Multiple sequence alignment - TraesCS1B01G384400

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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 TraesCS1B01G384400 chr1B 100.000 2636 0 0 1 2636 617087427 617090062 0.000000e+00 4868.0
1 TraesCS1B01G384400 chr1B 87.841 806 70 16 1844 2631 617284673 617285468 0.000000e+00 920.0
2 TraesCS1B01G384400 chr1B 93.377 604 32 1 1 604 617283602 617284197 0.000000e+00 887.0
3 TraesCS1B01G384400 chr1B 90.984 244 18 1 657 896 617284192 617284435 2.530000e-85 326.0
4 TraesCS1B01G384400 chr1B 91.928 223 17 1 831 1053 617284438 617284659 7.080000e-81 311.0
5 TraesCS1B01G384400 chr1B 90.811 185 17 0 1 185 617284013 617284197 5.630000e-62 248.0
6 TraesCS1B01G384400 chr1A 88.951 1964 185 16 1 1939 545473754 545475710 0.000000e+00 2396.0
7 TraesCS1B01G384400 chr1A 87.609 1953 207 19 1 1938 528297612 528295680 0.000000e+00 2233.0
8 TraesCS1B01G384400 chr1A 86.449 214 27 1 2 215 528297192 528296981 1.580000e-57 233.0
9 TraesCS1B01G384400 chr7D 88.047 1782 175 18 180 1943 616459554 616457793 0.000000e+00 2076.0
10 TraesCS1B01G384400 chr7D 91.121 214 17 1 2 215 616459312 616459101 3.320000e-74 289.0
11 TraesCS1B01G384400 chr7D 93.085 188 10 1 1 188 616460145 616459961 3.340000e-69 272.0
12 TraesCS1B01G384400 chr7D 75.720 243 45 6 863 1104 12475848 12476077 2.770000e-20 110.0
13 TraesCS1B01G384400 chr7D 89.362 47 5 0 866 912 12471737 12471783 2.830000e-05 60.2
14 TraesCS1B01G384400 chr1D 93.534 897 52 3 1 897 450203014 450203904 0.000000e+00 1330.0
15 TraesCS1B01G384400 chr4A 76.731 361 71 8 747 1103 725589095 725588744 3.460000e-44 189.0
16 TraesCS1B01G384400 chr4A 84.615 91 13 1 245 335 725589095 725589006 3.610000e-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 TraesCS1B01G384400 chr1B 617087427 617090062 2635 False 4868.0 4868 100.0000 1 2636 1 chr1B.!!$F1 2635
1 TraesCS1B01G384400 chr1B 617283602 617285468 1866 False 538.4 920 90.9882 1 2631 5 chr1B.!!$F2 2630
2 TraesCS1B01G384400 chr1A 545473754 545475710 1956 False 2396.0 2396 88.9510 1 1939 1 chr1A.!!$F1 1938
3 TraesCS1B01G384400 chr1A 528295680 528297612 1932 True 1233.0 2233 87.0290 1 1938 2 chr1A.!!$R1 1937
4 TraesCS1B01G384400 chr7D 616457793 616460145 2352 True 879.0 2076 90.7510 1 1943 3 chr7D.!!$R1 1942
5 TraesCS1B01G384400 chr1D 450203014 450203904 890 False 1330.0 1330 93.5340 1 897 1 chr1D.!!$F1 896

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
331 751 0.250945 TATCCACCGCCAAACTGCAA 60.251 50.0 0.00 0.00 0.00 4.08 F
1501 2000 0.175531 GGGTAATGCATGCGCCTTTT 59.824 50.0 14.09 4.22 37.32 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 2073 0.178953 ATTGAGGTTGCCCAGCTTGT 60.179 50.00 0.00 0.0 31.44 3.16 R
2410 2940 3.679502 AGAAACTTGTTTTGTGTGCTTGC 59.320 39.13 0.06 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
78 83 8.512956 TGGTAATAGAGAGAGCATTAATACGAC 58.487 37.037 0.00 0.00 0.00 4.34
85 90 6.787225 AGAGAGCATTAATACGACGATATCC 58.213 40.000 0.00 0.00 0.00 2.59
331 751 0.250945 TATCCACCGCCAAACTGCAA 60.251 50.000 0.00 0.00 0.00 4.08
351 771 6.245408 TGCAAACTACATTTATGAAGTCCCT 58.755 36.000 0.00 0.00 0.00 4.20
392 812 9.333724 TGAATATCATTTGGATATCCATGATCG 57.666 33.333 31.00 19.26 46.23 3.69
397 817 4.462508 TTGGATATCCATGATCGAGAGC 57.537 45.455 25.07 0.00 46.97 4.09
399 819 4.860022 TGGATATCCATGATCGAGAGCTA 58.140 43.478 20.98 0.00 42.01 3.32
409 829 4.891260 TGATCGAGAGCTATTGCATTCAT 58.109 39.130 1.12 0.00 42.74 2.57
534 955 5.393124 ACGATCAACATATTTGTGCACAAG 58.607 37.500 29.50 21.00 37.15 3.16
672 1096 9.791820 CAACCAATACATATATGCATACAATGG 57.208 33.333 24.33 19.27 0.00 3.16
686 1110 6.154445 GCATACAATGGACATCAATCATTCC 58.846 40.000 0.00 0.00 0.00 3.01
687 1111 6.239092 GCATACAATGGACATCAATCATTCCA 60.239 38.462 0.00 0.00 42.34 3.53
703 1127 6.264771 TCATTCCAATATCCATGACCAAGA 57.735 37.500 0.00 0.00 0.00 3.02
721 1149 8.498575 TGACCAAGATATGTTACATTAATGGGA 58.501 33.333 19.37 4.42 0.00 4.37
827 1255 5.136828 TCATTTGTATATCCACCGCCAAAT 58.863 37.500 0.00 0.00 33.97 2.32
897 1393 8.844865 ACCTATGCATATCACCTCAATCTATA 57.155 34.615 6.92 0.00 0.00 1.31
900 1396 9.747293 CTATGCATATCACCTCAATCTATACAG 57.253 37.037 6.92 0.00 0.00 2.74
901 1397 6.939622 TGCATATCACCTCAATCTATACAGG 58.060 40.000 0.00 0.00 0.00 4.00
912 1408 5.310331 TCAATCTATACAGGCATCCATCCAA 59.690 40.000 0.00 0.00 0.00 3.53
920 1416 0.394762 GCATCCATCCAAGTCTGCCA 60.395 55.000 0.00 0.00 0.00 4.92
1045 1541 4.630505 CCATCATCTTCTCTGCCATAATCG 59.369 45.833 0.00 0.00 0.00 3.34
1061 1557 5.297776 CCATAATCGTCATGCTCTTTTCCTT 59.702 40.000 0.00 0.00 0.00 3.36
1084 1580 1.069765 ACCACTGCTCAGACCAACG 59.930 57.895 3.60 0.00 0.00 4.10
1086 1582 0.249868 CCACTGCTCAGACCAACGAA 60.250 55.000 3.60 0.00 0.00 3.85
1090 1586 0.318699 TGCTCAGACCAACGAAGACG 60.319 55.000 0.00 0.00 45.75 4.18
1104 1600 2.594592 GACGTTGGTGGCAAGCCT 60.595 61.111 12.96 0.00 36.94 4.58
1109 1605 0.823356 GTTGGTGGCAAGCCTGAGAA 60.823 55.000 12.96 0.00 36.94 2.87
1120 1616 1.283321 AGCCTGAGAAGACCCATTTCC 59.717 52.381 0.00 0.00 0.00 3.13
1131 1627 1.613437 ACCCATTTCCTTGTTGAAGCG 59.387 47.619 0.00 0.00 0.00 4.68
1140 1636 2.029124 CCTTGTTGAAGCGTGCAAAAAC 59.971 45.455 0.00 0.00 0.00 2.43
1155 1651 3.796178 GCAAAAACGCTTCAATCAACTCA 59.204 39.130 0.00 0.00 0.00 3.41
1161 1657 3.681897 ACGCTTCAATCAACTCATCTGAC 59.318 43.478 0.00 0.00 0.00 3.51
1162 1658 3.241900 CGCTTCAATCAACTCATCTGACG 60.242 47.826 0.00 0.00 0.00 4.35
1194 1693 2.869897 GAAGAATTCTGCGTCTCGACT 58.130 47.619 9.17 0.00 43.23 4.18
1200 1699 2.047560 TGCGTCTCGACTCTCCGA 60.048 61.111 0.00 0.00 37.03 4.55
1211 1710 0.827925 ACTCTCCGACAGGACAAGCA 60.828 55.000 0.00 0.00 42.75 3.91
1235 1734 1.339055 TGATGAGGCAAAGGACCTTCG 60.339 52.381 7.34 0.00 37.77 3.79
1248 1747 2.750350 CTTCGTGACCTGGCCCTT 59.250 61.111 0.00 0.00 0.00 3.95
1263 1762 2.084546 GCCCTTGTTGGTGTAGACATC 58.915 52.381 0.00 0.00 0.00 3.06
1303 1802 1.199624 CGCAAGTGGCAAAGTCAAAC 58.800 50.000 0.00 0.00 45.17 2.93
1306 1805 2.348362 GCAAGTGGCAAAGTCAAACAAC 59.652 45.455 0.00 0.00 43.97 3.32
1308 1807 4.244862 CAAGTGGCAAAGTCAAACAACTT 58.755 39.130 0.00 0.00 41.20 2.66
1319 1818 4.640201 AGTCAAACAACTTATGCACAGTGT 59.360 37.500 1.61 0.00 0.00 3.55
1343 1842 3.342909 TGGCACATCAACAGCACG 58.657 55.556 0.00 0.00 0.00 5.34
1398 1897 0.320421 CGGTGACCGTCCTCAATGTT 60.320 55.000 17.28 0.00 42.73 2.71
1437 1936 1.376812 CTACCGTGGTCCCAAAGGC 60.377 63.158 0.00 0.00 31.82 4.35
1446 1945 0.313987 GTCCCAAAGGCGGTGAAAAG 59.686 55.000 0.00 0.00 0.00 2.27
1457 1956 0.704664 GGTGAAAAGGATGGACCCCT 59.295 55.000 0.00 0.00 40.05 4.79
1493 1992 1.398041 CGACTGTGTGGGTAATGCATG 59.602 52.381 0.00 0.00 0.00 4.06
1496 1995 1.226660 GTGTGGGTAATGCATGCGC 60.227 57.895 14.09 0.00 39.24 6.09
1501 2000 0.175531 GGGTAATGCATGCGCCTTTT 59.824 50.000 14.09 4.22 37.32 2.27
1530 2029 0.242017 GTGGGCATGAGCTTGTTGAC 59.758 55.000 0.00 0.00 41.70 3.18
1540 2039 1.181098 GCTTGTTGACATGCCTGGGT 61.181 55.000 10.01 0.00 40.04 4.51
1541 2040 0.599558 CTTGTTGACATGCCTGGGTG 59.400 55.000 0.00 0.00 0.00 4.61
1563 2062 3.549423 GGGAGGCGTTGTACAAAGAAAAC 60.549 47.826 23.28 10.78 0.00 2.43
1574 2073 5.525745 TGTACAAAGAAAACATTGAGCTCGA 59.474 36.000 6.01 6.01 0.00 4.04
1606 2105 3.159213 ACCTCAATGTTGCCTTGATGA 57.841 42.857 0.00 0.00 32.50 2.92
1623 2122 6.239120 CCTTGATGACACCATATTGGGATTTC 60.239 42.308 0.00 0.00 43.37 2.17
1730 2229 5.596845 TGATAGTTTCTATATGCGTGCACA 58.403 37.500 18.64 0.00 0.00 4.57
1745 2244 1.417517 TGCACAGTGTGAAGATGTCCT 59.582 47.619 27.37 0.00 35.23 3.85
1749 2248 4.621510 GCACAGTGTGAAGATGTCCTATCA 60.622 45.833 27.37 0.00 35.23 2.15
1757 2256 6.126681 TGTGAAGATGTCCTATCAATGTCCAT 60.127 38.462 0.00 0.00 0.00 3.41
1760 2259 6.505048 AGATGTCCTATCAATGTCCATTCA 57.495 37.500 0.00 0.00 0.00 2.57
1825 2341 0.387929 GCATGACATGGATGCCAAGG 59.612 55.000 17.03 0.00 40.37 3.61
1834 2350 0.110104 GGATGCCAAGGAGGATCTGG 59.890 60.000 0.00 0.00 41.22 3.86
1835 2351 0.842635 GATGCCAAGGAGGATCTGGT 59.157 55.000 0.00 0.00 41.22 4.00
1868 2384 8.146053 CATCAGTATGGGTAGTTTATATGGGA 57.854 38.462 0.00 0.00 36.16 4.37
1872 2388 6.783977 AGTATGGGTAGTTTATATGGGACGAA 59.216 38.462 0.00 0.00 0.00 3.85
1995 2511 2.517650 TTTGTGCCACGGGAAATTTC 57.482 45.000 9.83 9.83 0.00 2.17
1997 2513 2.570415 TGTGCCACGGGAAATTTCTA 57.430 45.000 17.42 0.00 0.00 2.10
2048 2565 3.621715 GTCAGACAAACTTCTCGTGGTTT 59.378 43.478 0.00 0.00 36.27 3.27
2062 2579 2.030007 CGTGGTTTGTGAGCCATCAATT 60.030 45.455 0.00 0.00 38.50 2.32
2063 2580 3.578688 GTGGTTTGTGAGCCATCAATTC 58.421 45.455 0.00 0.00 38.50 2.17
2110 2627 4.381825 GCAAATCACATTATGGGCAGTCAA 60.382 41.667 0.00 0.00 0.00 3.18
2111 2628 4.989279 AATCACATTATGGGCAGTCAAC 57.011 40.909 0.00 0.00 0.00 3.18
2112 2629 2.722094 TCACATTATGGGCAGTCAACC 58.278 47.619 0.00 0.00 0.00 3.77
2114 2631 2.684881 CACATTATGGGCAGTCAACCTC 59.315 50.000 0.00 0.00 0.00 3.85
2121 2638 2.107378 TGGGCAGTCAACCTCATGTTAA 59.893 45.455 0.00 0.00 34.69 2.01
2130 2647 9.559958 CAGTCAACCTCATGTTAAAACAATATC 57.440 33.333 0.00 0.00 43.03 1.63
2138 2655 9.912634 CTCATGTTAAAACAATATCACAAACCT 57.087 29.630 0.00 0.00 43.03 3.50
2261 2791 6.301169 AGTGACCAATAAGTTTCTCCCTAG 57.699 41.667 0.00 0.00 0.00 3.02
2263 2793 6.674419 AGTGACCAATAAGTTTCTCCCTAGAT 59.326 38.462 0.00 0.00 0.00 1.98
2264 2794 7.844779 AGTGACCAATAAGTTTCTCCCTAGATA 59.155 37.037 0.00 0.00 0.00 1.98
2265 2795 8.652290 GTGACCAATAAGTTTCTCCCTAGATAT 58.348 37.037 0.00 0.00 0.00 1.63
2277 2807 8.511604 TTCTCCCTAGATATTTTTGCTTCTTG 57.488 34.615 0.00 0.00 0.00 3.02
2300 2830 9.099454 CTTGGTAATCTATGACTCCTGTAAAAC 57.901 37.037 0.00 0.00 0.00 2.43
2301 2831 8.141298 TGGTAATCTATGACTCCTGTAAAACA 57.859 34.615 0.00 0.00 0.00 2.83
2303 2833 9.262358 GGTAATCTATGACTCCTGTAAAACATC 57.738 37.037 0.00 0.00 0.00 3.06
2312 2842 5.182001 ACTCCTGTAAAACATCTGCACATTC 59.818 40.000 0.00 0.00 0.00 2.67
2318 2848 5.534207 AAAACATCTGCACATTCCAAGAA 57.466 34.783 0.00 0.00 0.00 2.52
2319 2849 5.534207 AAACATCTGCACATTCCAAGAAA 57.466 34.783 0.00 0.00 0.00 2.52
2355 2885 5.049828 GTGGGAATGGAGTGAAAACAAAAG 58.950 41.667 0.00 0.00 0.00 2.27
2356 2886 4.100808 TGGGAATGGAGTGAAAACAAAAGG 59.899 41.667 0.00 0.00 0.00 3.11
2357 2887 4.503123 GGGAATGGAGTGAAAACAAAAGGG 60.503 45.833 0.00 0.00 0.00 3.95
2358 2888 4.343814 GGAATGGAGTGAAAACAAAAGGGA 59.656 41.667 0.00 0.00 0.00 4.20
2398 2928 9.632807 GTTTGTAACATATTAGCCATGTTTTCA 57.367 29.630 6.07 4.53 42.52 2.69
2419 2949 7.636259 TTCACATATTTAAAAGCAAGCACAC 57.364 32.000 0.00 0.00 0.00 3.82
2430 2960 3.663025 AGCAAGCACACAAAACAAGTTT 58.337 36.364 0.00 0.00 0.00 2.66
2431 2961 3.679502 AGCAAGCACACAAAACAAGTTTC 59.320 39.130 0.00 0.00 31.45 2.78
2435 2966 3.679502 AGCACACAAAACAAGTTTCTTGC 59.320 39.130 9.06 5.85 31.45 4.01
2449 2980 5.880341 AGTTTCTTGCAGTTCAGTGTTAAC 58.120 37.500 0.00 0.00 0.00 2.01
2450 2981 5.414454 AGTTTCTTGCAGTTCAGTGTTAACA 59.586 36.000 3.59 3.59 0.00 2.41
2456 2987 6.884096 TGCAGTTCAGTGTTAACAAAATTG 57.116 33.333 10.51 12.40 0.00 2.32
2459 2990 6.529829 GCAGTTCAGTGTTAACAAAATTGTGA 59.470 34.615 10.51 4.20 41.31 3.58
2498 3029 9.936759 AAAATTTGTCCAAGTACTTCAGAAAAA 57.063 25.926 17.13 17.13 0.00 1.94
2500 3031 9.533253 AATTTGTCCAAGTACTTCAGAAAAATG 57.467 29.630 22.59 6.35 28.25 2.32
2501 3032 7.873719 TTGTCCAAGTACTTCAGAAAAATGA 57.126 32.000 4.77 0.00 0.00 2.57
2502 3033 8.463930 TTGTCCAAGTACTTCAGAAAAATGAT 57.536 30.769 4.77 0.00 0.00 2.45
2586 3117 7.333528 ACACAAGAGCTTATTCTTTTGTTCA 57.666 32.000 2.64 0.00 42.41 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 83 5.230182 TGTTGATCCTCATTTCGGATATCG 58.770 41.667 0.00 0.00 41.24 2.92
85 90 6.415867 GCACAAATATGTTGATCCTCATTTCG 59.584 38.462 5.31 0.00 37.82 3.46
190 610 1.273048 TGCCCACTTTGAATGTCATGC 59.727 47.619 0.00 0.00 0.00 4.06
392 812 5.303971 AGGTACATGAATGCAATAGCTCTC 58.696 41.667 0.00 0.00 42.74 3.20
409 829 4.405680 ACACATCTAGCTTGCATAGGTACA 59.594 41.667 0.00 0.00 35.80 2.90
495 916 6.095300 TGTTGATCGTCATTTTGCATATCCTT 59.905 34.615 0.00 0.00 0.00 3.36
503 924 7.385650 CACAAATATGTTGATCGTCATTTTGC 58.614 34.615 20.45 0.00 37.82 3.68
512 933 5.393124 ACTTGTGCACAAATATGTTGATCG 58.607 37.500 30.62 17.39 37.82 3.69
561 982 4.381185 CCATGAATGCAACACAACTATGCT 60.381 41.667 0.00 0.00 40.66 3.79
609 1033 3.668141 TGCCCACTTTGGATATCATGT 57.332 42.857 4.83 0.00 40.96 3.21
672 1096 8.242053 GTCATGGATATTGGAATGATTGATGTC 58.758 37.037 0.00 0.00 32.07 3.06
686 1110 9.506018 TGTAACATATCTTGGTCATGGATATTG 57.494 33.333 0.00 0.00 32.41 1.90
754 1182 5.872070 TGTACATATGTTGACGCTCATTTCA 59.128 36.000 14.77 0.00 0.00 2.69
897 1393 1.064906 CAGACTTGGATGGATGCCTGT 60.065 52.381 0.00 0.00 0.00 4.00
900 1396 1.105759 GGCAGACTTGGATGGATGCC 61.106 60.000 0.00 0.00 45.61 4.40
901 1397 0.394762 TGGCAGACTTGGATGGATGC 60.395 55.000 0.00 0.00 0.00 3.91
1045 1541 3.127721 GTGGCTAAGGAAAAGAGCATGAC 59.872 47.826 0.00 0.00 37.98 3.06
1061 1557 1.544825 GGTCTGAGCAGTGGTGGCTA 61.545 60.000 0.00 0.00 42.78 3.93
1084 1580 1.282875 GCTTGCCACCAACGTCTTC 59.717 57.895 0.00 0.00 0.00 2.87
1086 1582 2.594592 GGCTTGCCACCAACGTCT 60.595 61.111 6.79 0.00 0.00 4.18
1090 1586 0.823356 TTCTCAGGCTTGCCACCAAC 60.823 55.000 14.54 0.00 0.00 3.77
1104 1600 4.141274 TCAACAAGGAAATGGGTCTTCTCA 60.141 41.667 0.00 0.00 0.00 3.27
1109 1605 2.893489 GCTTCAACAAGGAAATGGGTCT 59.107 45.455 0.00 0.00 0.00 3.85
1120 1616 2.284401 CGTTTTTGCACGCTTCAACAAG 60.284 45.455 0.00 0.00 32.43 3.16
1131 1627 3.551485 AGTTGATTGAAGCGTTTTTGCAC 59.449 39.130 0.00 0.00 37.31 4.57
1140 1636 3.241900 CGTCAGATGAGTTGATTGAAGCG 60.242 47.826 0.00 0.00 0.00 4.68
1155 1651 4.400567 TCTTCTGTGATGTGATCGTCAGAT 59.599 41.667 10.13 0.00 40.10 2.90
1194 1693 0.539669 TCTGCTTGTCCTGTCGGAGA 60.540 55.000 0.00 0.00 40.84 3.71
1200 1699 1.973515 TCATCACTCTGCTTGTCCTGT 59.026 47.619 0.00 0.00 0.00 4.00
1211 1710 1.280421 GGTCCTTTGCCTCATCACTCT 59.720 52.381 0.00 0.00 0.00 3.24
1235 1734 1.903404 CCAACAAGGGCCAGGTCAC 60.903 63.158 6.18 0.00 0.00 3.67
1248 1747 3.007940 CCTTGAGGATGTCTACACCAACA 59.992 47.826 0.00 0.00 37.39 3.33
1263 1762 3.152341 GGCAATGATATGTCCCTTGAGG 58.848 50.000 6.18 0.00 0.00 3.86
1296 1795 4.640201 ACACTGTGCATAAGTTGTTTGACT 59.360 37.500 7.90 0.00 0.00 3.41
1303 1802 5.422666 TTCTTGACACTGTGCATAAGTTG 57.577 39.130 7.90 2.53 0.00 3.16
1306 1805 4.673580 GCCATTCTTGACACTGTGCATAAG 60.674 45.833 7.90 9.84 0.00 1.73
1308 1807 2.749076 GCCATTCTTGACACTGTGCATA 59.251 45.455 7.90 0.00 0.00 3.14
1319 1818 2.229543 GCTGTTGATGTGCCATTCTTGA 59.770 45.455 0.00 0.00 0.00 3.02
1343 1842 4.389576 CGCACAAACTGAGGCGGC 62.390 66.667 0.00 0.00 39.53 6.53
1362 1861 2.279517 GCGGCGTCATAGTCCAGG 60.280 66.667 9.37 0.00 0.00 4.45
1398 1897 0.675083 CCTTGAGCATGGTGTTGCAA 59.325 50.000 0.00 0.00 45.23 4.08
1437 1936 0.679960 GGGGTCCATCCTTTTCACCG 60.680 60.000 0.00 0.00 36.25 4.94
1446 1945 5.600669 AATAAAAGGATAGGGGTCCATCC 57.399 43.478 0.00 0.00 40.90 3.51
1457 1956 6.819649 CACACAGTCGGGTAAATAAAAGGATA 59.180 38.462 0.00 0.00 0.00 2.59
1488 1987 2.257980 CCGAAAAAGGCGCATGCA 59.742 55.556 19.57 0.00 45.35 3.96
1496 1995 1.165270 CCCACAGTAGCCGAAAAAGG 58.835 55.000 0.00 0.00 0.00 3.11
1501 2000 1.078497 CATGCCCACAGTAGCCGAA 60.078 57.895 0.00 0.00 0.00 4.30
1540 2039 0.759959 TCTTTGTACAACGCCTCCCA 59.240 50.000 8.07 0.00 0.00 4.37
1541 2040 1.886886 TTCTTTGTACAACGCCTCCC 58.113 50.000 8.07 0.00 0.00 4.30
1574 2073 0.178953 ATTGAGGTTGCCCAGCTTGT 60.179 50.000 0.00 0.00 31.44 3.16
1606 2105 3.642141 GGGTGAAATCCCAATATGGTGT 58.358 45.455 0.00 0.00 46.30 4.16
1730 2229 6.305272 ACATTGATAGGACATCTTCACACT 57.695 37.500 0.00 0.00 0.00 3.55
1757 2256 1.089112 CAATGAGCGCATCCAGTGAA 58.911 50.000 11.47 0.00 32.35 3.18
1760 2259 2.627515 ATACAATGAGCGCATCCAGT 57.372 45.000 11.47 5.01 32.35 4.00
1766 2265 3.733727 CGTGTACATATACAATGAGCGCA 59.266 43.478 11.47 0.00 42.99 6.09
1825 2341 2.592308 GGGCCACACCAGATCCTC 59.408 66.667 4.39 0.00 42.05 3.71
1834 2350 3.100545 CATACTGATGGGGCCACAC 57.899 57.895 11.75 4.99 0.00 3.82
1961 2477 7.706179 CCGTGGCACAAAATCTAATTTATTGAT 59.294 33.333 19.09 0.00 44.16 2.57
2048 2565 2.170166 GGGTTGAATTGATGGCTCACA 58.830 47.619 0.00 0.00 0.00 3.58
2051 2568 4.081531 TGAAATGGGTTGAATTGATGGCTC 60.082 41.667 0.00 0.00 0.00 4.70
2062 2579 6.833416 CCCTTTATCATACTGAAATGGGTTGA 59.167 38.462 0.00 0.00 33.04 3.18
2063 2580 6.461509 GCCCTTTATCATACTGAAATGGGTTG 60.462 42.308 15.78 0.00 36.04 3.77
2110 2627 9.691362 GTTTGTGATATTGTTTTAACATGAGGT 57.309 29.630 0.00 0.00 38.95 3.85
2111 2628 9.139174 GGTTTGTGATATTGTTTTAACATGAGG 57.861 33.333 0.00 0.00 38.95 3.86
2112 2629 9.912634 AGGTTTGTGATATTGTTTTAACATGAG 57.087 29.630 0.00 0.00 38.95 2.90
2121 2638 6.978080 GTGTGTGAAGGTTTGTGATATTGTTT 59.022 34.615 0.00 0.00 0.00 2.83
2130 2647 3.799281 AATGGTGTGTGAAGGTTTGTG 57.201 42.857 0.00 0.00 0.00 3.33
2138 2655 9.469807 GTATTATTTTGTCAAATGGTGTGTGAA 57.530 29.630 0.00 0.00 34.29 3.18
2167 2684 9.723601 ATATTGTGTGCTATTTTGGAAATTTGT 57.276 25.926 0.00 0.00 0.00 2.83
2175 2692 7.333528 AGTGGTATATTGTGTGCTATTTTGG 57.666 36.000 0.00 0.00 0.00 3.28
2176 2693 8.458052 TGAAGTGGTATATTGTGTGCTATTTTG 58.542 33.333 0.00 0.00 0.00 2.44
2219 2736 9.667107 TGGTCACTTTGGAAAATAGATAGTAAG 57.333 33.333 0.00 0.00 0.00 2.34
2240 2757 8.798975 ATATCTAGGGAGAAACTTATTGGTCA 57.201 34.615 0.00 0.00 34.61 4.02
2264 2794 9.247861 AGTCATAGATTACCAAGAAGCAAAAAT 57.752 29.630 0.00 0.00 0.00 1.82
2265 2795 8.635765 AGTCATAGATTACCAAGAAGCAAAAA 57.364 30.769 0.00 0.00 0.00 1.94
2272 2802 8.603898 TTACAGGAGTCATAGATTACCAAGAA 57.396 34.615 0.00 0.00 0.00 2.52
2277 2807 9.262358 GATGTTTTACAGGAGTCATAGATTACC 57.738 37.037 0.00 0.00 0.00 2.85
2283 2813 6.036517 GTGCAGATGTTTTACAGGAGTCATAG 59.963 42.308 0.00 0.00 0.00 2.23
2300 2830 9.976511 ATATATTTTTCTTGGAATGTGCAGATG 57.023 29.630 0.00 0.00 0.00 2.90
2312 2842 9.627123 TTCCCACTGACTATATATTTTTCTTGG 57.373 33.333 0.00 0.00 0.00 3.61
2318 2848 8.949421 ACTCCATTCCCACTGACTATATATTTT 58.051 33.333 0.00 0.00 0.00 1.82
2319 2849 8.378565 CACTCCATTCCCACTGACTATATATTT 58.621 37.037 0.00 0.00 0.00 1.40
2332 2862 4.664150 TTTGTTTTCACTCCATTCCCAC 57.336 40.909 0.00 0.00 0.00 4.61
2398 2928 8.334632 GTTTTGTGTGCTTGCTTTTAAATATGT 58.665 29.630 0.00 0.00 0.00 2.29
2410 2940 3.679502 AGAAACTTGTTTTGTGTGCTTGC 59.320 39.130 0.06 0.00 0.00 4.01
2419 2949 5.634859 ACTGAACTGCAAGAAACTTGTTTTG 59.365 36.000 12.07 0.00 37.43 2.44
2430 2960 5.888691 TTTGTTAACACTGAACTGCAAGA 57.111 34.783 8.07 0.00 37.43 3.02
2431 2961 7.063308 ACAATTTTGTTAACACTGAACTGCAAG 59.937 33.333 8.07 0.00 38.47 4.01
2435 2966 8.633075 ATCACAATTTTGTTAACACTGAACTG 57.367 30.769 8.07 6.62 39.91 3.16
2471 3002 9.936759 TTTTCTGAAGTACTTGGACAAATTTTT 57.063 25.926 14.14 0.00 0.00 1.94
2472 3003 9.936759 TTTTTCTGAAGTACTTGGACAAATTTT 57.063 25.926 14.14 0.00 0.00 1.82
2474 3005 9.533253 CATTTTTCTGAAGTACTTGGACAAATT 57.467 29.630 14.14 7.97 0.00 1.82
2475 3006 8.912988 TCATTTTTCTGAAGTACTTGGACAAAT 58.087 29.630 14.14 16.45 0.00 2.32
2485 3016 7.915397 ACACAACACATCATTTTTCTGAAGTAC 59.085 33.333 0.00 0.00 0.00 2.73
2490 3021 8.545229 AAAAACACAACACATCATTTTTCTGA 57.455 26.923 0.00 0.00 0.00 3.27
2555 3086 9.435688 AAAAGAATAAGCTCTTGTGTTGTTTTT 57.564 25.926 0.00 0.00 35.79 1.94


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

AutoCloner maintained by Alex Coulton.