Multiple sequence alignment - TraesCS6B01G032500

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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 TraesCS6B01G032500 chr6B 100.000 4243 0 0 1 4243 18945297 18941055 0.000000e+00 7836.0
1 TraesCS6B01G032500 chr6B 95.927 3806 137 12 445 4243 19118838 19122632 0.000000e+00 6154.0
2 TraesCS6B01G032500 chr6B 91.111 180 13 3 1 177 244847140 244847319 1.520000e-59 241.0
3 TraesCS6B01G032500 chr6B 89.944 179 16 2 1 177 3390379 3390201 3.300000e-56 230.0
4 TraesCS6B01G032500 chr6A 92.525 3438 231 16 694 4115 11841890 11838463 0.000000e+00 4902.0
5 TraesCS6B01G032500 chr6A 92.091 3401 233 20 193 3582 11886998 11883623 0.000000e+00 4758.0
6 TraesCS6B01G032500 chr6A 90.707 2249 159 27 193 2430 11855035 11852826 0.000000e+00 2950.0
7 TraesCS6B01G032500 chr6A 89.796 1911 131 28 2343 4243 11852819 11850963 0.000000e+00 2390.0
8 TraesCS6B01G032500 chr6A 89.944 179 16 2 1 177 293629 293451 3.300000e-56 230.0
9 TraesCS6B01G032500 chr6D 92.629 3419 198 26 193 3596 10346459 10343080 0.000000e+00 4868.0
10 TraesCS6B01G032500 chr6D 92.586 3399 206 18 193 3582 10373905 10370544 0.000000e+00 4839.0
11 TraesCS6B01G032500 chr6D 93.434 2909 178 7 693 3598 10337944 10335046 0.000000e+00 4301.0
12 TraesCS6B01G032500 chr6D 91.615 644 44 9 3605 4243 10343104 10342466 0.000000e+00 881.0
13 TraesCS6B01G032500 chr6D 88.326 454 32 3 3662 4115 10335030 10334598 3.760000e-145 525.0
14 TraesCS6B01G032500 chr6D 89.974 379 28 8 3869 4243 10351542 10351170 8.250000e-132 481.0
15 TraesCS6B01G032500 chr5B 89.447 199 17 4 1 195 425186292 425186094 9.110000e-62 248.0
16 TraesCS6B01G032500 chr5B 72.537 477 101 20 1696 2149 537535669 537535200 1.240000e-25 128.0
17 TraesCS6B01G032500 chr2B 87.817 197 21 3 1 195 682919356 682919551 1.190000e-55 228.0
18 TraesCS6B01G032500 chr2B 86.869 198 19 7 3 196 55545908 55546102 9.240000e-52 215.0
19 TraesCS6B01G032500 chr2B 100.000 28 0 0 29 56 5708215 5708188 8.000000e-03 52.8
20 TraesCS6B01G032500 chrUn 89.583 48 4 1 10 57 365942311 365942265 4.580000e-05 60.2
21 TraesCS6B01G032500 chr2D 89.362 47 4 1 10 56 5645874 5645919 1.650000e-04 58.4
22 TraesCS6B01G032500 chr5D 96.875 32 1 0 10 41 62062709 62062678 2.000000e-03 54.7


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 TraesCS6B01G032500 chr6B 18941055 18945297 4242 True 7836.0 7836 100.0000 1 4243 1 chr6B.!!$R2 4242
1 TraesCS6B01G032500 chr6B 19118838 19122632 3794 False 6154.0 6154 95.9270 445 4243 1 chr6B.!!$F1 3798
2 TraesCS6B01G032500 chr6A 11838463 11841890 3427 True 4902.0 4902 92.5250 694 4115 1 chr6A.!!$R2 3421
3 TraesCS6B01G032500 chr6A 11883623 11886998 3375 True 4758.0 4758 92.0910 193 3582 1 chr6A.!!$R3 3389
4 TraesCS6B01G032500 chr6A 11850963 11855035 4072 True 2670.0 2950 90.2515 193 4243 2 chr6A.!!$R4 4050
5 TraesCS6B01G032500 chr6D 10370544 10373905 3361 True 4839.0 4839 92.5860 193 3582 1 chr6D.!!$R2 3389
6 TraesCS6B01G032500 chr6D 10342466 10346459 3993 True 2874.5 4868 92.1220 193 4243 2 chr6D.!!$R4 4050
7 TraesCS6B01G032500 chr6D 10334598 10337944 3346 True 2413.0 4301 90.8800 693 4115 2 chr6D.!!$R3 3422

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
920 939 0.599204 AGTGTCGCAATTTCGTCGGT 60.599 50.0 0.0 0.0 0.00 4.69 F
1500 1520 0.405585 TCCTGCCCAAAGAAGAAGGG 59.594 55.0 0.0 0.0 45.68 3.95 F
1885 1905 0.677731 ATGGTTGCTGATGGACACCG 60.678 55.0 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2328 4.283978 AGTTTGTCAATGCCATTCATTCCA 59.716 37.5 0.00 0.0 43.21 3.53 R
2934 3033 0.771755 AGTCACCAAGGGGGAGTTTC 59.228 55.0 0.00 0.0 34.72 2.78 R
3804 3951 0.912006 GAAGGAGAGGGCCAGGTTCT 60.912 60.0 6.18 0.0 0.00 3.01 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
44 45 9.991388 ATGTTCTTGTTTCAAAATTTGTTCATG 57.009 25.926 5.56 6.42 0.00 3.07
45 46 9.212641 TGTTCTTGTTTCAAAATTTGTTCATGA 57.787 25.926 5.56 0.00 0.00 3.07
51 52 9.170734 TGTTTCAAAATTTGTTCATGAATTCCA 57.829 25.926 12.12 2.04 30.81 3.53
63 64 9.299963 TGTTCATGAATTCCAAAAATATTAGCG 57.700 29.630 12.12 0.00 0.00 4.26
64 65 9.301153 GTTCATGAATTCCAAAAATATTAGCGT 57.699 29.630 12.12 0.00 0.00 5.07
65 66 9.868277 TTCATGAATTCCAAAAATATTAGCGTT 57.132 25.926 3.38 0.00 0.00 4.84
66 67 9.868277 TCATGAATTCCAAAAATATTAGCGTTT 57.132 25.926 2.27 0.00 0.00 3.60
68 69 8.696410 TGAATTCCAAAAATATTAGCGTTTCC 57.304 30.769 2.27 0.00 0.00 3.13
69 70 8.307483 TGAATTCCAAAAATATTAGCGTTTCCA 58.693 29.630 2.27 0.00 0.00 3.53
70 71 9.145865 GAATTCCAAAAATATTAGCGTTTCCAA 57.854 29.630 0.00 0.00 0.00 3.53
71 72 9.495572 AATTCCAAAAATATTAGCGTTTCCAAA 57.504 25.926 0.00 0.00 0.00 3.28
72 73 9.665719 ATTCCAAAAATATTAGCGTTTCCAAAT 57.334 25.926 0.00 0.00 0.00 2.32
73 74 9.495572 TTCCAAAAATATTAGCGTTTCCAAATT 57.504 25.926 0.00 0.00 0.00 1.82
74 75 9.495572 TCCAAAAATATTAGCGTTTCCAAATTT 57.504 25.926 0.00 0.00 0.00 1.82
80 81 3.942539 AGCGTTTCCAAATTTTTGTGC 57.057 38.095 2.63 0.00 36.45 4.57
81 82 3.265791 AGCGTTTCCAAATTTTTGTGCA 58.734 36.364 2.63 0.00 36.45 4.57
82 83 3.309410 AGCGTTTCCAAATTTTTGTGCAG 59.691 39.130 0.00 0.00 36.45 4.41
83 84 3.308323 GCGTTTCCAAATTTTTGTGCAGA 59.692 39.130 0.00 0.00 36.45 4.26
84 85 4.550639 GCGTTTCCAAATTTTTGTGCAGAG 60.551 41.667 0.00 0.00 36.45 3.35
85 86 4.566360 CGTTTCCAAATTTTTGTGCAGAGT 59.434 37.500 0.00 0.00 36.45 3.24
86 87 5.063312 CGTTTCCAAATTTTTGTGCAGAGTT 59.937 36.000 0.00 0.00 36.45 3.01
87 88 6.402011 CGTTTCCAAATTTTTGTGCAGAGTTT 60.402 34.615 0.00 0.00 36.45 2.66
88 89 6.660887 TTCCAAATTTTTGTGCAGAGTTTC 57.339 33.333 0.00 0.00 36.45 2.78
89 90 5.728471 TCCAAATTTTTGTGCAGAGTTTCA 58.272 33.333 0.00 0.00 36.45 2.69
90 91 6.169094 TCCAAATTTTTGTGCAGAGTTTCAA 58.831 32.000 0.00 0.00 36.45 2.69
91 92 6.822676 TCCAAATTTTTGTGCAGAGTTTCAAT 59.177 30.769 0.00 0.00 36.45 2.57
92 93 7.984050 TCCAAATTTTTGTGCAGAGTTTCAATA 59.016 29.630 0.00 0.00 36.45 1.90
93 94 8.610896 CCAAATTTTTGTGCAGAGTTTCAATAA 58.389 29.630 0.00 0.00 36.45 1.40
94 95 9.985318 CAAATTTTTGTGCAGAGTTTCAATAAA 57.015 25.926 0.00 0.00 33.59 1.40
95 96 9.986833 AAATTTTTGTGCAGAGTTTCAATAAAC 57.013 25.926 0.00 0.00 44.47 2.01
108 109 7.148355 GTTTCAATAAACGTCCCCTTTATCA 57.852 36.000 0.00 0.00 35.96 2.15
109 110 7.595604 GTTTCAATAAACGTCCCCTTTATCAA 58.404 34.615 0.00 0.00 35.96 2.57
110 111 7.762588 TTCAATAAACGTCCCCTTTATCAAA 57.237 32.000 0.00 0.00 0.00 2.69
111 112 7.762588 TCAATAAACGTCCCCTTTATCAAAA 57.237 32.000 0.00 0.00 0.00 2.44
112 113 8.179509 TCAATAAACGTCCCCTTTATCAAAAA 57.820 30.769 0.00 0.00 0.00 1.94
113 114 8.808092 TCAATAAACGTCCCCTTTATCAAAAAT 58.192 29.630 0.00 0.00 0.00 1.82
114 115 9.430623 CAATAAACGTCCCCTTTATCAAAAATT 57.569 29.630 0.00 0.00 0.00 1.82
116 117 7.722795 AAACGTCCCCTTTATCAAAAATTTG 57.277 32.000 0.00 0.00 39.48 2.32
117 118 6.413783 ACGTCCCCTTTATCAAAAATTTGT 57.586 33.333 5.84 0.00 39.18 2.83
118 119 6.822442 ACGTCCCCTTTATCAAAAATTTGTT 58.178 32.000 5.84 0.93 39.18 2.83
119 120 6.926826 ACGTCCCCTTTATCAAAAATTTGTTC 59.073 34.615 5.84 0.00 39.18 3.18
120 121 6.926272 CGTCCCCTTTATCAAAAATTTGTTCA 59.074 34.615 5.84 0.00 39.18 3.18
121 122 7.095816 CGTCCCCTTTATCAAAAATTTGTTCAC 60.096 37.037 5.84 0.00 39.18 3.18
122 123 7.713073 GTCCCCTTTATCAAAAATTTGTTCACA 59.287 33.333 5.84 0.00 39.18 3.58
123 124 8.435982 TCCCCTTTATCAAAAATTTGTTCACAT 58.564 29.630 5.84 0.00 39.18 3.21
124 125 9.717942 CCCCTTTATCAAAAATTTGTTCACATA 57.282 29.630 5.84 0.00 39.18 2.29
141 142 9.978044 TGTTCACATATTCAAAATTGTTCATGA 57.022 25.926 0.00 0.00 0.00 3.07
253 254 8.724229 CATTGAAGTTTTGACTGAGATGATACA 58.276 33.333 0.00 0.00 0.00 2.29
279 280 9.660544 ATTTTTACCAGGCAATATAGAAATCCT 57.339 29.630 0.00 0.00 0.00 3.24
335 339 7.011669 TGGTAAAACTTTCTACTCGGAAACAAG 59.988 37.037 0.00 0.00 32.63 3.16
337 341 4.067972 ACTTTCTACTCGGAAACAAGCA 57.932 40.909 0.00 0.00 32.63 3.91
399 407 6.716173 ACTCTCTAATCGGGGACTATAAACTC 59.284 42.308 0.00 0.00 0.00 3.01
400 408 6.607970 TCTCTAATCGGGGACTATAAACTCA 58.392 40.000 0.00 0.00 0.00 3.41
464 476 4.460382 CACTTAGGTGACCGTACTTCCTAA 59.540 45.833 0.00 0.00 45.61 2.69
591 608 0.998928 TGTCCATGGCCACCACTAAT 59.001 50.000 8.16 0.00 35.80 1.73
592 609 1.357420 TGTCCATGGCCACCACTAATT 59.643 47.619 8.16 0.00 35.80 1.40
593 610 2.578480 TGTCCATGGCCACCACTAATTA 59.422 45.455 8.16 0.00 35.80 1.40
594 611 3.010696 TGTCCATGGCCACCACTAATTAA 59.989 43.478 8.16 0.00 35.80 1.40
731 748 1.337167 GGATCACAAAGGCAAGCAACC 60.337 52.381 0.00 0.00 0.00 3.77
920 939 0.599204 AGTGTCGCAATTTCGTCGGT 60.599 50.000 0.00 0.00 0.00 4.69
1201 1221 4.378874 GCTTCTACATCAACAAAGGTGAGC 60.379 45.833 0.00 0.00 0.00 4.26
1468 1488 3.940852 TCAGTACTTATTCGACGGCACTA 59.059 43.478 0.00 0.00 0.00 2.74
1478 1498 3.599343 TCGACGGCACTACTTACTCTAA 58.401 45.455 0.00 0.00 0.00 2.10
1500 1520 0.405585 TCCTGCCCAAAGAAGAAGGG 59.594 55.000 0.00 0.00 45.68 3.95
1506 1526 2.557452 GCCCAAAGAAGAAGGGGATGAA 60.557 50.000 0.00 0.00 43.57 2.57
1612 1632 3.724128 GCGCATGAATCATAGCTTGATCG 60.724 47.826 0.30 10.25 44.51 3.69
1661 1681 6.929049 TCAGTACTTAAATCTGTGTTGTCCAG 59.071 38.462 0.00 0.00 0.00 3.86
1799 1819 1.026182 TTGTCACAGGCCGATGATGC 61.026 55.000 14.21 4.52 0.00 3.91
1885 1905 0.677731 ATGGTTGCTGATGGACACCG 60.678 55.000 0.00 0.00 0.00 4.94
1944 1964 2.241685 AGATGGCAATGCTTCTCTCCTT 59.758 45.455 4.82 0.00 0.00 3.36
2120 2140 1.678101 GCCTCCTGTATTTCATGCACC 59.322 52.381 0.00 0.00 0.00 5.01
2151 2172 8.706322 ATGATCCTACAAGGTTTGTTTTTAGT 57.294 30.769 0.00 0.00 42.22 2.24
2255 2277 6.035975 GCTTTGTCTTGTTGTGTGCTTTAAAT 59.964 34.615 0.00 0.00 0.00 1.40
2289 2312 7.317390 TGTAGCTTAGATCAATACACGAACAA 58.683 34.615 0.00 0.00 0.00 2.83
2293 2316 9.547753 AGCTTAGATCAATACACGAACAATATT 57.452 29.630 0.00 0.00 0.00 1.28
2305 2328 6.704493 ACACGAACAATATTCAGTGTAGTTGT 59.296 34.615 10.96 0.00 40.48 3.32
2322 2345 3.833650 AGTTGTGGAATGAATGGCATTGA 59.166 39.130 19.07 10.17 46.90 2.57
2598 2695 6.149973 CAGCTGAAGAATGGAAGTTCATGTAA 59.850 38.462 8.42 0.00 30.03 2.41
2601 2698 8.341173 GCTGAAGAATGGAAGTTCATGTAATAG 58.659 37.037 5.01 0.00 30.03 1.73
2702 2799 5.077134 TCACTCATGTTACTCTGGATGTG 57.923 43.478 0.00 0.00 0.00 3.21
2934 3033 6.025749 TGTCAAGTGTACAATCCAGTCTAG 57.974 41.667 0.00 0.00 0.00 2.43
2996 3096 7.254227 TGTTTCTTTACTTTTCACGCTGTAT 57.746 32.000 0.00 0.00 0.00 2.29
3014 3114 6.092944 CGCTGTATAAGGAAAAATACACCACA 59.907 38.462 0.00 0.00 34.47 4.17
3276 3376 5.957771 ACCAATAAACTAGAGCTCCATCA 57.042 39.130 10.93 0.00 0.00 3.07
3357 3457 4.819630 TGTGACAACCTGGAAAGTTATGAC 59.180 41.667 0.00 0.00 0.00 3.06
3521 3624 7.335422 CCCTAGTCTTGTATCATGATTTATGCC 59.665 40.741 14.65 0.00 36.70 4.40
3591 3694 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
3592 3695 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
3593 3696 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
3594 3697 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3595 3698 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3596 3699 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3597 3700 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3598 3701 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3599 3702 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3600 3703 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3601 3704 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3602 3705 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3603 3706 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3604 3707 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3605 3708 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3606 3709 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3607 3710 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3608 3711 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3609 3712 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3610 3713 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3611 3714 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3612 3715 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3613 3716 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3614 3717 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3615 3718 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3616 3719 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3635 3782 6.666678 AGAGAGAGAGAGAGAAGATGACAAT 58.333 40.000 0.00 0.00 0.00 2.71
3719 3866 1.417890 GGTAGGTGCTATGCAGATGGT 59.582 52.381 0.00 0.00 40.08 3.55
3743 3890 4.072131 GCAAACCTGATTGAGTCAACCTA 58.928 43.478 7.96 0.00 36.14 3.08
3804 3951 4.897509 ACATCACTCTCAACCTTCATCA 57.102 40.909 0.00 0.00 0.00 3.07
3812 3959 3.008375 TCTCAACCTTCATCAGAACCTGG 59.992 47.826 0.00 0.00 31.51 4.45
3852 4000 2.936202 ACTCATAATCCAAGCCGCAAT 58.064 42.857 0.00 0.00 0.00 3.56
3867 4015 3.868369 GCCGCAATTGCTATATACTCCCA 60.868 47.826 26.86 0.00 39.32 4.37
3910 4058 7.658982 TCATAGCTTTCTTCTGGCAATATACAG 59.341 37.037 0.00 0.00 36.07 2.74
3952 4100 5.480642 TCTCAATATCTGCTTCTCCCATC 57.519 43.478 0.00 0.00 0.00 3.51
4020 4168 1.070710 CAGTTGCGTACGCGGTTTTTA 60.071 47.619 32.65 12.85 45.51 1.52
4082 4230 2.037772 TGGACCAACTCTCTTCTTCAGC 59.962 50.000 0.00 0.00 0.00 4.26
4083 4231 2.301583 GGACCAACTCTCTTCTTCAGCT 59.698 50.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.991388 CATGAACAAATTTTGAAACAAGAACAT 57.009 25.926 15.81 5.11 0.00 2.71
19 20 9.212641 TCATGAACAAATTTTGAAACAAGAACA 57.787 25.926 15.81 3.36 0.00 3.18
25 26 9.170734 TGGAATTCATGAACAAATTTTGAAACA 57.829 25.926 11.07 11.62 30.81 2.83
37 38 9.299963 CGCTAATATTTTTGGAATTCATGAACA 57.700 29.630 11.07 1.31 0.00 3.18
38 39 9.301153 ACGCTAATATTTTTGGAATTCATGAAC 57.699 29.630 11.07 0.00 0.00 3.18
39 40 9.868277 AACGCTAATATTTTTGGAATTCATGAA 57.132 25.926 11.26 11.26 0.00 2.57
40 41 9.868277 AAACGCTAATATTTTTGGAATTCATGA 57.132 25.926 7.93 0.00 0.00 3.07
42 43 9.313118 GGAAACGCTAATATTTTTGGAATTCAT 57.687 29.630 7.93 0.00 0.00 2.57
43 44 8.307483 TGGAAACGCTAATATTTTTGGAATTCA 58.693 29.630 7.93 0.00 0.00 2.57
44 45 8.696410 TGGAAACGCTAATATTTTTGGAATTC 57.304 30.769 0.00 0.00 0.00 2.17
45 46 9.495572 TTTGGAAACGCTAATATTTTTGGAATT 57.504 25.926 0.00 0.00 0.00 2.17
46 47 9.665719 ATTTGGAAACGCTAATATTTTTGGAAT 57.334 25.926 0.00 0.00 0.00 3.01
47 48 9.495572 AATTTGGAAACGCTAATATTTTTGGAA 57.504 25.926 0.00 0.00 0.00 3.53
48 49 9.495572 AAATTTGGAAACGCTAATATTTTTGGA 57.504 25.926 0.00 0.00 0.00 3.53
54 55 8.227119 GCACAAAAATTTGGAAACGCTAATATT 58.773 29.630 10.38 0.00 42.34 1.28
55 56 7.386299 TGCACAAAAATTTGGAAACGCTAATAT 59.614 29.630 10.38 0.00 42.34 1.28
56 57 6.701841 TGCACAAAAATTTGGAAACGCTAATA 59.298 30.769 10.38 0.00 42.34 0.98
57 58 5.525378 TGCACAAAAATTTGGAAACGCTAAT 59.475 32.000 10.38 0.00 42.34 1.73
58 59 4.870426 TGCACAAAAATTTGGAAACGCTAA 59.130 33.333 10.38 0.00 42.34 3.09
59 60 4.433615 TGCACAAAAATTTGGAAACGCTA 58.566 34.783 10.38 0.00 42.34 4.26
60 61 3.265791 TGCACAAAAATTTGGAAACGCT 58.734 36.364 10.38 0.00 42.34 5.07
61 62 3.308323 TCTGCACAAAAATTTGGAAACGC 59.692 39.130 10.38 5.54 42.34 4.84
62 63 4.566360 ACTCTGCACAAAAATTTGGAAACG 59.434 37.500 10.38 0.00 42.34 3.60
63 64 6.421377 AACTCTGCACAAAAATTTGGAAAC 57.579 33.333 10.38 0.00 42.34 2.78
64 65 6.652481 TGAAACTCTGCACAAAAATTTGGAAA 59.348 30.769 10.38 0.00 42.34 3.13
65 66 6.169094 TGAAACTCTGCACAAAAATTTGGAA 58.831 32.000 10.38 0.00 42.34 3.53
66 67 5.728471 TGAAACTCTGCACAAAAATTTGGA 58.272 33.333 10.38 0.00 42.34 3.53
67 68 6.419980 TTGAAACTCTGCACAAAAATTTGG 57.580 33.333 10.38 0.00 42.34 3.28
68 69 9.985318 TTTATTGAAACTCTGCACAAAAATTTG 57.015 25.926 4.40 4.40 43.62 2.32
69 70 9.986833 GTTTATTGAAACTCTGCACAAAAATTT 57.013 25.926 0.00 0.00 41.55 1.82
70 71 8.327429 CGTTTATTGAAACTCTGCACAAAAATT 58.673 29.630 0.00 0.00 42.44 1.82
71 72 7.491048 ACGTTTATTGAAACTCTGCACAAAAAT 59.509 29.630 0.00 0.00 42.44 1.82
72 73 6.809196 ACGTTTATTGAAACTCTGCACAAAAA 59.191 30.769 0.00 0.00 42.44 1.94
73 74 6.326375 ACGTTTATTGAAACTCTGCACAAAA 58.674 32.000 0.00 0.00 42.44 2.44
74 75 5.885881 ACGTTTATTGAAACTCTGCACAAA 58.114 33.333 0.00 0.00 42.44 2.83
75 76 5.493133 ACGTTTATTGAAACTCTGCACAA 57.507 34.783 0.00 0.00 42.44 3.33
76 77 4.024387 GGACGTTTATTGAAACTCTGCACA 60.024 41.667 0.00 0.00 42.44 4.57
77 78 4.464112 GGACGTTTATTGAAACTCTGCAC 58.536 43.478 0.00 0.00 42.44 4.57
78 79 3.500680 GGGACGTTTATTGAAACTCTGCA 59.499 43.478 0.00 0.00 42.44 4.41
79 80 3.119955 GGGGACGTTTATTGAAACTCTGC 60.120 47.826 0.00 0.00 42.44 4.26
80 81 4.324267 AGGGGACGTTTATTGAAACTCTG 58.676 43.478 0.00 0.00 42.44 3.35
81 82 4.635699 AGGGGACGTTTATTGAAACTCT 57.364 40.909 0.00 0.00 42.44 3.24
82 83 5.700722 AAAGGGGACGTTTATTGAAACTC 57.299 39.130 0.00 0.00 45.01 3.01
91 92 8.422566 ACAAATTTTTGATAAAGGGGACGTTTA 58.577 29.630 9.88 0.00 44.57 2.01
92 93 7.276658 ACAAATTTTTGATAAAGGGGACGTTT 58.723 30.769 9.88 0.00 43.59 3.60
93 94 6.822442 ACAAATTTTTGATAAAGGGGACGTT 58.178 32.000 9.88 0.00 40.55 3.99
94 95 6.413783 ACAAATTTTTGATAAAGGGGACGT 57.586 33.333 9.88 0.00 40.55 4.34
95 96 6.926272 TGAACAAATTTTTGATAAAGGGGACG 59.074 34.615 9.88 0.00 40.55 4.79
96 97 7.713073 TGTGAACAAATTTTTGATAAAGGGGAC 59.287 33.333 9.88 0.00 40.55 4.46
97 98 7.796054 TGTGAACAAATTTTTGATAAAGGGGA 58.204 30.769 9.88 0.00 40.55 4.81
98 99 8.620116 ATGTGAACAAATTTTTGATAAAGGGG 57.380 30.769 9.88 0.00 40.55 4.79
115 116 9.978044 TCATGAACAATTTTGAATATGTGAACA 57.022 25.926 0.00 0.00 0.00 3.18
253 254 9.660544 AGGATTTCTATATTGCCTGGTAAAAAT 57.339 29.630 0.16 2.81 0.00 1.82
311 315 6.849811 GCTTGTTTCCGAGTAGAAAGTTTTAC 59.150 38.462 0.00 0.00 36.45 2.01
335 339 2.489971 TGTACTGTGTAAGCCAACTGC 58.510 47.619 0.00 0.00 41.71 4.40
337 341 5.228945 AGAATGTACTGTGTAAGCCAACT 57.771 39.130 0.00 0.00 0.00 3.16
377 385 6.896021 TGAGTTTATAGTCCCCGATTAGAG 57.104 41.667 0.00 0.00 0.00 2.43
399 407 5.423886 AGTAAAAATGTGTGGGTTTGGTTG 58.576 37.500 0.00 0.00 0.00 3.77
400 408 5.187967 TGAGTAAAAATGTGTGGGTTTGGTT 59.812 36.000 0.00 0.00 0.00 3.67
532 545 9.927668 AACAAATGACCATGGAAGTATTAAAAG 57.072 29.630 21.47 6.86 0.00 2.27
731 748 2.609244 CCTTTTTATTGTGGTGGCGTGG 60.609 50.000 0.00 0.00 0.00 4.94
790 808 9.319143 CATTTAAACCAAAAATGGTAACTGTCA 57.681 29.630 0.12 0.00 42.20 3.58
861 880 3.065371 CGTTTCAGGCAAGTGAAGAAACT 59.935 43.478 12.62 0.00 43.41 2.66
920 939 1.469335 GGGACGGTGAGGTGAAGTCA 61.469 60.000 0.00 0.00 33.84 3.41
1201 1221 1.256812 GGGATGAAGTTTGGGGTGTG 58.743 55.000 0.00 0.00 0.00 3.82
1327 1347 0.327924 ATGAGGACGTTGCCATTCCA 59.672 50.000 0.00 0.00 0.00 3.53
1402 1422 1.767681 GAGGATGTCCATGCCTCTCTT 59.232 52.381 8.59 0.00 43.79 2.85
1468 1488 5.514500 TTGGGCAGGATTTTAGAGTAAGT 57.486 39.130 0.00 0.00 0.00 2.24
1478 1498 3.168292 CCTTCTTCTTTGGGCAGGATTT 58.832 45.455 0.00 0.00 0.00 2.17
1500 1520 8.268850 ACACATACAAGTAAGACAATTCATCC 57.731 34.615 0.00 0.00 0.00 3.51
1506 1526 7.174772 TGCATCAACACATACAAGTAAGACAAT 59.825 33.333 0.00 0.00 0.00 2.71
1612 1632 3.372554 GACGAGGGGGCTGCTGTAC 62.373 68.421 0.00 0.00 0.00 2.90
1661 1681 4.980434 CAGCTGGCACATAGATTTTATTGC 59.020 41.667 5.57 0.00 38.20 3.56
1799 1819 6.216569 ACAACGATTAGATATACACCAGCAG 58.783 40.000 0.00 0.00 0.00 4.24
1885 1905 6.416455 TCAACAAACATCTCACGCAAATAAAC 59.584 34.615 0.00 0.00 0.00 2.01
1944 1964 4.780815 CATTGTCTCCTGCCTGGTTTATA 58.219 43.478 0.00 0.00 37.07 0.98
2120 2140 4.510167 AACCTTGTAGGATCATCCTTGG 57.490 45.455 12.79 11.73 46.91 3.61
2220 2242 7.647715 ACACAACAAGACAAAGCAACATAATAC 59.352 33.333 0.00 0.00 0.00 1.89
2289 2312 8.896744 CATTCATTCCACAACTACACTGAATAT 58.103 33.333 0.00 0.00 32.47 1.28
2293 2316 5.003160 CCATTCATTCCACAACTACACTGA 58.997 41.667 0.00 0.00 0.00 3.41
2305 2328 4.283978 AGTTTGTCAATGCCATTCATTCCA 59.716 37.500 0.00 0.00 43.21 3.53
2355 2452 6.946340 ACTACACCATGACTATTGATGAACA 58.054 36.000 0.00 0.00 0.00 3.18
2506 2603 6.215845 ACAACAATAGTCATGACCAAAAAGC 58.784 36.000 22.21 0.00 0.00 3.51
2509 2606 7.068103 AGACAACAACAATAGTCATGACCAAAA 59.932 33.333 22.21 6.26 33.56 2.44
2511 2608 6.061441 AGACAACAACAATAGTCATGACCAA 58.939 36.000 22.21 11.43 33.56 3.67
2729 2826 7.712797 TCCTTTCTCGCAAAAAGAAAAACTAT 58.287 30.769 4.51 0.00 41.02 2.12
2934 3033 0.771755 AGTCACCAAGGGGGAGTTTC 59.228 55.000 0.00 0.00 34.72 2.78
2996 3096 6.014156 CCCCAAATGTGGTGTATTTTTCCTTA 60.014 38.462 0.00 0.00 44.30 2.69
3014 3114 3.979501 AGATGCTTCCATACCCCAAAT 57.020 42.857 0.00 0.00 0.00 2.32
3276 3376 9.228949 GGATGCATTTATTCTCAACTCATCTAT 57.771 33.333 0.00 0.00 0.00 1.98
3357 3457 6.352516 AGCTCTAGATATTGAAAACAGGTGG 58.647 40.000 0.00 0.00 0.00 4.61
3462 3565 9.232473 GAGGTAATAACAAGGTGAAGAAAATCT 57.768 33.333 0.00 0.00 0.00 2.40
3521 3624 8.226819 TCCAGATACAATAGAGTAGACAACAG 57.773 38.462 0.00 0.00 0.00 3.16
3591 3694 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3592 3695 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3593 3696 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3594 3697 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3595 3698 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3596 3699 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3597 3700 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3598 3701 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3599 3702 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3600 3703 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3601 3704 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3602 3705 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3603 3706 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3604 3707 5.596361 TCTTCTCTCTCTCTCTCTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
3605 3708 5.523588 TCTTCTCTCTCTCTCTCTCTCTCT 58.476 45.833 0.00 0.00 0.00 3.10
3606 3709 5.860941 TCTTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
3607 3710 5.901853 TCATCTTCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
3608 3711 5.988561 GTCATCTTCTCTCTCTCTCTCTCTC 59.011 48.000 0.00 0.00 0.00 3.20
3609 3712 5.426509 TGTCATCTTCTCTCTCTCTCTCTCT 59.573 44.000 0.00 0.00 0.00 3.10
3610 3713 5.674525 TGTCATCTTCTCTCTCTCTCTCTC 58.325 45.833 0.00 0.00 0.00 3.20
3611 3714 5.698741 TGTCATCTTCTCTCTCTCTCTCT 57.301 43.478 0.00 0.00 0.00 3.10
3612 3715 6.949352 ATTGTCATCTTCTCTCTCTCTCTC 57.051 41.667 0.00 0.00 0.00 3.20
3613 3716 8.219868 TGATATTGTCATCTTCTCTCTCTCTCT 58.780 37.037 0.00 0.00 0.00 3.10
3614 3717 8.394971 TGATATTGTCATCTTCTCTCTCTCTC 57.605 38.462 0.00 0.00 0.00 3.20
3615 3718 8.632679 GTTGATATTGTCATCTTCTCTCTCTCT 58.367 37.037 0.00 0.00 36.54 3.10
3616 3719 8.632679 AGTTGATATTGTCATCTTCTCTCTCTC 58.367 37.037 0.00 0.00 34.02 3.20
3635 3782 3.153919 GGGGCAAACAACAGAGTTGATA 58.846 45.455 15.99 0.00 0.00 2.15
3719 3866 3.068024 GGTTGACTCAATCAGGTTTGCAA 59.932 43.478 0.00 0.00 38.99 4.08
3743 3890 4.524802 TTCATGGGCTCCATTATTGAGT 57.475 40.909 4.15 0.00 42.23 3.41
3804 3951 0.912006 GAAGGAGAGGGCCAGGTTCT 60.912 60.000 6.18 0.00 0.00 3.01
3852 4000 3.587498 AGCCACTGGGAGTATATAGCAA 58.413 45.455 0.00 0.00 35.59 3.91
3867 4015 4.502950 GCTATGAGCTTGAGATTAGCCACT 60.503 45.833 0.00 0.00 39.47 4.00
4082 4230 0.529378 GGGAGCTTCCACATTGCAAG 59.471 55.000 6.02 0.00 38.64 4.01
4083 4231 0.899717 GGGGAGCTTCCACATTGCAA 60.900 55.000 14.70 0.00 40.54 4.08
4197 4350 9.755804 TGTGAACTTTTATAAAATGCATGAACA 57.244 25.926 10.97 7.25 0.00 3.18


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

AutoCloner maintained by Alex Coulton.