Multiple sequence alignment - TraesCS1B01G288600

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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 TraesCS1B01G288600 chr1B 100.000 3796 0 0 1 3796 503350632 503354427 0.000000e+00 7011.0
1 TraesCS1B01G288600 chr1D 91.595 2320 110 29 1 2275 376620120 376622399 0.000000e+00 3125.0
2 TraesCS1B01G288600 chr1D 93.794 1273 58 13 2355 3609 376622396 376623665 0.000000e+00 1893.0
3 TraesCS1B01G288600 chr1A 93.095 2013 81 24 297 2275 476908493 476910481 0.000000e+00 2894.0
4 TraesCS1B01G288600 chr1A 89.885 1473 80 24 2356 3796 476910479 476911914 0.000000e+00 1831.0
5 TraesCS1B01G288600 chr1A 81.677 322 41 13 1 307 476907968 476908286 6.290000e-63 252.0
6 TraesCS1B01G288600 chr1A 100.000 91 0 0 2272 2362 133496464 133496554 6.520000e-38 169.0
7 TraesCS1B01G288600 chr7B 96.970 99 1 1 2272 2368 285453487 285453585 8.440000e-37 165.0
8 TraesCS1B01G288600 chr7B 96.040 101 1 2 2272 2370 719465290 719465191 1.090000e-35 161.0
9 TraesCS1B01G288600 chr3B 95.960 99 4 0 2260 2358 612117831 612117733 1.090000e-35 161.0
10 TraesCS1B01G288600 chr2D 96.907 97 2 1 2261 2357 371692494 371692589 1.090000e-35 161.0
11 TraesCS1B01G288600 chr5D 96.000 100 1 3 2260 2358 475004840 475004937 3.920000e-35 159.0
12 TraesCS1B01G288600 chr7D 91.818 110 8 1 2248 2357 550104556 550104664 6.570000e-33 152.0
13 TraesCS1B01G288600 chr7D 93.204 103 5 2 2256 2357 58488135 58488034 2.360000e-32 150.0
14 TraesCS1B01G288600 chr7D 94.737 38 1 1 3603 3640 49871813 49871777 1.470000e-04 58.4
15 TraesCS1B01G288600 chr6B 89.916 119 8 4 2251 2367 390047013 390046897 2.360000e-32 150.0


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 TraesCS1B01G288600 chr1B 503350632 503354427 3795 False 7011 7011 100.0000 1 3796 1 chr1B.!!$F1 3795
1 TraesCS1B01G288600 chr1D 376620120 376623665 3545 False 2509 3125 92.6945 1 3609 2 chr1D.!!$F1 3608
2 TraesCS1B01G288600 chr1A 476907968 476911914 3946 False 1659 2894 88.2190 1 3796 3 chr1A.!!$F2 3795

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
592 840 0.387202 CATGCGGATCCGTCTCTTCT 59.613 55.000 33.33 9.32 42.09 2.85 F
931 1179 0.462759 CTGTTCCCAGCCCTCGATTC 60.463 60.000 0.00 0.00 0.00 2.52 F
1478 1741 1.000938 CAAAGCCAACTTGTCTGCTCC 60.001 52.381 0.00 0.00 35.85 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 2061 0.615331 TGAGAAGAGTGTGGCATCCC 59.385 55.000 0.0 0.0 0.0 3.85 R
2356 2649 1.004745 CAGGACCCAATGCTTAGTGGT 59.995 52.381 0.0 0.0 32.6 4.16 R
3256 3582 1.202325 CCATGGCAATCAACATCACCG 60.202 52.381 0.0 0.0 0.0 4.94 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
65 66 1.750399 ATCGGTGCTTGGTGATGCC 60.750 57.895 0.00 0.00 37.90 4.40
66 67 3.443045 CGGTGCTTGGTGATGCCC 61.443 66.667 0.00 0.00 36.04 5.36
98 99 1.895231 AGTTTGGAAACGCGGGGTC 60.895 57.895 12.47 4.00 43.51 4.46
150 167 9.081997 TGATAAAAGTTCACATGAAAAACACAC 57.918 29.630 0.00 0.00 35.58 3.82
164 181 5.544136 AAAACACACAAATTTTCACAGCC 57.456 34.783 0.00 0.00 0.00 4.85
169 186 1.070601 ACAAATTTTCACAGCCAGCCC 59.929 47.619 0.00 0.00 0.00 5.19
170 187 1.070445 CAAATTTTCACAGCCAGCCCA 59.930 47.619 0.00 0.00 0.00 5.36
173 190 1.422531 TTTTCACAGCCAGCCCATTT 58.577 45.000 0.00 0.00 0.00 2.32
174 191 0.680618 TTTCACAGCCAGCCCATTTG 59.319 50.000 0.00 0.00 0.00 2.32
175 192 0.469705 TTCACAGCCAGCCCATTTGT 60.470 50.000 0.00 0.00 0.00 2.83
176 193 0.469705 TCACAGCCAGCCCATTTGTT 60.470 50.000 0.00 0.00 0.00 2.83
177 194 1.202989 TCACAGCCAGCCCATTTGTTA 60.203 47.619 0.00 0.00 0.00 2.41
179 196 1.075374 ACAGCCAGCCCATTTGTTAGA 59.925 47.619 0.00 0.00 0.00 2.10
331 568 5.503498 TGTTCACGGTGATTTCTAAAAACG 58.497 37.500 12.26 0.00 0.00 3.60
348 586 9.719279 TCTAAAAACGAAAATTACACGAAACAT 57.281 25.926 0.00 0.00 0.00 2.71
366 604 7.005958 CGAAACATGATAGCATAATGAGTTCG 58.994 38.462 0.00 14.50 36.76 3.95
394 632 1.239296 CCACATGGCATAGGCGGATG 61.239 60.000 0.00 8.08 42.47 3.51
443 685 2.201732 CACAGCGGTATCGTGCTTTAT 58.798 47.619 0.00 0.00 40.03 1.40
444 686 3.377439 CACAGCGGTATCGTGCTTTATA 58.623 45.455 0.00 0.00 40.03 0.98
525 773 1.067084 ATCTGCACCAGATCGAGCG 59.933 57.895 2.02 0.00 46.83 5.03
526 774 1.387295 ATCTGCACCAGATCGAGCGA 61.387 55.000 2.02 0.00 46.83 4.93
592 840 0.387202 CATGCGGATCCGTCTCTTCT 59.613 55.000 33.33 9.32 42.09 2.85
736 984 1.135731 GCGACTCTCCGTCTGTCTG 59.864 63.158 0.00 0.00 40.59 3.51
740 988 2.223157 CGACTCTCCGTCTGTCTGATTC 60.223 54.545 0.00 0.00 40.59 2.52
763 1011 1.059369 CTTGACGCTCGATTTGCCG 59.941 57.895 0.00 0.00 0.00 5.69
764 1012 1.626654 CTTGACGCTCGATTTGCCGT 61.627 55.000 0.00 0.00 0.00 5.68
765 1013 1.623081 TTGACGCTCGATTTGCCGTC 61.623 55.000 12.58 12.58 35.88 4.79
766 1014 2.048597 ACGCTCGATTTGCCGTCA 60.049 55.556 0.00 0.00 0.00 4.35
768 1016 2.802667 CGCTCGATTTGCCGTCAGG 61.803 63.158 0.00 0.00 41.62 3.86
781 1029 0.508641 CGTCAGGCATACATAAGCGC 59.491 55.000 0.00 0.00 0.00 5.92
816 1064 4.102054 TCTGCCTTGCTATGATCTTGATGA 59.898 41.667 0.00 0.00 0.00 2.92
824 1072 7.550597 TGCTATGATCTTGATGATTCCTAGT 57.449 36.000 0.00 0.00 35.14 2.57
825 1073 7.609960 TGCTATGATCTTGATGATTCCTAGTC 58.390 38.462 0.00 0.00 35.14 2.59
826 1074 7.041107 GCTATGATCTTGATGATTCCTAGTCC 58.959 42.308 0.00 0.00 35.14 3.85
827 1075 7.093377 GCTATGATCTTGATGATTCCTAGTCCT 60.093 40.741 0.00 0.00 35.14 3.85
828 1076 9.473007 CTATGATCTTGATGATTCCTAGTCCTA 57.527 37.037 0.00 0.00 35.14 2.94
829 1077 7.773489 TGATCTTGATGATTCCTAGTCCTAG 57.227 40.000 0.00 0.00 35.14 3.02
833 1081 6.711194 TCTTGATGATTCCTAGTCCTAGTACG 59.289 42.308 0.96 0.00 0.00 3.67
849 1097 3.671716 AGTACGCCTTTTCCCTGTAAAG 58.328 45.455 0.00 0.00 33.42 1.85
931 1179 0.462759 CTGTTCCCAGCCCTCGATTC 60.463 60.000 0.00 0.00 0.00 2.52
1053 1301 2.978010 GTGCCCTTCACACCACCG 60.978 66.667 0.00 0.00 44.98 4.94
1124 1372 2.027837 GGCTTTGGCAATCCTTTGATGT 60.028 45.455 0.00 0.00 40.87 3.06
1228 1477 4.154918 ACGTTCTGGCTTCTTCATGATTTC 59.845 41.667 0.00 0.00 0.00 2.17
1283 1546 5.582269 TCATCTGCTATTTTTGTCTCCGAAG 59.418 40.000 0.00 0.00 0.00 3.79
1289 1552 5.390991 GCTATTTTTGTCTCCGAAGTTCTGG 60.391 44.000 0.56 4.50 0.00 3.86
1307 1570 4.101114 TCTGGTAGAACAGATTAAGCCCA 58.899 43.478 0.00 0.00 42.26 5.36
1314 1577 6.313519 AGAACAGATTAAGCCCAAGATACA 57.686 37.500 0.00 0.00 0.00 2.29
1327 1590 5.992217 GCCCAAGATACACTATCAACTAAGG 59.008 44.000 0.00 0.00 37.65 2.69
1354 1617 3.648339 TGTTTCTCTGCTGATTTTGCC 57.352 42.857 0.00 0.00 0.00 4.52
1372 1635 1.421382 CCGTTGCAATGCTTTTCTGG 58.579 50.000 13.42 0.00 0.00 3.86
1373 1636 1.421382 CGTTGCAATGCTTTTCTGGG 58.579 50.000 6.82 0.00 0.00 4.45
1410 1673 2.103373 CTAGTAGGTGAGCTTCAGCCA 58.897 52.381 10.45 0.00 45.34 4.75
1428 1691 8.579850 TTCAGCCACTGAAATTTCATAACTAT 57.420 30.769 20.76 4.09 45.84 2.12
1433 1696 8.034804 GCCACTGAAATTTCATAACTATGGTTT 58.965 33.333 20.76 0.00 36.46 3.27
1440 1703 9.807649 AAATTTCATAACTATGGTTTCATGCTC 57.192 29.630 0.00 0.00 36.92 4.26
1478 1741 1.000938 CAAAGCCAACTTGTCTGCTCC 60.001 52.381 0.00 0.00 35.85 4.70
1622 1885 5.355350 AGATTTGTAAGTAATGTGGCAGCTC 59.645 40.000 0.00 0.00 0.00 4.09
1774 2040 2.099921 CTGATTCGGTGTAGGGACTGAG 59.900 54.545 0.00 0.00 41.52 3.35
1884 2150 2.311542 TCAACCTGGCAATGGAAGGTAT 59.688 45.455 0.00 0.00 43.62 2.73
1901 2189 6.764560 GGAAGGTATATCGACCAAAGCTTTTA 59.235 38.462 9.53 0.00 42.47 1.52
1918 2206 7.494922 AGCTTTTATTTCTCTCTCTCTTCCT 57.505 36.000 0.00 0.00 0.00 3.36
1990 2280 4.968626 TGTTGACATTGATTCGTGTATGC 58.031 39.130 0.00 0.00 0.00 3.14
1995 2285 5.855925 TGACATTGATTCGTGTATGCAAAAC 59.144 36.000 0.00 0.00 0.00 2.43
2275 2568 8.902806 TCACAAACACAAAGATTGAAAGATACT 58.097 29.630 0.00 0.00 34.43 2.12
2276 2569 9.173939 CACAAACACAAAGATTGAAAGATACTC 57.826 33.333 0.00 0.00 34.43 2.59
2278 2571 7.454260 AACACAAAGATTGAAAGATACTCCC 57.546 36.000 0.00 0.00 0.00 4.30
2279 2572 6.784031 ACACAAAGATTGAAAGATACTCCCT 58.216 36.000 0.00 0.00 0.00 4.20
2280 2573 6.881602 ACACAAAGATTGAAAGATACTCCCTC 59.118 38.462 0.00 0.00 0.00 4.30
2281 2574 6.317391 CACAAAGATTGAAAGATACTCCCTCC 59.683 42.308 0.00 0.00 0.00 4.30
2282 2575 4.946478 AGATTGAAAGATACTCCCTCCG 57.054 45.455 0.00 0.00 0.00 4.63
2283 2576 4.290942 AGATTGAAAGATACTCCCTCCGT 58.709 43.478 0.00 0.00 0.00 4.69
2284 2577 5.455872 AGATTGAAAGATACTCCCTCCGTA 58.544 41.667 0.00 0.00 0.00 4.02
2285 2578 5.897824 AGATTGAAAGATACTCCCTCCGTAA 59.102 40.000 0.00 0.00 0.00 3.18
2286 2579 6.383147 AGATTGAAAGATACTCCCTCCGTAAA 59.617 38.462 0.00 0.00 0.00 2.01
2287 2580 5.334724 TGAAAGATACTCCCTCCGTAAAC 57.665 43.478 0.00 0.00 0.00 2.01
2288 2581 5.021458 TGAAAGATACTCCCTCCGTAAACT 58.979 41.667 0.00 0.00 0.00 2.66
2289 2582 6.189859 TGAAAGATACTCCCTCCGTAAACTA 58.810 40.000 0.00 0.00 0.00 2.24
2290 2583 6.664816 TGAAAGATACTCCCTCCGTAAACTAA 59.335 38.462 0.00 0.00 0.00 2.24
2291 2584 7.343833 TGAAAGATACTCCCTCCGTAAACTAAT 59.656 37.037 0.00 0.00 0.00 1.73
2292 2585 8.773033 AAAGATACTCCCTCCGTAAACTAATA 57.227 34.615 0.00 0.00 0.00 0.98
2293 2586 8.953223 AAGATACTCCCTCCGTAAACTAATAT 57.047 34.615 0.00 0.00 0.00 1.28
2298 2591 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2299 2592 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2300 2593 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2301 2594 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2302 2595 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2303 2596 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2304 2597 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2305 2598 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2306 2599 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2351 2644 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2352 2645 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2353 2646 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2354 2647 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2355 2648 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2359 2652 9.940974 TTATATTAGTTTACAGAGGGAGTACCA 57.059 33.333 0.00 0.00 43.89 3.25
2360 2653 5.990120 TTAGTTTACAGAGGGAGTACCAC 57.010 43.478 0.00 0.00 43.89 4.16
2361 2654 4.129317 AGTTTACAGAGGGAGTACCACT 57.871 45.455 0.00 0.00 43.89 4.00
2362 2655 5.266709 AGTTTACAGAGGGAGTACCACTA 57.733 43.478 0.00 0.00 43.89 2.74
2431 2724 4.285020 TCAGAAGGATGAGTGCATAGAGT 58.715 43.478 0.00 0.00 34.11 3.24
2655 2949 1.225854 GCACGCGACAAGAGCATTC 60.226 57.895 15.93 0.00 34.19 2.67
2718 3012 3.411446 TGTTGAGCGACCTGAATTTCAT 58.589 40.909 0.00 0.00 0.00 2.57
2729 3023 6.486657 CGACCTGAATTTCATACCAACCATAT 59.513 38.462 0.00 0.00 0.00 1.78
2768 3062 2.905415 ACCCTTTTCAGGCATCATCA 57.095 45.000 0.00 0.00 39.20 3.07
2837 3131 0.819666 GGCAGCTTCCCGGAATAAGG 60.820 60.000 0.73 0.00 0.00 2.69
2891 3185 2.238144 CAGAAGCAATCTCTTCCTCCCA 59.762 50.000 0.41 0.00 42.52 4.37
2937 3231 0.463654 TGGCGAGCTTGCGGAATAAT 60.464 50.000 19.73 0.00 35.06 1.28
3009 3303 8.533569 TGTGTAACTGGATCAGACAGATATAA 57.466 34.615 4.68 0.00 39.24 0.98
3020 3314 5.071788 TCAGACAGATATAATGAACCCACCC 59.928 44.000 0.00 0.00 0.00 4.61
3050 3344 9.733556 TTATGTTCAATCCTAGCTTCTTTTACA 57.266 29.630 0.00 0.00 0.00 2.41
3061 3355 9.774742 CCTAGCTTCTTTTACATGTGTTTTATC 57.225 33.333 9.11 0.00 0.00 1.75
3085 3387 8.511604 TCTCAGAAATTTTCTTCTTCTTGTGT 57.488 30.769 8.95 0.00 38.11 3.72
3148 3450 7.220108 GGCAATTCTTGAACCGAACAATATTAC 59.780 37.037 0.00 0.00 0.00 1.89
3153 3458 3.619483 TGAACCGAACAATATTACTGCCG 59.381 43.478 0.00 0.00 0.00 5.69
3175 3500 4.491441 CGACATGATCATGAACAGTTCACG 60.491 45.833 36.37 21.62 43.48 4.35
3219 3545 0.732571 ATGATTAGGGTGCGCAAACG 59.267 50.000 14.00 0.00 44.07 3.60
3256 3582 0.980231 ATGGTGGACTCTGGAGGAGC 60.980 60.000 2.58 0.00 45.48 4.70
3258 3584 2.363018 TGGACTCTGGAGGAGCGG 60.363 66.667 2.58 0.00 45.48 5.52
3302 3628 1.767692 GATGGGGTGAGTGTTGGGT 59.232 57.895 0.00 0.00 0.00 4.51
3466 3796 3.769300 GACCCAATTATTGCCAGGAAAGT 59.231 43.478 0.00 0.00 0.00 2.66
3487 3822 2.066262 TGCGCGGAAAAGTTTAGAGAG 58.934 47.619 8.83 0.00 0.00 3.20
3499 3834 8.621532 AAAAGTTTAGAGAGCACAATGATGTA 57.378 30.769 0.00 0.00 37.82 2.29
3519 3854 0.613260 AAAGGCGTAGATGGTGCTCA 59.387 50.000 0.00 0.00 0.00 4.26
3558 3893 0.392193 GTGCCTGCTGCTAGTCACAT 60.392 55.000 0.00 0.00 42.00 3.21
3564 3899 3.593096 CTGCTGCTAGTCACATTTCAGA 58.407 45.455 0.00 0.00 0.00 3.27
3573 3908 7.339466 TGCTAGTCACATTTCAGAGACATACTA 59.661 37.037 0.00 0.00 32.48 1.82
3644 3979 4.089351 GCGTTTTTAAAATCATGTGGACCG 59.911 41.667 0.55 0.00 0.00 4.79
3665 4000 4.551388 CGAAGGAGCCATAATGAGTCTAC 58.449 47.826 0.00 0.00 0.00 2.59
3667 4002 3.567397 AGGAGCCATAATGAGTCTACGT 58.433 45.455 0.00 0.00 0.00 3.57
3672 4007 3.185188 GCCATAATGAGTCTACGTGCATG 59.815 47.826 3.82 3.82 0.00 4.06
3693 4028 1.212688 CTGCAGGATTGGTGGGTATCA 59.787 52.381 5.57 0.00 0.00 2.15
3694 4029 1.638070 TGCAGGATTGGTGGGTATCAA 59.362 47.619 0.00 0.00 0.00 2.57
3709 4044 5.647658 TGGGTATCAAAGCTGTTGTTATCTG 59.352 40.000 0.00 0.00 0.00 2.90
3710 4045 5.066505 GGGTATCAAAGCTGTTGTTATCTGG 59.933 44.000 0.00 0.00 0.00 3.86
3734 4069 2.551912 CGGGACTTTGTGTGCACCC 61.552 63.158 15.69 2.52 38.87 4.61
3755 4090 3.163630 GGTGCATTGCATCGGTTTATT 57.836 42.857 15.49 0.00 41.91 1.40
3756 4091 4.300189 GGTGCATTGCATCGGTTTATTA 57.700 40.909 15.49 0.00 41.91 0.98
3757 4092 4.677584 GGTGCATTGCATCGGTTTATTAA 58.322 39.130 15.49 0.00 41.91 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.044092 TAAGAGGAGGGGCATCACCA 59.956 55.000 0.00 0.00 42.05 4.17
65 66 1.065126 CAAACTGGCCTAAGAGGAGGG 60.065 57.143 3.32 0.00 37.67 4.30
66 67 1.065126 CCAAACTGGCCTAAGAGGAGG 60.065 57.143 3.32 0.00 37.67 4.30
129 130 7.721286 TTTGTGTGTTTTTCATGTGAACTTT 57.279 28.000 0.00 0.00 33.13 2.66
150 167 1.070445 TGGGCTGGCTGTGAAAATTTG 59.930 47.619 0.00 0.00 0.00 2.32
164 181 1.094785 CCCGTCTAACAAATGGGCTG 58.905 55.000 0.00 0.00 36.18 4.85
169 186 4.941263 TCCTCATTTCCCGTCTAACAAATG 59.059 41.667 0.00 0.00 37.51 2.32
170 187 5.174037 TCCTCATTTCCCGTCTAACAAAT 57.826 39.130 0.00 0.00 0.00 2.32
173 190 4.202377 TGTTTCCTCATTTCCCGTCTAACA 60.202 41.667 0.00 0.00 0.00 2.41
174 191 4.153655 GTGTTTCCTCATTTCCCGTCTAAC 59.846 45.833 0.00 0.00 0.00 2.34
175 192 4.202377 TGTGTTTCCTCATTTCCCGTCTAA 60.202 41.667 0.00 0.00 0.00 2.10
176 193 3.325425 TGTGTTTCCTCATTTCCCGTCTA 59.675 43.478 0.00 0.00 0.00 2.59
177 194 2.105821 TGTGTTTCCTCATTTCCCGTCT 59.894 45.455 0.00 0.00 0.00 4.18
179 196 2.649531 TGTGTTTCCTCATTTCCCGT 57.350 45.000 0.00 0.00 0.00 5.28
219 236 2.609427 TCTCTTCCAAGATCATGCCG 57.391 50.000 0.00 0.00 33.93 5.69
291 310 8.028938 ACCGTGAACAATTATTTACGTAGTAGT 58.971 33.333 12.04 0.98 46.93 2.73
293 312 8.026026 TCACCGTGAACAATTATTTACGTAGTA 58.974 33.333 12.04 0.00 45.11 1.82
331 568 8.841444 ATGCTATCATGTTTCGTGTAATTTTC 57.159 30.769 0.00 0.00 0.00 2.29
348 586 4.546570 CGTCCGAACTCATTATGCTATCA 58.453 43.478 0.00 0.00 0.00 2.15
394 632 1.680338 GTGGGCTCTCTCTCTCTCTC 58.320 60.000 0.00 0.00 0.00 3.20
443 685 1.071699 GGGAATGCGGCAGATAAGGTA 59.928 52.381 9.25 0.00 0.00 3.08
444 686 0.179018 GGGAATGCGGCAGATAAGGT 60.179 55.000 9.25 0.00 0.00 3.50
525 773 3.843240 CTCGGCTCGCGTTGCTTC 61.843 66.667 21.30 9.05 0.00 3.86
592 840 2.668212 CGCTTGCCCGGTTCAGAA 60.668 61.111 0.00 0.00 0.00 3.02
712 960 1.153997 GACGGAGAGTCGCCTTCAC 60.154 63.158 13.53 0.00 40.43 3.18
723 971 2.493675 CAAGGAATCAGACAGACGGAGA 59.506 50.000 0.00 0.00 0.00 3.71
763 1011 0.868406 GGCGCTTATGTATGCCTGAC 59.132 55.000 7.64 0.00 44.16 3.51
764 1012 3.305709 GGCGCTTATGTATGCCTGA 57.694 52.632 7.64 0.00 44.16 3.86
768 1016 2.032549 CAGTTGAGGCGCTTATGTATGC 60.033 50.000 7.64 0.00 0.00 3.14
769 1017 3.198068 ACAGTTGAGGCGCTTATGTATG 58.802 45.455 7.64 1.23 0.00 2.39
770 1018 3.543680 ACAGTTGAGGCGCTTATGTAT 57.456 42.857 7.64 0.00 0.00 2.29
771 1019 3.446161 AGTACAGTTGAGGCGCTTATGTA 59.554 43.478 7.64 4.86 0.00 2.29
772 1020 2.233922 AGTACAGTTGAGGCGCTTATGT 59.766 45.455 7.64 5.88 0.00 2.29
773 1021 2.860735 GAGTACAGTTGAGGCGCTTATG 59.139 50.000 7.64 0.00 0.00 1.90
774 1022 2.761208 AGAGTACAGTTGAGGCGCTTAT 59.239 45.455 7.64 0.00 0.00 1.73
775 1023 2.094700 CAGAGTACAGTTGAGGCGCTTA 60.095 50.000 7.64 0.00 0.00 3.09
776 1024 0.969894 AGAGTACAGTTGAGGCGCTT 59.030 50.000 7.64 0.00 0.00 4.68
777 1025 0.244994 CAGAGTACAGTTGAGGCGCT 59.755 55.000 7.64 0.00 0.00 5.92
778 1026 1.355066 GCAGAGTACAGTTGAGGCGC 61.355 60.000 0.00 0.00 0.00 6.53
781 1029 2.693069 CAAGGCAGAGTACAGTTGAGG 58.307 52.381 0.00 0.00 0.00 3.86
816 1064 3.880168 AGGCGTACTAGGACTAGGAAT 57.120 47.619 2.99 0.00 37.49 3.01
824 1072 1.829222 CAGGGAAAAGGCGTACTAGGA 59.171 52.381 0.00 0.00 0.00 2.94
825 1073 1.553704 ACAGGGAAAAGGCGTACTAGG 59.446 52.381 0.00 0.00 0.00 3.02
826 1074 4.460948 TTACAGGGAAAAGGCGTACTAG 57.539 45.455 0.00 0.00 0.00 2.57
827 1075 4.284234 ACTTTACAGGGAAAAGGCGTACTA 59.716 41.667 0.00 0.00 38.09 1.82
828 1076 3.072038 ACTTTACAGGGAAAAGGCGTACT 59.928 43.478 0.00 0.00 38.09 2.73
829 1077 3.405831 ACTTTACAGGGAAAAGGCGTAC 58.594 45.455 0.00 0.00 38.09 3.67
833 1081 4.796290 GCTTCAACTTTACAGGGAAAAGGC 60.796 45.833 0.00 0.00 38.09 4.35
849 1097 1.865865 TCTGGTGAGAACGCTTCAAC 58.134 50.000 0.00 0.00 0.00 3.18
1053 1301 0.825010 CCATACCTGCATTGGGAGCC 60.825 60.000 0.00 0.00 0.00 4.70
1228 1477 8.861086 TCAGCTCCTATATACTTTTTAGTCCAG 58.139 37.037 0.00 0.00 0.00 3.86
1242 1491 7.460071 AGCAGATGAAAAATCAGCTCCTATAT 58.540 34.615 0.00 0.00 36.36 0.86
1289 1552 7.224949 GTGTATCTTGGGCTTAATCTGTTCTAC 59.775 40.741 0.00 0.00 0.00 2.59
1307 1570 9.368416 TCTATGCCTTAGTTGATAGTGTATCTT 57.632 33.333 0.00 0.00 36.17 2.40
1314 1577 8.709308 AGAAACATCTATGCCTTAGTTGATAGT 58.291 33.333 8.19 0.00 33.56 2.12
1354 1617 1.000385 TCCCAGAAAAGCATTGCAACG 60.000 47.619 11.91 0.00 0.00 4.10
1390 1653 2.103373 TGGCTGAAGCTCACCTACTAG 58.897 52.381 1.74 0.00 41.70 2.57
1392 1655 0.610687 GTGGCTGAAGCTCACCTACT 59.389 55.000 1.74 0.00 41.70 2.57
1440 1703 1.243342 TGAGCCCCTGAAATTGCACG 61.243 55.000 0.00 0.00 0.00 5.34
1622 1885 9.859427 ATGTTGTAAATATGGAACTCAATGTTG 57.141 29.630 0.00 0.00 39.30 3.33
1774 2040 1.063166 GCAAACTAGCTGCGCCATC 59.937 57.895 4.18 0.00 0.00 3.51
1795 2061 0.615331 TGAGAAGAGTGTGGCATCCC 59.385 55.000 0.00 0.00 0.00 3.85
1884 2150 8.041323 AGAGAGAAATAAAAGCTTTGGTCGATA 58.959 33.333 13.54 0.07 0.00 2.92
1901 2189 4.073425 ACCCAGGAAGAGAGAGAGAAAT 57.927 45.455 0.00 0.00 0.00 2.17
1918 2206 2.025416 AGCATATACCACTTGCAACCCA 60.025 45.455 0.00 0.00 38.84 4.51
1990 2280 2.157738 CTGCTCAGAAGGAGGGTTTTG 58.842 52.381 0.00 0.00 44.22 2.44
2275 2568 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2276 2569 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2278 2571 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2279 2572 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2280 2573 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2325 2618 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2326 2619 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2327 2620 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2328 2621 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2329 2622 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2333 2626 9.940974 TGGTACTCCCTCTGTAAACTAATATAA 57.059 33.333 0.00 0.00 0.00 0.98
2334 2627 9.359653 GTGGTACTCCCTCTGTAAACTAATATA 57.640 37.037 0.00 0.00 0.00 0.86
2335 2628 8.066247 AGTGGTACTCCCTCTGTAAACTAATAT 58.934 37.037 0.00 0.00 35.71 1.28
2336 2629 7.416731 AGTGGTACTCCCTCTGTAAACTAATA 58.583 38.462 0.00 0.00 35.71 0.98
2337 2630 6.262207 AGTGGTACTCCCTCTGTAAACTAAT 58.738 40.000 0.00 0.00 35.71 1.73
2338 2631 5.648247 AGTGGTACTCCCTCTGTAAACTAA 58.352 41.667 0.00 0.00 35.71 2.24
2339 2632 5.266709 AGTGGTACTCCCTCTGTAAACTA 57.733 43.478 0.00 0.00 35.71 2.24
2340 2633 4.129317 AGTGGTACTCCCTCTGTAAACT 57.871 45.455 0.00 0.00 35.71 2.66
2341 2634 5.624052 GCTTAGTGGTACTCCCTCTGTAAAC 60.624 48.000 0.00 0.00 37.61 2.01
2342 2635 4.465305 GCTTAGTGGTACTCCCTCTGTAAA 59.535 45.833 0.00 0.00 37.61 2.01
2343 2636 4.021916 GCTTAGTGGTACTCCCTCTGTAA 58.978 47.826 0.00 0.00 37.61 2.41
2344 2637 3.010920 TGCTTAGTGGTACTCCCTCTGTA 59.989 47.826 0.00 0.00 37.61 2.74
2345 2638 2.225293 TGCTTAGTGGTACTCCCTCTGT 60.225 50.000 0.00 0.00 37.61 3.41
2346 2639 2.457598 TGCTTAGTGGTACTCCCTCTG 58.542 52.381 0.00 0.00 37.61 3.35
2347 2640 2.921834 TGCTTAGTGGTACTCCCTCT 57.078 50.000 0.00 0.00 40.21 3.69
2348 2641 3.432326 CCAATGCTTAGTGGTACTCCCTC 60.432 52.174 0.00 0.00 0.00 4.30
2349 2642 2.505819 CCAATGCTTAGTGGTACTCCCT 59.494 50.000 0.00 0.00 0.00 4.20
2350 2643 2.421529 CCCAATGCTTAGTGGTACTCCC 60.422 54.545 0.00 0.00 32.60 4.30
2351 2644 2.238898 ACCCAATGCTTAGTGGTACTCC 59.761 50.000 0.00 0.00 32.60 3.85
2352 2645 3.532542 GACCCAATGCTTAGTGGTACTC 58.467 50.000 0.00 0.00 32.60 2.59
2353 2646 2.238898 GGACCCAATGCTTAGTGGTACT 59.761 50.000 0.00 0.00 32.60 2.73
2354 2647 2.238898 AGGACCCAATGCTTAGTGGTAC 59.761 50.000 0.00 0.00 32.60 3.34
2355 2648 2.238646 CAGGACCCAATGCTTAGTGGTA 59.761 50.000 0.00 0.00 32.60 3.25
2356 2649 1.004745 CAGGACCCAATGCTTAGTGGT 59.995 52.381 0.00 0.00 32.60 4.16
2357 2650 1.281867 TCAGGACCCAATGCTTAGTGG 59.718 52.381 0.00 0.00 34.44 4.00
2358 2651 2.026822 AGTCAGGACCCAATGCTTAGTG 60.027 50.000 0.00 0.00 0.00 2.74
2359 2652 2.269940 AGTCAGGACCCAATGCTTAGT 58.730 47.619 0.00 0.00 0.00 2.24
2360 2653 3.054802 AGAAGTCAGGACCCAATGCTTAG 60.055 47.826 0.00 0.00 0.00 2.18
2361 2654 2.912956 AGAAGTCAGGACCCAATGCTTA 59.087 45.455 0.00 0.00 0.00 3.09
2362 2655 1.707427 AGAAGTCAGGACCCAATGCTT 59.293 47.619 0.00 0.00 0.00 3.91
2449 2742 9.766277 GAATTTGTCATTCAGAGTATTTGAGAC 57.234 33.333 0.00 0.00 0.00 3.36
2655 2949 5.280945 TGTGAAAAATCCAGAAAAAGAGCG 58.719 37.500 0.00 0.00 0.00 5.03
2718 3012 4.415881 ACGCATTCAGATATGGTTGGTA 57.584 40.909 0.00 0.00 0.00 3.25
2729 3023 4.933400 GGGTAAAGAAGTAACGCATTCAGA 59.067 41.667 0.00 0.00 0.00 3.27
2768 3062 2.350514 GGCTTCTGCTCTGCACCT 59.649 61.111 0.00 0.00 39.59 4.00
2837 3131 4.627611 ATACATGTGCACTCAAAGCATC 57.372 40.909 19.41 0.00 44.79 3.91
2891 3185 1.916181 ACGAAGGTGGGAAATGGAGAT 59.084 47.619 0.00 0.00 0.00 2.75
2937 3231 8.726988 GCACTATGTATTACCAAAAACTCTTGA 58.273 33.333 0.00 0.00 0.00 3.02
3009 3303 3.825908 ACATAAACAGGGTGGGTTCAT 57.174 42.857 0.00 0.00 0.00 2.57
3020 3314 7.856145 AGAAGCTAGGATTGAACATAAACAG 57.144 36.000 0.00 0.00 0.00 3.16
3061 3355 9.578439 AAACACAAGAAGAAGAAAATTTCTGAG 57.422 29.630 9.21 0.00 40.59 3.35
3078 3380 8.292448 GCAGAAATTCTTCAGATAAACACAAGA 58.708 33.333 0.00 0.00 33.64 3.02
3085 3387 6.458751 GCATCGGCAGAAATTCTTCAGATAAA 60.459 38.462 7.74 0.00 40.72 1.40
3148 3450 2.282407 TGTTCATGATCATGTCGGCAG 58.718 47.619 30.01 7.95 39.72 4.85
3175 3500 5.156355 CAGCATTTGGACTTGTATGTGTTC 58.844 41.667 0.00 0.00 0.00 3.18
3219 3545 2.621998 CCATTCAACTCCCATCTGATGC 59.378 50.000 12.17 0.00 0.00 3.91
3256 3582 1.202325 CCATGGCAATCAACATCACCG 60.202 52.381 0.00 0.00 0.00 4.94
3258 3584 1.930567 GCCATGGCAATCAACATCAC 58.069 50.000 32.08 0.00 41.49 3.06
3287 3613 1.377612 GGTACCCAACACTCACCCC 59.622 63.158 0.00 0.00 0.00 4.95
3302 3628 4.263949 TGGACAAGAGTCAGAGAGATGGTA 60.264 45.833 0.00 0.00 46.80 3.25
3466 3796 2.478894 CTCTCTAAACTTTTCCGCGCAA 59.521 45.455 8.75 0.00 0.00 4.85
3487 3822 3.216147 ACGCCTTTTACATCATTGTGC 57.784 42.857 0.00 0.00 36.53 4.57
3499 3834 1.003118 TGAGCACCATCTACGCCTTTT 59.997 47.619 0.00 0.00 0.00 2.27
3519 3854 1.010935 CATTGAGTGCTGACGCGACT 61.011 55.000 15.93 4.72 39.65 4.18
3558 3893 9.955102 TTCAGTAGTACTAGTATGTCTCTGAAA 57.045 33.333 18.57 8.51 36.00 2.69
3564 3899 9.848710 TTGCTATTCAGTAGTACTAGTATGTCT 57.151 33.333 9.94 1.36 32.72 3.41
3573 3908 9.137459 ACAGTGATATTGCTATTCAGTAGTACT 57.863 33.333 0.00 0.00 32.72 2.73
3609 3944 9.751542 TGATTTTAAAAACGCAGGAATAGAAAA 57.248 25.926 4.44 0.00 0.00 2.29
3610 3945 9.921637 ATGATTTTAAAAACGCAGGAATAGAAA 57.078 25.926 4.44 0.00 0.00 2.52
3611 3946 9.352784 CATGATTTTAAAAACGCAGGAATAGAA 57.647 29.630 4.44 0.00 0.00 2.10
3612 3947 8.519526 ACATGATTTTAAAAACGCAGGAATAGA 58.480 29.630 15.54 0.00 0.00 1.98
3613 3948 8.586273 CACATGATTTTAAAAACGCAGGAATAG 58.414 33.333 15.54 4.47 0.00 1.73
3614 3949 7.543868 CCACATGATTTTAAAAACGCAGGAATA 59.456 33.333 15.54 0.00 0.00 1.75
3615 3950 6.368516 CCACATGATTTTAAAAACGCAGGAAT 59.631 34.615 15.54 0.00 0.00 3.01
3616 3951 5.694006 CCACATGATTTTAAAAACGCAGGAA 59.306 36.000 15.54 0.00 0.00 3.36
3617 3952 5.010112 TCCACATGATTTTAAAAACGCAGGA 59.990 36.000 15.54 11.42 0.00 3.86
3618 3953 5.118510 GTCCACATGATTTTAAAAACGCAGG 59.881 40.000 4.44 8.05 0.00 4.85
3619 3954 5.118510 GGTCCACATGATTTTAAAAACGCAG 59.881 40.000 4.44 0.00 0.00 5.18
3620 3955 4.985409 GGTCCACATGATTTTAAAAACGCA 59.015 37.500 4.44 4.56 0.00 5.24
3621 3956 4.089351 CGGTCCACATGATTTTAAAAACGC 59.911 41.667 4.44 0.00 0.00 4.84
3622 3957 5.453648 TCGGTCCACATGATTTTAAAAACG 58.546 37.500 4.44 0.00 0.00 3.60
3623 3958 6.364976 CCTTCGGTCCACATGATTTTAAAAAC 59.635 38.462 4.44 2.82 0.00 2.43
3624 3959 6.265649 TCCTTCGGTCCACATGATTTTAAAAA 59.734 34.615 4.44 0.00 0.00 1.94
3625 3960 5.770663 TCCTTCGGTCCACATGATTTTAAAA 59.229 36.000 2.51 2.51 0.00 1.52
3626 3961 5.317808 TCCTTCGGTCCACATGATTTTAAA 58.682 37.500 0.00 0.00 0.00 1.52
3630 3965 2.941415 GCTCCTTCGGTCCACATGATTT 60.941 50.000 0.00 0.00 0.00 2.17
3644 3979 4.038162 ACGTAGACTCATTATGGCTCCTTC 59.962 45.833 0.00 0.00 0.00 3.46
3653 3988 4.053983 CAGCATGCACGTAGACTCATTAT 58.946 43.478 21.98 0.00 0.00 1.28
3672 4007 0.106519 ATACCCACCAATCCTGCAGC 60.107 55.000 8.66 0.00 0.00 5.25
3693 4028 3.821033 GTCCACCAGATAACAACAGCTTT 59.179 43.478 0.00 0.00 0.00 3.51
3694 4029 3.412386 GTCCACCAGATAACAACAGCTT 58.588 45.455 0.00 0.00 0.00 3.74
3709 4044 1.599797 CACAAAGTCCCGGTCCACC 60.600 63.158 0.00 0.00 0.00 4.61
3710 4045 1.147600 ACACAAAGTCCCGGTCCAC 59.852 57.895 0.00 0.00 0.00 4.02
3734 4069 0.449786 TAAACCGATGCAATGCACCG 59.550 50.000 16.17 16.17 46.28 4.94


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

AutoCloner maintained by Alex Coulton.