGG 59.560 55.000 0.00 0.00 0.00 4.79
2535 5613 1.139989 ACAACACGAGCATTCAGACG 58.860 50.000 0.00 0.00 0.00 4.18
2536 5614 2.287915 ACAACAACACGAGCATTCAGAC 59.712 45.455 0.00 0.00 0.00 3.51
2537 5615 2.560504 ACAACAACACGAGCATTCAGA 58.439 42.857 0.00 0.00 0.00 3.27
2538 5616 3.291585 GAACAACAACACGAGCATTCAG 58.708 45.455 0.00 0.00 0.00 3.02
2539 5617 2.032799 GGAACAACAACACGAGCATTCA 59.967 45.455 0.00 0.00 0.00 2.57
2540 5618 2.032799 TGGAACAACAACACGAGCATTC 59.967 45.455 0.00 0.00 31.92 2.67
2541 5619 2.020720 TGGAACAACAACACGAGCATT 58.979 42.857 0.00 0.00 31.92 3.56


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

AutoCloner maintained by Alex Coulton.