Multiple sequence alignment - TraesCS1D01G202300

Loading Multiple Alignment...

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 TraesCS1D01G202300 chr1D 100.000 3988 0 0 1 3988 285440920 285444907 0.000000e+00 7365.0
1 TraesCS1D01G202300 chr1A 93.187 3611 137 47 1 3536 357061509 357065085 0.000000e+00 5204.0
2 TraesCS1D01G202300 chr1A 93.895 344 16 3 3647 3988 357065264 357065604 7.640000e-142 514.0
3 TraesCS1D01G202300 chr1A 90.244 82 3 2 3545 3626 357065206 357065282 7.050000e-18 102.0
4 TraesCS1D01G202300 chr1B 94.901 2687 86 24 854 3508 388008547 388011214 0.000000e+00 4156.0
5 TraesCS1D01G202300 chr1B 90.505 653 36 14 204 841 388007861 388008502 0.000000e+00 839.0
6 TraesCS1D01G202300 chr1B 90.860 372 24 4 3624 3988 388011275 388011643 1.290000e-134 490.0
7 TraesCS1D01G202300 chr1B 90.972 144 7 2 1 138 388007478 388007621 5.260000e-44 189.0
8 TraesCS1D01G202300 chr1B 88.889 45 5 0 3545 3589 388011281 388011325 5.570000e-04 56.5
9 TraesCS1D01G202300 chr5B 87.588 427 34 6 2250 2665 545197224 545197642 1.000000e-130 477.0
10 TraesCS1D01G202300 chr5B 79.755 163 31 2 1649 1810 213250625 213250786 2.520000e-22 117.0
11 TraesCS1D01G202300 chr3B 86.744 430 38 8 2250 2668 61688216 61687795 1.010000e-125 460.0
12 TraesCS1D01G202300 chr6D 79.439 214 31 8 1651 1858 335375780 335375574 5.370000e-29 139.0
13 TraesCS1D01G202300 chr6A 79.439 214 31 9 1651 1858 475000348 475000142 5.370000e-29 139.0
14 TraesCS1D01G202300 chr4D 83.088 136 23 0 1639 1774 70119460 70119595 1.500000e-24 124.0
15 TraesCS1D01G202300 chr4B 83.088 136 23 0 1639 1774 103773320 103773455 1.500000e-24 124.0
16 TraesCS1D01G202300 chr5D 77.404 208 45 2 1652 1858 197152205 197151999 5.410000e-24 122.0
17 TraesCS1D01G202300 chr5A 76.786 224 48 4 1637 1858 227923938 227924159 5.410000e-24 122.0
18 TraesCS1D01G202300 chr2D 77.564 156 30 4 1502 1656 509941945 509942096 5.490000e-14 89.8
19 TraesCS1D01G202300 chr2A 77.564 156 30 4 1502 1656 653678188 653678339 5.490000e-14 89.8


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 TraesCS1D01G202300 chr1D 285440920 285444907 3987 False 7365.0 7365 100.0000 1 3988 1 chr1D.!!$F1 3987
1 TraesCS1D01G202300 chr1A 357061509 357065604 4095 False 1940.0 5204 92.4420 1 3988 3 chr1A.!!$F1 3987
2 TraesCS1D01G202300 chr1B 388007478 388011643 4165 False 1146.1 4156 91.2254 1 3988 5 chr1B.!!$F1 3987

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
160 189 0.248661 CGCGTAGATGTGCAGCTACT 60.249 55.0 20.59 4.48 45.33 2.57 F
687 896 0.804933 AACGTAAATCTCCTCGGCGC 60.805 55.0 0.00 0.00 0.00 6.53 F
1161 1413 0.105194 TCACCTTCTCCTCCACCACA 60.105 55.0 0.00 0.00 0.00 4.17 F
2571 2823 0.390866 CAACTGCATCCTGCTCGACT 60.391 55.0 0.34 0.00 45.31 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1413 0.179009 CGATGGGGATGATGCTGGTT 60.179 55.0 0.0 0.0 0.00 3.67 R
2678 2942 0.391130 TACCTGTGTGATTCTGCGGC 60.391 55.0 0.0 0.0 0.00 6.53 R
2885 3161 0.176449 TGTCGCAGGTCCATCTCATG 59.824 55.0 0.0 0.0 0.00 3.07 R
3374 3655 0.548031 TGCTCTGGGGCAAGGAATAG 59.452 55.0 0.0 0.0 39.43 1.73 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
116 127 2.581409 GATGTACGACCGGCCACG 60.581 66.667 0.00 8.18 40.55 4.94
130 141 2.350498 CGGCCACGTCGAATTAAAGAAT 59.650 45.455 2.24 0.00 29.41 2.40
160 189 0.248661 CGCGTAGATGTGCAGCTACT 60.249 55.000 20.59 4.48 45.33 2.57
161 190 1.002792 CGCGTAGATGTGCAGCTACTA 60.003 52.381 20.59 3.69 45.33 1.82
162 191 2.386249 GCGTAGATGTGCAGCTACTAC 58.614 52.381 20.59 11.81 45.33 2.73
163 192 2.033550 GCGTAGATGTGCAGCTACTACT 59.966 50.000 20.59 0.00 45.33 2.57
164 193 3.250280 GCGTAGATGTGCAGCTACTACTA 59.750 47.826 20.59 0.00 45.33 1.82
165 194 4.774586 CGTAGATGTGCAGCTACTACTAC 58.225 47.826 20.59 7.65 45.33 2.73
166 195 4.272748 CGTAGATGTGCAGCTACTACTACA 59.727 45.833 20.59 7.16 45.33 2.74
167 196 5.049336 CGTAGATGTGCAGCTACTACTACAT 60.049 44.000 20.59 10.30 45.33 2.29
179 208 7.326305 CAGCTACTACTACATTTTAGCCATACG 59.674 40.741 0.00 0.00 36.60 3.06
180 209 7.014038 AGCTACTACTACATTTTAGCCATACGT 59.986 37.037 0.00 0.00 36.60 3.57
181 210 8.292448 GCTACTACTACATTTTAGCCATACGTA 58.708 37.037 0.00 0.00 30.87 3.57
183 212 7.134815 ACTACTACATTTTAGCCATACGTACG 58.865 38.462 15.01 15.01 0.00 3.67
184 213 5.894807 ACTACATTTTAGCCATACGTACGT 58.105 37.500 25.98 25.98 0.00 3.57
185 214 5.973565 ACTACATTTTAGCCATACGTACGTC 59.026 40.000 26.53 10.66 0.00 4.34
229 419 1.590442 CGTTCGGTTGACGTTGAACAC 60.590 52.381 12.01 3.24 44.69 3.32
341 542 9.793252 ATGACAGTAAATCATTTGTAATTCTGC 57.207 29.630 0.00 0.00 32.77 4.26
349 550 9.709495 AAATCATTTGTAATTCTGCTTGCTTTA 57.291 25.926 0.00 0.00 0.00 1.85
377 578 1.644786 GAGTCGGGGCGTTTCCAATG 61.645 60.000 0.00 0.00 36.21 2.82
407 608 8.192774 CCATGATAATAATGCACTCAGTTGTTT 58.807 33.333 0.00 0.00 0.00 2.83
412 613 7.698836 AATAATGCACTCAGTTGTTTTTGAC 57.301 32.000 0.00 0.00 0.00 3.18
415 616 2.096819 GCACTCAGTTGTTTTTGACGGA 59.903 45.455 0.00 0.00 0.00 4.69
547 756 5.186021 CCGCTAGAGATACTCCCATAATTGT 59.814 44.000 0.00 0.00 0.00 2.71
581 790 3.252458 ACCTGCCAATTCTCGTTTGTTAC 59.748 43.478 0.00 0.00 0.00 2.50
659 868 8.801299 CAGCTTCAGATCTAATCTAGTAATGGA 58.199 37.037 0.00 0.00 37.58 3.41
660 869 9.023962 AGCTTCAGATCTAATCTAGTAATGGAG 57.976 37.037 0.00 0.00 37.58 3.86
661 870 8.802267 GCTTCAGATCTAATCTAGTAATGGAGT 58.198 37.037 0.00 0.00 37.58 3.85
682 891 7.497249 TGGAGTAGTAGTAACGTAAATCTCCTC 59.503 40.741 0.00 5.84 38.63 3.71
687 896 0.804933 AACGTAAATCTCCTCGGCGC 60.805 55.000 0.00 0.00 0.00 6.53
798 1014 2.232298 CTCTGCTCCCTGGTTCCGTC 62.232 65.000 0.00 0.00 0.00 4.79
827 1047 5.045578 TCCAAACTTCCAATTCAACCCAAAA 60.046 36.000 0.00 0.00 0.00 2.44
846 1066 4.906065 AAAGGTACGTCTTTTGGTTTCC 57.094 40.909 0.00 0.00 33.62 3.13
848 1068 4.160642 AGGTACGTCTTTTGGTTTCCTT 57.839 40.909 0.00 0.00 0.00 3.36
849 1069 3.881089 AGGTACGTCTTTTGGTTTCCTTG 59.119 43.478 0.00 0.00 0.00 3.61
850 1070 3.004002 GGTACGTCTTTTGGTTTCCTTGG 59.996 47.826 0.00 0.00 0.00 3.61
851 1071 2.730382 ACGTCTTTTGGTTTCCTTGGT 58.270 42.857 0.00 0.00 0.00 3.67
852 1072 3.093814 ACGTCTTTTGGTTTCCTTGGTT 58.906 40.909 0.00 0.00 0.00 3.67
872 1124 5.583061 TGGTTGATAATTTCGTTGCGTATCT 59.417 36.000 0.00 0.00 0.00 1.98
1161 1413 0.105194 TCACCTTCTCCTCCACCACA 60.105 55.000 0.00 0.00 0.00 4.17
1191 1443 4.530857 CCCATCGTCTCCACGGCC 62.531 72.222 0.00 0.00 46.70 6.13
1206 1458 3.726144 GCCAAGCAGGAGGGCTCT 61.726 66.667 0.00 0.00 45.07 4.09
1215 1467 4.959596 GAGGGCTCTGCGATCGCC 62.960 72.222 35.12 20.33 43.03 5.54
1629 1881 2.125512 ATGAAGGACGGCAGCGTC 60.126 61.111 6.93 6.93 38.09 5.19
2334 2586 3.315949 AAGTGGAAGGCGGCGGTA 61.316 61.111 9.78 0.00 0.00 4.02
2406 2658 0.391528 TCATGGACATGAGCACCGTG 60.392 55.000 10.75 8.97 42.42 4.94
2569 2821 1.078918 CCAACTGCATCCTGCTCGA 60.079 57.895 0.34 0.00 45.31 4.04
2571 2823 0.390866 CAACTGCATCCTGCTCGACT 60.391 55.000 0.34 0.00 45.31 4.18
2609 2870 4.644103 CAGAATGGAATTAACCTGCTGG 57.356 45.455 8.29 8.29 36.07 4.85
2988 3264 1.679032 GGTCGGCAAAGAAGGCATAGT 60.679 52.381 0.00 0.00 0.00 2.12
2989 3265 1.666189 GTCGGCAAAGAAGGCATAGTC 59.334 52.381 0.00 0.00 0.00 2.59
2990 3266 1.277842 TCGGCAAAGAAGGCATAGTCA 59.722 47.619 0.00 0.00 0.00 3.41
3004 3280 2.167398 TAGTCACGAACCAGCAGCCC 62.167 60.000 0.00 0.00 0.00 5.19
3079 3355 5.010719 AGTCGACACTTTGATAGAACAAGGA 59.989 40.000 19.50 0.00 32.52 3.36
3200 3480 7.331687 ACACAACAGTTGATTCTTTTTCTTTGG 59.668 33.333 20.56 0.00 0.00 3.28
3209 3489 8.719645 TGATTCTTTTTCTTTGGGGAAAGATA 57.280 30.769 0.00 0.00 38.46 1.98
3227 3507 6.713731 AAGATAAGGGGAGGTAAAGTTTGA 57.286 37.500 0.00 0.00 0.00 2.69
3283 3564 2.229062 TGCATGTCTATAGCTAGTCGGC 59.771 50.000 0.00 0.00 0.00 5.54
3288 3569 1.880675 TCTATAGCTAGTCGGCACTGC 59.119 52.381 0.00 0.00 33.62 4.40
3324 3605 1.136828 TCAAGCGGGGTGGCTATAAT 58.863 50.000 0.00 0.00 43.93 1.28
3373 3654 4.983671 ACGAAGTGATAGTGATGCAGTA 57.016 40.909 0.00 0.00 42.51 2.74
3374 3655 4.673441 ACGAAGTGATAGTGATGCAGTAC 58.327 43.478 0.00 0.00 42.51 2.73
3375 3656 4.399618 ACGAAGTGATAGTGATGCAGTACT 59.600 41.667 10.12 10.12 42.51 2.73
3457 3747 0.034477 CCAATGTGTACCTCACCCCC 60.034 60.000 0.00 0.00 45.61 5.40
3479 3769 7.094334 CCCCCAATCTCTTTGTTTTCTAGTTAC 60.094 40.741 0.00 0.00 33.15 2.50
3483 3773 8.836413 CAATCTCTTTGTTTTCTAGTTACACCA 58.164 33.333 0.00 0.00 0.00 4.17
3515 3809 0.385223 CTGACGCTGCAGCTTTGAAC 60.385 55.000 34.22 15.09 39.32 3.18
3522 3816 3.330267 GCTGCAGCTTTGAACTAGTACT 58.670 45.455 31.33 0.00 38.21 2.73
3523 3817 4.495422 GCTGCAGCTTTGAACTAGTACTA 58.505 43.478 31.33 1.89 38.21 1.82
3577 3983 6.405731 GCATTGCATAATTGACCAAAGGACTA 60.406 38.462 3.15 0.00 0.00 2.59
3578 3984 7.546358 CATTGCATAATTGACCAAAGGACTAA 58.454 34.615 0.00 0.00 0.00 2.24
3589 3995 7.179966 TGACCAAAGGACTAATGAGTAGAGTA 58.820 38.462 0.00 0.00 35.45 2.59
3590 3996 7.339721 TGACCAAAGGACTAATGAGTAGAGTAG 59.660 40.741 0.00 0.00 35.45 2.57
3591 3997 7.411808 ACCAAAGGACTAATGAGTAGAGTAGA 58.588 38.462 0.00 0.00 35.45 2.59
3592 3998 7.558444 ACCAAAGGACTAATGAGTAGAGTAGAG 59.442 40.741 0.00 0.00 35.45 2.43
3614 4020 2.240279 AGAGTAGTGACCACTGACCAC 58.760 52.381 12.54 3.22 42.52 4.16
3615 4021 1.272769 GAGTAGTGACCACTGACCACC 59.727 57.143 12.54 0.00 42.52 4.61
3616 4022 1.045407 GTAGTGACCACTGACCACCA 58.955 55.000 12.54 0.00 42.52 4.17
3617 4023 1.623811 GTAGTGACCACTGACCACCAT 59.376 52.381 12.54 0.00 42.52 3.55
3618 4024 0.397941 AGTGACCACTGACCACCATG 59.602 55.000 1.31 0.00 40.75 3.66
3619 4025 0.396435 GTGACCACTGACCACCATGA 59.604 55.000 0.00 0.00 0.00 3.07
3620 4026 0.396435 TGACCACTGACCACCATGAC 59.604 55.000 0.00 0.00 0.00 3.06
3621 4027 0.687354 GACCACTGACCACCATGACT 59.313 55.000 0.00 0.00 0.00 3.41
3622 4028 1.899814 GACCACTGACCACCATGACTA 59.100 52.381 0.00 0.00 0.00 2.59
3623 4029 1.623811 ACCACTGACCACCATGACTAC 59.376 52.381 0.00 0.00 0.00 2.73
3624 4030 1.902508 CCACTGACCACCATGACTACT 59.097 52.381 0.00 0.00 0.00 2.57
3625 4031 2.354103 CCACTGACCACCATGACTACTG 60.354 54.545 0.00 0.00 0.00 2.74
3626 4032 1.902508 ACTGACCACCATGACTACTGG 59.097 52.381 0.00 0.00 39.80 4.00
3627 4033 2.179427 CTGACCACCATGACTACTGGA 58.821 52.381 0.00 0.00 37.22 3.86
3628 4034 2.167281 CTGACCACCATGACTACTGGAG 59.833 54.545 0.00 0.00 37.22 3.86
3629 4035 2.225267 TGACCACCATGACTACTGGAGA 60.225 50.000 0.00 0.00 37.22 3.71
3630 4036 2.428890 GACCACCATGACTACTGGAGAG 59.571 54.545 0.00 0.00 37.22 3.20
3631 4037 2.225394 ACCACCATGACTACTGGAGAGT 60.225 50.000 0.00 0.00 37.22 3.24
3632 4038 3.011369 ACCACCATGACTACTGGAGAGTA 59.989 47.826 0.00 0.00 37.22 2.59
3642 4048 3.191078 ACTGGAGAGTAGATGCATTGC 57.809 47.619 0.00 0.46 0.00 3.56
3643 4049 2.502947 ACTGGAGAGTAGATGCATTGCA 59.497 45.455 14.72 14.72 44.86 4.08
3644 4050 4.346127 TACTGGAGAGTAGATGCATTGCAT 59.654 41.667 23.61 23.61 41.88 3.96
3645 4051 5.539955 TACTGGAGAGTAGATGCATTGCATA 59.460 40.000 23.44 7.06 40.46 3.14
3646 4052 6.041979 TACTGGAGAGTAGATGCATTGCATAA 59.958 38.462 23.44 12.41 40.46 1.90
3647 4053 7.952445 TACTGGAGAGTAGATGCATTGCATAAC 60.952 40.741 23.44 21.92 40.46 1.89
3730 4142 1.281419 TCCGCTCCCATTTACCTTCA 58.719 50.000 0.00 0.00 0.00 3.02
3759 4171 3.222855 CCGCTCTCTCCGCTCCAT 61.223 66.667 0.00 0.00 0.00 3.41
3763 4175 1.391157 GCTCTCTCCGCTCCATGACT 61.391 60.000 0.00 0.00 0.00 3.41
3814 4226 3.474570 GTCCCATGCCTCGAGCCT 61.475 66.667 6.99 0.00 42.71 4.58
3817 4229 2.586245 CCATGCCTCGAGCCTGAA 59.414 61.111 6.99 0.00 39.28 3.02
3823 4235 4.148825 CTCGAGCCTGAACCCGGG 62.149 72.222 22.25 22.25 41.93 5.73
3901 4313 2.278013 GCGTTCTCCTCGTAGCCG 60.278 66.667 0.00 0.00 0.00 5.52
3919 4331 4.758251 CCATCGCTGCCACGGTCA 62.758 66.667 0.00 0.00 0.00 4.02
3964 4376 1.750018 CGATGGCCTTGATGCACCA 60.750 57.895 3.32 0.00 36.43 4.17
3978 4390 2.920912 ACCACCCATCACGACCGT 60.921 61.111 0.00 0.00 0.00 4.83
3981 4393 2.032634 CACCCATCACGACCGTTGG 61.033 63.158 6.35 6.35 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.594310 GTGGAGTGAGGGAGTGAGC 59.406 63.158 0.00 0.00 0.00 4.26
116 127 7.509986 CGCGTGAATTTCATTCTTTAATTCGAC 60.510 37.037 1.78 0.00 39.80 4.20
130 141 1.323235 CATCTACGCGCGTGAATTTCA 59.677 47.619 42.78 21.95 0.00 2.69
160 189 7.026631 ACGTACGTATGGCTAAAATGTAGTA 57.973 36.000 21.41 0.00 0.00 1.82
161 190 5.894807 ACGTACGTATGGCTAAAATGTAGT 58.105 37.500 21.41 0.00 0.00 2.73
162 191 5.400485 GGACGTACGTATGGCTAAAATGTAG 59.600 44.000 22.87 0.00 0.00 2.74
163 192 5.280945 GGACGTACGTATGGCTAAAATGTA 58.719 41.667 22.87 0.00 0.00 2.29
164 193 4.114794 GGACGTACGTATGGCTAAAATGT 58.885 43.478 22.87 0.00 0.00 2.71
165 194 3.180980 CGGACGTACGTATGGCTAAAATG 59.819 47.826 22.87 0.76 0.00 2.32
166 195 3.181487 ACGGACGTACGTATGGCTAAAAT 60.181 43.478 27.27 0.00 46.58 1.82
167 196 2.163412 ACGGACGTACGTATGGCTAAAA 59.837 45.455 27.27 0.00 46.58 1.52
179 208 2.510691 CCCCATGCACGGACGTAC 60.511 66.667 0.00 0.00 0.00 3.67
180 209 4.460683 GCCCCATGCACGGACGTA 62.461 66.667 0.00 0.00 40.77 3.57
229 419 4.691860 AAGATTGACTGATTTCCTTGCG 57.308 40.909 0.00 0.00 0.00 4.85
280 470 3.798337 GGTGAAAACAAGTCACATGCTTG 59.202 43.478 9.28 9.28 45.94 4.01
338 529 0.244721 GGCCAACCTAAAGCAAGCAG 59.755 55.000 0.00 0.00 0.00 4.24
341 542 0.804989 CTCGGCCAACCTAAAGCAAG 59.195 55.000 2.24 0.00 0.00 4.01
377 578 6.488006 ACTGAGTGCATTATTATCATGGGTTC 59.512 38.462 0.00 0.00 0.00 3.62
407 608 0.039798 CGTCGTCTTCCTCCGTCAAA 60.040 55.000 0.00 0.00 0.00 2.69
412 613 1.064296 CCATCGTCGTCTTCCTCCG 59.936 63.158 0.00 0.00 0.00 4.63
415 616 1.135139 CATCACCATCGTCGTCTTCCT 59.865 52.381 0.00 0.00 0.00 3.36
547 756 1.304381 GGCAGGTTGATTGGGCAGA 60.304 57.895 0.00 0.00 0.00 4.26
582 791 3.424433 CGCCTAAACAAAACGACCAGATC 60.424 47.826 0.00 0.00 0.00 2.75
659 868 6.481644 CCGAGGAGATTTACGTTACTACTACT 59.518 42.308 0.00 0.00 0.00 2.57
660 869 6.654122 CCGAGGAGATTTACGTTACTACTAC 58.346 44.000 0.00 0.00 0.00 2.73
661 870 5.237344 GCCGAGGAGATTTACGTTACTACTA 59.763 44.000 0.00 0.00 0.00 1.82
760 972 1.625818 AGGTTGCGAGGTCTTGAAGAT 59.374 47.619 0.00 0.00 0.00 2.40
798 1014 4.935352 TGAATTGGAAGTTTGGAACCAG 57.065 40.909 0.00 0.00 33.85 4.00
827 1047 3.851458 AGGAAACCAAAAGACGTACCT 57.149 42.857 0.00 0.00 0.00 3.08
841 1061 6.128929 GCAACGAAATTATCAACCAAGGAAAC 60.129 38.462 0.00 0.00 0.00 2.78
842 1062 5.923684 GCAACGAAATTATCAACCAAGGAAA 59.076 36.000 0.00 0.00 0.00 3.13
843 1063 5.465935 GCAACGAAATTATCAACCAAGGAA 58.534 37.500 0.00 0.00 0.00 3.36
845 1065 3.851403 CGCAACGAAATTATCAACCAAGG 59.149 43.478 0.00 0.00 0.00 3.61
846 1066 4.472286 ACGCAACGAAATTATCAACCAAG 58.528 39.130 0.00 0.00 0.00 3.61
848 1068 5.583061 AGATACGCAACGAAATTATCAACCA 59.417 36.000 0.00 0.00 0.00 3.67
849 1069 5.901884 CAGATACGCAACGAAATTATCAACC 59.098 40.000 0.00 0.00 0.00 3.77
850 1070 5.901884 CCAGATACGCAACGAAATTATCAAC 59.098 40.000 0.00 0.00 0.00 3.18
851 1071 5.583061 ACCAGATACGCAACGAAATTATCAA 59.417 36.000 0.00 0.00 0.00 2.57
852 1072 5.113383 ACCAGATACGCAACGAAATTATCA 58.887 37.500 0.00 0.00 0.00 2.15
872 1124 2.433491 CACGCGATTTCCGGACCA 60.433 61.111 15.93 0.00 39.04 4.02
954 1206 2.269520 CTGCGGATGGGATTGGGTCA 62.270 60.000 0.00 0.00 0.00 4.02
995 1247 0.647410 CTTGCTGTACTTCATCGCCG 59.353 55.000 0.00 0.00 0.00 6.46
1161 1413 0.179009 CGATGGGGATGATGCTGGTT 60.179 55.000 0.00 0.00 0.00 3.67
1689 1941 1.352156 GCGACACGGTCAGGATGTTC 61.352 60.000 5.15 0.00 37.40 3.18
1998 2250 0.677288 TCTTCTTGAGCCGGTCGAAA 59.323 50.000 1.90 0.00 0.00 3.46
2296 2548 1.733041 CGTCGTCGTGCTTCATGGT 60.733 57.895 0.00 0.00 0.00 3.55
2331 2583 0.446616 GCGCCTTGTAGTGCTTTACC 59.553 55.000 0.00 0.00 40.17 2.85
2332 2584 3.969795 GCGCCTTGTAGTGCTTTAC 57.030 52.632 0.00 0.00 40.17 2.01
2442 2694 0.598942 CGACGTTCATGACCCACACA 60.599 55.000 0.00 0.00 0.00 3.72
2609 2870 1.900545 AAGGCCTCGCACCTAGGAAC 61.901 60.000 17.98 5.70 36.14 3.62
2613 2874 1.439644 GAGAAGGCCTCGCACCTAG 59.560 63.158 5.23 0.00 36.14 3.02
2678 2942 0.391130 TACCTGTGTGATTCTGCGGC 60.391 55.000 0.00 0.00 0.00 6.53
2879 3155 0.842635 AGGTCCATCTCATGCCCTTC 59.157 55.000 0.00 0.00 29.14 3.46
2885 3161 0.176449 TGTCGCAGGTCCATCTCATG 59.824 55.000 0.00 0.00 0.00 3.07
2909 3185 1.699730 TCTCCTTGTTCTCGGTGTCA 58.300 50.000 0.00 0.00 0.00 3.58
2988 3264 4.329545 GGGGCTGCTGGTTCGTGA 62.330 66.667 0.00 0.00 0.00 4.35
2989 3265 4.641645 TGGGGCTGCTGGTTCGTG 62.642 66.667 0.00 0.00 0.00 4.35
2990 3266 4.335647 CTGGGGCTGCTGGTTCGT 62.336 66.667 0.00 0.00 0.00 3.85
3004 3280 2.566833 TGGTCAATTCCTGTCACTGG 57.433 50.000 0.00 0.00 0.00 4.00
3079 3355 9.492730 AATTTATTTTGATGACTATGAACCCCT 57.507 29.630 0.00 0.00 0.00 4.79
3130 3408 8.985922 TGGATCCTCCTATATGAATATGACAAG 58.014 37.037 14.23 0.00 37.46 3.16
3200 3480 4.477581 ACTTTACCTCCCCTTATCTTTCCC 59.522 45.833 0.00 0.00 0.00 3.97
3209 3489 4.354087 ACTCATCAAACTTTACCTCCCCTT 59.646 41.667 0.00 0.00 0.00 3.95
3227 3507 6.407202 GGATAACAACTTACAGGTGACTCAT 58.593 40.000 0.00 0.00 40.21 2.90
3373 3654 0.548510 GCTCTGGGGCAAGGAATAGT 59.451 55.000 0.00 0.00 0.00 2.12
3374 3655 0.548031 TGCTCTGGGGCAAGGAATAG 59.452 55.000 0.00 0.00 39.43 1.73
3375 3656 0.548031 CTGCTCTGGGGCAAGGAATA 59.452 55.000 0.00 0.00 41.94 1.75
3457 3747 8.836413 TGGTGTAACTAGAAAACAAAGAGATTG 58.164 33.333 0.00 0.00 40.33 2.67
3501 3795 3.330267 AGTACTAGTTCAAAGCTGCAGC 58.670 45.455 31.53 31.53 42.49 5.25
3515 3809 6.956047 TGCGTCTTGTATCATGTAGTACTAG 58.044 40.000 1.87 2.38 0.00 2.57
3522 3816 5.901552 TGATTCTGCGTCTTGTATCATGTA 58.098 37.500 0.00 0.00 0.00 2.29
3523 3817 4.758688 TGATTCTGCGTCTTGTATCATGT 58.241 39.130 0.00 0.00 0.00 3.21
3577 3983 9.204337 TCACTACTCTACTCTACTCTACTCATT 57.796 37.037 0.00 0.00 0.00 2.57
3578 3984 8.636213 GTCACTACTCTACTCTACTCTACTCAT 58.364 40.741 0.00 0.00 0.00 2.90
3589 3995 4.566070 GGTCAGTGGTCACTACTCTACTCT 60.566 50.000 3.06 0.00 40.20 3.24
3590 3996 3.690628 GGTCAGTGGTCACTACTCTACTC 59.309 52.174 3.06 0.00 40.20 2.59
3591 3997 3.074094 TGGTCAGTGGTCACTACTCTACT 59.926 47.826 3.06 0.00 40.20 2.57
3592 3998 3.190953 GTGGTCAGTGGTCACTACTCTAC 59.809 52.174 3.06 0.00 40.20 2.59
3618 4024 8.348944 TGCAATGCATCTACTCTCCAGTAGTC 62.349 46.154 2.72 2.14 42.30 2.59
3619 4025 6.623916 TGCAATGCATCTACTCTCCAGTAGT 61.624 44.000 2.72 0.00 42.30 2.73
3620 4026 4.202192 TGCAATGCATCTACTCTCCAGTAG 60.202 45.833 2.72 3.17 42.66 2.57
3621 4027 3.706086 TGCAATGCATCTACTCTCCAGTA 59.294 43.478 2.72 0.00 31.71 2.74
3622 4028 2.502947 TGCAATGCATCTACTCTCCAGT 59.497 45.455 2.72 0.00 31.71 4.00
3623 4029 3.189618 TGCAATGCATCTACTCTCCAG 57.810 47.619 2.72 0.00 31.71 3.86
3635 4041 4.220163 TCATTTGGTCAGTTATGCAATGCA 59.780 37.500 11.44 11.44 44.86 3.96
3636 4042 4.563976 GTCATTTGGTCAGTTATGCAATGC 59.436 41.667 0.00 0.00 0.00 3.56
3637 4043 5.957798 AGTCATTTGGTCAGTTATGCAATG 58.042 37.500 0.00 0.00 0.00 2.82
3638 4044 6.886459 AGTAGTCATTTGGTCAGTTATGCAAT 59.114 34.615 0.00 0.00 0.00 3.56
3639 4045 6.149308 CAGTAGTCATTTGGTCAGTTATGCAA 59.851 38.462 0.00 0.00 0.00 4.08
3640 4046 5.643348 CAGTAGTCATTTGGTCAGTTATGCA 59.357 40.000 0.00 0.00 0.00 3.96
3641 4047 5.874810 TCAGTAGTCATTTGGTCAGTTATGC 59.125 40.000 0.00 0.00 0.00 3.14
3642 4048 7.905604 TTCAGTAGTCATTTGGTCAGTTATG 57.094 36.000 0.00 0.00 0.00 1.90
3643 4049 9.823647 CTATTCAGTAGTCATTTGGTCAGTTAT 57.176 33.333 0.00 0.00 0.00 1.89
3644 4050 9.031537 TCTATTCAGTAGTCATTTGGTCAGTTA 57.968 33.333 0.00 0.00 0.00 2.24
3645 4051 7.907389 TCTATTCAGTAGTCATTTGGTCAGTT 58.093 34.615 0.00 0.00 0.00 3.16
3646 4052 7.179338 ACTCTATTCAGTAGTCATTTGGTCAGT 59.821 37.037 0.00 0.00 0.00 3.41
3647 4053 7.490725 CACTCTATTCAGTAGTCATTTGGTCAG 59.509 40.741 0.00 0.00 0.00 3.51
3648 4054 7.323420 CACTCTATTCAGTAGTCATTTGGTCA 58.677 38.462 0.00 0.00 0.00 4.02
3649 4055 6.758886 CCACTCTATTCAGTAGTCATTTGGTC 59.241 42.308 0.00 0.00 0.00 4.02
3650 4056 6.213600 ACCACTCTATTCAGTAGTCATTTGGT 59.786 38.462 0.00 0.00 0.00 3.67
3651 4057 6.536582 CACCACTCTATTCAGTAGTCATTTGG 59.463 42.308 0.00 0.00 0.00 3.28
3652 4058 6.536582 CCACCACTCTATTCAGTAGTCATTTG 59.463 42.308 0.00 0.00 0.00 2.32
3653 4059 6.644347 CCACCACTCTATTCAGTAGTCATTT 58.356 40.000 0.00 0.00 0.00 2.32
3742 4154 3.222855 ATGGAGCGGAGAGAGCGG 61.223 66.667 0.00 0.00 40.04 5.52
3759 4171 1.581934 CAAGTCGTCAAGGCAAGTCA 58.418 50.000 0.00 0.00 0.00 3.41
3763 4175 1.785041 GCAGCAAGTCGTCAAGGCAA 61.785 55.000 0.00 0.00 0.00 4.52
3802 4214 2.586792 GGTTCAGGCTCGAGGCAT 59.413 61.111 36.63 20.93 44.01 4.40
3838 4250 1.350351 GATACCAGCAGCATGGGAGAT 59.650 52.381 13.53 5.73 45.25 2.75
3919 4331 2.293677 CCCTACGATACTGCAATCTCGT 59.706 50.000 13.09 13.09 45.40 4.18
3964 4376 2.047213 AACCAACGGTCGTGATGGGT 62.047 55.000 15.75 8.61 37.26 4.51


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

AutoCloner maintained by Alex Coulton.