Multiple sequence alignment - TraesCS1B01G012900

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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 TraesCS1B01G012900 chr1B 100.000 4298 0 0 1 4298 6280521 6284818 0.000000e+00 7938.0
1 TraesCS1B01G012900 chr1B 88.359 3565 383 19 146 3700 5694450 5697992 0.000000e+00 4255.0
2 TraesCS1B01G012900 chr1B 87.571 3170 358 22 545 3697 629652649 629655799 0.000000e+00 3639.0
3 TraesCS1B01G012900 chr1B 87.615 3157 352 23 550 3700 6060402 6063525 0.000000e+00 3627.0
4 TraesCS1B01G012900 chr1B 84.661 3540 470 38 194 3700 6488174 6484675 0.000000e+00 3461.0
5 TraesCS1B01G012900 chr1B 84.221 3099 439 27 617 3700 7256971 7253908 0.000000e+00 2968.0
6 TraesCS1B01G012900 chr1B 82.676 3244 482 42 475 3700 22714640 22711459 0.000000e+00 2804.0
7 TraesCS1B01G012900 chr1B 84.081 2651 349 41 194 2811 5985493 5988103 0.000000e+00 2490.0
8 TraesCS1B01G012900 chr1B 89.279 569 58 3 3732 4298 5697967 5698534 0.000000e+00 710.0
9 TraesCS1B01G012900 chr1B 88.889 540 59 1 3760 4298 6484672 6484133 0.000000e+00 664.0
10 TraesCS1B01G012900 chr1B 86.995 569 71 3 3732 4298 5989042 5989609 4.690000e-179 638.0
11 TraesCS1B01G012900 chr1B 87.319 552 67 3 3749 4298 22151434 22150884 2.820000e-176 628.0
12 TraesCS1B01G012900 chr1A 85.848 3533 435 32 198 3700 6341685 6338188 0.000000e+00 3694.0
13 TraesCS1B01G012900 chr1A 85.270 3537 439 42 194 3700 5506406 5502922 0.000000e+00 3570.0
14 TraesCS1B01G012900 chr1A 84.275 2779 351 45 68 2811 4497203 4499930 0.000000e+00 2632.0
15 TraesCS1B01G012900 chr1A 82.660 2053 310 29 194 2230 6012948 6010926 0.000000e+00 1777.0
16 TraesCS1B01G012900 chr1A 89.455 569 57 3 3732 4298 4500806 4501373 0.000000e+00 715.0
17 TraesCS1B01G012900 chr1A 89.267 559 57 3 3742 4298 5502937 5502380 0.000000e+00 697.0
18 TraesCS1B01G012900 chr1A 88.225 569 64 3 3732 4298 4505017 4505584 0.000000e+00 676.0
19 TraesCS1B01G012900 chr1A 88.551 559 61 3 3742 4298 6338203 6337646 0.000000e+00 675.0
20 TraesCS1B01G012900 chr1A 81.662 349 52 8 3361 3700 4500486 4500831 3.270000e-71 279.0
21 TraesCS1B01G012900 chr1D 89.328 2680 264 13 1035 3700 77380 74709 0.000000e+00 3345.0
22 TraesCS1B01G012900 chr1D 84.688 3089 433 25 619 3700 5135218 5132163 0.000000e+00 3048.0
23 TraesCS1B01G012900 chr1D 86.819 569 72 3 3732 4298 5132188 5131621 2.180000e-177 632.0
24 TraesCS1B01G012900 chr1D 86.770 257 32 2 3445 3700 4196196 4195941 7.030000e-73 285.0
25 TraesCS1B01G012900 chr1D 75.676 148 21 12 550 688 3168246 3168387 4.640000e-05 60.2


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 TraesCS1B01G012900 chr1B 6280521 6284818 4297 False 7938.0 7938 100.00000 1 4298 1 chr1B.!!$F2 4297
1 TraesCS1B01G012900 chr1B 629652649 629655799 3150 False 3639.0 3639 87.57100 545 3697 1 chr1B.!!$F3 3152
2 TraesCS1B01G012900 chr1B 6060402 6063525 3123 False 3627.0 3627 87.61500 550 3700 1 chr1B.!!$F1 3150
3 TraesCS1B01G012900 chr1B 7253908 7256971 3063 True 2968.0 2968 84.22100 617 3700 1 chr1B.!!$R1 3083
4 TraesCS1B01G012900 chr1B 22711459 22714640 3181 True 2804.0 2804 82.67600 475 3700 1 chr1B.!!$R3 3225
5 TraesCS1B01G012900 chr1B 5694450 5698534 4084 False 2482.5 4255 88.81900 146 4298 2 chr1B.!!$F4 4152
6 TraesCS1B01G012900 chr1B 6484133 6488174 4041 True 2062.5 3461 86.77500 194 4298 2 chr1B.!!$R4 4104
7 TraesCS1B01G012900 chr1B 5985493 5989609 4116 False 1564.0 2490 85.53800 194 4298 2 chr1B.!!$F5 4104
8 TraesCS1B01G012900 chr1B 22150884 22151434 550 True 628.0 628 87.31900 3749 4298 1 chr1B.!!$R2 549
9 TraesCS1B01G012900 chr1A 6337646 6341685 4039 True 2184.5 3694 87.19950 198 4298 2 chr1A.!!$R3 4100
10 TraesCS1B01G012900 chr1A 5502380 5506406 4026 True 2133.5 3570 87.26850 194 4298 2 chr1A.!!$R2 4104
11 TraesCS1B01G012900 chr1A 6010926 6012948 2022 True 1777.0 1777 82.66000 194 2230 1 chr1A.!!$R1 2036
12 TraesCS1B01G012900 chr1A 4497203 4505584 8381 False 1075.5 2632 85.90425 68 4298 4 chr1A.!!$F1 4230
13 TraesCS1B01G012900 chr1D 74709 77380 2671 True 3345.0 3345 89.32800 1035 3700 1 chr1D.!!$R1 2665
14 TraesCS1B01G012900 chr1D 5131621 5135218 3597 True 1840.0 3048 85.75350 619 4298 2 chr1D.!!$R3 3679

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
312 317 0.034059 AACTTCACTGGAGTCGCCTG 59.966 55.0 0.00 0.00 41.12 4.85 F
364 372 0.323957 TCTGAATCTGCTGCTGCTGT 59.676 50.0 17.00 1.31 40.48 4.40 F
461 488 0.325933 CTGGGTGTTGCTGATCAGGA 59.674 55.0 23.89 19.17 0.00 3.86 F
463 490 0.326264 GGGTGTTGCTGATCAGGAGT 59.674 55.0 23.89 0.00 0.00 3.85 F
1083 1138 0.534203 TTGGGTTGAGGCAGACGTTC 60.534 55.0 0.00 0.00 0.00 3.95 F
1550 1611 0.605589 AGGCTGAAGGTCTGTCTTCG 59.394 55.0 0.00 0.00 44.38 3.79 F
2202 2282 1.089920 AGGAATGTGTCGCTGCAATC 58.910 50.0 0.00 0.00 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1973 0.109153 ACTGCTTCATGTGTGCTGGA 59.891 50.000 14.29 0.00 0.00 3.86 R
2237 2317 3.314913 TGACAAGAACAAATGTCGTGCAT 59.685 39.130 0.00 0.00 46.99 3.96 R
2336 2416 3.758755 TCAATGAGCTTCGCATAGGAT 57.241 42.857 0.00 0.00 0.00 3.24 R
2428 2508 5.412594 TCAAGTGATGCAGATACTTTGGTTC 59.587 40.000 9.51 0.00 32.69 3.62 R
2995 3182 0.109597 GCACTGCATCCGGACAAAAG 60.110 55.000 6.12 4.88 0.00 2.27 R
3002 3189 0.379669 GAAGATTGCACTGCATCCGG 59.620 55.000 4.10 0.00 38.76 5.14 R
3747 8073 0.111061 TGCATTCAGGCCTCAGTGTT 59.889 50.000 0.00 0.00 0.00 3.32 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
21 22 3.494378 CTGGTTCGCCTCAGCATG 58.506 61.111 0.00 0.00 39.83 4.06
22 23 1.078918 CTGGTTCGCCTCAGCATGA 60.079 57.895 0.00 0.00 46.23 3.07
39 40 5.368256 GCATGAGGCTAGTCAAATAATGG 57.632 43.478 0.00 0.00 40.25 3.16
40 41 4.823989 GCATGAGGCTAGTCAAATAATGGT 59.176 41.667 0.00 0.00 40.25 3.55
41 42 5.997746 GCATGAGGCTAGTCAAATAATGGTA 59.002 40.000 0.00 0.00 40.25 3.25
42 43 6.486657 GCATGAGGCTAGTCAAATAATGGTAA 59.513 38.462 0.00 0.00 40.25 2.85
43 44 7.175641 GCATGAGGCTAGTCAAATAATGGTAAT 59.824 37.037 0.00 0.00 40.25 1.89
44 45 8.725148 CATGAGGCTAGTCAAATAATGGTAATC 58.275 37.037 0.00 0.00 0.00 1.75
45 46 8.034313 TGAGGCTAGTCAAATAATGGTAATCT 57.966 34.615 0.00 0.00 0.00 2.40
46 47 7.933577 TGAGGCTAGTCAAATAATGGTAATCTG 59.066 37.037 0.00 0.00 0.00 2.90
47 48 6.712547 AGGCTAGTCAAATAATGGTAATCTGC 59.287 38.462 0.00 0.00 0.00 4.26
48 49 6.072452 GGCTAGTCAAATAATGGTAATCTGCC 60.072 42.308 0.00 0.00 0.00 4.85
49 50 6.347725 GCTAGTCAAATAATGGTAATCTGCCG 60.348 42.308 0.00 0.00 0.00 5.69
50 51 4.821805 AGTCAAATAATGGTAATCTGCCGG 59.178 41.667 0.00 0.00 0.00 6.13
51 52 3.568007 TCAAATAATGGTAATCTGCCGGC 59.432 43.478 22.73 22.73 0.00 6.13
52 53 2.200373 ATAATGGTAATCTGCCGGCC 57.800 50.000 26.77 6.80 0.00 6.13
53 54 1.136828 TAATGGTAATCTGCCGGCCT 58.863 50.000 26.77 8.42 0.00 5.19
54 55 0.466189 AATGGTAATCTGCCGGCCTG 60.466 55.000 26.77 17.37 0.00 4.85
55 56 2.902343 GGTAATCTGCCGGCCTGC 60.902 66.667 26.77 12.95 0.00 4.85
56 57 2.902343 GTAATCTGCCGGCCTGCC 60.902 66.667 26.77 2.75 0.00 4.85
57 58 3.407083 TAATCTGCCGGCCTGCCA 61.407 61.111 26.77 2.93 35.37 4.92
58 59 2.756042 TAATCTGCCGGCCTGCCAT 61.756 57.895 26.77 7.92 35.37 4.40
59 60 1.414866 TAATCTGCCGGCCTGCCATA 61.415 55.000 26.77 6.83 35.37 2.74
60 61 2.687418 AATCTGCCGGCCTGCCATAG 62.687 60.000 26.77 13.09 35.37 2.23
61 62 4.181010 CTGCCGGCCTGCCATAGT 62.181 66.667 26.77 0.00 35.37 2.12
62 63 4.488136 TGCCGGCCTGCCATAGTG 62.488 66.667 26.77 0.00 35.37 2.74
63 64 4.489771 GCCGGCCTGCCATAGTGT 62.490 66.667 18.11 0.00 35.37 3.55
64 65 2.203070 CCGGCCTGCCATAGTGTC 60.203 66.667 9.17 0.00 35.37 3.67
65 66 2.584064 CGGCCTGCCATAGTGTCA 59.416 61.111 9.17 0.00 35.37 3.58
66 67 1.146930 CGGCCTGCCATAGTGTCAT 59.853 57.895 9.17 0.00 35.37 3.06
67 68 0.392706 CGGCCTGCCATAGTGTCATA 59.607 55.000 9.17 0.00 35.37 2.15
68 69 1.606480 CGGCCTGCCATAGTGTCATAG 60.606 57.143 9.17 0.00 35.37 2.23
69 70 1.271054 GGCCTGCCATAGTGTCATAGG 60.271 57.143 2.58 0.00 35.81 2.57
70 71 1.879796 GCCTGCCATAGTGTCATAGGC 60.880 57.143 0.00 0.00 45.41 3.93
73 74 2.620251 GCCATAGTGTCATAGGCACA 57.380 50.000 4.46 0.00 44.59 4.57
74 75 2.487934 GCCATAGTGTCATAGGCACAG 58.512 52.381 4.46 0.00 44.59 3.66
75 76 2.487934 CCATAGTGTCATAGGCACAGC 58.512 52.381 4.46 0.00 39.17 4.40
76 77 2.103771 CCATAGTGTCATAGGCACAGCT 59.896 50.000 4.46 0.00 39.17 4.24
111 112 5.083122 TGGCTTCCATTTTCCTCACAATTA 58.917 37.500 0.00 0.00 0.00 1.40
112 113 5.185635 TGGCTTCCATTTTCCTCACAATTAG 59.814 40.000 0.00 0.00 0.00 1.73
118 119 5.472148 CATTTTCCTCACAATTAGCAAGCA 58.528 37.500 0.00 0.00 0.00 3.91
119 120 4.503741 TTTCCTCACAATTAGCAAGCAC 57.496 40.909 0.00 0.00 0.00 4.40
120 121 3.138884 TCCTCACAATTAGCAAGCACA 57.861 42.857 0.00 0.00 0.00 4.57
121 122 2.813754 TCCTCACAATTAGCAAGCACAC 59.186 45.455 0.00 0.00 0.00 3.82
122 123 2.553602 CCTCACAATTAGCAAGCACACA 59.446 45.455 0.00 0.00 0.00 3.72
124 125 4.321452 CCTCACAATTAGCAAGCACACATT 60.321 41.667 0.00 0.00 0.00 2.71
125 126 5.199024 TCACAATTAGCAAGCACACATTT 57.801 34.783 0.00 0.00 0.00 2.32
127 128 5.009911 TCACAATTAGCAAGCACACATTTCT 59.990 36.000 0.00 0.00 0.00 2.52
128 129 5.693104 CACAATTAGCAAGCACACATTTCTT 59.307 36.000 0.00 0.00 0.00 2.52
129 130 5.693104 ACAATTAGCAAGCACACATTTCTTG 59.307 36.000 0.00 0.00 39.95 3.02
143 144 1.621992 TTCTTGCTCACGTCTCCTCT 58.378 50.000 0.00 0.00 0.00 3.69
144 145 0.884514 TCTTGCTCACGTCTCCTCTG 59.115 55.000 0.00 0.00 0.00 3.35
254 259 3.182967 CCGTTTGTCAGAGTAGAGCATC 58.817 50.000 0.00 0.00 0.00 3.91
277 282 2.045045 CCGCCCACACATCCATGT 60.045 61.111 0.00 0.00 42.84 3.21
312 317 0.034059 AACTTCACTGGAGTCGCCTG 59.966 55.000 0.00 0.00 41.12 4.85
315 320 1.758440 TTCACTGGAGTCGCCTGCTT 61.758 55.000 0.00 0.00 39.08 3.91
317 322 2.210013 ACTGGAGTCGCCTGCTTGA 61.210 57.895 0.00 0.00 39.08 3.02
323 331 3.630013 TCGCCTGCTTGAGTGCCT 61.630 61.111 0.00 0.00 0.00 4.75
325 333 2.033141 GCCTGCTTGAGTGCCTCA 59.967 61.111 1.25 1.25 38.87 3.86
330 338 1.449246 GCTTGAGTGCCTCATCGCT 60.449 57.895 5.83 0.00 40.39 4.93
342 350 4.796231 ATCGCTGGCGTCGACCAC 62.796 66.667 10.58 3.41 38.88 4.16
364 372 0.323957 TCTGAATCTGCTGCTGCTGT 59.676 50.000 17.00 1.31 40.48 4.40
365 373 0.727970 CTGAATCTGCTGCTGCTGTC 59.272 55.000 17.00 10.81 40.48 3.51
373 381 4.377708 TGCTGCTGTCGCCGACAT 62.378 61.111 21.54 0.00 41.94 3.06
374 382 3.857854 GCTGCTGTCGCCGACATG 61.858 66.667 21.54 15.23 41.94 3.21
377 385 3.545481 GCTGTCGCCGACATGACG 61.545 66.667 21.54 10.11 41.94 4.35
378 386 3.545481 CTGTCGCCGACATGACGC 61.545 66.667 21.54 6.95 41.94 5.19
383 391 3.554692 GCCGACATGACGCCGAAG 61.555 66.667 12.17 0.00 0.00 3.79
384 392 3.554692 CCGACATGACGCCGAAGC 61.555 66.667 12.17 0.00 0.00 3.86
385 393 3.554692 CGACATGACGCCGAAGCC 61.555 66.667 4.36 0.00 34.57 4.35
386 394 2.434185 GACATGACGCCGAAGCCA 60.434 61.111 0.00 0.00 34.57 4.75
409 430 2.920645 CGACGTGCCTGTGAGGACT 61.921 63.158 0.00 0.00 37.67 3.85
412 433 0.826256 ACGTGCCTGTGAGGACTACA 60.826 55.000 0.00 0.00 37.67 2.74
423 444 2.501723 TGAGGACTACATCTTCCTTGCC 59.498 50.000 0.00 0.00 42.68 4.52
428 449 2.038557 ACTACATCTTCCTTGCCGTTGT 59.961 45.455 0.00 0.00 0.00 3.32
432 453 2.623878 TCTTCCTTGCCGTTGTTGTA 57.376 45.000 0.00 0.00 0.00 2.41
449 476 0.328258 GTATTGCTGGTCCTGGGTGT 59.672 55.000 0.00 0.00 0.00 4.16
461 488 0.325933 CTGGGTGTTGCTGATCAGGA 59.674 55.000 23.89 19.17 0.00 3.86
463 490 0.326264 GGGTGTTGCTGATCAGGAGT 59.674 55.000 23.89 0.00 0.00 3.85
518 548 9.191995 GATCGGATTTTGACTTGTAATTTGTTT 57.808 29.630 0.00 0.00 0.00 2.83
571 622 3.434984 GTCTTGCTCACACCATTCTCTTC 59.565 47.826 0.00 0.00 0.00 2.87
572 623 3.326006 TCTTGCTCACACCATTCTCTTCT 59.674 43.478 0.00 0.00 0.00 2.85
573 624 3.325293 TGCTCACACCATTCTCTTCTC 57.675 47.619 0.00 0.00 0.00 2.87
609 663 0.603975 GCACCTGTGTTGGAGGAGTC 60.604 60.000 0.00 0.00 34.37 3.36
630 684 0.673644 CTTCCGAGCGTTCCAATGGT 60.674 55.000 0.00 0.00 0.00 3.55
679 733 1.883638 GCTTTGGTGTCCATGCTGAGA 60.884 52.381 0.00 0.00 33.08 3.27
791 845 1.584495 CTGGACGTCATCACCGACA 59.416 57.895 18.91 2.22 35.54 4.35
825 880 1.922821 GGCCAATAGAGAAGGGGCA 59.077 57.895 0.00 0.00 46.37 5.36
833 888 1.372501 AGAGAAGGGGCAAAAGCCTA 58.627 50.000 6.45 0.00 0.00 3.93
838 893 1.210885 AGGGGCAAAAGCCTAGCTCT 61.211 55.000 6.45 0.00 38.25 4.09
1017 1072 2.821969 CAGAATGGGTAGCAAGCTTTGT 59.178 45.455 0.00 0.00 0.00 2.83
1080 1135 0.535102 ACTTTGGGTTGAGGCAGACG 60.535 55.000 0.00 0.00 0.00 4.18
1083 1138 0.534203 TTGGGTTGAGGCAGACGTTC 60.534 55.000 0.00 0.00 0.00 3.95
1108 1163 3.084039 GTGTCCAATCAATTGAGGCAGA 58.916 45.455 14.54 5.35 40.14 4.26
1109 1164 3.084039 TGTCCAATCAATTGAGGCAGAC 58.916 45.455 14.54 16.27 40.14 3.51
1110 1165 3.084039 GTCCAATCAATTGAGGCAGACA 58.916 45.455 14.54 0.00 40.14 3.41
1131 1186 1.227853 ACCGGTGTCAAAGGAGTGC 60.228 57.895 6.12 0.00 0.00 4.40
1238 1293 1.352352 ACCTGGTGAAGCTAGCAATGT 59.648 47.619 18.83 0.00 0.00 2.71
1378 1433 3.549019 CGTCTCTGATACCTTCGATGTGG 60.549 52.174 0.00 0.00 0.00 4.17
1383 1438 4.649218 TCTGATACCTTCGATGTGGATTCA 59.351 41.667 6.63 7.46 0.00 2.57
1412 1467 5.957771 AAGAGTATAGTTGAAGCATCCCA 57.042 39.130 0.00 0.00 0.00 4.37
1420 1475 3.319122 AGTTGAAGCATCCCACAAGAAAC 59.681 43.478 0.00 0.00 0.00 2.78
1424 1479 2.173519 AGCATCCCACAAGAAACATGG 58.826 47.619 0.00 0.00 0.00 3.66
1463 1518 5.097742 TCACTGGAGAGACTTCAAAAACA 57.902 39.130 0.00 0.00 0.00 2.83
1550 1611 0.605589 AGGCTGAAGGTCTGTCTTCG 59.394 55.000 0.00 0.00 44.38 3.79
1600 1661 3.204526 ACGACAACCCGTGATAAACAAA 58.795 40.909 0.00 0.00 41.70 2.83
1618 1679 7.686438 AAACAAATTTCTGAAATTATGGGCC 57.314 32.000 24.18 0.00 40.05 5.80
1621 1682 5.357742 AATTTCTGAAATTATGGGCCCAC 57.642 39.130 31.51 14.57 39.21 4.61
1737 1802 2.101582 GCTAGTCGAGATGGTTGGTGAT 59.898 50.000 0.00 0.00 0.00 3.06
1742 1807 3.248602 GTCGAGATGGTTGGTGATATTGC 59.751 47.826 0.00 0.00 0.00 3.56
1743 1808 3.118445 TCGAGATGGTTGGTGATATTGCA 60.118 43.478 0.00 0.00 0.00 4.08
1875 1946 2.223340 CGAGGAATCTGGAATTTTGCCG 60.223 50.000 0.00 0.00 0.00 5.69
1885 1956 3.694072 TGGAATTTTGCCGATACTCAAGG 59.306 43.478 0.00 0.00 0.00 3.61
1902 1973 5.995897 ACTCAAGGTTAGCTACAACGATTTT 59.004 36.000 0.00 0.00 0.00 1.82
2037 2108 5.782845 ACAGGAGGAAGATAGTCTTGAAACT 59.217 40.000 0.00 0.00 36.73 2.66
2044 2115 8.482128 AGGAAGATAGTCTTGAAACTATTGGAG 58.518 37.037 0.00 0.00 41.45 3.86
2092 2163 6.778821 TCAAGGTCATTCTTTCTGGACATAA 58.221 36.000 0.00 0.00 32.00 1.90
2106 2177 6.431722 TCTGGACATAAAGGAATTTAAGGGG 58.568 40.000 0.00 0.00 0.00 4.79
2112 2192 4.759793 AAAGGAATTTAAGGGGGACAGT 57.240 40.909 0.00 0.00 0.00 3.55
2202 2282 1.089920 AGGAATGTGTCGCTGCAATC 58.910 50.000 0.00 0.00 0.00 2.67
2232 2312 4.301628 CAAGTCAAATTGAGTGGCTTTCC 58.698 43.478 3.83 0.00 38.86 3.13
2237 2317 5.007034 TCAAATTGAGTGGCTTTCCGATAA 58.993 37.500 0.00 0.00 34.14 1.75
2241 2321 2.288666 GAGTGGCTTTCCGATAATGCA 58.711 47.619 0.00 0.00 34.14 3.96
2336 2416 7.338957 TGCCATTCAAACACTGATATGTGATAA 59.661 33.333 1.47 0.00 40.12 1.75
2449 2529 4.263462 TGGAACCAAAGTATCTGCATCACT 60.263 41.667 0.00 0.00 0.00 3.41
2464 2544 4.469586 TGCATCACTTGAGGTACCTTGATA 59.530 41.667 21.22 8.87 0.00 2.15
2549 2629 1.203287 GGACCTTTCCAATTGCTCTGC 59.797 52.381 0.00 0.00 42.30 4.26
2618 2698 3.703556 CACCTCTACACTCATGGATGTCT 59.296 47.826 6.09 0.00 0.00 3.41
2676 2756 1.967066 ACTAAGCTGCAGACACTCACT 59.033 47.619 20.43 0.00 0.00 3.41
2739 2822 5.106038 TGTTGGAGAGCTGCATGATTTAAAG 60.106 40.000 1.02 0.00 0.00 1.85
2781 2867 4.442375 ACGTCAGGTAGAGAATGTTGAG 57.558 45.455 0.00 0.00 0.00 3.02
2786 2872 6.459923 GTCAGGTAGAGAATGTTGAGAAAGT 58.540 40.000 0.00 0.00 0.00 2.66
2830 3015 4.899502 TGGAAACAAGAAGGATCTCAGTC 58.100 43.478 0.00 0.00 37.44 3.51
2835 3020 6.672266 AACAAGAAGGATCTCAGTCAACTA 57.328 37.500 0.00 0.00 33.77 2.24
2843 3028 8.779354 AAGGATCTCAGTCAACTAACATTAAC 57.221 34.615 0.00 0.00 0.00 2.01
2859 3046 5.261216 ACATTAACATGGAGTAAGGTTGGG 58.739 41.667 0.00 0.00 34.27 4.12
2955 3142 2.995258 GTGCATGGGTATGTTGCAAAAG 59.005 45.455 0.00 0.00 46.91 2.27
2995 3182 5.694674 TTTTTGTTGTGAAAGATTGCGAC 57.305 34.783 0.00 0.00 0.00 5.19
3002 3189 4.597079 TGTGAAAGATTGCGACTTTTGTC 58.403 39.130 0.00 0.00 45.55 3.18
3004 3191 2.969443 AAGATTGCGACTTTTGTCCG 57.031 45.000 0.00 0.00 46.25 4.79
3048 3235 2.038557 TCCAAGACTGAAGGTGCTTACC 59.961 50.000 0.00 0.00 0.00 2.85
3055 3242 4.104831 ACTGAAGGTGCTTACCCTAGAAT 58.895 43.478 0.00 0.00 0.00 2.40
3093 3280 4.054369 AGGGATGGTGGGAAATAGATGAA 58.946 43.478 0.00 0.00 0.00 2.57
3103 3290 6.015918 TGGGAAATAGATGAAAGGCAAGAAA 58.984 36.000 0.00 0.00 0.00 2.52
3258 3556 3.238597 TGCCCTAAAGGTGCTCAAAATT 58.761 40.909 9.82 0.00 38.26 1.82
3295 3593 2.171568 TCAGAGATGGGATGCAGTCT 57.828 50.000 0.00 0.00 0.00 3.24
3315 3613 4.767928 GTCTAAGAGACTCAAGGAGGACAA 59.232 45.833 5.02 0.00 41.88 3.18
3448 7756 3.793144 GCTCAGCGTTTCCTGCCG 61.793 66.667 0.00 0.00 32.87 5.69
3453 7761 0.589223 CAGCGTTTCCTGCCGTAAAA 59.411 50.000 0.00 0.00 0.00 1.52
3456 7764 1.002142 GCGTTTCCTGCCGTAAAAGTT 60.002 47.619 0.00 0.00 0.00 2.66
3468 7776 5.242838 TGCCGTAAAAGTTCTCAAAATGGAT 59.757 36.000 0.00 0.00 0.00 3.41
3512 7838 2.019984 GGATGCAGTTGAAGGGACATC 58.980 52.381 0.00 0.00 34.54 3.06
3513 7839 2.618816 GGATGCAGTTGAAGGGACATCA 60.619 50.000 0.00 0.00 36.49 3.07
3689 8015 4.530161 ACTGAGGCTAGAAGACACAGAAAT 59.470 41.667 13.23 0.00 43.51 2.17
3700 8026 7.901029 AGAAGACACAGAAATAACATCAGAGA 58.099 34.615 0.00 0.00 0.00 3.10
3701 8027 7.816995 AGAAGACACAGAAATAACATCAGAGAC 59.183 37.037 0.00 0.00 0.00 3.36
3702 8028 6.997655 AGACACAGAAATAACATCAGAGACA 58.002 36.000 0.00 0.00 0.00 3.41
3703 8029 7.445121 AGACACAGAAATAACATCAGAGACAA 58.555 34.615 0.00 0.00 0.00 3.18
3704 8030 7.386299 AGACACAGAAATAACATCAGAGACAAC 59.614 37.037 0.00 0.00 0.00 3.32
3705 8031 6.992123 ACACAGAAATAACATCAGAGACAACA 59.008 34.615 0.00 0.00 0.00 3.33
3706 8032 7.663081 ACACAGAAATAACATCAGAGACAACAT 59.337 33.333 0.00 0.00 0.00 2.71
3707 8033 8.173775 CACAGAAATAACATCAGAGACAACATC 58.826 37.037 0.00 0.00 0.00 3.06
3708 8034 7.879677 ACAGAAATAACATCAGAGACAACATCA 59.120 33.333 0.00 0.00 0.00 3.07
3709 8035 8.388853 CAGAAATAACATCAGAGACAACATCAG 58.611 37.037 0.00 0.00 0.00 2.90
3710 8036 8.316946 AGAAATAACATCAGAGACAACATCAGA 58.683 33.333 0.00 0.00 0.00 3.27
3711 8037 8.489990 AAATAACATCAGAGACAACATCAGAG 57.510 34.615 0.00 0.00 0.00 3.35
3712 8038 4.468765 ACATCAGAGACAACATCAGAGG 57.531 45.455 0.00 0.00 0.00 3.69
3713 8039 4.092279 ACATCAGAGACAACATCAGAGGA 58.908 43.478 0.00 0.00 0.00 3.71
3714 8040 4.715792 ACATCAGAGACAACATCAGAGGAT 59.284 41.667 0.00 0.00 0.00 3.24
3725 8051 3.552875 CATCAGAGGATGCTCCAATTGT 58.447 45.455 11.06 0.00 44.03 2.71
3726 8052 2.995283 TCAGAGGATGCTCCAATTGTG 58.005 47.619 11.06 1.56 39.61 3.33
3727 8053 3.687551 ATCAGAGGATGCTCCAATTGTGG 60.688 47.826 11.06 0.00 39.61 4.17
3728 8054 5.921853 ATCAGAGGATGCTCCAATTGTGGA 61.922 45.833 11.06 0.00 41.25 4.02
3755 8081 8.704234 GTTAGAACTCATAGAAACAACACTGAG 58.296 37.037 0.00 0.00 36.92 3.35
3785 8112 2.159627 GCACTTCAATTGTACCGGTGAG 59.840 50.000 19.93 4.60 0.00 3.51
3802 8129 3.688673 GGTGAGAGCAAAGAGAAATGGAG 59.311 47.826 0.00 0.00 0.00 3.86
3804 8131 3.008813 TGAGAGCAAAGAGAAATGGAGCT 59.991 43.478 0.00 0.00 0.00 4.09
3816 8143 5.227593 AGAAATGGAGCTAGAAATCCCCTA 58.772 41.667 0.00 0.00 34.47 3.53
3846 8173 1.350684 TGGAGTTAGGATGCTGCAACA 59.649 47.619 6.36 0.00 30.30 3.33
3847 8174 2.224744 TGGAGTTAGGATGCTGCAACAA 60.225 45.455 6.36 0.00 30.30 2.83
3858 8185 3.719924 TGCTGCAACAAATTCTTTGGAG 58.280 40.909 0.00 13.22 44.81 3.86
3859 8186 3.384146 TGCTGCAACAAATTCTTTGGAGA 59.616 39.130 18.87 6.62 42.15 3.71
3896 8223 3.682858 CGTGGGACTATTTTGTACACCTG 59.317 47.826 0.00 0.00 0.00 4.00
3902 8229 6.436218 GGGACTATTTTGTACACCTGGAAAAT 59.564 38.462 0.00 4.55 33.64 1.82
3916 8243 6.426633 CACCTGGAAAATTTGGAAATTGGTAC 59.573 38.462 0.00 0.00 38.53 3.34
3919 8246 7.334171 CCTGGAAAATTTGGAAATTGGTACATC 59.666 37.037 0.00 0.00 38.53 3.06
4005 8332 5.569059 GTGATTACAAACTGCGAAAATCTGG 59.431 40.000 0.00 0.00 0.00 3.86
4015 8342 2.880890 GCGAAAATCTGGCTGGATATGT 59.119 45.455 0.00 0.00 0.00 2.29
4089 8416 5.241728 GGTTTGGAGTCTCTTTGCTTACAAT 59.758 40.000 0.00 0.00 35.21 2.71
4137 8464 0.101399 CGTCCCGACATCTCTCAAGG 59.899 60.000 0.00 0.00 0.00 3.61
4142 8469 3.519510 TCCCGACATCTCTCAAGGAAATT 59.480 43.478 0.00 0.00 0.00 1.82
4168 8495 8.469309 AATATTAGTGGATGCATTAAGCTTGT 57.531 30.769 9.86 0.00 45.94 3.16
4178 8505 6.528537 TGCATTAAGCTTGTGTCCATATTT 57.471 33.333 9.86 0.00 45.94 1.40
4223 8550 7.039363 CCATAGTTAGTCCAAGGATCTTCTAGG 60.039 44.444 0.00 0.00 0.00 3.02
4282 8609 3.474600 CATCCTCACCCATGAATCACTC 58.525 50.000 0.00 0.00 33.30 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.078918 TCATGCTGAGGCGAACCAG 60.079 57.895 0.00 0.00 42.25 4.00
5 6 1.078918 CTCATGCTGAGGCGAACCA 60.079 57.895 5.54 0.00 40.71 3.67
6 7 3.805267 CTCATGCTGAGGCGAACC 58.195 61.111 5.54 0.00 40.71 3.62
17 18 4.823989 ACCATTATTTGACTAGCCTCATGC 59.176 41.667 0.00 0.00 41.71 4.06
18 19 8.627208 ATTACCATTATTTGACTAGCCTCATG 57.373 34.615 0.00 0.00 0.00 3.07
19 20 8.664079 AGATTACCATTATTTGACTAGCCTCAT 58.336 33.333 0.00 0.00 0.00 2.90
20 21 7.933577 CAGATTACCATTATTTGACTAGCCTCA 59.066 37.037 0.00 0.00 0.00 3.86
21 22 7.095017 GCAGATTACCATTATTTGACTAGCCTC 60.095 40.741 0.00 0.00 0.00 4.70
22 23 6.712547 GCAGATTACCATTATTTGACTAGCCT 59.287 38.462 0.00 0.00 0.00 4.58
23 24 6.072452 GGCAGATTACCATTATTTGACTAGCC 60.072 42.308 0.00 0.00 0.00 3.93
24 25 6.347725 CGGCAGATTACCATTATTTGACTAGC 60.348 42.308 0.00 0.00 0.00 3.42
25 26 6.147821 CCGGCAGATTACCATTATTTGACTAG 59.852 42.308 0.00 0.00 0.00 2.57
26 27 5.995282 CCGGCAGATTACCATTATTTGACTA 59.005 40.000 0.00 0.00 0.00 2.59
27 28 4.821805 CCGGCAGATTACCATTATTTGACT 59.178 41.667 0.00 0.00 0.00 3.41
28 29 4.556699 GCCGGCAGATTACCATTATTTGAC 60.557 45.833 24.80 0.00 0.00 3.18
29 30 3.568007 GCCGGCAGATTACCATTATTTGA 59.432 43.478 24.80 0.00 0.00 2.69
30 31 3.305335 GGCCGGCAGATTACCATTATTTG 60.305 47.826 30.85 0.00 0.00 2.32
31 32 2.890945 GGCCGGCAGATTACCATTATTT 59.109 45.455 30.85 0.00 0.00 1.40
32 33 2.108250 AGGCCGGCAGATTACCATTATT 59.892 45.455 30.85 0.00 0.00 1.40
33 34 1.705186 AGGCCGGCAGATTACCATTAT 59.295 47.619 30.85 0.00 0.00 1.28
34 35 1.136828 AGGCCGGCAGATTACCATTA 58.863 50.000 30.85 0.00 0.00 1.90
35 36 0.466189 CAGGCCGGCAGATTACCATT 60.466 55.000 30.85 0.00 0.00 3.16
36 37 1.149174 CAGGCCGGCAGATTACCAT 59.851 57.895 30.85 0.00 0.00 3.55
37 38 2.589540 CAGGCCGGCAGATTACCA 59.410 61.111 30.85 0.00 0.00 3.25
38 39 2.902343 GCAGGCCGGCAGATTACC 60.902 66.667 30.85 8.87 0.00 2.85
39 40 2.902343 GGCAGGCCGGCAGATTAC 60.902 66.667 30.85 9.73 40.76 1.89
46 47 4.489771 ACACTATGGCAGGCCGGC 62.490 66.667 21.18 21.18 39.42 6.13
47 48 2.203070 GACACTATGGCAGGCCGG 60.203 66.667 5.74 0.00 39.42 6.13
48 49 0.392706 TATGACACTATGGCAGGCCG 59.607 55.000 5.74 0.00 39.76 6.13
49 50 1.271054 CCTATGACACTATGGCAGGCC 60.271 57.143 2.62 2.62 39.76 5.19
50 51 1.879796 GCCTATGACACTATGGCAGGC 60.880 57.143 0.00 0.00 39.76 4.85
51 52 2.175878 GCCTATGACACTATGGCAGG 57.824 55.000 0.00 0.00 39.76 4.85
54 55 2.487934 CTGTGCCTATGACACTATGGC 58.512 52.381 0.00 0.00 43.49 4.40
55 56 2.103771 AGCTGTGCCTATGACACTATGG 59.896 50.000 0.00 0.00 38.86 2.74
56 57 3.129109 CAGCTGTGCCTATGACACTATG 58.871 50.000 5.25 0.00 38.86 2.23
57 58 2.103771 CCAGCTGTGCCTATGACACTAT 59.896 50.000 13.81 0.00 38.86 2.12
58 59 1.482182 CCAGCTGTGCCTATGACACTA 59.518 52.381 13.81 0.00 38.86 2.74
59 60 0.251354 CCAGCTGTGCCTATGACACT 59.749 55.000 13.81 0.00 38.86 3.55
60 61 1.372087 GCCAGCTGTGCCTATGACAC 61.372 60.000 13.81 0.00 38.55 3.67
61 62 1.078214 GCCAGCTGTGCCTATGACA 60.078 57.895 13.81 0.00 0.00 3.58
62 63 1.821332 GGCCAGCTGTGCCTATGAC 60.821 63.158 28.74 6.48 45.70 3.06
63 64 2.591753 GGCCAGCTGTGCCTATGA 59.408 61.111 28.74 0.00 45.70 2.15
118 119 2.802816 GAGACGTGAGCAAGAAATGTGT 59.197 45.455 0.00 0.00 0.00 3.72
119 120 2.158449 GGAGACGTGAGCAAGAAATGTG 59.842 50.000 0.00 0.00 0.00 3.21
120 121 2.037772 AGGAGACGTGAGCAAGAAATGT 59.962 45.455 0.00 0.00 0.00 2.71
121 122 2.670414 GAGGAGACGTGAGCAAGAAATG 59.330 50.000 0.00 0.00 0.00 2.32
122 123 2.564947 AGAGGAGACGTGAGCAAGAAAT 59.435 45.455 0.00 0.00 0.00 2.17
124 125 1.270826 CAGAGGAGACGTGAGCAAGAA 59.729 52.381 0.00 0.00 0.00 2.52
125 126 0.884514 CAGAGGAGACGTGAGCAAGA 59.115 55.000 0.00 0.00 0.00 3.02
127 128 1.328279 TTCAGAGGAGACGTGAGCAA 58.672 50.000 0.00 0.00 31.08 3.91
128 129 1.328279 TTTCAGAGGAGACGTGAGCA 58.672 50.000 0.00 0.00 31.08 4.26
129 130 2.663826 ATTTCAGAGGAGACGTGAGC 57.336 50.000 0.00 0.00 31.08 4.26
130 131 3.516615 GGAATTTCAGAGGAGACGTGAG 58.483 50.000 0.00 0.00 31.08 3.51
131 132 2.233922 GGGAATTTCAGAGGAGACGTGA 59.766 50.000 0.00 0.00 0.00 4.35
143 144 2.459644 CCAGCTTGATGGGGAATTTCA 58.540 47.619 0.00 0.00 36.64 2.69
144 145 1.137675 GCCAGCTTGATGGGGAATTTC 59.862 52.381 7.05 0.00 40.97 2.17
177 178 1.231963 GATGGGTGGGGGTAGGATTT 58.768 55.000 0.00 0.00 0.00 2.17
323 331 4.492160 GGTCGACGCCAGCGATGA 62.492 66.667 20.32 12.54 42.83 2.92
325 333 4.796231 GTGGTCGACGCCAGCGAT 62.796 66.667 20.32 2.73 42.83 4.58
335 343 0.171231 CAGATTCAGAGCGTGGTCGA 59.829 55.000 0.00 0.00 39.71 4.20
342 350 2.007549 CAGCAGCAGATTCAGAGCG 58.992 57.895 0.00 0.00 0.00 5.03
370 378 2.434884 CTGGCTTCGGCGTCATGT 60.435 61.111 6.85 0.00 42.91 3.21
371 379 3.869272 GCTGGCTTCGGCGTCATG 61.869 66.667 6.85 0.00 42.91 3.07
373 381 4.393155 ATGCTGGCTTCGGCGTCA 62.393 61.111 6.85 0.83 45.43 4.35
377 385 3.567797 GTCGATGCTGGCTTCGGC 61.568 66.667 23.47 20.35 41.77 5.54
378 386 3.257561 CGTCGATGCTGGCTTCGG 61.258 66.667 23.47 10.38 41.77 4.30
380 388 3.084579 CACGTCGATGCTGGCTTC 58.915 61.111 4.06 0.00 0.00 3.86
384 392 3.190849 CAGGCACGTCGATGCTGG 61.191 66.667 10.61 0.00 45.38 4.85
385 393 2.433145 ACAGGCACGTCGATGCTG 60.433 61.111 10.61 9.54 45.38 4.41
386 394 2.433145 CACAGGCACGTCGATGCT 60.433 61.111 10.61 0.00 45.38 3.79
409 430 2.811431 CAACAACGGCAAGGAAGATGTA 59.189 45.455 0.00 0.00 0.00 2.29
412 433 1.981256 ACAACAACGGCAAGGAAGAT 58.019 45.000 0.00 0.00 0.00 2.40
423 444 2.095768 CAGGACCAGCAATACAACAACG 60.096 50.000 0.00 0.00 0.00 4.10
428 449 1.072266 ACCCAGGACCAGCAATACAA 58.928 50.000 0.00 0.00 0.00 2.41
432 453 0.540365 CAACACCCAGGACCAGCAAT 60.540 55.000 0.00 0.00 0.00 3.56
449 476 1.206610 GAGCTCACTCCTGATCAGCAA 59.793 52.381 17.76 6.53 36.90 3.91
461 488 2.792878 AGTTACCTACACGAGCTCACT 58.207 47.619 15.40 3.03 0.00 3.41
463 490 3.630769 CCATAGTTACCTACACGAGCTCA 59.369 47.826 15.40 0.00 0.00 4.26
473 500 5.452776 CCGATCTTGCAACCATAGTTACCTA 60.453 44.000 0.00 0.00 33.27 3.08
518 548 7.921041 ATGTAGAGATTGGGATCTGTTCTTA 57.079 36.000 0.00 0.00 42.66 2.10
519 549 6.821616 ATGTAGAGATTGGGATCTGTTCTT 57.178 37.500 0.00 0.00 42.66 2.52
520 550 9.030452 GTATATGTAGAGATTGGGATCTGTTCT 57.970 37.037 0.00 0.00 42.66 3.01
521 551 8.807118 TGTATATGTAGAGATTGGGATCTGTTC 58.193 37.037 0.00 0.00 42.66 3.18
522 552 8.727100 TGTATATGTAGAGATTGGGATCTGTT 57.273 34.615 0.00 0.00 42.66 3.16
523 553 8.756927 CATGTATATGTAGAGATTGGGATCTGT 58.243 37.037 0.00 0.00 42.66 3.41
524 554 8.756927 ACATGTATATGTAGAGATTGGGATCTG 58.243 37.037 2.87 0.00 45.45 2.90
525 555 8.907829 ACATGTATATGTAGAGATTGGGATCT 57.092 34.615 2.87 0.00 45.45 2.75
571 622 4.418392 GTGCACTGCAGAAATTAATGGAG 58.582 43.478 23.35 9.05 40.08 3.86
572 623 3.193267 GGTGCACTGCAGAAATTAATGGA 59.807 43.478 23.35 4.31 40.08 3.41
573 624 3.194116 AGGTGCACTGCAGAAATTAATGG 59.806 43.478 23.35 0.00 40.08 3.16
659 713 0.524862 CTCAGCATGGACACCAAAGC 59.475 55.000 9.46 9.46 36.95 3.51
661 715 1.699083 TCTCTCAGCATGGACACCAAA 59.301 47.619 0.00 0.00 36.95 3.28
691 745 1.008403 ACTGGTCCAGGAGGTAGCTA 58.992 55.000 23.06 0.00 35.51 3.32
838 893 2.512056 AGGCTACTCTCTTGAGCTCCTA 59.488 50.000 12.15 0.00 43.85 2.94
876 931 6.740905 GTGCTTCGTATTTGAATTCATCGAAA 59.259 34.615 23.95 13.17 35.06 3.46
914 969 7.573283 GCTTTTTGTAGTGTCCATTCTTCCTAC 60.573 40.741 0.00 0.00 0.00 3.18
915 970 6.430000 GCTTTTTGTAGTGTCCATTCTTCCTA 59.570 38.462 0.00 0.00 0.00 2.94
1017 1072 6.441924 GGACATTGATATCCTCCAGAATCCTA 59.558 42.308 0.00 0.00 31.75 2.94
1110 1165 1.342672 ACTCCTTTGACACCGGTGGT 61.343 55.000 36.47 22.65 35.62 4.16
1122 1177 0.250640 CTGTCTGCCTGCACTCCTTT 60.251 55.000 0.00 0.00 0.00 3.11
1220 1275 4.128925 TCTACATTGCTAGCTTCACCAG 57.871 45.455 17.23 6.40 0.00 4.00
1238 1293 3.292492 TGGGAACTACTGCGAGATCTA 57.708 47.619 0.00 0.00 0.00 1.98
1378 1433 7.717568 TCAACTATACTCTTAGCCACTGAATC 58.282 38.462 0.00 0.00 0.00 2.52
1383 1438 5.422331 TGCTTCAACTATACTCTTAGCCACT 59.578 40.000 0.00 0.00 0.00 4.00
1412 1467 5.620206 TGTCTGTATCACCATGTTTCTTGT 58.380 37.500 0.00 0.00 0.00 3.16
1420 1475 4.943093 TGATGGTTTGTCTGTATCACCATG 59.057 41.667 6.86 0.00 46.24 3.66
1424 1479 4.393062 CCAGTGATGGTTTGTCTGTATCAC 59.607 45.833 0.00 0.00 44.81 3.06
1441 1496 5.097742 TGTTTTTGAAGTCTCTCCAGTGA 57.902 39.130 0.00 0.00 0.00 3.41
1463 1518 2.880629 ATACCTCTGCCCGCTGACCT 62.881 60.000 0.00 0.00 0.00 3.85
1550 1611 1.829533 CTACCCATGCCACCATGCC 60.830 63.158 0.00 0.00 45.97 4.40
1600 1661 4.360889 TGTGGGCCCATAATTTCAGAAAT 58.639 39.130 31.45 2.20 0.00 2.17
1617 1678 5.614324 TGAGATTGTAGGTTCTATGTGGG 57.386 43.478 0.00 0.00 0.00 4.61
1618 1679 7.050377 ACATTGAGATTGTAGGTTCTATGTGG 58.950 38.462 0.00 0.00 35.66 4.17
1621 1682 9.778993 CAAAACATTGAGATTGTAGGTTCTATG 57.221 33.333 0.00 0.00 0.00 2.23
1704 1769 1.439644 GACTAGCTCGGGAGGCTTG 59.560 63.158 0.00 0.00 40.74 4.01
1737 1802 2.677836 GCCACGACATCTCTTTGCAATA 59.322 45.455 0.00 0.00 0.00 1.90
1742 1807 2.266554 GAGAGCCACGACATCTCTTTG 58.733 52.381 0.00 0.00 37.32 2.77
1743 1808 1.205893 GGAGAGCCACGACATCTCTTT 59.794 52.381 0.00 0.00 39.53 2.52
1770 1835 1.376424 AGATCCCAGTGCAGTTGCG 60.376 57.895 0.00 0.00 45.83 4.85
1875 1946 5.888105 TCGTTGTAGCTAACCTTGAGTATC 58.112 41.667 0.00 0.00 0.00 2.24
1885 1956 4.153475 TGCTGGAAAATCGTTGTAGCTAAC 59.847 41.667 0.00 0.00 0.00 2.34
1902 1973 0.109153 ACTGCTTCATGTGTGCTGGA 59.891 50.000 14.29 0.00 0.00 3.86
2037 2108 9.412460 AGCTCAATGAAAATATGTTCTCCAATA 57.588 29.630 7.16 0.00 0.00 1.90
2044 2115 8.347771 TGATGCTAGCTCAATGAAAATATGTTC 58.652 33.333 17.23 0.00 0.00 3.18
2057 2128 3.920231 ATGACCTTGATGCTAGCTCAA 57.080 42.857 17.23 19.57 0.00 3.02
2092 2163 3.660669 TCACTGTCCCCCTTAAATTCCTT 59.339 43.478 0.00 0.00 0.00 3.36
2106 2177 7.440523 AGTTCTGAAACAATAATCACTGTCC 57.559 36.000 0.00 0.00 37.88 4.02
2112 2192 8.334263 TGCATGTAGTTCTGAAACAATAATCA 57.666 30.769 0.00 0.00 37.88 2.57
2173 2253 3.442273 GCGACACATTCCTTTCCCATAAA 59.558 43.478 0.00 0.00 0.00 1.40
2202 2282 5.284079 CACTCAATTTGACTTGGTTCCTTG 58.716 41.667 0.00 0.00 0.00 3.61
2232 2312 4.897224 AGAACAAATGTCGTGCATTATCG 58.103 39.130 8.01 0.00 46.29 2.92
2237 2317 3.314913 TGACAAGAACAAATGTCGTGCAT 59.685 39.130 0.00 0.00 46.99 3.96
2241 2321 4.574421 TCACATGACAAGAACAAATGTCGT 59.426 37.500 0.00 0.00 46.99 4.34
2336 2416 3.758755 TCAATGAGCTTCGCATAGGAT 57.241 42.857 0.00 0.00 0.00 3.24
2408 2488 8.472007 TGGTTCCAGTAGAAATAATTTTGTGT 57.528 30.769 0.00 0.00 35.85 3.72
2417 2497 7.769044 GCAGATACTTTGGTTCCAGTAGAAATA 59.231 37.037 9.08 0.00 35.85 1.40
2428 2508 5.412594 TCAAGTGATGCAGATACTTTGGTTC 59.587 40.000 9.51 0.00 32.69 3.62
2449 2529 7.038302 ACTGTTTGAGATATCAAGGTACCTCAA 60.038 37.037 16.64 9.80 38.42 3.02
2464 2544 9.512588 AAGTGATTTGATAGAACTGTTTGAGAT 57.487 29.630 0.00 0.00 0.00 2.75
2517 2597 1.673920 GAAAGGTCCAACGTTTGCAGA 59.326 47.619 0.00 0.00 36.46 4.26
2541 2621 1.547820 AGTCGATCAAGAGCAGAGCAA 59.452 47.619 0.00 0.00 0.00 3.91
2618 2698 0.610174 AGGCATGCTCTTCAACTCGA 59.390 50.000 18.92 0.00 0.00 4.04
2676 2756 4.164843 AGGAACTCCTGCTACAAAAACA 57.835 40.909 0.00 0.00 46.55 2.83
2739 2822 1.946745 GCTCTAGCTGACCACCAATC 58.053 55.000 0.00 0.00 38.21 2.67
2781 2867 3.403038 TGCCACTTCTGCTTCTACTTTC 58.597 45.455 0.00 0.00 0.00 2.62
2786 2872 2.106511 AGGTTTGCCACTTCTGCTTCTA 59.893 45.455 0.00 0.00 37.19 2.10
2830 3015 8.561738 ACCTTACTCCATGTTAATGTTAGTTG 57.438 34.615 0.00 0.00 32.93 3.16
2835 3020 5.714806 CCCAACCTTACTCCATGTTAATGTT 59.285 40.000 0.00 0.00 31.27 2.71
2843 3028 3.496870 GCTATCCCCAACCTTACTCCATG 60.497 52.174 0.00 0.00 0.00 3.66
2874 3061 3.601443 CCATGAGGTTCGAACTTCTCT 57.399 47.619 32.20 19.95 36.15 3.10
2977 3164 4.630894 AAAGTCGCAATCTTTCACAACA 57.369 36.364 0.00 0.00 30.57 3.33
2995 3182 0.109597 GCACTGCATCCGGACAAAAG 60.110 55.000 6.12 4.88 0.00 2.27
3002 3189 0.379669 GAAGATTGCACTGCATCCGG 59.620 55.000 4.10 0.00 38.76 5.14
3004 3191 2.089980 AGTGAAGATTGCACTGCATCC 58.910 47.619 4.10 0.00 44.39 3.51
3048 3235 7.363793 CCCTCAAAACCCAACAAATATTCTAGG 60.364 40.741 0.00 0.00 0.00 3.02
3055 3242 4.530161 CCATCCCTCAAAACCCAACAAATA 59.470 41.667 0.00 0.00 0.00 1.40
3093 3280 7.657354 GGAAATATTGTCTGTTTTTCTTGCCTT 59.343 33.333 0.00 0.00 0.00 4.35
3103 3290 6.265196 TCAAGCACAGGAAATATTGTCTGTTT 59.735 34.615 16.62 10.04 38.27 2.83
3206 3393 6.055588 GCTGAGTGTACCAATGTATAACCAT 58.944 40.000 0.00 0.00 0.00 3.55
3258 3556 6.591935 TCTCTGAAAGCTCTCCAAGTTTTTA 58.408 36.000 0.00 0.00 38.39 1.52
3295 3593 7.979786 ATATTTGTCCTCCTTGAGTCTCTTA 57.020 36.000 0.65 0.00 0.00 2.10
3311 3609 7.214467 TCCAGACAAGGAAACAATATTTGTC 57.786 36.000 7.40 7.40 44.81 3.18
3315 3613 6.139679 TCCTCCAGACAAGGAAACAATATT 57.860 37.500 0.00 0.00 39.99 1.28
3453 7761 7.911651 TCTCTAAGTCATCCATTTTGAGAACT 58.088 34.615 0.00 0.00 32.51 3.01
3456 7764 6.441924 ACCTCTCTAAGTCATCCATTTTGAGA 59.558 38.462 0.00 0.00 33.73 3.27
3468 7776 5.420421 CCATCTCTGAAACCTCTCTAAGTCA 59.580 44.000 0.00 0.00 0.00 3.41
3512 7838 5.123027 GGTAGTTTCTCAAGCTGAGGAAATG 59.877 44.000 13.84 0.00 43.15 2.32
3513 7839 5.221925 TGGTAGTTTCTCAAGCTGAGGAAAT 60.222 40.000 10.56 10.56 43.15 2.17
3560 7886 5.010012 AGTTTTGGTGCTTCAGGTAAATCTG 59.990 40.000 0.00 0.00 36.17 2.90
3689 8015 5.716703 TCCTCTGATGTTGTCTCTGATGTTA 59.283 40.000 0.00 0.00 0.00 2.41
3728 8054 8.421784 TCAGTGTTGTTTCTATGAGTTCTAACT 58.578 33.333 0.00 0.00 43.16 2.24
3729 8055 8.589335 TCAGTGTTGTTTCTATGAGTTCTAAC 57.411 34.615 0.00 0.00 0.00 2.34
3730 8056 7.872993 CCTCAGTGTTGTTTCTATGAGTTCTAA 59.127 37.037 0.00 0.00 33.86 2.10
3731 8057 7.378966 CCTCAGTGTTGTTTCTATGAGTTCTA 58.621 38.462 0.00 0.00 33.86 2.10
3732 8058 6.226787 CCTCAGTGTTGTTTCTATGAGTTCT 58.773 40.000 0.00 0.00 33.86 3.01
3733 8059 5.106908 GCCTCAGTGTTGTTTCTATGAGTTC 60.107 44.000 0.00 0.00 33.86 3.01
3734 8060 4.757149 GCCTCAGTGTTGTTTCTATGAGTT 59.243 41.667 0.00 0.00 33.86 3.01
3735 8061 4.319177 GCCTCAGTGTTGTTTCTATGAGT 58.681 43.478 0.00 0.00 33.86 3.41
3736 8062 3.686726 GGCCTCAGTGTTGTTTCTATGAG 59.313 47.826 0.00 0.00 35.14 2.90
3737 8063 3.327757 AGGCCTCAGTGTTGTTTCTATGA 59.672 43.478 0.00 0.00 0.00 2.15
3738 8064 3.438087 CAGGCCTCAGTGTTGTTTCTATG 59.562 47.826 0.00 0.00 0.00 2.23
3739 8065 3.327757 TCAGGCCTCAGTGTTGTTTCTAT 59.672 43.478 0.00 0.00 0.00 1.98
3740 8066 2.703536 TCAGGCCTCAGTGTTGTTTCTA 59.296 45.455 0.00 0.00 0.00 2.10
3741 8067 1.490490 TCAGGCCTCAGTGTTGTTTCT 59.510 47.619 0.00 0.00 0.00 2.52
3742 8068 1.967319 TCAGGCCTCAGTGTTGTTTC 58.033 50.000 0.00 0.00 0.00 2.78
3743 8069 2.435372 TTCAGGCCTCAGTGTTGTTT 57.565 45.000 0.00 0.00 0.00 2.83
3744 8070 2.233271 CATTCAGGCCTCAGTGTTGTT 58.767 47.619 0.00 0.00 0.00 2.83
3745 8071 1.901591 CATTCAGGCCTCAGTGTTGT 58.098 50.000 0.00 0.00 0.00 3.32
3746 8072 0.524862 GCATTCAGGCCTCAGTGTTG 59.475 55.000 0.00 0.00 0.00 3.33
3747 8073 0.111061 TGCATTCAGGCCTCAGTGTT 59.889 50.000 0.00 0.00 0.00 3.32
3785 8112 4.764172 TCTAGCTCCATTTCTCTTTGCTC 58.236 43.478 0.00 0.00 0.00 4.26
3802 8129 6.483640 CACAACTGTAATAGGGGATTTCTAGC 59.516 42.308 0.00 0.00 0.00 3.42
3804 8131 6.674861 TCCACAACTGTAATAGGGGATTTCTA 59.325 38.462 0.00 0.00 0.00 2.10
3816 8143 5.045578 AGCATCCTAACTCCACAACTGTAAT 60.046 40.000 0.00 0.00 0.00 1.89
3846 8173 4.218312 AGTGCACCTTCTCCAAAGAATTT 58.782 39.130 14.63 0.00 40.68 1.82
3847 8174 3.837355 AGTGCACCTTCTCCAAAGAATT 58.163 40.909 14.63 0.00 40.68 2.17
3858 8185 0.737715 CACGGCTCTAGTGCACCTTC 60.738 60.000 14.63 0.00 32.52 3.46
3859 8186 1.293498 CACGGCTCTAGTGCACCTT 59.707 57.895 14.63 0.00 32.52 3.50
3896 8223 6.312672 CGGATGTACCAATTTCCAAATTTTCC 59.687 38.462 0.00 0.00 36.52 3.13
3902 8229 5.013547 ACATCGGATGTACCAATTTCCAAA 58.986 37.500 21.49 0.00 42.78 3.28
4005 8332 3.323403 AGAGGAGCTTGTACATATCCAGC 59.677 47.826 18.52 14.07 32.21 4.85
4044 8371 3.562393 CCTCTCAGGTGTTCACTCCTAGA 60.562 52.174 0.21 4.44 37.73 2.43
4045 8372 2.757868 CCTCTCAGGTGTTCACTCCTAG 59.242 54.545 0.21 0.00 37.73 3.02
4046 8373 2.808919 CCTCTCAGGTGTTCACTCCTA 58.191 52.381 0.21 0.00 37.73 2.94
4068 8395 6.650807 CAGTATTGTAAGCAAAGAGACTCCAA 59.349 38.462 0.00 0.00 38.21 3.53
4089 8416 5.720041 ACATCTCTACTAAACTTGGGCAGTA 59.280 40.000 0.00 0.00 32.94 2.74
4142 8469 9.573166 ACAAGCTTAATGCATCCACTAATATTA 57.427 29.630 0.00 0.00 45.94 0.98
4154 8481 6.720112 AATATGGACACAAGCTTAATGCAT 57.280 33.333 0.00 7.29 45.94 3.96
4178 8505 4.689549 ATGCCCTGCTGCTTGCCA 62.690 61.111 0.00 0.00 42.00 4.92
4197 8524 6.739331 AGAAGATCCTTGGACTAACTATGG 57.261 41.667 0.00 0.00 0.00 2.74
4200 8527 7.091902 ACTCCTAGAAGATCCTTGGACTAACTA 60.092 40.741 0.00 0.00 34.09 2.24
4240 8567 2.158842 GGCAACTCTGATACAGCTCCAT 60.159 50.000 0.00 0.00 0.00 3.41
4243 8570 2.680312 TGGCAACTCTGATACAGCTC 57.320 50.000 0.00 0.00 37.61 4.09


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

AutoCloner maintained by Alex Coulton.