Multiple sequence alignment - TraesCS3A01G443600

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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 TraesCS3A01G443600 chr3A 100.000 5710 0 0 1 5710 685114414 685120123 0.000000e+00 10545
1 TraesCS3A01G443600 chr3D 95.310 4307 145 27 650 4946 548242390 548246649 0.000000e+00 6782
2 TraesCS3A01G443600 chr3D 86.935 796 55 26 4948 5710 548246698 548247477 0.000000e+00 848
3 TraesCS3A01G443600 chr3D 93.229 576 29 4 4 577 548241822 548242389 0.000000e+00 839
4 TraesCS3A01G443600 chr3B 94.979 3545 135 20 706 4233 725702581 725706099 0.000000e+00 5520
5 TraesCS3A01G443600 chr3B 95.308 1492 56 8 4218 5705 725706149 725707630 0.000000e+00 2355
6 TraesCS3A01G443600 chr3B 86.486 296 31 6 345 635 725702280 725702571 3.320000e-82 316
7 TraesCS3A01G443600 chr7B 95.701 442 18 1 3954 4394 603668317 603667876 0.000000e+00 710
8 TraesCS3A01G443600 chr7B 96.030 403 12 3 3231 3632 603669425 603669026 0.000000e+00 652
9 TraesCS3A01G443600 chr7B 97.857 280 6 0 3646 3925 603668590 603668311 8.600000e-133 484
10 TraesCS3A01G443600 chr7B 92.347 196 14 1 4458 4653 603667766 603667572 1.570000e-70 278


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 TraesCS3A01G443600 chr3A 685114414 685120123 5709 False 10545.000000 10545 100.000000 1 5710 1 chr3A.!!$F1 5709
1 TraesCS3A01G443600 chr3D 548241822 548247477 5655 False 2823.000000 6782 91.824667 4 5710 3 chr3D.!!$F1 5706
2 TraesCS3A01G443600 chr3B 725702280 725707630 5350 False 2730.333333 5520 92.257667 345 5705 3 chr3B.!!$F1 5360
3 TraesCS3A01G443600 chr7B 603667572 603669425 1853 True 531.000000 710 95.483750 3231 4653 4 chr7B.!!$R1 1422

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
532 536 0.108945 ACGGTAGCGTAGTGAAAGGC 60.109 55.000 19.91 0.0 0.00 4.35 F
1159 1170 0.178891 TTTGCCTCTGACCCCTCTCT 60.179 55.000 0.00 0.0 0.00 3.10 F
1625 1641 0.179067 AGCACGAAAACGACAGGGAA 60.179 50.000 0.00 0.0 0.00 3.97 F
2900 2922 1.001597 GGGACGACAAGGAGCTATACG 60.002 57.143 0.00 0.0 0.00 3.06 F
3947 4395 1.136891 ACCTTTGCTGCAGGTTTCAAC 59.863 47.619 17.12 0.0 42.45 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1726 0.038159 AGGTCTTCAGAAAGGCGTCG 60.038 55.000 0.0 0.0 38.03 5.12 R
3135 3157 0.746659 AAGGCACCAGAAACTGTTGC 59.253 50.000 11.7 11.7 46.64 4.17 R
3173 3195 2.097466 GGTGGTTTGTAGGAATCATGCG 59.903 50.000 0.0 0.0 0.00 4.73 R
4676 5254 2.305635 TGCTTTCATAACCAGCTCCTCA 59.694 45.455 0.0 0.0 34.42 3.86 R
5351 5999 2.328099 CCACACCCTCTTCGCTTGC 61.328 63.158 0.0 0.0 0.00 4.01 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
80 81 2.870435 GCCCCGCACACATAATACCTAG 60.870 54.545 0.00 0.00 0.00 3.02
188 189 7.793948 AAAGTTGACCTATCAGTACTAAGGT 57.206 36.000 18.80 18.80 45.02 3.50
216 217 2.699846 AGGAATTTCTGGCAAACAAGCA 59.300 40.909 0.00 0.00 35.83 3.91
263 264 8.349245 CACCAAGAGTTTTTATATTGTCACACA 58.651 33.333 0.00 0.00 0.00 3.72
288 289 1.399089 TCGTATTGCGTCATCAGTCGA 59.601 47.619 0.00 0.00 42.13 4.20
289 290 2.032924 TCGTATTGCGTCATCAGTCGAT 59.967 45.455 0.00 0.00 42.13 3.59
320 321 2.319438 ACTAGGAGGGAGGAGGAACATT 59.681 50.000 0.00 0.00 0.00 2.71
333 334 2.573915 AGGAACATTGGAGGAAGGAGAC 59.426 50.000 0.00 0.00 0.00 3.36
344 345 3.178865 AGGAAGGAGACGGGTTAATGAA 58.821 45.455 0.00 0.00 0.00 2.57
407 410 1.886422 AGGGGATGAAGGAAGAGGAC 58.114 55.000 0.00 0.00 0.00 3.85
449 452 0.384309 GACGATGGTCATGCTCGGTA 59.616 55.000 2.59 0.00 42.91 4.02
481 484 2.848887 CAGTGAATCGACTCGATGTCAC 59.151 50.000 27.68 27.68 46.30 3.67
482 485 2.488153 AGTGAATCGACTCGATGTCACA 59.512 45.455 31.40 21.06 46.30 3.58
483 486 2.594654 GTGAATCGACTCGATGTCACAC 59.405 50.000 28.69 23.32 46.30 3.82
484 487 2.488153 TGAATCGACTCGATGTCACACT 59.512 45.455 14.62 0.00 46.30 3.55
485 488 3.687698 TGAATCGACTCGATGTCACACTA 59.312 43.478 14.62 0.00 46.30 2.74
486 489 3.677190 ATCGACTCGATGTCACACTAC 57.323 47.619 13.20 0.00 45.24 2.73
493 497 1.404035 CGATGTCACACTACCGATGGA 59.596 52.381 0.00 0.00 0.00 3.41
496 500 2.244695 TGTCACACTACCGATGGAAGT 58.755 47.619 0.00 0.00 0.00 3.01
507 511 6.724441 ACTACCGATGGAAGTGGATATCATTA 59.276 38.462 4.83 0.00 0.00 1.90
513 517 7.603784 CGATGGAAGTGGATATCATTATCAACA 59.396 37.037 4.83 0.00 40.10 3.33
532 536 0.108945 ACGGTAGCGTAGTGAAAGGC 60.109 55.000 19.91 0.00 0.00 4.35
539 543 1.373748 GTAGTGAAAGGCGCGGACA 60.374 57.895 8.83 0.00 0.00 4.02
549 553 1.702491 GGCGCGGACAGTAATGAACC 61.702 60.000 8.83 0.00 0.00 3.62
594 598 3.763356 GGGTCGGGGACACGGTAC 61.763 72.222 0.00 0.00 33.68 3.34
599 603 3.059099 GGGGACACGGTACCGAAA 58.941 61.111 39.52 0.00 37.42 3.46
635 639 3.256383 GGGGGTGCGTTTACATTTTAACT 59.744 43.478 0.00 0.00 0.00 2.24
637 641 4.478699 GGGTGCGTTTACATTTTAACTCC 58.521 43.478 0.00 0.00 0.00 3.85
638 642 4.153256 GGTGCGTTTACATTTTAACTCCG 58.847 43.478 0.00 0.00 0.00 4.63
639 643 4.319694 GGTGCGTTTACATTTTAACTCCGT 60.320 41.667 0.00 0.00 0.00 4.69
641 645 4.272991 TGCGTTTACATTTTAACTCCGTGT 59.727 37.500 0.00 0.00 0.00 4.49
642 646 5.207033 GCGTTTACATTTTAACTCCGTGTT 58.793 37.500 0.00 0.00 42.31 3.32
643 647 5.337773 GCGTTTACATTTTAACTCCGTGTTC 59.662 40.000 0.00 0.00 39.89 3.18
644 648 5.557405 CGTTTACATTTTAACTCCGTGTTCG 59.443 40.000 0.00 0.00 39.89 3.95
645 649 6.561902 CGTTTACATTTTAACTCCGTGTTCGA 60.562 38.462 0.00 0.00 39.89 3.71
646 650 6.841443 TTACATTTTAACTCCGTGTTCGAA 57.159 33.333 0.00 0.00 39.89 3.71
647 651 5.338614 ACATTTTAACTCCGTGTTCGAAG 57.661 39.130 0.00 0.00 39.89 3.79
648 652 5.051816 ACATTTTAACTCCGTGTTCGAAGA 58.948 37.500 0.00 0.00 39.89 2.87
693 697 5.564048 AGAAACGTATCCTAGTGTGACTC 57.436 43.478 0.00 0.00 0.00 3.36
743 747 7.601508 AGACGTATTCCTAAATTTCACGTTTCT 59.398 33.333 0.00 0.00 37.58 2.52
745 749 6.892951 CGTATTCCTAAATTTCACGTTTCTCG 59.107 38.462 0.00 0.00 46.00 4.04
775 779 3.008375 TGGAGGAGGAAGAAGACAACATG 59.992 47.826 0.00 0.00 0.00 3.21
776 780 3.261897 GGAGGAGGAAGAAGACAACATGA 59.738 47.826 0.00 0.00 0.00 3.07
777 781 4.249661 GAGGAGGAAGAAGACAACATGAC 58.750 47.826 0.00 0.00 0.00 3.06
1152 1163 1.815003 CTCATTGGTTTGCCTCTGACC 59.185 52.381 0.00 0.00 35.27 4.02
1154 1165 0.251787 ATTGGTTTGCCTCTGACCCC 60.252 55.000 0.00 0.00 35.27 4.95
1155 1166 1.360393 TTGGTTTGCCTCTGACCCCT 61.360 55.000 0.00 0.00 35.27 4.79
1157 1168 1.492993 GGTTTGCCTCTGACCCCTCT 61.493 60.000 0.00 0.00 0.00 3.69
1159 1170 0.178891 TTTGCCTCTGACCCCTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
1165 1176 2.654863 CTCTGACCCCTCTCTCTCTTC 58.345 57.143 0.00 0.00 0.00 2.87
1176 1187 4.401202 CCTCTCTCTCTTCCTTTACCTGTC 59.599 50.000 0.00 0.00 0.00 3.51
1178 1189 3.442076 TCTCTCTTCCTTTACCTGTCCC 58.558 50.000 0.00 0.00 0.00 4.46
1179 1190 3.173965 CTCTCTTCCTTTACCTGTCCCA 58.826 50.000 0.00 0.00 0.00 4.37
1183 1194 5.189145 TCTCTTCCTTTACCTGTCCCATTAC 59.811 44.000 0.00 0.00 0.00 1.89
1344 1359 4.423732 GAAAGCACGCATATTGGTTTGAT 58.576 39.130 7.58 0.00 43.03 2.57
1409 1424 9.601217 GCTCAAAGAAATCCTAATAACTGTAGA 57.399 33.333 0.00 0.00 0.00 2.59
1416 1431 9.892130 GAAATCCTAATAACTGTAGATATGGGG 57.108 37.037 0.00 0.00 0.00 4.96
1464 1479 0.822164 ACACACATACTAGCGGGGTC 59.178 55.000 0.00 0.00 0.00 4.46
1531 1546 5.246203 TCACCTGTCTTAGTTTCTACATGCT 59.754 40.000 0.00 0.00 0.00 3.79
1567 1583 3.824443 CGTCTTTTGGGTTTATGGGACTT 59.176 43.478 0.00 0.00 0.00 3.01
1570 1586 5.480422 GTCTTTTGGGTTTATGGGACTTCAT 59.520 40.000 0.00 0.00 0.00 2.57
1625 1641 0.179067 AGCACGAAAACGACAGGGAA 60.179 50.000 0.00 0.00 0.00 3.97
1709 1725 6.769822 AGTTTGATGATATGATGGTGAGAACC 59.230 38.462 0.00 0.00 0.00 3.62
1710 1726 5.233083 TGATGATATGATGGTGAGAACCC 57.767 43.478 0.00 0.00 0.00 4.11
1728 1745 1.014564 CCGACGCCTTTCTGAAGACC 61.015 60.000 0.00 0.00 34.71 3.85
1733 1750 2.222027 CGCCTTTCTGAAGACCTGTTT 58.778 47.619 0.00 0.00 34.71 2.83
1759 1776 8.464770 TTCATACATTTTCATACTTTTGCTGC 57.535 30.769 0.00 0.00 0.00 5.25
1789 1806 8.375506 AGACTGATCTGTACAACCATCTTAAAA 58.624 33.333 5.09 0.00 32.29 1.52
1797 1814 6.712998 TGTACAACCATCTTAAAAAGCTGCTA 59.287 34.615 0.90 0.00 0.00 3.49
1805 1822 8.031277 CCATCTTAAAAAGCTGCTAATTTCTGT 58.969 33.333 14.29 0.00 0.00 3.41
1845 1862 9.049523 TGAAGCAGATTTGATGTATTCAGTATC 57.950 33.333 0.00 0.00 35.27 2.24
2003 2021 2.099098 ACTTGTTTGGGAGAAAGCGTTG 59.901 45.455 0.00 0.00 0.00 4.10
2021 2039 5.989168 AGCGTTGCTAATATGTTATGTAGCA 59.011 36.000 0.25 0.25 45.39 3.49
2178 2197 4.246458 GTTAATGTCCACTCACTCCAGAC 58.754 47.826 0.00 0.00 0.00 3.51
2179 2198 1.270907 ATGTCCACTCACTCCAGACC 58.729 55.000 0.00 0.00 0.00 3.85
2199 2218 2.618709 CCGCACCTCCTTATCCAAAATC 59.381 50.000 0.00 0.00 0.00 2.17
2204 2223 5.297029 GCACCTCCTTATCCAAAATCACTAC 59.703 44.000 0.00 0.00 0.00 2.73
2205 2224 6.653989 CACCTCCTTATCCAAAATCACTACT 58.346 40.000 0.00 0.00 0.00 2.57
2206 2225 7.635089 GCACCTCCTTATCCAAAATCACTACTA 60.635 40.741 0.00 0.00 0.00 1.82
2207 2226 7.928706 CACCTCCTTATCCAAAATCACTACTAG 59.071 40.741 0.00 0.00 0.00 2.57
2208 2227 7.844779 ACCTCCTTATCCAAAATCACTACTAGA 59.155 37.037 0.00 0.00 0.00 2.43
2482 2504 7.491682 AGGTTTTCATGTATTATTGATGTGGC 58.508 34.615 0.00 0.00 0.00 5.01
2498 2520 1.351350 GTGGCACCCTAGACCTTTTCT 59.649 52.381 6.29 0.00 38.51 2.52
2670 2692 6.391227 TTTTTCTTCATGGAGAAAGTGGAC 57.609 37.500 24.76 0.00 44.05 4.02
2858 2880 5.435291 AGCCAGTGATAGATTCCAAGAAAG 58.565 41.667 0.00 0.00 0.00 2.62
2900 2922 1.001597 GGGACGACAAGGAGCTATACG 60.002 57.143 0.00 0.00 0.00 3.06
2929 2951 7.410800 ACGTATACGACTTGAAACAATGAAA 57.589 32.000 30.77 0.00 43.02 2.69
2951 2973 6.463995 AATTGAGGTTTGTGCTGTTCTTAA 57.536 33.333 0.00 0.00 0.00 1.85
2992 3014 3.448301 TCCCAATAAGCTGCCATCTTTTG 59.552 43.478 0.00 0.00 0.00 2.44
3011 3033 8.027524 TCTTTTGGTCTTCTATGCTCTCATAT 57.972 34.615 0.00 0.00 34.88 1.78
3135 3157 5.782893 TGATTTTGGTTTGAGGTTGTAGG 57.217 39.130 0.00 0.00 0.00 3.18
3155 3177 2.497107 CAACAGTTTCTGGTGCCTTG 57.503 50.000 1.85 0.00 42.40 3.61
3198 3220 4.380843 TGATTCCTACAAACCACCATGT 57.619 40.909 0.00 0.00 0.00 3.21
3200 3222 4.042809 TGATTCCTACAAACCACCATGTCT 59.957 41.667 0.00 0.00 0.00 3.41
3638 3661 1.649171 CTCGTCGGTTCACTCGAAATG 59.351 52.381 0.00 0.00 38.42 2.32
3830 4278 5.978814 TCTTTTGACCTGCTAGGATTACTC 58.021 41.667 8.91 0.00 37.67 2.59
3947 4395 1.136891 ACCTTTGCTGCAGGTTTCAAC 59.863 47.619 17.12 0.00 42.45 3.18
4095 4543 4.584325 TCAGCAAAATAGAGGCTTGTGTTT 59.416 37.500 0.00 0.00 35.27 2.83
4100 4548 7.829211 AGCAAAATAGAGGCTTGTGTTTATAGA 59.171 33.333 0.00 0.00 33.21 1.98
4251 4764 8.134895 TGCTACTTCAAACCACTATTTTTCTTG 58.865 33.333 0.00 0.00 0.00 3.02
4445 5023 6.482308 TGAGTTCTTACAGCCTTTTCTTGTAC 59.518 38.462 0.00 0.00 0.00 2.90
4448 5026 5.925509 TCTTACAGCCTTTTCTTGTACTGT 58.074 37.500 0.00 0.00 41.06 3.55
4456 5034 6.206829 AGCCTTTTCTTGTACTGTTTCATACC 59.793 38.462 0.00 0.00 0.00 2.73
4676 5254 6.491714 AATGAGATCATTGGTGCTACTACT 57.508 37.500 7.26 0.00 44.22 2.57
4697 5275 2.305635 TGAGGAGCTGGTTATGAAAGCA 59.694 45.455 0.00 0.00 40.68 3.91
4717 5295 4.686554 AGCAAGACAAAGCTAGTAAACTCG 59.313 41.667 0.00 0.00 39.78 4.18
4733 5311 6.993902 AGTAAACTCGATTTGAACCAGGTAAA 59.006 34.615 0.00 0.00 0.00 2.01
4751 5329 7.255139 CCAGGTAAACTTCTTGTAAACTCTTGG 60.255 40.741 0.00 0.00 0.00 3.61
4808 5386 2.747989 CAAGAAGTGCTGACATGCTGAT 59.252 45.455 0.00 0.00 0.00 2.90
4812 5390 3.623906 AGTGCTGACATGCTGATACTT 57.376 42.857 0.00 0.00 0.00 2.24
4818 5396 5.352293 TGCTGACATGCTGATACTTAGTTTG 59.648 40.000 0.00 0.00 0.00 2.93
4893 5471 0.522180 GAAGTTGAGGAGAGACGCGA 59.478 55.000 15.93 0.00 0.00 5.87
4984 5609 9.722184 GGTGTAAGAATTAAATATCCCCTACTC 57.278 37.037 0.00 0.00 28.70 2.59
5014 5641 4.647564 ATGGAGATGTTCAAGGAAGTGT 57.352 40.909 0.00 0.00 0.00 3.55
5122 5755 3.895656 GGGTATTTTCCTTCCCCTTATGC 59.104 47.826 0.00 0.00 34.32 3.14
5125 5758 4.513406 ATTTTCCTTCCCCTTATGCGTA 57.487 40.909 0.00 0.00 0.00 4.42
5351 5999 2.419297 GGAGGTACATGTGCAGGAGAAG 60.419 54.545 16.11 0.00 0.00 2.85
5705 6364 0.309922 CTTGCTGCTGTGTTGTCTGG 59.690 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.217799 CAGGGTAGAGGTCATTTTATTTATGGA 58.782 37.037 0.00 0.00 0.00 3.41
39 40 3.322828 GGCGGATTAATACAGGTAGGTCA 59.677 47.826 0.00 0.00 0.00 4.02
48 49 0.533308 GTGCGGGGCGGATTAATACA 60.533 55.000 0.00 0.00 0.00 2.29
182 183 6.116126 CCAGAAATTCCTTAGGTGACCTTAG 58.884 44.000 10.53 10.55 34.61 2.18
183 184 5.572885 GCCAGAAATTCCTTAGGTGACCTTA 60.573 44.000 10.53 0.00 34.61 2.69
184 185 4.811063 GCCAGAAATTCCTTAGGTGACCTT 60.811 45.833 10.53 0.00 34.61 3.50
185 186 3.308473 GCCAGAAATTCCTTAGGTGACCT 60.308 47.826 10.00 10.00 37.71 3.85
186 187 3.017442 GCCAGAAATTCCTTAGGTGACC 58.983 50.000 0.00 0.00 0.00 4.02
187 188 3.686016 TGCCAGAAATTCCTTAGGTGAC 58.314 45.455 0.00 0.00 0.00 3.67
188 189 4.380843 TTGCCAGAAATTCCTTAGGTGA 57.619 40.909 0.00 0.00 0.00 4.02
216 217 7.499292 TGGTGAGATTGTTGATTCAAAATTGT 58.501 30.769 0.00 0.00 0.00 2.71
266 267 6.267956 ATCGACTGATGACGCAATACGACT 62.268 45.833 0.00 0.00 37.43 4.18
288 289 2.023015 TCCCTCCTAGTCACATGGTCAT 60.023 50.000 0.00 0.00 0.00 3.06
289 290 1.361197 TCCCTCCTAGTCACATGGTCA 59.639 52.381 0.00 0.00 0.00 4.02
297 298 1.288335 GTTCCTCCTCCCTCCTAGTCA 59.712 57.143 0.00 0.00 0.00 3.41
320 321 0.410663 TAACCCGTCTCCTTCCTCCA 59.589 55.000 0.00 0.00 0.00 3.86
333 334 4.528920 TGTATCCCCTTTTCATTAACCCG 58.471 43.478 0.00 0.00 0.00 5.28
344 345 3.718956 CCTCCTCTTCATGTATCCCCTTT 59.281 47.826 0.00 0.00 0.00 3.11
407 410 4.452733 GGTCCGCCCCTTCACTCG 62.453 72.222 0.00 0.00 0.00 4.18
449 452 4.707448 AGTCGATTCACTGGTAAGACAGAT 59.293 41.667 0.00 0.00 40.97 2.90
481 484 4.280929 TGATATCCACTTCCATCGGTAGTG 59.719 45.833 11.62 11.62 46.18 2.74
482 485 4.480115 TGATATCCACTTCCATCGGTAGT 58.520 43.478 0.00 0.00 33.63 2.73
483 486 5.667539 ATGATATCCACTTCCATCGGTAG 57.332 43.478 0.00 0.00 0.00 3.18
484 487 7.398904 TGATAATGATATCCACTTCCATCGGTA 59.601 37.037 0.00 0.00 37.68 4.02
485 488 4.982241 AATGATATCCACTTCCATCGGT 57.018 40.909 0.00 0.00 0.00 4.69
486 489 6.643388 TGATAATGATATCCACTTCCATCGG 58.357 40.000 0.00 0.00 37.68 4.18
493 497 6.591935 ACCGTGTTGATAATGATATCCACTT 58.408 36.000 0.00 0.00 37.68 3.16
496 500 6.163476 GCTACCGTGTTGATAATGATATCCA 58.837 40.000 0.00 0.00 37.68 3.41
532 536 0.457166 TCGGTTCATTACTGTCCGCG 60.457 55.000 0.00 0.00 39.15 6.46
539 543 6.206829 CCTCTTTCCTTTTTCGGTTCATTACT 59.793 38.462 0.00 0.00 0.00 2.24
549 553 2.737252 CGGTCTCCTCTTTCCTTTTTCG 59.263 50.000 0.00 0.00 0.00 3.46
594 598 2.499685 CCTCGCCCTAGGTTTCGG 59.500 66.667 8.29 0.00 31.46 4.30
617 621 4.609708 CACGGAGTTAAAATGTAAACGCAC 59.390 41.667 0.00 0.00 41.61 5.34
624 628 6.144402 GTCTTCGAACACGGAGTTAAAATGTA 59.856 38.462 0.00 0.00 41.61 2.29
637 641 2.704193 GACGCCGTCTTCGAACACG 61.704 63.158 17.61 17.61 39.71 4.49
638 642 2.704193 CGACGCCGTCTTCGAACAC 61.704 63.158 16.07 0.00 36.24 3.32
639 643 2.391238 TTCGACGCCGTCTTCGAACA 62.391 55.000 16.07 0.00 44.45 3.18
641 645 1.008652 TTTCGACGCCGTCTTCGAA 60.009 52.632 16.07 11.69 46.54 3.71
642 646 1.727022 GTTTCGACGCCGTCTTCGA 60.727 57.895 16.07 5.49 40.51 3.71
643 647 2.761354 GTTTCGACGCCGTCTTCG 59.239 61.111 16.07 2.80 35.59 3.79
644 648 2.713894 CCGTTTCGACGCCGTCTTC 61.714 63.158 16.07 2.17 37.05 2.87
645 649 2.732094 CCGTTTCGACGCCGTCTT 60.732 61.111 16.07 0.00 37.05 3.01
646 650 4.712425 CCCGTTTCGACGCCGTCT 62.712 66.667 16.07 0.00 37.05 4.18
647 651 4.705519 TCCCGTTTCGACGCCGTC 62.706 66.667 7.29 7.29 37.05 4.79
653 657 5.276067 CGTTTCTATATTGTCCCGTTTCGAC 60.276 44.000 0.00 0.00 0.00 4.20
672 676 4.142730 ACGAGTCACACTAGGATACGTTTC 60.143 45.833 0.00 0.00 46.39 2.78
693 697 4.811024 TCCACACTAGGATACGTAGTTACG 59.189 45.833 9.93 9.93 43.19 3.18
754 758 3.261897 TCATGTTGTCTTCTTCCTCCTCC 59.738 47.826 0.00 0.00 0.00 4.30
775 779 0.740737 AAGCACACCAAGCTGTTGTC 59.259 50.000 0.00 0.00 42.53 3.18
776 780 0.457035 CAAGCACACCAAGCTGTTGT 59.543 50.000 0.00 0.00 42.53 3.32
777 781 0.249155 CCAAGCACACCAAGCTGTTG 60.249 55.000 0.00 0.00 42.53 3.33
1144 1155 0.926293 AGAGAGAGAGGGGTCAGAGG 59.074 60.000 0.00 0.00 0.00 3.69
1152 1163 3.704061 CAGGTAAAGGAAGAGAGAGAGGG 59.296 52.174 0.00 0.00 0.00 4.30
1154 1165 4.401202 GGACAGGTAAAGGAAGAGAGAGAG 59.599 50.000 0.00 0.00 0.00 3.20
1155 1166 4.345854 GGACAGGTAAAGGAAGAGAGAGA 58.654 47.826 0.00 0.00 0.00 3.10
1157 1168 3.181410 TGGGACAGGTAAAGGAAGAGAGA 60.181 47.826 0.00 0.00 0.00 3.10
1159 1170 3.269592 TGGGACAGGTAAAGGAAGAGA 57.730 47.619 0.00 0.00 0.00 3.10
1414 1429 4.158949 GTGGTATGAAATGTACAAACCCCC 59.841 45.833 0.00 0.00 0.00 5.40
1416 1431 5.014202 AGGTGGTATGAAATGTACAAACCC 58.986 41.667 0.00 0.00 33.86 4.11
1418 1433 6.882678 AGGTAGGTGGTATGAAATGTACAAAC 59.117 38.462 0.00 0.00 0.00 2.93
1419 1434 7.023171 AGGTAGGTGGTATGAAATGTACAAA 57.977 36.000 0.00 0.00 0.00 2.83
1464 1479 5.440610 ACTTGATAGCCACATTAGGAAAGG 58.559 41.667 0.00 0.00 0.00 3.11
1548 1563 7.178451 AGTTATGAAGTCCCATAAACCCAAAAG 59.822 37.037 0.00 0.00 39.76 2.27
1567 1583 6.728200 CAACAGAGTTTGCTTTCAGTTATGA 58.272 36.000 0.00 0.00 0.00 2.15
1625 1641 3.008813 TCTTGCAGAGCTTCAGGAATTCT 59.991 43.478 5.23 0.00 0.00 2.40
1709 1725 1.014564 GGTCTTCAGAAAGGCGTCGG 61.015 60.000 0.00 0.00 38.03 4.79
1710 1726 0.038159 AGGTCTTCAGAAAGGCGTCG 60.038 55.000 0.00 0.00 38.03 5.12
1733 1750 8.924691 GCAGCAAAAGTATGAAAATGTATGAAA 58.075 29.630 0.00 0.00 0.00 2.69
1749 1766 2.923121 TCAGTCTGAAGCAGCAAAAGT 58.077 42.857 0.00 0.00 0.00 2.66
1751 1768 3.748083 AGATCAGTCTGAAGCAGCAAAA 58.252 40.909 6.64 0.00 32.13 2.44
1789 1806 3.190118 GCACTGACAGAAATTAGCAGCTT 59.810 43.478 10.08 0.00 0.00 3.74
1797 1814 6.808829 TCAATTTCAAGCACTGACAGAAATT 58.191 32.000 10.08 7.17 44.90 1.82
2003 2021 9.630098 AATTGCAATGCTACATAACATATTAGC 57.370 29.630 13.82 0.00 37.95 3.09
2021 2039 4.630940 CGAATTGGGCACTTAAATTGCAAT 59.369 37.500 5.99 5.99 42.12 3.56
2178 2197 2.122783 TTTTGGATAAGGAGGTGCGG 57.877 50.000 0.00 0.00 0.00 5.69
2179 2198 3.065371 GTGATTTTGGATAAGGAGGTGCG 59.935 47.826 0.00 0.00 0.00 5.34
2199 2218 4.696479 AATGGCCCTGAATCTAGTAGTG 57.304 45.455 0.00 0.00 0.00 2.74
2204 2223 6.966534 AAAATGTAATGGCCCTGAATCTAG 57.033 37.500 0.00 0.00 0.00 2.43
2205 2224 6.667414 ACAAAAATGTAATGGCCCTGAATCTA 59.333 34.615 0.00 0.00 0.00 1.98
2206 2225 5.484998 ACAAAAATGTAATGGCCCTGAATCT 59.515 36.000 0.00 0.00 0.00 2.40
2207 2226 5.733676 ACAAAAATGTAATGGCCCTGAATC 58.266 37.500 0.00 0.00 0.00 2.52
2208 2227 5.760484 ACAAAAATGTAATGGCCCTGAAT 57.240 34.783 0.00 0.00 0.00 2.57
2214 2233 5.008514 AGCAAACAACAAAAATGTAATGGCC 59.991 36.000 0.00 0.00 0.00 5.36
2482 2504 5.491323 AAGAGAAGAAAAGGTCTAGGGTG 57.509 43.478 0.00 0.00 34.56 4.61
2556 2578 3.242188 GGTAAGTATAAGGTTTGCACGCG 60.242 47.826 3.53 3.53 0.00 6.01
2595 2617 5.327616 TCCGAAATATGACGTACTGGAAA 57.672 39.130 0.00 0.00 0.00 3.13
2670 2692 3.494626 GCCATGTACGAGTTATGACCATG 59.505 47.826 0.00 0.00 0.00 3.66
2858 2880 5.303971 CCCTTCACCAACTAGATCATCATC 58.696 45.833 0.00 0.00 0.00 2.92
2900 2922 6.201556 TGTTTCAAGTCGTATACGTTCAAC 57.798 37.500 23.67 14.77 40.80 3.18
2929 2951 5.221244 GGTTAAGAACAGCACAAACCTCAAT 60.221 40.000 0.00 0.00 34.79 2.57
2951 2973 4.534500 TGGGATTGTGATAGTGTAACAGGT 59.466 41.667 0.00 0.00 41.43 4.00
2992 3014 7.449247 AGGAAAATATGAGAGCATAGAAGACC 58.551 38.462 0.00 0.00 40.14 3.85
3011 3033 5.183140 GCAGGCTACAATGAAAGTAGGAAAA 59.817 40.000 0.00 0.00 39.42 2.29
3135 3157 0.746659 AAGGCACCAGAAACTGTTGC 59.253 50.000 11.70 11.70 46.64 4.17
3173 3195 2.097466 GGTGGTTTGTAGGAATCATGCG 59.903 50.000 0.00 0.00 0.00 4.73
3198 3220 5.559770 TGTGCCATCAGAAATTAGTTCAGA 58.440 37.500 0.00 0.00 38.86 3.27
3200 3222 5.711506 ACATGTGCCATCAGAAATTAGTTCA 59.288 36.000 0.00 0.00 38.86 3.18
3358 3380 6.575162 AACTTTTGGACATAACCACATCTC 57.425 37.500 0.00 0.00 39.85 2.75
3422 3444 7.211966 ACCATGATTTATCTTCAGCATAAGC 57.788 36.000 0.00 0.00 42.56 3.09
3638 3661 2.728007 ACCCAGAAATCAGCTTTAGGC 58.272 47.619 0.00 0.00 42.19 3.93
3905 4353 5.047590 GGTAAATTCCATCAACCCGAAAAGT 60.048 40.000 0.00 0.00 0.00 2.66
3910 4358 4.310022 AAGGTAAATTCCATCAACCCGA 57.690 40.909 0.00 0.00 0.00 5.14
3947 4395 5.163513 GTTTTGATAGGTTGCCATGTTCTG 58.836 41.667 0.00 0.00 0.00 3.02
4191 4639 2.767505 ACCTCAACAGTAGCTTTTCCG 58.232 47.619 0.00 0.00 0.00 4.30
4197 4645 4.344978 TCTGACATACCTCAACAGTAGCT 58.655 43.478 0.00 0.00 0.00 3.32
4287 4800 5.523438 TCCTAACATGTTGGGAAACAAAC 57.477 39.130 34.06 0.00 45.45 2.93
4445 5023 2.492881 TGGCAATGCAGGTATGAAACAG 59.507 45.455 7.79 0.00 0.00 3.16
4448 5026 2.754552 GACTGGCAATGCAGGTATGAAA 59.245 45.455 7.79 0.00 0.00 2.69
4456 5034 4.499188 CCTTTCATATGACTGGCAATGCAG 60.499 45.833 7.79 5.36 0.00 4.41
4544 5122 6.043938 AGGGATAACAATACGATGGGTAATGT 59.956 38.462 0.00 0.00 45.02 2.71
4605 5183 9.620259 AACAATTCTTCCTATAGAATCCTGAAC 57.380 33.333 0.00 0.00 42.53 3.18
4676 5254 2.305635 TGCTTTCATAACCAGCTCCTCA 59.694 45.455 0.00 0.00 34.42 3.86
4697 5275 7.656137 TCAAATCGAGTTTACTAGCTTTGTCTT 59.344 33.333 14.50 0.00 36.64 3.01
4717 5295 7.039313 ACAAGAAGTTTACCTGGTTCAAATC 57.961 36.000 3.84 0.00 0.00 2.17
4733 5311 4.137543 CTGGCCAAGAGTTTACAAGAAGT 58.862 43.478 7.01 0.00 0.00 3.01
4767 5345 8.561738 TTCTTGGAGTAATCCAGAAACATTAC 57.438 34.615 12.37 0.00 41.35 1.89
4818 5396 2.903784 ACTTGCCCCCTTAAAATGGAAC 59.096 45.455 0.00 0.00 0.00 3.62
4893 5471 5.407407 AGAATCTACGACCAAATCACAGT 57.593 39.130 0.00 0.00 0.00 3.55
4977 5602 5.531122 TCTCCATATTTGTTCGAGTAGGG 57.469 43.478 0.00 0.00 0.00 3.53
4984 5609 6.316140 TCCTTGAACATCTCCATATTTGTTCG 59.684 38.462 9.33 0.00 46.87 3.95
4993 5618 4.647564 ACACTTCCTTGAACATCTCCAT 57.352 40.909 0.00 0.00 0.00 3.41
5039 5667 8.374743 CCAATCCAGGGAATTTCTTTTCTTTAA 58.625 33.333 0.00 0.00 0.00 1.52
5060 5688 4.219288 AGAACAGATCCAGCAAAACCAATC 59.781 41.667 0.00 0.00 0.00 2.67
5122 5755 4.671766 GCTCACAGGGCTTTATGTTTTACG 60.672 45.833 0.00 0.00 0.00 3.18
5125 5758 3.230134 TGCTCACAGGGCTTTATGTTTT 58.770 40.909 0.00 0.00 0.00 2.43
5190 5823 2.783135 ACTGTTACATGGCTGGACAAG 58.217 47.619 0.00 0.00 0.00 3.16
5351 5999 2.328099 CCACACCCTCTTCGCTTGC 61.328 63.158 0.00 0.00 0.00 4.01
5381 6031 3.977244 CACCCCCAAACGCTGTGC 61.977 66.667 0.00 0.00 0.00 4.57
5668 6327 3.741075 GCAAGAACAAGAAAACCAAGGGG 60.741 47.826 0.00 0.00 41.29 4.79
5669 6328 3.132824 AGCAAGAACAAGAAAACCAAGGG 59.867 43.478 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.