Multiple sequence alignment - TraesCS4A01G332400

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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 TraesCS4A01G332400 chr4A 100.000 3469 0 0 1 3469 616661076 616664544 0.000000e+00 6407.0
1 TraesCS4A01G332400 chr4A 78.898 1289 217 37 944 2216 616120896 616119647 0.000000e+00 822.0
2 TraesCS4A01G332400 chr4A 100.000 398 0 0 3754 4151 616664829 616665226 0.000000e+00 736.0
3 TraesCS4A01G332400 chr5D 95.380 3333 108 13 170 3469 551470690 551467371 0.000000e+00 5260.0
4 TraesCS4A01G332400 chr5D 79.612 1339 233 26 944 2258 551545969 551544647 0.000000e+00 924.0
5 TraesCS4A01G332400 chr5D 79.228 1218 214 28 995 2192 542411210 542410012 0.000000e+00 811.0
6 TraesCS4A01G332400 chr5D 78.477 1287 237 30 995 2258 552407684 552408953 0.000000e+00 806.0
7 TraesCS4A01G332400 chr5D 83.388 614 88 10 1606 2216 552068206 552068808 1.300000e-154 556.0
8 TraesCS4A01G332400 chr5D 84.375 512 66 9 2479 2987 552409069 552409569 1.340000e-134 490.0
9 TraesCS4A01G332400 chr5D 99.528 212 0 1 3940 4151 551466873 551466663 6.510000e-103 385.0
10 TraesCS4A01G332400 chr5D 80.037 536 87 15 2652 3176 557952009 557951483 3.030000e-101 379.0
11 TraesCS4A01G332400 chr5D 81.663 469 62 16 2835 3280 552739986 552739519 6.560000e-98 368.0
12 TraesCS4A01G332400 chr5D 98.315 178 3 0 3761 3938 551467101 551466924 3.120000e-81 313.0
13 TraesCS4A01G332400 chr5B 91.540 1312 95 12 870 2171 699731356 699730051 0.000000e+00 1794.0
14 TraesCS4A01G332400 chr5B 77.785 1643 255 65 653 2258 699282875 699281306 0.000000e+00 911.0
15 TraesCS4A01G332400 chr5B 75.882 1559 261 62 653 2157 697869456 697867959 0.000000e+00 689.0
16 TraesCS4A01G332400 chr5B 86.016 615 75 6 1650 2258 703894156 703893547 0.000000e+00 649.0
17 TraesCS4A01G332400 chr5B 81.695 814 114 15 2474 3280 698261748 698260963 0.000000e+00 645.0
18 TraesCS4A01G332400 chr5B 75.962 1248 252 40 995 2218 703859469 703858246 2.140000e-167 599.0
19 TraesCS4A01G332400 chr5B 89.035 456 43 2 3 451 530709722 530709267 3.620000e-155 558.0
20 TraesCS4A01G332400 chr5B 78.867 847 153 12 1302 2142 699645474 699644648 2.180000e-152 549.0
21 TraesCS4A01G332400 chr5B 81.566 396 61 9 2813 3197 697809425 697809819 2.410000e-82 316.0
22 TraesCS4A01G332400 chr5B 85.522 297 25 10 492 776 699774017 699773727 1.130000e-75 294.0
23 TraesCS4A01G332400 chr5B 83.505 291 31 13 552 834 699731642 699731361 5.330000e-64 255.0
24 TraesCS4A01G332400 chr5B 79.896 383 37 8 859 1233 699615716 699615366 1.150000e-60 244.0
25 TraesCS4A01G332400 chr5B 79.896 383 37 8 859 1233 699645825 699645475 1.150000e-60 244.0
26 TraesCS4A01G332400 chr5B 83.019 265 30 11 560 815 699737816 699737558 4.180000e-55 226.0
27 TraesCS4A01G332400 chr5B 87.013 154 12 5 606 752 698274066 698273914 2.570000e-37 167.0
28 TraesCS4A01G332400 chr4B 89.542 459 41 2 3 455 546576050 546575593 3.600000e-160 575.0
29 TraesCS4A01G332400 chr4B 91.866 209 14 3 2277 2482 130063324 130063532 5.250000e-74 289.0
30 TraesCS4A01G332400 chr3B 89.427 454 42 1 3 450 49869555 49870008 6.020000e-158 568.0
31 TraesCS4A01G332400 chr3B 88.865 458 42 4 1 450 810450250 810449794 4.690000e-154 555.0
32 TraesCS4A01G332400 chr3B 88.248 468 46 4 3 463 758628403 758628868 6.070000e-153 551.0
33 TraesCS4A01G332400 chr3B 93.651 189 12 0 2294 2482 575317883 575318071 2.440000e-72 283.0
34 TraesCS4A01G332400 chr6D 88.937 461 42 4 3 454 61601268 61600808 1.010000e-155 560.0
35 TraesCS4A01G332400 chr6D 88.660 97 9 2 3937 4033 202976774 202976868 2.620000e-22 117.0
36 TraesCS4A01G332400 chr2B 89.035 456 43 2 3 451 436266545 436266090 3.620000e-155 558.0
37 TraesCS4A01G332400 chr2B 77.451 204 21 17 3842 4033 87413348 87413538 9.500000e-17 99.0
38 TraesCS4A01G332400 chr7A 88.840 457 44 2 3 452 10222562 10222106 4.690000e-154 555.0
39 TraesCS4A01G332400 chr7A 93.158 190 13 0 2294 2483 641845563 641845752 3.160000e-71 279.0
40 TraesCS4A01G332400 chr1A 76.211 929 187 27 1286 2194 33236677 33235763 1.050000e-125 460.0
41 TraesCS4A01G332400 chr1A 82.910 433 67 3 2698 3126 33227533 33227104 2.340000e-102 383.0
42 TraesCS4A01G332400 chr1A 82.910 433 65 5 2698 3125 33302842 33302414 8.420000e-102 381.0
43 TraesCS4A01G332400 chr1A 89.552 67 7 0 3214 3280 33226983 33226917 7.390000e-13 86.1
44 TraesCS4A01G332400 chr1D 83.011 465 72 3 2686 3146 34654683 34654222 8.300000e-112 414.0
45 TraesCS4A01G332400 chr1D 88.525 61 7 0 3220 3280 34654115 34654055 1.600000e-09 75.0
46 TraesCS4A01G332400 chr1B 81.938 454 73 5 2698 3146 53075861 53075412 3.920000e-100 375.0
47 TraesCS4A01G332400 chr1B 91.045 67 6 0 3214 3280 53075311 53075245 1.590000e-14 91.6
48 TraesCS4A01G332400 chr5A 94.709 189 10 0 2294 2482 520388851 520388663 1.130000e-75 294.0
49 TraesCS4A01G332400 chr5A 93.651 189 12 0 2294 2482 185717291 185717479 2.440000e-72 283.0
50 TraesCS4A01G332400 chr5A 92.347 196 14 1 2288 2482 166733909 166733714 1.140000e-70 278.0
51 TraesCS4A01G332400 chr6A 92.000 200 16 0 2283 2482 489613556 489613357 8.790000e-72 281.0
52 TraesCS4A01G332400 chr6A 90.000 210 21 0 2294 2503 425147627 425147418 5.290000e-69 272.0
53 TraesCS4A01G332400 chr6A 92.784 97 5 2 3937 4033 290256937 290256843 5.600000e-29 139.0
54 TraesCS4A01G332400 chr2A 86.905 84 5 4 3952 4033 55969927 55970006 5.720000e-14 89.8
55 TraesCS4A01G332400 chr2D 86.585 82 4 6 3952 4033 55260699 55260773 2.660000e-12 84.2
56 TraesCS4A01G332400 chr2D 84.706 85 9 3 3951 4033 55245751 55245833 9.560000e-12 82.4
57 TraesCS4A01G332400 chr2D 86.250 80 4 6 3952 4031 55239484 55239556 3.440000e-11 80.5


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 TraesCS4A01G332400 chr4A 616661076 616665226 4150 False 3571.50 6407 100.0000 1 4151 2 chr4A.!!$F1 4150
1 TraesCS4A01G332400 chr4A 616119647 616120896 1249 True 822.00 822 78.8980 944 2216 1 chr4A.!!$R1 1272
2 TraesCS4A01G332400 chr5D 551466663 551470690 4027 True 1986.00 5260 97.7410 170 4151 3 chr5D.!!$R5 3981
3 TraesCS4A01G332400 chr5D 551544647 551545969 1322 True 924.00 924 79.6120 944 2258 1 chr5D.!!$R2 1314
4 TraesCS4A01G332400 chr5D 542410012 542411210 1198 True 811.00 811 79.2280 995 2192 1 chr5D.!!$R1 1197
5 TraesCS4A01G332400 chr5D 552407684 552409569 1885 False 648.00 806 81.4260 995 2987 2 chr5D.!!$F2 1992
6 TraesCS4A01G332400 chr5D 552068206 552068808 602 False 556.00 556 83.3880 1606 2216 1 chr5D.!!$F1 610
7 TraesCS4A01G332400 chr5D 557951483 557952009 526 True 379.00 379 80.0370 2652 3176 1 chr5D.!!$R4 524
8 TraesCS4A01G332400 chr5B 699730051 699731642 1591 True 1024.50 1794 87.5225 552 2171 2 chr5B.!!$R12 1619
9 TraesCS4A01G332400 chr5B 699281306 699282875 1569 True 911.00 911 77.7850 653 2258 1 chr5B.!!$R5 1605
10 TraesCS4A01G332400 chr5B 697867959 697869456 1497 True 689.00 689 75.8820 653 2157 1 chr5B.!!$R2 1504
11 TraesCS4A01G332400 chr5B 703893547 703894156 609 True 649.00 649 86.0160 1650 2258 1 chr5B.!!$R10 608
12 TraesCS4A01G332400 chr5B 698260963 698261748 785 True 645.00 645 81.6950 2474 3280 1 chr5B.!!$R3 806
13 TraesCS4A01G332400 chr5B 703858246 703859469 1223 True 599.00 599 75.9620 995 2218 1 chr5B.!!$R9 1223
14 TraesCS4A01G332400 chr5B 699644648 699645825 1177 True 396.50 549 79.3815 859 2142 2 chr5B.!!$R11 1283
15 TraesCS4A01G332400 chr1A 33235763 33236677 914 True 460.00 460 76.2110 1286 2194 1 chr1A.!!$R1 908
16 TraesCS4A01G332400 chr1A 33226917 33227533 616 True 234.55 383 86.2310 2698 3280 2 chr1A.!!$R3 582
17 TraesCS4A01G332400 chr1D 34654055 34654683 628 True 244.50 414 85.7680 2686 3280 2 chr1D.!!$R1 594
18 TraesCS4A01G332400 chr1B 53075245 53075861 616 True 233.30 375 86.4915 2698 3280 2 chr1B.!!$R1 582

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
74 75 0.038435 TTCCGACGGTGCGTTTATCA 60.038 50.0 14.79 0.0 41.37 2.15 F
151 152 0.095935 CGGATCTCGTCGTTGTACGT 59.904 55.0 0.00 0.0 43.14 3.57 F
1713 1852 0.034089 TCGAGCTCATCTCTGTCCCA 60.034 55.0 15.40 0.0 39.70 4.37 F
2450 2713 0.872388 CGGTAAGCGATAAATGGGCC 59.128 55.0 0.00 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1632 1.127567 TGTAAGCCTGGTGAGCCACT 61.128 55.0 0.00 0.00 40.46 4.00 R
1848 1989 1.311859 TTGCACTCCTTGACAAGCAG 58.688 50.0 9.85 7.16 33.14 4.24 R
2987 3255 0.449388 CTTCAATCCAACAGCTCGCC 59.551 55.0 0.00 0.00 0.00 5.54 R
3754 4061 0.329261 CAGGAGTGGCAGGGATTCAA 59.671 55.0 0.00 0.00 0.00 2.69 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
26 27 4.883354 GGCGGCCCCCTGAAGATG 62.883 72.222 8.12 0.00 0.00 2.90
27 28 4.883354 GCGGCCCCCTGAAGATGG 62.883 72.222 0.00 0.00 0.00 3.51
28 29 3.089874 CGGCCCCCTGAAGATGGA 61.090 66.667 0.00 0.00 0.00 3.41
29 30 2.679342 CGGCCCCCTGAAGATGGAA 61.679 63.158 0.00 0.00 0.00 3.53
30 31 1.933629 GGCCCCCTGAAGATGGAAT 59.066 57.895 0.00 0.00 0.00 3.01
31 32 1.149101 GGCCCCCTGAAGATGGAATA 58.851 55.000 0.00 0.00 0.00 1.75
32 33 1.499007 GGCCCCCTGAAGATGGAATAA 59.501 52.381 0.00 0.00 0.00 1.40
33 34 2.091333 GGCCCCCTGAAGATGGAATAAA 60.091 50.000 0.00 0.00 0.00 1.40
34 35 3.225940 GCCCCCTGAAGATGGAATAAAG 58.774 50.000 0.00 0.00 0.00 1.85
35 36 3.837355 CCCCCTGAAGATGGAATAAAGG 58.163 50.000 0.00 0.00 0.00 3.11
36 37 3.205282 CCCCCTGAAGATGGAATAAAGGT 59.795 47.826 0.00 0.00 0.00 3.50
37 38 4.464947 CCCCTGAAGATGGAATAAAGGTC 58.535 47.826 0.00 0.00 0.00 3.85
38 39 4.166919 CCCCTGAAGATGGAATAAAGGTCT 59.833 45.833 0.00 0.00 0.00 3.85
39 40 5.372373 CCCTGAAGATGGAATAAAGGTCTC 58.628 45.833 0.00 0.00 0.00 3.36
40 41 5.372373 CCTGAAGATGGAATAAAGGTCTCC 58.628 45.833 0.00 0.00 0.00 3.71
41 42 5.372373 CTGAAGATGGAATAAAGGTCTCCC 58.628 45.833 0.00 0.00 0.00 4.30
42 43 4.166144 TGAAGATGGAATAAAGGTCTCCCC 59.834 45.833 0.00 0.00 0.00 4.81
43 44 2.706190 AGATGGAATAAAGGTCTCCCCG 59.294 50.000 0.00 0.00 38.74 5.73
44 45 0.544697 TGGAATAAAGGTCTCCCCGC 59.455 55.000 0.00 0.00 38.74 6.13
45 46 0.179026 GGAATAAAGGTCTCCCCGCC 60.179 60.000 0.00 0.00 38.74 6.13
46 47 0.837940 GAATAAAGGTCTCCCCGCCT 59.162 55.000 0.00 0.00 38.74 5.52
47 48 2.044758 GAATAAAGGTCTCCCCGCCTA 58.955 52.381 0.00 0.00 38.74 3.93
48 49 1.718280 ATAAAGGTCTCCCCGCCTAG 58.282 55.000 0.00 0.00 38.74 3.02
49 50 1.047034 TAAAGGTCTCCCCGCCTAGC 61.047 60.000 0.00 0.00 38.74 3.42
50 51 4.862823 AGGTCTCCCCGCCTAGCC 62.863 72.222 0.00 0.00 38.74 3.93
61 62 3.846430 CCTAGCCCCCGTTCCGAC 61.846 72.222 0.00 0.00 0.00 4.79
70 71 3.332409 CGTTCCGACGGTGCGTTT 61.332 61.111 14.79 0.00 45.32 3.60
71 72 2.015627 CGTTCCGACGGTGCGTTTA 61.016 57.895 14.79 0.00 45.32 2.01
72 73 1.346378 CGTTCCGACGGTGCGTTTAT 61.346 55.000 14.79 0.00 45.32 1.40
73 74 0.367887 GTTCCGACGGTGCGTTTATC 59.632 55.000 14.79 0.00 41.37 1.75
74 75 0.038435 TTCCGACGGTGCGTTTATCA 60.038 50.000 14.79 0.00 41.37 2.15
75 76 0.733566 TCCGACGGTGCGTTTATCAC 60.734 55.000 14.79 0.00 41.37 3.06
76 77 0.734942 CCGACGGTGCGTTTATCACT 60.735 55.000 5.48 0.00 41.37 3.41
77 78 0.365523 CGACGGTGCGTTTATCACTG 59.634 55.000 0.86 0.86 41.37 3.66
78 79 3.599412 ACGGTGCGTTTATCACTGT 57.401 47.368 2.10 2.10 46.05 3.55
80 81 0.365523 CGGTGCGTTTATCACTGTCG 59.634 55.000 0.00 0.00 36.38 4.35
81 82 0.719465 GGTGCGTTTATCACTGTCGG 59.281 55.000 0.00 0.00 34.97 4.79
82 83 1.425412 GTGCGTTTATCACTGTCGGT 58.575 50.000 0.00 0.00 0.00 4.69
83 84 1.126113 GTGCGTTTATCACTGTCGGTG 59.874 52.381 5.35 5.35 46.60 4.94
84 85 0.719465 GCGTTTATCACTGTCGGTGG 59.281 55.000 11.94 0.00 45.38 4.61
85 86 1.355971 CGTTTATCACTGTCGGTGGG 58.644 55.000 11.94 0.00 45.38 4.61
86 87 1.084289 GTTTATCACTGTCGGTGGGC 58.916 55.000 11.94 0.00 45.38 5.36
87 88 0.687920 TTTATCACTGTCGGTGGGCA 59.312 50.000 11.94 0.00 45.38 5.36
88 89 0.908910 TTATCACTGTCGGTGGGCAT 59.091 50.000 11.94 1.22 45.38 4.40
89 90 0.177836 TATCACTGTCGGTGGGCATG 59.822 55.000 11.94 0.00 45.38 4.06
90 91 1.841302 ATCACTGTCGGTGGGCATGT 61.841 55.000 11.94 0.00 45.38 3.21
91 92 2.032528 ACTGTCGGTGGGCATGTG 59.967 61.111 0.00 0.00 0.00 3.21
92 93 2.747460 CTGTCGGTGGGCATGTGG 60.747 66.667 0.00 0.00 0.00 4.17
93 94 3.245346 TGTCGGTGGGCATGTGGA 61.245 61.111 0.00 0.00 0.00 4.02
94 95 2.436646 GTCGGTGGGCATGTGGAG 60.437 66.667 0.00 0.00 0.00 3.86
95 96 3.716195 TCGGTGGGCATGTGGAGG 61.716 66.667 0.00 0.00 0.00 4.30
96 97 4.033776 CGGTGGGCATGTGGAGGT 62.034 66.667 0.00 0.00 0.00 3.85
97 98 2.361610 GGTGGGCATGTGGAGGTG 60.362 66.667 0.00 0.00 0.00 4.00
98 99 2.436109 GTGGGCATGTGGAGGTGT 59.564 61.111 0.00 0.00 0.00 4.16
99 100 1.973281 GTGGGCATGTGGAGGTGTG 60.973 63.158 0.00 0.00 0.00 3.82
100 101 2.436109 GGGCATGTGGAGGTGTGT 59.564 61.111 0.00 0.00 0.00 3.72
101 102 1.675641 GGGCATGTGGAGGTGTGTC 60.676 63.158 0.00 0.00 0.00 3.67
102 103 1.376466 GGCATGTGGAGGTGTGTCT 59.624 57.895 0.00 0.00 0.00 3.41
103 104 0.674895 GGCATGTGGAGGTGTGTCTC 60.675 60.000 0.00 0.00 0.00 3.36
108 109 2.657237 GGAGGTGTGTCTCCGGTG 59.343 66.667 0.00 0.00 43.19 4.94
109 110 2.657237 GAGGTGTGTCTCCGGTGG 59.343 66.667 0.00 0.00 0.00 4.61
110 111 1.906824 GAGGTGTGTCTCCGGTGGA 60.907 63.158 0.00 0.00 0.00 4.02
111 112 1.229209 AGGTGTGTCTCCGGTGGAT 60.229 57.895 0.00 0.00 0.00 3.41
112 113 1.218316 GGTGTGTCTCCGGTGGATC 59.782 63.158 0.00 0.63 0.00 3.36
113 114 1.258445 GGTGTGTCTCCGGTGGATCT 61.258 60.000 0.00 0.00 0.00 2.75
114 115 1.471119 GTGTGTCTCCGGTGGATCTA 58.529 55.000 0.00 0.00 0.00 1.98
115 116 2.032620 GTGTGTCTCCGGTGGATCTAT 58.967 52.381 0.00 0.00 0.00 1.98
116 117 2.431057 GTGTGTCTCCGGTGGATCTATT 59.569 50.000 0.00 0.00 0.00 1.73
117 118 3.104512 TGTGTCTCCGGTGGATCTATTT 58.895 45.455 0.00 0.00 0.00 1.40
118 119 3.517901 TGTGTCTCCGGTGGATCTATTTT 59.482 43.478 0.00 0.00 0.00 1.82
119 120 4.019681 TGTGTCTCCGGTGGATCTATTTTT 60.020 41.667 0.00 0.00 0.00 1.94
120 121 4.332819 GTGTCTCCGGTGGATCTATTTTTG 59.667 45.833 0.00 0.00 0.00 2.44
121 122 4.019681 TGTCTCCGGTGGATCTATTTTTGT 60.020 41.667 0.00 0.00 0.00 2.83
122 123 4.941873 GTCTCCGGTGGATCTATTTTTGTT 59.058 41.667 0.00 0.00 0.00 2.83
123 124 4.941263 TCTCCGGTGGATCTATTTTTGTTG 59.059 41.667 0.00 0.00 0.00 3.33
124 125 4.658063 TCCGGTGGATCTATTTTTGTTGT 58.342 39.130 0.00 0.00 0.00 3.32
125 126 5.806818 TCCGGTGGATCTATTTTTGTTGTA 58.193 37.500 0.00 0.00 0.00 2.41
126 127 6.419791 TCCGGTGGATCTATTTTTGTTGTAT 58.580 36.000 0.00 0.00 0.00 2.29
127 128 6.887545 TCCGGTGGATCTATTTTTGTTGTATT 59.112 34.615 0.00 0.00 0.00 1.89
128 129 7.394923 TCCGGTGGATCTATTTTTGTTGTATTT 59.605 33.333 0.00 0.00 0.00 1.40
129 130 7.487829 CCGGTGGATCTATTTTTGTTGTATTTG 59.512 37.037 0.00 0.00 0.00 2.32
130 131 7.009174 CGGTGGATCTATTTTTGTTGTATTTGC 59.991 37.037 0.00 0.00 0.00 3.68
131 132 8.034804 GGTGGATCTATTTTTGTTGTATTTGCT 58.965 33.333 0.00 0.00 0.00 3.91
132 133 9.076596 GTGGATCTATTTTTGTTGTATTTGCTC 57.923 33.333 0.00 0.00 0.00 4.26
133 134 7.967854 TGGATCTATTTTTGTTGTATTTGCTCG 59.032 33.333 0.00 0.00 0.00 5.03
134 135 7.432252 GGATCTATTTTTGTTGTATTTGCTCGG 59.568 37.037 0.00 0.00 0.00 4.63
135 136 7.441890 TCTATTTTTGTTGTATTTGCTCGGA 57.558 32.000 0.00 0.00 0.00 4.55
136 137 8.050778 TCTATTTTTGTTGTATTTGCTCGGAT 57.949 30.769 0.00 0.00 0.00 4.18
137 138 8.181573 TCTATTTTTGTTGTATTTGCTCGGATC 58.818 33.333 0.00 0.00 0.00 3.36
138 139 5.957842 TTTTGTTGTATTTGCTCGGATCT 57.042 34.783 0.00 0.00 0.00 2.75
139 140 5.545658 TTTGTTGTATTTGCTCGGATCTC 57.454 39.130 0.00 0.00 0.00 2.75
140 141 3.186909 TGTTGTATTTGCTCGGATCTCG 58.813 45.455 0.00 0.00 40.90 4.04
141 142 3.187700 GTTGTATTTGCTCGGATCTCGT 58.812 45.455 0.00 0.00 40.32 4.18
142 143 3.079960 TGTATTTGCTCGGATCTCGTC 57.920 47.619 0.00 0.00 40.32 4.20
143 144 2.044860 GTATTTGCTCGGATCTCGTCG 58.955 52.381 0.00 0.00 40.32 5.12
144 145 0.456221 ATTTGCTCGGATCTCGTCGT 59.544 50.000 0.00 0.00 40.32 4.34
145 146 0.242825 TTTGCTCGGATCTCGTCGTT 59.757 50.000 0.00 0.00 40.32 3.85
146 147 0.456142 TTGCTCGGATCTCGTCGTTG 60.456 55.000 0.00 0.00 40.32 4.10
147 148 1.136984 GCTCGGATCTCGTCGTTGT 59.863 57.895 0.00 0.00 40.32 3.32
148 149 0.376152 GCTCGGATCTCGTCGTTGTA 59.624 55.000 0.00 0.00 40.32 2.41
149 150 1.855223 GCTCGGATCTCGTCGTTGTAC 60.855 57.143 0.00 0.00 40.32 2.90
150 151 0.371301 TCGGATCTCGTCGTTGTACG 59.629 55.000 0.00 0.00 44.19 3.67
151 152 0.095935 CGGATCTCGTCGTTGTACGT 59.904 55.000 0.00 0.00 43.14 3.57
152 153 1.464687 CGGATCTCGTCGTTGTACGTT 60.465 52.381 0.00 0.00 43.14 3.99
153 154 2.172365 GGATCTCGTCGTTGTACGTTC 58.828 52.381 0.00 0.00 43.14 3.95
154 155 1.830633 GATCTCGTCGTTGTACGTTCG 59.169 52.381 0.00 6.26 43.14 3.95
155 156 0.858583 TCTCGTCGTTGTACGTTCGA 59.141 50.000 0.00 15.78 43.14 3.71
156 157 3.349972 TCGTCGTTGTACGTTCGAG 57.650 52.632 0.00 3.55 43.14 4.04
157 158 0.581529 TCGTCGTTGTACGTTCGAGT 59.418 50.000 0.00 0.00 43.14 4.18
158 159 0.693817 CGTCGTTGTACGTTCGAGTG 59.306 55.000 0.00 1.36 43.14 3.51
159 160 1.746760 GTCGTTGTACGTTCGAGTGT 58.253 50.000 0.00 0.00 43.14 3.55
160 161 1.705559 GTCGTTGTACGTTCGAGTGTC 59.294 52.381 0.00 0.00 43.14 3.67
161 162 1.599071 TCGTTGTACGTTCGAGTGTCT 59.401 47.619 0.00 0.00 43.14 3.41
162 163 2.032054 TCGTTGTACGTTCGAGTGTCTT 59.968 45.455 0.00 0.00 43.14 3.01
163 164 2.399754 CGTTGTACGTTCGAGTGTCTTC 59.600 50.000 0.00 0.00 36.74 2.87
164 165 2.305252 TGTACGTTCGAGTGTCTTCG 57.695 50.000 0.00 0.00 41.79 3.79
165 166 1.069703 TGTACGTTCGAGTGTCTTCGG 60.070 52.381 0.00 0.00 40.83 4.30
166 167 0.518636 TACGTTCGAGTGTCTTCGGG 59.481 55.000 0.00 0.00 40.83 5.14
167 168 1.285023 CGTTCGAGTGTCTTCGGGT 59.715 57.895 0.00 0.00 40.83 5.28
168 169 0.318445 CGTTCGAGTGTCTTCGGGTT 60.318 55.000 0.00 0.00 40.83 4.11
177 178 1.702957 TGTCTTCGGGTTGGATCCTTT 59.297 47.619 14.23 0.00 0.00 3.11
181 182 3.010138 TCTTCGGGTTGGATCCTTTTGAT 59.990 43.478 14.23 0.00 36.01 2.57
199 200 9.319143 CCTTTTGATCTACGTTATTCTTCATCT 57.681 33.333 0.00 0.00 0.00 2.90
206 207 5.475273 ACGTTATTCTTCATCTACGACGA 57.525 39.130 0.00 0.00 33.60 4.20
210 211 6.414109 CGTTATTCTTCATCTACGACGATTGT 59.586 38.462 0.00 0.00 0.00 2.71
215 216 5.571741 TCTTCATCTACGACGATTGTTGTTC 59.428 40.000 11.39 0.00 39.83 3.18
221 222 1.864711 CGACGATTGTTGTTCTGGTGT 59.135 47.619 0.00 0.00 0.00 4.16
232 233 1.279271 GTTCTGGTGTGCTGGTCCTAT 59.721 52.381 0.00 0.00 0.00 2.57
234 235 0.107508 CTGGTGTGCTGGTCCTATGG 60.108 60.000 0.00 0.00 0.00 2.74
255 256 1.403249 GGCCTTAGCACGACGACTTTA 60.403 52.381 0.00 0.00 42.56 1.85
259 260 3.423571 CTTAGCACGACGACTTTACGAT 58.576 45.455 0.00 0.00 37.03 3.73
263 264 2.910482 GCACGACGACTTTACGATTGTA 59.090 45.455 0.00 0.00 37.03 2.41
269 270 7.109395 CACGACGACTTTACGATTGTATACTAC 59.891 40.741 0.00 0.00 37.03 2.73
289 290 1.257936 CAACAAGTTGTGTCCGACTCG 59.742 52.381 9.79 0.00 40.60 4.18
313 314 4.530857 GGAGGGGTGATGACGGCG 62.531 72.222 4.80 4.80 0.00 6.46
330 331 2.512515 GGCTCGCTTTCGGCTCAT 60.513 61.111 0.00 0.00 39.13 2.90
340 341 1.159285 TTCGGCTCATTTCAGTGCTG 58.841 50.000 0.00 0.00 36.10 4.41
355 356 1.355916 GCTGGTAGTCGTCGCTAGG 59.644 63.158 0.00 0.00 0.00 3.02
372 373 0.629596 AGGTGGTCTACGGATCTGGA 59.370 55.000 6.47 0.00 0.00 3.86
381 382 4.991687 GTCTACGGATCTGGATGGAATTTC 59.008 45.833 6.47 0.00 0.00 2.17
383 384 6.015350 GTCTACGGATCTGGATGGAATTTCTA 60.015 42.308 6.47 0.00 0.00 2.10
424 425 7.148590 CGTTGTACTGTCATGATTGAAGATGAA 60.149 37.037 0.00 0.00 32.48 2.57
432 433 9.841295 TGTCATGATTGAAGATGAATAGATTGA 57.159 29.630 0.00 0.00 32.48 2.57
475 476 9.763837 AATATAAGGTGGTTTTTAGGCTAGTTT 57.236 29.630 0.00 0.00 0.00 2.66
594 595 3.811497 ACACAAAGTCCGGCTAGTTTAAC 59.189 43.478 0.00 0.00 0.00 2.01
721 748 2.817258 TCCAATCGAATCCACACCAAAC 59.183 45.455 0.00 0.00 0.00 2.93
857 906 2.109387 GCGGGGTGTGTGTGTGTA 59.891 61.111 0.00 0.00 0.00 2.90
1062 1124 2.413351 GACAGGATCAGCGCGCTA 59.587 61.111 36.02 22.05 0.00 4.26
1326 1439 3.181967 CGCTTCTTCCTGTCGGCG 61.182 66.667 0.00 0.00 36.89 6.46
1496 1632 0.606604 GACTACCCACTCGCTTTCCA 59.393 55.000 0.00 0.00 0.00 3.53
1713 1852 0.034089 TCGAGCTCATCTCTGTCCCA 60.034 55.000 15.40 0.00 39.70 4.37
1848 1989 2.467826 GCCATTCCTGCTGAGCGAC 61.468 63.158 0.00 0.00 0.00 5.19
1902 2046 2.756760 ACTGCATCTCAATTTTCGCCAT 59.243 40.909 0.00 0.00 0.00 4.40
2177 2355 7.732996 AGTTTACAGTAAGCCTTTGACTCTAA 58.267 34.615 3.66 0.00 0.00 2.10
2221 2399 1.688735 CTTGGCCTGGATATGACTCGA 59.311 52.381 3.32 0.00 0.00 4.04
2266 2529 7.759886 CCGATATATAGCATTAACGGATATGGG 59.240 40.741 0.00 0.00 41.30 4.00
2315 2578 4.908601 ATGTTGGGGATATCGCTTATCA 57.091 40.909 18.21 12.87 38.82 2.15
2363 2626 2.621526 GGGGTAAATCGGCCAGTTTATG 59.378 50.000 2.24 0.00 0.00 1.90
2379 2642 2.631160 TATGGGCATTTCGGTCGATT 57.369 45.000 0.00 0.00 0.00 3.34
2380 2643 1.762708 ATGGGCATTTCGGTCGATTT 58.237 45.000 0.00 0.00 0.00 2.17
2421 2684 9.942850 TGATTTATCAGCCGATTTATCTTATCA 57.057 29.630 0.00 0.00 32.73 2.15
2427 2690 6.265422 TCAGCCGATTTATCTTATCAGTCAGA 59.735 38.462 0.00 0.00 0.00 3.27
2446 2709 3.245284 CAGACACCGGTAAGCGATAAATG 59.755 47.826 6.87 0.00 0.00 2.32
2450 2713 0.872388 CGGTAAGCGATAAATGGGCC 59.128 55.000 0.00 0.00 0.00 5.80
2531 2794 4.385447 CGACGTTCCATTTGAATTTTGCAT 59.615 37.500 0.00 0.00 34.90 3.96
2608 2872 5.615925 AAGAGTTACCCGAAGCATATTCT 57.384 39.130 0.00 0.00 0.00 2.40
2780 3047 7.489113 GCATGGGTTGATGTCAAGTTAAATTAG 59.511 37.037 0.00 0.00 36.39 1.73
2785 3052 9.537848 GGTTGATGTCAAGTTAAATTAGTAACG 57.462 33.333 0.00 0.00 38.71 3.18
2987 3255 5.552870 AACTACATAAGGCTAGTCATGGG 57.447 43.478 0.00 0.00 0.00 4.00
3000 3268 3.329889 ATGGGGCGAGCTGTTGGA 61.330 61.111 0.00 0.00 0.00 3.53
3332 3639 0.033504 GCCCGAGAAGTGTGTCAAGA 59.966 55.000 0.00 0.00 0.00 3.02
3365 3672 6.402658 GCTTAGTTCTGGAGCTCAATTACAAC 60.403 42.308 17.19 8.77 33.72 3.32
3820 4127 3.682377 TGTGTGTACCATCTGTATTTGCG 59.318 43.478 0.00 0.00 0.00 4.85
3837 4144 3.420300 TGCGTTGGTAAACCCTATCAA 57.580 42.857 0.00 0.00 32.23 2.57
4082 4438 5.640783 TGTTCAGCATGTGAAGATAGAACTG 59.359 40.000 9.93 0.00 46.18 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.883354 CATCTTCAGGGGGCCGCC 62.883 72.222 31.08 31.08 0.00 6.13
10 11 4.883354 CCATCTTCAGGGGGCCGC 62.883 72.222 13.58 13.58 0.00 6.53
11 12 1.999634 ATTCCATCTTCAGGGGGCCG 62.000 60.000 0.00 0.00 0.00 6.13
12 13 1.149101 TATTCCATCTTCAGGGGGCC 58.851 55.000 0.00 0.00 0.00 5.80
13 14 3.225940 CTTTATTCCATCTTCAGGGGGC 58.774 50.000 0.00 0.00 0.00 5.80
14 15 3.205282 ACCTTTATTCCATCTTCAGGGGG 59.795 47.826 0.00 0.00 0.00 5.40
15 16 4.166919 AGACCTTTATTCCATCTTCAGGGG 59.833 45.833 0.00 0.00 0.00 4.79
16 17 5.372373 GAGACCTTTATTCCATCTTCAGGG 58.628 45.833 0.00 0.00 0.00 4.45
17 18 5.372373 GGAGACCTTTATTCCATCTTCAGG 58.628 45.833 0.00 0.00 0.00 3.86
54 55 0.367887 GATAAACGCACCGTCGGAAC 59.632 55.000 20.51 8.29 39.99 3.62
55 56 0.038435 TGATAAACGCACCGTCGGAA 60.038 50.000 20.51 0.00 39.99 4.30
56 57 0.733566 GTGATAAACGCACCGTCGGA 60.734 55.000 20.51 0.00 39.99 4.55
57 58 0.734942 AGTGATAAACGCACCGTCGG 60.735 55.000 10.48 10.48 39.99 4.79
58 59 0.365523 CAGTGATAAACGCACCGTCG 59.634 55.000 0.00 0.00 39.99 5.12
59 60 1.389106 GACAGTGATAAACGCACCGTC 59.611 52.381 0.00 0.00 39.99 4.79
60 61 1.425412 GACAGTGATAAACGCACCGT 58.575 50.000 0.00 0.00 43.97 4.83
61 62 0.365523 CGACAGTGATAAACGCACCG 59.634 55.000 0.00 0.00 36.95 4.94
62 63 0.719465 CCGACAGTGATAAACGCACC 59.281 55.000 0.00 0.00 36.95 5.01
63 64 1.425412 ACCGACAGTGATAAACGCAC 58.575 50.000 0.00 0.00 36.53 5.34
64 65 3.898380 ACCGACAGTGATAAACGCA 57.102 47.368 0.00 0.00 0.00 5.24
73 74 2.032528 ACATGCCCACCGACAGTG 59.967 61.111 0.00 0.00 46.83 3.66
74 75 2.032528 CACATGCCCACCGACAGT 59.967 61.111 0.00 0.00 0.00 3.55
75 76 2.747460 CCACATGCCCACCGACAG 60.747 66.667 0.00 0.00 0.00 3.51
76 77 3.245346 TCCACATGCCCACCGACA 61.245 61.111 0.00 0.00 0.00 4.35
77 78 2.436646 CTCCACATGCCCACCGAC 60.437 66.667 0.00 0.00 0.00 4.79
78 79 3.716195 CCTCCACATGCCCACCGA 61.716 66.667 0.00 0.00 0.00 4.69
79 80 4.033776 ACCTCCACATGCCCACCG 62.034 66.667 0.00 0.00 0.00 4.94
80 81 2.361610 CACCTCCACATGCCCACC 60.362 66.667 0.00 0.00 0.00 4.61
81 82 1.973281 CACACCTCCACATGCCCAC 60.973 63.158 0.00 0.00 0.00 4.61
82 83 2.410322 GACACACCTCCACATGCCCA 62.410 60.000 0.00 0.00 0.00 5.36
83 84 1.675641 GACACACCTCCACATGCCC 60.676 63.158 0.00 0.00 0.00 5.36
84 85 0.674895 GAGACACACCTCCACATGCC 60.675 60.000 0.00 0.00 0.00 4.40
85 86 2.846371 GAGACACACCTCCACATGC 58.154 57.895 0.00 0.00 0.00 4.06
92 93 1.258445 ATCCACCGGAGACACACCTC 61.258 60.000 9.46 0.00 34.05 3.85
93 94 1.229209 ATCCACCGGAGACACACCT 60.229 57.895 9.46 0.00 34.05 4.00
94 95 1.218316 GATCCACCGGAGACACACC 59.782 63.158 9.46 0.00 34.05 4.16
95 96 1.471119 TAGATCCACCGGAGACACAC 58.529 55.000 9.46 0.00 34.05 3.82
96 97 2.454336 ATAGATCCACCGGAGACACA 57.546 50.000 9.46 0.00 34.05 3.72
97 98 3.821421 AAATAGATCCACCGGAGACAC 57.179 47.619 9.46 2.93 34.05 3.67
98 99 4.019681 ACAAAAATAGATCCACCGGAGACA 60.020 41.667 9.46 0.00 34.05 3.41
99 100 4.514401 ACAAAAATAGATCCACCGGAGAC 58.486 43.478 9.46 0.00 34.05 3.36
100 101 4.837093 ACAAAAATAGATCCACCGGAGA 57.163 40.909 9.46 4.59 34.05 3.71
101 102 4.700213 ACAACAAAAATAGATCCACCGGAG 59.300 41.667 9.46 0.00 34.05 4.63
102 103 4.658063 ACAACAAAAATAGATCCACCGGA 58.342 39.130 9.46 0.00 35.55 5.14
103 104 6.693315 ATACAACAAAAATAGATCCACCGG 57.307 37.500 0.00 0.00 0.00 5.28
104 105 7.009174 GCAAATACAACAAAAATAGATCCACCG 59.991 37.037 0.00 0.00 0.00 4.94
105 106 8.034804 AGCAAATACAACAAAAATAGATCCACC 58.965 33.333 0.00 0.00 0.00 4.61
106 107 8.986477 AGCAAATACAACAAAAATAGATCCAC 57.014 30.769 0.00 0.00 0.00 4.02
107 108 7.967854 CGAGCAAATACAACAAAAATAGATCCA 59.032 33.333 0.00 0.00 0.00 3.41
108 109 7.432252 CCGAGCAAATACAACAAAAATAGATCC 59.568 37.037 0.00 0.00 0.00 3.36
109 110 8.181573 TCCGAGCAAATACAACAAAAATAGATC 58.818 33.333 0.00 0.00 0.00 2.75
110 111 8.050778 TCCGAGCAAATACAACAAAAATAGAT 57.949 30.769 0.00 0.00 0.00 1.98
111 112 7.441890 TCCGAGCAAATACAACAAAAATAGA 57.558 32.000 0.00 0.00 0.00 1.98
112 113 8.184192 AGATCCGAGCAAATACAACAAAAATAG 58.816 33.333 0.00 0.00 0.00 1.73
113 114 8.050778 AGATCCGAGCAAATACAACAAAAATA 57.949 30.769 0.00 0.00 0.00 1.40
114 115 6.924111 AGATCCGAGCAAATACAACAAAAAT 58.076 32.000 0.00 0.00 0.00 1.82
115 116 6.325919 AGATCCGAGCAAATACAACAAAAA 57.674 33.333 0.00 0.00 0.00 1.94
116 117 5.390461 CGAGATCCGAGCAAATACAACAAAA 60.390 40.000 0.00 0.00 41.76 2.44
117 118 4.092821 CGAGATCCGAGCAAATACAACAAA 59.907 41.667 0.00 0.00 41.76 2.83
118 119 3.616821 CGAGATCCGAGCAAATACAACAA 59.383 43.478 0.00 0.00 41.76 2.83
119 120 3.186909 CGAGATCCGAGCAAATACAACA 58.813 45.455 0.00 0.00 41.76 3.33
120 121 3.187700 ACGAGATCCGAGCAAATACAAC 58.812 45.455 10.05 0.00 41.76 3.32
121 122 3.444916 GACGAGATCCGAGCAAATACAA 58.555 45.455 10.05 0.00 41.76 2.41
122 123 2.540973 CGACGAGATCCGAGCAAATACA 60.541 50.000 10.05 0.00 41.76 2.29
123 124 2.044860 CGACGAGATCCGAGCAAATAC 58.955 52.381 10.05 0.00 41.76 1.89
124 125 1.674441 ACGACGAGATCCGAGCAAATA 59.326 47.619 0.00 0.00 41.76 1.40
125 126 0.456221 ACGACGAGATCCGAGCAAAT 59.544 50.000 0.00 0.00 41.76 2.32
126 127 0.242825 AACGACGAGATCCGAGCAAA 59.757 50.000 0.00 0.00 41.76 3.68
127 128 0.456142 CAACGACGAGATCCGAGCAA 60.456 55.000 0.00 0.00 41.76 3.91
128 129 1.136774 CAACGACGAGATCCGAGCA 59.863 57.895 0.00 0.00 41.76 4.26
129 130 0.376152 TACAACGACGAGATCCGAGC 59.624 55.000 0.00 2.24 41.76 5.03
130 131 1.591632 CGTACAACGACGAGATCCGAG 60.592 57.143 0.00 6.49 46.05 4.63
131 132 0.371301 CGTACAACGACGAGATCCGA 59.629 55.000 0.00 0.00 46.05 4.55
132 133 0.095935 ACGTACAACGACGAGATCCG 59.904 55.000 0.00 0.51 46.05 4.18
133 134 2.172365 GAACGTACAACGACGAGATCC 58.828 52.381 0.00 0.00 46.05 3.36
134 135 1.830633 CGAACGTACAACGACGAGATC 59.169 52.381 0.00 0.00 46.05 2.75
135 136 1.460743 TCGAACGTACAACGACGAGAT 59.539 47.619 16.61 0.00 46.05 2.75
136 137 0.858583 TCGAACGTACAACGACGAGA 59.141 50.000 16.61 5.49 46.05 4.04
137 138 3.349972 TCGAACGTACAACGACGAG 57.650 52.632 16.61 0.00 46.05 4.18
138 139 0.581529 ACTCGAACGTACAACGACGA 59.418 50.000 18.28 18.28 46.05 4.20
139 140 0.693817 CACTCGAACGTACAACGACG 59.306 55.000 6.44 11.00 46.05 5.12
140 141 1.705559 GACACTCGAACGTACAACGAC 59.294 52.381 6.44 0.00 46.05 4.34
141 142 1.599071 AGACACTCGAACGTACAACGA 59.401 47.619 6.44 0.00 46.05 3.85
142 143 4.955556 CGAAGACACTCGAACGTACAACG 61.956 52.174 0.00 0.00 43.66 4.10
143 144 2.399754 CGAAGACACTCGAACGTACAAC 59.600 50.000 0.00 0.00 41.44 3.32
144 145 2.602933 CCGAAGACACTCGAACGTACAA 60.603 50.000 0.00 0.00 41.44 2.41
145 146 1.069703 CCGAAGACACTCGAACGTACA 60.070 52.381 0.00 0.00 41.44 2.90
146 147 1.599992 CCGAAGACACTCGAACGTAC 58.400 55.000 0.00 0.00 41.44 3.67
147 148 0.518636 CCCGAAGACACTCGAACGTA 59.481 55.000 0.00 0.00 41.44 3.57
148 149 1.285023 CCCGAAGACACTCGAACGT 59.715 57.895 0.00 0.00 41.44 3.99
149 150 0.318445 AACCCGAAGACACTCGAACG 60.318 55.000 0.00 0.00 41.44 3.95
150 151 1.137513 CAACCCGAAGACACTCGAAC 58.862 55.000 0.00 0.00 41.44 3.95
151 152 0.032952 CCAACCCGAAGACACTCGAA 59.967 55.000 0.00 0.00 41.44 3.71
152 153 0.824595 TCCAACCCGAAGACACTCGA 60.825 55.000 0.00 0.00 41.44 4.04
153 154 0.246635 ATCCAACCCGAAGACACTCG 59.753 55.000 0.00 0.00 38.58 4.18
154 155 1.405661 GGATCCAACCCGAAGACACTC 60.406 57.143 6.95 0.00 0.00 3.51
155 156 0.613777 GGATCCAACCCGAAGACACT 59.386 55.000 6.95 0.00 0.00 3.55
156 157 0.613777 AGGATCCAACCCGAAGACAC 59.386 55.000 15.82 0.00 0.00 3.67
157 158 1.358152 AAGGATCCAACCCGAAGACA 58.642 50.000 15.82 0.00 0.00 3.41
158 159 2.488153 CAAAAGGATCCAACCCGAAGAC 59.512 50.000 15.82 0.00 0.00 3.01
159 160 2.373836 TCAAAAGGATCCAACCCGAAGA 59.626 45.455 15.82 0.00 0.00 2.87
160 161 2.790433 TCAAAAGGATCCAACCCGAAG 58.210 47.619 15.82 0.00 0.00 3.79
161 162 2.961531 TCAAAAGGATCCAACCCGAA 57.038 45.000 15.82 0.00 0.00 4.30
162 163 2.999331 GATCAAAAGGATCCAACCCGA 58.001 47.619 15.82 3.92 45.58 5.14
177 178 8.833493 TCGTAGATGAAGAATAACGTAGATCAA 58.167 33.333 0.00 0.00 32.33 2.57
199 200 3.054166 CACCAGAACAACAATCGTCGTA 58.946 45.455 0.00 0.00 0.00 3.43
200 201 1.864711 CACCAGAACAACAATCGTCGT 59.135 47.619 0.00 0.00 0.00 4.34
206 207 1.682854 CCAGCACACCAGAACAACAAT 59.317 47.619 0.00 0.00 0.00 2.71
210 211 0.465460 GGACCAGCACACCAGAACAA 60.465 55.000 0.00 0.00 0.00 2.83
215 216 0.107508 CCATAGGACCAGCACACCAG 60.108 60.000 0.00 0.00 0.00 4.00
221 222 3.096495 GGCCCCATAGGACCAGCA 61.096 66.667 0.00 0.00 37.96 4.41
232 233 4.077184 CGTCGTGCTAAGGCCCCA 62.077 66.667 0.00 0.00 37.74 4.96
234 235 2.502692 AAGTCGTCGTGCTAAGGCCC 62.503 60.000 0.00 0.00 37.74 5.80
263 264 4.986659 GTCGGACACAACTTGTTGTAGTAT 59.013 41.667 17.26 5.47 39.17 2.12
269 270 1.257936 CGAGTCGGACACAACTTGTTG 59.742 52.381 11.27 11.44 39.17 3.33
289 290 3.171388 ATCACCCCTCCATCGCCC 61.171 66.667 0.00 0.00 0.00 6.13
320 321 1.536766 CAGCACTGAAATGAGCCGAAA 59.463 47.619 0.00 0.00 0.00 3.46
323 324 0.957395 ACCAGCACTGAAATGAGCCG 60.957 55.000 0.00 0.00 0.00 5.52
329 330 2.671351 CGACGACTACCAGCACTGAAAT 60.671 50.000 0.00 0.00 0.00 2.17
330 331 1.335597 CGACGACTACCAGCACTGAAA 60.336 52.381 0.00 0.00 0.00 2.69
340 341 1.028868 ACCACCTAGCGACGACTACC 61.029 60.000 0.00 0.00 0.00 3.18
355 356 1.341531 CCATCCAGATCCGTAGACCAC 59.658 57.143 0.00 0.00 0.00 4.16
527 528 1.379044 GTGTGCCAGCCTTGCCTAT 60.379 57.895 0.00 0.00 0.00 2.57
535 536 1.660560 CTAATGCCAGTGTGCCAGCC 61.661 60.000 1.78 0.00 0.00 4.85
536 537 1.660560 CCTAATGCCAGTGTGCCAGC 61.661 60.000 1.78 0.00 0.00 4.85
594 595 0.107945 GGTGCTGTGCTAGAGAAGGG 60.108 60.000 0.00 0.00 0.00 3.95
721 748 1.869767 GAGATGCATGGTTAGCTTCGG 59.130 52.381 2.46 0.00 40.07 4.30
806 855 2.049985 GGTGAGATCGGATCCGCG 60.050 66.667 29.62 7.20 39.59 6.46
848 897 1.304254 GCCACACACATACACACACA 58.696 50.000 0.00 0.00 0.00 3.72
849 898 0.234625 CGCCACACACATACACACAC 59.765 55.000 0.00 0.00 0.00 3.82
852 901 0.320334 CTCCGCCACACACATACACA 60.320 55.000 0.00 0.00 0.00 3.72
855 904 2.452813 CGCTCCGCCACACACATAC 61.453 63.158 0.00 0.00 0.00 2.39
856 905 2.125713 CGCTCCGCCACACACATA 60.126 61.111 0.00 0.00 0.00 2.29
1033 1092 2.064723 ATCCTGTCGTCATCTCGGCG 62.065 60.000 0.00 0.00 38.32 6.46
1062 1124 3.641925 GAGGAGGAGGTCGTCGGGT 62.642 68.421 0.00 0.00 30.65 5.28
1240 1315 2.426023 GGTCAGCAACCTCCGTGT 59.574 61.111 1.21 0.00 45.45 4.49
1496 1632 1.127567 TGTAAGCCTGGTGAGCCACT 61.128 55.000 0.00 0.00 40.46 4.00
1713 1852 2.291741 GCACTGCACTTTACTGAGCTTT 59.708 45.455 0.00 0.00 0.00 3.51
1848 1989 1.311859 TTGCACTCCTTGACAAGCAG 58.688 50.000 9.85 7.16 33.14 4.24
1902 2046 7.450014 TCCACAGAAATTAGCTTTACCATTTGA 59.550 33.333 0.00 0.00 0.00 2.69
2204 2382 2.175202 AGATCGAGTCATATCCAGGCC 58.825 52.381 0.00 0.00 0.00 5.19
2247 2425 5.012664 TGTGTCCCATATCCGTTAATGCTAT 59.987 40.000 0.00 0.00 0.00 2.97
2307 2570 4.677378 CGACTGATAAGTTCCTGATAAGCG 59.323 45.833 0.00 0.00 0.00 4.68
2315 2578 4.466370 TCATTGGTCGACTGATAAGTTCCT 59.534 41.667 16.46 0.00 0.00 3.36
2363 2626 2.875933 TGATAAATCGACCGAAATGCCC 59.124 45.455 0.00 0.00 0.00 5.36
2369 2632 5.158494 CGATATGGTGATAAATCGACCGAA 58.842 41.667 0.00 0.00 42.88 4.30
2379 2642 7.619965 TGATAAATCAGCCGATATGGTGATAA 58.380 34.615 7.84 2.09 37.45 1.75
2380 2643 7.181569 TGATAAATCAGCCGATATGGTGATA 57.818 36.000 7.84 0.00 37.45 2.15
2421 2684 0.892358 TCGCTTACCGGTGTCTGACT 60.892 55.000 19.93 0.00 37.59 3.41
2427 2690 2.557317 CCATTTATCGCTTACCGGTGT 58.443 47.619 19.93 0.00 37.59 4.16
2450 2713 9.119329 GATATCTTCCGATATTCCGATAAATCG 57.881 37.037 5.38 5.38 43.92 3.34
2508 2771 3.733224 TGCAAAATTCAAATGGAACGTCG 59.267 39.130 0.00 0.00 38.60 5.12
2732 2997 7.664082 TGCAAAACAATGTAATAATGGTTGG 57.336 32.000 0.00 0.00 0.00 3.77
2738 3003 8.099537 TCAACCCATGCAAAACAATGTAATAAT 58.900 29.630 0.00 0.00 0.00 1.28
2780 3047 7.267600 GCATACAAGACAAATAACACACGTTAC 59.732 37.037 0.00 0.00 40.35 2.50
2785 3052 5.183140 AGGGCATACAAGACAAATAACACAC 59.817 40.000 0.00 0.00 0.00 3.82
2987 3255 0.449388 CTTCAATCCAACAGCTCGCC 59.551 55.000 0.00 0.00 0.00 5.54
3000 3268 3.369147 CACGCAACTCGATTCTCTTCAAT 59.631 43.478 0.00 0.00 41.67 2.57
3332 3639 6.070538 TGAGCTCCAGAACTAAGCTTTCTTAT 60.071 38.462 12.15 0.00 46.01 1.73
3753 4060 0.329596 AGGAGTGGCAGGGATTCAAC 59.670 55.000 0.00 0.00 0.00 3.18
3754 4061 0.329261 CAGGAGTGGCAGGGATTCAA 59.671 55.000 0.00 0.00 0.00 2.69
3755 4062 1.993653 CAGGAGTGGCAGGGATTCA 59.006 57.895 0.00 0.00 0.00 2.57
3756 4063 1.452833 GCAGGAGTGGCAGGGATTC 60.453 63.158 0.00 0.00 0.00 2.52
3757 4064 0.621571 TAGCAGGAGTGGCAGGGATT 60.622 55.000 0.00 0.00 0.00 3.01
3758 4065 0.621571 TTAGCAGGAGTGGCAGGGAT 60.622 55.000 0.00 0.00 0.00 3.85
3759 4066 1.229496 TTAGCAGGAGTGGCAGGGA 60.229 57.895 0.00 0.00 0.00 4.20
3766 4073 5.543507 AATAGGAGATGTTAGCAGGAGTG 57.456 43.478 0.00 0.00 0.00 3.51
3820 4127 8.528643 AGCTAAAATTTGATAGGGTTTACCAAC 58.471 33.333 0.69 0.00 43.89 3.77
3837 4144 3.947196 TCGTGATCCATGCAGCTAAAATT 59.053 39.130 0.00 0.00 0.00 1.82
3938 4245 5.581605 TGTTGCTCTCTGAATTGTTGTTTC 58.418 37.500 0.00 0.00 0.00 2.78
4082 4438 7.494952 GTGTATCTATACCTTTGTTCAGGTTCC 59.505 40.741 0.00 0.00 45.76 3.62


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

AutoCloner maintained by Alex Coulton.