Multiple sequence alignment - TraesCS2A01G284100

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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 TraesCS2A01G284100 chr2A 100.000 5331 0 0 1 5331 476218017 476223347 0.000000e+00 9845.0
1 TraesCS2A01G284100 chr2A 96.471 85 2 1 5196 5279 477279933 477280017 7.200000e-29 139.0
2 TraesCS2A01G284100 chr2D 96.919 3181 50 12 602 3742 355978959 355982131 0.000000e+00 5288.0
3 TraesCS2A01G284100 chr2D 97.616 713 15 2 3755 4467 355982244 355982954 0.000000e+00 1221.0
4 TraesCS2A01G284100 chr2D 92.164 855 36 14 4481 5331 355982938 355983765 0.000000e+00 1179.0
5 TraesCS2A01G284100 chr2D 83.023 430 35 15 3 428 355978306 355978701 6.570000e-94 355.0
6 TraesCS2A01G284100 chr2D 96.512 86 2 1 5195 5279 342055943 342055858 2.000000e-29 141.0
7 TraesCS2A01G284100 chr2B 89.506 1620 84 38 758 2313 423828004 423829601 0.000000e+00 1971.0
8 TraesCS2A01G284100 chr2B 97.458 1141 29 0 2602 3742 423830152 423831292 0.000000e+00 1947.0
9 TraesCS2A01G284100 chr2B 96.792 717 18 3 3755 4468 423831405 423832119 0.000000e+00 1192.0
10 TraesCS2A01G284100 chr2B 91.445 865 38 10 4480 5331 423832101 423832942 0.000000e+00 1155.0
11 TraesCS2A01G284100 chr2B 77.990 209 30 11 561 761 423827531 423827731 3.370000e-22 117.0
12 TraesCS2A01G284100 chr3D 94.958 238 10 1 5094 5331 419377104 419376869 6.520000e-99 372.0
13 TraesCS2A01G284100 chr5D 95.506 89 3 1 5192 5279 8375848 8375936 2.000000e-29 141.0
14 TraesCS2A01G284100 chr5D 85.135 74 8 3 237 308 40181354 40181426 7.410000e-09 73.1
15 TraesCS2A01G284100 chr3B 95.506 89 3 1 5192 5279 12001010 12001098 2.000000e-29 141.0
16 TraesCS2A01G284100 chr5B 95.349 86 3 1 5195 5279 606531373 606531288 9.310000e-28 135.0
17 TraesCS2A01G284100 chr3A 94.382 89 4 1 5192 5279 328622838 328622926 9.310000e-28 135.0


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 TraesCS2A01G284100 chr2A 476218017 476223347 5330 False 9845.00 9845 100.0000 1 5331 1 chr2A.!!$F1 5330
1 TraesCS2A01G284100 chr2D 355978306 355983765 5459 False 2010.75 5288 92.4305 3 5331 4 chr2D.!!$F1 5328
2 TraesCS2A01G284100 chr2B 423827531 423832942 5411 False 1276.40 1971 90.6382 561 5331 5 chr2B.!!$F1 4770

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
19 20 0.038526 GCCGTCTCGTCTTCCTGAAA 60.039 55.0 0.0 0.0 0.00 2.69 F
438 464 0.180171 TGGGATGGTGGCAGATTACG 59.820 55.0 0.0 0.0 0.00 3.18 F
2332 2878 0.471617 ACACAGCCTCAGTTGCTTCT 59.528 50.0 0.0 0.0 36.81 2.85 F
3554 4324 0.392729 GTCAGATGAGCCAAGCTGCT 60.393 55.0 0.0 0.0 46.37 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 2449 0.867746 TCTGTTGCATCAACTCACGC 59.132 50.0 10.52 0.0 43.85 5.34 R
2370 2916 1.219646 GCAAGCAACAAATGTGTGGG 58.780 50.0 0.00 0.0 38.27 4.61 R
3745 4515 0.320421 GGTACTGAAGAGCACCGCAA 60.320 55.0 0.00 0.0 0.00 4.85 R
5025 5919 0.183492 AGGAGTTTTGCTGCCAGACA 59.817 50.0 0.00 0.0 36.05 3.41 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
19 20 0.038526 GCCGTCTCGTCTTCCTGAAA 60.039 55.000 0.00 0.00 0.00 2.69
21 22 2.931320 GCCGTCTCGTCTTCCTGAAAAT 60.931 50.000 0.00 0.00 0.00 1.82
26 27 4.932200 GTCTCGTCTTCCTGAAAATGACAT 59.068 41.667 0.00 0.00 0.00 3.06
30 31 7.117812 TCTCGTCTTCCTGAAAATGACATAAAC 59.882 37.037 0.00 0.00 0.00 2.01
36 37 7.696992 TCCTGAAAATGACATAAACCCTAAC 57.303 36.000 0.00 0.00 0.00 2.34
105 106 3.461773 CCAGATCCACCGCGTCCT 61.462 66.667 4.92 0.00 0.00 3.85
223 225 3.004171 TGTGTTGTTGGGCGTATACATC 58.996 45.455 3.32 0.00 0.00 3.06
224 226 2.029970 GTGTTGTTGGGCGTATACATCG 59.970 50.000 3.32 0.00 0.00 3.84
226 228 2.674357 GTTGTTGGGCGTATACATCGTT 59.326 45.455 3.32 0.00 0.00 3.85
229 231 3.371591 TGTTGGGCGTATACATCGTTTTC 59.628 43.478 3.32 0.00 0.00 2.29
236 238 5.321516 GCGTATACATCGTTTTCTGCTTTT 58.678 37.500 3.32 0.00 0.00 2.27
290 293 6.403866 AACATTTGTCCATGTTTGCTAGAA 57.596 33.333 0.00 0.00 43.54 2.10
291 294 6.403866 ACATTTGTCCATGTTTGCTAGAAA 57.596 33.333 0.00 0.00 33.29 2.52
292 295 6.815089 ACATTTGTCCATGTTTGCTAGAAAA 58.185 32.000 0.00 0.00 33.29 2.29
293 296 7.271511 ACATTTGTCCATGTTTGCTAGAAAAA 58.728 30.769 0.00 0.00 33.29 1.94
341 344 4.884668 TGTCGGAACAGGACTTTTAGAT 57.115 40.909 0.00 0.00 35.45 1.98
357 360 5.746990 TTTAGATAGATCCTAGCAAGCCC 57.253 43.478 0.00 0.00 0.00 5.19
438 464 0.180171 TGGGATGGTGGCAGATTACG 59.820 55.000 0.00 0.00 0.00 3.18
446 477 3.823873 TGGTGGCAGATTACGAAACATTT 59.176 39.130 0.00 0.00 0.00 2.32
486 521 9.760077 TGTCTCCTTATAAATCTCGGAATAAAC 57.240 33.333 0.00 0.00 0.00 2.01
495 530 4.467198 TCTCGGAATAAACTCAACCTCC 57.533 45.455 0.00 0.00 0.00 4.30
496 531 3.835978 TCTCGGAATAAACTCAACCTCCA 59.164 43.478 0.00 0.00 0.00 3.86
497 532 4.469945 TCTCGGAATAAACTCAACCTCCAT 59.530 41.667 0.00 0.00 0.00 3.41
498 533 5.045869 TCTCGGAATAAACTCAACCTCCATT 60.046 40.000 0.00 0.00 0.00 3.16
499 534 5.183228 TCGGAATAAACTCAACCTCCATTC 58.817 41.667 0.00 0.00 0.00 2.67
507 564 1.486310 TCAACCTCCATTCTCCCATCG 59.514 52.381 0.00 0.00 0.00 3.84
524 581 4.264638 GCGCGCTCTCTCCTCCTC 62.265 72.222 26.67 0.00 0.00 3.71
525 582 3.591835 CGCGCTCTCTCCTCCTCC 61.592 72.222 5.56 0.00 0.00 4.30
526 583 2.123897 GCGCTCTCTCCTCCTCCT 60.124 66.667 0.00 0.00 0.00 3.69
527 584 2.193536 GCGCTCTCTCCTCCTCCTC 61.194 68.421 0.00 0.00 0.00 3.71
528 585 1.528309 CGCTCTCTCCTCCTCCTCC 60.528 68.421 0.00 0.00 0.00 4.30
529 586 1.152546 GCTCTCTCCTCCTCCTCCC 60.153 68.421 0.00 0.00 0.00 4.30
530 587 1.943730 GCTCTCTCCTCCTCCTCCCA 61.944 65.000 0.00 0.00 0.00 4.37
531 588 0.633921 CTCTCTCCTCCTCCTCCCAA 59.366 60.000 0.00 0.00 0.00 4.12
532 589 1.007721 CTCTCTCCTCCTCCTCCCAAA 59.992 57.143 0.00 0.00 0.00 3.28
533 590 1.437149 TCTCTCCTCCTCCTCCCAAAA 59.563 52.381 0.00 0.00 0.00 2.44
534 591 2.158004 TCTCTCCTCCTCCTCCCAAAAA 60.158 50.000 0.00 0.00 0.00 1.94
651 757 2.220224 CGATCGAGCACTGCGTCTG 61.220 63.158 10.26 0.00 0.00 3.51
670 776 2.451191 TTGCCACTGCTGGGACTCA 61.451 57.895 0.00 0.00 37.69 3.41
693 799 5.919141 CAGATTGCTTTTCTCCTCAACTTTG 59.081 40.000 0.00 0.00 0.00 2.77
729 846 2.067197 AGGTCTTCCCTTCCCGTTG 58.933 57.895 0.00 0.00 42.73 4.10
752 869 4.276642 GCCATCATTTCCTCTTCTTCCTT 58.723 43.478 0.00 0.00 0.00 3.36
798 1194 1.536662 ACCTCCACCTGACCTGACC 60.537 63.158 0.00 0.00 0.00 4.02
799 1195 1.229336 CCTCCACCTGACCTGACCT 60.229 63.158 0.00 0.00 0.00 3.85
800 1196 1.548357 CCTCCACCTGACCTGACCTG 61.548 65.000 0.00 0.00 0.00 4.00
801 1197 0.542938 CTCCACCTGACCTGACCTGA 60.543 60.000 0.00 0.00 0.00 3.86
802 1198 0.832135 TCCACCTGACCTGACCTGAC 60.832 60.000 0.00 0.00 0.00 3.51
828 1224 2.031674 AAAAGCAAAGCCAAGCGCCT 62.032 50.000 2.29 0.00 38.78 5.52
841 1237 3.049227 GCGCCTTGCCATTAAAAGG 57.951 52.632 0.00 0.02 44.92 3.11
940 1358 3.181487 CCATTCCACCATCGAAATCCAAC 60.181 47.826 0.00 0.00 0.00 3.77
1376 1822 0.952497 TCTGCCGCTGCTTCTTTCTG 60.952 55.000 0.70 0.00 38.71 3.02
1381 1827 1.196354 CCGCTGCTTCTTTCTGTCTTG 59.804 52.381 0.00 0.00 0.00 3.02
1385 1831 3.852572 GCTGCTTCTTTCTGTCTTGCTTG 60.853 47.826 0.00 0.00 0.00 4.01
1437 1923 3.486542 GCGCTGCTTCTTTCTTAGATTGG 60.487 47.826 0.00 0.00 31.54 3.16
1635 2138 6.838090 TGAGGGGCACATGATCATTAAATAAA 59.162 34.615 5.16 0.00 0.00 1.40
1743 2250 3.004734 CCGGCTTTCTTGTGAAATTGACT 59.995 43.478 0.00 0.00 40.85 3.41
1947 2455 4.566759 TCTTCAATTCTTTATCGGCGTGAG 59.433 41.667 6.85 0.97 0.00 3.51
1976 2484 9.591404 GATGCAACAGAGATTATTCTTAATTCG 57.409 33.333 0.00 0.00 30.30 3.34
2069 2577 3.615155 GCCTTATCTGGATTAGATGGCC 58.385 50.000 0.00 0.00 43.89 5.36
2078 2586 4.298626 TGGATTAGATGGCCAAGTAGTCT 58.701 43.478 10.96 10.71 0.00 3.24
2096 2604 8.806429 AGTAGTCTAGTCTTACTTCCTAAACC 57.194 38.462 0.00 0.00 0.00 3.27
2134 2642 7.388776 TCCAAATTTCTCACATGTCAGAAGTAG 59.611 37.037 12.19 6.37 30.32 2.57
2135 2643 7.173907 CCAAATTTCTCACATGTCAGAAGTAGT 59.826 37.037 12.19 0.00 30.32 2.73
2332 2878 0.471617 ACACAGCCTCAGTTGCTTCT 59.528 50.000 0.00 0.00 36.81 2.85
2370 2916 4.034510 GTGTGCAGCTCAGGATAATGTAAC 59.965 45.833 0.00 0.00 0.00 2.50
2503 3073 5.619625 ACTACAGAGAGAATGCAAAAAGC 57.380 39.130 0.00 0.00 45.96 3.51
3129 3899 5.718649 TTCTCTCACAGTGTTTCTTTTCG 57.281 39.130 0.00 0.00 0.00 3.46
3170 3940 3.075005 ATCCCCGTGGTCCTGACG 61.075 66.667 0.00 0.00 36.56 4.35
3554 4324 0.392729 GTCAGATGAGCCAAGCTGCT 60.393 55.000 0.00 0.00 46.37 4.24
3742 4512 9.177608 TGCTATCATTTTTCAGTAGCTGTATTT 57.822 29.630 0.00 0.00 38.76 1.40
3761 4531 1.388547 TTTTTGCGGTGCTCTTCAGT 58.611 45.000 0.00 0.00 0.00 3.41
3762 4532 2.248280 TTTTGCGGTGCTCTTCAGTA 57.752 45.000 0.00 0.00 0.00 2.74
3763 4533 1.508632 TTTGCGGTGCTCTTCAGTAC 58.491 50.000 0.00 0.00 34.59 2.73
4000 4869 3.013921 TGCTGTTTCTGAACTTTTCGGT 58.986 40.909 0.00 0.00 37.33 4.69
4117 4986 0.743701 ATGAAGCTGAGAGGCAAGCG 60.744 55.000 0.00 0.00 34.17 4.68
4240 5109 2.029110 TGTCAGCTCGTTGATCATGTCA 60.029 45.455 0.00 0.00 34.25 3.58
4283 5152 3.375782 GCTTGAGCCTTGTCATTGTTT 57.624 42.857 0.00 0.00 34.31 2.83
4486 5358 3.935371 TTTTTGGAAGGGCAGACCA 57.065 47.368 0.00 0.00 43.89 4.02
4487 5359 2.397044 TTTTTGGAAGGGCAGACCAT 57.603 45.000 0.00 0.00 43.89 3.55
4488 5360 2.397044 TTTTGGAAGGGCAGACCATT 57.603 45.000 0.00 0.00 44.30 3.16
4489 5361 2.397044 TTTGGAAGGGCAGACCATTT 57.603 45.000 0.00 0.00 40.88 2.32
4490 5362 2.397044 TTGGAAGGGCAGACCATTTT 57.603 45.000 0.00 0.00 40.88 1.82
4583 5455 9.618890 ACTGTGTATTTATCTGTCAAATGCTAT 57.381 29.630 0.00 0.00 31.60 2.97
4728 5601 6.954944 TGAACTTGTGACTAGTAAATGTTGC 58.045 36.000 0.00 0.00 0.00 4.17
4902 5788 6.351711 CCTTGACTGTGATCTTAGTTCCATCT 60.352 42.308 0.00 0.00 0.00 2.90
4960 5854 3.244491 ACTTGCAGATCTGGCCATCTATC 60.244 47.826 23.89 10.35 31.47 2.08
4961 5855 2.617658 TGCAGATCTGGCCATCTATCT 58.382 47.619 23.89 12.64 31.47 1.98
4962 5856 3.782992 TGCAGATCTGGCCATCTATCTA 58.217 45.455 23.89 7.73 31.47 1.98
4963 5857 4.359996 TGCAGATCTGGCCATCTATCTAT 58.640 43.478 23.89 3.09 31.47 1.98
4964 5858 4.405036 TGCAGATCTGGCCATCTATCTATC 59.595 45.833 23.89 15.60 31.47 2.08
4965 5859 4.650588 GCAGATCTGGCCATCTATCTATCT 59.349 45.833 23.89 11.16 31.47 1.98
4966 5860 5.832595 GCAGATCTGGCCATCTATCTATCTA 59.167 44.000 23.89 0.00 31.47 1.98
4967 5861 6.494491 GCAGATCTGGCCATCTATCTATCTAT 59.506 42.308 23.89 1.40 31.47 1.98
4968 5862 7.309377 GCAGATCTGGCCATCTATCTATCTATC 60.309 44.444 23.89 0.00 31.47 2.08
4969 5863 7.946219 CAGATCTGGCCATCTATCTATCTATCT 59.054 40.741 19.52 6.90 31.47 1.98
4970 5864 9.181462 AGATCTGGCCATCTATCTATCTATCTA 57.819 37.037 18.86 0.00 30.84 1.98
4971 5865 9.979897 GATCTGGCCATCTATCTATCTATCTAT 57.020 37.037 5.51 0.00 0.00 1.98
4972 5866 9.979897 ATCTGGCCATCTATCTATCTATCTATC 57.020 37.037 5.51 0.00 0.00 2.08
4973 5867 9.181462 TCTGGCCATCTATCTATCTATCTATCT 57.819 37.037 5.51 0.00 0.00 1.98
5025 5919 4.137116 TCATATGGACGCTGCTACTTTT 57.863 40.909 2.13 0.00 0.00 2.27
5065 5959 4.695928 CCTAGAGACTTTGTTGTTTAGGCC 59.304 45.833 0.00 0.00 0.00 5.19
5072 5966 4.464597 ACTTTGTTGTTTAGGCCTGTGAAA 59.535 37.500 17.99 5.09 0.00 2.69
5116 6010 1.202806 TCTTCCTTTGGTGACTGGCAG 60.203 52.381 14.16 14.16 0.00 4.85
5128 6022 2.235898 TGACTGGCAGCATGTGTATGTA 59.764 45.455 15.89 0.00 39.31 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.038526 TTTCAGGAAGACGAGACGGC 60.039 55.000 0.00 0.00 33.59 5.68
1 2 2.433868 TTTTCAGGAAGACGAGACGG 57.566 50.000 0.00 0.00 0.00 4.79
48 49 9.453830 AGAGGACTCCCTATTTAGATGTTTTAT 57.546 33.333 0.00 0.00 44.53 1.40
49 50 8.855804 AGAGGACTCCCTATTTAGATGTTTTA 57.144 34.615 0.00 0.00 44.53 1.52
64 65 4.475135 GCCGGCAAGAGGACTCCC 62.475 72.222 24.80 0.00 0.00 4.30
89 90 2.021068 ATGAGGACGCGGTGGATCTG 62.021 60.000 12.47 0.00 0.00 2.90
114 115 1.601419 TTCGTCTCCGGTGGCCTTAG 61.601 60.000 3.32 0.00 33.95 2.18
120 121 2.125912 CTGCTTCGTCTCCGGTGG 60.126 66.667 0.00 0.00 33.95 4.61
125 126 3.760035 TCGGGCTGCTTCGTCTCC 61.760 66.667 13.39 0.00 0.00 3.71
150 151 0.321653 TTTCTCTGCTTTCCTCCGGC 60.322 55.000 0.00 0.00 0.00 6.13
151 152 1.443802 GTTTCTCTGCTTTCCTCCGG 58.556 55.000 0.00 0.00 0.00 5.14
155 156 4.538089 AGATTAGGGTTTCTCTGCTTTCCT 59.462 41.667 0.00 0.00 0.00 3.36
156 157 4.849518 AGATTAGGGTTTCTCTGCTTTCC 58.150 43.478 0.00 0.00 0.00 3.13
158 159 7.603180 AAAAAGATTAGGGTTTCTCTGCTTT 57.397 32.000 0.00 0.00 0.00 3.51
185 186 1.201429 ACACATCCGCCTCCTCCTTT 61.201 55.000 0.00 0.00 0.00 3.11
186 187 1.613630 ACACATCCGCCTCCTCCTT 60.614 57.895 0.00 0.00 0.00 3.36
223 225 4.732923 TCACGAAATGAAAAGCAGAAAACG 59.267 37.500 0.00 0.00 33.02 3.60
224 226 6.417635 TCATCACGAAATGAAAAGCAGAAAAC 59.582 34.615 0.00 0.00 41.93 2.43
226 228 6.070897 TCATCACGAAATGAAAAGCAGAAA 57.929 33.333 0.00 0.00 41.93 2.52
252 254 6.192234 ACAAATGTTTCATTGCTTGCAAAA 57.808 29.167 12.17 0.47 0.00 2.44
254 256 4.272991 GGACAAATGTTTCATTGCTTGCAA 59.727 37.500 10.57 10.57 0.00 4.08
321 324 6.205101 TCTATCTAAAAGTCCTGTTCCGAC 57.795 41.667 0.00 0.00 0.00 4.79
322 325 6.040616 GGATCTATCTAAAAGTCCTGTTCCGA 59.959 42.308 0.00 0.00 0.00 4.55
323 326 6.041069 AGGATCTATCTAAAAGTCCTGTTCCG 59.959 42.308 0.00 0.00 34.92 4.30
324 327 7.368198 AGGATCTATCTAAAAGTCCTGTTCC 57.632 40.000 0.00 0.00 34.92 3.62
325 328 8.085909 GCTAGGATCTATCTAAAAGTCCTGTTC 58.914 40.741 2.15 0.00 36.77 3.18
326 329 7.565398 TGCTAGGATCTATCTAAAAGTCCTGTT 59.435 37.037 2.15 0.00 36.77 3.16
327 330 7.069986 TGCTAGGATCTATCTAAAAGTCCTGT 58.930 38.462 2.15 0.00 36.77 4.00
328 331 7.531857 TGCTAGGATCTATCTAAAAGTCCTG 57.468 40.000 2.15 0.00 36.77 3.86
329 332 7.256154 GCTTGCTAGGATCTATCTAAAAGTCCT 60.256 40.741 0.00 0.00 39.32 3.85
330 333 6.871492 GCTTGCTAGGATCTATCTAAAAGTCC 59.129 42.308 0.00 0.00 0.00 3.85
331 334 6.871492 GGCTTGCTAGGATCTATCTAAAAGTC 59.129 42.308 0.00 0.00 0.00 3.01
332 335 6.239743 GGGCTTGCTAGGATCTATCTAAAAGT 60.240 42.308 0.00 0.00 0.00 2.66
333 336 6.013812 AGGGCTTGCTAGGATCTATCTAAAAG 60.014 42.308 0.00 0.00 0.00 2.27
334 337 5.846714 AGGGCTTGCTAGGATCTATCTAAAA 59.153 40.000 0.00 0.00 0.00 1.52
335 338 5.407049 AGGGCTTGCTAGGATCTATCTAAA 58.593 41.667 0.00 0.00 0.00 1.85
336 339 5.017093 AGGGCTTGCTAGGATCTATCTAA 57.983 43.478 0.00 0.00 0.00 2.10
337 340 4.683766 AGGGCTTGCTAGGATCTATCTA 57.316 45.455 0.00 0.00 0.00 1.98
338 341 3.558608 AGGGCTTGCTAGGATCTATCT 57.441 47.619 0.00 0.00 0.00 1.98
341 344 4.862641 AAAAAGGGCTTGCTAGGATCTA 57.137 40.909 0.00 0.00 0.00 1.98
375 378 3.423848 GCCGAAAAATGAGGCTTGG 57.576 52.632 0.00 0.00 46.83 3.61
438 464 7.441458 AGACACTACTAGTTGACCAAATGTTTC 59.559 37.037 11.43 0.00 0.00 2.78
446 477 4.383931 AGGAGACACTACTAGTTGACCA 57.616 45.455 11.43 0.00 0.00 4.02
477 512 5.186198 AGAATGGAGGTTGAGTTTATTCCG 58.814 41.667 0.00 0.00 0.00 4.30
486 521 2.484417 CGATGGGAGAATGGAGGTTGAG 60.484 54.545 0.00 0.00 0.00 3.02
495 530 4.005472 GCGCGCGATGGGAGAATG 62.005 66.667 37.18 0.00 0.00 2.67
496 531 4.227134 AGCGCGCGATGGGAGAAT 62.227 61.111 37.18 0.00 0.00 2.40
497 532 4.873129 GAGCGCGCGATGGGAGAA 62.873 66.667 37.18 0.00 0.00 2.87
507 564 4.264638 GAGGAGGAGAGAGCGCGC 62.265 72.222 26.66 26.66 0.00 6.86
531 588 4.281657 GGGTGATGAGCCCTAATCTTTTT 58.718 43.478 0.00 0.00 42.81 1.94
532 589 3.685550 CGGGTGATGAGCCCTAATCTTTT 60.686 47.826 0.00 0.00 43.92 2.27
533 590 2.158755 CGGGTGATGAGCCCTAATCTTT 60.159 50.000 0.00 0.00 43.92 2.52
534 591 1.417890 CGGGTGATGAGCCCTAATCTT 59.582 52.381 0.00 0.00 43.92 2.40
535 592 1.051812 CGGGTGATGAGCCCTAATCT 58.948 55.000 0.00 0.00 43.92 2.40
536 593 1.048601 TCGGGTGATGAGCCCTAATC 58.951 55.000 0.00 0.00 43.92 1.75
537 594 0.759346 GTCGGGTGATGAGCCCTAAT 59.241 55.000 0.00 0.00 43.92 1.73
538 595 1.335132 GGTCGGGTGATGAGCCCTAA 61.335 60.000 0.00 0.00 43.92 2.69
539 596 1.760875 GGTCGGGTGATGAGCCCTA 60.761 63.158 0.00 0.00 43.92 3.53
540 597 3.083997 GGTCGGGTGATGAGCCCT 61.084 66.667 0.00 0.00 43.92 5.19
541 598 3.391665 CTGGTCGGGTGATGAGCCC 62.392 68.421 0.00 0.00 42.68 5.19
542 599 1.327690 TACTGGTCGGGTGATGAGCC 61.328 60.000 0.00 0.00 36.28 4.70
553 610 2.092323 TGAGGATGACTGTACTGGTCG 58.908 52.381 4.66 0.00 36.58 4.79
651 757 1.968540 GAGTCCCAGCAGTGGCAAC 60.969 63.158 0.00 0.00 43.44 4.17
670 776 5.010415 CCAAAGTTGAGGAGAAAAGCAATCT 59.990 40.000 0.00 0.00 0.00 2.40
693 799 1.676006 CCTTTACACCCATCGAATGCC 59.324 52.381 0.00 0.00 0.00 4.40
729 846 2.954989 GGAAGAAGAGGAAATGATGGCC 59.045 50.000 0.00 0.00 0.00 5.36
940 1358 1.002857 AATTGGAGGGAGGTCAAGGG 58.997 55.000 0.00 0.00 0.00 3.95
1119 1565 4.845580 AGCGCGGCCTTGAGGATG 62.846 66.667 8.83 0.00 37.39 3.51
1376 1822 5.586339 AGAAAGAAAGAAAGCAAGCAAGAC 58.414 37.500 0.00 0.00 0.00 3.01
1381 1827 7.531280 AAAGAAAGAAAGAAAGAAAGCAAGC 57.469 32.000 0.00 0.00 0.00 4.01
1635 2138 1.668826 TCCAGCCAGTAACCCTCATT 58.331 50.000 0.00 0.00 0.00 2.57
1941 2449 0.867746 TCTGTTGCATCAACTCACGC 59.132 50.000 10.52 0.00 43.85 5.34
2078 2586 8.342270 ACATAGGAGGTTTAGGAAGTAAGACTA 58.658 37.037 0.00 0.00 0.00 2.59
2096 2604 7.391554 TGTGAGAAATTTGGAGAAACATAGGAG 59.608 37.037 0.00 0.00 0.00 3.69
2332 2878 2.159324 TGCACACGAACATTTGCTTGAA 60.159 40.909 0.00 0.00 35.91 2.69
2370 2916 1.219646 GCAAGCAACAAATGTGTGGG 58.780 50.000 0.00 0.00 38.27 4.61
2503 3073 8.195165 TGGAGAAGACCATACCAATTCTATAG 57.805 38.462 0.00 0.00 34.77 1.31
2557 3129 0.179006 GGAATCCTGGCCATCTGGAC 60.179 60.000 14.13 3.30 44.59 4.02
3129 3899 4.515432 GCGATCGGTAAAATAAGCAAGAC 58.485 43.478 18.30 0.00 0.00 3.01
3170 3940 9.346725 CTTGGATATTCAGTTTTCAAGCTAAAC 57.653 33.333 2.88 2.88 36.08 2.01
3554 4324 2.554893 GTTATGCCCGTCTTTGAAACCA 59.445 45.455 0.00 0.00 0.00 3.67
3742 4512 1.388547 ACTGAAGAGCACCGCAAAAA 58.611 45.000 0.00 0.00 0.00 1.94
3745 4515 0.320421 GGTACTGAAGAGCACCGCAA 60.320 55.000 0.00 0.00 0.00 4.85
3746 4516 1.185618 AGGTACTGAAGAGCACCGCA 61.186 55.000 0.00 0.00 37.18 5.69
3747 4517 0.458716 GAGGTACTGAAGAGCACCGC 60.459 60.000 0.00 0.00 41.55 5.68
3748 4518 1.133407 GAGAGGTACTGAAGAGCACCG 59.867 57.143 0.00 0.00 41.55 4.94
3749 4519 2.171840 TGAGAGGTACTGAAGAGCACC 58.828 52.381 0.00 0.00 41.55 5.01
3750 4520 3.944055 TTGAGAGGTACTGAAGAGCAC 57.056 47.619 0.00 0.00 41.55 4.40
3751 4521 5.489792 AATTTGAGAGGTACTGAAGAGCA 57.510 39.130 0.00 0.00 41.55 4.26
3752 4522 6.348868 CCAAAATTTGAGAGGTACTGAAGAGC 60.349 42.308 7.37 0.00 41.55 4.09
3753 4523 6.348868 GCCAAAATTTGAGAGGTACTGAAGAG 60.349 42.308 7.37 0.00 41.55 2.85
3755 4525 5.335976 GGCCAAAATTTGAGAGGTACTGAAG 60.336 44.000 7.37 0.00 41.55 3.02
3756 4526 4.522789 GGCCAAAATTTGAGAGGTACTGAA 59.477 41.667 7.37 0.00 41.55 3.02
3757 4527 4.079253 GGCCAAAATTTGAGAGGTACTGA 58.921 43.478 7.37 0.00 41.55 3.41
3758 4528 3.826157 TGGCCAAAATTTGAGAGGTACTG 59.174 43.478 0.61 0.00 41.55 2.74
3760 4530 3.193479 CCTGGCCAAAATTTGAGAGGTAC 59.807 47.826 7.01 0.00 0.00 3.34
3761 4531 3.430453 CCTGGCCAAAATTTGAGAGGTA 58.570 45.455 7.01 0.00 0.00 3.08
3762 4532 2.250924 CCTGGCCAAAATTTGAGAGGT 58.749 47.619 7.01 0.00 0.00 3.85
3763 4533 1.066645 GCCTGGCCAAAATTTGAGAGG 60.067 52.381 7.01 9.69 0.00 3.69
3764 4534 1.897802 AGCCTGGCCAAAATTTGAGAG 59.102 47.619 16.57 0.09 0.00 3.20
4000 4869 2.941453 TTGCGCCAAAGTGTTTTACA 57.059 40.000 4.18 0.00 0.00 2.41
4283 5152 2.089980 GTAGACTCGCTTGGTCCTGTA 58.910 52.381 0.00 0.00 34.56 2.74
4408 5280 8.677148 ACAAACTTTAGCTTCTTGTATCTTGA 57.323 30.769 0.00 0.00 0.00 3.02
4432 5304 9.855021 AAATGGTCTGCAACTATATAAACAAAC 57.145 29.630 0.00 0.00 0.00 2.93
4468 5340 2.397044 ATGGTCTGCCCTTCCAAAAA 57.603 45.000 0.00 0.00 34.80 1.94
4469 5341 2.397044 AATGGTCTGCCCTTCCAAAA 57.603 45.000 0.00 0.00 34.80 2.44
4470 5342 2.397044 AAATGGTCTGCCCTTCCAAA 57.603 45.000 0.00 0.00 34.80 3.28
4471 5343 2.397044 AAAATGGTCTGCCCTTCCAA 57.603 45.000 0.00 0.00 34.80 3.53
4472 5344 3.756082 ATAAAATGGTCTGCCCTTCCA 57.244 42.857 0.00 0.00 35.64 3.53
4473 5345 4.793201 ACTATAAAATGGTCTGCCCTTCC 58.207 43.478 0.00 0.00 0.00 3.46
4474 5346 6.775594 AAACTATAAAATGGTCTGCCCTTC 57.224 37.500 0.00 0.00 0.00 3.46
4475 5347 9.350951 GTATAAACTATAAAATGGTCTGCCCTT 57.649 33.333 0.00 0.00 0.00 3.95
4476 5348 8.724310 AGTATAAACTATAAAATGGTCTGCCCT 58.276 33.333 0.00 0.00 32.84 5.19
4477 5349 8.784043 CAGTATAAACTATAAAATGGTCTGCCC 58.216 37.037 0.00 0.00 33.48 5.36
4478 5350 9.338622 ACAGTATAAACTATAAAATGGTCTGCC 57.661 33.333 0.00 0.00 33.48 4.85
4488 5360 9.316730 CGGGTTGCTTACAGTATAAACTATAAA 57.683 33.333 0.00 0.00 33.48 1.40
4489 5361 8.477256 ACGGGTTGCTTACAGTATAAACTATAA 58.523 33.333 0.00 0.00 33.48 0.98
4490 5362 8.010733 ACGGGTTGCTTACAGTATAAACTATA 57.989 34.615 0.00 0.00 33.48 1.31
4583 5455 5.836358 AGGGTTCATTACAGCCAAAGTAAAA 59.164 36.000 0.00 0.00 35.33 1.52
4828 5714 5.007921 GCATGAAAACTCCAGCAACAAAATT 59.992 36.000 0.00 0.00 0.00 1.82
4836 5722 6.377996 ACATAAATAGCATGAAAACTCCAGCA 59.622 34.615 0.00 0.00 0.00 4.41
4920 5806 2.979240 AGTAGCTTGAAGTTAGGCAGC 58.021 47.619 0.00 0.00 0.00 5.25
4974 5868 7.890127 GCAGCCCAGATAGATAGATAGATAGAT 59.110 40.741 0.00 0.00 0.00 1.98
4975 5869 7.230747 GCAGCCCAGATAGATAGATAGATAGA 58.769 42.308 0.00 0.00 0.00 1.98
4976 5870 6.434028 GGCAGCCCAGATAGATAGATAGATAG 59.566 46.154 0.00 0.00 0.00 2.08
4977 5871 6.310941 GGCAGCCCAGATAGATAGATAGATA 58.689 44.000 0.00 0.00 0.00 1.98
4978 5872 5.147032 GGCAGCCCAGATAGATAGATAGAT 58.853 45.833 0.00 0.00 0.00 1.98
4979 5873 4.541705 GGCAGCCCAGATAGATAGATAGA 58.458 47.826 0.00 0.00 0.00 1.98
4980 5874 3.640967 GGGCAGCCCAGATAGATAGATAG 59.359 52.174 27.33 0.00 44.65 2.08
4981 5875 3.647636 GGGCAGCCCAGATAGATAGATA 58.352 50.000 27.33 0.00 44.65 1.98
4982 5876 2.476199 GGGCAGCCCAGATAGATAGAT 58.524 52.381 27.33 0.00 44.65 1.98
4983 5877 1.944177 GGGCAGCCCAGATAGATAGA 58.056 55.000 27.33 0.00 44.65 1.98
5025 5919 0.183492 AGGAGTTTTGCTGCCAGACA 59.817 50.000 0.00 0.00 36.05 3.41
5072 5966 9.857656 AGATCACTTGGATAATAATGTGTCATT 57.142 29.630 0.00 0.80 36.00 2.57
5116 6010 4.212847 CAGGATCAGCTTACATACACATGC 59.787 45.833 0.00 0.00 35.39 4.06
5119 6013 4.466015 TGACAGGATCAGCTTACATACACA 59.534 41.667 0.00 0.00 31.91 3.72
5120 6014 4.806247 GTGACAGGATCAGCTTACATACAC 59.194 45.833 0.00 0.00 38.28 2.90


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

AutoCloner maintained by Alex Coulton.