Multiple sequence alignment - TraesCS1D01G099700

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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 TraesCS1D01G099700 chr1D 100.000 4862 0 0 1 4862 86929638 86924777 0.000000e+00 8979.0
1 TraesCS1D01G099700 chr1B 93.886 3320 140 22 1564 4831 139673444 139670136 0.000000e+00 4948.0
2 TraesCS1D01G099700 chr1B 93.683 1583 65 17 1 1564 139675056 139673490 0.000000e+00 2337.0
3 TraesCS1D01G099700 chr1A 91.539 2151 114 17 2485 4606 82532553 82530442 0.000000e+00 2902.0
4 TraesCS1D01G099700 chr1A 93.158 1593 62 19 1 1564 82535260 82533686 0.000000e+00 2294.0
5 TraesCS1D01G099700 chr1A 94.492 944 29 15 1564 2487 82533640 82532700 0.000000e+00 1434.0
6 TraesCS1D01G099700 chr1A 89.130 138 8 3 4724 4855 82528616 82528480 1.080000e-36 165.0
7 TraesCS1D01G099700 chr1A 93.878 49 3 0 1516 1564 586371576 586371624 1.880000e-09 75.0
8 TraesCS1D01G099700 chr6D 100.000 42 0 0 1523 1564 470575088 470575047 1.450000e-10 78.7
9 TraesCS1D01G099700 chr4B 95.833 48 2 0 1517 1564 660460893 660460940 1.450000e-10 78.7
10 TraesCS1D01G099700 chr4B 83.784 74 9 3 1491 1563 580533851 580533780 3.140000e-07 67.6
11 TraesCS1D01G099700 chr6B 94.000 50 1 2 1516 1564 539706319 539706271 1.880000e-09 75.0
12 TraesCS1D01G099700 chr3D 92.453 53 3 1 1520 1571 443261490 443261438 1.880000e-09 75.0
13 TraesCS1D01G099700 chr3D 85.135 74 8 3 1496 1568 528186685 528186756 6.750000e-09 73.1


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 TraesCS1D01G099700 chr1D 86924777 86929638 4861 True 8979.00 8979 100.00000 1 4862 1 chr1D.!!$R1 4861
1 TraesCS1D01G099700 chr1B 139670136 139675056 4920 True 3642.50 4948 93.78450 1 4831 2 chr1B.!!$R1 4830
2 TraesCS1D01G099700 chr1A 82528480 82535260 6780 True 1698.75 2902 92.07975 1 4855 4 chr1A.!!$R1 4854

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
107 115 0.107654 GGGTCGAGGATTCAAGGTGG 60.108 60.0 0.0 0.0 0.00 4.61 F
500 526 0.236711 CTGCTCTTGTTGTCCTTGCG 59.763 55.0 0.0 0.0 0.00 4.85 F
531 557 0.396974 CTCCCCTGCTCTGCTCTAGT 60.397 60.0 0.0 0.0 0.00 2.57 F
1897 1986 0.550914 TTGACTTGCCAGTTGTCCCT 59.449 50.0 0.0 0.0 31.22 4.20 F
2911 3185 0.178953 AACACAGCAGAAGCCCCAAT 60.179 50.0 0.0 0.0 43.56 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 1986 0.033781 GCACCAGCAGGCATGAAAAA 59.966 50.000 0.62 0.00 41.58 1.94 R
2446 2551 0.323629 TGAAGGTGGTAAGAAGGCGG 59.676 55.000 0.00 0.00 0.00 6.13 R
2769 3043 7.039644 GGTTTAGGATAAGATCTCCGAGATTGA 60.040 40.741 12.26 1.92 34.53 2.57 R
3099 3373 0.109597 GCAATGGACTTCTTGGCACG 60.110 55.000 0.00 0.00 0.00 5.34 R
4177 4481 0.037975 CAACCAACCATGCCTCAAGC 60.038 55.000 0.00 0.00 44.14 4.01 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 3.041940 GGCTGTCGGTGGTTCGTG 61.042 66.667 0.00 0.00 0.00 4.35
75 76 2.229062 CCTTTTTCCCTTTCGCTTCCTC 59.771 50.000 0.00 0.00 0.00 3.71
77 78 0.321298 TTTCCCTTTCGCTTCCTCCG 60.321 55.000 0.00 0.00 0.00 4.63
78 79 2.798148 TTCCCTTTCGCTTCCTCCGC 62.798 60.000 0.00 0.00 0.00 5.54
107 115 0.107654 GGGTCGAGGATTCAAGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
124 132 3.069318 GAGGGAGAGTCGGCGGTT 61.069 66.667 7.21 0.00 0.00 4.44
156 164 2.354259 GTTGGTCTGCTCATCTCTTGG 58.646 52.381 0.00 0.00 0.00 3.61
257 265 2.358737 CTTTCTTGGCTCCGGCGT 60.359 61.111 6.01 0.00 39.81 5.68
263 271 4.742649 TGGCTCCGGCGTCTCTCT 62.743 66.667 6.01 0.00 39.81 3.10
332 340 6.238842 CCATATCATTCCATGCGTTCTCTTTT 60.239 38.462 0.00 0.00 0.00 2.27
333 341 4.685169 TCATTCCATGCGTTCTCTTTTC 57.315 40.909 0.00 0.00 0.00 2.29
335 343 4.393062 TCATTCCATGCGTTCTCTTTTCTC 59.607 41.667 0.00 0.00 0.00 2.87
337 345 4.008074 TCCATGCGTTCTCTTTTCTCTT 57.992 40.909 0.00 0.00 0.00 2.85
462 488 2.812591 CTGAATCAGCTGCTCTTGTGTT 59.187 45.455 9.47 0.00 0.00 3.32
486 512 4.989279 TTTTAATGGGAATCAGCTGCTC 57.011 40.909 9.47 7.98 0.00 4.26
500 526 0.236711 CTGCTCTTGTTGTCCTTGCG 59.763 55.000 0.00 0.00 0.00 4.85
501 527 0.463654 TGCTCTTGTTGTCCTTGCGT 60.464 50.000 0.00 0.00 0.00 5.24
531 557 0.396974 CTCCCCTGCTCTGCTCTAGT 60.397 60.000 0.00 0.00 0.00 2.57
532 558 0.927029 TCCCCTGCTCTGCTCTAGTA 59.073 55.000 0.00 0.00 0.00 1.82
533 559 1.036707 CCCCTGCTCTGCTCTAGTAC 58.963 60.000 0.00 0.00 0.00 2.73
572 598 8.737168 TCATAAAAGTACCAATGAATCCTCTG 57.263 34.615 0.00 0.00 0.00 3.35
596 622 3.119708 GGACTGCAGTTTATTGCTTCCAG 60.120 47.826 22.65 0.00 44.38 3.86
614 640 7.039293 TGCTTCCAGTAGTCTTACTCATTGTTA 60.039 37.037 0.00 0.00 38.05 2.41
631 657 2.571653 TGTTAGTATGGTTGCCTCTGCT 59.428 45.455 0.00 0.00 38.71 4.24
662 692 7.496591 CCAGCATTATGTTTATTGCTTCCATTT 59.503 33.333 0.00 0.00 41.02 2.32
837 867 2.939103 ACTGCTTGATTGATACTTCCGC 59.061 45.455 0.00 0.00 0.00 5.54
973 1012 4.504858 GTGATGTAGTTTAGTGGGTCCAG 58.495 47.826 0.00 0.00 0.00 3.86
1280 1319 7.037658 TGTTGATGCCCCTAGATATTGCTTATA 60.038 37.037 0.00 0.00 0.00 0.98
1377 1416 7.345422 ACCCAAATTTTTGCAGCTTATTTTT 57.655 28.000 0.00 0.00 36.86 1.94
1378 1417 7.201835 ACCCAAATTTTTGCAGCTTATTTTTG 58.798 30.769 0.00 0.00 36.86 2.44
1479 1518 5.581085 TCCTTTATCTTAAGCTTCTGCGAAC 59.419 40.000 0.00 0.00 45.42 3.95
1486 1525 1.059994 GCTTCTGCGAACATGCTCG 59.940 57.895 14.06 14.06 41.84 5.03
1490 1529 2.357396 TGCGAACATGCTCGTGCT 60.357 55.556 18.87 0.00 40.99 4.40
1498 1537 4.436050 CGAACATGCTCGTGCTATTCTTTT 60.436 41.667 10.33 0.00 40.48 2.27
1514 1553 6.849588 ATTCTTTTCTTCATTGCACAAACC 57.150 33.333 0.00 0.00 0.00 3.27
1518 1557 4.686191 TTCTTCATTGCACAAACCCATT 57.314 36.364 0.00 0.00 0.00 3.16
1521 1560 4.344679 TCTTCATTGCACAAACCCATTCTT 59.655 37.500 0.00 0.00 0.00 2.52
1551 1590 6.565999 CGTCCCAAAATAAGTGTCTCAACTTC 60.566 42.308 0.00 0.00 40.77 3.01
1553 1592 6.486657 TCCCAAAATAAGTGTCTCAACTTCAG 59.513 38.462 0.00 0.00 40.77 3.02
1555 1594 7.444183 CCCAAAATAAGTGTCTCAACTTCAGTA 59.556 37.037 0.00 0.00 40.77 2.74
1556 1595 8.283291 CCAAAATAAGTGTCTCAACTTCAGTAC 58.717 37.037 0.00 0.00 40.77 2.73
1615 1700 3.225104 TGCCCTTTCCATCAGCAATATC 58.775 45.455 0.00 0.00 0.00 1.63
1683 1772 9.787435 TTTAATTCACTTGGAATATAGCCGTAT 57.213 29.630 0.00 0.00 45.46 3.06
1690 1779 4.755411 TGGAATATAGCCGTATAGCAAGC 58.245 43.478 0.00 0.00 34.23 4.01
1711 1800 2.614987 CCAGCCTCTCCTTCAGTCAAAG 60.615 54.545 0.00 0.00 0.00 2.77
1827 1916 7.118535 TGCAATAAGTCAAAGCGAAACAGTATA 59.881 33.333 0.00 0.00 0.00 1.47
1897 1986 0.550914 TTGACTTGCCAGTTGTCCCT 59.449 50.000 0.00 0.00 31.22 4.20
1941 2030 8.296713 GCAGTAAAAACAAATCCAAGTAGATGA 58.703 33.333 0.00 0.00 0.00 2.92
1977 2066 7.298122 GTTGTCATGTGGTATGTAGTTTTCTG 58.702 38.462 0.00 0.00 0.00 3.02
1981 2070 3.329520 TGTGGTATGTAGTTTTCTGCCCT 59.670 43.478 0.00 0.00 0.00 5.19
2046 2141 7.877097 GTCATCTAGATTCAGCATTTGGACTAT 59.123 37.037 1.33 0.00 0.00 2.12
2047 2142 7.876582 TCATCTAGATTCAGCATTTGGACTATG 59.123 37.037 1.33 0.00 0.00 2.23
2048 2143 7.129457 TCTAGATTCAGCATTTGGACTATGT 57.871 36.000 0.00 0.00 0.00 2.29
2049 2144 7.568349 TCTAGATTCAGCATTTGGACTATGTT 58.432 34.615 0.00 0.00 0.00 2.71
2051 2146 6.860080 AGATTCAGCATTTGGACTATGTTTG 58.140 36.000 0.00 0.00 0.00 2.93
2052 2147 5.389859 TTCAGCATTTGGACTATGTTTGG 57.610 39.130 0.00 0.00 0.00 3.28
2053 2148 3.193267 TCAGCATTTGGACTATGTTTGGC 59.807 43.478 0.00 0.00 0.00 4.52
2077 2175 9.667989 GGCAACGTTTTCTTTATACTTCTTTTA 57.332 29.630 0.00 0.00 0.00 1.52
2279 2384 1.290955 GGCCGGTTTAAAACTGCCC 59.709 57.895 23.94 9.30 40.79 5.36
2445 2550 4.829064 TTGAAGCAGCGTGAGTATTTTT 57.171 36.364 0.00 0.00 0.00 1.94
2446 2551 4.404507 TGAAGCAGCGTGAGTATTTTTC 57.595 40.909 0.00 0.00 0.00 2.29
2769 3043 0.611896 AGCAAAGCAATAACCGCCCT 60.612 50.000 0.00 0.00 0.00 5.19
2910 3184 1.108727 CAACACAGCAGAAGCCCCAA 61.109 55.000 0.00 0.00 43.56 4.12
2911 3185 0.178953 AACACAGCAGAAGCCCCAAT 60.179 50.000 0.00 0.00 43.56 3.16
2914 3188 2.170166 CACAGCAGAAGCCCCAATTTA 58.830 47.619 0.00 0.00 43.56 1.40
2924 3198 1.407618 GCCCCAATTTACGATGGTTCC 59.592 52.381 0.00 0.00 34.79 3.62
2926 3200 3.093057 CCCCAATTTACGATGGTTCCAA 58.907 45.455 0.00 0.00 34.79 3.53
2927 3201 3.511934 CCCCAATTTACGATGGTTCCAAA 59.488 43.478 0.00 0.00 34.79 3.28
2966 3240 2.038269 AACCGCCACCAACTATGCG 61.038 57.895 0.00 0.00 46.14 4.73
2980 3254 1.070758 CTATGCGCTCCATGTACCCTT 59.929 52.381 9.73 0.00 35.34 3.95
2992 3266 3.383698 TGTACCCTTCTCCACCTAGAG 57.616 52.381 0.00 0.00 35.04 2.43
2994 3268 1.394532 ACCCTTCTCCACCTAGAGGA 58.605 55.000 1.60 0.00 38.94 3.71
3002 3276 2.900546 CTCCACCTAGAGGACAGTTTGT 59.099 50.000 1.60 0.00 38.94 2.83
3052 3326 5.335504 GCTCTTCTTCCATGTTTTCCTGAAG 60.336 44.000 0.00 0.00 0.00 3.02
3069 3343 1.130054 AAGCTGCTCCTGTCCTTCCA 61.130 55.000 1.00 0.00 0.00 3.53
3081 3355 1.891150 GTCCTTCCACGGTACTTCTCA 59.109 52.381 0.00 0.00 0.00 3.27
3094 3368 1.280457 CTTCTCACCTTACCCTGCCT 58.720 55.000 0.00 0.00 0.00 4.75
3099 3373 0.831307 CACCTTACCCTGCCTCCTAC 59.169 60.000 0.00 0.00 0.00 3.18
3102 3376 0.460311 CTTACCCTGCCTCCTACGTG 59.540 60.000 0.00 0.00 0.00 4.49
3165 3439 3.053917 GGGAAAGGCAAGGGTATACTGAA 60.054 47.826 2.25 0.00 0.00 3.02
3187 3461 0.990374 AGTTGAGCTTCCTGATGCCT 59.010 50.000 0.00 0.00 32.53 4.75
3315 3589 2.351244 TAGTGCTGCCTCCGTGGAG 61.351 63.158 9.02 9.02 41.63 3.86
3328 3602 2.431057 TCCGTGGAGGAGAATAAAGCTC 59.569 50.000 0.00 0.00 45.98 4.09
3336 3610 4.066646 GGAGAATAAAGCTCCTCAGACC 57.933 50.000 0.00 0.00 46.70 3.85
3362 3636 2.042831 GCTCCACAGCACATCCACC 61.043 63.158 0.00 0.00 46.06 4.61
3366 3640 2.048222 ACAGCACATCCACCGTCG 60.048 61.111 0.00 0.00 0.00 5.12
3413 3687 8.325046 AGATAATAAAGAGTCAAAGAAGCCAGT 58.675 33.333 0.00 0.00 0.00 4.00
3424 3698 1.277557 AGAAGCCAGTAGAACAGCCAG 59.722 52.381 0.00 0.00 0.00 4.85
3430 3704 2.498167 CAGTAGAACAGCCAGCAAAGT 58.502 47.619 0.00 0.00 0.00 2.66
3431 3705 2.880890 CAGTAGAACAGCCAGCAAAGTT 59.119 45.455 0.00 0.00 0.00 2.66
3432 3706 2.880890 AGTAGAACAGCCAGCAAAGTTG 59.119 45.455 0.00 0.00 0.00 3.16
3442 3716 3.491447 GCCAGCAAAGTTGTCATTGTCTT 60.491 43.478 0.00 0.00 0.00 3.01
3446 3720 4.158394 AGCAAAGTTGTCATTGTCTTGTGT 59.842 37.500 0.00 0.00 0.00 3.72
3477 3751 3.804036 TGTTGTACAAAGACCTGTCCAG 58.196 45.455 10.51 0.00 0.00 3.86
3643 3917 4.324267 GTCAGGTTTGTTATACCAGCAGT 58.676 43.478 0.00 0.00 38.16 4.40
3720 3994 1.718757 CTAGGCCAAATGCTGCGGTC 61.719 60.000 5.01 0.00 40.92 4.79
3728 4005 2.472695 AATGCTGCGGTCAACTCTAA 57.527 45.000 0.00 0.00 0.00 2.10
4012 4291 1.685224 GGGAGGGTTCATGCTCACA 59.315 57.895 0.00 0.00 0.00 3.58
4029 4308 0.478072 ACAATCACCAGGCCTGTTCA 59.522 50.000 30.63 14.21 0.00 3.18
4139 4442 7.652524 TGAGATAAGAATCAGCAGTCTAGTT 57.347 36.000 0.00 0.00 34.28 2.24
4177 4481 6.230654 GTTTGTTTTGTTCAAACTGTTAGCG 58.769 36.000 12.33 0.00 46.08 4.26
4200 4504 1.686052 TGAGGCATGGTTGGTTGAAAC 59.314 47.619 0.00 0.00 0.00 2.78
4211 4515 4.442192 GGTTGGTTGAAACTTATGTGGCAA 60.442 41.667 0.00 0.00 0.00 4.52
4258 4563 0.531974 GTGTGTTGTTCCAGCTCCGA 60.532 55.000 0.00 0.00 0.00 4.55
4339 4644 4.509737 GGAGTGCGGCGTAGGACC 62.510 72.222 9.37 3.96 32.59 4.46
4555 4860 3.758931 GGCGATGTGGGGTTTGGC 61.759 66.667 0.00 0.00 0.00 4.52
4572 4877 1.578206 GGCGAGCTCCAGGTGAAAAC 61.578 60.000 8.47 0.00 0.00 2.43
4608 4914 1.425267 TAATGCCGGCGACAATGACG 61.425 55.000 23.90 0.02 0.00 4.35
4614 4920 0.248907 CGGCGACAATGACGTCCTAT 60.249 55.000 14.12 0.00 31.91 2.57
4697 6749 0.827368 AGAGCTCTCCGGGTGAAATC 59.173 55.000 11.45 1.89 0.00 2.17
4698 6750 0.827368 GAGCTCTCCGGGTGAAATCT 59.173 55.000 6.43 0.00 0.00 2.40
4699 6751 0.827368 AGCTCTCCGGGTGAAATCTC 59.173 55.000 0.00 0.00 0.00 2.75
4700 6752 0.537188 GCTCTCCGGGTGAAATCTCA 59.463 55.000 0.00 0.00 0.00 3.27
4716 6768 5.859205 AATCTCAAGTTTCTGCTTTGGTT 57.141 34.783 0.00 0.00 0.00 3.67
4812 6882 5.863397 TCTTGCCGATTGCTTGAAAATAAAG 59.137 36.000 0.00 0.00 42.00 1.85
4850 6921 2.547299 ACAACATTGGGGCATGTTTG 57.453 45.000 0.00 0.06 38.78 2.93
4855 6926 3.212685 ACATTGGGGCATGTTTGTTTTG 58.787 40.909 0.00 0.00 0.00 2.44
4856 6927 3.118112 ACATTGGGGCATGTTTGTTTTGA 60.118 39.130 0.00 0.00 0.00 2.69
4857 6928 2.906691 TGGGGCATGTTTGTTTTGAG 57.093 45.000 0.00 0.00 0.00 3.02
4858 6929 2.392662 TGGGGCATGTTTGTTTTGAGA 58.607 42.857 0.00 0.00 0.00 3.27
4859 6930 2.768527 TGGGGCATGTTTGTTTTGAGAA 59.231 40.909 0.00 0.00 0.00 2.87
4860 6931 3.198635 TGGGGCATGTTTGTTTTGAGAAA 59.801 39.130 0.00 0.00 0.00 2.52
4861 6932 3.809279 GGGGCATGTTTGTTTTGAGAAAG 59.191 43.478 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.241213 GGGAAAAAGGCAGCGAAGAC 59.759 55.000 0.00 0.00 0.00 3.01
75 76 4.452733 GACCCCTCTCAACCGCGG 62.453 72.222 26.86 26.86 0.00 6.46
77 78 3.358076 CTCGACCCCTCTCAACCGC 62.358 68.421 0.00 0.00 0.00 5.68
78 79 2.711922 CCTCGACCCCTCTCAACCG 61.712 68.421 0.00 0.00 0.00 4.44
79 80 0.688087 ATCCTCGACCCCTCTCAACC 60.688 60.000 0.00 0.00 0.00 3.77
81 82 1.273041 TGAATCCTCGACCCCTCTCAA 60.273 52.381 0.00 0.00 0.00 3.02
107 115 2.560051 GAAACCGCCGACTCTCCCTC 62.560 65.000 0.00 0.00 0.00 4.30
124 132 1.006571 GACCAACCTGCGACGAGAA 60.007 57.895 0.00 0.00 0.00 2.87
156 164 1.658114 GAACCAAGCCCCACGAAAC 59.342 57.895 0.00 0.00 0.00 2.78
257 265 8.707796 AACCTAATCGTATCCAATTAGAGAGA 57.292 34.615 4.17 0.00 37.56 3.10
263 271 8.092687 GGCTAAGAACCTAATCGTATCCAATTA 58.907 37.037 0.00 0.00 0.00 1.40
332 340 5.775195 TGATTAACTGACACAGAGGAAGAGA 59.225 40.000 5.76 0.00 35.18 3.10
333 341 6.030548 TGATTAACTGACACAGAGGAAGAG 57.969 41.667 5.76 0.00 35.18 2.85
335 343 6.030548 TCTGATTAACTGACACAGAGGAAG 57.969 41.667 5.76 0.00 35.18 3.46
337 345 5.651387 CTCTGATTAACTGACACAGAGGA 57.349 43.478 0.00 0.00 45.86 3.71
468 494 3.054139 ACAAGAGCAGCTGATTCCCATTA 60.054 43.478 20.43 0.00 0.00 1.90
470 496 1.284198 ACAAGAGCAGCTGATTCCCAT 59.716 47.619 20.43 0.99 0.00 4.00
486 512 0.381801 AAGCACGCAAGGACAACAAG 59.618 50.000 0.00 0.00 46.39 3.16
500 526 1.000396 AGGGGAGGCAATGAAGCAC 60.000 57.895 0.00 0.00 35.83 4.40
501 527 1.000521 CAGGGGAGGCAATGAAGCA 60.001 57.895 0.00 0.00 35.83 3.91
531 557 8.375493 ACTTTTATGAGGATTCACTGGTAGTA 57.625 34.615 0.00 0.00 35.83 1.82
532 558 7.259088 ACTTTTATGAGGATTCACTGGTAGT 57.741 36.000 0.00 0.00 35.83 2.73
533 559 7.711339 GGTACTTTTATGAGGATTCACTGGTAG 59.289 40.741 0.00 0.00 35.83 3.18
572 598 3.127721 GGAAGCAATAAACTGCAGTCCTC 59.872 47.826 21.95 5.44 45.18 3.71
614 640 2.418746 CGTTAGCAGAGGCAACCATACT 60.419 50.000 0.00 0.00 44.61 2.12
631 657 5.067153 AGCAATAAACATAATGCTGGCGTTA 59.933 36.000 9.28 9.28 46.66 3.18
645 675 5.394005 CCGGATCAAATGGAAGCAATAAACA 60.394 40.000 0.00 0.00 0.00 2.83
662 692 3.521937 AGGAACAAATAAGTCCCGGATCA 59.478 43.478 0.73 0.00 0.00 2.92
719 749 7.663905 GCAGTAGATAAGAAGAGGTCTCAGATA 59.336 40.741 0.55 0.00 34.56 1.98
727 757 6.211584 TCTTGTTGCAGTAGATAAGAAGAGGT 59.788 38.462 0.00 0.00 31.39 3.85
837 867 5.563842 GTGAAGAAATGCATACCTTCGAAG 58.436 41.667 24.09 18.51 38.20 3.79
973 1012 3.428589 GCATCCACCTCAAGAATCAAAGC 60.429 47.826 0.00 0.00 0.00 3.51
1280 1319 3.168035 TCCAATGTTAATGTGGCCAGT 57.832 42.857 5.11 0.00 32.10 4.00
1377 1416 7.032580 CAGTTTTATTTGTCTTTGTCCACACA 58.967 34.615 0.00 0.00 0.00 3.72
1378 1417 7.033185 ACAGTTTTATTTGTCTTTGTCCACAC 58.967 34.615 0.00 0.00 0.00 3.82
1414 1453 7.012327 GCCAGTCACTTGCATATTAAGTATTCA 59.988 37.037 0.00 0.00 36.29 2.57
1415 1454 7.012327 TGCCAGTCACTTGCATATTAAGTATTC 59.988 37.037 0.00 0.00 36.29 1.75
1468 1507 1.059994 CGAGCATGTTCGCAGAAGC 59.940 57.895 19.05 0.00 45.90 3.86
1479 1518 4.871993 AGAAAAGAATAGCACGAGCATG 57.128 40.909 7.77 0.00 45.49 4.06
1486 1525 6.151691 TGTGCAATGAAGAAAAGAATAGCAC 58.848 36.000 0.00 0.00 46.21 4.40
1490 1529 6.928492 GGGTTTGTGCAATGAAGAAAAGAATA 59.072 34.615 0.00 0.00 0.00 1.75
1498 1537 3.896888 AGAATGGGTTTGTGCAATGAAGA 59.103 39.130 0.00 0.00 0.00 2.87
1514 1553 0.618458 TTGGGACGGAGGAAGAATGG 59.382 55.000 0.00 0.00 0.00 3.16
1518 1557 3.585732 ACTTATTTTGGGACGGAGGAAGA 59.414 43.478 0.00 0.00 0.00 2.87
1521 1560 2.640826 ACACTTATTTTGGGACGGAGGA 59.359 45.455 0.00 0.00 0.00 3.71
1555 1594 7.809806 GCAGATTAAGCAAATACTCAAAGTTGT 59.190 33.333 0.00 0.00 0.00 3.32
1556 1595 8.025445 AGCAGATTAAGCAAATACTCAAAGTTG 58.975 33.333 0.00 0.00 0.00 3.16
1607 1692 5.449107 ACGAATGGTACTACGATATTGCT 57.551 39.130 0.00 0.00 0.00 3.91
1671 1756 4.759782 CTGGCTTGCTATACGGCTATATT 58.240 43.478 0.00 0.00 0.00 1.28
1680 1769 1.270571 GGAGAGGCTGGCTTGCTATAC 60.271 57.143 4.82 0.00 0.00 1.47
1683 1772 0.911525 AAGGAGAGGCTGGCTTGCTA 60.912 55.000 4.82 0.00 0.00 3.49
1690 1779 0.979665 TTGACTGAAGGAGAGGCTGG 59.020 55.000 0.00 0.00 0.00 4.85
1711 1800 7.062605 CCACAGCACAGATGAAATTTATTGTTC 59.937 37.037 0.00 0.00 0.00 3.18
1827 1916 7.623278 ACCTTCCCAACCAATACATCATAAATT 59.377 33.333 0.00 0.00 0.00 1.82
1897 1986 0.033781 GCACCAGCAGGCATGAAAAA 59.966 50.000 0.62 0.00 41.58 1.94
1941 2030 9.342308 CATACCACATGACAACCTTAAATATCT 57.658 33.333 0.00 0.00 0.00 1.98
1977 2066 4.499357 CGGTAGAGATGTACTACAAAGGGC 60.499 50.000 0.00 0.00 41.08 5.19
1981 2070 5.474532 ACACACGGTAGAGATGTACTACAAA 59.525 40.000 0.00 0.00 41.08 2.83
2046 2141 6.797454 AGTATAAAGAAAACGTTGCCAAACA 58.203 32.000 0.00 0.00 35.94 2.83
2047 2142 7.646526 AGAAGTATAAAGAAAACGTTGCCAAAC 59.353 33.333 0.00 0.00 0.00 2.93
2048 2143 7.708998 AGAAGTATAAAGAAAACGTTGCCAAA 58.291 30.769 0.00 0.00 0.00 3.28
2049 2144 7.266922 AGAAGTATAAAGAAAACGTTGCCAA 57.733 32.000 0.00 0.00 0.00 4.52
2051 2146 8.570096 AAAAGAAGTATAAAGAAAACGTTGCC 57.430 30.769 0.00 0.00 0.00 4.52
2279 2384 8.516234 GGTCCAGATCTAATAGTAGTGTACATG 58.484 40.741 0.00 0.00 0.00 3.21
2445 2550 0.611714 GAAGGTGGTAAGAAGGCGGA 59.388 55.000 0.00 0.00 0.00 5.54
2446 2551 0.323629 TGAAGGTGGTAAGAAGGCGG 59.676 55.000 0.00 0.00 0.00 6.13
2769 3043 7.039644 GGTTTAGGATAAGATCTCCGAGATTGA 60.040 40.741 12.26 1.92 34.53 2.57
2883 3157 1.299620 CTGCTGTGTTGCTTGCACC 60.300 57.895 0.00 0.00 36.11 5.01
2910 3184 5.010617 GCCCATATTTGGAACCATCGTAAAT 59.989 40.000 3.41 0.00 46.92 1.40
2911 3185 4.339814 GCCCATATTTGGAACCATCGTAAA 59.660 41.667 3.41 0.00 46.92 2.01
2914 3188 2.306847 GCCCATATTTGGAACCATCGT 58.693 47.619 3.41 0.00 46.92 3.73
2924 3198 3.959535 ACCTTGTGTTGCCCATATTTG 57.040 42.857 0.00 0.00 0.00 2.32
2926 3200 3.900601 TGAAACCTTGTGTTGCCCATATT 59.099 39.130 0.00 0.00 37.23 1.28
2927 3201 3.505386 TGAAACCTTGTGTTGCCCATAT 58.495 40.909 0.00 0.00 37.23 1.78
2966 3240 1.134371 GTGGAGAAGGGTACATGGAGC 60.134 57.143 0.00 0.00 0.00 4.70
2980 3254 3.165875 CAAACTGTCCTCTAGGTGGAGA 58.834 50.000 5.78 4.50 35.52 3.71
2992 3266 0.242017 GCTGGCATGACAAACTGTCC 59.758 55.000 1.11 0.00 46.40 4.02
2994 3268 0.467844 TGGCTGGCATGACAAACTGT 60.468 50.000 1.11 0.00 0.00 3.55
3052 3326 1.376553 GTGGAAGGACAGGAGCAGC 60.377 63.158 0.00 0.00 0.00 5.25
3069 3343 2.174360 GGGTAAGGTGAGAAGTACCGT 58.826 52.381 0.00 0.00 43.06 4.83
3081 3355 0.686769 CGTAGGAGGCAGGGTAAGGT 60.687 60.000 0.00 0.00 0.00 3.50
3094 3368 0.606604 GGACTTCTTGGCACGTAGGA 59.393 55.000 2.87 0.00 0.00 2.94
3099 3373 0.109597 GCAATGGACTTCTTGGCACG 60.110 55.000 0.00 0.00 0.00 5.34
3102 3376 0.529378 CTGGCAATGGACTTCTTGGC 59.471 55.000 2.29 2.29 45.30 4.52
3165 3439 2.157738 GCATCAGGAAGCTCAACTGTT 58.842 47.619 10.77 0.00 34.02 3.16
3187 3461 4.161565 AGCAGTGTATCCGGATAAAACTGA 59.838 41.667 40.62 19.95 39.82 3.41
3328 3602 0.248843 GAGCTTGACAGGGTCTGAGG 59.751 60.000 9.33 0.00 35.18 3.86
3336 3610 1.071987 TGCTGTGGAGCTTGACAGG 59.928 57.895 21.32 8.69 46.39 4.00
3362 3636 2.027625 GGTTCCACCTTCTGCGACG 61.028 63.158 0.00 0.00 34.73 5.12
3366 3640 4.522789 TCTTTATTTGGTTCCACCTTCTGC 59.477 41.667 0.00 0.00 39.58 4.26
3385 3659 9.520515 TGGCTTCTTTGACTCTTTATTATCTTT 57.479 29.630 0.00 0.00 0.00 2.52
3391 3665 7.680730 TCTACTGGCTTCTTTGACTCTTTATT 58.319 34.615 0.00 0.00 0.00 1.40
3413 3687 2.878406 GACAACTTTGCTGGCTGTTCTA 59.122 45.455 0.00 0.00 0.00 2.10
3424 3698 4.423732 ACACAAGACAATGACAACTTTGC 58.576 39.130 0.00 0.00 35.48 3.68
3430 3704 4.886489 TGATCCAACACAAGACAATGACAA 59.114 37.500 0.00 0.00 0.00 3.18
3431 3705 4.459330 TGATCCAACACAAGACAATGACA 58.541 39.130 0.00 0.00 0.00 3.58
3432 3706 5.413833 AGATGATCCAACACAAGACAATGAC 59.586 40.000 0.00 0.00 0.00 3.06
3442 3716 4.967036 TGTACAACAGATGATCCAACACA 58.033 39.130 0.00 0.00 0.00 3.72
3446 3720 5.705441 GGTCTTTGTACAACAGATGATCCAA 59.295 40.000 8.07 0.00 0.00 3.53
3487 3761 2.736719 CGTGCTGAACAGGACTAGGATG 60.737 54.545 20.32 4.28 45.96 3.51
3621 3895 4.154195 CACTGCTGGTATAACAAACCTGAC 59.846 45.833 0.00 0.00 37.98 3.51
3720 3994 1.677217 GCTGCTCCAGGGTTAGAGTTG 60.677 57.143 0.00 0.00 32.47 3.16
3751 4028 1.452833 GGATCTGAACAGCAGGCCC 60.453 63.158 0.00 0.00 44.98 5.80
3816 4093 2.202610 CTCGCCGTCGAAGCATCA 60.203 61.111 9.17 0.00 44.98 3.07
3819 4096 2.430244 GAACTCGCCGTCGAAGCA 60.430 61.111 9.17 0.00 44.98 3.91
4012 4291 1.004044 CTCTGAACAGGCCTGGTGATT 59.996 52.381 35.42 21.13 34.19 2.57
4029 4308 9.672673 ACAACAAAGCAGTATAATATGAACTCT 57.327 29.630 0.00 0.00 0.00 3.24
4139 4442 0.183492 ACAAACAGAAGCAGCCTCCA 59.817 50.000 0.00 0.00 0.00 3.86
4177 4481 0.037975 CAACCAACCATGCCTCAAGC 60.038 55.000 0.00 0.00 44.14 4.01
4200 4504 1.066605 GCTCCAGCATTGCCACATAAG 59.933 52.381 4.70 0.00 41.59 1.73
4211 4515 4.457496 CCGACCACGCTCCAGCAT 62.457 66.667 0.00 0.00 42.21 3.79
4275 4580 2.841988 GCCCCACCACCAAGCAAA 60.842 61.111 0.00 0.00 0.00 3.68
4538 4843 3.758931 GCCAAACCCCACATCGCC 61.759 66.667 0.00 0.00 0.00 5.54
4555 4860 2.544726 GGTTTTCACCTGGAGCTCG 58.455 57.895 7.83 0.00 40.44 5.03
4572 4877 1.600023 TTAACCGAAGTTGGTGCAGG 58.400 50.000 0.00 0.00 42.89 4.85
4608 4914 0.804933 GGGCAACGACGTCATAGGAC 60.805 60.000 17.16 3.52 37.97 3.85
4614 4920 1.434555 CAATTAGGGCAACGACGTCA 58.565 50.000 17.16 0.00 37.60 4.35
4697 6749 3.709987 CCAACCAAAGCAGAAACTTGAG 58.290 45.455 0.00 0.00 0.00 3.02
4698 6750 2.159114 GCCAACCAAAGCAGAAACTTGA 60.159 45.455 0.00 0.00 0.00 3.02
4699 6751 2.204237 GCCAACCAAAGCAGAAACTTG 58.796 47.619 0.00 0.00 0.00 3.16
4700 6752 1.830477 TGCCAACCAAAGCAGAAACTT 59.170 42.857 0.00 0.00 33.08 2.66
4779 6849 1.557269 AATCGGCAAGACCTCTGCCT 61.557 55.000 11.76 0.00 45.86 4.75
4812 6882 6.442952 TGTTGTATGTTAACATTGGAACAGC 58.557 36.000 25.31 22.37 38.86 4.40
4839 6909 3.467374 TTCTCAAAACAAACATGCCCC 57.533 42.857 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.