Multiple sequence alignment - TraesCS2D01G151200

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 TraesCS2D01G151200 chr2D 100.000 2260 0 0 2029 4288 94318470 94316211 0.000000e+00 4174
1 TraesCS2D01G151200 chr2D 100.000 1760 0 0 1 1760 94320498 94318739 0.000000e+00 3251
2 TraesCS2D01G151200 chr2B 91.912 2275 120 39 2031 4278 146441725 146439488 0.000000e+00 3123
3 TraesCS2D01G151200 chr2B 91.104 1821 66 35 1 1760 146443542 146441757 0.000000e+00 2377
4 TraesCS2D01G151200 chr2A 92.690 2011 85 27 2031 4003 92317550 92315564 0.000000e+00 2843
5 TraesCS2D01G151200 chr2A 89.499 1057 39 32 747 1760 92318610 92317583 0.000000e+00 1271
6 TraesCS2D01G151200 chr2A 93.952 463 6 12 350 796 92319064 92318608 0.000000e+00 680
7 TraesCS2D01G151200 chr2A 93.314 344 16 7 1 338 92319491 92319149 6.400000e-138 501
8 TraesCS2D01G151200 chr2A 87.171 304 30 6 3923 4224 92315560 92315264 1.910000e-88 337
9 TraesCS2D01G151200 chr5A 88.205 195 20 2 1106 1297 453877108 453876914 3.340000e-56 230
10 TraesCS2D01G151200 chr5D 87.179 195 22 2 1106 1297 352219252 352219446 7.220000e-53 219
11 TraesCS2D01G151200 chr5D 83.152 184 31 0 1113 1296 558247753 558247570 7.370000e-38 169
12 TraesCS2D01G151200 chr5B 87.179 195 22 2 1106 1297 416851128 416850934 7.220000e-53 219
13 TraesCS2D01G151200 chr4A 84.239 184 29 0 1113 1296 610490444 610490261 3.410000e-41 180
14 TraesCS2D01G151200 chr1B 83.957 187 28 2 1108 1293 595176892 595177077 1.230000e-40 178
15 TraesCS2D01G151200 chr1D 82.888 187 30 2 1108 1293 439022280 439022465 2.650000e-37 167


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 TraesCS2D01G151200 chr2D 94316211 94320498 4287 True 3712.5 4174 100.0000 1 4288 2 chr2D.!!$R1 4287
1 TraesCS2D01G151200 chr2B 146439488 146443542 4054 True 2750.0 3123 91.5080 1 4278 2 chr2B.!!$R1 4277
2 TraesCS2D01G151200 chr2A 92315264 92319491 4227 True 1126.4 2843 91.3252 1 4224 5 chr2A.!!$R1 4223

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
763 859 0.316114 GCGTGTCATGTGTGTGTGTG 60.316 55.0 0.00 0.0 0.00 3.82 F
1690 1900 0.108585 TTCCTGGTCTGTGACAAGCC 59.891 55.0 0.00 0.0 32.58 4.35 F
2077 2294 0.179076 GGTGGCCATTTATGCAAGCC 60.179 55.0 9.72 0.0 44.13 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1924 0.736325 GTGATGGACGCGTTGTAGCT 60.736 55.0 15.53 0.00 34.4 3.32 R
2819 3057 1.096967 GGTGATGGTGATGATGCGCA 61.097 55.0 14.96 14.96 0.0 6.09 R
3965 4320 0.033504 TGACACTCCGTTGGCTTCTC 59.966 55.0 0.00 0.00 0.0 2.87 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
97 101 6.668323 TGTAAATTTCTGCAGCTTCAGTAAC 58.332 36.000 13.22 0.04 35.63 2.50
116 120 2.960819 ACTACCTTGTGTCAAGATCGC 58.039 47.619 10.54 0.00 0.00 4.58
141 145 2.233186 GACACTAGCCGTAGAACCCTTT 59.767 50.000 0.00 0.00 0.00 3.11
195 202 2.028203 GCAAGAGCCAAGAGAGAGAACT 60.028 50.000 0.00 0.00 33.58 3.01
257 264 0.940991 GCGCCTTGTCTTGCCAAAAG 60.941 55.000 0.00 0.00 0.00 2.27
357 437 2.854185 GCACACAAGTTTTTGCTGAGAC 59.146 45.455 0.00 0.00 37.85 3.36
418 498 1.072173 TGCTGCACATTGACCAGTACT 59.928 47.619 0.00 0.00 0.00 2.73
419 499 2.301583 TGCTGCACATTGACCAGTACTA 59.698 45.455 0.00 0.00 0.00 1.82
420 500 3.244387 TGCTGCACATTGACCAGTACTAA 60.244 43.478 0.00 0.00 0.00 2.24
421 501 3.372206 GCTGCACATTGACCAGTACTAAG 59.628 47.826 0.00 0.00 0.00 2.18
456 536 3.600388 AGCACATTAGGACTGTAGCAAC 58.400 45.455 0.00 0.00 0.00 4.17
505 586 2.290323 CGACCCTTCCTTGTGATTTCCT 60.290 50.000 0.00 0.00 0.00 3.36
677 773 1.450491 GAGAAGGAAAGAGGGCGGC 60.450 63.158 0.00 0.00 0.00 6.53
758 854 2.281484 GGGGCGTGTCATGTGTGT 60.281 61.111 0.00 0.00 0.00 3.72
759 855 2.616330 GGGGCGTGTCATGTGTGTG 61.616 63.158 0.00 0.00 0.00 3.82
760 856 1.891919 GGGCGTGTCATGTGTGTGT 60.892 57.895 0.00 0.00 0.00 3.72
761 857 1.279539 GGCGTGTCATGTGTGTGTG 59.720 57.895 0.00 0.00 0.00 3.82
762 858 1.436195 GGCGTGTCATGTGTGTGTGT 61.436 55.000 0.00 0.00 0.00 3.72
763 859 0.316114 GCGTGTCATGTGTGTGTGTG 60.316 55.000 0.00 0.00 0.00 3.82
764 860 1.006086 CGTGTCATGTGTGTGTGTGT 58.994 50.000 0.00 0.00 0.00 3.72
765 861 1.267483 CGTGTCATGTGTGTGTGTGTG 60.267 52.381 0.00 0.00 0.00 3.82
766 862 1.737236 GTGTCATGTGTGTGTGTGTGT 59.263 47.619 0.00 0.00 0.00 3.72
767 863 1.736681 TGTCATGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
768 864 1.737236 GTCATGTGTGTGTGTGTGTGT 59.263 47.619 0.00 0.00 0.00 3.72
769 865 1.736681 TCATGTGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
770 866 1.468127 CATGTGTGTGTGTGTGTGTGT 59.532 47.619 0.00 0.00 0.00 3.72
771 867 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
777 935 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
794 952 5.182190 TGTGTGTTTTTATGTGTGTGAGTGT 59.818 36.000 0.00 0.00 0.00 3.55
829 987 5.971493 ACTGGAGATATAGCTAAAGAGGGT 58.029 41.667 0.00 0.00 0.00 4.34
851 1009 3.392616 TCAGCCTTTCTTTCTTCCTCACT 59.607 43.478 0.00 0.00 0.00 3.41
934 1097 1.003696 CTTCTTCTTCTCCACCCACCC 59.996 57.143 0.00 0.00 0.00 4.61
974 1140 0.755698 CTAGGTAGAAGCAGCGGGGA 60.756 60.000 0.00 0.00 0.00 4.81
994 1160 1.267806 AGTACGTACGTGTGGTTGAGG 59.732 52.381 30.25 0.00 0.00 3.86
1327 1493 1.070758 CATTATCTGCTGCCCCGTACT 59.929 52.381 0.00 0.00 0.00 2.73
1356 1545 3.221771 TGCATGTTTAGTCCAGCAAGTT 58.778 40.909 0.00 0.00 0.00 2.66
1389 1582 7.857569 TGTTCGATTTGTTTCGTTAATCTTCT 58.142 30.769 0.00 0.00 40.03 2.85
1422 1624 3.772853 TAGGGCGTCCATGGCATGC 62.773 63.158 22.02 9.90 35.84 4.06
1432 1634 1.604438 CCATGGCATGCATATGTGTGC 60.604 52.381 22.02 19.74 45.25 4.57
1439 1641 1.353103 GCATATGTGTGCGGAGTGC 59.647 57.895 4.29 0.00 46.70 4.40
1446 1648 1.668793 TGTGCGGAGTGCTCATGTG 60.669 57.895 1.41 0.00 46.63 3.21
1447 1649 1.669115 GTGCGGAGTGCTCATGTGT 60.669 57.895 1.41 0.00 46.63 3.72
1448 1650 1.668793 TGCGGAGTGCTCATGTGTG 60.669 57.895 1.41 0.00 46.63 3.82
1449 1651 3.031964 GCGGAGTGCTCATGTGTGC 62.032 63.158 1.41 0.40 41.73 4.57
1450 1652 2.733671 CGGAGTGCTCATGTGTGCG 61.734 63.158 1.41 0.00 37.35 5.34
1451 1653 2.477845 GAGTGCTCATGTGTGCGC 59.522 61.111 0.00 0.00 43.08 6.09
1452 1654 3.031964 GAGTGCTCATGTGTGCGCC 62.032 63.158 4.18 0.00 43.58 6.53
1453 1655 4.450122 GTGCTCATGTGTGCGCCG 62.450 66.667 4.18 0.00 38.62 6.46
1454 1656 4.986645 TGCTCATGTGTGCGCCGT 62.987 61.111 4.18 0.00 35.22 5.68
1455 1657 4.450122 GCTCATGTGTGCGCCGTG 62.450 66.667 4.18 0.75 29.89 4.94
1456 1658 3.043713 CTCATGTGTGCGCCGTGT 61.044 61.111 4.18 0.00 0.00 4.49
1457 1659 2.590291 TCATGTGTGCGCCGTGTT 60.590 55.556 4.18 0.00 0.00 3.32
1458 1660 2.127270 CATGTGTGCGCCGTGTTC 60.127 61.111 4.18 0.00 0.00 3.18
1459 1661 2.590291 ATGTGTGCGCCGTGTTCA 60.590 55.556 4.18 0.00 0.00 3.18
1460 1662 1.965930 ATGTGTGCGCCGTGTTCAT 60.966 52.632 4.18 0.00 0.00 2.57
1461 1663 2.127270 GTGTGCGCCGTGTTCATG 60.127 61.111 4.18 0.00 0.00 3.07
1462 1664 2.590291 TGTGCGCCGTGTTCATGT 60.590 55.556 4.18 0.00 0.00 3.21
1463 1665 2.173382 GTGCGCCGTGTTCATGTC 59.827 61.111 4.18 0.00 0.00 3.06
1481 1683 6.234177 TCATGTCCAAGTTTTGTTTGGTTTT 58.766 32.000 4.14 0.00 44.35 2.43
1588 1794 5.288804 TGCAAAAGTTAATGCACCTCTTTC 58.711 37.500 11.14 0.00 46.87 2.62
1679 1889 3.418684 TTAGTTCCTTGCTTCCTGGTC 57.581 47.619 0.00 0.00 0.00 4.02
1690 1900 0.108585 TTCCTGGTCTGTGACAAGCC 59.891 55.000 0.00 0.00 32.58 4.35
1704 1917 3.046390 GACAAGCCGTCGAATAGATCAG 58.954 50.000 0.00 0.00 34.19 2.90
1711 1924 3.004419 CCGTCGAATAGATCAGGCTGTAA 59.996 47.826 15.27 0.00 0.00 2.41
1748 1965 6.071672 TCCATCACACTGTTCTTTTGTTGAAA 60.072 34.615 0.00 0.00 0.00 2.69
1749 1966 6.757947 CCATCACACTGTTCTTTTGTTGAAAT 59.242 34.615 0.00 0.00 0.00 2.17
1750 1967 7.254185 CCATCACACTGTTCTTTTGTTGAAATG 60.254 37.037 0.00 0.00 0.00 2.32
1751 1968 6.098679 TCACACTGTTCTTTTGTTGAAATGG 58.901 36.000 0.00 0.00 0.00 3.16
1753 1970 6.589523 CACACTGTTCTTTTGTTGAAATGGAA 59.410 34.615 0.00 0.00 0.00 3.53
2049 2266 4.983671 CCCCATTTCTTACTACTTTGGC 57.016 45.455 0.00 0.00 0.00 4.52
2053 2270 6.184789 CCCATTTCTTACTACTTTGGCCTTA 58.815 40.000 3.32 0.00 0.00 2.69
2077 2294 0.179076 GGTGGCCATTTATGCAAGCC 60.179 55.000 9.72 0.00 44.13 4.35
2081 2298 1.481772 GGCCATTTATGCAAGCCAGAA 59.518 47.619 0.00 0.00 43.32 3.02
2086 2303 5.221303 GCCATTTATGCAAGCCAGAAGATTA 60.221 40.000 0.00 0.00 0.00 1.75
2103 2320 9.261180 CAGAAGATTATTCGGCTAATCAGTTAA 57.739 33.333 15.59 0.00 39.53 2.01
2119 2336 7.636150 ATCAGTTAATCCATCAGTTTTCTGG 57.364 36.000 0.00 0.00 46.94 3.86
2130 2347 5.885230 TCAGTTTTCTGGCAAGATGTATG 57.115 39.130 0.00 0.00 46.94 2.39
2131 2348 4.156556 TCAGTTTTCTGGCAAGATGTATGC 59.843 41.667 0.00 0.00 46.94 3.14
2140 2361 5.379187 TGGCAAGATGTATGCATGATAAGT 58.621 37.500 10.16 0.00 45.60 2.24
2197 2418 9.914131 GGTTTCTTCTTTTAAAGCATGAGTTAT 57.086 29.630 0.00 0.00 34.17 1.89
2284 2508 5.420725 TGTGGATGCATACTAAGAAGTGT 57.579 39.130 11.02 0.00 36.36 3.55
2382 2606 2.209690 TGACACTATCCACAGGTCGA 57.790 50.000 0.00 0.00 0.00 4.20
2468 2703 4.205323 TGACATGACTACTATACGTGCG 57.795 45.455 0.00 0.00 0.00 5.34
2469 2704 2.971915 GACATGACTACTATACGTGCGC 59.028 50.000 0.00 0.00 0.00 6.09
2563 2799 9.582648 ACTATTGGGTGTTGATTTTTAACTAGT 57.417 29.630 0.00 0.00 0.00 2.57
2801 3039 3.626924 AACACCTTCTCGCCGCCT 61.627 61.111 0.00 0.00 0.00 5.52
2858 3099 0.670546 CGGTGTACCAGCACTTCCAG 60.671 60.000 1.50 0.00 39.21 3.86
2867 3108 1.743252 GCACTTCCAGGAAGAGCCG 60.743 63.158 31.41 19.18 45.59 5.52
3237 3481 3.825160 AAGAAGAAGCGGGCGCACA 62.825 57.895 11.77 0.00 44.88 4.57
3463 3714 4.279671 GGATCAATGAGGTCATCGAGTAGT 59.720 45.833 0.00 0.00 35.10 2.73
3464 3715 5.473846 GGATCAATGAGGTCATCGAGTAGTA 59.526 44.000 0.00 0.00 35.10 1.82
3465 3716 6.016192 GGATCAATGAGGTCATCGAGTAGTAA 60.016 42.308 0.00 0.00 35.10 2.24
3466 3717 6.378710 TCAATGAGGTCATCGAGTAGTAAG 57.621 41.667 0.00 0.00 35.10 2.34
3471 3722 5.100344 AGGTCATCGAGTAGTAAGTCTGA 57.900 43.478 0.00 0.00 0.00 3.27
3566 3817 4.334552 TCTTGATATGTTCTTTGCTGCCA 58.665 39.130 0.00 0.00 0.00 4.92
3580 3831 4.165486 GCCATTGCCCCCATGCAC 62.165 66.667 0.00 0.00 41.88 4.57
3581 3832 2.684294 CCATTGCCCCCATGCACA 60.684 61.111 0.00 0.00 41.88 4.57
3665 3922 7.386299 GCAAAGTGTTCTCTTCTTTCTCTCATA 59.614 37.037 0.00 0.00 30.41 2.15
3666 3923 9.265901 CAAAGTGTTCTCTTCTTTCTCTCATAA 57.734 33.333 0.00 0.00 30.41 1.90
3667 3924 9.487790 AAAGTGTTCTCTTCTTTCTCTCATAAG 57.512 33.333 0.00 0.00 0.00 1.73
3668 3925 8.189119 AGTGTTCTCTTCTTTCTCTCATAAGT 57.811 34.615 0.00 0.00 0.00 2.24
3669 3926 8.303876 AGTGTTCTCTTCTTTCTCTCATAAGTC 58.696 37.037 0.00 0.00 0.00 3.01
3671 3928 8.811017 TGTTCTCTTCTTTCTCTCATAAGTCAT 58.189 33.333 0.00 0.00 0.00 3.06
3679 3936 8.762645 TCTTTCTCTCATAAGTCATAACATGGT 58.237 33.333 0.00 0.00 0.00 3.55
3732 3991 7.308229 CCGTATCCTCTTCAATTCAATTGGATC 60.308 40.741 10.30 0.00 40.61 3.36
3883 4145 9.681062 TCATTAGGAATTTTTCGTAAGGATTCT 57.319 29.630 10.96 0.00 42.30 2.40
3902 4171 4.790765 TCTAATCCTGTGAGTGTGACAG 57.209 45.455 0.00 0.00 40.55 3.51
3926 4195 3.502211 ACACGGTGATGATTTTGAAGGAC 59.498 43.478 16.29 0.00 0.00 3.85
3936 4291 4.518590 TGATTTTGAAGGACGCAAATCTCA 59.481 37.500 0.00 0.00 35.41 3.27
3973 4328 4.371624 TTCCTTTGAATCAGAGAAGCCA 57.628 40.909 2.01 0.00 0.00 4.75
3986 4341 1.072331 AGAAGCCAACGGAGTGTCAAT 59.928 47.619 0.00 0.00 45.00 2.57
4004 4359 7.224753 AGTGTCAATATACGAGCCTACAATTTG 59.775 37.037 0.00 0.00 0.00 2.32
4047 4403 5.891551 AGCCTACTTTGGACAAAAAGAAGAA 59.108 36.000 3.82 0.00 39.12 2.52
4051 4407 9.599866 CCTACTTTGGACAAAAAGAAGAAAATT 57.400 29.630 3.82 0.00 39.12 1.82
4106 4462 3.603158 TGTATTGGAGAGCGCAGTTTA 57.397 42.857 11.47 0.00 0.00 2.01
4119 4475 4.941263 AGCGCAGTTTAATGGACAATCTTA 59.059 37.500 11.47 0.00 0.00 2.10
4124 4480 7.360861 CGCAGTTTAATGGACAATCTTAGTTGA 60.361 37.037 0.00 0.00 33.37 3.18
4135 4491 9.436957 GGACAATCTTAGTTGAGTGAGATTAAA 57.563 33.333 5.77 0.00 36.88 1.52
4150 4506 7.985752 AGTGAGATTAAAGAATACCTAAACCCG 59.014 37.037 0.00 0.00 0.00 5.28
4217 4573 7.916914 AAATTTACATTTACGGTGAGCTAGT 57.083 32.000 0.00 0.00 30.22 2.57
4281 4637 6.919775 AATATCTAGGTGTCACATACTCCC 57.080 41.667 5.12 0.00 41.82 4.30
4282 4638 2.651455 TCTAGGTGTCACATACTCCCG 58.349 52.381 5.12 0.00 41.82 5.14
4283 4639 1.681793 CTAGGTGTCACATACTCCCGG 59.318 57.143 5.12 0.00 41.82 5.73
4284 4640 0.252103 AGGTGTCACATACTCCCGGT 60.252 55.000 5.12 0.00 41.82 5.28
4285 4641 0.175073 GGTGTCACATACTCCCGGTC 59.825 60.000 5.12 0.00 35.99 4.79
4286 4642 0.175073 GTGTCACATACTCCCGGTCC 59.825 60.000 0.00 0.00 0.00 4.46
4287 4643 0.040646 TGTCACATACTCCCGGTCCT 59.959 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 101 2.926200 CTGCGATCTTGACACAAGGTAG 59.074 50.000 10.84 6.17 0.00 3.18
116 120 1.134560 GTTCTACGGCTAGTGTCCCTG 59.865 57.143 0.00 0.00 0.00 4.45
156 160 3.788227 TGCTGTTACTTGTGGGATTCT 57.212 42.857 0.00 0.00 0.00 2.40
161 165 1.537202 GCTCTTGCTGTTACTTGTGGG 59.463 52.381 0.00 0.00 36.03 4.61
195 202 4.574828 GGAAGACTAGTCAAACAGTGCAAA 59.425 41.667 24.44 0.00 0.00 3.68
257 264 7.226325 CAGACCCACATCAATTCTATCTTCTTC 59.774 40.741 0.00 0.00 0.00 2.87
338 345 3.129287 CAGGTCTCAGCAAAAACTTGTGT 59.871 43.478 0.00 0.00 0.00 3.72
339 346 3.378112 TCAGGTCTCAGCAAAAACTTGTG 59.622 43.478 0.00 0.00 0.00 3.33
357 437 2.676839 GCACACTGATCAGATGTTCAGG 59.323 50.000 29.27 16.06 42.95 3.86
418 498 9.803315 CTAATGTGCTTAGTTGAGTCATACTTA 57.197 33.333 11.53 4.47 33.47 2.24
419 499 7.766278 CCTAATGTGCTTAGTTGAGTCATACTT 59.234 37.037 11.53 0.00 35.94 2.24
420 500 7.124298 TCCTAATGTGCTTAGTTGAGTCATACT 59.876 37.037 11.17 11.17 35.94 2.12
421 501 7.222999 GTCCTAATGTGCTTAGTTGAGTCATAC 59.777 40.741 0.00 0.00 35.94 2.39
456 536 4.037089 TGCAACTGAATTAGCATATGCAGG 59.963 41.667 28.62 12.26 45.16 4.85
505 586 1.832167 GCCAAGGTGGTGCTGGAAA 60.832 57.895 0.00 0.00 40.46 3.13
677 773 4.124943 AGCTGCTGCCTGGATGGG 62.125 66.667 12.44 0.00 40.80 4.00
758 854 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
759 855 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
760 856 3.717400 AAAAACACACACACACACACA 57.283 38.095 0.00 0.00 0.00 3.72
761 857 5.060323 CACATAAAAACACACACACACACAC 59.940 40.000 0.00 0.00 0.00 3.82
762 858 5.157067 CACATAAAAACACACACACACACA 58.843 37.500 0.00 0.00 0.00 3.72
763 859 5.060323 CACACATAAAAACACACACACACAC 59.940 40.000 0.00 0.00 0.00 3.82
764 860 5.157067 CACACATAAAAACACACACACACA 58.843 37.500 0.00 0.00 0.00 3.72
765 861 5.060323 CACACACATAAAAACACACACACAC 59.940 40.000 0.00 0.00 0.00 3.82
766 862 5.048713 TCACACACATAAAAACACACACACA 60.049 36.000 0.00 0.00 0.00 3.72
767 863 5.394802 TCACACACATAAAAACACACACAC 58.605 37.500 0.00 0.00 0.00 3.82
768 864 5.182190 ACTCACACACATAAAAACACACACA 59.818 36.000 0.00 0.00 0.00 3.72
769 865 5.511377 CACTCACACACATAAAAACACACAC 59.489 40.000 0.00 0.00 0.00 3.82
770 866 5.182190 ACACTCACACACATAAAAACACACA 59.818 36.000 0.00 0.00 0.00 3.72
771 867 5.511377 CACACTCACACACATAAAAACACAC 59.489 40.000 0.00 0.00 0.00 3.82
777 935 5.423886 TGTCTCACACTCACACACATAAAA 58.576 37.500 0.00 0.00 0.00 1.52
794 952 2.959465 TCTCCAGTCTCACTGTCTCA 57.041 50.000 3.07 0.00 44.50 3.27
829 987 3.392616 AGTGAGGAAGAAAGAAAGGCTGA 59.607 43.478 0.00 0.00 0.00 4.26
934 1097 1.818060 CTCAGGGACTCAGTCACTCAG 59.182 57.143 6.60 0.00 43.51 3.35
974 1140 1.267806 CCTCAACCACACGTACGTACT 59.732 52.381 22.34 6.25 0.00 2.73
994 1160 0.613012 ACAAGGAAAGCCATGGCCTC 60.613 55.000 33.14 27.18 43.17 4.70
1110 1276 3.883744 CTTGGTCAGGAACGGCGCT 62.884 63.158 6.90 0.00 0.00 5.92
1327 1493 3.081061 GGACTAAACATGCATGTGTGGA 58.919 45.455 32.95 15.00 41.61 4.02
1356 1545 4.732923 CGAAACAAATCGAACAAAGAGCAA 59.267 37.500 0.00 0.00 45.48 3.91
1389 1582 1.339342 GCCCTAACTAGCAAACCGGAA 60.339 52.381 9.46 0.00 0.00 4.30
1422 1624 0.933097 GAGCACTCCGCACACATATG 59.067 55.000 0.00 0.00 46.13 1.78
1432 1634 2.733671 CGCACACATGAGCACTCCG 61.734 63.158 0.00 0.00 0.00 4.63
1439 1641 2.498761 GAACACGGCGCACACATGAG 62.499 60.000 10.83 0.00 0.00 2.90
1446 1648 2.173382 GACATGAACACGGCGCAC 59.827 61.111 10.83 0.00 0.00 5.34
1447 1649 3.047280 GGACATGAACACGGCGCA 61.047 61.111 10.83 0.00 0.00 6.09
1448 1650 2.513065 CTTGGACATGAACACGGCGC 62.513 60.000 6.90 0.00 0.00 6.53
1449 1651 1.227999 ACTTGGACATGAACACGGCG 61.228 55.000 4.80 4.80 0.00 6.46
1450 1652 0.951558 AACTTGGACATGAACACGGC 59.048 50.000 0.00 0.00 0.00 5.68
1451 1653 3.181491 ACAAAACTTGGACATGAACACGG 60.181 43.478 0.00 0.00 34.12 4.94
1452 1654 4.027572 ACAAAACTTGGACATGAACACG 57.972 40.909 0.00 0.00 34.12 4.49
1453 1655 5.063312 CCAAACAAAACTTGGACATGAACAC 59.937 40.000 0.00 0.00 45.31 3.32
1454 1656 5.174395 CCAAACAAAACTTGGACATGAACA 58.826 37.500 0.00 0.00 45.31 3.18
1455 1657 5.175127 ACCAAACAAAACTTGGACATGAAC 58.825 37.500 8.54 0.00 45.31 3.18
1456 1658 5.413309 ACCAAACAAAACTTGGACATGAA 57.587 34.783 8.54 0.00 45.31 2.57
1457 1659 5.413309 AACCAAACAAAACTTGGACATGA 57.587 34.783 8.54 0.00 45.31 3.07
1458 1660 6.072783 ACAAAACCAAACAAAACTTGGACATG 60.073 34.615 8.54 0.00 45.31 3.21
1459 1661 6.000840 ACAAAACCAAACAAAACTTGGACAT 58.999 32.000 8.54 0.00 45.31 3.06
1460 1662 5.368989 ACAAAACCAAACAAAACTTGGACA 58.631 33.333 8.54 0.00 45.31 4.02
1461 1663 5.933187 ACAAAACCAAACAAAACTTGGAC 57.067 34.783 8.54 0.00 45.31 4.02
1462 1664 8.622948 AAATACAAAACCAAACAAAACTTGGA 57.377 26.923 8.54 0.00 45.31 3.53
1481 1683 8.997323 CCATTGCTTTGACCAAATTAAAATACA 58.003 29.630 0.00 0.00 0.00 2.29
1588 1794 3.490526 CACCTCGCAAACAAAATCTTTGG 59.509 43.478 4.30 0.00 0.00 3.28
1690 1900 2.783828 ACAGCCTGATCTATTCGACG 57.216 50.000 0.00 0.00 0.00 5.12
1704 1917 1.012486 ACGCGTTGTAGCTTACAGCC 61.012 55.000 5.58 0.00 43.77 4.85
1711 1924 0.736325 GTGATGGACGCGTTGTAGCT 60.736 55.000 15.53 0.00 34.40 3.32
1716 1929 1.221466 ACAGTGTGATGGACGCGTTG 61.221 55.000 15.53 6.73 40.28 4.10
2028 2245 3.699538 GGCCAAAGTAGTAAGAAATGGGG 59.300 47.826 0.00 0.00 0.00 4.96
2029 2246 4.600062 AGGCCAAAGTAGTAAGAAATGGG 58.400 43.478 5.01 0.00 0.00 4.00
2049 2266 4.680440 GCATAAATGGCCACCAAAGTAAGG 60.680 45.833 8.16 0.00 36.95 2.69
2053 2270 2.255406 TGCATAAATGGCCACCAAAGT 58.745 42.857 8.16 0.00 36.95 2.66
2064 2281 7.325338 CGAATAATCTTCTGGCTTGCATAAATG 59.675 37.037 0.00 0.00 0.00 2.32
2077 2294 7.721286 AACTGATTAGCCGAATAATCTTCTG 57.279 36.000 15.91 9.17 41.03 3.02
2081 2298 8.375506 TGGATTAACTGATTAGCCGAATAATCT 58.624 33.333 15.91 4.29 41.03 2.40
2086 2303 6.533730 TGATGGATTAACTGATTAGCCGAAT 58.466 36.000 0.00 0.00 0.00 3.34
2103 2320 4.038271 TCTTGCCAGAAAACTGATGGAT 57.962 40.909 0.00 0.00 36.09 3.41
2105 2322 3.508793 ACATCTTGCCAGAAAACTGATGG 59.491 43.478 0.00 0.00 35.51 3.51
2119 2336 6.348295 CCTCACTTATCATGCATACATCTTGC 60.348 42.308 0.00 0.00 40.55 4.01
2130 2347 2.604046 ACGGTCCTCACTTATCATGC 57.396 50.000 0.00 0.00 0.00 4.06
2131 2348 4.695455 ACAAAACGGTCCTCACTTATCATG 59.305 41.667 0.00 0.00 0.00 3.07
2140 2361 5.506649 GCAAATAGAAACAAAACGGTCCTCA 60.507 40.000 0.00 0.00 0.00 3.86
2197 2418 1.677576 GCATATGGCAAGTGCAGCTAA 59.322 47.619 18.79 0.00 44.36 3.09
2284 2508 6.921857 GTGTACAAGCTTCTGAGTACAAACTA 59.078 38.462 22.11 4.22 45.65 2.24
2357 2581 5.091261 ACCTGTGGATAGTGTCAATCTTC 57.909 43.478 0.00 0.00 0.00 2.87
2372 2596 7.207383 TCTACATACATAAATTCGACCTGTGG 58.793 38.462 0.00 0.00 0.00 4.17
2382 2606 7.922382 AGGGCATAGCTCTACATACATAAATT 58.078 34.615 0.00 0.00 37.75 1.82
2489 2725 3.181451 GGGAGAGATACATGACATGGCAA 60.181 47.826 19.39 5.25 33.60 4.52
2731 2969 3.372730 GCGGCACCATTGAAGGCA 61.373 61.111 0.00 0.00 0.00 4.75
2819 3057 1.096967 GGTGATGGTGATGATGCGCA 61.097 55.000 14.96 14.96 0.00 6.09
2822 3060 1.168407 CCGGGTGATGGTGATGATGC 61.168 60.000 0.00 0.00 0.00 3.91
3108 3352 2.029073 CCTGCACGAGTTGGACGT 59.971 61.111 0.00 0.00 44.83 4.34
3260 3507 1.958205 GCTTCCGAGATCATGGGCG 60.958 63.158 0.00 0.00 0.00 6.13
3261 3508 1.958205 CGCTTCCGAGATCATGGGC 60.958 63.158 0.00 0.00 36.29 5.36
3262 3509 1.742146 TCGCTTCCGAGATCATGGG 59.258 57.895 0.00 0.00 38.82 4.00
3463 3714 6.316640 CGTTCCTAACTCATCTCTCAGACTTA 59.683 42.308 0.00 0.00 0.00 2.24
3464 3715 5.124776 CGTTCCTAACTCATCTCTCAGACTT 59.875 44.000 0.00 0.00 0.00 3.01
3465 3716 4.638421 CGTTCCTAACTCATCTCTCAGACT 59.362 45.833 0.00 0.00 0.00 3.24
3466 3717 4.396790 ACGTTCCTAACTCATCTCTCAGAC 59.603 45.833 0.00 0.00 0.00 3.51
3471 3722 5.113446 TCCTACGTTCCTAACTCATCTCT 57.887 43.478 0.00 0.00 0.00 3.10
3566 3817 2.737881 GCATGTGCATGGGGGCAAT 61.738 57.895 13.28 0.00 46.93 3.56
3665 3922 9.088987 ACTTTTTCCATTACCATGTTATGACTT 57.911 29.630 0.00 0.00 0.00 3.01
3666 3923 8.650143 ACTTTTTCCATTACCATGTTATGACT 57.350 30.769 0.00 0.00 0.00 3.41
3668 3925 9.967451 TCTACTTTTTCCATTACCATGTTATGA 57.033 29.630 0.00 0.00 0.00 2.15
3672 3929 8.934023 TCTTCTACTTTTTCCATTACCATGTT 57.066 30.769 0.00 0.00 0.00 2.71
3732 3991 7.636259 TGAAGAAAATTTATGCACCTTTTCG 57.364 32.000 14.21 0.00 40.69 3.46
3760 4022 6.173339 GTCTCCAACTCTCCATGTCAAATTA 58.827 40.000 0.00 0.00 0.00 1.40
3762 4024 4.042062 TGTCTCCAACTCTCCATGTCAAAT 59.958 41.667 0.00 0.00 0.00 2.32
3763 4025 3.390967 TGTCTCCAACTCTCCATGTCAAA 59.609 43.478 0.00 0.00 0.00 2.69
3766 4028 2.354203 GGTGTCTCCAACTCTCCATGTC 60.354 54.545 0.00 0.00 35.97 3.06
3767 4029 1.625818 GGTGTCTCCAACTCTCCATGT 59.374 52.381 0.00 0.00 35.97 3.21
3768 4030 1.625315 TGGTGTCTCCAACTCTCCATG 59.375 52.381 0.00 0.00 44.12 3.66
3769 4031 2.030027 TGGTGTCTCCAACTCTCCAT 57.970 50.000 0.00 0.00 44.12 3.41
3770 4032 3.550692 TGGTGTCTCCAACTCTCCA 57.449 52.632 0.00 0.00 44.12 3.86
3883 4145 2.632512 TGCTGTCACACTCACAGGATTA 59.367 45.455 2.21 0.00 41.49 1.75
3896 4158 0.599991 TCATCACCGTGTGCTGTCAC 60.600 55.000 0.00 0.00 43.40 3.67
3902 4171 2.987413 TCAAAATCATCACCGTGTGC 57.013 45.000 0.00 0.00 32.98 4.57
3910 4179 4.844998 TTTGCGTCCTTCAAAATCATCA 57.155 36.364 0.00 0.00 31.27 3.07
3914 4183 5.046910 TGAGATTTGCGTCCTTCAAAATC 57.953 39.130 0.00 0.00 37.04 2.17
3965 4320 0.033504 TGACACTCCGTTGGCTTCTC 59.966 55.000 0.00 0.00 0.00 2.87
3973 4328 3.490419 GGCTCGTATATTGACACTCCGTT 60.490 47.826 0.00 0.00 0.00 4.44
3986 4341 8.251026 CCTCATATCAAATTGTAGGCTCGTATA 58.749 37.037 0.00 0.00 0.00 1.47
4004 4359 2.159028 GCTTATCTCCGCCCCTCATATC 60.159 54.545 0.00 0.00 0.00 1.63
4079 4435 0.940126 GCTCTCCAATACATGCGTGG 59.060 55.000 11.36 0.00 0.00 4.94
4106 4462 7.009179 TCTCACTCAACTAAGATTGTCCATT 57.991 36.000 0.00 0.00 0.00 3.16
4124 4480 7.985752 CGGGTTTAGGTATTCTTTAATCTCACT 59.014 37.037 0.00 0.00 0.00 3.41
4135 4491 2.835764 TCACAGCGGGTTTAGGTATTCT 59.164 45.455 0.00 0.00 0.00 2.40
4144 4500 0.107831 TGCTAGTTCACAGCGGGTTT 59.892 50.000 0.00 0.00 42.13 3.27
4150 4506 3.253188 TGTTGGAATTGCTAGTTCACAGC 59.747 43.478 0.00 0.00 39.56 4.40


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

AutoCloner maintained by Alex Coulton.