Multiple sequence alignment - TraesCS3A01G252000

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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 TraesCS3A01G252000 chr3A 100.000 7160 0 0 1 7160 471826820 471819661 0.000000e+00 13223.0
1 TraesCS3A01G252000 chr3D 95.746 6512 197 33 2 6464 352958521 352952041 0.000000e+00 10418.0
2 TraesCS3A01G252000 chr3D 84.992 613 54 15 6463 7039 352951990 352951380 8.000000e-164 588.0
3 TraesCS3A01G252000 chr3D 82.258 310 36 15 6520 6817 64836209 64835907 4.290000e-62 250.0
4 TraesCS3A01G252000 chr3D 94.915 118 2 3 7043 7160 352951405 352951292 1.590000e-41 182.0
5 TraesCS3A01G252000 chr3B 92.857 3696 196 36 734 4403 452113558 452109905 0.000000e+00 5301.0
6 TraesCS3A01G252000 chr3B 93.327 1139 48 13 4420 5544 452109298 452108174 0.000000e+00 1657.0
7 TraesCS3A01G252000 chr3B 95.309 938 27 10 5541 6464 452108138 452107204 0.000000e+00 1472.0
8 TraesCS3A01G252000 chr3B 84.203 747 54 27 6463 7153 452107063 452106325 0.000000e+00 667.0
9 TraesCS3A01G252000 chr3B 84.807 362 48 4 391 747 452114427 452114068 2.460000e-94 357.0
10 TraesCS3A01G252000 chr3B 78.372 393 46 23 6509 6870 58154613 58154229 1.210000e-52 219.0
11 TraesCS3A01G252000 chr3B 92.308 39 1 2 6763 6799 407466383 407466345 4.000000e-03 54.7
12 TraesCS3A01G252000 chr5D 80.749 374 44 16 6521 6870 379088257 379087888 4.260000e-67 267.0
13 TraesCS3A01G252000 chr5D 93.023 43 3 0 6903 6945 409996303 409996345 6.000000e-06 63.9
14 TraesCS3A01G252000 chr5D 91.304 46 4 0 6902 6947 453868205 453868160 6.000000e-06 63.9
15 TraesCS3A01G252000 chrUn 83.162 291 39 9 6520 6804 28336053 28335767 2.560000e-64 257.0
16 TraesCS3A01G252000 chr1B 79.452 365 55 18 6520 6870 689826141 689825783 2.580000e-59 241.0
17 TraesCS3A01G252000 chr5B 81.879 298 40 9 6516 6803 478929432 478929725 9.280000e-59 239.0
18 TraesCS3A01G252000 chr5B 81.356 295 37 12 6556 6837 499161360 499161649 2.600000e-54 224.0
19 TraesCS3A01G252000 chr5B 97.297 37 1 0 6905 6941 687879719 687879683 6.000000e-06 63.9
20 TraesCS3A01G252000 chr5A 94.872 39 2 0 6907 6945 521040426 521040464 2.160000e-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 TraesCS3A01G252000 chr3A 471819661 471826820 7159 True 13223.000000 13223 100.000000 1 7160 1 chr3A.!!$R1 7159
1 TraesCS3A01G252000 chr3D 352951292 352958521 7229 True 3729.333333 10418 91.884333 2 7160 3 chr3D.!!$R2 7158
2 TraesCS3A01G252000 chr3B 452106325 452114427 8102 True 1890.800000 5301 90.100600 391 7153 5 chr3B.!!$R3 6762

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
886 1418 0.106519 CTCCGGGGGAGCATTTCAAT 60.107 55.000 0.0 0.0 43.29 2.57 F
1750 2285 0.387239 GCTCGTGTCATGGGTTTTGC 60.387 55.000 0.0 0.0 0.00 3.68 F
2886 3440 1.470098 GCAGTGGGCAAAGTACATGAG 59.530 52.381 0.0 0.0 43.97 2.90 F
4630 5786 1.202405 GGTTTGCTTGTGTCCTGGTTG 60.202 52.381 0.0 0.0 0.00 3.77 F
5059 6216 0.402121 GAAGACTGACTTGCCCCCTT 59.598 55.000 0.0 0.0 39.13 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 2369 0.098376 GCAGCAAGCTAGCATCACAC 59.902 55.000 18.83 0.00 41.15 3.82 R
3452 4011 1.193462 TTTCGGCCTCGGAACCCTTA 61.193 55.000 0.00 0.00 36.95 2.69 R
4875 6032 0.112412 ACCCCCAACAAGCTAACAGG 59.888 55.000 0.00 0.00 0.00 4.00 R
5506 6681 1.542472 TCGTGTCGAGCTCCACATAAA 59.458 47.619 17.41 3.65 0.00 1.40 R
6869 8279 0.029834 AACGCAAAGCAGACAAGCAG 59.970 50.000 0.00 0.00 36.85 4.24 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
31 32 0.179040 GGACGACGAGAGGGAGATCT 60.179 60.000 0.00 0.00 0.00 2.75
74 75 0.548682 ACCATGGTGCCTCTCTTCCT 60.549 55.000 18.99 0.00 0.00 3.36
82 83 0.687354 GCCTCTCTTCCTCACACCAA 59.313 55.000 0.00 0.00 0.00 3.67
141 142 2.124570 CGGTTGGGCCTCATGGAG 60.125 66.667 4.53 0.00 34.57 3.86
157 158 4.587520 AGGTTGCCTCCATCCTCA 57.412 55.556 0.00 0.00 36.64 3.86
186 187 3.046374 GGGAGAGGAAGCCCTATGTTTA 58.954 50.000 0.00 0.00 44.53 2.01
191 192 4.907875 AGAGGAAGCCCTATGTTTATGCTA 59.092 41.667 0.00 0.00 44.53 3.49
193 194 6.044871 AGAGGAAGCCCTATGTTTATGCTAAT 59.955 38.462 0.00 0.00 44.53 1.73
202 203 2.863740 TGTTTATGCTAATCCGTGAGCG 59.136 45.455 0.00 0.00 41.83 5.03
213 214 2.665603 GTGAGCGCTCTTCCCCTT 59.334 61.111 35.27 0.00 0.00 3.95
214 215 1.898154 GTGAGCGCTCTTCCCCTTA 59.102 57.895 35.27 12.31 0.00 2.69
215 216 0.460459 GTGAGCGCTCTTCCCCTTAC 60.460 60.000 35.27 19.97 0.00 2.34
221 222 2.376109 CGCTCTTCCCCTTACTGACTA 58.624 52.381 0.00 0.00 0.00 2.59
226 227 2.615986 TCCCCTTACTGACTACTGCA 57.384 50.000 0.00 0.00 0.00 4.41
238 239 2.366916 GACTACTGCAGCTACCCATCAT 59.633 50.000 15.27 0.00 0.00 2.45
251 252 5.011943 GCTACCCATCATCAAGAGAGAAGAT 59.988 44.000 0.00 0.00 0.00 2.40
258 259 7.233144 CCATCATCAAGAGAGAAGATAAGAGGA 59.767 40.741 0.00 0.00 0.00 3.71
266 267 7.056635 AGAGAGAAGATAAGAGGAGAGAACAG 58.943 42.308 0.00 0.00 0.00 3.16
274 275 5.832539 AAGAGGAGAGAACAGAAAATGGA 57.167 39.130 0.00 0.00 0.00 3.41
286 287 3.873952 CAGAAAATGGAAGGGAGATCGAC 59.126 47.826 0.00 0.00 0.00 4.20
296 297 1.153349 GAGATCGACCAGGTTGGGC 60.153 63.158 7.02 0.00 44.03 5.36
297 298 2.124695 GATCGACCAGGTTGGGCC 60.125 66.667 7.02 0.00 44.91 5.80
309 310 1.760086 TTGGGCCCCACAACAACAG 60.760 57.895 22.27 0.00 30.78 3.16
343 344 0.343372 TCCCCTCCAGCTTCCTACAT 59.657 55.000 0.00 0.00 0.00 2.29
359 360 2.592102 ACATGCCTTTGTCCATGACT 57.408 45.000 7.53 0.00 40.92 3.41
384 385 0.947244 CAAGAGCTTCAACGTGCCTT 59.053 50.000 0.00 0.00 0.00 4.35
414 415 3.018856 GTGATGGACAAATGCCATGAGA 58.981 45.455 12.15 0.00 45.81 3.27
424 425 3.548745 ATGCCATGAGATCGACAAAGA 57.451 42.857 0.00 0.00 0.00 2.52
425 426 3.548745 TGCCATGAGATCGACAAAGAT 57.451 42.857 0.00 0.00 0.00 2.40
426 427 4.670896 TGCCATGAGATCGACAAAGATA 57.329 40.909 0.00 0.00 0.00 1.98
461 462 2.427095 CTGTCACCACACGGATATCTCA 59.573 50.000 2.05 0.00 35.59 3.27
463 464 1.404035 TCACCACACGGATATCTCACG 59.596 52.381 2.05 0.42 35.59 4.35
514 516 4.595538 GTGGTGGACGCGGTGACA 62.596 66.667 12.47 0.00 0.00 3.58
605 607 6.377429 GGGGAAAGAAGTCGAGGATTTAAATT 59.623 38.462 1.43 0.00 0.00 1.82
607 609 7.120726 GGGAAAGAAGTCGAGGATTTAAATTGA 59.879 37.037 1.43 0.00 0.00 2.57
622 624 1.855513 ATTGAACGACGACGAAACCA 58.144 45.000 15.32 3.22 42.66 3.67
822 1352 0.533491 CTTGGCCATGGTTGGTGATG 59.467 55.000 14.67 0.00 45.57 3.07
885 1417 1.302949 CTCCGGGGGAGCATTTCAA 59.697 57.895 0.00 0.00 43.29 2.69
886 1418 0.106519 CTCCGGGGGAGCATTTCAAT 60.107 55.000 0.00 0.00 43.29 2.57
901 1433 9.448294 GAGCATTTCAATAGCAAATAAAGAGAG 57.552 33.333 0.00 0.00 0.00 3.20
903 1435 9.448294 GCATTTCAATAGCAAATAAAGAGAGAG 57.552 33.333 0.00 0.00 0.00 3.20
1128 1662 4.467107 AGCCCCGTCCTCTCCTCC 62.467 72.222 0.00 0.00 0.00 4.30
1175 1709 2.671070 CATCCCCTGAAGCACCGT 59.329 61.111 0.00 0.00 0.00 4.83
1200 1734 2.588620 CTTCCCATCTACTACCTCGCT 58.411 52.381 0.00 0.00 0.00 4.93
1329 1863 1.000843 TGTGTGCGATGCTCTGTTAGT 59.999 47.619 0.00 0.00 0.00 2.24
1419 1953 1.950909 AGACGAGAATCTGATCCCGAC 59.049 52.381 11.38 6.86 0.00 4.79
1509 2043 3.717294 CGTTGGGAGGGAGGGTGG 61.717 72.222 0.00 0.00 0.00 4.61
1541 2075 6.911250 TGATCTGGACTGTACAGTAAAAGA 57.089 37.500 27.98 26.33 42.66 2.52
1543 2077 7.907389 TGATCTGGACTGTACAGTAAAAGATT 58.093 34.615 29.72 20.76 42.66 2.40
1589 2123 5.183228 ACTATTGGTGGTCGAAATAGTTGG 58.817 41.667 11.82 0.00 41.91 3.77
1750 2285 0.387239 GCTCGTGTCATGGGTTTTGC 60.387 55.000 0.00 0.00 0.00 3.68
1832 2369 6.099341 GCTGGTAAAATAGTTGGATTTGGTG 58.901 40.000 0.00 0.00 0.00 4.17
1947 2485 6.044682 GGAAATGCAATTAGCTAAGCACATT 58.955 36.000 19.29 18.58 45.94 2.71
1987 2525 2.353889 CTGTGCAGTTATGTGATGCCTC 59.646 50.000 0.00 0.00 39.22 4.70
1992 2530 3.746751 GCAGTTATGTGATGCCTCCAGAT 60.747 47.826 0.00 0.00 33.81 2.90
2201 2739 2.303311 GTTCTTCCTCTGTTAGGCACCT 59.697 50.000 0.00 0.00 46.10 4.00
2340 2878 9.010029 TCTTCTTAACAATTCCTCCAATGTAAC 57.990 33.333 0.00 0.00 0.00 2.50
2533 3074 8.592155 GTTTGAAGACGGGCATAAATATTTTTC 58.408 33.333 5.91 1.75 0.00 2.29
2619 3167 8.201554 TGAATGATGAATACACTCTTAGCAAC 57.798 34.615 0.00 0.00 0.00 4.17
2705 3253 3.490348 CTGTTTCCTTCACTGGAACCAT 58.510 45.455 0.00 0.00 44.83 3.55
2706 3254 3.221771 TGTTTCCTTCACTGGAACCATG 58.778 45.455 0.00 0.00 44.83 3.66
2729 3277 4.718961 AGTTCCTGGCATGACAATATACC 58.281 43.478 1.11 0.00 0.00 2.73
2751 3302 5.107133 CCAGGCAAGCTAAATCTTGAATTG 58.893 41.667 7.60 2.74 44.61 2.32
2808 3362 6.151985 AGCCATTTGAGTCCTAGATATAGACG 59.848 42.308 0.00 0.00 35.65 4.18
2886 3440 1.470098 GCAGTGGGCAAAGTACATGAG 59.530 52.381 0.00 0.00 43.97 2.90
2902 3456 9.594936 AAGTACATGAGCTTACTCCTAGATATT 57.405 33.333 0.00 0.00 42.74 1.28
2929 3483 8.004801 TCTCCTGTTCTCCAGATACATTGTATA 58.995 37.037 9.27 0.00 44.49 1.47
3007 3561 5.043248 GTGGTCCAATTGTTTCTTCAAGTG 58.957 41.667 4.43 0.00 41.19 3.16
3305 3863 2.885266 CCATTTGAGGAGCATGAGGATG 59.115 50.000 0.00 0.00 0.00 3.51
3317 3875 6.239600 GGAGCATGAGGATGGTATGTAAGTTA 60.240 42.308 0.00 0.00 40.47 2.24
3355 3914 9.345517 CAGATTTTACCATGTTTAATGACACTG 57.654 33.333 0.00 0.00 31.30 3.66
3381 3940 6.886459 TGCTCTAGCTTACCTGATTGAAATTT 59.114 34.615 3.26 0.00 42.66 1.82
3452 4011 3.010250 GGACTGGGTTCAAGGGATAAACT 59.990 47.826 0.00 0.00 0.00 2.66
3462 4021 4.080751 TCAAGGGATAAACTAAGGGTTCCG 60.081 45.833 0.00 0.00 37.12 4.30
3846 4410 8.679288 AATGATCACGAGATGAATTTTCAAAC 57.321 30.769 0.00 0.00 41.93 2.93
3881 4445 4.098914 TGACCAACATAAGGATATGCCC 57.901 45.455 0.00 0.00 42.26 5.36
3979 4543 3.904800 TGACAGACTCAGGTCAACAAA 57.095 42.857 0.00 0.00 44.36 2.83
4138 4702 1.685517 CATGATCCTGGAAGCTCTCGA 59.314 52.381 0.00 0.00 0.00 4.04
4290 4855 5.358725 TGCTCAGGTATACAACTAACATCGA 59.641 40.000 5.01 0.00 0.00 3.59
4479 5635 6.239120 CCTGATCTTTGACATGGTGAAAAAGT 60.239 38.462 0.00 0.00 30.85 2.66
4630 5786 1.202405 GGTTTGCTTGTGTCCTGGTTG 60.202 52.381 0.00 0.00 0.00 3.77
4852 6009 6.574350 ACGAGACTACCAGAATTATGAAAGG 58.426 40.000 0.54 0.00 0.00 3.11
4875 6032 5.808030 GGTTATGAGTGCTGAAGTAGTTCTC 59.192 44.000 11.52 4.42 33.38 2.87
4993 6150 8.603304 TCCTAGGCTTAGTTGAACTTCTAATTT 58.397 33.333 1.97 0.00 0.00 1.82
5020 6177 4.414337 TGCTTAATTGCAAACTGGGTTT 57.586 36.364 1.71 0.00 40.29 3.27
5058 6215 1.492993 GGAAGACTGACTTGCCCCCT 61.493 60.000 0.00 0.00 40.32 4.79
5059 6216 0.402121 GAAGACTGACTTGCCCCCTT 59.598 55.000 0.00 0.00 39.13 3.95
5118 6275 6.559429 TCTCTTCCTAACTAACTACCTGGTT 58.441 40.000 3.84 0.00 0.00 3.67
5146 6303 0.443869 CTGGTGCGACTGTTATGTGC 59.556 55.000 0.00 0.00 0.00 4.57
5179 6336 1.140852 TGAATCCACTCCATTAGGCCG 59.859 52.381 0.00 0.00 33.74 6.13
5238 6413 0.676782 CCCTTCAAACTACGGCAGGG 60.677 60.000 0.00 0.00 35.21 4.45
5241 6416 0.978151 TTCAAACTACGGCAGGGCTA 59.022 50.000 0.00 0.00 0.00 3.93
5273 6448 4.081862 TCCACACGAATCTTAATTCTCCGT 60.082 41.667 0.00 0.00 39.36 4.69
5285 6460 7.103641 TCTTAATTCTCCGTATGGATTATGCC 58.896 38.462 3.55 0.00 45.33 4.40
5291 6466 2.279741 CGTATGGATTATGCCGGGATG 58.720 52.381 20.08 0.00 0.00 3.51
5353 6528 1.768870 CTGGGTAGAGTATTGGTGGGG 59.231 57.143 0.00 0.00 0.00 4.96
5387 6562 1.134220 AGGAAGTCTCGTTGTGCCAAA 60.134 47.619 0.00 0.00 0.00 3.28
5506 6681 6.402550 CGCTGCATCTCAAGTTACAAGTTATT 60.403 38.462 0.00 0.00 0.00 1.40
5524 6699 5.581085 AGTTATTTTATGTGGAGCTCGACAC 59.419 40.000 30.53 21.95 37.41 3.67
5593 6807 2.301346 GGTGGCTGGATCCAAACTATG 58.699 52.381 17.00 3.82 37.96 2.23
5623 6837 6.426587 AGTTTACCAGACATGCAATATCCTT 58.573 36.000 0.00 0.00 0.00 3.36
5625 6839 3.559069 ACCAGACATGCAATATCCTTGG 58.441 45.455 0.00 0.00 0.00 3.61
5634 6848 2.376518 GCAATATCCTTGGATCCCCTCA 59.623 50.000 9.90 0.00 0.00 3.86
5636 6850 4.660168 CAATATCCTTGGATCCCCTCAAG 58.340 47.826 9.90 5.92 39.83 3.02
5851 7080 0.038310 GCAAAGGGTCTAGGCCAGTT 59.962 55.000 16.93 4.94 0.00 3.16
5966 7195 0.257039 AAAGGATCGGCAAGATGGCT 59.743 50.000 2.37 0.00 41.25 4.75
6021 7250 2.690173 GCTCTACGAGCGATGTATGT 57.310 50.000 0.00 0.00 45.85 2.29
6227 7458 1.768275 ACATGGATGGATGGAAGCGTA 59.232 47.619 0.00 0.00 0.00 4.42
6274 7505 2.218759 GCGTGTTGTCTCTGTGTTGTAG 59.781 50.000 0.00 0.00 0.00 2.74
6424 7655 1.940613 GCCGCCTTTTCCTGTATGTAG 59.059 52.381 0.00 0.00 0.00 2.74
6455 7686 2.158900 AGTTTGGTCATATGCTCCCTCG 60.159 50.000 12.12 0.00 0.00 4.63
6456 7687 0.758734 TTGGTCATATGCTCCCTCGG 59.241 55.000 12.12 0.00 0.00 4.63
6457 7688 1.004440 GGTCATATGCTCCCTCGGC 60.004 63.158 0.00 0.00 0.00 5.54
6458 7689 1.748403 GTCATATGCTCCCTCGGCA 59.252 57.895 0.00 0.00 44.05 5.69
6459 7690 0.106708 GTCATATGCTCCCTCGGCAA 59.893 55.000 0.00 0.00 43.14 4.52
6460 7691 0.836606 TCATATGCTCCCTCGGCAAA 59.163 50.000 0.00 0.00 43.14 3.68
6536 7918 2.902608 TGTCTCCTGGGTGAACAGTAT 58.097 47.619 0.00 0.00 36.75 2.12
6605 7987 9.892130 TGTGGTAAAATTTAAGGAATGTTTGTT 57.108 25.926 0.00 0.00 0.00 2.83
6736 8127 3.574284 TTTTTGCCATGACTTCCATCG 57.426 42.857 0.00 0.00 31.94 3.84
6747 8138 4.831107 TGACTTCCATCGATGTGATTTCA 58.169 39.130 23.27 18.64 34.13 2.69
6749 8140 5.525012 TGACTTCCATCGATGTGATTTCATC 59.475 40.000 23.27 10.24 40.29 2.92
6838 8248 7.447374 TTTGATTTTACGGTTCACATCAGAT 57.553 32.000 0.00 0.00 0.00 2.90
6840 8250 5.937540 TGATTTTACGGTTCACATCAGATGT 59.062 36.000 10.53 10.53 46.22 3.06
6850 8260 4.454678 TCACATCAGATGTATTTGAGCCC 58.545 43.478 15.98 0.00 42.70 5.19
6869 8279 1.676006 CCGGGTGCAGAATGGTATTTC 59.324 52.381 0.00 0.00 35.86 2.17
6883 8293 4.144297 TGGTATTTCTGCTTGTCTGCTTT 58.856 39.130 0.00 0.00 0.00 3.51
6885 8295 2.497107 TTTCTGCTTGTCTGCTTTGC 57.503 45.000 0.00 0.00 0.00 3.68
6886 8296 0.308684 TTCTGCTTGTCTGCTTTGCG 59.691 50.000 0.00 0.00 0.00 4.85
6904 8323 4.839668 TGCGTTTTGTTATTAGTGCCTT 57.160 36.364 0.00 0.00 0.00 4.35
6911 8330 9.021863 CGTTTTGTTATTAGTGCCTTTGTTTTA 57.978 29.630 0.00 0.00 0.00 1.52
6958 8377 5.897377 AAATTGGAACGGAGGAAGTATTG 57.103 39.130 0.00 0.00 0.00 1.90
6991 8410 0.704076 AGGGCTGCTTTTGGTGGATA 59.296 50.000 0.00 0.00 0.00 2.59
7032 8451 1.736126 CTGAAATCATGTGACGCTGCT 59.264 47.619 0.00 0.00 0.00 4.24
7100 8548 1.595093 CCGATGGTTGGCCTTTGTCC 61.595 60.000 3.32 0.00 35.27 4.02
7137 8585 0.532115 GCAGATTCGCCCATGGTTTT 59.468 50.000 11.73 0.00 0.00 2.43
7153 8601 0.516877 TTTTTGTCCTCTGCGATGCG 59.483 50.000 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.817084 TCTCGTCGTCCTCTTTTGTCTTA 59.183 43.478 0.00 0.00 0.00 2.10
2 3 2.226912 CTCTCGTCGTCCTCTTTTGTCT 59.773 50.000 0.00 0.00 0.00 3.41
3 4 2.586900 CTCTCGTCGTCCTCTTTTGTC 58.413 52.381 0.00 0.00 0.00 3.18
4 5 1.269998 CCTCTCGTCGTCCTCTTTTGT 59.730 52.381 0.00 0.00 0.00 2.83
5 6 1.402984 CCCTCTCGTCGTCCTCTTTTG 60.403 57.143 0.00 0.00 0.00 2.44
9 10 1.222387 CTCCCTCTCGTCGTCCTCT 59.778 63.158 0.00 0.00 0.00 3.69
10 11 0.179040 ATCTCCCTCTCGTCGTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
11 12 0.179040 GATCTCCCTCTCGTCGTCCT 60.179 60.000 0.00 0.00 0.00 3.85
12 13 0.179040 AGATCTCCCTCTCGTCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
15 16 2.139917 CACTAGATCTCCCTCTCGTCG 58.860 57.143 0.00 0.00 0.00 5.12
31 32 2.646175 GCGGCTGACCTGGTCACTA 61.646 63.158 25.12 5.29 37.67 2.74
51 52 1.448540 GAGAGGCACCATGGTCGTG 60.449 63.158 16.53 5.29 0.00 4.35
52 53 1.194781 AAGAGAGGCACCATGGTCGT 61.195 55.000 16.53 11.59 0.00 4.34
62 63 0.471780 TGGTGTGAGGAAGAGAGGCA 60.472 55.000 0.00 0.00 0.00 4.75
74 75 0.665835 GCGTGTTGGATTTGGTGTGA 59.334 50.000 0.00 0.00 0.00 3.58
82 83 0.250513 GAGAGGGAGCGTGTTGGATT 59.749 55.000 0.00 0.00 0.00 3.01
141 142 0.038166 TTGTGAGGATGGAGGCAACC 59.962 55.000 0.00 0.00 37.17 3.77
144 145 1.300963 GCTTGTGAGGATGGAGGCA 59.699 57.895 0.00 0.00 0.00 4.75
146 147 1.676746 CATGCTTGTGAGGATGGAGG 58.323 55.000 0.58 0.00 45.07 4.30
157 158 0.034670 GCTTCCTCTCCCATGCTTGT 60.035 55.000 0.00 0.00 0.00 3.16
186 187 0.598680 GAGCGCTCACGGATTAGCAT 60.599 55.000 31.91 0.00 38.70 3.79
191 192 1.153549 GGAAGAGCGCTCACGGATT 60.154 57.895 36.87 22.90 40.57 3.01
193 194 3.760035 GGGAAGAGCGCTCACGGA 61.760 66.667 36.87 0.00 40.57 4.69
202 203 3.131400 CAGTAGTCAGTAAGGGGAAGAGC 59.869 52.174 0.00 0.00 0.00 4.09
213 214 2.291346 TGGGTAGCTGCAGTAGTCAGTA 60.291 50.000 16.64 0.00 34.21 2.74
214 215 1.187087 GGGTAGCTGCAGTAGTCAGT 58.813 55.000 16.64 0.00 34.21 3.41
215 216 1.186200 TGGGTAGCTGCAGTAGTCAG 58.814 55.000 16.64 0.00 34.79 3.51
221 222 1.206878 TGATGATGGGTAGCTGCAGT 58.793 50.000 16.64 4.79 0.00 4.40
226 227 3.921104 TCTCTCTTGATGATGGGTAGCT 58.079 45.455 0.00 0.00 0.00 3.32
238 239 7.206789 TCTCTCCTCTTATCTTCTCTCTTGA 57.793 40.000 0.00 0.00 0.00 3.02
251 252 6.935240 TCCATTTTCTGTTCTCTCCTCTTA 57.065 37.500 0.00 0.00 0.00 2.10
258 259 4.599241 TCTCCCTTCCATTTTCTGTTCTCT 59.401 41.667 0.00 0.00 0.00 3.10
266 267 3.206964 GGTCGATCTCCCTTCCATTTTC 58.793 50.000 0.00 0.00 0.00 2.29
274 275 0.905357 CAACCTGGTCGATCTCCCTT 59.095 55.000 0.00 0.00 0.00 3.95
286 287 4.232061 TTGTGGGGCCCAACCTGG 62.232 66.667 30.70 0.00 39.10 4.45
296 297 3.294493 CCGGCTGTTGTTGTGGGG 61.294 66.667 0.00 0.00 0.00 4.96
297 298 2.518349 ACCGGCTGTTGTTGTGGG 60.518 61.111 0.00 0.00 0.00 4.61
302 303 1.227853 GAGGTCACCGGCTGTTGTT 60.228 57.895 0.00 0.00 0.00 2.83
343 344 1.271543 CCTCAGTCATGGACAAAGGCA 60.272 52.381 0.00 0.00 34.60 4.75
359 360 1.412710 ACGTTGAAGCTCTTGACCTCA 59.587 47.619 0.00 0.00 0.00 3.86
384 385 0.032815 TTGTCCATCACGTCGAGCAA 59.967 50.000 0.00 0.00 0.00 3.91
394 395 3.369242 TCTCATGGCATTTGTCCATCA 57.631 42.857 0.00 0.00 42.11 3.07
414 415 7.615582 TGAAATTGAAGCTATCTTTGTCGAT 57.384 32.000 0.00 0.00 31.48 3.59
424 425 6.094603 GTGGTGACAGATGAAATTGAAGCTAT 59.905 38.462 0.00 0.00 44.46 2.97
425 426 5.412594 GTGGTGACAGATGAAATTGAAGCTA 59.587 40.000 0.00 0.00 44.46 3.32
426 427 4.217118 GTGGTGACAGATGAAATTGAAGCT 59.783 41.667 0.00 0.00 44.46 3.74
461 462 2.363795 TCCCTCGAAGATGGGCGT 60.364 61.111 2.54 0.00 42.79 5.68
463 464 2.812619 CCCTCCCTCGAAGATGGGC 61.813 68.421 2.54 0.00 42.79 5.36
548 550 0.249868 CTTCCTCACTTCCACGCACA 60.250 55.000 0.00 0.00 0.00 4.57
584 586 8.015658 CGTTCAATTTAAATCCTCGACTTCTTT 58.984 33.333 0.10 0.00 0.00 2.52
605 607 1.788308 GAATGGTTTCGTCGTCGTTCA 59.212 47.619 1.33 0.00 38.33 3.18
647 652 6.374333 ACATAATTTGTAACTGGCACACCTAG 59.626 38.462 0.00 0.00 36.57 3.02
649 654 5.076873 ACATAATTTGTAACTGGCACACCT 58.923 37.500 0.00 0.00 36.57 4.00
732 737 8.747538 AAGCAAGATATTACTTACCCGAATTT 57.252 30.769 0.00 0.00 0.00 1.82
822 1352 7.793036 ACTCAAAAGGGATAAGTACTCCATAC 58.207 38.462 0.00 0.00 34.24 2.39
885 1417 9.389755 GAGGTTTTCTCTCTCTTTATTTGCTAT 57.610 33.333 0.00 0.00 39.38 2.97
886 1418 7.545965 CGAGGTTTTCTCTCTCTTTATTTGCTA 59.454 37.037 0.00 0.00 40.30 3.49
1128 1662 1.519455 GAGGTCGATGTTGGAGCGG 60.519 63.158 0.00 0.00 37.02 5.52
1175 1709 0.750850 GTAGTAGATGGGAAGCGGCA 59.249 55.000 1.45 0.00 0.00 5.69
1353 1887 3.944123 CCGGTCCGGGAATCACTA 58.056 61.111 23.59 0.00 44.15 2.74
1509 2043 7.766278 ACTGTACAGTCCAGATCATAAAACATC 59.234 37.037 22.95 0.00 36.92 3.06
1589 2123 6.324819 CCATGACCAGTGACAACATAAAATC 58.675 40.000 0.00 0.00 0.00 2.17
1750 2285 0.909623 ATTCCAACCTCCTACACCCG 59.090 55.000 0.00 0.00 0.00 5.28
1832 2369 0.098376 GCAGCAAGCTAGCATCACAC 59.902 55.000 18.83 0.00 41.15 3.82
1889 2426 7.888250 AGGGATCCATAAAAATCACTTCTTC 57.112 36.000 15.23 0.00 31.54 2.87
1947 2485 2.423892 CAGCTCTTACGCTAGAACTCCA 59.576 50.000 0.00 0.00 38.41 3.86
1987 2525 7.429633 ACTTACTCAATCTGAATCGTATCTGG 58.570 38.462 0.00 0.00 0.00 3.86
1992 2530 9.653287 ATCAAAACTTACTCAATCTGAATCGTA 57.347 29.630 0.00 0.00 0.00 3.43
2099 2637 7.865385 GTGAAGTAATTTGCTGGTTAAATGTGA 59.135 33.333 0.00 0.00 0.00 3.58
2158 2696 5.205056 ACAAACTCCCAACTAAAACCATGA 58.795 37.500 0.00 0.00 0.00 3.07
2401 2941 1.396996 CTGGGTTGCGTTTATCGAAGG 59.603 52.381 0.00 0.00 42.86 3.46
2619 3167 9.398170 CGGGCACAATTTAGAATAATATTTCTG 57.602 33.333 0.00 0.00 36.63 3.02
2705 3253 2.885135 ATTGTCATGCCAGGAACTCA 57.115 45.000 0.00 0.00 34.60 3.41
2706 3254 4.757149 GGTATATTGTCATGCCAGGAACTC 59.243 45.833 0.00 0.00 34.60 3.01
2729 3277 5.957798 TCAATTCAAGATTTAGCTTGCCTG 58.042 37.500 2.96 1.35 43.78 4.85
2853 3407 3.952535 GCCCACTGCATAAATTTCTACG 58.047 45.455 0.00 0.00 40.77 3.51
2886 3440 7.533289 ACAGGAGAAATATCTAGGAGTAAGC 57.467 40.000 0.00 0.00 35.54 3.09
2929 3483 9.959721 TTTCTAAGTCTATCTATTGGCTTGTTT 57.040 29.630 2.20 0.00 30.61 2.83
3305 3863 9.148104 CTGAAGGTACAACTTAACTTACATACC 57.852 37.037 0.00 0.00 0.00 2.73
3317 3875 7.724061 ACATGGTAAAATCTGAAGGTACAACTT 59.276 33.333 0.00 0.00 0.00 2.66
3355 3914 4.392921 TCAATCAGGTAAGCTAGAGCAC 57.607 45.455 4.01 0.00 45.16 4.40
3381 3940 3.953712 TTGTCCTGAAAGTCGCAGATA 57.046 42.857 0.00 0.00 40.67 1.98
3452 4011 1.193462 TTTCGGCCTCGGAACCCTTA 61.193 55.000 0.00 0.00 36.95 2.69
3462 4021 2.391389 CGAAGGTGCTTTCGGCCTC 61.391 63.158 0.00 0.00 44.56 4.70
3809 4370 7.282332 TCTCGTGATCATTAGACAGAATCAT 57.718 36.000 0.00 0.00 0.00 2.45
3810 4371 6.699575 TCTCGTGATCATTAGACAGAATCA 57.300 37.500 0.00 0.00 0.00 2.57
3830 4394 7.704789 ACTGCTTTGTTTGAAAATTCATCTC 57.295 32.000 0.00 0.00 37.00 2.75
3846 4410 3.820467 TGTTGGTCATTCCTACTGCTTTG 59.180 43.478 0.00 0.00 41.34 2.77
4138 4702 2.554032 CCATTTGGCTCTTTCAGTTCGT 59.446 45.455 0.00 0.00 0.00 3.85
4290 4855 9.860898 GGAAAATGCTTATAATTCTCACTTGTT 57.139 29.630 0.00 0.00 0.00 2.83
4479 5635 2.557924 GTCATGAAACATGGGCTCACAA 59.442 45.455 0.00 0.00 0.00 3.33
4852 6009 5.808030 GGAGAACTACTTCAGCACTCATAAC 59.192 44.000 0.00 0.00 33.85 1.89
4875 6032 0.112412 ACCCCCAACAAGCTAACAGG 59.888 55.000 0.00 0.00 0.00 4.00
5020 6177 7.844779 AGTCTTCCCTATAAAAGAGACACCATA 59.155 37.037 0.00 0.00 32.40 2.74
5058 6215 9.886132 GTTAGGAAGGTGAGTTATATTCTCAAA 57.114 33.333 10.48 0.74 42.42 2.69
5059 6216 9.268282 AGTTAGGAAGGTGAGTTATATTCTCAA 57.732 33.333 10.48 0.00 42.42 3.02
5118 6275 1.179174 AGTCGCACCAGCAGTAGTCA 61.179 55.000 0.00 0.00 42.27 3.41
5146 6303 3.508793 AGTGGATTCAAACAAGCATGAGG 59.491 43.478 0.00 0.00 0.00 3.86
5179 6336 7.677454 AAATGAAAAGGAAAATTGGAGATGC 57.323 32.000 0.00 0.00 0.00 3.91
5208 6368 5.401674 CGTAGTTTGAAGGGAGAATATACGC 59.598 44.000 0.00 0.00 0.00 4.42
5209 6369 5.919141 CCGTAGTTTGAAGGGAGAATATACG 59.081 44.000 0.00 0.00 33.87 3.06
5210 6370 5.695363 GCCGTAGTTTGAAGGGAGAATATAC 59.305 44.000 0.00 0.00 0.00 1.47
5212 6372 4.163458 TGCCGTAGTTTGAAGGGAGAATAT 59.837 41.667 0.00 0.00 0.00 1.28
5238 6413 5.527582 AGATTCGTGTGGATTTGGTAATAGC 59.472 40.000 0.00 0.00 0.00 2.97
5241 6416 7.931578 TTAAGATTCGTGTGGATTTGGTAAT 57.068 32.000 0.00 0.00 0.00 1.89
5273 6448 1.064758 GGCATCCCGGCATAATCCATA 60.065 52.381 0.00 0.00 40.76 2.74
5285 6460 1.308998 GTAAGGAATGTGGCATCCCG 58.691 55.000 2.00 0.00 36.31 5.14
5291 6466 1.548719 GGGTTTGGTAAGGAATGTGGC 59.451 52.381 0.00 0.00 0.00 5.01
5353 6528 5.013258 AGACTTCCTATACCCCCTGTATC 57.987 47.826 0.00 0.00 40.64 2.24
5387 6562 4.530710 AATCACAACATCTGCTGCAAAT 57.469 36.364 3.02 0.00 0.00 2.32
5506 6681 1.542472 TCGTGTCGAGCTCCACATAAA 59.458 47.619 17.41 3.65 0.00 1.40
5524 6699 6.968131 TTCTCAATACAACCTTGAATCTCG 57.032 37.500 0.00 0.00 32.53 4.04
5593 6807 3.187637 TGCATGTCTGGTAAACTAAACGC 59.812 43.478 0.00 0.00 0.00 4.84
5634 6848 5.305139 ACGTACAAACAAGCTCAAAACTT 57.695 34.783 0.00 0.00 0.00 2.66
5636 6850 6.088350 TCAAAACGTACAAACAAGCTCAAAAC 59.912 34.615 0.00 0.00 0.00 2.43
6021 7250 5.378230 AAATTGCTGGAGGATGAGTATGA 57.622 39.130 0.00 0.00 0.00 2.15
6100 7330 3.867984 GCCTCTCCTCTTGAACCTGAAAG 60.868 52.174 0.00 0.00 0.00 2.62
6424 7655 5.973565 GCATATGACCAAACTTGCATTAGAC 59.026 40.000 6.97 0.00 0.00 2.59
6605 7987 6.514048 TTTCGTGATGAATTTGTGCATACACA 60.514 34.615 0.00 0.00 45.08 3.72
6660 8048 7.647907 ACATTTTCAGAGCATTGATTTTGTC 57.352 32.000 0.00 0.00 0.00 3.18
6661 8049 8.981647 GTAACATTTTCAGAGCATTGATTTTGT 58.018 29.630 0.00 0.00 0.00 2.83
6662 8050 9.199982 AGTAACATTTTCAGAGCATTGATTTTG 57.800 29.630 0.00 0.00 0.00 2.44
6663 8051 9.768662 AAGTAACATTTTCAGAGCATTGATTTT 57.231 25.926 0.00 0.00 0.00 1.82
6664 8052 9.768662 AAAGTAACATTTTCAGAGCATTGATTT 57.231 25.926 0.00 0.00 0.00 2.17
6665 8053 9.415544 GAAAGTAACATTTTCAGAGCATTGATT 57.584 29.630 0.00 0.00 35.22 2.57
6825 8235 5.220931 GGCTCAAATACATCTGATGTGAACC 60.221 44.000 28.67 18.81 44.60 3.62
6833 8243 1.140852 CCCGGGCTCAAATACATCTGA 59.859 52.381 8.08 0.00 0.00 3.27
6838 8248 1.377987 GCACCCGGGCTCAAATACA 60.378 57.895 24.08 0.00 0.00 2.29
6840 8250 1.077787 CTGCACCCGGGCTCAAATA 60.078 57.895 24.08 0.00 34.04 1.40
6850 8260 2.355756 CAGAAATACCATTCTGCACCCG 59.644 50.000 4.31 0.00 46.88 5.28
6869 8279 0.029834 AACGCAAAGCAGACAAGCAG 59.970 50.000 0.00 0.00 36.85 4.24
6877 8287 5.387342 GCACTAATAACAAAACGCAAAGCAG 60.387 40.000 0.00 0.00 0.00 4.24
6883 8293 4.839668 AAGGCACTAATAACAAAACGCA 57.160 36.364 0.00 0.00 38.49 5.24
6885 8295 7.458038 AAACAAAGGCACTAATAACAAAACG 57.542 32.000 0.00 0.00 38.49 3.60
6917 8336 8.248945 TCCAATTTAAACTAAAACCACGACAAA 58.751 29.630 0.00 0.00 0.00 2.83
6958 8377 1.172812 AGCCCTCACTTCCGCAAAAC 61.173 55.000 0.00 0.00 0.00 2.43
6991 8410 3.510360 AGATCACAGGCTGTACGTTAAGT 59.490 43.478 21.59 0.05 0.00 2.24
7100 8548 3.569701 TCTGCTTTTAGGTGCCTTCTTTG 59.430 43.478 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.