Multiple sequence alignment - TraesCS3D01G272700

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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 TraesCS3D01G272700 chr3D 100.000 8424 0 0 1 8424 378228804 378237227 0.000000e+00 15557.0
1 TraesCS3D01G272700 chr3D 90.323 186 16 2 2804 2987 71517844 71517659 8.450000e-60 243.0
2 TraesCS3D01G272700 chr3A 97.446 4111 65 15 2536 6623 502384266 502388359 0.000000e+00 6974.0
3 TraesCS3D01G272700 chr3A 95.950 1506 44 5 1163 2651 502382761 502384266 0.000000e+00 2427.0
4 TraesCS3D01G272700 chr3A 91.723 1776 103 21 6665 8424 502388360 502390107 0.000000e+00 2425.0
5 TraesCS3D01G272700 chr3A 93.196 779 38 4 1 765 502381461 502382238 0.000000e+00 1131.0
6 TraesCS3D01G272700 chr3A 91.489 188 14 2 2804 2989 83748187 83748000 3.020000e-64 257.0
7 TraesCS3D01G272700 chr3A 93.529 170 11 0 2804 2973 34532615 34532446 3.900000e-63 254.0
8 TraesCS3D01G272700 chr3A 94.410 161 2 3 830 989 502382258 502382412 3.040000e-59 241.0
9 TraesCS3D01G272700 chr3B 95.860 3140 89 21 2461 5570 493118507 493121635 0.000000e+00 5040.0
10 TraesCS3D01G272700 chr3B 94.620 2881 99 23 5555 8424 493121866 493124701 0.000000e+00 4410.0
11 TraesCS3D01G272700 chr3B 94.878 1191 34 12 833 2013 493117342 493118515 0.000000e+00 1836.0
12 TraesCS3D01G272700 chr3B 85.014 347 45 3 197 537 493116664 493117009 6.260000e-91 346.0
13 TraesCS3D01G272700 chr3B 93.370 181 12 0 21 201 493088220 493088400 1.390000e-67 268.0
14 TraesCS3D01G272700 chr3B 93.529 170 11 0 2804 2973 42630984 42630815 3.900000e-63 254.0
15 TraesCS3D01G272700 chr3B 89.922 129 4 2 554 681 493117070 493117190 3.150000e-34 158.0
16 TraesCS3D01G272700 chr6D 92.982 171 12 0 2801 2971 304099283 304099453 5.050000e-62 250.0
17 TraesCS3D01G272700 chr1D 92.941 170 12 0 2803 2972 175820003 175819834 1.820000e-61 248.0
18 TraesCS3D01G272700 chr1D 80.435 92 15 3 3620 3709 376065750 376065660 5.460000e-07 67.6
19 TraesCS3D01G272700 chr7B 92.308 169 13 0 2804 2972 152467773 152467605 3.040000e-59 241.0
20 TraesCS3D01G272700 chr5B 83.544 79 13 0 8261 8339 689366721 689366799 3.260000e-09 75.0
21 TraesCS3D01G272700 chr5A 100.000 29 0 0 510 538 674826786 674826758 4.000000e-03 54.7
22 TraesCS3D01G272700 chr5A 100.000 29 0 0 510 538 674867545 674867517 4.000000e-03 54.7
23 TraesCS3D01G272700 chr5A 100.000 29 0 0 510 538 674908764 674908736 4.000000e-03 54.7
24 TraesCS3D01G272700 chr2B 100.000 29 0 0 510 538 555328488 555328516 4.000000e-03 54.7
25 TraesCS3D01G272700 chr2A 100.000 29 0 0 510 538 762821752 762821724 4.000000e-03 54.7
26 TraesCS3D01G272700 chr1B 100.000 29 0 0 510 538 679550305 679550277 4.000000e-03 54.7


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 TraesCS3D01G272700 chr3D 378228804 378237227 8423 False 15557.0 15557 100.0000 1 8424 1 chr3D.!!$F1 8423
1 TraesCS3D01G272700 chr3A 502381461 502390107 8646 False 2639.6 6974 94.5450 1 8424 5 chr3A.!!$F1 8423
2 TraesCS3D01G272700 chr3B 493116664 493124701 8037 False 2358.0 5040 92.0588 197 8424 5 chr3B.!!$F2 8227

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
782 862 0.104409 AACACCACCTTCCCCTCTCT 60.104 55.000 0.00 0.0 0.00 3.10 F
783 863 0.104409 ACACCACCTTCCCCTCTCTT 60.104 55.000 0.00 0.0 0.00 2.85 F
908 991 0.109039 GCTCTCACGAACCCTCTCAC 60.109 60.000 0.00 0.0 0.00 3.51 F
1188 1446 0.337082 TGACCTCCATCTTACCCCGA 59.663 55.000 0.00 0.0 0.00 5.14 F
2334 2609 1.088306 CTCGTCAAGTCGGACTAGCT 58.912 55.000 11.71 0.0 35.63 3.32 F
3156 3557 0.038159 GAGAAGGTCGGTCTGTGGTG 60.038 60.000 0.00 0.0 0.00 4.17 F
4618 5031 1.202879 CCTACTGGGTGCCTTGTTTGA 60.203 52.381 0.00 0.0 0.00 2.69 F
5494 5918 1.689273 TGGTGTGTGGGTAATTTTGGC 59.311 47.619 0.00 0.0 0.00 4.52 F
6174 6848 0.694771 AGAGCTTGGCCTGACATTCA 59.305 50.000 3.32 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 2617 1.192534 GAGGAAGCGTTGAGAAACGTG 59.807 52.381 12.05 0.00 46.91 4.49 R
2497 2772 2.166459 CCTGAAACACGATCCAGCTCTA 59.834 50.000 0.00 0.00 0.00 2.43 R
2753 3143 2.382882 TGTTGGAGGCAATTGTTCACA 58.617 42.857 7.40 4.64 0.00 3.58 R
3007 3408 4.263331 CCGGGGCCTACATCAATAAAGTAT 60.263 45.833 0.84 0.00 0.00 2.12 R
3203 3604 4.808895 GTGAACCATTCCCAACTTTTTCAC 59.191 41.667 0.00 0.00 36.05 3.18 R
4630 5044 0.249238 GCTGGCGATAGAGGACTGTG 60.249 60.000 0.00 0.00 39.76 3.66 R
5660 6329 0.617820 ACCCGAGTAAGGTCCATGCT 60.618 55.000 0.00 0.00 28.99 3.79 R
7308 7989 0.040425 AAACAACGGTTCGCATCAGC 60.040 50.000 0.00 0.00 35.82 4.26 R
7680 8363 0.030369 GACGTGTATAGGCCCGTCTG 59.970 60.000 18.89 0.00 44.55 3.51 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
47 48 4.689062 TCCCCTCCACTGATATATCTTCC 58.311 47.826 13.79 0.00 0.00 3.46
76 77 1.587547 GACTACCGTACCGACTAGGG 58.412 60.000 0.00 0.00 46.96 3.53
88 89 1.271163 CGACTAGGGTTTCTTGGGCAA 60.271 52.381 0.00 0.00 0.00 4.52
140 141 2.303175 TGCTCCTGGTTTGGTTGTTAC 58.697 47.619 0.00 0.00 0.00 2.50
172 173 8.479313 TCTAGTCTTGTTATGTACTGCATTTG 57.521 34.615 0.00 0.00 38.94 2.32
184 185 4.669206 ACTGCATTTGTGAAAATGGTGA 57.331 36.364 11.88 0.00 39.79 4.02
205 206 6.407299 GGTGATTGTGATTTTGAATATGGGCT 60.407 38.462 0.00 0.00 0.00 5.19
237 238 5.448654 TGAAGATAACCTGGATGGAAATGG 58.551 41.667 0.00 0.00 39.71 3.16
301 302 2.710377 TCGTGCAGATAAAGCCAATGT 58.290 42.857 0.00 0.00 0.00 2.71
303 304 3.871006 TCGTGCAGATAAAGCCAATGTAG 59.129 43.478 0.00 0.00 0.00 2.74
313 314 1.133976 AGCCAATGTAGGATGGACAGC 60.134 52.381 0.00 0.00 39.12 4.40
360 364 3.334691 ACGTGAATGTTGATGGTAGGTG 58.665 45.455 0.00 0.00 0.00 4.00
419 423 2.028112 TGTTGTGTGCATCTAGGACTCC 60.028 50.000 0.00 0.00 39.64 3.85
422 426 1.827969 GTGTGCATCTAGGACTCCTGT 59.172 52.381 7.98 0.00 39.64 4.00
492 501 0.612744 TCGTGTTGGAGATGATGCCA 59.387 50.000 0.00 0.00 0.00 4.92
505 514 6.239430 GGAGATGATGCCAACTCAGTATCTTA 60.239 42.308 0.00 0.00 42.09 2.10
506 515 6.757237 AGATGATGCCAACTCAGTATCTTAG 58.243 40.000 0.00 0.00 0.00 2.18
512 521 4.688021 CCAACTCAGTATCTTAGAGGTGC 58.312 47.826 0.00 0.00 43.87 5.01
524 533 0.175760 AGAGGTGCGTGCGTTCATAT 59.824 50.000 0.00 0.00 0.00 1.78
525 534 0.301687 GAGGTGCGTGCGTTCATATG 59.698 55.000 0.00 0.00 0.00 1.78
584 638 1.177895 TCGTGTTGCCATGTTGCCAT 61.178 50.000 0.00 0.00 0.00 4.40
715 795 0.636101 CCCTCAATTCCCATTCCCCA 59.364 55.000 0.00 0.00 0.00 4.96
779 859 2.082140 AAAAACACCACCTTCCCCTC 57.918 50.000 0.00 0.00 0.00 4.30
780 860 1.231963 AAAACACCACCTTCCCCTCT 58.768 50.000 0.00 0.00 0.00 3.69
781 861 0.771755 AAACACCACCTTCCCCTCTC 59.228 55.000 0.00 0.00 0.00 3.20
782 862 0.104409 AACACCACCTTCCCCTCTCT 60.104 55.000 0.00 0.00 0.00 3.10
783 863 0.104409 ACACCACCTTCCCCTCTCTT 60.104 55.000 0.00 0.00 0.00 2.85
784 864 1.068121 CACCACCTTCCCCTCTCTTT 58.932 55.000 0.00 0.00 0.00 2.52
785 865 1.425448 CACCACCTTCCCCTCTCTTTT 59.575 52.381 0.00 0.00 0.00 2.27
786 866 2.144450 ACCACCTTCCCCTCTCTTTTT 58.856 47.619 0.00 0.00 0.00 1.94
811 891 2.882137 TGAGACAAACGTTCCCCATTTC 59.118 45.455 0.00 0.00 0.00 2.17
813 893 3.562182 AGACAAACGTTCCCCATTTCTT 58.438 40.909 0.00 0.00 0.00 2.52
816 896 5.092554 ACAAACGTTCCCCATTTCTTTTT 57.907 34.783 0.00 0.00 0.00 1.94
903 986 3.382832 CCCGCTCTCACGAACCCT 61.383 66.667 0.00 0.00 34.06 4.34
904 987 2.182030 CCGCTCTCACGAACCCTC 59.818 66.667 0.00 0.00 34.06 4.30
905 988 2.344203 CCGCTCTCACGAACCCTCT 61.344 63.158 0.00 0.00 34.06 3.69
906 989 1.137825 CGCTCTCACGAACCCTCTC 59.862 63.158 0.00 0.00 34.06 3.20
907 990 1.587043 CGCTCTCACGAACCCTCTCA 61.587 60.000 0.00 0.00 34.06 3.27
908 991 0.109039 GCTCTCACGAACCCTCTCAC 60.109 60.000 0.00 0.00 0.00 3.51
1036 1119 3.319198 GCGGGAGGGTGTCTGGAA 61.319 66.667 0.00 0.00 0.00 3.53
1188 1446 0.337082 TGACCTCCATCTTACCCCGA 59.663 55.000 0.00 0.00 0.00 5.14
1292 1563 2.186903 CCCGTGGGAAGGATGACG 59.813 66.667 0.00 0.00 37.50 4.35
1385 1656 2.888863 CTCTCCTCTGCACCCGAC 59.111 66.667 0.00 0.00 0.00 4.79
1386 1657 3.057547 CTCTCCTCTGCACCCGACG 62.058 68.421 0.00 0.00 0.00 5.12
1387 1658 3.062466 CTCCTCTGCACCCGACGA 61.062 66.667 0.00 0.00 0.00 4.20
1629 1902 3.308323 GGTTTCGTGTACAAAACGGTGTA 59.692 43.478 14.11 0.00 41.34 2.90
1649 1922 6.644592 GGTGTATATTTTGTTGCTTTTGAGCA 59.355 34.615 0.00 0.00 43.81 4.26
1712 1986 4.230657 CTGTGACTCGCAGTATATTAGGC 58.769 47.826 10.95 0.00 37.23 3.93
1944 2219 6.097554 ACAGTAACTCCTGAATCTGGTATGAG 59.902 42.308 6.07 0.00 36.30 2.90
2023 2298 4.021192 TCATGACAAGGGAGAAATTTTGGC 60.021 41.667 0.00 0.00 0.00 4.52
2053 2328 6.928492 CCAACCACATATTTGTTAAAGCAAGT 59.072 34.615 0.00 0.00 32.34 3.16
2214 2489 1.270625 GGATTCCTTGTGTCACGACCA 60.271 52.381 0.00 0.00 0.00 4.02
2237 2512 7.394359 ACCACATTTCATAGCATTATATGTCCC 59.606 37.037 0.00 0.00 35.16 4.46
2334 2609 1.088306 CTCGTCAAGTCGGACTAGCT 58.912 55.000 11.71 0.00 35.63 3.32
2342 2617 4.335874 TCAAGTCGGACTAGCTTATGACTC 59.664 45.833 11.71 0.00 35.77 3.36
2353 2628 4.883083 AGCTTATGACTCACGTTTCTCAA 58.117 39.130 0.00 0.00 0.00 3.02
2745 3135 6.116126 AGTCCATCCAAATCAAGTACTTAGC 58.884 40.000 8.04 0.00 0.00 3.09
2753 3143 6.039047 CCAAATCAAGTACTTAGCAGATGCAT 59.961 38.462 8.04 0.00 45.16 3.96
3058 3459 8.660373 ACATTTCTATCGACTGAAAAAGCTTAG 58.340 33.333 15.50 0.00 36.06 2.18
3088 3489 3.720002 TCTTCCCCTACAGAAAGTGGTTT 59.280 43.478 0.00 0.00 0.00 3.27
3156 3557 0.038159 GAGAAGGTCGGTCTGTGGTG 60.038 60.000 0.00 0.00 0.00 4.17
3203 3604 3.397482 CTTCTGGTGTTGTTCAGGAGAG 58.603 50.000 0.00 0.00 38.56 3.20
3531 3932 5.780958 AGAAAAAGGTACCTAATGAGCCT 57.219 39.130 16.67 3.69 0.00 4.58
3924 4331 6.963242 CACAAGTCATTAGTCATGTAATGTGC 59.037 38.462 13.05 9.12 46.80 4.57
4198 4611 7.732593 AGAAATATCTAGTGAAGATGTAGGCCT 59.267 37.037 11.78 11.78 44.95 5.19
4618 5031 1.202879 CCTACTGGGTGCCTTGTTTGA 60.203 52.381 0.00 0.00 0.00 2.69
4619 5032 2.555227 CCTACTGGGTGCCTTGTTTGAT 60.555 50.000 0.00 0.00 0.00 2.57
4621 5034 3.237268 ACTGGGTGCCTTGTTTGATAA 57.763 42.857 0.00 0.00 0.00 1.75
4624 5037 3.571590 TGGGTGCCTTGTTTGATAAAGT 58.428 40.909 0.00 0.00 0.00 2.66
4625 5038 4.730966 TGGGTGCCTTGTTTGATAAAGTA 58.269 39.130 0.00 0.00 0.00 2.24
4630 5044 6.090763 GGTGCCTTGTTTGATAAAGTAAATGC 59.909 38.462 0.00 0.00 0.00 3.56
4927 5341 8.479313 AAAGGTCTGAATCAAAGAACAAAAAC 57.521 30.769 0.00 0.00 33.56 2.43
5032 5446 6.070824 ACCAAAAGACCAAAACAAACTCAGAT 60.071 34.615 0.00 0.00 0.00 2.90
5494 5918 1.689273 TGGTGTGTGGGTAATTTTGGC 59.311 47.619 0.00 0.00 0.00 4.52
5495 5919 1.967779 GGTGTGTGGGTAATTTTGGCT 59.032 47.619 0.00 0.00 0.00 4.75
5571 6240 5.598830 TCAGTTTGGGGTTGTTGCTTTATTA 59.401 36.000 0.00 0.00 0.00 0.98
5605 6274 9.926751 CATATTTTCACTAAGTAATCAGTGCAG 57.073 33.333 0.00 0.00 41.58 4.41
5660 6329 7.340232 AGCTAATCCTGTTCTTCAATAATGCAA 59.660 33.333 0.00 0.00 0.00 4.08
5857 6526 3.240134 GAAGAGCACGAGGTGGGCA 62.240 63.158 0.00 0.00 33.64 5.36
5953 6622 2.124507 AATGGCACCAGTAGCACGGT 62.125 55.000 0.00 0.00 35.27 4.83
5994 6668 9.615660 ATGGTCCTATTGTTAATCAGGTATAGA 57.384 33.333 0.00 0.00 0.00 1.98
5995 6669 9.442062 TGGTCCTATTGTTAATCAGGTATAGAA 57.558 33.333 0.00 0.00 0.00 2.10
6174 6848 0.694771 AGAGCTTGGCCTGACATTCA 59.305 50.000 3.32 0.00 0.00 2.57
6208 6882 3.228188 TGCCAGTTTGTCCTTTCATCT 57.772 42.857 0.00 0.00 0.00 2.90
6257 6932 4.661993 TTTATCAACGTTAGCTGCACTG 57.338 40.909 0.00 0.00 0.00 3.66
6444 7122 5.491070 CATACAACAGAGAGAACCCAATGA 58.509 41.667 0.00 0.00 0.00 2.57
6449 7127 3.007398 ACAGAGAGAACCCAATGACAGTC 59.993 47.826 0.00 0.00 0.00 3.51
6629 7310 3.118261 TGCCAACTCAAGAGAAGTTGACT 60.118 43.478 15.57 0.00 43.81 3.41
6666 7347 0.961753 GGAGGAAACCAGCAAAGTGG 59.038 55.000 0.00 0.00 44.01 4.00
6729 7410 2.737180 CTGTGAGCAGACCGTGGT 59.263 61.111 0.00 0.00 45.28 4.16
7005 7686 4.142381 ACCTTCAGTGCAAGTCAAGTTTTC 60.142 41.667 0.00 0.00 0.00 2.29
7042 7723 3.823304 AGTTTGAACTCTGGATTGCTTCC 59.177 43.478 0.00 0.00 38.93 3.46
7152 7833 6.740110 TGTTTCTCTATAGAGCCTCGAATTC 58.260 40.000 22.81 9.82 41.80 2.17
7308 7989 2.237143 TGGGTAGCCATGTTGAGAGAAG 59.763 50.000 10.27 0.00 0.00 2.85
7360 8041 7.036996 TCTTGTAAACATGCTGTGAATTGAA 57.963 32.000 0.00 0.00 0.00 2.69
7412 8095 7.636363 GTTTAATGAAACGAGATCAATGACG 57.364 36.000 0.00 0.00 35.90 4.35
7492 8175 6.539649 TCTTGGTTCTCGTTCTGTTTTATG 57.460 37.500 0.00 0.00 0.00 1.90
7564 8247 2.408565 TCTTTCTTCCTGTGTCCCAGT 58.591 47.619 0.00 0.00 39.74 4.00
7680 8363 2.239907 ACCTAGTTGGGCTCCTCAAATC 59.760 50.000 0.00 0.00 41.11 2.17
7681 8364 2.239654 CCTAGTTGGGCTCCTCAAATCA 59.760 50.000 0.00 0.00 0.00 2.57
7682 8365 2.503895 AGTTGGGCTCCTCAAATCAG 57.496 50.000 0.00 0.00 0.00 2.90
7683 8366 1.988107 AGTTGGGCTCCTCAAATCAGA 59.012 47.619 0.00 0.00 0.00 3.27
7687 8370 0.462759 GGCTCCTCAAATCAGACGGG 60.463 60.000 0.00 0.00 0.00 5.28
7796 8497 1.536284 GCCTCCGTTTCCTACATCTCG 60.536 57.143 0.00 0.00 0.00 4.04
7821 8522 3.636231 CCGTCCTCCACCCTTGCA 61.636 66.667 0.00 0.00 0.00 4.08
7822 8523 2.358737 CGTCCTCCACCCTTGCAC 60.359 66.667 0.00 0.00 0.00 4.57
7864 8565 1.349026 CCATCCATCGCCCTAGATGTT 59.651 52.381 6.27 0.00 44.76 2.71
7865 8566 2.420642 CATCCATCGCCCTAGATGTTG 58.579 52.381 6.27 1.01 44.76 3.33
7931 8632 2.027745 ACGTTGTCATGGAGCTCTTGAT 60.028 45.455 14.64 0.53 33.08 2.57
7941 8642 1.446099 GCTCTTGATCGTGGCGACA 60.446 57.895 0.00 0.00 39.18 4.35
7989 8690 2.694760 GGAGCGGCAAAGGAAGCAG 61.695 63.158 1.45 0.00 0.00 4.24
8058 8759 2.028130 GATGTCGAGGAGGATGTGTCT 58.972 52.381 0.00 0.00 0.00 3.41
8154 8855 1.964223 ACCGACAATGATCCGATAGCT 59.036 47.619 0.00 0.00 0.00 3.32
8158 8859 4.240888 CGACAATGATCCGATAGCTGAAT 58.759 43.478 0.00 0.00 0.00 2.57
8164 8865 0.249868 TCCGATAGCTGAATTGGGCG 60.250 55.000 0.00 0.00 31.98 6.13
8165 8866 0.249868 CCGATAGCTGAATTGGGCGA 60.250 55.000 0.00 0.00 0.00 5.54
8168 8869 2.158449 CGATAGCTGAATTGGGCGATTC 59.842 50.000 0.00 5.55 36.73 2.52
8175 8876 1.455383 AATTGGGCGATTCCGGATGC 61.455 55.000 4.15 10.37 36.06 3.91
8217 8918 2.502080 CGACGAGGTGTGCGACTC 60.502 66.667 0.00 0.00 0.00 3.36
8236 8937 2.941616 GCCGCAATTCCAAAGGGCA 61.942 57.895 0.00 0.00 40.24 5.36
8314 9016 3.451178 GTCCTAGCAGGAGATGGTACAAA 59.549 47.826 5.28 0.00 46.90 2.83
8339 9041 9.860898 AATTTTGCTCTATTTTGTATCACTTCC 57.139 29.630 0.00 0.00 0.00 3.46
8417 9121 6.449635 TTTCGAATCATGGTCATTTTAGGG 57.550 37.500 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.013006 TGGAGGGGAGAGTTAGGGTTA 58.987 52.381 0.00 0.00 0.00 2.85
47 48 1.086067 TACGGTAGTCGGCGACAGAG 61.086 60.000 37.71 26.86 44.45 3.35
88 89 4.349930 ACTTGTGGTAATCCTGGTACTTGT 59.650 41.667 0.00 0.00 34.23 3.16
140 141 4.849883 ACATAACAAGACTAGAGCGATCG 58.150 43.478 11.69 11.69 0.00 3.69
172 173 7.712264 TCAAAATCACAATCACCATTTTCAC 57.288 32.000 0.00 0.00 0.00 3.18
184 185 6.795144 TCAGCCCATATTCAAAATCACAAT 57.205 33.333 0.00 0.00 0.00 2.71
205 206 6.806668 TCCAGGTTATCTTCATACACATCA 57.193 37.500 0.00 0.00 0.00 3.07
237 238 6.091713 GGCATTCAAAGGATGCAATATTATGC 59.908 38.462 11.99 0.00 46.58 3.14
301 302 3.005897 GCTTATTCTCGCTGTCCATCCTA 59.994 47.826 0.00 0.00 0.00 2.94
303 304 2.139118 GCTTATTCTCGCTGTCCATCC 58.861 52.381 0.00 0.00 0.00 3.51
419 423 7.099764 ACACTTATGATCAGGACTACAAACAG 58.900 38.462 0.09 0.00 0.00 3.16
422 426 7.450074 ACAACACTTATGATCAGGACTACAAA 58.550 34.615 0.09 0.00 0.00 2.83
492 501 4.017808 ACGCACCTCTAAGATACTGAGTT 58.982 43.478 0.00 0.00 0.00 3.01
505 514 0.175760 ATATGAACGCACGCACCTCT 59.824 50.000 0.00 0.00 0.00 3.69
506 515 0.301687 CATATGAACGCACGCACCTC 59.698 55.000 0.00 0.00 0.00 3.85
512 521 2.219445 CACTCATCCATATGAACGCACG 59.781 50.000 3.65 0.00 41.57 5.34
524 533 1.284313 TGCCCACATACACTCATCCA 58.716 50.000 0.00 0.00 0.00 3.41
525 534 2.498167 GATGCCCACATACACTCATCC 58.502 52.381 0.00 0.00 36.35 3.51
617 671 1.482182 ACACATTATGCTCTCCGCTCA 59.518 47.619 0.00 0.00 40.11 4.26
730 810 4.678574 CGAATAGGGGAACGTGATGTTGTA 60.679 45.833 0.00 0.00 42.09 2.41
737 817 0.609151 TTGCGAATAGGGGAACGTGA 59.391 50.000 0.00 0.00 0.00 4.35
765 845 1.068121 AAAGAGAGGGGAAGGTGGTG 58.932 55.000 0.00 0.00 0.00 4.17
767 847 2.980246 AAAAAGAGAGGGGAAGGTGG 57.020 50.000 0.00 0.00 0.00 4.61
786 866 3.090037 TGGGGAACGTTTGTCTCAAAAA 58.910 40.909 0.46 0.00 0.00 1.94
787 867 2.724454 TGGGGAACGTTTGTCTCAAAA 58.276 42.857 0.46 0.00 0.00 2.44
788 868 2.421751 TGGGGAACGTTTGTCTCAAA 57.578 45.000 0.46 0.00 0.00 2.69
789 869 2.649531 ATGGGGAACGTTTGTCTCAA 57.350 45.000 0.46 0.00 0.00 3.02
790 870 2.649531 AATGGGGAACGTTTGTCTCA 57.350 45.000 0.46 2.08 0.00 3.27
791 871 3.146847 AGAAATGGGGAACGTTTGTCTC 58.853 45.455 0.46 0.00 38.38 3.36
792 872 3.223674 AGAAATGGGGAACGTTTGTCT 57.776 42.857 0.46 0.00 38.38 3.41
793 873 4.316205 AAAGAAATGGGGAACGTTTGTC 57.684 40.909 0.46 0.00 38.38 3.18
822 902 2.092914 AGAAATGGGGAACGTGATCTCC 60.093 50.000 0.00 0.00 40.67 3.71
825 905 4.514401 AGTTAGAAATGGGGAACGTGATC 58.486 43.478 0.00 0.00 0.00 2.92
827 907 3.307199 GGAGTTAGAAATGGGGAACGTGA 60.307 47.826 0.00 0.00 0.00 4.35
831 911 3.353557 GTGGGAGTTAGAAATGGGGAAC 58.646 50.000 0.00 0.00 0.00 3.62
902 985 3.609703 CGGGAGGGTGAGTGAGAG 58.390 66.667 0.00 0.00 0.00 3.20
1027 1110 1.129437 GATTTCGCAGCTTCCAGACAC 59.871 52.381 0.00 0.00 0.00 3.67
1036 1119 0.177604 CTCAGGGAGATTTCGCAGCT 59.822 55.000 3.07 0.00 38.65 4.24
1188 1446 3.470888 CCCGGCGATGGAGAAGGT 61.471 66.667 9.30 0.00 0.00 3.50
1649 1922 9.353999 GTTATAAATCCGCAATGAAGAAAACTT 57.646 29.630 0.00 0.00 0.00 2.66
1718 1992 7.869429 CCACCTCCTTTCATGCAAATTATATTC 59.131 37.037 0.00 0.00 0.00 1.75
1725 1999 2.564062 CACCACCTCCTTTCATGCAAAT 59.436 45.455 0.00 0.00 0.00 2.32
1732 2006 2.409064 TCCTACACCACCTCCTTTCA 57.591 50.000 0.00 0.00 0.00 2.69
1944 2219 8.479313 TGCATATTATTTCATATCTCACGGTC 57.521 34.615 0.00 0.00 0.00 4.79
1991 2266 5.573219 TCTCCCTTGTCATGATTGTTCATT 58.427 37.500 0.00 0.00 40.70 2.57
2023 2298 3.848272 ACAAATATGTGGTTGGCTTCG 57.152 42.857 0.00 0.00 38.69 3.79
2031 2306 6.493458 AGGACTTGCTTTAACAAATATGTGGT 59.507 34.615 0.00 0.00 40.46 4.16
2032 2307 6.924111 AGGACTTGCTTTAACAAATATGTGG 58.076 36.000 0.00 0.00 40.46 4.17
2053 2328 1.434188 TCCCTTGCAACTCTGAAGGA 58.566 50.000 0.00 0.00 38.93 3.36
2214 2489 6.891908 GGGGGACATATAATGCTATGAAATGT 59.108 38.462 0.00 0.00 34.01 2.71
2237 2512 1.656818 GATGGCGTGTGGATTGTGGG 61.657 60.000 0.00 0.00 0.00 4.61
2317 2592 3.064958 TCATAAGCTAGTCCGACTTGACG 59.935 47.826 13.37 0.00 40.26 4.35
2342 2617 1.192534 GAGGAAGCGTTGAGAAACGTG 59.807 52.381 12.05 0.00 46.91 4.49
2369 2644 9.705103 ACCTTTTAGACCTAATTTTATAACCCC 57.295 33.333 0.00 0.00 0.00 4.95
2402 2677 7.268586 TGTACAAACATTTGCAAACTTACCAT 58.731 30.769 15.41 0.55 41.79 3.55
2497 2772 2.166459 CCTGAAACACGATCCAGCTCTA 59.834 50.000 0.00 0.00 0.00 2.43
2745 3135 2.927477 GGCAATTGTTCACATGCATCTG 59.073 45.455 7.40 0.00 40.51 2.90
2753 3143 2.382882 TGTTGGAGGCAATTGTTCACA 58.617 42.857 7.40 4.64 0.00 3.58
3007 3408 4.263331 CCGGGGCCTACATCAATAAAGTAT 60.263 45.833 0.84 0.00 0.00 2.12
3088 3489 5.104235 GGGAGATTTAGGGTAAGCCTTGTAA 60.104 44.000 0.00 0.00 34.45 2.41
3156 3557 5.413833 AGATGTTTTGCCCATATCGATGATC 59.586 40.000 8.54 0.00 34.73 2.92
3203 3604 4.808895 GTGAACCATTCCCAACTTTTTCAC 59.191 41.667 0.00 0.00 36.05 3.18
3901 4304 6.458751 GGGCACATTACATGACTAATGACTTG 60.459 42.308 18.16 10.13 38.72 3.16
4198 4611 7.771183 ACAAGCAAGAGTGAACAAAATAAGAA 58.229 30.769 0.00 0.00 0.00 2.52
4618 5031 7.653713 CGATAGAGGACTGTGCATTTACTTTAT 59.346 37.037 1.24 0.00 39.76 1.40
4619 5032 6.978659 CGATAGAGGACTGTGCATTTACTTTA 59.021 38.462 1.24 0.00 39.76 1.85
4621 5034 5.352284 CGATAGAGGACTGTGCATTTACTT 58.648 41.667 1.24 0.00 39.76 2.24
4624 5037 3.492656 GGCGATAGAGGACTGTGCATTTA 60.493 47.826 1.24 0.00 39.76 1.40
4625 5038 2.555199 GCGATAGAGGACTGTGCATTT 58.445 47.619 1.24 0.00 39.76 2.32
4630 5044 0.249238 GCTGGCGATAGAGGACTGTG 60.249 60.000 0.00 0.00 39.76 3.66
4927 5341 1.227999 ACGCAAGGTCATTGACGGTG 61.228 55.000 10.56 11.32 41.83 4.94
5044 5458 7.226128 GCACAGAAATCATCAGAATCAGATGTA 59.774 37.037 13.98 3.66 42.63 2.29
5322 5737 5.806366 GCATGCCAAAATAGAATGCTTTT 57.194 34.783 6.36 0.00 40.34 2.27
5331 5746 3.194116 AGGTCAACAGCATGCCAAAATAG 59.806 43.478 15.66 0.00 42.53 1.73
5333 5748 1.972795 AGGTCAACAGCATGCCAAAAT 59.027 42.857 15.66 0.00 42.53 1.82
5424 5848 1.334160 TGCAGAAGGGTGACGACTTA 58.666 50.000 0.00 0.00 0.00 2.24
5494 5918 2.291741 GGCAACAACCTGAAACTGAGAG 59.708 50.000 0.00 0.00 0.00 3.20
5495 5919 2.092429 AGGCAACAACCTGAAACTGAGA 60.092 45.455 0.00 0.00 39.13 3.27
5660 6329 0.617820 ACCCGAGTAAGGTCCATGCT 60.618 55.000 0.00 0.00 28.99 3.79
5857 6526 2.353803 GGAGTACGCTCATTGTTCTGGT 60.354 50.000 0.00 0.00 43.37 4.00
5994 6668 6.551601 ACTGTAGAGGTGCATAGTTAGCTATT 59.448 38.462 0.00 0.00 35.85 1.73
5995 6669 6.071984 ACTGTAGAGGTGCATAGTTAGCTAT 58.928 40.000 0.00 0.00 38.38 2.97
5996 6670 5.446860 ACTGTAGAGGTGCATAGTTAGCTA 58.553 41.667 0.00 0.00 0.00 3.32
5997 6671 4.282496 ACTGTAGAGGTGCATAGTTAGCT 58.718 43.478 0.00 0.00 0.00 3.32
5998 6672 4.657436 ACTGTAGAGGTGCATAGTTAGC 57.343 45.455 0.00 0.00 0.00 3.09
6174 6848 4.961438 AACTGGCATTTCAAACCTGATT 57.039 36.364 0.00 0.00 0.00 2.57
6208 6882 1.273048 GTGGCCAGAAATGCATGTTGA 59.727 47.619 5.11 0.00 0.00 3.18
6244 6919 1.334059 CCAACAACAGTGCAGCTAACG 60.334 52.381 0.00 0.00 0.00 3.18
6415 7093 5.069781 GGGTTCTCTCTGTTGTATGCTATCT 59.930 44.000 0.00 0.00 0.00 1.98
6444 7122 2.969821 TGGTTTGCCCAATAGACTGT 57.030 45.000 0.00 0.00 41.50 3.55
6666 7347 0.391661 TTCTGCATTCCTCGAGGTGC 60.392 55.000 30.53 30.53 37.61 5.01
6729 7410 1.547820 TGCAGTTTTGGTTGACAGCAA 59.452 42.857 0.00 0.00 35.72 3.91
6853 7534 1.988107 AGCCCAGGAATGTTCTTCTCA 59.012 47.619 0.00 0.00 0.00 3.27
7005 7686 3.242518 TCAAACTTGTCGAGTAGCATCG 58.757 45.455 0.00 0.09 44.07 3.84
7042 7723 1.829849 TCAGTCATCTTCTCTGGCTGG 59.170 52.381 5.20 0.00 44.56 4.85
7152 7833 1.285280 TCCAGGTGTACCCAATCAGG 58.715 55.000 0.00 0.00 36.42 3.86
7308 7989 0.040425 AAACAACGGTTCGCATCAGC 60.040 50.000 0.00 0.00 35.82 4.26
7412 8095 4.944619 TGTCACAGATCCCAGATATGAC 57.055 45.455 6.24 7.43 36.40 3.06
7447 8130 5.987953 AGAGCACGATCGTACTGTTATAGTA 59.012 40.000 25.14 0.00 40.89 1.82
7452 8135 3.427098 CCAAGAGCACGATCGTACTGTTA 60.427 47.826 25.22 0.00 0.00 2.41
7455 8138 1.135373 ACCAAGAGCACGATCGTACTG 60.135 52.381 25.14 13.04 0.00 2.74
7492 8175 5.655488 TCGAAGAAGAGATTGATCCAGTTC 58.345 41.667 0.00 0.00 0.00 3.01
7564 8247 5.526111 GTGTACAGCACAAAAAGAACCTCTA 59.474 40.000 0.00 0.00 46.91 2.43
7636 8319 3.009723 ACGATTTTATGGCAGGTCAGTG 58.990 45.455 0.00 0.00 0.00 3.66
7638 8321 3.063997 GTCACGATTTTATGGCAGGTCAG 59.936 47.826 0.00 0.00 0.00 3.51
7680 8363 0.030369 GACGTGTATAGGCCCGTCTG 59.970 60.000 18.89 0.00 44.55 3.51
7681 8364 2.412605 GACGTGTATAGGCCCGTCT 58.587 57.895 18.89 0.00 44.55 4.18
7683 8366 1.312815 GTAGACGTGTATAGGCCCGT 58.687 55.000 0.00 0.00 36.04 5.28
7846 8547 2.037772 GACAACATCTAGGGCGATGGAT 59.962 50.000 5.85 0.00 43.92 3.41
7850 8551 2.363680 CAGAGACAACATCTAGGGCGAT 59.636 50.000 0.00 0.00 38.00 4.58
7931 8632 1.771073 CTTGCAACTTGTCGCCACGA 61.771 55.000 0.00 0.00 0.00 4.35
7941 8642 1.308998 CGTTCTCCACCTTGCAACTT 58.691 50.000 0.00 0.00 0.00 2.66
7989 8690 3.482783 GTCGCTTCCTGCTCGTGC 61.483 66.667 1.71 1.71 40.11 5.34
8130 8831 2.576893 CGGATCATTGTCGGTCGCG 61.577 63.158 0.00 0.00 0.00 5.87
8142 8843 2.550855 GCCCAATTCAGCTATCGGATCA 60.551 50.000 0.00 0.00 0.00 2.92
8154 8855 0.182537 ATCCGGAATCGCCCAATTCA 59.817 50.000 9.01 0.00 37.38 2.57
8158 8859 2.515991 GCATCCGGAATCGCCCAA 60.516 61.111 9.01 0.00 34.56 4.12
8164 8865 2.489971 TCCGTAAATGCATCCGGAATC 58.510 47.619 24.43 3.39 45.71 2.52
8165 8866 2.631160 TCCGTAAATGCATCCGGAAT 57.369 45.000 24.43 0.00 45.71 3.01
8168 8869 1.267832 CGTTTCCGTAAATGCATCCGG 60.268 52.381 20.42 20.42 41.75 5.14
8175 8876 0.179210 CGCCACCGTTTCCGTAAATG 60.179 55.000 0.00 0.00 0.00 2.32
8217 8918 2.181525 CCCTTTGGAATTGCGGCG 59.818 61.111 0.51 0.51 0.00 6.46
8236 8937 0.028902 GAGTTGCCGTGCTTTTTCGT 59.971 50.000 0.00 0.00 0.00 3.85
8314 9016 9.247861 AGGAAGTGATACAAAATAGAGCAAAAT 57.752 29.630 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.