Multiple sequence alignment - TraesCS7D01G183500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G183500 chr7D 100.000 3091 0 0 1 3091 136893371 136890281 0.000000e+00 5709
1 TraesCS7D01G183500 chr7D 88.576 569 38 14 2488 3049 136864581 136864033 0.000000e+00 665
2 TraesCS7D01G183500 chr7D 80.717 446 32 16 2623 3056 136925094 136925497 6.480000e-77 298
3 TraesCS7D01G183500 chr7A 89.791 2635 144 64 535 3091 136757396 136754809 0.000000e+00 3260
4 TraesCS7D01G183500 chr7A 84.236 609 54 19 2486 3091 136467263 136466694 3.480000e-154 555
5 TraesCS7D01G183500 chr7A 82.997 347 28 8 2571 2917 136536458 136536143 5.040000e-73 285
6 TraesCS7D01G183500 chr7A 92.857 70 5 0 2714 2783 136451695 136451626 5.450000e-18 102
7 TraesCS7D01G183500 chr7B 90.049 1638 100 22 1466 3091 100332692 100331106 0.000000e+00 2063
8 TraesCS7D01G183500 chr7B 86.340 1142 65 37 242 1333 100333945 100332845 0.000000e+00 1160
9 TraesCS7D01G183500 chr7B 91.878 197 15 1 1 197 100334222 100334027 1.090000e-69 274


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 TraesCS7D01G183500 chr7D 136890281 136893371 3090 True 5709.000000 5709 100.000000 1 3091 1 chr7D.!!$R2 3090
1 TraesCS7D01G183500 chr7D 136864033 136864581 548 True 665.000000 665 88.576000 2488 3049 1 chr7D.!!$R1 561
2 TraesCS7D01G183500 chr7A 136754809 136757396 2587 True 3260.000000 3260 89.791000 535 3091 1 chr7A.!!$R4 2556
3 TraesCS7D01G183500 chr7A 136466694 136467263 569 True 555.000000 555 84.236000 2486 3091 1 chr7A.!!$R2 605
4 TraesCS7D01G183500 chr7B 100331106 100334222 3116 True 1165.666667 2063 89.422333 1 3091 3 chr7B.!!$R1 3090

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
623 685 0.240945 AACGGAATCCAGCAAAAGCG 59.759 50.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2362 1.052287 GCGCCAACGATTTTCTGTTG 58.948 50.0 0.0 0.0 43.93 3.33 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
21 22 3.190878 CCAGCGGGATCTTTGTGC 58.809 61.111 0.00 0.00 35.59 4.57
29 30 2.706890 GGGATCTTTGTGCCGTTTCTA 58.293 47.619 0.00 0.00 0.00 2.10
99 100 8.797438 ACTATATCTCATGTCGACACACATTAT 58.203 33.333 22.71 16.67 34.60 1.28
105 106 6.598525 TCATGTCGACACACATTATTGTTTC 58.401 36.000 22.71 0.00 34.60 2.78
109 110 8.317891 TGTCGACACACATTATTGTTTCTATT 57.682 30.769 15.76 0.00 32.34 1.73
111 112 9.607285 GTCGACACACATTATTGTTTCTATTTT 57.393 29.630 11.55 0.00 32.34 1.82
153 154 0.902531 TCAAGTAGCCTTCTTCCCCG 59.097 55.000 0.00 0.00 0.00 5.73
159 160 2.125106 CCTTCTTCCCCGCTTCCG 60.125 66.667 0.00 0.00 0.00 4.30
210 211 8.524870 AGTCAAATGCTTTTATGTTTGATCAC 57.475 30.769 0.00 0.00 41.11 3.06
211 212 7.326789 AGTCAAATGCTTTTATGTTTGATCACG 59.673 33.333 0.00 0.00 41.11 4.35
212 213 7.114811 GTCAAATGCTTTTATGTTTGATCACGT 59.885 33.333 0.00 0.00 41.11 4.49
213 214 7.651304 TCAAATGCTTTTATGTTTGATCACGTT 59.349 29.630 0.00 0.00 36.11 3.99
214 215 7.945033 AATGCTTTTATGTTTGATCACGTTT 57.055 28.000 0.00 0.00 0.00 3.60
215 216 9.469807 AAATGCTTTTATGTTTGATCACGTTTA 57.530 25.926 0.00 0.00 0.00 2.01
216 217 9.638239 AATGCTTTTATGTTTGATCACGTTTAT 57.362 25.926 0.00 0.00 0.00 1.40
218 219 9.767684 TGCTTTTATGTTTGATCACGTTTATAG 57.232 29.630 0.00 0.00 0.00 1.31
219 220 9.982291 GCTTTTATGTTTGATCACGTTTATAGA 57.018 29.630 0.00 0.00 0.00 1.98
288 341 8.718102 AATCTAGATTACGAGCTAAGCAAAAA 57.282 30.769 16.50 0.00 0.00 1.94
323 376 7.987268 ATATATTGCGTGATGAGTATAACGG 57.013 36.000 0.00 0.00 0.00 4.44
328 381 2.789339 CGTGATGAGTATAACGGCACTG 59.211 50.000 0.00 0.00 0.00 3.66
336 389 1.832883 ATAACGGCACTGATTTGGCA 58.167 45.000 0.00 0.00 42.14 4.92
355 408 9.905713 ATTTGGCAGTGTAGATATTTTTCTCTA 57.094 29.630 0.00 0.00 0.00 2.43
376 429 9.702494 TCTCTATATGCACTTGATCAAACATAG 57.298 33.333 20.94 14.66 0.00 2.23
382 438 8.970691 ATGCACTTGATCAAACATAGTTAAAC 57.029 30.769 9.88 0.00 0.00 2.01
485 547 2.584391 GGCGGAGAAGAGTGGTGGT 61.584 63.158 0.00 0.00 0.00 4.16
486 548 1.255667 GGCGGAGAAGAGTGGTGGTA 61.256 60.000 0.00 0.00 0.00 3.25
496 558 0.324368 AGTGGTGGTATCCGAGAGCA 60.324 55.000 0.00 0.00 0.00 4.26
522 584 2.749076 TGTGCATTTCATACTGACAGCC 59.251 45.455 1.25 0.00 0.00 4.85
524 586 2.279741 GCATTTCATACTGACAGCCGA 58.720 47.619 1.25 0.00 0.00 5.54
525 587 2.286294 GCATTTCATACTGACAGCCGAG 59.714 50.000 1.25 0.00 0.00 4.63
526 588 2.672961 TTTCATACTGACAGCCGAGG 57.327 50.000 1.25 0.00 0.00 4.63
527 589 1.847328 TTCATACTGACAGCCGAGGA 58.153 50.000 1.25 0.00 0.00 3.71
528 590 1.393603 TCATACTGACAGCCGAGGAG 58.606 55.000 1.25 0.00 0.00 3.69
529 591 1.064685 TCATACTGACAGCCGAGGAGA 60.065 52.381 1.25 0.00 0.00 3.71
530 592 1.751351 CATACTGACAGCCGAGGAGAA 59.249 52.381 1.25 0.00 0.00 2.87
585 647 2.546584 CCAAAGAAAGAGTGGCAAAGGC 60.547 50.000 0.00 0.00 40.13 4.35
600 662 3.369921 GGCCAAAGGGACAGCAAG 58.630 61.111 0.00 0.00 44.16 4.01
607 669 1.308998 AAGGGACAGCAAGTGAAACG 58.691 50.000 0.00 0.00 45.86 3.60
623 685 0.240945 AACGGAATCCAGCAAAAGCG 59.759 50.000 0.00 0.00 0.00 4.68
874 988 1.446366 GCCGCCCCTCCTTAACTAG 59.554 63.158 0.00 0.00 0.00 2.57
902 1041 2.612251 CCTCCTCCTCCCTCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
903 1042 2.612251 CTCCTCCTCCCTCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
904 1043 2.018086 CTCCTCCTCCCTCCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
905 1044 2.015726 TCCTCCTCCCTCCCTCCTC 61.016 68.421 0.00 0.00 0.00 3.71
906 1045 2.328589 CCTCCTCCCTCCCTCCTCA 61.329 68.421 0.00 0.00 0.00 3.86
1307 1463 1.776662 TACATGTAAGCCTCGAGCCT 58.223 50.000 6.99 0.00 45.47 4.58
1308 1464 0.176680 ACATGTAAGCCTCGAGCCTG 59.823 55.000 6.99 0.00 45.47 4.85
1309 1465 1.144936 ATGTAAGCCTCGAGCCTGC 59.855 57.895 6.99 5.38 45.47 4.85
1311 1467 3.838271 TAAGCCTCGAGCCTGCCG 61.838 66.667 6.99 0.00 45.47 5.69
1325 1481 0.661020 CTGCCGTCGTTTGGTTTTCT 59.339 50.000 0.00 0.00 0.00 2.52
1336 1561 2.433868 TGGTTTTCTCTCCGACTTCG 57.566 50.000 0.00 0.00 39.44 3.79
1338 1563 2.101917 TGGTTTTCTCTCCGACTTCGTT 59.898 45.455 0.00 0.00 37.74 3.85
1349 1574 2.159476 CCGACTTCGTTATCTTCCGTGA 60.159 50.000 0.00 0.00 37.74 4.35
1355 1580 7.287050 ACTTCGTTATCTTCCGTGAAAATAC 57.713 36.000 0.00 0.00 0.00 1.89
1359 1584 5.062934 CGTTATCTTCCGTGAAAATACTGCA 59.937 40.000 0.00 0.00 0.00 4.41
1368 1593 7.995289 TCCGTGAAAATACTGCATAATCATTT 58.005 30.769 0.00 0.00 0.00 2.32
1388 1613 0.250252 TGCTGCCATGAGACGTGAAA 60.250 50.000 0.00 0.00 0.00 2.69
1401 1629 5.522460 TGAGACGTGAAAGATCGAACTTTTT 59.478 36.000 20.00 7.07 39.71 1.94
1436 1664 5.935448 GCAGTTTTGCTTTGTTTTACGTA 57.065 34.783 0.00 0.00 46.95 3.57
1437 1665 5.710314 GCAGTTTTGCTTTGTTTTACGTAC 58.290 37.500 0.00 0.00 46.95 3.67
1438 1666 5.551187 GCAGTTTTGCTTTGTTTTACGTACG 60.551 40.000 15.01 15.01 46.95 3.67
1441 1669 6.901357 AGTTTTGCTTTGTTTTACGTACGTAG 59.099 34.615 25.56 16.37 31.71 3.51
1454 1682 3.789756 ACGTACGTAGCAGATTTGATTCG 59.210 43.478 21.41 0.00 39.05 3.34
1458 1686 4.242475 ACGTAGCAGATTTGATTCGTTCA 58.758 39.130 0.37 0.00 42.67 3.18
1468 1696 2.959516 TGATTCGTTCACGCTGATCTT 58.040 42.857 0.00 0.00 39.60 2.40
1472 1700 1.148310 CGTTCACGCTGATCTTTGGT 58.852 50.000 0.00 0.00 0.00 3.67
1503 1731 6.547510 AGGTTGATGGTTAATCTAATCTTGCC 59.452 38.462 0.00 0.00 36.15 4.52
1512 1740 9.004717 GGTTAATCTAATCTTGCCCTTCTTATC 57.995 37.037 0.00 0.00 0.00 1.75
1537 1765 6.318900 CCCGGCTCTATGTTTTTAGAGAAATT 59.681 38.462 11.65 0.00 45.37 1.82
1569 1797 4.202315 ACTTGGGGCTTTAATTTGGTTGAC 60.202 41.667 0.00 0.00 0.00 3.18
1632 1861 3.120786 GCAGAGCAACAATCAAATGCAAC 60.121 43.478 0.00 0.00 42.45 4.17
1637 1866 5.571277 AGCAACAATCAAATGCAACAAAAC 58.429 33.333 0.00 0.00 42.45 2.43
1667 1899 5.103290 TGGTTTTAGTCGTTGCATTTCTC 57.897 39.130 0.00 0.00 0.00 2.87
1740 1973 7.488792 TGATGACAAGAACACTCAAAAACAATG 59.511 33.333 0.00 0.00 0.00 2.82
1763 1996 1.497991 TGTTTCTCTTTCGTCCAGCG 58.502 50.000 0.00 0.00 43.01 5.18
1803 2043 5.163120 ACCTCTGCATCATTCATAGGATGTT 60.163 40.000 0.00 0.00 42.90 2.71
1816 2056 0.253327 GGATGTTGAGTGGGTCTCCC 59.747 60.000 0.00 0.00 45.71 4.30
1831 2074 3.072622 GGTCTCCCACCTCCAATAATACC 59.927 52.174 0.00 0.00 42.84 2.73
1832 2075 3.714798 GTCTCCCACCTCCAATAATACCA 59.285 47.826 0.00 0.00 0.00 3.25
1833 2076 3.714798 TCTCCCACCTCCAATAATACCAC 59.285 47.826 0.00 0.00 0.00 4.16
1834 2077 3.716872 CTCCCACCTCCAATAATACCACT 59.283 47.826 0.00 0.00 0.00 4.00
1844 2087 5.719563 TCCAATAATACCACTCACTCACAGA 59.280 40.000 0.00 0.00 0.00 3.41
1946 2196 4.963953 CCGAGCTTAATATTTCTTGTTGCG 59.036 41.667 0.00 0.00 0.00 4.85
2021 2271 1.254284 ACCTGGACGAGCTCAAGGAG 61.254 60.000 22.04 9.83 0.00 3.69
2101 2351 2.645567 CGCCTAGCATCGACCGAT 59.354 61.111 0.00 0.00 34.81 4.18
2102 2352 1.442857 CGCCTAGCATCGACCGATC 60.443 63.158 1.46 0.00 31.62 3.69
2286 2540 2.110899 TGGAATTGGGGCTAGGTGAAAA 59.889 45.455 0.00 0.00 0.00 2.29
2287 2541 2.760650 GGAATTGGGGCTAGGTGAAAAG 59.239 50.000 0.00 0.00 0.00 2.27
2457 2713 2.368875 TGTCTGAAAGTCTGTCCCCTTC 59.631 50.000 0.00 0.00 33.76 3.46
2461 2717 2.106511 TGAAAGTCTGTCCCCTTCTTGG 59.893 50.000 0.00 0.00 0.00 3.61
2566 2826 2.556622 AGTTTCACCATTAACCTTGGCG 59.443 45.455 0.00 0.00 37.81 5.69
2567 2827 2.554893 GTTTCACCATTAACCTTGGCGA 59.445 45.455 0.00 0.00 37.81 5.54
2568 2828 1.816074 TCACCATTAACCTTGGCGAC 58.184 50.000 0.00 0.00 37.81 5.19
2569 2829 1.349688 TCACCATTAACCTTGGCGACT 59.650 47.619 0.00 0.00 37.81 4.18
2671 2939 1.456296 CATGACACTGACATGTGGGG 58.544 55.000 1.15 0.00 41.84 4.96
2680 2948 3.266772 ACTGACATGTGGGGTGATTATGT 59.733 43.478 1.15 0.00 34.91 2.29
2687 2955 2.946990 GTGGGGTGATTATGTTAACCGG 59.053 50.000 0.00 0.00 33.24 5.28
2763 3032 5.887598 TGGTTGTAATTGGATCAAGATCTGG 59.112 40.000 9.69 0.00 37.92 3.86
2937 3209 2.850695 TGGTAAACCCCAAAACCTGT 57.149 45.000 0.00 0.00 32.99 4.00
3016 3288 2.470821 GCATTTTGCAGGATCTGATGC 58.529 47.619 0.29 0.29 44.26 3.91
3017 3289 2.100916 GCATTTTGCAGGATCTGATGCT 59.899 45.455 5.79 5.79 44.26 3.79
3018 3290 3.430374 GCATTTTGCAGGATCTGATGCTT 60.430 43.478 9.11 0.00 44.26 3.91
3019 3291 3.861276 TTTTGCAGGATCTGATGCTTG 57.139 42.857 9.11 6.59 42.98 4.01
3020 3292 1.100510 TTGCAGGATCTGATGCTTGC 58.899 50.000 19.01 19.01 42.98 4.01
3021 3293 1.093496 TGCAGGATCTGATGCTTGCG 61.093 55.000 19.82 8.91 42.98 4.85
3022 3294 0.812811 GCAGGATCTGATGCTTGCGA 60.813 55.000 9.11 0.00 39.38 5.10
3023 3295 0.935898 CAGGATCTGATGCTTGCGAC 59.064 55.000 9.11 0.00 32.44 5.19
3024 3296 0.538584 AGGATCTGATGCTTGCGACA 59.461 50.000 5.79 0.00 0.00 4.35
3025 3297 0.935898 GGATCTGATGCTTGCGACAG 59.064 55.000 1.51 10.74 0.00 3.51
3026 3298 0.304098 GATCTGATGCTTGCGACAGC 59.696 55.000 0.00 0.00 45.41 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.534729 AGAAACGGCACAAAGATCCC 58.465 50.000 0.00 0.00 0.00 3.85
116 117 9.075678 GCTACTTGATATACCACTAGGAAGTTA 57.924 37.037 0.00 0.00 38.69 2.24
118 119 6.494146 GGCTACTTGATATACCACTAGGAAGT 59.506 42.308 0.00 0.00 38.69 3.01
137 138 0.910088 AAGCGGGGAAGAAGGCTACT 60.910 55.000 0.00 0.00 34.82 2.57
234 235 4.019501 TGGCGGGGTAGTTTGTAATCTAAA 60.020 41.667 0.00 0.00 0.00 1.85
235 236 3.518705 TGGCGGGGTAGTTTGTAATCTAA 59.481 43.478 0.00 0.00 0.00 2.10
236 237 3.106054 TGGCGGGGTAGTTTGTAATCTA 58.894 45.455 0.00 0.00 0.00 1.98
237 238 1.910671 TGGCGGGGTAGTTTGTAATCT 59.089 47.619 0.00 0.00 0.00 2.40
238 239 2.406596 TGGCGGGGTAGTTTGTAATC 57.593 50.000 0.00 0.00 0.00 1.75
239 240 2.883122 TTGGCGGGGTAGTTTGTAAT 57.117 45.000 0.00 0.00 0.00 1.89
240 241 2.653234 TTTGGCGGGGTAGTTTGTAA 57.347 45.000 0.00 0.00 0.00 2.41
306 359 1.521423 GTGCCGTTATACTCATCACGC 59.479 52.381 0.00 0.00 31.77 5.34
317 370 1.745087 CTGCCAAATCAGTGCCGTTAT 59.255 47.619 0.00 0.00 0.00 1.89
320 373 1.228245 ACTGCCAAATCAGTGCCGT 60.228 52.632 0.00 0.00 44.88 5.68
328 381 8.897752 AGAGAAAAATATCTACACTGCCAAATC 58.102 33.333 0.00 0.00 0.00 2.17
359 412 8.289618 TCAGTTTAACTATGTTTGATCAAGTGC 58.710 33.333 8.41 4.26 0.00 4.40
432 494 2.566529 CGCTGCTGGACACGAGTA 59.433 61.111 0.00 0.00 0.00 2.59
438 500 4.704833 GGCTTCCGCTGCTGGACA 62.705 66.667 11.72 4.72 37.89 4.02
439 501 4.704833 TGGCTTCCGCTGCTGGAC 62.705 66.667 11.72 3.51 37.89 4.02
454 516 1.275291 TCTCCGCCTTTTCTACAGTGG 59.725 52.381 0.00 0.00 0.00 4.00
455 517 2.743636 TCTCCGCCTTTTCTACAGTG 57.256 50.000 0.00 0.00 0.00 3.66
456 518 2.897969 TCTTCTCCGCCTTTTCTACAGT 59.102 45.455 0.00 0.00 0.00 3.55
457 519 3.056465 ACTCTTCTCCGCCTTTTCTACAG 60.056 47.826 0.00 0.00 0.00 2.74
485 547 3.342719 TGCACATTTTTGCTCTCGGATA 58.657 40.909 0.00 0.00 43.41 2.59
486 548 2.161855 TGCACATTTTTGCTCTCGGAT 58.838 42.857 0.00 0.00 43.41 4.18
522 584 0.467290 CCTCCTCCTCCTTCTCCTCG 60.467 65.000 0.00 0.00 0.00 4.63
524 586 0.933700 CTCCTCCTCCTCCTTCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
525 587 0.105709 CCTCCTCCTCCTCCTTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
526 588 0.930726 TCCTCCTCCTCCTCCTTCTC 59.069 60.000 0.00 0.00 0.00 2.87
527 589 0.933700 CTCCTCCTCCTCCTCCTTCT 59.066 60.000 0.00 0.00 0.00 2.85
528 590 0.105709 CCTCCTCCTCCTCCTCCTTC 60.106 65.000 0.00 0.00 0.00 3.46
529 591 0.556380 TCCTCCTCCTCCTCCTCCTT 60.556 60.000 0.00 0.00 0.00 3.36
530 592 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
585 647 1.691196 TTCACTTGCTGTCCCTTTGG 58.309 50.000 0.00 0.00 0.00 3.28
586 648 2.541588 CGTTTCACTTGCTGTCCCTTTG 60.542 50.000 0.00 0.00 0.00 2.77
593 655 1.880027 GGATTCCGTTTCACTTGCTGT 59.120 47.619 0.00 0.00 0.00 4.40
595 657 2.154462 CTGGATTCCGTTTCACTTGCT 58.846 47.619 0.00 0.00 0.00 3.91
600 662 3.308530 CTTTTGCTGGATTCCGTTTCAC 58.691 45.455 0.00 0.00 0.00 3.18
607 669 0.603065 AACCGCTTTTGCTGGATTCC 59.397 50.000 0.00 0.00 44.80 3.01
623 685 3.414700 CACACGGAGCTCGCAACC 61.415 66.667 7.83 0.00 43.89 3.77
902 1041 4.803426 GCGAGTGGCGAGGTGAGG 62.803 72.222 0.00 0.00 44.57 3.86
903 1042 4.803426 GGCGAGTGGCGAGGTGAG 62.803 72.222 0.00 0.00 44.92 3.51
905 1044 4.457496 ATGGCGAGTGGCGAGGTG 62.457 66.667 0.00 0.00 44.92 4.00
906 1045 4.148825 GATGGCGAGTGGCGAGGT 62.149 66.667 0.00 0.00 44.92 3.85
973 1123 4.157120 CCGCCTAGGTTCCACCGG 62.157 72.222 11.31 9.76 44.90 5.28
974 1124 3.072468 TCCGCCTAGGTTCCACCG 61.072 66.667 11.31 3.85 44.90 4.94
975 1125 1.677637 CTCTCCGCCTAGGTTCCACC 61.678 65.000 11.31 0.00 41.99 4.61
976 1126 1.677637 CCTCTCCGCCTAGGTTCCAC 61.678 65.000 11.31 0.00 41.99 4.02
989 1139 2.833582 TCGTCATCGCCCCTCTCC 60.834 66.667 0.00 0.00 36.96 3.71
990 1140 2.413765 GTCGTCATCGCCCCTCTC 59.586 66.667 0.00 0.00 36.96 3.20
991 1141 3.518998 CGTCGTCATCGCCCCTCT 61.519 66.667 0.00 0.00 36.96 3.69
1307 1463 0.658897 GAGAAAACCAAACGACGGCA 59.341 50.000 0.00 0.00 0.00 5.69
1308 1464 0.942252 AGAGAAAACCAAACGACGGC 59.058 50.000 0.00 0.00 0.00 5.68
1309 1465 1.529865 GGAGAGAAAACCAAACGACGG 59.470 52.381 0.00 0.00 0.00 4.79
1311 1467 2.220363 GTCGGAGAGAAAACCAAACGAC 59.780 50.000 0.00 0.00 41.79 4.34
1312 1468 2.101917 AGTCGGAGAGAAAACCAAACGA 59.898 45.455 0.00 0.00 36.95 3.85
1315 1471 3.128349 CGAAGTCGGAGAGAAAACCAAA 58.872 45.455 0.00 0.00 36.95 3.28
1325 1481 2.353889 CGGAAGATAACGAAGTCGGAGA 59.646 50.000 5.60 0.00 45.00 3.71
1336 1561 6.417191 TGCAGTATTTTCACGGAAGATAAC 57.583 37.500 0.00 0.00 0.00 1.89
1338 1563 8.902540 ATTATGCAGTATTTTCACGGAAGATA 57.097 30.769 0.00 0.00 0.00 1.98
1349 1574 7.011669 GGCAGCAAAATGATTATGCAGTATTTT 59.988 33.333 0.00 0.00 42.45 1.82
1355 1580 3.787785 TGGCAGCAAAATGATTATGCAG 58.212 40.909 0.00 0.00 42.45 4.41
1359 1584 5.506815 CGTCTCATGGCAGCAAAATGATTAT 60.507 40.000 0.00 0.00 30.31 1.28
1368 1593 0.250252 TTCACGTCTCATGGCAGCAA 60.250 50.000 0.00 0.00 0.00 3.91
1401 1629 3.821033 GCAAAACTGCTCTAGGGAAGAAA 59.179 43.478 3.95 0.00 32.46 2.52
1403 1631 2.639839 AGCAAAACTGCTCTAGGGAAGA 59.360 45.455 3.95 0.00 42.12 2.87
1404 1632 3.064900 AGCAAAACTGCTCTAGGGAAG 57.935 47.619 0.00 0.00 42.12 3.46
1407 1635 2.887152 ACAAAGCAAAACTGCTCTAGGG 59.113 45.455 0.00 0.00 45.54 3.53
1417 1645 5.913305 ACGTACGTAAAACAAAGCAAAAC 57.087 34.783 21.41 0.00 0.00 2.43
1436 1664 4.091509 GTGAACGAATCAAATCTGCTACGT 59.908 41.667 0.00 0.00 40.50 3.57
1437 1665 4.569029 GTGAACGAATCAAATCTGCTACG 58.431 43.478 0.00 0.00 40.50 3.51
1438 1666 4.569029 CGTGAACGAATCAAATCTGCTAC 58.431 43.478 0.00 0.00 40.50 3.58
1441 1669 2.159653 AGCGTGAACGAATCAAATCTGC 60.160 45.455 7.10 0.00 40.50 4.26
1454 1682 4.492570 CGAATACCAAAGATCAGCGTGAAC 60.493 45.833 0.00 0.00 0.00 3.18
1458 1686 3.448686 CTCGAATACCAAAGATCAGCGT 58.551 45.455 0.00 0.00 0.00 5.07
1468 1696 3.992943 ACCATCAACCTCGAATACCAA 57.007 42.857 0.00 0.00 0.00 3.67
1472 1700 9.706691 GATTAGATTAACCATCAACCTCGAATA 57.293 33.333 0.00 0.00 33.75 1.75
1503 1731 2.900546 ACATAGAGCCGGGATAAGAAGG 59.099 50.000 2.18 0.00 0.00 3.46
1512 1740 4.402056 TCTCTAAAAACATAGAGCCGGG 57.598 45.455 2.18 0.00 45.60 5.73
1537 1765 6.926630 ATTAAAGCCCCAAGTCACAAAATA 57.073 33.333 0.00 0.00 0.00 1.40
1569 1797 1.083015 CAAGCCGGTGTTCGTTTCG 60.083 57.895 1.90 0.00 37.11 3.46
1632 1861 6.635239 ACGACTAAAACCAATCGATTGTTTTG 59.365 34.615 33.01 28.02 33.54 2.44
1637 1866 4.553429 GCAACGACTAAAACCAATCGATTG 59.447 41.667 27.66 27.66 37.97 2.67
1655 1887 1.740025 GGGGAGAAGAGAAATGCAACG 59.260 52.381 0.00 0.00 0.00 4.10
1740 1973 3.059529 GCTGGACGAAAGAGAAACAACTC 60.060 47.826 0.00 0.00 37.19 3.01
1756 1989 2.154798 TACAGAGTGCACCGCTGGAC 62.155 60.000 29.70 9.86 39.00 4.02
1763 1996 2.143925 GAGGTTGTTACAGAGTGCACC 58.856 52.381 14.63 5.12 0.00 5.01
1816 2056 5.104941 TGAGTGAGTGGTATTATTGGAGGTG 60.105 44.000 0.00 0.00 0.00 4.00
1831 2074 1.683385 TCTGTGGTCTGTGAGTGAGTG 59.317 52.381 0.00 0.00 0.00 3.51
1832 2075 2.073252 TCTGTGGTCTGTGAGTGAGT 57.927 50.000 0.00 0.00 0.00 3.41
1833 2076 2.824936 AGATCTGTGGTCTGTGAGTGAG 59.175 50.000 0.00 0.00 0.00 3.51
1834 2077 2.560105 CAGATCTGTGGTCTGTGAGTGA 59.440 50.000 14.95 0.00 38.58 3.41
1844 2087 3.755378 GACAAGAAATGCAGATCTGTGGT 59.245 43.478 23.38 6.54 0.00 4.16
2101 2351 5.235616 ACGATTTTCTGTTGTTTTAGCTCGA 59.764 36.000 0.00 0.00 0.00 4.04
2102 2352 5.440685 ACGATTTTCTGTTGTTTTAGCTCG 58.559 37.500 0.00 0.00 0.00 5.03
2107 2357 4.735822 CGCCAACGATTTTCTGTTGTTTTA 59.264 37.500 0.00 0.00 42.99 1.52
2111 2361 1.599419 GCGCCAACGATTTTCTGTTGT 60.599 47.619 0.00 0.00 42.99 3.32
2112 2362 1.052287 GCGCCAACGATTTTCTGTTG 58.948 50.000 0.00 0.00 43.93 3.33
2193 2443 8.221100 GCAATATACACAATAACACGACATAGG 58.779 37.037 0.00 0.00 0.00 2.57
2194 2444 8.978539 AGCAATATACACAATAACACGACATAG 58.021 33.333 0.00 0.00 0.00 2.23
2286 2540 2.670934 CGAAGCCACCTGCAAGCT 60.671 61.111 0.00 0.00 44.83 3.74
2287 2541 3.741476 CCGAAGCCACCTGCAAGC 61.741 66.667 0.00 0.00 44.83 4.01
2408 2664 5.184711 GGAGAGCTCAAGTTCTTGATTCAT 58.815 41.667 17.77 3.73 35.71 2.57
2423 2679 3.393089 TTCAGACAACTTGGAGAGCTC 57.607 47.619 5.27 5.27 0.00 4.09
2457 2713 7.095271 ACACAAACAACATTTCAAAAGTCCAAG 60.095 33.333 0.00 0.00 0.00 3.61
2461 2717 7.951565 CAGAACACAAACAACATTTCAAAAGTC 59.048 33.333 0.00 0.00 0.00 3.01
2466 2722 7.821652 TCTACAGAACACAAACAACATTTCAA 58.178 30.769 0.00 0.00 0.00 2.69
2468 2724 8.856490 ATTCTACAGAACACAAACAACATTTC 57.144 30.769 0.00 0.00 36.80 2.17
2566 2826 3.971871 GTCGATCGATCAATCAGTCAGTC 59.028 47.826 22.50 0.00 0.00 3.51
2567 2827 3.243234 GGTCGATCGATCAATCAGTCAGT 60.243 47.826 23.20 0.00 0.00 3.41
2568 2828 3.243201 TGGTCGATCGATCAATCAGTCAG 60.243 47.826 28.02 5.61 31.55 3.51
2569 2829 2.687935 TGGTCGATCGATCAATCAGTCA 59.312 45.455 28.02 2.43 31.55 3.41
2680 2948 8.513774 GTCAAGGTCAATAATAAAACCGGTTAA 58.486 33.333 22.60 12.73 36.87 2.01
2687 2955 8.736244 TGGCTTAGTCAAGGTCAATAATAAAAC 58.264 33.333 0.00 0.00 31.96 2.43
2763 3032 1.607628 GATGCAGGACAGATCAATGGC 59.392 52.381 0.00 0.00 0.00 4.40
2799 3068 5.340803 TGTGAGATTCTACTAACATGTCGC 58.659 41.667 0.00 0.00 0.00 5.19
2801 3070 6.868622 ACCTGTGAGATTCTACTAACATGTC 58.131 40.000 0.00 0.00 31.71 3.06
2867 3139 1.524165 GCAGCTGGGCTCTGATCAG 60.524 63.158 17.07 17.07 36.40 2.90
2937 3209 1.022451 GTTTAATCGGGCGGCTGTCA 61.022 55.000 18.34 0.00 0.00 3.58
2996 3268 2.100916 AGCATCAGATCCTGCAAAATGC 59.899 45.455 13.19 9.12 45.29 3.56
3002 3274 1.093496 CGCAAGCATCAGATCCTGCA 61.093 55.000 13.19 0.00 40.88 4.41
3012 3284 1.011463 CATCGCTGTCGCAAGCATC 60.011 57.895 9.41 0.00 43.73 3.91
3013 3285 1.020861 TTCATCGCTGTCGCAAGCAT 61.021 50.000 9.41 0.82 43.73 3.79
3014 3286 1.227342 TTTCATCGCTGTCGCAAGCA 61.227 50.000 9.41 0.00 43.73 3.91
3015 3287 0.110238 TTTTCATCGCTGTCGCAAGC 60.110 50.000 0.00 0.00 39.94 4.01
3016 3288 1.595609 GTTTTCATCGCTGTCGCAAG 58.404 50.000 0.00 0.00 35.30 4.01
3017 3289 0.110867 CGTTTTCATCGCTGTCGCAA 60.111 50.000 0.00 0.00 35.30 4.85
3018 3290 1.218875 ACGTTTTCATCGCTGTCGCA 61.219 50.000 0.00 0.00 35.30 5.10
3019 3291 0.711670 TACGTTTTCATCGCTGTCGC 59.288 50.000 0.00 0.00 35.26 5.19
3020 3292 2.034842 GGATACGTTTTCATCGCTGTCG 60.035 50.000 0.00 0.00 0.00 4.35
3021 3293 2.927477 TGGATACGTTTTCATCGCTGTC 59.073 45.455 0.00 0.00 42.51 3.51
3022 3294 2.930040 CTGGATACGTTTTCATCGCTGT 59.070 45.455 0.00 0.00 42.51 4.40
3023 3295 2.285834 GCTGGATACGTTTTCATCGCTG 60.286 50.000 0.00 0.00 42.51 5.18
3024 3296 1.933853 GCTGGATACGTTTTCATCGCT 59.066 47.619 0.00 0.00 42.51 4.93
3025 3297 1.663643 TGCTGGATACGTTTTCATCGC 59.336 47.619 0.00 0.00 42.51 4.58
3026 3298 3.186909 TCTGCTGGATACGTTTTCATCG 58.813 45.455 0.00 0.00 42.51 3.84


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

AutoCloner maintained by Alex Coulton.