Multiple sequence alignment - TraesCS5D01G209700

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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 TraesCS5D01G209700 chr5D 100.000 3766 0 0 1 3766 317454671 317450906 0.000000e+00 6955.0
1 TraesCS5D01G209700 chr5D 84.733 131 20 0 26 156 256007308 256007178 8.490000e-27 132.0
2 TraesCS5D01G209700 chr5D 98.148 54 1 0 209 262 317452230 317452283 1.110000e-15 95.3
3 TraesCS5D01G209700 chr5D 93.651 63 4 0 2380 2442 317454401 317454463 1.110000e-15 95.3
4 TraesCS5D01G209700 chr5B 93.733 2601 94 18 712 3253 367213598 367211008 0.000000e+00 3836.0
5 TraesCS5D01G209700 chr5B 93.359 512 22 3 3233 3743 367210977 367210477 0.000000e+00 747.0
6 TraesCS5D01G209700 chr5B 87.363 182 17 3 275 450 367213774 367213593 1.770000e-48 204.0
7 TraesCS5D01G209700 chr5B 98.214 56 1 0 210 265 367211837 367211892 8.610000e-17 99.0
8 TraesCS5D01G209700 chr5A 95.831 1799 47 8 1976 3766 412103915 412102137 0.000000e+00 2881.0
9 TraesCS5D01G209700 chr5A 93.700 1238 40 15 712 1919 412105146 412103917 0.000000e+00 1820.0
10 TraesCS5D01G209700 chr5A 87.719 171 14 2 26 195 412105953 412105789 3.840000e-45 193.0
11 TraesCS5D01G209700 chr5A 92.000 100 4 3 354 453 412105236 412105141 1.820000e-28 137.0
12 TraesCS5D01G209700 chr5A 98.246 57 1 0 209 265 412103450 412103506 2.390000e-17 100.0
13 TraesCS5D01G209700 chr1B 94.737 266 11 3 447 710 211479123 211478859 9.740000e-111 411.0
14 TraesCS5D01G209700 chr7A 94.697 264 13 1 451 713 44210559 44210822 3.500000e-110 409.0
15 TraesCS5D01G209700 chr7A 81.675 191 28 6 10 195 164091791 164091979 6.520000e-33 152.0
16 TraesCS5D01G209700 chr7A 79.330 179 25 9 26 195 610072834 610072659 8.550000e-22 115.0
17 TraesCS5D01G209700 chr1D 94.340 265 13 2 451 713 97740151 97740415 4.530000e-109 405.0
18 TraesCS5D01G209700 chr4D 94.318 264 14 1 451 713 479154485 479154222 1.630000e-108 403.0
19 TraesCS5D01G209700 chr4D 85.075 201 26 4 1636 1834 390598131 390598329 6.380000e-48 202.0
20 TraesCS5D01G209700 chr3D 94.656 262 11 3 452 711 447584884 447585144 1.630000e-108 403.0
21 TraesCS5D01G209700 chr3B 93.985 266 14 2 449 712 507455407 507455142 5.860000e-108 401.0
22 TraesCS5D01G209700 chr2B 93.985 266 14 2 449 712 245947960 245948225 5.860000e-108 401.0
23 TraesCS5D01G209700 chr2B 93.680 269 13 4 447 713 357919822 357919556 2.110000e-107 399.0
24 TraesCS5D01G209700 chr6A 92.989 271 17 2 452 720 608292180 608292450 9.800000e-106 394.0
25 TraesCS5D01G209700 chr6A 85.470 234 28 6 1621 1850 491027825 491028056 4.860000e-59 239.0
26 TraesCS5D01G209700 chr6A 83.770 191 29 2 1642 1831 56134606 56134795 2.990000e-41 180.0
27 TraesCS5D01G209700 chr6B 85.043 234 29 6 1621 1850 527043547 527043778 2.260000e-57 233.0
28 TraesCS5D01G209700 chr4B 86.070 201 24 4 1636 1834 480590889 480591087 2.950000e-51 213.0
29 TraesCS5D01G209700 chr4B 84.733 131 20 0 26 156 25963655 25963525 8.490000e-27 132.0
30 TraesCS5D01G209700 chr4A 86.070 201 24 4 1636 1834 72294412 72294610 2.950000e-51 213.0
31 TraesCS5D01G209700 chr4A 81.714 175 28 4 23 195 200222442 200222614 3.920000e-30 143.0
32 TraesCS5D01G209700 chrUn 83.770 191 29 2 1642 1831 20367270 20367459 2.990000e-41 180.0
33 TraesCS5D01G209700 chr3A 85.496 131 19 0 26 156 154735513 154735643 1.820000e-28 137.0
34 TraesCS5D01G209700 chr2A 81.564 179 22 9 26 195 728019794 728019970 1.820000e-28 137.0
35 TraesCS5D01G209700 chr2A 79.330 179 27 8 26 195 763162392 763162215 2.380000e-22 117.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G209700 chr5D 317450906 317454671 3765 True 6955.000000 6955 100.0000 1 3766 1 chr5D.!!$R2 3765
1 TraesCS5D01G209700 chr5B 367210477 367213774 3297 True 1595.666667 3836 91.4850 275 3743 3 chr5B.!!$R1 3468
2 TraesCS5D01G209700 chr5A 412102137 412105953 3816 True 1257.750000 2881 92.3125 26 3766 4 chr5A.!!$R1 3740

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
224 226 0.039256 TTTCGGCGCGTACTTGTAGT 60.039 50.0 8.43 0.0 0.00 2.73 F
949 1431 0.107897 AAATCGCACCTATCACGGCA 60.108 50.0 0.00 0.0 0.00 5.69 F
988 1474 0.393673 CCGAGCTCAGAGTGGAGAGA 60.394 60.0 15.40 0.0 37.05 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 2066 0.673333 TGGTGGTAAGATGCACAGCG 60.673 55.000 0.00 0.0 34.32 5.18 R
2639 3152 2.126307 CACTCTGACAGGGCGACG 60.126 66.667 0.98 0.0 0.00 5.12 R
2831 3344 2.417516 CCGCCTCTGTACATCCCG 59.582 66.667 0.00 0.0 0.00 5.14 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
23 24 6.239217 TCCATGCAGTATGTTCTATGAAGT 57.761 37.500 0.00 0.00 39.31 3.01
24 25 6.653020 TCCATGCAGTATGTTCTATGAAGTT 58.347 36.000 0.00 0.00 39.31 2.66
181 183 0.766131 TTCTTTAAGGCGGACCACCA 59.234 50.000 0.32 0.00 39.06 4.17
195 197 2.557924 GACCACCATGTTCTCAAATGCA 59.442 45.455 0.00 0.00 0.00 3.96
197 199 2.821378 CCACCATGTTCTCAAATGCAGA 59.179 45.455 0.00 0.00 0.00 4.26
198 200 3.256383 CCACCATGTTCTCAAATGCAGAA 59.744 43.478 0.00 0.00 0.00 3.02
199 201 4.262121 CCACCATGTTCTCAAATGCAGAAA 60.262 41.667 0.00 0.00 31.60 2.52
200 202 5.291178 CACCATGTTCTCAAATGCAGAAAA 58.709 37.500 0.00 0.00 31.60 2.29
201 203 5.929992 CACCATGTTCTCAAATGCAGAAAAT 59.070 36.000 0.00 0.00 31.60 1.82
202 204 7.092079 CACCATGTTCTCAAATGCAGAAAATA 58.908 34.615 0.00 0.00 31.60 1.40
203 205 7.599621 CACCATGTTCTCAAATGCAGAAAATAA 59.400 33.333 0.00 0.00 31.60 1.40
204 206 8.149647 ACCATGTTCTCAAATGCAGAAAATAAA 58.850 29.630 0.00 0.00 31.60 1.40
205 207 9.158233 CCATGTTCTCAAATGCAGAAAATAAAT 57.842 29.630 0.00 0.00 31.60 1.40
217 219 4.648754 GAAAATAAATTTCGGCGCGTAC 57.351 40.909 8.43 0.00 38.21 3.67
218 220 4.336932 GAAAATAAATTTCGGCGCGTACT 58.663 39.130 8.43 0.00 38.21 2.73
219 221 4.345271 AAATAAATTTCGGCGCGTACTT 57.655 36.364 8.43 0.00 0.00 2.24
220 222 2.791417 TAAATTTCGGCGCGTACTTG 57.209 45.000 8.43 0.00 0.00 3.16
221 223 0.869730 AAATTTCGGCGCGTACTTGT 59.130 45.000 8.43 0.00 0.00 3.16
222 224 1.712401 AATTTCGGCGCGTACTTGTA 58.288 45.000 8.43 0.00 0.00 2.41
223 225 1.274596 ATTTCGGCGCGTACTTGTAG 58.725 50.000 8.43 0.00 0.00 2.74
224 226 0.039256 TTTCGGCGCGTACTTGTAGT 60.039 50.000 8.43 0.00 0.00 2.73
225 227 0.039256 TTCGGCGCGTACTTGTAGTT 60.039 50.000 8.43 0.00 0.00 2.24
226 228 0.730155 TCGGCGCGTACTTGTAGTTG 60.730 55.000 8.43 0.00 0.00 3.16
227 229 0.730155 CGGCGCGTACTTGTAGTTGA 60.730 55.000 8.43 0.00 0.00 3.18
228 230 0.712222 GGCGCGTACTTGTAGTTGAC 59.288 55.000 8.43 0.00 0.00 3.18
229 231 0.712222 GCGCGTACTTGTAGTTGACC 59.288 55.000 8.43 0.00 0.00 4.02
230 232 1.343506 CGCGTACTTGTAGTTGACCC 58.656 55.000 0.00 0.00 0.00 4.46
231 233 1.068055 CGCGTACTTGTAGTTGACCCT 60.068 52.381 0.00 0.00 0.00 4.34
232 234 2.334838 GCGTACTTGTAGTTGACCCTG 58.665 52.381 0.00 0.00 0.00 4.45
233 235 2.288640 GCGTACTTGTAGTTGACCCTGT 60.289 50.000 0.00 0.00 0.00 4.00
234 236 3.057315 GCGTACTTGTAGTTGACCCTGTA 60.057 47.826 0.00 0.00 0.00 2.74
235 237 4.730657 CGTACTTGTAGTTGACCCTGTAG 58.269 47.826 0.00 0.00 0.00 2.74
236 238 3.679824 ACTTGTAGTTGACCCTGTAGC 57.320 47.619 0.00 0.00 0.00 3.58
237 239 2.029290 ACTTGTAGTTGACCCTGTAGCG 60.029 50.000 0.00 0.00 0.00 4.26
238 240 0.892755 TGTAGTTGACCCTGTAGCGG 59.107 55.000 0.00 0.00 0.00 5.52
239 241 0.459759 GTAGTTGACCCTGTAGCGGC 60.460 60.000 0.00 0.00 0.00 6.53
240 242 1.610554 TAGTTGACCCTGTAGCGGCC 61.611 60.000 0.00 0.00 0.00 6.13
241 243 4.077184 TTGACCCTGTAGCGGCCG 62.077 66.667 24.05 24.05 0.00 6.13
278 280 3.933048 GAGCCCTGCCACTGTGCAT 62.933 63.158 1.29 0.00 41.16 3.96
289 455 4.082841 TGCCACTGTGCATACATGTAAAAG 60.083 41.667 10.14 0.58 36.04 2.27
325 491 9.796120 TTAACGTGTTTGATTTTTCTCAGAAAT 57.204 25.926 0.00 0.00 0.00 2.17
349 515 5.731599 TTTTAAACCAGACGCGAAGTTTA 57.268 34.783 15.93 16.80 34.46 2.01
350 516 5.731599 TTTAAACCAGACGCGAAGTTTAA 57.268 34.783 23.09 23.09 40.84 1.52
352 518 4.619437 AAACCAGACGCGAAGTTTAAAA 57.381 36.364 15.93 0.00 30.94 1.52
353 519 4.619437 AACCAGACGCGAAGTTTAAAAA 57.381 36.364 15.93 0.00 0.00 1.94
450 913 9.893305 ACCACTACGATTTTCATTTCTTTTTAG 57.107 29.630 0.00 0.00 0.00 1.85
457 920 9.556030 CGATTTTCATTTCTTTTTAGTACTCCC 57.444 33.333 0.00 0.00 0.00 4.30
461 924 7.324388 TCATTTCTTTTTAGTACTCCCTCCA 57.676 36.000 0.00 0.00 0.00 3.86
462 925 7.928873 TCATTTCTTTTTAGTACTCCCTCCAT 58.071 34.615 0.00 0.00 0.00 3.41
463 926 8.390921 TCATTTCTTTTTAGTACTCCCTCCATT 58.609 33.333 0.00 0.00 0.00 3.16
464 927 9.025041 CATTTCTTTTTAGTACTCCCTCCATTT 57.975 33.333 0.00 0.00 0.00 2.32
465 928 9.601810 ATTTCTTTTTAGTACTCCCTCCATTTT 57.398 29.630 0.00 0.00 0.00 1.82
466 929 9.429109 TTTCTTTTTAGTACTCCCTCCATTTTT 57.571 29.630 0.00 0.00 0.00 1.94
491 954 9.959749 TTTTTAATCCGCATATAAGATTTGGTC 57.040 29.630 0.00 0.00 32.64 4.02
492 955 8.684386 TTTAATCCGCATATAAGATTTGGTCA 57.316 30.769 0.00 0.00 32.64 4.02
493 956 8.684386 TTAATCCGCATATAAGATTTGGTCAA 57.316 30.769 0.00 0.00 32.64 3.18
494 957 7.581213 AATCCGCATATAAGATTTGGTCAAA 57.419 32.000 0.00 0.00 34.46 2.69
495 958 7.581213 ATCCGCATATAAGATTTGGTCAAAA 57.419 32.000 0.00 0.00 33.56 2.44
496 959 7.581213 TCCGCATATAAGATTTGGTCAAAAT 57.419 32.000 0.00 0.00 41.33 1.82
622 1085 9.850198 TTATTGATTTCATAGTGTGGATGATGA 57.150 29.630 0.00 0.00 33.41 2.92
623 1086 8.935614 ATTGATTTCATAGTGTGGATGATGAT 57.064 30.769 0.00 0.00 33.41 2.45
626 1089 9.662947 TGATTTCATAGTGTGGATGATGATATC 57.337 33.333 0.00 0.00 37.32 1.63
627 1090 9.887629 GATTTCATAGTGTGGATGATGATATCT 57.112 33.333 3.98 0.00 35.56 1.98
631 1094 9.716531 TCATAGTGTGGATGATGATATCTTTTC 57.283 33.333 3.98 0.00 0.00 2.29
632 1095 8.944029 CATAGTGTGGATGATGATATCTTTTCC 58.056 37.037 3.98 8.88 0.00 3.13
633 1096 7.146715 AGTGTGGATGATGATATCTTTTCCT 57.853 36.000 16.16 2.60 0.00 3.36
634 1097 8.267620 AGTGTGGATGATGATATCTTTTCCTA 57.732 34.615 16.16 8.00 0.00 2.94
635 1098 8.888419 AGTGTGGATGATGATATCTTTTCCTAT 58.112 33.333 16.16 0.00 0.00 2.57
688 1151 9.597999 GATTTTGACCAAATCTTTTATGCAAAC 57.402 29.630 5.04 0.00 45.30 2.93
689 1152 8.729805 TTTTGACCAAATCTTTTATGCAAACT 57.270 26.923 0.00 0.00 0.00 2.66
690 1153 9.823647 TTTTGACCAAATCTTTTATGCAAACTA 57.176 25.926 0.00 0.00 0.00 2.24
691 1154 9.823647 TTTGACCAAATCTTTTATGCAAACTAA 57.176 25.926 0.00 0.00 0.00 2.24
692 1155 9.823647 TTGACCAAATCTTTTATGCAAACTAAA 57.176 25.926 0.00 0.00 0.00 1.85
693 1156 9.823647 TGACCAAATCTTTTATGCAAACTAAAA 57.176 25.926 0.00 0.00 0.00 1.52
701 1164 9.026074 TCTTTTATGCAAACTAAAAAGAAACGG 57.974 29.630 15.72 2.14 42.13 4.44
702 1165 8.928270 TTTTATGCAAACTAAAAAGAAACGGA 57.072 26.923 0.00 0.00 0.00 4.69
703 1166 8.568732 TTTATGCAAACTAAAAAGAAACGGAG 57.431 30.769 0.00 0.00 0.00 4.63
704 1167 4.927422 TGCAAACTAAAAAGAAACGGAGG 58.073 39.130 0.00 0.00 0.00 4.30
705 1168 4.202070 TGCAAACTAAAAAGAAACGGAGGG 60.202 41.667 0.00 0.00 0.00 4.30
706 1169 4.037089 GCAAACTAAAAAGAAACGGAGGGA 59.963 41.667 0.00 0.00 0.00 4.20
707 1170 5.758924 CAAACTAAAAAGAAACGGAGGGAG 58.241 41.667 0.00 0.00 0.00 4.30
708 1171 4.701651 ACTAAAAAGAAACGGAGGGAGT 57.298 40.909 0.00 0.00 0.00 3.85
709 1172 5.813513 ACTAAAAAGAAACGGAGGGAGTA 57.186 39.130 0.00 0.00 0.00 2.59
710 1173 5.545588 ACTAAAAAGAAACGGAGGGAGTAC 58.454 41.667 0.00 0.00 0.00 2.73
711 1174 4.701651 AAAAAGAAACGGAGGGAGTACT 57.298 40.909 0.00 0.00 0.00 2.73
712 1175 4.701651 AAAAGAAACGGAGGGAGTACTT 57.298 40.909 0.00 0.00 0.00 2.24
721 1184 9.473640 GAAACGGAGGGAGTACTTATTAATTAG 57.526 37.037 0.00 0.00 0.00 1.73
891 1362 1.333619 GAGAAAAAGGCGCTCACACAA 59.666 47.619 7.64 0.00 0.00 3.33
893 1364 1.065551 GAAAAAGGCGCTCACACAACT 59.934 47.619 7.64 0.00 0.00 3.16
906 1377 2.230992 CACACAACTGGAGAGAGAGAGG 59.769 54.545 0.00 0.00 0.00 3.69
949 1431 0.107897 AAATCGCACCTATCACGGCA 60.108 50.000 0.00 0.00 0.00 5.69
988 1474 0.393673 CCGAGCTCAGAGTGGAGAGA 60.394 60.000 15.40 0.00 37.05 3.10
1546 2047 3.495193 TGCATTCTACGTACGTTCAGTC 58.505 45.455 27.92 12.02 0.00 3.51
1553 2054 3.722728 ACGTACGTTCAGTCTTTCCTT 57.277 42.857 16.72 0.00 0.00 3.36
1565 2066 2.093394 GTCTTTCCTTGCTACTCTCCCC 60.093 54.545 0.00 0.00 0.00 4.81
1613 2124 4.442706 TGCTAATCCGAAGCTAAAGAAGG 58.557 43.478 0.00 0.00 40.73 3.46
1876 2387 1.133388 GCATCCCATTCTTCCCCATCA 60.133 52.381 0.00 0.00 0.00 3.07
1962 2473 3.202906 GTGGAAGAAGCGCACCATAATA 58.797 45.455 11.47 0.00 34.87 0.98
1969 2480 8.082242 GGAAGAAGCGCACCATAATAAATTTAT 58.918 33.333 11.47 4.81 0.00 1.40
1972 2483 9.062524 AGAAGCGCACCATAATAAATTTATGTA 57.937 29.630 11.47 6.93 32.07 2.29
1973 2484 9.672086 GAAGCGCACCATAATAAATTTATGTAA 57.328 29.630 11.47 1.67 32.07 2.41
1974 2485 9.458374 AAGCGCACCATAATAAATTTATGTAAC 57.542 29.630 11.47 1.46 32.07 2.50
2306 2819 1.068083 CGTGGATGAGACCCCGATG 59.932 63.158 0.00 0.00 0.00 3.84
2387 2900 3.717294 GCCACCATCTGGGACGGT 61.717 66.667 0.54 0.00 41.02 4.83
2468 2981 2.049433 CAGTTCGGCGACCTCGTT 60.049 61.111 10.16 0.00 42.22 3.85
2831 3344 2.509336 CGGCACCGAGGATGACAC 60.509 66.667 2.01 0.00 42.83 3.67
3046 3559 5.758784 AGCTTAGCGTTTATTATTGTCTCCC 59.241 40.000 0.00 0.00 0.00 4.30
3119 3645 1.137872 GCTCCTAGTCCCATCACTGTG 59.862 57.143 0.17 0.17 0.00 3.66
3231 3760 1.130373 GTGATCTCGCGCCATTTTCAA 59.870 47.619 0.00 0.00 0.00 2.69
3424 4008 4.223953 TCACCGGCTAGGAAAGATTCTAT 58.776 43.478 0.00 0.00 45.00 1.98
3425 4009 5.391256 TCACCGGCTAGGAAAGATTCTATA 58.609 41.667 0.00 0.00 45.00 1.31
3566 4150 2.743752 CGATTGTGTGGCTCCTGCG 61.744 63.158 0.00 0.00 40.82 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.239217 ACTTCATAGAACATACTGCATGGA 57.761 37.500 0.00 0.00 39.13 3.41
1 2 6.765036 AGAACTTCATAGAACATACTGCATGG 59.235 38.462 0.00 0.00 39.13 3.66
2 3 7.783090 AGAACTTCATAGAACATACTGCATG 57.217 36.000 0.00 0.00 40.78 4.06
3 4 9.486497 CATAGAACTTCATAGAACATACTGCAT 57.514 33.333 0.00 0.00 0.00 3.96
4 5 8.478066 ACATAGAACTTCATAGAACATACTGCA 58.522 33.333 0.00 0.00 0.00 4.41
5 6 8.879342 ACATAGAACTTCATAGAACATACTGC 57.121 34.615 0.00 0.00 0.00 4.40
122 123 9.645059 AGAAATATGACATATGAACGATCGAAT 57.355 29.630 24.34 14.19 0.00 3.34
165 166 0.402504 ACATGGTGGTCCGCCTTAAA 59.597 50.000 22.20 2.13 34.70 1.52
169 170 2.185310 GAGAACATGGTGGTCCGCCT 62.185 60.000 22.20 1.45 33.71 5.52
195 197 3.481112 ACGCGCCGAAATTTATTTTCT 57.519 38.095 5.73 0.00 41.37 2.52
197 199 4.345271 AGTACGCGCCGAAATTTATTTT 57.655 36.364 5.73 0.00 0.00 1.82
198 200 4.092816 CAAGTACGCGCCGAAATTTATTT 58.907 39.130 5.73 0.00 0.00 1.40
199 201 3.125658 ACAAGTACGCGCCGAAATTTATT 59.874 39.130 5.73 0.00 0.00 1.40
200 202 2.674357 ACAAGTACGCGCCGAAATTTAT 59.326 40.909 5.73 0.00 0.00 1.40
201 203 2.067766 ACAAGTACGCGCCGAAATTTA 58.932 42.857 5.73 0.00 0.00 1.40
202 204 0.869730 ACAAGTACGCGCCGAAATTT 59.130 45.000 5.73 0.00 0.00 1.82
203 205 1.657094 CTACAAGTACGCGCCGAAATT 59.343 47.619 5.73 0.00 0.00 1.82
204 206 1.274596 CTACAAGTACGCGCCGAAAT 58.725 50.000 5.73 0.00 0.00 2.17
205 207 0.039256 ACTACAAGTACGCGCCGAAA 60.039 50.000 5.73 0.00 0.00 3.46
206 208 0.039256 AACTACAAGTACGCGCCGAA 60.039 50.000 5.73 0.00 0.00 4.30
207 209 0.730155 CAACTACAAGTACGCGCCGA 60.730 55.000 5.73 0.00 0.00 5.54
208 210 0.730155 TCAACTACAAGTACGCGCCG 60.730 55.000 5.73 0.00 0.00 6.46
209 211 0.712222 GTCAACTACAAGTACGCGCC 59.288 55.000 5.73 0.00 0.00 6.53
210 212 0.712222 GGTCAACTACAAGTACGCGC 59.288 55.000 5.73 0.00 0.00 6.86
211 213 1.068055 AGGGTCAACTACAAGTACGCG 60.068 52.381 3.53 3.53 28.60 6.01
212 214 2.288640 ACAGGGTCAACTACAAGTACGC 60.289 50.000 0.00 0.00 0.00 4.42
213 215 3.655276 ACAGGGTCAACTACAAGTACG 57.345 47.619 0.00 0.00 0.00 3.67
214 216 4.492611 GCTACAGGGTCAACTACAAGTAC 58.507 47.826 0.00 0.00 0.00 2.73
215 217 3.192001 CGCTACAGGGTCAACTACAAGTA 59.808 47.826 0.00 0.00 0.00 2.24
216 218 2.029290 CGCTACAGGGTCAACTACAAGT 60.029 50.000 0.00 0.00 0.00 3.16
217 219 2.607187 CGCTACAGGGTCAACTACAAG 58.393 52.381 0.00 0.00 0.00 3.16
218 220 1.274167 CCGCTACAGGGTCAACTACAA 59.726 52.381 0.00 0.00 0.00 2.41
219 221 0.892755 CCGCTACAGGGTCAACTACA 59.107 55.000 0.00 0.00 0.00 2.74
220 222 0.459759 GCCGCTACAGGGTCAACTAC 60.460 60.000 0.00 0.00 0.00 2.73
221 223 1.610554 GGCCGCTACAGGGTCAACTA 61.611 60.000 0.00 0.00 0.00 2.24
222 224 2.663196 GCCGCTACAGGGTCAACT 59.337 61.111 0.00 0.00 0.00 3.16
223 225 2.436115 GGCCGCTACAGGGTCAAC 60.436 66.667 0.00 0.00 0.00 3.18
224 226 4.077184 CGGCCGCTACAGGGTCAA 62.077 66.667 14.67 0.00 0.00 3.18
260 262 4.648626 TGCACAGTGGCAGGGCTC 62.649 66.667 1.84 0.00 39.25 4.70
268 270 4.675146 GCCTTTTACATGTATGCACAGTGG 60.675 45.833 6.36 2.79 38.30 4.00
271 273 4.700268 TGCCTTTTACATGTATGCACAG 57.300 40.909 6.36 0.00 38.30 3.66
278 280 8.779303 CGTTAATATGGATGCCTTTTACATGTA 58.221 33.333 0.08 0.08 0.00 2.29
289 455 5.493133 TCAAACACGTTAATATGGATGCC 57.507 39.130 0.00 0.00 0.00 4.40
330 496 5.731599 TTTTAAACTTCGCGTCTGGTTTA 57.268 34.783 5.77 13.76 34.40 2.01
352 518 8.241367 AGCGATGGAAGTCGTTTTTATTATTTT 58.759 29.630 0.00 0.00 43.27 1.82
353 519 7.758495 AGCGATGGAAGTCGTTTTTATTATTT 58.242 30.769 0.00 0.00 43.27 1.40
465 928 9.959749 GACCAAATCTTATATGCGGATTAAAAA 57.040 29.630 0.00 0.00 0.00 1.94
466 929 9.126151 TGACCAAATCTTATATGCGGATTAAAA 57.874 29.630 0.00 0.00 0.00 1.52
467 930 8.684386 TGACCAAATCTTATATGCGGATTAAA 57.316 30.769 0.00 0.00 0.00 1.52
468 931 8.684386 TTGACCAAATCTTATATGCGGATTAA 57.316 30.769 0.00 0.00 0.00 1.40
469 932 8.684386 TTTGACCAAATCTTATATGCGGATTA 57.316 30.769 0.00 0.00 0.00 1.75
470 933 7.581213 TTTGACCAAATCTTATATGCGGATT 57.419 32.000 0.00 0.00 0.00 3.01
471 934 7.581213 TTTTGACCAAATCTTATATGCGGAT 57.419 32.000 0.00 0.00 0.00 4.18
472 935 7.581213 ATTTTGACCAAATCTTATATGCGGA 57.419 32.000 0.00 0.00 27.71 5.54
473 936 7.858052 GATTTTGACCAAATCTTATATGCGG 57.142 36.000 5.04 0.00 45.30 5.69
485 948 9.495572 ACTTTACAAAGTTTGATTTTGACCAAA 57.504 25.926 22.23 6.72 46.52 3.28
596 1059 9.850198 TCATCATCCACACTATGAAATCAATAA 57.150 29.630 0.00 0.00 36.95 1.40
598 1061 8.935614 ATCATCATCCACACTATGAAATCAAT 57.064 30.769 0.00 0.00 36.95 2.57
600 1063 9.662947 GATATCATCATCCACACTATGAAATCA 57.337 33.333 0.00 0.00 36.95 2.57
601 1064 9.887629 AGATATCATCATCCACACTATGAAATC 57.112 33.333 5.32 0.00 36.95 2.17
605 1068 9.716531 GAAAAGATATCATCATCCACACTATGA 57.283 33.333 5.32 0.00 37.73 2.15
606 1069 8.944029 GGAAAAGATATCATCATCCACACTATG 58.056 37.037 5.32 0.00 32.42 2.23
607 1070 8.888419 AGGAAAAGATATCATCATCCACACTAT 58.112 33.333 5.32 0.00 33.71 2.12
608 1071 8.267620 AGGAAAAGATATCATCATCCACACTA 57.732 34.615 5.32 0.00 33.71 2.74
609 1072 7.146715 AGGAAAAGATATCATCATCCACACT 57.853 36.000 5.32 0.00 33.71 3.55
663 1126 9.341078 AGTTTGCATAAAAGATTTGGTCAAAAT 57.659 25.926 0.00 0.00 41.33 1.82
664 1127 8.729805 AGTTTGCATAAAAGATTTGGTCAAAA 57.270 26.923 0.00 0.00 33.56 2.44
665 1128 9.823647 TTAGTTTGCATAAAAGATTTGGTCAAA 57.176 25.926 0.00 0.00 34.46 2.69
666 1129 9.823647 TTTAGTTTGCATAAAAGATTTGGTCAA 57.176 25.926 0.00 0.00 0.00 3.18
667 1130 9.823647 TTTTAGTTTGCATAAAAGATTTGGTCA 57.176 25.926 0.61 0.00 30.63 4.02
675 1138 9.026074 CCGTTTCTTTTTAGTTTGCATAAAAGA 57.974 29.630 12.89 12.89 41.97 2.52
676 1139 9.026074 TCCGTTTCTTTTTAGTTTGCATAAAAG 57.974 29.630 4.43 0.00 38.38 2.27
677 1140 8.928270 TCCGTTTCTTTTTAGTTTGCATAAAA 57.072 26.923 0.61 0.61 31.89 1.52
678 1141 7.650104 CCTCCGTTTCTTTTTAGTTTGCATAAA 59.350 33.333 0.00 0.00 0.00 1.40
679 1142 7.142680 CCTCCGTTTCTTTTTAGTTTGCATAA 58.857 34.615 0.00 0.00 0.00 1.90
680 1143 6.294286 CCCTCCGTTTCTTTTTAGTTTGCATA 60.294 38.462 0.00 0.00 0.00 3.14
681 1144 5.508994 CCCTCCGTTTCTTTTTAGTTTGCAT 60.509 40.000 0.00 0.00 0.00 3.96
682 1145 4.202070 CCCTCCGTTTCTTTTTAGTTTGCA 60.202 41.667 0.00 0.00 0.00 4.08
683 1146 4.037089 TCCCTCCGTTTCTTTTTAGTTTGC 59.963 41.667 0.00 0.00 0.00 3.68
684 1147 5.298527 ACTCCCTCCGTTTCTTTTTAGTTTG 59.701 40.000 0.00 0.00 0.00 2.93
685 1148 5.443283 ACTCCCTCCGTTTCTTTTTAGTTT 58.557 37.500 0.00 0.00 0.00 2.66
686 1149 5.045012 ACTCCCTCCGTTTCTTTTTAGTT 57.955 39.130 0.00 0.00 0.00 2.24
687 1150 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
688 1151 5.791666 AGTACTCCCTCCGTTTCTTTTTAG 58.208 41.667 0.00 0.00 0.00 1.85
689 1152 5.813513 AGTACTCCCTCCGTTTCTTTTTA 57.186 39.130 0.00 0.00 0.00 1.52
690 1153 4.701651 AGTACTCCCTCCGTTTCTTTTT 57.298 40.909 0.00 0.00 0.00 1.94
691 1154 4.701651 AAGTACTCCCTCCGTTTCTTTT 57.298 40.909 0.00 0.00 0.00 2.27
692 1155 6.370186 AATAAGTACTCCCTCCGTTTCTTT 57.630 37.500 0.00 0.00 0.00 2.52
693 1156 7.486407 TTAATAAGTACTCCCTCCGTTTCTT 57.514 36.000 0.00 0.00 0.00 2.52
694 1157 7.672122 ATTAATAAGTACTCCCTCCGTTTCT 57.328 36.000 0.00 0.00 0.00 2.52
695 1158 9.473640 CTAATTAATAAGTACTCCCTCCGTTTC 57.526 37.037 0.00 0.00 0.00 2.78
696 1159 8.985922 ACTAATTAATAAGTACTCCCTCCGTTT 58.014 33.333 0.00 0.00 0.00 3.60
697 1160 8.544687 ACTAATTAATAAGTACTCCCTCCGTT 57.455 34.615 0.00 0.00 0.00 4.44
698 1161 9.819754 ATACTAATTAATAAGTACTCCCTCCGT 57.180 33.333 0.00 0.00 31.30 4.69
756 1219 3.015293 CTACTGCGCGCACACCAAG 62.015 63.158 33.09 22.04 0.00 3.61
891 1362 1.846439 CTCTCCCTCTCTCTCTCCAGT 59.154 57.143 0.00 0.00 0.00 4.00
893 1364 2.126882 CTCTCTCCCTCTCTCTCTCCA 58.873 57.143 0.00 0.00 0.00 3.86
906 1377 1.039856 GTGATGGGCTCTCTCTCTCC 58.960 60.000 0.00 0.00 0.00 3.71
988 1474 1.608717 GACGCCATCTCCACACCTCT 61.609 60.000 0.00 0.00 0.00 3.69
1042 1535 4.393778 GACGGGGAGGAGGTGGGA 62.394 72.222 0.00 0.00 0.00 4.37
1278 1771 1.554042 GCACCCGCATATTACGTCGG 61.554 60.000 4.25 4.25 41.41 4.79
1546 2047 1.134670 CGGGGAGAGTAGCAAGGAAAG 60.135 57.143 0.00 0.00 0.00 2.62
1553 2054 2.037367 ACAGCGGGGAGAGTAGCA 59.963 61.111 0.00 0.00 0.00 3.49
1565 2066 0.673333 TGGTGGTAAGATGCACAGCG 60.673 55.000 0.00 0.00 34.32 5.18
1613 2124 1.989165 TGCGAAAACACAAACAAGCAC 59.011 42.857 0.00 0.00 0.00 4.40
1969 2480 8.150296 CACACCAGGAATATCATCATAGTTACA 58.850 37.037 0.00 0.00 0.00 2.41
1972 2483 6.329986 TCCACACCAGGAATATCATCATAGTT 59.670 38.462 0.00 0.00 33.93 2.24
1973 2484 5.846164 TCCACACCAGGAATATCATCATAGT 59.154 40.000 0.00 0.00 33.93 2.12
1974 2485 6.364568 TCCACACCAGGAATATCATCATAG 57.635 41.667 0.00 0.00 33.93 2.23
2306 2819 2.352032 CGTCCTCACCACCTCCCTC 61.352 68.421 0.00 0.00 0.00 4.30
2639 3152 2.126307 CACTCTGACAGGGCGACG 60.126 66.667 0.98 0.00 0.00 5.12
2831 3344 2.417516 CCGCCTCTGTACATCCCG 59.582 66.667 0.00 0.00 0.00 5.14
3046 3559 4.552365 ATGGCGCGGATGGTCCAG 62.552 66.667 8.83 0.00 35.91 3.86
3119 3645 1.364901 GGCCATGTACATGCATGCC 59.635 57.895 27.86 27.86 43.46 4.40
3231 3760 2.177580 CAACAGTGCGTTCCACCGT 61.178 57.895 0.00 0.00 45.83 4.83
3317 3899 4.832608 GTACGCTTGCCTCCCCCG 62.833 72.222 0.00 0.00 0.00 5.73
3424 4008 3.345737 GCACAGCGTCATGTAGCTA 57.654 52.632 15.09 0.00 42.52 3.32
3425 4009 4.192000 GCACAGCGTCATGTAGCT 57.808 55.556 10.92 10.92 45.74 3.32
3447 4031 0.109272 GCGTCTGACATGAACGAGGA 60.109 55.000 8.73 1.86 0.00 3.71
3485 4069 2.761354 CGCGAACGACCGAACTTC 59.239 61.111 0.00 0.00 43.93 3.01
3566 4150 1.002366 CATAGCAGCGTTCTGTCCAC 58.998 55.000 0.00 0.00 42.29 4.02


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

AutoCloner maintained by Alex Coulton.