Multiple sequence alignment - TraesCS6D01G052300

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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 TraesCS6D01G052300 chr6D 100.000 3821 0 0 1 3821 24878716 24882536 0.000000e+00 7057.0
1 TraesCS6D01G052300 chr6D 96.456 1411 28 4 744 2149 24714311 24712918 0.000000e+00 2309.0
2 TraesCS6D01G052300 chr6D 94.453 1334 72 2 1212 2544 24451283 24449951 0.000000e+00 2052.0
3 TraesCS6D01G052300 chr6D 78.133 1939 322 59 860 2727 24914217 24916124 0.000000e+00 1138.0
4 TraesCS6D01G052300 chr6D 96.462 537 15 3 2977 3513 24693031 24692499 0.000000e+00 883.0
5 TraesCS6D01G052300 chr6D 92.188 512 17 11 2597 3086 24449944 24449434 0.000000e+00 702.0
6 TraesCS6D01G052300 chr6D 84.896 576 80 3 2409 2984 24344056 24344624 3.310000e-160 575.0
7 TraesCS6D01G052300 chr6D 84.896 576 80 3 2409 2984 24395271 24394703 3.310000e-160 575.0
8 TraesCS6D01G052300 chr6D 87.273 495 32 7 725 1219 24451891 24451428 1.560000e-148 536.0
9 TraesCS6D01G052300 chr6D 77.825 947 140 39 2064 2984 24670601 24669699 4.370000e-144 521.0
10 TraesCS6D01G052300 chr6D 77.287 973 164 35 991 1924 24470297 24469343 1.570000e-143 520.0
11 TraesCS6D01G052300 chr6D 92.615 325 19 2 2545 2869 24712604 24712285 2.690000e-126 462.0
12 TraesCS6D01G052300 chr6D 90.881 318 24 1 2186 2498 24712924 24712607 4.560000e-114 422.0
13 TraesCS6D01G052300 chr6D 88.000 300 19 8 3167 3464 24449297 24449013 4.730000e-89 339.0
14 TraesCS6D01G052300 chr6D 92.130 216 15 1 2216 2429 24224582 24224367 1.720000e-78 303.0
15 TraesCS6D01G052300 chr6D 97.273 110 3 0 2868 2977 24700050 24699941 1.810000e-43 187.0
16 TraesCS6D01G052300 chr6D 89.262 149 13 1 3463 3608 24448985 24448837 2.340000e-42 183.0
17 TraesCS6D01G052300 chr6D 78.049 164 18 13 3186 3345 24344888 24345037 1.890000e-13 87.9
18 TraesCS6D01G052300 chr6D 78.710 155 15 13 3195 3345 24394430 24394290 1.890000e-13 87.9
19 TraesCS6D01G052300 chr6D 90.164 61 5 1 651 710 24452345 24452285 1.140000e-10 78.7
20 TraesCS6D01G052300 chr6A 92.058 2279 139 24 725 2977 23344785 23342523 0.000000e+00 3168.0
21 TraesCS6D01G052300 chr6A 93.453 1833 93 14 1279 3086 23426290 23428120 0.000000e+00 2695.0
22 TraesCS6D01G052300 chr6A 90.845 568 10 14 2977 3526 23333218 23332675 0.000000e+00 723.0
23 TraesCS6D01G052300 chr6A 85.333 300 17 12 3167 3464 23428265 23428539 6.250000e-73 285.0
24 TraesCS6D01G052300 chr6A 97.279 147 4 0 3675 3821 23332255 23332109 2.280000e-62 250.0
25 TraesCS6D01G052300 chr6A 100.000 30 0 0 3635 3664 23332609 23332580 5.330000e-04 56.5
26 TraesCS6D01G052300 chr6B 87.246 2266 260 16 725 2984 40253600 40251358 0.000000e+00 2556.0
27 TraesCS6D01G052300 chr6B 79.066 2226 358 69 794 2984 39677702 39675550 0.000000e+00 1430.0
28 TraesCS6D01G052300 chr6B 77.915 969 164 33 991 1924 40146410 40145457 3.330000e-155 558.0
29 TraesCS6D01G052300 chr6B 84.468 573 80 6 2272 2839 40590476 40591044 1.200000e-154 556.0
30 TraesCS6D01G052300 chr6B 95.918 49 2 0 681 729 40253685 40253637 3.160000e-11 80.5
31 TraesCS6D01G052300 chr6B 95.652 46 2 0 3525 3570 40250901 40250856 1.470000e-09 75.0
32 TraesCS6D01G052300 chr5D 91.479 622 48 4 1 619 456742374 456741755 0.000000e+00 850.0
33 TraesCS6D01G052300 chr5D 89.855 621 60 3 1 619 50861298 50860679 0.000000e+00 795.0
34 TraesCS6D01G052300 chr1D 91.391 604 50 2 17 619 468337960 468337358 0.000000e+00 826.0
35 TraesCS6D01G052300 chr7B 90.244 615 57 3 1 613 61125842 61126455 0.000000e+00 800.0
36 TraesCS6D01G052300 chr3D 90.579 605 55 2 14 616 506059728 506060332 0.000000e+00 800.0
37 TraesCS6D01G052300 chr5A 89.951 617 61 1 4 619 505293222 505292606 0.000000e+00 795.0
38 TraesCS6D01G052300 chr2D 89.902 614 59 3 5 616 249877066 249877678 0.000000e+00 787.0
39 TraesCS6D01G052300 chr7D 89.482 618 60 3 1 616 575166192 575166806 0.000000e+00 776.0
40 TraesCS6D01G052300 chr4B 88.835 618 66 3 1 616 43231598 43232214 0.000000e+00 756.0


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 TraesCS6D01G052300 chr6D 24878716 24882536 3820 False 7057.000000 7057 100.000000 1 3821 1 chr6D.!!$F1 3820
1 TraesCS6D01G052300 chr6D 24914217 24916124 1907 False 1138.000000 1138 78.133000 860 2727 1 chr6D.!!$F2 1867
2 TraesCS6D01G052300 chr6D 24712285 24714311 2026 True 1064.333333 2309 93.317333 744 2869 3 chr6D.!!$R8 2125
3 TraesCS6D01G052300 chr6D 24692499 24693031 532 True 883.000000 883 96.462000 2977 3513 1 chr6D.!!$R4 536
4 TraesCS6D01G052300 chr6D 24448837 24452345 3508 True 648.450000 2052 90.223333 651 3608 6 chr6D.!!$R7 2957
5 TraesCS6D01G052300 chr6D 24669699 24670601 902 True 521.000000 521 77.825000 2064 2984 1 chr6D.!!$R3 920
6 TraesCS6D01G052300 chr6D 24469343 24470297 954 True 520.000000 520 77.287000 991 1924 1 chr6D.!!$R2 933
7 TraesCS6D01G052300 chr6D 24344056 24345037 981 False 331.450000 575 81.472500 2409 3345 2 chr6D.!!$F3 936
8 TraesCS6D01G052300 chr6D 24394290 24395271 981 True 331.450000 575 81.803000 2409 3345 2 chr6D.!!$R6 936
9 TraesCS6D01G052300 chr6A 23342523 23344785 2262 True 3168.000000 3168 92.058000 725 2977 1 chr6A.!!$R1 2252
10 TraesCS6D01G052300 chr6A 23426290 23428539 2249 False 1490.000000 2695 89.393000 1279 3464 2 chr6A.!!$F1 2185
11 TraesCS6D01G052300 chr6A 23332109 23333218 1109 True 343.166667 723 96.041333 2977 3821 3 chr6A.!!$R2 844
12 TraesCS6D01G052300 chr6B 39675550 39677702 2152 True 1430.000000 1430 79.066000 794 2984 1 chr6B.!!$R1 2190
13 TraesCS6D01G052300 chr6B 40250856 40253685 2829 True 903.833333 2556 92.938667 681 3570 3 chr6B.!!$R3 2889
14 TraesCS6D01G052300 chr6B 40145457 40146410 953 True 558.000000 558 77.915000 991 1924 1 chr6B.!!$R2 933
15 TraesCS6D01G052300 chr6B 40590476 40591044 568 False 556.000000 556 84.468000 2272 2839 1 chr6B.!!$F1 567
16 TraesCS6D01G052300 chr5D 456741755 456742374 619 True 850.000000 850 91.479000 1 619 1 chr5D.!!$R2 618
17 TraesCS6D01G052300 chr5D 50860679 50861298 619 True 795.000000 795 89.855000 1 619 1 chr5D.!!$R1 618
18 TraesCS6D01G052300 chr1D 468337358 468337960 602 True 826.000000 826 91.391000 17 619 1 chr1D.!!$R1 602
19 TraesCS6D01G052300 chr7B 61125842 61126455 613 False 800.000000 800 90.244000 1 613 1 chr7B.!!$F1 612
20 TraesCS6D01G052300 chr3D 506059728 506060332 604 False 800.000000 800 90.579000 14 616 1 chr3D.!!$F1 602
21 TraesCS6D01G052300 chr5A 505292606 505293222 616 True 795.000000 795 89.951000 4 619 1 chr5A.!!$R1 615
22 TraesCS6D01G052300 chr2D 249877066 249877678 612 False 787.000000 787 89.902000 5 616 1 chr2D.!!$F1 611
23 TraesCS6D01G052300 chr7D 575166192 575166806 614 False 776.000000 776 89.482000 1 616 1 chr7D.!!$F1 615
24 TraesCS6D01G052300 chr4B 43231598 43232214 616 False 756.000000 756 88.835000 1 616 1 chr4B.!!$F1 615

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
616 629 0.111446 TCTGACCGGAAAATTGGGCA 59.889 50.0 9.46 0.0 42.32 5.36 F
644 657 0.306533 GACCGAAAACAAGCAGCGAA 59.693 50.0 0.00 0.0 0.00 4.70 F
736 1128 0.620556 GGGCAAGAGTGAATCAGGGA 59.379 55.0 0.00 0.0 0.00 4.20 F
2451 3176 0.946221 GCTGAACGAGTGGAGTGTGG 60.946 60.0 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
2445 3170 1.420138 ACGGAAATCAGGTTCCACACT 59.580 47.619 4.93 0.0 46.45 3.55 R
2451 3176 1.523758 AGTGCACGGAAATCAGGTTC 58.476 50.000 12.01 0.0 0.00 3.62 R
2460 3185 2.739913 GCATACAAACTAGTGCACGGAA 59.260 45.455 12.01 0.0 37.52 4.30 R
3563 4536 0.464036 ACAGTCGAGAGGCACAAACA 59.536 50.000 0.00 0.0 38.99 2.83 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
82 83 3.068691 CGGGCTCCTCCTTGACGA 61.069 66.667 0.00 0.00 34.39 4.20
114 115 3.707640 CTCGTCCGGCTCCTCCTCT 62.708 68.421 0.00 0.00 0.00 3.69
367 374 3.842923 CGGATCTGCTGCCGGAGT 61.843 66.667 5.05 0.00 43.67 3.85
387 394 2.105128 CGTCCGGAGCTCCACATC 59.895 66.667 31.67 16.90 35.14 3.06
462 474 1.229853 AGAAGGGGTGGGGAATCGT 60.230 57.895 0.00 0.00 0.00 3.73
509 521 1.377366 TTTCGACCCGCAAACAAGCA 61.377 50.000 0.00 0.00 0.00 3.91
518 530 0.527385 GCAAACAAGCAGCGAAACCA 60.527 50.000 0.00 0.00 0.00 3.67
616 629 0.111446 TCTGACCGGAAAATTGGGCA 59.889 50.000 9.46 0.00 42.32 5.36
619 632 1.272425 TGACCGGAAAATTGGGCAGAT 60.272 47.619 9.46 0.00 38.72 2.90
620 633 1.134946 GACCGGAAAATTGGGCAGATG 59.865 52.381 9.46 0.00 31.69 2.90
621 634 1.272425 ACCGGAAAATTGGGCAGATGA 60.272 47.619 9.46 0.00 0.00 2.92
622 635 1.406539 CCGGAAAATTGGGCAGATGAG 59.593 52.381 0.00 0.00 0.00 2.90
623 636 1.202336 CGGAAAATTGGGCAGATGAGC 60.202 52.381 0.00 0.00 0.00 4.26
624 637 2.105766 GGAAAATTGGGCAGATGAGCT 58.894 47.619 0.00 0.00 34.17 4.09
635 648 2.839486 AGATGAGCTGACCGAAAACA 57.161 45.000 0.00 0.00 0.00 2.83
636 649 3.126001 AGATGAGCTGACCGAAAACAA 57.874 42.857 0.00 0.00 0.00 2.83
637 650 3.070018 AGATGAGCTGACCGAAAACAAG 58.930 45.455 0.00 0.00 0.00 3.16
638 651 0.944386 TGAGCTGACCGAAAACAAGC 59.056 50.000 0.00 0.00 0.00 4.01
639 652 0.944386 GAGCTGACCGAAAACAAGCA 59.056 50.000 0.00 0.00 0.00 3.91
640 653 0.947244 AGCTGACCGAAAACAAGCAG 59.053 50.000 0.00 0.00 0.00 4.24
641 654 0.661483 GCTGACCGAAAACAAGCAGC 60.661 55.000 0.00 0.00 41.38 5.25
642 655 0.384725 CTGACCGAAAACAAGCAGCG 60.385 55.000 0.00 0.00 0.00 5.18
643 656 0.812014 TGACCGAAAACAAGCAGCGA 60.812 50.000 0.00 0.00 0.00 4.93
644 657 0.306533 GACCGAAAACAAGCAGCGAA 59.693 50.000 0.00 0.00 0.00 4.70
645 658 0.736053 ACCGAAAACAAGCAGCGAAA 59.264 45.000 0.00 0.00 0.00 3.46
646 659 1.120437 CCGAAAACAAGCAGCGAAAC 58.880 50.000 0.00 0.00 0.00 2.78
647 660 1.268539 CCGAAAACAAGCAGCGAAACT 60.269 47.619 0.00 0.00 0.00 2.66
658 671 1.993370 CAGCGAAACTGTACACTAGCC 59.007 52.381 0.00 0.00 41.86 3.93
662 675 2.987149 CGAAACTGTACACTAGCCTGTG 59.013 50.000 0.00 5.30 43.07 3.66
679 692 1.089920 GTGCTGTGCGGAATCAATCT 58.910 50.000 0.00 0.00 0.00 2.40
718 1069 2.841795 TCCTAGGGTTAGGGTTTCAGG 58.158 52.381 9.46 0.00 45.60 3.86
736 1128 0.620556 GGGCAAGAGTGAATCAGGGA 59.379 55.000 0.00 0.00 0.00 4.20
819 1211 2.030562 CAAGGGTGGCGTTCGTCT 59.969 61.111 0.00 0.00 0.00 4.18
976 1396 2.281484 GTGTTCCCGCAGCTTCCA 60.281 61.111 0.00 0.00 0.00 3.53
1993 2637 8.093307 TCTCTATCCATCTTTGCATATCAGTTC 58.907 37.037 0.00 0.00 0.00 3.01
2105 2759 3.320626 CGACTGCACTTTGAGATCTGAA 58.679 45.455 0.00 0.00 0.00 3.02
2108 2762 2.414481 CTGCACTTTGAGATCTGAACCG 59.586 50.000 0.00 0.00 0.00 4.44
2264 2962 7.031226 TGAAATTGCTTATATGCTTCCTGTC 57.969 36.000 11.48 3.47 0.00 3.51
2445 3170 1.872952 CATTGTTGCTGAACGAGTGGA 59.127 47.619 0.00 0.00 34.49 4.02
2451 3176 0.946221 GCTGAACGAGTGGAGTGTGG 60.946 60.000 0.00 0.00 0.00 4.17
2459 3184 1.625818 GAGTGGAGTGTGGAACCTGAT 59.374 52.381 0.00 0.00 34.36 2.90
2460 3185 2.039084 GAGTGGAGTGTGGAACCTGATT 59.961 50.000 0.00 0.00 34.36 2.57
2522 3247 7.664082 TCTTGAGAATCTGACACTTCAATTC 57.336 36.000 0.00 0.00 33.69 2.17
2523 3248 7.219322 TCTTGAGAATCTGACACTTCAATTCA 58.781 34.615 0.00 0.00 34.74 2.57
2707 3446 0.107654 ACCAGCGGCTATTTCAGGAC 60.108 55.000 0.26 0.00 0.00 3.85
2936 3679 7.930217 ACACGATCATTATCTATTTTGTTGGG 58.070 34.615 0.00 0.00 0.00 4.12
3013 3824 1.004679 GCAAACATGGGTGGCCTTG 60.005 57.895 3.32 0.00 0.00 3.61
3121 4016 4.974645 ACCTCCCATTCGCTATAATTCA 57.025 40.909 0.00 0.00 0.00 2.57
3139 4035 0.963962 CAGGTTCATGTGCAAGCCTT 59.036 50.000 0.00 0.00 0.00 4.35
3242 4180 2.488153 GGATTCGGTTTCAAGAGTTGGG 59.512 50.000 0.00 0.00 0.00 4.12
3390 4333 8.902540 TTGAAAAACTCATAGCTGTCTTTCTA 57.097 30.769 0.00 0.00 32.78 2.10
3563 4536 6.318648 ACTGTAACACAAACATGAGTCATTGT 59.681 34.615 1.86 3.74 36.49 2.71
3597 4573 1.303074 CTGTCCAGCAGCATGTGGT 60.303 57.895 0.00 0.00 38.11 4.16
3632 4608 0.754217 AAGGCCGCTGCATGAATGAT 60.754 50.000 1.55 0.00 40.13 2.45
3633 4609 1.007734 GGCCGCTGCATGAATGATG 60.008 57.895 1.55 0.00 40.13 3.07
3664 4673 8.057536 ACTGACAGGAGTTAATAGACTTACTG 57.942 38.462 7.51 0.00 39.14 2.74
3665 4674 7.889073 ACTGACAGGAGTTAATAGACTTACTGA 59.111 37.037 7.51 0.00 37.86 3.41
3666 4675 8.053026 TGACAGGAGTTAATAGACTTACTGAC 57.947 38.462 13.73 9.92 37.86 3.51
3667 4676 7.668469 TGACAGGAGTTAATAGACTTACTGACA 59.332 37.037 13.73 11.61 37.86 3.58
3668 4677 8.057536 ACAGGAGTTAATAGACTTACTGACAG 57.942 38.462 0.00 0.00 37.86 3.51
3669 4678 7.122948 ACAGGAGTTAATAGACTTACTGACAGG 59.877 40.741 7.51 0.00 37.86 4.00
3670 4679 7.339721 CAGGAGTTAATAGACTTACTGACAGGA 59.660 40.741 7.51 0.00 37.23 3.86
3671 4680 7.558444 AGGAGTTAATAGACTTACTGACAGGAG 59.442 40.741 7.51 6.96 0.00 3.69
3672 4681 7.339976 GGAGTTAATAGACTTACTGACAGGAGT 59.660 40.741 7.51 10.18 0.00 3.85
3673 4682 8.653036 AGTTAATAGACTTACTGACAGGAGTT 57.347 34.615 7.51 4.83 0.00 3.01
3699 5022 0.535102 AGAGCAACCAAGAACCACCG 60.535 55.000 0.00 0.00 0.00 4.94
3714 5037 2.509336 CCGGTGCTGGTTCTAGCG 60.509 66.667 0.00 0.00 46.61 4.26
3737 5060 6.143758 GCGAGCACAATATGAAAAAGAAAACA 59.856 34.615 0.00 0.00 0.00 2.83
3739 5062 8.368126 CGAGCACAATATGAAAAAGAAAACATC 58.632 33.333 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.106569 TCGGGCCGGAAGACTATGTA 60.107 55.000 27.98 0.00 0.00 2.29
82 83 0.516439 GACGAGTTCGACTTCGTCCT 59.484 55.000 27.73 8.66 39.98 3.85
114 115 1.305046 GAGGGAGTGGTCGGAGGAA 60.305 63.158 0.00 0.00 0.00 3.36
213 220 2.348998 ACGGAGGACTACGACCGT 59.651 61.111 11.45 3.96 46.17 4.83
222 229 3.878519 CGGAGCGAGACGGAGGAC 61.879 72.222 0.00 0.00 0.00 3.85
478 490 0.984432 GGTCGAAACCCTATCCCCCA 60.984 60.000 0.00 0.00 39.93 4.96
509 521 3.510360 ACCGCTATATCTATGGTTTCGCT 59.490 43.478 0.00 0.00 0.00 4.93
518 530 1.400737 GCCCCGACCGCTATATCTAT 58.599 55.000 0.00 0.00 0.00 1.98
573 586 3.849951 CCCGCATACTCGCCTGGT 61.850 66.667 0.00 0.00 0.00 4.00
576 589 3.917760 GAGCCCGCATACTCGCCT 61.918 66.667 0.00 0.00 0.00 5.52
616 629 2.839486 TGTTTTCGGTCAGCTCATCT 57.161 45.000 0.00 0.00 0.00 2.90
619 632 0.944386 GCTTGTTTTCGGTCAGCTCA 59.056 50.000 0.00 0.00 0.00 4.26
620 633 0.944386 TGCTTGTTTTCGGTCAGCTC 59.056 50.000 0.00 0.00 0.00 4.09
621 634 0.947244 CTGCTTGTTTTCGGTCAGCT 59.053 50.000 0.00 0.00 0.00 4.24
622 635 0.661483 GCTGCTTGTTTTCGGTCAGC 60.661 55.000 0.00 0.00 39.82 4.26
623 636 0.384725 CGCTGCTTGTTTTCGGTCAG 60.385 55.000 0.00 0.00 0.00 3.51
624 637 0.812014 TCGCTGCTTGTTTTCGGTCA 60.812 50.000 0.00 0.00 0.00 4.02
625 638 0.306533 TTCGCTGCTTGTTTTCGGTC 59.693 50.000 0.00 0.00 0.00 4.79
626 639 0.736053 TTTCGCTGCTTGTTTTCGGT 59.264 45.000 0.00 0.00 0.00 4.69
627 640 1.120437 GTTTCGCTGCTTGTTTTCGG 58.880 50.000 0.00 0.00 0.00 4.30
628 641 1.775208 CAGTTTCGCTGCTTGTTTTCG 59.225 47.619 0.00 0.00 38.52 3.46
639 652 1.893801 AGGCTAGTGTACAGTTTCGCT 59.106 47.619 8.85 0.00 0.00 4.93
640 653 1.993370 CAGGCTAGTGTACAGTTTCGC 59.007 52.381 8.85 9.28 0.00 4.70
641 654 2.987149 CACAGGCTAGTGTACAGTTTCG 59.013 50.000 8.85 0.00 34.83 3.46
642 655 2.737252 GCACAGGCTAGTGTACAGTTTC 59.263 50.000 8.85 1.12 41.52 2.78
643 656 2.767505 GCACAGGCTAGTGTACAGTTT 58.232 47.619 8.85 0.00 41.52 2.66
644 657 2.457366 GCACAGGCTAGTGTACAGTT 57.543 50.000 8.85 0.00 41.52 3.16
658 671 0.806868 ATTGATTCCGCACAGCACAG 59.193 50.000 0.00 0.00 0.00 3.66
662 675 4.991056 TCTATTAGATTGATTCCGCACAGC 59.009 41.667 0.00 0.00 0.00 4.40
670 683 5.390356 GCGGCTGCTTCTATTAGATTGATTC 60.390 44.000 11.21 0.00 38.39 2.52
679 692 2.878406 GGAAATGCGGCTGCTTCTATTA 59.122 45.455 20.27 0.00 43.34 0.98
718 1069 1.680249 GGTCCCTGATTCACTCTTGCC 60.680 57.143 0.00 0.00 0.00 4.52
736 1128 2.512286 CACATCGCAGCCATCGGT 60.512 61.111 0.00 0.00 0.00 4.69
1411 2028 0.540597 GGAGGGCCATCCAAATAGCC 60.541 60.000 31.31 0.92 44.99 3.93
1498 2118 3.378112 TCCAGTGTTGAACAGCTTGAAAG 59.622 43.478 0.00 0.00 0.00 2.62
1993 2637 5.143916 GTGGCTACACTATTTTCGTCATG 57.856 43.478 0.00 0.00 44.29 3.07
2105 2759 6.603997 ACAAGACTATCTCAACTAGAATCGGT 59.396 38.462 0.00 0.00 37.89 4.69
2156 2850 2.282407 TCACATCATGAACATGCGGAG 58.718 47.619 0.00 4.06 38.65 4.63
2445 3170 1.420138 ACGGAAATCAGGTTCCACACT 59.580 47.619 4.93 0.00 46.45 3.55
2451 3176 1.523758 AGTGCACGGAAATCAGGTTC 58.476 50.000 12.01 0.00 0.00 3.62
2459 3184 3.187637 GCATACAAACTAGTGCACGGAAA 59.812 43.478 12.01 0.00 37.52 3.13
2460 3185 2.739913 GCATACAAACTAGTGCACGGAA 59.260 45.455 12.01 0.00 37.52 4.30
2707 3446 8.517878 ACATTTCACTTTGATAATCTTCAGGTG 58.482 33.333 0.00 0.00 34.96 4.00
2936 3679 7.658261 TGACATGCCTCACTGTATAATACTAC 58.342 38.462 0.00 0.00 0.00 2.73
3013 3824 1.406539 CCATGTTTCATAGCAGCACCC 59.593 52.381 0.00 0.00 0.00 4.61
3096 3959 7.458397 TGAATTATAGCGAATGGGAGGTATTT 58.542 34.615 0.00 0.00 33.69 1.40
3121 4016 1.202976 AGAAGGCTTGCACATGAACCT 60.203 47.619 3.46 0.00 0.00 3.50
3139 4035 3.558931 TTGCTCTGTTCCTTGACAAGA 57.441 42.857 16.99 0.20 0.00 3.02
3242 4180 3.443925 GCGGCCCAAAAGCTCCTC 61.444 66.667 0.00 0.00 0.00 3.71
3390 4333 7.609760 TGCAAATTATAAGAGTTCACACGAT 57.390 32.000 0.00 0.00 0.00 3.73
3563 4536 0.464036 ACAGTCGAGAGGCACAAACA 59.536 50.000 0.00 0.00 38.99 2.83
3618 4594 1.306148 AGACCATCATTCATGCAGCG 58.694 50.000 0.00 0.00 0.00 5.18
3664 4673 4.207891 TGCTCTGGAATTAACTCCTGTC 57.792 45.455 4.33 2.07 36.35 3.51
3665 4674 4.327680 GTTGCTCTGGAATTAACTCCTGT 58.672 43.478 4.33 0.00 36.35 4.00
3666 4675 3.691609 GGTTGCTCTGGAATTAACTCCTG 59.308 47.826 4.33 3.96 36.35 3.86
3667 4676 3.330701 TGGTTGCTCTGGAATTAACTCCT 59.669 43.478 4.33 0.00 36.35 3.69
3668 4677 3.686016 TGGTTGCTCTGGAATTAACTCC 58.314 45.455 0.00 0.00 35.88 3.85
3669 4678 5.003804 TCTTGGTTGCTCTGGAATTAACTC 58.996 41.667 0.00 0.00 0.00 3.01
3670 4679 4.985538 TCTTGGTTGCTCTGGAATTAACT 58.014 39.130 0.00 0.00 0.00 2.24
3671 4680 5.461526 GTTCTTGGTTGCTCTGGAATTAAC 58.538 41.667 0.00 0.00 0.00 2.01
3672 4681 4.522789 GGTTCTTGGTTGCTCTGGAATTAA 59.477 41.667 0.00 0.00 0.00 1.40
3673 4682 4.079253 GGTTCTTGGTTGCTCTGGAATTA 58.921 43.478 0.00 0.00 0.00 1.40
3699 5022 1.811679 GCTCGCTAGAACCAGCACC 60.812 63.158 0.00 0.00 41.88 5.01
3714 5037 8.368126 CGATGTTTTCTTTTTCATATTGTGCTC 58.632 33.333 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.