Multiple sequence alignment - TraesCS2D01G118600

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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 TraesCS2D01G118600 chr2D 100.000 4253 0 0 1 4253 67977465 67973213 0.000000e+00 7854
1 TraesCS2D01G118600 chr2B 93.053 3613 149 37 689 4253 102414504 102418062 0.000000e+00 5188
2 TraesCS2D01G118600 chr2B 84.680 594 61 13 70 651 102413933 102414508 2.220000e-157 566
3 TraesCS2D01G118600 chr2A 94.118 3145 125 28 833 3934 66577047 66580174 0.000000e+00 4728
4 TraesCS2D01G118600 chr2A 86.065 775 75 16 1 769 66576073 66576820 0.000000e+00 802
5 TraesCS2D01G118600 chr2A 96.000 150 3 3 4026 4173 66580181 66580329 1.530000e-59 241
6 TraesCS2D01G118600 chr2A 96.512 86 3 0 4164 4249 66580569 66580654 4.430000e-30 143
7 TraesCS2D01G118600 chr2A 90.090 111 8 3 3932 4042 68155823 68155930 1.590000e-29 141
8 TraesCS2D01G118600 chr1D 93.814 97 6 0 3933 4029 354518921 354519017 3.430000e-31 147
9 TraesCS2D01G118600 chr5B 89.565 115 11 1 3922 4036 693583909 693583796 1.230000e-30 145
10 TraesCS2D01G118600 chr3B 91.509 106 8 1 3925 4029 256253702 256253807 1.230000e-30 145
11 TraesCS2D01G118600 chr4D 90.741 108 9 1 3930 4037 509117705 509117811 4.430000e-30 143
12 TraesCS2D01G118600 chr1B 91.346 104 9 0 3930 4033 301264582 301264479 4.430000e-30 143
13 TraesCS2D01G118600 chr1A 90.566 106 10 0 3932 4037 386427576 386427681 1.590000e-29 141
14 TraesCS2D01G118600 chrUn 88.596 114 11 2 3918 4030 71312968 71312856 2.060000e-28 137


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 TraesCS2D01G118600 chr2D 67973213 67977465 4252 True 7854.0 7854 100.00000 1 4253 1 chr2D.!!$R1 4252
1 TraesCS2D01G118600 chr2B 102413933 102418062 4129 False 2877.0 5188 88.86650 70 4253 2 chr2B.!!$F1 4183
2 TraesCS2D01G118600 chr2A 66576073 66580654 4581 False 1478.5 4728 93.17375 1 4249 4 chr2A.!!$F2 4248

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
332 334 0.178068 GCCCCACGAGCTTATTCTGA 59.822 55.0 0.0 0.0 0.00 3.27 F
394 398 0.178990 GGGTGACAAGCTTTGGAGGT 60.179 55.0 0.0 0.0 34.43 3.85 F
956 1171 0.677414 GACGAGAAGACGGAGGTCCT 60.677 60.0 0.0 0.0 44.54 3.85 F
1995 2246 0.101399 CAATGGACGAGGACGAGGAG 59.899 60.0 0.0 0.0 42.66 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1887 0.193574 TTCCAGGAGACCAGGTCCTT 59.806 55.000 16.72 0.00 42.12 3.36 R
1637 1888 0.545548 GTTCCAGGAGACCAGGTCCT 60.546 60.000 16.72 4.85 46.01 3.85 R
1997 2248 1.206849 TGCCATTGTACAGAGCGATGA 59.793 47.619 6.13 0.00 31.13 2.92 R
3308 3561 0.106708 AGTCGCTGCCTTTTCTCACA 59.893 50.000 0.00 0.00 0.00 3.58 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
31 32 4.703897 TGATCATAACGAAATCCCTCCAC 58.296 43.478 0.00 0.00 0.00 4.02
43 44 4.821589 CTCCACGGGCCGCTCTTC 62.822 72.222 28.71 0.00 0.00 2.87
87 88 2.664851 CAAGACTGGCGGCGAACA 60.665 61.111 12.98 7.95 0.00 3.18
102 103 2.050691 CGAACAAACGATGCCCAAAAG 58.949 47.619 0.00 0.00 35.09 2.27
117 118 2.058829 AAAAGCACTTGTGGGCGTCG 62.059 55.000 2.81 0.00 34.54 5.12
126 127 1.153628 GTGGGCGTCGTAGCTTCAT 60.154 57.895 0.00 0.00 37.29 2.57
129 130 0.459585 GGGCGTCGTAGCTTCATTCA 60.460 55.000 0.00 0.00 37.29 2.57
146 147 4.093850 TCATTCACAATCGTGCAGAGAATG 59.906 41.667 13.35 13.35 43.28 2.67
266 268 1.480954 TCCTCCTCCATTACTCAACGC 59.519 52.381 0.00 0.00 0.00 4.84
290 292 2.667470 AGGGCGTAGAGAGAATAAGCA 58.333 47.619 0.00 0.00 30.42 3.91
292 294 4.408276 AGGGCGTAGAGAGAATAAGCATA 58.592 43.478 0.00 0.00 30.42 3.14
332 334 0.178068 GCCCCACGAGCTTATTCTGA 59.822 55.000 0.00 0.00 0.00 3.27
352 354 1.375908 AGCTTTCGCTGAATCCGCA 60.376 52.632 0.00 0.00 46.86 5.69
394 398 0.178990 GGGTGACAAGCTTTGGAGGT 60.179 55.000 0.00 0.00 34.43 3.85
400 406 1.064017 ACAAGCTTTGGAGGTGGTTGA 60.064 47.619 0.00 0.00 40.35 3.18
414 420 2.659244 TTGACGTCCACCGAACGC 60.659 61.111 14.12 0.00 43.76 4.84
461 467 4.065110 GCAAGACGCCAAACTCCT 57.935 55.556 0.00 0.00 32.94 3.69
462 468 1.869690 GCAAGACGCCAAACTCCTC 59.130 57.895 0.00 0.00 32.94 3.71
465 471 2.678190 GCAAGACGCCAAACTCCTCTAT 60.678 50.000 0.00 0.00 32.94 1.98
467 473 2.457598 AGACGCCAAACTCCTCTATGA 58.542 47.619 0.00 0.00 0.00 2.15
497 503 8.648693 CCCTAAACCTAAAGCTACTATGTACAT 58.351 37.037 13.93 13.93 0.00 2.29
515 521 2.046507 GAGTGCACCTGGCTCCAG 60.047 66.667 14.63 8.93 45.15 3.86
529 535 1.684386 CTCCAGCCCGCATCTTCTCT 61.684 60.000 0.00 0.00 0.00 3.10
555 561 2.425312 AGCAACACCGACAACAAAATCA 59.575 40.909 0.00 0.00 0.00 2.57
556 562 2.788786 GCAACACCGACAACAAAATCAG 59.211 45.455 0.00 0.00 0.00 2.90
557 563 3.488384 GCAACACCGACAACAAAATCAGA 60.488 43.478 0.00 0.00 0.00 3.27
565 578 4.379813 CGACAACAAAATCAGAGATTGGGG 60.380 45.833 3.68 0.00 0.00 4.96
598 611 7.452880 AGCACATTGTATTTAGCTCTCAAAA 57.547 32.000 0.00 0.00 0.00 2.44
621 634 4.723789 AGAGGCTATGAGAAGGATGGAAAA 59.276 41.667 0.00 0.00 0.00 2.29
622 635 5.046288 AGGCTATGAGAAGGATGGAAAAG 57.954 43.478 0.00 0.00 0.00 2.27
628 641 4.666512 TGAGAAGGATGGAAAAGGAAAGG 58.333 43.478 0.00 0.00 0.00 3.11
630 643 4.928263 AGAAGGATGGAAAAGGAAAGGAG 58.072 43.478 0.00 0.00 0.00 3.69
631 644 3.093057 AGGATGGAAAAGGAAAGGAGC 57.907 47.619 0.00 0.00 0.00 4.70
718 737 5.216566 TCAGTTTCGACAACAAACAAGAG 57.783 39.130 11.33 0.00 36.38 2.85
719 738 4.094294 TCAGTTTCGACAACAAACAAGAGG 59.906 41.667 11.33 0.00 36.38 3.69
738 757 8.723365 ACAAGAGGGACAATATATATTCCAACA 58.277 33.333 13.25 0.00 0.00 3.33
772 978 5.300286 AGAAGGACAACATATTGCTATTGCC 59.700 40.000 0.00 0.00 39.66 4.52
775 981 5.242393 AGGACAACATATTGCTATTGCCATC 59.758 40.000 0.00 0.00 39.66 3.51
816 1022 1.684983 TCCTCCGACGAACAGAACTTT 59.315 47.619 0.00 0.00 0.00 2.66
817 1023 2.101917 TCCTCCGACGAACAGAACTTTT 59.898 45.455 0.00 0.00 0.00 2.27
822 1028 3.137563 GACGAACAGAACTTTTCGACG 57.862 47.619 23.36 5.63 46.01 5.12
846 1056 1.364626 CGCTGAAACAGGCTAGCAGG 61.365 60.000 18.24 10.23 35.98 4.85
889 1104 0.798776 ATCTGCAGCAAACACGCTAC 59.201 50.000 9.47 0.00 41.38 3.58
893 1108 1.270094 TGCAGCAAACACGCTACTAGT 60.270 47.619 0.00 0.00 41.38 2.57
894 1109 2.029739 TGCAGCAAACACGCTACTAGTA 60.030 45.455 1.89 1.89 41.38 1.82
896 1111 3.243177 GCAGCAAACACGCTACTAGTATC 59.757 47.826 2.33 0.00 41.38 2.24
897 1112 4.421058 CAGCAAACACGCTACTAGTATCA 58.579 43.478 2.33 0.00 41.38 2.15
898 1113 4.500837 CAGCAAACACGCTACTAGTATCAG 59.499 45.833 2.33 0.80 41.38 2.90
899 1114 3.243177 GCAAACACGCTACTAGTATCAGC 59.757 47.826 2.33 4.50 0.00 4.26
900 1115 4.673441 CAAACACGCTACTAGTATCAGCT 58.327 43.478 12.99 0.05 33.03 4.24
901 1116 4.985538 AACACGCTACTAGTATCAGCTT 57.014 40.909 12.99 2.47 33.03 3.74
902 1117 4.555348 ACACGCTACTAGTATCAGCTTC 57.445 45.455 12.99 0.00 33.03 3.86
903 1118 3.002451 ACACGCTACTAGTATCAGCTTCG 59.998 47.826 12.99 5.15 33.03 3.79
953 1168 3.576004 CGACGAGAAGACGGAGGT 58.424 61.111 0.00 0.00 37.61 3.85
954 1169 1.424635 CGACGAGAAGACGGAGGTC 59.575 63.158 0.00 0.00 43.76 3.85
955 1170 1.801983 GACGAGAAGACGGAGGTCC 59.198 63.158 0.00 0.00 44.54 4.46
956 1171 0.677414 GACGAGAAGACGGAGGTCCT 60.677 60.000 0.00 0.00 44.54 3.85
977 1210 4.386413 GCAGCTGCCACTTGTAGT 57.614 55.556 28.76 0.00 34.31 2.73
978 1211 3.532896 GCAGCTGCCACTTGTAGTA 57.467 52.632 28.76 0.00 34.31 1.82
979 1212 1.079503 GCAGCTGCCACTTGTAGTAC 58.920 55.000 28.76 0.00 34.31 2.73
980 1213 1.726853 CAGCTGCCACTTGTAGTACC 58.273 55.000 0.00 0.00 0.00 3.34
981 1214 1.276421 CAGCTGCCACTTGTAGTACCT 59.724 52.381 0.00 0.00 0.00 3.08
982 1215 2.496070 CAGCTGCCACTTGTAGTACCTA 59.504 50.000 0.00 0.00 0.00 3.08
1149 1400 2.360852 GTCCCCGACCTCGTCTCA 60.361 66.667 0.00 0.00 37.74 3.27
1637 1888 4.207281 CGAGGAGATGCCGGCGAA 62.207 66.667 23.90 5.15 43.43 4.70
1947 2198 4.147449 CAGTCCATGGGCGAGCGA 62.147 66.667 11.52 0.00 0.00 4.93
1995 2246 0.101399 CAATGGACGAGGACGAGGAG 59.899 60.000 0.00 0.00 42.66 3.69
1996 2247 0.323542 AATGGACGAGGACGAGGAGT 60.324 55.000 0.00 0.00 42.66 3.85
1997 2248 0.323542 ATGGACGAGGACGAGGAGTT 60.324 55.000 0.00 0.00 42.66 3.01
2009 2260 1.671328 CGAGGAGTTCATCGCTCTGTA 59.329 52.381 3.16 0.00 43.10 2.74
2067 2318 1.153647 CACCTTCGTGGCGCTCATA 60.154 57.895 7.64 0.00 40.22 2.15
2110 2361 4.227134 CGAGGGACGGGCAGATGG 62.227 72.222 0.00 0.00 38.46 3.51
2137 2388 4.329545 TGTGCCTCAAGACCGGCC 62.330 66.667 0.00 0.00 45.71 6.13
2327 2578 0.460987 GCCTTCTCGTGGATGGTCAG 60.461 60.000 11.94 0.00 40.27 3.51
2431 2682 4.778143 CGTACCACTGCCAGGCCC 62.778 72.222 9.64 0.00 0.00 5.80
2629 2880 1.511305 GGCCTCTTCGACGACATGA 59.489 57.895 0.00 0.00 0.00 3.07
2632 2883 1.469940 GCCTCTTCGACGACATGATGT 60.470 52.381 0.00 0.00 0.00 3.06
2640 2891 1.153568 CGACATGATGTGCTCCGGT 60.154 57.895 1.23 0.00 0.00 5.28
2682 2933 3.827898 CTCTCGGTCCTCACGGCC 61.828 72.222 0.00 0.00 0.00 6.13
2850 3101 1.970114 GATGCAGATGCCATCCGGG 60.970 63.158 0.00 0.00 41.18 5.73
3223 3474 6.349694 GGAGATGAAACTTTTGAAGGACCATC 60.350 42.308 0.00 0.00 34.58 3.51
3308 3561 6.126409 TGACCATCAAAAAGGAAACTACACT 58.874 36.000 0.00 0.00 42.68 3.55
3324 3577 0.236711 CACTGTGAGAAAAGGCAGCG 59.763 55.000 0.32 0.00 32.65 5.18
3361 3614 0.670546 CGAACTGGGTGGTGCTACAG 60.671 60.000 0.00 0.00 37.01 2.74
3415 3668 1.333791 GCAAAACGTTCTCGGTCAAGG 60.334 52.381 0.00 0.00 41.85 3.61
3447 3700 6.903883 ACACTATCTTAACATAAGCAACCG 57.096 37.500 0.00 0.00 0.00 4.44
3494 3747 6.618805 GCGAGAACAAGGATGACTAAAACTTC 60.619 42.308 0.00 0.00 0.00 3.01
3662 3915 1.543429 CCTGAAAGAGAAGGCACCGTT 60.543 52.381 0.00 0.00 34.07 4.44
3827 4080 5.712217 ACATGATAAACGACACCAATACG 57.288 39.130 0.00 0.00 0.00 3.06
3895 4148 1.609208 AGTGACAGCCTTGCGAAAAT 58.391 45.000 0.00 0.00 0.00 1.82
3896 4149 1.956477 AGTGACAGCCTTGCGAAAATT 59.044 42.857 0.00 0.00 0.00 1.82
3897 4150 3.146066 AGTGACAGCCTTGCGAAAATTA 58.854 40.909 0.00 0.00 0.00 1.40
3898 4151 3.568007 AGTGACAGCCTTGCGAAAATTAA 59.432 39.130 0.00 0.00 0.00 1.40
3946 4206 1.045407 GCATATACTCCCACCGTCCA 58.955 55.000 0.00 0.00 0.00 4.02
3950 4210 2.781681 ATACTCCCACCGTCCAAAAG 57.218 50.000 0.00 0.00 0.00 2.27
3961 4221 3.133362 ACCGTCCAAAAGTAAGTGTCTCA 59.867 43.478 0.00 0.00 0.00 3.27
3962 4222 4.124238 CCGTCCAAAAGTAAGTGTCTCAA 58.876 43.478 0.00 0.00 0.00 3.02
3965 4225 4.275196 GTCCAAAAGTAAGTGTCTCAACCC 59.725 45.833 0.00 0.00 0.00 4.11
3971 4231 6.587206 AAGTAAGTGTCTCAACCCTAGTAC 57.413 41.667 0.00 0.00 0.00 2.73
3978 4238 5.465724 GTGTCTCAACCCTAGTACAACTTTG 59.534 44.000 0.00 0.00 0.00 2.77
3979 4239 5.129815 TGTCTCAACCCTAGTACAACTTTGT 59.870 40.000 0.00 0.00 44.86 2.83
4022 4282 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
4105 4365 9.494271 TGGATTGTTCTAATATTATCTCAGTGC 57.506 33.333 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.494398 CCGTGGAGGGATTTCGTTATGAT 60.494 47.826 0.00 0.00 35.97 2.45
43 44 0.108329 ACCGTGGACAATTCTAGCCG 60.108 55.000 0.00 0.00 0.00 5.52
83 84 1.792367 GCTTTTGGGCATCGTTTGTTC 59.208 47.619 0.00 0.00 0.00 3.18
87 88 1.039856 AGTGCTTTTGGGCATCGTTT 58.960 45.000 0.00 0.00 44.34 3.60
102 103 2.356553 TACGACGCCCACAAGTGC 60.357 61.111 0.00 0.00 0.00 4.40
107 108 1.884075 ATGAAGCTACGACGCCCACA 61.884 55.000 0.00 0.00 0.00 4.17
129 130 2.738846 GACACATTCTCTGCACGATTGT 59.261 45.455 0.00 0.00 0.00 2.71
171 172 1.220206 CGACAAGGGATGCAGAGCT 59.780 57.895 0.00 0.00 0.00 4.09
176 177 0.465705 GATCTCCGACAAGGGATGCA 59.534 55.000 0.00 0.00 41.52 3.96
205 206 1.208358 CTACAGTTCGGTCGTCGCA 59.792 57.895 0.00 0.00 39.05 5.10
233 234 1.231751 AGGAGGAGATGGGGTGGAGA 61.232 60.000 0.00 0.00 0.00 3.71
266 268 2.990066 ATTCTCTCTACGCCCTTTGG 57.010 50.000 0.00 0.00 0.00 3.28
275 277 8.032451 GGGAAGATGTATGCTTATTCTCTCTAC 58.968 40.741 4.53 0.00 0.00 2.59
290 292 4.100373 GGCTGGATCTAGGGAAGATGTAT 58.900 47.826 8.31 0.00 45.35 2.29
292 294 2.334023 GGCTGGATCTAGGGAAGATGT 58.666 52.381 8.31 0.00 45.35 3.06
343 345 0.613260 AACTACAGGCTGCGGATTCA 59.387 50.000 15.89 0.00 0.00 2.57
352 354 0.036875 GTGAAGGGCAACTACAGGCT 59.963 55.000 0.00 0.00 0.00 4.58
394 398 1.227321 GTTCGGTGGACGTCAACCA 60.227 57.895 35.49 22.41 44.69 3.67
400 406 2.814183 GATCAGCGTTCGGTGGACGT 62.814 60.000 20.97 0.00 44.69 4.34
461 467 7.696017 AGCTTTAGGTTTAGGGTTTTCATAGA 58.304 34.615 0.00 0.00 0.00 1.98
462 468 7.939784 AGCTTTAGGTTTAGGGTTTTCATAG 57.060 36.000 0.00 0.00 0.00 2.23
465 471 6.844829 AGTAGCTTTAGGTTTAGGGTTTTCA 58.155 36.000 0.00 0.00 0.00 2.69
467 473 8.388589 ACATAGTAGCTTTAGGTTTAGGGTTTT 58.611 33.333 0.00 0.00 0.00 2.43
497 503 2.848679 TGGAGCCAGGTGCACTCA 60.849 61.111 17.98 1.69 44.83 3.41
515 521 1.522580 GGTCAGAGAAGATGCGGGC 60.523 63.158 0.00 0.00 0.00 6.13
529 535 1.092921 GTTGTCGGTGTTGCTGGTCA 61.093 55.000 0.00 0.00 0.00 4.02
565 578 4.440127 CAATGTGCTTGGGCCCGC 62.440 66.667 19.37 16.59 37.74 6.13
598 611 3.627041 TCCATCCTTCTCATAGCCTCT 57.373 47.619 0.00 0.00 0.00 3.69
605 618 5.015603 TCCTTTCCTTTTCCATCCTTCTCAT 59.984 40.000 0.00 0.00 0.00 2.90
678 697 9.840427 CGAAACTGAATGATAATAACAAGGTTT 57.160 29.630 0.00 0.00 0.00 3.27
680 699 8.665685 GTCGAAACTGAATGATAATAACAAGGT 58.334 33.333 0.00 0.00 0.00 3.50
683 702 9.820229 GTTGTCGAAACTGAATGATAATAACAA 57.180 29.630 0.00 0.00 0.00 2.83
684 703 8.994170 TGTTGTCGAAACTGAATGATAATAACA 58.006 29.630 10.41 0.00 0.00 2.41
685 704 9.820229 TTGTTGTCGAAACTGAATGATAATAAC 57.180 29.630 10.41 0.00 0.00 1.89
687 706 9.820229 GTTTGTTGTCGAAACTGAATGATAATA 57.180 29.630 10.41 0.00 31.74 0.98
688 707 8.349245 TGTTTGTTGTCGAAACTGAATGATAAT 58.651 29.630 10.41 0.00 34.88 1.28
689 708 7.698628 TGTTTGTTGTCGAAACTGAATGATAA 58.301 30.769 10.41 0.00 34.88 1.75
690 709 7.252965 TGTTTGTTGTCGAAACTGAATGATA 57.747 32.000 10.41 0.00 34.88 2.15
691 710 6.130298 TGTTTGTTGTCGAAACTGAATGAT 57.870 33.333 10.41 0.00 34.88 2.45
692 711 5.553290 TGTTTGTTGTCGAAACTGAATGA 57.447 34.783 10.41 0.00 34.88 2.57
693 712 6.027131 TCTTGTTTGTTGTCGAAACTGAATG 58.973 36.000 10.41 0.00 34.88 2.67
694 713 6.189677 TCTTGTTTGTTGTCGAAACTGAAT 57.810 33.333 10.41 0.00 34.88 2.57
695 714 5.391523 CCTCTTGTTTGTTGTCGAAACTGAA 60.392 40.000 10.41 4.84 34.88 3.02
696 715 4.094294 CCTCTTGTTTGTTGTCGAAACTGA 59.906 41.667 10.41 0.00 34.88 3.41
697 716 4.342772 CCTCTTGTTTGTTGTCGAAACTG 58.657 43.478 10.41 0.00 34.88 3.16
698 717 3.377172 CCCTCTTGTTTGTTGTCGAAACT 59.623 43.478 10.41 0.00 34.88 2.66
699 718 3.375922 TCCCTCTTGTTTGTTGTCGAAAC 59.624 43.478 0.00 0.00 34.48 2.78
700 719 3.375922 GTCCCTCTTGTTTGTTGTCGAAA 59.624 43.478 0.00 0.00 0.00 3.46
718 737 9.981114 CCTTTTTGTTGGAATATATATTGTCCC 57.019 33.333 12.74 8.42 0.00 4.46
719 738 9.981114 CCCTTTTTGTTGGAATATATATTGTCC 57.019 33.333 12.74 9.26 0.00 4.02
738 757 3.103742 TGTTGTCCTTCTTGCCCTTTTT 58.896 40.909 0.00 0.00 0.00 1.94
772 978 0.447406 TCCATGAAAACTGCGCGATG 59.553 50.000 12.10 3.22 0.00 3.84
775 981 1.396648 TGTATCCATGAAAACTGCGCG 59.603 47.619 0.00 0.00 0.00 6.86
816 1022 1.299544 TTTCAGCGTGCTCGTCGAA 60.300 52.632 10.18 9.70 39.49 3.71
817 1023 2.014554 GTTTCAGCGTGCTCGTCGA 61.015 57.895 10.18 3.96 39.49 4.20
822 1028 0.670546 TAGCCTGTTTCAGCGTGCTC 60.671 55.000 0.00 0.00 31.27 4.26
846 1056 2.097250 GCTTGCAAAATTTCAGTGCGTC 60.097 45.455 0.00 0.00 41.27 5.19
893 1108 5.585844 TGAATTGATTCTTGCGAAGCTGATA 59.414 36.000 5.42 0.00 45.75 2.15
894 1109 4.397103 TGAATTGATTCTTGCGAAGCTGAT 59.603 37.500 5.42 0.00 45.75 2.90
896 1111 4.087510 TGAATTGATTCTTGCGAAGCTG 57.912 40.909 5.42 0.00 45.75 4.24
897 1112 4.771590 TTGAATTGATTCTTGCGAAGCT 57.228 36.364 5.42 0.00 45.75 3.74
898 1113 4.201561 GCTTTGAATTGATTCTTGCGAAGC 60.202 41.667 0.00 0.00 45.76 3.86
899 1114 4.919168 TGCTTTGAATTGATTCTTGCGAAG 59.081 37.500 5.42 0.00 37.67 3.79
900 1115 4.869215 TGCTTTGAATTGATTCTTGCGAA 58.131 34.783 5.42 0.00 37.67 4.70
901 1116 4.216042 TCTGCTTTGAATTGATTCTTGCGA 59.784 37.500 5.42 6.18 37.67 5.10
902 1117 4.322804 GTCTGCTTTGAATTGATTCTTGCG 59.677 41.667 5.42 0.00 37.67 4.85
903 1118 4.322804 CGTCTGCTTTGAATTGATTCTTGC 59.677 41.667 5.42 7.08 37.67 4.01
943 1158 2.584391 GCCACAGGACCTCCGTCTT 61.584 63.158 0.00 0.00 42.08 3.01
947 1162 4.767255 GCTGCCACAGGACCTCCG 62.767 72.222 0.00 0.00 42.08 4.63
949 1164 2.046507 CAGCTGCCACAGGACCTC 60.047 66.667 0.00 0.00 31.21 3.85
950 1165 4.341783 GCAGCTGCCACAGGACCT 62.342 66.667 28.76 0.00 34.31 3.85
976 1209 4.776435 AGGTGGAGAGACTAGTAGGTAC 57.224 50.000 0.00 0.00 0.00 3.34
977 1210 5.786224 TCTAGGTGGAGAGACTAGTAGGTA 58.214 45.833 0.00 0.00 36.47 3.08
978 1211 4.633351 TCTAGGTGGAGAGACTAGTAGGT 58.367 47.826 0.00 0.00 36.47 3.08
979 1212 5.556915 CATCTAGGTGGAGAGACTAGTAGG 58.443 50.000 0.00 0.00 36.47 3.18
980 1213 5.001232 GCATCTAGGTGGAGAGACTAGTAG 58.999 50.000 4.87 0.00 36.47 2.57
981 1214 4.202482 GGCATCTAGGTGGAGAGACTAGTA 60.202 50.000 4.87 0.00 36.47 1.82
982 1215 3.435890 GGCATCTAGGTGGAGAGACTAGT 60.436 52.174 4.87 0.00 36.47 2.57
1139 1390 2.442272 CGGGGGATGAGACGAGGT 60.442 66.667 0.00 0.00 0.00 3.85
1149 1400 4.256180 GAGAATGCGGCGGGGGAT 62.256 66.667 9.78 0.00 0.00 3.85
1246 1497 0.471211 AGGGAGTTGGACACGAAGGA 60.471 55.000 0.00 0.00 0.00 3.36
1487 1738 1.682451 CCGAACTATCCCAAGGCCGA 61.682 60.000 0.00 0.00 0.00 5.54
1617 1868 2.186903 GCCGGCATCTCCTCGAAA 59.813 61.111 24.80 0.00 0.00 3.46
1636 1887 0.193574 TTCCAGGAGACCAGGTCCTT 59.806 55.000 16.72 0.00 42.12 3.36
1637 1888 0.545548 GTTCCAGGAGACCAGGTCCT 60.546 60.000 16.72 4.85 46.01 3.85
1947 2198 1.546476 GTGGTCCAAGAGATGACGTCT 59.454 52.381 17.92 0.00 40.81 4.18
1959 2210 4.837298 TCCATTGAAATGATTGTGGTCCAA 59.163 37.500 4.58 0.00 38.70 3.53
1995 2246 2.030946 GCCATTGTACAGAGCGATGAAC 59.969 50.000 6.13 0.00 31.13 3.18
1996 2247 2.279741 GCCATTGTACAGAGCGATGAA 58.720 47.619 6.13 0.00 31.13 2.57
1997 2248 1.206849 TGCCATTGTACAGAGCGATGA 59.793 47.619 6.13 0.00 31.13 2.92
2004 2255 1.375853 GCCGCATGCCATTGTACAGA 61.376 55.000 13.15 0.00 0.00 3.41
2009 2260 3.511595 CTCGCCGCATGCCATTGT 61.512 61.111 13.15 0.00 36.24 2.71
2137 2388 4.821589 GGCGGCCTTGTCGGAGAG 62.822 72.222 12.87 0.00 36.95 3.20
2327 2578 2.432628 CGTCGGGTCTCAAGCACC 60.433 66.667 0.00 0.00 0.00 5.01
2583 2834 1.805945 GTCGTAGCTCCCGTGCTTG 60.806 63.158 0.00 0.00 43.74 4.01
2616 2867 1.585668 GAGCACATCATGTCGTCGAAG 59.414 52.381 0.00 0.00 0.00 3.79
2629 2880 4.722700 GGCCACACCGGAGCACAT 62.723 66.667 9.46 0.00 36.56 3.21
2682 2933 1.450312 CTCCCCTTTGTAGCGGCAG 60.450 63.158 1.45 0.00 0.00 4.85
2817 3068 1.747145 CATCATGAGCTCCTCGGCT 59.253 57.895 12.15 0.00 46.11 5.52
3223 3474 1.973138 CTTTCTGTTTCCATGCGCAG 58.027 50.000 18.32 8.11 0.00 5.18
3275 3528 9.898152 TTTCCTTTTTGATGGTCAAACTATTTT 57.102 25.926 4.72 0.00 45.03 1.82
3280 3533 6.544928 AGTTTCCTTTTTGATGGTCAAACT 57.455 33.333 4.72 0.00 45.03 2.66
3308 3561 0.106708 AGTCGCTGCCTTTTCTCACA 59.893 50.000 0.00 0.00 0.00 3.58
3324 3577 3.132629 TCGAGTAAACTGATGCGAGTC 57.867 47.619 0.00 0.00 0.00 3.36
3334 3587 2.044758 ACCACCCAGTTCGAGTAAACT 58.955 47.619 0.00 0.00 40.08 2.66
3335 3588 2.140717 CACCACCCAGTTCGAGTAAAC 58.859 52.381 0.00 0.00 0.00 2.01
3407 3660 7.490000 AGATAGTGTAGAATTAACCTTGACCG 58.510 38.462 0.00 0.00 0.00 4.79
3447 3700 5.834239 CAAATCTTGCCAGTTTCACATTC 57.166 39.130 0.00 0.00 0.00 2.67
3494 3747 1.714899 AAATCGCTTGGATTCCGGCG 61.715 55.000 26.34 26.34 44.59 6.46
3662 3915 6.762702 TGAAGTACCGACACTGATACAATA 57.237 37.500 0.00 0.00 0.00 1.90
3862 4115 1.547820 TGTCACTTAGCTCTCAGCCAG 59.452 52.381 0.00 0.00 43.77 4.85
3895 4148 2.490115 CACCGCCTTGTTGCCTAATTAA 59.510 45.455 0.00 0.00 0.00 1.40
3896 4149 2.088423 CACCGCCTTGTTGCCTAATTA 58.912 47.619 0.00 0.00 0.00 1.40
3897 4150 0.887933 CACCGCCTTGTTGCCTAATT 59.112 50.000 0.00 0.00 0.00 1.40
3898 4151 0.251165 ACACCGCCTTGTTGCCTAAT 60.251 50.000 0.00 0.00 0.00 1.73
3934 4187 2.224450 ACTTACTTTTGGACGGTGGGAG 60.224 50.000 0.00 0.00 0.00 4.30
3935 4188 1.770061 ACTTACTTTTGGACGGTGGGA 59.230 47.619 0.00 0.00 0.00 4.37
3936 4189 1.877443 CACTTACTTTTGGACGGTGGG 59.123 52.381 0.00 0.00 0.00 4.61
3937 4190 2.546789 GACACTTACTTTTGGACGGTGG 59.453 50.000 0.00 0.00 0.00 4.61
3938 4191 3.463944 AGACACTTACTTTTGGACGGTG 58.536 45.455 0.00 0.00 0.00 4.94
3939 4192 3.133362 TGAGACACTTACTTTTGGACGGT 59.867 43.478 0.00 0.00 0.00 4.83
3946 4206 6.496144 ACTAGGGTTGAGACACTTACTTTT 57.504 37.500 0.00 0.00 40.79 2.27
3950 4210 5.972107 TGTACTAGGGTTGAGACACTTAC 57.028 43.478 0.00 0.00 40.79 2.34
3997 4257 5.935789 TCCGTCCCAAAATAAGTGTCTTAAG 59.064 40.000 0.00 0.00 0.00 1.85
4022 4282 7.755822 GTCGTTGAATCATAGTATCATACTCCC 59.244 40.741 0.00 0.00 40.14 4.30
4105 4365 6.506147 TGAAACAATTTGAAGTGACTCATGG 58.494 36.000 2.79 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.