Multiple sequence alignment - TraesCS4A01G333000

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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 TraesCS4A01G333000 chr4A 100.000 3469 0 0 1 3469 616898536 616895068 0.000000e+00 6407.0
1 TraesCS4A01G333000 chr4A 78.615 491 94 9 1712 2195 616229886 616229400 7.230000e-82 315.0
2 TraesCS4A01G333000 chr4A 76.449 552 88 28 1043 1558 616885943 616885398 9.550000e-66 261.0
3 TraesCS4A01G333000 chr5D 88.111 2170 175 48 85 2200 551056660 551058800 0.000000e+00 2501.0
4 TraesCS4A01G333000 chr5D 87.962 731 71 12 2306 3026 551058894 551059617 0.000000e+00 846.0
5 TraesCS4A01G333000 chr5D 87.709 659 62 9 989 1646 543503744 543503104 0.000000e+00 750.0
6 TraesCS4A01G333000 chr5D 90.071 564 54 2 1638 2200 543503148 543502586 0.000000e+00 730.0
7 TraesCS4A01G333000 chr5D 89.130 368 37 2 3044 3409 543501206 543500840 4.080000e-124 455.0
8 TraesCS4A01G333000 chr5D 89.790 333 23 6 2704 3026 543502125 543501794 1.930000e-112 416.0
9 TraesCS4A01G333000 chr5D 77.796 617 108 18 1030 1624 552422783 552422174 1.530000e-93 353.0
10 TraesCS4A01G333000 chr5D 79.691 453 82 9 1742 2186 552422095 552421645 5.590000e-83 318.0
11 TraesCS4A01G333000 chr5D 96.226 159 5 1 3019 3177 551060213 551060370 3.430000e-65 259.0
12 TraesCS4A01G333000 chr5D 74.677 620 94 29 1041 1606 551336839 551337449 2.100000e-52 217.0
13 TraesCS4A01G333000 chr5D 81.553 103 10 3 1336 1429 543536472 543536370 3.710000e-10 76.8
14 TraesCS4A01G333000 chr5D 90.385 52 5 0 2201 2252 551058841 551058892 6.210000e-08 69.4
15 TraesCS4A01G333000 chr5B 84.346 856 98 13 2198 3026 685321903 685321057 0.000000e+00 806.0
16 TraesCS4A01G333000 chr5B 89.252 642 66 2 1005 1646 685323092 685322454 0.000000e+00 800.0
17 TraesCS4A01G333000 chr5B 88.785 642 69 2 1005 1646 685503751 685504389 0.000000e+00 784.0
18 TraesCS4A01G333000 chr5B 89.803 559 55 2 1643 2200 685504350 685504907 0.000000e+00 715.0
19 TraesCS4A01G333000 chr5B 88.948 561 60 2 1641 2200 685322495 685321936 0.000000e+00 691.0
20 TraesCS4A01G333000 chr5B 83.710 620 59 14 2200 2807 685504945 685505534 6.550000e-152 547.0
21 TraesCS4A01G333000 chr5B 75.563 1199 214 45 1038 2198 700237576 700236419 5.130000e-143 518.0
22 TraesCS4A01G333000 chr5B 87.834 337 32 7 3078 3409 685320511 685320179 1.510000e-103 387.0
23 TraesCS4A01G333000 chr5B 87.834 337 32 7 3078 3409 685506093 685506425 1.510000e-103 387.0
24 TraesCS4A01G333000 chr5B 76.155 541 97 24 1043 1558 699354084 699354617 4.440000e-64 255.0
25 TraesCS4A01G333000 chr5B 79.822 337 66 2 1865 2200 685444523 685444858 9.620000e-61 244.0
26 TraesCS4A01G333000 chr5B 75.126 595 110 22 988 1558 703488438 703489018 9.620000e-61 244.0
27 TraesCS4A01G333000 chr5B 79.641 334 66 2 1868 2200 685422084 685421752 4.470000e-59 239.0
28 TraesCS4A01G333000 chr5B 76.409 479 76 21 974 1429 699597055 699597519 1.250000e-54 224.0
29 TraesCS4A01G333000 chr5B 82.857 140 19 5 2564 2701 685501173 685501309 1.690000e-23 121.0
30 TraesCS4A01G333000 chr5B 78.621 145 22 7 1469 1610 700007470 700007608 1.720000e-13 87.9
31 TraesCS4A01G333000 chr5B 87.097 62 8 0 2847 2908 677749610 677749549 1.730000e-08 71.3
32 TraesCS4A01G333000 chr1D 80.193 621 87 18 1009 1610 22968957 22968354 1.910000e-117 433.0
33 TraesCS4A01G333000 chr1B 79.435 637 93 24 998 1610 39517735 39517113 1.930000e-112 416.0
34 TraesCS4A01G333000 chr1B 77.247 523 86 18 1030 1522 115748992 115749511 3.410000e-70 276.0
35 TraesCS4A01G333000 chr1B 78.125 416 87 4 1782 2195 327488145 327488558 9.550000e-66 261.0
36 TraesCS4A01G333000 chr7D 77.593 482 79 17 1728 2196 22655231 22655696 7.380000e-67 265.0
37 TraesCS4A01G333000 chr1A 77.961 304 48 13 1324 1610 24152015 24151714 4.600000e-39 172.0
38 TraesCS4A01G333000 chr4B 100.000 28 0 0 1004 1031 657170553 657170580 6.000000e-03 52.8


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 TraesCS4A01G333000 chr4A 616895068 616898536 3468 True 6407.00 6407 100.0000 1 3469 1 chr4A.!!$R3 3468
1 TraesCS4A01G333000 chr4A 616885398 616885943 545 True 261.00 261 76.4490 1043 1558 1 chr4A.!!$R2 515
2 TraesCS4A01G333000 chr5D 551056660 551060370 3710 False 918.85 2501 90.6710 85 3177 4 chr5D.!!$F2 3092
3 TraesCS4A01G333000 chr5D 543500840 543503744 2904 True 587.75 750 89.1750 989 3409 4 chr5D.!!$R2 2420
4 TraesCS4A01G333000 chr5D 552421645 552422783 1138 True 335.50 353 78.7435 1030 2186 2 chr5D.!!$R3 1156
5 TraesCS4A01G333000 chr5D 551336839 551337449 610 False 217.00 217 74.6770 1041 1606 1 chr5D.!!$F1 565
6 TraesCS4A01G333000 chr5B 685320179 685323092 2913 True 671.00 806 87.5950 1005 3409 4 chr5B.!!$R4 2404
7 TraesCS4A01G333000 chr5B 700236419 700237576 1157 True 518.00 518 75.5630 1038 2198 1 chr5B.!!$R3 1160
8 TraesCS4A01G333000 chr5B 685501173 685506425 5252 False 510.80 784 86.5978 1005 3409 5 chr5B.!!$F6 2404
9 TraesCS4A01G333000 chr5B 699354084 699354617 533 False 255.00 255 76.1550 1043 1558 1 chr5B.!!$F2 515
10 TraesCS4A01G333000 chr5B 703488438 703489018 580 False 244.00 244 75.1260 988 1558 1 chr5B.!!$F5 570
11 TraesCS4A01G333000 chr1D 22968354 22968957 603 True 433.00 433 80.1930 1009 1610 1 chr1D.!!$R1 601
12 TraesCS4A01G333000 chr1B 39517113 39517735 622 True 416.00 416 79.4350 998 1610 1 chr1B.!!$R1 612
13 TraesCS4A01G333000 chr1B 115748992 115749511 519 False 276.00 276 77.2470 1030 1522 1 chr1B.!!$F1 492

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
326 329 0.030807 TAGTAGGGTAGGGTTGGGGC 60.031 60.0 0.00 0.00 0.00 5.80 F
529 542 0.039617 CGCTCGAGCTCCCTTCTATG 60.040 60.0 32.88 11.25 39.32 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 3814 3.101437 TCCATAGCTTCTTCCACCGTAA 58.899 45.455 0.00 0.0 0.00 3.18 R
2517 4274 1.135199 CACTGATTGCAAGACCCATGC 60.135 52.381 4.94 0.0 44.08 4.06 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
20 21 3.928727 CAAGCACCATGATGACACTTT 57.071 42.857 0.00 0.00 0.00 2.66
22 23 4.726416 CAAGCACCATGATGACACTTTAC 58.274 43.478 0.00 0.00 0.00 2.01
23 24 4.019792 AGCACCATGATGACACTTTACA 57.980 40.909 0.00 0.00 0.00 2.41
24 25 4.397420 AGCACCATGATGACACTTTACAA 58.603 39.130 0.00 0.00 0.00 2.41
25 26 4.826733 AGCACCATGATGACACTTTACAAA 59.173 37.500 0.00 0.00 0.00 2.83
27 28 5.702865 CACCATGATGACACTTTACAAAGG 58.297 41.667 6.66 0.00 40.31 3.11
28 29 5.473162 CACCATGATGACACTTTACAAAGGA 59.527 40.000 6.66 0.00 40.31 3.36
30 31 5.392380 CCATGATGACACTTTACAAAGGAGC 60.392 44.000 6.66 0.00 40.31 4.70
31 32 4.713553 TGATGACACTTTACAAAGGAGCA 58.286 39.130 6.66 1.96 40.31 4.26
32 33 4.515191 TGATGACACTTTACAAAGGAGCAC 59.485 41.667 6.66 0.00 40.31 4.40
33 34 3.211045 TGACACTTTACAAAGGAGCACC 58.789 45.455 6.66 0.00 40.31 5.01
34 35 2.218603 ACACTTTACAAAGGAGCACCG 58.781 47.619 6.66 0.00 40.31 4.94
35 36 1.069227 CACTTTACAAAGGAGCACCGC 60.069 52.381 6.66 0.00 40.31 5.68
36 37 0.521735 CTTTACAAAGGAGCACCGCC 59.478 55.000 0.00 0.00 41.83 6.13
38 39 2.058125 TTACAAAGGAGCACCGCCCA 62.058 55.000 0.00 0.00 41.83 5.36
40 41 1.978617 CAAAGGAGCACCGCCCAAT 60.979 57.895 0.00 0.00 41.83 3.16
41 42 1.978617 AAAGGAGCACCGCCCAATG 60.979 57.895 0.00 0.00 41.83 2.82
42 43 2.713531 AAAGGAGCACCGCCCAATGT 62.714 55.000 0.00 0.00 41.83 2.71
43 44 2.676471 GGAGCACCGCCCAATGTT 60.676 61.111 0.00 0.00 0.00 2.71
45 46 1.971167 GAGCACCGCCCAATGTTGA 60.971 57.895 0.00 0.00 0.00 3.18
46 47 1.926511 GAGCACCGCCCAATGTTGAG 61.927 60.000 0.00 0.00 0.00 3.02
47 48 1.971167 GCACCGCCCAATGTTGAGA 60.971 57.895 0.00 0.00 0.00 3.27
49 50 0.240945 CACCGCCCAATGTTGAGAAC 59.759 55.000 0.00 0.00 0.00 3.01
50 51 0.893727 ACCGCCCAATGTTGAGAACC 60.894 55.000 0.00 0.00 0.00 3.62
52 53 0.240945 CGCCCAATGTTGAGAACCAC 59.759 55.000 0.00 0.00 0.00 4.16
53 54 0.603065 GCCCAATGTTGAGAACCACC 59.397 55.000 0.00 0.00 0.00 4.61
54 55 1.993956 CCCAATGTTGAGAACCACCA 58.006 50.000 0.00 0.00 0.00 4.17
55 56 2.528564 CCCAATGTTGAGAACCACCAT 58.471 47.619 0.00 0.00 28.28 3.55
56 57 2.231964 CCCAATGTTGAGAACCACCATG 59.768 50.000 0.00 0.00 27.74 3.66
57 58 2.231964 CCAATGTTGAGAACCACCATGG 59.768 50.000 11.19 11.19 45.02 3.66
66 67 4.722193 CCACCATGGTTTCGAGCT 57.278 55.556 16.84 0.00 31.35 4.09
67 68 2.174334 CCACCATGGTTTCGAGCTG 58.826 57.895 16.84 0.54 31.35 4.24
68 69 1.503542 CACCATGGTTTCGAGCTGC 59.496 57.895 16.84 0.00 0.00 5.25
70 71 0.957395 ACCATGGTTTCGAGCTGCAG 60.957 55.000 13.00 10.11 0.00 4.41
73 74 0.613260 ATGGTTTCGAGCTGCAGGTA 59.387 50.000 20.22 0.27 0.00 3.08
74 75 0.394938 TGGTTTCGAGCTGCAGGTAA 59.605 50.000 20.22 7.80 0.00 2.85
75 76 1.079503 GGTTTCGAGCTGCAGGTAAG 58.920 55.000 20.22 15.92 0.00 2.34
77 78 2.413837 GTTTCGAGCTGCAGGTAAGAA 58.586 47.619 23.83 23.83 0.00 2.52
78 79 2.080286 TTCGAGCTGCAGGTAAGAAC 57.920 50.000 23.83 10.78 0.00 3.01
118 119 0.535335 TTGTAGAGGCATCGACCACC 59.465 55.000 9.14 0.00 30.61 4.61
121 122 0.033503 TAGAGGCATCGACCACCAGA 60.034 55.000 0.00 0.00 0.00 3.86
129 130 2.762535 TCGACCACCAGAAGATTTCC 57.237 50.000 0.00 0.00 0.00 3.13
138 139 3.896888 ACCAGAAGATTTCCATTGTTGCA 59.103 39.130 0.00 0.00 0.00 4.08
145 146 7.386848 AGAAGATTTCCATTGTTGCAGAATTTG 59.613 33.333 0.00 0.00 0.00 2.32
149 150 7.475771 TTTCCATTGTTGCAGAATTTGTTAC 57.524 32.000 0.00 0.00 0.00 2.50
192 194 4.219944 ACGGAGCTTACATACAAAGACTCA 59.780 41.667 0.00 0.00 33.00 3.41
193 195 4.800993 CGGAGCTTACATACAAAGACTCAG 59.199 45.833 0.00 0.00 33.00 3.35
194 196 5.112686 GGAGCTTACATACAAAGACTCAGG 58.887 45.833 0.00 0.00 33.00 3.86
212 214 5.905913 ACTCAGGTAGTTTCAGGGCTTATAT 59.094 40.000 0.00 0.00 33.35 0.86
213 215 7.073854 ACTCAGGTAGTTTCAGGGCTTATATA 58.926 38.462 0.00 0.00 33.35 0.86
214 216 7.735321 ACTCAGGTAGTTTCAGGGCTTATATAT 59.265 37.037 0.00 0.00 33.35 0.86
215 217 9.256228 CTCAGGTAGTTTCAGGGCTTATATATA 57.744 37.037 0.00 0.00 0.00 0.86
217 219 9.654663 CAGGTAGTTTCAGGGCTTATATATAAC 57.345 37.037 0.81 0.00 0.00 1.89
219 221 9.433153 GGTAGTTTCAGGGCTTATATATAACAC 57.567 37.037 0.81 1.11 0.00 3.32
220 222 9.991906 GTAGTTTCAGGGCTTATATATAACACA 57.008 33.333 0.81 0.00 0.00 3.72
223 225 9.284968 GTTTCAGGGCTTATATATAACACATGT 57.715 33.333 0.81 0.00 0.00 3.21
224 226 9.860650 TTTCAGGGCTTATATATAACACATGTT 57.139 29.630 0.00 2.32 41.73 2.71
254 256 9.593565 TGTTACCCATCAATAATATAATTGGCA 57.406 29.630 0.00 0.00 37.44 4.92
259 261 7.417116 CCCATCAATAATATAATTGGCAGGAGC 60.417 40.741 0.00 0.00 37.44 4.70
260 262 7.123098 CCATCAATAATATAATTGGCAGGAGCA 59.877 37.037 0.00 0.00 44.61 4.26
261 263 7.692460 TCAATAATATAATTGGCAGGAGCAG 57.308 36.000 0.00 0.00 44.61 4.24
263 265 4.729552 AATATAATTGGCAGGAGCAGGA 57.270 40.909 0.00 0.00 44.61 3.86
264 266 2.355010 ATAATTGGCAGGAGCAGGAC 57.645 50.000 0.00 0.00 44.61 3.85
265 267 0.991146 TAATTGGCAGGAGCAGGACA 59.009 50.000 0.00 0.00 44.61 4.02
266 268 0.333993 AATTGGCAGGAGCAGGACAT 59.666 50.000 0.00 0.00 44.61 3.06
267 269 1.216064 ATTGGCAGGAGCAGGACATA 58.784 50.000 0.00 0.00 44.61 2.29
268 270 0.253044 TTGGCAGGAGCAGGACATAC 59.747 55.000 0.00 0.00 44.61 2.39
293 296 6.151648 CCTATAGGCACAAAATCATACCCATG 59.848 42.308 5.67 0.00 0.00 3.66
300 303 6.735694 GCACAAAATCATACCCATGACATACC 60.736 42.308 0.00 0.00 43.89 2.73
311 314 4.838423 CCCATGACATACCCATGACTAGTA 59.162 45.833 0.00 0.00 42.89 1.82
313 316 5.047021 CCATGACATACCCATGACTAGTAGG 60.047 48.000 0.00 0.00 42.89 3.18
322 325 3.641906 CCATGACTAGTAGGGTAGGGTTG 59.358 52.174 0.00 0.00 0.00 3.77
325 328 1.293153 ACTAGTAGGGTAGGGTTGGGG 59.707 57.143 1.45 0.00 0.00 4.96
326 329 0.030807 TAGTAGGGTAGGGTTGGGGC 60.031 60.000 0.00 0.00 0.00 5.80
351 354 2.477863 GCCCATAGTCACGAAAATGTGC 60.478 50.000 0.00 0.00 39.73 4.57
353 356 3.378112 CCCATAGTCACGAAAATGTGCAT 59.622 43.478 0.00 0.00 39.73 3.96
355 358 2.995466 AGTCACGAAAATGTGCATGG 57.005 45.000 0.00 0.00 39.73 3.66
356 359 2.503331 AGTCACGAAAATGTGCATGGA 58.497 42.857 0.00 0.00 39.73 3.41
407 410 6.899393 TGCTCATGGGTAAAATTATCATCC 57.101 37.500 0.00 0.00 0.00 3.51
412 415 9.236006 CTCATGGGTAAAATTATCATCCTTAGG 57.764 37.037 0.00 0.00 0.00 2.69
414 417 7.161715 TGGGTAAAATTATCATCCTTAGGCT 57.838 36.000 0.00 0.00 0.00 4.58
417 420 7.391833 GGGTAAAATTATCATCCTTAGGCTCAG 59.608 40.741 0.00 0.00 0.00 3.35
418 421 6.890979 AAAATTATCATCCTTAGGCTCAGC 57.109 37.500 0.00 0.00 0.00 4.26
419 422 3.667497 TTATCATCCTTAGGCTCAGCG 57.333 47.619 0.00 0.00 0.00 5.18
439 442 4.776322 TCCGCTTGATGCCGTGGG 62.776 66.667 0.00 0.00 38.78 4.61
457 460 2.485795 GGCACCACTTTGGCAACGA 61.486 57.895 10.99 0.00 42.67 3.85
529 542 0.039617 CGCTCGAGCTCCCTTCTATG 60.040 60.000 32.88 11.25 39.32 2.23
536 549 2.102252 GAGCTCCCTTCTATGTGACCAG 59.898 54.545 0.87 0.00 0.00 4.00
548 561 1.153524 TGACCAGCCCACATTGCTT 59.846 52.632 0.00 0.00 36.81 3.91
570 583 3.532155 CGGAGCGGGAGGAGGAAG 61.532 72.222 0.00 0.00 0.00 3.46
664 696 2.501610 GCTAGGTTCCGCTCCCTG 59.498 66.667 0.00 0.00 32.08 4.45
740 772 4.703645 TTTGTTGTTGATTGTTGGACGA 57.296 36.364 0.00 0.00 0.00 4.20
746 778 6.016693 TGTTGTTGATTGTTGGACGACATAAT 60.017 34.615 0.00 0.00 32.88 1.28
749 781 8.275015 TGTTGATTGTTGGACGACATAATATT 57.725 30.769 0.00 0.00 0.00 1.28
786 818 6.050454 TGTTGTTGTACGATCACGAAAAAT 57.950 33.333 0.00 0.00 42.66 1.82
790 822 6.716438 TGTTGTACGATCACGAAAAATTTGA 58.284 32.000 0.00 0.00 42.66 2.69
795 827 5.689819 ACGATCACGAAAAATTTGAGAAGG 58.310 37.500 0.00 0.00 42.66 3.46
797 829 6.017440 ACGATCACGAAAAATTTGAGAAGGAA 60.017 34.615 0.00 0.00 42.66 3.36
798 830 6.855914 CGATCACGAAAAATTTGAGAAGGAAA 59.144 34.615 0.00 0.00 42.66 3.13
799 831 7.378461 CGATCACGAAAAATTTGAGAAGGAAAA 59.622 33.333 0.00 0.00 42.66 2.29
810 842 8.953368 ATTTGAGAAGGAAAATATTTCATGGC 57.047 30.769 0.10 0.00 0.00 4.40
812 844 6.866480 TGAGAAGGAAAATATTTCATGGCAC 58.134 36.000 0.10 0.00 0.00 5.01
813 845 6.664816 TGAGAAGGAAAATATTTCATGGCACT 59.335 34.615 0.10 0.00 0.00 4.40
814 846 7.105241 AGAAGGAAAATATTTCATGGCACTC 57.895 36.000 0.10 0.00 0.00 3.51
815 847 5.859205 AGGAAAATATTTCATGGCACTCC 57.141 39.130 0.10 2.42 0.00 3.85
864 911 4.773323 AGTTGCTGATAGCCTGAAAAAC 57.227 40.909 0.00 0.00 41.51 2.43
895 942 9.376075 TCAAAATCTGAAAATTTTAACACAGCA 57.624 25.926 2.75 0.00 36.86 4.41
896 943 9.640974 CAAAATCTGAAAATTTTAACACAGCAG 57.359 29.630 2.75 5.42 36.86 4.24
897 944 7.412137 AATCTGAAAATTTTAACACAGCAGC 57.588 32.000 2.75 0.00 0.00 5.25
898 945 4.975502 TCTGAAAATTTTAACACAGCAGCG 59.024 37.500 2.75 0.00 0.00 5.18
899 946 4.047822 TGAAAATTTTAACACAGCAGCGG 58.952 39.130 2.75 0.00 0.00 5.52
900 947 4.202060 TGAAAATTTTAACACAGCAGCGGA 60.202 37.500 2.75 0.00 0.00 5.54
901 948 4.314740 AAATTTTAACACAGCAGCGGAA 57.685 36.364 0.00 0.00 0.00 4.30
902 949 4.314740 AATTTTAACACAGCAGCGGAAA 57.685 36.364 0.00 0.00 0.00 3.13
903 950 2.766970 TTTAACACAGCAGCGGAAAC 57.233 45.000 0.00 0.00 0.00 2.78
904 951 1.961793 TTAACACAGCAGCGGAAACT 58.038 45.000 0.00 0.00 0.00 2.66
905 952 1.225855 TAACACAGCAGCGGAAACTG 58.774 50.000 0.00 0.00 40.80 3.16
906 953 1.447317 AACACAGCAGCGGAAACTGG 61.447 55.000 0.00 0.00 38.16 4.00
908 955 1.302033 ACAGCAGCGGAAACTGGAG 60.302 57.895 0.00 0.00 38.16 3.86
910 957 0.603707 CAGCAGCGGAAACTGGAGAA 60.604 55.000 0.00 0.00 38.16 2.87
911 958 0.321122 AGCAGCGGAAACTGGAGAAG 60.321 55.000 0.00 0.00 38.16 2.85
912 959 1.916697 GCAGCGGAAACTGGAGAAGC 61.917 60.000 0.00 0.00 38.16 3.86
919 966 3.553095 AACTGGAGAAGCCCACGCC 62.553 63.158 0.00 0.00 34.97 5.68
982 1052 0.463833 ATCCGATTGAAACCCTCGCC 60.464 55.000 0.00 0.00 0.00 5.54
1083 2670 3.468326 GATCTTCCTCCGCCTGCCC 62.468 68.421 0.00 0.00 0.00 5.36
1524 3183 1.153349 GGTTGTCCTCATCGGCCTC 60.153 63.158 0.00 0.00 0.00 4.70
1627 3307 4.885907 GCTCTGATTCTCATTTTGATGGGA 59.114 41.667 0.00 0.00 0.00 4.37
1662 3354 3.486542 GCTCTGATTCTCGTTTTGATGGC 60.487 47.826 0.00 0.00 0.00 4.40
1943 3641 5.411103 ACCCTCTATCTATGGTCAAGACT 57.589 43.478 0.00 0.00 0.00 3.24
1998 3696 8.147058 ACTCAGCATAAAGTCATCGATCTAAAT 58.853 33.333 0.00 0.00 0.00 1.40
2116 3814 8.768955 GCATCTACGAGATTAATTTGAAGACAT 58.231 33.333 0.00 0.00 31.32 3.06
2244 3986 8.888716 GTTGGTGGAACAATTTAAAAGTTTGAT 58.111 29.630 6.96 0.00 44.16 2.57
2261 4003 5.183904 AGTTTGATTGTTTAGTCAGATGGGC 59.816 40.000 0.00 0.00 0.00 5.36
2318 4060 3.427161 GCTTGAGCAAACTTTGAGTGT 57.573 42.857 5.65 0.00 41.59 3.55
2326 4068 5.985781 AGCAAACTTTGAGTGTTATGTACG 58.014 37.500 5.65 0.00 0.00 3.67
2328 4070 5.144359 CAAACTTTGAGTGTTATGTACGCC 58.856 41.667 0.00 0.00 38.02 5.68
2358 4100 8.439993 TTTTACATCTAATTATGCTTACGCCA 57.560 30.769 0.00 0.00 34.43 5.69
2362 4104 4.131596 TCTAATTATGCTTACGCCAACCC 58.868 43.478 0.00 0.00 34.43 4.11
2364 4106 2.201921 TTATGCTTACGCCAACCCAA 57.798 45.000 0.00 0.00 34.43 4.12
2366 4108 0.965363 ATGCTTACGCCAACCCAAGG 60.965 55.000 0.00 0.00 34.43 3.61
2388 4130 6.531021 AGGGTGCAATTGTATATAGTACCAC 58.469 40.000 7.40 2.46 36.80 4.16
2396 4138 9.181805 CAATTGTATATAGTACCACGTCTTCTG 57.818 37.037 0.00 0.00 0.00 3.02
2424 4171 8.902806 GGAATCACACTGATAAATCCATGTTTA 58.097 33.333 0.00 0.00 35.76 2.01
2459 4206 1.069022 CCCTGCAAGACATTGACAACG 60.069 52.381 0.00 0.00 38.83 4.10
2485 4232 2.332063 TGAGTATGCTTAAGGGCAGC 57.668 50.000 4.29 0.00 45.75 5.25
2514 4271 8.239314 GCAACATGAGAAATGACTATTTGAAGA 58.761 33.333 0.00 0.00 36.66 2.87
2517 4274 6.968131 TGAGAAATGACTATTTGAAGACGG 57.032 37.500 0.00 0.00 36.66 4.79
2530 4287 2.359850 GACGGCATGGGTCTTGCA 60.360 61.111 0.00 0.00 41.95 4.08
2709 4468 7.061441 CAGCATCAGTTATGTGCTTAGTTTTTG 59.939 37.037 0.00 0.00 46.29 2.44
2729 4488 8.611757 GTTTTTGAATTGGCTTGAAAATGTACT 58.388 29.630 0.00 0.00 31.38 2.73
2731 4490 6.403866 TGAATTGGCTTGAAAATGTACTGT 57.596 33.333 0.00 0.00 0.00 3.55
2741 4500 4.202419 TGAAAATGTACTGTGGGCACTAGT 60.202 41.667 0.00 0.00 0.00 2.57
2759 4518 6.373779 CACTAGTTTTGTCTTGCCATTGTAG 58.626 40.000 0.00 0.00 0.00 2.74
2889 4648 1.602311 CTGGCTCATTGGTATGCCTC 58.398 55.000 0.16 0.00 45.11 4.70
2900 4659 9.252962 CTCATTGGTATGCCTCAATTAATTTTC 57.747 33.333 0.16 0.00 31.95 2.29
2930 4689 7.553881 TTTATTAATGCTAGAGGTCAAGTGC 57.446 36.000 0.00 0.00 0.00 4.40
2942 4701 3.003480 GGTCAAGTGCCTGATGTTACTC 58.997 50.000 0.00 0.00 0.00 2.59
2972 4732 8.265055 AGTAAAAGTATAGCATGCAGTTCCTTA 58.735 33.333 21.98 1.26 0.00 2.69
3027 5419 9.490663 GTATAGCATGTAAACTGAAATGTTGTC 57.509 33.333 0.00 0.00 0.00 3.18
3182 5592 7.243091 AGGTAATTGTAATGGTTTGTTAGGGT 58.757 34.615 0.00 0.00 0.00 4.34
3194 5604 5.712917 GGTTTGTTAGGGTTGTGGAATATGA 59.287 40.000 0.00 0.00 0.00 2.15
3224 5634 2.020720 CTATGTGCTGGACTCGACTCT 58.979 52.381 0.00 0.00 0.00 3.24
3226 5636 2.130272 TGTGCTGGACTCGACTCTAT 57.870 50.000 0.00 0.00 0.00 1.98
3232 5642 3.226777 CTGGACTCGACTCTATGGGATT 58.773 50.000 0.00 0.00 0.00 3.01
3235 5645 3.004944 GGACTCGACTCTATGGGATTCAC 59.995 52.174 0.00 0.00 0.00 3.18
3243 5653 4.653341 ACTCTATGGGATTCACTCTGAAGG 59.347 45.833 0.00 0.00 40.05 3.46
3268 5679 7.554835 GGTTAACATGGTAATCTGTTATGTGGA 59.445 37.037 6.46 0.00 37.60 4.02
3277 5688 3.449918 TCTGTTATGTGGATGGGACTCA 58.550 45.455 0.00 0.00 0.00 3.41
3278 5689 3.452264 TCTGTTATGTGGATGGGACTCAG 59.548 47.826 0.00 0.00 0.00 3.35
3292 5703 2.224402 GGACTCAGGATGCTGGTATTCC 60.224 54.545 14.84 10.74 34.76 3.01
3301 5712 6.774656 CAGGATGCTGGTATTCCTCTATTTTT 59.225 38.462 6.28 0.00 37.80 1.94
3321 5733 5.483685 TTTCACATAGTAGCTTCCTGTGT 57.516 39.130 17.49 13.56 38.61 3.72
3323 5735 6.599356 TTCACATAGTAGCTTCCTGTGTTA 57.401 37.500 17.49 7.68 38.61 2.41
3326 5738 7.620880 TCACATAGTAGCTTCCTGTGTTATTT 58.379 34.615 17.49 0.00 38.61 1.40
3416 5832 9.476928 ACTTTATAGCGGGTATAGATTGTATCT 57.523 33.333 6.97 0.00 43.33 1.98
3421 5837 7.534723 AGCGGGTATAGATTGTATCTTAACA 57.465 36.000 0.00 0.00 40.76 2.41
3422 5838 7.959175 AGCGGGTATAGATTGTATCTTAACAA 58.041 34.615 0.00 0.00 43.16 2.83
3423 5839 8.088981 AGCGGGTATAGATTGTATCTTAACAAG 58.911 37.037 0.00 0.00 42.33 3.16
3424 5840 7.871463 GCGGGTATAGATTGTATCTTAACAAGT 59.129 37.037 0.00 0.00 42.33 3.16
3425 5841 9.193133 CGGGTATAGATTGTATCTTAACAAGTG 57.807 37.037 0.00 0.00 42.33 3.16
3432 5848 8.762645 AGATTGTATCTTAACAAGTGAGGATCA 58.237 33.333 0.00 0.00 42.40 2.92
3433 5849 9.553064 GATTGTATCTTAACAAGTGAGGATCAT 57.447 33.333 0.00 0.00 43.71 2.45
3434 5850 9.911788 ATTGTATCTTAACAAGTGAGGATCATT 57.088 29.630 0.00 0.00 43.71 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.764679 TTGTAAAGTGTCATCATGGTGC 57.235 40.909 0.00 0.00 0.00 5.01
5 6 5.630121 TCCTTTGTAAAGTGTCATCATGGT 58.370 37.500 3.90 0.00 34.20 3.55
7 8 5.181811 TGCTCCTTTGTAAAGTGTCATCATG 59.818 40.000 3.90 0.00 34.20 3.07
8 9 5.182001 GTGCTCCTTTGTAAAGTGTCATCAT 59.818 40.000 3.90 0.00 34.20 2.45
10 11 4.083271 GGTGCTCCTTTGTAAAGTGTCATC 60.083 45.833 0.00 0.00 34.20 2.92
11 12 3.821033 GGTGCTCCTTTGTAAAGTGTCAT 59.179 43.478 0.00 0.00 34.20 3.06
13 14 2.223377 CGGTGCTCCTTTGTAAAGTGTC 59.777 50.000 2.85 0.00 34.20 3.67
14 15 2.218603 CGGTGCTCCTTTGTAAAGTGT 58.781 47.619 2.85 0.00 34.20 3.55
15 16 1.069227 GCGGTGCTCCTTTGTAAAGTG 60.069 52.381 2.85 0.00 34.20 3.16
16 17 1.235724 GCGGTGCTCCTTTGTAAAGT 58.764 50.000 2.85 0.00 34.20 2.66
18 19 0.891904 GGGCGGTGCTCCTTTGTAAA 60.892 55.000 2.85 0.00 0.00 2.01
20 21 2.058125 TTGGGCGGTGCTCCTTTGTA 62.058 55.000 2.85 0.00 0.00 2.41
21 22 2.713531 ATTGGGCGGTGCTCCTTTGT 62.714 55.000 2.85 0.00 0.00 2.83
22 23 1.978617 ATTGGGCGGTGCTCCTTTG 60.979 57.895 2.85 0.00 0.00 2.77
23 24 1.978617 CATTGGGCGGTGCTCCTTT 60.979 57.895 2.85 0.00 0.00 3.11
24 25 2.361610 CATTGGGCGGTGCTCCTT 60.362 61.111 2.85 0.00 0.00 3.36
25 26 3.210012 AACATTGGGCGGTGCTCCT 62.210 57.895 2.85 0.00 0.00 3.69
27 28 1.926511 CTCAACATTGGGCGGTGCTC 61.927 60.000 0.00 0.00 0.00 4.26
28 29 1.973281 CTCAACATTGGGCGGTGCT 60.973 57.895 0.00 0.00 0.00 4.40
30 31 0.240945 GTTCTCAACATTGGGCGGTG 59.759 55.000 0.00 0.00 0.00 4.94
31 32 0.893727 GGTTCTCAACATTGGGCGGT 60.894 55.000 0.00 0.00 0.00 5.68
32 33 0.893270 TGGTTCTCAACATTGGGCGG 60.893 55.000 0.00 0.00 0.00 6.13
33 34 0.240945 GTGGTTCTCAACATTGGGCG 59.759 55.000 0.00 0.00 0.00 6.13
34 35 0.603065 GGTGGTTCTCAACATTGGGC 59.397 55.000 0.00 0.00 32.12 5.36
35 36 1.993956 TGGTGGTTCTCAACATTGGG 58.006 50.000 0.00 0.00 38.32 4.12
49 50 1.926511 GCAGCTCGAAACCATGGTGG 61.927 60.000 20.60 11.33 45.02 4.61
50 51 1.236616 TGCAGCTCGAAACCATGGTG 61.237 55.000 20.60 6.21 0.00 4.17
52 53 1.651240 CCTGCAGCTCGAAACCATGG 61.651 60.000 11.19 11.19 0.00 3.66
53 54 0.957395 ACCTGCAGCTCGAAACCATG 60.957 55.000 8.66 0.00 0.00 3.66
54 55 0.613260 TACCTGCAGCTCGAAACCAT 59.387 50.000 8.66 0.00 0.00 3.55
55 56 0.394938 TTACCTGCAGCTCGAAACCA 59.605 50.000 8.66 0.00 0.00 3.67
56 57 1.079503 CTTACCTGCAGCTCGAAACC 58.920 55.000 8.66 0.00 0.00 3.27
57 58 2.080286 TCTTACCTGCAGCTCGAAAC 57.920 50.000 8.66 0.00 0.00 2.78
58 59 2.413837 GTTCTTACCTGCAGCTCGAAA 58.586 47.619 8.66 0.00 0.00 3.46
59 60 1.337823 GGTTCTTACCTGCAGCTCGAA 60.338 52.381 8.66 5.10 41.53 3.71
60 61 0.246635 GGTTCTTACCTGCAGCTCGA 59.753 55.000 8.66 0.00 41.53 4.04
62 63 1.443802 GTGGTTCTTACCTGCAGCTC 58.556 55.000 8.66 0.00 45.27 4.09
63 64 0.036875 GGTGGTTCTTACCTGCAGCT 59.963 55.000 8.66 0.00 45.27 4.24
64 65 0.250727 TGGTGGTTCTTACCTGCAGC 60.251 55.000 8.66 0.00 45.27 5.25
65 66 2.086869 CATGGTGGTTCTTACCTGCAG 58.913 52.381 6.78 6.78 45.27 4.41
66 67 1.702401 TCATGGTGGTTCTTACCTGCA 59.298 47.619 0.00 0.00 45.27 4.41
67 68 2.084546 GTCATGGTGGTTCTTACCTGC 58.915 52.381 0.00 0.00 45.27 4.85
68 69 3.417069 TGTCATGGTGGTTCTTACCTG 57.583 47.619 0.00 0.00 45.27 4.00
70 71 5.242838 TGAAATTGTCATGGTGGTTCTTACC 59.757 40.000 0.00 0.00 45.26 2.85
84 85 5.048782 GCCTCTACAACACATGAAATTGTCA 60.049 40.000 14.32 5.58 41.67 3.58
85 86 5.048782 TGCCTCTACAACACATGAAATTGTC 60.049 40.000 14.32 4.64 37.68 3.18
86 87 4.826733 TGCCTCTACAACACATGAAATTGT 59.173 37.500 14.97 14.97 39.75 2.71
87 88 5.375417 TGCCTCTACAACACATGAAATTG 57.625 39.130 0.00 3.24 0.00 2.32
88 89 5.163723 CGATGCCTCTACAACACATGAAATT 60.164 40.000 0.00 0.00 0.00 1.82
89 90 4.333649 CGATGCCTCTACAACACATGAAAT 59.666 41.667 0.00 0.00 0.00 2.17
118 119 5.381174 TCTGCAACAATGGAAATCTTCTG 57.619 39.130 0.00 0.00 0.00 3.02
121 122 6.993902 ACAAATTCTGCAACAATGGAAATCTT 59.006 30.769 0.00 0.00 0.00 2.40
129 130 5.406175 CCCAGTAACAAATTCTGCAACAATG 59.594 40.000 0.00 0.00 0.00 2.82
138 139 5.203528 CCCATCATCCCAGTAACAAATTCT 58.796 41.667 0.00 0.00 0.00 2.40
145 146 1.133792 CCACCCCATCATCCCAGTAAC 60.134 57.143 0.00 0.00 0.00 2.50
149 150 2.771321 CCCCACCCCATCATCCCAG 61.771 68.421 0.00 0.00 0.00 4.45
192 194 9.388672 TGTTATATATAAGCCCTGAAACTACCT 57.611 33.333 5.39 0.00 0.00 3.08
193 195 9.433153 GTGTTATATATAAGCCCTGAAACTACC 57.567 37.037 5.39 0.00 0.00 3.18
194 196 9.991906 TGTGTTATATATAAGCCCTGAAACTAC 57.008 33.333 5.39 0.00 0.00 2.73
212 214 9.386010 GATGGGTAACAGTTAACATGTGTTATA 57.614 33.333 17.10 10.38 38.55 0.98
213 215 7.885922 TGATGGGTAACAGTTAACATGTGTTAT 59.114 33.333 17.10 6.92 38.55 1.89
214 216 7.225011 TGATGGGTAACAGTTAACATGTGTTA 58.775 34.615 10.60 10.97 37.68 2.41
215 217 6.065374 TGATGGGTAACAGTTAACATGTGTT 58.935 36.000 10.60 14.05 39.43 3.32
217 219 6.567687 TTGATGGGTAACAGTTAACATGTG 57.432 37.500 10.60 0.00 39.74 3.21
251 253 1.147153 GGTATGTCCTGCTCCTGCC 59.853 63.158 0.00 0.00 38.71 4.85
261 263 6.296026 TGATTTTGTGCCTATAGGTATGTCC 58.704 40.000 20.10 4.58 37.57 4.02
263 265 7.883311 GGTATGATTTTGTGCCTATAGGTATGT 59.117 37.037 20.10 1.96 37.57 2.29
264 266 7.336931 GGGTATGATTTTGTGCCTATAGGTATG 59.663 40.741 20.10 0.00 37.57 2.39
265 267 7.018149 TGGGTATGATTTTGTGCCTATAGGTAT 59.982 37.037 20.10 0.00 37.57 2.73
266 268 6.330514 TGGGTATGATTTTGTGCCTATAGGTA 59.669 38.462 20.10 13.34 37.57 3.08
267 269 5.133660 TGGGTATGATTTTGTGCCTATAGGT 59.866 40.000 20.10 0.00 37.57 3.08
268 270 5.630121 TGGGTATGATTTTGTGCCTATAGG 58.370 41.667 15.01 15.01 38.53 2.57
273 276 3.701040 GTCATGGGTATGATTTTGTGCCT 59.299 43.478 0.00 0.00 44.62 4.75
300 303 3.614568 ACCCTACCCTACTAGTCATGG 57.385 52.381 0.00 0.73 0.00 3.66
311 314 2.939353 GTGCCCCAACCCTACCCT 60.939 66.667 0.00 0.00 0.00 4.34
313 316 2.355115 CAGTGCCCCAACCCTACC 59.645 66.667 0.00 0.00 0.00 3.18
325 328 0.391130 TTCGTGACTATGGGCAGTGC 60.391 55.000 6.55 6.55 0.00 4.40
326 329 2.093306 TTTCGTGACTATGGGCAGTG 57.907 50.000 0.00 0.00 0.00 3.66
336 339 2.503331 TCCATGCACATTTTCGTGACT 58.497 42.857 0.00 0.00 39.34 3.41
401 404 0.034616 GCGCTGAGCCTAAGGATGAT 59.965 55.000 0.00 0.00 40.81 2.45
414 417 3.774528 ATCAAGCGGAGGCGCTGA 61.775 61.111 7.64 0.57 45.26 4.26
436 439 3.686098 TTGCCAAAGTGGTGCCCCA 62.686 57.895 0.00 0.00 40.46 4.96
439 442 2.027460 CGTTGCCAAAGTGGTGCC 59.973 61.111 0.00 0.00 40.46 5.01
442 445 0.818040 GAGGTCGTTGCCAAAGTGGT 60.818 55.000 0.00 0.00 40.46 4.16
443 446 1.515521 GGAGGTCGTTGCCAAAGTGG 61.516 60.000 0.00 0.00 41.55 4.00
445 448 1.228154 GGGAGGTCGTTGCCAAAGT 60.228 57.895 0.00 0.00 0.00 2.66
513 526 2.025155 GTCACATAGAAGGGAGCTCGA 58.975 52.381 7.83 0.00 0.00 4.04
529 542 1.181098 AAGCAATGTGGGCTGGTCAC 61.181 55.000 0.00 0.00 41.66 3.67
536 549 4.086547 GGGGCAAGCAATGTGGGC 62.087 66.667 0.00 0.00 0.00 5.36
625 639 4.729918 GCCAGCTCCACCCCACTG 62.730 72.222 0.00 0.00 0.00 3.66
645 677 3.081409 GGGAGCGGAACCTAGCCA 61.081 66.667 0.00 0.00 0.00 4.75
672 704 1.080839 GATCCTCGATCGCTCCAGC 60.081 63.158 11.09 0.00 37.78 4.85
675 707 2.517650 AAAAGATCCTCGATCGCTCC 57.482 50.000 11.09 0.00 43.17 4.70
697 729 9.354673 ACAAATCTCTTTTAAACTCCATTGAGA 57.645 29.630 0.00 0.00 41.42 3.27
698 730 9.971922 AACAAATCTCTTTTAAACTCCATTGAG 57.028 29.630 0.00 0.00 44.62 3.02
703 735 8.744652 TCAACAACAAATCTCTTTTAAACTCCA 58.255 29.630 0.00 0.00 0.00 3.86
711 743 8.040132 TCCAACAATCAACAACAAATCTCTTTT 58.960 29.630 0.00 0.00 0.00 2.27
712 744 7.492344 GTCCAACAATCAACAACAAATCTCTTT 59.508 33.333 0.00 0.00 0.00 2.52
756 788 8.463456 TCGTGATCGTACAACAACAATAATTA 57.537 30.769 0.00 0.00 38.33 1.40
761 793 5.660629 TTTCGTGATCGTACAACAACAAT 57.339 34.783 0.00 0.00 38.33 2.71
769 801 6.772770 TCTCAAATTTTTCGTGATCGTACA 57.227 33.333 0.00 0.00 38.33 2.90
774 806 8.574196 TTTTCCTTCTCAAATTTTTCGTGATC 57.426 30.769 0.00 0.00 0.00 2.92
786 818 7.818930 GTGCCATGAAATATTTTCCTTCTCAAA 59.181 33.333 1.43 0.00 0.00 2.69
790 822 6.097412 GGAGTGCCATGAAATATTTTCCTTCT 59.903 38.462 1.43 0.00 0.00 2.85
795 827 5.596836 TGGGAGTGCCATGAAATATTTTC 57.403 39.130 0.00 0.00 35.15 2.29
797 829 5.540400 CATGGGAGTGCCATGAAATATTT 57.460 39.130 33.71 0.00 45.40 1.40
805 837 1.411246 CCAAATCATGGGAGTGCCATG 59.589 52.381 31.98 31.98 46.27 3.66
807 839 3.286404 CCAAATCATGGGAGTGCCA 57.714 52.632 5.57 5.57 46.27 4.92
820 852 6.546772 ACTTGAAATGGTTTGATTTGCCAAAT 59.453 30.769 1.47 1.47 38.18 2.32
864 911 8.738554 TGTTAAAATTTTCAGATTTTGACGACG 58.261 29.630 6.72 0.00 43.12 5.12
895 942 1.003233 GGCTTCTCCAGTTTCCGCT 60.003 57.895 0.00 0.00 34.01 5.52
896 943 2.041115 GGGCTTCTCCAGTTTCCGC 61.041 63.158 0.00 0.00 36.21 5.54
897 944 0.955919 GTGGGCTTCTCCAGTTTCCG 60.956 60.000 0.00 0.00 37.50 4.30
898 945 0.955919 CGTGGGCTTCTCCAGTTTCC 60.956 60.000 0.00 0.00 37.50 3.13
899 946 1.578206 GCGTGGGCTTCTCCAGTTTC 61.578 60.000 0.00 0.00 37.50 2.78
900 947 1.600916 GCGTGGGCTTCTCCAGTTT 60.601 57.895 0.00 0.00 37.50 2.66
901 948 2.032681 GCGTGGGCTTCTCCAGTT 59.967 61.111 0.00 0.00 37.50 3.16
902 949 4.021925 GGCGTGGGCTTCTCCAGT 62.022 66.667 0.00 0.00 37.50 4.00
905 952 4.821589 CTCGGCGTGGGCTTCTCC 62.822 72.222 6.85 0.00 39.81 3.71
933 980 3.818787 GAGCTGGGCAACATGCGG 61.819 66.667 0.00 0.00 46.21 5.69
937 984 1.708341 AAGTTTGAGCTGGGCAACAT 58.292 45.000 0.00 0.00 39.74 2.71
943 990 0.969149 GGGGAAAAGTTTGAGCTGGG 59.031 55.000 0.00 0.00 0.00 4.45
982 1052 3.979497 GGTTGGGGGTGGGTGGAG 61.979 72.222 0.00 0.00 0.00 3.86
1524 3183 3.497262 CACCATCATCCTCATTCATGTCG 59.503 47.826 0.00 0.00 0.00 4.35
1943 3641 3.531538 GCAACTCCGTTGGAATCTATCA 58.468 45.455 8.60 0.00 42.99 2.15
1998 3696 4.772100 GGATTTTGAATGGGGAGAAGTTCA 59.228 41.667 5.50 0.00 0.00 3.18
2116 3814 3.101437 TCCATAGCTTCTTCCACCGTAA 58.899 45.455 0.00 0.00 0.00 3.18
2244 3986 3.788227 ACTGCCCATCTGACTAAACAA 57.212 42.857 0.00 0.00 0.00 2.83
2301 4043 6.292649 CGTACATAACACTCAAAGTTTGCTCA 60.293 38.462 10.90 0.00 0.00 4.26
2318 4060 6.050432 AGATGTAAAATTCGGGCGTACATAA 58.950 36.000 0.00 0.00 35.94 1.90
2326 4068 7.593825 AGCATAATTAGATGTAAAATTCGGGC 58.406 34.615 0.00 0.00 0.00 6.13
2358 4100 2.390225 TACAATTGCACCCTTGGGTT 57.610 45.000 8.91 0.00 0.00 4.11
2362 4104 6.995686 TGGTACTATATACAATTGCACCCTTG 59.004 38.462 5.05 0.00 0.00 3.61
2364 4106 6.531021 GTGGTACTATATACAATTGCACCCT 58.469 40.000 5.05 0.00 0.00 4.34
2366 4108 5.987347 ACGTGGTACTATATACAATTGCACC 59.013 40.000 5.05 1.41 0.00 5.01
2396 4138 6.319658 ACATGGATTTATCAGTGTGATTCCAC 59.680 38.462 9.85 0.00 41.45 4.02
2459 4206 4.515567 GCCCTTAAGCATACTCAACCATAC 59.484 45.833 0.00 0.00 0.00 2.39
2485 4232 6.446781 AATAGTCATTTCTCATGTTGCCTG 57.553 37.500 0.00 0.00 0.00 4.85
2514 4271 1.304381 ATTGCAAGACCCATGCCGT 60.304 52.632 4.94 0.00 43.16 5.68
2517 4274 1.135199 CACTGATTGCAAGACCCATGC 60.135 52.381 4.94 0.00 44.08 4.06
2530 4287 4.402793 AGCTACCGAATACTGACACTGATT 59.597 41.667 0.00 0.00 0.00 2.57
2579 4336 7.384660 GCTGACAAAATCCAACAACATTATGAA 59.615 33.333 0.00 0.00 0.00 2.57
2585 4342 4.669206 TGCTGACAAAATCCAACAACAT 57.331 36.364 0.00 0.00 0.00 2.71
2709 4468 5.634859 CCACAGTACATTTTCAAGCCAATTC 59.365 40.000 0.00 0.00 0.00 2.17
2729 4488 2.948979 CAAGACAAAACTAGTGCCCACA 59.051 45.455 0.00 0.00 0.00 4.17
2731 4490 1.953686 GCAAGACAAAACTAGTGCCCA 59.046 47.619 0.00 0.00 0.00 5.36
2741 4500 6.321181 AGAGTTTCTACAATGGCAAGACAAAA 59.679 34.615 0.00 0.00 0.00 2.44
2791 4550 6.684686 CCATCATCAATGTTCTCTGTTTTGT 58.315 36.000 0.00 0.00 33.13 2.83
2908 4667 5.366768 AGGCACTTGACCTCTAGCATTAATA 59.633 40.000 0.00 0.00 27.25 0.98
2913 4672 1.209019 CAGGCACTTGACCTCTAGCAT 59.791 52.381 0.00 0.00 34.60 3.79
2930 4689 9.877178 ATACTTTTACTCTTGAGTAACATCAGG 57.123 33.333 19.19 10.20 34.42 3.86
2942 4701 7.545362 ACTGCATGCTATACTTTTACTCTTG 57.455 36.000 20.33 0.00 0.00 3.02
2972 4732 6.377996 TCAGTACATTGCTTGCTGGATAAAAT 59.622 34.615 0.00 0.00 0.00 1.82
3027 5419 2.031420 CACCATCTTGGCATATTGCTCG 60.031 50.000 0.00 0.00 42.67 5.03
3182 5592 4.102524 AGCGGTTAGGATCATATTCCACAA 59.897 41.667 0.00 0.00 38.32 3.33
3224 5634 6.214615 TGTTAACCTTCAGAGTGAATCCCATA 59.785 38.462 2.48 0.00 35.59 2.74
3226 5636 4.349636 TGTTAACCTTCAGAGTGAATCCCA 59.650 41.667 2.48 0.00 35.59 4.37
3232 5642 4.974645 ACCATGTTAACCTTCAGAGTGA 57.025 40.909 2.48 0.00 0.00 3.41
3235 5645 7.106239 ACAGATTACCATGTTAACCTTCAGAG 58.894 38.462 2.48 0.00 0.00 3.35
3243 5653 8.500753 TCCACATAACAGATTACCATGTTAAC 57.499 34.615 0.00 0.00 43.14 2.01
3268 5679 0.622738 ACCAGCATCCTGAGTCCCAT 60.623 55.000 0.00 0.00 41.77 4.00
3277 5688 6.521527 AAAATAGAGGAATACCAGCATCCT 57.478 37.500 0.00 0.00 46.14 3.24
3278 5689 6.772716 TGAAAAATAGAGGAATACCAGCATCC 59.227 38.462 0.00 0.00 38.94 3.51
3292 5703 9.039870 CAGGAAGCTACTATGTGAAAAATAGAG 57.960 37.037 0.00 0.00 36.15 2.43
3301 5712 6.791867 ATAACACAGGAAGCTACTATGTGA 57.208 37.500 21.25 8.32 43.02 3.58
3344 5756 9.803315 CAGTTAACTGCAGAATTCTGTATACTA 57.197 33.333 30.88 17.25 45.45 1.82
3378 5794 5.892119 CCCGCTATAAAGTATATGGAGGAGA 59.108 44.000 3.75 0.00 29.38 3.71
3410 5826 9.817809 GTAATGATCCTCACTTGTTAAGATACA 57.182 33.333 0.00 0.00 0.00 2.29
3411 5827 9.817809 TGTAATGATCCTCACTTGTTAAGATAC 57.182 33.333 0.00 0.00 0.00 2.24
3413 5829 9.739276 TTTGTAATGATCCTCACTTGTTAAGAT 57.261 29.630 0.00 0.00 0.00 2.40
3414 5830 9.567776 TTTTGTAATGATCCTCACTTGTTAAGA 57.432 29.630 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.