Multiple sequence alignment - TraesCS2B01G220300

Loading Multiple Alignment...

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 TraesCS2B01G220300 chr2B 100.000 3989 0 0 1 3989 210670437 210666449 0.000000e+00 7367.0
1 TraesCS2B01G220300 chr2B 80.800 125 16 7 3361 3481 679624777 679624657 1.530000e-14 91.6
2 TraesCS2B01G220300 chr2B 78.689 122 24 2 3361 3481 106206625 106206745 3.300000e-11 80.5
3 TraesCS2B01G220300 chr2D 96.802 1970 57 5 1278 3246 152664380 152662416 0.000000e+00 3284.0
4 TraesCS2B01G220300 chr2D 89.311 1132 58 16 167 1275 152665506 152664415 0.000000e+00 1362.0
5 TraesCS2B01G220300 chr2D 87.276 503 44 8 3504 3989 503913795 503913296 1.250000e-154 556.0
6 TraesCS2B01G220300 chr2D 86.345 498 52 9 3504 3987 3772591 3772096 2.730000e-146 529.0
7 TraesCS2B01G220300 chr2D 91.045 134 8 2 3244 3376 152662302 152662172 1.140000e-40 178.0
8 TraesCS2B01G220300 chr2D 94.340 106 6 0 20 125 152665796 152665691 3.190000e-36 163.0
9 TraesCS2B01G220300 chr2A 97.071 1400 37 4 1263 2662 148851249 148852644 0.000000e+00 2355.0
10 TraesCS2B01G220300 chr2A 91.395 1348 93 15 2647 3989 148852671 148854000 0.000000e+00 1825.0
11 TraesCS2B01G220300 chr2A 84.506 1336 100 36 1 1275 148849925 148851214 0.000000e+00 1221.0
12 TraesCS2B01G220300 chr2A 85.170 499 58 7 3505 3989 18014188 18014684 7.700000e-137 497.0
13 TraesCS2B01G220300 chr5D 86.029 1632 179 23 997 2625 250416297 250417882 0.000000e+00 1705.0
14 TraesCS2B01G220300 chr5D 86.750 400 39 6 3504 3889 542299105 542299504 2.200000e-117 433.0
15 TraesCS2B01G220300 chr5B 85.977 1633 176 30 997 2625 283235066 283236649 0.000000e+00 1698.0
16 TraesCS2B01G220300 chr5B 86.573 499 49 9 3505 3989 684060301 684060795 5.870000e-148 534.0
17 TraesCS2B01G220300 chr5A 85.915 1633 179 27 997 2625 333739778 333741363 0.000000e+00 1694.0
18 TraesCS2B01G220300 chr3B 88.668 503 42 3 3501 3989 489693920 489694421 2.050000e-167 599.0
19 TraesCS2B01G220300 chr7D 88.283 495 43 3 3501 3981 414101774 414102267 2.670000e-161 579.0
20 TraesCS2B01G220300 chr1D 87.873 503 46 5 3501 3989 211805514 211806015 9.610000e-161 577.0
21 TraesCS2B01G220300 chr1D 87.273 495 48 10 3509 3989 486753011 486752518 5.830000e-153 551.0
22 TraesCS2B01G220300 chr7B 86.774 499 49 5 3501 3985 410629064 410629559 1.260000e-149 540.0
23 TraesCS2B01G220300 chr6A 86.008 486 61 7 3504 3985 454693712 454693230 7.640000e-142 514.0
24 TraesCS2B01G220300 chr3D 82.099 486 71 12 3504 3981 41801342 41801819 6.210000e-108 401.0
25 TraesCS2B01G220300 chr4D 83.696 92 14 1 3361 3452 253768354 253768444 7.100000e-13 86.1
26 TraesCS2B01G220300 chr7A 80.233 86 17 0 3396 3481 272549433 272549518 9.250000e-07 65.8


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 TraesCS2B01G220300 chr2B 210666449 210670437 3988 True 7367.000000 7367 100.000000 1 3989 1 chr2B.!!$R1 3988
1 TraesCS2B01G220300 chr2D 152662172 152665796 3624 True 1246.750000 3284 92.874500 20 3376 4 chr2D.!!$R3 3356
2 TraesCS2B01G220300 chr2A 148849925 148854000 4075 False 1800.333333 2355 90.990667 1 3989 3 chr2A.!!$F2 3988
3 TraesCS2B01G220300 chr5D 250416297 250417882 1585 False 1705.000000 1705 86.029000 997 2625 1 chr5D.!!$F1 1628
4 TraesCS2B01G220300 chr5B 283235066 283236649 1583 False 1698.000000 1698 85.977000 997 2625 1 chr5B.!!$F1 1628
5 TraesCS2B01G220300 chr5A 333739778 333741363 1585 False 1694.000000 1694 85.915000 997 2625 1 chr5A.!!$F1 1628
6 TraesCS2B01G220300 chr3B 489693920 489694421 501 False 599.000000 599 88.668000 3501 3989 1 chr3B.!!$F1 488
7 TraesCS2B01G220300 chr1D 211805514 211806015 501 False 577.000000 577 87.873000 3501 3989 1 chr1D.!!$F1 488

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
353 523 0.101399 TGCGGCGATCTCTTCTCTTC 59.899 55.0 12.98 0.0 0.00 2.87 F
791 968 0.461961 ATACCAAGGTGAGAGAGCGC 59.538 55.0 0.00 0.0 0.00 5.92 F
1635 1902 0.673644 CGTGGGCGATGAGGTTCTTT 60.674 55.0 0.00 0.0 41.33 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1902 0.322816 GCTGCATTTGGGAGAGTGGA 60.323 55.0 0.00 0.0 37.05 4.02 R
2347 2614 0.596341 ACAAAACATCCCGCGCAAAC 60.596 50.0 8.75 0.0 0.00 2.93 R
3370 3799 0.170561 ACGATCTTGTCTTCGTCCCG 59.829 55.0 0.00 0.0 44.72 5.14 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
37 38 0.319986 TCTAAACACCGCGTGCATCA 60.320 50.000 4.92 0.00 36.98 3.07
92 93 2.554032 CTCAGTCAAACCCTCGCATTTT 59.446 45.455 0.00 0.00 0.00 1.82
137 143 7.404985 TCAAGTACGCTTAATTACGAGTAGAG 58.595 38.462 5.92 0.00 32.87 2.43
300 451 2.079925 CTTCTTGCTTGGCACTACTCC 58.920 52.381 0.00 0.00 38.71 3.85
302 453 1.699634 TCTTGCTTGGCACTACTCCTT 59.300 47.619 0.00 0.00 38.71 3.36
323 474 3.382111 CGGAGGAGGACAAGTGCT 58.618 61.111 0.00 0.00 0.00 4.40
324 475 1.674057 CGGAGGAGGACAAGTGCTT 59.326 57.895 0.00 0.00 0.00 3.91
325 476 0.390472 CGGAGGAGGACAAGTGCTTC 60.390 60.000 0.00 0.00 0.00 3.86
326 477 0.980423 GGAGGAGGACAAGTGCTTCT 59.020 55.000 1.80 1.80 39.79 2.85
327 478 1.349357 GGAGGAGGACAAGTGCTTCTT 59.651 52.381 3.93 0.00 36.97 2.52
328 479 2.614229 GGAGGAGGACAAGTGCTTCTTC 60.614 54.545 3.93 0.00 36.97 2.87
330 481 1.349357 GGAGGACAAGTGCTTCTTCCT 59.651 52.381 10.04 10.04 35.58 3.36
331 482 2.224646 GGAGGACAAGTGCTTCTTCCTT 60.225 50.000 11.08 0.00 35.58 3.36
332 483 3.070748 GAGGACAAGTGCTTCTTCCTTC 58.929 50.000 11.08 4.30 34.09 3.46
333 484 1.801178 GGACAAGTGCTTCTTCCTTCG 59.199 52.381 0.00 0.00 33.63 3.79
353 523 0.101399 TGCGGCGATCTCTTCTCTTC 59.899 55.000 12.98 0.00 0.00 2.87
437 614 1.002274 AGGTGGTTTGTTTGCCCCA 59.998 52.632 0.00 0.00 0.00 4.96
459 636 2.358737 CTTGCCGCCGTCCTCTTT 60.359 61.111 0.00 0.00 0.00 2.52
519 696 3.903932 GAGCCTTGCGCCTGTTTGC 62.904 63.158 4.18 0.00 38.78 3.68
521 698 3.297620 CCTTGCGCCTGTTTGCCT 61.298 61.111 4.18 0.00 0.00 4.75
559 736 1.084370 CCAAATCCGCCGTCTCACTC 61.084 60.000 0.00 0.00 0.00 3.51
582 759 1.801309 GCTCTTCGATCTCCCCTCCG 61.801 65.000 0.00 0.00 0.00 4.63
712 889 2.203209 CCCGAATACTGGCCCAGC 60.203 66.667 11.63 0.00 34.37 4.85
742 919 1.668419 CATGGTCCGATGGTTCTTCC 58.332 55.000 0.00 0.00 0.00 3.46
774 951 4.540824 CGCAAGATCGATCTGAGTTCATA 58.459 43.478 27.93 0.00 37.19 2.15
785 962 4.416516 TCTGAGTTCATACCAAGGTGAGA 58.583 43.478 1.07 0.00 0.00 3.27
787 964 4.416516 TGAGTTCATACCAAGGTGAGAGA 58.583 43.478 1.07 0.00 0.00 3.10
791 968 0.461961 ATACCAAGGTGAGAGAGCGC 59.538 55.000 0.00 0.00 0.00 5.92
844 1023 3.634568 ACCATTTCGCGTCATTTTTCA 57.365 38.095 5.77 0.00 0.00 2.69
872 1051 7.035840 AGAGCATTTCGCATCATTAATTTCT 57.964 32.000 0.00 0.00 46.13 2.52
876 1056 5.514274 TTTCGCATCATTAATTTCTCCCC 57.486 39.130 0.00 0.00 0.00 4.81
887 1067 9.270707 TCATTAATTTCTCCCCAGATTCATTTT 57.729 29.630 0.00 0.00 0.00 1.82
929 1109 7.982919 TGTGCTTAGTAGTTTCTGTTCTTGTAA 59.017 33.333 0.00 0.00 0.00 2.41
970 1165 3.340814 TTTCAGCTTGGATCCAGAGTC 57.659 47.619 15.53 11.04 0.00 3.36
1016 1211 0.674534 ATAATGTCGCCGAGGAGACC 59.325 55.000 20.39 6.15 42.82 3.85
1056 1251 4.300803 TGTTCATGCTCATGCTTTTCAAC 58.699 39.130 5.04 4.48 38.65 3.18
1082 1277 4.606210 TCAGGTACTTACTAGCACATGGA 58.394 43.478 0.00 0.00 34.60 3.41
1083 1278 5.208890 TCAGGTACTTACTAGCACATGGAT 58.791 41.667 0.00 0.00 34.60 3.41
1084 1279 5.069119 TCAGGTACTTACTAGCACATGGATG 59.931 44.000 0.00 0.00 34.60 3.51
1085 1280 4.058817 GGTACTTACTAGCACATGGATGC 58.941 47.826 0.00 0.00 46.50 3.91
1139 1361 6.260271 CACATGATTAGCATCTCATTGTGTCT 59.740 38.462 0.00 0.00 34.15 3.41
1233 1455 6.242396 TGAACTGAAGGGGAAAAATCGATAA 58.758 36.000 0.00 0.00 0.00 1.75
1239 1461 7.599171 TGAAGGGGAAAAATCGATAAAGAAAC 58.401 34.615 0.00 0.00 0.00 2.78
1253 1476 8.936864 TCGATAAAGAAACCTGAAGAGAATTTC 58.063 33.333 0.00 0.00 0.00 2.17
1256 1479 6.890979 AAGAAACCTGAAGAGAATTTCCTG 57.109 37.500 0.00 0.00 30.17 3.86
1307 1574 9.910511 TTTCTATCTAATTTTTCGTCGCATAAC 57.089 29.630 0.00 0.00 0.00 1.89
1312 1579 5.908240 AATTTTTCGTCGCATAACAATCG 57.092 34.783 0.00 0.00 0.00 3.34
1320 1587 1.130373 CGCATAACAATCGGTTGCTGT 59.870 47.619 8.70 0.00 40.73 4.40
1466 1733 4.498894 TGATTCAGACCATCAGATGCTT 57.501 40.909 4.68 0.00 0.00 3.91
1595 1862 2.190578 GCTGCCTACATTCCGGCT 59.809 61.111 0.00 0.00 46.42 5.52
1635 1902 0.673644 CGTGGGCGATGAGGTTCTTT 60.674 55.000 0.00 0.00 41.33 2.52
1757 2024 6.760440 AGTCCTCACTCAATGGATATGATT 57.240 37.500 0.00 0.00 32.03 2.57
1760 2027 5.013495 TCCTCACTCAATGGATATGATTCCC 59.987 44.000 0.00 0.00 34.67 3.97
2177 2444 6.039270 GCCATGTGCTAAATAATTCTGGTACA 59.961 38.462 0.00 0.00 36.87 2.90
2220 2487 6.238484 CCAAGTAAGCACATACCTATTTGAGC 60.238 42.308 0.00 0.00 0.00 4.26
2347 2614 0.108329 AATAACACTGACTCGCCGGG 60.108 55.000 2.18 0.00 0.00 5.73
2730 3039 7.232118 ACCTAAACAAATTTCCTCCTGAATG 57.768 36.000 0.00 0.00 31.67 2.67
2820 3130 6.919721 TGTAAGCTCAAACTTCTTTTGTTGT 58.080 32.000 0.00 0.00 44.47 3.32
2922 3232 0.040067 GCCAAGACAGTTTTGCCTCG 60.040 55.000 0.00 0.00 0.00 4.63
3022 3332 7.500992 ACTGTATGTTGTATTTCGGATGAGAT 58.499 34.615 0.00 0.00 0.00 2.75
3206 3516 3.188667 GGAAGGGCTACTTTCTTGAAACG 59.811 47.826 0.00 0.00 40.21 3.60
3314 3743 2.497675 AGGATCTTAGCTCAGCGTTTCA 59.502 45.455 0.00 0.00 0.00 2.69
3370 3799 2.409012 CAAAACGCCCCAATGTTTACC 58.591 47.619 0.00 0.00 37.31 2.85
3394 3823 2.080286 CGAAGACAAGATCGTTGGGT 57.920 50.000 8.95 0.00 34.48 4.51
3410 3839 2.866351 TGGGTTGGCCTAACTAAACAC 58.134 47.619 3.32 0.00 39.31 3.32
3413 3842 2.228103 GGTTGGCCTAACTAAACACTGC 59.772 50.000 3.32 0.00 39.31 4.40
3423 3852 1.737793 CTAAACACTGCGACCATTCCC 59.262 52.381 0.00 0.00 0.00 3.97
3476 3905 3.461085 AGCCTCCACATTTGATGTCCTAT 59.539 43.478 0.00 0.00 42.70 2.57
3489 3918 5.464069 TGATGTCCTATACTCTTAGCCCAA 58.536 41.667 0.00 0.00 0.00 4.12
3490 3919 5.903010 TGATGTCCTATACTCTTAGCCCAAA 59.097 40.000 0.00 0.00 0.00 3.28
3606 4035 0.946221 CGTCGCTTGGCACTTCTCTT 60.946 55.000 0.00 0.00 0.00 2.85
3609 4038 3.003480 GTCGCTTGGCACTTCTCTTTAT 58.997 45.455 0.00 0.00 0.00 1.40
3647 4076 1.001974 TGGTGCTCGCAGTAAGACAAT 59.998 47.619 0.00 0.00 0.00 2.71
3657 4086 1.423541 AGTAAGACAATGTGGGTGGCA 59.576 47.619 0.00 0.00 0.00 4.92
3698 4127 2.835895 GTTGGGCGGTGGTTTGGT 60.836 61.111 0.00 0.00 0.00 3.67
3708 4137 0.818938 GTGGTTTGGTTGGTCGGTTT 59.181 50.000 0.00 0.00 0.00 3.27
3729 4158 3.822035 TTGGGCGGTGGGGTTTGA 61.822 61.111 0.00 0.00 0.00 2.69
3769 4227 2.750815 GGTTCGTCCGACTCCAATG 58.249 57.895 0.00 0.00 0.00 2.82
3770 4228 1.359459 GGTTCGTCCGACTCCAATGC 61.359 60.000 0.00 0.00 0.00 3.56
3771 4229 1.445410 TTCGTCCGACTCCAATGCG 60.445 57.895 0.00 0.00 0.00 4.73
3772 4230 2.829043 TTCGTCCGACTCCAATGCGG 62.829 60.000 0.00 0.00 46.08 5.69
3773 4231 2.264794 GTCCGACTCCAATGCGGT 59.735 61.111 0.00 0.00 45.02 5.68
3774 4232 2.100631 GTCCGACTCCAATGCGGTG 61.101 63.158 0.00 0.00 45.02 4.94
3775 4233 3.499737 CCGACTCCAATGCGGTGC 61.500 66.667 0.00 0.00 40.17 5.01
3776 4234 3.499737 CGACTCCAATGCGGTGCC 61.500 66.667 0.00 0.00 35.57 5.01
3777 4235 2.359850 GACTCCAATGCGGTGCCA 60.360 61.111 0.00 0.00 35.57 4.92
3778 4236 2.672996 ACTCCAATGCGGTGCCAC 60.673 61.111 0.00 0.00 35.57 5.01
3811 4269 2.745037 GGTGTCGGTGGTAGCCAA 59.255 61.111 0.00 0.00 34.18 4.52
3826 4284 1.852626 CCAACCCCCACTTCCCTCT 60.853 63.158 0.00 0.00 0.00 3.69
3899 4358 2.356125 GCATCCCTTCTTGAAGGTGCTA 60.356 50.000 25.13 12.48 38.31 3.49
3940 4399 1.302832 CCTCAGGCTGTGGTGGTTC 60.303 63.158 24.09 0.00 0.00 3.62
3948 4407 1.802337 CTGTGGTGGTTCGTCTCCGA 61.802 60.000 0.00 0.00 42.41 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.490759 GAGGTGATGCACGCGGTG 61.491 66.667 12.47 7.75 34.83 4.94
25 26 4.760047 GGAGGTGATGCACGCGGT 62.760 66.667 12.47 0.00 34.83 5.68
28 29 2.359850 TTGGGAGGTGATGCACGC 60.360 61.111 0.00 0.00 34.83 5.34
37 38 2.915869 TGTAGATCCAACTTGGGAGGT 58.084 47.619 8.01 0.00 41.08 3.85
137 143 6.285990 TCTGTGTCTTGGGAGTTTAACTTAC 58.714 40.000 0.00 0.00 0.00 2.34
315 466 2.213499 CACGAAGGAAGAAGCACTTGT 58.787 47.619 0.00 0.00 39.13 3.16
332 483 1.941734 GAGAAGAGATCGCCGCACG 60.942 63.158 0.00 0.00 45.62 5.34
333 484 0.179124 AAGAGAAGAGATCGCCGCAC 60.179 55.000 0.00 0.00 0.00 5.34
373 544 2.364317 TCCCTGCTTCCTCCTCCG 60.364 66.667 0.00 0.00 0.00 4.63
380 551 3.803162 GGAGCCCTCCCTGCTTCC 61.803 72.222 2.81 0.00 43.94 3.46
400 577 2.446036 GTATCCCGCTGGTCCCCT 60.446 66.667 0.00 0.00 0.00 4.79
417 594 1.445518 GGGCAAACAAACCACCTGG 59.554 57.895 0.00 0.00 42.17 4.45
519 696 1.745653 GGGCGGAAAATCAGAGAAAGG 59.254 52.381 0.00 0.00 0.00 3.11
521 698 1.615919 GGGGGCGGAAAATCAGAGAAA 60.616 52.381 0.00 0.00 0.00 2.52
638 815 1.218316 GGGCGGAAGAGTGGTAGTG 59.782 63.158 0.00 0.00 0.00 2.74
712 889 2.510906 GACCATGGACGGATGGGG 59.489 66.667 21.47 0.08 46.46 4.96
716 893 1.748403 CATCGGACCATGGACGGAT 59.252 57.895 24.49 24.49 32.47 4.18
742 919 0.854853 CGATCTTGCGCGCTGAAAAG 60.855 55.000 33.29 25.59 0.00 2.27
774 951 2.164865 CTGCGCTCTCTCACCTTGGT 62.165 60.000 9.73 0.00 0.00 3.67
785 962 1.869767 GTGCATAATAAGCTGCGCTCT 59.130 47.619 9.73 2.40 43.69 4.09
791 968 5.550232 TCACACAAGTGCATAATAAGCTG 57.450 39.130 0.00 0.00 45.49 4.24
794 971 6.324042 TGCATTCACACAAGTGCATAATAAG 58.676 36.000 0.00 0.00 45.49 1.73
802 981 1.458064 GCAATGCATTCACACAAGTGC 59.542 47.619 9.53 3.52 45.49 4.40
808 987 3.788333 ATGGTAGCAATGCATTCACAC 57.212 42.857 9.53 7.08 0.00 3.82
844 1023 9.754382 AAATTAATGATGCGAAATGCTCTTATT 57.246 25.926 0.00 0.00 46.63 1.40
872 1051 4.531339 TGAAATGCAAAATGAATCTGGGGA 59.469 37.500 0.00 0.00 0.00 4.81
876 1056 6.395629 ACTCCTGAAATGCAAAATGAATCTG 58.604 36.000 0.00 0.00 0.00 2.90
887 1067 2.694628 AGCACAAAACTCCTGAAATGCA 59.305 40.909 0.00 0.00 34.27 3.96
970 1165 2.111384 TCTACTAGGGGCTTCTTGCAG 58.889 52.381 0.00 0.00 45.15 4.41
1056 1251 3.119602 TGTGCTAGTAAGTACCTGAAGCG 60.120 47.826 0.00 0.00 37.52 4.68
1082 1277 6.039270 ACCGTGTAATTTAATACAGCATGCAT 59.961 34.615 21.98 10.24 42.53 3.96
1083 1278 5.355630 ACCGTGTAATTTAATACAGCATGCA 59.644 36.000 21.98 0.00 42.53 3.96
1084 1279 5.681105 CACCGTGTAATTTAATACAGCATGC 59.319 40.000 10.51 10.51 42.53 4.06
1085 1280 5.681105 GCACCGTGTAATTTAATACAGCATG 59.319 40.000 0.00 0.00 46.00 4.06
1181 1403 7.065204 GGCAAACAAAGTATGTTTTCCTCAAAA 59.935 33.333 13.19 0.00 45.86 2.44
1221 1443 9.548208 CTCTTCAGGTTTCTTTATCGATTTTTC 57.452 33.333 1.71 0.00 0.00 2.29
1233 1455 5.772169 CCAGGAAATTCTCTTCAGGTTTCTT 59.228 40.000 0.00 0.00 31.03 2.52
1239 1461 4.639310 CACATCCAGGAAATTCTCTTCAGG 59.361 45.833 0.00 0.00 0.00 3.86
1253 1476 7.279536 GCAGATATATGATTGTACACATCCAGG 59.720 40.741 0.39 0.00 0.00 4.45
1256 1479 8.783833 AAGCAGATATATGATTGTACACATCC 57.216 34.615 0.00 0.00 0.00 3.51
1284 1551 9.864034 ATTGTTATGCGACGAAAAATTAGATAG 57.136 29.630 0.00 0.00 0.00 2.08
1300 1567 1.130373 ACAGCAACCGATTGTTATGCG 59.870 47.619 0.00 0.00 38.17 4.73
1307 1574 3.705604 ACAGAAAAACAGCAACCGATTG 58.294 40.909 0.00 0.00 38.99 2.67
1312 1579 5.351189 ACAATTGAACAGAAAAACAGCAACC 59.649 36.000 13.59 0.00 0.00 3.77
1320 1587 6.707440 TGCTCCTACAATTGAACAGAAAAA 57.293 33.333 13.59 0.00 0.00 1.94
1595 1862 3.976306 CGGCGATATACGTGATGTTTGTA 59.024 43.478 0.00 0.00 44.60 2.41
1635 1902 0.322816 GCTGCATTTGGGAGAGTGGA 60.323 55.000 0.00 0.00 37.05 4.02
2177 2444 1.132500 GGTTATCTGGCTGGCTAGGT 58.868 55.000 0.00 1.60 0.00 3.08
2347 2614 0.596341 ACAAAACATCCCGCGCAAAC 60.596 50.000 8.75 0.00 0.00 2.93
2706 3015 6.782494 ACATTCAGGAGGAAATTTGTTTAGGT 59.218 34.615 0.00 0.00 39.39 3.08
2730 3039 1.544724 TCCATGGCCTGCAAGTTTAC 58.455 50.000 6.96 0.00 0.00 2.01
2820 3130 5.421056 ACCAAACCTCATCGTCAGTATAGAA 59.579 40.000 0.00 0.00 0.00 2.10
3137 3447 4.935352 TTCAAAATAAGTGCACCTTGCT 57.065 36.364 14.63 0.00 45.31 3.91
3138 3448 4.990426 ACATTCAAAATAAGTGCACCTTGC 59.010 37.500 14.63 0.00 45.29 4.01
3370 3799 0.170561 ACGATCTTGTCTTCGTCCCG 59.829 55.000 0.00 0.00 44.72 5.14
3389 3818 3.117436 AGTGTTTAGTTAGGCCAACCCAA 60.117 43.478 5.01 2.42 37.93 4.12
3390 3819 2.444010 AGTGTTTAGTTAGGCCAACCCA 59.556 45.455 5.01 0.13 37.93 4.51
3394 3823 2.147958 CGCAGTGTTTAGTTAGGCCAA 58.852 47.619 5.01 0.00 0.00 4.52
3404 3833 1.349688 AGGGAATGGTCGCAGTGTTTA 59.650 47.619 0.00 0.00 39.15 2.01
3410 3839 1.115467 ACTCTAGGGAATGGTCGCAG 58.885 55.000 0.00 0.00 39.15 5.18
3413 3842 4.120589 GCTTTAACTCTAGGGAATGGTCG 58.879 47.826 0.00 0.00 0.00 4.79
3444 3873 2.205022 TGTGGAGGCTGGAAATCTTG 57.795 50.000 0.00 0.00 0.00 3.02
3445 3874 3.463048 AATGTGGAGGCTGGAAATCTT 57.537 42.857 0.00 0.00 0.00 2.40
3454 3883 1.637553 AGGACATCAAATGTGGAGGCT 59.362 47.619 0.00 0.00 45.03 4.58
3476 3905 7.039504 CCGGTAATATACTTTGGGCTAAGAGTA 60.040 40.741 0.00 7.28 0.00 2.59
3489 3918 2.486918 GTTGCGGCCGGTAATATACTT 58.513 47.619 29.38 0.00 0.00 2.24
3490 3919 1.603678 CGTTGCGGCCGGTAATATACT 60.604 52.381 29.38 0.00 0.00 2.12
3606 4035 3.695830 ACACGAGGCCAAGAAGAATAA 57.304 42.857 5.01 0.00 0.00 1.40
3609 4038 1.593196 CAACACGAGGCCAAGAAGAA 58.407 50.000 5.01 0.00 0.00 2.52
3666 4095 2.046411 AACACCATGCGCCATCGA 60.046 55.556 4.18 0.00 38.10 3.59
3698 4127 1.526455 CCCAACCGAAACCGACCAA 60.526 57.895 0.00 0.00 0.00 3.67
3729 4158 1.826385 CAAGGATTTCTCCCGCACTT 58.174 50.000 0.00 0.00 43.21 3.16
3763 4221 3.582242 ATGGTGGCACCGCATTGGA 62.582 57.895 30.14 12.56 42.58 3.53
3764 4222 2.561549 GAATGGTGGCACCGCATTGG 62.562 60.000 30.14 0.00 42.58 3.16
3765 4223 1.153784 GAATGGTGGCACCGCATTG 60.154 57.895 30.14 0.00 42.58 2.82
3766 4224 2.350458 GGAATGGTGGCACCGCATT 61.350 57.895 30.14 24.22 42.58 3.56
3767 4225 2.755469 GGAATGGTGGCACCGCAT 60.755 61.111 30.14 19.10 42.58 4.73
3768 4226 3.505790 AAGGAATGGTGGCACCGCA 62.506 57.895 30.14 15.66 42.58 5.69
3769 4227 2.676471 AAGGAATGGTGGCACCGC 60.676 61.111 30.14 21.24 42.58 5.68
3770 4228 0.609131 AAGAAGGAATGGTGGCACCG 60.609 55.000 30.14 0.00 42.58 4.94
3771 4229 0.890683 CAAGAAGGAATGGTGGCACC 59.109 55.000 29.75 29.75 39.22 5.01
3772 4230 1.909700 TCAAGAAGGAATGGTGGCAC 58.090 50.000 9.70 9.70 0.00 5.01
3773 4231 2.517959 CTTCAAGAAGGAATGGTGGCA 58.482 47.619 1.86 0.00 34.87 4.92
3811 4269 1.305887 CGTAGAGGGAAGTGGGGGT 60.306 63.158 0.00 0.00 0.00 4.95
3826 4284 3.393106 GGTTTCCCCCGGCTCGTA 61.393 66.667 0.00 0.00 0.00 3.43
3860 4318 4.175489 GACGCCGACGAGCTGCTA 62.175 66.667 0.15 0.00 43.93 3.49
3899 4358 1.153628 GATCTGCCGCGTACCAAGT 60.154 57.895 4.92 0.00 0.00 3.16
3926 4385 2.100879 GAGACGAACCACCACAGCCT 62.101 60.000 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.