Multiple sequence alignment - TraesCS7B01G310900

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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 TraesCS7B01G310900 chr7B 100.000 2138 0 0 1 2138 556459533 556457396 0.000000e+00 3949.0
1 TraesCS7B01G310900 chr7B 100.000 1037 0 0 2448 3484 556457086 556456050 0.000000e+00 1916.0
2 TraesCS7B01G310900 chr7B 100.000 202 0 0 3926 4127 556455608 556455407 1.400000e-99 374.0
3 TraesCS7B01G310900 chr7B 95.000 120 5 1 2020 2138 692194954 692194835 1.960000e-43 187.0
4 TraesCS7B01G310900 chr7B 94.167 120 6 1 2020 2138 579495846 579495727 9.110000e-42 182.0
5 TraesCS7B01G310900 chr7B 93.333 120 7 1 2020 2138 579497405 579497286 4.240000e-40 176.0
6 TraesCS7B01G310900 chr7D 91.982 1534 57 20 527 2019 522504697 522503189 0.000000e+00 2091.0
7 TraesCS7B01G310900 chr7D 93.545 945 36 9 2450 3383 522503196 522502266 0.000000e+00 1384.0
8 TraesCS7B01G310900 chr7D 94.444 162 9 0 160 321 522505395 522505234 2.460000e-62 250.0
9 TraesCS7B01G310900 chr7D 95.620 137 6 0 1 137 522510082 522509946 1.930000e-53 220.0
10 TraesCS7B01G310900 chr7D 83.838 198 17 7 343 525 522505059 522504862 1.520000e-39 174.0
11 TraesCS7B01G310900 chr7D 87.000 100 9 1 3957 4052 522501957 522501858 4.360000e-20 110.0
12 TraesCS7B01G310900 chr7A 94.235 1301 52 9 735 2019 602806635 602805342 0.000000e+00 1965.0
13 TraesCS7B01G310900 chr7A 93.888 949 35 11 2450 3383 602805349 602804409 0.000000e+00 1410.0
14 TraesCS7B01G310900 chr7A 87.291 598 43 12 1 570 602807371 602806779 0.000000e+00 652.0
15 TraesCS7B01G310900 chr6B 87.917 960 98 11 1001 1947 11574687 11575641 0.000000e+00 1114.0
16 TraesCS7B01G310900 chr6B 87.846 650 70 3 2477 3126 11577456 11578096 0.000000e+00 754.0
17 TraesCS7B01G310900 chr6D 87.063 943 106 11 1012 1946 6319416 6320350 0.000000e+00 1051.0
18 TraesCS7B01G310900 chr6D 88.280 657 68 4 2470 3126 6320578 6321225 0.000000e+00 778.0
19 TraesCS7B01G310900 chr6D 85.823 656 84 4 2472 3127 6328274 6328920 0.000000e+00 688.0
20 TraesCS7B01G310900 chr6A 86.757 959 108 13 1001 1946 5861556 5862508 0.000000e+00 1050.0
21 TraesCS7B01G310900 chr6A 87.399 373 38 3 2754 3126 5863053 5863416 1.770000e-113 420.0
22 TraesCS7B01G310900 chr6A 89.167 120 10 1 419 535 573531034 573530915 3.320000e-31 147.0
23 TraesCS7B01G310900 chr6A 73.191 235 55 8 2480 2710 64506064 64505834 1.230000e-10 78.7
24 TraesCS7B01G310900 chr1D 78.594 626 122 11 2497 3115 492534871 492534251 1.790000e-108 403.0
25 TraesCS7B01G310900 chr1A 78.130 631 123 14 2497 3118 590996272 590995648 1.800000e-103 387.0
26 TraesCS7B01G310900 chr1B 77.636 626 128 11 2497 3115 685232258 685231638 1.810000e-98 370.0
27 TraesCS7B01G310900 chr1B 92.437 119 8 1 2021 2138 446026676 446026794 7.100000e-38 169.0
28 TraesCS7B01G310900 chr2B 74.964 695 150 18 1116 1798 792677574 792678256 8.670000e-77 298.0
29 TraesCS7B01G310900 chr2B 93.043 115 7 1 2025 2138 362663495 362663381 2.550000e-37 167.0
30 TraesCS7B01G310900 chr2D 94.215 121 6 1 2019 2138 595226677 595226797 2.530000e-42 183.0
31 TraesCS7B01G310900 chrUn 94.167 120 6 1 2020 2138 312869603 312869484 9.110000e-42 182.0
32 TraesCS7B01G310900 chrUn 94.167 120 6 1 2020 2138 312874226 312874345 9.110000e-42 182.0
33 TraesCS7B01G310900 chrUn 94.167 120 6 1 2020 2138 340781387 340781268 9.110000e-42 182.0
34 TraesCS7B01G310900 chr3B 93.443 61 2 2 4068 4127 666472143 666472084 5.680000e-14 89.8


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 TraesCS7B01G310900 chr7B 556455407 556459533 4126 True 2079.666667 3949 100.000000 1 4127 3 chr7B.!!$R2 4126
1 TraesCS7B01G310900 chr7D 522501858 522505395 3537 True 801.800000 2091 90.161800 160 4052 5 chr7D.!!$R2 3892
2 TraesCS7B01G310900 chr7A 602804409 602807371 2962 True 1342.333333 1965 91.804667 1 3383 3 chr7A.!!$R1 3382
3 TraesCS7B01G310900 chr6B 11574687 11578096 3409 False 934.000000 1114 87.881500 1001 3126 2 chr6B.!!$F1 2125
4 TraesCS7B01G310900 chr6D 6319416 6321225 1809 False 914.500000 1051 87.671500 1012 3126 2 chr6D.!!$F2 2114
5 TraesCS7B01G310900 chr6D 6328274 6328920 646 False 688.000000 688 85.823000 2472 3127 1 chr6D.!!$F1 655
6 TraesCS7B01G310900 chr6A 5861556 5863416 1860 False 735.000000 1050 87.078000 1001 3126 2 chr6A.!!$F1 2125
7 TraesCS7B01G310900 chr1D 492534251 492534871 620 True 403.000000 403 78.594000 2497 3115 1 chr1D.!!$R1 618
8 TraesCS7B01G310900 chr1A 590995648 590996272 624 True 387.000000 387 78.130000 2497 3118 1 chr1A.!!$R1 621
9 TraesCS7B01G310900 chr1B 685231638 685232258 620 True 370.000000 370 77.636000 2497 3115 1 chr1B.!!$R1 618
10 TraesCS7B01G310900 chr2B 792677574 792678256 682 False 298.000000 298 74.964000 1116 1798 1 chr2B.!!$F1 682

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
582 1006 0.102481 GCGGAGTGTCGGATACATGT 59.898 55.0 2.69 2.69 41.1 3.21 F
2018 4266 0.320683 TCAGTCGTCCAATGTGCCTG 60.321 55.0 0.00 0.00 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 4295 0.033109 ATTAAGAGCACTTGGCCCCC 60.033 55.0 6.66 0.0 46.50 5.4 R
3451 6001 0.107557 AACCGGTTGTTCGTGAGGTT 60.108 50.0 21.56 0.0 37.17 3.5 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
40 41 6.376018 TGCTTGGTAAAGTTGGTATGATAACC 59.624 38.462 0.00 0.00 36.57 2.85
64 65 5.627182 AGTCTGGTATGATTGAATCTGCT 57.373 39.130 6.73 0.00 0.00 4.24
69 70 4.571984 TGGTATGATTGAATCTGCTTCACG 59.428 41.667 6.73 0.00 43.54 4.35
81 82 1.337728 TGCTTCACGACCACCATACAG 60.338 52.381 0.00 0.00 0.00 2.74
92 93 0.323725 ACCATACAGGGCCTTGCTTG 60.324 55.000 16.02 12.39 43.89 4.01
121 130 3.129502 CGTCATGCTGTGCTGGGG 61.130 66.667 0.00 0.00 0.00 4.96
249 258 5.341872 AGAGTTCAGGAATCAGATGACAG 57.658 43.478 0.00 0.00 0.00 3.51
272 281 4.030529 GCATAACATTTGCGTGAATGTCAC 59.969 41.667 15.55 0.00 46.53 3.67
323 502 1.066645 GCCCAGCTTTTCATCCAAAGG 60.067 52.381 0.00 0.00 34.75 3.11
328 507 5.125356 CCAGCTTTTCATCCAAAGGTTTTT 58.875 37.500 0.00 0.00 41.49 1.94
331 510 4.808895 GCTTTTCATCCAAAGGTTTTTCGT 59.191 37.500 0.00 0.00 34.75 3.85
336 515 6.308371 TCATCCAAAGGTTTTTCGTAGTTC 57.692 37.500 0.00 0.00 0.00 3.01
353 532 5.632347 CGTAGTTCGATACAGTTGAAAAGGT 59.368 40.000 0.00 0.00 42.86 3.50
368 547 2.767644 AAGGTAACAAAAGCCAGGGT 57.232 45.000 0.00 0.00 41.41 4.34
369 548 1.995376 AGGTAACAAAAGCCAGGGTG 58.005 50.000 0.00 0.00 41.41 4.61
441 632 4.952335 AGGTCATCATTTCTGATTGTTCCC 59.048 41.667 0.00 0.00 40.20 3.97
446 637 4.280819 TCATTTCTGATTGTTCCCCCATC 58.719 43.478 0.00 0.00 0.00 3.51
459 660 2.090210 TCCCCCATCAAGGTAGATGCTA 60.090 50.000 0.00 0.00 43.15 3.49
513 717 5.973651 TGAATGTCATCATTTCTCGCTAC 57.026 39.130 0.00 0.00 43.33 3.58
521 725 2.002586 CATTTCTCGCTACACCACCAG 58.997 52.381 0.00 0.00 0.00 4.00
525 729 1.542915 TCTCGCTACACCACCAGTAAC 59.457 52.381 0.00 0.00 0.00 2.50
570 994 1.593006 GTTCATTCATACCGCGGAGTG 59.407 52.381 35.90 27.74 38.04 3.51
571 995 0.821517 TCATTCATACCGCGGAGTGT 59.178 50.000 35.90 12.54 35.45 3.55
572 996 1.202371 TCATTCATACCGCGGAGTGTC 60.202 52.381 35.90 0.00 35.45 3.67
573 997 0.248907 ATTCATACCGCGGAGTGTCG 60.249 55.000 35.90 13.56 35.45 4.35
579 1003 2.795973 CGCGGAGTGTCGGATACA 59.204 61.111 7.64 0.00 35.06 2.29
580 1004 1.359117 CGCGGAGTGTCGGATACAT 59.641 57.895 7.64 0.00 41.10 2.29
581 1005 0.934901 CGCGGAGTGTCGGATACATG 60.935 60.000 7.64 0.00 41.10 3.21
582 1006 0.102481 GCGGAGTGTCGGATACATGT 59.898 55.000 2.69 2.69 41.10 3.21
583 1007 1.470979 GCGGAGTGTCGGATACATGTT 60.471 52.381 2.30 0.00 41.10 2.71
584 1008 2.888594 CGGAGTGTCGGATACATGTTT 58.111 47.619 2.30 0.00 41.10 2.83
585 1009 2.603110 CGGAGTGTCGGATACATGTTTG 59.397 50.000 2.30 0.00 41.10 2.93
586 1010 3.674955 CGGAGTGTCGGATACATGTTTGA 60.675 47.826 2.30 0.00 41.10 2.69
587 1011 4.442706 GGAGTGTCGGATACATGTTTGAT 58.557 43.478 2.30 0.00 41.10 2.57
588 1012 4.271049 GGAGTGTCGGATACATGTTTGATG 59.729 45.833 2.30 0.00 41.10 3.07
589 1013 4.832248 AGTGTCGGATACATGTTTGATGT 58.168 39.130 2.30 0.00 41.10 3.06
590 1014 5.972935 AGTGTCGGATACATGTTTGATGTA 58.027 37.500 2.30 0.00 41.10 2.29
591 1015 6.582636 AGTGTCGGATACATGTTTGATGTAT 58.417 36.000 2.30 6.96 45.01 2.29
592 1016 7.722363 AGTGTCGGATACATGTTTGATGTATA 58.278 34.615 2.30 0.00 43.10 1.47
593 1017 8.367911 AGTGTCGGATACATGTTTGATGTATAT 58.632 33.333 2.30 0.00 43.10 0.86
594 1018 8.988934 GTGTCGGATACATGTTTGATGTATATT 58.011 33.333 2.30 0.00 43.10 1.28
595 1019 9.554395 TGTCGGATACATGTTTGATGTATATTT 57.446 29.630 2.30 0.00 43.10 1.40
652 1076 6.426980 TGATATGCTCAAGTGATTGAACAC 57.573 37.500 0.00 0.00 40.60 3.32
656 1080 3.002246 TGCTCAAGTGATTGAACACGTTC 59.998 43.478 2.89 2.89 44.35 3.95
668 1092 5.728351 TGAACACGTTCAGAAACCTTTAG 57.272 39.130 8.51 0.00 43.90 1.85
669 1093 5.180271 TGAACACGTTCAGAAACCTTTAGT 58.820 37.500 8.51 0.00 43.90 2.24
670 1094 6.339730 TGAACACGTTCAGAAACCTTTAGTA 58.660 36.000 8.51 0.00 43.90 1.82
677 1101 8.529476 ACGTTCAGAAACCTTTAGTATATCTGT 58.471 33.333 0.00 0.00 36.20 3.41
708 1157 4.617253 ACTAACTGTGCACATTCACCTA 57.383 40.909 22.00 3.10 36.17 3.08
724 1173 5.818678 TCACCTACACAGTTTCCATACTT 57.181 39.130 0.00 0.00 0.00 2.24
725 1174 6.921486 TCACCTACACAGTTTCCATACTTA 57.079 37.500 0.00 0.00 0.00 2.24
728 1177 5.544948 ACCTACACAGTTTCCATACTTACCA 59.455 40.000 0.00 0.00 0.00 3.25
730 1179 6.761714 CCTACACAGTTTCCATACTTACCATC 59.238 42.308 0.00 0.00 0.00 3.51
731 1180 5.175859 ACACAGTTTCCATACTTACCATCG 58.824 41.667 0.00 0.00 0.00 3.84
736 1208 5.363005 AGTTTCCATACTTACCATCGCTACT 59.637 40.000 0.00 0.00 0.00 2.57
738 1210 5.954296 TCCATACTTACCATCGCTACTAC 57.046 43.478 0.00 0.00 0.00 2.73
740 1212 5.472478 TCCATACTTACCATCGCTACTACTG 59.528 44.000 0.00 0.00 0.00 2.74
748 1220 1.460504 TCGCTACTACTGGTCCTGTG 58.539 55.000 11.49 4.61 0.00 3.66
795 1267 2.374184 GCAAATGGTGGTAGGCATACA 58.626 47.619 11.12 0.00 33.21 2.29
830 1302 5.468072 CGAAAGCTGCAAGAGACCATATTAT 59.532 40.000 1.02 0.00 34.07 1.28
831 1303 6.017605 CGAAAGCTGCAAGAGACCATATTATT 60.018 38.462 1.02 0.00 34.07 1.40
832 1304 7.171508 CGAAAGCTGCAAGAGACCATATTATTA 59.828 37.037 1.02 0.00 34.07 0.98
833 1305 8.930846 AAAGCTGCAAGAGACCATATTATTAT 57.069 30.769 1.02 0.00 34.07 1.28
835 1307 9.664332 AAGCTGCAAGAGACCATATTATTATAG 57.336 33.333 1.02 0.00 34.07 1.31
911 1383 4.202419 ACCTGTACAGTTTTGCCAGTCATA 60.202 41.667 21.18 0.00 0.00 2.15
1019 1506 2.969238 GCATCTCGTCGCCATGGG 60.969 66.667 15.13 3.69 0.00 4.00
1257 1750 3.681835 AGCTCCGTCGTGGTGGTC 61.682 66.667 0.00 0.00 37.38 4.02
1755 2253 1.615392 GCCAGGTTGAAGAAACTGCAT 59.385 47.619 0.00 0.00 44.49 3.96
1967 2474 0.974010 ATCTACTTCGTTCCCGGCCA 60.974 55.000 2.24 0.00 33.95 5.36
2011 4259 1.270839 CCACAACCTCAGTCGTCCAAT 60.271 52.381 0.00 0.00 0.00 3.16
2012 4260 1.800586 CACAACCTCAGTCGTCCAATG 59.199 52.381 0.00 0.00 0.00 2.82
2013 4261 1.416401 ACAACCTCAGTCGTCCAATGT 59.584 47.619 0.00 0.00 0.00 2.71
2014 4262 1.800586 CAACCTCAGTCGTCCAATGTG 59.199 52.381 0.00 0.00 0.00 3.21
2015 4263 0.320771 ACCTCAGTCGTCCAATGTGC 60.321 55.000 0.00 0.00 0.00 4.57
2018 4266 0.320683 TCAGTCGTCCAATGTGCCTG 60.321 55.000 0.00 0.00 0.00 4.85
2019 4267 1.672356 AGTCGTCCAATGTGCCTGC 60.672 57.895 0.00 0.00 0.00 4.85
2020 4268 1.965930 GTCGTCCAATGTGCCTGCA 60.966 57.895 0.00 0.00 0.00 4.41
2021 4269 1.672030 TCGTCCAATGTGCCTGCAG 60.672 57.895 6.78 6.78 0.00 4.41
2022 4270 1.968017 CGTCCAATGTGCCTGCAGT 60.968 57.895 13.81 0.00 0.00 4.40
2023 4271 1.582968 GTCCAATGTGCCTGCAGTG 59.417 57.895 13.81 5.37 34.64 3.66
2024 4272 2.967397 CCAATGTGCCTGCAGTGG 59.033 61.111 13.81 8.72 46.02 4.00
2048 4296 6.305693 CGGAGCCAGAAAAATTCTATTAGG 57.694 41.667 0.00 0.00 38.11 2.69
2049 4297 5.239525 CGGAGCCAGAAAAATTCTATTAGGG 59.760 44.000 0.00 0.00 38.11 3.53
2050 4298 5.536538 GGAGCCAGAAAAATTCTATTAGGGG 59.463 44.000 0.00 0.00 38.11 4.79
2051 4299 5.458595 AGCCAGAAAAATTCTATTAGGGGG 58.541 41.667 0.00 0.00 38.11 5.40
2052 4300 4.039245 GCCAGAAAAATTCTATTAGGGGGC 59.961 45.833 0.00 0.00 38.11 5.80
2053 4301 4.588951 CCAGAAAAATTCTATTAGGGGGCC 59.411 45.833 0.00 0.00 38.11 5.80
2054 4302 5.208121 CAGAAAAATTCTATTAGGGGGCCA 58.792 41.667 4.39 0.00 38.11 5.36
2055 4303 5.660864 CAGAAAAATTCTATTAGGGGGCCAA 59.339 40.000 4.39 0.00 38.11 4.52
2056 4304 5.899547 AGAAAAATTCTATTAGGGGGCCAAG 59.100 40.000 4.39 0.00 38.49 3.61
2057 4305 4.899898 AAATTCTATTAGGGGGCCAAGT 57.100 40.909 4.39 0.00 0.00 3.16
2058 4306 3.884037 ATTCTATTAGGGGGCCAAGTG 57.116 47.619 4.39 0.00 0.00 3.16
2059 4307 0.843984 TCTATTAGGGGGCCAAGTGC 59.156 55.000 4.39 0.00 40.16 4.40
2060 4308 0.846693 CTATTAGGGGGCCAAGTGCT 59.153 55.000 4.39 0.00 40.92 4.40
2061 4309 0.843984 TATTAGGGGGCCAAGTGCTC 59.156 55.000 4.39 0.00 40.99 4.26
2062 4310 0.921256 ATTAGGGGGCCAAGTGCTCT 60.921 55.000 4.39 0.00 41.66 4.09
2063 4311 1.140134 TTAGGGGGCCAAGTGCTCTT 61.140 55.000 4.39 0.00 41.66 2.85
2064 4312 0.252974 TAGGGGGCCAAGTGCTCTTA 60.253 55.000 4.39 0.00 41.66 2.10
2065 4313 1.140134 AGGGGGCCAAGTGCTCTTAA 61.140 55.000 4.39 0.00 41.66 1.85
2066 4314 0.033109 GGGGGCCAAGTGCTCTTAAT 60.033 55.000 4.39 0.00 41.66 1.40
2067 4315 1.214424 GGGGGCCAAGTGCTCTTAATA 59.786 52.381 4.39 0.00 41.66 0.98
2068 4316 2.298610 GGGGCCAAGTGCTCTTAATAC 58.701 52.381 4.39 0.00 41.66 1.89
2069 4317 2.092375 GGGGCCAAGTGCTCTTAATACT 60.092 50.000 4.39 0.00 41.66 2.12
2070 4318 2.945668 GGGCCAAGTGCTCTTAATACTG 59.054 50.000 4.39 0.00 37.53 2.74
2071 4319 3.370527 GGGCCAAGTGCTCTTAATACTGA 60.371 47.826 4.39 0.00 37.53 3.41
2072 4320 4.455606 GGCCAAGTGCTCTTAATACTGAT 58.544 43.478 0.00 0.00 40.92 2.90
2073 4321 4.884164 GGCCAAGTGCTCTTAATACTGATT 59.116 41.667 0.00 0.00 40.92 2.57
2074 4322 5.220931 GGCCAAGTGCTCTTAATACTGATTG 60.221 44.000 0.00 0.00 40.92 2.67
2075 4323 5.586243 GCCAAGTGCTCTTAATACTGATTGA 59.414 40.000 0.00 0.00 36.87 2.57
2076 4324 6.238320 GCCAAGTGCTCTTAATACTGATTGAG 60.238 42.308 0.00 0.00 36.87 3.02
2077 4325 6.259608 CCAAGTGCTCTTAATACTGATTGAGG 59.740 42.308 0.00 0.00 31.20 3.86
2078 4326 6.798427 AGTGCTCTTAATACTGATTGAGGA 57.202 37.500 0.00 0.00 31.20 3.71
2079 4327 6.815089 AGTGCTCTTAATACTGATTGAGGAG 58.185 40.000 0.00 0.00 31.20 3.69
2080 4328 5.988561 GTGCTCTTAATACTGATTGAGGAGG 59.011 44.000 0.00 0.00 31.20 4.30
2081 4329 5.070981 TGCTCTTAATACTGATTGAGGAGGG 59.929 44.000 0.00 0.00 31.20 4.30
2082 4330 5.546526 CTCTTAATACTGATTGAGGAGGGC 58.453 45.833 0.00 0.00 31.20 5.19
2083 4331 5.219739 TCTTAATACTGATTGAGGAGGGCT 58.780 41.667 0.00 0.00 31.20 5.19
2084 4332 6.382087 TCTTAATACTGATTGAGGAGGGCTA 58.618 40.000 0.00 0.00 31.20 3.93
2085 4333 6.844388 TCTTAATACTGATTGAGGAGGGCTAA 59.156 38.462 0.00 0.00 31.20 3.09
2086 4334 5.975988 AATACTGATTGAGGAGGGCTAAA 57.024 39.130 0.00 0.00 0.00 1.85
2087 4335 3.922171 ACTGATTGAGGAGGGCTAAAG 57.078 47.619 0.00 0.00 0.00 1.85
2088 4336 2.092699 ACTGATTGAGGAGGGCTAAAGC 60.093 50.000 0.00 0.00 41.14 3.51
2089 4337 1.915489 TGATTGAGGAGGGCTAAAGCA 59.085 47.619 4.07 0.00 44.36 3.91
2090 4338 2.511218 TGATTGAGGAGGGCTAAAGCAT 59.489 45.455 4.07 0.00 44.36 3.79
2091 4339 2.717639 TTGAGGAGGGCTAAAGCATC 57.282 50.000 4.07 1.37 44.36 3.91
2092 4340 1.583556 TGAGGAGGGCTAAAGCATCA 58.416 50.000 4.07 0.00 44.36 3.07
2093 4341 1.210478 TGAGGAGGGCTAAAGCATCAC 59.790 52.381 4.07 1.41 44.36 3.06
2094 4342 1.488393 GAGGAGGGCTAAAGCATCACT 59.512 52.381 4.07 1.77 44.36 3.41
2095 4343 1.918957 AGGAGGGCTAAAGCATCACTT 59.081 47.619 4.07 0.00 44.36 3.16
2097 4345 3.523564 AGGAGGGCTAAAGCATCACTTTA 59.476 43.478 4.07 0.00 46.95 1.85
2105 4353 4.589216 AAAGCATCACTTTAGCAGCAAA 57.411 36.364 0.00 0.00 46.95 3.68
2106 4354 4.589216 AAGCATCACTTTAGCAGCAAAA 57.411 36.364 0.00 0.00 33.71 2.44
2107 4355 3.905784 AGCATCACTTTAGCAGCAAAAC 58.094 40.909 0.00 0.00 0.00 2.43
2108 4356 3.318839 AGCATCACTTTAGCAGCAAAACA 59.681 39.130 0.00 0.00 0.00 2.83
2109 4357 4.021719 AGCATCACTTTAGCAGCAAAACAT 60.022 37.500 0.00 0.00 0.00 2.71
2110 4358 4.325472 GCATCACTTTAGCAGCAAAACATC 59.675 41.667 0.00 0.00 0.00 3.06
2111 4359 5.463286 CATCACTTTAGCAGCAAAACATCA 58.537 37.500 0.00 0.00 0.00 3.07
2112 4360 4.858935 TCACTTTAGCAGCAAAACATCAC 58.141 39.130 0.00 0.00 0.00 3.06
2113 4361 4.580167 TCACTTTAGCAGCAAAACATCACT 59.420 37.500 0.00 0.00 0.00 3.41
2114 4362 5.762711 TCACTTTAGCAGCAAAACATCACTA 59.237 36.000 0.00 0.00 0.00 2.74
2115 4363 6.262049 TCACTTTAGCAGCAAAACATCACTAA 59.738 34.615 0.00 0.00 0.00 2.24
2116 4364 7.040478 TCACTTTAGCAGCAAAACATCACTAAT 60.040 33.333 0.00 0.00 0.00 1.73
2117 4365 7.596248 CACTTTAGCAGCAAAACATCACTAATT 59.404 33.333 0.00 0.00 0.00 1.40
2118 4366 8.143835 ACTTTAGCAGCAAAACATCACTAATTT 58.856 29.630 0.00 0.00 0.00 1.82
2119 4367 8.519492 TTTAGCAGCAAAACATCACTAATTTC 57.481 30.769 0.00 0.00 0.00 2.17
2120 4368 6.088016 AGCAGCAAAACATCACTAATTTCA 57.912 33.333 0.00 0.00 0.00 2.69
2121 4369 5.922544 AGCAGCAAAACATCACTAATTTCAC 59.077 36.000 0.00 0.00 0.00 3.18
2122 4370 5.691305 GCAGCAAAACATCACTAATTTCACA 59.309 36.000 0.00 0.00 0.00 3.58
2123 4371 6.346040 GCAGCAAAACATCACTAATTTCACAC 60.346 38.462 0.00 0.00 0.00 3.82
2124 4372 6.919662 CAGCAAAACATCACTAATTTCACACT 59.080 34.615 0.00 0.00 0.00 3.55
2125 4373 6.919662 AGCAAAACATCACTAATTTCACACTG 59.080 34.615 0.00 0.00 0.00 3.66
2126 4374 6.697019 GCAAAACATCACTAATTTCACACTGT 59.303 34.615 0.00 0.00 0.00 3.55
2127 4375 7.222611 GCAAAACATCACTAATTTCACACTGTT 59.777 33.333 0.00 0.00 0.00 3.16
2128 4376 8.745837 CAAAACATCACTAATTTCACACTGTTC 58.254 33.333 0.00 0.00 0.00 3.18
2129 4377 7.566760 AACATCACTAATTTCACACTGTTCA 57.433 32.000 0.00 0.00 0.00 3.18
2130 4378 7.750229 ACATCACTAATTTCACACTGTTCAT 57.250 32.000 0.00 0.00 0.00 2.57
2131 4379 7.810658 ACATCACTAATTTCACACTGTTCATC 58.189 34.615 0.00 0.00 0.00 2.92
2132 4380 7.445096 ACATCACTAATTTCACACTGTTCATCA 59.555 33.333 0.00 0.00 0.00 3.07
2134 4382 7.216494 TCACTAATTTCACACTGTTCATCAGA 58.784 34.615 1.79 0.00 46.27 3.27
2135 4383 7.714813 TCACTAATTTCACACTGTTCATCAGAA 59.285 33.333 1.79 0.00 46.27 3.02
2136 4384 8.344831 CACTAATTTCACACTGTTCATCAGAAA 58.655 33.333 1.79 0.00 46.27 2.52
2137 4385 8.902806 ACTAATTTCACACTGTTCATCAGAAAA 58.097 29.630 1.79 0.00 46.27 2.29
3144 5433 5.507315 CGCATAAACAAAAACAGAGGGAAGT 60.507 40.000 0.00 0.00 0.00 3.01
3178 5469 3.570125 TGTCGTGATGATCTATGGAGGAC 59.430 47.826 0.00 0.00 0.00 3.85
3185 5476 2.625314 TGATCTATGGAGGACAAGCTCG 59.375 50.000 0.00 0.00 0.00 5.03
3191 5482 1.016653 GGAGGACAAGCTCGAGTTGC 61.017 60.000 15.13 12.08 0.00 4.17
3217 5508 2.285977 GTATTGTTGTCGATGGGGGTC 58.714 52.381 0.00 0.00 0.00 4.46
3218 5509 0.034477 ATTGTTGTCGATGGGGGTCC 60.034 55.000 0.00 0.00 0.00 4.46
3219 5510 2.132089 TTGTTGTCGATGGGGGTCCC 62.132 60.000 0.00 0.00 45.71 4.46
3220 5511 2.124085 TTGTCGATGGGGGTCCCT 59.876 61.111 8.15 0.00 45.70 4.20
3222 5513 2.365105 GTCGATGGGGGTCCCTCA 60.365 66.667 14.63 14.63 45.70 3.86
3224 5515 3.480133 CGATGGGGGTCCCTCACC 61.480 72.222 14.56 0.54 45.70 4.02
3231 5522 2.346365 GGTCCCTCACCGTTGACC 59.654 66.667 0.00 0.00 40.40 4.02
3232 5523 2.048503 GTCCCTCACCGTTGACCG 60.049 66.667 0.00 0.00 0.00 4.79
3233 5524 2.522436 TCCCTCACCGTTGACCGT 60.522 61.111 0.00 0.00 33.66 4.83
3234 5525 2.135581 TCCCTCACCGTTGACCGTT 61.136 57.895 0.00 0.00 33.66 4.44
3235 5526 1.666872 CCCTCACCGTTGACCGTTC 60.667 63.158 0.00 0.00 33.66 3.95
3236 5527 1.666872 CCTCACCGTTGACCGTTCC 60.667 63.158 0.00 0.00 33.66 3.62
3237 5528 1.666872 CTCACCGTTGACCGTTCCC 60.667 63.158 0.00 0.00 33.66 3.97
3307 5607 9.646427 TGGAAAATAACATTTTATGTACCAAGC 57.354 29.630 0.00 0.00 44.07 4.01
3333 5634 8.710551 CAATATTGCTTTGCTGTCACAAATTAA 58.289 29.630 1.74 0.00 38.76 1.40
3359 5660 8.472683 AGATCATTTCACGTAAAAGAGAAGAG 57.527 34.615 0.00 0.00 29.01 2.85
3370 5671 2.822707 AGAGAAGAGGGCAATGCAAT 57.177 45.000 7.79 0.00 0.00 3.56
3374 5675 1.339291 GAAGAGGGCAATGCAATAGGC 59.661 52.381 7.79 0.00 45.13 3.93
3422 5972 9.758651 ATATTGTTGTGCTACTATGTTATCGAA 57.241 29.630 0.00 0.00 0.00 3.71
3425 5975 8.487313 TGTTGTGCTACTATGTTATCGAAAAT 57.513 30.769 0.00 0.00 0.00 1.82
3426 5976 8.387354 TGTTGTGCTACTATGTTATCGAAAATG 58.613 33.333 0.00 0.00 0.00 2.32
3427 5977 6.943981 TGTGCTACTATGTTATCGAAAATGC 58.056 36.000 0.00 0.00 0.00 3.56
3428 5978 6.761242 TGTGCTACTATGTTATCGAAAATGCT 59.239 34.615 0.00 0.00 0.00 3.79
3430 5980 8.761497 GTGCTACTATGTTATCGAAAATGCTAA 58.239 33.333 0.00 0.00 0.00 3.09
3432 5982 9.582223 GCTACTATGTTATCGAAAATGCTAAAC 57.418 33.333 0.00 0.00 0.00 2.01
3434 5984 8.732746 ACTATGTTATCGAAAATGCTAAACCT 57.267 30.769 0.00 0.00 0.00 3.50
3435 5985 9.826574 ACTATGTTATCGAAAATGCTAAACCTA 57.173 29.630 0.00 0.00 0.00 3.08
3437 5987 6.996106 TGTTATCGAAAATGCTAAACCTACG 58.004 36.000 0.00 0.00 0.00 3.51
3438 5988 6.591062 TGTTATCGAAAATGCTAAACCTACGT 59.409 34.615 0.00 0.00 0.00 3.57
3439 5989 7.758980 TGTTATCGAAAATGCTAAACCTACGTA 59.241 33.333 0.00 0.00 0.00 3.57
3440 5990 8.594687 GTTATCGAAAATGCTAAACCTACGTAA 58.405 33.333 0.00 0.00 0.00 3.18
3441 5991 7.599630 ATCGAAAATGCTAAACCTACGTAAA 57.400 32.000 0.00 0.00 0.00 2.01
3442 5992 6.820459 TCGAAAATGCTAAACCTACGTAAAC 58.180 36.000 0.00 0.00 0.00 2.01
3443 5993 6.646240 TCGAAAATGCTAAACCTACGTAAACT 59.354 34.615 0.00 0.00 0.00 2.66
3444 5994 6.952083 CGAAAATGCTAAACCTACGTAAACTC 59.048 38.462 0.00 0.00 0.00 3.01
3445 5995 7.148689 CGAAAATGCTAAACCTACGTAAACTCT 60.149 37.037 0.00 0.00 0.00 3.24
3446 5996 7.974482 AAATGCTAAACCTACGTAAACTCTT 57.026 32.000 0.00 0.00 0.00 2.85
3447 5997 9.492973 AAAATGCTAAACCTACGTAAACTCTTA 57.507 29.630 0.00 0.00 0.00 2.10
3448 5998 8.471361 AATGCTAAACCTACGTAAACTCTTAC 57.529 34.615 0.00 0.00 35.08 2.34
3460 6010 4.836125 AAACTCTTACGTAACCTCACGA 57.164 40.909 3.29 0.00 44.69 4.35
3461 6011 4.836125 AACTCTTACGTAACCTCACGAA 57.164 40.909 3.29 0.00 44.69 3.85
3462 6012 4.152607 ACTCTTACGTAACCTCACGAAC 57.847 45.455 3.29 0.00 44.69 3.95
3463 6013 3.565482 ACTCTTACGTAACCTCACGAACA 59.435 43.478 3.29 0.00 44.69 3.18
3464 6014 4.036734 ACTCTTACGTAACCTCACGAACAA 59.963 41.667 3.29 0.00 44.69 2.83
3465 6015 4.290155 TCTTACGTAACCTCACGAACAAC 58.710 43.478 3.29 0.00 44.69 3.32
3466 6016 1.856802 ACGTAACCTCACGAACAACC 58.143 50.000 2.26 0.00 44.69 3.77
3467 6017 0.780002 CGTAACCTCACGAACAACCG 59.220 55.000 0.00 0.00 44.69 4.44
3468 6018 1.142474 GTAACCTCACGAACAACCGG 58.858 55.000 0.00 0.00 0.00 5.28
3469 6019 0.752054 TAACCTCACGAACAACCGGT 59.248 50.000 0.00 0.00 0.00 5.28
3470 6020 0.107557 AACCTCACGAACAACCGGTT 60.108 50.000 15.86 15.86 44.10 4.44
3979 6529 8.381636 CCCTCTCTCCTTGTATGATGAAATAAT 58.618 37.037 0.00 0.00 0.00 1.28
3980 6530 9.434420 CCTCTCTCCTTGTATGATGAAATAATC 57.566 37.037 0.00 0.00 0.00 1.75
3981 6531 9.434420 CTCTCTCCTTGTATGATGAAATAATCC 57.566 37.037 0.00 0.00 0.00 3.01
3983 6533 9.736414 CTCTCCTTGTATGATGAAATAATCCAT 57.264 33.333 0.00 0.00 0.00 3.41
3993 6543 6.555738 TGATGAAATAATCCATGCCATTTCCT 59.444 34.615 12.82 6.88 36.84 3.36
4015 6569 8.830915 TCCTGCAAAATATAGAAATAACCCAA 57.169 30.769 0.00 0.00 0.00 4.12
4052 6606 4.445557 TGGCATTATAAGGGCACATACA 57.554 40.909 20.80 0.00 40.39 2.29
4053 6607 4.996793 TGGCATTATAAGGGCACATACAT 58.003 39.130 20.80 0.00 40.39 2.29
4054 6608 5.392995 TGGCATTATAAGGGCACATACATT 58.607 37.500 20.80 0.00 40.39 2.71
4055 6609 5.243507 TGGCATTATAAGGGCACATACATTG 59.756 40.000 20.80 0.00 40.39 2.82
4056 6610 5.336690 GGCATTATAAGGGCACATACATTGG 60.337 44.000 17.66 0.00 35.18 3.16
4057 6611 5.243730 GCATTATAAGGGCACATACATTGGT 59.756 40.000 0.00 0.00 0.00 3.67
4058 6612 6.239289 GCATTATAAGGGCACATACATTGGTT 60.239 38.462 0.00 0.00 0.00 3.67
4059 6613 6.707440 TTATAAGGGCACATACATTGGTTG 57.293 37.500 0.00 0.00 0.00 3.77
4060 6614 2.897271 AGGGCACATACATTGGTTGA 57.103 45.000 0.00 0.00 0.00 3.18
4061 6615 3.386932 AGGGCACATACATTGGTTGAT 57.613 42.857 0.00 0.00 0.00 2.57
4062 6616 3.290710 AGGGCACATACATTGGTTGATC 58.709 45.455 0.00 0.00 0.00 2.92
4063 6617 2.362077 GGGCACATACATTGGTTGATCC 59.638 50.000 0.00 0.00 0.00 3.36
4064 6618 2.362077 GGCACATACATTGGTTGATCCC 59.638 50.000 0.00 0.00 34.77 3.85
4065 6619 2.362077 GCACATACATTGGTTGATCCCC 59.638 50.000 0.00 0.00 34.77 4.81
4066 6620 3.630168 CACATACATTGGTTGATCCCCA 58.370 45.455 0.00 0.00 34.77 4.96
4067 6621 4.217510 CACATACATTGGTTGATCCCCAT 58.782 43.478 2.32 0.00 34.77 4.00
4068 6622 4.038282 CACATACATTGGTTGATCCCCATG 59.962 45.833 2.32 2.06 34.11 3.66
4069 6623 2.925966 ACATTGGTTGATCCCCATGT 57.074 45.000 2.32 2.63 35.51 3.21
4070 6624 2.738743 ACATTGGTTGATCCCCATGTC 58.261 47.619 2.32 0.00 35.46 3.06
4071 6625 1.677576 CATTGGTTGATCCCCATGTCG 59.322 52.381 2.32 0.00 34.77 4.35
4072 6626 0.695924 TTGGTTGATCCCCATGTCGT 59.304 50.000 2.32 0.00 34.77 4.34
4073 6627 0.251916 TGGTTGATCCCCATGTCGTC 59.748 55.000 0.00 0.00 34.77 4.20
4074 6628 0.463833 GGTTGATCCCCATGTCGTCC 60.464 60.000 0.00 0.00 0.00 4.79
4075 6629 0.463833 GTTGATCCCCATGTCGTCCC 60.464 60.000 0.00 0.00 0.00 4.46
4076 6630 1.632018 TTGATCCCCATGTCGTCCCC 61.632 60.000 0.00 0.00 0.00 4.81
4077 6631 3.161450 ATCCCCATGTCGTCCCCG 61.161 66.667 0.00 0.00 0.00 5.73
4078 6632 3.995809 ATCCCCATGTCGTCCCCGT 62.996 63.158 0.00 0.00 35.01 5.28
4079 6633 4.467084 CCCCATGTCGTCCCCGTG 62.467 72.222 0.00 0.00 35.01 4.94
4080 6634 4.467084 CCCATGTCGTCCCCGTGG 62.467 72.222 0.00 0.00 38.48 4.94
4081 6635 4.467084 CCATGTCGTCCCCGTGGG 62.467 72.222 0.00 0.00 46.11 4.61
4108 6662 2.202974 GGTAAACCCTAGCCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
4109 6663 2.893895 GTAAACCCTAGCCGCCGC 60.894 66.667 0.00 0.00 0.00 6.53
4110 6664 4.165486 TAAACCCTAGCCGCCGCC 62.165 66.667 0.00 0.00 34.57 6.13
4121 6675 4.794439 CGCCGCCACTCGATCACA 62.794 66.667 0.00 0.00 41.67 3.58
4122 6676 3.188786 GCCGCCACTCGATCACAC 61.189 66.667 0.00 0.00 41.67 3.82
4123 6677 2.509336 CCGCCACTCGATCACACC 60.509 66.667 0.00 0.00 41.67 4.16
4124 6678 2.509336 CGCCACTCGATCACACCC 60.509 66.667 0.00 0.00 41.67 4.61
4125 6679 2.662596 GCCACTCGATCACACCCA 59.337 61.111 0.00 0.00 0.00 4.51
4126 6680 1.221840 GCCACTCGATCACACCCAT 59.778 57.895 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.821470 AGCAGATTCAATCATACCAGACTTG 59.179 40.000 0.00 0.00 0.00 3.16
64 65 0.611200 CCCTGTATGGTGGTCGTGAA 59.389 55.000 0.00 0.00 0.00 3.18
69 70 0.394352 CAAGGCCCTGTATGGTGGTC 60.394 60.000 0.00 0.00 0.00 4.02
92 93 4.101448 ATGACGGGCTGGTGAGGC 62.101 66.667 0.00 0.00 44.21 4.70
249 258 4.030529 GTGACATTCACGCAAATGTTATGC 59.969 41.667 14.89 5.59 46.99 3.14
272 281 8.355913 GGCCTTTTCTCTAAATATCAGAAATGG 58.644 37.037 15.97 15.97 45.58 3.16
331 510 8.143193 TGTTACCTTTTCAACTGTATCGAACTA 58.857 33.333 0.00 0.00 0.00 2.24
336 515 7.112984 GCTTTTGTTACCTTTTCAACTGTATCG 59.887 37.037 0.00 0.00 0.00 2.92
389 569 8.654485 TTATCCTTGGTTGTAGACTTGTAGTA 57.346 34.615 0.00 0.00 0.00 1.82
441 632 4.630644 ATGTAGCATCTACCTTGATGGG 57.369 45.455 6.62 0.00 42.82 4.00
446 637 6.932356 ATGTTCAATGTAGCATCTACCTTG 57.068 37.500 12.65 12.65 0.00 3.61
459 660 7.596248 GCATCAAGTTTGAACTATGTTCAATGT 59.404 33.333 21.44 12.07 41.13 2.71
465 666 6.435277 AGATGGCATCAAGTTTGAACTATGTT 59.565 34.615 27.93 0.00 41.13 2.71
484 688 6.145338 AGAAATGATGACATTCAAGATGGC 57.855 37.500 0.00 0.00 44.67 4.40
513 717 2.094182 AGCATCTACGTTACTGGTGGTG 60.094 50.000 0.00 0.00 0.00 4.17
652 1076 8.808529 CACAGATATACTAAAGGTTTCTGAACG 58.191 37.037 4.21 0.00 36.61 3.95
677 1101 7.686438 ATGTGCACAGTTAGTATTTCATTCA 57.314 32.000 25.84 0.00 0.00 2.57
687 1111 3.492102 AGGTGAATGTGCACAGTTAGT 57.508 42.857 25.84 4.67 40.52 2.24
708 1157 5.175859 CGATGGTAAGTATGGAAACTGTGT 58.824 41.667 0.00 0.00 0.00 3.72
724 1173 2.174210 AGGACCAGTAGTAGCGATGGTA 59.826 50.000 0.00 0.00 45.92 3.25
728 1177 2.025155 CACAGGACCAGTAGTAGCGAT 58.975 52.381 0.00 0.00 0.00 4.58
730 1179 0.456221 CCACAGGACCAGTAGTAGCG 59.544 60.000 0.00 0.00 0.00 4.26
731 1180 1.558233 ACCACAGGACCAGTAGTAGC 58.442 55.000 0.00 0.00 0.00 3.58
748 1220 2.547826 GATGGTTTAGTGTCGCCTACC 58.452 52.381 0.00 0.00 0.00 3.18
795 1267 1.405661 GCAGCTTTCGCTTACCTACCT 60.406 52.381 0.00 0.00 46.47 3.08
833 1305 9.082313 ACAGCTTTTACTTACCAACTACTACTA 57.918 33.333 0.00 0.00 0.00 1.82
834 1306 7.871463 CACAGCTTTTACTTACCAACTACTACT 59.129 37.037 0.00 0.00 0.00 2.57
835 1307 7.117379 CCACAGCTTTTACTTACCAACTACTAC 59.883 40.741 0.00 0.00 0.00 2.73
1019 1506 2.514824 GCAACGGGAGAGGGATGC 60.515 66.667 0.00 0.00 0.00 3.91
1967 2474 1.078214 CCATGCCGGTCACAGTCAT 60.078 57.895 1.90 0.00 0.00 3.06
2024 4272 4.639135 AATAGAATTTTTCTGGCTCCGC 57.361 40.909 0.07 0.00 40.94 5.54
2025 4273 5.239525 CCCTAATAGAATTTTTCTGGCTCCG 59.760 44.000 0.07 0.00 40.94 4.63
2026 4274 5.536538 CCCCTAATAGAATTTTTCTGGCTCC 59.463 44.000 0.07 0.00 40.94 4.70
2027 4275 5.536538 CCCCCTAATAGAATTTTTCTGGCTC 59.463 44.000 0.07 0.00 40.94 4.70
2028 4276 5.458595 CCCCCTAATAGAATTTTTCTGGCT 58.541 41.667 0.07 0.00 40.94 4.75
2029 4277 4.039245 GCCCCCTAATAGAATTTTTCTGGC 59.961 45.833 0.07 0.00 40.94 4.85
2030 4278 4.588951 GGCCCCCTAATAGAATTTTTCTGG 59.411 45.833 0.00 0.00 40.94 3.86
2031 4279 5.208121 TGGCCCCCTAATAGAATTTTTCTG 58.792 41.667 0.00 0.00 40.94 3.02
2032 4280 5.481615 TGGCCCCCTAATAGAATTTTTCT 57.518 39.130 0.00 0.00 43.72 2.52
2033 4281 5.661312 ACTTGGCCCCCTAATAGAATTTTTC 59.339 40.000 0.00 0.00 0.00 2.29
2034 4282 5.425217 CACTTGGCCCCCTAATAGAATTTTT 59.575 40.000 0.00 0.00 0.00 1.94
2035 4283 4.962362 CACTTGGCCCCCTAATAGAATTTT 59.038 41.667 0.00 0.00 0.00 1.82
2036 4284 4.546674 CACTTGGCCCCCTAATAGAATTT 58.453 43.478 0.00 0.00 0.00 1.82
2037 4285 3.691311 GCACTTGGCCCCCTAATAGAATT 60.691 47.826 0.00 0.00 36.11 2.17
2038 4286 2.158460 GCACTTGGCCCCCTAATAGAAT 60.158 50.000 0.00 0.00 36.11 2.40
2039 4287 1.214424 GCACTTGGCCCCCTAATAGAA 59.786 52.381 0.00 0.00 36.11 2.10
2040 4288 0.843984 GCACTTGGCCCCCTAATAGA 59.156 55.000 0.00 0.00 36.11 1.98
2041 4289 0.846693 AGCACTTGGCCCCCTAATAG 59.153 55.000 0.00 0.00 46.50 1.73
2042 4290 0.843984 GAGCACTTGGCCCCCTAATA 59.156 55.000 0.00 0.00 46.50 0.98
2043 4291 0.921256 AGAGCACTTGGCCCCCTAAT 60.921 55.000 0.00 0.00 46.50 1.73
2044 4292 1.140134 AAGAGCACTTGGCCCCCTAA 61.140 55.000 0.00 0.00 46.50 2.69
2045 4293 0.252974 TAAGAGCACTTGGCCCCCTA 60.253 55.000 6.66 0.00 46.50 3.53
2046 4294 1.140134 TTAAGAGCACTTGGCCCCCT 61.140 55.000 6.66 0.00 46.50 4.79
2047 4295 0.033109 ATTAAGAGCACTTGGCCCCC 60.033 55.000 6.66 0.00 46.50 5.40
2048 4296 2.092375 AGTATTAAGAGCACTTGGCCCC 60.092 50.000 6.66 0.00 46.50 5.80
2049 4297 2.945668 CAGTATTAAGAGCACTTGGCCC 59.054 50.000 6.66 0.00 46.50 5.80
2050 4298 3.873910 TCAGTATTAAGAGCACTTGGCC 58.126 45.455 6.66 0.00 46.50 5.36
2051 4299 5.586243 TCAATCAGTATTAAGAGCACTTGGC 59.414 40.000 6.66 0.00 45.30 4.52
2052 4300 6.259608 CCTCAATCAGTATTAAGAGCACTTGG 59.740 42.308 6.66 0.00 37.53 3.61
2053 4301 7.044181 TCCTCAATCAGTATTAAGAGCACTTG 58.956 38.462 6.66 0.00 37.53 3.16
2054 4302 7.187824 TCCTCAATCAGTATTAAGAGCACTT 57.812 36.000 1.05 1.05 39.81 3.16
2055 4303 6.183360 CCTCCTCAATCAGTATTAAGAGCACT 60.183 42.308 0.00 0.00 0.00 4.40
2056 4304 5.988561 CCTCCTCAATCAGTATTAAGAGCAC 59.011 44.000 0.00 0.00 0.00 4.40
2057 4305 5.070981 CCCTCCTCAATCAGTATTAAGAGCA 59.929 44.000 0.00 0.00 0.00 4.26
2058 4306 5.546526 CCCTCCTCAATCAGTATTAAGAGC 58.453 45.833 0.00 0.00 0.00 4.09
2059 4307 5.306678 AGCCCTCCTCAATCAGTATTAAGAG 59.693 44.000 0.00 0.00 0.00 2.85
2060 4308 5.219739 AGCCCTCCTCAATCAGTATTAAGA 58.780 41.667 0.00 0.00 0.00 2.10
2061 4309 5.559148 AGCCCTCCTCAATCAGTATTAAG 57.441 43.478 0.00 0.00 0.00 1.85
2062 4310 7.446106 TTTAGCCCTCCTCAATCAGTATTAA 57.554 36.000 0.00 0.00 0.00 1.40
2063 4311 6.464465 GCTTTAGCCCTCCTCAATCAGTATTA 60.464 42.308 0.00 0.00 34.31 0.98
2064 4312 5.688766 GCTTTAGCCCTCCTCAATCAGTATT 60.689 44.000 0.00 0.00 34.31 1.89
2065 4313 4.202409 GCTTTAGCCCTCCTCAATCAGTAT 60.202 45.833 0.00 0.00 34.31 2.12
2066 4314 3.134804 GCTTTAGCCCTCCTCAATCAGTA 59.865 47.826 0.00 0.00 34.31 2.74
2067 4315 2.092699 GCTTTAGCCCTCCTCAATCAGT 60.093 50.000 0.00 0.00 34.31 3.41
2068 4316 2.092753 TGCTTTAGCCCTCCTCAATCAG 60.093 50.000 0.00 0.00 41.18 2.90
2069 4317 1.915489 TGCTTTAGCCCTCCTCAATCA 59.085 47.619 0.00 0.00 41.18 2.57
2070 4318 2.717639 TGCTTTAGCCCTCCTCAATC 57.282 50.000 0.00 0.00 41.18 2.67
2071 4319 2.511218 TGATGCTTTAGCCCTCCTCAAT 59.489 45.455 0.00 0.00 41.18 2.57
2072 4320 1.915489 TGATGCTTTAGCCCTCCTCAA 59.085 47.619 0.00 0.00 41.18 3.02
2073 4321 1.210478 GTGATGCTTTAGCCCTCCTCA 59.790 52.381 0.00 0.00 41.18 3.86
2074 4322 1.488393 AGTGATGCTTTAGCCCTCCTC 59.512 52.381 0.00 0.00 41.18 3.71
2075 4323 1.589414 AGTGATGCTTTAGCCCTCCT 58.411 50.000 0.00 0.00 41.18 3.69
2076 4324 2.426842 AAGTGATGCTTTAGCCCTCC 57.573 50.000 0.00 0.00 41.18 4.30
2083 4331 5.703978 TTTGCTGCTAAAGTGATGCTTTA 57.296 34.783 0.00 0.00 44.90 1.85
2085 4333 4.202141 TGTTTTGCTGCTAAAGTGATGCTT 60.202 37.500 9.43 0.00 39.52 3.91
2086 4334 3.318839 TGTTTTGCTGCTAAAGTGATGCT 59.681 39.130 9.43 0.00 0.00 3.79
2087 4335 3.641648 TGTTTTGCTGCTAAAGTGATGC 58.358 40.909 9.43 0.00 0.00 3.91
2088 4336 5.344128 GTGATGTTTTGCTGCTAAAGTGATG 59.656 40.000 9.43 0.00 0.00 3.07
2089 4337 5.242393 AGTGATGTTTTGCTGCTAAAGTGAT 59.758 36.000 9.43 3.11 0.00 3.06
2090 4338 4.580167 AGTGATGTTTTGCTGCTAAAGTGA 59.420 37.500 9.43 0.00 0.00 3.41
2091 4339 4.863491 AGTGATGTTTTGCTGCTAAAGTG 58.137 39.130 9.43 0.00 0.00 3.16
2092 4340 6.633500 TTAGTGATGTTTTGCTGCTAAAGT 57.367 33.333 9.43 2.33 0.00 2.66
2093 4341 8.524870 AAATTAGTGATGTTTTGCTGCTAAAG 57.475 30.769 9.43 0.00 0.00 1.85
2094 4342 8.140628 TGAAATTAGTGATGTTTTGCTGCTAAA 58.859 29.630 5.17 5.17 0.00 1.85
2095 4343 7.594758 GTGAAATTAGTGATGTTTTGCTGCTAA 59.405 33.333 0.00 0.00 0.00 3.09
2096 4344 7.083858 GTGAAATTAGTGATGTTTTGCTGCTA 58.916 34.615 0.00 0.00 0.00 3.49
2097 4345 5.922544 GTGAAATTAGTGATGTTTTGCTGCT 59.077 36.000 0.00 0.00 0.00 4.24
2098 4346 5.691305 TGTGAAATTAGTGATGTTTTGCTGC 59.309 36.000 0.00 0.00 0.00 5.25
2099 4347 6.919662 AGTGTGAAATTAGTGATGTTTTGCTG 59.080 34.615 0.00 0.00 0.00 4.41
2100 4348 6.919662 CAGTGTGAAATTAGTGATGTTTTGCT 59.080 34.615 0.00 0.00 0.00 3.91
2101 4349 6.697019 ACAGTGTGAAATTAGTGATGTTTTGC 59.303 34.615 0.00 0.00 0.00 3.68
2102 4350 8.633075 AACAGTGTGAAATTAGTGATGTTTTG 57.367 30.769 0.00 0.00 0.00 2.44
2103 4351 8.465999 TGAACAGTGTGAAATTAGTGATGTTTT 58.534 29.630 0.00 0.00 0.00 2.43
2104 4352 7.995289 TGAACAGTGTGAAATTAGTGATGTTT 58.005 30.769 0.00 0.00 0.00 2.83
2105 4353 7.566760 TGAACAGTGTGAAATTAGTGATGTT 57.433 32.000 0.00 0.00 0.00 2.71
2106 4354 7.445096 TGATGAACAGTGTGAAATTAGTGATGT 59.555 33.333 0.00 0.00 0.00 3.06
2107 4355 7.809665 TGATGAACAGTGTGAAATTAGTGATG 58.190 34.615 0.00 0.00 0.00 3.07
2108 4356 7.879677 TCTGATGAACAGTGTGAAATTAGTGAT 59.120 33.333 0.00 0.00 45.86 3.06
2109 4357 7.216494 TCTGATGAACAGTGTGAAATTAGTGA 58.784 34.615 0.00 0.00 45.86 3.41
2110 4358 7.425577 TCTGATGAACAGTGTGAAATTAGTG 57.574 36.000 0.00 0.00 45.86 2.74
2111 4359 8.450578 TTTCTGATGAACAGTGTGAAATTAGT 57.549 30.769 0.00 0.00 45.86 2.24
2447 4695 2.304180 AGCAGAGTTAATCAGGCACAGT 59.696 45.455 0.04 0.00 34.07 3.55
2448 4696 2.983229 AGCAGAGTTAATCAGGCACAG 58.017 47.619 0.04 0.00 34.07 3.66
2655 4907 2.743636 GGAACGTCTCCTTGATGACA 57.256 50.000 8.87 0.00 41.61 3.58
2970 5259 2.658707 GAACGAGTGCACCAGCGTC 61.659 63.158 23.97 15.93 46.23 5.19
3105 5394 1.229428 ATGCGATTTGGTATGCCGAG 58.771 50.000 0.00 0.00 37.67 4.63
3185 5476 4.578601 GACAACAATACATAGCGCAACTC 58.421 43.478 11.47 0.00 0.00 3.01
3191 5482 3.184379 CCCATCGACAACAATACATAGCG 59.816 47.826 0.00 0.00 0.00 4.26
3217 5508 1.666872 GAACGGTCAACGGTGAGGG 60.667 63.158 1.63 0.24 46.88 4.30
3218 5509 1.666872 GGAACGGTCAACGGTGAGG 60.667 63.158 1.63 0.68 46.88 3.86
3219 5510 1.666872 GGGAACGGTCAACGGTGAG 60.667 63.158 1.63 0.00 46.88 3.51
3220 5511 1.688269 AAGGGAACGGTCAACGGTGA 61.688 55.000 0.00 0.00 46.88 4.02
3224 5515 0.584876 GTTGAAGGGAACGGTCAACG 59.415 55.000 1.31 0.00 44.54 4.10
3226 5517 3.842007 TTAGTTGAAGGGAACGGTCAA 57.158 42.857 1.31 0.00 37.05 3.18
3227 5518 3.842007 TTTAGTTGAAGGGAACGGTCA 57.158 42.857 1.31 0.00 0.00 4.02
3228 5519 5.936372 ACTATTTTAGTTGAAGGGAACGGTC 59.064 40.000 0.00 0.00 34.86 4.79
3230 5521 6.812879 AACTATTTTAGTTGAAGGGAACGG 57.187 37.500 0.00 0.00 46.58 4.44
3307 5607 6.715344 ATTTGTGACAGCAAAGCAATATTG 57.285 33.333 11.27 11.27 41.00 1.90
3333 5634 8.833231 TCTTCTCTTTTACGTGAAATGATCTT 57.167 30.769 5.92 0.00 32.45 2.40
3359 5660 3.817709 TTTTAGCCTATTGCATTGCCC 57.182 42.857 6.12 0.00 44.83 5.36
3383 5684 5.588648 GCACAACAATATACATGGTGTACCT 59.411 40.000 9.94 0.00 46.54 3.08
3385 5686 6.677781 AGCACAACAATATACATGGTGTAC 57.322 37.500 9.94 5.88 46.54 2.90
3404 5954 7.178712 AGCATTTTCGATAACATAGTAGCAC 57.821 36.000 0.00 0.00 0.00 4.40
3417 5967 7.332678 AGTTTACGTAGGTTTAGCATTTTCGAT 59.667 33.333 0.00 0.00 0.00 3.59
3420 5970 8.026341 AGAGTTTACGTAGGTTTAGCATTTTC 57.974 34.615 0.00 0.00 0.00 2.29
3422 5972 7.974482 AAGAGTTTACGTAGGTTTAGCATTT 57.026 32.000 0.00 0.00 0.00 2.32
3437 5987 5.689819 TCGTGAGGTTACGTAAGAGTTTAC 58.310 41.667 8.60 3.21 44.06 2.01
3438 5988 5.940192 TCGTGAGGTTACGTAAGAGTTTA 57.060 39.130 8.60 0.00 44.06 2.01
3439 5989 4.836125 TCGTGAGGTTACGTAAGAGTTT 57.164 40.909 8.60 0.00 44.06 2.66
3440 5990 4.036734 TGTTCGTGAGGTTACGTAAGAGTT 59.963 41.667 8.60 0.00 44.06 3.01
3441 5991 3.565482 TGTTCGTGAGGTTACGTAAGAGT 59.435 43.478 8.60 0.00 44.06 3.24
3442 5992 4.151258 TGTTCGTGAGGTTACGTAAGAG 57.849 45.455 8.60 0.00 44.06 2.85
3443 5993 4.290155 GTTGTTCGTGAGGTTACGTAAGA 58.710 43.478 8.60 0.00 44.06 2.10
3444 5994 3.426525 GGTTGTTCGTGAGGTTACGTAAG 59.573 47.826 8.60 0.00 44.06 2.34
3445 5995 3.380142 GGTTGTTCGTGAGGTTACGTAA 58.620 45.455 3.29 3.29 44.06 3.18
3446 5996 2.604373 CGGTTGTTCGTGAGGTTACGTA 60.604 50.000 0.00 0.00 44.06 3.57
3447 5997 1.856802 GGTTGTTCGTGAGGTTACGT 58.143 50.000 0.00 0.00 44.06 3.57
3448 5998 0.780002 CGGTTGTTCGTGAGGTTACG 59.220 55.000 0.00 0.00 44.98 3.18
3449 5999 1.142474 CCGGTTGTTCGTGAGGTTAC 58.858 55.000 0.00 0.00 0.00 2.50
3450 6000 0.752054 ACCGGTTGTTCGTGAGGTTA 59.248 50.000 0.00 0.00 0.00 2.85
3451 6001 0.107557 AACCGGTTGTTCGTGAGGTT 60.108 50.000 21.56 0.00 37.17 3.50
3452 6002 0.531311 GAACCGGTTGTTCGTGAGGT 60.531 55.000 27.87 0.00 43.65 3.85
3453 6003 2.231820 GAACCGGTTGTTCGTGAGG 58.768 57.895 27.87 0.00 43.65 3.86
3948 6498 6.215431 TCATCATACAAGGAGAGAGGGAAAAA 59.785 38.462 0.00 0.00 0.00 1.94
3949 6499 5.726308 TCATCATACAAGGAGAGAGGGAAAA 59.274 40.000 0.00 0.00 0.00 2.29
3950 6500 5.280499 TCATCATACAAGGAGAGAGGGAAA 58.720 41.667 0.00 0.00 0.00 3.13
3951 6501 4.883759 TCATCATACAAGGAGAGAGGGAA 58.116 43.478 0.00 0.00 0.00 3.97
3952 6502 4.542906 TCATCATACAAGGAGAGAGGGA 57.457 45.455 0.00 0.00 0.00 4.20
3953 6503 5.620738 TTTCATCATACAAGGAGAGAGGG 57.379 43.478 0.00 0.00 0.00 4.30
3954 6504 9.434420 GATTATTTCATCATACAAGGAGAGAGG 57.566 37.037 0.00 0.00 0.00 3.69
3955 6505 9.434420 GGATTATTTCATCATACAAGGAGAGAG 57.566 37.037 0.00 0.00 0.00 3.20
3970 6520 6.743208 GCAGGAAATGGCATGGATTATTTCAT 60.743 38.462 0.00 0.00 39.87 2.57
3979 6529 1.642112 TTTGCAGGAAATGGCATGGA 58.358 45.000 0.00 0.00 40.17 3.41
3980 6530 2.476126 TTTTGCAGGAAATGGCATGG 57.524 45.000 0.00 0.00 40.17 3.66
3981 6531 6.751157 TCTATATTTTGCAGGAAATGGCATG 58.249 36.000 0.00 0.00 40.17 4.06
3983 6533 6.788598 TTCTATATTTTGCAGGAAATGGCA 57.211 33.333 6.62 0.00 38.46 4.92
3993 6543 7.124901 TGGCTTGGGTTATTTCTATATTTTGCA 59.875 33.333 0.00 0.00 0.00 4.08
4047 6601 4.217510 ACATGGGGATCAACCAATGTATG 58.782 43.478 11.80 8.14 42.06 2.39
4052 6606 1.284785 ACGACATGGGGATCAACCAAT 59.715 47.619 11.80 4.42 42.17 3.16
4053 6607 0.695924 ACGACATGGGGATCAACCAA 59.304 50.000 11.80 0.00 42.17 3.67
4054 6608 0.251916 GACGACATGGGGATCAACCA 59.748 55.000 10.39 10.39 43.22 3.67
4055 6609 0.463833 GGACGACATGGGGATCAACC 60.464 60.000 0.00 0.00 38.08 3.77
4056 6610 0.463833 GGGACGACATGGGGATCAAC 60.464 60.000 0.00 0.00 0.00 3.18
4057 6611 1.632018 GGGGACGACATGGGGATCAA 61.632 60.000 0.00 0.00 0.00 2.57
4058 6612 2.070039 GGGGACGACATGGGGATCA 61.070 63.158 0.00 0.00 0.00 2.92
4059 6613 2.829592 GGGGACGACATGGGGATC 59.170 66.667 0.00 0.00 0.00 3.36
4091 6645 2.202974 CGGCGGCTAGGGTTTACC 60.203 66.667 7.61 0.00 40.67 2.85
4092 6646 2.893895 GCGGCGGCTAGGGTTTAC 60.894 66.667 9.78 0.00 35.83 2.01
4093 6647 4.165486 GGCGGCGGCTAGGGTTTA 62.165 66.667 27.22 0.00 39.81 2.01
4104 6658 4.794439 TGTGATCGAGTGGCGGCG 62.794 66.667 0.51 0.51 41.33 6.46
4105 6659 3.188786 GTGTGATCGAGTGGCGGC 61.189 66.667 0.00 0.00 41.33 6.53
4106 6660 2.509336 GGTGTGATCGAGTGGCGG 60.509 66.667 0.00 0.00 41.33 6.13
4107 6661 2.509336 GGGTGTGATCGAGTGGCG 60.509 66.667 0.00 0.00 42.69 5.69
4108 6662 1.221840 ATGGGTGTGATCGAGTGGC 59.778 57.895 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.