Multiple sequence alignment - TraesCS6A01G066800

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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 TraesCS6A01G066800 chr6A 100.000 3155 0 0 1 3155 35582595 35579441 0.000000e+00 5827
1 TraesCS6A01G066800 chr6B 93.822 2347 95 25 811 3155 65175280 65172982 0.000000e+00 3485
2 TraesCS6A01G066800 chr6B 88.529 2066 207 14 1095 3155 15225632 15223592 0.000000e+00 2475
3 TraesCS6A01G066800 chr6B 85.825 1164 152 8 1412 2568 52573770 52572613 0.000000e+00 1223
4 TraesCS6A01G066800 chr6B 90.397 604 38 4 2553 3155 52572446 52571862 0.000000e+00 776
5 TraesCS6A01G066800 chr6B 85.102 443 52 12 172 603 65211555 65211116 1.040000e-119 440
6 TraesCS6A01G066800 chr6B 80.760 421 77 4 1754 2173 15298768 15298351 3.030000e-85 326
7 TraesCS6A01G066800 chr6B 78.156 499 66 18 2690 3155 14628142 14627654 8.620000e-71 278
8 TraesCS6A01G066800 chr6D 87.155 2172 251 11 988 3155 8894045 8896192 0.000000e+00 2440
9 TraesCS6A01G066800 chr6D 87.014 1748 198 12 1412 3155 8402243 8400521 0.000000e+00 1943
10 TraesCS6A01G066800 chr6D 84.464 1223 165 17 942 2156 8899468 8900673 0.000000e+00 1182
11 TraesCS6A01G066800 chr6D 81.046 1224 225 7 991 2211 8967575 8968794 0.000000e+00 968
12 TraesCS6A01G066800 chr6D 76.860 726 115 34 2214 2911 7654186 7654886 8.320000e-96 361
13 TraesCS6A01G066800 chr6D 77.427 443 54 16 2748 3155 7997563 7997132 4.100000e-54 222
14 TraesCS6A01G066800 chr1B 86.394 2249 254 25 932 3155 630644674 630646895 0.000000e+00 2410
15 TraesCS6A01G066800 chr1B 86.611 1546 177 13 1023 2566 630649577 630651094 0.000000e+00 1681
16 TraesCS6A01G066800 chr1B 87.862 552 31 15 2633 3155 630651115 630651659 1.610000e-172 616
17 TraesCS6A01G066800 chr3A 82.894 1251 194 15 953 2189 45938025 45936781 0.000000e+00 1107
18 TraesCS6A01G066800 chrUn 93.785 708 36 3 746 1452 101047633 101048333 0.000000e+00 1057
19 TraesCS6A01G066800 chrUn 90.791 695 59 4 56 746 101045197 101045890 0.000000e+00 924
20 TraesCS6A01G066800 chr3D 82.515 1201 203 4 994 2189 33330498 33329300 0.000000e+00 1048


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 TraesCS6A01G066800 chr6A 35579441 35582595 3154 True 5827.0 5827 100.000000 1 3155 1 chr6A.!!$R1 3154
1 TraesCS6A01G066800 chr6B 65172982 65175280 2298 True 3485.0 3485 93.822000 811 3155 1 chr6B.!!$R4 2344
2 TraesCS6A01G066800 chr6B 15223592 15225632 2040 True 2475.0 2475 88.529000 1095 3155 1 chr6B.!!$R2 2060
3 TraesCS6A01G066800 chr6B 52571862 52573770 1908 True 999.5 1223 88.111000 1412 3155 2 chr6B.!!$R6 1743
4 TraesCS6A01G066800 chr6D 8400521 8402243 1722 True 1943.0 1943 87.014000 1412 3155 1 chr6D.!!$R2 1743
5 TraesCS6A01G066800 chr6D 8894045 8900673 6628 False 1811.0 2440 85.809500 942 3155 2 chr6D.!!$F3 2213
6 TraesCS6A01G066800 chr6D 8967575 8968794 1219 False 968.0 968 81.046000 991 2211 1 chr6D.!!$F2 1220
7 TraesCS6A01G066800 chr6D 7654186 7654886 700 False 361.0 361 76.860000 2214 2911 1 chr6D.!!$F1 697
8 TraesCS6A01G066800 chr1B 630644674 630651659 6985 False 1569.0 2410 86.955667 932 3155 3 chr1B.!!$F1 2223
9 TraesCS6A01G066800 chr3A 45936781 45938025 1244 True 1107.0 1107 82.894000 953 2189 1 chr3A.!!$R1 1236
10 TraesCS6A01G066800 chrUn 101045197 101048333 3136 False 990.5 1057 92.288000 56 1452 2 chrUn.!!$F1 1396
11 TraesCS6A01G066800 chr3D 33329300 33330498 1198 True 1048.0 1048 82.515000 994 2189 1 chr3D.!!$R1 1195

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
623 627 0.178068 ATCATCTTTGACGGGTCGGG 59.822 55.0 0.00 0.0 33.85 5.14 F
1125 2898 0.396695 TCCCGAACCCTAGCTTCGAT 60.397 55.0 17.76 0.0 42.57 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 3548 0.900421 TCAGCATCTGACCACCTGAG 59.100 55.0 0.00 0.0 35.39 3.35 R
3096 5108 0.251653 ACCCAGTGGCTCTCGAACTA 60.252 55.0 2.61 0.0 33.59 2.24 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
23 24 6.673154 GACCACAAATACCTACATAACACC 57.327 41.667 0.00 0.00 0.00 4.16
24 25 6.129414 ACCACAAATACCTACATAACACCA 57.871 37.500 0.00 0.00 0.00 4.17
25 26 5.941647 ACCACAAATACCTACATAACACCAC 59.058 40.000 0.00 0.00 0.00 4.16
26 27 6.177610 CCACAAATACCTACATAACACCACT 58.822 40.000 0.00 0.00 0.00 4.00
27 28 6.315393 CCACAAATACCTACATAACACCACTC 59.685 42.308 0.00 0.00 0.00 3.51
28 29 6.315393 CACAAATACCTACATAACACCACTCC 59.685 42.308 0.00 0.00 0.00 3.85
29 30 6.214819 ACAAATACCTACATAACACCACTCCT 59.785 38.462 0.00 0.00 0.00 3.69
30 31 7.400915 ACAAATACCTACATAACACCACTCCTA 59.599 37.037 0.00 0.00 0.00 2.94
31 32 7.983166 AATACCTACATAACACCACTCCTAA 57.017 36.000 0.00 0.00 0.00 2.69
32 33 8.562949 AATACCTACATAACACCACTCCTAAT 57.437 34.615 0.00 0.00 0.00 1.73
33 34 9.664777 AATACCTACATAACACCACTCCTAATA 57.335 33.333 0.00 0.00 0.00 0.98
34 35 7.357429 ACCTACATAACACCACTCCTAATAC 57.643 40.000 0.00 0.00 0.00 1.89
35 36 7.130775 ACCTACATAACACCACTCCTAATACT 58.869 38.462 0.00 0.00 0.00 2.12
36 37 7.287235 ACCTACATAACACCACTCCTAATACTC 59.713 40.741 0.00 0.00 0.00 2.59
37 38 7.287005 CCTACATAACACCACTCCTAATACTCA 59.713 40.741 0.00 0.00 0.00 3.41
38 39 7.113658 ACATAACACCACTCCTAATACTCAG 57.886 40.000 0.00 0.00 0.00 3.35
39 40 4.473477 AACACCACTCCTAATACTCAGC 57.527 45.455 0.00 0.00 0.00 4.26
40 41 3.441101 ACACCACTCCTAATACTCAGCA 58.559 45.455 0.00 0.00 0.00 4.41
41 42 4.033709 ACACCACTCCTAATACTCAGCAT 58.966 43.478 0.00 0.00 0.00 3.79
42 43 5.208890 ACACCACTCCTAATACTCAGCATA 58.791 41.667 0.00 0.00 0.00 3.14
43 44 5.069251 ACACCACTCCTAATACTCAGCATAC 59.931 44.000 0.00 0.00 0.00 2.39
44 45 5.069119 CACCACTCCTAATACTCAGCATACA 59.931 44.000 0.00 0.00 0.00 2.29
45 46 5.661312 ACCACTCCTAATACTCAGCATACAA 59.339 40.000 0.00 0.00 0.00 2.41
46 47 6.156256 ACCACTCCTAATACTCAGCATACAAA 59.844 38.462 0.00 0.00 0.00 2.83
47 48 7.147479 ACCACTCCTAATACTCAGCATACAAAT 60.147 37.037 0.00 0.00 0.00 2.32
48 49 8.367911 CCACTCCTAATACTCAGCATACAAATA 58.632 37.037 0.00 0.00 0.00 1.40
49 50 9.935241 CACTCCTAATACTCAGCATACAAATAT 57.065 33.333 0.00 0.00 0.00 1.28
62 63 8.972349 CAGCATACAAATATATCTACCATAGCG 58.028 37.037 0.00 0.00 0.00 4.26
63 64 8.144478 AGCATACAAATATATCTACCATAGCGG 58.856 37.037 0.00 0.00 42.50 5.52
73 74 2.967076 CATAGCGGCGCGGAACAT 60.967 61.111 27.59 10.56 0.00 2.71
81 82 3.186047 CGCGGAACATCGACACCC 61.186 66.667 0.00 0.00 0.00 4.61
102 103 1.005867 TACGGCCGAGGAAACACAC 60.006 57.895 35.90 0.00 0.00 3.82
114 115 2.427506 GAAACACACTCCATCTCCACC 58.572 52.381 0.00 0.00 0.00 4.61
122 123 2.248686 ACTCCATCTCCACCTCCTACAT 59.751 50.000 0.00 0.00 0.00 2.29
123 124 3.310954 ACTCCATCTCCACCTCCTACATT 60.311 47.826 0.00 0.00 0.00 2.71
147 148 1.593750 GATCTAGCAGCACCAGCCG 60.594 63.158 0.00 0.00 43.56 5.52
166 167 0.826715 GAGCCTCTATCACCAGCACA 59.173 55.000 0.00 0.00 0.00 4.57
175 176 4.954970 ACCAGCACACCAAGGCCG 62.955 66.667 0.00 0.00 0.00 6.13
176 177 4.954970 CCAGCACACCAAGGCCGT 62.955 66.667 0.00 0.00 0.00 5.68
192 193 1.063006 CGTCGGCATTGGAAGCATG 59.937 57.895 0.00 0.00 0.00 4.06
195 196 1.065273 CGGCATTGGAAGCATGAGC 59.935 57.895 0.00 0.00 42.56 4.26
214 215 1.271054 GCTGATCACACAACTCCAGGT 60.271 52.381 0.00 0.00 0.00 4.00
233 236 2.276116 GGACAGGACCTGCTCGACA 61.276 63.158 21.95 0.00 34.37 4.35
234 237 1.608717 GGACAGGACCTGCTCGACAT 61.609 60.000 21.95 0.00 34.37 3.06
237 240 0.247460 CAGGACCTGCTCGACATTGA 59.753 55.000 8.99 0.00 0.00 2.57
242 245 1.019673 CCTGCTCGACATTGAATGGG 58.980 55.000 10.27 1.27 33.60 4.00
248 251 3.282021 CTCGACATTGAATGGGTCCAAT 58.718 45.455 10.27 0.00 33.66 3.16
255 258 3.541242 TGAATGGGTCCAATTCCAGTT 57.459 42.857 15.36 0.00 36.38 3.16
258 261 4.044065 TGAATGGGTCCAATTCCAGTTAGT 59.956 41.667 15.36 0.00 36.38 2.24
260 263 5.994416 ATGGGTCCAATTCCAGTTAGTAT 57.006 39.130 0.00 0.00 36.38 2.12
264 267 4.443034 GGTCCAATTCCAGTTAGTATCGCT 60.443 45.833 0.00 0.00 0.00 4.93
271 274 2.616960 CAGTTAGTATCGCTGCCAACA 58.383 47.619 0.00 0.00 0.00 3.33
274 277 4.094887 CAGTTAGTATCGCTGCCAACAAAT 59.905 41.667 0.00 0.00 0.00 2.32
342 345 2.193536 AAAGGACCGCACAACAGCC 61.194 57.895 0.00 0.00 0.00 4.85
344 347 2.902423 AAGGACCGCACAACAGCCAA 62.902 55.000 0.00 0.00 0.00 4.52
372 375 3.566853 CCGCTCGCGCAATGTCAT 61.567 61.111 8.75 0.00 38.24 3.06
383 386 2.076100 GCAATGTCATCTGGTCGAACA 58.924 47.619 1.69 1.69 0.00 3.18
396 399 2.582978 GAACACCGCTACCCCTCC 59.417 66.667 0.00 0.00 0.00 4.30
402 405 3.849951 CGCTACCCCTCCGCACAT 61.850 66.667 0.00 0.00 0.00 3.21
440 443 2.587194 CATCGGCGCCTTCTGGAG 60.587 66.667 26.68 6.92 36.16 3.86
458 461 1.210204 AGGACCATCATGCACCACCT 61.210 55.000 0.00 0.00 0.00 4.00
459 462 0.546122 GGACCATCATGCACCACCTA 59.454 55.000 0.00 0.00 0.00 3.08
460 463 1.143684 GGACCATCATGCACCACCTAT 59.856 52.381 0.00 0.00 0.00 2.57
461 464 2.498167 GACCATCATGCACCACCTATC 58.502 52.381 0.00 0.00 0.00 2.08
462 465 2.105477 GACCATCATGCACCACCTATCT 59.895 50.000 0.00 0.00 0.00 1.98
470 474 5.425217 TCATGCACCACCTATCTTCTTCTAA 59.575 40.000 0.00 0.00 0.00 2.10
494 498 1.408405 CCAATCATGCTCCACTGCTCT 60.408 52.381 0.00 0.00 0.00 4.09
514 518 4.148825 GCTCTCCCCGTCGTGCAT 62.149 66.667 0.00 0.00 0.00 3.96
623 627 0.178068 ATCATCTTTGACGGGTCGGG 59.822 55.000 0.00 0.00 33.85 5.14
625 629 2.589157 ATCTTTGACGGGTCGGGCA 61.589 57.895 0.00 0.00 0.00 5.36
678 682 2.575993 CTGTGAGCACGGGAGGAG 59.424 66.667 0.00 0.00 34.12 3.69
689 693 2.726351 GGGAGGAGGGTCTTGAGCG 61.726 68.421 0.00 0.00 0.00 5.03
751 2498 2.514803 CGGTGGAGATGGGAACTTTTT 58.485 47.619 0.00 0.00 0.00 1.94
759 2506 8.147704 GTGGAGATGGGAACTTTTTATTTTCAA 58.852 33.333 0.00 0.00 0.00 2.69
809 2556 9.558648 TGAATGTATTTTCACATTTCGAATCTG 57.441 29.630 0.00 2.51 46.53 2.90
907 2655 3.030291 AGATCAGAGATCAGACCACACC 58.970 50.000 9.43 0.00 0.00 4.16
913 2668 3.589654 ATCAGACCACACCCACGCG 62.590 63.158 3.53 3.53 0.00 6.01
1125 2898 0.396695 TCCCGAACCCTAGCTTCGAT 60.397 55.000 17.76 0.00 42.57 3.59
1463 3237 0.830444 TACCACCTGCACCTCTTCGT 60.830 55.000 0.00 0.00 0.00 3.85
1558 3332 0.885196 GCCCAATGTTGCGTTCCTTA 59.115 50.000 0.00 0.00 0.00 2.69
1645 3419 1.533469 AAGCTTAGAGTGCGTCCGGT 61.533 55.000 0.00 0.00 35.28 5.28
1732 3506 3.730761 CTGTTGCACGCCTCAGCC 61.731 66.667 0.00 0.00 34.57 4.85
1774 3548 2.161211 GTGGAGCACTTGAAGAAGATGC 59.839 50.000 0.00 0.00 36.90 3.91
1855 3629 0.610174 TTCTAGTGACAGGCTGCAGG 59.390 55.000 17.12 0.73 0.00 4.85
1917 3691 0.877071 CATACATTGCTCATCGGCCC 59.123 55.000 0.00 0.00 0.00 5.80
2021 3795 8.333984 TCTAGATCATGACCGGGACTATTATAA 58.666 37.037 6.32 0.00 0.00 0.98
2025 3799 7.092137 TCATGACCGGGACTATTATAATACG 57.908 40.000 6.32 4.09 0.00 3.06
2174 3948 1.276622 ACCAAGAACGGGCTATGAGT 58.723 50.000 0.00 0.00 0.00 3.41
2262 4036 4.438744 CGGTGTTCTTTGCCTAATTGGATC 60.439 45.833 0.00 0.00 38.35 3.36
2273 4047 4.336713 GCCTAATTGGATCTTGGTTGTCTC 59.663 45.833 0.00 0.00 38.35 3.36
2279 4053 4.624913 TGGATCTTGGTTGTCTCCTCTAT 58.375 43.478 0.00 0.00 0.00 1.98
2312 4086 6.479001 GGTACATGTCAATTTAGTGTCGCTAT 59.521 38.462 0.00 0.00 0.00 2.97
2470 4247 5.958380 AGTGTGTGAGATCAGGGTATTTCTA 59.042 40.000 0.00 0.00 0.00 2.10
2630 4616 5.791336 AGTCTCAAAATTTCCCTTTGGAC 57.209 39.130 0.00 0.00 41.57 4.02
2797 4798 8.798859 AAGATATTGACTGTACAAGAAAGCAT 57.201 30.769 0.00 0.00 33.22 3.79
2985 4997 7.513371 TTTTTATCACCTTTCGAAAGCCTTA 57.487 32.000 28.68 15.39 34.69 2.69
2986 4998 7.696992 TTTTATCACCTTTCGAAAGCCTTAT 57.303 32.000 28.68 20.06 34.69 1.73
2987 4999 8.795842 TTTTATCACCTTTCGAAAGCCTTATA 57.204 30.769 28.68 19.23 34.69 0.98
2988 5000 8.795842 TTTATCACCTTTCGAAAGCCTTATAA 57.204 30.769 28.68 22.65 34.69 0.98
3040 5052 4.677182 AGATAGGCCATGTTGTTTCCTTT 58.323 39.130 5.01 0.00 0.00 3.11
3096 5108 3.779444 TCTGGATGACTGTTAGGACTGT 58.221 45.455 0.00 0.00 40.18 3.55
3144 5156 2.028130 TGCCACACAAGTAAAACCCAG 58.972 47.619 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.093082 GTGGTGTTATGTAGGTATTTGTGGTC 59.907 42.308 0.00 0.00 0.00 4.02
1 2 5.941647 GTGGTGTTATGTAGGTATTTGTGGT 59.058 40.000 0.00 0.00 0.00 4.16
2 3 6.177610 AGTGGTGTTATGTAGGTATTTGTGG 58.822 40.000 0.00 0.00 0.00 4.17
5 6 6.650120 AGGAGTGGTGTTATGTAGGTATTTG 58.350 40.000 0.00 0.00 0.00 2.32
6 7 6.886178 AGGAGTGGTGTTATGTAGGTATTT 57.114 37.500 0.00 0.00 0.00 1.40
7 8 7.983166 TTAGGAGTGGTGTTATGTAGGTATT 57.017 36.000 0.00 0.00 0.00 1.89
8 9 9.086758 GTATTAGGAGTGGTGTTATGTAGGTAT 57.913 37.037 0.00 0.00 0.00 2.73
10 11 7.130775 AGTATTAGGAGTGGTGTTATGTAGGT 58.869 38.462 0.00 0.00 0.00 3.08
11 12 7.287005 TGAGTATTAGGAGTGGTGTTATGTAGG 59.713 40.741 0.00 0.00 0.00 3.18
12 13 8.234136 TGAGTATTAGGAGTGGTGTTATGTAG 57.766 38.462 0.00 0.00 0.00 2.74
13 14 7.201884 GCTGAGTATTAGGAGTGGTGTTATGTA 60.202 40.741 0.00 0.00 0.00 2.29
14 15 6.407074 GCTGAGTATTAGGAGTGGTGTTATGT 60.407 42.308 0.00 0.00 0.00 2.29
15 16 5.986135 GCTGAGTATTAGGAGTGGTGTTATG 59.014 44.000 0.00 0.00 0.00 1.90
16 17 5.661312 TGCTGAGTATTAGGAGTGGTGTTAT 59.339 40.000 0.00 0.00 0.00 1.89
17 18 5.020795 TGCTGAGTATTAGGAGTGGTGTTA 58.979 41.667 0.00 0.00 0.00 2.41
18 19 3.838317 TGCTGAGTATTAGGAGTGGTGTT 59.162 43.478 0.00 0.00 0.00 3.32
19 20 3.441101 TGCTGAGTATTAGGAGTGGTGT 58.559 45.455 0.00 0.00 0.00 4.16
20 21 4.679373 ATGCTGAGTATTAGGAGTGGTG 57.321 45.455 0.00 0.00 0.00 4.17
21 22 5.208890 TGTATGCTGAGTATTAGGAGTGGT 58.791 41.667 0.00 0.00 0.00 4.16
22 23 5.791336 TGTATGCTGAGTATTAGGAGTGG 57.209 43.478 0.00 0.00 0.00 4.00
23 24 9.935241 ATATTTGTATGCTGAGTATTAGGAGTG 57.065 33.333 0.00 0.00 0.00 3.51
36 37 8.972349 CGCTATGGTAGATATATTTGTATGCTG 58.028 37.037 0.00 0.00 0.00 4.41
37 38 8.144478 CCGCTATGGTAGATATATTTGTATGCT 58.856 37.037 0.00 0.00 0.00 3.79
38 39 7.095607 GCCGCTATGGTAGATATATTTGTATGC 60.096 40.741 0.00 0.00 41.21 3.14
39 40 7.114953 CGCCGCTATGGTAGATATATTTGTATG 59.885 40.741 0.00 0.00 41.21 2.39
40 41 7.145985 CGCCGCTATGGTAGATATATTTGTAT 58.854 38.462 0.00 0.00 41.21 2.29
41 42 6.500910 CGCCGCTATGGTAGATATATTTGTA 58.499 40.000 0.00 0.00 41.21 2.41
42 43 5.348986 CGCCGCTATGGTAGATATATTTGT 58.651 41.667 0.00 0.00 41.21 2.83
43 44 4.209288 GCGCCGCTATGGTAGATATATTTG 59.791 45.833 0.00 0.00 41.21 2.32
44 45 4.369182 GCGCCGCTATGGTAGATATATTT 58.631 43.478 0.00 0.00 41.21 1.40
45 46 3.550233 CGCGCCGCTATGGTAGATATATT 60.550 47.826 7.78 0.00 41.21 1.28
46 47 2.031069 CGCGCCGCTATGGTAGATATAT 60.031 50.000 7.78 0.00 41.21 0.86
47 48 1.332686 CGCGCCGCTATGGTAGATATA 59.667 52.381 7.78 0.00 41.21 0.86
48 49 0.100682 CGCGCCGCTATGGTAGATAT 59.899 55.000 7.78 0.00 41.21 1.63
49 50 1.504900 CGCGCCGCTATGGTAGATA 59.495 57.895 7.78 0.00 41.21 1.98
50 51 2.258591 CGCGCCGCTATGGTAGAT 59.741 61.111 7.78 0.00 41.21 1.98
51 52 3.973516 CCGCGCCGCTATGGTAGA 61.974 66.667 7.78 0.00 41.21 2.59
52 53 3.493830 TTCCGCGCCGCTATGGTAG 62.494 63.158 7.78 0.00 41.21 3.18
53 54 3.529314 TTCCGCGCCGCTATGGTA 61.529 61.111 7.78 0.00 41.21 3.25
56 57 2.943345 GATGTTCCGCGCCGCTATG 61.943 63.158 7.78 0.00 0.00 2.23
57 58 2.661866 GATGTTCCGCGCCGCTAT 60.662 61.111 7.78 0.00 0.00 2.97
62 63 3.849953 GTGTCGATGTTCCGCGCC 61.850 66.667 0.00 0.00 0.00 6.53
63 64 3.849953 GGTGTCGATGTTCCGCGC 61.850 66.667 0.00 0.00 0.00 6.86
73 74 3.376078 GGCCGTACAGGGTGTCGA 61.376 66.667 0.00 0.00 41.48 4.20
81 82 1.012486 GTGTTTCCTCGGCCGTACAG 61.012 60.000 27.15 15.59 0.00 2.74
102 103 2.461300 TGTAGGAGGTGGAGATGGAG 57.539 55.000 0.00 0.00 0.00 3.86
114 115 4.202295 TGCTAGATCTTGCCAATGTAGGAG 60.202 45.833 23.51 1.67 0.00 3.69
122 123 1.679944 GGTGCTGCTAGATCTTGCCAA 60.680 52.381 23.51 7.70 0.00 4.52
123 124 0.107508 GGTGCTGCTAGATCTTGCCA 60.108 55.000 23.51 13.83 0.00 4.92
147 148 0.826715 TGTGCTGGTGATAGAGGCTC 59.173 55.000 6.34 6.34 0.00 4.70
175 176 0.379669 CTCATGCTTCCAATGCCGAC 59.620 55.000 0.00 0.00 0.00 4.79
176 177 1.378882 GCTCATGCTTCCAATGCCGA 61.379 55.000 0.00 0.00 36.03 5.54
192 193 2.344950 CTGGAGTTGTGTGATCAGCTC 58.655 52.381 0.00 0.00 42.25 4.09
195 196 2.420642 CACCTGGAGTTGTGTGATCAG 58.579 52.381 0.00 0.00 0.00 2.90
198 199 1.072331 GTCCACCTGGAGTTGTGTGAT 59.928 52.381 0.00 0.00 46.49 3.06
214 215 2.117423 TCGAGCAGGTCCTGTCCA 59.883 61.111 20.24 3.09 33.43 4.02
233 236 4.065214 ACTGGAATTGGACCCATTCAAT 57.935 40.909 17.62 2.51 35.37 2.57
234 237 3.541242 ACTGGAATTGGACCCATTCAA 57.459 42.857 17.62 7.73 0.00 2.69
237 240 4.675063 ACTAACTGGAATTGGACCCATT 57.325 40.909 0.00 0.00 0.00 3.16
242 245 4.508124 CAGCGATACTAACTGGAATTGGAC 59.492 45.833 0.00 0.00 0.00 4.02
248 251 1.828595 TGGCAGCGATACTAACTGGAA 59.171 47.619 0.00 0.00 31.94 3.53
255 258 3.625764 GGAATTTGTTGGCAGCGATACTA 59.374 43.478 0.00 0.00 0.00 1.82
258 261 1.748493 GGGAATTTGTTGGCAGCGATA 59.252 47.619 0.00 0.00 0.00 2.92
260 263 1.861542 CGGGAATTTGTTGGCAGCGA 61.862 55.000 0.00 0.00 0.00 4.93
264 267 1.365633 GTGCGGGAATTTGTTGGCA 59.634 52.632 0.00 0.00 0.00 4.92
271 274 3.747976 GCTGCGGTGCGGGAATTT 61.748 61.111 0.00 0.00 35.15 1.82
369 372 1.080093 GCGGTGTTCGACCAGATGA 60.080 57.895 0.00 0.00 46.55 2.92
372 375 1.582968 GTAGCGGTGTTCGACCAGA 59.417 57.895 0.00 0.00 46.55 3.86
417 420 3.969250 GAAGGCGCCGATGTGGGAA 62.969 63.158 23.20 0.00 38.63 3.97
420 423 3.197790 CAGAAGGCGCCGATGTGG 61.198 66.667 23.20 6.11 42.50 4.17
440 443 0.546122 TAGGTGGTGCATGATGGTCC 59.454 55.000 0.00 0.00 0.00 4.46
448 451 5.426833 AGTTAGAAGAAGATAGGTGGTGCAT 59.573 40.000 0.00 0.00 0.00 3.96
458 461 7.071698 AGCATGATTGGGAGTTAGAAGAAGATA 59.928 37.037 0.00 0.00 0.00 1.98
459 462 6.060788 GCATGATTGGGAGTTAGAAGAAGAT 58.939 40.000 0.00 0.00 0.00 2.40
460 463 5.190528 AGCATGATTGGGAGTTAGAAGAAGA 59.809 40.000 0.00 0.00 0.00 2.87
461 464 5.435291 AGCATGATTGGGAGTTAGAAGAAG 58.565 41.667 0.00 0.00 0.00 2.85
462 465 5.431765 GAGCATGATTGGGAGTTAGAAGAA 58.568 41.667 0.00 0.00 0.00 2.52
470 474 1.064906 CAGTGGAGCATGATTGGGAGT 60.065 52.381 0.00 0.00 0.00 3.85
494 498 3.680786 CACGACGGGGAGAGCACA 61.681 66.667 0.00 0.00 0.00 4.57
514 518 0.680280 GGAGTCCTCTAGTGTGGCGA 60.680 60.000 0.41 0.00 0.00 5.54
591 595 1.077787 GATGATGGGCGTGGGTTCA 60.078 57.895 0.00 0.00 0.00 3.18
604 608 0.178068 CCCGACCCGTCAAAGATGAT 59.822 55.000 0.00 0.00 38.01 2.45
664 668 4.316823 ACCCTCCTCCCGTGCTCA 62.317 66.667 0.00 0.00 0.00 4.26
678 682 2.501610 CCTAGCCGCTCAAGACCC 59.498 66.667 0.00 0.00 0.00 4.46
724 728 4.147449 CATCTCCACCGCGAGCCA 62.147 66.667 8.23 0.00 0.00 4.75
819 2566 3.132111 TCACATGCCACGTCATACACTAT 59.868 43.478 0.00 0.00 0.00 2.12
820 2567 2.494073 TCACATGCCACGTCATACACTA 59.506 45.455 0.00 0.00 0.00 2.74
821 2568 1.275010 TCACATGCCACGTCATACACT 59.725 47.619 0.00 0.00 0.00 3.55
907 2655 3.041940 GTGGAGTGGTTCGCGTGG 61.042 66.667 5.77 0.00 0.00 4.94
913 2668 2.032071 CCGGTGGTGGAGTGGTTC 59.968 66.667 0.00 0.00 0.00 3.62
967 2722 4.129148 AAGGAGATTGGCGGGGGC 62.129 66.667 0.00 0.00 0.00 5.80
968 2723 2.193248 GAAGGAGATTGGCGGGGG 59.807 66.667 0.00 0.00 0.00 5.40
969 2724 1.147153 GAGAAGGAGATTGGCGGGG 59.853 63.158 0.00 0.00 0.00 5.73
970 2725 1.147153 GGAGAAGGAGATTGGCGGG 59.853 63.158 0.00 0.00 0.00 6.13
1510 3284 2.506438 CTCGAGGTCGGCCGAAAC 60.506 66.667 32.93 25.50 40.50 2.78
1558 3332 1.192146 TCACCTAGCCCGCACTCTTT 61.192 55.000 0.00 0.00 0.00 2.52
1732 3506 2.279784 GGCGGCGATCTTCTCCTG 60.280 66.667 12.98 0.00 0.00 3.86
1772 3546 1.196766 AGCATCTGACCACCTGAGCA 61.197 55.000 0.00 0.00 0.00 4.26
1774 3548 0.900421 TCAGCATCTGACCACCTGAG 59.100 55.000 0.00 0.00 35.39 3.35
1917 3691 2.161012 CAGGCTATAATTGAGCATGGCG 59.839 50.000 16.67 0.00 45.54 5.69
2025 3799 2.622436 ACCTTTTCGCTGATACAGAGC 58.378 47.619 2.81 0.00 32.44 4.09
2174 3948 3.199677 GCGCCATACACAGTTACCAATA 58.800 45.455 0.00 0.00 0.00 1.90
2262 4036 6.983307 CAGACATAATAGAGGAGACAACCAAG 59.017 42.308 0.00 0.00 0.00 3.61
2441 4218 2.344950 CCTGATCTCACACACTCTTGC 58.655 52.381 0.00 0.00 0.00 4.01
2630 4616 0.312416 TTCCACAATTGTTTCCGCCG 59.688 50.000 8.77 0.00 0.00 6.46
2735 4735 4.832248 TGCAGGAAAACGAAGACTATCAT 58.168 39.130 0.00 0.00 0.00 2.45
2739 4739 3.746045 ACTGCAGGAAAACGAAGACTA 57.254 42.857 19.93 0.00 0.00 2.59
2988 5000 9.667107 TGTGCTTGATAAAGCTTAAGTAATACT 57.333 29.630 16.00 0.00 45.66 2.12
3016 5028 4.273318 AGGAAACAACATGGCCTATCTTC 58.727 43.478 3.32 0.00 0.00 2.87
3096 5108 0.251653 ACCCAGTGGCTCTCGAACTA 60.252 55.000 2.61 0.00 33.59 2.24


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

AutoCloner maintained by Alex Coulton.