Multiple sequence alignment - TraesCS4D01G200500

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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 TraesCS4D01G200500 chr4D 100.000 3853 0 0 1 3853 347516148 347520000 0.000000e+00 7116.0
1 TraesCS4D01G200500 chr4B 89.747 2019 92 46 1 1962 428020340 428022300 0.000000e+00 2475.0
2 TraesCS4D01G200500 chr4B 90.000 670 30 12 2436 3076 428022635 428023296 0.000000e+00 832.0
3 TraesCS4D01G200500 chr4B 89.902 307 12 11 2089 2390 428022333 428022625 1.010000e-100 377.0
4 TraesCS4D01G200500 chr4B 92.000 150 11 1 3077 3225 12112659 12112510 3.900000e-50 209.0
5 TraesCS4D01G200500 chr4A 89.256 2029 101 44 1 1962 117897694 117895716 0.000000e+00 2431.0
6 TraesCS4D01G200500 chr4A 88.141 877 54 16 2240 3076 117895271 117894405 0.000000e+00 998.0
7 TraesCS4D01G200500 chr6D 90.569 615 52 5 3226 3839 469580086 469580695 0.000000e+00 809.0
8 TraesCS4D01G200500 chr5D 88.339 626 67 5 3226 3848 399612763 399612141 0.000000e+00 747.0
9 TraesCS4D01G200500 chr5D 82.828 99 12 4 1963 2056 412619537 412619439 2.470000e-12 84.2
10 TraesCS4D01G200500 chr2A 87.662 616 70 6 3227 3839 773383795 773383183 0.000000e+00 712.0
11 TraesCS4D01G200500 chr1B 87.102 628 78 3 3226 3850 589132555 589133182 0.000000e+00 708.0
12 TraesCS4D01G200500 chr1B 91.391 151 12 1 3072 3222 11133326 11133475 5.050000e-49 206.0
13 TraesCS4D01G200500 chr1B 83.000 100 12 4 1963 2057 448296394 448296493 6.860000e-13 86.1
14 TraesCS4D01G200500 chr1B 82.353 102 9 6 1963 2057 540341650 540341551 3.190000e-11 80.5
15 TraesCS4D01G200500 chr5B 86.867 632 78 5 3226 3853 614364818 614364188 0.000000e+00 702.0
16 TraesCS4D01G200500 chr5B 86.371 631 82 4 3226 3853 403154819 403154190 0.000000e+00 686.0
17 TraesCS4D01G200500 chr5B 92.667 150 11 0 3076 3225 614364922 614364773 2.330000e-52 217.0
18 TraesCS4D01G200500 chr5B 92.000 150 12 0 3076 3225 699242910 699242761 1.080000e-50 211.0
19 TraesCS4D01G200500 chr7D 86.581 626 82 2 3227 3850 148121211 148121836 0.000000e+00 689.0
20 TraesCS4D01G200500 chr6B 86.486 629 80 5 3226 3850 599981205 599981832 0.000000e+00 686.0
21 TraesCS4D01G200500 chr6B 92.208 154 10 2 3074 3225 76215783 76215630 2.330000e-52 217.0
22 TraesCS4D01G200500 chr2B 86.371 631 83 3 3226 3853 653684588 653683958 0.000000e+00 686.0
23 TraesCS4D01G200500 chr2B 92.000 150 11 1 3077 3225 263697807 263697658 3.900000e-50 209.0
24 TraesCS4D01G200500 chr2B 82.692 104 9 6 1960 2056 46595467 46595366 2.470000e-12 84.2
25 TraesCS4D01G200500 chr2D 92.667 150 11 0 3076 3225 484880997 484881146 2.330000e-52 217.0
26 TraesCS4D01G200500 chr2D 82.243 107 12 4 1963 2063 71761525 71761630 6.860000e-13 86.1
27 TraesCS4D01G200500 chr2D 82.105 95 11 5 1972 2061 294975955 294976048 4.130000e-10 76.8
28 TraesCS4D01G200500 chr7A 91.558 154 12 1 3072 3225 93492908 93493060 1.080000e-50 211.0
29 TraesCS4D01G200500 chr7B 90.968 155 14 0 3071 3225 684574630 684574476 3.900000e-50 209.0
30 TraesCS4D01G200500 chr5A 81.553 103 14 4 1964 2061 90044654 90044756 3.190000e-11 80.5
31 TraesCS4D01G200500 chr3A 81.553 103 14 4 1964 2061 198035935 198036037 3.190000e-11 80.5
32 TraesCS4D01G200500 chr6A 80.769 104 13 5 1963 2060 396295170 396295068 1.480000e-09 75.0


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 TraesCS4D01G200500 chr4D 347516148 347520000 3852 False 7116.0 7116 100.0000 1 3853 1 chr4D.!!$F1 3852
1 TraesCS4D01G200500 chr4B 428020340 428023296 2956 False 1228.0 2475 89.8830 1 3076 3 chr4B.!!$F1 3075
2 TraesCS4D01G200500 chr4A 117894405 117897694 3289 True 1714.5 2431 88.6985 1 3076 2 chr4A.!!$R1 3075
3 TraesCS4D01G200500 chr6D 469580086 469580695 609 False 809.0 809 90.5690 3226 3839 1 chr6D.!!$F1 613
4 TraesCS4D01G200500 chr5D 399612141 399612763 622 True 747.0 747 88.3390 3226 3848 1 chr5D.!!$R1 622
5 TraesCS4D01G200500 chr2A 773383183 773383795 612 True 712.0 712 87.6620 3227 3839 1 chr2A.!!$R1 612
6 TraesCS4D01G200500 chr1B 589132555 589133182 627 False 708.0 708 87.1020 3226 3850 1 chr1B.!!$F3 624
7 TraesCS4D01G200500 chr5B 403154190 403154819 629 True 686.0 686 86.3710 3226 3853 1 chr5B.!!$R1 627
8 TraesCS4D01G200500 chr5B 614364188 614364922 734 True 459.5 702 89.7670 3076 3853 2 chr5B.!!$R3 777
9 TraesCS4D01G200500 chr7D 148121211 148121836 625 False 689.0 689 86.5810 3227 3850 1 chr7D.!!$F1 623
10 TraesCS4D01G200500 chr6B 599981205 599981832 627 False 686.0 686 86.4860 3226 3850 1 chr6B.!!$F1 624
11 TraesCS4D01G200500 chr2B 653683958 653684588 630 True 686.0 686 86.3710 3226 3853 1 chr2B.!!$R3 627

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
188 200 0.179018 ATTGCAGATTACGAGGCCCC 60.179 55.0 0.00 0.00 0.00 5.80 F
299 311 0.393402 TCTCAGTCCCACATGCATGC 60.393 55.0 26.53 11.82 0.00 4.06 F
1063 1151 0.813821 GCCACCTTCTTGGATTGCTC 59.186 55.0 0.00 0.00 39.24 4.26 F
2505 2910 0.035534 ATACCGATTGTGCTGTGCCA 60.036 50.0 0.00 0.00 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 1159 0.250513 ATCTGTCCTGGAAACCGAGC 59.749 55.0 0.0 0.0 0.00 5.03 R
1157 1245 0.621082 TCCCCATTAACACGCCATCA 59.379 50.0 0.0 0.0 0.00 3.07 R
2681 3094 1.069255 GCTCGTCGTTCCCTTCTTTC 58.931 55.0 0.0 0.0 0.00 2.62 R
3503 3947 0.028374 CGAAACGTGTGTTGGGTTCC 59.972 55.0 0.0 0.0 38.62 3.62 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
41 42 0.750249 AAAACCCACGGGCAAAAGAG 59.250 50.000 0.69 0.00 39.32 2.85
42 43 1.744320 AAACCCACGGGCAAAAGAGC 61.744 55.000 0.69 0.00 39.32 4.09
43 44 3.737172 CCCACGGGCAAAAGAGCG 61.737 66.667 0.00 0.00 34.64 5.03
44 45 3.737172 CCACGGGCAAAAGAGCGG 61.737 66.667 0.00 0.00 34.64 5.52
45 46 4.404654 CACGGGCAAAAGAGCGGC 62.405 66.667 0.00 0.00 34.64 6.53
46 47 4.947147 ACGGGCAAAAGAGCGGCA 62.947 61.111 1.45 0.00 34.64 5.69
47 48 3.669344 CGGGCAAAAGAGCGGCAA 61.669 61.111 1.45 0.00 34.64 4.52
49 50 1.373371 GGGCAAAAGAGCGGCAAAG 60.373 57.895 1.45 0.00 34.64 2.77
50 51 1.373371 GGCAAAAGAGCGGCAAAGG 60.373 57.895 1.45 0.00 34.64 3.11
51 52 1.363807 GCAAAAGAGCGGCAAAGGT 59.636 52.632 1.45 0.00 0.00 3.50
52 53 0.940991 GCAAAAGAGCGGCAAAGGTG 60.941 55.000 1.45 0.00 0.00 4.00
53 54 0.667993 CAAAAGAGCGGCAAAGGTGA 59.332 50.000 1.45 0.00 0.00 4.02
188 200 0.179018 ATTGCAGATTACGAGGCCCC 60.179 55.000 0.00 0.00 0.00 5.80
269 281 8.786898 TCTTTTCTTTTATCAGTGGAATCAGTG 58.213 33.333 0.00 0.00 43.77 3.66
297 309 1.133884 CCATCTCAGTCCCACATGCAT 60.134 52.381 0.00 0.00 0.00 3.96
298 310 1.947456 CATCTCAGTCCCACATGCATG 59.053 52.381 25.09 25.09 0.00 4.06
299 311 0.393402 TCTCAGTCCCACATGCATGC 60.393 55.000 26.53 11.82 0.00 4.06
343 355 0.820891 CAAGGGCTGAGCTTGTGTGT 60.821 55.000 3.72 0.00 0.00 3.72
344 356 0.820891 AAGGGCTGAGCTTGTGTGTG 60.821 55.000 3.72 0.00 0.00 3.82
345 357 2.641559 GGCTGAGCTTGTGTGTGC 59.358 61.111 3.72 0.00 0.00 4.57
349 361 2.126417 CTGAGCTTGTGTGTGCTGCC 62.126 60.000 0.00 0.00 39.91 4.85
354 366 1.527034 CTTGTGTGTGCTGCCACTAT 58.473 50.000 17.81 0.00 42.54 2.12
364 376 3.941483 GTGCTGCCACTATACAATTGACT 59.059 43.478 13.59 0.97 38.93 3.41
411 426 2.295253 GCTGACGCCAACTGTATAGT 57.705 50.000 0.00 0.00 39.32 2.12
412 427 3.431922 GCTGACGCCAACTGTATAGTA 57.568 47.619 0.00 0.00 35.69 1.82
434 449 2.741211 GGTTTCGACACCGCCTCC 60.741 66.667 4.72 0.00 35.37 4.30
453 468 1.012086 CCATGTGACTCCTGCATTCG 58.988 55.000 0.00 0.00 0.00 3.34
498 513 3.688185 CCATGGGATCATTATGCTTCTCG 59.312 47.826 2.85 0.00 0.00 4.04
505 520 5.049198 GGATCATTATGCTTCTCGATTTGCA 60.049 40.000 8.41 8.41 39.83 4.08
509 524 7.259882 TCATTATGCTTCTCGATTTGCAAATT 58.740 30.769 24.81 9.69 38.96 1.82
536 551 5.065474 CCTACGTTGGAGAAAACTGTGAAAA 59.935 40.000 10.83 0.00 0.00 2.29
538 553 4.698304 ACGTTGGAGAAAACTGTGAAAAGA 59.302 37.500 0.00 0.00 0.00 2.52
539 554 5.182380 ACGTTGGAGAAAACTGTGAAAAGAA 59.818 36.000 0.00 0.00 0.00 2.52
540 555 6.127730 ACGTTGGAGAAAACTGTGAAAAGAAT 60.128 34.615 0.00 0.00 0.00 2.40
541 556 6.197096 CGTTGGAGAAAACTGTGAAAAGAATG 59.803 38.462 0.00 0.00 0.00 2.67
542 557 6.773976 TGGAGAAAACTGTGAAAAGAATGT 57.226 33.333 0.00 0.00 0.00 2.71
543 558 7.873719 TGGAGAAAACTGTGAAAAGAATGTA 57.126 32.000 0.00 0.00 0.00 2.29
683 705 1.216990 CAAATCCCCTGCCTCCTACT 58.783 55.000 0.00 0.00 0.00 2.57
707 747 3.610791 CTCGACGCTTCTCACGCCA 62.611 63.158 0.00 0.00 0.00 5.69
714 754 1.864862 CTTCTCACGCCAGCAACAG 59.135 57.895 0.00 0.00 0.00 3.16
720 776 1.014044 CACGCCAGCAACAGACGTAT 61.014 55.000 0.00 0.00 34.79 3.06
781 841 2.672996 AATTCAGCAACCGCCGCT 60.673 55.556 0.00 0.00 41.47 5.52
823 883 1.615392 AGCCATTCACCTCAAAAGCAC 59.385 47.619 0.00 0.00 0.00 4.40
825 885 1.068333 CCATTCACCTCAAAAGCACCG 60.068 52.381 0.00 0.00 0.00 4.94
840 900 3.511595 CCGGCGTGCATGCAGATT 61.512 61.111 30.79 0.00 36.28 2.40
870 930 3.093278 CAGAAGCGCCTAAAGCCG 58.907 61.111 2.29 0.00 38.78 5.52
969 1053 3.506096 CTCGGGTACGCTGCGAGA 61.506 66.667 30.47 13.26 40.69 4.04
973 1057 2.408022 GGTACGCTGCGAGATCGT 59.592 61.111 30.47 7.50 42.22 3.73
980 1064 4.492160 TGCGAGATCGTGGCGTCC 62.492 66.667 3.94 0.00 42.22 4.79
1063 1151 0.813821 GCCACCTTCTTGGATTGCTC 59.186 55.000 0.00 0.00 39.24 4.26
1065 1153 1.339055 CCACCTTCTTGGATTGCTCGA 60.339 52.381 0.00 0.00 39.24 4.04
1071 1159 2.011947 TCTTGGATTGCTCGATGCTTG 58.988 47.619 8.07 0.00 43.37 4.01
1207 1296 3.425659 GATCAGTTCCTGAGCCCTTTTT 58.574 45.455 0.00 0.00 44.08 1.94
1341 1430 3.721706 AAGGCGGCCAAGGAGGAG 61.722 66.667 23.09 0.00 41.22 3.69
1390 1479 4.406972 CACTTCTCCTCTATCCACATTCCA 59.593 45.833 0.00 0.00 0.00 3.53
1395 1484 5.090139 CTCCTCTATCCACATTCCATACCT 58.910 45.833 0.00 0.00 0.00 3.08
1398 1487 7.950803 TCCTCTATCCACATTCCATACCTATA 58.049 38.462 0.00 0.00 0.00 1.31
1412 1501 5.397109 CCATACCTATACGTCAACCCCTTTT 60.397 44.000 0.00 0.00 0.00 2.27
1416 1505 6.117488 ACCTATACGTCAACCCCTTTTATTG 58.883 40.000 0.00 0.00 0.00 1.90
1434 1523 3.688694 TTGCTACTGTTGGTTCGGTAT 57.311 42.857 0.00 0.00 0.00 2.73
1494 1583 1.593787 CTTGAGAAGCGGCTCTCCA 59.406 57.895 19.63 12.14 41.09 3.86
1546 1635 2.509916 GCTGAGGAGGGCCATCAG 59.490 66.667 20.75 22.16 39.96 2.90
1845 1952 1.751162 AAGGAGGAGGAGAGTCGCG 60.751 63.158 0.00 0.00 0.00 5.87
1887 2000 2.981977 GAAGTGCGGTTCCGGTGACA 62.982 60.000 13.16 0.00 0.00 3.58
1889 2002 3.542676 TGCGGTTCCGGTGACAGT 61.543 61.111 13.16 0.00 0.00 3.55
1892 2005 2.668550 GGTTCCGGTGACAGTGCC 60.669 66.667 0.00 0.00 0.00 5.01
1937 2050 4.053526 TACGCGGCGTGCAGGTTA 62.054 61.111 35.53 13.11 46.97 2.85
1962 2075 5.830991 ACAATGAGTGCCTTTTTACTGGTTA 59.169 36.000 0.00 0.00 0.00 2.85
1963 2076 6.016276 ACAATGAGTGCCTTTTTACTGGTTAG 60.016 38.462 0.00 0.00 0.00 2.34
1966 2079 5.993441 TGAGTGCCTTTTTACTGGTTAGTAC 59.007 40.000 0.00 0.00 39.06 2.73
1967 2080 6.183361 TGAGTGCCTTTTTACTGGTTAGTACT 60.183 38.462 0.00 0.00 39.06 2.73
1968 2081 6.598503 AGTGCCTTTTTACTGGTTAGTACTT 58.401 36.000 0.00 0.00 39.06 2.24
1969 2082 6.709397 AGTGCCTTTTTACTGGTTAGTACTTC 59.291 38.462 0.00 0.00 39.06 3.01
1970 2083 5.999600 TGCCTTTTTACTGGTTAGTACTTCC 59.000 40.000 0.00 5.25 39.06 3.46
1971 2084 6.183361 TGCCTTTTTACTGGTTAGTACTTCCT 60.183 38.462 0.00 0.00 39.06 3.36
1972 2085 6.370994 GCCTTTTTACTGGTTAGTACTTCCTC 59.629 42.308 0.00 0.00 39.06 3.71
1973 2086 6.877855 CCTTTTTACTGGTTAGTACTTCCTCC 59.122 42.308 0.00 0.00 39.06 4.30
1974 2087 5.649782 TTTACTGGTTAGTACTTCCTCCG 57.350 43.478 0.00 1.18 39.06 4.63
1975 2088 3.166560 ACTGGTTAGTACTTCCTCCGT 57.833 47.619 0.00 1.75 34.74 4.69
1976 2089 3.087781 ACTGGTTAGTACTTCCTCCGTC 58.912 50.000 0.00 0.00 34.74 4.79
1977 2090 2.426381 CTGGTTAGTACTTCCTCCGTCC 59.574 54.545 0.00 0.00 0.00 4.79
1978 2091 1.753649 GGTTAGTACTTCCTCCGTCCC 59.246 57.143 0.00 0.00 0.00 4.46
1981 2094 2.019807 AGTACTTCCTCCGTCCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1982 2095 2.332117 AGTACTTCCTCCGTCCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1983 2096 2.910977 AGTACTTCCTCCGTCCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1985 2098 4.533311 AGTACTTCCTCCGTCCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
1986 2099 3.951663 ACTTCCTCCGTCCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
1987 2100 3.329814 ACTTCCTCCGTCCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
1988 2101 3.343941 TCCTCCGTCCCAAAATAAGTG 57.656 47.619 0.00 0.00 0.00 3.16
1990 2103 3.839490 TCCTCCGTCCCAAAATAAGTGTA 59.161 43.478 0.00 0.00 0.00 2.90
1991 2104 4.472108 TCCTCCGTCCCAAAATAAGTGTAT 59.528 41.667 0.00 0.00 0.00 2.29
1992 2105 4.814771 CCTCCGTCCCAAAATAAGTGTATC 59.185 45.833 0.00 0.00 0.00 2.24
1993 2106 4.435425 TCCGTCCCAAAATAAGTGTATCG 58.565 43.478 0.00 0.00 0.00 2.92
1994 2107 4.160065 TCCGTCCCAAAATAAGTGTATCGA 59.840 41.667 0.00 0.00 0.00 3.59
1995 2108 4.269363 CCGTCCCAAAATAAGTGTATCGAC 59.731 45.833 0.00 0.00 0.00 4.20
1996 2109 5.107133 CGTCCCAAAATAAGTGTATCGACT 58.893 41.667 0.00 0.00 0.00 4.18
1997 2110 5.231568 CGTCCCAAAATAAGTGTATCGACTC 59.768 44.000 0.00 0.00 0.00 3.36
1998 2111 6.338937 GTCCCAAAATAAGTGTATCGACTCT 58.661 40.000 0.00 0.00 0.00 3.24
1999 2112 7.486647 GTCCCAAAATAAGTGTATCGACTCTA 58.513 38.462 0.00 0.00 0.00 2.43
2000 2113 7.648510 GTCCCAAAATAAGTGTATCGACTCTAG 59.351 40.741 0.00 0.00 0.00 2.43
2001 2114 7.341256 TCCCAAAATAAGTGTATCGACTCTAGT 59.659 37.037 0.00 0.00 0.00 2.57
2002 2115 8.627403 CCCAAAATAAGTGTATCGACTCTAGTA 58.373 37.037 0.00 0.00 0.00 1.82
2003 2116 9.448294 CCAAAATAAGTGTATCGACTCTAGTAC 57.552 37.037 0.00 0.00 0.00 2.73
2004 2117 9.999009 CAAAATAAGTGTATCGACTCTAGTACA 57.001 33.333 0.00 0.00 0.00 2.90
2008 2121 7.684937 AAGTGTATCGACTCTAGTACAAAGT 57.315 36.000 0.00 0.00 0.00 2.66
2009 2122 7.684937 AGTGTATCGACTCTAGTACAAAGTT 57.315 36.000 0.00 0.00 0.00 2.66
2010 2123 8.783833 AGTGTATCGACTCTAGTACAAAGTTA 57.216 34.615 0.00 0.00 0.00 2.24
2011 2124 9.393512 AGTGTATCGACTCTAGTACAAAGTTAT 57.606 33.333 0.00 0.00 0.00 1.89
2044 2157 8.973182 ACTAAGTTTGAAACACTTATTTTGGGA 58.027 29.630 11.02 0.00 36.39 4.37
2045 2158 9.981114 CTAAGTTTGAAACACTTATTTTGGGAT 57.019 29.630 11.02 0.00 36.39 3.85
2046 2159 8.661352 AAGTTTGAAACACTTATTTTGGGATG 57.339 30.769 11.02 0.00 32.48 3.51
2047 2160 7.216494 AGTTTGAAACACTTATTTTGGGATGG 58.784 34.615 11.02 0.00 0.00 3.51
2048 2161 6.985653 TTGAAACACTTATTTTGGGATGGA 57.014 33.333 0.00 0.00 0.00 3.41
2049 2162 6.588719 TGAAACACTTATTTTGGGATGGAG 57.411 37.500 0.00 0.00 0.00 3.86
2050 2163 5.480073 TGAAACACTTATTTTGGGATGGAGG 59.520 40.000 0.00 0.00 0.00 4.30
2051 2164 4.946160 ACACTTATTTTGGGATGGAGGA 57.054 40.909 0.00 0.00 0.00 3.71
2052 2165 5.269554 ACACTTATTTTGGGATGGAGGAA 57.730 39.130 0.00 0.00 0.00 3.36
2053 2166 5.264395 ACACTTATTTTGGGATGGAGGAAG 58.736 41.667 0.00 0.00 0.00 3.46
2054 2167 5.222337 ACACTTATTTTGGGATGGAGGAAGT 60.222 40.000 0.00 0.00 0.00 3.01
2055 2168 6.011981 ACACTTATTTTGGGATGGAGGAAGTA 60.012 38.462 0.00 0.00 0.00 2.24
2056 2169 7.062957 CACTTATTTTGGGATGGAGGAAGTAT 58.937 38.462 0.00 0.00 0.00 2.12
2057 2170 7.561356 CACTTATTTTGGGATGGAGGAAGTATT 59.439 37.037 0.00 0.00 0.00 1.89
2058 2171 8.787818 ACTTATTTTGGGATGGAGGAAGTATTA 58.212 33.333 0.00 0.00 0.00 0.98
2059 2172 9.640952 CTTATTTTGGGATGGAGGAAGTATTAA 57.359 33.333 0.00 0.00 0.00 1.40
2063 2176 9.998752 TTTTGGGATGGAGGAAGTATTAATTAA 57.001 29.630 0.00 0.00 0.00 1.40
2064 2177 9.640952 TTTGGGATGGAGGAAGTATTAATTAAG 57.359 33.333 3.94 0.00 0.00 1.85
2065 2178 8.575736 TGGGATGGAGGAAGTATTAATTAAGA 57.424 34.615 3.94 0.00 0.00 2.10
2066 2179 8.660435 TGGGATGGAGGAAGTATTAATTAAGAG 58.340 37.037 3.94 0.00 0.00 2.85
2067 2180 8.661345 GGGATGGAGGAAGTATTAATTAAGAGT 58.339 37.037 3.94 0.00 0.00 3.24
2087 2200 7.440523 AGAGTTGATAACAGTTGATTGGTTC 57.559 36.000 0.00 0.00 0.00 3.62
2108 2221 7.884877 TGGTTCATTGCTCTATGGATTATTAGG 59.115 37.037 0.00 0.00 0.00 2.69
2111 2224 7.108194 TCATTGCTCTATGGATTATTAGGCTG 58.892 38.462 0.00 0.00 0.00 4.85
2120 2233 5.904941 TGGATTATTAGGCTGTTTTGCATG 58.095 37.500 0.00 0.00 34.04 4.06
2121 2234 4.746611 GGATTATTAGGCTGTTTTGCATGC 59.253 41.667 11.82 11.82 34.04 4.06
2122 2235 4.797800 TTATTAGGCTGTTTTGCATGCA 57.202 36.364 18.46 18.46 34.04 3.96
2123 2236 3.899052 ATTAGGCTGTTTTGCATGCAT 57.101 38.095 23.37 6.28 34.04 3.96
2127 2240 1.283736 GCTGTTTTGCATGCATAGGC 58.716 50.000 23.37 16.96 41.68 3.93
2145 2258 2.093447 AGGCGTTTCCAGATTACTCCTG 60.093 50.000 0.00 0.00 37.29 3.86
2158 2275 5.426833 AGATTACTCCTGGTTTATGCAGAGT 59.573 40.000 6.28 6.28 0.00 3.24
2188 2305 2.925078 TCCGACAGGAATTAGGGGG 58.075 57.895 0.00 0.00 45.12 5.40
2278 2664 1.936547 GTACTGCATGCCTCACTTAGC 59.063 52.381 16.68 0.00 0.00 3.09
2349 2742 2.416747 GTGCACATCTGTACTTCAGCA 58.583 47.619 13.17 0.00 43.32 4.41
2369 2762 0.534203 TCCCTCTTTGTGTGTTCCGC 60.534 55.000 0.00 0.00 0.00 5.54
2398 2795 0.815615 CCAGGATAGGAAGCCGTTGC 60.816 60.000 0.00 0.00 35.82 4.17
2402 2799 1.472026 GGATAGGAAGCCGTTGCGTAA 60.472 52.381 0.00 0.00 44.33 3.18
2410 2807 4.408694 GAAGCCGTTGCGTAATTTGTTAT 58.591 39.130 0.00 0.00 44.33 1.89
2414 2811 2.524302 CGTTGCGTAATTTGTTATGCCG 59.476 45.455 9.21 4.13 38.35 5.69
2477 2882 8.736244 TCTTTTTATAGCACCCACTATGTTTTC 58.264 33.333 0.00 0.00 34.66 2.29
2480 2885 0.179200 GCACCCACTATGTTTTCGCG 60.179 55.000 0.00 0.00 0.00 5.87
2504 2909 0.378257 CATACCGATTGTGCTGTGCC 59.622 55.000 0.00 0.00 0.00 5.01
2505 2910 0.035534 ATACCGATTGTGCTGTGCCA 60.036 50.000 0.00 0.00 0.00 4.92
2520 2925 4.226761 CTGTGCCAAACTAACGGAATTTC 58.773 43.478 0.00 0.00 0.00 2.17
2525 2930 4.723248 CCAAACTAACGGAATTTCTCTGC 58.277 43.478 0.00 0.00 33.14 4.26
2526 2931 4.394795 CAAACTAACGGAATTTCTCTGCG 58.605 43.478 0.00 0.00 33.14 5.18
2600 3005 3.452024 GAGCTACCGCGACGAGGAC 62.452 68.421 25.04 12.59 42.32 3.85
2676 3089 0.820871 CGAGACCAAGGAGAAGGAGG 59.179 60.000 0.00 0.00 0.00 4.30
2677 3090 1.617263 CGAGACCAAGGAGAAGGAGGA 60.617 57.143 0.00 0.00 0.00 3.71
2678 3091 2.758130 GAGACCAAGGAGAAGGAGGAT 58.242 52.381 0.00 0.00 0.00 3.24
2679 3092 2.433970 GAGACCAAGGAGAAGGAGGATG 59.566 54.545 0.00 0.00 0.00 3.51
2680 3093 2.045047 AGACCAAGGAGAAGGAGGATGA 59.955 50.000 0.00 0.00 0.00 2.92
2681 3094 2.433970 GACCAAGGAGAAGGAGGATGAG 59.566 54.545 0.00 0.00 0.00 2.90
2689 3102 4.141733 GGAGAAGGAGGATGAGAAAGAAGG 60.142 50.000 0.00 0.00 0.00 3.46
2693 3106 3.521531 AGGAGGATGAGAAAGAAGGGAAC 59.478 47.826 0.00 0.00 0.00 3.62
2698 3111 1.958579 TGAGAAAGAAGGGAACGACGA 59.041 47.619 0.00 0.00 0.00 4.20
2842 3267 1.890510 TCGCGCACCGAGAGCTATA 60.891 57.895 8.75 0.00 41.89 1.31
2917 3356 0.322456 TGGTCTCAAAAGCATCCCGG 60.322 55.000 0.00 0.00 0.00 5.73
2979 3418 7.119116 CACTTGCACTGGTGTATTTATCTACAA 59.881 37.037 2.64 0.00 33.59 2.41
3008 3449 6.965866 TGGGAGTATATATGCTGGAATAAGGT 59.034 38.462 8.17 0.00 0.00 3.50
3038 3479 1.525619 GTGAGACGTTGTAGTGGTTGC 59.474 52.381 0.00 0.00 0.00 4.17
3152 3595 2.097036 TCACGTAAGGACCGACATGAT 58.903 47.619 0.00 0.00 46.39 2.45
3179 3622 7.608308 AACTGAAAAGATAGCAGAACATCTC 57.392 36.000 0.00 0.00 33.94 2.75
3180 3623 6.945218 ACTGAAAAGATAGCAGAACATCTCT 58.055 36.000 0.00 0.00 33.94 3.10
3191 3634 3.924144 AGAACATCTCTGAGCTTGACAC 58.076 45.455 12.47 5.44 31.12 3.67
3192 3635 2.758736 ACATCTCTGAGCTTGACACC 57.241 50.000 12.47 0.00 0.00 4.16
3193 3636 1.973515 ACATCTCTGAGCTTGACACCA 59.026 47.619 12.47 0.00 0.00 4.17
3194 3637 2.369860 ACATCTCTGAGCTTGACACCAA 59.630 45.455 12.47 0.00 0.00 3.67
3195 3638 2.533266 TCTCTGAGCTTGACACCAAC 57.467 50.000 0.00 0.00 0.00 3.77
3196 3639 1.143305 CTCTGAGCTTGACACCAACG 58.857 55.000 0.00 0.00 0.00 4.10
3197 3640 0.464036 TCTGAGCTTGACACCAACGT 59.536 50.000 0.00 0.00 0.00 3.99
3198 3641 0.861837 CTGAGCTTGACACCAACGTC 59.138 55.000 0.00 0.00 36.40 4.34
3199 3642 0.531974 TGAGCTTGACACCAACGTCC 60.532 55.000 0.00 0.00 34.88 4.79
3200 3643 1.557443 GAGCTTGACACCAACGTCCG 61.557 60.000 0.00 0.00 34.88 4.79
3201 3644 1.885850 GCTTGACACCAACGTCCGT 60.886 57.895 0.00 0.00 34.88 4.69
3202 3645 1.828331 GCTTGACACCAACGTCCGTC 61.828 60.000 0.00 0.00 34.88 4.79
3203 3646 0.528901 CTTGACACCAACGTCCGTCA 60.529 55.000 0.00 0.00 36.63 4.35
3204 3647 0.806884 TTGACACCAACGTCCGTCAC 60.807 55.000 8.31 0.00 38.07 3.67
3205 3648 1.227031 GACACCAACGTCCGTCACA 60.227 57.895 0.00 0.00 0.00 3.58
3206 3649 0.599204 GACACCAACGTCCGTCACAT 60.599 55.000 0.00 0.00 0.00 3.21
3207 3650 0.878523 ACACCAACGTCCGTCACATG 60.879 55.000 0.00 0.00 0.00 3.21
3208 3651 1.959226 ACCAACGTCCGTCACATGC 60.959 57.895 0.00 0.00 0.00 4.06
3209 3652 2.677003 CCAACGTCCGTCACATGCC 61.677 63.158 0.00 0.00 0.00 4.40
3210 3653 1.667830 CAACGTCCGTCACATGCCT 60.668 57.895 0.00 0.00 0.00 4.75
3211 3654 1.374252 AACGTCCGTCACATGCCTC 60.374 57.895 0.00 0.00 0.00 4.70
3212 3655 2.509336 CGTCCGTCACATGCCTCC 60.509 66.667 0.00 0.00 0.00 4.30
3213 3656 2.509336 GTCCGTCACATGCCTCCG 60.509 66.667 0.00 0.00 0.00 4.63
3214 3657 3.770040 TCCGTCACATGCCTCCGG 61.770 66.667 0.00 0.00 39.98 5.14
3237 3680 1.544093 CCACCACACTGAGCTTGACAT 60.544 52.381 0.00 0.00 0.00 3.06
3251 3694 1.666553 GACATCAACGCCCGTCACA 60.667 57.895 0.00 0.00 0.00 3.58
3276 3719 2.273449 GGCACCACCATAGCAGCT 59.727 61.111 0.00 0.00 38.86 4.24
3336 3779 3.386867 GACGCGGCTTCATTGCTGG 62.387 63.158 12.47 0.00 39.56 4.85
3387 3831 1.915141 ACCAGAAGTGAAGCCATTGG 58.085 50.000 0.00 0.00 0.00 3.16
3474 3918 1.944676 CGACTAAGACGCCGATGGC 60.945 63.158 0.00 0.00 46.75 4.40
3503 3947 2.290514 ACACCTGTCATCCATCAACCAG 60.291 50.000 0.00 0.00 0.00 4.00
3511 3955 1.153539 TCCATCAACCAGGAACCCAA 58.846 50.000 0.00 0.00 0.00 4.12
3542 3986 2.287103 CGTCTTCCAGATGTCGTCGATA 59.713 50.000 0.00 0.00 0.00 2.92
3544 3988 3.312973 GTCTTCCAGATGTCGTCGATACT 59.687 47.826 0.00 0.00 0.00 2.12
3569 4013 0.463295 CAATCTGCATCCGCTCCTGT 60.463 55.000 0.00 0.00 39.64 4.00
3574 4018 1.615883 CTGCATCCGCTCCTGTACTAT 59.384 52.381 0.00 0.00 39.64 2.12
3653 4098 1.972198 GTGTCCACCACGAGGATGA 59.028 57.895 5.68 0.00 37.52 2.92
3684 4129 2.361757 CACACCATCCTTGCTTGAACAA 59.638 45.455 0.00 0.00 0.00 2.83
3808 4255 3.432252 AGACGATGAACAGCCTAAAAACG 59.568 43.478 0.00 0.00 0.00 3.60
3839 4288 7.402862 ACTTTAGCCTAAAACTATCCACACAT 58.597 34.615 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.328099 CCTCACTCACCTTTGCCGC 61.328 63.158 0.00 0.00 0.00 6.53
42 43 1.071471 ACCTCACTCACCTTTGCCG 59.929 57.895 0.00 0.00 0.00 5.69
43 44 0.108585 TCACCTCACTCACCTTTGCC 59.891 55.000 0.00 0.00 0.00 4.52
44 45 1.808945 CATCACCTCACTCACCTTTGC 59.191 52.381 0.00 0.00 0.00 3.68
45 46 2.430465 CCATCACCTCACTCACCTTTG 58.570 52.381 0.00 0.00 0.00 2.77
46 47 1.352352 CCCATCACCTCACTCACCTTT 59.648 52.381 0.00 0.00 0.00 3.11
47 48 0.987294 CCCATCACCTCACTCACCTT 59.013 55.000 0.00 0.00 0.00 3.50
49 50 1.604378 CCCCATCACCTCACTCACC 59.396 63.158 0.00 0.00 0.00 4.02
50 51 1.078143 GCCCCATCACCTCACTCAC 60.078 63.158 0.00 0.00 0.00 3.51
51 52 2.300967 GGCCCCATCACCTCACTCA 61.301 63.158 0.00 0.00 0.00 3.41
52 53 2.592308 GGCCCCATCACCTCACTC 59.408 66.667 0.00 0.00 0.00 3.51
53 54 3.402681 CGGCCCCATCACCTCACT 61.403 66.667 0.00 0.00 0.00 3.41
74 82 4.332637 CCGCTTGCGCTTGCTGTT 62.333 61.111 19.33 0.00 40.12 3.16
188 200 1.679977 CATGTGGGGTCTTGGCCTG 60.680 63.158 3.32 0.00 0.00 4.85
343 355 4.220693 AGTCAATTGTATAGTGGCAGCA 57.779 40.909 5.13 0.00 0.00 4.41
344 356 4.913376 CAAGTCAATTGTATAGTGGCAGC 58.087 43.478 5.13 0.00 33.95 5.25
364 376 1.872952 CATGGCAACTCGACTCAACAA 59.127 47.619 0.00 0.00 37.61 2.83
410 425 2.286025 GGCGGTGTCGAAACCATAATAC 59.714 50.000 24.47 6.04 40.53 1.89
411 426 2.168936 AGGCGGTGTCGAAACCATAATA 59.831 45.455 24.47 0.00 40.53 0.98
412 427 1.065709 AGGCGGTGTCGAAACCATAAT 60.066 47.619 24.47 4.34 40.53 1.28
434 449 1.012086 CGAATGCAGGAGTCACATGG 58.988 55.000 0.00 0.00 0.00 3.66
453 468 6.592607 TGGTTCACGTTCATAAATAGAACTCC 59.407 38.462 8.80 0.00 42.37 3.85
459 474 5.820423 TCCCATGGTTCACGTTCATAAATAG 59.180 40.000 11.73 0.00 0.00 1.73
498 513 5.095490 CCAACGTAGGAGAATTTGCAAATC 58.905 41.667 24.28 16.84 0.00 2.17
633 655 0.737715 GAGATGACCACAGTGACGGC 60.738 60.000 0.62 0.00 0.00 5.68
707 747 2.952978 CCCTCTCTATACGTCTGTTGCT 59.047 50.000 0.00 0.00 0.00 3.91
714 754 2.638855 TCTCCCTCCCTCTCTATACGTC 59.361 54.545 0.00 0.00 0.00 4.34
720 776 0.927767 GGTGTCTCCCTCCCTCTCTA 59.072 60.000 0.00 0.00 0.00 2.43
781 841 4.424867 AGGGTATGGCGGGGTGGA 62.425 66.667 0.00 0.00 0.00 4.02
823 883 3.459378 GAATCTGCATGCACGCCGG 62.459 63.158 18.46 6.94 0.00 6.13
825 885 1.063649 CTGAATCTGCATGCACGCC 59.936 57.895 18.46 6.97 0.00 5.68
908 968 3.112709 GAAGAGGTGTGCGTCCGC 61.113 66.667 4.42 4.42 42.35 5.54
980 1064 4.722700 CTCCCGGCCACCCTTGTG 62.723 72.222 2.24 0.00 42.39 3.33
1063 1151 1.298157 TGGAAACCGAGCAAGCATCG 61.298 55.000 0.00 1.20 39.86 3.84
1065 1153 0.962356 CCTGGAAACCGAGCAAGCAT 60.962 55.000 0.00 0.00 0.00 3.79
1071 1159 0.250513 ATCTGTCCTGGAAACCGAGC 59.749 55.000 0.00 0.00 0.00 5.03
1157 1245 0.621082 TCCCCATTAACACGCCATCA 59.379 50.000 0.00 0.00 0.00 3.07
1207 1296 2.028203 TGCGATCCACACAAATGAGAGA 60.028 45.455 0.00 0.00 0.00 3.10
1368 1457 4.624913 TGGAATGTGGATAGAGGAGAAGT 58.375 43.478 0.00 0.00 0.00 3.01
1379 1468 5.778241 TGACGTATAGGTATGGAATGTGGAT 59.222 40.000 0.00 0.00 0.00 3.41
1390 1479 5.963214 AAAAGGGGTTGACGTATAGGTAT 57.037 39.130 0.00 0.00 0.00 2.73
1395 1484 5.747342 AGCAATAAAAGGGGTTGACGTATA 58.253 37.500 0.00 0.00 0.00 1.47
1398 1487 2.871453 AGCAATAAAAGGGGTTGACGT 58.129 42.857 0.00 0.00 0.00 4.34
1412 1501 3.688694 ACCGAACCAACAGTAGCAATA 57.311 42.857 0.00 0.00 0.00 1.90
1416 1505 3.121544 GCTATACCGAACCAACAGTAGC 58.878 50.000 0.00 0.00 0.00 3.58
1434 1523 8.020819 CCGAATCACAGAACAAAATTAAAGCTA 58.979 33.333 0.00 0.00 0.00 3.32
1494 1583 1.550976 GTCCCTGATCTTGACCTCGTT 59.449 52.381 0.00 0.00 0.00 3.85
1845 1952 2.486042 GTCGTCAGAGTCCTCCGC 59.514 66.667 0.00 0.00 0.00 5.54
1887 2000 1.374252 GATCAACGTCACCGGCACT 60.374 57.895 0.00 0.00 38.78 4.40
1889 2002 2.431771 CGATCAACGTCACCGGCA 60.432 61.111 0.00 0.00 38.78 5.69
1937 2050 4.649218 ACCAGTAAAAAGGCACTCATTGTT 59.351 37.500 0.00 0.00 38.49 2.83
1962 2075 2.019807 TTTGGGACGGAGGAAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
1963 2076 2.845363 TTTTGGGACGGAGGAAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1966 2079 3.689649 CACTTATTTTGGGACGGAGGAAG 59.310 47.826 0.00 0.00 0.00 3.46
1967 2080 3.073356 ACACTTATTTTGGGACGGAGGAA 59.927 43.478 0.00 0.00 0.00 3.36
1968 2081 2.640826 ACACTTATTTTGGGACGGAGGA 59.359 45.455 0.00 0.00 0.00 3.71
1969 2082 3.067684 ACACTTATTTTGGGACGGAGG 57.932 47.619 0.00 0.00 0.00 4.30
1970 2083 4.506654 CGATACACTTATTTTGGGACGGAG 59.493 45.833 0.00 0.00 0.00 4.63
1971 2084 4.160065 TCGATACACTTATTTTGGGACGGA 59.840 41.667 0.00 0.00 0.00 4.69
1972 2085 4.269363 GTCGATACACTTATTTTGGGACGG 59.731 45.833 0.00 0.00 0.00 4.79
1973 2086 5.107133 AGTCGATACACTTATTTTGGGACG 58.893 41.667 0.00 0.00 0.00 4.79
1974 2087 6.338937 AGAGTCGATACACTTATTTTGGGAC 58.661 40.000 0.00 0.00 0.00 4.46
1975 2088 6.540438 AGAGTCGATACACTTATTTTGGGA 57.460 37.500 0.00 0.00 0.00 4.37
1976 2089 7.490000 ACTAGAGTCGATACACTTATTTTGGG 58.510 38.462 0.00 0.00 0.00 4.12
1977 2090 9.448294 GTACTAGAGTCGATACACTTATTTTGG 57.552 37.037 0.00 0.00 0.00 3.28
1978 2091 9.999009 TGTACTAGAGTCGATACACTTATTTTG 57.001 33.333 0.00 0.00 0.00 2.44
1982 2095 9.393512 ACTTTGTACTAGAGTCGATACACTTAT 57.606 33.333 0.00 0.00 0.00 1.73
1983 2096 8.783833 ACTTTGTACTAGAGTCGATACACTTA 57.216 34.615 0.00 0.00 0.00 2.24
1985 2098 7.684937 AACTTTGTACTAGAGTCGATACACT 57.315 36.000 0.00 0.00 0.00 3.55
2018 2131 8.973182 TCCCAAAATAAGTGTTTCAAACTTAGT 58.027 29.630 1.10 0.00 41.95 2.24
2019 2132 9.981114 ATCCCAAAATAAGTGTTTCAAACTTAG 57.019 29.630 1.10 0.00 41.95 2.18
2020 2133 9.757227 CATCCCAAAATAAGTGTTTCAAACTTA 57.243 29.630 1.10 0.00 42.63 2.24
2021 2134 7.714813 CCATCCCAAAATAAGTGTTTCAAACTT 59.285 33.333 1.10 0.00 40.82 2.66
2022 2135 7.070571 TCCATCCCAAAATAAGTGTTTCAAACT 59.929 33.333 1.10 0.00 0.00 2.66
2023 2136 7.213678 TCCATCCCAAAATAAGTGTTTCAAAC 58.786 34.615 0.00 0.00 0.00 2.93
2024 2137 7.366847 TCCATCCCAAAATAAGTGTTTCAAA 57.633 32.000 0.00 0.00 0.00 2.69
2025 2138 6.014669 CCTCCATCCCAAAATAAGTGTTTCAA 60.015 38.462 0.00 0.00 0.00 2.69
2026 2139 5.480073 CCTCCATCCCAAAATAAGTGTTTCA 59.520 40.000 0.00 0.00 0.00 2.69
2027 2140 5.714806 TCCTCCATCCCAAAATAAGTGTTTC 59.285 40.000 0.00 0.00 0.00 2.78
2028 2141 5.650283 TCCTCCATCCCAAAATAAGTGTTT 58.350 37.500 0.00 0.00 0.00 2.83
2029 2142 5.269554 TCCTCCATCCCAAAATAAGTGTT 57.730 39.130 0.00 0.00 0.00 3.32
2030 2143 4.946160 TCCTCCATCCCAAAATAAGTGT 57.054 40.909 0.00 0.00 0.00 3.55
2031 2144 5.264395 ACTTCCTCCATCCCAAAATAAGTG 58.736 41.667 0.00 0.00 0.00 3.16
2032 2145 5.536497 ACTTCCTCCATCCCAAAATAAGT 57.464 39.130 0.00 0.00 0.00 2.24
2033 2146 9.640952 TTAATACTTCCTCCATCCCAAAATAAG 57.359 33.333 0.00 0.00 0.00 1.73
2037 2150 9.998752 TTAATTAATACTTCCTCCATCCCAAAA 57.001 29.630 0.00 0.00 0.00 2.44
2038 2151 9.640952 CTTAATTAATACTTCCTCCATCCCAAA 57.359 33.333 0.00 0.00 0.00 3.28
2039 2152 9.009675 TCTTAATTAATACTTCCTCCATCCCAA 57.990 33.333 0.00 0.00 0.00 4.12
2040 2153 8.575736 TCTTAATTAATACTTCCTCCATCCCA 57.424 34.615 0.00 0.00 0.00 4.37
2041 2154 8.661345 ACTCTTAATTAATACTTCCTCCATCCC 58.339 37.037 0.00 0.00 0.00 3.85
2059 2172 9.520515 ACCAATCAACTGTTATCAACTCTTAAT 57.479 29.630 0.00 0.00 0.00 1.40
2060 2173 8.918202 ACCAATCAACTGTTATCAACTCTTAA 57.082 30.769 0.00 0.00 0.00 1.85
2061 2174 8.918202 AACCAATCAACTGTTATCAACTCTTA 57.082 30.769 0.00 0.00 0.00 2.10
2062 2175 7.502226 TGAACCAATCAACTGTTATCAACTCTT 59.498 33.333 0.00 0.00 34.30 2.85
2063 2176 6.998074 TGAACCAATCAACTGTTATCAACTCT 59.002 34.615 0.00 0.00 34.30 3.24
2064 2177 7.202016 TGAACCAATCAACTGTTATCAACTC 57.798 36.000 0.00 0.00 34.30 3.01
2065 2178 7.765695 ATGAACCAATCAACTGTTATCAACT 57.234 32.000 0.00 0.00 42.54 3.16
2066 2179 7.148755 GCAATGAACCAATCAACTGTTATCAAC 60.149 37.037 0.00 0.00 42.54 3.18
2067 2180 6.867816 GCAATGAACCAATCAACTGTTATCAA 59.132 34.615 0.00 0.00 42.54 2.57
2068 2181 6.209192 AGCAATGAACCAATCAACTGTTATCA 59.791 34.615 0.00 0.00 42.54 2.15
2069 2182 6.624423 AGCAATGAACCAATCAACTGTTATC 58.376 36.000 0.00 0.00 42.54 1.75
2070 2183 6.435277 AGAGCAATGAACCAATCAACTGTTAT 59.565 34.615 0.00 0.00 42.54 1.89
2071 2184 5.769662 AGAGCAATGAACCAATCAACTGTTA 59.230 36.000 0.00 0.00 42.54 2.41
2084 2197 7.609532 AGCCTAATAATCCATAGAGCAATGAAC 59.390 37.037 0.00 0.00 0.00 3.18
2087 2200 6.883217 ACAGCCTAATAATCCATAGAGCAATG 59.117 38.462 0.00 0.00 0.00 2.82
2108 2221 1.283736 GCCTATGCATGCAAAACAGC 58.716 50.000 26.68 18.64 37.47 4.40
2111 2224 1.994916 AACGCCTATGCATGCAAAAC 58.005 45.000 26.68 13.43 37.32 2.43
2120 2233 3.467803 AGTAATCTGGAAACGCCTATGC 58.532 45.455 0.00 0.00 37.63 3.14
2121 2234 4.058817 GGAGTAATCTGGAAACGCCTATG 58.941 47.826 0.00 0.00 37.63 2.23
2122 2235 3.967987 AGGAGTAATCTGGAAACGCCTAT 59.032 43.478 8.95 0.00 40.99 2.57
2123 2236 3.132289 CAGGAGTAATCTGGAAACGCCTA 59.868 47.826 9.88 0.00 40.86 3.93
2145 2258 9.181805 GAGAAAAGTAAAAACTCTGCATAAACC 57.818 33.333 0.00 0.00 0.00 3.27
2150 2267 5.763204 TCGGAGAAAAGTAAAAACTCTGCAT 59.237 36.000 0.00 0.00 34.97 3.96
2158 2275 7.576861 AATTCCTGTCGGAGAAAAGTAAAAA 57.423 32.000 0.00 0.00 41.25 1.94
2207 2327 6.631971 ACAACATGATGAAACACACATGTA 57.368 33.333 10.29 0.00 43.29 2.29
2278 2664 6.978343 TCTGTCCTAAACACAATTATTCCG 57.022 37.500 0.00 0.00 33.24 4.30
2349 2742 1.882352 GCGGAACACACAAAGAGGGAT 60.882 52.381 0.00 0.00 0.00 3.85
2369 2762 4.640647 GCTTCCTATCCTGGTAAAAAGGTG 59.359 45.833 0.00 0.00 36.14 4.00
2398 2795 2.353269 TGGAGCGGCATAACAAATTACG 59.647 45.455 1.45 0.00 0.00 3.18
2402 2799 3.023119 TCAATGGAGCGGCATAACAAAT 58.977 40.909 1.45 0.00 0.00 2.32
2410 2807 2.288666 GTAAGAATCAATGGAGCGGCA 58.711 47.619 1.45 0.00 0.00 5.69
2414 2811 6.073331 GCATCTACTGTAAGAATCAATGGAGC 60.073 42.308 0.00 0.00 37.43 4.70
2477 2882 1.221466 ACAATCGGTATGATGGCGCG 61.221 55.000 0.00 0.00 37.39 6.86
2480 2885 1.265095 CAGCACAATCGGTATGATGGC 59.735 52.381 0.00 0.00 37.39 4.40
2504 2909 4.394795 CGCAGAGAAATTCCGTTAGTTTG 58.605 43.478 0.00 0.00 0.00 2.93
2505 2910 3.435671 CCGCAGAGAAATTCCGTTAGTTT 59.564 43.478 0.00 0.00 0.00 2.66
2525 2930 1.141449 CTCTTCTCTCCTGCTGCCG 59.859 63.158 0.00 0.00 0.00 5.69
2526 2931 1.153389 GCTCTTCTCTCCTGCTGCC 60.153 63.158 0.00 0.00 0.00 4.85
2676 3089 2.924290 CGTCGTTCCCTTCTTTCTCATC 59.076 50.000 0.00 0.00 0.00 2.92
2677 3090 2.561419 TCGTCGTTCCCTTCTTTCTCAT 59.439 45.455 0.00 0.00 0.00 2.90
2678 3091 1.958579 TCGTCGTTCCCTTCTTTCTCA 59.041 47.619 0.00 0.00 0.00 3.27
2679 3092 2.597520 CTCGTCGTTCCCTTCTTTCTC 58.402 52.381 0.00 0.00 0.00 2.87
2680 3093 1.336980 GCTCGTCGTTCCCTTCTTTCT 60.337 52.381 0.00 0.00 0.00 2.52
2681 3094 1.069255 GCTCGTCGTTCCCTTCTTTC 58.931 55.000 0.00 0.00 0.00 2.62
2948 3387 2.128771 ACACCAGTGCAAGTGAAAGT 57.871 45.000 17.05 2.71 40.62 2.66
2952 3391 5.804639 AGATAAATACACCAGTGCAAGTGA 58.195 37.500 17.05 4.33 40.62 3.41
2979 3418 4.157246 TCCAGCATATATACTCCCAACGT 58.843 43.478 0.00 0.00 0.00 3.99
3008 3449 6.474427 CACTACAACGTCTCACAAGAGTAAAA 59.526 38.462 0.00 0.00 42.66 1.52
3016 3457 3.191669 CAACCACTACAACGTCTCACAA 58.808 45.455 0.00 0.00 0.00 3.33
3118 3561 8.558700 GGTCCTTACGTGACTTGTAATTTAAAA 58.441 33.333 0.00 0.00 31.85 1.52
3119 3562 7.095691 CGGTCCTTACGTGACTTGTAATTTAAA 60.096 37.037 0.00 0.00 31.85 1.52
3125 3568 2.884012 TCGGTCCTTACGTGACTTGTAA 59.116 45.455 0.00 0.00 33.22 2.41
3152 3595 9.507329 AGATGTTCTGCTATCTTTTCAGTTTTA 57.493 29.630 0.00 0.00 29.64 1.52
3179 3622 0.861837 GACGTTGGTGTCAAGCTCAG 59.138 55.000 0.00 0.00 38.75 3.35
3180 3623 0.531974 GGACGTTGGTGTCAAGCTCA 60.532 55.000 0.00 0.00 40.72 4.26
3181 3624 1.557443 CGGACGTTGGTGTCAAGCTC 61.557 60.000 0.00 0.00 40.72 4.09
3182 3625 1.594293 CGGACGTTGGTGTCAAGCT 60.594 57.895 0.00 0.00 40.72 3.74
3183 3626 1.828331 GACGGACGTTGGTGTCAAGC 61.828 60.000 0.00 0.00 40.72 4.01
3184 3627 0.528901 TGACGGACGTTGGTGTCAAG 60.529 55.000 9.64 0.00 40.72 3.02
3185 3628 0.806884 GTGACGGACGTTGGTGTCAA 60.807 55.000 12.55 0.00 42.43 3.18
3186 3629 1.227031 GTGACGGACGTTGGTGTCA 60.227 57.895 0.00 8.43 40.72 3.58
3187 3630 0.599204 ATGTGACGGACGTTGGTGTC 60.599 55.000 0.00 0.00 38.17 3.67
3188 3631 0.878523 CATGTGACGGACGTTGGTGT 60.879 55.000 0.00 0.00 0.00 4.16
3189 3632 1.859398 CATGTGACGGACGTTGGTG 59.141 57.895 0.00 0.00 0.00 4.17
3190 3633 1.959226 GCATGTGACGGACGTTGGT 60.959 57.895 0.00 0.00 0.00 3.67
3191 3634 2.677003 GGCATGTGACGGACGTTGG 61.677 63.158 0.00 0.00 0.00 3.77
3192 3635 1.626654 GAGGCATGTGACGGACGTTG 61.627 60.000 0.00 0.00 0.00 4.10
3193 3636 1.374252 GAGGCATGTGACGGACGTT 60.374 57.895 0.00 0.00 0.00 3.99
3194 3637 2.261671 GAGGCATGTGACGGACGT 59.738 61.111 0.00 0.00 0.00 4.34
3195 3638 2.509336 GGAGGCATGTGACGGACG 60.509 66.667 0.00 0.00 0.00 4.79
3196 3639 2.509336 CGGAGGCATGTGACGGAC 60.509 66.667 0.00 0.00 0.00 4.79
3197 3640 3.770040 CCGGAGGCATGTGACGGA 61.770 66.667 12.71 0.00 46.14 4.69
3209 3652 3.941188 AGTGTGGTGGTGCCGGAG 61.941 66.667 5.05 0.00 41.21 4.63
3210 3653 4.248842 CAGTGTGGTGGTGCCGGA 62.249 66.667 5.05 0.00 41.21 5.14
3211 3654 4.248842 TCAGTGTGGTGGTGCCGG 62.249 66.667 0.00 0.00 41.21 6.13
3212 3655 2.666190 CTCAGTGTGGTGGTGCCG 60.666 66.667 0.00 0.00 41.21 5.69
3213 3656 2.965716 AAGCTCAGTGTGGTGGTGCC 62.966 60.000 0.00 0.00 37.90 5.01
3214 3657 1.526917 AAGCTCAGTGTGGTGGTGC 60.527 57.895 0.00 0.00 0.00 5.01
3215 3658 0.179048 TCAAGCTCAGTGTGGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
3216 3659 0.179045 GTCAAGCTCAGTGTGGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
3217 3660 0.179048 TGTCAAGCTCAGTGTGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
3218 3661 1.802960 GATGTCAAGCTCAGTGTGGTG 59.197 52.381 0.00 0.00 0.00 4.17
3219 3662 1.417517 TGATGTCAAGCTCAGTGTGGT 59.582 47.619 0.00 0.00 0.00 4.16
3220 3663 2.174363 TGATGTCAAGCTCAGTGTGG 57.826 50.000 0.00 0.00 0.00 4.17
3221 3664 2.096565 CGTTGATGTCAAGCTCAGTGTG 60.097 50.000 0.00 0.00 36.39 3.82
3222 3665 2.138320 CGTTGATGTCAAGCTCAGTGT 58.862 47.619 0.00 0.00 36.39 3.55
3223 3666 1.136141 GCGTTGATGTCAAGCTCAGTG 60.136 52.381 0.00 0.00 36.39 3.66
3224 3667 1.151668 GCGTTGATGTCAAGCTCAGT 58.848 50.000 0.00 0.00 36.39 3.41
3237 3680 3.047280 GCATGTGACGGGCGTTGA 61.047 61.111 0.00 0.00 0.00 3.18
3276 3719 4.524316 TCCGTCAATCTTTTCTTCGGTA 57.476 40.909 0.00 0.00 38.04 4.02
3385 3829 2.083774 GGTCTGATTCGTTCAATGCCA 58.916 47.619 0.00 0.00 32.78 4.92
3386 3830 1.062587 CGGTCTGATTCGTTCAATGCC 59.937 52.381 0.00 0.00 32.78 4.40
3387 3831 1.062587 CCGGTCTGATTCGTTCAATGC 59.937 52.381 0.00 0.00 32.78 3.56
3388 3832 1.665679 CCCGGTCTGATTCGTTCAATG 59.334 52.381 0.00 0.00 32.78 2.82
3389 3833 1.406887 CCCCGGTCTGATTCGTTCAAT 60.407 52.381 0.00 0.00 32.78 2.57
3447 3891 1.079336 GTCTTAGTCGTGGTGGGGC 60.079 63.158 0.00 0.00 0.00 5.80
3474 3918 1.156736 GATGACAGGTGTGGTTTCCG 58.843 55.000 0.00 0.00 0.00 4.30
3503 3947 0.028374 CGAAACGTGTGTTGGGTTCC 59.972 55.000 0.00 0.00 38.62 3.62
3511 3955 1.135527 TCTGGAAGACGAAACGTGTGT 59.864 47.619 0.62 0.00 41.37 3.72
3542 3986 1.676916 CGGATGCAGATTGTGGTCAGT 60.677 52.381 0.00 0.00 0.00 3.41
3544 3988 1.026182 GCGGATGCAGATTGTGGTCA 61.026 55.000 0.00 0.00 42.15 4.02
3621 4066 3.916392 GACACGTGTCCTCGGGCTG 62.916 68.421 33.62 0.00 39.07 4.85
3635 4080 0.389948 GTCATCCTCGTGGTGGACAC 60.390 60.000 18.57 0.00 46.78 3.67
3653 4098 3.909258 GATGGTGTGGCGACGACGT 62.909 63.158 9.33 0.00 41.98 4.34
3779 4226 3.071479 GGCTGTTCATCGTCTTGGTTTA 58.929 45.455 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.