Multiple sequence alignment - TraesCS7A01G297700

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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 TraesCS7A01G297700 chr7A 100.000 3660 0 0 1 3660 401605093 401608752 0.000000e+00 6759
1 TraesCS7A01G297700 chr7A 98.870 177 1 1 1659 1835 605175710 605175535 7.630000e-82 315
2 TraesCS7A01G297700 chr7A 96.809 188 3 3 1655 1841 18962205 18962390 9.870000e-81 311
3 TraesCS7A01G297700 chr1A 98.317 1842 14 5 1836 3660 276863818 276861977 0.000000e+00 3214
4 TraesCS7A01G297700 chr1A 97.525 808 20 0 853 1660 276864618 276863811 0.000000e+00 1382
5 TraesCS7A01G297700 chr1A 94.624 465 19 2 214 672 276865461 276864997 0.000000e+00 715
6 TraesCS7A01G297700 chr1A 94.444 216 12 0 2 217 74549930 74550145 2.110000e-87 333
7 TraesCS7A01G297700 chr1A 98.864 176 1 1 1660 1835 259053003 259052829 2.740000e-81 313
8 TraesCS7A01G297700 chr1A 97.778 180 3 1 1659 1838 115360127 115359949 3.550000e-80 309
9 TraesCS7A01G297700 chr7D 96.276 1853 40 7 1836 3660 283703148 283701297 0.000000e+00 3013
10 TraesCS7A01G297700 chr7D 95.000 820 37 2 842 1660 283703957 283703141 0.000000e+00 1284
11 TraesCS7A01G297700 chr7D 95.349 215 10 0 2 216 219932232 219932018 3.500000e-90 342
12 TraesCS7A01G297700 chr7D 94.884 215 11 0 2 216 224991521 224991735 1.630000e-88 337
13 TraesCS7A01G297700 chr7D 97.183 71 2 0 774 844 283704058 283703988 1.790000e-23 121
14 TraesCS7A01G297700 chr6D 95.894 1851 36 11 1836 3660 273428833 273426997 0.000000e+00 2961
15 TraesCS7A01G297700 chr6D 96.375 800 28 1 862 1660 273429625 273428826 0.000000e+00 1315
16 TraesCS7A01G297700 chr6D 93.281 640 26 4 211 844 273430641 273430013 0.000000e+00 928
17 TraesCS7A01G297700 chr4B 91.027 1850 123 22 1836 3660 294454714 294452883 0.000000e+00 2457
18 TraesCS7A01G297700 chr4B 91.786 560 38 3 2473 3031 410074530 410075082 0.000000e+00 773
19 TraesCS7A01G297700 chr4B 85.447 749 74 10 841 1557 294459093 294458348 0.000000e+00 747
20 TraesCS7A01G297700 chr4B 85.219 548 63 9 1117 1660 242922202 242921669 6.910000e-152 547
21 TraesCS7A01G297700 chr4B 88.262 443 39 7 215 648 126087078 126086640 5.420000e-143 518
22 TraesCS7A01G297700 chr4B 89.276 373 25 6 1091 1453 410074146 410074513 1.550000e-123 453
23 TraesCS7A01G297700 chr4B 97.973 148 3 0 1836 1983 242921676 242921529 1.300000e-64 257
24 TraesCS7A01G297700 chr4B 92.025 163 12 1 1499 1660 294454869 294454707 1.020000e-55 228
25 TraesCS7A01G297700 chr4B 85.787 197 23 2 650 846 294459312 294459121 1.720000e-48 204
26 TraesCS7A01G297700 chr1D 92.796 1166 53 24 215 1371 72468172 72469315 0.000000e+00 1659
27 TraesCS7A01G297700 chr7B 91.732 1149 75 11 2473 3602 254251093 254249946 0.000000e+00 1578
28 TraesCS7A01G297700 chr7B 91.369 1147 82 6 2473 3602 256085916 256087062 0.000000e+00 1554
29 TraesCS7A01G297700 chr7B 89.333 375 25 4 1089 1453 254251479 254251110 1.200000e-124 457
30 TraesCS7A01G297700 chr7B 88.564 376 26 4 1089 1454 256085532 256085900 1.210000e-119 440
31 TraesCS7A01G297700 chr7B 98.883 179 1 1 1659 1837 672656372 672656195 5.900000e-83 318
32 TraesCS7A01G297700 chr7B 93.333 180 6 1 3487 3660 264476358 264476537 1.010000e-65 261
33 TraesCS7A01G297700 chr7B 93.243 74 5 0 3529 3602 254251933 254251860 3.860000e-20 110
34 TraesCS7A01G297700 chr1B 91.630 1147 79 9 2473 3602 380312068 380313214 0.000000e+00 1570
35 TraesCS7A01G297700 chr1B 91.558 1149 75 10 2473 3602 398649117 398650262 0.000000e+00 1565
36 TraesCS7A01G297700 chr1B 91.297 1149 80 10 2473 3602 116769823 116768676 0.000000e+00 1550
37 TraesCS7A01G297700 chr1B 89.567 393 31 4 257 645 157456562 157456176 1.180000e-134 490
38 TraesCS7A01G297700 chr1B 89.333 375 25 4 1089 1453 380311682 380312051 1.200000e-124 457
39 TraesCS7A01G297700 chr1B 88.800 375 27 4 1089 1453 116770209 116769840 2.590000e-121 446
40 TraesCS7A01G297700 chr1B 88.533 375 29 3 1089 1453 398648730 398649100 3.350000e-120 442
41 TraesCS7A01G297700 chr3B 92.484 958 57 9 2473 3415 587004849 587005806 0.000000e+00 1356
42 TraesCS7A01G297700 chr3B 87.045 440 51 2 215 649 546151933 546151495 3.280000e-135 492
43 TraesCS7A01G297700 chr3B 89.067 375 26 4 1089 1453 587004463 587004832 5.570000e-123 451
44 TraesCS7A01G297700 chr3B 88.889 81 9 0 842 922 330781122 330781042 2.330000e-17 100
45 TraesCS7A01G297700 chrUn 100.000 437 0 0 2201 2637 476060741 476061177 0.000000e+00 808
46 TraesCS7A01G297700 chrUn 96.296 189 4 3 1652 1839 116285846 116286032 1.280000e-79 307
47 TraesCS7A01G297700 chr5D 93.622 439 22 2 215 648 123559019 123559456 0.000000e+00 651
48 TraesCS7A01G297700 chr5D 96.279 215 8 0 2 216 496460569 496460783 1.620000e-93 353
49 TraesCS7A01G297700 chr5D 95.370 216 10 0 1 216 561510587 561510372 9.730000e-91 344
50 TraesCS7A01G297700 chr3A 93.593 437 21 4 215 645 330448097 330448532 0.000000e+00 645
51 TraesCS7A01G297700 chr3D 87.443 438 45 7 214 645 95959882 95960315 2.540000e-136 496
52 TraesCS7A01G297700 chr3D 94.907 216 11 0 1 216 202127431 202127216 4.530000e-89 339
53 TraesCS7A01G297700 chr2D 95.349 215 10 0 2 216 513351593 513351379 3.500000e-90 342
54 TraesCS7A01G297700 chr2D 94.884 215 11 0 2 216 584685256 584685042 1.630000e-88 337
55 TraesCS7A01G297700 chr2A 95.349 215 10 0 2 216 194568576 194568362 3.500000e-90 342
56 TraesCS7A01G297700 chr2A 94.937 79 4 0 212 290 201075085 201075163 1.380000e-24 124
57 TraesCS7A01G297700 chr6A 98.870 177 1 1 1659 1835 168007030 168007205 7.630000e-82 315
58 TraesCS7A01G297700 chr4A 98.864 176 1 1 1661 1836 733434532 733434358 2.740000e-81 313
59 TraesCS7A01G297700 chr5B 98.315 178 2 1 1661 1838 291789293 291789117 9.870000e-81 311
60 TraesCS7A01G297700 chr2B 96.053 76 3 0 215 290 672813396 672813471 1.380000e-24 124


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 TraesCS7A01G297700 chr7A 401605093 401608752 3659 False 6759.000000 6759 100.000000 1 3660 1 chr7A.!!$F2 3659
1 TraesCS7A01G297700 chr1A 276861977 276865461 3484 True 1770.333333 3214 96.822000 214 3660 3 chr1A.!!$R3 3446
2 TraesCS7A01G297700 chr7D 283701297 283704058 2761 True 1472.666667 3013 96.153000 774 3660 3 chr7D.!!$R2 2886
3 TraesCS7A01G297700 chr6D 273426997 273430641 3644 True 1734.666667 2961 95.183333 211 3660 3 chr6D.!!$R1 3449
4 TraesCS7A01G297700 chr4B 294452883 294459312 6429 True 909.000000 2457 88.571500 650 3660 4 chr4B.!!$R3 3010
5 TraesCS7A01G297700 chr4B 410074146 410075082 936 False 613.000000 773 90.531000 1091 3031 2 chr4B.!!$F1 1940
6 TraesCS7A01G297700 chr4B 242921529 242922202 673 True 402.000000 547 91.596000 1117 1983 2 chr4B.!!$R2 866
7 TraesCS7A01G297700 chr1D 72468172 72469315 1143 False 1659.000000 1659 92.796000 215 1371 1 chr1D.!!$F1 1156
8 TraesCS7A01G297700 chr7B 256085532 256087062 1530 False 997.000000 1554 89.966500 1089 3602 2 chr7B.!!$F2 2513
9 TraesCS7A01G297700 chr7B 254249946 254251933 1987 True 715.000000 1578 91.436000 1089 3602 3 chr7B.!!$R2 2513
10 TraesCS7A01G297700 chr1B 380311682 380313214 1532 False 1013.500000 1570 90.481500 1089 3602 2 chr1B.!!$F1 2513
11 TraesCS7A01G297700 chr1B 398648730 398650262 1532 False 1003.500000 1565 90.045500 1089 3602 2 chr1B.!!$F2 2513
12 TraesCS7A01G297700 chr1B 116768676 116770209 1533 True 998.000000 1550 90.048500 1089 3602 2 chr1B.!!$R2 2513
13 TraesCS7A01G297700 chr3B 587004463 587005806 1343 False 903.500000 1356 90.775500 1089 3415 2 chr3B.!!$F1 2326

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
109 110 0.106708 GGACATATGGAGCGCCTGAA 59.893 55.0 8.34 0.0 34.31 3.02 F
115 116 0.174162 ATGGAGCGCCTGAAATTTGC 59.826 50.0 8.34 0.0 34.31 3.68 F
1689 5648 0.672711 AAAAGCGTCCCTAAGGCGAC 60.673 55.0 0.00 0.0 43.57 5.19 F
1741 5700 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.0 0.00 0.0 44.64 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 5681 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.0 30.80 3.13 R
1723 5682 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.0 30.80 2.29 R
2637 6617 3.056179 TCACTCGTCACCAATAAGCATGA 60.056 43.478 0.00 0.0 0.00 3.07 R
3612 7646 3.831323 TGGAGCCTCATTTGAAGAACAA 58.169 40.909 0.00 0.0 36.65 2.83 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
18 19 3.092088 ACAAATCCCGGGTACTCCA 57.908 52.632 22.86 0.00 34.36 3.86
19 20 1.591768 ACAAATCCCGGGTACTCCAT 58.408 50.000 22.86 1.44 34.36 3.41
20 21 2.766736 ACAAATCCCGGGTACTCCATA 58.233 47.619 22.86 0.00 34.36 2.74
21 22 3.323775 ACAAATCCCGGGTACTCCATAT 58.676 45.455 22.86 0.00 34.36 1.78
22 23 3.072476 ACAAATCCCGGGTACTCCATATG 59.928 47.826 22.86 10.08 34.36 1.78
24 25 2.005370 TCCCGGGTACTCCATATGTC 57.995 55.000 22.86 0.00 34.36 3.06
25 26 0.974383 CCCGGGTACTCCATATGTCC 59.026 60.000 14.18 0.00 34.36 4.02
26 27 1.482553 CCCGGGTACTCCATATGTCCT 60.483 57.143 14.18 0.00 34.36 3.85
28 29 3.090037 CCGGGTACTCCATATGTCCTAG 58.910 54.545 1.24 0.00 34.36 3.02
33 34 5.839606 GGGTACTCCATATGTCCTAGTTTCT 59.160 44.000 1.24 0.00 35.00 2.52
35 36 7.177041 GGGTACTCCATATGTCCTAGTTTCTAG 59.823 44.444 1.24 0.00 35.00 2.43
37 38 6.136857 ACTCCATATGTCCTAGTTTCTAGCA 58.863 40.000 1.24 0.00 0.00 3.49
38 39 6.041069 ACTCCATATGTCCTAGTTTCTAGCAC 59.959 42.308 1.24 0.00 0.00 4.40
39 40 5.897250 TCCATATGTCCTAGTTTCTAGCACA 59.103 40.000 1.24 3.52 0.00 4.57
41 42 6.703607 CCATATGTCCTAGTTTCTAGCACAAG 59.296 42.308 4.93 0.26 0.00 3.16
42 43 5.746990 ATGTCCTAGTTTCTAGCACAAGT 57.253 39.130 4.93 0.00 0.00 3.16
43 44 5.135508 TGTCCTAGTTTCTAGCACAAGTC 57.864 43.478 0.00 0.00 0.00 3.01
45 46 5.246203 TGTCCTAGTTTCTAGCACAAGTCAT 59.754 40.000 0.00 0.00 0.00 3.06
46 47 5.578727 GTCCTAGTTTCTAGCACAAGTCATG 59.421 44.000 0.00 0.00 0.00 3.07
47 48 4.331168 CCTAGTTTCTAGCACAAGTCATGC 59.669 45.833 0.00 0.00 43.74 4.06
48 49 3.743521 AGTTTCTAGCACAAGTCATGCA 58.256 40.909 0.00 0.00 45.92 3.96
49 50 3.750130 AGTTTCTAGCACAAGTCATGCAG 59.250 43.478 0.00 0.00 45.92 4.41
52 53 4.006780 TCTAGCACAAGTCATGCAGAAA 57.993 40.909 0.00 0.00 45.92 2.52
53 54 4.388485 TCTAGCACAAGTCATGCAGAAAA 58.612 39.130 0.00 0.00 45.92 2.29
54 55 5.005740 TCTAGCACAAGTCATGCAGAAAAT 58.994 37.500 0.00 0.00 45.92 1.82
56 57 3.570975 AGCACAAGTCATGCAGAAAATCA 59.429 39.130 0.00 0.00 45.92 2.57
57 58 4.219944 AGCACAAGTCATGCAGAAAATCAT 59.780 37.500 0.00 0.00 45.92 2.45
58 59 4.326278 GCACAAGTCATGCAGAAAATCATG 59.674 41.667 0.00 0.00 42.88 3.07
59 60 5.705902 CACAAGTCATGCAGAAAATCATGA 58.294 37.500 0.00 0.00 44.62 3.07
68 69 8.552865 TCATGCAGAAAATCATGAAAAGTTTTG 58.447 29.630 5.36 4.15 44.08 2.44
69 70 7.249186 TGCAGAAAATCATGAAAAGTTTTGG 57.751 32.000 5.36 3.84 0.00 3.28
70 71 6.138088 GCAGAAAATCATGAAAAGTTTTGGC 58.862 36.000 5.36 8.73 0.00 4.52
71 72 6.238429 GCAGAAAATCATGAAAAGTTTTGGCA 60.238 34.615 5.36 0.00 0.00 4.92
73 74 7.801315 CAGAAAATCATGAAAAGTTTTGGCATG 59.199 33.333 17.73 17.73 36.20 4.06
75 76 6.790285 AATCATGAAAAGTTTTGGCATGAC 57.210 33.333 24.16 0.00 41.39 3.06
76 77 5.273674 TCATGAAAAGTTTTGGCATGACA 57.726 34.783 20.56 0.00 37.61 3.58
77 78 5.856156 TCATGAAAAGTTTTGGCATGACAT 58.144 33.333 20.56 8.77 37.61 3.06
79 80 6.766944 TCATGAAAAGTTTTGGCATGACATTT 59.233 30.769 20.56 0.00 37.61 2.32
81 82 4.816786 AAAGTTTTGGCATGACATTTGC 57.183 36.364 0.00 0.00 39.41 3.68
82 83 3.756933 AGTTTTGGCATGACATTTGCT 57.243 38.095 0.00 0.00 40.03 3.91
83 84 4.870123 AGTTTTGGCATGACATTTGCTA 57.130 36.364 0.00 0.00 40.03 3.49
85 86 5.609423 AGTTTTGGCATGACATTTGCTAAA 58.391 33.333 0.00 8.09 45.14 1.85
88 89 6.542574 TTTGGCATGACATTTGCTAAAAAG 57.457 33.333 0.00 0.00 44.27 2.27
90 91 4.989797 TGGCATGACATTTGCTAAAAAGTG 59.010 37.500 0.00 0.00 40.03 3.16
91 92 4.389687 GGCATGACATTTGCTAAAAAGTGG 59.610 41.667 0.00 0.00 40.03 4.00
92 93 5.229423 GCATGACATTTGCTAAAAAGTGGA 58.771 37.500 0.00 0.00 37.14 4.02
93 94 5.119125 GCATGACATTTGCTAAAAAGTGGAC 59.881 40.000 0.00 0.00 37.14 4.02
94 95 5.843673 TGACATTTGCTAAAAAGTGGACA 57.156 34.783 0.00 0.00 27.77 4.02
96 97 7.517614 TGACATTTGCTAAAAAGTGGACATA 57.482 32.000 0.00 0.00 27.77 2.29
97 98 8.121305 TGACATTTGCTAAAAAGTGGACATAT 57.879 30.769 0.00 0.00 27.77 1.78
98 99 8.028354 TGACATTTGCTAAAAAGTGGACATATG 58.972 33.333 0.00 0.00 27.77 1.78
99 100 7.322664 ACATTTGCTAAAAAGTGGACATATGG 58.677 34.615 7.80 0.00 0.00 2.74
100 101 7.178274 ACATTTGCTAAAAAGTGGACATATGGA 59.822 33.333 7.80 0.00 0.00 3.41
101 102 6.757897 TTGCTAAAAAGTGGACATATGGAG 57.242 37.500 7.80 0.00 0.00 3.86
102 103 4.640201 TGCTAAAAAGTGGACATATGGAGC 59.360 41.667 7.80 0.00 0.00 4.70
103 104 4.260784 GCTAAAAAGTGGACATATGGAGCG 60.261 45.833 7.80 0.00 0.00 5.03
104 105 1.668419 AAAGTGGACATATGGAGCGC 58.332 50.000 7.80 0.00 0.00 5.92
105 106 0.179045 AAGTGGACATATGGAGCGCC 60.179 55.000 2.29 0.00 0.00 6.53
109 110 0.106708 GGACATATGGAGCGCCTGAA 59.893 55.000 8.34 0.00 34.31 3.02
110 111 1.475034 GGACATATGGAGCGCCTGAAA 60.475 52.381 8.34 0.00 34.31 2.69
112 113 2.880890 GACATATGGAGCGCCTGAAATT 59.119 45.455 8.34 0.00 34.31 1.82
113 114 3.290710 ACATATGGAGCGCCTGAAATTT 58.709 40.909 8.34 0.00 34.31 1.82
114 115 3.067180 ACATATGGAGCGCCTGAAATTTG 59.933 43.478 8.34 0.95 34.31 2.32
115 116 0.174162 ATGGAGCGCCTGAAATTTGC 59.826 50.000 8.34 0.00 34.31 3.68
116 117 1.153765 GGAGCGCCTGAAATTTGCC 60.154 57.895 2.29 0.00 0.00 4.52
117 118 1.514873 GAGCGCCTGAAATTTGCCG 60.515 57.895 2.29 0.00 0.00 5.69
118 119 2.506881 GCGCCTGAAATTTGCCGG 60.507 61.111 0.00 0.00 0.00 6.13
119 120 2.988688 GCGCCTGAAATTTGCCGGA 61.989 57.895 5.05 0.00 0.00 5.14
120 121 1.583986 CGCCTGAAATTTGCCGGAA 59.416 52.632 5.05 0.00 0.00 4.30
144 145 5.452078 GGAAATGAATCAATATTCCGGCA 57.548 39.130 0.00 0.00 40.78 5.69
145 146 5.841810 GGAAATGAATCAATATTCCGGCAA 58.158 37.500 0.00 0.00 40.78 4.52
146 147 6.279882 GGAAATGAATCAATATTCCGGCAAA 58.720 36.000 0.00 0.00 40.78 3.68
147 148 6.760770 GGAAATGAATCAATATTCCGGCAAAA 59.239 34.615 0.00 0.00 40.78 2.44
148 149 7.254421 GGAAATGAATCAATATTCCGGCAAAAC 60.254 37.037 0.00 0.00 40.78 2.43
149 150 5.651387 TGAATCAATATTCCGGCAAAACA 57.349 34.783 0.00 0.00 40.78 2.83
150 151 6.219417 TGAATCAATATTCCGGCAAAACAT 57.781 33.333 0.00 0.00 40.78 2.71
151 152 7.340122 TGAATCAATATTCCGGCAAAACATA 57.660 32.000 0.00 0.00 40.78 2.29
152 153 7.424803 TGAATCAATATTCCGGCAAAACATAG 58.575 34.615 0.00 0.00 40.78 2.23
153 154 5.766150 TCAATATTCCGGCAAAACATAGG 57.234 39.130 0.00 0.00 0.00 2.57
154 155 5.197451 TCAATATTCCGGCAAAACATAGGT 58.803 37.500 0.00 0.00 0.00 3.08
155 156 5.298276 TCAATATTCCGGCAAAACATAGGTC 59.702 40.000 0.00 0.00 0.00 3.85
156 157 2.570415 TTCCGGCAAAACATAGGTCA 57.430 45.000 0.00 0.00 0.00 4.02
157 158 1.816074 TCCGGCAAAACATAGGTCAC 58.184 50.000 0.00 0.00 0.00 3.67
159 160 1.737793 CCGGCAAAACATAGGTCACTC 59.262 52.381 0.00 0.00 0.00 3.51
160 161 1.393539 CGGCAAAACATAGGTCACTCG 59.606 52.381 0.00 0.00 0.00 4.18
161 162 1.737793 GGCAAAACATAGGTCACTCGG 59.262 52.381 0.00 0.00 0.00 4.63
164 165 4.439057 GCAAAACATAGGTCACTCGGATA 58.561 43.478 0.00 0.00 0.00 2.59
165 166 5.057149 GCAAAACATAGGTCACTCGGATAT 58.943 41.667 0.00 0.00 0.00 1.63
166 167 5.527582 GCAAAACATAGGTCACTCGGATATT 59.472 40.000 0.00 0.00 0.00 1.28
167 168 6.292919 GCAAAACATAGGTCACTCGGATATTC 60.293 42.308 0.00 0.00 0.00 1.75
168 169 6.732896 AAACATAGGTCACTCGGATATTCT 57.267 37.500 0.00 0.00 0.00 2.40
169 170 6.732896 AACATAGGTCACTCGGATATTCTT 57.267 37.500 0.00 0.00 0.00 2.52
170 171 6.334102 ACATAGGTCACTCGGATATTCTTC 57.666 41.667 0.00 0.00 0.00 2.87
171 172 3.992260 AGGTCACTCGGATATTCTTCG 57.008 47.619 0.00 0.00 0.00 3.79
172 173 3.552875 AGGTCACTCGGATATTCTTCGA 58.447 45.455 0.00 0.00 0.00 3.71
173 174 3.315749 AGGTCACTCGGATATTCTTCGAC 59.684 47.826 0.00 0.00 0.00 4.20
174 175 3.066342 GGTCACTCGGATATTCTTCGACA 59.934 47.826 0.00 0.00 0.00 4.35
175 176 4.261656 GGTCACTCGGATATTCTTCGACAT 60.262 45.833 0.00 0.00 0.00 3.06
176 177 5.282510 GTCACTCGGATATTCTTCGACATT 58.717 41.667 0.00 0.00 0.00 2.71
177 178 5.399892 GTCACTCGGATATTCTTCGACATTC 59.600 44.000 0.00 0.00 0.00 2.67
178 179 5.067283 TCACTCGGATATTCTTCGACATTCA 59.933 40.000 0.00 0.00 0.00 2.57
180 181 5.749109 ACTCGGATATTCTTCGACATTCAAC 59.251 40.000 0.00 0.00 0.00 3.18
182 183 4.808895 CGGATATTCTTCGACATTCAACCA 59.191 41.667 0.00 0.00 0.00 3.67
183 184 5.293324 CGGATATTCTTCGACATTCAACCAA 59.707 40.000 0.00 0.00 0.00 3.67
184 185 6.487103 GGATATTCTTCGACATTCAACCAAC 58.513 40.000 0.00 0.00 0.00 3.77
185 186 6.093495 GGATATTCTTCGACATTCAACCAACA 59.907 38.462 0.00 0.00 0.00 3.33
186 187 5.964958 ATTCTTCGACATTCAACCAACAT 57.035 34.783 0.00 0.00 0.00 2.71
187 188 5.766150 TTCTTCGACATTCAACCAACATT 57.234 34.783 0.00 0.00 0.00 2.71
188 189 5.107109 TCTTCGACATTCAACCAACATTG 57.893 39.130 0.00 0.00 0.00 2.82
189 190 3.281341 TCGACATTCAACCAACATTGC 57.719 42.857 0.00 0.00 0.00 3.56
190 191 2.620585 TCGACATTCAACCAACATTGCA 59.379 40.909 0.00 0.00 0.00 4.08
193 194 4.269603 CGACATTCAACCAACATTGCAAAA 59.730 37.500 1.71 0.00 0.00 2.44
194 195 5.050227 CGACATTCAACCAACATTGCAAAAT 60.050 36.000 1.71 0.00 0.00 1.82
195 196 6.303021 ACATTCAACCAACATTGCAAAATC 57.697 33.333 1.71 0.00 0.00 2.17
196 197 5.821470 ACATTCAACCAACATTGCAAAATCA 59.179 32.000 1.71 0.00 0.00 2.57
197 198 6.487331 ACATTCAACCAACATTGCAAAATCAT 59.513 30.769 1.71 0.00 0.00 2.45
198 199 7.660617 ACATTCAACCAACATTGCAAAATCATA 59.339 29.630 1.71 0.00 0.00 2.15
199 200 8.670135 CATTCAACCAACATTGCAAAATCATAT 58.330 29.630 1.71 0.00 0.00 1.78
200 201 9.887629 ATTCAACCAACATTGCAAAATCATATA 57.112 25.926 1.71 0.00 0.00 0.86
201 202 9.716531 TTCAACCAACATTGCAAAATCATATAA 57.283 25.926 1.71 0.00 0.00 0.98
202 203 9.149225 TCAACCAACATTGCAAAATCATATAAC 57.851 29.630 1.71 0.00 0.00 1.89
203 204 8.933807 CAACCAACATTGCAAAATCATATAACA 58.066 29.630 1.71 0.00 0.00 2.41
205 206 9.316730 ACCAACATTGCAAAATCATATAACATC 57.683 29.630 1.71 0.00 0.00 3.06
271 272 2.503356 AGAATGCTCCCTCGATCAGTTT 59.497 45.455 0.00 0.00 0.00 2.66
389 390 0.745486 CAATGACTGATGGGCTCGCA 60.745 55.000 0.00 0.00 0.00 5.10
481 487 1.827399 AATCCTGGTCGCGGAGTTGT 61.827 55.000 6.13 0.00 33.29 3.32
748 755 4.373116 GAGCTCAACCGGGCGTCA 62.373 66.667 9.40 0.00 0.00 4.35
767 774 3.839432 CGGCCGGAGAAGGAGGAC 61.839 72.222 20.10 0.00 0.00 3.85
846 853 4.416738 GCCACCACCCTCCTCTGC 62.417 72.222 0.00 0.00 0.00 4.26
847 854 3.721706 CCACCACCCTCCTCTGCC 61.722 72.222 0.00 0.00 0.00 4.85
848 855 2.930019 CACCACCCTCCTCTGCCA 60.930 66.667 0.00 0.00 0.00 4.92
999 1376 3.141488 GAAGGAGGAGAGGCGCGA 61.141 66.667 12.10 0.00 0.00 5.87
1064 1442 0.733150 GCTCGATGGTAAGTTTGGCC 59.267 55.000 0.00 0.00 0.00 5.36
1169 1569 1.210478 TGCTTCCAGAGGATAAGGCAC 59.790 52.381 0.00 0.00 0.00 5.01
1270 1670 5.636123 TCAGTTACAATTACAACATGGGGT 58.364 37.500 0.00 0.00 0.00 4.95
1335 1755 3.585862 AGTTATGACTAAGTGCCACACG 58.414 45.455 0.00 0.00 35.26 4.49
1410 1831 6.630863 CGGTTTGTCCCCATAGTCTATGTTTA 60.631 42.308 16.89 1.22 34.36 2.01
1492 1913 5.848036 CAGATTAAGTGACTGAAAGCAAACG 59.152 40.000 0.00 0.00 37.60 3.60
1660 5619 8.280497 CGTGTACCATTTTCAGGTATTAATAGC 58.720 37.037 15.39 15.39 43.08 2.97
1661 5620 9.338622 GTGTACCATTTTCAGGTATTAATAGCT 57.661 33.333 19.18 19.18 43.08 3.32
1679 5638 9.777575 TTAATAGCTATGTTTTTAAAAGCGTCC 57.222 29.630 12.15 6.23 38.23 4.79
1680 5639 5.055642 AGCTATGTTTTTAAAAGCGTCCC 57.944 39.130 12.15 5.94 38.23 4.46
1681 5640 4.765339 AGCTATGTTTTTAAAAGCGTCCCT 59.235 37.500 12.15 7.78 38.23 4.20
1682 5641 5.941647 AGCTATGTTTTTAAAAGCGTCCCTA 59.058 36.000 12.15 0.00 38.23 3.53
1683 5642 6.431852 AGCTATGTTTTTAAAAGCGTCCCTAA 59.568 34.615 12.15 0.00 38.23 2.69
1684 5643 6.745907 GCTATGTTTTTAAAAGCGTCCCTAAG 59.254 38.462 12.15 6.18 0.00 2.18
1685 5644 5.441709 TGTTTTTAAAAGCGTCCCTAAGG 57.558 39.130 9.79 0.00 0.00 2.69
1686 5645 4.232221 GTTTTTAAAAGCGTCCCTAAGGC 58.768 43.478 0.14 0.00 39.09 4.35
1687 5646 1.729284 TTAAAAGCGTCCCTAAGGCG 58.271 50.000 0.00 0.00 43.57 5.52
1688 5647 0.896923 TAAAAGCGTCCCTAAGGCGA 59.103 50.000 0.00 0.00 43.57 5.54
1689 5648 0.672711 AAAAGCGTCCCTAAGGCGAC 60.673 55.000 0.00 0.00 43.57 5.19
1690 5649 1.823169 AAAGCGTCCCTAAGGCGACA 61.823 55.000 0.00 0.00 43.57 4.35
1691 5650 2.502692 AAGCGTCCCTAAGGCGACAC 62.503 60.000 0.00 0.30 43.57 3.67
1692 5651 2.183555 CGTCCCTAAGGCGACACC 59.816 66.667 0.00 0.00 35.49 4.16
1704 5663 4.787999 GACACCTAGGCGTCGAAG 57.212 61.111 14.00 0.00 0.00 3.79
1705 5664 1.516603 GACACCTAGGCGTCGAAGC 60.517 63.158 14.00 15.40 0.00 3.86
1706 5665 2.579787 CACCTAGGCGTCGAAGCG 60.580 66.667 17.05 4.02 38.18 4.68
1715 5674 4.516195 GTCGAAGCGCTCCCCCTC 62.516 72.222 12.06 2.47 0.00 4.30
1723 5682 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
1733 5692 1.161843 TCCGCTTTGGAAAATCGACC 58.838 50.000 0.00 0.00 46.38 4.79
1734 5693 0.179200 CCGCTTTGGAAAATCGACCG 60.179 55.000 0.00 0.00 42.00 4.79
1735 5694 0.793104 CGCTTTGGAAAATCGACCGC 60.793 55.000 0.00 0.00 0.00 5.68
1736 5695 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
1737 5696 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
1738 5697 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
1739 5698 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
1740 5699 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
1741 5700 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
1742 5701 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
1760 5719 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
1768 5727 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
1769 5728 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
1811 5770 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
1812 5771 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
1813 5772 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
1814 5773 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
1815 5774 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
1834 5793 3.047613 GGCGTCGCCTTAAAAACATAG 57.952 47.619 28.98 0.00 46.69 2.23
1835 5794 2.674357 GGCGTCGCCTTAAAAACATAGA 59.326 45.455 28.98 0.00 46.69 1.98
1836 5795 3.311596 GGCGTCGCCTTAAAAACATAGAT 59.688 43.478 28.98 0.00 46.69 1.98
1837 5796 4.201881 GGCGTCGCCTTAAAAACATAGATT 60.202 41.667 28.98 0.00 46.69 2.40
1838 5797 5.006941 GGCGTCGCCTTAAAAACATAGATTA 59.993 40.000 28.98 0.00 46.69 1.75
1839 5798 6.457257 GGCGTCGCCTTAAAAACATAGATTAA 60.457 38.462 28.98 0.00 46.69 1.40
1840 5799 7.130269 GCGTCGCCTTAAAAACATAGATTAAT 58.870 34.615 5.75 0.00 0.00 1.40
1841 5800 8.277713 GCGTCGCCTTAAAAACATAGATTAATA 58.722 33.333 5.75 0.00 0.00 0.98
1842 5801 9.793245 CGTCGCCTTAAAAACATAGATTAATAG 57.207 33.333 0.00 0.00 0.00 1.73
1934 5893 3.365868 CGCTTATGGTTTTGCTGCAGTAA 60.366 43.478 13.67 13.67 0.00 2.24
2199 6170 7.718334 TGATAACTCTTCACCTGACATTCTA 57.282 36.000 0.00 0.00 0.00 2.10
2637 6617 3.766545 ACTTGGCACCTAATGTCAACAT 58.233 40.909 0.00 0.00 45.92 2.71
2687 6667 2.235402 AGAAGGCTGCAATGGAATTTGG 59.765 45.455 0.50 0.00 31.22 3.28
3053 7075 7.439056 CACCATTGTAAAGAGCAATTTCAGTTT 59.561 33.333 0.00 0.00 34.68 2.66
3612 7646 4.401202 CCCCGTTTTTGTTCTATAGGCATT 59.599 41.667 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.537143 GACATATGGAGTACCCGGGAT 58.463 52.381 32.02 14.63 37.93 3.85
7 8 2.011122 AGGACATATGGAGTACCCGG 57.989 55.000 7.80 0.00 37.93 5.73
8 9 3.764218 ACTAGGACATATGGAGTACCCG 58.236 50.000 7.80 0.69 37.93 5.28
9 10 5.839606 AGAAACTAGGACATATGGAGTACCC 59.160 44.000 7.80 0.00 34.81 3.69
10 11 6.980416 AGAAACTAGGACATATGGAGTACC 57.020 41.667 7.80 2.81 0.00 3.34
13 14 6.041069 GTGCTAGAAACTAGGACATATGGAGT 59.959 42.308 19.88 2.13 36.17 3.85
14 15 6.040955 TGTGCTAGAAACTAGGACATATGGAG 59.959 42.308 22.32 1.51 40.20 3.86
15 16 5.897250 TGTGCTAGAAACTAGGACATATGGA 59.103 40.000 22.32 5.73 40.20 3.41
16 17 6.161855 TGTGCTAGAAACTAGGACATATGG 57.838 41.667 22.32 0.00 40.20 2.74
18 19 7.124298 TGACTTGTGCTAGAAACTAGGACATAT 59.876 37.037 25.05 18.62 43.56 1.78
19 20 6.436218 TGACTTGTGCTAGAAACTAGGACATA 59.564 38.462 25.05 17.41 43.56 2.29
20 21 5.246203 TGACTTGTGCTAGAAACTAGGACAT 59.754 40.000 25.05 15.94 43.56 3.06
21 22 4.587262 TGACTTGTGCTAGAAACTAGGACA 59.413 41.667 22.32 22.32 42.68 4.02
22 23 5.135508 TGACTTGTGCTAGAAACTAGGAC 57.864 43.478 18.62 18.62 36.58 3.85
24 25 4.331168 GCATGACTTGTGCTAGAAACTAGG 59.669 45.833 0.00 0.00 39.45 3.02
25 26 4.931601 TGCATGACTTGTGCTAGAAACTAG 59.068 41.667 0.00 0.00 42.92 2.57
26 27 4.893608 TGCATGACTTGTGCTAGAAACTA 58.106 39.130 0.00 0.00 42.92 2.24
28 29 3.748048 TCTGCATGACTTGTGCTAGAAAC 59.252 43.478 0.00 0.00 42.92 2.78
33 34 4.761227 TGATTTTCTGCATGACTTGTGCTA 59.239 37.500 0.00 0.00 42.92 3.49
35 36 3.904571 TGATTTTCTGCATGACTTGTGC 58.095 40.909 0.00 0.00 42.81 4.57
37 38 5.970317 TCATGATTTTCTGCATGACTTGT 57.030 34.783 0.00 0.00 44.17 3.16
42 43 8.552865 CAAAACTTTTCATGATTTTCTGCATGA 58.447 29.630 0.00 0.00 46.50 3.07
43 44 7.801315 CCAAAACTTTTCATGATTTTCTGCATG 59.199 33.333 0.00 0.00 42.41 4.06
45 46 6.238429 GCCAAAACTTTTCATGATTTTCTGCA 60.238 34.615 0.00 0.00 0.00 4.41
46 47 6.138088 GCCAAAACTTTTCATGATTTTCTGC 58.862 36.000 0.00 2.43 0.00 4.26
47 48 7.249186 TGCCAAAACTTTTCATGATTTTCTG 57.751 32.000 0.00 0.00 0.00 3.02
48 49 7.716123 TCATGCCAAAACTTTTCATGATTTTCT 59.284 29.630 11.77 0.00 38.70 2.52
49 50 7.799914 GTCATGCCAAAACTTTTCATGATTTTC 59.200 33.333 16.08 5.74 43.37 2.29
52 53 6.289834 TGTCATGCCAAAACTTTTCATGATT 58.710 32.000 16.08 0.00 43.37 2.57
53 54 5.856156 TGTCATGCCAAAACTTTTCATGAT 58.144 33.333 16.08 0.00 43.37 2.45
54 55 5.273674 TGTCATGCCAAAACTTTTCATGA 57.726 34.783 11.77 11.77 40.56 3.07
56 57 6.513720 GCAAATGTCATGCCAAAACTTTTCAT 60.514 34.615 0.00 0.00 37.85 2.57
57 58 5.220815 GCAAATGTCATGCCAAAACTTTTCA 60.221 36.000 0.00 0.00 37.85 2.69
58 59 5.007921 AGCAAATGTCATGCCAAAACTTTTC 59.992 36.000 0.00 0.00 44.91 2.29
59 60 4.883006 AGCAAATGTCATGCCAAAACTTTT 59.117 33.333 0.00 0.00 44.91 2.27
61 62 4.075963 AGCAAATGTCATGCCAAAACTT 57.924 36.364 0.00 0.00 44.91 2.66
62 63 3.756933 AGCAAATGTCATGCCAAAACT 57.243 38.095 0.00 0.00 44.91 2.66
63 64 5.921004 TTTAGCAAATGTCATGCCAAAAC 57.079 34.783 0.00 0.00 44.91 2.43
64 65 6.541641 ACTTTTTAGCAAATGTCATGCCAAAA 59.458 30.769 2.01 2.01 44.91 2.44
65 66 6.018098 CACTTTTTAGCAAATGTCATGCCAAA 60.018 34.615 0.00 0.00 44.91 3.28
68 69 4.389687 CCACTTTTTAGCAAATGTCATGCC 59.610 41.667 0.00 0.00 44.91 4.40
69 70 5.119125 GTCCACTTTTTAGCAAATGTCATGC 59.881 40.000 0.00 0.00 44.15 4.06
70 71 6.215121 TGTCCACTTTTTAGCAAATGTCATG 58.785 36.000 0.00 0.00 29.87 3.07
71 72 6.403866 TGTCCACTTTTTAGCAAATGTCAT 57.596 33.333 0.00 0.00 29.87 3.06
73 74 7.489113 CCATATGTCCACTTTTTAGCAAATGTC 59.511 37.037 1.24 0.00 29.87 3.06
75 76 7.546358 TCCATATGTCCACTTTTTAGCAAATG 58.454 34.615 1.24 0.00 0.00 2.32
76 77 7.631377 GCTCCATATGTCCACTTTTTAGCAAAT 60.631 37.037 1.24 0.00 0.00 2.32
77 78 6.350110 GCTCCATATGTCCACTTTTTAGCAAA 60.350 38.462 1.24 0.00 0.00 3.68
79 80 4.640201 GCTCCATATGTCCACTTTTTAGCA 59.360 41.667 1.24 0.00 0.00 3.49
81 82 4.260784 GCGCTCCATATGTCCACTTTTTAG 60.261 45.833 0.00 0.00 0.00 1.85
82 83 3.625764 GCGCTCCATATGTCCACTTTTTA 59.374 43.478 0.00 0.00 0.00 1.52
83 84 2.423538 GCGCTCCATATGTCCACTTTTT 59.576 45.455 0.00 0.00 0.00 1.94
85 86 1.668419 GCGCTCCATATGTCCACTTT 58.332 50.000 0.00 0.00 0.00 2.66
88 89 0.882042 CAGGCGCTCCATATGTCCAC 60.882 60.000 7.64 0.00 33.74 4.02
90 91 0.106708 TTCAGGCGCTCCATATGTCC 59.893 55.000 7.64 0.00 33.74 4.02
91 92 1.953559 TTTCAGGCGCTCCATATGTC 58.046 50.000 7.64 0.00 33.74 3.06
92 93 2.645838 ATTTCAGGCGCTCCATATGT 57.354 45.000 7.64 0.00 33.74 2.29
93 94 3.635331 CAAATTTCAGGCGCTCCATATG 58.365 45.455 7.64 0.00 33.74 1.78
94 95 2.035066 GCAAATTTCAGGCGCTCCATAT 59.965 45.455 7.64 0.00 33.74 1.78
96 97 0.174162 GCAAATTTCAGGCGCTCCAT 59.826 50.000 7.64 0.00 33.74 3.41
97 98 1.586028 GCAAATTTCAGGCGCTCCA 59.414 52.632 7.64 0.00 33.74 3.86
98 99 1.153765 GGCAAATTTCAGGCGCTCC 60.154 57.895 7.64 0.00 0.00 4.70
99 100 1.514873 CGGCAAATTTCAGGCGCTC 60.515 57.895 7.64 0.00 46.46 5.03
100 101 2.568090 CGGCAAATTTCAGGCGCT 59.432 55.556 7.64 0.00 46.46 5.92
103 104 0.732538 CGTTCCGGCAAATTTCAGGC 60.733 55.000 0.00 0.00 0.00 4.85
104 105 0.109319 CCGTTCCGGCAAATTTCAGG 60.109 55.000 0.00 0.00 41.17 3.86
105 106 3.399879 CCGTTCCGGCAAATTTCAG 57.600 52.632 0.00 0.00 41.17 3.02
113 114 9.536049 GAATATTGATTCATTTCCGTTCCGGCA 62.536 40.741 0.00 0.00 42.75 5.69
114 115 7.273040 GAATATTGATTCATTTCCGTTCCGGC 61.273 42.308 0.00 0.00 42.75 6.13
115 116 6.142817 GAATATTGATTCATTTCCGTTCCGG 58.857 40.000 0.00 0.00 43.53 5.14
116 117 6.142817 GGAATATTGATTCATTTCCGTTCCG 58.857 40.000 0.00 0.00 42.95 4.30
122 123 5.452078 TGCCGGAATATTGATTCATTTCC 57.548 39.130 5.05 11.02 42.95 3.13
123 124 7.277539 TGTTTTGCCGGAATATTGATTCATTTC 59.722 33.333 5.05 0.00 42.95 2.17
129 130 6.323739 ACCTATGTTTTGCCGGAATATTGATT 59.676 34.615 5.05 0.00 0.00 2.57
130 131 5.833131 ACCTATGTTTTGCCGGAATATTGAT 59.167 36.000 5.05 0.00 0.00 2.57
131 132 5.197451 ACCTATGTTTTGCCGGAATATTGA 58.803 37.500 5.05 0.00 0.00 2.57
132 133 5.067153 TGACCTATGTTTTGCCGGAATATTG 59.933 40.000 5.05 0.00 0.00 1.90
133 134 5.067283 GTGACCTATGTTTTGCCGGAATATT 59.933 40.000 5.05 0.00 0.00 1.28
135 136 3.942748 GTGACCTATGTTTTGCCGGAATA 59.057 43.478 5.05 0.00 0.00 1.75
137 138 2.156098 GTGACCTATGTTTTGCCGGAA 58.844 47.619 5.05 0.00 0.00 4.30
138 139 1.349688 AGTGACCTATGTTTTGCCGGA 59.650 47.619 5.05 0.00 0.00 5.14
139 140 1.737793 GAGTGACCTATGTTTTGCCGG 59.262 52.381 0.00 0.00 0.00 6.13
140 141 1.393539 CGAGTGACCTATGTTTTGCCG 59.606 52.381 0.00 0.00 0.00 5.69
141 142 1.737793 CCGAGTGACCTATGTTTTGCC 59.262 52.381 0.00 0.00 0.00 4.52
142 143 2.695359 TCCGAGTGACCTATGTTTTGC 58.305 47.619 0.00 0.00 0.00 3.68
143 144 6.986817 AGAATATCCGAGTGACCTATGTTTTG 59.013 38.462 0.00 0.00 0.00 2.44
144 145 7.125792 AGAATATCCGAGTGACCTATGTTTT 57.874 36.000 0.00 0.00 0.00 2.43
145 146 6.732896 AGAATATCCGAGTGACCTATGTTT 57.267 37.500 0.00 0.00 0.00 2.83
146 147 6.515200 CGAAGAATATCCGAGTGACCTATGTT 60.515 42.308 0.00 0.00 0.00 2.71
147 148 5.048643 CGAAGAATATCCGAGTGACCTATGT 60.049 44.000 0.00 0.00 0.00 2.29
148 149 5.181433 TCGAAGAATATCCGAGTGACCTATG 59.819 44.000 0.00 0.00 0.00 2.23
149 150 5.181622 GTCGAAGAATATCCGAGTGACCTAT 59.818 44.000 0.00 0.00 39.69 2.57
150 151 4.514441 GTCGAAGAATATCCGAGTGACCTA 59.486 45.833 0.00 0.00 39.69 3.08
151 152 3.315749 GTCGAAGAATATCCGAGTGACCT 59.684 47.826 0.00 0.00 39.69 3.85
152 153 3.066342 TGTCGAAGAATATCCGAGTGACC 59.934 47.826 0.00 0.00 39.69 4.02
153 154 4.288670 TGTCGAAGAATATCCGAGTGAC 57.711 45.455 0.00 0.00 39.69 3.67
154 155 5.067283 TGAATGTCGAAGAATATCCGAGTGA 59.933 40.000 0.00 0.00 39.69 3.41
155 156 5.281727 TGAATGTCGAAGAATATCCGAGTG 58.718 41.667 0.00 0.00 39.69 3.51
156 157 5.515797 TGAATGTCGAAGAATATCCGAGT 57.484 39.130 0.00 0.00 39.69 4.18
157 158 5.175856 GGTTGAATGTCGAAGAATATCCGAG 59.824 44.000 0.00 0.00 39.69 4.63
159 160 4.808895 TGGTTGAATGTCGAAGAATATCCG 59.191 41.667 0.00 0.00 39.69 4.18
160 161 6.093495 TGTTGGTTGAATGTCGAAGAATATCC 59.907 38.462 0.00 0.00 39.69 2.59
161 162 7.072177 TGTTGGTTGAATGTCGAAGAATATC 57.928 36.000 0.00 0.00 39.69 1.63
164 165 5.964958 ATGTTGGTTGAATGTCGAAGAAT 57.035 34.783 0.00 0.00 39.69 2.40
165 166 5.518812 CAATGTTGGTTGAATGTCGAAGAA 58.481 37.500 0.00 0.00 39.69 2.52
166 167 4.556501 GCAATGTTGGTTGAATGTCGAAGA 60.557 41.667 0.00 0.00 0.00 2.87
167 168 3.670055 GCAATGTTGGTTGAATGTCGAAG 59.330 43.478 0.00 0.00 0.00 3.79
168 169 3.067320 TGCAATGTTGGTTGAATGTCGAA 59.933 39.130 0.00 0.00 0.00 3.71
169 170 2.620585 TGCAATGTTGGTTGAATGTCGA 59.379 40.909 0.00 0.00 0.00 4.20
170 171 3.010624 TGCAATGTTGGTTGAATGTCG 57.989 42.857 0.00 0.00 0.00 4.35
171 172 5.731599 TTTTGCAATGTTGGTTGAATGTC 57.268 34.783 0.00 0.00 0.00 3.06
172 173 5.821470 TGATTTTGCAATGTTGGTTGAATGT 59.179 32.000 0.00 0.00 0.00 2.71
173 174 6.301687 TGATTTTGCAATGTTGGTTGAATG 57.698 33.333 0.00 0.00 0.00 2.67
174 175 8.795842 ATATGATTTTGCAATGTTGGTTGAAT 57.204 26.923 0.00 0.00 0.00 2.57
175 176 9.716531 TTATATGATTTTGCAATGTTGGTTGAA 57.283 25.926 0.00 0.00 0.00 2.69
176 177 9.149225 GTTATATGATTTTGCAATGTTGGTTGA 57.851 29.630 0.00 0.00 0.00 3.18
177 178 8.933807 TGTTATATGATTTTGCAATGTTGGTTG 58.066 29.630 0.00 0.00 0.00 3.77
178 179 9.669887 ATGTTATATGATTTTGCAATGTTGGTT 57.330 25.926 0.00 0.00 0.00 3.67
180 181 9.315525 TGATGTTATATGATTTTGCAATGTTGG 57.684 29.630 0.00 0.00 0.00 3.77
208 209 9.461312 AGCCTCTGTATTGTTTTAAATATGTCA 57.539 29.630 0.00 0.00 0.00 3.58
211 212 9.884465 GCTAGCCTCTGTATTGTTTTAAATATG 57.116 33.333 2.29 0.00 0.00 1.78
212 213 9.067986 GGCTAGCCTCTGTATTGTTTTAAATAT 57.932 33.333 27.17 0.00 0.00 1.28
271 272 2.852495 GATCCAACGGCCAGCGAAGA 62.852 60.000 2.24 0.00 0.00 2.87
389 390 1.582610 CCAGCCAATAAACACGCGGT 61.583 55.000 12.47 2.05 0.00 5.68
597 603 2.000825 GAAGGGGGAGAAGGGATGCC 62.001 65.000 0.00 0.00 0.00 4.40
718 725 1.985116 GAGCTCCTCCTTCCGTGGT 60.985 63.158 0.87 0.00 0.00 4.16
846 853 1.281899 GATCTCGCCGAAAGAACTGG 58.718 55.000 0.00 0.00 0.00 4.00
847 854 1.281899 GGATCTCGCCGAAAGAACTG 58.718 55.000 0.00 0.00 0.00 3.16
848 855 0.895530 TGGATCTCGCCGAAAGAACT 59.104 50.000 0.00 0.00 0.00 3.01
974 1351 1.002274 TCTCCTCCTTCTCTGGCCC 59.998 63.158 0.00 0.00 0.00 5.80
1064 1442 3.307674 GCTCGCTGAGATATGAGAACAG 58.692 50.000 9.32 0.00 0.00 3.16
1137 1537 2.158475 TCTGGAAGCAAACTGGGAATGT 60.158 45.455 0.00 0.00 0.00 2.71
1169 1569 1.376037 GCAGGTTCACCTCTTCCCG 60.376 63.158 0.00 0.00 46.65 5.14
1270 1670 7.225931 GTGTTCCACAGTAATAGACACTTGAAA 59.774 37.037 0.00 0.00 34.08 2.69
1335 1755 6.072286 ACCTGAACAGACATTCACATTCATTC 60.072 38.462 3.19 0.00 34.84 2.67
1542 5500 6.864685 TGCAACAGAAATTTAAGAAGCTGATG 59.135 34.615 8.76 8.19 31.82 3.07
1660 5619 7.248437 CCTTAGGGACGCTTTTAAAAACATAG 58.752 38.462 1.66 0.00 33.58 2.23
1661 5620 6.349528 GCCTTAGGGACGCTTTTAAAAACATA 60.350 38.462 0.00 0.00 33.58 2.29
1662 5621 5.566032 GCCTTAGGGACGCTTTTAAAAACAT 60.566 40.000 0.00 0.00 33.58 2.71
1663 5622 4.261698 GCCTTAGGGACGCTTTTAAAAACA 60.262 41.667 0.00 0.00 33.58 2.83
1664 5623 4.232221 GCCTTAGGGACGCTTTTAAAAAC 58.768 43.478 0.00 0.00 33.58 2.43
1665 5624 3.058085 CGCCTTAGGGACGCTTTTAAAAA 60.058 43.478 0.00 0.00 33.58 1.94
1666 5625 2.485038 CGCCTTAGGGACGCTTTTAAAA 59.515 45.455 0.00 0.00 33.58 1.52
1667 5626 2.078392 CGCCTTAGGGACGCTTTTAAA 58.922 47.619 0.00 0.00 33.58 1.52
1668 5627 1.275856 TCGCCTTAGGGACGCTTTTAA 59.724 47.619 0.00 0.00 34.09 1.52
1669 5628 0.896923 TCGCCTTAGGGACGCTTTTA 59.103 50.000 0.00 0.00 34.09 1.52
1670 5629 0.672711 GTCGCCTTAGGGACGCTTTT 60.673 55.000 0.00 0.00 44.82 2.27
1671 5630 1.079336 GTCGCCTTAGGGACGCTTT 60.079 57.895 0.00 0.00 44.82 3.51
1672 5631 2.577593 GTCGCCTTAGGGACGCTT 59.422 61.111 0.00 0.00 44.82 4.68
1688 5647 2.572284 GCTTCGACGCCTAGGTGT 59.428 61.111 27.94 27.94 42.00 4.16
1689 5648 2.579787 CGCTTCGACGCCTAGGTG 60.580 66.667 21.04 21.04 0.00 4.00
1698 5657 4.516195 GAGGGGGAGCGCTTCGAC 62.516 72.222 13.26 5.82 0.00 4.20
1706 5665 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
1707 5666 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
1714 5673 1.161843 GGTCGATTTTCCAAAGCGGA 58.838 50.000 7.00 0.00 44.40 5.54
1715 5674 0.179200 CGGTCGATTTTCCAAAGCGG 60.179 55.000 7.00 0.00 0.00 5.52
1716 5675 0.793104 GCGGTCGATTTTCCAAAGCG 60.793 55.000 0.54 0.54 0.00 4.68
1717 5676 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
1718 5677 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
1719 5678 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
1720 5679 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
1721 5680 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
1722 5681 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
1723 5682 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
1724 5683 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
1725 5684 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
1743 5702 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
1751 5710 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
1752 5711 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
1798 5757 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
1799 5758 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
1800 5759 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
1801 5760 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
1802 5761 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
1803 5762 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
1815 5774 4.531659 ATCTATGTTTTTAAGGCGACGC 57.468 40.909 12.43 12.43 0.00 5.19
1816 5775 9.793245 CTATTAATCTATGTTTTTAAGGCGACG 57.207 33.333 0.00 0.00 0.00 5.12
1819 5778 9.382244 GCACTATTAATCTATGTTTTTAAGGCG 57.618 33.333 0.00 0.00 0.00 5.52
1835 5794 9.490379 GCCTTAATGTAGTACTGCACTATTAAT 57.510 33.333 16.34 0.00 41.77 1.40
1836 5795 8.479689 TGCCTTAATGTAGTACTGCACTATTAA 58.520 33.333 16.34 14.82 41.77 1.40
1837 5796 8.014070 TGCCTTAATGTAGTACTGCACTATTA 57.986 34.615 16.34 8.42 41.77 0.98
1838 5797 6.884832 TGCCTTAATGTAGTACTGCACTATT 58.115 36.000 16.34 9.39 41.77 1.73
1839 5798 6.479972 TGCCTTAATGTAGTACTGCACTAT 57.520 37.500 16.34 8.20 41.77 2.12
1840 5799 5.925506 TGCCTTAATGTAGTACTGCACTA 57.074 39.130 16.34 6.94 38.80 2.74
1841 5800 4.819105 TGCCTTAATGTAGTACTGCACT 57.181 40.909 16.34 8.08 41.62 4.40
1842 5801 7.226720 ACATATTGCCTTAATGTAGTACTGCAC 59.773 37.037 16.34 2.04 32.21 4.57
1934 5893 2.952978 AGACGAATAGATGCCGAGTCTT 59.047 45.455 0.00 0.00 34.27 3.01
2637 6617 3.056179 TCACTCGTCACCAATAAGCATGA 60.056 43.478 0.00 0.00 0.00 3.07
2687 6667 7.070074 TGAGAAGAGGGAGAAACATACCTAATC 59.930 40.741 0.00 0.00 32.42 1.75
3053 7075 4.080356 CCACAGGGGACAGAATCTTCAATA 60.080 45.833 0.00 0.00 40.01 1.90
3612 7646 3.831323 TGGAGCCTCATTTGAAGAACAA 58.169 40.909 0.00 0.00 36.65 2.83


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

AutoCloner maintained by Alex Coulton.