Multiple sequence alignment - TraesCS1A01G230400

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 TraesCS1A01G230400 chr1A 100.000 5389 0 0 1 5389 403022147 403027535 0.000000e+00 9952.0
1 TraesCS1A01G230400 chr1A 85.714 91 13 0 479 569 292892078 292891988 4.440000e-16 97.1
2 TraesCS1A01G230400 chr1D 94.378 4820 170 48 620 5389 319936374 319931606 0.000000e+00 7306.0
3 TraesCS1A01G230400 chr1D 86.724 467 45 10 8 466 319936827 319936370 2.240000e-138 503.0
4 TraesCS1A01G230400 chr1B 93.128 4831 185 58 629 5389 432825179 432820426 0.000000e+00 6946.0
5 TraesCS1A01G230400 chr1B 88.636 88 10 0 482 569 115142278 115142191 2.050000e-19 108.0
6 TraesCS1A01G230400 chr2A 87.859 313 36 2 5011 5322 621265122 621265433 3.070000e-97 366.0
7 TraesCS1A01G230400 chr2A 84.192 291 44 2 4072 4362 62299896 62299608 1.140000e-71 281.0
8 TraesCS1A01G230400 chr2D 87.540 313 37 2 5011 5322 478118173 478118484 1.430000e-95 361.0
9 TraesCS1A01G230400 chr2D 85.223 291 41 2 4072 4362 61980659 61980371 1.130000e-76 298.0
10 TraesCS1A01G230400 chr2B 87.540 313 37 2 5011 5322 560458447 560458758 1.430000e-95 361.0
11 TraesCS1A01G230400 chr3D 87.085 271 33 2 1369 1638 460497244 460497513 6.780000e-79 305.0
12 TraesCS1A01G230400 chr3A 86.716 271 34 2 1369 1638 602917575 602917844 3.150000e-77 300.0
13 TraesCS1A01G230400 chr4A 86.131 274 36 2 1379 1652 114592031 114591760 1.470000e-75 294.0
14 TraesCS1A01G230400 chr4A 87.097 93 10 2 481 572 6040292 6040383 2.660000e-18 104.0
15 TraesCS1A01G230400 chr4D 86.194 268 36 1 1377 1643 350492644 350492911 6.830000e-74 289.0
16 TraesCS1A01G230400 chr4B 85.556 270 39 0 1377 1646 433641740 433642009 3.180000e-72 283.0
17 TraesCS1A01G230400 chr4B 83.495 103 17 0 478 580 26790042 26790144 4.440000e-16 97.1
18 TraesCS1A01G230400 chr7B 87.368 95 12 0 477 571 6172923 6172829 5.710000e-20 110.0
19 TraesCS1A01G230400 chr7B 88.636 88 10 0 482 569 629223318 629223231 2.050000e-19 108.0
20 TraesCS1A01G230400 chr7B 86.170 94 13 0 481 574 60780550 60780457 9.550000e-18 102.0
21 TraesCS1A01G230400 chr5A 87.640 89 11 0 478 566 609785882 609785970 2.660000e-18 104.0
22 TraesCS1A01G230400 chr7A 83.962 106 17 0 464 569 32008450 32008555 9.550000e-18 102.0


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 TraesCS1A01G230400 chr1A 403022147 403027535 5388 False 9952.0 9952 100.000 1 5389 1 chr1A.!!$F1 5388
1 TraesCS1A01G230400 chr1D 319931606 319936827 5221 True 3904.5 7306 90.551 8 5389 2 chr1D.!!$R1 5381
2 TraesCS1A01G230400 chr1B 432820426 432825179 4753 True 6946.0 6946 93.128 629 5389 1 chr1B.!!$R2 4760

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
852 888 0.875059 GGCCGCAGCATAAATACCTC 59.125 55.0 0.00 0.0 42.56 3.85 F
1860 1907 0.103026 GCGATTGCAAGGGGGATTTC 59.897 55.0 4.94 0.0 42.15 2.17 F
2739 2822 0.244450 TGTTACACGAGGTTAGCGGG 59.756 55.0 0.00 0.0 38.32 6.13 F
3196 3280 0.319900 CCGCCCGTGGAATCTAGATG 60.320 60.0 5.86 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 2365 0.322187 TAGCGGAAAAAGGGACAGCC 60.322 55.000 0.0 0.0 0.00 4.85 R
2895 2978 0.536724 GGACAACCCCAAATCCATGC 59.463 55.000 0.0 0.0 0.00 4.06 R
4065 4165 0.771755 AACCCCTCAACCTGGAAGAC 59.228 55.000 0.0 0.0 34.07 3.01 R
4557 4658 1.268352 GTATAGCTGAGACTGGCGGAG 59.732 57.143 0.0 0.0 0.00 4.63 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
27 28 4.342092 GCTCCATGCTTAATAACACCCAAT 59.658 41.667 0.00 0.00 38.95 3.16
28 29 5.507985 GCTCCATGCTTAATAACACCCAATC 60.508 44.000 0.00 0.00 38.95 2.67
30 31 5.954752 TCCATGCTTAATAACACCCAATCAA 59.045 36.000 0.00 0.00 0.00 2.57
44 45 9.533831 AACACCCAATCAATCTCTTACTAAAAT 57.466 29.630 0.00 0.00 0.00 1.82
88 90 1.099879 ACTTAGGTCCGATACGCGCT 61.100 55.000 5.73 0.00 39.11 5.92
99 101 1.531149 GATACGCGCTAAACATGGCAT 59.469 47.619 5.73 0.00 0.00 4.40
109 113 6.074356 GCGCTAAACATGGCATTAAATTAAGG 60.074 38.462 0.00 0.00 0.00 2.69
204 208 8.986477 TTTTGGTCTAAACTTAGGTACGATAC 57.014 34.615 0.00 0.00 0.00 2.24
217 221 1.919240 ACGATACGCCCCAGATATGA 58.081 50.000 0.00 0.00 0.00 2.15
246 250 9.976511 ATAATTCAAGACATTGCAAATCCTATG 57.023 29.630 1.71 0.00 36.30 2.23
271 277 8.002433 GTGAAACAACGTAAATGCACATTTAT 57.998 30.769 16.52 2.17 39.86 1.40
273 279 7.862873 TGAAACAACGTAAATGCACATTTATCA 59.137 29.630 16.52 11.96 42.93 2.15
329 335 2.756840 AACTTAGACTTGGTACGCCC 57.243 50.000 0.00 0.00 0.00 6.13
338 344 0.985760 TTGGTACGCCCCAAGTATGT 59.014 50.000 2.43 0.00 39.56 2.29
383 392 3.303938 ACAGTCCCTCTATGAGACCATG 58.696 50.000 0.00 0.00 34.31 3.66
384 393 2.632028 CAGTCCCTCTATGAGACCATGG 59.368 54.545 11.19 11.19 34.31 3.66
466 475 6.786967 ACGGATGAAGTACTATAGTGGTTT 57.213 37.500 15.90 6.82 0.00 3.27
467 476 7.179076 ACGGATGAAGTACTATAGTGGTTTT 57.821 36.000 15.90 4.45 0.00 2.43
468 477 7.263496 ACGGATGAAGTACTATAGTGGTTTTC 58.737 38.462 15.90 12.72 0.00 2.29
469 478 7.093640 ACGGATGAAGTACTATAGTGGTTTTCA 60.094 37.037 15.90 17.00 0.00 2.69
471 480 9.262358 GGATGAAGTACTATAGTGGTTTTCATC 57.738 37.037 28.71 28.71 40.62 2.92
472 481 9.817809 GATGAAGTACTATAGTGGTTTTCATCA 57.182 33.333 29.88 19.17 40.78 3.07
476 485 9.745880 AAGTACTATAGTGGTTTTCATCATACG 57.254 33.333 15.90 0.00 0.00 3.06
477 486 9.128404 AGTACTATAGTGGTTTTCATCATACGA 57.872 33.333 15.90 0.00 0.00 3.43
478 487 9.740239 GTACTATAGTGGTTTTCATCATACGAA 57.260 33.333 15.90 0.00 0.00 3.85
480 489 9.661563 ACTATAGTGGTTTTCATCATACGAAAA 57.338 29.630 4.10 0.00 39.42 2.29
556 565 8.133754 TGACGAAAACGTTCTTATATTATGGG 57.866 34.615 0.00 0.00 0.00 4.00
557 566 7.980662 TGACGAAAACGTTCTTATATTATGGGA 59.019 33.333 0.00 0.00 0.00 4.37
558 567 8.134905 ACGAAAACGTTCTTATATTATGGGAC 57.865 34.615 0.00 0.00 0.00 4.46
574 583 4.620086 TGGGACAGAGGGAGTAATAGAA 57.380 45.455 0.00 0.00 0.00 2.10
575 584 4.955335 TGGGACAGAGGGAGTAATAGAAA 58.045 43.478 0.00 0.00 0.00 2.52
576 585 4.962995 TGGGACAGAGGGAGTAATAGAAAG 59.037 45.833 0.00 0.00 0.00 2.62
577 586 4.345547 GGGACAGAGGGAGTAATAGAAAGG 59.654 50.000 0.00 0.00 0.00 3.11
578 587 4.963628 GGACAGAGGGAGTAATAGAAAGGT 59.036 45.833 0.00 0.00 0.00 3.50
579 588 5.425862 GGACAGAGGGAGTAATAGAAAGGTT 59.574 44.000 0.00 0.00 0.00 3.50
580 589 6.070136 GGACAGAGGGAGTAATAGAAAGGTTT 60.070 42.308 0.00 0.00 0.00 3.27
581 590 7.331089 ACAGAGGGAGTAATAGAAAGGTTTT 57.669 36.000 0.00 0.00 0.00 2.43
582 591 7.756614 ACAGAGGGAGTAATAGAAAGGTTTTT 58.243 34.615 0.00 0.00 0.00 1.94
583 592 7.665974 ACAGAGGGAGTAATAGAAAGGTTTTTG 59.334 37.037 0.00 0.00 0.00 2.44
584 593 7.883311 CAGAGGGAGTAATAGAAAGGTTTTTGA 59.117 37.037 0.00 0.00 0.00 2.69
585 594 8.445588 AGAGGGAGTAATAGAAAGGTTTTTGAA 58.554 33.333 0.00 0.00 0.00 2.69
586 595 9.074576 GAGGGAGTAATAGAAAGGTTTTTGAAA 57.925 33.333 0.00 0.00 0.00 2.69
587 596 8.857098 AGGGAGTAATAGAAAGGTTTTTGAAAC 58.143 33.333 0.00 0.00 0.00 2.78
588 597 8.857098 GGGAGTAATAGAAAGGTTTTTGAAACT 58.143 33.333 3.85 0.00 0.00 2.66
597 606 9.733556 AGAAAGGTTTTTGAAACTAATGGTTTT 57.266 25.926 0.00 0.00 46.77 2.43
673 682 4.577246 GCTAGCCGCCGACTGAGG 62.577 72.222 2.29 0.00 0.00 3.86
806 840 2.993264 GGTCGGGTCCCACGAGAA 60.993 66.667 9.12 0.00 41.50 2.87
807 841 2.260743 GTCGGGTCCCACGAGAAC 59.739 66.667 9.12 0.00 41.50 3.01
808 842 2.993264 TCGGGTCCCACGAGAACC 60.993 66.667 9.12 0.00 40.54 3.62
809 843 3.307906 CGGGTCCCACGAGAACCA 61.308 66.667 9.12 0.00 44.56 3.67
810 844 2.663196 GGGTCCCACGAGAACCAG 59.337 66.667 1.78 0.00 43.70 4.00
852 888 0.875059 GGCCGCAGCATAAATACCTC 59.125 55.000 0.00 0.00 42.56 3.85
1206 1247 2.188994 GCCATCTTCTGCCTCGCT 59.811 61.111 0.00 0.00 0.00 4.93
1697 1744 2.226437 TCGATGCTTTGACTTTTCCTGC 59.774 45.455 0.00 0.00 0.00 4.85
1705 1752 0.799393 GACTTTTCCTGCCTTCTCGC 59.201 55.000 0.00 0.00 0.00 5.03
1860 1907 0.103026 GCGATTGCAAGGGGGATTTC 59.897 55.000 4.94 0.00 42.15 2.17
1938 2002 1.269257 CGCGATACAGAGCTTGATCCA 60.269 52.381 0.00 0.00 0.00 3.41
2058 2127 4.891756 CCAATCTTGATAGGGAACAAGCAT 59.108 41.667 0.00 0.00 41.91 3.79
2086 2155 2.844122 CATCACATGATGCACACAGG 57.156 50.000 8.86 5.96 44.44 4.00
2099 2168 2.669391 GCACACAGGCATAGCAAAAGTC 60.669 50.000 0.00 0.00 0.00 3.01
2147 2221 4.716784 TGTGGCATCTCTAGACCAGTTTAT 59.283 41.667 0.14 0.00 31.46 1.40
2235 2309 1.833630 TGGATCTGGTTGAGCTGTAGG 59.166 52.381 0.00 0.00 0.00 3.18
2260 2334 6.477360 GGCTAGCTTAACTCTGACATAAAGAC 59.523 42.308 15.72 0.00 0.00 3.01
2270 2344 6.659668 ACTCTGACATAAAGACAGTACAGCTA 59.340 38.462 0.00 0.00 40.29 3.32
2273 2347 7.813148 TCTGACATAAAGACAGTACAGCTAAAC 59.187 37.037 0.00 0.00 40.29 2.01
2291 2365 1.221840 CCGTGAGATCCAAGTGGGG 59.778 63.158 0.00 0.00 37.22 4.96
2356 2430 0.518636 CATGACCTTCCTGTTGCGTG 59.481 55.000 0.00 0.00 0.00 5.34
2431 2507 3.510719 CAATATTGCGTGTTCCTTTGGG 58.489 45.455 1.74 0.00 0.00 4.12
2641 2723 7.234577 GGTAAGAACTCTCCTCAATCCTCATAT 59.765 40.741 0.00 0.00 0.00 1.78
2668 2750 5.423015 TCCAGCTCATTCTTAAGTGTGATC 58.577 41.667 1.63 4.37 0.00 2.92
2687 2769 5.515626 GTGATCGTGTTAGGTGTCTCATTAC 59.484 44.000 0.00 0.00 0.00 1.89
2738 2821 2.068837 TTGTTACACGAGGTTAGCGG 57.931 50.000 0.00 0.00 0.00 5.52
2739 2822 0.244450 TGTTACACGAGGTTAGCGGG 59.756 55.000 0.00 0.00 38.32 6.13
2895 2978 1.507140 TTGGGGGTAGGTATGCTGAG 58.493 55.000 0.00 0.00 0.00 3.35
2983 3067 2.922955 TGTGGGGGTGGATTGAGAATAA 59.077 45.455 0.00 0.00 0.00 1.40
3015 3099 7.524717 AACATATTGCCAGTTGGGTTATATC 57.475 36.000 0.00 0.00 39.65 1.63
3016 3100 6.852404 ACATATTGCCAGTTGGGTTATATCT 58.148 36.000 0.00 0.00 39.65 1.98
3017 3101 7.984475 ACATATTGCCAGTTGGGTTATATCTA 58.016 34.615 0.00 0.00 39.65 1.98
3075 3159 3.006247 GGAGAGCAGTGATGAGGTTTTC 58.994 50.000 0.00 0.00 0.00 2.29
3146 3230 4.521256 CCTCGTTTACTCAATTTGGGGAAA 59.479 41.667 2.35 2.35 0.00 3.13
3196 3280 0.319900 CCGCCCGTGGAATCTAGATG 60.320 60.000 5.86 0.00 0.00 2.90
3232 3316 2.030805 GCGTGGTTTGATTCTTTCTGCT 60.031 45.455 0.00 0.00 0.00 4.24
3233 3317 3.558505 CGTGGTTTGATTCTTTCTGCTG 58.441 45.455 0.00 0.00 0.00 4.41
3391 3476 1.029947 AACGCGCATAAAAGGAGGGG 61.030 55.000 5.73 0.00 0.00 4.79
3442 3527 3.487574 GTCGTCGCTCCATTTTCTATGAG 59.512 47.826 0.00 0.00 0.00 2.90
3464 3549 5.522456 AGTGCATTTGTCATGTACTGTTTG 58.478 37.500 4.95 0.00 42.04 2.93
3636 3724 7.148018 CCTTGAGGTATTTGTCATTTGTGCTAT 60.148 37.037 0.00 0.00 0.00 2.97
3678 3766 4.681512 GCACTGAAATTTCCATTCCATCCC 60.682 45.833 15.48 0.00 0.00 3.85
3681 3769 6.380846 CACTGAAATTTCCATTCCATCCCTAA 59.619 38.462 15.48 0.00 0.00 2.69
3757 3845 3.070302 AGGTTAGGATTGCTCGGATCTTC 59.930 47.826 0.00 0.00 0.00 2.87
3856 3944 2.149578 CTGCTGTGCTCTGCTAGTTTT 58.850 47.619 16.89 0.00 38.91 2.43
3884 3972 7.674471 ACTGTAAGCTTCCTTTTATTCTCAC 57.326 36.000 0.00 0.00 37.60 3.51
3887 3975 8.099364 TGTAAGCTTCCTTTTATTCTCACAAG 57.901 34.615 0.00 0.00 32.47 3.16
3893 3982 8.515414 GCTTCCTTTTATTCTCACAAGTAACAT 58.485 33.333 0.00 0.00 0.00 2.71
4065 4165 3.609103 ATGCGCTTTCTAAAATAGCCG 57.391 42.857 9.73 0.00 0.00 5.52
4325 4425 1.280457 GTCTTCCCCTCATGGTCACT 58.720 55.000 0.00 0.00 0.00 3.41
4365 4465 2.202878 GCGACCAAGATAGCGCCA 60.203 61.111 2.29 0.00 43.33 5.69
4557 4658 3.896648 TCATTTTTGTCTGTCGCCTTC 57.103 42.857 0.00 0.00 0.00 3.46
4648 4753 9.224267 CTGGATCTTCTAATTCTTTGTTGAGAA 57.776 33.333 0.00 0.00 39.76 2.87
4693 4798 6.951062 TTACATGTTGTTTCAGAATGTGGA 57.049 33.333 2.30 0.00 37.40 4.02
4694 4799 7.523293 TTACATGTTGTTTCAGAATGTGGAT 57.477 32.000 2.30 0.00 37.40 3.41
4695 4800 6.017400 ACATGTTGTTTCAGAATGTGGATC 57.983 37.500 0.00 0.00 37.40 3.36
4696 4801 5.771666 ACATGTTGTTTCAGAATGTGGATCT 59.228 36.000 0.00 0.00 37.40 2.75
4703 4809 3.453868 TCAGAATGTGGATCTTCCCAGA 58.546 45.455 0.00 0.00 36.78 3.86
4813 4920 6.600822 AGCACAGTATTTACATGCTTTCATCT 59.399 34.615 11.57 0.00 43.79 2.90
4814 4921 6.690098 GCACAGTATTTACATGCTTTCATCTG 59.310 38.462 0.00 0.00 37.50 2.90
4820 4927 2.168496 ACATGCTTTCATCTGCTGCTT 58.832 42.857 0.00 0.00 0.00 3.91
4823 4930 2.082231 TGCTTTCATCTGCTGCTTCTC 58.918 47.619 0.00 0.00 0.00 2.87
4835 4944 2.606551 GCTGCTTCTCTTTTCCTTGCAC 60.607 50.000 0.00 0.00 0.00 4.57
4975 5084 4.452733 CTCCGACGGGGCACTTCC 62.453 72.222 15.25 0.00 34.94 3.46
5003 5112 2.539338 GCCGTGTTCAGGTTTGCGA 61.539 57.895 0.00 0.00 0.00 5.10
5317 5426 2.289882 TGAGCTTGTTCCTCCTGATGTG 60.290 50.000 0.00 0.00 0.00 3.21
5318 5427 0.807496 GCTTGTTCCTCCTGATGTGC 59.193 55.000 0.00 0.00 0.00 4.57
5329 5438 2.021964 CTGATGTGCTCGCGCTTGAG 62.022 60.000 5.56 6.92 39.05 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.287222 TGGGTGTTATTAAGCATGGAGC 58.713 45.455 0.00 0.00 46.19 4.70
5 6 5.593909 TGATTGGGTGTTATTAAGCATGGAG 59.406 40.000 0.00 0.00 0.00 3.86
6 7 5.514169 TGATTGGGTGTTATTAAGCATGGA 58.486 37.500 0.00 0.00 0.00 3.41
20 21 9.793252 CAATTTTAGTAAGAGATTGATTGGGTG 57.207 33.333 8.76 0.00 31.15 4.61
64 66 3.851105 CGCGTATCGGACCTAAGTTTAGG 60.851 52.174 14.86 14.86 44.07 2.69
65 67 3.294943 CGCGTATCGGACCTAAGTTTAG 58.705 50.000 0.00 0.00 33.78 1.85
78 80 0.111266 GCCATGTTTAGCGCGTATCG 60.111 55.000 8.43 0.00 42.12 2.92
88 90 8.481314 TGATGCCTTAATTTAATGCCATGTTTA 58.519 29.630 12.12 0.00 0.00 2.01
171 175 9.014297 ACCTAAGTTTAGACCAAAATGAATCAG 57.986 33.333 0.51 0.00 32.47 2.90
199 203 1.544246 TGTCATATCTGGGGCGTATCG 59.456 52.381 0.00 0.00 0.00 2.92
204 208 5.003160 TGAATTATTGTCATATCTGGGGCG 58.997 41.667 0.00 0.00 0.00 6.13
217 221 8.316214 AGGATTTGCAATGTCTTGAATTATTGT 58.684 29.630 0.00 0.00 34.04 2.71
235 239 4.794169 ACGTTGTTTCACATAGGATTTGC 58.206 39.130 0.00 0.00 0.00 3.68
246 250 5.881637 AATGTGCATTTACGTTGTTTCAC 57.118 34.783 0.00 0.00 0.00 3.18
298 304 8.803397 ACCAAGTCTAAGTTTAGAACAAAGTT 57.197 30.769 3.30 0.00 41.12 2.66
300 306 8.485591 CGTACCAAGTCTAAGTTTAGAACAAAG 58.514 37.037 3.30 0.00 41.12 2.77
315 321 3.894832 TTGGGGCGTACCAAGTCT 58.105 55.556 8.58 0.00 45.19 3.24
358 367 4.597507 TGGTCTCATAGAGGGACTGTTTTT 59.402 41.667 0.00 0.00 41.55 1.94
364 373 2.248686 ACCATGGTCTCATAGAGGGACT 59.751 50.000 13.00 0.00 34.21 3.85
366 375 4.420206 CATACCATGGTCTCATAGAGGGA 58.580 47.826 23.76 0.00 31.33 4.20
383 392 7.736893 AGATACTCAGAAATTACCACCATACC 58.263 38.462 0.00 0.00 0.00 2.73
535 544 9.321562 TCTGTCCCATAATATAAGAACGTTTTC 57.678 33.333 0.46 0.00 0.00 2.29
536 545 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
537 546 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
538 547 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
539 548 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
540 549 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
541 550 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
542 551 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
543 552 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
544 553 8.666129 TTACTCCCTCTGTCCCATAATATAAG 57.334 38.462 0.00 0.00 0.00 1.73
546 555 9.937876 CTATTACTCCCTCTGTCCCATAATATA 57.062 37.037 0.00 0.00 0.00 0.86
547 556 8.633724 TCTATTACTCCCTCTGTCCCATAATAT 58.366 37.037 0.00 0.00 0.00 1.28
548 557 8.008104 TCTATTACTCCCTCTGTCCCATAATA 57.992 38.462 0.00 0.00 0.00 0.98
549 558 6.875469 TCTATTACTCCCTCTGTCCCATAAT 58.125 40.000 0.00 0.00 0.00 1.28
550 559 6.289482 TCTATTACTCCCTCTGTCCCATAA 57.711 41.667 0.00 0.00 0.00 1.90
551 560 5.942977 TCTATTACTCCCTCTGTCCCATA 57.057 43.478 0.00 0.00 0.00 2.74
552 561 4.834406 TCTATTACTCCCTCTGTCCCAT 57.166 45.455 0.00 0.00 0.00 4.00
553 562 4.620086 TTCTATTACTCCCTCTGTCCCA 57.380 45.455 0.00 0.00 0.00 4.37
554 563 4.345547 CCTTTCTATTACTCCCTCTGTCCC 59.654 50.000 0.00 0.00 0.00 4.46
555 564 4.963628 ACCTTTCTATTACTCCCTCTGTCC 59.036 45.833 0.00 0.00 0.00 4.02
556 565 6.547930 AACCTTTCTATTACTCCCTCTGTC 57.452 41.667 0.00 0.00 0.00 3.51
557 566 6.954352 AAACCTTTCTATTACTCCCTCTGT 57.046 37.500 0.00 0.00 0.00 3.41
558 567 7.883311 TCAAAAACCTTTCTATTACTCCCTCTG 59.117 37.037 0.00 0.00 0.00 3.35
559 568 7.985589 TCAAAAACCTTTCTATTACTCCCTCT 58.014 34.615 0.00 0.00 0.00 3.69
560 569 8.631480 TTCAAAAACCTTTCTATTACTCCCTC 57.369 34.615 0.00 0.00 0.00 4.30
561 570 8.857098 GTTTCAAAAACCTTTCTATTACTCCCT 58.143 33.333 0.00 0.00 0.00 4.20
562 571 8.857098 AGTTTCAAAAACCTTTCTATTACTCCC 58.143 33.333 0.00 0.00 0.00 4.30
611 620 7.646526 GCTTCTACGAAATTAACCTGTGTTTTT 59.353 33.333 0.00 0.00 35.87 1.94
612 621 7.136772 GCTTCTACGAAATTAACCTGTGTTTT 58.863 34.615 0.00 0.00 35.87 2.43
613 622 6.565247 CGCTTCTACGAAATTAACCTGTGTTT 60.565 38.462 0.00 0.00 33.58 2.83
614 623 5.107220 CGCTTCTACGAAATTAACCTGTGTT 60.107 40.000 0.00 0.00 35.15 3.32
615 624 4.387862 CGCTTCTACGAAATTAACCTGTGT 59.612 41.667 0.00 0.00 34.06 3.72
616 625 4.201685 CCGCTTCTACGAAATTAACCTGTG 60.202 45.833 0.00 0.00 34.06 3.66
617 626 3.930848 CCGCTTCTACGAAATTAACCTGT 59.069 43.478 0.00 0.00 34.06 4.00
618 627 3.930848 ACCGCTTCTACGAAATTAACCTG 59.069 43.478 0.00 0.00 34.06 4.00
619 628 4.179298 GACCGCTTCTACGAAATTAACCT 58.821 43.478 0.00 0.00 34.06 3.50
620 629 3.000376 CGACCGCTTCTACGAAATTAACC 60.000 47.826 0.00 0.00 34.06 2.85
621 630 3.000376 CCGACCGCTTCTACGAAATTAAC 60.000 47.826 0.00 0.00 34.06 2.01
622 631 3.181397 CCGACCGCTTCTACGAAATTAA 58.819 45.455 0.00 0.00 34.06 1.40
623 632 2.801063 CCGACCGCTTCTACGAAATTA 58.199 47.619 0.00 0.00 34.06 1.40
624 633 1.636988 CCGACCGCTTCTACGAAATT 58.363 50.000 0.00 0.00 34.06 1.82
625 634 0.804933 GCCGACCGCTTCTACGAAAT 60.805 55.000 0.00 0.00 34.06 2.17
626 635 1.444895 GCCGACCGCTTCTACGAAA 60.445 57.895 0.00 0.00 34.06 3.46
627 636 2.180017 GCCGACCGCTTCTACGAA 59.820 61.111 0.00 0.00 34.06 3.85
781 811 4.383861 GGACCCGACCCGTTGGAC 62.384 72.222 2.40 0.00 36.15 4.02
832 868 0.474184 AGGTATTTATGCTGCGGCCT 59.526 50.000 16.57 7.99 37.74 5.19
834 870 0.875059 GGAGGTATTTATGCTGCGGC 59.125 55.000 11.65 11.65 39.26 6.53
852 888 1.079256 TGTCAGAGGTGGGAGAGGG 59.921 63.158 0.00 0.00 0.00 4.30
922 959 2.158959 CGTGTAAGAGGAAGCGCGG 61.159 63.158 8.83 0.00 0.00 6.46
1705 1752 6.690957 TGCAAGGAAATAAAAATTAGCGATCG 59.309 34.615 11.69 11.69 0.00 3.69
1820 1867 3.956199 GCAGATTCCCAATCCAGAAATGA 59.044 43.478 0.00 0.00 38.71 2.57
1921 1969 5.755861 GGTAACTTGGATCAAGCTCTGTATC 59.244 44.000 7.48 0.00 44.43 2.24
1922 1970 5.675538 GGTAACTTGGATCAAGCTCTGTAT 58.324 41.667 7.48 0.00 44.43 2.29
1923 1971 4.381612 CGGTAACTTGGATCAAGCTCTGTA 60.382 45.833 7.48 0.00 44.43 2.74
1924 1972 3.617531 CGGTAACTTGGATCAAGCTCTGT 60.618 47.826 7.48 0.00 44.43 3.41
1938 2002 2.713863 TGTGGTGGAAACGGTAACTT 57.286 45.000 0.00 0.00 0.00 2.66
1993 2060 5.313623 CGTTTGATTGAACTAAACGCTAGG 58.686 41.667 13.07 0.00 46.32 3.02
2016 2083 4.216411 TGGCAGATTCTACTAACCCAAC 57.784 45.455 0.00 0.00 0.00 3.77
2058 2127 0.549469 ATCATGTGATGCAGAGGCCA 59.451 50.000 5.01 0.00 40.13 5.36
2086 2155 6.530913 TGATAGAATCGACTTTTGCTATGC 57.469 37.500 0.00 0.00 0.00 3.14
2235 2309 6.477360 GTCTTTATGTCAGAGTTAAGCTAGCC 59.523 42.308 12.13 0.00 0.00 3.93
2260 2334 3.570926 TCTCACGGTTTAGCTGTACTG 57.429 47.619 0.00 1.54 34.32 2.74
2270 2344 1.271379 CCCACTTGGATCTCACGGTTT 60.271 52.381 0.00 0.00 37.39 3.27
2273 2347 1.221840 CCCCACTTGGATCTCACGG 59.778 63.158 0.00 0.00 37.39 4.94
2291 2365 0.322187 TAGCGGAAAAAGGGACAGCC 60.322 55.000 0.00 0.00 0.00 4.85
2328 2402 3.136443 ACAGGAAGGTCATGTGAAGTGAA 59.864 43.478 0.00 0.00 40.17 3.18
2356 2430 3.006247 TCCAAAAGGTTGTTGCAAAAGC 58.994 40.909 0.00 7.99 32.40 3.51
2431 2507 4.274459 GGTCAAGGATCACACATAGCATTC 59.726 45.833 0.00 0.00 0.00 2.67
2488 2570 0.524862 CCAGTCCAAGCATGTTGAGC 59.475 55.000 8.90 0.00 0.00 4.26
2641 2723 4.287067 ACACTTAAGAATGAGCTGGAGGAA 59.713 41.667 10.09 0.00 0.00 3.36
2668 2750 4.806330 ACAGTAATGAGACACCTAACACG 58.194 43.478 0.00 0.00 0.00 4.49
2817 2900 5.005740 TCCAGAAGACCAGAAACATCATTG 58.994 41.667 0.00 0.00 0.00 2.82
2895 2978 0.536724 GGACAACCCCAAATCCATGC 59.463 55.000 0.00 0.00 0.00 4.06
2983 3067 7.941790 ACCCAACTGGCAATATGTTTTATTTTT 59.058 29.630 0.00 0.00 37.83 1.94
3075 3159 9.125906 CTTCAGCTCAAGAACATTTCTATTTTG 57.874 33.333 0.00 0.00 39.61 2.44
3146 3230 3.200165 GCTAGTAAGATTCCAACACCCCT 59.800 47.826 0.00 0.00 0.00 4.79
3203 3287 3.365265 CAAACCACGCAGGAGGCC 61.365 66.667 0.00 0.00 41.22 5.19
3232 3316 3.010138 CCTACCAGAATTGTCCCTTTCCA 59.990 47.826 0.00 0.00 0.00 3.53
3233 3317 3.010250 ACCTACCAGAATTGTCCCTTTCC 59.990 47.826 0.00 0.00 0.00 3.13
3424 3509 3.198068 GCACTCATAGAAAATGGAGCGA 58.802 45.455 0.00 0.00 0.00 4.93
3425 3510 2.938451 TGCACTCATAGAAAATGGAGCG 59.062 45.455 0.00 0.00 0.00 5.03
3442 3527 5.518812 TCAAACAGTACATGACAAATGCAC 58.481 37.500 0.00 0.00 0.00 4.57
3636 3724 8.956533 TCAGTGCTTGCAACAATATATTAGTA 57.043 30.769 0.00 0.00 0.00 1.82
3681 3769 8.362464 TCACTACACATACAGACCTATTTTCT 57.638 34.615 0.00 0.00 0.00 2.52
3757 3845 2.406616 GCGTGGGCCATAGGTGTTG 61.407 63.158 10.70 0.00 0.00 3.33
3884 3972 6.676950 TGTTACAGCATTTGGATGTTACTTG 58.323 36.000 4.00 0.00 45.58 3.16
3887 3975 6.035843 CCATGTTACAGCATTTGGATGTTAC 58.964 40.000 0.00 0.00 45.58 2.50
3893 3982 2.824936 CCACCATGTTACAGCATTTGGA 59.175 45.455 8.70 0.00 33.99 3.53
4065 4165 0.771755 AACCCCTCAACCTGGAAGAC 59.228 55.000 0.00 0.00 34.07 3.01
4154 4254 1.973812 GACAACCTTGGCCAGCTCC 60.974 63.158 5.11 0.00 0.00 4.70
4325 4425 1.447838 GATCCGCTTGCGGAAGTCA 60.448 57.895 35.03 16.62 41.79 3.41
4548 4649 4.069232 CTGGCGGAGAAGGCGACA 62.069 66.667 0.00 0.00 39.82 4.35
4557 4658 1.268352 GTATAGCTGAGACTGGCGGAG 59.732 57.143 0.00 0.00 0.00 4.63
4688 4793 1.588239 AGCATCTGGGAAGATCCACA 58.412 50.000 0.00 0.00 38.64 4.17
4689 4794 2.092753 TGAAGCATCTGGGAAGATCCAC 60.093 50.000 0.00 0.00 38.64 4.02
4690 4795 2.172082 CTGAAGCATCTGGGAAGATCCA 59.828 50.000 0.00 0.00 38.64 3.41
4691 4796 2.486907 CCTGAAGCATCTGGGAAGATCC 60.487 54.545 6.95 0.00 40.13 3.36
4693 4798 2.485659 TCCTGAAGCATCTGGGAAGAT 58.514 47.619 14.00 0.00 43.09 2.40
4694 4799 1.956869 TCCTGAAGCATCTGGGAAGA 58.043 50.000 14.00 0.00 43.09 2.87
4695 4800 2.641305 CTTCCTGAAGCATCTGGGAAG 58.359 52.381 20.69 20.69 43.05 3.46
4696 4801 2.795231 CTTCCTGAAGCATCTGGGAA 57.205 50.000 14.00 13.60 43.09 3.97
4725 4831 6.981559 ACTCTGAAGTTTCTTGTGTTCTAGAC 59.018 38.462 0.00 0.00 28.74 2.59
4783 4890 3.731867 GCATGTAAATACTGTGCTGCACC 60.732 47.826 28.17 11.75 36.40 5.01
4794 4901 5.684626 GCAGCAGATGAAAGCATGTAAATAC 59.315 40.000 0.00 0.00 34.11 1.89
4813 4920 1.610522 GCAAGGAAAAGAGAAGCAGCA 59.389 47.619 0.00 0.00 0.00 4.41
4814 4921 1.610522 TGCAAGGAAAAGAGAAGCAGC 59.389 47.619 0.00 0.00 0.00 5.25
4820 4927 4.016444 ACTGTTTGTGCAAGGAAAAGAGA 58.984 39.130 13.21 0.00 30.89 3.10
4823 4930 3.865164 GGAACTGTTTGTGCAAGGAAAAG 59.135 43.478 0.00 0.00 0.00 2.27
4835 4944 8.349245 TGTAGAATGTAAACATGGAACTGTTTG 58.651 33.333 11.37 0.00 46.11 2.93
4895 5004 2.420568 GGACAGCCCGGTGTCGATA 61.421 63.158 17.99 0.00 46.72 2.92
4997 5106 2.793272 CGCAGCCATCATCGCAAA 59.207 55.556 0.00 0.00 0.00 3.68
5099 5208 1.501582 AGACCATCAAGCTCTACCCC 58.498 55.000 0.00 0.00 0.00 4.95
5318 5427 4.821589 GACCCCCTCAAGCGCGAG 62.822 72.222 12.10 3.12 0.00 5.03
5329 5438 4.426313 CCGCCTTCAAGGACCCCC 62.426 72.222 7.98 0.00 37.67 5.40


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

AutoCloner maintained by Alex Coulton.