Multiple sequence alignment - TraesCS3B01G222600

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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 TraesCS3B01G222600 chr3B 100.000 5265 0 0 1 5265 284003565 284008829 0.000000e+00 9723.0
1 TraesCS3B01G222600 chr3B 100.000 3182 0 0 5561 8742 284009125 284012306 0.000000e+00 5877.0
2 TraesCS3B01G222600 chr3A 96.751 5294 132 22 1 5265 296931213 296925931 0.000000e+00 8787.0
3 TraesCS3B01G222600 chr3A 95.312 3221 89 17 5562 8742 296925880 296922682 0.000000e+00 5055.0
4 TraesCS3B01G222600 chr3D 96.773 4431 101 16 1 4416 231718580 231722983 0.000000e+00 7352.0
5 TraesCS3B01G222600 chr3D 96.621 2427 54 10 5576 7981 231728043 231730462 0.000000e+00 4002.0
6 TraesCS3B01G222600 chr3D 97.708 829 15 2 4437 5265 231727027 231727851 0.000000e+00 1423.0
7 TraesCS3B01G222600 chr3D 92.324 469 12 4 7966 8434 231730502 231730946 0.000000e+00 645.0
8 TraesCS3B01G222600 chr3D 91.845 233 17 2 8511 8742 231730976 231731207 3.040000e-84 324.0
9 TraesCS3B01G222600 chr3D 96.970 33 1 0 6569 6601 57152968 57153000 1.000000e-03 56.5
10 TraesCS3B01G222600 chr5D 88.920 361 26 5 4444 4790 43208518 43208158 4.850000e-117 433.0
11 TraesCS3B01G222600 chr5D 83.803 142 15 6 6467 6606 506087728 506087863 2.560000e-25 128.0
12 TraesCS3B01G222600 chr5B 91.519 283 16 4 4444 4718 40783879 40783597 4.950000e-102 383.0
13 TraesCS3B01G222600 chr5A 91.584 202 15 2 4440 4640 33003707 33003507 2.400000e-70 278.0
14 TraesCS3B01G222600 chr5A 87.500 80 5 2 4818 4892 33002740 33002661 4.350000e-13 87.9
15 TraesCS3B01G222600 chr7D 92.708 96 5 2 6467 6561 588081883 588081789 4.260000e-28 137.0
16 TraesCS3B01G222600 chr7A 92.708 96 5 2 6467 6561 679957124 679957030 4.260000e-28 137.0
17 TraesCS3B01G222600 chr4D 88.333 120 7 3 6438 6556 37050732 37050619 4.260000e-28 137.0
18 TraesCS3B01G222600 chr2D 92.632 95 7 0 6467 6561 512769238 512769332 4.260000e-28 137.0
19 TraesCS3B01G222600 chr2B 92.708 96 5 2 6467 6561 153858329 153858235 4.260000e-28 137.0
20 TraesCS3B01G222600 chr6D 84.507 142 13 4 6090 6223 24601162 24601022 1.980000e-26 132.0
21 TraesCS3B01G222600 chrUn 88.462 52 5 1 523 573 69337902 69337953 2.640000e-05 62.1
22 TraesCS3B01G222600 chrUn 88.462 52 5 1 523 573 69355487 69355538 2.640000e-05 62.1
23 TraesCS3B01G222600 chr4A 94.118 34 2 0 6569 6602 37805173 37805206 1.600000e-02 52.8


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 TraesCS3B01G222600 chr3B 284003565 284012306 8741 False 7800.0 9723 100.0000 1 8742 2 chr3B.!!$F1 8741
1 TraesCS3B01G222600 chr3A 296922682 296931213 8531 True 6921.0 8787 96.0315 1 8742 2 chr3A.!!$R1 8741
2 TraesCS3B01G222600 chr3D 231718580 231722983 4403 False 7352.0 7352 96.7730 1 4416 1 chr3D.!!$F2 4415
3 TraesCS3B01G222600 chr3D 231727027 231731207 4180 False 1598.5 4002 94.6245 4437 8742 4 chr3D.!!$F3 4305

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
403 410 0.394762 TGTCCCTACCGAGTATGCGT 60.395 55.000 0.0 0.0 0.00 5.24 F
1014 1036 0.750546 ACTCGATGGGATTCGACGGA 60.751 55.000 0.0 0.0 42.81 4.69 F
2511 2543 0.465705 ACCCCAGTGCATCATCTACG 59.534 55.000 0.0 0.0 0.00 3.51 F
3109 3143 0.179108 GCTGCTAGACCCCTTACACG 60.179 60.000 0.0 0.0 0.00 4.49 F
3592 3626 0.733150 GCCCCGAAAGACATAGTTGC 59.267 55.000 0.0 0.0 0.00 4.17 F
4854 4889 0.322997 TGCAAACCGACCCCCAATAG 60.323 55.000 0.0 0.0 0.00 1.73 F
5248 5283 2.886081 ACAATTCTTTTGCACGCACAA 58.114 38.095 0.0 0.0 0.00 3.33 F
6376 6431 6.238842 CCAACATGCATTTCCGAATAATCTCT 60.239 38.462 0.0 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2158 1.572447 CAACACCGGGTGCTTTACG 59.428 57.895 26.62 1.72 36.98 3.18 R
2815 2849 2.310233 CGACCAACTGAGGTGTGCG 61.310 63.158 0.00 0.00 43.38 5.34 R
3911 3946 1.048601 GGTGGACAGGTGAGAGAACA 58.951 55.000 0.00 0.00 0.00 3.18 R
4196 4231 2.742053 TCGCAATCCTTTTCTGTGCTAC 59.258 45.455 0.00 0.00 32.99 3.58 R
5560 5595 2.346766 TTGCCAGAGAAAAGCTGTCA 57.653 45.000 0.00 0.00 0.00 3.58 R
6432 6487 2.308275 ACTGAACGGAGGGAGTAGTAGT 59.692 50.000 0.00 0.00 0.00 2.73 R
6826 6881 2.664851 CAACGCGAGGCTCCACAA 60.665 61.111 15.93 0.00 0.00 3.33 R
8124 8276 0.457035 CCATGCCAAAATAGCGCAGT 59.543 50.000 11.47 0.00 35.66 4.40 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
32 33 2.835431 CAACGCCCACCAACCCAA 60.835 61.111 0.00 0.00 0.00 4.12
78 79 2.547218 GGCATCCCGAGCGAGTAATAAA 60.547 50.000 0.00 0.00 0.00 1.40
87 88 5.449588 CCGAGCGAGTAATAAACCTGAGTAA 60.450 44.000 0.00 0.00 0.00 2.24
173 175 2.743752 CGATGCGAGGCCAACACAG 61.744 63.158 5.01 0.00 0.00 3.66
196 198 3.318539 CTGTCTGGCATGCACGCAC 62.319 63.158 21.36 10.44 0.00 5.34
197 199 3.356267 GTCTGGCATGCACGCACA 61.356 61.111 21.36 6.72 0.00 4.57
198 200 3.051479 TCTGGCATGCACGCACAG 61.051 61.111 21.36 16.52 33.84 3.66
199 201 3.359523 CTGGCATGCACGCACAGT 61.360 61.111 21.36 0.00 0.00 3.55
204 211 4.687215 ATGCACGCACAGTCGGCT 62.687 61.111 0.00 0.00 0.00 5.52
230 237 1.133513 ACTGAACAGTTGGATGGGCAA 60.134 47.619 1.32 0.00 38.83 4.52
270 277 2.107041 TTGAACGCCCGAGGTGACAT 62.107 55.000 10.01 0.00 36.58 3.06
399 406 2.019984 GACGTTGTCCCTACCGAGTAT 58.980 52.381 0.00 0.00 0.00 2.12
403 410 0.394762 TGTCCCTACCGAGTATGCGT 60.395 55.000 0.00 0.00 0.00 5.24
418 425 2.202878 CGTGGGCATACCGGTCTG 60.203 66.667 12.40 14.19 44.64 3.51
421 428 3.480133 GGGCATACCGGTCTGGCT 61.480 66.667 34.93 5.87 43.94 4.75
425 433 1.961180 GCATACCGGTCTGGCTCAGT 61.961 60.000 20.34 0.00 43.94 3.41
457 466 2.045926 GGGCCAACGATGCTGACT 60.046 61.111 4.39 0.00 0.00 3.41
478 487 8.791327 TGACTAGCAAAAACATCTCATAATCA 57.209 30.769 0.00 0.00 0.00 2.57
617 626 3.826157 CTGCATTTGGACTCCAACCTTAA 59.174 43.478 10.25 0.00 43.82 1.85
667 676 1.561076 CTCAATCAGTGACATCCCCCA 59.439 52.381 0.00 0.00 31.13 4.96
674 684 1.692749 TGACATCCCCCAGTAGCCC 60.693 63.158 0.00 0.00 0.00 5.19
832 848 1.552337 TCTCTCATCAAGGCTCCACAC 59.448 52.381 0.00 0.00 0.00 3.82
833 849 1.554160 CTCTCATCAAGGCTCCACACT 59.446 52.381 0.00 0.00 0.00 3.55
834 850 1.552337 TCTCATCAAGGCTCCACACTC 59.448 52.381 0.00 0.00 0.00 3.51
938 957 3.735029 GCCACCGTCTCGACTCGT 61.735 66.667 0.00 0.00 0.00 4.18
1014 1036 0.750546 ACTCGATGGGATTCGACGGA 60.751 55.000 0.00 0.00 42.81 4.69
1261 1283 2.525877 GGGAGCCCCACCGCTATA 60.526 66.667 5.45 0.00 44.65 1.31
1321 1343 4.742201 GAGAACAGCTCGCCGCCA 62.742 66.667 0.00 0.00 40.39 5.69
1734 1765 4.200838 TGTGCTTTCGATCCACTGATTA 57.799 40.909 10.60 0.00 0.00 1.75
2139 2170 2.048877 ACGACCGTAAAGCACCCG 60.049 61.111 0.00 0.00 0.00 5.28
2177 2208 7.240674 TCTACTTTTGTTGCTTTATACATGCG 58.759 34.615 0.00 0.00 0.00 4.73
2301 2332 9.653287 CCTTTTGTTATGACTGACAAGATAGTA 57.347 33.333 0.00 0.00 37.12 1.82
2511 2543 0.465705 ACCCCAGTGCATCATCTACG 59.534 55.000 0.00 0.00 0.00 3.51
2815 2849 2.436417 TGGCAGATGTAAACCTGAAGC 58.564 47.619 0.00 0.00 32.37 3.86
2905 2939 5.502544 GCACTTTGGAGACTATTTCGTATGC 60.503 44.000 0.00 0.00 0.00 3.14
3109 3143 0.179108 GCTGCTAGACCCCTTACACG 60.179 60.000 0.00 0.00 0.00 4.49
3173 3207 9.931210 GTGCTACATATGTTCCAAAAACTATAC 57.069 33.333 14.77 0.00 0.00 1.47
3592 3626 0.733150 GCCCCGAAAGACATAGTTGC 59.267 55.000 0.00 0.00 0.00 4.17
3800 3835 6.737720 AGCATGTGATAGTTCTTCATCCTA 57.262 37.500 0.00 0.00 0.00 2.94
3911 3946 7.759433 GCAAACTGGTAGCATTATGTTGTTAAT 59.241 33.333 0.00 0.00 0.00 1.40
3994 4029 6.748333 TTATTGCTGAGAATGAAGGTGAAG 57.252 37.500 0.00 0.00 0.00 3.02
4040 4075 6.312426 CAGACATCAGAAGACAATAGAACCAC 59.688 42.308 0.00 0.00 0.00 4.16
4046 4081 9.793259 ATCAGAAGACAATAGAACCACTTTTTA 57.207 29.630 0.00 0.00 0.00 1.52
4104 4139 9.733556 TGCTCCTACAAATAAGAGATTGTTTTA 57.266 29.630 0.00 0.00 40.14 1.52
4196 4231 2.119457 GTTTGCTTGCAGAAGTTTCCG 58.881 47.619 0.00 0.00 0.00 4.30
4268 4303 1.166129 CAACTGAGCAAGCTGAGCAT 58.834 50.000 7.39 0.00 30.30 3.79
4388 4423 6.709643 CCTATTCAGCAAATACTTTCGTCAG 58.290 40.000 0.00 0.00 0.00 3.51
4443 4478 6.486993 CCAGTACTACAGCTAGATACACATGA 59.513 42.308 0.00 0.00 0.00 3.07
4854 4889 0.322997 TGCAAACCGACCCCCAATAG 60.323 55.000 0.00 0.00 0.00 1.73
5243 5278 6.324522 TGTTTTGTACAATTCTTTTGCACG 57.675 33.333 9.56 0.00 32.64 5.34
5248 5283 2.886081 ACAATTCTTTTGCACGCACAA 58.114 38.095 0.00 0.00 0.00 3.33
5684 5719 7.640597 ACTATTATGGGCTAACAAAAAGGTC 57.359 36.000 0.00 0.00 0.00 3.85
5740 5775 9.965824 AAGTTTCAAGGTTTGTATACTTCAATG 57.034 29.630 4.17 0.00 0.00 2.82
6016 6062 6.875076 TGCTATCTTGTCTAAGTTAGGTTCC 58.125 40.000 10.02 0.00 36.99 3.62
6376 6431 6.238842 CCAACATGCATTTCCGAATAATCTCT 60.239 38.462 0.00 0.00 0.00 3.10
6563 6618 7.690228 TCCAAAACGTCTTATAATTCGGATTG 58.310 34.615 0.00 13.48 0.00 2.67
6893 6948 5.835280 AGAAAAAGGTTGGATGTCTCATGTT 59.165 36.000 0.00 0.00 0.00 2.71
7044 7100 7.165485 AGGCAACACATTATAGACACACTTAA 58.835 34.615 0.00 0.00 41.41 1.85
7182 7239 5.627182 ATGCTTCCTACATCATCTCTGTT 57.373 39.130 0.00 0.00 0.00 3.16
7225 7282 1.065636 TCTTCTTGCTGCCAGAGGATG 60.066 52.381 10.85 1.49 0.00 3.51
7285 7344 8.324163 AGCCAAAACTAGTTTCATACAGTTAG 57.676 34.615 20.78 0.00 31.94 2.34
7361 7420 6.108097 GCTGTAAGTAAGCTGAATTACACC 57.892 41.667 18.13 9.91 37.98 4.16
7362 7421 5.642063 GCTGTAAGTAAGCTGAATTACACCA 59.358 40.000 18.13 0.76 37.98 4.17
7363 7422 6.148811 GCTGTAAGTAAGCTGAATTACACCAA 59.851 38.462 18.13 0.37 37.98 3.67
7364 7423 7.624344 GCTGTAAGTAAGCTGAATTACACCAAG 60.624 40.741 18.13 10.87 37.98 3.61
7365 7424 7.221450 TGTAAGTAAGCTGAATTACACCAAGT 58.779 34.615 18.13 0.00 37.98 3.16
7366 7425 8.369424 TGTAAGTAAGCTGAATTACACCAAGTA 58.631 33.333 18.13 0.00 37.98 2.24
7367 7426 9.211485 GTAAGTAAGCTGAATTACACCAAGTAA 57.789 33.333 15.15 0.00 46.10 2.24
7368 7427 7.907214 AGTAAGCTGAATTACACCAAGTAAG 57.093 36.000 0.00 0.00 45.31 2.34
7369 7428 5.629079 AAGCTGAATTACACCAAGTAAGC 57.371 39.130 0.00 0.00 45.31 3.09
7370 7429 4.911390 AGCTGAATTACACCAAGTAAGCT 58.089 39.130 0.00 0.00 45.31 3.74
7371 7430 4.697352 AGCTGAATTACACCAAGTAAGCTG 59.303 41.667 0.00 0.00 45.31 4.24
7372 7431 4.695455 GCTGAATTACACCAAGTAAGCTGA 59.305 41.667 0.00 0.00 45.31 4.26
7373 7432 5.181245 GCTGAATTACACCAAGTAAGCTGAA 59.819 40.000 0.00 0.00 45.31 3.02
7374 7433 6.127897 GCTGAATTACACCAAGTAAGCTGAAT 60.128 38.462 0.00 0.00 45.31 2.57
7375 7434 7.575720 GCTGAATTACACCAAGTAAGCTGAATT 60.576 37.037 0.00 0.00 45.31 2.17
7376 7435 8.856153 TGAATTACACCAAGTAAGCTGAATTA 57.144 30.769 0.00 0.00 45.31 1.40
7377 7436 8.726988 TGAATTACACCAAGTAAGCTGAATTAC 58.273 33.333 0.00 0.00 45.31 1.89
7378 7437 8.630054 AATTACACCAAGTAAGCTGAATTACA 57.370 30.769 0.00 0.00 45.31 2.41
7379 7438 5.941948 ACACCAAGTAAGCTGAATTACAC 57.058 39.130 0.00 0.00 37.98 2.90
7464 7561 2.359850 GTGTGATGCCCCGCTTGA 60.360 61.111 0.00 0.00 0.00 3.02
7475 7572 1.202582 CCCCGCTTGATAGTCTATCCG 59.797 57.143 15.81 12.08 34.26 4.18
7493 7590 0.459237 CGAGCAGCCTCAAGTAGTGG 60.459 60.000 0.00 0.00 38.00 4.00
7494 7591 0.898320 GAGCAGCCTCAAGTAGTGGA 59.102 55.000 0.00 0.00 38.03 4.02
7643 7740 6.211587 TGAAAAGGCCAACATCATATTCAG 57.788 37.500 5.01 0.00 0.00 3.02
7996 8148 7.494298 AGTTGTTTATTCAAAATCCAACCACAC 59.506 33.333 0.00 0.00 32.56 3.82
8124 8276 6.293735 GCTACAACCATTATAGCGCCAAATAA 60.294 38.462 2.29 6.85 32.61 1.40
8287 8443 7.433680 ACATTAGAAAACAACACCCAATCTTC 58.566 34.615 0.00 0.00 0.00 2.87
8340 8496 1.478510 CTACTGGCGACTCTCACCAAT 59.521 52.381 0.00 0.00 26.66 3.16
8357 8513 8.708378 TCTCACCAATACTCATTATGACTCAAT 58.292 33.333 0.00 0.00 0.00 2.57
8497 8667 3.763902 CTTCCATGGTAGATCGCGATAG 58.236 50.000 23.76 7.72 0.00 2.08
8513 8683 5.182570 TCGCGATAGTTAACATGGCTATAGT 59.817 40.000 3.71 0.00 39.35 2.12
8532 8702 0.904865 TTCAGACCTCCCTGCGATGT 60.905 55.000 0.00 0.00 34.28 3.06
8556 8727 7.753132 TGTCGCATAAAAGCTATTTAAAACCTG 59.247 33.333 0.00 0.00 0.00 4.00
8611 8782 0.103937 CTGAAGCCCATCCTCTCGTC 59.896 60.000 0.00 0.00 0.00 4.20
8640 8811 3.270877 GAGAACAACACTGACAACCTGT 58.729 45.455 0.00 0.00 0.00 4.00
8648 8819 4.787551 ACACTGACAACCTGTGGATAAAA 58.212 39.130 0.00 0.00 45.52 1.52
8650 8821 4.216257 CACTGACAACCTGTGGATAAAAGG 59.784 45.833 0.00 0.00 39.96 3.11
8656 8827 4.302559 ACCTGTGGATAAAAGGTTCCTC 57.697 45.455 0.00 0.00 41.65 3.71
8657 8828 3.655777 ACCTGTGGATAAAAGGTTCCTCA 59.344 43.478 0.00 0.00 41.65 3.86
8698 8869 0.597637 CGGTGGTGCGGTGAGATATC 60.598 60.000 0.00 0.00 0.00 1.63
8712 8883 6.073873 CGGTGAGATATCTCTTCATTTCTTGC 60.074 42.308 28.51 3.68 43.25 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.455217 CCCTCGTCCCGGTATGTCT 60.455 63.158 0.00 0.00 0.00 3.41
72 73 5.721000 TCGGTTCCCTTACTCAGGTTTATTA 59.279 40.000 0.00 0.00 42.02 0.98
78 79 1.622312 GTTCGGTTCCCTTACTCAGGT 59.378 52.381 0.00 0.00 42.02 4.00
87 88 2.428622 CCGGTTGTTCGGTTCCCT 59.571 61.111 0.00 0.00 44.60 4.20
173 175 1.078637 TGCATGCCAGACAGCTCTC 60.079 57.895 16.68 0.00 0.00 3.20
196 198 3.052082 CAGTTGCCCAGCCGACTG 61.052 66.667 0.00 0.00 44.05 3.51
197 199 2.818169 TTCAGTTGCCCAGCCGACT 61.818 57.895 0.00 0.00 0.00 4.18
198 200 2.281484 TTCAGTTGCCCAGCCGAC 60.281 61.111 0.00 0.00 0.00 4.79
199 201 2.281484 GTTCAGTTGCCCAGCCGA 60.281 61.111 0.00 0.00 0.00 5.54
204 211 0.257328 TCCAACTGTTCAGTTGCCCA 59.743 50.000 29.20 17.54 45.53 5.36
270 277 4.560743 TTGGCCTCACAGCGTGCA 62.561 61.111 3.32 0.00 32.98 4.57
403 410 3.792736 GCCAGACCGGTATGCCCA 61.793 66.667 23.87 0.00 36.97 5.36
412 419 0.888619 TAGTTCACTGAGCCAGACCG 59.111 55.000 8.91 0.00 35.18 4.79
418 425 1.218316 CCGGGTAGTTCACTGAGCC 59.782 63.158 0.00 0.00 0.00 4.70
421 428 2.642254 CCGCCGGGTAGTTCACTGA 61.642 63.158 2.18 0.00 0.00 3.41
457 466 9.230122 TGACTTGATTATGAGATGTTTTTGCTA 57.770 29.630 0.00 0.00 0.00 3.49
516 525 2.101640 AAATGCCCTTGGTTGTCCTT 57.898 45.000 0.00 0.00 34.23 3.36
580 589 3.896648 ATGCAGTCGTTTTACAGTTGG 57.103 42.857 0.00 0.00 0.00 3.77
587 596 3.500680 GGAGTCCAAATGCAGTCGTTTTA 59.499 43.478 3.60 0.00 29.41 1.52
617 626 3.755434 GCTCTTGCAAGCTGTGGT 58.245 55.556 21.99 0.00 39.27 4.16
653 662 0.179000 GCTACTGGGGGATGTCACTG 59.821 60.000 0.00 0.00 0.00 3.66
667 676 0.611062 TCACGCTACAGTGGGCTACT 60.611 55.000 0.00 0.00 42.10 2.57
674 684 0.598562 ACCACTCTCACGCTACAGTG 59.401 55.000 0.00 0.00 43.11 3.66
832 848 5.045578 TCCCAGTCCAATAGAAAGAAAGGAG 60.046 44.000 0.00 0.00 0.00 3.69
833 849 4.849810 TCCCAGTCCAATAGAAAGAAAGGA 59.150 41.667 0.00 0.00 0.00 3.36
834 850 4.944317 GTCCCAGTCCAATAGAAAGAAAGG 59.056 45.833 0.00 0.00 0.00 3.11
938 957 2.270850 GGCGTTAGGTGGGATGCA 59.729 61.111 0.00 0.00 0.00 3.96
1014 1036 2.592574 TCGGACACGACGACCAGT 60.593 61.111 0.00 0.00 45.59 4.00
2006 2037 8.520835 TTACTCTGAATATCATGTAATGCGAC 57.479 34.615 0.00 0.00 46.21 5.19
2127 2158 1.572447 CAACACCGGGTGCTTTACG 59.428 57.895 26.62 1.72 36.98 3.18
2139 2170 5.123936 ACAAAAGTAGAGAGAACCAACACC 58.876 41.667 0.00 0.00 0.00 4.16
2177 2208 4.523083 TCCAATGATAACCACCAGTAAGC 58.477 43.478 0.00 0.00 0.00 3.09
2301 2332 5.633182 CACAGTAAGTTTGCCGCAAATTTAT 59.367 36.000 26.81 17.18 37.66 1.40
2302 2333 4.979197 CACAGTAAGTTTGCCGCAAATTTA 59.021 37.500 22.78 22.78 35.51 1.40
2483 2515 2.684001 TGCACTGGGGTATAGAAACG 57.316 50.000 0.00 0.00 0.00 3.60
2511 2543 7.074502 CAGAGCTTAGATCTGAACAAACAAAC 58.925 38.462 21.38 0.00 45.80 2.93
2616 2650 4.023707 GCAAGCAGTAAGAGAAAGCTTTGA 60.024 41.667 18.30 0.00 43.06 2.69
2695 2729 7.601856 CCCACACAAATAGACAAATGTAACAT 58.398 34.615 0.00 0.00 0.00 2.71
2815 2849 2.310233 CGACCAACTGAGGTGTGCG 61.310 63.158 0.00 0.00 43.38 5.34
2905 2939 7.376336 GTGTGTTACTCTCACTAGCATATTACG 59.624 40.741 0.00 0.00 37.51 3.18
3173 3207 8.993121 TGAAAGAGAAGTTAAATAGCTCAGTTG 58.007 33.333 0.00 0.00 0.00 3.16
3592 3626 6.967199 GGCGAGATTTAGATTTTGTAAACCAG 59.033 38.462 0.00 0.00 0.00 4.00
3656 3690 2.045536 CTGAGCTGAAGGGGTGCC 60.046 66.667 0.00 0.00 0.00 5.01
3695 3729 4.978580 GGAAATGTGAGTTCTTCAGCAAAC 59.021 41.667 0.00 0.00 36.21 2.93
3911 3946 1.048601 GGTGGACAGGTGAGAGAACA 58.951 55.000 0.00 0.00 0.00 3.18
3994 4029 3.568007 TGACTGTTCCCTACAAACATTGC 59.432 43.478 0.00 0.00 36.14 3.56
4196 4231 2.742053 TCGCAATCCTTTTCTGTGCTAC 59.258 45.455 0.00 0.00 32.99 3.58
4268 4303 8.574251 ACATTATCTAGTTACAATGTTTGCCA 57.426 30.769 0.00 0.00 38.18 4.92
4388 4423 3.639094 TGCTGCTCCCTAGTTAAGAGATC 59.361 47.826 0.00 0.00 0.00 2.75
4443 4478 9.638176 ATCAGATTTTCATTTAGGCTTCTGTAT 57.362 29.630 0.00 0.00 33.00 2.29
4854 4889 8.595533 GTTTTCAACTTTTCTGAATGGAAGTTC 58.404 33.333 13.15 0.00 39.55 3.01
5159 5194 6.964370 GCAAAACCAGTTAATCAACCAAAAAC 59.036 34.615 0.00 0.00 35.05 2.43
5560 5595 2.346766 TTGCCAGAGAAAAGCTGTCA 57.653 45.000 0.00 0.00 0.00 3.58
5684 5719 4.020751 TGAGACTGTCTTCCAGAATCCTTG 60.021 45.833 12.27 0.00 44.49 3.61
5711 5746 7.996644 TGAAGTATACAAACCTTGAAACTTCCT 59.003 33.333 18.84 0.00 41.18 3.36
6014 6060 8.815912 TCGAGATTATTCTGGATTTATGATGGA 58.184 33.333 0.00 0.00 32.45 3.41
6016 6062 9.866798 TCTCGAGATTATTCTGGATTTATGATG 57.133 33.333 12.08 0.00 36.31 3.07
6087 6133 9.791820 CATCTCTATGTTCATGTGCATTTTTAA 57.208 29.630 9.31 0.00 0.00 1.52
6089 6135 7.833786 ACATCTCTATGTTCATGTGCATTTTT 58.166 30.769 9.31 0.00 44.07 1.94
6094 6140 7.955918 AGTATACATCTCTATGTTCATGTGCA 58.044 34.615 5.50 0.00 44.07 4.57
6095 6141 9.566530 CTAGTATACATCTCTATGTTCATGTGC 57.433 37.037 5.50 0.00 44.07 4.57
6357 6412 9.778741 AATAGTAAGAGATTATTCGGAAATGCA 57.221 29.630 0.00 0.00 0.00 3.96
6417 6472 9.761504 GGGAGTAGTAGTTTATTCTGGATTTAC 57.238 37.037 0.00 0.00 0.00 2.01
6432 6487 2.308275 ACTGAACGGAGGGAGTAGTAGT 59.692 50.000 0.00 0.00 0.00 2.73
6435 6490 3.666345 ATACTGAACGGAGGGAGTAGT 57.334 47.619 0.00 0.00 0.00 2.73
6826 6881 2.664851 CAACGCGAGGCTCCACAA 60.665 61.111 15.93 0.00 0.00 3.33
6893 6948 7.039644 GGATAGGAGATTTTCGGACTCATAGAA 60.040 40.741 0.00 0.00 32.15 2.10
7044 7100 6.710295 TCTGCAAATAACACTGGCGATATAAT 59.290 34.615 0.00 0.00 0.00 1.28
7182 7239 3.135901 GGAGCAACCAAGCTTTCTAGCA 61.136 50.000 0.00 0.00 46.75 3.49
7225 7282 3.620488 TCAAATGCCTCACCTCCATTAC 58.380 45.455 0.00 0.00 0.00 1.89
7285 7344 7.698836 AACATTCACAAACTTAATCTGCAAC 57.301 32.000 0.00 0.00 0.00 4.17
7361 7420 6.913170 ACATTGGTGTAATTCAGCTTACTTG 58.087 36.000 0.00 0.00 43.97 3.16
7362 7421 7.370383 CAACATTGGTGTAATTCAGCTTACTT 58.630 34.615 0.00 0.00 43.97 2.24
7363 7422 6.071952 CCAACATTGGTGTAATTCAGCTTACT 60.072 38.462 0.20 0.00 43.43 2.24
7364 7423 6.092748 CCAACATTGGTGTAATTCAGCTTAC 58.907 40.000 0.20 0.00 43.43 2.34
7365 7424 6.266168 CCAACATTGGTGTAATTCAGCTTA 57.734 37.500 0.20 0.00 43.43 3.09
7366 7425 5.138125 CCAACATTGGTGTAATTCAGCTT 57.862 39.130 0.20 0.00 43.43 3.74
7367 7426 4.789012 CCAACATTGGTGTAATTCAGCT 57.211 40.909 0.20 0.00 43.43 4.24
7464 7561 2.224892 TGAGGCTGCTCGGATAGACTAT 60.225 50.000 0.00 0.00 30.84 2.12
7475 7572 0.898320 TCCACTACTTGAGGCTGCTC 59.102 55.000 0.00 0.00 0.00 4.26
7493 7590 5.041191 AGAGAATATGGTCCAACATGGTC 57.959 43.478 0.00 0.00 39.03 4.02
7494 7591 5.195940 CAAGAGAATATGGTCCAACATGGT 58.804 41.667 0.00 0.00 39.03 3.55
7643 7740 1.692519 ACTACTGTTGTCAGGGTCCAC 59.307 52.381 0.00 0.00 45.14 4.02
8108 8260 4.404507 CGCAGTTATTTGGCGCTATAAT 57.595 40.909 7.64 7.36 44.49 1.28
8124 8276 0.457035 CCATGCCAAAATAGCGCAGT 59.543 50.000 11.47 0.00 35.66 4.40
8287 8443 4.220602 CCAAGGTAAAACAATCTCCCAAGG 59.779 45.833 0.00 0.00 0.00 3.61
8457 8615 9.941664 CATGGAAGCTATTTACAATGTAAGAAG 57.058 33.333 5.94 8.71 32.05 2.85
8497 8667 6.583562 AGGTCTGAACTATAGCCATGTTAAC 58.416 40.000 0.00 0.00 0.00 2.01
8513 8683 0.904865 ACATCGCAGGGAGGTCTGAA 60.905 55.000 0.00 0.00 33.69 3.02
8532 8702 7.121463 TCCAGGTTTTAAATAGCTTTTATGCGA 59.879 33.333 0.00 0.00 38.13 5.10
8556 8727 8.122472 TCATTTTAAGGTTCTCTCCAAAATCC 57.878 34.615 0.00 0.00 32.40 3.01
8611 8782 2.280524 TGTTGTTCTCGTGGCGGG 60.281 61.111 0.00 0.00 0.00 6.13
8622 8793 2.091541 CCACAGGTTGTCAGTGTTGTT 58.908 47.619 0.00 0.00 0.00 2.83
8640 8811 5.843019 AAGTCTGAGGAACCTTTTATCCA 57.157 39.130 0.00 0.00 38.23 3.41
8648 8819 1.421646 CACCCAAAGTCTGAGGAACCT 59.578 52.381 0.00 0.00 0.00 3.50
8650 8821 2.158813 TGACACCCAAAGTCTGAGGAAC 60.159 50.000 0.00 0.00 36.94 3.62
8652 8823 1.416401 GTGACACCCAAAGTCTGAGGA 59.584 52.381 0.00 0.00 36.94 3.71
8654 8825 1.140852 TGGTGACACCCAAAGTCTGAG 59.859 52.381 22.00 0.00 37.50 3.35
8655 8826 1.208706 TGGTGACACCCAAAGTCTGA 58.791 50.000 22.00 0.00 37.50 3.27
8656 8827 1.949525 CTTGGTGACACCCAAAGTCTG 59.050 52.381 22.00 1.38 43.68 3.51
8657 8828 1.843851 TCTTGGTGACACCCAAAGTCT 59.156 47.619 22.00 0.00 43.68 3.24
8659 8830 2.052782 GTCTTGGTGACACCCAAAGT 57.947 50.000 22.00 0.00 43.68 2.66
8679 8850 0.597637 GATATCTCACCGCACCACCG 60.598 60.000 0.00 0.00 0.00 4.94
8698 8869 4.227538 CAAGCACTGCAAGAAATGAAGAG 58.772 43.478 3.30 0.00 36.73 2.85
8712 8883 2.670934 AAGGCCGAGCAAGCACTG 60.671 61.111 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.