Multiple sequence alignment - TraesCS2D01G101800

Loading Multiple Alignment...

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 TraesCS2D01G101800 chr2D 100.000 4825 0 0 1 4825 55056072 55060896 0.000000e+00 8911.0
1 TraesCS2D01G101800 chr2B 91.041 4956 175 103 1 4825 86209691 86214508 0.000000e+00 6444.0
2 TraesCS2D01G101800 chr2B 91.736 363 13 9 3969 4328 765341707 765341359 5.610000e-134 488.0
3 TraesCS2D01G101800 chr2A 91.386 4365 163 86 501 4771 55850440 55854685 0.000000e+00 5781.0
4 TraesCS2D01G101800 chr2A 87.954 523 21 12 5 507 55849766 55850266 3.240000e-161 579.0
5 TraesCS2D01G101800 chr2A 95.556 45 1 1 4781 4825 55854678 55854721 2.410000e-08 71.3
6 TraesCS2D01G101800 chr7B 91.119 822 35 20 3974 4781 502266496 502265699 0.000000e+00 1079.0
7 TraesCS2D01G101800 chr7B 90.146 822 44 20 3974 4781 66954569 66953771 0.000000e+00 1035.0
8 TraesCS2D01G101800 chr7B 100.000 30 0 0 3526 3555 530373146 530373117 6.750000e-04 56.5
9 TraesCS2D01G101800 chr3D 85.338 266 30 7 2173 2436 11399632 11399890 2.860000e-67 267.0
10 TraesCS2D01G101800 chr4A 89.691 194 20 0 2356 2549 469513112 469513305 1.040000e-61 248.0
11 TraesCS2D01G101800 chr4B 89.175 194 21 0 2356 2549 149938152 149937959 4.820000e-60 243.0
12 TraesCS2D01G101800 chr3B 84.906 159 20 4 2287 2443 747699332 747699488 1.800000e-34 158.0
13 TraesCS2D01G101800 chr5D 91.262 103 9 0 2882 2984 236662764 236662662 1.810000e-29 141.0
14 TraesCS2D01G101800 chr5A 91.262 103 9 0 2882 2984 318756941 318757043 1.810000e-29 141.0
15 TraesCS2D01G101800 chr5B 90.291 103 10 0 2882 2984 268432472 268432574 8.420000e-28 135.0
16 TraesCS2D01G101800 chr7D 100.000 30 0 0 3526 3555 501088776 501088747 6.750000e-04 56.5


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 TraesCS2D01G101800 chr2D 55056072 55060896 4824 False 8911.000000 8911 100.000 1 4825 1 chr2D.!!$F1 4824
1 TraesCS2D01G101800 chr2B 86209691 86214508 4817 False 6444.000000 6444 91.041 1 4825 1 chr2B.!!$F1 4824
2 TraesCS2D01G101800 chr2A 55849766 55854721 4955 False 2143.766667 5781 91.632 5 4825 3 chr2A.!!$F1 4820
3 TraesCS2D01G101800 chr7B 502265699 502266496 797 True 1079.000000 1079 91.119 3974 4781 1 chr7B.!!$R2 807
4 TraesCS2D01G101800 chr7B 66953771 66954569 798 True 1035.000000 1035 90.146 3974 4781 1 chr7B.!!$R1 807

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
935 1225 0.179176 TTGTTGTTGTGCTGTGCGAC 60.179 50.0 0.00 0.0 0.00 5.19 F
2025 2383 0.393402 TCGCCAACTACGAGCTCCTA 60.393 55.0 8.47 0.0 33.96 2.94 F
2066 2424 0.803768 CATCTCACCGGTTGCTCTCG 60.804 60.0 2.97 0.0 0.00 4.04 F
3638 4019 0.397254 ACCACCATCTCCTACCTCCG 60.397 60.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2317 2678 1.287425 GTTAATCCCGGCGAGTCTTG 58.713 55.0 9.30 0.0 0.0 3.02 R
3429 3807 0.104855 TCCGCGCTGCAGATTAGATT 59.895 50.0 20.43 0.0 0.0 2.40 R
3772 4157 0.178998 GACAGCCTGCATCCATCCAT 60.179 55.0 0.00 0.0 0.0 3.41 R
4523 4959 0.815734 CCTGTCCGTCACTTCCGTAT 59.184 55.0 0.00 0.0 0.0 3.06 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
29 30 4.430765 GACGGAAAGGCGAGGCGA 62.431 66.667 0.00 0.00 0.00 5.54
33 34 4.459089 GAAAGGCGAGGCGAGGCT 62.459 66.667 0.00 0.00 46.93 4.58
34 35 3.075005 AAAGGCGAGGCGAGGCTA 61.075 61.111 11.15 0.00 44.05 3.93
35 36 2.962697 GAAAGGCGAGGCGAGGCTAG 62.963 65.000 11.15 0.30 44.05 3.42
196 213 2.429069 CGCGGCAAAGGACAAAGC 60.429 61.111 0.00 0.00 0.00 3.51
197 214 2.429069 GCGGCAAAGGACAAAGCG 60.429 61.111 0.00 0.00 0.00 4.68
198 215 2.255252 CGGCAAAGGACAAAGCGG 59.745 61.111 0.00 0.00 0.00 5.52
199 216 2.650778 GGCAAAGGACAAAGCGGG 59.349 61.111 0.00 0.00 0.00 6.13
200 217 2.650778 GCAAAGGACAAAGCGGGG 59.349 61.111 0.00 0.00 0.00 5.73
348 373 3.963724 CAGCGGTAACAACAGTAAAAACG 59.036 43.478 0.00 0.00 0.00 3.60
349 374 3.870419 AGCGGTAACAACAGTAAAAACGA 59.130 39.130 0.00 0.00 0.00 3.85
350 375 4.025480 AGCGGTAACAACAGTAAAAACGAG 60.025 41.667 0.00 0.00 0.00 4.18
400 428 1.682854 CCGGGTTGATTGATTGGATGG 59.317 52.381 0.00 0.00 0.00 3.51
422 459 3.303526 GCGGTACTATTGGTAATTTGGCG 60.304 47.826 0.00 0.00 31.56 5.69
462 504 1.093159 GAGCACAGGAAGAATGCAGG 58.907 55.000 0.00 0.00 41.97 4.85
680 942 2.851071 CGGCTCCCTCGTCATCTCC 61.851 68.421 0.00 0.00 0.00 3.71
681 943 2.725008 GCTCCCTCGTCATCTCCG 59.275 66.667 0.00 0.00 0.00 4.63
682 944 2.725008 CTCCCTCGTCATCTCCGC 59.275 66.667 0.00 0.00 0.00 5.54
683 945 1.826054 CTCCCTCGTCATCTCCGCT 60.826 63.158 0.00 0.00 0.00 5.52
684 946 1.791103 CTCCCTCGTCATCTCCGCTC 61.791 65.000 0.00 0.00 0.00 5.03
685 947 2.725008 CCTCGTCATCTCCGCTCC 59.275 66.667 0.00 0.00 0.00 4.70
821 1105 2.576406 CGCAAGTAGTATAGCTCGCTC 58.424 52.381 0.00 0.00 0.00 5.03
826 1110 3.255725 AGTAGTATAGCTCGCTCGCTAG 58.744 50.000 9.26 0.00 44.88 3.42
827 1111 0.800012 AGTATAGCTCGCTCGCTAGC 59.200 55.000 4.06 4.06 44.88 3.42
836 1120 1.008309 GCTCGCTAGCTAACCCTCG 60.008 63.158 13.93 0.00 45.85 4.63
837 1121 1.008309 CTCGCTAGCTAACCCTCGC 60.008 63.158 13.93 0.00 0.00 5.03
838 1122 1.448922 CTCGCTAGCTAACCCTCGCT 61.449 60.000 13.93 0.00 40.15 4.93
839 1123 1.299468 CGCTAGCTAACCCTCGCTG 60.299 63.158 13.93 0.00 37.05 5.18
840 1124 1.592939 GCTAGCTAACCCTCGCTGC 60.593 63.158 7.70 0.00 37.05 5.25
841 1125 1.068250 CTAGCTAACCCTCGCTGCC 59.932 63.158 0.00 0.00 37.05 4.85
842 1126 2.685387 CTAGCTAACCCTCGCTGCCG 62.685 65.000 0.00 0.00 37.05 5.69
858 1147 4.796231 CGCCCACGAACGAGGGAG 62.796 72.222 27.92 22.29 46.98 4.30
860 1149 3.382832 CCCACGAACGAGGGAGCT 61.383 66.667 21.47 0.00 46.98 4.09
861 1150 2.182030 CCACGAACGAGGGAGCTC 59.818 66.667 4.71 4.71 0.00 4.09
862 1151 2.344203 CCACGAACGAGGGAGCTCT 61.344 63.158 14.64 0.00 0.00 4.09
863 1152 1.137825 CACGAACGAGGGAGCTCTC 59.862 63.158 14.64 10.30 0.00 3.20
869 1158 2.364448 GAGGGAGCTCTCGGGGTT 60.364 66.667 14.64 0.00 0.00 4.11
880 1169 1.416401 TCTCGGGGTTATTCATGGAGC 59.584 52.381 0.00 0.00 0.00 4.70
881 1170 1.417890 CTCGGGGTTATTCATGGAGCT 59.582 52.381 0.00 0.00 0.00 4.09
885 1174 2.225467 GGGTTATTCATGGAGCTGCTC 58.775 52.381 21.17 21.17 0.00 4.26
935 1225 0.179176 TTGTTGTTGTGCTGTGCGAC 60.179 50.000 0.00 0.00 0.00 5.19
975 1294 3.630312 TGTGAGGTTGTTTGCTAGGTTTC 59.370 43.478 0.00 0.00 0.00 2.78
982 1310 3.537580 TGTTTGCTAGGTTTCGTTGAGT 58.462 40.909 0.00 0.00 0.00 3.41
1461 1816 2.602267 TTCTTCGGCGGGGACTCA 60.602 61.111 7.21 0.00 0.00 3.41
1511 1866 2.811317 CCAGCTCGCGTTCCTCAC 60.811 66.667 5.77 0.00 0.00 3.51
1564 1919 4.421479 AGCTCCCGCTGTTCGACG 62.421 66.667 0.00 0.00 46.86 5.12
1756 2114 4.947147 AAAACGGGAGCGCCTGCA 62.947 61.111 16.16 0.00 44.98 4.41
2014 2372 3.953775 CCACCACCCTCGCCAACT 61.954 66.667 0.00 0.00 0.00 3.16
2025 2383 0.393402 TCGCCAACTACGAGCTCCTA 60.393 55.000 8.47 0.00 33.96 2.94
2041 2399 2.286872 TCCTAGCTCTCGTTTCTACCG 58.713 52.381 0.00 0.00 0.00 4.02
2049 2407 2.124860 GTTTCTACCGGCGGGCAT 60.125 61.111 31.78 12.31 36.48 4.40
2066 2424 0.803768 CATCTCACCGGTTGCTCTCG 60.804 60.000 2.97 0.00 0.00 4.04
2317 2678 3.438017 CTACCTCCGCTCTGCCTGC 62.438 68.421 0.00 0.00 0.00 4.85
2321 2682 3.306595 CTCCGCTCTGCCTGCAAGA 62.307 63.158 0.00 0.00 34.07 3.02
2553 2914 1.576421 GACAAGTTCAGGCAAGCCG 59.424 57.895 5.28 1.09 41.95 5.52
2598 2959 2.690778 CCGGCAGCAGCAACTAACC 61.691 63.158 2.65 0.00 44.61 2.85
2599 2960 1.965930 CGGCAGCAGCAACTAACCA 60.966 57.895 2.65 0.00 44.61 3.67
2622 2988 4.733165 AGACATCCCCATGACCATTTATG 58.267 43.478 0.00 0.00 33.72 1.90
2994 3367 4.821589 CTCAAGACCCGCTCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
3221 3599 1.234615 TGCGGCTTCCTTTTTCCTCG 61.235 55.000 0.00 0.00 0.00 4.63
3225 3603 1.335964 GGCTTCCTTTTTCCTCGCAAC 60.336 52.381 0.00 0.00 0.00 4.17
3412 3790 4.525912 AAGCATTTCACCAAACTGATCC 57.474 40.909 0.00 0.00 0.00 3.36
3424 3802 3.372440 AACTGATCCTTTAGCCCCTTG 57.628 47.619 0.00 0.00 0.00 3.61
3427 3805 1.340991 TGATCCTTTAGCCCCTTGTGC 60.341 52.381 0.00 0.00 0.00 4.57
3429 3807 1.663911 TCCTTTAGCCCCTTGTGCTA 58.336 50.000 0.00 0.00 40.23 3.49
3430 3808 1.989586 TCCTTTAGCCCCTTGTGCTAA 59.010 47.619 0.84 0.84 46.55 3.09
3599 3977 1.517694 CGGCATCAACAGCAATGGC 60.518 57.895 0.00 0.00 43.05 4.40
3638 4019 0.397254 ACCACCATCTCCTACCTCCG 60.397 60.000 0.00 0.00 0.00 4.63
3772 4157 3.008923 TGATTGGTGTGCTGAAGGTATCA 59.991 43.478 0.00 0.00 36.38 2.15
3773 4158 3.719268 TTGGTGTGCTGAAGGTATCAT 57.281 42.857 0.00 0.00 37.44 2.45
3774 4159 2.989909 TGGTGTGCTGAAGGTATCATG 58.010 47.619 0.00 0.00 37.44 3.07
3775 4160 2.292267 GGTGTGCTGAAGGTATCATGG 58.708 52.381 0.00 0.00 37.44 3.66
3850 4239 5.982516 GCTGAATGGAAGTGAGTGATACTAG 59.017 44.000 0.00 0.00 0.00 2.57
3892 4284 1.636003 CCCTCTCTTTTTACCAGCCCT 59.364 52.381 0.00 0.00 0.00 5.19
3909 4301 0.111253 CCTTCAACACCTTGCTCCCT 59.889 55.000 0.00 0.00 0.00 4.20
3923 4315 4.778213 TGCTCCCTAGTAAAATCATGCT 57.222 40.909 0.00 0.00 0.00 3.79
3976 4384 5.548056 TGTCTTAACCTTGGATCCTTCTCTT 59.452 40.000 14.23 0.73 0.00 2.85
4031 4439 7.775053 AAAGGAATAGTGCAACATAGGAAAA 57.225 32.000 0.00 0.00 41.43 2.29
4157 4569 1.376037 GACCACAAGAGGCGAAGGG 60.376 63.158 0.00 0.00 0.00 3.95
4229 4643 0.106015 TACGTTAGGGCCCCTCCTAC 60.106 60.000 21.43 8.73 38.97 3.18
4243 4657 4.781621 CCCCTCCTACTATTACCATTACCC 59.218 50.000 0.00 0.00 0.00 3.69
4244 4658 4.781621 CCCTCCTACTATTACCATTACCCC 59.218 50.000 0.00 0.00 0.00 4.95
4286 4700 7.614583 TGTTAGTTGATTACTCCTGCTACTACT 59.385 37.037 0.00 0.00 38.33 2.57
4287 4701 9.118300 GTTAGTTGATTACTCCTGCTACTACTA 57.882 37.037 0.00 0.00 38.33 1.82
4288 4702 9.690913 TTAGTTGATTACTCCTGCTACTACTAA 57.309 33.333 0.00 0.00 38.33 2.24
4406 4842 5.358922 AGCCACTAGTAGTAGTAGTTCTCG 58.641 45.833 13.97 4.55 37.40 4.04
4442 4878 2.772077 TAGGTGCGATGTTTAGCCAA 57.228 45.000 0.00 0.00 0.00 4.52
4523 4959 2.849880 GCAAGACAGTGCAACAAGAA 57.150 45.000 0.00 0.00 44.29 2.52
4564 5000 2.830923 CAGGGATGCATAGCTAGCTAGT 59.169 50.000 27.42 14.41 31.45 2.57
4576 5012 3.071023 AGCTAGCTAGTTTGTGTTGGTGA 59.929 43.478 17.69 0.00 0.00 4.02
4585 5021 6.236017 AGTTTGTGTTGGTGATTACGTATG 57.764 37.500 0.00 0.00 0.00 2.39
4586 5022 5.761234 AGTTTGTGTTGGTGATTACGTATGT 59.239 36.000 0.00 0.00 0.00 2.29
4587 5023 6.930164 AGTTTGTGTTGGTGATTACGTATGTA 59.070 34.615 0.00 0.00 0.00 2.29
4588 5024 7.604927 AGTTTGTGTTGGTGATTACGTATGTAT 59.395 33.333 0.00 0.00 0.00 2.29
4589 5025 6.895607 TGTGTTGGTGATTACGTATGTATG 57.104 37.500 0.00 0.00 0.00 2.39
4590 5026 6.399743 TGTGTTGGTGATTACGTATGTATGT 58.600 36.000 0.00 0.00 0.00 2.29
4591 5027 7.545489 TGTGTTGGTGATTACGTATGTATGTA 58.455 34.615 0.00 0.00 0.00 2.29
4592 5028 7.488792 TGTGTTGGTGATTACGTATGTATGTAC 59.511 37.037 0.00 0.00 0.00 2.90
4751 5196 3.499737 GCGTTGGCCGTGGATCAG 61.500 66.667 0.00 0.00 39.32 2.90
4784 5230 4.233635 GGCAGCGCATTCAGCTCG 62.234 66.667 11.47 0.00 44.06 5.03
4785 5231 4.233635 GCAGCGCATTCAGCTCGG 62.234 66.667 11.47 0.00 44.06 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.901650 GCCTTTCCGTCGCTTCACAG 61.902 60.000 0.00 0.00 0.00 3.66
25 26 1.603425 GCTAAAGCTACTAGCCTCGCC 60.603 57.143 14.20 0.00 43.77 5.54
26 27 1.773410 GCTAAAGCTACTAGCCTCGC 58.227 55.000 14.20 0.00 43.77 5.03
57 63 4.458989 TCCTTTCCTCCGTTTGATTTGATG 59.541 41.667 0.00 0.00 0.00 3.07
281 298 1.806542 GCGTGTGTGATTGACTGGAAT 59.193 47.619 0.00 0.00 0.00 3.01
322 347 1.204062 CTGTTGTTACCGCTGCGTG 59.796 57.895 21.59 14.46 0.00 5.34
323 348 0.032403 TACTGTTGTTACCGCTGCGT 59.968 50.000 21.59 11.45 0.00 5.24
324 349 1.141645 TTACTGTTGTTACCGCTGCG 58.858 50.000 16.34 16.34 0.00 5.18
325 350 3.612472 TTTTACTGTTGTTACCGCTGC 57.388 42.857 0.00 0.00 0.00 5.25
348 373 0.179205 GTGCTGCGCTGTGATTTCTC 60.179 55.000 16.05 0.00 0.00 2.87
349 374 1.871772 GTGCTGCGCTGTGATTTCT 59.128 52.632 16.05 0.00 0.00 2.52
350 375 1.510623 CGTGCTGCGCTGTGATTTC 60.511 57.895 16.05 0.00 0.00 2.17
382 410 1.067516 CGCCATCCAATCAATCAACCC 59.932 52.381 0.00 0.00 0.00 4.11
384 412 1.750778 ACCGCCATCCAATCAATCAAC 59.249 47.619 0.00 0.00 0.00 3.18
400 428 3.303526 CGCCAAATTACCAATAGTACCGC 60.304 47.826 0.00 0.00 0.00 5.68
422 459 2.420466 GGGCGGACGGATAGGAAC 59.580 66.667 0.00 0.00 0.00 3.62
462 504 1.679153 TGTCACCGCCTTTTCTTTTCC 59.321 47.619 0.00 0.00 0.00 3.13
489 541 6.322712 CCCCCATTTATAAAAACTCGATCCAA 59.677 38.462 1.21 0.00 0.00 3.53
555 790 2.795297 GCTCGTCGTCTCAGAGGG 59.205 66.667 0.00 0.00 32.96 4.30
557 792 2.401592 CCGCTCGTCGTCTCAGAG 59.598 66.667 0.00 0.00 36.19 3.35
558 793 3.125573 CCCGCTCGTCGTCTCAGA 61.126 66.667 0.00 0.00 36.19 3.27
666 928 1.824329 GAGCGGAGATGACGAGGGA 60.824 63.158 0.00 0.00 0.00 4.20
675 937 1.152830 GGAGGAGAGGAGCGGAGAT 59.847 63.158 0.00 0.00 0.00 2.75
716 978 1.676014 CCCTATGTATAAGCTGGCCGC 60.676 57.143 11.02 11.02 39.57 6.53
717 979 1.899814 TCCCTATGTATAAGCTGGCCG 59.100 52.381 0.00 0.00 0.00 6.13
718 980 3.173965 TCTCCCTATGTATAAGCTGGCC 58.826 50.000 0.00 0.00 0.00 5.36
719 981 5.181748 CAATCTCCCTATGTATAAGCTGGC 58.818 45.833 0.00 0.00 0.00 4.85
821 1105 1.299468 CAGCGAGGGTTAGCTAGCG 60.299 63.158 9.55 0.00 42.52 4.26
841 1125 4.796231 CTCCCTCGTTCGTGGGCG 62.796 72.222 22.43 15.36 43.04 6.13
855 1144 1.120530 TGAATAACCCCGAGAGCTCC 58.879 55.000 10.93 0.68 0.00 4.70
856 1145 2.548920 CCATGAATAACCCCGAGAGCTC 60.549 54.545 5.27 5.27 0.00 4.09
857 1146 1.417890 CCATGAATAACCCCGAGAGCT 59.582 52.381 0.00 0.00 0.00 4.09
858 1147 1.416401 TCCATGAATAACCCCGAGAGC 59.584 52.381 0.00 0.00 0.00 4.09
859 1148 2.548920 GCTCCATGAATAACCCCGAGAG 60.549 54.545 0.00 0.00 0.00 3.20
860 1149 1.416401 GCTCCATGAATAACCCCGAGA 59.584 52.381 0.00 0.00 0.00 4.04
861 1150 1.417890 AGCTCCATGAATAACCCCGAG 59.582 52.381 0.00 0.00 0.00 4.63
862 1151 1.140852 CAGCTCCATGAATAACCCCGA 59.859 52.381 0.00 0.00 0.00 5.14
863 1152 1.597742 CAGCTCCATGAATAACCCCG 58.402 55.000 0.00 0.00 0.00 5.73
864 1153 1.133668 AGCAGCTCCATGAATAACCCC 60.134 52.381 0.00 0.00 0.00 4.95
865 1154 2.225467 GAGCAGCTCCATGAATAACCC 58.775 52.381 11.84 0.00 0.00 4.11
866 1155 1.869767 CGAGCAGCTCCATGAATAACC 59.130 52.381 17.16 0.00 0.00 2.85
867 1156 2.541762 GACGAGCAGCTCCATGAATAAC 59.458 50.000 17.16 0.00 0.00 1.89
868 1157 2.432146 AGACGAGCAGCTCCATGAATAA 59.568 45.455 17.16 0.00 0.00 1.40
869 1158 2.034878 AGACGAGCAGCTCCATGAATA 58.965 47.619 17.16 0.00 0.00 1.75
935 1225 0.250513 CACCCCTTCTTCCTCCTTCG 59.749 60.000 0.00 0.00 0.00 3.79
975 1294 0.318699 TCGACCAAGCTCACTCAACG 60.319 55.000 0.00 0.00 0.00 4.10
982 1310 1.960040 ATGCCGATCGACCAAGCTCA 61.960 55.000 18.66 0.00 0.00 4.26
1324 1673 4.681978 GGAGAACACCGGCTGCGT 62.682 66.667 0.00 0.00 0.00 5.24
1328 1677 2.203788 TCCTGGAGAACACCGGCT 60.204 61.111 0.00 0.00 35.17 5.52
1461 1816 1.945522 CTCGTCGAGGATCAGCGAT 59.054 57.895 14.68 0.00 38.91 4.58
1926 2284 2.357881 CTGAGGCACTTGCTCGCA 60.358 61.111 0.38 0.00 41.55 5.10
2025 2383 1.511768 GCCGGTAGAAACGAGAGCT 59.488 57.895 1.90 0.00 0.00 4.09
2049 2407 2.636412 CCGAGAGCAACCGGTGAGA 61.636 63.158 8.52 0.00 40.78 3.27
2057 2415 1.424493 CCTGCGAATCCGAGAGCAAC 61.424 60.000 0.00 0.00 39.26 4.17
2317 2678 1.287425 GTTAATCCCGGCGAGTCTTG 58.713 55.000 9.30 0.00 0.00 3.02
2321 2682 2.497770 CGGTTAATCCCGGCGAGT 59.502 61.111 9.30 0.00 44.32 4.18
2590 2951 3.433306 TGGGGATGTCTTGGTTAGTTG 57.567 47.619 0.00 0.00 0.00 3.16
2598 2959 2.742428 ATGGTCATGGGGATGTCTTG 57.258 50.000 0.00 0.00 0.00 3.02
2599 2960 3.763557 AAATGGTCATGGGGATGTCTT 57.236 42.857 0.00 0.00 0.00 3.01
2622 2988 2.666190 TGCAGAGCAACAGCGGAC 60.666 61.111 0.00 0.00 34.76 4.79
2760 3126 8.699749 CATGCATATGAACATGAACAATCAATC 58.300 33.333 14.72 0.00 45.23 2.67
2761 3127 8.587952 CATGCATATGAACATGAACAATCAAT 57.412 30.769 14.72 0.00 45.23 2.57
3021 3394 3.365265 GTGGGGCTGAACGGCTTG 61.365 66.667 5.60 0.00 38.46 4.01
3221 3599 1.729131 CCGTTGACCGCATTGTTGC 60.729 57.895 0.00 0.00 45.78 4.17
3225 3603 2.034879 AGCTCCGTTGACCGCATTG 61.035 57.895 0.00 0.00 34.38 2.82
3311 3689 3.818210 TGATGGTGATTTGTTTAGCGTGT 59.182 39.130 0.00 0.00 0.00 4.49
3312 3690 4.418013 TGATGGTGATTTGTTTAGCGTG 57.582 40.909 0.00 0.00 0.00 5.34
3424 3802 2.096516 GCGCTGCAGATTAGATTAGCAC 60.097 50.000 20.43 0.00 0.00 4.40
3427 3805 1.723542 CCGCGCTGCAGATTAGATTAG 59.276 52.381 20.43 0.00 0.00 1.73
3429 3807 0.104855 TCCGCGCTGCAGATTAGATT 59.895 50.000 20.43 0.00 0.00 2.40
3430 3808 0.319383 CTCCGCGCTGCAGATTAGAT 60.319 55.000 20.43 0.00 0.00 1.98
3431 3809 1.066422 CTCCGCGCTGCAGATTAGA 59.934 57.895 20.43 7.33 0.00 2.10
3548 3926 2.664851 TTGCAACCTGTCGAGGCG 60.665 61.111 0.00 0.00 44.33 5.52
3557 3935 4.323477 TAGGCCGCGTTGCAACCT 62.323 61.111 23.42 16.34 37.32 3.50
3638 4019 1.680338 GTGAGGGTATGTCCAATGCC 58.320 55.000 0.00 0.00 38.11 4.40
3772 4157 0.178998 GACAGCCTGCATCCATCCAT 60.179 55.000 0.00 0.00 0.00 3.41
3773 4158 1.225426 GACAGCCTGCATCCATCCA 59.775 57.895 0.00 0.00 0.00 3.41
3774 4159 1.527844 GGACAGCCTGCATCCATCC 60.528 63.158 7.39 0.00 32.35 3.51
3775 4160 1.530771 AGGACAGCCTGCATCCATC 59.469 57.895 13.11 0.00 44.90 3.51
3850 4239 4.065789 GGGTGCTTACTATGATTAGGCAC 58.934 47.826 7.80 7.80 44.99 5.01
3892 4284 2.054799 ACTAGGGAGCAAGGTGTTGAA 58.945 47.619 0.00 0.00 35.46 2.69
3909 4301 8.965819 TGAAAAAGGCATAGCATGATTTTACTA 58.034 29.630 0.00 0.00 33.33 1.82
3923 4315 6.945435 TCATTCCAGTAAGTGAAAAAGGCATA 59.055 34.615 0.00 0.00 0.00 3.14
3976 4384 4.002982 CTGCTAGTATTCCTGCACAACAA 58.997 43.478 0.00 0.00 0.00 2.83
4031 4439 4.158394 TGCTGCAACTTCTTCACTCTTTTT 59.842 37.500 0.00 0.00 0.00 1.94
4177 4589 1.337118 TTAAAGCCTTGGGGTTGCTG 58.663 50.000 1.66 0.00 43.04 4.41
4229 4643 9.342308 CTAATGCATATGGGGTAATGGTAATAG 57.658 37.037 0.00 0.00 0.00 1.73
4243 4657 9.325198 TCAACTAACAGTAACTAATGCATATGG 57.675 33.333 0.00 0.00 0.00 2.74
4286 4700 6.931790 TGGTTGTTGGTGGTAGTACTATTA 57.068 37.500 5.75 0.00 0.00 0.98
4287 4701 5.829062 TGGTTGTTGGTGGTAGTACTATT 57.171 39.130 5.75 0.00 0.00 1.73
4288 4702 5.829062 TTGGTTGTTGGTGGTAGTACTAT 57.171 39.130 5.75 0.00 0.00 2.12
4295 4718 4.350225 TGGTAGTATTGGTTGTTGGTGGTA 59.650 41.667 0.00 0.00 0.00 3.25
4399 4835 5.892160 TGTGCTACTATTACACGAGAACT 57.108 39.130 0.00 0.00 37.11 3.01
4400 4836 7.378995 CCTAATGTGCTACTATTACACGAGAAC 59.621 40.741 0.00 0.00 37.11 3.01
4401 4837 7.067859 ACCTAATGTGCTACTATTACACGAGAA 59.932 37.037 0.00 0.00 37.11 2.87
4442 4878 7.970102 TGTGGTAGTATTCCTCTGTACTTTTT 58.030 34.615 0.00 0.00 33.48 1.94
4523 4959 0.815734 CCTGTCCGTCACTTCCGTAT 59.184 55.000 0.00 0.00 0.00 3.06
4564 5000 7.388224 ACATACATACGTAATCACCAACACAAA 59.612 33.333 0.00 0.00 0.00 2.83
4585 5021 9.687210 TCATCCAGTGAAATTATACGTACATAC 57.313 33.333 0.00 0.00 32.78 2.39
4751 5196 2.269241 CCGAGCAAGAAGGGACCC 59.731 66.667 0.59 0.59 0.00 4.46
4773 5218 1.300971 TTCAGTGCCGAGCTGAATGC 61.301 55.000 0.00 0.00 44.90 3.56
4784 5230 2.584492 AAAAACACAGCTTCAGTGCC 57.416 45.000 2.73 0.00 40.59 5.01


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

AutoCloner maintained by Alex Coulton.