Multiple sequence alignment - TraesCS3A01G213300

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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 TraesCS3A01G213300 chr3A 100.000 2874 0 0 1 2874 384733280 384730407 0.000000e+00 5308.0
1 TraesCS3A01G213300 chr3D 91.402 2082 120 18 2 2069 291977139 291975103 0.000000e+00 2798.0
2 TraesCS3A01G213300 chr3D 85.697 825 81 18 2061 2873 291974913 291974114 0.000000e+00 835.0
3 TraesCS3A01G213300 chr3B 90.545 1375 84 23 423 1781 385190412 385189068 0.000000e+00 1777.0
4 TraesCS3A01G213300 chr3B 87.571 708 72 14 2174 2870 385185825 385185123 0.000000e+00 806.0
5 TraesCS3A01G213300 chr3B 93.909 394 20 4 2 393 385190881 385190490 2.470000e-165 592.0
6 TraesCS3A01G213300 chr3B 90.402 323 22 3 1775 2097 385186792 385186479 1.590000e-112 416.0
7 TraesCS3A01G213300 chr5A 77.800 509 87 20 2136 2630 333444265 333443769 1.010000e-74 291.0
8 TraesCS3A01G213300 chr7A 81.633 245 38 7 2389 2630 563342891 563343131 2.260000e-46 196.0
9 TraesCS3A01G213300 chr6D 82.231 242 29 7 939 1170 13154327 13154564 2.260000e-46 196.0
10 TraesCS3A01G213300 chr6D 78.846 208 35 6 193 398 13153160 13153360 6.460000e-27 132.0
11 TraesCS3A01G213300 chr6B 85.621 153 16 3 1024 1170 23605917 23605765 3.830000e-34 156.0
12 TraesCS3A01G213300 chr6B 89.091 110 12 0 1193 1302 23605583 23605474 1.390000e-28 137.0
13 TraesCS3A01G213300 chr6A 84.677 124 11 4 1775 1892 14386530 14386651 1.810000e-22 117.0
14 TraesCS3A01G213300 chr6A 90.164 61 4 2 2570 2629 310195395 310195336 8.540000e-11 78.7
15 TraesCS3A01G213300 chr6A 90.164 61 4 2 2570 2629 356201005 356200946 8.540000e-11 78.7
16 TraesCS3A01G213300 chrUn 90.164 61 4 2 2570 2629 329534977 329534918 8.540000e-11 78.7
17 TraesCS3A01G213300 chr7B 90.164 61 4 2 2570 2629 68187063 68187122 8.540000e-11 78.7
18 TraesCS3A01G213300 chr7B 90.164 61 4 2 2570 2629 516317021 516316962 8.540000e-11 78.7
19 TraesCS3A01G213300 chr7B 90.164 61 4 2 2570 2629 566747504 566747563 8.540000e-11 78.7


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 TraesCS3A01G213300 chr3A 384730407 384733280 2873 True 5308.00 5308 100.00000 1 2874 1 chr3A.!!$R1 2873
1 TraesCS3A01G213300 chr3D 291974114 291977139 3025 True 1816.50 2798 88.54950 2 2873 2 chr3D.!!$R1 2871
2 TraesCS3A01G213300 chr3B 385185123 385190881 5758 True 897.75 1777 90.60675 2 2870 4 chr3B.!!$R1 2868

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
644 726 0.238289 CAACAACGTCCATGCACTCC 59.762 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 5376 0.321122 AGTTTGCCTGAGCCTTCGAG 60.321 55.0 0.0 0.0 38.69 4.04 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
198 200 0.744414 CTTCGGATTGGTCGCATGGT 60.744 55.000 0.00 0.00 0.00 3.55
244 246 7.480222 TCCCCCTATGAAAGAATTAAGGATT 57.520 36.000 0.00 0.00 0.00 3.01
245 247 7.526918 TCCCCCTATGAAAGAATTAAGGATTC 58.473 38.462 0.00 0.00 43.71 2.52
258 260 5.579384 TTAAGGATTCAAACACGTACACG 57.421 39.130 0.00 0.00 46.33 4.49
298 300 4.588899 TCTTGGAGAACAATGGTACCATG 58.411 43.478 28.00 21.84 38.65 3.66
437 443 0.734889 CATCAAGAATGTGCCCCGAC 59.265 55.000 0.00 0.00 0.00 4.79
439 445 2.046314 AAGAATGTGCCCCGACCG 60.046 61.111 0.00 0.00 0.00 4.79
502 580 6.055231 TGAAACCTTGAAACGTCTAACATG 57.945 37.500 0.00 0.00 0.00 3.21
504 582 5.418310 AACCTTGAAACGTCTAACATGTG 57.582 39.130 0.00 0.00 0.00 3.21
508 586 5.924254 CCTTGAAACGTCTAACATGTGTCTA 59.076 40.000 0.00 0.00 30.14 2.59
536 614 6.575162 ACGAATATTTTCTTGGAAGCTTGT 57.425 33.333 2.10 0.00 0.00 3.16
590 672 3.572604 AGAAACCTTAGAACGTCCGAG 57.427 47.619 0.00 0.00 0.00 4.63
620 702 1.388065 TTTGCGGTGTGGAAACAGGG 61.388 55.000 0.00 0.00 44.46 4.45
621 703 3.670377 GCGGTGTGGAAACAGGGC 61.670 66.667 0.00 0.00 44.46 5.19
622 704 3.353836 CGGTGTGGAAACAGGGCG 61.354 66.667 0.00 0.00 44.46 6.13
623 705 3.670377 GGTGTGGAAACAGGGCGC 61.670 66.667 0.00 0.00 44.46 6.53
624 706 4.025401 GTGTGGAAACAGGGCGCG 62.025 66.667 0.00 0.00 44.46 6.86
628 710 4.700365 GGAAACAGGGCGCGCAAC 62.700 66.667 34.42 24.63 0.00 4.17
644 726 0.238289 CAACAACGTCCATGCACTCC 59.762 55.000 0.00 0.00 0.00 3.85
663 745 1.681780 CCATACACCTTCCCGCAACAT 60.682 52.381 0.00 0.00 0.00 2.71
726 812 4.082571 GCTTGTTGATGTGTCCAGCTTAAT 60.083 41.667 0.00 0.00 0.00 1.40
731 817 4.264253 TGATGTGTCCAGCTTAATCTTGG 58.736 43.478 0.00 0.00 0.00 3.61
853 939 1.528076 TGTTGCATGTTCAGGCCGT 60.528 52.632 6.97 0.00 0.00 5.68
854 940 1.210155 GTTGCATGTTCAGGCCGTC 59.790 57.895 6.97 0.00 0.00 4.79
856 942 3.499737 GCATGTTCAGGCCGTCCG 61.500 66.667 0.00 0.00 37.47 4.79
869 955 2.030401 CGTCCGCCAACCGATTCAA 61.030 57.895 0.00 0.00 40.02 2.69
928 1014 2.126228 GACGTGACCGGCGAATCA 60.126 61.111 9.30 9.33 38.78 2.57
977 1066 4.284550 GAAGGCAGCCACACCCCA 62.285 66.667 15.80 0.00 0.00 4.96
1012 1101 1.079819 CGCACCTCACACACTAGGG 60.080 63.158 0.00 0.00 37.18 3.53
1013 1102 1.532604 CGCACCTCACACACTAGGGA 61.533 60.000 0.00 0.00 37.18 4.20
1014 1103 0.685097 GCACCTCACACACTAGGGAA 59.315 55.000 0.00 0.00 37.18 3.97
1111 1200 4.695791 GGACCCCCAACCTCCCCT 62.696 72.222 0.00 0.00 0.00 4.79
1113 1202 1.999568 GACCCCCAACCTCCCCTAC 61.000 68.421 0.00 0.00 0.00 3.18
1229 1318 3.552875 CAAGAAGTCATGCATCCTGGAT 58.447 45.455 2.57 2.57 0.00 3.41
1311 1400 4.584518 CACCAGGTGCCTGTGCCA 62.585 66.667 16.15 0.00 42.15 4.92
1321 1412 2.666190 CTGTGCCACACCGTCCAG 60.666 66.667 0.00 0.00 32.73 3.86
1323 1414 2.110213 GTGCCACACCGTCCAGAA 59.890 61.111 0.00 0.00 0.00 3.02
1325 1416 0.889186 GTGCCACACCGTCCAGAAAT 60.889 55.000 0.00 0.00 0.00 2.17
1332 1425 0.951558 ACCGTCCAGAAATGCAACAC 59.048 50.000 0.00 0.00 0.00 3.32
1348 1441 3.626977 CAACACGCATTTTACTTGCTCA 58.373 40.909 0.00 0.00 37.96 4.26
1366 1464 3.489785 GCTCATACGTACATAACCAGCAC 59.510 47.826 0.00 0.00 0.00 4.40
1415 1513 2.098117 GTGGATTGCTACAAGGCATGTC 59.902 50.000 0.00 0.00 42.70 3.06
1426 1524 0.038166 AGGCATGTCGGACCAAATGT 59.962 50.000 5.55 0.00 0.00 2.71
1467 1574 1.458588 GGCCAAACCCAGGTCCAAA 60.459 57.895 0.00 0.00 0.00 3.28
1468 1575 1.471829 GGCCAAACCCAGGTCCAAAG 61.472 60.000 0.00 0.00 0.00 2.77
1469 1576 2.049435 CCAAACCCAGGTCCAAAGC 58.951 57.895 0.00 0.00 0.00 3.51
1470 1577 1.471829 CCAAACCCAGGTCCAAAGCC 61.472 60.000 0.00 0.00 0.00 4.35
1471 1578 0.758685 CAAACCCAGGTCCAAAGCCA 60.759 55.000 0.00 0.00 0.00 4.75
1472 1579 0.759060 AAACCCAGGTCCAAAGCCAC 60.759 55.000 0.00 0.00 0.00 5.01
1473 1580 2.283173 CCCAGGTCCAAAGCCACC 60.283 66.667 0.00 0.00 0.00 4.61
1474 1581 2.520458 CCAGGTCCAAAGCCACCA 59.480 61.111 0.00 0.00 34.80 4.17
1475 1582 1.152567 CCAGGTCCAAAGCCACCAA 60.153 57.895 0.00 0.00 34.80 3.67
1476 1583 0.542702 CCAGGTCCAAAGCCACCAAT 60.543 55.000 0.00 0.00 34.80 3.16
1573 1680 2.917227 AAGCCAACCCCGCCAAAG 60.917 61.111 0.00 0.00 0.00 2.77
1637 1744 0.380733 CACTAGCTGTATCCGCGTCA 59.619 55.000 4.92 0.00 0.00 4.35
1654 1761 0.740149 TCAAGCAACACCAGCAACAG 59.260 50.000 0.00 0.00 0.00 3.16
1669 1776 3.799753 CAGCTGATGGGTGTACGC 58.200 61.111 8.42 0.00 38.49 4.42
1700 1807 6.530181 CGTCTATGCACACATACTTTCAAGTA 59.470 38.462 1.89 1.89 44.84 2.24
1701 1808 7.462856 CGTCTATGCACACATACTTTCAAGTAC 60.463 40.741 1.42 0.00 43.67 2.73
1703 1810 6.875948 ATGCACACATACTTTCAAGTACAA 57.124 33.333 1.42 0.00 43.67 2.41
1704 1811 6.055231 TGCACACATACTTTCAAGTACAAC 57.945 37.500 1.42 0.00 43.67 3.32
1705 1812 5.820423 TGCACACATACTTTCAAGTACAACT 59.180 36.000 1.42 0.00 43.67 3.16
1706 1813 6.018262 TGCACACATACTTTCAAGTACAACTC 60.018 38.462 1.42 0.00 43.67 3.01
1707 1814 6.018262 GCACACATACTTTCAAGTACAACTCA 60.018 38.462 1.42 0.00 43.67 3.41
1731 1838 7.807907 TCACGATATATACAGCACAACAGTATG 59.192 37.037 0.00 0.00 46.00 2.39
1734 1841 7.008719 CGATATATACAGCACAACAGTATGAGC 59.991 40.741 0.00 0.00 39.69 4.26
1746 1853 0.313672 GTATGAGCAGAGCCCTCGAG 59.686 60.000 5.13 5.13 31.98 4.04
1748 1855 1.108727 ATGAGCAGAGCCCTCGAGAG 61.109 60.000 15.71 0.16 31.98 3.20
1781 1888 9.144747 CAGTATATGTAGAGGTGTTATGATTGC 57.855 37.037 0.00 0.00 0.00 3.56
1783 1890 9.360093 GTATATGTAGAGGTGTTATGATTGCTC 57.640 37.037 0.00 0.00 0.00 4.26
1784 1891 5.939764 TGTAGAGGTGTTATGATTGCTCT 57.060 39.130 0.00 0.00 0.00 4.09
1916 4305 4.103153 AGAAGTTGATTCCTTGTGTGAGGA 59.897 41.667 0.00 0.00 43.99 3.71
1931 4320 1.209128 GAGGATGCGGATGTAACACG 58.791 55.000 0.00 0.00 0.00 4.49
1977 4366 2.622942 GCCTCACCAAAACAATGTCTGA 59.377 45.455 0.00 0.00 0.00 3.27
1978 4367 3.304928 GCCTCACCAAAACAATGTCTGAG 60.305 47.826 0.00 0.00 0.00 3.35
1987 4376 3.040147 ACAATGTCTGAGTAACCCACG 57.960 47.619 0.00 0.00 0.00 4.94
1995 4384 5.362717 TGTCTGAGTAACCCACGATTATGAT 59.637 40.000 0.00 0.00 0.00 2.45
2047 4436 7.032580 TGTAATAATTATTGCCTTGCACACAC 58.967 34.615 18.98 6.66 38.71 3.82
2104 5268 9.250624 CTAGTTCTAGATTAGGGAAATGTTTCG 57.749 37.037 0.00 0.00 38.06 3.46
2105 5269 7.621796 AGTTCTAGATTAGGGAAATGTTTCGT 58.378 34.615 0.00 0.00 38.06 3.85
2143 5317 0.734253 GCTTCACGTCGCTCTCACAT 60.734 55.000 0.00 0.00 0.00 3.21
2163 5337 2.323213 CACAGTGTGCACATCAGCA 58.677 52.632 24.69 0.00 43.35 4.41
2171 5345 2.181954 TGCACATCAGCACATACACA 57.818 45.000 0.00 0.00 40.11 3.72
2172 5346 2.713877 TGCACATCAGCACATACACAT 58.286 42.857 0.00 0.00 40.11 3.21
2195 5369 2.838225 ACACGGGCCTAGCGCTAT 60.838 61.111 19.19 0.00 39.38 2.97
2196 5370 2.356313 CACGGGCCTAGCGCTATG 60.356 66.667 19.19 16.65 39.38 2.23
2197 5371 2.520982 ACGGGCCTAGCGCTATGA 60.521 61.111 21.97 0.57 39.38 2.15
2198 5372 1.908793 ACGGGCCTAGCGCTATGAT 60.909 57.895 21.97 0.00 39.38 2.45
2199 5373 1.446792 CGGGCCTAGCGCTATGATG 60.447 63.158 21.97 8.99 39.38 3.07
2200 5374 1.078848 GGGCCTAGCGCTATGATGG 60.079 63.158 21.97 18.09 38.48 3.51
2201 5375 1.743252 GGCCTAGCGCTATGATGGC 60.743 63.158 28.37 28.37 39.61 4.40
2202 5376 1.743252 GCCTAGCGCTATGATGGCC 60.743 63.158 26.85 13.85 34.81 5.36
2203 5377 1.978473 CCTAGCGCTATGATGGCCT 59.022 57.895 19.19 0.00 0.00 5.19
2257 5440 1.407656 ATACGCGATGGTCCCCATGT 61.408 55.000 15.93 0.00 45.26 3.21
2279 5462 0.701147 CAGCCCTCCTTTTTCCTCCT 59.299 55.000 0.00 0.00 0.00 3.69
2323 5509 4.461781 TCTCTTACCTTTCTTGTACCTCCG 59.538 45.833 0.00 0.00 0.00 4.63
2324 5510 4.410099 TCTTACCTTTCTTGTACCTCCGA 58.590 43.478 0.00 0.00 0.00 4.55
2335 5521 1.259142 TACCTCCGACCCGCATCAAA 61.259 55.000 0.00 0.00 0.00 2.69
2336 5522 2.106683 CCTCCGACCCGCATCAAAC 61.107 63.158 0.00 0.00 0.00 2.93
2378 5564 1.473258 TGCATCCGGCTAAGCAAAAT 58.527 45.000 0.00 0.00 45.15 1.82
2381 5567 2.796032 GCATCCGGCTAAGCAAAATGTC 60.796 50.000 0.00 0.00 40.25 3.06
2385 5571 1.202177 CGGCTAAGCAAAATGTCGCAT 60.202 47.619 0.00 0.00 0.00 4.73
2386 5572 2.731968 CGGCTAAGCAAAATGTCGCATT 60.732 45.455 0.00 0.09 0.00 3.56
2387 5573 2.854185 GGCTAAGCAAAATGTCGCATTC 59.146 45.455 5.70 0.00 0.00 2.67
2431 5622 1.064685 AGAAAATAGGAGGGGGCAACG 60.065 52.381 0.00 0.00 37.60 4.10
2476 5667 1.269726 GGGTGTTGCAACCATTGACAG 60.270 52.381 26.14 0.00 41.64 3.51
2512 5704 4.095036 CCTAGATCGAAAAAGCTTCAACCC 59.905 45.833 0.00 0.00 0.00 4.11
2518 5710 3.066760 CGAAAAAGCTTCAACCCTCAACT 59.933 43.478 0.00 0.00 0.00 3.16
2519 5711 4.440112 CGAAAAAGCTTCAACCCTCAACTT 60.440 41.667 0.00 0.00 0.00 2.66
2540 5732 1.527433 GGAAGCTTCAACCAGCCACC 61.527 60.000 27.02 3.24 41.12 4.61
2554 5746 1.676006 AGCCACCGTCAAACTGAAAAG 59.324 47.619 0.00 0.00 0.00 2.27
2605 5797 4.342352 CATAGGTGGAAAAAGCTTCGAC 57.658 45.455 0.00 0.00 0.00 4.20
2639 5832 1.322538 GCTTCAACCGCATGGGGAAT 61.323 55.000 33.50 19.09 41.60 3.01
2660 5853 3.096092 TGCTTCAACCTGTGGAAAAAGT 58.904 40.909 0.00 0.00 0.00 2.66
2668 5861 4.093743 ACCTGTGGAAAAAGTTTCAACCT 58.906 39.130 5.92 0.00 0.00 3.50
2687 5882 4.886579 ACCTGCATGGAAAAATCTTCAAC 58.113 39.130 8.91 0.00 39.71 3.18
2689 5884 4.262549 CCTGCATGGAAAAATCTTCAACCA 60.263 41.667 0.00 0.00 38.35 3.67
2690 5885 4.630111 TGCATGGAAAAATCTTCAACCAC 58.370 39.130 0.00 0.00 0.00 4.16
2713 5908 3.064820 GTGAGAAAAAGCTTCAACCGACA 59.935 43.478 0.00 0.00 0.00 4.35
2715 5910 2.031683 AGAAAAAGCTTCAACCGACACG 59.968 45.455 0.00 0.00 0.00 4.49
2717 5912 2.101209 AAAGCTTCAACCGACACGCG 62.101 55.000 3.53 3.53 40.47 6.01
2748 5943 4.427661 GCGACGTGGAGAGCTGCT 62.428 66.667 0.00 0.00 0.00 4.24
2754 5949 2.926779 TGGAGAGCTGCTGCCAGT 60.927 61.111 7.01 0.00 41.26 4.00
2769 5964 1.520192 CAGTGGCATGGCGGTACTA 59.480 57.895 15.27 0.00 0.00 1.82
2777 5973 0.394762 ATGGCGGTACTACGAGGACA 60.395 55.000 0.00 0.00 35.47 4.02
2789 5985 2.042464 ACGAGGACATGCTATGATGGT 58.958 47.619 0.00 0.00 0.00 3.55
2818 6014 1.823470 TGCTGCAACGACAAAGGCT 60.823 52.632 0.00 0.00 0.00 4.58
2822 6018 0.812014 TGCAACGACAAAGGCTTCGA 60.812 50.000 13.54 0.00 38.63 3.71
2840 6036 1.762419 GACGTGCTACAAGACGACAA 58.238 50.000 0.00 0.00 38.94 3.18
2866 6062 0.387750 GTTACGAGGGCGACGACTTT 60.388 55.000 0.00 0.00 41.64 2.66
2870 6066 1.219522 CGAGGGCGACGACTTTTTGT 61.220 55.000 0.00 0.00 40.82 2.83
2873 6069 0.379316 GGGCGACGACTTTTTGTTGT 59.621 50.000 0.00 0.00 45.46 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.900635 AAATGTATTCTCATTCGGGCAC 57.099 40.909 0.00 0.00 37.09 5.01
72 74 7.680730 AGACCATATGTAATAAGGACATGGAC 58.319 38.462 1.24 0.00 40.01 4.02
228 230 7.936584 ACGTGTTTGAATCCTTAATTCTTTCA 58.063 30.769 0.00 0.00 43.61 2.69
290 292 5.835113 AAATGTGAAGCATACATGGTACC 57.165 39.130 4.43 4.43 38.67 3.34
396 402 3.181504 GGTTACCCATGTTCACGCATAAC 60.182 47.826 0.00 0.00 0.00 1.89
437 443 1.838077 ACTACAAGAAATCCTCCCCGG 59.162 52.381 0.00 0.00 0.00 5.73
439 445 5.952347 TCTTACTACAAGAAATCCTCCCC 57.048 43.478 0.00 0.00 0.00 4.81
445 451 7.806690 TGTGCACATTCTTACTACAAGAAATC 58.193 34.615 17.42 0.00 39.43 2.17
479 557 5.587043 ACATGTTAGACGTTTCAAGGTTTCA 59.413 36.000 0.00 0.00 0.00 2.69
529 607 6.980397 CCAAGTTGAAACAGAATAACAAGCTT 59.020 34.615 3.87 0.00 0.00 3.74
536 614 5.860941 TTGCCCAAGTTGAAACAGAATAA 57.139 34.783 3.87 0.00 0.00 1.40
543 625 4.211164 GTGCTTATTTGCCCAAGTTGAAAC 59.789 41.667 3.87 0.00 0.00 2.78
590 672 2.009774 ACACCGCAAATGAGACATAGC 58.990 47.619 0.00 0.00 0.00 2.97
620 702 4.383602 ATGGACGTTGTTGCGCGC 62.384 61.111 27.26 27.26 34.88 6.86
621 703 2.499520 CATGGACGTTGTTGCGCG 60.500 61.111 0.00 0.00 34.88 6.86
622 704 2.800746 GCATGGACGTTGTTGCGC 60.801 61.111 0.00 0.00 34.88 6.09
623 705 1.725625 GTGCATGGACGTTGTTGCG 60.726 57.895 0.10 0.00 37.92 4.85
624 706 0.385974 GAGTGCATGGACGTTGTTGC 60.386 55.000 12.02 9.72 35.67 4.17
625 707 0.238289 GGAGTGCATGGACGTTGTTG 59.762 55.000 12.02 0.00 0.00 3.33
626 708 0.179032 TGGAGTGCATGGACGTTGTT 60.179 50.000 12.02 0.00 0.00 2.83
627 709 0.036732 ATGGAGTGCATGGACGTTGT 59.963 50.000 12.02 0.00 0.00 3.32
628 710 1.665679 GTATGGAGTGCATGGACGTTG 59.334 52.381 12.02 0.00 0.00 4.10
644 726 1.401552 CATGTTGCGGGAAGGTGTATG 59.598 52.381 0.00 0.00 0.00 2.39
663 745 1.032794 TGCCACAAATTAACCGTGCA 58.967 45.000 0.00 0.00 0.00 4.57
768 854 3.120385 CCAGCTTCGCATGCGTGA 61.120 61.111 36.50 25.22 40.74 4.35
789 875 1.027357 CCCTCATGCTTAATGCGCTT 58.973 50.000 9.73 0.00 46.63 4.68
828 914 2.352030 CCTGAACATGCAACACACATCC 60.352 50.000 0.00 0.00 0.00 3.51
829 915 2.923605 GCCTGAACATGCAACACACATC 60.924 50.000 0.00 0.00 0.00 3.06
830 916 1.000060 GCCTGAACATGCAACACACAT 60.000 47.619 0.00 0.00 0.00 3.21
831 917 0.385029 GCCTGAACATGCAACACACA 59.615 50.000 0.00 0.00 0.00 3.72
832 918 0.318955 GGCCTGAACATGCAACACAC 60.319 55.000 0.00 0.00 0.00 3.82
837 923 1.971167 GGACGGCCTGAACATGCAA 60.971 57.895 0.00 0.00 0.00 4.08
853 939 1.470890 GAAATTGAATCGGTTGGCGGA 59.529 47.619 0.00 0.00 0.00 5.54
854 940 1.793714 CGAAATTGAATCGGTTGGCGG 60.794 52.381 0.00 0.00 36.68 6.13
856 942 2.629639 ACGAAATTGAATCGGTTGGC 57.370 45.000 3.31 0.00 44.32 4.52
869 955 1.735571 GTGCACGGGACAATACGAAAT 59.264 47.619 0.00 0.00 0.00 2.17
915 1001 1.153353 GTTCTTTGATTCGCCGGTCA 58.847 50.000 1.90 0.00 0.00 4.02
928 1014 8.621073 AGAAAGGTGGTATAAATAGGGTTCTTT 58.379 33.333 0.00 0.00 0.00 2.52
976 1065 1.607509 GCGTGGAGATGGAGATGGATG 60.608 57.143 0.00 0.00 0.00 3.51
977 1066 0.683973 GCGTGGAGATGGAGATGGAT 59.316 55.000 0.00 0.00 0.00 3.41
1111 1200 1.706305 ACTGGGTTTCATTTCCGGGTA 59.294 47.619 0.00 0.00 0.00 3.69
1113 1202 0.887933 CACTGGGTTTCATTTCCGGG 59.112 55.000 0.00 0.00 0.00 5.73
1217 1306 3.220110 CTTGTAGCAATCCAGGATGCAT 58.780 45.455 19.91 0.00 31.97 3.96
1229 1318 1.234615 GCGGCAGTTCCTTGTAGCAA 61.235 55.000 0.00 0.00 0.00 3.91
1304 1393 2.658679 TTCTGGACGGTGTGGCACAG 62.659 60.000 22.75 13.14 41.80 3.66
1306 1395 0.889186 ATTTCTGGACGGTGTGGCAC 60.889 55.000 11.55 11.55 0.00 5.01
1309 1398 0.888736 TGCATTTCTGGACGGTGTGG 60.889 55.000 0.00 0.00 0.00 4.17
1310 1399 0.950836 TTGCATTTCTGGACGGTGTG 59.049 50.000 0.00 0.00 0.00 3.82
1311 1400 0.951558 GTTGCATTTCTGGACGGTGT 59.048 50.000 0.00 0.00 0.00 4.16
1335 1428 8.823818 GGTTATGTACGTATGAGCAAGTAAAAT 58.176 33.333 0.00 0.00 0.00 1.82
1348 1441 3.379372 AGTCGTGCTGGTTATGTACGTAT 59.621 43.478 0.00 0.00 42.45 3.06
1366 1464 4.927978 ATCTGTAATCAAGGGAGAGTCG 57.072 45.455 0.00 0.00 0.00 4.18
1415 1513 2.544903 GGTTGTGGAAACATTTGGTCCG 60.545 50.000 0.00 0.00 46.14 4.79
1426 1524 0.179023 GGTACGGGTGGTTGTGGAAA 60.179 55.000 0.00 0.00 0.00 3.13
1459 1557 1.187567 GCATTGGTGGCTTTGGACCT 61.188 55.000 0.00 0.00 32.98 3.85
1555 1662 3.225069 CTTTGGCGGGGTTGGCTTG 62.225 63.158 0.00 0.00 35.06 4.01
1578 1685 2.288186 GCTTTGTCTTCGGCCTATTAGC 59.712 50.000 0.00 0.00 0.00 3.09
1584 1691 2.185310 ATCGGCTTTGTCTTCGGCCT 62.185 55.000 0.00 0.00 42.13 5.19
1585 1692 1.745489 ATCGGCTTTGTCTTCGGCC 60.745 57.895 0.00 0.00 41.02 6.13
1589 1696 1.425428 CGGCATCGGCTTTGTCTTC 59.575 57.895 0.00 0.00 40.87 2.87
1637 1744 1.438814 GCTGTTGCTGGTGTTGCTT 59.561 52.632 0.00 0.00 36.03 3.91
1654 1761 2.165301 GTCGCGTACACCCATCAGC 61.165 63.158 5.77 0.00 0.00 4.26
1658 1765 2.180017 GTCGTCGCGTACACCCAT 59.820 61.111 5.77 0.00 0.00 4.00
1669 1776 0.453782 TGTGTGCATAGACGTCGTCG 60.454 55.000 19.11 7.03 37.67 5.12
1700 1807 6.144078 TGTGCTGTATATATCGTGAGTTGT 57.856 37.500 0.00 0.00 0.00 3.32
1701 1808 6.475402 TGTTGTGCTGTATATATCGTGAGTTG 59.525 38.462 0.00 0.00 0.00 3.16
1703 1810 6.144078 TGTTGTGCTGTATATATCGTGAGT 57.856 37.500 0.00 0.00 0.00 3.41
1704 1811 6.209361 ACTGTTGTGCTGTATATATCGTGAG 58.791 40.000 0.00 0.00 0.00 3.51
1705 1812 6.144078 ACTGTTGTGCTGTATATATCGTGA 57.856 37.500 0.00 0.00 0.00 4.35
1706 1813 7.807907 TCATACTGTTGTGCTGTATATATCGTG 59.192 37.037 0.00 0.00 39.29 4.35
1707 1814 7.882179 TCATACTGTTGTGCTGTATATATCGT 58.118 34.615 0.00 0.00 39.29 3.73
1731 1838 1.034838 TTCTCTCGAGGGCTCTGCTC 61.035 60.000 13.56 0.00 0.00 4.26
1734 1841 2.751166 TTTTTCTCTCGAGGGCTCTG 57.249 50.000 13.56 0.00 0.00 3.35
1820 4209 4.582701 AGAGCTGATGGATTACTTCTCG 57.417 45.455 0.00 0.00 0.00 4.04
1821 4210 7.049799 ACTTAGAGCTGATGGATTACTTCTC 57.950 40.000 0.00 0.00 0.00 2.87
1822 4211 8.540507 TTACTTAGAGCTGATGGATTACTTCT 57.459 34.615 0.00 0.00 0.00 2.85
1823 4212 9.036671 GTTTACTTAGAGCTGATGGATTACTTC 57.963 37.037 0.00 0.00 0.00 3.01
1824 4213 8.763601 AGTTTACTTAGAGCTGATGGATTACTT 58.236 33.333 0.00 0.00 0.00 2.24
1825 4214 8.200792 CAGTTTACTTAGAGCTGATGGATTACT 58.799 37.037 0.00 0.00 0.00 2.24
1826 4215 7.439655 CCAGTTTACTTAGAGCTGATGGATTAC 59.560 40.741 0.00 0.00 0.00 1.89
1827 4216 7.419057 CCCAGTTTACTTAGAGCTGATGGATTA 60.419 40.741 0.00 0.00 0.00 1.75
1828 4217 6.352516 CCAGTTTACTTAGAGCTGATGGATT 58.647 40.000 0.00 0.00 0.00 3.01
1916 4305 1.933181 CATGTCGTGTTACATCCGCAT 59.067 47.619 0.00 0.00 38.01 4.73
1931 4320 9.831737 GCATGTGGATATTAAGAATTACATGTC 57.168 33.333 0.00 10.82 43.50 3.06
1977 4366 7.732025 TGATAACATCATAATCGTGGGTTACT 58.268 34.615 0.00 0.00 33.59 2.24
1978 4367 7.956420 TGATAACATCATAATCGTGGGTTAC 57.044 36.000 0.00 0.00 33.59 2.50
2047 4436 5.382618 AAAGACCTTATCAAGCTTTGCAG 57.617 39.130 0.00 0.00 0.00 4.41
2125 5299 0.987715 CATGTGAGAGCGACGTGAAG 59.012 55.000 0.00 0.00 32.91 3.02
2126 5300 1.008875 GCATGTGAGAGCGACGTGAA 61.009 55.000 0.00 0.00 32.91 3.18
2159 5333 1.135603 GTGGTGCATGTGTATGTGCTG 60.136 52.381 0.00 0.00 41.78 4.41
2160 5334 1.167851 GTGGTGCATGTGTATGTGCT 58.832 50.000 0.00 0.00 41.78 4.40
2161 5335 0.880441 TGTGGTGCATGTGTATGTGC 59.120 50.000 0.00 0.00 41.61 4.57
2163 5337 1.155889 CGTGTGGTGCATGTGTATGT 58.844 50.000 0.00 0.00 36.65 2.29
2165 5339 0.676466 CCCGTGTGGTGCATGTGTAT 60.676 55.000 0.00 0.00 32.30 2.29
2166 5340 1.302112 CCCGTGTGGTGCATGTGTA 60.302 57.895 0.00 0.00 32.30 2.90
2167 5341 2.594303 CCCGTGTGGTGCATGTGT 60.594 61.111 0.00 0.00 32.30 3.72
2168 5342 4.041917 GCCCGTGTGGTGCATGTG 62.042 66.667 0.00 0.00 36.04 3.21
2170 5344 3.620419 TAGGCCCGTGTGGTGCATG 62.620 63.158 0.00 0.00 34.28 4.06
2171 5345 3.326578 TAGGCCCGTGTGGTGCAT 61.327 61.111 0.00 0.00 34.28 3.96
2172 5346 4.015406 CTAGGCCCGTGTGGTGCA 62.015 66.667 0.00 0.00 34.28 4.57
2201 5375 1.003355 TTTGCCTGAGCCTTCGAGG 60.003 57.895 0.00 0.00 38.69 4.63
2202 5376 0.321122 AGTTTGCCTGAGCCTTCGAG 60.321 55.000 0.00 0.00 38.69 4.04
2203 5377 0.603707 CAGTTTGCCTGAGCCTTCGA 60.604 55.000 0.00 0.00 44.49 3.71
2257 5440 1.073923 GAGGAAAAAGGAGGGCTGTCA 59.926 52.381 0.00 0.00 0.00 3.58
2279 5462 7.671302 AGAGATAAGGCAAGCGATAATTAAGA 58.329 34.615 0.00 0.00 0.00 2.10
2323 5509 2.000447 GAGTAGTGTTTGATGCGGGTC 59.000 52.381 0.00 0.00 0.00 4.46
2324 5510 1.338769 GGAGTAGTGTTTGATGCGGGT 60.339 52.381 0.00 0.00 0.00 5.28
2335 5521 5.621193 ACATTTTTGTAGCAGGAGTAGTGT 58.379 37.500 0.00 0.00 0.00 3.55
2336 5522 6.373779 CAACATTTTTGTAGCAGGAGTAGTG 58.626 40.000 0.00 0.00 0.00 2.74
2378 5564 2.076100 AGCTTTTCGATGAATGCGACA 58.924 42.857 0.00 0.00 37.52 4.35
2381 5567 1.398041 TCCAGCTTTTCGATGAATGCG 59.602 47.619 0.00 0.00 30.79 4.73
2385 5571 1.804151 CGGTTCCAGCTTTTCGATGAA 59.196 47.619 0.00 0.00 0.00 2.57
2386 5572 1.001520 TCGGTTCCAGCTTTTCGATGA 59.998 47.619 0.00 0.00 0.00 2.92
2387 5573 1.438651 TCGGTTCCAGCTTTTCGATG 58.561 50.000 0.00 0.00 0.00 3.84
2431 5622 0.804989 CGGTGGTTCCAGCATCTTTC 59.195 55.000 18.88 0.00 34.50 2.62
2476 5667 6.481954 TTCGATCTAGGCTTGAAGTTTTTC 57.518 37.500 2.10 0.00 0.00 2.29
2512 5704 2.294512 GGTTGAAGCTTCCCAAGTTGAG 59.705 50.000 23.42 0.00 0.00 3.02
2518 5710 0.827507 GGCTGGTTGAAGCTTCCCAA 60.828 55.000 23.42 10.15 43.06 4.12
2519 5711 1.228552 GGCTGGTTGAAGCTTCCCA 60.229 57.895 23.42 21.23 43.06 4.37
2540 5732 3.143807 TGCAACCTTTTCAGTTTGACG 57.856 42.857 0.00 0.00 0.00 4.35
2585 5777 3.344515 GGTCGAAGCTTTTTCCACCTAT 58.655 45.455 0.00 0.00 28.84 2.57
2639 5832 3.096092 ACTTTTTCCACAGGTTGAAGCA 58.904 40.909 0.00 0.00 0.00 3.91
2660 5853 5.549742 AGATTTTTCCATGCAGGTTGAAA 57.450 34.783 0.00 0.00 39.02 2.69
2668 5861 4.630111 GTGGTTGAAGATTTTTCCATGCA 58.370 39.130 0.00 0.00 0.00 3.96
2687 5882 3.363178 GTTGAAGCTTTTTCTCACGTGG 58.637 45.455 17.00 6.71 0.00 4.94
2689 5884 2.031683 CGGTTGAAGCTTTTTCTCACGT 59.968 45.455 0.00 0.00 0.00 4.49
2690 5885 2.286833 TCGGTTGAAGCTTTTTCTCACG 59.713 45.455 0.00 0.02 0.00 4.35
2717 5912 4.373116 TCGCCGCTCTCACCAACC 62.373 66.667 0.00 0.00 0.00 3.77
2754 5949 2.011741 CTCGTAGTACCGCCATGCCA 62.012 60.000 0.00 0.00 0.00 4.92
2766 5961 3.256879 CCATCATAGCATGTCCTCGTAGT 59.743 47.826 0.00 0.00 0.00 2.73
2769 5964 2.042464 ACCATCATAGCATGTCCTCGT 58.958 47.619 0.00 0.00 0.00 4.18
2777 5973 0.477204 AGCAGGCACCATCATAGCAT 59.523 50.000 0.00 0.00 0.00 3.79
2818 6014 0.587768 TCGTCTTGTAGCACGTCGAA 59.412 50.000 0.00 0.00 37.30 3.71
2822 6018 1.484356 GTTGTCGTCTTGTAGCACGT 58.516 50.000 0.00 0.00 37.30 4.49
2840 6036 0.249405 TCGCCCTCGTAACAAAACGT 60.249 50.000 0.00 0.00 43.31 3.99
2852 6048 0.942252 AACAAAAAGTCGTCGCCCTC 59.058 50.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.