Multiple sequence alignment - TraesCS2A01G279300

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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 TraesCS2A01G279300 chr2A 100.000 4367 0 0 1 4367 464857921 464853555 0.000000e+00 8065
1 TraesCS2A01G279300 chr2B 96.287 3205 76 14 399 3576 415317038 415313850 0.000000e+00 5219
2 TraesCS2A01G279300 chr2B 90.361 415 23 4 1 414 415317455 415317057 2.990000e-146 529
3 TraesCS2A01G279300 chr2B 92.958 284 16 2 3643 3923 415313859 415313577 1.130000e-110 411
4 TraesCS2A01G279300 chr2B 86.510 341 38 4 4033 4365 415313533 415313193 6.900000e-98 368
5 TraesCS2A01G279300 chr2B 92.143 140 11 0 1 140 415325403 415325264 9.580000e-47 198
6 TraesCS2A01G279300 chr2D 97.045 2640 50 15 963 3576 349562247 349559610 0.000000e+00 4418
7 TraesCS2A01G279300 chr2D 92.057 705 35 6 1 702 349564440 349563754 0.000000e+00 972
8 TraesCS2A01G279300 chr2D 95.423 284 9 2 3643 3923 349559619 349559337 2.400000e-122 449
9 TraesCS2A01G279300 chr2D 96.234 239 3 4 689 926 349562812 349562579 1.900000e-103 387
10 TraesCS2A01G279300 chr2D 89.916 238 14 4 4032 4259 349559295 349559058 9.180000e-77 298
11 TraesCS2A01G279300 chr2D 93.902 164 10 0 4204 4367 349559063 349558900 9.380000e-62 248
12 TraesCS2A01G279300 chr2D 92.982 114 8 0 3923 4036 383552232 383552119 2.700000e-37 167
13 TraesCS2A01G279300 chr4D 83.267 1769 208 59 1832 3572 445339113 445337405 0.000000e+00 1546
14 TraesCS2A01G279300 chr4A 83.080 1779 220 62 1832 3572 22730283 22728548 0.000000e+00 1543
15 TraesCS2A01G279300 chr4B 82.260 1770 231 62 1832 3572 554816801 554815086 0.000000e+00 1452
16 TraesCS2A01G279300 chr7A 95.536 112 5 0 3923 4034 666808026 666808137 3.470000e-41 180
17 TraesCS2A01G279300 chr1D 92.623 122 7 1 3915 4036 315462378 315462497 1.610000e-39 174
18 TraesCS2A01G279300 chr3A 94.595 111 6 0 3923 4033 492706538 492706428 5.810000e-39 172
19 TraesCS2A01G279300 chr7B 93.750 112 7 0 3923 4034 296754947 296755058 7.510000e-38 169
20 TraesCS2A01G279300 chr1B 93.750 112 7 0 3923 4034 647545206 647545317 7.510000e-38 169
21 TraesCS2A01G279300 chr1B 93.694 111 7 0 3923 4033 570480321 570480431 2.700000e-37 167
22 TraesCS2A01G279300 chr5B 93.694 111 7 0 3923 4033 116826274 116826384 2.700000e-37 167
23 TraesCS2A01G279300 chr5A 93.694 111 7 0 3923 4033 377924993 377925103 2.700000e-37 167


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 TraesCS2A01G279300 chr2A 464853555 464857921 4366 True 8065.000000 8065 100.000000 1 4367 1 chr2A.!!$R1 4366
1 TraesCS2A01G279300 chr2B 415313193 415317455 4262 True 1631.750000 5219 91.529000 1 4365 4 chr2B.!!$R2 4364
2 TraesCS2A01G279300 chr2D 349558900 349564440 5540 True 1128.666667 4418 94.096167 1 4367 6 chr2D.!!$R2 4366
3 TraesCS2A01G279300 chr4D 445337405 445339113 1708 True 1546.000000 1546 83.267000 1832 3572 1 chr4D.!!$R1 1740
4 TraesCS2A01G279300 chr4A 22728548 22730283 1735 True 1543.000000 1543 83.080000 1832 3572 1 chr4A.!!$R1 1740
5 TraesCS2A01G279300 chr4B 554815086 554816801 1715 True 1452.000000 1452 82.260000 1832 3572 1 chr4B.!!$R1 1740

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
98 99 0.038890 GGCAAGCTTTCTTCCCTCCT 59.961 55.0 0.0 0.0 27.19 3.69 F
1110 2401 0.464916 GGGTTCCTGTTGTCGGTTGT 60.465 55.0 0.0 0.0 0.00 3.32 F
1200 2492 0.039180 GGGGTTTGGTAGGGTCTTGG 59.961 60.0 0.0 0.0 0.00 3.61 F
1550 2845 0.250124 TTGGTCATTCTTCGTGGCGT 60.250 50.0 0.0 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 2492 0.250640 CCTCATGCCCATGCTAGTCC 60.251 60.000 3.41 0.00 38.65 3.85 R
2181 3493 3.444703 ACTTCGAACATAGCCAGCTAG 57.555 47.619 5.49 0.85 31.45 3.42 R
2536 3859 4.259356 GGCTTTAACGGAACCAGATAAGT 58.741 43.478 0.00 0.00 0.00 2.24 R
3519 4880 3.692593 CACCACAGATGAATGCTGAATCA 59.307 43.478 0.00 0.00 36.86 2.57 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
44 45 4.208632 CACCTCGTGGATTGCTCC 57.791 61.111 11.17 0.00 42.45 4.70
81 82 2.844451 TTGGCTTTGACACGCAGGC 61.844 57.895 0.00 0.00 0.00 4.85
98 99 0.038890 GGCAAGCTTTCTTCCCTCCT 59.961 55.000 0.00 0.00 27.19 3.69
116 118 2.501723 TCCTCCCTCTCATTTTTCTCCG 59.498 50.000 0.00 0.00 0.00 4.63
143 145 0.534203 TTCGTTTGCCTCCGCTTTCT 60.534 50.000 0.00 0.00 35.36 2.52
192 194 1.568504 TGGATAGGAACCGAGTGCTT 58.431 50.000 0.00 0.00 0.00 3.91
328 330 9.643693 CATTTTAGGATTGCACTAGAACATTTT 57.356 29.630 0.00 0.00 0.00 1.82
416 452 3.889196 TCAAACAATCGTGTAGTTGGC 57.111 42.857 0.00 0.00 36.80 4.52
454 493 1.134907 CCACCAGCAAAAGATGGATGC 60.135 52.381 6.79 0.00 39.02 3.91
533 572 3.776340 TCTTTTTCAACAAACGAAGGGC 58.224 40.909 0.00 0.00 0.00 5.19
682 721 2.736995 GCTAGCCGTGCGACAACA 60.737 61.111 2.29 0.00 0.00 3.33
795 1791 5.818136 TTCCATTCCGCATTTCTTTCTAG 57.182 39.130 0.00 0.00 0.00 2.43
796 1792 4.843728 TCCATTCCGCATTTCTTTCTAGT 58.156 39.130 0.00 0.00 0.00 2.57
797 1793 5.984725 TCCATTCCGCATTTCTTTCTAGTA 58.015 37.500 0.00 0.00 0.00 1.82
814 1810 8.706322 TTTCTAGTATTTTCTTTCTGCCCTTT 57.294 30.769 0.00 0.00 0.00 3.11
815 1811 7.923414 TCTAGTATTTTCTTTCTGCCCTTTC 57.077 36.000 0.00 0.00 0.00 2.62
1078 2369 1.919918 CAACAACCAAATGTGCGTGT 58.080 45.000 0.00 0.00 32.81 4.49
1110 2401 0.464916 GGGTTCCTGTTGTCGGTTGT 60.465 55.000 0.00 0.00 0.00 3.32
1111 2402 0.661020 GGTTCCTGTTGTCGGTTGTG 59.339 55.000 0.00 0.00 0.00 3.33
1177 2469 1.679981 TTGTTGGATGGAGGGGATCA 58.320 50.000 0.00 0.00 0.00 2.92
1200 2492 0.039180 GGGGTTTGGTAGGGTCTTGG 59.961 60.000 0.00 0.00 0.00 3.61
1343 2635 0.463833 GATCCTTAGGTGCCCCGTTG 60.464 60.000 0.00 0.00 35.12 4.10
1539 2834 3.377253 ACTGATGCTGGATTGGTCATT 57.623 42.857 0.00 0.00 0.00 2.57
1549 2844 1.062587 GATTGGTCATTCTTCGTGGCG 59.937 52.381 0.00 0.00 0.00 5.69
1550 2845 0.250124 TTGGTCATTCTTCGTGGCGT 60.250 50.000 0.00 0.00 0.00 5.68
1553 2848 0.865769 GTCATTCTTCGTGGCGTGTT 59.134 50.000 0.00 0.00 0.00 3.32
1617 2912 2.095161 CCACAGAACTGAGTACTCGTCC 60.095 54.545 17.85 7.13 0.00 4.79
1681 2976 7.002879 ACTTATGCCTGATCTCATATTGCTTT 58.997 34.615 0.00 0.00 0.00 3.51
2181 3493 3.258372 TGACATCTGAGGTGGTTCACTAC 59.742 47.826 0.00 0.00 34.40 2.73
2536 3859 4.827692 ACACGCCTGATCAAATGTTAGTA 58.172 39.130 0.00 0.00 0.00 1.82
2538 3861 4.870426 CACGCCTGATCAAATGTTAGTACT 59.130 41.667 0.00 0.00 0.00 2.73
2695 4029 4.793216 CGGTACAAAGCACATTTTCTATGC 59.207 41.667 0.00 0.00 39.74 3.14
2708 4042 7.861372 CACATTTTCTATGCCATCTTTGAGATC 59.139 37.037 0.00 0.00 31.32 2.75
2766 4100 5.921962 TCCAGTCTATGCATATATTCGCT 57.078 39.130 6.92 0.00 0.00 4.93
3401 4762 5.826643 ACTTATTTAACAGCCATTCCCTCA 58.173 37.500 0.00 0.00 0.00 3.86
3517 4878 1.546029 GGATGGCCAACTCTTTGTTCC 59.454 52.381 10.96 4.71 36.63 3.62
3519 4880 2.380064 TGGCCAACTCTTTGTTCCAT 57.620 45.000 0.61 0.00 36.63 3.41
3576 4940 8.757877 TGGCATGCGGCTAATGATATATATATA 58.242 33.333 12.44 4.92 44.01 0.86
3577 4941 9.770097 GGCATGCGGCTAATGATATATATATAT 57.230 33.333 13.97 13.97 44.01 0.86
3748 5118 8.252417 CCTGATGGTTCAACATTCAAATTATGA 58.748 33.333 0.00 0.00 35.85 2.15
3767 5137 8.883954 ATTATGATATCGGCTTGATCACTATG 57.116 34.615 0.00 0.00 38.57 2.23
3851 5221 8.236586 CGAAATAAAGTTGATTTCCAGTCATGA 58.763 33.333 16.88 0.00 39.23 3.07
3914 5284 3.600617 TCCCCCAAAAGTCATTAATCCCT 59.399 43.478 0.00 0.00 0.00 4.20
3916 5286 5.103686 TCCCCCAAAAGTCATTAATCCCTAG 60.104 44.000 0.00 0.00 0.00 3.02
3955 5325 9.755804 TTTCACAAACATTGATATACTTTTGCA 57.244 25.926 0.00 0.00 0.00 4.08
3956 5326 8.741101 TCACAAACATTGATATACTTTTGCAC 57.259 30.769 0.00 0.00 0.00 4.57
3957 5327 8.355913 TCACAAACATTGATATACTTTTGCACA 58.644 29.630 0.00 0.00 0.00 4.57
3958 5328 8.976471 CACAAACATTGATATACTTTTGCACAA 58.024 29.630 0.00 0.00 0.00 3.33
3959 5329 9.539825 ACAAACATTGATATACTTTTGCACAAA 57.460 25.926 0.00 0.00 0.00 2.83
3960 5330 9.796062 CAAACATTGATATACTTTTGCACAAAC 57.204 29.630 0.00 0.00 0.00 2.93
3962 5332 9.709495 AACATTGATATACTTTTGCACAAACAT 57.291 25.926 0.00 0.00 0.00 2.71
3963 5333 9.142515 ACATTGATATACTTTTGCACAAACATG 57.857 29.630 0.00 0.00 0.00 3.21
3964 5334 8.597227 CATTGATATACTTTTGCACAAACATGG 58.403 33.333 0.00 0.00 0.00 3.66
3965 5335 7.225784 TGATATACTTTTGCACAAACATGGT 57.774 32.000 0.00 0.00 0.00 3.55
3966 5336 7.312154 TGATATACTTTTGCACAAACATGGTC 58.688 34.615 0.00 0.00 0.00 4.02
3967 5337 3.883830 ACTTTTGCACAAACATGGTCA 57.116 38.095 0.00 0.00 0.00 4.02
3968 5338 4.199432 ACTTTTGCACAAACATGGTCAA 57.801 36.364 0.00 0.00 0.00 3.18
3969 5339 4.573900 ACTTTTGCACAAACATGGTCAAA 58.426 34.783 0.00 0.00 0.00 2.69
3970 5340 4.391523 ACTTTTGCACAAACATGGTCAAAC 59.608 37.500 0.00 0.00 0.00 2.93
3971 5341 3.883830 TTGCACAAACATGGTCAAACT 57.116 38.095 0.00 0.00 0.00 2.66
3972 5342 3.883830 TGCACAAACATGGTCAAACTT 57.116 38.095 0.00 0.00 0.00 2.66
3973 5343 4.199432 TGCACAAACATGGTCAAACTTT 57.801 36.364 0.00 0.00 0.00 2.66
3974 5344 3.931468 TGCACAAACATGGTCAAACTTTG 59.069 39.130 0.00 0.00 0.00 2.77
3975 5345 4.180057 GCACAAACATGGTCAAACTTTGA 58.820 39.130 9.03 0.00 37.33 2.69
3976 5346 4.268405 GCACAAACATGGTCAAACTTTGAG 59.732 41.667 4.36 3.65 41.01 3.02
3977 5347 5.649557 CACAAACATGGTCAAACTTTGAGA 58.350 37.500 4.36 0.00 41.01 3.27
3978 5348 6.275335 CACAAACATGGTCAAACTTTGAGAT 58.725 36.000 4.36 0.00 41.01 2.75
3979 5349 6.199531 CACAAACATGGTCAAACTTTGAGATG 59.800 38.462 15.82 15.82 41.01 2.90
3980 5350 5.458041 AACATGGTCAAACTTTGAGATGG 57.542 39.130 19.03 8.78 41.01 3.51
3981 5351 4.473444 ACATGGTCAAACTTTGAGATGGT 58.527 39.130 19.03 9.23 41.01 3.55
3982 5352 4.895297 ACATGGTCAAACTTTGAGATGGTT 59.105 37.500 19.03 5.35 41.01 3.67
3983 5353 5.363580 ACATGGTCAAACTTTGAGATGGTTT 59.636 36.000 19.03 0.74 41.01 3.27
3984 5354 5.261209 TGGTCAAACTTTGAGATGGTTTG 57.739 39.130 4.36 10.36 46.18 2.93
3990 5360 6.625873 AAACTTTGAGATGGTTTGACTCTC 57.374 37.500 0.00 0.00 36.72 3.20
3991 5361 4.646572 ACTTTGAGATGGTTTGACTCTCC 58.353 43.478 0.00 0.00 35.59 3.71
3992 5362 4.103153 ACTTTGAGATGGTTTGACTCTCCA 59.897 41.667 0.00 0.00 35.59 3.86
3993 5363 4.705110 TTGAGATGGTTTGACTCTCCAA 57.295 40.909 0.00 0.00 35.59 3.53
3994 5364 4.008074 TGAGATGGTTTGACTCTCCAAC 57.992 45.455 0.00 0.00 35.59 3.77
3995 5365 3.390967 TGAGATGGTTTGACTCTCCAACA 59.609 43.478 0.00 0.00 35.59 3.33
3996 5366 4.141505 TGAGATGGTTTGACTCTCCAACAA 60.142 41.667 0.00 0.00 35.59 2.83
3997 5367 4.792068 AGATGGTTTGACTCTCCAACAAA 58.208 39.130 0.00 0.00 34.80 2.83
3998 5368 4.823989 AGATGGTTTGACTCTCCAACAAAG 59.176 41.667 0.00 0.00 34.86 2.77
3999 5369 3.963129 TGGTTTGACTCTCCAACAAAGT 58.037 40.909 0.00 0.00 34.86 2.66
4000 5370 4.340617 TGGTTTGACTCTCCAACAAAGTT 58.659 39.130 0.00 0.00 34.86 2.66
4001 5371 4.157656 TGGTTTGACTCTCCAACAAAGTTG 59.842 41.667 3.00 3.00 34.86 3.16
4002 5372 4.440112 GGTTTGACTCTCCAACAAAGTTGG 60.440 45.833 20.09 20.09 40.87 3.77
4003 5373 3.924114 TGACTCTCCAACAAAGTTGGA 57.076 42.857 25.17 25.17 45.61 3.53
4004 5374 4.229304 TGACTCTCCAACAAAGTTGGAA 57.771 40.909 26.25 17.81 46.85 3.53
4005 5375 4.199310 TGACTCTCCAACAAAGTTGGAAG 58.801 43.478 26.25 24.81 46.85 3.46
4006 5376 4.200092 GACTCTCCAACAAAGTTGGAAGT 58.800 43.478 27.33 27.33 46.85 3.01
4007 5377 5.104693 TGACTCTCCAACAAAGTTGGAAGTA 60.105 40.000 27.19 18.52 46.85 2.24
4008 5378 5.123936 ACTCTCCAACAAAGTTGGAAGTAC 58.876 41.667 26.25 0.00 46.85 2.73
4009 5379 5.105567 TCTCCAACAAAGTTGGAAGTACA 57.894 39.130 26.25 8.75 46.85 2.90
4010 5380 4.879545 TCTCCAACAAAGTTGGAAGTACAC 59.120 41.667 26.25 0.00 46.85 2.90
4011 5381 4.850680 TCCAACAAAGTTGGAAGTACACT 58.149 39.130 24.83 0.00 44.90 3.55
4012 5382 4.879545 TCCAACAAAGTTGGAAGTACACTC 59.120 41.667 24.83 0.00 44.90 3.51
4013 5383 4.881850 CCAACAAAGTTGGAAGTACACTCT 59.118 41.667 21.24 0.00 42.06 3.24
4014 5384 5.357032 CCAACAAAGTTGGAAGTACACTCTT 59.643 40.000 21.24 0.00 42.06 2.85
4015 5385 6.127730 CCAACAAAGTTGGAAGTACACTCTTT 60.128 38.462 21.24 0.00 42.06 2.52
4016 5386 7.066525 CCAACAAAGTTGGAAGTACACTCTTTA 59.933 37.037 21.24 0.00 42.06 1.85
4017 5387 8.455682 CAACAAAGTTGGAAGTACACTCTTTAA 58.544 33.333 2.05 0.00 0.00 1.52
4018 5388 8.570068 ACAAAGTTGGAAGTACACTCTTTAAA 57.430 30.769 0.00 0.00 0.00 1.52
4019 5389 8.674607 ACAAAGTTGGAAGTACACTCTTTAAAG 58.325 33.333 9.04 9.04 0.00 1.85
4020 5390 7.803279 AAGTTGGAAGTACACTCTTTAAAGG 57.197 36.000 15.13 8.48 0.00 3.11
4021 5391 7.133133 AGTTGGAAGTACACTCTTTAAAGGA 57.867 36.000 15.13 1.82 0.00 3.36
4022 5392 7.746703 AGTTGGAAGTACACTCTTTAAAGGAT 58.253 34.615 15.13 1.07 0.00 3.24
4023 5393 7.661847 AGTTGGAAGTACACTCTTTAAAGGATG 59.338 37.037 15.13 14.75 0.00 3.51
4024 5394 6.472887 TGGAAGTACACTCTTTAAAGGATGG 58.527 40.000 15.13 5.64 0.00 3.51
4025 5395 6.271391 TGGAAGTACACTCTTTAAAGGATGGA 59.729 38.462 15.13 7.76 0.00 3.41
4026 5396 6.819146 GGAAGTACACTCTTTAAAGGATGGAG 59.181 42.308 15.13 7.51 0.00 3.86
4027 5397 6.301169 AGTACACTCTTTAAAGGATGGAGG 57.699 41.667 15.13 2.85 0.00 4.30
4028 5398 4.576330 ACACTCTTTAAAGGATGGAGGG 57.424 45.455 15.13 8.51 34.07 4.30
4029 5399 4.175962 ACACTCTTTAAAGGATGGAGGGA 58.824 43.478 15.13 0.00 32.45 4.20
4030 5400 4.226168 ACACTCTTTAAAGGATGGAGGGAG 59.774 45.833 15.13 4.81 32.45 4.30
4076 5446 6.708949 ACGAAGTCTCAACAAATTTAGGCTAA 59.291 34.615 2.04 2.04 29.74 3.09
4078 5448 7.095187 CGAAGTCTCAACAAATTTAGGCTAACT 60.095 37.037 6.43 0.00 0.00 2.24
4090 5460 1.511768 GCTAACTCGAGCGTCCCTT 59.488 57.895 13.61 0.12 31.57 3.95
4100 5470 2.650778 CGTCCCTTTTGGCCTTGC 59.349 61.111 3.32 0.00 38.58 4.01
4101 5471 2.650778 GTCCCTTTTGGCCTTGCG 59.349 61.111 3.32 0.00 38.58 4.85
4194 5577 4.023107 TGCCAAAATTAATCGGTTTCGTCA 60.023 37.500 0.00 0.00 37.69 4.35
4197 5580 6.318628 CCAAAATTAATCGGTTTCGTCATCA 58.681 36.000 0.00 0.00 37.69 3.07
4219 5602 1.479368 GCCAAGCCCCAATTTGGTCA 61.479 55.000 14.26 0.00 44.52 4.02
4223 5606 0.712380 AGCCCCAATTTGGTCAGGAT 59.288 50.000 14.26 4.55 35.17 3.24
4350 5783 1.918467 CTTCCTCCAGCTCCCATGCA 61.918 60.000 0.00 0.00 34.99 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.383456 AAGCTTGCCTGCGTGTCAAA 61.383 50.000 0.00 0.00 38.13 2.69
81 82 1.340502 GGGAGGAGGGAAGAAAGCTTG 60.341 57.143 0.00 0.00 33.61 4.01
98 99 3.173965 AGACGGAGAAAAATGAGAGGGA 58.826 45.455 0.00 0.00 0.00 4.20
116 118 2.412847 CGGAGGCAAACGAATGAAAGAC 60.413 50.000 0.00 0.00 0.00 3.01
143 145 2.191400 CATGTCCAGGAGAGGAAGGAA 58.809 52.381 0.00 0.00 39.92 3.36
192 194 9.062524 GTTATTGTTGGGAATACACATATAGCA 57.937 33.333 0.00 0.00 0.00 3.49
281 283 3.720002 TGTAGATTAAATGGTCCTCCCCC 59.280 47.826 0.00 0.00 0.00 5.40
282 284 5.584551 ATGTAGATTAAATGGTCCTCCCC 57.415 43.478 0.00 0.00 0.00 4.81
283 285 7.898014 AAAATGTAGATTAAATGGTCCTCCC 57.102 36.000 0.00 0.00 0.00 4.30
284 286 9.067986 CCTAAAATGTAGATTAAATGGTCCTCC 57.932 37.037 0.00 0.00 0.00 4.30
285 287 9.847224 TCCTAAAATGTAGATTAAATGGTCCTC 57.153 33.333 0.00 0.00 0.00 3.71
298 300 8.318412 TGTTCTAGTGCAATCCTAAAATGTAGA 58.682 33.333 0.00 0.00 0.00 2.59
328 330 1.144691 TGGTGGACATGGGTCAAGAA 58.855 50.000 0.00 0.00 46.17 2.52
329 331 1.073763 CTTGGTGGACATGGGTCAAGA 59.926 52.381 0.00 0.00 46.17 3.02
416 452 1.548719 TGGTAACGAGACCATGGACAG 59.451 52.381 21.47 13.14 44.79 3.51
533 572 9.337396 TCCATTGGCTGTATACTTTAATACTTG 57.663 33.333 4.17 0.00 34.13 3.16
594 633 0.827368 AAGGTCCAGCTAGCTACAGC 59.173 55.000 18.86 15.81 42.12 4.40
682 721 0.809636 GCTTTGCCACCTTTGCGTTT 60.810 50.000 0.00 0.00 0.00 3.60
795 1791 6.657117 AGAGAGAAAGGGCAGAAAGAAAATAC 59.343 38.462 0.00 0.00 0.00 1.89
796 1792 6.784031 AGAGAGAAAGGGCAGAAAGAAAATA 58.216 36.000 0.00 0.00 0.00 1.40
797 1793 5.639139 AGAGAGAAAGGGCAGAAAGAAAAT 58.361 37.500 0.00 0.00 0.00 1.82
808 1804 2.031870 GGAGAGAGAGAGAGAAAGGGC 58.968 57.143 0.00 0.00 0.00 5.19
814 1810 1.843851 GAGGTGGGAGAGAGAGAGAGA 59.156 57.143 0.00 0.00 0.00 3.10
815 1811 1.475034 CGAGGTGGGAGAGAGAGAGAG 60.475 61.905 0.00 0.00 0.00 3.20
1177 2469 0.775542 GACCCTACCAAACCCCAGTT 59.224 55.000 0.00 0.00 38.03 3.16
1200 2492 0.250640 CCTCATGCCCATGCTAGTCC 60.251 60.000 3.41 0.00 38.65 3.85
1343 2635 2.492484 AGTTCGACACTCCATAGACACC 59.508 50.000 0.00 0.00 0.00 4.16
1553 2848 5.921408 AGTTTCAGTTGCACAAACGTAAAAA 59.079 32.000 0.00 0.00 44.04 1.94
1558 2853 4.688511 TTAGTTTCAGTTGCACAAACGT 57.311 36.364 0.00 0.00 44.04 3.99
1681 2976 0.325933 CCAATCCCACAGACTGCAGA 59.674 55.000 23.35 0.00 0.00 4.26
2160 3472 3.511934 AGTAGTGAACCACCTCAGATGTC 59.488 47.826 0.00 0.00 34.49 3.06
2181 3493 3.444703 ACTTCGAACATAGCCAGCTAG 57.555 47.619 5.49 0.85 31.45 3.42
2536 3859 4.259356 GGCTTTAACGGAACCAGATAAGT 58.741 43.478 0.00 0.00 0.00 2.24
2538 3861 4.289238 TGGCTTTAACGGAACCAGATAA 57.711 40.909 0.00 0.00 0.00 1.75
3401 4762 7.503549 AGAAGACCAAATTCTTGAAAGCAATT 58.496 30.769 0.00 0.00 35.90 2.32
3517 4878 4.338400 ACCACAGATGAATGCTGAATCATG 59.662 41.667 0.00 0.00 36.45 3.07
3519 4880 3.692593 CACCACAGATGAATGCTGAATCA 59.307 43.478 0.00 0.00 36.86 2.57
3651 5015 8.739972 GGAGCTAATTCTTAACTCAAATTTCCA 58.260 33.333 0.00 0.00 31.54 3.53
3748 5118 6.606796 AGATCTCATAGTGATCAAGCCGATAT 59.393 38.462 0.00 0.00 41.85 1.63
3767 5137 5.067023 CAGGGCCACTCAAATTTAAGATCTC 59.933 44.000 6.18 0.00 0.00 2.75
3929 5299 9.755804 TGCAAAAGTATATCAATGTTTGTGAAA 57.244 25.926 0.00 0.00 0.00 2.69
3931 5301 8.355913 TGTGCAAAAGTATATCAATGTTTGTGA 58.644 29.630 0.00 0.00 0.00 3.58
3932 5302 8.518151 TGTGCAAAAGTATATCAATGTTTGTG 57.482 30.769 0.00 0.00 0.00 3.33
3933 5303 9.539825 TTTGTGCAAAAGTATATCAATGTTTGT 57.460 25.926 0.00 0.00 0.00 2.83
3934 5304 9.796062 GTTTGTGCAAAAGTATATCAATGTTTG 57.204 29.630 0.00 0.00 31.33 2.93
3935 5305 9.539825 TGTTTGTGCAAAAGTATATCAATGTTT 57.460 25.926 0.00 0.00 31.33 2.83
3936 5306 9.709495 ATGTTTGTGCAAAAGTATATCAATGTT 57.291 25.926 0.00 0.00 31.33 2.71
3937 5307 9.142515 CATGTTTGTGCAAAAGTATATCAATGT 57.857 29.630 0.00 0.00 31.33 2.71
3941 5311 7.040132 TGACCATGTTTGTGCAAAAGTATATCA 60.040 33.333 0.00 0.00 31.33 2.15
3942 5312 7.312154 TGACCATGTTTGTGCAAAAGTATATC 58.688 34.615 0.00 0.00 31.33 1.63
3943 5313 7.225784 TGACCATGTTTGTGCAAAAGTATAT 57.774 32.000 0.00 0.00 31.33 0.86
3944 5314 6.641169 TGACCATGTTTGTGCAAAAGTATA 57.359 33.333 0.00 0.00 31.33 1.47
3945 5315 5.528043 TGACCATGTTTGTGCAAAAGTAT 57.472 34.783 0.00 0.00 31.33 2.12
3946 5316 4.991153 TGACCATGTTTGTGCAAAAGTA 57.009 36.364 0.00 0.00 31.33 2.24
3948 5318 4.630940 AGTTTGACCATGTTTGTGCAAAAG 59.369 37.500 0.00 0.00 30.65 2.27
3949 5319 4.573900 AGTTTGACCATGTTTGTGCAAAA 58.426 34.783 0.00 0.00 30.65 2.44
3952 5322 3.883830 AAGTTTGACCATGTTTGTGCA 57.116 38.095 0.00 0.00 0.00 4.57
3955 5325 5.913137 TCTCAAAGTTTGACCATGTTTGT 57.087 34.783 14.35 0.00 35.46 2.83
3956 5326 5.693104 CCATCTCAAAGTTTGACCATGTTTG 59.307 40.000 14.35 2.86 35.46 2.93
3957 5327 5.363580 ACCATCTCAAAGTTTGACCATGTTT 59.636 36.000 14.35 6.35 35.46 2.83
3958 5328 4.895297 ACCATCTCAAAGTTTGACCATGTT 59.105 37.500 14.35 5.76 35.46 2.71
3959 5329 4.473444 ACCATCTCAAAGTTTGACCATGT 58.527 39.130 14.35 7.14 35.46 3.21
3960 5330 5.458041 AACCATCTCAAAGTTTGACCATG 57.542 39.130 14.35 16.83 35.46 3.66
3967 5337 5.532779 GGAGAGTCAAACCATCTCAAAGTTT 59.467 40.000 4.05 0.00 41.03 2.66
3968 5338 5.066593 GGAGAGTCAAACCATCTCAAAGTT 58.933 41.667 4.05 0.00 41.03 2.66
3969 5339 4.103153 TGGAGAGTCAAACCATCTCAAAGT 59.897 41.667 4.05 0.00 41.03 2.66
3970 5340 4.645535 TGGAGAGTCAAACCATCTCAAAG 58.354 43.478 4.05 0.00 41.03 2.77
3971 5341 4.705110 TGGAGAGTCAAACCATCTCAAA 57.295 40.909 4.05 0.00 41.03 2.69
3972 5342 4.141505 TGTTGGAGAGTCAAACCATCTCAA 60.142 41.667 4.05 0.00 41.03 3.02
3973 5343 3.390967 TGTTGGAGAGTCAAACCATCTCA 59.609 43.478 4.05 3.66 41.03 3.27
3974 5344 4.008074 TGTTGGAGAGTCAAACCATCTC 57.992 45.455 4.93 0.00 39.00 2.75
3975 5345 4.437682 TTGTTGGAGAGTCAAACCATCT 57.562 40.909 4.93 0.00 33.56 2.90
3976 5346 4.580580 ACTTTGTTGGAGAGTCAAACCATC 59.419 41.667 4.93 5.33 33.56 3.51
3977 5347 4.536765 ACTTTGTTGGAGAGTCAAACCAT 58.463 39.130 4.93 0.00 33.56 3.55
3978 5348 3.963129 ACTTTGTTGGAGAGTCAAACCA 58.037 40.909 0.00 0.00 0.00 3.67
3979 5349 4.440112 CCAACTTTGTTGGAGAGTCAAACC 60.440 45.833 21.06 0.00 42.06 3.27
3980 5350 4.398044 TCCAACTTTGTTGGAGAGTCAAAC 59.602 41.667 23.38 0.00 43.17 2.93
3981 5351 4.594970 TCCAACTTTGTTGGAGAGTCAAA 58.405 39.130 23.38 4.13 43.17 2.69
3982 5352 4.229304 TCCAACTTTGTTGGAGAGTCAA 57.771 40.909 23.38 4.76 43.17 3.18
3983 5353 3.924114 TCCAACTTTGTTGGAGAGTCA 57.076 42.857 23.38 5.39 43.17 3.41
3989 5359 4.850680 AGTGTACTTCCAACTTTGTTGGA 58.149 39.130 23.38 23.38 46.08 3.53
3990 5360 4.881850 AGAGTGTACTTCCAACTTTGTTGG 59.118 41.667 19.97 19.97 40.87 3.77
3991 5361 6.436843 AAGAGTGTACTTCCAACTTTGTTG 57.563 37.500 3.69 3.69 0.00 3.33
3992 5362 8.570068 TTAAAGAGTGTACTTCCAACTTTGTT 57.430 30.769 0.00 0.00 31.02 2.83
3993 5363 8.570068 TTTAAAGAGTGTACTTCCAACTTTGT 57.430 30.769 0.00 0.00 31.02 2.83
3994 5364 8.129211 CCTTTAAAGAGTGTACTTCCAACTTTG 58.871 37.037 16.98 0.00 31.02 2.77
3995 5365 8.050930 TCCTTTAAAGAGTGTACTTCCAACTTT 58.949 33.333 16.98 0.00 32.26 2.66
3996 5366 7.571025 TCCTTTAAAGAGTGTACTTCCAACTT 58.429 34.615 16.98 0.00 0.00 2.66
3997 5367 7.133133 TCCTTTAAAGAGTGTACTTCCAACT 57.867 36.000 16.98 0.00 0.00 3.16
3998 5368 7.094762 CCATCCTTTAAAGAGTGTACTTCCAAC 60.095 40.741 16.98 0.00 0.00 3.77
3999 5369 6.940298 CCATCCTTTAAAGAGTGTACTTCCAA 59.060 38.462 16.98 0.00 0.00 3.53
4000 5370 6.271391 TCCATCCTTTAAAGAGTGTACTTCCA 59.729 38.462 16.98 0.00 0.00 3.53
4001 5371 6.708285 TCCATCCTTTAAAGAGTGTACTTCC 58.292 40.000 16.98 0.00 0.00 3.46
4002 5372 6.819146 CCTCCATCCTTTAAAGAGTGTACTTC 59.181 42.308 16.98 0.00 0.00 3.01
4003 5373 6.296489 CCCTCCATCCTTTAAAGAGTGTACTT 60.296 42.308 16.98 0.00 0.00 2.24
4004 5374 5.189934 CCCTCCATCCTTTAAAGAGTGTACT 59.810 44.000 16.98 0.00 0.00 2.73
4005 5375 5.189145 TCCCTCCATCCTTTAAAGAGTGTAC 59.811 44.000 16.98 0.00 0.00 2.90
4006 5376 5.347124 TCCCTCCATCCTTTAAAGAGTGTA 58.653 41.667 16.98 1.50 0.00 2.90
4007 5377 4.175962 TCCCTCCATCCTTTAAAGAGTGT 58.824 43.478 16.98 0.00 0.00 3.55
4008 5378 4.226168 ACTCCCTCCATCCTTTAAAGAGTG 59.774 45.833 16.98 13.36 31.21 3.51
4009 5379 4.439860 ACTCCCTCCATCCTTTAAAGAGT 58.560 43.478 16.98 6.02 0.00 3.24
4010 5380 6.755542 ATACTCCCTCCATCCTTTAAAGAG 57.244 41.667 16.98 7.03 0.00 2.85
4011 5381 7.525158 AAATACTCCCTCCATCCTTTAAAGA 57.475 36.000 16.98 3.50 0.00 2.52
4012 5382 8.470002 CAAAAATACTCCCTCCATCCTTTAAAG 58.530 37.037 8.32 8.32 0.00 1.85
4013 5383 7.093509 GCAAAAATACTCCCTCCATCCTTTAAA 60.094 37.037 0.00 0.00 0.00 1.52
4014 5384 6.379988 GCAAAAATACTCCCTCCATCCTTTAA 59.620 38.462 0.00 0.00 0.00 1.52
4015 5385 5.891551 GCAAAAATACTCCCTCCATCCTTTA 59.108 40.000 0.00 0.00 0.00 1.85
4016 5386 4.711846 GCAAAAATACTCCCTCCATCCTTT 59.288 41.667 0.00 0.00 0.00 3.11
4017 5387 4.017130 AGCAAAAATACTCCCTCCATCCTT 60.017 41.667 0.00 0.00 0.00 3.36
4018 5388 3.529319 AGCAAAAATACTCCCTCCATCCT 59.471 43.478 0.00 0.00 0.00 3.24
4019 5389 3.903467 AGCAAAAATACTCCCTCCATCC 58.097 45.455 0.00 0.00 0.00 3.51
4020 5390 5.418840 TCAAAGCAAAAATACTCCCTCCATC 59.581 40.000 0.00 0.00 0.00 3.51
4021 5391 5.332743 TCAAAGCAAAAATACTCCCTCCAT 58.667 37.500 0.00 0.00 0.00 3.41
4022 5392 4.735369 TCAAAGCAAAAATACTCCCTCCA 58.265 39.130 0.00 0.00 0.00 3.86
4023 5393 5.010282 TCTCAAAGCAAAAATACTCCCTCC 58.990 41.667 0.00 0.00 0.00 4.30
4024 5394 6.575162 TTCTCAAAGCAAAAATACTCCCTC 57.425 37.500 0.00 0.00 0.00 4.30
4025 5395 6.976934 TTTCTCAAAGCAAAAATACTCCCT 57.023 33.333 0.00 0.00 0.00 4.20
4026 5396 6.983890 TGTTTTCTCAAAGCAAAAATACTCCC 59.016 34.615 0.00 0.00 0.00 4.30
4027 5397 7.305993 CGTGTTTTCTCAAAGCAAAAATACTCC 60.306 37.037 0.00 0.00 34.08 3.85
4028 5398 7.431084 TCGTGTTTTCTCAAAGCAAAAATACTC 59.569 33.333 0.00 0.00 34.08 2.59
4029 5399 7.254852 TCGTGTTTTCTCAAAGCAAAAATACT 58.745 30.769 0.00 0.00 34.08 2.12
4030 5400 7.444558 TCGTGTTTTCTCAAAGCAAAAATAC 57.555 32.000 0.00 0.00 33.34 1.89
4076 5446 1.004918 CCAAAAGGGACGCTCGAGT 60.005 57.895 15.13 0.00 40.01 4.18
4078 5448 2.358247 GCCAAAAGGGACGCTCGA 60.358 61.111 0.00 0.00 40.01 4.04
4100 5470 2.408835 GGGATGCAAATGACGGCG 59.591 61.111 4.80 4.80 0.00 6.46
4101 5471 2.785425 GGGGGATGCAAATGACGGC 61.785 63.158 0.00 0.00 0.00 5.68
4194 5577 2.803593 AATTGGGGCTTGGCGGTGAT 62.804 55.000 0.00 0.00 0.00 3.06
4197 5580 2.203773 AAATTGGGGCTTGGCGGT 60.204 55.556 0.00 0.00 0.00 5.68
4231 5614 0.393132 ACGTCATCTCTGAGCTCGGA 60.393 55.000 23.72 23.72 30.18 4.55
4276 5709 2.431954 AATTCCGGTCTCCTCGACTA 57.568 50.000 0.00 0.00 42.44 2.59
4286 5719 4.375272 GGTAAAGTAGGCTAATTCCGGTC 58.625 47.826 7.77 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.