Multiple sequence alignment - TraesCS5B01G455500

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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 TraesCS5B01G455500 chr5B 100.000 5406 0 0 1 5406 629894667 629900072 0.000000e+00 9984.0
1 TraesCS5B01G455500 chr5B 92.826 2788 130 24 1 2768 628693487 628696224 0.000000e+00 3976.0
2 TraesCS5B01G455500 chr5B 92.755 2788 136 28 1 2768 625113934 625116675 0.000000e+00 3969.0
3 TraesCS5B01G455500 chr5B 92.724 2584 133 20 1 2548 626837027 626839591 0.000000e+00 3679.0
4 TraesCS5B01G455500 chr5B 92.631 2592 128 22 1 2548 623166051 623168623 0.000000e+00 3670.0
5 TraesCS5B01G455500 chr5B 96.368 1955 55 6 2539 4492 623171263 623173202 0.000000e+00 3203.0
6 TraesCS5B01G455500 chr5B 96.317 1955 56 6 2539 4492 626842230 626844169 0.000000e+00 3197.0
7 TraesCS5B01G455500 chr5B 94.143 1878 88 7 2773 4643 633176722 633174860 0.000000e+00 2839.0
8 TraesCS5B01G455500 chr5B 96.376 1683 58 3 2773 4453 625117263 625118944 0.000000e+00 2767.0
9 TraesCS5B01G455500 chr5B 96.316 1683 59 3 2773 4453 628696812 628698493 0.000000e+00 2761.0
10 TraesCS5B01G455500 chr5B 91.472 1454 79 18 888 2322 633179460 633178033 0.000000e+00 1956.0
11 TraesCS5B01G455500 chr5B 92.526 669 32 8 4739 5406 623176473 623177124 0.000000e+00 942.0
12 TraesCS5B01G455500 chr5B 92.526 669 32 8 4739 5406 626847439 626848090 0.000000e+00 942.0
13 TraesCS5B01G455500 chr5B 90.826 654 52 3 4753 5406 625121281 625121926 0.000000e+00 869.0
14 TraesCS5B01G455500 chr5B 90.826 654 52 3 4753 5406 628700830 628701475 0.000000e+00 869.0
15 TraesCS5B01G455500 chr5B 95.911 269 10 1 4489 4757 623176108 623176375 8.320000e-118 435.0
16 TraesCS5B01G455500 chr5B 95.911 269 10 1 4489 4757 626847074 626847341 8.320000e-118 435.0
17 TraesCS5B01G455500 chr5B 92.486 173 3 3 4576 4738 625120957 625121129 7.000000e-59 239.0
18 TraesCS5B01G455500 chr5B 92.486 173 3 3 4576 4738 628700506 628700678 7.000000e-59 239.0
19 TraesCS5B01G455500 chr5B 80.932 236 39 4 5170 5405 700187940 700187711 1.200000e-41 182.0
20 TraesCS5B01G455500 chr5B 94.253 87 4 1 4452 4537 625119059 625119145 1.220000e-26 132.0
21 TraesCS5B01G455500 chr5B 94.253 87 4 1 4452 4537 628698608 628698694 1.220000e-26 132.0
22 TraesCS5B01G455500 chr5B 100.000 31 0 0 4808 4838 633174784 633174754 2.100000e-04 58.4
23 TraesCS5B01G455500 chr5A 94.006 1902 97 7 2874 4759 625733836 625731936 0.000000e+00 2865.0
24 TraesCS5B01G455500 chr5A 92.844 1607 81 13 888 2475 625738874 625737283 0.000000e+00 2300.0
25 TraesCS5B01G455500 chr5A 91.022 323 8 7 2461 2768 625737250 625736934 3.010000e-112 416.0
26 TraesCS5B01G455500 chr5A 78.011 714 100 29 4743 5405 625731819 625731112 3.920000e-106 396.0
27 TraesCS5B01G455500 chr5A 78.484 409 44 13 62 448 535155224 535154838 1.510000e-55 228.0
28 TraesCS5B01G455500 chr5A 97.959 98 2 0 2773 2870 625734890 625734793 2.590000e-38 171.0
29 TraesCS5B01G455500 chrUn 96.567 699 9 5 2539 3237 349938901 349939584 0.000000e+00 1144.0
30 TraesCS5B01G455500 chrUn 96.567 699 9 5 2539 3237 349941194 349941877 0.000000e+00 1144.0
31 TraesCS5B01G455500 chr6A 84.016 1026 156 7 3168 4188 32898759 32897737 0.000000e+00 979.0
32 TraesCS5B01G455500 chr6A 76.225 1367 211 66 1003 2301 32900815 32899495 2.140000e-173 619.0
33 TraesCS5B01G455500 chr6A 85.766 274 36 3 174 444 463161953 463162226 2.460000e-73 287.0
34 TraesCS5B01G455500 chr6D 83.821 1026 158 7 3168 4188 29771042 29772064 0.000000e+00 968.0
35 TraesCS5B01G455500 chr6D 80.323 991 181 12 3219 4202 468096600 468095617 0.000000e+00 737.0
36 TraesCS5B01G455500 chr6D 77.132 1360 202 60 1000 2301 29769000 29770308 0.000000e+00 688.0
37 TraesCS5B01G455500 chr5D 88.042 669 65 9 4743 5406 297089206 297088548 0.000000e+00 778.0
38 TraesCS5B01G455500 chr5D 87.792 385 34 7 4130 4504 297092972 297092591 6.430000e-119 438.0
39 TraesCS5B01G455500 chr5D 89.912 228 17 3 4536 4757 297089551 297089324 6.850000e-74 289.0
40 TraesCS5B01G455500 chr5D 79.218 409 42 13 62 448 421546875 421546488 1.500000e-60 244.0
41 TraesCS5B01G455500 chr5D 100.000 28 0 0 446 473 135232567 135232594 1.000000e-02 52.8
42 TraesCS5B01G455500 chr3B 88.129 278 32 1 171 448 741337457 741337733 4.040000e-86 329.0
43 TraesCS5B01G455500 chr3B 74.603 504 105 16 4909 5397 595362999 595363494 3.300000e-47 200.0
44 TraesCS5B01G455500 chr4B 78.016 514 91 14 4907 5402 526925684 526926193 2.450000e-78 303.0
45 TraesCS5B01G455500 chr4B 74.306 432 69 29 446 850 7877944 7877528 1.570000e-30 145.0
46 TraesCS5B01G455500 chr7B 75.960 495 100 13 4913 5398 233586913 233586429 2.520000e-58 237.0
47 TraesCS5B01G455500 chr7D 88.806 134 14 1 316 448 535570308 535570175 4.330000e-36 163.0
48 TraesCS5B01G455500 chr7D 86.184 152 19 2 65 215 535577690 535577540 4.330000e-36 163.0
49 TraesCS5B01G455500 chr6B 82.927 164 28 0 1080 1243 714336614 714336451 1.210000e-31 148.0
50 TraesCS5B01G455500 chr3D 75.069 361 55 26 4907 5253 20619516 20619177 9.440000e-28 135.0
51 TraesCS5B01G455500 chr1D 75.333 300 55 12 567 850 483359279 483358983 5.680000e-25 126.0
52 TraesCS5B01G455500 chr2A 76.630 184 30 10 4914 5091 685356977 685357153 7.460000e-14 89.8
53 TraesCS5B01G455500 chr1B 92.593 54 3 1 12 65 328920581 328920529 5.810000e-10 76.8


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 TraesCS5B01G455500 chr5B 629894667 629900072 5405 False 9984.000000 9984 100.0000 1 5406 1 chr5B.!!$F1 5405
1 TraesCS5B01G455500 chr5B 626837027 626848090 11063 False 2063.250000 3679 94.3695 1 5406 4 chr5B.!!$F4 5405
2 TraesCS5B01G455500 chr5B 623166051 623177124 11073 False 2062.500000 3670 94.3590 1 5406 4 chr5B.!!$F2 5405
3 TraesCS5B01G455500 chr5B 633174754 633179460 4706 True 1617.800000 2839 95.2050 888 4838 3 chr5B.!!$R2 3950
4 TraesCS5B01G455500 chr5B 628693487 628701475 7988 False 1595.400000 3976 93.3414 1 5406 5 chr5B.!!$F5 5405
5 TraesCS5B01G455500 chr5B 625113934 625121926 7992 False 1595.200000 3969 93.3392 1 5406 5 chr5B.!!$F3 5405
6 TraesCS5B01G455500 chr5A 625731112 625738874 7762 True 1229.600000 2865 90.7684 888 5405 5 chr5A.!!$R2 4517
7 TraesCS5B01G455500 chrUn 349938901 349941877 2976 False 1144.000000 1144 96.5670 2539 3237 2 chrUn.!!$F1 698
8 TraesCS5B01G455500 chr6A 32897737 32900815 3078 True 799.000000 979 80.1205 1003 4188 2 chr6A.!!$R1 3185
9 TraesCS5B01G455500 chr6D 29769000 29772064 3064 False 828.000000 968 80.4765 1000 4188 2 chr6D.!!$F1 3188
10 TraesCS5B01G455500 chr6D 468095617 468096600 983 True 737.000000 737 80.3230 3219 4202 1 chr6D.!!$R1 983
11 TraesCS5B01G455500 chr5D 297088548 297092972 4424 True 501.666667 778 88.5820 4130 5406 3 chr5D.!!$R2 1276
12 TraesCS5B01G455500 chr4B 526925684 526926193 509 False 303.000000 303 78.0160 4907 5402 1 chr4B.!!$F1 495

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
235 256 0.323451 GAGGGCTTGGGGATTTTCGT 60.323 55.000 0.00 0.0 0.0 3.85 F
994 1026 1.086634 AGAAAAGCAGATCTCGCGCC 61.087 55.000 0.00 0.0 0.0 6.53 F
1262 1321 0.036732 ACAGACACCAACCGCATCAT 59.963 50.000 0.00 0.0 0.0 2.45 F
1362 1436 1.221840 GGTGGACATGTCAGCCGAT 59.778 57.895 26.47 0.0 0.0 4.18 F
2960 11691 2.276732 AAGGTCCACAACTCCACATG 57.723 50.000 0.00 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1292 0.677731 CCATGATGCGGTTGGTGTCT 60.678 55.000 0.00 0.0 0.00 3.41 R
1891 2036 1.070577 GTTGACACAGTAGCTGTTGCG 60.071 52.381 0.00 0.0 42.59 4.85 R
3039 11770 2.260844 TGCCTTGTCCTCTTTGAGTG 57.739 50.000 0.00 0.0 0.00 3.51 R
3044 11775 2.587522 GGACTTTGCCTTGTCCTCTTT 58.412 47.619 10.61 0.0 46.65 2.52 R
4805 20300 0.036671 GGTAGTTAGGCGTGCCAGTT 60.037 55.000 14.29 0.0 38.92 3.16 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
77 78 3.998672 CCCCGTGGCGTGTGTACT 61.999 66.667 0.00 0.00 0.00 2.73
120 121 3.713936 CGTAGGATCTGACGCAACA 57.286 52.632 6.94 0.00 31.49 3.33
235 256 0.323451 GAGGGCTTGGGGATTTTCGT 60.323 55.000 0.00 0.00 0.00 3.85
241 262 2.045731 GGGGATTTTCGTGGCGGA 60.046 61.111 0.00 0.00 0.00 5.54
303 325 2.594131 CACATATACTGGTCGAGGGGA 58.406 52.381 0.00 0.00 0.00 4.81
304 326 2.963101 CACATATACTGGTCGAGGGGAA 59.037 50.000 0.00 0.00 0.00 3.97
335 357 1.268640 GCCACCGCAAAAGTTTTACGA 60.269 47.619 20.02 0.00 34.03 3.43
343 365 1.244816 AAAGTTTTACGAGCCAGGCC 58.755 50.000 8.22 0.00 0.00 5.19
444 466 1.135915 CGGTGTCTGCTAGAGATGCTT 59.864 52.381 0.00 0.00 31.63 3.91
469 491 1.536766 CTTGTTGAAGGCATTGCTCGA 59.463 47.619 8.82 0.00 0.00 4.04
507 529 5.306678 TGTGAAAACCTAAATTCTGGCCATT 59.693 36.000 5.51 0.00 0.00 3.16
519 541 3.653164 TCTGGCCATTAGTCCATGACTA 58.347 45.455 5.51 0.00 41.51 2.59
549 571 3.430862 GACGGCGGCAATTGAGCA 61.431 61.111 22.04 0.00 35.83 4.26
550 572 3.667429 GACGGCGGCAATTGAGCAC 62.667 63.158 22.04 13.32 35.83 4.40
552 574 3.372730 GGCGGCAATTGAGCACCA 61.373 61.111 22.04 0.00 35.83 4.17
556 578 1.885871 GGCAATTGAGCACCACTCC 59.114 57.895 10.34 0.00 45.61 3.85
564 586 1.152030 AGCACCACTCCCTTCCTGA 60.152 57.895 0.00 0.00 0.00 3.86
577 599 2.287608 CCTTCCTGAAAAGGCGTTGTTC 60.288 50.000 0.00 0.34 39.47 3.18
615 637 4.790765 TCCATATGGCGTCTTGAGATAG 57.209 45.455 17.58 0.00 34.44 2.08
643 665 5.050091 GTGCGAATATGGTCTTTCATGTAGG 60.050 44.000 0.00 0.00 0.00 3.18
646 668 6.292919 GCGAATATGGTCTTTCATGTAGGTTC 60.293 42.308 0.00 0.00 0.00 3.62
649 671 2.307686 TGGTCTTTCATGTAGGTTCCCC 59.692 50.000 0.00 0.00 0.00 4.81
757 781 1.761449 TGGTGTTGACTGTGTGCATT 58.239 45.000 0.00 0.00 0.00 3.56
767 791 3.005554 ACTGTGTGCATTCTGACTATGC 58.994 45.455 7.25 7.25 46.63 3.14
775 799 3.431346 GCATTCTGACTATGCAGAGGACA 60.431 47.826 13.85 11.24 45.93 4.02
776 800 4.763073 CATTCTGACTATGCAGAGGACAA 58.237 43.478 13.85 0.20 44.93 3.18
790 814 2.532531 GGACAAATGTGTGCTCATCG 57.467 50.000 0.00 0.00 42.49 3.84
882 906 1.372128 GTTAAGTCCGTGGCGACGT 60.372 57.895 20.00 3.93 44.54 4.34
980 1012 6.946340 AGCCAAGAAGAAAAAGGAAAGAAAA 58.054 32.000 0.00 0.00 0.00 2.29
981 1013 7.044181 AGCCAAGAAGAAAAAGGAAAGAAAAG 58.956 34.615 0.00 0.00 0.00 2.27
982 1014 6.238211 GCCAAGAAGAAAAAGGAAAGAAAAGC 60.238 38.462 0.00 0.00 0.00 3.51
983 1015 6.818142 CCAAGAAGAAAAAGGAAAGAAAAGCA 59.182 34.615 0.00 0.00 0.00 3.91
988 1020 7.594351 AGAAAAAGGAAAGAAAAGCAGATCT 57.406 32.000 0.00 0.00 0.00 2.75
994 1026 1.086634 AGAAAAGCAGATCTCGCGCC 61.087 55.000 0.00 0.00 0.00 6.53
1001 1045 2.279517 GATCTCGCGCCGGAACAT 60.280 61.111 5.05 0.00 0.00 2.71
1158 1205 1.303282 GAGCATCCCGTTCCCCTTT 59.697 57.895 0.00 0.00 0.00 3.11
1262 1321 0.036732 ACAGACACCAACCGCATCAT 59.963 50.000 0.00 0.00 0.00 2.45
1362 1436 1.221840 GGTGGACATGTCAGCCGAT 59.778 57.895 26.47 0.00 0.00 4.18
1452 1526 3.628646 AACCCAGGCCATGACGCTC 62.629 63.158 5.01 0.00 0.00 5.03
1771 1892 2.282958 TCTTCTCCACGCCGGACT 60.283 61.111 5.05 0.00 39.64 3.85
1801 1922 3.260483 CGCTGCTGATGGAGACGC 61.260 66.667 0.00 0.00 33.10 5.19
2053 2210 3.688185 TCGTTGACCTACTAGTAGCACAG 59.312 47.826 22.39 12.28 31.95 3.66
2328 2629 7.011763 CACTTCAACTGCTAATACATATGCTGT 59.988 37.037 1.58 0.00 42.13 4.40
2443 3034 6.771188 ATGAAGTCTGAAAAGAAGTGTACG 57.229 37.500 0.00 0.00 0.00 3.67
2459 3050 9.701098 AGAAGTGTACGTAATAAGTCAAAATGA 57.299 29.630 0.00 0.00 0.00 2.57
2494 3132 2.341101 CGTACACGACCCCTGCTCT 61.341 63.158 0.00 0.00 43.02 4.09
2960 11691 2.276732 AAGGTCCACAACTCCACATG 57.723 50.000 0.00 0.00 0.00 3.21
3039 11770 2.338500 CTTACTTTGTGAGGGTCGCTC 58.662 52.381 9.91 9.91 0.00 5.03
3322 12057 4.684724 AGAATGGTGGACCTACACTAGAA 58.315 43.478 0.00 0.00 41.09 2.10
3611 12346 3.118956 CGAATTTCTCTCTGGTGGTAGCT 60.119 47.826 0.00 0.00 0.00 3.32
3982 12717 6.769822 AGAAGGCCATACATTCTGACAATAAG 59.230 38.462 5.01 0.00 32.19 1.73
4019 12754 0.662619 CCTTGAAGCTCGCAACAACA 59.337 50.000 0.00 0.00 0.00 3.33
4040 12775 4.245660 CAAGAGCAGAATAACCGAGTTGA 58.754 43.478 0.23 0.00 0.00 3.18
4132 12867 2.029020 TCTCAACCTTGACGTGGATCAG 60.029 50.000 0.00 0.00 32.90 2.90
4332 13073 2.480845 ACTTGGTTGTAACTCACTCGC 58.519 47.619 0.00 0.00 0.00 5.03
4377 13126 5.991328 AGCAATTGTACGTCTTCCATATG 57.009 39.130 7.40 0.00 0.00 1.78
4805 20300 2.404923 TCCACAAACACAAACTCCGA 57.595 45.000 0.00 0.00 0.00 4.55
4836 20331 2.810852 CCTAACTACCTCCGTCGGTATC 59.189 54.545 11.88 0.00 38.76 2.24
4837 20332 1.303309 AACTACCTCCGTCGGTATCG 58.697 55.000 11.88 0.00 38.76 2.92
4838 20333 0.465705 ACTACCTCCGTCGGTATCGA 59.534 55.000 11.88 0.00 43.86 3.59
4952 20483 8.351461 CCTCTATAACCGGTTAGAGAAGTAAAG 58.649 40.741 37.58 28.14 41.21 1.85
5077 20612 2.143122 CTTGCGGCTGAGTAAAAGTCA 58.857 47.619 0.00 0.00 0.00 3.41
5101 20647 0.547471 TCTCCTCCATTGCCTGTCCA 60.547 55.000 0.00 0.00 0.00 4.02
5160 20721 2.928361 CACTGGCACGTCGTTGTC 59.072 61.111 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 1.738099 GCGTGTTGCGTCAGATCCT 60.738 57.895 0.00 0.00 43.66 3.24
221 242 1.506262 CGCCACGAAAATCCCCAAG 59.494 57.895 0.00 0.00 0.00 3.61
235 256 2.201490 CCTATCCCTCCTCCGCCA 59.799 66.667 0.00 0.00 0.00 5.69
241 262 1.236282 CCCGAACCCTATCCCTCCT 59.764 63.158 0.00 0.00 0.00 3.69
343 365 0.160182 GAACAGACACCGTAAACGCG 59.840 55.000 3.53 3.53 38.18 6.01
427 449 4.467795 AGGTAAAAGCATCTCTAGCAGACA 59.532 41.667 0.00 0.00 32.26 3.41
480 502 6.183361 TGGCCAGAATTTAGGTTTTCACATTT 60.183 34.615 0.00 0.00 0.00 2.32
483 505 4.219115 TGGCCAGAATTTAGGTTTTCACA 58.781 39.130 0.00 0.00 0.00 3.58
495 517 4.079558 AGTCATGGACTAATGGCCAGAATT 60.080 41.667 13.05 2.90 41.51 2.17
507 529 2.515854 GATCCGGCTAGTCATGGACTA 58.484 52.381 0.00 6.01 41.51 2.59
541 563 1.272147 GGAAGGGAGTGGTGCTCAATT 60.272 52.381 0.00 0.00 45.88 2.32
549 571 1.425448 CCTTTTCAGGAAGGGAGTGGT 59.575 52.381 0.00 0.00 44.19 4.16
550 572 1.888391 GCCTTTTCAGGAAGGGAGTGG 60.888 57.143 5.87 0.00 44.19 4.00
552 574 0.036875 CGCCTTTTCAGGAAGGGAGT 59.963 55.000 5.87 0.00 44.19 3.85
556 578 1.318576 ACAACGCCTTTTCAGGAAGG 58.681 50.000 0.00 0.00 44.19 3.46
564 586 4.712122 TTCTTCAAGAACAACGCCTTTT 57.288 36.364 0.00 0.00 0.00 2.27
577 599 6.939163 CCATATGGATAAGGAGGTTCTTCAAG 59.061 42.308 17.49 0.00 37.39 3.02
590 612 5.139435 TCTCAAGACGCCATATGGATAAG 57.861 43.478 26.47 14.48 37.39 1.73
593 615 4.774726 ACTATCTCAAGACGCCATATGGAT 59.225 41.667 26.47 12.36 37.39 3.41
615 637 5.041951 TGAAAGACCATATTCGCACAAAC 57.958 39.130 0.00 0.00 0.00 2.93
643 665 2.017049 CAAAGTGATCGGATGGGGAAC 58.983 52.381 0.00 0.00 0.00 3.62
646 668 0.546122 TCCAAAGTGATCGGATGGGG 59.454 55.000 0.00 0.00 0.00 4.96
649 671 8.408601 AGAAATAAAATCCAAAGTGATCGGATG 58.591 33.333 0.00 0.00 39.51 3.51
733 756 1.132262 CACACAGTCAACACCAACACC 59.868 52.381 0.00 0.00 0.00 4.16
757 781 4.223700 ACATTTGTCCTCTGCATAGTCAGA 59.776 41.667 0.00 0.00 40.50 3.27
767 791 2.497138 TGAGCACACATTTGTCCTCTG 58.503 47.619 4.63 0.00 31.66 3.35
775 799 3.066621 ACAAACACGATGAGCACACATTT 59.933 39.130 0.00 0.00 0.00 2.32
776 800 2.618241 ACAAACACGATGAGCACACATT 59.382 40.909 0.00 0.00 0.00 2.71
790 814 9.793252 AATAAAGCATCATGAGAATACAAACAC 57.207 29.630 0.09 0.00 0.00 3.32
882 906 1.248486 ACAGCGAGTCAACTGAGCTA 58.752 50.000 15.22 0.00 35.65 3.32
953 980 6.365520 TCTTTCCTTTTTCTTCTTGGCTAGT 58.634 36.000 0.00 0.00 0.00 2.57
981 1013 4.873129 TTCCGGCGCGAGATCTGC 62.873 66.667 12.10 3.35 0.00 4.26
982 1014 2.956964 GTTCCGGCGCGAGATCTG 60.957 66.667 12.10 0.00 0.00 2.90
983 1015 2.786495 ATGTTCCGGCGCGAGATCT 61.786 57.895 12.10 0.00 0.00 2.75
1245 1292 0.677731 CCATGATGCGGTTGGTGTCT 60.678 55.000 0.00 0.00 0.00 3.41
1453 1527 3.499737 CTCCGTGATGCCGTTGCC 61.500 66.667 0.00 0.00 36.33 4.52
1454 1528 3.499737 CCTCCGTGATGCCGTTGC 61.500 66.667 0.00 0.00 38.26 4.17
1455 1529 2.819595 CCCTCCGTGATGCCGTTG 60.820 66.667 0.00 0.00 0.00 4.10
1456 1530 4.096003 CCCCTCCGTGATGCCGTT 62.096 66.667 0.00 0.00 0.00 4.44
1581 1684 2.676822 TTCCTCACCGCGAGCTCT 60.677 61.111 8.23 0.00 40.78 4.09
1592 1701 4.351938 CGCACGACCCGTTCCTCA 62.352 66.667 0.00 0.00 38.32 3.86
1801 1922 4.436998 GTCGAGCACCACGGGGAG 62.437 72.222 12.96 2.38 38.05 4.30
1891 2036 1.070577 GTTGACACAGTAGCTGTTGCG 60.071 52.381 0.00 0.00 42.59 4.85
2053 2210 3.018149 AGTCGTCTAAGACAGGATGGAC 58.982 50.000 0.00 0.00 43.62 4.02
2179 2341 3.432326 CCTCCCAGCCTGTTCTTACATAC 60.432 52.174 0.00 0.00 32.86 2.39
2436 3027 8.092687 ACCTCATTTTGACTTATTACGTACACT 58.907 33.333 0.00 0.00 0.00 3.55
2437 3028 8.248117 ACCTCATTTTGACTTATTACGTACAC 57.752 34.615 0.00 0.00 0.00 2.90
2442 3033 8.335356 CCATGTACCTCATTTTGACTTATTACG 58.665 37.037 0.00 0.00 34.09 3.18
2443 3034 9.391006 TCCATGTACCTCATTTTGACTTATTAC 57.609 33.333 0.00 0.00 34.09 1.89
2459 3050 4.081406 TGTACGTAGTTGTCCATGTACCT 58.919 43.478 0.00 0.00 37.78 3.08
2960 11691 5.054477 TCTATACCAAGCGGAAGTATTTGC 58.946 41.667 0.00 0.00 35.59 3.68
3039 11770 2.260844 TGCCTTGTCCTCTTTGAGTG 57.739 50.000 0.00 0.00 0.00 3.51
3044 11775 2.587522 GGACTTTGCCTTGTCCTCTTT 58.412 47.619 10.61 0.00 46.65 2.52
3611 12346 3.753815 TGCTGTGAAGAATGTCATCCAA 58.246 40.909 0.00 0.00 0.00 3.53
3982 12717 7.964604 TTCAAGGAAGCTCTTTACTAAGTTC 57.035 36.000 0.00 0.00 32.98 3.01
4011 12746 4.229876 GGTTATTCTGCTCTTGTTGTTGC 58.770 43.478 0.00 0.00 0.00 4.17
4019 12754 4.537135 TCAACTCGGTTATTCTGCTCTT 57.463 40.909 0.00 0.00 0.00 2.85
4040 12775 3.255725 CTGCCGCAATTTCATTGTCAAT 58.744 40.909 0.00 0.00 42.20 2.57
4132 12867 0.676184 TATCTGCCATCGCTGGTCTC 59.324 55.000 7.21 0.00 45.10 3.36
4332 13073 5.856126 AACACGAATACATGGTTACACAG 57.144 39.130 0.00 0.00 0.00 3.66
4377 13126 3.192001 TGTGAAGATGATTGCTCCTTTGC 59.808 43.478 0.00 0.00 0.00 3.68
4550 19887 1.906105 AAGGGCTAACGATTCCGGCA 61.906 55.000 0.00 0.00 40.78 5.69
4632 19977 1.475280 CCTTCCGATCTCGTGTAACCA 59.525 52.381 0.00 0.00 37.74 3.67
4703 20061 6.015688 TGACATACCGTACTGAAGACTTTTCT 60.016 38.462 0.00 0.00 0.00 2.52
4739 20103 0.249657 GCTGAGTCCGAAGCCCTATG 60.250 60.000 0.00 0.00 33.12 2.23
4805 20300 0.036671 GGTAGTTAGGCGTGCCAGTT 60.037 55.000 14.29 0.00 38.92 3.16
4836 20331 3.191581 AGGTTCATCTGGCTACGATATCG 59.808 47.826 23.18 23.18 46.33 2.92
4837 20332 4.218635 TCAGGTTCATCTGGCTACGATATC 59.781 45.833 0.00 0.00 35.58 1.63
4838 20333 4.152647 TCAGGTTCATCTGGCTACGATAT 58.847 43.478 0.00 0.00 35.58 1.63
4839 20334 3.562182 TCAGGTTCATCTGGCTACGATA 58.438 45.455 0.00 0.00 35.58 2.92
4840 20335 2.388735 TCAGGTTCATCTGGCTACGAT 58.611 47.619 0.00 0.00 35.58 3.73
4989 20521 0.546747 ACTCCCTTGACGGATTGGGA 60.547 55.000 7.98 7.98 45.58 4.37
5077 20612 2.586792 GCAATGGAGGAGAGGCGT 59.413 61.111 0.00 0.00 0.00 5.68
5160 20721 1.007964 CGGAGCCTACAGAGCATCG 60.008 63.158 0.00 0.00 42.67 3.84
5362 20923 3.136809 TGTCTAGAAGAGGAGCCGATACT 59.863 47.826 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.