Multiple sequence alignment - TraesCS3A01G344000

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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 TraesCS3A01G344000 chr3A 100.000 6704 0 0 1 6704 593348174 593341471 0.000000e+00 12381
1 TraesCS3A01G344000 chr3A 79.385 325 43 13 2968 3291 653189538 653189839 2.450000e-49 207
2 TraesCS3A01G344000 chr3A 97.297 111 3 0 6594 6704 593341174 593341284 8.880000e-44 189
3 TraesCS3A01G344000 chr3B 93.425 6312 270 56 27 6258 591372869 591366623 0.000000e+00 9223
4 TraesCS3A01G344000 chr3B 83.806 247 32 6 6316 6561 252610593 252610832 1.880000e-55 228
5 TraesCS3A01G344000 chr3D 92.966 2417 91 20 650 3051 449744964 449742612 0.000000e+00 3448
6 TraesCS3A01G344000 chr3D 92.251 1626 86 19 3705 5310 449742047 449740442 0.000000e+00 2268
7 TraesCS3A01G344000 chr3D 93.308 1300 70 10 5309 6593 449739953 449738656 0.000000e+00 1903
8 TraesCS3A01G344000 chr3D 88.889 675 59 11 1 671 449745635 449744973 0.000000e+00 817
9 TraesCS3A01G344000 chr3D 89.929 566 27 12 3086 3629 449742611 449742054 0.000000e+00 702
10 TraesCS3A01G344000 chr3D 87.349 166 12 1 5145 5310 449740183 449740027 1.490000e-41 182
11 TraesCS3A01G344000 chr3D 94.118 102 6 0 5309 5410 449740283 449740182 9.000000e-34 156
12 TraesCS3A01G344000 chr2B 86.166 253 26 5 6307 6558 793327965 793328209 1.430000e-66 265
13 TraesCS3A01G344000 chr2B 84.362 243 31 2 6320 6562 610844740 610844505 1.450000e-56 231
14 TraesCS3A01G344000 chr2B 83.871 248 30 5 6317 6561 163570457 163570697 1.880000e-55 228
15 TraesCS3A01G344000 chr2B 97.368 114 3 0 6591 6704 636413691 636413578 1.910000e-45 195
16 TraesCS3A01G344000 chr2B 97.321 112 3 0 6593 6704 636394100 636394211 2.470000e-44 191
17 TraesCS3A01G344000 chr2B 96.460 113 4 0 6592 6704 227681728 227681840 3.190000e-43 187
18 TraesCS3A01G344000 chr4B 80.997 321 52 7 2973 3291 647702324 647702637 5.190000e-61 246
19 TraesCS3A01G344000 chr4B 83.936 249 30 2 6317 6561 1991628 1991870 5.230000e-56 230
20 TraesCS3A01G344000 chr6D 85.837 233 27 1 6329 6561 45485510 45485284 6.720000e-60 243
21 TraesCS3A01G344000 chr2D 84.959 246 30 4 6316 6561 38791433 38791195 6.720000e-60 243
22 TraesCS3A01G344000 chr2D 95.763 118 4 1 6587 6704 566589156 566589040 8.880000e-44 189
23 TraesCS3A01G344000 chr7D 84.375 256 28 5 6307 6562 41993090 41992847 2.420000e-59 241
24 TraesCS3A01G344000 chr7D 80.556 324 40 12 2968 3291 16730863 16730563 1.880000e-55 228
25 TraesCS3A01G344000 chr7D 80.717 223 31 8 2966 3184 501092113 501092327 5.380000e-36 163
26 TraesCS3A01G344000 chr4A 81.231 325 38 12 2968 3292 594659497 594659798 2.420000e-59 241
27 TraesCS3A01G344000 chr6A 80.556 324 40 10 2968 3291 126295096 126295396 1.880000e-55 228
28 TraesCS3A01G344000 chr1A 85.507 207 29 1 2968 3174 532736815 532737020 1.460000e-51 215
29 TraesCS3A01G344000 chr1A 84.038 213 31 2 2968 3180 541517792 541517583 1.140000e-47 202
30 TraesCS3A01G344000 chr6B 97.321 112 3 0 6593 6704 265822984 265822873 2.470000e-44 191
31 TraesCS3A01G344000 chr6B 96.396 111 4 0 6594 6704 662061769 662061879 4.130000e-42 183
32 TraesCS3A01G344000 chr2A 96.522 115 4 0 6590 6704 737479128 737479014 2.470000e-44 191
33 TraesCS3A01G344000 chr7B 96.460 113 4 0 6592 6704 708580972 708580860 3.190000e-43 187
34 TraesCS3A01G344000 chrUn 90.000 90 9 0 3159 3248 367564070 367563981 4.250000e-22 117


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 TraesCS3A01G344000 chr3A 593341471 593348174 6703 True 12381.000000 12381 100.000000 1 6704 1 chr3A.!!$R1 6703
1 TraesCS3A01G344000 chr3B 591366623 591372869 6246 True 9223.000000 9223 93.425000 27 6258 1 chr3B.!!$R1 6231
2 TraesCS3A01G344000 chr3D 449738656 449745635 6979 True 1353.714286 3448 91.258571 1 6593 7 chr3D.!!$R1 6592

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
306 308 0.343372 ACATCCTCCCAGAGCCCTTA 59.657 55.000 0.00 0.0 0.00 2.69 F
1278 1376 0.042731 TCCGAGATCCTTCCCCTGTT 59.957 55.000 0.00 0.0 0.00 3.16 F
1542 1652 0.110192 GCAGCGGTGTTTCTGTTAGC 60.110 55.000 17.07 0.0 33.09 3.09 F
2182 2292 0.512952 GTAGACAGTTTGGTGCTGCG 59.487 55.000 0.00 0.0 37.47 5.18 F
2191 2301 0.605050 TTGGTGCTGCGTTGCTATGA 60.605 50.000 0.00 0.0 0.00 2.15 F
3390 3506 3.247411 CCGATCATTGTTGCTTATGCGTA 59.753 43.478 0.00 0.0 43.34 4.42 F
4285 4427 1.383248 ATAGCTTCCACCTCCGCCT 60.383 57.895 0.00 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1837 0.038166 TGAGCATTTCCCTCCACACC 59.962 55.000 0.00 0.0 0.00 4.16 R
2163 2273 0.512952 CGCAGCACCAAACTGTCTAC 59.487 55.000 0.00 0.0 37.47 2.59 R
2666 2776 7.278646 TGCAAATAAGCACAACAACATAAAACA 59.721 29.630 0.00 0.0 40.11 2.83 R
3932 4074 1.202927 CCTTGGGAGGCTCAACTTGAA 60.203 52.381 17.69 0.0 35.94 2.69 R
3946 4088 5.982890 ATATGAACAGTTGAAACCTTGGG 57.017 39.130 0.00 0.0 0.00 4.12 R
4719 4878 0.033504 GAGAAGTGTCGCCCTGTCAA 59.966 55.000 0.00 0.0 0.00 3.18 R
6225 6919 0.031178 CTCAGGCCAAACAGCAACAC 59.969 55.000 5.01 0.0 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
23 24 2.754946 AATCTAAGACCGGCGTTCAA 57.245 45.000 7.31 0.00 0.00 2.69
48 49 8.059798 ACTAGTTGACAAATACAGTATACCGT 57.940 34.615 0.00 0.00 0.00 4.83
52 53 3.800531 ACAAATACAGTATACCGTGGGC 58.199 45.455 1.83 0.00 0.00 5.36
54 55 1.985473 ATACAGTATACCGTGGGCGA 58.015 50.000 1.83 0.00 41.33 5.54
91 92 1.272425 CCTAACATTGGGTTGGCCTCA 60.272 52.381 3.32 0.00 40.73 3.86
95 96 2.934838 ATTGGGTTGGCCTCAGGGG 61.935 63.158 3.32 0.00 38.36 4.79
104 105 3.086600 CCTCAGGGGCCAGGAGTC 61.087 72.222 18.70 0.00 30.32 3.36
105 106 2.040278 CTCAGGGGCCAGGAGTCT 59.960 66.667 4.39 0.00 0.00 3.24
106 107 2.284921 TCAGGGGCCAGGAGTCTG 60.285 66.667 4.39 1.86 40.59 3.51
189 191 2.032528 CAAGCCACGAAGCTCCCA 59.967 61.111 4.49 0.00 44.11 4.37
240 242 2.101082 CCCTAGCTCTCGTCCCTTTTAC 59.899 54.545 0.00 0.00 0.00 2.01
244 246 2.897969 AGCTCTCGTCCCTTTTACAAGA 59.102 45.455 0.00 0.00 30.57 3.02
246 248 3.586892 CTCTCGTCCCTTTTACAAGACC 58.413 50.000 0.00 0.00 30.57 3.85
296 298 4.622695 GCTCAATAGCTCATACATCCTCCC 60.623 50.000 0.00 0.00 45.85 4.30
297 299 4.492646 TCAATAGCTCATACATCCTCCCA 58.507 43.478 0.00 0.00 0.00 4.37
306 308 0.343372 ACATCCTCCCAGAGCCCTTA 59.657 55.000 0.00 0.00 0.00 2.69
309 311 0.417841 TCCTCCCAGAGCCCTTACTT 59.582 55.000 0.00 0.00 0.00 2.24
321 323 1.273896 CCCTTACTTGAGTCCTCCCCT 60.274 57.143 0.00 0.00 0.00 4.79
381 384 1.088306 ACCGAGACTCTGACGACATC 58.912 55.000 0.35 0.00 0.00 3.06
409 412 5.497464 TCACCTATCACAGATGGTTTTGA 57.503 39.130 0.00 0.00 0.00 2.69
435 438 2.427453 CTCTACCACATGCGGTTAGACT 59.573 50.000 11.37 0.00 40.67 3.24
438 441 1.071699 ACCACATGCGGTTAGACTGTT 59.928 47.619 0.00 0.00 34.91 3.16
452 455 3.275143 AGACTGTTCGATCTCGTGATCT 58.725 45.455 21.45 5.36 45.10 2.75
473 476 7.553760 TGATCTGTATCACTGCATACATGTTTT 59.446 33.333 2.30 0.00 38.34 2.43
476 479 7.174772 TCTGTATCACTGCATACATGTTTTGTT 59.825 33.333 2.30 0.00 38.34 2.83
527 530 2.080286 ACACTCCAGATTACACGTGC 57.920 50.000 17.22 0.00 0.00 5.34
547 550 2.068519 CTCGATGCAAACACACAGCTA 58.931 47.619 0.00 0.00 0.00 3.32
552 555 1.535028 TGCAAACACACAGCTATTCGG 59.465 47.619 0.00 0.00 0.00 4.30
576 579 0.459585 TCTAACCGCACTCGCATTCC 60.460 55.000 0.00 0.00 38.40 3.01
594 597 1.137872 TCCACACAAATTTGGGCACAC 59.862 47.619 20.40 0.00 34.06 3.82
638 667 3.947834 GTGAGATTTACAATCACCCCCTG 59.052 47.826 0.00 0.00 37.88 4.45
658 687 1.472480 GGTTGAACATTGGATGGACGG 59.528 52.381 0.00 0.00 33.60 4.79
725 784 4.477302 CTTACGAAAGCCGAAAAGGAAA 57.523 40.909 0.00 0.00 45.00 3.13
726 785 4.464112 CTTACGAAAGCCGAAAAGGAAAG 58.536 43.478 0.00 0.00 45.00 2.62
727 786 2.567985 ACGAAAGCCGAAAAGGAAAGA 58.432 42.857 0.00 0.00 45.00 2.52
728 787 2.946990 ACGAAAGCCGAAAAGGAAAGAA 59.053 40.909 0.00 0.00 45.00 2.52
737 796 5.234329 GCCGAAAAGGAAAGAAAAGGAAAAG 59.766 40.000 0.00 0.00 45.00 2.27
879 951 1.627297 AAACTCCTCCATCCTCCGCC 61.627 60.000 0.00 0.00 0.00 6.13
919 991 2.513204 CCTCCGCCGTCTCGTCTA 60.513 66.667 0.00 0.00 0.00 2.59
921 993 3.152937 CTCCGCCGTCTCGTCTACG 62.153 68.421 0.00 0.00 40.01 3.51
951 1023 3.700350 CCACCCTCCCTCCCCTCT 61.700 72.222 0.00 0.00 0.00 3.69
952 1024 2.041405 CACCCTCCCTCCCCTCTC 60.041 72.222 0.00 0.00 0.00 3.20
953 1025 3.369388 ACCCTCCCTCCCCTCTCC 61.369 72.222 0.00 0.00 0.00 3.71
954 1026 3.039526 CCCTCCCTCCCCTCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
955 1027 2.612251 CCTCCCTCCCCTCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
956 1028 2.612251 CTCCCTCCCCTCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
957 1029 3.036959 TCCCTCCCCTCTCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
958 1030 4.179599 CCCTCCCCTCTCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
959 1031 3.039526 CCTCCCCTCTCCTCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
960 1032 2.612251 CTCCCCTCTCCTCCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
961 1033 2.018086 CTCCCCTCTCCTCCCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
962 1034 2.015726 TCCCCTCTCCTCCCCTCTC 61.016 68.421 0.00 0.00 0.00 3.20
963 1035 2.612251 CCCTCTCCTCCCCTCTCC 59.388 72.222 0.00 0.00 0.00 3.71
964 1036 2.018086 CCCTCTCCTCCCCTCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
965 1037 1.541672 CCTCTCCTCCCCTCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
966 1038 1.541672 CTCTCCTCCCCTCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
967 1039 2.015726 TCTCCTCCCCTCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
968 1040 2.204624 TCCTCCCCTCTCCTCCCA 60.205 66.667 0.00 0.00 0.00 4.37
969 1041 2.041405 CCTCCCCTCTCCTCCCAC 60.041 72.222 0.00 0.00 0.00 4.61
970 1042 2.041405 CTCCCCTCTCCTCCCACC 60.041 72.222 0.00 0.00 0.00 4.61
1271 1369 0.591170 CGCTCTCTCCGAGATCCTTC 59.409 60.000 0.00 0.00 42.62 3.46
1277 1375 0.397816 CTCCGAGATCCTTCCCCTGT 60.398 60.000 0.00 0.00 0.00 4.00
1278 1376 0.042731 TCCGAGATCCTTCCCCTGTT 59.957 55.000 0.00 0.00 0.00 3.16
1364 1462 4.599047 ATCTGATCTGCTAGGTTGTAGC 57.401 45.455 0.00 0.00 40.76 3.58
1388 1486 1.626321 TCACCTCACCCGCATTTCTAA 59.374 47.619 0.00 0.00 0.00 2.10
1389 1487 1.737793 CACCTCACCCGCATTTCTAAC 59.262 52.381 0.00 0.00 0.00 2.34
1390 1488 1.339727 ACCTCACCCGCATTTCTAACC 60.340 52.381 0.00 0.00 0.00 2.85
1391 1489 1.379527 CTCACCCGCATTTCTAACCC 58.620 55.000 0.00 0.00 0.00 4.11
1413 1511 6.096423 ACCCTTTATTTTATTTTCCTCTCGCC 59.904 38.462 0.00 0.00 0.00 5.54
1459 1557 1.911464 GCGCCTTTACAATTTTCGCTC 59.089 47.619 0.00 0.00 38.29 5.03
1539 1649 0.814457 TTTGCAGCGGTGTTTCTGTT 59.186 45.000 17.07 0.00 33.09 3.16
1541 1651 1.225855 TGCAGCGGTGTTTCTGTTAG 58.774 50.000 17.07 0.00 33.09 2.34
1542 1652 0.110192 GCAGCGGTGTTTCTGTTAGC 60.110 55.000 17.07 0.00 33.09 3.09
1547 1657 1.196808 CGGTGTTTCTGTTAGCGCATT 59.803 47.619 11.47 0.00 0.00 3.56
1584 1694 5.545658 ATGTTTCTGTGTGCTAAATACCG 57.454 39.130 0.00 0.00 0.00 4.02
1691 1801 4.340950 GGTGATGACAAGGAAAAGGAAACA 59.659 41.667 0.00 0.00 0.00 2.83
1694 1804 5.532406 TGATGACAAGGAAAAGGAAACAGAG 59.468 40.000 0.00 0.00 0.00 3.35
1712 1822 5.355596 ACAGAGAAGATTGAAATAGAGCCG 58.644 41.667 0.00 0.00 0.00 5.52
2009 2119 1.619654 CAGTTGGCAACCTCAATGGA 58.380 50.000 25.81 0.00 39.71 3.41
2081 2191 5.203528 AGGCATTATGTTGGTAGCATTTCT 58.796 37.500 0.00 0.00 0.00 2.52
2163 2273 7.558161 TGGCTTTGTTAGATCATCAGTTATG 57.442 36.000 0.00 0.00 36.88 1.90
2167 2277 9.534565 GCTTTGTTAGATCATCAGTTATGTAGA 57.465 33.333 0.00 0.00 36.89 2.59
2182 2292 0.512952 GTAGACAGTTTGGTGCTGCG 59.487 55.000 0.00 0.00 37.47 5.18
2191 2301 0.605050 TTGGTGCTGCGTTGCTATGA 60.605 50.000 0.00 0.00 0.00 2.15
2289 2399 5.163713 CCTTAACTTCATGCTAACTGGAAGC 60.164 44.000 0.00 0.00 40.21 3.86
2507 2617 3.385577 GCATAGCTACTTCTGCCAGTAC 58.614 50.000 5.86 0.00 0.00 2.73
2890 3001 6.201806 CCTCTATCTAAATTTGACAGCTTCCG 59.798 42.308 0.00 0.00 0.00 4.30
3390 3506 3.247411 CCGATCATTGTTGCTTATGCGTA 59.753 43.478 0.00 0.00 43.34 4.42
3713 3852 4.456911 AGACAAATTCTGCATGTACAGTGG 59.543 41.667 0.33 0.00 38.84 4.00
3946 4088 6.375455 TGGAATTTAGATTCAAGTTGAGCCTC 59.625 38.462 5.56 5.08 42.82 4.70
3966 4108 3.891366 CTCCCAAGGTTTCAACTGTTCAT 59.109 43.478 0.00 0.00 0.00 2.57
4285 4427 1.383248 ATAGCTTCCACCTCCGCCT 60.383 57.895 0.00 0.00 0.00 5.52
4319 4461 6.149142 TGCCAGGATTTAATTGAATTTTGTGC 59.851 34.615 0.00 5.86 0.00 4.57
4475 4617 2.806608 TGAACTACGTCGCTTCCTTT 57.193 45.000 0.00 0.00 0.00 3.11
4476 4618 3.102052 TGAACTACGTCGCTTCCTTTT 57.898 42.857 0.00 0.00 0.00 2.27
4482 4624 4.624452 ACTACGTCGCTTCCTTTTATGTTC 59.376 41.667 0.00 0.00 0.00 3.18
4483 4625 2.740447 ACGTCGCTTCCTTTTATGTTCC 59.260 45.455 0.00 0.00 0.00 3.62
4485 4627 3.062234 CGTCGCTTCCTTTTATGTTCCTC 59.938 47.826 0.00 0.00 0.00 3.71
4487 4629 4.093556 GTCGCTTCCTTTTATGTTCCTCTG 59.906 45.833 0.00 0.00 0.00 3.35
4488 4630 3.181506 CGCTTCCTTTTATGTTCCTCTGC 60.182 47.826 0.00 0.00 0.00 4.26
4489 4631 3.129462 GCTTCCTTTTATGTTCCTCTGCC 59.871 47.826 0.00 0.00 0.00 4.85
4531 4682 3.836949 ACTGCATAAAATGGCTTGTTCG 58.163 40.909 0.00 0.00 0.00 3.95
4532 4683 2.599973 CTGCATAAAATGGCTTGTTCGC 59.400 45.455 0.00 0.00 0.00 4.70
4662 4821 7.453752 AGACCACCTCTCATTTTTACTGTACTA 59.546 37.037 0.00 0.00 0.00 1.82
4719 4878 2.146146 TTGCCTCTGCTGCAATCCCT 62.146 55.000 3.02 0.00 43.36 4.20
5067 5235 9.632638 ATTGCTGTCAAATAATACTAGTTGGAT 57.367 29.630 0.00 0.00 34.56 3.41
5136 5307 2.387510 AGTTCTTCCTCTAGTTCCCCCT 59.612 50.000 0.00 0.00 0.00 4.79
5177 5350 6.473758 GTGAAGTTCCTTCCCTTAACTGTAT 58.526 40.000 0.00 0.00 39.51 2.29
5210 5807 0.908910 AATGTGACACCCTGCGGATA 59.091 50.000 2.45 0.00 0.00 2.59
5218 5825 2.565645 CCCTGCGGATAGGACGAGG 61.566 68.421 0.00 0.00 40.42 4.63
5219 5826 2.565645 CCTGCGGATAGGACGAGGG 61.566 68.421 0.00 0.00 40.42 4.30
5220 5827 1.828660 CTGCGGATAGGACGAGGGT 60.829 63.158 0.00 0.00 0.00 4.34
5221 5828 2.076622 CTGCGGATAGGACGAGGGTG 62.077 65.000 0.00 0.00 0.00 4.61
5222 5829 2.857744 GCGGATAGGACGAGGGTGG 61.858 68.421 0.00 0.00 0.00 4.61
5223 5830 2.857744 CGGATAGGACGAGGGTGGC 61.858 68.421 0.00 0.00 0.00 5.01
5224 5831 2.728817 GATAGGACGAGGGTGGCG 59.271 66.667 0.00 0.00 0.00 5.69
5225 5832 1.826921 GATAGGACGAGGGTGGCGA 60.827 63.158 0.00 0.00 0.00 5.54
5226 5833 1.797211 GATAGGACGAGGGTGGCGAG 61.797 65.000 0.00 0.00 0.00 5.03
5448 6131 8.851541 ATGTCCAAATAAATCAGCATTTTGTT 57.148 26.923 0.00 0.00 33.95 2.83
5462 6145 3.460857 TTTTGTTAATTTGCAGGCGGT 57.539 38.095 0.00 0.00 0.00 5.68
5557 6242 2.356665 TGTTTGCAAAGGCCACTAGA 57.643 45.000 13.26 0.00 40.13 2.43
5561 6246 0.401738 TGCAAAGGCCACTAGAGCTT 59.598 50.000 5.01 0.00 40.13 3.74
5677 6362 0.109723 GACTGGTGGCCACAAAGGTA 59.890 55.000 35.78 13.91 40.61 3.08
5873 6558 7.014905 ACACTTCTCTAGGTTATACAACACACA 59.985 37.037 0.00 0.00 36.29 3.72
5899 6584 3.738982 TGAATCATATGACCGCGGAAAT 58.261 40.909 35.90 25.48 0.00 2.17
6152 6845 9.661187 GTATCAATCTGTTCATCATTCATGTTC 57.339 33.333 0.00 0.00 33.66 3.18
6225 6919 0.318699 TCGGTTTGTCTCGCTCAGTG 60.319 55.000 0.00 0.00 0.00 3.66
6252 6946 1.202879 TGTTTGGCCTGAGGGTAACAG 60.203 52.381 3.32 0.00 39.74 3.16
6318 7014 9.884636 TGTTTGCTAGATTGTATTGTACTGTAT 57.115 29.630 0.00 0.00 0.00 2.29
6334 7032 4.603131 ACTGTATTACCTCCGTTCTGGTA 58.397 43.478 0.00 0.00 39.52 3.25
6339 7037 7.663827 TGTATTACCTCCGTTCTGGTATATTG 58.336 38.462 0.00 0.00 38.45 1.90
6342 7040 3.387050 ACCTCCGTTCTGGTATATTGGTC 59.613 47.826 0.00 0.00 39.52 4.02
6345 7043 3.640029 TCCGTTCTGGTATATTGGTCCTC 59.360 47.826 0.00 0.00 39.52 3.71
6349 7047 5.163447 CGTTCTGGTATATTGGTCCTCTTCA 60.163 44.000 0.00 0.00 0.00 3.02
6359 7057 5.643379 TTGGTCCTCTTCATATTTTGTGC 57.357 39.130 0.00 0.00 0.00 4.57
6360 7058 4.016444 TGGTCCTCTTCATATTTTGTGCC 58.984 43.478 0.00 0.00 0.00 5.01
6361 7059 4.016444 GGTCCTCTTCATATTTTGTGCCA 58.984 43.478 0.00 0.00 0.00 4.92
6375 7073 7.814264 ATTTTGTGCCAAAATTTGACCATAA 57.186 28.000 15.79 5.97 0.00 1.90
6411 7109 8.604640 AATTGACAAAATGTTAATGCATGTCA 57.395 26.923 0.00 4.80 36.80 3.58
6462 7160 7.624360 TCCGAACATAGTTTTTAATGATGCT 57.376 32.000 0.00 0.00 0.00 3.79
6532 7232 7.875554 GTCAAAATTTGGCCCAAAATACTAAGA 59.124 33.333 13.87 2.85 36.90 2.10
6544 7244 8.683615 CCCAAAATACTAAGAGGACCAATAAAC 58.316 37.037 0.00 0.00 0.00 2.01
6576 7276 7.096312 CGGAGTTAGTATTTACTTATTGCCGAC 60.096 40.741 0.00 0.00 37.73 4.79
6593 7293 5.277825 TGCCGACTTTGTCAATTTGTTTAG 58.722 37.500 0.00 0.00 32.09 1.85
6594 7294 5.066634 TGCCGACTTTGTCAATTTGTTTAGA 59.933 36.000 0.00 0.00 32.09 2.10
6595 7295 5.625311 GCCGACTTTGTCAATTTGTTTAGAG 59.375 40.000 0.00 0.00 32.09 2.43
6596 7296 6.142817 CCGACTTTGTCAATTTGTTTAGAGG 58.857 40.000 0.00 0.00 32.09 3.69
6597 7297 6.238648 CCGACTTTGTCAATTTGTTTAGAGGT 60.239 38.462 0.00 0.00 32.09 3.85
6598 7298 7.041644 CCGACTTTGTCAATTTGTTTAGAGGTA 60.042 37.037 0.00 0.00 32.09 3.08
6599 7299 8.339714 CGACTTTGTCAATTTGTTTAGAGGTAA 58.660 33.333 0.00 0.00 32.09 2.85
6604 7304 8.856153 TGTCAATTTGTTTAGAGGTAATAGCA 57.144 30.769 0.00 0.00 0.00 3.49
6605 7305 8.726988 TGTCAATTTGTTTAGAGGTAATAGCAC 58.273 33.333 0.00 0.00 0.00 4.40
6606 7306 8.182227 GTCAATTTGTTTAGAGGTAATAGCACC 58.818 37.037 0.00 0.00 39.02 5.01
6607 7307 7.338449 TCAATTTGTTTAGAGGTAATAGCACCC 59.662 37.037 0.00 0.00 39.62 4.61
6608 7308 4.395959 TGTTTAGAGGTAATAGCACCCG 57.604 45.455 0.00 0.00 39.62 5.28
6609 7309 4.025360 TGTTTAGAGGTAATAGCACCCGA 58.975 43.478 0.00 0.00 39.62 5.14
6610 7310 4.098960 TGTTTAGAGGTAATAGCACCCGAG 59.901 45.833 0.00 0.00 39.62 4.63
6611 7311 2.750141 AGAGGTAATAGCACCCGAGA 57.250 50.000 0.00 0.00 39.62 4.04
6612 7312 3.246416 AGAGGTAATAGCACCCGAGAT 57.754 47.619 0.00 0.00 39.62 2.75
6613 7313 3.158676 AGAGGTAATAGCACCCGAGATC 58.841 50.000 0.00 0.00 39.62 2.75
6614 7314 2.231721 GAGGTAATAGCACCCGAGATCC 59.768 54.545 0.00 0.00 39.62 3.36
6615 7315 1.968493 GGTAATAGCACCCGAGATCCA 59.032 52.381 0.00 0.00 31.91 3.41
6616 7316 2.288886 GGTAATAGCACCCGAGATCCAC 60.289 54.545 0.00 0.00 31.91 4.02
6617 7317 1.496060 AATAGCACCCGAGATCCACA 58.504 50.000 0.00 0.00 0.00 4.17
6618 7318 1.496060 ATAGCACCCGAGATCCACAA 58.504 50.000 0.00 0.00 0.00 3.33
6619 7319 1.271856 TAGCACCCGAGATCCACAAA 58.728 50.000 0.00 0.00 0.00 2.83
6620 7320 0.321653 AGCACCCGAGATCCACAAAC 60.322 55.000 0.00 0.00 0.00 2.93
6621 7321 0.321653 GCACCCGAGATCCACAAACT 60.322 55.000 0.00 0.00 0.00 2.66
6622 7322 1.882352 GCACCCGAGATCCACAAACTT 60.882 52.381 0.00 0.00 0.00 2.66
6623 7323 1.806542 CACCCGAGATCCACAAACTTG 59.193 52.381 0.00 0.00 0.00 3.16
6624 7324 0.804989 CCCGAGATCCACAAACTTGC 59.195 55.000 0.00 0.00 0.00 4.01
6625 7325 1.522668 CCGAGATCCACAAACTTGCA 58.477 50.000 0.00 0.00 0.00 4.08
6626 7326 1.197721 CCGAGATCCACAAACTTGCAC 59.802 52.381 0.00 0.00 0.00 4.57
6627 7327 1.197721 CGAGATCCACAAACTTGCACC 59.802 52.381 0.00 0.00 0.00 5.01
6628 7328 1.197721 GAGATCCACAAACTTGCACCG 59.802 52.381 0.00 0.00 0.00 4.94
6629 7329 1.202758 AGATCCACAAACTTGCACCGA 60.203 47.619 0.00 0.00 0.00 4.69
6630 7330 1.606668 GATCCACAAACTTGCACCGAA 59.393 47.619 0.00 0.00 0.00 4.30
6631 7331 1.686355 TCCACAAACTTGCACCGAAT 58.314 45.000 0.00 0.00 0.00 3.34
6632 7332 1.336440 TCCACAAACTTGCACCGAATG 59.664 47.619 0.00 0.00 0.00 2.67
6633 7333 1.066908 CCACAAACTTGCACCGAATGT 59.933 47.619 0.00 0.00 0.00 2.71
6647 7347 4.647611 ACCGAATGTGATGTTTTAGTCCA 58.352 39.130 0.00 0.00 0.00 4.02
6648 7348 5.067273 ACCGAATGTGATGTTTTAGTCCAA 58.933 37.500 0.00 0.00 0.00 3.53
6649 7349 5.533154 ACCGAATGTGATGTTTTAGTCCAAA 59.467 36.000 0.00 0.00 0.00 3.28
6650 7350 6.039941 ACCGAATGTGATGTTTTAGTCCAAAA 59.960 34.615 0.00 0.00 33.66 2.44
6662 7362 6.463995 TTTAGTCCAAAACTTGCAGAATGT 57.536 33.333 0.00 0.00 39.55 2.71
6663 7363 4.311816 AGTCCAAAACTTGCAGAATGTG 57.688 40.909 0.00 0.00 33.83 3.21
6664 7364 3.953612 AGTCCAAAACTTGCAGAATGTGA 59.046 39.130 0.00 0.00 33.83 3.58
6665 7365 4.044426 GTCCAAAACTTGCAGAATGTGAC 58.956 43.478 0.00 0.00 39.31 3.67
6666 7366 3.953612 TCCAAAACTTGCAGAATGTGACT 59.046 39.130 0.00 0.00 39.31 3.41
6667 7367 4.046462 CCAAAACTTGCAGAATGTGACTG 58.954 43.478 0.00 0.00 39.31 3.51
6668 7368 4.202040 CCAAAACTTGCAGAATGTGACTGA 60.202 41.667 0.00 0.00 39.31 3.41
6669 7369 4.825546 AAACTTGCAGAATGTGACTGAG 57.174 40.909 0.00 0.00 39.31 3.35
6670 7370 2.775890 ACTTGCAGAATGTGACTGAGG 58.224 47.619 0.00 0.00 39.31 3.86
6671 7371 2.369860 ACTTGCAGAATGTGACTGAGGA 59.630 45.455 0.00 0.00 39.31 3.71
6672 7372 2.462456 TGCAGAATGTGACTGAGGAC 57.538 50.000 0.00 0.00 39.31 3.85
6673 7373 1.973515 TGCAGAATGTGACTGAGGACT 59.026 47.619 0.00 0.00 39.31 3.85
6674 7374 2.028658 TGCAGAATGTGACTGAGGACTC 60.029 50.000 0.00 0.00 39.31 3.36
6675 7375 2.676463 GCAGAATGTGACTGAGGACTCC 60.676 54.545 0.00 0.00 39.31 3.85
6676 7376 2.564504 CAGAATGTGACTGAGGACTCCA 59.435 50.000 0.00 0.00 37.54 3.86
6677 7377 2.564947 AGAATGTGACTGAGGACTCCAC 59.435 50.000 0.00 0.00 0.00 4.02
6678 7378 2.015456 ATGTGACTGAGGACTCCACA 57.985 50.000 10.74 10.74 41.24 4.17
6679 7379 1.788229 TGTGACTGAGGACTCCACAA 58.212 50.000 7.22 0.00 35.16 3.33
6680 7380 2.115427 TGTGACTGAGGACTCCACAAA 58.885 47.619 7.22 0.00 35.16 2.83
6681 7381 2.158957 TGTGACTGAGGACTCCACAAAC 60.159 50.000 7.22 0.00 35.16 2.93
6682 7382 2.103263 GTGACTGAGGACTCCACAAACT 59.897 50.000 0.00 0.00 0.00 2.66
6683 7383 2.771943 TGACTGAGGACTCCACAAACTT 59.228 45.455 0.00 0.00 0.00 2.66
6684 7384 3.134458 GACTGAGGACTCCACAAACTTG 58.866 50.000 0.00 0.00 0.00 3.16
6685 7385 2.771943 ACTGAGGACTCCACAAACTTGA 59.228 45.455 0.00 0.00 0.00 3.02
6686 7386 3.134458 CTGAGGACTCCACAAACTTGAC 58.866 50.000 0.00 0.00 0.00 3.18
6687 7387 2.503765 TGAGGACTCCACAAACTTGACA 59.496 45.455 0.00 0.00 0.00 3.58
6688 7388 2.872858 GAGGACTCCACAAACTTGACAC 59.127 50.000 0.00 0.00 0.00 3.67
6689 7389 1.947456 GGACTCCACAAACTTGACACC 59.053 52.381 0.00 0.00 0.00 4.16
6690 7390 1.947456 GACTCCACAAACTTGACACCC 59.053 52.381 0.00 0.00 0.00 4.61
6691 7391 1.564348 ACTCCACAAACTTGACACCCT 59.436 47.619 0.00 0.00 0.00 4.34
6692 7392 2.775384 ACTCCACAAACTTGACACCCTA 59.225 45.455 0.00 0.00 0.00 3.53
6693 7393 3.394606 ACTCCACAAACTTGACACCCTAT 59.605 43.478 0.00 0.00 0.00 2.57
6694 7394 3.750371 TCCACAAACTTGACACCCTATG 58.250 45.455 0.00 0.00 0.00 2.23
6702 7402 6.239008 CAAACTTGACACCCTATGTGATGTTT 60.239 38.462 0.00 5.21 46.49 2.83
6703 7403 6.323739 AAACTTGACACCCTATGTGATGTTTT 59.676 34.615 0.00 0.00 44.66 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.677842 ACTAGTTGAACGCCGGTCTT 59.322 50.000 2.87 0.00 0.00 3.01
23 24 7.972277 CACGGTATACTGTATTTGTCAACTAGT 59.028 37.037 16.95 0.00 33.39 2.57
33 34 2.694628 TCGCCCACGGTATACTGTATTT 59.305 45.455 16.95 0.00 40.63 1.40
54 55 4.070552 GCTTCCCAGCCGACGAGT 62.071 66.667 0.00 0.00 40.61 4.18
97 98 0.250513 GGGCTAACACCAGACTCCTG 59.749 60.000 0.00 0.00 40.09 3.86
103 104 0.981277 GGGCTAGGGCTAACACCAGA 60.981 60.000 0.00 0.00 38.73 3.86
104 105 1.271840 TGGGCTAGGGCTAACACCAG 61.272 60.000 0.00 0.00 38.73 4.00
105 106 0.623324 ATGGGCTAGGGCTAACACCA 60.623 55.000 0.00 0.00 38.73 4.17
106 107 0.108774 GATGGGCTAGGGCTAACACC 59.891 60.000 0.00 0.00 38.73 4.16
108 109 0.397957 TCGATGGGCTAGGGCTAACA 60.398 55.000 0.00 0.00 38.73 2.41
109 110 0.977395 ATCGATGGGCTAGGGCTAAC 59.023 55.000 0.00 0.00 38.73 2.34
110 111 1.267121 GATCGATGGGCTAGGGCTAA 58.733 55.000 0.54 0.00 38.73 3.09
152 154 1.470098 GCACGCCAAGATCATGTTTCT 59.530 47.619 0.00 0.00 0.00 2.52
189 191 3.227276 CCTAGCCGACCTCGCCAT 61.227 66.667 0.00 0.00 38.18 4.40
240 242 0.035056 CTACCCTTGGCCTGGTCTTG 60.035 60.000 14.34 4.73 36.04 3.02
244 246 1.923909 GACCTACCCTTGGCCTGGT 60.924 63.158 15.12 15.12 38.69 4.00
246 248 1.987855 TCGACCTACCCTTGGCCTG 60.988 63.158 3.32 0.00 0.00 4.85
296 298 2.167487 GAGGACTCAAGTAAGGGCTCTG 59.833 54.545 0.00 0.00 0.00 3.35
297 299 2.462723 GAGGACTCAAGTAAGGGCTCT 58.537 52.381 0.00 0.00 0.00 4.09
306 308 2.316372 ACATAGAGGGGAGGACTCAAGT 59.684 50.000 1.32 0.00 37.43 3.16
309 311 4.834406 AATACATAGAGGGGAGGACTCA 57.166 45.455 1.32 0.00 37.43 3.41
352 354 1.076677 AGAGTCTCGGTGGGTTCCTTA 59.923 52.381 0.00 0.00 0.00 2.69
353 355 0.178929 AGAGTCTCGGTGGGTTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
381 384 4.038522 ACCATCTGTGATAGGTGATCGAAG 59.961 45.833 0.00 0.00 40.09 3.79
409 412 0.465705 CCGCATGTGGTAGAGATGGT 59.534 55.000 17.59 0.00 0.00 3.55
452 455 6.816134 ACAAAACATGTATGCAGTGATACA 57.184 33.333 0.00 14.00 41.63 2.29
493 496 4.081406 TGGAGTGTAAAGTTAGCGGTAGA 58.919 43.478 0.00 0.00 0.00 2.59
500 503 7.061905 CACGTGTAATCTGGAGTGTAAAGTTAG 59.938 40.741 7.58 0.00 0.00 2.34
527 530 0.870393 AGCTGTGTGTTTGCATCGAG 59.130 50.000 0.00 0.00 0.00 4.04
552 555 1.266466 GCGAGTGCGGTTAGAGTTAC 58.734 55.000 0.00 0.00 38.16 2.50
566 569 3.552684 CCAAATTTGTGTGGAATGCGAGT 60.553 43.478 16.73 0.00 37.03 4.18
576 579 2.306341 TGTGTGCCCAAATTTGTGTG 57.694 45.000 16.73 6.37 0.00 3.82
594 597 5.008911 CACACATGGTATTGGTACATGGATG 59.991 44.000 8.51 3.00 39.30 3.51
638 667 1.472480 CCGTCCATCCAATGTTCAACC 59.528 52.381 0.00 0.00 0.00 3.77
658 687 1.035923 TGAGATCCGAGGAGACATGC 58.964 55.000 0.00 0.00 0.00 4.06
719 778 6.153851 TCGTTTCCTTTTCCTTTTCTTTCCTT 59.846 34.615 0.00 0.00 0.00 3.36
720 779 5.655090 TCGTTTCCTTTTCCTTTTCTTTCCT 59.345 36.000 0.00 0.00 0.00 3.36
721 780 5.898174 TCGTTTCCTTTTCCTTTTCTTTCC 58.102 37.500 0.00 0.00 0.00 3.13
722 781 7.921214 AGATTCGTTTCCTTTTCCTTTTCTTTC 59.079 33.333 0.00 0.00 0.00 2.62
723 782 7.706607 CAGATTCGTTTCCTTTTCCTTTTCTTT 59.293 33.333 0.00 0.00 0.00 2.52
724 783 7.147897 ACAGATTCGTTTCCTTTTCCTTTTCTT 60.148 33.333 0.00 0.00 0.00 2.52
725 784 6.321435 ACAGATTCGTTTCCTTTTCCTTTTCT 59.679 34.615 0.00 0.00 0.00 2.52
726 785 6.504398 ACAGATTCGTTTCCTTTTCCTTTTC 58.496 36.000 0.00 0.00 0.00 2.29
727 786 6.465439 ACAGATTCGTTTCCTTTTCCTTTT 57.535 33.333 0.00 0.00 0.00 2.27
728 787 6.294010 GCTACAGATTCGTTTCCTTTTCCTTT 60.294 38.462 0.00 0.00 0.00 3.11
737 796 5.332707 GGATTTTGCTACAGATTCGTTTCC 58.667 41.667 0.00 0.00 0.00 3.13
879 951 3.603365 GGCACGAAGGAAATGGGG 58.397 61.111 0.00 0.00 0.00 4.96
919 991 4.371417 TGGCGAGGGGTAGACCGT 62.371 66.667 0.00 0.00 41.60 4.83
921 993 3.468140 GGTGGCGAGGGGTAGACC 61.468 72.222 0.00 0.00 39.11 3.85
948 1020 1.541672 GGAGGAGAGGGGAGGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
949 1021 2.015726 GGGAGGAGAGGGGAGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
950 1022 2.328589 TGGGAGGAGAGGGGAGGAG 61.329 68.421 0.00 0.00 0.00 3.69
951 1023 2.204624 TGGGAGGAGAGGGGAGGA 60.205 66.667 0.00 0.00 0.00 3.71
952 1024 2.041405 GTGGGAGGAGAGGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
953 1025 2.041405 GGTGGGAGGAGAGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
954 1026 2.540910 AGGTGGGAGGAGAGGGGA 60.541 66.667 0.00 0.00 0.00 4.81
955 1027 2.041405 GAGGTGGGAGGAGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
956 1028 2.041405 GGAGGTGGGAGGAGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
957 1029 2.041405 GGGAGGTGGGAGGAGAGG 60.041 72.222 0.00 0.00 0.00 3.69
958 1030 2.041405 GGGGAGGTGGGAGGAGAG 60.041 72.222 0.00 0.00 0.00 3.20
959 1031 4.075793 CGGGGAGGTGGGAGGAGA 62.076 72.222 0.00 0.00 0.00 3.71
960 1032 4.075793 TCGGGGAGGTGGGAGGAG 62.076 72.222 0.00 0.00 0.00 3.69
961 1033 4.075793 CTCGGGGAGGTGGGAGGA 62.076 72.222 0.00 0.00 0.00 3.71
1278 1376 2.724454 TCACCACCGGAAACAGAAAAA 58.276 42.857 9.46 0.00 0.00 1.94
1291 1389 0.318120 CAAAACAGGGCATCACCACC 59.682 55.000 0.00 0.00 42.05 4.61
1364 1462 2.469465 AATGCGGGTGAGGTGACCAG 62.469 60.000 3.63 0.00 37.80 4.00
1388 1486 6.096423 GGCGAGAGGAAAATAAAATAAAGGGT 59.904 38.462 0.00 0.00 0.00 4.34
1389 1487 6.096282 TGGCGAGAGGAAAATAAAATAAAGGG 59.904 38.462 0.00 0.00 0.00 3.95
1390 1488 6.972901 GTGGCGAGAGGAAAATAAAATAAAGG 59.027 38.462 0.00 0.00 0.00 3.11
1391 1489 6.687105 CGTGGCGAGAGGAAAATAAAATAAAG 59.313 38.462 0.00 0.00 0.00 1.85
1413 1511 0.732571 ATTATTTCAGCCCGTGCGTG 59.267 50.000 0.00 0.00 44.33 5.34
1459 1557 0.107508 ATCCTCAATGCACTCCACGG 60.108 55.000 0.00 0.00 0.00 4.94
1539 1649 2.742053 GTCAAAAGACCTCAATGCGCTA 59.258 45.455 9.73 0.00 0.00 4.26
1541 1651 1.725931 CGTCAAAAGACCTCAATGCGC 60.726 52.381 0.00 0.00 0.00 6.09
1542 1652 1.798223 TCGTCAAAAGACCTCAATGCG 59.202 47.619 0.00 0.00 0.00 4.73
1547 1657 4.511454 CAGAAACATCGTCAAAAGACCTCA 59.489 41.667 0.00 0.00 0.00 3.86
1564 1674 6.657836 ATACGGTATTTAGCACACAGAAAC 57.342 37.500 0.00 0.00 0.00 2.78
1584 1694 3.674997 TCACAGTTCAGCCAAGGAATAC 58.325 45.455 0.00 0.00 0.00 1.89
1691 1801 4.651503 TCCGGCTCTATTTCAATCTTCTCT 59.348 41.667 0.00 0.00 0.00 3.10
1694 1804 4.061596 CCTCCGGCTCTATTTCAATCTTC 58.938 47.826 0.00 0.00 0.00 2.87
1712 1822 4.423209 ACCTCCTGGGCCTCCTCC 62.423 72.222 4.53 0.00 39.10 4.30
1727 1837 0.038166 TGAGCATTTCCCTCCACACC 59.962 55.000 0.00 0.00 0.00 4.16
1799 1909 2.111384 GCCCTCTTGGAGTAGACATCA 58.889 52.381 0.00 0.00 35.39 3.07
2009 2119 9.331466 ACATGATAATCCTTATACTCTGATGGT 57.669 33.333 0.00 0.00 0.00 3.55
2094 2204 3.865164 CGTCAACTTGCAGCATGAGTATA 59.135 43.478 14.99 0.00 39.69 1.47
2131 2241 4.158394 TGATCTAACAAAGCCATTTCCTGC 59.842 41.667 0.00 0.00 0.00 4.85
2163 2273 0.512952 CGCAGCACCAAACTGTCTAC 59.487 55.000 0.00 0.00 37.47 2.59
2167 2277 1.433064 CAACGCAGCACCAAACTGT 59.567 52.632 0.00 0.00 37.47 3.55
2182 2292 2.260844 TGCAGCCCTATCATAGCAAC 57.739 50.000 0.00 0.00 0.00 4.17
2191 2301 9.759473 ATTAATACTATTCAATTGCAGCCCTAT 57.241 29.630 0.00 0.00 0.00 2.57
2666 2776 7.278646 TGCAAATAAGCACAACAACATAAAACA 59.721 29.630 0.00 0.00 40.11 2.83
3390 3506 8.919145 TGGACCAATTATCAAAGTTAACTGTTT 58.081 29.630 9.34 0.00 0.00 2.83
3594 3731 7.584108 TCTATGTTTACAGCATTGTTTGACAG 58.416 34.615 0.00 0.00 38.76 3.51
3713 3852 7.412137 AAAAATCTGCATGAAAAACACTAGC 57.588 32.000 0.00 0.00 0.00 3.42
3742 3883 6.596888 TCAAACAGAATCACATCCTCAAGATC 59.403 38.462 0.00 0.00 30.59 2.75
3783 3925 3.694072 GCAGCACCCATAGTCATGTAAAA 59.306 43.478 0.00 0.00 0.00 1.52
3932 4074 1.202927 CCTTGGGAGGCTCAACTTGAA 60.203 52.381 17.69 0.00 35.94 2.69
3946 4088 5.982890 ATATGAACAGTTGAAACCTTGGG 57.017 39.130 0.00 0.00 0.00 4.12
4285 4427 7.619050 TCAATTAAATCCTGGCATTGCTAAAA 58.381 30.769 8.82 0.00 0.00 1.52
4319 4461 3.740397 CCACCCATGCTGCACACG 61.740 66.667 3.57 0.00 0.00 4.49
4328 4470 3.767902 AACATTTGGAAACCACCCATG 57.232 42.857 0.00 0.00 30.78 3.66
4475 4617 1.675714 CGCACAGGCAGAGGAACATAA 60.676 52.381 0.00 0.00 41.24 1.90
4476 4618 0.108186 CGCACAGGCAGAGGAACATA 60.108 55.000 0.00 0.00 41.24 2.29
4482 4624 2.352814 GGTATATACGCACAGGCAGAGG 60.353 54.545 6.79 0.00 41.24 3.69
4483 4625 2.558795 AGGTATATACGCACAGGCAGAG 59.441 50.000 6.79 0.00 41.24 3.35
4485 4627 2.677199 CAGGTATATACGCACAGGCAG 58.323 52.381 6.79 0.00 41.24 4.85
4487 4629 1.270094 TGCAGGTATATACGCACAGGC 60.270 52.381 10.35 6.69 0.00 4.85
4488 4630 2.812358 TGCAGGTATATACGCACAGG 57.188 50.000 10.35 0.00 0.00 4.00
4489 4631 3.736252 GTCTTGCAGGTATATACGCACAG 59.264 47.826 13.12 12.99 33.29 3.66
4531 4682 1.956629 TAGAGCCCTTGTAGCCACGC 61.957 60.000 0.00 0.00 0.00 5.34
4532 4683 0.179108 GTAGAGCCCTTGTAGCCACG 60.179 60.000 0.00 0.00 0.00 4.94
4630 4789 2.898729 ATGAGAGGTGGTCTATTGCG 57.101 50.000 0.00 0.00 34.71 4.85
4662 4821 5.512576 GGAAAGAACTATGTGGTACAGTGGT 60.513 44.000 0.00 0.00 41.80 4.16
4719 4878 0.033504 GAGAAGTGTCGCCCTGTCAA 59.966 55.000 0.00 0.00 0.00 3.18
4938 5106 5.349270 CACATTTGGGTTGATAATTGTGCAG 59.651 40.000 0.00 0.00 33.91 4.41
4944 5112 8.542080 ACATTCATCACATTTGGGTTGATAATT 58.458 29.630 0.00 0.00 0.00 1.40
4993 5161 8.343168 ACTATGTGATAGATACTTCCACTAGC 57.657 38.462 0.00 0.00 36.68 3.42
5067 5235 2.034124 GTTGACGGGGGCTAGTACATA 58.966 52.381 0.00 0.00 0.00 2.29
5136 5307 5.192176 ACTTCACCCCTTAACACGTTTTTA 58.808 37.500 0.00 0.00 0.00 1.52
5177 5350 5.761234 GGTGTCACATTTCTACCTAACAACA 59.239 40.000 5.12 0.00 0.00 3.33
5218 5825 1.324005 AACTAGAGGAGCTCGCCACC 61.324 60.000 7.83 0.00 35.36 4.61
5219 5826 0.101579 GAACTAGAGGAGCTCGCCAC 59.898 60.000 7.83 0.00 35.36 5.01
5220 5827 1.038130 GGAACTAGAGGAGCTCGCCA 61.038 60.000 7.83 0.00 35.36 5.69
5221 5828 1.737201 GGAACTAGAGGAGCTCGCC 59.263 63.158 7.83 1.47 35.36 5.54
5222 5829 1.737201 GGGAACTAGAGGAGCTCGC 59.263 63.158 7.83 2.06 35.36 5.03
5223 5830 0.395862 TGGGGAACTAGAGGAGCTCG 60.396 60.000 7.83 0.00 35.36 5.03
5224 5831 1.867363 TTGGGGAACTAGAGGAGCTC 58.133 55.000 4.71 4.71 0.00 4.09
5225 5832 2.577772 ATTGGGGAACTAGAGGAGCT 57.422 50.000 0.00 0.00 0.00 4.09
5226 5833 3.653835 AAATTGGGGAACTAGAGGAGC 57.346 47.619 0.00 0.00 0.00 4.70
5250 5857 6.428465 TGAAGAGCGTGTAAATGTCCAAAATA 59.572 34.615 0.00 0.00 0.00 1.40
5251 5858 5.240623 TGAAGAGCGTGTAAATGTCCAAAAT 59.759 36.000 0.00 0.00 0.00 1.82
5432 6115 8.719648 CCTGCAAATTAACAAAATGCTGATTTA 58.280 29.630 0.00 0.00 37.94 1.40
5448 6131 2.418368 ATCAGACCGCCTGCAAATTA 57.582 45.000 0.00 0.00 42.62 1.40
5451 6134 1.327303 AAAATCAGACCGCCTGCAAA 58.673 45.000 0.00 0.00 42.62 3.68
5561 6246 4.785511 TTTTCGTGGTCCAACTCAAAAA 57.214 36.364 0.00 0.00 0.00 1.94
5677 6362 1.181741 TCTGAACTGCTCTCGGTGCT 61.182 55.000 0.00 0.00 0.00 4.40
5873 6558 3.264947 CGCGGTCATATGATTCATCCAT 58.735 45.455 9.02 0.00 0.00 3.41
5899 6584 4.523943 CACCATCAATCTTCAGAACCCAAA 59.476 41.667 0.00 0.00 0.00 3.28
6105 6798 4.949121 ACATACTAGAGACCTTCAAGGGT 58.051 43.478 8.75 0.00 40.58 4.34
6146 6839 9.554724 AACTACGTTGCATAAATAAAGAACATG 57.445 29.630 0.00 0.00 0.00 3.21
6152 6845 9.814507 TGTTACAACTACGTTGCATAAATAAAG 57.185 29.630 6.64 0.00 46.20 1.85
6225 6919 0.031178 CTCAGGCCAAACAGCAACAC 59.969 55.000 5.01 0.00 0.00 3.32
6271 6967 8.928733 CAAACATTAAGCAACAAAAGATAGCAT 58.071 29.630 0.00 0.00 0.00 3.79
6281 6977 7.432869 ACAATCTAGCAAACATTAAGCAACAA 58.567 30.769 0.00 0.00 0.00 2.83
6318 7014 4.964262 ACCAATATACCAGAACGGAGGTAA 59.036 41.667 0.00 0.00 43.14 2.85
6334 7032 7.014615 GGCACAAAATATGAAGAGGACCAATAT 59.985 37.037 0.00 0.00 0.00 1.28
6339 7037 4.016444 TGGCACAAAATATGAAGAGGACC 58.984 43.478 0.00 0.00 31.92 4.46
6385 7083 9.053840 TGACATGCATTAACATTTTGTCAATTT 57.946 25.926 10.64 0.00 31.39 1.82
6388 7086 9.702494 TTATGACATGCATTAACATTTTGTCAA 57.298 25.926 15.55 5.51 35.43 3.18
6439 7137 9.950680 AATAGCATCATTAAAAACTATGTTCGG 57.049 29.630 0.00 0.00 0.00 4.30
6495 7195 5.942826 GGCCAAATTTTGACCATGGATTTAA 59.057 36.000 21.47 7.63 32.85 1.52
6512 7212 5.656859 GTCCTCTTAGTATTTTGGGCCAAAT 59.343 40.000 30.82 21.74 33.19 2.32
6519 7219 8.683615 GGTTTATTGGTCCTCTTAGTATTTTGG 58.316 37.037 0.00 0.00 0.00 3.28
6529 7229 3.307480 CGTCCTGGTTTATTGGTCCTCTT 60.307 47.826 0.00 0.00 0.00 2.85
6532 7232 1.280998 CCGTCCTGGTTTATTGGTCCT 59.719 52.381 0.00 0.00 0.00 3.85
6544 7244 5.848833 AGTAAATACTAACTCCGTCCTGG 57.151 43.478 0.00 0.00 34.13 4.45
6593 7293 2.231721 GGATCTCGGGTGCTATTACCTC 59.768 54.545 0.00 0.00 40.66 3.85
6594 7294 2.249139 GGATCTCGGGTGCTATTACCT 58.751 52.381 0.00 0.00 40.66 3.08
6595 7295 1.968493 TGGATCTCGGGTGCTATTACC 59.032 52.381 0.00 0.00 40.10 2.85
6596 7296 2.364324 TGTGGATCTCGGGTGCTATTAC 59.636 50.000 0.00 0.00 0.00 1.89
6597 7297 2.673258 TGTGGATCTCGGGTGCTATTA 58.327 47.619 0.00 0.00 0.00 0.98
6598 7298 1.496060 TGTGGATCTCGGGTGCTATT 58.504 50.000 0.00 0.00 0.00 1.73
6599 7299 1.496060 TTGTGGATCTCGGGTGCTAT 58.504 50.000 0.00 0.00 0.00 2.97
6600 7300 1.066430 GTTTGTGGATCTCGGGTGCTA 60.066 52.381 0.00 0.00 0.00 3.49
6601 7301 0.321653 GTTTGTGGATCTCGGGTGCT 60.322 55.000 0.00 0.00 0.00 4.40
6602 7302 0.321653 AGTTTGTGGATCTCGGGTGC 60.322 55.000 0.00 0.00 0.00 5.01
6603 7303 1.806542 CAAGTTTGTGGATCTCGGGTG 59.193 52.381 0.00 0.00 0.00 4.61
6604 7304 1.882352 GCAAGTTTGTGGATCTCGGGT 60.882 52.381 0.00 0.00 0.00 5.28
6605 7305 0.804989 GCAAGTTTGTGGATCTCGGG 59.195 55.000 0.00 0.00 0.00 5.14
6606 7306 1.197721 GTGCAAGTTTGTGGATCTCGG 59.802 52.381 0.00 0.00 0.00 4.63
6607 7307 1.197721 GGTGCAAGTTTGTGGATCTCG 59.802 52.381 0.00 0.00 0.00 4.04
6608 7308 1.197721 CGGTGCAAGTTTGTGGATCTC 59.802 52.381 0.00 0.00 0.00 2.75
6609 7309 1.202758 TCGGTGCAAGTTTGTGGATCT 60.203 47.619 0.00 0.00 0.00 2.75
6610 7310 1.234821 TCGGTGCAAGTTTGTGGATC 58.765 50.000 0.00 0.00 0.00 3.36
6611 7311 1.686355 TTCGGTGCAAGTTTGTGGAT 58.314 45.000 0.00 0.00 0.00 3.41
6612 7312 1.336440 CATTCGGTGCAAGTTTGTGGA 59.664 47.619 0.00 0.00 0.00 4.02
6613 7313 1.066908 ACATTCGGTGCAAGTTTGTGG 59.933 47.619 0.00 0.00 0.00 4.17
6614 7314 2.118683 CACATTCGGTGCAAGTTTGTG 58.881 47.619 0.00 1.41 41.36 3.33
6615 7315 2.490328 CACATTCGGTGCAAGTTTGT 57.510 45.000 0.00 0.00 41.36 2.83
6624 7324 7.945457 TTTTGGACTAAAACATCACATTCGGTG 60.945 37.037 0.00 0.00 39.80 4.94
6625 7325 4.647611 TGGACTAAAACATCACATTCGGT 58.352 39.130 0.00 0.00 0.00 4.69
6626 7326 5.621197 TTGGACTAAAACATCACATTCGG 57.379 39.130 0.00 0.00 0.00 4.30
6638 7338 6.756074 CACATTCTGCAAGTTTTGGACTAAAA 59.244 34.615 0.00 0.00 37.72 1.52
6639 7339 6.096141 TCACATTCTGCAAGTTTTGGACTAAA 59.904 34.615 0.00 0.00 37.72 1.85
6640 7340 5.592282 TCACATTCTGCAAGTTTTGGACTAA 59.408 36.000 0.00 0.00 37.72 2.24
6641 7341 5.008613 GTCACATTCTGCAAGTTTTGGACTA 59.991 40.000 0.00 0.00 37.72 2.59
6642 7342 3.953612 TCACATTCTGCAAGTTTTGGACT 59.046 39.130 0.00 0.00 41.47 3.85
6643 7343 4.044426 GTCACATTCTGCAAGTTTTGGAC 58.956 43.478 0.00 0.00 33.76 4.02
6644 7344 3.953612 AGTCACATTCTGCAAGTTTTGGA 59.046 39.130 0.00 0.00 33.76 3.53
6645 7345 4.046462 CAGTCACATTCTGCAAGTTTTGG 58.954 43.478 0.00 0.00 33.76 3.28
6646 7346 4.923893 TCAGTCACATTCTGCAAGTTTTG 58.076 39.130 0.00 0.00 33.76 2.44
6647 7347 4.037208 CCTCAGTCACATTCTGCAAGTTTT 59.963 41.667 0.00 0.00 33.76 2.43
6648 7348 3.567164 CCTCAGTCACATTCTGCAAGTTT 59.433 43.478 0.00 0.00 33.76 2.66
6649 7349 3.144506 CCTCAGTCACATTCTGCAAGTT 58.855 45.455 0.00 0.00 33.76 2.66
6650 7350 2.369860 TCCTCAGTCACATTCTGCAAGT 59.630 45.455 0.00 0.00 33.76 3.16
6651 7351 2.740981 GTCCTCAGTCACATTCTGCAAG 59.259 50.000 0.00 0.00 33.48 4.01
6652 7352 2.369860 AGTCCTCAGTCACATTCTGCAA 59.630 45.455 0.00 0.00 33.48 4.08
6653 7353 1.973515 AGTCCTCAGTCACATTCTGCA 59.026 47.619 0.00 0.00 33.48 4.41
6654 7354 2.615869 GAGTCCTCAGTCACATTCTGC 58.384 52.381 0.00 0.00 33.48 4.26
6655 7355 2.564504 TGGAGTCCTCAGTCACATTCTG 59.435 50.000 11.33 0.00 0.00 3.02
6656 7356 2.564947 GTGGAGTCCTCAGTCACATTCT 59.435 50.000 11.33 0.00 0.00 2.40
6657 7357 2.300152 TGTGGAGTCCTCAGTCACATTC 59.700 50.000 11.33 0.00 0.00 2.67
6658 7358 2.329267 TGTGGAGTCCTCAGTCACATT 58.671 47.619 11.33 0.00 0.00 2.71
6659 7359 2.015456 TGTGGAGTCCTCAGTCACAT 57.985 50.000 11.33 0.00 0.00 3.21
6660 7360 1.788229 TTGTGGAGTCCTCAGTCACA 58.212 50.000 13.39 3.98 0.00 3.58
6661 7361 2.103263 AGTTTGTGGAGTCCTCAGTCAC 59.897 50.000 13.39 11.58 0.00 3.67
6662 7362 2.398588 AGTTTGTGGAGTCCTCAGTCA 58.601 47.619 13.39 0.00 0.00 3.41
6663 7363 3.134458 CAAGTTTGTGGAGTCCTCAGTC 58.866 50.000 13.39 10.67 0.00 3.51
6664 7364 2.771943 TCAAGTTTGTGGAGTCCTCAGT 59.228 45.455 13.39 1.28 0.00 3.41
6665 7365 3.134458 GTCAAGTTTGTGGAGTCCTCAG 58.866 50.000 13.39 3.03 0.00 3.35
6666 7366 2.503765 TGTCAAGTTTGTGGAGTCCTCA 59.496 45.455 11.33 10.57 0.00 3.86
6667 7367 2.872858 GTGTCAAGTTTGTGGAGTCCTC 59.127 50.000 11.33 7.59 0.00 3.71
6668 7368 2.421529 GGTGTCAAGTTTGTGGAGTCCT 60.422 50.000 11.33 0.00 0.00 3.85
6669 7369 1.947456 GGTGTCAAGTTTGTGGAGTCC 59.053 52.381 0.73 0.73 0.00 3.85
6670 7370 1.947456 GGGTGTCAAGTTTGTGGAGTC 59.053 52.381 0.00 0.00 0.00 3.36
6671 7371 1.564348 AGGGTGTCAAGTTTGTGGAGT 59.436 47.619 0.00 0.00 0.00 3.85
6672 7372 2.348411 AGGGTGTCAAGTTTGTGGAG 57.652 50.000 0.00 0.00 0.00 3.86
6673 7373 3.137544 ACATAGGGTGTCAAGTTTGTGGA 59.862 43.478 0.00 0.00 35.77 4.02
6674 7374 3.253188 CACATAGGGTGTCAAGTTTGTGG 59.747 47.826 0.00 0.00 42.75 4.17
6675 7375 4.488126 CACATAGGGTGTCAAGTTTGTG 57.512 45.455 0.00 0.00 42.75 3.33


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

AutoCloner maintained by Alex Coulton.