Multiple sequence alignment - TraesCS2B01G401800

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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 TraesCS2B01G401800 chr2B 100.000 2499 0 0 1 2499 570655110 570657608 0.000000e+00 4615.0
1 TraesCS2B01G401800 chr2B 91.525 59 5 0 5 63 241926285 241926343 5.730000e-12 82.4
2 TraesCS2B01G401800 chr2D 92.705 2440 101 38 109 2499 485748651 485751062 0.000000e+00 3448.0
3 TraesCS2B01G401800 chr2D 91.525 59 5 0 5 63 412117265 412117323 5.730000e-12 82.4
4 TraesCS2B01G401800 chr2A 89.749 917 40 24 1226 2099 631203083 631203988 0.000000e+00 1123.0
5 TraesCS2B01G401800 chr2A 89.452 493 32 7 246 732 631201955 631202433 2.750000e-169 604.0
6 TraesCS2B01G401800 chr2A 90.682 440 25 5 760 1195 631202663 631203090 2.790000e-159 571.0
7 TraesCS2B01G401800 chr2A 93.651 315 9 3 2195 2499 631204018 631204331 6.300000e-126 460.0
8 TraesCS2B01G401800 chr2A 93.220 59 4 0 5 63 2784759 2784817 1.230000e-13 87.9
9 TraesCS2B01G401800 chr7A 96.491 57 2 0 5 61 498937260 498937204 7.360000e-16 95.3
10 TraesCS2B01G401800 chr5D 94.545 55 3 0 5 59 484305048 484304994 4.430000e-13 86.1
11 TraesCS2B01G401800 chr5B 94.545 55 3 0 5 59 595370723 595370669 4.430000e-13 86.1
12 TraesCS2B01G401800 chr5B 90.476 63 6 0 1 63 13084217 13084279 1.590000e-12 84.2
13 TraesCS2B01G401800 chr3B 94.545 55 3 0 5 59 369105729 369105675 4.430000e-13 86.1
14 TraesCS2B01G401800 chr1D 93.103 58 3 1 6 63 293904713 293904769 1.590000e-12 84.2


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 TraesCS2B01G401800 chr2B 570655110 570657608 2498 False 4615.0 4615 100.0000 1 2499 1 chr2B.!!$F2 2498
1 TraesCS2B01G401800 chr2D 485748651 485751062 2411 False 3448.0 3448 92.7050 109 2499 1 chr2D.!!$F2 2390
2 TraesCS2B01G401800 chr2A 631201955 631204331 2376 False 689.5 1123 90.8835 246 2499 4 chr2A.!!$F2 2253

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
482 487 0.179081 GGCAGGTGGACCTACGAATC 60.179 60.0 0.0 0.0 46.65 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 2517 0.031585 TCGTCTGGAAACACGAGTGG 59.968 55.0 8.19 0.0 34.4 4.0 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
28 29 8.722480 CATGTAGTTCATGTTGGAATCTCTAA 57.278 34.615 1.75 0.00 46.18 2.10
29 30 9.166173 CATGTAGTTCATGTTGGAATCTCTAAA 57.834 33.333 1.75 0.00 46.18 1.85
30 31 9.739276 ATGTAGTTCATGTTGGAATCTCTAAAA 57.261 29.630 0.00 0.00 35.19 1.52
31 32 9.567776 TGTAGTTCATGTTGGAATCTCTAAAAA 57.432 29.630 0.00 0.00 0.00 1.94
33 34 8.924511 AGTTCATGTTGGAATCTCTAAAAAGA 57.075 30.769 0.00 0.00 0.00 2.52
34 35 9.354673 AGTTCATGTTGGAATCTCTAAAAAGAA 57.645 29.630 0.00 0.00 0.00 2.52
54 55 8.919777 AAAGAATTATATTTAGGAACGGAGGG 57.080 34.615 0.00 0.00 0.00 4.30
55 56 7.867160 AGAATTATATTTAGGAACGGAGGGA 57.133 36.000 0.00 0.00 0.00 4.20
56 57 7.908453 AGAATTATATTTAGGAACGGAGGGAG 58.092 38.462 0.00 0.00 0.00 4.30
57 58 7.513091 AGAATTATATTTAGGAACGGAGGGAGT 59.487 37.037 0.00 0.00 0.00 3.85
58 59 8.731591 AATTATATTTAGGAACGGAGGGAGTA 57.268 34.615 0.00 0.00 0.00 2.59
59 60 8.912614 ATTATATTTAGGAACGGAGGGAGTAT 57.087 34.615 0.00 0.00 0.00 2.12
60 61 8.731591 TTATATTTAGGAACGGAGGGAGTATT 57.268 34.615 0.00 0.00 0.00 1.89
61 62 5.970501 ATTTAGGAACGGAGGGAGTATTT 57.029 39.130 0.00 0.00 0.00 1.40
62 63 5.349061 TTTAGGAACGGAGGGAGTATTTC 57.651 43.478 0.00 0.00 0.00 2.17
63 64 2.117051 AGGAACGGAGGGAGTATTTCC 58.883 52.381 0.00 0.00 46.00 3.13
77 78 5.763698 GGAGTATTTCCCAACTGGTATTAGC 59.236 44.000 0.00 0.00 40.37 3.09
78 79 5.365619 AGTATTTCCCAACTGGTATTAGCG 58.634 41.667 0.00 0.00 34.77 4.26
79 80 2.702592 TTCCCAACTGGTATTAGCGG 57.297 50.000 0.13 0.13 34.77 5.52
80 81 1.575419 TCCCAACTGGTATTAGCGGT 58.425 50.000 1.47 1.47 36.65 5.68
81 82 2.749600 TCCCAACTGGTATTAGCGGTA 58.250 47.619 7.73 0.00 33.46 4.02
82 83 3.311091 TCCCAACTGGTATTAGCGGTAT 58.689 45.455 7.73 0.00 33.46 2.73
83 84 3.712733 TCCCAACTGGTATTAGCGGTATT 59.287 43.478 7.73 0.00 33.46 1.89
84 85 4.900652 TCCCAACTGGTATTAGCGGTATTA 59.099 41.667 7.73 0.00 33.46 0.98
85 86 5.011329 TCCCAACTGGTATTAGCGGTATTAG 59.989 44.000 7.73 0.19 33.46 1.73
86 87 4.689345 CCAACTGGTATTAGCGGTATTAGC 59.311 45.833 15.23 15.23 33.46 3.09
88 89 5.135508 ACTGGTATTAGCGGTATTAGCTG 57.864 43.478 20.88 20.88 45.60 4.24
89 90 4.831155 ACTGGTATTAGCGGTATTAGCTGA 59.169 41.667 25.51 10.46 45.60 4.26
90 91 5.130292 TGGTATTAGCGGTATTAGCTGAC 57.870 43.478 20.04 0.00 45.60 3.51
91 92 4.585581 TGGTATTAGCGGTATTAGCTGACA 59.414 41.667 20.04 4.29 45.60 3.58
92 93 5.245301 TGGTATTAGCGGTATTAGCTGACAT 59.755 40.000 20.04 2.26 45.60 3.06
93 94 5.805994 GGTATTAGCGGTATTAGCTGACATC 59.194 44.000 14.96 0.00 45.60 3.06
94 95 5.730296 ATTAGCGGTATTAGCTGACATCT 57.270 39.130 0.00 0.00 45.60 2.90
95 96 6.835819 ATTAGCGGTATTAGCTGACATCTA 57.164 37.500 0.00 0.00 45.60 1.98
96 97 6.644248 TTAGCGGTATTAGCTGACATCTAA 57.356 37.500 0.00 1.44 45.60 2.10
97 98 5.127693 AGCGGTATTAGCTGACATCTAAG 57.872 43.478 0.00 0.00 44.22 2.18
98 99 4.827835 AGCGGTATTAGCTGACATCTAAGA 59.172 41.667 0.00 0.00 44.22 2.10
99 100 4.918583 GCGGTATTAGCTGACATCTAAGAC 59.081 45.833 13.06 13.06 37.46 3.01
100 101 5.507482 GCGGTATTAGCTGACATCTAAGACA 60.507 44.000 19.79 1.63 38.99 3.41
101 102 6.682746 CGGTATTAGCTGACATCTAAGACAT 58.317 40.000 19.79 2.04 38.99 3.06
102 103 6.804295 CGGTATTAGCTGACATCTAAGACATC 59.196 42.308 19.79 7.62 38.99 3.06
103 104 7.308891 CGGTATTAGCTGACATCTAAGACATCT 60.309 40.741 19.79 1.17 38.99 2.90
104 105 8.364142 GGTATTAGCTGACATCTAAGACATCTT 58.636 37.037 19.79 0.00 38.99 2.40
105 106 9.405587 GTATTAGCTGACATCTAAGACATCTTC 57.594 37.037 15.48 0.00 37.85 2.87
106 107 7.652524 TTAGCTGACATCTAAGACATCTTCT 57.347 36.000 0.00 0.00 37.40 2.85
107 108 6.543430 AGCTGACATCTAAGACATCTTCTT 57.457 37.500 0.00 0.00 46.91 2.52
123 124 6.645415 ACATCTTCTTGTTTTACGTCTTCGAT 59.355 34.615 0.00 0.00 40.62 3.59
128 129 7.416154 TCTTGTTTTACGTCTTCGATTTGAT 57.584 32.000 0.00 0.00 40.62 2.57
131 132 9.250986 CTTGTTTTACGTCTTCGATTTGATTAG 57.749 33.333 0.00 0.00 40.62 1.73
219 220 1.000506 TGACGACCTAAGTTCCTGTGC 59.999 52.381 0.00 0.00 0.00 4.57
258 259 4.825422 TCCGGAGAGATTATTCATCATGC 58.175 43.478 0.00 0.00 33.75 4.06
259 260 4.284234 TCCGGAGAGATTATTCATCATGCA 59.716 41.667 0.00 0.00 33.75 3.96
276 277 0.249398 GCAAGGACACACCGGATACT 59.751 55.000 9.46 0.00 44.74 2.12
290 291 4.760204 ACCGGATACTTGAGAAACCAAAAG 59.240 41.667 9.46 0.00 0.00 2.27
349 350 7.168219 AGCAACATAGGAGTGTCTTGATTTTA 58.832 34.615 0.00 0.00 0.00 1.52
350 351 7.831193 AGCAACATAGGAGTGTCTTGATTTTAT 59.169 33.333 0.00 0.00 0.00 1.40
446 451 4.804868 AAAAACGTACACCCCAAAACTT 57.195 36.364 0.00 0.00 0.00 2.66
452 457 1.362355 CACCCCAAAACTTCCACGC 59.638 57.895 0.00 0.00 0.00 5.34
480 485 1.534476 TGGCAGGTGGACCTACGAA 60.534 57.895 0.00 0.00 46.65 3.85
482 487 0.179081 GGCAGGTGGACCTACGAATC 60.179 60.000 0.00 0.00 46.65 2.52
540 545 1.152756 GAATTCCCCATCCACCCCG 60.153 63.158 0.00 0.00 0.00 5.73
587 593 4.697756 CATCCCACCACCGCACGT 62.698 66.667 0.00 0.00 0.00 4.49
599 605 1.223187 CCGCACGTAATTACCCATCC 58.777 55.000 10.01 0.00 0.00 3.51
600 606 1.473610 CCGCACGTAATTACCCATCCA 60.474 52.381 10.01 0.00 0.00 3.41
691 697 1.523524 GGGCGTAATTCCCTCCGAA 59.476 57.895 0.00 0.00 40.66 4.30
718 724 4.140599 CCTTCTCTGGCGCGCTCT 62.141 66.667 32.29 0.00 0.00 4.09
737 743 6.094061 CGCTCTAGTATAAATAGGAGGCAAC 58.906 44.000 0.00 0.00 0.00 4.17
806 1014 3.368501 CCTCCTCCCCCTCCTCCA 61.369 72.222 0.00 0.00 0.00 3.86
813 1021 2.040278 CCCCTCCTCCAGTGCTCT 59.960 66.667 0.00 0.00 0.00 4.09
844 1054 2.092861 TCCTCCGATCTTTCTCTCGTCT 60.093 50.000 0.00 0.00 33.11 4.18
847 1057 1.666700 CCGATCTTTCTCTCGTCTCGT 59.333 52.381 0.00 0.00 33.11 4.18
857 1067 0.318445 CTCGTCTCGTCCCGTTGTTT 60.318 55.000 0.00 0.00 0.00 2.83
880 1090 3.839432 CCTCCTCTCGTTCGGCCC 61.839 72.222 0.00 0.00 0.00 5.80
938 1150 1.918293 ACGGCCATCAACCTCCTGA 60.918 57.895 2.24 0.00 0.00 3.86
1030 1247 1.740025 CATCAGAAACCGCTTTCCTCC 59.260 52.381 0.00 0.00 37.12 4.30
1045 1262 4.458829 TCCCCATCGACGGCTCCT 62.459 66.667 0.00 0.00 0.00 3.69
1048 1265 2.427245 CCCATCGACGGCTCCTCTT 61.427 63.158 0.00 0.00 0.00 2.85
1212 1429 4.823732 CCCAGCCCTAGCCCCAGA 62.824 72.222 0.00 0.00 41.25 3.86
1213 1430 3.167105 CCAGCCCTAGCCCCAGAG 61.167 72.222 0.00 0.00 41.25 3.35
1214 1431 3.871395 CAGCCCTAGCCCCAGAGC 61.871 72.222 0.00 0.00 41.25 4.09
1217 1434 3.167105 CCCTAGCCCCAGAGCCTG 61.167 72.222 0.00 0.00 0.00 4.85
1218 1435 3.871395 CCTAGCCCCAGAGCCTGC 61.871 72.222 0.00 0.00 0.00 4.85
1219 1436 3.085947 CTAGCCCCAGAGCCTGCA 61.086 66.667 0.00 0.00 0.00 4.41
1220 1437 3.085947 TAGCCCCAGAGCCTGCAG 61.086 66.667 6.78 6.78 0.00 4.41
1279 1499 1.153086 CAAGCTGCTAGCCGGGAAT 60.153 57.895 13.29 0.00 43.77 3.01
1423 1643 2.436292 GAGCTGTCCTGGCTGCTG 60.436 66.667 20.69 6.35 42.37 4.41
1654 1881 7.876936 TTCCTAGATCTAGCGAGAAAACTTA 57.123 36.000 22.33 3.44 34.61 2.24
1723 1950 7.413548 GGCACTGCTAGTCTTTAATTTCTTCTC 60.414 40.741 0.00 0.00 0.00 2.87
2056 2327 2.596452 CGCGTGGTAGATATGTCATCC 58.404 52.381 0.00 0.00 0.00 3.51
2081 2352 6.691818 CCATCTGTGTATGTTTCGTAGTAGTC 59.308 42.308 0.00 0.00 0.00 2.59
2125 2402 2.639065 ACGTGGTGCCGATTGATTATT 58.361 42.857 0.00 0.00 0.00 1.40
2135 2412 4.635223 CCGATTGATTATTCAGAGAGGCA 58.365 43.478 0.00 0.00 32.27 4.75
2178 2456 4.825422 AGATGATGCGTATATCCTTGTGG 58.175 43.478 0.00 0.00 0.00 4.17
2185 2463 5.004448 TGCGTATATCCTTGTGGTTTTGAA 58.996 37.500 0.00 0.00 34.23 2.69
2224 2502 1.358152 TTGGATCAAGGGACGAAGGT 58.642 50.000 0.00 0.00 0.00 3.50
2237 2515 1.185618 CGAAGGTGGTCTGGTCTGGA 61.186 60.000 0.00 0.00 0.00 3.86
2327 2614 5.295431 TGTTGTTTCCATTGATCGATGAC 57.705 39.130 22.50 13.77 0.00 3.06
2329 2616 5.240403 TGTTGTTTCCATTGATCGATGACAA 59.760 36.000 22.50 20.03 0.00 3.18
2340 2627 4.335315 TGATCGATGACAAGTATTTTGGCC 59.665 41.667 0.54 0.00 0.00 5.36
2381 2668 3.367025 CCGTTACGACCTGTCTTGATTTC 59.633 47.826 6.24 0.00 0.00 2.17
2470 2757 1.133181 TGCTGGTCAATGGTGGGAGA 61.133 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.739276 TTTTAGAGATTCCAACATGAACTACAT 57.261 29.630 0.00 0.00 40.17 2.29
5 6 9.567776 TTTTTAGAGATTCCAACATGAACTACA 57.432 29.630 0.00 0.00 0.00 2.74
8 9 8.924511 TCTTTTTAGAGATTCCAACATGAACT 57.075 30.769 0.00 0.00 0.00 3.01
28 29 9.350951 CCCTCCGTTCCTAAATATAATTCTTTT 57.649 33.333 0.00 0.00 0.00 2.27
29 30 8.720537 TCCCTCCGTTCCTAAATATAATTCTTT 58.279 33.333 0.00 0.00 0.00 2.52
30 31 8.271398 TCCCTCCGTTCCTAAATATAATTCTT 57.729 34.615 0.00 0.00 0.00 2.52
31 32 7.513091 ACTCCCTCCGTTCCTAAATATAATTCT 59.487 37.037 0.00 0.00 0.00 2.40
32 33 7.677892 ACTCCCTCCGTTCCTAAATATAATTC 58.322 38.462 0.00 0.00 0.00 2.17
33 34 7.628501 ACTCCCTCCGTTCCTAAATATAATT 57.371 36.000 0.00 0.00 0.00 1.40
34 35 8.912614 ATACTCCCTCCGTTCCTAAATATAAT 57.087 34.615 0.00 0.00 0.00 1.28
35 36 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
36 37 8.731591 AAATACTCCCTCCGTTCCTAAATATA 57.268 34.615 0.00 0.00 0.00 0.86
37 38 7.256583 GGAAATACTCCCTCCGTTCCTAAATAT 60.257 40.741 0.00 0.00 38.44 1.28
38 39 6.042437 GGAAATACTCCCTCCGTTCCTAAATA 59.958 42.308 0.00 0.00 38.44 1.40
39 40 5.163227 GGAAATACTCCCTCCGTTCCTAAAT 60.163 44.000 0.00 0.00 38.44 1.40
40 41 4.162888 GGAAATACTCCCTCCGTTCCTAAA 59.837 45.833 0.00 0.00 38.44 1.85
41 42 3.708121 GGAAATACTCCCTCCGTTCCTAA 59.292 47.826 0.00 0.00 38.44 2.69
42 43 3.303049 GGAAATACTCCCTCCGTTCCTA 58.697 50.000 0.00 0.00 38.44 2.94
43 44 2.117051 GGAAATACTCCCTCCGTTCCT 58.883 52.381 0.00 0.00 38.44 3.36
44 45 2.616634 GGAAATACTCCCTCCGTTCC 57.383 55.000 0.00 0.00 38.44 3.62
53 54 5.763698 GCTAATACCAGTTGGGAAATACTCC 59.236 44.000 2.79 0.00 44.54 3.85
54 55 5.465724 CGCTAATACCAGTTGGGAAATACTC 59.534 44.000 2.79 0.00 41.15 2.59
55 56 5.365619 CGCTAATACCAGTTGGGAAATACT 58.634 41.667 2.79 0.00 41.15 2.12
56 57 4.514066 CCGCTAATACCAGTTGGGAAATAC 59.486 45.833 2.79 0.00 41.15 1.89
57 58 4.164604 ACCGCTAATACCAGTTGGGAAATA 59.835 41.667 2.79 0.00 41.15 1.40
58 59 3.053917 ACCGCTAATACCAGTTGGGAAAT 60.054 43.478 2.79 0.00 41.15 2.17
59 60 2.306512 ACCGCTAATACCAGTTGGGAAA 59.693 45.455 2.79 0.00 41.15 3.13
60 61 1.910671 ACCGCTAATACCAGTTGGGAA 59.089 47.619 2.79 0.00 41.15 3.97
61 62 1.575419 ACCGCTAATACCAGTTGGGA 58.425 50.000 2.79 0.00 41.15 4.37
62 63 3.764237 ATACCGCTAATACCAGTTGGG 57.236 47.619 2.79 0.00 44.81 4.12
63 64 4.689345 GCTAATACCGCTAATACCAGTTGG 59.311 45.833 0.00 0.00 42.17 3.77
64 65 5.405571 CAGCTAATACCGCTAATACCAGTTG 59.594 44.000 0.00 0.00 35.63 3.16
65 66 5.303589 TCAGCTAATACCGCTAATACCAGTT 59.696 40.000 0.00 0.00 35.63 3.16
66 67 4.831155 TCAGCTAATACCGCTAATACCAGT 59.169 41.667 0.00 0.00 35.63 4.00
67 68 5.162075 GTCAGCTAATACCGCTAATACCAG 58.838 45.833 0.00 0.00 35.63 4.00
68 69 4.585581 TGTCAGCTAATACCGCTAATACCA 59.414 41.667 0.00 0.00 35.63 3.25
69 70 5.130292 TGTCAGCTAATACCGCTAATACC 57.870 43.478 0.00 0.00 35.63 2.73
70 71 6.622549 AGATGTCAGCTAATACCGCTAATAC 58.377 40.000 0.00 0.00 35.63 1.89
71 72 6.835819 AGATGTCAGCTAATACCGCTAATA 57.164 37.500 0.00 0.00 35.63 0.98
72 73 5.730296 AGATGTCAGCTAATACCGCTAAT 57.270 39.130 0.00 0.00 35.63 1.73
73 74 6.489022 TCTTAGATGTCAGCTAATACCGCTAA 59.511 38.462 10.84 0.00 35.63 3.09
74 75 6.002082 TCTTAGATGTCAGCTAATACCGCTA 58.998 40.000 10.84 0.00 35.63 4.26
75 76 4.827835 TCTTAGATGTCAGCTAATACCGCT 59.172 41.667 10.84 0.00 38.49 5.52
76 77 4.918583 GTCTTAGATGTCAGCTAATACCGC 59.081 45.833 10.84 0.00 0.00 5.68
77 78 6.073327 TGTCTTAGATGTCAGCTAATACCG 57.927 41.667 18.36 6.31 29.11 4.02
78 79 7.891561 AGATGTCTTAGATGTCAGCTAATACC 58.108 38.462 18.36 8.39 29.11 2.73
79 80 9.405587 GAAGATGTCTTAGATGTCAGCTAATAC 57.594 37.037 15.70 15.70 36.11 1.89
80 81 9.360901 AGAAGATGTCTTAGATGTCAGCTAATA 57.639 33.333 10.84 1.63 36.11 0.98
81 82 8.248904 AGAAGATGTCTTAGATGTCAGCTAAT 57.751 34.615 10.84 0.00 36.11 1.73
82 83 7.652524 AGAAGATGTCTTAGATGTCAGCTAA 57.347 36.000 10.05 10.05 36.11 3.09
83 84 7.123397 ACAAGAAGATGTCTTAGATGTCAGCTA 59.877 37.037 0.00 0.00 45.25 3.32
84 85 6.070881 ACAAGAAGATGTCTTAGATGTCAGCT 60.071 38.462 0.00 0.00 45.25 4.24
85 86 6.105333 ACAAGAAGATGTCTTAGATGTCAGC 58.895 40.000 0.00 0.00 45.25 4.26
86 87 8.545229 AAACAAGAAGATGTCTTAGATGTCAG 57.455 34.615 0.00 0.00 45.25 3.51
87 88 8.908786 AAAACAAGAAGATGTCTTAGATGTCA 57.091 30.769 0.00 0.00 45.25 3.58
89 90 8.926710 CGTAAAACAAGAAGATGTCTTAGATGT 58.073 33.333 0.00 0.00 45.25 3.06
90 91 8.926710 ACGTAAAACAAGAAGATGTCTTAGATG 58.073 33.333 0.00 0.00 45.25 2.90
91 92 9.141400 GACGTAAAACAAGAAGATGTCTTAGAT 57.859 33.333 0.00 0.00 45.25 1.98
92 93 8.358148 AGACGTAAAACAAGAAGATGTCTTAGA 58.642 33.333 0.00 0.00 45.25 2.10
93 94 8.522178 AGACGTAAAACAAGAAGATGTCTTAG 57.478 34.615 0.00 0.00 45.25 2.18
94 95 8.882415 AAGACGTAAAACAAGAAGATGTCTTA 57.118 30.769 6.10 0.00 45.25 2.10
95 96 7.306632 CGAAGACGTAAAACAAGAAGATGTCTT 60.307 37.037 7.35 7.35 44.26 3.01
96 97 6.144080 CGAAGACGTAAAACAAGAAGATGTCT 59.856 38.462 0.00 0.00 35.83 3.41
97 98 6.143438 TCGAAGACGTAAAACAAGAAGATGTC 59.857 38.462 0.00 0.00 40.69 3.06
98 99 5.981315 TCGAAGACGTAAAACAAGAAGATGT 59.019 36.000 0.00 0.00 40.69 3.06
99 100 6.448053 TCGAAGACGTAAAACAAGAAGATG 57.552 37.500 0.00 0.00 40.69 2.90
100 101 7.653767 AATCGAAGACGTAAAACAAGAAGAT 57.346 32.000 0.00 0.00 42.51 2.40
101 102 7.223193 TCAAATCGAAGACGTAAAACAAGAAGA 59.777 33.333 0.00 0.00 42.51 2.87
102 103 7.342194 TCAAATCGAAGACGTAAAACAAGAAG 58.658 34.615 0.00 0.00 42.51 2.85
103 104 7.236674 TCAAATCGAAGACGTAAAACAAGAA 57.763 32.000 0.00 0.00 42.51 2.52
104 105 6.831727 TCAAATCGAAGACGTAAAACAAGA 57.168 33.333 0.00 0.00 42.51 3.02
105 106 9.250986 CTAATCAAATCGAAGACGTAAAACAAG 57.749 33.333 0.00 0.00 42.51 3.16
106 107 7.742963 GCTAATCAAATCGAAGACGTAAAACAA 59.257 33.333 0.00 0.00 42.51 2.83
107 108 7.095565 TGCTAATCAAATCGAAGACGTAAAACA 60.096 33.333 0.00 0.00 42.51 2.83
189 190 5.526506 ACTTAGGTCGTCAGTTTAACAGT 57.473 39.130 0.00 0.00 0.00 3.55
190 191 5.404667 GGAACTTAGGTCGTCAGTTTAACAG 59.595 44.000 0.00 0.00 30.71 3.16
191 192 5.069516 AGGAACTTAGGTCGTCAGTTTAACA 59.930 40.000 0.00 0.00 27.25 2.41
219 220 5.661312 TCTCCGGATGGGAATATAAGTATGG 59.339 44.000 3.57 0.00 46.61 2.74
258 259 2.028476 TCAAGTATCCGGTGTGTCCTTG 60.028 50.000 0.00 6.99 0.00 3.61
259 260 2.233922 CTCAAGTATCCGGTGTGTCCTT 59.766 50.000 0.00 0.00 0.00 3.36
290 291 8.730680 TCCTTTGCTGATAAATCTACAAACTTC 58.269 33.333 6.78 0.00 32.74 3.01
353 354 9.793259 TCAAGACACTCCTAATTGTAGAAAATT 57.207 29.630 0.00 0.00 34.24 1.82
372 377 5.104941 CCCGGATAGGCATATAATCAAGACA 60.105 44.000 0.73 0.00 39.21 3.41
373 378 5.360591 CCCGGATAGGCATATAATCAAGAC 58.639 45.833 0.73 0.00 39.21 3.01
374 379 5.614324 CCCGGATAGGCATATAATCAAGA 57.386 43.478 0.73 0.00 39.21 3.02
446 451 4.994471 CAGTGGCAGCTGCGTGGA 62.994 66.667 31.19 13.04 43.26 4.02
480 485 1.098050 GATTTTGCAGCTGGGTCGAT 58.902 50.000 17.12 0.00 0.00 3.59
482 487 0.962356 AGGATTTTGCAGCTGGGTCG 60.962 55.000 17.12 0.00 0.00 4.79
563 569 1.234615 CGGTGGTGGGATGTGTGTTC 61.235 60.000 0.00 0.00 0.00 3.18
587 593 2.787035 GGGAAGGGTGGATGGGTAATTA 59.213 50.000 0.00 0.00 0.00 1.40
599 605 3.400054 GGGGAGACGGGAAGGGTG 61.400 72.222 0.00 0.00 0.00 4.61
600 606 3.936566 TGGGGAGACGGGAAGGGT 61.937 66.667 0.00 0.00 0.00 4.34
643 649 1.674057 CTTTCGTGCAGAGGGACCT 59.326 57.895 0.00 0.00 30.51 3.85
703 709 0.746923 TACTAGAGCGCGCCAGAGAA 60.747 55.000 30.33 7.11 0.00 2.87
718 724 4.848086 GGGGGTTGCCTCCTATTTATACTA 59.152 45.833 0.00 0.00 42.03 1.82
803 1011 2.680352 GACGGGGAGAGCACTGGA 60.680 66.667 0.00 0.00 0.00 3.86
804 1012 2.681778 AGACGGGGAGAGCACTGG 60.682 66.667 0.00 0.00 0.00 4.00
806 1014 1.379309 GAGAGACGGGGAGAGCACT 60.379 63.158 0.00 0.00 0.00 4.40
813 1021 2.340673 GATCGGAGGAGAGACGGGGA 62.341 65.000 0.00 0.00 0.00 4.81
847 1057 1.462627 AGGGGAGGAAACAACGGGA 60.463 57.895 0.00 0.00 0.00 5.14
857 1067 1.306970 GAACGAGAGGAGGGGAGGA 59.693 63.158 0.00 0.00 0.00 3.71
880 1090 1.626654 CGGTAACTTCACAGCGCAGG 61.627 60.000 11.47 3.29 0.00 4.85
885 1097 1.429463 CAGGACGGTAACTTCACAGC 58.571 55.000 0.00 0.00 36.36 4.40
949 1161 9.958180 AAGAAATAAAAACAATTATTGGGAGGG 57.042 29.630 9.88 0.00 36.03 4.30
987 1201 6.271537 TGGGATATGTATGTATGTGGAGGAT 58.728 40.000 0.00 0.00 0.00 3.24
1030 1247 2.427245 AAGAGGAGCCGTCGATGGG 61.427 63.158 24.85 13.14 0.00 4.00
1078 1295 0.459899 TCAGCGACATATCAACGGCT 59.540 50.000 0.00 0.00 0.00 5.52
1195 1412 4.823732 TCTGGGGCTAGGGCTGGG 62.824 72.222 0.00 0.00 38.73 4.45
1213 1430 2.436646 TCGGCTTTAGCTGCAGGC 60.437 61.111 17.12 9.69 46.62 4.85
1214 1431 2.467826 GCTCGGCTTTAGCTGCAGG 61.468 63.158 17.12 0.00 46.62 4.85
1215 1432 3.096791 GCTCGGCTTTAGCTGCAG 58.903 61.111 10.11 10.11 46.62 4.41
1220 1437 0.673644 TTGGACAGCTCGGCTTTAGC 60.674 55.000 0.00 0.00 36.40 3.09
1260 1477 3.976701 TTCCCGGCTAGCAGCTTGC 62.977 63.158 19.41 19.41 45.46 4.01
1279 1499 2.203788 AGGAACTCGTGGGCCAGA 60.204 61.111 6.40 5.95 0.00 3.86
1423 1643 4.090588 TGGGCCCCGTTCGTCATC 62.091 66.667 22.27 0.00 0.00 2.92
1654 1881 4.320494 GCTAAGTACAACAGCAACAGCAAT 60.320 41.667 8.10 0.00 35.35 3.56
1723 1950 1.581934 ACACGCATGAATGATACGGG 58.418 50.000 0.00 0.00 0.00 5.28
2056 2327 6.561614 ACTACTACGAAACATACACAGATGG 58.438 40.000 0.00 0.00 0.00 3.51
2090 2361 5.277538 GGCACCACGTACTACTGTATACTAC 60.278 48.000 4.17 0.00 0.00 2.73
2125 2402 1.699083 TCACAACCAATGCCTCTCTGA 59.301 47.619 0.00 0.00 0.00 3.27
2185 2463 9.822185 GATCCAATAAACAAAATCTAAATGGCT 57.178 29.630 0.00 0.00 0.00 4.75
2237 2515 0.106149 GTCTGGAAACACGAGTGGGT 59.894 55.000 8.19 0.00 35.60 4.51
2239 2517 0.031585 TCGTCTGGAAACACGAGTGG 59.968 55.000 8.19 0.00 34.40 4.00
2240 2518 1.847818 TTCGTCTGGAAACACGAGTG 58.152 50.000 1.13 1.13 39.56 3.51
2241 2519 2.470821 CTTTCGTCTGGAAACACGAGT 58.529 47.619 0.00 0.00 39.56 4.18
2242 2520 1.192534 GCTTTCGTCTGGAAACACGAG 59.807 52.381 0.00 0.00 39.56 4.18
2327 2614 1.994916 CGCAAGGGCCAAAATACTTG 58.005 50.000 6.18 9.01 42.31 3.16
2329 2616 1.890174 GCGCAAGGGCCAAAATACT 59.110 52.632 6.18 0.00 36.38 2.12
2381 2668 3.058501 GCGATCCCCGTGTATTTAAATGG 60.059 47.826 11.05 3.34 41.15 3.16
2470 2757 1.522355 CACATTCGCATCGCCCTCT 60.522 57.895 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.