Multiple sequence alignment - TraesCS6D01G377000

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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 TraesCS6D01G377000 chr6D 100.000 2993 0 0 1 2993 459736690 459733698 0.000000e+00 5528.0
1 TraesCS6D01G377000 chr6D 83.920 995 104 31 1982 2946 459715719 459714751 0.000000e+00 900.0
2 TraesCS6D01G377000 chr6A 93.203 2310 98 31 728 2991 605392207 605389911 0.000000e+00 3341.0
3 TraesCS6D01G377000 chr6A 81.579 684 68 29 8 637 605393026 605392347 2.060000e-141 512.0
4 TraesCS6D01G377000 chr6B 93.992 1498 38 19 812 2276 699019033 699017555 0.000000e+00 2220.0
5 TraesCS6D01G377000 chr6B 86.207 377 21 12 309 672 699019536 699019178 2.180000e-101 379.0
6 TraesCS6D01G377000 chr6B 84.171 398 41 17 2308 2693 699017459 699017072 1.700000e-97 366.0
7 TraesCS6D01G377000 chr6B 85.350 157 21 2 164 318 508812847 508812691 8.590000e-36 161.0
8 TraesCS6D01G377000 chr5D 85.973 221 23 7 1222 1440 87173742 87173528 2.320000e-56 230.0
9 TraesCS6D01G377000 chr5D 83.425 181 27 3 128 307 565282686 565282508 6.640000e-37 165.0
10 TraesCS6D01G377000 chr5A 86.957 207 23 4 1222 1426 80155800 80155596 2.320000e-56 230.0
11 TraesCS6D01G377000 chr2B 85.567 194 27 1 1206 1398 211614087 211614280 5.060000e-48 202.0
12 TraesCS6D01G377000 chr2B 81.768 181 25 4 132 306 765556402 765556224 8.650000e-31 145.0
13 TraesCS6D01G377000 chr2B 80.226 177 31 4 129 302 495146741 495146566 2.420000e-26 130.0
14 TraesCS6D01G377000 chr2A 83.019 212 32 4 1218 1426 146825246 146825036 3.940000e-44 189.0
15 TraesCS6D01G377000 chr3A 82.967 182 26 4 128 307 562912899 562912721 3.090000e-35 159.0
16 TraesCS6D01G377000 chr7A 83.832 167 21 5 128 292 53293499 53293337 1.440000e-33 154.0
17 TraesCS6D01G377000 chr7D 81.143 175 26 6 137 307 41058107 41057936 1.870000e-27 134.0
18 TraesCS6D01G377000 chr7D 81.410 156 21 4 153 302 125907603 125907756 1.460000e-23 121.0
19 TraesCS6D01G377000 chr3D 79.651 172 26 7 131 300 2800564 2800400 6.780000e-22 115.0
20 TraesCS6D01G377000 chr1D 80.822 146 20 6 1228 1369 366475660 366475519 1.130000e-19 108.0
21 TraesCS6D01G377000 chr1A 80.822 146 20 6 1228 1369 465496876 465497017 1.130000e-19 108.0
22 TraesCS6D01G377000 chr1B 76.364 220 34 14 1156 1369 491232489 491232696 5.280000e-18 102.0
23 TraesCS6D01G377000 chr4D 88.732 71 3 3 2920 2990 4019005 4018940 6.880000e-12 82.4
24 TraesCS6D01G377000 chr4D 87.324 71 4 3 2920 2990 4000035 3999970 3.200000e-10 76.8
25 TraesCS6D01G377000 chr4D 87.324 71 4 3 2920 2990 4002742 4002677 3.200000e-10 76.8
26 TraesCS6D01G377000 chr4D 87.324 71 4 3 2920 2990 4005453 4005388 3.200000e-10 76.8
27 TraesCS6D01G377000 chr4D 87.324 71 4 3 2920 2990 4008162 4008097 3.200000e-10 76.8
28 TraesCS6D01G377000 chr4D 87.324 71 4 3 2920 2990 4010873 4010808 3.200000e-10 76.8
29 TraesCS6D01G377000 chr4D 87.324 71 4 3 2920 2990 4013585 4013520 3.200000e-10 76.8
30 TraesCS6D01G377000 chr4D 87.324 71 4 3 2920 2990 4021718 4021653 3.200000e-10 76.8


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 TraesCS6D01G377000 chr6D 459733698 459736690 2992 True 5528.000000 5528 100.000000 1 2993 1 chr6D.!!$R2 2992
1 TraesCS6D01G377000 chr6D 459714751 459715719 968 True 900.000000 900 83.920000 1982 2946 1 chr6D.!!$R1 964
2 TraesCS6D01G377000 chr6A 605389911 605393026 3115 True 1926.500000 3341 87.391000 8 2991 2 chr6A.!!$R1 2983
3 TraesCS6D01G377000 chr6B 699017072 699019536 2464 True 988.333333 2220 88.123333 309 2693 3 chr6B.!!$R2 2384

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
685 832 0.323629 TCAAACCCCCTCATCGTCAC 59.676 55.0 0.0 0.0 0.0 3.67 F
1075 1222 0.038166 TTCATGCACAACCTCCTCCC 59.962 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1830 1.257750 CGGGAGTGGGAGTGTGATGA 61.258 60.000 0.0 0.0 0.0 2.92 R
2962 3294 1.202976 CCCCTTGCTATGATTCCTGGG 60.203 57.143 0.0 0.0 0.0 4.45 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
46 47 2.730672 GCTTTGCTCACGACGCGAT 61.731 57.895 15.93 0.00 0.00 4.58
53 54 4.840288 CACGACGCGATGCCGGTA 62.840 66.667 15.93 0.00 36.06 4.02
54 55 3.896133 ACGACGCGATGCCGGTAT 61.896 61.111 15.93 4.04 36.06 2.73
72 73 4.985409 CGGTATATGCAGAAGGAAGAAGAC 59.015 45.833 0.00 0.00 0.00 3.01
140 170 7.865530 TGATATATTTTAGGGTGTGGCTAGA 57.134 36.000 0.00 0.00 0.00 2.43
149 179 2.103373 GGTGTGGCTAGATCTCAGTCA 58.897 52.381 0.00 0.17 0.00 3.41
167 197 6.867662 CAGTCAACTGAGATTTAACCAAGT 57.132 37.500 4.05 0.00 46.59 3.16
184 214 9.979578 TTAACCAAGTCTTAGTCAAATAACGTA 57.020 29.630 0.00 0.00 0.00 3.57
259 321 9.579768 AATGTAAGATCTGACGAATATAGCATC 57.420 33.333 5.72 0.00 0.00 3.91
260 322 7.244192 TGTAAGATCTGACGAATATAGCATCG 58.756 38.462 5.72 4.40 44.33 3.84
272 334 7.094762 ACGAATATAGCATCGACTGAGACATAA 60.095 37.037 11.05 0.00 41.43 1.90
273 335 7.912773 CGAATATAGCATCGACTGAGACATAAT 59.087 37.037 0.00 0.00 41.43 1.28
274 336 9.232082 GAATATAGCATCGACTGAGACATAATC 57.768 37.037 0.00 0.00 0.00 1.75
275 337 4.926140 AGCATCGACTGAGACATAATCA 57.074 40.909 0.00 0.00 0.00 2.57
276 338 5.268118 AGCATCGACTGAGACATAATCAA 57.732 39.130 0.00 0.00 0.00 2.57
277 339 5.288015 AGCATCGACTGAGACATAATCAAG 58.712 41.667 0.00 0.00 0.00 3.02
278 340 5.046529 GCATCGACTGAGACATAATCAAGT 58.953 41.667 0.00 0.00 31.11 3.16
279 341 5.174761 GCATCGACTGAGACATAATCAAGTC 59.825 44.000 0.00 0.00 38.79 3.01
307 369 3.862267 CGACTGAGATTTAGCAAGACTGG 59.138 47.826 0.00 0.00 0.00 4.00
340 402 8.492415 AAGGGTCTGTGCTACTTAATATATGA 57.508 34.615 0.00 0.00 0.00 2.15
368 430 8.869897 GTTTGACCTTCCTAAAAGAAAAGTTTG 58.130 33.333 0.00 0.00 0.00 2.93
387 449 2.993545 TGAGCATCGTTTTTGTTTCCG 58.006 42.857 0.00 0.00 38.61 4.30
413 475 0.385974 GTGCCATGTTGCAGACGAAC 60.386 55.000 0.00 0.00 43.02 3.95
420 482 0.928229 GTTGCAGACGAACAGAACGT 59.072 50.000 0.00 0.00 46.58 3.99
454 523 1.134610 CGGCCGGAGTGGTTTATAACT 60.135 52.381 20.10 0.00 41.21 2.24
538 613 2.165167 ACATGACAATGACCAGCCAAG 58.835 47.619 0.00 0.00 37.24 3.61
640 718 5.485662 AGAAGCATCAATAAACTAACGGC 57.514 39.130 0.00 0.00 0.00 5.68
646 724 3.255725 TCAATAAACTAACGGCGGTCAG 58.744 45.455 13.24 7.51 0.00 3.51
647 725 2.997986 CAATAAACTAACGGCGGTCAGT 59.002 45.455 13.24 8.22 0.00 3.41
648 726 2.068837 TAAACTAACGGCGGTCAGTG 57.931 50.000 13.24 0.00 0.00 3.66
668 752 4.435436 CAGTAGTGCGCGGGCTCA 62.435 66.667 25.62 9.87 40.82 4.26
679 763 3.100111 GGGCTCAAACCCCCTCAT 58.900 61.111 0.00 0.00 45.00 2.90
680 764 1.076705 GGGCTCAAACCCCCTCATC 60.077 63.158 0.00 0.00 45.00 2.92
681 765 1.452108 GGCTCAAACCCCCTCATCG 60.452 63.158 0.00 0.00 0.00 3.84
685 832 0.323629 TCAAACCCCCTCATCGTCAC 59.676 55.000 0.00 0.00 0.00 3.67
716 863 4.351938 CGCCCCACGTCGTCTCAA 62.352 66.667 0.00 0.00 36.87 3.02
717 864 2.029964 GCCCCACGTCGTCTCAAA 59.970 61.111 0.00 0.00 0.00 2.69
718 865 2.315386 GCCCCACGTCGTCTCAAAC 61.315 63.158 0.00 0.00 0.00 2.93
719 866 1.666872 CCCCACGTCGTCTCAAACC 60.667 63.158 0.00 0.00 0.00 3.27
720 867 1.666872 CCCACGTCGTCTCAAACCC 60.667 63.158 0.00 0.00 0.00 4.11
721 868 1.666872 CCACGTCGTCTCAAACCCC 60.667 63.158 0.00 0.00 0.00 4.95
722 869 2.019951 CACGTCGTCTCAAACCCCG 61.020 63.158 0.00 0.00 0.00 5.73
723 870 2.195567 ACGTCGTCTCAAACCCCGA 61.196 57.895 0.00 0.00 0.00 5.14
724 871 1.731969 CGTCGTCTCAAACCCCGAC 60.732 63.158 0.00 0.00 44.51 4.79
725 872 1.373873 GTCGTCTCAAACCCCGACC 60.374 63.158 0.00 0.00 42.76 4.79
726 873 2.047560 CGTCTCAAACCCCGACCC 60.048 66.667 0.00 0.00 0.00 4.46
727 874 2.580601 CGTCTCAAACCCCGACCCT 61.581 63.158 0.00 0.00 0.00 4.34
728 875 1.295746 GTCTCAAACCCCGACCCTC 59.704 63.158 0.00 0.00 0.00 4.30
729 876 2.264794 CTCAAACCCCGACCCTCG 59.735 66.667 0.00 0.00 40.07 4.63
730 877 2.524887 TCAAACCCCGACCCTCGT 60.525 61.111 0.00 0.00 38.40 4.18
731 878 2.047560 CAAACCCCGACCCTCGTC 60.048 66.667 0.00 0.00 38.40 4.20
744 891 1.202076 CCCTCGTCGTACGTCCTTAAC 60.202 57.143 16.05 3.73 43.14 2.01
745 892 1.464608 CCTCGTCGTACGTCCTTAACA 59.535 52.381 16.05 0.00 43.14 2.41
762 909 2.202570 AAATCCGTCGGTCGCTCG 60.203 61.111 11.88 0.00 38.35 5.03
1075 1222 0.038166 TTCATGCACAACCTCCTCCC 59.962 55.000 0.00 0.00 0.00 4.30
1077 1224 1.852157 ATGCACAACCTCCTCCCCA 60.852 57.895 0.00 0.00 0.00 4.96
1078 1225 1.434513 ATGCACAACCTCCTCCCCAA 61.435 55.000 0.00 0.00 0.00 4.12
1103 1295 5.659440 AGTTCAGACCAGAGAGAGAATTC 57.341 43.478 0.00 0.00 0.00 2.17
1491 1686 4.511636 CTCAAGAAGAGCGCCTCC 57.488 61.111 2.29 0.00 37.59 4.30
1534 1732 2.173669 CAGCCCGCTGTTACCATCG 61.174 63.158 8.57 0.00 39.10 3.84
1671 1872 1.134371 GGCCTCTCTAACCACATGACC 60.134 57.143 0.00 0.00 0.00 4.02
1837 2041 0.320771 GCCGGAGAAGCAAGAAGACA 60.321 55.000 5.05 0.00 0.00 3.41
1980 2184 0.179702 TGGCAGGTCTCTCATCATGC 59.820 55.000 0.00 0.00 40.01 4.06
2084 2293 4.023291 GGGAGCCAATTCCATACAGAAAA 58.977 43.478 0.00 0.00 39.09 2.29
2085 2294 4.466015 GGGAGCCAATTCCATACAGAAAAA 59.534 41.667 0.00 0.00 39.09 1.94
2171 2390 6.547141 AGATGAGTGGATTTTGAAGTGTTGAA 59.453 34.615 0.00 0.00 0.00 2.69
2286 2590 8.510505 CCTGGGATTTATAGTAGTAGTTACGAC 58.489 40.741 0.00 0.00 37.35 4.34
2482 2795 4.953868 CGGTCGGCGGTTGTCACA 62.954 66.667 7.21 0.00 0.00 3.58
2512 2825 0.977395 GGCCTAGGTGAGACAACTGT 59.023 55.000 11.31 0.00 31.86 3.55
2524 2837 2.885644 AACTGTCGCGCGCCTATG 60.886 61.111 27.95 15.94 0.00 2.23
2575 2895 7.714377 AGGTGAGATTAAGCAGACATAAATCAG 59.286 37.037 0.00 0.00 0.00 2.90
2637 2957 8.599055 TCTTTGCATCTACAATAGCTGAATAG 57.401 34.615 0.00 0.00 0.00 1.73
2641 2961 7.674120 TGCATCTACAATAGCTGAATAGACAT 58.326 34.615 0.00 0.00 0.00 3.06
2721 3043 6.366061 TCCGCATTCTTATGTAAATCGATGAG 59.634 38.462 0.00 0.00 34.12 2.90
2755 3079 7.421087 AAATAGAGGAAGTAAGGGTGAGTAC 57.579 40.000 0.00 0.00 0.00 2.73
2768 3092 4.341520 AGGGTGAGTACGAGAAATCATACC 59.658 45.833 0.00 0.00 0.00 2.73
2830 3156 6.108687 GATGGTGTATCAACAGATGAACTGA 58.891 40.000 0.00 0.00 42.54 3.41
2961 3293 2.022195 CATGACCATCAAGCTTCCCAG 58.978 52.381 0.00 0.00 0.00 4.45
2977 3309 0.475475 CCAGCCCAGGAATCATAGCA 59.525 55.000 0.00 0.00 0.00 3.49
2991 3323 3.278574 TCATAGCAAGGGGTGAAATTCG 58.721 45.455 0.00 0.00 0.00 3.34
2992 3324 3.054728 TCATAGCAAGGGGTGAAATTCGA 60.055 43.478 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.568612 CTCTCAGCCTTCGTCGCA 59.431 61.111 0.00 0.00 0.00 5.10
1 2 2.202676 CCTCTCAGCCTTCGTCGC 60.203 66.667 0.00 0.00 0.00 5.19
2 3 2.202676 GCCTCTCAGCCTTCGTCG 60.203 66.667 0.00 0.00 0.00 5.12
3 4 2.202676 CGCCTCTCAGCCTTCGTC 60.203 66.667 0.00 0.00 0.00 4.20
4 5 3.764466 CCGCCTCTCAGCCTTCGT 61.764 66.667 0.00 0.00 0.00 3.85
6 7 2.427245 TAGCCGCCTCTCAGCCTTC 61.427 63.158 0.00 0.00 0.00 3.46
46 47 1.419381 TCCTTCTGCATATACCGGCA 58.581 50.000 0.00 0.00 38.52 5.69
53 54 5.355596 CGAAGTCTTCTTCCTTCTGCATAT 58.644 41.667 10.81 0.00 45.02 1.78
54 55 4.382040 CCGAAGTCTTCTTCCTTCTGCATA 60.382 45.833 10.81 0.00 45.02 3.14
127 129 1.007721 ACTGAGATCTAGCCACACCCT 59.992 52.381 0.00 0.00 0.00 4.34
149 179 8.429641 TGACTAAGACTTGGTTAAATCTCAGTT 58.570 33.333 5.60 0.00 0.00 3.16
211 273 8.576442 ACATTGAGATCCGTGTTTCTTTTATTT 58.424 29.630 0.00 0.00 0.00 1.40
212 274 8.110860 ACATTGAGATCCGTGTTTCTTTTATT 57.889 30.769 0.00 0.00 0.00 1.40
213 275 7.687941 ACATTGAGATCCGTGTTTCTTTTAT 57.312 32.000 0.00 0.00 0.00 1.40
214 276 8.610248 TTACATTGAGATCCGTGTTTCTTTTA 57.390 30.769 0.00 0.00 0.00 1.52
215 277 7.444183 TCTTACATTGAGATCCGTGTTTCTTTT 59.556 33.333 0.00 0.00 0.00 2.27
216 278 6.934645 TCTTACATTGAGATCCGTGTTTCTTT 59.065 34.615 0.00 0.00 0.00 2.52
217 279 6.464222 TCTTACATTGAGATCCGTGTTTCTT 58.536 36.000 0.00 0.00 0.00 2.52
218 280 6.037786 TCTTACATTGAGATCCGTGTTTCT 57.962 37.500 0.00 0.00 0.00 2.52
219 281 6.758886 AGATCTTACATTGAGATCCGTGTTTC 59.241 38.462 9.76 0.00 46.88 2.78
220 282 6.536582 CAGATCTTACATTGAGATCCGTGTTT 59.463 38.462 9.76 0.00 46.88 2.83
221 283 6.045318 CAGATCTTACATTGAGATCCGTGTT 58.955 40.000 9.76 0.00 46.88 3.32
226 288 6.078202 TCGTCAGATCTTACATTGAGATCC 57.922 41.667 7.77 0.00 46.88 3.36
227 289 9.853555 ATATTCGTCAGATCTTACATTGAGATC 57.146 33.333 7.77 6.09 46.32 2.75
248 310 9.232082 GATTATGTCTCAGTCGATGCTATATTC 57.768 37.037 0.00 0.00 0.00 1.75
281 343 4.560819 GTCTTGCTAAATCTCAGTCGACTG 59.439 45.833 34.76 34.76 45.08 3.51
282 344 4.461081 AGTCTTGCTAAATCTCAGTCGACT 59.539 41.667 13.58 13.58 0.00 4.18
283 345 4.560819 CAGTCTTGCTAAATCTCAGTCGAC 59.439 45.833 7.70 7.70 0.00 4.20
284 346 4.380973 CCAGTCTTGCTAAATCTCAGTCGA 60.381 45.833 0.00 0.00 0.00 4.20
285 347 3.862267 CCAGTCTTGCTAAATCTCAGTCG 59.138 47.826 0.00 0.00 0.00 4.18
286 348 4.826556 ACCAGTCTTGCTAAATCTCAGTC 58.173 43.478 0.00 0.00 0.00 3.51
295 357 6.214819 ACCCTTAGAAATACCAGTCTTGCTAA 59.785 38.462 0.00 0.00 0.00 3.09
297 359 4.536489 ACCCTTAGAAATACCAGTCTTGCT 59.464 41.667 0.00 0.00 0.00 3.91
298 360 4.844884 ACCCTTAGAAATACCAGTCTTGC 58.155 43.478 0.00 0.00 0.00 4.01
307 369 6.223351 AGTAGCACAGACCCTTAGAAATAC 57.777 41.667 0.00 0.00 0.00 1.89
340 402 8.306313 ACTTTTCTTTTAGGAAGGTCAAACAT 57.694 30.769 0.00 0.00 0.00 2.71
368 430 2.994849 ACGGAAACAAAAACGATGCTC 58.005 42.857 0.00 0.00 0.00 4.26
387 449 0.109365 TGCAACATGGCACGCATAAC 60.109 50.000 0.00 0.00 39.25 1.89
413 475 2.290093 GGTAGACCTATCCGACGTTCTG 59.710 54.545 0.00 0.00 0.00 3.02
420 482 1.228367 GGCCGGTAGACCTATCCGA 60.228 63.158 1.90 0.00 46.05 4.55
454 523 2.614520 TCTTCGTCCGTGCATTTCAAAA 59.385 40.909 0.00 0.00 0.00 2.44
538 613 1.663643 TCGCCGTGCTCAAATATGAAC 59.336 47.619 0.00 0.00 34.49 3.18
640 718 0.734253 GCACTACTGAGCACTGACCG 60.734 60.000 0.00 0.00 0.00 4.79
646 724 3.181967 CCGCGCACTACTGAGCAC 61.182 66.667 8.75 0.00 42.99 4.40
647 725 4.435436 CCCGCGCACTACTGAGCA 62.435 66.667 8.75 0.00 42.99 4.26
668 752 0.840722 AGGTGACGATGAGGGGGTTT 60.841 55.000 0.00 0.00 0.00 3.27
672 756 0.905357 AAGAAGGTGACGATGAGGGG 59.095 55.000 0.00 0.00 0.00 4.79
674 758 3.056536 TGAAGAAGAAGGTGACGATGAGG 60.057 47.826 0.00 0.00 0.00 3.86
676 760 4.382040 GGATGAAGAAGAAGGTGACGATGA 60.382 45.833 0.00 0.00 0.00 2.92
677 761 3.868077 GGATGAAGAAGAAGGTGACGATG 59.132 47.826 0.00 0.00 0.00 3.84
678 762 3.429547 CGGATGAAGAAGAAGGTGACGAT 60.430 47.826 0.00 0.00 0.00 3.73
679 763 2.094700 CGGATGAAGAAGAAGGTGACGA 60.095 50.000 0.00 0.00 0.00 4.20
680 764 2.263077 CGGATGAAGAAGAAGGTGACG 58.737 52.381 0.00 0.00 0.00 4.35
681 765 2.003301 GCGGATGAAGAAGAAGGTGAC 58.997 52.381 0.00 0.00 0.00 3.67
685 832 0.464554 GGGGCGGATGAAGAAGAAGG 60.465 60.000 0.00 0.00 0.00 3.46
711 858 2.280552 CGAGGGTCGGGGTTTGAGA 61.281 63.158 0.00 0.00 36.00 3.27
712 859 2.264794 CGAGGGTCGGGGTTTGAG 59.735 66.667 0.00 0.00 36.00 3.02
713 860 2.524887 ACGAGGGTCGGGGTTTGA 60.525 61.111 0.86 0.00 45.59 2.69
714 861 2.047560 GACGAGGGTCGGGGTTTG 60.048 66.667 0.86 0.00 45.59 2.93
722 869 1.301677 AAGGACGTACGACGAGGGTC 61.302 60.000 24.41 6.76 46.05 4.46
723 870 0.036388 TAAGGACGTACGACGAGGGT 60.036 55.000 24.41 0.00 46.05 4.34
724 871 1.086696 TTAAGGACGTACGACGAGGG 58.913 55.000 24.41 0.00 46.05 4.30
725 872 1.464608 TGTTAAGGACGTACGACGAGG 59.535 52.381 24.41 0.00 46.05 4.63
726 873 2.880822 TGTTAAGGACGTACGACGAG 57.119 50.000 24.41 0.00 46.05 4.18
727 874 3.617540 TTTGTTAAGGACGTACGACGA 57.382 42.857 24.41 5.26 46.05 4.20
729 876 3.301642 CGGATTTGTTAAGGACGTACGAC 59.698 47.826 24.41 16.49 0.00 4.34
730 877 3.057596 ACGGATTTGTTAAGGACGTACGA 60.058 43.478 24.41 0.00 0.00 3.43
731 878 3.244976 ACGGATTTGTTAAGGACGTACG 58.755 45.455 15.01 15.01 0.00 3.67
732 879 3.301642 CGACGGATTTGTTAAGGACGTAC 59.698 47.826 0.00 0.00 32.84 3.67
733 880 3.500982 CGACGGATTTGTTAAGGACGTA 58.499 45.455 0.00 0.00 32.84 3.57
734 881 2.331194 CGACGGATTTGTTAAGGACGT 58.669 47.619 0.00 0.00 35.64 4.34
744 891 2.505498 CGAGCGACCGACGGATTTG 61.505 63.158 23.38 3.89 42.83 2.32
745 892 2.202570 CGAGCGACCGACGGATTT 60.203 61.111 23.38 0.00 42.83 2.17
792 939 4.647615 ATCCGGGCTTCGATCGCG 62.648 66.667 11.09 7.70 42.43 5.87
793 940 3.038417 CATCCGGGCTTCGATCGC 61.038 66.667 11.09 0.00 42.43 4.58
1037 1184 1.608425 ATTTAAGGGAGGGGAGGTGG 58.392 55.000 0.00 0.00 0.00 4.61
1039 1186 2.942905 TGAATTTAAGGGAGGGGAGGT 58.057 47.619 0.00 0.00 0.00 3.85
1075 1222 4.708177 TCTCTCTGGTCTGAACTTTTTGG 58.292 43.478 0.00 0.00 0.00 3.28
1077 1224 5.878406 TCTCTCTCTGGTCTGAACTTTTT 57.122 39.130 0.00 0.00 0.00 1.94
1078 1225 5.878406 TTCTCTCTCTGGTCTGAACTTTT 57.122 39.130 0.00 0.00 0.00 2.27
1103 1295 2.295885 GGAACTGGAGCTCCATTGATG 58.704 52.381 35.11 24.48 46.46 3.07
1632 1830 1.257750 CGGGAGTGGGAGTGTGATGA 61.258 60.000 0.00 0.00 0.00 2.92
1635 1833 2.603473 CCGGGAGTGGGAGTGTGA 60.603 66.667 0.00 0.00 0.00 3.58
1980 2184 2.737252 GCGAAACCTTCAACCTCTAGTG 59.263 50.000 0.00 0.00 0.00 2.74
2084 2293 5.075493 GGCCATCATTCCTCATACAATCTT 58.925 41.667 0.00 0.00 0.00 2.40
2085 2294 4.105217 TGGCCATCATTCCTCATACAATCT 59.895 41.667 0.00 0.00 0.00 2.40
2286 2590 2.028190 CTCTAGCCGCATCCCGTG 59.972 66.667 0.00 0.00 34.38 4.94
2501 2814 2.729491 CGCGCGACAGTTGTCTCA 60.729 61.111 28.94 0.00 42.66 3.27
2512 2825 4.583866 TGATGCATAGGCGCGCGA 62.584 61.111 37.18 14.30 45.35 5.87
2524 2837 1.694150 TGACTATAGGCCACCTGATGC 59.306 52.381 5.01 0.00 34.61 3.91
2637 2957 9.291664 GGAAGCGACTAGTGAATATAATATGTC 57.708 37.037 0.00 0.00 0.00 3.06
2641 2961 7.309621 GGTGGGAAGCGACTAGTGAATATAATA 60.310 40.741 0.00 0.00 0.00 0.98
2755 3079 3.426859 CGCTTGCTAGGTATGATTTCTCG 59.573 47.826 0.00 0.00 0.00 4.04
2768 3092 3.444703 AGTGAAGTATCCGCTTGCTAG 57.555 47.619 0.00 0.00 0.00 3.42
2900 3232 7.969690 TCCTTGCCCATTTCTATTGAATTTA 57.030 32.000 0.00 0.00 31.56 1.40
2902 3234 6.872585 TTCCTTGCCCATTTCTATTGAATT 57.127 33.333 0.00 0.00 31.56 2.17
2961 3293 1.613836 CCTTGCTATGATTCCTGGGC 58.386 55.000 0.00 0.00 0.00 5.36
2962 3294 1.202976 CCCCTTGCTATGATTCCTGGG 60.203 57.143 0.00 0.00 0.00 4.45
2969 3301 3.885297 CGAATTTCACCCCTTGCTATGAT 59.115 43.478 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.