Multiple sequence alignment - TraesCS3B01G154400

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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 TraesCS3B01G154400 chr3B 100.000 4367 0 0 1 4367 146983366 146979000 0.000000e+00 8065.0
1 TraesCS3B01G154400 chr3B 92.434 2987 178 18 837 3812 172981886 172978937 0.000000e+00 4220.0
2 TraesCS3B01G154400 chr3B 91.799 2829 193 22 804 3620 172052044 172054845 0.000000e+00 3903.0
3 TraesCS3B01G154400 chr3B 91.968 2764 184 21 869 3620 172170467 172173204 0.000000e+00 3840.0
4 TraesCS3B01G154400 chr3B 87.267 322 31 5 117 428 172091579 172091900 4.150000e-95 359.0
5 TraesCS3B01G154400 chr3B 87.267 322 30 5 117 428 172211093 172211413 1.490000e-94 357.0
6 TraesCS3B01G154400 chr3B 85.154 357 36 11 3951 4299 172978870 172978523 2.500000e-92 350.0
7 TraesCS3B01G154400 chr3B 93.103 174 11 1 1 173 173000330 173000157 2.020000e-63 254.0
8 TraesCS3B01G154400 chr3B 87.736 106 8 3 3683 3784 172978968 172978864 7.670000e-23 119.0
9 TraesCS3B01G154400 chr3B 76.736 288 19 15 500 784 172092050 172092292 2.760000e-22 117.0
10 TraesCS3B01G154400 chr3B 87.379 103 5 3 683 784 172211655 172211750 1.280000e-20 111.0
11 TraesCS3B01G154400 chr3B 100.000 28 0 0 632 659 172211621 172211648 8.000000e-03 52.8
12 TraesCS3B01G154400 chr3D 92.206 2938 189 17 508 3432 121269200 121266290 0.000000e+00 4120.0
13 TraesCS3B01G154400 chr3D 92.332 2856 184 10 617 3455 121335050 121332213 0.000000e+00 4028.0
14 TraesCS3B01G154400 chr3D 85.142 774 67 21 3136 3890 121185628 121184884 0.000000e+00 749.0
15 TraesCS3B01G154400 chr3D 91.529 425 29 6 3877 4299 121261872 121261453 2.930000e-161 579.0
16 TraesCS3B01G154400 chr3D 91.076 437 22 8 3466 3890 121262345 121261914 3.790000e-160 575.0
17 TraesCS3B01G154400 chr3D 90.090 444 26 7 3 428 121269790 121269347 1.060000e-155 560.0
18 TraesCS3B01G154400 chr3D 88.050 318 30 4 8 318 116075218 116074902 1.920000e-98 370.0
19 TraesCS3B01G154400 chr3A 92.823 2689 157 16 1225 3890 127822363 127819688 0.000000e+00 3864.0
20 TraesCS3B01G154400 chr3A 88.710 558 27 20 687 1227 127834905 127834367 0.000000e+00 649.0
21 TraesCS3B01G154400 chr3A 90.281 463 33 11 3912 4367 127819621 127819164 2.910000e-166 595.0
22 TraesCS3B01G154400 chr3A 92.032 251 20 0 1 251 127835215 127834965 1.930000e-93 353.0
23 TraesCS3B01G154400 chr1B 92.860 2689 149 19 837 3508 456714318 456711656 0.000000e+00 3862.0
24 TraesCS3B01G154400 chr1B 93.094 2534 159 9 909 3430 642701479 642698950 0.000000e+00 3696.0
25 TraesCS3B01G154400 chr6D 92.302 2650 173 20 804 3432 452128110 452125471 0.000000e+00 3735.0
26 TraesCS3B01G154400 chr1A 84.842 442 43 12 1 428 440781384 440780953 1.450000e-114 424.0
27 TraesCS3B01G154400 chr1A 78.694 291 39 16 508 784 440780899 440780618 5.810000e-39 172.0
28 TraesCS3B01G154400 chr1D 88.060 268 25 5 1 262 341030730 341030464 1.180000e-80 311.0
29 TraesCS3B01G154400 chr1D 78.966 290 36 18 508 784 341030308 341030031 1.610000e-39 174.0


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 TraesCS3B01G154400 chr3B 146979000 146983366 4366 True 8065.0 8065 100.000000 1 4367 1 chr3B.!!$R1 4366
1 TraesCS3B01G154400 chr3B 172052044 172054845 2801 False 3903.0 3903 91.799000 804 3620 1 chr3B.!!$F1 2816
2 TraesCS3B01G154400 chr3B 172170467 172173204 2737 False 3840.0 3840 91.968000 869 3620 1 chr3B.!!$F2 2751
3 TraesCS3B01G154400 chr3B 172978523 172981886 3363 True 1563.0 4220 88.441333 837 4299 3 chr3B.!!$R3 3462
4 TraesCS3B01G154400 chr3B 172091579 172092292 713 False 238.0 359 82.001500 117 784 2 chr3B.!!$F3 667
5 TraesCS3B01G154400 chr3D 121332213 121335050 2837 True 4028.0 4028 92.332000 617 3455 1 chr3D.!!$R3 2838
6 TraesCS3B01G154400 chr3D 121261453 121269790 8337 True 1458.5 4120 91.225250 3 4299 4 chr3D.!!$R4 4296
7 TraesCS3B01G154400 chr3D 121184884 121185628 744 True 749.0 749 85.142000 3136 3890 1 chr3D.!!$R2 754
8 TraesCS3B01G154400 chr3A 127819164 127822363 3199 True 2229.5 3864 91.552000 1225 4367 2 chr3A.!!$R1 3142
9 TraesCS3B01G154400 chr3A 127834367 127835215 848 True 501.0 649 90.371000 1 1227 2 chr3A.!!$R2 1226
10 TraesCS3B01G154400 chr1B 456711656 456714318 2662 True 3862.0 3862 92.860000 837 3508 1 chr1B.!!$R1 2671
11 TraesCS3B01G154400 chr1B 642698950 642701479 2529 True 3696.0 3696 93.094000 909 3430 1 chr1B.!!$R2 2521
12 TraesCS3B01G154400 chr6D 452125471 452128110 2639 True 3735.0 3735 92.302000 804 3432 1 chr6D.!!$R1 2628
13 TraesCS3B01G154400 chr1A 440780618 440781384 766 True 298.0 424 81.768000 1 784 2 chr1A.!!$R1 783
14 TraesCS3B01G154400 chr1D 341030031 341030730 699 True 242.5 311 83.513000 1 784 2 chr1D.!!$R1 783

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
746 890 0.038618 TGCAGCTACACCTACACGTG 60.039 55.0 15.48 15.48 39.75 4.49 F
1233 1420 0.463833 GGATCAACAAGGTAGCCCGG 60.464 60.0 0.00 0.00 35.12 5.73 F
2442 2629 0.252193 AGAGGGAGCTGCAAGAGACT 60.252 55.0 7.79 0.00 34.07 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2122 0.395724 TCAGCAGCTGGGAGACGATA 60.396 55.0 22.62 0.0 31.51 2.92 R
2922 3109 0.036010 CCTTGAAGATCTGGTGCCGT 60.036 55.0 0.00 0.0 0.00 5.68 R
4074 8285 1.269012 AATTCCAACCCACCATGCTG 58.731 50.0 0.00 0.0 0.00 4.41 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
51 60 5.492895 TGAACCGCCAAATACTAAGAATGA 58.507 37.500 0.00 0.00 0.00 2.57
72 81 5.503002 TGACACTCACAAATGATGATCCAT 58.497 37.500 0.00 0.00 33.22 3.41
130 139 8.819974 ACATCAAAGCAACAAACTAATTTCTTG 58.180 29.630 0.00 0.00 29.58 3.02
136 146 8.947055 AGCAACAAACTAATTTCTTGAATGTT 57.053 26.923 0.00 0.00 28.13 2.71
192 204 4.537135 TCCAGTATGACACACTCCTTTC 57.463 45.455 0.00 0.00 39.69 2.62
241 257 2.987413 ACTGCGCGAAATGAAATTGA 57.013 40.000 12.10 0.00 36.10 2.57
334 350 3.801997 CCTCGGCCAGGCTCCATT 61.802 66.667 12.43 0.00 34.56 3.16
335 351 2.443394 CCTCGGCCAGGCTCCATTA 61.443 63.158 12.43 0.00 34.56 1.90
337 353 0.976641 CTCGGCCAGGCTCCATTATA 59.023 55.000 12.43 0.00 0.00 0.98
338 354 1.347707 CTCGGCCAGGCTCCATTATAA 59.652 52.381 12.43 0.00 0.00 0.98
342 358 1.873591 GCCAGGCTCCATTATAACACG 59.126 52.381 3.29 0.00 0.00 4.49
343 359 1.873591 CCAGGCTCCATTATAACACGC 59.126 52.381 0.00 0.00 0.00 5.34
344 360 2.560504 CAGGCTCCATTATAACACGCA 58.439 47.619 0.00 0.00 0.00 5.24
345 361 2.942376 CAGGCTCCATTATAACACGCAA 59.058 45.455 0.00 0.00 0.00 4.85
393 419 5.782893 AAAATGAAAACTGACGGATTGGA 57.217 34.783 0.00 0.00 0.00 3.53
428 454 5.012239 AGGACATGAGCACACATAATGTTT 58.988 37.500 0.00 0.00 40.64 2.83
429 455 5.477984 AGGACATGAGCACACATAATGTTTT 59.522 36.000 0.00 0.00 40.64 2.43
431 457 6.349611 GGACATGAGCACACATAATGTTTTCT 60.350 38.462 0.00 0.00 40.64 2.52
432 458 6.985117 ACATGAGCACACATAATGTTTTCTT 58.015 32.000 0.00 0.00 40.64 2.52
433 459 7.436118 ACATGAGCACACATAATGTTTTCTTT 58.564 30.769 0.00 0.00 40.64 2.52
434 460 7.927629 ACATGAGCACACATAATGTTTTCTTTT 59.072 29.630 0.00 0.00 40.64 2.27
435 461 8.767085 CATGAGCACACATAATGTTTTCTTTTT 58.233 29.630 0.00 0.00 40.64 1.94
436 462 8.351495 TGAGCACACATAATGTTTTCTTTTTC 57.649 30.769 0.00 0.00 40.64 2.29
439 515 8.196771 AGCACACATAATGTTTTCTTTTTCAGA 58.803 29.630 0.00 0.00 40.64 3.27
466 546 1.888018 GCCTCCGTACACTGCAGTA 59.112 57.895 21.20 1.09 0.00 2.74
473 553 0.736325 GTACACTGCAGTAGCCACCG 60.736 60.000 21.20 7.85 41.13 4.94
476 556 1.908793 ACTGCAGTAGCCACCGTCT 60.909 57.895 20.16 0.00 41.13 4.18
477 557 1.153745 CTGCAGTAGCCACCGTCTC 60.154 63.158 5.25 0.00 41.13 3.36
498 578 1.069358 GGACCGAGGTGGAGATGAATC 59.931 57.143 0.00 0.00 42.00 2.52
503 583 1.342819 GAGGTGGAGATGAATCGAGGG 59.657 57.143 0.00 0.00 0.00 4.30
504 584 1.062886 AGGTGGAGATGAATCGAGGGA 60.063 52.381 0.00 0.00 0.00 4.20
505 585 1.342819 GGTGGAGATGAATCGAGGGAG 59.657 57.143 0.00 0.00 0.00 4.30
506 586 2.311463 GTGGAGATGAATCGAGGGAGA 58.689 52.381 0.00 0.00 0.00 3.71
520 621 3.031013 GAGGGAGAAGAGGGAGAAGAAG 58.969 54.545 0.00 0.00 0.00 2.85
526 627 3.769300 AGAAGAGGGAGAAGAAGAGAAGC 59.231 47.826 0.00 0.00 0.00 3.86
539 647 4.443266 GAAGCAGCTCCGGTCGCT 62.443 66.667 13.89 13.89 38.49 4.93
609 717 1.984570 CTCTTCCGACCTCCTGCCA 60.985 63.158 0.00 0.00 0.00 4.92
668 807 1.138036 CACCGCTGTTCATGCATGG 59.862 57.895 25.97 10.98 0.00 3.66
669 808 1.002257 ACCGCTGTTCATGCATGGA 60.002 52.632 25.97 16.13 0.00 3.41
670 809 1.308069 ACCGCTGTTCATGCATGGAC 61.308 55.000 28.29 28.29 36.81 4.02
671 810 1.028330 CCGCTGTTCATGCATGGACT 61.028 55.000 32.85 0.00 37.20 3.85
672 811 0.098200 CGCTGTTCATGCATGGACTG 59.902 55.000 32.85 31.76 37.20 3.51
673 812 1.456296 GCTGTTCATGCATGGACTGA 58.544 50.000 36.16 20.00 37.40 3.41
674 813 2.022195 GCTGTTCATGCATGGACTGAT 58.978 47.619 36.16 0.00 37.40 2.90
675 814 2.223502 GCTGTTCATGCATGGACTGATG 60.224 50.000 36.16 24.13 37.40 3.07
738 882 1.729149 GCGTTGATTTGCAGCTACACC 60.729 52.381 0.00 0.00 0.00 4.16
740 884 3.000041 CGTTGATTTGCAGCTACACCTA 59.000 45.455 0.00 0.00 0.00 3.08
741 885 3.181520 CGTTGATTTGCAGCTACACCTAC 60.182 47.826 0.00 0.00 0.00 3.18
742 886 3.694043 TGATTTGCAGCTACACCTACA 57.306 42.857 0.00 0.00 0.00 2.74
743 887 3.334691 TGATTTGCAGCTACACCTACAC 58.665 45.455 0.00 0.00 0.00 2.90
744 888 1.790755 TTTGCAGCTACACCTACACG 58.209 50.000 0.00 0.00 0.00 4.49
745 889 0.677288 TTGCAGCTACACCTACACGT 59.323 50.000 0.00 0.00 0.00 4.49
746 890 0.038618 TGCAGCTACACCTACACGTG 60.039 55.000 15.48 15.48 39.75 4.49
834 981 3.767230 CGTGTGAAGTGCGCGAGG 61.767 66.667 12.10 0.00 41.71 4.63
866 1013 1.732259 CCAACCGGAGTCGAATTCTTG 59.268 52.381 9.46 0.00 39.00 3.02
969 1144 5.496127 ACGAGAGTAATACACGAGAGACGG 61.496 50.000 10.32 0.00 46.88 4.79
983 1162 0.753479 AGACGGAGCAGGTCGATCAT 60.753 55.000 0.00 0.00 39.38 2.45
1203 1390 3.371063 GACGACACCTGCGAGGGA 61.371 66.667 7.06 0.00 40.58 4.20
1210 1397 1.837051 ACCTGCGAGGGACACAAGA 60.837 57.895 7.06 0.00 40.58 3.02
1233 1420 0.463833 GGATCAACAAGGTAGCCCGG 60.464 60.000 0.00 0.00 35.12 5.73
1242 1429 1.686800 GGTAGCCCGGTCCAACCTA 60.687 63.158 0.00 0.00 35.66 3.08
1245 1432 2.786512 TAGCCCGGTCCAACCTACGT 62.787 60.000 0.00 0.00 35.66 3.57
1277 1464 4.934942 CGTCGTGTCGGTGCACCA 62.935 66.667 34.16 19.11 36.08 4.17
1392 1579 2.967397 CCCTACTTCGTGGACGCA 59.033 61.111 0.00 0.00 39.60 5.24
1503 1690 3.567478 CTACTGTGTCGTGGCGCCA 62.567 63.158 29.03 29.03 0.00 5.69
1594 1781 3.583276 GACGACGTGGGTGGCATGA 62.583 63.158 4.58 0.00 0.00 3.07
1707 1894 2.604152 CTCCTCTACGGCCCTCCT 59.396 66.667 0.00 0.00 0.00 3.69
1884 2071 6.294955 CCTCCATCATCTTCATTGACGAGATA 60.295 42.308 1.46 0.00 30.07 1.98
1899 2086 2.029470 CGAGATAGACTCCATTGCTCCC 60.029 54.545 0.00 0.00 42.18 4.30
2007 2194 2.755469 ATTGTCATGGGCGCCACC 60.755 61.111 30.85 12.89 35.80 4.61
2367 2554 2.279584 TCCGCGCTTCGTGAAACA 60.280 55.556 5.56 0.00 39.94 2.83
2373 2560 0.575390 CGCTTCGTGAAACAGTCGTT 59.425 50.000 0.00 0.00 35.74 3.85
2442 2629 0.252193 AGAGGGAGCTGCAAGAGACT 60.252 55.000 7.79 0.00 34.07 3.24
2703 2890 1.136502 GTGCTTTTCTTCGACGAGCTG 60.137 52.381 0.00 0.00 34.56 4.24
2736 2923 2.668632 CAAAGGGGCGGCAGAGTA 59.331 61.111 12.47 0.00 0.00 2.59
3092 3279 4.766891 GGACATTGAAAAGGACATGGAGAA 59.233 41.667 0.00 0.00 0.00 2.87
3168 3361 0.034059 CGGAGATTAAGGCGGCTCAT 59.966 55.000 13.70 7.75 0.00 2.90
3455 3666 4.265556 CGTCGATCACTTCTTTCCATGTAC 59.734 45.833 0.00 0.00 0.00 2.90
3456 3667 5.411781 GTCGATCACTTCTTTCCATGTACT 58.588 41.667 0.00 0.00 0.00 2.73
3457 3668 5.517054 GTCGATCACTTCTTTCCATGTACTC 59.483 44.000 0.00 0.00 0.00 2.59
3458 3669 4.806247 CGATCACTTCTTTCCATGTACTCC 59.194 45.833 0.00 0.00 0.00 3.85
3535 7659 9.814899 AGTTGATGATATAAGAAGTTCTCTGTG 57.185 33.333 5.70 0.00 33.37 3.66
3620 7744 0.095245 CGTGGATTGCACGCAACTAG 59.905 55.000 17.65 0.00 38.88 2.57
3719 7849 7.385205 TGAGCTGTAAGAACATGAGTTTCTTAC 59.615 37.037 25.87 25.87 41.83 2.34
3739 7869 7.889469 TCTTACTATTGAACCTGTAAGAACGT 58.111 34.615 10.71 0.00 44.14 3.99
3813 7943 2.173782 TGTGGCTCCCAACAGACTTTTA 59.826 45.455 0.00 0.00 34.18 1.52
3854 7995 2.691011 GTTGTTCTGCACCACCCTTTTA 59.309 45.455 0.00 0.00 0.00 1.52
3939 8146 2.333417 GCGAGGTCTCTGTGGACGA 61.333 63.158 0.00 0.00 37.12 4.20
3942 8149 0.179124 GAGGTCTCTGTGGACGATGC 60.179 60.000 0.00 0.00 37.12 3.91
3985 8192 2.492090 GTGATGCTCGGCTCGTCT 59.508 61.111 0.00 0.00 0.00 4.18
3992 8199 3.997064 CTCGGCTCGTCTGGCTTGG 62.997 68.421 0.00 0.00 0.00 3.61
4026 8234 1.879380 CAAATGGTCACAGAGGCGAAA 59.121 47.619 0.00 0.00 0.00 3.46
4067 8278 6.538945 TCCTACTTTGGGGCAATTAATTTC 57.461 37.500 0.00 0.00 0.00 2.17
4074 8285 7.228507 ACTTTGGGGCAATTAATTTCTGAAAAC 59.771 33.333 6.95 0.00 0.00 2.43
4106 8317 4.381185 GGGTTGGAATTTAAGGCTTAACCG 60.381 45.833 18.87 0.00 46.52 4.44
4130 8341 7.273381 CCGTTATCAGTTTCATGAAAATGGAAC 59.727 37.037 35.19 32.91 43.91 3.62
4165 8377 6.640092 GTGCTCCTTTTCTCTGAAAAATCTTG 59.360 38.462 6.87 0.00 0.00 3.02
4170 8382 6.015603 CCTTTTCTCTGAAAAATCTTGAGGCT 60.016 38.462 6.87 0.00 0.00 4.58
4177 8389 8.918202 TCTGAAAAATCTTGAGGCTTTAACTA 57.082 30.769 0.00 0.00 0.00 2.24
4198 8410 7.404671 ACTACTTGTCCAAACAAAGTTTGAT 57.595 32.000 22.23 7.64 44.53 2.57
4215 8428 6.453092 AGTTTGATTTTCATGCTCTTCCTTG 58.547 36.000 0.00 0.00 0.00 3.61
4221 8434 2.771089 TCATGCTCTTCCTTGTGTCAC 58.229 47.619 0.00 0.00 0.00 3.67
4254 8471 7.518370 GCTTTAAAGATTCAGTCACGAGTTTCA 60.518 37.037 19.48 0.00 0.00 2.69
4346 8566 6.109156 TCGGCCTTTGCATTATAGATAGAA 57.891 37.500 0.00 0.00 40.13 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 60 4.885907 GGATGGATCATCATTTGTGAGTGT 59.114 41.667 9.68 0.00 42.13 3.55
72 81 4.071423 TCGTCAATGCTGATTTTTCAGGA 58.929 39.130 5.24 2.55 42.08 3.86
154 164 5.543507 ACTGGATAATGCTCCAAGACTAG 57.456 43.478 0.00 0.00 44.59 2.57
213 229 2.826979 TTTCGCGCAGTTTGTGTTTA 57.173 40.000 8.75 0.00 0.00 2.01
241 257 5.527026 AACCCTCTTTTGATTCTCATCCT 57.473 39.130 0.00 0.00 0.00 3.24
262 278 3.839490 TCCCCAACTGTAAGATCCGTTAA 59.161 43.478 0.00 0.00 37.43 2.01
367 393 7.229707 TCCAATCCGTCAGTTTTCATTTTTCTA 59.770 33.333 0.00 0.00 0.00 2.10
376 402 4.315803 TCTCTTCCAATCCGTCAGTTTTC 58.684 43.478 0.00 0.00 0.00 2.29
382 408 3.260632 TCATGTTCTCTTCCAATCCGTCA 59.739 43.478 0.00 0.00 0.00 4.35
428 454 2.226437 GCGCCAGTGATCTGAAAAAGAA 59.774 45.455 0.00 0.00 43.76 2.52
429 455 1.806542 GCGCCAGTGATCTGAAAAAGA 59.193 47.619 0.00 0.00 43.76 2.52
431 457 0.881118 GGCGCCAGTGATCTGAAAAA 59.119 50.000 24.80 0.00 43.76 1.94
432 458 0.036732 AGGCGCCAGTGATCTGAAAA 59.963 50.000 31.54 0.00 43.76 2.29
433 459 0.391661 GAGGCGCCAGTGATCTGAAA 60.392 55.000 31.54 0.00 43.76 2.69
434 460 1.219124 GAGGCGCCAGTGATCTGAA 59.781 57.895 31.54 0.00 43.76 3.02
435 461 2.725312 GGAGGCGCCAGTGATCTGA 61.725 63.158 31.54 0.00 43.76 3.27
436 462 2.202987 GGAGGCGCCAGTGATCTG 60.203 66.667 31.54 0.00 41.01 2.90
439 515 2.758327 TACGGAGGCGCCAGTGAT 60.758 61.111 31.54 7.13 35.94 3.06
442 518 4.065281 GTGTACGGAGGCGCCAGT 62.065 66.667 31.54 26.03 35.94 4.00
476 556 1.753078 CATCTCCACCTCGGTCCGA 60.753 63.158 14.54 14.54 35.57 4.55
477 557 1.320344 TTCATCTCCACCTCGGTCCG 61.320 60.000 4.39 4.39 35.57 4.79
482 562 1.000827 CCTCGATTCATCTCCACCTCG 60.001 57.143 0.00 0.00 0.00 4.63
487 567 2.755952 TCTCCCTCGATTCATCTCCA 57.244 50.000 0.00 0.00 0.00 3.86
498 578 1.064314 TCTTCTCCCTCTTCTCCCTCG 60.064 57.143 0.00 0.00 0.00 4.63
503 583 4.142160 GCTTCTCTTCTTCTCCCTCTTCTC 60.142 50.000 0.00 0.00 0.00 2.87
504 584 3.769300 GCTTCTCTTCTTCTCCCTCTTCT 59.231 47.826 0.00 0.00 0.00 2.85
505 585 3.513515 TGCTTCTCTTCTTCTCCCTCTTC 59.486 47.826 0.00 0.00 0.00 2.87
506 586 3.515104 CTGCTTCTCTTCTTCTCCCTCTT 59.485 47.826 0.00 0.00 0.00 2.85
520 621 2.202676 CGACCGGAGCTGCTTCTC 60.203 66.667 9.46 0.00 0.00 2.87
561 669 2.817423 GCCTCGCCATCAGCTTTCG 61.817 63.158 0.00 0.00 40.39 3.46
578 686 3.731653 GAAGAGCTCTCCCGCTGGC 62.732 68.421 18.55 0.00 41.08 4.85
581 689 3.144193 CGGAAGAGCTCTCCCGCT 61.144 66.667 29.14 6.51 44.33 5.52
609 717 0.036732 TTCTGCGCTGGAAGTGGAAT 59.963 50.000 14.70 0.00 46.58 3.01
668 807 2.011046 GCTTGCTGGAGTCCATCAGTC 61.011 57.143 13.56 6.58 31.09 3.51
669 808 0.035630 GCTTGCTGGAGTCCATCAGT 60.036 55.000 13.56 0.00 31.09 3.41
670 809 0.747283 GGCTTGCTGGAGTCCATCAG 60.747 60.000 13.56 9.95 31.09 2.90
671 810 1.300963 GGCTTGCTGGAGTCCATCA 59.699 57.895 13.56 12.56 30.82 3.07
672 811 1.452833 GGGCTTGCTGGAGTCCATC 60.453 63.158 13.56 9.52 41.18 3.51
673 812 2.679716 GGGCTTGCTGGAGTCCAT 59.320 61.111 13.56 0.00 41.18 3.41
674 813 3.650950 GGGGCTTGCTGGAGTCCA 61.651 66.667 12.40 12.40 43.38 4.02
675 814 3.334054 AGGGGCTTGCTGGAGTCC 61.334 66.667 0.73 0.73 40.79 3.85
738 882 3.369385 GTCATATTCGTCCCACGTGTAG 58.631 50.000 15.65 5.60 43.14 2.74
740 884 1.468565 CGTCATATTCGTCCCACGTGT 60.469 52.381 15.65 0.00 43.14 4.49
741 885 1.197055 CGTCATATTCGTCCCACGTG 58.803 55.000 9.08 9.08 43.14 4.49
742 886 0.813184 ACGTCATATTCGTCCCACGT 59.187 50.000 0.00 0.00 43.14 4.49
743 887 1.197055 CACGTCATATTCGTCCCACG 58.803 55.000 0.00 0.00 44.19 4.94
744 888 2.572191 TCACGTCATATTCGTCCCAC 57.428 50.000 0.00 0.00 39.55 4.61
745 889 2.732912 CGTTCACGTCATATTCGTCCCA 60.733 50.000 0.00 0.00 39.55 4.37
746 890 1.850441 CGTTCACGTCATATTCGTCCC 59.150 52.381 0.00 0.00 39.55 4.46
789 933 7.120285 TCCGAGTCGAGATTTACTAAAAGAGAA 59.880 37.037 15.64 0.00 0.00 2.87
790 934 6.596888 TCCGAGTCGAGATTTACTAAAAGAGA 59.403 38.462 15.64 0.00 0.00 3.10
791 935 6.783162 TCCGAGTCGAGATTTACTAAAAGAG 58.217 40.000 15.64 0.00 0.00 2.85
792 936 6.748333 TCCGAGTCGAGATTTACTAAAAGA 57.252 37.500 15.64 0.00 0.00 2.52
793 937 6.021626 CGTTCCGAGTCGAGATTTACTAAAAG 60.022 42.308 15.64 0.00 0.00 2.27
834 981 2.437895 GGTTGGAAGGCCCGTAGC 60.438 66.667 0.00 0.00 42.60 3.58
969 1144 2.100584 ACTCTCAATGATCGACCTGCTC 59.899 50.000 0.00 0.00 0.00 4.26
974 1149 4.331168 CCTTTCAACTCTCAATGATCGACC 59.669 45.833 0.00 0.00 0.00 4.79
983 1162 2.426522 CCATCGCCTTTCAACTCTCAA 58.573 47.619 0.00 0.00 0.00 3.02
1203 1390 4.202503 ACCTTGTTGATCCTCATCTTGTGT 60.203 41.667 0.00 0.00 0.00 3.72
1210 1397 2.173569 GGGCTACCTTGTTGATCCTCAT 59.826 50.000 0.00 0.00 0.00 2.90
1233 1420 2.664436 GCGCACACGTAGGTTGGAC 61.664 63.158 0.30 0.00 42.83 4.02
1277 1464 0.318445 GTACTTGACGTCGTGGCACT 60.318 55.000 16.72 0.00 0.00 4.40
1289 1476 1.592131 ACGCGTTTGCCGTACTTGA 60.592 52.632 5.58 0.00 39.32 3.02
1392 1579 3.385749 CTTGTGGAGCGGGCGGTAT 62.386 63.158 0.00 0.00 0.00 2.73
1503 1690 2.292016 CTCGCAGAATATCTCCGTGTCT 59.708 50.000 0.00 0.00 34.09 3.41
1594 1781 1.205893 GATCAGAGTCAGCGGTTTCCT 59.794 52.381 0.00 0.00 0.00 3.36
1822 2009 1.276421 CTCTTCGAAGGCCTTCCTCAA 59.724 52.381 34.54 23.91 43.40 3.02
1884 2071 1.004044 CTGTTGGGAGCAATGGAGTCT 59.996 52.381 0.00 0.00 0.00 3.24
1899 2086 1.337260 CCGTGAGTCTTCTCCCTGTTG 60.337 57.143 0.00 0.00 39.75 3.33
1935 2122 0.395724 TCAGCAGCTGGGAGACGATA 60.396 55.000 22.62 0.00 31.51 2.92
1983 2170 1.298157 CGCCCATGACAATGACGTGT 61.298 55.000 0.00 0.00 35.67 4.49
2007 2194 2.990967 ATGCTGTTGGGGCGGTTG 60.991 61.111 0.00 0.00 0.00 3.77
2688 2875 0.959553 AGTCCAGCTCGTCGAAGAAA 59.040 50.000 1.95 0.00 39.69 2.52
2703 2890 2.280628 CTTTGGGTTGCTATCGAGTCC 58.719 52.381 0.00 0.00 0.00 3.85
2922 3109 0.036010 CCTTGAAGATCTGGTGCCGT 60.036 55.000 0.00 0.00 0.00 5.68
2952 3139 1.672356 CTTGGCCACGGGAGACTTG 60.672 63.158 3.88 0.00 0.00 3.16
3092 3279 0.915364 GTCTTTCCCCATCCTCTGCT 59.085 55.000 0.00 0.00 0.00 4.24
3204 3397 3.250323 CTGATGTCGGCGTCGCTG 61.250 66.667 20.19 20.19 36.13 5.18
3426 3620 4.477780 GAAAGAAGTGATCGACGAGAACT 58.522 43.478 3.01 6.55 0.00 3.01
3518 7642 6.360370 AAGCACCACAGAGAACTTCTTATA 57.640 37.500 0.00 0.00 32.41 0.98
3535 7659 3.065371 CCTACGAATGAATGGAAAGCACC 59.935 47.826 0.00 0.00 0.00 5.01
3620 7744 2.255316 GTTGAGAGAGAAGCGTGCTAC 58.745 52.381 0.00 0.00 0.00 3.58
3719 7849 6.157211 ACTCACGTTCTTACAGGTTCAATAG 58.843 40.000 0.00 0.00 0.00 1.73
3738 7868 6.035327 GCATGAAATATTTGCCTTCAACTCAC 59.965 38.462 5.17 0.00 33.08 3.51
3739 7869 6.101332 GCATGAAATATTTGCCTTCAACTCA 58.899 36.000 5.17 0.00 33.08 3.41
3854 7995 2.241430 GGGTAGAACCAATGGCCTTAGT 59.759 50.000 3.32 0.00 41.02 2.24
3979 8186 2.125912 CGACCCAAGCCAGACGAG 60.126 66.667 0.00 0.00 0.00 4.18
4026 8234 6.879400 AGTAGGAAGCGATGTAAGAGATTTT 58.121 36.000 0.00 0.00 0.00 1.82
4074 8285 1.269012 AATTCCAACCCACCATGCTG 58.731 50.000 0.00 0.00 0.00 4.41
4106 8317 9.132521 CAGTTCCATTTTCATGAAACTGATAAC 57.867 33.333 29.87 28.27 34.20 1.89
4165 8377 5.529800 TGTTTGGACAAGTAGTTAAAGCCTC 59.470 40.000 0.00 0.00 31.49 4.70
4170 8382 9.413048 CAAACTTTGTTTGGACAAGTAGTTAAA 57.587 29.630 13.49 0.00 45.80 1.52
4177 8389 7.659390 TGAAAATCAAACTTTGTTTGGACAAGT 59.341 29.630 18.98 1.42 45.80 3.16
4198 8410 4.036734 GTGACACAAGGAAGAGCATGAAAA 59.963 41.667 0.00 0.00 0.00 2.29
4215 8428 7.862372 TGAATCTTTAAAGCATTTCAGTGACAC 59.138 33.333 10.51 0.00 40.09 3.67
4221 8434 7.269937 CGTGACTGAATCTTTAAAGCATTTCAG 59.730 37.037 29.70 29.70 40.09 3.02
4309 8529 3.039202 GCCGAACACCTGCCATTCG 62.039 63.158 0.00 0.00 43.71 3.34
4325 8545 8.579863 ACATTTTCTATCTATAATGCAAAGGCC 58.420 33.333 0.00 0.00 40.13 5.19
4346 8566 2.159382 CGGCAACCCTCTTGTACATTT 58.841 47.619 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.