Multiple sequence alignment - TraesCS7D01G278400

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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 TraesCS7D01G278400 chr7D 100.000 4902 0 0 1 4902 268556009 268551108 0.000000e+00 9053.0
1 TraesCS7D01G278400 chr7A 94.891 3308 82 27 1642 4902 294412970 294409703 0.000000e+00 5092.0
2 TraesCS7D01G278400 chr7A 84.112 1605 126 71 66 1636 294414518 294413009 0.000000e+00 1432.0
3 TraesCS7D01G278400 chr7A 96.226 53 2 0 451 503 42987580 42987528 2.430000e-13 87.9
4 TraesCS7D01G278400 chr7B 93.522 3489 98 45 1472 4902 248548781 248545363 0.000000e+00 5073.0
5 TraesCS7D01G278400 chr7B 90.319 909 52 12 578 1473 248549755 248548870 0.000000e+00 1158.0
6 TraesCS7D01G278400 chr7B 90.152 396 24 4 75 455 248550167 248549772 7.330000e-138 501.0
7 TraesCS7D01G278400 chr7B 95.455 44 2 0 535 578 248549771 248549728 2.450000e-08 71.3
8 TraesCS7D01G278400 chr4B 95.000 60 3 0 443 502 358091511 358091452 1.450000e-15 95.3
9 TraesCS7D01G278400 chr4B 94.545 55 3 0 448 502 68101443 68101497 8.740000e-13 86.1
10 TraesCS7D01G278400 chr1B 96.296 54 2 0 449 502 325262094 325262147 6.760000e-14 89.8
11 TraesCS7D01G278400 chr1B 88.060 67 7 1 435 500 54875751 54875685 1.460000e-10 78.7
12 TraesCS7D01G278400 chr5A 94.545 55 3 0 448 502 36368134 36368080 8.740000e-13 86.1
13 TraesCS7D01G278400 chr4D 93.220 59 3 1 444 502 504226810 504226753 8.740000e-13 86.1
14 TraesCS7D01G278400 chr1A 91.803 61 4 1 443 502 261378676 261378616 3.140000e-12 84.2


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 TraesCS7D01G278400 chr7D 268551108 268556009 4901 True 9053.000 9053 100.0000 1 4902 1 chr7D.!!$R1 4901
1 TraesCS7D01G278400 chr7A 294409703 294414518 4815 True 3262.000 5092 89.5015 66 4902 2 chr7A.!!$R2 4836
2 TraesCS7D01G278400 chr7B 248545363 248550167 4804 True 1700.825 5073 92.3620 75 4902 4 chr7B.!!$R1 4827

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
825 852 0.110238 CCTTCCGTGTTTGCATCGTG 60.110 55.0 0.00 0.0 0.00 4.35 F
1191 1237 0.107459 GGATGGAGGAGTGAGTTGGC 60.107 60.0 0.00 0.0 0.00 4.52 F
1499 1636 0.478072 AGCACCCAACTGGACAATCA 59.522 50.0 0.00 0.0 37.39 2.57 F
2924 3127 0.185901 TGCTGGGTGGAGCTTTCTTT 59.814 50.0 0.00 0.0 39.90 2.52 F
3288 3491 1.859302 AAACTCAAAAGGGGTGCACA 58.141 45.0 20.43 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 2416 1.266718 TGCAAAGCCATCGTGAAGTTC 59.733 47.619 0.00 0.00 0.00 3.01 R
2924 3127 0.961019 GGTTGACATTTCCAGCTGCA 59.039 50.000 8.66 0.00 0.00 4.41 R
3039 3242 3.699538 TCCGTAGATCTGCACAGTTGTAT 59.300 43.478 11.58 0.00 0.00 2.29 R
3841 4046 0.602638 TTGGCACATCGACTGTCCAC 60.603 55.000 1.55 4.07 39.30 4.02 R
4234 4456 1.271856 TCAGGTTTAGCCCGACATGA 58.728 50.000 0.00 0.00 38.26 3.07 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
40 41 4.277552 CCTGGGTGGCTCGATCTA 57.722 61.111 0.00 0.00 0.00 1.98
41 42 2.045280 CCTGGGTGGCTCGATCTAG 58.955 63.158 0.00 0.00 0.00 2.43
42 43 1.365633 CTGGGTGGCTCGATCTAGC 59.634 63.158 10.68 10.68 41.99 3.42
49 50 3.966104 CTCGATCTAGCCGCGCCA 61.966 66.667 0.00 0.00 0.00 5.69
50 51 3.888079 CTCGATCTAGCCGCGCCAG 62.888 68.421 0.00 0.00 0.00 4.85
51 52 3.966104 CGATCTAGCCGCGCCAGA 61.966 66.667 0.00 2.35 0.00 3.86
52 53 2.653702 GATCTAGCCGCGCCAGAT 59.346 61.111 13.13 13.13 0.00 2.90
53 54 1.445238 GATCTAGCCGCGCCAGATC 60.445 63.158 19.97 19.97 38.32 2.75
54 55 1.872197 GATCTAGCCGCGCCAGATCT 61.872 60.000 24.07 0.00 40.91 2.75
55 56 2.152297 ATCTAGCCGCGCCAGATCTG 62.152 60.000 16.24 16.24 0.00 2.90
64 65 4.555610 CCAGATCTGGCTCTTGGC 57.444 61.111 28.45 0.00 44.73 4.52
161 162 2.853542 TCCTGGAGTGCAGGCCAA 60.854 61.111 25.07 6.12 39.60 4.52
205 206 9.921637 CTCTGACCTCTTATTAAATAGCTTAGG 57.078 37.037 0.00 0.00 0.00 2.69
210 211 9.155785 ACCTCTTATTAAATAGCTTAGGCACTA 57.844 33.333 0.00 0.00 41.75 2.74
328 334 9.081997 GTGAGACAAAAACAACATTATTTCACA 57.918 29.630 0.00 0.00 0.00 3.58
347 353 1.153449 CCAATTGCGACGGAGGCTA 60.153 57.895 0.00 0.00 0.00 3.93
382 388 3.246619 CTCGAGAAGGCACTGAACTAAC 58.753 50.000 6.58 0.00 40.86 2.34
406 418 1.606668 ACCCACATGTAACACGCAAAG 59.393 47.619 0.00 0.00 0.00 2.77
456 474 6.420903 GTCAAATCAAACAAAAAGCTACTCCC 59.579 38.462 0.00 0.00 0.00 4.30
462 480 2.289506 ACAAAAAGCTACTCCCTCCGTC 60.290 50.000 0.00 0.00 0.00 4.79
463 481 0.903236 AAAAGCTACTCCCTCCGTCC 59.097 55.000 0.00 0.00 0.00 4.79
464 482 1.321074 AAAGCTACTCCCTCCGTCCG 61.321 60.000 0.00 0.00 0.00 4.79
468 486 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
473 491 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
477 495 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
478 496 3.581755 TCCGTCCGAAAATACTTGTCAG 58.418 45.455 0.00 0.00 0.00 3.51
489 507 8.454106 CGAAAATACTTGTCAGAGAAATGGATT 58.546 33.333 0.00 0.00 0.00 3.01
498 516 9.823647 TTGTCAGAGAAATGGATTTATCTAGAC 57.176 33.333 19.32 19.32 43.99 2.59
499 517 8.138074 TGTCAGAGAAATGGATTTATCTAGACG 58.862 37.037 19.95 8.66 43.99 4.18
500 518 8.138712 GTCAGAGAAATGGATTTATCTAGACGT 58.861 37.037 8.53 0.00 43.99 4.34
501 519 9.350951 TCAGAGAAATGGATTTATCTAGACGTA 57.649 33.333 8.53 0.00 43.99 3.57
502 520 9.400638 CAGAGAAATGGATTTATCTAGACGTAC 57.599 37.037 8.53 0.00 43.99 3.67
503 521 8.291032 AGAGAAATGGATTTATCTAGACGTACG 58.709 37.037 15.01 15.01 43.99 3.67
504 522 7.368833 AGAAATGGATTTATCTAGACGTACGG 58.631 38.462 21.06 1.09 0.00 4.02
505 523 6.889301 AATGGATTTATCTAGACGTACGGA 57.111 37.500 21.06 7.34 0.00 4.69
506 524 5.679734 TGGATTTATCTAGACGTACGGAC 57.320 43.478 21.06 13.04 0.00 4.79
515 533 4.198625 CGTACGGACGGAGAGAGT 57.801 61.111 13.75 0.00 45.63 3.24
516 534 3.352447 CGTACGGACGGAGAGAGTA 57.648 57.895 13.75 0.00 45.63 2.59
517 535 1.863267 CGTACGGACGGAGAGAGTAT 58.137 55.000 13.75 0.00 45.63 2.12
518 536 1.526041 CGTACGGACGGAGAGAGTATG 59.474 57.143 13.75 0.00 45.63 2.39
519 537 2.559440 GTACGGACGGAGAGAGTATGT 58.441 52.381 0.00 0.00 0.00 2.29
520 538 2.996249 ACGGACGGAGAGAGTATGTA 57.004 50.000 0.00 0.00 0.00 2.29
521 539 2.559440 ACGGACGGAGAGAGTATGTAC 58.441 52.381 0.00 0.00 0.00 2.90
522 540 2.170187 ACGGACGGAGAGAGTATGTACT 59.830 50.000 0.00 0.00 39.71 2.73
523 541 3.386078 ACGGACGGAGAGAGTATGTACTA 59.614 47.826 0.00 0.00 36.50 1.82
524 542 4.040217 ACGGACGGAGAGAGTATGTACTAT 59.960 45.833 0.00 0.00 36.50 2.12
525 543 4.996122 CGGACGGAGAGAGTATGTACTATT 59.004 45.833 0.00 0.00 36.50 1.73
526 544 6.162079 CGGACGGAGAGAGTATGTACTATTA 58.838 44.000 0.00 0.00 36.50 0.98
527 545 6.817641 CGGACGGAGAGAGTATGTACTATTAT 59.182 42.308 0.00 0.00 36.50 1.28
528 546 7.333921 CGGACGGAGAGAGTATGTACTATTATT 59.666 40.741 0.00 0.00 36.50 1.40
529 547 8.452534 GGACGGAGAGAGTATGTACTATTATTG 58.547 40.741 0.00 0.00 36.50 1.90
533 551 8.679100 GGAGAGAGTATGTACTATTATTGCGAT 58.321 37.037 0.00 0.00 36.50 4.58
571 589 4.461781 CCTTTGCTTTCTGGACATGATTCT 59.538 41.667 0.00 0.00 0.00 2.40
671 691 5.070313 GCTCTATCCCATCTAATCCAGATCC 59.930 48.000 0.00 0.00 42.40 3.36
681 701 0.896019 ATCCAGATCCGACGGCCTAG 60.896 60.000 9.66 2.14 0.00 3.02
683 703 1.528542 CAGATCCGACGGCCTAGGA 60.529 63.158 14.75 12.19 38.56 2.94
691 711 4.208686 CGGCCTAGGAGACACGGC 62.209 72.222 14.75 0.00 44.39 5.68
716 736 1.595382 GATCCGACGGGCATTCCAG 60.595 63.158 15.25 0.00 34.36 3.86
743 764 6.633583 GCAAGATCTCATCTTCCTTTTCCCTA 60.634 42.308 0.00 0.00 46.17 3.53
744 765 7.341805 CAAGATCTCATCTTCCTTTTCCCTAA 58.658 38.462 0.00 0.00 46.17 2.69
825 852 0.110238 CCTTCCGTGTTTGCATCGTG 60.110 55.000 0.00 0.00 0.00 4.35
863 891 1.508632 CGAGGCTCGTTGGAAAAAGA 58.491 50.000 27.92 0.00 34.72 2.52
876 904 3.458118 TGGAAAAAGAAGGACAGTCTGGA 59.542 43.478 4.53 0.00 0.00 3.86
877 905 4.068599 GGAAAAAGAAGGACAGTCTGGAG 58.931 47.826 4.53 0.00 0.00 3.86
878 906 4.202367 GGAAAAAGAAGGACAGTCTGGAGA 60.202 45.833 4.53 0.00 0.00 3.71
879 907 5.368989 GAAAAAGAAGGACAGTCTGGAGAA 58.631 41.667 4.53 0.00 0.00 2.87
938 971 1.288350 CTCTGCTCGCATCTTCCTTG 58.712 55.000 0.00 0.00 0.00 3.61
939 972 0.610174 TCTGCTCGCATCTTCCTTGT 59.390 50.000 0.00 0.00 0.00 3.16
941 974 1.129998 CTGCTCGCATCTTCCTTGTTG 59.870 52.381 0.00 0.00 0.00 3.33
942 975 1.270785 TGCTCGCATCTTCCTTGTTGA 60.271 47.619 0.00 0.00 0.00 3.18
944 977 2.421424 GCTCGCATCTTCCTTGTTGATT 59.579 45.455 0.00 0.00 0.00 2.57
945 978 3.486542 GCTCGCATCTTCCTTGTTGATTC 60.487 47.826 0.00 0.00 0.00 2.52
1128 1174 3.619038 GCTTCGATTCCCTGTTACTTCTG 59.381 47.826 0.00 0.00 0.00 3.02
1139 1185 1.877443 GTTACTTCTGCGCTTTCCCAA 59.123 47.619 9.73 0.00 0.00 4.12
1140 1186 2.488153 GTTACTTCTGCGCTTTCCCAAT 59.512 45.455 9.73 0.00 0.00 3.16
1141 1187 1.168714 ACTTCTGCGCTTTCCCAATC 58.831 50.000 9.73 0.00 0.00 2.67
1142 1188 0.453390 CTTCTGCGCTTTCCCAATCC 59.547 55.000 9.73 0.00 0.00 3.01
1143 1189 0.965363 TTCTGCGCTTTCCCAATCCC 60.965 55.000 9.73 0.00 0.00 3.85
1144 1190 1.678635 CTGCGCTTTCCCAATCCCA 60.679 57.895 9.73 0.00 0.00 4.37
1163 1209 3.119388 CCCACCTGTTGCTGACATTAATG 60.119 47.826 14.01 14.01 37.69 1.90
1179 1225 7.231925 TGACATTAATGAATGGAATGGATGGAG 59.768 37.037 22.16 0.00 45.83 3.86
1185 1231 2.268796 TGGAATGGATGGAGGAGTGA 57.731 50.000 0.00 0.00 0.00 3.41
1188 1234 2.507471 GGAATGGATGGAGGAGTGAGTT 59.493 50.000 0.00 0.00 0.00 3.01
1189 1235 3.539604 GAATGGATGGAGGAGTGAGTTG 58.460 50.000 0.00 0.00 0.00 3.16
1191 1237 0.107459 GGATGGAGGAGTGAGTTGGC 60.107 60.000 0.00 0.00 0.00 4.52
1193 1239 0.617413 ATGGAGGAGTGAGTTGGCTG 59.383 55.000 0.00 0.00 0.00 4.85
1194 1240 1.298014 GGAGGAGTGAGTTGGCTGG 59.702 63.158 0.00 0.00 0.00 4.85
1195 1241 1.194781 GGAGGAGTGAGTTGGCTGGA 61.195 60.000 0.00 0.00 0.00 3.86
1267 1314 3.965780 AAGCTCCGGTTTGCTTTTG 57.034 47.368 20.23 0.00 45.91 2.44
1362 1409 4.758251 TGCCGTGCCACCATCTCG 62.758 66.667 0.00 0.00 0.00 4.04
1366 1413 1.141665 CGTGCCACCATCTCGATCA 59.858 57.895 0.00 0.00 0.00 2.92
1426 1473 2.160417 GTGGAGTCGAGCAGGAAAATTG 59.840 50.000 0.00 0.00 0.00 2.32
1499 1636 0.478072 AGCACCCAACTGGACAATCA 59.522 50.000 0.00 0.00 37.39 2.57
1504 1641 2.819608 ACCCAACTGGACAATCAATTCG 59.180 45.455 0.00 0.00 37.39 3.34
1552 1692 3.884169 CGGCACCGTAATTAATTGATGG 58.116 45.455 11.05 11.30 34.35 3.51
1553 1693 3.314080 CGGCACCGTAATTAATTGATGGT 59.686 43.478 11.05 11.89 34.35 3.55
1554 1694 4.512198 CGGCACCGTAATTAATTGATGGTA 59.488 41.667 11.05 0.00 34.35 3.25
1555 1695 5.180492 CGGCACCGTAATTAATTGATGGTAT 59.820 40.000 11.05 0.00 34.35 2.73
1558 1698 7.604927 GGCACCGTAATTAATTGATGGTATAGA 59.395 37.037 11.05 0.00 0.00 1.98
1575 1715 7.553334 TGGTATAGAAGTTGTATCTTCACACC 58.447 38.462 8.73 11.03 44.18 4.16
1599 1739 3.888323 ACATAGTGACATCGATCTCAGCT 59.112 43.478 3.36 7.17 0.00 4.24
1639 1779 6.996509 ACTTTCATGACTGGCAAATGTTTAT 58.003 32.000 0.00 0.00 0.00 1.40
1645 1818 9.183368 TCATGACTGGCAAATGTTTATGTTATA 57.817 29.630 0.00 0.00 0.00 0.98
1671 1844 1.032014 TCTTGCCAAGTTCCAGCAAC 58.968 50.000 4.04 0.00 41.35 4.17
1779 1952 4.582656 ACTTTGCAAATGTTACACTGGCTA 59.417 37.500 13.23 0.00 28.79 3.93
1788 1961 5.420725 TGTTACACTGGCTATCAATGTCT 57.579 39.130 0.00 0.00 37.07 3.41
1791 1964 6.071051 TGTTACACTGGCTATCAATGTCTACA 60.071 38.462 0.00 0.00 37.07 2.74
1827 2000 4.950744 GCATGCGCAACTCAAACT 57.049 50.000 17.11 0.00 38.36 2.66
1936 2133 7.218614 CCTGCTTTCTCTGATTTCTAGATGAT 58.781 38.462 0.00 0.00 0.00 2.45
1948 2145 8.309656 TGATTTCTAGATGATAGCATGACGATT 58.690 33.333 0.00 0.00 34.11 3.34
1957 2154 3.198409 AGCATGACGATTCTAATGGCA 57.802 42.857 0.00 0.00 0.00 4.92
2206 2403 1.674359 ACGATGGTTCACACTGCAAA 58.326 45.000 0.00 0.00 0.00 3.68
2219 2416 4.847757 CACACTGCAAATCTGTACATTTCG 59.152 41.667 0.00 0.00 0.00 3.46
2268 2465 7.446931 TGGATGTTTCTTGTTTAGTTGATGCTA 59.553 33.333 0.00 0.00 0.00 3.49
2269 2466 7.965107 GGATGTTTCTTGTTTAGTTGATGCTAG 59.035 37.037 0.00 0.00 0.00 3.42
2270 2467 8.621532 ATGTTTCTTGTTTAGTTGATGCTAGA 57.378 30.769 0.00 0.00 0.00 2.43
2379 2580 5.679734 AATCGATTGTACAAGATGCCATC 57.320 39.130 14.65 0.00 0.00 3.51
2627 2828 4.025040 TGCTGACTTTGTTCATGGATCT 57.975 40.909 0.00 0.00 0.00 2.75
2813 3014 7.661437 CAGGATAAAGCTATTTACCATGCTGTA 59.339 37.037 0.00 0.00 33.78 2.74
2815 3016 8.454106 GGATAAAGCTATTTACCATGCTGTATG 58.546 37.037 0.00 0.00 36.45 2.39
2924 3127 0.185901 TGCTGGGTGGAGCTTTCTTT 59.814 50.000 0.00 0.00 39.90 2.52
3058 3261 6.796426 TGAGTATACAACTGTGCAGATCTAC 58.204 40.000 5.50 0.00 39.07 2.59
3179 3382 4.777366 TCCTTGATACCAGTGTCATCTTCA 59.223 41.667 0.00 0.00 30.87 3.02
3180 3383 5.426509 TCCTTGATACCAGTGTCATCTTCAT 59.573 40.000 0.00 0.00 30.87 2.57
3288 3491 1.859302 AAACTCAAAAGGGGTGCACA 58.141 45.000 20.43 0.00 0.00 4.57
3724 3929 6.909909 CAGTCCACTGGTTTAAATTCTAACC 58.090 40.000 12.49 12.49 43.28 2.85
3841 4046 2.068837 ATGCACCAATTTCAGTTGCG 57.931 45.000 0.00 0.00 0.00 4.85
4093 4304 8.984891 TTGTGACAACATTGATTCCAAATATC 57.015 30.769 0.00 0.00 35.83 1.63
4164 4375 1.153066 TTGCTTTGTGCCCGTCTCA 60.153 52.632 0.00 0.00 42.00 3.27
4234 4456 6.096001 GGAAGATCTATTTGCTCATGTTTGGT 59.904 38.462 0.00 0.00 0.00 3.67
4236 4458 6.182627 AGATCTATTTGCTCATGTTTGGTCA 58.817 36.000 0.00 0.00 0.00 4.02
4304 4526 4.246458 GAGTTGGCACTACTTCCTACTTG 58.754 47.826 0.00 0.00 38.27 3.16
4383 4606 5.163468 ACCGATTGCCATGCATTATTTTGTA 60.163 36.000 0.00 0.00 38.76 2.41
4390 4615 8.789825 TGCCATGCATTATTTTGTAAAATTCT 57.210 26.923 7.78 0.00 35.41 2.40
4656 4904 9.547279 TGGAGAAGATAAGGTGCATATATCTTA 57.453 33.333 21.59 12.19 43.11 2.10
4836 5084 2.923655 TGATGTCGTCGAAGCTTGATTC 59.076 45.455 2.10 0.00 0.00 2.52
4856 5104 7.377398 TGATTCGTTCATTCATTCAATGGTTT 58.623 30.769 0.00 0.00 42.18 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.045280 CTAGATCGAGCCACCCAGG 58.955 63.158 0.00 0.00 41.84 4.45
24 25 1.365633 GCTAGATCGAGCCACCCAG 59.634 63.158 16.26 0.00 36.38 4.45
25 26 3.538614 GCTAGATCGAGCCACCCA 58.461 61.111 16.26 0.00 36.38 4.51
32 33 3.888079 CTGGCGCGGCTAGATCGAG 62.888 68.421 33.23 16.57 39.54 4.04
33 34 3.966104 CTGGCGCGGCTAGATCGA 61.966 66.667 33.23 10.46 39.54 3.59
34 35 3.966104 TCTGGCGCGGCTAGATCG 61.966 66.667 33.23 14.05 41.04 3.69
38 39 2.355599 CAGATCTGGCGCGGCTAG 60.356 66.667 33.23 25.99 38.51 3.42
39 40 3.916544 CCAGATCTGGCGCGGCTA 61.917 66.667 33.23 21.49 44.73 3.93
48 49 2.178890 GCGCCAAGAGCCAGATCTG 61.179 63.158 16.24 16.24 38.78 2.90
49 50 2.188994 GCGCCAAGAGCCAGATCT 59.811 61.111 0.00 0.00 38.78 2.75
161 162 1.737793 GAGAATTGGTCGCAATTCCGT 59.262 47.619 18.91 7.19 46.94 4.69
183 184 8.151596 AGTGCCTAAGCTATTTAATAAGAGGTC 58.848 37.037 0.00 0.00 40.80 3.85
328 334 1.895020 TAGCCTCCGTCGCAATTGGT 61.895 55.000 7.72 0.00 0.00 3.67
347 353 0.811915 CTCGAGGTGTCGGTCAGAAT 59.188 55.000 3.91 0.00 46.80 2.40
382 388 2.744741 TGCGTGTTACATGTGGGTAATG 59.255 45.455 9.11 0.00 35.83 1.90
406 418 4.102649 GGCTACATGTGCGTAATTTTTCC 58.897 43.478 9.11 0.00 0.00 3.13
456 474 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
462 480 6.371548 TCCATTTCTCTGACAAGTATTTTCGG 59.628 38.462 0.00 0.00 0.00 4.30
463 481 7.364522 TCCATTTCTCTGACAAGTATTTTCG 57.635 36.000 0.00 0.00 0.00 3.46
473 491 8.138074 CGTCTAGATAAATCCATTTCTCTGACA 58.862 37.037 17.75 0.00 35.08 3.58
477 495 8.291032 CGTACGTCTAGATAAATCCATTTCTCT 58.709 37.037 7.22 5.54 37.15 3.10
478 496 7.537991 CCGTACGTCTAGATAAATCCATTTCTC 59.462 40.741 15.21 0.00 0.00 2.87
498 516 8.648843 TAGTACATACTCTCTCCGTCCGTACG 62.649 50.000 8.69 8.69 41.89 3.67
499 517 2.559440 ACATACTCTCTCCGTCCGTAC 58.441 52.381 0.00 0.00 0.00 3.67
500 518 2.996249 ACATACTCTCTCCGTCCGTA 57.004 50.000 0.00 0.00 0.00 4.02
501 519 2.170187 AGTACATACTCTCTCCGTCCGT 59.830 50.000 0.00 0.00 0.00 4.69
502 520 2.836262 AGTACATACTCTCTCCGTCCG 58.164 52.381 0.00 0.00 0.00 4.79
503 521 8.452534 CAATAATAGTACATACTCTCTCCGTCC 58.547 40.741 0.00 0.00 37.73 4.79
504 522 7.964011 GCAATAATAGTACATACTCTCTCCGTC 59.036 40.741 0.00 0.00 37.73 4.79
505 523 7.361031 CGCAATAATAGTACATACTCTCTCCGT 60.361 40.741 0.00 0.00 37.73 4.69
506 524 6.962116 CGCAATAATAGTACATACTCTCTCCG 59.038 42.308 0.00 0.00 37.73 4.63
507 525 8.041829 TCGCAATAATAGTACATACTCTCTCC 57.958 38.462 0.00 0.00 37.73 3.71
508 526 9.497030 CATCGCAATAATAGTACATACTCTCTC 57.503 37.037 0.00 0.00 37.73 3.20
509 527 8.462811 CCATCGCAATAATAGTACATACTCTCT 58.537 37.037 0.00 0.00 37.73 3.10
510 528 8.459635 TCCATCGCAATAATAGTACATACTCTC 58.540 37.037 0.00 0.00 37.73 3.20
511 529 8.349568 TCCATCGCAATAATAGTACATACTCT 57.650 34.615 0.00 0.00 37.73 3.24
512 530 8.244802 ACTCCATCGCAATAATAGTACATACTC 58.755 37.037 0.00 0.00 37.73 2.59
513 531 8.029522 CACTCCATCGCAATAATAGTACATACT 58.970 37.037 0.00 0.00 40.24 2.12
514 532 7.813148 ACACTCCATCGCAATAATAGTACATAC 59.187 37.037 0.00 0.00 0.00 2.39
515 533 7.812669 CACACTCCATCGCAATAATAGTACATA 59.187 37.037 0.00 0.00 0.00 2.29
516 534 6.646653 CACACTCCATCGCAATAATAGTACAT 59.353 38.462 0.00 0.00 0.00 2.29
517 535 5.983118 CACACTCCATCGCAATAATAGTACA 59.017 40.000 0.00 0.00 0.00 2.90
518 536 5.405571 CCACACTCCATCGCAATAATAGTAC 59.594 44.000 0.00 0.00 0.00 2.73
519 537 5.510690 CCCACACTCCATCGCAATAATAGTA 60.511 44.000 0.00 0.00 0.00 1.82
520 538 4.380531 CCACACTCCATCGCAATAATAGT 58.619 43.478 0.00 0.00 0.00 2.12
521 539 3.748048 CCCACACTCCATCGCAATAATAG 59.252 47.826 0.00 0.00 0.00 1.73
522 540 3.495983 CCCCACACTCCATCGCAATAATA 60.496 47.826 0.00 0.00 0.00 0.98
523 541 2.575532 CCCACACTCCATCGCAATAAT 58.424 47.619 0.00 0.00 0.00 1.28
524 542 1.408127 CCCCACACTCCATCGCAATAA 60.408 52.381 0.00 0.00 0.00 1.40
525 543 0.180171 CCCCACACTCCATCGCAATA 59.820 55.000 0.00 0.00 0.00 1.90
526 544 1.077501 CCCCACACTCCATCGCAAT 60.078 57.895 0.00 0.00 0.00 3.56
527 545 1.561769 ATCCCCACACTCCATCGCAA 61.562 55.000 0.00 0.00 0.00 4.85
528 546 1.995066 ATCCCCACACTCCATCGCA 60.995 57.895 0.00 0.00 0.00 5.10
529 547 1.524621 CATCCCCACACTCCATCGC 60.525 63.158 0.00 0.00 0.00 4.58
533 551 1.434513 AAAGGCATCCCCACACTCCA 61.435 55.000 0.00 0.00 35.39 3.86
580 598 4.637534 ACGAATGAATCATGTCCAGAAAGG 59.362 41.667 0.00 0.00 39.47 3.11
581 599 5.808042 ACGAATGAATCATGTCCAGAAAG 57.192 39.130 0.00 0.00 0.00 2.62
583 601 7.864108 AATAACGAATGAATCATGTCCAGAA 57.136 32.000 0.00 0.00 0.00 3.02
584 602 9.559732 AATAATAACGAATGAATCATGTCCAGA 57.440 29.630 0.00 0.00 0.00 3.86
585 603 9.603298 CAATAATAACGAATGAATCATGTCCAG 57.397 33.333 0.00 0.00 0.00 3.86
586 604 8.075574 GCAATAATAACGAATGAATCATGTCCA 58.924 33.333 0.00 0.00 0.00 4.02
587 605 7.538678 GGCAATAATAACGAATGAATCATGTCC 59.461 37.037 0.00 0.00 0.00 4.02
589 607 7.370383 GGGCAATAATAACGAATGAATCATGT 58.630 34.615 0.00 0.00 0.00 3.21
590 608 6.808212 GGGGCAATAATAACGAATGAATCATG 59.192 38.462 0.00 0.00 0.00 3.07
592 610 5.242838 GGGGGCAATAATAACGAATGAATCA 59.757 40.000 0.00 0.00 0.00 2.57
594 612 5.722021 GGGGGCAATAATAACGAATGAAT 57.278 39.130 0.00 0.00 0.00 2.57
671 691 2.799371 GTGTCTCCTAGGCCGTCG 59.201 66.667 2.96 0.00 0.00 5.12
683 703 3.649277 GATCAGCGTGGCCGTGTCT 62.649 63.158 0.00 0.00 36.15 3.41
691 711 4.873129 CCCGTCGGATCAGCGTGG 62.873 72.222 14.39 0.00 0.00 4.94
710 730 2.104451 AGATGAGATCTTGCGCTGGAAT 59.896 45.455 9.73 0.00 35.76 3.01
743 764 3.747579 CTGCTGGGGCTGGGGATT 61.748 66.667 0.00 0.00 39.59 3.01
825 852 2.159057 TCGCTTCCCCGGACTTTTATAC 60.159 50.000 0.73 0.00 0.00 1.47
863 891 4.656112 TCTTTCTTTCTCCAGACTGTCCTT 59.344 41.667 3.76 0.00 0.00 3.36
876 904 2.106684 ACCTCGCCCTTTCTTTCTTTCT 59.893 45.455 0.00 0.00 0.00 2.52
877 905 2.505405 ACCTCGCCCTTTCTTTCTTTC 58.495 47.619 0.00 0.00 0.00 2.62
878 906 2.623416 CAACCTCGCCCTTTCTTTCTTT 59.377 45.455 0.00 0.00 0.00 2.52
879 907 2.230660 CAACCTCGCCCTTTCTTTCTT 58.769 47.619 0.00 0.00 0.00 2.52
938 971 3.555966 AGGGGAATCGGAATGAATCAAC 58.444 45.455 0.00 0.00 0.00 3.18
939 972 3.744214 CGAGGGGAATCGGAATGAATCAA 60.744 47.826 0.00 0.00 39.04 2.57
941 974 2.417719 CGAGGGGAATCGGAATGAATC 58.582 52.381 0.00 0.00 39.04 2.52
942 975 1.543429 GCGAGGGGAATCGGAATGAAT 60.543 52.381 0.00 0.00 42.94 2.57
944 977 1.048724 AGCGAGGGGAATCGGAATGA 61.049 55.000 0.00 0.00 42.94 2.57
945 978 0.679505 TAGCGAGGGGAATCGGAATG 59.320 55.000 0.00 0.00 42.94 2.67
995 1033 3.537874 CGTCCTCCCCCATCGTCC 61.538 72.222 0.00 0.00 0.00 4.79
1066 1104 1.057275 GGGAGGGAGGGATTGAGGAC 61.057 65.000 0.00 0.00 0.00 3.85
1128 1174 2.710902 GGTGGGATTGGGAAAGCGC 61.711 63.158 0.00 0.00 0.00 5.92
1139 1185 0.700564 ATGTCAGCAACAGGTGGGAT 59.299 50.000 0.00 0.00 42.37 3.85
1140 1186 0.478072 AATGTCAGCAACAGGTGGGA 59.522 50.000 0.00 0.00 42.37 4.37
1141 1187 2.198827 TAATGTCAGCAACAGGTGGG 57.801 50.000 0.00 0.00 42.37 4.61
1142 1188 3.758023 TCATTAATGTCAGCAACAGGTGG 59.242 43.478 14.97 0.00 42.37 4.61
1143 1189 5.375417 TTCATTAATGTCAGCAACAGGTG 57.625 39.130 14.97 0.00 42.37 4.00
1144 1190 5.105635 CCATTCATTAATGTCAGCAACAGGT 60.106 40.000 14.97 0.00 42.37 4.00
1163 1209 3.137176 TCACTCCTCCATCCATTCCATTC 59.863 47.826 0.00 0.00 0.00 2.67
1179 1225 1.205893 CTACTCCAGCCAACTCACTCC 59.794 57.143 0.00 0.00 0.00 3.85
1185 1231 0.545309 TCTGCCTACTCCAGCCAACT 60.545 55.000 0.00 0.00 0.00 3.16
1188 1234 1.289160 ATTTCTGCCTACTCCAGCCA 58.711 50.000 0.00 0.00 0.00 4.75
1189 1235 2.426842 AATTTCTGCCTACTCCAGCC 57.573 50.000 0.00 0.00 0.00 4.85
1191 1237 4.124851 ACGTAATTTCTGCCTACTCCAG 57.875 45.455 0.00 0.00 0.00 3.86
1193 1239 4.032558 CGAAACGTAATTTCTGCCTACTCC 59.967 45.833 0.00 0.00 44.03 3.85
1194 1240 4.624452 ACGAAACGTAATTTCTGCCTACTC 59.376 41.667 0.00 0.00 44.03 2.59
1195 1241 4.563061 ACGAAACGTAATTTCTGCCTACT 58.437 39.130 0.00 0.00 44.03 2.57
1267 1314 0.726256 GCAGAGCAGAGCAGTAAAGC 59.274 55.000 0.00 0.00 0.00 3.51
1278 1325 3.476646 CACGTGCGAGCAGAGCAG 61.477 66.667 0.82 0.05 46.10 4.24
1362 1409 1.927174 CGAGAAACCGTGGTGATGATC 59.073 52.381 0.00 0.00 0.00 2.92
1366 1413 0.037605 GGACGAGAAACCGTGGTGAT 60.038 55.000 0.00 0.00 43.49 3.06
1426 1473 6.701400 AGAAAACTGAACCACAATTGCATTAC 59.299 34.615 5.05 0.00 0.00 1.89
1499 1636 8.788325 AGCAAAAGAGTTACTAATACCGAATT 57.212 30.769 0.00 0.00 0.00 2.17
1547 1687 8.977412 TGTGAAGATACAACTTCTATACCATCA 58.023 33.333 0.00 0.00 44.34 3.07
1548 1688 9.250624 GTGTGAAGATACAACTTCTATACCATC 57.749 37.037 0.00 0.00 44.34 3.51
1549 1689 8.204836 GGTGTGAAGATACAACTTCTATACCAT 58.795 37.037 4.06 0.00 44.34 3.55
1550 1690 7.179516 TGGTGTGAAGATACAACTTCTATACCA 59.820 37.037 17.97 17.97 44.34 3.25
1552 1692 8.870879 GTTGGTGTGAAGATACAACTTCTATAC 58.129 37.037 0.00 0.00 44.34 1.47
1553 1693 8.590204 TGTTGGTGTGAAGATACAACTTCTATA 58.410 33.333 0.00 0.00 44.34 1.31
1554 1694 7.450074 TGTTGGTGTGAAGATACAACTTCTAT 58.550 34.615 0.00 0.00 44.34 1.98
1555 1695 6.822442 TGTTGGTGTGAAGATACAACTTCTA 58.178 36.000 0.00 0.00 44.34 2.10
1558 1698 7.173218 CACTATGTTGGTGTGAAGATACAACTT 59.827 37.037 0.00 0.00 41.32 2.66
1575 1715 4.443725 GCTGAGATCGATGTCACTATGTTG 59.556 45.833 20.37 10.58 0.00 3.33
1671 1844 6.183360 TGGCAAAGGCAATAATATAGTTTGGG 60.183 38.462 0.00 0.00 43.71 4.12
1779 1952 4.159693 TGGTACGAAGCTGTAGACATTGAT 59.840 41.667 0.00 0.00 0.00 2.57
1788 1961 3.021695 AGCATACTGGTACGAAGCTGTA 58.978 45.455 0.00 0.00 40.39 2.74
1791 1964 1.471676 GCAGCATACTGGTACGAAGCT 60.472 52.381 0.00 0.00 44.63 3.74
1936 2133 4.335400 TGCCATTAGAATCGTCATGCTA 57.665 40.909 0.00 0.00 0.00 3.49
1948 2145 4.314522 TGGTTCTCCAAATGCCATTAGA 57.685 40.909 0.00 0.00 41.25 2.10
2059 2256 4.702131 AGAAGAAGCAAAACTCAACAGTGT 59.298 37.500 0.00 0.00 31.06 3.55
2103 2300 4.752101 CACTGTCCTTTGAAGACTCGAAAT 59.248 41.667 0.00 0.00 35.21 2.17
2107 2304 2.797156 CACACTGTCCTTTGAAGACTCG 59.203 50.000 0.00 0.00 35.21 4.18
2206 2403 5.466819 TCGTGAAGTTCGAAATGTACAGAT 58.533 37.500 0.00 0.00 34.36 2.90
2219 2416 1.266718 TGCAAAGCCATCGTGAAGTTC 59.733 47.619 0.00 0.00 0.00 3.01
2379 2580 2.930040 CACCCACTAGTGCAAATACGAG 59.070 50.000 17.86 0.26 0.00 4.18
2627 2828 6.126863 AGAGACAAATTACCAAGACCATCA 57.873 37.500 0.00 0.00 0.00 3.07
2924 3127 0.961019 GGTTGACATTTCCAGCTGCA 59.039 50.000 8.66 0.00 0.00 4.41
2971 3174 7.753309 AATAATGCACCAGTGTTTAGTACAA 57.247 32.000 0.00 0.00 38.80 2.41
3028 3231 6.423905 TCTGCACAGTTGTATACTCAAAGTTC 59.576 38.462 4.17 0.00 33.85 3.01
3039 3242 3.699538 TCCGTAGATCTGCACAGTTGTAT 59.300 43.478 11.58 0.00 0.00 2.29
3179 3382 7.212976 CCATACTCACACAAGTTGAGCTATAT 58.787 38.462 10.54 0.00 33.30 0.86
3180 3383 6.406961 CCCATACTCACACAAGTTGAGCTATA 60.407 42.308 10.54 0.00 33.30 1.31
3841 4046 0.602638 TTGGCACATCGACTGTCCAC 60.603 55.000 1.55 4.07 39.30 4.02
3985 4191 5.415701 TCCTATGCTTGCTTCTAAAAACAGG 59.584 40.000 0.00 0.00 0.00 4.00
4164 4375 6.780457 AATATGCCTGCTAAACAAAGACAT 57.220 33.333 0.00 0.00 0.00 3.06
4234 4456 1.271856 TCAGGTTTAGCCCGACATGA 58.728 50.000 0.00 0.00 38.26 3.07
4236 4458 2.119495 AGATCAGGTTTAGCCCGACAT 58.881 47.619 0.00 0.00 38.26 3.06
4383 4606 6.817641 TGTCATGTTTGAAGCACAAGAATTTT 59.182 30.769 0.00 0.00 39.77 1.82
4390 4615 4.915158 TCATGTCATGTTTGAAGCACAA 57.085 36.364 12.54 0.00 36.65 3.33
4531 4767 8.908786 TTATTATGTTGGAGAAGGACATCATC 57.091 34.615 0.00 0.00 35.72 2.92
4656 4904 7.439655 TCAAGTAAAACCGCAGCAAAATTTATT 59.560 29.630 0.00 0.00 0.00 1.40
4836 5084 5.919707 TGTCAAACCATTGAATGAATGAACG 59.080 36.000 6.76 0.00 46.66 3.95
4837 5085 7.439056 ACTTGTCAAACCATTGAATGAATGAAC 59.561 33.333 6.76 0.51 46.66 3.18
4856 5104 5.920840 CACGTCTCATCTTCTTTACTTGTCA 59.079 40.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.