Multiple sequence alignment - TraesCS1A01G340600

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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 TraesCS1A01G340600 chr1A 100.000 2902 0 0 1570 4471 530730942 530728041 0.000000e+00 5360.0
1 TraesCS1A01G340600 chr1A 100.000 1151 0 0 1 1151 530732511 530731361 0.000000e+00 2126.0
2 TraesCS1A01G340600 chr1A 85.356 478 28 13 1805 2255 504761976 504762438 1.470000e-124 457.0
3 TraesCS1A01G340600 chr1A 83.750 400 23 17 1883 2255 349295680 349295296 1.540000e-89 340.0
4 TraesCS1A01G340600 chr1A 93.151 73 2 3 4401 4471 530727207 530727278 2.200000e-18 104.0
5 TraesCS1A01G340600 chr1B 90.595 2371 131 30 1570 3875 583688183 583685840 0.000000e+00 3059.0
6 TraesCS1A01G340600 chr1B 87.924 1002 79 22 1 992 583689568 583688599 0.000000e+00 1142.0
7 TraesCS1A01G340600 chr1B 88.961 462 43 5 3861 4320 583685799 583685344 8.400000e-157 564.0
8 TraesCS1A01G340600 chr1B 84.902 510 55 16 1898 2388 23667655 23668161 3.110000e-136 496.0
9 TraesCS1A01G340600 chr1B 84.674 522 36 12 1898 2388 6412926 6413434 8.700000e-132 481.0
10 TraesCS1A01G340600 chr1B 95.050 101 4 1 4314 4413 543009443 543009343 1.660000e-34 158.0
11 TraesCS1A01G340600 chr1D 90.349 2321 128 30 1570 3825 432205261 432202972 0.000000e+00 2957.0
12 TraesCS1A01G340600 chr1D 84.441 752 26 25 450 1151 432206058 432205348 0.000000e+00 656.0
13 TraesCS1A01G340600 chr1D 84.512 523 35 23 1898 2388 15184471 15184979 4.050000e-130 475.0
14 TraesCS1A01G340600 chr1D 91.026 234 15 5 73 305 432206574 432206346 1.210000e-80 311.0
15 TraesCS1A01G340600 chr1D 91.228 171 12 3 3 171 432229710 432229541 3.480000e-56 230.0
16 TraesCS1A01G340600 chr5D 95.668 554 24 0 2791 3344 378331049 378330496 0.000000e+00 891.0
17 TraesCS1A01G340600 chr5D 95.512 557 25 0 2788 3344 559439998 559440554 0.000000e+00 891.0
18 TraesCS1A01G340600 chr5D 95.332 557 26 0 2788 3344 296177967 296178523 0.000000e+00 885.0
19 TraesCS1A01G340600 chr5D 90.271 627 46 9 3699 4320 559440559 559441175 0.000000e+00 806.0
20 TraesCS1A01G340600 chr5D 90.112 627 47 10 3699 4320 80202329 80201713 0.000000e+00 800.0
21 TraesCS1A01G340600 chr5D 90.112 627 45 11 3699 4320 378330491 378329877 0.000000e+00 798.0
22 TraesCS1A01G340600 chr5D 89.650 628 47 11 3699 4320 296178528 296179143 0.000000e+00 784.0
23 TraesCS1A01G340600 chr5D 96.047 430 17 0 2791 3220 80203081 80202652 0.000000e+00 701.0
24 TraesCS1A01G340600 chr5D 88.475 564 17 11 1570 2120 80203837 80203309 4.880000e-179 638.0
25 TraesCS1A01G340600 chr5D 87.943 564 20 10 1570 2120 296177214 296177742 4.910000e-174 621.0
26 TraesCS1A01G340600 chr5D 88.104 538 16 12 1596 2120 378331779 378331277 2.980000e-166 595.0
27 TraesCS1A01G340600 chr5D 85.333 450 27 9 1802 2223 398002384 398002822 3.200000e-116 429.0
28 TraesCS1A01G340600 chr5D 90.847 295 12 4 1830 2120 559439490 559439773 9.080000e-102 381.0
29 TraesCS1A01G340600 chr5D 92.576 229 7 3 1570 1789 559439260 559439487 2.010000e-83 320.0
30 TraesCS1A01G340600 chr5D 90.476 168 10 1 2564 2725 296177796 296177963 2.710000e-52 217.0
31 TraesCS1A01G340600 chr5D 89.881 168 11 1 2564 2725 80203255 80203088 1.260000e-50 211.0
32 TraesCS1A01G340600 chr5D 89.881 168 11 1 2564 2725 378331223 378331056 1.260000e-50 211.0
33 TraesCS1A01G340600 chr5D 89.881 168 11 1 2564 2725 559439827 559439994 1.260000e-50 211.0
34 TraesCS1A01G340600 chr5D 92.913 127 8 1 3219 3344 80202460 80202334 2.750000e-42 183.0
35 TraesCS1A01G340600 chr5D 93.750 96 3 2 1056 1151 394992075 394992167 1.680000e-29 141.0
36 TraesCS1A01G340600 chr5D 91.176 102 3 2 1570 1665 394992251 394992352 2.810000e-27 134.0
37 TraesCS1A01G340600 chr5A 85.164 519 36 10 1898 2388 439770074 439769569 1.120000e-135 494.0
38 TraesCS1A01G340600 chr5A 83.750 400 23 13 1883 2255 584085285 584084901 1.540000e-89 340.0
39 TraesCS1A01G340600 chr5A 98.901 91 1 0 4323 4413 703192970 703192880 3.580000e-36 163.0
40 TraesCS1A01G340600 chr5A 100.000 58 0 0 4414 4471 423034426 423034483 1.700000e-19 108.0
41 TraesCS1A01G340600 chr5A 96.610 59 1 1 4414 4471 662623996 662624054 3.680000e-16 97.1
42 TraesCS1A01G340600 chr3A 84.231 520 40 12 1898 2388 227067869 227068375 6.770000e-128 468.0
43 TraesCS1A01G340600 chr3A 98.901 91 1 0 4323 4413 26529434 26529524 3.580000e-36 163.0
44 TraesCS1A01G340600 chr3A 92.593 108 7 1 2282 2388 726476795 726476902 2.150000e-33 154.0
45 TraesCS1A01G340600 chr3A 96.923 65 1 1 4407 4471 142907882 142907945 1.700000e-19 108.0
46 TraesCS1A01G340600 chr3A 100.000 58 0 0 4414 4471 142922906 142922849 1.700000e-19 108.0
47 TraesCS1A01G340600 chr3A 94.545 55 3 0 1056 1110 714029171 714029117 7.970000e-13 86.1
48 TraesCS1A01G340600 chr7A 84.728 478 31 13 1805 2255 595385524 595385986 1.480000e-119 440.0
49 TraesCS1A01G340600 chr7A 97.802 91 2 0 4323 4413 45063478 45063568 1.660000e-34 158.0
50 TraesCS1A01G340600 chr7A 94.545 55 3 0 1056 1110 71731704 71731758 7.970000e-13 86.1
51 TraesCS1A01G340600 chr2A 84.728 478 31 16 1805 2255 692539638 692540100 1.480000e-119 440.0
52 TraesCS1A01G340600 chr2A 82.469 405 49 14 1898 2284 535696795 535696395 7.170000e-88 335.0
53 TraesCS1A01G340600 chr2A 97.802 91 2 0 4323 4413 42960553 42960643 1.660000e-34 158.0
54 TraesCS1A01G340600 chr2A 92.727 55 4 0 1056 1110 617004284 617004338 3.710000e-11 80.5
55 TraesCS1A01G340600 chr5B 83.925 479 33 16 1805 2255 13315010 13314548 6.920000e-113 418.0
56 TraesCS1A01G340600 chr5B 90.950 221 18 2 2167 2386 564768558 564768339 3.380000e-76 296.0
57 TraesCS1A01G340600 chr4B 83.891 478 34 20 1805 2255 652496460 652496921 2.490000e-112 416.0
58 TraesCS1A01G340600 chr4B 83.857 223 20 7 1900 2120 653272464 653272256 9.810000e-47 198.0
59 TraesCS1A01G340600 chr4B 98.901 91 1 0 4323 4413 40215527 40215437 3.580000e-36 163.0
60 TraesCS1A01G340600 chr4B 85.417 96 11 2 1056 1151 627802331 627802239 3.680000e-16 97.1
61 TraesCS1A01G340600 chr2D 83.408 223 21 6 1900 2120 1689535 1689327 4.560000e-45 193.0
62 TraesCS1A01G340600 chr2B 98.901 91 1 0 4323 4413 531144962 531145052 3.580000e-36 163.0
63 TraesCS1A01G340600 chrUn 97.802 91 2 0 4323 4413 48224269 48224359 1.660000e-34 158.0
64 TraesCS1A01G340600 chrUn 97.802 91 2 0 4323 4413 48225577 48225667 1.660000e-34 158.0
65 TraesCS1A01G340600 chrUn 85.294 136 17 2 1016 1151 401330765 401330897 2.170000e-28 137.0
66 TraesCS1A01G340600 chr7D 91.667 96 5 2 1056 1151 503944154 503944062 3.630000e-26 130.0
67 TraesCS1A01G340600 chr7D 96.774 62 1 1 4411 4471 4255281 4255220 7.910000e-18 102.0
68 TraesCS1A01G340600 chr3D 98.276 58 1 0 4414 4471 497962099 497962156 7.910000e-18 102.0
69 TraesCS1A01G340600 chr3D 95.082 61 1 2 4411 4471 49541378 49541436 1.320000e-15 95.3
70 TraesCS1A01G340600 chr3D 96.552 58 1 1 4414 4471 49546692 49546636 1.320000e-15 95.3
71 TraesCS1A01G340600 chr3B 92.727 55 4 0 1056 1110 644434455 644434401 3.710000e-11 80.5
72 TraesCS1A01G340600 chr4A 100.000 35 0 0 1084 1118 13035294 13035328 1.040000e-06 65.8
73 TraesCS1A01G340600 chr6A 94.872 39 2 0 1084 1122 56944527 56944489 1.340000e-05 62.1


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 TraesCS1A01G340600 chr1A 530728041 530732511 4470 True 3743.000000 5360 100.000000 1 4471 2 chr1A.!!$R2 4470
1 TraesCS1A01G340600 chr1B 583685344 583689568 4224 True 1588.333333 3059 89.160000 1 4320 3 chr1B.!!$R2 4319
2 TraesCS1A01G340600 chr1B 23667655 23668161 506 False 496.000000 496 84.902000 1898 2388 1 chr1B.!!$F2 490
3 TraesCS1A01G340600 chr1B 6412926 6413434 508 False 481.000000 481 84.674000 1898 2388 1 chr1B.!!$F1 490
4 TraesCS1A01G340600 chr1D 432202972 432206574 3602 True 1308.000000 2957 88.605333 73 3825 3 chr1D.!!$R2 3752
5 TraesCS1A01G340600 chr1D 15184471 15184979 508 False 475.000000 475 84.512000 1898 2388 1 chr1D.!!$F1 490
6 TraesCS1A01G340600 chr5D 296177214 296179143 1929 False 626.750000 885 90.850250 1570 4320 4 chr5D.!!$F2 2750
7 TraesCS1A01G340600 chr5D 378329877 378331779 1902 True 623.750000 891 90.941250 1596 4320 4 chr5D.!!$R2 2724
8 TraesCS1A01G340600 chr5D 559439260 559441175 1915 False 521.800000 891 91.817400 1570 4320 5 chr5D.!!$F4 2750
9 TraesCS1A01G340600 chr5D 80201713 80203837 2124 True 506.600000 800 91.485600 1570 4320 5 chr5D.!!$R1 2750
10 TraesCS1A01G340600 chr5A 439769569 439770074 505 True 494.000000 494 85.164000 1898 2388 1 chr5A.!!$R1 490
11 TraesCS1A01G340600 chr3A 227067869 227068375 506 False 468.000000 468 84.231000 1898 2388 1 chr3A.!!$F3 490

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
327 331 0.247934 CCGCCCGCGAATACTTTTTC 60.248 55.0 8.23 0.0 42.83 2.29 F
635 816 0.313672 TTTGTGTTGCATTCTCCGCC 59.686 50.0 0.00 0.0 0.00 6.13 F
2054 2306 0.179163 GCTTTGCGTAGGTTCATGGC 60.179 55.0 0.00 0.0 0.00 4.40 F
3102 3418 0.625849 TCAATTCCTCTGCCCTTCCC 59.374 55.0 0.00 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2193 0.239347 GAATCTACCATGCGCATGCC 59.761 55.0 38.76 19.07 41.78 4.40 R
2558 2854 0.038618 GGTGCCATGAAACCGAAACC 60.039 55.0 0.00 0.00 0.00 3.27 R
3257 3767 0.622665 AGACCATGAAGCCTCCTTGG 59.377 55.0 0.00 0.93 39.35 3.61 R
4417 5005 0.035056 CAGGGGGTGATGTGGACTTC 60.035 60.0 0.00 0.00 0.00 3.01 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
55 56 6.697641 ATTCACCAAGTTTTAGAGTCCCTA 57.302 37.500 0.00 0.00 0.00 3.53
58 59 5.011738 TCACCAAGTTTTAGAGTCCCTACAG 59.988 44.000 0.00 0.00 0.00 2.74
69 70 2.586792 CCTACAGGACCAGGCAGC 59.413 66.667 0.00 0.00 37.39 5.25
90 91 3.561213 CAGAGTGCTGGCGATGCG 61.561 66.667 0.00 0.00 38.51 4.73
137 138 7.548097 TCTGATAACTAGTCTGCTAACTTTGG 58.452 38.462 0.00 0.00 0.00 3.28
222 226 1.004560 CTCGCAGTTGAAGGCCAGA 60.005 57.895 5.01 0.00 0.00 3.86
227 231 1.887956 GCAGTTGAAGGCCAGAATCCA 60.888 52.381 5.01 0.00 0.00 3.41
230 234 3.512724 CAGTTGAAGGCCAGAATCCATTT 59.487 43.478 5.01 0.00 0.00 2.32
241 245 3.129287 CAGAATCCATTTGCTGTACCCAC 59.871 47.826 0.00 0.00 0.00 4.61
242 246 2.897271 ATCCATTTGCTGTACCCACA 57.103 45.000 0.00 0.00 0.00 4.17
299 303 2.481952 GCAGACTCTAGTGCTTGGTTTG 59.518 50.000 0.00 0.00 36.71 2.93
325 329 1.376295 ACCGCCCGCGAATACTTTT 60.376 52.632 8.23 0.00 42.83 2.27
327 331 0.247934 CCGCCCGCGAATACTTTTTC 60.248 55.000 8.23 0.00 42.83 2.29
329 333 0.247934 GCCCGCGAATACTTTTTCGG 60.248 55.000 8.23 0.00 46.52 4.30
336 340 4.491441 CGCGAATACTTTTTCGGTTACCTC 60.491 45.833 0.00 0.00 46.52 3.85
337 341 4.628766 GCGAATACTTTTTCGGTTACCTCT 59.371 41.667 0.00 0.00 46.52 3.69
339 343 6.531439 CGAATACTTTTTCGGTTACCTCTTG 58.469 40.000 0.00 0.00 43.59 3.02
340 344 6.366877 CGAATACTTTTTCGGTTACCTCTTGA 59.633 38.462 0.00 0.00 43.59 3.02
359 363 7.772757 CCTCTTGATGATGATGATGATGATGAT 59.227 37.037 0.00 0.00 0.00 2.45
385 389 2.724744 GCAACACAGCTTTGCTTTTG 57.275 45.000 13.22 5.96 44.96 2.44
412 416 2.356553 TTCCCTTTCCGCGACACG 60.357 61.111 8.23 0.00 43.15 4.49
422 426 2.742372 GCGACACGGGACAAGCAT 60.742 61.111 0.00 0.00 0.00 3.79
437 441 5.806654 ACAAGCATTTGTAATCCCAAACT 57.193 34.783 0.00 0.00 45.45 2.66
438 442 5.540911 ACAAGCATTTGTAATCCCAAACTG 58.459 37.500 0.00 0.00 45.45 3.16
504 663 2.277247 GTGCGTGTGTGTGTGTGC 60.277 61.111 0.00 0.00 0.00 4.57
594 775 1.299468 CTCGTGGCATCTCCGCTAC 60.299 63.158 0.00 0.00 43.21 3.58
627 808 1.066908 CTGGACCGTTTTGTGTTGCAT 59.933 47.619 0.00 0.00 0.00 3.96
632 813 2.223711 ACCGTTTTGTGTTGCATTCTCC 60.224 45.455 0.00 0.00 0.00 3.71
635 816 0.313672 TTTGTGTTGCATTCTCCGCC 59.686 50.000 0.00 0.00 0.00 6.13
642 823 1.321805 TGCATTCTCCGCCCCAAATG 61.322 55.000 0.00 0.00 33.31 2.32
652 833 2.755655 CCGCCCCAAATGTGTATGTAAA 59.244 45.455 0.00 0.00 0.00 2.01
675 856 5.565509 ACTTTGATCTTCTCCTTTCCTTCC 58.434 41.667 0.00 0.00 0.00 3.46
687 868 3.307059 CCTTTCCTTCCTCGTGAACATCT 60.307 47.826 0.00 0.00 0.00 2.90
694 875 5.348997 CCTTCCTCGTGAACATCTAGTTTTC 59.651 44.000 0.00 0.00 41.51 2.29
695 876 5.723672 TCCTCGTGAACATCTAGTTTTCT 57.276 39.130 0.00 0.00 41.51 2.52
696 877 6.097915 TCCTCGTGAACATCTAGTTTTCTT 57.902 37.500 0.00 0.00 41.51 2.52
697 878 6.522054 TCCTCGTGAACATCTAGTTTTCTTT 58.478 36.000 0.00 0.00 41.51 2.52
698 879 6.990349 TCCTCGTGAACATCTAGTTTTCTTTT 59.010 34.615 0.00 0.00 41.51 2.27
699 880 7.497909 TCCTCGTGAACATCTAGTTTTCTTTTT 59.502 33.333 0.00 0.00 41.51 1.94
700 881 7.798982 CCTCGTGAACATCTAGTTTTCTTTTTC 59.201 37.037 0.00 0.00 41.51 2.29
701 882 8.433421 TCGTGAACATCTAGTTTTCTTTTTCT 57.567 30.769 0.00 0.00 41.51 2.52
702 883 8.889717 TCGTGAACATCTAGTTTTCTTTTTCTT 58.110 29.630 0.00 0.00 41.51 2.52
703 884 9.159470 CGTGAACATCTAGTTTTCTTTTTCTTC 57.841 33.333 0.00 0.00 41.51 2.87
704 885 9.452065 GTGAACATCTAGTTTTCTTTTTCTTCC 57.548 33.333 0.00 0.00 41.51 3.46
800 1015 4.054780 TCTCGAAATTAACTCGGATGGG 57.945 45.455 8.49 0.00 36.93 4.00
879 1100 1.582610 AAAAGCATACCGCCACCACG 61.583 55.000 0.00 0.00 44.04 4.94
905 1126 2.280186 GGCATCCACCCGATCGAC 60.280 66.667 18.66 0.00 0.00 4.20
1015 1236 4.741239 ACATGGCCTCCTCCCCGT 62.741 66.667 3.32 0.00 0.00 5.28
1089 1310 2.815647 CAGTCGCCCTTCTTCCGC 60.816 66.667 0.00 0.00 0.00 5.54
1927 2170 5.645497 ACCATGATGCTCTTCTTTACTTGTC 59.355 40.000 0.00 0.00 0.00 3.18
1950 2193 1.520342 GAGGAAGCTGTAGCCTGCG 60.520 63.158 0.00 0.00 43.38 5.18
2048 2300 1.028905 TTTGCTGCTTTGCGTAGGTT 58.971 45.000 0.00 0.00 35.36 3.50
2049 2301 0.591170 TTGCTGCTTTGCGTAGGTTC 59.409 50.000 0.00 0.00 35.36 3.62
2050 2302 0.533978 TGCTGCTTTGCGTAGGTTCA 60.534 50.000 0.00 0.00 35.36 3.18
2051 2303 0.804989 GCTGCTTTGCGTAGGTTCAT 59.195 50.000 0.00 0.00 0.00 2.57
2052 2304 1.466360 GCTGCTTTGCGTAGGTTCATG 60.466 52.381 0.00 0.00 0.00 3.07
2053 2305 1.131126 CTGCTTTGCGTAGGTTCATGG 59.869 52.381 0.00 0.00 0.00 3.66
2054 2306 0.179163 GCTTTGCGTAGGTTCATGGC 60.179 55.000 0.00 0.00 0.00 4.40
2089 2341 1.310933 CCATGTGCTTGCTCCTGTCC 61.311 60.000 0.00 0.00 0.00 4.02
2227 2505 1.517257 CAGGAGCCGTCACTTAGCG 60.517 63.158 0.00 0.00 0.00 4.26
2237 2515 2.462565 CGTCACTTAGCGTTTTTGTTGC 59.537 45.455 0.00 0.00 0.00 4.17
2456 2738 3.497262 GGTTTCTGTTCTACCTTTCGGTG 59.503 47.826 0.00 0.00 45.18 4.94
2503 2785 9.848172 CAACAGTTGTATTAATTTGCTTTGTTC 57.152 29.630 4.99 0.00 0.00 3.18
2633 2929 8.394971 TGATTGTCTACTTGTTCAATTCACAT 57.605 30.769 0.00 0.00 31.87 3.21
2720 3022 6.515272 TGCATTCTCTTTATTCCAGTTTCC 57.485 37.500 0.00 0.00 0.00 3.13
2752 3054 6.872020 GTGTCACTATTTCTTAGCTACACCAA 59.128 38.462 0.00 0.00 39.09 3.67
2784 3086 3.859118 TTGGGTCCCCATGCGTGTG 62.859 63.158 5.75 0.00 46.64 3.82
2785 3087 4.344865 GGGTCCCCATGCGTGTGT 62.345 66.667 4.96 0.00 35.81 3.72
2786 3088 3.055719 GGTCCCCATGCGTGTGTG 61.056 66.667 4.96 0.00 0.00 3.82
2787 3089 2.281484 GTCCCCATGCGTGTGTGT 60.281 61.111 4.96 0.00 0.00 3.72
2788 3090 1.004320 GTCCCCATGCGTGTGTGTA 60.004 57.895 4.96 0.00 0.00 2.90
2789 3091 1.004320 TCCCCATGCGTGTGTGTAC 60.004 57.895 4.96 0.00 0.00 2.90
2842 3148 3.698029 ACATGAAACACACAGTGAAGC 57.302 42.857 7.81 0.00 36.96 3.86
2858 3164 1.138859 GAAGCTGGTTTTGGCCTGTTT 59.861 47.619 3.32 0.00 34.65 2.83
2865 3171 3.257127 TGGTTTTGGCCTGTTTAGTATGC 59.743 43.478 3.32 0.00 0.00 3.14
2872 3181 4.830046 TGGCCTGTTTAGTATGCTTTTCAA 59.170 37.500 3.32 0.00 0.00 2.69
2875 3184 6.212955 GCCTGTTTAGTATGCTTTTCAACAA 58.787 36.000 0.00 0.00 0.00 2.83
3013 3328 3.326880 TCCGGAACCTAGCTCTTTTCTTT 59.673 43.478 0.00 0.00 0.00 2.52
3035 3350 9.567776 TCTTTACAAATGTTTATCTCAGTTCCA 57.432 29.630 0.00 0.00 0.00 3.53
3095 3411 1.739466 TGCGACAATCAATTCCTCTGC 59.261 47.619 0.00 0.00 0.00 4.26
3102 3418 0.625849 TCAATTCCTCTGCCCTTCCC 59.374 55.000 0.00 0.00 0.00 3.97
3257 3767 2.139118 GATAGGCTCGCTGGAATCAAC 58.861 52.381 0.00 0.00 0.00 3.18
3281 3791 0.915364 GAGGCTTCATGGTCTCCCTT 59.085 55.000 0.00 0.00 32.35 3.95
3310 3820 3.777106 ATCACTTGTCCTGAAGAGCAA 57.223 42.857 0.00 0.00 0.00 3.91
3410 3920 1.663702 GCGTCGTACAACAGGCAGT 60.664 57.895 0.00 0.00 0.00 4.40
3413 3923 1.137513 GTCGTACAACAGGCAGTGTC 58.862 55.000 0.00 0.00 39.03 3.67
3440 3950 3.303132 CGCCAGCGAAATCTATTGTAACC 60.303 47.826 6.06 0.00 42.83 2.85
3501 4011 4.804261 GCCTGTGGACCAATGATATACCTC 60.804 50.000 0.00 0.00 0.00 3.85
3504 4014 4.347876 TGTGGACCAATGATATACCTCCAG 59.652 45.833 0.00 0.00 0.00 3.86
3509 4019 4.780021 ACCAATGATATACCTCCAGCCTAG 59.220 45.833 0.00 0.00 0.00 3.02
3516 4026 0.326048 ACCTCCAGCCTAGCATGTCT 60.326 55.000 0.00 0.00 0.00 3.41
3517 4027 0.392336 CCTCCAGCCTAGCATGTCTC 59.608 60.000 0.00 0.00 0.00 3.36
3525 4035 2.871022 GCCTAGCATGTCTCATCTGTTG 59.129 50.000 0.00 0.00 0.00 3.33
3532 4042 4.201792 GCATGTCTCATCTGTTGTGTGATC 60.202 45.833 0.00 0.00 0.00 2.92
3533 4043 4.879197 TGTCTCATCTGTTGTGTGATCT 57.121 40.909 0.00 0.00 0.00 2.75
3550 4065 1.725641 TCTGTCACGGTGATTGATGC 58.274 50.000 14.78 0.59 0.00 3.91
3551 4066 1.276138 TCTGTCACGGTGATTGATGCT 59.724 47.619 14.78 0.00 0.00 3.79
3554 4069 2.028567 TGTCACGGTGATTGATGCTGTA 60.029 45.455 14.78 0.00 0.00 2.74
3556 4071 1.328680 CACGGTGATTGATGCTGTAGC 59.671 52.381 0.74 0.00 42.50 3.58
3569 4084 3.528009 GCTGTAGCAAGTGAGTTTGTC 57.472 47.619 0.00 0.00 41.59 3.18
3570 4085 2.224314 GCTGTAGCAAGTGAGTTTGTCC 59.776 50.000 0.00 0.00 41.59 4.02
3572 4087 1.194772 GTAGCAAGTGAGTTTGTCCGC 59.805 52.381 0.00 0.00 0.00 5.54
3573 4088 1.166531 AGCAAGTGAGTTTGTCCGCC 61.167 55.000 0.00 0.00 0.00 6.13
3574 4089 1.444119 GCAAGTGAGTTTGTCCGCCA 61.444 55.000 0.00 0.00 0.00 5.69
3577 4095 1.308998 AGTGAGTTTGTCCGCCAAAG 58.691 50.000 0.00 0.00 43.52 2.77
3585 4103 4.338710 TCCGCCAAAGGGTTCGGG 62.339 66.667 0.00 0.00 39.48 5.14
3593 4111 0.037734 AAAGGGTTCGGGAGCGAAAT 59.962 50.000 0.00 0.00 0.00 2.17
3595 4113 0.037734 AGGGTTCGGGAGCGAAATTT 59.962 50.000 0.00 0.00 0.00 1.82
3617 4135 2.100087 GAGAGAATCCGGAGAAGTGGAC 59.900 54.545 11.34 0.00 37.02 4.02
3659 4186 7.807433 GTGATGTAACAGTTATGAATGTGCAAA 59.193 33.333 0.00 0.00 0.00 3.68
3660 4187 8.355913 TGATGTAACAGTTATGAATGTGCAAAA 58.644 29.630 0.00 0.00 0.00 2.44
3671 4198 6.414408 TGAATGTGCAAAATTTTCACGTTT 57.586 29.167 25.08 19.65 33.69 3.60
3720 4247 4.438200 CGGCTGTTGTAACTTTGTGTTCTT 60.438 41.667 0.00 0.00 39.89 2.52
3776 4303 6.875726 TGAATGACGAAACTGAGATCTCAATT 59.124 34.615 25.09 19.52 39.39 2.32
3777 4304 8.034804 TGAATGACGAAACTGAGATCTCAATTA 58.965 33.333 25.09 7.74 39.39 1.40
3809 4336 2.279741 GTCCGCTGCAATCTACATGAA 58.720 47.619 0.00 0.00 0.00 2.57
3902 4485 4.014847 ACATCGTTTACAATGGCATTCG 57.985 40.909 10.36 10.66 0.00 3.34
3924 4507 0.712380 AGGAATGCAGGGGGTTCATT 59.288 50.000 0.00 0.00 33.57 2.57
3970 4553 7.739022 TTATTGTCATAAGCAAATTTCGCTG 57.261 32.000 13.49 5.44 40.35 5.18
4004 4587 3.879295 ACCTCAGTTGTTTGACAGACATG 59.121 43.478 0.00 0.00 0.00 3.21
4073 4657 4.546674 TGAACTCTCCACATAGATAGCCA 58.453 43.478 0.00 0.00 0.00 4.75
4092 4676 2.634453 CCAAAAGCTTCACCCCAAATCT 59.366 45.455 0.00 0.00 0.00 2.40
4109 4693 6.206243 CCCAAATCTTATATCTTGTCCTGCAG 59.794 42.308 6.78 6.78 0.00 4.41
4111 4695 7.500227 CCAAATCTTATATCTTGTCCTGCAGAA 59.500 37.037 17.39 0.00 0.00 3.02
4156 4740 2.588539 CGAGTCGTTCGTATTGAGTGTG 59.411 50.000 3.82 0.00 44.27 3.82
4210 4794 2.688446 TGAGAGCGTTCGTATTGGATCT 59.312 45.455 0.00 0.00 0.00 2.75
4211 4795 3.881089 TGAGAGCGTTCGTATTGGATCTA 59.119 43.478 0.00 0.00 0.00 1.98
4212 4796 4.220572 GAGAGCGTTCGTATTGGATCTAC 58.779 47.826 0.00 0.00 0.00 2.59
4213 4797 3.884091 AGAGCGTTCGTATTGGATCTACT 59.116 43.478 0.00 0.00 0.00 2.57
4235 4821 3.914312 AGTGTGGTCATAGAACGTTCAG 58.086 45.455 28.78 17.94 0.00 3.02
4261 4847 3.433306 TTTTCAATCAGGGTCATCCGT 57.567 42.857 0.00 0.00 41.52 4.69
4269 4855 0.038166 AGGGTCATCCGTGTGCATTT 59.962 50.000 0.00 0.00 41.52 2.32
4328 4916 8.798975 TGGGAATAGATAGATTTACTCAACCT 57.201 34.615 0.00 0.00 0.00 3.50
4329 4917 8.651389 TGGGAATAGATAGATTTACTCAACCTG 58.349 37.037 0.00 0.00 0.00 4.00
4330 4918 8.652290 GGGAATAGATAGATTTACTCAACCTGT 58.348 37.037 0.00 0.00 0.00 4.00
4331 4919 9.482627 GGAATAGATAGATTTACTCAACCTGTG 57.517 37.037 0.00 0.00 0.00 3.66
4332 4920 9.482627 GAATAGATAGATTTACTCAACCTGTGG 57.517 37.037 0.00 0.00 0.00 4.17
4333 4921 6.875972 AGATAGATTTACTCAACCTGTGGT 57.124 37.500 0.00 0.00 37.65 4.16
4343 4931 2.525105 AACCTGTGGTTGAGTTGGTT 57.475 45.000 0.71 0.00 45.07 3.67
4344 4932 3.655615 AACCTGTGGTTGAGTTGGTTA 57.344 42.857 0.71 0.00 45.07 2.85
4345 4933 3.208747 ACCTGTGGTTGAGTTGGTTAG 57.791 47.619 0.00 0.00 27.29 2.34
4346 4934 2.158667 ACCTGTGGTTGAGTTGGTTAGG 60.159 50.000 0.00 0.00 27.29 2.69
4347 4935 2.158667 CCTGTGGTTGAGTTGGTTAGGT 60.159 50.000 0.00 0.00 0.00 3.08
4348 4936 2.878406 CTGTGGTTGAGTTGGTTAGGTG 59.122 50.000 0.00 0.00 0.00 4.00
4349 4937 2.227194 GTGGTTGAGTTGGTTAGGTGG 58.773 52.381 0.00 0.00 0.00 4.61
4350 4938 2.128535 TGGTTGAGTTGGTTAGGTGGA 58.871 47.619 0.00 0.00 0.00 4.02
4351 4939 2.158726 TGGTTGAGTTGGTTAGGTGGAC 60.159 50.000 0.00 0.00 0.00 4.02
4352 4940 2.158726 GGTTGAGTTGGTTAGGTGGACA 60.159 50.000 0.00 0.00 0.00 4.02
4353 4941 3.139077 GTTGAGTTGGTTAGGTGGACAG 58.861 50.000 0.00 0.00 0.00 3.51
4354 4942 2.404559 TGAGTTGGTTAGGTGGACAGT 58.595 47.619 0.00 0.00 0.00 3.55
4355 4943 2.104111 TGAGTTGGTTAGGTGGACAGTG 59.896 50.000 0.00 0.00 0.00 3.66
4356 4944 1.420138 AGTTGGTTAGGTGGACAGTGG 59.580 52.381 0.00 0.00 0.00 4.00
4357 4945 1.142262 GTTGGTTAGGTGGACAGTGGT 59.858 52.381 0.00 0.00 0.00 4.16
4358 4946 2.369532 GTTGGTTAGGTGGACAGTGGTA 59.630 50.000 0.00 0.00 0.00 3.25
4359 4947 2.910544 TGGTTAGGTGGACAGTGGTAT 58.089 47.619 0.00 0.00 0.00 2.73
4360 4948 2.835764 TGGTTAGGTGGACAGTGGTATC 59.164 50.000 0.00 0.00 0.00 2.24
4361 4949 2.169978 GGTTAGGTGGACAGTGGTATCC 59.830 54.545 0.00 0.00 35.37 2.59
4362 4950 2.169978 GTTAGGTGGACAGTGGTATCCC 59.830 54.545 0.00 0.00 33.69 3.85
4363 4951 0.417841 AGGTGGACAGTGGTATCCCT 59.582 55.000 0.00 0.00 33.69 4.20
4364 4952 1.649633 AGGTGGACAGTGGTATCCCTA 59.350 52.381 0.00 0.00 33.69 3.53
4365 4953 2.045326 AGGTGGACAGTGGTATCCCTAA 59.955 50.000 0.00 0.00 33.69 2.69
4366 4954 2.169978 GGTGGACAGTGGTATCCCTAAC 59.830 54.545 0.00 0.00 33.69 2.34
4367 4955 2.169978 GTGGACAGTGGTATCCCTAACC 59.830 54.545 0.00 0.00 37.53 2.85
4368 4956 1.767088 GGACAGTGGTATCCCTAACCC 59.233 57.143 0.00 0.00 36.06 4.11
4369 4957 2.474112 GACAGTGGTATCCCTAACCCA 58.526 52.381 0.00 0.00 36.06 4.51
4370 4958 3.046374 GACAGTGGTATCCCTAACCCAT 58.954 50.000 0.00 0.00 36.06 4.00
4371 4959 3.046374 ACAGTGGTATCCCTAACCCATC 58.954 50.000 0.00 0.00 36.06 3.51
4372 4960 3.045634 CAGTGGTATCCCTAACCCATCA 58.954 50.000 0.00 0.00 36.06 3.07
4373 4961 3.071602 CAGTGGTATCCCTAACCCATCAG 59.928 52.174 0.00 0.00 36.06 2.90
4374 4962 2.372172 GTGGTATCCCTAACCCATCAGG 59.628 54.545 0.00 0.00 43.78 3.86
4390 4978 3.363787 AGGGTTCAAATCCTGGTGC 57.636 52.632 0.00 0.00 38.36 5.01
4391 4979 0.779997 AGGGTTCAAATCCTGGTGCT 59.220 50.000 0.00 0.00 38.36 4.40
4392 4980 1.177401 GGGTTCAAATCCTGGTGCTC 58.823 55.000 0.00 0.00 0.00 4.26
4393 4981 0.804989 GGTTCAAATCCTGGTGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
4394 4982 0.169009 GTTCAAATCCTGGTGCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
4395 4983 0.250684 TTCAAATCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
4396 4984 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
4397 4985 0.813184 CAAATCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
4398 4986 2.016318 CAAATCCTGGTGCTCGCATTA 58.984 47.619 0.00 0.00 0.00 1.90
4399 4987 2.620115 CAAATCCTGGTGCTCGCATTAT 59.380 45.455 0.00 0.00 0.00 1.28
4400 4988 2.645838 ATCCTGGTGCTCGCATTATT 57.354 45.000 0.00 0.00 0.00 1.40
4401 4989 1.953559 TCCTGGTGCTCGCATTATTC 58.046 50.000 0.00 0.00 0.00 1.75
4402 4990 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
4403 4991 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
4404 4992 1.600957 CTGGTGCTCGCATTATTCCTG 59.399 52.381 0.00 0.00 0.00 3.86
4405 4993 1.209261 TGGTGCTCGCATTATTCCTGA 59.791 47.619 0.00 0.00 0.00 3.86
4406 4994 2.288666 GGTGCTCGCATTATTCCTGAA 58.711 47.619 0.00 0.00 0.00 3.02
4407 4995 2.880890 GGTGCTCGCATTATTCCTGAAT 59.119 45.455 0.00 0.00 34.93 2.57
4408 4996 3.316308 GGTGCTCGCATTATTCCTGAATT 59.684 43.478 0.00 0.00 32.50 2.17
4409 4997 4.202050 GGTGCTCGCATTATTCCTGAATTT 60.202 41.667 0.00 0.00 32.50 1.82
4410 4998 5.008613 GGTGCTCGCATTATTCCTGAATTTA 59.991 40.000 0.00 0.00 32.50 1.40
4411 4999 6.294176 GGTGCTCGCATTATTCCTGAATTTAT 60.294 38.462 0.00 0.00 32.50 1.40
4412 5000 7.141363 GTGCTCGCATTATTCCTGAATTTATT 58.859 34.615 0.00 0.00 32.50 1.40
4413 5001 7.113965 GTGCTCGCATTATTCCTGAATTTATTG 59.886 37.037 0.00 0.00 32.50 1.90
4414 5002 7.013178 TGCTCGCATTATTCCTGAATTTATTGA 59.987 33.333 0.00 0.00 32.50 2.57
4415 5003 7.862372 GCTCGCATTATTCCTGAATTTATTGAA 59.138 33.333 0.00 0.00 32.50 2.69
4416 5004 9.734620 CTCGCATTATTCCTGAATTTATTGAAA 57.265 29.630 0.00 0.00 32.50 2.69
4417 5005 9.734620 TCGCATTATTCCTGAATTTATTGAAAG 57.265 29.630 0.00 0.00 32.50 2.62
4418 5006 9.734620 CGCATTATTCCTGAATTTATTGAAAGA 57.265 29.630 0.00 0.00 32.50 2.52
4424 5012 8.704849 TTCCTGAATTTATTGAAAGAAGTCCA 57.295 30.769 0.00 0.00 0.00 4.02
4425 5013 8.110860 TCCTGAATTTATTGAAAGAAGTCCAC 57.889 34.615 0.00 0.00 0.00 4.02
4426 5014 7.723616 TCCTGAATTTATTGAAAGAAGTCCACA 59.276 33.333 0.00 0.00 0.00 4.17
4427 5015 8.526147 CCTGAATTTATTGAAAGAAGTCCACAT 58.474 33.333 0.00 0.00 0.00 3.21
4428 5016 9.565213 CTGAATTTATTGAAAGAAGTCCACATC 57.435 33.333 0.00 0.00 0.00 3.06
4429 5017 9.076781 TGAATTTATTGAAAGAAGTCCACATCA 57.923 29.630 0.00 0.00 0.00 3.07
4430 5018 9.346725 GAATTTATTGAAAGAAGTCCACATCAC 57.653 33.333 0.00 0.00 0.00 3.06
4431 5019 6.817765 TTATTGAAAGAAGTCCACATCACC 57.182 37.500 0.00 0.00 0.00 4.02
4432 5020 3.140325 TGAAAGAAGTCCACATCACCC 57.860 47.619 0.00 0.00 0.00 4.61
4433 5021 2.224769 TGAAAGAAGTCCACATCACCCC 60.225 50.000 0.00 0.00 0.00 4.95
4434 5022 0.698818 AAGAAGTCCACATCACCCCC 59.301 55.000 0.00 0.00 0.00 5.40
4435 5023 0.178861 AGAAGTCCACATCACCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
4436 5024 0.035056 GAAGTCCACATCACCCCCTG 60.035 60.000 0.00 0.00 0.00 4.45
4437 5025 0.772124 AAGTCCACATCACCCCCTGT 60.772 55.000 0.00 0.00 0.00 4.00
4438 5026 1.002134 GTCCACATCACCCCCTGTG 60.002 63.158 0.00 0.00 46.88 3.66
4440 5028 3.170362 CACATCACCCCCTGTGGT 58.830 61.111 0.00 0.00 45.48 4.16
4441 5029 1.460255 CACATCACCCCCTGTGGTT 59.540 57.895 0.00 0.00 45.48 3.67
4442 5030 0.178964 CACATCACCCCCTGTGGTTT 60.179 55.000 0.00 0.00 45.48 3.27
4443 5031 0.112412 ACATCACCCCCTGTGGTTTC 59.888 55.000 0.00 0.00 45.48 2.78
4444 5032 0.112218 CATCACCCCCTGTGGTTTCA 59.888 55.000 0.00 0.00 45.48 2.69
4445 5033 0.405585 ATCACCCCCTGTGGTTTCAG 59.594 55.000 0.00 0.00 45.48 3.02
4446 5034 0.696143 TCACCCCCTGTGGTTTCAGA 60.696 55.000 0.00 0.00 45.48 3.27
4447 5035 0.184933 CACCCCCTGTGGTTTCAGAA 59.815 55.000 0.00 0.00 41.52 3.02
4448 5036 0.930726 ACCCCCTGTGGTTTCAGAAA 59.069 50.000 0.00 0.00 33.91 2.52
4449 5037 1.328279 CCCCCTGTGGTTTCAGAAAC 58.672 55.000 16.63 16.63 40.65 2.78
4458 5046 2.983402 GTTTCAGAAACCGGCTAACC 57.017 50.000 14.34 0.00 35.35 2.85
4459 5047 1.538512 GTTTCAGAAACCGGCTAACCC 59.461 52.381 14.34 0.00 35.35 4.11
4460 5048 0.766131 TTCAGAAACCGGCTAACCCA 59.234 50.000 0.00 0.00 0.00 4.51
4461 5049 0.035739 TCAGAAACCGGCTAACCCAC 59.964 55.000 0.00 0.00 0.00 4.61
4462 5050 0.958876 CAGAAACCGGCTAACCCACC 60.959 60.000 0.00 0.00 0.00 4.61
4463 5051 1.676635 GAAACCGGCTAACCCACCC 60.677 63.158 0.00 0.00 0.00 4.61
4464 5052 3.214190 AAACCGGCTAACCCACCCC 62.214 63.158 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.897436 TCATGAATCACGAGCCTTCAG 58.103 47.619 0.00 0.00 32.82 3.02
14 15 5.334414 GGTGAATATTCATGAATCACGAGCC 60.334 44.000 23.95 15.62 39.73 4.70
55 56 4.341783 GCTGCTGCCTGGTCCTGT 62.342 66.667 3.85 0.00 0.00 4.00
90 91 4.708726 AGCAATACCAAAGATGCAACTC 57.291 40.909 0.00 0.00 41.18 3.01
100 101 8.540388 AGACTAGTTATCAGAAGCAATACCAAA 58.460 33.333 0.00 0.00 0.00 3.28
222 226 2.825532 GTGTGGGTACAGCAAATGGATT 59.174 45.455 0.00 0.00 37.52 3.01
241 245 1.306148 ATCAAGCGATGCATGAGGTG 58.694 50.000 2.46 0.00 39.56 4.00
242 246 1.945394 GAATCAAGCGATGCATGAGGT 59.055 47.619 2.46 0.00 39.56 3.85
318 322 7.391620 TCATCAAGAGGTAACCGAAAAAGTAT 58.608 34.615 0.00 0.00 37.17 2.12
325 329 5.128663 TCATCATCATCAAGAGGTAACCGAA 59.871 40.000 0.00 0.00 37.17 4.30
327 331 4.948847 TCATCATCATCAAGAGGTAACCG 58.051 43.478 0.00 0.00 37.17 4.44
328 332 6.528321 TCATCATCATCATCAAGAGGTAACC 58.472 40.000 0.00 0.00 37.17 2.85
329 333 7.876582 TCATCATCATCATCATCAAGAGGTAAC 59.123 37.037 0.00 0.00 0.00 2.50
336 340 8.498054 TCATCATCATCATCATCATCATCAAG 57.502 34.615 0.00 0.00 0.00 3.02
339 343 9.771534 ACTATCATCATCATCATCATCATCATC 57.228 33.333 0.00 0.00 0.00 2.92
340 344 9.553064 CACTATCATCATCATCATCATCATCAT 57.447 33.333 0.00 0.00 0.00 2.45
359 363 3.902261 CAAAGCTGTGTTGCACTATCA 57.098 42.857 0.00 0.00 35.11 2.15
394 398 2.664436 CGTGTCGCGGAAAGGGAAC 61.664 63.158 6.13 0.00 43.70 3.62
395 399 2.356553 CGTGTCGCGGAAAGGGAA 60.357 61.111 6.13 0.00 43.70 3.97
412 416 3.096092 TGGGATTACAAATGCTTGTCCC 58.904 45.455 6.99 6.99 42.25 4.46
414 418 5.634859 CAGTTTGGGATTACAAATGCTTGTC 59.365 40.000 0.00 0.00 42.25 3.18
422 426 8.387813 AGATAACCTACAGTTTGGGATTACAAA 58.612 33.333 0.00 0.00 40.05 2.83
431 435 5.429130 GGGAGAAGATAACCTACAGTTTGG 58.571 45.833 0.00 0.00 40.05 3.28
491 650 4.250431 GGGCGCACACACACACAC 62.250 66.667 10.83 0.00 0.00 3.82
492 651 4.785453 TGGGCGCACACACACACA 62.785 61.111 9.15 0.00 0.00 3.72
493 652 3.468266 CTTGGGCGCACACACACAC 62.468 63.158 14.54 0.00 0.00 3.82
494 653 3.208383 CTTGGGCGCACACACACA 61.208 61.111 14.54 0.00 0.00 3.72
504 663 4.303257 GAGGTTTCCTCTTGGGCG 57.697 61.111 8.38 0.00 46.41 6.13
613 794 2.043411 CGGAGAATGCAACACAAAACG 58.957 47.619 0.00 0.00 0.00 3.60
627 808 0.693622 TACACATTTGGGGCGGAGAA 59.306 50.000 0.00 0.00 0.00 2.87
632 813 3.442273 AGTTTACATACACATTTGGGGCG 59.558 43.478 0.00 0.00 0.00 6.13
635 816 8.522830 AGATCAAAGTTTACATACACATTTGGG 58.477 33.333 0.00 0.00 0.00 4.12
642 823 8.779354 AGGAGAAGATCAAAGTTTACATACAC 57.221 34.615 0.00 0.00 0.00 2.90
652 833 5.311913 AGGAAGGAAAGGAGAAGATCAAAGT 59.688 40.000 0.00 0.00 0.00 2.66
675 856 8.552034 AGAAAAAGAAAACTAGATGTTCACGAG 58.448 33.333 0.00 0.00 38.03 4.18
773 988 3.491267 CCGAGTTAATTTCGAGATCCTGC 59.509 47.826 12.28 0.00 40.36 4.85
780 995 3.793559 ACCCATCCGAGTTAATTTCGAG 58.206 45.455 12.28 4.89 40.36 4.04
944 1165 4.500116 GAGCTGGACTCGGACGGC 62.500 72.222 0.00 0.00 35.18 5.68
951 1172 0.035915 GAGGGTTTGGAGCTGGACTC 60.036 60.000 0.00 0.00 45.45 3.36
952 1173 0.768221 TGAGGGTTTGGAGCTGGACT 60.768 55.000 0.00 0.00 0.00 3.85
954 1175 0.110486 GTTGAGGGTTTGGAGCTGGA 59.890 55.000 0.00 0.00 0.00 3.86
955 1176 0.895559 GGTTGAGGGTTTGGAGCTGG 60.896 60.000 0.00 0.00 0.00 4.85
956 1177 0.895559 GGGTTGAGGGTTTGGAGCTG 60.896 60.000 0.00 0.00 0.00 4.24
957 1178 1.460699 GGGTTGAGGGTTTGGAGCT 59.539 57.895 0.00 0.00 0.00 4.09
958 1179 1.606601 GGGGTTGAGGGTTTGGAGC 60.607 63.158 0.00 0.00 0.00 4.70
959 1180 1.076727 GGGGGTTGAGGGTTTGGAG 59.923 63.158 0.00 0.00 0.00 3.86
1739 1972 4.106925 GGAGTGCAGGGGCTGGAG 62.107 72.222 0.00 0.00 41.91 3.86
1927 2170 2.746362 CAGGCTACAGCTTCCTCAAAAG 59.254 50.000 0.54 0.00 41.70 2.27
1950 2193 0.239347 GAATCTACCATGCGCATGCC 59.761 55.000 38.76 19.07 41.78 4.40
2048 2300 1.380246 GGCCATGAACCTGCCATGA 60.380 57.895 0.00 0.00 44.70 3.07
2049 2301 3.213264 GGCCATGAACCTGCCATG 58.787 61.111 0.00 0.00 44.70 3.66
2050 2302 2.866523 CAGGGCCATGAACCTGCCAT 62.867 60.000 13.35 6.94 46.78 4.40
2051 2303 3.588817 CAGGGCCATGAACCTGCCA 62.589 63.158 13.35 0.00 46.78 4.92
2052 2304 2.757099 CAGGGCCATGAACCTGCC 60.757 66.667 13.35 11.18 46.78 4.85
2089 2341 1.170442 TGCTGTTGCTCATGGACATG 58.830 50.000 5.95 5.95 40.48 3.21
2212 2490 1.145803 AAAACGCTAAGTGACGGCTC 58.854 50.000 0.00 0.00 0.00 4.70
2227 2505 5.741982 CCTATATAAGGCACGCAACAAAAAC 59.258 40.000 0.00 0.00 38.97 2.43
2237 2515 6.173339 ACCAATTCATCCTATATAAGGCACG 58.827 40.000 0.00 0.00 46.10 5.34
2277 2555 4.223032 AGCGAGAATCTGTAGAAGGGAAAA 59.777 41.667 0.00 0.00 0.00 2.29
2334 2616 9.241919 TGATGTCTCAATATAACACCACATTTT 57.758 29.630 0.00 0.00 0.00 1.82
2456 2738 3.071747 TGGGAAAACATAAAAACAGGGGC 59.928 43.478 0.00 0.00 0.00 5.80
2503 2785 4.174411 TGTCGAGTCACAGTTCATTAGG 57.826 45.455 0.00 0.00 0.00 2.69
2511 2807 5.196341 TCAAGTTTATGTCGAGTCACAGT 57.804 39.130 0.00 0.00 0.00 3.55
2558 2854 0.038618 GGTGCCATGAAACCGAAACC 60.039 55.000 0.00 0.00 0.00 3.27
2633 2929 4.558226 ATCTGAGTGAAGCCATACAACA 57.442 40.909 0.00 0.00 0.00 3.33
2752 3054 0.465460 ACCCAACTTGATGTGCACGT 60.465 50.000 12.38 12.38 0.00 4.49
2789 3091 3.735820 GCCAAATCATACACCACAGCATG 60.736 47.826 0.00 0.00 46.00 4.06
2842 3148 4.618227 GCATACTAAACAGGCCAAAACCAG 60.618 45.833 5.01 0.00 0.00 4.00
2858 3164 7.270757 ACATGTGTTGTTGAAAAGCATACTA 57.729 32.000 0.00 0.00 33.74 1.82
2872 3181 4.955811 TCCAGACTAGAACATGTGTTGT 57.044 40.909 0.00 1.81 41.53 3.32
2875 3184 7.124901 ACAGATTATCCAGACTAGAACATGTGT 59.875 37.037 0.00 0.00 0.00 3.72
2926 3235 6.603599 ACAGGCCAGAGAAACCTATAAAAATC 59.396 38.462 5.01 0.00 30.84 2.17
2993 3308 5.235516 TGTAAAGAAAAGAGCTAGGTTCCG 58.764 41.667 0.00 0.00 0.00 4.30
3084 3400 0.627986 AGGGAAGGGCAGAGGAATTG 59.372 55.000 0.00 0.00 0.00 2.32
3095 3411 4.367039 TTGTCAGTTTAAGAGGGAAGGG 57.633 45.455 0.00 0.00 0.00 3.95
3257 3767 0.622665 AGACCATGAAGCCTCCTTGG 59.377 55.000 0.00 0.93 39.35 3.61
3281 3791 3.323691 TCAGGACAAGTGATTTCGAAGGA 59.676 43.478 0.00 0.00 0.00 3.36
3310 3820 1.143684 ACTGGTTTGATGCTCCTGTGT 59.856 47.619 0.00 0.00 33.41 3.72
3317 3827 1.915141 CTCCCAACTGGTTTGATGCT 58.085 50.000 0.00 0.00 37.39 3.79
3440 3950 5.561532 GCCGAATATCAAGTCCATCACATTG 60.562 44.000 0.00 0.00 0.00 2.82
3501 4011 1.693062 AGATGAGACATGCTAGGCTGG 59.307 52.381 0.00 0.00 0.00 4.85
3504 4014 2.871022 CAACAGATGAGACATGCTAGGC 59.129 50.000 0.00 0.00 0.00 3.93
3509 4019 3.069289 TCACACAACAGATGAGACATGC 58.931 45.455 0.00 0.00 0.00 4.06
3516 4026 4.605640 TGACAGATCACACAACAGATGA 57.394 40.909 0.00 0.00 0.00 2.92
3532 4042 1.395954 CAGCATCAATCACCGTGACAG 59.604 52.381 2.57 0.00 0.00 3.51
3533 4043 1.270785 ACAGCATCAATCACCGTGACA 60.271 47.619 2.57 0.00 0.00 3.58
3550 4065 2.476619 CGGACAAACTCACTTGCTACAG 59.523 50.000 0.00 0.00 0.00 2.74
3551 4066 2.479837 CGGACAAACTCACTTGCTACA 58.520 47.619 0.00 0.00 0.00 2.74
3554 4069 1.166531 GGCGGACAAACTCACTTGCT 61.167 55.000 0.00 0.00 0.00 3.91
3556 4071 1.021202 TTGGCGGACAAACTCACTTG 58.979 50.000 0.00 0.00 35.79 3.16
3557 4072 1.676006 CTTTGGCGGACAAACTCACTT 59.324 47.619 4.55 0.00 43.81 3.16
3560 4075 0.821711 CCCTTTGGCGGACAAACTCA 60.822 55.000 4.55 0.00 43.81 3.41
3569 4084 4.338710 TCCCGAACCCTTTGGCGG 62.339 66.667 0.00 0.00 43.20 6.13
3570 4085 2.746277 CTCCCGAACCCTTTGGCG 60.746 66.667 0.00 0.00 32.45 5.69
3572 4087 2.746277 CGCTCCCGAACCCTTTGG 60.746 66.667 0.00 0.00 36.29 3.28
3573 4088 2.345991 TCGCTCCCGAACCCTTTG 59.654 61.111 0.00 0.00 41.17 2.77
3585 4103 3.001736 CCGGATTCTCTCAAATTTCGCTC 59.998 47.826 0.00 0.00 0.00 5.03
3593 4111 3.055819 CCACTTCTCCGGATTCTCTCAAA 60.056 47.826 3.57 0.00 0.00 2.69
3595 4113 2.103373 CCACTTCTCCGGATTCTCTCA 58.897 52.381 3.57 0.00 0.00 3.27
3617 4135 7.978975 TGTTACATCACCAAAGAAAAGAAAAGG 59.021 33.333 0.00 0.00 0.00 3.11
3659 4186 9.289303 GCAGATCATAACATAAACGTGAAAATT 57.711 29.630 0.00 0.00 0.00 1.82
3660 4187 8.677300 AGCAGATCATAACATAAACGTGAAAAT 58.323 29.630 0.00 0.00 0.00 1.82
3671 4198 7.389232 CCCACATCTTAGCAGATCATAACATA 58.611 38.462 0.00 0.00 37.71 2.29
3720 4247 1.302752 GCTCATGACAGCACCCACA 60.303 57.895 2.23 0.00 39.43 4.17
3755 4282 6.925211 ACTAATTGAGATCTCAGTTTCGTCA 58.075 36.000 30.97 16.34 39.66 4.35
3776 4303 6.745159 TTGCAGCGGACAAAATAAATACTA 57.255 33.333 0.00 0.00 0.00 1.82
3777 4304 5.637006 TTGCAGCGGACAAAATAAATACT 57.363 34.783 0.00 0.00 0.00 2.12
3794 4321 9.872721 ATATATCAGAGTTCATGTAGATTGCAG 57.127 33.333 0.00 0.00 0.00 4.41
3852 4380 7.231317 CCACATTACCAATTCAATATAGTGGCT 59.769 37.037 0.00 0.00 35.75 4.75
3875 4458 4.083217 TGCCATTGTAAACGATGTAACCAC 60.083 41.667 9.04 0.00 36.28 4.16
3902 4485 3.607084 AACCCCCTGCATTCCTGGC 62.607 63.158 0.00 0.00 0.00 4.85
3910 4493 1.076549 GGTCAATGAACCCCCTGCA 59.923 57.895 0.00 0.00 32.82 4.41
3924 4507 4.901197 TGCTTCTTGTAATACAGGGTCA 57.099 40.909 2.68 0.00 0.00 4.02
3970 4553 4.826556 ACAACTGAGGTAGCTCATTCTTC 58.173 43.478 24.03 0.00 32.39 2.87
3988 4571 5.689383 ATACACCATGTCTGTCAAACAAC 57.311 39.130 0.00 0.00 0.00 3.32
3995 4578 6.238484 GGCTGAATTTATACACCATGTCTGTC 60.238 42.308 0.00 0.00 0.00 3.51
4004 4587 4.642429 AGGATCGGCTGAATTTATACACC 58.358 43.478 0.00 0.00 0.00 4.16
4073 4657 7.841222 AGATATAAGATTTGGGGTGAAGCTTTT 59.159 33.333 0.00 0.00 34.82 2.27
4092 4676 5.357742 TGCTTCTGCAGGACAAGATATAA 57.642 39.130 15.13 0.00 45.31 0.98
4111 4695 8.783093 TCGGATTCGATTGAAATTATTAATGCT 58.217 29.630 0.00 0.00 40.88 3.79
4117 4701 6.479001 ACGACTCGGATTCGATTGAAATTATT 59.521 34.615 22.15 0.00 45.04 1.40
4138 4722 1.389106 GCCACACTCAATACGAACGAC 59.611 52.381 0.14 0.00 0.00 4.34
4142 4726 3.394674 TTCTGCCACACTCAATACGAA 57.605 42.857 0.00 0.00 0.00 3.85
4182 4766 5.251081 CAATACGAACGCTCTCAAATCAAG 58.749 41.667 0.00 0.00 0.00 3.02
4210 4794 5.706833 TGAACGTTCTATGACCACACTAGTA 59.293 40.000 27.32 0.00 0.00 1.82
4211 4795 4.521639 TGAACGTTCTATGACCACACTAGT 59.478 41.667 27.32 0.00 0.00 2.57
4212 4796 5.055642 TGAACGTTCTATGACCACACTAG 57.944 43.478 27.32 0.00 0.00 2.57
4213 4797 4.521639 ACTGAACGTTCTATGACCACACTA 59.478 41.667 27.32 3.11 0.00 2.74
4235 4821 6.238484 CGGATGACCCTGATTGAAAATTAGAC 60.238 42.308 0.00 0.00 0.00 2.59
4261 4847 6.152492 TGAGCAATATTAGTTGGAAATGCACA 59.848 34.615 0.00 0.00 35.11 4.57
4325 4913 2.158667 CCTAACCAACTCAACCACAGGT 60.159 50.000 0.00 0.00 37.65 4.00
4326 4914 2.158667 ACCTAACCAACTCAACCACAGG 60.159 50.000 0.00 0.00 0.00 4.00
4327 4915 2.878406 CACCTAACCAACTCAACCACAG 59.122 50.000 0.00 0.00 0.00 3.66
4328 4916 2.422235 CCACCTAACCAACTCAACCACA 60.422 50.000 0.00 0.00 0.00 4.17
4329 4917 2.158726 TCCACCTAACCAACTCAACCAC 60.159 50.000 0.00 0.00 0.00 4.16
4330 4918 2.128535 TCCACCTAACCAACTCAACCA 58.871 47.619 0.00 0.00 0.00 3.67
4331 4919 2.158726 TGTCCACCTAACCAACTCAACC 60.159 50.000 0.00 0.00 0.00 3.77
4332 4920 3.139077 CTGTCCACCTAACCAACTCAAC 58.861 50.000 0.00 0.00 0.00 3.18
4333 4921 2.775384 ACTGTCCACCTAACCAACTCAA 59.225 45.455 0.00 0.00 0.00 3.02
4334 4922 2.104111 CACTGTCCACCTAACCAACTCA 59.896 50.000 0.00 0.00 0.00 3.41
4335 4923 2.550208 CCACTGTCCACCTAACCAACTC 60.550 54.545 0.00 0.00 0.00 3.01
4336 4924 1.420138 CCACTGTCCACCTAACCAACT 59.580 52.381 0.00 0.00 0.00 3.16
4337 4925 1.142262 ACCACTGTCCACCTAACCAAC 59.858 52.381 0.00 0.00 0.00 3.77
4338 4926 1.513858 ACCACTGTCCACCTAACCAA 58.486 50.000 0.00 0.00 0.00 3.67
4339 4927 2.402182 TACCACTGTCCACCTAACCA 57.598 50.000 0.00 0.00 0.00 3.67
4340 4928 2.169978 GGATACCACTGTCCACCTAACC 59.830 54.545 0.00 0.00 34.57 2.85
4341 4929 3.538634 GGATACCACTGTCCACCTAAC 57.461 52.381 0.00 0.00 34.57 2.34
4372 4960 0.779997 AGCACCAGGATTTGAACCCT 59.220 50.000 0.00 0.00 0.00 4.34
4373 4961 1.177401 GAGCACCAGGATTTGAACCC 58.823 55.000 0.00 0.00 0.00 4.11
4374 4962 0.804989 CGAGCACCAGGATTTGAACC 59.195 55.000 0.00 0.00 0.00 3.62
4375 4963 0.169009 GCGAGCACCAGGATTTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
4376 4964 0.250684 TGCGAGCACCAGGATTTGAA 60.251 50.000 0.00 0.00 0.00 2.69
4377 4965 0.035152 ATGCGAGCACCAGGATTTGA 60.035 50.000 0.00 0.00 0.00 2.69
4378 4966 0.813184 AATGCGAGCACCAGGATTTG 59.187 50.000 0.00 0.00 0.00 2.32
4379 4967 2.418368 TAATGCGAGCACCAGGATTT 57.582 45.000 0.00 0.00 31.11 2.17
4380 4968 2.645838 ATAATGCGAGCACCAGGATT 57.354 45.000 0.00 0.00 33.17 3.01
4381 4969 2.498167 GAATAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
4382 4970 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
4383 4971 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
4384 4972 1.600957 CAGGAATAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
4385 4973 1.209261 TCAGGAATAATGCGAGCACCA 59.791 47.619 0.00 0.00 0.00 4.17
4386 4974 1.953559 TCAGGAATAATGCGAGCACC 58.046 50.000 0.00 0.00 0.00 5.01
4387 4975 4.558538 AATTCAGGAATAATGCGAGCAC 57.441 40.909 0.00 0.00 0.00 4.40
4388 4976 6.882610 ATAAATTCAGGAATAATGCGAGCA 57.117 33.333 0.00 0.00 0.00 4.26
4389 4977 7.362662 TCAATAAATTCAGGAATAATGCGAGC 58.637 34.615 0.00 0.00 0.00 5.03
4390 4978 9.734620 TTTCAATAAATTCAGGAATAATGCGAG 57.265 29.630 0.00 0.00 0.00 5.03
4391 4979 9.734620 CTTTCAATAAATTCAGGAATAATGCGA 57.265 29.630 0.00 0.00 0.00 5.10
4392 4980 9.734620 TCTTTCAATAAATTCAGGAATAATGCG 57.265 29.630 0.00 0.00 0.00 4.73
4398 4986 9.312904 TGGACTTCTTTCAATAAATTCAGGAAT 57.687 29.630 0.00 0.00 0.00 3.01
4399 4987 8.576442 GTGGACTTCTTTCAATAAATTCAGGAA 58.424 33.333 0.00 0.00 0.00 3.36
4400 4988 7.723616 TGTGGACTTCTTTCAATAAATTCAGGA 59.276 33.333 0.00 0.00 0.00 3.86
4401 4989 7.885297 TGTGGACTTCTTTCAATAAATTCAGG 58.115 34.615 0.00 0.00 0.00 3.86
4402 4990 9.565213 GATGTGGACTTCTTTCAATAAATTCAG 57.435 33.333 0.00 0.00 0.00 3.02
4403 4991 9.076781 TGATGTGGACTTCTTTCAATAAATTCA 57.923 29.630 0.00 0.00 0.00 2.57
4404 4992 9.346725 GTGATGTGGACTTCTTTCAATAAATTC 57.653 33.333 0.00 0.00 0.00 2.17
4405 4993 8.306761 GGTGATGTGGACTTCTTTCAATAAATT 58.693 33.333 0.00 0.00 0.00 1.82
4406 4994 7.093771 GGGTGATGTGGACTTCTTTCAATAAAT 60.094 37.037 0.00 0.00 0.00 1.40
4407 4995 6.208599 GGGTGATGTGGACTTCTTTCAATAAA 59.791 38.462 0.00 0.00 0.00 1.40
4408 4996 5.710099 GGGTGATGTGGACTTCTTTCAATAA 59.290 40.000 0.00 0.00 0.00 1.40
4409 4997 5.253330 GGGTGATGTGGACTTCTTTCAATA 58.747 41.667 0.00 0.00 0.00 1.90
4410 4998 4.082125 GGGTGATGTGGACTTCTTTCAAT 58.918 43.478 0.00 0.00 0.00 2.57
4411 4999 3.486383 GGGTGATGTGGACTTCTTTCAA 58.514 45.455 0.00 0.00 0.00 2.69
4412 5000 2.224769 GGGGTGATGTGGACTTCTTTCA 60.225 50.000 0.00 0.00 0.00 2.69
4413 5001 2.437413 GGGGTGATGTGGACTTCTTTC 58.563 52.381 0.00 0.00 0.00 2.62
4414 5002 1.075536 GGGGGTGATGTGGACTTCTTT 59.924 52.381 0.00 0.00 0.00 2.52
4415 5003 0.698818 GGGGGTGATGTGGACTTCTT 59.301 55.000 0.00 0.00 0.00 2.52
4416 5004 0.178861 AGGGGGTGATGTGGACTTCT 60.179 55.000 0.00 0.00 0.00 2.85
4417 5005 0.035056 CAGGGGGTGATGTGGACTTC 60.035 60.000 0.00 0.00 0.00 3.01
4418 5006 0.772124 ACAGGGGGTGATGTGGACTT 60.772 55.000 0.00 0.00 0.00 3.01
4419 5007 1.151810 ACAGGGGGTGATGTGGACT 60.152 57.895 0.00 0.00 0.00 3.85
4420 5008 3.495729 ACAGGGGGTGATGTGGAC 58.504 61.111 0.00 0.00 0.00 4.02
4429 5017 0.930726 TTTCTGAAACCACAGGGGGT 59.069 50.000 0.00 0.00 45.04 4.95
4430 5018 1.328279 GTTTCTGAAACCACAGGGGG 58.672 55.000 19.96 0.00 42.91 5.40
4439 5027 1.538512 GGGTTAGCCGGTTTCTGAAAC 59.461 52.381 21.92 21.92 40.65 2.78
4440 5028 1.143277 TGGGTTAGCCGGTTTCTGAAA 59.857 47.619 1.90 0.00 34.97 2.69
4441 5029 0.766131 TGGGTTAGCCGGTTTCTGAA 59.234 50.000 1.90 0.00 34.97 3.02
4442 5030 0.035739 GTGGGTTAGCCGGTTTCTGA 59.964 55.000 1.90 0.00 34.97 3.27
4443 5031 0.958876 GGTGGGTTAGCCGGTTTCTG 60.959 60.000 1.90 0.00 34.97 3.02
4444 5032 1.377612 GGTGGGTTAGCCGGTTTCT 59.622 57.895 1.90 0.00 34.97 2.52
4445 5033 1.676635 GGGTGGGTTAGCCGGTTTC 60.677 63.158 1.90 0.00 37.17 2.78
4446 5034 2.437449 GGGTGGGTTAGCCGGTTT 59.563 61.111 1.90 0.00 37.17 3.27


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

AutoCloner maintained by Alex Coulton.