Multiple sequence alignment - TraesCS5B01G152900

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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 TraesCS5B01G152900 chr5B 100.000 3329 0 0 1 3329 282044238 282047566 0.000000e+00 6148.0
1 TraesCS5B01G152900 chr5B 87.943 141 12 5 602 739 243851147 243851009 9.560000e-36 161.0
2 TraesCS5B01G152900 chr5B 87.368 95 12 0 1664 1758 616904622 616904716 3.510000e-20 110.0
3 TraesCS5B01G152900 chr5D 94.336 2984 100 26 400 3329 249256660 249259628 0.000000e+00 4510.0
4 TraesCS5B01G152900 chr5A 91.282 1342 88 19 114 1434 331940354 331941687 0.000000e+00 1803.0
5 TraesCS5B01G152900 chr5A 96.078 918 32 3 1780 2695 331943560 331944475 0.000000e+00 1493.0
6 TraesCS5B01G152900 chr5A 95.400 500 21 2 2831 3329 331944470 331944968 0.000000e+00 795.0
7 TraesCS5B01G152900 chr5A 91.837 98 8 0 1682 1779 592618837 592618934 1.610000e-28 137.0
8 TraesCS5B01G152900 chr5A 87.736 106 13 0 1664 1769 362159347 362159452 1.250000e-24 124.0
9 TraesCS5B01G152900 chr5A 91.463 82 6 1 1435 1516 331941725 331941805 9.760000e-21 111.0
10 TraesCS5B01G152900 chrUn 100.000 427 0 0 1931 2357 476491497 476491923 0.000000e+00 789.0
11 TraesCS5B01G152900 chr6B 90.000 130 10 3 602 729 233039360 233039232 7.390000e-37 165.0
12 TraesCS5B01G152900 chr1D 89.844 128 8 4 600 725 79358260 79358136 3.440000e-35 159.0
13 TraesCS5B01G152900 chr1D 96.250 80 2 1 1664 1743 462192447 462192369 2.700000e-26 130.0
14 TraesCS5B01G152900 chr1D 100.000 30 0 0 1638 1667 471759074 471759103 4.640000e-04 56.5
15 TraesCS5B01G152900 chr1B 89.683 126 10 3 602 725 130540304 130540180 1.240000e-34 158.0
16 TraesCS5B01G152900 chr6D 87.970 133 12 4 602 732 134289095 134288965 1.600000e-33 154.0
17 TraesCS5B01G152900 chr6D 100.000 30 0 0 1638 1667 417471223 417471252 4.640000e-04 56.5
18 TraesCS5B01G152900 chr4A 88.550 131 9 6 607 734 137187127 137187000 1.600000e-33 154.0
19 TraesCS5B01G152900 chr4A 87.395 119 14 1 1664 1781 11301207 11301325 5.790000e-28 135.0
20 TraesCS5B01G152900 chr3A 90.517 116 9 2 1664 1778 550706757 550706643 5.750000e-33 152.0
21 TraesCS5B01G152900 chr7B 85.417 144 16 5 601 740 86331647 86331505 9.630000e-31 145.0
22 TraesCS5B01G152900 chr7B 97.059 34 1 0 1634 1667 706468743 706468710 1.290000e-04 58.4
23 TraesCS5B01G152900 chr3B 93.407 91 6 0 1691 1781 446748011 446748101 5.790000e-28 135.0
24 TraesCS5B01G152900 chr2B 87.931 116 12 2 1665 1779 787527148 787527034 5.790000e-28 135.0
25 TraesCS5B01G152900 chr3D 88.785 107 12 0 1673 1779 593235075 593235181 7.490000e-27 132.0
26 TraesCS5B01G152900 chr2D 80.952 126 22 1 1651 1776 13242187 13242310 7.600000e-17 99.0
27 TraesCS5B01G152900 chr2D 100.000 30 0 0 1638 1667 630131588 630131559 4.640000e-04 56.5
28 TraesCS5B01G152900 chr7D 83.333 108 13 5 1638 1741 108518146 108518252 9.830000e-16 95.3
29 TraesCS5B01G152900 chr7D 96.970 33 1 0 1635 1667 513211551 513211583 4.640000e-04 56.5
30 TraesCS5B01G152900 chr7D 97.059 34 0 1 1635 1667 619358577 619358610 4.640000e-04 56.5
31 TraesCS5B01G152900 chr1A 100.000 30 0 0 1638 1667 571578907 571578936 4.640000e-04 56.5


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 TraesCS5B01G152900 chr5B 282044238 282047566 3328 False 6148.0 6148 100.00000 1 3329 1 chr5B.!!$F1 3328
1 TraesCS5B01G152900 chr5D 249256660 249259628 2968 False 4510.0 4510 94.33600 400 3329 1 chr5D.!!$F1 2929
2 TraesCS5B01G152900 chr5A 331940354 331944968 4614 False 1050.5 1803 93.55575 114 3329 4 chr5A.!!$F3 3215

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
189 190 0.034896 TTGGCTCGGGACAAAGAGTC 59.965 55.000 0.0 0.0 46.83 3.36 F
280 282 1.074699 GGGACCTCCTATTCCCCGT 60.075 63.158 0.0 0.0 45.40 5.28 F
816 840 1.760613 TGGCCCAGAGTATTTACCGAG 59.239 52.381 0.0 0.0 0.00 4.63 F
1390 1416 2.236146 ACAGTTACGCATCTCCCATTCA 59.764 45.455 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 3349 0.037734 TCGACTGAGACCTAGCCACA 59.962 55.000 0.00 0.0 0.00 4.17 R
1643 3351 0.328592 AGTCGACTGAGACCTAGCCA 59.671 55.000 19.30 0.0 41.83 4.75 R
1644 3352 0.736053 CAGTCGACTGAGACCTAGCC 59.264 60.000 36.73 0.0 46.59 3.93 R
2469 4219 1.977854 TCACAGTACAATGCCACCTCT 59.022 47.619 0.00 0.0 0.00 3.69 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
26 27 9.952030 ATTTTTAAACAGGGAAAAAGAAAGACA 57.048 25.926 0.00 0.00 37.79 3.41
27 28 9.952030 TTTTTAAACAGGGAAAAAGAAAGACAT 57.048 25.926 0.00 0.00 32.30 3.06
28 29 8.940768 TTTAAACAGGGAAAAAGAAAGACATG 57.059 30.769 0.00 0.00 0.00 3.21
29 30 6.790232 AAACAGGGAAAAAGAAAGACATGA 57.210 33.333 0.00 0.00 0.00 3.07
30 31 6.790232 AACAGGGAAAAAGAAAGACATGAA 57.210 33.333 0.00 0.00 0.00 2.57
31 32 6.396829 ACAGGGAAAAAGAAAGACATGAAG 57.603 37.500 0.00 0.00 0.00 3.02
32 33 6.129179 ACAGGGAAAAAGAAAGACATGAAGA 58.871 36.000 0.00 0.00 0.00 2.87
33 34 6.779539 ACAGGGAAAAAGAAAGACATGAAGAT 59.220 34.615 0.00 0.00 0.00 2.40
34 35 7.944554 ACAGGGAAAAAGAAAGACATGAAGATA 59.055 33.333 0.00 0.00 0.00 1.98
35 36 8.964772 CAGGGAAAAAGAAAGACATGAAGATAT 58.035 33.333 0.00 0.00 0.00 1.63
84 85 7.803487 AGGAAAAATCCTTTGAAGATTGGAT 57.197 32.000 0.00 0.00 40.65 3.41
85 86 8.899887 AGGAAAAATCCTTTGAAGATTGGATA 57.100 30.769 0.00 0.00 38.25 2.59
86 87 9.498039 AGGAAAAATCCTTTGAAGATTGGATAT 57.502 29.630 0.00 0.00 38.25 1.63
94 95 9.753674 TCCTTTGAAGATTGGATATAAAACTGT 57.246 29.630 0.00 0.00 0.00 3.55
97 98 7.786178 TGAAGATTGGATATAAAACTGTCCG 57.214 36.000 0.00 0.00 33.39 4.79
98 99 6.260050 TGAAGATTGGATATAAAACTGTCCGC 59.740 38.462 0.00 0.00 33.39 5.54
99 100 5.063880 AGATTGGATATAAAACTGTCCGCC 58.936 41.667 0.00 0.00 33.39 6.13
100 101 3.916359 TGGATATAAAACTGTCCGCCA 57.084 42.857 0.00 0.00 33.39 5.69
101 102 4.223556 TGGATATAAAACTGTCCGCCAA 57.776 40.909 0.00 0.00 33.39 4.52
102 103 4.590918 TGGATATAAAACTGTCCGCCAAA 58.409 39.130 0.00 0.00 33.39 3.28
103 104 5.010933 TGGATATAAAACTGTCCGCCAAAA 58.989 37.500 0.00 0.00 33.39 2.44
104 105 5.124776 TGGATATAAAACTGTCCGCCAAAAG 59.875 40.000 0.00 0.00 33.39 2.27
105 106 3.934457 ATAAAACTGTCCGCCAAAAGG 57.066 42.857 0.00 0.00 0.00 3.11
106 107 1.480789 AAAACTGTCCGCCAAAAGGT 58.519 45.000 0.00 0.00 0.00 3.50
107 108 1.480789 AAACTGTCCGCCAAAAGGTT 58.519 45.000 0.00 0.00 0.00 3.50
108 109 2.351706 AACTGTCCGCCAAAAGGTTA 57.648 45.000 0.00 0.00 0.00 2.85
109 110 2.351706 ACTGTCCGCCAAAAGGTTAA 57.648 45.000 0.00 0.00 0.00 2.01
110 111 2.657143 ACTGTCCGCCAAAAGGTTAAA 58.343 42.857 0.00 0.00 0.00 1.52
111 112 2.621526 ACTGTCCGCCAAAAGGTTAAAG 59.378 45.455 0.00 0.00 0.00 1.85
112 113 2.621526 CTGTCCGCCAAAAGGTTAAAGT 59.378 45.455 0.00 0.00 0.00 2.66
142 143 3.182173 GCACACAAAATGTCCAAACATCG 59.818 43.478 0.00 0.00 45.48 3.84
143 144 3.182173 CACACAAAATGTCCAAACATCGC 59.818 43.478 0.00 0.00 45.48 4.58
146 147 3.244976 CAAAATGTCCAAACATCGCCTC 58.755 45.455 0.00 0.00 45.48 4.70
149 150 0.669318 TGTCCAAACATCGCCTCGAC 60.669 55.000 0.00 0.00 39.18 4.20
164 165 1.067060 CTCGACGATGTGCCCATAGAA 59.933 52.381 0.00 0.00 0.00 2.10
167 168 2.285220 CGACGATGTGCCCATAGAAAAG 59.715 50.000 0.00 0.00 0.00 2.27
180 181 1.056660 AGAAAAGAGTTGGCTCGGGA 58.943 50.000 0.00 0.00 46.03 5.14
182 183 0.472471 AAAAGAGTTGGCTCGGGACA 59.528 50.000 0.00 0.00 46.03 4.02
184 185 0.472471 AAGAGTTGGCTCGGGACAAA 59.528 50.000 4.31 0.00 42.74 2.83
185 186 0.035458 AGAGTTGGCTCGGGACAAAG 59.965 55.000 4.31 0.00 42.74 2.77
187 188 0.035458 AGTTGGCTCGGGACAAAGAG 59.965 55.000 4.31 0.00 42.74 2.85
188 189 0.250338 GTTGGCTCGGGACAAAGAGT 60.250 55.000 4.31 0.00 42.74 3.24
189 190 0.034896 TTGGCTCGGGACAAAGAGTC 59.965 55.000 0.00 0.00 46.83 3.36
219 221 3.700538 TGAGGCTTTTTATGATGGTGCT 58.299 40.909 0.00 0.00 0.00 4.40
241 243 9.914131 GTGCTTCAAATAGTTAGGATTTTTCTT 57.086 29.630 0.00 0.00 0.00 2.52
280 282 1.074699 GGGACCTCCTATTCCCCGT 60.075 63.158 0.00 0.00 45.40 5.28
394 397 4.837093 AACAGCTATTGGTGGCTTAGTA 57.163 40.909 10.97 0.00 40.57 1.82
536 541 7.118101 GGTACAATGTATACTGAAAAACCGTCA 59.882 37.037 4.17 0.00 0.00 4.35
650 655 1.762419 TCGGATGTTTATAGACGCGC 58.238 50.000 5.73 0.00 0.00 6.86
688 693 9.990360 TGTTCACTCATTTTAGTCTGTATGTAA 57.010 29.630 0.00 0.00 0.00 2.41
732 737 6.531021 ACATCTTATAATTGGTACGGAAGGG 58.469 40.000 0.00 0.00 0.00 3.95
792 816 3.651803 AAAATGAAAACCGGCGAATGA 57.348 38.095 9.30 0.00 0.00 2.57
793 817 3.651803 AAATGAAAACCGGCGAATGAA 57.348 38.095 9.30 0.00 0.00 2.57
816 840 1.760613 TGGCCCAGAGTATTTACCGAG 59.239 52.381 0.00 0.00 0.00 4.63
853 879 4.730949 TTGCGTATAGGAGCAAGTAGTT 57.269 40.909 6.21 0.00 46.83 2.24
863 889 6.076981 AGGAGCAAGTAGTTCAATTTGTTG 57.923 37.500 0.00 0.00 0.00 3.33
1087 1113 3.016971 CAGCCACCCCATCCTCCA 61.017 66.667 0.00 0.00 0.00 3.86
1102 1128 2.507992 CCAGCACTCTCCGCTTCG 60.508 66.667 0.00 0.00 37.72 3.79
1214 1240 2.429930 CACCCAGACTTTGCCCGA 59.570 61.111 0.00 0.00 0.00 5.14
1372 1398 2.481449 GCCTCCGTCAAGGTATACACAG 60.481 54.545 5.01 0.00 41.99 3.66
1390 1416 2.236146 ACAGTTACGCATCTCCCATTCA 59.764 45.455 0.00 0.00 0.00 2.57
1633 3341 6.861572 CAGTTATCTCTCTACACGTTTTGACA 59.138 38.462 0.00 0.00 0.00 3.58
1634 3342 7.542477 CAGTTATCTCTCTACACGTTTTGACAT 59.458 37.037 0.00 0.00 0.00 3.06
1635 3343 8.088981 AGTTATCTCTCTACACGTTTTGACATT 58.911 33.333 0.00 0.00 0.00 2.71
1636 3344 6.712241 ATCTCTCTACACGTTTTGACATTG 57.288 37.500 0.00 0.00 0.00 2.82
1637 3345 5.838529 TCTCTCTACACGTTTTGACATTGA 58.161 37.500 0.00 0.00 0.00 2.57
1638 3346 5.920840 TCTCTCTACACGTTTTGACATTGAG 59.079 40.000 0.00 0.00 0.00 3.02
1639 3347 4.988540 TCTCTACACGTTTTGACATTGAGG 59.011 41.667 0.00 0.00 0.00 3.86
1640 3348 4.062293 TCTACACGTTTTGACATTGAGGG 58.938 43.478 0.00 0.00 0.00 4.30
1641 3349 2.650322 ACACGTTTTGACATTGAGGGT 58.350 42.857 0.00 0.00 0.00 4.34
1642 3350 2.357637 ACACGTTTTGACATTGAGGGTG 59.642 45.455 0.00 0.00 0.00 4.61
1643 3351 2.357637 CACGTTTTGACATTGAGGGTGT 59.642 45.455 0.00 0.00 0.00 4.16
1644 3352 2.357637 ACGTTTTGACATTGAGGGTGTG 59.642 45.455 0.00 0.00 0.00 3.82
1645 3353 2.287547 CGTTTTGACATTGAGGGTGTGG 60.288 50.000 0.00 0.00 0.00 4.17
1646 3354 1.327303 TTTGACATTGAGGGTGTGGC 58.673 50.000 0.00 0.00 0.00 5.01
1647 3355 0.478072 TTGACATTGAGGGTGTGGCT 59.522 50.000 0.00 0.00 0.00 4.75
1648 3356 1.357137 TGACATTGAGGGTGTGGCTA 58.643 50.000 0.00 0.00 0.00 3.93
1649 3357 1.278985 TGACATTGAGGGTGTGGCTAG 59.721 52.381 0.00 0.00 0.00 3.42
1650 3358 0.620556 ACATTGAGGGTGTGGCTAGG 59.379 55.000 0.00 0.00 0.00 3.02
1651 3359 0.620556 CATTGAGGGTGTGGCTAGGT 59.379 55.000 0.00 0.00 0.00 3.08
1652 3360 0.912486 ATTGAGGGTGTGGCTAGGTC 59.088 55.000 0.00 0.00 0.00 3.85
1653 3361 0.178903 TTGAGGGTGTGGCTAGGTCT 60.179 55.000 0.00 0.00 0.00 3.85
1744 3494 7.445707 ACAGATATAGCATCGACTGAGACTTTA 59.554 37.037 0.00 0.00 0.00 1.85
1810 3560 9.823647 CATACTACTTGAGGATTTGATAACACT 57.176 33.333 0.00 0.00 0.00 3.55
1929 3679 3.661648 AAGGCGCCACCAGGGAAT 61.662 61.111 31.54 0.00 43.14 3.01
2357 4107 7.514721 TCTCACCTTGGAGTTTAAGTAATGTT 58.485 34.615 0.00 0.00 36.30 2.71
2469 4219 8.616942 TCAGAAACACGTTGATTCAATTTAGAA 58.383 29.630 1.78 0.00 32.41 2.10
2474 4224 6.710744 ACACGTTGATTCAATTTAGAAGAGGT 59.289 34.615 1.78 0.00 0.00 3.85
2475 4225 7.017645 CACGTTGATTCAATTTAGAAGAGGTG 58.982 38.462 1.78 0.00 0.00 4.00
2602 4353 6.791867 AGCTACATGAGAAAGTATGTGGTA 57.208 37.500 0.00 0.00 37.86 3.25
2737 4488 1.200948 GATGTTTCCTGTTGCCTCAGC 59.799 52.381 0.48 0.00 40.48 4.26
2836 4587 2.093500 ACTGTGCTCAAGAGTGTTCACA 60.093 45.455 5.74 7.64 36.94 3.58
2887 4638 4.919774 TGAGGAGTCAAGAGAGTAGTCT 57.080 45.455 0.00 0.00 34.86 3.24
3260 5011 5.928264 GGTTCTCTATTGTTGCATTTTTGCT 59.072 36.000 0.00 0.00 35.49 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.952030 TGTCTTTCTTTTTCCCTGTTTAAAAAT 57.048 25.926 0.00 0.00 34.90 1.82
1 2 9.952030 ATGTCTTTCTTTTTCCCTGTTTAAAAA 57.048 25.926 0.00 0.00 34.39 1.94
2 3 9.377312 CATGTCTTTCTTTTTCCCTGTTTAAAA 57.623 29.630 0.00 0.00 0.00 1.52
3 4 8.754080 TCATGTCTTTCTTTTTCCCTGTTTAAA 58.246 29.630 0.00 0.00 0.00 1.52
4 5 8.299990 TCATGTCTTTCTTTTTCCCTGTTTAA 57.700 30.769 0.00 0.00 0.00 1.52
5 6 7.889873 TCATGTCTTTCTTTTTCCCTGTTTA 57.110 32.000 0.00 0.00 0.00 2.01
6 7 6.790232 TCATGTCTTTCTTTTTCCCTGTTT 57.210 33.333 0.00 0.00 0.00 2.83
7 8 6.607198 TCTTCATGTCTTTCTTTTTCCCTGTT 59.393 34.615 0.00 0.00 0.00 3.16
8 9 6.129179 TCTTCATGTCTTTCTTTTTCCCTGT 58.871 36.000 0.00 0.00 0.00 4.00
9 10 6.639632 TCTTCATGTCTTTCTTTTTCCCTG 57.360 37.500 0.00 0.00 0.00 4.45
60 61 7.803487 ATCCAATCTTCAAAGGATTTTTCCT 57.197 32.000 0.00 0.00 43.04 3.36
68 69 9.753674 ACAGTTTTATATCCAATCTTCAAAGGA 57.246 29.630 0.00 0.00 34.12 3.36
71 72 8.673711 CGGACAGTTTTATATCCAATCTTCAAA 58.326 33.333 0.00 0.00 0.00 2.69
72 73 7.201696 GCGGACAGTTTTATATCCAATCTTCAA 60.202 37.037 0.00 0.00 0.00 2.69
73 74 6.260050 GCGGACAGTTTTATATCCAATCTTCA 59.740 38.462 0.00 0.00 0.00 3.02
74 75 6.293462 GGCGGACAGTTTTATATCCAATCTTC 60.293 42.308 0.00 0.00 0.00 2.87
75 76 5.531287 GGCGGACAGTTTTATATCCAATCTT 59.469 40.000 0.00 0.00 0.00 2.40
76 77 5.063880 GGCGGACAGTTTTATATCCAATCT 58.936 41.667 0.00 0.00 0.00 2.40
77 78 4.819630 TGGCGGACAGTTTTATATCCAATC 59.180 41.667 0.00 0.00 0.00 2.67
78 79 4.787551 TGGCGGACAGTTTTATATCCAAT 58.212 39.130 0.00 0.00 0.00 3.16
79 80 4.223556 TGGCGGACAGTTTTATATCCAA 57.776 40.909 0.00 0.00 0.00 3.53
80 81 3.916359 TGGCGGACAGTTTTATATCCA 57.084 42.857 0.00 0.00 0.00 3.41
81 82 5.449999 CCTTTTGGCGGACAGTTTTATATCC 60.450 44.000 0.00 0.00 0.00 2.59
82 83 5.124936 ACCTTTTGGCGGACAGTTTTATATC 59.875 40.000 0.00 0.00 45.59 1.63
83 84 5.014202 ACCTTTTGGCGGACAGTTTTATAT 58.986 37.500 0.00 0.00 45.59 0.86
84 85 4.400120 ACCTTTTGGCGGACAGTTTTATA 58.600 39.130 0.00 0.00 45.59 0.98
85 86 3.227614 ACCTTTTGGCGGACAGTTTTAT 58.772 40.909 0.00 0.00 45.59 1.40
86 87 2.657143 ACCTTTTGGCGGACAGTTTTA 58.343 42.857 0.00 0.00 45.59 1.52
87 88 1.480789 ACCTTTTGGCGGACAGTTTT 58.519 45.000 0.00 0.00 45.59 2.43
88 89 1.480789 AACCTTTTGGCGGACAGTTT 58.519 45.000 0.00 0.00 45.59 2.66
89 90 2.351706 TAACCTTTTGGCGGACAGTT 57.648 45.000 0.00 0.00 45.59 3.16
90 91 2.351706 TTAACCTTTTGGCGGACAGT 57.648 45.000 0.00 0.00 45.59 3.55
91 92 2.621526 ACTTTAACCTTTTGGCGGACAG 59.378 45.455 0.00 0.00 45.59 3.51
92 93 2.657143 ACTTTAACCTTTTGGCGGACA 58.343 42.857 0.00 0.00 45.59 4.02
93 94 4.834357 TTACTTTAACCTTTTGGCGGAC 57.166 40.909 0.00 0.00 45.59 4.79
94 95 5.848833 TTTTACTTTAACCTTTTGGCGGA 57.151 34.783 0.00 0.00 45.59 5.54
126 127 2.095263 CGAGGCGATGTTTGGACATTTT 60.095 45.455 0.00 0.00 46.27 1.82
134 135 4.162640 TCGTCGAGGCGATGTTTG 57.837 55.556 8.64 0.00 42.61 2.93
142 143 2.363711 TATGGGCACATCGTCGAGGC 62.364 60.000 3.67 7.26 38.53 4.70
143 144 0.319040 CTATGGGCACATCGTCGAGG 60.319 60.000 3.67 5.17 38.53 4.63
146 147 1.934589 TTTCTATGGGCACATCGTCG 58.065 50.000 3.67 0.00 38.53 5.12
149 150 3.535561 ACTCTTTTCTATGGGCACATCG 58.464 45.455 3.67 0.00 38.53 3.84
164 165 0.472471 TTGTCCCGAGCCAACTCTTT 59.528 50.000 0.00 0.00 41.09 2.52
167 168 0.034896 TCTTTGTCCCGAGCCAACTC 59.965 55.000 0.00 0.00 39.75 3.01
180 181 4.911390 CCTCAAATAGGTGGACTCTTTGT 58.089 43.478 0.00 0.00 41.47 2.83
219 221 8.964420 CGCAAGAAAAATCCTAACTATTTGAA 57.036 30.769 0.00 0.00 43.02 2.69
241 243 4.191544 CCAATCCTGACTATTTTCTCGCA 58.808 43.478 0.00 0.00 0.00 5.10
255 257 2.373502 GGAATAGGAGGTCCCAATCCTG 59.626 54.545 8.18 0.00 45.65 3.86
280 282 1.372997 GACAGCTCGGCGTTGAAGA 60.373 57.895 6.85 0.00 0.00 2.87
310 312 1.000506 GGGTGTAGAGTGAGCGTTGAA 59.999 52.381 0.00 0.00 0.00 2.69
311 313 0.601558 GGGTGTAGAGTGAGCGTTGA 59.398 55.000 0.00 0.00 0.00 3.18
352 355 2.010145 TTTAGATGAGTGAGCGCCAC 57.990 50.000 17.87 17.87 46.03 5.01
374 377 4.837093 TTACTAAGCCACCAATAGCTGT 57.163 40.909 0.00 0.00 39.87 4.40
510 513 7.118101 TGACGGTTTTTCAGTATACATTGTACC 59.882 37.037 5.50 4.63 0.00 3.34
536 541 6.935167 ACACAACACTTCTTGAAGGAAAAAT 58.065 32.000 13.97 0.00 0.00 1.82
646 651 2.034076 GAACAAACACACTAAAGCGCG 58.966 47.619 0.00 0.00 0.00 6.86
650 655 8.687824 AAAATGAGTGAACAAACACACTAAAG 57.312 30.769 0.00 0.00 45.54 1.85
771 777 3.983741 TCATTCGCCGGTTTTCATTTTT 58.016 36.364 1.90 0.00 0.00 1.94
776 782 0.239879 GCTTCATTCGCCGGTTTTCA 59.760 50.000 1.90 0.00 0.00 2.69
777 783 0.521735 AGCTTCATTCGCCGGTTTTC 59.478 50.000 1.90 0.00 0.00 2.29
787 811 0.034670 ACTCTGGGCCAGCTTCATTC 60.035 55.000 29.02 0.00 0.00 2.67
792 816 2.092375 GGTAAATACTCTGGGCCAGCTT 60.092 50.000 29.02 19.08 0.00 3.74
793 817 1.490910 GGTAAATACTCTGGGCCAGCT 59.509 52.381 29.02 17.70 0.00 4.24
853 879 5.096443 AGCCCAACTTTTCAACAAATTGA 57.904 34.783 0.00 0.00 43.28 2.57
882 908 2.202837 GCCGACGGCCTAATCGTT 60.203 61.111 28.74 0.00 44.06 3.85
906 932 0.614697 TCTCGAACTGGGCTGGATGA 60.615 55.000 0.00 0.00 0.00 2.92
1372 1398 2.906354 ACTGAATGGGAGATGCGTAAC 58.094 47.619 0.00 0.00 0.00 2.50
1390 1416 9.125026 GTTCCATGATGTAAATGAAATCCTACT 57.875 33.333 0.00 0.00 0.00 2.57
1508 1571 1.747206 GCAAGACCGTGGGATAGCAAT 60.747 52.381 0.00 0.00 0.00 3.56
1633 3341 0.912486 GACCTAGCCACACCCTCAAT 59.088 55.000 0.00 0.00 0.00 2.57
1634 3342 0.178903 AGACCTAGCCACACCCTCAA 60.179 55.000 0.00 0.00 0.00 3.02
1635 3343 0.614979 GAGACCTAGCCACACCCTCA 60.615 60.000 0.00 0.00 0.00 3.86
1636 3344 0.614979 TGAGACCTAGCCACACCCTC 60.615 60.000 0.00 0.00 0.00 4.30
1637 3345 0.616111 CTGAGACCTAGCCACACCCT 60.616 60.000 0.00 0.00 0.00 4.34
1638 3346 0.905337 ACTGAGACCTAGCCACACCC 60.905 60.000 0.00 0.00 0.00 4.61
1639 3347 0.533032 GACTGAGACCTAGCCACACC 59.467 60.000 0.00 0.00 0.00 4.16
1640 3348 0.171455 CGACTGAGACCTAGCCACAC 59.829 60.000 0.00 0.00 0.00 3.82
1641 3349 0.037734 TCGACTGAGACCTAGCCACA 59.962 55.000 0.00 0.00 0.00 4.17
1642 3350 0.452585 GTCGACTGAGACCTAGCCAC 59.547 60.000 8.70 0.00 35.22 5.01
1643 3351 0.328592 AGTCGACTGAGACCTAGCCA 59.671 55.000 19.30 0.00 41.83 4.75
1644 3352 0.736053 CAGTCGACTGAGACCTAGCC 59.264 60.000 36.73 0.00 46.59 3.93
1744 3494 9.360093 CTAAGTCTCAGTCGATTGAAACTTAAT 57.640 33.333 26.87 12.88 39.09 1.40
1755 3505 4.013728 AGTCTTGCTAAGTCTCAGTCGAT 58.986 43.478 0.00 0.00 0.00 3.59
1805 3555 6.952773 TTGCAACCTGTAGAAATAAGTGTT 57.047 33.333 0.00 0.00 0.00 3.32
1810 3560 7.335924 GTCTGGTATTGCAACCTGTAGAAATAA 59.664 37.037 0.00 0.00 40.44 1.40
1929 3679 2.517402 GTGTGGTTCCCGGCAACA 60.517 61.111 11.12 0.00 0.00 3.33
2357 4107 7.010923 GTCACATTTTGCACCTGATAAAACAAA 59.989 33.333 0.00 0.00 0.00 2.83
2469 4219 1.977854 TCACAGTACAATGCCACCTCT 59.022 47.619 0.00 0.00 0.00 3.69
2474 4224 3.243367 GCAAGTTTCACAGTACAATGCCA 60.243 43.478 0.00 0.00 0.00 4.92
2475 4225 3.004734 AGCAAGTTTCACAGTACAATGCC 59.995 43.478 0.00 0.00 32.89 4.40
2602 4353 3.438087 CCAGCGATTTTCTCACTTCATGT 59.562 43.478 0.00 0.00 0.00 3.21
2697 4448 6.336566 ACATCTCAGTTATCAGCTAGTTGTG 58.663 40.000 6.47 0.00 0.00 3.33
2836 4587 5.181245 CAGATCCAAACACTTCGGTAACATT 59.819 40.000 0.00 0.00 0.00 2.71
2887 4638 8.868522 ATCAATCTGTTCCAGAAATCTACAAA 57.131 30.769 0.00 0.00 44.04 2.83
3097 4848 3.244561 TGCCTCCAGTAGAAACTTTCCTG 60.245 47.826 0.00 0.35 31.97 3.86
3245 4996 7.462731 CAGAAAGTAAAGCAAAAATGCAACAA 58.537 30.769 3.41 0.00 37.25 2.83
3260 5011 8.999431 CACTCTTTAGTAATGGCAGAAAGTAAA 58.001 33.333 0.00 0.35 33.48 2.01


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

AutoCloner maintained by Alex Coulton.