Multiple sequence alignment - TraesCS3D01G168400

Loading Multiple Alignment...

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 TraesCS3D01G168400 chr3D 100.000 2380 0 0 1 2380 142997717 143000096 0.000000e+00 4396.0
1 TraesCS3D01G168400 chr3D 85.325 477 63 4 2 476 360691939 360691468 9.890000e-134 486.0
2 TraesCS3D01G168400 chr3D 87.351 419 50 2 1 419 149769499 149769914 5.950000e-131 477.0
3 TraesCS3D01G168400 chr3D 87.136 412 50 2 7 418 141411053 141410645 4.630000e-127 464.0
4 TraesCS3D01G168400 chr3B 89.264 1630 98 30 1 1580 204847829 204849431 0.000000e+00 1969.0
5 TraesCS3D01G168400 chr3B 87.879 594 60 7 1586 2171 204849553 204850142 0.000000e+00 688.0
6 TraesCS3D01G168400 chr3B 86.449 428 55 2 7 434 215572569 215572145 1.290000e-127 466.0
7 TraesCS3D01G168400 chr3B 86.215 428 56 1 7 434 221912923 221912499 5.990000e-126 460.0
8 TraesCS3D01G168400 chr3B 90.141 213 19 2 2169 2379 204850408 204850620 2.330000e-70 276.0
9 TraesCS3D01G168400 chr3B 88.312 77 3 1 1586 1656 204849474 204849550 1.170000e-13 87.9
10 TraesCS3D01G168400 chr3A 90.102 1475 79 29 1 1432 162751698 162753148 0.000000e+00 1853.0
11 TraesCS3D01G168400 chr3A 86.842 418 52 2 1 418 159832458 159832044 4.630000e-127 464.0
12 TraesCS3D01G168400 chr3A 87.136 412 50 2 7 418 166923885 166923477 4.630000e-127 464.0
13 TraesCS3D01G168400 chr6B 79.032 186 26 9 1927 2110 288299541 288299715 5.380000e-22 115.0


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 TraesCS3D01G168400 chr3D 142997717 143000096 2379 False 4396.000 4396 100.000 1 2380 1 chr3D.!!$F1 2379
1 TraesCS3D01G168400 chr3B 204847829 204850620 2791 False 755.225 1969 88.899 1 2379 4 chr3B.!!$F1 2378
2 TraesCS3D01G168400 chr3A 162751698 162753148 1450 False 1853.000 1853 90.102 1 1432 1 chr3A.!!$F1 1431

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
398 400 1.070134 CGAAGTCCACCACCAAGAAGA 59.93 52.381 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2098 0.11734 AAGGTGGTCTGAGGTAGGCT 59.883 55.0 0.0 0.0 0.0 4.58 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
49 50 2.032528 CCCTTGAAGCGGCACTCA 59.967 61.111 1.45 1.26 0.00 3.41
125 126 1.904771 CCACATCGCTTGGTCCCTA 59.095 57.895 0.00 0.00 0.00 3.53
133 135 2.608368 TTGGTCCCTACCCCCGTG 60.608 66.667 0.00 0.00 46.16 4.94
214 216 1.826921 GACGTCCTCCTGCCGGATA 60.827 63.158 5.05 0.00 39.01 2.59
217 219 2.122989 TCCTCCTGCCGGATACCC 60.123 66.667 5.05 0.00 39.01 3.69
388 390 2.126031 GTCGCCTCGAAGTCCACC 60.126 66.667 0.00 0.00 37.72 4.61
398 400 1.070134 CGAAGTCCACCACCAAGAAGA 59.930 52.381 0.00 0.00 0.00 2.87
400 402 3.551846 GAAGTCCACCACCAAGAAGAAA 58.448 45.455 0.00 0.00 0.00 2.52
406 408 3.189287 CCACCACCAAGAAGAAATCGAAG 59.811 47.826 0.00 0.00 0.00 3.79
475 477 3.730761 GCCATGATCGGCGCCATC 61.731 66.667 28.98 25.74 43.52 3.51
476 478 3.417224 CCATGATCGGCGCCATCG 61.417 66.667 28.98 13.22 39.07 3.84
486 488 2.633657 CGCCATCGCCATGTAAGC 59.366 61.111 0.00 0.00 0.00 3.09
487 489 1.889105 CGCCATCGCCATGTAAGCT 60.889 57.895 0.00 0.00 0.00 3.74
525 531 2.174319 GGATCGCCTCGCAAACTCC 61.174 63.158 0.00 0.00 0.00 3.85
534 540 2.747686 GCAAACTCCAGACCGGGA 59.252 61.111 6.32 0.00 34.36 5.14
643 649 1.801178 GGAGGCGAAATCGGATTCATC 59.199 52.381 3.28 0.00 40.23 2.92
656 667 4.738252 TCGGATTCATCTTCGTAATCGTTG 59.262 41.667 0.00 0.00 38.33 4.10
874 893 1.129437 GCTGGCAGTTCGAGTTCAATC 59.871 52.381 17.16 0.00 0.00 2.67
923 944 4.459390 TTCGATTTCGGACATAGTTCCA 57.541 40.909 0.00 0.00 40.29 3.53
929 950 6.348213 CGATTTCGGACATAGTTCCAAACTTT 60.348 38.462 0.00 0.00 38.09 2.66
931 952 4.963373 TCGGACATAGTTCCAAACTTTCA 58.037 39.130 0.00 0.00 42.81 2.69
933 954 5.823570 TCGGACATAGTTCCAAACTTTCAAA 59.176 36.000 0.00 0.00 42.81 2.69
948 969 1.729131 CAAATTCGCACACGCACCC 60.729 57.895 0.00 0.00 39.84 4.61
1133 1157 4.899239 CTGGATCCTCGGGTGCGC 62.899 72.222 14.23 0.00 0.00 6.09
1170 1201 1.755395 GCTCCCTCATGCATGCCAA 60.755 57.895 22.25 3.99 0.00 4.52
1173 1204 1.380785 CCCTCATGCATGCCAACCT 60.381 57.895 22.25 0.00 0.00 3.50
1178 1209 0.457166 CATGCATGCCAACCTGAACG 60.457 55.000 14.93 0.00 0.00 3.95
1179 1210 2.126346 GCATGCCAACCTGAACGC 60.126 61.111 6.36 0.00 0.00 4.84
1228 1259 0.320771 TGGTTTCTCTGCTTCGGCTC 60.321 55.000 0.00 0.00 42.37 4.70
1406 1462 4.764172 CTCAATTGTCCTTCTGGAGTAGG 58.236 47.826 5.13 0.00 44.16 3.18
1462 1520 1.293498 GCTGAACGAGAGGCCAGAA 59.707 57.895 5.01 0.00 36.98 3.02
1472 1530 5.728471 ACGAGAGGCCAGAAATATGATATG 58.272 41.667 5.01 0.00 0.00 1.78
1488 1546 5.723492 TGATATGATCGTGTTTCTGCTTG 57.277 39.130 0.00 0.00 0.00 4.01
1500 1558 1.595109 CTGCTTGCCACGTCTCACA 60.595 57.895 0.00 0.00 0.00 3.58
1501 1559 1.153269 TGCTTGCCACGTCTCACAA 60.153 52.632 0.00 0.00 0.00 3.33
1502 1560 1.279840 GCTTGCCACGTCTCACAAC 59.720 57.895 0.00 0.00 0.00 3.32
1503 1561 1.160329 GCTTGCCACGTCTCACAACT 61.160 55.000 0.00 0.00 0.00 3.16
1505 1563 1.261619 CTTGCCACGTCTCACAACTTC 59.738 52.381 0.00 0.00 0.00 3.01
1507 1565 1.202639 TGCCACGTCTCACAACTTCAT 60.203 47.619 0.00 0.00 0.00 2.57
1508 1566 2.036604 TGCCACGTCTCACAACTTCATA 59.963 45.455 0.00 0.00 0.00 2.15
1509 1567 3.262420 GCCACGTCTCACAACTTCATAT 58.738 45.455 0.00 0.00 0.00 1.78
1510 1568 3.062639 GCCACGTCTCACAACTTCATATG 59.937 47.826 0.00 0.00 0.00 1.78
1511 1569 4.245660 CCACGTCTCACAACTTCATATGT 58.754 43.478 1.90 0.00 0.00 2.29
1512 1570 5.407502 CCACGTCTCACAACTTCATATGTA 58.592 41.667 1.90 0.00 0.00 2.29
1513 1571 6.042777 CCACGTCTCACAACTTCATATGTAT 58.957 40.000 1.90 0.00 0.00 2.29
1514 1572 6.199154 CCACGTCTCACAACTTCATATGTATC 59.801 42.308 1.90 0.00 0.00 2.24
1515 1573 6.975197 CACGTCTCACAACTTCATATGTATCT 59.025 38.462 1.90 0.00 0.00 1.98
1516 1574 6.975197 ACGTCTCACAACTTCATATGTATCTG 59.025 38.462 1.90 0.00 0.00 2.90
1517 1575 6.074623 CGTCTCACAACTTCATATGTATCTGC 60.075 42.308 1.90 0.00 0.00 4.26
1519 1577 6.098838 TCTCACAACTTCATATGTATCTGCCT 59.901 38.462 1.90 0.00 0.00 4.75
1520 1578 6.653020 TCACAACTTCATATGTATCTGCCTT 58.347 36.000 1.90 0.00 0.00 4.35
1521 1579 6.539826 TCACAACTTCATATGTATCTGCCTTG 59.460 38.462 1.90 0.00 0.00 3.61
1562 1628 4.642429 ACAGTTTAGGACGATGCTTTTCT 58.358 39.130 0.00 0.00 0.00 2.52
1580 1646 3.194005 TCTTGACCCTGACACAACTTC 57.806 47.619 0.00 0.00 0.00 3.01
1581 1647 2.503765 TCTTGACCCTGACACAACTTCA 59.496 45.455 0.00 0.00 0.00 3.02
1582 1648 3.136443 TCTTGACCCTGACACAACTTCAT 59.864 43.478 0.00 0.00 0.00 2.57
1583 1649 4.346709 TCTTGACCCTGACACAACTTCATA 59.653 41.667 0.00 0.00 0.00 2.15
1584 1650 4.908601 TGACCCTGACACAACTTCATAT 57.091 40.909 0.00 0.00 0.00 1.78
1596 1778 8.948631 ACACAACTTCATATGTATCTACCTTG 57.051 34.615 1.90 0.00 0.00 3.61
1651 1839 4.412843 TCTGGATGGTTAAAAGGGGAAAC 58.587 43.478 0.00 0.00 0.00 2.78
1692 1880 1.640917 TGAGCTCCGGTCTTTTAGGT 58.359 50.000 12.15 0.00 0.00 3.08
1713 1902 5.825679 AGGTTGCAACACATTTGTAGTCTTA 59.174 36.000 29.55 0.00 33.55 2.10
1721 1910 8.383619 CAACACATTTGTAGTCTTAGCATCTAC 58.616 37.037 0.00 0.00 33.55 2.59
1748 1937 4.617530 CGGACCTCTCAAACGTCTAATCAA 60.618 45.833 0.00 0.00 0.00 2.57
1749 1938 5.235516 GGACCTCTCAAACGTCTAATCAAA 58.764 41.667 0.00 0.00 0.00 2.69
1754 1943 6.295039 TCTCAAACGTCTAATCAAACAACC 57.705 37.500 0.00 0.00 0.00 3.77
1771 1960 2.258591 CTGGTCACTGTCCGGACG 59.741 66.667 28.70 23.92 34.87 4.79
1776 1965 3.612681 CACTGTCCGGACGGGTGT 61.613 66.667 39.46 26.29 41.89 4.16
1777 1966 3.612681 ACTGTCCGGACGGGTGTG 61.613 66.667 39.46 22.03 41.89 3.82
1785 1974 1.911766 GGACGGGTGTGAGGAGGAA 60.912 63.158 0.00 0.00 0.00 3.36
1817 2006 2.052782 ACCACAACCCTCACTTTGTC 57.947 50.000 0.00 0.00 33.59 3.18
1819 2008 1.409521 CCACAACCCTCACTTTGTCCA 60.410 52.381 0.00 0.00 33.59 4.02
1828 2017 3.244353 CCTCACTTTGTCCAGACATGTCT 60.244 47.826 22.89 22.89 41.52 3.41
1851 2040 6.386927 TCTGACAAGTCCACAAATCCCTATAT 59.613 38.462 0.00 0.00 0.00 0.86
1866 2055 6.874278 TCCCTATATCCAACTCATATGTGG 57.126 41.667 9.45 7.06 0.00 4.17
1871 2060 2.845659 TCCAACTCATATGTGGGGAGT 58.154 47.619 13.34 3.07 43.35 3.85
1878 2067 5.915628 ACTCATATGTGGGGAGTATATGGA 58.084 41.667 9.45 0.00 39.95 3.41
1879 2068 5.960811 ACTCATATGTGGGGAGTATATGGAG 59.039 44.000 9.45 0.00 39.95 3.86
1880 2069 6.165742 TCATATGTGGGGAGTATATGGAGA 57.834 41.667 1.90 0.00 36.13 3.71
1881 2070 6.756270 TCATATGTGGGGAGTATATGGAGAT 58.244 40.000 1.90 0.00 36.13 2.75
1882 2071 6.612863 TCATATGTGGGGAGTATATGGAGATG 59.387 42.308 1.90 0.00 36.13 2.90
1884 2073 4.566837 TGTGGGGAGTATATGGAGATGTT 58.433 43.478 0.00 0.00 0.00 2.71
1885 2074 4.593206 TGTGGGGAGTATATGGAGATGTTC 59.407 45.833 0.00 0.00 0.00 3.18
1887 2076 3.195825 GGGGAGTATATGGAGATGTTCGG 59.804 52.174 0.00 0.00 0.00 4.30
1888 2077 3.195825 GGGAGTATATGGAGATGTTCGGG 59.804 52.174 0.00 0.00 0.00 5.14
1889 2078 3.368531 GGAGTATATGGAGATGTTCGGGC 60.369 52.174 0.00 0.00 0.00 6.13
1896 2085 2.514824 GATGTTCGGGCAGCCCTC 60.515 66.667 28.80 14.86 42.67 4.30
1919 2108 3.946242 TAGGATGCAGCCTACCTCA 57.054 52.632 26.62 6.46 39.50 3.86
1920 2109 1.709578 TAGGATGCAGCCTACCTCAG 58.290 55.000 26.62 0.00 39.50 3.35
1926 2115 1.901085 CAGCCTACCTCAGACCACC 59.099 63.158 0.00 0.00 0.00 4.61
1930 2119 1.351350 GCCTACCTCAGACCACCTTTT 59.649 52.381 0.00 0.00 0.00 2.27
1931 2120 2.615747 GCCTACCTCAGACCACCTTTTC 60.616 54.545 0.00 0.00 0.00 2.29
1932 2121 2.907042 CCTACCTCAGACCACCTTTTCT 59.093 50.000 0.00 0.00 0.00 2.52
1933 2122 3.055747 CCTACCTCAGACCACCTTTTCTC 60.056 52.174 0.00 0.00 0.00 2.87
1936 2125 3.459969 ACCTCAGACCACCTTTTCTCTTT 59.540 43.478 0.00 0.00 0.00 2.52
1937 2126 4.068599 CCTCAGACCACCTTTTCTCTTTC 58.931 47.826 0.00 0.00 0.00 2.62
1938 2127 3.728845 TCAGACCACCTTTTCTCTTTCG 58.271 45.455 0.00 0.00 0.00 3.46
1939 2128 3.386726 TCAGACCACCTTTTCTCTTTCGA 59.613 43.478 0.00 0.00 0.00 3.71
1949 2138 5.353678 CCTTTTCTCTTTCGATCTTCATGCT 59.646 40.000 0.00 0.00 0.00 3.79
1980 2169 7.172868 TCATATGCATTTGACTGGACAATTT 57.827 32.000 14.89 0.00 0.00 1.82
1982 2171 4.933505 TGCATTTGACTGGACAATTTGA 57.066 36.364 2.79 0.00 0.00 2.69
1987 2176 6.514947 CATTTGACTGGACAATTTGAAAGGA 58.485 36.000 2.79 0.00 0.00 3.36
1993 2182 5.711976 ACTGGACAATTTGAAAGGATGTAGG 59.288 40.000 2.79 0.00 0.00 3.18
1997 2186 5.016831 ACAATTTGAAAGGATGTAGGGGAC 58.983 41.667 2.79 0.00 0.00 4.46
2039 2229 0.507358 GAAGACTCAAACGGACACGC 59.493 55.000 0.00 0.00 46.04 5.34
2042 2232 2.280524 CTCAAACGGACACGCCCA 60.281 61.111 0.00 0.00 46.04 5.36
2088 2278 5.451798 CGGATGTTTGGGGGATCAAAATTAG 60.452 44.000 0.00 0.00 38.21 1.73
2095 2285 3.324846 GGGGGATCAAAATTAGCCAATCC 59.675 47.826 0.00 0.00 33.44 3.01
2096 2286 4.607293 GGGATCAAAATTAGCCAATCCC 57.393 45.455 2.65 2.65 44.01 3.85
2098 2288 3.888930 GGATCAAAATTAGCCAATCCCGA 59.111 43.478 0.00 0.00 0.00 5.14
2104 2294 8.335532 TCAAAATTAGCCAATCCCGATTATAG 57.664 34.615 0.00 0.00 0.00 1.31
2107 2297 8.511604 AAATTAGCCAATCCCGATTATAGATG 57.488 34.615 0.00 0.00 0.00 2.90
2110 2300 4.018960 AGCCAATCCCGATTATAGATGCTT 60.019 41.667 0.00 0.00 0.00 3.91
2112 2302 5.392380 GCCAATCCCGATTATAGATGCTTTG 60.392 44.000 0.00 0.00 0.00 2.77
2117 2307 5.991606 TCCCGATTATAGATGCTTTGACAAG 59.008 40.000 0.00 0.00 0.00 3.16
2118 2308 5.760253 CCCGATTATAGATGCTTTGACAAGT 59.240 40.000 0.00 0.00 31.86 3.16
2126 2316 5.825507 AGATGCTTTGACAAGTTTTGAGTC 58.174 37.500 0.00 0.00 31.86 3.36
2133 2323 1.141053 ACAAGTTTTGAGTCGGCCTCT 59.859 47.619 0.00 0.00 41.11 3.69
2134 2324 1.532868 CAAGTTTTGAGTCGGCCTCTG 59.467 52.381 0.00 0.00 41.11 3.35
2161 2351 1.003839 CCTTGACAAGGCGGTGCTA 60.004 57.895 21.10 0.00 42.78 3.49
2184 2642 9.670719 GCTAATGAAATTACTTGGAAGCTATTC 57.329 33.333 0.00 0.00 37.87 1.75
2199 2657 2.693069 CTATTCAGCATAGAAGGCCCG 58.307 52.381 0.00 0.00 37.65 6.13
2231 2690 1.220206 CGGCCTCTCACATGAAGCT 59.780 57.895 0.00 0.00 0.00 3.74
2258 2717 0.538516 TGGAACAACCGGGAACCATG 60.539 55.000 6.32 0.00 45.03 3.66
2274 2733 5.049474 GGAACCATGGAAGCACAAAATTTTC 60.049 40.000 21.47 6.54 0.00 2.29
2277 2736 3.170791 TGGAAGCACAAAATTTTCGCA 57.829 38.095 19.06 1.66 0.00 5.10
2283 2742 3.059166 GCACAAAATTTTCGCATGACCT 58.941 40.909 14.22 0.00 0.00 3.85
2286 2745 5.348451 GCACAAAATTTTCGCATGACCTATT 59.652 36.000 14.22 0.00 0.00 1.73
2289 2748 6.586082 ACAAAATTTTCGCATGACCTATTGTC 59.414 34.615 0.00 0.00 44.72 3.18
2290 2749 4.900635 ATTTTCGCATGACCTATTGTCC 57.099 40.909 0.00 0.00 43.78 4.02
2291 2750 3.342377 TTTCGCATGACCTATTGTCCA 57.658 42.857 0.00 0.00 43.78 4.02
2292 2751 2.602257 TCGCATGACCTATTGTCCAG 57.398 50.000 0.00 0.00 43.78 3.86
2293 2752 0.940126 CGCATGACCTATTGTCCAGC 59.060 55.000 0.00 0.00 43.78 4.85
2294 2753 1.743431 CGCATGACCTATTGTCCAGCA 60.743 52.381 0.00 0.00 43.78 4.41
2295 2754 1.672881 GCATGACCTATTGTCCAGCAC 59.327 52.381 0.00 0.00 43.78 4.40
2296 2755 2.681976 GCATGACCTATTGTCCAGCACT 60.682 50.000 0.00 0.00 43.78 4.40
2336 2796 0.323725 TTGCAAAGGAGAGGATGGCC 60.324 55.000 0.00 0.00 0.00 5.36
2371 2831 3.074538 ACCCCAGTTATGCAAAAGAGAGT 59.925 43.478 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.034879 CCGCACCATGCTCGAGTTT 61.035 57.895 15.13 0.00 42.25 2.66
109 110 1.905512 GGTAGGGACCAAGCGATGT 59.094 57.895 0.00 0.00 46.12 3.06
217 219 1.374758 GTTCTGCAGGGACCTCACG 60.375 63.158 15.13 0.00 0.00 4.35
388 390 5.683859 CAAGACTTCGATTTCTTCTTGGTG 58.316 41.667 6.15 0.00 39.58 4.17
398 400 1.198637 GCTGCAGCAAGACTTCGATTT 59.801 47.619 33.36 0.00 41.59 2.17
400 402 0.036577 AGCTGCAGCAAGACTTCGAT 60.037 50.000 38.24 12.75 45.16 3.59
406 408 1.801332 CCATGAGCTGCAGCAAGAC 59.199 57.895 38.24 25.09 45.16 3.01
470 472 1.650912 CAGCTTACATGGCGATGGC 59.349 57.895 13.62 6.96 33.39 4.40
476 478 2.100991 GCACGCAGCTTACATGGC 59.899 61.111 0.00 0.00 41.15 4.40
525 531 1.375523 CCCGAGTTTTCCCGGTCTG 60.376 63.158 0.00 0.00 43.93 3.51
534 540 4.216257 CACACTGATTCAATCCCGAGTTTT 59.784 41.667 0.00 0.00 0.00 2.43
643 649 0.025001 CTGCGCCAACGATTACGAAG 59.975 55.000 4.18 0.00 43.93 3.79
686 697 1.003839 TCATGAGGTCGGTTGCCAC 60.004 57.895 0.00 0.00 0.00 5.01
846 865 1.739562 GAACTGCCAGCACCGAGAG 60.740 63.158 0.00 0.00 0.00 3.20
847 866 2.343758 GAACTGCCAGCACCGAGA 59.656 61.111 0.00 0.00 0.00 4.04
874 893 2.159626 CGGTTGGTAAATAACGCTGTGG 60.160 50.000 0.00 0.00 0.00 4.17
906 927 6.488683 TGAAAGTTTGGAACTATGTCCGAAAT 59.511 34.615 0.00 0.00 41.78 2.17
923 944 2.533942 GCGTGTGCGAATTTGAAAGTTT 59.466 40.909 0.00 0.00 41.33 2.66
948 969 3.620300 TTCCGCAGCGTCCTACGTG 62.620 63.158 15.05 0.00 44.73 4.49
1170 1201 4.643387 GCACCCAGGCGTTCAGGT 62.643 66.667 0.00 0.00 0.00 4.00
1173 1204 2.594303 CAAGCACCCAGGCGTTCA 60.594 61.111 0.00 0.00 39.27 3.18
1179 1210 1.898574 AAAGTCGCAAGCACCCAGG 60.899 57.895 0.00 0.00 37.18 4.45
1195 1226 5.299279 CAGAGAAACCAAAGTCTAAGCCAAA 59.701 40.000 0.00 0.00 0.00 3.28
1247 1303 1.449601 CAGCGCCGACCTACCAATT 60.450 57.895 2.29 0.00 0.00 2.32
1248 1304 2.186903 CAGCGCCGACCTACCAAT 59.813 61.111 2.29 0.00 0.00 3.16
1462 1520 8.501580 CAAGCAGAAACACGATCATATCATATT 58.498 33.333 0.00 0.00 0.00 1.28
1472 1530 0.874390 TGGCAAGCAGAAACACGATC 59.126 50.000 0.00 0.00 0.00 3.69
1488 1546 1.512926 ATGAAGTTGTGAGACGTGGC 58.487 50.000 0.00 0.00 0.00 5.01
1500 1558 7.112122 TGTTCAAGGCAGATACATATGAAGTT 58.888 34.615 10.38 0.00 0.00 2.66
1501 1559 6.653020 TGTTCAAGGCAGATACATATGAAGT 58.347 36.000 10.38 0.00 0.00 3.01
1502 1560 7.228108 ACATGTTCAAGGCAGATACATATGAAG 59.772 37.037 10.38 0.00 0.00 3.02
1503 1561 7.056006 ACATGTTCAAGGCAGATACATATGAA 58.944 34.615 10.38 0.00 0.00 2.57
1505 1563 6.872628 ACATGTTCAAGGCAGATACATATG 57.127 37.500 0.00 0.00 0.00 1.78
1507 1565 6.653020 AGAACATGTTCAAGGCAGATACATA 58.347 36.000 33.92 0.00 41.84 2.29
1508 1566 5.503927 AGAACATGTTCAAGGCAGATACAT 58.496 37.500 33.92 11.09 41.84 2.29
1509 1567 4.910195 AGAACATGTTCAAGGCAGATACA 58.090 39.130 33.92 0.00 41.84 2.29
1510 1568 5.886960 AAGAACATGTTCAAGGCAGATAC 57.113 39.130 33.92 9.03 41.84 2.24
1511 1569 6.240894 AGAAAGAACATGTTCAAGGCAGATA 58.759 36.000 33.92 0.00 41.84 1.98
1512 1570 5.075493 AGAAAGAACATGTTCAAGGCAGAT 58.925 37.500 33.92 13.10 41.84 2.90
1513 1571 4.464008 AGAAAGAACATGTTCAAGGCAGA 58.536 39.130 33.92 0.00 41.84 4.26
1514 1572 4.612259 CGAGAAAGAACATGTTCAAGGCAG 60.612 45.833 33.92 19.56 41.84 4.85
1515 1573 3.250762 CGAGAAAGAACATGTTCAAGGCA 59.749 43.478 33.92 0.00 41.84 4.75
1516 1574 3.498397 TCGAGAAAGAACATGTTCAAGGC 59.502 43.478 33.92 21.56 41.84 4.35
1517 1575 4.991056 TCTCGAGAAAGAACATGTTCAAGG 59.009 41.667 33.92 18.94 41.84 3.61
1519 1577 5.356426 TGTCTCGAGAAAGAACATGTTCAA 58.644 37.500 33.92 13.24 41.84 2.69
1520 1578 4.944048 TGTCTCGAGAAAGAACATGTTCA 58.056 39.130 33.92 15.08 41.84 3.18
1521 1579 4.985409 ACTGTCTCGAGAAAGAACATGTTC 59.015 41.667 34.34 27.69 39.78 3.18
1562 1628 3.576078 ATGAAGTTGTGTCAGGGTCAA 57.424 42.857 0.00 0.00 0.00 3.18
1583 1649 9.046296 GTCATCGATTTTTCAAGGTAGATACAT 57.954 33.333 0.00 0.00 0.00 2.29
1584 1650 8.258007 AGTCATCGATTTTTCAAGGTAGATACA 58.742 33.333 0.00 0.00 0.00 2.29
1596 1778 9.302345 TCTACAGAACATAGTCATCGATTTTTC 57.698 33.333 0.00 0.00 0.00 2.29
1651 1839 5.623264 TCATGTTAACTTTTGCAATCGTTCG 59.377 36.000 14.72 3.99 0.00 3.95
1692 1880 5.298026 TGCTAAGACTACAAATGTGTTGCAA 59.702 36.000 0.00 0.00 39.30 4.08
1713 1902 0.824759 GAGGTCCGGTTGTAGATGCT 59.175 55.000 0.00 0.00 0.00 3.79
1721 1910 0.249741 ACGTTTGAGAGGTCCGGTTG 60.250 55.000 0.00 0.00 0.00 3.77
1748 1937 0.179056 CGGACAGTGACCAGGTTGTT 60.179 55.000 12.19 0.00 0.00 2.83
1749 1938 1.445942 CGGACAGTGACCAGGTTGT 59.554 57.895 12.19 0.00 0.00 3.32
1754 1943 2.258591 CGTCCGGACAGTGACCAG 59.741 66.667 32.80 11.27 0.00 4.00
1785 1974 2.235155 GGTTGTGGTTGGGTGACTTTTT 59.765 45.455 0.00 0.00 0.00 1.94
1819 2008 2.700371 TGTGGACTTGTCAGACATGTCT 59.300 45.455 32.74 22.89 46.38 3.41
1828 2017 4.927267 ATAGGGATTTGTGGACTTGTCA 57.073 40.909 3.08 0.00 0.00 3.58
1829 2018 5.998363 GGATATAGGGATTTGTGGACTTGTC 59.002 44.000 0.00 0.00 0.00 3.18
1831 2020 5.940617 TGGATATAGGGATTTGTGGACTTG 58.059 41.667 0.00 0.00 0.00 3.16
1834 2023 5.941788 AGTTGGATATAGGGATTTGTGGAC 58.058 41.667 0.00 0.00 0.00 4.02
1851 2040 2.845659 ACTCCCCACATATGAGTTGGA 58.154 47.619 10.38 8.82 35.93 3.53
1866 2055 3.195825 CCCGAACATCTCCATATACTCCC 59.804 52.174 0.00 0.00 0.00 4.30
1871 2060 2.028112 GCTGCCCGAACATCTCCATATA 60.028 50.000 0.00 0.00 0.00 0.86
1887 2076 2.072487 TCCTACATGGAGGGCTGCC 61.072 63.158 24.45 11.05 40.56 4.85
1888 2077 3.647367 TCCTACATGGAGGGCTGC 58.353 61.111 24.45 0.00 40.56 5.25
1909 2098 0.117340 AAGGTGGTCTGAGGTAGGCT 59.883 55.000 0.00 0.00 0.00 4.58
1933 2122 5.729974 TTGATGAGCATGAAGATCGAAAG 57.270 39.130 0.00 0.00 34.70 2.62
1936 2125 4.952460 TGATTGATGAGCATGAAGATCGA 58.048 39.130 0.00 0.00 34.70 3.59
1937 2126 5.864628 ATGATTGATGAGCATGAAGATCG 57.135 39.130 0.00 0.00 34.70 3.69
1938 2127 7.148239 TGCATATGATTGATGAGCATGAAGATC 60.148 37.037 6.97 0.00 34.70 2.75
1939 2128 6.659242 TGCATATGATTGATGAGCATGAAGAT 59.341 34.615 6.97 0.00 34.70 2.40
1949 2138 6.773685 TCCAGTCAAATGCATATGATTGATGA 59.226 34.615 13.21 8.76 35.89 2.92
1980 2169 3.459828 TCATGTCCCCTACATCCTTTCA 58.540 45.455 0.00 0.00 46.15 2.69
1982 2171 4.796606 CAATCATGTCCCCTACATCCTTT 58.203 43.478 0.00 0.00 46.15 3.11
2010 2199 3.725740 CGTTTGAGTCTTCATTTGTGCAC 59.274 43.478 10.75 10.75 32.27 4.57
2015 2204 4.527564 GTGTCCGTTTGAGTCTTCATTTG 58.472 43.478 0.00 0.00 32.27 2.32
2052 2242 2.896854 CATCCGTGGATGTGCCCG 60.897 66.667 18.76 0.00 44.93 6.13
2070 2260 3.796111 TGGCTAATTTTGATCCCCCAAA 58.204 40.909 0.00 0.00 34.56 3.28
2073 2263 3.324846 GGATTGGCTAATTTTGATCCCCC 59.675 47.826 0.00 0.00 0.00 5.40
2088 2278 3.878778 AGCATCTATAATCGGGATTGGC 58.121 45.455 4.21 0.00 32.50 4.52
2095 2285 6.851222 ACTTGTCAAAGCATCTATAATCGG 57.149 37.500 0.00 0.00 36.84 4.18
2096 2286 9.003112 CAAAACTTGTCAAAGCATCTATAATCG 57.997 33.333 0.00 0.00 36.84 3.34
2104 2294 4.672413 CGACTCAAAACTTGTCAAAGCATC 59.328 41.667 0.00 0.00 36.84 3.91
2107 2297 3.363178 CCGACTCAAAACTTGTCAAAGC 58.637 45.455 0.00 0.00 36.84 3.51
2110 2300 1.673920 GGCCGACTCAAAACTTGTCAA 59.326 47.619 0.00 0.00 0.00 3.18
2112 2302 1.531578 GAGGCCGACTCAAAACTTGTC 59.468 52.381 0.00 0.00 45.85 3.18
2150 2340 4.270008 AGTAATTTCATTAGCACCGCCTT 58.730 39.130 0.00 0.00 0.00 4.35
2161 2351 8.193438 GCTGAATAGCTTCCAAGTAATTTCATT 58.807 33.333 0.00 0.00 46.57 2.57
2184 2642 2.592861 GCCGGGCCTTCTATGCTG 60.593 66.667 8.12 0.00 0.00 4.41
2185 2643 2.770048 AGCCGGGCCTTCTATGCT 60.770 61.111 17.02 0.00 0.00 3.79
2199 2657 3.521796 GCCGCCAAATCCTCAGCC 61.522 66.667 0.00 0.00 0.00 4.85
2248 2707 0.893270 TTGTGCTTCCATGGTTCCCG 60.893 55.000 12.58 0.00 0.00 5.14
2258 2717 3.740321 TCATGCGAAAATTTTGTGCTTCC 59.260 39.130 19.69 1.23 0.00 3.46
2301 2761 2.892374 TGCAACATGTCGGTCATCTAG 58.108 47.619 0.00 0.00 34.09 2.43
2311 2771 2.783135 TCCTCTCCTTTGCAACATGTC 58.217 47.619 0.00 0.00 0.00 3.06
2336 2796 1.005924 ACTGGGGTAGCCCTCAATTTG 59.994 52.381 29.64 13.17 42.04 2.32


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

AutoCloner maintained by Alex Coulton.