Multiple sequence alignment - TraesCS1A01G090100

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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 TraesCS1A01G090100 chr1A 100.000 7251 0 0 1 7251 80189207 80196457 0.000000e+00 13391.0
1 TraesCS1A01G090100 chr1A 84.512 594 65 10 6681 7251 396280873 396281462 4.910000e-156 562.0
2 TraesCS1A01G090100 chr1A 99.029 103 1 0 740 842 80189259 80189361 1.240000e-42 185.0
3 TraesCS1A01G090100 chr1A 99.029 103 1 0 53 155 80189946 80190048 1.240000e-42 185.0
4 TraesCS1A01G090100 chr1D 96.067 6001 140 32 740 6688 85643673 85649629 0.000000e+00 9686.0
5 TraesCS1A01G090100 chr1D 89.147 387 24 3 6883 7251 85649797 85650183 3.960000e-127 466.0
6 TraesCS1A01G090100 chr1D 94.194 155 8 1 1 155 85643622 85643775 1.220000e-57 235.0
7 TraesCS1A01G090100 chr1D 94.702 151 8 0 378 528 326240217 326240067 1.220000e-57 235.0
8 TraesCS1A01G090100 chr1B 95.785 5124 126 31 740 5818 138036600 138041678 0.000000e+00 8183.0
9 TraesCS1A01G090100 chr1B 93.789 950 47 9 5774 6716 138041690 138042634 0.000000e+00 1417.0
10 TraesCS1A01G090100 chr1B 89.808 520 31 5 6750 7251 138042638 138043153 0.000000e+00 647.0
11 TraesCS1A01G090100 chr1B 90.196 204 16 4 174 377 616609424 616609225 5.580000e-66 263.0
12 TraesCS1A01G090100 chr1B 96.599 147 5 0 378 524 497443789 497443643 2.020000e-60 244.0
13 TraesCS1A01G090100 chr4A 93.675 585 32 4 169 751 374357369 374357950 0.000000e+00 870.0
14 TraesCS1A01G090100 chr4A 93.702 524 31 2 169 691 377550001 377549479 0.000000e+00 784.0
15 TraesCS1A01G090100 chr4A 91.388 209 16 2 169 377 695985190 695985396 1.190000e-72 285.0
16 TraesCS1A01G090100 chr4A 94.771 153 7 1 379 530 7158303 7158151 3.380000e-58 237.0
17 TraesCS1A01G090100 chr4A 97.826 46 1 0 1539 1584 662286503 662286458 6.030000e-11 80.5
18 TraesCS1A01G090100 chr4A 95.745 47 1 1 699 744 590978974 590978928 2.810000e-09 75.0
19 TraesCS1A01G090100 chr4A 100.000 30 0 0 5276 5305 537547418 537547447 1.000000e-03 56.5
20 TraesCS1A01G090100 chr7B 84.497 587 65 9 6687 7251 13321439 13320857 2.290000e-154 556.0
21 TraesCS1A01G090100 chr2D 83.959 586 69 8 6687 7251 370049499 370048918 8.280000e-149 538.0
22 TraesCS1A01G090100 chr2D 96.599 147 4 1 378 524 506464774 506464629 7.270000e-60 243.0
23 TraesCS1A01G090100 chr2D 95.302 149 7 0 378 526 54130574 54130426 3.380000e-58 237.0
24 TraesCS1A01G090100 chr2D 100.000 45 0 0 1539 1583 130726046 130726002 4.660000e-12 84.2
25 TraesCS1A01G090100 chr3D 83.932 585 68 9 6687 7250 47429033 47428454 2.980000e-148 536.0
26 TraesCS1A01G090100 chr3D 97.203 143 4 0 378 520 573150844 573150702 7.270000e-60 243.0
27 TraesCS1A01G090100 chr6B 83.503 588 68 12 6687 7251 290708658 290709239 8.340000e-144 521.0
28 TraesCS1A01G090100 chr6B 83.163 588 70 12 6687 7251 290686975 290687556 1.800000e-140 510.0
29 TraesCS1A01G090100 chr3A 83.505 582 68 9 6687 7247 59463739 59463165 1.080000e-142 518.0
30 TraesCS1A01G090100 chr6D 83.135 587 73 10 6687 7251 386638105 386638687 5.020000e-141 512.0
31 TraesCS1A01G090100 chr2A 94.776 268 14 0 169 436 363528330 363528063 1.130000e-112 418.0
32 TraesCS1A01G090100 chr2A 92.857 280 15 4 469 746 363528063 363527787 1.130000e-107 401.0
33 TraesCS1A01G090100 chr2A 96.000 50 2 0 6639 6688 610112992 610113041 1.680000e-11 82.4
34 TraesCS1A01G090100 chr4B 91.388 209 16 2 169 377 226130324 226130118 1.190000e-72 285.0
35 TraesCS1A01G090100 chr4B 100.000 44 0 0 1538 1581 131352008 131352051 1.680000e-11 82.4
36 TraesCS1A01G090100 chr4B 94.118 51 1 2 1540 1589 83310533 83310582 7.800000e-10 76.8
37 TraesCS1A01G090100 chr2B 91.388 209 16 2 169 377 17854749 17854955 1.190000e-72 285.0
38 TraesCS1A01G090100 chr2B 97.931 145 3 0 378 522 131288134 131287990 1.210000e-62 252.0
39 TraesCS1A01G090100 chr2B 93.478 46 2 1 699 743 551248951 551248906 4.690000e-07 67.6
40 TraesCS1A01G090100 chrUn 89.706 204 17 4 174 377 254203766 254203567 2.600000e-64 257.0
41 TraesCS1A01G090100 chr5B 89.372 207 18 4 171 377 692999234 692999436 2.600000e-64 257.0
42 TraesCS1A01G090100 chr5B 92.188 64 3 1 1540 1601 706166244 706166181 1.000000e-13 89.8
43 TraesCS1A01G090100 chr5B 100.000 32 0 0 710 741 325960688 325960719 7.860000e-05 60.2
44 TraesCS1A01G090100 chr5D 87.302 126 11 4 615 739 277316574 277316453 9.810000e-29 139.0
45 TraesCS1A01G090100 chr5D 90.196 102 8 2 520 619 277317164 277317063 1.640000e-26 132.0
46 TraesCS1A01G090100 chr7D 89.216 102 9 2 520 619 78537620 78537519 7.640000e-25 126.0
47 TraesCS1A01G090100 chr7D 100.000 29 0 0 5276 5304 403773186 403773214 4.000000e-03 54.7
48 TraesCS1A01G090100 chr7A 98.148 54 1 0 6630 6683 191265544 191265597 2.150000e-15 95.3
49 TraesCS1A01G090100 chr5A 91.045 67 5 1 6622 6688 45292750 45292815 1.000000e-13 89.8
50 TraesCS1A01G090100 chr5A 100.000 43 0 0 1539 1581 382114857 382114899 6.030000e-11 80.5
51 TraesCS1A01G090100 chr4D 85.227 88 10 3 520 607 331032513 331032429 3.600000e-13 87.9
52 TraesCS1A01G090100 chr3B 89.474 57 5 1 1536 1591 794596349 794596293 3.630000e-08 71.3
53 TraesCS1A01G090100 chr3B 100.000 29 0 0 5276 5304 710390441 710390413 4.000000e-03 54.7


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 TraesCS1A01G090100 chr1A 80189207 80196457 7250 False 13391.000000 13391 100.000000 1 7251 1 chr1A.!!$F1 7250
1 TraesCS1A01G090100 chr1A 396280873 396281462 589 False 562.000000 562 84.512000 6681 7251 1 chr1A.!!$F2 570
2 TraesCS1A01G090100 chr1D 85643622 85650183 6561 False 3462.333333 9686 93.136000 1 7251 3 chr1D.!!$F1 7250
3 TraesCS1A01G090100 chr1B 138036600 138043153 6553 False 3415.666667 8183 93.127333 740 7251 3 chr1B.!!$F1 6511
4 TraesCS1A01G090100 chr4A 374357369 374357950 581 False 870.000000 870 93.675000 169 751 1 chr4A.!!$F1 582
5 TraesCS1A01G090100 chr4A 377549479 377550001 522 True 784.000000 784 93.702000 169 691 1 chr4A.!!$R2 522
6 TraesCS1A01G090100 chr7B 13320857 13321439 582 True 556.000000 556 84.497000 6687 7251 1 chr7B.!!$R1 564
7 TraesCS1A01G090100 chr2D 370048918 370049499 581 True 538.000000 538 83.959000 6687 7251 1 chr2D.!!$R3 564
8 TraesCS1A01G090100 chr3D 47428454 47429033 579 True 536.000000 536 83.932000 6687 7250 1 chr3D.!!$R1 563
9 TraesCS1A01G090100 chr6B 290708658 290709239 581 False 521.000000 521 83.503000 6687 7251 1 chr6B.!!$F2 564
10 TraesCS1A01G090100 chr6B 290686975 290687556 581 False 510.000000 510 83.163000 6687 7251 1 chr6B.!!$F1 564
11 TraesCS1A01G090100 chr3A 59463165 59463739 574 True 518.000000 518 83.505000 6687 7247 1 chr3A.!!$R1 560
12 TraesCS1A01G090100 chr6D 386638105 386638687 582 False 512.000000 512 83.135000 6687 7251 1 chr6D.!!$F1 564
13 TraesCS1A01G090100 chr2A 363527787 363528330 543 True 409.500000 418 93.816500 169 746 2 chr2A.!!$R1 577

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
111 112 0.039527 ACGGCCGACAAAGCAAAATC 60.040 50.000 35.90 0.0 0.00 2.17 F
112 113 0.039617 CGGCCGACAAAGCAAAATCA 60.040 50.000 24.07 0.0 0.00 2.57 F
732 734 0.179051 TTGTAACGCACGGGTCCTTT 60.179 50.000 0.00 0.0 0.00 3.11 F
733 735 0.179051 TGTAACGCACGGGTCCTTTT 60.179 50.000 0.00 0.0 0.00 2.27 F
734 736 0.236449 GTAACGCACGGGTCCTTTTG 59.764 55.000 0.00 0.0 0.00 2.44 F
1493 1509 0.322906 CCCTCAGAAAACCAGGAGGC 60.323 60.000 0.00 0.0 44.45 4.70 F
2053 2070 2.170397 TCACATTGCATCACGGGACTAT 59.830 45.455 0.00 0.0 0.00 2.12 F
3869 3921 3.138283 TCCCTGTTGGTTCTCATCAACTT 59.862 43.478 0.00 0.0 42.48 2.66 F
4244 4296 1.937191 AGCACCTTAACCAAATGGGG 58.063 50.000 4.17 0.0 42.91 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 1262 1.693083 GCCATTCCCGAAGACGAACG 61.693 60.000 0.00 0.00 42.66 3.95 R
1493 1509 1.740025 GGAAAATGCAGTCGGAGAAGG 59.260 52.381 0.00 0.00 39.69 3.46 R
1683 1699 1.765904 TGCCCAGTAACAACAGAGTCA 59.234 47.619 0.00 0.00 0.00 3.41 R
2053 2070 6.682423 ATCATCAAATATTGACAAGTCGCA 57.318 33.333 0.00 0.00 43.48 5.10 R
2889 2926 9.352784 GCTTTTGTTGCATATAGTTCATTACAA 57.647 29.630 0.00 0.00 0.00 2.41 R
3509 3559 1.719709 CTGATGGCATGTCACGCAG 59.280 57.895 15.12 15.12 0.00 5.18 R
3899 3951 0.178068 TTTCAGCCTGCTCGGTATCC 59.822 55.000 0.00 0.00 34.25 2.59 R
5404 5461 2.244695 CCCAACCCCAAGTTTAGTTCC 58.755 52.381 0.00 0.00 36.18 3.62 R
6311 6431 1.299541 CTACAATAACGCAGGCAGGG 58.700 55.000 0.00 0.00 0.00 4.45 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.919666 TAAAGCAAGCAAGCGATTCC 57.080 45.000 0.00 0.00 40.15 3.01
20 21 0.244721 AAAGCAAGCAAGCGATTCCC 59.755 50.000 0.00 0.00 40.15 3.97
21 22 0.895100 AAGCAAGCAAGCGATTCCCA 60.895 50.000 0.00 0.00 40.15 4.37
29 30 4.973168 AGCAAGCGATTCCCAATATTCTA 58.027 39.130 0.00 0.00 0.00 2.10
35 36 4.702131 GCGATTCCCAATATTCTAGGCATT 59.298 41.667 0.00 0.00 0.00 3.56
36 37 5.183904 GCGATTCCCAATATTCTAGGCATTT 59.816 40.000 0.00 0.00 0.00 2.32
96 97 8.515473 AGAAACAAAATCAAACTTATAACGGC 57.485 30.769 0.00 0.00 0.00 5.68
97 98 7.597369 AGAAACAAAATCAAACTTATAACGGCC 59.403 33.333 0.00 0.00 0.00 6.13
98 99 5.395642 ACAAAATCAAACTTATAACGGCCG 58.604 37.500 26.86 26.86 0.00 6.13
99 100 5.181622 ACAAAATCAAACTTATAACGGCCGA 59.818 36.000 35.90 11.57 0.00 5.54
100 101 4.870221 AATCAAACTTATAACGGCCGAC 57.130 40.909 35.90 0.00 0.00 4.79
101 102 3.316071 TCAAACTTATAACGGCCGACA 57.684 42.857 35.90 19.57 0.00 4.35
102 103 3.661944 TCAAACTTATAACGGCCGACAA 58.338 40.909 35.90 17.04 0.00 3.18
103 104 4.063689 TCAAACTTATAACGGCCGACAAA 58.936 39.130 35.90 18.33 0.00 2.83
104 105 4.152759 TCAAACTTATAACGGCCGACAAAG 59.847 41.667 35.90 27.52 0.00 2.77
105 106 2.004733 ACTTATAACGGCCGACAAAGC 58.995 47.619 35.90 0.00 0.00 3.51
106 107 2.004017 CTTATAACGGCCGACAAAGCA 58.996 47.619 35.90 8.33 0.00 3.91
107 108 2.096220 TATAACGGCCGACAAAGCAA 57.904 45.000 35.90 7.55 0.00 3.91
108 109 1.240256 ATAACGGCCGACAAAGCAAA 58.760 45.000 35.90 5.86 0.00 3.68
109 110 1.022735 TAACGGCCGACAAAGCAAAA 58.977 45.000 35.90 0.73 0.00 2.44
110 111 0.387565 AACGGCCGACAAAGCAAAAT 59.612 45.000 35.90 0.00 0.00 1.82
111 112 0.039527 ACGGCCGACAAAGCAAAATC 60.040 50.000 35.90 0.00 0.00 2.17
112 113 0.039617 CGGCCGACAAAGCAAAATCA 60.040 50.000 24.07 0.00 0.00 2.57
113 114 1.402720 CGGCCGACAAAGCAAAATCAT 60.403 47.619 24.07 0.00 0.00 2.45
114 115 2.159448 CGGCCGACAAAGCAAAATCATA 60.159 45.455 24.07 0.00 0.00 2.15
115 116 3.671971 CGGCCGACAAAGCAAAATCATAA 60.672 43.478 24.07 0.00 0.00 1.90
116 117 4.432712 GGCCGACAAAGCAAAATCATAAT 58.567 39.130 0.00 0.00 0.00 1.28
117 118 4.869861 GGCCGACAAAGCAAAATCATAATT 59.130 37.500 0.00 0.00 0.00 1.40
118 119 5.351189 GGCCGACAAAGCAAAATCATAATTT 59.649 36.000 0.00 0.00 36.64 1.82
119 120 6.128309 GGCCGACAAAGCAAAATCATAATTTT 60.128 34.615 0.00 0.00 44.12 1.82
132 133 8.586570 AAATCATAATTTTGAAACACGCTTCA 57.413 26.923 2.59 0.00 30.79 3.02
133 134 8.586570 AATCATAATTTTGAAACACGCTTCAA 57.413 26.923 2.59 4.35 42.21 2.69
139 140 3.684103 TGAAACACGCTTCAAATTCGT 57.316 38.095 0.00 0.00 32.39 3.85
140 141 3.613563 TGAAACACGCTTCAAATTCGTC 58.386 40.909 0.00 0.00 32.39 4.20
141 142 2.294479 AACACGCTTCAAATTCGTCG 57.706 45.000 0.00 0.00 33.84 5.12
142 143 1.493772 ACACGCTTCAAATTCGTCGA 58.506 45.000 0.00 0.00 33.84 4.20
143 144 1.862201 ACACGCTTCAAATTCGTCGAA 59.138 42.857 10.61 10.61 33.84 3.71
144 145 2.478894 ACACGCTTCAAATTCGTCGAAT 59.521 40.909 14.69 14.69 33.84 3.34
145 146 3.059188 ACACGCTTCAAATTCGTCGAATT 60.059 39.130 24.09 24.09 43.07 2.17
146 147 3.534516 CACGCTTCAAATTCGTCGAATTC 59.465 43.478 28.29 16.76 40.77 2.17
147 148 3.185594 ACGCTTCAAATTCGTCGAATTCA 59.814 39.130 28.29 17.60 40.77 2.57
148 149 4.148166 CGCTTCAAATTCGTCGAATTCAA 58.852 39.130 28.29 22.17 40.77 2.69
149 150 4.610951 CGCTTCAAATTCGTCGAATTCAAA 59.389 37.500 28.29 22.80 40.77 2.69
150 151 5.114871 CGCTTCAAATTCGTCGAATTCAAAA 59.885 36.000 28.29 20.91 40.77 2.44
151 152 6.344624 CGCTTCAAATTCGTCGAATTCAAAAA 60.345 34.615 28.29 19.03 40.77 1.94
152 153 6.997912 GCTTCAAATTCGTCGAATTCAAAAAG 59.002 34.615 28.29 25.19 40.77 2.27
153 154 7.305993 GCTTCAAATTCGTCGAATTCAAAAAGT 60.306 33.333 28.29 12.15 40.77 2.66
154 155 9.165014 CTTCAAATTCGTCGAATTCAAAAAGTA 57.835 29.630 28.29 10.96 40.77 2.24
155 156 8.483743 TCAAATTCGTCGAATTCAAAAAGTAC 57.516 30.769 28.29 0.00 40.77 2.73
156 157 8.123575 TCAAATTCGTCGAATTCAAAAAGTACA 58.876 29.630 28.29 4.09 40.77 2.90
157 158 8.738554 CAAATTCGTCGAATTCAAAAAGTACAA 58.261 29.630 28.29 0.00 40.77 2.41
158 159 8.844441 AATTCGTCGAATTCAAAAAGTACAAA 57.156 26.923 24.09 0.00 37.68 2.83
159 160 8.844441 ATTCGTCGAATTCAAAAAGTACAAAA 57.156 26.923 14.69 0.00 0.00 2.44
160 161 8.670804 TTCGTCGAATTCAAAAAGTACAAAAA 57.329 26.923 2.90 0.00 0.00 1.94
161 162 8.844441 TCGTCGAATTCAAAAAGTACAAAAAT 57.156 26.923 6.22 0.00 0.00 1.82
162 163 8.738554 TCGTCGAATTCAAAAAGTACAAAAATG 58.261 29.630 6.22 0.00 0.00 2.32
163 164 8.528295 CGTCGAATTCAAAAAGTACAAAAATGT 58.472 29.630 6.22 0.00 0.00 2.71
204 205 5.441500 ACGATCATGAGAGAGAGGACTAAA 58.558 41.667 0.09 0.00 0.00 1.85
254 255 2.224606 CTCTTCACCAAGTGTGTGCAT 58.775 47.619 0.00 0.00 45.61 3.96
309 310 2.464157 TGATATGTTGCACACGGTCA 57.536 45.000 0.00 0.00 0.00 4.02
310 311 2.984562 TGATATGTTGCACACGGTCAT 58.015 42.857 0.00 0.00 0.00 3.06
321 322 5.182487 TGCACACGGTCATAGAATGTAAAT 58.818 37.500 0.00 0.00 0.00 1.40
365 367 3.555527 TGAATTCTCTGAGATGCCTGG 57.444 47.619 8.42 0.00 0.00 4.45
370 372 2.042404 CTCTGAGATGCCTGGCTCCC 62.042 65.000 21.03 8.71 0.00 4.30
454 456 5.403897 TTCACTTAGTTTGAGCTCGTTTG 57.596 39.130 9.64 0.00 0.00 2.93
485 487 2.867624 TGAATTGAGCTGAGCCAACTT 58.132 42.857 0.00 2.63 0.00 2.66
649 651 3.567164 CACCCAAAGCAGACATCATATCC 59.433 47.826 0.00 0.00 0.00 2.59
656 658 5.057843 AGCAGACATCATATCCCATGTTT 57.942 39.130 0.00 0.00 33.22 2.83
657 659 5.068636 AGCAGACATCATATCCCATGTTTC 58.931 41.667 0.00 0.00 33.22 2.78
658 660 4.823442 GCAGACATCATATCCCATGTTTCA 59.177 41.667 0.00 0.00 33.22 2.69
659 661 5.300034 GCAGACATCATATCCCATGTTTCAA 59.700 40.000 0.00 0.00 33.22 2.69
660 662 6.183360 GCAGACATCATATCCCATGTTTCAAA 60.183 38.462 0.00 0.00 33.22 2.69
661 663 7.198390 CAGACATCATATCCCATGTTTCAAAC 58.802 38.462 0.00 0.00 33.22 2.93
662 664 7.067859 CAGACATCATATCCCATGTTTCAAACT 59.932 37.037 1.10 0.00 33.22 2.66
663 665 8.274322 AGACATCATATCCCATGTTTCAAACTA 58.726 33.333 1.10 0.00 33.22 2.24
664 666 8.455903 ACATCATATCCCATGTTTCAAACTAG 57.544 34.615 1.10 0.00 28.27 2.57
665 667 6.942532 TCATATCCCATGTTTCAAACTAGC 57.057 37.500 1.10 0.00 0.00 3.42
666 668 6.422333 TCATATCCCATGTTTCAAACTAGCA 58.578 36.000 1.10 0.00 0.00 3.49
667 669 7.062322 TCATATCCCATGTTTCAAACTAGCAT 58.938 34.615 1.10 0.00 0.00 3.79
668 670 5.841957 ATCCCATGTTTCAAACTAGCATC 57.158 39.130 1.10 0.00 0.00 3.91
669 671 4.016444 TCCCATGTTTCAAACTAGCATCC 58.984 43.478 1.10 0.00 0.00 3.51
670 672 3.763360 CCCATGTTTCAAACTAGCATCCA 59.237 43.478 1.10 0.00 0.00 3.41
671 673 4.220382 CCCATGTTTCAAACTAGCATCCAA 59.780 41.667 1.10 0.00 0.00 3.53
672 674 5.105228 CCCATGTTTCAAACTAGCATCCAAT 60.105 40.000 1.10 0.00 0.00 3.16
673 675 6.400568 CCATGTTTCAAACTAGCATCCAATT 58.599 36.000 1.10 0.00 0.00 2.32
674 676 6.875195 CCATGTTTCAAACTAGCATCCAATTT 59.125 34.615 1.10 0.00 0.00 1.82
675 677 7.388500 CCATGTTTCAAACTAGCATCCAATTTT 59.612 33.333 1.10 0.00 0.00 1.82
676 678 8.776470 CATGTTTCAAACTAGCATCCAATTTTT 58.224 29.630 1.10 0.00 0.00 1.94
677 679 8.364129 TGTTTCAAACTAGCATCCAATTTTTC 57.636 30.769 1.10 0.00 0.00 2.29
678 680 7.440856 TGTTTCAAACTAGCATCCAATTTTTCC 59.559 33.333 1.10 0.00 0.00 3.13
679 681 6.036577 TCAAACTAGCATCCAATTTTTCCC 57.963 37.500 0.00 0.00 0.00 3.97
680 682 5.046663 TCAAACTAGCATCCAATTTTTCCCC 60.047 40.000 0.00 0.00 0.00 4.81
681 683 3.374764 ACTAGCATCCAATTTTTCCCCC 58.625 45.455 0.00 0.00 0.00 5.40
728 730 2.848310 CGTTGTAACGCACGGGTC 59.152 61.111 4.08 0.00 46.06 4.46
729 731 2.660612 CGTTGTAACGCACGGGTCC 61.661 63.158 4.08 0.00 46.06 4.46
730 732 1.301165 GTTGTAACGCACGGGTCCT 60.301 57.895 0.00 0.00 0.00 3.85
731 733 0.881600 GTTGTAACGCACGGGTCCTT 60.882 55.000 0.00 0.00 0.00 3.36
732 734 0.179051 TTGTAACGCACGGGTCCTTT 60.179 50.000 0.00 0.00 0.00 3.11
733 735 0.179051 TGTAACGCACGGGTCCTTTT 60.179 50.000 0.00 0.00 0.00 2.27
734 736 0.236449 GTAACGCACGGGTCCTTTTG 59.764 55.000 0.00 0.00 0.00 2.44
735 737 1.508808 TAACGCACGGGTCCTTTTGC 61.509 55.000 0.00 0.00 0.00 3.68
736 738 2.978010 CGCACGGGTCCTTTTGCT 60.978 61.111 7.88 0.00 32.56 3.91
737 739 1.669760 CGCACGGGTCCTTTTGCTA 60.670 57.895 7.88 0.00 32.56 3.49
738 740 1.635663 CGCACGGGTCCTTTTGCTAG 61.636 60.000 7.88 0.00 32.56 3.42
787 791 7.081976 ACAAAATCAAACTTATAACGGCTGAC 58.918 34.615 0.00 0.00 0.00 3.51
844 848 9.712410 CAAATTCGTCGAATTCAAAAAGTAATG 57.288 29.630 28.29 16.89 40.77 1.90
845 849 9.672086 AAATTCGTCGAATTCAAAAAGTAATGA 57.328 25.926 28.29 0.00 40.77 2.57
846 850 8.880768 ATTCGTCGAATTCAAAAAGTAATGAG 57.119 30.769 14.69 0.00 0.00 2.90
847 851 6.827641 TCGTCGAATTCAAAAAGTAATGAGG 58.172 36.000 6.22 0.00 0.00 3.86
902 908 2.814336 GCCATTTTGTTTCTCCGTCTCT 59.186 45.455 0.00 0.00 0.00 3.10
1246 1262 0.460109 GGCATGGTTGGAATTTCGCC 60.460 55.000 0.00 0.00 0.00 5.54
1485 1501 3.857549 GAAGGCATTCCCTCAGAAAAC 57.142 47.619 0.00 0.00 45.62 2.43
1493 1509 0.322906 CCCTCAGAAAACCAGGAGGC 60.323 60.000 0.00 0.00 44.45 4.70
1530 1546 2.940514 TCCATAAGAGACCCACTGGA 57.059 50.000 0.00 0.00 34.81 3.86
1627 1643 7.288560 TGTTATGGTTTAAGAAGGTAACACCA 58.711 34.615 0.00 0.00 41.95 4.17
1632 1648 7.288560 TGGTTTAAGAAGGTAACACCATAACA 58.711 34.615 0.00 0.00 41.95 2.41
1637 1653 6.038997 AGAAGGTAACACCATAACAGACTC 57.961 41.667 0.00 0.00 41.95 3.36
1672 1688 4.391830 TCTTGCAGGTTGCTATTTTACTCG 59.608 41.667 2.48 0.00 45.31 4.18
1682 1698 8.114905 GGTTGCTATTTTACTCGTTAGTTGATC 58.885 37.037 0.00 0.00 37.15 2.92
1683 1699 8.870879 GTTGCTATTTTACTCGTTAGTTGATCT 58.129 33.333 0.00 0.00 37.15 2.75
1930 1947 3.196469 TGGATACAGGAGCTCTTGTTCTG 59.804 47.826 33.02 22.67 46.17 3.02
2053 2070 2.170397 TCACATTGCATCACGGGACTAT 59.830 45.455 0.00 0.00 0.00 2.12
2069 2086 5.057149 GGGACTATGCGACTTGTCAATATT 58.943 41.667 1.59 0.00 0.00 1.28
2430 2447 3.420893 TGACTTGCTTCCCCTAATGTTG 58.579 45.455 0.00 0.00 0.00 3.33
2453 2476 6.143206 TGTCTGACTTCCTTGGATATCCATA 58.857 40.000 25.07 14.39 46.97 2.74
2889 2926 7.049799 TGTGCTTCATTTTTAGGCTTTTAGT 57.950 32.000 0.00 0.00 0.00 2.24
3060 3097 8.215050 TGTTGAGTTTGTTAAGAATTAGGAGGA 58.785 33.333 0.00 0.00 0.00 3.71
3109 3146 9.569122 ACAACTGTCAATAGTACTGGTATTTTT 57.431 29.630 5.39 0.00 0.00 1.94
3509 3559 6.082491 GGACTTATTCCCAATTTGGCACAAC 61.082 44.000 10.10 0.00 40.89 3.32
3672 3722 6.363577 TGCGAGGAATTGTCTTTCATAATC 57.636 37.500 0.00 0.00 0.00 1.75
3813 3865 9.959721 ATTTGGTCATCTTGTACTTTAGTGTAT 57.040 29.630 0.00 0.00 0.00 2.29
3814 3866 8.771920 TTGGTCATCTTGTACTTTAGTGTATG 57.228 34.615 0.00 0.00 0.00 2.39
3869 3921 3.138283 TCCCTGTTGGTTCTCATCAACTT 59.862 43.478 0.00 0.00 42.48 2.66
3899 3951 2.424246 GGAGAGTGAGGAAGAGGTAACG 59.576 54.545 0.00 0.00 46.39 3.18
4214 4266 3.055602 TGCTCTCTGCTCTGCTTTCATTA 60.056 43.478 0.00 0.00 43.37 1.90
4244 4296 1.937191 AGCACCTTAACCAAATGGGG 58.063 50.000 4.17 0.00 42.91 4.96
4260 4312 6.405842 CCAAATGGGGAACATAAACTCTTAGC 60.406 42.308 0.00 0.00 39.40 3.09
4778 4831 5.671493 CCGAAGTAGGAGAAACATATGGTT 58.329 41.667 5.47 5.47 42.98 3.67
5327 5384 4.941713 ACACTCTCAAGTTCCCTATCTCT 58.058 43.478 0.00 0.00 31.71 3.10
5381 5438 6.174720 TGAAACCTGAAGTGAGTAAGTCAT 57.825 37.500 0.00 0.00 37.56 3.06
5404 5461 3.068165 TCGCAGTAGTATCCATGAACCTG 59.932 47.826 0.00 0.00 0.00 4.00
5568 5625 7.121315 GCAGTTCCTTCCTTGTATAGTTTGATT 59.879 37.037 0.00 0.00 0.00 2.57
5749 5812 3.784701 AGTCTTACACGAGATGCGATT 57.215 42.857 0.00 0.00 44.57 3.34
5811 5931 3.034635 CCTCTCACAATACCTACAGGCT 58.965 50.000 0.00 0.00 39.32 4.58
6175 6295 5.813383 ACTATTGCCAGCATGCTTATAGAT 58.187 37.500 26.64 17.62 34.06 1.98
6181 6301 3.306294 CCAGCATGCTTATAGATGTCCGA 60.306 47.826 19.98 0.00 31.97 4.55
6287 6407 2.125753 GGTGCTCCGCTGTCTCAG 60.126 66.667 0.00 0.00 34.12 3.35
6486 6606 2.096248 TGTTTGAACGGTGAAAGCCTT 58.904 42.857 0.00 0.00 0.00 4.35
6581 6703 2.028476 TGTAACTGCAGAACCTATGCGT 60.028 45.455 23.35 0.00 46.87 5.24
6588 6710 2.419574 GCAGAACCTATGCGTTCCCTTA 60.420 50.000 3.78 0.00 42.63 2.69
6595 6717 1.609208 ATGCGTTCCCTTATGGATGC 58.391 50.000 0.00 0.00 44.66 3.91
6652 6778 2.217429 TTTTCAACGGAGGCAAAAGC 57.783 45.000 0.00 0.00 0.00 3.51
6654 6780 1.398692 TTCAACGGAGGCAAAAGCTT 58.601 45.000 0.00 0.00 0.00 3.74
6655 6781 1.398692 TCAACGGAGGCAAAAGCTTT 58.601 45.000 5.69 5.69 0.00 3.51
6656 6782 1.066908 TCAACGGAGGCAAAAGCTTTG 59.933 47.619 13.54 8.26 0.00 2.77
6668 6794 5.418676 GCAAAAGCTTTGCCTTATCCATTA 58.581 37.500 13.54 0.00 39.38 1.90
6669 6795 5.874261 GCAAAAGCTTTGCCTTATCCATTAA 59.126 36.000 13.54 0.00 39.38 1.40
6736 6900 0.322456 CTCCGGCAATGACCCAAAGA 60.322 55.000 0.00 0.00 0.00 2.52
6755 6919 2.026822 AGATTTGCCTCGGTGAAGATGT 60.027 45.455 0.00 0.00 0.00 3.06
6780 6944 2.354729 CAAGATTGGCGGTGGGGA 59.645 61.111 0.00 0.00 0.00 4.81
6781 6945 2.046285 CAAGATTGGCGGTGGGGAC 61.046 63.158 0.00 0.00 0.00 4.46
6782 6946 2.534396 AAGATTGGCGGTGGGGACA 61.534 57.895 0.00 0.00 38.70 4.02
6830 6994 3.057174 TGTTTCGCTTGTTCCAAACTGTT 60.057 39.130 0.00 0.00 31.29 3.16
6852 7016 4.026052 TCAAGAGACTAGCATGGTGATGA 58.974 43.478 7.89 0.00 0.00 2.92
6881 7045 2.745906 CTTGTTGATTTGGCGCGCCA 62.746 55.000 46.88 46.88 45.63 5.69
6919 7083 1.663695 CACCACTCTTCAACCGTGTT 58.336 50.000 0.00 0.00 0.00 3.32
6939 7103 1.341482 TGAACAAGGGCCACACAGAAA 60.341 47.619 6.18 0.00 0.00 2.52
7073 7240 0.108709 CATCACAATTTGGCCACCCG 60.109 55.000 3.88 0.00 0.00 5.28
7118 7285 3.070159 TCCAGATTCTATCTTGAAGGGCG 59.930 47.826 0.00 0.00 37.58 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.674997 TGCCTAGAATATTGGGAATCGC 58.325 45.455 0.00 0.00 0.00 4.58
19 20 6.772716 ACTACCACAAATGCCTAGAATATTGG 59.227 38.462 0.00 0.00 0.00 3.16
20 21 7.807977 ACTACCACAAATGCCTAGAATATTG 57.192 36.000 0.00 0.00 0.00 1.90
21 22 7.937394 GGTACTACCACAAATGCCTAGAATATT 59.063 37.037 0.00 0.00 38.42 1.28
29 30 5.508280 TTTAGGTACTACCACAAATGCCT 57.492 39.130 8.01 0.00 42.67 4.75
77 78 5.181622 TGTCGGCCGTTATAAGTTTGATTTT 59.818 36.000 27.15 0.00 0.00 1.82
78 79 4.696402 TGTCGGCCGTTATAAGTTTGATTT 59.304 37.500 27.15 0.00 0.00 2.17
79 80 4.255301 TGTCGGCCGTTATAAGTTTGATT 58.745 39.130 27.15 0.00 0.00 2.57
80 81 3.864243 TGTCGGCCGTTATAAGTTTGAT 58.136 40.909 27.15 0.00 0.00 2.57
81 82 3.316071 TGTCGGCCGTTATAAGTTTGA 57.684 42.857 27.15 0.00 0.00 2.69
82 83 4.399978 CTTTGTCGGCCGTTATAAGTTTG 58.600 43.478 27.15 2.61 0.00 2.93
83 84 3.120095 GCTTTGTCGGCCGTTATAAGTTT 60.120 43.478 27.15 0.00 0.00 2.66
84 85 2.417586 GCTTTGTCGGCCGTTATAAGTT 59.582 45.455 27.15 0.00 0.00 2.66
85 86 2.004733 GCTTTGTCGGCCGTTATAAGT 58.995 47.619 27.15 0.00 0.00 2.24
86 87 2.004017 TGCTTTGTCGGCCGTTATAAG 58.996 47.619 27.15 22.53 0.00 1.73
87 88 2.096220 TGCTTTGTCGGCCGTTATAA 57.904 45.000 27.15 8.64 0.00 0.98
88 89 2.096220 TTGCTTTGTCGGCCGTTATA 57.904 45.000 27.15 1.49 0.00 0.98
89 90 1.240256 TTTGCTTTGTCGGCCGTTAT 58.760 45.000 27.15 0.00 0.00 1.89
90 91 1.022735 TTTTGCTTTGTCGGCCGTTA 58.977 45.000 27.15 12.81 0.00 3.18
91 92 0.387565 ATTTTGCTTTGTCGGCCGTT 59.612 45.000 27.15 0.00 0.00 4.44
92 93 0.039527 GATTTTGCTTTGTCGGCCGT 60.040 50.000 27.15 0.00 0.00 5.68
93 94 0.039617 TGATTTTGCTTTGTCGGCCG 60.040 50.000 22.12 22.12 0.00 6.13
94 95 2.368655 ATGATTTTGCTTTGTCGGCC 57.631 45.000 0.00 0.00 0.00 6.13
95 96 6.407475 AAATTATGATTTTGCTTTGTCGGC 57.593 33.333 0.00 0.00 31.48 5.54
106 107 9.039870 TGAAGCGTGTTTCAAAATTATGATTTT 57.960 25.926 2.50 2.50 44.24 1.82
107 108 8.586570 TGAAGCGTGTTTCAAAATTATGATTT 57.413 26.923 0.00 0.00 37.06 2.17
108 109 8.586570 TTGAAGCGTGTTTCAAAATTATGATT 57.413 26.923 9.07 0.00 42.39 2.57
118 119 4.022464 ACGAATTTGAAGCGTGTTTCAA 57.978 36.364 7.65 7.65 43.32 2.69
119 120 3.613563 GACGAATTTGAAGCGTGTTTCA 58.386 40.909 0.00 0.00 38.51 2.69
120 121 2.645647 CGACGAATTTGAAGCGTGTTTC 59.354 45.455 0.00 0.00 38.51 2.78
121 122 2.285756 TCGACGAATTTGAAGCGTGTTT 59.714 40.909 0.00 0.00 38.51 2.83
122 123 1.862201 TCGACGAATTTGAAGCGTGTT 59.138 42.857 0.00 0.00 38.51 3.32
123 124 1.493772 TCGACGAATTTGAAGCGTGT 58.506 45.000 0.00 0.00 38.51 4.49
124 125 2.570468 TTCGACGAATTTGAAGCGTG 57.430 45.000 6.10 0.00 38.51 5.34
125 126 3.185594 TGAATTCGACGAATTTGAAGCGT 59.814 39.130 30.50 11.35 41.56 5.07
126 127 3.731855 TGAATTCGACGAATTTGAAGCG 58.268 40.909 30.50 0.74 41.56 4.68
127 128 6.432802 TTTTGAATTCGACGAATTTGAAGC 57.567 33.333 30.50 19.98 41.56 3.86
128 129 8.050121 ACTTTTTGAATTCGACGAATTTGAAG 57.950 30.769 30.50 27.78 41.56 3.02
129 130 7.979115 ACTTTTTGAATTCGACGAATTTGAA 57.021 28.000 30.50 24.34 41.56 2.69
130 131 8.123575 TGTACTTTTTGAATTCGACGAATTTGA 58.876 29.630 30.50 20.96 41.56 2.69
131 132 8.264022 TGTACTTTTTGAATTCGACGAATTTG 57.736 30.769 30.50 19.53 41.56 2.32
132 133 8.844441 TTGTACTTTTTGAATTCGACGAATTT 57.156 26.923 30.50 18.22 41.56 1.82
133 134 8.844441 TTTGTACTTTTTGAATTCGACGAATT 57.156 26.923 30.43 30.43 43.77 2.17
134 135 8.844441 TTTTGTACTTTTTGAATTCGACGAAT 57.156 26.923 17.19 17.19 33.25 3.34
135 136 8.670804 TTTTTGTACTTTTTGAATTCGACGAA 57.329 26.923 13.48 13.48 0.00 3.85
136 137 8.738554 CATTTTTGTACTTTTTGAATTCGACGA 58.261 29.630 0.04 0.00 0.00 4.20
137 138 8.528295 ACATTTTTGTACTTTTTGAATTCGACG 58.472 29.630 0.04 0.00 0.00 5.12
225 226 4.080863 ACACTTGGTGAAGAGCCCTTATAG 60.081 45.833 4.62 0.00 36.96 1.31
347 349 1.845143 AGCCAGGCATCTCAGAGAATT 59.155 47.619 15.80 0.00 0.00 2.17
365 367 3.491267 CGATCTCGAGTAAAAATGGGAGC 59.509 47.826 13.13 0.00 43.02 4.70
370 372 6.895040 GCTTGTAACGATCTCGAGTAAAAATG 59.105 38.462 13.13 0.00 43.02 2.32
454 456 7.381678 GGCTCAGCTCAATTCATATGAAAATTC 59.618 37.037 21.50 10.21 37.61 2.17
649 651 5.389859 TTGGATGCTAGTTTGAAACATGG 57.610 39.130 11.02 1.19 0.00 3.66
656 658 5.046663 GGGGAAAAATTGGATGCTAGTTTGA 60.047 40.000 0.00 0.00 0.00 2.69
657 659 5.178061 GGGGAAAAATTGGATGCTAGTTTG 58.822 41.667 0.00 0.00 0.00 2.93
658 660 4.225042 GGGGGAAAAATTGGATGCTAGTTT 59.775 41.667 0.00 0.00 0.00 2.66
659 661 3.774766 GGGGGAAAAATTGGATGCTAGTT 59.225 43.478 0.00 0.00 0.00 2.24
660 662 3.374764 GGGGGAAAAATTGGATGCTAGT 58.625 45.455 0.00 0.00 0.00 2.57
678 680 3.317455 TTGATGGATCAATTGAGGGGG 57.683 47.619 14.54 0.00 41.51 5.40
712 714 0.881600 AAGGACCCGTGCGTTACAAC 60.882 55.000 0.00 0.00 0.00 3.32
713 715 0.179051 AAAGGACCCGTGCGTTACAA 60.179 50.000 0.00 0.00 0.00 2.41
714 716 0.179051 AAAAGGACCCGTGCGTTACA 60.179 50.000 0.00 0.00 0.00 2.41
715 717 0.236449 CAAAAGGACCCGTGCGTTAC 59.764 55.000 0.00 0.00 0.00 2.50
716 718 1.508808 GCAAAAGGACCCGTGCGTTA 61.509 55.000 0.00 0.00 0.00 3.18
717 719 2.841160 GCAAAAGGACCCGTGCGTT 61.841 57.895 0.00 0.00 0.00 4.84
718 720 2.386064 TAGCAAAAGGACCCGTGCGT 62.386 55.000 6.11 0.00 41.90 5.24
719 721 1.635663 CTAGCAAAAGGACCCGTGCG 61.636 60.000 6.11 0.00 41.90 5.34
720 722 0.605589 ACTAGCAAAAGGACCCGTGC 60.606 55.000 3.92 3.92 37.26 5.34
721 723 1.892209 AACTAGCAAAAGGACCCGTG 58.108 50.000 0.00 0.00 0.00 4.94
722 724 3.994931 ATAACTAGCAAAAGGACCCGT 57.005 42.857 0.00 0.00 0.00 5.28
723 725 4.514401 AGAATAACTAGCAAAAGGACCCG 58.486 43.478 0.00 0.00 0.00 5.28
724 726 7.933215 TTAAGAATAACTAGCAAAAGGACCC 57.067 36.000 0.00 0.00 0.00 4.46
760 762 8.138712 TCAGCCGTTATAAGTTTGATTTTGTTT 58.861 29.630 0.00 0.00 0.00 2.83
844 848 0.032267 GTACCTAGCCGTGATGCCTC 59.968 60.000 0.00 0.00 0.00 4.70
845 849 0.686441 TGTACCTAGCCGTGATGCCT 60.686 55.000 0.00 0.00 0.00 4.75
846 850 0.177141 TTGTACCTAGCCGTGATGCC 59.823 55.000 0.00 0.00 0.00 4.40
847 851 2.240493 ATTGTACCTAGCCGTGATGC 57.760 50.000 0.00 0.00 0.00 3.91
1246 1262 1.693083 GCCATTCCCGAAGACGAACG 61.693 60.000 0.00 0.00 42.66 3.95
1493 1509 1.740025 GGAAAATGCAGTCGGAGAAGG 59.260 52.381 0.00 0.00 39.69 3.46
1627 1643 4.011023 AGCACACGACTAGAGTCTGTTAT 58.989 43.478 1.86 1.08 42.66 1.89
1632 1648 2.483014 AGAGCACACGACTAGAGTCT 57.517 50.000 8.01 0.00 42.66 3.24
1672 1688 7.868415 AGTAACAACAGAGTCAGATCAACTAAC 59.132 37.037 0.00 0.00 0.00 2.34
1682 1698 2.224281 TGCCCAGTAACAACAGAGTCAG 60.224 50.000 0.00 0.00 0.00 3.51
1683 1699 1.765904 TGCCCAGTAACAACAGAGTCA 59.234 47.619 0.00 0.00 0.00 3.41
1930 1947 6.970484 ACGGCAAGTTTTATCATGGAATATC 58.030 36.000 0.00 0.00 0.00 1.63
2053 2070 6.682423 ATCATCAAATATTGACAAGTCGCA 57.318 33.333 0.00 0.00 43.48 5.10
2889 2926 9.352784 GCTTTTGTTGCATATAGTTCATTACAA 57.647 29.630 0.00 0.00 0.00 2.41
3509 3559 1.719709 CTGATGGCATGTCACGCAG 59.280 57.895 15.12 15.12 0.00 5.18
3845 3897 3.140325 TGATGAGAACCAACAGGGAAC 57.860 47.619 0.00 0.00 41.15 3.62
3869 3921 6.070538 CCTCTTCCTCACTCTCCTGAAAATAA 60.071 42.308 0.00 0.00 0.00 1.40
3899 3951 0.178068 TTTCAGCCTGCTCGGTATCC 59.822 55.000 0.00 0.00 34.25 2.59
4068 4120 3.327172 AGGAACATATCTGCAGAGGGATG 59.673 47.826 22.96 23.69 0.00 3.51
4166 4218 7.603024 AGATTTTAACCTCTTTCGACGAAGATT 59.397 33.333 10.61 5.06 35.27 2.40
4214 4266 7.833285 TTGGTTAAGGTGCTTTAGAAGAAAT 57.167 32.000 0.00 0.00 0.00 2.17
4244 4296 7.042389 GGAGTAGCATGCTAAGAGTTTATGTTC 60.042 40.741 28.44 11.46 0.00 3.18
4260 4312 6.446781 ACATTGAAGATTTGGAGTAGCATG 57.553 37.500 0.00 0.00 0.00 4.06
4931 4984 5.123227 TCCTTCCGAATAAATTACTGCCAG 58.877 41.667 0.00 0.00 0.00 4.85
5048 5101 9.658475 TGAAACGAATAAGTACAGAATTGTTTG 57.342 29.630 10.14 1.65 38.76 2.93
5381 5438 3.704566 AGGTTCATGGATACTACTGCGAA 59.295 43.478 0.00 0.00 37.61 4.70
5404 5461 2.244695 CCCAACCCCAAGTTTAGTTCC 58.755 52.381 0.00 0.00 36.18 3.62
5568 5625 6.000840 TGGTTGTTAGATGATTGTGCAGTTA 58.999 36.000 0.00 0.00 0.00 2.24
5749 5812 7.473735 TTTTGGTCACATTAATATTCCTGCA 57.526 32.000 0.00 0.00 0.00 4.41
5811 5931 8.976471 CACAATTGGCATCGCATTAATATTTTA 58.024 29.630 10.83 0.00 0.00 1.52
5824 5944 4.359971 TCTGATTTCACAATTGGCATCG 57.640 40.909 10.83 3.21 0.00 3.84
5946 6066 4.115516 CGGTTGTCATGAGGTCAATAGAG 58.884 47.826 0.00 0.00 0.00 2.43
5948 6068 4.115516 CTCGGTTGTCATGAGGTCAATAG 58.884 47.826 0.00 0.00 0.00 1.73
6175 6295 3.706373 GCCCAGAAGCCTCGGACA 61.706 66.667 0.00 0.00 0.00 4.02
6311 6431 1.299541 CTACAATAACGCAGGCAGGG 58.700 55.000 0.00 0.00 0.00 4.45
6486 6606 9.079833 GCGTTCAAGTAAATACTTCACATACTA 57.920 33.333 2.88 0.00 44.19 1.82
6588 6710 5.012046 TCAGGTACAAATAGATCGCATCCAT 59.988 40.000 0.00 0.00 0.00 3.41
6595 6717 7.800380 GCAAATTCATCAGGTACAAATAGATCG 59.200 37.037 0.00 0.00 0.00 3.69
6668 6794 7.644551 CGCGAGTAACTGTATTCTCTCTTATTT 59.355 37.037 0.00 0.00 0.00 1.40
6669 6795 7.133513 CGCGAGTAACTGTATTCTCTCTTATT 58.866 38.462 0.00 0.00 0.00 1.40
6736 6900 2.496899 ACATCTTCACCGAGGCAAAT 57.503 45.000 0.00 0.00 0.00 2.32
6755 6919 1.083489 CCGCCAATCTTGCTTTCGTA 58.917 50.000 0.00 0.00 0.00 3.43
6780 6944 8.879427 AGGGTTTTTAAGCATAATAAGAGTGT 57.121 30.769 0.00 0.00 0.00 3.55
6788 6952 9.581099 CGAAACATAAGGGTTTTTAAGCATAAT 57.419 29.630 0.00 0.00 40.85 1.28
6830 6994 4.026052 TCATCACCATGCTAGTCTCTTGA 58.974 43.478 0.00 0.00 0.00 3.02
6852 7016 1.720781 AATCAACAAGCCAAGGCCTT 58.279 45.000 13.78 13.78 43.17 4.35
6881 7045 2.956987 GCAAGCACTTGTGCCGAT 59.043 55.556 20.39 6.34 42.31 4.18
6887 7051 2.278404 TGGTGGGCAAGCACTTGT 59.722 55.556 11.77 0.00 42.31 3.16
6919 7083 0.257328 TTCTGTGTGGCCCTTGTTCA 59.743 50.000 0.00 0.00 0.00 3.18
6939 7103 2.107750 CATGCTCGGGCTCGACAT 59.892 61.111 3.45 11.50 40.88 3.06
7073 7240 1.668047 GCAGACAGATTGGCAAAGTGC 60.668 52.381 3.01 3.67 44.08 4.40
7210 7393 2.970639 GCAGTGGGCAGTACTCGA 59.029 61.111 0.00 0.00 43.97 4.04


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

AutoCloner maintained by Alex Coulton.