Multiple sequence alignment - TraesCS6A01G318300

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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 TraesCS6A01G318300 chr6A 100.000 4469 0 0 1 4469 554458709 554463177 0.000000e+00 8253.0
1 TraesCS6A01G318300 chr6A 83.405 464 49 16 72 514 596354622 596354166 5.380000e-109 405.0
2 TraesCS6A01G318300 chr6A 83.981 206 23 7 312 507 596341119 596340914 5.900000e-44 189.0
3 TraesCS6A01G318300 chr6B 96.063 3708 88 18 506 4174 613111636 613115324 0.000000e+00 5986.0
4 TraesCS6A01G318300 chr6B 93.090 521 28 6 1 515 613111026 613111544 0.000000e+00 756.0
5 TraesCS6A01G318300 chr6B 95.690 232 6 2 4242 4469 613115325 613115556 1.960000e-98 370.0
6 TraesCS6A01G318300 chr6B 95.652 69 3 0 4174 4242 27336757 27336825 1.310000e-20 111.0
7 TraesCS6A01G318300 chr6B 94.366 71 2 1 4174 4242 132677767 132677697 1.700000e-19 108.0
8 TraesCS6A01G318300 chr6D 95.680 3727 76 32 506 4175 408651015 408654713 0.000000e+00 5912.0
9 TraesCS6A01G318300 chr6D 94.027 519 25 6 1 515 408650416 408650932 0.000000e+00 782.0
10 TraesCS6A01G318300 chr6D 85.906 447 52 6 67 507 450820720 450820279 2.430000e-127 466.0
11 TraesCS6A01G318300 chr6D 95.671 231 9 1 4240 4469 408654712 408654942 1.960000e-98 370.0
12 TraesCS6A01G318300 chr6D 91.304 69 5 1 3835 3902 411616993 411616925 4.760000e-15 93.5
13 TraesCS6A01G318300 chr3D 82.000 400 49 14 72 464 335628992 335628609 7.210000e-83 318.0
14 TraesCS6A01G318300 chr3D 90.217 92 6 3 3819 3908 237809572 237809662 2.820000e-22 117.0
15 TraesCS6A01G318300 chr3B 81.047 401 51 17 72 464 434048881 434048498 3.380000e-76 296.0
16 TraesCS6A01G318300 chr3B 90.217 92 6 3 3819 3908 345690130 345690220 2.820000e-22 117.0
17 TraesCS6A01G318300 chr3A 81.000 400 53 14 72 464 453601966 453601583 3.380000e-76 296.0
18 TraesCS6A01G318300 chr3A 91.667 72 6 0 4174 4245 126162987 126163058 2.840000e-17 100.0
19 TraesCS6A01G318300 chr1D 90.909 99 5 4 3817 3914 320590034 320589939 3.630000e-26 130.0
20 TraesCS6A01G318300 chr1D 92.308 91 6 1 3819 3908 319515834 319515744 1.300000e-25 128.0
21 TraesCS6A01G318300 chr7B 98.551 69 1 0 4173 4241 329086216 329086148 6.070000e-24 122.0
22 TraesCS6A01G318300 chr7B 91.954 87 7 0 4174 4260 536665595 536665509 6.070000e-24 122.0
23 TraesCS6A01G318300 chr7B 97.917 48 1 0 3855 3902 660336593 660336546 2.860000e-12 84.2
24 TraesCS6A01G318300 chr4A 93.902 82 3 2 3823 3902 567678338 567678257 6.070000e-24 122.0
25 TraesCS6A01G318300 chr7D 97.222 72 1 1 4174 4244 597539403 597539474 2.180000e-23 121.0
26 TraesCS6A01G318300 chr7D 90.805 87 4 3 4174 4256 219832026 219832112 3.650000e-21 113.0
27 TraesCS6A01G318300 chr7D 95.652 46 2 0 3847 3892 80779811 80779766 1.720000e-09 75.0
28 TraesCS6A01G318300 chr2B 93.671 79 4 1 3825 3902 754008455 754008533 2.820000e-22 117.0
29 TraesCS6A01G318300 chr2B 92.593 81 5 1 3825 3904 139078987 139078907 1.020000e-21 115.0
30 TraesCS6A01G318300 chr2B 94.118 68 2 1 4174 4239 57174141 57174074 7.910000e-18 102.0
31 TraesCS6A01G318300 chr5A 92.958 71 3 1 4174 4242 11018437 11018507 7.910000e-18 102.0
32 TraesCS6A01G318300 chr5A 87.500 72 9 0 4101 4172 651446596 651446525 2.860000e-12 84.2
33 TraesCS6A01G318300 chr5D 84.416 77 7 4 3829 3901 369035638 369035563 2.230000e-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 TraesCS6A01G318300 chr6A 554458709 554463177 4468 False 8253.000000 8253 100.000000 1 4469 1 chr6A.!!$F1 4468
1 TraesCS6A01G318300 chr6B 613111026 613115556 4530 False 2370.666667 5986 94.947667 1 4469 3 chr6B.!!$F2 4468
2 TraesCS6A01G318300 chr6D 408650416 408654942 4526 False 2354.666667 5912 95.126000 1 4469 3 chr6D.!!$F1 4468

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
971 1103 0.458669 TCCCAAATCTAGTCGCCGAC 59.541 55.000 9.71 9.71 0.00 4.79 F
1080 1235 0.468214 TAGCTCTCGTCCCCATGGAG 60.468 60.000 15.22 0.00 42.85 3.86 F
2543 2698 1.141657 AGAGCTGCCAGTTCAGAAACA 59.858 47.619 11.30 0.00 37.88 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2523 2678 1.141657 TGTTTCTGAACTGGCAGCTCT 59.858 47.619 15.89 0.00 36.70 4.09 R
2718 2873 2.132996 CCCAGCAACAAGGGCAACA 61.133 57.895 0.00 0.00 38.44 3.33 R
4176 4368 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 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
60 61 1.903877 ATGCGGTGAGAACAGGGGAG 61.904 60.000 0.00 0.00 0.00 4.30
65 67 2.353803 CGGTGAGAACAGGGGAGTTTAG 60.354 54.545 0.00 0.00 0.00 1.85
114 116 3.859961 ACGTGAATATGAAGAACAGAGCG 59.140 43.478 0.00 0.00 0.00 5.03
138 141 2.829120 AGAAAGGAGACCTTCTTCCTCG 59.171 50.000 3.45 0.00 43.92 4.63
220 223 1.632422 CCTGTGCAATTTCGGAATGC 58.368 50.000 8.93 8.93 0.00 3.56
243 246 2.178984 ACCCTCATTTTTCACCTCCCAA 59.821 45.455 0.00 0.00 0.00 4.12
274 277 2.143925 GTTTTCAAGGGAGGTCAGTCG 58.856 52.381 0.00 0.00 0.00 4.18
280 283 2.060050 AGGGAGGTCAGTCGACATAG 57.940 55.000 19.50 7.34 44.54 2.23
282 285 1.394618 GGAGGTCAGTCGACATAGCT 58.605 55.000 19.50 18.74 44.54 3.32
474 482 2.432146 TGACAGGACTGCATAGTGATCC 59.568 50.000 0.00 0.00 37.25 3.36
545 655 1.964552 TTTAGAAAACGAACGGGGCA 58.035 45.000 0.00 0.00 0.00 5.36
661 772 3.064987 CTGGTCGCGGAGTAGGGTG 62.065 68.421 6.13 0.00 0.00 4.61
682 800 2.146061 CCCCTCCATCCCTGAGCTC 61.146 68.421 6.82 6.82 0.00 4.09
743 867 7.387948 GGTGAAGCTTCTATGTTCAGAGTTTTA 59.612 37.037 26.09 0.00 30.94 1.52
768 900 3.520290 TTTGAGACACGTGTTCAGAGT 57.480 42.857 24.26 3.52 0.00 3.24
844 976 6.099341 GCTTTCATCCATGTTTTACGGAAAT 58.901 36.000 0.00 0.00 31.18 2.17
845 977 7.254852 GCTTTCATCCATGTTTTACGGAAATA 58.745 34.615 0.00 0.00 31.18 1.40
846 978 7.220108 GCTTTCATCCATGTTTTACGGAAATAC 59.780 37.037 0.00 0.00 31.18 1.89
847 979 6.352682 TCATCCATGTTTTACGGAAATACG 57.647 37.500 0.00 0.00 40.31 3.06
848 980 6.107343 TCATCCATGTTTTACGGAAATACGA 58.893 36.000 0.00 0.00 37.61 3.43
849 981 6.256975 TCATCCATGTTTTACGGAAATACGAG 59.743 38.462 0.00 0.00 37.61 4.18
850 982 5.481105 TCCATGTTTTACGGAAATACGAGT 58.519 37.500 0.00 0.00 37.61 4.18
851 983 6.629128 TCCATGTTTTACGGAAATACGAGTA 58.371 36.000 0.00 0.00 37.61 2.59
852 984 6.753279 TCCATGTTTTACGGAAATACGAGTAG 59.247 38.462 0.00 0.00 37.61 2.57
853 985 6.532657 CCATGTTTTACGGAAATACGAGTAGT 59.467 38.462 0.00 0.00 37.61 2.73
871 1003 1.421646 AGTACATTCCATAGGGCCAGC 59.578 52.381 6.18 0.00 0.00 4.85
888 1020 2.038975 CCACCTCTTCCCTCCCGA 59.961 66.667 0.00 0.00 0.00 5.14
889 1021 2.060980 CCACCTCTTCCCTCCCGAG 61.061 68.421 0.00 0.00 0.00 4.63
912 1044 3.665675 GACTCTGCATTCGCCCCGT 62.666 63.158 0.00 0.00 37.32 5.28
971 1103 0.458669 TCCCAAATCTAGTCGCCGAC 59.541 55.000 9.71 9.71 0.00 4.79
987 1124 4.514577 ACCTCGCCGCATCCTTCG 62.515 66.667 0.00 0.00 0.00 3.79
1080 1235 0.468214 TAGCTCTCGTCCCCATGGAG 60.468 60.000 15.22 0.00 42.85 3.86
1098 1253 2.997315 CAGGACGAGGACCAGGCA 60.997 66.667 0.00 0.00 0.00 4.75
1494 1649 2.022129 CGCCGTCATCCCGCTTATC 61.022 63.158 0.00 0.00 0.00 1.75
2117 2272 2.148916 CGGCAGGTTATCGCAGATAA 57.851 50.000 6.83 6.83 45.12 1.75
2543 2698 1.141657 AGAGCTGCCAGTTCAGAAACA 59.858 47.619 11.30 0.00 37.88 2.83
2547 2702 2.358898 GCTGCCAGTTCAGAAACAAGAA 59.641 45.455 0.00 0.00 37.88 2.52
2718 2873 0.178921 TCTCAGGAGGTCCACTGCTT 60.179 55.000 8.36 0.00 46.85 3.91
2879 3034 1.153489 CTCGATGGGGCACTGACAG 60.153 63.158 0.00 0.00 0.00 3.51
2901 3056 9.288576 GACAGGTTTTCATATGGATCATATTCA 57.711 33.333 2.13 0.00 35.18 2.57
2973 3128 7.684529 AGAGTGTTGGTGATAGAATCTTCTTT 58.315 34.615 0.00 0.00 38.70 2.52
3122 3277 8.721478 TGAGAAAATAGTTGTCAGTTATGAAGC 58.279 33.333 0.00 0.00 37.14 3.86
3136 3291 8.677300 TCAGTTATGAAGCCAAAGATATTGTTC 58.323 33.333 0.00 0.00 30.61 3.18
3221 3376 3.118629 TCAGTTCTGCATGACCCATCTAC 60.119 47.826 0.00 0.00 0.00 2.59
3758 3944 7.094291 TGACATTTCTATGACATTGTGATGCAA 60.094 33.333 0.00 0.00 37.21 4.08
3760 3946 8.905850 ACATTTCTATGACATTGTGATGCAATA 58.094 29.630 0.00 0.00 39.18 1.90
3833 4020 7.234988 GTGGTTATATGGTATTCCCTCTGTACT 59.765 40.741 0.00 0.00 0.00 2.73
3924 4115 8.635877 AGTTGTTATGACTCTCGATATTGTTC 57.364 34.615 0.00 0.00 0.00 3.18
4000 4191 8.591114 ATTTCAGGATTCAGTCTCATTGATTT 57.409 30.769 0.00 0.00 0.00 2.17
4007 4198 8.680903 GGATTCAGTCTCATTGATTTATTGTGT 58.319 33.333 0.00 0.00 0.00 3.72
4031 4222 4.098914 TGTTGCTTATTCTGGAAGGTGT 57.901 40.909 0.00 0.00 0.00 4.16
4032 4223 3.820467 TGTTGCTTATTCTGGAAGGTGTG 59.180 43.478 0.00 0.00 0.00 3.82
4036 4227 4.892934 TGCTTATTCTGGAAGGTGTGTTTT 59.107 37.500 0.00 0.00 0.00 2.43
4165 4357 5.882000 CAGTGTGATATCCATTCTTTCACCA 59.118 40.000 0.00 0.00 36.68 4.17
4175 4367 6.177610 TCCATTCTTTCACCATACAACCTAC 58.822 40.000 0.00 0.00 0.00 3.18
4176 4368 6.012858 TCCATTCTTTCACCATACAACCTACT 60.013 38.462 0.00 0.00 0.00 2.57
4177 4369 6.316390 CCATTCTTTCACCATACAACCTACTC 59.684 42.308 0.00 0.00 0.00 2.59
4178 4370 5.416271 TCTTTCACCATACAACCTACTCC 57.584 43.478 0.00 0.00 0.00 3.85
4179 4371 4.224370 TCTTTCACCATACAACCTACTCCC 59.776 45.833 0.00 0.00 0.00 4.30
4180 4372 3.484953 TCACCATACAACCTACTCCCT 57.515 47.619 0.00 0.00 0.00 4.20
4181 4373 3.371965 TCACCATACAACCTACTCCCTC 58.628 50.000 0.00 0.00 0.00 4.30
4182 4374 2.434702 CACCATACAACCTACTCCCTCC 59.565 54.545 0.00 0.00 0.00 4.30
4183 4375 1.687123 CCATACAACCTACTCCCTCCG 59.313 57.143 0.00 0.00 0.00 4.63
4184 4376 2.385803 CATACAACCTACTCCCTCCGT 58.614 52.381 0.00 0.00 0.00 4.69
4185 4377 2.134789 TACAACCTACTCCCTCCGTC 57.865 55.000 0.00 0.00 0.00 4.79
4186 4378 0.614134 ACAACCTACTCCCTCCGTCC 60.614 60.000 0.00 0.00 0.00 4.79
4187 4379 1.379576 AACCTACTCCCTCCGTCCG 60.380 63.158 0.00 0.00 0.00 4.79
4188 4380 2.518825 CCTACTCCCTCCGTCCGG 60.519 72.222 0.00 0.00 0.00 5.14
4189 4381 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
4190 4382 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
4191 4383 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
4192 4384 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4193 4385 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4194 4386 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4195 4387 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4196 4388 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4197 4389 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4198 4390 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4199 4391 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4200 4392 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
4201 4393 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
4202 4394 2.428171 CCGTCCGGAAATACTTGTCCTA 59.572 50.000 5.23 0.00 37.50 2.94
4203 4395 3.490419 CCGTCCGGAAATACTTGTCCTAG 60.490 52.174 5.23 0.00 37.50 3.02
4204 4396 3.379372 CGTCCGGAAATACTTGTCCTAGA 59.621 47.826 5.23 0.00 0.00 2.43
4205 4397 4.142315 CGTCCGGAAATACTTGTCCTAGAA 60.142 45.833 5.23 0.00 0.00 2.10
4206 4398 5.622914 CGTCCGGAAATACTTGTCCTAGAAA 60.623 44.000 5.23 0.00 0.00 2.52
4207 4399 6.346896 GTCCGGAAATACTTGTCCTAGAAAT 58.653 40.000 5.23 0.00 0.00 2.17
4208 4400 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
4209 4401 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
4210 4402 6.113411 CGGAAATACTTGTCCTAGAAATGGT 58.887 40.000 0.00 0.00 0.00 3.55
4211 4403 6.598064 CGGAAATACTTGTCCTAGAAATGGTT 59.402 38.462 0.00 0.00 0.00 3.67
4212 4404 7.767198 CGGAAATACTTGTCCTAGAAATGGTTA 59.233 37.037 0.00 0.00 0.00 2.85
4213 4405 9.110502 GGAAATACTTGTCCTAGAAATGGTTAG 57.889 37.037 0.00 0.00 0.00 2.34
4214 4406 9.110502 GAAATACTTGTCCTAGAAATGGTTAGG 57.889 37.037 0.00 0.00 38.22 2.69
4215 4407 7.989947 ATACTTGTCCTAGAAATGGTTAGGA 57.010 36.000 0.00 0.00 42.36 2.94
4222 4414 7.989947 TCCTAGAAATGGTTAGGACAAGTAT 57.010 36.000 0.00 0.00 40.32 2.12
4223 4415 8.388656 TCCTAGAAATGGTTAGGACAAGTATT 57.611 34.615 0.00 0.00 40.32 1.89
4224 4416 8.832735 TCCTAGAAATGGTTAGGACAAGTATTT 58.167 33.333 0.00 0.00 40.32 1.40
4225 4417 9.110502 CCTAGAAATGGTTAGGACAAGTATTTC 57.889 37.037 0.00 0.00 39.02 2.17
4226 4418 7.939784 AGAAATGGTTAGGACAAGTATTTCC 57.060 36.000 0.00 0.00 35.01 3.13
4227 4419 6.598064 AGAAATGGTTAGGACAAGTATTTCCG 59.402 38.462 0.00 0.00 36.95 4.30
4228 4420 4.210724 TGGTTAGGACAAGTATTTCCGG 57.789 45.455 0.00 0.00 36.95 5.14
4229 4421 3.839490 TGGTTAGGACAAGTATTTCCGGA 59.161 43.478 0.00 0.00 36.95 5.14
4230 4422 4.186926 GGTTAGGACAAGTATTTCCGGAC 58.813 47.826 1.83 0.00 36.95 4.79
4231 4423 2.667473 AGGACAAGTATTTCCGGACG 57.333 50.000 1.83 0.00 36.95 4.79
4232 4424 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
4233 4425 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
4234 4426 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
4235 4427 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4236 4428 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4237 4429 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4238 4430 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4239 4431 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
4240 4432 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4256 4448 7.417570 CGGAGGGAGTATTAGTTTGACTATGTT 60.418 40.741 0.00 0.00 29.64 2.71
4267 4459 9.891828 TTAGTTTGACTATGTTTGCAGTAAATG 57.108 29.630 0.00 0.00 29.64 2.32
4328 4520 6.462909 CCAAGAAGCAGGTAACCAATCTTTTT 60.463 38.462 0.00 0.00 37.17 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 8.734030 CGTTGTTCAGAATTCAGTTTTCTAAAC 58.266 33.333 8.44 0.00 33.65 2.01
65 67 6.629252 GTCTCGTTGTTCAGAATTCAGTTTTC 59.371 38.462 8.44 0.00 0.00 2.29
114 116 5.235850 AGGAAGAAGGTCTCCTTTCTTTC 57.764 43.478 2.48 6.68 44.82 2.62
138 141 1.952635 GCTTGTTGCTGCTGTTGCC 60.953 57.895 0.00 0.00 38.71 4.52
214 217 2.566724 TGAAAAATGAGGGTGGCATTCC 59.433 45.455 0.00 0.00 35.06 3.01
220 223 2.171003 GGAGGTGAAAAATGAGGGTGG 58.829 52.381 0.00 0.00 0.00 4.61
243 246 1.402787 CTTGAAAACAGGTGGCTGGT 58.597 50.000 0.00 0.00 0.00 4.00
274 277 7.617041 AAACTTGATTAAGACCAGCTATGTC 57.383 36.000 3.94 7.34 37.36 3.06
303 307 8.478066 TCTTCTCATGCTTTGCTATAGTAAAGA 58.522 33.333 34.18 23.32 46.24 2.52
304 308 8.654230 TCTTCTCATGCTTTGCTATAGTAAAG 57.346 34.615 28.91 28.91 46.13 1.85
449 457 4.318332 TCACTATGCAGTCCTGTCAAAAG 58.682 43.478 0.00 1.27 30.46 2.27
454 462 2.544694 CGGATCACTATGCAGTCCTGTC 60.545 54.545 0.00 0.00 30.46 3.51
474 482 1.004560 TTCTGAGCTTGAGGCCACG 60.005 57.895 5.01 0.00 43.05 4.94
502 510 1.153989 CTCGATCTAGGCCTCCCCA 59.846 63.158 9.68 0.00 35.39 4.96
828 960 5.789710 ACTCGTATTTCCGTAAAACATGG 57.210 39.130 0.00 0.00 34.18 3.66
844 976 4.763793 GCCCTATGGAATGTACTACTCGTA 59.236 45.833 0.00 0.00 0.00 3.43
845 977 3.573110 GCCCTATGGAATGTACTACTCGT 59.427 47.826 0.00 0.00 0.00 4.18
846 978 3.056749 GGCCCTATGGAATGTACTACTCG 60.057 52.174 0.00 0.00 0.00 4.18
847 979 3.901844 TGGCCCTATGGAATGTACTACTC 59.098 47.826 0.00 0.00 0.00 2.59
848 980 3.904339 CTGGCCCTATGGAATGTACTACT 59.096 47.826 0.00 0.00 0.00 2.57
849 981 3.557264 GCTGGCCCTATGGAATGTACTAC 60.557 52.174 0.00 0.00 0.00 2.73
850 982 2.637872 GCTGGCCCTATGGAATGTACTA 59.362 50.000 0.00 0.00 0.00 1.82
851 983 1.421646 GCTGGCCCTATGGAATGTACT 59.578 52.381 0.00 0.00 0.00 2.73
852 984 1.545651 GGCTGGCCCTATGGAATGTAC 60.546 57.143 0.00 0.00 0.00 2.90
853 985 0.771127 GGCTGGCCCTATGGAATGTA 59.229 55.000 0.00 0.00 0.00 2.29
871 1003 2.038975 TCGGGAGGGAAGAGGTGG 59.961 66.667 0.00 0.00 0.00 4.61
888 1020 1.513158 CGAATGCAGAGTCGGGACT 59.487 57.895 0.00 0.00 45.84 3.85
889 1021 2.167861 GCGAATGCAGAGTCGGGAC 61.168 63.158 16.18 0.00 40.03 4.46
900 1032 1.702491 GAACTGTACGGGGCGAATGC 61.702 60.000 6.65 0.00 41.71 3.56
902 1034 0.108329 CAGAACTGTACGGGGCGAAT 60.108 55.000 6.65 0.00 0.00 3.34
912 1044 2.340731 TGGTTTAGGGCCAGAACTGTA 58.659 47.619 17.80 6.21 0.00 2.74
987 1124 3.406595 CTCCATTGGGGTCTCCGGC 62.407 68.421 2.09 0.00 38.76 6.13
1080 1235 4.459089 GCCTGGTCCTCGTCCTGC 62.459 72.222 0.00 0.00 0.00 4.85
2523 2678 1.141657 TGTTTCTGAACTGGCAGCTCT 59.858 47.619 15.89 0.00 36.70 4.09
2543 2698 3.011032 ACCCAATCTCTGAATGGCTTCTT 59.989 43.478 0.00 0.00 31.70 2.52
2547 2702 3.463048 AAACCCAATCTCTGAATGGCT 57.537 42.857 0.00 0.00 31.70 4.75
2718 2873 2.132996 CCCAGCAACAAGGGCAACA 61.133 57.895 0.00 0.00 38.44 3.33
2879 3034 9.850628 CATGTGAATATGATCCATATGAAAACC 57.149 33.333 3.65 0.00 37.17 3.27
2901 3056 2.357154 GGAAGACCCAATAGCCACATGT 60.357 50.000 0.00 0.00 34.14 3.21
3122 3277 8.298854 TGTTGTCATCTTGAACAATATCTTTGG 58.701 33.333 0.00 0.00 0.00 3.28
3136 3291 7.317390 TCATCCAAATCAATGTTGTCATCTTG 58.683 34.615 0.00 0.00 32.56 3.02
3798 3985 7.289084 GGAATACCATATAACCACACCCAAATT 59.711 37.037 0.00 0.00 35.97 1.82
3924 4115 3.694072 TGGCAACTTGGAGAAATATTCCG 59.306 43.478 0.00 0.00 35.77 4.30
4000 4191 6.488344 TCCAGAATAAGCAACAACACACAATA 59.512 34.615 0.00 0.00 0.00 1.90
4007 4198 4.278170 CACCTTCCAGAATAAGCAACAACA 59.722 41.667 0.00 0.00 0.00 3.33
4031 4222 6.047870 ACATGCTTTGCAGTTCATAAAAACA 58.952 32.000 0.00 0.00 43.65 2.83
4032 4223 6.529463 ACATGCTTTGCAGTTCATAAAAAC 57.471 33.333 0.00 0.00 43.65 2.43
4036 4227 6.016360 ACACTAACATGCTTTGCAGTTCATAA 60.016 34.615 0.00 0.00 43.65 1.90
4165 4357 2.664015 GACGGAGGGAGTAGGTTGTAT 58.336 52.381 0.00 0.00 0.00 2.29
4175 4367 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4176 4368 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4177 4369 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4178 4370 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4179 4371 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
4180 4372 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
4181 4373 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
4182 4374 2.667473 AGGACAAGTATTTCCGGACG 57.333 50.000 1.83 0.00 36.95 4.79
4183 4375 4.996788 TCTAGGACAAGTATTTCCGGAC 57.003 45.455 1.83 0.00 36.95 4.79
4184 4376 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
4185 4377 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
4186 4378 6.113411 ACCATTTCTAGGACAAGTATTTCCG 58.887 40.000 0.00 0.00 36.95 4.30
4187 4379 7.939784 AACCATTTCTAGGACAAGTATTTCC 57.060 36.000 0.00 0.00 0.00 3.13
4188 4380 9.110502 CCTAACCATTTCTAGGACAAGTATTTC 57.889 37.037 0.00 0.00 37.47 2.17
4189 4381 8.832735 TCCTAACCATTTCTAGGACAAGTATTT 58.167 33.333 0.00 0.00 39.02 1.40
4190 4382 8.388656 TCCTAACCATTTCTAGGACAAGTATT 57.611 34.615 0.00 0.00 39.02 1.89
4191 4383 7.989947 TCCTAACCATTTCTAGGACAAGTAT 57.010 36.000 0.00 0.00 39.02 2.12
4198 4390 7.989947 ATACTTGTCCTAACCATTTCTAGGA 57.010 36.000 0.00 0.00 41.16 2.94
4199 4391 9.110502 GAAATACTTGTCCTAACCATTTCTAGG 57.889 37.037 0.00 0.00 36.74 3.02
4200 4392 9.110502 GGAAATACTTGTCCTAACCATTTCTAG 57.889 37.037 0.00 0.00 33.51 2.43
4201 4393 7.767198 CGGAAATACTTGTCCTAACCATTTCTA 59.233 37.037 0.00 0.00 33.51 2.10
4202 4394 6.598064 CGGAAATACTTGTCCTAACCATTTCT 59.402 38.462 0.00 0.00 33.51 2.52
4203 4395 6.183360 CCGGAAATACTTGTCCTAACCATTTC 60.183 42.308 0.00 0.00 32.66 2.17
4204 4396 5.650703 CCGGAAATACTTGTCCTAACCATTT 59.349 40.000 0.00 0.00 0.00 2.32
4205 4397 5.045432 TCCGGAAATACTTGTCCTAACCATT 60.045 40.000 0.00 0.00 0.00 3.16
4206 4398 4.472108 TCCGGAAATACTTGTCCTAACCAT 59.528 41.667 0.00 0.00 0.00 3.55
4207 4399 3.839490 TCCGGAAATACTTGTCCTAACCA 59.161 43.478 0.00 0.00 0.00 3.67
4208 4400 4.186926 GTCCGGAAATACTTGTCCTAACC 58.813 47.826 5.23 0.00 0.00 2.85
4209 4401 3.861689 CGTCCGGAAATACTTGTCCTAAC 59.138 47.826 5.23 0.00 0.00 2.34
4210 4402 3.119029 CCGTCCGGAAATACTTGTCCTAA 60.119 47.826 5.23 0.00 37.50 2.69
4211 4403 2.428171 CCGTCCGGAAATACTTGTCCTA 59.572 50.000 5.23 0.00 37.50 2.94
4212 4404 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
4213 4405 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
4214 4406 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4215 4407 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4216 4408 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4217 4409 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4218 4410 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4219 4411 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4220 4412 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4221 4413 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4222 4414 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
4223 4415 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
4224 4416 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
4225 4417 1.245732 CTAATACTCCCTCCGTCCGG 58.754 60.000 0.00 0.00 0.00 5.14
4226 4418 1.978454 ACTAATACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
4227 4419 3.703052 TCAAACTAATACTCCCTCCGTCC 59.297 47.826 0.00 0.00 0.00 4.79
4228 4420 4.401837 AGTCAAACTAATACTCCCTCCGTC 59.598 45.833 0.00 0.00 0.00 4.79
4229 4421 4.351127 AGTCAAACTAATACTCCCTCCGT 58.649 43.478 0.00 0.00 0.00 4.69
4230 4422 6.040616 ACATAGTCAAACTAATACTCCCTCCG 59.959 42.308 0.00 0.00 33.89 4.63
4231 4423 7.362802 ACATAGTCAAACTAATACTCCCTCC 57.637 40.000 0.00 0.00 33.89 4.30
4232 4424 9.099454 CAAACATAGTCAAACTAATACTCCCTC 57.901 37.037 0.00 0.00 33.89 4.30
4233 4425 7.553044 GCAAACATAGTCAAACTAATACTCCCT 59.447 37.037 0.00 0.00 33.89 4.20
4234 4426 7.335924 TGCAAACATAGTCAAACTAATACTCCC 59.664 37.037 0.00 0.00 33.89 4.30
4235 4427 8.263940 TGCAAACATAGTCAAACTAATACTCC 57.736 34.615 0.00 0.00 33.89 3.85
4236 4428 8.936864 ACTGCAAACATAGTCAAACTAATACTC 58.063 33.333 0.00 0.00 33.89 2.59
4237 4429 8.848474 ACTGCAAACATAGTCAAACTAATACT 57.152 30.769 0.00 0.00 33.89 2.12
4256 4448 8.954950 TTTCCTTCAAAAATCATTTACTGCAA 57.045 26.923 0.00 0.00 0.00 4.08
4267 4459 6.073058 GGTTTCCAGCATTTCCTTCAAAAATC 60.073 38.462 0.00 0.00 0.00 2.17
4422 4618 8.561738 TTTAGGGAGCTCAGTAAATTTAAGTG 57.438 34.615 17.19 1.26 0.00 3.16


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

AutoCloner maintained by Alex Coulton.