Multiple sequence alignment - TraesCS4A01G142200

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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 TraesCS4A01G142200 chr4A 100.000 4723 0 0 1 4723 225617014 225612292 0.000000e+00 8722.0
1 TraesCS4A01G142200 chr4A 85.484 1116 116 25 734 1809 700326461 700325352 0.000000e+00 1122.0
2 TraesCS4A01G142200 chr4A 93.870 522 24 5 220 733 568133219 568132698 0.000000e+00 780.0
3 TraesCS4A01G142200 chr4A 93.644 236 15 0 1974 2209 700325320 700325085 2.090000e-93 353.0
4 TraesCS4A01G142200 chr4A 92.342 222 14 1 1 219 35645118 35645339 3.550000e-81 313.0
5 TraesCS4A01G142200 chr7A 96.478 3549 116 6 973 4514 696325781 696322235 0.000000e+00 5853.0
6 TraesCS4A01G142200 chr7A 90.274 329 23 5 733 1059 696325978 696325657 5.650000e-114 422.0
7 TraesCS4A01G142200 chr7A 90.476 294 20 5 1913 2201 125259507 125259797 9.590000e-102 381.0
8 TraesCS4A01G142200 chr7A 94.737 95 4 1 1822 1915 125259271 125259365 3.810000e-31 147.0
9 TraesCS4A01G142200 chr7D 96.798 2592 80 2 2134 4722 185353444 185356035 0.000000e+00 4324.0
10 TraesCS4A01G142200 chr7D 90.764 2317 191 14 2416 4720 619378575 619380880 0.000000e+00 3072.0
11 TraesCS4A01G142200 chr7D 91.863 1020 69 12 730 1744 185352407 185353417 0.000000e+00 1411.0
12 TraesCS4A01G142200 chr7D 93.295 522 30 5 216 733 271185464 271185984 0.000000e+00 765.0
13 TraesCS4A01G142200 chr7D 90.283 566 46 7 733 1293 30490241 30489680 0.000000e+00 732.0
14 TraesCS4A01G142200 chr7D 88.776 294 25 5 1913 2201 120317045 120317335 2.090000e-93 353.0
15 TraesCS4A01G142200 chr7D 95.789 95 3 1 1822 1915 120316809 120316903 8.190000e-33 152.0
16 TraesCS4A01G142200 chr6D 96.605 2592 85 3 2134 4722 28132545 28129954 0.000000e+00 4296.0
17 TraesCS4A01G142200 chr6D 91.005 2368 193 13 2363 4720 433716687 433719044 0.000000e+00 3175.0
18 TraesCS4A01G142200 chr6D 90.675 2370 199 13 2363 4720 18944029 18941670 0.000000e+00 3133.0
19 TraesCS4A01G142200 chr6D 94.036 721 40 1 1027 1744 28133292 28132572 0.000000e+00 1090.0
20 TraesCS4A01G142200 chr6D 90.214 327 25 4 720 1046 28134155 28133836 2.030000e-113 420.0
21 TraesCS4A01G142200 chr6D 92.411 224 13 2 1 220 270844328 270844105 2.740000e-82 316.0
22 TraesCS4A01G142200 chr6D 95.122 41 2 0 3316 3356 18942910 18942870 1.100000e-06 65.8
23 TraesCS4A01G142200 chr6D 95.122 41 2 0 3316 3356 433717805 433717845 1.100000e-06 65.8
24 TraesCS4A01G142200 chr1A 96.430 2437 84 2 2289 4722 576626005 576623569 0.000000e+00 4015.0
25 TraesCS4A01G142200 chr1A 90.376 2369 204 15 2363 4720 493628328 493625973 0.000000e+00 3090.0
26 TraesCS4A01G142200 chr1A 95.160 1343 57 6 935 2272 582877886 582876547 0.000000e+00 2113.0
27 TraesCS4A01G142200 chr1A 89.347 1042 82 19 733 1748 576627358 576626320 0.000000e+00 1282.0
28 TraesCS4A01G142200 chr1A 89.863 365 30 3 733 1097 582878119 582877762 3.330000e-126 462.0
29 TraesCS4A01G142200 chr1A 92.342 222 14 1 1 219 127154516 127154737 3.550000e-81 313.0
30 TraesCS4A01G142200 chr1A 91.892 222 15 1 1 219 245111956 245112177 1.650000e-79 307.0
31 TraesCS4A01G142200 chr5B 96.105 2439 90 3 2289 4722 75248049 75245611 0.000000e+00 3973.0
32 TraesCS4A01G142200 chr5B 92.540 630 46 1 1120 1748 75248993 75248364 0.000000e+00 902.0
33 TraesCS4A01G142200 chr5B 85.673 342 34 7 724 1064 75249610 75249283 3.500000e-91 346.0
34 TraesCS4A01G142200 chr1D 91.431 2369 182 12 2363 4720 349548857 349546499 0.000000e+00 3230.0
35 TraesCS4A01G142200 chr1D 90.372 2368 182 22 2363 4720 225560821 225558490 0.000000e+00 3068.0
36 TraesCS4A01G142200 chr1D 93.617 517 27 2 220 733 92904880 92905393 0.000000e+00 767.0
37 TraesCS4A01G142200 chr1D 93.274 223 11 2 1 219 155564404 155564626 4.560000e-85 326.0
38 TraesCS4A01G142200 chr5A 91.251 2366 191 10 2363 4720 456479528 456481885 0.000000e+00 3208.0
39 TraesCS4A01G142200 chr5A 85.665 579 53 18 728 1281 68559515 68558942 2.450000e-162 582.0
40 TraesCS4A01G142200 chr5A 92.342 222 14 1 1 219 117590283 117590504 3.550000e-81 313.0
41 TraesCS4A01G142200 chr5A 91.765 85 7 0 2257 2341 224559739 224559655 8.300000e-23 119.0
42 TraesCS4A01G142200 chr7B 91.178 2369 188 13 2363 4720 4400829 4398471 0.000000e+00 3197.0
43 TraesCS4A01G142200 chr7B 89.324 281 20 7 1927 2201 81687729 81688005 1.260000e-90 344.0
44 TraesCS4A01G142200 chr7B 94.681 94 4 1 1823 1915 81687480 81687573 1.370000e-30 145.0
45 TraesCS4A01G142200 chr7B 89.412 85 9 0 2257 2341 508295055 508294971 1.800000e-19 108.0
46 TraesCS4A01G142200 chr2D 90.882 2369 193 14 2363 4720 568723296 568725652 0.000000e+00 3157.0
47 TraesCS4A01G142200 chr2D 93.629 518 28 2 219 733 261375360 261374845 0.000000e+00 769.0
48 TraesCS4A01G142200 chr3D 90.756 2369 190 18 2363 4720 349857175 349859525 0.000000e+00 3134.0
49 TraesCS4A01G142200 chr3D 94.626 521 24 2 216 733 121677110 121676591 0.000000e+00 804.0
50 TraesCS4A01G142200 chr4B 90.182 2363 192 12 2368 4720 253777234 253774902 0.000000e+00 3042.0
51 TraesCS4A01G142200 chr3B 90.000 1030 85 13 733 1744 490024486 490023457 0.000000e+00 1315.0
52 TraesCS4A01G142200 chrUn 92.567 713 52 1 1017 1729 382168103 382168814 0.000000e+00 1022.0
53 TraesCS4A01G142200 chrUn 87.629 291 18 7 733 1005 346762635 346762925 5.900000e-84 322.0
54 TraesCS4A01G142200 chr4D 94.242 521 25 2 216 733 168224436 168223918 0.000000e+00 791.0
55 TraesCS4A01G142200 chr4D 93.474 521 28 2 216 733 123066117 123065600 0.000000e+00 769.0
56 TraesCS4A01G142200 chr4D 92.817 529 33 4 209 733 335532582 335532055 0.000000e+00 761.0
57 TraesCS4A01G142200 chr4D 92.411 224 13 2 1 220 310059109 310059332 2.740000e-82 316.0
58 TraesCS4A01G142200 chr4D 92.377 223 13 2 1 219 310051836 310052058 9.870000e-82 315.0
59 TraesCS4A01G142200 chr4D 96.875 32 1 0 4077 4108 205902569 205902538 2.000000e-03 54.7
60 TraesCS4A01G142200 chr2A 93.462 520 28 2 220 733 650496944 650496425 0.000000e+00 767.0
61 TraesCS4A01G142200 chr3A 92.342 222 13 2 1 219 246573880 246574100 3.550000e-81 313.0
62 TraesCS4A01G142200 chr6B 100.000 40 0 0 1675 1714 40426791 40426830 1.820000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G142200 chr4A 225612292 225617014 4722 True 8722.000000 8722 100.000000 1 4723 1 chr4A.!!$R1 4722
1 TraesCS4A01G142200 chr4A 568132698 568133219 521 True 780.000000 780 93.870000 220 733 1 chr4A.!!$R2 513
2 TraesCS4A01G142200 chr4A 700325085 700326461 1376 True 737.500000 1122 89.564000 734 2209 2 chr4A.!!$R3 1475
3 TraesCS4A01G142200 chr7A 696322235 696325978 3743 True 3137.500000 5853 93.376000 733 4514 2 chr7A.!!$R1 3781
4 TraesCS4A01G142200 chr7A 125259271 125259797 526 False 264.000000 381 92.606500 1822 2201 2 chr7A.!!$F1 379
5 TraesCS4A01G142200 chr7D 619378575 619380880 2305 False 3072.000000 3072 90.764000 2416 4720 1 chr7D.!!$F2 2304
6 TraesCS4A01G142200 chr7D 185352407 185356035 3628 False 2867.500000 4324 94.330500 730 4722 2 chr7D.!!$F4 3992
7 TraesCS4A01G142200 chr7D 271185464 271185984 520 False 765.000000 765 93.295000 216 733 1 chr7D.!!$F1 517
8 TraesCS4A01G142200 chr7D 30489680 30490241 561 True 732.000000 732 90.283000 733 1293 1 chr7D.!!$R1 560
9 TraesCS4A01G142200 chr7D 120316809 120317335 526 False 252.500000 353 92.282500 1822 2201 2 chr7D.!!$F3 379
10 TraesCS4A01G142200 chr6D 28129954 28134155 4201 True 1935.333333 4296 93.618333 720 4722 3 chr6D.!!$R3 4002
11 TraesCS4A01G142200 chr6D 433716687 433719044 2357 False 1620.400000 3175 93.063500 2363 4720 2 chr6D.!!$F1 2357
12 TraesCS4A01G142200 chr6D 18941670 18944029 2359 True 1599.400000 3133 92.898500 2363 4720 2 chr6D.!!$R2 2357
13 TraesCS4A01G142200 chr1A 493625973 493628328 2355 True 3090.000000 3090 90.376000 2363 4720 1 chr1A.!!$R1 2357
14 TraesCS4A01G142200 chr1A 576623569 576627358 3789 True 2648.500000 4015 92.888500 733 4722 2 chr1A.!!$R2 3989
15 TraesCS4A01G142200 chr1A 582876547 582878119 1572 True 1287.500000 2113 92.511500 733 2272 2 chr1A.!!$R3 1539
16 TraesCS4A01G142200 chr5B 75245611 75249610 3999 True 1740.333333 3973 91.439333 724 4722 3 chr5B.!!$R1 3998
17 TraesCS4A01G142200 chr1D 349546499 349548857 2358 True 3230.000000 3230 91.431000 2363 4720 1 chr1D.!!$R2 2357
18 TraesCS4A01G142200 chr1D 225558490 225560821 2331 True 3068.000000 3068 90.372000 2363 4720 1 chr1D.!!$R1 2357
19 TraesCS4A01G142200 chr1D 92904880 92905393 513 False 767.000000 767 93.617000 220 733 1 chr1D.!!$F1 513
20 TraesCS4A01G142200 chr5A 456479528 456481885 2357 False 3208.000000 3208 91.251000 2363 4720 1 chr5A.!!$F2 2357
21 TraesCS4A01G142200 chr5A 68558942 68559515 573 True 582.000000 582 85.665000 728 1281 1 chr5A.!!$R1 553
22 TraesCS4A01G142200 chr7B 4398471 4400829 2358 True 3197.000000 3197 91.178000 2363 4720 1 chr7B.!!$R1 2357
23 TraesCS4A01G142200 chr7B 81687480 81688005 525 False 244.500000 344 92.002500 1823 2201 2 chr7B.!!$F1 378
24 TraesCS4A01G142200 chr2D 568723296 568725652 2356 False 3157.000000 3157 90.882000 2363 4720 1 chr2D.!!$F1 2357
25 TraesCS4A01G142200 chr2D 261374845 261375360 515 True 769.000000 769 93.629000 219 733 1 chr2D.!!$R1 514
26 TraesCS4A01G142200 chr3D 349857175 349859525 2350 False 3134.000000 3134 90.756000 2363 4720 1 chr3D.!!$F1 2357
27 TraesCS4A01G142200 chr3D 121676591 121677110 519 True 804.000000 804 94.626000 216 733 1 chr3D.!!$R1 517
28 TraesCS4A01G142200 chr4B 253774902 253777234 2332 True 3042.000000 3042 90.182000 2368 4720 1 chr4B.!!$R1 2352
29 TraesCS4A01G142200 chr3B 490023457 490024486 1029 True 1315.000000 1315 90.000000 733 1744 1 chr3B.!!$R1 1011
30 TraesCS4A01G142200 chrUn 382168103 382168814 711 False 1022.000000 1022 92.567000 1017 1729 1 chrUn.!!$F2 712
31 TraesCS4A01G142200 chr4D 168223918 168224436 518 True 791.000000 791 94.242000 216 733 1 chr4D.!!$R2 517
32 TraesCS4A01G142200 chr4D 123065600 123066117 517 True 769.000000 769 93.474000 216 733 1 chr4D.!!$R1 517
33 TraesCS4A01G142200 chr4D 335532055 335532582 527 True 761.000000 761 92.817000 209 733 1 chr4D.!!$R4 524
34 TraesCS4A01G142200 chr2A 650496425 650496944 519 True 767.000000 767 93.462000 220 733 1 chr2A.!!$R1 513

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
201 202 0.105964 CACAAACTCGGTGGGACTGA 59.894 55.000 0.00 0.00 32.65 3.41 F
716 732 0.250513 GACGAAGGCTCCCAAGTGAT 59.749 55.000 0.00 0.00 0.00 3.06 F
1583 2361 0.392706 TCTCTCAAGTTGCAAGCCGA 59.607 50.000 0.00 0.00 0.00 5.54 F
1666 2444 1.217882 GGAGACGACACCTGTGTTTG 58.782 55.000 4.16 3.53 45.05 2.93 F
2478 3502 1.768870 TGTTAGGAAGCTAGGGATGGC 59.231 52.381 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 2148 0.321564 CAATGTTCAGAGACCGGGCA 60.322 55.000 11.69 0.0 0.0 5.36 R
2461 3485 0.267658 TGGCCATCCCTAGCTTCCTA 59.732 55.000 0.00 0.0 0.0 2.94 R
2948 3984 0.895100 GCTGGTGGTGCTCATTGGAA 60.895 55.000 0.00 0.0 0.0 3.53 R
3311 4347 1.133513 TGCACCACCTCTTCAACCAAT 60.134 47.619 0.00 0.0 0.0 3.16 R
4425 5494 3.295093 TGGCTGAAATTGAAGTGTTCCA 58.705 40.909 0.00 0.0 0.0 3.53 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
19 20 2.270352 CTCCACACAAAACCTAGCCA 57.730 50.000 0.00 0.00 0.00 4.75
20 21 2.795329 CTCCACACAAAACCTAGCCAT 58.205 47.619 0.00 0.00 0.00 4.40
21 22 3.157087 CTCCACACAAAACCTAGCCATT 58.843 45.455 0.00 0.00 0.00 3.16
22 23 4.331968 CTCCACACAAAACCTAGCCATTA 58.668 43.478 0.00 0.00 0.00 1.90
23 24 4.929479 TCCACACAAAACCTAGCCATTAT 58.071 39.130 0.00 0.00 0.00 1.28
24 25 6.068461 TCCACACAAAACCTAGCCATTATA 57.932 37.500 0.00 0.00 0.00 0.98
25 26 5.883673 TCCACACAAAACCTAGCCATTATAC 59.116 40.000 0.00 0.00 0.00 1.47
26 27 5.650266 CCACACAAAACCTAGCCATTATACA 59.350 40.000 0.00 0.00 0.00 2.29
27 28 6.404293 CCACACAAAACCTAGCCATTATACAC 60.404 42.308 0.00 0.00 0.00 2.90
28 29 6.150307 CACACAAAACCTAGCCATTATACACA 59.850 38.462 0.00 0.00 0.00 3.72
29 30 6.717540 ACACAAAACCTAGCCATTATACACAA 59.282 34.615 0.00 0.00 0.00 3.33
30 31 7.396055 ACACAAAACCTAGCCATTATACACAAT 59.604 33.333 0.00 0.00 0.00 2.71
31 32 8.250332 CACAAAACCTAGCCATTATACACAATT 58.750 33.333 0.00 0.00 0.00 2.32
32 33 8.811994 ACAAAACCTAGCCATTATACACAATTT 58.188 29.630 0.00 0.00 0.00 1.82
35 36 8.459911 AACCTAGCCATTATACACAATTTACC 57.540 34.615 0.00 0.00 0.00 2.85
36 37 7.579105 ACCTAGCCATTATACACAATTTACCA 58.421 34.615 0.00 0.00 0.00 3.25
37 38 8.056400 ACCTAGCCATTATACACAATTTACCAA 58.944 33.333 0.00 0.00 0.00 3.67
38 39 8.908903 CCTAGCCATTATACACAATTTACCAAA 58.091 33.333 0.00 0.00 0.00 3.28
39 40 9.730420 CTAGCCATTATACACAATTTACCAAAC 57.270 33.333 0.00 0.00 0.00 2.93
40 41 8.361169 AGCCATTATACACAATTTACCAAACT 57.639 30.769 0.00 0.00 0.00 2.66
41 42 8.466798 AGCCATTATACACAATTTACCAAACTC 58.533 33.333 0.00 0.00 0.00 3.01
42 43 8.247562 GCCATTATACACAATTTACCAAACTCA 58.752 33.333 0.00 0.00 0.00 3.41
47 48 5.852827 ACACAATTTACCAAACTCAATGGG 58.147 37.500 0.00 0.00 42.48 4.00
48 49 5.600484 ACACAATTTACCAAACTCAATGGGA 59.400 36.000 0.00 0.00 42.48 4.37
49 50 5.925969 CACAATTTACCAAACTCAATGGGAC 59.074 40.000 0.00 0.00 42.48 4.46
50 51 5.011635 ACAATTTACCAAACTCAATGGGACC 59.988 40.000 0.00 0.00 42.48 4.46
51 52 3.885976 TTACCAAACTCAATGGGACCA 57.114 42.857 0.00 0.00 42.48 4.02
52 53 2.765689 ACCAAACTCAATGGGACCAA 57.234 45.000 0.00 0.00 42.48 3.67
53 54 3.039252 ACCAAACTCAATGGGACCAAA 57.961 42.857 0.00 0.00 42.48 3.28
54 55 3.586429 ACCAAACTCAATGGGACCAAAT 58.414 40.909 0.00 0.00 42.48 2.32
55 56 3.578282 ACCAAACTCAATGGGACCAAATC 59.422 43.478 0.00 0.00 42.48 2.17
56 57 3.577848 CCAAACTCAATGGGACCAAATCA 59.422 43.478 0.00 0.00 34.15 2.57
57 58 4.223477 CCAAACTCAATGGGACCAAATCAT 59.777 41.667 0.00 0.00 34.15 2.45
58 59 5.172934 CAAACTCAATGGGACCAAATCATG 58.827 41.667 0.00 0.00 0.00 3.07
59 60 4.320546 ACTCAATGGGACCAAATCATGA 57.679 40.909 0.00 0.00 0.00 3.07
60 61 4.676109 ACTCAATGGGACCAAATCATGAA 58.324 39.130 0.00 0.00 0.00 2.57
61 62 5.085920 ACTCAATGGGACCAAATCATGAAA 58.914 37.500 0.00 0.00 0.00 2.69
62 63 5.047092 ACTCAATGGGACCAAATCATGAAAC 60.047 40.000 0.00 0.00 0.00 2.78
63 64 5.085920 TCAATGGGACCAAATCATGAAACT 58.914 37.500 0.00 0.00 0.00 2.66
64 65 5.185635 TCAATGGGACCAAATCATGAAACTC 59.814 40.000 0.00 0.00 0.00 3.01
65 66 4.111255 TGGGACCAAATCATGAAACTCA 57.889 40.909 0.00 0.00 0.00 3.41
66 67 4.081406 TGGGACCAAATCATGAAACTCAG 58.919 43.478 0.00 0.00 0.00 3.35
67 68 4.082125 GGGACCAAATCATGAAACTCAGT 58.918 43.478 0.00 0.00 0.00 3.41
68 69 4.156739 GGGACCAAATCATGAAACTCAGTC 59.843 45.833 0.00 2.63 0.00 3.51
69 70 4.761739 GGACCAAATCATGAAACTCAGTCA 59.238 41.667 0.00 0.00 0.00 3.41
70 71 5.106396 GGACCAAATCATGAAACTCAGTCAG 60.106 44.000 0.00 0.00 0.00 3.51
71 72 5.624159 ACCAAATCATGAAACTCAGTCAGA 58.376 37.500 0.00 0.00 0.00 3.27
72 73 5.471456 ACCAAATCATGAAACTCAGTCAGAC 59.529 40.000 0.00 0.00 0.00 3.51
73 74 5.106396 CCAAATCATGAAACTCAGTCAGACC 60.106 44.000 0.00 0.00 0.00 3.85
74 75 3.303881 TCATGAAACTCAGTCAGACCG 57.696 47.619 0.00 0.00 0.00 4.79
75 76 2.890945 TCATGAAACTCAGTCAGACCGA 59.109 45.455 0.00 0.00 0.00 4.69
76 77 2.795175 TGAAACTCAGTCAGACCGAC 57.205 50.000 0.00 0.00 45.77 4.79
89 90 5.916969 GTCAGACCGACTTAGTTCAAAATG 58.083 41.667 0.00 0.00 41.81 2.32
90 91 5.465724 GTCAGACCGACTTAGTTCAAAATGT 59.534 40.000 0.00 0.00 41.81 2.71
91 92 5.465390 TCAGACCGACTTAGTTCAAAATGTG 59.535 40.000 0.00 0.00 0.00 3.21
92 93 5.465390 CAGACCGACTTAGTTCAAAATGTGA 59.535 40.000 0.00 0.00 0.00 3.58
93 94 6.018262 CAGACCGACTTAGTTCAAAATGTGAA 60.018 38.462 0.00 0.00 44.20 3.18
106 107 8.568732 TTCAAAATGTGAACGTTAGGATTTTC 57.431 30.769 15.46 0.00 41.47 2.29
107 108 6.853872 TCAAAATGTGAACGTTAGGATTTTCG 59.146 34.615 15.46 12.59 31.51 3.46
108 109 4.939509 ATGTGAACGTTAGGATTTTCGG 57.060 40.909 0.00 0.00 0.00 4.30
109 110 3.731089 TGTGAACGTTAGGATTTTCGGT 58.269 40.909 0.00 0.00 0.00 4.69
110 111 3.495377 TGTGAACGTTAGGATTTTCGGTG 59.505 43.478 0.00 0.00 0.00 4.94
111 112 3.068560 TGAACGTTAGGATTTTCGGTGG 58.931 45.455 0.00 0.00 0.00 4.61
112 113 2.103537 ACGTTAGGATTTTCGGTGGG 57.896 50.000 0.00 0.00 0.00 4.61
113 114 1.624813 ACGTTAGGATTTTCGGTGGGA 59.375 47.619 0.00 0.00 0.00 4.37
114 115 2.004733 CGTTAGGATTTTCGGTGGGAC 58.995 52.381 0.00 0.00 0.00 4.46
115 116 2.362736 GTTAGGATTTTCGGTGGGACC 58.637 52.381 0.00 0.00 34.05 4.46
124 125 4.857251 GGTGGGACCGACATGATC 57.143 61.111 9.04 0.00 0.00 2.92
125 126 1.904771 GGTGGGACCGACATGATCA 59.095 57.895 9.04 0.00 0.00 2.92
126 127 0.251916 GGTGGGACCGACATGATCAA 59.748 55.000 9.04 0.00 0.00 2.57
127 128 1.369625 GTGGGACCGACATGATCAAC 58.630 55.000 0.00 0.00 0.00 3.18
128 129 1.066143 GTGGGACCGACATGATCAACT 60.066 52.381 0.00 0.00 0.00 3.16
129 130 1.207089 TGGGACCGACATGATCAACTC 59.793 52.381 0.00 0.00 0.00 3.01
130 131 1.560923 GGACCGACATGATCAACTCG 58.439 55.000 15.23 15.23 0.00 4.18
132 133 2.977700 CCGACATGATCAACTCGGG 58.022 57.895 26.15 14.02 41.69 5.14
133 134 0.459899 CCGACATGATCAACTCGGGA 59.540 55.000 26.15 0.00 41.69 5.14
134 135 1.560923 CGACATGATCAACTCGGGAC 58.439 55.000 14.63 0.00 0.00 4.46
135 136 1.802880 CGACATGATCAACTCGGGACC 60.803 57.143 14.63 0.00 0.00 4.46
136 137 0.175760 ACATGATCAACTCGGGACCG 59.824 55.000 3.96 3.96 41.35 4.79
137 138 0.459899 CATGATCAACTCGGGACCGA 59.540 55.000 13.40 13.40 46.87 4.69
145 146 3.521605 TCGGGACCGATGTGCTAG 58.478 61.111 9.76 0.00 44.01 3.42
146 147 2.125326 TCGGGACCGATGTGCTAGG 61.125 63.158 9.76 0.00 44.01 3.02
147 148 2.822399 GGGACCGATGTGCTAGGG 59.178 66.667 0.00 0.00 32.62 3.53
148 149 2.064581 GGGACCGATGTGCTAGGGT 61.065 63.158 0.00 0.00 34.94 4.34
149 150 1.623542 GGGACCGATGTGCTAGGGTT 61.624 60.000 0.00 0.00 31.66 4.11
150 151 1.117150 GGACCGATGTGCTAGGGTTA 58.883 55.000 0.00 0.00 31.66 2.85
151 152 1.068741 GGACCGATGTGCTAGGGTTAG 59.931 57.143 0.00 0.00 31.66 2.34
152 153 1.068741 GACCGATGTGCTAGGGTTAGG 59.931 57.143 0.00 0.00 31.66 2.69
153 154 0.393077 CCGATGTGCTAGGGTTAGGG 59.607 60.000 0.00 0.00 0.00 3.53
154 155 1.120530 CGATGTGCTAGGGTTAGGGT 58.879 55.000 0.00 0.00 0.00 4.34
155 156 2.313317 CGATGTGCTAGGGTTAGGGTA 58.687 52.381 0.00 0.00 0.00 3.69
156 157 2.696707 CGATGTGCTAGGGTTAGGGTAA 59.303 50.000 0.00 0.00 0.00 2.85
157 158 3.133362 CGATGTGCTAGGGTTAGGGTAAA 59.867 47.826 0.00 0.00 0.00 2.01
158 159 4.383335 CGATGTGCTAGGGTTAGGGTAAAA 60.383 45.833 0.00 0.00 0.00 1.52
159 160 4.290711 TGTGCTAGGGTTAGGGTAAAAC 57.709 45.455 0.00 0.00 0.00 2.43
160 161 3.009363 TGTGCTAGGGTTAGGGTAAAACC 59.991 47.826 0.00 0.00 44.75 3.27
161 162 3.265221 GTGCTAGGGTTAGGGTAAAACCT 59.735 47.826 5.09 0.00 44.83 3.50
162 163 3.520721 TGCTAGGGTTAGGGTAAAACCTC 59.479 47.826 0.00 0.00 44.83 3.85
163 164 3.520721 GCTAGGGTTAGGGTAAAACCTCA 59.479 47.826 0.00 0.00 44.83 3.86
164 165 4.019051 GCTAGGGTTAGGGTAAAACCTCAA 60.019 45.833 0.00 0.00 44.83 3.02
165 166 4.377762 AGGGTTAGGGTAAAACCTCAAC 57.622 45.455 5.09 0.00 44.83 3.18
166 167 3.985452 AGGGTTAGGGTAAAACCTCAACT 59.015 43.478 5.09 0.00 44.83 3.16
167 168 4.417854 AGGGTTAGGGTAAAACCTCAACTT 59.582 41.667 5.09 0.00 44.83 2.66
168 169 4.521639 GGGTTAGGGTAAAACCTCAACTTG 59.478 45.833 5.09 0.00 44.83 3.16
169 170 4.521639 GGTTAGGGTAAAACCTCAACTTGG 59.478 45.833 0.00 0.00 42.63 3.61
170 171 3.965470 AGGGTAAAACCTCAACTTGGT 57.035 42.857 0.00 0.00 38.64 3.67
177 178 1.675552 ACCTCAACTTGGTTTGACCG 58.324 50.000 0.00 0.00 42.58 4.79
178 179 1.210967 ACCTCAACTTGGTTTGACCGA 59.789 47.619 0.00 0.00 42.58 4.69
179 180 2.158667 ACCTCAACTTGGTTTGACCGAT 60.159 45.455 0.00 0.00 42.58 4.18
180 181 2.884639 CCTCAACTTGGTTTGACCGATT 59.115 45.455 0.00 0.00 42.58 3.34
181 182 4.069304 CCTCAACTTGGTTTGACCGATTA 58.931 43.478 0.00 0.00 42.58 1.75
182 183 4.083484 CCTCAACTTGGTTTGACCGATTAC 60.083 45.833 0.00 0.00 42.58 1.89
183 184 4.452825 TCAACTTGGTTTGACCGATTACA 58.547 39.130 0.00 0.00 42.58 2.41
184 185 4.273969 TCAACTTGGTTTGACCGATTACAC 59.726 41.667 0.00 0.00 42.58 2.90
185 186 3.811083 ACTTGGTTTGACCGATTACACA 58.189 40.909 0.00 0.00 42.58 3.72
186 187 4.200874 ACTTGGTTTGACCGATTACACAA 58.799 39.130 0.00 0.00 42.58 3.33
187 188 4.641094 ACTTGGTTTGACCGATTACACAAA 59.359 37.500 0.00 0.00 42.58 2.83
188 189 4.555348 TGGTTTGACCGATTACACAAAC 57.445 40.909 0.00 0.00 46.04 2.93
189 190 4.200874 TGGTTTGACCGATTACACAAACT 58.799 39.130 16.92 0.00 46.03 2.66
190 191 4.273969 TGGTTTGACCGATTACACAAACTC 59.726 41.667 16.92 10.34 46.03 3.01
191 192 4.451557 GTTTGACCGATTACACAAACTCG 58.548 43.478 0.00 0.00 44.51 4.18
195 196 1.730064 CCGATTACACAAACTCGGTGG 59.270 52.381 1.81 0.00 44.30 4.61
196 197 1.730064 CGATTACACAAACTCGGTGGG 59.270 52.381 0.00 0.00 40.54 4.61
197 198 2.610976 CGATTACACAAACTCGGTGGGA 60.611 50.000 0.00 0.00 40.54 4.37
198 199 2.243602 TTACACAAACTCGGTGGGAC 57.756 50.000 0.00 0.00 40.54 4.46
199 200 1.416243 TACACAAACTCGGTGGGACT 58.584 50.000 0.00 0.00 40.54 3.85
200 201 0.179056 ACACAAACTCGGTGGGACTG 60.179 55.000 0.00 0.00 40.54 3.51
201 202 0.105964 CACAAACTCGGTGGGACTGA 59.894 55.000 0.00 0.00 32.65 3.41
202 203 1.056660 ACAAACTCGGTGGGACTGAT 58.943 50.000 0.00 0.00 32.23 2.90
203 204 1.420138 ACAAACTCGGTGGGACTGATT 59.580 47.619 0.00 0.00 32.23 2.57
204 205 2.158667 ACAAACTCGGTGGGACTGATTT 60.159 45.455 0.00 0.00 32.23 2.17
205 206 2.884639 CAAACTCGGTGGGACTGATTTT 59.115 45.455 0.00 0.00 36.99 1.82
206 207 2.185004 ACTCGGTGGGACTGATTTTG 57.815 50.000 0.00 0.00 32.23 2.44
207 208 1.271379 ACTCGGTGGGACTGATTTTGG 60.271 52.381 0.00 0.00 32.23 3.28
208 209 0.768622 TCGGTGGGACTGATTTTGGT 59.231 50.000 0.00 0.00 0.00 3.67
209 210 1.979308 TCGGTGGGACTGATTTTGGTA 59.021 47.619 0.00 0.00 0.00 3.25
210 211 2.372504 TCGGTGGGACTGATTTTGGTAA 59.627 45.455 0.00 0.00 0.00 2.85
211 212 3.009695 TCGGTGGGACTGATTTTGGTAAT 59.990 43.478 0.00 0.00 0.00 1.89
212 213 4.225492 TCGGTGGGACTGATTTTGGTAATA 59.775 41.667 0.00 0.00 0.00 0.98
213 214 4.944930 CGGTGGGACTGATTTTGGTAATAA 59.055 41.667 0.00 0.00 0.00 1.40
214 215 5.065988 CGGTGGGACTGATTTTGGTAATAAG 59.934 44.000 0.00 0.00 0.00 1.73
240 241 2.093973 TGAAAGGATCGAGAAGAGGTGC 60.094 50.000 0.00 0.00 0.00 5.01
246 247 3.057596 GGATCGAGAAGAGGTGCATAGAG 60.058 52.174 0.00 0.00 0.00 2.43
247 248 2.302260 TCGAGAAGAGGTGCATAGAGG 58.698 52.381 0.00 0.00 0.00 3.69
248 249 1.339610 CGAGAAGAGGTGCATAGAGGG 59.660 57.143 0.00 0.00 0.00 4.30
372 387 5.987953 GCAAGCATGACAAGAGTATATGAGA 59.012 40.000 0.00 0.00 0.00 3.27
375 390 7.594351 AGCATGACAAGAGTATATGAGAAGA 57.406 36.000 0.00 0.00 0.00 2.87
377 392 8.649591 AGCATGACAAGAGTATATGAGAAGAAT 58.350 33.333 0.00 0.00 0.00 2.40
398 413 9.492973 AAGAATAAAGTAAAGCATGCAATTTGT 57.507 25.926 21.98 6.66 0.00 2.83
410 425 7.558604 AGCATGCAATTTGTAAGGATGTAAAT 58.441 30.769 21.98 0.00 34.16 1.40
533 549 0.881159 CACGAAGGGTAACGGTTGCA 60.881 55.000 11.05 0.00 37.60 4.08
657 673 3.538591 TCTTCACGAAGTAGGCGATCTA 58.461 45.455 6.68 0.00 41.61 1.98
701 717 3.744238 TCAACTCCACAATCTTGACGA 57.256 42.857 0.00 0.00 0.00 4.20
716 732 0.250513 GACGAAGGCTCCCAAGTGAT 59.749 55.000 0.00 0.00 0.00 3.06
933 959 0.907704 ACTTATCCACACCGCTCCCA 60.908 55.000 0.00 0.00 0.00 4.37
977 1074 3.518998 GCAGAGTCGCCTCCGCTA 61.519 66.667 0.00 0.00 37.98 4.26
1251 2029 3.317603 TCGATCTGAACAGCAACATCA 57.682 42.857 0.00 0.00 0.00 3.07
1353 2131 2.603776 GTGGGAGGTCCGTGTCCT 60.604 66.667 0.00 0.00 38.76 3.85
1367 2145 3.028098 TCCTAGGGCGGAGGAGGT 61.028 66.667 9.46 0.00 38.22 3.85
1370 2148 3.717924 CTAGGGCGGAGGAGGTCGT 62.718 68.421 0.00 0.00 0.00 4.34
1455 2233 2.425592 CTGTTGGTGACGGAGGCA 59.574 61.111 0.00 0.00 36.72 4.75
1583 2361 0.392706 TCTCTCAAGTTGCAAGCCGA 59.607 50.000 0.00 0.00 0.00 5.54
1657 2435 3.619038 GGATTTGAAGATGGAGACGACAC 59.381 47.826 0.00 0.00 0.00 3.67
1666 2444 1.217882 GGAGACGACACCTGTGTTTG 58.782 55.000 4.16 3.53 45.05 2.93
1720 2498 2.426522 TGTCCATGTGTTCTTGCTAGC 58.573 47.619 8.10 8.10 0.00 3.42
1725 2504 4.523943 TCCATGTGTTCTTGCTAGCAAAAT 59.476 37.500 28.95 13.65 35.33 1.82
1777 2647 7.618502 TGTAGTAAATTGTTGGTATGCGAAT 57.381 32.000 0.00 0.00 0.00 3.34
1787 2657 7.106439 TGTTGGTATGCGAATTTCCATATTT 57.894 32.000 9.40 0.00 0.00 1.40
1942 2958 7.336396 AGTTGTCATTTATACTGAACCCTACC 58.664 38.462 0.00 0.00 0.00 3.18
2044 3067 9.981114 AATTTGTAGAAACCACTGAAATAAAGG 57.019 29.630 0.00 0.00 0.00 3.11
2124 3147 1.974957 TGTCTGGTGCAGCCTTTACTA 59.025 47.619 14.36 0.00 38.35 1.82
2132 3155 2.637872 TGCAGCCTTTACTAGACCTTGT 59.362 45.455 0.00 0.00 0.00 3.16
2162 3186 6.300354 AGCGTACAATATTTACCAATGCTC 57.700 37.500 0.00 0.00 0.00 4.26
2251 3275 9.897744 CTTTAGAAATTGTTGTCAGATTTAGCA 57.102 29.630 0.00 0.00 0.00 3.49
2430 3454 3.768633 GGCTGATTGGACAGACGAT 57.231 52.632 0.00 0.00 39.94 3.73
2478 3502 1.768870 TGTTAGGAAGCTAGGGATGGC 59.231 52.381 0.00 0.00 0.00 4.40
2546 3570 8.984891 ATGAAGACAAAATTTTATGAATGCGA 57.015 26.923 2.44 0.00 0.00 5.10
2739 3771 6.366877 GCAAATTACAGTTGAATTGCTCACAT 59.633 34.615 0.00 0.00 32.21 3.21
2786 3819 7.493320 TGTCCTAATTACCTAACTAATGTTGCG 59.507 37.037 0.00 0.00 37.59 4.85
2921 3957 9.656040 CATAGATGAAGAGGAAGAAGAATATGG 57.344 37.037 0.00 0.00 0.00 2.74
2927 3963 4.472833 AGAGGAAGAAGAATATGGTGCTGT 59.527 41.667 0.00 0.00 0.00 4.40
2948 3984 2.631545 TCGATGATGGACATGAGCAGAT 59.368 45.455 0.00 0.00 39.56 2.90
3137 4173 1.819305 GCAGGAAGCAAAGGACAAGGA 60.819 52.381 0.00 0.00 44.79 3.36
3143 4179 4.371786 GAAGCAAAGGACAAGGAAAAAGG 58.628 43.478 0.00 0.00 0.00 3.11
3284 4320 5.879223 AGGCAAACAGAGTCATATTTGAGAG 59.121 40.000 14.50 0.00 34.62 3.20
3311 4347 3.255888 ACAAGTGATGACGCTAGACTGAA 59.744 43.478 0.00 0.00 35.69 3.02
3824 4889 4.137116 AGTGCGCTTGTTGATTCCTATA 57.863 40.909 9.73 0.00 0.00 1.31
3856 4921 4.761739 TCCACCAAAAGAATGTCATCAGTC 59.238 41.667 0.00 0.00 38.71 3.51
3859 4924 5.049474 CACCAAAAGAATGTCATCAGTCGAA 60.049 40.000 0.00 0.00 42.50 3.71
3888 4953 4.009675 GGCATGTTTCTGTGGATAGTTGA 58.990 43.478 0.00 0.00 0.00 3.18
4425 5494 4.725790 GCACAATGCCTAGAGGAAAAAT 57.274 40.909 0.00 0.00 37.42 1.82
4449 5518 4.687483 GGAACACTTCAATTTCAGCCATTG 59.313 41.667 0.00 0.00 33.55 2.82
4474 5543 6.516739 TCACTTAGAAATGTCATCGAGAGT 57.483 37.500 0.00 0.00 0.00 3.24
4582 5651 2.136728 TGCATTGCACTGCACAATTTC 58.863 42.857 25.93 0.00 46.76 2.17
4676 5745 0.889186 GCCAACGACCACTCCAACAT 60.889 55.000 0.00 0.00 0.00 2.71
4722 5791 8.954350 GGATAGTGCTGCTATGAATCAATTTAT 58.046 33.333 0.00 0.00 40.30 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.650266 TGTATAATGGCTAGGTTTTGTGTGG 59.350 40.000 0.00 0.00 0.00 4.17
3 4 6.150307 TGTGTATAATGGCTAGGTTTTGTGTG 59.850 38.462 0.00 0.00 0.00 3.82
9 10 8.909923 GGTAAATTGTGTATAATGGCTAGGTTT 58.090 33.333 0.00 0.00 0.00 3.27
10 11 8.056400 TGGTAAATTGTGTATAATGGCTAGGTT 58.944 33.333 0.00 0.00 0.00 3.50
11 12 7.579105 TGGTAAATTGTGTATAATGGCTAGGT 58.421 34.615 0.00 0.00 0.00 3.08
12 13 8.458573 TTGGTAAATTGTGTATAATGGCTAGG 57.541 34.615 0.00 0.00 0.00 3.02
13 14 9.730420 GTTTGGTAAATTGTGTATAATGGCTAG 57.270 33.333 0.00 0.00 0.00 3.42
14 15 9.469097 AGTTTGGTAAATTGTGTATAATGGCTA 57.531 29.630 0.00 0.00 0.00 3.93
15 16 8.361169 AGTTTGGTAAATTGTGTATAATGGCT 57.639 30.769 0.00 0.00 0.00 4.75
16 17 8.247562 TGAGTTTGGTAAATTGTGTATAATGGC 58.752 33.333 0.00 0.00 0.00 4.40
21 22 8.744652 CCCATTGAGTTTGGTAAATTGTGTATA 58.255 33.333 0.00 0.00 31.99 1.47
22 23 7.453126 TCCCATTGAGTTTGGTAAATTGTGTAT 59.547 33.333 0.00 0.00 31.99 2.29
23 24 6.778069 TCCCATTGAGTTTGGTAAATTGTGTA 59.222 34.615 0.00 0.00 31.99 2.90
24 25 5.600484 TCCCATTGAGTTTGGTAAATTGTGT 59.400 36.000 0.00 0.00 31.99 3.72
25 26 5.925969 GTCCCATTGAGTTTGGTAAATTGTG 59.074 40.000 0.00 0.00 31.99 3.33
26 27 5.011635 GGTCCCATTGAGTTTGGTAAATTGT 59.988 40.000 0.00 0.00 31.99 2.71
27 28 5.011533 TGGTCCCATTGAGTTTGGTAAATTG 59.988 40.000 0.00 0.00 31.99 2.32
28 29 5.151454 TGGTCCCATTGAGTTTGGTAAATT 58.849 37.500 0.00 0.00 31.99 1.82
29 30 4.746466 TGGTCCCATTGAGTTTGGTAAAT 58.254 39.130 0.00 0.00 31.99 1.40
30 31 4.186077 TGGTCCCATTGAGTTTGGTAAA 57.814 40.909 0.00 0.00 31.99 2.01
31 32 3.885976 TGGTCCCATTGAGTTTGGTAA 57.114 42.857 0.00 0.00 31.99 2.85
32 33 3.885976 TTGGTCCCATTGAGTTTGGTA 57.114 42.857 0.00 0.00 31.99 3.25
33 34 2.765689 TTGGTCCCATTGAGTTTGGT 57.234 45.000 0.00 0.00 31.99 3.67
34 35 3.577848 TGATTTGGTCCCATTGAGTTTGG 59.422 43.478 0.00 0.00 0.00 3.28
35 36 4.870123 TGATTTGGTCCCATTGAGTTTG 57.130 40.909 0.00 0.00 0.00 2.93
36 37 5.085920 TCATGATTTGGTCCCATTGAGTTT 58.914 37.500 0.00 0.00 0.00 2.66
37 38 4.676109 TCATGATTTGGTCCCATTGAGTT 58.324 39.130 0.00 0.00 0.00 3.01
38 39 4.320546 TCATGATTTGGTCCCATTGAGT 57.679 40.909 0.00 0.00 0.00 3.41
39 40 5.186409 AGTTTCATGATTTGGTCCCATTGAG 59.814 40.000 0.00 0.00 0.00 3.02
40 41 5.085920 AGTTTCATGATTTGGTCCCATTGA 58.914 37.500 0.00 0.00 0.00 2.57
41 42 5.047164 TGAGTTTCATGATTTGGTCCCATTG 60.047 40.000 0.00 0.00 0.00 2.82
42 43 5.085920 TGAGTTTCATGATTTGGTCCCATT 58.914 37.500 0.00 0.00 0.00 3.16
43 44 4.676109 TGAGTTTCATGATTTGGTCCCAT 58.324 39.130 0.00 0.00 0.00 4.00
44 45 4.081406 CTGAGTTTCATGATTTGGTCCCA 58.919 43.478 0.00 0.00 0.00 4.37
45 46 4.082125 ACTGAGTTTCATGATTTGGTCCC 58.918 43.478 0.00 0.00 0.00 4.46
46 47 4.761739 TGACTGAGTTTCATGATTTGGTCC 59.238 41.667 0.00 0.00 0.00 4.46
47 48 5.702670 TCTGACTGAGTTTCATGATTTGGTC 59.297 40.000 0.00 2.10 0.00 4.02
48 49 5.471456 GTCTGACTGAGTTTCATGATTTGGT 59.529 40.000 0.00 0.00 0.00 3.67
49 50 5.106396 GGTCTGACTGAGTTTCATGATTTGG 60.106 44.000 7.85 0.00 0.00 3.28
50 51 5.390251 CGGTCTGACTGAGTTTCATGATTTG 60.390 44.000 11.20 0.00 0.00 2.32
51 52 4.692625 CGGTCTGACTGAGTTTCATGATTT 59.307 41.667 11.20 0.00 0.00 2.17
52 53 4.021104 TCGGTCTGACTGAGTTTCATGATT 60.021 41.667 15.13 0.00 0.00 2.57
53 54 3.511540 TCGGTCTGACTGAGTTTCATGAT 59.488 43.478 15.13 0.00 0.00 2.45
54 55 2.890945 TCGGTCTGACTGAGTTTCATGA 59.109 45.455 15.13 0.00 0.00 3.07
55 56 2.989840 GTCGGTCTGACTGAGTTTCATG 59.010 50.000 19.21 0.00 44.58 3.07
56 57 3.305398 GTCGGTCTGACTGAGTTTCAT 57.695 47.619 19.21 0.00 44.58 2.57
57 58 2.795175 GTCGGTCTGACTGAGTTTCA 57.205 50.000 19.21 0.00 44.58 2.69
67 68 5.465390 CACATTTTGAACTAAGTCGGTCTGA 59.535 40.000 0.00 0.00 0.00 3.27
68 69 5.465390 TCACATTTTGAACTAAGTCGGTCTG 59.535 40.000 0.00 0.00 0.00 3.51
69 70 5.607477 TCACATTTTGAACTAAGTCGGTCT 58.393 37.500 0.00 0.00 0.00 3.85
70 71 5.917541 TCACATTTTGAACTAAGTCGGTC 57.082 39.130 0.00 0.00 0.00 4.79
81 82 7.377397 CGAAAATCCTAACGTTCACATTTTGAA 59.623 33.333 20.25 0.00 42.26 2.69
82 83 6.853872 CGAAAATCCTAACGTTCACATTTTGA 59.146 34.615 20.25 4.46 0.00 2.69
83 84 6.087555 CCGAAAATCCTAACGTTCACATTTTG 59.912 38.462 20.25 13.53 0.00 2.44
84 85 6.146898 CCGAAAATCCTAACGTTCACATTTT 58.853 36.000 17.36 17.36 0.00 1.82
85 86 5.239963 ACCGAAAATCCTAACGTTCACATTT 59.760 36.000 2.82 4.80 0.00 2.32
86 87 4.758165 ACCGAAAATCCTAACGTTCACATT 59.242 37.500 2.82 0.00 0.00 2.71
87 88 4.153475 CACCGAAAATCCTAACGTTCACAT 59.847 41.667 2.82 0.00 0.00 3.21
88 89 3.495377 CACCGAAAATCCTAACGTTCACA 59.505 43.478 2.82 0.00 0.00 3.58
89 90 3.120442 CCACCGAAAATCCTAACGTTCAC 60.120 47.826 2.82 0.00 0.00 3.18
90 91 3.068560 CCACCGAAAATCCTAACGTTCA 58.931 45.455 2.82 0.00 0.00 3.18
91 92 2.417586 CCCACCGAAAATCCTAACGTTC 59.582 50.000 2.82 0.00 0.00 3.95
92 93 2.038820 TCCCACCGAAAATCCTAACGTT 59.961 45.455 5.88 5.88 0.00 3.99
93 94 1.624813 TCCCACCGAAAATCCTAACGT 59.375 47.619 0.00 0.00 0.00 3.99
94 95 2.004733 GTCCCACCGAAAATCCTAACG 58.995 52.381 0.00 0.00 0.00 3.18
95 96 2.362736 GGTCCCACCGAAAATCCTAAC 58.637 52.381 0.00 0.00 0.00 2.34
96 97 2.793288 GGTCCCACCGAAAATCCTAA 57.207 50.000 0.00 0.00 0.00 2.69
107 108 0.251916 TTGATCATGTCGGTCCCACC 59.748 55.000 0.00 0.00 34.05 4.61
108 109 1.066143 AGTTGATCATGTCGGTCCCAC 60.066 52.381 0.00 0.00 0.00 4.61
109 110 1.207089 GAGTTGATCATGTCGGTCCCA 59.793 52.381 0.00 0.00 0.00 4.37
110 111 1.802880 CGAGTTGATCATGTCGGTCCC 60.803 57.143 15.96 0.00 0.00 4.46
111 112 1.560923 CGAGTTGATCATGTCGGTCC 58.439 55.000 15.96 0.00 0.00 4.46
112 113 1.560923 CCGAGTTGATCATGTCGGTC 58.439 55.000 26.92 7.08 45.62 4.79
113 114 3.741029 CCGAGTTGATCATGTCGGT 57.259 52.632 26.92 0.00 45.62 4.69
115 116 1.560923 GTCCCGAGTTGATCATGTCG 58.439 55.000 16.55 16.55 0.00 4.35
116 117 1.802880 CGGTCCCGAGTTGATCATGTC 60.803 57.143 0.00 0.00 42.83 3.06
117 118 0.175760 CGGTCCCGAGTTGATCATGT 59.824 55.000 0.00 0.00 42.83 3.21
118 119 0.459899 TCGGTCCCGAGTTGATCATG 59.540 55.000 3.90 0.00 44.01 3.07
119 120 2.896278 TCGGTCCCGAGTTGATCAT 58.104 52.632 3.90 0.00 44.01 2.45
120 121 4.426971 TCGGTCCCGAGTTGATCA 57.573 55.556 3.90 0.00 44.01 2.92
129 130 2.417516 CCTAGCACATCGGTCCCG 59.582 66.667 0.00 0.00 41.35 5.14
130 131 1.623542 AACCCTAGCACATCGGTCCC 61.624 60.000 0.00 0.00 0.00 4.46
131 132 1.068741 CTAACCCTAGCACATCGGTCC 59.931 57.143 0.00 0.00 0.00 4.46
132 133 1.068741 CCTAACCCTAGCACATCGGTC 59.931 57.143 0.00 0.00 0.00 4.79
133 134 1.120530 CCTAACCCTAGCACATCGGT 58.879 55.000 0.00 0.00 0.00 4.69
134 135 0.393077 CCCTAACCCTAGCACATCGG 59.607 60.000 0.00 0.00 0.00 4.18
135 136 1.120530 ACCCTAACCCTAGCACATCG 58.879 55.000 0.00 0.00 0.00 3.84
136 137 4.765813 TTTACCCTAACCCTAGCACATC 57.234 45.455 0.00 0.00 0.00 3.06
137 138 4.324797 GGTTTTACCCTAACCCTAGCACAT 60.325 45.833 0.00 0.00 39.29 3.21
138 139 3.009363 GGTTTTACCCTAACCCTAGCACA 59.991 47.826 0.00 0.00 39.29 4.57
139 140 3.265221 AGGTTTTACCCTAACCCTAGCAC 59.735 47.826 0.00 0.00 44.96 4.40
140 141 3.520721 GAGGTTTTACCCTAACCCTAGCA 59.479 47.826 0.00 0.00 44.96 3.49
141 142 3.520721 TGAGGTTTTACCCTAACCCTAGC 59.479 47.826 0.00 0.00 44.96 3.42
142 143 5.250082 AGTTGAGGTTTTACCCTAACCCTAG 59.750 44.000 0.00 0.00 44.96 3.02
143 144 5.164897 AGTTGAGGTTTTACCCTAACCCTA 58.835 41.667 0.00 0.00 44.96 3.53
144 145 3.985452 AGTTGAGGTTTTACCCTAACCCT 59.015 43.478 0.00 0.00 44.96 4.34
145 146 4.377762 AGTTGAGGTTTTACCCTAACCC 57.622 45.455 0.00 0.00 44.96 4.11
146 147 4.521639 CCAAGTTGAGGTTTTACCCTAACC 59.478 45.833 3.87 0.00 44.34 2.85
147 148 5.135383 ACCAAGTTGAGGTTTTACCCTAAC 58.865 41.667 3.87 0.00 39.75 2.34
148 149 5.391577 ACCAAGTTGAGGTTTTACCCTAA 57.608 39.130 3.87 0.00 39.75 2.69
149 150 5.391577 AACCAAGTTGAGGTTTTACCCTA 57.608 39.130 3.87 0.00 46.85 3.53
150 151 3.965470 ACCAAGTTGAGGTTTTACCCT 57.035 42.857 3.87 0.00 39.75 4.34
158 159 1.210967 TCGGTCAAACCAAGTTGAGGT 59.789 47.619 3.87 0.00 38.47 3.85
159 160 1.961793 TCGGTCAAACCAAGTTGAGG 58.038 50.000 3.87 0.00 38.47 3.86
160 161 4.513692 TGTAATCGGTCAAACCAAGTTGAG 59.486 41.667 3.87 0.00 38.47 3.02
161 162 4.273969 GTGTAATCGGTCAAACCAAGTTGA 59.726 41.667 3.87 0.00 38.47 3.18
162 163 4.035792 TGTGTAATCGGTCAAACCAAGTTG 59.964 41.667 0.00 0.00 38.47 3.16
163 164 4.200874 TGTGTAATCGGTCAAACCAAGTT 58.799 39.130 0.00 0.00 38.47 2.66
164 165 3.811083 TGTGTAATCGGTCAAACCAAGT 58.189 40.909 0.00 0.00 38.47 3.16
165 166 4.822036 TTGTGTAATCGGTCAAACCAAG 57.178 40.909 0.00 0.00 38.47 3.61
166 167 4.641094 AGTTTGTGTAATCGGTCAAACCAA 59.359 37.500 13.47 0.00 45.79 3.67
167 168 4.200874 AGTTTGTGTAATCGGTCAAACCA 58.799 39.130 13.47 0.00 45.79 3.67
168 169 4.609783 CGAGTTTGTGTAATCGGTCAAACC 60.610 45.833 13.47 0.00 45.79 3.27
169 170 4.451557 CGAGTTTGTGTAATCGGTCAAAC 58.548 43.478 10.36 10.36 45.33 2.93
170 171 4.718858 CGAGTTTGTGTAATCGGTCAAA 57.281 40.909 0.00 0.00 0.00 2.69
176 177 1.730064 CCCACCGAGTTTGTGTAATCG 59.270 52.381 0.00 0.00 35.02 3.34
177 178 2.740447 GTCCCACCGAGTTTGTGTAATC 59.260 50.000 0.00 0.00 31.71 1.75
178 179 2.370849 AGTCCCACCGAGTTTGTGTAAT 59.629 45.455 0.00 0.00 31.71 1.89
179 180 1.764134 AGTCCCACCGAGTTTGTGTAA 59.236 47.619 0.00 0.00 31.71 2.41
180 181 1.069513 CAGTCCCACCGAGTTTGTGTA 59.930 52.381 0.00 0.00 31.71 2.90
181 182 0.179056 CAGTCCCACCGAGTTTGTGT 60.179 55.000 0.00 0.00 31.71 3.72
182 183 0.105964 TCAGTCCCACCGAGTTTGTG 59.894 55.000 0.00 0.00 0.00 3.33
183 184 1.056660 ATCAGTCCCACCGAGTTTGT 58.943 50.000 0.00 0.00 0.00 2.83
184 185 2.185004 AATCAGTCCCACCGAGTTTG 57.815 50.000 0.00 0.00 0.00 2.93
185 186 2.884639 CAAAATCAGTCCCACCGAGTTT 59.115 45.455 0.00 0.00 0.00 2.66
186 187 2.504367 CAAAATCAGTCCCACCGAGTT 58.496 47.619 0.00 0.00 0.00 3.01
187 188 1.271379 CCAAAATCAGTCCCACCGAGT 60.271 52.381 0.00 0.00 0.00 4.18
188 189 1.271379 ACCAAAATCAGTCCCACCGAG 60.271 52.381 0.00 0.00 0.00 4.63
189 190 0.768622 ACCAAAATCAGTCCCACCGA 59.231 50.000 0.00 0.00 0.00 4.69
190 191 2.483014 TACCAAAATCAGTCCCACCG 57.517 50.000 0.00 0.00 0.00 4.94
191 192 5.163550 GCTTATTACCAAAATCAGTCCCACC 60.164 44.000 0.00 0.00 0.00 4.61
192 193 5.417580 TGCTTATTACCAAAATCAGTCCCAC 59.582 40.000 0.00 0.00 0.00 4.61
193 194 5.575157 TGCTTATTACCAAAATCAGTCCCA 58.425 37.500 0.00 0.00 0.00 4.37
194 195 6.524101 TTGCTTATTACCAAAATCAGTCCC 57.476 37.500 0.00 0.00 0.00 4.46
195 196 8.250332 TCATTTGCTTATTACCAAAATCAGTCC 58.750 33.333 0.00 0.00 34.93 3.85
196 197 9.638239 TTCATTTGCTTATTACCAAAATCAGTC 57.362 29.630 0.00 0.00 34.93 3.51
197 198 9.995003 TTTCATTTGCTTATTACCAAAATCAGT 57.005 25.926 0.00 0.00 34.93 3.41
199 200 9.434420 CCTTTCATTTGCTTATTACCAAAATCA 57.566 29.630 0.00 0.00 34.93 2.57
200 201 9.651913 TCCTTTCATTTGCTTATTACCAAAATC 57.348 29.630 0.00 0.00 34.93 2.17
202 203 9.651913 GATCCTTTCATTTGCTTATTACCAAAA 57.348 29.630 0.00 0.00 34.93 2.44
203 204 7.973388 CGATCCTTTCATTTGCTTATTACCAAA 59.027 33.333 0.00 0.00 35.64 3.28
204 205 7.338196 TCGATCCTTTCATTTGCTTATTACCAA 59.662 33.333 0.00 0.00 0.00 3.67
205 206 6.826231 TCGATCCTTTCATTTGCTTATTACCA 59.174 34.615 0.00 0.00 0.00 3.25
206 207 7.226720 TCTCGATCCTTTCATTTGCTTATTACC 59.773 37.037 0.00 0.00 0.00 2.85
207 208 8.142994 TCTCGATCCTTTCATTTGCTTATTAC 57.857 34.615 0.00 0.00 0.00 1.89
208 209 8.731275 TTCTCGATCCTTTCATTTGCTTATTA 57.269 30.769 0.00 0.00 0.00 0.98
209 210 7.554118 TCTTCTCGATCCTTTCATTTGCTTATT 59.446 33.333 0.00 0.00 0.00 1.40
210 211 7.050377 TCTTCTCGATCCTTTCATTTGCTTAT 58.950 34.615 0.00 0.00 0.00 1.73
211 212 6.406370 TCTTCTCGATCCTTTCATTTGCTTA 58.594 36.000 0.00 0.00 0.00 3.09
212 213 5.248640 TCTTCTCGATCCTTTCATTTGCTT 58.751 37.500 0.00 0.00 0.00 3.91
213 214 4.836825 TCTTCTCGATCCTTTCATTTGCT 58.163 39.130 0.00 0.00 0.00 3.91
214 215 4.034975 CCTCTTCTCGATCCTTTCATTTGC 59.965 45.833 0.00 0.00 0.00 3.68
372 387 9.492973 ACAAATTGCATGCTTTACTTTATTCTT 57.507 25.926 20.33 0.00 0.00 2.52
377 392 8.580720 TCCTTACAAATTGCATGCTTTACTTTA 58.419 29.630 20.33 0.00 0.00 1.85
398 413 6.103946 TCCAATCCCATCCATTTACATCCTTA 59.896 38.462 0.00 0.00 0.00 2.69
410 425 0.034186 GCACACTCCAATCCCATCCA 60.034 55.000 0.00 0.00 0.00 3.41
485 501 3.706594 AGTCTCCATCAACGTGGATGTAT 59.293 43.478 27.21 8.92 46.67 2.29
533 549 4.680537 AGCCCTCCGTGGACTCGT 62.681 66.667 0.00 0.00 38.35 4.18
657 673 0.763035 AGGAGTTTGTACGGGCAAGT 59.237 50.000 0.00 0.00 0.00 3.16
701 717 1.972588 AGGTATCACTTGGGAGCCTT 58.027 50.000 0.00 0.00 0.00 4.35
905 922 0.613260 TGTGGATAAGTTGAGGCGCT 59.387 50.000 7.64 0.00 0.00 5.92
914 931 0.907704 TGGGAGCGGTGTGGATAAGT 60.908 55.000 0.00 0.00 0.00 2.24
987 1084 2.737180 CGACTGGAGGTGCAGTGT 59.263 61.111 9.07 0.00 0.00 3.55
1210 1985 1.235756 GAATCCCATTCCCCTCCCTT 58.764 55.000 0.00 0.00 33.17 3.95
1251 2029 1.969862 CCAAGTCGGGGTAGTCGTT 59.030 57.895 0.00 0.00 0.00 3.85
1303 2081 2.670148 GGAGGAAGACCATGGCCGT 61.670 63.158 13.04 0.00 38.94 5.68
1307 2085 1.475751 CCAATCGGAGGAAGACCATGG 60.476 57.143 11.19 11.19 38.94 3.66
1353 2131 3.736224 ACGACCTCCTCCGCCCTA 61.736 66.667 0.00 0.00 0.00 3.53
1367 2145 2.599281 TTCAGAGACCGGGCACGA 60.599 61.111 11.66 2.04 44.60 4.35
1370 2148 0.321564 CAATGTTCAGAGACCGGGCA 60.322 55.000 11.69 0.00 0.00 5.36
1430 2208 4.254709 TCACCAACAGCTGCGCCT 62.255 61.111 15.27 0.00 0.00 5.52
1455 2233 2.765807 CCTCCCACGCCCTCTGAT 60.766 66.667 0.00 0.00 0.00 2.90
1657 2435 3.485463 TTACCTCTCCACAAACACAGG 57.515 47.619 0.00 0.00 0.00 4.00
1666 2444 5.998363 ACAACTCAGAAATTTACCTCTCCAC 59.002 40.000 0.00 0.00 0.00 4.02
1725 2504 9.421806 CTTTTGTTCATAAGTGGCATGAAAATA 57.578 29.630 0.00 0.00 42.44 1.40
1777 2647 8.669946 TGTCATTCGTAGCATAAATATGGAAA 57.330 30.769 2.82 0.00 34.32 3.13
1787 2657 6.270815 GGTAGTTCTTGTCATTCGTAGCATA 58.729 40.000 0.00 0.00 0.00 3.14
1972 2991 4.564406 CCAACTTGCCAAGTCTGTCTATCT 60.564 45.833 11.11 0.00 41.91 1.98
2044 3067 2.233922 TGGTTAGCTAGTGCCTCTGTTC 59.766 50.000 10.90 0.00 40.80 3.18
2124 3147 4.890088 TGTACGCTAAATGAACAAGGTCT 58.110 39.130 0.00 0.00 0.00 3.85
2251 3275 5.815740 CAGAAGGTGCTTGTAAATACGGTAT 59.184 40.000 0.00 0.00 0.00 2.73
2461 3485 0.267658 TGGCCATCCCTAGCTTCCTA 59.732 55.000 0.00 0.00 0.00 2.94
2478 3502 1.001048 CAAGCACCATTCACACAGTGG 60.001 52.381 5.31 0.00 38.96 4.00
2739 3771 9.474313 AGGACAAGGCTAAATAATGTAATCAAA 57.526 29.630 0.00 0.00 0.00 2.69
2786 3819 4.566488 ATGTTCTGACATCTGGTCTTTCCC 60.566 45.833 0.00 0.00 42.83 3.97
2807 3840 1.136305 CAGGATTGCCAGCCTTGAATG 59.864 52.381 0.00 0.00 36.29 2.67
2921 3957 1.596260 CATGTCCATCATCGACAGCAC 59.404 52.381 0.00 0.00 43.17 4.40
2927 3963 2.034124 TCTGCTCATGTCCATCATCGA 58.966 47.619 0.00 0.00 34.09 3.59
2948 3984 0.895100 GCTGGTGGTGCTCATTGGAA 60.895 55.000 0.00 0.00 0.00 3.53
3137 4173 5.817296 GTGCTGTTTGATTTCTTCCCTTTTT 59.183 36.000 0.00 0.00 0.00 1.94
3143 4179 4.320608 TTGGTGCTGTTTGATTTCTTCC 57.679 40.909 0.00 0.00 0.00 3.46
3284 4320 4.026475 GTCTAGCGTCATCACTTGTAATGC 60.026 45.833 0.00 0.00 0.00 3.56
3311 4347 1.133513 TGCACCACCTCTTCAACCAAT 60.134 47.619 0.00 0.00 0.00 3.16
3569 4633 3.431346 GCTTCATCATCACTACTGCTCCA 60.431 47.826 0.00 0.00 0.00 3.86
3824 4889 5.422012 ACATTCTTTTGGTGGACTTCAAACT 59.578 36.000 0.00 0.00 33.29 2.66
3856 4921 4.269603 CACAGAAACATGCCTAGAGATTCG 59.730 45.833 0.00 0.00 0.00 3.34
3859 4924 3.776969 TCCACAGAAACATGCCTAGAGAT 59.223 43.478 0.00 0.00 0.00 2.75
3888 4953 5.397334 GCTTGTCTTAGAGATTGAGGGGAAT 60.397 44.000 0.00 0.00 0.00 3.01
4425 5494 3.295093 TGGCTGAAATTGAAGTGTTCCA 58.705 40.909 0.00 0.00 0.00 3.53
4449 5518 6.809196 ACTCTCGATGACATTTCTAAGTGAAC 59.191 38.462 0.00 0.00 33.88 3.18
4474 5543 6.582677 TTGTTCTTCAAGACTCCAAAACAA 57.417 33.333 0.00 0.00 34.15 2.83
4582 5651 9.979578 ATATCAGCTAGTTGACTTTCTCTAATG 57.020 33.333 11.84 0.00 0.00 1.90
4676 5745 8.663167 ACTATCCATCTCATTGGTTGAATCATA 58.337 33.333 0.00 0.00 38.01 2.15


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

AutoCloner maintained by Alex Coulton.