Multiple sequence alignment - TraesCS1D01G132700

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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 TraesCS1D01G132700 chr1D 100.000 3401 0 0 3004 6404 159142000 159145400 0.000000e+00 6281.0
1 TraesCS1D01G132700 chr1D 100.000 2828 0 0 1 2828 159138997 159141824 0.000000e+00 5223.0
2 TraesCS1D01G132700 chr1D 91.456 316 21 4 392 702 276505103 276504789 4.590000e-116 429.0
3 TraesCS1D01G132700 chr1D 80.645 124 22 2 6041 6163 70582311 70582433 1.900000e-15 95.3
4 TraesCS1D01G132700 chr1A 95.672 3281 76 22 3004 6249 233922635 233925884 0.000000e+00 5212.0
5 TraesCS1D01G132700 chr1A 93.928 2668 98 18 2 2648 233919983 233922607 0.000000e+00 3971.0
6 TraesCS1D01G132700 chr1A 91.909 309 20 3 396 699 376346528 376346220 1.650000e-115 427.0
7 TraesCS1D01G132700 chr1A 93.798 258 15 1 3448 3705 37396569 37396313 2.800000e-103 387.0
8 TraesCS1D01G132700 chr1A 97.030 101 3 0 6304 6404 233925882 233925982 3.070000e-38 171.0
9 TraesCS1D01G132700 chr1B 94.774 3272 103 30 3004 6244 217562096 217565330 0.000000e+00 5033.0
10 TraesCS1D01G132700 chr1B 94.121 2024 69 21 808 2828 217559998 217561974 0.000000e+00 3033.0
11 TraesCS1D01G132700 chr2B 87.407 405 38 1 5 396 463454412 463454008 2.720000e-123 453.0
12 TraesCS1D01G132700 chr2B 82.843 408 29 13 2 396 333037517 333037896 1.720000e-85 327.0
13 TraesCS1D01G132700 chr2B 80.412 97 15 4 5919 6013 547933241 547933335 3.200000e-08 71.3
14 TraesCS1D01G132700 chr2B 87.755 49 6 0 6034 6082 114518791 114518839 2.490000e-04 58.4
15 TraesCS1D01G132700 chr2D 91.746 315 20 4 396 705 213696995 213697308 3.550000e-117 433.0
16 TraesCS1D01G132700 chr2D 89.970 329 26 6 389 714 171840933 171840609 9.930000e-113 418.0
17 TraesCS1D01G132700 chr2D 82.379 227 27 7 173 386 576485797 576486023 1.100000e-42 185.0
18 TraesCS1D01G132700 chr6A 91.429 315 22 5 394 704 235919606 235919293 1.650000e-115 427.0
19 TraesCS1D01G132700 chr6A 91.167 317 24 3 393 706 588602432 588602117 1.650000e-115 427.0
20 TraesCS1D01G132700 chr7D 90.654 321 25 4 396 711 539381773 539382093 7.680000e-114 422.0
21 TraesCS1D01G132700 chr7B 85.922 412 39 5 2 396 80702107 80702516 7.680000e-114 422.0
22 TraesCS1D01G132700 chr7B 90.000 60 6 0 3031 3090 657372186 657372245 1.910000e-10 78.7
23 TraesCS1D01G132700 chr7B 88.333 60 7 0 3031 3090 657604652 657604711 8.910000e-09 73.1
24 TraesCS1D01G132700 chr7B 93.478 46 3 0 3045 3090 657594935 657594980 1.150000e-07 69.4
25 TraesCS1D01G132700 chr4B 96.124 258 10 0 3448 3705 333372417 333372160 7.680000e-114 422.0
26 TraesCS1D01G132700 chr3A 90.625 320 26 3 393 708 395477615 395477934 7.680000e-114 422.0
27 TraesCS1D01G132700 chr3A 85.955 178 11 2 233 396 703418398 703418221 1.830000e-40 178.0
28 TraesCS1D01G132700 chr3A 82.857 70 8 4 5949 6016 513924107 513924174 6.930000e-05 60.2
29 TraesCS1D01G132700 chrUn 95.349 258 12 0 3448 3705 114953319 114953062 1.660000e-110 411.0
30 TraesCS1D01G132700 chrUn 80.412 97 15 4 5919 6013 2139038 2139132 3.200000e-08 71.3
31 TraesCS1D01G132700 chr4A 95.349 258 11 1 3448 3705 610428503 610428759 5.980000e-110 409.0
32 TraesCS1D01G132700 chr4A 93.411 258 17 0 3448 3705 555158802 555158545 3.620000e-102 383.0
33 TraesCS1D01G132700 chr5A 85.086 409 46 4 2 396 540568229 540567822 2.780000e-108 403.0
34 TraesCS1D01G132700 chr3B 94.186 258 15 0 3448 3705 365739429 365739686 1.670000e-105 394.0
35 TraesCS1D01G132700 chr3B 86.957 69 7 2 5949 6016 763241439 763241506 6.890000e-10 76.8
36 TraesCS1D01G132700 chr3B 84.286 70 7 4 5949 6016 513807422 513807489 1.490000e-06 65.8
37 TraesCS1D01G132700 chr2A 93.411 258 16 1 3448 3705 132706233 132705977 1.300000e-101 381.0
38 TraesCS1D01G132700 chr2A 89.252 214 23 0 2 215 714440506 714440719 1.060000e-67 268.0
39 TraesCS1D01G132700 chr2A 82.524 206 22 11 204 396 714516526 714516730 1.100000e-37 169.0
40 TraesCS1D01G132700 chr2A 83.582 67 11 0 6029 6095 74585752 74585818 5.360000e-06 63.9
41 TraesCS1D01G132700 chr2A 87.500 56 4 3 6044 6098 74785830 74785883 1.930000e-05 62.1
42 TraesCS1D01G132700 chr4D 84.536 97 11 4 5920 6013 10752446 10752541 6.840000e-15 93.5
43 TraesCS1D01G132700 chr3D 87.719 57 2 5 5963 6016 394187297 394187351 1.930000e-05 62.1


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 TraesCS1D01G132700 chr1D 159138997 159145400 6403 False 5752 6281 100.000000 1 6404 2 chr1D.!!$F2 6403
1 TraesCS1D01G132700 chr1A 233919983 233925982 5999 False 3118 5212 95.543333 2 6404 3 chr1A.!!$F1 6402
2 TraesCS1D01G132700 chr1B 217559998 217565330 5332 False 4033 5033 94.447500 808 6244 2 chr1B.!!$F1 5436

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
69 70 0.037303 CCCTGACAGATTGGTGCACT 59.963 55.000 17.98 0.0 0.00 4.40 F
929 951 0.179215 CATCGAGTTTGTTGAGGCGC 60.179 55.000 0.00 0.0 0.00 6.53 F
1458 1480 0.250793 TCTCGTGGTGTTGTGGTGTT 59.749 50.000 0.00 0.0 0.00 3.32 F
1530 1552 1.489481 TGGATGCGAGGAGACAAGAT 58.511 50.000 0.00 0.0 0.00 2.40 F
2401 2424 2.180086 TGGGGATGCTCCTAGTATGTCT 59.820 50.000 2.79 0.0 36.57 3.41 F
3135 3160 2.227194 GGGGCTTTTATATGTGGACCG 58.773 52.381 0.00 0.0 0.00 4.79 F
4693 4745 2.254546 ATTTGTGCTTCCGTGACTCA 57.745 45.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1133 1155 0.697079 TAGGCGGAGGATAGATCGGT 59.303 55.000 0.00 0.0 0.00 4.69 R
2619 2642 2.092319 TAGGCGCTAGGCAGATGCAG 62.092 60.000 7.64 0.0 46.16 4.41 R
3183 3222 2.165030 GGGTCACTGAATTGCTGAATGG 59.835 50.000 0.00 0.0 0.00 3.16 R
3473 3512 2.301346 CCCTTGTCAGATGTAATGGCC 58.699 52.381 0.00 0.0 0.00 5.36 R
3924 3967 5.734720 CCAACTCAGAAAGCCTACATCTAA 58.265 41.667 0.00 0.0 0.00 2.10 R
4892 4944 2.457366 AACTACAGAAGGGTCAAGCG 57.543 50.000 0.00 0.0 0.00 4.68 R
6374 6445 0.320421 GTCGTGGCTTTGGCAGAGTA 60.320 55.000 6.91 0.0 39.19 2.59 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
69 70 0.037303 CCCTGACAGATTGGTGCACT 59.963 55.000 17.98 0.00 0.00 4.40
86 87 2.703416 CACTAGCAGGACAAGCAATCA 58.297 47.619 0.00 0.00 0.00 2.57
87 88 2.676839 CACTAGCAGGACAAGCAATCAG 59.323 50.000 0.00 0.00 0.00 2.90
105 106 3.076621 TCAGCATTCAGACATGGACAAC 58.923 45.455 0.00 0.00 0.00 3.32
141 142 3.054728 TGTTGGGTATGTGGACACTATGG 60.055 47.826 3.91 0.00 0.00 2.74
145 146 3.467803 GGTATGTGGACACTATGGAAGC 58.532 50.000 3.91 0.00 0.00 3.86
147 148 2.472695 TGTGGACACTATGGAAGCAC 57.527 50.000 3.91 0.00 0.00 4.40
150 151 0.462047 GGACACTATGGAAGCACCGG 60.462 60.000 0.00 0.00 42.61 5.28
163 164 1.922135 GCACCGGAATGCAATCGTGT 61.922 55.000 9.46 1.37 45.39 4.49
198 199 1.768870 CCCTCCTTACATCGGGTCATT 59.231 52.381 0.00 0.00 31.89 2.57
200 201 2.434336 CCTCCTTACATCGGGTCATTGA 59.566 50.000 0.00 0.00 0.00 2.57
283 297 4.103785 ACCATTTCATAGTGGAGCTAGCAT 59.896 41.667 18.83 1.44 38.86 3.79
316 330 1.078426 CCAACTAGGCCGGTTCTGG 60.078 63.158 12.96 10.18 0.00 3.86
338 352 1.630244 CGGCAGAGTAGTGCTTGCAC 61.630 60.000 16.98 16.98 43.45 4.57
340 354 0.946221 GCAGAGTAGTGCTTGCACGT 60.946 55.000 18.32 8.69 40.54 4.49
352 366 5.077424 GTGCTTGCACGTAATTACTTGTAC 58.923 41.667 19.70 8.32 0.00 2.90
358 372 5.863397 TGCACGTAATTACTTGTACCACTAC 59.137 40.000 19.70 5.05 0.00 2.73
361 375 7.754924 GCACGTAATTACTTGTACCACTACTTA 59.245 37.037 19.70 0.00 0.00 2.24
416 430 2.024941 AGGCTTCCTTTGGTTCATAGGG 60.025 50.000 4.94 0.00 34.20 3.53
420 434 4.080526 GCTTCCTTTGGTTCATAGGGTAGA 60.081 45.833 4.94 0.00 34.20 2.59
434 448 8.258850 TCATAGGGTAGAAAAATCGTAGGAAT 57.741 34.615 0.00 0.00 0.00 3.01
442 456 9.917872 GTAGAAAAATCGTAGGAATAGAAAAGC 57.082 33.333 0.00 0.00 0.00 3.51
455 469 8.061304 AGGAATAGAAAAGCCATAGGAAATGAA 58.939 33.333 0.00 0.00 0.00 2.57
521 535 6.131264 AGATGCCCTTTGATTCACATCATAA 58.869 36.000 13.54 0.00 39.28 1.90
522 536 6.781014 AGATGCCCTTTGATTCACATCATAAT 59.219 34.615 13.54 0.00 39.28 1.28
564 582 8.713971 TCTAGGCTGATGTTTATTTTCCTATGA 58.286 33.333 0.00 0.00 0.00 2.15
610 629 7.502060 TCTCCATAGGAATAGGATTCCATTC 57.498 40.000 18.17 11.30 41.00 2.67
625 644 3.773560 TCCATTCCTACAAACCAAAGGG 58.226 45.455 0.00 0.00 41.29 3.95
630 649 2.162681 CCTACAAACCAAAGGGCTCTG 58.837 52.381 0.00 0.00 37.90 3.35
633 652 2.310538 ACAAACCAAAGGGCTCTGAAG 58.689 47.619 0.00 0.00 37.90 3.02
636 655 1.376649 ACCAAAGGGCTCTGAAGGAT 58.623 50.000 6.25 0.00 37.90 3.24
695 716 6.660949 ACAAGATTCCTCTAAACCAAATGAGG 59.339 38.462 0.00 0.00 45.36 3.86
696 717 5.196695 AGATTCCTCTAAACCAAATGAGGC 58.803 41.667 0.00 0.00 44.09 4.70
698 719 2.919602 TCCTCTAAACCAAATGAGGCCT 59.080 45.455 3.86 3.86 44.09 5.19
719 740 5.991606 GCCTTAAGTAGATGATATGCACACA 59.008 40.000 0.97 0.00 0.00 3.72
723 744 5.767816 AGTAGATGATATGCACACACGTA 57.232 39.130 0.00 0.00 0.00 3.57
724 745 6.332735 AGTAGATGATATGCACACACGTAT 57.667 37.500 0.00 0.00 0.00 3.06
838 859 2.123982 CATTCTGCCTCAGCCCCC 60.124 66.667 0.00 0.00 38.69 5.40
878 899 1.445716 CTACTGTAGGGCTCGTCCGG 61.446 65.000 6.95 0.00 34.94 5.14
929 951 0.179215 CATCGAGTTTGTTGAGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
1014 1036 2.432456 GCGATGGCGATGGCGATA 60.432 61.111 0.00 0.00 37.76 2.92
1133 1155 5.486332 AGATCCCCATCCATTTACTCCTTA 58.514 41.667 0.00 0.00 0.00 2.69
1157 1179 3.433957 CGATCTATCCTCCGCCTATATCG 59.566 52.174 0.00 0.00 0.00 2.92
1454 1476 1.948104 TTCTTCTCGTGGTGTTGTGG 58.052 50.000 0.00 0.00 0.00 4.17
1455 1477 0.828022 TCTTCTCGTGGTGTTGTGGT 59.172 50.000 0.00 0.00 0.00 4.16
1458 1480 0.250793 TCTCGTGGTGTTGTGGTGTT 59.749 50.000 0.00 0.00 0.00 3.32
1530 1552 1.489481 TGGATGCGAGGAGACAAGAT 58.511 50.000 0.00 0.00 0.00 2.40
1532 1554 2.237143 TGGATGCGAGGAGACAAGATTT 59.763 45.455 0.00 0.00 0.00 2.17
1571 1593 6.541934 TCACCATCATTTTATTTGATGCCA 57.458 33.333 7.90 0.00 45.89 4.92
1621 1643 5.458452 TGTTTTATTGTGCTTTCTTGCTTCG 59.542 36.000 0.00 0.00 0.00 3.79
1699 1721 7.665561 TTTATGTTTTTAATCCTTGCTTGCC 57.334 32.000 0.00 0.00 0.00 4.52
1853 1876 2.225491 TGCTTTCACGCTACCATTTGTC 59.775 45.455 0.00 0.00 0.00 3.18
2008 2031 9.143631 CTTCCTGTGAAATTATTTGTTTGGATC 57.856 33.333 0.00 0.00 0.00 3.36
2190 2213 8.877864 ATTTTCATTCCAACCTGTTCTGTATA 57.122 30.769 0.00 0.00 0.00 1.47
2401 2424 2.180086 TGGGGATGCTCCTAGTATGTCT 59.820 50.000 2.79 0.00 36.57 3.41
2673 2696 4.439153 CGCACACCTGAAATCATGCTTAAT 60.439 41.667 5.49 0.00 0.00 1.40
2763 2786 8.685838 AGTGCTTTTTCTAACCAGTAACATAA 57.314 30.769 0.00 0.00 0.00 1.90
2809 2832 6.989169 GGCACTTCTACTGATGTTATCTTCAT 59.011 38.462 0.00 0.00 0.00 2.57
3135 3160 2.227194 GGGGCTTTTATATGTGGACCG 58.773 52.381 0.00 0.00 0.00 4.79
3924 3967 9.822185 AAGTATTTTCTTTTCTGCAGTTTCATT 57.178 25.926 14.67 0.00 0.00 2.57
4159 4202 4.325972 TCTGTTCACTGAGCATGCATTAA 58.674 39.130 21.98 2.19 0.00 1.40
4174 4217 7.543172 AGCATGCATTAACATTTCAAGTAGTTG 59.457 33.333 21.98 3.73 34.67 3.16
4243 4286 8.669243 AGTTTCTCATTCTTAGAATAAAAGGCG 58.331 33.333 7.18 0.00 33.17 5.52
4336 4379 8.565896 TTCACTTACAATGAAGCATCACTTAT 57.434 30.769 0.00 0.00 39.29 1.73
4427 4471 3.519107 TCTCTGCCTTGTATCATTGGACA 59.481 43.478 0.00 0.00 0.00 4.02
4468 4512 5.588845 TGGGATCAATGGAAGGTTTATGTT 58.411 37.500 0.00 0.00 0.00 2.71
4693 4745 2.254546 ATTTGTGCTTCCGTGACTCA 57.745 45.000 0.00 0.00 0.00 3.41
4892 4944 1.693467 TGTGTAAGTCGTGCGTCATC 58.307 50.000 0.00 0.00 0.00 2.92
5042 5097 5.664457 TGTAATTTTGTTGCCACAACATCA 58.336 33.333 13.42 4.61 42.87 3.07
5420 5485 4.576463 GGGATGATGATGAAACTTTACGCT 59.424 41.667 0.00 0.00 0.00 5.07
5546 5611 3.006672 GGGACGGATATGCCTTGTG 57.993 57.895 0.00 0.00 0.00 3.33
5565 5630 0.811281 GGCGCTATCAACCTTGCTTT 59.189 50.000 7.64 0.00 0.00 3.51
5611 5676 8.049117 AGATGTCCACTTATAATTTGAAGCAGA 58.951 33.333 0.00 0.00 0.00 4.26
5676 5743 6.992715 GCAATAATTAGCCTGACTAAAGGAGA 59.007 38.462 0.00 0.00 43.99 3.71
5696 5763 8.674263 AGGAGATGCTTTAAGAATATGTCTTG 57.326 34.615 0.00 0.00 46.48 3.02
5960 6030 9.875708 TTGGACATACCTATATAATTGCCTTTT 57.124 29.630 0.00 0.00 39.86 2.27
5985 6055 8.537049 TGGTCAAAATATTTCAGCAATTTCAG 57.463 30.769 0.10 0.00 0.00 3.02
6102 6172 5.874810 TCCTTTGGTCGAAATGATAACAGAG 59.125 40.000 0.00 0.00 0.00 3.35
6113 6183 8.274248 CGAAATGATAACAGAGATCACTGAATG 58.726 37.037 24.57 1.63 40.63 2.67
6240 6311 6.825610 TGCCTTGAACTTATTTGGAATTGTT 58.174 32.000 0.00 0.00 0.00 2.83
6247 6318 9.255304 TGAACTTATTTGGAATTGTTAACAAGC 57.745 29.630 24.22 18.11 39.47 4.01
6248 6319 9.255304 GAACTTATTTGGAATTGTTAACAAGCA 57.745 29.630 24.22 4.06 39.47 3.91
6249 6320 9.606631 AACTTATTTGGAATTGTTAACAAGCAA 57.393 25.926 24.22 11.22 39.47 3.91
6250 6321 9.606631 ACTTATTTGGAATTGTTAACAAGCAAA 57.393 25.926 24.22 15.85 39.47 3.68
6253 6324 7.913674 TTTGGAATTGTTAACAAGCAAAAGT 57.086 28.000 24.22 4.98 39.47 2.66
6254 6325 9.606631 ATTTGGAATTGTTAACAAGCAAAAGTA 57.393 25.926 24.22 7.89 39.47 2.24
6255 6326 9.436957 TTTGGAATTGTTAACAAGCAAAAGTAA 57.563 25.926 24.22 9.79 39.47 2.24
6256 6327 8.641499 TGGAATTGTTAACAAGCAAAAGTAAG 57.359 30.769 24.22 0.00 39.47 2.34
6257 6328 7.708752 TGGAATTGTTAACAAGCAAAAGTAAGG 59.291 33.333 24.22 0.00 39.47 2.69
6258 6329 7.923878 GGAATTGTTAACAAGCAAAAGTAAGGA 59.076 33.333 24.22 0.00 39.47 3.36
6259 6330 8.871686 AATTGTTAACAAGCAAAAGTAAGGAG 57.128 30.769 24.22 0.00 39.47 3.69
6260 6331 7.633193 TTGTTAACAAGCAAAAGTAAGGAGA 57.367 32.000 17.01 0.00 0.00 3.71
6261 6332 7.633193 TGTTAACAAGCAAAAGTAAGGAGAA 57.367 32.000 5.64 0.00 0.00 2.87
6262 6333 8.057536 TGTTAACAAGCAAAAGTAAGGAGAAA 57.942 30.769 5.64 0.00 0.00 2.52
6263 6334 8.524487 TGTTAACAAGCAAAAGTAAGGAGAAAA 58.476 29.630 5.64 0.00 0.00 2.29
6264 6335 9.361315 GTTAACAAGCAAAAGTAAGGAGAAAAA 57.639 29.630 0.00 0.00 0.00 1.94
6337 6408 1.199789 CAGCGGATTTGCAAACTGCTA 59.800 47.619 30.35 7.97 45.31 3.49
6353 6424 2.874701 CTGCTACCTATGACCAATGTGC 59.125 50.000 0.00 0.00 0.00 4.57
6374 6445 3.739519 GCAGCATCTCCTCGTACTTCATT 60.740 47.826 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.878088 GACTCCATCGTCGTGCCTATA 59.122 52.381 0.00 0.00 0.00 1.31
50 51 0.037303 AGTGCACCAATCTGTCAGGG 59.963 55.000 14.63 0.00 0.00 4.45
69 70 1.003464 TGCTGATTGCTTGTCCTGCTA 59.997 47.619 0.00 0.00 43.37 3.49
86 87 3.079578 CTGTTGTCCATGTCTGAATGCT 58.920 45.455 0.00 0.00 0.00 3.79
87 88 3.076621 TCTGTTGTCCATGTCTGAATGC 58.923 45.455 0.00 0.00 0.00 3.56
98 99 1.414550 TGGTGATCGTTCTGTTGTCCA 59.585 47.619 0.00 0.00 0.00 4.02
105 106 1.739466 CCCAACATGGTGATCGTTCTG 59.261 52.381 13.74 0.00 35.17 3.02
141 142 0.248215 CGATTGCATTCCGGTGCTTC 60.248 55.000 17.03 12.60 45.27 3.86
145 146 0.521291 AACACGATTGCATTCCGGTG 59.479 50.000 0.00 12.31 0.00 4.94
147 148 0.247655 CGAACACGATTGCATTCCGG 60.248 55.000 0.00 0.00 0.00 5.14
225 226 0.672401 TTAAACCCGCTCGCTTCCAG 60.672 55.000 0.00 0.00 0.00 3.86
258 259 3.185246 AGCTCCACTATGAAATGGTCG 57.815 47.619 0.00 0.00 35.00 4.79
283 297 3.107402 AGTTGGCCTACTCATCTCTCA 57.893 47.619 14.58 0.00 0.00 3.27
313 327 3.077556 ACTACTCTGCCGGGCCAG 61.078 66.667 17.97 14.72 0.00 4.85
316 330 3.316573 AAGCACTACTCTGCCGGGC 62.317 63.158 13.32 13.32 37.96 6.13
319 333 1.374631 TGCAAGCACTACTCTGCCG 60.375 57.895 0.00 0.00 37.96 5.69
352 366 6.940298 TGAAAGAAACCCTTCATAAGTAGTGG 59.060 38.462 0.00 0.00 33.02 4.00
398 412 5.693769 TCTACCCTATGAACCAAAGGAAG 57.306 43.478 0.00 0.00 31.64 3.46
399 413 6.457159 TTTCTACCCTATGAACCAAAGGAA 57.543 37.500 0.00 0.00 31.64 3.36
401 415 7.415206 CGATTTTTCTACCCTATGAACCAAAGG 60.415 40.741 0.00 0.00 0.00 3.11
416 430 9.917872 GCTTTTCTATTCCTACGATTTTTCTAC 57.082 33.333 0.00 0.00 0.00 2.59
420 434 7.696992 TGGCTTTTCTATTCCTACGATTTTT 57.303 32.000 0.00 0.00 0.00 1.94
434 448 8.686334 GTCATTTCATTTCCTATGGCTTTTCTA 58.314 33.333 0.00 0.00 0.00 2.10
442 456 9.293404 AGATACATGTCATTTCATTTCCTATGG 57.707 33.333 0.00 0.00 0.00 2.74
490 504 5.184671 GTGAATCAAAGGGCATCTTCTTTCT 59.815 40.000 0.00 0.00 33.94 2.52
496 510 4.346730 TGATGTGAATCAAAGGGCATCTT 58.653 39.130 10.68 0.00 37.28 2.40
530 548 8.682936 AATAAACATCAGCCTAGACTTAATGG 57.317 34.615 0.00 0.00 0.00 3.16
535 553 7.406104 AGGAAAATAAACATCAGCCTAGACTT 58.594 34.615 0.00 0.00 0.00 3.01
543 561 9.807649 ACATTTCATAGGAAAATAAACATCAGC 57.192 29.630 6.65 0.00 45.52 4.26
564 582 9.129532 GGAGAATTCTTCATATCCTTCACATTT 57.870 33.333 9.87 0.00 0.00 2.32
578 596 8.748179 ATCCTATTCCTATGGAGAATTCTTCA 57.252 34.615 18.85 18.85 35.59 3.02
579 597 9.665719 GAATCCTATTCCTATGGAGAATTCTTC 57.334 37.037 9.87 8.30 35.59 2.87
588 606 6.642733 GGAATGGAATCCTATTCCTATGGA 57.357 41.667 23.95 0.29 45.66 3.41
610 629 2.162681 CAGAGCCCTTTGGTTTGTAGG 58.837 52.381 0.00 0.00 0.00 3.18
614 633 1.615392 CCTTCAGAGCCCTTTGGTTTG 59.385 52.381 0.00 0.00 0.00 2.93
679 700 5.946377 ACTTAAGGCCTCATTTGGTTTAGAG 59.054 40.000 5.23 0.00 0.00 2.43
695 716 5.991606 TGTGTGCATATCATCTACTTAAGGC 59.008 40.000 7.53 0.00 0.00 4.35
696 717 6.144563 CGTGTGTGCATATCATCTACTTAAGG 59.855 42.308 7.53 0.00 0.00 2.69
698 719 6.569780 ACGTGTGTGCATATCATCTACTTAA 58.430 36.000 0.00 0.00 0.00 1.85
838 859 2.356069 GCATCGAAGGGCCTCTTTAAAG 59.644 50.000 6.46 9.04 35.50 1.85
895 916 1.381735 GATGGGAAAGGCTTGGGGG 60.382 63.158 0.00 0.00 0.00 5.40
898 919 0.035056 ACTCGATGGGAAAGGCTTGG 60.035 55.000 0.00 0.00 0.00 3.61
944 966 5.114081 GGATCTGGAATTTCTTGCAAATGG 58.886 41.667 0.00 0.00 31.82 3.16
1133 1155 0.697079 TAGGCGGAGGATAGATCGGT 59.303 55.000 0.00 0.00 0.00 4.69
1157 1179 4.629092 GACCGGATATTTAGAGAACCACC 58.371 47.826 9.46 0.00 0.00 4.61
1252 1274 2.831685 TACATTCGCAGAACACAGGT 57.168 45.000 0.00 0.00 45.90 4.00
1530 1552 6.924913 TGGTGAATCCCAAACAATCATAAA 57.075 33.333 0.00 0.00 34.77 1.40
1532 1554 6.193504 TGATGGTGAATCCCAAACAATCATA 58.806 36.000 0.00 0.00 38.20 2.15
1571 1593 7.902920 AATGCCATAATCTTTGGACAGTAAT 57.097 32.000 0.00 0.00 36.26 1.89
1621 1643 3.747193 CATAATGCACGGTTCACAGTTC 58.253 45.455 0.00 0.00 0.00 3.01
1682 1704 3.007723 TGCATGGCAAGCAAGGATTAAAA 59.992 39.130 15.86 0.00 39.39 1.52
1699 1721 9.524106 ACAAACATTATGTCATATCTTTGCATG 57.476 29.630 0.00 0.00 0.00 4.06
1909 1932 7.176589 ACCTTCAAACCAGTAAATTTCAACA 57.823 32.000 0.00 0.00 0.00 3.33
2190 2213 4.077300 ACGACATCATTCCATGTATGCT 57.923 40.909 0.00 0.00 37.11 3.79
2205 2228 6.959639 AATTCAGGCCAATAAATACGACAT 57.040 33.333 5.01 0.00 0.00 3.06
2619 2642 2.092319 TAGGCGCTAGGCAGATGCAG 62.092 60.000 7.64 0.00 46.16 4.41
2673 2696 3.895656 ACAACAGCAGTAAGACCTAGTGA 59.104 43.478 0.00 0.00 33.30 3.41
2725 2748 3.402681 GCACTCCTAGGGCAGGCA 61.403 66.667 9.46 0.00 45.95 4.75
2763 2786 4.337555 GCCATCATTTACTGCTCAGATGTT 59.662 41.667 3.60 0.00 32.98 2.71
3096 3121 2.641305 CCCCTCAAAATCAGAGCTCAG 58.359 52.381 17.77 8.39 0.00 3.35
3135 3160 3.877508 CCCGTTTCAATCACTAATCCCTC 59.122 47.826 0.00 0.00 0.00 4.30
3183 3222 2.165030 GGGTCACTGAATTGCTGAATGG 59.835 50.000 0.00 0.00 0.00 3.16
3191 3230 3.480470 AGAACTGTGGGTCACTGAATTG 58.520 45.455 10.97 0.00 36.91 2.32
3293 3332 6.369890 TGCAAAAAGAACAAAACAACAGCATA 59.630 30.769 0.00 0.00 0.00 3.14
3473 3512 2.301346 CCCTTGTCAGATGTAATGGCC 58.699 52.381 0.00 0.00 0.00 5.36
3924 3967 5.734720 CCAACTCAGAAAGCCTACATCTAA 58.265 41.667 0.00 0.00 0.00 2.10
4159 4202 7.661437 TCAGCTAATGTCAACTACTTGAAATGT 59.339 33.333 0.00 0.00 38.17 2.71
4243 4286 5.783111 AGATAAAACCTGGAAAACACATGC 58.217 37.500 0.00 0.00 0.00 4.06
4427 4471 5.688220 TCCCAGAATTAGATACTCCCTCT 57.312 43.478 0.00 0.00 0.00 3.69
4468 4512 9.753674 AAATTCACACTCAGAGGGAAAATATAA 57.246 29.630 6.71 0.00 0.00 0.98
4892 4944 2.457366 AACTACAGAAGGGTCAAGCG 57.543 50.000 0.00 0.00 0.00 4.68
4904 4956 7.880160 TCCCCAAATATTGATGAAACTACAG 57.120 36.000 0.00 0.00 0.00 2.74
5249 5314 9.278978 TGCTGATGTGTTAAGTGATACTTTTAA 57.721 29.630 0.00 0.00 39.51 1.52
5546 5611 0.811281 AAAGCAAGGTTGATAGCGCC 59.189 50.000 2.29 0.00 0.00 6.53
5565 5630 5.384063 TCTGCTGAACTTTGAACAAAACA 57.616 34.783 1.76 2.68 0.00 2.83
5676 5743 8.680903 CAAGACCAAGACATATTCTTAAAGCAT 58.319 33.333 0.00 0.00 43.23 3.79
5692 5759 4.770010 ACTTTGGACAAAACAAGACCAAGA 59.230 37.500 0.00 0.00 40.72 3.02
5696 5763 3.780902 CCACTTTGGACAAAACAAGACC 58.219 45.455 0.00 0.00 40.96 3.85
5960 6030 8.149647 ACTGAAATTGCTGAAATATTTTGACCA 58.850 29.630 1.43 0.00 0.00 4.02
5985 6055 8.976986 AAATGATTTGAAATTCTGCTCACTAC 57.023 30.769 0.00 0.00 0.00 2.73
6052 6122 9.393512 ACCAAAATTTTCACTTGAATTTGATCA 57.606 25.926 14.13 0.00 35.32 2.92
6113 6183 7.328249 TGCCGAAAATCACTAAATTTCAATGAC 59.672 33.333 0.00 0.00 33.68 3.06
6278 6349 8.844244 GCTTCTGAACATGTAAATCCAAGATAT 58.156 33.333 0.00 0.00 0.00 1.63
6279 6350 7.828717 TGCTTCTGAACATGTAAATCCAAGATA 59.171 33.333 0.00 0.00 0.00 1.98
6280 6351 6.660521 TGCTTCTGAACATGTAAATCCAAGAT 59.339 34.615 0.00 0.00 0.00 2.40
6281 6352 6.003326 TGCTTCTGAACATGTAAATCCAAGA 58.997 36.000 0.00 0.00 0.00 3.02
6282 6353 6.258230 TGCTTCTGAACATGTAAATCCAAG 57.742 37.500 0.00 0.13 0.00 3.61
6283 6354 6.839124 ATGCTTCTGAACATGTAAATCCAA 57.161 33.333 0.00 0.00 0.00 3.53
6284 6355 6.839124 AATGCTTCTGAACATGTAAATCCA 57.161 33.333 0.00 0.00 0.00 3.41
6285 6356 9.241317 CAATAATGCTTCTGAACATGTAAATCC 57.759 33.333 0.00 0.00 0.00 3.01
6287 6358 9.793252 GTCAATAATGCTTCTGAACATGTAAAT 57.207 29.630 0.00 0.00 0.00 1.40
6288 6359 8.791675 TGTCAATAATGCTTCTGAACATGTAAA 58.208 29.630 0.00 0.00 0.00 2.01
6289 6360 8.334263 TGTCAATAATGCTTCTGAACATGTAA 57.666 30.769 0.00 0.00 0.00 2.41
6290 6361 7.920160 TGTCAATAATGCTTCTGAACATGTA 57.080 32.000 0.00 0.00 0.00 2.29
6291 6362 6.822667 TGTCAATAATGCTTCTGAACATGT 57.177 33.333 0.00 0.00 0.00 3.21
6292 6363 7.971722 TGATTGTCAATAATGCTTCTGAACATG 59.028 33.333 0.00 0.00 0.00 3.21
6293 6364 8.058667 TGATTGTCAATAATGCTTCTGAACAT 57.941 30.769 0.00 0.00 0.00 2.71
6294 6365 7.451501 TGATTGTCAATAATGCTTCTGAACA 57.548 32.000 0.00 0.00 0.00 3.18
6295 6366 6.471519 GCTGATTGTCAATAATGCTTCTGAAC 59.528 38.462 0.00 0.00 0.00 3.18
6296 6367 6.558009 GCTGATTGTCAATAATGCTTCTGAA 58.442 36.000 0.00 0.00 0.00 3.02
6297 6368 5.220719 CGCTGATTGTCAATAATGCTTCTGA 60.221 40.000 0.00 0.00 0.00 3.27
6298 6369 4.968181 CGCTGATTGTCAATAATGCTTCTG 59.032 41.667 0.00 0.00 0.00 3.02
6299 6370 4.036027 CCGCTGATTGTCAATAATGCTTCT 59.964 41.667 0.00 0.00 0.00 2.85
6300 6371 4.035558 TCCGCTGATTGTCAATAATGCTTC 59.964 41.667 0.00 0.00 0.00 3.86
6301 6372 3.947196 TCCGCTGATTGTCAATAATGCTT 59.053 39.130 0.00 0.00 0.00 3.91
6302 6373 3.544684 TCCGCTGATTGTCAATAATGCT 58.455 40.909 0.00 0.00 0.00 3.79
6337 6408 1.004628 TGCTGCACATTGGTCATAGGT 59.995 47.619 0.00 0.00 0.00 3.08
6353 6424 3.724508 ATGAAGTACGAGGAGATGCTG 57.275 47.619 0.00 0.00 0.00 4.41
6374 6445 0.320421 GTCGTGGCTTTGGCAGAGTA 60.320 55.000 6.91 0.00 39.19 2.59


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

AutoCloner maintained by Alex Coulton.