Multiple sequence alignment - TraesCS1B01G456200

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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 TraesCS1B01G456200 chr1B 100.000 3979 0 0 1 3979 670898473 670902451 0.000000e+00 7348.0
1 TraesCS1B01G456200 chr1B 87.099 1744 196 22 1718 3449 670947538 670949264 0.000000e+00 1947.0
2 TraesCS1B01G456200 chr1B 84.897 1993 228 35 1452 3427 670957005 670958941 0.000000e+00 1945.0
3 TraesCS1B01G456200 chr1B 87.439 1433 156 9 1723 3134 670917383 670918812 0.000000e+00 1628.0
4 TraesCS1B01G456200 chr1B 87.755 539 65 1 1149 1686 670916769 670917307 2.610000e-176 628.0
5 TraesCS1B01G456200 chr1B 84.778 427 47 13 13 430 670945651 670946068 2.860000e-111 412.0
6 TraesCS1B01G456200 chr1B 82.750 400 52 11 3166 3558 670918810 670919199 1.370000e-89 340.0
7 TraesCS1B01G456200 chr1B 84.112 214 18 6 720 917 670946420 670946633 4.060000e-45 193.0
8 TraesCS1B01G456200 chr1B 81.395 215 20 7 423 625 670946213 670946419 1.480000e-34 158.0
9 TraesCS1B01G456200 chr1B 84.375 64 10 0 1189 1252 670274412 670274349 3.320000e-06 63.9
10 TraesCS1B01G456200 chrUn 94.325 2643 142 5 1300 3936 1926840 1929480 0.000000e+00 4043.0
11 TraesCS1B01G456200 chrUn 87.299 3173 316 40 573 3728 1822770 1825872 0.000000e+00 3546.0
12 TraesCS1B01G456200 chrUn 88.229 1954 217 12 1174 3115 1944240 1946192 0.000000e+00 2322.0
13 TraesCS1B01G456200 chrUn 85.729 946 77 22 423 1356 1925952 1926851 0.000000e+00 946.0
14 TraesCS1B01G456200 chrUn 95.062 81 4 0 117 197 1818697 1818777 1.160000e-25 128.0
15 TraesCS1B01G456200 chrUn 81.646 158 26 3 261 416 116432598 116432754 1.160000e-25 128.0
16 TraesCS1B01G456200 chrUn 93.182 44 3 0 3936 3979 268464919 268464876 9.230000e-07 65.8
17 TraesCS1B01G456200 chrUn 93.182 44 3 0 3936 3979 288951379 288951422 9.230000e-07 65.8
18 TraesCS1B01G456200 chr1D 90.152 2701 188 22 407 3091 482368744 482371382 0.000000e+00 3443.0
19 TraesCS1B01G456200 chr1D 90.905 2474 198 10 1258 3729 482323691 482326139 0.000000e+00 3297.0
20 TraesCS1B01G456200 chr1D 88.191 1973 219 9 1151 3118 482517366 482515403 0.000000e+00 2340.0
21 TraesCS1B01G456200 chr1D 86.391 1668 194 19 1452 3116 482492939 482491302 0.000000e+00 1792.0
22 TraesCS1B01G456200 chr1D 80.428 654 61 23 573 1222 482323098 482323688 1.700000e-118 436.0
23 TraesCS1B01G456200 chr1D 82.082 413 44 17 1 410 482356806 482357191 3.830000e-85 326.0
24 TraesCS1B01G456200 chr1D 79.368 475 60 22 654 1110 482517828 482517374 2.320000e-77 300.0
25 TraesCS1B01G456200 chr1D 78.788 231 29 13 40 267 482522575 482522362 1.930000e-28 137.0
26 TraesCS1B01G456200 chr1D 93.827 81 5 0 117 197 482322746 482322826 5.400000e-24 122.0
27 TraesCS1B01G456200 chr1A 85.053 1987 230 34 1452 3427 579575778 579573848 0.000000e+00 1962.0
28 TraesCS1B01G456200 chr6B 85.185 162 21 3 257 416 683376066 683376226 3.180000e-36 163.0
29 TraesCS1B01G456200 chr6B 84.314 153 22 2 266 416 700776477 700776629 8.910000e-32 148.0
30 TraesCS1B01G456200 chr6B 83.582 134 18 4 284 414 146665294 146665162 5.400000e-24 122.0
31 TraesCS1B01G456200 chr2A 84.286 140 18 4 280 416 2959020 2959158 2.490000e-27 134.0
32 TraesCS1B01G456200 chr5D 81.646 158 22 7 276 430 509956208 509956055 1.500000e-24 124.0
33 TraesCS1B01G456200 chr4D 80.892 157 22 6 265 416 463336495 463336342 2.510000e-22 117.0
34 TraesCS1B01G456200 chr7B 79.630 162 27 6 264 420 633671899 633672059 1.170000e-20 111.0
35 TraesCS1B01G456200 chr4A 84.615 78 10 2 3547 3624 3002583 3002658 4.260000e-10 76.8
36 TraesCS1B01G456200 chr4A 93.182 44 3 0 3936 3979 714906438 714906395 9.230000e-07 65.8


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 TraesCS1B01G456200 chr1B 670898473 670902451 3978 False 7348.000000 7348 100.000000 1 3979 1 chr1B.!!$F1 3978
1 TraesCS1B01G456200 chr1B 670957005 670958941 1936 False 1945.000000 1945 84.897000 1452 3427 1 chr1B.!!$F2 1975
2 TraesCS1B01G456200 chr1B 670916769 670919199 2430 False 865.333333 1628 85.981333 1149 3558 3 chr1B.!!$F3 2409
3 TraesCS1B01G456200 chr1B 670945651 670949264 3613 False 677.500000 1947 84.346000 13 3449 4 chr1B.!!$F4 3436
4 TraesCS1B01G456200 chrUn 1925952 1929480 3528 False 2494.500000 4043 90.027000 423 3936 2 chrUn.!!$F5 3513
5 TraesCS1B01G456200 chrUn 1944240 1946192 1952 False 2322.000000 2322 88.229000 1174 3115 1 chrUn.!!$F1 1941
6 TraesCS1B01G456200 chrUn 1818697 1825872 7175 False 1837.000000 3546 91.180500 117 3728 2 chrUn.!!$F4 3611
7 TraesCS1B01G456200 chr1D 482368744 482371382 2638 False 3443.000000 3443 90.152000 407 3091 1 chr1D.!!$F2 2684
8 TraesCS1B01G456200 chr1D 482491302 482492939 1637 True 1792.000000 1792 86.391000 1452 3116 1 chr1D.!!$R1 1664
9 TraesCS1B01G456200 chr1D 482515403 482517828 2425 True 1320.000000 2340 83.779500 654 3118 2 chr1D.!!$R3 2464
10 TraesCS1B01G456200 chr1D 482322746 482326139 3393 False 1285.000000 3297 88.386667 117 3729 3 chr1D.!!$F3 3612
11 TraesCS1B01G456200 chr1A 579573848 579575778 1930 True 1962.000000 1962 85.053000 1452 3427 1 chr1A.!!$R1 1975

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
547 4464 1.243902 GCACAAGAATTTCGTCCCCA 58.756 50.0 0.0 0.0 0.00 4.96 F
1103 5152 0.385598 CTTCGTGTCTCGTCGCAGAA 60.386 55.0 0.0 0.0 39.69 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 6105 0.827507 AAGGCACATTCCAAAGGCGT 60.828 50.0 0.00 0.0 0.00 5.68 R
3002 7301 0.527113 TAAGCTAGCCGTGCGTACAA 59.473 50.0 12.13 0.0 35.28 2.41 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
25 26 1.429423 GCAAAGCTCACATACGCCC 59.571 57.895 0.00 0.00 0.00 6.13
33 34 2.203153 ACATACGCCCGGGCAATC 60.203 61.111 42.78 16.34 42.06 2.67
210 3968 3.689161 TCTTTGCACCCATTAATCTGTCG 59.311 43.478 0.00 0.00 0.00 4.35
213 3971 1.593006 GCACCCATTAATCTGTCGTCG 59.407 52.381 0.00 0.00 0.00 5.12
225 3984 6.542574 AATCTGTCGTCGTCCTAGTATTAG 57.457 41.667 0.00 0.00 0.00 1.73
278 4039 8.948145 ACAGGTATATAGTACTCGCTCTATTTG 58.052 37.037 0.00 0.00 0.00 2.32
293 4054 8.988934 TCGCTCTATTTGTAAATATAAGCCTTG 58.011 33.333 17.29 9.85 36.83 3.61
326 4088 7.977789 TTAATACGGACTACATACGGATGTA 57.022 36.000 19.32 19.32 44.77 2.29
366 4128 8.854614 AGAGTGTAGATTCACTTATTTTGCTT 57.145 30.769 0.98 0.00 46.81 3.91
374 4136 7.803189 AGATTCACTTATTTTGCTTTGTACGTG 59.197 33.333 0.00 0.00 0.00 4.49
377 4139 5.623673 CACTTATTTTGCTTTGTACGTGGTC 59.376 40.000 0.00 0.00 0.00 4.02
384 4147 4.570930 TGCTTTGTACGTGGTCATATTGA 58.429 39.130 0.00 0.00 0.00 2.57
385 4148 4.998033 TGCTTTGTACGTGGTCATATTGAA 59.002 37.500 0.00 0.00 0.00 2.69
390 4153 7.915293 TTGTACGTGGTCATATTGAAATCTT 57.085 32.000 0.00 0.00 0.00 2.40
431 4346 6.370186 AGGAACGGGGAGAATATTATTACC 57.630 41.667 0.00 0.00 0.00 2.85
485 4400 2.864946 CGAGCTCTCCATCACAATTCAG 59.135 50.000 12.85 0.00 0.00 3.02
516 4431 1.884075 AAGTCGAGGCCGTGTGCATA 61.884 55.000 0.00 0.00 43.89 3.14
517 4432 2.165301 GTCGAGGCCGTGTGCATAC 61.165 63.158 3.05 3.05 43.89 2.39
518 4433 2.125713 CGAGGCCGTGTGCATACA 60.126 61.111 14.34 0.00 43.89 2.29
547 4464 1.243902 GCACAAGAATTTCGTCCCCA 58.756 50.000 0.00 0.00 0.00 4.96
553 4470 3.669939 AGAATTTCGTCCCCATGGATT 57.330 42.857 15.22 2.36 44.28 3.01
558 4475 1.506025 TCGTCCCCATGGATTCATCA 58.494 50.000 15.22 0.00 44.28 3.07
757 4733 2.124570 GTGCGTGCCTCATCCCAT 60.125 61.111 0.00 0.00 0.00 4.00
767 4744 3.860605 CATCCCATCCCGTGCCGA 61.861 66.667 0.00 0.00 0.00 5.54
768 4745 2.849162 ATCCCATCCCGTGCCGAT 60.849 61.111 0.00 0.00 0.00 4.18
783 4760 2.581354 GATGCCGCTGACCTGACT 59.419 61.111 0.00 0.00 0.00 3.41
853 4849 4.521062 GCCGAGCATGCGTCCTCT 62.521 66.667 13.01 0.00 0.00 3.69
908 4906 1.277739 CCACGATGCGATGCACATC 59.722 57.895 5.86 5.86 43.04 3.06
984 5004 2.183046 GCGGTGGAGACAGAGAGC 59.817 66.667 0.00 0.00 44.46 4.09
1042 5083 1.635817 CCAGATGGTGGGGGTACTGG 61.636 65.000 0.00 0.00 43.63 4.00
1093 5134 1.587054 CCGCTTCTCCTTCGTGTCT 59.413 57.895 0.00 0.00 0.00 3.41
1102 5151 1.206831 CTTCGTGTCTCGTCGCAGA 59.793 57.895 0.00 0.00 40.80 4.26
1103 5152 0.385598 CTTCGTGTCTCGTCGCAGAA 60.386 55.000 0.00 0.00 39.69 3.02
1122 5171 1.874915 CGCCGGCGTTTCTTCGATA 60.875 57.895 39.71 0.00 34.35 2.92
1167 5216 2.352805 GGCAGGACCACCAAGGAG 59.647 66.667 0.00 0.00 41.22 3.69
1170 5219 2.936032 AGGACCACCAAGGAGGCC 60.936 66.667 0.00 0.00 43.14 5.19
1172 5221 3.637273 GACCACCAAGGAGGCCGT 61.637 66.667 0.00 0.00 43.14 5.68
1269 5318 3.803082 CTCGCCATGCCACCGTTG 61.803 66.667 0.00 0.00 0.00 4.10
1336 5430 1.006571 GTGTTGAAGGTCGAGCGGA 60.007 57.895 9.28 0.00 0.00 5.54
1350 5444 4.096003 CGGATTCACCACCCGGCT 62.096 66.667 0.00 0.00 39.59 5.52
1410 5504 0.393077 CGTCCTTGGTGGTCAGAGTT 59.607 55.000 0.00 0.00 37.07 3.01
1728 6014 7.981102 ACCACTCCTTACTAAAACATCTTTC 57.019 36.000 0.00 0.00 0.00 2.62
1819 6105 0.181114 CTGCTCCGATTCCCCATCAA 59.819 55.000 0.00 0.00 0.00 2.57
1829 6115 1.304052 CCCCATCAACGCCTTTGGA 60.304 57.895 0.00 0.00 35.69 3.53
1988 6274 6.903534 TCTCCATCACCTACCTTCTAAAGATT 59.096 38.462 0.00 0.00 0.00 2.40
2201 6487 2.675423 TCTAGTGGTGAGCGGCGT 60.675 61.111 9.37 0.00 0.00 5.68
2444 6730 0.745845 CTAGCGTTGCTTCCATGGCT 60.746 55.000 6.96 0.00 40.44 4.75
2531 6817 1.170919 ACGTGTCTCTAGTGGTGCGT 61.171 55.000 0.00 0.00 0.00 5.24
2564 6850 0.250770 GGGGGTTCAAGTTCTCGCTT 60.251 55.000 0.00 0.00 0.00 4.68
2633 6919 3.742882 CGGTGTTATATGCATCAGAGGTG 59.257 47.826 0.19 0.00 0.00 4.00
2929 7221 0.679505 AGCTACAAGACGAGTGGCAA 59.320 50.000 10.30 0.00 44.71 4.52
2994 7287 0.535335 TTAGGAGGTCCATGCACGAC 59.465 55.000 7.14 7.14 38.89 4.34
3119 7440 4.141620 ACATAGTTGCAGATTAGGAGTGGG 60.142 45.833 0.00 0.00 0.00 4.61
3137 7460 1.065551 GGGCCGTGAGCAATTTACATC 59.934 52.381 0.00 0.00 46.50 3.06
3265 7596 8.428186 ACTCTATTCTCGTCTCAAGTAACTAG 57.572 38.462 0.00 0.00 0.00 2.57
3269 7600 6.872628 TTCTCGTCTCAAGTAACTAGACAA 57.127 37.500 0.00 0.00 39.69 3.18
3340 7680 3.546724 TGGCTTAGTGTGTTGCAACTTA 58.453 40.909 28.61 15.52 0.00 2.24
3341 7681 3.314080 TGGCTTAGTGTGTTGCAACTTAC 59.686 43.478 28.61 24.52 0.00 2.34
3342 7682 3.314080 GGCTTAGTGTGTTGCAACTTACA 59.686 43.478 28.61 22.19 0.00 2.41
3343 7683 4.201970 GGCTTAGTGTGTTGCAACTTACAA 60.202 41.667 28.61 19.45 0.00 2.41
3344 7684 4.733405 GCTTAGTGTGTTGCAACTTACAAC 59.267 41.667 28.61 18.58 46.05 3.32
3432 7776 2.095853 CCGTGACATGCTTTCCACATAC 59.904 50.000 0.00 0.00 0.00 2.39
3436 7780 2.749076 GACATGCTTTCCACATACTGCA 59.251 45.455 0.00 0.00 34.88 4.41
3453 7797 2.693074 CTGCACAAAACCAAGGTTACCT 59.307 45.455 4.68 0.00 37.35 3.08
3464 7809 0.978146 AGGTTACCTCTGATGGCGCT 60.978 55.000 7.64 0.00 0.00 5.92
3471 7817 1.005340 CTCTGATGGCGCTTTCTCAC 58.995 55.000 7.64 0.00 0.00 3.51
3477 7823 1.508632 TGGCGCTTTCTCACACTTAC 58.491 50.000 7.64 0.00 0.00 2.34
3627 7973 2.248248 GGATACAGACGGGATCATGGA 58.752 52.381 0.00 0.00 0.00 3.41
3697 8043 1.270305 TGCTAACCTATCAGCATCGGC 60.270 52.381 0.00 0.00 42.68 5.54
3749 8095 2.009774 CGATTCGAAGCAGGTGGAAAT 58.990 47.619 14.56 0.00 0.00 2.17
3753 8099 1.071542 TCGAAGCAGGTGGAAATGACA 59.928 47.619 0.00 0.00 0.00 3.58
3762 8108 5.356751 GCAGGTGGAAATGACATACACAATA 59.643 40.000 15.44 0.00 33.91 1.90
3772 8118 6.753107 TGACATACACAATAAGAGTCGAGA 57.247 37.500 0.00 0.00 0.00 4.04
3807 8153 8.802267 TCAATTAAAACCTAGCTTTGCTTACAT 58.198 29.630 0.00 0.00 40.44 2.29
3835 8181 0.473501 GCCCTCATCCCATCTCCTCT 60.474 60.000 0.00 0.00 0.00 3.69
3843 8189 0.332632 CCCATCTCCTCTTTTGGGCA 59.667 55.000 0.00 0.00 42.23 5.36
3849 8195 2.242196 TCTCCTCTTTTGGGCATTAGGG 59.758 50.000 0.00 0.00 0.00 3.53
3873 8220 1.544759 CCGGAAGTAGGCTTTTGGTGT 60.545 52.381 0.00 0.00 34.61 4.16
3875 8222 2.583143 GGAAGTAGGCTTTTGGTGTGT 58.417 47.619 0.00 0.00 34.61 3.72
3884 8231 2.806244 GCTTTTGGTGTGTCGTGTCTAT 59.194 45.455 0.00 0.00 0.00 1.98
3893 8240 4.857588 GTGTGTCGTGTCTATTAGTTCTGG 59.142 45.833 0.00 0.00 0.00 3.86
3901 8248 5.986135 GTGTCTATTAGTTCTGGCTACCATG 59.014 44.000 0.00 0.00 30.82 3.66
3910 8257 2.093500 TCTGGCTACCATGCAGTTACTG 60.093 50.000 8.18 8.18 30.82 2.74
3938 8285 3.001395 CGTATGGCTCGGAACTAAGAG 57.999 52.381 0.00 0.00 37.54 2.85
3939 8286 2.287668 CGTATGGCTCGGAACTAAGAGG 60.288 54.545 0.00 0.00 35.19 3.69
3942 8289 3.354131 GCTCGGAACTAAGAGGCTG 57.646 57.895 0.00 0.00 35.19 4.85
3943 8290 0.533032 GCTCGGAACTAAGAGGCTGT 59.467 55.000 0.00 0.00 35.19 4.40
3944 8291 1.066787 GCTCGGAACTAAGAGGCTGTT 60.067 52.381 1.39 1.39 35.19 3.16
3945 8292 2.613223 GCTCGGAACTAAGAGGCTGTTT 60.613 50.000 0.90 0.00 35.19 2.83
3946 8293 2.996621 CTCGGAACTAAGAGGCTGTTTG 59.003 50.000 0.90 2.91 0.00 2.93
3947 8294 2.076863 CGGAACTAAGAGGCTGTTTGG 58.923 52.381 0.90 0.00 0.00 3.28
3948 8295 2.289444 CGGAACTAAGAGGCTGTTTGGA 60.289 50.000 0.90 0.00 0.00 3.53
3949 8296 3.619979 CGGAACTAAGAGGCTGTTTGGAT 60.620 47.826 0.90 0.00 0.00 3.41
3950 8297 3.942115 GGAACTAAGAGGCTGTTTGGATC 59.058 47.826 0.90 4.06 0.00 3.36
3951 8298 3.252974 ACTAAGAGGCTGTTTGGATCG 57.747 47.619 0.90 0.00 0.00 3.69
3952 8299 1.936547 CTAAGAGGCTGTTTGGATCGC 59.063 52.381 0.90 0.00 0.00 4.58
3953 8300 0.036732 AAGAGGCTGTTTGGATCGCA 59.963 50.000 0.00 0.00 0.00 5.10
3954 8301 0.392193 AGAGGCTGTTTGGATCGCAG 60.392 55.000 0.00 0.00 0.00 5.18
3956 8303 2.486966 GCTGTTTGGATCGCAGCC 59.513 61.111 14.97 0.00 46.93 4.85
3957 8304 3.056313 GCTGTTTGGATCGCAGCCC 62.056 63.158 14.97 0.00 46.93 5.19
3958 8305 1.377725 CTGTTTGGATCGCAGCCCT 60.378 57.895 0.00 0.00 0.00 5.19
3959 8306 1.372087 CTGTTTGGATCGCAGCCCTC 61.372 60.000 0.00 0.00 0.00 4.30
3960 8307 2.125147 TTTGGATCGCAGCCCTCG 60.125 61.111 0.00 0.00 0.00 4.63
3961 8308 3.680620 TTTGGATCGCAGCCCTCGG 62.681 63.158 0.00 0.00 0.00 4.63
3978 8325 3.704151 GCAGCCCAGCCAGAAAAT 58.296 55.556 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.957395 ATGTGAGCTTTGCCTCCGTG 60.957 55.000 0.00 0.00 0.00 4.94
1 2 0.613260 TATGTGAGCTTTGCCTCCGT 59.387 50.000 0.00 0.00 0.00 4.69
2 3 1.009829 GTATGTGAGCTTTGCCTCCG 58.990 55.000 0.00 0.00 0.00 4.63
3 4 1.009829 CGTATGTGAGCTTTGCCTCC 58.990 55.000 0.00 0.00 0.00 4.30
4 5 0.375106 GCGTATGTGAGCTTTGCCTC 59.625 55.000 0.00 0.00 0.00 4.70
5 6 1.026718 GGCGTATGTGAGCTTTGCCT 61.027 55.000 0.00 0.00 38.00 4.75
6 7 1.429423 GGCGTATGTGAGCTTTGCC 59.571 57.895 0.00 0.00 0.00 4.52
7 8 1.429423 GGGCGTATGTGAGCTTTGC 59.571 57.895 0.00 0.00 0.00 3.68
8 9 1.705337 CCGGGCGTATGTGAGCTTTG 61.705 60.000 0.00 0.00 0.00 2.77
9 10 1.449601 CCGGGCGTATGTGAGCTTT 60.450 57.895 0.00 0.00 0.00 3.51
10 11 2.186903 CCGGGCGTATGTGAGCTT 59.813 61.111 0.00 0.00 0.00 3.74
11 12 3.849951 CCCGGGCGTATGTGAGCT 61.850 66.667 8.08 0.00 0.00 4.09
33 34 3.046390 GGAAGCTCTCATCAATCGTACG 58.954 50.000 9.53 9.53 0.00 3.67
170 175 6.589523 TGCAAAGAATAAAATGGTGCATGTAC 59.410 34.615 5.22 5.22 35.72 2.90
264 4025 9.635520 GGCTTATATTTACAAATAGAGCGAGTA 57.364 33.333 17.56 0.00 40.80 2.59
265 4026 8.368668 AGGCTTATATTTACAAATAGAGCGAGT 58.631 33.333 17.56 9.00 40.80 4.18
296 4058 8.250332 TCCGTATGTAGTCCGTATTAAAAACTT 58.750 33.333 0.00 0.00 0.00 2.66
299 4061 8.196771 ACATCCGTATGTAGTCCGTATTAAAAA 58.803 33.333 0.00 0.00 44.66 1.94
353 4115 5.516090 ACCACGTACAAAGCAAAATAAGTG 58.484 37.500 0.00 0.00 0.00 3.16
355 4117 5.753744 TGACCACGTACAAAGCAAAATAAG 58.246 37.500 0.00 0.00 0.00 1.73
357 4119 5.950758 ATGACCACGTACAAAGCAAAATA 57.049 34.783 0.00 0.00 0.00 1.40
366 4128 7.915293 AAGATTTCAATATGACCACGTACAA 57.085 32.000 0.00 0.00 0.00 2.41
416 4179 6.195600 TGGTGGGTGGTAATAATATTCTCC 57.804 41.667 0.00 0.00 0.00 3.71
431 4346 1.610086 ATGCATGGGTTGGTGGGTG 60.610 57.895 0.00 0.00 0.00 4.61
485 4400 1.134965 CCTCGACTTGGACAGATGGTC 60.135 57.143 0.00 0.00 46.20 4.02
516 4431 0.315886 TCTTGTGCGTGTATCGGTGT 59.684 50.000 0.00 0.00 40.26 4.16
517 4432 1.424403 TTCTTGTGCGTGTATCGGTG 58.576 50.000 0.00 0.00 40.26 4.94
518 4433 2.380084 ATTCTTGTGCGTGTATCGGT 57.620 45.000 0.00 0.00 40.26 4.69
519 4434 3.670203 GAAATTCTTGTGCGTGTATCGG 58.330 45.455 0.00 0.00 40.26 4.18
520 4435 3.181534 ACGAAATTCTTGTGCGTGTATCG 60.182 43.478 0.00 0.00 43.12 2.92
521 4436 4.322101 ACGAAATTCTTGTGCGTGTATC 57.678 40.909 0.00 0.00 33.52 2.24
522 4437 3.124636 GGACGAAATTCTTGTGCGTGTAT 59.875 43.478 0.00 0.00 35.09 2.29
523 4438 2.477375 GGACGAAATTCTTGTGCGTGTA 59.523 45.455 0.00 0.00 35.09 2.90
524 4439 1.263217 GGACGAAATTCTTGTGCGTGT 59.737 47.619 0.00 0.00 35.09 4.49
547 4464 0.819259 CCGGCGGTTGATGAATCCAT 60.819 55.000 19.97 0.00 35.29 3.41
553 4470 4.090588 GTCCCCGGCGGTTGATGA 62.091 66.667 26.32 10.05 0.00 2.92
637 4597 2.645567 CGTCACCGTCAGCAGTCT 59.354 61.111 0.00 0.00 0.00 3.24
657 4625 2.421619 GCCATTGCTACAGAGATAGCC 58.578 52.381 2.51 0.00 45.95 3.93
767 4744 1.517832 GTAGTCAGGTCAGCGGCAT 59.482 57.895 1.45 0.00 0.00 4.40
768 4745 2.646175 GGTAGTCAGGTCAGCGGCA 61.646 63.158 1.45 0.00 0.00 5.69
840 4836 1.729470 CCGAGTAGAGGACGCATGCT 61.729 60.000 17.13 2.38 0.00 3.79
843 4839 2.491022 GCCCGAGTAGAGGACGCAT 61.491 63.158 0.00 0.00 0.00 4.73
853 4849 1.491668 ATACACACATGGCCCGAGTA 58.508 50.000 0.00 0.00 0.00 2.59
908 4906 1.021390 GGTGACTGGCGAGTGAATGG 61.021 60.000 5.94 0.00 30.16 3.16
1312 5361 2.853914 GACCTTCAACACGCTCGC 59.146 61.111 0.00 0.00 0.00 5.03
1322 5416 0.108804 GTGAATCCGCTCGACCTTCA 60.109 55.000 0.00 0.00 0.00 3.02
1336 5430 2.034066 CACAGCCGGGTGGTGAAT 59.966 61.111 34.98 13.26 45.48 2.57
1437 5531 4.393155 TCCCGCATGCTGTCGCTT 62.393 61.111 17.13 0.00 36.97 4.68
1728 6014 6.149308 TGCAAGTTCACATGGTTATTAGACAG 59.851 38.462 0.00 0.00 0.00 3.51
1819 6105 0.827507 AAGGCACATTCCAAAGGCGT 60.828 50.000 0.00 0.00 0.00 5.68
1829 6115 2.629656 GCTCACGCCAAGGCACATT 61.630 57.895 12.19 0.00 42.06 2.71
1988 6274 1.342174 ACGGCCTCGAAGTAGAAAACA 59.658 47.619 0.00 0.00 40.11 2.83
2141 6427 2.284625 TCGAGGCACAGGATGGGT 60.285 61.111 0.00 0.00 45.57 4.51
2201 6487 2.043939 TGGGTTGGCTACCTTAGAGAGA 59.956 50.000 17.47 0.00 46.86 3.10
2444 6730 1.285078 TCTCCAGAGATCCTCGTCCAA 59.715 52.381 0.00 0.00 35.36 3.53
2531 6817 4.440808 TGAACCCCCTAAAGAGGTTGATA 58.559 43.478 8.57 0.00 43.88 2.15
2564 6850 2.359354 GTGTACGCCCACCATGCA 60.359 61.111 0.00 0.00 0.00 3.96
2633 6919 1.577328 CCCGTGTCAGCATGTTGTCC 61.577 60.000 9.54 2.63 37.40 4.02
2666 6952 2.028130 ACAACGGCAATTCCTGACAAA 58.972 42.857 0.00 0.00 28.94 2.83
2828 7114 3.582208 AGAGAACAAGCTCCTTGACATCT 59.418 43.478 11.56 10.74 43.42 2.90
2855 7141 6.934083 GCTTGGAATTGGAACTAAAATTTGGA 59.066 34.615 0.00 0.00 0.00 3.53
2929 7221 1.679305 ACAGGAGACTCGCCGACAT 60.679 57.895 0.00 0.00 40.21 3.06
2957 7249 2.038387 AACACTTTGCTCTTCCGTGT 57.962 45.000 0.00 0.00 40.22 4.49
3002 7301 0.527113 TAAGCTAGCCGTGCGTACAA 59.473 50.000 12.13 0.00 35.28 2.41
3119 7440 1.856014 GCGATGTAAATTGCTCACGGC 60.856 52.381 0.00 0.00 42.22 5.68
3137 7460 6.019559 CCGACAATTATATCACTATCATGGCG 60.020 42.308 0.00 0.00 0.00 5.69
3265 7596 5.163457 TGTCCTTCCAATTTTCAGGTTTGTC 60.163 40.000 0.00 0.00 0.00 3.18
3269 7600 6.099557 TGAAATGTCCTTCCAATTTTCAGGTT 59.900 34.615 0.00 0.00 31.53 3.50
3340 7680 5.762279 TGAAAACCTCCCTTCTAAAGTTGT 58.238 37.500 0.00 0.00 0.00 3.32
3341 7681 6.709018 TTGAAAACCTCCCTTCTAAAGTTG 57.291 37.500 0.00 0.00 0.00 3.16
3342 7682 6.895756 ACTTTGAAAACCTCCCTTCTAAAGTT 59.104 34.615 0.00 0.00 33.77 2.66
3343 7683 6.432581 ACTTTGAAAACCTCCCTTCTAAAGT 58.567 36.000 0.00 0.00 33.29 2.66
3344 7684 6.961360 ACTTTGAAAACCTCCCTTCTAAAG 57.039 37.500 0.00 0.00 32.28 1.85
3432 7776 2.693074 AGGTAACCTTGGTTTTGTGCAG 59.307 45.455 10.52 0.00 37.17 4.41
3436 7780 4.513406 TCAGAGGTAACCTTGGTTTTGT 57.487 40.909 10.52 0.00 31.76 2.83
3453 7797 0.321346 TGTGAGAAAGCGCCATCAGA 59.679 50.000 2.29 0.00 0.00 3.27
3464 7809 6.116806 TGTAAGCAAAGGTAAGTGTGAGAAA 58.883 36.000 0.00 0.00 0.00 2.52
3616 7962 0.249489 GTCCGAACTCCATGATCCCG 60.249 60.000 0.00 0.00 0.00 5.14
3697 8043 2.734606 TGAAGTTATGGAGCAACGAACG 59.265 45.455 0.00 0.00 0.00 3.95
3749 8095 6.753107 TCTCGACTCTTATTGTGTATGTCA 57.247 37.500 0.00 0.00 0.00 3.58
3753 8099 9.877178 AGAAAAATCTCGACTCTTATTGTGTAT 57.123 29.630 0.00 0.00 0.00 2.29
3807 8153 0.839946 GGGATGAGGGCTCTTTGCTA 59.160 55.000 0.00 0.00 42.39 3.49
3835 8181 1.888826 CGGTGACCCTAATGCCCAAAA 60.889 52.381 0.00 0.00 0.00 2.44
3843 8189 2.395619 CCTACTTCCGGTGACCCTAAT 58.604 52.381 0.00 0.00 0.00 1.73
3849 8195 1.804748 CAAAAGCCTACTTCCGGTGAC 59.195 52.381 0.00 0.00 34.05 3.67
3873 8220 3.762288 AGCCAGAACTAATAGACACGACA 59.238 43.478 0.00 0.00 0.00 4.35
3875 8222 4.337555 GGTAGCCAGAACTAATAGACACGA 59.662 45.833 0.00 0.00 0.00 4.35
3884 8231 2.571653 ACTGCATGGTAGCCAGAACTAA 59.428 45.455 4.53 0.00 36.75 2.24
3893 8240 2.932614 CAGACAGTAACTGCATGGTAGC 59.067 50.000 0.00 0.00 34.37 3.58
3901 8248 0.317479 ACGGTCCAGACAGTAACTGC 59.683 55.000 1.54 0.00 37.94 4.40
3910 8257 1.065928 CGAGCCATACGGTCCAGAC 59.934 63.158 0.00 0.00 35.44 3.51
3931 8278 2.678190 GCGATCCAAACAGCCTCTTAGT 60.678 50.000 0.00 0.00 0.00 2.24
3936 8283 2.093216 CTGCGATCCAAACAGCCTC 58.907 57.895 0.00 0.00 0.00 4.70
3937 8284 4.308526 CTGCGATCCAAACAGCCT 57.691 55.556 0.00 0.00 0.00 4.58
3940 8287 1.372087 GAGGGCTGCGATCCAAACAG 61.372 60.000 0.00 0.00 34.48 3.16
3941 8288 1.377202 GAGGGCTGCGATCCAAACA 60.377 57.895 0.00 0.00 0.00 2.83
3942 8289 2.464459 CGAGGGCTGCGATCCAAAC 61.464 63.158 0.00 0.00 0.00 2.93
3943 8290 2.125147 CGAGGGCTGCGATCCAAA 60.125 61.111 0.00 0.00 0.00 3.28
3944 8291 4.161295 CCGAGGGCTGCGATCCAA 62.161 66.667 0.00 0.00 0.00 3.53
3961 8308 3.704151 ATTTTCTGGCTGGGCTGC 58.296 55.556 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.