Multiple sequence alignment - TraesCS1D01G000900

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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 TraesCS1D01G000900 chr1D 100.000 2322 0 0 1 2322 215924 218245 0.000000e+00 4289.0
1 TraesCS1D01G000900 chr1D 94.000 100 5 1 289 387 200465101 200465200 1.440000e-32 150.0
2 TraesCS1D01G000900 chr1A 90.325 1354 83 26 519 1833 4048775 4047431 0.000000e+00 1731.0
3 TraesCS1D01G000900 chr1A 90.026 381 28 7 1944 2322 4047304 4046932 3.470000e-133 484.0
4 TraesCS1D01G000900 chr1A 92.208 231 17 1 1 231 4049550 4049321 2.220000e-85 326.0
5 TraesCS1D01G000900 chr1A 95.522 67 2 1 230 296 4049018 4048953 3.160000e-19 106.0
6 TraesCS1D01G000900 chr1A 85.057 87 12 1 720 805 4052441 4052355 1.140000e-13 87.9
7 TraesCS1D01G000900 chr1B 88.417 1390 80 33 519 1833 5160307 5158924 0.000000e+00 1600.0
8 TraesCS1D01G000900 chr1B 91.832 453 30 6 1871 2322 5158856 5158410 1.960000e-175 625.0
9 TraesCS1D01G000900 chr1B 91.554 296 14 6 1 296 5160787 5160503 4.650000e-107 398.0
10 TraesCS1D01G000900 chr3D 92.920 113 7 1 282 394 77359415 77359526 1.850000e-36 163.0
11 TraesCS1D01G000900 chr3D 94.737 95 3 2 291 384 560556325 560556232 1.860000e-31 147.0
12 TraesCS1D01G000900 chr2D 98.824 85 1 0 295 379 31708491 31708407 4.000000e-33 152.0
13 TraesCS1D01G000900 chr7A 93.939 99 4 2 285 382 213151255 213151352 5.170000e-32 148.0
14 TraesCS1D01G000900 chr4A 96.629 89 3 0 291 379 644038558 644038470 5.170000e-32 148.0
15 TraesCS1D01G000900 chr7D 94.624 93 5 0 291 383 80504126 80504218 6.690000e-31 145.0
16 TraesCS1D01G000900 chr6D 92.233 103 7 1 284 386 25851212 25851111 6.690000e-31 145.0
17 TraesCS1D01G000900 chr2A 90.476 105 8 2 286 390 48468003 48468105 1.120000e-28 137.0


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 TraesCS1D01G000900 chr1D 215924 218245 2321 False 4289.000000 4289 100.0000 1 2322 1 chr1D.!!$F1 2321
1 TraesCS1D01G000900 chr1A 4046932 4052441 5509 True 546.980000 1731 90.6276 1 2322 5 chr1A.!!$R1 2321
2 TraesCS1D01G000900 chr1B 5158410 5160787 2377 True 874.333333 1600 90.6010 1 2322 3 chr1B.!!$R1 2321

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
99 2991 0.961019 TTCTTGGGAAGTGCATGCAC 59.039 50.0 37.87 37.87 46.5 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 4685 0.310543 TTGCAATGAACCTGTGTCGC 59.689 50.0 0.0 0.0 0.0 5.19 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
65 2957 3.876320 ACCATGGCATTGTTTGTTTTCAC 59.124 39.130 13.04 0.00 0.00 3.18
67 2959 2.911484 TGGCATTGTTTGTTTTCACCC 58.089 42.857 0.00 0.00 0.00 4.61
97 2989 2.036346 ACTTTTCTTGGGAAGTGCATGC 59.964 45.455 11.82 11.82 34.96 4.06
99 2991 0.961019 TTCTTGGGAAGTGCATGCAC 59.039 50.000 37.87 37.87 46.50 4.57
114 3006 1.882912 TGCACGCTTCTCAACTCATT 58.117 45.000 0.00 0.00 0.00 2.57
134 3026 7.602644 ACTCATTATTTCGTATGTTGTGTCTGT 59.397 33.333 0.00 0.00 0.00 3.41
157 3049 8.487313 TGTTGGCACTACTTATAAGTGTATTG 57.513 34.615 25.27 16.92 45.01 1.90
206 3098 3.244526 TGTTGCACATATCACTCCACTGT 60.245 43.478 0.00 0.00 0.00 3.55
282 3477 5.614308 ACATCAATCTAGATTGCATCGGAA 58.386 37.500 32.11 18.36 45.77 4.30
305 3500 5.216614 GTTTCTGAAACTACTCCCTCTGT 57.783 43.478 22.55 0.00 38.35 3.41
306 3501 6.342338 GTTTCTGAAACTACTCCCTCTGTA 57.658 41.667 22.55 0.00 38.35 2.74
307 3502 6.756221 GTTTCTGAAACTACTCCCTCTGTAA 58.244 40.000 22.55 0.00 38.35 2.41
308 3503 6.989155 TTCTGAAACTACTCCCTCTGTAAA 57.011 37.500 0.00 0.00 0.00 2.01
309 3504 6.342338 TCTGAAACTACTCCCTCTGTAAAC 57.658 41.667 0.00 0.00 0.00 2.01
310 3505 6.075984 TCTGAAACTACTCCCTCTGTAAACT 58.924 40.000 0.00 0.00 0.00 2.66
311 3506 7.236529 TCTGAAACTACTCCCTCTGTAAACTA 58.763 38.462 0.00 0.00 0.00 2.24
312 3507 7.727186 TCTGAAACTACTCCCTCTGTAAACTAA 59.273 37.037 0.00 0.00 0.00 2.24
313 3508 8.431910 TGAAACTACTCCCTCTGTAAACTAAT 57.568 34.615 0.00 0.00 0.00 1.73
314 3509 9.537852 TGAAACTACTCCCTCTGTAAACTAATA 57.462 33.333 0.00 0.00 0.00 0.98
322 3517 9.680315 CTCCCTCTGTAAACTAATATAAGAACG 57.320 37.037 0.00 0.00 0.00 3.95
323 3518 9.193806 TCCCTCTGTAAACTAATATAAGAACGT 57.806 33.333 0.00 0.00 0.00 3.99
324 3519 9.813446 CCCTCTGTAAACTAATATAAGAACGTT 57.187 33.333 0.00 0.00 0.00 3.99
342 3537 9.978044 AAGAACGTTTAGATCACTAAAGTAGTT 57.022 29.630 0.46 0.00 45.42 2.24
374 3569 8.953368 ACACTTTTATATTAGTTTACGGAGGG 57.047 34.615 0.00 0.00 0.00 4.30
375 3570 8.761689 ACACTTTTATATTAGTTTACGGAGGGA 58.238 33.333 0.00 0.00 0.00 4.20
376 3571 9.257651 CACTTTTATATTAGTTTACGGAGGGAG 57.742 37.037 0.00 0.00 0.00 4.30
377 3572 8.985922 ACTTTTATATTAGTTTACGGAGGGAGT 58.014 33.333 0.00 0.00 0.00 3.85
380 3575 9.646522 TTTATATTAGTTTACGGAGGGAGTAGT 57.353 33.333 0.00 0.00 0.00 2.73
381 3576 9.646522 TTATATTAGTTTACGGAGGGAGTAGTT 57.353 33.333 0.00 0.00 0.00 2.24
382 3577 6.864151 ATTAGTTTACGGAGGGAGTAGTTT 57.136 37.500 0.00 0.00 0.00 2.66
383 3578 4.532314 AGTTTACGGAGGGAGTAGTTTG 57.468 45.455 0.00 0.00 0.00 2.93
384 3579 3.899980 AGTTTACGGAGGGAGTAGTTTGT 59.100 43.478 0.00 0.00 0.00 2.83
385 3580 5.079643 AGTTTACGGAGGGAGTAGTTTGTA 58.920 41.667 0.00 0.00 0.00 2.41
386 3581 5.539955 AGTTTACGGAGGGAGTAGTTTGTAA 59.460 40.000 0.00 0.00 0.00 2.41
387 3582 6.212187 AGTTTACGGAGGGAGTAGTTTGTAAT 59.788 38.462 0.00 0.00 0.00 1.89
388 3583 4.467198 ACGGAGGGAGTAGTTTGTAATG 57.533 45.455 0.00 0.00 0.00 1.90
389 3584 3.836562 ACGGAGGGAGTAGTTTGTAATGT 59.163 43.478 0.00 0.00 0.00 2.71
390 3585 4.285260 ACGGAGGGAGTAGTTTGTAATGTT 59.715 41.667 0.00 0.00 0.00 2.71
391 3586 4.868734 CGGAGGGAGTAGTTTGTAATGTTC 59.131 45.833 0.00 0.00 0.00 3.18
392 3587 5.337330 CGGAGGGAGTAGTTTGTAATGTTCT 60.337 44.000 0.00 0.00 0.00 3.01
393 3588 6.127535 CGGAGGGAGTAGTTTGTAATGTTCTA 60.128 42.308 0.00 0.00 0.00 2.10
394 3589 7.040494 GGAGGGAGTAGTTTGTAATGTTCTAC 58.960 42.308 0.00 0.00 33.46 2.59
395 3590 7.310237 GGAGGGAGTAGTTTGTAATGTTCTACA 60.310 40.741 0.00 0.00 35.05 2.74
396 3591 7.612677 AGGGAGTAGTTTGTAATGTTCTACAG 58.387 38.462 0.00 0.00 33.44 2.74
397 3592 6.817140 GGGAGTAGTTTGTAATGTTCTACAGG 59.183 42.308 0.00 0.00 33.44 4.00
398 3593 7.384477 GGAGTAGTTTGTAATGTTCTACAGGT 58.616 38.462 0.00 0.00 33.44 4.00
399 3594 7.876582 GGAGTAGTTTGTAATGTTCTACAGGTT 59.123 37.037 0.00 0.00 33.44 3.50
400 3595 8.603242 AGTAGTTTGTAATGTTCTACAGGTTG 57.397 34.615 0.00 0.00 33.44 3.77
401 3596 8.208903 AGTAGTTTGTAATGTTCTACAGGTTGT 58.791 33.333 0.00 0.00 33.44 3.32
405 3618 8.614346 GTTTGTAATGTTCTACAGGTTGTTACA 58.386 33.333 0.00 0.00 33.44 2.41
429 3642 6.262944 CACATAAACCAGATTAGCATGCCTTA 59.737 38.462 15.66 0.00 0.00 2.69
451 3664 8.718734 CCTTACACTGAACTAAGTTTGTAATCC 58.281 37.037 0.00 0.00 30.87 3.01
538 3806 8.352137 TGACATGATTCAATATTCTGTTGGTT 57.648 30.769 0.00 0.00 0.00 3.67
584 3852 5.367302 TGTGCGGATCATTCAGATAATCAA 58.633 37.500 0.00 0.00 37.00 2.57
710 3981 9.713713 GGGAAATTTATTTAGCAGGTAAAAACA 57.286 29.630 8.84 0.00 34.21 2.83
827 4099 5.511234 AGCAATCACATTCTTATTCCAGC 57.489 39.130 0.00 0.00 0.00 4.85
838 4110 3.767673 TCTTATTCCAGCCGAACAGTAGT 59.232 43.478 0.00 0.00 31.79 2.73
858 4132 2.874701 GTTGAATGCCGTATGCTCAGAT 59.125 45.455 0.00 0.00 42.00 2.90
866 4140 6.096673 TGCCGTATGCTCAGATTAGAAATA 57.903 37.500 0.00 0.00 42.00 1.40
871 4145 7.413438 CCGTATGCTCAGATTAGAAATATTGGC 60.413 40.741 0.00 0.00 0.00 4.52
883 4157 5.012239 AGAAATATTGGCTTCAACTCAGCA 58.988 37.500 0.00 0.00 39.21 4.41
895 4171 5.888691 TCAACTCAGCAGTCTCTAACTAG 57.111 43.478 0.00 0.00 36.07 2.57
922 4198 4.962155 AGAAAGACCTGTAACAAGTCCAG 58.038 43.478 0.00 0.00 0.00 3.86
924 4200 5.130477 AGAAAGACCTGTAACAAGTCCAGAA 59.870 40.000 0.00 0.00 0.00 3.02
938 4214 4.990526 AGTCCAGAACAAAATCCAGATGT 58.009 39.130 0.00 0.00 0.00 3.06
945 4221 4.978083 ACAAAATCCAGATGTGCAGATC 57.022 40.909 15.79 15.79 0.00 2.75
950 4226 2.102578 TCCAGATGTGCAGATCGAAGA 58.897 47.619 17.31 12.52 45.75 2.87
957 4233 6.089685 CAGATGTGCAGATCGAAGATGATAAG 59.910 42.308 17.31 0.00 45.12 1.73
959 4235 3.431572 GTGCAGATCGAAGATGATAAGCC 59.568 47.826 0.00 0.00 45.12 4.35
960 4236 3.070015 TGCAGATCGAAGATGATAAGCCA 59.930 43.478 0.00 0.00 45.12 4.75
961 4237 4.252073 GCAGATCGAAGATGATAAGCCAT 58.748 43.478 0.00 0.00 45.12 4.40
962 4238 4.329528 GCAGATCGAAGATGATAAGCCATC 59.670 45.833 0.00 0.00 45.12 3.51
1041 4320 0.892063 GGTCACCTCTGTCAGTCTCC 59.108 60.000 0.00 0.00 0.00 3.71
1134 4413 2.647297 GGTGTCTGCAAGCAAGGC 59.353 61.111 0.00 0.00 0.00 4.35
1150 4429 3.084039 CAAGGCAGCAGAAACCTCAATA 58.916 45.455 0.00 0.00 31.86 1.90
1151 4430 3.659183 AGGCAGCAGAAACCTCAATAT 57.341 42.857 0.00 0.00 0.00 1.28
1154 4433 3.282021 GCAGCAGAAACCTCAATATGGA 58.718 45.455 0.00 0.00 0.00 3.41
1179 4473 6.691754 TTATGAACTTCAAACTCAGCAACA 57.308 33.333 0.00 0.00 0.00 3.33
1243 4547 8.182227 GCAGGAAGTACACAATTAATTACCTTC 58.818 37.037 0.00 7.80 0.00 3.46
1245 4549 9.975218 AGGAAGTACACAATTAATTACCTTCAT 57.025 29.630 17.18 12.04 0.00 2.57
1377 4681 7.802251 CAGTTAGCATATAATCTGAAGCAAAGC 59.198 37.037 0.00 0.00 0.00 3.51
1379 4683 6.315091 AGCATATAATCTGAAGCAAAGCTG 57.685 37.500 0.00 0.00 39.62 4.24
1380 4684 5.826737 AGCATATAATCTGAAGCAAAGCTGT 59.173 36.000 0.00 0.00 39.62 4.40
1381 4685 5.913514 GCATATAATCTGAAGCAAAGCTGTG 59.086 40.000 0.00 0.00 39.62 3.66
1382 4686 2.719426 AATCTGAAGCAAAGCTGTGC 57.281 45.000 21.92 21.92 45.28 4.57
1573 4911 7.170151 TCAAATGCAGATGAAACACAAAATCAG 59.830 33.333 1.95 0.00 0.00 2.90
1579 4917 7.031372 CAGATGAAACACAAAATCAGGTATGG 58.969 38.462 0.00 0.00 0.00 2.74
1580 4918 5.720371 TGAAACACAAAATCAGGTATGGG 57.280 39.130 0.00 0.00 0.00 4.00
1604 4942 3.072330 TCAATATAGGAAAGGATGGCGCA 59.928 43.478 10.83 0.00 0.00 6.09
1608 4946 0.034186 AGGAAAGGATGGCGCAATGA 60.034 50.000 10.83 0.00 0.00 2.57
1646 4984 2.425592 CACGAGGCCACTGACCAA 59.574 61.111 5.01 0.00 0.00 3.67
1647 4985 1.227823 CACGAGGCCACTGACCAAA 60.228 57.895 5.01 0.00 0.00 3.28
1726 5064 0.037975 CAGGGTCAAAATGCAGCACC 60.038 55.000 0.00 0.00 0.00 5.01
1772 5110 4.220163 ACGAGCAAAGCTAGTAGTAAAGGT 59.780 41.667 2.91 0.00 42.25 3.50
1785 5128 7.868792 AGTAGTAAAGGTTCTAAACTCCCTT 57.131 36.000 0.00 0.00 38.94 3.95
1853 5251 7.106239 ACAGCTAGCATAACTATCAACAAACT 58.894 34.615 18.83 0.00 0.00 2.66
1877 5275 4.640789 AACAGGTACATTCGTGCAAAAA 57.359 36.364 0.00 0.00 0.00 1.94
1910 5308 7.105588 AGCACATGTATCTGTTCAATCTTGTA 58.894 34.615 0.00 0.00 0.00 2.41
1936 5334 6.704512 CAAAGGTATTTGCATGGTAACAAC 57.295 37.500 0.00 0.00 44.79 3.32
1937 5335 6.454795 CAAAGGTATTTGCATGGTAACAACT 58.545 36.000 0.00 0.00 44.79 3.16
1969 5367 8.796475 TCTTTAGCTTTTCTTAATGCAATCTGT 58.204 29.630 0.00 0.00 37.00 3.41
2123 5521 1.198759 CGAACCCTTTCTCCCCTGGA 61.199 60.000 0.00 0.00 0.00 3.86
2124 5522 0.328592 GAACCCTTTCTCCCCTGGAC 59.671 60.000 0.00 0.00 0.00 4.02
2125 5523 0.402861 AACCCTTTCTCCCCTGGACA 60.403 55.000 0.00 0.00 0.00 4.02
2126 5524 0.402861 ACCCTTTCTCCCCTGGACAA 60.403 55.000 0.00 0.00 0.00 3.18
2127 5525 0.777446 CCCTTTCTCCCCTGGACAAA 59.223 55.000 0.00 0.00 0.00 2.83
2128 5526 1.146982 CCCTTTCTCCCCTGGACAAAA 59.853 52.381 0.00 0.00 0.00 2.44
2129 5527 2.519013 CCTTTCTCCCCTGGACAAAAG 58.481 52.381 0.00 0.00 33.07 2.27
2130 5528 2.108250 CCTTTCTCCCCTGGACAAAAGA 59.892 50.000 11.90 0.00 34.17 2.52
2164 5562 4.824479 TTGCTCATACACCTCATCAGAA 57.176 40.909 0.00 0.00 0.00 3.02
2165 5563 5.363562 TTGCTCATACACCTCATCAGAAT 57.636 39.130 0.00 0.00 0.00 2.40
2166 5564 5.363562 TGCTCATACACCTCATCAGAATT 57.636 39.130 0.00 0.00 0.00 2.17
2168 5566 6.888105 TGCTCATACACCTCATCAGAATTAA 58.112 36.000 0.00 0.00 0.00 1.40
2169 5567 7.512130 TGCTCATACACCTCATCAGAATTAAT 58.488 34.615 0.00 0.00 0.00 1.40
2170 5568 7.994911 TGCTCATACACCTCATCAGAATTAATT 59.005 33.333 0.00 0.00 0.00 1.40
2171 5569 8.502387 GCTCATACACCTCATCAGAATTAATTC 58.498 37.037 18.70 18.70 37.06 2.17
2194 5592 6.962182 TCTTGAAGATGGGATAACAGAACAT 58.038 36.000 0.00 0.00 0.00 2.71
2212 5610 3.791586 GGCTCCAGCAGTCCCTCC 61.792 72.222 0.03 0.00 44.36 4.30
2219 5617 1.687493 AGCAGTCCCTCCTACCAGC 60.687 63.158 0.00 0.00 0.00 4.85
2226 5624 2.055042 CCTCCTACCAGCGCAGAGT 61.055 63.158 11.47 6.15 0.00 3.24
2250 5648 1.937899 CGGAAGTTCTCAACGGTTTGT 59.062 47.619 2.25 0.00 36.23 2.83
2268 5666 1.484653 TGTGGAACGTCATCCCCATAG 59.515 52.381 3.84 0.00 42.39 2.23
2286 5684 1.207791 AGAGCCCGATGACAATCCTT 58.792 50.000 0.00 0.00 0.00 3.36
2292 5690 2.617788 CCCGATGACAATCCTTCCAACA 60.618 50.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 2957 4.283212 TCCCAAGAAAAGTAAATGCAAGGG 59.717 41.667 0.00 0.00 0.00 3.95
67 2959 6.421801 CACTTCCCAAGAAAAGTAAATGCAAG 59.578 38.462 0.00 0.00 34.05 4.01
97 2989 5.163953 ACGAAATAATGAGTTGAGAAGCGTG 60.164 40.000 0.00 0.00 0.00 5.34
99 2991 5.456192 ACGAAATAATGAGTTGAGAAGCG 57.544 39.130 0.00 0.00 0.00 4.68
114 3006 5.106869 GCCAACAGACACAACATACGAAATA 60.107 40.000 0.00 0.00 0.00 1.40
134 3026 8.941977 CAACAATACACTTATAAGTAGTGCCAA 58.058 33.333 17.62 4.80 45.38 4.52
157 3049 5.382618 AGAACTTTGATGAGCAATCCAAC 57.617 39.130 0.00 0.00 36.15 3.77
296 3491 9.680315 CGTTCTTATATTAGTTTACAGAGGGAG 57.320 37.037 0.00 0.00 0.00 4.30
298 3493 9.813446 AACGTTCTTATATTAGTTTACAGAGGG 57.187 33.333 0.00 0.00 0.00 4.30
316 3511 9.978044 AACTACTTTAGTGATCTAAACGTTCTT 57.022 29.630 0.00 0.00 40.05 2.52
348 3543 9.387257 CCCTCCGTAAACTAATATAAAAGTGTT 57.613 33.333 0.00 0.00 0.00 3.32
349 3544 8.761689 TCCCTCCGTAAACTAATATAAAAGTGT 58.238 33.333 0.00 0.00 0.00 3.55
350 3545 9.257651 CTCCCTCCGTAAACTAATATAAAAGTG 57.742 37.037 0.00 0.00 0.00 3.16
351 3546 8.985922 ACTCCCTCCGTAAACTAATATAAAAGT 58.014 33.333 0.00 0.00 0.00 2.66
354 3549 9.646522 ACTACTCCCTCCGTAAACTAATATAAA 57.353 33.333 0.00 0.00 0.00 1.40
355 3550 9.646522 AACTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
356 3551 9.646522 AAACTACTCCCTCCGTAAACTAATATA 57.353 33.333 0.00 0.00 0.00 0.86
357 3552 8.419442 CAAACTACTCCCTCCGTAAACTAATAT 58.581 37.037 0.00 0.00 0.00 1.28
358 3553 7.397192 ACAAACTACTCCCTCCGTAAACTAATA 59.603 37.037 0.00 0.00 0.00 0.98
359 3554 6.212187 ACAAACTACTCCCTCCGTAAACTAAT 59.788 38.462 0.00 0.00 0.00 1.73
360 3555 5.539955 ACAAACTACTCCCTCCGTAAACTAA 59.460 40.000 0.00 0.00 0.00 2.24
361 3556 5.079643 ACAAACTACTCCCTCCGTAAACTA 58.920 41.667 0.00 0.00 0.00 2.24
362 3557 3.899980 ACAAACTACTCCCTCCGTAAACT 59.100 43.478 0.00 0.00 0.00 2.66
363 3558 4.263018 ACAAACTACTCCCTCCGTAAAC 57.737 45.455 0.00 0.00 0.00 2.01
364 3559 6.014327 ACATTACAAACTACTCCCTCCGTAAA 60.014 38.462 0.00 0.00 0.00 2.01
365 3560 5.481473 ACATTACAAACTACTCCCTCCGTAA 59.519 40.000 0.00 0.00 0.00 3.18
366 3561 5.018809 ACATTACAAACTACTCCCTCCGTA 58.981 41.667 0.00 0.00 0.00 4.02
367 3562 3.836562 ACATTACAAACTACTCCCTCCGT 59.163 43.478 0.00 0.00 0.00 4.69
368 3563 4.467198 ACATTACAAACTACTCCCTCCG 57.533 45.455 0.00 0.00 0.00 4.63
369 3564 6.051179 AGAACATTACAAACTACTCCCTCC 57.949 41.667 0.00 0.00 0.00 4.30
370 3565 7.609056 TGTAGAACATTACAAACTACTCCCTC 58.391 38.462 0.00 0.00 35.78 4.30
371 3566 7.310485 CCTGTAGAACATTACAAACTACTCCCT 60.310 40.741 0.00 0.00 35.78 4.20
372 3567 6.817140 CCTGTAGAACATTACAAACTACTCCC 59.183 42.308 0.00 0.00 35.78 4.30
373 3568 7.384477 ACCTGTAGAACATTACAAACTACTCC 58.616 38.462 0.00 0.00 35.78 3.85
374 3569 8.709646 CAACCTGTAGAACATTACAAACTACTC 58.290 37.037 0.00 0.00 35.78 2.59
375 3570 8.208903 ACAACCTGTAGAACATTACAAACTACT 58.791 33.333 0.00 0.00 35.78 2.57
376 3571 8.374327 ACAACCTGTAGAACATTACAAACTAC 57.626 34.615 0.00 0.00 33.44 2.73
377 3572 8.967664 AACAACCTGTAGAACATTACAAACTA 57.032 30.769 0.00 0.00 33.44 2.24
378 3573 7.875327 AACAACCTGTAGAACATTACAAACT 57.125 32.000 0.00 0.00 33.44 2.66
379 3574 8.614346 TGTAACAACCTGTAGAACATTACAAAC 58.386 33.333 0.00 0.00 30.33 2.93
380 3575 8.614346 GTGTAACAACCTGTAGAACATTACAAA 58.386 33.333 5.30 0.00 33.24 2.83
381 3576 8.145316 GTGTAACAACCTGTAGAACATTACAA 57.855 34.615 5.30 0.00 33.24 2.41
382 3577 7.718272 GTGTAACAACCTGTAGAACATTACA 57.282 36.000 0.00 0.00 36.32 2.41
400 3595 6.912591 GCATGCTAATCTGGTTTATGTGTAAC 59.087 38.462 11.37 0.00 37.35 2.50
401 3596 6.039270 GGCATGCTAATCTGGTTTATGTGTAA 59.961 38.462 18.92 0.00 0.00 2.41
405 3618 4.796606 AGGCATGCTAATCTGGTTTATGT 58.203 39.130 18.92 0.00 0.00 2.29
429 3642 7.226720 CACAGGATTACAAACTTAGTTCAGTGT 59.773 37.037 11.64 9.05 0.00 3.55
451 3664 3.684788 GTGTATCTTTACAGGCCACACAG 59.315 47.826 5.01 0.00 38.98 3.66
560 3828 4.992951 TGATTATCTGAATGATCCGCACAG 59.007 41.667 0.00 0.00 36.65 3.66
584 3852 4.797275 GCAGATTTAGCAAGCAAAACCTGT 60.797 41.667 0.00 0.00 0.00 4.00
671 3940 0.615331 ATTTCCCTCGAGCTGCAGAA 59.385 50.000 20.43 0.00 0.00 3.02
718 3989 5.074102 TCCATGAAATGCCTGGATATCTCTT 59.926 40.000 0.00 0.00 44.97 2.85
745 4016 2.037901 TGCCTTGTGAATTTTCTGGCA 58.962 42.857 0.00 0.00 45.31 4.92
827 4099 1.393539 CGGCATTCAACTACTGTTCGG 59.606 52.381 0.00 0.00 33.52 4.30
858 4132 6.658816 TGCTGAGTTGAAGCCAATATTTCTAA 59.341 34.615 0.00 0.00 40.06 2.10
866 4140 2.157738 GACTGCTGAGTTGAAGCCAAT 58.842 47.619 0.00 0.00 40.06 3.16
871 4145 5.132897 AGTTAGAGACTGCTGAGTTGAAG 57.867 43.478 0.00 0.00 37.17 3.02
883 4157 7.183293 AGGTCTTTCTCCTACTAGTTAGAGACT 59.817 40.741 19.00 12.21 36.62 3.24
895 4171 6.099159 ACTTGTTACAGGTCTTTCTCCTAC 57.901 41.667 0.00 0.00 33.54 3.18
922 4198 4.771590 TCTGCACATCTGGATTTTGTTC 57.228 40.909 0.00 0.00 0.00 3.18
924 4200 3.376234 CGATCTGCACATCTGGATTTTGT 59.624 43.478 0.30 0.00 0.00 2.83
938 4214 3.070015 TGGCTTATCATCTTCGATCTGCA 59.930 43.478 0.00 0.00 0.00 4.41
950 4226 6.995091 GGTCTGAGTTTTAGATGGCTTATCAT 59.005 38.462 4.71 0.00 38.31 2.45
957 4233 3.686726 CAGTGGTCTGAGTTTTAGATGGC 59.313 47.826 0.00 0.00 43.76 4.40
959 4235 5.152623 TCCAGTGGTCTGAGTTTTAGATG 57.847 43.478 9.54 0.00 43.76 2.90
960 4236 5.799213 CTTCCAGTGGTCTGAGTTTTAGAT 58.201 41.667 9.54 0.00 43.76 1.98
961 4237 4.503296 GCTTCCAGTGGTCTGAGTTTTAGA 60.503 45.833 9.54 0.00 43.76 2.10
962 4238 3.748568 GCTTCCAGTGGTCTGAGTTTTAG 59.251 47.826 9.54 0.00 43.76 1.85
1134 4413 6.461110 AATTCCATATTGAGGTTTCTGCTG 57.539 37.500 0.00 0.00 0.00 4.41
1150 4429 7.177216 TGCTGAGTTTGAAGTTCATAATTCCAT 59.823 33.333 6.36 0.00 0.00 3.41
1151 4430 6.489700 TGCTGAGTTTGAAGTTCATAATTCCA 59.510 34.615 6.36 0.52 0.00 3.53
1154 4433 7.715657 TGTTGCTGAGTTTGAAGTTCATAATT 58.284 30.769 6.36 1.49 0.00 1.40
1214 4518 8.610035 GGTAATTAATTGTGTACTTCCTGCTAC 58.390 37.037 11.05 0.00 0.00 3.58
1243 4547 3.863424 GCCAATTCTTCATCTGCACAATG 59.137 43.478 0.00 0.00 0.00 2.82
1245 4549 3.057104 CAGCCAATTCTTCATCTGCACAA 60.057 43.478 0.00 0.00 0.00 3.33
1379 4683 0.385974 GCAATGAACCTGTGTCGCAC 60.386 55.000 3.44 3.44 34.56 5.34
1380 4684 0.817229 TGCAATGAACCTGTGTCGCA 60.817 50.000 0.00 0.00 0.00 5.10
1381 4685 0.310543 TTGCAATGAACCTGTGTCGC 59.689 50.000 0.00 0.00 0.00 5.19
1382 4686 1.333308 TGTTGCAATGAACCTGTGTCG 59.667 47.619 0.59 0.00 0.00 4.35
1383 4687 2.098934 TGTGTTGCAATGAACCTGTGTC 59.901 45.455 0.59 0.00 0.00 3.67
1384 4688 2.098614 TGTGTTGCAATGAACCTGTGT 58.901 42.857 0.59 0.00 0.00 3.72
1385 4689 2.867287 TGTGTTGCAATGAACCTGTG 57.133 45.000 0.59 0.00 0.00 3.66
1386 4690 3.888323 TGTATGTGTTGCAATGAACCTGT 59.112 39.130 0.59 0.00 0.00 4.00
1387 4691 4.502171 TGTATGTGTTGCAATGAACCTG 57.498 40.909 0.59 0.00 0.00 4.00
1573 4911 5.250774 TCCTTTCCTATATTGAGCCCATACC 59.749 44.000 0.00 0.00 0.00 2.73
1579 4917 4.013050 GCCATCCTTTCCTATATTGAGCC 58.987 47.826 0.00 0.00 0.00 4.70
1580 4918 3.686726 CGCCATCCTTTCCTATATTGAGC 59.313 47.826 0.00 0.00 0.00 4.26
1604 4942 7.451255 TGGTAAGAATTCAAGGTGATTGTCATT 59.549 33.333 8.44 0.00 40.05 2.57
1608 4946 5.181245 CGTGGTAAGAATTCAAGGTGATTGT 59.819 40.000 8.44 0.00 40.05 2.71
1647 4985 5.009010 CACAAGTGCATCCTACTCTGTTTTT 59.991 40.000 0.00 0.00 0.00 1.94
1726 5064 6.251163 CGTGTACCTGCATTCAATTTGTTATG 59.749 38.462 0.00 3.65 0.00 1.90
1772 5110 4.288887 GGGAGAAGGAAAGGGAGTTTAGAA 59.711 45.833 0.00 0.00 0.00 2.10
1785 5128 1.229853 GGGACTGGGGGAGAAGGAA 60.230 63.158 0.00 0.00 0.00 3.36
1853 5251 2.839975 TGCACGAATGTACCTGTTTCA 58.160 42.857 0.00 0.00 0.00 2.69
1877 5275 8.109705 TGAACAGATACATGTGCTTATTTGTT 57.890 30.769 9.11 11.31 36.33 2.83
1879 5277 9.229784 GATTGAACAGATACATGTGCTTATTTG 57.770 33.333 9.11 1.97 32.52 2.32
1893 5291 7.665559 ACCTTTGCTTACAAGATTGAACAGATA 59.334 33.333 0.00 0.00 37.04 1.98
1897 5295 7.759489 ATACCTTTGCTTACAAGATTGAACA 57.241 32.000 0.00 0.00 37.04 3.18
1925 5323 7.766278 AGCTAAAGACTATCAGTTGTTACCATG 59.234 37.037 0.00 0.00 0.00 3.66
1936 5334 9.928236 GCATTAAGAAAAGCTAAAGACTATCAG 57.072 33.333 0.00 0.00 0.00 2.90
1937 5335 9.448438 TGCATTAAGAAAAGCTAAAGACTATCA 57.552 29.630 0.00 0.00 30.67 2.15
2136 5534 6.660521 TGATGAGGTGTATGAGCAATTTTTCT 59.339 34.615 0.00 0.00 0.00 2.52
2139 5537 6.182627 TCTGATGAGGTGTATGAGCAATTTT 58.817 36.000 0.00 0.00 0.00 1.82
2146 5544 9.775854 AGAATTAATTCTGATGAGGTGTATGAG 57.224 33.333 26.26 0.00 44.91 2.90
2152 5550 9.170734 TCTTCAAGAATTAATTCTGATGAGGTG 57.829 33.333 27.25 19.84 45.83 4.00
2165 5563 9.973661 TTCTGTTATCCCATCTTCAAGAATTAA 57.026 29.630 0.00 0.00 0.00 1.40
2166 5564 9.396022 GTTCTGTTATCCCATCTTCAAGAATTA 57.604 33.333 0.00 0.00 0.00 1.40
2168 5566 7.405292 TGTTCTGTTATCCCATCTTCAAGAAT 58.595 34.615 0.00 0.00 0.00 2.40
2169 5567 6.778821 TGTTCTGTTATCCCATCTTCAAGAA 58.221 36.000 0.00 0.00 0.00 2.52
2170 5568 6.373005 TGTTCTGTTATCCCATCTTCAAGA 57.627 37.500 0.00 0.00 0.00 3.02
2171 5569 6.039047 CCATGTTCTGTTATCCCATCTTCAAG 59.961 42.308 0.00 0.00 0.00 3.02
2174 5572 4.276926 GCCATGTTCTGTTATCCCATCTTC 59.723 45.833 0.00 0.00 0.00 2.87
2175 5573 4.079558 AGCCATGTTCTGTTATCCCATCTT 60.080 41.667 0.00 0.00 0.00 2.40
2194 5592 3.005539 GAGGGACTGCTGGAGCCA 61.006 66.667 10.63 0.00 41.55 4.75
2226 5624 0.878523 CCGTTGAGAACTTCCGTGCA 60.879 55.000 0.00 0.00 0.00 4.57
2250 5648 2.039418 CTCTATGGGGATGACGTTCCA 58.961 52.381 8.50 3.74 37.53 3.53
2268 5666 1.587547 GAAGGATTGTCATCGGGCTC 58.412 55.000 0.00 0.00 0.00 4.70
2286 5684 1.003118 CCTGTCGGGAAGAATGTTGGA 59.997 52.381 0.00 0.00 37.23 3.53


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

AutoCloner maintained by Alex Coulton.