Multiple sequence alignment - TraesCS6A01G261500

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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 TraesCS6A01G261500 chr6A 100.000 6158 0 0 1 6158 484858028 484851871 0.000000e+00 11372
1 TraesCS6A01G261500 chr6D 94.435 5265 192 53 907 6150 344309678 344304494 0.000000e+00 8006
2 TraesCS6A01G261500 chr6D 87.309 654 39 22 282 914 344332918 344332288 0.000000e+00 708
3 TraesCS6A01G261500 chr6D 95.968 248 8 2 29 276 344333252 344333007 9.610000e-108 401
4 TraesCS6A01G261500 chr6B 95.650 2322 76 17 1696 3998 519852436 519850121 0.000000e+00 3705
5 TraesCS6A01G261500 chr6B 93.862 1450 71 14 4698 6142 519847652 519846216 0.000000e+00 2169
6 TraesCS6A01G261500 chr6B 94.697 660 20 5 3995 4642 519848301 519847645 0.000000e+00 1011
7 TraesCS6A01G261500 chr6B 88.350 824 42 21 280 1067 520086302 520085497 0.000000e+00 941
8 TraesCS6A01G261500 chr6B 88.253 647 49 9 1059 1697 519853093 519852466 0.000000e+00 749
9 TraesCS6A01G261500 chr6B 92.308 299 16 4 8 302 520086637 520086342 9.550000e-113 418
10 TraesCS6A01G261500 chr2D 88.584 219 17 5 5943 6158 197870567 197870780 6.120000e-65 259
11 TraesCS6A01G261500 chr1D 82.741 197 24 4 5951 6142 462485861 462485670 3.820000e-37 167
12 TraesCS6A01G261500 chr2A 80.296 203 24 7 5941 6143 603369611 603369425 8.320000e-29 139
13 TraesCS6A01G261500 chr7D 79.808 208 19 12 5941 6147 52698464 52698279 5.010000e-26 130


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 TraesCS6A01G261500 chr6A 484851871 484858028 6157 True 11372.0 11372 100.0000 1 6158 1 chr6A.!!$R1 6157
1 TraesCS6A01G261500 chr6D 344304494 344309678 5184 True 8006.0 8006 94.4350 907 6150 1 chr6D.!!$R1 5243
2 TraesCS6A01G261500 chr6D 344332288 344333252 964 True 554.5 708 91.6385 29 914 2 chr6D.!!$R2 885
3 TraesCS6A01G261500 chr6B 519846216 519853093 6877 True 1908.5 3705 93.1155 1059 6142 4 chr6B.!!$R1 5083
4 TraesCS6A01G261500 chr6B 520085497 520086637 1140 True 679.5 941 90.3290 8 1067 2 chr6B.!!$R2 1059

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
753 877 0.105039 GTCATAGGGGCCTTGTCTCG 59.895 60.00 0.84 0.00 0.00 4.04 F
1054 1193 0.107081 TTCGTTCTTTCCGCCTTCCA 59.893 50.00 0.00 0.00 0.00 3.53 F
2077 2265 0.249531 TCAGTTTAGCACGCGGTTGA 60.250 50.00 12.47 0.00 0.00 3.18 F
2078 2266 0.796312 CAGTTTAGCACGCGGTTGAT 59.204 50.00 12.47 0.88 0.00 2.57 F
3368 3570 1.032014 TGTTGGCAGCTGGAAAGAAC 58.968 50.00 17.12 0.00 0.00 3.01 F
4527 6587 3.876914 AGATTCAAGTGAAACAACGCAGA 59.123 39.13 0.00 0.00 41.43 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2476 2664 0.457337 GCGCAAGAAATCCAGCCTTG 60.457 55.000 0.30 0.0 40.00 3.61 R
2732 2920 0.683973 CCTGAAGATCTCCATCCGGG 59.316 60.000 0.00 0.0 38.37 5.73 R
3132 3320 0.178998 CTCCATGAGAATGCCCCAGG 60.179 60.000 0.00 0.0 0.00 4.45 R
4024 6051 1.815003 CAGGCTTCTGGAAACCATCAC 59.185 52.381 5.70 0.0 34.96 3.06 R
4539 6599 2.803956 TGGAAATCCTTCGTCGTTTCAC 59.196 45.455 0.44 0.0 36.82 3.18 R
5858 7922 0.519519 TATGTGCGGAAAAAGCGTGG 59.480 50.000 0.00 0.0 37.44 4.94 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
205 206 2.093973 CGTTCCACTTCCTGCAGACTAT 60.094 50.000 17.39 0.00 0.00 2.12
210 211 3.452474 CACTTCCTGCAGACTATACAGC 58.548 50.000 17.39 0.00 0.00 4.40
305 370 3.064931 GAGTAACGGAGGACTTTTGGTG 58.935 50.000 0.00 0.00 0.00 4.17
340 447 9.347934 GATAATAGGATGTCGACATAAGAAGTG 57.652 37.037 30.04 0.00 36.57 3.16
352 459 4.082136 ACATAAGAAGTGACGGAGGAGTTC 60.082 45.833 0.00 0.00 0.00 3.01
468 575 1.069765 CCGTCCATGGGAGGAATCG 59.930 63.158 18.09 9.18 39.66 3.34
588 698 4.653888 AAAGGTCGTTGGCCCCGG 62.654 66.667 11.51 0.00 0.00 5.73
671 795 5.760253 ACATTCACAAAAGAAGACGATCTGT 59.240 36.000 0.00 0.00 0.00 3.41
683 807 1.450312 GATCTGTGCACCTTCCCGG 60.450 63.158 15.69 0.00 39.35 5.73
745 869 4.256180 CTGGCGGTCATAGGGGCC 62.256 72.222 0.00 0.00 45.76 5.80
746 870 4.815973 TGGCGGTCATAGGGGCCT 62.816 66.667 0.84 0.00 45.75 5.19
747 871 3.489513 GGCGGTCATAGGGGCCTT 61.490 66.667 0.84 0.00 42.29 4.35
750 874 1.146263 CGGTCATAGGGGCCTTGTC 59.854 63.158 0.84 0.00 0.00 3.18
752 876 0.470341 GGTCATAGGGGCCTTGTCTC 59.530 60.000 0.84 0.00 0.00 3.36
753 877 0.105039 GTCATAGGGGCCTTGTCTCG 59.895 60.000 0.84 0.00 0.00 4.04
802 940 1.664965 GAGCGGCGATATGACACCC 60.665 63.158 12.98 0.00 0.00 4.61
972 1110 0.537188 CTCCATGGCAGTTCGTAGGT 59.463 55.000 6.96 0.00 0.00 3.08
973 1111 1.754803 CTCCATGGCAGTTCGTAGGTA 59.245 52.381 6.96 0.00 0.00 3.08
974 1112 1.754803 TCCATGGCAGTTCGTAGGTAG 59.245 52.381 6.96 0.00 0.00 3.18
975 1113 1.202533 CCATGGCAGTTCGTAGGTAGG 60.203 57.143 0.00 0.00 0.00 3.18
976 1114 0.464452 ATGGCAGTTCGTAGGTAGGC 59.536 55.000 0.00 0.00 0.00 3.93
977 1115 1.143401 GGCAGTTCGTAGGTAGGCC 59.857 63.158 0.00 0.00 0.00 5.19
978 1116 1.226888 GCAGTTCGTAGGTAGGCCG 60.227 63.158 0.00 0.00 40.50 6.13
979 1117 1.941999 GCAGTTCGTAGGTAGGCCGT 61.942 60.000 0.00 0.00 40.50 5.68
980 1118 1.382522 CAGTTCGTAGGTAGGCCGTA 58.617 55.000 0.00 0.00 40.50 4.02
981 1119 1.332997 CAGTTCGTAGGTAGGCCGTAG 59.667 57.143 0.00 0.00 40.50 3.51
993 1131 3.458163 CCGTAGGCGCCTTCCTCA 61.458 66.667 37.74 14.26 46.14 3.86
1009 1147 4.255833 TCCTCATTGCAAATGTGGTTTC 57.744 40.909 19.90 0.00 35.04 2.78
1041 1180 4.325472 AGATTCGTTTACGGACATTCGTTC 59.675 41.667 2.09 0.00 43.59 3.95
1054 1193 0.107081 TTCGTTCTTTCCGCCTTCCA 59.893 50.000 0.00 0.00 0.00 3.53
1147 1286 2.901042 CCCCCTCGGCTCTTGTAC 59.099 66.667 0.00 0.00 0.00 2.90
1497 1636 2.367107 GTCTCCCCTCCCCCTTCC 60.367 72.222 0.00 0.00 0.00 3.46
1531 1672 2.079925 GTTGATGTTGCCAGTCTCTCC 58.920 52.381 0.00 0.00 0.00 3.71
1595 1742 4.708177 ACATATTTCAGGTCGCTAGCATT 58.292 39.130 16.45 0.00 0.00 3.56
1618 1765 2.291282 TGTTATCCGGCCCTCATTTGTT 60.291 45.455 0.00 0.00 0.00 2.83
1619 1766 2.758423 GTTATCCGGCCCTCATTTGTTT 59.242 45.455 0.00 0.00 0.00 2.83
1620 1767 1.474330 ATCCGGCCCTCATTTGTTTC 58.526 50.000 0.00 0.00 0.00 2.78
1621 1768 0.610785 TCCGGCCCTCATTTGTTTCC 60.611 55.000 0.00 0.00 0.00 3.13
1649 1796 6.484308 TGCTAATACCCCTAATTTTAGCGTTC 59.516 38.462 9.89 0.00 44.78 3.95
1732 1909 2.234896 TTGGTGGGCATGAACATGAT 57.765 45.000 17.40 0.00 41.20 2.45
1800 1981 6.484643 ACACTTATAGCTGCTGATTTGTATGG 59.515 38.462 13.43 0.00 0.00 2.74
1860 2048 7.297936 TCTGTTCCACTGTGAGAAATAACTA 57.702 36.000 9.86 0.00 0.00 2.24
1866 2054 8.547967 TCCACTGTGAGAAATAACTAAACATC 57.452 34.615 9.86 0.00 0.00 3.06
1937 2125 2.286365 TCCTGGTGAAATGTCAACCC 57.714 50.000 0.00 0.00 41.16 4.11
2035 2223 3.961480 ATGCCTTTCCTTTTTAGCACC 57.039 42.857 0.00 0.00 32.26 5.01
2077 2265 0.249531 TCAGTTTAGCACGCGGTTGA 60.250 50.000 12.47 0.00 0.00 3.18
2078 2266 0.796312 CAGTTTAGCACGCGGTTGAT 59.204 50.000 12.47 0.88 0.00 2.57
2284 2472 7.298374 TCTCCAGGCTCAGTTATAGATCTTTA 58.702 38.462 0.00 0.00 0.00 1.85
2465 2653 1.833630 CTGACTGCTGGGTATCTGGAA 59.166 52.381 0.00 0.00 0.00 3.53
2476 2664 4.137543 GGGTATCTGGAAATGATGTGGAC 58.862 47.826 0.00 0.00 0.00 4.02
2620 2808 8.674607 CACAATAAGATGTACCCTTTTCCTAAC 58.325 37.037 3.41 0.00 30.84 2.34
2726 2914 4.142271 TGGTTTCGCAATCCATTTCCATAC 60.142 41.667 0.00 0.00 0.00 2.39
2732 2920 6.791303 TCGCAATCCATTTCCATACTTTTAC 58.209 36.000 0.00 0.00 0.00 2.01
3132 3320 3.172229 TGCCACCAAGCTTAAAAACAC 57.828 42.857 0.00 0.00 0.00 3.32
3357 3559 6.702723 TCAATTTCTGAGAATTTTGTTGGCAG 59.297 34.615 14.25 0.00 0.00 4.85
3368 3570 1.032014 TGTTGGCAGCTGGAAAGAAC 58.968 50.000 17.12 0.00 0.00 3.01
3558 3760 8.891720 ACAATTGGTAGTTTAAGTTTGACGTAA 58.108 29.630 10.83 0.00 0.00 3.18
3925 4129 5.106948 CGTTCATCTGTTTGATAAGCACTGT 60.107 40.000 0.00 0.00 33.36 3.55
4060 6094 5.248477 AGAAGCCTGACACATAGTTTCCTTA 59.752 40.000 0.00 0.00 0.00 2.69
4402 6436 9.092876 TCATTTGGTAAAGTGAATGAAAAACAC 57.907 29.630 0.00 0.00 36.05 3.32
4434 6468 6.625532 AAATTTCCCTTTGATGGCACTATT 57.374 33.333 0.00 0.00 0.00 1.73
4474 6508 9.578439 GATTCAAAGGAATGGAGTAAAGAAATG 57.422 33.333 0.00 0.00 43.69 2.32
4527 6587 3.876914 AGATTCAAGTGAAACAACGCAGA 59.123 39.130 0.00 0.00 41.43 4.26
4539 6599 4.228912 ACAACGCAGAATTTCCAGAAAG 57.771 40.909 0.00 0.00 33.32 2.62
4540 6600 3.632145 ACAACGCAGAATTTCCAGAAAGT 59.368 39.130 0.00 0.00 33.32 2.66
4541 6601 3.904136 ACGCAGAATTTCCAGAAAGTG 57.096 42.857 0.00 0.00 33.32 3.16
4542 6602 3.476552 ACGCAGAATTTCCAGAAAGTGA 58.523 40.909 0.00 0.00 33.32 3.41
4543 6603 3.882888 ACGCAGAATTTCCAGAAAGTGAA 59.117 39.130 0.00 0.00 33.32 3.18
4544 6604 4.338118 ACGCAGAATTTCCAGAAAGTGAAA 59.662 37.500 0.00 0.00 35.17 2.69
4545 6605 4.676924 CGCAGAATTTCCAGAAAGTGAAAC 59.323 41.667 0.00 0.00 33.64 2.78
4546 6606 4.676924 GCAGAATTTCCAGAAAGTGAAACG 59.323 41.667 0.00 0.00 45.86 3.60
4547 6607 5.505654 GCAGAATTTCCAGAAAGTGAAACGA 60.506 40.000 0.00 0.00 45.86 3.85
4548 6608 5.909610 CAGAATTTCCAGAAAGTGAAACGAC 59.090 40.000 0.00 0.00 45.86 4.34
4549 6609 3.936902 TTTCCAGAAAGTGAAACGACG 57.063 42.857 0.00 0.00 45.86 5.12
4550 6610 2.875087 TCCAGAAAGTGAAACGACGA 57.125 45.000 0.00 0.00 45.86 4.20
4551 6611 3.167921 TCCAGAAAGTGAAACGACGAA 57.832 42.857 0.00 0.00 45.86 3.85
4552 6612 3.120792 TCCAGAAAGTGAAACGACGAAG 58.879 45.455 0.00 0.00 45.86 3.79
4617 6677 7.945033 TGACATTGCTTTGACTTTTATTTCC 57.055 32.000 0.00 0.00 0.00 3.13
4681 6741 9.461312 TCATGTATAAAACTTATGTGCTTTCCT 57.539 29.630 0.00 0.00 0.00 3.36
4756 6816 9.947669 CCTGTGTAGTCTGTACACTAATTATAC 57.052 37.037 14.60 0.00 45.77 1.47
4887 6947 5.731591 AGAAAATCGAAATACCGAGGAAGT 58.268 37.500 0.00 0.00 42.21 3.01
4957 7018 8.531146 CCACTAGAAAATGGAAACCAATTGTAT 58.469 33.333 4.43 0.00 38.34 2.29
5047 7108 5.598005 CCCATTGAGGCAAGGAAATATACAA 59.402 40.000 0.00 0.00 35.39 2.41
5076 7137 5.657474 AGCTGGTAGAATCATGCAAATTTG 58.343 37.500 14.03 14.03 0.00 2.32
5088 7149 7.703298 TCATGCAAATTTGAGAAAGTTCAAG 57.297 32.000 22.31 4.95 38.25 3.02
5172 7233 1.841277 ACCAGGACTACCAACAACACA 59.159 47.619 0.00 0.00 38.94 3.72
5187 7248 4.976987 ACAACACAGAAACTGTAAAACCG 58.023 39.130 4.08 0.00 43.43 4.44
5189 7250 3.011119 ACACAGAAACTGTAAAACCGCA 58.989 40.909 4.08 0.00 43.43 5.69
5217 7278 9.239551 GTCCTACAGGAGGTAAATTTGTATTTT 57.760 33.333 0.00 0.00 46.49 1.82
5218 7279 9.816787 TCCTACAGGAGGTAAATTTGTATTTTT 57.183 29.630 0.00 0.00 46.76 1.94
5362 7426 6.510317 GCGGATCAACTTTAGATTTAGCAGTC 60.510 42.308 0.00 0.00 0.00 3.51
5691 7755 7.735917 TCAAGTACTCTCTCTGATTCCAAAAA 58.264 34.615 0.00 0.00 0.00 1.94
5726 7790 7.027778 CAGTTTACCTTAGTTCAAAACTGCT 57.972 36.000 11.84 0.00 45.63 4.24
5731 7795 5.681639 ACCTTAGTTCAAAACTGCTACACT 58.318 37.500 2.65 0.00 42.84 3.55
5768 7832 5.984323 CGGAGGGAGTAAGTTTTATAAGCTC 59.016 44.000 0.00 0.00 0.00 4.09
5790 7854 8.630917 AGCTCTGAATAATTTTCTTGGATCATG 58.369 33.333 0.00 0.00 0.00 3.07
5858 7922 2.611518 AGCGCTCAACTCTGAATGTAC 58.388 47.619 2.64 0.00 0.00 2.90
5863 7927 2.668457 CTCAACTCTGAATGTACCACGC 59.332 50.000 0.00 0.00 0.00 5.34
5871 7935 2.224549 TGAATGTACCACGCTTTTTCCG 59.775 45.455 0.00 0.00 0.00 4.30
5887 7951 6.529829 GCTTTTTCCGCACATATAATTGTTCA 59.470 34.615 0.00 0.00 0.00 3.18
6107 8178 2.038557 ACGGGATAACAGTGCTTTGTCT 59.961 45.455 0.00 0.00 0.00 3.41
6113 8184 3.764885 AACAGTGCTTTGTCTGTGAAC 57.235 42.857 0.00 0.00 42.95 3.18
6150 8221 3.153919 AGTGTAACATTTGGCGTTCCAT 58.846 40.909 0.00 0.00 40.51 3.41
6151 8222 3.572255 AGTGTAACATTTGGCGTTCCATT 59.428 39.130 0.00 0.00 40.51 3.16
6152 8223 4.762765 AGTGTAACATTTGGCGTTCCATTA 59.237 37.500 0.00 0.00 40.51 1.90
6153 8224 5.092781 GTGTAACATTTGGCGTTCCATTAG 58.907 41.667 0.00 0.00 38.57 1.73
6154 8225 4.762765 TGTAACATTTGGCGTTCCATTAGT 59.237 37.500 0.00 0.00 43.05 2.24
6155 8226 4.864704 AACATTTGGCGTTCCATTAGTT 57.135 36.364 0.00 0.00 43.05 2.24
6156 8227 4.864704 ACATTTGGCGTTCCATTAGTTT 57.135 36.364 0.00 0.00 43.05 2.66
6157 8228 5.208463 ACATTTGGCGTTCCATTAGTTTT 57.792 34.783 0.00 0.00 43.05 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.749808 TCGTCAATAAGTACTGTACTTCAGAG 58.250 38.462 30.45 20.17 45.38 3.35
8 9 8.739649 AAGTTCGTCAATAAGTACTGTACTTC 57.260 34.615 30.45 17.72 45.38 3.01
10 11 8.786898 TGTAAGTTCGTCAATAAGTACTGTACT 58.213 33.333 14.53 14.53 41.73 2.73
11 12 8.955061 TGTAAGTTCGTCAATAAGTACTGTAC 57.045 34.615 9.93 9.93 0.00 2.90
12 13 8.239314 CCTGTAAGTTCGTCAATAAGTACTGTA 58.761 37.037 0.00 0.00 0.00 2.74
13 14 7.088905 CCTGTAAGTTCGTCAATAAGTACTGT 58.911 38.462 0.00 0.00 0.00 3.55
19 20 3.306166 CGGCCTGTAAGTTCGTCAATAAG 59.694 47.826 0.00 0.00 0.00 1.73
20 21 3.255725 CGGCCTGTAAGTTCGTCAATAA 58.744 45.455 0.00 0.00 0.00 1.40
22 23 1.001633 ACGGCCTGTAAGTTCGTCAAT 59.998 47.619 0.00 0.00 36.26 2.57
27 28 1.474017 CGATACGGCCTGTAAGTTCG 58.526 55.000 0.00 7.84 36.44 3.95
205 206 0.107703 CCTGAATTGCCCGAGCTGTA 60.108 55.000 0.00 0.00 40.80 2.74
267 271 9.304335 TCCGTTACTCCTTATATGTTATCATGA 57.696 33.333 0.00 0.00 35.70 3.07
278 282 6.127253 CCAAAAGTCCTCCGTTACTCCTTATA 60.127 42.308 0.00 0.00 0.00 0.98
279 283 5.338137 CCAAAAGTCCTCCGTTACTCCTTAT 60.338 44.000 0.00 0.00 0.00 1.73
280 284 4.020839 CCAAAAGTCCTCCGTTACTCCTTA 60.021 45.833 0.00 0.00 0.00 2.69
305 370 5.648526 TCGACATCCTATTATCAGCTACTCC 59.351 44.000 0.00 0.00 0.00 3.85
340 447 1.380524 TCGATCAGAACTCCTCCGTC 58.619 55.000 0.00 0.00 0.00 4.79
352 459 2.656651 CTCGCCGCCTTCGATCAG 60.657 66.667 0.00 0.00 38.10 2.90
588 698 1.700955 TCTATCTAACCACCGGGAGC 58.299 55.000 6.32 0.00 38.05 4.70
745 869 2.811317 GACGCAGGCCGAGACAAG 60.811 66.667 0.00 0.00 41.02 3.16
746 870 4.717629 CGACGCAGGCCGAGACAA 62.718 66.667 0.00 0.00 41.02 3.18
914 1052 0.530211 CGGAGATGGAGCAAGAGCAG 60.530 60.000 0.00 0.00 45.49 4.24
952 1090 0.811616 CCTACGAACTGCCATGGAGC 60.812 60.000 18.40 0.45 0.00 4.70
962 1100 1.673168 CTACGGCCTACCTACGAACT 58.327 55.000 0.00 0.00 0.00 3.01
963 1101 0.665298 CCTACGGCCTACCTACGAAC 59.335 60.000 0.00 0.00 0.00 3.95
976 1114 2.311688 AATGAGGAAGGCGCCTACGG 62.312 60.000 33.07 0.00 38.73 4.02
977 1115 1.144057 AATGAGGAAGGCGCCTACG 59.856 57.895 33.07 0.00 38.73 3.51
978 1116 1.440145 GCAATGAGGAAGGCGCCTAC 61.440 60.000 33.07 25.58 38.73 3.18
979 1117 1.153168 GCAATGAGGAAGGCGCCTA 60.153 57.895 33.07 15.07 38.73 3.93
980 1118 2.439156 GCAATGAGGAAGGCGCCT 60.439 61.111 27.08 27.08 42.17 5.52
981 1119 1.876497 TTTGCAATGAGGAAGGCGCC 61.876 55.000 21.89 21.89 0.00 6.53
982 1120 0.174162 ATTTGCAATGAGGAAGGCGC 59.826 50.000 0.00 0.00 0.00 6.53
983 1121 1.203052 ACATTTGCAATGAGGAAGGCG 59.797 47.619 0.00 0.00 0.00 5.52
984 1122 2.613691 CACATTTGCAATGAGGAAGGC 58.386 47.619 0.00 0.00 0.00 4.35
985 1123 2.564062 ACCACATTTGCAATGAGGAAGG 59.436 45.455 22.33 12.10 34.51 3.46
986 1124 3.947910 ACCACATTTGCAATGAGGAAG 57.052 42.857 22.33 1.69 34.51 3.46
987 1125 4.502950 GGAAACCACATTTGCAATGAGGAA 60.503 41.667 22.33 1.33 38.45 3.36
993 1131 1.344114 AGCGGAAACCACATTTGCAAT 59.656 42.857 0.00 0.00 38.49 3.56
1009 1147 2.284288 CGTAAACGAATCTCGAAAGCGG 60.284 50.000 2.59 0.00 43.74 5.52
1099 1238 2.356793 GTGCGCTGACTGCTGAGT 60.357 61.111 9.73 0.00 40.11 3.41
1144 1283 1.717348 GCCATTGCGGGTTACGTAC 59.283 57.895 0.00 0.00 46.52 3.67
1145 1284 4.205287 GCCATTGCGGGTTACGTA 57.795 55.556 0.00 0.00 46.52 3.57
1223 1362 4.070552 GGAGGCGGCTTCGAGTGT 62.071 66.667 14.76 0.00 35.61 3.55
1351 1490 4.248842 CCCACACGACCTGCACCA 62.249 66.667 0.00 0.00 0.00 4.17
1450 1589 1.227263 AGATCGTCGGCGGAAATGG 60.227 57.895 10.62 0.00 38.89 3.16
1497 1636 0.978146 ATCAACGAGGAGGAGGTGGG 60.978 60.000 0.00 0.00 0.00 4.61
1531 1672 5.059833 ACAGAACTGAAAAGTAAGGCAGAG 58.940 41.667 8.87 0.00 32.86 3.35
1568 1709 6.765989 TGCTAGCGACCTGAAATATGTAATTT 59.234 34.615 10.77 0.00 0.00 1.82
1595 1742 1.507140 AATGAGGGCCGGATAACAGA 58.493 50.000 5.05 0.00 0.00 3.41
1618 1765 9.416284 CTAAAATTAGGGGTATTAGCAAAGGAA 57.584 33.333 0.00 0.00 0.00 3.36
1619 1766 7.504574 GCTAAAATTAGGGGTATTAGCAAAGGA 59.495 37.037 10.10 0.00 44.80 3.36
1620 1767 7.521585 CGCTAAAATTAGGGGTATTAGCAAAGG 60.522 40.741 14.06 0.00 45.38 3.11
1621 1768 7.012989 ACGCTAAAATTAGGGGTATTAGCAAAG 59.987 37.037 18.00 3.29 45.38 2.77
1649 1796 4.191544 TGATCAGTTGATTCTAAAGGCCG 58.808 43.478 0.00 0.00 34.37 6.13
1732 1909 7.772757 AGGGTTTGCAGATTTTAACATCAAAAA 59.227 29.630 4.50 0.00 31.54 1.94
1860 2048 7.318141 CACAAGGCTAATCATTTGAGATGTTT 58.682 34.615 0.00 0.00 0.00 2.83
1937 2125 8.986929 ACAGGAATGATTAAAATAAGGAGGAG 57.013 34.615 0.00 0.00 0.00 3.69
1995 2183 5.641209 GGCATAAGGCTAATCACTGACATAG 59.359 44.000 0.00 0.00 44.01 2.23
2014 2202 4.219725 GTGGTGCTAAAAAGGAAAGGCATA 59.780 41.667 0.00 0.00 32.38 3.14
2035 2223 4.934075 ACACATTTCATCTGATGACGTG 57.066 40.909 26.53 26.53 39.39 4.49
2078 2266 9.748708 GAAAGCAATTCAATTTGGTAGCATATA 57.251 29.630 0.00 0.00 36.36 0.86
2284 2472 2.224606 CATGCCGGAAGCTATCAATGT 58.775 47.619 5.05 0.00 44.23 2.71
2369 2557 3.508012 AGGTATGGATCTCAGTACATCGC 59.492 47.826 0.00 0.00 0.00 4.58
2465 2653 1.355381 TCCAGCCTTGTCCACATCATT 59.645 47.619 0.00 0.00 0.00 2.57
2476 2664 0.457337 GCGCAAGAAATCCAGCCTTG 60.457 55.000 0.30 0.00 40.00 3.61
2586 2774 7.054124 AGGGTACATCTTATTGTGTTGGTATG 58.946 38.462 0.00 0.00 0.00 2.39
2620 2808 5.356882 TGACCTTTTCAAGTTCGCTATTG 57.643 39.130 0.00 0.00 0.00 1.90
2638 2826 7.246674 TCAGTTTATGCTTATCGATTTGACC 57.753 36.000 1.71 0.00 0.00 4.02
2726 2914 4.141711 TGAAGATCTCCATCCGGGTAAAAG 60.142 45.833 0.00 0.00 38.11 2.27
2732 2920 0.683973 CCTGAAGATCTCCATCCGGG 59.316 60.000 0.00 0.00 38.37 5.73
3132 3320 0.178998 CTCCATGAGAATGCCCCAGG 60.179 60.000 0.00 0.00 0.00 4.45
3357 3559 5.689383 TCAAGTACATTGTTCTTTCCAGC 57.311 39.130 5.99 0.00 40.05 4.85
3368 3570 8.918961 TGTAAACAAACCTTTCAAGTACATTG 57.081 30.769 0.00 0.00 40.52 2.82
3558 3760 5.420104 CCATCCAAATTTGAGCCTTAAGTCT 59.580 40.000 19.86 0.00 0.00 3.24
3925 4129 6.405278 TTGATTCTACAACTGTCTCTGTCA 57.595 37.500 0.00 0.00 0.00 3.58
4016 6043 6.442541 TTCTGGAAACCATCACTTAAGGTA 57.557 37.500 7.53 0.00 34.63 3.08
4024 6051 1.815003 CAGGCTTCTGGAAACCATCAC 59.185 52.381 5.70 0.00 34.96 3.06
4030 6057 1.967319 TGTGTCAGGCTTCTGGAAAC 58.033 50.000 0.00 0.00 38.96 2.78
4060 6094 3.612795 AAAGGGCTTCCACTAAAAGGT 57.387 42.857 0.00 0.00 0.00 3.50
4124 6158 7.485595 TCATTCTTGAACATTGCGACAATTATG 59.514 33.333 2.86 0.00 0.00 1.90
4402 6436 7.809806 GCCATCAAAGGGAAATTTATATTCTCG 59.190 37.037 0.00 0.00 32.40 4.04
4474 6508 9.817809 TCAGATGATAGTGGTAGTTTCATTTAC 57.182 33.333 0.00 0.00 0.00 2.01
4498 6532 6.073602 CGTTGTTTCACTTGAATCTGAGATCA 60.074 38.462 0.00 0.00 33.54 2.92
4527 6587 4.573201 TCGTCGTTTCACTTTCTGGAAATT 59.427 37.500 0.00 0.00 35.66 1.82
4539 6599 2.803956 TGGAAATCCTTCGTCGTTTCAC 59.196 45.455 0.44 0.00 36.82 3.18
4540 6600 3.064207 CTGGAAATCCTTCGTCGTTTCA 58.936 45.455 0.44 0.00 36.82 2.69
4541 6601 3.323243 TCTGGAAATCCTTCGTCGTTTC 58.677 45.455 0.44 0.00 36.82 2.78
4542 6602 3.396260 TCTGGAAATCCTTCGTCGTTT 57.604 42.857 0.44 0.00 36.82 3.60
4543 6603 3.396260 TTCTGGAAATCCTTCGTCGTT 57.604 42.857 0.44 0.00 36.82 3.85
4544 6604 3.396260 TTTCTGGAAATCCTTCGTCGT 57.604 42.857 0.44 0.00 36.82 4.34
4545 6605 3.932710 TCATTTCTGGAAATCCTTCGTCG 59.067 43.478 5.68 0.00 38.84 5.12
4546 6606 4.201724 CGTCATTTCTGGAAATCCTTCGTC 60.202 45.833 5.68 0.00 38.84 4.20
4547 6607 3.684788 CGTCATTTCTGGAAATCCTTCGT 59.315 43.478 5.68 0.00 38.84 3.85
4548 6608 3.684788 ACGTCATTTCTGGAAATCCTTCG 59.315 43.478 5.68 9.83 38.84 3.79
4549 6609 6.737254 TTACGTCATTTCTGGAAATCCTTC 57.263 37.500 5.68 0.00 38.84 3.46
4550 6610 7.362920 CCATTTACGTCATTTCTGGAAATCCTT 60.363 37.037 5.68 0.00 38.84 3.36
4551 6611 6.095440 CCATTTACGTCATTTCTGGAAATCCT 59.905 38.462 5.68 0.00 38.84 3.24
4552 6612 6.265577 CCATTTACGTCATTTCTGGAAATCC 58.734 40.000 5.68 0.00 38.84 3.01
4617 6677 3.308053 CACATGACTCGAATAAGCACAGG 59.692 47.826 0.00 0.00 0.00 4.00
4658 6718 9.391006 CCTAGGAAAGCACATAAGTTTTATACA 57.609 33.333 1.05 0.00 0.00 2.29
4659 6719 8.343366 GCCTAGGAAAGCACATAAGTTTTATAC 58.657 37.037 14.75 0.00 0.00 1.47
4660 6720 8.272173 AGCCTAGGAAAGCACATAAGTTTTATA 58.728 33.333 14.75 0.00 0.00 0.98
4661 6721 7.119387 AGCCTAGGAAAGCACATAAGTTTTAT 58.881 34.615 14.75 0.00 0.00 1.40
4662 6722 6.481643 AGCCTAGGAAAGCACATAAGTTTTA 58.518 36.000 14.75 0.00 0.00 1.52
4663 6723 5.325239 AGCCTAGGAAAGCACATAAGTTTT 58.675 37.500 14.75 0.00 0.00 2.43
4675 6735 3.425162 ACAAACCAGAGCCTAGGAAAG 57.575 47.619 14.75 0.00 0.00 2.62
4681 6741 3.326588 ACACATGTACAAACCAGAGCCTA 59.673 43.478 0.00 0.00 0.00 3.93
4733 6793 9.643652 GTCGTATAATTAGTGTACAGACTACAC 57.356 37.037 0.00 0.90 45.89 2.90
4756 6816 4.375698 CACTATTGAACTGCAAAAACGTCG 59.624 41.667 0.00 0.00 40.48 5.12
4899 6960 3.790089 AATTCCTTCCTCGGTTCTGTT 57.210 42.857 0.00 0.00 0.00 3.16
4957 7018 5.581126 AAACACTTCTCTTTTGCATGACA 57.419 34.783 0.00 0.00 0.00 3.58
5047 7108 5.439721 TGCATGATTCTACCAGCTACAATT 58.560 37.500 0.00 0.00 0.00 2.32
5076 7137 8.173130 TCGAACAACTTAAACTTGAACTTTCTC 58.827 33.333 0.00 0.00 0.00 2.87
5088 7149 8.836959 AAAACTCTCATTCGAACAACTTAAAC 57.163 30.769 0.00 0.00 0.00 2.01
5096 7157 7.094805 CCAATAAGGAAAACTCTCATTCGAACA 60.095 37.037 0.00 0.00 41.22 3.18
5172 7233 3.252458 GGACATGCGGTTTTACAGTTTCT 59.748 43.478 0.00 0.00 0.00 2.52
5263 7324 8.365060 TGAATTCATAGGATCAAACCAAATGT 57.635 30.769 3.38 0.00 31.77 2.71
5318 7382 9.734620 TGATCCGCAATTATCTTTTAGAATTTG 57.265 29.630 0.00 0.00 26.31 2.32
5691 7755 4.976224 AAGGTAAACTGCGACACTTTTT 57.024 36.364 0.00 0.00 0.00 1.94
5745 7809 6.987404 CAGAGCTTATAAAACTTACTCCCTCC 59.013 42.308 0.00 0.00 0.00 4.30
5790 7854 5.914033 TGCATTTAGGATCCTACACTACAC 58.086 41.667 21.57 7.95 0.00 2.90
5858 7922 0.519519 TATGTGCGGAAAAAGCGTGG 59.480 50.000 0.00 0.00 37.44 4.94
5863 7927 8.459521 TTGAACAATTATATGTGCGGAAAAAG 57.540 30.769 0.00 0.00 30.88 2.27
5945 8010 2.528564 CTTCCCAGAGCCAAAAATCCA 58.471 47.619 0.00 0.00 0.00 3.41
6074 8145 3.805422 TGTTATCCCGTATCGCATGAAAC 59.195 43.478 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.