Multiple sequence alignment - TraesCS5D01G099100

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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 TraesCS5D01G099100 chr5D 100.000 3948 0 0 1 3948 110792640 110796587 0.000000e+00 7291.0
1 TraesCS5D01G099100 chr5D 88.856 341 33 5 3607 3946 520247466 520247802 7.890000e-112 414.0
2 TraesCS5D01G099100 chr5D 88.473 347 31 6 3607 3948 238387093 238387435 1.020000e-110 411.0
3 TraesCS5D01G099100 chr5D 86.880 343 40 5 3607 3948 482905008 482904670 2.880000e-101 379.0
4 TraesCS5D01G099100 chr5D 85.591 347 40 9 3607 3948 288544123 288543782 4.850000e-94 355.0
5 TraesCS5D01G099100 chr5A 91.523 1852 106 22 164 1982 116035856 116034023 0.000000e+00 2503.0
6 TraesCS5D01G099100 chr5A 94.762 1470 55 9 2013 3476 116034019 116032566 0.000000e+00 2268.0
7 TraesCS5D01G099100 chr5A 90.773 401 30 6 3549 3948 116032565 116032171 2.700000e-146 529.0
8 TraesCS5D01G099100 chr5A 96.063 127 5 0 1 127 116035980 116035854 1.440000e-49 207.0
9 TraesCS5D01G099100 chr5B 90.808 1893 90 31 164 1983 122102789 122100908 0.000000e+00 2455.0
10 TraesCS5D01G099100 chr5B 88.606 1492 119 25 2059 3512 122100880 122099402 0.000000e+00 1766.0
11 TraesCS5D01G099100 chr5B 95.276 127 6 0 1 127 122102913 122102787 6.690000e-48 202.0
12 TraesCS5D01G099100 chr5B 97.059 34 0 1 2004 2036 510729605 510729572 5.510000e-04 56.5
13 TraesCS5D01G099100 chr5B 96.970 33 0 1 1971 2003 89058095 89058126 2.000000e-03 54.7
14 TraesCS5D01G099100 chr2B 86.297 343 37 10 3610 3948 643677126 643676790 8.060000e-97 364.0
15 TraesCS5D01G099100 chr2B 85.423 343 43 7 3608 3948 670343184 670342847 2.260000e-92 350.0
16 TraesCS5D01G099100 chrUn 84.703 353 40 12 3601 3948 26707051 26706708 1.360000e-89 340.0
17 TraesCS5D01G099100 chrUn 95.556 135 6 0 1459 1593 58870827 58870693 2.390000e-52 217.0
18 TraesCS5D01G099100 chr3D 84.726 347 42 9 3607 3948 467488580 467488920 1.760000e-88 337.0
19 TraesCS5D01G099100 chr6A 79.480 346 57 11 395 729 608085409 608085751 2.370000e-57 233.0
20 TraesCS5D01G099100 chr2D 77.136 398 78 8 344 730 30677509 30677904 6.640000e-53 219.0
21 TraesCS5D01G099100 chr2D 77.250 400 73 12 343 729 188282392 188282786 6.640000e-53 219.0
22 TraesCS5D01G099100 chr4A 94.815 135 7 0 1459 1593 437483912 437483778 1.110000e-50 211.0
23 TraesCS5D01G099100 chr4D 92.908 141 10 0 1453 1593 129776536 129776676 5.170000e-49 206.0
24 TraesCS5D01G099100 chr6B 79.522 293 48 9 465 747 82528392 82528102 8.650000e-47 198.0
25 TraesCS5D01G099100 chr7D 79.636 275 52 4 366 638 59870180 59870452 1.120000e-45 195.0
26 TraesCS5D01G099100 chr7D 97.143 35 0 1 2004 2037 423587157 423587191 1.530000e-04 58.4
27 TraesCS5D01G099100 chr3A 75.534 421 82 13 344 747 78184206 78183790 1.870000e-43 187.0
28 TraesCS5D01G099100 chr3A 94.737 38 1 1 2000 2036 127352318 127352281 1.530000e-04 58.4
29 TraesCS5D01G099100 chr1B 75.000 392 80 13 345 723 681804797 681805183 8.780000e-37 165.0
30 TraesCS5D01G099100 chr1B 85.401 137 18 2 1453 1588 659780378 659780243 1.480000e-29 141.0
31 TraesCS5D01G099100 chr7A 77.143 280 44 17 483 748 83107763 83107490 1.140000e-30 145.0
32 TraesCS5D01G099100 chr7A 80.435 138 25 2 1452 1588 121398162 121398298 1.940000e-18 104.0
33 TraesCS5D01G099100 chr1A 84.783 138 19 2 1452 1588 569139386 569139250 1.910000e-28 137.0
34 TraesCS5D01G099100 chr1A 97.059 34 0 1 2004 2036 493216571 493216538 5.510000e-04 56.5
35 TraesCS5D01G099100 chr3B 74.618 327 59 17 415 730 142840331 142840018 5.360000e-24 122.0
36 TraesCS5D01G099100 chr3B 72.953 403 75 26 364 747 816062912 816062525 4.170000e-20 110.0
37 TraesCS5D01G099100 chr7B 81.159 138 24 2 1452 1588 77432156 77432292 4.170000e-20 110.0
38 TraesCS5D01G099100 chr7B 100.000 28 0 0 363 390 191894756 191894783 7.000000e-03 52.8


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 TraesCS5D01G099100 chr5D 110792640 110796587 3947 False 7291.000000 7291 100.000000 1 3948 1 chr5D.!!$F1 3947
1 TraesCS5D01G099100 chr5A 116032171 116035980 3809 True 1376.750000 2503 93.280250 1 3948 4 chr5A.!!$R1 3947
2 TraesCS5D01G099100 chr5B 122099402 122102913 3511 True 1474.333333 2455 91.563333 1 3512 3 chr5B.!!$R2 3511

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
659 669 0.107456 CTCCAATGAGGGGGTGATCG 59.893 60.0 0.0 0.0 38.24 3.69 F
2413 2502 0.250467 AGCTCAACTGTGACGCCAAT 60.250 50.0 0.0 0.0 31.87 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2632 2721 1.075374 TCTTCAACCCAATCCCCACTG 59.925 52.381 0.00 0.00 0.0 3.66 R
3693 3813 1.090728 TCAGCGAAACTTTGTGCACA 58.909 45.000 17.42 17.42 0.0 4.57 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
124 125 5.297776 CGCATCTAATTCTTCCATGTCCTTT 59.702 40.000 0.00 0.00 0.00 3.11
125 126 6.183360 CGCATCTAATTCTTCCATGTCCTTTT 60.183 38.462 0.00 0.00 0.00 2.27
126 127 7.550712 GCATCTAATTCTTCCATGTCCTTTTT 58.449 34.615 0.00 0.00 0.00 1.94
148 149 5.730296 TTTTTGCGGGATTAATTCTTCCA 57.270 34.783 8.42 0.00 33.43 3.53
149 150 5.930837 TTTTGCGGGATTAATTCTTCCAT 57.069 34.783 8.42 0.00 33.43 3.41
150 151 4.916983 TTGCGGGATTAATTCTTCCATG 57.083 40.909 8.42 0.00 33.43 3.66
151 152 3.897239 TGCGGGATTAATTCTTCCATGT 58.103 40.909 8.42 0.00 33.43 3.21
152 153 3.882888 TGCGGGATTAATTCTTCCATGTC 59.117 43.478 8.42 0.38 33.43 3.06
153 154 3.253432 GCGGGATTAATTCTTCCATGTCC 59.747 47.826 8.42 0.00 33.43 4.02
154 155 4.718961 CGGGATTAATTCTTCCATGTCCT 58.281 43.478 8.42 0.00 33.43 3.85
155 156 5.133221 CGGGATTAATTCTTCCATGTCCTT 58.867 41.667 8.42 0.00 33.43 3.36
156 157 6.296026 CGGGATTAATTCTTCCATGTCCTTA 58.704 40.000 8.42 0.00 33.43 2.69
157 158 6.942576 CGGGATTAATTCTTCCATGTCCTTAT 59.057 38.462 8.42 0.00 33.43 1.73
158 159 7.448469 CGGGATTAATTCTTCCATGTCCTTATT 59.552 37.037 8.42 0.00 33.43 1.40
159 160 8.797438 GGGATTAATTCTTCCATGTCCTTATTC 58.203 37.037 8.42 0.00 33.43 1.75
160 161 8.507249 GGATTAATTCTTCCATGTCCTTATTCG 58.493 37.037 0.00 0.00 31.99 3.34
161 162 8.980481 ATTAATTCTTCCATGTCCTTATTCGT 57.020 30.769 0.00 0.00 0.00 3.85
162 163 6.683974 AATTCTTCCATGTCCTTATTCGTG 57.316 37.500 0.00 0.00 0.00 4.35
189 190 7.857734 TCGTGAGCATTTTAGGATTTATTGA 57.142 32.000 0.00 0.00 0.00 2.57
220 221 1.088340 CAGGCAGCTGATCGTTCCAG 61.088 60.000 20.43 0.33 34.88 3.86
265 266 4.157289 GTGGTGATGCTTCTCAATTGTCAT 59.843 41.667 5.13 3.02 0.00 3.06
271 272 2.912967 GCTTCTCAATTGTCATTGCGTG 59.087 45.455 5.13 0.00 39.90 5.34
275 276 3.058983 TCTCAATTGTCATTGCGTGTGTC 60.059 43.478 5.13 0.00 39.90 3.67
392 401 0.485543 TAGCCTCCATCCCGGTGATA 59.514 55.000 0.00 0.00 35.57 2.15
399 408 3.895656 CTCCATCCCGGTGATACTTCTAA 59.104 47.826 0.00 0.00 35.57 2.10
469 478 1.144969 TGCGGTCGACATTTGTCTTC 58.855 50.000 18.91 0.00 42.66 2.87
471 480 1.732259 GCGGTCGACATTTGTCTTCAT 59.268 47.619 18.91 0.00 42.66 2.57
512 521 4.436451 GGTCTTCGTTCGTCTTTGTTTGTT 60.436 41.667 0.00 0.00 0.00 2.83
521 530 7.433979 GTTCGTCTTTGTTTGTTTGTTTACAG 58.566 34.615 0.00 0.00 0.00 2.74
533 542 7.266922 TGTTTGTTTACAGATTGTACCCTTC 57.733 36.000 0.00 0.00 31.69 3.46
559 568 0.248661 ATGCGTCTCTTCATCGTCGG 60.249 55.000 0.00 0.00 0.00 4.79
585 595 2.031163 GTTCAGGTGCGCTGTCCT 59.969 61.111 9.73 11.25 33.96 3.85
597 607 3.321968 TGCGCTGTCCTATGTGATCTTAT 59.678 43.478 9.73 0.00 0.00 1.73
629 639 7.527457 GCTTCCCAACTGTTTACTGTAATAAG 58.473 38.462 0.37 5.02 0.00 1.73
642 652 3.211045 TGTAATAAGATTTGCCCGGCTC 58.789 45.455 11.61 0.00 0.00 4.70
644 654 0.550914 ATAAGATTTGCCCGGCTCCA 59.449 50.000 11.61 0.00 0.00 3.86
653 663 4.195334 CCGGCTCCAATGAGGGGG 62.195 72.222 0.00 0.00 38.82 5.40
658 668 0.179006 GCTCCAATGAGGGGGTGATC 60.179 60.000 0.00 0.00 38.82 2.92
659 669 0.107456 CTCCAATGAGGGGGTGATCG 59.893 60.000 0.00 0.00 38.24 3.69
660 670 1.149174 CCAATGAGGGGGTGATCGG 59.851 63.158 0.00 0.00 0.00 4.18
681 699 1.860078 CACCTTCGGCTCGTTCAAC 59.140 57.895 0.00 0.00 0.00 3.18
861 896 2.634815 TTGTACGGTGCCCTTTGTAA 57.365 45.000 0.00 0.00 0.00 2.41
962 1014 1.397672 CGCATTCTCTCTCTCCCTCA 58.602 55.000 0.00 0.00 0.00 3.86
1120 1172 8.343168 TCTGTCTCTAGAACTAGAAAAAGGAG 57.657 38.462 11.82 0.00 41.22 3.69
1121 1173 8.164733 TCTGTCTCTAGAACTAGAAAAAGGAGA 58.835 37.037 11.82 0.00 41.22 3.71
1896 1974 4.707448 ACGCCTCTTCTATCTTTCTCTTCA 59.293 41.667 0.00 0.00 0.00 3.02
1988 2066 7.954788 TTTTTCAAACAAATTATTCCCTCCG 57.045 32.000 0.00 0.00 0.00 4.63
1989 2067 6.658188 TTTCAAACAAATTATTCCCTCCGT 57.342 33.333 0.00 0.00 0.00 4.69
1990 2068 7.762588 TTTCAAACAAATTATTCCCTCCGTA 57.237 32.000 0.00 0.00 0.00 4.02
1991 2069 7.762588 TTCAAACAAATTATTCCCTCCGTAA 57.237 32.000 0.00 0.00 0.00 3.18
1992 2070 7.762588 TCAAACAAATTATTCCCTCCGTAAA 57.237 32.000 0.00 0.00 0.00 2.01
1993 2071 7.822658 TCAAACAAATTATTCCCTCCGTAAAG 58.177 34.615 0.00 0.00 0.00 1.85
1994 2072 7.666388 TCAAACAAATTATTCCCTCCGTAAAGA 59.334 33.333 0.00 0.00 0.00 2.52
1995 2073 8.301002 CAAACAAATTATTCCCTCCGTAAAGAA 58.699 33.333 0.00 0.00 0.00 2.52
1996 2074 8.411991 AACAAATTATTCCCTCCGTAAAGAAA 57.588 30.769 0.00 0.00 0.00 2.52
1997 2075 8.589701 ACAAATTATTCCCTCCGTAAAGAAAT 57.410 30.769 0.00 0.00 0.00 2.17
1998 2076 9.689501 ACAAATTATTCCCTCCGTAAAGAAATA 57.310 29.630 0.00 0.00 0.00 1.40
2003 2081 7.981102 ATTCCCTCCGTAAAGAAATATAAGC 57.019 36.000 0.00 0.00 0.00 3.09
2004 2082 6.742559 TCCCTCCGTAAAGAAATATAAGCT 57.257 37.500 0.00 0.00 0.00 3.74
2005 2083 7.844493 TCCCTCCGTAAAGAAATATAAGCTA 57.156 36.000 0.00 0.00 0.00 3.32
2006 2084 8.253867 TCCCTCCGTAAAGAAATATAAGCTAA 57.746 34.615 0.00 0.00 0.00 3.09
2007 2085 8.707449 TCCCTCCGTAAAGAAATATAAGCTAAA 58.293 33.333 0.00 0.00 0.00 1.85
2008 2086 8.989980 CCCTCCGTAAAGAAATATAAGCTAAAG 58.010 37.037 0.00 0.00 0.00 1.85
2009 2087 8.496751 CCTCCGTAAAGAAATATAAGCTAAAGC 58.503 37.037 0.00 0.00 42.49 3.51
2096 2174 8.506168 TTATAGTTCATTTTCTCCACATGGAC 57.494 34.615 0.00 0.00 39.78 4.02
2148 2235 8.718734 AGAGTTGCCGAAAATTTAACTTACTAG 58.281 33.333 5.09 0.00 32.23 2.57
2191 2278 8.244113 ACTAAGGTGTCTTTTGCTAATTAATGC 58.756 33.333 0.00 0.00 34.59 3.56
2222 2311 2.194201 TTCCTTTCCCTCGCGAAAAT 57.806 45.000 11.33 0.00 31.56 1.82
2253 2342 9.656040 TGCAATTAATTAGTTTTCTTCATGCAT 57.344 25.926 0.00 0.00 0.00 3.96
2271 2360 7.944061 TCATGCATCATAAATGTTTCCCTAAG 58.056 34.615 0.00 0.00 0.00 2.18
2279 2368 8.250332 TCATAAATGTTTCCCTAAGTGCATTTC 58.750 33.333 0.00 0.00 37.59 2.17
2288 2377 2.101640 AAGTGCATTTCCCCCTTTGT 57.898 45.000 0.00 0.00 0.00 2.83
2297 2386 2.397044 TCCCCCTTTGTTTCTTGCAT 57.603 45.000 0.00 0.00 0.00 3.96
2413 2502 0.250467 AGCTCAACTGTGACGCCAAT 60.250 50.000 0.00 0.00 31.87 3.16
2461 2550 0.901124 ATCTATGGATGCCTCGCCTC 59.099 55.000 0.00 0.00 0.00 4.70
2632 2721 1.683917 AGCGTGGGAGAGATGATACAC 59.316 52.381 0.00 0.00 0.00 2.90
2648 2737 0.178964 ACACAGTGGGGATTGGGTTG 60.179 55.000 5.31 0.00 0.00 3.77
2707 2796 3.389329 AGACTTTCCAGCTTCAAGACTCA 59.611 43.478 3.77 0.00 0.00 3.41
2710 2799 3.393089 TTCCAGCTTCAAGACTCAGAC 57.607 47.619 0.00 0.00 0.00 3.51
2753 2842 2.438614 CCGAGTCCGAGAGCCTCA 60.439 66.667 0.00 0.00 38.22 3.86
2823 2916 9.951866 ATTTATATTCTATGTTGGAAAAGGGGT 57.048 29.630 0.00 0.00 0.00 4.95
3178 3278 1.873591 CTCCAAAGTCCCAACGTCTTG 59.126 52.381 0.00 0.00 0.00 3.02
3323 3423 1.090052 GCTAATGTCCCGTGTGGAGC 61.090 60.000 0.00 0.00 46.38 4.70
3406 3517 7.949006 ACCCTAAGTCTCTAAACTAGAAGTTGA 59.051 37.037 0.00 0.00 38.66 3.18
3425 3536 7.393841 AGTTGATTTAGACGAACTAGTAGCT 57.606 36.000 0.00 0.00 32.30 3.32
3499 3619 6.222038 ACATGTATTCGAACACTACTCCAT 57.778 37.500 8.23 0.00 30.75 3.41
3501 3621 7.103641 ACATGTATTCGAACACTACTCCATTT 58.896 34.615 8.23 0.00 30.75 2.32
3514 3634 8.982723 ACACTACTCCATTTATATATGCTAGGG 58.017 37.037 0.00 1.41 0.00 3.53
3515 3635 8.982723 CACTACTCCATTTATATATGCTAGGGT 58.017 37.037 0.00 0.00 0.00 4.34
3516 3636 9.203163 ACTACTCCATTTATATATGCTAGGGTC 57.797 37.037 0.00 0.00 0.00 4.46
3517 3637 9.427821 CTACTCCATTTATATATGCTAGGGTCT 57.572 37.037 0.00 0.00 0.00 3.85
3518 3638 8.686739 ACTCCATTTATATATGCTAGGGTCTT 57.313 34.615 0.00 0.00 0.00 3.01
3519 3639 9.117223 ACTCCATTTATATATGCTAGGGTCTTT 57.883 33.333 0.00 0.00 0.00 2.52
3520 3640 9.606631 CTCCATTTATATATGCTAGGGTCTTTC 57.393 37.037 0.00 0.00 0.00 2.62
3521 3641 8.548877 TCCATTTATATATGCTAGGGTCTTTCC 58.451 37.037 0.00 0.00 0.00 3.13
3534 3654 4.659111 GGTCTTTCCCCTTTTCGAAAAA 57.341 40.909 22.67 6.71 0.00 1.94
3678 3798 1.933115 AAAATCCCGCGTGTGCATCC 61.933 55.000 4.92 0.00 42.97 3.51
3693 3813 4.065088 GTGCATCCGGACATTATATGTGT 58.935 43.478 6.12 0.00 45.03 3.72
3709 3829 0.913876 GTGTGTGCACAAAGTTTCGC 59.086 50.000 23.59 10.93 43.77 4.70
3712 3832 1.090728 TGTGCACAAAGTTTCGCTGA 58.909 45.000 19.28 0.00 0.00 4.26
3775 3896 3.819564 TGCCTCGTCAATAGCTGTAAT 57.180 42.857 0.00 0.00 0.00 1.89
3778 3899 4.119862 GCCTCGTCAATAGCTGTAATCAA 58.880 43.478 0.00 0.00 0.00 2.57
3783 3904 5.463392 TCGTCAATAGCTGTAATCAAGCATC 59.537 40.000 0.00 0.00 0.00 3.91
3784 3905 5.611197 CGTCAATAGCTGTAATCAAGCATCG 60.611 44.000 0.00 0.00 0.00 3.84
3791 3912 6.032094 AGCTGTAATCAAGCATCGAAAATTG 58.968 36.000 0.00 0.00 0.00 2.32
3794 3915 7.144722 TGTAATCAAGCATCGAAAATTGTCT 57.855 32.000 0.00 0.00 0.00 3.41
3866 3987 4.448210 ACGCACATATAAAGTCCGGATTT 58.552 39.130 7.81 6.99 0.00 2.17
3871 3992 6.563381 GCACATATAAAGTCCGGATTTACACG 60.563 42.308 13.15 9.69 0.00 4.49
3875 3996 2.169146 GTCCGGATTTACACGCGGG 61.169 63.158 6.92 6.92 0.00 6.13
3882 4003 3.431856 GGATTTACACGCGGGATTTTTC 58.568 45.455 19.19 4.85 0.00 2.29
3886 4007 1.296056 ACACGCGGGATTTTTCCTCG 61.296 55.000 19.19 0.00 34.10 4.63
3927 4048 6.042552 TCAAAATGTGTATTTGGACAATGGGT 59.957 34.615 0.00 0.00 38.12 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 5.730296 TGGAAGAATTAATCCCGCAAAAA 57.270 34.783 6.55 0.00 34.68 1.94
127 128 5.186797 ACATGGAAGAATTAATCCCGCAAAA 59.813 36.000 0.00 0.00 34.68 2.44
128 129 4.709397 ACATGGAAGAATTAATCCCGCAAA 59.291 37.500 0.00 0.00 34.68 3.68
129 130 4.277476 ACATGGAAGAATTAATCCCGCAA 58.723 39.130 0.00 0.00 34.68 4.85
130 131 3.882888 GACATGGAAGAATTAATCCCGCA 59.117 43.478 0.00 0.00 34.68 5.69
131 132 3.253432 GGACATGGAAGAATTAATCCCGC 59.747 47.826 0.00 0.00 34.68 6.13
132 133 4.718961 AGGACATGGAAGAATTAATCCCG 58.281 43.478 0.00 1.76 34.68 5.14
133 134 8.712228 AATAAGGACATGGAAGAATTAATCCC 57.288 34.615 0.00 0.00 34.68 3.85
134 135 8.507249 CGAATAAGGACATGGAAGAATTAATCC 58.493 37.037 0.00 2.66 36.21 3.01
135 136 9.057089 ACGAATAAGGACATGGAAGAATTAATC 57.943 33.333 0.00 0.00 0.00 1.75
136 137 8.840321 CACGAATAAGGACATGGAAGAATTAAT 58.160 33.333 0.00 0.00 0.00 1.40
137 138 8.044309 TCACGAATAAGGACATGGAAGAATTAA 58.956 33.333 0.00 0.00 0.00 1.40
138 139 7.561251 TCACGAATAAGGACATGGAAGAATTA 58.439 34.615 0.00 0.00 0.00 1.40
139 140 6.414732 TCACGAATAAGGACATGGAAGAATT 58.585 36.000 0.00 0.00 0.00 2.17
140 141 5.989477 TCACGAATAAGGACATGGAAGAAT 58.011 37.500 0.00 0.00 0.00 2.40
141 142 5.414789 TCACGAATAAGGACATGGAAGAA 57.585 39.130 0.00 0.00 0.00 2.52
142 143 5.614324 ATCACGAATAAGGACATGGAAGA 57.386 39.130 0.00 0.00 0.00 2.87
143 144 5.050769 CGAATCACGAATAAGGACATGGAAG 60.051 44.000 0.00 0.00 45.77 3.46
144 145 4.808895 CGAATCACGAATAAGGACATGGAA 59.191 41.667 0.00 0.00 45.77 3.53
145 146 4.142026 ACGAATCACGAATAAGGACATGGA 60.142 41.667 0.00 0.00 45.77 3.41
146 147 4.025730 CACGAATCACGAATAAGGACATGG 60.026 45.833 0.00 0.00 45.77 3.66
147 148 4.803613 TCACGAATCACGAATAAGGACATG 59.196 41.667 0.00 0.00 45.77 3.21
148 149 5.006153 TCACGAATCACGAATAAGGACAT 57.994 39.130 0.00 0.00 45.77 3.06
149 150 4.421058 CTCACGAATCACGAATAAGGACA 58.579 43.478 0.00 0.00 45.77 4.02
150 151 3.243177 GCTCACGAATCACGAATAAGGAC 59.757 47.826 0.00 0.00 45.77 3.85
151 152 3.119280 TGCTCACGAATCACGAATAAGGA 60.119 43.478 0.00 0.00 45.77 3.36
152 153 3.186909 TGCTCACGAATCACGAATAAGG 58.813 45.455 0.00 0.00 45.77 2.69
153 154 5.395325 AATGCTCACGAATCACGAATAAG 57.605 39.130 0.00 0.00 45.77 1.73
154 155 5.794687 AAATGCTCACGAATCACGAATAA 57.205 34.783 0.00 0.00 45.77 1.40
155 156 5.794687 AAAATGCTCACGAATCACGAATA 57.205 34.783 0.00 0.00 45.77 1.75
156 157 4.685169 AAAATGCTCACGAATCACGAAT 57.315 36.364 0.00 0.00 45.77 3.34
157 158 4.092821 CCTAAAATGCTCACGAATCACGAA 59.907 41.667 0.00 0.00 45.77 3.85
158 159 3.616821 CCTAAAATGCTCACGAATCACGA 59.383 43.478 0.00 0.00 45.77 4.35
160 161 5.741388 ATCCTAAAATGCTCACGAATCAC 57.259 39.130 0.00 0.00 0.00 3.06
161 162 6.757897 AAATCCTAAAATGCTCACGAATCA 57.242 33.333 0.00 0.00 0.00 2.57
162 163 9.173939 CAATAAATCCTAAAATGCTCACGAATC 57.826 33.333 0.00 0.00 0.00 2.52
189 190 1.849039 AGCTGCCTGGAATCACCTATT 59.151 47.619 0.00 0.00 39.86 1.73
220 221 2.203126 CCGGAGAGCTGAATGCCC 60.203 66.667 0.00 0.00 44.23 5.36
235 236 0.460987 GAAGCATCACCACTCCTCCG 60.461 60.000 0.00 0.00 0.00 4.63
265 266 3.946308 TTACATTTTCGACACACGCAA 57.054 38.095 0.00 0.00 42.26 4.85
356 364 2.214347 GCTAGGCGGGAAGAATCTTTC 58.786 52.381 0.00 0.00 0.00 2.62
392 401 2.694109 GCCCTCCTATGACGTTAGAAGT 59.306 50.000 0.00 0.00 0.00 3.01
399 408 1.681327 ACACGCCCTCCTATGACGT 60.681 57.895 0.00 0.00 37.47 4.34
512 521 4.998672 CGGAAGGGTACAATCTGTAAACAA 59.001 41.667 0.00 0.00 34.21 2.83
521 530 4.246458 GCATAGATCGGAAGGGTACAATC 58.754 47.826 0.00 0.00 0.00 2.67
533 542 3.497118 GATGAAGAGACGCATAGATCGG 58.503 50.000 0.00 0.00 0.00 4.18
559 568 0.592247 CGCACCTGAACAACAACTGC 60.592 55.000 0.00 0.00 0.00 4.40
597 607 1.300620 CAGTTGGGAAGCGTCGTGA 60.301 57.895 0.00 0.00 0.00 4.35
629 639 1.037030 TCATTGGAGCCGGGCAAATC 61.037 55.000 23.09 10.11 0.00 2.17
642 652 1.149174 CCGATCACCCCCTCATTGG 59.851 63.158 0.00 0.00 0.00 3.16
644 654 2.919043 GCCGATCACCCCCTCATT 59.081 61.111 0.00 0.00 0.00 2.57
653 663 3.554692 CGAAGGTGCGCCGATCAC 61.555 66.667 20.43 0.00 40.50 3.06
676 694 3.990092 ACGATGACTACAAGCAGTTGAA 58.010 40.909 0.00 0.00 37.10 2.69
861 896 2.533365 CGCGCGTACGTATTTTCACAAT 60.533 45.455 24.19 0.00 42.83 2.71
962 1014 3.574826 AGAGGAAGTAGAAAAGTGAGCGT 59.425 43.478 0.00 0.00 0.00 5.07
1120 1172 1.667724 CCATGACGCCATGTTCTCTTC 59.332 52.381 10.93 0.00 46.68 2.87
1121 1173 1.003580 ACCATGACGCCATGTTCTCTT 59.996 47.619 10.93 0.00 46.68 2.85
2007 2085 9.995003 CTCACTCCATAAAGAAATATAAGAGCT 57.005 33.333 0.00 0.00 0.00 4.09
2008 2086 9.771534 ACTCACTCCATAAAGAAATATAAGAGC 57.228 33.333 0.00 0.00 0.00 4.09
2253 2342 7.716799 AATGCACTTAGGGAAACATTTATGA 57.283 32.000 0.00 0.00 0.00 2.15
2271 2360 2.368548 AGAAACAAAGGGGGAAATGCAC 59.631 45.455 0.00 0.00 0.00 4.57
2279 2368 3.768757 TCATATGCAAGAAACAAAGGGGG 59.231 43.478 0.00 0.00 0.00 5.40
2288 2377 4.462483 GGACCACCTTTCATATGCAAGAAA 59.538 41.667 15.61 10.60 33.17 2.52
2297 2386 4.721776 AGCTATCTTGGACCACCTTTCATA 59.278 41.667 0.00 0.00 37.04 2.15
2407 2496 1.164411 TGAACTTGGTGCTATTGGCG 58.836 50.000 0.00 0.00 45.43 5.69
2413 2502 2.436417 GCATCCTTGAACTTGGTGCTA 58.564 47.619 0.00 0.00 32.07 3.49
2569 2658 3.942130 TCATATGACTCCGATGCGAAT 57.058 42.857 0.00 0.00 0.00 3.34
2632 2721 1.075374 TCTTCAACCCAATCCCCACTG 59.925 52.381 0.00 0.00 0.00 3.66
2648 2737 4.321527 CCAAAACCCTTGATTCTGCTCTTC 60.322 45.833 0.00 0.00 0.00 2.87
2707 2796 2.902608 TGTACCCATCCAGACAAGTCT 58.097 47.619 0.00 0.00 41.37 3.24
2710 2799 2.356125 CCCTTGTACCCATCCAGACAAG 60.356 54.545 6.63 6.63 45.41 3.16
2753 2842 5.302823 CCTCCAAACTCCAAAAATTCTCAGT 59.697 40.000 0.00 0.00 0.00 3.41
2822 2915 6.237123 CGACCATAAATCGTATATGCACGTAC 60.237 42.308 0.00 0.00 42.51 3.67
2823 2916 5.796437 CGACCATAAATCGTATATGCACGTA 59.204 40.000 0.00 0.00 42.51 3.57
2975 3073 5.359860 ACACCTGACCCAAAAAGTAGAAAAG 59.640 40.000 0.00 0.00 0.00 2.27
2980 3078 4.204012 TGAACACCTGACCCAAAAAGTAG 58.796 43.478 0.00 0.00 0.00 2.57
3178 3278 4.520492 TGAAAAGGCCAGAGACTTGAAATC 59.480 41.667 5.01 0.00 0.00 2.17
3323 3423 4.273480 AGTTGTTCTCTGTGAAATTCGGTG 59.727 41.667 0.00 0.00 36.30 4.94
3471 3591 7.758528 GGAGTAGTGTTCGAATACATGTAGTTT 59.241 37.037 24.38 1.37 0.00 2.66
3477 3597 7.539712 AAATGGAGTAGTGTTCGAATACATG 57.460 36.000 24.38 0.00 0.00 3.21
3483 3603 9.419297 GCATATATAAATGGAGTAGTGTTCGAA 57.581 33.333 0.00 0.00 0.00 3.71
3485 3605 8.988064 AGCATATATAAATGGAGTAGTGTTCG 57.012 34.615 0.00 0.00 0.00 3.95
3513 3633 4.659111 TTTTTCGAAAAGGGGAAAGACC 57.341 40.909 21.53 0.00 34.03 3.85
3547 3667 9.553064 CTTTTTGAGAAGACCTGTAGCATATAT 57.447 33.333 0.00 0.00 0.00 0.86
3556 3676 5.418840 TCTTTTGCTTTTTGAGAAGACCTGT 59.581 36.000 0.00 0.00 0.00 4.00
3660 3780 2.406616 GGATGCACACGCGGGATTT 61.407 57.895 19.19 0.00 42.97 2.17
3661 3781 2.824041 GGATGCACACGCGGGATT 60.824 61.111 19.19 0.00 42.97 3.01
3670 3790 4.064388 CACATATAATGTCCGGATGCACA 58.936 43.478 7.81 0.55 42.70 4.57
3678 3798 4.195744 GTGCACACACATATAATGTCCG 57.804 45.455 13.17 0.00 46.61 4.79
3693 3813 1.090728 TCAGCGAAACTTTGTGCACA 58.909 45.000 17.42 17.42 0.00 4.57
3759 3880 4.754322 TGCTTGATTACAGCTATTGACGA 58.246 39.130 0.00 0.00 0.00 4.20
3763 3884 5.912360 TCGATGCTTGATTACAGCTATTG 57.088 39.130 0.00 0.00 0.00 1.90
3769 3890 7.246311 AGACAATTTTCGATGCTTGATTACAG 58.754 34.615 7.97 0.00 0.00 2.74
3825 3946 2.574450 GTACCCAAAGTTCCGGTGAAA 58.426 47.619 0.00 0.00 30.79 2.69
3841 3962 3.054878 CCGGACTTTATATGTGCGTACC 58.945 50.000 15.18 0.00 45.36 3.34
3866 3987 1.729284 GAGGAAAAATCCCGCGTGTA 58.271 50.000 4.92 0.00 0.00 2.90
3871 3992 4.365899 AAATTACGAGGAAAAATCCCGC 57.634 40.909 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.