Multiple sequence alignment - TraesCS5D01G042500

Loading Multiple Alignment...

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 TraesCS5D01G042500 chr5D 100.000 2663 0 0 1 2663 42075549 42078211 0.000000e+00 4918
1 TraesCS5D01G042500 chr5D 80.063 1580 254 36 433 1982 499865159 499863611 0.000000e+00 1116
2 TraesCS5D01G042500 chr5D 85.877 439 45 10 2234 2663 499863237 499862807 4.040000e-123 451
3 TraesCS5D01G042500 chr5A 92.192 1268 45 12 1146 2379 30638329 30639576 0.000000e+00 1744
4 TraesCS5D01G042500 chr5A 88.235 170 15 3 431 595 30637931 30638100 5.810000e-47 198
5 TraesCS5D01G042500 chrUn 83.973 1460 204 13 694 2132 95438041 95439491 0.000000e+00 1373
6 TraesCS5D01G042500 chrUn 85.597 243 15 5 325 567 65779513 65779291 1.230000e-58 237
7 TraesCS5D01G042500 chr6A 84.222 1369 202 12 626 1989 9461576 9462935 0.000000e+00 1319
8 TraesCS5D01G042500 chr6A 83.075 1353 217 9 633 1980 9355310 9356655 0.000000e+00 1219
9 TraesCS5D01G042500 chr6B 82.300 1565 236 29 443 1984 16433073 16434619 0.000000e+00 1317
10 TraesCS5D01G042500 chr6B 83.894 1279 187 18 630 1901 670592574 670591308 0.000000e+00 1203
11 TraesCS5D01G042500 chr6B 80.107 1498 275 10 506 1989 15397956 15396468 0.000000e+00 1094
12 TraesCS5D01G042500 chr6B 83.185 672 70 15 2027 2661 15233256 15232591 2.300000e-160 575
13 TraesCS5D01G042500 chr6B 83.284 670 63 16 2027 2661 16268934 16269589 2.970000e-159 571
14 TraesCS5D01G042500 chr6B 79.695 591 73 25 2097 2663 15396378 15395811 1.500000e-102 383
15 TraesCS5D01G042500 chr6B 80.652 491 60 15 2193 2663 16434909 16435384 5.460000e-92 348
16 TraesCS5D01G042500 chr6B 84.262 305 37 4 2370 2663 52979678 52979374 1.210000e-73 287
17 TraesCS5D01G042500 chr6B 79.903 413 41 20 2097 2495 670591147 670590763 5.650000e-67 265
18 TraesCS5D01G042500 chr6B 81.639 305 34 9 2370 2663 16340398 16340691 1.590000e-57 233
19 TraesCS5D01G042500 chr6B 77.982 218 30 9 2085 2287 15713638 15713424 1.290000e-23 121
20 TraesCS5D01G042500 chr6B 91.463 82 7 0 2085 2166 16434726 16434807 2.170000e-21 113
21 TraesCS5D01G042500 chr2B 82.010 1562 236 36 449 1989 54016728 54015191 0.000000e+00 1286
22 TraesCS5D01G042500 chr2B 83.774 1362 196 17 606 1962 54043910 54042569 0.000000e+00 1267
23 TraesCS5D01G042500 chr2B 80.584 582 67 19 2085 2629 89492185 89492757 8.880000e-110 407
24 TraesCS5D01G042500 chr2B 78.636 220 25 12 2085 2287 709252208 709251994 2.780000e-25 126
25 TraesCS5D01G042500 chr1B 79.136 1505 285 23 503 1989 662153019 662154512 0.000000e+00 1013
26 TraesCS5D01G042500 chr7B 84.386 839 111 15 501 1331 32348080 32347254 0.000000e+00 806
27 TraesCS5D01G042500 chr5B 83.383 674 67 18 2027 2661 556624963 556624296 1.370000e-162 582
28 TraesCS5D01G042500 chr5B 85.388 438 48 9 2234 2663 621236541 621236112 8.750000e-120 440
29 TraesCS5D01G042500 chr5B 80.961 583 74 21 2097 2663 556794174 556793613 6.810000e-116 427
30 TraesCS5D01G042500 chr6D 75.330 1289 270 37 430 1689 8893967 8895236 2.300000e-160 575
31 TraesCS5D01G042500 chr6D 82.212 416 43 14 2097 2490 33896609 33897015 1.980000e-86 329
32 TraesCS5D01G042500 chr6D 77.143 245 39 10 430 660 8402507 8402266 2.780000e-25 126
33 TraesCS5D01G042500 chr6D 90.244 82 8 0 2085 2166 8551216 8551135 1.010000e-19 108
34 TraesCS5D01G042500 chr3D 86.275 306 30 5 2370 2663 582881304 582881609 3.310000e-84 322


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 TraesCS5D01G042500 chr5D 42075549 42078211 2662 False 4918.000000 4918 100.0000 1 2663 1 chr5D.!!$F1 2662
1 TraesCS5D01G042500 chr5D 499862807 499865159 2352 True 783.500000 1116 82.9700 433 2663 2 chr5D.!!$R1 2230
2 TraesCS5D01G042500 chr5A 30637931 30639576 1645 False 971.000000 1744 90.2135 431 2379 2 chr5A.!!$F1 1948
3 TraesCS5D01G042500 chrUn 95438041 95439491 1450 False 1373.000000 1373 83.9730 694 2132 1 chrUn.!!$F1 1438
4 TraesCS5D01G042500 chr6A 9461576 9462935 1359 False 1319.000000 1319 84.2220 626 1989 1 chr6A.!!$F2 1363
5 TraesCS5D01G042500 chr6A 9355310 9356655 1345 False 1219.000000 1219 83.0750 633 1980 1 chr6A.!!$F1 1347
6 TraesCS5D01G042500 chr6B 15395811 15397956 2145 True 738.500000 1094 79.9010 506 2663 2 chr6B.!!$R4 2157
7 TraesCS5D01G042500 chr6B 670590763 670592574 1811 True 734.000000 1203 81.8985 630 2495 2 chr6B.!!$R5 1865
8 TraesCS5D01G042500 chr6B 16433073 16435384 2311 False 592.666667 1317 84.8050 443 2663 3 chr6B.!!$F3 2220
9 TraesCS5D01G042500 chr6B 15232591 15233256 665 True 575.000000 575 83.1850 2027 2661 1 chr6B.!!$R1 634
10 TraesCS5D01G042500 chr6B 16268934 16269589 655 False 571.000000 571 83.2840 2027 2661 1 chr6B.!!$F1 634
11 TraesCS5D01G042500 chr2B 54015191 54016728 1537 True 1286.000000 1286 82.0100 449 1989 1 chr2B.!!$R1 1540
12 TraesCS5D01G042500 chr2B 54042569 54043910 1341 True 1267.000000 1267 83.7740 606 1962 1 chr2B.!!$R2 1356
13 TraesCS5D01G042500 chr2B 89492185 89492757 572 False 407.000000 407 80.5840 2085 2629 1 chr2B.!!$F1 544
14 TraesCS5D01G042500 chr1B 662153019 662154512 1493 False 1013.000000 1013 79.1360 503 1989 1 chr1B.!!$F1 1486
15 TraesCS5D01G042500 chr7B 32347254 32348080 826 True 806.000000 806 84.3860 501 1331 1 chr7B.!!$R1 830
16 TraesCS5D01G042500 chr5B 556624296 556624963 667 True 582.000000 582 83.3830 2027 2661 1 chr5B.!!$R1 634
17 TraesCS5D01G042500 chr5B 556793613 556794174 561 True 427.000000 427 80.9610 2097 2663 1 chr5B.!!$R2 566
18 TraesCS5D01G042500 chr6D 8893967 8895236 1269 False 575.000000 575 75.3300 430 1689 1 chr6D.!!$F1 1259

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
623 664 0.037160 GGCCGTTTCCTCAAACCCTA 59.963 55.0 0.0 0.0 39.07 3.53 F
1144 1189 0.249398 GATCACCGCCAACCTACAGT 59.751 55.0 0.0 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1605 0.174617 GCCTTCTCGGTCTCCTTGAG 59.825 60.0 0.0 0.0 34.25 3.02 R
2611 3049 0.323816 TGCCCACAGGACAAAACACA 60.324 50.0 0.0 0.0 33.47 3.72 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
21 22 4.990543 TGTGCTCAATTTGAGTAACTCG 57.009 40.909 23.66 2.36 45.94 4.18
22 23 4.627058 TGTGCTCAATTTGAGTAACTCGA 58.373 39.130 23.66 8.00 45.94 4.04
23 24 4.447724 TGTGCTCAATTTGAGTAACTCGAC 59.552 41.667 23.66 9.94 45.94 4.20
24 25 4.447724 GTGCTCAATTTGAGTAACTCGACA 59.552 41.667 23.66 10.53 45.94 4.35
25 26 5.050363 GTGCTCAATTTGAGTAACTCGACAA 60.050 40.000 23.66 0.00 45.94 3.18
26 27 5.525745 TGCTCAATTTGAGTAACTCGACAAA 59.474 36.000 23.66 0.00 45.94 2.83
27 28 6.037720 TGCTCAATTTGAGTAACTCGACAAAA 59.962 34.615 23.66 0.00 45.94 2.44
28 29 6.910433 GCTCAATTTGAGTAACTCGACAAAAA 59.090 34.615 23.66 0.00 45.94 1.94
50 51 5.458041 AACTGATGTTTTGGATTGACAGG 57.542 39.130 0.00 0.00 31.37 4.00
51 52 4.473444 ACTGATGTTTTGGATTGACAGGT 58.527 39.130 0.00 0.00 0.00 4.00
52 53 4.279169 ACTGATGTTTTGGATTGACAGGTG 59.721 41.667 0.00 0.00 0.00 4.00
53 54 4.214310 TGATGTTTTGGATTGACAGGTGT 58.786 39.130 0.00 0.00 0.00 4.16
54 55 4.037803 TGATGTTTTGGATTGACAGGTGTG 59.962 41.667 0.00 0.00 0.00 3.82
55 56 3.360867 TGTTTTGGATTGACAGGTGTGT 58.639 40.909 0.00 0.00 40.71 3.72
56 57 3.766591 TGTTTTGGATTGACAGGTGTGTT 59.233 39.130 0.00 0.00 36.88 3.32
57 58 4.142271 TGTTTTGGATTGACAGGTGTGTTC 60.142 41.667 0.00 0.00 36.88 3.18
58 59 1.877637 TGGATTGACAGGTGTGTTCG 58.122 50.000 0.00 0.00 36.88 3.95
59 60 1.414550 TGGATTGACAGGTGTGTTCGA 59.585 47.619 0.00 0.00 36.88 3.71
60 61 2.158885 TGGATTGACAGGTGTGTTCGAA 60.159 45.455 0.00 0.00 36.88 3.71
61 62 2.480419 GGATTGACAGGTGTGTTCGAAG 59.520 50.000 0.00 0.00 36.88 3.79
62 63 2.684001 TTGACAGGTGTGTTCGAAGT 57.316 45.000 0.00 0.00 36.88 3.01
63 64 1.934589 TGACAGGTGTGTTCGAAGTG 58.065 50.000 0.00 0.00 36.88 3.16
64 65 1.206132 TGACAGGTGTGTTCGAAGTGT 59.794 47.619 0.00 0.00 36.88 3.55
65 66 2.427812 TGACAGGTGTGTTCGAAGTGTA 59.572 45.455 0.00 0.00 36.88 2.90
66 67 3.069016 TGACAGGTGTGTTCGAAGTGTAT 59.931 43.478 0.00 0.00 36.88 2.29
67 68 3.650139 ACAGGTGTGTTCGAAGTGTATC 58.350 45.455 0.00 0.00 30.30 2.24
68 69 3.069016 ACAGGTGTGTTCGAAGTGTATCA 59.931 43.478 0.00 0.00 30.30 2.15
69 70 3.675225 CAGGTGTGTTCGAAGTGTATCAG 59.325 47.826 0.00 0.00 0.00 2.90
70 71 3.321111 AGGTGTGTTCGAAGTGTATCAGT 59.679 43.478 0.00 0.00 0.00 3.41
71 72 3.428870 GGTGTGTTCGAAGTGTATCAGTG 59.571 47.826 0.00 0.00 0.00 3.66
72 73 3.057019 TGTGTTCGAAGTGTATCAGTGC 58.943 45.455 0.00 0.00 0.00 4.40
73 74 2.090658 GTGTTCGAAGTGTATCAGTGCG 59.909 50.000 0.00 0.00 37.20 5.34
74 75 2.030628 TGTTCGAAGTGTATCAGTGCGA 60.031 45.455 0.00 3.86 42.32 5.10
75 76 3.179830 GTTCGAAGTGTATCAGTGCGAT 58.820 45.455 0.00 0.00 43.30 4.58
76 77 3.503827 TCGAAGTGTATCAGTGCGATT 57.496 42.857 3.86 0.00 39.59 3.34
77 78 4.625972 TCGAAGTGTATCAGTGCGATTA 57.374 40.909 3.86 0.00 39.59 1.75
78 79 4.348656 TCGAAGTGTATCAGTGCGATTAC 58.651 43.478 3.86 0.00 39.59 1.89
79 80 4.102649 CGAAGTGTATCAGTGCGATTACA 58.897 43.478 0.00 0.00 38.02 2.41
80 81 4.740205 CGAAGTGTATCAGTGCGATTACAT 59.260 41.667 0.00 0.00 38.02 2.29
81 82 5.108217 CGAAGTGTATCAGTGCGATTACATC 60.108 44.000 0.00 0.00 38.02 3.06
82 83 5.262588 AGTGTATCAGTGCGATTACATCA 57.737 39.130 0.00 0.00 35.39 3.07
83 84 5.043903 AGTGTATCAGTGCGATTACATCAC 58.956 41.667 0.00 0.00 35.39 3.06
84 85 5.043903 GTGTATCAGTGCGATTACATCACT 58.956 41.667 0.00 0.00 41.29 3.41
85 86 5.520288 GTGTATCAGTGCGATTACATCACTT 59.480 40.000 0.00 0.00 38.85 3.16
86 87 6.695713 GTGTATCAGTGCGATTACATCACTTA 59.304 38.462 0.00 0.00 38.85 2.24
87 88 6.695713 TGTATCAGTGCGATTACATCACTTAC 59.304 38.462 0.00 0.00 38.85 2.34
88 89 5.066968 TCAGTGCGATTACATCACTTACA 57.933 39.130 0.00 0.00 38.85 2.41
89 90 5.474825 TCAGTGCGATTACATCACTTACAA 58.525 37.500 0.00 0.00 38.85 2.41
90 91 5.929415 TCAGTGCGATTACATCACTTACAAA 59.071 36.000 0.00 0.00 38.85 2.83
91 92 6.593770 TCAGTGCGATTACATCACTTACAAAT 59.406 34.615 0.00 0.00 38.85 2.32
92 93 7.119116 TCAGTGCGATTACATCACTTACAAATT 59.881 33.333 0.00 0.00 38.85 1.82
93 94 8.387354 CAGTGCGATTACATCACTTACAAATTA 58.613 33.333 0.00 0.00 38.85 1.40
94 95 9.109393 AGTGCGATTACATCACTTACAAATTAT 57.891 29.630 0.00 0.00 37.78 1.28
95 96 9.158364 GTGCGATTACATCACTTACAAATTATG 57.842 33.333 0.00 0.00 0.00 1.90
96 97 8.341903 TGCGATTACATCACTTACAAATTATGG 58.658 33.333 0.00 0.00 0.00 2.74
97 98 7.323656 GCGATTACATCACTTACAAATTATGGC 59.676 37.037 0.00 0.00 0.00 4.40
98 99 7.803189 CGATTACATCACTTACAAATTATGGCC 59.197 37.037 0.00 0.00 0.00 5.36
99 100 5.499139 ACATCACTTACAAATTATGGCCG 57.501 39.130 0.00 0.00 0.00 6.13
100 101 4.338118 ACATCACTTACAAATTATGGCCGG 59.662 41.667 0.00 0.00 0.00 6.13
101 102 4.223556 TCACTTACAAATTATGGCCGGA 57.776 40.909 5.05 0.00 0.00 5.14
102 103 4.787551 TCACTTACAAATTATGGCCGGAT 58.212 39.130 5.05 0.00 0.00 4.18
103 104 4.819630 TCACTTACAAATTATGGCCGGATC 59.180 41.667 5.05 0.00 0.00 3.36
104 105 3.813166 ACTTACAAATTATGGCCGGATCG 59.187 43.478 5.05 0.00 0.00 3.69
105 106 2.631160 ACAAATTATGGCCGGATCGA 57.369 45.000 5.05 0.00 0.00 3.59
106 107 3.140325 ACAAATTATGGCCGGATCGAT 57.860 42.857 5.05 0.00 0.00 3.59
107 108 2.813754 ACAAATTATGGCCGGATCGATG 59.186 45.455 5.05 0.00 0.00 3.84
108 109 1.453155 AATTATGGCCGGATCGATGC 58.547 50.000 5.05 4.17 0.00 3.91
109 110 0.615331 ATTATGGCCGGATCGATGCT 59.385 50.000 15.31 0.00 0.00 3.79
110 111 0.037326 TTATGGCCGGATCGATGCTC 60.037 55.000 15.31 6.44 0.00 4.26
111 112 1.888436 TATGGCCGGATCGATGCTCC 61.888 60.000 15.31 15.13 0.00 4.70
112 113 3.620785 GGCCGGATCGATGCTCCT 61.621 66.667 15.31 0.00 0.00 3.69
113 114 2.423446 GCCGGATCGATGCTCCTT 59.577 61.111 15.31 0.00 0.00 3.36
114 115 1.666234 GCCGGATCGATGCTCCTTC 60.666 63.158 15.31 0.00 0.00 3.46
115 116 2.045280 CCGGATCGATGCTCCTTCT 58.955 57.895 15.31 0.00 0.00 2.85
116 117 0.038709 CCGGATCGATGCTCCTTCTC 60.039 60.000 15.31 0.00 0.00 2.87
117 118 0.038709 CGGATCGATGCTCCTTCTCC 60.039 60.000 15.31 0.48 0.00 3.71
118 119 1.043816 GGATCGATGCTCCTTCTCCA 58.956 55.000 9.99 0.00 0.00 3.86
119 120 1.622811 GGATCGATGCTCCTTCTCCAT 59.377 52.381 9.99 0.00 0.00 3.41
120 121 2.353605 GGATCGATGCTCCTTCTCCATC 60.354 54.545 9.99 0.00 33.71 3.51
123 124 2.437200 GATGCTCCTTCTCCATCGAG 57.563 55.000 0.00 0.00 37.48 4.04
124 125 1.686052 GATGCTCCTTCTCCATCGAGT 59.314 52.381 0.00 0.00 37.40 4.18
125 126 2.437085 TGCTCCTTCTCCATCGAGTA 57.563 50.000 0.00 0.00 37.40 2.59
126 127 2.025155 TGCTCCTTCTCCATCGAGTAC 58.975 52.381 0.00 0.00 37.40 2.73
127 128 2.025155 GCTCCTTCTCCATCGAGTACA 58.975 52.381 0.00 0.00 37.40 2.90
128 129 2.625790 GCTCCTTCTCCATCGAGTACAT 59.374 50.000 0.00 0.00 37.40 2.29
129 130 3.305064 GCTCCTTCTCCATCGAGTACATC 60.305 52.174 0.00 0.00 37.40 3.06
130 131 3.885901 CTCCTTCTCCATCGAGTACATCA 59.114 47.826 0.00 0.00 37.40 3.07
131 132 4.474394 TCCTTCTCCATCGAGTACATCAT 58.526 43.478 0.00 0.00 37.40 2.45
132 133 5.631119 TCCTTCTCCATCGAGTACATCATA 58.369 41.667 0.00 0.00 37.40 2.15
133 134 6.249192 TCCTTCTCCATCGAGTACATCATAT 58.751 40.000 0.00 0.00 37.40 1.78
134 135 6.721668 TCCTTCTCCATCGAGTACATCATATT 59.278 38.462 0.00 0.00 37.40 1.28
135 136 7.032580 CCTTCTCCATCGAGTACATCATATTC 58.967 42.308 0.00 0.00 37.40 1.75
136 137 7.093988 CCTTCTCCATCGAGTACATCATATTCT 60.094 40.741 0.00 0.00 37.40 2.40
137 138 7.767250 TCTCCATCGAGTACATCATATTCTT 57.233 36.000 0.00 0.00 37.40 2.52
138 139 8.863872 TCTCCATCGAGTACATCATATTCTTA 57.136 34.615 0.00 0.00 37.40 2.10
139 140 8.951243 TCTCCATCGAGTACATCATATTCTTAG 58.049 37.037 0.00 0.00 37.40 2.18
140 141 7.539436 TCCATCGAGTACATCATATTCTTAGC 58.461 38.462 0.00 0.00 0.00 3.09
141 142 6.470556 CCATCGAGTACATCATATTCTTAGCG 59.529 42.308 0.00 0.00 0.00 4.26
142 143 5.939457 TCGAGTACATCATATTCTTAGCGG 58.061 41.667 0.00 0.00 0.00 5.52
143 144 5.472478 TCGAGTACATCATATTCTTAGCGGT 59.528 40.000 0.00 0.00 0.00 5.68
144 145 6.652062 TCGAGTACATCATATTCTTAGCGGTA 59.348 38.462 0.00 0.00 0.00 4.02
145 146 7.336176 TCGAGTACATCATATTCTTAGCGGTAT 59.664 37.037 0.00 0.00 0.00 2.73
146 147 7.640630 CGAGTACATCATATTCTTAGCGGTATC 59.359 40.741 0.00 0.00 0.00 2.24
147 148 8.582657 AGTACATCATATTCTTAGCGGTATCT 57.417 34.615 0.00 0.00 0.00 1.98
148 149 9.026121 AGTACATCATATTCTTAGCGGTATCTT 57.974 33.333 0.00 0.00 0.00 2.40
149 150 9.640963 GTACATCATATTCTTAGCGGTATCTTT 57.359 33.333 0.00 0.00 0.00 2.52
151 152 9.561069 ACATCATATTCTTAGCGGTATCTTTTT 57.439 29.630 0.00 0.00 0.00 1.94
152 153 9.817365 CATCATATTCTTAGCGGTATCTTTTTG 57.183 33.333 0.00 0.00 0.00 2.44
153 154 8.958119 TCATATTCTTAGCGGTATCTTTTTGT 57.042 30.769 0.00 0.00 0.00 2.83
154 155 8.826710 TCATATTCTTAGCGGTATCTTTTTGTG 58.173 33.333 0.00 0.00 0.00 3.33
155 156 8.612619 CATATTCTTAGCGGTATCTTTTTGTGT 58.387 33.333 0.00 0.00 0.00 3.72
156 157 5.856126 TCTTAGCGGTATCTTTTTGTGTG 57.144 39.130 0.00 0.00 0.00 3.82
157 158 5.302360 TCTTAGCGGTATCTTTTTGTGTGT 58.698 37.500 0.00 0.00 0.00 3.72
158 159 5.761234 TCTTAGCGGTATCTTTTTGTGTGTT 59.239 36.000 0.00 0.00 0.00 3.32
159 160 4.911514 AGCGGTATCTTTTTGTGTGTTT 57.088 36.364 0.00 0.00 0.00 2.83
160 161 5.257082 AGCGGTATCTTTTTGTGTGTTTT 57.743 34.783 0.00 0.00 0.00 2.43
161 162 5.656480 AGCGGTATCTTTTTGTGTGTTTTT 58.344 33.333 0.00 0.00 0.00 1.94
231 232 9.612066 TTTTTAGCAATTTGAGACAAATCCTTT 57.388 25.926 9.60 1.44 0.00 3.11
232 233 9.612066 TTTTAGCAATTTGAGACAAATCCTTTT 57.388 25.926 9.60 0.00 0.00 2.27
233 234 9.612066 TTTAGCAATTTGAGACAAATCCTTTTT 57.388 25.926 9.60 0.00 0.00 1.94
303 304 8.924691 CAAATCTTTTTGTGTTGTTGAAAGAGA 58.075 29.630 0.00 0.00 39.04 3.10
304 305 9.487790 AAATCTTTTTGTGTTGTTGAAAGAGAA 57.512 25.926 0.00 0.00 39.04 2.87
305 306 9.487790 AATCTTTTTGTGTTGTTGAAAGAGAAA 57.512 25.926 0.00 0.00 39.04 2.52
306 307 8.519492 TCTTTTTGTGTTGTTGAAAGAGAAAG 57.481 30.769 0.00 0.00 32.97 2.62
307 308 8.356657 TCTTTTTGTGTTGTTGAAAGAGAAAGA 58.643 29.630 0.00 0.00 32.97 2.52
308 309 8.519492 TTTTTGTGTTGTTGAAAGAGAAAGAG 57.481 30.769 0.00 0.00 0.00 2.85
309 310 7.447374 TTTGTGTTGTTGAAAGAGAAAGAGA 57.553 32.000 0.00 0.00 0.00 3.10
310 311 7.447374 TTGTGTTGTTGAAAGAGAAAGAGAA 57.553 32.000 0.00 0.00 0.00 2.87
311 312 7.447374 TGTGTTGTTGAAAGAGAAAGAGAAA 57.553 32.000 0.00 0.00 0.00 2.52
312 313 7.881142 TGTGTTGTTGAAAGAGAAAGAGAAAA 58.119 30.769 0.00 0.00 0.00 2.29
313 314 8.356657 TGTGTTGTTGAAAGAGAAAGAGAAAAA 58.643 29.630 0.00 0.00 0.00 1.94
340 341 8.675705 AAGAAGAGAAAGAGAAAGAGAAAAGG 57.324 34.615 0.00 0.00 0.00 3.11
341 342 6.710295 AGAAGAGAAAGAGAAAGAGAAAAGGC 59.290 38.462 0.00 0.00 0.00 4.35
342 343 6.186420 AGAGAAAGAGAAAGAGAAAAGGCT 57.814 37.500 0.00 0.00 0.00 4.58
343 344 6.230472 AGAGAAAGAGAAAGAGAAAAGGCTC 58.770 40.000 0.00 0.00 35.11 4.70
344 345 5.934781 AGAAAGAGAAAGAGAAAAGGCTCA 58.065 37.500 0.00 0.00 37.37 4.26
345 346 6.360618 AGAAAGAGAAAGAGAAAAGGCTCAA 58.639 36.000 0.00 0.00 37.37 3.02
346 347 7.003482 AGAAAGAGAAAGAGAAAAGGCTCAAT 58.997 34.615 0.00 0.00 37.37 2.57
347 348 8.160106 AGAAAGAGAAAGAGAAAAGGCTCAATA 58.840 33.333 0.00 0.00 37.37 1.90
348 349 7.920160 AAGAGAAAGAGAAAAGGCTCAATAG 57.080 36.000 0.00 0.00 37.37 1.73
349 350 7.014988 AGAGAAAGAGAAAAGGCTCAATAGT 57.985 36.000 0.00 0.00 37.37 2.12
350 351 7.457561 AGAGAAAGAGAAAAGGCTCAATAGTT 58.542 34.615 0.00 0.00 37.37 2.24
351 352 7.941790 AGAGAAAGAGAAAAGGCTCAATAGTTT 59.058 33.333 0.00 0.00 37.37 2.66
352 353 8.470657 AGAAAGAGAAAAGGCTCAATAGTTTT 57.529 30.769 0.00 0.00 37.37 2.43
353 354 9.574516 AGAAAGAGAAAAGGCTCAATAGTTTTA 57.425 29.630 0.00 0.00 37.37 1.52
381 382 5.424121 AGAACAAAATTCTCTTCCACACG 57.576 39.130 0.00 0.00 0.00 4.49
382 383 5.123227 AGAACAAAATTCTCTTCCACACGA 58.877 37.500 0.00 0.00 0.00 4.35
383 384 5.237344 AGAACAAAATTCTCTTCCACACGAG 59.763 40.000 0.00 0.00 0.00 4.18
384 385 4.451900 ACAAAATTCTCTTCCACACGAGT 58.548 39.130 0.00 0.00 0.00 4.18
385 386 4.511826 ACAAAATTCTCTTCCACACGAGTC 59.488 41.667 0.00 0.00 0.00 3.36
386 387 4.336889 AAATTCTCTTCCACACGAGTCA 57.663 40.909 0.00 0.00 0.00 3.41
387 388 4.543590 AATTCTCTTCCACACGAGTCAT 57.456 40.909 0.00 0.00 0.00 3.06
388 389 3.577649 TTCTCTTCCACACGAGTCATC 57.422 47.619 0.00 0.00 0.00 2.92
389 390 1.819288 TCTCTTCCACACGAGTCATCC 59.181 52.381 0.00 0.00 0.00 3.51
390 391 1.546029 CTCTTCCACACGAGTCATCCA 59.454 52.381 0.00 0.00 0.00 3.41
391 392 1.546029 TCTTCCACACGAGTCATCCAG 59.454 52.381 0.00 0.00 0.00 3.86
392 393 0.037326 TTCCACACGAGTCATCCAGC 60.037 55.000 0.00 0.00 0.00 4.85
393 394 1.448540 CCACACGAGTCATCCAGCC 60.449 63.158 0.00 0.00 0.00 4.85
394 395 1.448540 CACACGAGTCATCCAGCCC 60.449 63.158 0.00 0.00 0.00 5.19
395 396 1.913262 ACACGAGTCATCCAGCCCA 60.913 57.895 0.00 0.00 0.00 5.36
396 397 1.153489 CACGAGTCATCCAGCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
397 398 2.202987 CGAGTCATCCAGCCCAGC 60.203 66.667 0.00 0.00 0.00 4.85
398 399 2.191641 GAGTCATCCAGCCCAGCC 59.808 66.667 0.00 0.00 0.00 4.85
399 400 3.412624 GAGTCATCCAGCCCAGCCC 62.413 68.421 0.00 0.00 0.00 5.19
400 401 3.731728 GTCATCCAGCCCAGCCCA 61.732 66.667 0.00 0.00 0.00 5.36
401 402 2.940467 TCATCCAGCCCAGCCCAA 60.940 61.111 0.00 0.00 0.00 4.12
402 403 2.757099 CATCCAGCCCAGCCCAAC 60.757 66.667 0.00 0.00 0.00 3.77
403 404 4.066139 ATCCAGCCCAGCCCAACC 62.066 66.667 0.00 0.00 0.00 3.77
416 417 4.387343 CAACCCAGCCCAGCCCAT 62.387 66.667 0.00 0.00 0.00 4.00
417 418 3.604133 AACCCAGCCCAGCCCATT 61.604 61.111 0.00 0.00 0.00 3.16
418 419 2.245379 AACCCAGCCCAGCCCATTA 61.245 57.895 0.00 0.00 0.00 1.90
419 420 1.593166 AACCCAGCCCAGCCCATTAT 61.593 55.000 0.00 0.00 0.00 1.28
420 421 1.228675 CCCAGCCCAGCCCATTATC 60.229 63.158 0.00 0.00 0.00 1.75
421 422 1.601759 CCAGCCCAGCCCATTATCG 60.602 63.158 0.00 0.00 0.00 2.92
422 423 1.601759 CAGCCCAGCCCATTATCGG 60.602 63.158 0.00 0.00 0.00 4.18
423 424 2.078665 AGCCCAGCCCATTATCGGT 61.079 57.895 0.00 0.00 0.00 4.69
424 425 1.600916 GCCCAGCCCATTATCGGTC 60.601 63.158 0.00 0.00 0.00 4.79
425 426 1.836391 CCCAGCCCATTATCGGTCA 59.164 57.895 0.00 0.00 0.00 4.02
426 427 0.535102 CCCAGCCCATTATCGGTCAC 60.535 60.000 0.00 0.00 0.00 3.67
427 428 0.535102 CCAGCCCATTATCGGTCACC 60.535 60.000 0.00 0.00 0.00 4.02
428 429 0.535102 CAGCCCATTATCGGTCACCC 60.535 60.000 0.00 0.00 0.00 4.61
479 489 3.728373 GGCCGTCATTCCCCACCT 61.728 66.667 0.00 0.00 0.00 4.00
554 568 1.605202 GCATCCTCGCTCATCTCTTCC 60.605 57.143 0.00 0.00 0.00 3.46
567 584 2.269023 TCTCTTCCATTCTCCAGCCAA 58.731 47.619 0.00 0.00 0.00 4.52
622 663 1.228459 GGCCGTTTCCTCAAACCCT 60.228 57.895 0.00 0.00 39.07 4.34
623 664 0.037160 GGCCGTTTCCTCAAACCCTA 59.963 55.000 0.00 0.00 39.07 3.53
892 934 3.126879 TCGCGTCCCGACATACGT 61.127 61.111 5.77 0.00 41.89 3.57
942 984 0.657840 CCGCAAGAAATCCATCGTCC 59.342 55.000 0.00 0.00 43.02 4.79
974 1016 3.072468 TACCTGGGCGTCTTCGGG 61.072 66.667 0.00 0.00 37.56 5.14
1005 1047 1.702957 ACCTTCTTCCGGGTGATGAAA 59.297 47.619 0.00 0.00 36.88 2.69
1108 1153 0.316442 CGATATTGCCAAGCTGTGCG 60.316 55.000 3.56 0.00 0.00 5.34
1118 1163 2.049063 GCTGTGCGTCCGAAGACT 60.049 61.111 0.00 0.00 41.16 3.24
1140 1185 3.543884 GTTGATCACCGCCAACCTA 57.456 52.632 0.00 0.00 37.32 3.08
1144 1189 0.249398 GATCACCGCCAACCTACAGT 59.751 55.000 0.00 0.00 0.00 3.55
1379 1445 3.479269 GCGCAGTTCCGAGTTCCG 61.479 66.667 0.30 0.00 38.18 4.30
1380 1446 2.257371 CGCAGTTCCGAGTTCCGA 59.743 61.111 0.00 0.00 41.76 4.55
1515 1586 2.048444 ATGGATTGCTCAAGCGTGAT 57.952 45.000 1.88 0.00 45.83 3.06
1534 1605 0.243907 TCCGAGCTACAGTGCTGTTC 59.756 55.000 10.28 1.73 44.17 3.18
1577 1648 4.842531 TCAGGAAGAAGTTCATATGCCA 57.157 40.909 5.50 0.00 33.93 4.92
1640 1711 1.144913 TGCTTGTAAAGGGGAAGTGCT 59.855 47.619 0.00 0.00 46.35 4.40
1771 1846 8.415553 GTGTGATGGAATTGATAATTTGATCCA 58.584 33.333 0.00 0.00 0.00 3.41
2039 2299 9.961265 GCAAATTTAGGTAAGTAGTCTTTTTGT 57.039 29.630 0.00 0.00 35.36 2.83
2092 2364 2.037208 CGGGCCCAGGGTCAATTT 59.963 61.111 24.92 0.00 0.00 1.82
2172 2459 5.517770 GGTTTGCTCATATGCAGACATTTTC 59.482 40.000 11.22 0.00 45.95 2.29
2333 2717 1.002990 TGTGCAGGGCTCACATCTG 60.003 57.895 0.00 0.00 39.29 2.90
2334 2718 1.002868 GTGCAGGGCTCACATCTGT 60.003 57.895 0.00 0.00 34.73 3.41
2397 2781 3.510459 TCAAACTCTCACATGGAGGAGA 58.490 45.455 14.80 13.32 44.19 3.71
2440 2840 8.741603 TTAAGTAAACTTAGTTGCCTCTGTTT 57.258 30.769 0.00 0.00 39.36 2.83
2441 2841 6.619801 AGTAAACTTAGTTGCCTCTGTTTG 57.380 37.500 0.00 0.00 32.34 2.93
2444 2844 4.900635 ACTTAGTTGCCTCTGTTTGTTG 57.099 40.909 0.00 0.00 0.00 3.33
2501 2907 5.742446 GCACTTGCTGCTAGTAATGTTATC 58.258 41.667 15.96 0.00 43.33 1.75
2512 2922 6.642950 GCTAGTAATGTTATCGAGACAAGCAT 59.357 38.462 15.10 3.24 30.28 3.79
2516 2926 8.818057 AGTAATGTTATCGAGACAAGCATTAAC 58.182 33.333 8.28 1.47 31.80 2.01
2529 2939 8.076178 AGACAAGCATTAACTTTGTATTGTGTC 58.924 33.333 0.00 0.00 31.07 3.67
2573 3011 4.408270 TGCACCATGGCCATAAATTATGTT 59.592 37.500 20.30 0.00 34.36 2.71
2574 3012 4.990426 GCACCATGGCCATAAATTATGTTC 59.010 41.667 20.30 4.55 34.36 3.18
2629 3070 0.820871 TTGTGTTTTGTCCTGTGGGC 59.179 50.000 0.00 0.00 0.00 5.36
2634 3075 2.158986 TGTTTTGTCCTGTGGGCAATTG 60.159 45.455 4.39 0.00 32.06 2.32
2650 3091 2.807392 CAATTGTTTGTGCCAATCACCC 59.193 45.455 0.00 0.00 45.03 4.61
2657 3098 2.166346 TGCCAATCACCCCCAGGAA 61.166 57.895 0.00 0.00 36.73 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.895297 ACCTGTCAATCCAAAACATCAGTT 59.105 37.500 0.00 0.00 40.40 3.16
29 30 4.279169 CACCTGTCAATCCAAAACATCAGT 59.721 41.667 0.00 0.00 0.00 3.41
30 31 4.279169 ACACCTGTCAATCCAAAACATCAG 59.721 41.667 0.00 0.00 0.00 2.90
31 32 4.037803 CACACCTGTCAATCCAAAACATCA 59.962 41.667 0.00 0.00 0.00 3.07
32 33 4.037923 ACACACCTGTCAATCCAAAACATC 59.962 41.667 0.00 0.00 0.00 3.06
33 34 3.960102 ACACACCTGTCAATCCAAAACAT 59.040 39.130 0.00 0.00 0.00 2.71
34 35 3.360867 ACACACCTGTCAATCCAAAACA 58.639 40.909 0.00 0.00 0.00 2.83
35 36 4.359706 GAACACACCTGTCAATCCAAAAC 58.640 43.478 0.00 0.00 0.00 2.43
36 37 3.066064 CGAACACACCTGTCAATCCAAAA 59.934 43.478 0.00 0.00 0.00 2.44
37 38 2.616376 CGAACACACCTGTCAATCCAAA 59.384 45.455 0.00 0.00 0.00 3.28
38 39 2.158885 TCGAACACACCTGTCAATCCAA 60.159 45.455 0.00 0.00 0.00 3.53
39 40 1.414550 TCGAACACACCTGTCAATCCA 59.585 47.619 0.00 0.00 0.00 3.41
40 41 2.163818 TCGAACACACCTGTCAATCC 57.836 50.000 0.00 0.00 0.00 3.01
41 42 3.059597 CACTTCGAACACACCTGTCAATC 60.060 47.826 0.00 0.00 0.00 2.67
42 43 2.872245 CACTTCGAACACACCTGTCAAT 59.128 45.455 0.00 0.00 0.00 2.57
43 44 2.276201 CACTTCGAACACACCTGTCAA 58.724 47.619 0.00 0.00 0.00 3.18
44 45 1.206132 ACACTTCGAACACACCTGTCA 59.794 47.619 0.00 0.00 0.00 3.58
45 46 1.935933 ACACTTCGAACACACCTGTC 58.064 50.000 0.00 0.00 0.00 3.51
46 47 3.069016 TGATACACTTCGAACACACCTGT 59.931 43.478 0.00 0.00 0.00 4.00
47 48 3.649073 TGATACACTTCGAACACACCTG 58.351 45.455 0.00 0.00 0.00 4.00
48 49 3.321111 ACTGATACACTTCGAACACACCT 59.679 43.478 0.00 0.00 0.00 4.00
49 50 3.428870 CACTGATACACTTCGAACACACC 59.571 47.826 0.00 0.00 0.00 4.16
50 51 3.120991 GCACTGATACACTTCGAACACAC 60.121 47.826 0.00 0.00 0.00 3.82
51 52 3.057019 GCACTGATACACTTCGAACACA 58.943 45.455 0.00 0.00 0.00 3.72
52 53 2.090658 CGCACTGATACACTTCGAACAC 59.909 50.000 0.00 0.00 0.00 3.32
53 54 2.030628 TCGCACTGATACACTTCGAACA 60.031 45.455 0.00 0.00 0.00 3.18
54 55 2.592194 TCGCACTGATACACTTCGAAC 58.408 47.619 0.00 0.00 0.00 3.95
55 56 3.503827 ATCGCACTGATACACTTCGAA 57.496 42.857 0.00 0.00 34.83 3.71
56 57 3.503827 AATCGCACTGATACACTTCGA 57.496 42.857 0.00 0.00 35.84 3.71
57 58 4.102649 TGTAATCGCACTGATACACTTCG 58.897 43.478 0.00 0.00 35.84 3.79
58 59 6.204075 GATGTAATCGCACTGATACACTTC 57.796 41.667 0.00 0.00 35.84 3.01
73 74 7.803189 CGGCCATAATTTGTAAGTGATGTAATC 59.197 37.037 2.24 0.00 45.83 1.75
74 75 7.255451 CCGGCCATAATTTGTAAGTGATGTAAT 60.255 37.037 2.24 0.00 0.00 1.89
75 76 6.038825 CCGGCCATAATTTGTAAGTGATGTAA 59.961 38.462 2.24 0.00 0.00 2.41
76 77 5.529430 CCGGCCATAATTTGTAAGTGATGTA 59.471 40.000 2.24 0.00 0.00 2.29
77 78 4.338118 CCGGCCATAATTTGTAAGTGATGT 59.662 41.667 2.24 0.00 0.00 3.06
78 79 4.578516 TCCGGCCATAATTTGTAAGTGATG 59.421 41.667 2.24 0.00 0.00 3.07
79 80 4.787551 TCCGGCCATAATTTGTAAGTGAT 58.212 39.130 2.24 0.00 0.00 3.06
80 81 4.223556 TCCGGCCATAATTTGTAAGTGA 57.776 40.909 2.24 0.00 0.00 3.41
81 82 4.319477 CGATCCGGCCATAATTTGTAAGTG 60.319 45.833 2.24 0.00 0.00 3.16
82 83 3.813166 CGATCCGGCCATAATTTGTAAGT 59.187 43.478 2.24 0.00 0.00 2.24
83 84 4.062293 TCGATCCGGCCATAATTTGTAAG 58.938 43.478 2.24 0.00 0.00 2.34
84 85 4.074627 TCGATCCGGCCATAATTTGTAA 57.925 40.909 2.24 0.00 0.00 2.41
85 86 3.755112 TCGATCCGGCCATAATTTGTA 57.245 42.857 2.24 0.00 0.00 2.41
86 87 2.631160 TCGATCCGGCCATAATTTGT 57.369 45.000 2.24 0.00 0.00 2.83
87 88 2.414559 GCATCGATCCGGCCATAATTTG 60.415 50.000 2.24 0.00 0.00 2.32
88 89 1.812571 GCATCGATCCGGCCATAATTT 59.187 47.619 2.24 0.00 0.00 1.82
89 90 1.003580 AGCATCGATCCGGCCATAATT 59.996 47.619 2.24 0.00 0.00 1.40
90 91 0.615331 AGCATCGATCCGGCCATAAT 59.385 50.000 2.24 0.00 0.00 1.28
91 92 0.037326 GAGCATCGATCCGGCCATAA 60.037 55.000 2.24 0.00 0.00 1.90
92 93 1.591703 GAGCATCGATCCGGCCATA 59.408 57.895 2.24 0.00 0.00 2.74
93 94 2.345244 GAGCATCGATCCGGCCAT 59.655 61.111 2.24 0.00 0.00 4.40
94 95 3.928779 GGAGCATCGATCCGGCCA 61.929 66.667 2.24 0.00 34.37 5.36
95 96 3.170490 AAGGAGCATCGATCCGGCC 62.170 63.158 0.00 0.00 43.66 6.13
96 97 1.666234 GAAGGAGCATCGATCCGGC 60.666 63.158 0.00 0.00 43.66 6.13
97 98 0.038709 GAGAAGGAGCATCGATCCGG 60.039 60.000 0.00 0.00 43.66 5.14
98 99 0.038709 GGAGAAGGAGCATCGATCCG 60.039 60.000 0.00 0.00 43.66 4.18
99 100 1.043816 TGGAGAAGGAGCATCGATCC 58.956 55.000 0.00 0.00 38.56 3.36
100 101 2.670789 CGATGGAGAAGGAGCATCGATC 60.671 54.545 0.14 0.00 45.28 3.69
101 102 1.271934 CGATGGAGAAGGAGCATCGAT 59.728 52.381 0.14 0.00 45.28 3.59
102 103 0.670706 CGATGGAGAAGGAGCATCGA 59.329 55.000 0.14 0.00 45.28 3.59
103 104 0.670706 TCGATGGAGAAGGAGCATCG 59.329 55.000 0.06 0.06 44.25 3.84
104 105 1.686052 ACTCGATGGAGAAGGAGCATC 59.314 52.381 12.14 0.00 43.27 3.91
105 106 1.786937 ACTCGATGGAGAAGGAGCAT 58.213 50.000 12.14 0.00 43.27 3.79
106 107 2.025155 GTACTCGATGGAGAAGGAGCA 58.975 52.381 12.14 0.00 43.27 4.26
107 108 2.025155 TGTACTCGATGGAGAAGGAGC 58.975 52.381 12.14 0.00 43.27 4.70
108 109 3.885901 TGATGTACTCGATGGAGAAGGAG 59.114 47.826 12.14 0.00 43.27 3.69
109 110 3.898482 TGATGTACTCGATGGAGAAGGA 58.102 45.455 12.14 0.00 43.27 3.36
110 111 4.862902 ATGATGTACTCGATGGAGAAGG 57.137 45.455 12.14 0.00 43.27 3.46
111 112 7.825681 AGAATATGATGTACTCGATGGAGAAG 58.174 38.462 12.14 0.00 43.27 2.85
112 113 7.767250 AGAATATGATGTACTCGATGGAGAA 57.233 36.000 12.14 0.00 43.27 2.87
113 114 7.767250 AAGAATATGATGTACTCGATGGAGA 57.233 36.000 12.14 0.00 43.27 3.71
114 115 7.700234 GCTAAGAATATGATGTACTCGATGGAG 59.300 40.741 2.78 2.78 46.13 3.86
115 116 7.539436 GCTAAGAATATGATGTACTCGATGGA 58.461 38.462 0.00 0.00 0.00 3.41
116 117 6.470556 CGCTAAGAATATGATGTACTCGATGG 59.529 42.308 0.00 0.00 0.00 3.51
117 118 6.470556 CCGCTAAGAATATGATGTACTCGATG 59.529 42.308 0.00 0.00 0.00 3.84
118 119 6.151312 ACCGCTAAGAATATGATGTACTCGAT 59.849 38.462 0.00 0.00 0.00 3.59
119 120 5.472478 ACCGCTAAGAATATGATGTACTCGA 59.528 40.000 0.00 0.00 0.00 4.04
120 121 5.700846 ACCGCTAAGAATATGATGTACTCG 58.299 41.667 0.00 0.00 0.00 4.18
121 122 8.679100 AGATACCGCTAAGAATATGATGTACTC 58.321 37.037 0.00 0.00 0.00 2.59
122 123 8.582657 AGATACCGCTAAGAATATGATGTACT 57.417 34.615 0.00 0.00 0.00 2.73
123 124 9.640963 AAAGATACCGCTAAGAATATGATGTAC 57.359 33.333 0.00 0.00 0.00 2.90
125 126 9.561069 AAAAAGATACCGCTAAGAATATGATGT 57.439 29.630 0.00 0.00 0.00 3.06
126 127 9.817365 CAAAAAGATACCGCTAAGAATATGATG 57.183 33.333 0.00 0.00 0.00 3.07
127 128 9.561069 ACAAAAAGATACCGCTAAGAATATGAT 57.439 29.630 0.00 0.00 0.00 2.45
128 129 8.826710 CACAAAAAGATACCGCTAAGAATATGA 58.173 33.333 0.00 0.00 0.00 2.15
129 130 8.612619 ACACAAAAAGATACCGCTAAGAATATG 58.387 33.333 0.00 0.00 0.00 1.78
130 131 8.612619 CACACAAAAAGATACCGCTAAGAATAT 58.387 33.333 0.00 0.00 0.00 1.28
131 132 7.604927 ACACACAAAAAGATACCGCTAAGAATA 59.395 33.333 0.00 0.00 0.00 1.75
132 133 6.430000 ACACACAAAAAGATACCGCTAAGAAT 59.570 34.615 0.00 0.00 0.00 2.40
133 134 5.761234 ACACACAAAAAGATACCGCTAAGAA 59.239 36.000 0.00 0.00 0.00 2.52
134 135 5.302360 ACACACAAAAAGATACCGCTAAGA 58.698 37.500 0.00 0.00 0.00 2.10
135 136 5.607119 ACACACAAAAAGATACCGCTAAG 57.393 39.130 0.00 0.00 0.00 2.18
136 137 6.380095 AAACACACAAAAAGATACCGCTAA 57.620 33.333 0.00 0.00 0.00 3.09
137 138 6.380095 AAAACACACAAAAAGATACCGCTA 57.620 33.333 0.00 0.00 0.00 4.26
138 139 4.911514 AAACACACAAAAAGATACCGCT 57.088 36.364 0.00 0.00 0.00 5.52
139 140 5.959652 AAAAACACACAAAAAGATACCGC 57.040 34.783 0.00 0.00 0.00 5.68
176 177 8.225603 AGAGATTTGTCTCAAGTTGCTAAAAA 57.774 30.769 8.04 0.00 39.12 1.94
177 178 7.807977 AGAGATTTGTCTCAAGTTGCTAAAA 57.192 32.000 8.04 0.00 39.12 1.52
178 179 7.807977 AAGAGATTTGTCTCAAGTTGCTAAA 57.192 32.000 8.04 0.00 39.12 1.85
179 180 7.807977 AAAGAGATTTGTCTCAAGTTGCTAA 57.192 32.000 8.04 0.00 39.12 3.09
180 181 7.807977 AAAAGAGATTTGTCTCAAGTTGCTA 57.192 32.000 8.04 0.00 39.12 3.49
181 182 6.705863 AAAAGAGATTTGTCTCAAGTTGCT 57.294 33.333 8.04 0.00 39.12 3.91
205 206 9.612066 AAAGGATTTGTCTCAAATTGCTAAAAA 57.388 25.926 8.72 0.00 36.60 1.94
206 207 9.612066 AAAAGGATTTGTCTCAAATTGCTAAAA 57.388 25.926 8.72 0.00 39.02 1.52
207 208 9.612066 AAAAAGGATTTGTCTCAAATTGCTAAA 57.388 25.926 8.72 0.00 39.02 1.85
278 279 9.487790 TTCTCTTTCAACAACACAAAAAGATTT 57.512 25.926 0.00 0.00 35.91 2.17
279 280 9.487790 TTTCTCTTTCAACAACACAAAAAGATT 57.512 25.926 0.00 0.00 35.91 2.40
280 281 9.143631 CTTTCTCTTTCAACAACACAAAAAGAT 57.856 29.630 0.00 0.00 35.91 2.40
281 282 8.356657 TCTTTCTCTTTCAACAACACAAAAAGA 58.643 29.630 0.00 0.00 35.36 2.52
282 283 8.519492 TCTTTCTCTTTCAACAACACAAAAAG 57.481 30.769 0.00 0.00 0.00 2.27
283 284 8.356657 TCTCTTTCTCTTTCAACAACACAAAAA 58.643 29.630 0.00 0.00 0.00 1.94
284 285 7.881142 TCTCTTTCTCTTTCAACAACACAAAA 58.119 30.769 0.00 0.00 0.00 2.44
285 286 7.447374 TCTCTTTCTCTTTCAACAACACAAA 57.553 32.000 0.00 0.00 0.00 2.83
286 287 7.447374 TTCTCTTTCTCTTTCAACAACACAA 57.553 32.000 0.00 0.00 0.00 3.33
287 288 7.447374 TTTCTCTTTCTCTTTCAACAACACA 57.553 32.000 0.00 0.00 0.00 3.72
288 289 8.742554 TTTTTCTCTTTCTCTTTCAACAACAC 57.257 30.769 0.00 0.00 0.00 3.32
314 315 9.119418 CCTTTTCTCTTTCTCTTTCTCTTCTTT 57.881 33.333 0.00 0.00 0.00 2.52
315 316 7.228507 GCCTTTTCTCTTTCTCTTTCTCTTCTT 59.771 37.037 0.00 0.00 0.00 2.52
316 317 6.710295 GCCTTTTCTCTTTCTCTTTCTCTTCT 59.290 38.462 0.00 0.00 0.00 2.85
317 318 6.710295 AGCCTTTTCTCTTTCTCTTTCTCTTC 59.290 38.462 0.00 0.00 0.00 2.87
318 319 6.600388 AGCCTTTTCTCTTTCTCTTTCTCTT 58.400 36.000 0.00 0.00 0.00 2.85
319 320 6.183361 TGAGCCTTTTCTCTTTCTCTTTCTCT 60.183 38.462 0.00 0.00 34.29 3.10
320 321 5.994668 TGAGCCTTTTCTCTTTCTCTTTCTC 59.005 40.000 0.00 0.00 34.29 2.87
321 322 5.934781 TGAGCCTTTTCTCTTTCTCTTTCT 58.065 37.500 0.00 0.00 34.29 2.52
322 323 6.625873 TTGAGCCTTTTCTCTTTCTCTTTC 57.374 37.500 0.00 0.00 34.29 2.62
323 324 7.941790 ACTATTGAGCCTTTTCTCTTTCTCTTT 59.058 33.333 0.00 0.00 34.29 2.52
324 325 7.457561 ACTATTGAGCCTTTTCTCTTTCTCTT 58.542 34.615 0.00 0.00 34.29 2.85
325 326 7.014988 ACTATTGAGCCTTTTCTCTTTCTCT 57.985 36.000 0.00 0.00 34.29 3.10
326 327 7.680442 AACTATTGAGCCTTTTCTCTTTCTC 57.320 36.000 0.00 0.00 34.29 2.87
327 328 8.470657 AAAACTATTGAGCCTTTTCTCTTTCT 57.529 30.769 0.00 0.00 34.29 2.52
355 356 8.717821 CGTGTGGAAGAGAATTTTGTTCTAATA 58.282 33.333 5.94 0.00 0.00 0.98
356 357 7.444183 TCGTGTGGAAGAGAATTTTGTTCTAAT 59.556 33.333 5.94 0.00 0.00 1.73
357 358 6.764085 TCGTGTGGAAGAGAATTTTGTTCTAA 59.236 34.615 5.94 0.00 0.00 2.10
358 359 6.285224 TCGTGTGGAAGAGAATTTTGTTCTA 58.715 36.000 5.94 0.00 0.00 2.10
359 360 5.123227 TCGTGTGGAAGAGAATTTTGTTCT 58.877 37.500 5.94 0.00 0.00 3.01
360 361 5.007724 ACTCGTGTGGAAGAGAATTTTGTTC 59.992 40.000 0.00 0.00 37.87 3.18
361 362 4.881850 ACTCGTGTGGAAGAGAATTTTGTT 59.118 37.500 0.00 0.00 37.87 2.83
362 363 4.451900 ACTCGTGTGGAAGAGAATTTTGT 58.548 39.130 0.00 0.00 37.87 2.83
363 364 4.511454 TGACTCGTGTGGAAGAGAATTTTG 59.489 41.667 0.00 0.00 37.87 2.44
364 365 4.703897 TGACTCGTGTGGAAGAGAATTTT 58.296 39.130 0.00 0.00 37.87 1.82
365 366 4.336889 TGACTCGTGTGGAAGAGAATTT 57.663 40.909 0.00 0.00 37.87 1.82
366 367 4.499183 GATGACTCGTGTGGAAGAGAATT 58.501 43.478 0.00 0.00 37.87 2.17
367 368 3.118956 GGATGACTCGTGTGGAAGAGAAT 60.119 47.826 0.00 0.00 37.87 2.40
368 369 2.231478 GGATGACTCGTGTGGAAGAGAA 59.769 50.000 0.00 0.00 37.87 2.87
369 370 1.819288 GGATGACTCGTGTGGAAGAGA 59.181 52.381 0.00 0.00 37.87 3.10
370 371 1.546029 TGGATGACTCGTGTGGAAGAG 59.454 52.381 0.00 0.00 40.16 2.85
371 372 1.546029 CTGGATGACTCGTGTGGAAGA 59.454 52.381 0.00 0.00 0.00 2.87
372 373 2.001812 CTGGATGACTCGTGTGGAAG 57.998 55.000 0.00 0.00 0.00 3.46
373 374 0.037326 GCTGGATGACTCGTGTGGAA 60.037 55.000 0.00 0.00 0.00 3.53
374 375 1.591703 GCTGGATGACTCGTGTGGA 59.408 57.895 0.00 0.00 0.00 4.02
375 376 1.448540 GGCTGGATGACTCGTGTGG 60.449 63.158 0.00 0.00 0.00 4.17
376 377 1.448540 GGGCTGGATGACTCGTGTG 60.449 63.158 0.00 0.00 0.00 3.82
377 378 1.892819 CTGGGCTGGATGACTCGTGT 61.893 60.000 0.00 0.00 0.00 4.49
378 379 1.153489 CTGGGCTGGATGACTCGTG 60.153 63.158 0.00 0.00 0.00 4.35
379 380 3.023949 GCTGGGCTGGATGACTCGT 62.024 63.158 0.00 0.00 0.00 4.18
380 381 2.202987 GCTGGGCTGGATGACTCG 60.203 66.667 0.00 0.00 0.00 4.18
381 382 2.191641 GGCTGGGCTGGATGACTC 59.808 66.667 0.00 0.00 0.00 3.36
382 383 3.415087 GGGCTGGGCTGGATGACT 61.415 66.667 0.00 0.00 0.00 3.41
383 384 3.286694 TTGGGCTGGGCTGGATGAC 62.287 63.158 0.00 0.00 0.00 3.06
384 385 2.940467 TTGGGCTGGGCTGGATGA 60.940 61.111 0.00 0.00 0.00 2.92
385 386 2.757099 GTTGGGCTGGGCTGGATG 60.757 66.667 0.00 0.00 0.00 3.51
386 387 4.066139 GGTTGGGCTGGGCTGGAT 62.066 66.667 0.00 0.00 0.00 3.41
399 400 2.512986 TAATGGGCTGGGCTGGGTTG 62.513 60.000 0.00 0.00 0.00 3.77
400 401 1.593166 ATAATGGGCTGGGCTGGGTT 61.593 55.000 0.00 0.00 0.00 4.11
401 402 2.011617 GATAATGGGCTGGGCTGGGT 62.012 60.000 0.00 0.00 0.00 4.51
402 403 1.228675 GATAATGGGCTGGGCTGGG 60.229 63.158 0.00 0.00 0.00 4.45
403 404 1.601759 CGATAATGGGCTGGGCTGG 60.602 63.158 0.00 0.00 0.00 4.85
404 405 1.601759 CCGATAATGGGCTGGGCTG 60.602 63.158 0.00 0.00 0.00 4.85
405 406 2.056906 GACCGATAATGGGCTGGGCT 62.057 60.000 0.00 0.00 32.64 5.19
406 407 1.600916 GACCGATAATGGGCTGGGC 60.601 63.158 0.00 0.00 32.64 5.36
407 408 0.535102 GTGACCGATAATGGGCTGGG 60.535 60.000 0.00 0.00 38.15 4.45
408 409 0.535102 GGTGACCGATAATGGGCTGG 60.535 60.000 0.00 0.00 38.15 4.85
409 410 0.535102 GGGTGACCGATAATGGGCTG 60.535 60.000 0.00 0.00 43.64 4.85
410 411 1.837090 GGGTGACCGATAATGGGCT 59.163 57.895 0.00 0.00 43.64 5.19
411 412 4.475527 GGGTGACCGATAATGGGC 57.524 61.111 0.00 0.00 43.64 5.36
435 436 1.154207 CGAGAGCGAGAGTTTGCGA 60.154 57.895 0.00 0.00 40.82 5.10
469 475 3.090532 GGCGAGGAGGTGGGGAAT 61.091 66.667 0.00 0.00 0.00 3.01
554 568 1.407989 GGGAGAGTTGGCTGGAGAATG 60.408 57.143 0.00 0.00 0.00 2.67
567 584 0.106116 GAGGTGGGATACGGGAGAGT 60.106 60.000 0.00 0.00 37.60 3.24
604 621 0.037160 TAGGGTTTGAGGAAACGGCC 59.963 55.000 0.00 0.00 42.20 6.13
860 902 2.663188 CGATAAGCCGAGGCCAGC 60.663 66.667 10.95 4.62 43.17 4.85
911 953 0.796312 TCTTGCGGAATTTGTCGAGC 59.204 50.000 0.00 0.00 0.00 5.03
942 984 0.905357 AGGTAGTACTGCAGCTTGGG 59.095 55.000 15.27 0.00 0.00 4.12
974 1016 0.035915 GAAGAAGGTGTGGGAGGAGC 60.036 60.000 0.00 0.00 0.00 4.70
1005 1047 1.094073 GCGAGAGGACATTGCAGCAT 61.094 55.000 0.00 0.00 0.00 3.79
1108 1153 2.231478 TGATCAACCTCAGTCTTCGGAC 59.769 50.000 0.00 0.00 44.75 4.79
1140 1185 1.593787 CATCGCCTGGAGACACTGT 59.406 57.895 1.07 0.00 35.60 3.55
1379 1445 1.407989 CCAGCCCCACTTCAGAGATTC 60.408 57.143 0.00 0.00 0.00 2.52
1380 1446 0.622665 CCAGCCCCACTTCAGAGATT 59.377 55.000 0.00 0.00 0.00 2.40
1515 1586 0.243907 GAACAGCACTGTAGCTCGGA 59.756 55.000 3.26 0.00 44.54 4.55
1534 1605 0.174617 GCCTTCTCGGTCTCCTTGAG 59.825 60.000 0.00 0.00 34.25 3.02
1577 1648 0.957395 CTGTGCGGCTTCCTTGTGAT 60.957 55.000 0.00 0.00 0.00 3.06
1640 1711 5.007039 GCTCATGCGAATCTGAAATTAGACA 59.993 40.000 0.00 0.00 0.00 3.41
1771 1846 9.658799 GTGATAGCATTACATACCAGTATTCAT 57.341 33.333 0.00 0.00 0.00 2.57
1814 1889 5.175856 CGAAGAAGTTCATAACCGATCCATC 59.824 44.000 5.50 0.00 32.36 3.51
2039 2299 4.015872 CAACTTCCCCTACAGTTGCTTA 57.984 45.455 0.00 0.00 42.52 3.09
2333 2717 7.786178 TCCACATTTAGCAGATAACATGTAC 57.214 36.000 0.00 0.00 30.60 2.90
2334 2718 7.041167 GCATCCACATTTAGCAGATAACATGTA 60.041 37.037 0.00 0.00 30.60 2.29
2429 2829 3.636300 AGCATAACAACAAACAGAGGCAA 59.364 39.130 0.00 0.00 0.00 4.52
2501 2907 7.269084 CACAATACAAAGTTAATGCTTGTCTCG 59.731 37.037 3.82 0.00 29.61 4.04
2512 2922 9.562408 TCCACAATAGACACAATACAAAGTTAA 57.438 29.630 0.00 0.00 0.00 2.01
2516 2926 9.912634 AAAATCCACAATAGACACAATACAAAG 57.087 29.630 0.00 0.00 0.00 2.77
2529 2939 5.163591 TGCAGAGCATGAAAATCCACAATAG 60.164 40.000 0.00 0.00 31.71 1.73
2573 3011 6.946340 TCTTAAGCTGACATCCACAATAAGA 58.054 36.000 0.00 0.00 0.00 2.10
2574 3012 7.798596 ATCTTAAGCTGACATCCACAATAAG 57.201 36.000 0.00 0.00 0.00 1.73
2609 3047 1.412343 GCCCACAGGACAAAACACAAT 59.588 47.619 0.00 0.00 33.47 2.71
2611 3049 0.323816 TGCCCACAGGACAAAACACA 60.324 50.000 0.00 0.00 33.47 3.72
2612 3050 0.820871 TTGCCCACAGGACAAAACAC 59.179 50.000 0.00 0.00 33.47 3.32
2618 3059 1.411977 CAAACAATTGCCCACAGGACA 59.588 47.619 5.05 0.00 33.47 4.02
2645 3086 4.761163 TGAACTTCCTGGGGGTGA 57.239 55.556 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.