Multiple sequence alignment - TraesCS5B01G264800

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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 TraesCS5B01G264800 chr5B 100.000 4325 0 0 1 4325 448663942 448659618 0.000000e+00 7987.0
1 TraesCS5B01G264800 chr5A 93.006 4032 151 56 372 4325 476898495 476894517 0.000000e+00 5762.0
2 TraesCS5B01G264800 chr5A 86.059 373 43 7 10 379 476899725 476899359 4.050000e-105 392.0
3 TraesCS5B01G264800 chr5D 93.402 2622 123 19 1692 4297 375802772 375800185 0.000000e+00 3838.0
4 TraesCS5B01G264800 chr5D 87.500 1048 74 29 445 1466 375804022 375803006 0.000000e+00 1157.0
5 TraesCS5B01G264800 chr5D 92.969 256 18 0 2650 2905 459224877 459225132 1.470000e-99 374.0
6 TraesCS5B01G264800 chr5D 100.000 28 0 0 2455 2482 459224857 459224830 8.000000e-03 52.8
7 TraesCS5B01G264800 chr4D 95.037 403 17 3 2340 2741 25433235 25433635 7.890000e-177 630.0
8 TraesCS5B01G264800 chr7D 75.451 998 208 25 2305 3294 212809598 212808630 6.600000e-123 451.0
9 TraesCS5B01G264800 chr7B 91.016 256 23 0 2650 2905 130117186 130116931 3.200000e-91 346.0
10 TraesCS5B01G264800 chr7B 83.228 316 47 5 5 316 524776041 524776354 7.080000e-73 285.0
11 TraesCS5B01G264800 chr7B 95.238 84 2 2 2822 2905 647452105 647452024 9.760000e-27 132.0
12 TraesCS5B01G264800 chr6A 85.449 323 38 7 1 317 46121262 46121581 1.160000e-85 327.0
13 TraesCS5B01G264800 chr6A 85.449 323 38 7 1 317 46150268 46150587 1.160000e-85 327.0
14 TraesCS5B01G264800 chr6A 84.923 325 37 9 1 317 45983619 45983939 6.980000e-83 318.0
15 TraesCS5B01G264800 chr6B 86.557 305 29 9 22 317 78617044 78616743 4.170000e-85 326.0
16 TraesCS5B01G264800 chr7A 84.228 298 39 4 5 297 503529181 503528887 2.550000e-72 283.0
17 TraesCS5B01G264800 chr3D 81.739 230 29 8 18 243 567212446 567212666 3.440000e-41 180.0
18 TraesCS5B01G264800 chr4A 80.000 190 23 10 17 201 430430556 430430377 4.540000e-25 126.0
19 TraesCS5B01G264800 chrUn 98.361 61 1 0 3706 3766 16375979 16376039 1.640000e-19 108.0
20 TraesCS5B01G264800 chrUn 95.312 64 3 0 3706 3769 67440121 67440184 7.650000e-18 102.0
21 TraesCS5B01G264800 chr6D 96.875 64 2 0 3706 3769 379559341 379559278 1.640000e-19 108.0
22 TraesCS5B01G264800 chr2B 98.361 61 1 0 3706 3766 56928472 56928532 1.640000e-19 108.0
23 TraesCS5B01G264800 chr2B 98.361 61 1 0 3706 3766 787156089 787156149 1.640000e-19 108.0
24 TraesCS5B01G264800 chr2D 96.721 61 2 0 3706 3766 352792640 352792700 7.650000e-18 102.0
25 TraesCS5B01G264800 chr1A 96.721 61 2 0 3706 3766 380321257 380321317 7.650000e-18 102.0


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 TraesCS5B01G264800 chr5B 448659618 448663942 4324 True 7987.0 7987 100.0000 1 4325 1 chr5B.!!$R1 4324
1 TraesCS5B01G264800 chr5A 476894517 476899725 5208 True 3077.0 5762 89.5325 10 4325 2 chr5A.!!$R1 4315
2 TraesCS5B01G264800 chr5D 375800185 375804022 3837 True 2497.5 3838 90.4510 445 4297 2 chr5D.!!$R2 3852
3 TraesCS5B01G264800 chr7D 212808630 212809598 968 True 451.0 451 75.4510 2305 3294 1 chr7D.!!$R1 989

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
972 1895 0.320374 TGACCCGTCACTGTTCATCC 59.680 55.000 0.0 0.0 34.14 3.51 F
1266 2195 1.205655 GAGGACTACCCCGTGTTTACC 59.794 57.143 0.0 0.0 36.73 2.85 F
3025 4019 0.390340 GAAGATGAGCTGCGTGGTGA 60.390 55.000 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
1876 2867 0.108424 CAGGAGGAGAAGCCGTTGAG 60.108 60.0 0.00 0.0 43.43 3.02 R
3214 4208 0.107456 CTCAACGGATCATCCTGGGG 59.893 60.0 1.10 0.0 33.30 4.96 R
4148 5168 1.014044 GCTCCGCGATCTGTTCAACA 61.014 55.0 8.23 0.0 0.00 3.33 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
39 41 7.383572 CACATCCCTCTCTTATTTACGATTCAG 59.616 40.741 0.00 0.00 0.00 3.02
40 42 7.070074 ACATCCCTCTCTTATTTACGATTCAGT 59.930 37.037 0.00 0.00 0.00 3.41
42 44 6.605995 TCCCTCTCTTATTTACGATTCAGTCA 59.394 38.462 0.00 0.00 0.00 3.41
43 45 7.123697 TCCCTCTCTTATTTACGATTCAGTCAA 59.876 37.037 0.00 0.00 0.00 3.18
53 55 7.716768 TTACGATTCAGTCAACATTACAACA 57.283 32.000 0.00 0.00 0.00 3.33
54 56 6.801539 ACGATTCAGTCAACATTACAACAT 57.198 33.333 0.00 0.00 0.00 2.71
84 86 0.539438 AGGGATGAGCTCGCTAGGAG 60.539 60.000 9.64 4.39 44.74 3.69
96 98 2.151202 CGCTAGGAGGCTCAACAAAAA 58.849 47.619 17.69 0.00 0.00 1.94
97 99 2.160417 CGCTAGGAGGCTCAACAAAAAG 59.840 50.000 17.69 3.56 0.00 2.27
108 110 8.465273 AGGCTCAACAAAAAGAAACTATTACT 57.535 30.769 0.00 0.00 0.00 2.24
114 116 9.807386 CAACAAAAAGAAACTATTACTAGACGG 57.193 33.333 0.00 0.00 0.00 4.79
115 117 8.543862 ACAAAAAGAAACTATTACTAGACGGG 57.456 34.615 0.00 0.00 0.00 5.28
116 118 7.118825 ACAAAAAGAAACTATTACTAGACGGGC 59.881 37.037 0.00 0.00 0.00 6.13
117 119 4.933505 AGAAACTATTACTAGACGGGCC 57.066 45.455 0.00 0.00 0.00 5.80
118 120 3.640498 AGAAACTATTACTAGACGGGCCC 59.360 47.826 13.57 13.57 0.00 5.80
119 121 3.325359 AACTATTACTAGACGGGCCCT 57.675 47.619 22.43 6.87 0.00 5.19
120 122 3.325359 ACTATTACTAGACGGGCCCTT 57.675 47.619 22.43 11.59 0.00 3.95
122 124 4.405548 ACTATTACTAGACGGGCCCTTAG 58.594 47.826 22.43 19.83 0.00 2.18
123 125 1.406903 TTACTAGACGGGCCCTTAGC 58.593 55.000 22.43 6.05 42.60 3.09
158 160 1.745653 GGAGCAACACAATTAGCCTCC 59.254 52.381 0.00 0.00 0.00 4.30
169 171 1.040646 TTAGCCTCCCTGATAGTGCG 58.959 55.000 0.00 0.00 0.00 5.34
174 176 1.009829 CTCCCTGATAGTGCGCAAAC 58.990 55.000 14.00 0.00 0.00 2.93
184 186 2.268298 AGTGCGCAAACGAGGTATAAG 58.732 47.619 14.00 0.00 43.93 1.73
185 187 2.094390 AGTGCGCAAACGAGGTATAAGA 60.094 45.455 14.00 0.00 43.93 2.10
190 192 4.421948 CGCAAACGAGGTATAAGAGAAGT 58.578 43.478 0.00 0.00 43.93 3.01
195 197 5.599999 ACGAGGTATAAGAGAAGTTGCAT 57.400 39.130 0.00 0.00 0.00 3.96
197 199 4.210120 CGAGGTATAAGAGAAGTTGCATGC 59.790 45.833 11.82 11.82 0.00 4.06
214 216 4.093850 TGCATGCGATATGATAGCAATCAC 59.906 41.667 14.09 0.00 44.79 3.06
223 225 9.154847 CGATATGATAGCAATCACCAAAGATTA 57.845 33.333 0.00 0.00 44.79 1.75
230 232 4.816385 GCAATCACCAAAGATTAGATCCGA 59.184 41.667 0.00 0.00 36.13 4.55
233 235 5.614324 TCACCAAAGATTAGATCCGATGT 57.386 39.130 0.00 0.00 0.00 3.06
242 244 2.073252 AGATCCGATGTACCTGCAGA 57.927 50.000 17.39 0.00 0.00 4.26
261 263 4.305769 CAGATCGTCCTCCTTCATTCATC 58.694 47.826 0.00 0.00 0.00 2.92
267 269 4.363999 GTCCTCCTTCATTCATCGTACTG 58.636 47.826 0.00 0.00 0.00 2.74
275 277 6.986817 CCTTCATTCATCGTACTGATAACCTT 59.013 38.462 0.00 0.00 34.83 3.50
320 322 3.130340 AGTTTGTTGCAACCGATTGACTT 59.870 39.130 26.14 0.41 38.15 3.01
334 336 7.649973 ACCGATTGACTTAGTAGATGTGTATC 58.350 38.462 0.00 0.00 0.00 2.24
335 337 6.797513 CCGATTGACTTAGTAGATGTGTATCG 59.202 42.308 0.00 0.00 38.38 2.92
368 370 8.186821 CCCTATAAAACTGATTTGAGCTTTCAG 58.813 37.037 12.59 12.59 42.05 3.02
375 377 5.694910 ACTGATTTGAGCTTTCAGCAATTTG 59.305 36.000 13.58 0.00 45.56 2.32
403 1276 2.288825 TGTTTTTCAACGGTTTGGTGCA 60.289 40.909 0.00 0.00 35.40 4.57
404 1277 1.997669 TTTTCAACGGTTTGGTGCAC 58.002 45.000 8.80 8.80 33.06 4.57
405 1278 1.178276 TTTCAACGGTTTGGTGCACT 58.822 45.000 17.98 0.00 33.06 4.40
417 1290 2.528797 GTGCACTGGTACACCTTCG 58.471 57.895 10.32 0.00 36.82 3.79
421 1294 0.902531 CACTGGTACACCTTCGGGAT 59.097 55.000 0.00 0.00 38.77 3.85
423 1296 2.105766 ACTGGTACACCTTCGGGATAC 58.894 52.381 0.00 0.00 38.77 2.24
437 1315 5.717078 TCGGGATACAGTGTATTCCATAC 57.283 43.478 31.54 13.30 39.74 2.39
442 1320 3.179443 ACAGTGTATTCCATACGCCTG 57.821 47.619 0.00 7.50 45.05 4.85
443 1321 2.500098 ACAGTGTATTCCATACGCCTGT 59.500 45.455 0.00 10.81 45.05 4.00
451 1333 1.148157 CCATACGCCTGTTCTCAGCG 61.148 60.000 1.59 1.59 42.31 5.18
538 1423 7.039082 CCTTAATTCTTGGTTTGGATTGGAAGA 60.039 37.037 0.00 0.00 0.00 2.87
645 1542 3.517602 ACAAACGAAAAGCCCAAAAGAC 58.482 40.909 0.00 0.00 0.00 3.01
666 1567 2.094675 GCTGCCAGCCTCTTCAAAATA 58.905 47.619 5.06 0.00 34.48 1.40
685 1587 2.285743 GCAGTTCCCTCCCTCCCT 60.286 66.667 0.00 0.00 0.00 4.20
694 1599 4.761304 TCCCTCCCTCCCTCCCCT 62.761 72.222 0.00 0.00 0.00 4.79
730 1641 2.262915 CTCCACCACCTCACTCGC 59.737 66.667 0.00 0.00 0.00 5.03
731 1642 2.203640 TCCACCACCTCACTCGCT 60.204 61.111 0.00 0.00 0.00 4.93
741 1652 4.467062 CACTCGCTCTCGCTCGCA 62.467 66.667 0.00 0.00 35.26 5.10
762 1673 4.279043 GCCGCACCAACCACAACC 62.279 66.667 0.00 0.00 0.00 3.77
763 1674 2.830827 CCGCACCAACCACAACCA 60.831 61.111 0.00 0.00 0.00 3.67
764 1675 2.721231 CGCACCAACCACAACCAG 59.279 61.111 0.00 0.00 0.00 4.00
765 1676 2.118404 CGCACCAACCACAACCAGT 61.118 57.895 0.00 0.00 0.00 4.00
766 1677 1.733526 GCACCAACCACAACCAGTC 59.266 57.895 0.00 0.00 0.00 3.51
767 1678 1.734388 GCACCAACCACAACCAGTCC 61.734 60.000 0.00 0.00 0.00 3.85
768 1679 1.106944 CACCAACCACAACCAGTCCC 61.107 60.000 0.00 0.00 0.00 4.46
769 1680 1.286305 ACCAACCACAACCAGTCCCT 61.286 55.000 0.00 0.00 0.00 4.20
819 1730 1.533711 CCCTCCGCTCCATTCCATT 59.466 57.895 0.00 0.00 0.00 3.16
820 1731 0.536006 CCCTCCGCTCCATTCCATTC 60.536 60.000 0.00 0.00 0.00 2.67
822 1733 0.471617 CTCCGCTCCATTCCATTCCT 59.528 55.000 0.00 0.00 0.00 3.36
823 1734 0.918983 TCCGCTCCATTCCATTCCTT 59.081 50.000 0.00 0.00 0.00 3.36
972 1895 0.320374 TGACCCGTCACTGTTCATCC 59.680 55.000 0.00 0.00 34.14 3.51
1266 2195 1.205655 GAGGACTACCCCGTGTTTACC 59.794 57.143 0.00 0.00 36.73 2.85
1416 2349 1.525995 CCCACTGTTCTTGCCGTGT 60.526 57.895 0.00 0.00 0.00 4.49
1417 2350 1.648720 CCACTGTTCTTGCCGTGTG 59.351 57.895 0.00 0.00 0.00 3.82
1519 2482 7.144722 TGGTGCAGTAATGTTAAATTCAGAG 57.855 36.000 0.00 0.00 0.00 3.35
1520 2483 6.714810 TGGTGCAGTAATGTTAAATTCAGAGT 59.285 34.615 0.00 0.00 0.00 3.24
1521 2484 7.094805 TGGTGCAGTAATGTTAAATTCAGAGTC 60.095 37.037 0.00 0.00 0.00 3.36
1522 2485 7.119846 GGTGCAGTAATGTTAAATTCAGAGTCT 59.880 37.037 0.00 0.00 0.00 3.24
1523 2486 7.959651 GTGCAGTAATGTTAAATTCAGAGTCTG 59.040 37.037 14.36 14.36 0.00 3.51
1524 2487 7.877612 TGCAGTAATGTTAAATTCAGAGTCTGA 59.122 33.333 19.10 19.10 38.87 3.27
1667 2658 1.872313 GACGGACCTGTACGATCCTAG 59.128 57.143 9.23 0.00 39.85 3.02
1669 2660 2.295885 CGGACCTGTACGATCCTAGTT 58.704 52.381 0.00 0.00 39.85 2.24
1676 2667 3.021695 TGTACGATCCTAGTTCACCCTG 58.978 50.000 0.00 0.00 0.00 4.45
1698 2689 5.072055 TGTGAGAAGGATTGCATTTCTGAA 58.928 37.500 7.68 0.00 31.67 3.02
1734 2725 2.370281 ACATGGTGCAGACTTACGAG 57.630 50.000 0.00 0.00 0.00 4.18
1807 2798 3.379445 GCCGGTCCGAGAACTGGA 61.379 66.667 14.39 0.00 46.94 3.86
2061 3052 2.435938 TTCAAGATGCCGCCGTCC 60.436 61.111 0.00 0.00 0.00 4.79
2064 3055 3.706373 AAGATGCCGCCGTCCTGT 61.706 61.111 0.00 0.00 0.00 4.00
2217 3208 1.376466 GGCAAAGCAGAGAGGGTCA 59.624 57.895 0.00 0.00 0.00 4.02
2239 3230 2.699321 CAGATCCTCTCATGGCTCTTCA 59.301 50.000 0.00 0.00 30.96 3.02
2340 3331 3.334054 AAGGAGTGGGGGCTGCTC 61.334 66.667 0.00 0.00 36.11 4.26
2352 3343 2.101965 CTGCTCTCGCTGGACTCG 59.898 66.667 0.00 0.00 36.97 4.18
2370 3361 2.498726 CTCAGGAAGGAGCTCGCC 59.501 66.667 7.83 9.14 0.00 5.54
2592 3583 2.187946 CGAGAGCTGCCCGGAAAT 59.812 61.111 0.73 0.00 0.00 2.17
3025 4019 0.390340 GAAGATGAGCTGCGTGGTGA 60.390 55.000 0.00 0.00 0.00 4.02
3048 4042 4.007644 CTGAGCTGGTCGTGGCCA 62.008 66.667 0.00 0.00 36.97 5.36
3205 4199 2.284625 AGGACATCCTGCCGGACA 60.285 61.111 5.05 1.09 46.55 4.02
3225 4222 3.882326 CGGCAGCCCCAGGATGAT 61.882 66.667 5.63 0.00 42.34 2.45
3306 4303 2.023673 TGCAAGGTCCTCACAACAAAG 58.976 47.619 0.00 0.00 0.00 2.77
3307 4304 1.269257 GCAAGGTCCTCACAACAAAGC 60.269 52.381 0.00 0.00 0.00 3.51
3308 4305 2.023673 CAAGGTCCTCACAACAAAGCA 58.976 47.619 0.00 0.00 0.00 3.91
3309 4306 1.972872 AGGTCCTCACAACAAAGCAG 58.027 50.000 0.00 0.00 0.00 4.24
3336 4333 4.993029 AGACCAGTAGCATAACTGTCTC 57.007 45.455 11.46 6.81 44.45 3.36
3409 4406 2.158813 AGTGTGGTGTGAGGGTAACTTG 60.159 50.000 0.00 0.00 0.00 3.16
3471 4468 2.302733 TCAGAGTAGGCAATTGAGCACA 59.697 45.455 10.34 0.00 35.83 4.57
3521 4518 4.248174 TCCTCCATTGTTTATGCCATGA 57.752 40.909 0.00 0.00 32.60 3.07
3569 4574 3.676093 ACATGATGCTCAGATGCTATGG 58.324 45.455 0.00 0.00 0.00 2.74
3572 4577 4.004196 TGATGCTCAGATGCTATGGAAG 57.996 45.455 0.00 0.00 0.00 3.46
3631 4647 6.431543 TGTTCTGAACACTACTTCTCTAGGAG 59.568 42.308 18.69 0.00 41.03 3.69
3637 4653 6.827586 ACACTACTTCTCTAGGAGAAACTG 57.172 41.667 10.55 3.37 46.18 3.16
3640 4656 6.882140 CACTACTTCTCTAGGAGAAACTGAGA 59.118 42.308 10.55 0.00 46.18 3.27
3644 4660 4.020543 TCTCTAGGAGAAACTGAGAAGCC 58.979 47.826 0.00 0.00 35.59 4.35
3645 4661 4.023291 CTCTAGGAGAAACTGAGAAGCCT 58.977 47.826 0.00 0.00 0.00 4.58
3685 4701 6.175471 AGAAGATGAAGACATTACATGTGCA 58.825 36.000 9.11 0.00 45.03 4.57
3752 4772 9.195411 TGATGCTTCATTTTGAGTCAATAAAAC 57.805 29.630 6.36 0.00 0.00 2.43
3876 4896 3.107402 ACTCTATGTTCAGGGCTCTCA 57.893 47.619 0.00 0.00 0.00 3.27
3987 5007 1.748122 CTCCCACATGAGCAGGTGC 60.748 63.158 9.55 0.00 41.31 5.01
4005 5025 3.336568 AGCTGGATGGGCTGCAGT 61.337 61.111 16.64 0.00 44.65 4.40
4062 5082 2.654912 GGTGTCGAAGCAACGGACG 61.655 63.158 0.00 0.00 0.00 4.79
4131 5151 5.008415 CACCCTTGATATGATCAGCAGTTTC 59.992 44.000 0.09 0.00 40.94 2.78
4262 5282 5.232838 GGATGAAACAAAACAGAAGTTGCAG 59.767 40.000 0.00 0.00 38.17 4.41
4272 5292 3.587506 ACAGAAGTTGCAGGGTAGGTTAT 59.412 43.478 0.00 0.00 0.00 1.89
4305 5325 3.230976 TGAAAGCTGGAGTAGTGACTGA 58.769 45.455 0.00 0.00 35.45 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.970859 AGAGAGGGATGTGATATAAAAACAAG 57.029 34.615 0.00 0.00 0.00 3.16
8 9 9.749340 TCGTAAATAAGAGAGGGATGTGATATA 57.251 33.333 0.00 0.00 0.00 0.86
15 16 7.437748 ACTGAATCGTAAATAAGAGAGGGATG 58.562 38.462 0.00 0.00 0.00 3.51
27 28 8.779303 TGTTGTAATGTTGACTGAATCGTAAAT 58.221 29.630 0.00 0.00 0.00 1.40
51 53 7.327064 AGCTCATCCCTCTCATATTAAATGT 57.673 36.000 0.00 0.00 0.00 2.71
53 55 6.638610 CGAGCTCATCCCTCTCATATTAAAT 58.361 40.000 15.40 0.00 0.00 1.40
54 56 5.567623 GCGAGCTCATCCCTCTCATATTAAA 60.568 44.000 15.40 0.00 0.00 1.52
61 63 0.183731 TAGCGAGCTCATCCCTCTCA 59.816 55.000 15.40 0.00 0.00 3.27
84 86 9.827411 CTAGTAATAGTTTCTTTTTGTTGAGCC 57.173 33.333 0.00 0.00 0.00 4.70
96 98 3.640498 GGGCCCGTCTAGTAATAGTTTCT 59.360 47.826 5.69 0.00 0.00 2.52
97 99 3.640498 AGGGCCCGTCTAGTAATAGTTTC 59.360 47.826 18.44 0.00 0.00 2.78
122 124 4.654091 TGCTCCTAAATTAGCAATTGGC 57.346 40.909 7.72 0.00 45.36 4.52
136 138 3.370527 GGAGGCTAATTGTGTTGCTCCTA 60.371 47.826 0.00 0.00 0.00 2.94
138 140 1.745653 GGAGGCTAATTGTGTTGCTCC 59.254 52.381 0.00 0.00 0.00 4.70
147 149 3.406764 GCACTATCAGGGAGGCTAATTG 58.593 50.000 0.00 0.00 0.00 2.32
150 152 1.040646 CGCACTATCAGGGAGGCTAA 58.959 55.000 0.00 0.00 0.00 3.09
158 160 0.647410 CTCGTTTGCGCACTATCAGG 59.353 55.000 11.12 0.00 38.14 3.86
169 171 5.446073 GCAACTTCTCTTATACCTCGTTTGC 60.446 44.000 0.00 0.00 0.00 3.68
174 176 4.210120 GCATGCAACTTCTCTTATACCTCG 59.790 45.833 14.21 0.00 0.00 4.63
184 186 5.445673 GCTATCATATCGCATGCAACTTCTC 60.446 44.000 19.57 0.00 0.00 2.87
185 187 4.391216 GCTATCATATCGCATGCAACTTCT 59.609 41.667 19.57 0.00 0.00 2.85
190 192 4.696402 TGATTGCTATCATATCGCATGCAA 59.304 37.500 19.57 0.00 41.94 4.08
195 197 4.270245 TGGTGATTGCTATCATATCGCA 57.730 40.909 13.92 0.66 42.49 5.10
197 199 7.606858 ATCTTTGGTGATTGCTATCATATCG 57.393 36.000 13.92 3.32 42.49 2.92
214 216 5.928839 CAGGTACATCGGATCTAATCTTTGG 59.071 44.000 0.00 0.00 0.00 3.28
223 225 2.073252 TCTGCAGGTACATCGGATCT 57.927 50.000 15.13 0.00 0.00 2.75
224 226 2.669670 CGATCTGCAGGTACATCGGATC 60.670 54.545 21.59 10.88 39.56 3.36
226 228 0.668535 CGATCTGCAGGTACATCGGA 59.331 55.000 21.59 0.00 35.54 4.55
230 232 1.683917 GAGGACGATCTGCAGGTACAT 59.316 52.381 15.13 0.00 0.00 2.29
233 235 0.259065 AGGAGGACGATCTGCAGGTA 59.741 55.000 15.13 0.00 0.00 3.08
242 244 2.695666 ACGATGAATGAAGGAGGACGAT 59.304 45.455 0.00 0.00 0.00 3.73
291 293 8.414814 TCAATCGGTTGCAACAAACTAATTGTC 61.415 37.037 29.55 7.83 41.99 3.18
297 299 3.880490 AGTCAATCGGTTGCAACAAACTA 59.120 39.130 29.55 10.89 35.26 2.24
320 322 4.755629 GGCAGAGACGATACACATCTACTA 59.244 45.833 0.00 0.00 0.00 1.82
334 336 4.386867 TCAGTTTTATAGGGCAGAGACG 57.613 45.455 0.00 0.00 0.00 4.18
335 337 6.823689 TCAAATCAGTTTTATAGGGCAGAGAC 59.176 38.462 0.00 0.00 0.00 3.36
368 370 7.163357 CCGTTGAAAAACATGTTTACAAATTGC 59.837 33.333 28.63 20.63 33.98 3.56
375 377 6.091034 ACCAAACCGTTGAAAAACATGTTTAC 59.909 34.615 23.53 19.35 36.83 2.01
437 1315 1.493311 GAAACGCTGAGAACAGGCG 59.507 57.895 5.03 5.03 43.62 5.52
442 1320 0.238553 GCTTGGGAAACGCTGAGAAC 59.761 55.000 0.00 0.00 0.00 3.01
443 1321 0.889186 GGCTTGGGAAACGCTGAGAA 60.889 55.000 0.00 0.00 0.00 2.87
451 1333 3.680786 GGCACGGGCTTGGGAAAC 61.681 66.667 10.74 0.00 40.87 2.78
538 1423 1.888436 TTGGAGCAGCCGATTCGTCT 61.888 55.000 5.20 0.00 40.66 4.18
628 1525 0.030235 GCGTCTTTTGGGCTTTTCGT 59.970 50.000 0.00 0.00 0.00 3.85
645 1542 1.518056 TTTTGAAGAGGCTGGCAGCG 61.518 55.000 31.22 0.63 43.62 5.18
685 1587 3.707189 GAGGGGGAAGGGGAGGGA 61.707 72.222 0.00 0.00 0.00 4.20
694 1599 4.257810 TGGACGTGGGAGGGGGAA 62.258 66.667 0.00 0.00 0.00 3.97
758 1669 1.190643 GGAGAGAGAGGGACTGGTTG 58.809 60.000 0.00 0.00 41.55 3.77
759 1670 0.041982 GGGAGAGAGAGGGACTGGTT 59.958 60.000 0.00 0.00 41.55 3.67
760 1671 1.700985 GGGAGAGAGAGGGACTGGT 59.299 63.158 0.00 0.00 41.55 4.00
762 1673 0.686112 GTGGGGAGAGAGAGGGACTG 60.686 65.000 0.00 0.00 41.55 3.51
764 1675 1.755008 CGTGGGGAGAGAGAGGGAC 60.755 68.421 0.00 0.00 0.00 4.46
765 1676 1.506907 TTCGTGGGGAGAGAGAGGGA 61.507 60.000 0.00 0.00 0.00 4.20
766 1677 0.397816 ATTCGTGGGGAGAGAGAGGG 60.398 60.000 0.00 0.00 0.00 4.30
767 1678 1.410882 GAATTCGTGGGGAGAGAGAGG 59.589 57.143 0.00 0.00 0.00 3.69
768 1679 1.410882 GGAATTCGTGGGGAGAGAGAG 59.589 57.143 0.00 0.00 0.00 3.20
769 1680 1.273041 TGGAATTCGTGGGGAGAGAGA 60.273 52.381 0.00 0.00 0.00 3.10
819 1730 1.392534 GTGGGGAGGAGGAGAAGGA 59.607 63.158 0.00 0.00 0.00 3.36
820 1731 1.690985 GGTGGGGAGGAGGAGAAGG 60.691 68.421 0.00 0.00 0.00 3.46
822 1733 2.454941 GGGTGGGGAGGAGGAGAA 59.545 66.667 0.00 0.00 0.00 2.87
823 1734 4.075793 CGGGTGGGGAGGAGGAGA 62.076 72.222 0.00 0.00 0.00 3.71
1285 2218 1.346395 ACACGGTGACATGTGGTACAT 59.654 47.619 16.29 0.00 44.52 2.29
1310 2243 1.070758 AGAGAAGCCAAGAACGCAGAA 59.929 47.619 0.00 0.00 0.00 3.02
1312 2245 1.462670 GAAGAGAAGCCAAGAACGCAG 59.537 52.381 0.00 0.00 0.00 5.18
1316 2249 1.443802 CGGGAAGAGAAGCCAAGAAC 58.556 55.000 0.00 0.00 0.00 3.01
1394 2327 2.270986 GGCAAGAACAGTGGGGCAG 61.271 63.158 0.00 0.00 0.00 4.85
1395 2328 2.203480 GGCAAGAACAGTGGGGCA 60.203 61.111 0.00 0.00 0.00 5.36
1477 2414 1.726791 CCAACTGTTGCTAGCGTACTG 59.273 52.381 14.94 18.69 0.00 2.74
1478 2415 1.343465 ACCAACTGTTGCTAGCGTACT 59.657 47.619 14.94 0.00 0.00 2.73
1519 2482 2.615869 GCAACCATGAGAGACTCAGAC 58.384 52.381 5.02 0.00 44.08 3.51
1520 2483 1.552337 GGCAACCATGAGAGACTCAGA 59.448 52.381 5.02 0.00 44.08 3.27
1521 2484 1.277273 TGGCAACCATGAGAGACTCAG 59.723 52.381 5.02 0.00 44.08 3.35
1522 2485 1.351076 TGGCAACCATGAGAGACTCA 58.649 50.000 5.02 3.95 44.99 3.41
1523 2486 2.559440 GATGGCAACCATGAGAGACTC 58.441 52.381 3.30 0.00 45.26 3.36
1524 2487 1.134580 CGATGGCAACCATGAGAGACT 60.135 52.381 3.30 0.00 45.26 3.24
1554 2517 4.251760 GCGATCATAGCCTCGTGG 57.748 61.111 0.00 0.00 37.23 4.94
1663 2654 2.234908 CCTTCTCACAGGGTGAACTAGG 59.765 54.545 0.33 4.17 42.26 3.02
1667 2658 3.077359 CAATCCTTCTCACAGGGTGAAC 58.923 50.000 0.33 0.00 42.26 3.18
1669 2660 1.003580 GCAATCCTTCTCACAGGGTGA 59.996 52.381 0.00 0.00 40.50 4.02
1676 2667 5.633830 TTCAGAAATGCAATCCTTCTCAC 57.366 39.130 0.00 0.00 0.00 3.51
1698 2689 3.305813 CCATGTTCAGTTGAGCAAGCAAT 60.306 43.478 2.80 0.00 38.71 3.56
1807 2798 2.045926 GTCCAAGGTGATGCCGCT 60.046 61.111 0.00 0.00 43.70 5.52
1876 2867 0.108424 CAGGAGGAGAAGCCGTTGAG 60.108 60.000 0.00 0.00 43.43 3.02
1956 2947 1.526917 GGCCGGATGGATCCTGTTG 60.527 63.158 14.23 0.40 44.93 3.33
1960 2951 0.695803 AGAAAGGCCGGATGGATCCT 60.696 55.000 14.23 0.00 44.93 3.24
2239 3230 0.606673 GCCTTCTTCTTCGCCTTGGT 60.607 55.000 0.00 0.00 0.00 3.67
2340 3331 2.101965 CTGAGCGAGTCCAGCGAG 59.898 66.667 0.00 0.00 40.04 5.03
2409 3400 2.413765 GACGACCTCATCTCGGCC 59.586 66.667 0.00 0.00 32.64 6.13
2586 3577 3.140141 ACCGGCATGCCATTTCCG 61.140 61.111 34.93 19.77 41.41 4.30
2589 3580 2.713967 GCTCACCGGCATGCCATTT 61.714 57.895 34.93 16.37 35.37 2.32
3066 4060 2.383527 GGCGACGAAGAAGCACTGG 61.384 63.158 0.00 0.00 35.55 4.00
3214 4208 0.107456 CTCAACGGATCATCCTGGGG 59.893 60.000 1.10 0.00 33.30 4.96
3223 4220 2.168521 TGATCTTCACCCTCAACGGATC 59.831 50.000 0.00 0.00 33.16 3.36
3224 4221 2.187958 TGATCTTCACCCTCAACGGAT 58.812 47.619 0.00 0.00 33.16 4.18
3225 4222 1.639722 TGATCTTCACCCTCAACGGA 58.360 50.000 0.00 0.00 33.16 4.69
3306 4303 0.529555 GCTACTGGTCTAGCTGCTGC 60.530 60.000 13.43 7.62 36.88 5.25
3307 4304 0.820226 TGCTACTGGTCTAGCTGCTG 59.180 55.000 13.43 2.51 40.02 4.41
3308 4305 1.786937 ATGCTACTGGTCTAGCTGCT 58.213 50.000 7.57 7.57 40.02 4.24
3309 4306 3.068873 AGTTATGCTACTGGTCTAGCTGC 59.931 47.826 0.00 0.00 40.02 5.25
3336 4333 9.897744 AACAAAGTTACACATAATGAACATGAG 57.102 29.630 0.00 0.00 0.00 2.90
3569 4574 4.141620 TGAAGTAATCAGGGGAGATGCTTC 60.142 45.833 0.00 0.00 39.12 3.86
3572 4577 3.845781 TGAAGTAATCAGGGGAGATGC 57.154 47.619 0.00 0.00 33.04 3.91
3603 4613 8.740906 CCTAGAGAAGTAGTGTTCAGAACAATA 58.259 37.037 17.83 17.66 44.16 1.90
3604 4614 7.451877 TCCTAGAGAAGTAGTGTTCAGAACAAT 59.548 37.037 19.51 19.51 44.16 2.71
3605 4615 6.776116 TCCTAGAGAAGTAGTGTTCAGAACAA 59.224 38.462 17.83 0.19 44.16 2.83
3606 4616 6.304624 TCCTAGAGAAGTAGTGTTCAGAACA 58.695 40.000 12.24 12.24 39.52 3.18
3607 4617 6.655848 TCTCCTAGAGAAGTAGTGTTCAGAAC 59.344 42.308 6.32 6.32 35.59 3.01
3631 4647 1.902938 AGGCAAGGCTTCTCAGTTTC 58.097 50.000 0.00 0.00 0.00 2.78
3637 4653 2.499693 AGTTCTCTAGGCAAGGCTTCTC 59.500 50.000 0.00 0.00 0.00 2.87
3640 4656 3.704061 CTCTAGTTCTCTAGGCAAGGCTT 59.296 47.826 0.17 0.00 42.66 4.35
3644 4660 6.545666 TCATCTTCTCTAGTTCTCTAGGCAAG 59.454 42.308 3.02 5.56 42.66 4.01
3645 4661 6.427441 TCATCTTCTCTAGTTCTCTAGGCAA 58.573 40.000 3.02 0.00 42.66 4.52
3752 4772 1.141053 CCTCTTCCGATAAAGGGTGGG 59.859 57.143 0.00 0.00 0.00 4.61
3876 4896 3.392616 CTCAGGTACCCCTAAGCATCATT 59.607 47.826 8.74 0.00 39.89 2.57
3906 4926 3.645268 AATGCCCTTCCCGCTGTCC 62.645 63.158 0.00 0.00 0.00 4.02
4062 5082 1.522580 GATCTCCAGTTCAGGCGCC 60.523 63.158 21.89 21.89 0.00 6.53
4148 5168 1.014044 GCTCCGCGATCTGTTCAACA 61.014 55.000 8.23 0.00 0.00 3.33
4262 5282 7.074653 TCAGAAATGTCCATATAACCTACCC 57.925 40.000 0.00 0.00 0.00 3.69
4272 5292 5.178096 TCCAGCTTTCAGAAATGTCCATA 57.822 39.130 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.