Multiple sequence alignment - TraesCS4D01G365900

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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 TraesCS4D01G365900 chr4D 100.000 9691 0 0 1 9691 509668400 509678090 0.000000e+00 17897.0
1 TraesCS4D01G365900 chr4D 82.971 276 28 8 1896 2162 509669939 509670204 2.100000e-56 231.0
2 TraesCS4D01G365900 chr4D 82.971 276 28 8 1540 1805 509670295 509670561 2.100000e-56 231.0
3 TraesCS4D01G365900 chr4D 84.034 238 22 8 9395 9628 509681174 509681399 2.120000e-51 215.0
4 TraesCS4D01G365900 chr4D 85.561 187 12 5 6300 6486 509674527 509674698 2.150000e-41 182.0
5 TraesCS4D01G365900 chr4D 85.561 187 12 5 6128 6299 509674699 509674885 2.150000e-41 182.0
6 TraesCS4D01G365900 chr6B 99.903 3106 3 0 2601 5706 339386146 339383041 0.000000e+00 5720.0
7 TraesCS4D01G365900 chr6B 85.703 1259 133 31 7537 8767 15940324 15941563 0.000000e+00 1284.0
8 TraesCS4D01G365900 chr6B 76.452 1618 198 103 295 1800 15936997 15938543 0.000000e+00 708.0
9 TraesCS4D01G365900 chr6B 84.935 697 62 16 1931 2607 15938418 15939091 0.000000e+00 665.0
10 TraesCS4D01G365900 chr6B 93.536 263 16 1 5705 5967 15939115 15939376 3.280000e-104 390.0
11 TraesCS4D01G365900 chr6B 84.135 416 49 11 6383 6790 15939533 15939939 4.240000e-103 387.0
12 TraesCS4D01G365900 chr6B 91.386 267 16 2 7123 7389 15939948 15940207 9.250000e-95 359.0
13 TraesCS4D01G365900 chr6B 87.454 271 28 1 6029 6299 15939372 15939636 3.400000e-79 307.0
14 TraesCS4D01G365900 chr6B 80.222 450 42 18 1935 2377 632000993 632000584 2.650000e-75 294.0
15 TraesCS4D01G365900 chr6B 87.755 98 1 7 8898 8987 15941715 15941809 4.790000e-18 104.0
16 TraesCS4D01G365900 chr6A 99.711 3113 8 1 2601 5712 76516302 76519414 0.000000e+00 5698.0
17 TraesCS4D01G365900 chr6A 83.333 1944 189 71 7123 8986 9043544 9041656 0.000000e+00 1670.0
18 TraesCS4D01G365900 chr6A 85.889 737 63 12 1899 2610 9045128 9044408 0.000000e+00 747.0
19 TraesCS4D01G365900 chr6A 79.599 1147 126 57 725 1805 9045952 9044848 0.000000e+00 723.0
20 TraesCS4D01G365900 chr6A 84.778 427 54 8 6383 6799 9043969 9043544 1.510000e-112 418.0
21 TraesCS4D01G365900 chr6A 93.536 263 16 1 5705 5967 9044387 9044126 3.280000e-104 390.0
22 TraesCS4D01G365900 chr3B 99.647 3113 10 1 2601 5712 332925981 332929093 0.000000e+00 5686.0
23 TraesCS4D01G365900 chr3B 99.615 3114 10 2 2601 5712 695918154 695915041 0.000000e+00 5683.0
24 TraesCS4D01G365900 chr3B 99.453 3106 17 0 2601 5706 463461937 463465042 0.000000e+00 5642.0
25 TraesCS4D01G365900 chr3B 79.556 450 39 15 1935 2377 45147607 45147204 1.240000e-68 272.0
26 TraesCS4D01G365900 chr3B 93.182 88 4 1 1802 1887 551513891 551513978 2.840000e-25 128.0
27 TraesCS4D01G365900 chr5D 99.678 3106 10 0 2601 5706 565528479 565525374 0.000000e+00 5681.0
28 TraesCS4D01G365900 chr5D 92.222 90 5 1 1802 1889 51811466 51811555 1.020000e-24 126.0
29 TraesCS4D01G365900 chr1A 99.518 3113 11 2 2601 5712 7340432 7343541 0.000000e+00 5662.0
30 TraesCS4D01G365900 chr1A 99.356 3106 19 1 2601 5706 517048271 517045167 0.000000e+00 5624.0
31 TraesCS4D01G365900 chr1B 99.453 3106 17 0 2601 5706 357015676 357012571 0.000000e+00 5642.0
32 TraesCS4D01G365900 chr1B 95.181 83 2 1 1805 1885 628049892 628049810 7.900000e-26 130.0
33 TraesCS4D01G365900 chr4B 94.925 3074 94 21 5704 8759 657168747 657165718 0.000000e+00 4756.0
34 TraesCS4D01G365900 chr4B 88.966 1450 80 23 386 1805 657170893 657169494 0.000000e+00 1718.0
35 TraesCS4D01G365900 chr4B 94.118 731 27 3 1880 2607 657169487 657168770 0.000000e+00 1098.0
36 TraesCS4D01G365900 chr4B 85.424 295 24 7 1899 2174 657169776 657169482 1.230000e-73 289.0
37 TraesCS4D01G365900 chr4B 89.778 225 8 2 1 210 657171369 657171145 3.450000e-69 274.0
38 TraesCS4D01G365900 chr4B 91.279 172 15 0 6131 6302 657168148 657167977 1.630000e-57 235.0
39 TraesCS4D01G365900 chr4B 84.492 187 14 5 6303 6489 657168320 657168149 4.650000e-38 171.0
40 TraesCS4D01G365900 chr4B 97.727 44 0 1 228 271 657171155 657171113 3.750000e-09 75.0
41 TraesCS4D01G365900 chr5A 94.295 2261 76 19 6625 8873 698515406 698517625 0.000000e+00 3411.0
42 TraesCS4D01G365900 chr5A 88.409 1458 81 32 378 1778 698511917 698513343 0.000000e+00 1676.0
43 TraesCS4D01G365900 chr5A 97.059 952 19 3 1656 2607 698513500 698514442 0.000000e+00 1594.0
44 TraesCS4D01G365900 chr5A 93.136 947 31 4 5705 6651 698514466 698515378 0.000000e+00 1358.0
45 TraesCS4D01G365900 chr5A 89.091 275 23 7 1 272 698511510 698511780 1.560000e-87 335.0
46 TraesCS4D01G365900 chr5A 92.442 172 13 0 6128 6299 698515043 698515214 7.520000e-61 246.0
47 TraesCS4D01G365900 chr5A 84.916 179 12 5 6308 6486 698514879 698515042 6.020000e-37 167.0
48 TraesCS4D01G365900 chr5A 91.346 104 5 1 8872 8975 698517683 698517782 1.310000e-28 139.0
49 TraesCS4D01G365900 chr5A 97.260 73 2 0 9024 9096 698517874 698517946 3.670000e-24 124.0
50 TraesCS4D01G365900 chr5A 79.310 145 13 8 1534 1661 698513197 698513341 1.730000e-12 86.1
51 TraesCS4D01G365900 chr6D 90.160 935 74 10 7441 8357 8799591 8800525 0.000000e+00 1201.0
52 TraesCS4D01G365900 chr6D 79.261 1596 174 97 295 1805 8796483 8798006 0.000000e+00 968.0
53 TraesCS4D01G365900 chr6D 86.813 728 59 13 1899 2607 8797733 8798442 0.000000e+00 778.0
54 TraesCS4D01G365900 chr6D 87.260 416 44 9 6383 6790 8798883 8799297 5.300000e-127 466.0
55 TraesCS4D01G365900 chr6D 93.536 263 15 2 5705 5967 8798466 8798726 3.280000e-104 390.0
56 TraesCS4D01G365900 chr6D 89.542 306 18 6 7123 7421 8799306 8799604 9.190000e-100 375.0
57 TraesCS4D01G365900 chr6D 88.192 271 26 1 6029 6299 8798722 8798986 1.570000e-82 318.0
58 TraesCS4D01G365900 chr6D 83.502 297 38 7 8480 8767 8800604 8800898 5.770000e-67 267.0
59 TraesCS4D01G365900 chr6D 90.526 95 4 2 8898 8987 8801050 8801144 4.750000e-23 121.0
60 TraesCS4D01G365900 chr2D 94.198 293 11 1 9405 9691 551856419 551856127 8.930000e-120 442.0
61 TraesCS4D01G365900 chr2D 88.372 258 27 2 9423 9677 551847370 551847113 3.400000e-79 307.0
62 TraesCS4D01G365900 chr2D 84.914 232 32 3 9403 9634 551834670 551834442 2.100000e-56 231.0
63 TraesCS4D01G365900 chr2D 81.250 240 6 6 9167 9406 551856772 551856572 3.620000e-34 158.0
64 TraesCS4D01G365900 chr2D 92.045 88 3 2 8891 8974 551858326 551858239 4.750000e-23 121.0
65 TraesCS4D01G365900 chr2A 93.127 291 15 3 9405 9691 692580968 692580679 1.160000e-113 422.0
66 TraesCS4D01G365900 chr2A 87.209 258 30 2 9423 9677 692526527 692526270 3.420000e-74 291.0
67 TraesCS4D01G365900 chr2A 86.207 174 4 6 9233 9406 692581278 692581125 4.650000e-38 171.0
68 TraesCS4D01G365900 chr2A 88.406 138 4 3 8897 9027 692584339 692584207 1.300000e-33 156.0
69 TraesCS4D01G365900 chr2A 95.181 83 2 1 1805 1885 39327499 39327417 7.900000e-26 130.0
70 TraesCS4D01G365900 chr2A 92.308 91 3 3 1802 1889 617178809 617178898 1.020000e-24 126.0
71 TraesCS4D01G365900 chr7B 80.222 450 42 19 1935 2377 577362756 577362347 2.650000e-75 294.0
72 TraesCS4D01G365900 chr3A 95.294 85 2 1 1802 1884 99426188 99426272 6.110000e-27 134.0
73 TraesCS4D01G365900 chr4A 74.603 315 73 4 7608 7917 660920328 660920640 2.200000e-26 132.0
74 TraesCS4D01G365900 chr7D 73.941 307 77 1 7608 7911 46888258 46888564 4.750000e-23 121.0
75 TraesCS4D01G365900 chr7D 89.583 96 8 1 1802 1895 471560760 471560665 4.750000e-23 121.0
76 TraesCS4D01G365900 chr7D 73.482 313 80 1 7608 7917 46839603 46839291 2.210000e-21 115.0
77 TraesCS4D01G365900 chr7D 97.297 37 0 1 7680 7716 473093840 473093805 2.920000e-05 62.1
78 TraesCS4D01G365900 chr5B 90.426 94 6 2 1805 1895 246182703 246182610 4.750000e-23 121.0
79 TraesCS4D01G365900 chr3D 72.333 300 72 10 7616 7909 283316767 283317061 6.240000e-12 84.2


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 TraesCS4D01G365900 chr4D 509668400 509678090 9690 False 17897.000000 17897 100.000000 1 9691 1 chr4D.!!$F1 9690
1 TraesCS4D01G365900 chr4D 509669939 509674885 4946 False 206.500000 231 84.266000 1540 6486 4 chr4D.!!$F3 4946
2 TraesCS4D01G365900 chr6B 339383041 339386146 3105 True 5720.000000 5720 99.903000 2601 5706 1 chr6B.!!$R1 3105
3 TraesCS4D01G365900 chr6B 15936997 15941809 4812 False 525.500000 1284 86.419500 295 8987 8 chr6B.!!$F1 8692
4 TraesCS4D01G365900 chr6A 76516302 76519414 3112 False 5698.000000 5698 99.711000 2601 5712 1 chr6A.!!$F1 3111
5 TraesCS4D01G365900 chr6A 9041656 9045952 4296 True 789.600000 1670 85.427000 725 8986 5 chr6A.!!$R1 8261
6 TraesCS4D01G365900 chr3B 332925981 332929093 3112 False 5686.000000 5686 99.647000 2601 5712 1 chr3B.!!$F1 3111
7 TraesCS4D01G365900 chr3B 695915041 695918154 3113 True 5683.000000 5683 99.615000 2601 5712 1 chr3B.!!$R2 3111
8 TraesCS4D01G365900 chr3B 463461937 463465042 3105 False 5642.000000 5642 99.453000 2601 5706 1 chr3B.!!$F2 3105
9 TraesCS4D01G365900 chr5D 565525374 565528479 3105 True 5681.000000 5681 99.678000 2601 5706 1 chr5D.!!$R1 3105
10 TraesCS4D01G365900 chr1A 7340432 7343541 3109 False 5662.000000 5662 99.518000 2601 5712 1 chr1A.!!$F1 3111
11 TraesCS4D01G365900 chr1A 517045167 517048271 3104 True 5624.000000 5624 99.356000 2601 5706 1 chr1A.!!$R1 3105
12 TraesCS4D01G365900 chr1B 357012571 357015676 3105 True 5642.000000 5642 99.453000 2601 5706 1 chr1B.!!$R1 3105
13 TraesCS4D01G365900 chr4B 657165718 657171369 5651 True 1077.000000 4756 90.838625 1 8759 8 chr4B.!!$R1 8758
14 TraesCS4D01G365900 chr5A 698511510 698517946 6436 False 913.610000 3411 90.726400 1 9096 10 chr5A.!!$F1 9095
15 TraesCS4D01G365900 chr6D 8796483 8801144 4661 False 542.666667 1201 87.643556 295 8987 9 chr6D.!!$F1 8692
16 TraesCS4D01G365900 chr2D 551856127 551858326 2199 True 240.333333 442 89.164333 8891 9691 3 chr2D.!!$R3 800
17 TraesCS4D01G365900 chr2A 692580679 692584339 3660 True 249.666667 422 89.246667 8897 9691 3 chr2A.!!$R3 794

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
867 1062 0.029567 CTAGCCTAGTTGTCGGAGCG 59.970 60.0 0.00 0.0 0.00 5.03 F
1756 2369 0.896923 TGAATGCATCAACCCCTTGC 59.103 50.0 0.00 0.0 34.30 4.01 F
2299 3191 5.073827 AGGTAGCTCCTCATACTCATACTCA 59.926 44.0 0.00 0.0 44.42 3.41 F
6367 7278 5.255687 TGCTGGAATTAATGCTTTCAGAGA 58.744 37.5 0.54 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 3199 4.768968 ACCACGAATTAGTACAGTACAGGT 59.231 41.667 13.37 4.84 0.00 4.00 R
6372 7283 4.453478 GCACTAACCTTGTTACCACTAACC 59.547 45.833 0.00 0.00 32.52 2.85 R
6378 7289 2.158740 TGCAGCACTAACCTTGTTACCA 60.159 45.455 0.00 0.00 0.00 3.25 R
9224 12751 0.037605 GGATTCAGGTTCGACCACGT 60.038 55.000 6.78 0.00 41.95 4.49 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
98 99 1.219124 GTGATTCAGCAGCTCGGGA 59.781 57.895 0.00 0.00 0.00 5.14
110 111 4.056584 TCGGGAGCGGGGAGAAGA 62.057 66.667 0.00 0.00 0.00 2.87
121 136 1.764454 GGAGAAGAGAGGGAGGGGC 60.764 68.421 0.00 0.00 0.00 5.80
305 320 2.183046 GACAGACAGAGCGGAGGC 59.817 66.667 0.00 0.00 40.37 4.70
354 369 0.491371 AAAGGAAAGGATGGGCCCAA 59.509 50.000 32.58 13.16 37.37 4.12
357 372 0.325577 GGAAAGGATGGGCCCAACAT 60.326 55.000 32.58 23.16 37.37 2.71
444 566 1.906574 TCCTACAAAACTCCGCATCCT 59.093 47.619 0.00 0.00 0.00 3.24
615 763 2.038820 CCAAATGCATGTGAAACCCCTT 59.961 45.455 18.93 0.00 34.36 3.95
620 772 0.409484 CATGTGAAACCCCTTCCCCT 59.591 55.000 0.00 0.00 34.36 4.79
710 866 2.632541 CTACGCTAGCCTCGTCGG 59.367 66.667 9.66 0.00 40.89 4.79
803 960 2.896443 GCTCTTCCCCGACCAGAG 59.104 66.667 0.00 0.00 37.67 3.35
804 961 2.896443 CTCTTCCCCGACCAGAGC 59.104 66.667 0.00 0.00 0.00 4.09
805 962 3.068691 TCTTCCCCGACCAGAGCG 61.069 66.667 0.00 0.00 0.00 5.03
806 963 4.821589 CTTCCCCGACCAGAGCGC 62.822 72.222 0.00 0.00 0.00 5.92
852 1047 1.904378 CGAGAGGCCCTACCCTAGC 60.904 68.421 0.00 0.00 40.58 3.42
858 1053 0.105090 GGCCCTACCCTAGCCTAGTT 60.105 60.000 0.00 0.00 43.62 2.24
864 1059 0.333993 ACCCTAGCCTAGTTGTCGGA 59.666 55.000 0.00 0.00 0.00 4.55
867 1062 0.029567 CTAGCCTAGTTGTCGGAGCG 59.970 60.000 0.00 0.00 0.00 5.03
970 1192 3.134127 ATTTCCGCGCCTCTTGCC 61.134 61.111 0.00 0.00 36.24 4.52
1215 1463 4.129737 TACGCACGCTCCAGCTCC 62.130 66.667 0.00 0.00 39.32 4.70
1315 1584 3.431725 GCCTGTGTGCGGCTTACC 61.432 66.667 0.00 0.00 44.17 2.85
1508 1779 8.534496 TCATGTTCTAGACTGAATCTGAATGAA 58.466 33.333 0.00 0.00 38.49 2.57
1509 1780 9.327628 CATGTTCTAGACTGAATCTGAATGAAT 57.672 33.333 0.00 0.00 38.49 2.57
1510 1781 8.713737 TGTTCTAGACTGAATCTGAATGAATG 57.286 34.615 0.00 0.00 38.49 2.67
1511 1782 7.767659 TGTTCTAGACTGAATCTGAATGAATGG 59.232 37.037 0.00 0.00 38.49 3.16
1512 1783 7.666063 TCTAGACTGAATCTGAATGAATGGA 57.334 36.000 0.00 0.00 38.49 3.41
1513 1784 8.260099 TCTAGACTGAATCTGAATGAATGGAT 57.740 34.615 0.00 0.00 38.49 3.41
1514 1785 8.148999 TCTAGACTGAATCTGAATGAATGGATG 58.851 37.037 0.00 0.00 38.49 3.51
1515 1786 6.062749 AGACTGAATCTGAATGAATGGATGG 58.937 40.000 0.00 0.00 35.81 3.51
1516 1787 6.009908 ACTGAATCTGAATGAATGGATGGA 57.990 37.500 0.00 0.00 0.00 3.41
1517 1788 6.611785 ACTGAATCTGAATGAATGGATGGAT 58.388 36.000 0.00 0.00 0.00 3.41
1518 1789 6.490381 ACTGAATCTGAATGAATGGATGGATG 59.510 38.462 0.00 0.00 0.00 3.51
1519 1790 5.773176 TGAATCTGAATGAATGGATGGATGG 59.227 40.000 0.00 0.00 0.00 3.51
1520 1791 5.594199 ATCTGAATGAATGGATGGATGGA 57.406 39.130 0.00 0.00 0.00 3.41
1521 1792 5.594199 TCTGAATGAATGGATGGATGGAT 57.406 39.130 0.00 0.00 0.00 3.41
1522 1793 5.321927 TCTGAATGAATGGATGGATGGATG 58.678 41.667 0.00 0.00 0.00 3.51
1523 1794 4.412843 TGAATGAATGGATGGATGGATGG 58.587 43.478 0.00 0.00 0.00 3.51
1692 2299 2.949447 AGTCACAGGTTGATTTGCCTT 58.051 42.857 0.00 0.00 36.32 4.35
1693 2300 4.098914 AGTCACAGGTTGATTTGCCTTA 57.901 40.909 0.00 0.00 36.32 2.69
1756 2369 0.896923 TGAATGCATCAACCCCTTGC 59.103 50.000 0.00 0.00 34.30 4.01
2296 3188 6.373216 CACTAGGTAGCTCCTCATACTCATAC 59.627 46.154 0.00 0.00 44.42 2.39
2297 3189 5.592587 AGGTAGCTCCTCATACTCATACT 57.407 43.478 0.00 0.00 44.42 2.12
2298 3190 5.566469 AGGTAGCTCCTCATACTCATACTC 58.434 45.833 0.00 0.00 44.42 2.59
2299 3191 5.073827 AGGTAGCTCCTCATACTCATACTCA 59.926 44.000 0.00 0.00 44.42 3.41
2300 3192 5.949354 GGTAGCTCCTCATACTCATACTCAT 59.051 44.000 0.00 0.00 0.00 2.90
2301 3193 7.037225 AGGTAGCTCCTCATACTCATACTCATA 60.037 40.741 0.00 0.00 44.42 2.15
2302 3194 7.066525 GGTAGCTCCTCATACTCATACTCATAC 59.933 44.444 0.00 0.00 0.00 2.39
2303 3195 6.789268 AGCTCCTCATACTCATACTCATACT 58.211 40.000 0.00 0.00 0.00 2.12
2304 3196 6.884295 AGCTCCTCATACTCATACTCATACTC 59.116 42.308 0.00 0.00 0.00 2.59
2305 3197 6.657117 GCTCCTCATACTCATACTCATACTCA 59.343 42.308 0.00 0.00 0.00 3.41
2306 3198 7.339212 GCTCCTCATACTCATACTCATACTCAT 59.661 40.741 0.00 0.00 0.00 2.90
2307 3199 9.898152 CTCCTCATACTCATACTCATACTCATA 57.102 37.037 0.00 0.00 0.00 2.15
6367 7278 5.255687 TGCTGGAATTAATGCTTTCAGAGA 58.744 37.500 0.54 0.00 0.00 3.10
6368 7279 5.711506 TGCTGGAATTAATGCTTTCAGAGAA 59.288 36.000 0.54 0.00 0.00 2.87
6369 7280 6.127814 TGCTGGAATTAATGCTTTCAGAGAAG 60.128 38.462 0.54 0.00 0.00 2.85
6370 7281 6.094603 GCTGGAATTAATGCTTTCAGAGAAGA 59.905 38.462 0.54 0.00 0.00 2.87
6371 7282 7.362401 GCTGGAATTAATGCTTTCAGAGAAGAA 60.362 37.037 0.54 0.00 0.00 2.52
6372 7283 8.048534 TGGAATTAATGCTTTCAGAGAAGAAG 57.951 34.615 0.00 0.00 0.00 2.85
6373 7284 7.121759 TGGAATTAATGCTTTCAGAGAAGAAGG 59.878 37.037 0.00 0.00 0.00 3.46
6374 7285 7.121907 GGAATTAATGCTTTCAGAGAAGAAGGT 59.878 37.037 0.00 0.00 0.00 3.50
6375 7286 8.414629 AATTAATGCTTTCAGAGAAGAAGGTT 57.585 30.769 0.00 0.00 0.00 3.50
6376 7287 9.520515 AATTAATGCTTTCAGAGAAGAAGGTTA 57.479 29.630 0.00 0.00 0.00 2.85
6377 7288 8.553459 TTAATGCTTTCAGAGAAGAAGGTTAG 57.447 34.615 0.00 0.00 0.00 2.34
6378 7289 5.552870 TGCTTTCAGAGAAGAAGGTTAGT 57.447 39.130 0.00 0.00 0.00 2.24
6379 7290 5.300752 TGCTTTCAGAGAAGAAGGTTAGTG 58.699 41.667 0.00 0.00 0.00 2.74
6380 7291 4.693095 GCTTTCAGAGAAGAAGGTTAGTGG 59.307 45.833 0.00 0.00 0.00 4.00
6381 7292 5.743422 GCTTTCAGAGAAGAAGGTTAGTGGT 60.743 44.000 0.00 0.00 0.00 4.16
6486 7412 3.005367 CCAACCCATAGCTTTCGTTTTGT 59.995 43.478 0.00 0.00 0.00 2.83
6621 7554 3.470709 CACGTGCCTTATGGATCTTGAT 58.529 45.455 0.82 0.00 34.57 2.57
6622 7555 3.496130 CACGTGCCTTATGGATCTTGATC 59.504 47.826 0.82 2.21 34.57 2.92
6672 7659 3.559238 AATTTACTGTTGCGCTGGAAG 57.441 42.857 9.73 3.56 0.00 3.46
6731 7723 2.013400 TCTAACTCTGCTCTGCTCTCG 58.987 52.381 0.00 0.00 0.00 4.04
6890 7883 3.645884 CTGCTGTCAAAAAGGGTGAATG 58.354 45.455 0.00 0.00 0.00 2.67
7353 8346 4.225942 AGGTCCTTCATTCTAATGACAGCA 59.774 41.667 4.89 0.00 44.54 4.41
7402 8401 5.885912 AGGTACGTATTGGCTGAATTCATTT 59.114 36.000 8.96 0.00 0.00 2.32
7434 8436 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
7435 8437 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
7436 8438 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
7437 8439 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
7438 8440 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
7439 8441 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
7440 8442 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
7441 8443 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
7442 8444 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
7443 8445 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
7444 8446 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
7445 8447 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
7446 8448 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
7447 8449 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
7448 8450 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
7507 8518 5.867174 GCGTGTATTTTTAATGGCCTTTTCT 59.133 36.000 9.46 0.00 0.00 2.52
7515 8526 3.855689 AATGGCCTTTTCTTCATGACG 57.144 42.857 3.32 0.00 0.00 4.35
8127 9146 2.125753 GTGGAGCGAGCAGTGGAG 60.126 66.667 0.00 0.00 0.00 3.86
8369 9401 2.162408 AGGTACGTACGGTTTCTACAGC 59.838 50.000 21.06 1.23 0.00 4.40
8378 9410 6.914215 CGTACGGTTTCTACAGCAGATTTATA 59.086 38.462 7.57 0.00 31.77 0.98
8380 9412 7.772332 ACGGTTTCTACAGCAGATTTATAAG 57.228 36.000 0.00 0.00 31.77 1.73
8419 9452 7.892771 TGTGATAGATAGATAGACAGGCTGATT 59.107 37.037 23.66 11.02 0.00 2.57
8455 9490 6.074302 GCATGGACGTGTGATTAATACAGTAG 60.074 42.308 0.00 0.00 0.00 2.57
8692 9824 0.042431 AGGCCTCTGATGGAGTGAGT 59.958 55.000 0.00 0.00 40.30 3.41
8693 9825 0.177604 GGCCTCTGATGGAGTGAGTG 59.822 60.000 0.00 0.00 40.30 3.51
8694 9826 1.189752 GCCTCTGATGGAGTGAGTGA 58.810 55.000 0.00 0.00 40.30 3.41
8695 9827 1.136695 GCCTCTGATGGAGTGAGTGAG 59.863 57.143 0.00 0.00 40.30 3.51
8696 9828 1.755959 CCTCTGATGGAGTGAGTGAGG 59.244 57.143 0.00 0.00 40.30 3.86
8713 9846 6.412362 AGTGAGGCTCATGGTAAATACTAG 57.588 41.667 21.84 0.00 0.00 2.57
8717 9850 6.267014 TGAGGCTCATGGTAAATACTAGTACC 59.733 42.308 14.43 5.11 40.28 3.34
8797 9957 3.067320 GGAGAGAAGGTTTATGCCATTGC 59.933 47.826 0.00 0.00 38.26 3.56
8798 9958 3.026694 AGAGAAGGTTTATGCCATTGCC 58.973 45.455 0.00 0.00 36.33 4.52
8822 9993 6.708949 CCAGGTATAGAAGAGAGTAGAGTGTC 59.291 46.154 0.00 0.00 0.00 3.67
8823 9994 7.419750 CCAGGTATAGAAGAGAGTAGAGTGTCT 60.420 44.444 0.00 0.00 0.00 3.41
8827 10012 5.957842 AGAAGAGAGTAGAGTGTCTGTTG 57.042 43.478 0.00 0.00 0.00 3.33
8991 11317 1.668419 GATGCCGAGGTTATGCTGTT 58.332 50.000 0.00 0.00 0.00 3.16
8992 11318 2.017049 GATGCCGAGGTTATGCTGTTT 58.983 47.619 0.00 0.00 0.00 2.83
8993 11319 1.904287 TGCCGAGGTTATGCTGTTTT 58.096 45.000 0.00 0.00 0.00 2.43
8994 11320 1.539388 TGCCGAGGTTATGCTGTTTTG 59.461 47.619 0.00 0.00 0.00 2.44
8995 11321 1.135402 GCCGAGGTTATGCTGTTTTGG 60.135 52.381 0.00 0.00 0.00 3.28
9058 11428 1.941294 CCTGCAGATTGAGATGACAGC 59.059 52.381 17.39 0.00 0.00 4.40
9092 11462 1.238439 ATCGTCTTGGGTGCAGTTTG 58.762 50.000 0.00 0.00 0.00 2.93
9096 11466 2.794631 CGTCTTGGGTGCAGTTTGTTTC 60.795 50.000 0.00 0.00 0.00 2.78
9097 11467 1.754226 TCTTGGGTGCAGTTTGTTTCC 59.246 47.619 0.00 0.00 0.00 3.13
9098 11468 0.457851 TTGGGTGCAGTTTGTTTCCG 59.542 50.000 0.00 0.00 0.00 4.30
9101 11471 1.677052 GGGTGCAGTTTGTTTCCGTTA 59.323 47.619 0.00 0.00 0.00 3.18
9103 11473 3.243602 GGGTGCAGTTTGTTTCCGTTAAT 60.244 43.478 0.00 0.00 0.00 1.40
9104 11474 3.733727 GGTGCAGTTTGTTTCCGTTAATG 59.266 43.478 0.00 0.00 0.00 1.90
9105 11475 4.498345 GGTGCAGTTTGTTTCCGTTAATGA 60.498 41.667 0.00 0.00 0.00 2.57
9106 11476 5.219633 GTGCAGTTTGTTTCCGTTAATGAT 58.780 37.500 0.00 0.00 0.00 2.45
9128 11498 7.509546 TGATTTTATTTTGGTTGGTAGGCAAA 58.490 30.769 0.00 0.00 0.00 3.68
9136 11506 4.469657 TGGTTGGTAGGCAAATGGATATC 58.530 43.478 0.00 0.00 0.00 1.63
9138 11508 5.079643 GGTTGGTAGGCAAATGGATATCAT 58.920 41.667 4.83 0.00 37.79 2.45
9140 11510 6.719370 GGTTGGTAGGCAAATGGATATCATTA 59.281 38.462 4.83 0.00 44.68 1.90
9142 11512 9.461312 GTTGGTAGGCAAATGGATATCATTATA 57.539 33.333 4.83 0.00 44.68 0.98
9143 11513 9.461312 TTGGTAGGCAAATGGATATCATTATAC 57.539 33.333 4.83 5.16 44.68 1.47
9144 11514 8.835734 TGGTAGGCAAATGGATATCATTATACT 58.164 33.333 4.83 4.88 44.68 2.12
9146 11516 9.331282 GTAGGCAAATGGATATCATTATACTCC 57.669 37.037 4.83 0.00 44.68 3.85
9189 12708 2.178580 CTTACTTGGGTGGGTACGGTA 58.821 52.381 0.00 0.00 0.00 4.02
9190 12709 2.548464 TACTTGGGTGGGTACGGTAT 57.452 50.000 0.00 0.00 0.00 2.73
9191 12710 1.197812 ACTTGGGTGGGTACGGTATC 58.802 55.000 0.00 0.00 0.00 2.24
9192 12711 0.103572 CTTGGGTGGGTACGGTATCG 59.896 60.000 0.00 0.00 43.02 2.92
9224 12751 2.662596 CTGGGAAGCTGCACCGTA 59.337 61.111 1.02 0.00 0.00 4.02
9225 12752 1.741770 CTGGGAAGCTGCACCGTAC 60.742 63.158 1.02 0.00 0.00 3.67
9226 12753 2.813908 GGGAAGCTGCACCGTACG 60.814 66.667 8.69 8.69 0.00 3.67
9227 12754 2.048503 GGAAGCTGCACCGTACGT 60.049 61.111 15.21 0.00 0.00 3.57
9287 14417 4.168291 CAGCCTCCGCCTCCCTTC 62.168 72.222 0.00 0.00 34.57 3.46
9290 14420 4.806339 CCTCCGCCTCCCTTCCCT 62.806 72.222 0.00 0.00 0.00 4.20
9339 14469 2.375345 GCCTCCCTCCCCAAATCGA 61.375 63.158 0.00 0.00 0.00 3.59
9344 14474 0.773644 CCCTCCCCAAATCGATCCAT 59.226 55.000 0.00 0.00 0.00 3.41
9346 14476 1.271597 CCTCCCCAAATCGATCCATCC 60.272 57.143 0.00 0.00 0.00 3.51
9347 14477 1.421268 CTCCCCAAATCGATCCATCCA 59.579 52.381 0.00 0.00 0.00 3.41
9348 14478 1.849692 TCCCCAAATCGATCCATCCAA 59.150 47.619 0.00 0.00 0.00 3.53
9349 14479 2.446666 TCCCCAAATCGATCCATCCAAT 59.553 45.455 0.00 0.00 0.00 3.16
9350 14480 2.821969 CCCCAAATCGATCCATCCAATC 59.178 50.000 0.00 0.00 0.00 2.67
9351 14481 2.821969 CCCAAATCGATCCATCCAATCC 59.178 50.000 0.00 0.00 0.00 3.01
9352 14482 3.489355 CCAAATCGATCCATCCAATCCA 58.511 45.455 0.00 0.00 0.00 3.41
9353 14483 3.890756 CCAAATCGATCCATCCAATCCAA 59.109 43.478 0.00 0.00 0.00 3.53
9369 14499 0.878416 CCAAAGCGTTCCAAATCGGA 59.122 50.000 0.00 0.00 44.40 4.55
9462 14749 2.551912 CCACAACCCGCACAAGGAC 61.552 63.158 0.00 0.00 0.00 3.85
9596 14883 4.899239 GGTGGCCAGGAGATCGCG 62.899 72.222 5.11 0.00 0.00 5.87
9669 14962 2.034053 TGGCGATTTCGTTGAAAAGCTT 59.966 40.909 16.71 0.00 42.22 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 2.042435 CCCTCTCTTCTCCCCGCT 60.042 66.667 0.00 0.00 0.00 5.52
103 104 1.764454 GCCCCTCCCTCTCTTCTCC 60.764 68.421 0.00 0.00 0.00 3.71
105 106 0.944999 TATGCCCCTCCCTCTCTTCT 59.055 55.000 0.00 0.00 0.00 2.85
106 107 1.052617 GTATGCCCCTCCCTCTCTTC 58.947 60.000 0.00 0.00 0.00 2.87
108 109 1.237458 GGTATGCCCCTCCCTCTCT 59.763 63.158 0.00 0.00 0.00 3.10
110 111 1.237458 GAGGTATGCCCCTCCCTCT 59.763 63.158 0.00 0.00 44.49 3.69
178 193 2.815647 CGCTGGGAAGAAGACGGC 60.816 66.667 0.00 0.00 0.00 5.68
284 299 3.775654 CCGCTCTGTCTGTCCCCC 61.776 72.222 0.00 0.00 0.00 5.40
285 300 2.680352 TCCGCTCTGTCTGTCCCC 60.680 66.667 0.00 0.00 0.00 4.81
286 301 2.716017 CCTCCGCTCTGTCTGTCCC 61.716 68.421 0.00 0.00 0.00 4.46
287 302 2.888863 CCTCCGCTCTGTCTGTCC 59.111 66.667 0.00 0.00 0.00 4.02
288 303 2.183046 GCCTCCGCTCTGTCTGTC 59.817 66.667 0.00 0.00 0.00 3.51
289 304 3.753434 CGCCTCCGCTCTGTCTGT 61.753 66.667 0.00 0.00 0.00 3.41
290 305 4.504916 CCGCCTCCGCTCTGTCTG 62.505 72.222 0.00 0.00 0.00 3.51
366 381 1.814169 GGCCGGTCGGAGTGAAATC 60.814 63.158 14.15 0.00 37.50 2.17
367 382 2.267961 GGCCGGTCGGAGTGAAAT 59.732 61.111 14.15 0.00 37.50 2.17
368 383 4.011517 GGGCCGGTCGGAGTGAAA 62.012 66.667 14.15 0.00 37.50 2.69
444 566 3.452627 GGTTATGGAAGAAGAGAGCAGGA 59.547 47.826 0.00 0.00 0.00 3.86
757 913 2.686835 AGAGAGGAGCACAGGGGC 60.687 66.667 0.00 0.00 0.00 5.80
852 1047 2.202756 GCCGCTCCGACAACTAGG 60.203 66.667 0.00 0.00 0.00 3.02
878 1078 4.373116 GCGAGAGTTCCGCCACCA 62.373 66.667 0.00 0.00 46.22 4.17
896 1096 1.749638 GCTCTCGTCGGGGAAGAGA 60.750 63.158 11.68 10.13 42.80 3.10
899 1099 4.856607 GCGCTCTCGTCGGGGAAG 62.857 72.222 0.00 0.00 38.14 3.46
970 1192 3.853330 CGCACGCCCTGTTCATCG 61.853 66.667 0.00 0.00 0.00 3.84
1077 1299 3.412879 GAGGACGTAGGCGCTGGAC 62.413 68.421 7.64 1.72 42.83 4.02
1216 1464 2.521958 TAAGAAGGAGCTGGGCGTGC 62.522 60.000 0.00 0.00 0.00 5.34
1224 1472 1.096416 CGACGAGGTAAGAAGGAGCT 58.904 55.000 0.00 0.00 0.00 4.09
1313 1582 4.581391 CCCCCACTGAAGGTAGGT 57.419 61.111 0.00 0.00 0.00 3.08
1508 1779 2.651190 TCCATCCATCCATCCATCCAT 58.349 47.619 0.00 0.00 0.00 3.41
1509 1780 2.136974 TCCATCCATCCATCCATCCA 57.863 50.000 0.00 0.00 0.00 3.41
1510 1781 2.421107 CGATCCATCCATCCATCCATCC 60.421 54.545 0.00 0.00 0.00 3.51
1511 1782 2.502947 TCGATCCATCCATCCATCCATC 59.497 50.000 0.00 0.00 0.00 3.51
1512 1783 2.238144 GTCGATCCATCCATCCATCCAT 59.762 50.000 0.00 0.00 0.00 3.41
1513 1784 1.625315 GTCGATCCATCCATCCATCCA 59.375 52.381 0.00 0.00 0.00 3.41
1514 1785 1.065854 GGTCGATCCATCCATCCATCC 60.066 57.143 0.00 0.00 35.97 3.51
1515 1786 1.065854 GGGTCGATCCATCCATCCATC 60.066 57.143 10.69 0.00 38.11 3.51
1516 1787 0.987294 GGGTCGATCCATCCATCCAT 59.013 55.000 10.69 0.00 38.11 3.41
1517 1788 1.127567 GGGGTCGATCCATCCATCCA 61.128 60.000 18.43 0.00 38.11 3.41
1518 1789 1.679898 GGGGTCGATCCATCCATCC 59.320 63.158 18.43 0.00 38.11 3.51
1519 1790 0.838122 AGGGGGTCGATCCATCCATC 60.838 60.000 18.43 0.00 38.11 3.51
1520 1791 0.401979 AAGGGGGTCGATCCATCCAT 60.402 55.000 18.43 0.00 38.11 3.41
1521 1792 1.004230 AAGGGGGTCGATCCATCCA 59.996 57.895 18.43 0.00 38.11 3.41
1522 1793 1.345715 ACAAGGGGGTCGATCCATCC 61.346 60.000 18.43 9.66 38.11 3.51
1523 1794 1.420430 TACAAGGGGGTCGATCCATC 58.580 55.000 18.43 8.17 38.11 3.51
1756 2369 8.143835 AGTAAAGAAATCAATTCAACCAACAGG 58.856 33.333 0.00 0.00 40.72 4.00
2296 3188 9.557061 TTAGTACAGTACAGGTATGAGTATGAG 57.443 37.037 13.37 0.00 0.00 2.90
2300 3192 9.049523 CGAATTAGTACAGTACAGGTATGAGTA 57.950 37.037 13.37 0.00 0.00 2.59
2301 3193 7.555554 ACGAATTAGTACAGTACAGGTATGAGT 59.444 37.037 13.37 1.13 0.00 3.41
2302 3194 7.856398 CACGAATTAGTACAGTACAGGTATGAG 59.144 40.741 13.37 0.56 0.00 2.90
2303 3195 7.201758 CCACGAATTAGTACAGTACAGGTATGA 60.202 40.741 13.37 0.00 0.00 2.15
2304 3196 6.916387 CCACGAATTAGTACAGTACAGGTATG 59.084 42.308 13.37 1.63 0.00 2.39
2305 3197 6.604795 ACCACGAATTAGTACAGTACAGGTAT 59.395 38.462 13.37 0.00 0.00 2.73
2306 3198 5.945784 ACCACGAATTAGTACAGTACAGGTA 59.054 40.000 13.37 0.00 0.00 3.08
2307 3199 4.768968 ACCACGAATTAGTACAGTACAGGT 59.231 41.667 13.37 4.84 0.00 4.00
6367 7278 5.641789 ACCTTGTTACCACTAACCTTCTT 57.358 39.130 0.00 0.00 32.52 2.52
6368 7279 5.641789 AACCTTGTTACCACTAACCTTCT 57.358 39.130 0.00 0.00 32.52 2.85
6369 7280 6.426025 CACTAACCTTGTTACCACTAACCTTC 59.574 42.308 0.00 0.00 32.52 3.46
6370 7281 6.293698 CACTAACCTTGTTACCACTAACCTT 58.706 40.000 0.00 0.00 32.52 3.50
6371 7282 5.744007 GCACTAACCTTGTTACCACTAACCT 60.744 44.000 0.00 0.00 32.52 3.50
6372 7283 4.453478 GCACTAACCTTGTTACCACTAACC 59.547 45.833 0.00 0.00 32.52 2.85
6373 7284 5.178809 CAGCACTAACCTTGTTACCACTAAC 59.821 44.000 0.00 0.00 33.92 2.34
6374 7285 5.302360 CAGCACTAACCTTGTTACCACTAA 58.698 41.667 0.00 0.00 0.00 2.24
6375 7286 4.801581 GCAGCACTAACCTTGTTACCACTA 60.802 45.833 0.00 0.00 0.00 2.74
6376 7287 3.740115 CAGCACTAACCTTGTTACCACT 58.260 45.455 0.00 0.00 0.00 4.00
6377 7288 2.225727 GCAGCACTAACCTTGTTACCAC 59.774 50.000 0.00 0.00 0.00 4.16
6378 7289 2.158740 TGCAGCACTAACCTTGTTACCA 60.159 45.455 0.00 0.00 0.00 3.25
6379 7290 2.500229 TGCAGCACTAACCTTGTTACC 58.500 47.619 0.00 0.00 0.00 2.85
6380 7291 4.766404 ATTGCAGCACTAACCTTGTTAC 57.234 40.909 0.00 0.00 0.00 2.50
6381 7292 5.534654 AGAAATTGCAGCACTAACCTTGTTA 59.465 36.000 0.00 0.00 0.00 2.41
6395 7306 5.865552 CCTGTCAATAACCAAGAAATTGCAG 59.134 40.000 0.00 0.00 36.11 4.41
6704 7695 2.992543 CAGAGCAGAGTTAGAGTGCAAC 59.007 50.000 0.00 0.00 39.80 4.17
6890 7883 7.938563 TTAAACATTTGTGCTGAATTGGTAC 57.061 32.000 0.00 0.00 0.00 3.34
6923 7916 4.895889 TCGACATCAATAAGGATCAGAGGT 59.104 41.667 0.00 0.00 0.00 3.85
7353 8346 2.890945 GGTTGAAATGCTTGGTACTGGT 59.109 45.455 0.00 0.00 0.00 4.00
7402 8401 6.352516 AGAAGAAGAAGAAGAAGAAGCACAA 58.647 36.000 0.00 0.00 0.00 3.33
7434 8436 6.520272 TCACCAGAAGAAGAAGAAGAAGAAG 58.480 40.000 0.00 0.00 0.00 2.85
7435 8437 6.485830 TCACCAGAAGAAGAAGAAGAAGAA 57.514 37.500 0.00 0.00 0.00 2.52
7436 8438 5.510520 GCTCACCAGAAGAAGAAGAAGAAGA 60.511 44.000 0.00 0.00 0.00 2.87
7437 8439 4.690280 GCTCACCAGAAGAAGAAGAAGAAG 59.310 45.833 0.00 0.00 0.00 2.85
7438 8440 4.346418 AGCTCACCAGAAGAAGAAGAAGAA 59.654 41.667 0.00 0.00 0.00 2.52
7439 8441 3.900601 AGCTCACCAGAAGAAGAAGAAGA 59.099 43.478 0.00 0.00 0.00 2.87
7440 8442 3.995705 CAGCTCACCAGAAGAAGAAGAAG 59.004 47.826 0.00 0.00 0.00 2.85
7441 8443 3.389329 ACAGCTCACCAGAAGAAGAAGAA 59.611 43.478 0.00 0.00 0.00 2.52
7442 8444 2.968574 ACAGCTCACCAGAAGAAGAAGA 59.031 45.455 0.00 0.00 0.00 2.87
7443 8445 3.399440 ACAGCTCACCAGAAGAAGAAG 57.601 47.619 0.00 0.00 0.00 2.85
7444 8446 3.845781 AACAGCTCACCAGAAGAAGAA 57.154 42.857 0.00 0.00 0.00 2.52
7445 8447 3.118261 ACAAACAGCTCACCAGAAGAAGA 60.118 43.478 0.00 0.00 0.00 2.87
7446 8448 3.209410 ACAAACAGCTCACCAGAAGAAG 58.791 45.455 0.00 0.00 0.00 2.85
7447 8449 3.281727 ACAAACAGCTCACCAGAAGAA 57.718 42.857 0.00 0.00 0.00 2.52
7448 8450 3.281727 AACAAACAGCTCACCAGAAGA 57.718 42.857 0.00 0.00 0.00 2.87
7484 8486 7.596995 TGAAGAAAAGGCCATTAAAAATACACG 59.403 33.333 5.01 0.00 0.00 4.49
7489 8491 7.331687 CGTCATGAAGAAAAGGCCATTAAAAAT 59.668 33.333 5.01 0.00 0.00 1.82
7507 8518 1.150827 CTGCTTCACTGCGTCATGAA 58.849 50.000 0.00 0.00 35.36 2.57
7515 8526 0.742635 GACCCTAGCTGCTTCACTGC 60.743 60.000 7.79 0.00 43.18 4.40
7585 8601 1.401761 AACAGGCACTTGCATCAACA 58.598 45.000 3.15 0.00 44.36 3.33
7740 8759 4.101448 GGGATCGCTGGTGTGCCT 62.101 66.667 1.84 0.00 35.27 4.75
8127 9146 1.139058 ACATCAGTAATCTGGCCGTCC 59.861 52.381 0.00 0.00 41.59 4.79
8369 9401 6.803320 CACAAACTGCCACACTTATAAATCTG 59.197 38.462 0.00 0.00 0.00 2.90
8378 9410 1.832883 TCACACAAACTGCCACACTT 58.167 45.000 0.00 0.00 0.00 3.16
8380 9412 3.138304 TCTATCACACAAACTGCCACAC 58.862 45.455 0.00 0.00 0.00 3.82
8419 9452 2.682352 CACGTCCATGCACCAAATGATA 59.318 45.455 0.00 0.00 0.00 2.15
8422 9455 0.597568 ACACGTCCATGCACCAAATG 59.402 50.000 0.00 0.00 0.00 2.32
8423 9456 0.597568 CACACGTCCATGCACCAAAT 59.402 50.000 0.00 0.00 0.00 2.32
8455 9490 0.179192 CACACACACACACACACAGC 60.179 55.000 0.00 0.00 0.00 4.40
8692 9824 6.267014 GGTACTAGTATTTACCATGAGCCTCA 59.733 42.308 5.75 0.00 38.14 3.86
8693 9825 6.267014 TGGTACTAGTATTTACCATGAGCCTC 59.733 42.308 10.61 0.00 42.35 4.70
8694 9826 6.141083 TGGTACTAGTATTTACCATGAGCCT 58.859 40.000 10.61 0.00 42.35 4.58
8695 9827 6.415206 TGGTACTAGTATTTACCATGAGCC 57.585 41.667 10.61 1.78 42.35 4.70
8713 9846 5.583495 CACTCTGTTAGACTAGCATGGTAC 58.417 45.833 0.00 0.00 0.00 3.34
8717 9850 4.111198 CAGCACTCTGTTAGACTAGCATG 58.889 47.826 0.00 0.00 35.61 4.06
8797 9957 6.597562 ACACTCTACTCTCTTCTATACCTGG 58.402 44.000 0.00 0.00 0.00 4.45
8798 9958 7.441157 CAGACACTCTACTCTCTTCTATACCTG 59.559 44.444 0.00 0.00 0.00 4.00
8822 9993 1.001378 GCAGCTGGTACCAAACAACAG 60.001 52.381 17.11 3.21 0.00 3.16
8823 9994 1.028905 GCAGCTGGTACCAAACAACA 58.971 50.000 17.11 0.00 0.00 3.33
8827 10012 1.537202 CAGAAGCAGCTGGTACCAAAC 59.463 52.381 20.51 11.23 32.26 2.93
8888 10135 2.131854 CTCTCCTCTCCTCTCCTGGTA 58.868 57.143 0.00 0.00 0.00 3.25
8947 10202 6.348376 CCAATCCAATCCAACCAAAATTTTCG 60.348 38.462 0.00 0.00 0.00 3.46
8991 11317 1.133637 TGCCAAAGACACTAGCCCAAA 60.134 47.619 0.00 0.00 0.00 3.28
8992 11318 0.476338 TGCCAAAGACACTAGCCCAA 59.524 50.000 0.00 0.00 0.00 4.12
8993 11319 0.698238 ATGCCAAAGACACTAGCCCA 59.302 50.000 0.00 0.00 0.00 5.36
8994 11320 1.474077 CAATGCCAAAGACACTAGCCC 59.526 52.381 0.00 0.00 0.00 5.19
8995 11321 2.436417 TCAATGCCAAAGACACTAGCC 58.564 47.619 0.00 0.00 0.00 3.93
9058 11428 5.049198 CCAAGACGATATCCACATTCCATTG 60.049 44.000 0.00 0.00 0.00 2.82
9096 11466 8.541133 ACCAACCAAAATAAAATCATTAACGG 57.459 30.769 0.00 0.00 0.00 4.44
9101 11471 7.684529 TGCCTACCAACCAAAATAAAATCATT 58.315 30.769 0.00 0.00 0.00 2.57
9103 11473 6.672266 TGCCTACCAACCAAAATAAAATCA 57.328 33.333 0.00 0.00 0.00 2.57
9104 11474 7.971183 TTTGCCTACCAACCAAAATAAAATC 57.029 32.000 0.00 0.00 31.97 2.17
9105 11475 7.392953 CCATTTGCCTACCAACCAAAATAAAAT 59.607 33.333 0.00 0.00 32.85 1.82
9106 11476 6.712547 CCATTTGCCTACCAACCAAAATAAAA 59.287 34.615 0.00 0.00 32.85 1.52
9113 11483 2.685106 TCCATTTGCCTACCAACCAA 57.315 45.000 0.00 0.00 31.97 3.67
9114 11484 2.917713 ATCCATTTGCCTACCAACCA 57.082 45.000 0.00 0.00 31.97 3.67
9115 11485 4.469657 TGATATCCATTTGCCTACCAACC 58.530 43.478 0.00 0.00 31.97 3.77
9116 11486 6.655078 AATGATATCCATTTGCCTACCAAC 57.345 37.500 0.00 0.00 42.55 3.77
9165 11679 2.774687 GTACCCACCCAAGTAAGTGTG 58.225 52.381 0.00 0.00 31.88 3.82
9173 12692 0.103572 CGATACCGTACCCACCCAAG 59.896 60.000 0.00 0.00 0.00 3.61
9189 12708 3.461061 CCAGCTTCACACATGATACGAT 58.539 45.455 0.00 0.00 33.85 3.73
9190 12709 2.418609 CCCAGCTTCACACATGATACGA 60.419 50.000 0.00 0.00 33.85 3.43
9191 12710 1.935873 CCCAGCTTCACACATGATACG 59.064 52.381 0.00 0.00 33.85 3.06
9192 12711 3.266510 TCCCAGCTTCACACATGATAC 57.733 47.619 0.00 0.00 33.85 2.24
9193 12712 3.877559 CTTCCCAGCTTCACACATGATA 58.122 45.455 0.00 0.00 33.85 2.15
9194 12713 2.719739 CTTCCCAGCTTCACACATGAT 58.280 47.619 0.00 0.00 33.85 2.45
9195 12714 1.883638 GCTTCCCAGCTTCACACATGA 60.884 52.381 0.00 0.00 43.51 3.07
9196 12715 0.524862 GCTTCCCAGCTTCACACATG 59.475 55.000 0.00 0.00 43.51 3.21
9224 12751 0.037605 GGATTCAGGTTCGACCACGT 60.038 55.000 6.78 0.00 41.95 4.49
9225 12752 1.076533 CGGATTCAGGTTCGACCACG 61.077 60.000 6.78 0.00 41.95 4.94
9226 12753 0.245539 TCGGATTCAGGTTCGACCAC 59.754 55.000 6.78 0.00 41.95 4.16
9227 12754 0.530744 CTCGGATTCAGGTTCGACCA 59.469 55.000 6.78 0.00 41.95 4.02
9282 14412 5.045140 TCCAGTGTTATAAAGAAGGGAAGGG 60.045 44.000 0.00 0.00 0.00 3.95
9283 14413 6.062258 TCCAGTGTTATAAAGAAGGGAAGG 57.938 41.667 0.00 0.00 0.00 3.46
9284 14414 6.116126 CCTCCAGTGTTATAAAGAAGGGAAG 58.884 44.000 0.00 0.00 0.00 3.46
9285 14415 5.572885 GCCTCCAGTGTTATAAAGAAGGGAA 60.573 44.000 0.00 0.00 0.00 3.97
9286 14416 4.080526 GCCTCCAGTGTTATAAAGAAGGGA 60.081 45.833 0.00 0.00 0.00 4.20
9287 14417 4.080299 AGCCTCCAGTGTTATAAAGAAGGG 60.080 45.833 0.00 0.00 0.00 3.95
9288 14418 4.878397 CAGCCTCCAGTGTTATAAAGAAGG 59.122 45.833 0.00 0.00 0.00 3.46
9289 14419 4.878397 CCAGCCTCCAGTGTTATAAAGAAG 59.122 45.833 0.00 0.00 0.00 2.85
9290 14420 4.534500 TCCAGCCTCCAGTGTTATAAAGAA 59.466 41.667 0.00 0.00 0.00 2.52
9339 14469 2.442236 ACGCTTTGGATTGGATGGAT 57.558 45.000 0.00 0.00 0.00 3.41
9344 14474 1.988293 TTGGAACGCTTTGGATTGGA 58.012 45.000 0.00 0.00 0.00 3.53
9346 14476 2.916716 CGATTTGGAACGCTTTGGATTG 59.083 45.455 0.00 0.00 0.00 2.67
9347 14477 2.094752 CCGATTTGGAACGCTTTGGATT 60.095 45.455 0.00 0.00 42.00 3.01
9348 14478 1.472480 CCGATTTGGAACGCTTTGGAT 59.528 47.619 0.00 0.00 42.00 3.41
9349 14479 0.878416 CCGATTTGGAACGCTTTGGA 59.122 50.000 0.00 0.00 42.00 3.53
9350 14480 0.878416 TCCGATTTGGAACGCTTTGG 59.122 50.000 0.00 0.00 46.38 3.28
9369 14499 4.211920 TGACGGGTGGATTTTTCTTTCTT 58.788 39.130 0.00 0.00 0.00 2.52
9435 14722 2.418356 GGGTTGTGGTCGTCGTCA 59.582 61.111 0.00 0.00 0.00 4.35
9596 14883 0.905357 ATACACCTGGTGACTGAGCC 59.095 55.000 32.30 0.00 36.96 4.70
9651 14944 4.317291 CGGTTAAGCTTTTCAACGAAATCG 59.683 41.667 3.20 0.00 46.33 3.34
9669 14962 0.599558 CGTCCTCCTTGTCACGGTTA 59.400 55.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.