Multiple sequence alignment - TraesCS2A01G069200

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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 TraesCS2A01G069200 chr2A 100.000 2629 0 0 1 2629 30314307 30311679 0.000000e+00 4855.0
1 TraesCS2A01G069200 chr2A 92.908 282 8 5 2360 2629 423774613 423774894 1.470000e-107 399.0
2 TraesCS2A01G069200 chr2A 90.769 65 3 1 1596 1657 30312234 30312170 1.680000e-12 84.2
3 TraesCS2A01G069200 chr2A 90.769 65 3 1 2074 2138 30312712 30312651 1.680000e-12 84.2
4 TraesCS2A01G069200 chr2B 90.417 1607 82 26 785 2370 45617274 45618829 0.000000e+00 2049.0
5 TraesCS2A01G069200 chr2B 87.547 795 73 14 1 789 45703177 45702403 0.000000e+00 896.0
6 TraesCS2A01G069200 chr2B 81.739 115 14 5 2028 2140 45618008 45618117 3.600000e-14 89.8
7 TraesCS2A01G069200 chr2D 89.920 1508 107 25 882 2370 28429341 28427860 0.000000e+00 1901.0
8 TraesCS2A01G069200 chr2D 83.495 103 13 4 2028 2128 28428661 28428561 2.790000e-15 93.5
9 TraesCS2A01G069200 chr6A 98.855 262 1 2 2369 2629 613972472 613972732 1.430000e-127 466.0
10 TraesCS2A01G069200 chr6A 98.755 241 3 0 2389 2629 86115590 86115350 1.870000e-116 429.0
11 TraesCS2A01G069200 chr6A 93.502 277 7 1 2364 2629 105585567 105585843 4.080000e-108 401.0
12 TraesCS2A01G069200 chr5A 99.585 241 1 0 2389 2629 630124057 630123817 8.640000e-120 440.0
13 TraesCS2A01G069200 chr5A 96.183 262 10 0 2368 2629 458228102 458228363 1.870000e-116 429.0
14 TraesCS2A01G069200 chr5A 80.989 263 38 4 2365 2616 673512539 673512800 5.740000e-47 198.0
15 TraesCS2A01G069200 chr3A 99.585 241 1 0 2389 2629 363316255 363316015 8.640000e-120 440.0
16 TraesCS2A01G069200 chr3A 95.736 258 11 0 2372 2629 712633978 712633721 1.460000e-112 416.0
17 TraesCS2A01G069200 chr3B 96.911 259 8 0 2371 2629 145959990 145960248 4.020000e-118 435.0
18 TraesCS2A01G069200 chr5D 98.755 241 3 0 2389 2629 352931687 352931927 1.870000e-116 429.0
19 TraesCS2A01G069200 chr1B 95.420 262 9 2 2370 2628 591442051 591442312 5.240000e-112 414.0
20 TraesCS2A01G069200 chr7A 85.153 229 27 6 1173 1394 469981671 469981443 7.320000e-56 228.0
21 TraesCS2A01G069200 chr4A 80.882 272 39 3 2356 2615 596766388 596766658 4.440000e-48 202.0


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 TraesCS2A01G069200 chr2A 30311679 30314307 2628 True 1674.466667 4855 93.8460 1 2629 3 chr2A.!!$R1 2628
1 TraesCS2A01G069200 chr2B 45617274 45618829 1555 False 1069.400000 2049 86.0780 785 2370 2 chr2B.!!$F1 1585
2 TraesCS2A01G069200 chr2B 45702403 45703177 774 True 896.000000 896 87.5470 1 789 1 chr2B.!!$R1 788
3 TraesCS2A01G069200 chr2D 28427860 28429341 1481 True 997.250000 1901 86.7075 882 2370 2 chr2D.!!$R1 1488

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
944 951 0.035036 GGTCGGCCTTCTTATAGCCC 59.965 60.0 0.0 0.0 44.13 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2370 2434 0.11319 CTCCAAACCAAAGGAGGCCT 59.887 55.0 3.86 3.86 46.11 5.19 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
44 45 9.705290 AATGGGTAATCTTTAATGTGTTTTGAC 57.295 29.630 0.00 0.00 0.00 3.18
45 46 8.472007 TGGGTAATCTTTAATGTGTTTTGACT 57.528 30.769 0.00 0.00 0.00 3.41
46 47 9.575868 TGGGTAATCTTTAATGTGTTTTGACTA 57.424 29.630 0.00 0.00 0.00 2.59
70 71 9.810231 CTATAATGGTTTTTGAATTTTGTGTGC 57.190 29.630 0.00 0.00 0.00 4.57
75 76 5.389935 GGTTTTTGAATTTTGTGTGCGTGAA 60.390 36.000 0.00 0.00 0.00 3.18
76 77 5.845985 TTTTGAATTTTGTGTGCGTGAAA 57.154 30.435 0.00 0.00 0.00 2.69
87 89 1.035923 TGCGTGAAAGGGATTTTGCA 58.964 45.000 0.00 0.00 0.00 4.08
91 93 3.311048 GCGTGAAAGGGATTTTGCAAAAA 59.689 39.130 27.10 11.93 0.00 1.94
92 94 4.024133 GCGTGAAAGGGATTTTGCAAAAAT 60.024 37.500 27.10 15.86 0.00 1.82
99 101 4.747540 GGATTTTGCAAAAATCCCACAC 57.252 40.909 27.10 11.32 46.22 3.82
109 111 8.076910 TGCAAAAATCCCACACTGATAATAAT 57.923 30.769 0.00 0.00 0.00 1.28
137 139 1.004745 ACGATTTGGCCCATTGAGAGT 59.995 47.619 0.00 0.00 0.00 3.24
139 141 1.753073 GATTTGGCCCATTGAGAGTGG 59.247 52.381 0.00 0.00 36.47 4.00
159 161 1.325476 GGGTCCCGTGTACACCTAGG 61.325 65.000 20.11 17.29 0.00 3.02
165 167 3.069289 CCCGTGTACACCTAGGAAAAAC 58.931 50.000 17.98 8.45 0.00 2.43
173 175 6.502863 TGTACACCTAGGAAAAACCCTCTATT 59.497 38.462 17.98 0.00 40.05 1.73
187 189 4.202631 ACCCTCTATTGTTTTGTGCCCTAA 60.203 41.667 0.00 0.00 0.00 2.69
199 201 6.656632 TTTGTGCCCTAATGTTTTGTATCA 57.343 33.333 0.00 0.00 0.00 2.15
207 209 9.683069 GCCCTAATGTTTTGTATCATAGAATTG 57.317 33.333 0.00 0.00 0.00 2.32
293 295 9.656040 TTATTAACCTTGCTAGTTCGATTGTTA 57.344 29.630 0.00 0.00 0.00 2.41
303 305 6.255887 GCTAGTTCGATTGTTATGTAGCAACT 59.744 38.462 0.00 0.00 33.39 3.16
308 310 6.811954 TCGATTGTTATGTAGCAACTCCATA 58.188 36.000 0.00 0.00 0.00 2.74
316 318 8.458843 GTTATGTAGCAACTCCATAACACATTT 58.541 33.333 14.53 0.00 45.12 2.32
322 324 6.493458 AGCAACTCCATAACACATTTTAAGGT 59.507 34.615 0.00 0.00 0.00 3.50
338 340 5.968528 TTAAGGTCAACACGCCATTTAAT 57.031 34.783 0.00 0.00 0.00 1.40
342 344 4.634443 AGGTCAACACGCCATTTAATACTC 59.366 41.667 0.00 0.00 0.00 2.59
345 347 5.123344 GTCAACACGCCATTTAATACTCCTT 59.877 40.000 0.00 0.00 0.00 3.36
346 348 5.708230 TCAACACGCCATTTAATACTCCTTT 59.292 36.000 0.00 0.00 0.00 3.11
427 433 0.692476 AGCATACAAGTGTGCCCTCA 59.308 50.000 16.67 0.00 46.93 3.86
438 444 2.548480 GTGTGCCCTCACTACAACTTTC 59.452 50.000 0.00 0.00 43.49 2.62
451 457 8.208903 TCACTACAACTTTCTTTTTAGTAGGCT 58.791 33.333 0.00 0.00 33.60 4.58
452 458 8.496751 CACTACAACTTTCTTTTTAGTAGGCTC 58.503 37.037 0.00 0.00 33.60 4.70
453 459 6.541111 ACAACTTTCTTTTTAGTAGGCTCG 57.459 37.500 0.00 0.00 0.00 5.03
454 460 5.469084 ACAACTTTCTTTTTAGTAGGCTCGG 59.531 40.000 0.00 0.00 0.00 4.63
462 468 8.431910 TCTTTTTAGTAGGCTCGGGATATATT 57.568 34.615 0.00 0.00 0.00 1.28
464 470 7.549147 TTTTAGTAGGCTCGGGATATATTGT 57.451 36.000 0.00 0.00 0.00 2.71
507 513 7.707035 AGATACACTATCTCTTTTTAAGCACCG 59.293 37.037 0.00 0.00 41.55 4.94
520 526 9.651718 CTTTTTAAGCACCGTAAATATCTCATC 57.348 33.333 0.00 0.00 0.00 2.92
527 533 5.629849 CACCGTAAATATCTCATCGAAGACC 59.370 44.000 0.00 0.00 42.51 3.85
529 535 4.852104 CGTAAATATCTCATCGAAGACCGG 59.148 45.833 0.00 0.00 42.51 5.28
542 548 1.830279 AGACCGGAACTATCGTGTCA 58.170 50.000 9.46 0.00 33.51 3.58
564 570 5.992829 TCAAATGCTGCTTTTGACATGATTT 59.007 32.000 28.93 9.64 37.97 2.17
567 573 3.243941 TGCTGCTTTTGACATGATTTGCT 60.244 39.130 0.00 0.00 0.00 3.91
580 586 3.911868 TGATTTGCTGGGTTGAAATTCG 58.088 40.909 0.00 0.00 0.00 3.34
582 588 3.363341 TTTGCTGGGTTGAAATTCGTC 57.637 42.857 0.00 0.00 0.00 4.20
588 594 1.401018 GGGTTGAAATTCGTCAAGGCG 60.401 52.381 0.00 0.00 38.17 5.52
590 596 0.110419 TTGAAATTCGTCAAGGCGCG 60.110 50.000 0.00 0.00 32.56 6.86
606 612 2.568090 CGCTTGCCACCATGAACC 59.432 61.111 0.00 0.00 0.00 3.62
609 615 2.988684 TTGCCACCATGAACCGGC 60.989 61.111 0.00 0.64 45.11 6.13
620 626 2.922740 TGAACCGGCCATTAGTATCC 57.077 50.000 0.00 0.00 0.00 2.59
621 627 1.069513 TGAACCGGCCATTAGTATCCG 59.930 52.381 0.00 0.00 41.41 4.18
622 628 1.342174 GAACCGGCCATTAGTATCCGA 59.658 52.381 0.00 0.00 44.23 4.55
623 629 0.677842 ACCGGCCATTAGTATCCGAC 59.322 55.000 0.00 0.00 44.23 4.79
625 631 1.069513 CCGGCCATTAGTATCCGACAA 59.930 52.381 2.24 0.00 44.23 3.18
626 632 2.289444 CCGGCCATTAGTATCCGACAAT 60.289 50.000 2.24 0.00 44.23 2.71
627 633 2.736721 CGGCCATTAGTATCCGACAATG 59.263 50.000 2.24 0.00 44.23 2.82
628 634 3.074412 GGCCATTAGTATCCGACAATGG 58.926 50.000 0.00 7.64 43.01 3.16
630 636 3.498397 GCCATTAGTATCCGACAATGGTG 59.502 47.826 12.40 0.00 42.60 4.17
651 657 1.001633 GAGCCTAACCCTTTGTCGACA 59.998 52.381 15.76 15.76 0.00 4.35
693 699 9.051679 ACTTTGAATTTTACAAACCCTAAATGC 57.948 29.630 0.00 0.00 34.30 3.56
697 703 2.883122 TACAAACCCTAAATGCCGGT 57.117 45.000 1.90 0.00 0.00 5.28
716 723 2.430694 GGTTTGGTCCACTTTTTGCTCT 59.569 45.455 0.00 0.00 0.00 4.09
717 724 3.447742 GTTTGGTCCACTTTTTGCTCTG 58.552 45.455 0.00 0.00 0.00 3.35
762 769 1.242989 TCGCCAGCAGTATTTTGCAA 58.757 45.000 0.00 0.00 46.47 4.08
782 789 7.288810 TGCAAGAGTATTCAACAGGAAAAAT 57.711 32.000 0.00 0.00 39.39 1.82
783 790 8.402798 TGCAAGAGTATTCAACAGGAAAAATA 57.597 30.769 0.00 0.00 39.39 1.40
794 801 9.944079 TTCAACAGGAAAAATATATATTGGGGA 57.056 29.630 8.74 0.00 30.98 4.81
824 831 5.896073 TTGGACAAAATGTATTGGGGTTT 57.104 34.783 0.00 0.00 34.56 3.27
829 836 5.800296 ACAAAATGTATTGGGGTTTTAGGC 58.200 37.500 0.00 0.00 34.56 3.93
848 855 2.098298 CCGCTCATTTGCCGAACG 59.902 61.111 0.00 0.00 0.00 3.95
855 862 1.883275 TCATTTGCCGAACGTTTCCAT 59.117 42.857 0.46 0.00 0.00 3.41
862 869 2.846693 CCGAACGTTTCCATTTAGCAC 58.153 47.619 0.46 0.00 0.00 4.40
870 877 3.660970 TTCCATTTAGCACATGGGCTA 57.339 42.857 25.84 25.84 43.70 3.93
872 879 4.991789 TCCATTTAGCACATGGGCTATA 57.008 40.909 29.55 24.71 45.18 1.31
921 928 5.944007 ACTTAGCCGAACATTTCCACTTTAT 59.056 36.000 0.00 0.00 0.00 1.40
925 932 5.925969 AGCCGAACATTTCCACTTTATTTTG 59.074 36.000 0.00 0.00 0.00 2.44
943 950 0.756903 TGGTCGGCCTTCTTATAGCC 59.243 55.000 7.97 0.00 43.53 3.93
944 951 0.035036 GGTCGGCCTTCTTATAGCCC 59.965 60.000 0.00 0.00 44.13 5.19
945 952 0.756903 GTCGGCCTTCTTATAGCCCA 59.243 55.000 0.00 0.00 44.13 5.36
946 953 1.348036 GTCGGCCTTCTTATAGCCCAT 59.652 52.381 0.00 0.00 44.13 4.00
947 954 1.623811 TCGGCCTTCTTATAGCCCATC 59.376 52.381 0.00 0.00 44.13 3.51
948 955 1.625818 CGGCCTTCTTATAGCCCATCT 59.374 52.381 0.00 0.00 44.13 2.90
949 956 2.613977 CGGCCTTCTTATAGCCCATCTG 60.614 54.545 0.00 0.00 44.13 2.90
950 957 2.639839 GGCCTTCTTATAGCCCATCTGA 59.360 50.000 0.00 0.00 41.00 3.27
951 958 3.265479 GGCCTTCTTATAGCCCATCTGAT 59.735 47.826 0.00 0.00 41.00 2.90
952 959 4.471386 GGCCTTCTTATAGCCCATCTGATA 59.529 45.833 0.00 0.00 41.00 2.15
953 960 5.396213 GGCCTTCTTATAGCCCATCTGATAG 60.396 48.000 0.00 0.00 41.00 2.08
954 961 5.188751 GCCTTCTTATAGCCCATCTGATAGT 59.811 44.000 0.00 0.00 0.00 2.12
955 962 6.381420 GCCTTCTTATAGCCCATCTGATAGTA 59.619 42.308 0.00 0.00 0.00 1.82
956 963 7.070571 GCCTTCTTATAGCCCATCTGATAGTAT 59.929 40.741 0.00 0.00 0.00 2.12
957 964 8.637986 CCTTCTTATAGCCCATCTGATAGTATC 58.362 40.741 2.97 2.97 0.00 2.24
958 965 9.194972 CTTCTTATAGCCCATCTGATAGTATCA 57.805 37.037 12.28 12.28 37.76 2.15
1027 1058 3.993535 GCAGAAGGCAACAGAGGG 58.006 61.111 0.00 0.00 43.97 4.30
1078 1120 2.607134 AGGAGCAGAGCCAGCAGT 60.607 61.111 0.00 0.00 0.00 4.40
1079 1121 2.125188 GGAGCAGAGCCAGCAGTC 60.125 66.667 0.00 0.00 0.00 3.51
1082 1124 2.508887 GCAGAGCCAGCAGTCGAG 60.509 66.667 0.00 0.00 0.00 4.04
1083 1125 2.999485 GCAGAGCCAGCAGTCGAGA 61.999 63.158 0.00 0.00 0.00 4.04
1084 1126 1.139308 CAGAGCCAGCAGTCGAGAG 59.861 63.158 0.00 0.00 0.00 3.20
1085 1127 1.001517 AGAGCCAGCAGTCGAGAGA 60.002 57.895 0.00 0.00 38.16 3.10
1086 1128 1.031571 AGAGCCAGCAGTCGAGAGAG 61.032 60.000 0.00 0.00 43.49 3.20
1087 1129 1.001517 AGCCAGCAGTCGAGAGAGA 60.002 57.895 0.00 0.00 43.49 3.10
1088 1130 0.610509 AGCCAGCAGTCGAGAGAGAA 60.611 55.000 0.00 0.00 43.49 2.87
1089 1131 0.179140 GCCAGCAGTCGAGAGAGAAG 60.179 60.000 0.00 0.00 43.49 2.85
1090 1132 0.179140 CCAGCAGTCGAGAGAGAAGC 60.179 60.000 0.00 0.00 43.49 3.86
1168 1210 1.350193 CGAAGCTGTACATCACGCTT 58.650 50.000 17.20 17.20 44.23 4.68
1276 1318 4.658786 ACCACGCCCTCCCTCCTT 62.659 66.667 0.00 0.00 0.00 3.36
1492 1534 2.794350 GGTGATGCTTCGGTTTGTTTTG 59.206 45.455 0.00 0.00 0.00 2.44
1497 1539 2.926838 TGCTTCGGTTTGTTTTGCTTTC 59.073 40.909 0.00 0.00 0.00 2.62
1498 1540 2.034926 GCTTCGGTTTGTTTTGCTTTCG 60.035 45.455 0.00 0.00 0.00 3.46
1499 1541 1.551145 TCGGTTTGTTTTGCTTTCGC 58.449 45.000 0.00 0.00 0.00 4.70
1541 1588 1.574428 GTGTTCGACGCAATGCCTT 59.426 52.632 0.00 0.00 0.00 4.35
1564 1611 0.838987 AGGGTTGGCGTCCTCCTTTA 60.839 55.000 0.00 0.00 0.00 1.85
1578 1625 7.173390 GCGTCCTCCTTTATAATAGAAATGCTT 59.827 37.037 0.00 0.00 0.00 3.91
1675 1722 8.637986 TGATTGTTATATTGAAATGTAAGGCCC 58.362 33.333 0.00 0.00 0.00 5.80
1682 1729 4.046286 TGAAATGTAAGGCCCAAGTCAT 57.954 40.909 0.00 0.00 0.00 3.06
1912 1959 8.451748 GGCTTTTGGCTATACTTTATGCTATAC 58.548 37.037 0.00 0.00 42.31 1.47
1961 2008 6.579666 TCAAGACATGCTTTGCTATTTTCT 57.420 33.333 0.00 0.00 33.60 2.52
1963 2010 8.284945 TCAAGACATGCTTTGCTATTTTCTAT 57.715 30.769 0.00 0.00 33.60 1.98
1991 2038 9.463443 AGTTTGTCTAAAATACATTTTGCACTC 57.537 29.630 9.64 3.73 40.00 3.51
2042 2091 1.818060 TGATTTTGGCACCCTCATTCG 59.182 47.619 0.00 0.00 0.00 3.34
2084 2148 9.376075 AGTAATCTGTGATGTCTTGACTTAATG 57.624 33.333 2.35 0.00 0.00 1.90
2110 2174 7.176690 GGGAATAAGTGAAGAATTTCCTGTGAA 59.823 37.037 0.00 0.00 32.09 3.18
2212 2276 7.397892 TGTCTTGTTTTTAATGTCCAGTTCA 57.602 32.000 0.00 0.00 0.00 3.18
2311 2375 4.888326 TCCAGCCATGCTTAACAAATTT 57.112 36.364 0.00 0.00 36.40 1.82
2360 2424 8.815565 TTTGCACTATATGTGAAAATTCCCTA 57.184 30.769 8.81 0.00 46.27 3.53
2373 2437 9.582431 GTGAAAATTCCCTAGTAAATTTTAGGC 57.418 33.333 17.99 10.89 42.26 3.93
2374 2438 8.755028 TGAAAATTCCCTAGTAAATTTTAGGCC 58.245 33.333 17.99 0.00 42.26 5.19
2375 2439 8.911018 AAAATTCCCTAGTAAATTTTAGGCCT 57.089 30.769 11.78 11.78 41.10 5.19
2376 2440 8.534954 AAATTCCCTAGTAAATTTTAGGCCTC 57.465 34.615 9.68 0.00 36.02 4.70
2377 2441 5.641789 TCCCTAGTAAATTTTAGGCCTCC 57.358 43.478 9.68 0.00 36.02 4.30
2378 2442 5.294473 TCCCTAGTAAATTTTAGGCCTCCT 58.706 41.667 9.68 0.00 36.02 3.69
2379 2443 5.734634 TCCCTAGTAAATTTTAGGCCTCCTT 59.265 40.000 9.68 0.00 36.02 3.36
2380 2444 6.218938 TCCCTAGTAAATTTTAGGCCTCCTTT 59.781 38.462 9.68 7.76 36.02 3.11
2381 2445 6.321435 CCCTAGTAAATTTTAGGCCTCCTTTG 59.679 42.308 9.68 0.00 36.02 2.77
2382 2446 6.321435 CCTAGTAAATTTTAGGCCTCCTTTGG 59.679 42.308 9.68 0.00 34.61 3.28
2383 2447 5.651303 AGTAAATTTTAGGCCTCCTTTGGT 58.349 37.500 9.68 0.00 34.61 3.67
2384 2448 6.082031 AGTAAATTTTAGGCCTCCTTTGGTT 58.918 36.000 9.68 0.00 34.61 3.67
2385 2449 5.904984 AAATTTTAGGCCTCCTTTGGTTT 57.095 34.783 9.68 0.00 34.61 3.27
2386 2450 4.890158 ATTTTAGGCCTCCTTTGGTTTG 57.110 40.909 9.68 0.00 34.61 2.93
2387 2451 2.302587 TTAGGCCTCCTTTGGTTTGG 57.697 50.000 9.68 0.00 34.61 3.28
2388 2452 1.451449 TAGGCCTCCTTTGGTTTGGA 58.549 50.000 9.68 0.00 34.61 3.53
2389 2453 0.113190 AGGCCTCCTTTGGTTTGGAG 59.887 55.000 0.00 0.00 46.91 3.86
2396 2460 5.551305 CTCCTTTGGTTTGGAGGAATTTT 57.449 39.130 0.00 0.00 44.44 1.82
2397 2461 6.664428 CTCCTTTGGTTTGGAGGAATTTTA 57.336 37.500 0.00 0.00 44.44 1.52
2398 2462 6.664428 TCCTTTGGTTTGGAGGAATTTTAG 57.336 37.500 0.00 0.00 36.67 1.85
2399 2463 6.377912 TCCTTTGGTTTGGAGGAATTTTAGA 58.622 36.000 0.00 0.00 36.67 2.10
2400 2464 6.493458 TCCTTTGGTTTGGAGGAATTTTAGAG 59.507 38.462 0.00 0.00 36.67 2.43
2401 2465 6.295292 CCTTTGGTTTGGAGGAATTTTAGAGG 60.295 42.308 0.00 0.00 32.11 3.69
2402 2466 5.592587 TGGTTTGGAGGAATTTTAGAGGA 57.407 39.130 0.00 0.00 0.00 3.71
2403 2467 6.152638 TGGTTTGGAGGAATTTTAGAGGAT 57.847 37.500 0.00 0.00 0.00 3.24
2404 2468 7.278724 TGGTTTGGAGGAATTTTAGAGGATA 57.721 36.000 0.00 0.00 0.00 2.59
2405 2469 7.346471 TGGTTTGGAGGAATTTTAGAGGATAG 58.654 38.462 0.00 0.00 0.00 2.08
2406 2470 6.773200 GGTTTGGAGGAATTTTAGAGGATAGG 59.227 42.308 0.00 0.00 0.00 2.57
2407 2471 7.366551 GGTTTGGAGGAATTTTAGAGGATAGGA 60.367 40.741 0.00 0.00 0.00 2.94
2408 2472 7.954539 TTGGAGGAATTTTAGAGGATAGGAT 57.045 36.000 0.00 0.00 0.00 3.24
2409 2473 7.954539 TGGAGGAATTTTAGAGGATAGGATT 57.045 36.000 0.00 0.00 0.00 3.01
2410 2474 7.978925 TGGAGGAATTTTAGAGGATAGGATTC 58.021 38.462 0.00 0.00 0.00 2.52
2411 2475 7.796637 TGGAGGAATTTTAGAGGATAGGATTCT 59.203 37.037 0.00 0.00 0.00 2.40
2412 2476 8.664992 GGAGGAATTTTAGAGGATAGGATTCTT 58.335 37.037 0.00 0.00 0.00 2.52
2442 2506 3.895704 TTTCCTTTAGAGCCCTTTGGT 57.104 42.857 0.00 0.00 0.00 3.67
2443 2507 3.895704 TTCCTTTAGAGCCCTTTGGTT 57.104 42.857 0.00 0.00 0.00 3.67
2444 2508 3.434940 TCCTTTAGAGCCCTTTGGTTC 57.565 47.619 0.00 0.00 41.91 3.62
2445 2509 2.714250 TCCTTTAGAGCCCTTTGGTTCA 59.286 45.455 0.00 0.00 43.89 3.18
2446 2510 3.333680 TCCTTTAGAGCCCTTTGGTTCAT 59.666 43.478 0.00 0.00 43.89 2.57
2447 2511 4.538490 TCCTTTAGAGCCCTTTGGTTCATA 59.462 41.667 0.00 0.00 43.89 2.15
2448 2512 4.884164 CCTTTAGAGCCCTTTGGTTCATAG 59.116 45.833 0.00 0.00 43.89 2.23
2449 2513 4.503714 TTAGAGCCCTTTGGTTCATAGG 57.496 45.455 0.00 0.00 43.89 2.57
2450 2514 2.562296 AGAGCCCTTTGGTTCATAGGA 58.438 47.619 6.07 0.00 43.89 2.94
2451 2515 2.919602 AGAGCCCTTTGGTTCATAGGAA 59.080 45.455 6.07 0.00 43.89 3.36
2452 2516 3.529319 AGAGCCCTTTGGTTCATAGGAAT 59.471 43.478 6.07 0.00 43.89 3.01
2453 2517 3.633986 GAGCCCTTTGGTTCATAGGAATG 59.366 47.826 6.07 0.00 41.28 2.67
2454 2518 2.695147 GCCCTTTGGTTCATAGGAATGG 59.305 50.000 6.07 0.00 35.14 3.16
2455 2519 3.627237 GCCCTTTGGTTCATAGGAATGGA 60.627 47.826 6.07 0.00 35.14 3.41
2456 2520 4.808042 CCCTTTGGTTCATAGGAATGGAT 58.192 43.478 6.07 0.00 35.14 3.41
2457 2521 5.211201 CCCTTTGGTTCATAGGAATGGATT 58.789 41.667 6.07 0.00 35.14 3.01
2458 2522 5.302823 CCCTTTGGTTCATAGGAATGGATTC 59.697 44.000 6.07 0.00 35.14 2.52
2492 2556 3.493767 GGATTGGTTCCTATCCTCCAC 57.506 52.381 19.71 0.00 41.78 4.02
2493 2557 2.777692 GGATTGGTTCCTATCCTCCACA 59.222 50.000 19.71 0.00 41.78 4.17
2494 2558 3.395941 GGATTGGTTCCTATCCTCCACAT 59.604 47.826 19.71 0.00 41.78 3.21
2495 2559 4.141158 GGATTGGTTCCTATCCTCCACATT 60.141 45.833 19.71 0.00 41.78 2.71
2496 2560 4.946160 TTGGTTCCTATCCTCCACATTT 57.054 40.909 0.00 0.00 0.00 2.32
2497 2561 4.503714 TGGTTCCTATCCTCCACATTTC 57.496 45.455 0.00 0.00 0.00 2.17
2498 2562 3.849574 TGGTTCCTATCCTCCACATTTCA 59.150 43.478 0.00 0.00 0.00 2.69
2499 2563 4.478317 TGGTTCCTATCCTCCACATTTCAT 59.522 41.667 0.00 0.00 0.00 2.57
2500 2564 5.669904 TGGTTCCTATCCTCCACATTTCATA 59.330 40.000 0.00 0.00 0.00 2.15
2501 2565 6.183361 TGGTTCCTATCCTCCACATTTCATAG 60.183 42.308 0.00 0.00 0.00 2.23
2502 2566 6.234177 GTTCCTATCCTCCACATTTCATAGG 58.766 44.000 0.00 0.00 35.93 2.57
2503 2567 5.726560 TCCTATCCTCCACATTTCATAGGA 58.273 41.667 2.01 2.01 39.61 2.94
2504 2568 6.150332 TCCTATCCTCCACATTTCATAGGAA 58.850 40.000 3.47 0.00 39.17 3.36
2505 2569 6.619437 TCCTATCCTCCACATTTCATAGGAAA 59.381 38.462 4.85 4.85 46.36 3.13
2506 2570 7.128728 TCCTATCCTCCACATTTCATAGGAAAA 59.871 37.037 6.65 0.00 45.52 2.29
2507 2571 7.946776 CCTATCCTCCACATTTCATAGGAAAAT 59.053 37.037 6.65 0.00 45.52 1.82
2510 2574 9.713684 ATCCTCCACATTTCATAGGAAAATAAA 57.286 29.630 6.65 0.00 45.52 1.40
2511 2575 9.540538 TCCTCCACATTTCATAGGAAAATAAAA 57.459 29.630 6.65 0.00 45.52 1.52
2525 2589 8.512966 AGGAAAATAAAAATGAGCCTAGACTC 57.487 34.615 0.00 0.00 37.19 3.36
2534 2598 4.908601 TGAGCCTAGACTCAATGGAAAA 57.091 40.909 6.25 0.00 43.59 2.29
2535 2599 5.241403 TGAGCCTAGACTCAATGGAAAAA 57.759 39.130 6.25 0.00 43.59 1.94
2536 2600 5.819991 TGAGCCTAGACTCAATGGAAAAAT 58.180 37.500 6.25 0.00 43.59 1.82
2537 2601 6.248433 TGAGCCTAGACTCAATGGAAAAATT 58.752 36.000 6.25 0.00 43.59 1.82
2538 2602 6.375455 TGAGCCTAGACTCAATGGAAAAATTC 59.625 38.462 6.25 0.00 43.59 2.17
2539 2603 6.183360 GAGCCTAGACTCAATGGAAAAATTCC 60.183 42.308 0.51 2.12 42.14 3.01
2540 2604 8.285329 GAGCCTAGACTCAATGGAAAAATTCCT 61.285 40.741 10.28 0.00 42.21 3.36
2551 2615 5.984233 GGAAAAATTCCTTTGGTGTCAAC 57.016 39.130 1.86 0.00 46.57 3.18
2552 2616 4.814234 GGAAAAATTCCTTTGGTGTCAACC 59.186 41.667 1.86 0.00 46.57 3.77
2569 2633 5.356882 TCAACCAAATGACATCTCGTTTC 57.643 39.130 0.00 0.00 33.97 2.78
2570 2634 4.215399 TCAACCAAATGACATCTCGTTTCC 59.785 41.667 0.00 0.00 33.97 3.13
2571 2635 4.021102 ACCAAATGACATCTCGTTTCCT 57.979 40.909 0.00 0.00 33.97 3.36
2572 2636 5.160607 ACCAAATGACATCTCGTTTCCTA 57.839 39.130 0.00 0.00 33.97 2.94
2573 2637 5.745227 ACCAAATGACATCTCGTTTCCTAT 58.255 37.500 0.00 0.00 33.97 2.57
2574 2638 6.180472 ACCAAATGACATCTCGTTTCCTATT 58.820 36.000 0.00 0.00 33.97 1.73
2575 2639 6.316390 ACCAAATGACATCTCGTTTCCTATTC 59.684 38.462 0.00 0.00 33.97 1.75
2576 2640 6.238484 CCAAATGACATCTCGTTTCCTATTCC 60.238 42.308 0.00 0.00 33.97 3.01
2577 2641 5.878406 ATGACATCTCGTTTCCTATTCCT 57.122 39.130 0.00 0.00 0.00 3.36
2578 2642 6.978674 ATGACATCTCGTTTCCTATTCCTA 57.021 37.500 0.00 0.00 0.00 2.94
2579 2643 6.145338 TGACATCTCGTTTCCTATTCCTAC 57.855 41.667 0.00 0.00 0.00 3.18
2580 2644 5.892119 TGACATCTCGTTTCCTATTCCTACT 59.108 40.000 0.00 0.00 0.00 2.57
2581 2645 6.039493 TGACATCTCGTTTCCTATTCCTACTC 59.961 42.308 0.00 0.00 0.00 2.59
2582 2646 5.892119 ACATCTCGTTTCCTATTCCTACTCA 59.108 40.000 0.00 0.00 0.00 3.41
2583 2647 6.551601 ACATCTCGTTTCCTATTCCTACTCAT 59.448 38.462 0.00 0.00 0.00 2.90
2584 2648 7.724506 ACATCTCGTTTCCTATTCCTACTCATA 59.275 37.037 0.00 0.00 0.00 2.15
2585 2649 7.747155 TCTCGTTTCCTATTCCTACTCATAG 57.253 40.000 0.00 0.00 0.00 2.23
2602 2666 9.853555 CTACTCATAGGATTTGAGATACATGTC 57.146 37.037 0.00 0.00 42.63 3.06
2603 2667 8.255111 ACTCATAGGATTTGAGATACATGTCA 57.745 34.615 0.00 0.00 42.63 3.58
2604 2668 8.878211 ACTCATAGGATTTGAGATACATGTCAT 58.122 33.333 0.00 0.00 42.63 3.06
2605 2669 9.368674 CTCATAGGATTTGAGATACATGTCATC 57.631 37.037 0.00 4.47 42.63 2.92
2606 2670 9.097946 TCATAGGATTTGAGATACATGTCATCT 57.902 33.333 0.00 9.42 35.43 2.90
2607 2671 9.368674 CATAGGATTTGAGATACATGTCATCTC 57.631 37.037 24.04 24.04 45.76 2.75
2616 2680 8.755696 GAGATACATGTCATCTCATTTCCTAC 57.244 38.462 24.95 8.46 45.17 3.18
2617 2681 8.255111 AGATACATGTCATCTCATTTCCTACA 57.745 34.615 0.00 0.00 0.00 2.74
2618 2682 8.708378 AGATACATGTCATCTCATTTCCTACAA 58.292 33.333 0.00 0.00 0.00 2.41
2619 2683 9.330063 GATACATGTCATCTCATTTCCTACAAA 57.670 33.333 0.00 0.00 0.00 2.83
2620 2684 9.685276 ATACATGTCATCTCATTTCCTACAAAA 57.315 29.630 0.00 0.00 0.00 2.44
2621 2685 8.585471 ACATGTCATCTCATTTCCTACAAAAT 57.415 30.769 0.00 0.00 0.00 1.82
2622 2686 9.028284 ACATGTCATCTCATTTCCTACAAAATT 57.972 29.630 0.00 0.00 0.00 1.82
2623 2687 9.512435 CATGTCATCTCATTTCCTACAAAATTC 57.488 33.333 0.00 0.00 0.00 2.17
2624 2688 8.055279 TGTCATCTCATTTCCTACAAAATTCC 57.945 34.615 0.00 0.00 0.00 3.01
2625 2689 7.890127 TGTCATCTCATTTCCTACAAAATTCCT 59.110 33.333 0.00 0.00 0.00 3.36
2626 2690 9.396022 GTCATCTCATTTCCTACAAAATTCCTA 57.604 33.333 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 9.810231 GCACACAAAATTCAAAAACCATTATAG 57.190 29.630 0.00 0.00 0.00 1.31
45 46 8.491152 CGCACACAAAATTCAAAAACCATTATA 58.509 29.630 0.00 0.00 0.00 0.98
46 47 7.011857 ACGCACACAAAATTCAAAAACCATTAT 59.988 29.630 0.00 0.00 0.00 1.28
47 48 6.313905 ACGCACACAAAATTCAAAAACCATTA 59.686 30.769 0.00 0.00 0.00 1.90
48 49 5.123027 ACGCACACAAAATTCAAAAACCATT 59.877 32.000 0.00 0.00 0.00 3.16
49 50 4.633565 ACGCACACAAAATTCAAAAACCAT 59.366 33.333 0.00 0.00 0.00 3.55
50 51 3.997021 ACGCACACAAAATTCAAAAACCA 59.003 34.783 0.00 0.00 0.00 3.67
51 52 4.092091 TCACGCACACAAAATTCAAAAACC 59.908 37.500 0.00 0.00 0.00 3.27
52 53 5.196809 TCACGCACACAAAATTCAAAAAC 57.803 34.783 0.00 0.00 0.00 2.43
64 65 1.686355 AAATCCCTTTCACGCACACA 58.314 45.000 0.00 0.00 0.00 3.72
65 66 2.393764 CAAAATCCCTTTCACGCACAC 58.606 47.619 0.00 0.00 0.00 3.82
70 71 5.334028 GGATTTTTGCAAAATCCCTTTCACG 60.334 40.000 24.39 0.00 46.22 4.35
109 111 7.721842 TCTCAATGGGCCAAATCGTTATTATTA 59.278 33.333 11.89 0.00 0.00 0.98
112 114 5.441500 TCTCAATGGGCCAAATCGTTATTA 58.558 37.500 11.89 0.00 0.00 0.98
115 117 3.278574 CTCTCAATGGGCCAAATCGTTA 58.721 45.455 11.89 0.00 0.00 3.18
116 118 2.094675 CTCTCAATGGGCCAAATCGTT 58.905 47.619 11.89 0.00 0.00 3.85
117 119 1.004745 ACTCTCAATGGGCCAAATCGT 59.995 47.619 11.89 0.00 0.00 3.73
118 120 1.402968 CACTCTCAATGGGCCAAATCG 59.597 52.381 11.89 0.00 0.00 3.34
137 139 2.924101 GTGTACACGGGACCCCCA 60.924 66.667 10.84 0.00 45.83 4.96
139 141 1.305213 TAGGTGTACACGGGACCCC 60.305 63.158 19.41 4.13 0.00 4.95
159 161 5.465390 GGCACAAAACAATAGAGGGTTTTTC 59.535 40.000 0.00 0.00 42.73 2.29
165 167 2.807676 AGGGCACAAAACAATAGAGGG 58.192 47.619 0.00 0.00 0.00 4.30
173 175 5.091261 ACAAAACATTAGGGCACAAAACA 57.909 34.783 0.00 0.00 0.00 2.83
293 295 7.466746 AAAATGTGTTATGGAGTTGCTACAT 57.533 32.000 0.13 0.00 38.71 2.29
303 305 7.520776 CGTGTTGACCTTAAAATGTGTTATGGA 60.521 37.037 2.77 0.00 34.13 3.41
308 310 4.356289 GCGTGTTGACCTTAAAATGTGTT 58.644 39.130 0.00 0.00 0.00 3.32
316 318 5.968528 ATTAAATGGCGTGTTGACCTTAA 57.031 34.783 0.00 0.00 0.00 1.85
322 324 4.839121 AGGAGTATTAAATGGCGTGTTGA 58.161 39.130 0.00 0.00 0.00 3.18
338 340 8.202461 TCTCACTGGATTTTCTTAAAGGAGTA 57.798 34.615 0.00 0.00 0.00 2.59
342 344 8.633561 ACTTTTCTCACTGGATTTTCTTAAAGG 58.366 33.333 0.00 0.00 0.00 3.11
345 347 7.559897 ACCACTTTTCTCACTGGATTTTCTTAA 59.440 33.333 0.00 0.00 0.00 1.85
346 348 7.060421 ACCACTTTTCTCACTGGATTTTCTTA 58.940 34.615 0.00 0.00 0.00 2.10
354 356 3.072330 TGCATACCACTTTTCTCACTGGA 59.928 43.478 0.00 0.00 0.00 3.86
427 433 7.384387 CGAGCCTACTAAAAAGAAAGTTGTAGT 59.616 37.037 0.00 0.00 0.00 2.73
438 444 8.095169 ACAATATATCCCGAGCCTACTAAAAAG 58.905 37.037 0.00 0.00 0.00 2.27
486 492 7.591006 TTACGGTGCTTAAAAAGAGATAGTG 57.409 36.000 0.00 0.00 0.00 2.74
507 513 6.010294 TCCGGTCTTCGATGAGATATTTAC 57.990 41.667 0.00 0.00 42.43 2.01
529 535 8.970220 CAAAAGCAGCATTTGACACGATAGTTC 61.970 40.741 16.53 0.00 42.81 3.01
542 548 5.334569 GCAAATCATGTCAAAAGCAGCATTT 60.335 36.000 0.00 0.00 0.00 2.32
564 570 1.974265 TGACGAATTTCAACCCAGCA 58.026 45.000 0.00 0.00 0.00 4.41
567 573 1.611491 GCCTTGACGAATTTCAACCCA 59.389 47.619 0.00 0.00 32.02 4.51
588 594 2.126346 GTTCATGGTGGCAAGCGC 60.126 61.111 0.00 0.00 37.44 5.92
590 596 2.568090 CGGTTCATGGTGGCAAGC 59.432 61.111 0.00 0.00 0.00 4.01
606 612 2.519377 TTGTCGGATACTAATGGCCG 57.481 50.000 0.00 0.00 44.83 6.13
609 615 4.065088 CCACCATTGTCGGATACTAATGG 58.935 47.826 17.26 17.26 44.20 3.16
610 616 4.956085 TCCACCATTGTCGGATACTAATG 58.044 43.478 0.00 0.00 0.00 1.90
620 626 1.369625 GTTAGGCTCCACCATTGTCG 58.630 55.000 0.00 0.00 43.14 4.35
621 627 1.682087 GGGTTAGGCTCCACCATTGTC 60.682 57.143 15.72 0.00 43.14 3.18
622 628 0.331616 GGGTTAGGCTCCACCATTGT 59.668 55.000 15.72 0.00 43.14 2.71
623 629 0.625849 AGGGTTAGGCTCCACCATTG 59.374 55.000 15.72 0.00 43.14 2.82
625 631 1.005924 CAAAGGGTTAGGCTCCACCAT 59.994 52.381 15.72 7.50 43.14 3.55
626 632 0.404040 CAAAGGGTTAGGCTCCACCA 59.596 55.000 15.72 0.00 43.14 4.17
627 633 0.404426 ACAAAGGGTTAGGCTCCACC 59.596 55.000 7.17 7.17 39.61 4.61
628 634 1.822506 GACAAAGGGTTAGGCTCCAC 58.177 55.000 0.00 0.00 0.00 4.02
630 636 0.611714 TCGACAAAGGGTTAGGCTCC 59.388 55.000 0.00 0.00 0.00 4.70
651 657 9.729281 AAATTCAAAGTTAATGCTTCATTCCAT 57.271 25.926 0.00 0.00 35.54 3.41
669 675 7.171678 CGGCATTTAGGGTTTGTAAAATTCAAA 59.828 33.333 0.00 0.00 33.28 2.69
692 698 0.462375 AAAAAGTGGACCAAACCGGC 59.538 50.000 0.00 0.00 39.03 6.13
693 699 1.804746 GCAAAAAGTGGACCAAACCGG 60.805 52.381 0.00 0.00 42.50 5.28
697 703 3.096092 ACAGAGCAAAAAGTGGACCAAA 58.904 40.909 0.00 0.00 0.00 3.28
716 723 2.930019 CCTCCTCTGGTGCCCACA 60.930 66.667 0.40 0.00 0.00 4.17
717 724 4.416738 GCCTCCTCTGGTGCCCAC 62.417 72.222 0.00 0.00 0.00 4.61
726 733 2.224402 GGCGAAAATATCAGCCTCCTCT 60.224 50.000 0.00 0.00 41.51 3.69
735 742 6.264832 CAAAATACTGCTGGCGAAAATATCA 58.735 36.000 0.00 0.00 0.00 2.15
782 789 9.494055 TGTCCAAAACAAAATCCCCAATATATA 57.506 29.630 0.00 0.00 34.03 0.86
783 790 8.386012 TGTCCAAAACAAAATCCCCAATATAT 57.614 30.769 0.00 0.00 34.03 0.86
807 814 4.867608 CGCCTAAAACCCCAATACATTTTG 59.132 41.667 0.00 0.00 0.00 2.44
824 831 2.760159 GCAAATGAGCGGCGCCTAA 61.760 57.895 30.40 15.16 0.00 2.69
848 855 2.497273 AGCCCATGTGCTAAATGGAAAC 59.503 45.455 0.00 4.35 46.44 2.78
855 862 5.104109 ACCTTCTTATAGCCCATGTGCTAAA 60.104 40.000 14.05 8.76 46.23 1.85
862 869 5.704515 CAGATTGACCTTCTTATAGCCCATG 59.295 44.000 0.00 0.00 0.00 3.66
870 877 3.738281 CGTCCGCAGATTGACCTTCTTAT 60.738 47.826 0.00 0.00 0.00 1.73
872 879 1.673033 CGTCCGCAGATTGACCTTCTT 60.673 52.381 0.00 0.00 0.00 2.52
921 928 3.275999 GCTATAAGAAGGCCGACCAAAA 58.724 45.455 0.00 0.00 39.06 2.44
925 932 3.608760 GGCTATAAGAAGGCCGACC 57.391 57.895 0.00 0.00 36.37 4.79
948 955 6.596309 ATCGAGAAATGGCTGATACTATCA 57.404 37.500 0.00 0.00 37.76 2.15
949 956 7.990917 TCTATCGAGAAATGGCTGATACTATC 58.009 38.462 0.00 0.00 0.00 2.08
950 957 7.946381 TCTATCGAGAAATGGCTGATACTAT 57.054 36.000 0.00 0.00 0.00 2.12
951 958 7.831690 AGATCTATCGAGAAATGGCTGATACTA 59.168 37.037 0.00 0.00 34.61 1.82
952 959 6.663093 AGATCTATCGAGAAATGGCTGATACT 59.337 38.462 0.00 0.00 34.61 2.12
953 960 6.862209 AGATCTATCGAGAAATGGCTGATAC 58.138 40.000 0.00 0.00 34.61 2.24
954 961 6.096141 GGAGATCTATCGAGAAATGGCTGATA 59.904 42.308 0.00 0.00 34.61 2.15
955 962 5.105392 GGAGATCTATCGAGAAATGGCTGAT 60.105 44.000 0.00 0.00 34.61 2.90
956 963 4.219507 GGAGATCTATCGAGAAATGGCTGA 59.780 45.833 0.00 0.00 34.61 4.26
957 964 4.493547 GGAGATCTATCGAGAAATGGCTG 58.506 47.826 0.00 0.00 34.61 4.85
958 965 3.192422 CGGAGATCTATCGAGAAATGGCT 59.808 47.826 11.23 0.00 34.61 4.75
959 966 3.191581 TCGGAGATCTATCGAGAAATGGC 59.808 47.826 14.31 0.00 34.61 4.40
1013 1040 1.340114 CCCTAACCCTCTGTTGCCTTC 60.340 57.143 0.00 0.00 37.83 3.46
1078 1120 2.209273 CTCATCTCGCTTCTCTCTCGA 58.791 52.381 0.00 0.00 0.00 4.04
1079 1121 1.334059 GCTCATCTCGCTTCTCTCTCG 60.334 57.143 0.00 0.00 0.00 4.04
1082 1124 0.317770 CCGCTCATCTCGCTTCTCTC 60.318 60.000 0.00 0.00 0.00 3.20
1083 1125 1.732917 CCGCTCATCTCGCTTCTCT 59.267 57.895 0.00 0.00 0.00 3.10
1084 1126 1.299773 CCCGCTCATCTCGCTTCTC 60.300 63.158 0.00 0.00 0.00 2.87
1085 1127 1.733402 CTCCCGCTCATCTCGCTTCT 61.733 60.000 0.00 0.00 0.00 2.85
1086 1128 1.299773 CTCCCGCTCATCTCGCTTC 60.300 63.158 0.00 0.00 0.00 3.86
1087 1129 2.811101 CTCCCGCTCATCTCGCTT 59.189 61.111 0.00 0.00 0.00 4.68
1088 1130 3.910490 GCTCCCGCTCATCTCGCT 61.910 66.667 0.00 0.00 0.00 4.93
1276 1318 3.259314 ACCTGGGTGAGCATGCCA 61.259 61.111 15.66 9.53 0.00 4.92
1471 1513 2.793278 AAACAAACCGAAGCATCACC 57.207 45.000 0.00 0.00 0.00 4.02
1578 1625 3.407698 TCAAGTTGCCAAAGATCGCTAA 58.592 40.909 0.00 0.00 0.00 3.09
1582 1629 4.797471 TCAATTCAAGTTGCCAAAGATCG 58.203 39.130 0.00 0.00 0.00 3.69
1588 1635 3.237746 TCCCATCAATTCAAGTTGCCAA 58.762 40.909 0.00 0.00 0.00 4.52
1590 1637 3.959535 TTCCCATCAATTCAAGTTGCC 57.040 42.857 0.00 0.00 0.00 4.52
1657 1704 6.194235 TGACTTGGGCCTTACATTTCAATAT 58.806 36.000 4.53 0.00 0.00 1.28
1675 1722 5.163824 ACGCAACATCAACTGATATGACTTG 60.164 40.000 8.21 0.00 32.63 3.16
1682 1729 3.063861 GCATCACGCAACATCAACTGATA 59.936 43.478 0.00 0.00 41.79 2.15
1859 1906 1.954733 GCCCATCATACCAACAGTGCA 60.955 52.381 0.00 0.00 0.00 4.57
1861 1908 2.019249 CTGCCCATCATACCAACAGTG 58.981 52.381 0.00 0.00 0.00 3.66
1912 1959 5.221126 GGCTGCATCTCCCAAAACTAAATAG 60.221 44.000 0.50 0.00 0.00 1.73
1928 1975 1.269102 GCATGTCTTGATGGCTGCATC 60.269 52.381 0.50 3.67 0.00 3.91
1979 2026 8.891671 AAATTTTCACATAGAGTGCAAAATGT 57.108 26.923 13.64 0.00 44.37 2.71
2019 2067 4.621274 CGAATGAGGGTGCCAAAATCAATT 60.621 41.667 0.00 0.00 0.00 2.32
2084 2148 6.659242 TCACAGGAAATTCTTCACTTATTCCC 59.341 38.462 0.00 0.00 37.61 3.97
2098 2162 7.166804 CGTAAAATTGAACGTTCACAGGAAATT 59.833 33.333 29.74 21.19 36.83 1.82
2110 2174 7.170320 ACAATCAGTAGTCGTAAAATTGAACGT 59.830 33.333 11.31 0.00 39.99 3.99
2164 2228 4.438744 GCTGCAACAGTTACAACAGACTTT 60.439 41.667 0.00 0.00 33.43 2.66
2212 2276 6.209391 ACAGCCAGTCTGCATAAACTTTTATT 59.791 34.615 0.00 0.00 46.76 1.40
2291 2355 4.567971 TGAAATTTGTTAAGCATGGCTGG 58.432 39.130 0.00 0.00 39.62 4.85
2311 2375 8.908786 AAACACATTCTAGATGAACTTCTTGA 57.091 30.769 0.00 0.00 37.52 3.02
2360 2424 5.651303 ACCAAAGGAGGCCTAAAATTTACT 58.349 37.500 4.42 0.00 31.13 2.24
2370 2434 0.113190 CTCCAAACCAAAGGAGGCCT 59.887 55.000 3.86 3.86 46.11 5.19
2371 2435 2.658548 CTCCAAACCAAAGGAGGCC 58.341 57.895 0.00 0.00 46.11 5.19
2375 2439 6.377912 TCTAAAATTCCTCCAAACCAAAGGA 58.622 36.000 0.00 0.00 37.42 3.36
2376 2440 6.295292 CCTCTAAAATTCCTCCAAACCAAAGG 60.295 42.308 0.00 0.00 0.00 3.11
2377 2441 6.493458 TCCTCTAAAATTCCTCCAAACCAAAG 59.507 38.462 0.00 0.00 0.00 2.77
2378 2442 6.377912 TCCTCTAAAATTCCTCCAAACCAAA 58.622 36.000 0.00 0.00 0.00 3.28
2379 2443 5.959512 TCCTCTAAAATTCCTCCAAACCAA 58.040 37.500 0.00 0.00 0.00 3.67
2380 2444 5.592587 TCCTCTAAAATTCCTCCAAACCA 57.407 39.130 0.00 0.00 0.00 3.67
2381 2445 6.773200 CCTATCCTCTAAAATTCCTCCAAACC 59.227 42.308 0.00 0.00 0.00 3.27
2382 2446 7.574607 TCCTATCCTCTAAAATTCCTCCAAAC 58.425 38.462 0.00 0.00 0.00 2.93
2383 2447 7.765149 TCCTATCCTCTAAAATTCCTCCAAA 57.235 36.000 0.00 0.00 0.00 3.28
2384 2448 7.954539 ATCCTATCCTCTAAAATTCCTCCAA 57.045 36.000 0.00 0.00 0.00 3.53
2385 2449 7.796637 AGAATCCTATCCTCTAAAATTCCTCCA 59.203 37.037 0.00 0.00 0.00 3.86
2386 2450 8.213489 AGAATCCTATCCTCTAAAATTCCTCC 57.787 38.462 0.00 0.00 0.00 4.30
2420 2484 4.552674 ACCAAAGGGCTCTAAAGGAAAAA 58.447 39.130 5.94 0.00 37.90 1.94
2421 2485 4.193240 ACCAAAGGGCTCTAAAGGAAAA 57.807 40.909 5.94 0.00 37.90 2.29
2422 2486 3.895704 ACCAAAGGGCTCTAAAGGAAA 57.104 42.857 5.94 0.00 37.90 3.13
2423 2487 3.139397 TGAACCAAAGGGCTCTAAAGGAA 59.861 43.478 5.94 0.00 37.90 3.36
2424 2488 2.714250 TGAACCAAAGGGCTCTAAAGGA 59.286 45.455 5.94 0.00 37.90 3.36
2425 2489 3.154827 TGAACCAAAGGGCTCTAAAGG 57.845 47.619 0.00 0.00 37.90 3.11
2426 2490 4.884164 CCTATGAACCAAAGGGCTCTAAAG 59.116 45.833 0.00 0.00 37.90 1.85
2427 2491 4.538490 TCCTATGAACCAAAGGGCTCTAAA 59.462 41.667 0.00 0.00 37.90 1.85
2428 2492 4.108570 TCCTATGAACCAAAGGGCTCTAA 58.891 43.478 0.00 0.00 37.90 2.10
2429 2493 3.731431 TCCTATGAACCAAAGGGCTCTA 58.269 45.455 0.00 0.00 37.90 2.43
2430 2494 2.562296 TCCTATGAACCAAAGGGCTCT 58.438 47.619 0.00 0.00 37.90 4.09
2431 2495 3.366052 TTCCTATGAACCAAAGGGCTC 57.634 47.619 0.00 0.00 37.90 4.70
2432 2496 3.628257 CCATTCCTATGAACCAAAGGGCT 60.628 47.826 0.00 0.00 33.50 5.19
2433 2497 2.695147 CCATTCCTATGAACCAAAGGGC 59.305 50.000 0.00 0.00 33.50 5.19
2434 2498 4.249638 TCCATTCCTATGAACCAAAGGG 57.750 45.455 0.00 0.00 35.37 3.95
2435 2499 6.396829 GAATCCATTCCTATGAACCAAAGG 57.603 41.667 0.00 0.00 33.37 3.11
2473 2537 4.713792 ATGTGGAGGATAGGAACCAATC 57.286 45.455 0.00 0.00 34.11 2.67
2474 2538 5.044179 TGAAATGTGGAGGATAGGAACCAAT 60.044 40.000 0.00 0.00 34.11 3.16
2475 2539 4.290985 TGAAATGTGGAGGATAGGAACCAA 59.709 41.667 0.00 0.00 34.11 3.67
2476 2540 3.849574 TGAAATGTGGAGGATAGGAACCA 59.150 43.478 0.00 0.00 0.00 3.67
2477 2541 4.503714 TGAAATGTGGAGGATAGGAACC 57.496 45.455 0.00 0.00 0.00 3.62
2478 2542 6.043243 TCCTATGAAATGTGGAGGATAGGAAC 59.957 42.308 0.00 0.00 38.86 3.62
2479 2543 6.150332 TCCTATGAAATGTGGAGGATAGGAA 58.850 40.000 0.00 0.00 38.86 3.36
2480 2544 5.726560 TCCTATGAAATGTGGAGGATAGGA 58.273 41.667 0.00 0.00 39.29 2.94
2481 2545 6.439636 TTCCTATGAAATGTGGAGGATAGG 57.560 41.667 0.00 0.00 36.22 2.57
2482 2546 8.930846 ATTTTCCTATGAAATGTGGAGGATAG 57.069 34.615 0.00 0.00 40.08 2.08
2484 2548 9.713684 TTTATTTTCCTATGAAATGTGGAGGAT 57.286 29.630 0.00 0.00 40.08 3.24
2485 2549 9.540538 TTTTATTTTCCTATGAAATGTGGAGGA 57.459 29.630 0.00 0.00 40.08 3.71
2499 2563 9.614792 GAGTCTAGGCTCATTTTTATTTTCCTA 57.385 33.333 19.57 0.00 35.67 2.94
2500 2564 8.109634 TGAGTCTAGGCTCATTTTTATTTTCCT 58.890 33.333 23.07 0.00 40.23 3.36
2501 2565 8.281212 TGAGTCTAGGCTCATTTTTATTTTCC 57.719 34.615 23.07 0.00 40.23 3.13
2504 2568 8.689972 CCATTGAGTCTAGGCTCATTTTTATTT 58.310 33.333 26.91 3.37 43.99 1.40
2505 2569 8.055181 TCCATTGAGTCTAGGCTCATTTTTATT 58.945 33.333 26.91 4.66 43.99 1.40
2506 2570 7.577303 TCCATTGAGTCTAGGCTCATTTTTAT 58.423 34.615 26.91 14.49 43.99 1.40
2507 2571 6.957631 TCCATTGAGTCTAGGCTCATTTTTA 58.042 36.000 26.91 12.75 43.99 1.52
2508 2572 5.819991 TCCATTGAGTCTAGGCTCATTTTT 58.180 37.500 26.91 10.30 43.99 1.94
2509 2573 5.441718 TCCATTGAGTCTAGGCTCATTTT 57.558 39.130 26.91 12.69 43.99 1.82
2510 2574 5.441718 TTCCATTGAGTCTAGGCTCATTT 57.558 39.130 26.91 15.12 43.99 2.32
2511 2575 5.441718 TTTCCATTGAGTCTAGGCTCATT 57.558 39.130 26.91 20.33 43.99 2.57
2512 2576 5.441718 TTTTCCATTGAGTCTAGGCTCAT 57.558 39.130 26.91 14.39 43.99 2.90
2513 2577 4.908601 TTTTCCATTGAGTCTAGGCTCA 57.091 40.909 23.07 23.07 43.03 4.26
2514 2578 6.765915 AATTTTTCCATTGAGTCTAGGCTC 57.234 37.500 17.74 17.74 36.12 4.70
2515 2579 6.765915 GAATTTTTCCATTGAGTCTAGGCT 57.234 37.500 0.00 0.00 0.00 4.58
2526 2590 8.334633 GGTTGACACCAAAGGAATTTTTCCATT 61.335 37.037 8.87 0.31 46.88 3.16
2527 2591 6.911529 GGTTGACACCAAAGGAATTTTTCCAT 60.912 38.462 8.87 0.00 46.88 3.41
2528 2592 5.627968 GGTTGACACCAAAGGAATTTTTCCA 60.628 40.000 8.87 0.00 46.88 3.53
2529 2593 4.814234 GGTTGACACCAAAGGAATTTTTCC 59.186 41.667 0.00 0.00 45.80 3.13
2530 2594 5.984233 GGTTGACACCAAAGGAATTTTTC 57.016 39.130 0.00 0.00 43.61 2.29
2546 2610 4.749245 AACGAGATGTCATTTGGTTGAC 57.251 40.909 3.39 0.00 45.05 3.18
2547 2611 4.215399 GGAAACGAGATGTCATTTGGTTGA 59.785 41.667 4.80 0.00 0.00 3.18
2548 2612 4.216257 AGGAAACGAGATGTCATTTGGTTG 59.784 41.667 4.80 0.00 0.00 3.77
2549 2613 4.398319 AGGAAACGAGATGTCATTTGGTT 58.602 39.130 0.00 0.00 0.00 3.67
2550 2614 4.021102 AGGAAACGAGATGTCATTTGGT 57.979 40.909 0.00 0.00 0.00 3.67
2551 2615 6.238484 GGAATAGGAAACGAGATGTCATTTGG 60.238 42.308 0.00 0.00 0.00 3.28
2552 2616 6.540189 AGGAATAGGAAACGAGATGTCATTTG 59.460 38.462 0.00 0.00 0.00 2.32
2553 2617 6.653989 AGGAATAGGAAACGAGATGTCATTT 58.346 36.000 0.00 0.00 0.00 2.32
2554 2618 6.240549 AGGAATAGGAAACGAGATGTCATT 57.759 37.500 0.00 0.00 0.00 2.57
2555 2619 5.878406 AGGAATAGGAAACGAGATGTCAT 57.122 39.130 0.00 0.00 0.00 3.06
2556 2620 5.892119 AGTAGGAATAGGAAACGAGATGTCA 59.108 40.000 0.00 0.00 0.00 3.58
2557 2621 6.039493 TGAGTAGGAATAGGAAACGAGATGTC 59.961 42.308 0.00 0.00 0.00 3.06
2558 2622 5.892119 TGAGTAGGAATAGGAAACGAGATGT 59.108 40.000 0.00 0.00 0.00 3.06
2559 2623 6.392625 TGAGTAGGAATAGGAAACGAGATG 57.607 41.667 0.00 0.00 0.00 2.90
2560 2624 8.343168 CTATGAGTAGGAATAGGAAACGAGAT 57.657 38.462 0.00 0.00 0.00 2.75
2561 2625 7.747155 CTATGAGTAGGAATAGGAAACGAGA 57.253 40.000 0.00 0.00 0.00 4.04
2576 2640 9.853555 GACATGTATCTCAAATCCTATGAGTAG 57.146 37.037 0.00 0.00 43.77 2.57
2577 2641 9.367160 TGACATGTATCTCAAATCCTATGAGTA 57.633 33.333 0.00 0.00 43.77 2.59
2578 2642 8.255111 TGACATGTATCTCAAATCCTATGAGT 57.745 34.615 0.00 0.00 43.77 3.41
2579 2643 9.368674 GATGACATGTATCTCAAATCCTATGAG 57.631 37.037 0.00 0.00 44.53 2.90
2580 2644 9.097946 AGATGACATGTATCTCAAATCCTATGA 57.902 33.333 0.00 0.00 29.05 2.15
2581 2645 9.368674 GAGATGACATGTATCTCAAATCCTATG 57.631 37.037 24.95 0.00 46.22 2.23
2591 2655 8.363390 TGTAGGAAATGAGATGACATGTATCTC 58.637 37.037 24.04 24.04 46.82 2.75
2592 2656 8.255111 TGTAGGAAATGAGATGACATGTATCT 57.745 34.615 14.05 14.05 37.59 1.98
2593 2657 8.893219 TTGTAGGAAATGAGATGACATGTATC 57.107 34.615 0.00 2.87 0.00 2.24
2594 2658 9.685276 TTTTGTAGGAAATGAGATGACATGTAT 57.315 29.630 0.00 0.00 0.00 2.29
2595 2659 9.685276 ATTTTGTAGGAAATGAGATGACATGTA 57.315 29.630 0.00 0.00 0.00 2.29
2596 2660 8.585471 ATTTTGTAGGAAATGAGATGACATGT 57.415 30.769 0.00 0.00 0.00 3.21
2597 2661 9.512435 GAATTTTGTAGGAAATGAGATGACATG 57.488 33.333 0.00 0.00 30.06 3.21
2598 2662 8.689972 GGAATTTTGTAGGAAATGAGATGACAT 58.310 33.333 0.00 0.00 30.06 3.06
2599 2663 7.890127 AGGAATTTTGTAGGAAATGAGATGACA 59.110 33.333 0.00 0.00 30.06 3.58
2600 2664 8.286191 AGGAATTTTGTAGGAAATGAGATGAC 57.714 34.615 0.00 0.00 30.06 3.06


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

AutoCloner maintained by Alex Coulton.