Multiple sequence alignment - TraesCS5B01G500200

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 TraesCS5B01G500200 chr5B 100.000 4227 0 0 1 4227 666206065 666210291 0.000000e+00 7806.0
1 TraesCS5B01G500200 chr5D 92.733 3729 137 44 1 3686 528977154 528980791 0.000000e+00 5262.0
2 TraesCS5B01G500200 chr5D 92.182 550 32 6 3682 4226 528980875 528981418 0.000000e+00 767.0
3 TraesCS5B01G500200 chr5A 90.607 1959 129 20 1671 3609 657206181 657208104 0.000000e+00 2547.0
4 TraesCS5B01G500200 chr5A 89.802 1461 76 28 1 1429 657204612 657206031 0.000000e+00 1805.0
5 TraesCS5B01G500200 chr5A 87.316 339 26 9 3663 3992 657208111 657208441 5.160000e-99 372.0
6 TraesCS5B01G500200 chr4B 94.872 39 2 0 3606 3644 587902387 587902425 1.270000e-05 62.1


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 TraesCS5B01G500200 chr5B 666206065 666210291 4226 False 7806.000000 7806 100.000000 1 4227 1 chr5B.!!$F1 4226
1 TraesCS5B01G500200 chr5D 528977154 528981418 4264 False 3014.500000 5262 92.457500 1 4226 2 chr5D.!!$F1 4225
2 TraesCS5B01G500200 chr5A 657204612 657208441 3829 False 1574.666667 2547 89.241667 1 3992 3 chr5A.!!$F1 3991

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
959 982 0.694444 GGCCTCCCTGGACCAGATTA 60.694 60.000 23.77 6.64 38.13 1.75 F
960 983 0.761802 GCCTCCCTGGACCAGATTAG 59.238 60.000 23.77 15.32 38.35 1.73 F
1569 1651 1.197721 CTGGTGAACTTGAATGCGGTC 59.802 52.381 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 2023 0.108041 CAACTCATTGGCAATGGGGC 60.108 55.0 36.0 0.0 43.84 5.8 R
2563 2676 0.607620 GAGCCTTGTCAGAGAGCAGT 59.392 55.0 0.0 0.0 0.00 4.4 R
3548 3673 0.610174 TCTCTGCAAGACGAAGGCAT 59.390 50.0 0.0 0.0 38.67 4.4 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
280 281 2.266055 CACTTGTCGAGGAGGGCC 59.734 66.667 0.00 0.00 0.00 5.80
439 440 3.482783 GCGAAGTCCTGCAGCGTC 61.483 66.667 8.66 2.61 0.00 5.19
719 720 1.615384 GGTGGTCGTAGTGGTAGGAGT 60.615 57.143 0.00 0.00 0.00 3.85
722 723 2.092753 TGGTCGTAGTGGTAGGAGTAGG 60.093 54.545 0.00 0.00 0.00 3.18
723 724 2.171448 GGTCGTAGTGGTAGGAGTAGGA 59.829 54.545 0.00 0.00 0.00 2.94
724 725 3.202097 GTCGTAGTGGTAGGAGTAGGAC 58.798 54.545 0.00 0.00 32.43 3.85
833 851 2.003301 GAGAGATTTTTCCGCTCGCTT 58.997 47.619 0.00 0.00 33.98 4.68
908 930 3.972227 CGTGAGGGAAACAGGCTG 58.028 61.111 14.16 14.16 0.00 4.85
923 945 4.410400 CTGAGCCCAACCCGTCCC 62.410 72.222 0.00 0.00 0.00 4.46
957 980 2.367512 GGCCTCCCTGGACCAGAT 60.368 66.667 23.77 0.00 38.13 2.90
958 981 2.003548 GGCCTCCCTGGACCAGATT 61.004 63.158 23.77 0.00 38.13 2.40
959 982 0.694444 GGCCTCCCTGGACCAGATTA 60.694 60.000 23.77 6.64 38.13 1.75
960 983 0.761802 GCCTCCCTGGACCAGATTAG 59.238 60.000 23.77 15.32 38.35 1.73
961 984 1.692762 GCCTCCCTGGACCAGATTAGA 60.693 57.143 23.77 12.26 38.35 2.10
987 1010 2.197643 GAACAGAAGCAGCAGCAGCC 62.198 60.000 6.10 0.00 45.49 4.85
1415 1493 4.421058 CCGCCTTGCTTTATTTTCCTTAC 58.579 43.478 0.00 0.00 0.00 2.34
1416 1494 4.157840 CCGCCTTGCTTTATTTTCCTTACT 59.842 41.667 0.00 0.00 0.00 2.24
1419 1497 6.458342 CGCCTTGCTTTATTTTCCTTACTAGG 60.458 42.308 0.00 0.00 43.46 3.02
1436 1517 1.638529 AGGATTAGGATCGGCCTCTG 58.361 55.000 0.00 0.00 46.97 3.35
1443 1524 3.046870 ATCGGCCTCTGCTCGATC 58.953 61.111 0.00 0.00 42.97 3.69
1444 1525 1.530419 ATCGGCCTCTGCTCGATCT 60.530 57.895 0.00 0.00 42.97 2.75
1445 1526 1.523154 ATCGGCCTCTGCTCGATCTC 61.523 60.000 0.00 0.00 42.97 2.75
1446 1527 2.733945 GGCCTCTGCTCGATCTCC 59.266 66.667 0.00 0.00 37.74 3.71
1447 1528 2.334653 GCCTCTGCTCGATCTCCG 59.665 66.667 0.00 0.00 40.25 4.63
1448 1529 3.038280 CCTCTGCTCGATCTCCGG 58.962 66.667 0.00 0.00 39.14 5.14
1449 1530 2.334653 CTCTGCTCGATCTCCGGC 59.665 66.667 0.00 0.00 39.14 6.13
1450 1531 3.534970 CTCTGCTCGATCTCCGGCG 62.535 68.421 0.00 0.00 37.30 6.46
1451 1532 4.637489 CTGCTCGATCTCCGGCGG 62.637 72.222 22.51 22.51 37.30 6.13
1466 1547 4.598894 CGGGAGGCAGCCGATGAG 62.599 72.222 5.55 0.00 0.00 2.90
1569 1651 1.197721 CTGGTGAACTTGAATGCGGTC 59.802 52.381 0.00 0.00 0.00 4.79
1584 1666 2.094494 TGCGGTCTCAGAATCTCTCAAC 60.094 50.000 0.00 0.00 0.00 3.18
1589 1671 5.106118 CGGTCTCAGAATCTCTCAACTGTTA 60.106 44.000 0.00 0.00 0.00 2.41
1604 1686 6.509656 TCAACTGTTAAAGTCTATCGTGTGT 58.490 36.000 0.00 0.00 38.56 3.72
1667 1749 7.125792 AGGAAATTGGGTGATACTGTACTAG 57.874 40.000 0.00 0.00 0.00 2.57
1669 1751 7.842743 AGGAAATTGGGTGATACTGTACTAGTA 59.157 37.037 0.00 0.00 45.50 1.82
1670 1752 7.924947 GGAAATTGGGTGATACTGTACTAGTAC 59.075 40.741 23.58 23.58 44.30 2.73
1672 1754 4.454678 TGGGTGATACTGTACTAGTACCG 58.545 47.826 26.41 22.84 44.30 4.02
1677 1759 6.253746 GTGATACTGTACTAGTACCGTGTTG 58.746 44.000 29.67 16.16 44.30 3.33
1682 1764 7.921786 ACTGTACTAGTACCGTGTTGTATTA 57.078 36.000 26.41 5.96 38.04 0.98
1683 1765 8.511604 ACTGTACTAGTACCGTGTTGTATTAT 57.488 34.615 26.41 1.67 38.04 1.28
1687 1769 6.270815 ACTAGTACCGTGTTGTATTATGCTG 58.729 40.000 0.00 0.00 0.00 4.41
1696 1778 6.478673 CGTGTTGTATTATGCTGTGGAATCTA 59.521 38.462 0.00 0.00 0.00 1.98
1697 1779 7.306807 CGTGTTGTATTATGCTGTGGAATCTAG 60.307 40.741 0.00 0.00 0.00 2.43
1761 1843 6.441093 TTTTGCTCTTATGCCTACAAGATG 57.559 37.500 0.00 0.00 30.70 2.90
1930 2023 1.967066 CCTAGCTGACCCTGATACTGG 59.033 57.143 0.00 0.00 0.00 4.00
2004 2097 4.572985 TTCAGTGCACTTCATTCCTTTG 57.427 40.909 18.94 2.53 0.00 2.77
2013 2107 5.671329 GCACTTCATTCCTTTGTCGTGTATC 60.671 44.000 0.00 0.00 0.00 2.24
2077 2184 5.549742 TGGACTTGCCAATGAAATTTCTT 57.450 34.783 18.64 10.06 45.87 2.52
2078 2185 5.927819 TGGACTTGCCAATGAAATTTCTTT 58.072 33.333 18.64 15.29 45.87 2.52
2079 2186 7.060383 TGGACTTGCCAATGAAATTTCTTTA 57.940 32.000 18.64 0.00 45.87 1.85
2080 2187 7.153985 TGGACTTGCCAATGAAATTTCTTTAG 58.846 34.615 18.64 12.55 45.87 1.85
2081 2188 6.091305 GGACTTGCCAATGAAATTTCTTTAGC 59.909 38.462 21.93 21.93 31.22 3.09
2082 2189 6.523840 ACTTGCCAATGAAATTTCTTTAGCA 58.476 32.000 25.25 25.25 37.25 3.49
2083 2190 6.991531 ACTTGCCAATGAAATTTCTTTAGCAA 59.008 30.769 31.12 31.12 42.15 3.91
2084 2191 7.498570 ACTTGCCAATGAAATTTCTTTAGCAAA 59.501 29.630 31.87 22.88 42.96 3.68
2085 2192 7.982761 TGCCAATGAAATTTCTTTAGCAAAT 57.017 28.000 26.17 7.30 36.56 2.32
2086 2193 8.393671 TGCCAATGAAATTTCTTTAGCAAATT 57.606 26.923 26.17 11.81 36.56 1.82
2087 2194 8.848182 TGCCAATGAAATTTCTTTAGCAAATTT 58.152 25.926 26.17 4.59 43.15 1.82
2132 2239 4.141018 GGATGTGGGGATTTATTGTAGGGT 60.141 45.833 0.00 0.00 0.00 4.34
2149 2256 3.893521 AGGGTAACAAATATTGTCCCGG 58.106 45.455 11.98 0.00 46.84 5.73
2157 2264 9.063615 GTAACAAATATTGTCCCGGAGATATTT 57.936 33.333 0.73 16.28 44.59 1.40
2234 2344 1.452651 CATGAGCATCCCAAGGCGT 60.453 57.895 0.00 0.00 37.25 5.68
2245 2355 1.543429 CCCAAGGCGTCTCTTCAGTTT 60.543 52.381 0.00 0.00 0.00 2.66
2246 2356 2.289444 CCCAAGGCGTCTCTTCAGTTTA 60.289 50.000 0.00 0.00 0.00 2.01
2311 2421 4.429854 AGGCATCCCTCTACAAAAGATC 57.570 45.455 0.00 0.00 36.46 2.75
2506 2619 1.202976 ACTGCCCAGATTCAGCTTGTT 60.203 47.619 1.69 0.00 33.80 2.83
2524 2637 1.243342 TTGCAAGCCATCCGGAAGTG 61.243 55.000 9.01 2.34 0.00 3.16
2551 2664 3.705051 ACCATGTGATGATTCCTTTGCT 58.295 40.909 0.00 0.00 0.00 3.91
2563 2676 2.585330 TCCTTTGCTCTTGTTGATGCA 58.415 42.857 0.00 0.00 0.00 3.96
2716 2829 2.358898 AGCAACAGACATCAACCAACAC 59.641 45.455 0.00 0.00 0.00 3.32
3046 3159 5.188359 CCATTTGATGAATGAGAAGGGGTTT 59.812 40.000 0.56 0.00 46.59 3.27
3142 3255 0.241749 CTGGCGCAAATGCTTCTCAA 59.758 50.000 10.83 0.00 39.32 3.02
3148 3261 1.800286 GCAAATGCTTCTCAATCCGGC 60.800 52.381 0.00 0.00 38.21 6.13
3181 3294 2.307309 CGAGTCGTGGCTTTCGCAA 61.307 57.895 3.82 0.00 38.10 4.85
3244 3357 1.355381 TGACATCATCAGTTTGGGCCT 59.645 47.619 4.53 0.00 31.91 5.19
3283 3396 1.066908 CGAAGCAAGGAAACCTTTGCA 59.933 47.619 18.84 0.00 41.69 4.08
3350 3469 0.398318 GTTCAGACCTGCCTGTCCTT 59.602 55.000 0.00 0.00 35.83 3.36
3375 3494 2.910688 ACACGAACCAGACTGACATT 57.089 45.000 3.32 0.00 0.00 2.71
3388 3507 4.993584 AGACTGACATTGTGAACTTAGCTG 59.006 41.667 0.00 0.00 0.00 4.24
3439 3560 5.813080 AGTCGCAATATACCAAACTTTCC 57.187 39.130 0.00 0.00 0.00 3.13
3476 3597 5.066893 ACAGCTGTCTTATTATGTTGGCATG 59.933 40.000 15.25 0.00 36.58 4.06
3548 3673 8.257830 TGAATGTGACATACGCTGTTAAATTA 57.742 30.769 0.00 0.00 38.54 1.40
3588 3713 4.074970 GAGAAATTCTGCCCAACTTCTGA 58.925 43.478 0.00 0.00 0.00 3.27
3610 3735 7.065085 TCTGAATCTGTGCAAAATTAGCTACTC 59.935 37.037 0.00 0.00 0.00 2.59
3618 3743 4.626529 GCAAAATTAGCTACTCCCTCCAGT 60.627 45.833 0.00 0.00 0.00 4.00
3627 3752 4.838986 GCTACTCCCTCCAGTCCATATTAA 59.161 45.833 0.00 0.00 0.00 1.40
3660 3786 5.045869 CCTTTAGTTGTGATTGGAGGGAGTA 60.046 44.000 0.00 0.00 0.00 2.59
3686 3812 9.744468 ACAAAAATTTGATGTCTGTTTAGTACC 57.256 29.630 12.54 0.00 40.55 3.34
3699 3913 4.638421 TGTTTAGTACCATGGTATGCTTGC 59.362 41.667 27.03 13.23 32.82 4.01
3700 3914 4.771114 TTAGTACCATGGTATGCTTGCT 57.229 40.909 27.03 19.26 32.82 3.91
3706 3920 2.219458 CATGGTATGCTTGCTCTCCTG 58.781 52.381 0.00 0.00 0.00 3.86
3740 3954 2.655090 TGCATCTGGGTTTGTTCTCA 57.345 45.000 0.00 0.00 0.00 3.27
3761 3975 1.372656 GTCGCGTCGTTTGTTTTGAG 58.627 50.000 5.77 0.00 0.00 3.02
3763 3977 1.862201 TCGCGTCGTTTGTTTTGAGAT 59.138 42.857 5.77 0.00 0.00 2.75
3768 3982 5.338559 CGCGTCGTTTGTTTTGAGATATTTT 59.661 36.000 0.00 0.00 0.00 1.82
3769 3983 6.517034 CGCGTCGTTTGTTTTGAGATATTTTA 59.483 34.615 0.00 0.00 0.00 1.52
3834 4048 0.179137 TGTCGCGTCTAGAATGCAGG 60.179 55.000 16.05 3.73 40.11 4.85
3865 4079 1.149288 TGTAGTGGACTTGGGAGGAGT 59.851 52.381 0.00 0.00 0.00 3.85
3889 4103 2.054232 ATCTGCCATGAGCTTTCCTG 57.946 50.000 0.00 0.00 44.23 3.86
3945 4164 8.201464 TCATATTTGCTAGTAAACCTGATCGAA 58.799 33.333 8.24 0.00 0.00 3.71
3967 4186 2.551459 CACAGAAACTTCAGCAAGGAGG 59.449 50.000 0.00 0.00 33.37 4.30
3973 4192 2.800250 ACTTCAGCAAGGAGGAAATGG 58.200 47.619 0.00 0.00 33.37 3.16
3975 4194 0.323725 TCAGCAAGGAGGAAATGGCC 60.324 55.000 0.00 0.00 0.00 5.36
4022 4242 3.005684 CAGTTGCAACAAAGCCATAAGGA 59.994 43.478 30.11 0.00 36.89 3.36
4053 4273 9.977762 CAAGAATTTTTATTTTCTTGCATAGCC 57.022 29.630 11.20 0.00 46.79 3.93
4063 4283 2.745281 TCTTGCATAGCCGGTACAAAAC 59.255 45.455 1.90 0.00 0.00 2.43
4170 4394 7.987458 ACTCATCCTTCGTCAAACATTACATAT 59.013 33.333 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.148825 GAGATGCGCCACGACCCT 62.149 66.667 4.18 0.00 0.00 4.34
707 708 2.159043 CGTCGTCCTACTCCTACCACTA 60.159 54.545 0.00 0.00 0.00 2.74
719 720 2.513204 CGCCTCCTCGTCGTCCTA 60.513 66.667 0.00 0.00 0.00 2.94
722 723 4.517703 CGTCGCCTCCTCGTCGTC 62.518 72.222 0.00 0.00 36.56 4.20
860 878 1.612442 TTCCTCCTCCCAACTCCCG 60.612 63.158 0.00 0.00 0.00 5.14
957 980 4.800914 GCTGCTTCTGTTCTGGACTTCTAA 60.801 45.833 0.00 0.00 0.00 2.10
958 981 3.306364 GCTGCTTCTGTTCTGGACTTCTA 60.306 47.826 0.00 0.00 0.00 2.10
959 982 2.549778 GCTGCTTCTGTTCTGGACTTCT 60.550 50.000 0.00 0.00 0.00 2.85
960 983 1.803555 GCTGCTTCTGTTCTGGACTTC 59.196 52.381 0.00 0.00 0.00 3.01
961 984 1.141657 TGCTGCTTCTGTTCTGGACTT 59.858 47.619 0.00 0.00 0.00 3.01
1058 1128 2.023307 AGAGGAAGGGGACGGATTTAGA 60.023 50.000 0.00 0.00 0.00 2.10
1062 1132 0.691413 GGAGAGGAAGGGGACGGATT 60.691 60.000 0.00 0.00 0.00 3.01
1142 1212 1.602920 GGAAACCTCCAAAGCGCAAAG 60.603 52.381 11.47 0.00 41.96 2.77
1234 1304 1.579932 GCGACAGACGAGGAAGACA 59.420 57.895 0.00 0.00 45.77 3.41
1380 1451 3.787001 GGCGGGAGGGTGAGAAGG 61.787 72.222 0.00 0.00 0.00 3.46
1424 1502 2.569354 ATCGAGCAGAGGCCGATCC 61.569 63.158 0.00 0.00 44.47 3.36
1425 1503 3.046870 ATCGAGCAGAGGCCGATC 58.953 61.111 0.00 0.00 44.47 3.69
1449 1530 4.598894 CTCATCGGCTGCCTCCCG 62.599 72.222 17.92 3.19 46.88 5.14
1450 1531 2.134287 TACTCATCGGCTGCCTCCC 61.134 63.158 17.92 0.00 0.00 4.30
1451 1532 1.068250 GTACTCATCGGCTGCCTCC 59.932 63.158 17.92 0.00 0.00 4.30
1452 1533 1.319541 TAGTACTCATCGGCTGCCTC 58.680 55.000 17.92 0.00 0.00 4.70
1465 1546 2.818432 CGCCTACCGGATTCATAGTACT 59.182 50.000 9.46 0.00 0.00 2.73
1466 1547 2.670509 GCGCCTACCGGATTCATAGTAC 60.671 54.545 9.46 0.00 37.44 2.73
1493 1575 2.046314 CATCGACACCCACCCACC 60.046 66.667 0.00 0.00 0.00 4.61
1494 1576 1.375523 GTCATCGACACCCACCCAC 60.376 63.158 0.00 0.00 32.09 4.61
1495 1577 1.198094 ATGTCATCGACACCCACCCA 61.198 55.000 0.00 0.00 45.65 4.51
1496 1578 0.462047 GATGTCATCGACACCCACCC 60.462 60.000 0.00 0.00 45.65 4.61
1497 1579 3.065575 GATGTCATCGACACCCACC 57.934 57.895 0.00 0.00 45.65 4.61
1569 1651 8.087750 AGACTTTAACAGTTGAGAGATTCTGAG 58.912 37.037 0.00 0.00 35.01 3.35
1584 1666 4.625742 CCCACACACGATAGACTTTAACAG 59.374 45.833 0.00 0.00 41.38 3.16
1589 1671 4.020573 TGATTCCCACACACGATAGACTTT 60.021 41.667 0.00 0.00 41.38 2.66
1604 1686 6.572182 AGAAGAATCTGAAGATGATTCCCA 57.428 37.500 11.39 0.00 46.43 4.37
1653 1735 6.128172 ACAACACGGTACTAGTACAGTATCAC 60.128 42.308 30.15 13.71 40.41 3.06
1667 1749 4.033587 CCACAGCATAATACAACACGGTAC 59.966 45.833 0.00 0.00 0.00 3.34
1669 1751 3.006940 CCACAGCATAATACAACACGGT 58.993 45.455 0.00 0.00 0.00 4.83
1670 1752 3.266636 TCCACAGCATAATACAACACGG 58.733 45.455 0.00 0.00 0.00 4.94
1672 1754 6.683974 AGATTCCACAGCATAATACAACAC 57.316 37.500 0.00 0.00 0.00 3.32
1677 1759 9.765795 AAACTACTAGATTCCACAGCATAATAC 57.234 33.333 0.00 0.00 0.00 1.89
1682 1764 4.878397 GCAAACTACTAGATTCCACAGCAT 59.122 41.667 0.00 0.00 0.00 3.79
1683 1765 4.020218 AGCAAACTACTAGATTCCACAGCA 60.020 41.667 0.00 0.00 0.00 4.41
1687 1769 6.043411 CCTACAGCAAACTACTAGATTCCAC 58.957 44.000 0.00 0.00 0.00 4.02
1696 1778 7.112779 AGCAAATATTCCTACAGCAAACTACT 58.887 34.615 0.00 0.00 0.00 2.57
1697 1779 7.321745 AGCAAATATTCCTACAGCAAACTAC 57.678 36.000 0.00 0.00 0.00 2.73
1787 1874 3.440522 GGAGCACTAGAACAAAATCCACC 59.559 47.826 0.00 0.00 0.00 4.61
1869 1962 8.511604 AGATAAGTGTGATGTTGGGAAATAAG 57.488 34.615 0.00 0.00 0.00 1.73
1898 1991 3.306613 GTCAGCTAGGGTAAGGGTACAT 58.693 50.000 0.00 0.00 31.21 2.29
1930 2023 0.108041 CAACTCATTGGCAATGGGGC 60.108 55.000 36.00 0.00 43.84 5.80
2013 2107 6.375455 AGCAAACAGGATAAAACATAGGTGAG 59.625 38.462 0.00 0.00 0.00 3.51
2132 2239 9.062524 CAAATATCTCCGGGACAATATTTGTTA 57.937 33.333 28.40 9.02 45.52 2.41
2157 2264 7.867305 TCCAAAGTTAACAACACATACTTCA 57.133 32.000 8.61 0.00 0.00 3.02
2506 2619 1.675310 CACTTCCGGATGGCTTGCA 60.675 57.895 20.44 0.00 34.14 4.08
2551 2664 2.038164 AGAGAGCAGTGCATCAACAAGA 59.962 45.455 19.20 0.00 0.00 3.02
2563 2676 0.607620 GAGCCTTGTCAGAGAGCAGT 59.392 55.000 0.00 0.00 0.00 4.40
2683 2796 2.094130 GTCTGTTGCTAGGTACTGGGTC 60.094 54.545 0.00 0.00 41.52 4.46
2716 2829 1.284982 CTTGAGTTGTCTCCACGGCG 61.285 60.000 4.80 4.80 39.75 6.46
3034 3147 0.960364 GCGATGCAAACCCCTTCTCA 60.960 55.000 0.00 0.00 0.00 3.27
3046 3159 0.878086 TCAACAGAACACGCGATGCA 60.878 50.000 15.93 0.00 0.00 3.96
3142 3255 3.133014 CGTGGAGATCTGCCGGAT 58.867 61.111 12.15 0.00 37.37 4.18
3148 3261 4.193334 TCGGCGCGTGGAGATCTG 62.193 66.667 8.43 0.00 0.00 2.90
3178 3291 5.694231 AAAAGGATTTGAAAGGCAATTGC 57.306 34.783 22.47 22.47 39.02 3.56
3244 3357 7.167535 TGCTTCGATATATTTCATGATGGGAA 58.832 34.615 0.00 0.00 0.00 3.97
3283 3396 6.463995 ACACATTACCGCCATATGAATTTT 57.536 33.333 3.65 0.00 0.00 1.82
3350 3469 2.429250 TCAGTCTGGTTCGTGTTCTCAA 59.571 45.455 0.00 0.00 0.00 3.02
3375 3494 3.930336 CTGGATCACAGCTAAGTTCACA 58.070 45.455 0.00 0.00 40.97 3.58
3388 3507 3.119708 GGTTTGATTGCTCACTGGATCAC 60.120 47.826 0.00 0.00 0.00 3.06
3476 3597 5.556382 GCACATATACACACTAACACGCATC 60.556 44.000 0.00 0.00 0.00 3.91
3548 3673 0.610174 TCTCTGCAAGACGAAGGCAT 59.390 50.000 0.00 0.00 38.67 4.40
3588 3713 5.358160 GGGAGTAGCTAATTTTGCACAGATT 59.642 40.000 0.00 0.00 0.00 2.40
3610 3735 4.997395 CGTCAATTAATATGGACTGGAGGG 59.003 45.833 11.00 0.00 33.25 4.30
3618 3743 7.506114 ACTAAAGGAGCGTCAATTAATATGGA 58.494 34.615 0.00 0.00 0.00 3.41
3627 3752 4.002906 TCACAACTAAAGGAGCGTCAAT 57.997 40.909 0.00 0.00 0.00 2.57
3660 3786 9.744468 GGTACTAAACAGACATCAAATTTTTGT 57.256 29.630 3.72 3.72 39.18 2.83
3686 3812 2.219458 CAGGAGAGCAAGCATACCATG 58.781 52.381 0.00 0.00 0.00 3.66
3706 3920 4.564406 CCAGATGCATCTTCCTGGGTATAC 60.564 50.000 26.70 0.00 41.76 1.47
3740 3954 0.027063 CAAAACAAACGACGCGACCT 59.973 50.000 15.93 0.00 0.00 3.85
3774 3988 7.222224 AGCTCGTAAAATTCTCCACTAATTACG 59.778 37.037 8.40 8.40 43.05 3.18
3781 3995 4.003648 CCAAGCTCGTAAAATTCTCCACT 58.996 43.478 0.00 0.00 0.00 4.00
3786 4000 3.871594 CCGATCCAAGCTCGTAAAATTCT 59.128 43.478 0.00 0.00 34.36 2.40
3795 4009 1.227350 TGCATCCGATCCAAGCTCG 60.227 57.895 0.00 0.00 35.92 5.03
3834 4048 2.094854 AGTCCACTACATCGGTTCGAAC 60.095 50.000 20.14 20.14 39.99 3.95
3842 4056 1.137086 CCTCCCAAGTCCACTACATCG 59.863 57.143 0.00 0.00 0.00 3.84
3865 4079 3.194116 GGAAAGCTCATGGCAGATTCAAA 59.806 43.478 8.58 0.00 44.79 2.69
3889 4103 4.483476 AAAATTGGTACTCACTCGCAAC 57.517 40.909 0.00 0.00 0.00 4.17
3930 4149 4.866508 TCTGTGTTCGATCAGGTTTACT 57.133 40.909 11.09 0.00 33.13 2.24
3931 4150 5.465724 AGTTTCTGTGTTCGATCAGGTTTAC 59.534 40.000 11.09 2.86 33.13 2.01
3932 4151 5.607477 AGTTTCTGTGTTCGATCAGGTTTA 58.393 37.500 11.09 0.00 33.13 2.01
3945 4164 3.209410 CTCCTTGCTGAAGTTTCTGTGT 58.791 45.455 1.59 0.00 0.00 3.72
3967 4186 3.907894 TTGTTGTAACTCGGCCATTTC 57.092 42.857 2.24 0.00 0.00 2.17
3973 4192 4.483476 AGTCATTTTGTTGTAACTCGGC 57.517 40.909 0.00 0.00 0.00 5.54
4034 4254 5.652994 ACCGGCTATGCAAGAAAATAAAA 57.347 34.783 0.00 0.00 0.00 1.52
4053 4273 6.861055 AGCATAATTTGTTCTGTTTTGTACCG 59.139 34.615 0.00 0.00 0.00 4.02
4063 4283 6.688637 TGATCTCCAGCATAATTTGTTCTG 57.311 37.500 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.