Multiple sequence alignment - TraesCS5D01G340200

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 TraesCS5D01G340200 chr5D 100.000 4937 0 0 1 4937 428709497 428704561 0.000000e+00 9118.0
1 TraesCS5D01G340200 chr5D 90.865 208 16 2 4301 4505 329124706 329124913 4.870000e-70 276.0
2 TraesCS5D01G340200 chr5D 90.000 70 3 3 547 616 66974044 66973979 2.450000e-13 87.9
3 TraesCS5D01G340200 chr5D 88.571 70 4 4 547 616 412829174 412829239 1.140000e-11 82.4
4 TraesCS5D01G340200 chr5A 91.921 4221 182 65 238 4388 544541421 544537290 0.000000e+00 5758.0
5 TraesCS5D01G340200 chr5A 89.806 412 34 6 4528 4935 544535956 544535549 5.660000e-144 521.0
6 TraesCS5D01G340200 chr5A 90.741 162 13 2 1 161 544541607 544541447 1.080000e-51 215.0
7 TraesCS5D01G340200 chr5B 92.536 3403 139 42 1591 4937 517857792 517854449 0.000000e+00 4771.0
8 TraesCS5D01G340200 chr5B 88.464 1569 90 42 1 1541 517859298 517857793 0.000000e+00 1810.0
9 TraesCS5D01G340200 chr3B 91.346 208 15 2 4301 4505 201522389 201522182 1.050000e-71 281.0
10 TraesCS5D01G340200 chr2D 91.346 208 15 2 4301 4505 272798519 272798726 1.050000e-71 281.0
11 TraesCS5D01G340200 chr2D 88.060 67 4 3 550 616 75397921 75397859 5.300000e-10 76.8
12 TraesCS5D01G340200 chrUn 90.865 208 16 2 4301 4505 93416631 93416838 4.870000e-70 276.0
13 TraesCS5D01G340200 chr6D 90.865 208 16 2 4301 4505 168246910 168246703 4.870000e-70 276.0
14 TraesCS5D01G340200 chr6D 87.143 70 5 2 547 616 472139064 472139129 5.300000e-10 76.8
15 TraesCS5D01G340200 chr1D 90.865 208 16 2 4301 4505 144238418 144238211 4.870000e-70 276.0
16 TraesCS5D01G340200 chr1D 90.865 208 16 2 4301 4505 254521441 254521234 4.870000e-70 276.0
17 TraesCS5D01G340200 chr1A 90.865 208 16 2 4301 4505 584778824 584778617 4.870000e-70 276.0
18 TraesCS5D01G340200 chr1B 90.625 64 2 2 553 616 677283421 677283480 1.140000e-11 82.4
19 TraesCS5D01G340200 chr3D 84.524 84 7 5 535 616 454000668 454000747 1.470000e-10 78.7
20 TraesCS5D01G340200 chr3A 86.111 72 5 4 534 605 674751139 674751205 6.860000e-09 73.1


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 TraesCS5D01G340200 chr5D 428704561 428709497 4936 True 9118.000000 9118 100.000000 1 4937 1 chr5D.!!$R2 4936
1 TraesCS5D01G340200 chr5A 544535549 544541607 6058 True 2164.666667 5758 90.822667 1 4935 3 chr5A.!!$R1 4934
2 TraesCS5D01G340200 chr5B 517854449 517859298 4849 True 3290.500000 4771 90.500000 1 4937 2 chr5B.!!$R1 4936

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
196 198 0.250295 TTCTTTCCACGACCAGCCAG 60.250 55.000 0.00 0.0 0.00 4.85 F
1354 1383 0.396695 CTCTTCCAGGTACCGCCCTA 60.397 60.000 6.18 0.0 38.26 3.53 F
1495 1537 0.174162 GCCGTACGGATTGGTGTACT 59.826 55.000 37.62 0.0 38.99 2.73 F
1547 1589 0.537188 ACCATTGATTCGACGAGGCT 59.463 50.000 0.00 0.0 0.00 4.58 F
1548 1590 0.933097 CCATTGATTCGACGAGGCTG 59.067 55.000 0.00 0.0 0.00 4.85 F
3012 3098 1.345112 GGGAATGGGAAGGGGTAGAGA 60.345 57.143 0.00 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1439 0.466189 CCCCACTGCTTATCGCCAAT 60.466 55.000 0.00 0.0 38.05 3.16 R
3012 3098 0.253044 ATTAGCCTCACCACGTGCAT 59.747 50.000 10.91 0.0 32.98 3.96 R
3255 3341 0.912486 GACCACCATAGCCACCTCTT 59.088 55.000 0.00 0.0 0.00 2.85 R
3483 3590 2.572191 TAACAAGGGACGTAGATGCG 57.428 50.000 0.00 0.0 37.94 4.73 R
3491 3598 3.004862 AGCGGTTTATTAACAAGGGACG 58.995 45.455 0.00 0.0 35.92 4.79 R
4792 6117 0.319813 GCGGAAGTGCTTGGCATTTT 60.320 50.000 2.14 0.0 41.91 1.82 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
35 36 1.289160 ATGGTTTGGCTAGGCTCTGA 58.711 50.000 18.18 0.00 0.00 3.27
46 47 0.411452 AGGCTCTGACCCAGAAGAGA 59.589 55.000 3.92 0.00 42.15 3.10
151 153 2.573462 AGCTCTCTACCTGCATGGAAAA 59.427 45.455 8.91 0.00 39.71 2.29
174 176 1.232621 GGCAGTACAACCCCACGAAC 61.233 60.000 0.00 0.00 0.00 3.95
196 198 0.250295 TTCTTTCCACGACCAGCCAG 60.250 55.000 0.00 0.00 0.00 4.85
252 255 5.924356 TCGCATTTATGACCCAAGAATCTA 58.076 37.500 0.00 0.00 0.00 1.98
309 312 6.208644 ACAAGCAAAGACACATATGAACAAC 58.791 36.000 10.38 0.00 0.00 3.32
341 344 8.868522 ACCTAATCAAGAAGTGAAATCAATCA 57.131 30.769 0.00 0.00 40.50 2.57
526 536 5.088739 CCGAAAATGAATTTCTTGAGACGG 58.911 41.667 0.00 0.00 44.35 4.79
730 746 3.944233 AACCGTCGCGTTGGTTGC 61.944 61.111 28.06 4.01 46.41 4.17
1163 1192 1.248101 TTGCGTGGATCTGAGACGGA 61.248 55.000 8.23 3.58 33.68 4.69
1164 1193 1.226717 GCGTGGATCTGAGACGGAC 60.227 63.158 8.23 0.00 33.68 4.79
1165 1194 1.062685 CGTGGATCTGAGACGGACG 59.937 63.158 0.00 0.00 0.00 4.79
1166 1195 1.433879 GTGGATCTGAGACGGACGG 59.566 63.158 0.00 0.00 0.00 4.79
1167 1196 1.001269 TGGATCTGAGACGGACGGT 60.001 57.895 0.00 0.00 0.00 4.83
1352 1381 2.732619 CCTCTTCCAGGTACCGCCC 61.733 68.421 6.18 0.00 37.53 6.13
1353 1382 1.686110 CTCTTCCAGGTACCGCCCT 60.686 63.158 6.18 0.00 38.26 5.19
1354 1383 0.396695 CTCTTCCAGGTACCGCCCTA 60.397 60.000 6.18 0.00 38.26 3.53
1355 1384 0.685458 TCTTCCAGGTACCGCCCTAC 60.685 60.000 6.18 0.00 38.26 3.18
1358 1387 2.440796 CAGGTACCGCCCTACCGA 60.441 66.667 6.18 0.00 41.18 4.69
1359 1388 2.440980 AGGTACCGCCCTACCGAC 60.441 66.667 6.18 0.00 41.18 4.79
1360 1389 3.892581 GGTACCGCCCTACCGACG 61.893 72.222 0.00 0.00 0.00 5.12
1361 1390 4.559229 GTACCGCCCTACCGACGC 62.559 72.222 0.00 0.00 0.00 5.19
1410 1439 4.263572 CCCGGTTGTGTGGCCTGA 62.264 66.667 3.32 0.00 0.00 3.86
1412 1441 1.603455 CCGGTTGTGTGGCCTGATT 60.603 57.895 3.32 0.00 0.00 2.57
1489 1523 1.153046 ATTGGGCCGTACGGATTGG 60.153 57.895 37.62 11.43 37.50 3.16
1493 1535 1.516892 GGCCGTACGGATTGGTGTA 59.483 57.895 37.62 0.00 37.50 2.90
1494 1536 0.807275 GGCCGTACGGATTGGTGTAC 60.807 60.000 37.62 15.83 38.03 2.90
1495 1537 0.174162 GCCGTACGGATTGGTGTACT 59.826 55.000 37.62 0.00 38.99 2.73
1496 1538 1.404583 GCCGTACGGATTGGTGTACTT 60.405 52.381 37.62 0.00 38.99 2.24
1497 1539 2.159254 GCCGTACGGATTGGTGTACTTA 60.159 50.000 37.62 0.00 38.99 2.24
1498 1540 3.699067 CCGTACGGATTGGTGTACTTAG 58.301 50.000 30.64 0.00 38.99 2.18
1499 1541 3.129287 CCGTACGGATTGGTGTACTTAGT 59.871 47.826 30.64 0.00 38.99 2.24
1500 1542 4.335315 CCGTACGGATTGGTGTACTTAGTA 59.665 45.833 30.64 0.00 38.99 1.82
1501 1543 5.266242 CGTACGGATTGGTGTACTTAGTAC 58.734 45.833 14.99 14.99 38.99 2.73
1502 1544 4.361451 ACGGATTGGTGTACTTAGTACG 57.639 45.455 16.48 5.78 41.41 3.67
1505 1547 3.181497 GGATTGGTGTACTTAGTACGCGA 60.181 47.826 24.03 19.73 46.55 5.87
1546 1588 1.327764 GAACCATTGATTCGACGAGGC 59.672 52.381 0.00 0.00 0.00 4.70
1547 1589 0.537188 ACCATTGATTCGACGAGGCT 59.463 50.000 0.00 0.00 0.00 4.58
1548 1590 0.933097 CCATTGATTCGACGAGGCTG 59.067 55.000 0.00 0.00 0.00 4.85
1560 1602 1.379642 CGAGGCTGGGAGGAAATTGC 61.380 60.000 0.00 0.00 0.00 3.56
1727 1771 7.078228 GCGAATTAGGCATAGTTTTTGGATAG 58.922 38.462 0.00 0.00 0.00 2.08
1763 1807 7.652524 ACAGATAGATGTTGTACTCTCATGT 57.347 36.000 0.00 0.00 0.00 3.21
1764 1808 7.711846 ACAGATAGATGTTGTACTCTCATGTC 58.288 38.462 0.00 0.00 0.00 3.06
1785 1829 4.963953 GTCGTGTGATTTGTCACTTCAAAG 59.036 41.667 9.64 0.00 40.00 2.77
1921 1971 4.913335 TCTCTAATAATTGACGGCGACT 57.087 40.909 16.62 0.00 0.00 4.18
1956 2006 3.574284 TGTTTTGATGATTTCGCCTGG 57.426 42.857 0.00 0.00 0.00 4.45
1986 2041 4.589216 TGAGTTTCCTTTGATGGCTTTG 57.411 40.909 0.00 0.00 0.00 2.77
1992 2047 8.189119 AGTTTCCTTTGATGGCTTTGTTTATA 57.811 30.769 0.00 0.00 0.00 0.98
1994 2049 7.775053 TTCCTTTGATGGCTTTGTTTATAGT 57.225 32.000 0.00 0.00 0.00 2.12
2014 2069 4.533222 AGTTGTTCGATAAAAACGCAAGG 58.467 39.130 0.00 0.00 46.39 3.61
2017 2072 3.315749 TGTTCGATAAAAACGCAAGGGTT 59.684 39.130 0.00 0.00 46.39 4.11
2018 2073 3.546002 TCGATAAAAACGCAAGGGTTG 57.454 42.857 3.17 0.00 46.39 3.77
2030 2085 2.801063 CAAGGGTTGCGATGCTTTATG 58.199 47.619 0.00 0.00 0.00 1.90
2031 2086 2.418368 AGGGTTGCGATGCTTTATGA 57.582 45.000 0.00 0.00 0.00 2.15
2032 2087 2.936202 AGGGTTGCGATGCTTTATGAT 58.064 42.857 0.00 0.00 0.00 2.45
2033 2088 3.290710 AGGGTTGCGATGCTTTATGATT 58.709 40.909 0.00 0.00 0.00 2.57
2034 2089 3.067180 AGGGTTGCGATGCTTTATGATTG 59.933 43.478 0.00 0.00 0.00 2.67
2035 2090 2.791004 GGTTGCGATGCTTTATGATTGC 59.209 45.455 0.00 0.00 0.00 3.56
2036 2091 3.437428 GTTGCGATGCTTTATGATTGCA 58.563 40.909 0.00 0.00 37.23 4.08
2037 2092 3.069074 TGCGATGCTTTATGATTGCAC 57.931 42.857 0.00 0.00 39.63 4.57
2038 2093 2.422832 TGCGATGCTTTATGATTGCACA 59.577 40.909 0.00 0.00 39.63 4.57
2082 2137 4.106029 GGCTGATGCTTTGCCATATATG 57.894 45.455 5.68 5.68 45.46 1.78
2216 2271 5.940192 TGTGAACTATGCATTCGACTTTT 57.060 34.783 3.54 0.00 0.00 2.27
2352 2407 3.371965 AGGCCTACTTCCGTAAGAATCA 58.628 45.455 1.29 0.00 43.02 2.57
2438 2509 2.418976 CTGTGCTCTTGTGATGACATGG 59.581 50.000 0.00 0.00 30.13 3.66
2561 2637 7.990314 TGCTAGCTGTATATCTGATACTAGGAG 59.010 40.741 17.23 4.92 0.00 3.69
2766 2852 8.496707 AACATTGCAAATTGGATTATTCTTCC 57.503 30.769 1.71 0.00 0.00 3.46
2772 2858 5.458041 AATTGGATTATTCTTCCGCATGG 57.542 39.130 0.00 0.00 35.94 3.66
2806 2892 8.122952 GGTTGAGTTAATTGTATGTGCAGATAC 58.877 37.037 23.45 23.45 0.00 2.24
2876 2962 3.737559 ATGAAGAAGGTATTGGGCACA 57.262 42.857 0.00 0.00 0.00 4.57
3012 3098 1.345112 GGGAATGGGAAGGGGTAGAGA 60.345 57.143 0.00 0.00 0.00 3.10
3160 3246 2.241941 TGGGAAAATGAGCATGCTCCTA 59.758 45.455 37.92 24.80 42.09 2.94
3491 3598 4.658071 CCAAATTGGTTGTACGCATCTAC 58.342 43.478 3.34 0.00 35.23 2.59
3525 3635 2.133742 AACCGCTGCATCTGTGTTGC 62.134 55.000 0.00 0.00 40.55 4.17
3803 3913 4.616553 TGACTAGATTTGTAGGGGTAGCA 58.383 43.478 0.00 0.00 0.00 3.49
3827 3937 5.689961 ACCGTTATGATTGTGCTTTGTTTTC 59.310 36.000 0.00 0.00 0.00 2.29
4064 4174 6.207691 TGGAATAGGAAAAACATAGCTTGC 57.792 37.500 0.00 0.00 0.00 4.01
4230 4342 6.153340 ACAAAATGTTCAATATCACAGGGAGG 59.847 38.462 0.00 0.00 0.00 4.30
4283 4399 1.598701 GGGCTGCCTTGTGGTCATTC 61.599 60.000 19.68 0.00 35.27 2.67
4284 4400 0.610232 GGCTGCCTTGTGGTCATTCT 60.610 55.000 12.43 0.00 35.27 2.40
4285 4401 0.524862 GCTGCCTTGTGGTCATTCTG 59.475 55.000 0.00 0.00 35.27 3.02
4289 4416 1.270550 GCCTTGTGGTCATTCTGGTTG 59.729 52.381 0.00 0.00 35.27 3.77
4300 4427 6.206634 TGGTCATTCTGGTTGAACAAATCTAC 59.793 38.462 0.00 0.00 37.84 2.59
4365 4604 8.141909 GGTTATAACTGATAAAAAGGCAATCCC 58.858 37.037 15.05 0.00 31.66 3.85
4370 4609 5.779771 ACTGATAAAAAGGCAATCCCAAAGA 59.220 36.000 0.00 0.00 35.39 2.52
4376 4615 2.529632 AGGCAATCCCAAAGAAACTCC 58.470 47.619 0.00 0.00 35.39 3.85
4386 4625 4.081142 CCCAAAGAAACTCCAGTTTTTGGT 60.081 41.667 22.70 4.92 45.43 3.67
4394 4633 2.507339 CCAGTTTTTGGTGCGATTGT 57.493 45.000 0.00 0.00 42.41 2.71
4551 5875 3.637432 CTGATACTGCGAGGTGATTCTC 58.363 50.000 0.00 0.00 0.00 2.87
4615 5939 3.518634 AGTCTTTCTCGATGAAGAGCC 57.481 47.619 9.99 2.14 38.12 4.70
4694 6018 1.523711 CCTCGGCGGTGCATTGTAT 60.524 57.895 7.21 0.00 0.00 2.29
4695 6019 1.643292 CTCGGCGGTGCATTGTATG 59.357 57.895 7.21 0.00 0.00 2.39
4755 6079 0.944311 GGTCGTACCGCCATGCTATG 60.944 60.000 0.00 0.00 0.00 2.23
4791 6116 0.248417 CGGTGAGCTCTGATGTCTCG 60.248 60.000 16.19 3.64 0.00 4.04
4792 6117 1.098869 GGTGAGCTCTGATGTCTCGA 58.901 55.000 16.19 0.00 0.00 4.04
4796 6121 4.180057 GTGAGCTCTGATGTCTCGAAAAT 58.820 43.478 16.19 0.00 0.00 1.82
4797 6122 4.032672 GTGAGCTCTGATGTCTCGAAAATG 59.967 45.833 16.19 0.00 0.00 2.32
4798 6123 2.935201 AGCTCTGATGTCTCGAAAATGC 59.065 45.455 0.00 0.00 0.00 3.56
4800 6125 3.264947 CTCTGATGTCTCGAAAATGCCA 58.735 45.455 0.00 0.00 0.00 4.92
4802 6127 3.686241 TCTGATGTCTCGAAAATGCCAAG 59.314 43.478 0.00 0.00 0.00 3.61
4919 6246 1.463444 GGTGCTTGACGGACAATGTAC 59.537 52.381 0.00 0.00 37.88 2.90
4928 6255 1.134640 CGGACAATGTACGAATCCCCA 60.135 52.381 13.54 0.00 43.34 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 5.163152 ACAAGTTTCAAGATCTCTTCTGGGT 60.163 40.000 0.00 0.00 33.93 4.51
46 47 5.825593 TCTAGTCCCACAAGTTTCAAGAT 57.174 39.130 0.00 0.00 0.00 2.40
151 153 0.179001 GTGGGGTTGTACTGCCAACT 60.179 55.000 9.68 0.00 43.36 3.16
174 176 0.804989 GCTGGTCGTGGAAAGAATGG 59.195 55.000 0.00 0.00 0.00 3.16
196 198 3.879180 ATGGTTCGTGGGGTTGGGC 62.879 63.158 0.00 0.00 0.00 5.36
225 227 1.378531 TGGGTCATAAATGCGAGTGC 58.621 50.000 0.00 0.00 43.20 4.40
252 255 0.375803 GTCGGTGCCGCGAAATATTT 59.624 50.000 8.23 0.00 39.59 1.40
309 312 7.510549 TTCACTTCTTGATTAGGTTTGAAGG 57.489 36.000 0.00 0.00 36.28 3.46
340 343 5.946972 TCCTCTTCTCTTCCTGTAGTACTTG 59.053 44.000 0.00 0.00 0.00 3.16
341 344 6.012333 TCTCCTCTTCTCTTCCTGTAGTACTT 60.012 42.308 0.00 0.00 0.00 2.24
349 352 5.940617 TCTATCTCTCCTCTTCTCTTCCTG 58.059 45.833 0.00 0.00 0.00 3.86
526 536 3.024547 GGGCCAGAGGGAGTAATTTTTC 58.975 50.000 4.39 0.00 35.59 2.29
659 675 1.873591 CGACCCAACAGAAGAAACTGG 59.126 52.381 0.00 0.00 41.59 4.00
730 746 2.556286 GAAGGGCTTTCCAAGGACG 58.444 57.895 0.00 0.00 38.24 4.79
774 800 2.361104 TGTGCGGCTGGGATTTCC 60.361 61.111 0.00 0.00 0.00 3.13
1163 1192 1.820481 CGACCAAACCAACCACCGT 60.820 57.895 0.00 0.00 0.00 4.83
1164 1193 3.027292 CGACCAAACCAACCACCG 58.973 61.111 0.00 0.00 0.00 4.94
1165 1194 2.725641 GCGACCAAACCAACCACC 59.274 61.111 0.00 0.00 0.00 4.61
1166 1195 2.330041 CGCGACCAAACCAACCAC 59.670 61.111 0.00 0.00 0.00 4.16
1167 1196 3.587933 GCGCGACCAAACCAACCA 61.588 61.111 12.10 0.00 0.00 3.67
1361 1390 1.135286 GCGATTCAAAGGGGCTGAAAG 60.135 52.381 0.00 0.00 36.43 2.62
1410 1439 0.466189 CCCCACTGCTTATCGCCAAT 60.466 55.000 0.00 0.00 38.05 3.16
1412 1441 1.847798 AACCCCACTGCTTATCGCCA 61.848 55.000 0.00 0.00 38.05 5.69
1502 1544 2.587612 TGAAAACACACGCTTATCGC 57.412 45.000 0.00 0.00 43.23 4.58
1505 1547 3.058570 TCGCATTGAAAACACACGCTTAT 60.059 39.130 0.00 0.00 0.00 1.73
1541 1583 1.379642 GCAATTTCCTCCCAGCCTCG 61.380 60.000 0.00 0.00 0.00 4.63
1544 1586 2.234143 GATAGCAATTTCCTCCCAGCC 58.766 52.381 0.00 0.00 0.00 4.85
1545 1587 2.158549 AGGATAGCAATTTCCTCCCAGC 60.159 50.000 0.00 0.00 37.89 4.85
1546 1588 3.872459 AGGATAGCAATTTCCTCCCAG 57.128 47.619 0.00 0.00 37.89 4.45
1560 1602 7.716799 AGGCATCAGAGTAATAAGAGGATAG 57.283 40.000 0.00 0.00 0.00 2.08
1569 1611 5.815581 ACCAAACAAGGCATCAGAGTAATA 58.184 37.500 0.00 0.00 0.00 0.98
1570 1612 4.666512 ACCAAACAAGGCATCAGAGTAAT 58.333 39.130 0.00 0.00 0.00 1.89
1571 1613 4.098914 ACCAAACAAGGCATCAGAGTAA 57.901 40.909 0.00 0.00 0.00 2.24
1785 1829 3.551082 CACGATCTCAGATTCTTCAGTGC 59.449 47.826 0.00 0.00 0.00 4.40
1921 1971 6.714356 TCATCAAAACATGGATGTGACTAACA 59.286 34.615 0.00 0.00 44.79 2.41
1956 2006 5.545658 TCAAAGGAAACTCATAATCGCAC 57.454 39.130 0.00 0.00 42.68 5.34
1986 2041 8.644264 TGCGTTTTTATCGAACAACTATAAAC 57.356 30.769 0.00 0.00 29.86 2.01
1992 2047 4.533222 CCTTGCGTTTTTATCGAACAACT 58.467 39.130 0.00 0.00 0.00 3.16
1994 2049 3.315749 ACCCTTGCGTTTTTATCGAACAA 59.684 39.130 0.00 0.00 0.00 2.83
2014 2069 2.791004 GCAATCATAAAGCATCGCAACC 59.209 45.455 0.00 0.00 0.00 3.77
2017 2072 2.422832 TGTGCAATCATAAAGCATCGCA 59.577 40.909 0.00 0.00 40.78 5.10
2018 2073 2.785477 GTGTGCAATCATAAAGCATCGC 59.215 45.455 0.00 0.00 40.78 4.58
2019 2074 4.018649 TGTGTGCAATCATAAAGCATCG 57.981 40.909 0.00 0.00 40.78 3.84
2020 2075 4.990257 ACTGTGTGCAATCATAAAGCATC 58.010 39.130 0.00 0.00 40.78 3.91
2021 2076 5.395682 AACTGTGTGCAATCATAAAGCAT 57.604 34.783 0.00 0.00 40.78 3.79
2022 2077 4.852134 AACTGTGTGCAATCATAAAGCA 57.148 36.364 0.00 0.00 35.63 3.91
2023 2078 5.463061 ACAAAACTGTGTGCAATCATAAAGC 59.537 36.000 0.00 0.00 0.00 3.51
2024 2079 7.467557 AACAAAACTGTGTGCAATCATAAAG 57.532 32.000 0.00 0.00 0.00 1.85
2026 2081 7.840342 AAAACAAAACTGTGTGCAATCATAA 57.160 28.000 0.00 0.00 0.00 1.90
2027 2082 7.840342 AAAAACAAAACTGTGTGCAATCATA 57.160 28.000 0.00 0.00 0.00 2.15
2028 2083 6.740411 AAAAACAAAACTGTGTGCAATCAT 57.260 29.167 0.00 0.00 0.00 2.45
2029 2084 7.332926 ACATAAAAACAAAACTGTGTGCAATCA 59.667 29.630 0.00 0.00 0.00 2.57
2030 2085 7.683746 ACATAAAAACAAAACTGTGTGCAATC 58.316 30.769 0.00 0.00 0.00 2.67
2031 2086 7.608308 ACATAAAAACAAAACTGTGTGCAAT 57.392 28.000 0.00 0.00 0.00 3.56
2032 2087 7.386299 AGAACATAAAAACAAAACTGTGTGCAA 59.614 29.630 0.00 0.00 0.00 4.08
2033 2088 6.870965 AGAACATAAAAACAAAACTGTGTGCA 59.129 30.769 0.00 0.00 0.00 4.57
2034 2089 7.148656 ACAGAACATAAAAACAAAACTGTGTGC 60.149 33.333 0.00 0.00 35.31 4.57
2035 2090 8.161610 CACAGAACATAAAAACAAAACTGTGTG 58.838 33.333 0.41 0.00 43.89 3.82
2036 2091 7.330700 CCACAGAACATAAAAACAAAACTGTGT 59.669 33.333 17.70 0.00 45.91 3.72
2037 2092 7.673776 GCCACAGAACATAAAAACAAAACTGTG 60.674 37.037 1.23 1.23 46.48 3.66
2038 2093 6.312672 GCCACAGAACATAAAAACAAAACTGT 59.687 34.615 0.00 0.00 36.69 3.55
2082 2137 1.873591 CGCAACCCTTATCCTGTATGC 59.126 52.381 0.00 0.00 0.00 3.14
2414 2485 2.299867 TGTCATCACAAGAGCACAGCTA 59.700 45.455 0.00 0.00 39.88 3.32
2438 2509 1.747924 GCCTGCAGGGAGAAAAGATTC 59.252 52.381 33.46 8.84 37.23 2.52
2766 2852 3.470709 ACTCAACCTATCATTCCATGCG 58.529 45.455 0.00 0.00 0.00 4.73
2806 2892 0.464013 CAGCAGGCAGAGGAGATTGG 60.464 60.000 0.00 0.00 0.00 3.16
3012 3098 0.253044 ATTAGCCTCACCACGTGCAT 59.747 50.000 10.91 0.00 32.98 3.96
3160 3246 1.221635 TACCCATTGCCTGCATAGGT 58.778 50.000 11.45 11.45 46.41 3.08
3255 3341 0.912486 GACCACCATAGCCACCTCTT 59.088 55.000 0.00 0.00 0.00 2.85
3483 3590 2.572191 TAACAAGGGACGTAGATGCG 57.428 50.000 0.00 0.00 37.94 4.73
3491 3598 3.004862 AGCGGTTTATTAACAAGGGACG 58.995 45.455 0.00 0.00 35.92 4.79
3525 3635 3.403057 CGACCACGACCTGCAACG 61.403 66.667 0.00 6.16 42.66 4.10
3803 3913 4.846779 AACAAAGCACAATCATAACGGT 57.153 36.364 0.00 0.00 0.00 4.83
3827 3937 8.994429 ACAATTAGTCTGACATCTACTTTGAG 57.006 34.615 10.88 0.00 0.00 3.02
3914 4024 4.642437 TGGCACAATGTAACAGAGAACAAA 59.358 37.500 0.00 0.00 31.92 2.83
3984 4094 9.394477 AGCGAAAAGAAATCAAATTGTAAGTAC 57.606 29.630 0.00 0.00 0.00 2.73
4098 4208 9.136952 GACTGATCTTCAAAGAAAAATCATTGG 57.863 33.333 0.00 0.00 38.77 3.16
4218 4330 2.477104 TGAGATGCCTCCCTGTGATA 57.523 50.000 0.00 0.00 38.66 2.15
4256 4368 0.409484 ACAAGGCAGCCCCATAGTTT 59.591 50.000 8.22 0.00 35.39 2.66
4266 4382 0.524862 CAGAATGACCACAAGGCAGC 59.475 55.000 0.00 0.00 39.69 5.25
4283 4399 5.465390 TGTCTTCGTAGATTTGTTCAACCAG 59.535 40.000 0.00 0.00 35.04 4.00
4284 4400 5.361427 TGTCTTCGTAGATTTGTTCAACCA 58.639 37.500 0.00 0.00 35.04 3.67
4285 4401 5.465724 ACTGTCTTCGTAGATTTGTTCAACC 59.534 40.000 0.00 0.00 35.04 3.77
4300 4427 8.182227 TCATAGCGGATTATTATACTGTCTTCG 58.818 37.037 0.00 0.00 0.00 3.79
4376 4615 3.443037 TCAACAATCGCACCAAAAACTG 58.557 40.909 0.00 0.00 0.00 3.16
4386 4625 3.673902 TCTCATTTCCTCAACAATCGCA 58.326 40.909 0.00 0.00 0.00 5.10
4394 4633 9.927668 GGTAAAATTCAATTCTCATTTCCTCAA 57.072 29.630 0.00 0.00 0.00 3.02
4551 5875 3.127895 ACGAGAATCTCAAGAGGAAGACG 59.872 47.826 11.18 0.00 0.00 4.18
4694 6018 2.438795 GCAACCCCCTAGCCAACA 59.561 61.111 0.00 0.00 0.00 3.33
4769 6094 1.079543 ACATCAGAGCTCACCGTGC 60.080 57.895 17.77 0.00 0.00 5.34
4771 6096 0.814457 GAGACATCAGAGCTCACCGT 59.186 55.000 17.77 7.15 0.00 4.83
4791 6116 1.701704 CGGAAGTGCTTGGCATTTTC 58.298 50.000 2.14 6.49 41.91 2.29
4792 6117 0.319813 GCGGAAGTGCTTGGCATTTT 60.320 50.000 2.14 0.00 41.91 1.82
4802 6127 3.435186 GAGGGCAAGCGGAAGTGC 61.435 66.667 0.00 0.00 40.14 4.40
4859 6184 3.845259 GCCCTACCGCGACATCCA 61.845 66.667 8.23 0.00 0.00 3.41
4903 6228 3.306166 GGATTCGTACATTGTCCGTCAAG 59.694 47.826 1.62 0.00 39.55 3.02


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

AutoCloner maintained by Alex Coulton.