Multiple sequence alignment - TraesCS2D01G105600

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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 TraesCS2D01G105600 chr2D 100.000 2831 0 0 1 2831 57148514 57145684 0.000000e+00 5228
1 TraesCS2D01G105600 chr2D 75.867 692 115 27 1108 1774 23159947 23159283 3.540000e-79 305
2 TraesCS2D01G105600 chr2D 77.946 331 61 7 1429 1755 606198363 606198685 2.220000e-46 196
3 TraesCS2D01G105600 chr2A 86.318 2200 144 77 166 2255 58387039 58384887 0.000000e+00 2250
4 TraesCS2D01G105600 chr2B 89.008 1674 103 37 774 2407 90442243 90440611 0.000000e+00 1997
5 TraesCS2D01G105600 chr2B 94.250 400 22 1 2433 2831 90440376 90439977 6.700000e-171 610
6 TraesCS2D01G105600 chr2B 83.481 563 42 22 128 646 90444156 90443601 7.100000e-131 477
7 TraesCS2D01G105600 chr6A 77.132 551 88 22 1248 1774 578685830 578686366 4.620000e-73 285
8 TraesCS2D01G105600 chr1B 78.630 365 56 13 1417 1768 641140771 641140416 3.670000e-54 222
9 TraesCS2D01G105600 chr3B 84.234 222 31 2 1545 1763 57228585 57228365 2.210000e-51 213
10 TraesCS2D01G105600 chr3B 84.475 219 28 4 1543 1757 187530394 187530610 7.950000e-51 211
11 TraesCS2D01G105600 chr5D 78.614 332 61 4 1429 1757 26423793 26423469 7.950000e-51 211
12 TraesCS2D01G105600 chr5D 86.598 194 20 1 1562 1755 558941633 558941446 2.860000e-50 209
13 TraesCS2D01G105600 chr7B 74.933 375 71 15 1298 1663 584233982 584234342 1.760000e-32 150
14 TraesCS2D01G105600 chr5B 74.933 375 71 14 1298 1663 623106489 623106129 1.760000e-32 150
15 TraesCS2D01G105600 chr4D 78.733 221 35 7 1144 1362 488262357 488262147 1.370000e-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 TraesCS2D01G105600 chr2D 57145684 57148514 2830 True 5228 5228 100.000 1 2831 1 chr2D.!!$R2 2830
1 TraesCS2D01G105600 chr2D 23159283 23159947 664 True 305 305 75.867 1108 1774 1 chr2D.!!$R1 666
2 TraesCS2D01G105600 chr2A 58384887 58387039 2152 True 2250 2250 86.318 166 2255 1 chr2A.!!$R1 2089
3 TraesCS2D01G105600 chr2B 90439977 90444156 4179 True 1028 1997 88.913 128 2831 3 chr2B.!!$R1 2703
4 TraesCS2D01G105600 chr6A 578685830 578686366 536 False 285 285 77.132 1248 1774 1 chr6A.!!$F1 526

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
99 100 0.1078 ATGACTGGCTGCAGCACTAG 60.108 55.0 37.63 30.83 44.36 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 3295 1.001378 CGCCCCAAGAAACTTTCACAG 60.001 52.381 4.34 0.0 0.0 3.66 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
17 18 4.504596 TCCCCCATGCCACGATGC 62.505 66.667 0.00 0.00 0.00 3.91
18 19 4.818863 CCCCCATGCCACGATGCA 62.819 66.667 6.12 6.12 46.94 3.96
19 20 3.520862 CCCCATGCCACGATGCAC 61.521 66.667 5.80 0.00 45.48 4.57
20 21 3.879682 CCCATGCCACGATGCACG 61.880 66.667 5.80 7.07 45.48 5.34
21 22 4.541482 CCATGCCACGATGCACGC 62.541 66.667 5.80 0.00 45.48 5.34
22 23 4.874282 CATGCCACGATGCACGCG 62.874 66.667 3.53 3.53 45.48 6.01
25 26 4.580044 GCCACGATGCACGCGATG 62.580 66.667 15.93 8.90 46.94 3.84
26 27 3.928769 CCACGATGCACGCGATGG 61.929 66.667 15.93 14.85 46.94 3.51
27 28 2.885164 CACGATGCACGCGATGGA 60.885 61.111 15.93 9.47 46.94 3.41
28 29 2.583319 ACGATGCACGCGATGGAG 60.583 61.111 15.93 1.48 46.94 3.86
29 30 3.993234 CGATGCACGCGATGGAGC 61.993 66.667 15.93 10.82 34.51 4.70
72 73 4.511617 CGGAGCATCTAGAATTCTAGCA 57.488 45.455 30.07 21.23 44.24 3.49
73 74 4.484236 CGGAGCATCTAGAATTCTAGCAG 58.516 47.826 30.07 24.89 44.24 4.24
74 75 4.022416 CGGAGCATCTAGAATTCTAGCAGT 60.022 45.833 30.07 18.62 44.24 4.40
75 76 5.182190 CGGAGCATCTAGAATTCTAGCAGTA 59.818 44.000 30.07 17.69 44.24 2.74
76 77 6.620678 GGAGCATCTAGAATTCTAGCAGTAG 58.379 44.000 30.07 19.74 44.24 2.57
77 78 6.024552 AGCATCTAGAATTCTAGCAGTAGC 57.975 41.667 30.07 25.67 44.24 3.58
78 79 5.538053 AGCATCTAGAATTCTAGCAGTAGCA 59.462 40.000 30.07 16.15 44.24 3.49
79 80 5.863397 GCATCTAGAATTCTAGCAGTAGCAG 59.137 44.000 30.07 12.42 44.24 4.24
80 81 6.294453 GCATCTAGAATTCTAGCAGTAGCAGA 60.294 42.308 30.07 16.70 44.24 4.26
81 82 7.577426 GCATCTAGAATTCTAGCAGTAGCAGAT 60.577 40.741 30.07 17.96 44.24 2.90
82 83 7.213216 TCTAGAATTCTAGCAGTAGCAGATG 57.787 40.000 30.07 9.64 44.24 2.90
83 84 7.001073 TCTAGAATTCTAGCAGTAGCAGATGA 58.999 38.462 30.07 11.52 44.24 2.92
84 85 5.841810 AGAATTCTAGCAGTAGCAGATGAC 58.158 41.667 6.06 0.00 45.49 3.06
85 86 5.598005 AGAATTCTAGCAGTAGCAGATGACT 59.402 40.000 6.06 0.00 45.49 3.41
86 87 4.645762 TTCTAGCAGTAGCAGATGACTG 57.354 45.455 0.00 0.00 45.49 3.51
87 88 2.954989 TCTAGCAGTAGCAGATGACTGG 59.045 50.000 4.36 0.00 45.49 4.00
88 89 0.177604 AGCAGTAGCAGATGACTGGC 59.822 55.000 4.36 0.00 45.49 4.85
89 90 0.177604 GCAGTAGCAGATGACTGGCT 59.822 55.000 4.36 0.00 42.77 4.75
90 91 1.937278 CAGTAGCAGATGACTGGCTG 58.063 55.000 0.00 0.00 43.62 4.85
94 95 3.499050 CAGATGACTGGCTGCAGC 58.501 61.111 30.88 30.88 40.14 5.25
95 96 1.376812 CAGATGACTGGCTGCAGCA 60.377 57.895 37.63 23.01 44.36 4.41
96 97 1.376942 AGATGACTGGCTGCAGCAC 60.377 57.895 37.63 26.73 44.36 4.40
97 98 1.376942 GATGACTGGCTGCAGCACT 60.377 57.895 37.63 20.34 44.36 4.40
98 99 0.107993 GATGACTGGCTGCAGCACTA 60.108 55.000 37.63 22.57 44.36 2.74
99 100 0.107800 ATGACTGGCTGCAGCACTAG 60.108 55.000 37.63 30.83 44.36 2.57
100 101 2.046507 ACTGGCTGCAGCACTAGC 60.047 61.111 37.63 21.50 44.36 3.42
119 120 2.791383 CTAAGCTAGCTGTGCGATCT 57.209 50.000 20.16 1.78 35.28 2.75
120 121 2.660490 CTAAGCTAGCTGTGCGATCTC 58.340 52.381 20.16 0.00 35.28 2.75
121 122 1.110442 AAGCTAGCTGTGCGATCTCT 58.890 50.000 20.16 0.00 35.28 3.10
122 123 1.974265 AGCTAGCTGTGCGATCTCTA 58.026 50.000 18.57 0.00 35.28 2.43
123 124 2.302260 AGCTAGCTGTGCGATCTCTAA 58.698 47.619 18.57 0.00 35.28 2.10
124 125 2.034053 AGCTAGCTGTGCGATCTCTAAC 59.966 50.000 18.57 0.00 35.28 2.34
125 126 2.223595 GCTAGCTGTGCGATCTCTAACA 60.224 50.000 7.70 0.00 0.00 2.41
126 127 3.735208 GCTAGCTGTGCGATCTCTAACAA 60.735 47.826 7.70 0.00 0.00 2.83
145 146 2.715536 GGCTAACTAATTGCCCCCG 58.284 57.895 0.00 0.00 40.71 5.73
146 147 0.822121 GGCTAACTAATTGCCCCCGG 60.822 60.000 0.00 0.00 40.71 5.73
266 267 2.124151 ACCGAATCATGGCTGCCC 60.124 61.111 17.53 0.00 0.00 5.36
280 281 2.134630 CTGCCCCTGCCTCAAGAACT 62.135 60.000 0.00 0.00 36.33 3.01
281 282 0.840288 TGCCCCTGCCTCAAGAACTA 60.840 55.000 0.00 0.00 36.33 2.24
282 283 0.393132 GCCCCTGCCTCAAGAACTAC 60.393 60.000 0.00 0.00 0.00 2.73
283 284 0.108138 CCCCTGCCTCAAGAACTACG 60.108 60.000 0.00 0.00 0.00 3.51
298 299 6.639632 AGAACTACGTAGTAACTTGGTTCA 57.360 37.500 27.59 0.00 45.13 3.18
311 312 3.577415 ACTTGGTTCACACTCCTACCTAC 59.423 47.826 0.00 0.00 0.00 3.18
312 313 3.537795 TGGTTCACACTCCTACCTACT 57.462 47.619 0.00 0.00 0.00 2.57
313 314 4.662966 TGGTTCACACTCCTACCTACTA 57.337 45.455 0.00 0.00 0.00 1.82
315 316 4.768968 TGGTTCACACTCCTACCTACTAAC 59.231 45.833 0.00 0.00 0.00 2.34
316 317 4.159321 GGTTCACACTCCTACCTACTAACC 59.841 50.000 0.00 0.00 0.00 2.85
321 322 3.626670 CACTCCTACCTACTAACCACTCG 59.373 52.174 0.00 0.00 0.00 4.18
358 359 6.339730 TGTGAAGAAACTCATGTGCAAAAAT 58.660 32.000 0.00 0.00 0.00 1.82
367 387 2.810439 TGTGCAAAAATGCTGGGTAC 57.190 45.000 2.22 0.00 35.49 3.34
384 404 5.914033 TGGGTACAGACAATAATCAGTAGC 58.086 41.667 0.00 0.00 37.97 3.58
412 436 2.031870 GGCCTATGGTAAAAAGCTGGG 58.968 52.381 0.00 0.00 0.00 4.45
416 440 2.532250 ATGGTAAAAAGCTGGGGAGG 57.468 50.000 0.00 0.00 0.00 4.30
504 567 6.019762 CACATGTCTGTCGAATTCAAATCAG 58.980 40.000 6.22 7.81 31.62 2.90
515 578 5.339611 CGAATTCAAATCAGACGTTTTGACC 59.660 40.000 11.62 5.19 39.43 4.02
560 627 3.567579 TAGTCCGGGTCCGTCGGTT 62.568 63.158 11.88 0.56 46.82 4.44
596 663 2.124011 AATTGCGCACTTGACACAAG 57.876 45.000 11.12 9.51 0.00 3.16
603 670 2.537529 CGCACTTGACACAAGTTGACAG 60.538 50.000 10.54 1.60 31.27 3.51
607 674 4.072131 ACTTGACACAAGTTGACAGTGTT 58.928 39.130 10.54 0.00 45.65 3.32
640 707 6.645003 CACACAGTTTACAGCAGATGTTACTA 59.355 38.462 0.00 0.00 39.96 1.82
641 708 6.645415 ACACAGTTTACAGCAGATGTTACTAC 59.355 38.462 0.00 0.00 39.96 2.73
642 709 5.862323 ACAGTTTACAGCAGATGTTACTACG 59.138 40.000 0.00 0.00 39.96 3.51
643 710 4.863131 AGTTTACAGCAGATGTTACTACGC 59.137 41.667 0.00 0.00 39.96 4.42
644 711 4.443913 TTACAGCAGATGTTACTACGCA 57.556 40.909 0.00 0.00 39.96 5.24
645 712 3.313012 ACAGCAGATGTTACTACGCAA 57.687 42.857 0.00 0.00 39.96 4.85
646 713 3.861840 ACAGCAGATGTTACTACGCAAT 58.138 40.909 0.00 0.00 39.96 3.56
647 714 3.865745 ACAGCAGATGTTACTACGCAATC 59.134 43.478 0.00 0.00 39.96 2.67
648 715 4.115516 CAGCAGATGTTACTACGCAATCT 58.884 43.478 0.00 0.00 0.00 2.40
649 716 4.026228 CAGCAGATGTTACTACGCAATCTG 60.026 45.833 6.60 6.60 37.63 2.90
650 717 3.865745 GCAGATGTTACTACGCAATCTGT 59.134 43.478 11.41 0.00 37.11 3.41
651 718 4.259970 GCAGATGTTACTACGCAATCTGTG 60.260 45.833 11.41 0.00 37.11 3.66
672 739 1.063806 CACGCAAGACAGTGAGCTAC 58.936 55.000 0.00 0.00 40.56 3.58
673 740 0.387367 ACGCAAGACAGTGAGCTACG 60.387 55.000 0.00 4.61 43.62 3.51
674 741 1.678269 CGCAAGACAGTGAGCTACGC 61.678 60.000 0.00 0.17 43.02 4.42
678 748 2.738846 CAAGACAGTGAGCTACGCATTT 59.261 45.455 0.00 0.00 0.00 2.32
683 753 5.643777 AGACAGTGAGCTACGCATTTAAAAT 59.356 36.000 0.00 0.00 0.00 1.82
686 756 6.072728 ACAGTGAGCTACGCATTTAAAATGAA 60.073 34.615 0.00 0.00 0.00 2.57
692 762 7.090173 AGCTACGCATTTAAAATGAACAATGT 58.910 30.769 0.00 0.00 0.00 2.71
697 767 8.085296 ACGCATTTAAAATGAACAATGTAAGGA 58.915 29.630 0.00 0.00 0.00 3.36
798 2148 1.006832 GATTGTTATGTGACGCCGCT 58.993 50.000 0.00 0.00 0.00 5.52
917 2271 1.918293 CCAGCCTCCCCACTGTACA 60.918 63.158 0.00 0.00 31.76 2.90
918 2272 1.599047 CAGCCTCCCCACTGTACAG 59.401 63.158 21.44 21.44 0.00 2.74
970 2324 2.410466 GCTAGCTAGCGTGAGACCT 58.590 57.895 28.89 0.00 39.82 3.85
971 2325 0.309612 GCTAGCTAGCGTGAGACCTC 59.690 60.000 28.89 0.98 39.82 3.85
992 2351 4.803426 CCTGACGCCCTCTCGTGC 62.803 72.222 0.00 0.00 43.42 5.34
1028 2387 1.517832 CGGCCTCCTGGTTCTACAG 59.482 63.158 0.00 0.00 38.21 2.74
1291 2663 3.487764 TTCGACGTGGTCACCGTGG 62.488 63.158 0.00 0.00 38.92 4.94
1468 2849 2.579787 CGCGGCTCTACGTGAAGG 60.580 66.667 0.00 0.00 46.47 3.46
1862 3273 2.028484 ACGTGTGCCCGTGTACAG 59.972 61.111 0.00 0.00 40.08 2.74
1863 3274 2.028484 CGTGTGCCCGTGTACAGT 59.972 61.111 0.00 0.00 37.79 3.55
1884 3295 0.445043 GTACGAAAATGGCGGTGGTC 59.555 55.000 0.00 0.00 0.00 4.02
1901 3312 3.066760 GTGGTCTGTGAAAGTTTCTTGGG 59.933 47.826 16.33 5.01 0.00 4.12
2014 3432 1.372683 GGTGCTCTGCTCTGGTTCA 59.627 57.895 0.00 0.00 0.00 3.18
2017 3435 0.604780 TGCTCTGCTCTGGTTCAAGC 60.605 55.000 0.00 0.00 39.02 4.01
2043 3471 0.919300 CATCGATCGTGTGCTGTCTG 59.081 55.000 15.94 0.00 0.00 3.51
2044 3472 0.803768 ATCGATCGTGTGCTGTCTGC 60.804 55.000 15.94 0.00 43.25 4.26
2045 3473 1.445066 CGATCGTGTGCTGTCTGCT 60.445 57.895 7.03 0.00 43.37 4.24
2178 3620 2.421248 GGAGTACGGACTAGGTAGCTGT 60.421 54.545 0.00 0.55 35.45 4.40
2210 3661 1.205657 GCATATACGGTGTGACACGG 58.794 55.000 19.78 19.78 39.91 4.94
2234 3688 3.906998 TGCACATGTACAAAAATTCGGG 58.093 40.909 0.00 0.00 0.00 5.14
2242 3696 9.016438 ACATGTACAAAAATTCGGGTAAGTTAT 57.984 29.630 0.00 0.00 0.00 1.89
2243 3697 9.849166 CATGTACAAAAATTCGGGTAAGTTATT 57.151 29.630 0.00 0.00 0.00 1.40
2273 3727 2.126228 TTTCCTAGCGTGCGTCCG 60.126 61.111 0.00 0.00 0.00 4.79
2288 3742 1.356938 GTCCGACCGTTCTTTCCATC 58.643 55.000 0.00 0.00 0.00 3.51
2289 3743 1.067071 GTCCGACCGTTCTTTCCATCT 60.067 52.381 0.00 0.00 0.00 2.90
2290 3744 1.621814 TCCGACCGTTCTTTCCATCTT 59.378 47.619 0.00 0.00 0.00 2.40
2332 3786 9.516314 AAAGAAAAGAAGATAAAAAGAACGTGG 57.484 29.630 0.00 0.00 0.00 4.94
2333 3787 7.649057 AGAAAAGAAGATAAAAAGAACGTGGG 58.351 34.615 0.00 0.00 0.00 4.61
2342 3796 9.020731 AGATAAAAAGAACGTGGGATTTGTTAT 57.979 29.630 0.00 0.00 0.00 1.89
2363 3817 9.825109 TGTTATCTCCGTACAATAATTTGATCA 57.175 29.630 0.00 0.00 36.64 2.92
2378 3832 2.849942 TGATCAATACAAGGCATCCCG 58.150 47.619 0.00 0.00 35.76 5.14
2400 3854 5.472137 CCGGAAAGACAAGAAAATTCCACTA 59.528 40.000 0.00 0.00 39.59 2.74
2441 4104 0.035056 GTACAGCTGGGCATGAACCT 60.035 55.000 19.93 0.00 0.00 3.50
2477 4140 2.737039 GCACCCAAACGAAGCAAAAAGA 60.737 45.455 0.00 0.00 0.00 2.52
2511 4175 2.088178 GCAGCCGCAAAAACATCCG 61.088 57.895 0.00 0.00 38.36 4.18
2513 4177 0.454957 CAGCCGCAAAAACATCCGAG 60.455 55.000 0.00 0.00 0.00 4.63
2547 4211 2.844348 TGATCCCCAAGGGTTAGTCTTC 59.156 50.000 4.11 0.00 44.74 2.87
2550 4214 1.272807 CCCAAGGGTTAGTCTTCCGA 58.727 55.000 0.00 0.00 0.00 4.55
2564 4228 1.307355 TTCCGATGTCGACGCCACTA 61.307 55.000 11.62 0.00 43.02 2.74
2602 4266 4.878397 CACTATTGAAAAGAGCCGGAAGAT 59.122 41.667 5.05 0.00 39.15 2.40
2605 4269 2.977914 TGAAAAGAGCCGGAAGATGAG 58.022 47.619 5.05 0.00 0.00 2.90
2629 4293 2.128853 ATTGCCTTGACGCCAACACG 62.129 55.000 0.00 0.00 39.50 4.49
2639 4303 0.653323 CGCCAACACGAAGAAACACG 60.653 55.000 0.00 0.00 34.06 4.49
2695 4359 7.981225 GCAAACACCACCTATCAAATCAAATAT 59.019 33.333 0.00 0.00 0.00 1.28
2698 4362 6.486657 ACACCACCTATCAAATCAAATATCGG 59.513 38.462 0.00 0.00 0.00 4.18
2715 4379 1.691196 CGGTACCCGGGATAACTACA 58.309 55.000 32.02 0.00 44.15 2.74
2716 4380 2.242043 CGGTACCCGGGATAACTACAT 58.758 52.381 32.02 2.92 44.15 2.29
2725 4389 4.997395 CCGGGATAACTACATCTTTGATGG 59.003 45.833 11.55 0.00 0.00 3.51
2748 4412 5.300539 GGAAGATCCAAAGGAAGCTTATTCC 59.699 44.000 0.00 0.00 36.28 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.504596 GCATCGTGGCATGGGGGA 62.505 66.667 6.90 0.00 0.00 4.81
1 2 4.818863 TGCATCGTGGCATGGGGG 62.819 66.667 6.90 0.00 39.25 5.40
2 3 3.520862 GTGCATCGTGGCATGGGG 61.521 66.667 6.90 0.51 46.92 4.96
3 4 3.879682 CGTGCATCGTGGCATGGG 61.880 66.667 6.90 0.89 46.92 4.00
11 12 2.583319 CTCCATCGCGTGCATCGT 60.583 61.111 5.77 0.00 42.13 3.73
12 13 3.993234 GCTCCATCGCGTGCATCG 61.993 66.667 5.77 5.14 43.12 3.84
20 21 3.934684 GCAGCTTCGCTCCATCGC 61.935 66.667 0.00 0.00 36.40 4.58
21 22 2.510012 TGCAGCTTCGCTCCATCG 60.510 61.111 0.00 0.00 36.40 3.84
22 23 2.178890 CCTGCAGCTTCGCTCCATC 61.179 63.158 8.66 0.00 36.40 3.51
23 24 2.124819 CCTGCAGCTTCGCTCCAT 60.125 61.111 8.66 0.00 36.40 3.41
24 25 3.630013 ACCTGCAGCTTCGCTCCA 61.630 61.111 8.66 0.00 36.40 3.86
25 26 3.123620 CACCTGCAGCTTCGCTCC 61.124 66.667 8.66 0.00 36.40 4.70
26 27 3.797546 GCACCTGCAGCTTCGCTC 61.798 66.667 8.66 0.00 36.40 5.03
47 48 6.622146 CTAGAATTCTAGATGCTCCGCGCA 62.622 50.000 30.83 1.04 46.80 6.09
48 49 0.787183 GAATTCTAGATGCTCCGCGC 59.213 55.000 0.00 0.00 39.77 6.86
49 50 2.430546 AGAATTCTAGATGCTCCGCG 57.569 50.000 6.06 0.00 0.00 6.46
50 51 3.249917 GCTAGAATTCTAGATGCTCCGC 58.750 50.000 36.09 20.50 46.80 5.54
51 52 4.022416 ACTGCTAGAATTCTAGATGCTCCG 60.022 45.833 36.09 20.52 46.80 4.63
52 53 5.467035 ACTGCTAGAATTCTAGATGCTCC 57.533 43.478 36.09 21.71 46.80 4.70
53 54 6.092748 GCTACTGCTAGAATTCTAGATGCTC 58.907 44.000 36.09 22.29 46.80 4.26
54 55 5.538053 TGCTACTGCTAGAATTCTAGATGCT 59.462 40.000 36.09 20.70 46.80 3.79
55 56 5.777802 TGCTACTGCTAGAATTCTAGATGC 58.222 41.667 36.09 28.54 46.80 3.91
56 57 7.213216 TCTGCTACTGCTAGAATTCTAGATG 57.787 40.000 36.09 28.58 46.80 2.90
57 58 7.669304 TCATCTGCTACTGCTAGAATTCTAGAT 59.331 37.037 36.09 24.75 46.80 1.98
58 59 7.001073 TCATCTGCTACTGCTAGAATTCTAGA 58.999 38.462 36.09 23.02 46.80 2.43
59 60 7.040478 AGTCATCTGCTACTGCTAGAATTCTAG 60.040 40.741 30.38 30.38 46.63 2.43
60 61 6.775142 AGTCATCTGCTACTGCTAGAATTCTA 59.225 38.462 14.42 14.42 40.48 2.10
61 62 5.598005 AGTCATCTGCTACTGCTAGAATTCT 59.402 40.000 13.56 13.56 40.48 2.40
62 63 5.691305 CAGTCATCTGCTACTGCTAGAATTC 59.309 44.000 0.00 0.00 36.96 2.17
63 64 5.453057 CCAGTCATCTGCTACTGCTAGAATT 60.453 44.000 0.00 0.00 41.45 2.17
64 65 4.039004 CCAGTCATCTGCTACTGCTAGAAT 59.961 45.833 0.00 0.00 41.45 2.40
65 66 3.382865 CCAGTCATCTGCTACTGCTAGAA 59.617 47.826 0.00 0.00 41.45 2.10
66 67 2.954989 CCAGTCATCTGCTACTGCTAGA 59.045 50.000 0.00 0.00 41.45 2.43
67 68 2.545532 GCCAGTCATCTGCTACTGCTAG 60.546 54.545 0.00 0.00 41.45 3.42
68 69 1.410517 GCCAGTCATCTGCTACTGCTA 59.589 52.381 0.00 0.00 41.45 3.49
69 70 0.177604 GCCAGTCATCTGCTACTGCT 59.822 55.000 0.00 0.00 41.45 4.24
70 71 0.177604 AGCCAGTCATCTGCTACTGC 59.822 55.000 0.00 0.00 41.45 4.40
71 72 1.937278 CAGCCAGTCATCTGCTACTG 58.063 55.000 0.00 0.00 42.25 2.74
77 78 1.376812 TGCTGCAGCCAGTCATCTG 60.377 57.895 34.64 0.00 41.26 2.90
78 79 1.376942 GTGCTGCAGCCAGTCATCT 60.377 57.895 34.64 0.00 41.26 2.90
79 80 0.107993 TAGTGCTGCAGCCAGTCATC 60.108 55.000 34.64 15.66 41.26 2.92
80 81 0.107800 CTAGTGCTGCAGCCAGTCAT 60.108 55.000 34.64 16.32 41.26 3.06
81 82 1.294459 CTAGTGCTGCAGCCAGTCA 59.706 57.895 34.64 14.24 41.26 3.41
82 83 2.105466 GCTAGTGCTGCAGCCAGTC 61.105 63.158 34.64 21.24 41.26 3.51
83 84 2.046507 GCTAGTGCTGCAGCCAGT 60.047 61.111 34.64 25.16 41.26 4.00
100 101 2.293122 AGAGATCGCACAGCTAGCTTAG 59.707 50.000 16.46 11.72 0.00 2.18
101 102 2.302260 AGAGATCGCACAGCTAGCTTA 58.698 47.619 16.46 0.00 0.00 3.09
102 103 1.110442 AGAGATCGCACAGCTAGCTT 58.890 50.000 16.46 3.91 0.00 3.74
103 104 1.974265 TAGAGATCGCACAGCTAGCT 58.026 50.000 12.68 12.68 0.00 3.32
104 105 2.223595 TGTTAGAGATCGCACAGCTAGC 60.224 50.000 6.62 6.62 0.00 3.42
105 106 3.699779 TGTTAGAGATCGCACAGCTAG 57.300 47.619 0.00 0.00 0.00 3.42
106 107 3.181486 CCTTGTTAGAGATCGCACAGCTA 60.181 47.826 0.00 0.00 0.00 3.32
107 108 2.417924 CCTTGTTAGAGATCGCACAGCT 60.418 50.000 0.00 0.00 0.00 4.24
108 109 1.929836 CCTTGTTAGAGATCGCACAGC 59.070 52.381 0.00 0.00 0.00 4.40
109 110 1.929836 GCCTTGTTAGAGATCGCACAG 59.070 52.381 0.00 0.00 0.00 3.66
110 111 1.550524 AGCCTTGTTAGAGATCGCACA 59.449 47.619 0.00 0.00 0.00 4.57
111 112 2.301577 AGCCTTGTTAGAGATCGCAC 57.698 50.000 0.00 0.00 0.00 5.34
112 113 3.447586 AGTTAGCCTTGTTAGAGATCGCA 59.552 43.478 0.00 0.00 0.00 5.10
113 114 4.048241 AGTTAGCCTTGTTAGAGATCGC 57.952 45.455 0.00 0.00 0.00 4.58
114 115 7.306866 GCAATTAGTTAGCCTTGTTAGAGATCG 60.307 40.741 0.00 0.00 0.00 3.69
115 116 7.041712 GGCAATTAGTTAGCCTTGTTAGAGATC 60.042 40.741 0.00 0.00 44.92 2.75
116 117 6.768381 GGCAATTAGTTAGCCTTGTTAGAGAT 59.232 38.462 0.00 0.00 44.92 2.75
117 118 6.113411 GGCAATTAGTTAGCCTTGTTAGAGA 58.887 40.000 0.00 0.00 44.92 3.10
118 119 6.364945 GGCAATTAGTTAGCCTTGTTAGAG 57.635 41.667 0.00 0.00 44.92 2.43
163 164 0.529555 TCGCTTTGCTTTGGTTTGCC 60.530 50.000 0.00 0.00 0.00 4.52
164 165 1.258720 CTTCGCTTTGCTTTGGTTTGC 59.741 47.619 0.00 0.00 0.00 3.68
167 168 0.249447 GGCTTCGCTTTGCTTTGGTT 60.249 50.000 0.00 0.00 0.00 3.67
266 267 2.492484 ACTACGTAGTTCTTGAGGCAGG 59.508 50.000 22.45 0.00 37.78 4.85
280 281 5.278463 GGAGTGTGAACCAAGTTACTACGTA 60.278 44.000 0.00 0.00 0.00 3.57
281 282 4.500375 GGAGTGTGAACCAAGTTACTACGT 60.500 45.833 0.00 0.00 0.00 3.57
282 283 3.985925 GGAGTGTGAACCAAGTTACTACG 59.014 47.826 0.00 0.00 0.00 3.51
283 284 5.211174 AGGAGTGTGAACCAAGTTACTAC 57.789 43.478 0.00 0.00 0.00 2.73
298 299 4.598022 GAGTGGTTAGTAGGTAGGAGTGT 58.402 47.826 0.00 0.00 0.00 3.55
311 312 3.797184 GCAGGAGATAAGCGAGTGGTTAG 60.797 52.174 0.00 0.00 41.03 2.34
312 313 2.100916 GCAGGAGATAAGCGAGTGGTTA 59.899 50.000 0.00 0.00 41.85 2.85
313 314 1.134670 GCAGGAGATAAGCGAGTGGTT 60.135 52.381 0.00 0.00 39.56 3.67
315 316 0.749649 AGCAGGAGATAAGCGAGTGG 59.250 55.000 0.00 0.00 0.00 4.00
316 317 1.135915 ACAGCAGGAGATAAGCGAGTG 59.864 52.381 0.00 0.00 0.00 3.51
321 322 3.533606 TCTTCACAGCAGGAGATAAGC 57.466 47.619 0.00 0.00 0.00 3.09
358 359 4.225042 ACTGATTATTGTCTGTACCCAGCA 59.775 41.667 0.00 0.00 38.66 4.41
367 387 4.260375 GCAACGGCTACTGATTATTGTCTG 60.260 45.833 0.00 0.00 36.96 3.51
384 404 0.107410 TTACCATAGGCCTGCAACGG 60.107 55.000 17.99 10.78 0.00 4.44
397 417 1.716503 ACCTCCCCAGCTTTTTACCAT 59.283 47.619 0.00 0.00 0.00 3.55
446 497 0.752376 ATCGAAGACCGGGGAGAGAC 60.752 60.000 6.32 0.00 42.51 3.36
447 498 0.465824 GATCGAAGACCGGGGAGAGA 60.466 60.000 6.32 0.00 42.51 3.10
504 567 2.223409 GGTCCACAAAGGTCAAAACGTC 60.223 50.000 0.00 0.00 39.02 4.34
515 578 1.266718 CACGGAACATGGTCCACAAAG 59.733 52.381 29.00 14.76 37.56 2.77
560 627 5.725590 GCGCAATTATTTTACAGTAGCACGA 60.726 40.000 0.30 0.00 0.00 4.35
565 632 7.216317 GTCAAGTGCGCAATTATTTTACAGTAG 59.784 37.037 23.88 6.29 0.00 2.57
596 663 2.666022 GTGGCAAACAAACACTGTCAAC 59.334 45.455 0.00 0.00 37.23 3.18
603 670 2.362169 ACTGTGTGGCAAACAAACAC 57.638 45.000 12.36 4.33 42.37 3.32
607 674 3.674682 GCTGTAAACTGTGTGGCAAACAA 60.675 43.478 12.36 0.00 41.57 2.83
643 710 0.110056 GTCTTGCGTGGCACAGATTG 60.110 55.000 19.09 1.44 41.80 2.67
644 711 0.534877 TGTCTTGCGTGGCACAGATT 60.535 50.000 19.09 0.00 41.80 2.40
645 712 0.952497 CTGTCTTGCGTGGCACAGAT 60.952 55.000 19.09 0.00 41.80 2.90
646 713 1.595109 CTGTCTTGCGTGGCACAGA 60.595 57.895 19.09 10.24 41.80 3.41
647 714 1.889105 ACTGTCTTGCGTGGCACAG 60.889 57.895 19.09 11.48 41.80 3.66
648 715 2.179547 CACTGTCTTGCGTGGCACA 61.180 57.895 19.09 0.00 38.71 4.57
649 716 1.835483 CTCACTGTCTTGCGTGGCAC 61.835 60.000 7.79 7.79 38.71 5.01
650 717 1.595109 CTCACTGTCTTGCGTGGCA 60.595 57.895 0.00 0.00 36.47 4.92
651 718 2.959357 GCTCACTGTCTTGCGTGGC 61.959 63.158 0.00 0.00 0.00 5.01
652 719 0.038251 TAGCTCACTGTCTTGCGTGG 60.038 55.000 0.00 0.00 0.00 4.94
653 720 1.063806 GTAGCTCACTGTCTTGCGTG 58.936 55.000 0.00 0.00 0.00 5.34
672 739 8.459521 TCCTTACATTGTTCATTTTAAATGCG 57.540 30.769 12.39 0.67 34.13 4.73
673 740 9.638239 TCTCCTTACATTGTTCATTTTAAATGC 57.362 29.630 12.39 1.20 34.13 3.56
697 767 9.692325 ACCTCATGCTAAATCTATTTCTTTTCT 57.308 29.630 0.00 0.00 0.00 2.52
729 799 3.924686 CCGATTAGGATATCCCGAAAACG 59.075 47.826 18.56 17.96 45.00 3.60
763 2103 0.749454 AATCTGGCATCTGTTCCGGC 60.749 55.000 0.00 0.00 0.00 6.13
850 2200 1.259316 GCACTTTTTATGGCGCGAAG 58.741 50.000 12.10 4.90 0.00 3.79
925 2279 1.002033 CTCTGGCTTTGTGTTGCACTC 60.002 52.381 0.00 0.00 35.11 3.51
963 2317 1.967535 CGTCAGGCTTGAGGTCTCA 59.032 57.895 10.12 0.00 35.12 3.27
967 2321 4.021925 GGGCGTCAGGCTTGAGGT 62.022 66.667 18.22 0.00 40.46 3.85
968 2322 3.672295 GAGGGCGTCAGGCTTGAGG 62.672 68.421 13.63 13.63 42.94 3.86
969 2323 2.125350 GAGGGCGTCAGGCTTGAG 60.125 66.667 0.00 0.00 42.94 3.02
970 2324 2.604686 AGAGGGCGTCAGGCTTGA 60.605 61.111 10.15 0.00 42.94 3.02
971 2325 2.125350 GAGAGGGCGTCAGGCTTG 60.125 66.667 10.15 0.00 42.94 4.01
1270 2639 1.211969 CGGTGACCACGTCGAAGAT 59.788 57.895 5.05 0.00 40.67 2.40
1757 3153 4.717629 CGTCGTCGAGCCAGGCAA 62.718 66.667 15.80 0.00 39.71 4.52
1853 3264 4.560035 CCATTTTCGTACTACTGTACACGG 59.440 45.833 13.93 0.00 46.88 4.94
1861 3272 2.613691 CACCGCCATTTTCGTACTACT 58.386 47.619 0.00 0.00 0.00 2.57
1862 3273 1.662122 CCACCGCCATTTTCGTACTAC 59.338 52.381 0.00 0.00 0.00 2.73
1863 3274 1.275856 ACCACCGCCATTTTCGTACTA 59.724 47.619 0.00 0.00 0.00 1.82
1884 3295 1.001378 CGCCCCAAGAAACTTTCACAG 60.001 52.381 4.34 0.00 0.00 3.66
1999 3417 1.304509 GGCTTGAACCAGAGCAGAGC 61.305 60.000 0.00 0.00 40.63 4.09
2014 3432 3.258225 CGATCGATGAGAACGGCTT 57.742 52.632 10.26 0.00 40.78 4.35
2045 3473 4.579340 CGGCTACTCCTATCTGTAAAGACA 59.421 45.833 0.00 0.00 0.00 3.41
2178 3620 3.366985 CCGTATATGCGTAGATGCTTCCA 60.367 47.826 12.30 0.00 35.36 3.53
2210 3661 4.201608 CCGAATTTTTGTACATGTGCATGC 60.202 41.667 17.69 11.82 42.39 4.06
2242 3696 6.039047 CACGCTAGGAAAGGTACTATCAGTAA 59.961 42.308 0.00 0.00 38.49 2.24
2243 3697 5.530171 CACGCTAGGAAAGGTACTATCAGTA 59.470 44.000 0.00 0.00 38.49 2.74
2244 3698 4.338682 CACGCTAGGAAAGGTACTATCAGT 59.661 45.833 0.00 0.00 38.49 3.41
2309 3763 7.645402 TCCCACGTTCTTTTTATCTTCTTTTC 58.355 34.615 0.00 0.00 0.00 2.29
2311 3765 7.761038 ATCCCACGTTCTTTTTATCTTCTTT 57.239 32.000 0.00 0.00 0.00 2.52
2321 3775 6.072119 GGAGATAACAAATCCCACGTTCTTTT 60.072 38.462 0.00 0.00 0.00 2.27
2342 3796 9.825109 TGTATTGATCAAATTATTGTACGGAGA 57.175 29.630 13.09 0.00 37.79 3.71
2360 3814 1.774254 TCCGGGATGCCTTGTATTGAT 59.226 47.619 0.00 0.00 0.00 2.57
2363 3817 2.241176 TCTTTCCGGGATGCCTTGTATT 59.759 45.455 0.00 0.00 0.00 1.89
2373 3827 4.462834 GGAATTTTCTTGTCTTTCCGGGAT 59.537 41.667 0.00 0.00 0.00 3.85
2378 3832 9.594478 TTTTTAGTGGAATTTTCTTGTCTTTCC 57.406 29.630 0.00 0.00 37.06 3.13
2407 3861 4.996788 GCTGTACCTTAGCTGTACCTTA 57.003 45.455 9.61 0.00 38.21 2.69
2408 3862 3.889520 GCTGTACCTTAGCTGTACCTT 57.110 47.619 9.61 0.00 38.21 3.50
2441 4104 0.676184 GGTGCATATCGCTCTCCAGA 59.324 55.000 0.00 0.00 43.06 3.86
2477 4140 2.190578 GCGCCTAGATTGTGGCCT 59.809 61.111 3.32 0.00 45.90 5.19
2493 4157 2.088178 CGGATGTTTTTGCGGCTGC 61.088 57.895 11.65 11.65 43.20 5.25
2498 4162 0.878416 TTCCCTCGGATGTTTTTGCG 59.122 50.000 0.00 0.00 0.00 4.85
2547 4211 1.298413 CTAGTGGCGTCGACATCGG 60.298 63.158 17.16 0.00 40.29 4.18
2564 4228 1.705002 TAGTGGTGTTGTGGGCAGCT 61.705 55.000 0.00 0.00 35.60 4.24
2602 4266 2.013563 GCGTCAAGGCAATGATCCTCA 61.014 52.381 0.00 0.00 32.45 3.86
2605 4269 1.729881 GGCGTCAAGGCAATGATCC 59.270 57.895 0.00 0.00 45.92 3.36
2617 4281 0.653636 GTTTCTTCGTGTTGGCGTCA 59.346 50.000 0.00 0.00 0.00 4.35
2639 4303 1.073768 GTCCGAAGAGCGAGCAACTC 61.074 60.000 0.00 0.00 44.57 3.01
2650 4314 2.341101 GCCGTCTCAGGTCCGAAGA 61.341 63.158 0.00 0.00 0.00 2.87
2698 4362 5.069516 TCAAAGATGTAGTTATCCCGGGTAC 59.930 44.000 22.86 15.70 0.00 3.34
2725 4389 5.300539 GGGAATAAGCTTCCTTTGGATCTTC 59.699 44.000 0.00 0.00 38.61 2.87
2748 4412 1.672356 CTTCGGCTCCAACAGTGGG 60.672 63.158 0.00 0.00 46.01 4.61
2763 4427 3.381590 GGTCTTTGGTTATCCATGGCTTC 59.618 47.826 6.96 0.00 43.91 3.86


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

AutoCloner maintained by Alex Coulton.