Multiple sequence alignment - TraesCS5D01G132500

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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 TraesCS5D01G132500 chr5D 100.000 5167 0 0 1 5167 210987438 210992604 0.000000e+00 9542.0
1 TraesCS5D01G132500 chr5D 95.833 120 5 0 2626 2745 210989944 210990063 1.470000e-45 195.0
2 TraesCS5D01G132500 chr5D 95.833 120 5 0 2507 2626 210990063 210990182 1.470000e-45 195.0
3 TraesCS5D01G132500 chr5A 95.035 2417 72 10 924 3310 273447839 273450237 0.000000e+00 3755.0
4 TraesCS5D01G132500 chr5A 94.185 963 23 11 3745 4679 273452011 273452968 0.000000e+00 1437.0
5 TraesCS5D01G132500 chr5A 94.727 512 12 5 436 935 273447282 273447790 0.000000e+00 782.0
6 TraesCS5D01G132500 chr5A 97.778 405 6 1 3307 3711 273451211 273451612 0.000000e+00 695.0
7 TraesCS5D01G132500 chr5A 89.521 334 23 5 4840 5164 273453509 273453839 3.720000e-111 412.0
8 TraesCS5D01G132500 chr5A 97.500 120 3 0 2626 2745 273449432 273449551 6.780000e-49 206.0
9 TraesCS5D01G132500 chr5A 95.000 120 6 0 2507 2626 273449551 273449670 6.830000e-44 189.0
10 TraesCS5D01G132500 chr5B 95.235 1700 49 6 922 2598 224624511 224622821 0.000000e+00 2662.0
11 TraesCS5D01G132500 chr5B 95.802 1215 33 11 3763 4969 224620930 224619726 0.000000e+00 1945.0
12 TraesCS5D01G132500 chr5B 96.693 1028 25 3 2507 3532 224622538 224621518 0.000000e+00 1701.0
13 TraesCS5D01G132500 chr5B 90.402 646 23 13 304 935 224625179 224624559 0.000000e+00 813.0
14 TraesCS5D01G132500 chr5B 98.352 182 2 1 3530 3710 224621404 224621223 8.350000e-83 318.0
15 TraesCS5D01G132500 chr5B 97.987 149 3 0 2597 2745 224622567 224622419 5.130000e-65 259.0
16 TraesCS5D01G132500 chr5B 86.475 244 18 7 4936 5167 224619725 224619485 2.390000e-63 254.0
17 TraesCS5D01G132500 chr5B 90.000 180 16 2 1 178 224626281 224626102 1.120000e-56 231.0
18 TraesCS5D01G132500 chr5B 96.739 92 3 0 2626 2717 224622912 224622821 2.490000e-33 154.0
19 TraesCS5D01G132500 chr4D 78.421 190 29 7 4 182 341540526 341540714 4.230000e-21 113.0
20 TraesCS5D01G132500 chr4D 81.053 95 18 0 1207 1301 44205209 44205115 5.550000e-10 76.8
21 TraesCS5D01G132500 chr4B 83.158 95 16 0 1207 1301 63998055 63997961 2.560000e-13 87.9
22 TraesCS5D01G132500 chr4A 81.053 95 18 0 1207 1301 555746304 555746398 5.550000e-10 76.8
23 TraesCS5D01G132500 chr6B 75.676 148 33 3 1 147 661546701 661546846 2.580000e-08 71.3
24 TraesCS5D01G132500 chr3B 79.798 99 12 3 36 126 521801393 521801295 1.200000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G132500 chr5D 210987438 210992604 5166 False 3310.666667 9542 97.222000 1 5167 3 chr5D.!!$F1 5166
1 TraesCS5D01G132500 chr5A 273447282 273453839 6557 False 1068.000000 3755 94.820857 436 5164 7 chr5A.!!$F1 4728
2 TraesCS5D01G132500 chr5B 224619485 224626281 6796 True 926.333333 2662 94.187222 1 5167 9 chr5B.!!$R1 5166

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
185 188 0.179163 GGCACAAGAAACGCTATGGC 60.179 55.0 0.00 0.0 0.00 4.40 F
377 1202 0.323269 TTCGCCATGCCCATTTCAGA 60.323 50.0 0.00 0.0 0.00 3.27 F
1338 2241 0.464735 TGGGTGTGTAGTGTGGTTGC 60.465 55.0 0.00 0.0 0.00 4.17 F
2249 3175 2.096496 CACGAAGCACAATGGGATTCTC 59.904 50.0 11.86 0.0 0.00 2.87 F
3725 6248 0.251341 ATGGCTGACCCTGTTTGTCC 60.251 55.0 0.00 0.0 33.59 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1941 0.107800 AGATCGCAGCACTTGAGCAT 60.108 50.0 0.00 0.0 36.85 3.79 R
1654 2557 0.250295 CTCCACGGAAAACTGCCTCA 60.250 55.0 0.00 0.0 0.00 3.86 R
2840 4260 0.037419 ATTTGAACGCAACATGGCCC 60.037 50.0 0.00 0.0 32.79 5.80 R
3729 6252 0.182537 TGACTCAAGTTGTGGGGTGG 59.817 55.0 9.58 0.0 28.49 4.61 R
4931 8231 0.107410 TATTAGGGGTGTGCTTGCCG 60.107 55.0 0.00 0.0 0.00 5.69 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
31 32 1.227497 GCCGCCTCATCTCTCCAAG 60.227 63.158 0.00 0.00 0.00 3.61
32 33 1.227497 CCGCCTCATCTCTCCAAGC 60.227 63.158 0.00 0.00 0.00 4.01
37 39 2.903798 CCTCATCTCTCCAAGCAAGAC 58.096 52.381 0.00 0.00 0.00 3.01
39 41 3.260740 CTCATCTCTCCAAGCAAGACAC 58.739 50.000 0.00 0.00 0.00 3.67
89 92 2.815647 CGAAGCCCTCTTGTCGGC 60.816 66.667 0.00 0.00 46.09 5.54
130 133 2.681097 GCCTTCATGACCCTAAGACCAC 60.681 54.545 0.00 0.00 0.00 4.16
134 137 3.724478 TCATGACCCTAAGACCACAGAT 58.276 45.455 0.00 0.00 0.00 2.90
140 143 2.159226 CCCTAAGACCACAGATGACGAC 60.159 54.545 0.00 0.00 0.00 4.34
178 181 2.966309 GCGGGAGGCACAAGAAACG 61.966 63.158 0.00 0.00 42.87 3.60
179 182 2.954611 GGGAGGCACAAGAAACGC 59.045 61.111 0.00 0.00 0.00 4.84
180 183 1.600916 GGGAGGCACAAGAAACGCT 60.601 57.895 0.00 0.00 0.00 5.07
181 184 0.321298 GGGAGGCACAAGAAACGCTA 60.321 55.000 0.00 0.00 0.00 4.26
182 185 1.679032 GGGAGGCACAAGAAACGCTAT 60.679 52.381 0.00 0.00 0.00 2.97
183 186 1.398390 GGAGGCACAAGAAACGCTATG 59.602 52.381 0.00 0.00 0.00 2.23
184 187 1.398390 GAGGCACAAGAAACGCTATGG 59.602 52.381 0.00 0.00 0.00 2.74
185 188 0.179163 GGCACAAGAAACGCTATGGC 60.179 55.000 0.00 0.00 0.00 4.40
196 199 4.181010 CTATGGCGGCTGGGTGCT 62.181 66.667 11.43 0.00 42.39 4.40
197 200 4.175337 TATGGCGGCTGGGTGCTC 62.175 66.667 11.43 0.00 42.39 4.26
203 206 3.695606 GGCTGGGTGCTCAGTCGA 61.696 66.667 0.71 0.00 42.39 4.20
204 207 2.125753 GCTGGGTGCTCAGTCGAG 60.126 66.667 0.71 0.00 42.66 4.04
215 218 2.338500 CTCAGTCGAGCCAAAAGGTAC 58.662 52.381 0.00 0.00 31.00 3.34
217 220 0.963962 AGTCGAGCCAAAAGGTACGA 59.036 50.000 0.00 0.00 0.00 3.43
220 223 1.683790 CGAGCCAAAAGGTACGAGCG 61.684 60.000 0.00 0.00 0.00 5.03
231 234 1.670730 TACGAGCGTCCCGTGTGTA 60.671 57.895 0.00 0.00 40.76 2.90
245 248 7.148804 CGTCCCGTGTGTATATTGATATTCAAG 60.149 40.741 0.00 0.00 40.05 3.02
266 269 6.765989 TCAAGAATTAATATGCTACGTGCCTT 59.234 34.615 0.00 0.00 42.00 4.35
267 270 7.282224 TCAAGAATTAATATGCTACGTGCCTTT 59.718 33.333 0.00 0.00 42.00 3.11
268 271 8.556194 CAAGAATTAATATGCTACGTGCCTTTA 58.444 33.333 0.00 0.00 42.00 1.85
272 275 5.986004 AATATGCTACGTGCCTTTACTTC 57.014 39.130 0.00 0.00 42.00 3.01
276 656 4.885413 TGCTACGTGCCTTTACTTCTTTA 58.115 39.130 0.00 0.00 42.00 1.85
302 682 3.649096 TTGACGTCAACATGCCCG 58.351 55.556 26.53 0.00 0.00 6.13
306 686 1.908066 GACGTCAACATGCCCGGTTC 61.908 60.000 11.55 0.00 0.00 3.62
322 1147 5.508320 GCCCGGTTCAGATTTTCTTTTAACA 60.508 40.000 0.00 0.00 0.00 2.41
324 1149 6.238925 CCCGGTTCAGATTTTCTTTTAACACT 60.239 38.462 0.00 0.00 0.00 3.55
339 1164 8.332464 TCTTTTAACACTGTACAATCAAAGTCG 58.668 33.333 0.00 0.00 0.00 4.18
340 1165 6.533819 TTAACACTGTACAATCAAAGTCGG 57.466 37.500 0.00 0.00 0.00 4.79
348 1173 4.488126 ACAATCAAAGTCGGTTCACATG 57.512 40.909 0.00 0.00 0.00 3.21
373 1198 1.608918 TGGTTCGCCATGCCCATTT 60.609 52.632 0.00 0.00 43.56 2.32
377 1202 0.323269 TTCGCCATGCCCATTTCAGA 60.323 50.000 0.00 0.00 0.00 3.27
428 1254 9.133627 GAGAAATAGAAAATTTTCTTGACTGGC 57.866 33.333 32.37 17.74 44.70 4.85
502 1328 0.810031 ACGCACCCACGATAGCAATC 60.810 55.000 0.00 0.00 42.67 2.67
687 1526 4.504916 CCGCCTCGTCTGCCTCAG 62.505 72.222 0.00 0.00 0.00 3.35
859 1699 1.745320 CGATCCGTGGAGGGGTAAGG 61.745 65.000 0.00 0.00 41.52 2.69
863 1703 4.484872 GTGGAGGGGTAAGGGCGC 62.485 72.222 0.00 0.00 0.00 6.53
1042 1941 4.121669 GACGGCTCGCTGCTCTCA 62.122 66.667 0.00 0.00 42.39 3.27
1162 2061 6.500751 TCTCCAGTTTCTTACCTCCATTTACT 59.499 38.462 0.00 0.00 0.00 2.24
1294 2197 8.465999 GTGGTTGATGATGGTGTGATTAATAAA 58.534 33.333 0.00 0.00 0.00 1.40
1338 2241 0.464735 TGGGTGTGTAGTGTGGTTGC 60.465 55.000 0.00 0.00 0.00 4.17
1534 2437 7.060633 GTCCATGTTGTTTTGTTCGTGATATTC 59.939 37.037 0.00 0.00 0.00 1.75
1545 2448 4.297299 TCGTGATATTCGGTTGGTACTC 57.703 45.455 0.00 0.00 0.00 2.59
1654 2557 2.794103 TGCAGTATGAACATTGGCAGT 58.206 42.857 0.00 0.00 39.69 4.40
1693 2596 9.798994 CGTGGAGTTATCTAAAACACTATAAGT 57.201 33.333 0.00 0.00 0.00 2.24
1747 2650 4.037446 GTCACATGTGTTATGTGTTTGGGT 59.963 41.667 24.63 0.00 46.82 4.51
1828 2731 9.372369 CACTAGCTAACTTTTGAGTAGCTTTAT 57.628 33.333 9.49 0.00 43.10 1.40
1829 2732 9.589111 ACTAGCTAACTTTTGAGTAGCTTTATC 57.411 33.333 9.49 0.00 43.10 1.75
1830 2733 7.527084 AGCTAACTTTTGAGTAGCTTTATCG 57.473 36.000 0.00 0.00 40.80 2.92
2249 3175 2.096496 CACGAAGCACAATGGGATTCTC 59.904 50.000 11.86 0.00 0.00 2.87
2417 3344 5.246429 AGTCTAGTTTTTCCCTCTTCGATGT 59.754 40.000 0.00 0.00 0.00 3.06
2427 3354 4.695455 TCCCTCTTCGATGTGACAATTTTC 59.305 41.667 0.00 0.00 0.00 2.29
2460 3387 7.056006 TGGATCTTCAATTATTGCTGCTTAGA 58.944 34.615 0.00 0.00 0.00 2.10
2477 3404 8.538039 GCTGCTTAGAAAATGAATATGAAAAGC 58.462 33.333 0.00 0.00 36.90 3.51
2497 3424 2.938756 GCTAGCTGGCTGTTGACTTCAT 60.939 50.000 15.78 0.00 0.00 2.57
2520 3447 2.121786 GCAGATGCACACAAACTGTTG 58.878 47.619 0.00 0.00 41.59 3.33
2538 3465 7.525688 ACTGTTGTCATTGATATACTCAACG 57.474 36.000 9.59 7.75 46.37 4.10
2661 4081 8.713971 TGTTATCATTGATATACTCAACCCTGT 58.286 33.333 7.19 0.00 46.37 4.00
2684 4104 9.529325 CTGTAATTTAGACGAACTATCATTGGA 57.471 33.333 0.00 0.00 0.00 3.53
2790 4210 2.626149 GGGAGGGTGGTGTGTAGATACT 60.626 54.545 0.00 0.00 0.00 2.12
2809 4229 7.770662 AGATACTTATGGATCCCAGTCTTAGA 58.229 38.462 9.90 0.00 36.75 2.10
2840 4260 9.586435 TCATACACACTCATCTGTTATTACTTG 57.414 33.333 0.00 0.00 0.00 3.16
2858 4278 1.365633 GGGCCATGTTGCGTTCAAA 59.634 52.632 4.39 0.00 33.37 2.69
2931 4351 8.768957 TCAATCTCTTCTTGAGTTCTTGTATG 57.231 34.615 0.00 0.00 43.13 2.39
3004 4424 9.716531 CATCTGTTCTTCTAATCTTATGCCATA 57.283 33.333 0.00 0.00 0.00 2.74
3115 4542 6.128418 GCCTATTGTGAACTCTTTCTGTTCTC 60.128 42.308 7.89 5.30 42.86 2.87
3133 4560 8.721478 TCTGTTCTCTTGTATTTTGTTATGAGC 58.279 33.333 0.00 0.00 0.00 4.26
3227 4654 0.457443 TGTGGTGAGAGAGCTATGCG 59.543 55.000 0.00 0.00 0.00 4.73
3269 4696 2.159014 AGTTAACCGTGTGAAGCACTCA 60.159 45.455 0.88 0.00 45.57 3.41
3277 4704 4.440112 CCGTGTGAAGCACTCATACATAGA 60.440 45.833 13.55 0.00 44.25 1.98
3278 4705 5.102313 CGTGTGAAGCACTCATACATAGAA 58.898 41.667 13.55 0.00 44.25 2.10
3323 5729 8.390921 TCCTTCCATCTTAATGTTACTCCTTTT 58.609 33.333 0.00 0.00 0.00 2.27
3711 6234 4.780021 CCCATATCTAAGGTCTGTATGGCT 59.220 45.833 4.58 0.00 40.14 4.75
3712 6235 5.337894 CCCATATCTAAGGTCTGTATGGCTG 60.338 48.000 4.58 0.00 40.14 4.85
3713 6236 5.481824 CCATATCTAAGGTCTGTATGGCTGA 59.518 44.000 0.00 0.00 36.46 4.26
3714 6237 4.946478 ATCTAAGGTCTGTATGGCTGAC 57.054 45.455 0.00 0.00 42.90 3.51
3718 6241 3.768633 GTCTGTATGGCTGACCCTG 57.231 57.895 0.00 0.00 39.30 4.45
3719 6242 0.905357 GTCTGTATGGCTGACCCTGT 59.095 55.000 0.00 0.00 39.30 4.00
3720 6243 1.279271 GTCTGTATGGCTGACCCTGTT 59.721 52.381 0.00 0.00 39.30 3.16
3721 6244 1.985159 TCTGTATGGCTGACCCTGTTT 59.015 47.619 0.00 0.00 33.59 2.83
3722 6245 2.086869 CTGTATGGCTGACCCTGTTTG 58.913 52.381 0.00 0.00 33.59 2.93
3723 6246 1.423541 TGTATGGCTGACCCTGTTTGT 59.576 47.619 0.00 0.00 33.59 2.83
3724 6247 2.084546 GTATGGCTGACCCTGTTTGTC 58.915 52.381 0.00 0.00 33.59 3.18
3725 6248 0.251341 ATGGCTGACCCTGTTTGTCC 60.251 55.000 0.00 0.00 33.59 4.02
3726 6249 1.603739 GGCTGACCCTGTTTGTCCC 60.604 63.158 0.00 0.00 31.60 4.46
3727 6250 1.603739 GCTGACCCTGTTTGTCCCC 60.604 63.158 0.00 0.00 31.60 4.81
3728 6251 1.074951 CTGACCCTGTTTGTCCCCC 59.925 63.158 0.00 0.00 31.60 5.40
3743 6266 2.203625 CCCCCACCCCACAACTTG 60.204 66.667 0.00 0.00 0.00 3.16
3802 6690 2.354704 CCGTGGGATACATGTGTGAAGT 60.355 50.000 9.11 0.00 34.14 3.01
4285 7177 2.945668 GGCGATATCCTTCTTGTGCTTT 59.054 45.455 0.00 0.00 0.00 3.51
4418 7310 7.985184 TGTTCCTTATGTATAAACGCTCTTCAT 59.015 33.333 0.00 0.00 0.00 2.57
4431 7342 4.585162 ACGCTCTTCATATACCTAGTTGCT 59.415 41.667 0.00 0.00 0.00 3.91
4537 7449 1.226888 GTACTCCCGTGCCATCGTC 60.227 63.158 0.00 0.00 0.00 4.20
4545 7457 1.434555 CGTGCCATCGTCCAGTTTTA 58.565 50.000 0.00 0.00 0.00 1.52
4672 7592 9.979270 TTTTACTTTACACATTTGCATTGTTTG 57.021 25.926 0.31 0.00 0.00 2.93
4707 7705 1.379044 GCAAGTGCCTGCATAGGGT 60.379 57.895 0.00 0.00 44.75 4.34
4723 7721 2.031120 AGGGTGTTTGTGTTGACATGG 58.969 47.619 0.00 0.00 30.13 3.66
4740 7739 3.009473 ACATGGTTGCTCTTCCTATGTGT 59.991 43.478 0.00 0.00 30.54 3.72
4784 7783 4.469657 TGTTTCTTGGTCTTAACATGGCT 58.530 39.130 0.00 0.00 0.00 4.75
4862 8162 2.931512 GAGCATCTATAGCCGGACTC 57.068 55.000 5.05 0.00 0.00 3.36
4865 8165 1.889829 GCATCTATAGCCGGACTCTGT 59.110 52.381 5.05 0.00 0.00 3.41
4869 8169 5.509163 GCATCTATAGCCGGACTCTGTAAAA 60.509 44.000 5.05 0.00 0.00 1.52
4872 8172 6.069331 TCTATAGCCGGACTCTGTAAAATCT 58.931 40.000 5.05 0.00 0.00 2.40
4888 8188 0.252197 ATCTGCACCCCTAAACGTCC 59.748 55.000 0.00 0.00 0.00 4.79
4891 8191 2.435410 CACCCCTAAACGTCCGCC 60.435 66.667 0.00 0.00 0.00 6.13
4928 8228 4.292186 AGCTTGCTTCTCATTTGTCCTA 57.708 40.909 0.00 0.00 0.00 2.94
4930 8230 4.006319 GCTTGCTTCTCATTTGTCCTACT 58.994 43.478 0.00 0.00 0.00 2.57
4931 8231 4.094146 GCTTGCTTCTCATTTGTCCTACTC 59.906 45.833 0.00 0.00 0.00 2.59
4932 8232 3.849911 TGCTTCTCATTTGTCCTACTCG 58.150 45.455 0.00 0.00 0.00 4.18
4947 8277 2.925706 TCGGCAAGCACACCCCTA 60.926 61.111 0.00 0.00 0.00 3.53
5040 8382 7.424227 AAATAAAGCACAATTCAACACATGG 57.576 32.000 0.00 0.00 0.00 3.66
5061 8403 8.723311 ACATGGCAAAAGAAAATATGACAATTG 58.277 29.630 3.24 3.24 33.86 2.32
5091 8433 7.136772 ACATGCGATACAAGAATGAATCATTG 58.863 34.615 13.82 3.34 33.90 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.422399 TGAGTTTATTAAGGTTTGTGTCTTGC 58.578 34.615 0.00 0.00 0.00 4.01
32 33 9.796120 TTTGAGTTTATTAAGGTTTGTGTCTTG 57.204 29.630 0.00 0.00 0.00 3.02
130 133 0.027716 CCGGTCTACGTCGTCATCTG 59.972 60.000 0.00 0.00 42.24 2.90
134 137 3.792047 CGCCGGTCTACGTCGTCA 61.792 66.667 0.00 0.00 39.36 4.35
160 163 2.954611 GTTTCTTGTGCCTCCCGC 59.045 61.111 0.00 0.00 38.31 6.13
187 190 2.125753 CTCGACTGAGCACCCAGC 60.126 66.667 0.00 0.00 46.19 4.85
195 198 2.338500 GTACCTTTTGGCTCGACTGAG 58.662 52.381 0.00 0.00 45.59 3.35
196 199 1.336517 CGTACCTTTTGGCTCGACTGA 60.337 52.381 0.00 0.00 45.59 3.41
197 200 1.068474 CGTACCTTTTGGCTCGACTG 58.932 55.000 0.00 0.00 45.59 3.51
198 201 0.963962 TCGTACCTTTTGGCTCGACT 59.036 50.000 0.00 0.00 45.59 4.18
199 202 1.347320 CTCGTACCTTTTGGCTCGAC 58.653 55.000 0.00 0.00 45.59 4.20
200 203 0.389426 GCTCGTACCTTTTGGCTCGA 60.389 55.000 0.00 0.00 45.59 4.04
201 204 1.683790 CGCTCGTACCTTTTGGCTCG 61.684 60.000 0.00 0.00 45.59 5.03
202 205 0.669625 ACGCTCGTACCTTTTGGCTC 60.670 55.000 0.00 0.00 45.59 4.70
203 206 0.669625 GACGCTCGTACCTTTTGGCT 60.670 55.000 0.00 0.00 45.59 4.75
204 207 1.632948 GGACGCTCGTACCTTTTGGC 61.633 60.000 0.00 0.00 45.59 4.52
220 223 7.870954 TCTTGAATATCAATATACACACGGGAC 59.129 37.037 0.00 0.00 35.59 4.46
260 263 6.148976 ACTCGGAAATAAAGAAGTAAAGGCAC 59.851 38.462 0.00 0.00 0.00 5.01
261 264 6.235664 ACTCGGAAATAAAGAAGTAAAGGCA 58.764 36.000 0.00 0.00 0.00 4.75
266 269 6.925165 ACGTCAACTCGGAAATAAAGAAGTAA 59.075 34.615 0.00 0.00 34.94 2.24
267 270 6.449698 ACGTCAACTCGGAAATAAAGAAGTA 58.550 36.000 0.00 0.00 34.94 2.24
268 271 5.295152 ACGTCAACTCGGAAATAAAGAAGT 58.705 37.500 0.00 0.00 34.94 3.01
272 275 5.585500 TTGACGTCAACTCGGAAATAAAG 57.415 39.130 26.53 0.00 34.94 1.85
300 680 6.636850 CAGTGTTAAAAGAAAATCTGAACCGG 59.363 38.462 0.00 0.00 0.00 5.28
302 682 9.447040 GTACAGTGTTAAAAGAAAATCTGAACC 57.553 33.333 0.00 0.00 0.00 3.62
322 1147 4.510340 GTGAACCGACTTTGATTGTACAGT 59.490 41.667 0.00 0.00 0.00 3.55
324 1149 4.443621 TGTGAACCGACTTTGATTGTACA 58.556 39.130 0.00 0.00 0.00 2.90
336 1161 0.889186 AACCTGGCATGTGAACCGAC 60.889 55.000 0.00 0.00 0.00 4.79
339 1164 0.827507 ACCAACCTGGCATGTGAACC 60.828 55.000 0.00 0.00 42.67 3.62
340 1165 1.000274 GAACCAACCTGGCATGTGAAC 60.000 52.381 0.00 0.00 42.67 3.18
402 1228 9.133627 GCCAGTCAAGAAAATTTTCTATTTCTC 57.866 33.333 28.95 17.20 46.22 2.87
403 1229 8.641541 TGCCAGTCAAGAAAATTTTCTATTTCT 58.358 29.630 28.95 21.11 46.22 2.52
404 1230 8.816640 TGCCAGTCAAGAAAATTTTCTATTTC 57.183 30.769 28.95 19.66 46.22 2.17
405 1231 9.211485 CATGCCAGTCAAGAAAATTTTCTATTT 57.789 29.630 28.95 14.42 46.22 1.40
407 1233 6.815142 GCATGCCAGTCAAGAAAATTTTCTAT 59.185 34.615 28.95 17.93 46.22 1.98
408 1234 6.015180 AGCATGCCAGTCAAGAAAATTTTCTA 60.015 34.615 28.95 15.08 46.22 2.10
410 1236 4.992951 AGCATGCCAGTCAAGAAAATTTTC 59.007 37.500 21.00 21.00 37.45 2.29
411 1237 4.964593 AGCATGCCAGTCAAGAAAATTTT 58.035 34.783 15.66 2.28 0.00 1.82
412 1238 4.612264 AGCATGCCAGTCAAGAAAATTT 57.388 36.364 15.66 0.00 0.00 1.82
413 1239 4.159135 CCTAGCATGCCAGTCAAGAAAATT 59.841 41.667 15.66 0.00 0.00 1.82
414 1240 3.698040 CCTAGCATGCCAGTCAAGAAAAT 59.302 43.478 15.66 0.00 0.00 1.82
415 1241 3.084039 CCTAGCATGCCAGTCAAGAAAA 58.916 45.455 15.66 0.00 0.00 2.29
416 1242 2.040278 ACCTAGCATGCCAGTCAAGAAA 59.960 45.455 15.66 0.00 0.00 2.52
417 1243 1.630369 ACCTAGCATGCCAGTCAAGAA 59.370 47.619 15.66 0.00 0.00 2.52
418 1244 1.065926 CACCTAGCATGCCAGTCAAGA 60.066 52.381 15.66 0.00 0.00 3.02
419 1245 1.376543 CACCTAGCATGCCAGTCAAG 58.623 55.000 15.66 0.00 0.00 3.02
420 1246 0.035152 CCACCTAGCATGCCAGTCAA 60.035 55.000 15.66 0.00 0.00 3.18
421 1247 0.909133 TCCACCTAGCATGCCAGTCA 60.909 55.000 15.66 0.00 0.00 3.41
422 1248 0.179062 CTCCACCTAGCATGCCAGTC 60.179 60.000 15.66 0.00 0.00 3.51
423 1249 1.910722 CTCCACCTAGCATGCCAGT 59.089 57.895 15.66 6.55 0.00 4.00
424 1250 1.525535 GCTCCACCTAGCATGCCAG 60.526 63.158 15.66 10.65 42.30 4.85
425 1251 2.591753 GCTCCACCTAGCATGCCA 59.408 61.111 15.66 0.00 42.30 4.92
426 1252 2.203266 GGCTCCACCTAGCATGCC 60.203 66.667 15.66 0.00 44.64 4.40
427 1253 2.590007 CGGCTCCACCTAGCATGC 60.590 66.667 10.51 10.51 44.64 4.06
428 1254 1.068753 CTCGGCTCCACCTAGCATG 59.931 63.158 0.00 0.00 44.64 4.06
522 1361 0.895530 TCCGCTCTTCCTGTCGATTT 59.104 50.000 0.00 0.00 0.00 2.17
863 1703 3.905678 AATCGCGCTCTCCTCCGG 61.906 66.667 5.56 0.00 0.00 5.14
1042 1941 0.107800 AGATCGCAGCACTTGAGCAT 60.108 50.000 0.00 0.00 36.85 3.79
1162 2061 3.258372 GGTACGAGATATTGGCTGATCCA 59.742 47.826 0.00 0.00 44.85 3.41
1294 2197 6.335777 ACGAAATCGGCATAACTTACTAACT 58.664 36.000 7.81 0.00 44.95 2.24
1306 2209 0.608035 ACACCCAACGAAATCGGCAT 60.608 50.000 7.81 0.00 44.95 4.40
1338 2241 1.901591 ATGGGAGTGCAAGTTGTCAG 58.098 50.000 4.48 0.00 0.00 3.51
1348 2251 2.368221 AGATTGAGCTCTATGGGAGTGC 59.632 50.000 15.60 0.00 43.62 4.40
1534 2437 5.347012 ACAAATAAAACGAGTACCAACCG 57.653 39.130 0.00 0.00 0.00 4.44
1545 2448 5.309652 AGCGCAAAAGAACAAATAAAACG 57.690 34.783 11.47 0.00 0.00 3.60
1654 2557 0.250295 CTCCACGGAAAACTGCCTCA 60.250 55.000 0.00 0.00 0.00 3.86
1693 2596 5.398603 TGACCAAAACTTCAAAGCTCAAA 57.601 34.783 0.00 0.00 0.00 2.69
1747 2650 1.545428 GGAGACATGTGGGAGTGCAAA 60.545 52.381 1.15 0.00 0.00 3.68
1810 2713 6.704493 TGACACGATAAAGCTACTCAAAAGTT 59.296 34.615 0.00 0.00 36.92 2.66
1828 2731 3.194861 GCTGCCATAACTTATGACACGA 58.805 45.455 9.97 0.00 38.45 4.35
1829 2732 2.287915 GGCTGCCATAACTTATGACACG 59.712 50.000 15.17 1.76 38.45 4.49
1830 2733 3.545703 AGGCTGCCATAACTTATGACAC 58.454 45.455 22.65 1.33 38.45 3.67
2249 3175 4.201428 GCTCGCACAAATTCTTCAAATTCG 60.201 41.667 0.00 0.00 0.00 3.34
2460 3387 6.982724 GCCAGCTAGCTTTTCATATTCATTTT 59.017 34.615 16.46 0.00 0.00 1.82
2477 3404 2.462456 TGAAGTCAACAGCCAGCTAG 57.538 50.000 0.00 0.00 0.00 3.42
2497 3424 1.067364 CAGTTTGTGTGCATCTGCCAA 59.933 47.619 0.00 0.00 41.18 4.52
2538 3465 5.718649 TGATAGTTCGTCTAAATTGCAGC 57.281 39.130 0.00 0.00 31.94 5.25
2684 4104 2.440409 CAAGCTGCAACCACTAGGATT 58.560 47.619 1.02 0.00 38.69 3.01
2790 4210 5.529289 ACTGTCTAAGACTGGGATCCATAA 58.471 41.667 15.23 0.00 36.14 1.90
2809 4229 5.474578 ACAGATGAGTGTGTATGAACTGT 57.525 39.130 0.00 0.00 28.73 3.55
2840 4260 0.037419 ATTTGAACGCAACATGGCCC 60.037 50.000 0.00 0.00 32.79 5.80
2858 4278 5.467735 GCATGCAAGAAACCAAAGAAGAAAT 59.532 36.000 14.21 0.00 0.00 2.17
2890 4310 3.441572 AGATTGAGACAAAAGGGCATTCG 59.558 43.478 0.00 0.00 0.00 3.34
2931 4351 1.334556 TGACCGATGCAAATGCTATGC 59.665 47.619 6.97 2.57 44.08 3.14
2941 4361 3.544684 AGCATAAATTCTGACCGATGCA 58.455 40.909 7.34 0.00 41.65 3.96
3133 4560 8.251026 TGACAGTATGAACAAATGGACTACTAG 58.749 37.037 0.00 0.00 39.69 2.57
3227 4654 6.648725 ACTCGATTTAGTTATTGCTGACAC 57.351 37.500 0.00 0.00 0.00 3.67
3269 4696 4.406003 AGAAGGGCGTCAGTTTCTATGTAT 59.594 41.667 0.00 0.00 0.00 2.29
3277 4704 0.465460 TTGCAGAAGGGCGTCAGTTT 60.465 50.000 0.00 0.00 36.28 2.66
3278 4705 0.250901 ATTGCAGAAGGGCGTCAGTT 60.251 50.000 0.00 0.00 36.28 3.16
3711 6234 3.257133 GGGGGACAAACAGGGTCA 58.743 61.111 0.00 0.00 37.00 4.02
3726 6249 2.203625 CAAGTTGTGGGGTGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
3727 6250 1.228552 CTCAAGTTGTGGGGTGGGG 60.229 63.158 2.11 0.00 0.00 4.96
3728 6251 0.537371 GACTCAAGTTGTGGGGTGGG 60.537 60.000 9.58 0.00 28.49 4.61
3729 6252 0.182537 TGACTCAAGTTGTGGGGTGG 59.817 55.000 9.58 0.00 28.49 4.61
3730 6253 1.949525 CTTGACTCAAGTTGTGGGGTG 59.050 52.381 10.27 0.00 36.79 4.61
3731 6254 2.348411 CTTGACTCAAGTTGTGGGGT 57.652 50.000 10.27 2.38 36.79 4.95
3740 6263 6.925718 TGATCAGTAAGACAACTTGACTCAAG 59.074 38.462 16.01 16.01 45.85 3.02
3741 6264 6.816136 TGATCAGTAAGACAACTTGACTCAA 58.184 36.000 0.00 0.00 37.53 3.02
3742 6265 6.040955 ACTGATCAGTAAGACAACTTGACTCA 59.959 38.462 26.87 0.00 40.43 3.41
3743 6266 6.451393 ACTGATCAGTAAGACAACTTGACTC 58.549 40.000 26.87 0.00 40.43 3.36
3802 6690 7.254898 CGATCCTTAAGAATTTAGCATGCTGAA 60.255 37.037 30.42 27.58 0.00 3.02
4097 6989 6.726379 TGTGGTAATATCCCTGTTGATGAAA 58.274 36.000 0.00 0.00 0.00 2.69
4418 7310 3.889538 ACTCGCATGAGCAACTAGGTATA 59.110 43.478 0.00 0.00 46.69 1.47
4431 7342 7.227087 CTGATTATCAGTTGCTACTCGCATGA 61.227 42.308 13.65 0.00 41.17 3.07
4480 7391 6.697019 AGAACAACCAAATGAATGAACGAAAG 59.303 34.615 0.00 0.00 0.00 2.62
4537 7449 2.098117 GCTATGCAGCCACTAAAACTGG 59.902 50.000 0.00 0.00 42.37 4.00
4672 7592 3.056313 GCTTCGGACAAGGCATGCC 62.056 63.158 30.12 30.12 0.00 4.40
4707 7705 2.495270 AGCAACCATGTCAACACAAACA 59.505 40.909 0.00 0.00 35.64 2.83
4723 7721 2.744202 CACCACACATAGGAAGAGCAAC 59.256 50.000 0.00 0.00 0.00 4.17
4740 7739 3.686227 AAGGATGGGCAATTATCACCA 57.314 42.857 0.00 0.00 37.41 4.17
4784 7783 2.222886 CGTAACCAACCATGACCAACA 58.777 47.619 0.00 0.00 0.00 3.33
4818 7817 8.304596 TCTAAGGTTGACTTAAGATGTACACAG 58.695 37.037 10.09 0.00 40.97 3.66
4862 8162 4.142687 CGTTTAGGGGTGCAGATTTTACAG 60.143 45.833 0.00 0.00 0.00 2.74
4865 8165 4.004982 GACGTTTAGGGGTGCAGATTTTA 58.995 43.478 0.00 0.00 0.00 1.52
4869 8169 0.252197 GGACGTTTAGGGGTGCAGAT 59.748 55.000 0.00 0.00 0.00 2.90
4872 8172 2.344500 CGGACGTTTAGGGGTGCA 59.656 61.111 0.00 0.00 0.00 4.57
4891 8191 2.417516 CTATCTGGGGACACGCCG 59.582 66.667 0.00 0.00 39.47 6.46
4903 8203 4.880696 GGACAAATGAGAAGCAAGCTATCT 59.119 41.667 0.00 0.91 0.00 1.98
4928 8228 4.643387 GGGGTGTGCTTGCCGAGT 62.643 66.667 0.00 0.00 0.00 4.18
4930 8230 1.847798 ATTAGGGGTGTGCTTGCCGA 61.848 55.000 0.00 0.00 0.00 5.54
4931 8231 0.107410 TATTAGGGGTGTGCTTGCCG 60.107 55.000 0.00 0.00 0.00 5.69
4932 8232 2.362077 CAATATTAGGGGTGTGCTTGCC 59.638 50.000 0.00 0.00 0.00 4.52
4947 8277 6.156602 TGCATGGATTCAAGGGTTTCAATATT 59.843 34.615 0.00 0.00 0.00 1.28
5061 8403 9.322776 GATTCATTCTTGTATCGCATGTTTATC 57.677 33.333 0.00 0.00 0.00 1.75
5071 8413 6.038603 ACACCCAATGATTCATTCTTGTATCG 59.961 38.462 8.95 0.00 33.61 2.92


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

AutoCloner maintained by Alex Coulton.