Multiple sequence alignment - TraesCS1A01G316100

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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 TraesCS1A01G316100 chr1A 100.000 4209 0 0 1 4209 508198117 508202325 0.000000e+00 7773.0
1 TraesCS1A01G316100 chr1A 94.118 85 5 0 143 227 398448531 398448615 3.420000e-26 130.0
2 TraesCS1A01G316100 chr4A 98.823 4077 22 5 1 4073 47627474 47631528 0.000000e+00 7239.0
3 TraesCS1A01G316100 chr4A 89.209 139 15 0 4071 4209 720091940 720092078 1.560000e-39 174.0
4 TraesCS1A01G316100 chr4A 91.860 86 6 1 793 877 595422502 595422587 7.390000e-23 119.0
5 TraesCS1A01G316100 chr4D 95.316 2882 102 15 138 3000 416450789 416447922 0.000000e+00 4543.0
6 TraesCS1A01G316100 chr4D 89.655 145 15 0 3108 3252 416447886 416447742 7.190000e-43 185.0
7 TraesCS1A01G316100 chr4D 84.000 200 13 8 3882 4073 416447132 416446944 1.560000e-39 174.0
8 TraesCS1A01G316100 chr4D 95.876 97 1 3 3013 3107 494801286 494801381 2.030000e-33 154.0
9 TraesCS1A01G316100 chr4D 85.612 139 15 5 781 915 7893697 7893560 1.580000e-29 141.0
10 TraesCS1A01G316100 chr4B 94.114 2854 122 20 143 2979 513100584 513097760 0.000000e+00 4298.0
11 TraesCS1A01G316100 chr4B 91.698 265 20 2 3110 3374 513097613 513097351 2.390000e-97 366.0
12 TraesCS1A01G316100 chr4B 95.789 95 4 0 3013 3107 585819124 585819030 2.030000e-33 154.0
13 TraesCS1A01G316100 chr4B 100.000 42 0 0 2979 3020 513097658 513097617 1.250000e-10 78.7
14 TraesCS1A01G316100 chr7D 95.000 120 6 0 28 147 431926830 431926949 5.560000e-44 189.0
15 TraesCS1A01G316100 chr7D 92.562 121 8 1 30 149 182605349 182605469 5.590000e-39 172.0
16 TraesCS1A01G316100 chr7D 93.162 117 7 1 31 146 247324144 247324260 2.010000e-38 171.0
17 TraesCS1A01G316100 chr7D 95.876 97 1 3 3013 3107 70086450 70086545 2.030000e-33 154.0
18 TraesCS1A01G316100 chr6A 91.304 138 12 0 4072 4209 558040095 558039958 5.560000e-44 189.0
19 TraesCS1A01G316100 chr6A 86.614 127 15 2 4074 4199 66266608 66266733 5.670000e-29 139.0
20 TraesCS1A01G316100 chr5D 92.126 127 10 0 27 153 369304980 369304854 3.340000e-41 180.0
21 TraesCS1A01G316100 chr1B 93.277 119 8 0 28 146 487947625 487947743 4.330000e-40 176.0
22 TraesCS1A01G316100 chr1B 88.971 136 15 0 4074 4209 56382257 56382392 7.240000e-38 169.0
23 TraesCS1A01G316100 chr1B 87.302 126 16 0 4074 4199 170577417 170577542 1.220000e-30 145.0
24 TraesCS1A01G316100 chr1B 85.401 137 20 0 4073 4209 353274171 353274035 4.390000e-30 143.0
25 TraesCS1A01G316100 chr1B 94.118 85 5 0 143 227 429584085 429584169 3.420000e-26 130.0
26 TraesCS1A01G316100 chr3B 88.722 133 13 2 15 146 655032731 655032862 1.210000e-35 161.0
27 TraesCS1A01G316100 chr3B 97.849 93 1 1 3019 3110 127291869 127291961 4.360000e-35 159.0
28 TraesCS1A01G316100 chr3B 94.186 86 5 0 143 228 489361686 489361771 9.500000e-27 132.0
29 TraesCS1A01G316100 chr3A 94.340 106 5 1 145 249 535190050 535189945 1.210000e-35 161.0
30 TraesCS1A01G316100 chr6B 89.231 130 11 3 26 154 444741805 444741678 4.360000e-35 159.0
31 TraesCS1A01G316100 chr6B 94.118 102 3 3 3004 3104 27938410 27938509 7.290000e-33 152.0
32 TraesCS1A01G316100 chr5A 95.098 102 3 2 3011 3110 27637146 27637045 4.360000e-35 159.0
33 TraesCS1A01G316100 chr6D 95.876 97 1 3 3013 3107 333950611 333950516 2.030000e-33 154.0
34 TraesCS1A01G316100 chr3D 86.957 138 16 2 29 165 208640709 208640573 2.030000e-33 154.0
35 TraesCS1A01G316100 chr3D 95.876 97 1 3 3013 3107 531382489 531382394 2.030000e-33 154.0
36 TraesCS1A01G316100 chr3D 91.429 105 6 2 145 249 415165390 415165491 1.580000e-29 141.0
37 TraesCS1A01G316100 chr3D 95.294 85 4 0 143 227 375211111 375211195 7.340000e-28 135.0
38 TraesCS1A01G316100 chr5B 86.923 130 17 0 4070 4199 663517256 663517385 3.390000e-31 147.0
39 TraesCS1A01G316100 chr2B 85.294 136 20 0 4074 4209 647897277 647897412 1.580000e-29 141.0
40 TraesCS1A01G316100 chr2B 84.173 139 22 0 4064 4202 24026300 24026162 7.340000e-28 135.0


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 TraesCS1A01G316100 chr1A 508198117 508202325 4208 False 7773.0 7773 100.000000 1 4209 1 chr1A.!!$F2 4208
1 TraesCS1A01G316100 chr4A 47627474 47631528 4054 False 7239.0 7239 98.823000 1 4073 1 chr4A.!!$F1 4072
2 TraesCS1A01G316100 chr4D 416446944 416450789 3845 True 1634.0 4543 89.657000 138 4073 3 chr4D.!!$R2 3935
3 TraesCS1A01G316100 chr4B 513097351 513100584 3233 True 1580.9 4298 95.270667 143 3374 3 chr4B.!!$R2 3231

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
39 40 7.554476 GCAATTGAGAATTTTAGTACTCCCTCT 59.446 37.037 10.34 0.0 0.00 3.69 F
1064 1087 2.950065 TTCCCCATCCCCAACCCC 60.950 66.667 0.00 0.0 0.00 4.95 F
1359 1382 0.972471 GATTTGGGGGTGCTCAAGGG 60.972 60.000 0.00 0.0 0.00 3.95 F
2627 2653 2.099141 GCTGATGTCTTACAGGCACA 57.901 50.000 0.00 0.0 29.65 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1068 1091 1.274728 CGCAGAGATAAGGGAGATGGG 59.725 57.143 0.00 0.0 0.00 4.00 R
2627 2653 2.064581 GGGGTATGTCCAGGTCGCT 61.065 63.158 0.00 0.0 38.11 4.93 R
3079 3210 2.907696 TCCCTCCGTTCCAAATTACTCA 59.092 45.455 0.00 0.0 0.00 3.41 R
3659 3803 0.108567 GTGGCCGGAGAAGAAGAGTC 60.109 60.000 5.05 0.0 0.00 3.36 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
39 40 7.554476 GCAATTGAGAATTTTAGTACTCCCTCT 59.446 37.037 10.34 0.00 0.00 3.69
1064 1087 2.950065 TTCCCCATCCCCAACCCC 60.950 66.667 0.00 0.00 0.00 4.95
1065 1088 3.857746 TTCCCCATCCCCAACCCCA 62.858 63.158 0.00 0.00 0.00 4.96
1066 1089 3.280151 CCCCATCCCCAACCCCAA 61.280 66.667 0.00 0.00 0.00 4.12
1067 1090 2.038813 CCCATCCCCAACCCCAAC 59.961 66.667 0.00 0.00 0.00 3.77
1068 1091 2.038813 CCATCCCCAACCCCAACC 59.961 66.667 0.00 0.00 0.00 3.77
1069 1092 2.038813 CATCCCCAACCCCAACCC 59.961 66.667 0.00 0.00 0.00 4.11
1359 1382 0.972471 GATTTGGGGGTGCTCAAGGG 60.972 60.000 0.00 0.00 0.00 3.95
1648 1673 5.635120 ACTTTTGGTGCTCTTCCTATTTCT 58.365 37.500 0.00 0.00 0.00 2.52
2547 2573 6.837312 TGAGTTATATGACGGGGAATTCAAT 58.163 36.000 7.93 0.00 0.00 2.57
2627 2653 2.099141 GCTGATGTCTTACAGGCACA 57.901 50.000 0.00 0.00 29.65 4.57
2744 2770 7.821846 GTCTCTGTCCTGATGTTTAGATCTTTT 59.178 37.037 0.00 0.00 0.00 2.27
3430 3574 4.460382 TCCTCAAAATCCAGAATGTCTTGC 59.540 41.667 0.00 0.00 0.00 4.01
3630 3774 0.178964 TCTCCCTGGCCTTGTTTTGG 60.179 55.000 3.32 0.00 0.00 3.28
3635 3779 2.381838 CTGGCCTTGTTTTGGGTGGC 62.382 60.000 3.32 0.00 42.56 5.01
3659 3803 4.697756 TCGCCCGTTTCCAGCAGG 62.698 66.667 0.00 0.00 0.00 4.85
3987 4314 4.411013 AGGGAGATGGAAAAAGAAACTGG 58.589 43.478 0.00 0.00 0.00 4.00
4073 4405 4.456911 TGCAGTGCCTCTCTGAATTAAAAG 59.543 41.667 13.72 0.00 35.20 2.27
4074 4406 4.697352 GCAGTGCCTCTCTGAATTAAAAGA 59.303 41.667 2.85 0.00 35.20 2.52
4075 4407 5.163774 GCAGTGCCTCTCTGAATTAAAAGAG 60.164 44.000 2.85 6.11 41.13 2.85
4083 4415 9.267084 CCTCTCTGAATTAAAAGAGGTAATAGC 57.733 37.037 16.22 0.00 46.51 2.97
4084 4416 9.823647 CTCTCTGAATTAAAAGAGGTAATAGCA 57.176 33.333 10.73 0.00 40.34 3.49
4087 4419 9.561069 TCTGAATTAAAAGAGGTAATAGCATCC 57.439 33.333 0.00 0.00 0.00 3.51
4088 4420 8.691661 TGAATTAAAAGAGGTAATAGCATCCC 57.308 34.615 0.00 0.00 0.00 3.85
4089 4421 8.278639 TGAATTAAAAGAGGTAATAGCATCCCA 58.721 33.333 0.00 0.00 0.00 4.37
4090 4422 8.697507 AATTAAAAGAGGTAATAGCATCCCAG 57.302 34.615 0.00 0.00 0.00 4.45
4091 4423 4.713792 AAAGAGGTAATAGCATCCCAGG 57.286 45.455 0.00 0.00 0.00 4.45
4092 4424 3.352611 AGAGGTAATAGCATCCCAGGT 57.647 47.619 0.00 0.00 0.00 4.00
4093 4425 4.487282 AGAGGTAATAGCATCCCAGGTA 57.513 45.455 0.00 0.00 0.00 3.08
4094 4426 4.161102 AGAGGTAATAGCATCCCAGGTAC 58.839 47.826 0.00 0.00 0.00 3.34
4095 4427 3.248888 AGGTAATAGCATCCCAGGTACC 58.751 50.000 2.73 2.73 0.00 3.34
4096 4428 2.305052 GGTAATAGCATCCCAGGTACCC 59.695 54.545 8.74 0.00 0.00 3.69
4097 4429 2.514726 AATAGCATCCCAGGTACCCT 57.485 50.000 8.74 0.00 0.00 4.34
4098 4430 3.648683 AATAGCATCCCAGGTACCCTA 57.351 47.619 8.74 1.02 29.64 3.53
4099 4431 3.648683 ATAGCATCCCAGGTACCCTAA 57.351 47.619 8.74 0.00 29.64 2.69
4100 4432 1.508256 AGCATCCCAGGTACCCTAAC 58.492 55.000 8.74 0.00 29.64 2.34
4101 4433 1.009675 AGCATCCCAGGTACCCTAACT 59.990 52.381 8.74 0.00 29.64 2.24
4102 4434 1.844497 GCATCCCAGGTACCCTAACTT 59.156 52.381 8.74 0.00 29.64 2.66
4103 4435 2.421529 GCATCCCAGGTACCCTAACTTG 60.422 54.545 8.74 0.00 29.64 3.16
4104 4436 1.282382 TCCCAGGTACCCTAACTTGC 58.718 55.000 8.74 0.00 29.64 4.01
4105 4437 0.988832 CCCAGGTACCCTAACTTGCA 59.011 55.000 8.74 0.00 29.64 4.08
4106 4438 1.564348 CCCAGGTACCCTAACTTGCAT 59.436 52.381 8.74 0.00 29.64 3.96
4107 4439 2.775384 CCCAGGTACCCTAACTTGCATA 59.225 50.000 8.74 0.00 29.64 3.14
4108 4440 3.201266 CCCAGGTACCCTAACTTGCATAA 59.799 47.826 8.74 0.00 29.64 1.90
4109 4441 4.451900 CCAGGTACCCTAACTTGCATAAG 58.548 47.826 8.74 0.00 34.38 1.73
4110 4442 4.163458 CCAGGTACCCTAACTTGCATAAGA 59.837 45.833 8.74 0.00 33.21 2.10
4111 4443 5.163195 CCAGGTACCCTAACTTGCATAAGAT 60.163 44.000 8.74 0.00 33.21 2.40
4112 4444 5.760253 CAGGTACCCTAACTTGCATAAGATG 59.240 44.000 8.74 0.00 33.21 2.90
4113 4445 5.428783 AGGTACCCTAACTTGCATAAGATGT 59.571 40.000 8.74 0.00 32.94 3.06
4114 4446 5.527582 GGTACCCTAACTTGCATAAGATGTG 59.472 44.000 0.00 0.00 37.36 3.21
4115 4447 5.435686 ACCCTAACTTGCATAAGATGTGA 57.564 39.130 0.00 0.00 37.36 3.58
4116 4448 6.006275 ACCCTAACTTGCATAAGATGTGAT 57.994 37.500 0.00 0.00 37.36 3.06
4117 4449 7.136822 ACCCTAACTTGCATAAGATGTGATA 57.863 36.000 0.00 0.00 37.36 2.15
4118 4450 7.749666 ACCCTAACTTGCATAAGATGTGATAT 58.250 34.615 0.00 0.00 37.36 1.63
4119 4451 8.220559 ACCCTAACTTGCATAAGATGTGATATT 58.779 33.333 0.00 0.00 37.36 1.28
4120 4452 9.071276 CCCTAACTTGCATAAGATGTGATATTT 57.929 33.333 0.00 0.00 37.36 1.40
4127 4459 9.851686 TTGCATAAGATGTGATATTTTAGTCCT 57.148 29.630 0.00 0.00 0.00 3.85
4144 4476 9.877178 TTTTAGTCCTAAAATTGCAAAACTCAA 57.123 25.926 1.71 0.00 39.34 3.02
4146 4478 9.691362 TTAGTCCTAAAATTGCAAAACTCAATC 57.309 29.630 1.71 0.00 33.41 2.67
4147 4479 7.154656 AGTCCTAAAATTGCAAAACTCAATCC 58.845 34.615 1.71 0.00 33.41 3.01
4148 4480 6.368791 GTCCTAAAATTGCAAAACTCAATCCC 59.631 38.462 1.71 0.00 33.41 3.85
4149 4481 6.042552 TCCTAAAATTGCAAAACTCAATCCCA 59.957 34.615 1.71 0.00 33.41 4.37
4150 4482 6.880529 CCTAAAATTGCAAAACTCAATCCCAT 59.119 34.615 1.71 0.00 33.41 4.00
4151 4483 7.391275 CCTAAAATTGCAAAACTCAATCCCATT 59.609 33.333 1.71 0.00 33.41 3.16
4152 4484 9.434420 CTAAAATTGCAAAACTCAATCCCATTA 57.566 29.630 1.71 0.00 33.41 1.90
4153 4485 8.866970 AAAATTGCAAAACTCAATCCCATTAT 57.133 26.923 1.71 0.00 33.41 1.28
4154 4486 9.956640 AAAATTGCAAAACTCAATCCCATTATA 57.043 25.926 1.71 0.00 33.41 0.98
4155 4487 8.947055 AATTGCAAAACTCAATCCCATTATAC 57.053 30.769 1.71 0.00 33.41 1.47
4156 4488 6.463995 TGCAAAACTCAATCCCATTATACC 57.536 37.500 0.00 0.00 0.00 2.73
4157 4489 5.362430 TGCAAAACTCAATCCCATTATACCC 59.638 40.000 0.00 0.00 0.00 3.69
4158 4490 5.598417 GCAAAACTCAATCCCATTATACCCT 59.402 40.000 0.00 0.00 0.00 4.34
4159 4491 6.775629 GCAAAACTCAATCCCATTATACCCTA 59.224 38.462 0.00 0.00 0.00 3.53
4160 4492 7.286775 GCAAAACTCAATCCCATTATACCCTAA 59.713 37.037 0.00 0.00 0.00 2.69
4161 4493 8.630037 CAAAACTCAATCCCATTATACCCTAAC 58.370 37.037 0.00 0.00 0.00 2.34
4162 4494 7.707467 AACTCAATCCCATTATACCCTAACT 57.293 36.000 0.00 0.00 0.00 2.24
4163 4495 7.707467 ACTCAATCCCATTATACCCTAACTT 57.293 36.000 0.00 0.00 0.00 2.66
4164 4496 8.808240 ACTCAATCCCATTATACCCTAACTTA 57.192 34.615 0.00 0.00 0.00 2.24
4165 4497 8.657712 ACTCAATCCCATTATACCCTAACTTAC 58.342 37.037 0.00 0.00 0.00 2.34
4166 4498 8.570038 TCAATCCCATTATACCCTAACTTACA 57.430 34.615 0.00 0.00 0.00 2.41
4167 4499 8.434392 TCAATCCCATTATACCCTAACTTACAC 58.566 37.037 0.00 0.00 0.00 2.90
4168 4500 6.752285 TCCCATTATACCCTAACTTACACC 57.248 41.667 0.00 0.00 0.00 4.16
4169 4501 6.455241 TCCCATTATACCCTAACTTACACCT 58.545 40.000 0.00 0.00 0.00 4.00
4170 4502 6.556116 TCCCATTATACCCTAACTTACACCTC 59.444 42.308 0.00 0.00 0.00 3.85
4171 4503 6.328148 CCCATTATACCCTAACTTACACCTCA 59.672 42.308 0.00 0.00 0.00 3.86
4172 4504 7.017254 CCCATTATACCCTAACTTACACCTCAT 59.983 40.741 0.00 0.00 0.00 2.90
4173 4505 7.878127 CCATTATACCCTAACTTACACCTCATG 59.122 40.741 0.00 0.00 0.00 3.07
4174 4506 7.983166 TTATACCCTAACTTACACCTCATGT 57.017 36.000 0.00 0.00 46.06 3.21
4188 4520 4.589908 ACCTCATGTGATGTTTTAGTCCC 58.410 43.478 0.00 0.00 0.00 4.46
4189 4521 4.042809 ACCTCATGTGATGTTTTAGTCCCA 59.957 41.667 0.00 0.00 0.00 4.37
4190 4522 4.637534 CCTCATGTGATGTTTTAGTCCCAG 59.362 45.833 0.00 0.00 0.00 4.45
4191 4523 4.588899 TCATGTGATGTTTTAGTCCCAGG 58.411 43.478 0.00 0.00 0.00 4.45
4192 4524 2.790433 TGTGATGTTTTAGTCCCAGGC 58.210 47.619 0.00 0.00 0.00 4.85
4193 4525 2.092323 GTGATGTTTTAGTCCCAGGCC 58.908 52.381 0.00 0.00 0.00 5.19
4194 4526 1.707989 TGATGTTTTAGTCCCAGGCCA 59.292 47.619 5.01 0.00 0.00 5.36
4195 4527 2.109128 TGATGTTTTAGTCCCAGGCCAA 59.891 45.455 5.01 0.00 0.00 4.52
4196 4528 2.990740 TGTTTTAGTCCCAGGCCAAT 57.009 45.000 5.01 0.00 0.00 3.16
4197 4529 2.802719 TGTTTTAGTCCCAGGCCAATC 58.197 47.619 5.01 0.00 0.00 2.67
4198 4530 2.109128 TGTTTTAGTCCCAGGCCAATCA 59.891 45.455 5.01 0.00 0.00 2.57
4199 4531 2.755103 GTTTTAGTCCCAGGCCAATCAG 59.245 50.000 5.01 0.00 0.00 2.90
4200 4532 1.965414 TTAGTCCCAGGCCAATCAGA 58.035 50.000 5.01 0.00 0.00 3.27
4201 4533 1.500474 TAGTCCCAGGCCAATCAGAG 58.500 55.000 5.01 0.00 0.00 3.35
4202 4534 1.225704 GTCCCAGGCCAATCAGAGG 59.774 63.158 5.01 0.00 0.00 3.69
4203 4535 1.082766 TCCCAGGCCAATCAGAGGA 59.917 57.895 5.01 0.00 0.00 3.71
4204 4536 1.225704 CCCAGGCCAATCAGAGGAC 59.774 63.158 5.01 0.00 0.00 3.85
4205 4537 1.153289 CCAGGCCAATCAGAGGACG 60.153 63.158 5.01 0.00 39.93 4.79
4206 4538 1.617018 CCAGGCCAATCAGAGGACGA 61.617 60.000 5.01 0.00 39.93 4.20
4207 4539 0.460987 CAGGCCAATCAGAGGACGAC 60.461 60.000 5.01 0.00 39.93 4.34
4208 4540 0.904865 AGGCCAATCAGAGGACGACA 60.905 55.000 5.01 0.00 39.93 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.316390 AGGGAGTACTAAAATTCTCAATTGCG 59.684 38.462 0.00 0.00 0.00 4.85
39 40 2.369203 TGTGGACAAGTAATTCCGGACA 59.631 45.455 1.83 0.00 34.24 4.02
1064 1087 3.072184 CAGAGATAAGGGAGATGGGGTTG 59.928 52.174 0.00 0.00 0.00 3.77
1065 1088 3.321950 CAGAGATAAGGGAGATGGGGTT 58.678 50.000 0.00 0.00 0.00 4.11
1066 1089 2.983296 CAGAGATAAGGGAGATGGGGT 58.017 52.381 0.00 0.00 0.00 4.95
1067 1090 1.627834 GCAGAGATAAGGGAGATGGGG 59.372 57.143 0.00 0.00 0.00 4.96
1068 1091 1.274728 CGCAGAGATAAGGGAGATGGG 59.725 57.143 0.00 0.00 0.00 4.00
1069 1092 1.337635 GCGCAGAGATAAGGGAGATGG 60.338 57.143 0.30 0.00 0.00 3.51
2547 2573 3.359033 CAGGCCAATCCTCTGAAATTCA 58.641 45.455 5.01 0.00 45.52 2.57
2627 2653 2.064581 GGGGTATGTCCAGGTCGCT 61.065 63.158 0.00 0.00 38.11 4.93
2744 2770 8.397575 TGCTATGTCTACCAAACAAACAATTA 57.602 30.769 0.00 0.00 0.00 1.40
3079 3210 2.907696 TCCCTCCGTTCCAAATTACTCA 59.092 45.455 0.00 0.00 0.00 3.41
3411 3555 4.796038 AGGCAAGACATTCTGGATTTTG 57.204 40.909 0.00 0.00 0.00 2.44
3430 3574 2.601367 CCAACCACAGGGGCAAGG 60.601 66.667 0.00 0.00 42.05 3.61
3659 3803 0.108567 GTGGCCGGAGAAGAAGAGTC 60.109 60.000 5.05 0.00 0.00 3.36
3987 4314 3.300857 CGTGATATCTCATGTGGACGTC 58.699 50.000 7.13 7.13 34.30 4.34
4073 4405 3.261137 GGTACCTGGGATGCTATTACCTC 59.739 52.174 4.06 0.00 0.00 3.85
4074 4406 3.248888 GGTACCTGGGATGCTATTACCT 58.751 50.000 4.06 0.00 0.00 3.08
4075 4407 3.697619 GGTACCTGGGATGCTATTACC 57.302 52.381 4.06 0.00 0.00 2.85
4085 4417 8.984482 TCTTATGCAAGTTAGGGTACCTGGGA 62.984 46.154 12.72 0.00 46.00 4.37
4086 4418 6.867653 TCTTATGCAAGTTAGGGTACCTGGG 61.868 48.000 12.72 0.00 46.00 4.45
4087 4419 4.163458 TCTTATGCAAGTTAGGGTACCTGG 59.837 45.833 12.72 0.00 46.00 4.45
4088 4420 5.353394 TCTTATGCAAGTTAGGGTACCTG 57.647 43.478 12.72 1.69 46.00 4.00
4090 4422 5.527582 CACATCTTATGCAAGTTAGGGTACC 59.472 44.000 2.17 2.17 40.26 3.34
4091 4423 6.346096 TCACATCTTATGCAAGTTAGGGTAC 58.654 40.000 0.00 0.00 33.20 3.34
4092 4424 6.553953 TCACATCTTATGCAAGTTAGGGTA 57.446 37.500 0.00 0.00 33.20 3.69
4093 4425 5.435686 TCACATCTTATGCAAGTTAGGGT 57.564 39.130 0.00 0.00 33.20 4.34
4094 4426 8.627208 AATATCACATCTTATGCAAGTTAGGG 57.373 34.615 0.00 0.00 33.20 3.53
4101 4433 9.851686 AGGACTAAAATATCACATCTTATGCAA 57.148 29.630 0.00 0.00 0.00 4.08
4118 4450 9.877178 TTGAGTTTTGCAATTTTAGGACTAAAA 57.123 25.926 16.83 16.83 45.56 1.52
4120 4452 9.691362 GATTGAGTTTTGCAATTTTAGGACTAA 57.309 29.630 0.00 0.00 36.19 2.24
4121 4453 8.303876 GGATTGAGTTTTGCAATTTTAGGACTA 58.696 33.333 0.00 0.00 36.19 2.59
4122 4454 7.154656 GGATTGAGTTTTGCAATTTTAGGACT 58.845 34.615 0.00 0.00 36.19 3.85
4123 4455 6.368791 GGGATTGAGTTTTGCAATTTTAGGAC 59.631 38.462 0.00 0.00 36.19 3.85
4124 4456 6.042552 TGGGATTGAGTTTTGCAATTTTAGGA 59.957 34.615 0.00 0.00 36.19 2.94
4125 4457 6.229733 TGGGATTGAGTTTTGCAATTTTAGG 58.770 36.000 0.00 0.00 36.19 2.69
4126 4458 7.910441 ATGGGATTGAGTTTTGCAATTTTAG 57.090 32.000 0.00 0.00 36.19 1.85
4127 4459 9.956640 ATAATGGGATTGAGTTTTGCAATTTTA 57.043 25.926 0.00 0.00 36.19 1.52
4128 4460 8.866970 ATAATGGGATTGAGTTTTGCAATTTT 57.133 26.923 0.00 0.00 36.19 1.82
4129 4461 9.382275 GTATAATGGGATTGAGTTTTGCAATTT 57.618 29.630 0.00 0.00 36.19 1.82
4130 4462 7.986889 GGTATAATGGGATTGAGTTTTGCAATT 59.013 33.333 0.00 0.00 36.19 2.32
4131 4463 7.418942 GGGTATAATGGGATTGAGTTTTGCAAT 60.419 37.037 0.00 0.00 38.58 3.56
4132 4464 6.127196 GGGTATAATGGGATTGAGTTTTGCAA 60.127 38.462 0.00 0.00 0.00 4.08
4133 4465 5.362430 GGGTATAATGGGATTGAGTTTTGCA 59.638 40.000 0.00 0.00 0.00 4.08
4134 4466 5.598417 AGGGTATAATGGGATTGAGTTTTGC 59.402 40.000 0.00 0.00 0.00 3.68
4135 4467 8.630037 GTTAGGGTATAATGGGATTGAGTTTTG 58.370 37.037 0.00 0.00 0.00 2.44
4136 4468 8.566109 AGTTAGGGTATAATGGGATTGAGTTTT 58.434 33.333 0.00 0.00 0.00 2.43
4137 4469 8.114301 AGTTAGGGTATAATGGGATTGAGTTT 57.886 34.615 0.00 0.00 0.00 2.66
4138 4470 7.707467 AGTTAGGGTATAATGGGATTGAGTT 57.293 36.000 0.00 0.00 0.00 3.01
4139 4471 7.707467 AAGTTAGGGTATAATGGGATTGAGT 57.293 36.000 0.00 0.00 0.00 3.41
4140 4472 8.656806 TGTAAGTTAGGGTATAATGGGATTGAG 58.343 37.037 0.00 0.00 0.00 3.02
4141 4473 8.434392 GTGTAAGTTAGGGTATAATGGGATTGA 58.566 37.037 0.00 0.00 0.00 2.57
4142 4474 7.664318 GGTGTAAGTTAGGGTATAATGGGATTG 59.336 40.741 0.00 0.00 0.00 2.67
4143 4475 7.575129 AGGTGTAAGTTAGGGTATAATGGGATT 59.425 37.037 0.00 0.00 0.00 3.01
4144 4476 7.086920 AGGTGTAAGTTAGGGTATAATGGGAT 58.913 38.462 0.00 0.00 0.00 3.85
4145 4477 6.455241 AGGTGTAAGTTAGGGTATAATGGGA 58.545 40.000 0.00 0.00 0.00 4.37
4146 4478 6.328148 TGAGGTGTAAGTTAGGGTATAATGGG 59.672 42.308 0.00 0.00 0.00 4.00
4147 4479 7.369551 TGAGGTGTAAGTTAGGGTATAATGG 57.630 40.000 0.00 0.00 0.00 3.16
4148 4480 8.429641 ACATGAGGTGTAAGTTAGGGTATAATG 58.570 37.037 0.00 0.00 39.91 1.90
4149 4481 8.429641 CACATGAGGTGTAAGTTAGGGTATAAT 58.570 37.037 0.00 0.00 42.75 1.28
4150 4482 7.788026 CACATGAGGTGTAAGTTAGGGTATAA 58.212 38.462 0.00 0.00 42.75 0.98
4151 4483 7.356089 CACATGAGGTGTAAGTTAGGGTATA 57.644 40.000 0.00 0.00 42.75 1.47
4152 4484 6.235231 CACATGAGGTGTAAGTTAGGGTAT 57.765 41.667 0.00 0.00 42.75 2.73
4153 4485 5.670792 CACATGAGGTGTAAGTTAGGGTA 57.329 43.478 0.00 0.00 42.75 3.69
4154 4486 4.553330 CACATGAGGTGTAAGTTAGGGT 57.447 45.455 0.00 0.00 42.75 4.34
4166 4498 4.042809 TGGGACTAAAACATCACATGAGGT 59.957 41.667 0.00 0.00 41.21 3.85
4167 4499 4.588899 TGGGACTAAAACATCACATGAGG 58.411 43.478 0.00 0.00 0.00 3.86
4168 4500 4.637534 CCTGGGACTAAAACATCACATGAG 59.362 45.833 0.00 0.00 0.00 2.90
4169 4501 4.588899 CCTGGGACTAAAACATCACATGA 58.411 43.478 0.00 0.00 0.00 3.07
4170 4502 3.129287 GCCTGGGACTAAAACATCACATG 59.871 47.826 0.00 0.00 0.00 3.21
4171 4503 3.356290 GCCTGGGACTAAAACATCACAT 58.644 45.455 0.00 0.00 0.00 3.21
4172 4504 2.554344 GGCCTGGGACTAAAACATCACA 60.554 50.000 0.00 0.00 0.00 3.58
4173 4505 2.092323 GGCCTGGGACTAAAACATCAC 58.908 52.381 0.00 0.00 0.00 3.06
4174 4506 1.707989 TGGCCTGGGACTAAAACATCA 59.292 47.619 3.32 0.00 0.00 3.07
4175 4507 2.507407 TGGCCTGGGACTAAAACATC 57.493 50.000 3.32 0.00 0.00 3.06
4176 4508 2.990740 TTGGCCTGGGACTAAAACAT 57.009 45.000 3.32 0.00 0.00 2.71
4177 4509 2.109128 TGATTGGCCTGGGACTAAAACA 59.891 45.455 3.32 0.00 0.00 2.83
4178 4510 2.755103 CTGATTGGCCTGGGACTAAAAC 59.245 50.000 3.32 0.00 0.00 2.43
4179 4511 2.647299 TCTGATTGGCCTGGGACTAAAA 59.353 45.455 3.32 0.00 0.00 1.52
4180 4512 2.239654 CTCTGATTGGCCTGGGACTAAA 59.760 50.000 3.32 0.00 0.00 1.85
4181 4513 1.839994 CTCTGATTGGCCTGGGACTAA 59.160 52.381 3.32 0.00 0.00 2.24
4182 4514 1.500474 CTCTGATTGGCCTGGGACTA 58.500 55.000 3.32 0.00 0.00 2.59
4183 4515 1.277580 CCTCTGATTGGCCTGGGACT 61.278 60.000 3.32 0.00 0.00 3.85
4184 4516 1.225704 CCTCTGATTGGCCTGGGAC 59.774 63.158 3.32 0.00 0.00 4.46
4185 4517 1.082766 TCCTCTGATTGGCCTGGGA 59.917 57.895 3.32 0.00 0.00 4.37
4186 4518 1.225704 GTCCTCTGATTGGCCTGGG 59.774 63.158 3.32 0.00 0.00 4.45
4187 4519 1.153289 CGTCCTCTGATTGGCCTGG 60.153 63.158 3.32 0.00 0.00 4.45
4188 4520 0.460987 GTCGTCCTCTGATTGGCCTG 60.461 60.000 3.32 0.00 0.00 4.85
4189 4521 0.904865 TGTCGTCCTCTGATTGGCCT 60.905 55.000 3.32 0.00 0.00 5.19
4190 4522 1.596934 TGTCGTCCTCTGATTGGCC 59.403 57.895 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.