Multiple sequence alignment - TraesCS4B01G290100

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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 TraesCS4B01G290100 chr4B 100.000 2948 0 0 1 2948 574947889 574950836 0.000000e+00 5445.0
1 TraesCS4B01G290100 chr4B 85.714 56 7 1 398 452 193527067 193527012 1.140000e-04 58.4
2 TraesCS4B01G290100 chr4D 91.816 1454 66 30 554 1961 460479255 460480701 0.000000e+00 1977.0
3 TraesCS4B01G290100 chr4D 95.702 954 37 3 1996 2948 460480774 460481724 0.000000e+00 1531.0
4 TraesCS4B01G290100 chr4D 81.609 174 26 5 1060 1231 467949928 467949759 3.960000e-29 139.0
5 TraesCS4B01G290100 chr4D 82.075 106 17 2 250 354 88124608 88124712 4.050000e-14 89.8
6 TraesCS4B01G290100 chr4D 78.947 133 27 1 254 386 509464373 509464504 4.050000e-14 89.8
7 TraesCS4B01G290100 chr4A 91.463 1476 55 29 539 1961 7750477 7749020 0.000000e+00 1962.0
8 TraesCS4B01G290100 chr4A 93.396 954 40 14 1996 2948 7748945 7748014 0.000000e+00 1391.0
9 TraesCS4B01G290100 chr4A 88.079 151 12 6 13 160 7753144 7752997 1.090000e-39 174.0
10 TraesCS4B01G290100 chr2A 86.364 132 18 0 1080 1211 738921993 738922124 8.520000e-31 145.0
11 TraesCS4B01G290100 chr2D 84.848 132 20 0 1080 1211 607283912 607284043 1.840000e-27 134.0
12 TraesCS4B01G290100 chr2D 79.259 135 27 1 254 388 587101358 587101491 3.130000e-15 93.5
13 TraesCS4B01G290100 chr2B 83.333 132 22 0 1080 1211 739369408 739369277 3.990000e-24 122.0
14 TraesCS4B01G290100 chr7A 81.884 138 20 5 254 389 20051543 20051677 8.640000e-21 111.0
15 TraesCS4B01G290100 chr7A 78.195 133 28 1 254 386 28308862 28308731 1.880000e-12 84.2
16 TraesCS4B01G290100 chr3A 78.102 137 25 3 254 388 472574074 472573941 6.770000e-12 82.4
17 TraesCS4B01G290100 chr3A 87.500 56 5 2 401 454 574325111 574325056 2.450000e-06 63.9
18 TraesCS4B01G290100 chr6D 78.571 126 16 8 257 379 60315514 60315631 4.080000e-09 73.1
19 TraesCS4B01G290100 chr6D 94.872 39 1 1 257 294 60316248 60316286 3.170000e-05 60.2
20 TraesCS4B01G290100 chr5A 95.455 44 2 0 271 314 183434880 183434923 1.470000e-08 71.3


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 TraesCS4B01G290100 chr4B 574947889 574950836 2947 False 5445.000000 5445 100.000000 1 2948 1 chr4B.!!$F1 2947
1 TraesCS4B01G290100 chr4D 460479255 460481724 2469 False 1754.000000 1977 93.759000 554 2948 2 chr4D.!!$F3 2394
2 TraesCS4B01G290100 chr4A 7748014 7753144 5130 True 1175.666667 1962 90.979333 13 2948 3 chr4A.!!$R1 2935

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
674 2911 0.032678 CACTCACGCTCACAGGTCTT 59.967 55.0 0.0 0.0 0.0 3.01 F
809 3064 0.459237 CAGCTCCATCGTCACACTCC 60.459 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 4103 2.126031 GCGTCCCAGTCGAACTCC 60.126 66.667 0.0 0.0 0.00 3.85 R
2679 5031 1.274167 GTCCACTACATTGGTGTCGGA 59.726 52.381 0.0 0.0 39.77 4.55 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
19 20 1.195347 CGACATCATCGTGACTCAGC 58.805 55.000 0.00 0.00 46.25 4.26
20 21 1.202234 CGACATCATCGTGACTCAGCT 60.202 52.381 0.00 0.00 46.25 4.24
26 27 0.323816 ATCGTGACTCAGCTCCTCCA 60.324 55.000 0.00 0.00 0.00 3.86
138 141 2.593376 GCGCGATGCTGTTATCAGA 58.407 52.632 12.10 0.00 43.76 3.27
160 163 2.993899 GACAGATGTCGTGTAAACTGGG 59.006 50.000 0.00 0.00 35.12 4.45
162 165 2.993899 CAGATGTCGTGTAAACTGGGTC 59.006 50.000 0.00 0.00 0.00 4.46
163 166 2.897969 AGATGTCGTGTAAACTGGGTCT 59.102 45.455 0.00 0.00 0.00 3.85
165 168 3.102052 TGTCGTGTAAACTGGGTCTTC 57.898 47.619 0.00 0.00 0.00 2.87
167 170 3.133362 TGTCGTGTAAACTGGGTCTTCTT 59.867 43.478 0.00 0.00 0.00 2.52
168 171 3.739810 GTCGTGTAAACTGGGTCTTCTTC 59.260 47.826 0.00 0.00 0.00 2.87
180 1845 0.036732 TCTTCTTCCGCAACTGGCAT 59.963 50.000 0.00 0.00 45.17 4.40
201 2435 2.104331 GACGACGATGATGGCGGT 59.896 61.111 0.00 0.00 0.00 5.68
207 2441 0.107703 ACGATGATGGCGGTGACAAT 60.108 50.000 0.00 0.00 0.00 2.71
217 2451 3.376859 TGGCGGTGACAATGACATATTTC 59.623 43.478 0.00 0.00 0.00 2.17
239 2473 7.851822 TTCGAATTCATGTTCTAACTTTTGC 57.148 32.000 6.22 0.00 0.00 3.68
241 2475 6.073494 TCGAATTCATGTTCTAACTTTTGCGA 60.073 34.615 6.22 0.00 0.00 5.10
251 2485 7.117812 TGTTCTAACTTTTGCGAATCCTCTAAG 59.882 37.037 0.00 0.00 0.00 2.18
268 2503 6.729100 TCCTCTAAGTTATTCCCTCTGTTTCA 59.271 38.462 0.00 0.00 0.00 2.69
344 2579 9.442047 TTTTTAGTGTGTTTGTTCATCCATTTT 57.558 25.926 0.00 0.00 0.00 1.82
346 2581 9.743057 TTTAGTGTGTTTGTTCATCCATTTTAG 57.257 29.630 0.00 0.00 0.00 1.85
347 2582 7.346751 AGTGTGTTTGTTCATCCATTTTAGT 57.653 32.000 0.00 0.00 0.00 2.24
348 2583 7.425606 AGTGTGTTTGTTCATCCATTTTAGTC 58.574 34.615 0.00 0.00 0.00 2.59
349 2584 6.640907 GTGTGTTTGTTCATCCATTTTAGTCC 59.359 38.462 0.00 0.00 0.00 3.85
350 2585 6.322456 TGTGTTTGTTCATCCATTTTAGTCCA 59.678 34.615 0.00 0.00 0.00 4.02
382 2617 9.553064 AGTCCATACTGAAATATCACAAAGATC 57.447 33.333 0.00 0.00 34.71 2.75
397 2632 9.836179 ATCACAAAGATCTTATATACTCCCTCT 57.164 33.333 8.75 0.00 28.20 3.69
398 2633 9.083422 TCACAAAGATCTTATATACTCCCTCTG 57.917 37.037 8.75 0.96 0.00 3.35
399 2634 8.865090 CACAAAGATCTTATATACTCCCTCTGT 58.135 37.037 8.75 1.62 0.00 3.41
400 2635 9.440761 ACAAAGATCTTATATACTCCCTCTGTT 57.559 33.333 8.75 0.00 0.00 3.16
404 2639 9.747898 AGATCTTATATACTCCCTCTGTTAGTG 57.252 37.037 0.00 0.00 0.00 2.74
405 2640 9.742144 GATCTTATATACTCCCTCTGTTAGTGA 57.258 37.037 0.00 0.00 0.00 3.41
407 2642 9.742144 TCTTATATACTCCCTCTGTTAGTGATC 57.258 37.037 0.00 0.00 0.00 2.92
408 2643 9.747898 CTTATATACTCCCTCTGTTAGTGATCT 57.252 37.037 0.00 0.00 0.00 2.75
413 2648 7.118496 ACTCCCTCTGTTAGTGATCTAAATG 57.882 40.000 0.00 0.00 37.81 2.32
414 2649 6.897966 ACTCCCTCTGTTAGTGATCTAAATGA 59.102 38.462 0.00 0.00 37.81 2.57
415 2650 7.566879 ACTCCCTCTGTTAGTGATCTAAATGAT 59.433 37.037 0.00 0.00 37.81 2.45
437 2672 8.680820 TGATCTTATATTACTTTAGGGAGGGG 57.319 38.462 0.00 0.00 0.00 4.79
438 2673 8.246615 TGATCTTATATTACTTTAGGGAGGGGT 58.753 37.037 0.00 0.00 0.00 4.95
439 2674 9.779951 GATCTTATATTACTTTAGGGAGGGGTA 57.220 37.037 0.00 0.00 0.00 3.69
448 2683 5.554350 ACTTTAGGGAGGGGTATTTCAGAAA 59.446 40.000 0.00 0.00 0.00 2.52
451 2686 2.091830 GGGAGGGGTATTTCAGAAAGGG 60.092 54.545 1.28 0.00 0.00 3.95
476 2711 6.550481 GGGGAGTAGTACTCTAGTATTTTGCT 59.450 42.308 25.70 0.00 44.46 3.91
505 2742 7.775053 TCAAAACCTAAACTTAATCATGCCT 57.225 32.000 0.00 0.00 0.00 4.75
508 2745 9.921637 CAAAACCTAAACTTAATCATGCCTAAA 57.078 29.630 0.00 0.00 0.00 1.85
523 2760 7.778083 TCATGCCTAAATACGTAAGAAGAAGA 58.222 34.615 0.00 0.00 43.62 2.87
524 2761 8.255206 TCATGCCTAAATACGTAAGAAGAAGAA 58.745 33.333 0.00 0.00 43.62 2.52
525 2762 8.543774 CATGCCTAAATACGTAAGAAGAAGAAG 58.456 37.037 0.00 0.00 43.62 2.85
526 2763 7.833786 TGCCTAAATACGTAAGAAGAAGAAGA 58.166 34.615 0.00 0.00 43.62 2.87
527 2764 8.308931 TGCCTAAATACGTAAGAAGAAGAAGAA 58.691 33.333 0.00 0.00 43.62 2.52
528 2765 8.809478 GCCTAAATACGTAAGAAGAAGAAGAAG 58.191 37.037 0.00 0.00 43.62 2.85
534 2771 9.849166 ATACGTAAGAAGAAGAAGAAGAAGAAG 57.151 33.333 0.00 0.00 43.62 2.85
535 2772 7.942990 ACGTAAGAAGAAGAAGAAGAAGAAGA 58.057 34.615 0.00 0.00 43.62 2.87
536 2773 8.414778 ACGTAAGAAGAAGAAGAAGAAGAAGAA 58.585 33.333 0.00 0.00 43.62 2.52
537 2774 8.911662 CGTAAGAAGAAGAAGAAGAAGAAGAAG 58.088 37.037 0.00 0.00 43.02 2.85
538 2775 9.974980 GTAAGAAGAAGAAGAAGAAGAAGAAGA 57.025 33.333 0.00 0.00 0.00 2.87
540 2777 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
541 2778 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
542 2779 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
543 2780 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
544 2781 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
545 2782 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
546 2783 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
567 2804 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
645 2882 1.376683 GCCCTAACGGTCACATGCA 60.377 57.895 0.00 0.00 0.00 3.96
674 2911 0.032678 CACTCACGCTCACAGGTCTT 59.967 55.000 0.00 0.00 0.00 3.01
774 3024 4.582656 CACTCCTCTCTCACCCTACTTATG 59.417 50.000 0.00 0.00 0.00 1.90
809 3064 0.459237 CAGCTCCATCGTCACACTCC 60.459 60.000 0.00 0.00 0.00 3.85
868 3125 3.287222 CCAAAACCTCACTCCAACTTCA 58.713 45.455 0.00 0.00 0.00 3.02
956 3221 4.400884 CGCTACCTGGATATATTGCTCTCT 59.599 45.833 0.00 0.00 0.00 3.10
958 3223 6.095580 CGCTACCTGGATATATTGCTCTCTTA 59.904 42.308 0.00 0.00 0.00 2.10
960 3225 6.274157 ACCTGGATATATTGCTCTCTTACG 57.726 41.667 0.00 0.00 0.00 3.18
961 3226 5.775701 ACCTGGATATATTGCTCTCTTACGT 59.224 40.000 0.00 0.00 0.00 3.57
962 3227 6.071840 ACCTGGATATATTGCTCTCTTACGTC 60.072 42.308 0.00 0.00 0.00 4.34
963 3228 5.939457 TGGATATATTGCTCTCTTACGTCG 58.061 41.667 0.00 0.00 0.00 5.12
964 3229 5.472478 TGGATATATTGCTCTCTTACGTCGT 59.528 40.000 2.21 2.21 0.00 4.34
1251 3530 2.753966 CGCATTCCTCAACCTGCCG 61.754 63.158 0.00 0.00 0.00 5.69
1733 4036 2.125552 CAAGCATCAGGGCGTCGA 60.126 61.111 0.00 0.00 39.27 4.20
1968 4276 9.995003 ATCTGATGTCATATTCTTAAGACTTCC 57.005 33.333 4.18 0.00 33.03 3.46
1971 4279 8.642432 TGATGTCATATTCTTAAGACTTCCGAT 58.358 33.333 4.18 0.00 33.03 4.18
1972 4280 9.134734 GATGTCATATTCTTAAGACTTCCGATC 57.865 37.037 4.18 0.00 30.18 3.69
1975 4283 9.615295 GTCATATTCTTAAGACTTCCGATCTAC 57.385 37.037 4.18 0.00 0.00 2.59
1976 4284 9.350951 TCATATTCTTAAGACTTCCGATCTACA 57.649 33.333 4.18 0.00 0.00 2.74
1979 4287 5.833082 TCTTAAGACTTCCGATCTACATGC 58.167 41.667 0.00 0.00 0.00 4.06
1980 4288 5.359860 TCTTAAGACTTCCGATCTACATGCA 59.640 40.000 0.00 0.00 0.00 3.96
1982 4290 3.027412 AGACTTCCGATCTACATGCAGT 58.973 45.455 0.00 0.00 0.00 4.40
1983 4291 3.067461 AGACTTCCGATCTACATGCAGTC 59.933 47.826 0.00 0.00 0.00 3.51
1985 4293 3.181482 ACTTCCGATCTACATGCAGTCTG 60.181 47.826 0.00 0.00 0.00 3.51
1987 4295 3.225940 TCCGATCTACATGCAGTCTGAT 58.774 45.455 3.32 0.00 0.00 2.90
1990 4298 4.228317 CGATCTACATGCAGTCTGATCTG 58.772 47.826 3.32 0.00 37.79 2.90
1991 4299 4.023365 CGATCTACATGCAGTCTGATCTGA 60.023 45.833 3.32 0.00 37.79 3.27
1992 4300 5.335819 CGATCTACATGCAGTCTGATCTGAT 60.336 44.000 3.32 0.00 37.79 2.90
1993 4301 5.197682 TCTACATGCAGTCTGATCTGATG 57.802 43.478 3.32 6.62 37.61 3.07
1994 4302 4.891756 TCTACATGCAGTCTGATCTGATGA 59.108 41.667 3.32 0.00 37.61 2.92
2010 4358 4.532126 TCTGATGAGAGGTTTAGCTTCCAA 59.468 41.667 0.00 0.00 0.00 3.53
2025 4373 5.241662 AGCTTCCAAGTTCTTCATGTAGTC 58.758 41.667 0.00 0.00 0.00 2.59
2105 4453 2.435762 TTGGCGCGCATGAGCTAA 60.436 55.556 34.42 12.29 41.13 3.09
2107 4455 1.775039 TTGGCGCGCATGAGCTAATC 61.775 55.000 34.42 11.73 41.13 1.75
2231 4582 5.756195 TCACTCACTGTCAAAGGATTTTG 57.244 39.130 0.00 0.00 44.03 2.44
2291 4642 1.351350 GAGCTAAAGACACCCCCAACT 59.649 52.381 0.00 0.00 0.00 3.16
2304 4655 3.244981 ACCCCCAACTAGCGAAATAAACA 60.245 43.478 0.00 0.00 0.00 2.83
2305 4656 3.128068 CCCCCAACTAGCGAAATAAACAC 59.872 47.826 0.00 0.00 0.00 3.32
2363 4714 4.319984 GCATTCAGCATTCATAATCAGCGA 60.320 41.667 0.00 0.00 44.79 4.93
2400 4752 3.972950 TTGTGACAATACCACCAAACG 57.027 42.857 0.00 0.00 33.80 3.60
2467 4819 7.108194 ACACTGCATCCTTATGGTGATATATG 58.892 38.462 5.57 0.00 32.61 1.78
2570 4922 0.895100 TGGCAATCAAGGGTGTGCTC 60.895 55.000 0.00 0.00 37.17 4.26
2613 4965 7.208080 TCGGCCTAGTTAAGACTGAATTATTC 58.792 38.462 0.00 0.00 36.60 1.75
2648 5000 2.156098 GTACCAAATCGAGTTTGCCCA 58.844 47.619 0.00 0.00 44.69 5.36
2679 5031 1.692042 CAGAGCATCCCTCCCAGGT 60.692 63.158 0.00 0.00 41.74 4.00
2709 5061 1.796017 TGTAGTGGACTGGAACACCA 58.204 50.000 0.00 0.00 38.34 4.17
2853 5205 5.527951 AGACGAAGCATATGAGAGATGAAC 58.472 41.667 6.97 0.00 0.00 3.18
2888 5240 9.048446 TCCTCACATTTAAGTGTAAGTTGTTAC 57.952 33.333 2.99 0.00 40.37 2.50
2922 5274 9.383519 CTGGTAATGACATCAGTTTACAATACT 57.616 33.333 7.38 0.00 0.00 2.12
2940 5292 6.874134 ACAATACTACAGAACTAAAGCCAGTG 59.126 38.462 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.458951 GAGCTGAGTCACGATGATGTC 58.541 52.381 0.00 0.00 0.00 3.06
2 3 1.135915 GGAGCTGAGTCACGATGATGT 59.864 52.381 0.00 0.00 0.00 3.06
3 4 1.408340 AGGAGCTGAGTCACGATGATG 59.592 52.381 0.00 0.00 0.00 3.07
4 5 1.680735 GAGGAGCTGAGTCACGATGAT 59.319 52.381 0.00 0.00 0.00 2.45
5 6 1.098869 GAGGAGCTGAGTCACGATGA 58.901 55.000 0.00 0.00 0.00 2.92
6 7 0.102120 GGAGGAGCTGAGTCACGATG 59.898 60.000 0.00 0.00 0.00 3.84
7 8 0.323816 TGGAGGAGCTGAGTCACGAT 60.324 55.000 0.00 0.00 0.00 3.73
8 9 0.323816 ATGGAGGAGCTGAGTCACGA 60.324 55.000 0.00 0.00 0.00 4.35
9 10 1.393603 TATGGAGGAGCTGAGTCACG 58.606 55.000 0.00 0.00 0.00 4.35
10 11 2.030363 CGATATGGAGGAGCTGAGTCAC 60.030 54.545 0.00 0.00 0.00 3.67
11 12 2.234143 CGATATGGAGGAGCTGAGTCA 58.766 52.381 0.00 0.00 0.00 3.41
62 64 1.303317 TTGCTCCTTTCGGCCTTCC 60.303 57.895 0.00 0.00 0.00 3.46
83 86 1.303643 GCCTCCTCCACCACCTTTG 60.304 63.158 0.00 0.00 0.00 2.77
84 87 2.539081 GGCCTCCTCCACCACCTTT 61.539 63.158 0.00 0.00 0.00 3.11
92 95 2.829384 AAACGCTTGGCCTCCTCCA 61.829 57.895 3.32 0.00 0.00 3.86
95 98 1.898574 CACAAACGCTTGGCCTCCT 60.899 57.895 3.32 0.00 36.82 3.69
122 125 2.793790 CTGTCTCTGATAACAGCATCGC 59.206 50.000 7.22 0.00 43.17 4.58
123 126 4.298744 TCTGTCTCTGATAACAGCATCG 57.701 45.455 12.87 0.00 42.10 3.84
133 136 5.184096 AGTTTACACGACATCTGTCTCTGAT 59.816 40.000 8.57 0.00 42.66 2.90
136 139 4.321304 CCAGTTTACACGACATCTGTCTCT 60.321 45.833 8.57 0.00 42.66 3.10
137 140 3.921021 CCAGTTTACACGACATCTGTCTC 59.079 47.826 8.57 0.00 42.66 3.36
138 141 3.306088 CCCAGTTTACACGACATCTGTCT 60.306 47.826 8.57 0.00 42.66 3.41
155 158 0.250338 GTTGCGGAAGAAGACCCAGT 60.250 55.000 0.00 0.00 0.00 4.00
156 159 0.035458 AGTTGCGGAAGAAGACCCAG 59.965 55.000 0.00 0.00 0.00 4.45
157 160 0.250295 CAGTTGCGGAAGAAGACCCA 60.250 55.000 0.00 0.00 0.00 4.51
159 162 1.578206 GCCAGTTGCGGAAGAAGACC 61.578 60.000 0.00 0.00 0.00 3.85
160 163 0.884704 TGCCAGTTGCGGAAGAAGAC 60.885 55.000 0.00 0.00 45.60 3.01
162 165 0.169672 CATGCCAGTTGCGGAAGAAG 59.830 55.000 0.00 0.00 45.60 2.85
163 166 0.250684 TCATGCCAGTTGCGGAAGAA 60.251 50.000 0.00 0.00 45.60 2.52
165 168 1.503542 GTCATGCCAGTTGCGGAAG 59.496 57.895 0.00 0.00 45.60 3.46
167 170 2.741985 CGTCATGCCAGTTGCGGA 60.742 61.111 0.00 0.00 45.60 5.54
168 171 2.741985 TCGTCATGCCAGTTGCGG 60.742 61.111 0.00 0.00 45.60 5.69
180 1845 1.226575 GCCATCATCGTCGTCGTCA 60.227 57.895 1.33 0.00 38.33 4.35
201 2435 8.676401 ACATGAATTCGAAATATGTCATTGTCA 58.324 29.630 15.33 0.00 0.00 3.58
217 2451 6.077197 TCGCAAAAGTTAGAACATGAATTCG 58.923 36.000 0.00 0.00 33.57 3.34
239 2473 6.041069 ACAGAGGGAATAACTTAGAGGATTCG 59.959 42.308 0.00 0.00 0.00 3.34
241 2475 7.757242 AACAGAGGGAATAACTTAGAGGATT 57.243 36.000 0.00 0.00 0.00 3.01
322 2557 8.458573 ACTAAAATGGATGAACAAACACACTA 57.541 30.769 0.00 0.00 0.00 2.74
323 2558 7.346751 ACTAAAATGGATGAACAAACACACT 57.653 32.000 0.00 0.00 0.00 3.55
324 2559 6.640907 GGACTAAAATGGATGAACAAACACAC 59.359 38.462 0.00 0.00 0.00 3.82
325 2560 6.322456 TGGACTAAAATGGATGAACAAACACA 59.678 34.615 0.00 0.00 0.00 3.72
372 2607 9.083422 CAGAGGGAGTATATAAGATCTTTGTGA 57.917 37.037 14.36 0.00 0.00 3.58
382 2617 9.747898 AGATCACTAACAGAGGGAGTATATAAG 57.252 37.037 0.00 0.00 42.35 1.73
390 2625 7.353414 TCATTTAGATCACTAACAGAGGGAG 57.647 40.000 0.00 0.00 42.35 4.30
391 2626 7.921041 ATCATTTAGATCACTAACAGAGGGA 57.079 36.000 0.00 0.00 43.59 4.20
411 2646 9.285359 CCCCTCCCTAAAGTAATATAAGATCAT 57.715 37.037 0.00 0.00 0.00 2.45
412 2647 8.246615 ACCCCTCCCTAAAGTAATATAAGATCA 58.753 37.037 0.00 0.00 0.00 2.92
413 2648 8.682297 ACCCCTCCCTAAAGTAATATAAGATC 57.318 38.462 0.00 0.00 0.00 2.75
418 2653 9.917118 TGAAATACCCCTCCCTAAAGTAATATA 57.083 33.333 0.00 0.00 0.00 0.86
419 2654 8.823810 TGAAATACCCCTCCCTAAAGTAATAT 57.176 34.615 0.00 0.00 0.00 1.28
420 2655 8.075621 TCTGAAATACCCCTCCCTAAAGTAATA 58.924 37.037 0.00 0.00 0.00 0.98
421 2656 6.912561 TCTGAAATACCCCTCCCTAAAGTAAT 59.087 38.462 0.00 0.00 0.00 1.89
422 2657 6.273889 TCTGAAATACCCCTCCCTAAAGTAA 58.726 40.000 0.00 0.00 0.00 2.24
423 2658 5.857134 TCTGAAATACCCCTCCCTAAAGTA 58.143 41.667 0.00 0.00 0.00 2.24
424 2659 4.706616 TCTGAAATACCCCTCCCTAAAGT 58.293 43.478 0.00 0.00 0.00 2.66
425 2660 5.710409 TTCTGAAATACCCCTCCCTAAAG 57.290 43.478 0.00 0.00 0.00 1.85
426 2661 5.044402 CCTTTCTGAAATACCCCTCCCTAAA 60.044 44.000 2.88 0.00 0.00 1.85
427 2662 4.477213 CCTTTCTGAAATACCCCTCCCTAA 59.523 45.833 2.88 0.00 0.00 2.69
428 2663 4.045022 CCTTTCTGAAATACCCCTCCCTA 58.955 47.826 2.88 0.00 0.00 3.53
429 2664 2.853077 CCTTTCTGAAATACCCCTCCCT 59.147 50.000 2.88 0.00 0.00 4.20
430 2665 2.091830 CCCTTTCTGAAATACCCCTCCC 60.092 54.545 2.88 0.00 0.00 4.30
431 2666 2.091830 CCCCTTTCTGAAATACCCCTCC 60.092 54.545 2.88 0.00 0.00 4.30
432 2667 2.091830 CCCCCTTTCTGAAATACCCCTC 60.092 54.545 2.88 0.00 0.00 4.30
433 2668 1.930204 CCCCCTTTCTGAAATACCCCT 59.070 52.381 2.88 0.00 0.00 4.79
434 2669 2.454336 CCCCCTTTCTGAAATACCCC 57.546 55.000 2.88 0.00 0.00 4.95
451 2686 6.550481 AGCAAAATACTAGAGTACTACTCCCC 59.450 42.308 11.94 0.00 46.18 4.81
482 2717 9.921637 TTTAGGCATGATTAAGTTTAGGTTTTG 57.078 29.630 0.00 0.00 0.00 2.44
508 2745 9.849166 CTTCTTCTTCTTCTTCTTCTTACGTAT 57.151 33.333 0.00 0.00 0.00 3.06
523 2760 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
524 2761 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
525 2762 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
526 2763 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
527 2764 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
528 2765 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
529 2766 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
530 2767 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
531 2768 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
532 2769 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
533 2770 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
534 2771 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
535 2772 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
536 2773 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
537 2774 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
538 2775 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
539 2776 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
540 2777 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
541 2778 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
542 2779 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
543 2780 9.710900 ATCTTCTTCTTCTTCTTCTTCTTCTTC 57.289 33.333 0.00 0.00 0.00 2.87
544 2781 9.710900 GATCTTCTTCTTCTTCTTCTTCTTCTT 57.289 33.333 0.00 0.00 0.00 2.52
545 2782 9.093458 AGATCTTCTTCTTCTTCTTCTTCTTCT 57.907 33.333 0.00 0.00 0.00 2.85
590 2827 5.920273 CACGATGTAGGAAGCAAAACAAAAT 59.080 36.000 0.00 0.00 0.00 1.82
645 2882 3.374402 CGTGAGTGAGCTCCCGGT 61.374 66.667 12.15 0.00 38.61 5.28
755 3002 2.630580 GGCATAAGTAGGGTGAGAGAGG 59.369 54.545 0.00 0.00 0.00 3.69
809 3064 0.252284 AGTAGTGGAGTGGGTGAGGG 60.252 60.000 0.00 0.00 0.00 4.30
868 3125 0.885879 GCGGGGGAATTCGAAGTTTT 59.114 50.000 3.35 0.00 0.00 2.43
960 3225 2.486322 GCACGACGACGATGACGAC 61.486 63.158 15.32 0.00 42.66 4.34
961 3226 2.202260 GCACGACGACGATGACGA 60.202 61.111 15.32 0.00 42.66 4.20
962 3227 1.867812 ATGCACGACGACGATGACG 60.868 57.895 15.32 4.49 42.66 4.35
963 3228 1.625870 CATGCACGACGACGATGAC 59.374 57.895 15.32 5.98 42.66 3.06
964 3229 2.158330 GCATGCACGACGACGATGA 61.158 57.895 14.21 0.00 42.66 2.92
1755 4058 4.712425 CCGAACCCGAACGCGTCT 62.712 66.667 14.44 2.25 38.22 4.18
1800 4103 2.126031 GCGTCCCAGTCGAACTCC 60.126 66.667 0.00 0.00 0.00 3.85
1919 4225 3.556306 ATACGGGGATGGGCACGG 61.556 66.667 0.00 0.00 0.00 4.94
1949 4257 9.615295 GTAGATCGGAAGTCTTAAGAATATGAC 57.385 37.037 6.78 0.00 36.78 3.06
1961 4269 3.027412 ACTGCATGTAGATCGGAAGTCT 58.973 45.455 18.40 0.00 0.00 3.24
1962 4270 3.067461 AGACTGCATGTAGATCGGAAGTC 59.933 47.826 18.40 2.76 34.40 3.01
1963 4271 3.027412 AGACTGCATGTAGATCGGAAGT 58.973 45.455 18.40 0.00 0.00 3.01
1964 4272 3.067320 TCAGACTGCATGTAGATCGGAAG 59.933 47.826 18.40 5.28 0.00 3.46
1965 4273 3.023832 TCAGACTGCATGTAGATCGGAA 58.976 45.455 18.40 0.92 0.00 4.30
1968 4276 4.023365 TCAGATCAGACTGCATGTAGATCG 60.023 45.833 18.40 4.94 41.37 3.69
1971 4279 4.891756 TCATCAGATCAGACTGCATGTAGA 59.108 41.667 18.40 0.00 37.75 2.59
1972 4280 5.009811 TCTCATCAGATCAGACTGCATGTAG 59.990 44.000 9.50 9.50 37.75 2.74
1975 4283 4.303282 CTCTCATCAGATCAGACTGCATG 58.697 47.826 0.00 0.00 37.75 4.06
1976 4284 3.322541 CCTCTCATCAGATCAGACTGCAT 59.677 47.826 0.00 0.00 37.75 3.96
1977 4285 2.694109 CCTCTCATCAGATCAGACTGCA 59.306 50.000 0.00 0.00 37.75 4.41
1978 4286 2.694628 ACCTCTCATCAGATCAGACTGC 59.305 50.000 0.00 0.00 37.75 4.40
1979 4287 5.341872 AAACCTCTCATCAGATCAGACTG 57.658 43.478 0.00 0.00 39.02 3.51
1980 4288 5.068987 GCTAAACCTCTCATCAGATCAGACT 59.931 44.000 0.00 0.00 0.00 3.24
1982 4290 5.207354 AGCTAAACCTCTCATCAGATCAGA 58.793 41.667 0.00 0.00 0.00 3.27
1983 4291 5.534207 AGCTAAACCTCTCATCAGATCAG 57.466 43.478 0.00 0.00 0.00 2.90
1985 4293 5.163364 TGGAAGCTAAACCTCTCATCAGATC 60.163 44.000 0.00 0.00 0.00 2.75
1987 4295 4.096681 TGGAAGCTAAACCTCTCATCAGA 58.903 43.478 0.00 0.00 0.00 3.27
1990 4298 4.837972 ACTTGGAAGCTAAACCTCTCATC 58.162 43.478 0.00 0.00 0.00 2.92
1991 4299 4.917906 ACTTGGAAGCTAAACCTCTCAT 57.082 40.909 0.00 0.00 0.00 2.90
1992 4300 4.348168 AGAACTTGGAAGCTAAACCTCTCA 59.652 41.667 0.00 0.00 0.00 3.27
1993 4301 4.900684 AGAACTTGGAAGCTAAACCTCTC 58.099 43.478 0.00 0.00 0.00 3.20
1994 4302 4.984146 AGAACTTGGAAGCTAAACCTCT 57.016 40.909 0.00 0.00 0.00 3.69
2010 4358 4.511527 CATGCCAGACTACATGAAGAACT 58.488 43.478 10.71 0.00 45.23 3.01
2025 4373 6.506500 AACAGATCTAAAACTTCATGCCAG 57.493 37.500 0.00 0.00 0.00 4.85
2105 4453 3.075882 TCTCATTTTCCTGGTTGTGGGAT 59.924 43.478 0.00 0.00 0.00 3.85
2107 4455 2.558359 GTCTCATTTTCCTGGTTGTGGG 59.442 50.000 0.00 0.00 0.00 4.61
2231 4582 4.554330 GCATCGATCTTCTTGCTTTGGATC 60.554 45.833 0.00 0.00 32.41 3.36
2282 4633 3.244981 TGTTTATTTCGCTAGTTGGGGGT 60.245 43.478 0.00 0.00 0.00 4.95
2291 4642 5.236911 AGTTTTCACCGTGTTTATTTCGCTA 59.763 36.000 0.00 0.00 0.00 4.26
2304 4655 4.957296 AGTCTGATGTAAGTTTTCACCGT 58.043 39.130 0.00 0.00 0.00 4.83
2305 4656 5.679906 CAAGTCTGATGTAAGTTTTCACCG 58.320 41.667 0.00 0.00 0.00 4.94
2363 4714 6.976088 TGTCACAATTCACCGTCATATTTTT 58.024 32.000 0.00 0.00 0.00 1.94
2400 4752 3.040147 TGTCTTTCGACTCCACCAATC 57.960 47.619 0.00 0.00 40.86 2.67
2613 4965 4.572985 TTGGTACTATTGTATCGGACGG 57.427 45.455 0.00 0.00 32.63 4.79
2648 5000 7.093112 GGAGGGATGCTCTGATATACAAGTAAT 60.093 40.741 0.00 0.00 0.00 1.89
2679 5031 1.274167 GTCCACTACATTGGTGTCGGA 59.726 52.381 0.00 0.00 39.77 4.55
2709 5061 3.219281 GGAGAGGATAGAAGAGCTCGTT 58.781 50.000 8.37 2.98 0.00 3.85
2754 5106 4.823442 TCTGTCCGAAGTTACAGTGAACTA 59.177 41.667 0.00 0.00 42.96 2.24
2802 5154 2.497675 TCAGGTCAACTATGAGGTGCTC 59.502 50.000 0.00 0.00 35.88 4.26
2922 5274 3.762407 TGCACTGGCTTTAGTTCTGTA 57.238 42.857 0.00 0.00 41.91 2.74


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

AutoCloner maintained by Alex Coulton.