Multiple sequence alignment - TraesCS3B01G237300

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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 TraesCS3B01G237300 chr3B 100.000 2649 0 0 1380 4028 372240187 372242835 0.000000e+00 4892.0
1 TraesCS3B01G237300 chr3B 100.000 1120 0 0 1 1120 372238808 372239927 0.000000e+00 2069.0
2 TraesCS3B01G237300 chr3D 95.417 2509 77 17 1539 4028 278450479 278447990 0.000000e+00 3962.0
3 TraesCS3B01G237300 chr3D 97.048 813 19 1 1 813 278451381 278450574 0.000000e+00 1363.0
4 TraesCS3B01G237300 chr3D 97.391 115 3 0 828 942 278450592 278450478 3.180000e-46 196.0
5 TraesCS3B01G237300 chr3D 86.400 125 13 4 1490 1613 583473364 583473243 2.530000e-27 134.0
6 TraesCS3B01G237300 chr3D 89.286 56 3 3 1421 1473 38185281 38185336 2.600000e-07 67.6
7 TraesCS3B01G237300 chr3A 93.352 2557 116 28 1490 4028 360825001 360827521 0.000000e+00 3731.0
8 TraesCS3B01G237300 chr3A 96.921 812 18 3 3 813 360823759 360824564 0.000000e+00 1354.0
9 TraesCS3B01G237300 chr3A 93.667 300 11 3 828 1119 360824546 360824845 3.690000e-120 442.0
10 TraesCS3B01G237300 chr3A 93.878 49 3 0 1425 1473 647158973 647158925 1.550000e-09 75.0
11 TraesCS3B01G237300 chr5A 88.000 125 11 4 1490 1613 26532044 26532165 1.170000e-30 145.0
12 TraesCS3B01G237300 chr7D 88.889 117 8 5 1503 1616 34383203 34383089 5.430000e-29 139.0
13 TraesCS3B01G237300 chr5B 86.614 127 11 6 1487 1610 96754703 96754826 7.020000e-28 135.0
14 TraesCS3B01G237300 chr4B 85.246 122 14 4 1490 1610 50830881 50830999 5.470000e-24 122.0
15 TraesCS3B01G237300 chr4D 87.619 105 12 1 1509 1613 437033690 437033587 1.970000e-23 121.0
16 TraesCS3B01G237300 chr2A 83.846 130 15 5 1490 1616 516306371 516306245 7.070000e-23 119.0
17 TraesCS3B01G237300 chr7B 95.556 45 2 0 1426 1470 75778114 75778158 5.580000e-09 73.1
18 TraesCS3B01G237300 chr7B 95.556 45 2 0 1426 1470 100880558 100880602 5.580000e-09 73.1
19 TraesCS3B01G237300 chr7A 95.556 45 2 0 1429 1473 69967077 69967033 5.580000e-09 73.1
20 TraesCS3B01G237300 chr7A 95.556 45 2 0 1426 1470 676892780 676892824 5.580000e-09 73.1
21 TraesCS3B01G237300 chr4A 95.556 45 2 0 1429 1473 248663 248619 5.580000e-09 73.1
22 TraesCS3B01G237300 chr6D 95.349 43 2 0 1428 1470 97352513 97352555 7.220000e-08 69.4
23 TraesCS3B01G237300 chr6A 93.333 45 3 0 1429 1473 523352314 523352270 2.600000e-07 67.6


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 TraesCS3B01G237300 chr3B 372238808 372242835 4027 False 3480.500000 4892 100.000000 1 4028 2 chr3B.!!$F1 4027
1 TraesCS3B01G237300 chr3D 278447990 278451381 3391 True 1840.333333 3962 96.618667 1 4028 3 chr3D.!!$R2 4027
2 TraesCS3B01G237300 chr3A 360823759 360827521 3762 False 1842.333333 3731 94.646667 3 4028 3 chr3A.!!$F1 4025

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
638 640 1.254026 ACGAGCTGTACAAGGTAGCA 58.746 50.0 6.79 0.0 39.84 3.49 F
1442 1452 0.034337 TTGTGTACTCCCTCCGTTGC 59.966 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
2130 2147 0.034896 TTCCTTGTCCTCGGAGTTGC 59.965 55.000 4.02 0.0 0.0 4.17 R
3154 3180 1.135431 TGCCTTGTATTTGTGCGATGC 60.135 47.619 0.00 0.0 0.0 3.91 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
138 139 7.924541 AGGTAAAGTGGAACCTCATTTATGTA 58.075 34.615 0.00 0.00 42.60 2.29
263 264 4.165372 TGAGTGAAAAAGTGGGGTTAGACT 59.835 41.667 0.00 0.00 0.00 3.24
305 306 8.262933 AGGTAGCTTTACGGAAACAAGTATAAT 58.737 33.333 0.00 0.00 0.00 1.28
306 307 9.533253 GGTAGCTTTACGGAAACAAGTATAATA 57.467 33.333 0.00 0.00 0.00 0.98
309 310 9.310716 AGCTTTACGGAAACAAGTATAATACTC 57.689 33.333 0.00 0.00 38.26 2.59
533 535 4.499865 GCACCTCGTCTTAATCTGATGCTA 60.500 45.833 0.00 0.00 0.00 3.49
545 547 3.262420 TCTGATGCTAAGAAGAAACGCC 58.738 45.455 0.00 0.00 0.00 5.68
638 640 1.254026 ACGAGCTGTACAAGGTAGCA 58.746 50.000 6.79 0.00 39.84 3.49
674 676 2.649034 GACCACGACTTCTCCGCA 59.351 61.111 0.00 0.00 0.00 5.69
778 780 5.455392 CATTCAAATGTATTCGCCCATCTC 58.545 41.667 0.00 0.00 0.00 2.75
790 792 1.945819 GCCCATCTCGTCTCTTTTGCA 60.946 52.381 0.00 0.00 0.00 4.08
794 796 3.320626 CATCTCGTCTCTTTTGCAGACA 58.679 45.455 4.20 0.00 40.42 3.41
795 797 3.667497 TCTCGTCTCTTTTGCAGACAT 57.333 42.857 4.20 0.00 40.42 3.06
796 798 4.783764 TCTCGTCTCTTTTGCAGACATA 57.216 40.909 4.20 0.00 40.42 2.29
797 799 5.330455 TCTCGTCTCTTTTGCAGACATAT 57.670 39.130 4.20 0.00 40.42 1.78
798 800 6.451064 TCTCGTCTCTTTTGCAGACATATA 57.549 37.500 4.20 0.00 40.42 0.86
799 801 6.863275 TCTCGTCTCTTTTGCAGACATATAA 58.137 36.000 4.20 0.00 40.42 0.98
800 802 7.320399 TCTCGTCTCTTTTGCAGACATATAAA 58.680 34.615 4.20 0.00 40.42 1.40
801 803 7.981789 TCTCGTCTCTTTTGCAGACATATAAAT 59.018 33.333 4.20 0.00 40.42 1.40
802 804 7.909267 TCGTCTCTTTTGCAGACATATAAATG 58.091 34.615 4.20 0.00 40.42 2.32
804 806 7.637519 CGTCTCTTTTGCAGACATATAAATGTG 59.362 37.037 4.20 0.00 46.49 3.21
805 807 7.430502 GTCTCTTTTGCAGACATATAAATGTGC 59.569 37.037 0.00 2.70 46.49 4.57
806 808 7.337689 TCTCTTTTGCAGACATATAAATGTGCT 59.662 33.333 9.30 0.00 46.49 4.40
807 809 7.829725 TCTTTTGCAGACATATAAATGTGCTT 58.170 30.769 9.30 0.00 46.49 3.91
808 810 7.756272 TCTTTTGCAGACATATAAATGTGCTTG 59.244 33.333 9.30 0.00 46.49 4.01
809 811 6.513806 TTGCAGACATATAAATGTGCTTGT 57.486 33.333 9.30 0.00 46.49 3.16
810 812 6.513806 TGCAGACATATAAATGTGCTTGTT 57.486 33.333 9.30 0.00 46.49 2.83
811 813 6.923012 TGCAGACATATAAATGTGCTTGTTT 58.077 32.000 9.30 0.00 46.49 2.83
812 814 7.377398 TGCAGACATATAAATGTGCTTGTTTT 58.623 30.769 9.30 0.00 46.49 2.43
813 815 7.328982 TGCAGACATATAAATGTGCTTGTTTTG 59.671 33.333 9.30 0.00 46.49 2.44
814 816 7.669098 CAGACATATAAATGTGCTTGTTTTGC 58.331 34.615 0.00 0.00 46.49 3.68
815 817 6.527722 AGACATATAAATGTGCTTGTTTTGCG 59.472 34.615 0.00 0.00 46.49 4.85
816 818 5.062058 ACATATAAATGTGCTTGTTTTGCGC 59.938 36.000 0.00 0.00 44.79 6.09
818 820 4.898002 TGTGCTTGTTTTGCGCAA 57.102 44.444 21.02 21.02 46.07 4.85
819 821 3.128259 TGTGCTTGTTTTGCGCAAA 57.872 42.105 30.63 30.63 46.07 3.68
820 822 1.649664 TGTGCTTGTTTTGCGCAAAT 58.350 40.000 33.94 0.00 46.07 2.32
821 823 2.814269 TGTGCTTGTTTTGCGCAAATA 58.186 38.095 33.94 23.24 46.07 1.40
822 824 3.388308 TGTGCTTGTTTTGCGCAAATAT 58.612 36.364 33.94 0.00 46.07 1.28
823 825 4.550422 TGTGCTTGTTTTGCGCAAATATA 58.450 34.783 33.94 18.44 46.07 0.86
824 826 5.167121 TGTGCTTGTTTTGCGCAAATATAT 58.833 33.333 33.94 0.00 46.07 0.86
825 827 6.325596 TGTGCTTGTTTTGCGCAAATATATA 58.674 32.000 33.94 17.68 46.07 0.86
826 828 6.977502 TGTGCTTGTTTTGCGCAAATATATAT 59.022 30.769 33.94 0.00 46.07 0.86
865 867 2.969628 ACAGGCAGAGTGTATACAGC 57.030 50.000 5.62 6.04 0.00 4.40
966 968 2.076863 AGTTTGGTTATCGCAGTCAGC 58.923 47.619 0.00 0.00 40.87 4.26
1012 1014 2.837591 AGCAAATTTATGGTCCCAACCC 59.162 45.455 0.00 0.00 45.83 4.11
1076 1086 3.006003 ACGGTGTGTATGTGTGTATGTGA 59.994 43.478 0.00 0.00 0.00 3.58
1086 1096 8.470805 TGTATGTGTGTATGTGATGTGTATGTA 58.529 33.333 0.00 0.00 0.00 2.29
1119 1129 8.469200 TCTTTGAAGCTTTGGTTCCATTATATG 58.531 33.333 0.00 0.00 39.02 1.78
1417 1427 3.609103 ATGTGTTTGTTCACTCGCTTC 57.391 42.857 0.00 0.00 38.90 3.86
1436 1446 4.561105 CTTCAGTCTTTGTGTACTCCCTC 58.439 47.826 0.00 0.00 0.00 4.30
1441 1451 2.036733 TCTTTGTGTACTCCCTCCGTTG 59.963 50.000 0.00 0.00 0.00 4.10
1442 1452 0.034337 TTGTGTACTCCCTCCGTTGC 59.966 55.000 0.00 0.00 0.00 4.17
1502 1517 8.575649 TTTTTGTGGGTCTTTAGATATTCTCC 57.424 34.615 0.00 0.00 0.00 3.71
1503 1518 6.884472 TTGTGGGTCTTTAGATATTCTCCA 57.116 37.500 0.00 0.00 0.00 3.86
1504 1519 6.884472 TGTGGGTCTTTAGATATTCTCCAA 57.116 37.500 0.00 0.00 0.00 3.53
1505 1520 7.451731 TGTGGGTCTTTAGATATTCTCCAAT 57.548 36.000 0.00 0.00 0.00 3.16
1506 1521 8.561536 TGTGGGTCTTTAGATATTCTCCAATA 57.438 34.615 0.00 0.00 0.00 1.90
1507 1522 9.170890 TGTGGGTCTTTAGATATTCTCCAATAT 57.829 33.333 0.00 0.00 37.82 1.28
1508 1523 9.442047 GTGGGTCTTTAGATATTCTCCAATATG 57.558 37.037 0.00 0.00 35.63 1.78
1509 1524 9.392506 TGGGTCTTTAGATATTCTCCAATATGA 57.607 33.333 0.00 0.00 35.63 2.15
1510 1525 9.660180 GGGTCTTTAGATATTCTCCAATATGAC 57.340 37.037 0.00 0.00 35.63 3.06
1565 1580 6.006449 AGTGTAGGTTCATTCATTTTGCTCT 58.994 36.000 0.00 0.00 0.00 4.09
1671 1688 0.396417 ACAGTGATCGGAGGGAGGAG 60.396 60.000 0.00 0.00 0.00 3.69
1710 1727 3.034721 TGGTAGGCACAAAGAACGTAG 57.965 47.619 0.00 0.00 0.00 3.51
1711 1728 2.289195 TGGTAGGCACAAAGAACGTAGG 60.289 50.000 0.00 0.00 0.00 3.18
1712 1729 2.289257 GGTAGGCACAAAGAACGTAGGT 60.289 50.000 0.00 0.00 0.00 3.08
1713 1730 1.878953 AGGCACAAAGAACGTAGGTG 58.121 50.000 0.00 0.00 0.00 4.00
1714 1731 3.748021 GCACAAAGAACGTAGGTGC 57.252 52.632 12.09 12.09 46.53 5.01
1715 1732 0.110823 GCACAAAGAACGTAGGTGCG 60.111 55.000 12.09 0.00 44.32 5.34
1716 1733 0.511221 CACAAAGAACGTAGGTGCGG 59.489 55.000 0.00 0.00 35.98 5.69
1945 1962 0.380733 TGCTCGTGCACTACTATCCG 59.619 55.000 16.19 0.00 45.31 4.18
1970 1987 3.640407 GGAGCCTGGTGGTCAGCA 61.640 66.667 2.80 2.80 43.44 4.41
2026 2043 3.774702 GGCGTGCCTTTCGTCGTC 61.775 66.667 2.98 0.00 0.00 4.20
2081 2098 2.598099 TCGTACTGTCGGCACCCA 60.598 61.111 0.00 0.00 0.00 4.51
2162 2179 1.895798 ACAAGGAAGATGACGAGCTGA 59.104 47.619 0.00 0.00 0.00 4.26
2785 2803 2.954868 CGGCCATCGACTACGTGC 60.955 66.667 2.24 0.00 42.43 5.34
3047 3073 4.630111 TGAAACTTTGGCCATTTTAGCTG 58.370 39.130 6.09 0.00 0.00 4.24
3150 3176 2.762887 TGCCAACTTTCATGACCAAACA 59.237 40.909 0.00 0.00 0.00 2.83
3151 3177 3.123050 GCCAACTTTCATGACCAAACAC 58.877 45.455 0.00 0.00 0.00 3.32
3152 3178 3.371168 CCAACTTTCATGACCAAACACG 58.629 45.455 0.00 0.00 0.00 4.49
3154 3180 3.691049 ACTTTCATGACCAAACACGTG 57.309 42.857 15.48 15.48 0.00 4.49
3155 3181 2.223479 ACTTTCATGACCAAACACGTGC 60.223 45.455 17.22 0.00 0.00 5.34
3157 3183 1.603456 TCATGACCAAACACGTGCAT 58.397 45.000 17.22 6.87 0.00 3.96
3160 3186 1.440353 GACCAAACACGTGCATCGC 60.440 57.895 17.22 0.00 44.19 4.58
3231 3258 4.371786 TGTCAACAGCACAACTAGAGAAG 58.628 43.478 0.00 0.00 0.00 2.85
3235 3262 3.983741 ACAGCACAACTAGAGAAGTCAC 58.016 45.455 0.00 0.00 37.50 3.67
3236 3263 3.639094 ACAGCACAACTAGAGAAGTCACT 59.361 43.478 0.00 0.00 37.50 3.41
3302 3330 6.644347 TCCTCCATGTGTTTCTTTCTCTATC 58.356 40.000 0.00 0.00 0.00 2.08
3354 3382 1.536766 GTTTGATGCAGCAGTGTAGCA 59.463 47.619 4.20 12.81 43.14 3.49
3386 3414 1.000283 GGGGATACTCATCAGCTGACG 60.000 57.143 20.97 11.99 36.63 4.35
3392 3420 1.081892 CTCATCAGCTGACGGTTTGG 58.918 55.000 20.97 3.68 0.00 3.28
3394 3422 1.073025 ATCAGCTGACGGTTTGGCA 59.927 52.632 20.97 0.00 0.00 4.92
3422 3463 3.577848 ACCTGCTAATTTGGTGAATGCAA 59.422 39.130 0.00 0.00 29.46 4.08
3427 3468 4.389687 GCTAATTTGGTGAATGCAAACCTG 59.610 41.667 15.27 3.55 37.36 4.00
3449 3490 1.067776 GGATGCTAAGACCCGATACCG 60.068 57.143 0.00 0.00 0.00 4.02
3450 3491 1.884579 GATGCTAAGACCCGATACCGA 59.115 52.381 0.00 0.00 38.22 4.69
3464 3505 1.833787 TACCGACAACTCCCTTGGCC 61.834 60.000 0.00 0.00 33.72 5.36
3857 3898 3.508762 CATTGCTCTTGCCATCAAAGTC 58.491 45.455 0.00 0.00 38.71 3.01
3929 3970 4.951050 TATAAGCTCCTCTGCCACCCGT 62.951 54.545 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 5.908590 TCTCCATGACCATACATAGGATCT 58.091 41.667 0.00 0.00 32.06 2.75
263 264 1.730501 ACCTCGACGACAGTATTCGA 58.269 50.000 0.00 5.97 41.78 3.71
305 306 7.342026 TCTCTTGACATATTGCAGGTTAGAGTA 59.658 37.037 0.00 0.00 34.38 2.59
306 307 6.155221 TCTCTTGACATATTGCAGGTTAGAGT 59.845 38.462 0.00 0.00 34.38 3.24
307 308 6.577103 TCTCTTGACATATTGCAGGTTAGAG 58.423 40.000 0.00 0.00 34.20 2.43
308 309 6.155221 ACTCTCTTGACATATTGCAGGTTAGA 59.845 38.462 0.00 0.00 0.00 2.10
309 310 6.344500 ACTCTCTTGACATATTGCAGGTTAG 58.656 40.000 0.00 0.00 0.00 2.34
533 535 1.416401 TCCTGTCAGGCGTTTCTTCTT 59.584 47.619 14.64 0.00 34.61 2.52
545 547 1.202627 GCCAGCCTTAGATCCTGTCAG 60.203 57.143 0.00 0.00 0.00 3.51
638 640 3.134127 GCGAGGCCCAGCGATTTT 61.134 61.111 13.66 0.00 0.00 1.82
662 664 0.994995 CAATGACTGCGGAGAAGTCG 59.005 55.000 12.26 0.00 45.81 4.18
778 780 7.637519 CACATTTATATGTCTGCAAAAGAGACG 59.362 37.037 0.00 0.00 43.07 4.18
790 792 6.527722 CGCAAAACAAGCACATTTATATGTCT 59.472 34.615 0.00 0.00 43.07 3.41
794 796 5.167121 TGCGCAAAACAAGCACATTTATAT 58.833 33.333 8.16 0.00 35.81 0.86
795 797 4.550422 TGCGCAAAACAAGCACATTTATA 58.450 34.783 8.16 0.00 35.81 0.98
796 798 3.388308 TGCGCAAAACAAGCACATTTAT 58.612 36.364 8.16 0.00 35.81 1.40
797 799 2.814269 TGCGCAAAACAAGCACATTTA 58.186 38.095 8.16 0.00 35.81 1.40
798 800 1.649664 TGCGCAAAACAAGCACATTT 58.350 40.000 8.16 0.00 35.81 2.32
799 801 1.649664 TTGCGCAAAACAAGCACATT 58.350 40.000 22.78 0.00 40.92 2.71
800 802 1.649664 TTTGCGCAAAACAAGCACAT 58.350 40.000 31.98 0.00 40.92 3.21
801 803 1.649664 ATTTGCGCAAAACAAGCACA 58.350 40.000 36.42 13.69 40.92 4.57
802 804 5.701029 ATATATTTGCGCAAAACAAGCAC 57.299 34.783 36.42 0.00 40.92 4.40
825 827 9.965824 GCCTGTAAAACAAGCACATTTATATAT 57.034 29.630 0.00 0.00 35.69 0.86
826 828 8.961634 TGCCTGTAAAACAAGCACATTTATATA 58.038 29.630 0.00 0.00 40.30 0.86
944 946 3.682858 GCTGACTGCGATAACCAAACTTA 59.317 43.478 0.00 0.00 0.00 2.24
1012 1014 2.993899 GTCACGGTTGGTCAGATAGTTG 59.006 50.000 0.00 0.00 0.00 3.16
1049 1059 3.794717 ACACACATACACACCGTTGTTA 58.205 40.909 0.00 0.00 31.66 2.41
1051 1061 2.319136 ACACACATACACACCGTTGT 57.681 45.000 0.00 0.00 35.84 3.32
1063 1073 8.785329 TTTACATACACATCACATACACACAT 57.215 30.769 0.00 0.00 0.00 3.21
1064 1074 8.785329 ATTTACATACACATCACATACACACA 57.215 30.769 0.00 0.00 0.00 3.72
1086 1096 7.154656 GGAACCAAAGCTTCAAAGACATATTT 58.845 34.615 0.00 0.00 0.00 1.40
1389 1399 6.198216 GCGAGTGAACAAACACATTAAATTGT 59.802 34.615 0.00 0.00 42.45 2.71
1397 1407 2.942376 TGAAGCGAGTGAACAAACACAT 59.058 40.909 0.00 0.00 42.45 3.21
1417 1427 2.352814 CGGAGGGAGTACACAAAGACTG 60.353 54.545 0.00 0.00 0.00 3.51
1476 1491 9.190317 GGAGAATATCTAAAGACCCACAAAAAT 57.810 33.333 0.00 0.00 0.00 1.82
1478 1493 7.695055 TGGAGAATATCTAAAGACCCACAAAA 58.305 34.615 0.00 0.00 0.00 2.44
1479 1494 7.265599 TGGAGAATATCTAAAGACCCACAAA 57.734 36.000 0.00 0.00 0.00 2.83
1480 1495 6.884472 TGGAGAATATCTAAAGACCCACAA 57.116 37.500 0.00 0.00 0.00 3.33
1482 1497 9.442047 CATATTGGAGAATATCTAAAGACCCAC 57.558 37.037 0.00 0.00 33.21 4.61
1483 1498 9.392506 TCATATTGGAGAATATCTAAAGACCCA 57.607 33.333 0.00 0.00 33.21 4.51
1484 1499 9.660180 GTCATATTGGAGAATATCTAAAGACCC 57.340 37.037 0.00 0.00 33.21 4.46
1493 1508 9.737427 CCGTATGTAGTCATATTGGAGAATATC 57.263 37.037 0.00 0.00 38.56 1.63
1494 1509 9.475620 TCCGTATGTAGTCATATTGGAGAATAT 57.524 33.333 0.00 0.00 38.16 1.28
1495 1510 8.873186 TCCGTATGTAGTCATATTGGAGAATA 57.127 34.615 0.00 0.00 38.16 1.75
1496 1511 7.776618 TCCGTATGTAGTCATATTGGAGAAT 57.223 36.000 0.00 0.00 38.16 2.40
1497 1512 7.776618 ATCCGTATGTAGTCATATTGGAGAA 57.223 36.000 13.38 0.00 42.02 2.87
1512 1527 9.535170 AAGCTATGCCTATATATATCCGTATGT 57.465 33.333 0.00 0.00 0.00 2.29
1530 1545 5.263968 TGAACCTACACTCTAAGCTATGC 57.736 43.478 0.00 0.00 0.00 3.14
1536 1551 7.965107 GCAAAATGAATGAACCTACACTCTAAG 59.035 37.037 0.00 0.00 0.00 2.18
1540 1555 6.150140 AGAGCAAAATGAATGAACCTACACTC 59.850 38.462 0.00 0.00 0.00 3.51
1649 1666 2.091278 TCCTCCCTCCGATCACTGTTAT 60.091 50.000 0.00 0.00 0.00 1.89
1734 1751 0.461961 CCTCGTCACCCTCATTCTCC 59.538 60.000 0.00 0.00 0.00 3.71
2127 2144 1.294659 CTTGTCCTCGGAGTTGCTGC 61.295 60.000 4.02 0.00 0.00 5.25
2128 2145 0.671781 CCTTGTCCTCGGAGTTGCTG 60.672 60.000 4.02 0.00 0.00 4.41
2129 2146 0.832135 TCCTTGTCCTCGGAGTTGCT 60.832 55.000 4.02 0.00 0.00 3.91
2130 2147 0.034896 TTCCTTGTCCTCGGAGTTGC 59.965 55.000 4.02 0.00 0.00 4.17
2131 2148 1.618837 TCTTCCTTGTCCTCGGAGTTG 59.381 52.381 4.02 0.00 0.00 3.16
2132 2149 2.011122 TCTTCCTTGTCCTCGGAGTT 57.989 50.000 4.02 0.00 0.00 3.01
2162 2179 3.151022 GCTCAGTAGAGGCGCCCT 61.151 66.667 26.15 22.05 42.33 5.19
3070 3096 2.138320 GAGATCCCATGCATACACACG 58.862 52.381 0.00 0.00 0.00 4.49
3120 3146 9.194972 TGGTCATGAAAGTTGGCAATAATAATA 57.805 29.630 1.92 0.00 0.00 0.98
3121 3147 8.076910 TGGTCATGAAAGTTGGCAATAATAAT 57.923 30.769 1.92 0.00 0.00 1.28
3122 3148 7.473735 TGGTCATGAAAGTTGGCAATAATAA 57.526 32.000 1.92 0.00 0.00 1.40
3131 3157 3.181491 ACGTGTTTGGTCATGAAAGTTGG 60.181 43.478 0.00 0.00 0.00 3.77
3154 3180 1.135431 TGCCTTGTATTTGTGCGATGC 60.135 47.619 0.00 0.00 0.00 3.91
3155 3181 2.419673 TCTGCCTTGTATTTGTGCGATG 59.580 45.455 0.00 0.00 0.00 3.84
3157 3183 2.177394 TCTGCCTTGTATTTGTGCGA 57.823 45.000 0.00 0.00 0.00 5.10
3160 3186 7.081349 TCGTTAAAATCTGCCTTGTATTTGTG 58.919 34.615 0.00 0.00 0.00 3.33
3197 3224 3.313249 TGCTGTTGACAACTTCACATCTG 59.687 43.478 18.73 0.00 32.26 2.90
3224 3251 6.265649 AGCTAGTGTTTGAAGTGACTTCTCTA 59.734 38.462 24.09 16.10 40.73 2.43
3231 3258 5.696724 ACATGTAGCTAGTGTTTGAAGTGAC 59.303 40.000 0.00 0.00 0.00 3.67
3235 3262 4.142816 GGCACATGTAGCTAGTGTTTGAAG 60.143 45.833 16.34 2.68 35.75 3.02
3236 3263 3.751175 GGCACATGTAGCTAGTGTTTGAA 59.249 43.478 16.34 0.00 35.75 2.69
3302 3330 1.865788 CGATGTTGCTTGGGGTGTGG 61.866 60.000 0.00 0.00 0.00 4.17
3386 3414 3.965780 CAGGTTGTTCTGCCAAACC 57.034 52.632 0.00 0.00 32.27 3.27
3394 3422 4.469657 TCACCAAATTAGCAGGTTGTTCT 58.530 39.130 0.00 0.00 32.15 3.01
3422 3463 1.282157 GGGTCTTAGCATCCACAGGTT 59.718 52.381 0.00 0.00 0.00 3.50
3427 3468 2.288886 GGTATCGGGTCTTAGCATCCAC 60.289 54.545 0.00 0.00 0.00 4.02
3449 3490 1.973812 GCAGGCCAAGGGAGTTGTC 60.974 63.158 5.01 0.00 33.87 3.18
3450 3491 2.116125 GCAGGCCAAGGGAGTTGT 59.884 61.111 5.01 0.00 33.87 3.32
3857 3898 0.095935 CATCCGACTTTGAGCAAGCG 59.904 55.000 0.00 0.00 35.65 4.68
3929 3970 1.206811 TGGATGTGTGCATGGGAGGA 61.207 55.000 0.00 0.00 35.07 3.71


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

AutoCloner maintained by Alex Coulton.