Multiple sequence alignment - TraesCS3D01G189300

Loading Multiple Alignment...

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 TraesCS3D01G189300 chr3D 100.000 4518 0 0 1 4518 177039600 177044117 0.000000e+00 8344.0
1 TraesCS3D01G189300 chr3D 98.406 251 4 0 4017 4267 177057090 177057340 4.150000e-120 442.0
2 TraesCS3D01G189300 chr3D 81.967 427 57 13 2019 2429 604538797 604538375 1.200000e-90 344.0
3 TraesCS3D01G189300 chr3D 83.871 217 30 5 2234 2450 87735195 87734984 7.660000e-48 202.0
4 TraesCS3D01G189300 chr3D 87.209 86 11 0 3591 3676 47963350 47963265 1.030000e-16 99.0
5 TraesCS3D01G189300 chr3B 97.187 1991 36 7 2035 4016 256195724 256197703 0.000000e+00 3349.0
6 TraesCS3D01G189300 chr3B 95.920 1152 25 3 910 2039 256188898 256190049 0.000000e+00 1847.0
7 TraesCS3D01G189300 chr3B 86.458 96 11 2 3588 3682 778392730 778392824 2.220000e-18 104.0
8 TraesCS3D01G189300 chr3A 95.277 1609 53 10 777 2372 217817273 217818871 0.000000e+00 2529.0
9 TraesCS3D01G189300 chr3A 94.368 1669 47 13 2367 4016 217818931 217820571 0.000000e+00 2518.0
10 TraesCS3D01G189300 chr3A 91.358 729 57 5 1 726 217816548 217817273 0.000000e+00 992.0
11 TraesCS3D01G189300 chr7B 91.279 516 25 6 4017 4518 290060039 290059530 0.000000e+00 686.0
12 TraesCS3D01G189300 chr7B 90.979 521 23 8 4016 4518 19673090 19672576 0.000000e+00 680.0
13 TraesCS3D01G189300 chr5D 89.423 520 30 16 4017 4518 528812968 528812456 2.290000e-177 632.0
14 TraesCS3D01G189300 chr4A 88.676 521 31 6 4013 4518 3355192 3355699 1.070000e-170 610.0
15 TraesCS3D01G189300 chr4A 87.743 514 26 5 4017 4518 600798751 600798263 2.360000e-157 566.0
16 TraesCS3D01G189300 chr4A 83.774 265 31 2 4262 4514 16034568 16034832 1.620000e-59 241.0
17 TraesCS3D01G189300 chr4A 82.836 268 34 5 4259 4514 615153048 615153315 3.520000e-56 230.0
18 TraesCS3D01G189300 chr4A 82.090 268 36 7 4259 4514 734925127 734924860 7.610000e-53 219.0
19 TraesCS3D01G189300 chr4A 88.235 85 10 0 3591 3675 570973600 570973516 8.000000e-18 102.0
20 TraesCS3D01G189300 chr5B 91.295 448 21 3 4085 4518 124303285 124302842 3.010000e-166 595.0
21 TraesCS3D01G189300 chr5B 93.750 256 10 3 4017 4270 124295899 124295648 3.300000e-101 379.0
22 TraesCS3D01G189300 chr5A 88.109 513 34 5 4020 4518 554820908 554821407 6.510000e-163 584.0
23 TraesCS3D01G189300 chr5A 87.767 515 36 5 4018 4518 554814393 554814894 1.090000e-160 577.0
24 TraesCS3D01G189300 chr4B 88.889 405 25 5 4128 4518 28065138 28064740 8.790000e-132 481.0
25 TraesCS3D01G189300 chr4B 85.177 452 52 10 1982 2429 9670291 9669851 2.480000e-122 449.0
26 TraesCS3D01G189300 chr4B 85.714 91 11 2 3586 3675 41531412 41531501 1.340000e-15 95.3
27 TraesCS3D01G189300 chr2D 75.963 857 188 16 4 852 2720697 2719851 4.180000e-115 425.0
28 TraesCS3D01G189300 chr2D 82.787 488 57 20 1980 2450 329946888 329946411 1.170000e-110 411.0
29 TraesCS3D01G189300 chr7D 83.830 470 50 17 1981 2450 5162976 5162533 1.500000e-114 424.0
30 TraesCS3D01G189300 chr7D 82.189 466 65 11 1979 2429 601899411 601899873 7.090000e-103 385.0
31 TraesCS3D01G189300 chr6B 94.922 256 7 2 4017 4270 79430474 79430223 3.280000e-106 396.0
32 TraesCS3D01G189300 chr6B 94.141 256 9 2 4017 4270 79549931 79549680 7.090000e-103 385.0
33 TraesCS3D01G189300 chr6B 93.750 256 10 2 4017 4270 79636290 79636039 3.300000e-101 379.0
34 TraesCS3D01G189300 chrUn 81.725 487 66 16 1980 2451 306222555 306222077 7.090000e-103 385.0
35 TraesCS3D01G189300 chr2A 92.337 261 11 6 4014 4269 762797977 762798233 3.320000e-96 363.0
36 TraesCS3D01G189300 chr2A 90.698 86 8 0 3590 3675 34328214 34328129 1.030000e-21 115.0
37 TraesCS3D01G189300 chr2A 88.235 85 10 0 3591 3675 591279992 591280076 8.000000e-18 102.0
38 TraesCS3D01G189300 chr1D 84.932 365 28 12 4014 4359 454044381 454044025 1.200000e-90 344.0
39 TraesCS3D01G189300 chr7A 80.882 272 35 10 4259 4516 48218141 48218409 9.910000e-47 198.0
40 TraesCS3D01G189300 chr6D 86.517 89 12 0 3587 3675 78352685 78352773 1.030000e-16 99.0


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 TraesCS3D01G189300 chr3D 177039600 177044117 4517 False 8344 8344 100.000000 1 4518 1 chr3D.!!$F1 4517
1 TraesCS3D01G189300 chr3B 256195724 256197703 1979 False 3349 3349 97.187000 2035 4016 1 chr3B.!!$F2 1981
2 TraesCS3D01G189300 chr3B 256188898 256190049 1151 False 1847 1847 95.920000 910 2039 1 chr3B.!!$F1 1129
3 TraesCS3D01G189300 chr3A 217816548 217820571 4023 False 2013 2529 93.667667 1 4016 3 chr3A.!!$F1 4015
4 TraesCS3D01G189300 chr7B 290059530 290060039 509 True 686 686 91.279000 4017 4518 1 chr7B.!!$R2 501
5 TraesCS3D01G189300 chr7B 19672576 19673090 514 True 680 680 90.979000 4016 4518 1 chr7B.!!$R1 502
6 TraesCS3D01G189300 chr5D 528812456 528812968 512 True 632 632 89.423000 4017 4518 1 chr5D.!!$R1 501
7 TraesCS3D01G189300 chr4A 3355192 3355699 507 False 610 610 88.676000 4013 4518 1 chr4A.!!$F1 505
8 TraesCS3D01G189300 chr5A 554814393 554814894 501 False 577 577 87.767000 4018 4518 1 chr5A.!!$F1 500
9 TraesCS3D01G189300 chr2D 2719851 2720697 846 True 425 425 75.963000 4 852 1 chr2D.!!$R1 848

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
369 373 0.738389 CGCCCACCCAAACATGATAC 59.262 55.000 0.00 0.0 0.00 2.24 F
730 735 1.102154 CCAATGGTCCAGCGCATTTA 58.898 50.000 11.47 0.0 0.00 1.40 F
956 976 1.134491 GTTATCCCCCGAGTGGAACAG 60.134 57.143 0.00 0.0 41.80 3.16 F
1678 1730 5.327091 GCACAATGCAGTTATGTTCAGTAG 58.673 41.667 0.00 0.0 44.26 2.57 F
3330 3457 3.575965 AATTGAATGACCCGCTGAAAC 57.424 42.857 0.00 0.0 0.00 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 1210 2.271497 CAGCAGGAGGGAGCAAGG 59.729 66.667 0.00 0.0 0.00 3.61 R
1678 1730 2.280797 TCAGACACCAGCAACGGC 60.281 61.111 0.00 0.0 41.61 5.68 R
1913 1966 5.163581 GCAAGTGAGCAATGTAATCCTCAAT 60.164 40.000 0.00 0.0 36.23 2.57 R
3446 3573 6.024552 TCTTTGTGTTTTGCTGAACTTCTT 57.975 33.333 4.78 0.0 0.00 2.52 R
4213 4355 0.179121 TGTAACACGCTATGAGGCCG 60.179 55.000 0.00 0.0 0.00 6.13 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
38 39 1.374758 GTCAAGCGACAGGTGAGGG 60.375 63.158 0.00 0.00 42.13 4.30
53 54 2.877168 GTGAGGGATTTAGAGCATGCTG 59.123 50.000 28.27 0.00 0.00 4.41
74 75 5.686841 GCTGTTATTCATTATTCGCATGCAA 59.313 36.000 19.57 11.51 0.00 4.08
89 90 3.740764 GCATGCAAAGTGTTTTTGGGAGA 60.741 43.478 14.21 0.00 0.00 3.71
96 97 1.028905 TGTTTTTGGGAGAAGGCACG 58.971 50.000 0.00 0.00 0.00 5.34
120 121 6.910433 CGTATGTTGCTGGACATAAAATTACC 59.090 38.462 8.89 0.00 42.39 2.85
135 136 1.493854 TTACCACGCCTCCACCCAAT 61.494 55.000 0.00 0.00 0.00 3.16
159 160 3.260884 ACTTGGGCGAGAGACATTTCTTA 59.739 43.478 0.00 0.00 45.40 2.10
188 189 7.309177 TCACATGTTTTCAAAAGAAGAACGAA 58.691 30.769 0.00 0.00 0.00 3.85
194 195 5.890424 TTCAAAAGAAGAACGAACCACTT 57.110 34.783 0.00 0.00 0.00 3.16
199 200 7.281324 TCAAAAGAAGAACGAACCACTTTCATA 59.719 33.333 0.00 0.00 33.24 2.15
256 260 4.594920 TGGACCCATGATAAGGAGAAGATC 59.405 45.833 0.00 0.00 0.00 2.75
316 320 3.071023 TGGCTCTTTTGGATATACCTCGG 59.929 47.826 0.00 0.00 39.86 4.63
317 321 3.071167 GGCTCTTTTGGATATACCTCGGT 59.929 47.826 0.00 0.00 39.86 4.69
369 373 0.738389 CGCCCACCCAAACATGATAC 59.262 55.000 0.00 0.00 0.00 2.24
416 420 3.706389 TTGATAGAGATGGGGGTCTGA 57.294 47.619 0.00 0.00 0.00 3.27
425 429 2.348998 GGGGTCTGAGTGGTGCAG 59.651 66.667 0.00 0.00 34.71 4.41
451 455 2.358737 GCCAGGTCCCACAACTCG 60.359 66.667 0.00 0.00 0.00 4.18
511 515 3.390639 CAGATCCCTTGATAGTGGAAGCT 59.609 47.826 0.00 0.00 0.00 3.74
512 516 3.390639 AGATCCCTTGATAGTGGAAGCTG 59.609 47.826 0.00 0.00 0.00 4.24
521 525 2.355010 AGTGGAAGCTGCTTCTGTTT 57.645 45.000 33.75 18.54 40.07 2.83
527 531 3.505293 GGAAGCTGCTTCTGTTTGAGAAT 59.495 43.478 33.75 1.83 40.06 2.40
612 616 3.442273 GTGGTGAACCTTTGAAACACTCA 59.558 43.478 0.37 0.00 36.82 3.41
730 735 1.102154 CCAATGGTCCAGCGCATTTA 58.898 50.000 11.47 0.00 0.00 1.40
744 749 4.291540 CGCATTTATGTGCCAAGTATGT 57.708 40.909 0.00 0.00 42.06 2.29
750 755 5.459536 TTATGTGCCAAGTATGTTTGCAA 57.540 34.783 0.00 0.00 0.00 4.08
751 756 4.540359 ATGTGCCAAGTATGTTTGCAAT 57.460 36.364 0.00 0.00 0.00 3.56
752 757 3.651206 TGTGCCAAGTATGTTTGCAATG 58.349 40.909 0.00 0.00 0.00 2.82
753 758 3.069300 TGTGCCAAGTATGTTTGCAATGT 59.931 39.130 0.00 0.00 0.00 2.71
758 763 5.335583 GCCAAGTATGTTTGCAATGTGTCTA 60.336 40.000 0.00 0.00 0.00 2.59
760 765 6.748658 CCAAGTATGTTTGCAATGTGTCTATG 59.251 38.462 0.00 0.00 0.00 2.23
763 768 4.764679 TGTTTGCAATGTGTCTATGTCC 57.235 40.909 0.00 0.00 0.00 4.02
796 801 2.218603 CTCGAGACTCCTAGCTTCCTC 58.781 57.143 6.58 0.00 0.00 3.71
798 803 1.673920 CGAGACTCCTAGCTTCCTCAC 59.326 57.143 0.00 0.00 0.00 3.51
860 865 8.999431 TCGTTAGAATAAAGCTCTCACAATTTT 58.001 29.630 0.00 0.00 0.00 1.82
864 869 7.311408 AGAATAAAGCTCTCACAATTTTCTGC 58.689 34.615 0.00 0.00 0.00 4.26
865 870 4.924305 AAAGCTCTCACAATTTTCTGCA 57.076 36.364 0.00 0.00 0.00 4.41
866 871 4.924305 AAGCTCTCACAATTTTCTGCAA 57.076 36.364 0.00 0.00 0.00 4.08
867 872 4.924305 AGCTCTCACAATTTTCTGCAAA 57.076 36.364 0.00 0.00 0.00 3.68
868 873 5.266733 AGCTCTCACAATTTTCTGCAAAA 57.733 34.783 0.00 0.00 35.92 2.44
869 874 5.663456 AGCTCTCACAATTTTCTGCAAAAA 58.337 33.333 8.54 8.54 35.10 1.94
949 969 2.757099 ACGCGTTATCCCCCGAGT 60.757 61.111 5.58 0.00 32.26 4.18
956 976 1.134491 GTTATCCCCCGAGTGGAACAG 60.134 57.143 0.00 0.00 41.80 3.16
1678 1730 5.327091 GCACAATGCAGTTATGTTCAGTAG 58.673 41.667 0.00 0.00 44.26 2.57
3278 3405 7.618019 ATTCCTCACAGTCCAGCTAAATATA 57.382 36.000 0.00 0.00 0.00 0.86
3330 3457 3.575965 AATTGAATGACCCGCTGAAAC 57.424 42.857 0.00 0.00 0.00 2.78
3380 3507 5.079406 CCGTAGTTCATTGATGTTTTGACG 58.921 41.667 0.00 0.00 0.00 4.35
3446 3573 1.557099 AGGACTCGTGCTACCATCAA 58.443 50.000 0.00 0.00 0.00 2.57
3721 3848 5.272283 AGTTCTTAACTCACTTCACGGAA 57.728 39.130 0.00 0.00 37.02 4.30
3805 3932 2.125350 GGCGGCTGAGAAGTGAGG 60.125 66.667 0.00 0.00 0.00 3.86
3859 3986 8.767085 CAATTTTGCACATCTTTGAAAGTATGT 58.233 29.630 13.49 13.49 32.94 2.29
3866 4002 7.653311 GCACATCTTTGAAAGTATGTCCTTTTT 59.347 33.333 15.28 0.00 34.87 1.94
3867 4003 8.971321 CACATCTTTGAAAGTATGTCCTTTTTG 58.029 33.333 15.28 4.82 34.87 2.44
3895 4031 6.578020 TGGAAACTTATATTTAGTCGCACG 57.422 37.500 0.00 0.00 0.00 5.34
3924 4060 9.206870 TCATATGCATGTGTGTATTACATAGTG 57.793 33.333 21.13 1.50 42.24 2.74
3925 4061 8.992073 CATATGCATGTGTGTATTACATAGTGT 58.008 33.333 14.79 0.00 42.24 3.55
3926 4062 6.660887 TGCATGTGTGTATTACATAGTGTG 57.339 37.500 0.00 0.00 42.24 3.82
3927 4063 5.064579 TGCATGTGTGTATTACATAGTGTGC 59.935 40.000 13.24 13.24 42.24 4.57
3928 4064 5.064579 GCATGTGTGTATTACATAGTGTGCA 59.935 40.000 14.36 0.00 42.24 4.57
3929 4065 6.238456 GCATGTGTGTATTACATAGTGTGCAT 60.238 38.462 14.36 4.77 42.24 3.96
3930 4066 7.042119 GCATGTGTGTATTACATAGTGTGCATA 60.042 37.037 14.36 0.00 42.24 3.14
3931 4067 8.490355 CATGTGTGTATTACATAGTGTGCATAG 58.510 37.037 0.00 0.00 42.24 2.23
3932 4068 7.552459 TGTGTGTATTACATAGTGTGCATAGT 58.448 34.615 0.00 0.00 42.24 2.12
3942 4078 3.067106 AGTGTGCATAGTGTACAACAGC 58.933 45.455 0.00 0.20 44.19 4.40
3988 4124 4.943705 AGAAATGAGAGCGGCTTAAAATGA 59.056 37.500 2.97 0.00 0.00 2.57
3991 4127 2.027192 TGAGAGCGGCTTAAAATGACCT 60.027 45.455 2.97 0.00 0.00 3.85
4194 4334 8.737175 CAAAAAGAATAAACCTCCTAACTACCC 58.263 37.037 0.00 0.00 0.00 3.69
4211 4353 2.435586 CTGCCGTGAGCCTCAAGG 60.436 66.667 20.76 20.76 46.68 3.61
4338 4503 3.205338 GTGGGCAAAGCTTTTGTGAAAT 58.795 40.909 9.53 0.00 0.00 2.17
4385 4550 4.884164 GGAATGAACCGAATCTCCAATTCT 59.116 41.667 0.00 0.00 0.00 2.40
4427 4592 7.704047 TCTCTCACAAAATGATAGTCAATCTCG 59.296 37.037 0.00 0.00 36.48 4.04
4429 4594 7.489435 TCTCACAAAATGATAGTCAATCTCGAC 59.511 37.037 0.00 0.00 36.48 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.877168 CAGCATGCTCTAAATCCCTCAC 59.123 50.000 19.68 0.00 0.00 3.51
53 54 7.220683 ACACTTTGCATGCGAATAATGAATAAC 59.779 33.333 20.61 0.00 0.00 1.89
74 75 2.430694 GTGCCTTCTCCCAAAAACACTT 59.569 45.455 0.00 0.00 0.00 3.16
89 90 0.036164 TCCAGCAACATACGTGCCTT 59.964 50.000 0.00 0.00 0.00 4.35
96 97 7.700656 GTGGTAATTTTATGTCCAGCAACATAC 59.299 37.037 6.21 0.00 40.81 2.39
120 121 2.040544 GTGATTGGGTGGAGGCGTG 61.041 63.158 0.00 0.00 0.00 5.34
135 136 0.976641 AATGTCTCTCGCCCAAGTGA 59.023 50.000 0.00 0.00 0.00 3.41
159 160 9.252962 GTTCTTCTTTTGAAAACATGTGATCAT 57.747 29.630 12.96 0.00 38.07 2.45
194 195 6.215227 TGCCATATGGACCATATCACTATGAA 59.785 38.462 26.47 4.50 35.18 2.57
199 200 5.503927 GAATGCCATATGGACCATATCACT 58.496 41.667 26.47 9.88 35.18 3.41
205 209 1.788295 TGGGAATGCCATATGGACCAT 59.212 47.619 26.47 16.51 37.39 3.55
225 229 4.019860 CCTTATCATGGGTCCATCGATTCT 60.020 45.833 15.04 2.21 33.90 2.40
256 260 4.627611 TCTTACAGACTTTATCGGGTCG 57.372 45.455 0.00 0.00 37.52 4.79
316 320 0.591170 ACAGCACCAACGCATGTTAC 59.409 50.000 0.00 0.00 36.28 2.50
317 321 0.871722 GACAGCACCAACGCATGTTA 59.128 50.000 0.00 0.00 36.28 2.41
389 393 6.726764 AGACCCCCATCTCTATCAATAGTTAC 59.273 42.308 0.00 0.00 0.00 2.50
400 404 1.062886 CCACTCAGACCCCCATCTCTA 60.063 57.143 0.00 0.00 0.00 2.43
416 420 2.367202 CGATACCCCCTGCACCACT 61.367 63.158 0.00 0.00 0.00 4.00
425 429 3.557290 GGACCTGGCGATACCCCC 61.557 72.222 0.00 0.00 37.83 5.40
451 455 3.809905 CTTACTCCAGGCTCCCATAAAC 58.190 50.000 0.00 0.00 0.00 2.01
511 515 7.750229 AATAACTCATTCTCAAACAGAAGCA 57.250 32.000 0.00 0.00 44.71 3.91
512 516 9.468532 AAAAATAACTCATTCTCAAACAGAAGC 57.531 29.630 0.00 0.00 44.71 3.86
521 525 6.016024 AGTGCTGCAAAAATAACTCATTCTCA 60.016 34.615 2.77 0.00 0.00 3.27
527 531 4.274705 TCGAAGTGCTGCAAAAATAACTCA 59.725 37.500 2.77 0.00 0.00 3.41
570 574 0.179100 CTCCACGCAATCGGTCTCAT 60.179 55.000 0.00 0.00 40.69 2.90
647 652 3.916035 TGGCTAGCTCTCCTATTTCTGA 58.084 45.455 15.72 0.00 0.00 3.27
730 735 4.247258 CATTGCAAACATACTTGGCACAT 58.753 39.130 1.71 0.00 39.30 3.21
739 744 6.258160 GGACATAGACACATTGCAAACATAC 58.742 40.000 1.71 0.00 0.00 2.39
740 745 5.064579 CGGACATAGACACATTGCAAACATA 59.935 40.000 1.71 0.00 0.00 2.29
744 749 3.669536 TCGGACATAGACACATTGCAAA 58.330 40.909 1.71 0.00 0.00 3.68
750 755 3.525537 CAGCTTTCGGACATAGACACAT 58.474 45.455 0.00 0.00 0.00 3.21
751 756 2.353704 CCAGCTTTCGGACATAGACACA 60.354 50.000 0.00 0.00 0.00 3.72
752 757 2.271800 CCAGCTTTCGGACATAGACAC 58.728 52.381 0.00 0.00 0.00 3.67
753 758 1.405526 GCCAGCTTTCGGACATAGACA 60.406 52.381 0.00 0.00 0.00 3.41
758 763 0.905357 AGTAGCCAGCTTTCGGACAT 59.095 50.000 0.00 0.00 0.00 3.06
760 765 0.802607 CGAGTAGCCAGCTTTCGGAC 60.803 60.000 14.70 0.96 32.31 4.79
763 768 0.452184 TCTCGAGTAGCCAGCTTTCG 59.548 55.000 13.13 15.79 35.07 3.46
839 844 7.040201 TGCAGAAAATTGTGAGAGCTTTATTCT 60.040 33.333 0.00 0.00 0.00 2.40
949 969 1.408969 GGAGGGTTTTTGCTGTTCCA 58.591 50.000 0.00 0.00 0.00 3.53
956 976 1.609501 GGGAGGGGAGGGTTTTTGC 60.610 63.158 0.00 0.00 0.00 3.68
1175 1210 2.271497 CAGCAGGAGGGAGCAAGG 59.729 66.667 0.00 0.00 0.00 3.61
1609 1657 3.211232 TCCTCCAATACCCCAGATAGGAA 59.789 47.826 0.00 0.00 41.22 3.36
1678 1730 2.280797 TCAGACACCAGCAACGGC 60.281 61.111 0.00 0.00 41.61 5.68
1913 1966 5.163581 GCAAGTGAGCAATGTAATCCTCAAT 60.164 40.000 0.00 0.00 36.23 2.57
3330 3457 8.081208 AGAAAATGCGTTATCATCTACTCATG 57.919 34.615 0.00 0.00 0.00 3.07
3446 3573 6.024552 TCTTTGTGTTTTGCTGAACTTCTT 57.975 33.333 4.78 0.00 0.00 2.52
3679 3806 8.974060 AGAACTTAAGATCTCTCTCGAGTTAT 57.026 34.615 13.13 1.93 37.00 1.89
3721 3848 6.902771 ACTCTACGGTAGATCAATAATGCT 57.097 37.500 17.63 0.00 33.66 3.79
3805 3932 9.571810 TCACATCAATTAAATCAGTACAATTGC 57.428 29.630 5.05 0.00 37.96 3.56
3859 3986 6.976934 ATAAGTTTCCAAGAGCAAAAAGGA 57.023 33.333 0.00 0.00 0.00 3.36
3866 4002 7.011109 GCGACTAAATATAAGTTTCCAAGAGCA 59.989 37.037 0.00 0.00 0.00 4.26
3867 4003 7.011109 TGCGACTAAATATAAGTTTCCAAGAGC 59.989 37.037 0.00 0.00 0.00 4.09
3890 4026 1.437573 CATGCATATGACGCGTGCG 60.438 57.895 20.70 13.39 41.61 5.34
3895 4031 4.472691 AATACACACATGCATATGACGC 57.527 40.909 12.92 0.00 37.73 5.19
3924 4060 4.749245 AAAGCTGTTGTACACTATGCAC 57.251 40.909 0.00 0.00 0.00 4.57
3925 4061 5.760743 TGTTAAAGCTGTTGTACACTATGCA 59.239 36.000 0.00 0.00 0.00 3.96
3926 4062 6.236017 TGTTAAAGCTGTTGTACACTATGC 57.764 37.500 0.00 0.00 0.00 3.14
3942 4078 7.050377 TCTCCTGGATAATTCAGCTGTTAAAG 58.950 38.462 14.67 5.88 0.00 1.85
3999 4135 4.793071 TCTACACATTTGATGTTTTGGCG 58.207 39.130 0.00 0.00 42.70 5.69
4001 4137 7.209475 AGGTTTCTACACATTTGATGTTTTGG 58.791 34.615 0.00 0.00 42.70 3.28
4064 4201 8.088365 CGACTCCCACAATCAATATATACTCAA 58.912 37.037 0.00 0.00 0.00 3.02
4194 4334 2.435586 CCTTGAGGCTCACGGCAG 60.436 66.667 24.90 15.76 44.01 4.85
4211 4353 2.638330 TAACACGCTATGAGGCCGGC 62.638 60.000 21.18 21.18 0.00 6.13
4212 4354 0.874607 GTAACACGCTATGAGGCCGG 60.875 60.000 0.00 0.00 0.00 6.13
4213 4355 0.179121 TGTAACACGCTATGAGGCCG 60.179 55.000 0.00 0.00 0.00 6.13
4214 4356 2.018542 TTGTAACACGCTATGAGGCC 57.981 50.000 0.00 0.00 0.00 5.19
4215 4357 2.351726 CCTTTGTAACACGCTATGAGGC 59.648 50.000 0.00 0.00 0.00 4.70
4216 4358 2.936498 CCCTTTGTAACACGCTATGAGG 59.064 50.000 0.00 0.00 0.00 3.86
4217 4359 3.617263 GTCCCTTTGTAACACGCTATGAG 59.383 47.826 0.00 0.00 0.00 2.90
4218 4360 3.007074 TGTCCCTTTGTAACACGCTATGA 59.993 43.478 0.00 0.00 0.00 2.15
4219 4361 3.124636 GTGTCCCTTTGTAACACGCTATG 59.875 47.826 0.00 0.00 34.55 2.23
4220 4362 3.332034 GTGTCCCTTTGTAACACGCTAT 58.668 45.455 0.00 0.00 34.55 2.97
4221 4363 2.758009 GTGTCCCTTTGTAACACGCTA 58.242 47.619 0.00 0.00 34.55 4.26
4222 4364 1.589803 GTGTCCCTTTGTAACACGCT 58.410 50.000 0.00 0.00 34.55 5.07
4338 4503 2.886523 CAAAGGACCAAGTTGCAGATGA 59.113 45.455 0.00 0.00 0.00 2.92
4385 4550 3.181445 TGAGAGAAAGGGTTGCTAGCAAA 60.181 43.478 30.83 13.14 37.70 3.68
4427 4592 6.476380 TCTTTCATGCAAGAACAAAACATGTC 59.524 34.615 5.25 0.00 42.99 3.06
4429 4594 6.256104 TGTCTTTCATGCAAGAACAAAACATG 59.744 34.615 9.46 0.00 39.53 3.21


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

AutoCloner maintained by Alex Coulton.