Multiple sequence alignment - TraesCS7D01G479100

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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 TraesCS7D01G479100 chr7D 100.000 3036 0 0 1 3036 590418971 590415936 0.000000e+00 5607.0
1 TraesCS7D01G479100 chr7D 100.000 34 0 0 677 710 13024721 13024754 2.530000e-06 63.9
2 TraesCS7D01G479100 chr7B 93.473 3064 112 28 8 3036 665387121 665384111 0.000000e+00 4470.0
3 TraesCS7D01G479100 chr2A 86.269 335 39 7 2563 2894 398444789 398445119 1.040000e-94 357.0
4 TraesCS7D01G479100 chr2A 85.886 333 40 7 2565 2894 398871192 398870864 6.230000e-92 348.0
5 TraesCS7D01G479100 chr2A 100.000 42 0 0 2565 2606 29780354 29780395 9.020000e-11 78.7
6 TraesCS7D01G479100 chr2A 100.000 33 0 0 678 710 4969504 4969536 9.090000e-06 62.1
7 TraesCS7D01G479100 chr2A 100.000 33 0 0 678 710 509547617 509547585 9.090000e-06 62.1
8 TraesCS7D01G479100 chr3B 85.235 298 39 5 2600 2894 535555094 535554799 4.920000e-78 302.0
9 TraesCS7D01G479100 chr3B 91.111 45 3 1 680 723 75322084 75322040 3.270000e-05 60.2
10 TraesCS7D01G479100 chr6A 90.062 161 12 3 2564 2724 535425770 535425614 3.970000e-49 206.0
11 TraesCS7D01G479100 chr6A 89.474 76 7 1 2962 3036 11014187 11014112 8.960000e-16 95.3
12 TraesCS7D01G479100 chr6A 84.946 93 7 7 2558 2646 109146635 109146546 1.500000e-13 87.9
13 TraesCS7D01G479100 chr3D 87.898 157 18 1 2676 2831 68323121 68323277 1.860000e-42 183.0
14 TraesCS7D01G479100 chr3D 93.333 45 2 1 680 723 47784241 47784197 7.030000e-07 65.8
15 TraesCS7D01G479100 chr6B 87.500 88 9 2 2950 3036 17989328 17989414 1.930000e-17 100.0
16 TraesCS7D01G479100 chr6B 84.884 86 9 3 2563 2646 3168153 3168070 1.940000e-12 84.2
17 TraesCS7D01G479100 chr6D 88.158 76 6 3 2962 3036 9869035 9868962 1.500000e-13 87.9
18 TraesCS7D01G479100 chr5A 83.721 86 12 2 2563 2646 477574134 477574219 2.510000e-11 80.5
19 TraesCS7D01G479100 chrUn 95.455 44 1 1 2563 2606 401119748 401119706 5.430000e-08 69.4
20 TraesCS7D01G479100 chr5B 100.000 36 0 0 678 713 116684119 116684084 1.950000e-07 67.6
21 TraesCS7D01G479100 chr1D 100.000 34 0 0 678 711 77013421 77013454 2.530000e-06 63.9
22 TraesCS7D01G479100 chr4A 100.000 33 0 0 678 710 590111599 590111631 9.090000e-06 62.1
23 TraesCS7D01G479100 chr1B 94.737 38 2 0 1653 1690 133076050 133076087 3.270000e-05 60.2


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 TraesCS7D01G479100 chr7D 590415936 590418971 3035 True 5607 5607 100.000 1 3036 1 chr7D.!!$R1 3035
1 TraesCS7D01G479100 chr7B 665384111 665387121 3010 True 4470 4470 93.473 8 3036 1 chr7B.!!$R1 3028

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
107 108 0.109086 CGGCATACTCATCTAGGCGG 60.109 60.0 0.0 0.0 43.33 6.13 F
912 916 1.057851 AGTCAAACGGAAGGGGTGGA 61.058 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1156 1162 0.033991 AAGAGCGAGAGAGGCCTACA 60.034 55.0 4.42 0.0 0.0 2.74 R
2387 2419 0.034896 TTCTTCCTTCACTCCGGCAC 59.965 55.0 0.00 0.0 0.0 5.01 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
75 76 1.009675 GCTTGTGTGTGCTTCCACG 60.010 57.895 0.00 0.00 45.04 4.94
91 92 0.247814 CACGCAATGTCATCTTCGGC 60.248 55.000 6.37 0.00 0.00 5.54
92 93 0.673333 ACGCAATGTCATCTTCGGCA 60.673 50.000 6.37 0.00 0.00 5.69
93 94 0.659427 CGCAATGTCATCTTCGGCAT 59.341 50.000 0.00 0.00 0.00 4.40
94 95 1.866601 CGCAATGTCATCTTCGGCATA 59.133 47.619 0.00 0.00 0.00 3.14
95 96 2.348872 CGCAATGTCATCTTCGGCATAC 60.349 50.000 0.00 0.00 0.00 2.39
96 97 2.874701 GCAATGTCATCTTCGGCATACT 59.125 45.455 0.00 0.00 0.00 2.12
97 98 3.059325 GCAATGTCATCTTCGGCATACTC 60.059 47.826 0.00 0.00 0.00 2.59
98 99 4.122046 CAATGTCATCTTCGGCATACTCA 58.878 43.478 0.00 0.00 0.00 3.41
99 100 4.613925 ATGTCATCTTCGGCATACTCAT 57.386 40.909 0.00 0.00 0.00 2.90
100 101 3.982475 TGTCATCTTCGGCATACTCATC 58.018 45.455 0.00 0.00 0.00 2.92
101 102 3.638627 TGTCATCTTCGGCATACTCATCT 59.361 43.478 0.00 0.00 0.00 2.90
102 103 4.827284 TGTCATCTTCGGCATACTCATCTA 59.173 41.667 0.00 0.00 0.00 1.98
103 104 5.048434 TGTCATCTTCGGCATACTCATCTAG 60.048 44.000 0.00 0.00 0.00 2.43
104 105 4.460731 TCATCTTCGGCATACTCATCTAGG 59.539 45.833 0.00 0.00 0.00 3.02
105 106 2.558795 TCTTCGGCATACTCATCTAGGC 59.441 50.000 0.00 0.00 0.00 3.93
106 107 3.408389 CGGCATACTCATCTAGGCG 57.592 57.895 0.00 0.00 41.63 5.52
107 108 0.109086 CGGCATACTCATCTAGGCGG 60.109 60.000 0.00 0.00 43.33 6.13
108 109 1.257743 GGCATACTCATCTAGGCGGA 58.742 55.000 0.00 0.00 0.00 5.54
109 110 1.618837 GGCATACTCATCTAGGCGGAA 59.381 52.381 0.00 0.00 0.00 4.30
110 111 2.353208 GGCATACTCATCTAGGCGGAAG 60.353 54.545 0.00 0.00 0.00 3.46
111 112 2.297597 GCATACTCATCTAGGCGGAAGT 59.702 50.000 0.00 0.00 0.00 3.01
112 113 3.858877 GCATACTCATCTAGGCGGAAGTG 60.859 52.174 0.00 0.00 0.00 3.16
113 114 1.115467 ACTCATCTAGGCGGAAGTGG 58.885 55.000 0.00 0.00 0.00 4.00
173 174 4.755411 CTCTAAACTGAAGTTGGCGGATA 58.245 43.478 0.00 0.00 38.44 2.59
189 190 3.553922 GCGGATATCTTGACCTTGGAGAG 60.554 52.174 2.05 0.00 0.00 3.20
358 360 8.880878 AAATTACACACGTGCATATAGATGTA 57.119 30.769 17.22 11.15 35.30 2.29
437 439 9.739276 AGAGAACAAAATCATACATTTCTACCA 57.261 29.630 0.00 0.00 0.00 3.25
438 440 9.994432 GAGAACAAAATCATACATTTCTACCAG 57.006 33.333 0.00 0.00 0.00 4.00
439 441 9.739276 AGAACAAAATCATACATTTCTACCAGA 57.261 29.630 0.00 0.00 0.00 3.86
442 444 8.408601 ACAAAATCATACATTTCTACCAGATGC 58.591 33.333 0.00 0.00 0.00 3.91
443 445 8.407832 CAAAATCATACATTTCTACCAGATGCA 58.592 33.333 0.00 0.00 0.00 3.96
444 446 7.502120 AATCATACATTTCTACCAGATGCAC 57.498 36.000 0.00 0.00 0.00 4.57
445 447 6.239217 TCATACATTTCTACCAGATGCACT 57.761 37.500 0.00 0.00 0.00 4.40
446 448 7.360113 TCATACATTTCTACCAGATGCACTA 57.640 36.000 0.00 0.00 0.00 2.74
447 449 7.966812 TCATACATTTCTACCAGATGCACTAT 58.033 34.615 0.00 0.00 0.00 2.12
448 450 8.432013 TCATACATTTCTACCAGATGCACTATT 58.568 33.333 0.00 0.00 0.00 1.73
449 451 9.060347 CATACATTTCTACCAGATGCACTATTT 57.940 33.333 0.00 0.00 0.00 1.40
473 475 8.574251 TTACTATTGCATCTGTACCAAAATGT 57.426 30.769 0.00 0.00 0.00 2.71
547 549 8.863049 TGTAACGAAAGGAATATAAAAGTCGAC 58.137 33.333 7.70 7.70 0.00 4.20
593 597 7.944061 TCACACAAAAATGAGTTTCATCATCT 58.056 30.769 0.00 0.00 39.00 2.90
604 608 8.201554 TGAGTTTCATCATCTACATTTACAGC 57.798 34.615 0.00 0.00 0.00 4.40
725 729 8.049721 CAGAGGGAGTATTTGATAAGAAACCTT 58.950 37.037 0.00 0.00 0.00 3.50
779 783 1.208052 CGGGAGCAAGAAATCCTCTCA 59.792 52.381 0.00 0.00 35.80 3.27
912 916 1.057851 AGTCAAACGGAAGGGGTGGA 61.058 55.000 0.00 0.00 0.00 4.02
941 947 4.202419 GGGGAATATATATGCGTGGCCATA 60.202 45.833 9.72 0.00 32.67 2.74
1156 1162 1.485066 CCCACCTTGCTAGGAACGTAT 59.515 52.381 21.63 0.00 45.05 3.06
1179 1185 1.064314 AGGCCTCTCTCGCTCTTCTAA 60.064 52.381 0.00 0.00 0.00 2.10
1211 1217 3.818210 AGACGACTATATCCTGCTCTGTG 59.182 47.826 0.00 0.00 0.00 3.66
1213 1219 3.954904 ACGACTATATCCTGCTCTGTGTT 59.045 43.478 0.00 0.00 0.00 3.32
1223 1229 3.244561 CCTGCTCTGTGTTCCTTTTCCTA 60.245 47.826 0.00 0.00 0.00 2.94
1279 1285 0.107831 CGGTCAGGTCCCAGTTTTGA 59.892 55.000 0.00 0.00 0.00 2.69
1368 1374 9.859427 AATATTGAACTACCAAAATGTCACATG 57.141 29.630 0.00 0.00 0.00 3.21
1501 1511 7.762588 ACATAGTATTACTCAGATACGCCTT 57.237 36.000 0.00 0.00 35.61 4.35
1517 1527 2.030805 CGCCTTGGGAGAAAACTTTCTG 60.031 50.000 9.40 0.00 46.84 3.02
1518 1528 2.959030 GCCTTGGGAGAAAACTTTCTGT 59.041 45.455 9.40 0.00 46.84 3.41
1537 1547 8.768957 TTTCTGTTGAAATTGAACATGTTTCA 57.231 26.923 13.36 9.12 39.36 2.69
1548 1558 3.423539 ACATGTTTCAAGCCTAGCTCA 57.576 42.857 0.00 0.00 38.25 4.26
1579 1589 8.424133 ACATATATTGTCTATGCAACAGAGTCA 58.576 33.333 1.80 0.00 30.89 3.41
1643 1653 1.315257 CCTTGGGGTTGGCAATCTCG 61.315 60.000 10.81 0.00 0.00 4.04
1680 1690 1.841302 GATGTGTGGCTGGAGGTGGA 61.841 60.000 0.00 0.00 0.00 4.02
1694 1704 2.609610 TGGAGGCCCACCACTACC 60.610 66.667 14.29 0.02 37.58 3.18
1696 1706 3.001406 GAGGCCCACCACTACCGT 61.001 66.667 0.00 0.00 39.06 4.83
1771 1781 1.299976 GGTTGATGAGAGGGCCGTT 59.700 57.895 0.00 0.00 0.00 4.44
1828 1838 4.110036 TGTGTATGAGTCCAGATTGTCG 57.890 45.455 0.00 0.00 0.00 4.35
1852 1862 3.571590 CTCCAAGTACCTAGCTGGAGAT 58.428 50.000 10.80 0.00 43.99 2.75
2014 2032 2.802816 GTCGGATCTAATGCACATGTCC 59.197 50.000 0.00 0.00 0.00 4.02
2038 2056 9.830975 TCCGTGAAGAATGATCTAAAATGATTA 57.169 29.630 0.00 0.00 33.77 1.75
2091 2116 5.447624 ACTTTTTCGGTATTTGGTCAAGG 57.552 39.130 0.00 0.00 0.00 3.61
2216 2241 5.639506 ACATTTCAAGTGATTCCTGTAGTCG 59.360 40.000 0.00 0.00 0.00 4.18
2217 2242 3.868757 TCAAGTGATTCCTGTAGTCGG 57.131 47.619 0.00 0.00 0.00 4.79
2218 2243 3.162666 TCAAGTGATTCCTGTAGTCGGT 58.837 45.455 0.00 0.00 0.00 4.69
2219 2244 3.192844 TCAAGTGATTCCTGTAGTCGGTC 59.807 47.826 0.00 0.00 0.00 4.79
2252 2284 8.845413 AATAAAATTGAAGCCTTAATGCAACA 57.155 26.923 5.50 2.28 0.00 3.33
2262 2294 5.045869 AGCCTTAATGCAACAGGTCTAACTA 60.046 40.000 5.50 0.00 0.00 2.24
2290 2322 8.655935 AAAAATGACTTGGTCCTATGAGAAAT 57.344 30.769 0.00 0.00 0.00 2.17
2337 2369 8.959548 TCACAATAGATAAACGTTAGTCACCTA 58.040 33.333 0.00 0.00 0.00 3.08
2370 2402 4.210724 TGGGTCGGTCGATTTTCTAAAT 57.789 40.909 0.00 0.00 0.00 1.40
2387 2419 5.967088 TCTAAATCGACAGAAGAAAGGAGG 58.033 41.667 0.00 0.00 0.00 4.30
2402 2434 2.203788 AGGTGCCGGAGTGAAGGA 60.204 61.111 5.05 0.00 0.00 3.36
2410 2442 2.876079 GCCGGAGTGAAGGAAGAAACAT 60.876 50.000 5.05 0.00 0.00 2.71
2415 2447 4.067896 GAGTGAAGGAAGAAACATCTGCA 58.932 43.478 0.00 0.00 0.00 4.41
2476 2508 1.851114 TATTAGGGTGGGGGTGGGGT 61.851 60.000 0.00 0.00 0.00 4.95
2477 2509 3.766120 TATTAGGGTGGGGGTGGGGTC 62.766 61.905 0.00 0.00 0.00 4.46
2498 2530 0.728466 GAAGAACGTCGGGTCAGTCG 60.728 60.000 0.00 0.00 0.00 4.18
2503 2535 0.603707 ACGTCGGGTCAGTCGTCTTA 60.604 55.000 0.00 0.00 30.90 2.10
2534 2566 6.752091 ACAAATCCCCAAAATTCTAGGGTAT 58.248 36.000 8.50 0.00 41.16 2.73
2556 2588 7.174253 GGTATAAATCCCGTAAATGATGCTTCA 59.826 37.037 4.57 4.57 36.00 3.02
2606 2638 5.762825 AGCTTGCGTATCATTCATTGATT 57.237 34.783 0.00 0.00 42.62 2.57
2607 2639 6.866010 AGCTTGCGTATCATTCATTGATTA 57.134 33.333 0.00 0.00 42.62 1.75
2610 2642 8.190122 AGCTTGCGTATCATTCATTGATTAAAA 58.810 29.630 0.00 0.00 42.62 1.52
2611 2643 8.474577 GCTTGCGTATCATTCATTGATTAAAAG 58.525 33.333 0.00 0.00 42.62 2.27
2612 2644 8.854979 TTGCGTATCATTCATTGATTAAAAGG 57.145 30.769 0.00 0.00 42.62 3.11
2616 2648 9.669353 CGTATCATTCATTGATTAAAAGGGAAG 57.331 33.333 0.00 0.00 42.62 3.46
2619 2651 8.884124 TCATTCATTGATTAAAAGGGAAGAGT 57.116 30.769 0.00 0.00 0.00 3.24
2620 2652 8.742777 TCATTCATTGATTAAAAGGGAAGAGTG 58.257 33.333 0.00 0.00 0.00 3.51
2626 2659 9.753674 ATTGATTAAAAGGGAAGAGTGAATACA 57.246 29.630 0.00 0.00 0.00 2.29
2658 2691 4.754322 ACAACACATGCATAGACGACATA 58.246 39.130 0.00 0.00 0.00 2.29
2681 2714 4.135153 CGGAGCAGAGGGACACGG 62.135 72.222 0.00 0.00 0.00 4.94
2690 2723 4.394712 GGGACACGGGGTGCTCAG 62.395 72.222 0.89 0.00 38.05 3.35
2701 2734 1.246737 GGTGCTCAGCCCAAGGAAAG 61.247 60.000 0.00 0.00 0.00 2.62
2709 2742 2.965147 CAGCCCAAGGAAAGGAAAAGAA 59.035 45.455 0.00 0.00 0.00 2.52
2734 2767 0.250513 CGGCAAAACTCTCCTAGCCT 59.749 55.000 0.00 0.00 39.91 4.58
2747 2780 5.084519 TCTCCTAGCCTTGAGAAACAACTA 58.915 41.667 0.00 0.00 34.79 2.24
2748 2781 5.186021 TCTCCTAGCCTTGAGAAACAACTAG 59.814 44.000 0.00 0.00 36.14 2.57
2757 2790 7.134815 CCTTGAGAAACAACTAGAACACAATG 58.865 38.462 0.00 0.00 34.56 2.82
2782 2815 2.305927 CCAACCAGTATCCAACTCCACT 59.694 50.000 0.00 0.00 35.76 4.00
2783 2816 3.600388 CAACCAGTATCCAACTCCACTC 58.400 50.000 0.00 0.00 35.76 3.51
2786 2819 3.099905 CCAGTATCCAACTCCACTCTCA 58.900 50.000 0.00 0.00 35.76 3.27
2810 2844 4.072088 CCGCGGCGAACAAGACAC 62.072 66.667 25.92 0.00 0.00 3.67
2840 2874 1.838073 AAGGGGAACGGCGTCAAGAT 61.838 55.000 15.17 0.00 0.00 2.40
2925 2960 5.301551 TGACAAAACTACAACGTACTCCCTA 59.698 40.000 0.00 0.00 0.00 3.53
2938 2973 7.432350 ACGTACTCCCTAATCGTTTCTATAG 57.568 40.000 0.00 0.00 0.00 1.31
2956 2991 6.084277 TCTATAGCATAACACATACGCTTCG 58.916 40.000 0.00 0.00 34.18 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.298854 GCACAATTCTTTGGTACTTTCTACTC 58.701 38.462 0.00 0.00 37.15 2.59
3 4 6.379386 GGCACAATTCTTTGGTACTTTCTAC 58.621 40.000 0.00 0.00 37.15 2.59
6 7 4.226761 CGGCACAATTCTTTGGTACTTTC 58.773 43.478 0.00 0.00 37.15 2.62
7 8 3.634910 ACGGCACAATTCTTTGGTACTTT 59.365 39.130 0.00 0.00 37.15 2.66
8 9 3.219281 ACGGCACAATTCTTTGGTACTT 58.781 40.909 0.00 0.00 37.15 2.24
9 10 2.858745 ACGGCACAATTCTTTGGTACT 58.141 42.857 0.00 0.00 37.15 2.73
10 11 4.957759 ATACGGCACAATTCTTTGGTAC 57.042 40.909 0.00 0.00 37.15 3.34
11 12 6.408035 TCTTATACGGCACAATTCTTTGGTA 58.592 36.000 0.00 0.00 37.15 3.25
12 13 5.250200 TCTTATACGGCACAATTCTTTGGT 58.750 37.500 0.00 0.00 37.15 3.67
13 14 5.220854 CCTCTTATACGGCACAATTCTTTGG 60.221 44.000 0.00 0.00 37.15 3.28
75 76 2.874701 AGTATGCCGAAGATGACATTGC 59.125 45.455 0.00 0.00 0.00 3.56
91 92 3.305676 CCACTTCCGCCTAGATGAGTATG 60.306 52.174 0.00 0.00 0.00 2.39
92 93 2.894126 CCACTTCCGCCTAGATGAGTAT 59.106 50.000 0.00 0.00 0.00 2.12
93 94 2.307768 CCACTTCCGCCTAGATGAGTA 58.692 52.381 0.00 0.00 0.00 2.59
94 95 1.115467 CCACTTCCGCCTAGATGAGT 58.885 55.000 0.00 0.00 0.00 3.41
95 96 1.115467 ACCACTTCCGCCTAGATGAG 58.885 55.000 0.00 0.00 0.00 2.90
96 97 0.824109 CACCACTTCCGCCTAGATGA 59.176 55.000 0.00 0.00 0.00 2.92
97 98 0.824109 TCACCACTTCCGCCTAGATG 59.176 55.000 0.00 0.00 0.00 2.90
98 99 1.568504 TTCACCACTTCCGCCTAGAT 58.431 50.000 0.00 0.00 0.00 1.98
99 100 1.207089 CATTCACCACTTCCGCCTAGA 59.793 52.381 0.00 0.00 0.00 2.43
100 101 1.656652 CATTCACCACTTCCGCCTAG 58.343 55.000 0.00 0.00 0.00 3.02
101 102 0.251916 CCATTCACCACTTCCGCCTA 59.748 55.000 0.00 0.00 0.00 3.93
102 103 1.002134 CCATTCACCACTTCCGCCT 60.002 57.895 0.00 0.00 0.00 5.52
103 104 0.893727 AACCATTCACCACTTCCGCC 60.894 55.000 0.00 0.00 0.00 6.13
104 105 0.240945 CAACCATTCACCACTTCCGC 59.759 55.000 0.00 0.00 0.00 5.54
105 106 1.535462 GACAACCATTCACCACTTCCG 59.465 52.381 0.00 0.00 0.00 4.30
106 107 2.863809 AGACAACCATTCACCACTTCC 58.136 47.619 0.00 0.00 0.00 3.46
107 108 5.048713 CCTTTAGACAACCATTCACCACTTC 60.049 44.000 0.00 0.00 0.00 3.01
108 109 4.827284 CCTTTAGACAACCATTCACCACTT 59.173 41.667 0.00 0.00 0.00 3.16
109 110 4.104102 TCCTTTAGACAACCATTCACCACT 59.896 41.667 0.00 0.00 0.00 4.00
110 111 4.215613 GTCCTTTAGACAACCATTCACCAC 59.784 45.833 0.00 0.00 45.55 4.16
111 112 4.394729 GTCCTTTAGACAACCATTCACCA 58.605 43.478 0.00 0.00 45.55 4.17
173 174 1.661463 TGGCTCTCCAAGGTCAAGAT 58.339 50.000 0.00 0.00 39.99 2.40
189 190 1.932511 CTCTCTTCGAGAATGCTTGGC 59.067 52.381 0.00 0.00 42.62 4.52
248 249 4.525487 TGACGACCCTGAGTACATAGTTTT 59.475 41.667 0.00 0.00 0.00 2.43
335 337 9.569167 GTATACATCTATATGCACGTGTGTAAT 57.431 33.333 18.38 8.68 36.50 1.89
336 338 8.024865 GGTATACATCTATATGCACGTGTGTAA 58.975 37.037 18.38 0.95 36.50 2.41
442 444 8.887036 TGGTACAGATGCAATAGTAAATAGTG 57.113 34.615 0.00 0.00 32.55 2.74
443 445 9.899661 TTTGGTACAGATGCAATAGTAAATAGT 57.100 29.630 0.00 0.00 42.39 2.12
447 449 9.019656 ACATTTTGGTACAGATGCAATAGTAAA 57.980 29.630 0.00 0.00 42.39 2.01
448 450 8.574251 ACATTTTGGTACAGATGCAATAGTAA 57.426 30.769 0.00 0.00 42.39 2.24
449 451 9.674068 TTACATTTTGGTACAGATGCAATAGTA 57.326 29.630 0.00 0.00 42.39 1.82
473 475 7.255801 CCCTATGCAAAACTCAAAAAGGTCTTA 60.256 37.037 0.00 0.00 0.00 2.10
593 597 7.010645 CGTGTATACCACAATGCTGTAAATGTA 59.989 37.037 0.00 0.00 44.78 2.29
604 608 6.715344 AAAGTACACGTGTATACCACAATG 57.285 37.500 29.58 0.00 44.78 2.82
680 684 8.370182 TCCCTCTGTAACTTTTTATAAGACGTT 58.630 33.333 3.80 3.80 0.00 3.99
682 686 8.033626 ACTCCCTCTGTAACTTTTTATAAGACG 58.966 37.037 0.00 0.00 0.00 4.18
779 783 4.472108 TGTTCCACGAGGAGGGTTTTATAT 59.528 41.667 0.78 0.00 46.74 0.86
812 816 5.279406 CCTTGGTCAAAATATTTGTCTGCCA 60.279 40.000 0.39 6.07 0.00 4.92
890 894 1.073199 CCCCTTCCGTTTGACTGCT 59.927 57.895 0.00 0.00 0.00 4.24
912 916 2.698797 CGCATATATATTCCCCCGTCCT 59.301 50.000 0.00 0.00 0.00 3.85
941 947 7.467811 CGCTACAGAATATCTTTGCCTGAAATT 60.468 37.037 0.00 0.00 0.00 1.82
960 966 1.135660 TCGCTCTTCAAGTCGCTACAG 60.136 52.381 0.00 0.00 0.00 2.74
1132 1138 4.489771 CCTAGCAAGGTGGGCGGG 62.490 72.222 0.00 0.00 38.19 6.13
1143 1149 1.684983 GGCCTACATACGTTCCTAGCA 59.315 52.381 0.00 0.00 0.00 3.49
1146 1152 3.137913 AGAGAGGCCTACATACGTTCCTA 59.862 47.826 4.42 0.00 0.00 2.94
1156 1162 0.033991 AAGAGCGAGAGAGGCCTACA 60.034 55.000 4.42 0.00 0.00 2.74
1179 1185 6.096141 CAGGATATAGTCGTCTCATAGGCAAT 59.904 42.308 0.00 0.00 0.00 3.56
1211 1217 5.618418 GCAATACCAACGTAGGAAAAGGAAC 60.618 44.000 0.00 0.00 0.00 3.62
1213 1219 4.004982 GCAATACCAACGTAGGAAAAGGA 58.995 43.478 0.00 0.00 0.00 3.36
1279 1285 0.182775 AGGCAAAAGTCACCGTCCTT 59.817 50.000 0.00 0.00 0.00 3.36
1368 1374 1.197812 TACTTCCCCCGCTCCTAAAC 58.802 55.000 0.00 0.00 0.00 2.01
1434 1444 4.454678 TCCATGCTAAATTACTCTGCCTG 58.545 43.478 0.00 0.00 0.00 4.85
1496 1506 2.030805 CAGAAAGTTTTCTCCCAAGGCG 60.031 50.000 4.20 0.00 45.23 5.52
1501 1511 6.790232 ATTTCAACAGAAAGTTTTCTCCCA 57.210 33.333 4.20 0.00 45.23 4.37
1517 1527 6.258507 AGGCTTGAAACATGTTCAATTTCAAC 59.741 34.615 12.39 11.22 43.74 3.18
1518 1528 6.347696 AGGCTTGAAACATGTTCAATTTCAA 58.652 32.000 12.39 15.56 45.42 2.69
1537 1547 4.970860 ATATGTGATGTGAGCTAGGCTT 57.029 40.909 0.00 0.00 39.88 4.35
1548 1558 8.907222 TGTTGCATAGACAATATATGTGATGT 57.093 30.769 0.00 0.00 44.12 3.06
1643 1653 0.465705 TCGACCATTGCTGATCCCTC 59.534 55.000 0.00 0.00 0.00 4.30
1680 1690 3.001406 GACGGTAGTGGTGGGCCT 61.001 66.667 4.53 0.00 35.27 5.19
1712 1722 4.322349 CCGGATCCTGATCTCCATAAGAAC 60.322 50.000 10.75 0.00 37.61 3.01
1771 1781 3.071457 TCAGCTTGTCAATGTTCTCCTCA 59.929 43.478 0.00 0.00 0.00 3.86
1828 1838 1.410882 CCAGCTAGGTACTTGGAGCTC 59.589 57.143 4.71 4.71 43.61 4.09
1846 1856 1.473965 GCGAGGCTGATGAAATCTCCA 60.474 52.381 0.00 0.00 45.81 3.86
1852 1862 1.447838 GTCGGCGAGGCTGATGAAA 60.448 57.895 11.20 0.00 46.06 2.69
1984 2002 3.800604 GCATTAGATCCGACACCTTCCTC 60.801 52.174 0.00 0.00 0.00 3.71
2038 2056 6.869913 CACATTAATGAAAGAGTTGCCAACAT 59.130 34.615 22.16 0.00 0.00 2.71
2139 2164 2.224079 CGACTTGATTTCCCACTGTGTG 59.776 50.000 7.08 0.00 0.00 3.82
2186 2211 3.989817 GGAATCACTTGAAATGTGGCAAC 59.010 43.478 0.00 0.00 41.82 4.17
2216 2241 5.344933 GCTTCAATTTTATTTCACCACGACC 59.655 40.000 0.00 0.00 0.00 4.79
2217 2242 5.344933 GGCTTCAATTTTATTTCACCACGAC 59.655 40.000 0.00 0.00 0.00 4.34
2218 2243 5.242838 AGGCTTCAATTTTATTTCACCACGA 59.757 36.000 0.00 0.00 0.00 4.35
2219 2244 5.469479 AGGCTTCAATTTTATTTCACCACG 58.531 37.500 0.00 0.00 0.00 4.94
2333 2365 4.705023 CCGACCCAAATCAGATTTTTAGGT 59.295 41.667 16.80 16.80 32.96 3.08
2337 2369 3.190535 CGACCGACCCAAATCAGATTTTT 59.809 43.478 5.58 0.00 0.00 1.94
2370 2402 1.000955 GCACCTCCTTTCTTCTGTCGA 59.999 52.381 0.00 0.00 0.00 4.20
2372 2404 1.814793 GGCACCTCCTTTCTTCTGTC 58.185 55.000 0.00 0.00 0.00 3.51
2374 2406 0.674895 CCGGCACCTCCTTTCTTCTG 60.675 60.000 0.00 0.00 0.00 3.02
2387 2419 0.034896 TTCTTCCTTCACTCCGGCAC 59.965 55.000 0.00 0.00 0.00 5.01
2402 2434 1.072331 ACCGGACTGCAGATGTTTCTT 59.928 47.619 23.35 0.00 0.00 2.52
2442 2474 6.217487 CCACCCTAATATAGATCATGGGGAAA 59.783 42.308 0.00 0.00 37.56 3.13
2476 2508 1.859427 CTGACCCGACGTTCTTCCGA 61.859 60.000 0.00 0.00 0.00 4.55
2477 2509 1.443872 CTGACCCGACGTTCTTCCG 60.444 63.158 0.00 0.00 0.00 4.30
2479 2511 0.728466 CGACTGACCCGACGTTCTTC 60.728 60.000 0.00 0.00 0.00 2.87
2498 2530 7.712204 TTTGGGGATTTGTTTCCTATAAGAC 57.288 36.000 0.00 0.00 35.97 3.01
2503 2535 7.813087 AGAATTTTGGGGATTTGTTTCCTAT 57.187 32.000 0.00 0.00 35.97 2.57
2534 2566 7.581213 ATTGAAGCATCATTTACGGGATTTA 57.419 32.000 0.00 0.00 34.96 1.40
2579 2611 8.494735 TCAATGAATGATACGCAAGCTTTGCA 62.495 38.462 17.22 0.00 44.58 4.08
2606 2638 5.550403 ACCCTGTATTCACTCTTCCCTTTTA 59.450 40.000 0.00 0.00 0.00 1.52
2607 2639 4.354087 ACCCTGTATTCACTCTTCCCTTTT 59.646 41.667 0.00 0.00 0.00 2.27
2610 2642 3.207044 ACCCTGTATTCACTCTTCCCT 57.793 47.619 0.00 0.00 0.00 4.20
2611 2643 4.202367 CCATACCCTGTATTCACTCTTCCC 60.202 50.000 0.00 0.00 0.00 3.97
2612 2644 4.654262 TCCATACCCTGTATTCACTCTTCC 59.346 45.833 0.00 0.00 0.00 3.46
2616 2648 5.353394 TGTTCCATACCCTGTATTCACTC 57.647 43.478 0.00 0.00 0.00 3.51
2617 2649 5.013704 TGTTGTTCCATACCCTGTATTCACT 59.986 40.000 0.00 0.00 0.00 3.41
2618 2650 5.123344 GTGTTGTTCCATACCCTGTATTCAC 59.877 44.000 0.00 0.00 0.00 3.18
2619 2651 5.221945 TGTGTTGTTCCATACCCTGTATTCA 60.222 40.000 0.00 0.00 0.00 2.57
2620 2652 5.250200 TGTGTTGTTCCATACCCTGTATTC 58.750 41.667 0.00 0.00 0.00 1.75
2626 2659 2.224992 TGCATGTGTTGTTCCATACCCT 60.225 45.455 0.00 0.00 0.00 4.34
2647 2680 0.959553 CCGGGCACTATGTCGTCTAT 59.040 55.000 0.00 0.00 0.00 1.98
2648 2681 0.107066 TCCGGGCACTATGTCGTCTA 60.107 55.000 0.00 0.00 0.00 2.59
2690 2723 2.698274 TGTTCTTTTCCTTTCCTTGGGC 59.302 45.455 0.00 0.00 0.00 5.36
2701 2734 2.570442 TTGCCGTGTTGTTCTTTTCC 57.430 45.000 0.00 0.00 0.00 3.13
2709 2742 1.021968 GGAGAGTTTTGCCGTGTTGT 58.978 50.000 0.00 0.00 0.00 3.32
2734 2767 7.012327 CCTCATTGTGTTCTAGTTGTTTCTCAA 59.988 37.037 0.00 0.00 0.00 3.02
2747 2780 1.133513 TGGTTGGCCTCATTGTGTTCT 60.134 47.619 3.32 0.00 35.27 3.01
2748 2781 1.270550 CTGGTTGGCCTCATTGTGTTC 59.729 52.381 3.32 0.00 35.27 3.18
2757 2790 1.282157 AGTTGGATACTGGTTGGCCTC 59.718 52.381 3.32 0.00 35.19 4.70
2810 2844 1.882352 CGTTCCCCTTCTTGAAGGTGG 60.882 57.143 23.12 21.93 38.28 4.61
2824 2858 2.750888 GCATCTTGACGCCGTTCCC 61.751 63.158 0.00 0.00 0.00 3.97
2876 2910 4.425577 ACAATCGAAGCATCAAGGAAAC 57.574 40.909 0.00 0.00 0.00 2.78
2882 2916 3.932710 GTCACCTACAATCGAAGCATCAA 59.067 43.478 0.00 0.00 0.00 2.57
2911 2946 4.219288 AGAAACGATTAGGGAGTACGTTGT 59.781 41.667 0.00 0.00 44.27 3.32
2925 2960 8.912658 CGTATGTGTTATGCTATAGAAACGATT 58.087 33.333 3.21 0.00 0.00 3.34
2938 2973 2.858344 AGACGAAGCGTATGTGTTATGC 59.142 45.455 0.00 0.00 41.37 3.14
2956 2991 4.363999 CTCTCCAATACGGACATCAAGAC 58.636 47.826 0.00 0.00 39.64 3.01


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

AutoCloner maintained by Alex Coulton.