Multiple sequence alignment - TraesCS5A01G381400

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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 TraesCS5A01G381400 chr5A 100.000 2300 0 0 1 2300 579276224 579273925 0.000000e+00 4248.0
1 TraesCS5A01G381400 chr5A 96.974 1983 33 4 1 1982 579260262 579258306 0.000000e+00 3304.0
2 TraesCS5A01G381400 chr5A 85.346 621 62 24 1380 1982 423124816 423124207 1.170000e-172 616.0
3 TraesCS5A01G381400 chr5A 85.437 618 59 25 1380 1982 150293376 150292775 4.200000e-172 614.0
4 TraesCS5A01G381400 chr5A 88.612 281 30 2 1983 2263 512587099 512586821 7.870000e-90 340.0
5 TraesCS5A01G381400 chr5A 88.614 202 19 4 2061 2262 493012681 493012878 2.280000e-60 243.0
6 TraesCS5A01G381400 chr2A 88.592 1385 131 20 534 1905 627542489 627541119 0.000000e+00 1657.0
7 TraesCS5A01G381400 chr2A 85.149 1010 122 21 987 1982 627550087 627549092 0.000000e+00 1009.0
8 TraesCS5A01G381400 chr2A 85.340 764 86 19 1231 1982 188730164 188729415 0.000000e+00 767.0
9 TraesCS5A01G381400 chr2A 83.689 797 93 29 1204 1982 121945657 121944880 0.000000e+00 717.0
10 TraesCS5A01G381400 chr2A 83.000 800 106 21 1204 1982 656945710 656944920 0.000000e+00 697.0
11 TraesCS5A01G381400 chr2A 82.463 804 103 23 1204 1982 632672077 632671287 0.000000e+00 669.0
12 TraesCS5A01G381400 chr2A 85.113 618 64 19 1387 1982 141242501 141241890 7.030000e-170 606.0
13 TraesCS5A01G381400 chr2A 88.626 422 34 12 1 414 470690810 470691225 3.410000e-138 501.0
14 TraesCS5A01G381400 chr2A 88.416 423 29 16 1 414 470657640 470658051 2.050000e-135 492.0
15 TraesCS5A01G381400 chr2A 89.286 364 36 3 1 362 169103118 169102756 9.690000e-124 453.0
16 TraesCS5A01G381400 chr2A 94.241 191 9 2 534 722 627550265 627550075 8.040000e-75 291.0
17 TraesCS5A01G381400 chr5B 93.996 533 29 3 728 1257 215239145 215239677 0.000000e+00 804.0
18 TraesCS5A01G381400 chr5B 87.864 206 22 3 1982 2186 304295679 304295476 2.950000e-59 239.0
19 TraesCS5A01G381400 chr3B 93.091 550 32 6 710 1253 367436204 367435655 0.000000e+00 800.0
20 TraesCS5A01G381400 chr2D 93.433 533 31 4 728 1257 236106876 236107407 0.000000e+00 787.0
21 TraesCS5A01G381400 chr2D 91.478 575 36 11 684 1253 337477107 337477673 0.000000e+00 778.0
22 TraesCS5A01G381400 chr2D 91.419 571 37 11 684 1250 337469181 337469743 0.000000e+00 773.0
23 TraesCS5A01G381400 chr2D 100.000 28 0 0 2127 2154 534403756 534403729 4.000000e-03 52.8
24 TraesCS5A01G381400 chr4D 91.161 577 42 8 684 1257 141364086 141364656 0.000000e+00 774.0
25 TraesCS5A01G381400 chr4D 91.837 98 7 1 585 681 300349861 300349958 3.990000e-28 135.0
26 TraesCS5A01G381400 chr7A 84.131 794 96 24 1204 1982 458617860 458617082 0.000000e+00 741.0
27 TraesCS5A01G381400 chr7A 84.906 159 22 2 579 736 536813535 536813378 2.370000e-35 159.0
28 TraesCS5A01G381400 chr7A 83.544 158 24 2 580 736 536821582 536821426 1.840000e-31 147.0
29 TraesCS5A01G381400 chr1A 84.637 703 89 17 1290 1982 423609165 423609858 0.000000e+00 682.0
30 TraesCS5A01G381400 chr1A 87.522 569 54 13 1423 1982 416534298 416533738 1.930000e-180 641.0
31 TraesCS5A01G381400 chr1A 86.972 568 59 12 1423 1982 416522127 416521567 1.940000e-175 625.0
32 TraesCS5A01G381400 chr1A 90.054 372 33 4 1 371 284170706 284171074 1.600000e-131 479.0
33 TraesCS5A01G381400 chr1A 89.785 372 34 4 1 371 284162845 284163213 7.440000e-130 473.0
34 TraesCS5A01G381400 chr1A 86.592 179 23 1 2004 2182 27277974 27278151 1.800000e-46 196.0
35 TraesCS5A01G381400 chr4A 96.226 318 10 2 1984 2300 533001549 533001865 9.420000e-144 520.0
36 TraesCS5A01G381400 chr4A 89.779 362 32 4 1 362 75079313 75079669 2.080000e-125 459.0
37 TraesCS5A01G381400 chr4A 89.503 362 33 4 1 362 75022291 75022647 9.690000e-124 453.0
38 TraesCS5A01G381400 chr1D 85.616 438 42 17 1 426 372285660 372285232 7.540000e-120 440.0
39 TraesCS5A01G381400 chr1D 91.007 278 23 2 1987 2264 419995270 419995545 7.760000e-100 374.0
40 TraesCS5A01G381400 chr1D 95.683 139 4 2 2164 2300 49426762 49426900 2.970000e-54 222.0
41 TraesCS5A01G381400 chr1D 97.414 116 3 0 1982 2097 49426652 49426767 5.010000e-47 198.0
42 TraesCS5A01G381400 chr3A 84.078 358 47 8 544 895 253805210 253805563 1.020000e-88 337.0
43 TraesCS5A01G381400 chr3D 87.671 292 27 4 1980 2264 610371071 610371360 4.740000e-87 331.0


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 TraesCS5A01G381400 chr5A 579273925 579276224 2299 True 4248 4248 100.000 1 2300 1 chr5A.!!$R5 2299
1 TraesCS5A01G381400 chr5A 579258306 579260262 1956 True 3304 3304 96.974 1 1982 1 chr5A.!!$R4 1981
2 TraesCS5A01G381400 chr5A 423124207 423124816 609 True 616 616 85.346 1380 1982 1 chr5A.!!$R2 602
3 TraesCS5A01G381400 chr5A 150292775 150293376 601 True 614 614 85.437 1380 1982 1 chr5A.!!$R1 602
4 TraesCS5A01G381400 chr2A 627541119 627542489 1370 True 1657 1657 88.592 534 1905 1 chr2A.!!$R5 1371
5 TraesCS5A01G381400 chr2A 188729415 188730164 749 True 767 767 85.340 1231 1982 1 chr2A.!!$R4 751
6 TraesCS5A01G381400 chr2A 121944880 121945657 777 True 717 717 83.689 1204 1982 1 chr2A.!!$R1 778
7 TraesCS5A01G381400 chr2A 656944920 656945710 790 True 697 697 83.000 1204 1982 1 chr2A.!!$R7 778
8 TraesCS5A01G381400 chr2A 632671287 632672077 790 True 669 669 82.463 1204 1982 1 chr2A.!!$R6 778
9 TraesCS5A01G381400 chr2A 627549092 627550265 1173 True 650 1009 89.695 534 1982 2 chr2A.!!$R8 1448
10 TraesCS5A01G381400 chr2A 141241890 141242501 611 True 606 606 85.113 1387 1982 1 chr2A.!!$R2 595
11 TraesCS5A01G381400 chr5B 215239145 215239677 532 False 804 804 93.996 728 1257 1 chr5B.!!$F1 529
12 TraesCS5A01G381400 chr3B 367435655 367436204 549 True 800 800 93.091 710 1253 1 chr3B.!!$R1 543
13 TraesCS5A01G381400 chr2D 236106876 236107407 531 False 787 787 93.433 728 1257 1 chr2D.!!$F1 529
14 TraesCS5A01G381400 chr2D 337477107 337477673 566 False 778 778 91.478 684 1253 1 chr2D.!!$F3 569
15 TraesCS5A01G381400 chr2D 337469181 337469743 562 False 773 773 91.419 684 1250 1 chr2D.!!$F2 566
16 TraesCS5A01G381400 chr4D 141364086 141364656 570 False 774 774 91.161 684 1257 1 chr4D.!!$F1 573
17 TraesCS5A01G381400 chr7A 458617082 458617860 778 True 741 741 84.131 1204 1982 1 chr7A.!!$R1 778
18 TraesCS5A01G381400 chr1A 423609165 423609858 693 False 682 682 84.637 1290 1982 1 chr1A.!!$F4 692
19 TraesCS5A01G381400 chr1A 416533738 416534298 560 True 641 641 87.522 1423 1982 1 chr1A.!!$R2 559
20 TraesCS5A01G381400 chr1A 416521567 416522127 560 True 625 625 86.972 1423 1982 1 chr1A.!!$R1 559

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
174 175 0.183971 TTCCGGAGCTCCACCAAAAA 59.816 50.0 31.67 12.94 35.14 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2253 0.392193 CGGCAGATGAAAGAGCTGGT 60.392 55.0 0.0 0.0 0.0 4.0 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
115 116 5.028549 ACTCTCAAGTCTTTTCTGCTTCA 57.971 39.130 0.00 0.00 0.00 3.02
174 175 0.183971 TTCCGGAGCTCCACCAAAAA 59.816 50.000 31.67 12.94 35.14 1.94
178 179 0.811281 GGAGCTCCACCAAAAATCCG 59.189 55.000 28.43 0.00 35.64 4.18
323 324 3.264706 TGTGAGTCCGGGAAAATTATCCA 59.735 43.478 0.00 0.00 41.55 3.41
415 417 0.746659 GAGAGAAGAGAGAGCCCAGC 59.253 60.000 0.00 0.00 0.00 4.85
442 444 1.140134 CCTTTTCCCTCCCCACTGGA 61.140 60.000 0.00 0.00 42.41 3.86
1177 1208 1.278127 CACCAAGTACCCTTCGGATGT 59.722 52.381 0.00 0.00 0.00 3.06
1202 1233 1.201647 AGTTCGACTACATGGACCACG 59.798 52.381 0.00 0.00 0.00 4.94
1934 2025 7.181845 TCTGGCCCCATTTAAATTGTTTAGATT 59.818 33.333 0.00 0.00 0.00 2.40
1982 2075 6.798482 TCTTGCCATGCTAATCAACATTTAG 58.202 36.000 0.00 0.00 0.00 1.85
1983 2076 5.518848 TGCCATGCTAATCAACATTTAGG 57.481 39.130 0.00 0.00 0.00 2.69
1984 2077 4.341806 TGCCATGCTAATCAACATTTAGGG 59.658 41.667 0.00 0.00 0.00 3.53
1985 2078 4.262164 GCCATGCTAATCAACATTTAGGGG 60.262 45.833 0.00 0.00 0.00 4.79
1986 2079 4.895297 CCATGCTAATCAACATTTAGGGGT 59.105 41.667 0.00 0.00 0.00 4.95
1987 2080 5.363580 CCATGCTAATCAACATTTAGGGGTT 59.636 40.000 0.00 0.00 0.00 4.11
1988 2081 5.913137 TGCTAATCAACATTTAGGGGTTG 57.087 39.130 0.00 0.00 44.35 3.77
1989 2082 5.329399 TGCTAATCAACATTTAGGGGTTGT 58.671 37.500 0.00 0.00 43.64 3.32
1990 2083 5.777732 TGCTAATCAACATTTAGGGGTTGTT 59.222 36.000 0.00 0.00 43.64 2.83
1991 2084 6.268847 TGCTAATCAACATTTAGGGGTTGTTT 59.731 34.615 0.00 0.00 43.64 2.83
1992 2085 6.589907 GCTAATCAACATTTAGGGGTTGTTTG 59.410 38.462 0.00 0.00 43.64 2.93
1993 2086 4.946478 TCAACATTTAGGGGTTGTTTGG 57.054 40.909 0.00 0.00 43.64 3.28
1994 2087 4.547671 TCAACATTTAGGGGTTGTTTGGA 58.452 39.130 0.00 0.00 43.64 3.53
1995 2088 5.151454 TCAACATTTAGGGGTTGTTTGGAT 58.849 37.500 0.00 0.00 43.64 3.41
1996 2089 6.315714 TCAACATTTAGGGGTTGTTTGGATA 58.684 36.000 0.00 0.00 43.64 2.59
1997 2090 6.209788 TCAACATTTAGGGGTTGTTTGGATAC 59.790 38.462 0.00 0.00 43.64 2.24
1998 2091 4.703093 ACATTTAGGGGTTGTTTGGATACG 59.297 41.667 0.00 0.00 42.51 3.06
1999 2092 3.353370 TTAGGGGTTGTTTGGATACGG 57.647 47.619 0.00 0.00 42.51 4.02
2000 2093 1.069775 AGGGGTTGTTTGGATACGGT 58.930 50.000 0.00 0.00 42.51 4.83
2001 2094 1.170442 GGGGTTGTTTGGATACGGTG 58.830 55.000 0.00 0.00 42.51 4.94
2002 2095 1.170442 GGGTTGTTTGGATACGGTGG 58.830 55.000 0.00 0.00 42.51 4.61
2003 2096 1.546099 GGGTTGTTTGGATACGGTGGT 60.546 52.381 0.00 0.00 42.51 4.16
2004 2097 2.232399 GGTTGTTTGGATACGGTGGTT 58.768 47.619 0.00 0.00 42.51 3.67
2005 2098 2.624364 GGTTGTTTGGATACGGTGGTTT 59.376 45.455 0.00 0.00 42.51 3.27
2006 2099 3.068448 GGTTGTTTGGATACGGTGGTTTT 59.932 43.478 0.00 0.00 42.51 2.43
2007 2100 4.277921 GGTTGTTTGGATACGGTGGTTTTA 59.722 41.667 0.00 0.00 42.51 1.52
2008 2101 5.214417 GTTGTTTGGATACGGTGGTTTTAC 58.786 41.667 0.00 0.00 42.51 2.01
2009 2102 4.716794 TGTTTGGATACGGTGGTTTTACT 58.283 39.130 0.00 0.00 42.51 2.24
2010 2103 5.862845 TGTTTGGATACGGTGGTTTTACTA 58.137 37.500 0.00 0.00 42.51 1.82
2011 2104 6.294473 TGTTTGGATACGGTGGTTTTACTAA 58.706 36.000 0.00 0.00 42.51 2.24
2012 2105 6.769822 TGTTTGGATACGGTGGTTTTACTAAA 59.230 34.615 0.00 0.00 42.51 1.85
2013 2106 6.799926 TTGGATACGGTGGTTTTACTAAAC 57.200 37.500 0.00 0.00 40.78 2.01
2024 2117 5.524971 GTTTTACTAAACCAGTTTGGCCT 57.475 39.130 3.32 0.00 42.67 5.19
2025 2118 6.638096 GTTTTACTAAACCAGTTTGGCCTA 57.362 37.500 3.32 0.00 42.67 3.93
2026 2119 6.441274 GTTTTACTAAACCAGTTTGGCCTAC 58.559 40.000 3.32 1.81 42.67 3.18
2027 2120 3.868619 ACTAAACCAGTTTGGCCTACA 57.131 42.857 3.32 0.00 42.67 2.74
2028 2121 3.483421 ACTAAACCAGTTTGGCCTACAC 58.517 45.455 3.32 0.00 42.67 2.90
2029 2122 2.445682 AAACCAGTTTGGCCTACACA 57.554 45.000 3.32 0.00 42.67 3.72
2030 2123 2.675658 AACCAGTTTGGCCTACACAT 57.324 45.000 3.32 0.00 42.67 3.21
2031 2124 1.909700 ACCAGTTTGGCCTACACATG 58.090 50.000 3.32 0.00 42.67 3.21
2032 2125 1.144913 ACCAGTTTGGCCTACACATGT 59.855 47.619 3.32 0.00 42.67 3.21
2033 2126 2.238521 CCAGTTTGGCCTACACATGTT 58.761 47.619 3.32 0.00 0.00 2.71
2034 2127 2.627699 CCAGTTTGGCCTACACATGTTT 59.372 45.455 3.32 0.00 0.00 2.83
2035 2128 3.069443 CCAGTTTGGCCTACACATGTTTT 59.931 43.478 3.32 0.00 0.00 2.43
2036 2129 4.298332 CAGTTTGGCCTACACATGTTTTC 58.702 43.478 3.32 0.00 0.00 2.29
2037 2130 3.004315 AGTTTGGCCTACACATGTTTTCG 59.996 43.478 3.32 0.00 0.00 3.46
2038 2131 1.529226 TGGCCTACACATGTTTTCGG 58.471 50.000 3.32 0.00 0.00 4.30
2039 2132 1.202830 TGGCCTACACATGTTTTCGGT 60.203 47.619 3.32 0.00 0.00 4.69
2040 2133 1.883926 GGCCTACACATGTTTTCGGTT 59.116 47.619 0.00 0.00 0.00 4.44
2041 2134 3.075884 GGCCTACACATGTTTTCGGTTA 58.924 45.455 0.00 0.00 0.00 2.85
2042 2135 3.692593 GGCCTACACATGTTTTCGGTTAT 59.307 43.478 0.00 0.00 0.00 1.89
2043 2136 4.877251 GGCCTACACATGTTTTCGGTTATA 59.123 41.667 0.00 0.00 0.00 0.98
2044 2137 5.354792 GGCCTACACATGTTTTCGGTTATAA 59.645 40.000 0.00 0.00 0.00 0.98
2045 2138 6.253013 GCCTACACATGTTTTCGGTTATAAC 58.747 40.000 7.09 7.09 0.00 1.89
2046 2139 6.128227 GCCTACACATGTTTTCGGTTATAACA 60.128 38.462 17.16 0.00 36.35 2.41
2047 2140 7.573469 GCCTACACATGTTTTCGGTTATAACAA 60.573 37.037 17.16 1.32 35.62 2.83
2048 2141 8.291032 CCTACACATGTTTTCGGTTATAACAAA 58.709 33.333 17.16 7.38 35.62 2.83
2049 2142 7.917720 ACACATGTTTTCGGTTATAACAAAC 57.082 32.000 17.16 17.11 35.62 2.93
2050 2143 7.708998 ACACATGTTTTCGGTTATAACAAACT 58.291 30.769 21.30 10.90 35.62 2.66
2051 2144 8.838365 ACACATGTTTTCGGTTATAACAAACTA 58.162 29.630 21.30 13.24 35.62 2.24
2052 2145 9.666626 CACATGTTTTCGGTTATAACAAACTAA 57.333 29.630 21.30 10.03 35.62 2.24
2071 2164 9.078753 CAAACTAAAATTCTGTTTGGTTAACGT 57.921 29.630 16.48 0.00 43.70 3.99
2074 2167 9.720667 ACTAAAATTCTGTTTGGTTAACGTAAC 57.279 29.630 12.15 12.15 39.72 2.50
2075 2168 9.719279 CTAAAATTCTGTTTGGTTAACGTAACA 57.281 29.630 17.76 17.76 40.39 2.41
2076 2169 8.983307 AAAATTCTGTTTGGTTAACGTAACAA 57.017 26.923 18.73 7.86 40.39 2.83
2077 2170 8.983307 AAATTCTGTTTGGTTAACGTAACAAA 57.017 26.923 18.73 12.24 40.39 2.83
2078 2171 9.589111 AAATTCTGTTTGGTTAACGTAACAAAT 57.411 25.926 18.73 17.02 40.39 2.32
2079 2172 8.791355 ATTCTGTTTGGTTAACGTAACAAATC 57.209 30.769 18.73 10.54 40.39 2.17
2080 2173 6.727215 TCTGTTTGGTTAACGTAACAAATCC 58.273 36.000 18.73 6.97 40.39 3.01
2081 2174 6.318144 TCTGTTTGGTTAACGTAACAAATCCA 59.682 34.615 18.73 9.93 40.39 3.41
2082 2175 7.013464 TCTGTTTGGTTAACGTAACAAATCCAT 59.987 33.333 18.73 0.00 40.39 3.41
2083 2176 6.918569 TGTTTGGTTAACGTAACAAATCCATG 59.081 34.615 16.95 0.00 40.39 3.66
2084 2177 5.630661 TGGTTAACGTAACAAATCCATGG 57.369 39.130 4.97 4.97 40.39 3.66
2085 2178 5.314529 TGGTTAACGTAACAAATCCATGGA 58.685 37.500 18.88 18.88 40.39 3.41
2086 2179 5.946972 TGGTTAACGTAACAAATCCATGGAT 59.053 36.000 22.15 22.15 40.39 3.41
2087 2180 7.110810 TGGTTAACGTAACAAATCCATGGATA 58.889 34.615 27.54 8.93 40.39 2.59
2088 2181 7.610692 TGGTTAACGTAACAAATCCATGGATAA 59.389 33.333 27.54 11.06 40.39 1.75
2089 2182 8.126700 GGTTAACGTAACAAATCCATGGATAAG 58.873 37.037 27.54 22.89 40.39 1.73
2090 2183 6.693315 AACGTAACAAATCCATGGATAAGG 57.307 37.500 27.54 20.29 33.97 2.69
2091 2184 5.996644 ACGTAACAAATCCATGGATAAGGA 58.003 37.500 27.54 12.16 38.50 3.36
2092 2185 6.055588 ACGTAACAAATCCATGGATAAGGAG 58.944 40.000 27.54 16.64 37.34 3.69
2093 2186 6.126883 ACGTAACAAATCCATGGATAAGGAGA 60.127 38.462 27.54 9.11 37.34 3.71
2094 2187 6.936900 CGTAACAAATCCATGGATAAGGAGAT 59.063 38.462 27.54 7.36 37.34 2.75
2095 2188 7.118390 CGTAACAAATCCATGGATAAGGAGATC 59.882 40.741 27.54 12.60 37.34 2.75
2096 2189 6.776887 ACAAATCCATGGATAAGGAGATCT 57.223 37.500 27.54 5.79 37.34 2.75
2097 2190 7.159201 ACAAATCCATGGATAAGGAGATCTT 57.841 36.000 27.54 11.78 37.34 2.40
2098 2191 8.280258 ACAAATCCATGGATAAGGAGATCTTA 57.720 34.615 27.54 0.00 41.66 2.10
2099 2192 8.381636 ACAAATCCATGGATAAGGAGATCTTAG 58.618 37.037 27.54 11.25 40.85 2.18
2100 2193 8.381636 CAAATCCATGGATAAGGAGATCTTAGT 58.618 37.037 27.54 3.78 40.85 2.24
2101 2194 8.517323 AATCCATGGATAAGGAGATCTTAGTT 57.483 34.615 27.54 3.96 40.85 2.24
2102 2195 7.937700 TCCATGGATAAGGAGATCTTAGTTT 57.062 36.000 11.44 0.00 40.85 2.66
2103 2196 8.337118 TCCATGGATAAGGAGATCTTAGTTTT 57.663 34.615 11.44 0.00 40.85 2.43
2104 2197 9.447279 TCCATGGATAAGGAGATCTTAGTTTTA 57.553 33.333 11.44 0.00 40.85 1.52
2105 2198 9.717942 CCATGGATAAGGAGATCTTAGTTTTAG 57.282 37.037 5.56 0.00 40.85 1.85
2113 2206 9.660180 AAGGAGATCTTAGTTTTAGTAAAGCTG 57.340 33.333 19.01 6.42 33.77 4.24
2114 2207 8.261522 AGGAGATCTTAGTTTTAGTAAAGCTGG 58.738 37.037 19.01 12.63 33.77 4.85
2115 2208 8.258708 GGAGATCTTAGTTTTAGTAAAGCTGGA 58.741 37.037 19.01 16.33 33.77 3.86
2116 2209 9.654663 GAGATCTTAGTTTTAGTAAAGCTGGAA 57.345 33.333 19.01 7.98 33.77 3.53
2120 2213 8.843262 TCTTAGTTTTAGTAAAGCTGGAAAACC 58.157 33.333 19.01 0.00 36.79 3.27
2121 2214 6.068473 AGTTTTAGTAAAGCTGGAAAACCG 57.932 37.500 10.81 0.00 36.79 4.44
2122 2215 5.824097 AGTTTTAGTAAAGCTGGAAAACCGA 59.176 36.000 10.81 0.00 36.79 4.69
2123 2216 5.934935 TTTAGTAAAGCTGGAAAACCGAG 57.065 39.130 0.00 0.00 0.00 4.63
2124 2217 3.487120 AGTAAAGCTGGAAAACCGAGT 57.513 42.857 0.00 0.00 0.00 4.18
2125 2218 3.816994 AGTAAAGCTGGAAAACCGAGTT 58.183 40.909 0.00 0.00 0.00 3.01
2126 2219 4.204799 AGTAAAGCTGGAAAACCGAGTTT 58.795 39.130 0.00 0.00 37.34 2.66
2127 2220 5.370679 AGTAAAGCTGGAAAACCGAGTTTA 58.629 37.500 0.00 0.00 34.43 2.01
2128 2221 6.002082 AGTAAAGCTGGAAAACCGAGTTTAT 58.998 36.000 0.00 0.00 34.43 1.40
2129 2222 7.163441 AGTAAAGCTGGAAAACCGAGTTTATA 58.837 34.615 0.00 0.00 34.43 0.98
2130 2223 6.496338 AAAGCTGGAAAACCGAGTTTATAG 57.504 37.500 0.00 3.99 34.43 1.31
2131 2224 5.416271 AGCTGGAAAACCGAGTTTATAGA 57.584 39.130 3.01 0.00 34.43 1.98
2132 2225 5.801380 AGCTGGAAAACCGAGTTTATAGAA 58.199 37.500 3.01 0.00 34.43 2.10
2133 2226 6.235664 AGCTGGAAAACCGAGTTTATAGAAA 58.764 36.000 3.01 0.00 34.43 2.52
2134 2227 6.713450 AGCTGGAAAACCGAGTTTATAGAAAA 59.287 34.615 3.01 0.00 34.43 2.29
2135 2228 7.229907 AGCTGGAAAACCGAGTTTATAGAAAAA 59.770 33.333 3.01 0.00 34.43 1.94
2136 2229 7.325338 GCTGGAAAACCGAGTTTATAGAAAAAC 59.675 37.037 3.01 0.00 39.22 2.43
2137 2230 7.354257 TGGAAAACCGAGTTTATAGAAAAACG 58.646 34.615 3.01 3.89 42.83 3.60
2138 2231 7.226325 TGGAAAACCGAGTTTATAGAAAAACGA 59.774 33.333 10.13 0.00 42.83 3.85
2139 2232 7.531871 GGAAAACCGAGTTTATAGAAAAACGAC 59.468 37.037 10.13 2.11 42.83 4.34
2140 2233 7.719778 AAACCGAGTTTATAGAAAAACGACT 57.280 32.000 10.13 0.00 42.83 4.18
2141 2234 8.816640 AAACCGAGTTTATAGAAAAACGACTA 57.183 30.769 10.13 0.00 42.83 2.59
2142 2235 8.992835 AACCGAGTTTATAGAAAAACGACTAT 57.007 30.769 10.13 0.00 42.83 2.12
2143 2236 8.992835 ACCGAGTTTATAGAAAAACGACTATT 57.007 30.769 10.13 0.00 42.83 1.73
2144 2237 9.428097 ACCGAGTTTATAGAAAAACGACTATTT 57.572 29.630 10.13 0.00 42.83 1.40
2145 2238 9.685005 CCGAGTTTATAGAAAAACGACTATTTG 57.315 33.333 10.13 0.00 42.83 2.32
2162 2255 9.469239 CGACTATTTGACGTTTTTCTATAAACC 57.531 33.333 0.00 0.00 35.15 3.27
2165 2258 9.274065 CTATTTGACGTTTTTCTATAAACCAGC 57.726 33.333 0.00 0.00 35.15 4.85
2166 2259 6.870971 TTGACGTTTTTCTATAAACCAGCT 57.129 33.333 0.00 0.00 35.15 4.24
2167 2260 6.476243 TGACGTTTTTCTATAAACCAGCTC 57.524 37.500 0.00 0.00 35.15 4.09
2168 2261 6.228258 TGACGTTTTTCTATAAACCAGCTCT 58.772 36.000 0.00 0.00 35.15 4.09
2169 2262 6.708949 TGACGTTTTTCTATAAACCAGCTCTT 59.291 34.615 0.00 0.00 35.15 2.85
2170 2263 7.227910 TGACGTTTTTCTATAAACCAGCTCTTT 59.772 33.333 0.00 0.00 35.15 2.52
2171 2264 7.582352 ACGTTTTTCTATAAACCAGCTCTTTC 58.418 34.615 0.00 0.00 35.15 2.62
2172 2265 7.227910 ACGTTTTTCTATAAACCAGCTCTTTCA 59.772 33.333 0.00 0.00 35.15 2.69
2173 2266 8.237267 CGTTTTTCTATAAACCAGCTCTTTCAT 58.763 33.333 0.00 0.00 35.15 2.57
2174 2267 9.561270 GTTTTTCTATAAACCAGCTCTTTCATC 57.439 33.333 0.00 0.00 33.01 2.92
2175 2268 9.520515 TTTTTCTATAAACCAGCTCTTTCATCT 57.479 29.630 0.00 0.00 0.00 2.90
2176 2269 8.498054 TTTCTATAAACCAGCTCTTTCATCTG 57.502 34.615 0.00 0.00 0.00 2.90
2177 2270 6.051717 TCTATAAACCAGCTCTTTCATCTGC 58.948 40.000 0.00 0.00 0.00 4.26
2178 2271 1.831580 AACCAGCTCTTTCATCTGCC 58.168 50.000 0.00 0.00 0.00 4.85
2179 2272 0.392193 ACCAGCTCTTTCATCTGCCG 60.392 55.000 0.00 0.00 0.00 5.69
2180 2273 1.712977 CCAGCTCTTTCATCTGCCGC 61.713 60.000 0.00 0.00 0.00 6.53
2181 2274 1.451028 AGCTCTTTCATCTGCCGCC 60.451 57.895 0.00 0.00 0.00 6.13
2182 2275 2.817423 GCTCTTTCATCTGCCGCCG 61.817 63.158 0.00 0.00 0.00 6.46
2183 2276 2.817423 CTCTTTCATCTGCCGCCGC 61.817 63.158 0.00 0.00 0.00 6.53
2184 2277 4.228097 CTTTCATCTGCCGCCGCG 62.228 66.667 5.59 5.59 38.08 6.46
2185 2278 4.751093 TTTCATCTGCCGCCGCGA 62.751 61.111 15.93 0.00 38.08 5.87
2186 2279 4.529219 TTCATCTGCCGCCGCGAT 62.529 61.111 15.93 0.00 38.08 4.58
2187 2280 4.529219 TCATCTGCCGCCGCGATT 62.529 61.111 15.93 0.00 38.08 3.34
2188 2281 4.303603 CATCTGCCGCCGCGATTG 62.304 66.667 15.93 3.43 38.08 2.67
2194 2287 2.587753 CCGCCGCGATTGGTGTAT 60.588 61.111 15.93 0.00 37.84 2.29
2195 2288 2.625906 CGCCGCGATTGGTGTATG 59.374 61.111 8.23 0.00 34.75 2.39
2196 2289 2.881266 CGCCGCGATTGGTGTATGG 61.881 63.158 8.23 0.00 34.75 2.74
2197 2290 1.817941 GCCGCGATTGGTGTATGGT 60.818 57.895 8.23 0.00 0.00 3.55
2198 2291 1.373590 GCCGCGATTGGTGTATGGTT 61.374 55.000 8.23 0.00 0.00 3.67
2199 2292 0.655733 CCGCGATTGGTGTATGGTTC 59.344 55.000 8.23 0.00 0.00 3.62
2200 2293 1.364721 CGCGATTGGTGTATGGTTCA 58.635 50.000 0.00 0.00 0.00 3.18
2201 2294 1.327460 CGCGATTGGTGTATGGTTCAG 59.673 52.381 0.00 0.00 0.00 3.02
2202 2295 1.064060 GCGATTGGTGTATGGTTCAGC 59.936 52.381 0.00 0.00 0.00 4.26
2203 2296 2.632377 CGATTGGTGTATGGTTCAGCT 58.368 47.619 0.00 0.00 34.86 4.24
2204 2297 2.352651 CGATTGGTGTATGGTTCAGCTG 59.647 50.000 7.63 7.63 34.86 4.24
2205 2298 2.198827 TTGGTGTATGGTTCAGCTGG 57.801 50.000 15.13 0.00 34.86 4.85
2206 2299 0.322456 TGGTGTATGGTTCAGCTGGC 60.322 55.000 15.13 7.27 34.86 4.85
2207 2300 0.322456 GGTGTATGGTTCAGCTGGCA 60.322 55.000 15.13 0.00 0.00 4.92
2208 2301 0.804989 GTGTATGGTTCAGCTGGCAC 59.195 55.000 15.13 11.03 0.00 5.01
2209 2302 0.673333 TGTATGGTTCAGCTGGCACG 60.673 55.000 15.13 0.00 0.00 5.34
2210 2303 1.745115 TATGGTTCAGCTGGCACGC 60.745 57.895 15.13 6.25 0.00 5.34
2211 2304 2.462125 TATGGTTCAGCTGGCACGCA 62.462 55.000 15.13 11.21 0.00 5.24
2212 2305 3.058160 GGTTCAGCTGGCACGCAT 61.058 61.111 15.13 0.00 0.00 4.73
2213 2306 2.177531 GTTCAGCTGGCACGCATG 59.822 61.111 15.13 0.00 0.00 4.06
2214 2307 2.281692 TTCAGCTGGCACGCATGT 60.282 55.556 15.13 0.00 0.00 3.21
2215 2308 1.898094 TTCAGCTGGCACGCATGTT 60.898 52.632 15.13 0.00 0.00 2.71
2216 2309 2.126618 CAGCTGGCACGCATGTTG 60.127 61.111 5.57 0.00 0.00 3.33
2217 2310 2.281692 AGCTGGCACGCATGTTGA 60.282 55.556 10.71 0.00 0.00 3.18
2218 2311 2.177531 GCTGGCACGCATGTTGAG 59.822 61.111 0.00 0.00 0.00 3.02
2219 2312 2.620112 GCTGGCACGCATGTTGAGT 61.620 57.895 0.00 0.00 0.00 3.41
2220 2313 1.499056 CTGGCACGCATGTTGAGTC 59.501 57.895 0.00 0.00 0.00 3.36
2221 2314 0.952497 CTGGCACGCATGTTGAGTCT 60.952 55.000 0.00 0.00 0.00 3.24
2222 2315 0.534877 TGGCACGCATGTTGAGTCTT 60.535 50.000 0.00 0.00 0.00 3.01
2223 2316 0.593128 GGCACGCATGTTGAGTCTTT 59.407 50.000 0.00 0.00 0.00 2.52
2224 2317 1.400242 GGCACGCATGTTGAGTCTTTC 60.400 52.381 0.00 0.00 0.00 2.62
2225 2318 1.400242 GCACGCATGTTGAGTCTTTCC 60.400 52.381 0.00 0.00 0.00 3.13
2226 2319 1.197721 CACGCATGTTGAGTCTTTCCC 59.802 52.381 0.00 0.00 0.00 3.97
2227 2320 0.443869 CGCATGTTGAGTCTTTCCCG 59.556 55.000 0.00 0.00 0.00 5.14
2228 2321 1.808411 GCATGTTGAGTCTTTCCCGA 58.192 50.000 0.00 0.00 0.00 5.14
2229 2322 1.734465 GCATGTTGAGTCTTTCCCGAG 59.266 52.381 0.00 0.00 0.00 4.63
2230 2323 1.734465 CATGTTGAGTCTTTCCCGAGC 59.266 52.381 0.00 0.00 0.00 5.03
2231 2324 0.756294 TGTTGAGTCTTTCCCGAGCA 59.244 50.000 0.00 0.00 0.00 4.26
2232 2325 1.140052 TGTTGAGTCTTTCCCGAGCAA 59.860 47.619 0.00 0.00 0.00 3.91
2233 2326 1.531578 GTTGAGTCTTTCCCGAGCAAC 59.468 52.381 0.00 0.00 0.00 4.17
2234 2327 0.756294 TGAGTCTTTCCCGAGCAACA 59.244 50.000 0.00 0.00 0.00 3.33
2235 2328 1.140052 TGAGTCTTTCCCGAGCAACAA 59.860 47.619 0.00 0.00 0.00 2.83
2236 2329 1.531578 GAGTCTTTCCCGAGCAACAAC 59.468 52.381 0.00 0.00 0.00 3.32
2237 2330 1.141053 AGTCTTTCCCGAGCAACAACT 59.859 47.619 0.00 0.00 0.00 3.16
2238 2331 1.531578 GTCTTTCCCGAGCAACAACTC 59.468 52.381 0.00 0.00 0.00 3.01
2239 2332 1.140052 TCTTTCCCGAGCAACAACTCA 59.860 47.619 0.00 0.00 36.42 3.41
2240 2333 2.154462 CTTTCCCGAGCAACAACTCAT 58.846 47.619 0.00 0.00 36.42 2.90
2241 2334 1.808411 TTCCCGAGCAACAACTCATC 58.192 50.000 0.00 0.00 36.42 2.92
2242 2335 0.976641 TCCCGAGCAACAACTCATCT 59.023 50.000 0.00 0.00 36.42 2.90
2243 2336 1.066858 TCCCGAGCAACAACTCATCTC 60.067 52.381 0.00 0.00 36.42 2.75
2244 2337 0.994995 CCGAGCAACAACTCATCTCG 59.005 55.000 0.00 0.00 44.21 4.04
2245 2338 0.368227 CGAGCAACAACTCATCTCGC 59.632 55.000 0.00 0.00 39.82 5.03
2246 2339 1.432514 GAGCAACAACTCATCTCGCA 58.567 50.000 0.00 0.00 36.65 5.10
2247 2340 2.005451 GAGCAACAACTCATCTCGCAT 58.995 47.619 0.00 0.00 36.65 4.73
2248 2341 2.005451 AGCAACAACTCATCTCGCATC 58.995 47.619 0.00 0.00 0.00 3.91
2249 2342 1.267235 GCAACAACTCATCTCGCATCG 60.267 52.381 0.00 0.00 0.00 3.84
2250 2343 1.002366 AACAACTCATCTCGCATCGC 58.998 50.000 0.00 0.00 0.00 4.58
2251 2344 0.807667 ACAACTCATCTCGCATCGCC 60.808 55.000 0.00 0.00 0.00 5.54
2252 2345 1.227380 AACTCATCTCGCATCGCCC 60.227 57.895 0.00 0.00 0.00 6.13
2253 2346 1.960040 AACTCATCTCGCATCGCCCA 61.960 55.000 0.00 0.00 0.00 5.36
2254 2347 1.005275 CTCATCTCGCATCGCCCAT 60.005 57.895 0.00 0.00 0.00 4.00
2255 2348 1.289800 CTCATCTCGCATCGCCCATG 61.290 60.000 0.00 0.00 35.29 3.66
2256 2349 1.301165 CATCTCGCATCGCCCATGA 60.301 57.895 0.00 0.00 33.80 3.07
2257 2350 1.301244 ATCTCGCATCGCCCATGAC 60.301 57.895 0.00 0.00 33.80 3.06
2258 2351 2.721971 ATCTCGCATCGCCCATGACC 62.722 60.000 0.00 0.00 33.80 4.02
2259 2352 3.738429 CTCGCATCGCCCATGACCA 62.738 63.158 0.00 0.00 33.80 4.02
2260 2353 2.592574 CGCATCGCCCATGACCAT 60.593 61.111 0.00 0.00 33.80 3.55
2261 2354 2.610694 CGCATCGCCCATGACCATC 61.611 63.158 0.00 0.00 33.80 3.51
2262 2355 1.526686 GCATCGCCCATGACCATCA 60.527 57.895 0.00 0.00 33.80 3.07
2263 2356 1.789078 GCATCGCCCATGACCATCAC 61.789 60.000 0.00 0.00 33.80 3.06
2264 2357 0.179037 CATCGCCCATGACCATCACT 60.179 55.000 0.00 0.00 33.80 3.41
2265 2358 0.107456 ATCGCCCATGACCATCACTC 59.893 55.000 0.00 0.00 0.00 3.51
2266 2359 1.524621 CGCCCATGACCATCACTCC 60.525 63.158 0.00 0.00 0.00 3.85
2267 2360 1.152881 GCCCATGACCATCACTCCC 60.153 63.158 0.00 0.00 0.00 4.30
2268 2361 1.146930 CCCATGACCATCACTCCCG 59.853 63.158 0.00 0.00 0.00 5.14
2269 2362 1.524621 CCATGACCATCACTCCCGC 60.525 63.158 0.00 0.00 0.00 6.13
2270 2363 1.884464 CATGACCATCACTCCCGCG 60.884 63.158 0.00 0.00 0.00 6.46
2271 2364 2.359169 ATGACCATCACTCCCGCGT 61.359 57.895 4.92 0.00 0.00 6.01
2272 2365 2.202756 GACCATCACTCCCGCGTC 60.203 66.667 4.92 0.00 0.00 5.19
2273 2366 4.129737 ACCATCACTCCCGCGTCG 62.130 66.667 4.92 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.548877 TCCATGGAATACTTTATAATAGCTCCC 58.451 37.037 13.46 0.00 0.00 4.30
115 116 1.683385 GCAAGGTTTGAGGAGCAACTT 59.317 47.619 0.00 0.00 35.91 2.66
244 245 9.333724 GGCCATGATTGAAAGATTTAAATTCAT 57.666 29.630 0.00 3.15 33.45 2.57
323 324 1.141053 AGGGAAAGAAGTTGAGCACGT 59.859 47.619 0.00 0.00 0.00 4.49
415 417 1.680314 GAGGGAAAAGGCCTGGCTG 60.680 63.158 19.68 0.00 0.00 4.85
1177 1208 2.426024 GTCCATGTAGTCGAACTAGGCA 59.574 50.000 0.00 0.00 30.12 4.75
1202 1233 1.132073 GGTCGACGGTAGAGGAACTTC 59.868 57.143 9.92 0.00 41.55 3.01
1352 1386 5.287226 TCAGTGAGGAAGTAGTCGTTTTTC 58.713 41.667 0.00 0.00 0.00 2.29
1934 2025 8.100791 AGAGGTGAAGCATAACAAAACTATACA 58.899 33.333 0.00 0.00 0.00 2.29
1982 2075 1.170442 CACCGTATCCAAACAACCCC 58.830 55.000 0.00 0.00 0.00 4.95
1983 2076 1.170442 CCACCGTATCCAAACAACCC 58.830 55.000 0.00 0.00 0.00 4.11
1984 2077 1.900245 ACCACCGTATCCAAACAACC 58.100 50.000 0.00 0.00 0.00 3.77
1985 2078 3.994204 AAACCACCGTATCCAAACAAC 57.006 42.857 0.00 0.00 0.00 3.32
1986 2079 5.131784 AGTAAAACCACCGTATCCAAACAA 58.868 37.500 0.00 0.00 0.00 2.83
1987 2080 4.716794 AGTAAAACCACCGTATCCAAACA 58.283 39.130 0.00 0.00 0.00 2.83
1988 2081 6.799926 TTAGTAAAACCACCGTATCCAAAC 57.200 37.500 0.00 0.00 0.00 2.93
1989 2082 7.200778 GTTTAGTAAAACCACCGTATCCAAA 57.799 36.000 0.00 0.00 39.29 3.28
1990 2083 6.799926 GTTTAGTAAAACCACCGTATCCAA 57.200 37.500 0.00 0.00 39.29 3.53
2002 2095 5.524971 AGGCCAAACTGGTTTAGTAAAAC 57.475 39.130 5.01 3.57 43.58 2.43
2003 2096 6.039605 GTGTAGGCCAAACTGGTTTAGTAAAA 59.960 38.462 5.01 0.00 40.46 1.52
2004 2097 5.532032 GTGTAGGCCAAACTGGTTTAGTAAA 59.468 40.000 5.01 0.00 40.46 2.01
2005 2098 5.065235 GTGTAGGCCAAACTGGTTTAGTAA 58.935 41.667 5.01 0.00 40.46 2.24
2006 2099 4.102838 TGTGTAGGCCAAACTGGTTTAGTA 59.897 41.667 5.01 0.00 40.46 1.82
2007 2100 3.117813 TGTGTAGGCCAAACTGGTTTAGT 60.118 43.478 5.01 0.00 40.46 2.24
2008 2101 3.482436 TGTGTAGGCCAAACTGGTTTAG 58.518 45.455 5.01 0.00 40.46 1.85
2009 2102 3.579534 TGTGTAGGCCAAACTGGTTTA 57.420 42.857 5.01 0.00 40.46 2.01
2010 2103 2.445682 TGTGTAGGCCAAACTGGTTT 57.554 45.000 5.01 0.00 40.46 3.27
2011 2104 2.238521 CATGTGTAGGCCAAACTGGTT 58.761 47.619 5.01 0.00 40.46 3.67
2012 2105 1.144913 ACATGTGTAGGCCAAACTGGT 59.855 47.619 5.01 0.00 40.46 4.00
2013 2106 1.909700 ACATGTGTAGGCCAAACTGG 58.090 50.000 5.01 0.00 41.55 4.00
2014 2107 4.298332 GAAAACATGTGTAGGCCAAACTG 58.702 43.478 5.01 0.00 0.00 3.16
2015 2108 3.004315 CGAAAACATGTGTAGGCCAAACT 59.996 43.478 5.01 0.00 0.00 2.66
2016 2109 3.305110 CGAAAACATGTGTAGGCCAAAC 58.695 45.455 5.01 2.84 0.00 2.93
2017 2110 2.294791 CCGAAAACATGTGTAGGCCAAA 59.705 45.455 5.01 0.00 0.00 3.28
2018 2111 1.883275 CCGAAAACATGTGTAGGCCAA 59.117 47.619 5.01 0.00 0.00 4.52
2019 2112 1.202830 ACCGAAAACATGTGTAGGCCA 60.203 47.619 5.01 0.00 0.00 5.36
2020 2113 1.530323 ACCGAAAACATGTGTAGGCC 58.470 50.000 0.00 0.00 0.00 5.19
2021 2114 4.957759 ATAACCGAAAACATGTGTAGGC 57.042 40.909 0.00 0.00 0.00 3.93
2022 2115 7.367159 TGTTATAACCGAAAACATGTGTAGG 57.633 36.000 13.01 3.84 0.00 3.18
2023 2116 9.109533 GTTTGTTATAACCGAAAACATGTGTAG 57.890 33.333 18.23 0.00 33.44 2.74
2024 2117 8.838365 AGTTTGTTATAACCGAAAACATGTGTA 58.162 29.630 22.19 0.00 33.44 2.90
2025 2118 7.708998 AGTTTGTTATAACCGAAAACATGTGT 58.291 30.769 22.19 0.00 33.44 3.72
2026 2119 9.666626 TTAGTTTGTTATAACCGAAAACATGTG 57.333 29.630 22.19 0.00 33.44 3.21
2044 2137 9.078753 CGTTAACCAAACAGAATTTTAGTTTGT 57.921 29.630 20.26 11.58 46.43 2.83
2048 2141 9.720667 GTTACGTTAACCAAACAGAATTTTAGT 57.279 29.630 0.00 0.00 38.03 2.24
2049 2142 9.719279 TGTTACGTTAACCAAACAGAATTTTAG 57.281 29.630 13.60 0.00 38.03 1.85
2051 2144 8.983307 TTGTTACGTTAACCAAACAGAATTTT 57.017 26.923 15.85 0.00 38.03 1.82
2052 2145 8.983307 TTTGTTACGTTAACCAAACAGAATTT 57.017 26.923 15.85 0.00 38.03 1.82
2053 2146 9.240159 GATTTGTTACGTTAACCAAACAGAATT 57.760 29.630 15.85 3.65 38.03 2.17
2054 2147 7.863877 GGATTTGTTACGTTAACCAAACAGAAT 59.136 33.333 15.85 16.42 38.03 2.40
2055 2148 7.148120 TGGATTTGTTACGTTAACCAAACAGAA 60.148 33.333 15.85 13.87 38.03 3.02
2056 2149 6.318144 TGGATTTGTTACGTTAACCAAACAGA 59.682 34.615 15.85 13.51 38.03 3.41
2057 2150 6.496571 TGGATTTGTTACGTTAACCAAACAG 58.503 36.000 15.85 0.00 38.03 3.16
2058 2151 6.446781 TGGATTTGTTACGTTAACCAAACA 57.553 33.333 13.60 13.60 38.03 2.83
2059 2152 6.363896 CCATGGATTTGTTACGTTAACCAAAC 59.636 38.462 5.56 9.39 37.88 2.93
2060 2153 6.264744 TCCATGGATTTGTTACGTTAACCAAA 59.735 34.615 11.44 9.29 37.88 3.28
2061 2154 5.768662 TCCATGGATTTGTTACGTTAACCAA 59.231 36.000 11.44 0.00 37.88 3.67
2062 2155 5.314529 TCCATGGATTTGTTACGTTAACCA 58.685 37.500 11.44 0.00 37.88 3.67
2063 2156 5.883503 TCCATGGATTTGTTACGTTAACC 57.116 39.130 11.44 0.00 37.88 2.85
2064 2157 8.126700 CCTTATCCATGGATTTGTTACGTTAAC 58.873 37.037 31.70 0.00 36.41 2.01
2065 2158 8.047911 TCCTTATCCATGGATTTGTTACGTTAA 58.952 33.333 31.70 14.63 36.17 2.01
2066 2159 7.566569 TCCTTATCCATGGATTTGTTACGTTA 58.433 34.615 31.70 7.49 36.17 3.18
2067 2160 6.419791 TCCTTATCCATGGATTTGTTACGTT 58.580 36.000 31.70 7.48 36.17 3.99
2068 2161 5.996644 TCCTTATCCATGGATTTGTTACGT 58.003 37.500 31.70 8.26 36.17 3.57
2069 2162 6.288294 TCTCCTTATCCATGGATTTGTTACG 58.712 40.000 31.70 11.32 36.17 3.18
2070 2163 8.160106 AGATCTCCTTATCCATGGATTTGTTAC 58.840 37.037 31.70 15.85 36.17 2.50
2071 2164 8.280258 AGATCTCCTTATCCATGGATTTGTTA 57.720 34.615 31.70 11.38 36.17 2.41
2072 2165 7.159201 AGATCTCCTTATCCATGGATTTGTT 57.841 36.000 31.70 11.40 36.17 2.83
2073 2166 6.776887 AGATCTCCTTATCCATGGATTTGT 57.223 37.500 31.70 11.80 36.17 2.83
2074 2167 8.381636 ACTAAGATCTCCTTATCCATGGATTTG 58.618 37.037 31.70 22.38 36.80 2.32
2075 2168 8.517323 ACTAAGATCTCCTTATCCATGGATTT 57.483 34.615 31.70 18.13 36.80 2.17
2076 2169 8.517323 AACTAAGATCTCCTTATCCATGGATT 57.483 34.615 31.70 12.58 36.80 3.01
2077 2170 8.517323 AAACTAAGATCTCCTTATCCATGGAT 57.483 34.615 29.66 29.66 36.80 3.41
2078 2171 7.937700 AAACTAAGATCTCCTTATCCATGGA 57.062 36.000 18.88 18.88 36.80 3.41
2079 2172 9.717942 CTAAAACTAAGATCTCCTTATCCATGG 57.282 37.037 4.97 4.97 36.80 3.66
2087 2180 9.660180 CAGCTTTACTAAAACTAAGATCTCCTT 57.340 33.333 0.00 0.00 38.87 3.36
2088 2181 8.261522 CCAGCTTTACTAAAACTAAGATCTCCT 58.738 37.037 0.00 0.00 0.00 3.69
2089 2182 8.258708 TCCAGCTTTACTAAAACTAAGATCTCC 58.741 37.037 0.00 0.00 0.00 3.71
2090 2183 9.654663 TTCCAGCTTTACTAAAACTAAGATCTC 57.345 33.333 0.00 0.00 0.00 2.75
2094 2187 8.843262 GGTTTTCCAGCTTTACTAAAACTAAGA 58.157 33.333 13.87 0.00 37.16 2.10
2095 2188 7.801783 CGGTTTTCCAGCTTTACTAAAACTAAG 59.198 37.037 13.87 0.00 37.16 2.18
2096 2189 7.498570 TCGGTTTTCCAGCTTTACTAAAACTAA 59.501 33.333 13.87 5.22 37.16 2.24
2097 2190 6.991531 TCGGTTTTCCAGCTTTACTAAAACTA 59.008 34.615 13.87 5.43 37.16 2.24
2098 2191 5.824097 TCGGTTTTCCAGCTTTACTAAAACT 59.176 36.000 13.87 0.00 37.16 2.66
2099 2192 6.063640 TCGGTTTTCCAGCTTTACTAAAAC 57.936 37.500 0.00 0.00 36.63 2.43
2100 2193 5.824097 ACTCGGTTTTCCAGCTTTACTAAAA 59.176 36.000 0.00 0.00 40.70 1.52
2101 2194 5.370679 ACTCGGTTTTCCAGCTTTACTAAA 58.629 37.500 0.00 0.00 40.70 1.85
2102 2195 4.964593 ACTCGGTTTTCCAGCTTTACTAA 58.035 39.130 0.00 0.00 40.70 2.24
2103 2196 4.612264 ACTCGGTTTTCCAGCTTTACTA 57.388 40.909 0.00 0.00 40.70 1.82
2104 2197 3.487120 ACTCGGTTTTCCAGCTTTACT 57.513 42.857 0.00 0.00 40.70 2.24
2105 2198 4.563337 AAACTCGGTTTTCCAGCTTTAC 57.437 40.909 0.00 0.00 40.70 2.01
2106 2199 7.388437 TCTATAAACTCGGTTTTCCAGCTTTA 58.612 34.615 7.22 0.00 40.70 1.85
2107 2200 6.235664 TCTATAAACTCGGTTTTCCAGCTTT 58.764 36.000 7.22 0.00 40.70 3.51
2108 2201 5.801380 TCTATAAACTCGGTTTTCCAGCTT 58.199 37.500 7.22 0.00 40.70 3.74
2109 2202 5.416271 TCTATAAACTCGGTTTTCCAGCT 57.584 39.130 7.22 0.00 40.70 4.24
2110 2203 6.490566 TTTCTATAAACTCGGTTTTCCAGC 57.509 37.500 7.22 0.00 40.70 4.85
2111 2204 7.532884 CGTTTTTCTATAAACTCGGTTTTCCAG 59.467 37.037 7.22 3.99 37.01 3.86
2112 2205 7.226325 TCGTTTTTCTATAAACTCGGTTTTCCA 59.774 33.333 7.22 0.00 37.01 3.53
2113 2206 7.531871 GTCGTTTTTCTATAAACTCGGTTTTCC 59.468 37.037 7.22 0.00 37.01 3.13
2114 2207 8.278408 AGTCGTTTTTCTATAAACTCGGTTTTC 58.722 33.333 7.22 0.00 37.01 2.29
2115 2208 8.146479 AGTCGTTTTTCTATAAACTCGGTTTT 57.854 30.769 7.22 0.00 37.01 2.43
2116 2209 7.719778 AGTCGTTTTTCTATAAACTCGGTTT 57.280 32.000 7.11 7.11 39.24 3.27
2117 2210 8.992835 ATAGTCGTTTTTCTATAAACTCGGTT 57.007 30.769 0.00 0.00 36.18 4.44
2118 2211 8.992835 AATAGTCGTTTTTCTATAAACTCGGT 57.007 30.769 0.00 0.00 36.18 4.69
2119 2212 9.685005 CAAATAGTCGTTTTTCTATAAACTCGG 57.315 33.333 0.00 0.00 36.18 4.63
2136 2229 9.469239 GGTTTATAGAAAAACGTCAAATAGTCG 57.531 33.333 0.00 0.00 39.71 4.18
2139 2232 9.274065 GCTGGTTTATAGAAAAACGTCAAATAG 57.726 33.333 0.00 0.00 39.71 1.73
2140 2233 9.005777 AGCTGGTTTATAGAAAAACGTCAAATA 57.994 29.630 0.00 0.00 39.71 1.40
2141 2234 7.882179 AGCTGGTTTATAGAAAAACGTCAAAT 58.118 30.769 0.00 0.00 39.71 2.32
2142 2235 7.227910 AGAGCTGGTTTATAGAAAAACGTCAAA 59.772 33.333 0.00 0.00 39.71 2.69
2143 2236 6.708949 AGAGCTGGTTTATAGAAAAACGTCAA 59.291 34.615 0.00 0.00 39.71 3.18
2144 2237 6.228258 AGAGCTGGTTTATAGAAAAACGTCA 58.772 36.000 0.00 0.00 39.71 4.35
2145 2238 6.723131 AGAGCTGGTTTATAGAAAAACGTC 57.277 37.500 0.00 0.00 39.71 4.34
2146 2239 7.227910 TGAAAGAGCTGGTTTATAGAAAAACGT 59.772 33.333 0.00 0.00 39.71 3.99
2147 2240 7.581476 TGAAAGAGCTGGTTTATAGAAAAACG 58.419 34.615 0.00 0.00 39.71 3.60
2148 2241 9.561270 GATGAAAGAGCTGGTTTATAGAAAAAC 57.439 33.333 0.00 0.00 38.39 2.43
2149 2242 9.520515 AGATGAAAGAGCTGGTTTATAGAAAAA 57.479 29.630 0.00 0.00 0.00 1.94
2150 2243 8.950210 CAGATGAAAGAGCTGGTTTATAGAAAA 58.050 33.333 0.00 0.00 0.00 2.29
2151 2244 7.066284 GCAGATGAAAGAGCTGGTTTATAGAAA 59.934 37.037 0.00 0.00 0.00 2.52
2152 2245 6.540189 GCAGATGAAAGAGCTGGTTTATAGAA 59.460 38.462 0.00 0.00 0.00 2.10
2153 2246 6.051717 GCAGATGAAAGAGCTGGTTTATAGA 58.948 40.000 0.00 0.00 0.00 1.98
2154 2247 5.238214 GGCAGATGAAAGAGCTGGTTTATAG 59.762 44.000 0.00 0.00 0.00 1.31
2155 2248 5.126067 GGCAGATGAAAGAGCTGGTTTATA 58.874 41.667 0.00 0.00 0.00 0.98
2156 2249 3.950395 GGCAGATGAAAGAGCTGGTTTAT 59.050 43.478 0.00 0.00 0.00 1.40
2157 2250 3.347216 GGCAGATGAAAGAGCTGGTTTA 58.653 45.455 0.00 0.00 0.00 2.01
2158 2251 2.165998 GGCAGATGAAAGAGCTGGTTT 58.834 47.619 0.00 0.00 0.00 3.27
2159 2252 1.831580 GGCAGATGAAAGAGCTGGTT 58.168 50.000 0.00 0.00 0.00 3.67
2160 2253 0.392193 CGGCAGATGAAAGAGCTGGT 60.392 55.000 0.00 0.00 0.00 4.00
2161 2254 1.712977 GCGGCAGATGAAAGAGCTGG 61.713 60.000 0.00 0.00 34.05 4.85
2162 2255 1.712977 GGCGGCAGATGAAAGAGCTG 61.713 60.000 3.07 0.00 36.47 4.24
2163 2256 1.451028 GGCGGCAGATGAAAGAGCT 60.451 57.895 3.07 0.00 0.00 4.09
2164 2257 2.817423 CGGCGGCAGATGAAAGAGC 61.817 63.158 10.53 0.00 0.00 4.09
2165 2258 2.817423 GCGGCGGCAGATGAAAGAG 61.817 63.158 9.78 0.00 39.62 2.85
2166 2259 2.819595 GCGGCGGCAGATGAAAGA 60.820 61.111 9.78 0.00 39.62 2.52
2167 2260 4.228097 CGCGGCGGCAGATGAAAG 62.228 66.667 15.84 0.00 39.92 2.62
2168 2261 4.751093 TCGCGGCGGCAGATGAAA 62.751 61.111 23.46 0.00 39.92 2.69
2169 2262 4.529219 ATCGCGGCGGCAGATGAA 62.529 61.111 23.46 0.00 39.92 2.57
2170 2263 4.529219 AATCGCGGCGGCAGATGA 62.529 61.111 23.46 5.58 39.92 2.92
2171 2264 4.303603 CAATCGCGGCGGCAGATG 62.304 66.667 23.46 10.47 39.92 2.90
2177 2270 2.587753 ATACACCAATCGCGGCGG 60.588 61.111 23.46 8.74 0.00 6.13
2178 2271 2.625906 CATACACCAATCGCGGCG 59.374 61.111 17.70 17.70 0.00 6.46
2179 2272 1.373590 AACCATACACCAATCGCGGC 61.374 55.000 6.13 0.00 0.00 6.53
2180 2273 0.655733 GAACCATACACCAATCGCGG 59.344 55.000 6.13 0.00 0.00 6.46
2181 2274 1.327460 CTGAACCATACACCAATCGCG 59.673 52.381 0.00 0.00 0.00 5.87
2182 2275 1.064060 GCTGAACCATACACCAATCGC 59.936 52.381 0.00 0.00 0.00 4.58
2183 2276 2.352651 CAGCTGAACCATACACCAATCG 59.647 50.000 8.42 0.00 0.00 3.34
2184 2277 2.684881 CCAGCTGAACCATACACCAATC 59.315 50.000 17.39 0.00 0.00 2.67
2185 2278 2.726821 CCAGCTGAACCATACACCAAT 58.273 47.619 17.39 0.00 0.00 3.16
2186 2279 1.886222 GCCAGCTGAACCATACACCAA 60.886 52.381 17.39 0.00 0.00 3.67
2187 2280 0.322456 GCCAGCTGAACCATACACCA 60.322 55.000 17.39 0.00 0.00 4.17
2188 2281 0.322456 TGCCAGCTGAACCATACACC 60.322 55.000 17.39 0.00 0.00 4.16
2189 2282 0.804989 GTGCCAGCTGAACCATACAC 59.195 55.000 17.39 7.71 0.00 2.90
2190 2283 0.673333 CGTGCCAGCTGAACCATACA 60.673 55.000 17.39 0.00 0.00 2.29
2191 2284 1.982073 GCGTGCCAGCTGAACCATAC 61.982 60.000 17.39 3.79 0.00 2.39
2192 2285 1.745115 GCGTGCCAGCTGAACCATA 60.745 57.895 17.39 0.00 0.00 2.74
2193 2286 3.058160 GCGTGCCAGCTGAACCAT 61.058 61.111 17.39 0.00 0.00 3.55
2194 2287 3.848301 ATGCGTGCCAGCTGAACCA 62.848 57.895 17.39 12.89 38.13 3.67
2195 2288 3.058160 ATGCGTGCCAGCTGAACC 61.058 61.111 17.39 3.53 38.13 3.62
2196 2289 2.133742 AACATGCGTGCCAGCTGAAC 62.134 55.000 17.39 12.27 38.13 3.18
2197 2290 1.898094 AACATGCGTGCCAGCTGAA 60.898 52.632 17.39 0.00 38.13 3.02
2198 2291 2.281692 AACATGCGTGCCAGCTGA 60.282 55.556 17.39 0.00 38.13 4.26
2199 2292 2.126618 CAACATGCGTGCCAGCTG 60.127 61.111 6.78 6.78 38.13 4.24
2200 2293 2.281692 TCAACATGCGTGCCAGCT 60.282 55.556 5.64 0.00 38.13 4.24
2201 2294 2.177531 CTCAACATGCGTGCCAGC 59.822 61.111 5.64 0.00 37.71 4.85
2202 2295 0.952497 AGACTCAACATGCGTGCCAG 60.952 55.000 5.64 1.78 0.00 4.85
2203 2296 0.534877 AAGACTCAACATGCGTGCCA 60.535 50.000 5.64 0.00 0.00 4.92
2204 2297 0.593128 AAAGACTCAACATGCGTGCC 59.407 50.000 5.64 0.00 0.00 5.01
2205 2298 1.400242 GGAAAGACTCAACATGCGTGC 60.400 52.381 5.64 0.00 0.00 5.34
2206 2299 1.197721 GGGAAAGACTCAACATGCGTG 59.802 52.381 3.82 3.82 0.00 5.34
2207 2300 1.523758 GGGAAAGACTCAACATGCGT 58.476 50.000 0.00 0.00 0.00 5.24
2208 2301 0.443869 CGGGAAAGACTCAACATGCG 59.556 55.000 0.00 0.00 0.00 4.73
2209 2302 1.734465 CTCGGGAAAGACTCAACATGC 59.266 52.381 0.00 0.00 0.00 4.06
2210 2303 1.734465 GCTCGGGAAAGACTCAACATG 59.266 52.381 0.00 0.00 0.00 3.21
2211 2304 1.347707 TGCTCGGGAAAGACTCAACAT 59.652 47.619 0.00 0.00 0.00 2.71
2212 2305 0.756294 TGCTCGGGAAAGACTCAACA 59.244 50.000 0.00 0.00 0.00 3.33
2213 2306 1.531578 GTTGCTCGGGAAAGACTCAAC 59.468 52.381 0.00 0.00 0.00 3.18
2214 2307 1.140052 TGTTGCTCGGGAAAGACTCAA 59.860 47.619 0.00 0.00 0.00 3.02
2215 2308 0.756294 TGTTGCTCGGGAAAGACTCA 59.244 50.000 0.00 0.00 0.00 3.41
2216 2309 1.531578 GTTGTTGCTCGGGAAAGACTC 59.468 52.381 0.00 0.00 0.00 3.36
2217 2310 1.141053 AGTTGTTGCTCGGGAAAGACT 59.859 47.619 0.00 0.00 0.00 3.24
2218 2311 1.531578 GAGTTGTTGCTCGGGAAAGAC 59.468 52.381 0.00 0.00 0.00 3.01
2219 2312 1.140052 TGAGTTGTTGCTCGGGAAAGA 59.860 47.619 0.00 0.00 38.28 2.52
2220 2313 1.593196 TGAGTTGTTGCTCGGGAAAG 58.407 50.000 0.00 0.00 38.28 2.62
2221 2314 2.151202 GATGAGTTGTTGCTCGGGAAA 58.849 47.619 0.00 0.00 38.28 3.13
2222 2315 1.347707 AGATGAGTTGTTGCTCGGGAA 59.652 47.619 0.00 0.00 38.28 3.97
2223 2316 0.976641 AGATGAGTTGTTGCTCGGGA 59.023 50.000 0.00 0.00 38.28 5.14
2224 2317 1.363744 GAGATGAGTTGTTGCTCGGG 58.636 55.000 0.00 0.00 38.28 5.14
2225 2318 0.994995 CGAGATGAGTTGTTGCTCGG 59.005 55.000 0.00 0.00 43.25 4.63
2227 2320 1.432514 TGCGAGATGAGTTGTTGCTC 58.567 50.000 0.00 0.00 36.12 4.26
2228 2321 2.005451 GATGCGAGATGAGTTGTTGCT 58.995 47.619 0.00 0.00 0.00 3.91
2229 2322 1.267235 CGATGCGAGATGAGTTGTTGC 60.267 52.381 0.00 0.00 0.00 4.17
2230 2323 1.267235 GCGATGCGAGATGAGTTGTTG 60.267 52.381 0.00 0.00 0.00 3.33
2231 2324 1.002366 GCGATGCGAGATGAGTTGTT 58.998 50.000 0.00 0.00 0.00 2.83
2232 2325 0.807667 GGCGATGCGAGATGAGTTGT 60.808 55.000 0.00 0.00 0.00 3.32
2233 2326 1.493950 GGGCGATGCGAGATGAGTTG 61.494 60.000 0.00 0.00 0.00 3.16
2234 2327 1.227380 GGGCGATGCGAGATGAGTT 60.227 57.895 0.00 0.00 0.00 3.01
2235 2328 1.752358 ATGGGCGATGCGAGATGAGT 61.752 55.000 0.00 0.00 0.00 3.41
2236 2329 1.005275 ATGGGCGATGCGAGATGAG 60.005 57.895 0.00 0.00 0.00 2.90
2237 2330 1.301165 CATGGGCGATGCGAGATGA 60.301 57.895 0.00 0.00 0.00 2.92
2238 2331 1.301165 TCATGGGCGATGCGAGATG 60.301 57.895 4.42 0.00 31.32 2.90
2239 2332 1.301244 GTCATGGGCGATGCGAGAT 60.301 57.895 4.42 0.00 31.32 2.75
2240 2333 2.106938 GTCATGGGCGATGCGAGA 59.893 61.111 4.42 0.00 31.32 4.04
2241 2334 2.969238 GGTCATGGGCGATGCGAG 60.969 66.667 4.42 0.00 31.32 5.03
2242 2335 2.994387 GATGGTCATGGGCGATGCGA 62.994 60.000 4.42 0.00 31.32 5.10
2243 2336 2.592574 ATGGTCATGGGCGATGCG 60.593 61.111 4.42 0.00 31.32 4.73
2244 2337 1.526686 TGATGGTCATGGGCGATGC 60.527 57.895 4.42 0.37 31.32 3.91
2245 2338 0.179037 AGTGATGGTCATGGGCGATG 60.179 55.000 2.72 2.72 0.00 3.84
2246 2339 0.107456 GAGTGATGGTCATGGGCGAT 59.893 55.000 0.00 0.00 0.00 4.58
2247 2340 1.522092 GAGTGATGGTCATGGGCGA 59.478 57.895 0.00 0.00 0.00 5.54
2248 2341 1.524621 GGAGTGATGGTCATGGGCG 60.525 63.158 0.00 0.00 0.00 6.13
2249 2342 1.152881 GGGAGTGATGGTCATGGGC 60.153 63.158 0.00 0.00 0.00 5.36
2250 2343 1.146930 CGGGAGTGATGGTCATGGG 59.853 63.158 0.00 0.00 0.00 4.00
2251 2344 1.524621 GCGGGAGTGATGGTCATGG 60.525 63.158 0.00 0.00 0.00 3.66
2252 2345 1.884464 CGCGGGAGTGATGGTCATG 60.884 63.158 0.00 0.00 44.85 3.07
2253 2346 2.298158 GACGCGGGAGTGATGGTCAT 62.298 60.000 12.47 0.00 44.85 3.06
2254 2347 2.994995 ACGCGGGAGTGATGGTCA 60.995 61.111 12.47 0.00 44.85 4.02
2255 2348 2.202756 GACGCGGGAGTGATGGTC 60.203 66.667 12.47 0.00 44.85 4.02
2256 2349 4.129737 CGACGCGGGAGTGATGGT 62.130 66.667 12.47 0.00 44.85 3.55


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

AutoCloner maintained by Alex Coulton.