Multiple sequence alignment - TraesCS6A01G221500

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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 TraesCS6A01G221500 chr6A 100.000 5812 0 0 1 5812 411766957 411772768 0.000000e+00 10733.0
1 TraesCS6A01G221500 chr6A 89.175 582 20 19 4144 4709 441440964 441440410 0.000000e+00 686.0
2 TraesCS6A01G221500 chr6A 97.727 308 7 0 3973 4280 441441268 441440961 1.110000e-146 531.0
3 TraesCS6A01G221500 chr6A 92.000 275 13 3 3306 3579 440694501 440694235 1.530000e-100 377.0
4 TraesCS6A01G221500 chr6A 96.262 107 4 0 3807 3913 441443388 441443282 5.990000e-40 176.0
5 TraesCS6A01G221500 chr6A 84.615 169 26 0 135 303 302778680 302778848 1.000000e-37 169.0
6 TraesCS6A01G221500 chr6A 84.810 158 23 1 147 303 398098581 398098738 2.170000e-34 158.0
7 TraesCS6A01G221500 chr6A 100.000 51 0 0 3905 3955 441441316 441441266 1.720000e-15 95.3
8 TraesCS6A01G221500 chr6D 94.860 5389 188 30 26 5355 303056563 303061921 0.000000e+00 8335.0
9 TraesCS6A01G221500 chr6D 87.002 477 18 16 5362 5812 303062029 303062487 1.120000e-136 497.0
10 TraesCS6A01G221500 chr6B 96.895 1707 47 3 3655 5355 468735100 468736806 0.000000e+00 2854.0
11 TraesCS6A01G221500 chr6B 95.077 1747 77 5 855 2594 468731990 468733734 0.000000e+00 2741.0
12 TraesCS6A01G221500 chr6B 94.033 905 52 2 2584 3487 468733752 468734655 0.000000e+00 1371.0
13 TraesCS6A01G221500 chr6B 91.477 880 54 12 1 863 468730963 468731838 0.000000e+00 1190.0
14 TraesCS6A01G221500 chr6B 90.523 306 27 2 1652 1957 131684026 131683723 2.520000e-108 403.0
15 TraesCS6A01G221500 chr6B 93.033 244 8 2 5561 5804 468738574 468738808 1.200000e-91 348.0
16 TraesCS6A01G221500 chr6B 96.471 170 5 1 3489 3657 468734818 468734987 4.430000e-71 279.0
17 TraesCS6A01G221500 chr6B 85.093 161 22 2 147 306 9103055 9102896 4.660000e-36 163.0
18 TraesCS6A01G221500 chr7B 92.506 427 24 5 1538 1957 619156847 619156422 6.440000e-169 604.0
19 TraesCS6A01G221500 chr7B 83.080 591 40 21 972 1548 619158146 619157602 3.150000e-132 483.0
20 TraesCS6A01G221500 chr4A 91.017 423 32 3 1539 1957 68459557 68459137 3.040000e-157 566.0
21 TraesCS6A01G221500 chr4A 84.568 162 22 3 144 303 37771084 37771244 2.170000e-34 158.0
22 TraesCS6A01G221500 chr4A 81.757 148 23 4 3 148 161279714 161279569 2.840000e-23 121.0
23 TraesCS6A01G221500 chr1B 90.071 423 36 4 1539 1957 23988590 23989010 1.420000e-150 544.0
24 TraesCS6A01G221500 chr1B 90.071 423 36 4 1539 1957 24092073 24091653 1.420000e-150 544.0
25 TraesCS6A01G221500 chr5B 89.598 423 37 5 1539 1957 506660556 506660975 1.110000e-146 531.0
26 TraesCS6A01G221500 chr5B 91.541 331 22 3 1539 1865 56555438 56555766 8.880000e-123 451.0
27 TraesCS6A01G221500 chr5B 94.304 158 7 1 3296 3453 665744468 665744623 2.090000e-59 241.0
28 TraesCS6A01G221500 chr5B 84.337 166 23 3 143 306 534012415 534012251 6.030000e-35 159.0
29 TraesCS6A01G221500 chr2A 96.129 155 6 0 3295 3449 141506472 141506318 2.690000e-63 254.0
30 TraesCS6A01G221500 chr7D 95.425 153 7 0 3297 3449 34757018 34756866 1.620000e-60 244.0
31 TraesCS6A01G221500 chr2B 94.839 155 8 0 3295 3449 190023045 190022891 5.820000e-60 243.0
32 TraesCS6A01G221500 chr2B 84.337 166 23 3 2586 2750 38126363 38126200 6.030000e-35 159.0
33 TraesCS6A01G221500 chr2B 84.337 166 23 3 2586 2750 38173618 38173455 6.030000e-35 159.0
34 TraesCS6A01G221500 chr5D 94.304 158 7 1 3296 3453 528717277 528717432 2.090000e-59 241.0
35 TraesCS6A01G221500 chr5D 85.093 161 21 2 147 306 391220275 391220117 1.680000e-35 161.0
36 TraesCS6A01G221500 chr5A 94.304 158 7 1 3296 3453 656872284 656872439 2.090000e-59 241.0
37 TraesCS6A01G221500 chr3A 85.093 161 22 2 147 306 733185702 733185543 4.660000e-36 163.0
38 TraesCS6A01G221500 chr3A 83.951 162 23 3 147 306 599416253 599416093 1.010000e-32 152.0
39 TraesCS6A01G221500 chr3A 92.000 50 4 0 99 148 593345001 593345050 2.910000e-08 71.3
40 TraesCS6A01G221500 chrUn 84.663 163 22 3 2586 2747 368162156 368162316 6.030000e-35 159.0
41 TraesCS6A01G221500 chr1A 91.071 112 10 0 37 148 532737082 532736971 1.010000e-32 152.0
42 TraesCS6A01G221500 chr1A 93.878 49 3 0 3 51 532738277 532738229 2.250000e-09 75.0
43 TraesCS6A01G221500 chr3D 83.951 162 20 3 147 303 443256902 443257062 3.630000e-32 150.0
44 TraesCS6A01G221500 chr3D 92.000 50 4 0 99 148 449742523 449742572 2.910000e-08 71.3


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 TraesCS6A01G221500 chr6A 411766957 411772768 5811 False 10733.000000 10733 100.000000 1 5812 1 chr6A.!!$F3 5811
1 TraesCS6A01G221500 chr6A 441440410 441443388 2978 True 372.075000 686 95.791000 3807 4709 4 chr6A.!!$R2 902
2 TraesCS6A01G221500 chr6D 303056563 303062487 5924 False 4416.000000 8335 90.931000 26 5812 2 chr6D.!!$F1 5786
3 TraesCS6A01G221500 chr6B 468730963 468738808 7845 False 1463.833333 2854 94.497667 1 5804 6 chr6B.!!$F1 5803
4 TraesCS6A01G221500 chr7B 619156422 619158146 1724 True 543.500000 604 87.793000 972 1957 2 chr7B.!!$R1 985

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
21 22 1.000731 CAGGGCCTTTTTGATTCGCAA 59.999 47.619 1.32 0.00 33.88 4.85 F
1291 1497 0.106894 CCCTACCATCCCGCTCTTTC 59.893 60.000 0.00 0.00 0.00 2.62 F
1847 2834 2.094234 GCCCAAACTGTTCAGTTGTGTT 60.094 45.455 17.16 1.11 31.64 3.32 F
2762 3789 1.202222 GCACTGGCACACATAGCATTC 60.202 52.381 0.00 0.00 40.72 2.67 F
4261 7675 0.605589 GGCCTGGAAAACGTACAGCT 60.606 55.000 0.00 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 2571 1.417517 TCACCATGGATGATCCCGAAG 59.582 52.381 21.47 0.0 35.03 3.79 R
2482 3481 0.959372 ACAGCAGCAATGCAGGACTC 60.959 55.000 8.35 0.0 37.25 3.36 R
3208 4236 3.627395 AGACAAACGATAATCCCTGCA 57.373 42.857 0.00 0.0 0.00 4.41 R
4749 8181 0.764890 AACTCCTGCACTGTAGCCAA 59.235 50.000 0.00 0.0 0.00 4.52 R
5358 8799 0.033601 TTCTATTGTTGCGGGGGCAT 60.034 50.000 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
21 22 1.000731 CAGGGCCTTTTTGATTCGCAA 59.999 47.619 1.32 0.00 33.88 4.85
51 52 8.899427 TTCAAAATGCAGGAACATGAAAAATA 57.101 26.923 0.00 0.00 0.00 1.40
60 61 9.899226 GCAGGAACATGAAAAATATAGGAATAC 57.101 33.333 0.00 0.00 0.00 1.89
115 116 4.022329 TCGAGAAGTGTTTGATAGCACAGA 60.022 41.667 0.00 0.00 38.02 3.41
155 156 2.575805 AAGAAGTTTGAGGGCTCCTG 57.424 50.000 0.00 0.00 31.76 3.86
165 166 2.027192 TGAGGGCTCCTGTGATACAAAC 60.027 50.000 0.00 0.00 31.76 2.93
166 167 1.985159 AGGGCTCCTGTGATACAAACA 59.015 47.619 0.00 0.00 29.57 2.83
318 324 7.106239 ACTTTTCATCTACCGAATGAGATGTT 58.894 34.615 10.73 0.00 46.14 2.71
444 451 2.745308 CGATGGGGCCACATGGAGA 61.745 63.158 29.36 0.00 37.39 3.71
511 518 1.742768 GGTAGATCGGAGCAGGTGG 59.257 63.158 0.00 0.00 0.00 4.61
667 683 2.890474 CGATGAAACTCGCCCCGG 60.890 66.667 0.00 0.00 0.00 5.73
701 717 1.282875 GTTGCTTTCGTGGTCTGGC 59.717 57.895 0.00 0.00 0.00 4.85
1275 1481 3.155167 GAGGTCGCCGAATCCCCT 61.155 66.667 0.00 0.00 0.00 4.79
1291 1497 0.106894 CCCTACCATCCCGCTCTTTC 59.893 60.000 0.00 0.00 0.00 2.62
1471 1687 2.774439 TTTTCTTTCCGTGCTTCTGC 57.226 45.000 0.00 0.00 40.20 4.26
1525 1741 3.057876 GGAACATGCGATTGTGGTGTTAA 60.058 43.478 0.00 0.00 33.55 2.01
1590 2571 5.513495 CGAAGTAGACAGAGTGCTTTCATAC 59.487 44.000 0.00 0.00 0.00 2.39
1659 2645 2.423577 GGATACACTGCGTTTCTGGTT 58.576 47.619 0.00 0.00 0.00 3.67
1833 2820 3.453424 CCTTTTGTACACTTGCCCAAAC 58.547 45.455 0.00 0.00 0.00 2.93
1847 2834 2.094234 GCCCAAACTGTTCAGTTGTGTT 60.094 45.455 17.16 1.11 31.64 3.32
1997 2992 7.333423 TCGGTGTATTTGAGGTTTCATTAGAAG 59.667 37.037 0.00 0.00 34.71 2.85
2016 3011 6.613153 AGAAGAACAGTAAGTAGGATTGCT 57.387 37.500 0.00 0.00 0.00 3.91
2029 3024 3.798202 AGGATTGCTGAGACGGTTTATC 58.202 45.455 0.00 0.00 0.00 1.75
2197 3195 9.914834 TTAGACCAGTAATGGCTATTTTTGTAT 57.085 29.630 9.63 0.00 0.00 2.29
2354 3352 3.661944 TGTTTGTTTTGCCTGCCATATG 58.338 40.909 0.00 0.00 0.00 1.78
2376 3374 4.141937 TGGTCTGTGGTATATTCAGCAGTC 60.142 45.833 0.00 0.00 0.00 3.51
2517 3516 2.815503 TGCTGTCATCCTGTCATGTTTG 59.184 45.455 0.00 0.00 0.00 2.93
2546 3545 2.135139 TGTGTCGAATGTGACTTCTGC 58.865 47.619 0.00 0.00 39.64 4.26
2556 3555 8.194769 TCGAATGTGACTTCTGCAAACTATATA 58.805 33.333 0.00 0.00 0.00 0.86
2609 3636 2.238942 TGTTGTAGTCTGGCACACTG 57.761 50.000 5.61 0.00 0.00 3.66
2643 3670 1.264020 CGGATGTTGGTGTGAACTGTG 59.736 52.381 0.00 0.00 0.00 3.66
2762 3789 1.202222 GCACTGGCACACATAGCATTC 60.202 52.381 0.00 0.00 40.72 2.67
2764 3791 2.751259 CACTGGCACACATAGCATTCTT 59.249 45.455 0.00 0.00 0.00 2.52
2811 3838 3.388024 TGGTGCTTCTAGTTTGACTCACT 59.612 43.478 0.00 0.00 0.00 3.41
2815 3842 5.523916 GTGCTTCTAGTTTGACTCACTCAAA 59.476 40.000 0.00 0.00 45.05 2.69
2894 3922 6.995511 TTACCGATCTTCCTAAAATGGTTG 57.004 37.500 0.00 0.00 0.00 3.77
2951 3979 6.583562 ACTTCAGAGGTTGTAATATGTAGCC 58.416 40.000 0.00 0.00 0.00 3.93
2961 3989 7.767198 GGTTGTAATATGTAGCCTGTCTTACAA 59.233 37.037 0.00 0.00 36.06 2.41
2963 3991 8.942338 TGTAATATGTAGCCTGTCTTACAAAG 57.058 34.615 0.00 0.00 0.00 2.77
2964 3992 8.537016 TGTAATATGTAGCCTGTCTTACAAAGT 58.463 33.333 0.00 0.00 0.00 2.66
3071 4099 1.378531 TGGCAGTCAAAGTGTGTGTC 58.621 50.000 0.00 0.00 0.00 3.67
3072 4100 1.339535 TGGCAGTCAAAGTGTGTGTCA 60.340 47.619 0.00 0.00 0.00 3.58
3158 4186 9.372369 CTGGATCCTATTTATCCGAATAGAAAC 57.628 37.037 14.23 0.00 45.05 2.78
3208 4236 6.060788 GCAATCTTAGGAAGTGAAGATGGAT 58.939 40.000 3.66 0.00 40.68 3.41
3222 4250 2.909006 AGATGGATGCAGGGATTATCGT 59.091 45.455 0.00 0.00 0.00 3.73
3230 4258 5.092554 TGCAGGGATTATCGTTTGTCTTA 57.907 39.130 0.00 0.00 0.00 2.10
3306 4334 4.895889 CAGTGACAAGATATACTCCCTCCA 59.104 45.833 0.00 0.00 0.00 3.86
3396 4425 5.547465 TGTTCACTCATTTCAGTCCGTATT 58.453 37.500 0.00 0.00 0.00 1.89
3601 4793 6.513806 TCTGATACACAAATGACAAATGGG 57.486 37.500 0.00 0.00 0.00 4.00
3607 4799 1.460359 CAAATGACAAATGGGCAACGC 59.540 47.619 0.00 0.00 37.60 4.84
3743 5050 9.832445 TGTTAGTATCATTGAATTACTTCCCTC 57.168 33.333 5.50 0.00 0.00 4.30
4040 7321 2.446435 GTTTTGGCATCTAAGCTGGGA 58.554 47.619 0.00 0.00 34.17 4.37
4261 7675 0.605589 GGCCTGGAAAACGTACAGCT 60.606 55.000 0.00 0.00 0.00 4.24
4270 7684 1.804601 AACGTACAGCTTACAAGGGC 58.195 50.000 0.00 0.00 0.00 5.19
4376 7792 1.321743 CAGTCGTACGCTTTGATCTGC 59.678 52.381 11.24 0.00 0.00 4.26
4464 7882 6.693545 CCTCTGTCTCAATATGTAAGACGTTC 59.306 42.308 0.00 0.00 41.84 3.95
4716 8148 3.067833 CCTGCTGATGTGATATCTGCTG 58.932 50.000 18.53 17.37 41.57 4.41
4787 8219 1.082104 GCCAAAGGAAGAACACGCG 60.082 57.895 3.53 3.53 0.00 6.01
4887 8319 0.537143 TGAACTGGTTTGAGCCGCAT 60.537 50.000 0.00 0.00 0.00 4.73
4917 8349 8.177119 AGCACTGTTGTAAAATTGGAAATAGA 57.823 30.769 0.00 0.00 0.00 1.98
4971 8403 9.124807 GTACAATAATTGTTTAGCCAGTTTGTC 57.875 33.333 0.00 0.00 42.22 3.18
5021 8456 2.285368 AATGGGGACTGCCGGAGA 60.285 61.111 5.05 0.00 33.83 3.71
5085 8520 0.904865 ATGAGGTGGAGGCGAACAGA 60.905 55.000 0.00 0.00 0.00 3.41
5145 8580 9.256477 TGGTGTAAAAACATAGATATGATCGAC 57.744 33.333 6.84 0.08 37.15 4.20
5207 8642 3.763360 TGGAGATGCGGAATTTTTGACAT 59.237 39.130 0.00 0.00 0.00 3.06
5235 8670 3.064207 GACATTTACGGTCACAGCTTCA 58.936 45.455 0.00 0.00 35.36 3.02
5298 8733 1.402325 CGTATCCTTGGCGCGATGATA 60.402 52.381 12.10 7.35 0.00 2.15
5355 8796 1.339247 TGGGTTAGTGGGTTGTATGCG 60.339 52.381 0.00 0.00 0.00 4.73
5356 8797 1.375551 GGTTAGTGGGTTGTATGCGG 58.624 55.000 0.00 0.00 0.00 5.69
5357 8798 1.339342 GGTTAGTGGGTTGTATGCGGT 60.339 52.381 0.00 0.00 0.00 5.68
5358 8799 2.093553 GGTTAGTGGGTTGTATGCGGTA 60.094 50.000 0.00 0.00 0.00 4.02
5359 8800 3.432608 GGTTAGTGGGTTGTATGCGGTAT 60.433 47.826 0.00 0.00 0.00 2.73
5385 8927 3.303329 CCCGCAACAATAGAACATCATCG 60.303 47.826 0.00 0.00 0.00 3.84
5391 8933 7.340699 GCAACAATAGAACATCATCGTCTTAG 58.659 38.462 0.00 0.00 0.00 2.18
5407 8951 5.584649 TCGTCTTAGCATCCCATAACTTTTG 59.415 40.000 0.00 0.00 0.00 2.44
5408 8952 5.220854 CGTCTTAGCATCCCATAACTTTTGG 60.221 44.000 0.00 0.00 0.00 3.28
5409 8953 4.644685 TCTTAGCATCCCATAACTTTTGGC 59.355 41.667 0.00 0.00 32.60 4.52
5411 8955 2.762327 AGCATCCCATAACTTTTGGCAG 59.238 45.455 0.00 0.00 32.60 4.85
5412 8956 2.760092 GCATCCCATAACTTTTGGCAGA 59.240 45.455 0.00 0.00 32.60 4.26
5413 8957 3.385755 GCATCCCATAACTTTTGGCAGAT 59.614 43.478 0.00 0.00 32.60 2.90
5414 8958 4.500375 GCATCCCATAACTTTTGGCAGATC 60.500 45.833 0.00 0.00 32.60 2.75
5444 8988 3.726291 ACTTTCAAACATGGTTTCCGG 57.274 42.857 0.00 0.00 0.00 5.14
5446 8990 1.698506 TTCAAACATGGTTTCCGGCT 58.301 45.000 0.00 0.00 0.00 5.52
5447 8991 1.698506 TCAAACATGGTTTCCGGCTT 58.301 45.000 0.00 0.00 0.00 4.35
5448 8992 2.035632 TCAAACATGGTTTCCGGCTTT 58.964 42.857 0.00 0.00 0.00 3.51
5449 8993 2.035321 TCAAACATGGTTTCCGGCTTTC 59.965 45.455 0.00 0.00 0.00 2.62
5450 8994 0.966179 AACATGGTTTCCGGCTTTCC 59.034 50.000 0.00 0.00 0.00 3.13
5476 9020 6.682441 GCGAAGTTTTCTTTGAATTTGGTTTG 59.318 34.615 0.00 0.00 42.34 2.93
5478 9022 7.446001 AAGTTTTCTTTGAATTTGGTTTGCA 57.554 28.000 0.00 0.00 36.67 4.08
5502 9046 7.599171 CATATGATATTCACATTGGTGCACAT 58.401 34.615 20.43 0.73 44.87 3.21
5657 10674 4.301072 CCAGTCCTGGGAGATTGTTTAA 57.699 45.455 5.37 0.00 46.81 1.52
5760 10777 4.319549 CCAGAGAAAGCTACGTTTTTCCAC 60.320 45.833 13.09 9.56 34.60 4.02
5805 10822 5.300539 GGCCAAAATCCTTTCCTCTAAGATC 59.699 44.000 0.00 0.00 0.00 2.75
5808 10825 6.770303 CCAAAATCCTTTCCTCTAAGATCTCC 59.230 42.308 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.272212 TCTTGCGAATCAAAAAGGCCC 59.728 47.619 0.00 0.00 33.65 5.80
9 10 7.587028 GCATTTTGAAAATCTTGCGAATCAAAA 59.413 29.630 12.21 12.21 39.21 2.44
21 22 6.761312 TCATGTTCCTGCATTTTGAAAATCT 58.239 32.000 0.00 0.00 0.00 2.40
51 52 7.667575 AGAGAACATGACACTGTATTCCTAT 57.332 36.000 0.00 0.00 0.00 2.57
93 94 4.237724 TCTGTGCTATCAAACACTTCTCG 58.762 43.478 0.00 0.00 37.68 4.04
94 95 6.545504 TTTCTGTGCTATCAAACACTTCTC 57.454 37.500 0.00 0.00 37.68 2.87
220 225 8.915871 ATTTCAATCCTACAAATCAAACGATG 57.084 30.769 0.00 0.00 0.00 3.84
318 324 6.183360 GGTTTCTACACATGTTGAGTTGTTGA 60.183 38.462 0.00 0.00 31.97 3.18
444 451 1.805539 CACGCGTCGTCCATCATGT 60.806 57.895 9.86 0.00 38.32 3.21
511 518 0.312102 AAACTCGCAAAGAAGCCAGC 59.688 50.000 0.00 0.00 0.00 4.85
667 683 0.179189 CAACCGAATTCCGCTGCTTC 60.179 55.000 0.00 0.00 36.84 3.86
685 701 1.597854 CAGCCAGACCACGAAAGCA 60.598 57.895 0.00 0.00 0.00 3.91
701 717 0.313043 ACGGTTGTGGTCGACTACAG 59.687 55.000 29.71 22.15 38.56 2.74
778 798 1.298014 GACCACAGAAGCAGAGGGG 59.702 63.158 0.00 0.00 0.00 4.79
779 799 1.079543 CGACCACAGAAGCAGAGGG 60.080 63.158 0.00 0.00 0.00 4.30
782 802 1.666011 GTCCGACCACAGAAGCAGA 59.334 57.895 0.00 0.00 0.00 4.26
1275 1481 1.485066 GGAAGAAAGAGCGGGATGGTA 59.515 52.381 0.00 0.00 0.00 3.25
1291 1497 4.204573 CGCGTAGTAAATTCGAGAAGGAAG 59.795 45.833 0.00 0.00 0.00 3.46
1525 1741 3.259876 GCTTTTAACCTCCGGGGAAAATT 59.740 43.478 0.37 0.00 38.76 1.82
1590 2571 1.417517 TCACCATGGATGATCCCGAAG 59.582 52.381 21.47 0.00 35.03 3.79
1679 2665 4.164796 TGTGCATCTATTCCCAGTGAGAAT 59.835 41.667 5.15 5.15 37.67 2.40
1833 2820 8.826710 TGAAAATAGTAGAACACAACTGAACAG 58.173 33.333 0.00 0.00 0.00 3.16
1972 2967 6.978343 TCTAATGAAACCTCAAATACACCG 57.022 37.500 0.00 0.00 34.49 4.94
1997 2992 5.808030 GTCTCAGCAATCCTACTTACTGTTC 59.192 44.000 0.00 0.00 0.00 3.18
2016 3011 7.759886 CAGATACTCAAAAGATAAACCGTCTCA 59.240 37.037 0.00 0.00 0.00 3.27
2029 3024 4.695455 TCCTTTTCGGCAGATACTCAAAAG 59.305 41.667 0.00 0.00 32.83 2.27
2197 3195 7.739022 CACAAATTGCTTGCTCGATATTTAA 57.261 32.000 0.00 0.00 38.75 1.52
2354 3352 4.372656 GACTGCTGAATATACCACAGACC 58.627 47.826 0.00 0.00 34.07 3.85
2376 3374 2.478894 ACGCATCCTTGTGAAGTTTACG 59.521 45.455 0.00 0.00 36.82 3.18
2464 3463 8.897752 GCAGGACTCACTAAGAATGATTAAAAT 58.102 33.333 0.00 0.00 0.00 1.82
2472 3471 4.201891 GCAATGCAGGACTCACTAAGAATG 60.202 45.833 0.00 0.00 0.00 2.67
2482 3481 0.959372 ACAGCAGCAATGCAGGACTC 60.959 55.000 8.35 0.00 37.25 3.36
2517 3516 7.700322 AGTCACATTCGACACATAATCATAC 57.300 36.000 0.00 0.00 38.43 2.39
2582 3581 5.011227 TGTGCCAGACTACAACATACTGTTA 59.989 40.000 0.00 0.00 38.77 2.41
2609 3636 2.762745 ACATCCGTGGACAAGTACAAC 58.237 47.619 0.00 0.00 0.00 3.32
2700 3727 7.442364 ACTGCTTCGTATTGCATACTTATCATT 59.558 33.333 0.00 0.00 38.59 2.57
2701 3728 6.931281 ACTGCTTCGTATTGCATACTTATCAT 59.069 34.615 0.00 0.00 38.59 2.45
2719 3746 9.599322 GTGCATACATATATTGTAAACTGCTTC 57.401 33.333 15.32 9.68 43.84 3.86
2722 3749 8.017373 CCAGTGCATACATATATTGTAAACTGC 58.983 37.037 18.50 15.26 43.84 4.40
2764 3791 9.891828 CACAACTAAAATATGTGCAAAGAAGTA 57.108 29.630 0.00 0.00 38.14 2.24
2815 3842 7.491682 ATTGCACACAAGTGAAAGTAAAAGAT 58.508 30.769 7.28 0.00 46.22 2.40
2857 3885 9.557061 GGAAGATCGGTAATACTAAAGGAAATT 57.443 33.333 0.00 0.00 0.00 1.82
2870 3898 7.067008 CACAACCATTTTAGGAAGATCGGTAAT 59.933 37.037 0.00 0.00 0.00 1.89
2876 3904 5.904362 AGCACAACCATTTTAGGAAGATC 57.096 39.130 0.00 0.00 0.00 2.75
2987 4015 6.790285 CATTCCAGCTAAAATGCAAAGTTT 57.210 33.333 7.16 0.00 34.99 2.66
3071 4099 7.094205 ACACTTATCTAAGTCCCAAGCAATTTG 60.094 37.037 0.00 0.00 44.19 2.32
3072 4100 6.948309 ACACTTATCTAAGTCCCAAGCAATTT 59.052 34.615 0.00 0.00 44.19 1.82
3158 4186 9.236691 CTTTCGGATAAAATTAATCACACCATG 57.763 33.333 0.00 0.00 0.00 3.66
3177 4205 4.020573 TCACTTCCTAAGATTGCTTTCGGA 60.021 41.667 0.00 0.00 35.56 4.55
3208 4236 3.627395 AGACAAACGATAATCCCTGCA 57.373 42.857 0.00 0.00 0.00 4.41
3230 4258 8.259411 TGCAATACTTCAATAGAATTGGCAATT 58.741 29.630 24.57 24.57 32.31 2.32
3288 4316 5.905331 TGTGAATGGAGGGAGTATATCTTGT 59.095 40.000 0.00 0.00 0.00 3.16
3440 4469 9.041354 TGTTAATAATTTGCCAAATACTCCCTT 57.959 29.630 2.54 0.00 0.00 3.95
3489 4519 9.961265 CATGCAACTATCAATATTTGTTCTGAT 57.039 29.630 0.00 0.00 33.26 2.90
3607 4799 5.356470 CCAAGATCCTTCCTAGCAAAAAGAG 59.644 44.000 0.00 0.00 0.00 2.85
4040 7321 1.834263 ACTCTTAAGCCAGAATCCGCT 59.166 47.619 0.00 0.00 36.74 5.52
4261 7675 6.953101 TGATAATGTTCTACAGCCCTTGTAA 58.047 36.000 0.00 0.00 41.57 2.41
4270 7684 5.757320 CCAGAGCCTTGATAATGTTCTACAG 59.243 44.000 0.00 0.00 0.00 2.74
4352 7768 1.762419 TCAAAGCGTACGACTGTGAC 58.238 50.000 21.65 0.00 0.00 3.67
4487 7905 5.123027 CCTCTGCCTCAAAATGTAAGACTTC 59.877 44.000 0.00 0.00 0.00 3.01
4716 8148 2.357637 CACTCTCTACTACTGAGCTGGC 59.642 54.545 0.00 0.00 0.00 4.85
4749 8181 0.764890 AACTCCTGCACTGTAGCCAA 59.235 50.000 0.00 0.00 0.00 4.52
4787 8219 0.693049 TTGCCTCCACTTCCTTCTCC 59.307 55.000 0.00 0.00 0.00 3.71
4887 8319 7.987750 TCCAATTTTACAACAGTGCTACATA 57.012 32.000 0.00 0.00 0.00 2.29
4917 8349 5.830799 TTGCTGTGGATCATATAGGTCAT 57.169 39.130 0.00 0.00 0.00 3.06
4971 8403 0.035056 GTCCCCTCAAGTGTCCATGG 60.035 60.000 4.97 4.97 0.00 3.66
4986 8421 2.517650 TTGCCAACAAAATTCGTCCC 57.482 45.000 0.00 0.00 31.21 4.46
5021 8456 0.957395 CAGCACGTTGCCATTCTCCT 60.957 55.000 6.39 0.00 46.52 3.69
5085 8520 0.741326 CGTCACCCGACTGATCTCAT 59.259 55.000 0.00 0.00 40.23 2.90
5145 8580 7.643764 CACACAAATATGGGTAAAATAGAAGCG 59.356 37.037 0.00 0.00 42.77 4.68
5198 8633 7.010552 CCGTAAATGTCCAAACAATGTCAAAAA 59.989 33.333 0.00 0.00 39.30 1.94
5207 8642 3.945921 TGTGACCGTAAATGTCCAAACAA 59.054 39.130 0.00 0.00 39.30 2.83
5298 8733 5.798434 GCAAAACGAAACTACAAGTTGAAGT 59.202 36.000 10.54 0.00 38.66 3.01
5355 8796 0.466555 TATTGTTGCGGGGGCATACC 60.467 55.000 0.00 0.00 39.11 2.73
5356 8797 0.951558 CTATTGTTGCGGGGGCATAC 59.048 55.000 0.00 0.00 0.00 2.39
5357 8798 0.840617 TCTATTGTTGCGGGGGCATA 59.159 50.000 0.00 0.00 0.00 3.14
5358 8799 0.033601 TTCTATTGTTGCGGGGGCAT 60.034 50.000 0.00 0.00 0.00 4.40
5359 8800 0.963355 GTTCTATTGTTGCGGGGGCA 60.963 55.000 0.00 0.00 0.00 5.36
5368 8910 7.041721 TGCTAAGACGATGATGTTCTATTGTT 58.958 34.615 0.00 0.00 0.00 2.83
5385 8927 5.450550 GCCAAAAGTTATGGGATGCTAAGAC 60.451 44.000 0.00 0.00 38.44 3.01
5391 8933 2.760092 TCTGCCAAAAGTTATGGGATGC 59.240 45.455 0.00 0.00 37.67 3.91
5421 8965 4.979815 CCGGAAACCATGTTTGAAAGTTAC 59.020 41.667 0.00 0.00 0.00 2.50
5444 8988 2.401017 AAGAAAACTTCGCGGAAAGC 57.599 45.000 6.13 0.00 43.95 3.51
5446 8990 4.358494 TTCAAAGAAAACTTCGCGGAAA 57.642 36.364 6.13 0.00 34.02 3.13
5447 8991 4.561735 ATTCAAAGAAAACTTCGCGGAA 57.438 36.364 6.13 0.00 34.02 4.30
5448 8992 4.561735 AATTCAAAGAAAACTTCGCGGA 57.438 36.364 6.13 0.00 34.02 5.54
5449 8993 4.085107 CCAAATTCAAAGAAAACTTCGCGG 60.085 41.667 6.13 0.00 34.02 6.46
5450 8994 4.502645 ACCAAATTCAAAGAAAACTTCGCG 59.497 37.500 0.00 0.00 34.02 5.87
5451 8995 5.966636 ACCAAATTCAAAGAAAACTTCGC 57.033 34.783 0.00 0.00 34.02 4.70
5452 8996 6.682441 GCAAACCAAATTCAAAGAAAACTTCG 59.318 34.615 0.00 0.00 34.02 3.79
5476 9020 5.860182 GTGCACCAATGTGAATATCATATGC 59.140 40.000 5.22 0.00 45.76 3.14
5478 9022 7.770366 ATGTGCACCAATGTGAATATCATAT 57.230 32.000 15.69 0.00 45.76 1.78
5533 9077 4.024556 CCAACAACTTGACTCAGCTAACTG 60.025 45.833 0.00 0.00 45.95 3.16
5534 9078 4.130118 CCAACAACTTGACTCAGCTAACT 58.870 43.478 0.00 0.00 0.00 2.24
5535 9079 3.877508 ACCAACAACTTGACTCAGCTAAC 59.122 43.478 0.00 0.00 0.00 2.34
5536 9080 3.876914 CACCAACAACTTGACTCAGCTAA 59.123 43.478 0.00 0.00 0.00 3.09
5537 9081 3.118408 ACACCAACAACTTGACTCAGCTA 60.118 43.478 0.00 0.00 0.00 3.32
5538 9082 2.292267 CACCAACAACTTGACTCAGCT 58.708 47.619 0.00 0.00 0.00 4.24
5540 9084 2.285220 CGACACCAACAACTTGACTCAG 59.715 50.000 0.00 0.00 0.00 3.35
5541 9085 2.276201 CGACACCAACAACTTGACTCA 58.724 47.619 0.00 0.00 0.00 3.41
5542 9086 1.003866 GCGACACCAACAACTTGACTC 60.004 52.381 0.00 0.00 0.00 3.36
5543 9087 1.014352 GCGACACCAACAACTTGACT 58.986 50.000 0.00 0.00 0.00 3.41
5544 9088 1.014352 AGCGACACCAACAACTTGAC 58.986 50.000 0.00 0.00 0.00 3.18
5545 9089 1.013596 CAGCGACACCAACAACTTGA 58.986 50.000 0.00 0.00 0.00 3.02
5582 10599 2.040178 GACCCAATATCTCACCCGTCT 58.960 52.381 0.00 0.00 0.00 4.18
5657 10674 3.067742 CACACCTAATATCGAACCCGTCT 59.932 47.826 0.00 0.00 37.05 4.18
5710 10727 5.751586 ACTCCCAAGTAGTTTCTCAAAACA 58.248 37.500 4.09 0.00 45.94 2.83
5711 10728 7.422878 CTACTCCCAAGTAGTTTCTCAAAAC 57.577 40.000 4.75 0.00 46.70 2.43


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

AutoCloner maintained by Alex Coulton.