Multiple sequence alignment - TraesCS7D01G156400

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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 TraesCS7D01G156400 chr7D 100.000 9935 0 0 1 9935 104566515 104576449 0.000000e+00 18347
1 TraesCS7D01G156400 chr7D 97.436 78 1 1 7472 7548 104573910 104573987 2.250000e-26 132
2 TraesCS7D01G156400 chr7D 97.436 78 1 1 7396 7473 104573986 104574062 2.250000e-26 132
3 TraesCS7D01G156400 chr7D 95.385 65 3 0 2226 2290 104568680 104568744 4.910000e-18 104
4 TraesCS7D01G156400 chr7D 95.385 65 3 0 2166 2230 104568740 104568804 4.910000e-18 104
5 TraesCS7D01G156400 chr7A 95.697 9923 261 56 1 9850 108808687 108818516 0.000000e+00 15806
6 TraesCS7D01G156400 chr7A 86.747 664 64 13 1 648 418348780 418348125 0.000000e+00 717
7 TraesCS7D01G156400 chr7A 96.809 94 3 0 9842 9935 108818869 108818962 3.710000e-34 158
8 TraesCS7D01G156400 chr7A 98.734 79 0 1 7396 7474 108816140 108816217 1.350000e-28 139
9 TraesCS7D01G156400 chr7A 96.923 65 2 0 2166 2230 108810895 108810959 1.060000e-19 110
10 TraesCS7D01G156400 chr7A 95.385 65 3 0 2226 2290 108810835 108810899 4.910000e-18 104
11 TraesCS7D01G156400 chr7B 95.807 4674 126 32 5307 9935 62692650 62697298 0.000000e+00 7481
12 TraesCS7D01G156400 chr7B 97.368 2698 60 5 2226 4920 62689422 62692111 0.000000e+00 4578
13 TraesCS7D01G156400 chr7B 90.724 2264 142 34 1 2230 62687257 62689486 0.000000e+00 2955
14 TraesCS7D01G156400 chr7B 96.341 410 9 2 4906 5309 62692128 62692537 0.000000e+00 669
15 TraesCS7D01G156400 chr7B 89.130 322 16 6 9531 9846 62705298 62705606 5.630000e-102 383
16 TraesCS7D01G156400 chr7B 97.895 95 2 0 9841 9935 62706649 62706743 2.220000e-36 165
17 TraesCS7D01G156400 chr7B 96.154 78 2 1 7396 7473 62694822 62694898 1.050000e-24 126
18 TraesCS7D01G156400 chr7B 94.737 76 3 1 7474 7548 62694748 62694823 6.300000e-22 117
19 TraesCS7D01G156400 chr5B 87.671 657 57 11 8 648 453116217 453116865 0.000000e+00 743
20 TraesCS7D01G156400 chr3B 86.846 669 61 15 1 653 632817953 632817296 0.000000e+00 723
21 TraesCS7D01G156400 chr1D 90.522 517 40 4 1 512 10037978 10037466 0.000000e+00 675
22 TraesCS7D01G156400 chr1D 90.329 517 41 4 1 512 9923248 9923760 0.000000e+00 669
23 TraesCS7D01G156400 chr3A 86.455 598 57 13 1 582 56494791 56494202 1.410000e-177 634
24 TraesCS7D01G156400 chr3A 85.978 271 21 9 390 648 71904925 71904660 3.540000e-69 274
25 TraesCS7D01G156400 chrUn 82.294 401 51 13 235 632 74596487 74596104 7.440000e-86 329
26 TraesCS7D01G156400 chr5A 85.556 270 24 7 390 648 43682644 43682909 1.640000e-67 268
27 TraesCS7D01G156400 chr5A 85.556 270 24 7 390 648 43768700 43768965 1.640000e-67 268
28 TraesCS7D01G156400 chr4A 85.185 270 25 7 390 648 590625743 590625478 7.650000e-66 263
29 TraesCS7D01G156400 chr2A 85.185 270 25 7 390 648 779537837 779538102 7.650000e-66 263
30 TraesCS7D01G156400 chr2A 85.992 257 21 7 390 635 779441080 779441332 2.750000e-65 261
31 TraesCS7D01G156400 chr2A 83.026 271 29 9 390 648 35027436 35027171 7.760000e-56 230
32 TraesCS7D01G156400 chr2B 85.088 114 8 7 90 202 593657232 593657337 3.790000e-19 108


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 TraesCS7D01G156400 chr7D 104566515 104576449 9934 False 18347.000000 18347 100.0000 1 9935 1 chr7D.!!$F1 9934
1 TraesCS7D01G156400 chr7A 108808687 108818516 9829 False 15806.000000 15806 95.6970 1 9850 1 chr7A.!!$F1 9849
2 TraesCS7D01G156400 chr7A 418348125 418348780 655 True 717.000000 717 86.7470 1 648 1 chr7A.!!$R1 647
3 TraesCS7D01G156400 chr7B 62687257 62697298 10041 False 2654.333333 7481 95.1885 1 9935 6 chr7B.!!$F1 9934
4 TraesCS7D01G156400 chr7B 62705298 62706743 1445 False 274.000000 383 93.5125 9531 9935 2 chr7B.!!$F2 404
5 TraesCS7D01G156400 chr5B 453116217 453116865 648 False 743.000000 743 87.6710 8 648 1 chr5B.!!$F1 640
6 TraesCS7D01G156400 chr3B 632817296 632817953 657 True 723.000000 723 86.8460 1 653 1 chr3B.!!$R1 652
7 TraesCS7D01G156400 chr1D 10037466 10037978 512 True 675.000000 675 90.5220 1 512 1 chr1D.!!$R1 511
8 TraesCS7D01G156400 chr1D 9923248 9923760 512 False 669.000000 669 90.3290 1 512 1 chr1D.!!$F1 511
9 TraesCS7D01G156400 chr3A 56494202 56494791 589 True 634.000000 634 86.4550 1 582 1 chr3A.!!$R1 581

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
871 907 0.248907 CGAATGTCACGGCGGTAGAT 60.249 55.000 13.24 0.0 0.00 1.98 F
1958 2013 0.674895 GCAGGGTGTAGGCAGTTCTG 60.675 60.000 0.00 0.0 0.00 3.02 F
3311 3366 0.036164 ATGTTGCAGGCGGTGAGTAA 59.964 50.000 0.00 0.0 0.00 2.24 F
3462 3519 3.606687 GATCCGCTTTAGGAAAGAACCA 58.393 45.455 3.15 0.0 44.50 3.67 F
3884 3941 5.324409 AGGTTTAAGGAATGCTGAATGTCA 58.676 37.500 0.00 0.0 0.00 3.58 F
4136 4193 6.925610 TCCAAATACAACTGTGCTATCATC 57.074 37.500 0.00 0.0 0.00 2.92 F
5067 5162 2.236146 TGATATGTGTTTCCTCGGCAGT 59.764 45.455 0.00 0.0 0.00 4.40 F
5520 5733 0.535102 GGCTGTTATGGTGATCCCCG 60.535 60.000 0.00 0.0 0.00 5.73 F
6993 7213 0.440371 CAAGCGAAAGAGAGAACGGC 59.560 55.000 0.00 0.0 0.00 5.68 F
7959 8193 1.179814 GCCGACGGATATCCAGGTCT 61.180 60.000 20.50 0.0 35.14 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2223 0.110056 GAAGCACACAATCACCTGCG 60.110 55.000 0.00 0.00 34.69 5.18 R
3462 3519 3.782656 AGTACCGGTGATGGAAAAAGT 57.217 42.857 19.93 0.00 0.00 2.66 R
4363 4420 0.802494 GTCATAACACCAAGGGCACG 59.198 55.000 0.00 0.00 0.00 5.34 R
4686 4744 1.677217 GGAGCTGTGGTTCTTAGCTGG 60.677 57.143 2.33 0.00 46.95 4.85 R
4702 4760 2.574006 TTGCCCATATGATCTGGAGC 57.426 50.000 3.65 1.55 35.70 4.70 R
5374 5584 3.244249 ACTTCCAGTGACAAGAGGTAAGC 60.244 47.826 8.37 0.00 0.00 3.09 R
6399 6619 0.518636 CCAACTTGACGACATGGCTG 59.481 55.000 0.00 0.00 0.00 4.85 R
7254 7474 2.223711 GCTCTCTTCCTCGGAATCACTC 60.224 54.545 0.00 0.00 33.28 3.51 R
8148 8382 0.029567 GTCTATCTCCACTGGCGTCG 59.970 60.000 0.00 0.00 0.00 5.12 R
9773 10049 0.459585 TAAGGTCGAGCAATGTCGCC 60.460 55.000 18.15 0.00 39.90 5.54 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
33 34 4.278170 ACAAAATGTCACACACATGGTAGG 59.722 41.667 0.00 0.00 45.77 3.18
54 56 3.696051 GGGTAAATCATGCAGAGCAAAGA 59.304 43.478 0.00 0.00 43.62 2.52
86 91 1.660607 ACAAACATCAGCGATAGTGCG 59.339 47.619 0.00 0.00 40.67 5.34
221 231 3.671928 GCAAGCAGCACATCAAAAACTAG 59.328 43.478 0.00 0.00 44.79 2.57
222 232 4.557296 GCAAGCAGCACATCAAAAACTAGA 60.557 41.667 0.00 0.00 44.79 2.43
487 497 0.967380 CCTGCAGAAATTTCCCCGCT 60.967 55.000 17.39 0.00 0.00 5.52
572 607 2.035442 GGCCGCTCACCTCTTGAAC 61.035 63.158 0.00 0.00 32.21 3.18
636 671 2.757099 GCCCCTTCACCATGGCTG 60.757 66.667 13.04 9.79 40.77 4.85
637 672 2.757099 CCCCTTCACCATGGCTGC 60.757 66.667 13.04 0.00 0.00 5.25
638 673 2.757099 CCCTTCACCATGGCTGCC 60.757 66.667 13.04 12.87 0.00 4.85
761 797 1.676014 GGCTTATATGTAGGCAGCGGG 60.676 57.143 5.95 0.00 38.03 6.13
779 815 4.201679 CGGTATCTGGACGGCGCA 62.202 66.667 10.83 0.00 0.00 6.09
813 849 2.822399 GGGATGGACGGCTCGATT 59.178 61.111 1.50 0.00 0.00 3.34
869 905 1.138047 GACGAATGTCACGGCGGTAG 61.138 60.000 13.24 0.03 44.82 3.18
870 906 1.138036 CGAATGTCACGGCGGTAGA 59.862 57.895 13.24 2.96 0.00 2.59
871 907 0.248907 CGAATGTCACGGCGGTAGAT 60.249 55.000 13.24 0.00 0.00 1.98
872 908 1.209128 GAATGTCACGGCGGTAGATG 58.791 55.000 13.24 0.00 0.00 2.90
874 910 2.585247 GTCACGGCGGTAGATGGC 60.585 66.667 13.24 0.00 0.00 4.40
875 911 3.845259 TCACGGCGGTAGATGGCC 61.845 66.667 13.24 0.00 45.95 5.36
1097 1149 3.160748 GAGCTCTCCCTCCCAGGC 61.161 72.222 6.43 0.00 32.73 4.85
1127 1179 3.612247 CTCCTCCCGTGCCCAGTTG 62.612 68.421 0.00 0.00 0.00 3.16
1151 1203 4.824515 CCTCTCGCTCGTCCCCCT 62.825 72.222 0.00 0.00 0.00 4.79
1152 1204 3.213402 CTCTCGCTCGTCCCCCTC 61.213 72.222 0.00 0.00 0.00 4.30
1180 1233 4.436998 GTCGCCTGACCGGGTCTG 62.437 72.222 26.41 24.58 39.30 3.51
1285 1338 3.722082 CGCGAATTTGGAAGTTTCTCTCG 60.722 47.826 0.00 0.00 0.00 4.04
1287 1340 3.722082 CGAATTTGGAAGTTTCTCTCGCG 60.722 47.826 0.00 0.00 0.00 5.87
1348 1401 2.735134 CTGTAAATCCGGGCGCTATTAC 59.265 50.000 7.64 8.64 0.00 1.89
1395 1449 6.869913 TGGTAACTAGTCTATTTTGTTCGTGG 59.130 38.462 0.00 0.00 37.61 4.94
1483 1537 3.861840 TCTAGGCATGTCTACTTTGTGC 58.138 45.455 2.01 0.00 35.17 4.57
1484 1538 2.867109 AGGCATGTCTACTTTGTGCT 57.133 45.000 0.00 0.00 36.15 4.40
1564 1619 5.353394 TGATTTATTCTAGACAAGGCCGT 57.647 39.130 0.00 0.00 0.00 5.68
1626 1681 7.734924 TCCTTGATAATCACATGCTTATGTC 57.265 36.000 0.00 0.00 31.37 3.06
1630 1685 5.696270 TGATAATCACATGCTTATGTCGGTC 59.304 40.000 0.00 0.00 31.37 4.79
1637 1692 4.273480 ACATGCTTATGTCGGTCTTTATGC 59.727 41.667 0.00 0.00 0.00 3.14
1939 1994 8.960591 ACTTATTTGTCTTCACCTAATGAATGG 58.039 33.333 0.00 0.00 46.37 3.16
1958 2013 0.674895 GCAGGGTGTAGGCAGTTCTG 60.675 60.000 0.00 0.00 0.00 3.02
2168 2223 4.035208 CGCAATAGTCCTGGTAATGGAAAC 59.965 45.833 0.00 0.00 35.10 2.78
2183 2238 1.334960 GGAAACGCAGGTGATTGTGTG 60.335 52.381 0.00 0.00 40.67 3.82
2261 2316 4.707448 TGTGTGCTTCCCAAAGAAAGTTTA 59.293 37.500 0.00 0.00 34.14 2.01
2657 2712 5.063880 CAGGATGAAGATGAGAATGATGCA 58.936 41.667 0.00 0.00 39.69 3.96
2837 2892 6.033966 GGAATCAACTAAACCTAATTTGCGG 58.966 40.000 0.00 0.00 0.00 5.69
3311 3366 0.036164 ATGTTGCAGGCGGTGAGTAA 59.964 50.000 0.00 0.00 0.00 2.24
3374 3429 7.288810 TCTTGTTTGCCATGACTTAAAATCT 57.711 32.000 0.00 0.00 0.00 2.40
3462 3519 3.606687 GATCCGCTTTAGGAAAGAACCA 58.393 45.455 3.15 0.00 44.50 3.67
3778 3835 9.403583 ACGGGTATGATTTACATTTTCACTAAT 57.596 29.630 0.00 0.00 40.07 1.73
3884 3941 5.324409 AGGTTTAAGGAATGCTGAATGTCA 58.676 37.500 0.00 0.00 0.00 3.58
3962 4019 9.838975 CTGTCACTGTTTTATGCAATTTGTATA 57.161 29.630 3.40 3.40 0.00 1.47
4136 4193 6.925610 TCCAAATACAACTGTGCTATCATC 57.074 37.500 0.00 0.00 0.00 2.92
4476 4534 7.651304 GTGTTGTTTTGATTGTATTGACATGGA 59.349 33.333 0.00 0.00 34.86 3.41
4702 4760 3.356529 AATCCCAGCTAAGAACCACAG 57.643 47.619 0.00 0.00 0.00 3.66
4749 4807 4.687901 ATTTTGCCCAGTGCTTAGTTTT 57.312 36.364 0.00 0.00 42.00 2.43
5067 5162 2.236146 TGATATGTGTTTCCTCGGCAGT 59.764 45.455 0.00 0.00 0.00 4.40
5083 5178 5.651530 TCGGCAGTGACTTCTTTTCTATAG 58.348 41.667 0.00 0.00 0.00 1.31
5210 5305 4.863491 TGTGTCAACGTAAAGTAGGACTC 58.137 43.478 0.00 0.00 37.83 3.36
5374 5584 1.748591 GCTTTGGTGGGGCTCTATGAG 60.749 57.143 0.00 0.00 0.00 2.90
5455 5665 5.448632 GGTCAATATGTTCCCGTTTAGCAAG 60.449 44.000 0.00 0.00 0.00 4.01
5520 5733 0.535102 GGCTGTTATGGTGATCCCCG 60.535 60.000 0.00 0.00 0.00 5.73
6399 6619 6.560253 TCACAATTGTCTAAAGAGAAAGGC 57.440 37.500 8.48 0.00 31.96 4.35
6453 6673 2.910977 TCCTGTAAACCTTCCTCCTTCC 59.089 50.000 0.00 0.00 0.00 3.46
6993 7213 0.440371 CAAGCGAAAGAGAGAACGGC 59.560 55.000 0.00 0.00 0.00 5.68
7059 7279 8.090250 ACAACATTGATTTGGACATTCATTTG 57.910 30.769 0.00 0.00 0.00 2.32
7584 7818 3.862267 GGACTGATTCTCACATGTTCTCG 59.138 47.826 0.00 0.00 0.00 4.04
7625 7859 7.650890 CCGATCATTGATTGGTGATGAAATTA 58.349 34.615 20.83 0.00 38.46 1.40
7626 7860 8.136800 CCGATCATTGATTGGTGATGAAATTAA 58.863 33.333 20.83 0.00 38.46 1.40
7627 7861 9.518906 CGATCATTGATTGGTGATGAAATTAAA 57.481 29.630 6.04 0.00 35.33 1.52
7666 7900 7.233144 TCCTCCTGAATGATTTGAATGTTTTCA 59.767 33.333 0.00 0.00 40.09 2.69
7808 8042 2.099405 CCAGTGTCAAACCCAACAAGT 58.901 47.619 0.00 0.00 0.00 3.16
7830 8064 8.303876 CAAGTATTAAAACAGGTGGCTAAACAT 58.696 33.333 0.00 0.00 0.00 2.71
7837 8071 1.423541 AGGTGGCTAAACATGGTGTGA 59.576 47.619 0.00 0.00 0.00 3.58
7959 8193 1.179814 GCCGACGGATATCCAGGTCT 61.180 60.000 20.50 0.00 35.14 3.85
8362 8601 2.590007 GATCCAAGCAGCCGCGAT 60.590 61.111 8.23 0.00 45.49 4.58
8407 8646 2.279741 CTTTCTCGGATCGAATTGGCA 58.720 47.619 0.00 0.00 34.74 4.92
8644 8884 4.081420 GGAACTGCTGGATTTCTAGACAGA 60.081 45.833 11.27 0.00 34.92 3.41
8664 8904 2.749441 GCCCTTCAGTGAGGCAGC 60.749 66.667 16.50 8.73 46.34 5.25
8697 8942 6.072175 TGCAAATTTACAGGTCTTCCACATAC 60.072 38.462 0.00 0.00 35.89 2.39
8833 9078 0.332632 TCCAGGAAATCCTTGGCCTG 59.667 55.000 3.32 0.00 46.09 4.85
8955 9200 1.005630 GCACACGCAGAGGACTTCT 60.006 57.895 0.00 0.00 38.36 2.85
8956 9201 0.243907 GCACACGCAGAGGACTTCTA 59.756 55.000 0.00 0.00 38.36 2.10
8967 9212 3.772025 AGAGGACTTCTAAGGACATGTGG 59.228 47.826 1.15 0.00 33.23 4.17
8975 9220 2.550830 AAGGACATGTGGTGACAGAC 57.449 50.000 1.15 0.00 44.46 3.51
8976 9221 1.423584 AGGACATGTGGTGACAGACA 58.576 50.000 1.15 0.00 44.46 3.41
8977 9222 1.345741 AGGACATGTGGTGACAGACAG 59.654 52.381 1.15 0.00 44.46 3.51
8978 9223 1.344438 GGACATGTGGTGACAGACAGA 59.656 52.381 1.15 0.00 44.46 3.41
8979 9224 2.027745 GGACATGTGGTGACAGACAGAT 60.028 50.000 1.15 0.00 44.46 2.90
8980 9225 2.998670 GACATGTGGTGACAGACAGATG 59.001 50.000 1.15 12.84 44.46 2.90
8981 9226 2.369860 ACATGTGGTGACAGACAGATGT 59.630 45.455 13.82 13.82 43.90 3.06
8996 9241 5.540337 AGACAGATGTTTCTACTGGACTTCA 59.460 40.000 0.00 0.00 36.17 3.02
9006 9254 3.131709 ACTGGACTTCATGGTTCACAG 57.868 47.619 0.00 0.00 0.00 3.66
9086 9338 2.363018 CGAGGTCCCAGGAGAGCA 60.363 66.667 9.12 0.00 36.71 4.26
9529 9781 2.815647 CGCCGGGAGTGCTTCTTC 60.816 66.667 2.18 0.00 0.00 2.87
9767 10043 1.023513 CCTCCCGAAGTACGACGAGT 61.024 60.000 14.26 0.00 45.77 4.18
9792 10068 0.459585 GGCGACATTGCTCGACCTTA 60.460 55.000 11.20 0.00 35.48 2.69
9794 10070 1.560923 CGACATTGCTCGACCTTAGG 58.439 55.000 0.00 0.00 35.58 2.69
9795 10071 1.135083 CGACATTGCTCGACCTTAGGT 60.135 52.381 2.34 2.34 39.44 3.08
9796 10072 2.674177 CGACATTGCTCGACCTTAGGTT 60.674 50.000 4.99 0.00 35.25 3.50
9797 10073 2.673368 GACATTGCTCGACCTTAGGTTG 59.327 50.000 12.38 12.38 35.25 3.77
9798 10074 2.038557 ACATTGCTCGACCTTAGGTTGT 59.961 45.455 17.46 7.59 38.23 3.32
9799 10075 2.163818 TTGCTCGACCTTAGGTTGTG 57.836 50.000 17.46 15.93 38.23 3.33
9800 10076 1.045407 TGCTCGACCTTAGGTTGTGT 58.955 50.000 17.46 0.00 38.23 3.72
9885 11213 1.610038 TGTGGAATTGAAGCACTGCTG 59.390 47.619 3.73 0.00 39.62 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.558418 GTGTGTGACATTTTGTCCTACGT 59.442 43.478 5.27 0.00 46.40 3.57
19 20 4.584874 TGATTTACCCTACCATGTGTGTG 58.415 43.478 0.00 0.00 0.00 3.82
29 30 3.808728 TGCTCTGCATGATTTACCCTAC 58.191 45.455 0.00 0.00 31.71 3.18
33 34 4.970662 TCTTTGCTCTGCATGATTTACC 57.029 40.909 0.00 0.00 38.76 2.85
54 56 5.049828 GCTGATGTTTGTTTAAGGCTGTTT 58.950 37.500 0.00 0.00 0.00 2.83
86 91 2.810852 GCATCTAAGGTTAGCATCTGCC 59.189 50.000 0.00 0.00 43.38 4.85
190 196 2.737376 GCTGCTTGCTTGCTTGCC 60.737 61.111 0.00 0.00 38.95 4.52
208 218 2.711542 CCCGCCTCTAGTTTTTGATGT 58.288 47.619 0.00 0.00 0.00 3.06
515 525 1.226660 CCGTTCATTTCATGGCGGC 60.227 57.895 0.00 0.00 40.24 6.53
518 528 0.810648 TCTGCCGTTCATTTCATGGC 59.189 50.000 0.00 0.00 45.42 4.40
519 529 2.033801 GGATCTGCCGTTCATTTCATGG 59.966 50.000 0.00 0.00 0.00 3.66
520 530 3.344904 GGATCTGCCGTTCATTTCATG 57.655 47.619 0.00 0.00 0.00 3.07
533 544 2.279784 CCTTCTCGCCGGATCTGC 60.280 66.667 5.05 0.00 0.00 4.26
620 655 2.757099 GCAGCCATGGTGAAGGGG 60.757 66.667 14.67 0.00 32.22 4.79
1097 1149 3.878519 GAGGAGCGGACCTCGTCG 61.879 72.222 10.74 0.00 45.30 5.12
1180 1233 5.254115 AGGTGAAATTAGGGCTTACAGTTC 58.746 41.667 0.00 0.00 0.00 3.01
1253 1306 0.366871 CAAATTCGCGACCGACAGAG 59.633 55.000 9.15 0.00 44.30 3.35
1285 1338 2.061028 CAAAATTGCAGGTTTCCTCGC 58.939 47.619 0.39 0.00 0.00 5.03
1287 1340 3.751479 ACCAAAATTGCAGGTTTCCTC 57.249 42.857 0.39 0.00 29.58 3.71
1348 1401 2.553172 AGCTATTCGAACCCTAGTAGCG 59.447 50.000 16.42 0.00 39.47 4.26
1395 1449 1.379527 CGGCCATAAGAAGGGTGAAC 58.620 55.000 2.24 0.00 0.00 3.18
1483 1537 7.726216 TGGATGGTGACTAGAATGTATACAAG 58.274 38.462 10.14 5.21 0.00 3.16
1484 1538 7.669089 TGGATGGTGACTAGAATGTATACAA 57.331 36.000 10.14 0.00 0.00 2.41
1554 1609 0.387239 GCATTTCACACGGCCTTGTC 60.387 55.000 12.77 0.00 0.00 3.18
1556 1611 0.664166 GTGCATTTCACACGGCCTTG 60.664 55.000 7.87 7.87 44.98 3.61
1564 1619 4.335315 AGAACTTTCTTCGTGCATTTCACA 59.665 37.500 0.00 0.00 38.89 3.58
1575 1630 6.718454 AGATGATGAACAGAACTTTCTTCG 57.282 37.500 0.00 0.00 34.74 3.79
1622 1677 3.334583 ACAGTGCATAAAGACCGACAT 57.665 42.857 0.00 0.00 0.00 3.06
1626 1681 6.588756 TCTTTAGTTACAGTGCATAAAGACCG 59.411 38.462 10.80 0.00 37.48 4.79
1939 1994 0.674895 CAGAACTGCCTACACCCTGC 60.675 60.000 0.00 0.00 0.00 4.85
1958 2013 1.095600 GGGTAGCTTAGGCAAACAGC 58.904 55.000 0.00 0.00 41.70 4.40
2168 2223 0.110056 GAAGCACACAATCACCTGCG 60.110 55.000 0.00 0.00 34.69 5.18
2183 2238 2.687935 TGACAAACTTTCTGTGGGAAGC 59.312 45.455 0.00 0.00 35.16 3.86
2657 2712 3.999663 CCTCAATTTCGAGCTCAAAGTCT 59.000 43.478 15.40 0.85 0.00 3.24
2737 2792 6.331307 AGGCCTATGACCATCTTTCTTATTCT 59.669 38.462 1.29 0.00 0.00 2.40
3329 3384 9.598517 ACAAGATGAAAAAGAGTATTTGCAAAA 57.401 25.926 17.19 2.96 31.73 2.44
3330 3385 9.598517 AACAAGATGAAAAAGAGTATTTGCAAA 57.401 25.926 15.44 15.44 31.73 3.68
3331 3386 9.598517 AAACAAGATGAAAAAGAGTATTTGCAA 57.401 25.926 0.00 0.00 31.73 4.08
3332 3387 9.033481 CAAACAAGATGAAAAAGAGTATTTGCA 57.967 29.630 0.00 0.00 32.49 4.08
3462 3519 3.782656 AGTACCGGTGATGGAAAAAGT 57.217 42.857 19.93 0.00 0.00 2.66
3778 3835 6.975196 ACCATAATGCATGCCTTATAAACA 57.025 33.333 22.70 2.55 32.84 2.83
4006 4063 2.787035 ACCACCCAAAAGGAGACCTTAA 59.213 45.455 3.40 0.00 43.92 1.85
4136 4193 7.820648 AGAATGTTACATAGCCAAGAAAACAG 58.179 34.615 0.00 0.00 0.00 3.16
4363 4420 0.802494 GTCATAACACCAAGGGCACG 59.198 55.000 0.00 0.00 0.00 5.34
4414 4472 7.321745 ACCGACTCTTTAATGAATTCCATTC 57.678 36.000 2.27 0.00 43.96 2.67
4476 4534 3.629398 CAGCAGTTTGGAAACTCTCACTT 59.371 43.478 1.66 0.00 45.65 3.16
4686 4744 1.677217 GGAGCTGTGGTTCTTAGCTGG 60.677 57.143 2.33 0.00 46.95 4.85
4702 4760 2.574006 TTGCCCATATGATCTGGAGC 57.426 50.000 3.65 1.55 35.70 4.70
4749 4807 3.627577 GCTGAAAACTTGGTCAAGAGACA 59.372 43.478 16.55 9.78 46.80 3.41
5083 5178 6.042208 AGGGGCTTCAGTACTTAGAATATCAC 59.958 42.308 0.00 0.00 0.00 3.06
5374 5584 3.244249 ACTTCCAGTGACAAGAGGTAAGC 60.244 47.826 8.37 0.00 0.00 3.09
5796 6010 3.902881 TGGCACAACAAACTTCCAAAT 57.097 38.095 0.00 0.00 31.92 2.32
6399 6619 0.518636 CCAACTTGACGACATGGCTG 59.481 55.000 0.00 0.00 0.00 4.85
6453 6673 3.559504 CATCTGAGATATCACACGGACG 58.440 50.000 5.32 0.00 0.00 4.79
6993 7213 5.690409 GCTTGTGGATTCTTGCATATCAATG 59.310 40.000 0.00 0.00 33.57 2.82
7028 7248 7.722949 ATGTCCAAATCAATGTTGTTATCCT 57.277 32.000 0.00 0.00 0.00 3.24
7254 7474 2.223711 GCTCTCTTCCTCGGAATCACTC 60.224 54.545 0.00 0.00 33.28 3.51
7584 7818 1.295792 TCGGCTGATAATTTCGGTGC 58.704 50.000 0.00 0.00 32.85 5.01
7666 7900 4.768968 ACAACATGCAGAGAATAAAGGCTT 59.231 37.500 0.00 0.00 0.00 4.35
7808 8042 6.722129 ACCATGTTTAGCCACCTGTTTTAATA 59.278 34.615 0.00 0.00 0.00 0.98
7830 8064 2.404923 TCCGTTTTGAACTCACACCA 57.595 45.000 0.00 0.00 0.00 4.17
7837 8071 1.600485 ACGCGATTTCCGTTTTGAACT 59.400 42.857 15.93 0.00 41.15 3.01
7959 8193 1.941294 GATTCACTCGCTCGAGACCTA 59.059 52.381 23.95 8.08 44.53 3.08
8148 8382 0.029567 GTCTATCTCCACTGGCGTCG 59.970 60.000 0.00 0.00 0.00 5.12
8407 8646 7.147637 GGAGACAGGAAGGTGAAATATCTACTT 60.148 40.741 0.00 0.00 0.00 2.24
8622 8862 4.867608 GTCTGTCTAGAAATCCAGCAGTTC 59.132 45.833 0.00 0.00 34.01 3.01
8664 8904 5.471456 AGACCTGTAAATTTGCAGAGTCAAG 59.529 40.000 32.89 22.16 42.54 3.02
8697 8942 2.491693 GAGAGGGGAGCTCATAGATTCG 59.508 54.545 17.19 0.00 32.67 3.34
8737 8982 1.227823 CACTTCAACGCCACCTCCA 60.228 57.895 0.00 0.00 0.00 3.86
8833 9078 0.525029 GTACGACTACAAGAGCGCCC 60.525 60.000 2.29 0.00 0.00 6.13
8891 9136 2.032681 AACTGGCTGAACGAGGGC 59.967 61.111 0.00 0.00 0.00 5.19
8945 9190 3.772025 CCACATGTCCTTAGAAGTCCTCT 59.228 47.826 0.00 0.00 38.28 3.69
8946 9191 3.515901 ACCACATGTCCTTAGAAGTCCTC 59.484 47.826 0.00 0.00 0.00 3.71
8947 9192 3.261897 CACCACATGTCCTTAGAAGTCCT 59.738 47.826 0.00 0.00 0.00 3.85
8948 9193 3.260884 TCACCACATGTCCTTAGAAGTCC 59.739 47.826 0.00 0.00 0.00 3.85
8949 9194 4.246458 GTCACCACATGTCCTTAGAAGTC 58.754 47.826 0.00 0.00 0.00 3.01
8950 9195 3.646162 TGTCACCACATGTCCTTAGAAGT 59.354 43.478 0.00 0.00 0.00 3.01
8951 9196 4.021104 TCTGTCACCACATGTCCTTAGAAG 60.021 45.833 0.00 0.00 0.00 2.85
8955 9200 2.969262 TGTCTGTCACCACATGTCCTTA 59.031 45.455 0.00 0.00 0.00 2.69
8956 9201 1.768275 TGTCTGTCACCACATGTCCTT 59.232 47.619 0.00 0.00 0.00 3.36
8967 9212 4.926238 CCAGTAGAAACATCTGTCTGTCAC 59.074 45.833 9.93 0.00 0.00 3.67
8975 9220 5.583854 CCATGAAGTCCAGTAGAAACATCTG 59.416 44.000 0.00 0.00 0.00 2.90
8976 9221 5.249393 ACCATGAAGTCCAGTAGAAACATCT 59.751 40.000 0.00 0.00 0.00 2.90
8977 9222 5.491982 ACCATGAAGTCCAGTAGAAACATC 58.508 41.667 0.00 0.00 0.00 3.06
8978 9223 5.505181 ACCATGAAGTCCAGTAGAAACAT 57.495 39.130 0.00 0.00 0.00 2.71
8979 9224 4.974645 ACCATGAAGTCCAGTAGAAACA 57.025 40.909 0.00 0.00 0.00 2.83
8980 9225 5.179555 GTGAACCATGAAGTCCAGTAGAAAC 59.820 44.000 0.00 0.00 0.00 2.78
8981 9226 5.163248 TGTGAACCATGAAGTCCAGTAGAAA 60.163 40.000 0.00 0.00 0.00 2.52
8996 9241 0.842030 TCCCTCTGCCTGTGAACCAT 60.842 55.000 0.00 0.00 0.00 3.55
9006 9254 3.851128 GTACGCCCTCCCTCTGCC 61.851 72.222 0.00 0.00 0.00 4.85
9026 9278 1.277580 ATGGTCAGGAGGAAGGCCAG 61.278 60.000 5.01 0.00 36.29 4.85
9086 9338 4.157120 GCTCGGCATGGGGTACGT 62.157 66.667 0.00 0.00 0.00 3.57
9197 9449 4.143333 CACGTACCTCCGGCTGGG 62.143 72.222 12.87 11.33 35.24 4.45
9693 9960 2.513204 CCCTGCTCTGCATCACCG 60.513 66.667 0.00 0.00 38.13 4.94
9767 10043 1.515519 GAGCAATGTCGCCGTCGTA 60.516 57.895 0.00 0.00 36.96 3.43
9769 10045 3.902063 CGAGCAATGTCGCCGTCG 61.902 66.667 0.00 0.00 32.22 5.12
9770 10046 2.506217 TCGAGCAATGTCGCCGTC 60.506 61.111 0.00 0.00 39.90 4.79
9771 10047 2.809601 GTCGAGCAATGTCGCCGT 60.810 61.111 0.00 0.00 39.90 5.68
9772 10048 3.554692 GGTCGAGCAATGTCGCCG 61.555 66.667 10.30 0.00 39.90 6.46
9773 10049 0.459585 TAAGGTCGAGCAATGTCGCC 60.460 55.000 18.15 0.00 39.90 5.54
9774 10050 0.924090 CTAAGGTCGAGCAATGTCGC 59.076 55.000 18.15 0.00 39.90 5.19
9792 10068 1.252175 TTGCACACAACACACAACCT 58.748 45.000 0.00 0.00 0.00 3.50
9794 10070 1.925847 CCATTGCACACAACACACAAC 59.074 47.619 0.00 0.00 38.99 3.32
9795 10071 1.547820 ACCATTGCACACAACACACAA 59.452 42.857 0.00 0.00 38.99 3.33
9796 10072 1.135170 CACCATTGCACACAACACACA 60.135 47.619 0.00 0.00 38.99 3.72
9797 10073 1.558741 CACCATTGCACACAACACAC 58.441 50.000 0.00 0.00 38.99 3.82
9885 11213 1.282875 GGCAAACGACAGAACAGCC 59.717 57.895 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.