Multiple sequence alignment - TraesCS1A01G201500

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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 TraesCS1A01G201500 chr1A 100.000 2725 0 0 1 2725 362619670 362622394 0.000000e+00 5033.0
1 TraesCS1A01G201500 chr1A 86.555 357 19 10 2397 2725 502834210 502833855 1.540000e-97 366.0
2 TraesCS1A01G201500 chr1A 92.941 170 12 0 1516 1685 502835091 502834922 5.830000e-62 248.0
3 TraesCS1A01G201500 chr2D 96.054 887 27 4 1846 2725 429500554 429501439 0.000000e+00 1437.0
4 TraesCS1A01G201500 chr2D 96.860 414 10 2 1327 1740 429499151 429499561 0.000000e+00 689.0
5 TraesCS1A01G201500 chr2D 92.825 223 5 1 1107 1329 429498906 429499117 2.040000e-81 313.0
6 TraesCS1A01G201500 chr2D 80.893 403 43 21 460 846 93808628 93809012 1.230000e-73 287.0
7 TraesCS1A01G201500 chr6A 86.583 559 52 11 794 1329 36490540 36491098 1.810000e-166 595.0
8 TraesCS1A01G201500 chr6A 76.565 559 83 29 171 699 454682905 454683445 2.080000e-66 263.0
9 TraesCS1A01G201500 chr6A 85.930 199 18 5 651 846 507114657 507114848 1.280000e-48 204.0
10 TraesCS1A01G201500 chr6A 94.444 90 4 1 1329 1418 36491134 36491222 1.320000e-28 137.0
11 TraesCS1A01G201500 chr3A 85.714 567 52 17 1846 2395 36073030 36072476 3.040000e-159 571.0
12 TraesCS1A01G201500 chr3A 88.202 356 18 6 2394 2725 141554175 141554530 1.180000e-108 403.0
13 TraesCS1A01G201500 chr3A 86.517 356 20 6 2397 2725 708546042 708545688 1.540000e-97 366.0
14 TraesCS1A01G201500 chr3A 94.118 170 10 0 1516 1685 141553388 141553557 2.690000e-65 259.0
15 TraesCS1A01G201500 chr3A 83.516 182 16 4 1 172 633624186 633624363 1.010000e-34 158.0
16 TraesCS1A01G201500 chr3A 96.078 51 2 0 1796 1846 485291 485341 1.740000e-12 84.2
17 TraesCS1A01G201500 chr3A 96.078 51 2 0 1796 1846 495425 495475 1.740000e-12 84.2
18 TraesCS1A01G201500 chr2A 84.425 565 59 14 1846 2394 753816521 753817072 1.860000e-146 529.0
19 TraesCS1A01G201500 chr2A 77.444 532 83 30 1893 2395 53275963 53276486 1.600000e-72 283.0
20 TraesCS1A01G201500 chr2A 94.340 53 2 1 1797 1849 446550457 446550508 2.250000e-11 80.5
21 TraesCS1A01G201500 chr6D 89.884 346 21 6 2394 2725 331241893 331242238 1.500000e-117 433.0
22 TraesCS1A01G201500 chr6D 77.410 695 91 33 171 850 24030322 24030965 1.200000e-93 353.0
23 TraesCS1A01G201500 chr6D 85.135 222 23 5 628 846 366677149 366677363 4.570000e-53 219.0
24 TraesCS1A01G201500 chr6D 84.762 105 5 2 1701 1795 331241584 331241687 8.030000e-16 95.3
25 TraesCS1A01G201500 chr7D 83.750 480 53 16 870 1327 613873280 613872804 5.390000e-117 431.0
26 TraesCS1A01G201500 chr7D 75.892 701 88 37 171 850 548208148 548208788 1.600000e-72 283.0
27 TraesCS1A01G201500 chr7D 81.102 381 42 16 482 850 463876907 463876545 7.430000e-71 278.0
28 TraesCS1A01G201500 chr7D 81.006 358 37 10 1330 1685 613872765 613872437 3.480000e-64 255.0
29 TraesCS1A01G201500 chr7A 83.473 478 58 13 870 1327 705690272 705689796 2.510000e-115 425.0
30 TraesCS1A01G201500 chr7A 88.000 350 21 8 2397 2725 80916524 80916175 7.070000e-106 394.0
31 TraesCS1A01G201500 chr7A 86.908 359 19 9 2394 2725 2543636 2543993 7.120000e-101 377.0
32 TraesCS1A01G201500 chr7A 86.630 359 20 9 2394 2725 67566315 67566672 3.310000e-99 372.0
33 TraesCS1A01G201500 chr7A 85.434 357 39 5 1330 1685 705689755 705689411 2.580000e-95 359.0
34 TraesCS1A01G201500 chr4A 78.429 700 97 38 171 850 343932909 343933574 9.080000e-110 407.0
35 TraesCS1A01G201500 chr4A 86.275 357 20 10 2397 2725 12665935 12665580 7.170000e-96 361.0
36 TraesCS1A01G201500 chr4A 92.941 170 12 0 1516 1685 12666817 12666648 5.830000e-62 248.0
37 TraesCS1A01G201500 chr4A 95.918 49 2 0 2567 2615 577782276 577782324 2.250000e-11 80.5
38 TraesCS1A01G201500 chr4A 80.822 73 14 0 171 243 606636504 606636432 1.050000e-04 58.4
39 TraesCS1A01G201500 chr4A 80.822 73 14 0 171 243 606640363 606640291 1.050000e-04 58.4
40 TraesCS1A01G201500 chr4A 86.000 50 7 0 171 220 606632645 606632596 1.000000e-03 54.7
41 TraesCS1A01G201500 chr7B 82.609 483 58 17 870 1329 705256657 705256178 1.180000e-108 403.0
42 TraesCS1A01G201500 chr7B 87.042 355 21 6 2394 2725 575441777 575442129 7.120000e-101 377.0
43 TraesCS1A01G201500 chr7B 85.196 358 36 6 1330 1685 705256142 705255800 4.320000e-93 351.0
44 TraesCS1A01G201500 chr7B 95.294 170 8 0 1516 1685 622409111 622408942 1.240000e-68 270.0
45 TraesCS1A01G201500 chr7B 92.063 63 5 0 171 233 165107752 165107690 3.740000e-14 89.8
46 TraesCS1A01G201500 chr7B 86.567 67 8 1 171 236 708505398 708505332 3.760000e-09 73.1
47 TraesCS1A01G201500 chr4B 88.068 352 19 6 2397 2725 620097141 620096790 1.970000e-106 396.0
48 TraesCS1A01G201500 chr4B 86.969 353 22 3 2397 2725 145964674 145964322 2.560000e-100 375.0
49 TraesCS1A01G201500 chr3B 87.640 356 20 3 2394 2725 438574536 438574891 2.540000e-105 392.0
50 TraesCS1A01G201500 chr3B 87.006 354 21 5 2397 2725 492108482 492108129 2.560000e-100 375.0
51 TraesCS1A01G201500 chr3B 82.133 375 39 16 2039 2395 43543079 43542715 2.050000e-76 296.0
52 TraesCS1A01G201500 chr3B 82.143 364 37 11 467 826 49404909 49404570 1.230000e-73 287.0
53 TraesCS1A01G201500 chr3B 94.118 170 10 0 1516 1685 492109351 492109182 2.690000e-65 259.0
54 TraesCS1A01G201500 chr3B 80.159 126 19 6 169 291 498463223 498463345 3.740000e-14 89.8
55 TraesCS1A01G201500 chr5A 87.151 358 20 9 2394 2725 280766735 280767092 1.530000e-102 383.0
56 TraesCS1A01G201500 chr3D 77.730 696 97 29 171 850 28478525 28479178 9.210000e-100 374.0
57 TraesCS1A01G201500 chr3D 79.691 453 51 18 412 850 40718829 40718404 3.430000e-74 289.0
58 TraesCS1A01G201500 chr4D 82.161 398 40 19 465 850 450714425 450714803 2.040000e-81 313.0
59 TraesCS1A01G201500 chr4D 80.590 407 45 20 460 850 134537085 134537473 1.600000e-72 283.0
60 TraesCS1A01G201500 chr6B 94.253 174 9 1 1512 1685 125687430 125687602 5.790000e-67 265.0
61 TraesCS1A01G201500 chr6B 85.222 203 20 4 651 850 552399222 552399417 1.650000e-47 200.0
62 TraesCS1A01G201500 chrUn 79.319 382 51 11 464 841 38873714 38874071 2.710000e-60 243.0
63 TraesCS1A01G201500 chr1D 85.950 121 8 2 2614 2725 395849018 395849138 1.330000e-23 121.0


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 TraesCS1A01G201500 chr1A 362619670 362622394 2724 False 5033.00 5033 100.000000 1 2725 1 chr1A.!!$F1 2724
1 TraesCS1A01G201500 chr1A 502833855 502835091 1236 True 307.00 366 89.748000 1516 2725 2 chr1A.!!$R1 1209
2 TraesCS1A01G201500 chr2D 429498906 429501439 2533 False 813.00 1437 95.246333 1107 2725 3 chr2D.!!$F2 1618
3 TraesCS1A01G201500 chr6A 36490540 36491222 682 False 366.00 595 90.513500 794 1418 2 chr6A.!!$F3 624
4 TraesCS1A01G201500 chr6A 454682905 454683445 540 False 263.00 263 76.565000 171 699 1 chr6A.!!$F1 528
5 TraesCS1A01G201500 chr3A 36072476 36073030 554 True 571.00 571 85.714000 1846 2395 1 chr3A.!!$R1 549
6 TraesCS1A01G201500 chr3A 141553388 141554530 1142 False 331.00 403 91.160000 1516 2725 2 chr3A.!!$F4 1209
7 TraesCS1A01G201500 chr2A 753816521 753817072 551 False 529.00 529 84.425000 1846 2394 1 chr2A.!!$F3 548
8 TraesCS1A01G201500 chr2A 53275963 53276486 523 False 283.00 283 77.444000 1893 2395 1 chr2A.!!$F1 502
9 TraesCS1A01G201500 chr6D 24030322 24030965 643 False 353.00 353 77.410000 171 850 1 chr6D.!!$F1 679
10 TraesCS1A01G201500 chr6D 331241584 331242238 654 False 264.15 433 87.323000 1701 2725 2 chr6D.!!$F3 1024
11 TraesCS1A01G201500 chr7D 613872437 613873280 843 True 343.00 431 82.378000 870 1685 2 chr7D.!!$R2 815
12 TraesCS1A01G201500 chr7D 548208148 548208788 640 False 283.00 283 75.892000 171 850 1 chr7D.!!$F1 679
13 TraesCS1A01G201500 chr7A 705689411 705690272 861 True 392.00 425 84.453500 870 1685 2 chr7A.!!$R2 815
14 TraesCS1A01G201500 chr4A 343932909 343933574 665 False 407.00 407 78.429000 171 850 1 chr4A.!!$F1 679
15 TraesCS1A01G201500 chr4A 12665580 12666817 1237 True 304.50 361 89.608000 1516 2725 2 chr4A.!!$R1 1209
16 TraesCS1A01G201500 chr7B 705255800 705256657 857 True 377.00 403 83.902500 870 1685 2 chr7B.!!$R4 815
17 TraesCS1A01G201500 chr3B 492108129 492109351 1222 True 317.00 375 90.562000 1516 2725 2 chr3B.!!$R3 1209
18 TraesCS1A01G201500 chr3D 28478525 28479178 653 False 374.00 374 77.730000 171 850 1 chr3D.!!$F1 679

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
431 466 0.039618 ACAAAATCATCCCCTGCCGT 59.96 50.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 3593 1.747145 CCTGCGCCTGATCAGATCT 59.253 57.895 24.62 0.0 32.26 2.75 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
27 28 4.212213 CGAGAGGATTTTCGAGATACGT 57.788 45.455 0.00 0.00 43.13 3.57
28 29 3.969352 CGAGAGGATTTTCGAGATACGTG 59.031 47.826 0.00 0.00 43.13 4.49
29 30 3.707793 AGAGGATTTTCGAGATACGTGC 58.292 45.455 0.00 0.00 43.13 5.34
30 31 3.130516 AGAGGATTTTCGAGATACGTGCA 59.869 43.478 0.00 0.00 43.13 4.57
31 32 3.857052 AGGATTTTCGAGATACGTGCAA 58.143 40.909 0.00 0.00 43.13 4.08
32 33 4.250464 AGGATTTTCGAGATACGTGCAAA 58.750 39.130 0.00 0.00 43.13 3.68
33 34 4.876107 AGGATTTTCGAGATACGTGCAAAT 59.124 37.500 0.00 0.00 43.13 2.32
34 35 5.006746 AGGATTTTCGAGATACGTGCAAATC 59.993 40.000 0.00 0.00 43.13 2.17
35 36 5.220586 GGATTTTCGAGATACGTGCAAATCA 60.221 40.000 12.78 0.00 40.77 2.57
36 37 5.794687 TTTTCGAGATACGTGCAAATCAT 57.205 34.783 0.00 0.00 43.13 2.45
37 38 6.895607 TTTTCGAGATACGTGCAAATCATA 57.104 33.333 0.00 0.00 43.13 2.15
38 39 6.895607 TTTCGAGATACGTGCAAATCATAA 57.104 33.333 0.00 0.00 43.13 1.90
39 40 6.510746 TTCGAGATACGTGCAAATCATAAG 57.489 37.500 0.00 0.00 43.13 1.73
40 41 5.827666 TCGAGATACGTGCAAATCATAAGA 58.172 37.500 0.00 0.00 43.13 2.10
41 42 5.685954 TCGAGATACGTGCAAATCATAAGAC 59.314 40.000 0.00 0.00 43.13 3.01
42 43 5.687730 CGAGATACGTGCAAATCATAAGACT 59.312 40.000 0.00 0.00 37.22 3.24
43 44 6.345329 CGAGATACGTGCAAATCATAAGACTG 60.345 42.308 0.00 0.00 37.22 3.51
44 45 3.747099 ACGTGCAAATCATAAGACTGC 57.253 42.857 0.00 0.00 36.79 4.40
45 46 3.073678 ACGTGCAAATCATAAGACTGCA 58.926 40.909 3.18 3.18 41.24 4.41
46 47 3.125829 ACGTGCAAATCATAAGACTGCAG 59.874 43.478 13.48 13.48 42.99 4.41
47 48 3.125829 CGTGCAAATCATAAGACTGCAGT 59.874 43.478 21.88 21.88 42.99 4.40
48 49 4.656041 GTGCAAATCATAAGACTGCAGTC 58.344 43.478 34.82 34.82 42.99 3.51
56 57 4.561731 GACTGCAGTCGTCTGACC 57.438 61.111 29.84 6.63 46.74 4.02
57 58 1.442857 GACTGCAGTCGTCTGACCG 60.443 63.158 29.84 4.33 46.74 4.79
58 59 2.807045 CTGCAGTCGTCTGACCGC 60.807 66.667 14.02 0.00 46.53 5.68
59 60 4.357947 TGCAGTCGTCTGACCGCC 62.358 66.667 14.02 0.00 45.92 6.13
61 62 3.733960 CAGTCGTCTGACCGCCGA 61.734 66.667 3.36 0.00 46.74 5.54
62 63 3.432588 AGTCGTCTGACCGCCGAG 61.433 66.667 1.55 0.00 46.74 4.63
63 64 3.735029 GTCGTCTGACCGCCGAGT 61.735 66.667 1.55 0.00 39.30 4.18
64 65 2.981909 TCGTCTGACCGCCGAGTT 60.982 61.111 1.55 0.00 0.00 3.01
65 66 2.805353 CGTCTGACCGCCGAGTTG 60.805 66.667 1.55 0.00 0.00 3.16
66 67 3.112709 GTCTGACCGCCGAGTTGC 61.113 66.667 0.00 0.00 0.00 4.17
67 68 3.611674 TCTGACCGCCGAGTTGCA 61.612 61.111 0.00 0.00 0.00 4.08
68 69 3.114616 CTGACCGCCGAGTTGCAG 61.115 66.667 0.00 0.00 0.00 4.41
71 72 3.642778 GACCGCCGAGTTGCAGCTA 62.643 63.158 1.86 0.00 0.00 3.32
72 73 2.202932 CCGCCGAGTTGCAGCTAT 60.203 61.111 1.86 0.00 0.00 2.97
73 74 2.528743 CCGCCGAGTTGCAGCTATG 61.529 63.158 1.86 0.00 0.00 2.23
74 75 2.528743 CGCCGAGTTGCAGCTATGG 61.529 63.158 14.71 14.71 0.00 2.74
75 76 2.828128 GCCGAGTTGCAGCTATGGC 61.828 63.158 24.07 24.07 34.44 4.40
99 100 2.673074 GCCTTCGCGTATTGCTACA 58.327 52.632 5.77 0.00 43.27 2.74
100 101 1.003851 GCCTTCGCGTATTGCTACAA 58.996 50.000 5.77 0.00 43.27 2.41
101 102 1.395608 GCCTTCGCGTATTGCTACAAA 59.604 47.619 5.77 0.00 43.27 2.83
102 103 2.031683 GCCTTCGCGTATTGCTACAAAT 59.968 45.455 5.77 0.00 43.27 2.32
103 104 3.844943 GCCTTCGCGTATTGCTACAAATC 60.845 47.826 5.77 0.00 43.27 2.17
104 105 3.303132 CCTTCGCGTATTGCTACAAATCC 60.303 47.826 5.77 0.00 43.27 3.01
105 106 3.173668 TCGCGTATTGCTACAAATCCT 57.826 42.857 5.77 0.00 43.27 3.24
106 107 4.310357 TCGCGTATTGCTACAAATCCTA 57.690 40.909 5.77 0.00 43.27 2.94
107 108 4.046462 TCGCGTATTGCTACAAATCCTAC 58.954 43.478 5.77 0.00 43.27 3.18
108 109 3.183775 CGCGTATTGCTACAAATCCTACC 59.816 47.826 0.00 0.00 43.27 3.18
109 110 4.124238 GCGTATTGCTACAAATCCTACCA 58.876 43.478 0.00 0.00 41.73 3.25
110 111 4.573201 GCGTATTGCTACAAATCCTACCAA 59.427 41.667 0.00 0.00 41.73 3.67
111 112 5.065474 GCGTATTGCTACAAATCCTACCAAA 59.935 40.000 0.00 0.00 41.73 3.28
112 113 6.238648 GCGTATTGCTACAAATCCTACCAAAT 60.239 38.462 0.00 0.00 41.73 2.32
113 114 7.132213 CGTATTGCTACAAATCCTACCAAATG 58.868 38.462 0.00 0.00 0.00 2.32
114 115 4.981806 TGCTACAAATCCTACCAAATGC 57.018 40.909 0.00 0.00 0.00 3.56
115 116 3.699038 TGCTACAAATCCTACCAAATGCC 59.301 43.478 0.00 0.00 0.00 4.40
116 117 3.699038 GCTACAAATCCTACCAAATGCCA 59.301 43.478 0.00 0.00 0.00 4.92
117 118 4.342092 GCTACAAATCCTACCAAATGCCAT 59.658 41.667 0.00 0.00 0.00 4.40
118 119 4.741321 ACAAATCCTACCAAATGCCATG 57.259 40.909 0.00 0.00 0.00 3.66
119 120 4.352009 ACAAATCCTACCAAATGCCATGA 58.648 39.130 0.00 0.00 0.00 3.07
120 121 4.403432 ACAAATCCTACCAAATGCCATGAG 59.597 41.667 0.00 0.00 0.00 2.90
121 122 2.734755 TCCTACCAAATGCCATGAGG 57.265 50.000 0.00 0.00 38.23 3.86
122 123 2.204463 TCCTACCAAATGCCATGAGGA 58.796 47.619 0.00 0.00 36.89 3.71
123 124 2.092429 TCCTACCAAATGCCATGAGGAC 60.092 50.000 0.00 0.00 36.89 3.85
124 125 2.301346 CTACCAAATGCCATGAGGACC 58.699 52.381 0.00 0.00 36.89 4.46
125 126 0.409092 ACCAAATGCCATGAGGACCA 59.591 50.000 0.00 0.00 36.89 4.02
126 127 1.007479 ACCAAATGCCATGAGGACCAT 59.993 47.619 0.00 0.00 36.89 3.55
127 128 1.684983 CCAAATGCCATGAGGACCATC 59.315 52.381 0.00 0.00 36.89 3.51
128 129 1.684983 CAAATGCCATGAGGACCATCC 59.315 52.381 0.00 0.00 36.89 3.51
129 130 0.928505 AATGCCATGAGGACCATCCA 59.071 50.000 0.00 0.00 39.61 3.41
130 131 0.477204 ATGCCATGAGGACCATCCAG 59.523 55.000 0.00 0.00 39.61 3.86
131 132 0.621280 TGCCATGAGGACCATCCAGA 60.621 55.000 0.00 0.00 39.61 3.86
132 133 0.548031 GCCATGAGGACCATCCAGAA 59.452 55.000 0.00 0.00 39.61 3.02
133 134 1.064463 GCCATGAGGACCATCCAGAAA 60.064 52.381 0.00 0.00 39.61 2.52
134 135 2.928334 CCATGAGGACCATCCAGAAAG 58.072 52.381 0.00 0.00 39.61 2.62
135 136 2.240667 CCATGAGGACCATCCAGAAAGT 59.759 50.000 0.00 0.00 39.61 2.66
136 137 3.455910 CCATGAGGACCATCCAGAAAGTA 59.544 47.826 0.00 0.00 39.61 2.24
137 138 4.444022 CCATGAGGACCATCCAGAAAGTAG 60.444 50.000 0.00 0.00 39.61 2.57
138 139 2.501723 TGAGGACCATCCAGAAAGTAGC 59.498 50.000 0.00 0.00 39.61 3.58
139 140 2.501723 GAGGACCATCCAGAAAGTAGCA 59.498 50.000 0.00 0.00 39.61 3.49
140 141 2.503356 AGGACCATCCAGAAAGTAGCAG 59.497 50.000 0.00 0.00 39.61 4.24
141 142 2.284190 GACCATCCAGAAAGTAGCAGC 58.716 52.381 0.00 0.00 0.00 5.25
142 143 1.630369 ACCATCCAGAAAGTAGCAGCA 59.370 47.619 0.00 0.00 0.00 4.41
143 144 2.286872 CCATCCAGAAAGTAGCAGCAG 58.713 52.381 0.00 0.00 0.00 4.24
144 145 2.093288 CCATCCAGAAAGTAGCAGCAGA 60.093 50.000 0.00 0.00 0.00 4.26
145 146 2.751166 TCCAGAAAGTAGCAGCAGAC 57.249 50.000 0.00 0.00 0.00 3.51
146 147 1.067565 TCCAGAAAGTAGCAGCAGACG 60.068 52.381 0.00 0.00 0.00 4.18
147 148 1.067565 CCAGAAAGTAGCAGCAGACGA 60.068 52.381 0.00 0.00 0.00 4.20
148 149 1.989165 CAGAAAGTAGCAGCAGACGAC 59.011 52.381 0.00 0.00 0.00 4.34
149 150 0.985549 GAAAGTAGCAGCAGACGACG 59.014 55.000 0.00 0.00 0.00 5.12
150 151 1.009389 AAAGTAGCAGCAGACGACGC 61.009 55.000 0.00 0.00 0.00 5.19
151 152 3.241059 GTAGCAGCAGACGACGCG 61.241 66.667 3.53 3.53 0.00 6.01
164 165 2.429571 ACGCGCGTACGTCACAAT 60.430 55.556 37.08 4.68 44.43 2.71
165 166 1.154244 ACGCGCGTACGTCACAATA 60.154 52.632 37.08 0.00 44.43 1.90
166 167 1.129879 ACGCGCGTACGTCACAATAG 61.130 55.000 37.08 0.00 44.43 1.73
167 168 1.268946 GCGCGTACGTCACAATAGC 59.731 57.895 17.90 6.30 42.83 2.97
168 169 1.547134 CGCGTACGTCACAATAGCG 59.453 57.895 17.90 4.33 40.14 4.26
169 170 1.794455 CGCGTACGTCACAATAGCGG 61.794 60.000 17.90 0.00 42.04 5.52
233 235 2.032799 ACCACACAGCAAAATGTACACG 59.967 45.455 0.00 0.00 0.00 4.49
238 240 3.249799 CACAGCAAAATGTACACGGAAGA 59.750 43.478 0.00 0.00 0.00 2.87
243 245 4.498345 GCAAAATGTACACGGAAGAACCAA 60.498 41.667 0.00 0.00 38.90 3.67
255 257 4.689345 CGGAAGAACCAAAGACGTTAGATT 59.311 41.667 0.00 0.00 38.90 2.40
257 259 6.034683 CGGAAGAACCAAAGACGTTAGATTAG 59.965 42.308 0.00 0.00 38.90 1.73
263 265 7.653767 ACCAAAGACGTTAGATTAGTCAAAG 57.346 36.000 0.00 0.00 37.36 2.77
270 272 9.286946 AGACGTTAGATTAGTCAAAGTAAATCG 57.713 33.333 0.00 0.00 37.36 3.34
275 277 9.817809 TTAGATTAGTCAAAGTAAATCGCATCT 57.182 29.630 0.00 0.00 34.31 2.90
280 282 7.295952 AGTCAAAGTAAATCGCATCTAACAG 57.704 36.000 0.00 0.00 0.00 3.16
283 285 7.063544 GTCAAAGTAAATCGCATCTAACAGTCT 59.936 37.037 0.00 0.00 0.00 3.24
294 296 9.232473 TCGCATCTAACAGTCTATATTACATCT 57.768 33.333 0.00 0.00 0.00 2.90
323 326 2.033151 GTGACACAAACTAACGCTCCAC 60.033 50.000 0.00 0.00 0.00 4.02
329 332 5.472137 ACACAAACTAACGCTCCACATTAAT 59.528 36.000 0.00 0.00 0.00 1.40
363 374 2.283966 CCCACGTCCTGTCCCTCT 60.284 66.667 0.00 0.00 0.00 3.69
368 379 1.674651 CGTCCTGTCCCTCTCACGA 60.675 63.158 0.00 0.00 0.00 4.35
377 388 1.729470 CCCTCTCACGATCCACCTCG 61.729 65.000 0.00 0.00 44.14 4.63
413 424 2.399611 GCACATCACGCGCCTAAC 59.600 61.111 5.73 0.00 0.00 2.34
430 465 1.185315 AACAAAATCATCCCCTGCCG 58.815 50.000 0.00 0.00 0.00 5.69
431 466 0.039618 ACAAAATCATCCCCTGCCGT 59.960 50.000 0.00 0.00 0.00 5.68
457 494 4.806339 CCCCGCTTCCTCCCCTCT 62.806 72.222 0.00 0.00 0.00 3.69
458 495 2.282446 CCCGCTTCCTCCCCTCTA 59.718 66.667 0.00 0.00 0.00 2.43
465 502 2.042843 CCTCCCCTCTACCGTGCT 60.043 66.667 0.00 0.00 0.00 4.40
470 507 1.686110 CCCTCTACCGTGCTTCCCT 60.686 63.158 0.00 0.00 0.00 4.20
547 591 4.584966 ATCTCCCCTATTTCCCTCTCTT 57.415 45.455 0.00 0.00 0.00 2.85
648 693 1.302752 CACACCCTAAGCTGCAGCA 60.303 57.895 38.24 19.64 45.16 4.41
649 694 0.890542 CACACCCTAAGCTGCAGCAA 60.891 55.000 38.24 24.99 45.16 3.91
665 712 2.176273 CAAAGATGCCCGAGCGAGG 61.176 63.158 0.00 0.00 44.31 4.63
789 845 3.385384 CTGCTCCCTCGACCTGCA 61.385 66.667 0.00 0.00 0.00 4.41
790 846 3.368190 CTGCTCCCTCGACCTGCAG 62.368 68.421 6.78 6.78 43.71 4.41
826 882 4.127040 CAGCAGCTCCTCGACGCT 62.127 66.667 0.00 0.00 36.83 5.07
846 902 0.678048 GGCATCCGCTTCTTCCAAGT 60.678 55.000 0.00 0.00 38.60 3.16
850 906 1.508632 TCCGCTTCTTCCAAGTTTCG 58.491 50.000 0.00 0.00 0.00 3.46
860 916 5.369833 TCTTCCAAGTTTCGTATTGGTTCA 58.630 37.500 4.05 0.00 45.16 3.18
920 976 2.068915 TGCTGGATCTGAAGCACCA 58.931 52.632 12.33 0.00 44.26 4.17
931 987 2.971330 CTGAAGCACCAGATAGGGAGAT 59.029 50.000 0.00 0.00 43.89 2.75
950 1006 0.978667 TGCCCCTTCGTGTATGCCTA 60.979 55.000 0.00 0.00 0.00 3.93
955 1011 3.056749 CCCCTTCGTGTATGCCTAGATAC 60.057 52.174 0.00 0.00 0.00 2.24
957 1013 3.572682 CCTTCGTGTATGCCTAGATACCA 59.427 47.826 0.00 0.00 0.00 3.25
959 1015 5.452776 CCTTCGTGTATGCCTAGATACCAAA 60.453 44.000 0.00 0.00 0.00 3.28
961 1017 4.038763 TCGTGTATGCCTAGATACCAAAGG 59.961 45.833 0.00 0.00 0.00 3.11
978 1046 5.059833 CCAAAGGCAGAGTATTATGACCTC 58.940 45.833 0.00 0.00 0.00 3.85
1063 1131 1.669211 CGAGGTTCAACGAGGTCTTCC 60.669 57.143 0.00 0.00 0.00 3.46
1075 1143 1.244019 GGTCTTCCGCAAATGCCAGT 61.244 55.000 0.00 0.00 37.91 4.00
1079 1147 4.440127 CCGCAAATGCCAGTGCCC 62.440 66.667 0.00 0.00 37.47 5.36
1145 1216 6.473758 GGAGGGTATATATTTTCTGGTGGAC 58.526 44.000 0.00 0.00 0.00 4.02
1179 1250 4.322953 GGGTTGCCTGTGAATGAATCAATT 60.323 41.667 0.00 0.00 40.50 2.32
1200 1282 9.528018 TCAATTAAGATGGAGTTTTGTTTTGTC 57.472 29.630 0.00 0.00 0.00 3.18
1445 1568 5.547181 TGTGTTGAACGTGTTGTTTGATA 57.453 34.783 0.00 0.00 42.09 2.15
1446 1569 6.125327 TGTGTTGAACGTGTTGTTTGATAT 57.875 33.333 0.00 0.00 42.09 1.63
1475 1598 4.816925 GGCATGTATCCTTTCTCACCTTAC 59.183 45.833 0.00 0.00 0.00 2.34
1624 1748 4.321750 GCTTGGTGTGCTAGAACTACACTA 60.322 45.833 1.64 2.66 43.11 2.74
1627 1751 4.770531 TGGTGTGCTAGAACTACACTACAT 59.229 41.667 1.64 0.00 43.11 2.29
1749 3028 6.942576 AGTATGTTTAGCTTGGTGATTTGTCT 59.057 34.615 0.00 0.00 0.00 3.41
1792 3071 9.453572 TTTTATCTACTGCATCTGTTTTGATCT 57.546 29.630 0.00 0.00 0.00 2.75
1793 3072 9.453572 TTTATCTACTGCATCTGTTTTGATCTT 57.546 29.630 0.00 0.00 0.00 2.40
1794 3073 7.934855 ATCTACTGCATCTGTTTTGATCTTT 57.065 32.000 0.00 0.00 0.00 2.52
1796 3075 8.256611 TCTACTGCATCTGTTTTGATCTTTAC 57.743 34.615 0.00 0.00 0.00 2.01
1797 3076 5.931532 ACTGCATCTGTTTTGATCTTTACG 58.068 37.500 0.00 0.00 0.00 3.18
1798 3077 5.700832 ACTGCATCTGTTTTGATCTTTACGA 59.299 36.000 0.00 0.00 0.00 3.43
1799 3078 6.204688 ACTGCATCTGTTTTGATCTTTACGAA 59.795 34.615 0.00 0.00 0.00 3.85
1800 3079 6.964908 TGCATCTGTTTTGATCTTTACGAAA 58.035 32.000 0.00 0.00 0.00 3.46
1801 3080 7.592938 TGCATCTGTTTTGATCTTTACGAAAT 58.407 30.769 0.00 0.00 0.00 2.17
1802 3081 8.726068 TGCATCTGTTTTGATCTTTACGAAATA 58.274 29.630 0.00 0.00 0.00 1.40
1803 3082 9.214953 GCATCTGTTTTGATCTTTACGAAATAG 57.785 33.333 0.00 0.00 33.89 1.73
1804 3083 9.708222 CATCTGTTTTGATCTTTACGAAATAGG 57.292 33.333 0.00 0.00 33.62 2.57
1805 3084 7.748847 TCTGTTTTGATCTTTACGAAATAGGC 58.251 34.615 0.00 0.00 33.62 3.93
1806 3085 7.606456 TCTGTTTTGATCTTTACGAAATAGGCT 59.394 33.333 0.00 0.00 33.62 4.58
1807 3086 8.106247 TGTTTTGATCTTTACGAAATAGGCTT 57.894 30.769 0.00 0.00 0.00 4.35
1808 3087 8.573035 TGTTTTGATCTTTACGAAATAGGCTTT 58.427 29.630 0.00 0.00 0.00 3.51
1809 3088 9.062674 GTTTTGATCTTTACGAAATAGGCTTTC 57.937 33.333 0.00 0.00 0.00 2.62
1824 3103 3.955650 GCTTTCGCCCCACTATATAGA 57.044 47.619 16.79 0.00 0.00 1.98
1825 3104 4.473477 GCTTTCGCCCCACTATATAGAT 57.527 45.455 16.79 0.00 0.00 1.98
1826 3105 5.593679 GCTTTCGCCCCACTATATAGATA 57.406 43.478 16.79 0.00 0.00 1.98
1827 3106 6.163135 GCTTTCGCCCCACTATATAGATAT 57.837 41.667 16.79 0.00 0.00 1.63
1828 3107 7.286215 GCTTTCGCCCCACTATATAGATATA 57.714 40.000 16.79 0.00 0.00 0.86
1829 3108 7.371936 GCTTTCGCCCCACTATATAGATATAG 58.628 42.308 16.79 12.94 44.88 1.31
1830 3109 6.896021 TTCGCCCCACTATATAGATATAGC 57.104 41.667 16.79 10.58 43.77 2.97
1831 3110 5.948842 TCGCCCCACTATATAGATATAGCA 58.051 41.667 16.79 2.15 43.77 3.49
1832 3111 6.370453 TCGCCCCACTATATAGATATAGCAA 58.630 40.000 16.79 0.00 43.77 3.91
1833 3112 6.264744 TCGCCCCACTATATAGATATAGCAAC 59.735 42.308 16.79 2.74 43.77 4.17
1834 3113 6.516860 CGCCCCACTATATAGATATAGCAACC 60.517 46.154 16.79 2.49 43.77 3.77
1835 3114 6.555360 GCCCCACTATATAGATATAGCAACCT 59.445 42.308 16.79 0.00 43.77 3.50
1836 3115 7.256012 GCCCCACTATATAGATATAGCAACCTC 60.256 44.444 16.79 0.55 43.77 3.85
1837 3116 7.233757 CCCCACTATATAGATATAGCAACCTCC 59.766 44.444 16.79 0.00 43.77 4.30
1838 3117 7.233757 CCCACTATATAGATATAGCAACCTCCC 59.766 44.444 16.79 0.00 43.77 4.30
1839 3118 7.040340 CCACTATATAGATATAGCAACCTCCCG 60.040 44.444 16.79 0.00 43.77 5.14
1840 3119 7.720074 CACTATATAGATATAGCAACCTCCCGA 59.280 40.741 16.79 0.00 43.77 5.14
1841 3120 8.449625 ACTATATAGATATAGCAACCTCCCGAT 58.550 37.037 16.79 0.00 43.77 4.18
1842 3121 9.961264 CTATATAGATATAGCAACCTCCCGATA 57.039 37.037 3.44 0.00 36.77 2.92
1843 3122 6.963083 ATAGATATAGCAACCTCCCGATAC 57.037 41.667 0.00 0.00 0.00 2.24
1844 3123 4.673968 AGATATAGCAACCTCCCGATACA 58.326 43.478 0.00 0.00 0.00 2.29
2031 3447 6.358974 TCATTCTTTGATGACCAGTACAGA 57.641 37.500 0.00 0.00 31.35 3.41
2159 3583 0.403271 ACAGCAACCAAGAGATGCCT 59.597 50.000 0.00 0.00 40.93 4.75
2168 3593 1.839994 CAAGAGATGCCTAGGTCCCAA 59.160 52.381 11.31 0.00 0.00 4.12
2171 3596 2.090267 AGAGATGCCTAGGTCCCAAGAT 60.090 50.000 11.31 0.00 0.00 2.40
2181 3606 1.202746 GGTCCCAAGATCTGATCAGGC 60.203 57.143 22.42 14.51 0.00 4.85
2236 3683 3.573967 TGGCCTTTTCATCCTCTTGTTTC 59.426 43.478 3.32 0.00 0.00 2.78
2262 3711 3.319137 TTTCCATGGAGAAGTCGAGTG 57.681 47.619 15.53 0.00 0.00 3.51
2263 3712 1.924731 TCCATGGAGAAGTCGAGTGT 58.075 50.000 11.44 0.00 0.00 3.55
2264 3713 2.248248 TCCATGGAGAAGTCGAGTGTT 58.752 47.619 11.44 0.00 0.00 3.32
2265 3714 3.427573 TCCATGGAGAAGTCGAGTGTTA 58.572 45.455 11.44 0.00 0.00 2.41
2373 3822 6.849811 GCATTCAATCTACAATCATCAGTTCG 59.150 38.462 0.00 0.00 0.00 3.95
2439 3892 5.426689 TGCTCTTTTACTGATGGACTGAT 57.573 39.130 0.00 0.00 0.00 2.90
2485 3938 6.017109 GCCGTATTGATCCAAATGACAAGTAT 60.017 38.462 0.00 0.00 0.00 2.12
2644 4115 0.973632 TGCATACTGTCGACAAGGGT 59.026 50.000 20.49 16.15 0.00 4.34
2646 4117 1.067142 GCATACTGTCGACAAGGGTGA 60.067 52.381 20.49 1.63 0.00 4.02
2665 4137 4.573607 GGTGAGACGTTTTTCCTTAACTGT 59.426 41.667 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.009829 CGAAAATCCTCTCGGCCTTG 58.990 55.000 0.00 0.00 0.00 3.61
1 2 0.902531 TCGAAAATCCTCTCGGCCTT 59.097 50.000 0.00 0.00 35.76 4.35
2 3 0.461961 CTCGAAAATCCTCTCGGCCT 59.538 55.000 0.00 0.00 35.76 5.19
3 4 0.460311 TCTCGAAAATCCTCTCGGCC 59.540 55.000 0.00 0.00 35.76 6.13
4 5 2.517650 ATCTCGAAAATCCTCTCGGC 57.482 50.000 0.00 0.00 35.76 5.54
5 6 3.003482 ACGTATCTCGAAAATCCTCTCGG 59.997 47.826 0.00 0.00 42.86 4.63
6 7 3.969352 CACGTATCTCGAAAATCCTCTCG 59.031 47.826 0.00 0.00 42.86 4.04
7 8 3.731717 GCACGTATCTCGAAAATCCTCTC 59.268 47.826 0.00 0.00 42.86 3.20
8 9 3.130516 TGCACGTATCTCGAAAATCCTCT 59.869 43.478 0.00 0.00 42.86 3.69
9 10 3.444916 TGCACGTATCTCGAAAATCCTC 58.555 45.455 0.00 0.00 42.86 3.71
10 11 3.520290 TGCACGTATCTCGAAAATCCT 57.480 42.857 0.00 0.00 42.86 3.24
11 12 4.593597 TTTGCACGTATCTCGAAAATCC 57.406 40.909 0.00 0.00 42.86 3.01
12 13 5.795766 TGATTTGCACGTATCTCGAAAATC 58.204 37.500 8.61 8.61 41.48 2.17
13 14 5.794687 TGATTTGCACGTATCTCGAAAAT 57.205 34.783 0.00 0.00 42.86 1.82
14 15 5.794687 ATGATTTGCACGTATCTCGAAAA 57.205 34.783 0.00 0.00 42.86 2.29
15 16 6.754675 TCTTATGATTTGCACGTATCTCGAAA 59.245 34.615 0.00 0.00 42.86 3.46
16 17 6.198403 GTCTTATGATTTGCACGTATCTCGAA 59.802 38.462 0.00 0.00 42.86 3.71
17 18 5.685954 GTCTTATGATTTGCACGTATCTCGA 59.314 40.000 0.00 0.00 42.86 4.04
18 19 5.687730 AGTCTTATGATTTGCACGTATCTCG 59.312 40.000 0.00 0.00 46.00 4.04
19 20 6.563010 GCAGTCTTATGATTTGCACGTATCTC 60.563 42.308 11.00 0.00 36.40 2.75
20 21 5.235186 GCAGTCTTATGATTTGCACGTATCT 59.765 40.000 11.00 0.00 36.40 1.98
21 22 5.006649 TGCAGTCTTATGATTTGCACGTATC 59.993 40.000 13.31 0.00 39.21 2.24
22 23 4.875536 TGCAGTCTTATGATTTGCACGTAT 59.124 37.500 13.31 0.00 39.21 3.06
23 24 4.249661 TGCAGTCTTATGATTTGCACGTA 58.750 39.130 13.31 0.00 39.21 3.57
24 25 3.073678 TGCAGTCTTATGATTTGCACGT 58.926 40.909 13.31 0.00 39.21 4.49
25 26 3.125829 ACTGCAGTCTTATGATTTGCACG 59.874 43.478 15.25 12.17 39.21 5.34
26 27 4.656041 GACTGCAGTCTTATGATTTGCAC 58.344 43.478 34.54 8.05 39.21 4.57
27 28 3.371898 CGACTGCAGTCTTATGATTTGCA 59.628 43.478 36.78 15.29 42.66 4.08
28 29 3.372206 ACGACTGCAGTCTTATGATTTGC 59.628 43.478 36.78 13.43 42.66 3.68
29 30 4.867047 AGACGACTGCAGTCTTATGATTTG 59.133 41.667 36.78 23.20 45.74 2.32
30 31 4.867047 CAGACGACTGCAGTCTTATGATTT 59.133 41.667 36.78 15.43 45.74 2.17
31 32 4.158579 TCAGACGACTGCAGTCTTATGATT 59.841 41.667 33.94 16.77 45.74 2.57
32 33 3.696548 TCAGACGACTGCAGTCTTATGAT 59.303 43.478 33.94 18.78 45.74 2.45
33 34 3.081804 TCAGACGACTGCAGTCTTATGA 58.918 45.455 33.94 33.94 45.74 2.15
34 35 3.175152 GTCAGACGACTGCAGTCTTATG 58.825 50.000 36.78 33.89 45.74 1.90
35 36 2.164624 GGTCAGACGACTGCAGTCTTAT 59.835 50.000 36.78 26.47 45.74 1.73
36 37 1.540267 GGTCAGACGACTGCAGTCTTA 59.460 52.381 36.78 16.26 45.74 2.10
37 38 0.315568 GGTCAGACGACTGCAGTCTT 59.684 55.000 36.78 31.16 45.74 3.01
39 40 1.442857 CGGTCAGACGACTGCAGTC 60.443 63.158 32.73 32.73 41.53 3.51
40 41 2.645567 CGGTCAGACGACTGCAGT 59.354 61.111 21.88 21.88 41.53 4.40
49 50 3.112709 GCAACTCGGCGGTCAGAC 61.113 66.667 7.21 0.00 0.00 3.51
50 51 3.573772 CTGCAACTCGGCGGTCAGA 62.574 63.158 7.21 0.00 35.41 3.27
51 52 3.114616 CTGCAACTCGGCGGTCAG 61.115 66.667 7.21 0.00 35.41 3.51
58 59 3.414272 GCCATAGCTGCAACTCGG 58.586 61.111 1.02 0.00 35.50 4.63
87 88 4.124238 TGGTAGGATTTGTAGCAATACGC 58.876 43.478 0.00 0.00 42.91 4.42
88 89 6.671614 TTTGGTAGGATTTGTAGCAATACG 57.328 37.500 0.00 0.00 37.63 3.06
89 90 6.918022 GCATTTGGTAGGATTTGTAGCAATAC 59.082 38.462 0.00 0.00 37.63 1.89
90 91 6.040391 GGCATTTGGTAGGATTTGTAGCAATA 59.960 38.462 0.00 0.00 37.63 1.90
91 92 5.163416 GGCATTTGGTAGGATTTGTAGCAAT 60.163 40.000 0.00 0.00 37.63 3.56
92 93 4.159506 GGCATTTGGTAGGATTTGTAGCAA 59.840 41.667 0.00 0.00 36.38 3.91
93 94 3.699038 GGCATTTGGTAGGATTTGTAGCA 59.301 43.478 0.00 0.00 0.00 3.49
94 95 3.699038 TGGCATTTGGTAGGATTTGTAGC 59.301 43.478 0.00 0.00 0.00 3.58
95 96 5.593909 TCATGGCATTTGGTAGGATTTGTAG 59.406 40.000 0.00 0.00 0.00 2.74
96 97 5.514169 TCATGGCATTTGGTAGGATTTGTA 58.486 37.500 0.00 0.00 0.00 2.41
97 98 4.352009 TCATGGCATTTGGTAGGATTTGT 58.648 39.130 0.00 0.00 0.00 2.83
98 99 4.202182 CCTCATGGCATTTGGTAGGATTTG 60.202 45.833 0.00 0.00 0.00 2.32
99 100 3.962718 CCTCATGGCATTTGGTAGGATTT 59.037 43.478 0.00 0.00 0.00 2.17
100 101 3.205056 TCCTCATGGCATTTGGTAGGATT 59.795 43.478 13.25 0.00 0.00 3.01
101 102 2.785269 TCCTCATGGCATTTGGTAGGAT 59.215 45.455 13.25 0.00 0.00 3.24
102 103 2.092429 GTCCTCATGGCATTTGGTAGGA 60.092 50.000 13.25 10.41 0.00 2.94
103 104 2.301346 GTCCTCATGGCATTTGGTAGG 58.699 52.381 13.25 8.63 0.00 3.18
104 105 2.301346 GGTCCTCATGGCATTTGGTAG 58.699 52.381 13.25 0.00 0.00 3.18
105 106 1.638070 TGGTCCTCATGGCATTTGGTA 59.362 47.619 13.25 1.32 0.00 3.25
106 107 0.409092 TGGTCCTCATGGCATTTGGT 59.591 50.000 13.25 0.00 0.00 3.67
107 108 1.684983 GATGGTCCTCATGGCATTTGG 59.315 52.381 0.00 2.95 35.97 3.28
108 109 1.684983 GGATGGTCCTCATGGCATTTG 59.315 52.381 0.00 0.00 35.97 2.32
109 110 1.288633 TGGATGGTCCTCATGGCATTT 59.711 47.619 0.00 0.00 37.46 2.32
110 111 0.928505 TGGATGGTCCTCATGGCATT 59.071 50.000 0.00 0.00 37.46 3.56
111 112 0.477204 CTGGATGGTCCTCATGGCAT 59.523 55.000 0.00 0.00 37.46 4.40
112 113 0.621280 TCTGGATGGTCCTCATGGCA 60.621 55.000 0.00 0.00 37.46 4.92
113 114 0.548031 TTCTGGATGGTCCTCATGGC 59.452 55.000 0.00 0.00 37.46 4.40
114 115 2.240667 ACTTTCTGGATGGTCCTCATGG 59.759 50.000 0.00 0.00 37.46 3.66
115 116 3.641434 ACTTTCTGGATGGTCCTCATG 57.359 47.619 0.00 0.00 37.46 3.07
116 117 3.135530 GCTACTTTCTGGATGGTCCTCAT 59.864 47.826 0.00 0.00 37.46 2.90
117 118 2.501723 GCTACTTTCTGGATGGTCCTCA 59.498 50.000 0.00 0.00 37.46 3.86
118 119 2.501723 TGCTACTTTCTGGATGGTCCTC 59.498 50.000 0.00 0.00 37.46 3.71
119 120 2.503356 CTGCTACTTTCTGGATGGTCCT 59.497 50.000 0.00 0.00 37.46 3.85
120 121 2.911484 CTGCTACTTTCTGGATGGTCC 58.089 52.381 0.00 0.00 36.96 4.46
121 122 2.284190 GCTGCTACTTTCTGGATGGTC 58.716 52.381 0.00 0.00 0.00 4.02
122 123 1.630369 TGCTGCTACTTTCTGGATGGT 59.370 47.619 0.00 0.00 0.00 3.55
123 124 2.093288 TCTGCTGCTACTTTCTGGATGG 60.093 50.000 0.00 0.00 0.00 3.51
124 125 2.935201 GTCTGCTGCTACTTTCTGGATG 59.065 50.000 0.00 0.00 0.00 3.51
125 126 2.417924 CGTCTGCTGCTACTTTCTGGAT 60.418 50.000 0.00 0.00 0.00 3.41
126 127 1.067565 CGTCTGCTGCTACTTTCTGGA 60.068 52.381 0.00 0.00 0.00 3.86
127 128 1.067565 TCGTCTGCTGCTACTTTCTGG 60.068 52.381 0.00 0.00 0.00 3.86
128 129 1.989165 GTCGTCTGCTGCTACTTTCTG 59.011 52.381 0.00 0.00 0.00 3.02
129 130 1.401670 CGTCGTCTGCTGCTACTTTCT 60.402 52.381 0.00 0.00 0.00 2.52
130 131 0.985549 CGTCGTCTGCTGCTACTTTC 59.014 55.000 0.00 0.00 0.00 2.62
131 132 1.009389 GCGTCGTCTGCTGCTACTTT 61.009 55.000 0.00 0.00 0.00 2.66
132 133 1.444553 GCGTCGTCTGCTGCTACTT 60.445 57.895 0.00 0.00 0.00 2.24
133 134 2.179517 GCGTCGTCTGCTGCTACT 59.820 61.111 0.00 0.00 0.00 2.57
134 135 3.241059 CGCGTCGTCTGCTGCTAC 61.241 66.667 0.00 0.00 0.00 3.58
148 149 1.547134 CTATTGTGACGTACGCGCG 59.453 57.895 30.96 30.96 42.83 6.86
149 150 1.268946 GCTATTGTGACGTACGCGC 59.731 57.895 16.72 14.92 42.83 6.86
150 151 1.547134 CGCTATTGTGACGTACGCG 59.453 57.895 16.72 3.53 44.93 6.01
151 152 0.523968 TCCGCTATTGTGACGTACGC 60.524 55.000 16.72 8.98 0.00 4.42
152 153 2.041966 GATCCGCTATTGTGACGTACG 58.958 52.381 15.01 15.01 0.00 3.67
153 154 3.351020 AGATCCGCTATTGTGACGTAC 57.649 47.619 0.00 0.00 0.00 3.67
154 155 5.936372 AGTATAGATCCGCTATTGTGACGTA 59.064 40.000 0.00 0.00 40.30 3.57
155 156 4.760715 AGTATAGATCCGCTATTGTGACGT 59.239 41.667 0.00 0.00 40.30 4.34
156 157 5.298197 AGTATAGATCCGCTATTGTGACG 57.702 43.478 0.00 0.00 40.30 4.35
157 158 7.380431 AGTAGTATAGATCCGCTATTGTGAC 57.620 40.000 0.00 0.00 40.30 3.67
158 159 9.682465 AATAGTAGTATAGATCCGCTATTGTGA 57.318 33.333 0.00 0.00 40.30 3.58
166 167 9.505995 GCTCTTTTAATAGTAGTATAGATCCGC 57.494 37.037 0.00 0.00 0.00 5.54
198 199 5.362430 TGCTGTGTGGTTTTAGAGGAATTTT 59.638 36.000 0.00 0.00 0.00 1.82
201 202 4.098914 TGCTGTGTGGTTTTAGAGGAAT 57.901 40.909 0.00 0.00 0.00 3.01
203 205 3.569194 TTGCTGTGTGGTTTTAGAGGA 57.431 42.857 0.00 0.00 0.00 3.71
212 214 2.032799 CGTGTACATTTTGCTGTGTGGT 59.967 45.455 0.00 0.00 0.00 4.16
233 235 6.872547 ACTAATCTAACGTCTTTGGTTCTTCC 59.127 38.462 0.00 0.00 0.00 3.46
238 240 7.713942 ACTTTGACTAATCTAACGTCTTTGGTT 59.286 33.333 0.00 0.00 0.00 3.67
255 257 8.033038 ACTGTTAGATGCGATTTACTTTGACTA 58.967 33.333 0.00 0.00 0.00 2.59
257 259 7.061752 ACTGTTAGATGCGATTTACTTTGAC 57.938 36.000 0.00 0.00 0.00 3.18
300 302 2.610374 GGAGCGTTAGTTTGTGTCACAA 59.390 45.455 14.48 14.48 36.11 3.33
304 306 2.206750 TGTGGAGCGTTAGTTTGTGTC 58.793 47.619 0.00 0.00 0.00 3.67
323 326 3.514645 GTGCCTGGCAGAACAATTAATG 58.485 45.455 24.10 0.00 40.08 1.90
329 332 3.286751 GCGTGCCTGGCAGAACAA 61.287 61.111 24.10 0.00 40.08 2.83
347 358 1.606601 TGAGAGGGACAGGACGTGG 60.607 63.158 0.00 0.00 0.00 4.94
368 379 0.036010 CTTTGCCTGACGAGGTGGAT 60.036 55.000 0.00 0.00 42.15 3.41
407 418 2.101415 GCAGGGGATGATTTTGTTAGGC 59.899 50.000 0.00 0.00 0.00 3.93
408 419 2.695147 GGCAGGGGATGATTTTGTTAGG 59.305 50.000 0.00 0.00 0.00 2.69
413 424 0.457035 CACGGCAGGGGATGATTTTG 59.543 55.000 0.00 0.00 0.00 2.44
451 486 2.732619 GGGAAGCACGGTAGAGGGG 61.733 68.421 0.00 0.00 0.00 4.79
455 492 1.183549 GAGAAGGGAAGCACGGTAGA 58.816 55.000 0.00 0.00 0.00 2.59
457 494 1.262640 GGGAGAAGGGAAGCACGGTA 61.263 60.000 0.00 0.00 0.00 4.02
458 495 2.593956 GGGAGAAGGGAAGCACGGT 61.594 63.158 0.00 0.00 0.00 4.83
465 502 1.916777 GTCCGTGGGGAGAAGGGAA 60.917 63.158 0.00 0.00 44.97 3.97
519 562 2.633488 GAAATAGGGGAGATATGGCGC 58.367 52.381 0.00 0.00 0.00 6.53
526 569 4.173849 AGAAGAGAGGGAAATAGGGGAGAT 59.826 45.833 0.00 0.00 0.00 2.75
623 668 4.109675 CTTAGGGTGTGGGGCGGG 62.110 72.222 0.00 0.00 0.00 6.13
648 693 2.187946 CCTCGCTCGGGCATCTTT 59.812 61.111 8.62 0.00 38.60 2.52
667 714 3.917760 CACGCCTCGATCCCCTCC 61.918 72.222 0.00 0.00 0.00 4.30
790 846 1.057275 GGGACCAGGAGGAGGAATCC 61.057 65.000 0.00 0.00 38.69 3.01
826 882 0.677731 CTTGGAAGAAGCGGATGCCA 60.678 55.000 0.00 0.00 44.31 4.92
846 902 5.106869 CGAACCAAGATGAACCAATACGAAA 60.107 40.000 0.00 0.00 0.00 3.46
850 906 4.201822 GCTCGAACCAAGATGAACCAATAC 60.202 45.833 0.00 0.00 0.00 1.89
860 916 4.319177 GCTTATATGGCTCGAACCAAGAT 58.681 43.478 12.35 10.76 44.65 2.40
897 953 1.220206 CTTCAGATCCAGCACCGCT 59.780 57.895 0.00 0.00 40.77 5.52
931 987 0.978667 TAGGCATACACGAAGGGGCA 60.979 55.000 0.00 0.00 0.00 5.36
950 1006 7.445945 GTCATAATACTCTGCCTTTGGTATCT 58.554 38.462 0.00 0.00 0.00 1.98
955 1011 5.041191 AGGTCATAATACTCTGCCTTTGG 57.959 43.478 0.00 0.00 0.00 3.28
957 1013 7.056844 GTAGAGGTCATAATACTCTGCCTTT 57.943 40.000 0.00 0.00 41.38 3.11
961 1017 5.563085 CGTGGTAGAGGTCATAATACTCTGC 60.563 48.000 0.00 0.00 41.38 4.26
962 1018 5.763698 TCGTGGTAGAGGTCATAATACTCTG 59.236 44.000 0.00 0.00 41.38 3.35
1063 1131 4.781959 CGGGCACTGGCATTTGCG 62.782 66.667 13.32 0.00 43.71 4.85
1087 1155 2.709934 AGATGCCATGTAGGAAGCAGAT 59.290 45.455 0.00 0.00 41.22 2.90
1145 1216 1.067916 GGCAACCCAACAGCAAGTG 59.932 57.895 0.00 0.00 0.00 3.16
1200 1282 5.291858 TCATCGCTACACAAAGCTGAAATAG 59.708 40.000 0.00 0.00 40.49 1.73
1445 1568 6.543831 GTGAGAAAGGATACATGCCAGTTAAT 59.456 38.462 0.00 0.00 41.41 1.40
1446 1569 5.880332 GTGAGAAAGGATACATGCCAGTTAA 59.120 40.000 0.00 0.00 41.41 2.01
1475 1598 4.093998 GTCAACAGGATAATGTGTCTGCAG 59.906 45.833 7.63 7.63 32.52 4.41
1624 1748 7.286316 GGAGATTCTGAACAAATATTCCCATGT 59.714 37.037 0.00 0.00 0.00 3.21
1627 1751 6.730447 TGGAGATTCTGAACAAATATTCCCA 58.270 36.000 0.00 0.00 0.00 4.37
1770 3049 7.934855 AAAGATCAAAACAGATGCAGTAGAT 57.065 32.000 0.00 0.00 0.00 1.98
1771 3050 7.063426 CGTAAAGATCAAAACAGATGCAGTAGA 59.937 37.037 0.00 0.00 0.00 2.59
1772 3051 7.063426 TCGTAAAGATCAAAACAGATGCAGTAG 59.937 37.037 0.00 0.00 0.00 2.57
1774 3053 5.700832 TCGTAAAGATCAAAACAGATGCAGT 59.299 36.000 0.00 0.00 0.00 4.40
1776 3055 6.552859 TTCGTAAAGATCAAAACAGATGCA 57.447 33.333 0.00 0.00 0.00 3.96
1777 3056 9.214953 CTATTTCGTAAAGATCAAAACAGATGC 57.785 33.333 0.00 0.00 0.00 3.91
1778 3057 9.708222 CCTATTTCGTAAAGATCAAAACAGATG 57.292 33.333 0.00 0.00 0.00 2.90
1779 3058 8.398665 GCCTATTTCGTAAAGATCAAAACAGAT 58.601 33.333 0.00 0.00 0.00 2.90
1780 3059 7.606456 AGCCTATTTCGTAAAGATCAAAACAGA 59.394 33.333 0.00 0.00 0.00 3.41
1781 3060 7.752695 AGCCTATTTCGTAAAGATCAAAACAG 58.247 34.615 0.00 0.00 0.00 3.16
1782 3061 7.681939 AGCCTATTTCGTAAAGATCAAAACA 57.318 32.000 0.00 0.00 0.00 2.83
1783 3062 8.965986 AAAGCCTATTTCGTAAAGATCAAAAC 57.034 30.769 0.00 0.00 0.00 2.43
1784 3063 7.960738 CGAAAGCCTATTTCGTAAAGATCAAAA 59.039 33.333 13.11 0.00 44.25 2.44
1785 3064 7.461107 CGAAAGCCTATTTCGTAAAGATCAAA 58.539 34.615 13.11 0.00 44.25 2.69
1786 3065 7.000575 CGAAAGCCTATTTCGTAAAGATCAA 57.999 36.000 13.11 0.00 44.25 2.57
1787 3066 6.583912 CGAAAGCCTATTTCGTAAAGATCA 57.416 37.500 13.11 0.00 44.25 2.92
1804 3083 7.371936 CTATATCTATATAGTGGGGCGAAAGC 58.628 42.308 9.58 0.00 44.91 3.51
1805 3084 7.014326 TGCTATATCTATATAGTGGGGCGAAAG 59.986 40.741 15.21 0.00 42.58 2.62
1806 3085 6.837048 TGCTATATCTATATAGTGGGGCGAAA 59.163 38.462 15.21 0.00 42.58 3.46
1807 3086 6.370453 TGCTATATCTATATAGTGGGGCGAA 58.630 40.000 15.21 0.00 42.58 4.70
1808 3087 5.948842 TGCTATATCTATATAGTGGGGCGA 58.051 41.667 15.21 0.00 42.58 5.54
1809 3088 6.448006 GTTGCTATATCTATATAGTGGGGCG 58.552 44.000 15.21 0.00 42.58 6.13
1810 3089 6.555360 AGGTTGCTATATCTATATAGTGGGGC 59.445 42.308 15.21 9.23 42.58 5.80
1811 3090 7.233757 GGAGGTTGCTATATCTATATAGTGGGG 59.766 44.444 15.21 0.29 42.58 4.96
1812 3091 7.233757 GGGAGGTTGCTATATCTATATAGTGGG 59.766 44.444 15.21 0.00 42.58 4.61
1813 3092 7.040340 CGGGAGGTTGCTATATCTATATAGTGG 60.040 44.444 15.21 0.00 42.58 4.00
1814 3093 7.720074 TCGGGAGGTTGCTATATCTATATAGTG 59.280 40.741 15.21 0.00 42.58 2.74
1815 3094 7.813331 TCGGGAGGTTGCTATATCTATATAGT 58.187 38.462 15.21 0.62 42.58 2.12
1816 3095 8.871629 ATCGGGAGGTTGCTATATCTATATAG 57.128 38.462 11.20 11.20 43.16 1.31
1817 3096 9.736414 GTATCGGGAGGTTGCTATATCTATATA 57.264 37.037 0.00 0.00 0.00 0.86
1818 3097 8.225416 TGTATCGGGAGGTTGCTATATCTATAT 58.775 37.037 0.00 0.00 0.00 0.86
1819 3098 7.580007 TGTATCGGGAGGTTGCTATATCTATA 58.420 38.462 0.00 0.00 0.00 1.31
1820 3099 6.432581 TGTATCGGGAGGTTGCTATATCTAT 58.567 40.000 0.00 0.00 0.00 1.98
1821 3100 5.823312 TGTATCGGGAGGTTGCTATATCTA 58.177 41.667 0.00 0.00 0.00 1.98
1822 3101 4.673968 TGTATCGGGAGGTTGCTATATCT 58.326 43.478 0.00 0.00 0.00 1.98
1823 3102 5.401531 TTGTATCGGGAGGTTGCTATATC 57.598 43.478 0.00 0.00 0.00 1.63
1824 3103 5.721960 AGATTGTATCGGGAGGTTGCTATAT 59.278 40.000 0.00 0.00 0.00 0.86
1825 3104 5.047306 CAGATTGTATCGGGAGGTTGCTATA 60.047 44.000 0.00 0.00 0.00 1.31
1826 3105 3.904339 AGATTGTATCGGGAGGTTGCTAT 59.096 43.478 0.00 0.00 0.00 2.97
1827 3106 3.069586 CAGATTGTATCGGGAGGTTGCTA 59.930 47.826 0.00 0.00 0.00 3.49
1828 3107 2.119495 AGATTGTATCGGGAGGTTGCT 58.881 47.619 0.00 0.00 0.00 3.91
1829 3108 2.213499 CAGATTGTATCGGGAGGTTGC 58.787 52.381 0.00 0.00 0.00 4.17
1830 3109 3.543680 ACAGATTGTATCGGGAGGTTG 57.456 47.619 0.00 0.00 0.00 3.77
1831 3110 4.569719 AAACAGATTGTATCGGGAGGTT 57.430 40.909 0.00 0.00 0.00 3.50
1832 3111 4.019681 TCAAAACAGATTGTATCGGGAGGT 60.020 41.667 0.00 0.00 0.00 3.85
1833 3112 4.513442 TCAAAACAGATTGTATCGGGAGG 58.487 43.478 0.00 0.00 0.00 4.30
1834 3113 6.051717 AGATCAAAACAGATTGTATCGGGAG 58.948 40.000 0.00 0.00 0.00 4.30
1835 3114 5.989477 AGATCAAAACAGATTGTATCGGGA 58.011 37.500 0.00 0.00 0.00 5.14
1836 3115 6.683974 AAGATCAAAACAGATTGTATCGGG 57.316 37.500 0.00 0.00 0.00 5.14
1837 3116 8.970691 AAAAAGATCAAAACAGATTGTATCGG 57.029 30.769 0.00 0.00 0.00 4.18
1842 3121 9.598517 TGCTTTAAAAAGATCAAAACAGATTGT 57.401 25.926 6.64 0.00 38.28 2.71
1843 3122 9.853921 GTGCTTTAAAAAGATCAAAACAGATTG 57.146 29.630 6.64 0.00 38.28 2.67
1844 3123 9.598517 TGTGCTTTAAAAAGATCAAAACAGATT 57.401 25.926 6.64 0.00 38.28 2.40
2031 3447 9.965824 CATTGTAAAGGTTCTTAACAAGTTCAT 57.034 29.630 0.00 0.00 0.00 2.57
2159 3583 3.581101 CCTGATCAGATCTTGGGACCTA 58.419 50.000 24.62 0.00 0.00 3.08
2168 3593 1.747145 CCTGCGCCTGATCAGATCT 59.253 57.895 24.62 0.00 32.26 2.75
2171 3596 3.079478 AGCCTGCGCCTGATCAGA 61.079 61.111 24.62 2.81 34.57 3.27
2181 3606 2.625973 TTTTGCCAACACAGCCTGCG 62.626 55.000 0.00 0.00 0.00 5.18
2187 3612 2.539476 GTGTCCTTTTTGCCAACACAG 58.461 47.619 0.00 0.00 39.91 3.66
2236 3683 7.383572 CACTCGACTTCTCCATGGAAATATAAG 59.616 40.741 17.00 15.26 0.00 1.73
2262 3711 9.095065 TGTTCTTGACTTCTGTTAACTCTTAAC 57.905 33.333 7.22 0.00 44.43 2.01
2263 3712 9.661563 TTGTTCTTGACTTCTGTTAACTCTTAA 57.338 29.630 7.22 0.00 0.00 1.85
2264 3713 9.314321 CTTGTTCTTGACTTCTGTTAACTCTTA 57.686 33.333 7.22 0.00 0.00 2.10
2265 3714 7.201652 GCTTGTTCTTGACTTCTGTTAACTCTT 60.202 37.037 7.22 0.00 0.00 2.85
2373 3822 7.739295 TCAAATCTCGCATAACTGAACTTAAC 58.261 34.615 0.00 0.00 0.00 2.01
2439 3892 4.342378 GGCTGTTATACATCTCTGACCTCA 59.658 45.833 0.00 0.00 0.00 3.86
2485 3938 2.091541 GTAAGCAGGTTAGCATTGCCA 58.908 47.619 4.70 0.00 38.58 4.92
2490 3943 5.896073 ATTCTAGGTAAGCAGGTTAGCAT 57.104 39.130 20.68 10.27 40.95 3.79
2610 4074 7.444629 ACAGTATGCAATAATCATGCCTAAG 57.555 36.000 0.00 0.00 42.53 2.18
2644 4115 6.746745 AAACAGTTAAGGAAAAACGTCTCA 57.253 33.333 0.00 0.00 32.00 3.27
2673 4149 3.418684 AACCGAGCTCAACCAGTAATT 57.581 42.857 15.40 0.00 0.00 1.40
2674 4150 3.244422 TGAAACCGAGCTCAACCAGTAAT 60.244 43.478 15.40 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.