Multiple sequence alignment - TraesCS5B01G491900

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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 TraesCS5B01G491900 chr5B 100.000 6070 0 0 483 6552 660141930 660135861 0.000000e+00 11210.0
1 TraesCS5B01G491900 chr5B 100.000 161 0 0 1 161 660142412 660142252 1.380000e-76 298.0
2 TraesCS5B01G491900 chr5B 90.604 149 13 1 1286 1434 660140975 660140828 5.180000e-46 196.0
3 TraesCS5B01G491900 chr5B 90.604 149 13 1 1438 1585 660141127 660140979 5.180000e-46 196.0
4 TraesCS5B01G491900 chr5D 94.376 3627 147 23 502 4113 525666849 525663265 0.000000e+00 5515.0
5 TraesCS5B01G491900 chr5D 94.595 1554 54 10 4669 6206 525662929 525661390 0.000000e+00 2377.0
6 TraesCS5B01G491900 chr5D 87.385 325 22 5 6211 6535 525661340 525661035 8.080000e-94 355.0
7 TraesCS5B01G491900 chr5D 96.026 151 5 1 1435 1585 525666064 525665915 1.820000e-60 244.0
8 TraesCS5B01G491900 chr5D 88.272 162 10 5 9 161 525667079 525666918 1.120000e-42 185.0
9 TraesCS5B01G491900 chr5D 89.189 148 15 1 1286 1433 525665911 525665765 4.040000e-42 183.0
10 TraesCS5B01G491900 chr5A 90.372 4144 259 61 2451 6552 651988984 651984939 0.000000e+00 5313.0
11 TraesCS5B01G491900 chr5A 93.718 1544 72 8 924 2453 651990751 651989219 0.000000e+00 2290.0
12 TraesCS5B01G491900 chr5A 86.752 234 22 7 502 735 651991171 651990947 1.090000e-62 252.0
13 TraesCS5B01G491900 chr5A 95.302 149 7 0 1437 1585 651990377 651990229 3.050000e-58 237.0
14 TraesCS5B01G491900 chr5A 90.604 149 13 1 1286 1434 651990225 651990078 5.180000e-46 196.0
15 TraesCS5B01G491900 chr5A 88.757 169 8 2 1 161 651991405 651991240 5.180000e-46 196.0
16 TraesCS5B01G491900 chr5A 79.293 198 30 10 4417 4610 285396857 285396667 1.920000e-25 128.0
17 TraesCS5B01G491900 chr5A 86.458 96 10 2 815 908 651990900 651990806 1.160000e-17 102.0
18 TraesCS5B01G491900 chr6B 82.676 1547 227 26 2705 4228 484660565 484659037 0.000000e+00 1334.0
19 TraesCS5B01G491900 chr6B 87.097 62 8 0 2608 2669 20616641 20616702 3.280000e-08 71.3
20 TraesCS5B01G491900 chr7A 82.466 1557 219 23 2708 4235 14935536 14934005 0.000000e+00 1314.0
21 TraesCS5B01G491900 chr7A 82.759 174 23 6 4432 4602 721109719 721109550 1.470000e-31 148.0
22 TraesCS5B01G491900 chr7A 81.132 159 27 3 4432 4589 634399660 634399504 2.480000e-24 124.0
23 TraesCS5B01G491900 chr2B 81.988 1549 233 30 2708 4228 239631422 239629892 0.000000e+00 1273.0
24 TraesCS5B01G491900 chr2B 84.091 1188 161 18 3207 4371 66713674 66712492 0.000000e+00 1122.0
25 TraesCS5B01G491900 chr2B 83.133 1245 179 21 3152 4371 760253548 760254786 0.000000e+00 1107.0
26 TraesCS5B01G491900 chr3D 84.111 1221 162 18 3176 4374 358193269 358192059 0.000000e+00 1151.0
27 TraesCS5B01G491900 chr7B 83.623 1209 176 14 3183 4374 641750975 641749772 0.000000e+00 1116.0
28 TraesCS5B01G491900 chr7B 83.908 174 24 4 4432 4603 641684349 641684178 5.260000e-36 163.0
29 TraesCS5B01G491900 chr7B 81.325 166 22 8 4432 4595 572404640 572404482 6.900000e-25 126.0
30 TraesCS5B01G491900 chr3A 80.000 255 34 9 4180 4422 683533366 683533117 8.730000e-39 172.0
31 TraesCS5B01G491900 chr3A 79.429 175 30 5 4432 4603 589177213 589177042 1.150000e-22 119.0
32 TraesCS5B01G491900 chr3A 85.185 108 12 2 4316 4422 707618808 707618704 2.500000e-19 108.0
33 TraesCS5B01G491900 chr2D 82.105 190 30 4 4413 4600 627930514 627930701 6.800000e-35 159.0
34 TraesCS5B01G491900 chr2D 81.667 180 27 6 4434 4610 577686827 577687003 1.900000e-30 145.0
35 TraesCS5B01G491900 chr4B 86.239 109 12 3 4313 4421 590047703 590047598 1.490000e-21 115.0
36 TraesCS5B01G491900 chr4B 84.722 72 7 3 2607 2676 12095508 12095577 1.180000e-07 69.4


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 TraesCS5B01G491900 chr5B 660135861 660142412 6551 True 2975.000000 11210 95.302000 1 6552 4 chr5B.!!$R1 6551
1 TraesCS5B01G491900 chr5D 525661035 525667079 6044 True 1476.500000 5515 91.640500 9 6535 6 chr5D.!!$R1 6526
2 TraesCS5B01G491900 chr5A 651984939 651991405 6466 True 1226.571429 5313 90.280429 1 6552 7 chr5A.!!$R2 6551
3 TraesCS5B01G491900 chr6B 484659037 484660565 1528 True 1334.000000 1334 82.676000 2705 4228 1 chr6B.!!$R1 1523
4 TraesCS5B01G491900 chr7A 14934005 14935536 1531 True 1314.000000 1314 82.466000 2708 4235 1 chr7A.!!$R1 1527
5 TraesCS5B01G491900 chr2B 239629892 239631422 1530 True 1273.000000 1273 81.988000 2708 4228 1 chr2B.!!$R2 1520
6 TraesCS5B01G491900 chr2B 66712492 66713674 1182 True 1122.000000 1122 84.091000 3207 4371 1 chr2B.!!$R1 1164
7 TraesCS5B01G491900 chr2B 760253548 760254786 1238 False 1107.000000 1107 83.133000 3152 4371 1 chr2B.!!$F1 1219
8 TraesCS5B01G491900 chr3D 358192059 358193269 1210 True 1151.000000 1151 84.111000 3176 4374 1 chr3D.!!$R1 1198
9 TraesCS5B01G491900 chr7B 641749772 641750975 1203 True 1116.000000 1116 83.623000 3183 4374 1 chr7B.!!$R3 1191

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
736 748 0.179134 CTTGTCTCGGGGTAGCGAAG 60.179 60.000 0.00 0.00 0.00 3.79 F
1284 1349 0.109412 AACGTCGTAGCTACAGGTGC 60.109 55.000 23.21 7.26 0.00 5.01 F
1414 1479 0.318107 GCAGCACAAGTTCACGCATT 60.318 50.000 0.00 0.00 0.00 3.56 F
1452 1517 0.669619 TTGTGCACCTGCTGATGTTG 59.330 50.000 15.69 0.00 42.66 3.33 F
3400 3741 1.070615 TTGGCTGTAGCTGTTGCGA 59.929 52.632 0.00 0.00 45.42 5.10 F
4573 5048 0.458889 TTACGTGGCGCGCTTAAGAT 60.459 50.000 32.29 14.17 46.11 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2637 2941 0.759346 AGCCTTTATCCTACAGGGCG 59.241 55.000 0.0 0.0 43.68 6.13 R
3168 3498 0.611062 AGCAGCAACAGCACATCCAT 60.611 50.000 0.0 0.0 0.00 3.41 R
3169 3499 1.228337 AGCAGCAACAGCACATCCA 60.228 52.632 0.0 0.0 0.00 3.41 R
3421 3762 0.173708 GGAGTCAGAACTAGCCACGG 59.826 60.000 0.0 0.0 35.28 4.94 R
5185 5660 0.521291 TGTTGCATAGCTTGGCGTTC 59.479 50.000 0.0 0.0 0.00 3.95 R
6338 6883 0.244721 GCCTGTGAATGCAACCCTTC 59.755 55.000 0.0 0.0 0.00 3.46 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
68 69 3.537506 TCCCTCCCTCACCCACCA 61.538 66.667 0.00 0.00 0.00 4.17
71 72 3.706373 CTCCCTCACCCACCACCG 61.706 72.222 0.00 0.00 0.00 4.94
560 569 3.118482 ACGAGTAGTAGTAGTAGCAGGCA 60.118 47.826 0.00 0.00 0.00 4.75
594 603 5.147032 TGGAAATGAAACTCCCTGTTGAAT 58.853 37.500 0.00 0.00 39.13 2.57
629 639 9.234827 TGAATTGGATATATGCTGGTAGATTTG 57.765 33.333 5.77 0.00 0.00 2.32
658 670 3.972276 CCTCTCGGGCGCTAGAGC 61.972 72.222 22.47 10.35 38.33 4.09
722 734 8.519492 TTTTAACATTTGCAGCTTATCTTGTC 57.481 30.769 0.00 0.00 0.00 3.18
736 748 0.179134 CTTGTCTCGGGGTAGCGAAG 60.179 60.000 0.00 0.00 0.00 3.79
797 809 1.230149 TAACCATGGTGCCCCCTCT 60.230 57.895 20.60 1.86 0.00 3.69
865 878 1.271108 ACATGTATGGTGTTGGACGCA 60.271 47.619 0.00 0.00 0.00 5.24
949 1001 2.493675 GCCTTCTCCCTGGATTTGTTTC 59.506 50.000 0.00 0.00 0.00 2.78
1107 1166 2.284478 AGCAGGAGCAGGAGCAGA 60.284 61.111 0.00 0.00 45.49 4.26
1263 1328 1.025647 GTAGTCCTCCTCGTCGCAGT 61.026 60.000 0.00 0.00 0.00 4.40
1284 1349 0.109412 AACGTCGTAGCTACAGGTGC 60.109 55.000 23.21 7.26 0.00 5.01
1317 1382 9.125026 TCTGATGTTTTCTTCTTAGAAGCTTTT 57.875 29.630 16.49 0.00 41.25 2.27
1318 1383 9.741647 CTGATGTTTTCTTCTTAGAAGCTTTTT 57.258 29.630 16.49 0.00 41.25 1.94
1414 1479 0.318107 GCAGCACAAGTTCACGCATT 60.318 50.000 0.00 0.00 0.00 3.56
1426 1491 2.176546 CGCATTGTTGGCTGTCCG 59.823 61.111 0.00 0.00 34.14 4.79
1452 1517 0.669619 TTGTGCACCTGCTGATGTTG 59.330 50.000 15.69 0.00 42.66 3.33
1620 1685 1.656587 TCTGCACTGGAGTGGGTATT 58.343 50.000 8.82 0.00 45.72 1.89
2070 2135 2.174639 TGGTCAGTCAAATTGTCAGGGT 59.825 45.455 0.00 0.00 0.00 4.34
2076 2141 6.431234 GTCAGTCAAATTGTCAGGGTAGAATT 59.569 38.462 0.00 0.00 0.00 2.17
2077 2142 7.004086 TCAGTCAAATTGTCAGGGTAGAATTT 58.996 34.615 0.00 0.00 0.00 1.82
2078 2143 7.505585 TCAGTCAAATTGTCAGGGTAGAATTTT 59.494 33.333 0.00 0.00 0.00 1.82
2079 2144 8.143835 CAGTCAAATTGTCAGGGTAGAATTTTT 58.856 33.333 0.00 0.00 0.00 1.94
2080 2145 8.360390 AGTCAAATTGTCAGGGTAGAATTTTTC 58.640 33.333 0.00 0.00 0.00 2.29
2081 2146 8.141268 GTCAAATTGTCAGGGTAGAATTTTTCA 58.859 33.333 0.00 0.00 0.00 2.69
2082 2147 8.700051 TCAAATTGTCAGGGTAGAATTTTTCAA 58.300 29.630 0.00 0.00 0.00 2.69
2083 2148 9.492973 CAAATTGTCAGGGTAGAATTTTTCAAT 57.507 29.630 0.00 0.00 0.00 2.57
2124 2189 3.623960 CGACGTCACTTATCTCTTCCTCT 59.376 47.826 17.16 0.00 0.00 3.69
2206 2271 5.700402 AGCTGTTAGATGGGTATCAAAGT 57.300 39.130 0.00 0.00 35.70 2.66
2286 2351 6.190587 GGGACTAAGTAGAGTTGGGTAACTA 58.809 44.000 0.00 0.00 46.79 2.24
2380 2446 3.274288 CTGGAACTTGGTATCAGGAAGC 58.726 50.000 0.00 0.00 0.00 3.86
2407 2473 7.092079 TGAATTGAATGTGATGTTTCCATGTC 58.908 34.615 0.00 0.00 0.00 3.06
2420 2486 5.428457 TGTTTCCATGTCCCTACAGTATGAT 59.572 40.000 0.00 0.00 39.69 2.45
2637 2941 3.019564 ACAATGGTGCTATCTTTGGAGC 58.980 45.455 0.00 0.00 39.25 4.70
2663 2967 3.808728 TGTAGGATAAAGGCTGATGTGC 58.191 45.455 0.00 0.00 0.00 4.57
2911 3228 4.533124 TCCGGCGGCCTAGATCCA 62.533 66.667 23.83 0.00 0.00 3.41
3189 3519 1.521450 GGATGTGCTGTTGCTGCTGT 61.521 55.000 0.00 0.00 40.48 4.40
3400 3741 1.070615 TTGGCTGTAGCTGTTGCGA 59.929 52.632 0.00 0.00 45.42 5.10
3421 3762 2.583593 GCGTCGGATCTGACCAGC 60.584 66.667 25.58 20.46 35.40 4.85
3656 3998 2.357034 ACGATGGCGACGCTTGTT 60.357 55.556 20.77 1.82 41.64 2.83
3676 4019 2.972505 CGCCACGCACCTTCTTGT 60.973 61.111 0.00 0.00 0.00 3.16
3725 4069 1.878656 CTTCTCTCGCACTTCGGGGT 61.879 60.000 0.00 0.00 39.67 4.95
3819 4165 2.416107 CTGGAGTGGCTTGGCTTGGA 62.416 60.000 0.00 0.00 0.00 3.53
3954 4300 3.819652 TTGGCCAGCCTGGTGTGT 61.820 61.111 13.35 0.00 40.46 3.72
3984 4330 2.755876 AGCGTGGAGATCGGAGCA 60.756 61.111 0.00 0.00 0.00 4.26
3986 4332 3.069980 GCGTGGAGATCGGAGCAGT 62.070 63.158 0.00 0.00 0.00 4.40
4006 4352 1.087501 GGCTTCGGATCTGGTTGTTC 58.912 55.000 0.62 0.00 0.00 3.18
4010 4356 1.548081 TCGGATCTGGTTGTTCGGTA 58.452 50.000 0.62 0.00 0.00 4.02
4125 4471 1.202533 CGGCTCCGAAGATGGTTGTAT 60.203 52.381 1.35 0.00 42.83 2.29
4126 4472 2.035449 CGGCTCCGAAGATGGTTGTATA 59.965 50.000 1.35 0.00 42.83 1.47
4165 4511 4.687215 GTGGCAGAGCAGTCGGCA 62.687 66.667 0.00 0.00 44.96 5.69
4201 4547 2.911143 GGGATCGGTGTGGATGCT 59.089 61.111 0.00 0.00 35.37 3.79
4239 4597 4.758674 GGTTTTGGTTGTAGGGAGTTACTC 59.241 45.833 3.36 3.36 0.00 2.59
4248 4606 1.246737 GGGAGTTACTCGGGTGACGT 61.247 60.000 4.51 0.00 44.69 4.34
4252 4610 0.522076 GTTACTCGGGTGACGTAGCG 60.522 60.000 0.00 0.00 44.69 4.26
4344 4709 1.740332 CGGTTTTTGCCCGGGTTTCT 61.740 55.000 24.63 0.00 41.78 2.52
4345 4710 1.330234 GGTTTTTGCCCGGGTTTCTA 58.670 50.000 24.63 2.07 0.00 2.10
4543 5018 7.271511 TCACCCATTGTCCATATTTTATTTGC 58.728 34.615 0.00 0.00 0.00 3.68
4566 5041 3.617538 CTAGCTTACGTGGCGCGC 61.618 66.667 25.94 25.94 46.11 6.86
4573 5048 0.458889 TTACGTGGCGCGCTTAAGAT 60.459 50.000 32.29 14.17 46.11 2.40
4605 5080 1.507562 TCAACCACTGTACATGCACG 58.492 50.000 0.00 0.00 0.00 5.34
4608 5083 0.533978 ACCACTGTACATGCACGCAA 60.534 50.000 0.00 0.00 0.00 4.85
4868 5343 3.058914 CAGGGTAAAGTGAACTTTCAGCG 60.059 47.826 11.56 0.00 44.34 5.18
4870 5345 2.289547 GGTAAAGTGAACTTTCAGCGCA 59.710 45.455 11.47 0.00 44.34 6.09
5010 5485 7.823745 AATGTATTAGAAAGTTGGGCCATAG 57.176 36.000 7.26 0.00 0.00 2.23
5170 5645 2.173669 GCATATGGCGCGTGACTGT 61.174 57.895 8.43 0.00 0.00 3.55
5462 5937 3.889227 GCAACTGCATGGCGACTA 58.111 55.556 0.00 0.00 41.59 2.59
5593 6069 4.785453 CTGAAGCACCCCGCCCTC 62.785 72.222 0.00 0.00 44.04 4.30
5672 6148 0.749649 TTTTTGCTTGGTCGGTGCAT 59.250 45.000 0.00 0.00 36.55 3.96
5675 6151 4.120331 GCTTGGTCGGTGCATGCC 62.120 66.667 16.68 6.42 0.00 4.40
5682 6158 1.675310 TCGGTGCATGCCCTTCTTG 60.675 57.895 16.68 3.27 0.00 3.02
5683 6159 2.575461 GGTGCATGCCCTTCTTGC 59.425 61.111 16.68 0.00 43.74 4.01
5684 6160 1.980772 GGTGCATGCCCTTCTTGCT 60.981 57.895 16.68 0.00 43.80 3.91
5685 6161 1.509923 GTGCATGCCCTTCTTGCTC 59.490 57.895 16.68 0.00 43.80 4.26
5841 6319 2.093106 TCGAGTTTACCTGAGGAGCTC 58.907 52.381 4.99 4.71 0.00 4.09
5898 6376 3.304324 GCTCTGCTGAGTTGAAAGTTTCC 60.304 47.826 20.24 0.00 42.13 3.13
5917 6395 1.408127 CCGAGGGTTGTTGGATGCATA 60.408 52.381 0.00 0.00 0.00 3.14
5951 6444 2.880890 GTTGCAGATGTTGACTGTCCTT 59.119 45.455 5.17 0.00 37.64 3.36
5952 6445 3.213206 TGCAGATGTTGACTGTCCTTT 57.787 42.857 5.17 0.00 37.64 3.11
5964 6457 2.361104 TCCTTTGCGGTGATGGCC 60.361 61.111 0.00 0.00 0.00 5.36
5986 6479 4.142816 CCTTCCTTGCTGTTTCTTCATACG 60.143 45.833 0.00 0.00 0.00 3.06
6096 6589 2.357257 GGGATTCCAGAGGAAAGTTCCC 60.357 54.545 16.25 16.25 45.51 3.97
6107 6600 3.891049 GGAAAGTTCCCTGCAGATGTAT 58.109 45.455 17.39 0.00 41.62 2.29
6131 6624 2.223377 GGTTTGTAGGAAACGAGCACAG 59.777 50.000 0.00 0.00 0.00 3.66
6138 6631 2.362077 AGGAAACGAGCACAGCAATTTT 59.638 40.909 0.00 0.00 0.00 1.82
6141 6634 2.036556 ACGAGCACAGCAATTTTTCG 57.963 45.000 0.00 0.00 0.00 3.46
6155 6648 7.532546 CAGCAATTTTTCGTCGAAATACTGTTA 59.467 33.333 20.34 1.73 32.13 2.41
6226 6771 6.245890 TCCCTTTTGGTGTGAAAATTGATT 57.754 33.333 0.00 0.00 38.10 2.57
6228 6773 6.765512 TCCCTTTTGGTGTGAAAATTGATTTC 59.234 34.615 0.00 0.00 42.01 2.17
6251 6796 2.921754 GCAGCTTCATGATTTCAAGTGC 59.078 45.455 0.00 0.30 0.00 4.40
6254 6799 3.693085 AGCTTCATGATTTCAAGTGCGAT 59.307 39.130 0.00 0.00 0.00 4.58
6285 6830 3.209410 CATGGGGAAAGAAATCCTCTCG 58.791 50.000 0.00 0.00 40.90 4.04
6288 6833 3.073946 TGGGGAAAGAAATCCTCTCGTTT 59.926 43.478 0.00 0.00 40.90 3.60
6294 6839 4.195225 AGAAATCCTCTCGTTTCTCACC 57.805 45.455 0.00 0.00 39.75 4.02
6313 6858 4.709397 TCACCAAATTCTTGTTGTCTGGTT 59.291 37.500 0.00 0.00 33.46 3.67
6314 6859 5.888724 TCACCAAATTCTTGTTGTCTGGTTA 59.111 36.000 0.00 0.00 33.46 2.85
6334 6879 7.815383 TGGTTATCTGATAAATGATTGGACCT 58.185 34.615 11.46 0.00 0.00 3.85
6338 6883 9.565090 TTATCTGATAAATGATTGGACCTGAAG 57.435 33.333 7.62 0.00 0.00 3.02
6376 6922 1.276138 GCCCCAAGCAAAGCACTAAAT 59.724 47.619 0.00 0.00 42.97 1.40
6381 6927 5.812127 CCCCAAGCAAAGCACTAAATTAATC 59.188 40.000 0.00 0.00 0.00 1.75
6414 6960 1.922570 CTGAATGCTTTGCCTCATGC 58.077 50.000 0.00 0.00 41.77 4.06
6490 7039 6.935741 ATAGCACACACTTCAACTGTTTAA 57.064 33.333 0.00 0.00 0.00 1.52
6532 7081 2.544726 GTGGGTAGAGCACAGCAAC 58.455 57.895 0.00 0.00 0.00 4.17
6547 7101 2.613595 CAGCAACAGAGCTAACACACAA 59.386 45.455 0.00 0.00 44.54 3.33
6548 7102 2.614057 AGCAACAGAGCTAACACACAAC 59.386 45.455 0.00 0.00 44.50 3.32
6550 7104 3.546815 GCAACAGAGCTAACACACAACAG 60.547 47.826 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
539 548 3.464907 TGCCTGCTACTACTACTACTCG 58.535 50.000 0.00 0.00 0.00 4.18
560 569 6.079712 AGTTTCATTTCCAGTAAGGCCTAT 57.920 37.500 5.16 0.00 37.29 2.57
567 576 5.319043 ACAGGGAGTTTCATTTCCAGTAA 57.681 39.130 0.00 0.00 35.09 2.24
594 603 7.884877 CAGCATATATCCAATTCAAACCTAGGA 59.115 37.037 17.98 0.00 0.00 2.94
615 625 3.244561 CCCGTATCCAAATCTACCAGCAT 60.245 47.826 0.00 0.00 0.00 3.79
616 626 2.104111 CCCGTATCCAAATCTACCAGCA 59.896 50.000 0.00 0.00 0.00 4.41
629 639 2.631427 CGAGAGGAGACCCGTATCC 58.369 63.158 0.00 0.00 41.13 2.59
658 670 2.097925 GCGCGACAATCAACAAACAAAG 60.098 45.455 12.10 0.00 0.00 2.77
722 734 1.445716 ATCGACTTCGCTACCCCGAG 61.446 60.000 0.00 0.00 38.60 4.63
736 748 0.521735 GCAACCTGGTTTCCATCGAC 59.478 55.000 9.90 0.00 30.82 4.20
797 809 2.637872 CAGAAACTACAGGGACAAGGGA 59.362 50.000 0.00 0.00 0.00 4.20
863 876 2.738521 ATGGACACAGACGCGTGC 60.739 61.111 20.70 8.74 40.73 5.34
865 878 2.738521 GCATGGACACAGACGCGT 60.739 61.111 13.85 13.85 0.00 6.01
908 921 5.018809 AGGCAAAATCATGTCTACCAACAT 58.981 37.500 0.00 0.00 40.49 2.71
920 933 2.312741 TCCAGGGAGAAGGCAAAATCAT 59.687 45.455 0.00 0.00 0.00 2.45
949 1001 2.557056 TGAACTCCAACGGTCAGACTAG 59.443 50.000 0.00 0.00 0.00 2.57
1046 1099 3.391665 CTGCTCTTGGCCCTACCCG 62.392 68.421 0.00 0.00 40.92 5.28
1107 1166 0.536687 TCTTGCTGCTGCTCTTGCTT 60.537 50.000 17.00 0.00 40.48 3.91
1263 1328 1.198408 CACCTGTAGCTACGACGTTCA 59.802 52.381 18.74 0.00 0.00 3.18
1284 1349 3.499918 AGAAGAAAACATCAGAAGGTGCG 59.500 43.478 0.00 0.00 0.00 5.34
1371 1436 7.178274 TGCAGTTGGTATTCCAGTGAATATTTT 59.822 33.333 6.91 0.00 43.47 1.82
1414 1479 1.369692 CACTACCGGACAGCCAACA 59.630 57.895 9.46 0.00 0.00 3.33
1452 1517 3.499918 TGCAAGCAAGCTTCTAAGAAGAC 59.500 43.478 3.97 0.00 33.42 3.01
1620 1685 3.000041 GCTATGGTGTGTCGAATTGTCA 59.000 45.455 0.00 0.00 0.00 3.58
1736 1801 7.307694 TGCTTAAATAAATCAGACAAGCACAG 58.692 34.615 2.21 0.00 41.24 3.66
1839 1904 8.364142 TGTGGTTTAGTTAATGCAAAGCTATTT 58.636 29.630 0.00 0.00 32.36 1.40
1956 2021 9.739276 GTGCTAGGCATATATATCTCTAGAGAT 57.261 37.037 32.38 32.38 44.76 2.75
2077 2142 8.920665 CGGCAAGTAAATCACATAAAATTGAAA 58.079 29.630 0.00 0.00 0.00 2.69
2078 2143 8.300286 TCGGCAAGTAAATCACATAAAATTGAA 58.700 29.630 0.00 0.00 0.00 2.69
2079 2144 7.753132 GTCGGCAAGTAAATCACATAAAATTGA 59.247 33.333 0.00 0.00 0.00 2.57
2080 2145 7.253288 CGTCGGCAAGTAAATCACATAAAATTG 60.253 37.037 0.00 0.00 0.00 2.32
2081 2146 6.745450 CGTCGGCAAGTAAATCACATAAAATT 59.255 34.615 0.00 0.00 0.00 1.82
2082 2147 6.128117 ACGTCGGCAAGTAAATCACATAAAAT 60.128 34.615 0.00 0.00 0.00 1.82
2083 2148 5.179742 ACGTCGGCAAGTAAATCACATAAAA 59.820 36.000 0.00 0.00 0.00 1.52
2124 2189 1.965643 AGGTACGTGTTAGCCTTGACA 59.034 47.619 0.00 0.00 0.00 3.58
2244 2309 5.289510 AGTCCCACCTATTCAAATCCTACT 58.710 41.667 0.00 0.00 0.00 2.57
2407 2473 5.227569 TGTTATGGCATCATACTGTAGGG 57.772 43.478 1.65 0.00 35.75 3.53
2420 2486 2.158682 ACAACACAGACCTGTTATGGCA 60.159 45.455 13.28 0.00 42.83 4.92
2612 2916 5.754782 TCCAAAGATAGCACCATTGTACAT 58.245 37.500 0.00 0.00 0.00 2.29
2637 2941 0.759346 AGCCTTTATCCTACAGGGCG 59.241 55.000 0.00 0.00 43.68 6.13
3085 3415 4.379243 CCTCAAGAGCGCCCGTGT 62.379 66.667 2.29 0.00 0.00 4.49
3104 3434 1.895020 AAGGTAGATCCGCAACGCCA 61.895 55.000 0.00 0.00 41.99 5.69
3168 3498 0.611062 AGCAGCAACAGCACATCCAT 60.611 50.000 0.00 0.00 0.00 3.41
3169 3499 1.228337 AGCAGCAACAGCACATCCA 60.228 52.632 0.00 0.00 0.00 3.41
3189 3519 1.982395 CCTCATATCCGCCCCGCTA 60.982 63.158 0.00 0.00 0.00 4.26
3400 3741 3.148279 GTCAGATCCGACGCCCCT 61.148 66.667 0.00 0.00 0.00 4.79
3421 3762 0.173708 GGAGTCAGAACTAGCCACGG 59.826 60.000 0.00 0.00 35.28 4.94
3676 4019 0.599558 CCCTCGAACAACGACACCTA 59.400 55.000 0.00 0.00 46.45 3.08
3680 4023 1.180456 TAGGCCCTCGAACAACGACA 61.180 55.000 0.00 0.00 46.45 4.35
3725 4069 3.585732 CAGGAACCTGGAACTAGGGTTTA 59.414 47.826 12.54 0.00 42.54 2.01
3794 4139 0.951040 CCAAGCCACTCCAGAACGAC 60.951 60.000 0.00 0.00 0.00 4.34
3828 4174 2.510411 CACACACCACCAGAGCCA 59.490 61.111 0.00 0.00 0.00 4.75
3834 4180 4.248842 CGAGGCCACACACCACCA 62.249 66.667 5.01 0.00 0.00 4.17
3857 4203 2.259818 CGCTCAGACTTCCACGCT 59.740 61.111 0.00 0.00 0.00 5.07
3967 4313 2.755876 TGCTCCGATCTCCACGCT 60.756 61.111 0.00 0.00 0.00 5.07
3984 4330 0.036010 CAACCAGATCCGAAGCCACT 60.036 55.000 0.00 0.00 0.00 4.00
3986 4332 0.400213 AACAACCAGATCCGAAGCCA 59.600 50.000 0.00 0.00 0.00 4.75
3991 4337 1.548081 TACCGAACAACCAGATCCGA 58.452 50.000 0.00 0.00 0.00 4.55
4010 4356 4.514577 CGAGCAACCGGAGCCGAT 62.515 66.667 9.46 0.00 42.83 4.18
4125 4471 0.107831 AGCAACCAAAGCCGACACTA 59.892 50.000 0.00 0.00 0.00 2.74
4126 4472 1.152963 AGCAACCAAAGCCGACACT 60.153 52.632 0.00 0.00 0.00 3.55
4187 4533 0.390860 GCTCTAGCATCCACACCGAT 59.609 55.000 0.00 0.00 41.59 4.18
4252 4610 4.101448 ACACCAGATGAGCCGCCC 62.101 66.667 0.00 0.00 0.00 6.13
4278 4636 1.153249 CAACACACACACCGACCCT 60.153 57.895 0.00 0.00 0.00 4.34
4320 4678 4.518779 CGGGCAAAAACCGTTACG 57.481 55.556 0.00 0.00 46.03 3.18
4332 4697 5.757988 AGTTAATTAATAGAAACCCGGGCA 58.242 37.500 24.08 0.16 0.00 5.36
4543 5018 1.600663 CGCCACGTAAGCTAGAGATGG 60.601 57.143 8.00 0.00 45.62 3.51
4573 5048 4.286032 ACAGTGGTTGATAAGGCAGTCTTA 59.714 41.667 0.00 0.00 41.66 2.10
4713 5188 3.845398 TGGCCATTTTTCCATCAAAGGAT 59.155 39.130 0.00 0.00 37.56 3.24
4868 5343 4.922103 GGTGTACAAGTACAGTAAGAGTGC 59.078 45.833 12.96 0.00 45.61 4.40
4870 5345 5.832060 ACAGGTGTACAAGTACAGTAAGAGT 59.168 40.000 12.96 4.69 45.61 3.24
4995 5470 2.424956 CAAGAGCTATGGCCCAACTTTC 59.575 50.000 0.00 0.00 39.73 2.62
5164 5639 2.997315 CCTGAGGCGGGACAGTCA 60.997 66.667 2.17 0.00 32.93 3.41
5185 5660 0.521291 TGTTGCATAGCTTGGCGTTC 59.479 50.000 0.00 0.00 0.00 3.95
5347 5822 4.373116 GTCGTCTTCGGGCAGGCA 62.373 66.667 0.00 0.00 37.69 4.75
5458 5933 2.736978 CAGGTGTCGCAGATGATAGTC 58.263 52.381 0.00 0.00 40.67 2.59
5462 5937 1.520120 CGCAGGTGTCGCAGATGAT 60.520 57.895 0.00 0.00 40.67 2.45
5657 6133 3.364441 GCATGCACCGACCAAGCA 61.364 61.111 14.21 0.00 43.14 3.91
5672 6148 2.046892 GAGCGAGCAAGAAGGGCA 60.047 61.111 0.00 0.00 0.00 5.36
5675 6151 1.449246 CAGGGAGCGAGCAAGAAGG 60.449 63.158 0.00 0.00 0.00 3.46
5682 6158 4.021925 AACACCCAGGGAGCGAGC 62.022 66.667 14.54 0.00 0.00 5.03
5683 6159 2.046892 CAACACCCAGGGAGCGAG 60.047 66.667 14.54 0.00 0.00 5.03
5684 6160 3.636231 CCAACACCCAGGGAGCGA 61.636 66.667 14.54 0.00 0.00 4.93
5685 6161 3.491598 AACCAACACCCAGGGAGCG 62.492 63.158 14.54 2.22 0.00 5.03
5797 6273 8.272866 CGAAAGCGTGTCACATTGATATAATAA 58.727 33.333 3.42 0.00 0.00 1.40
5798 6274 7.650104 TCGAAAGCGTGTCACATTGATATAATA 59.350 33.333 3.42 0.00 38.98 0.98
5799 6275 6.478673 TCGAAAGCGTGTCACATTGATATAAT 59.521 34.615 3.42 0.00 38.98 1.28
5898 6376 2.036958 TATGCATCCAACAACCCTCG 57.963 50.000 0.19 0.00 0.00 4.63
5917 6395 0.606401 CTGCAACCCCAGAACACGAT 60.606 55.000 0.00 0.00 34.77 3.73
5951 6444 2.361104 GGAAGGCCATCACCGCAA 60.361 61.111 10.67 0.00 33.69 4.85
5952 6445 2.905996 AAGGAAGGCCATCACCGCA 61.906 57.895 10.67 0.00 36.29 5.69
5964 6457 4.452455 ACGTATGAAGAAACAGCAAGGAAG 59.548 41.667 0.00 0.00 0.00 3.46
6096 6589 4.271049 CCTACAAACCGAATACATCTGCAG 59.729 45.833 7.63 7.63 0.00 4.41
6107 6600 2.137523 GCTCGTTTCCTACAAACCGAA 58.862 47.619 0.00 0.00 0.00 4.30
6131 6624 6.669485 AACAGTATTTCGACGAAAAATTGC 57.331 33.333 25.32 13.51 35.11 3.56
6138 6631 7.894376 AGGAAATTAACAGTATTTCGACGAA 57.106 32.000 6.10 6.10 40.99 3.85
6141 6634 7.248437 CCCAAGGAAATTAACAGTATTTCGAC 58.752 38.462 0.00 0.00 40.99 4.20
6155 6648 0.686789 GCCAACAGCCCAAGGAAATT 59.313 50.000 0.00 0.00 34.35 1.82
6209 6754 4.054671 GCGGAAATCAATTTTCACACCAA 58.945 39.130 1.05 0.00 44.67 3.67
6226 6771 2.435422 TGAAATCATGAAGCTGCGGAA 58.565 42.857 0.00 0.00 0.00 4.30
6228 6773 2.163010 ACTTGAAATCATGAAGCTGCGG 59.837 45.455 0.00 0.00 0.00 5.69
6264 6809 3.209410 CGAGAGGATTTCTTTCCCCATG 58.791 50.000 0.00 0.00 35.87 3.66
6294 6839 7.874940 TCAGATAACCAGACAACAAGAATTTG 58.125 34.615 0.00 0.00 40.24 2.32
6313 6858 8.937835 TCTTCAGGTCCAATCATTTATCAGATA 58.062 33.333 0.00 0.00 0.00 1.98
6314 6859 7.809238 TCTTCAGGTCCAATCATTTATCAGAT 58.191 34.615 0.00 0.00 0.00 2.90
6334 6879 2.886523 CTGTGAATGCAACCCTTCTTCA 59.113 45.455 0.00 0.00 0.00 3.02
6338 6883 0.244721 GCCTGTGAATGCAACCCTTC 59.755 55.000 0.00 0.00 0.00 3.46
6376 6922 7.630026 CATTCAGCATTTGTACGCTAGATTAA 58.370 34.615 0.00 0.00 36.50 1.40
6381 6927 3.611517 GCATTCAGCATTTGTACGCTAG 58.388 45.455 0.00 0.00 44.79 3.42
6414 6960 0.677731 TGCCGAGAGAAAGCAATGGG 60.678 55.000 0.00 0.00 32.56 4.00
6471 7020 5.694816 TGTGTTAAACAGTTGAAGTGTGTG 58.305 37.500 6.40 0.00 30.99 3.82
6490 7039 3.181487 GCACCAACATCTTTTGACTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
6531 7080 3.819564 TCTGTTGTGTGTTAGCTCTGT 57.180 42.857 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.