Multiple sequence alignment - TraesCS6B01G342700

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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 TraesCS6B01G342700 chr6B 100.000 7983 0 0 1 7983 603363220 603355238 0.000000e+00 14742
1 TraesCS6B01G342700 chr6D 95.041 6695 161 67 7 6574 402497943 402491293 0.000000e+00 10366
2 TraesCS6B01G342700 chr6D 88.618 984 63 19 6631 7585 402491284 402490321 0.000000e+00 1151
3 TraesCS6B01G342700 chr6D 91.291 333 13 6 7662 7983 402490303 402489976 2.640000e-119 440
4 TraesCS6B01G342700 chr6A 92.653 5907 205 88 2 5788 549236304 549230507 0.000000e+00 8292
5 TraesCS6B01G342700 chr6A 93.682 1931 96 12 5787 7704 549230341 549228424 0.000000e+00 2867
6 TraesCS6B01G342700 chr6A 88.235 153 6 3 7835 7983 549228371 549228227 1.070000e-38 172
7 TraesCS6B01G342700 chr7A 89.655 87 8 1 3949 4035 470791899 470791984 8.470000e-20 110
8 TraesCS6B01G342700 chr7D 88.506 87 9 1 3949 4035 409518121 409518206 3.940000e-18 104


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 TraesCS6B01G342700 chr6B 603355238 603363220 7982 True 14742.000000 14742 100.000000 1 7983 1 chr6B.!!$R1 7982
1 TraesCS6B01G342700 chr6D 402489976 402497943 7967 True 3985.666667 10366 91.650000 7 7983 3 chr6D.!!$R1 7976
2 TraesCS6B01G342700 chr6A 549228227 549236304 8077 True 3777.000000 8292 91.523333 2 7983 3 chr6A.!!$R1 7981

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
279 313 0.179015 CCGTAGCTCTCTCCAGCCTA 60.179 60.000 0.00 0.0 40.65 3.93 F
728 819 0.247736 CACTGGAGTAAAGAGGCGCT 59.752 55.000 7.64 0.0 0.00 5.92 F
903 996 2.103934 CTCCCGCTCTCTCGCTTG 59.896 66.667 0.00 0.0 0.00 4.01 F
1278 1393 2.590007 GCGCTCGCCATCCTCATT 60.590 61.111 0.00 0.0 34.56 2.57 F
2082 2234 2.354203 CCTAGTTGGGTGAGTCTCTTGC 60.354 54.545 0.65 0.0 0.00 4.01 F
3364 3518 1.604278 GACACTGACTTTGTTGGCTCC 59.396 52.381 0.00 0.0 0.00 4.70 F
4506 4673 1.078143 GCGGGTCTCTTTGGCTGAT 60.078 57.895 0.00 0.0 0.00 2.90 F
4965 5132 0.586319 CGGTTGTGAAACGTGCATCT 59.414 50.000 0.00 0.0 42.39 2.90 F
6385 6727 1.398390 GTAAATCTGCGGGTTGCTCAG 59.602 52.381 0.00 0.0 46.63 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1733 0.036388 GATCAAGAGGCCCACAACGA 60.036 55.000 0.00 0.00 0.00 3.85 R
2063 2215 2.609747 AGCAAGAGACTCACCCAACTA 58.390 47.619 5.02 0.00 0.00 2.24 R
2065 2217 3.618690 ATAGCAAGAGACTCACCCAAC 57.381 47.619 5.02 0.00 0.00 3.77 R
3055 3209 0.837691 ATGACTCAGGAGGCCACACA 60.838 55.000 5.01 0.00 34.90 3.72 R
3929 4083 0.875059 GTTCCAACCTTCCAGCTTCG 59.125 55.000 0.00 0.00 0.00 3.79 R
4717 4884 0.175760 ATCAAGGTCACGTGATCGGG 59.824 55.000 23.12 17.94 41.04 5.14 R
5346 5513 0.324645 TCCACCTCCCTACCCGTAAC 60.325 60.000 0.00 0.00 0.00 2.50 R
6713 7055 0.038526 GTCGCCTCGAACCTGAAGAA 60.039 55.000 0.00 0.00 37.72 2.52 R
7196 7547 0.106967 GCCACCTCCTTCATCTTCCC 60.107 60.000 0.00 0.00 0.00 3.97 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
109 127 2.415426 GCTGGCTCTACCTCGCTC 59.585 66.667 0.00 0.00 40.22 5.03
110 128 2.718731 CTGGCTCTACCTCGCTCG 59.281 66.667 0.00 0.00 40.22 5.03
111 129 3.477224 CTGGCTCTACCTCGCTCGC 62.477 68.421 0.00 0.00 40.22 5.03
112 130 3.213402 GGCTCTACCTCGCTCGCT 61.213 66.667 0.00 0.00 34.51 4.93
173 195 2.018086 CCTCTCCCTCCCTCCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
175 197 2.197324 CTCCCTCCCTCCCTCTCG 59.803 72.222 0.00 0.00 0.00 4.04
176 198 2.617538 TCCCTCCCTCCCTCTCGT 60.618 66.667 0.00 0.00 0.00 4.18
206 232 1.541620 GGTTGGTTCCCTCCTCCCT 60.542 63.158 0.00 0.00 0.00 4.20
276 310 1.755008 ACCCGTAGCTCTCTCCAGC 60.755 63.158 0.00 0.00 39.99 4.85
279 313 0.179015 CCGTAGCTCTCTCCAGCCTA 60.179 60.000 0.00 0.00 40.65 3.93
373 413 2.187946 CGATCTCCGCCAGCCTTT 59.812 61.111 0.00 0.00 0.00 3.11
383 423 4.033776 CAGCCTTTCGCCCTCCCA 62.034 66.667 0.00 0.00 38.78 4.37
449 497 1.206578 CTAGCTAGCTCGCTCGCTC 59.793 63.158 23.26 0.00 42.81 5.03
450 498 2.493088 CTAGCTAGCTCGCTCGCTCG 62.493 65.000 23.26 11.08 42.81 5.03
576 645 3.066760 GGCCTTTGTCCAGAATATTTCCG 59.933 47.826 0.00 0.00 0.00 4.30
581 650 2.026729 TGTCCAGAATATTTCCGGCACA 60.027 45.455 0.00 0.00 0.00 4.57
728 819 0.247736 CACTGGAGTAAAGAGGCGCT 59.752 55.000 7.64 0.00 0.00 5.92
754 846 3.550030 GCTGCGGATTTTATTAATGCGGT 60.550 43.478 12.14 0.00 40.94 5.68
902 995 3.832492 GCTCCCGCTCTCTCGCTT 61.832 66.667 0.00 0.00 0.00 4.68
903 996 2.103934 CTCCCGCTCTCTCGCTTG 59.896 66.667 0.00 0.00 0.00 4.01
904 997 2.676822 TCCCGCTCTCTCGCTTGT 60.677 61.111 0.00 0.00 0.00 3.16
1028 1143 5.366460 GAGTAGTAGTAAATTGGGGGAAGC 58.634 45.833 0.00 0.00 0.00 3.86
1078 1193 4.752879 GCAAGTACGCGGCCAGGA 62.753 66.667 12.47 0.00 0.00 3.86
1278 1393 2.590007 GCGCTCGCCATCCTCATT 60.590 61.111 0.00 0.00 34.56 2.57
1376 1506 3.390175 TCTTCCTCTTCCTCCTCGATT 57.610 47.619 0.00 0.00 0.00 3.34
1377 1507 3.027412 TCTTCCTCTTCCTCCTCGATTG 58.973 50.000 0.00 0.00 0.00 2.67
1380 1510 2.961741 TCCTCTTCCTCCTCGATTGATG 59.038 50.000 0.00 0.00 0.00 3.07
1381 1511 2.697751 CCTCTTCCTCCTCGATTGATGT 59.302 50.000 0.00 0.00 0.00 3.06
1382 1512 3.891977 CCTCTTCCTCCTCGATTGATGTA 59.108 47.826 0.00 0.00 0.00 2.29
1384 1514 5.336372 CCTCTTCCTCCTCGATTGATGTATC 60.336 48.000 0.00 0.00 0.00 2.24
1385 1515 4.524714 TCTTCCTCCTCGATTGATGTATCC 59.475 45.833 0.00 0.00 0.00 2.59
1386 1516 2.820197 TCCTCCTCGATTGATGTATCCG 59.180 50.000 0.00 0.00 0.00 4.18
1495 1644 4.624015 CAAAACATGGTTGTTGCATCTCT 58.376 39.130 0.00 0.00 45.30 3.10
1583 1733 5.618195 CGGCACATTATTGTTTTAGTCGGTT 60.618 40.000 0.00 0.00 32.34 4.44
1789 1940 5.334802 CGACTCCATTTGTTTATGCTCACAA 60.335 40.000 0.00 0.00 0.00 3.33
1790 1941 6.594788 ACTCCATTTGTTTATGCTCACAAT 57.405 33.333 0.00 0.00 32.96 2.71
2070 2222 4.837093 TTTGGATACTGACCTAGTTGGG 57.163 45.455 0.00 0.00 40.89 4.12
2081 2233 2.900546 ACCTAGTTGGGTGAGTCTCTTG 59.099 50.000 0.65 0.00 41.11 3.02
2082 2234 2.354203 CCTAGTTGGGTGAGTCTCTTGC 60.354 54.545 0.65 0.00 0.00 4.01
2093 2245 8.325787 TGGGTGAGTCTCTTGCTATAATAAAAA 58.674 33.333 0.65 0.00 0.00 1.94
2128 2280 7.121315 GGATTAGGTGCAGTTTAAACTTGATCT 59.879 37.037 18.25 14.50 37.08 2.75
2156 2308 3.837355 ACTTTCTTGGATGCTCTTGGTT 58.163 40.909 0.00 0.00 0.00 3.67
2162 2314 5.569355 TCTTGGATGCTCTTGGTTATTCAA 58.431 37.500 0.00 0.00 0.00 2.69
2497 2649 3.084039 TGCATGATGGTTTCTTCTGTCC 58.916 45.455 0.00 0.00 0.00 4.02
2500 2652 3.485463 TGATGGTTTCTTCTGTCCGTT 57.515 42.857 0.00 0.00 0.00 4.44
2545 2698 3.988459 ACACGTTGTGTTGCAAGTC 57.012 47.368 0.00 0.00 45.08 3.01
2886 3039 7.276438 GCAGATGATTCGACATAGCATACAATA 59.724 37.037 7.59 0.00 34.12 1.90
2981 3134 7.281774 TCTCATTCAGCAATACAAAGATCCTTC 59.718 37.037 0.00 0.00 0.00 3.46
3095 3249 9.072375 AGTCATGACTCTAATCTAATCGAATCA 57.928 33.333 22.89 0.00 36.92 2.57
3364 3518 1.604278 GACACTGACTTTGTTGGCTCC 59.396 52.381 0.00 0.00 0.00 4.70
3600 3754 9.185192 CAAAGTCTCAGGTTTGACATTTATTTC 57.815 33.333 0.00 0.00 35.99 2.17
3743 3897 8.432805 TCCTTGGTATGAATATCTTCCTTTCTC 58.567 37.037 0.00 0.00 0.00 2.87
3759 3913 6.855836 TCCTTTCTCGTACATACATAACGTT 58.144 36.000 5.88 5.88 37.83 3.99
3929 4083 3.067106 TGTCCTTGATCGAGCAAAGTTC 58.933 45.455 17.83 9.62 0.00 3.01
4054 4208 9.776158 CATAGAGGTATCTTACTATTACAAGCG 57.224 37.037 0.00 0.00 36.96 4.68
4344 4498 4.873827 TCAAAGTAAGCAGTCAACTTTCGT 59.126 37.500 0.00 0.00 40.52 3.85
4394 4561 9.919348 CTTTGAATAATGTTGACCTTTTGTTTG 57.081 29.630 0.00 0.00 0.00 2.93
4506 4673 1.078143 GCGGGTCTCTTTGGCTGAT 60.078 57.895 0.00 0.00 0.00 2.90
4833 5000 5.106515 GGCAGATAGTTCAACTTCAAGGAAC 60.107 44.000 0.00 0.00 40.84 3.62
4908 5075 2.093711 GGGCGGGCAAATAAGTTTCATT 60.094 45.455 3.27 0.00 0.00 2.57
4956 5123 2.571212 ACATTCTCAGCGGTTGTGAAA 58.429 42.857 12.18 0.00 41.20 2.69
4965 5132 0.586319 CGGTTGTGAAACGTGCATCT 59.414 50.000 0.00 0.00 42.39 2.90
5346 5513 7.009179 TGAGAGGCTAATGTTCCCATATTAG 57.991 40.000 0.00 0.00 39.01 1.73
5350 5517 8.376270 AGAGGCTAATGTTCCCATATTAGTTAC 58.624 37.037 0.00 0.00 38.51 2.50
5363 5530 2.442236 TAGTTACGGGTAGGGAGGTG 57.558 55.000 0.00 0.00 0.00 4.00
5373 5540 2.158943 GGTAGGGAGGTGGAAAGATTCG 60.159 54.545 0.00 0.00 0.00 3.34
5383 5550 4.378459 GGTGGAAAGATTCGCACTACTTTG 60.378 45.833 0.00 0.00 33.61 2.77
5390 5557 5.978814 AGATTCGCACTACTTTGAGGTAAT 58.021 37.500 0.00 0.00 0.00 1.89
5391 5558 7.108841 AGATTCGCACTACTTTGAGGTAATA 57.891 36.000 0.00 0.00 0.00 0.98
5392 5559 6.979238 AGATTCGCACTACTTTGAGGTAATAC 59.021 38.462 0.00 0.00 0.00 1.89
5566 5733 6.092259 GGCAAGTTGTAGTTAATCGAATGACT 59.908 38.462 4.48 3.22 0.00 3.41
5588 5755 3.149196 GGAATGTCTCTGTGAGCCAAAA 58.851 45.455 0.00 0.00 0.00 2.44
5593 5760 3.181451 TGTCTCTGTGAGCCAAAATCAGT 60.181 43.478 0.00 0.00 0.00 3.41
5615 5782 4.010349 TCAGACAGAGATAAAGCACTCGA 58.990 43.478 0.00 0.00 38.08 4.04
5666 5841 5.660629 TGAAGCAATTTCTGTGCAATTTG 57.339 34.783 0.00 0.00 44.74 2.32
5812 6154 2.203153 GGGTGGACGTTGTGCTGT 60.203 61.111 0.00 0.00 0.00 4.40
5994 6336 7.530426 AAATTCTTCTTCAACACCTGCTTAT 57.470 32.000 0.00 0.00 0.00 1.73
6010 6352 7.554118 CACCTGCTTATTCTCTTTTCTCCATTA 59.446 37.037 0.00 0.00 0.00 1.90
6011 6353 8.109634 ACCTGCTTATTCTCTTTTCTCCATTAA 58.890 33.333 0.00 0.00 0.00 1.40
6012 6354 9.129532 CCTGCTTATTCTCTTTTCTCCATTAAT 57.870 33.333 0.00 0.00 0.00 1.40
6053 6395 4.041723 AGAAAAACCGTCGATGCTTTTTG 58.958 39.130 22.06 2.13 0.00 2.44
6385 6727 1.398390 GTAAATCTGCGGGTTGCTCAG 59.602 52.381 0.00 0.00 46.63 3.35
6522 6864 4.508047 GCCTGAGATGGATGGGTATGATTT 60.508 45.833 0.00 0.00 0.00 2.17
6534 6876 7.285401 GGATGGGTATGATTTTGTGTACTCATT 59.715 37.037 0.00 0.00 38.12 2.57
6685 7027 6.988580 TGTTGCTTGATAGTATCTCATCCTTG 59.011 38.462 11.40 0.00 0.00 3.61
6691 7033 7.055667 TGATAGTATCTCATCCTTGTTGACC 57.944 40.000 11.40 0.00 0.00 4.02
6700 7042 2.695359 TCCTTGTTGACCGCTGATTAC 58.305 47.619 0.00 0.00 0.00 1.89
6710 7052 4.141824 TGACCGCTGATTACCAATGTGATA 60.142 41.667 0.00 0.00 0.00 2.15
6713 7055 6.711277 ACCGCTGATTACCAATGTGATATAT 58.289 36.000 0.00 0.00 0.00 0.86
6745 7087 2.728922 GAGGCGACTAGACAAATACGG 58.271 52.381 0.00 0.00 44.43 4.02
6805 7147 0.685097 CGAGTTCAGGGGAAGGTTCA 59.315 55.000 0.00 0.00 32.62 3.18
6886 7228 4.183865 CCTACGAAGAGTGCATGAAATCA 58.816 43.478 3.54 0.00 0.00 2.57
7001 7343 3.001395 GATCTGATCGATCGAAACCGT 57.999 47.619 23.50 4.62 39.22 4.83
7096 7439 4.401022 TGCAACACTTTGGATGAGAAGAT 58.599 39.130 0.00 0.00 32.81 2.40
7102 7445 5.222007 ACACTTTGGATGAGAAGATGAAGGT 60.222 40.000 0.00 0.00 0.00 3.50
7217 7587 1.407989 GGAAGATGAAGGAGGTGGCTG 60.408 57.143 0.00 0.00 0.00 4.85
7284 7654 5.728471 AGTAGGCAGATGTATGTATGATGC 58.272 41.667 0.00 0.00 0.00 3.91
7333 7703 9.836864 TTTGAACATATATAACATCTCTGTGCT 57.163 29.630 0.00 0.00 35.22 4.40
7402 7779 4.599041 TGAGAAGAAAATATGTGGTGGGG 58.401 43.478 0.00 0.00 0.00 4.96
7407 7784 6.328934 AGAAGAAAATATGTGGTGGGGTTTTT 59.671 34.615 0.00 0.00 0.00 1.94
7410 7787 2.016905 TATGTGGTGGGGTTTTTGGG 57.983 50.000 0.00 0.00 0.00 4.12
7412 7789 0.688087 TGTGGTGGGGTTTTTGGGTC 60.688 55.000 0.00 0.00 0.00 4.46
7440 7822 3.823421 CGCCGCGTGTTCGTACTG 61.823 66.667 4.92 0.00 39.49 2.74
7441 7823 3.475774 GCCGCGTGTTCGTACTGG 61.476 66.667 4.92 0.00 39.49 4.00
7519 7901 1.021968 AACTGGGCGTGTGTCTTTTC 58.978 50.000 0.00 0.00 0.00 2.29
7526 7908 1.333258 GCGTGTGTCTTTTCTGTCTGC 60.333 52.381 0.00 0.00 0.00 4.26
7528 7910 2.288666 GTGTGTCTTTTCTGTCTGCCA 58.711 47.619 0.00 0.00 0.00 4.92
7534 7916 4.067896 GTCTTTTCTGTCTGCCAAGATGA 58.932 43.478 0.00 0.00 34.13 2.92
7535 7917 4.516698 GTCTTTTCTGTCTGCCAAGATGAA 59.483 41.667 0.00 0.00 34.13 2.57
7538 7920 3.606595 TCTGTCTGCCAAGATGAAGAG 57.393 47.619 0.00 0.00 34.13 2.85
7542 7924 4.067896 TGTCTGCCAAGATGAAGAGTTTC 58.932 43.478 0.00 0.00 34.13 2.78
7543 7925 4.202398 TGTCTGCCAAGATGAAGAGTTTCT 60.202 41.667 0.00 0.00 34.13 2.52
7556 7938 2.003301 GAGTTTCTTAGGCCTCTTGCG 58.997 52.381 9.68 0.00 42.61 4.85
7599 7981 5.163764 CCTCTGTAAATTGACGCATTTGCTA 60.164 40.000 0.51 0.00 39.32 3.49
7604 7986 1.890876 TTGACGCATTTGCTACTGGT 58.109 45.000 0.51 0.00 39.32 4.00
7618 8000 1.609208 ACTGGTAAGTTGCCTGCAAG 58.391 50.000 15.30 5.34 36.52 4.01
7631 8013 1.608590 CCTGCAAGAACGAATTGGTGT 59.391 47.619 0.00 0.00 34.07 4.16
7773 8155 1.067000 GCATTGTGTATTTGCTGGGCA 60.067 47.619 0.00 0.00 36.47 5.36
7774 8156 2.883574 CATTGTGTATTTGCTGGGCAG 58.116 47.619 0.00 0.00 40.61 4.85
7775 8157 2.284754 TTGTGTATTTGCTGGGCAGA 57.715 45.000 0.00 0.00 40.61 4.26
7776 8158 2.512692 TGTGTATTTGCTGGGCAGAT 57.487 45.000 0.00 1.50 40.61 2.90
7777 8159 2.093890 TGTGTATTTGCTGGGCAGATG 58.906 47.619 5.92 0.00 40.61 2.90
7792 8174 4.083110 GGGCAGATGGATGATAACGAAATG 60.083 45.833 0.00 0.00 0.00 2.32
7823 8205 1.669779 GCTTGGATGTCTCATGTCTGC 59.330 52.381 0.00 0.00 0.00 4.26
7830 8212 2.081462 TGTCTCATGTCTGCATTGCTG 58.919 47.619 10.49 9.74 31.99 4.41
7899 8301 1.421268 TCTGCCATGGTGTTTGACTCT 59.579 47.619 14.67 0.00 0.00 3.24
7970 8377 3.933722 AGTGCGCACTGCTCCTGT 61.934 61.111 40.34 15.76 46.63 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 4.115199 CAGTAGGGGGTGCCAGGC 62.115 72.222 3.66 3.66 0.00 4.85
75 76 3.411517 CCAGTAGGGGGTGCCAGG 61.412 72.222 0.00 0.00 0.00 4.45
76 77 4.115199 GCCAGTAGGGGGTGCCAG 62.115 72.222 0.00 0.00 37.04 4.85
175 197 2.674380 CAACCAGGCAGGCCAGAC 60.674 66.667 13.63 0.00 43.14 3.51
176 198 3.970410 CCAACCAGGCAGGCCAGA 61.970 66.667 13.63 0.00 43.14 3.86
225 251 4.530857 CTCGGTGGTGGCGATCCC 62.531 72.222 0.00 0.00 0.00 3.85
254 280 0.671251 GGAGAGAGCTACGGGTGATG 59.329 60.000 0.00 0.00 0.00 3.07
255 281 0.259065 TGGAGAGAGCTACGGGTGAT 59.741 55.000 0.00 0.00 0.00 3.06
256 282 0.394488 CTGGAGAGAGCTACGGGTGA 60.394 60.000 0.00 0.00 0.00 4.02
276 310 0.177373 TGCTGCTGATCTGCTGTAGG 59.823 55.000 25.05 12.60 39.95 3.18
279 313 1.078356 CCTGCTGCTGATCTGCTGT 60.078 57.895 25.05 0.00 39.95 4.40
373 413 2.674754 GTGGAATTGGGAGGGCGA 59.325 61.111 0.00 0.00 0.00 5.54
379 419 1.780488 TGGGTGGGTGGAATTGGGA 60.780 57.895 0.00 0.00 0.00 4.37
381 421 1.609210 GGTGGGTGGGTGGAATTGG 60.609 63.158 0.00 0.00 0.00 3.16
383 423 0.266152 TTTGGTGGGTGGGTGGAATT 59.734 50.000 0.00 0.00 0.00 2.17
513 578 2.182537 GGCAAGCCAATTGAGCGG 59.817 61.111 7.12 7.89 41.83 5.52
731 822 2.651703 CGCATTAATAAAATCCGCAGCG 59.348 45.455 8.18 8.18 35.42 5.18
734 825 4.640789 AACCGCATTAATAAAATCCGCA 57.359 36.364 0.00 0.00 0.00 5.69
735 826 5.116528 GCTAAACCGCATTAATAAAATCCGC 59.883 40.000 0.00 0.00 0.00 5.54
736 827 5.338559 CGCTAAACCGCATTAATAAAATCCG 59.661 40.000 0.00 0.00 0.00 4.18
772 864 4.151689 CAGCGGCGCTAAAATAATTAGCTA 59.848 41.667 35.90 0.00 43.77 3.32
773 865 3.058914 CAGCGGCGCTAAAATAATTAGCT 60.059 43.478 35.90 4.01 43.77 3.32
774 866 3.226347 CAGCGGCGCTAAAATAATTAGC 58.774 45.455 35.90 9.57 42.82 3.09
775 867 4.211374 AGACAGCGGCGCTAAAATAATTAG 59.789 41.667 35.90 19.91 36.40 1.73
899 992 3.634910 TGGTACCCAGAAGAAAAACAAGC 59.365 43.478 10.07 0.00 0.00 4.01
1028 1143 3.666122 CCCCCTTCTCCTCCATGG 58.334 66.667 4.97 4.97 37.10 3.66
1278 1393 1.712056 TCTCGAAGTGGAAGGTGGAA 58.288 50.000 0.00 0.00 0.00 3.53
1376 1506 4.749976 TGAACGAATGAACGGATACATCA 58.250 39.130 0.00 0.00 36.61 3.07
1377 1507 5.907197 ATGAACGAATGAACGGATACATC 57.093 39.130 0.00 0.00 37.61 3.06
1380 1510 4.025145 GGGAATGAACGAATGAACGGATAC 60.025 45.833 0.00 0.00 37.61 2.24
1381 1511 4.124238 GGGAATGAACGAATGAACGGATA 58.876 43.478 0.00 0.00 37.61 2.59
1382 1512 2.943033 GGGAATGAACGAATGAACGGAT 59.057 45.455 0.00 0.00 37.61 4.18
1384 1514 2.080693 TGGGAATGAACGAATGAACGG 58.919 47.619 0.00 0.00 37.61 4.44
1385 1515 3.126858 ACATGGGAATGAACGAATGAACG 59.873 43.478 0.00 0.00 39.31 3.95
1386 1516 4.662145 GACATGGGAATGAACGAATGAAC 58.338 43.478 0.00 0.00 0.00 3.18
1583 1733 0.036388 GATCAAGAGGCCCACAACGA 60.036 55.000 0.00 0.00 0.00 3.85
2063 2215 2.609747 AGCAAGAGACTCACCCAACTA 58.390 47.619 5.02 0.00 0.00 2.24
2065 2217 3.618690 ATAGCAAGAGACTCACCCAAC 57.381 47.619 5.02 0.00 0.00 3.77
2066 2218 5.957771 ATTATAGCAAGAGACTCACCCAA 57.042 39.130 5.02 0.00 0.00 4.12
2068 2220 8.732746 TTTTTATTATAGCAAGAGACTCACCC 57.267 34.615 5.02 0.00 0.00 4.61
2093 2245 4.603131 ACTGCACCTAATCCATGTGATTT 58.397 39.130 12.69 0.00 40.92 2.17
2128 2280 7.255590 CCAAGAGCATCCAAGAAAGTAAGAAAA 60.256 37.037 0.00 0.00 33.66 2.29
2156 2308 9.935682 GCGAATTGACAGATTTAAGATTGAATA 57.064 29.630 0.00 0.00 0.00 1.75
2162 2314 5.587844 AGCAGCGAATTGACAGATTTAAGAT 59.412 36.000 0.00 0.00 0.00 2.40
2308 2460 4.065088 CAAACGTTTCCTTCTCATGAGGA 58.935 43.478 22.42 13.61 0.00 3.71
2497 2649 5.447818 GCCCTCAATGAACTAAGAATCAACG 60.448 44.000 0.00 0.00 0.00 4.10
2500 2652 5.178096 TGCCCTCAATGAACTAAGAATCA 57.822 39.130 0.00 0.00 0.00 2.57
2541 2694 8.570068 TTTACACTGAACCAAACTTAAGACTT 57.430 30.769 10.09 0.00 0.00 3.01
2787 2940 7.257722 CAAATACAGGTTTTATGGGTCATCAC 58.742 38.462 0.00 0.00 0.00 3.06
2886 3039 9.331282 GATACATTAATGCAAGTTCTCTAGGTT 57.669 33.333 15.48 0.00 0.00 3.50
2981 3134 8.367911 TCTAAATATGTTGGCTATCACACTAGG 58.632 37.037 0.00 0.00 0.00 3.02
3055 3209 0.837691 ATGACTCAGGAGGCCACACA 60.838 55.000 5.01 0.00 34.90 3.72
3095 3249 2.027745 CACCAAGATAGCTGTCAGTGGT 60.028 50.000 24.35 24.35 38.55 4.16
3364 3518 4.398319 ACCAACATTAGTGGAAGGACAAG 58.602 43.478 0.00 0.00 0.00 3.16
3600 3754 1.065854 AGCCAAGTAGCCTAAGCACAG 60.066 52.381 0.00 0.00 43.56 3.66
3743 3897 7.375280 CCTTAGAGTGAACGTTATGTATGTACG 59.625 40.741 0.00 0.00 40.85 3.67
3756 3910 2.099427 GGCCTAGTCCTTAGAGTGAACG 59.901 54.545 0.00 0.00 0.00 3.95
3759 3913 3.205507 AGATGGCCTAGTCCTTAGAGTGA 59.794 47.826 3.32 0.00 0.00 3.41
3929 4083 0.875059 GTTCCAACCTTCCAGCTTCG 59.125 55.000 0.00 0.00 0.00 3.79
4506 4673 7.068348 ACTCGATTAGCTTCCATAGTTGAGTTA 59.932 37.037 0.00 0.00 32.55 2.24
4717 4884 0.175760 ATCAAGGTCACGTGATCGGG 59.824 55.000 23.12 17.94 41.04 5.14
4833 5000 4.503714 ACCAATACCAGTTCCACCATAG 57.496 45.455 0.00 0.00 0.00 2.23
4908 5075 0.619255 TCCCAATGGAAGGACGGCTA 60.619 55.000 0.00 0.00 37.86 3.93
4956 5123 6.256539 CACATGAAGTATCTTTAGATGCACGT 59.743 38.462 0.00 0.00 39.23 4.49
5065 5232 2.939103 GGTGATATCTTGTCACAGCACC 59.061 50.000 3.98 0.00 45.99 5.01
5161 5328 1.693627 ACTCACCTCGACTCTGTTGT 58.306 50.000 0.00 0.00 0.00 3.32
5172 5339 5.757850 AATGACAACAGAAAACTCACCTC 57.242 39.130 0.00 0.00 0.00 3.85
5249 5416 4.625607 ACAGCTAGAAACCAGTTAAGCT 57.374 40.909 0.00 8.39 40.79 3.74
5298 5465 2.873245 GCACATGTGAAAGCTCCTCTCA 60.873 50.000 29.80 0.00 0.00 3.27
5346 5513 0.324645 TCCACCTCCCTACCCGTAAC 60.325 60.000 0.00 0.00 0.00 2.50
5350 5517 0.616679 TCTTTCCACCTCCCTACCCG 60.617 60.000 0.00 0.00 0.00 5.28
5363 5530 4.093556 CCTCAAAGTAGTGCGAATCTTTCC 59.906 45.833 0.00 0.00 0.00 3.13
5373 5540 8.999220 AAACTAGTATTACCTCAAAGTAGTGC 57.001 34.615 0.00 0.00 0.00 4.40
5383 5550 9.583765 CACTTCCTACAAAACTAGTATTACCTC 57.416 37.037 0.00 0.00 0.00 3.85
5390 5557 8.685838 AAATTGCACTTCCTACAAAACTAGTA 57.314 30.769 0.00 0.00 0.00 1.82
5391 5558 7.582667 AAATTGCACTTCCTACAAAACTAGT 57.417 32.000 0.00 0.00 0.00 2.57
5392 5559 7.595130 GGAAAATTGCACTTCCTACAAAACTAG 59.405 37.037 12.24 0.00 38.48 2.57
5435 5602 7.906199 AAGCTCCTCTTGTATAAGTGATACT 57.094 36.000 3.17 0.00 41.08 2.12
5436 5603 8.198109 TGAAAGCTCCTCTTGTATAAGTGATAC 58.802 37.037 3.17 0.00 40.90 2.24
5437 5604 8.306313 TGAAAGCTCCTCTTGTATAAGTGATA 57.694 34.615 3.17 0.00 34.67 2.15
5444 5611 6.931281 GCACATATGAAAGCTCCTCTTGTATA 59.069 38.462 10.38 0.00 34.67 1.47
5566 5733 1.351076 TGGCTCACAGAGACATTCCA 58.649 50.000 0.00 0.00 43.49 3.53
5588 5755 5.421693 AGTGCTTTATCTCTGTCTGACTGAT 59.578 40.000 16.25 14.36 0.00 2.90
5593 5760 4.010349 TCGAGTGCTTTATCTCTGTCTGA 58.990 43.478 0.00 0.00 0.00 3.27
5615 5782 9.525409 CTTGATTTCTGTCACAGAGAAAAATTT 57.475 29.630 7.75 0.00 41.75 1.82
5666 5841 2.532250 AATCCCCATTGAGGTGGAAC 57.468 50.000 0.00 0.00 42.02 3.62
5812 6154 1.195115 GTCCTAGTCCACCTCATGCA 58.805 55.000 0.00 0.00 0.00 3.96
5852 6194 0.610174 CCTGCTCTGCCAAGTCTACA 59.390 55.000 0.00 0.00 0.00 2.74
6053 6395 2.941720 GCCTCCAGATGTCATTCTCAAC 59.058 50.000 0.00 0.00 0.00 3.18
6385 6727 1.009829 CATACTTCTTCAGTGCGGCC 58.990 55.000 0.00 0.00 35.97 6.13
6522 6864 4.245660 GCAGCAGAGTAATGAGTACACAA 58.754 43.478 0.00 0.00 34.88 3.33
6534 6876 5.551233 AGAAATAACAGTTGCAGCAGAGTA 58.449 37.500 2.55 0.00 0.00 2.59
6628 6970 9.143155 TGACACATAAAGCCTAGAGAACATATA 57.857 33.333 0.00 0.00 0.00 0.86
6629 6971 8.023021 TGACACATAAAGCCTAGAGAACATAT 57.977 34.615 0.00 0.00 0.00 1.78
6639 6981 6.952773 ACAAAACTTGACACATAAAGCCTA 57.047 33.333 0.00 0.00 0.00 3.93
6685 7027 2.747446 ACATTGGTAATCAGCGGTCAAC 59.253 45.455 0.00 0.00 0.00 3.18
6691 7033 8.484641 AGAATATATCACATTGGTAATCAGCG 57.515 34.615 0.00 0.00 0.00 5.18
6700 7042 7.657354 TCGAACCTGAAGAATATATCACATTGG 59.343 37.037 0.00 0.00 0.00 3.16
6710 7052 2.693591 TCGCCTCGAACCTGAAGAATAT 59.306 45.455 0.00 0.00 31.06 1.28
6713 7055 0.038526 GTCGCCTCGAACCTGAAGAA 60.039 55.000 0.00 0.00 37.72 2.52
6745 7087 3.424962 CGTTCGCTTTCTTCTCCATTTCC 60.425 47.826 0.00 0.00 0.00 3.13
6805 7147 3.560896 GCAAATGCCACTCAACAAATGTT 59.439 39.130 0.00 0.00 35.09 2.71
6886 7228 0.691078 ACACGTAGCCATCCATCCCT 60.691 55.000 0.00 0.00 0.00 4.20
6972 7314 1.708341 TCGATCAGATCATGAGGCCA 58.292 50.000 5.01 0.00 42.53 5.36
7001 7343 0.968901 ACCAACTGAGGCGTCGGATA 60.969 55.000 21.59 0.00 32.75 2.59
7014 7356 0.465460 TGGCTTCGCTTCAACCAACT 60.465 50.000 0.00 0.00 0.00 3.16
7096 7439 1.002430 CACTAGCTCAAGGCACCTTCA 59.998 52.381 0.00 0.00 44.79 3.02
7102 7445 2.610479 CGAAGTTCACTAGCTCAAGGCA 60.610 50.000 3.32 0.00 44.79 4.75
7156 7507 1.890625 GCAGAAATGCATGCCCACCA 61.891 55.000 16.68 0.00 36.41 4.17
7188 7539 2.615227 CTTCATCTTCCCCTGGGGCG 62.615 65.000 27.93 19.53 43.94 6.13
7191 7542 0.842635 CTCCTTCATCTTCCCCTGGG 59.157 60.000 5.50 5.50 0.00 4.45
7192 7543 0.842635 CCTCCTTCATCTTCCCCTGG 59.157 60.000 0.00 0.00 0.00 4.45
7194 7545 1.589414 CACCTCCTTCATCTTCCCCT 58.411 55.000 0.00 0.00 0.00 4.79
7196 7547 0.106967 GCCACCTCCTTCATCTTCCC 60.107 60.000 0.00 0.00 0.00 3.97
7197 7548 0.915364 AGCCACCTCCTTCATCTTCC 59.085 55.000 0.00 0.00 0.00 3.46
7284 7654 6.219417 AGAATGAACAGACAGGAGATACAG 57.781 41.667 0.00 0.00 0.00 2.74
7329 7699 2.330393 CACAGCACAGCACAGCAC 59.670 61.111 0.00 0.00 0.00 4.40
7330 7700 3.588906 GCACAGCACAGCACAGCA 61.589 61.111 0.00 0.00 0.00 4.41
7331 7701 3.285215 AGCACAGCACAGCACAGC 61.285 61.111 0.00 0.00 0.00 4.40
7332 7702 2.184830 ACAGCACAGCACAGCACAG 61.185 57.895 0.00 0.00 0.00 3.66
7333 7703 2.124612 ACAGCACAGCACAGCACA 60.125 55.556 0.00 0.00 0.00 4.57
7402 7779 2.414806 GAGAGGAGACGACCCAAAAAC 58.585 52.381 0.00 0.00 0.00 2.43
7407 7784 2.045242 CGGAGAGGAGACGACCCA 60.045 66.667 0.00 0.00 0.00 4.51
7410 7787 3.878519 CGGCGGAGAGGAGACGAC 61.879 72.222 0.00 0.00 42.33 4.34
7440 7822 6.738832 ATGAATCGATGATCATCAATCACC 57.261 37.500 30.13 16.15 47.00 4.02
7471 7853 3.309410 CACCCAACAGTTTGCATCAAAAC 59.691 43.478 0.00 0.00 39.80 2.43
7519 7901 3.331478 ACTCTTCATCTTGGCAGACAG 57.669 47.619 0.00 0.00 0.00 3.51
7526 7908 4.637977 GGCCTAAGAAACTCTTCATCTTGG 59.362 45.833 0.00 0.00 37.89 3.61
7528 7910 5.487131 AGAGGCCTAAGAAACTCTTCATCTT 59.513 40.000 4.42 0.00 36.99 2.40
7535 7917 2.354203 CGCAAGAGGCCTAAGAAACTCT 60.354 50.000 4.42 0.00 41.77 3.24
7538 7920 0.448197 GCGCAAGAGGCCTAAGAAAC 59.552 55.000 4.42 0.00 40.31 2.78
7556 7938 3.435186 GGGAAACAGAGCAGCGGC 61.435 66.667 0.00 0.00 41.61 6.53
7558 7940 2.747855 GGGGGAAACAGAGCAGCG 60.748 66.667 0.00 0.00 0.00 5.18
7586 7968 5.040588 AACTTACCAGTAGCAAATGCGTCA 61.041 41.667 0.00 0.00 38.11 4.35
7590 7972 3.501950 GCAACTTACCAGTAGCAAATGC 58.498 45.455 0.00 0.00 34.66 3.56
7618 8000 5.464965 AATCGACATACACCAATTCGTTC 57.535 39.130 0.00 0.00 0.00 3.95
7631 8013 2.092968 AGCTGCCCAGAAAATCGACATA 60.093 45.455 0.00 0.00 0.00 2.29
7700 8082 0.602905 GCGACAGGTAAGTTGGCTGT 60.603 55.000 0.00 0.00 0.00 4.40
7762 8144 1.063492 TCATCCATCTGCCCAGCAAAT 60.063 47.619 0.00 0.00 38.41 2.32
7773 8155 5.371526 ACTGCATTTCGTTATCATCCATCT 58.628 37.500 0.00 0.00 0.00 2.90
7774 8156 5.613360 CGACTGCATTTCGTTATCATCCATC 60.613 44.000 9.20 0.00 0.00 3.51
7775 8157 4.212004 CGACTGCATTTCGTTATCATCCAT 59.788 41.667 9.20 0.00 0.00 3.41
7776 8158 3.555547 CGACTGCATTTCGTTATCATCCA 59.444 43.478 9.20 0.00 0.00 3.41
7777 8159 3.802139 TCGACTGCATTTCGTTATCATCC 59.198 43.478 15.29 0.00 37.73 3.51
7823 8205 6.009115 TGCATTTCATATCTAGCAGCAATG 57.991 37.500 0.00 0.00 0.00 2.82
7830 8212 3.415212 TGCCCTGCATTTCATATCTAGC 58.585 45.455 0.00 0.00 31.71 3.42


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

AutoCloner maintained by Alex Coulton.