Multiple sequence alignment - TraesCS3D01G178200

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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 TraesCS3D01G178200 chr3D 100.000 4640 0 0 1 4640 159789315 159784676 0.000000e+00 8569.0
1 TraesCS3D01G178200 chr3D 81.650 594 64 22 4087 4638 520810567 520809977 7.080000e-123 451.0
2 TraesCS3D01G178200 chr3D 87.397 365 38 6 4089 4450 557761773 557761414 3.340000e-111 412.0
3 TraesCS3D01G178200 chr3D 89.163 203 20 2 4438 4640 523636764 523636964 7.710000e-63 252.0
4 TraesCS3D01G178200 chr3D 93.878 49 2 1 3859 3907 506177122 506177169 6.440000e-09 73.1
5 TraesCS3D01G178200 chr3B 95.458 4073 109 37 2 4050 236498945 236494925 0.000000e+00 6427.0
6 TraesCS3D01G178200 chr3B 85.211 568 65 8 4091 4640 451546824 451546258 2.420000e-157 566.0
7 TraesCS3D01G178200 chr3B 82.186 494 44 10 4041 4514 236494726 236494257 7.280000e-103 385.0
8 TraesCS3D01G178200 chr3B 94.000 50 2 1 3858 3907 342292905 342292857 1.790000e-09 75.0
9 TraesCS3D01G178200 chr3A 95.139 4094 122 21 1 4034 186043724 186039648 0.000000e+00 6386.0
10 TraesCS3D01G178200 chr3A 79.860 571 71 18 4089 4640 747603550 747603005 1.220000e-100 377.0
11 TraesCS3D01G178200 chr4A 81.415 1286 199 29 2162 3421 900272 901543 0.000000e+00 1014.0
12 TraesCS3D01G178200 chr4D 81.129 1293 197 30 2159 3420 629733 631009 0.000000e+00 992.0
13 TraesCS3D01G178200 chr4D 73.895 950 231 15 1080 2022 628615 629554 9.490000e-97 364.0
14 TraesCS3D01G178200 chr4B 86.218 907 116 7 2517 3420 1244614 1243714 0.000000e+00 974.0
15 TraesCS3D01G178200 chr4B 73.950 952 227 17 1080 2022 1246105 1245166 9.490000e-97 364.0
16 TraesCS3D01G178200 chr4B 74.160 863 148 53 2588 3415 654125473 654126295 5.870000e-74 289.0
17 TraesCS3D01G178200 chr4B 73.774 877 150 54 2588 3415 654130708 654131553 5.920000e-69 272.0
18 TraesCS3D01G178200 chr4B 73.092 773 155 46 2676 3411 638987633 638988389 4.670000e-55 226.0
19 TraesCS3D01G178200 chr4B 89.091 55 5 1 3853 3907 388392568 388392621 3.000000e-07 67.6
20 TraesCS3D01G178200 chr5D 81.502 892 149 15 2525 3411 425840488 425841368 0.000000e+00 719.0
21 TraesCS3D01G178200 chr5D 80.974 883 139 18 2541 3407 454977930 454978799 0.000000e+00 673.0
22 TraesCS3D01G178200 chr5D 80.974 883 139 18 2541 3407 455049178 455050047 0.000000e+00 673.0
23 TraesCS3D01G178200 chr5D 80.682 880 141 18 2541 3404 455221896 455222762 0.000000e+00 656.0
24 TraesCS3D01G178200 chr5D 81.250 768 120 15 2652 3407 455121047 455121802 2.390000e-167 599.0
25 TraesCS3D01G178200 chr5D 85.258 563 67 13 4089 4640 73814418 73813861 2.420000e-157 566.0
26 TraesCS3D01G178200 chr5D 86.427 361 46 3 4091 4450 460196979 460196621 4.350000e-105 392.0
27 TraesCS3D01G178200 chr5D 95.833 48 1 1 3861 3907 8010075 8010028 4.980000e-10 76.8
28 TraesCS3D01G178200 chr5A 81.348 890 154 11 2525 3411 540053546 540054426 0.000000e+00 713.0
29 TraesCS3D01G178200 chr5A 80.752 878 145 13 2542 3407 572391396 572392261 0.000000e+00 664.0
30 TraesCS3D01G178200 chr5A 94.000 50 2 1 3858 3907 450090187 450090235 1.790000e-09 75.0
31 TraesCS3D01G178200 chr5B 81.124 890 156 11 2525 3411 515185659 515186539 0.000000e+00 702.0
32 TraesCS3D01G178200 chr5B 76.516 775 142 32 2672 3420 6918998 6918238 2.020000e-103 387.0
33 TraesCS3D01G178200 chr5B 90.385 52 5 0 3856 3907 287072485 287072536 8.330000e-08 69.4
34 TraesCS3D01G178200 chr6D 85.198 581 50 12 4086 4640 200487828 200488398 8.720000e-157 564.0
35 TraesCS3D01G178200 chr1D 84.310 580 63 13 4087 4640 351509684 351510261 4.080000e-150 542.0
36 TraesCS3D01G178200 chr1D 92.000 50 4 0 3858 3907 216353328 216353377 2.320000e-08 71.3
37 TraesCS3D01G178200 chr2B 84.079 559 78 6 4091 4640 431170834 431170278 3.180000e-146 529.0
38 TraesCS3D01G178200 chr2B 83.979 568 72 11 4091 4640 211610638 211611204 1.140000e-145 527.0
39 TraesCS3D01G178200 chr2B 77.855 578 90 24 4091 4640 746714899 746715466 1.610000e-84 324.0
40 TraesCS3D01G178200 chr2D 84.256 578 50 13 4091 4630 139257551 139256977 4.110000e-145 525.0
41 TraesCS3D01G178200 chr7D 83.741 572 64 11 4089 4640 461392218 461391656 8.900000e-142 514.0
42 TraesCS3D01G178200 chr7D 78.444 784 149 12 2641 3414 25523007 25522234 1.160000e-135 494.0
43 TraesCS3D01G178200 chr7D 84.026 457 54 15 4089 4535 587829572 587829125 5.550000e-114 422.0
44 TraesCS3D01G178200 chr7B 81.765 510 78 14 4091 4595 240941248 240940749 3.340000e-111 412.0
45 TraesCS3D01G178200 chr7B 90.164 61 5 1 3848 3907 75150878 75150938 1.380000e-10 78.7
46 TraesCS3D01G178200 chr2A 80.354 509 58 19 4171 4640 719531860 719531355 9.560000e-92 348.0
47 TraesCS3D01G178200 chr2A 85.075 67 6 3 3844 3907 230388760 230388825 1.080000e-06 65.8
48 TraesCS3D01G178200 chr1A 74.074 216 45 8 2939 3150 549712274 549712482 1.380000e-10 78.7


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 TraesCS3D01G178200 chr3D 159784676 159789315 4639 True 8569 8569 100.000 1 4640 1 chr3D.!!$R1 4639
1 TraesCS3D01G178200 chr3D 520809977 520810567 590 True 451 451 81.650 4087 4638 1 chr3D.!!$R2 551
2 TraesCS3D01G178200 chr3B 236494257 236498945 4688 True 3406 6427 88.822 2 4514 2 chr3B.!!$R3 4512
3 TraesCS3D01G178200 chr3B 451546258 451546824 566 True 566 566 85.211 4091 4640 1 chr3B.!!$R2 549
4 TraesCS3D01G178200 chr3A 186039648 186043724 4076 True 6386 6386 95.139 1 4034 1 chr3A.!!$R1 4033
5 TraesCS3D01G178200 chr3A 747603005 747603550 545 True 377 377 79.860 4089 4640 1 chr3A.!!$R2 551
6 TraesCS3D01G178200 chr4A 900272 901543 1271 False 1014 1014 81.415 2162 3421 1 chr4A.!!$F1 1259
7 TraesCS3D01G178200 chr4D 628615 631009 2394 False 678 992 77.512 1080 3420 2 chr4D.!!$F1 2340
8 TraesCS3D01G178200 chr4B 1243714 1246105 2391 True 669 974 80.084 1080 3420 2 chr4B.!!$R1 2340
9 TraesCS3D01G178200 chr4B 654125473 654126295 822 False 289 289 74.160 2588 3415 1 chr4B.!!$F3 827
10 TraesCS3D01G178200 chr4B 654130708 654131553 845 False 272 272 73.774 2588 3415 1 chr4B.!!$F4 827
11 TraesCS3D01G178200 chr4B 638987633 638988389 756 False 226 226 73.092 2676 3411 1 chr4B.!!$F2 735
12 TraesCS3D01G178200 chr5D 425840488 425841368 880 False 719 719 81.502 2525 3411 1 chr5D.!!$F1 886
13 TraesCS3D01G178200 chr5D 454977930 454978799 869 False 673 673 80.974 2541 3407 1 chr5D.!!$F2 866
14 TraesCS3D01G178200 chr5D 455049178 455050047 869 False 673 673 80.974 2541 3407 1 chr5D.!!$F3 866
15 TraesCS3D01G178200 chr5D 455221896 455222762 866 False 656 656 80.682 2541 3404 1 chr5D.!!$F5 863
16 TraesCS3D01G178200 chr5D 455121047 455121802 755 False 599 599 81.250 2652 3407 1 chr5D.!!$F4 755
17 TraesCS3D01G178200 chr5D 73813861 73814418 557 True 566 566 85.258 4089 4640 1 chr5D.!!$R2 551
18 TraesCS3D01G178200 chr5A 540053546 540054426 880 False 713 713 81.348 2525 3411 1 chr5A.!!$F2 886
19 TraesCS3D01G178200 chr5A 572391396 572392261 865 False 664 664 80.752 2542 3407 1 chr5A.!!$F3 865
20 TraesCS3D01G178200 chr5B 515185659 515186539 880 False 702 702 81.124 2525 3411 1 chr5B.!!$F2 886
21 TraesCS3D01G178200 chr5B 6918238 6918998 760 True 387 387 76.516 2672 3420 1 chr5B.!!$R1 748
22 TraesCS3D01G178200 chr6D 200487828 200488398 570 False 564 564 85.198 4086 4640 1 chr6D.!!$F1 554
23 TraesCS3D01G178200 chr1D 351509684 351510261 577 False 542 542 84.310 4087 4640 1 chr1D.!!$F2 553
24 TraesCS3D01G178200 chr2B 431170278 431170834 556 True 529 529 84.079 4091 4640 1 chr2B.!!$R1 549
25 TraesCS3D01G178200 chr2B 211610638 211611204 566 False 527 527 83.979 4091 4640 1 chr2B.!!$F1 549
26 TraesCS3D01G178200 chr2B 746714899 746715466 567 False 324 324 77.855 4091 4640 1 chr2B.!!$F2 549
27 TraesCS3D01G178200 chr2D 139256977 139257551 574 True 525 525 84.256 4091 4630 1 chr2D.!!$R1 539
28 TraesCS3D01G178200 chr7D 461391656 461392218 562 True 514 514 83.741 4089 4640 1 chr7D.!!$R2 551
29 TraesCS3D01G178200 chr7D 25522234 25523007 773 True 494 494 78.444 2641 3414 1 chr7D.!!$R1 773
30 TraesCS3D01G178200 chr2A 719531355 719531860 505 True 348 348 80.354 4171 4640 1 chr2A.!!$R1 469

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
964 1030 0.096281 CTCGATCGCCTCTCTATCGC 59.904 60.0 11.09 0.0 41.66 4.58 F
968 1034 2.433646 ATCGCCTCTCTATCGCCCCT 62.434 60.0 0.00 0.0 0.00 4.79 F
2323 2441 0.251787 ATCCAAGGACCAGGCAAACC 60.252 55.0 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2441 0.806102 CCACCTATCACCGTCGCAAG 60.806 60.0 0.00 0.00 0.00 4.01 R
2895 3064 0.840617 TGTGGAGGTAGTGCAAACCA 59.159 50.0 18.95 6.49 39.64 3.67 R
3905 4160 0.249868 CATAGCGATCGGAAAGGCCA 60.250 55.0 18.30 0.00 35.94 5.36 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
240 241 1.537814 AATCTGTACCGACACCGCCA 61.538 55.000 0.00 0.00 0.00 5.69
309 310 4.197750 GCACTTCATCCATGTTCTCATCT 58.802 43.478 0.00 0.00 31.15 2.90
402 403 2.752903 TCACGAAGGTCGATGATCTTGA 59.247 45.455 4.40 0.00 43.74 3.02
478 479 0.763035 GGTGGTGTTAGTGACCTGGT 59.237 55.000 0.00 0.00 34.26 4.00
545 549 2.854777 CCTGCAAAAGACTAGATCGTCG 59.145 50.000 0.00 0.00 38.90 5.12
570 574 5.138125 ACATTTGATGGCTTTGTACCAAG 57.862 39.130 2.33 2.33 41.49 3.61
598 602 2.613026 TTTGCTCGAGGTTTCTGTCA 57.387 45.000 15.58 0.00 0.00 3.58
600 604 0.750249 TGCTCGAGGTTTCTGTCACA 59.250 50.000 15.58 0.00 0.00 3.58
601 605 1.140816 GCTCGAGGTTTCTGTCACAC 58.859 55.000 15.58 0.00 0.00 3.82
602 606 1.538204 GCTCGAGGTTTCTGTCACACA 60.538 52.381 15.58 0.00 0.00 3.72
603 607 2.868044 GCTCGAGGTTTCTGTCACACAT 60.868 50.000 15.58 0.00 0.00 3.21
605 609 3.804036 TCGAGGTTTCTGTCACACATTT 58.196 40.909 0.00 0.00 0.00 2.32
606 610 4.196193 TCGAGGTTTCTGTCACACATTTT 58.804 39.130 0.00 0.00 0.00 1.82
611 615 2.772568 TCTGTCACACATTTTTGGCG 57.227 45.000 0.00 0.00 0.00 5.69
612 616 2.020720 TCTGTCACACATTTTTGGCGT 58.979 42.857 0.00 0.00 0.00 5.68
613 617 2.118683 CTGTCACACATTTTTGGCGTG 58.881 47.619 0.00 0.00 36.70 5.34
614 618 1.474478 TGTCACACATTTTTGGCGTGT 59.526 42.857 0.00 0.00 44.45 4.49
618 622 2.994716 CACATTTTTGGCGTGTGTTG 57.005 45.000 0.00 0.00 38.66 3.33
619 623 1.592081 CACATTTTTGGCGTGTGTTGG 59.408 47.619 0.00 0.00 38.66 3.77
620 624 1.478510 ACATTTTTGGCGTGTGTTGGA 59.521 42.857 0.00 0.00 0.00 3.53
621 625 1.857837 CATTTTTGGCGTGTGTTGGAC 59.142 47.619 0.00 0.00 0.00 4.02
622 626 0.173708 TTTTTGGCGTGTGTTGGACC 59.826 50.000 0.00 0.00 0.00 4.46
664 713 3.009033 TGCAACAGGAAGTGGTAGCTATT 59.991 43.478 0.00 0.00 0.00 1.73
712 761 1.208293 GGAACTGTGGAGTGGAGATCC 59.792 57.143 0.00 0.00 37.35 3.36
717 766 3.551407 GGAGTGGAGATCCCCGGC 61.551 72.222 0.00 0.00 34.29 6.13
722 771 3.866582 GGAGATCCCCGGCACCTG 61.867 72.222 0.00 0.00 0.00 4.00
964 1030 0.096281 CTCGATCGCCTCTCTATCGC 59.904 60.000 11.09 0.00 41.66 4.58
968 1034 2.433646 ATCGCCTCTCTATCGCCCCT 62.434 60.000 0.00 0.00 0.00 4.79
2323 2441 0.251787 ATCCAAGGACCAGGCAAACC 60.252 55.000 0.00 0.00 0.00 3.27
3597 3823 2.523015 GACGACGACGACATAACCAAT 58.477 47.619 15.32 0.00 42.66 3.16
3727 3953 3.255888 TGTGTTGTGTTGTTGGTGCTAAA 59.744 39.130 0.00 0.00 0.00 1.85
3728 3954 4.081972 TGTGTTGTGTTGTTGGTGCTAAAT 60.082 37.500 0.00 0.00 0.00 1.40
3729 3955 4.867608 GTGTTGTGTTGTTGGTGCTAAATT 59.132 37.500 0.00 0.00 0.00 1.82
3802 4028 8.896744 CATGGAGATTTTGATAACTAGAAGCAA 58.103 33.333 0.00 0.00 0.00 3.91
3853 4089 5.692613 AGCTAAGGTACTAGCGAATACAG 57.307 43.478 8.11 0.00 38.49 2.74
3872 4108 8.664669 AATACAGTGGAATTTAATCAAGGGTT 57.335 30.769 0.00 0.00 0.00 4.11
3874 4110 6.758254 ACAGTGGAATTTAATCAAGGGTTTG 58.242 36.000 0.00 0.00 35.57 2.93
3909 4164 8.206325 CATCTAGATGTGACATAATTATGGCC 57.794 38.462 25.30 17.56 41.08 5.36
3910 4165 7.559335 TCTAGATGTGACATAATTATGGCCT 57.441 36.000 25.30 17.69 41.08 5.19
3911 4166 7.977818 TCTAGATGTGACATAATTATGGCCTT 58.022 34.615 25.30 15.42 41.08 4.35
3912 4167 8.439971 TCTAGATGTGACATAATTATGGCCTTT 58.560 33.333 25.30 11.73 41.08 3.11
3913 4168 7.516198 AGATGTGACATAATTATGGCCTTTC 57.484 36.000 25.30 18.34 41.08 2.62
3914 4169 6.491403 AGATGTGACATAATTATGGCCTTTCC 59.509 38.462 25.30 12.46 41.08 3.13
3915 4170 4.578516 TGTGACATAATTATGGCCTTTCCG 59.421 41.667 25.30 1.08 41.08 4.30
3916 4171 4.819630 GTGACATAATTATGGCCTTTCCGA 59.180 41.667 25.30 5.13 41.08 4.55
3919 4174 4.695455 ACATAATTATGGCCTTTCCGATCG 59.305 41.667 25.45 8.51 38.00 3.69
3921 4176 0.468226 TTATGGCCTTTCCGATCGCT 59.532 50.000 10.32 0.00 37.80 4.93
3927 4182 2.547218 GGCCTTTCCGATCGCTATGTTA 60.547 50.000 10.32 0.00 0.00 2.41
3928 4183 3.128349 GCCTTTCCGATCGCTATGTTAA 58.872 45.455 10.32 0.00 0.00 2.01
3936 4191 3.412386 GATCGCTATGTTAATGGCCCTT 58.588 45.455 0.00 0.00 36.98 3.95
3938 4193 1.880027 CGCTATGTTAATGGCCCTTCC 59.120 52.381 0.00 0.00 36.98 3.46
3946 4201 1.407656 AATGGCCCTTCCGATCGCTA 61.408 55.000 10.32 0.00 37.80 4.26
3953 4209 2.544267 CCCTTCCGATCGCTATGTTTTC 59.456 50.000 10.32 0.00 0.00 2.29
3960 4216 4.498177 CCGATCGCTATGTTTTCTCTCTCA 60.498 45.833 10.32 0.00 0.00 3.27
3980 4236 0.462225 TTCGCTTGTTTGTCACCCGA 60.462 50.000 0.00 0.00 0.00 5.14
3991 4247 2.685380 CACCCGAGCCTTCCCTCT 60.685 66.667 0.00 0.00 0.00 3.69
4061 4525 1.489560 CCCCTCCCACGAACTTTCCT 61.490 60.000 0.00 0.00 0.00 3.36
4068 4532 0.739813 CACGAACTTTCCTAGGCCCG 60.740 60.000 2.96 3.56 0.00 6.13
4122 4586 1.375523 GCGGTGACCCATTTCGTCT 60.376 57.895 0.00 0.00 0.00 4.18
4157 4621 2.047655 TCGGCGCGGACAGAAAAT 60.048 55.556 14.27 0.00 0.00 1.82
4185 4649 2.975799 GCGCCGACCCAAACAGAA 60.976 61.111 0.00 0.00 0.00 3.02
4204 4669 0.602638 AGCATGTCCGCTTTTCGTCA 60.603 50.000 0.00 0.00 39.99 4.35
4236 4702 2.107366 CATTCCCGGCCCATTTTTAGT 58.893 47.619 0.00 0.00 0.00 2.24
4240 4706 1.381165 CCGGCCCATTTTTAGTCGGG 61.381 60.000 0.00 0.00 42.03 5.14
4340 4830 0.110104 GCCATCCTCTCCCATTCCAG 59.890 60.000 0.00 0.00 0.00 3.86
4355 4852 2.670934 CAGCAGCAAACCCTCGCT 60.671 61.111 0.00 0.00 39.66 4.93
4356 4853 1.375908 CAGCAGCAAACCCTCGCTA 60.376 57.895 0.00 0.00 36.50 4.26
4403 4901 0.245539 CATTTTGCTGGTGCCTCTGG 59.754 55.000 0.00 0.00 38.71 3.86
4433 4931 2.819595 CCGCAACATCCACCTCCG 60.820 66.667 0.00 0.00 0.00 4.63
4492 5030 1.308216 CTTCCCATCCCCACTCCCT 60.308 63.158 0.00 0.00 0.00 4.20
4494 5032 2.286425 CCCATCCCCACTCCCTGT 60.286 66.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 241 2.797278 CCGGGCATTAGGACGAGCT 61.797 63.158 0.00 0.00 0.00 4.09
402 403 1.909302 CATCTACTCACCAACCACCCT 59.091 52.381 0.00 0.00 0.00 4.34
545 549 3.679502 GGTACAAAGCCATCAAATGTTGC 59.320 43.478 0.00 0.00 0.00 4.17
570 574 4.440839 AACCTCGAGCAAAATCATTTCC 57.559 40.909 6.99 0.00 0.00 3.13
600 604 1.478510 TCCAACACACGCCAAAAATGT 59.521 42.857 0.00 0.00 0.00 2.71
601 605 1.857837 GTCCAACACACGCCAAAAATG 59.142 47.619 0.00 0.00 0.00 2.32
602 606 1.202475 GGTCCAACACACGCCAAAAAT 60.202 47.619 0.00 0.00 0.00 1.82
603 607 0.173708 GGTCCAACACACGCCAAAAA 59.826 50.000 0.00 0.00 0.00 1.94
605 609 0.681564 AAGGTCCAACACACGCCAAA 60.682 50.000 0.00 0.00 0.00 3.28
606 610 0.681564 AAAGGTCCAACACACGCCAA 60.682 50.000 0.00 0.00 0.00 4.52
761 810 1.226211 CACGTCGCCGGTACTACAG 60.226 63.158 1.90 0.00 38.78 2.74
964 1030 2.066999 GGGAGCAGTGAGGTAGGGG 61.067 68.421 0.00 0.00 0.00 4.79
968 1034 1.001760 GGGAGGGAGCAGTGAGGTA 59.998 63.158 0.00 0.00 0.00 3.08
1698 1774 3.644399 GAGGCCGGAGTCGTTGGAC 62.644 68.421 5.05 0.00 43.76 4.02
1768 1844 4.530857 GCCGGCCGTGTAGCTGAT 62.531 66.667 26.12 0.00 42.00 2.90
2277 2395 2.897969 GGACCTGTCCTTCTCACTGTTA 59.102 50.000 9.11 0.00 46.16 2.41
2278 2396 1.694696 GGACCTGTCCTTCTCACTGTT 59.305 52.381 9.11 0.00 46.16 3.16
2323 2441 0.806102 CCACCTATCACCGTCGCAAG 60.806 60.000 0.00 0.00 0.00 4.01
2325 2443 2.889617 CCACCTATCACCGTCGCA 59.110 61.111 0.00 0.00 0.00 5.10
2649 2803 4.296265 GGGTTCGACCGCTTGATT 57.704 55.556 0.00 0.00 39.83 2.57
2895 3064 0.840617 TGTGGAGGTAGTGCAAACCA 59.159 50.000 18.95 6.49 39.64 3.67
3570 3796 2.812609 TCGTCGTCGTCCTCCTCG 60.813 66.667 1.33 0.00 38.33 4.63
3579 3805 1.511552 CGATTGGTTATGTCGTCGTCG 59.488 52.381 0.00 0.00 38.55 5.12
3802 4028 6.597672 TGAACACTGAGTGAAACACTAATGTT 59.402 34.615 20.97 18.64 45.44 2.71
3853 4089 6.993079 AGACAAACCCTTGATTAAATTCCAC 58.007 36.000 0.00 0.00 36.33 4.02
3894 4149 5.042463 TCGGAAAGGCCATAATTATGTCA 57.958 39.130 21.20 0.00 35.94 3.58
3895 4150 5.163854 CGATCGGAAAGGCCATAATTATGTC 60.164 44.000 21.20 10.89 35.94 3.06
3896 4151 4.695455 CGATCGGAAAGGCCATAATTATGT 59.305 41.667 21.20 5.15 35.94 2.29
3897 4152 4.437390 GCGATCGGAAAGGCCATAATTATG 60.437 45.833 18.30 17.11 35.94 1.90
3898 4153 3.689649 GCGATCGGAAAGGCCATAATTAT 59.310 43.478 18.30 0.00 35.94 1.28
3899 4154 3.071479 GCGATCGGAAAGGCCATAATTA 58.929 45.455 18.30 0.00 35.94 1.40
3900 4155 1.880027 GCGATCGGAAAGGCCATAATT 59.120 47.619 18.30 0.00 35.94 1.40
3901 4156 1.072331 AGCGATCGGAAAGGCCATAAT 59.928 47.619 18.30 0.00 35.94 1.28
3902 4157 0.468226 AGCGATCGGAAAGGCCATAA 59.532 50.000 18.30 0.00 35.94 1.90
3903 4158 1.334160 TAGCGATCGGAAAGGCCATA 58.666 50.000 18.30 0.00 35.94 2.74
3904 4159 0.687354 ATAGCGATCGGAAAGGCCAT 59.313 50.000 18.30 0.00 35.94 4.40
3905 4160 0.249868 CATAGCGATCGGAAAGGCCA 60.250 55.000 18.30 0.00 35.94 5.36
3906 4161 0.249911 ACATAGCGATCGGAAAGGCC 60.250 55.000 18.30 0.00 0.00 5.19
3907 4162 1.583054 AACATAGCGATCGGAAAGGC 58.417 50.000 18.30 0.00 0.00 4.35
3908 4163 4.152402 CCATTAACATAGCGATCGGAAAGG 59.848 45.833 18.30 2.70 0.00 3.11
3909 4164 4.377431 GCCATTAACATAGCGATCGGAAAG 60.377 45.833 18.30 0.00 0.00 2.62
3910 4165 3.496884 GCCATTAACATAGCGATCGGAAA 59.503 43.478 18.30 1.32 0.00 3.13
3911 4166 3.064207 GCCATTAACATAGCGATCGGAA 58.936 45.455 18.30 0.00 0.00 4.30
3912 4167 2.611971 GGCCATTAACATAGCGATCGGA 60.612 50.000 18.30 0.00 0.00 4.55
3913 4168 1.732259 GGCCATTAACATAGCGATCGG 59.268 52.381 18.30 2.04 0.00 4.18
3914 4169 1.732259 GGGCCATTAACATAGCGATCG 59.268 52.381 11.69 11.69 0.00 3.69
3915 4170 3.059352 AGGGCCATTAACATAGCGATC 57.941 47.619 6.18 0.00 0.00 3.69
3916 4171 3.412386 GAAGGGCCATTAACATAGCGAT 58.588 45.455 0.73 0.00 0.00 4.58
3919 4174 1.880027 CGGAAGGGCCATTAACATAGC 59.120 52.381 0.73 0.00 35.94 2.97
3921 4176 3.556213 CGATCGGAAGGGCCATTAACATA 60.556 47.826 0.73 0.00 35.94 2.29
3927 4182 1.407656 TAGCGATCGGAAGGGCCATT 61.408 55.000 18.30 0.07 35.94 3.16
3928 4183 1.194781 ATAGCGATCGGAAGGGCCAT 61.195 55.000 18.30 0.00 35.94 4.40
3936 4191 3.632604 AGAGAGAAAACATAGCGATCGGA 59.367 43.478 18.30 0.00 0.00 4.55
3938 4193 4.602006 TGAGAGAGAAAACATAGCGATCG 58.398 43.478 11.69 11.69 0.00 3.69
3946 4201 4.999950 ACAAGCGAATGAGAGAGAAAACAT 59.000 37.500 0.00 0.00 0.00 2.71
3953 4209 3.742882 TGACAAACAAGCGAATGAGAGAG 59.257 43.478 0.00 0.00 0.00 3.20
3960 4216 0.591170 CGGGTGACAAACAAGCGAAT 59.409 50.000 0.00 0.00 0.00 3.34
3980 4236 2.363172 GCCGAAGAGAGGGAAGGCT 61.363 63.158 0.00 0.00 41.21 4.58
3991 4247 2.813754 CAAAAAGGATGAGTGCCGAAGA 59.186 45.455 0.00 0.00 0.00 2.87
4044 4508 1.207329 CCTAGGAAAGTTCGTGGGAGG 59.793 57.143 1.05 0.00 43.68 4.30
4046 4510 0.611714 GCCTAGGAAAGTTCGTGGGA 59.388 55.000 14.75 0.00 43.68 4.37
4051 4515 1.153429 CCGGGCCTAGGAAAGTTCG 60.153 63.158 14.75 5.96 0.00 3.95
4068 4532 3.137687 CCCACAAACACAAGGCCC 58.862 61.111 0.00 0.00 0.00 5.80
4097 4561 3.894547 ATGGGTCACCGCGTTGGAC 62.895 63.158 3.08 8.59 42.00 4.02
4204 4669 2.070650 GGGAATGGGTCGGTAGGCT 61.071 63.158 0.00 0.00 0.00 4.58
4281 4771 2.446802 CCAGGGGGAGGAGTAGGC 60.447 72.222 0.00 0.00 35.59 3.93
4340 4830 2.754995 GCTAGCGAGGGTTTGCTGC 61.755 63.158 0.00 0.00 43.98 5.25
4355 4852 1.078918 TCGACGACGAAGGAGGCTA 60.079 57.895 7.68 0.00 45.74 3.93
4356 4853 2.359602 TCGACGACGAAGGAGGCT 60.360 61.111 7.68 0.00 45.74 4.58
4376 4873 4.054825 CAGCAAAATGGGCGGCGT 62.055 61.111 9.37 0.00 36.08 5.68
4494 5032 0.878523 CTTCTTGGTCGCGGTTGTGA 60.879 55.000 6.13 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.