Multiple sequence alignment - TraesCS1D01G419600

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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 TraesCS1D01G419600 chr1D 100.000 3218 0 0 1 3218 476568827 476565610 0.000000e+00 5943.0
1 TraesCS1D01G419600 chrUn 85.507 1104 138 16 200 1289 97784553 97785648 0.000000e+00 1133.0
2 TraesCS1D01G419600 chrUn 81.088 735 106 16 1428 2145 97785779 97786497 1.010000e-154 556.0
3 TraesCS1D01G419600 chrUn 88.701 177 20 0 92 268 97784412 97784588 1.940000e-52 217.0
4 TraesCS1D01G419600 chr6B 84.887 1105 144 17 200 1289 106511552 106512648 0.000000e+00 1094.0
5 TraesCS1D01G419600 chr6B 78.444 1118 157 49 1292 2351 106512690 106513781 0.000000e+00 652.0
6 TraesCS1D01G419600 chr6B 90.395 177 17 0 92 268 106511411 106511587 1.930000e-57 233.0
7 TraesCS1D01G419600 chr1B 90.995 744 27 16 1861 2596 662830556 662829845 0.000000e+00 966.0
8 TraesCS1D01G419600 chr1B 95.630 595 17 1 1280 1865 662836370 662835776 0.000000e+00 946.0
9 TraesCS1D01G419600 chr1B 93.098 623 32 6 2594 3206 662829460 662828839 0.000000e+00 902.0
10 TraesCS1D01G419600 chr1B 96.053 456 18 0 373 828 662836823 662836368 0.000000e+00 743.0
11 TraesCS1D01G419600 chr1B 94.925 335 17 0 40 374 662837213 662836879 2.840000e-145 525.0
12 TraesCS1D01G419600 chr1B 97.619 42 1 0 1 42 662837307 662837266 4.450000e-09 73.1
13 TraesCS1D01G419600 chr5D 79.217 1073 188 24 233 1289 528805549 528806602 0.000000e+00 713.0
14 TraesCS1D01G419600 chr5D 79.085 1071 172 31 233 1286 528764420 528765455 0.000000e+00 689.0
15 TraesCS1D01G419600 chr5D 78.972 1070 172 22 233 1289 528753218 528754247 0.000000e+00 680.0
16 TraesCS1D01G419600 chr5D 75.652 690 134 20 1292 1955 528754289 528754970 2.410000e-81 313.0
17 TraesCS1D01G419600 chr5D 88.194 144 17 0 92 235 528805441 528805584 4.270000e-39 172.0
18 TraesCS1D01G419600 chr5B 76.850 1054 175 36 233 1257 665940958 665941971 6.110000e-147 531.0
19 TraesCS1D01G419600 chr5B 86.806 144 19 0 92 235 665940850 665940993 9.240000e-36 161.0
20 TraesCS1D01G419600 chr5B 82.645 121 17 3 316 434 7018163 7018045 1.580000e-18 104.0


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 TraesCS1D01G419600 chr1D 476565610 476568827 3217 True 5943.000000 5943 100.000000 1 3218 1 chr1D.!!$R1 3217
1 TraesCS1D01G419600 chrUn 97784412 97786497 2085 False 635.333333 1133 85.098667 92 2145 3 chrUn.!!$F1 2053
2 TraesCS1D01G419600 chr6B 106511411 106513781 2370 False 659.666667 1094 84.575333 92 2351 3 chr6B.!!$F1 2259
3 TraesCS1D01G419600 chr1B 662828839 662830556 1717 True 934.000000 966 92.046500 1861 3206 2 chr1B.!!$R1 1345
4 TraesCS1D01G419600 chr1B 662835776 662837307 1531 True 571.775000 946 96.056750 1 1865 4 chr1B.!!$R2 1864
5 TraesCS1D01G419600 chr5D 528764420 528765455 1035 False 689.000000 689 79.085000 233 1286 1 chr5D.!!$F1 1053
6 TraesCS1D01G419600 chr5D 528753218 528754970 1752 False 496.500000 680 77.312000 233 1955 2 chr5D.!!$F2 1722
7 TraesCS1D01G419600 chr5D 528805441 528806602 1161 False 442.500000 713 83.705500 92 1289 2 chr5D.!!$F3 1197
8 TraesCS1D01G419600 chr5B 665940850 665941971 1121 False 346.000000 531 81.828000 92 1257 2 chr5B.!!$F1 1165

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
856 1044 0.823356 CTTGTTGGACCACCCACTGG 60.823 60.0 0.0 0.0 46.62 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2607 0.108585 GAAGGTCTCCACTTGTGGCA 59.891 55.0 14.49 1.47 0.0 4.92 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
90 146 4.768448 TCATTGTTCATGAAGCCTGACAAT 59.232 37.500 8.80 11.48 39.11 2.71
113 169 1.337071 CTTGATCATGCATGACCTGGC 59.663 52.381 30.92 17.38 40.03 4.85
207 263 6.709846 GGCTGACAGATCATAGAAAGCTATTT 59.290 38.462 6.65 0.00 35.13 1.40
231 287 4.597004 AGTCATCAATGAATCCACTTGCT 58.403 39.130 0.00 0.00 38.75 3.91
299 421 1.003866 GCATTTTATCGACCGTGGCTC 60.004 52.381 0.00 0.00 0.00 4.70
362 484 5.125417 GCCTATGTGTCTTGGATTTAAGCAA 59.875 40.000 0.00 0.00 0.00 3.91
381 560 4.097741 AGCAAATGTTGTGCACAAGAGTTA 59.902 37.500 32.81 18.39 44.74 2.24
436 624 1.926561 TCTCGATGCTTCATGGAACG 58.073 50.000 0.08 0.00 33.94 3.95
444 632 2.094442 TGCTTCATGGAACGTCGATGTA 60.094 45.455 11.40 0.00 34.71 2.29
445 633 2.281762 GCTTCATGGAACGTCGATGTAC 59.718 50.000 11.40 8.01 34.71 2.90
451 639 2.257034 GGAACGTCGATGTACCTGAAC 58.743 52.381 11.40 0.00 0.00 3.18
454 642 1.471684 ACGTCGATGTACCTGAACCTC 59.528 52.381 8.94 0.00 0.00 3.85
464 652 2.197465 ACCTGAACCTCCTGAATACCC 58.803 52.381 0.00 0.00 0.00 3.69
757 945 6.017026 GCCTGAAAGTTTTAGCAGACTAAAGT 60.017 38.462 1.89 0.00 46.36 2.66
851 1039 1.045911 TTTGGCTTGTTGGACCACCC 61.046 55.000 0.00 0.00 31.83 4.61
853 1041 2.200337 GGCTTGTTGGACCACCCAC 61.200 63.158 0.00 0.00 46.62 4.61
854 1042 1.152756 GCTTGTTGGACCACCCACT 60.153 57.895 0.00 0.00 46.62 4.00
855 1043 1.455383 GCTTGTTGGACCACCCACTG 61.455 60.000 0.00 0.00 46.62 3.66
856 1044 0.823356 CTTGTTGGACCACCCACTGG 60.823 60.000 0.00 0.00 46.62 4.00
861 1049 0.856982 TGGACCACCCACTGGAAAAT 59.143 50.000 0.00 0.00 43.95 1.82
864 1052 2.557452 GGACCACCCACTGGAAAATGAT 60.557 50.000 0.00 0.00 43.95 2.45
880 1097 1.225376 TGATGGGTTTCACGTGCGTC 61.225 55.000 11.67 7.98 0.00 5.19
893 1110 1.082117 GTGCGTCCGGTTGATAGTGG 61.082 60.000 0.00 0.00 0.00 4.00
898 1115 2.543861 CGTCCGGTTGATAGTGGATCTG 60.544 54.545 0.00 0.00 35.37 2.90
943 1163 5.012239 AGCATACAAATCCTGATGTGTTGT 58.988 37.500 8.19 4.92 39.76 3.32
958 1179 4.163552 TGTGTTGTGTATCGACGATCTTC 58.836 43.478 14.80 7.09 33.33 2.87
1039 1260 3.066621 TGAAACACTGTCATTGAAGTGGC 59.933 43.478 21.93 15.28 46.55 5.01
1040 1261 2.346766 ACACTGTCATTGAAGTGGCA 57.653 45.000 21.93 0.00 46.55 4.92
1041 1262 2.867624 ACACTGTCATTGAAGTGGCAT 58.132 42.857 21.93 8.27 46.55 4.40
1044 1265 2.165167 CTGTCATTGAAGTGGCATGGT 58.835 47.619 0.00 0.00 32.54 3.55
1073 1303 3.386768 ACACATCGAGTTGCTAACAGT 57.613 42.857 0.00 0.00 0.00 3.55
1078 1308 3.653539 TCGAGTTGCTAACAGTGCTAA 57.346 42.857 0.00 0.00 0.00 3.09
1104 1334 5.183140 GCCACCAAGCTCTGTAAAGAATTTA 59.817 40.000 0.00 0.00 40.09 1.40
1105 1335 6.623767 GCCACCAAGCTCTGTAAAGAATTTAG 60.624 42.308 0.00 0.00 41.97 1.85
1127 1357 5.476983 AGAGATAAGGGGTTACATGGATGA 58.523 41.667 0.00 0.00 0.00 2.92
1133 1363 3.137176 AGGGGTTACATGGATGACATCTG 59.863 47.826 14.95 8.97 37.84 2.90
1134 1364 2.880890 GGGTTACATGGATGACATCTGC 59.119 50.000 14.95 0.35 37.84 4.26
1156 1386 3.436704 CCCGCACTGGTTTATGCATATAG 59.563 47.826 7.36 6.73 42.17 1.31
1159 1389 3.191371 GCACTGGTTTATGCATATAGGCC 59.809 47.826 7.36 8.10 41.65 5.19
1189 1419 2.941720 CCTAATCTTGTGAGCTTGGAGC 59.058 50.000 0.00 0.00 42.84 4.70
1202 1432 2.294233 GCTTGGAGCTGTGTCATTTTCA 59.706 45.455 0.00 0.00 38.45 2.69
1232 1465 2.227194 CCTACCAACACTTGTCCAACC 58.773 52.381 0.00 0.00 0.00 3.77
1240 1473 0.629058 ACTTGTCCAACCACCCAACT 59.371 50.000 0.00 0.00 0.00 3.16
1258 1491 4.378459 CCAACTTACGCAAGATTGTTCTCC 60.378 45.833 1.47 0.00 43.62 3.71
1261 1494 1.298859 ACGCAAGATTGTTCTCCGCC 61.299 55.000 0.00 0.00 43.62 6.13
1267 1500 3.131709 AGATTGTTCTCCGCCATATGG 57.868 47.619 18.07 18.07 38.53 2.74
1269 1502 3.136443 AGATTGTTCTCCGCCATATGGAA 59.864 43.478 26.47 7.34 37.39 3.53
1275 1508 3.042682 TCTCCGCCATATGGAAAACCTA 58.957 45.455 26.47 0.88 37.39 3.08
1279 1512 4.080243 TCCGCCATATGGAAAACCTAGAAA 60.080 41.667 26.47 0.00 37.39 2.52
1311 1583 7.282585 ACATATTGGCTAAACTTGAGCATCTA 58.717 34.615 0.31 0.00 41.98 1.98
1447 1731 2.934364 GCCTCATCTTGTCCTGTGAGTG 60.934 54.545 0.00 0.00 37.08 3.51
1479 1766 2.092968 TGACTCAGAGTTGCCTTTGTGT 60.093 45.455 4.05 0.00 33.66 3.72
1659 1946 1.213013 GCTCACTTCTCTTCGGCGA 59.787 57.895 4.99 4.99 0.00 5.54
1737 2027 0.820226 AGCTGCAATCGCTCAGTCTA 59.180 50.000 1.02 0.00 39.64 2.59
1740 2030 2.730069 CTGCAATCGCTCAGTCTAGAG 58.270 52.381 0.00 0.00 39.64 2.43
2279 2607 3.382278 TGATCCTTGGAGCTCTTCTGAT 58.618 45.455 14.64 10.87 0.00 2.90
2286 2614 1.339438 GGAGCTCTTCTGATGCCACAA 60.339 52.381 14.64 0.00 0.00 3.33
2351 2679 6.577103 TCATTCACATGTTTTGTTGCCTTTA 58.423 32.000 0.00 0.00 36.00 1.85
2352 2680 6.478344 TCATTCACATGTTTTGTTGCCTTTAC 59.522 34.615 0.00 0.00 36.00 2.01
2353 2681 5.330455 TCACATGTTTTGTTGCCTTTACA 57.670 34.783 0.00 0.00 36.00 2.41
2354 2682 5.911752 TCACATGTTTTGTTGCCTTTACAT 58.088 33.333 0.00 0.00 36.00 2.29
2355 2683 5.752472 TCACATGTTTTGTTGCCTTTACATG 59.248 36.000 0.00 0.00 45.03 3.21
2356 2684 4.511082 ACATGTTTTGTTGCCTTTACATGC 59.489 37.500 11.65 0.00 43.97 4.06
2357 2685 4.399004 TGTTTTGTTGCCTTTACATGCT 57.601 36.364 0.00 0.00 0.00 3.79
2358 2686 4.118410 TGTTTTGTTGCCTTTACATGCTG 58.882 39.130 0.00 0.00 0.00 4.41
2359 2687 4.119136 GTTTTGTTGCCTTTACATGCTGT 58.881 39.130 0.00 0.00 0.00 4.40
2360 2688 3.367992 TTGTTGCCTTTACATGCTGTG 57.632 42.857 0.00 0.00 0.00 3.66
2361 2689 2.580962 TGTTGCCTTTACATGCTGTGA 58.419 42.857 0.00 0.00 0.00 3.58
2362 2690 2.553602 TGTTGCCTTTACATGCTGTGAG 59.446 45.455 0.00 0.00 0.00 3.51
2363 2691 2.554032 GTTGCCTTTACATGCTGTGAGT 59.446 45.455 0.00 0.00 0.00 3.41
2364 2692 2.153645 TGCCTTTACATGCTGTGAGTG 58.846 47.619 0.00 0.00 0.00 3.51
2365 2693 1.470098 GCCTTTACATGCTGTGAGTGG 59.530 52.381 0.00 0.00 0.00 4.00
2366 2694 2.875672 GCCTTTACATGCTGTGAGTGGA 60.876 50.000 0.00 0.00 0.00 4.02
2367 2695 3.411446 CCTTTACATGCTGTGAGTGGAA 58.589 45.455 0.00 0.00 0.00 3.53
2368 2696 3.438087 CCTTTACATGCTGTGAGTGGAAG 59.562 47.826 0.00 0.00 0.00 3.46
2369 2697 2.768253 TACATGCTGTGAGTGGAAGG 57.232 50.000 0.00 0.00 0.00 3.46
2370 2698 0.767375 ACATGCTGTGAGTGGAAGGT 59.233 50.000 0.00 0.00 0.00 3.50
2371 2699 1.143684 ACATGCTGTGAGTGGAAGGTT 59.856 47.619 0.00 0.00 0.00 3.50
2372 2700 2.371841 ACATGCTGTGAGTGGAAGGTTA 59.628 45.455 0.00 0.00 0.00 2.85
2373 2701 3.181445 ACATGCTGTGAGTGGAAGGTTAA 60.181 43.478 0.00 0.00 0.00 2.01
2374 2702 2.846193 TGCTGTGAGTGGAAGGTTAAC 58.154 47.619 0.00 0.00 0.00 2.01
2375 2703 2.152016 GCTGTGAGTGGAAGGTTAACC 58.848 52.381 17.41 17.41 0.00 2.85
2457 2785 0.971959 TCATTTGCCATGGTCCCTGC 60.972 55.000 14.67 0.00 0.00 4.85
2508 2840 6.545567 TGCTGGTGGACAATAATATGATGAT 58.454 36.000 0.00 0.00 0.00 2.45
2510 2842 6.883217 GCTGGTGGACAATAATATGATGATCT 59.117 38.462 0.00 0.00 0.00 2.75
2549 2881 6.734137 AGATAAAACTGACGCAAACAATTCA 58.266 32.000 0.00 0.00 0.00 2.57
2550 2882 6.857964 AGATAAAACTGACGCAAACAATTCAG 59.142 34.615 0.00 0.00 41.14 3.02
2561 2893 6.148948 CGCAAACAATTCAGTTTCATTCCTA 58.851 36.000 0.00 0.00 39.55 2.94
2580 2912 4.079558 TCCTATACTCCCTAACCAACGAGT 60.080 45.833 0.00 0.00 38.97 4.18
2614 3333 4.634004 TGCCTCCGTTTCATATTAGTTGTG 59.366 41.667 0.00 0.00 0.00 3.33
2632 3351 7.718272 AGTTGTGTTTGTACTAAATTAGCGA 57.282 32.000 0.00 0.00 0.00 4.93
2638 3357 8.919661 GTGTTTGTACTAAATTAGCGACTAACT 58.080 33.333 21.22 0.21 34.70 2.24
2837 3557 2.169769 TGGGACAGCGGGAGTATTTTAG 59.830 50.000 0.00 0.00 0.00 1.85
2844 3564 4.747108 CAGCGGGAGTATTTTAGACAGATG 59.253 45.833 0.00 0.00 0.00 2.90
2936 3656 2.999185 AAGCTCCTGATGGGGAAAAA 57.001 45.000 0.00 0.00 35.23 1.94
2968 3690 1.613928 TCCCGTATGCTGGAACCCA 60.614 57.895 0.00 0.00 0.00 4.51
2970 3692 0.106719 CCCGTATGCTGGAACCCATT 60.107 55.000 0.00 0.00 30.82 3.16
2987 3709 2.687425 CCATTGGGATGCGTGAAACATA 59.313 45.455 0.00 0.00 33.06 2.29
2999 3721 7.371126 TGCGTGAAACATATTCAGTTCATAA 57.629 32.000 0.00 0.00 35.74 1.90
3022 3747 6.128138 ACAGTAAGGGCTAGAAAACTGAAT 57.872 37.500 14.25 0.00 38.14 2.57
3051 3776 6.182627 TGCACCAGAATTATGTCAATCTTCT 58.817 36.000 0.00 0.00 0.00 2.85
3078 3803 5.470098 GCGGACATCATAAATATTGGACTGT 59.530 40.000 0.00 0.00 0.00 3.55
3150 3875 0.108424 AGCAGCTGCACTACTAGCAC 60.108 55.000 38.24 6.46 45.16 4.40
3159 3884 2.732366 CACTACTAGCACCGCATGTAG 58.268 52.381 13.22 13.22 40.01 2.74
3215 3944 7.447243 GCAATTTGCAAAGAACTCATCTATC 57.553 36.000 18.19 0.00 44.26 2.08
3216 3945 7.256286 GCAATTTGCAAAGAACTCATCTATCT 58.744 34.615 18.19 0.00 44.26 1.98
3217 3946 7.758528 GCAATTTGCAAAGAACTCATCTATCTT 59.241 33.333 18.19 0.00 44.26 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.215719 ACAACTAAGCAGGAAAGGTAAATTC 57.784 36.000 0.00 0.00 0.00 2.17
90 146 3.697542 CCAGGTCATGCATGATCAAGAAA 59.302 43.478 35.18 9.38 40.37 2.52
207 263 6.182627 AGCAAGTGGATTCATTGATGACTTA 58.817 36.000 0.00 0.00 36.36 2.24
362 484 4.568152 GGTAACTCTTGTGCACAACATT 57.432 40.909 27.96 21.71 38.99 2.71
381 560 7.942341 TGTTTTAGTTGACCAATAGAATCAGGT 59.058 33.333 0.00 0.00 37.00 4.00
436 624 2.100989 AGGAGGTTCAGGTACATCGAC 58.899 52.381 0.00 0.00 29.93 4.20
444 632 2.197465 GGGTATTCAGGAGGTTCAGGT 58.803 52.381 0.00 0.00 0.00 4.00
445 633 2.171448 CTGGGTATTCAGGAGGTTCAGG 59.829 54.545 0.00 0.00 0.00 3.86
451 639 1.620819 CGGATCTGGGTATTCAGGAGG 59.379 57.143 0.00 0.00 35.58 4.30
454 642 0.035458 GGCGGATCTGGGTATTCAGG 59.965 60.000 3.14 0.00 35.58 3.86
464 652 1.101635 TGTAGACTCCGGCGGATCTG 61.102 60.000 32.43 24.36 0.00 2.90
757 945 1.000486 AGCCGGAGAGGTTCAGCTA 60.000 57.895 5.05 0.00 43.70 3.32
851 1039 4.559153 GTGAAACCCATCATTTTCCAGTG 58.441 43.478 0.00 0.00 31.76 3.66
853 1041 3.255642 ACGTGAAACCCATCATTTTCCAG 59.744 43.478 0.00 0.00 31.76 3.86
854 1042 3.005261 CACGTGAAACCCATCATTTTCCA 59.995 43.478 10.90 0.00 31.76 3.53
855 1043 3.574614 CACGTGAAACCCATCATTTTCC 58.425 45.455 10.90 0.00 31.76 3.13
856 1044 2.986479 GCACGTGAAACCCATCATTTTC 59.014 45.455 22.23 0.00 33.15 2.29
861 1049 1.225376 GACGCACGTGAAACCCATCA 61.225 55.000 22.23 0.00 0.00 3.07
864 1052 2.589442 GGACGCACGTGAAACCCA 60.589 61.111 22.23 0.00 0.00 4.51
880 1097 1.541233 GCCAGATCCACTATCAACCGG 60.541 57.143 0.00 0.00 37.03 5.28
893 1110 1.066286 AGACAAGACTGCTGCCAGATC 60.066 52.381 0.00 0.00 41.77 2.75
898 1115 2.331132 GCCAGACAAGACTGCTGCC 61.331 63.158 0.00 0.00 36.67 4.85
943 1163 6.096695 TCACATTTTGAAGATCGTCGATACA 58.903 36.000 7.93 6.45 0.00 2.29
958 1179 6.348050 GCCTCTTCTACAGACTTCACATTTTG 60.348 42.308 0.00 0.00 0.00 2.44
1009 1230 7.099266 TCAATGACAGTGTTTCAATTCTGTT 57.901 32.000 2.39 0.00 40.53 3.16
1022 1243 2.094906 CCATGCCACTTCAATGACAGTG 60.095 50.000 14.37 14.37 40.23 3.66
1039 1260 1.135527 GATGTGTTCCATGCCACCATG 59.864 52.381 6.09 0.00 46.70 3.66
1040 1261 1.477553 GATGTGTTCCATGCCACCAT 58.522 50.000 6.09 2.63 32.56 3.55
1041 1262 0.959867 CGATGTGTTCCATGCCACCA 60.960 55.000 6.09 0.00 32.56 4.17
1044 1265 0.324614 ACTCGATGTGTTCCATGCCA 59.675 50.000 0.00 0.00 32.56 4.92
1048 1269 2.479566 AGCAACTCGATGTGTTCCAT 57.520 45.000 0.00 0.00 36.13 3.41
1059 1289 3.484229 GCATTAGCACTGTTAGCAACTCG 60.484 47.826 0.00 0.00 41.58 4.18
1073 1303 0.329261 AGAGCTTGGTGGCATTAGCA 59.671 50.000 16.97 0.00 44.61 3.49
1078 1308 2.040278 TCTTTACAGAGCTTGGTGGCAT 59.960 45.455 0.00 0.00 34.17 4.40
1104 1334 5.308237 GTCATCCATGTAACCCCTTATCTCT 59.692 44.000 0.00 0.00 0.00 3.10
1105 1335 5.071788 TGTCATCCATGTAACCCCTTATCTC 59.928 44.000 0.00 0.00 0.00 2.75
1112 1342 3.480470 CAGATGTCATCCATGTAACCCC 58.520 50.000 9.29 0.00 32.56 4.95
1113 1343 2.880890 GCAGATGTCATCCATGTAACCC 59.119 50.000 9.29 0.00 32.56 4.11
1127 1357 2.697147 AAACCAGTGCGGGCAGATGT 62.697 55.000 0.00 0.00 40.22 3.06
1133 1363 1.666209 ATGCATAAACCAGTGCGGGC 61.666 55.000 0.00 0.00 44.11 6.13
1134 1364 1.674359 TATGCATAAACCAGTGCGGG 58.326 50.000 3.27 0.00 44.11 6.13
1156 1386 6.299141 TCACAAGATTAGGAAGATATTGGCC 58.701 40.000 0.00 0.00 31.73 5.36
1159 1389 8.557864 CAAGCTCACAAGATTAGGAAGATATTG 58.442 37.037 0.00 0.00 33.24 1.90
1189 1419 4.084745 GCTGTTGCATTGAAAATGACACAG 60.085 41.667 18.52 18.52 39.41 3.66
1194 1424 4.321899 GGTAGGCTGTTGCATTGAAAATGA 60.322 41.667 0.00 0.00 41.91 2.57
1202 1432 1.613437 GTGTTGGTAGGCTGTTGCATT 59.387 47.619 0.00 0.00 41.91 3.56
1232 1465 2.552315 ACAATCTTGCGTAAGTTGGGTG 59.448 45.455 22.14 13.74 41.68 4.61
1240 1473 1.730064 GCGGAGAACAATCTTGCGTAA 59.270 47.619 0.00 0.00 35.54 3.18
1258 1491 5.357032 ACTTTTCTAGGTTTTCCATATGGCG 59.643 40.000 17.58 0.00 43.73 5.69
1269 1502 9.923143 GCCAATATGTTAAACTTTTCTAGGTTT 57.077 29.630 0.00 0.00 34.89 3.27
1311 1583 5.048846 AGTTGGGGCAATCGTATATTTCT 57.951 39.130 0.00 0.00 0.00 2.52
1447 1731 6.423042 GCAACTCTGAGTCAACTTTAAGTTC 58.577 40.000 11.31 0.00 36.03 3.01
1479 1766 2.886523 CTGGTGAAGCAAACTCCAATGA 59.113 45.455 0.00 0.00 31.94 2.57
1505 1792 5.593010 AGATAGCTAAATCACGAAGACCAC 58.407 41.667 0.00 0.00 0.00 4.16
1737 2027 6.148480 GTGATGTCAACTTATTGCACTTCTCT 59.852 38.462 0.00 0.00 35.63 3.10
1740 2030 6.246420 AGTGATGTCAACTTATTGCACTTC 57.754 37.500 0.00 0.00 33.96 3.01
1965 2257 2.601763 GGTCACTAAAACATACGAGCGG 59.398 50.000 0.00 0.00 0.00 5.52
2154 2458 4.615513 AGTAGGACTGCAAGGAAGTAGAT 58.384 43.478 0.00 0.00 39.30 1.98
2279 2607 0.108585 GAAGGTCTCCACTTGTGGCA 59.891 55.000 14.49 1.47 0.00 4.92
2286 2614 3.544698 TCCTAAGTGAAGGTCTCCACT 57.455 47.619 0.00 0.00 44.69 4.00
2352 2680 1.901591 AACCTTCCACTCACAGCATG 58.098 50.000 0.00 0.00 46.00 4.06
2353 2681 3.412386 GTTAACCTTCCACTCACAGCAT 58.588 45.455 0.00 0.00 0.00 3.79
2354 2682 2.486548 GGTTAACCTTCCACTCACAGCA 60.487 50.000 17.83 0.00 0.00 4.41
2355 2683 2.152016 GGTTAACCTTCCACTCACAGC 58.848 52.381 17.83 0.00 0.00 4.40
2356 2684 3.403038 CAGGTTAACCTTCCACTCACAG 58.597 50.000 24.99 5.68 46.09 3.66
2357 2685 2.486548 GCAGGTTAACCTTCCACTCACA 60.487 50.000 24.99 0.00 46.09 3.58
2358 2686 2.152016 GCAGGTTAACCTTCCACTCAC 58.848 52.381 24.99 3.56 46.09 3.51
2359 2687 2.054799 AGCAGGTTAACCTTCCACTCA 58.945 47.619 24.99 0.00 46.09 3.41
2360 2688 2.427506 CAGCAGGTTAACCTTCCACTC 58.572 52.381 24.99 9.51 46.09 3.51
2361 2689 1.545651 GCAGCAGGTTAACCTTCCACT 60.546 52.381 24.99 15.93 46.09 4.00
2362 2690 0.881796 GCAGCAGGTTAACCTTCCAC 59.118 55.000 24.99 13.99 46.09 4.02
2363 2691 0.771127 AGCAGCAGGTTAACCTTCCA 59.229 50.000 24.99 0.00 46.09 3.53
2364 2692 1.168714 CAGCAGCAGGTTAACCTTCC 58.831 55.000 24.99 17.68 46.09 3.46
2365 2693 1.897560 ACAGCAGCAGGTTAACCTTC 58.102 50.000 24.99 20.13 46.09 3.46
2366 2694 2.105821 TGTACAGCAGCAGGTTAACCTT 59.894 45.455 24.99 8.84 46.09 3.50
2367 2695 2.289694 CTGTACAGCAGCAGGTTAACCT 60.290 50.000 21.96 21.96 40.92 3.50
2368 2696 2.076863 CTGTACAGCAGCAGGTTAACC 58.923 52.381 17.41 17.41 38.52 2.85
2384 2712 8.362464 AGAAATCACAGATTAGTACCACTGTA 57.638 34.615 0.00 0.00 40.84 2.74
2401 2729 8.784994 TCAGGTAGATAGATACGAAGAAATCAC 58.215 37.037 0.00 0.00 0.00 3.06
2406 2734 8.919777 TTCATCAGGTAGATAGATACGAAGAA 57.080 34.615 0.00 0.00 34.43 2.52
2457 2785 8.153550 AGTTAAGCTTCCATCCATAGATAACAG 58.846 37.037 0.00 0.00 0.00 3.16
2508 2840 5.598416 TTATCTCGATTTCCAGAGCAAGA 57.402 39.130 0.00 0.00 34.66 3.02
2510 2842 6.092670 CAGTTTTATCTCGATTTCCAGAGCAA 59.907 38.462 0.00 0.00 34.66 3.91
2549 2881 6.906901 TGGTTAGGGAGTATAGGAATGAAACT 59.093 38.462 0.00 0.00 0.00 2.66
2550 2882 7.133133 TGGTTAGGGAGTATAGGAATGAAAC 57.867 40.000 0.00 0.00 0.00 2.78
2551 2883 7.571025 GTTGGTTAGGGAGTATAGGAATGAAA 58.429 38.462 0.00 0.00 0.00 2.69
2561 2893 2.167900 GCACTCGTTGGTTAGGGAGTAT 59.832 50.000 0.00 0.00 37.64 2.12
2580 2912 2.588439 GGAGGCATCAGCTGAGCA 59.412 61.111 27.83 8.05 41.70 4.26
2641 3360 6.820152 CCAATGCATATTCTCTCGATTCCATA 59.180 38.462 0.00 0.00 0.00 2.74
2643 3362 4.999311 CCAATGCATATTCTCTCGATTCCA 59.001 41.667 0.00 0.00 0.00 3.53
2644 3363 5.240891 TCCAATGCATATTCTCTCGATTCC 58.759 41.667 0.00 0.00 0.00 3.01
2645 3364 6.791887 TTCCAATGCATATTCTCTCGATTC 57.208 37.500 0.00 0.00 0.00 2.52
2646 3365 7.572523 TTTTCCAATGCATATTCTCTCGATT 57.427 32.000 0.00 0.00 0.00 3.34
2649 3369 6.732154 ACATTTTCCAATGCATATTCTCTCG 58.268 36.000 0.00 0.00 43.39 4.04
2676 3396 8.468399 TGCAAGACAAATCAAGCAATATCATTA 58.532 29.630 0.00 0.00 34.97 1.90
2679 3399 6.270156 TGCAAGACAAATCAAGCAATATCA 57.730 33.333 0.00 0.00 34.97 2.15
2692 3412 7.551974 TGAAATGAAAGGATTTTGCAAGACAAA 59.448 29.630 0.00 0.00 46.51 2.83
2782 3502 6.015434 GGTGTCCTTAAATTTCACTGGTCAAT 60.015 38.462 0.00 0.00 0.00 2.57
2837 3557 8.844244 ACAAGGAGCAAATATTATTCATCTGTC 58.156 33.333 0.00 0.00 0.00 3.51
2844 3564 9.282569 AGATGAGACAAGGAGCAAATATTATTC 57.717 33.333 0.00 0.00 0.00 1.75
2949 3669 1.146263 GGGTTCCAGCATACGGGAG 59.854 63.158 0.00 0.00 41.48 4.30
2950 3670 0.986019 ATGGGTTCCAGCATACGGGA 60.986 55.000 0.00 0.00 36.75 5.14
2968 3690 4.644234 TGAATATGTTTCACGCATCCCAAT 59.356 37.500 0.00 0.00 0.00 3.16
2970 3692 3.615155 TGAATATGTTTCACGCATCCCA 58.385 40.909 0.00 0.00 0.00 4.37
2987 3709 6.067217 AGCCCTTACTGTTATGAACTGAAT 57.933 37.500 3.60 0.00 34.78 2.57
2999 3721 5.562298 TTCAGTTTTCTAGCCCTTACTGT 57.438 39.130 0.00 0.00 35.64 3.55
3022 3747 6.587206 TTGACATAATTCTGGTGCAATTGA 57.413 33.333 10.34 0.00 0.00 2.57
3051 3776 5.700832 GTCCAATATTTATGATGTCCGCTCA 59.299 40.000 0.00 0.00 0.00 4.26
3078 3803 1.117994 TGTTGCTTTTGGTGCATGGA 58.882 45.000 0.00 0.00 40.34 3.41
3140 3865 2.099263 CACTACATGCGGTGCTAGTAGT 59.901 50.000 15.81 15.81 44.05 2.73
3150 3875 1.382522 AGCATTTCCACTACATGCGG 58.617 50.000 0.00 0.00 46.62 5.69
3159 3884 9.502091 TCAGGTTGTATATATAAGCATTTCCAC 57.498 33.333 19.50 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.