Multiple sequence alignment - TraesCS2D01G586800

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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 TraesCS2D01G586800 chr2D 100.000 2523 0 0 1 2523 644925454 644922932 0.000000e+00 4660.0
1 TraesCS2D01G586800 chr2D 87.164 1675 163 27 724 2380 644976041 644974401 0.000000e+00 1855.0
2 TraesCS2D01G586800 chr2D 93.249 1111 56 15 724 1823 644981534 644980432 0.000000e+00 1618.0
3 TraesCS2D01G586800 chr2D 75.258 776 139 34 925 1657 579511275 579510510 1.130000e-83 320.0
4 TraesCS2D01G586800 chr2B 96.399 2388 46 21 1 2374 790622651 790625012 0.000000e+00 3897.0
5 TraesCS2D01G586800 chr2B 86.181 1592 169 26 807 2380 790612614 790614172 0.000000e+00 1674.0
6 TraesCS2D01G586800 chr2B 86.275 255 34 1 1099 1352 790740483 790740737 2.470000e-70 276.0
7 TraesCS2D01G586800 chr2A 96.921 1689 35 7 701 2374 770291266 770289580 0.000000e+00 2815.0
8 TraesCS2D01G586800 chr2A 84.615 1209 129 27 1190 2380 770343037 770341868 0.000000e+00 1149.0
9 TraesCS2D01G586800 chr2A 95.634 710 22 4 1 705 770309989 770309284 0.000000e+00 1131.0
10 TraesCS2D01G586800 chr2A 90.106 283 28 0 807 1089 770343316 770343034 3.970000e-98 368.0
11 TraesCS2D01G586800 chr2A 91.358 81 6 1 724 804 770344977 770344898 2.650000e-20 110.0
12 TraesCS2D01G586800 chr2A 78.704 108 22 1 530 637 15063783 15063889 1.250000e-08 71.3
13 TraesCS2D01G586800 chr3B 89.051 1443 134 15 721 2147 48668842 48667408 0.000000e+00 1768.0
14 TraesCS2D01G586800 chr7B 84.455 431 63 4 1 429 48953189 48952761 3.000000e-114 422.0
15 TraesCS2D01G586800 chr1D 84.075 427 66 2 2 427 416395856 416396281 6.500000e-111 411.0
16 TraesCS2D01G586800 chr4B 83.991 431 61 6 3 429 369839827 369839401 8.400000e-110 407.0
17 TraesCS2D01G586800 chr1B 83.568 426 68 2 2 426 562744710 562745134 5.060000e-107 398.0
18 TraesCS2D01G586800 chr4A 83.411 428 65 6 2 427 413554645 413554222 2.350000e-105 392.0
19 TraesCS2D01G586800 chr4A 84.416 77 12 0 575 651 706511938 706511862 2.690000e-10 76.8
20 TraesCS2D01G586800 chr5B 83.178 428 66 6 1 425 585259082 585259506 1.090000e-103 387.0
21 TraesCS2D01G586800 chr3A 82.949 434 69 5 13 444 86111175 86111605 1.090000e-103 387.0
22 TraesCS2D01G586800 chr3D 82.906 117 15 5 535 649 587942350 587942237 1.600000e-17 100.0


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 TraesCS2D01G586800 chr2D 644922932 644925454 2522 True 4660.000000 4660 100.000 1 2523 1 chr2D.!!$R2 2522
1 TraesCS2D01G586800 chr2D 644974401 644976041 1640 True 1855.000000 1855 87.164 724 2380 1 chr2D.!!$R3 1656
2 TraesCS2D01G586800 chr2D 644980432 644981534 1102 True 1618.000000 1618 93.249 724 1823 1 chr2D.!!$R4 1099
3 TraesCS2D01G586800 chr2D 579510510 579511275 765 True 320.000000 320 75.258 925 1657 1 chr2D.!!$R1 732
4 TraesCS2D01G586800 chr2B 790622651 790625012 2361 False 3897.000000 3897 96.399 1 2374 1 chr2B.!!$F2 2373
5 TraesCS2D01G586800 chr2B 790612614 790614172 1558 False 1674.000000 1674 86.181 807 2380 1 chr2B.!!$F1 1573
6 TraesCS2D01G586800 chr2A 770289580 770291266 1686 True 2815.000000 2815 96.921 701 2374 1 chr2A.!!$R1 1673
7 TraesCS2D01G586800 chr2A 770309284 770309989 705 True 1131.000000 1131 95.634 1 705 1 chr2A.!!$R2 704
8 TraesCS2D01G586800 chr2A 770341868 770344977 3109 True 542.333333 1149 88.693 724 2380 3 chr2A.!!$R3 1656
9 TraesCS2D01G586800 chr3B 48667408 48668842 1434 True 1768.000000 1768 89.051 721 2147 1 chr3B.!!$R1 1426

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
105 106 6.77277 TGAAATTATCAAAGTCGTGAACGA 57.227 33.333 0.5 0.5 39.73 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 3641 1.351017 TCTAACCCCAAGCCTCAACAG 59.649 52.381 0.0 0.0 0.0 3.16 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
97 98 9.520204 CCACCAACATATGAAATTATCAAAGTC 57.480 33.333 10.38 0.00 42.54 3.01
105 106 6.772770 TGAAATTATCAAAGTCGTGAACGA 57.227 33.333 0.50 0.50 39.73 3.85
169 170 6.953520 TCCCATGTGTCCTTAAGAATGATTTT 59.046 34.615 3.36 0.00 0.00 1.82
551 558 8.316214 GGGTATATCGATGTCCTACCAAATTTA 58.684 37.037 20.44 0.00 34.74 1.40
685 693 7.849804 AGGTTTACATACATGCTTTCTACTG 57.150 36.000 0.00 0.00 0.00 2.74
1386 3002 6.053005 TGTTTCTGGAATGAACTACGAACTT 58.947 36.000 0.00 0.00 0.00 2.66
1798 3432 4.215399 CCGCAAGACCATTCAACTTTTCTA 59.785 41.667 0.00 0.00 43.02 2.10
1802 3436 7.425606 GCAAGACCATTCAACTTTTCTAAAGA 58.574 34.615 6.20 0.00 0.00 2.52
1922 3559 4.949238 TCCAATATCCAACAACTCATGGTG 59.051 41.667 0.00 0.00 46.87 4.17
2062 3699 1.288932 GGGTGACACTAGGGTAGGGTA 59.711 57.143 0.00 0.00 43.85 3.69
2063 3700 2.292455 GGGTGACACTAGGGTAGGGTAA 60.292 54.545 0.00 0.00 43.85 2.85
2143 3781 0.875059 GGCTGGAGGAGAAAAACACG 59.125 55.000 0.00 0.00 0.00 4.49
2307 3952 1.544825 CGGTCCTGAAGGAGAGCCAA 61.545 60.000 0.00 0.00 46.49 4.52
2398 4043 6.800072 AAAAATAAACACACCTCCTTTGGA 57.200 33.333 0.00 0.00 0.00 3.53
2399 4044 6.800072 AAAATAAACACACCTCCTTTGGAA 57.200 33.333 0.00 0.00 0.00 3.53
2400 4045 6.405278 AAATAAACACACCTCCTTTGGAAG 57.595 37.500 0.00 0.00 0.00 3.46
2401 4046 1.692411 AACACACCTCCTTTGGAAGC 58.308 50.000 0.00 0.00 0.00 3.86
2402 4047 0.178990 ACACACCTCCTTTGGAAGCC 60.179 55.000 0.00 0.00 0.00 4.35
2403 4048 0.111253 CACACCTCCTTTGGAAGCCT 59.889 55.000 0.00 0.00 0.00 4.58
2404 4049 1.351017 CACACCTCCTTTGGAAGCCTA 59.649 52.381 0.00 0.00 0.00 3.93
2405 4050 1.630878 ACACCTCCTTTGGAAGCCTAG 59.369 52.381 0.00 0.00 0.00 3.02
2406 4051 1.630878 CACCTCCTTTGGAAGCCTAGT 59.369 52.381 0.00 0.00 0.00 2.57
2407 4052 2.838202 CACCTCCTTTGGAAGCCTAGTA 59.162 50.000 0.00 0.00 0.00 1.82
2408 4053 3.263425 CACCTCCTTTGGAAGCCTAGTAA 59.737 47.826 0.00 0.00 0.00 2.24
2409 4054 3.263681 ACCTCCTTTGGAAGCCTAGTAAC 59.736 47.826 0.00 0.00 0.00 2.50
2410 4055 3.519913 CCTCCTTTGGAAGCCTAGTAACT 59.480 47.826 0.00 0.00 0.00 2.24
2411 4056 4.508662 CTCCTTTGGAAGCCTAGTAACTG 58.491 47.826 0.00 0.00 0.00 3.16
2412 4057 3.010420 CCTTTGGAAGCCTAGTAACTGC 58.990 50.000 0.00 0.00 0.00 4.40
2413 4058 2.781681 TTGGAAGCCTAGTAACTGCC 57.218 50.000 0.00 0.00 31.42 4.85
2414 4059 0.535335 TGGAAGCCTAGTAACTGCCG 59.465 55.000 0.00 0.00 33.82 5.69
2415 4060 0.535797 GGAAGCCTAGTAACTGCCGT 59.464 55.000 0.00 0.00 0.00 5.68
2416 4061 1.471153 GGAAGCCTAGTAACTGCCGTC 60.471 57.143 0.00 0.00 0.00 4.79
2417 4062 1.477295 GAAGCCTAGTAACTGCCGTCT 59.523 52.381 0.00 0.00 0.00 4.18
2418 4063 0.818296 AGCCTAGTAACTGCCGTCTG 59.182 55.000 0.00 0.00 0.00 3.51
2419 4064 0.531200 GCCTAGTAACTGCCGTCTGT 59.469 55.000 0.00 0.00 0.00 3.41
2420 4065 1.736032 GCCTAGTAACTGCCGTCTGTG 60.736 57.143 0.00 0.00 0.00 3.66
2421 4066 1.544691 CCTAGTAACTGCCGTCTGTGT 59.455 52.381 0.00 0.00 0.00 3.72
2422 4067 2.415625 CCTAGTAACTGCCGTCTGTGTC 60.416 54.545 0.00 0.00 0.00 3.67
2423 4068 0.039437 AGTAACTGCCGTCTGTGTCG 60.039 55.000 0.00 0.00 0.00 4.35
2424 4069 0.318445 GTAACTGCCGTCTGTGTCGT 60.318 55.000 0.00 0.00 0.00 4.34
2425 4070 0.039798 TAACTGCCGTCTGTGTCGTC 60.040 55.000 0.00 0.00 0.00 4.20
2426 4071 2.430921 CTGCCGTCTGTGTCGTCC 60.431 66.667 0.00 0.00 0.00 4.79
2427 4072 3.207547 CTGCCGTCTGTGTCGTCCA 62.208 63.158 0.00 0.00 0.00 4.02
2428 4073 2.261671 GCCGTCTGTGTCGTCCAT 59.738 61.111 0.00 0.00 0.00 3.41
2429 4074 2.094659 GCCGTCTGTGTCGTCCATG 61.095 63.158 0.00 0.00 0.00 3.66
2430 4075 1.446099 CCGTCTGTGTCGTCCATGG 60.446 63.158 4.97 4.97 0.00 3.66
2431 4076 1.446099 CGTCTGTGTCGTCCATGGG 60.446 63.158 13.02 0.00 0.00 4.00
2432 4077 1.873270 CGTCTGTGTCGTCCATGGGA 61.873 60.000 13.02 0.00 0.00 4.37
2433 4078 0.320374 GTCTGTGTCGTCCATGGGAA 59.680 55.000 13.02 0.00 31.38 3.97
2434 4079 1.052617 TCTGTGTCGTCCATGGGAAA 58.947 50.000 13.02 0.00 31.38 3.13
2435 4080 1.418264 TCTGTGTCGTCCATGGGAAAA 59.582 47.619 13.02 0.00 31.38 2.29
2436 4081 2.039746 TCTGTGTCGTCCATGGGAAAAT 59.960 45.455 13.02 0.00 31.38 1.82
2437 4082 2.158559 TGTGTCGTCCATGGGAAAATG 58.841 47.619 13.02 0.00 31.38 2.32
2438 4083 1.135402 GTGTCGTCCATGGGAAAATGC 60.135 52.381 13.02 0.00 31.38 3.56
2439 4084 0.098728 GTCGTCCATGGGAAAATGCG 59.901 55.000 13.02 5.85 31.38 4.73
2440 4085 1.226660 CGTCCATGGGAAAATGCGC 60.227 57.895 13.02 0.00 31.38 6.09
2441 4086 1.889454 GTCCATGGGAAAATGCGCA 59.111 52.632 14.96 14.96 31.38 6.09
2442 4087 0.179129 GTCCATGGGAAAATGCGCAG 60.179 55.000 18.32 0.00 34.06 5.18
2455 4100 2.034066 CGCAGCCTTCCCCTTGAA 59.966 61.111 0.00 0.00 0.00 2.69
2456 4101 2.335712 CGCAGCCTTCCCCTTGAAC 61.336 63.158 0.00 0.00 0.00 3.18
2457 4102 1.228552 GCAGCCTTCCCCTTGAACA 60.229 57.895 0.00 0.00 0.00 3.18
2458 4103 1.527433 GCAGCCTTCCCCTTGAACAC 61.527 60.000 0.00 0.00 0.00 3.32
2459 4104 0.178992 CAGCCTTCCCCTTGAACACA 60.179 55.000 0.00 0.00 0.00 3.72
2460 4105 0.111253 AGCCTTCCCCTTGAACACAG 59.889 55.000 0.00 0.00 0.00 3.66
2461 4106 0.110486 GCCTTCCCCTTGAACACAGA 59.890 55.000 0.00 0.00 0.00 3.41
2462 4107 1.884067 GCCTTCCCCTTGAACACAGAG 60.884 57.143 0.00 0.00 0.00 3.35
2463 4108 1.271597 CCTTCCCCTTGAACACAGAGG 60.272 57.143 0.00 0.00 0.00 3.69
2464 4109 1.699634 CTTCCCCTTGAACACAGAGGA 59.300 52.381 0.00 0.00 32.11 3.71
2465 4110 1.056660 TCCCCTTGAACACAGAGGAC 58.943 55.000 0.00 0.00 32.11 3.85
2466 4111 0.764890 CCCCTTGAACACAGAGGACA 59.235 55.000 0.00 0.00 32.11 4.02
2467 4112 1.142870 CCCCTTGAACACAGAGGACAA 59.857 52.381 0.00 0.00 32.11 3.18
2468 4113 2.222027 CCCTTGAACACAGAGGACAAC 58.778 52.381 0.00 0.00 32.11 3.32
2469 4114 2.421388 CCCTTGAACACAGAGGACAACA 60.421 50.000 0.00 0.00 32.11 3.33
2470 4115 3.480470 CCTTGAACACAGAGGACAACAT 58.520 45.455 0.00 0.00 32.11 2.71
2471 4116 4.504864 CCCTTGAACACAGAGGACAACATA 60.505 45.833 0.00 0.00 32.11 2.29
2472 4117 4.452455 CCTTGAACACAGAGGACAACATAC 59.548 45.833 0.00 0.00 32.11 2.39
2473 4118 4.002906 TGAACACAGAGGACAACATACC 57.997 45.455 0.00 0.00 0.00 2.73
2474 4119 3.389656 TGAACACAGAGGACAACATACCA 59.610 43.478 0.00 0.00 0.00 3.25
2475 4120 4.041567 TGAACACAGAGGACAACATACCAT 59.958 41.667 0.00 0.00 0.00 3.55
2476 4121 5.247337 TGAACACAGAGGACAACATACCATA 59.753 40.000 0.00 0.00 0.00 2.74
2477 4122 5.755409 ACACAGAGGACAACATACCATAA 57.245 39.130 0.00 0.00 0.00 1.90
2478 4123 6.121776 ACACAGAGGACAACATACCATAAA 57.878 37.500 0.00 0.00 0.00 1.40
2479 4124 6.539173 ACACAGAGGACAACATACCATAAAA 58.461 36.000 0.00 0.00 0.00 1.52
2480 4125 7.001674 ACACAGAGGACAACATACCATAAAAA 58.998 34.615 0.00 0.00 0.00 1.94
2481 4126 7.669722 ACACAGAGGACAACATACCATAAAAAT 59.330 33.333 0.00 0.00 0.00 1.82
2482 4127 8.184192 CACAGAGGACAACATACCATAAAAATC 58.816 37.037 0.00 0.00 0.00 2.17
2483 4128 8.109634 ACAGAGGACAACATACCATAAAAATCT 58.890 33.333 0.00 0.00 0.00 2.40
2484 4129 8.616076 CAGAGGACAACATACCATAAAAATCTC 58.384 37.037 0.00 0.00 0.00 2.75
2485 4130 7.775561 AGAGGACAACATACCATAAAAATCTCC 59.224 37.037 0.00 0.00 0.00 3.71
2486 4131 7.643123 AGGACAACATACCATAAAAATCTCCT 58.357 34.615 0.00 0.00 0.00 3.69
2487 4132 7.775561 AGGACAACATACCATAAAAATCTCCTC 59.224 37.037 0.00 0.00 0.00 3.71
2488 4133 7.254795 GGACAACATACCATAAAAATCTCCTCG 60.255 40.741 0.00 0.00 0.00 4.63
2489 4134 6.542370 ACAACATACCATAAAAATCTCCTCGG 59.458 38.462 0.00 0.00 0.00 4.63
2490 4135 6.494666 ACATACCATAAAAATCTCCTCGGA 57.505 37.500 0.00 0.00 0.00 4.55
2491 4136 7.079451 ACATACCATAAAAATCTCCTCGGAT 57.921 36.000 0.00 0.00 0.00 4.18
2492 4137 7.162082 ACATACCATAAAAATCTCCTCGGATC 58.838 38.462 0.00 0.00 0.00 3.36
2493 4138 4.632153 ACCATAAAAATCTCCTCGGATCG 58.368 43.478 0.00 0.00 0.00 3.69
2494 4139 3.433615 CCATAAAAATCTCCTCGGATCGC 59.566 47.826 0.00 0.00 0.00 4.58
2495 4140 1.571919 AAAAATCTCCTCGGATCGCG 58.428 50.000 0.00 0.00 0.00 5.87
2496 4141 0.460311 AAAATCTCCTCGGATCGCGT 59.540 50.000 5.77 0.00 0.00 6.01
2497 4142 0.249073 AAATCTCCTCGGATCGCGTG 60.249 55.000 5.77 0.00 0.00 5.34
2498 4143 2.076622 AATCTCCTCGGATCGCGTGG 62.077 60.000 5.77 14.67 0.00 4.94
2499 4144 4.271816 CTCCTCGGATCGCGTGGG 62.272 72.222 18.36 13.92 0.00 4.61
2501 4146 4.873129 CCTCGGATCGCGTGGGTG 62.873 72.222 5.77 0.00 0.00 4.61
2502 4147 4.129737 CTCGGATCGCGTGGGTGT 62.130 66.667 5.77 0.00 0.00 4.16
2503 4148 4.124351 TCGGATCGCGTGGGTGTC 62.124 66.667 5.77 0.00 0.00 3.67
2505 4150 4.430765 GGATCGCGTGGGTGTCGT 62.431 66.667 5.77 0.00 0.00 4.34
2506 4151 2.879462 GATCGCGTGGGTGTCGTC 60.879 66.667 5.77 0.00 0.00 4.20
2507 4152 3.620300 GATCGCGTGGGTGTCGTCA 62.620 63.158 5.77 0.00 0.00 4.35
2508 4153 2.884087 GATCGCGTGGGTGTCGTCAT 62.884 60.000 5.77 0.00 0.00 3.06
2509 4154 2.884087 ATCGCGTGGGTGTCGTCATC 62.884 60.000 5.77 0.00 0.00 2.92
2510 4155 2.261671 GCGTGGGTGTCGTCATCT 59.738 61.111 0.00 0.00 0.00 2.90
2511 4156 1.374252 GCGTGGGTGTCGTCATCTT 60.374 57.895 0.00 0.00 0.00 2.40
2512 4157 1.352156 GCGTGGGTGTCGTCATCTTC 61.352 60.000 0.00 0.00 0.00 2.87
2513 4158 0.736325 CGTGGGTGTCGTCATCTTCC 60.736 60.000 0.00 0.00 0.00 3.46
2514 4159 0.391263 GTGGGTGTCGTCATCTTCCC 60.391 60.000 0.05 0.05 35.85 3.97
2515 4160 1.221021 GGGTGTCGTCATCTTCCCC 59.779 63.158 0.00 0.00 0.00 4.81
2516 4161 1.153628 GGTGTCGTCATCTTCCCCG 60.154 63.158 0.00 0.00 0.00 5.73
2517 4162 1.810030 GTGTCGTCATCTTCCCCGC 60.810 63.158 0.00 0.00 0.00 6.13
2518 4163 1.982395 TGTCGTCATCTTCCCCGCT 60.982 57.895 0.00 0.00 0.00 5.52
2519 4164 0.681887 TGTCGTCATCTTCCCCGCTA 60.682 55.000 0.00 0.00 0.00 4.26
2520 4165 0.674534 GTCGTCATCTTCCCCGCTAT 59.325 55.000 0.00 0.00 0.00 2.97
2521 4166 1.884579 GTCGTCATCTTCCCCGCTATA 59.115 52.381 0.00 0.00 0.00 1.31
2522 4167 2.295349 GTCGTCATCTTCCCCGCTATAA 59.705 50.000 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 5.570262 TGTTTAGTTGATTCTCGTTCACG 57.430 39.130 0.00 0.00 41.45 4.35
105 106 9.214957 TCACGTTCATTATGTTTAGTTGATTCT 57.785 29.630 0.00 0.00 0.00 2.40
169 170 5.408604 GCCGAAAGTTCTTCTTGTAATGAGA 59.591 40.000 0.00 0.00 36.40 3.27
513 520 3.962063 TCGATATACCCTTAGTGTTGGCA 59.038 43.478 0.00 0.00 0.00 4.92
551 558 1.549950 CCAAATAGTGGCAGGGTTGGT 60.550 52.381 9.78 0.00 41.72 3.67
573 580 4.320608 ACAAGCACCACCACTATTTTTG 57.679 40.909 0.00 0.00 0.00 2.44
685 693 5.965922 AGGCATTATAAACTCACAAAAGGC 58.034 37.500 0.00 0.00 0.00 4.35
1386 3002 4.562143 CCAATGTCTGATGCCTCGATGATA 60.562 45.833 0.00 0.00 0.00 2.15
1710 3335 6.822676 TCATTTTTGTTTCATGCCTCTTTTGT 59.177 30.769 0.00 0.00 0.00 2.83
1922 3559 2.552315 TCACCTTCGAAATTTCACCAGC 59.448 45.455 17.99 0.00 0.00 4.85
2004 3641 1.351017 TCTAACCCCAAGCCTCAACAG 59.649 52.381 0.00 0.00 0.00 3.16
2231 3874 1.410517 GAACTAACTACCTACCCCCGC 59.589 57.143 0.00 0.00 0.00 6.13
2232 3875 2.738743 TGAACTAACTACCTACCCCCG 58.261 52.381 0.00 0.00 0.00 5.73
2307 3952 6.204688 CACCCATGTACTTATTGACGCATAAT 59.795 38.462 0.00 0.00 0.00 1.28
2377 4022 5.221441 GCTTCCAAAGGAGGTGTGTTTATTT 60.221 40.000 0.00 0.00 31.01 1.40
2380 4025 3.219281 GCTTCCAAAGGAGGTGTGTTTA 58.781 45.455 0.00 0.00 31.01 2.01
2381 4026 2.031870 GCTTCCAAAGGAGGTGTGTTT 58.968 47.619 0.00 0.00 31.01 2.83
2382 4027 1.692411 GCTTCCAAAGGAGGTGTGTT 58.308 50.000 0.00 0.00 31.01 3.32
2383 4028 0.178990 GGCTTCCAAAGGAGGTGTGT 60.179 55.000 0.00 0.00 31.01 3.72
2384 4029 0.111253 AGGCTTCCAAAGGAGGTGTG 59.889 55.000 0.00 0.00 31.01 3.82
2385 4030 1.630878 CTAGGCTTCCAAAGGAGGTGT 59.369 52.381 0.00 0.00 31.01 4.16
2386 4031 1.630878 ACTAGGCTTCCAAAGGAGGTG 59.369 52.381 0.00 0.00 31.01 4.00
2387 4032 2.046280 ACTAGGCTTCCAAAGGAGGT 57.954 50.000 0.00 0.00 31.01 3.85
2388 4033 3.519913 AGTTACTAGGCTTCCAAAGGAGG 59.480 47.826 0.00 0.00 31.21 4.30
2389 4034 4.508662 CAGTTACTAGGCTTCCAAAGGAG 58.491 47.826 0.00 0.00 31.21 3.69
2390 4035 3.307480 GCAGTTACTAGGCTTCCAAAGGA 60.307 47.826 0.00 0.00 0.00 3.36
2391 4036 3.010420 GCAGTTACTAGGCTTCCAAAGG 58.990 50.000 0.00 0.00 0.00 3.11
2392 4037 3.010420 GGCAGTTACTAGGCTTCCAAAG 58.990 50.000 0.00 0.00 0.00 2.77
2393 4038 2.614481 CGGCAGTTACTAGGCTTCCAAA 60.614 50.000 0.00 0.00 0.00 3.28
2394 4039 1.066430 CGGCAGTTACTAGGCTTCCAA 60.066 52.381 0.00 0.00 0.00 3.53
2395 4040 0.535335 CGGCAGTTACTAGGCTTCCA 59.465 55.000 0.00 0.00 0.00 3.53
2396 4041 0.535797 ACGGCAGTTACTAGGCTTCC 59.464 55.000 0.00 0.00 0.00 3.46
2397 4042 1.477295 AGACGGCAGTTACTAGGCTTC 59.523 52.381 0.00 6.71 0.00 3.86
2398 4043 1.204941 CAGACGGCAGTTACTAGGCTT 59.795 52.381 0.00 0.00 0.00 4.35
2399 4044 0.818296 CAGACGGCAGTTACTAGGCT 59.182 55.000 0.00 0.00 0.00 4.58
2400 4045 0.531200 ACAGACGGCAGTTACTAGGC 59.469 55.000 0.00 0.00 0.00 3.93
2401 4046 1.544691 ACACAGACGGCAGTTACTAGG 59.455 52.381 0.00 0.00 0.00 3.02
2402 4047 2.728225 CGACACAGACGGCAGTTACTAG 60.728 54.545 0.00 0.00 0.00 2.57
2403 4048 1.198408 CGACACAGACGGCAGTTACTA 59.802 52.381 0.00 0.00 0.00 1.82
2404 4049 0.039437 CGACACAGACGGCAGTTACT 60.039 55.000 0.00 0.00 0.00 2.24
2405 4050 0.318445 ACGACACAGACGGCAGTTAC 60.318 55.000 0.00 0.00 34.93 2.50
2406 4051 0.039798 GACGACACAGACGGCAGTTA 60.040 55.000 0.00 0.00 38.75 2.24
2407 4052 1.299926 GACGACACAGACGGCAGTT 60.300 57.895 0.00 0.00 38.75 3.16
2408 4053 2.335369 GACGACACAGACGGCAGT 59.665 61.111 0.00 0.00 38.75 4.40
2409 4054 2.430921 GGACGACACAGACGGCAG 60.431 66.667 0.00 0.00 40.86 4.85
2410 4055 2.570284 ATGGACGACACAGACGGCA 61.570 57.895 0.00 0.00 40.86 5.69
2411 4056 2.094659 CATGGACGACACAGACGGC 61.095 63.158 0.00 0.00 38.12 5.68
2412 4057 1.446099 CCATGGACGACACAGACGG 60.446 63.158 5.56 0.00 34.93 4.79
2413 4058 1.446099 CCCATGGACGACACAGACG 60.446 63.158 15.22 0.00 0.00 4.18
2414 4059 0.320374 TTCCCATGGACGACACAGAC 59.680 55.000 15.22 0.00 0.00 3.51
2415 4060 1.052617 TTTCCCATGGACGACACAGA 58.947 50.000 15.22 0.00 0.00 3.41
2416 4061 1.890876 TTTTCCCATGGACGACACAG 58.109 50.000 15.22 0.00 0.00 3.66
2417 4062 2.158559 CATTTTCCCATGGACGACACA 58.841 47.619 15.22 0.00 0.00 3.72
2418 4063 1.135402 GCATTTTCCCATGGACGACAC 60.135 52.381 15.22 0.00 0.00 3.67
2419 4064 1.173043 GCATTTTCCCATGGACGACA 58.827 50.000 15.22 0.00 0.00 4.35
2420 4065 0.098728 CGCATTTTCCCATGGACGAC 59.901 55.000 15.22 0.00 0.00 4.34
2421 4066 1.653094 GCGCATTTTCCCATGGACGA 61.653 55.000 15.22 0.00 0.00 4.20
2422 4067 1.226660 GCGCATTTTCCCATGGACG 60.227 57.895 15.22 6.22 0.00 4.79
2423 4068 0.179129 CTGCGCATTTTCCCATGGAC 60.179 55.000 15.22 0.00 0.00 4.02
2424 4069 1.947597 GCTGCGCATTTTCCCATGGA 61.948 55.000 15.22 0.00 0.00 3.41
2425 4070 1.519898 GCTGCGCATTTTCCCATGG 60.520 57.895 12.24 4.14 0.00 3.66
2426 4071 1.519898 GGCTGCGCATTTTCCCATG 60.520 57.895 12.24 0.00 0.00 3.66
2427 4072 1.259840 AAGGCTGCGCATTTTCCCAT 61.260 50.000 12.24 0.00 0.00 4.00
2428 4073 1.876497 GAAGGCTGCGCATTTTCCCA 61.876 55.000 12.24 0.00 31.02 4.37
2429 4074 1.153765 GAAGGCTGCGCATTTTCCC 60.154 57.895 12.24 6.82 31.02 3.97
2430 4075 1.153765 GGAAGGCTGCGCATTTTCC 60.154 57.895 23.31 23.31 31.02 3.13
2431 4076 1.153765 GGGAAGGCTGCGCATTTTC 60.154 57.895 12.24 14.78 31.02 2.29
2432 4077 2.649129 GGGGAAGGCTGCGCATTTT 61.649 57.895 12.24 5.62 31.02 1.82
2433 4078 3.070576 GGGGAAGGCTGCGCATTT 61.071 61.111 12.24 6.04 31.02 2.32
2434 4079 3.590466 AAGGGGAAGGCTGCGCATT 62.590 57.895 12.24 7.85 34.48 3.56
2435 4080 4.052518 AAGGGGAAGGCTGCGCAT 62.053 61.111 12.24 0.29 0.00 4.73
2437 4082 4.722700 TCAAGGGGAAGGCTGCGC 62.723 66.667 0.00 0.00 0.00 6.09
2438 4083 2.034066 TTCAAGGGGAAGGCTGCG 59.966 61.111 0.00 0.00 0.00 5.18
2439 4084 1.228552 TGTTCAAGGGGAAGGCTGC 60.229 57.895 0.00 0.00 35.82 5.25
2440 4085 0.178992 TGTGTTCAAGGGGAAGGCTG 60.179 55.000 0.00 0.00 35.82 4.85
2441 4086 0.111253 CTGTGTTCAAGGGGAAGGCT 59.889 55.000 0.00 0.00 35.82 4.58
2442 4087 0.110486 TCTGTGTTCAAGGGGAAGGC 59.890 55.000 0.00 0.00 35.82 4.35
2443 4088 1.271597 CCTCTGTGTTCAAGGGGAAGG 60.272 57.143 0.00 0.00 35.82 3.46
2444 4089 1.699634 TCCTCTGTGTTCAAGGGGAAG 59.300 52.381 0.00 0.00 35.82 3.46
2445 4090 1.420138 GTCCTCTGTGTTCAAGGGGAA 59.580 52.381 0.00 0.00 0.00 3.97
2446 4091 1.056660 GTCCTCTGTGTTCAAGGGGA 58.943 55.000 0.00 0.00 0.00 4.81
2447 4092 0.764890 TGTCCTCTGTGTTCAAGGGG 59.235 55.000 0.00 0.00 0.00 4.79
2448 4093 2.222027 GTTGTCCTCTGTGTTCAAGGG 58.778 52.381 0.00 0.00 0.00 3.95
2449 4094 2.917933 TGTTGTCCTCTGTGTTCAAGG 58.082 47.619 0.00 0.00 0.00 3.61
2450 4095 4.452455 GGTATGTTGTCCTCTGTGTTCAAG 59.548 45.833 0.00 0.00 0.00 3.02
2451 4096 4.141597 TGGTATGTTGTCCTCTGTGTTCAA 60.142 41.667 0.00 0.00 0.00 2.69
2452 4097 3.389656 TGGTATGTTGTCCTCTGTGTTCA 59.610 43.478 0.00 0.00 0.00 3.18
2453 4098 4.002906 TGGTATGTTGTCCTCTGTGTTC 57.997 45.455 0.00 0.00 0.00 3.18
2454 4099 4.640771 ATGGTATGTTGTCCTCTGTGTT 57.359 40.909 0.00 0.00 0.00 3.32
2455 4100 5.755409 TTATGGTATGTTGTCCTCTGTGT 57.245 39.130 0.00 0.00 0.00 3.72
2456 4101 7.447374 TTTTTATGGTATGTTGTCCTCTGTG 57.553 36.000 0.00 0.00 0.00 3.66
2457 4102 8.109634 AGATTTTTATGGTATGTTGTCCTCTGT 58.890 33.333 0.00 0.00 0.00 3.41
2458 4103 8.511604 AGATTTTTATGGTATGTTGTCCTCTG 57.488 34.615 0.00 0.00 0.00 3.35
2459 4104 7.775561 GGAGATTTTTATGGTATGTTGTCCTCT 59.224 37.037 0.00 0.00 0.00 3.69
2460 4105 7.775561 AGGAGATTTTTATGGTATGTTGTCCTC 59.224 37.037 0.00 0.00 0.00 3.71
2461 4106 7.643123 AGGAGATTTTTATGGTATGTTGTCCT 58.357 34.615 0.00 0.00 0.00 3.85
2462 4107 7.254795 CGAGGAGATTTTTATGGTATGTTGTCC 60.255 40.741 0.00 0.00 0.00 4.02
2463 4108 7.254795 CCGAGGAGATTTTTATGGTATGTTGTC 60.255 40.741 0.00 0.00 0.00 3.18
2464 4109 6.542370 CCGAGGAGATTTTTATGGTATGTTGT 59.458 38.462 0.00 0.00 0.00 3.32
2465 4110 6.765989 TCCGAGGAGATTTTTATGGTATGTTG 59.234 38.462 0.00 0.00 0.00 3.33
2466 4111 6.895782 TCCGAGGAGATTTTTATGGTATGTT 58.104 36.000 0.00 0.00 0.00 2.71
2467 4112 6.494666 TCCGAGGAGATTTTTATGGTATGT 57.505 37.500 0.00 0.00 0.00 2.29
2468 4113 6.311445 CGATCCGAGGAGATTTTTATGGTATG 59.689 42.308 0.00 0.00 0.00 2.39
2469 4114 6.398918 CGATCCGAGGAGATTTTTATGGTAT 58.601 40.000 0.00 0.00 0.00 2.73
2470 4115 5.779922 CGATCCGAGGAGATTTTTATGGTA 58.220 41.667 0.00 0.00 0.00 3.25
2471 4116 4.632153 CGATCCGAGGAGATTTTTATGGT 58.368 43.478 0.00 0.00 0.00 3.55
2472 4117 3.433615 GCGATCCGAGGAGATTTTTATGG 59.566 47.826 0.00 0.00 0.00 2.74
2473 4118 3.121944 CGCGATCCGAGGAGATTTTTATG 59.878 47.826 0.00 0.00 40.02 1.90
2474 4119 3.243771 ACGCGATCCGAGGAGATTTTTAT 60.244 43.478 15.93 0.00 41.02 1.40
2475 4120 2.100252 ACGCGATCCGAGGAGATTTTTA 59.900 45.455 15.93 0.00 41.02 1.52
2476 4121 1.134788 ACGCGATCCGAGGAGATTTTT 60.135 47.619 15.93 0.00 41.02 1.94
2477 4122 0.460311 ACGCGATCCGAGGAGATTTT 59.540 50.000 15.93 0.00 41.02 1.82
2478 4123 0.249073 CACGCGATCCGAGGAGATTT 60.249 55.000 15.93 0.00 41.02 2.17
2479 4124 1.360551 CACGCGATCCGAGGAGATT 59.639 57.895 15.93 0.00 41.02 2.40
2480 4125 3.034878 CACGCGATCCGAGGAGAT 58.965 61.111 15.93 0.00 41.02 2.75
2484 4129 4.873129 CACCCACGCGATCCGAGG 62.873 72.222 15.93 10.72 45.74 4.63
2485 4130 4.129737 ACACCCACGCGATCCGAG 62.130 66.667 15.93 0.00 41.02 4.63
2486 4131 4.124351 GACACCCACGCGATCCGA 62.124 66.667 15.93 0.00 41.02 4.55
2488 4133 4.430765 ACGACACCCACGCGATCC 62.431 66.667 15.93 0.00 0.00 3.36
2489 4134 2.879462 GACGACACCCACGCGATC 60.879 66.667 15.93 0.00 0.00 3.69
2490 4135 2.884087 GATGACGACACCCACGCGAT 62.884 60.000 15.93 0.00 0.00 4.58
2491 4136 3.620300 GATGACGACACCCACGCGA 62.620 63.158 15.93 0.00 0.00 5.87
2492 4137 3.179265 GATGACGACACCCACGCG 61.179 66.667 3.53 3.53 0.00 6.01
2493 4138 1.352156 GAAGATGACGACACCCACGC 61.352 60.000 0.00 0.00 0.00 5.34
2494 4139 0.736325 GGAAGATGACGACACCCACG 60.736 60.000 0.00 0.00 0.00 4.94
2495 4140 0.391263 GGGAAGATGACGACACCCAC 60.391 60.000 6.45 0.00 37.50 4.61
2496 4141 1.550130 GGGGAAGATGACGACACCCA 61.550 60.000 12.09 0.00 39.10 4.51
2497 4142 1.221021 GGGGAAGATGACGACACCC 59.779 63.158 3.22 3.22 36.90 4.61
2498 4143 1.153628 CGGGGAAGATGACGACACC 60.154 63.158 0.00 0.00 0.00 4.16
2499 4144 1.810030 GCGGGGAAGATGACGACAC 60.810 63.158 0.00 0.00 0.00 3.67
2500 4145 0.681887 TAGCGGGGAAGATGACGACA 60.682 55.000 0.00 0.00 0.00 4.35
2501 4146 0.674534 ATAGCGGGGAAGATGACGAC 59.325 55.000 0.00 0.00 0.00 4.34
2502 4147 2.281539 TATAGCGGGGAAGATGACGA 57.718 50.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.