Multiple sequence alignment - TraesCS4A01G022700

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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 TraesCS4A01G022700 chr4A 100.000 3862 0 0 1 3862 16245688 16249549 0.000000e+00 7132.0
1 TraesCS4A01G022700 chr4A 76.744 430 66 20 1696 2099 489434634 489434213 3.910000e-50 209.0
2 TraesCS4A01G022700 chr4B 95.321 3035 98 17 344 3356 563629778 563626766 0.000000e+00 4778.0
3 TraesCS4A01G022700 chr4B 96.000 175 7 0 3688 3862 563626504 563626330 6.320000e-73 285.0
4 TraesCS4A01G022700 chr4B 90.909 110 8 2 237 345 404771457 404771565 3.110000e-31 147.0
5 TraesCS4A01G022700 chr4D 94.822 2955 83 26 344 3279 450333414 450330511 0.000000e+00 4545.0
6 TraesCS4A01G022700 chr4D 89.796 392 25 5 3354 3745 450330282 450329906 4.480000e-134 488.0
7 TraesCS4A01G022700 chr4D 92.593 243 17 1 19 261 450333668 450333427 7.940000e-92 348.0
8 TraesCS4A01G022700 chr4D 77.404 416 62 18 1709 2099 93069536 93069944 6.500000e-53 219.0
9 TraesCS4A01G022700 chr7B 84.454 476 27 21 345 800 703006138 703005690 3.570000e-115 425.0
10 TraesCS4A01G022700 chr7B 91.892 222 17 1 41 261 703006373 703006152 3.750000e-80 309.0
11 TraesCS4A01G022700 chr7B 85.246 122 8 6 377 491 37373166 37373048 2.440000e-22 117.0
12 TraesCS4A01G022700 chr7B 85.915 71 9 1 3259 3329 23414444 23414513 1.490000e-09 75.0
13 TraesCS4A01G022700 chr1B 88.745 231 19 4 344 570 67349010 67349237 3.800000e-70 276.0
14 TraesCS4A01G022700 chr1B 91.111 135 11 1 10 143 67348775 67348909 8.520000e-42 182.0
15 TraesCS4A01G022700 chr1B 91.589 107 7 2 250 355 606365245 606365140 3.110000e-31 147.0
16 TraesCS4A01G022700 chr3B 97.826 92 2 0 258 349 569062595 569062504 3.990000e-35 159.0
17 TraesCS4A01G022700 chr3B 90.090 111 8 2 245 354 770343076 770342968 1.450000e-29 141.0
18 TraesCS4A01G022700 chr3B 86.957 69 9 0 2238 2306 624317596 624317528 1.150000e-10 78.7
19 TraesCS4A01G022700 chr3D 97.802 91 2 0 258 348 255449929 255449839 1.440000e-34 158.0
20 TraesCS4A01G022700 chr3D 93.269 104 6 1 252 354 153849597 153849494 6.680000e-33 152.0
21 TraesCS4A01G022700 chr3D 88.406 69 8 0 2238 2306 470487153 470487085 2.470000e-12 84.2
22 TraesCS4A01G022700 chr3D 88.235 51 4 2 3259 3308 62526872 62526921 4.170000e-05 60.2
23 TraesCS4A01G022700 chr5D 96.739 92 3 0 254 345 219763286 219763377 1.860000e-33 154.0
24 TraesCS4A01G022700 chr3A 94.898 98 3 2 249 346 54716970 54716875 6.680000e-33 152.0
25 TraesCS4A01G022700 chr3A 86.957 69 9 0 2238 2306 612524275 612524207 1.150000e-10 78.7
26 TraesCS4A01G022700 chr1D 95.789 95 3 1 258 351 387899501 387899595 6.680000e-33 152.0
27 TraesCS4A01G022700 chrUn 88.525 122 4 5 377 491 75656701 75656819 5.200000e-29 139.0
28 TraesCS4A01G022700 chr6B 87.705 122 5 5 377 491 674318504 674318622 2.420000e-27 134.0
29 TraesCS4A01G022700 chr2B 87.705 122 5 5 377 491 118306617 118306735 2.420000e-27 134.0
30 TraesCS4A01G022700 chr2B 100.000 28 0 0 3261 3288 661179730 661179703 7.000000e-03 52.8
31 TraesCS4A01G022700 chr7A 90.244 82 8 0 2016 2097 8916186 8916267 1.470000e-19 108.0
32 TraesCS4A01G022700 chr7D 90.000 80 8 0 2018 2097 8479815 8479894 1.900000e-18 104.0
33 TraesCS4A01G022700 chr7D 87.692 65 8 0 2235 2299 477932148 477932212 4.140000e-10 76.8
34 TraesCS4A01G022700 chr2A 86.364 66 9 0 2235 2300 138533219 138533284 5.350000e-09 73.1
35 TraesCS4A01G022700 chr5A 84.058 69 11 0 2238 2306 582919043 582918975 2.490000e-07 67.6
36 TraesCS4A01G022700 chr5A 84.058 69 11 0 2238 2306 616764482 616764414 2.490000e-07 67.6
37 TraesCS4A01G022700 chr6A 88.235 51 4 2 3259 3308 43576275 43576226 4.170000e-05 60.2


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 TraesCS4A01G022700 chr4A 16245688 16249549 3861 False 7132.000000 7132 100.000000 1 3862 1 chr4A.!!$F1 3861
1 TraesCS4A01G022700 chr4B 563626330 563629778 3448 True 2531.500000 4778 95.660500 344 3862 2 chr4B.!!$R1 3518
2 TraesCS4A01G022700 chr4D 450329906 450333668 3762 True 1793.666667 4545 92.403667 19 3745 3 chr4D.!!$R1 3726
3 TraesCS4A01G022700 chr7B 703005690 703006373 683 True 367.000000 425 88.173000 41 800 2 chr7B.!!$R2 759

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
555 563 0.319211 TTGTGTGCTCGGGAAGTACG 60.319 55.000 0.0 0.0 42.99 3.67 F
560 568 1.153881 GCTCGGGAAGTACGGTGAC 60.154 63.158 0.0 0.0 0.00 3.67 F
1416 1449 1.272147 GCTTTCCCCACCTTGATGAGT 60.272 52.381 0.0 0.0 0.00 3.41 F
2378 2411 0.237498 GCAACAAGCACGGTAAGGTC 59.763 55.000 0.0 0.0 44.79 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 1433 1.264749 CGGACTCATCAAGGTGGGGA 61.265 60.000 0.00 0.0 0.0 4.81 R
1720 1753 2.356780 GGTAGTGCCTGTACCGCCT 61.357 63.158 0.00 0.0 30.9 5.52 R
2712 2745 0.456995 CCGGCGTTGTTGTTGTTGTT 60.457 50.000 6.01 0.0 0.0 2.83 R
3458 3705 0.043183 TCATCTTCCTCCTCCCAGCA 59.957 55.000 0.00 0.0 0.0 4.41 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
77 79 5.259832 TCTGTAGATGATTCAGTGAGCAG 57.740 43.478 0.00 0.00 0.00 4.24
127 129 4.331968 TGTATGGATTCTTGGTGTGGTTC 58.668 43.478 0.00 0.00 0.00 3.62
215 217 5.746245 CGTACCAACTTGAAAAATTGCTTCA 59.254 36.000 0.23 0.23 0.00 3.02
256 258 2.298163 CAAGTTTGGCCTCTGAATTGCT 59.702 45.455 3.32 0.00 0.00 3.91
261 263 4.568072 TTGGCCTCTGAATTGCTAAGTA 57.432 40.909 3.32 0.00 0.00 2.24
262 264 3.873910 TGGCCTCTGAATTGCTAAGTAC 58.126 45.455 3.32 0.00 0.00 2.73
264 266 4.123506 GGCCTCTGAATTGCTAAGTACTC 58.876 47.826 0.00 0.00 0.00 2.59
265 267 4.123506 GCCTCTGAATTGCTAAGTACTCC 58.876 47.826 0.00 0.00 0.00 3.85
266 268 4.698575 CCTCTGAATTGCTAAGTACTCCC 58.301 47.826 0.00 0.00 0.00 4.30
267 269 4.407296 CCTCTGAATTGCTAAGTACTCCCT 59.593 45.833 0.00 0.00 0.00 4.20
268 270 5.452636 CCTCTGAATTGCTAAGTACTCCCTC 60.453 48.000 0.00 0.00 0.00 4.30
269 271 4.406003 TCTGAATTGCTAAGTACTCCCTCC 59.594 45.833 0.00 0.00 0.00 4.30
271 273 4.721776 TGAATTGCTAAGTACTCCCTCCAT 59.278 41.667 0.00 0.00 0.00 3.41
272 274 5.903010 TGAATTGCTAAGTACTCCCTCCATA 59.097 40.000 0.00 0.00 0.00 2.74
273 275 6.385759 TGAATTGCTAAGTACTCCCTCCATAA 59.614 38.462 0.00 0.00 0.00 1.90
274 276 6.824958 ATTGCTAAGTACTCCCTCCATAAA 57.175 37.500 0.00 0.00 0.00 1.40
275 277 5.609533 TGCTAAGTACTCCCTCCATAAAC 57.390 43.478 0.00 0.00 0.00 2.01
276 278 5.278061 TGCTAAGTACTCCCTCCATAAACT 58.722 41.667 0.00 0.00 0.00 2.66
277 279 6.437755 TGCTAAGTACTCCCTCCATAAACTA 58.562 40.000 0.00 0.00 0.00 2.24
278 280 6.899075 TGCTAAGTACTCCCTCCATAAACTAA 59.101 38.462 0.00 0.00 0.00 2.24
279 281 7.567622 TGCTAAGTACTCCCTCCATAAACTAAT 59.432 37.037 0.00 0.00 0.00 1.73
280 282 9.086758 GCTAAGTACTCCCTCCATAAACTAATA 57.913 37.037 0.00 0.00 0.00 0.98
287 289 8.817876 ACTCCCTCCATAAACTAATATAAGAGC 58.182 37.037 0.00 0.00 0.00 4.09
288 290 7.837863 TCCCTCCATAAACTAATATAAGAGCG 58.162 38.462 0.00 0.00 0.00 5.03
289 291 7.453752 TCCCTCCATAAACTAATATAAGAGCGT 59.546 37.037 0.00 0.00 0.00 5.07
290 292 8.095169 CCCTCCATAAACTAATATAAGAGCGTT 58.905 37.037 0.00 0.00 0.00 4.84
291 293 9.490379 CCTCCATAAACTAATATAAGAGCGTTT 57.510 33.333 0.00 0.00 0.00 3.60
307 309 8.828688 AAGAGCGTTTAGAACACTATTTTAGT 57.171 30.769 0.00 0.00 40.28 2.24
339 341 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
340 342 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
341 343 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
342 344 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
351 353 9.850198 ATTAGTTTACAGAGGGAGTAGTAGTAG 57.150 37.037 0.00 0.00 0.00 2.57
400 402 8.904834 GTTTATCTCAGGTCATGTCTAGTTAGA 58.095 37.037 0.00 0.00 0.00 2.10
423 426 3.786450 CCTTTTCCCCCTTGATAGGTACT 59.214 47.826 0.00 0.00 46.37 2.73
543 551 3.350833 AGAAGATTGAGGGATTGTGTGC 58.649 45.455 0.00 0.00 0.00 4.57
555 563 0.319211 TTGTGTGCTCGGGAAGTACG 60.319 55.000 0.00 0.00 42.99 3.67
560 568 1.153881 GCTCGGGAAGTACGGTGAC 60.154 63.158 0.00 0.00 0.00 3.67
576 584 3.195825 CGGTGACCTGAAGTTTATCCTCT 59.804 47.826 0.00 0.00 0.00 3.69
664 672 6.605471 TGCAGTAGAATTCTTTCACTCCTA 57.395 37.500 14.36 0.00 34.08 2.94
700 716 8.795513 TCTGAATGAATTTGCAGTTATTCTTGA 58.204 29.630 15.08 9.65 33.08 3.02
714 730 7.490725 CAGTTATTCTTGACTAGTCCACTCATG 59.509 40.741 20.11 4.49 0.00 3.07
735 757 6.763135 TCATGTCATACTTCTGCCTAATTCAC 59.237 38.462 0.00 0.00 0.00 3.18
742 764 5.482908 ACTTCTGCCTAATTCACTACAGTG 58.517 41.667 2.84 2.84 46.91 3.66
814 836 3.111098 GCTCCAAATCTTGCTATTTGCG 58.889 45.455 11.78 7.82 46.63 4.85
856 878 4.445452 GCAAGATGAAATTGCCTTCTGA 57.555 40.909 0.00 0.00 45.79 3.27
868 890 2.224597 TGCCTTCTGACAATTCTGAGCA 60.225 45.455 0.00 0.00 32.13 4.26
935 960 7.535997 ACACTGAAGACAAAACTTAAACCTTC 58.464 34.615 0.00 0.00 0.00 3.46
939 964 5.847111 AGACAAAACTTAAACCTTCCCAC 57.153 39.130 0.00 0.00 0.00 4.61
951 976 3.834447 TTCCCACGCGTCGACAGTG 62.834 63.158 25.40 25.40 35.79 3.66
972 1002 3.889538 TGGTACCCTTCTGATGATAGACG 59.110 47.826 10.07 0.00 0.00 4.18
973 1003 4.142790 GGTACCCTTCTGATGATAGACGA 58.857 47.826 0.00 0.00 0.00 4.20
974 1004 4.023021 GGTACCCTTCTGATGATAGACGAC 60.023 50.000 0.00 0.00 0.00 4.34
984 1014 1.926510 TGATAGACGACTGCATTTGCG 59.073 47.619 0.00 0.00 45.83 4.85
993 1023 2.221169 ACTGCATTTGCGTCTGAAGAA 58.779 42.857 0.00 0.00 45.83 2.52
1110 1140 1.388547 CCATGTCCAACCAATACCCG 58.611 55.000 0.00 0.00 0.00 5.28
1174 1204 2.202987 AGCAGAGCCACATAGCGC 60.203 61.111 0.00 0.00 38.01 5.92
1175 1205 2.512286 GCAGAGCCACATAGCGCA 60.512 61.111 11.47 0.00 38.01 6.09
1176 1206 2.817423 GCAGAGCCACATAGCGCAC 61.817 63.158 11.47 0.00 38.01 5.34
1416 1449 1.272147 GCTTTCCCCACCTTGATGAGT 60.272 52.381 0.00 0.00 0.00 3.41
1578 1611 2.035940 AGGAAGGACGACTCGGCT 59.964 61.111 3.84 0.00 34.07 5.52
1720 1753 0.839277 CATGCTGGACCAGGTGGATA 59.161 55.000 23.09 0.00 38.94 2.59
2101 2134 1.272872 ACTTCCTCCACCCGTAAGCTA 60.273 52.381 0.00 0.00 0.00 3.32
2102 2135 1.409427 CTTCCTCCACCCGTAAGCTAG 59.591 57.143 0.00 0.00 0.00 3.42
2103 2136 1.041447 TCCTCCACCCGTAAGCTAGC 61.041 60.000 6.62 6.62 0.00 3.42
2104 2137 1.043673 CCTCCACCCGTAAGCTAGCT 61.044 60.000 12.68 12.68 0.00 3.32
2285 2318 2.111251 GTCCGCCTATGGAAGCCC 59.889 66.667 0.00 0.00 40.44 5.19
2354 2387 0.454620 CCAACTCGTCGTCGGAGAAG 60.455 60.000 1.55 0.00 39.69 2.85
2378 2411 0.237498 GCAACAAGCACGGTAAGGTC 59.763 55.000 0.00 0.00 44.79 3.85
2643 2676 3.547249 GACGACGCCAGGTTCGTGA 62.547 63.158 19.68 0.00 40.59 4.35
3195 3232 9.252962 GGATATTGATGATTTGTTGATCCAAAC 57.747 33.333 0.00 0.00 37.16 2.93
3215 3252 4.422073 ACAGACACCAGTTTCTTGATCA 57.578 40.909 0.00 0.00 0.00 2.92
3236 3273 9.733556 TGATCAATACCAGTACAATACAAGTTT 57.266 29.630 0.00 0.00 0.00 2.66
3292 3344 3.927142 GTCCGGAATTACTTGTCACAGAG 59.073 47.826 5.23 0.00 0.00 3.35
3356 3408 5.873179 TTTCTGCGACAAGTAATTTAGGG 57.127 39.130 0.00 0.00 0.00 3.53
3357 3409 3.869065 TCTGCGACAAGTAATTTAGGGG 58.131 45.455 0.00 0.00 0.00 4.79
3394 3641 1.901948 TGTCCGAGCTCAAGACGGT 60.902 57.895 22.25 0.00 45.71 4.83
3444 3691 1.410882 GAGATGAAGGGACGGAGAAGG 59.589 57.143 0.00 0.00 0.00 3.46
3445 3692 1.007238 AGATGAAGGGACGGAGAAGGA 59.993 52.381 0.00 0.00 0.00 3.36
3447 3694 0.408309 TGAAGGGACGGAGAAGGAGA 59.592 55.000 0.00 0.00 0.00 3.71
3448 3695 1.007238 TGAAGGGACGGAGAAGGAGAT 59.993 52.381 0.00 0.00 0.00 2.75
3449 3696 1.410882 GAAGGGACGGAGAAGGAGATG 59.589 57.143 0.00 0.00 0.00 2.90
3450 3697 0.397816 AGGGACGGAGAAGGAGATGG 60.398 60.000 0.00 0.00 0.00 3.51
3451 3698 1.403687 GGGACGGAGAAGGAGATGGG 61.404 65.000 0.00 0.00 0.00 4.00
3454 3701 0.042731 ACGGAGAAGGAGATGGGGAA 59.957 55.000 0.00 0.00 0.00 3.97
3455 3702 0.755686 CGGAGAAGGAGATGGGGAAG 59.244 60.000 0.00 0.00 0.00 3.46
3456 3703 1.689575 CGGAGAAGGAGATGGGGAAGA 60.690 57.143 0.00 0.00 0.00 2.87
3457 3704 1.765904 GGAGAAGGAGATGGGGAAGAC 59.234 57.143 0.00 0.00 0.00 3.01
3458 3705 2.628290 GGAGAAGGAGATGGGGAAGACT 60.628 54.545 0.00 0.00 0.00 3.24
3499 3746 3.809905 AGGAGAGCCGTTGGATAATTTC 58.190 45.455 0.00 0.00 39.96 2.17
3500 3747 3.456277 AGGAGAGCCGTTGGATAATTTCT 59.544 43.478 0.00 0.00 39.96 2.52
3510 3757 7.277396 CCGTTGGATAATTTCTAGGGAACTTA 58.723 38.462 0.00 0.00 43.67 2.24
3525 3772 6.849151 AGGGAACTTACAAATAACTCCAAGT 58.151 36.000 0.00 0.00 37.44 3.16
3529 3776 9.244799 GGAACTTACAAATAACTCCAAGTTTTG 57.755 33.333 0.00 0.95 39.51 2.44
3536 3783 7.709182 ACAAATAACTCCAAGTTTTGTTTAGCC 59.291 33.333 0.00 0.00 36.36 3.93
3554 3801 1.742411 GCCCTTAGCAATGCAGACGTA 60.742 52.381 8.35 0.00 42.97 3.57
3560 3807 2.216046 AGCAATGCAGACGTATCATGG 58.784 47.619 8.35 0.00 0.00 3.66
3571 3818 1.541233 CGTATCATGGTTCTGCCCTCC 60.541 57.143 0.00 0.00 36.04 4.30
3572 3819 0.758734 TATCATGGTTCTGCCCTCCG 59.241 55.000 0.00 0.00 36.04 4.63
3573 3820 1.274703 ATCATGGTTCTGCCCTCCGT 61.275 55.000 0.00 0.00 36.04 4.69
3574 3821 0.616395 TCATGGTTCTGCCCTCCGTA 60.616 55.000 0.00 0.00 36.04 4.02
3603 3850 3.576550 ACTCTCCTGAACTTCTGAAGACC 59.423 47.826 23.36 13.90 0.00 3.85
3671 3918 4.160329 TGAACCTGATAAGGAGACAGTGT 58.840 43.478 1.89 0.00 0.00 3.55
3692 3939 3.853831 TGACAAATGCATCATGACACC 57.146 42.857 16.78 5.98 0.00 4.16
3756 4003 0.179065 TCATCAGATTCAGGCAGCCG 60.179 55.000 5.55 0.83 0.00 5.52
3758 4005 0.543277 ATCAGATTCAGGCAGCCGAA 59.457 50.000 17.47 17.47 0.00 4.30
3766 4013 1.009829 CAGGCAGCCGAAACATAGAC 58.990 55.000 5.55 0.00 0.00 2.59
3775 4022 2.285220 CCGAAACATAGACAATGGCTCG 59.715 50.000 0.00 0.00 40.62 5.03
3835 4082 1.583054 AACTTGTTCAGCGGACAGAC 58.417 50.000 0.00 0.00 0.00 3.51
3840 4087 1.202639 TGTTCAGCGGACAGACAACAT 60.203 47.619 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.233553 TGCTAAGATAAGCCTGTATCTACACAT 59.766 37.037 3.35 0.00 39.44 3.21
1 2 6.549736 TGCTAAGATAAGCCTGTATCTACACA 59.450 38.462 3.35 0.88 39.44 3.72
2 3 6.982852 TGCTAAGATAAGCCTGTATCTACAC 58.017 40.000 3.35 0.00 39.44 2.90
3 4 7.597288 TTGCTAAGATAAGCCTGTATCTACA 57.403 36.000 3.35 0.00 39.44 2.74
4 5 6.588373 GCTTGCTAAGATAAGCCTGTATCTAC 59.412 42.308 0.00 0.00 42.57 2.59
5 6 6.692486 GCTTGCTAAGATAAGCCTGTATCTA 58.308 40.000 0.00 0.00 42.57 1.98
6 7 5.546526 GCTTGCTAAGATAAGCCTGTATCT 58.453 41.667 0.00 0.00 42.57 1.98
7 8 5.854431 GCTTGCTAAGATAAGCCTGTATC 57.146 43.478 0.00 0.00 42.57 2.24
33 34 1.978617 ATGGACGCAAAGGGCAAGG 60.979 57.895 0.00 0.00 45.17 3.61
77 79 1.601166 AACACCTAACCGAAACCTGC 58.399 50.000 0.00 0.00 0.00 4.85
192 194 7.224557 ACATGAAGCAATTTTTCAAGTTGGTAC 59.775 33.333 0.00 0.00 38.01 3.34
215 217 5.244626 ACTTGCCAAGAATCAGCTAAAACAT 59.755 36.000 12.25 0.00 0.00 2.71
244 246 4.407296 AGGGAGTACTTAGCAATTCAGAGG 59.593 45.833 0.00 0.00 0.00 3.69
261 263 8.817876 GCTCTTATATTAGTTTATGGAGGGAGT 58.182 37.037 0.00 0.00 0.00 3.85
262 264 7.976734 CGCTCTTATATTAGTTTATGGAGGGAG 59.023 40.741 0.00 0.00 33.23 4.30
264 266 7.612677 ACGCTCTTATATTAGTTTATGGAGGG 58.387 38.462 0.00 0.00 35.06 4.30
265 267 9.490379 AAACGCTCTTATATTAGTTTATGGAGG 57.510 33.333 0.00 0.00 31.14 4.30
313 315 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
314 316 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
315 317 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
316 318 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
317 319 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
325 327 9.850198 CTACTACTACTCCCTCTGTAAACTAAT 57.150 37.037 0.00 0.00 0.00 1.73
326 328 7.772757 GCTACTACTACTCCCTCTGTAAACTAA 59.227 40.741 0.00 0.00 0.00 2.24
327 329 7.127032 AGCTACTACTACTCCCTCTGTAAACTA 59.873 40.741 0.00 0.00 0.00 2.24
328 330 6.069498 AGCTACTACTACTCCCTCTGTAAACT 60.069 42.308 0.00 0.00 0.00 2.66
329 331 6.038492 CAGCTACTACTACTCCCTCTGTAAAC 59.962 46.154 0.00 0.00 0.00 2.01
330 332 6.069789 TCAGCTACTACTACTCCCTCTGTAAA 60.070 42.308 0.00 0.00 0.00 2.01
331 333 5.427806 TCAGCTACTACTACTCCCTCTGTAA 59.572 44.000 0.00 0.00 0.00 2.41
332 334 4.967442 TCAGCTACTACTACTCCCTCTGTA 59.033 45.833 0.00 0.00 0.00 2.74
333 335 3.781407 TCAGCTACTACTACTCCCTCTGT 59.219 47.826 0.00 0.00 0.00 3.41
334 336 4.425180 TCAGCTACTACTACTCCCTCTG 57.575 50.000 0.00 0.00 0.00 3.35
335 337 6.963117 ATATCAGCTACTACTACTCCCTCT 57.037 41.667 0.00 0.00 0.00 3.69
336 338 8.411991 AAAATATCAGCTACTACTACTCCCTC 57.588 38.462 0.00 0.00 0.00 4.30
337 339 8.785184 AAAAATATCAGCTACTACTACTCCCT 57.215 34.615 0.00 0.00 0.00 4.20
363 365 7.732025 TGACCTGAGATAAACTAAGAACACAA 58.268 34.615 0.00 0.00 0.00 3.33
423 426 5.818678 AACACCAGTCCAAATCAGTAGTA 57.181 39.130 0.00 0.00 0.00 1.82
424 427 4.706842 AACACCAGTCCAAATCAGTAGT 57.293 40.909 0.00 0.00 0.00 2.73
425 428 5.048713 GGAAAACACCAGTCCAAATCAGTAG 60.049 44.000 0.00 0.00 0.00 2.57
426 429 4.825085 GGAAAACACCAGTCCAAATCAGTA 59.175 41.667 0.00 0.00 0.00 2.74
535 543 1.671850 CGTACTTCCCGAGCACACAAT 60.672 52.381 0.00 0.00 0.00 2.71
543 551 0.964358 AGGTCACCGTACTTCCCGAG 60.964 60.000 0.00 0.00 0.00 4.63
555 563 4.223032 TGAGAGGATAAACTTCAGGTCACC 59.777 45.833 0.00 0.00 0.00 4.02
560 568 5.894393 TCTACCTGAGAGGATAAACTTCAGG 59.106 44.000 15.29 15.29 46.13 3.86
603 611 4.989875 AGGATAGAATGGATCCAACAGG 57.010 45.455 20.67 0.00 44.71 4.00
700 716 6.096141 CAGAAGTATGACATGAGTGGACTAGT 59.904 42.308 0.00 0.00 0.00 2.57
714 730 7.265673 TGTAGTGAATTAGGCAGAAGTATGAC 58.734 38.462 0.00 0.00 0.00 3.06
735 757 1.988467 CTGTGCATCGACACACTGTAG 59.012 52.381 17.64 6.25 45.36 2.74
763 785 1.032794 TGGTAAAAACATGGTGCGCA 58.967 45.000 5.66 5.66 0.00 6.09
814 836 8.730680 TCTTGCTCCTAAATTCAAATTACAGTC 58.269 33.333 0.00 0.00 0.00 3.51
847 869 2.224597 TGCTCAGAATTGTCAGAAGGCA 60.225 45.455 0.00 0.00 0.00 4.75
856 878 5.645497 GTCAGTAAATCCTGCTCAGAATTGT 59.355 40.000 0.00 0.00 32.32 2.71
868 890 5.946377 GGATTGGAAACTGTCAGTAAATCCT 59.054 40.000 25.08 13.47 31.04 3.24
939 964 2.503375 GGTACCACTGTCGACGCG 60.503 66.667 11.62 3.53 0.00 6.01
972 1002 1.800586 TCTTCAGACGCAAATGCAGTC 59.199 47.619 16.88 16.88 42.21 3.51
973 1003 1.882912 TCTTCAGACGCAAATGCAGT 58.117 45.000 6.18 4.55 42.21 4.40
974 1004 2.481568 TCTTCTTCAGACGCAAATGCAG 59.518 45.455 6.18 1.33 42.21 4.41
984 1014 2.478831 GCCATCCGATCTTCTTCAGAC 58.521 52.381 0.00 0.00 32.83 3.51
993 1023 1.144057 GAACGTGGCCATCCGATCT 59.856 57.895 21.34 6.18 34.14 2.75
1065 1095 1.704628 TGGTGGTGGAATGACATGTCT 59.295 47.619 25.55 7.38 0.00 3.41
1348 1381 0.994247 TACTGGTAGAGGGACACCGA 59.006 55.000 0.00 0.00 43.47 4.69
1400 1433 1.264749 CGGACTCATCAAGGTGGGGA 61.265 60.000 0.00 0.00 0.00 4.81
1720 1753 2.356780 GGTAGTGCCTGTACCGCCT 61.357 63.158 0.00 0.00 30.90 5.52
2285 2318 3.432749 CCTTGTACATCTCCTCCACCATG 60.433 52.174 0.00 0.00 0.00 3.66
2372 2405 3.818787 GCCGCCTCGTCGACCTTA 61.819 66.667 10.58 0.00 0.00 2.69
2557 2590 2.669569 CGTGGTGGTTCAGGCTGG 60.670 66.667 15.73 0.00 0.00 4.85
2711 2744 0.637738 CGGCGTTGTTGTTGTTGTTG 59.362 50.000 0.00 0.00 0.00 3.33
2712 2745 0.456995 CCGGCGTTGTTGTTGTTGTT 60.457 50.000 6.01 0.00 0.00 2.83
2713 2746 1.137825 CCGGCGTTGTTGTTGTTGT 59.862 52.632 6.01 0.00 0.00 3.32
3195 3232 5.954296 ATTGATCAAGAAACTGGTGTCTG 57.046 39.130 14.54 0.00 0.00 3.51
3236 3273 5.865552 ACTAGTAGATAGCAAACGCGAAAAA 59.134 36.000 15.93 0.00 34.56 1.94
3332 3384 6.258160 CCCTAAATTACTTGTCGCAGAAATG 58.742 40.000 0.00 0.00 39.69 2.32
3415 3662 1.045350 CCCTTCATCTCCTCTGCCGA 61.045 60.000 0.00 0.00 0.00 5.54
3418 3665 0.103937 CGTCCCTTCATCTCCTCTGC 59.896 60.000 0.00 0.00 0.00 4.26
3420 3667 0.631753 TCCGTCCCTTCATCTCCTCT 59.368 55.000 0.00 0.00 0.00 3.69
3444 3691 0.179936 CCAGCAGTCTTCCCCATCTC 59.820 60.000 0.00 0.00 0.00 2.75
3445 3692 1.277580 CCCAGCAGTCTTCCCCATCT 61.278 60.000 0.00 0.00 0.00 2.90
3447 3694 1.229951 TCCCAGCAGTCTTCCCCAT 60.230 57.895 0.00 0.00 0.00 4.00
3448 3695 1.920325 CTCCCAGCAGTCTTCCCCA 60.920 63.158 0.00 0.00 0.00 4.96
3449 3696 2.674220 CCTCCCAGCAGTCTTCCCC 61.674 68.421 0.00 0.00 0.00 4.81
3450 3697 1.613630 TCCTCCCAGCAGTCTTCCC 60.614 63.158 0.00 0.00 0.00 3.97
3451 3698 1.621672 CCTCCTCCCAGCAGTCTTCC 61.622 65.000 0.00 0.00 0.00 3.46
3454 3701 0.617249 CTTCCTCCTCCCAGCAGTCT 60.617 60.000 0.00 0.00 0.00 3.24
3455 3702 0.616111 TCTTCCTCCTCCCAGCAGTC 60.616 60.000 0.00 0.00 0.00 3.51
3456 3703 0.043940 ATCTTCCTCCTCCCAGCAGT 59.956 55.000 0.00 0.00 0.00 4.40
3457 3704 0.469070 CATCTTCCTCCTCCCAGCAG 59.531 60.000 0.00 0.00 0.00 4.24
3458 3705 0.043183 TCATCTTCCTCCTCCCAGCA 59.957 55.000 0.00 0.00 0.00 4.41
3499 3746 8.101419 ACTTGGAGTTATTTGTAAGTTCCCTAG 58.899 37.037 0.00 0.00 0.00 3.02
3500 3747 7.981142 ACTTGGAGTTATTTGTAAGTTCCCTA 58.019 34.615 0.00 0.00 0.00 3.53
3510 3757 7.709182 GGCTAAACAAAACTTGGAGTTATTTGT 59.291 33.333 5.50 5.50 39.49 2.83
3517 3764 3.910989 AGGGCTAAACAAAACTTGGAGT 58.089 40.909 0.00 0.00 34.12 3.85
3519 3766 4.279922 GCTAAGGGCTAAACAAAACTTGGA 59.720 41.667 0.00 0.00 38.06 3.53
3525 3772 4.039730 TGCATTGCTAAGGGCTAAACAAAA 59.960 37.500 10.49 0.00 42.39 2.44
3529 3776 3.016736 TCTGCATTGCTAAGGGCTAAAC 58.983 45.455 10.49 0.00 42.39 2.01
3536 3783 3.457234 TGATACGTCTGCATTGCTAAGG 58.543 45.455 10.49 6.16 0.00 2.69
3554 3801 1.274703 ACGGAGGGCAGAACCATGAT 61.275 55.000 0.00 0.00 42.05 2.45
3560 3807 0.743097 ATACGTACGGAGGGCAGAAC 59.257 55.000 21.06 0.00 0.00 3.01
3571 3818 3.622163 AGTTCAGGAGAGTGATACGTACG 59.378 47.826 15.01 15.01 0.00 3.67
3572 3819 5.354792 AGAAGTTCAGGAGAGTGATACGTAC 59.645 44.000 5.50 0.00 0.00 3.67
3573 3820 5.354513 CAGAAGTTCAGGAGAGTGATACGTA 59.645 44.000 5.50 0.00 0.00 3.57
3574 3821 4.156922 CAGAAGTTCAGGAGAGTGATACGT 59.843 45.833 5.50 0.00 0.00 3.57
3603 3850 1.135199 CCAGCTTGTAAATGGCAGCAG 60.135 52.381 0.00 0.00 0.00 4.24
3658 3905 4.515191 GCATTTGTCAACACTGTCTCCTTA 59.485 41.667 0.00 0.00 0.00 2.69
3664 3911 4.227512 TGATGCATTTGTCAACACTGTC 57.772 40.909 0.00 0.00 0.00 3.51
3671 3918 3.366171 CGGTGTCATGATGCATTTGTCAA 60.366 43.478 0.00 0.00 0.00 3.18
3692 3939 3.155998 GACAAAATCTGAACATCACGCG 58.844 45.455 3.53 3.53 0.00 6.01
3756 4003 3.932710 TCACGAGCCATTGTCTATGTTTC 59.067 43.478 0.00 0.00 31.99 2.78
3758 4005 3.262420 GTCACGAGCCATTGTCTATGTT 58.738 45.455 0.00 0.00 31.99 2.71
3766 4013 2.002586 CCTTACTGTCACGAGCCATTG 58.997 52.381 0.00 0.00 0.00 2.82
3775 4022 8.828688 ATTGTTACTCTTAACCTTACTGTCAC 57.171 34.615 0.00 0.00 37.39 3.67
3835 4082 3.974401 GTCGAACCAATTGTGTGATGTTG 59.026 43.478 4.43 0.00 0.00 3.33
3840 4087 2.869801 GTGAGTCGAACCAATTGTGTGA 59.130 45.455 4.43 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.