Multiple sequence alignment - TraesCS2D01G099100

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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 TraesCS2D01G099100 chr2D 100.000 4226 0 0 1 4226 51161155 51156930 0.000000e+00 7805.0
1 TraesCS2D01G099100 chr2D 86.814 2351 284 14 869 3205 51253154 51255492 0.000000e+00 2601.0
2 TraesCS2D01G099100 chr2D 89.831 826 72 7 734 1551 51138026 51137205 0.000000e+00 1050.0
3 TraesCS2D01G099100 chr2D 81.152 191 27 7 416 599 51139801 51139613 1.220000e-30 145.0
4 TraesCS2D01G099100 chr2D 88.679 53 6 0 3359 3411 51130734 51130682 9.810000e-07 65.8
5 TraesCS2D01G099100 chr2A 96.567 3350 95 10 410 3742 52573732 52570386 0.000000e+00 5531.0
6 TraesCS2D01G099100 chr2A 86.188 2353 297 17 869 3205 52756522 52758862 0.000000e+00 2519.0
7 TraesCS2D01G099100 chr2A 82.934 334 39 6 601 927 761277785 761278107 6.920000e-73 285.0
8 TraesCS2D01G099100 chr2A 91.960 199 16 0 3797 3995 52570366 52570168 3.220000e-71 279.0
9 TraesCS2D01G099100 chr2A 91.489 188 13 3 4034 4221 52570169 52569985 5.420000e-64 255.0
10 TraesCS2D01G099100 chr2A 90.625 96 7 1 782 877 52428310 52428217 4.440000e-25 126.0
11 TraesCS2D01G099100 chr2B 94.697 3300 142 11 410 3686 79709678 79706389 0.000000e+00 5094.0
12 TraesCS2D01G099100 chr2B 86.522 2352 289 16 869 3205 80200438 80202776 0.000000e+00 2562.0
13 TraesCS2D01G099100 chr2B 84.910 2379 326 24 782 3137 79671968 79669600 0.000000e+00 2374.0
14 TraesCS2D01G099100 chr2B 81.684 2577 360 53 601 3124 794032143 794029626 0.000000e+00 2041.0
15 TraesCS2D01G099100 chr2B 90.909 385 21 5 1 377 79710150 79709772 4.880000e-139 505.0
16 TraesCS2D01G099100 chr2B 85.897 312 22 8 3932 4226 79706399 79706093 3.170000e-81 313.0
17 TraesCS2D01G099100 chr2B 90.594 202 14 3 457 658 79672387 79672191 3.240000e-66 263.0
18 TraesCS2D01G099100 chr7D 81.137 2709 454 34 508 3203 76396486 76399150 0.000000e+00 2119.0
19 TraesCS2D01G099100 chr7D 82.786 2039 326 18 1175 3203 79360862 79358839 0.000000e+00 1797.0
20 TraesCS2D01G099100 chr7D 81.237 1455 256 15 785 2232 79208594 79207150 0.000000e+00 1158.0
21 TraesCS2D01G099100 chr7D 78.011 714 115 27 475 1179 79376668 79375988 1.090000e-110 411.0
22 TraesCS2D01G099100 chr7A 81.943 2481 412 28 738 3203 80313655 80316114 0.000000e+00 2067.0
23 TraesCS2D01G099100 chr7A 83.704 2025 308 14 1187 3203 82155452 82153442 0.000000e+00 1892.0
24 TraesCS2D01G099100 chr7B 82.540 2291 366 24 778 3053 26654430 26652159 0.000000e+00 1984.0


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 TraesCS2D01G099100 chr2D 51156930 51161155 4225 True 7805.000000 7805 100.000000 1 4226 1 chr2D.!!$R2 4225
1 TraesCS2D01G099100 chr2D 51253154 51255492 2338 False 2601.000000 2601 86.814000 869 3205 1 chr2D.!!$F1 2336
2 TraesCS2D01G099100 chr2D 51137205 51139801 2596 True 597.500000 1050 85.491500 416 1551 2 chr2D.!!$R3 1135
3 TraesCS2D01G099100 chr2A 52756522 52758862 2340 False 2519.000000 2519 86.188000 869 3205 1 chr2A.!!$F1 2336
4 TraesCS2D01G099100 chr2A 52569985 52573732 3747 True 2021.666667 5531 93.338667 410 4221 3 chr2A.!!$R2 3811
5 TraesCS2D01G099100 chr2B 80200438 80202776 2338 False 2562.000000 2562 86.522000 869 3205 1 chr2B.!!$F1 2336
6 TraesCS2D01G099100 chr2B 794029626 794032143 2517 True 2041.000000 2041 81.684000 601 3124 1 chr2B.!!$R1 2523
7 TraesCS2D01G099100 chr2B 79706093 79710150 4057 True 1970.666667 5094 90.501000 1 4226 3 chr2B.!!$R3 4225
8 TraesCS2D01G099100 chr2B 79669600 79672387 2787 True 1318.500000 2374 87.752000 457 3137 2 chr2B.!!$R2 2680
9 TraesCS2D01G099100 chr7D 76396486 76399150 2664 False 2119.000000 2119 81.137000 508 3203 1 chr7D.!!$F1 2695
10 TraesCS2D01G099100 chr7D 79358839 79360862 2023 True 1797.000000 1797 82.786000 1175 3203 1 chr7D.!!$R2 2028
11 TraesCS2D01G099100 chr7D 79207150 79208594 1444 True 1158.000000 1158 81.237000 785 2232 1 chr7D.!!$R1 1447
12 TraesCS2D01G099100 chr7D 79375988 79376668 680 True 411.000000 411 78.011000 475 1179 1 chr7D.!!$R3 704
13 TraesCS2D01G099100 chr7A 80313655 80316114 2459 False 2067.000000 2067 81.943000 738 3203 1 chr7A.!!$F1 2465
14 TraesCS2D01G099100 chr7A 82153442 82155452 2010 True 1892.000000 1892 83.704000 1187 3203 1 chr7A.!!$R1 2016
15 TraesCS2D01G099100 chr7B 26652159 26654430 2271 True 1984.000000 1984 82.540000 778 3053 1 chr7B.!!$R1 2275

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
25 26 0.252284 TCTTCCCCTCTGTCTGTCCC 60.252 60.0 0.00 0.00 0.00 4.46 F
299 302 0.468029 CAACTGGTGGCCCTCAACTT 60.468 55.0 0.00 0.00 33.29 2.66 F
1909 3608 0.179048 TGCTATGTCCAAGGGCATCG 60.179 55.0 9.87 5.11 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 3286 1.587054 CCTCTTCGTCGCCAGAGTT 59.413 57.895 15.94 0.0 35.64 3.01 R
2214 3925 1.209504 GCACCAGCACCCACTATTCTA 59.790 52.381 0.00 0.0 41.58 2.10 R
3777 5525 0.038159 ACGACCTTGAGTAGCACAGC 60.038 55.000 0.00 0.0 0.00 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
23 24 2.167487 GACATCTTCCCCTCTGTCTGTC 59.833 54.545 0.00 0.00 36.07 3.51
25 26 0.252284 TCTTCCCCTCTGTCTGTCCC 60.252 60.000 0.00 0.00 0.00 4.46
29 30 1.364678 TCCCCTCTGTCTGTCCCATTA 59.635 52.381 0.00 0.00 0.00 1.90
65 66 1.350351 AGAGTTGCTGATGCTCTGGTT 59.650 47.619 0.00 0.00 38.09 3.67
66 67 1.736681 GAGTTGCTGATGCTCTGGTTC 59.263 52.381 0.00 0.00 40.48 3.62
85 86 5.068460 TGGTTCATAACAGTTGGGTCAAAAG 59.932 40.000 0.00 0.00 0.00 2.27
94 95 5.652452 ACAGTTGGGTCAAAAGATATTAGGC 59.348 40.000 0.00 0.00 0.00 3.93
99 100 6.013379 TGGGTCAAAAGATATTAGGCAACAA 58.987 36.000 0.00 0.00 41.41 2.83
135 137 1.830477 TCATGCAAAATACTTGGGCCC 59.170 47.619 17.59 17.59 0.00 5.80
141 143 1.089123 AAATACTTGGGCCCTGGGAA 58.911 50.000 25.70 7.85 0.00 3.97
142 144 1.089123 AATACTTGGGCCCTGGGAAA 58.911 50.000 25.70 7.41 0.00 3.13
163 165 7.939039 GGGAAATATTATCTGACATCCAACTCA 59.061 37.037 0.00 0.00 0.00 3.41
222 224 1.160137 CTGAAGGGCGTTTTCTCAGG 58.840 55.000 0.00 0.00 0.00 3.86
250 253 8.519799 AATCAGTTTACAAGTCCTTTTTCAGA 57.480 30.769 0.00 0.00 0.00 3.27
263 266 6.922957 GTCCTTTTTCAGATGCAATGTGTTTA 59.077 34.615 0.00 0.00 38.95 2.01
264 267 6.922957 TCCTTTTTCAGATGCAATGTGTTTAC 59.077 34.615 0.00 0.00 38.95 2.01
265 268 6.925165 CCTTTTTCAGATGCAATGTGTTTACT 59.075 34.615 0.00 0.00 38.95 2.24
266 269 7.439056 CCTTTTTCAGATGCAATGTGTTTACTT 59.561 33.333 0.00 0.00 38.95 2.24
267 270 8.715191 TTTTTCAGATGCAATGTGTTTACTTT 57.285 26.923 0.00 0.00 38.95 2.66
291 294 2.441750 TCCCTAATATCAACTGGTGGCC 59.558 50.000 0.00 0.00 0.00 5.36
296 299 1.367346 TATCAACTGGTGGCCCTCAA 58.633 50.000 0.00 0.00 0.00 3.02
299 302 0.468029 CAACTGGTGGCCCTCAACTT 60.468 55.000 0.00 0.00 33.29 2.66
301 304 1.145571 ACTGGTGGCCCTCAACTTTA 58.854 50.000 0.00 0.00 33.29 1.85
302 305 1.710809 ACTGGTGGCCCTCAACTTTAT 59.289 47.619 0.00 0.00 33.29 1.40
303 306 2.916934 ACTGGTGGCCCTCAACTTTATA 59.083 45.455 0.00 0.00 33.29 0.98
305 308 3.186283 TGGTGGCCCTCAACTTTATAGA 58.814 45.455 0.00 0.00 33.29 1.98
386 430 2.620115 CAGTGTTTGTGCAGATTGGTCT 59.380 45.455 0.00 0.00 34.14 3.85
406 450 1.371183 CTGGAACGCCAAGTCCAGA 59.629 57.895 13.35 0.00 45.41 3.86
427 497 6.310197 CAGACGTTTCTTCCATTTCTTCATC 58.690 40.000 0.00 0.00 0.00 2.92
434 504 2.910199 TCCATTTCTTCATCCAGCTCG 58.090 47.619 0.00 0.00 0.00 5.03
497 572 6.695713 GGTTTTGAGCGTAAAAGAAAATGACT 59.304 34.615 2.07 0.00 30.79 3.41
501 576 6.831769 TGAGCGTAAAAGAAAATGACTCATC 58.168 36.000 0.00 0.00 0.00 2.92
646 732 8.424274 AACCAGAAGCTGTTAATTTTGAAAAG 57.576 30.769 0.00 0.00 0.00 2.27
647 733 7.781056 ACCAGAAGCTGTTAATTTTGAAAAGA 58.219 30.769 0.00 0.00 0.00 2.52
812 2484 9.964354 CCCACATAATCTTATCATATCTTCCAA 57.036 33.333 0.00 0.00 0.00 3.53
932 2611 3.692101 CCGTGTTGTATAAAGATTGCCCA 59.308 43.478 0.00 0.00 0.00 5.36
973 2654 3.499537 GCATTGCCATCATCTTCATCGTA 59.500 43.478 0.00 0.00 0.00 3.43
1027 2710 4.500837 CGTCATTCACAAATCTCTCGGTAG 59.499 45.833 0.00 0.00 0.00 3.18
1309 2995 4.554363 CCGACGCCGAGCTCGATT 62.554 66.667 36.59 19.80 43.02 3.34
1600 3286 5.009631 CCAAGTCATTCATCAAGGGTGTTA 58.990 41.667 0.00 0.00 0.00 2.41
1909 3608 0.179048 TGCTATGTCCAAGGGCATCG 60.179 55.000 9.87 5.11 0.00 3.84
2214 3925 0.249322 CTCAACAGTCCAACGTCCGT 60.249 55.000 0.00 0.00 0.00 4.69
2709 4436 0.744414 GCACTGGCGGCTCAATCTTA 60.744 55.000 11.43 0.00 0.00 2.10
3219 4955 2.279784 GCTCTTCCGGCCTCATCG 60.280 66.667 0.00 0.00 0.00 3.84
3287 5024 5.934625 TCTTCCTGTTTAAGTCATCTTCAGC 59.065 40.000 0.00 0.00 35.36 4.26
3363 5103 7.707104 ACTTGCATTATGATTTACTTACTGGC 58.293 34.615 0.00 0.00 0.00 4.85
3494 5234 6.101997 ACCTTTTTGTTCAGAGCAAGAAAAG 58.898 36.000 13.44 13.44 32.06 2.27
3665 5413 4.766891 TCCCTCTAAATGCTCAACAAAAGG 59.233 41.667 0.00 0.00 0.00 3.11
3693 5441 6.915300 TGTGAAAATTGTTGGTGTTAATCTCG 59.085 34.615 0.00 0.00 0.00 4.04
3705 5453 4.863131 GTGTTAATCTCGTCAGTAGGGTTG 59.137 45.833 0.00 0.00 0.00 3.77
3716 5464 4.081087 GTCAGTAGGGTTGTATGGATGTGT 60.081 45.833 0.00 0.00 0.00 3.72
3725 5473 6.378582 GGTTGTATGGATGTGTAAGTTTGTG 58.621 40.000 0.00 0.00 0.00 3.33
3742 5490 2.626785 TGTGGGTTTCCTGGAGACATA 58.373 47.619 17.97 4.51 41.51 2.29
3743 5491 3.189606 TGTGGGTTTCCTGGAGACATAT 58.810 45.455 17.97 0.00 41.51 1.78
3744 5492 4.367166 TGTGGGTTTCCTGGAGACATATA 58.633 43.478 17.97 3.22 41.51 0.86
3745 5493 4.975147 TGTGGGTTTCCTGGAGACATATAT 59.025 41.667 17.97 0.00 41.51 0.86
3746 5494 5.163205 TGTGGGTTTCCTGGAGACATATATG 60.163 44.000 17.97 11.29 41.51 1.78
3747 5495 4.202461 TGGGTTTCCTGGAGACATATATGC 60.202 45.833 17.97 5.91 41.51 3.14
3748 5496 3.997021 GGTTTCCTGGAGACATATATGCG 59.003 47.826 17.97 0.00 41.51 4.73
3749 5497 4.503296 GGTTTCCTGGAGACATATATGCGT 60.503 45.833 17.97 0.00 41.51 5.24
3750 5498 4.955811 TTCCTGGAGACATATATGCGTT 57.044 40.909 12.79 0.00 41.51 4.84
3751 5499 4.521130 TCCTGGAGACATATATGCGTTC 57.479 45.455 12.79 7.71 41.51 3.95
3752 5500 3.258372 TCCTGGAGACATATATGCGTTCC 59.742 47.826 12.79 15.72 41.51 3.62
3763 5511 7.497595 ACATATATGCGTTCCTGAGTTTAAGA 58.502 34.615 12.79 0.00 0.00 2.10
3767 5515 5.401531 TGCGTTCCTGAGTTTAAGACTAT 57.598 39.130 0.00 0.00 39.19 2.12
3769 5517 6.228258 TGCGTTCCTGAGTTTAAGACTATTT 58.772 36.000 0.00 0.00 39.19 1.40
3770 5518 6.708949 TGCGTTCCTGAGTTTAAGACTATTTT 59.291 34.615 0.00 0.00 39.19 1.82
3771 5519 7.227910 TGCGTTCCTGAGTTTAAGACTATTTTT 59.772 33.333 0.00 0.00 39.19 1.94
3772 5520 8.715088 GCGTTCCTGAGTTTAAGACTATTTTTA 58.285 33.333 0.00 0.00 39.19 1.52
3783 5531 6.976636 AAGACTATTTTTAGAGAGCTGTGC 57.023 37.500 0.00 0.00 0.00 4.57
3784 5532 6.293004 AGACTATTTTTAGAGAGCTGTGCT 57.707 37.500 0.00 0.00 43.88 4.40
3785 5533 7.411486 AGACTATTTTTAGAGAGCTGTGCTA 57.589 36.000 0.00 0.00 39.88 3.49
3786 5534 7.262048 AGACTATTTTTAGAGAGCTGTGCTAC 58.738 38.462 0.00 0.00 39.88 3.58
3787 5535 7.123547 AGACTATTTTTAGAGAGCTGTGCTACT 59.876 37.037 0.00 0.00 39.88 2.57
3788 5536 7.262048 ACTATTTTTAGAGAGCTGTGCTACTC 58.738 38.462 0.00 0.00 39.88 2.59
3789 5537 5.468540 TTTTTAGAGAGCTGTGCTACTCA 57.531 39.130 15.62 1.32 39.88 3.41
3790 5538 5.468540 TTTTAGAGAGCTGTGCTACTCAA 57.531 39.130 15.62 5.75 39.88 3.02
3791 5539 4.710423 TTAGAGAGCTGTGCTACTCAAG 57.290 45.455 15.62 0.00 39.88 3.02
3792 5540 1.824230 AGAGAGCTGTGCTACTCAAGG 59.176 52.381 15.62 0.00 39.88 3.61
3793 5541 1.548269 GAGAGCTGTGCTACTCAAGGT 59.452 52.381 0.00 0.00 39.88 3.50
3794 5542 1.548269 AGAGCTGTGCTACTCAAGGTC 59.452 52.381 0.00 0.00 39.88 3.85
3795 5543 0.244994 AGCTGTGCTACTCAAGGTCG 59.755 55.000 0.00 0.00 36.99 4.79
3826 5574 6.925610 TGCCTTCACATATGAATACTTCAC 57.074 37.500 10.38 0.00 43.92 3.18
3835 5583 6.587990 ACATATGAATACTTCACTATGAGCGC 59.412 38.462 10.38 0.00 43.48 5.92
3866 5614 2.756760 AGATGCAAAATGCCGATCACTT 59.243 40.909 0.00 0.00 44.23 3.16
3878 5626 4.751600 TGCCGATCACTTGATATGCTAAAG 59.248 41.667 11.60 0.00 34.37 1.85
3898 5646 8.023128 GCTAAAGAAAAGTTAGAATGCACATCA 58.977 33.333 0.00 0.00 31.37 3.07
3900 5648 6.259550 AGAAAAGTTAGAATGCACATCACC 57.740 37.500 0.00 0.00 0.00 4.02
3903 5651 3.614092 AGTTAGAATGCACATCACCAGG 58.386 45.455 0.00 0.00 0.00 4.45
3905 5653 1.830279 AGAATGCACATCACCAGGTG 58.170 50.000 14.19 14.19 38.05 4.00
3910 5658 0.593128 GCACATCACCAGGTGTTGAC 59.407 55.000 29.99 19.73 36.91 3.18
3935 5683 4.621068 TGCTAGTGCTATCAAACATTGC 57.379 40.909 0.00 0.00 40.48 3.56
3960 5708 0.890683 CCACTTTCCATCAAGCACCC 59.109 55.000 0.00 0.00 0.00 4.61
3971 5719 0.540365 CAAGCACCCACATCCAGGTT 60.540 55.000 0.00 0.00 32.72 3.50
4003 5751 6.594788 ACAATGCATTCTTGTATGGTCTTT 57.405 33.333 9.53 0.00 35.15 2.52
4006 5754 5.885230 TGCATTCTTGTATGGTCTTTCAG 57.115 39.130 0.00 0.00 0.00 3.02
4068 5816 6.352222 GGAAGGACTAACTGAATCTCATTCCA 60.352 42.308 6.52 0.00 38.50 3.53
4103 5851 2.023673 CTGAGACGCTCAATCTCTCCT 58.976 52.381 10.12 0.00 42.68 3.69
4109 5857 5.194432 AGACGCTCAATCTCTCCTTTAGTA 58.806 41.667 0.00 0.00 0.00 1.82
4178 5944 1.434555 CACCGCATTCTGTTACCGAA 58.565 50.000 0.00 0.00 0.00 4.30
4185 5951 3.120304 GCATTCTGTTACCGAACTTCCAC 60.120 47.826 0.00 0.00 36.45 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.753073 CTCTTTGCTTGGCCTAATGGG 59.247 52.381 3.32 0.00 38.36 4.00
25 26 2.686915 CTCCTCTTTGCTTGGCCTAATG 59.313 50.000 3.32 0.00 0.00 1.90
29 30 0.327591 CTCTCCTCTTTGCTTGGCCT 59.672 55.000 3.32 0.00 0.00 5.19
65 66 8.877864 AATATCTTTTGACCCAACTGTTATGA 57.122 30.769 0.00 0.00 0.00 2.15
126 128 1.318934 ATATTTCCCAGGGCCCAAGT 58.681 50.000 27.56 8.80 0.00 3.16
135 137 7.941238 AGTTGGATGTCAGATAATATTTCCCAG 59.059 37.037 0.00 0.00 0.00 4.45
141 143 8.153550 GGACTGAGTTGGATGTCAGATAATATT 58.846 37.037 6.35 0.00 42.49 1.28
142 144 7.256475 GGGACTGAGTTGGATGTCAGATAATAT 60.256 40.741 6.35 0.00 42.49 1.28
163 165 0.250513 GAATCGCTCCTGTTGGGACT 59.749 55.000 0.00 0.00 39.58 3.85
222 224 9.581099 TGAAAAAGGACTTGTAAACTGATTTTC 57.419 29.630 0.00 0.00 35.01 2.29
250 253 6.010219 AGGGAGTAAAGTAAACACATTGCAT 58.990 36.000 0.00 0.00 0.00 3.96
263 266 7.365652 CCACCAGTTGATATTAGGGAGTAAAGT 60.366 40.741 0.00 0.00 0.00 2.66
264 267 6.992715 CCACCAGTTGATATTAGGGAGTAAAG 59.007 42.308 0.00 0.00 0.00 1.85
265 268 6.634039 GCCACCAGTTGATATTAGGGAGTAAA 60.634 42.308 0.00 0.00 0.00 2.01
266 269 5.163237 GCCACCAGTTGATATTAGGGAGTAA 60.163 44.000 0.00 0.00 0.00 2.24
267 270 4.347000 GCCACCAGTTGATATTAGGGAGTA 59.653 45.833 0.00 0.00 0.00 2.59
296 299 7.235812 ACCAGTTGAGTTCTTCCTCTATAAAGT 59.764 37.037 0.00 0.00 32.50 2.66
299 302 6.070767 CCACCAGTTGAGTTCTTCCTCTATAA 60.071 42.308 0.00 0.00 32.50 0.98
301 304 4.223923 CCACCAGTTGAGTTCTTCCTCTAT 59.776 45.833 0.00 0.00 32.50 1.98
302 305 3.578716 CCACCAGTTGAGTTCTTCCTCTA 59.421 47.826 0.00 0.00 32.50 2.43
303 306 2.370189 CCACCAGTTGAGTTCTTCCTCT 59.630 50.000 0.00 0.00 32.50 3.69
305 308 1.202818 GCCACCAGTTGAGTTCTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
386 430 0.320374 CTGGACTTGGCGTTCCAGTA 59.680 55.000 16.75 0.00 44.53 2.74
406 450 5.070001 TGGATGAAGAAATGGAAGAAACGT 58.930 37.500 0.00 0.00 0.00 3.99
427 497 7.491372 TCTTGAACAAATATTAGTACGAGCTGG 59.509 37.037 0.00 0.00 0.00 4.85
497 572 5.512942 TGAAATTAGGTGAGGTTGGATGA 57.487 39.130 0.00 0.00 0.00 2.92
501 576 5.256474 AGTCATGAAATTAGGTGAGGTTGG 58.744 41.667 0.00 0.00 0.00 3.77
599 682 6.499350 GGTTCTGTATCCCCACCTATAATGTA 59.501 42.308 0.00 0.00 0.00 2.29
600 683 5.309806 GGTTCTGTATCCCCACCTATAATGT 59.690 44.000 0.00 0.00 0.00 2.71
602 685 5.482580 TGGTTCTGTATCCCCACCTATAAT 58.517 41.667 0.00 0.00 0.00 1.28
603 686 4.898268 TGGTTCTGTATCCCCACCTATAA 58.102 43.478 0.00 0.00 0.00 0.98
604 687 4.171243 TCTGGTTCTGTATCCCCACCTATA 59.829 45.833 0.00 0.00 0.00 1.31
683 826 8.160521 TCGATTTTCTGAATGGTCTTTAACAA 57.839 30.769 0.00 0.00 0.00 2.83
910 2587 3.692101 TGGGCAATCTTTATACAACACGG 59.308 43.478 0.00 0.00 0.00 4.94
932 2611 5.579753 ATGCCAGAATAGGATCAATCACT 57.420 39.130 0.00 0.00 0.00 3.41
1027 2710 1.736681 GATGGTGAGCAAGAGAAGTGC 59.263 52.381 0.00 0.00 42.55 4.40
1600 3286 1.587054 CCTCTTCGTCGCCAGAGTT 59.413 57.895 15.94 0.00 35.64 3.01
1632 3318 3.755628 GCTGCCGTGGACGAGGTA 61.756 66.667 0.00 0.00 43.02 3.08
1909 3608 2.969806 CTGCGGCACACACCATGAC 61.970 63.158 0.00 0.00 0.00 3.06
2214 3925 1.209504 GCACCAGCACCCACTATTCTA 59.790 52.381 0.00 0.00 41.58 2.10
2709 4436 0.459237 CCTTTCGATGCTGCTCGTCT 60.459 55.000 16.79 0.00 39.62 4.18
3219 4955 1.002468 GGCACGTACATCATTCATGGC 60.002 52.381 0.00 0.00 36.72 4.40
3245 4981 9.220767 ACAGGAAGAAATAAAACATCTAGTGAC 57.779 33.333 0.00 0.00 0.00 3.67
3324 5064 5.678132 AATGCAAGTTTTTCTTCCATTGC 57.322 34.783 0.00 0.00 41.36 3.56
3494 5234 2.548480 CAGAAGTTTCCGTCCACCTTTC 59.452 50.000 0.00 0.00 0.00 2.62
3613 5361 5.806502 TGCATCAAAGCGGAAATAATTTCAG 59.193 36.000 0.00 0.00 41.43 3.02
3625 5373 0.942962 GGAGATCTGCATCAAAGCGG 59.057 55.000 9.69 0.00 42.28 5.52
3665 5413 9.260002 AGATTAACACCAACAATTTTCACATTC 57.740 29.630 0.00 0.00 0.00 2.67
3693 5441 4.081087 ACACATCCATACAACCCTACTGAC 60.081 45.833 0.00 0.00 0.00 3.51
3705 5453 5.007682 ACCCACAAACTTACACATCCATAC 58.992 41.667 0.00 0.00 0.00 2.39
3716 5464 3.460340 TCTCCAGGAAACCCACAAACTTA 59.540 43.478 0.00 0.00 0.00 2.24
3725 5473 4.327680 GCATATATGTCTCCAGGAAACCC 58.672 47.826 14.14 0.00 0.00 4.11
3742 5490 5.978814 AGTCTTAAACTCAGGAACGCATAT 58.021 37.500 0.00 0.00 30.02 1.78
3743 5491 5.401531 AGTCTTAAACTCAGGAACGCATA 57.598 39.130 0.00 0.00 30.02 3.14
3744 5492 4.273148 AGTCTTAAACTCAGGAACGCAT 57.727 40.909 0.00 0.00 30.02 4.73
3745 5493 3.746045 AGTCTTAAACTCAGGAACGCA 57.254 42.857 0.00 0.00 30.02 5.24
3746 5494 6.723131 AAATAGTCTTAAACTCAGGAACGC 57.277 37.500 0.00 0.00 39.55 4.84
3763 5511 7.093727 TGAGTAGCACAGCTCTCTAAAAATAGT 60.094 37.037 14.73 0.00 40.44 2.12
3767 5515 5.468540 TGAGTAGCACAGCTCTCTAAAAA 57.531 39.130 14.73 0.00 40.44 1.94
3769 5517 4.081972 CCTTGAGTAGCACAGCTCTCTAAA 60.082 45.833 14.73 6.79 40.44 1.85
3770 5518 3.445450 CCTTGAGTAGCACAGCTCTCTAA 59.555 47.826 14.73 9.37 40.44 2.10
3771 5519 3.020274 CCTTGAGTAGCACAGCTCTCTA 58.980 50.000 14.73 9.44 40.44 2.43
3772 5520 1.824230 CCTTGAGTAGCACAGCTCTCT 59.176 52.381 14.73 7.71 40.44 3.10
3773 5521 1.548269 ACCTTGAGTAGCACAGCTCTC 59.452 52.381 0.00 3.51 40.44 3.20
3774 5522 1.548269 GACCTTGAGTAGCACAGCTCT 59.452 52.381 0.00 0.00 40.44 4.09
3775 5523 1.734047 CGACCTTGAGTAGCACAGCTC 60.734 57.143 0.00 0.00 40.44 4.09
3776 5524 0.244994 CGACCTTGAGTAGCACAGCT 59.755 55.000 0.00 0.00 43.41 4.24
3777 5525 0.038159 ACGACCTTGAGTAGCACAGC 60.038 55.000 0.00 0.00 0.00 4.40
3778 5526 2.061773 CAACGACCTTGAGTAGCACAG 58.938 52.381 0.00 0.00 30.42 3.66
3779 5527 1.411246 ACAACGACCTTGAGTAGCACA 59.589 47.619 0.00 0.00 33.59 4.57
3780 5528 1.792949 CACAACGACCTTGAGTAGCAC 59.207 52.381 0.00 0.00 33.59 4.40
3781 5529 1.411246 ACACAACGACCTTGAGTAGCA 59.589 47.619 0.00 0.00 32.46 3.49
3782 5530 2.150397 ACACAACGACCTTGAGTAGC 57.850 50.000 0.00 0.00 32.46 3.58
3783 5531 3.303132 GCAAACACAACGACCTTGAGTAG 60.303 47.826 0.00 0.00 33.01 2.57
3784 5532 2.610374 GCAAACACAACGACCTTGAGTA 59.390 45.455 0.00 0.00 33.01 2.59
3785 5533 1.400494 GCAAACACAACGACCTTGAGT 59.600 47.619 0.00 0.00 35.40 3.41
3786 5534 1.268539 GGCAAACACAACGACCTTGAG 60.269 52.381 0.00 0.00 33.59 3.02
3787 5535 0.736053 GGCAAACACAACGACCTTGA 59.264 50.000 0.00 0.00 33.59 3.02
3788 5536 0.738389 AGGCAAACACAACGACCTTG 59.262 50.000 0.00 0.00 35.77 3.61
3789 5537 1.404035 GAAGGCAAACACAACGACCTT 59.596 47.619 0.00 0.00 40.14 3.50
3790 5538 1.021968 GAAGGCAAACACAACGACCT 58.978 50.000 0.00 0.00 0.00 3.85
3791 5539 0.736053 TGAAGGCAAACACAACGACC 59.264 50.000 0.00 0.00 0.00 4.79
3792 5540 1.131504 TGTGAAGGCAAACACAACGAC 59.868 47.619 8.47 0.00 42.72 4.34
3793 5541 1.454201 TGTGAAGGCAAACACAACGA 58.546 45.000 8.47 0.00 42.72 3.85
3794 5542 7.060986 ATTCATATGTGAAGGCAAACACAACG 61.061 38.462 10.79 7.06 46.75 4.10
3795 5543 6.158598 ATTCATATGTGAAGGCAAACACAAC 58.841 36.000 10.79 0.00 46.75 3.32
3849 5597 2.634982 TCAAGTGATCGGCATTTTGC 57.365 45.000 0.00 0.00 44.08 3.68
3856 5604 4.991056 TCTTTAGCATATCAAGTGATCGGC 59.009 41.667 0.00 3.35 36.05 5.54
3858 5606 8.607459 ACTTTTCTTTAGCATATCAAGTGATCG 58.393 33.333 0.00 0.00 36.05 3.69
3878 5626 6.012658 TGGTGATGTGCATTCTAACTTTTC 57.987 37.500 0.00 0.00 0.00 2.29
3898 5646 3.583086 ACTAGCATTAGTCAACACCTGGT 59.417 43.478 0.00 0.00 35.13 4.00
3900 5648 3.372206 GCACTAGCATTAGTCAACACCTG 59.628 47.826 0.00 0.00 38.05 4.00
3903 5651 6.042777 TGATAGCACTAGCATTAGTCAACAC 58.957 40.000 0.00 0.00 45.49 3.32
3905 5653 7.064609 TGTTTGATAGCACTAGCATTAGTCAAC 59.935 37.037 0.00 0.00 45.49 3.18
3910 5658 6.854892 GCAATGTTTGATAGCACTAGCATTAG 59.145 38.462 0.00 0.00 45.49 1.73
3960 5708 5.654603 TGTACTACTACAACCTGGATGTG 57.345 43.478 18.68 11.25 29.36 3.21
3971 5719 9.313118 CATACAAGAATGCATTGTACTACTACA 57.687 33.333 18.59 0.00 43.76 2.74
3995 5743 8.641498 AATGTCATTTTCTACTGAAAGACCAT 57.359 30.769 0.00 0.00 42.34 3.55
4024 5772 8.198778 GTCCTTCCATTGTAAAACTAACCAAAA 58.801 33.333 0.00 0.00 0.00 2.44
4027 5775 6.607019 AGTCCTTCCATTGTAAAACTAACCA 58.393 36.000 0.00 0.00 0.00 3.67
4042 5790 6.352222 GGAATGAGATTCAGTTAGTCCTTCCA 60.352 42.308 0.00 0.00 41.03 3.53
4103 5851 9.725019 ACAATGTTCAAGATCTCACATACTAAA 57.275 29.630 13.01 0.00 0.00 1.85
4143 5891 2.632377 CGGTGCATGAAATCCTGTAGT 58.368 47.619 0.00 0.00 0.00 2.73
4146 5894 0.608856 TGCGGTGCATGAAATCCTGT 60.609 50.000 0.00 0.00 31.71 4.00
4178 5944 0.472734 AGACAGGAGCCAGTGGAAGT 60.473 55.000 15.20 2.54 0.00 3.01
4185 5951 0.907486 TTCCATGAGACAGGAGCCAG 59.093 55.000 0.00 0.00 34.91 4.85


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

AutoCloner maintained by Alex Coulton.