Multiple sequence alignment - TraesCS4B01G178500

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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 TraesCS4B01G178500 chr4B 100.000 3077 0 0 1 3077 391156880 391159956 0.000000e+00 5683.0
1 TraesCS4B01G178500 chr4D 89.887 1681 58 19 231 1833 313887261 313885615 0.000000e+00 2060.0
2 TraesCS4B01G178500 chr4D 92.045 88 7 0 147 234 313918658 313918571 1.160000e-24 124.0
3 TraesCS4B01G178500 chr6D 92.886 1251 78 7 1833 3077 90927625 90926380 0.000000e+00 1807.0
4 TraesCS4B01G178500 chr6D 91.851 1264 83 16 1828 3077 444087166 444085909 0.000000e+00 1746.0
5 TraesCS4B01G178500 chr7D 92.590 1255 78 11 1831 3077 182599419 182600666 0.000000e+00 1788.0
6 TraesCS4B01G178500 chr7D 92.424 1254 75 13 1833 3077 69048030 69046788 0.000000e+00 1772.0
7 TraesCS4B01G178500 chr7D 91.799 1256 88 11 1831 3077 474004835 474003586 0.000000e+00 1735.0
8 TraesCS4B01G178500 chr1D 92.412 1252 84 9 1833 3077 478249346 478250593 0.000000e+00 1775.0
9 TraesCS4B01G178500 chr2D 92.283 1257 80 13 1833 3077 563965799 563967050 0.000000e+00 1768.0
10 TraesCS4B01G178500 chr2D 92.197 1256 81 12 1833 3077 603693932 603695181 0.000000e+00 1760.0
11 TraesCS4B01G178500 chr2D 91.952 1255 89 8 1831 3077 525939863 525938613 0.000000e+00 1748.0
12 TraesCS4B01G178500 chr4A 93.065 1067 38 9 790 1833 162813139 162814192 0.000000e+00 1528.0
13 TraesCS4B01G178500 chr4A 83.831 569 25 15 215 763 162812620 162813141 2.150000e-131 479.0
14 TraesCS4B01G178500 chr4A 81.166 223 15 9 4 212 162812322 162812531 1.480000e-33 154.0
15 TraesCS4B01G178500 chr3D 100.000 28 0 0 1216 1243 504003838 504003811 6.000000e-03 52.8


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 TraesCS4B01G178500 chr4B 391156880 391159956 3076 False 5683.000000 5683 100.000000 1 3077 1 chr4B.!!$F1 3076
1 TraesCS4B01G178500 chr4D 313885615 313887261 1646 True 2060.000000 2060 89.887000 231 1833 1 chr4D.!!$R1 1602
2 TraesCS4B01G178500 chr6D 90926380 90927625 1245 True 1807.000000 1807 92.886000 1833 3077 1 chr6D.!!$R1 1244
3 TraesCS4B01G178500 chr6D 444085909 444087166 1257 True 1746.000000 1746 91.851000 1828 3077 1 chr6D.!!$R2 1249
4 TraesCS4B01G178500 chr7D 182599419 182600666 1247 False 1788.000000 1788 92.590000 1831 3077 1 chr7D.!!$F1 1246
5 TraesCS4B01G178500 chr7D 69046788 69048030 1242 True 1772.000000 1772 92.424000 1833 3077 1 chr7D.!!$R1 1244
6 TraesCS4B01G178500 chr7D 474003586 474004835 1249 True 1735.000000 1735 91.799000 1831 3077 1 chr7D.!!$R2 1246
7 TraesCS4B01G178500 chr1D 478249346 478250593 1247 False 1775.000000 1775 92.412000 1833 3077 1 chr1D.!!$F1 1244
8 TraesCS4B01G178500 chr2D 563965799 563967050 1251 False 1768.000000 1768 92.283000 1833 3077 1 chr2D.!!$F1 1244
9 TraesCS4B01G178500 chr2D 603693932 603695181 1249 False 1760.000000 1760 92.197000 1833 3077 1 chr2D.!!$F2 1244
10 TraesCS4B01G178500 chr2D 525938613 525939863 1250 True 1748.000000 1748 91.952000 1831 3077 1 chr2D.!!$R1 1246
11 TraesCS4B01G178500 chr4A 162812322 162814192 1870 False 720.333333 1528 86.020667 4 1833 3 chr4A.!!$F1 1829

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
611 797 0.030773 CCACGTCCATGTCGATCGAT 59.969 55.0 22.5 2.68 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 2488 0.036858 TCATGCCATTTGACGTCCGA 60.037 50.0 14.12 1.25 0.0 4.55 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 7.582667 AATCTTGGACCGGGAAAATAATTAG 57.417 36.000 6.32 0.00 0.00 1.73
35 36 7.771826 TCTTGGACCGGGAAAATAATTAGTTAG 59.228 37.037 6.32 0.00 0.00 2.34
56 57 2.814336 GCCAAAATCGACAAGGACTCTT 59.186 45.455 0.00 0.00 0.00 2.85
57 58 4.000988 GCCAAAATCGACAAGGACTCTTA 58.999 43.478 0.00 0.00 0.00 2.10
61 62 6.017440 CCAAAATCGACAAGGACTCTTAACAA 60.017 38.462 0.00 0.00 0.00 2.83
74 75 9.588096 AGGACTCTTAACAATTTTTAGTTGGAT 57.412 29.630 0.00 0.00 0.00 3.41
121 122 1.905637 GGATTCTTTCCACAACGGGT 58.094 50.000 0.00 0.00 44.74 5.28
135 136 0.615827 ACGGGTAGGTTAGGTGGGTC 60.616 60.000 0.00 0.00 0.00 4.46
145 146 1.043116 TAGGTGGGTCGAGCATGAGG 61.043 60.000 17.59 0.00 0.00 3.86
163 178 2.544267 GAGGCTATGATTTTCGAACCCG 59.456 50.000 0.00 0.00 37.07 5.28
164 179 1.602377 GGCTATGATTTTCGAACCCGG 59.398 52.381 0.00 0.00 36.24 5.73
165 180 1.602377 GCTATGATTTTCGAACCCGGG 59.398 52.381 22.25 22.25 36.24 5.73
183 198 1.338200 GGGCCGTATTGCTCCATCTAG 60.338 57.143 0.00 0.00 0.00 2.43
197 212 3.635373 TCCATCTAGTTAACTAGTGGCGG 59.365 47.826 32.94 27.94 44.74 6.13
202 217 1.204941 AGTTAACTAGTGGCGGCTCTG 59.795 52.381 22.18 14.36 0.00 3.35
203 218 0.108329 TTAACTAGTGGCGGCTCTGC 60.108 55.000 22.18 4.73 0.00 4.26
212 227 1.094785 GGCGGCTCTGCAAATTAGAA 58.905 50.000 0.00 0.00 36.28 2.10
223 324 9.875675 GCTCTGCAAATTAGAATCAATTAGTAG 57.124 33.333 0.00 0.00 0.00 2.57
272 373 3.589988 ACACAACCTCAGATCGATCAAC 58.410 45.455 26.47 0.96 0.00 3.18
461 602 2.151369 TGGAACAGGAAGACCACCC 58.849 57.895 0.00 0.00 38.94 4.61
535 681 5.305644 CCCCTTTCAGATACACTAGCAGTAT 59.694 44.000 7.87 7.87 35.01 2.12
536 682 6.493802 CCCCTTTCAGATACACTAGCAGTATA 59.506 42.308 8.06 0.00 32.60 1.47
606 792 2.564458 CGTCCACGTCCATGTCGA 59.436 61.111 13.08 0.00 34.11 4.20
607 793 1.138883 CGTCCACGTCCATGTCGAT 59.861 57.895 13.08 0.00 34.11 3.59
608 794 0.866061 CGTCCACGTCCATGTCGATC 60.866 60.000 13.08 0.00 34.11 3.69
609 795 0.866061 GTCCACGTCCATGTCGATCG 60.866 60.000 9.36 9.36 0.00 3.69
610 796 1.027792 TCCACGTCCATGTCGATCGA 61.028 55.000 15.15 15.15 0.00 3.59
611 797 0.030773 CCACGTCCATGTCGATCGAT 59.969 55.000 22.50 2.68 0.00 3.59
612 798 1.399572 CACGTCCATGTCGATCGATC 58.600 55.000 22.50 15.68 0.00 3.69
613 799 1.021968 ACGTCCATGTCGATCGATCA 58.978 50.000 22.50 19.91 0.00 2.92
614 800 1.404035 ACGTCCATGTCGATCGATCAA 59.596 47.619 22.50 10.71 0.00 2.57
615 801 2.047040 CGTCCATGTCGATCGATCAAG 58.953 52.381 22.50 16.38 0.00 3.02
616 802 2.287009 CGTCCATGTCGATCGATCAAGA 60.287 50.000 22.50 16.98 0.00 3.02
617 803 3.610349 CGTCCATGTCGATCGATCAAGAT 60.610 47.826 22.50 8.24 0.00 2.40
618 804 3.917380 GTCCATGTCGATCGATCAAGATC 59.083 47.826 22.50 6.89 42.58 2.75
619 805 3.569701 TCCATGTCGATCGATCAAGATCA 59.430 43.478 22.50 12.77 45.39 2.92
620 806 4.037923 TCCATGTCGATCGATCAAGATCAA 59.962 41.667 22.50 6.11 45.39 2.57
621 807 4.928020 CCATGTCGATCGATCAAGATCAAT 59.072 41.667 22.50 7.86 45.39 2.57
628 814 5.574830 CGATCGATCAAGATCAATAACTCCC 59.425 44.000 24.40 0.00 45.39 4.30
636 822 1.044231 TCAATAACTCCCGCGCCCTA 61.044 55.000 0.00 0.00 0.00 3.53
662 848 1.552792 CCAGGAACCTTCACCTCTCTC 59.447 57.143 0.00 0.00 33.91 3.20
663 849 2.534990 CAGGAACCTTCACCTCTCTCT 58.465 52.381 0.00 0.00 33.91 3.10
664 850 2.495669 CAGGAACCTTCACCTCTCTCTC 59.504 54.545 0.00 0.00 33.91 3.20
665 851 2.381961 AGGAACCTTCACCTCTCTCTCT 59.618 50.000 0.00 0.00 0.00 3.10
668 854 3.825908 ACCTTCACCTCTCTCTCTCTT 57.174 47.619 0.00 0.00 0.00 2.85
691 877 2.596553 AAATTATCCCGCGCCGGTCA 62.597 55.000 14.57 1.10 46.80 4.02
767 953 3.075005 ACGCCCTATGACCGTGCT 61.075 61.111 0.00 0.00 33.46 4.40
790 976 4.971125 GCGGCCTGCGGGAGATAC 62.971 72.222 18.31 0.00 33.58 2.24
832 1031 4.090588 AATTCGCTCCGGCCGGAA 62.091 61.111 43.77 31.47 44.66 4.30
976 1175 1.671850 CGGCCGCACAACCCTATATAG 60.672 57.143 14.67 2.46 0.00 1.31
977 1176 1.439679 GCCGCACAACCCTATATAGC 58.560 55.000 4.04 0.00 0.00 2.97
978 1177 1.944430 GCCGCACAACCCTATATAGCC 60.944 57.143 4.04 0.00 0.00 3.93
979 1178 1.338769 CCGCACAACCCTATATAGCCC 60.339 57.143 4.04 0.00 0.00 5.19
1014 1214 3.324713 CCCCCATCACCTCCTCAC 58.675 66.667 0.00 0.00 0.00 3.51
1027 1227 0.840288 TCCTCACCCCAAAGCAGCTA 60.840 55.000 0.00 0.00 0.00 3.32
1028 1228 0.393537 CCTCACCCCAAAGCAGCTAG 60.394 60.000 0.00 0.00 0.00 3.42
1029 1229 1.002134 TCACCCCAAAGCAGCTAGC 60.002 57.895 6.62 6.62 46.19 3.42
1082 1282 2.037121 TCAGTCCGCTTCAACTTCATCA 59.963 45.455 0.00 0.00 0.00 3.07
1090 1290 1.432514 TCAACTTCATCACAGCGAGC 58.567 50.000 0.00 0.00 0.00 5.03
1116 1316 0.179150 CTCTCCTTGGCTTCGTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
1149 1358 4.916870 ACGTATTCGATCGAGATTGTTGA 58.083 39.130 18.54 0.64 40.62 3.18
1416 1637 1.452651 CCTACTCCTCGTACGGGCA 60.453 63.158 16.52 0.00 0.00 5.36
1534 1755 3.382832 CCTCCGCCGTTCCAGAGT 61.383 66.667 0.00 0.00 0.00 3.24
1592 1813 2.772515 GGCCAAGACTACTGGTAGGATT 59.227 50.000 11.73 4.00 37.49 3.01
1609 1830 2.035632 GATTGGAGATCGGTCACCTCT 58.964 52.381 13.57 0.38 36.22 3.69
1612 1833 1.187087 GGAGATCGGTCACCTCTTGT 58.813 55.000 4.72 0.00 32.90 3.16
1637 1858 3.940640 CGGTTCGGCATGCCATCG 61.941 66.667 34.93 24.68 35.37 3.84
1803 2025 3.699038 CTCCTTGTTCGAGATCTTCTCCT 59.301 47.826 0.00 0.00 40.34 3.69
1865 2087 0.802994 AGTTGTTGAACACGTCGCGA 60.803 50.000 3.71 3.71 34.17 5.87
1888 2114 1.852067 AAAAACTAGCTGCACGCCCG 61.852 55.000 1.02 0.25 40.39 6.13
1944 2172 1.154054 CAGCCGCGCTAAAATGCAA 60.154 52.632 5.56 0.00 36.40 4.08
1976 2207 1.154054 CCAGCAGCGCGCAAAAATA 60.154 52.632 35.10 0.00 46.13 1.40
1981 2212 0.728803 CAGCGCGCAAAAATACAGCA 60.729 50.000 35.10 0.00 0.00 4.41
1986 2217 0.724453 CGCAAAAATACAGCACGCGT 60.724 50.000 5.58 5.58 36.69 6.01
1993 2224 1.092348 ATACAGCACGCGTGACTCTA 58.908 50.000 41.19 26.51 0.00 2.43
2000 2231 0.387367 ACGCGTGACTCTAGCACAAG 60.387 55.000 12.93 0.00 36.06 3.16
2166 2408 4.002267 ACAATACAATGTCGAATGCACG 57.998 40.909 0.00 0.00 0.00 5.34
2171 2413 2.741517 ACAATGTCGAATGCACGAATCA 59.258 40.909 0.48 0.00 43.75 2.57
2172 2414 3.374988 ACAATGTCGAATGCACGAATCAT 59.625 39.130 0.48 0.00 43.75 2.45
2173 2415 3.597377 ATGTCGAATGCACGAATCATG 57.403 42.857 0.48 0.00 43.75 3.07
2228 2470 4.163839 CCACTCCTCAATGAGATCCTTCTT 59.836 45.833 12.53 0.00 36.22 2.52
2229 2471 5.117584 CACTCCTCAATGAGATCCTTCTTG 58.882 45.833 12.53 0.00 36.22 3.02
2232 2474 5.028802 TCCTCAATGAGATCCTTCTTGAGT 58.971 41.667 12.53 0.00 34.57 3.41
2243 2485 3.005554 CCTTCTTGAGTTCATCATGCGT 58.994 45.455 0.00 0.00 37.89 5.24
2246 2488 3.402110 TCTTGAGTTCATCATGCGTTGT 58.598 40.909 0.00 0.00 37.89 3.32
2247 2489 3.433274 TCTTGAGTTCATCATGCGTTGTC 59.567 43.478 0.00 0.00 37.89 3.18
2255 2497 2.019408 CATGCGTTGTCGGACGTCA 61.019 57.895 18.91 0.00 44.50 4.35
2315 2557 4.498520 CCTCCGTCGCACTCGCAT 62.499 66.667 0.00 0.00 38.40 4.73
2381 2623 3.315418 CACGCTCATTCTCGATGATCAT 58.685 45.455 8.25 8.25 43.59 2.45
2401 2643 5.882553 TCATTGTTATGCATGATCACACAC 58.117 37.500 10.16 0.00 0.00 3.82
2460 2702 2.171840 TCTAGCTGGTCCTCTCACAAC 58.828 52.381 0.00 0.00 0.00 3.32
2463 2705 0.394565 GCTGGTCCTCTCACAACAGT 59.605 55.000 0.00 0.00 0.00 3.55
2489 2731 2.107901 TGGGCTTGCAAAATCCCAAAAT 59.892 40.909 23.75 0.00 43.18 1.82
2514 2756 2.832129 TCTCCACATCTTTTCTAGCCGT 59.168 45.455 0.00 0.00 0.00 5.68
2656 2898 2.958355 ACCATTTGCTACAAACTGCACT 59.042 40.909 0.00 0.00 39.05 4.40
2704 2946 1.634960 TCATCAGTGGTGACCGGTTA 58.365 50.000 9.42 0.00 34.75 2.85
2715 2957 3.304190 GGTGACCGGTTAACAACATTGAC 60.304 47.826 9.42 0.00 0.00 3.18
2716 2958 3.312973 GTGACCGGTTAACAACATTGACA 59.687 43.478 9.42 0.00 0.00 3.58
2724 2966 6.524239 CGGTTAACAACATTGACATCATTCAG 59.476 38.462 8.10 0.00 0.00 3.02
2736 2978 3.181453 ACATCATTCAGAGATCCAGGCAG 60.181 47.826 0.00 0.00 0.00 4.85
2897 3143 0.257039 CCAAGCATACCAGGGAAGCT 59.743 55.000 0.00 0.00 37.08 3.74
2929 3175 1.762370 TCATCTCCAATAGCCTTGCGA 59.238 47.619 0.00 0.00 0.00 5.10
3053 3299 6.737720 AGCCAAGTGATCATCAACTAGATA 57.262 37.500 0.00 0.00 34.43 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.084546 CCCGGTCCAAGATTTTGTCTC 58.915 52.381 0.00 0.00 35.67 3.36
2 3 2.194201 TCCCGGTCCAAGATTTTGTC 57.806 50.000 0.00 0.00 32.21 3.18
31 32 3.751698 AGTCCTTGTCGATTTTGGCTAAC 59.248 43.478 0.00 0.00 0.00 2.34
35 36 2.427506 AGAGTCCTTGTCGATTTTGGC 58.572 47.619 0.00 0.00 0.00 4.52
118 119 0.324645 TCGACCCACCTAACCTACCC 60.325 60.000 0.00 0.00 0.00 3.69
121 122 0.040058 TGCTCGACCCACCTAACCTA 59.960 55.000 0.00 0.00 0.00 3.08
145 146 1.602377 CCCGGGTTCGAAAATCATAGC 59.398 52.381 14.18 0.00 39.00 2.97
151 166 2.182732 TACGGCCCGGGTTCGAAAAT 62.183 55.000 33.72 19.55 39.00 1.82
163 178 0.685097 TAGATGGAGCAATACGGCCC 59.315 55.000 0.00 0.00 0.00 5.80
164 179 1.344763 ACTAGATGGAGCAATACGGCC 59.655 52.381 0.00 0.00 0.00 6.13
165 180 2.821991 ACTAGATGGAGCAATACGGC 57.178 50.000 0.00 0.00 0.00 5.68
183 198 1.641577 CAGAGCCGCCACTAGTTAAC 58.358 55.000 0.00 0.00 0.00 2.01
197 212 9.875675 CTACTAATTGATTCTAATTTGCAGAGC 57.124 33.333 0.00 0.00 32.79 4.09
223 324 3.177487 GGCAGCTACAGTAGTAACGAAC 58.823 50.000 9.42 0.00 0.00 3.95
272 373 6.738114 TGAATTTTCTCACTGCCAGTTTTAG 58.262 36.000 0.00 0.00 0.00 1.85
369 510 5.285651 GGAATCGATCGAGATGTCTCTTTT 58.714 41.667 23.84 8.42 40.75 2.27
461 602 2.624838 AGTTCAAACCCTGCAACATCTG 59.375 45.455 0.00 0.00 0.00 2.90
535 681 3.772572 TCACTTGTGCCTAGGCTTGTATA 59.227 43.478 33.07 10.39 42.51 1.47
536 682 2.571653 TCACTTGTGCCTAGGCTTGTAT 59.428 45.455 33.07 14.25 42.51 2.29
604 790 5.574830 GGGAGTTATTGATCTTGATCGATCG 59.425 44.000 20.03 9.36 42.10 3.69
605 791 5.574830 CGGGAGTTATTGATCTTGATCGATC 59.425 44.000 18.72 18.72 40.13 3.69
606 792 5.473931 CGGGAGTTATTGATCTTGATCGAT 58.526 41.667 15.30 15.30 0.00 3.59
607 793 4.796290 GCGGGAGTTATTGATCTTGATCGA 60.796 45.833 3.32 3.32 0.00 3.59
608 794 3.430218 GCGGGAGTTATTGATCTTGATCG 59.570 47.826 6.19 0.00 0.00 3.69
609 795 3.430218 CGCGGGAGTTATTGATCTTGATC 59.570 47.826 0.00 3.82 0.00 2.92
610 796 3.393800 CGCGGGAGTTATTGATCTTGAT 58.606 45.455 0.00 0.00 0.00 2.57
611 797 2.821546 CGCGGGAGTTATTGATCTTGA 58.178 47.619 0.00 0.00 0.00 3.02
612 798 1.261619 GCGCGGGAGTTATTGATCTTG 59.738 52.381 8.83 0.00 0.00 3.02
613 799 1.583054 GCGCGGGAGTTATTGATCTT 58.417 50.000 8.83 0.00 0.00 2.40
614 800 0.249911 GGCGCGGGAGTTATTGATCT 60.250 55.000 8.83 0.00 0.00 2.75
615 801 1.228657 GGGCGCGGGAGTTATTGATC 61.229 60.000 8.83 0.00 0.00 2.92
616 802 1.227853 GGGCGCGGGAGTTATTGAT 60.228 57.895 8.83 0.00 0.00 2.57
617 803 1.044231 TAGGGCGCGGGAGTTATTGA 61.044 55.000 8.83 0.00 0.00 2.57
618 804 0.878961 GTAGGGCGCGGGAGTTATTG 60.879 60.000 8.83 0.00 0.00 1.90
619 805 1.047034 AGTAGGGCGCGGGAGTTATT 61.047 55.000 8.83 0.00 0.00 1.40
620 806 1.047034 AAGTAGGGCGCGGGAGTTAT 61.047 55.000 8.83 0.00 0.00 1.89
621 807 1.259840 AAAGTAGGGCGCGGGAGTTA 61.260 55.000 8.83 0.00 0.00 2.24
628 814 2.106683 CCTGGAAAAGTAGGGCGCG 61.107 63.158 0.00 0.00 0.00 6.86
636 822 2.514160 AGGTGAAGGTTCCTGGAAAAGT 59.486 45.455 11.40 0.00 32.29 2.66
662 848 4.786609 GCGCGGGATAATTTTGAAAGAGAG 60.787 45.833 8.83 0.00 0.00 3.20
663 849 3.064820 GCGCGGGATAATTTTGAAAGAGA 59.935 43.478 8.83 0.00 0.00 3.10
664 850 3.363178 GCGCGGGATAATTTTGAAAGAG 58.637 45.455 8.83 0.00 0.00 2.85
665 851 2.098443 GGCGCGGGATAATTTTGAAAGA 59.902 45.455 8.83 0.00 0.00 2.52
668 854 0.378962 CGGCGCGGGATAATTTTGAA 59.621 50.000 8.83 0.00 0.00 2.69
691 877 1.710244 TGGTGAGTGGGTTGATTGGAT 59.290 47.619 0.00 0.00 0.00 3.41
778 964 1.688735 TGATTGAGGTATCTCCCGCAG 59.311 52.381 0.00 0.00 39.23 5.18
779 965 1.788229 TGATTGAGGTATCTCCCGCA 58.212 50.000 0.00 0.00 39.23 5.69
780 966 2.910688 TTGATTGAGGTATCTCCCGC 57.089 50.000 0.00 0.00 39.23 6.13
781 967 3.134458 GCTTTGATTGAGGTATCTCCCG 58.866 50.000 0.00 0.00 39.23 5.14
782 968 3.481453 GGCTTTGATTGAGGTATCTCCC 58.519 50.000 0.00 0.00 39.23 4.30
783 969 3.481453 GGGCTTTGATTGAGGTATCTCC 58.519 50.000 0.00 0.00 39.23 3.71
784 970 3.117888 TGGGGCTTTGATTGAGGTATCTC 60.118 47.826 0.00 0.00 40.36 2.75
785 971 2.852449 TGGGGCTTTGATTGAGGTATCT 59.148 45.455 0.00 0.00 0.00 1.98
787 973 3.052642 ACATGGGGCTTTGATTGAGGTAT 60.053 43.478 0.00 0.00 0.00 2.73
788 974 2.311542 ACATGGGGCTTTGATTGAGGTA 59.688 45.455 0.00 0.00 0.00 3.08
789 975 1.077663 ACATGGGGCTTTGATTGAGGT 59.922 47.619 0.00 0.00 0.00 3.85
790 976 1.479323 CACATGGGGCTTTGATTGAGG 59.521 52.381 0.00 0.00 0.00 3.86
832 1031 5.394773 GCCGGATAATAATTTTGTTGTGGGT 60.395 40.000 5.05 0.00 0.00 4.51
836 1035 4.641094 TCCGCCGGATAATAATTTTGTTGT 59.359 37.500 5.05 0.00 0.00 3.32
870 1069 2.283821 GTGGATTGGCCCCTGCAA 60.284 61.111 0.00 0.00 40.13 4.08
963 1162 0.981943 GCGGGGCTATATAGGGTTGT 59.018 55.000 11.72 0.00 0.00 3.32
979 1178 4.656117 GTTTTGTTGGCGGGGCGG 62.656 66.667 0.00 0.00 0.00 6.13
1027 1227 3.878778 CTGAGCCAAGTTGGTTATAGCT 58.121 45.455 22.85 12.30 40.46 3.32
1028 1228 2.356069 GCTGAGCCAAGTTGGTTATAGC 59.644 50.000 22.85 22.80 40.46 2.97
1029 1229 3.624861 CAGCTGAGCCAAGTTGGTTATAG 59.375 47.826 22.85 18.00 40.46 1.31
1030 1230 3.609853 CAGCTGAGCCAAGTTGGTTATA 58.390 45.455 22.85 9.06 40.46 0.98
1031 1231 2.440409 CAGCTGAGCCAAGTTGGTTAT 58.560 47.619 22.85 9.72 40.46 1.89
1116 1316 2.256174 TCGAATACGTACAGCAGCAAC 58.744 47.619 0.00 0.00 40.69 4.17
1149 1358 0.390866 CACGCTCAGCTTGTCCATCT 60.391 55.000 0.00 0.00 0.00 2.90
1377 1586 0.178995 GGAGGAGTAGTAGGACGGGG 60.179 65.000 0.00 0.00 0.00 5.73
1534 1755 2.158871 GCCTCCCGTTTGGTCATACATA 60.159 50.000 0.00 0.00 34.77 2.29
1592 1813 1.186200 CAAGAGGTGACCGATCTCCA 58.814 55.000 0.00 0.00 40.42 3.86
1637 1858 5.297527 TCACACATATGCAAGTGATGGATTC 59.702 40.000 19.92 0.00 40.91 2.52
1709 1930 5.269189 TGACATTACCATCTCCAGTACAGA 58.731 41.667 0.00 0.00 0.00 3.41
1710 1931 5.598416 TGACATTACCATCTCCAGTACAG 57.402 43.478 0.00 0.00 0.00 2.74
1783 2005 3.779759 CAGGAGAAGATCTCGAACAAGG 58.220 50.000 0.00 0.00 44.28 3.61
1784 2006 3.186119 GCAGGAGAAGATCTCGAACAAG 58.814 50.000 0.00 0.00 44.28 3.16
1849 2071 2.582265 GCTCGCGACGTGTTCAACA 61.582 57.895 3.71 0.00 0.00 3.33
1851 2073 0.318022 TTAGCTCGCGACGTGTTCAA 60.318 50.000 3.71 0.00 0.00 2.69
1852 2074 0.318022 TTTAGCTCGCGACGTGTTCA 60.318 50.000 3.71 0.00 0.00 3.18
1857 2079 2.248487 CTAGTTTTTAGCTCGCGACGT 58.752 47.619 3.71 0.00 0.00 4.34
1976 2207 1.210413 CTAGAGTCACGCGTGCTGT 59.790 57.895 33.63 29.47 0.00 4.40
1981 2212 0.387367 CTTGTGCTAGAGTCACGCGT 60.387 55.000 5.58 5.58 37.26 6.01
1986 2217 2.908688 TGTTGCTTGTGCTAGAGTCA 57.091 45.000 0.00 0.00 40.48 3.41
2015 2246 8.031864 TGTGTTTGATCTTTTGCTTCTGTTTTA 58.968 29.630 0.00 0.00 0.00 1.52
2161 2403 2.546789 GAGCATCATCATGATTCGTGCA 59.453 45.455 26.12 0.00 34.28 4.57
2166 2408 5.007430 ACGACAAAGAGCATCATCATGATTC 59.993 40.000 5.16 0.49 34.28 2.52
2171 2413 3.201290 GGACGACAAAGAGCATCATCAT 58.799 45.455 0.00 0.00 37.82 2.45
2172 2414 2.028203 TGGACGACAAAGAGCATCATCA 60.028 45.455 0.00 0.00 37.82 3.07
2173 2415 2.621338 TGGACGACAAAGAGCATCATC 58.379 47.619 0.00 0.00 37.82 2.92
2228 2470 1.726248 CGACAACGCATGATGAACTCA 59.274 47.619 0.00 0.00 38.53 3.41
2229 2471 1.061131 CCGACAACGCATGATGAACTC 59.939 52.381 0.00 0.00 38.29 3.01
2232 2474 1.075542 GTCCGACAACGCATGATGAA 58.924 50.000 0.00 0.00 38.29 2.57
2243 2485 0.533085 TGCCATTTGACGTCCGACAA 60.533 50.000 14.12 0.00 0.00 3.18
2246 2488 0.036858 TCATGCCATTTGACGTCCGA 60.037 50.000 14.12 1.25 0.00 4.55
2247 2489 1.016627 ATCATGCCATTTGACGTCCG 58.983 50.000 14.12 0.00 0.00 4.79
2255 2497 2.961062 GTTGCCTCCTATCATGCCATTT 59.039 45.455 0.00 0.00 0.00 2.32
2381 2623 3.426025 GCGTGTGTGATCATGCATAACAA 60.426 43.478 0.00 0.00 46.02 2.83
2401 2643 0.445829 TTTGGTACATCATGCACGCG 59.554 50.000 3.53 3.53 39.30 6.01
2446 2688 4.974645 ATTTACTGTTGTGAGAGGACCA 57.025 40.909 0.00 0.00 0.00 4.02
2460 2702 4.392754 GGATTTTGCAAGCCCAATTTACTG 59.607 41.667 0.00 0.00 31.56 2.74
2489 2731 4.404073 GGCTAGAAAAGATGTGGAGAGAGA 59.596 45.833 0.00 0.00 0.00 3.10
2514 2756 2.655090 TTTCCACAATGCTCAGGTGA 57.345 45.000 0.00 0.00 34.52 4.02
2675 2917 5.882557 GGTCACCACTGATGAATAAGATTGT 59.117 40.000 0.00 0.00 0.00 2.71
2704 2946 7.148120 GGATCTCTGAATGATGTCAATGTTGTT 60.148 37.037 0.00 0.00 0.00 2.83
2715 2957 3.181453 ACTGCCTGGATCTCTGAATGATG 60.181 47.826 0.00 0.00 0.00 3.07
2716 2958 3.047115 ACTGCCTGGATCTCTGAATGAT 58.953 45.455 0.00 0.00 0.00 2.45
2724 2966 1.556911 TCTTTGGACTGCCTGGATCTC 59.443 52.381 0.00 0.00 34.31 2.75
2736 2978 2.747396 TTGGCATGCATTCTTTGGAC 57.253 45.000 21.36 0.00 0.00 4.02
2897 3143 1.270785 TGGAGATGAACAAAGCTCGCA 60.271 47.619 0.00 0.00 0.00 5.10
2929 3175 0.976641 TCTCCCAATGCTGAAGACGT 59.023 50.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.