Multiple sequence alignment - TraesCS3D01G344800

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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 TraesCS3D01G344800 chr3D 100.000 3674 0 0 1 3674 456599429 456595756 0.000000e+00 6785.0
1 TraesCS3D01G344800 chr3D 78.153 444 72 14 2143 2572 488118333 488117901 3.640000e-65 259.0
2 TraesCS3D01G344800 chr3D 75.644 427 93 6 2144 2563 488235630 488236052 6.220000e-48 202.0
3 TraesCS3D01G344800 chr3D 100.000 31 0 0 3437 3467 43027147 43027177 1.430000e-04 58.4
4 TraesCS3D01G344800 chr3A 92.064 2747 120 38 7 2699 599387145 599384443 0.000000e+00 3775.0
5 TraesCS3D01G344800 chr3A 87.327 1010 43 21 2694 3672 599383218 599382263 0.000000e+00 1077.0
6 TraesCS3D01G344800 chr3A 76.759 469 81 15 2120 2572 631728337 631727881 1.710000e-58 237.0
7 TraesCS3D01G344800 chr3B 95.235 1742 59 8 956 2680 603453548 603451814 0.000000e+00 2736.0
8 TraesCS3D01G344800 chr3B 94.222 675 29 7 2955 3621 603451506 603450834 0.000000e+00 1022.0
9 TraesCS3D01G344800 chr3B 89.773 704 57 8 247 940 603454299 603453601 0.000000e+00 887.0
10 TraesCS3D01G344800 chr3B 77.703 444 74 14 2143 2572 650953549 650953117 7.880000e-62 248.0
11 TraesCS3D01G344800 chr3B 76.168 428 91 6 2143 2563 651258024 651258447 7.990000e-52 215.0
12 TraesCS3D01G344800 chr1D 86.804 629 59 15 1006 1631 394673064 394672457 0.000000e+00 680.0
13 TraesCS3D01G344800 chr1D 83.929 448 70 2 2127 2573 394671104 394670658 9.430000e-116 427.0
14 TraesCS3D01G344800 chr1D 90.365 301 29 0 1733 2033 394671714 394671414 2.660000e-106 396.0
15 TraesCS3D01G344800 chr1A 86.570 618 61 12 1012 1627 490411643 490412240 0.000000e+00 662.0
16 TraesCS3D01G344800 chr1A 91.186 295 26 0 1733 2027 490413096 490413390 5.710000e-108 401.0
17 TraesCS3D01G344800 chr1A 94.231 52 3 0 191 242 561605676 561605727 3.040000e-11 80.5
18 TraesCS3D01G344800 chr1B 86.386 617 64 12 1012 1627 526747864 526748461 0.000000e+00 656.0
19 TraesCS3D01G344800 chr1B 83.705 448 71 2 2127 2573 526749871 526750317 4.390000e-114 422.0
20 TraesCS3D01G344800 chr1B 90.169 295 29 0 1733 2027 526749329 526749623 5.760000e-103 385.0
21 TraesCS3D01G344800 chr5D 80.519 616 108 12 1014 1623 540240501 540239892 2.580000e-126 462.0
22 TraesCS3D01G344800 chr5D 100.000 28 0 0 3464 3491 62479983 62480010 7.000000e-03 52.8
23 TraesCS3D01G344800 chr4A 80.357 616 109 12 1014 1623 628090307 628089698 1.200000e-124 457.0
24 TraesCS3D01G344800 chr4A 88.710 62 2 4 3436 3493 646603834 646603894 1.830000e-08 71.3
25 TraesCS3D01G344800 chr4A 88.889 45 3 2 3413 3457 386321090 386321048 2.000000e-03 54.7
26 TraesCS3D01G344800 chr5B 79.870 616 112 12 1014 1623 682538803 682538194 1.210000e-119 440.0
27 TraesCS3D01G344800 chr7B 91.391 302 25 1 1084 1384 6361103 6361404 2.640000e-111 412.0
28 TraesCS3D01G344800 chr7B 84.000 75 8 3 3436 3507 452258811 452258738 6.580000e-08 69.4
29 TraesCS3D01G344800 chr7B 93.023 43 3 0 3465 3507 99103435 99103477 3.060000e-06 63.9
30 TraesCS3D01G344800 chr7B 87.500 48 5 1 3464 3510 701174986 701174939 2.000000e-03 54.7
31 TraesCS3D01G344800 chr2B 85.401 137 12 2 2223 2359 627652307 627652435 6.400000e-28 135.0
32 TraesCS3D01G344800 chr2B 100.000 31 0 0 3437 3467 588071361 588071331 1.430000e-04 58.4
33 TraesCS3D01G344800 chr2A 90.698 43 4 0 3465 3507 153533072 153533114 1.430000e-04 58.4
34 TraesCS3D01G344800 chr5A 100.000 30 0 0 3432 3461 1098985 1099014 5.130000e-04 56.5
35 TraesCS3D01G344800 chr2D 100.000 30 0 0 3431 3460 616935171 616935200 5.130000e-04 56.5


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 TraesCS3D01G344800 chr3D 456595756 456599429 3673 True 6785.000000 6785 100.000000 1 3674 1 chr3D.!!$R1 3673
1 TraesCS3D01G344800 chr3A 599382263 599387145 4882 True 2426.000000 3775 89.695500 7 3672 2 chr3A.!!$R2 3665
2 TraesCS3D01G344800 chr3B 603450834 603454299 3465 True 1548.333333 2736 93.076667 247 3621 3 chr3B.!!$R2 3374
3 TraesCS3D01G344800 chr1D 394670658 394673064 2406 True 501.000000 680 87.032667 1006 2573 3 chr1D.!!$R1 1567
4 TraesCS3D01G344800 chr1A 490411643 490413390 1747 False 531.500000 662 88.878000 1012 2027 2 chr1A.!!$F2 1015
5 TraesCS3D01G344800 chr1B 526747864 526750317 2453 False 487.666667 656 86.753333 1012 2573 3 chr1B.!!$F1 1561
6 TraesCS3D01G344800 chr5D 540239892 540240501 609 True 462.000000 462 80.519000 1014 1623 1 chr5D.!!$R1 609
7 TraesCS3D01G344800 chr4A 628089698 628090307 609 True 457.000000 457 80.357000 1014 1623 1 chr4A.!!$R2 609
8 TraesCS3D01G344800 chr5B 682538194 682538803 609 True 440.000000 440 79.870000 1014 1623 1 chr5B.!!$R1 609

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
663 678 0.100682 CTCAGGTACGTGCGCAGTAT 59.899 55.0 12.22 0.77 0.00 2.12 F
1636 1707 0.037975 CTGGGTACGTTACGTTGCCT 60.038 55.0 17.42 0.00 41.54 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 1729 0.250424 AAGGTAAACCGAACCCGTGG 60.250 55.000 0.0 0.0 42.08 4.94 R
3429 6074 1.336125 GAACGGAGGGAGTACATACCG 59.664 57.143 0.0 0.0 44.77 4.02 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
33 34 1.202940 GGGGGCAATATGGACTTCTCC 60.203 57.143 0.00 0.00 37.04 3.71
38 39 3.244387 GGCAATATGGACTTCTCCTCTCC 60.244 52.174 0.00 0.00 37.48 3.71
60 61 5.548056 TCCCAAAGTAAGGAGAAGAAGTGAT 59.452 40.000 0.00 0.00 0.00 3.06
70 71 6.836242 AGGAGAAGAAGTGATAAATCATCCC 58.164 40.000 0.00 0.00 39.30 3.85
72 73 6.183361 GGAGAAGAAGTGATAAATCATCCCCT 60.183 42.308 0.00 0.00 39.30 4.79
94 96 1.749063 GTTGTTGGCCCTACCTAATGC 59.251 52.381 0.00 0.00 40.22 3.56
105 107 3.118738 CCTACCTAATGCCGAACTCTTGT 60.119 47.826 0.00 0.00 0.00 3.16
118 120 1.670811 ACTCTTGTTCACGCAACCTTG 59.329 47.619 0.00 0.00 33.51 3.61
146 149 1.654105 GTACTCTTGTTCACGCGGATG 59.346 52.381 12.47 0.00 0.00 3.51
148 151 0.670546 CTCTTGTTCACGCGGATGGT 60.671 55.000 12.47 0.00 0.00 3.55
239 242 4.479158 AGTGGCAAGTGATTTTCCCTTAA 58.521 39.130 0.00 0.00 0.00 1.85
245 248 7.875554 TGGCAAGTGATTTTCCCTTAAAATAAC 59.124 33.333 3.46 3.46 45.70 1.89
521 530 2.624636 CGTGGTTAACCGAGCCTAAAT 58.375 47.619 19.65 0.00 39.43 1.40
525 534 2.098607 GGTTAACCGAGCCTAAATTGCC 59.901 50.000 9.34 0.00 0.00 4.52
532 541 2.880268 CGAGCCTAAATTGCCATGATCA 59.120 45.455 0.00 0.00 0.00 2.92
569 581 6.647481 TGCAAGCTGTAGAAAATAACGAACTA 59.353 34.615 0.00 0.00 0.00 2.24
570 582 6.954297 GCAAGCTGTAGAAAATAACGAACTAC 59.046 38.462 0.00 0.00 35.47 2.73
663 678 0.100682 CTCAGGTACGTGCGCAGTAT 59.899 55.000 12.22 0.77 0.00 2.12
690 718 5.712917 CCTTTGGTACATTAAACAAGGGCTA 59.287 40.000 0.00 0.00 39.30 3.93
694 722 5.123936 GGTACATTAAACAAGGGCTAGGAG 58.876 45.833 0.00 0.00 0.00 3.69
711 739 3.854666 AGGAGAACGTGAGATGTTCATG 58.145 45.455 10.49 0.00 44.42 3.07
713 741 2.932614 GAGAACGTGAGATGTTCATGGG 59.067 50.000 10.49 0.00 44.42 4.00
767 795 3.056607 CCAATGAAACCGAGAAGCCAAAT 60.057 43.478 0.00 0.00 0.00 2.32
789 817 1.086696 CGCACGGGACATGAGAAAAT 58.913 50.000 0.00 0.00 0.00 1.82
790 818 1.468520 CGCACGGGACATGAGAAAATT 59.531 47.619 0.00 0.00 0.00 1.82
831 859 2.168503 GTGTCGACACGCCACACAA 61.169 57.895 31.03 0.00 40.22 3.33
906 940 2.581409 CGCCGCCTACTTGTACCG 60.581 66.667 0.00 0.00 0.00 4.02
953 1015 1.586028 GGTGCCCTACGTACGTGAA 59.414 57.895 30.25 11.03 0.00 3.18
954 1016 0.733909 GGTGCCCTACGTACGTGAAC 60.734 60.000 30.25 17.82 0.00 3.18
975 1046 2.410646 CGTGATCGATCAATCAATGGCG 60.411 50.000 28.83 20.37 38.75 5.69
978 1049 0.179048 TCGATCAATCAATGGCGGCT 60.179 50.000 11.43 0.00 0.00 5.52
1473 1544 3.134127 GCGTGGATGGCCTTCACC 61.134 66.667 19.49 10.41 34.31 4.02
1512 1583 1.374252 CTACACCGTCTGCGCCTTT 60.374 57.895 4.18 0.00 36.67 3.11
1542 1613 2.797278 CGGCGGCTTCCTCTACCAT 61.797 63.158 7.61 0.00 0.00 3.55
1630 1701 0.810648 TGCCTACTGGGTACGTTACG 59.189 55.000 2.19 2.19 37.43 3.18
1631 1702 0.811281 GCCTACTGGGTACGTTACGT 59.189 55.000 16.31 16.31 38.59 3.57
1632 1703 1.202348 GCCTACTGGGTACGTTACGTT 59.798 52.381 17.42 0.00 37.11 3.99
1633 1704 2.867429 CCTACTGGGTACGTTACGTTG 58.133 52.381 17.42 4.55 41.54 4.10
1634 1705 2.253603 CTACTGGGTACGTTACGTTGC 58.746 52.381 17.42 9.56 41.54 4.17
1636 1707 0.037975 CTGGGTACGTTACGTTGCCT 60.038 55.000 17.42 0.00 41.54 4.75
1637 1708 1.202114 CTGGGTACGTTACGTTGCCTA 59.798 52.381 17.42 15.16 41.54 3.93
1639 1710 2.159254 TGGGTACGTTACGTTGCCTATC 60.159 50.000 17.42 7.24 41.54 2.08
1640 1711 2.099756 GGGTACGTTACGTTGCCTATCT 59.900 50.000 17.42 0.00 41.54 1.98
1641 1712 3.315191 GGGTACGTTACGTTGCCTATCTA 59.685 47.826 17.42 0.00 41.54 1.98
1643 1714 5.181245 GGGTACGTTACGTTGCCTATCTATA 59.819 44.000 17.42 0.00 41.54 1.31
1644 1715 6.080406 GGTACGTTACGTTGCCTATCTATAC 58.920 44.000 17.42 3.03 41.54 1.47
1645 1716 4.776743 ACGTTACGTTGCCTATCTATACG 58.223 43.478 3.95 0.00 36.35 3.06
1647 1718 4.610122 CGTTACGTTGCCTATCTATACGTG 59.390 45.833 0.00 0.00 44.18 4.49
1649 1720 2.359848 ACGTTGCCTATCTATACGTGCA 59.640 45.455 0.00 0.00 43.02 4.57
1650 1721 3.181484 ACGTTGCCTATCTATACGTGCAA 60.181 43.478 0.00 0.00 43.02 4.08
1651 1722 3.987868 CGTTGCCTATCTATACGTGCAAT 59.012 43.478 8.61 0.00 40.38 3.56
1655 1726 3.181530 GCCTATCTATACGTGCAATTGCG 60.182 47.826 24.58 14.19 45.83 4.85
1656 1727 4.234574 CCTATCTATACGTGCAATTGCGA 58.765 43.478 24.58 14.21 45.83 5.10
1657 1728 4.090066 CCTATCTATACGTGCAATTGCGAC 59.910 45.833 24.58 20.59 45.83 5.19
1658 1729 2.198406 TCTATACGTGCAATTGCGACC 58.802 47.619 24.58 14.06 45.83 4.79
1946 3005 4.436998 GGACCTGCCTGGACGTCG 62.437 72.222 9.92 0.00 39.71 5.12
2035 3094 3.564027 GGCGCAGGTTCCGAATCG 61.564 66.667 10.83 0.00 0.00 3.34
2089 3362 3.634568 TGTGAATTTTGCTTACGGTGG 57.365 42.857 0.00 0.00 0.00 4.61
2111 3410 3.245990 GGCTTTGTCTTTTGTGTTGCATC 59.754 43.478 0.00 0.00 0.00 3.91
2577 3919 2.050714 GAGCGGTTCGACGTGTCA 60.051 61.111 0.00 0.00 35.98 3.58
2655 3997 1.053264 CAGCCATGGGAGCTAGAGGT 61.053 60.000 15.13 0.00 38.95 3.85
2699 4050 0.744281 CTGGTGCCCGTTGTTCTTTT 59.256 50.000 0.00 0.00 0.00 2.27
2794 5375 6.575162 TCTTTTGCTAATTTCAGAAGGGAC 57.425 37.500 9.32 0.00 0.00 4.46
2802 5383 7.094377 TGCTAATTTCAGAAGGGACATTTGTAC 60.094 37.037 0.00 0.00 0.00 2.90
2821 5402 7.987750 TTGTACTTTCCTACAATATGCAACA 57.012 32.000 0.00 0.00 32.72 3.33
2829 5410 7.377766 TCCTACAATATGCAACAGAGTTTTC 57.622 36.000 0.00 0.00 0.00 2.29
2830 5411 6.092122 TCCTACAATATGCAACAGAGTTTTCG 59.908 38.462 0.00 0.00 0.00 3.46
2837 5418 3.923461 TGCAACAGAGTTTTCGGTTTTTG 59.077 39.130 0.00 0.00 39.28 2.44
2849 5458 5.630661 TTCGGTTTTTGTTCAGTTCTTGA 57.369 34.783 0.00 0.00 0.00 3.02
2850 5459 5.630661 TCGGTTTTTGTTCAGTTCTTGAA 57.369 34.783 0.00 0.00 43.40 2.69
2921 5539 2.358957 CTTCGGTTCAGCAATCATGGA 58.641 47.619 0.00 0.00 0.00 3.41
2923 5541 0.734889 CGGTTCAGCAATCATGGACC 59.265 55.000 0.00 0.00 42.18 4.46
2924 5542 1.679944 CGGTTCAGCAATCATGGACCT 60.680 52.381 2.12 0.00 43.26 3.85
2925 5543 1.747355 GGTTCAGCAATCATGGACCTG 59.253 52.381 0.00 0.00 42.31 4.00
2926 5544 1.747355 GTTCAGCAATCATGGACCTGG 59.253 52.381 0.00 0.00 0.00 4.45
2927 5545 0.394762 TCAGCAATCATGGACCTGGC 60.395 55.000 0.00 0.00 0.00 4.85
2929 5547 0.682209 AGCAATCATGGACCTGGCAC 60.682 55.000 0.00 0.00 0.00 5.01
2931 5549 0.677731 CAATCATGGACCTGGCACGT 60.678 55.000 0.00 0.00 0.00 4.49
2932 5550 0.677731 AATCATGGACCTGGCACGTG 60.678 55.000 12.28 12.28 0.00 4.49
2935 5553 1.150536 ATGGACCTGGCACGTGTTT 59.849 52.632 18.38 0.00 0.00 2.83
2936 5554 0.467290 ATGGACCTGGCACGTGTTTT 60.467 50.000 18.38 0.00 0.00 2.43
2937 5555 0.180642 TGGACCTGGCACGTGTTTTA 59.819 50.000 18.38 0.29 0.00 1.52
2938 5556 1.310904 GGACCTGGCACGTGTTTTAA 58.689 50.000 18.38 0.00 0.00 1.52
2939 5557 1.677052 GGACCTGGCACGTGTTTTAAA 59.323 47.619 18.38 0.00 0.00 1.52
2940 5558 2.295070 GGACCTGGCACGTGTTTTAAAT 59.705 45.455 18.38 0.00 0.00 1.40
2941 5559 3.243602 GGACCTGGCACGTGTTTTAAATT 60.244 43.478 18.38 0.00 0.00 1.82
2942 5560 3.712187 ACCTGGCACGTGTTTTAAATTG 58.288 40.909 18.38 0.00 0.00 2.32
2943 5561 3.381908 ACCTGGCACGTGTTTTAAATTGA 59.618 39.130 18.38 0.00 0.00 2.57
2944 5562 4.142138 ACCTGGCACGTGTTTTAAATTGAA 60.142 37.500 18.38 0.00 0.00 2.69
2945 5563 4.987912 CCTGGCACGTGTTTTAAATTGAAT 59.012 37.500 18.38 0.00 0.00 2.57
3007 5652 6.091986 GGCAAGAACATTGTGAAACTTGAAAA 59.908 34.615 20.08 0.00 37.49 2.29
3118 5763 1.002250 ACACAGTAGCTTTCGTCGCG 61.002 55.000 0.00 0.00 0.00 5.87
3231 5876 1.509923 GAGCATTCAAGCTGCCCAC 59.490 57.895 0.00 0.00 46.75 4.61
3241 5886 3.283684 CTGCCCACGCCGTTTTCA 61.284 61.111 0.00 0.00 0.00 2.69
3367 6012 2.617274 GCGCACCTGGGAGTTTCAC 61.617 63.158 0.30 0.00 0.00 3.18
3429 6074 8.282592 GGTCTTTATTTGAAAAATGCAAAGGTC 58.717 33.333 0.00 0.00 38.48 3.85
3495 6144 8.194769 ACTAAAACCACAACAAGTATTTTGGAG 58.805 33.333 0.00 0.00 33.70 3.86
3600 6257 3.127791 ACCCCATTGGCAAATTATCCA 57.872 42.857 3.01 0.00 37.83 3.41
3614 6271 7.599998 GGCAAATTATCCAACCAATATGTCATC 59.400 37.037 0.00 0.00 0.00 2.92
3649 6306 5.696724 ACAAGAAGACAAAATCAGGACTACG 59.303 40.000 0.00 0.00 0.00 3.51
3667 6324 7.227910 AGGACTACGTAAAGCTGAAAAATCAAA 59.772 33.333 0.00 0.00 0.00 2.69
3672 6329 7.344441 ACGTAAAGCTGAAAAATCAAAATTGC 58.656 30.769 0.00 0.00 0.00 3.56
3673 6330 6.512647 CGTAAAGCTGAAAAATCAAAATTGCG 59.487 34.615 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.298525 ATATTGCCCCCTCCTCCCCA 62.299 60.000 0.00 0.00 0.00 4.96
5 6 1.466186 ATATTGCCCCCTCCTCCCC 60.466 63.158 0.00 0.00 0.00 4.81
6 7 1.770324 CATATTGCCCCCTCCTCCC 59.230 63.158 0.00 0.00 0.00 4.30
7 8 0.772124 TCCATATTGCCCCCTCCTCC 60.772 60.000 0.00 0.00 0.00 4.30
8 9 0.402121 GTCCATATTGCCCCCTCCTC 59.598 60.000 0.00 0.00 0.00 3.71
9 10 0.028642 AGTCCATATTGCCCCCTCCT 60.029 55.000 0.00 0.00 0.00 3.69
10 11 0.853530 AAGTCCATATTGCCCCCTCC 59.146 55.000 0.00 0.00 0.00 4.30
11 12 1.777272 AGAAGTCCATATTGCCCCCTC 59.223 52.381 0.00 0.00 0.00 4.30
18 19 3.969976 TGGGAGAGGAGAAGTCCATATTG 59.030 47.826 0.00 0.00 46.80 1.90
38 39 8.848474 TTTATCACTTCTTCTCCTTACTTTGG 57.152 34.615 0.00 0.00 0.00 3.28
60 61 3.513515 GCCAACAACAAGGGGATGATTTA 59.486 43.478 0.00 0.00 0.00 1.40
68 69 0.898326 GTAGGGCCAACAACAAGGGG 60.898 60.000 6.18 0.00 0.00 4.79
70 71 0.112412 AGGTAGGGCCAACAACAAGG 59.888 55.000 6.18 0.00 40.61 3.61
72 73 3.426615 CATTAGGTAGGGCCAACAACAA 58.573 45.455 6.18 0.00 40.61 2.83
126 129 1.654105 CATCCGCGTGAACAAGAGTAC 59.346 52.381 4.92 0.00 0.00 2.73
146 149 1.883084 GGACGATCGTGGCATCACC 60.883 63.158 28.12 14.85 40.65 4.02
148 151 0.179111 GAAGGACGATCGTGGCATCA 60.179 55.000 28.12 0.00 0.00 3.07
206 209 4.460263 TCACTTGCCACTTTATTGTGAGT 58.540 39.130 0.00 0.00 40.12 3.41
210 213 6.223120 GGAAAATCACTTGCCACTTTATTGT 58.777 36.000 0.00 0.00 0.00 2.71
211 214 5.639082 GGGAAAATCACTTGCCACTTTATTG 59.361 40.000 0.00 0.00 36.82 1.90
245 248 9.362539 CTGATATGAAAACCTCAAATTTCAAGG 57.637 33.333 12.62 12.62 45.56 3.61
321 329 3.085952 TGAATCCAGCCCGAATTTTCT 57.914 42.857 0.00 0.00 0.00 2.52
438 446 3.506455 ACGATATTTCCGATCTCGTGGAT 59.494 43.478 3.45 0.00 40.68 3.41
450 458 6.916440 AGTTTTTGGTACCAACGATATTTCC 58.084 36.000 27.08 7.55 35.46 3.13
521 530 3.448301 GGTTTGGATCTTGATCATGGCAA 59.552 43.478 12.02 4.90 0.00 4.52
525 534 3.697542 TGCAGGTTTGGATCTTGATCATG 59.302 43.478 12.02 0.00 0.00 3.07
532 541 1.891150 CAGCTTGCAGGTTTGGATCTT 59.109 47.619 0.00 0.00 0.00 2.40
569 581 1.473278 GCGTCTCCTTGTACAGCTAGT 59.527 52.381 0.00 0.00 0.00 2.57
570 582 1.746220 AGCGTCTCCTTGTACAGCTAG 59.254 52.381 1.99 0.00 0.00 3.42
690 718 3.368843 CCATGAACATCTCACGTTCTCCT 60.369 47.826 0.00 0.00 42.63 3.69
694 722 2.972625 TCCCATGAACATCTCACGTTC 58.027 47.619 0.00 0.00 42.52 3.95
711 739 2.242196 TCTCATGGATCTTTGGGTTCCC 59.758 50.000 0.12 0.12 33.89 3.97
744 772 1.073125 TGGCTTCTCGGTTTCATTGGA 59.927 47.619 0.00 0.00 0.00 3.53
767 795 4.758251 CTCATGTCCCGTGCGCCA 62.758 66.667 4.18 0.00 0.00 5.69
831 859 2.597805 AGTGACTCGACCGTGGCT 60.598 61.111 0.00 0.00 0.00 4.75
953 1015 2.545526 GCCATTGATTGATCGATCACGT 59.454 45.455 27.28 18.55 35.86 4.49
954 1016 2.410646 CGCCATTGATTGATCGATCACG 60.411 50.000 27.28 19.62 35.86 4.35
1542 1613 0.968901 AGTAGTCGATGACGCCCCAA 60.969 55.000 0.00 0.00 37.67 4.12
1630 1701 5.679906 CAATTGCACGTATAGATAGGCAAC 58.320 41.667 7.68 0.00 43.09 4.17
1631 1702 4.213270 GCAATTGCACGTATAGATAGGCAA 59.787 41.667 25.36 7.93 44.21 4.52
1632 1703 3.745975 GCAATTGCACGTATAGATAGGCA 59.254 43.478 25.36 0.00 41.59 4.75
1633 1704 3.181530 CGCAATTGCACGTATAGATAGGC 60.182 47.826 28.77 0.00 42.21 3.93
1634 1705 4.090066 GTCGCAATTGCACGTATAGATAGG 59.910 45.833 28.77 8.79 42.21 2.57
1636 1707 3.985279 GGTCGCAATTGCACGTATAGATA 59.015 43.478 28.77 0.00 42.21 1.98
1637 1708 2.800544 GGTCGCAATTGCACGTATAGAT 59.199 45.455 28.77 0.00 42.21 1.98
1639 1710 1.260561 GGGTCGCAATTGCACGTATAG 59.739 52.381 28.77 11.61 42.21 1.31
1640 1711 1.292061 GGGTCGCAATTGCACGTATA 58.708 50.000 28.77 5.02 42.21 1.47
1641 1712 0.675208 TGGGTCGCAATTGCACGTAT 60.675 50.000 28.77 0.00 42.21 3.06
1643 1714 2.593148 TGGGTCGCAATTGCACGT 60.593 55.556 28.77 0.00 42.21 4.49
1644 1715 2.126888 GTGGGTCGCAATTGCACG 60.127 61.111 28.77 14.48 42.21 5.34
1645 1716 2.126888 CGTGGGTCGCAATTGCAC 60.127 61.111 28.77 23.09 42.21 4.57
1647 1718 4.114997 CCCGTGGGTCGCAATTGC 62.115 66.667 20.76 20.76 38.35 3.56
1657 1728 1.672030 GGTAAACCGAACCCGTGGG 60.672 63.158 2.58 2.58 42.03 4.61
1658 1729 0.250424 AAGGTAAACCGAACCCGTGG 60.250 55.000 0.00 0.00 42.08 4.94
1946 3005 1.627550 GACGGCTTGCCGAAGAAGAC 61.628 60.000 35.96 15.52 36.94 3.01
2035 3094 2.841442 AGTACAGTTCAGTGAAGGCC 57.159 50.000 5.62 0.00 0.00 5.19
2036 3095 4.238514 CTGTAGTACAGTTCAGTGAAGGC 58.761 47.826 20.29 0.00 41.19 4.35
2071 3344 1.271102 GCCCACCGTAAGCAAAATTCA 59.729 47.619 0.00 0.00 0.00 2.57
2077 3350 0.466555 ACAAAGCCCACCGTAAGCAA 60.467 50.000 0.00 0.00 0.00 3.91
2080 3353 1.892209 AAGACAAAGCCCACCGTAAG 58.108 50.000 0.00 0.00 0.00 2.34
2082 3355 1.950909 CAAAAGACAAAGCCCACCGTA 59.049 47.619 0.00 0.00 0.00 4.02
2085 3358 1.480545 ACACAAAAGACAAAGCCCACC 59.519 47.619 0.00 0.00 0.00 4.61
2089 3362 2.615869 TGCAACACAAAAGACAAAGCC 58.384 42.857 0.00 0.00 0.00 4.35
2373 3715 4.051167 CCCACCTGCTGGATGCCA 62.051 66.667 17.64 0.00 43.95 4.92
2655 3997 6.624423 GCTTCTACTACAACTGAACGGTGATA 60.624 42.308 0.00 0.00 0.00 2.15
2699 4050 3.244582 TCTACTACAACTGCCCTTGGAA 58.755 45.455 0.00 0.00 0.00 3.53
2794 5375 9.289303 GTTGCATATTGTAGGAAAGTACAAATG 57.711 33.333 0.00 7.26 44.15 2.32
2802 5383 6.992063 ACTCTGTTGCATATTGTAGGAAAG 57.008 37.500 0.00 0.00 0.00 2.62
2821 5402 5.638596 ACTGAACAAAAACCGAAAACTCT 57.361 34.783 0.00 0.00 0.00 3.24
2869 5478 5.599732 TGCTTGACAACAATAACTGCATTT 58.400 33.333 0.00 0.00 35.37 2.32
2870 5479 5.199024 TGCTTGACAACAATAACTGCATT 57.801 34.783 0.00 0.00 35.37 3.56
2872 5481 4.548494 CATGCTTGACAACAATAACTGCA 58.452 39.130 0.00 0.00 36.90 4.41
2873 5482 3.922240 CCATGCTTGACAACAATAACTGC 59.078 43.478 0.22 0.00 35.37 4.40
2874 5483 5.375417 TCCATGCTTGACAACAATAACTG 57.625 39.130 0.22 0.00 35.37 3.16
2876 5485 6.636666 CATTCCATGCTTGACAACAATAAC 57.363 37.500 0.22 0.00 35.37 1.89
2921 5539 3.381908 TCAATTTAAAACACGTGCCAGGT 59.618 39.130 17.22 0.00 0.00 4.00
2923 5541 5.461737 ACATTCAATTTAAAACACGTGCCAG 59.538 36.000 17.22 0.00 0.00 4.85
2924 5542 5.352284 ACATTCAATTTAAAACACGTGCCA 58.648 33.333 17.22 0.00 0.00 4.92
2925 5543 5.898630 ACATTCAATTTAAAACACGTGCC 57.101 34.783 17.22 0.00 0.00 5.01
2926 5544 7.001347 GCTAACATTCAATTTAAAACACGTGC 58.999 34.615 17.22 0.00 0.00 5.34
2927 5545 8.055609 TGCTAACATTCAATTTAAAACACGTG 57.944 30.769 15.48 15.48 0.00 4.49
2929 5547 8.500837 TCTGCTAACATTCAATTTAAAACACG 57.499 30.769 0.00 0.00 0.00 4.49
2931 5549 9.255304 GGTTCTGCTAACATTCAATTTAAAACA 57.745 29.630 0.00 0.00 0.00 2.83
2932 5550 9.255304 TGGTTCTGCTAACATTCAATTTAAAAC 57.745 29.630 0.00 0.00 0.00 2.43
2935 5553 8.177119 ACTGGTTCTGCTAACATTCAATTTAA 57.823 30.769 5.14 0.00 0.00 1.52
2936 5554 7.759489 ACTGGTTCTGCTAACATTCAATTTA 57.241 32.000 5.14 0.00 0.00 1.40
2937 5555 6.655078 ACTGGTTCTGCTAACATTCAATTT 57.345 33.333 5.14 0.00 0.00 1.82
2938 5556 6.655078 AACTGGTTCTGCTAACATTCAATT 57.345 33.333 5.14 0.00 0.00 2.32
2939 5557 6.655078 AAACTGGTTCTGCTAACATTCAAT 57.345 33.333 5.14 0.00 0.00 2.57
2940 5558 6.016610 GGTAAACTGGTTCTGCTAACATTCAA 60.017 38.462 5.14 0.00 0.00 2.69
2941 5559 5.472137 GGTAAACTGGTTCTGCTAACATTCA 59.528 40.000 5.14 0.00 0.00 2.57
2942 5560 5.472137 TGGTAAACTGGTTCTGCTAACATTC 59.528 40.000 5.14 0.00 0.00 2.67
2943 5561 5.381757 TGGTAAACTGGTTCTGCTAACATT 58.618 37.500 5.14 0.00 0.00 2.71
2944 5562 4.980573 TGGTAAACTGGTTCTGCTAACAT 58.019 39.130 5.14 0.00 0.00 2.71
2945 5563 4.385825 CTGGTAAACTGGTTCTGCTAACA 58.614 43.478 5.14 0.00 0.00 2.41
3007 5652 4.764679 TTGCTCTGCAAAATCGTTATGT 57.235 36.364 2.24 0.00 45.96 2.29
3235 5880 2.033151 CGAGTGGGAGACGTTTGAAAAC 60.033 50.000 0.00 0.00 35.59 2.43
3241 5886 1.664306 GACCGAGTGGGAGACGTTT 59.336 57.895 0.00 0.00 40.75 3.60
3429 6074 1.336125 GAACGGAGGGAGTACATACCG 59.664 57.143 0.00 0.00 44.77 4.02
3480 6129 4.985538 TCCTCTGCTCCAAAATACTTGTT 58.014 39.130 0.00 0.00 0.00 2.83
3562 6219 5.505780 TGGGGTTGGTCACTATGAATAAAG 58.494 41.667 0.00 0.00 0.00 1.85
3631 6288 5.638234 GCTTTACGTAGTCCTGATTTTGTCT 59.362 40.000 0.00 0.00 43.93 3.41
3632 6289 5.638234 AGCTTTACGTAGTCCTGATTTTGTC 59.362 40.000 0.00 0.00 43.93 3.18
3633 6290 5.408604 CAGCTTTACGTAGTCCTGATTTTGT 59.591 40.000 10.95 0.00 43.93 2.83
3649 6306 7.750354 CGCAATTTTGATTTTTCAGCTTTAC 57.250 32.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.