Multiple sequence alignment - TraesCS6D01G108700

Loading Multiple Alignment...

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 TraesCS6D01G108700 chr6D 100.000 5005 0 0 1 5005 73494643 73499647 0.000000e+00 9243
1 TraesCS6D01G108700 chr6D 93.033 244 13 2 3389 3628 273093306 273093549 2.220000e-93 353
2 TraesCS6D01G108700 chr6D 86.905 168 18 4 2593 2758 305743073 305742908 8.560000e-43 185
3 TraesCS6D01G108700 chr6B 93.004 4460 168 62 605 5005 147677290 147681664 0.000000e+00 6375
4 TraesCS6D01G108700 chr6A 95.013 2306 88 10 1 2299 89891067 89893352 0.000000e+00 3596
5 TraesCS6D01G108700 chr6A 93.067 1875 69 27 3162 5005 89894348 89896192 0.000000e+00 2686
6 TraesCS6D01G108700 chr6A 96.420 866 29 2 2297 3161 89893322 89894186 0.000000e+00 1426
7 TraesCS6D01G108700 chr6A 86.316 95 7 6 605 698 617826462 617826551 1.150000e-16 99
8 TraesCS6D01G108700 chr4D 95.279 233 11 0 3387 3619 275616492 275616724 2.200000e-98 370
9 TraesCS6D01G108700 chr3A 94.583 240 10 2 3390 3626 76648141 76648380 7.920000e-98 368
10 TraesCS6D01G108700 chr3A 87.574 169 16 5 2593 2759 54660383 54660218 1.840000e-44 191
11 TraesCS6D01G108700 chr3B 94.215 242 11 1 3390 3628 480376942 480377183 2.850000e-97 366
12 TraesCS6D01G108700 chr3D 93.802 242 12 1 3390 3628 369414163 369414404 1.320000e-95 361
13 TraesCS6D01G108700 chr1D 92.063 252 17 1 3386 3634 486154363 486154614 7.970000e-93 351
14 TraesCS6D01G108700 chr7D 92.653 245 15 2 3387 3628 499792583 499792827 2.870000e-92 350
15 TraesCS6D01G108700 chr7D 82.759 116 16 4 605 719 184826795 184826683 3.190000e-17 100
16 TraesCS6D01G108700 chr5A 89.024 164 16 2 2593 2755 382336466 382336304 8.500000e-48 202
17 TraesCS6D01G108700 chr5D 88.344 163 17 2 2593 2754 443898154 443898315 1.420000e-45 195
18 TraesCS6D01G108700 chr2A 88.485 165 14 5 2593 2754 218122410 218122248 1.420000e-45 195
19 TraesCS6D01G108700 chr2D 87.654 162 19 1 2593 2754 22200812 22200972 2.380000e-43 187
20 TraesCS6D01G108700 chr7A 87.059 170 14 8 2593 2758 539543670 539543835 8.560000e-43 185


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 TraesCS6D01G108700 chr6D 73494643 73499647 5004 False 9243.000000 9243 100.000000 1 5005 1 chr6D.!!$F1 5004
1 TraesCS6D01G108700 chr6B 147677290 147681664 4374 False 6375.000000 6375 93.004000 605 5005 1 chr6B.!!$F1 4400
2 TraesCS6D01G108700 chr6A 89891067 89896192 5125 False 2569.333333 3596 94.833333 1 5005 3 chr6A.!!$F2 5004

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
181 182 0.036732 ACCTGGACATGTCGTGCAAT 59.963 50.0 19.33 0.26 46.3 3.56 F
344 345 0.249489 GTGTGTGAAGCCGTGTCTCT 60.249 55.0 0.00 0.00 0.0 3.10 F
592 593 0.390472 CGGAAGCTCAGAGGTGGAAC 60.390 60.0 1.99 0.00 0.0 3.62 F
842 855 0.473755 TCACCAGAAAAGGAGCAGCA 59.526 50.0 0.00 0.00 0.0 4.41 F
2440 2459 0.517316 GTTACCAAGGCTTGCACTCG 59.483 55.0 21.77 10.09 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1836 0.322975 ACCAAGCTAGCACTGACCTG 59.677 55.000 18.83 3.7 0.00 4.00 R
2278 2297 6.556495 AGAGCCAAGAATATCCAGATAGTGAA 59.444 38.462 0.00 0.0 0.00 3.18 R
2573 2592 5.163723 GCACATTGTATTCTGAAGCAAGCTA 60.164 40.000 13.10 0.0 0.00 3.32 R
2619 2638 5.582269 TCCTTTTCTATGCTTGATTGAGTCG 59.418 40.000 0.00 0.0 0.00 4.18 R
4015 4205 1.086634 GCGTCCTCTGAAGCATCCAC 61.087 60.000 0.00 0.0 44.24 4.02 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
32 33 0.830444 ACGGGACAAGGTCAGTGCTA 60.830 55.000 0.00 0.00 33.68 3.49
111 112 0.976641 TGACTTGGCTAGGTCACTGG 59.023 55.000 11.08 0.00 37.52 4.00
148 149 1.600663 GCATGGTCCTAGATGACGACG 60.601 57.143 0.00 0.00 36.07 5.12
164 165 0.247616 GACGAGCTCGACGTTAGACC 60.248 60.000 40.58 14.01 43.97 3.85
170 171 1.162698 CTCGACGTTAGACCTGGACA 58.837 55.000 0.00 0.00 0.00 4.02
181 182 0.036732 ACCTGGACATGTCGTGCAAT 59.963 50.000 19.33 0.26 46.30 3.56
202 203 6.592607 GCAATGACATGGATGTTTTTCTTCAT 59.407 34.615 0.00 0.00 41.95 2.57
237 238 3.951680 GACTCTTCAAGTTTGGTTTGGGA 59.048 43.478 0.00 0.00 38.74 4.37
242 243 2.817258 TCAAGTTTGGTTTGGGATAGCG 59.183 45.455 0.00 0.00 0.00 4.26
244 245 3.366052 AGTTTGGTTTGGGATAGCGAT 57.634 42.857 0.00 0.00 0.00 4.58
260 261 1.209128 CGATGCAACGACACTATCCC 58.791 55.000 11.36 0.00 35.09 3.85
270 271 5.596836 ACGACACTATCCCCGTATAAAAA 57.403 39.130 0.00 0.00 33.13 1.94
319 320 1.191647 GTTGGTGTGTTCGTCATCGAC 59.808 52.381 0.00 0.00 46.03 4.20
332 333 2.204461 ATCGACGGTGGGTGTGTGA 61.204 57.895 0.00 0.00 0.00 3.58
344 345 0.249489 GTGTGTGAAGCCGTGTCTCT 60.249 55.000 0.00 0.00 0.00 3.10
385 386 4.503643 CCGGTTGGTTTAGGTTTCTAGTGA 60.504 45.833 0.00 0.00 0.00 3.41
388 389 6.206048 CGGTTGGTTTAGGTTTCTAGTGAATT 59.794 38.462 0.00 0.00 31.56 2.17
403 404 4.369182 AGTGAATTCGTATGGATTCGACC 58.631 43.478 10.73 2.70 35.82 4.79
420 421 5.852282 TCGACCTACATTCATGATCTTCA 57.148 39.130 0.00 0.00 0.00 3.02
513 514 2.164624 ACTTCTCCTAGTGTGCATCGAC 59.835 50.000 0.00 0.00 0.00 4.20
537 538 4.952460 ACTTTTCAGCCGTTACTTCTACA 58.048 39.130 0.00 0.00 0.00 2.74
541 542 4.595762 TCAGCCGTTACTTCTACAAGTT 57.404 40.909 0.00 0.00 40.16 2.66
561 562 7.885922 ACAAGTTCTTGGGGTTTAAAATGTTTT 59.114 29.630 15.51 0.00 0.00 2.43
566 567 5.203060 TGGGGTTTAAAATGTTTTCTCCG 57.797 39.130 0.00 0.00 0.00 4.63
572 573 7.364970 GGTTTAAAATGTTTTCTCCGCTAAGA 58.635 34.615 0.00 0.00 0.00 2.10
584 585 0.452184 CGCTAAGACGGAAGCTCAGA 59.548 55.000 0.00 0.00 36.56 3.27
592 593 0.390472 CGGAAGCTCAGAGGTGGAAC 60.390 60.000 1.99 0.00 0.00 3.62
711 713 9.618890 CCCATGATACTTAATATATGACCTTGG 57.381 37.037 0.00 0.00 0.00 3.61
752 756 2.582052 CAGAACTTGGCCACCAGTAAA 58.418 47.619 3.88 0.00 33.81 2.01
753 757 3.157087 CAGAACTTGGCCACCAGTAAAT 58.843 45.455 3.88 0.00 33.81 1.40
754 758 3.191371 CAGAACTTGGCCACCAGTAAATC 59.809 47.826 3.88 1.98 33.81 2.17
825 838 7.682741 GCAGATAAAGCTATTCCAAAAGCATCA 60.683 37.037 0.00 0.00 41.32 3.07
826 839 7.646922 CAGATAAAGCTATTCCAAAAGCATCAC 59.353 37.037 0.00 0.00 41.32 3.06
842 855 0.473755 TCACCAGAAAAGGAGCAGCA 59.526 50.000 0.00 0.00 0.00 4.41
1479 1494 0.807496 GCAAATTTCGCTCTCCTGCT 59.193 50.000 5.65 0.00 0.00 4.24
1648 1663 2.102252 CCTCTCTTGGTGAGCTGTATCC 59.898 54.545 0.00 0.00 42.38 2.59
1818 1836 3.211045 TGTTAGGAAGGAAGTTGCACAC 58.789 45.455 0.00 0.00 0.00 3.82
1965 1983 1.856265 AAGCAAAGGCCGAAGAAGCG 61.856 55.000 0.00 0.00 42.56 4.68
2019 2037 2.746697 AGGTCGACCTCTTTCTGCA 58.253 52.632 31.69 0.00 44.77 4.41
2163 2181 7.444299 TGTAAATCAGTACCGAAGTTAGGTTT 58.556 34.615 13.25 3.18 42.81 3.27
2247 2266 3.386726 TGGTTTAGTGTCTAGTGCAGTGT 59.613 43.478 3.69 0.00 0.00 3.55
2267 2286 1.419762 TGTTAGTTGCCTGGCTTCTCA 59.580 47.619 21.03 9.91 0.00 3.27
2278 2297 3.434739 CCTGGCTTCTCATTGGCTCTATT 60.435 47.826 0.00 0.00 0.00 1.73
2282 2301 4.036144 GGCTTCTCATTGGCTCTATTTCAC 59.964 45.833 0.00 0.00 0.00 3.18
2283 2302 4.880696 GCTTCTCATTGGCTCTATTTCACT 59.119 41.667 0.00 0.00 0.00 3.41
2284 2303 6.051717 GCTTCTCATTGGCTCTATTTCACTA 58.948 40.000 0.00 0.00 0.00 2.74
2285 2304 6.709846 GCTTCTCATTGGCTCTATTTCACTAT 59.290 38.462 0.00 0.00 0.00 2.12
2286 2305 7.095271 GCTTCTCATTGGCTCTATTTCACTATC 60.095 40.741 0.00 0.00 0.00 2.08
2287 2306 7.609097 TCTCATTGGCTCTATTTCACTATCT 57.391 36.000 0.00 0.00 0.00 1.98
2288 2307 7.440198 TCTCATTGGCTCTATTTCACTATCTG 58.560 38.462 0.00 0.00 0.00 2.90
2289 2308 6.528321 TCATTGGCTCTATTTCACTATCTGG 58.472 40.000 0.00 0.00 0.00 3.86
2290 2309 6.327365 TCATTGGCTCTATTTCACTATCTGGA 59.673 38.462 0.00 0.00 0.00 3.86
2291 2310 6.753913 TTGGCTCTATTTCACTATCTGGAT 57.246 37.500 0.00 0.00 0.00 3.41
2292 2311 7.855784 TTGGCTCTATTTCACTATCTGGATA 57.144 36.000 0.00 0.00 0.00 2.59
2293 2312 8.441311 TTGGCTCTATTTCACTATCTGGATAT 57.559 34.615 0.00 0.00 0.00 1.63
2294 2313 8.441311 TGGCTCTATTTCACTATCTGGATATT 57.559 34.615 0.00 0.00 0.00 1.28
2295 2314 8.535335 TGGCTCTATTTCACTATCTGGATATTC 58.465 37.037 0.00 0.00 0.00 1.75
2296 2315 8.757877 GGCTCTATTTCACTATCTGGATATTCT 58.242 37.037 0.00 0.00 0.00 2.40
2300 2319 7.992754 ATTTCACTATCTGGATATTCTTGGC 57.007 36.000 0.00 0.00 0.00 4.52
2301 2320 6.753913 TTCACTATCTGGATATTCTTGGCT 57.246 37.500 0.00 0.00 0.00 4.75
2302 2321 6.352016 TCACTATCTGGATATTCTTGGCTC 57.648 41.667 0.00 0.00 0.00 4.70
2303 2322 6.080682 TCACTATCTGGATATTCTTGGCTCT 58.919 40.000 0.00 0.00 0.00 4.09
2304 2323 7.241628 TCACTATCTGGATATTCTTGGCTCTA 58.758 38.462 0.00 0.00 0.00 2.43
2305 2324 7.898100 TCACTATCTGGATATTCTTGGCTCTAT 59.102 37.037 0.00 0.00 0.00 1.98
2306 2325 9.194972 CACTATCTGGATATTCTTGGCTCTATA 57.805 37.037 0.00 0.00 0.00 1.31
2307 2326 9.950306 ACTATCTGGATATTCTTGGCTCTATAT 57.050 33.333 0.00 0.00 0.00 0.86
2309 2328 8.851106 ATCTGGATATTCTTGGCTCTATATCA 57.149 34.615 0.00 0.00 33.60 2.15
2350 2369 1.156736 CAAGGTTGTCCCGTAAGCTG 58.843 55.000 0.00 0.00 36.15 4.24
2440 2459 0.517316 GTTACCAAGGCTTGCACTCG 59.483 55.000 21.77 10.09 0.00 4.18
2551 2570 7.798982 GCTTCTTGAACACTTCTATTTGTACAC 59.201 37.037 0.00 0.00 0.00 2.90
2573 2592 5.348724 CACGTCACTGTTTATCTGTAGCAAT 59.651 40.000 0.00 0.00 0.00 3.56
2619 2638 4.214332 GCCCTAGTTATTGCACATCTAAGC 59.786 45.833 0.00 0.00 0.00 3.09
3113 3133 3.965379 TTACGTTGGATGCTGGTTCTA 57.035 42.857 0.00 0.00 0.00 2.10
3125 3145 4.645535 TGCTGGTTCTATGATATTCTGGC 58.354 43.478 0.00 0.00 0.00 4.85
3173 3354 8.131100 GCAACAATGTGCTTACATCAATATAGT 58.869 33.333 0.00 0.00 41.51 2.12
3312 3493 4.887071 TCATACACCTTTGAAAGTTGTGCT 59.113 37.500 16.88 3.12 34.81 4.40
3635 3825 4.569719 AACAACACCTTATACAGAGGGG 57.430 45.455 0.00 0.00 43.59 4.79
3639 3829 3.650948 ACACCTTATACAGAGGGGGTAC 58.349 50.000 0.00 0.00 42.21 3.34
3971 4161 1.016130 CACCAGAAGCACCAGTAGCG 61.016 60.000 0.00 0.00 37.01 4.26
4138 4330 2.032620 GGATGTACCGATGGTCTGACT 58.967 52.381 7.85 0.00 37.09 3.41
4139 4331 2.034812 GGATGTACCGATGGTCTGACTC 59.965 54.545 7.85 0.00 37.09 3.36
4185 4379 2.249844 AGACGTTTTTCGACATGGGT 57.750 45.000 0.00 0.00 42.86 4.51
4271 4485 0.829990 TCCTGCATGGCGTATGAGAA 59.170 50.000 6.06 0.00 39.21 2.87
4280 4494 5.505286 CATGGCGTATGAGAAAATCTGTTC 58.495 41.667 0.00 0.00 39.21 3.18
4293 4507 3.729526 ATCTGTTCGACAAATGCTTCG 57.270 42.857 0.00 0.00 36.55 3.79
4295 4509 1.798223 CTGTTCGACAAATGCTTCGGA 59.202 47.619 0.00 0.00 35.89 4.55
4350 4564 7.041372 GGATATGTGTACCAGATAATTTGCGTT 60.041 37.037 0.00 0.00 0.00 4.84
4412 4626 1.959710 TACCATACAAGAGGGTGGCA 58.040 50.000 0.00 0.00 43.79 4.92
4460 4677 5.331902 GCTGTGTGCGTGATATATTTTTGT 58.668 37.500 0.00 0.00 0.00 2.83
4467 4684 9.027129 TGTGCGTGATATATTTTTGTAGAGTAC 57.973 33.333 0.00 0.00 0.00 2.73
4505 4723 3.059884 CACAAAGCTTTCTCTCGCAGTA 58.940 45.455 9.23 0.00 0.00 2.74
4525 4743 4.982916 AGTAGTGTGAAGTTTACTCTTGCG 59.017 41.667 7.56 0.00 0.00 4.85
4533 4751 6.844779 GTGAAGTTTACTCTTGCGAAGTTTAC 59.155 38.462 0.00 0.00 0.00 2.01
4548 4766 5.063564 CGAAGTTTACTGGCATAGAAAGACC 59.936 44.000 0.00 0.00 0.00 3.85
4549 4767 5.763876 AGTTTACTGGCATAGAAAGACCT 57.236 39.130 0.00 0.00 0.00 3.85
4560 4778 1.150135 AGAAAGACCTGGGAGAGACCA 59.850 52.381 0.00 0.00 41.20 4.02
4561 4779 2.192263 GAAAGACCTGGGAGAGACCAT 58.808 52.381 0.00 0.00 40.36 3.55
4562 4780 1.577736 AAGACCTGGGAGAGACCATG 58.422 55.000 0.00 0.00 40.36 3.66
4563 4781 0.326048 AGACCTGGGAGAGACCATGG 60.326 60.000 11.19 11.19 40.36 3.66
4564 4782 0.325671 GACCTGGGAGAGACCATGGA 60.326 60.000 21.47 0.00 40.36 3.41
4565 4783 0.344790 ACCTGGGAGAGACCATGGAT 59.655 55.000 21.47 6.30 40.36 3.41
4707 4929 5.040635 GGTGTTGTTGGTTTCTATGTTGTG 58.959 41.667 0.00 0.00 0.00 3.33
4715 4937 2.890945 GTTTCTATGTTGTGGTGGCCTT 59.109 45.455 3.32 0.00 0.00 4.35
4730 4952 2.285024 CCTTGTGGGCATGTTGGGG 61.285 63.158 0.00 0.00 0.00 4.96
4765 4987 2.978010 CGGGGTTGTGAGTGTGGC 60.978 66.667 0.00 0.00 0.00 5.01
4838 5065 5.138125 ACACCTTATTGCTTTGGATTGTG 57.862 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.446161 CACTGACCTTGTCCCGTAATAGA 59.554 47.826 0.00 0.00 0.00 1.98
13 14 0.830444 TAGCACTGACCTTGTCCCGT 60.830 55.000 0.00 0.00 0.00 5.28
14 15 0.537188 ATAGCACTGACCTTGTCCCG 59.463 55.000 0.00 0.00 0.00 5.14
15 16 1.555075 TGATAGCACTGACCTTGTCCC 59.445 52.381 0.00 0.00 0.00 4.46
22 23 2.484417 CCACATCCTGATAGCACTGACC 60.484 54.545 0.00 0.00 0.00 4.02
24 25 2.470990 ACCACATCCTGATAGCACTGA 58.529 47.619 0.00 0.00 0.00 3.41
32 33 1.623311 TGTCGACAACCACATCCTGAT 59.377 47.619 17.62 0.00 0.00 2.90
62 63 1.121240 GATCACTAACATCGTCGCCG 58.879 55.000 0.00 0.00 0.00 6.46
68 69 1.548973 GCGCCGGATCACTAACATCG 61.549 60.000 5.05 0.00 0.00 3.84
92 93 0.976641 CCAGTGACCTAGCCAAGTCA 59.023 55.000 0.00 0.00 40.61 3.41
109 110 2.577563 TGCATCAAATCCCTCTTCTCCA 59.422 45.455 0.00 0.00 0.00 3.86
111 112 3.568853 CCATGCATCAAATCCCTCTTCTC 59.431 47.826 0.00 0.00 0.00 2.87
148 149 0.099082 CCAGGTCTAACGTCGAGCTC 59.901 60.000 14.31 2.73 37.14 4.09
157 158 2.607187 CACGACATGTCCAGGTCTAAC 58.393 52.381 20.03 0.00 39.71 2.34
159 160 0.530744 GCACGACATGTCCAGGTCTA 59.469 55.000 20.03 0.00 39.71 2.59
164 165 1.129251 GTCATTGCACGACATGTCCAG 59.871 52.381 20.03 13.28 33.43 3.86
181 182 6.653526 ACATGAAGAAAAACATCCATGTCA 57.346 33.333 0.00 0.00 40.80 3.58
202 203 5.602978 ACTTGAAGAGTCCCTAAAGAGAACA 59.397 40.000 0.00 0.00 31.20 3.18
237 238 2.863401 TAGTGTCGTTGCATCGCTAT 57.137 45.000 12.30 1.53 0.00 2.97
242 243 1.583054 GGGGATAGTGTCGTTGCATC 58.417 55.000 0.00 0.00 0.00 3.91
244 245 1.216977 CGGGGATAGTGTCGTTGCA 59.783 57.895 0.00 0.00 0.00 4.08
270 271 7.746703 ACCGGGAAAAGCTAAGAGAATATTAT 58.253 34.615 6.32 0.00 0.00 1.28
279 280 2.224354 ACGAAACCGGGAAAAGCTAAGA 60.224 45.455 6.32 0.00 0.00 2.10
280 281 2.148768 ACGAAACCGGGAAAAGCTAAG 58.851 47.619 6.32 0.00 0.00 2.18
281 282 2.259266 ACGAAACCGGGAAAAGCTAA 57.741 45.000 6.32 0.00 0.00 3.09
282 283 1.874872 CAACGAAACCGGGAAAAGCTA 59.125 47.619 6.32 0.00 0.00 3.32
283 284 0.666374 CAACGAAACCGGGAAAAGCT 59.334 50.000 6.32 0.00 0.00 3.74
284 285 0.318360 CCAACGAAACCGGGAAAAGC 60.318 55.000 6.32 0.00 0.00 3.51
285 286 1.026584 ACCAACGAAACCGGGAAAAG 58.973 50.000 6.32 0.00 0.00 2.27
286 287 0.739561 CACCAACGAAACCGGGAAAA 59.260 50.000 6.32 0.00 0.00 2.29
287 288 0.394080 ACACCAACGAAACCGGGAAA 60.394 50.000 6.32 0.00 0.00 3.13
288 289 1.096386 CACACCAACGAAACCGGGAA 61.096 55.000 6.32 0.00 0.00 3.97
319 320 2.978010 GGCTTCACACACCCACCG 60.978 66.667 0.00 0.00 0.00 4.94
322 323 2.203139 CACGGCTTCACACACCCA 60.203 61.111 0.00 0.00 0.00 4.51
344 345 2.367202 GGTCCCGGAAGATCAGCCA 61.367 63.158 0.73 0.00 0.00 4.75
365 366 7.041576 ACGAATTCACTAGAAACCTAAACCAAC 60.042 37.037 6.22 0.00 37.29 3.77
385 386 5.524971 TGTAGGTCGAATCCATACGAATT 57.475 39.130 0.00 0.00 40.12 2.17
388 389 4.581409 TGAATGTAGGTCGAATCCATACGA 59.419 41.667 0.00 0.00 36.18 3.43
420 421 6.599638 GGCTGATAAGGTCATGTAGAAACTTT 59.400 38.462 0.00 0.00 35.97 2.66
463 464 2.479730 CGCAATCTACAGAGCTAACCGT 60.480 50.000 0.00 0.00 0.00 4.83
513 514 3.057734 AGAAGTAACGGCTGAAAAGTCG 58.942 45.455 0.00 0.00 43.24 4.18
537 538 8.325787 AGAAAACATTTTAAACCCCAAGAACTT 58.674 29.630 0.00 0.00 0.00 2.66
541 542 6.461788 CGGAGAAAACATTTTAAACCCCAAGA 60.462 38.462 0.00 0.00 0.00 3.02
566 567 1.202359 CCTCTGAGCTTCCGTCTTAGC 60.202 57.143 0.00 0.00 37.66 3.09
572 573 0.832135 TTCCACCTCTGAGCTTCCGT 60.832 55.000 0.00 0.00 0.00 4.69
584 585 0.182775 AGCAAAACTCGGTTCCACCT 59.817 50.000 0.00 0.00 35.66 4.00
592 593 1.667724 CTCCTGCATAGCAAAACTCGG 59.332 52.381 0.00 0.00 38.41 4.63
656 658 8.707796 TTACAAACACACCCATAAATAAAGGA 57.292 30.769 0.00 0.00 0.00 3.36
704 706 3.552132 TTTTTCAAAAGGCCCAAGGTC 57.448 42.857 0.00 0.00 0.00 3.85
825 838 2.071778 TTTGCTGCTCCTTTTCTGGT 57.928 45.000 0.00 0.00 0.00 4.00
826 839 3.457610 TTTTTGCTGCTCCTTTTCTGG 57.542 42.857 0.00 0.00 0.00 3.86
909 922 0.169009 GCAAGATGGGTTGCGAACTC 59.831 55.000 0.00 0.00 43.24 3.01
1275 1290 2.125106 GCGCCTTCCTCGTCCATT 60.125 61.111 0.00 0.00 0.00 3.16
1479 1494 6.312141 TCCATCCAATCAAAGTACATCAGA 57.688 37.500 0.00 0.00 0.00 3.27
1648 1663 4.625742 TCGAAAGCTTCTCAACGGATAAAG 59.374 41.667 0.00 0.00 0.00 1.85
1818 1836 0.322975 ACCAAGCTAGCACTGACCTG 59.677 55.000 18.83 3.70 0.00 4.00
2267 2286 6.753913 TCCAGATAGTGAAATAGAGCCAAT 57.246 37.500 0.00 0.00 0.00 3.16
2278 2297 6.556495 AGAGCCAAGAATATCCAGATAGTGAA 59.444 38.462 0.00 0.00 0.00 3.18
2283 2302 9.942526 TGATATAGAGCCAAGAATATCCAGATA 57.057 33.333 0.00 0.00 32.64 1.98
2284 2303 8.703743 GTGATATAGAGCCAAGAATATCCAGAT 58.296 37.037 0.00 0.00 32.64 2.90
2285 2304 7.898100 AGTGATATAGAGCCAAGAATATCCAGA 59.102 37.037 0.00 0.00 32.64 3.86
2286 2305 8.076910 AGTGATATAGAGCCAAGAATATCCAG 57.923 38.462 0.00 0.00 32.64 3.86
2287 2306 9.720874 ATAGTGATATAGAGCCAAGAATATCCA 57.279 33.333 0.00 0.00 32.64 3.41
2291 2310 9.194972 CCAGATAGTGATATAGAGCCAAGAATA 57.805 37.037 0.00 0.00 0.00 1.75
2292 2311 7.898100 TCCAGATAGTGATATAGAGCCAAGAAT 59.102 37.037 0.00 0.00 0.00 2.40
2293 2312 7.241628 TCCAGATAGTGATATAGAGCCAAGAA 58.758 38.462 0.00 0.00 0.00 2.52
2294 2313 6.794534 TCCAGATAGTGATATAGAGCCAAGA 58.205 40.000 0.00 0.00 0.00 3.02
2295 2314 7.658525 ATCCAGATAGTGATATAGAGCCAAG 57.341 40.000 0.00 0.00 0.00 3.61
2296 2315 8.340002 AGTATCCAGATAGTGATATAGAGCCAA 58.660 37.037 0.00 0.00 0.00 4.52
2297 2316 7.877433 AGTATCCAGATAGTGATATAGAGCCA 58.123 38.462 0.00 0.00 0.00 4.75
2298 2317 8.217799 AGAGTATCCAGATAGTGATATAGAGCC 58.782 40.741 0.00 0.00 33.66 4.70
2299 2318 9.627123 AAGAGTATCCAGATAGTGATATAGAGC 57.373 37.037 0.00 0.00 33.66 4.09
2304 2323 8.948401 ACACAAGAGTATCCAGATAGTGATAT 57.052 34.615 9.64 0.00 33.66 1.63
2305 2324 9.286170 GTACACAAGAGTATCCAGATAGTGATA 57.714 37.037 9.64 0.00 33.66 2.15
2306 2325 7.780271 TGTACACAAGAGTATCCAGATAGTGAT 59.220 37.037 9.64 0.00 33.66 3.06
2307 2326 7.116736 TGTACACAAGAGTATCCAGATAGTGA 58.883 38.462 9.64 0.00 33.66 3.41
2308 2327 7.334844 TGTACACAAGAGTATCCAGATAGTG 57.665 40.000 0.00 2.02 33.66 2.74
2309 2328 7.956328 TTGTACACAAGAGTATCCAGATAGT 57.044 36.000 0.00 0.00 33.66 2.12
2350 2369 9.866798 TTCAGTTCTATGTAGCATCATATCATC 57.133 33.333 2.25 0.00 31.19 2.92
2551 2570 6.291849 GCTATTGCTACAGATAAACAGTGACG 60.292 42.308 0.00 0.00 36.03 4.35
2573 2592 5.163723 GCACATTGTATTCTGAAGCAAGCTA 60.164 40.000 13.10 0.00 0.00 3.32
2619 2638 5.582269 TCCTTTTCTATGCTTGATTGAGTCG 59.418 40.000 0.00 0.00 0.00 4.18
2654 2673 7.951347 AGATTCATGCAGGTATTTTCTTTCT 57.049 32.000 0.00 0.00 0.00 2.52
3113 3133 8.416329 GTTAAAACCATCTTGCCAGAATATCAT 58.584 33.333 0.00 0.00 30.76 2.45
3125 3145 8.915654 GTTGCTGATAAAGTTAAAACCATCTTG 58.084 33.333 0.00 0.00 0.00 3.02
3312 3493 2.741985 CGTCATCGGTTGCTGGCA 60.742 61.111 0.00 0.00 0.00 4.92
3841 4031 6.816640 TGAGATAACTGAACCGGTCAAAATAG 59.183 38.462 8.04 2.82 35.22 1.73
4015 4205 1.086634 GCGTCCTCTGAAGCATCCAC 61.087 60.000 0.00 0.00 44.24 4.02
4138 4330 2.682155 TATACACATGCGGCAACAGA 57.318 45.000 6.82 0.00 0.00 3.41
4139 4331 4.306600 TCTATATACACATGCGGCAACAG 58.693 43.478 6.82 2.58 0.00 3.16
4236 4430 1.554160 CAGGAGAGGATGTTGCTGTCT 59.446 52.381 0.00 0.00 29.00 3.41
4271 4485 4.466828 CGAAGCATTTGTCGAACAGATTT 58.533 39.130 0.00 0.00 39.64 2.17
4280 4494 2.159430 TGTCATTCCGAAGCATTTGTCG 59.841 45.455 0.00 0.00 37.01 4.35
4350 4564 3.395639 CAACCAAGTCGCTACCAAGTAA 58.604 45.455 0.00 0.00 0.00 2.24
4460 4677 7.437267 GTGTTTAGTTTTGCAGACTGTACTCTA 59.563 37.037 13.33 0.24 0.00 2.43
4467 4684 5.004726 GCTTTGTGTTTAGTTTTGCAGACTG 59.995 40.000 13.33 0.00 0.00 3.51
4471 4689 6.311200 AGAAAGCTTTGTGTTTAGTTTTGCAG 59.689 34.615 18.30 0.00 0.00 4.41
4505 4723 4.054780 TCGCAAGAGTAAACTTCACACT 57.945 40.909 0.00 0.00 45.01 3.55
4525 4743 6.092807 CAGGTCTTTCTATGCCAGTAAACTTC 59.907 42.308 0.00 0.00 0.00 3.01
4533 4751 1.839994 TCCCAGGTCTTTCTATGCCAG 59.160 52.381 0.00 0.00 0.00 4.85
4548 4766 2.570752 CCATATCCATGGTCTCTCCCAG 59.429 54.545 12.58 0.00 45.92 4.45
4549 4767 2.624495 CCATATCCATGGTCTCTCCCA 58.376 52.381 12.58 0.00 45.92 4.37
4560 4778 3.244665 TGAGCGCAAAGATCCATATCCAT 60.245 43.478 11.47 0.00 33.55 3.41
4561 4779 2.104622 TGAGCGCAAAGATCCATATCCA 59.895 45.455 11.47 0.00 33.55 3.41
4562 4780 2.771089 TGAGCGCAAAGATCCATATCC 58.229 47.619 11.47 0.00 33.55 2.59
4563 4781 4.379186 CCATTGAGCGCAAAGATCCATATC 60.379 45.833 11.47 0.00 37.59 1.63
4564 4782 3.504906 CCATTGAGCGCAAAGATCCATAT 59.495 43.478 11.47 0.00 37.59 1.78
4565 4783 2.880268 CCATTGAGCGCAAAGATCCATA 59.120 45.455 11.47 0.00 37.59 2.74
4659 4881 4.345859 ACAAGGACGGAACACTTATTCA 57.654 40.909 0.00 0.00 0.00 2.57
4715 4937 1.532794 GAACCCCAACATGCCCACA 60.533 57.895 0.00 0.00 0.00 4.17
4730 4952 2.295909 CCCGAGGATCAGATCTCAGAAC 59.704 54.545 10.36 0.00 33.17 3.01
4765 4987 7.814107 TCAATGCAAACTAAGGCAAAAAGATAG 59.186 33.333 0.00 0.00 44.20 2.08
4838 5065 1.825474 TCGGGAGAGAGACCAACAATC 59.175 52.381 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.