Multiple sequence alignment - TraesCS6A01G163300

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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 TraesCS6A01G163300 chr6A 100.000 5230 0 0 2694 7923 158907064 158912293 0.000000e+00 9659.0
1 TraesCS6A01G163300 chr6A 100.000 1096 0 0 1296 2391 158905666 158906761 0.000000e+00 2025.0
2 TraesCS6A01G163300 chr6A 100.000 1032 0 0 1 1032 158904371 158905402 0.000000e+00 1906.0
3 TraesCS6A01G163300 chr6A 82.495 1908 282 33 4988 6860 572136563 572138453 0.000000e+00 1626.0
4 TraesCS6A01G163300 chr6A 79.877 974 146 28 2873 3812 572134911 572135868 0.000000e+00 667.0
5 TraesCS6A01G163300 chr6B 95.117 5058 206 17 2880 7921 212629282 212624250 0.000000e+00 7934.0
6 TraesCS6A01G163300 chr6B 82.468 1483 217 22 5413 6860 643264124 643265598 0.000000e+00 1258.0
7 TraesCS6A01G163300 chr6B 89.028 1039 68 20 3 1030 212632149 212631146 0.000000e+00 1245.0
8 TraesCS6A01G163300 chr6B 91.562 877 36 11 1296 2146 212631142 212630278 0.000000e+00 1175.0
9 TraesCS6A01G163300 chr6B 79.550 978 146 32 2873 3812 643262400 643263361 0.000000e+00 649.0
10 TraesCS6A01G163300 chr6B 96.875 160 5 0 2232 2391 212630276 212630117 1.310000e-67 268.0
11 TraesCS6A01G163300 chr6B 92.308 195 4 1 2704 2898 212629480 212629297 4.710000e-67 267.0
12 TraesCS6A01G163300 chr6B 90.291 103 5 3 2135 2236 646750152 646750054 6.450000e-26 130.0
13 TraesCS6A01G163300 chr6B 88.785 107 7 3 2127 2232 13827510 13827612 8.350000e-25 126.0
14 TraesCS6A01G163300 chr6B 88.372 86 10 0 4268 4353 88219707 88219622 3.910000e-18 104.0
15 TraesCS6A01G163300 chr6B 79.330 179 7 4 1979 2144 212630101 212629940 1.820000e-16 99.0
16 TraesCS6A01G163300 chr6D 96.603 3297 90 8 4266 7545 120649773 120653064 0.000000e+00 5448.0
17 TraesCS6A01G163300 chr6D 96.126 1523 33 9 2694 4210 120648268 120649770 0.000000e+00 2462.0
18 TraesCS6A01G163300 chr6D 82.023 1908 281 36 4988 6860 427483218 427485098 0.000000e+00 1567.0
19 TraesCS6A01G163300 chr6D 89.453 1043 74 18 1 1028 120645949 120646970 0.000000e+00 1284.0
20 TraesCS6A01G163300 chr6D 79.979 974 145 27 2873 3812 427481493 427482450 0.000000e+00 673.0
21 TraesCS6A01G163300 chr6D 91.811 403 16 4 1761 2146 120647653 120648055 5.410000e-151 545.0
22 TraesCS6A01G163300 chr6D 94.412 340 15 4 7584 7921 120653058 120653395 3.280000e-143 520.0
23 TraesCS6A01G163300 chr6D 95.437 263 10 2 1296 1556 120646974 120647236 1.230000e-112 418.0
24 TraesCS6A01G163300 chr6D 95.706 163 7 0 2229 2391 120648052 120648214 6.100000e-66 263.0
25 TraesCS6A01G163300 chr6D 93.706 143 9 0 1564 1706 120647326 120647468 1.730000e-51 215.0
26 TraesCS6A01G163300 chr6D 76.331 338 49 24 133 445 368207215 368207546 1.380000e-32 152.0
27 TraesCS6A01G163300 chr6D 88.889 108 7 3 2136 2241 427344847 427344951 2.320000e-25 128.0
28 TraesCS6A01G163300 chrUn 80.208 1733 299 23 5162 6860 108321537 108323259 0.000000e+00 1260.0
29 TraesCS6A01G163300 chrUn 77.732 1455 268 34 5441 6860 134253664 134252231 0.000000e+00 841.0
30 TraesCS6A01G163300 chrUn 77.709 1458 269 34 5438 6860 134268163 134269599 0.000000e+00 841.0
31 TraesCS6A01G163300 chrUn 79.742 1086 196 12 5794 6860 331495126 331496206 0.000000e+00 765.0
32 TraesCS6A01G163300 chrUn 78.705 1019 149 30 2886 3863 108319406 108320397 1.130000e-172 617.0
33 TraesCS6A01G163300 chrUn 77.660 940 149 33 2881 3782 134255067 134254151 4.240000e-142 516.0
34 TraesCS6A01G163300 chrUn 77.660 940 149 33 2881 3782 134266763 134267679 4.240000e-142 516.0
35 TraesCS6A01G163300 chrUn 76.882 943 157 31 4047 4972 108320518 108321416 2.000000e-130 477.0
36 TraesCS6A01G163300 chrUn 83.696 276 34 7 3879 4145 134254136 134253863 4.750000e-62 250.0
37 TraesCS6A01G163300 chrUn 83.696 276 34 7 3879 4145 134267694 134267967 4.750000e-62 250.0
38 TraesCS6A01G163300 chr3B 77.924 1898 352 45 4988 6860 747822317 747824172 0.000000e+00 1122.0
39 TraesCS6A01G163300 chr3B 77.924 1898 352 45 4988 6860 747834793 747836648 0.000000e+00 1122.0
40 TraesCS6A01G163300 chr3B 77.883 1899 351 47 4988 6860 747838845 747840700 0.000000e+00 1116.0
41 TraesCS6A01G163300 chr3B 77.871 1898 353 45 4988 6860 747851320 747853175 0.000000e+00 1116.0
42 TraesCS6A01G163300 chr3B 78.143 517 88 14 3648 4160 747833448 747833943 9.990000e-79 305.0
43 TraesCS6A01G163300 chr3B 77.950 517 89 14 3648 4160 747820971 747821466 4.650000e-77 300.0
44 TraesCS6A01G163300 chr3B 77.563 517 91 14 3648 4160 747849975 747850470 1.010000e-73 289.0
45 TraesCS6A01G163300 chr3B 91.346 104 7 2 2143 2244 771737750 771737647 2.980000e-29 141.0
46 TraesCS6A01G163300 chr3B 87.963 108 7 4 2143 2248 10622597 10622494 1.080000e-23 122.0
47 TraesCS6A01G163300 chr5B 79.242 1609 277 39 5271 6846 419998322 419999906 0.000000e+00 1068.0
48 TraesCS6A01G163300 chr5B 78.346 254 39 15 70 315 38605253 38605498 4.950000e-32 150.0
49 TraesCS6A01G163300 chr5B 81.152 191 28 7 131 315 32127130 32126942 6.410000e-31 147.0
50 TraesCS6A01G163300 chr5B 89.216 102 9 2 2145 2244 594886817 594886918 8.350000e-25 126.0
51 TraesCS6A01G163300 chr5A 77.709 1458 266 37 5438 6860 706083332 706084765 0.000000e+00 837.0
52 TraesCS6A01G163300 chr5A 78.321 941 146 22 2881 3784 706081932 706082851 8.980000e-154 555.0
53 TraesCS6A01G163300 chr5A 81.283 187 28 7 133 315 36362329 36362146 2.300000e-30 145.0
54 TraesCS6A01G163300 chr3D 80.502 518 84 13 3653 4160 561170596 561171106 1.610000e-101 381.0
55 TraesCS6A01G163300 chr3D 80.347 519 85 11 3648 4156 561374158 561374669 2.090000e-100 377.0
56 TraesCS6A01G163300 chr3D 75.510 343 51 19 131 445 9673864 9673527 3.860000e-28 137.0
57 TraesCS6A01G163300 chr3D 73.633 311 48 23 133 416 345718547 345718850 1.100000e-13 89.8
58 TraesCS6A01G163300 chr3A 80.268 522 90 9 3648 4160 697260154 697260671 1.610000e-101 381.0
59 TraesCS6A01G163300 chr3A 82.000 250 45 0 6074 6323 678425205 678424956 6.230000e-51 213.0
60 TraesCS6A01G163300 chr4A 76.084 715 125 27 3523 4227 658402619 658401941 1.650000e-86 331.0
61 TraesCS6A01G163300 chr2D 75.362 414 71 25 55 445 467889011 467889416 3.800000e-38 171.0
62 TraesCS6A01G163300 chr2D 89.320 103 6 3 2144 2244 300888187 300888286 3.000000e-24 124.0
63 TraesCS6A01G163300 chr2D 95.122 41 2 0 2834 2874 172409710 172409750 1.850000e-06 65.8
64 TraesCS6A01G163300 chr2D 94.872 39 2 0 2837 2875 27924491 27924453 2.390000e-05 62.1
65 TraesCS6A01G163300 chr7B 80.628 191 24 11 133 315 7182457 7182642 1.390000e-27 135.0
66 TraesCS6A01G163300 chr4D 90.909 99 6 1 2140 2238 379147281 379147186 6.450000e-26 130.0
67 TraesCS6A01G163300 chr1A 91.667 96 5 1 2143 2238 558981463 558981555 6.450000e-26 130.0
68 TraesCS6A01G163300 chr1A 100.000 37 0 0 2837 2873 397738760 397738724 1.430000e-07 69.4
69 TraesCS6A01G163300 chr1D 100.000 38 0 0 2837 2874 316619703 316619666 3.970000e-08 71.3
70 TraesCS6A01G163300 chr1B 95.455 44 1 1 2837 2879 4516636 4516679 1.430000e-07 69.4
71 TraesCS6A01G163300 chr1B 97.368 38 1 0 2837 2874 428723303 428723266 1.850000e-06 65.8
72 TraesCS6A01G163300 chr2A 97.368 38 1 0 2837 2874 177658362 177658325 1.850000e-06 65.8
73 TraesCS6A01G163300 chr7D 96.875 32 0 1 2071 2101 6087657 6087688 1.400000e-02 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 TraesCS6A01G163300 chr6A 158904371 158912293 7922 False 4530.000000 9659 100.000000 1 7923 3 chr6A.!!$F1 7922
1 TraesCS6A01G163300 chr6A 572134911 572138453 3542 False 1146.500000 1626 81.186000 2873 6860 2 chr6A.!!$F2 3987
2 TraesCS6A01G163300 chr6B 212624250 212632149 7899 True 1831.333333 7934 90.703333 3 7921 6 chr6B.!!$R3 7918
3 TraesCS6A01G163300 chr6B 643262400 643265598 3198 False 953.500000 1258 81.009000 2873 6860 2 chr6B.!!$F2 3987
4 TraesCS6A01G163300 chr6D 120645949 120653395 7446 False 1394.375000 5448 94.156750 1 7921 8 chr6D.!!$F3 7920
5 TraesCS6A01G163300 chr6D 427481493 427485098 3605 False 1120.000000 1567 81.001000 2873 6860 2 chr6D.!!$F4 3987
6 TraesCS6A01G163300 chrUn 108319406 108323259 3853 False 784.666667 1260 78.598333 2886 6860 3 chrUn.!!$F2 3974
7 TraesCS6A01G163300 chrUn 331495126 331496206 1080 False 765.000000 765 79.742000 5794 6860 1 chrUn.!!$F1 1066
8 TraesCS6A01G163300 chrUn 134252231 134255067 2836 True 535.666667 841 79.696000 2881 6860 3 chrUn.!!$R1 3979
9 TraesCS6A01G163300 chrUn 134266763 134269599 2836 False 535.666667 841 79.688333 2881 6860 3 chrUn.!!$F3 3979
10 TraesCS6A01G163300 chr3B 747833448 747840700 7252 False 847.666667 1122 77.983333 3648 6860 3 chr3B.!!$F2 3212
11 TraesCS6A01G163300 chr3B 747820971 747824172 3201 False 711.000000 1122 77.937000 3648 6860 2 chr3B.!!$F1 3212
12 TraesCS6A01G163300 chr3B 747849975 747853175 3200 False 702.500000 1116 77.717000 3648 6860 2 chr3B.!!$F3 3212
13 TraesCS6A01G163300 chr5B 419998322 419999906 1584 False 1068.000000 1068 79.242000 5271 6846 1 chr5B.!!$F2 1575
14 TraesCS6A01G163300 chr5A 706081932 706084765 2833 False 696.000000 837 78.015000 2881 6860 2 chr5A.!!$F1 3979
15 TraesCS6A01G163300 chr3D 561170596 561171106 510 False 381.000000 381 80.502000 3653 4160 1 chr3D.!!$F2 507
16 TraesCS6A01G163300 chr3D 561374158 561374669 511 False 377.000000 377 80.347000 3648 4156 1 chr3D.!!$F3 508
17 TraesCS6A01G163300 chr3A 697260154 697260671 517 False 381.000000 381 80.268000 3648 4160 1 chr3A.!!$F1 512
18 TraesCS6A01G163300 chr4A 658401941 658402619 678 True 331.000000 331 76.084000 3523 4227 1 chr4A.!!$R1 704

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
428 439 1.008995 GCGTGCGTGTTGGACAATT 60.009 52.632 0.00 0.00 39.19 2.32 F
1739 1850 0.681887 TCGATGCGTTCCAGACCCTA 60.682 55.000 0.00 0.00 0.00 3.53 F
2299 2577 0.237498 GGACTGCAAACTACCGTTGC 59.763 55.000 2.24 2.24 32.65 4.17 F
2784 3394 1.215423 AGTGCTGGAGGGAGTTTGTTT 59.785 47.619 0.00 0.00 0.00 2.83 F
3600 4298 2.238144 ACTAGGTGCTGATGATGCAGTT 59.762 45.455 0.00 0.00 41.41 3.16 F
5080 6061 2.026356 CCTGTCCATCACCACCAATACA 60.026 50.000 0.00 0.00 0.00 2.29 F
5505 10543 3.554934 TCATTAGTAGGCATGGGCTTTG 58.445 45.455 0.00 0.00 39.70 2.77 F
6633 11710 0.252742 ACCGGAATTGGAGGAGGAGT 60.253 55.000 9.46 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2228 0.682209 AGTGCCCAGAATGCATCACC 60.682 55.000 0.0 0.0 41.46 4.02 R
2752 3362 1.209261 TCCAGCACTGTCACAACAAGA 59.791 47.619 0.0 0.0 34.24 3.02 R
3992 4828 0.395311 TGCGGGAGGTACTGGTCTAG 60.395 60.000 0.0 0.0 41.55 2.43 R
4401 5325 5.415701 TCCTTGCATTCTATGGAAAAGTGAC 59.584 40.000 0.0 0.0 40.14 3.67 R
5533 10571 2.139118 GAAAGAGCATACCGCATCTCC 58.861 52.381 0.0 0.0 46.13 3.71 R
6142 11210 0.178961 ACCCACTTTCCCTTGAAGCC 60.179 55.000 0.0 0.0 0.00 4.35 R
6738 11815 0.250640 CTCAACCAGCTTGCCTGTCT 60.251 55.000 0.0 0.0 40.06 3.41 R
7845 12942 0.888619 AGGATGAAAGCGACACGAGA 59.111 50.000 0.0 0.0 0.00 4.04 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
86 87 2.740714 GACATGGTTCCGCGAGCAC 61.741 63.158 8.23 0.00 0.00 4.40
218 219 2.423538 GCATTGACACCATGGTACCTTC 59.576 50.000 19.28 12.07 0.00 3.46
263 264 9.821662 GGCGTCTTATTATTCATAAAATGGTAC 57.178 33.333 0.00 0.00 0.00 3.34
298 301 5.008911 AGCTTTGATTTTGTCATTTTTGCCC 59.991 36.000 0.00 0.00 36.54 5.36
332 342 6.929896 CGGATGTCGTTCGAAAACTTTATAT 58.070 36.000 0.00 0.00 32.95 0.86
360 370 4.731720 CATCGACCATGCATGTTACAAAA 58.268 39.130 24.58 4.60 0.00 2.44
428 439 1.008995 GCGTGCGTGTTGGACAATT 60.009 52.632 0.00 0.00 39.19 2.32
573 587 9.973450 TGATTTAAATGAAAAGATCGGTCAAAA 57.027 25.926 5.17 0.00 0.00 2.44
582 596 4.336889 AGATCGGTCAAAACTGTCAAGA 57.663 40.909 0.00 0.00 33.20 3.02
585 599 4.066646 TCGGTCAAAACTGTCAAGATGA 57.933 40.909 0.00 0.00 33.20 2.92
629 643 7.015487 CCAAACCACCATCATTATTATCACCAT 59.985 37.037 0.00 0.00 0.00 3.55
631 645 6.851318 ACCACCATCATTATTATCACCATCA 58.149 36.000 0.00 0.00 0.00 3.07
635 649 8.631797 CACCATCATTATTATCACCATCAACAA 58.368 33.333 0.00 0.00 0.00 2.83
649 664 5.009610 ACCATCAACAACTACATCGCTTTTT 59.990 36.000 0.00 0.00 0.00 1.94
671 686 6.506464 TTTTACGTCTCGTCTTTTCTTCTG 57.494 37.500 0.00 0.00 41.54 3.02
672 687 2.395654 ACGTCTCGTCTTTTCTTCTGC 58.604 47.619 0.00 0.00 33.69 4.26
673 688 1.721926 CGTCTCGTCTTTTCTTCTGCC 59.278 52.381 0.00 0.00 0.00 4.85
674 689 2.608261 CGTCTCGTCTTTTCTTCTGCCT 60.608 50.000 0.00 0.00 0.00 4.75
675 690 3.366070 CGTCTCGTCTTTTCTTCTGCCTA 60.366 47.826 0.00 0.00 0.00 3.93
678 693 4.281182 TCTCGTCTTTTCTTCTGCCTACTT 59.719 41.667 0.00 0.00 0.00 2.24
921 945 4.144727 TCCTCCTCCGCCTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
976 1003 1.505538 CAGGGAGATAGAGGGAAGGGA 59.494 57.143 0.00 0.00 0.00 4.20
977 1004 2.090494 CAGGGAGATAGAGGGAAGGGAA 60.090 54.545 0.00 0.00 0.00 3.97
1030 1057 2.703007 GGCTCTCTCTCTCTCTCTCTCT 59.297 54.545 0.00 0.00 0.00 3.10
1031 1058 3.244044 GGCTCTCTCTCTCTCTCTCTCTC 60.244 56.522 0.00 0.00 0.00 3.20
1341 1369 2.698274 GCCCCATCCATTAAACGGATTT 59.302 45.455 6.98 0.00 41.48 2.17
1498 1527 5.545063 TGAAAGATTCCTTTGTTTTCCCC 57.455 39.130 0.00 0.00 42.30 4.81
1512 1541 2.133281 TTCCCCACTGCTCAATCATG 57.867 50.000 0.00 0.00 0.00 3.07
1517 1546 2.602878 CCACTGCTCAATCATGCAAAC 58.397 47.619 0.00 0.00 38.81 2.93
1519 1548 3.499048 CACTGCTCAATCATGCAAACTC 58.501 45.455 0.00 0.00 38.81 3.01
1546 1575 1.299773 GATGCGGAGGAAGCTCTCG 60.300 63.158 0.00 0.00 34.74 4.04
1552 1581 1.433534 GGAGGAAGCTCTCGTGTTTG 58.566 55.000 0.00 0.00 34.74 2.93
1658 1769 2.350057 TGTGGTTTGTTCGATGGGAA 57.650 45.000 0.00 0.00 0.00 3.97
1690 1801 5.261209 TCTGCATATTATGGTTTTGTGGC 57.739 39.130 5.84 0.00 0.00 5.01
1708 1819 1.671850 GGCGAGTTTGTTCGATGAGGA 60.672 52.381 0.00 0.00 43.03 3.71
1709 1820 2.066262 GCGAGTTTGTTCGATGAGGAA 58.934 47.619 0.00 0.00 43.03 3.36
1739 1850 0.681887 TCGATGCGTTCCAGACCCTA 60.682 55.000 0.00 0.00 0.00 3.53
1768 2009 2.033550 GGATCCGCCGTATATAGCAGAG 59.966 54.545 0.00 0.00 0.00 3.35
1769 2010 2.195741 TCCGCCGTATATAGCAGAGT 57.804 50.000 0.00 0.00 0.00 3.24
1971 2214 5.365619 GGTCCATTTGGTCTGATATACGTT 58.634 41.667 0.00 0.00 36.34 3.99
1973 2216 6.281405 GTCCATTTGGTCTGATATACGTTCT 58.719 40.000 0.00 0.00 36.34 3.01
1976 2219 7.827236 TCCATTTGGTCTGATATACGTTCTTTT 59.173 33.333 0.00 0.00 36.34 2.27
1977 2220 9.104965 CCATTTGGTCTGATATACGTTCTTTTA 57.895 33.333 0.00 0.00 0.00 1.52
2016 2263 2.237143 TCTGGGCACTAGAGTTGAATGG 59.763 50.000 0.00 0.00 42.32 3.16
2111 2389 3.066064 GTGGTCACACACAGCATTAACAA 59.934 43.478 0.00 0.00 46.90 2.83
2162 2440 7.545489 AGTAATACTCCCTCTGTAAAGAAACG 58.455 38.462 0.00 0.00 0.00 3.60
2163 2441 5.997384 ATACTCCCTCTGTAAAGAAACGT 57.003 39.130 0.00 0.00 0.00 3.99
2164 2442 7.472334 AATACTCCCTCTGTAAAGAAACGTA 57.528 36.000 0.00 0.00 0.00 3.57
2165 2443 5.796424 ACTCCCTCTGTAAAGAAACGTAA 57.204 39.130 0.00 0.00 0.00 3.18
2167 2445 5.537674 ACTCCCTCTGTAAAGAAACGTAAGA 59.462 40.000 0.00 0.00 43.62 2.10
2168 2446 6.022163 TCCCTCTGTAAAGAAACGTAAGAG 57.978 41.667 0.00 0.00 43.62 2.85
2169 2447 5.537674 TCCCTCTGTAAAGAAACGTAAGAGT 59.462 40.000 0.00 0.00 43.62 3.24
2170 2448 5.634020 CCCTCTGTAAAGAAACGTAAGAGTG 59.366 44.000 0.00 0.00 43.62 3.51
2171 2449 6.214399 CCTCTGTAAAGAAACGTAAGAGTGT 58.786 40.000 0.00 0.00 43.62 3.55
2172 2450 6.700520 CCTCTGTAAAGAAACGTAAGAGTGTT 59.299 38.462 0.00 0.00 43.62 3.32
2173 2451 7.224167 CCTCTGTAAAGAAACGTAAGAGTGTTT 59.776 37.037 0.00 0.00 40.77 2.83
2174 2452 9.241317 CTCTGTAAAGAAACGTAAGAGTGTTTA 57.759 33.333 0.00 0.00 38.35 2.01
2175 2453 9.241317 TCTGTAAAGAAACGTAAGAGTGTTTAG 57.759 33.333 0.00 0.00 38.35 1.85
2176 2454 9.241317 CTGTAAAGAAACGTAAGAGTGTTTAGA 57.759 33.333 0.00 0.00 38.35 2.10
2177 2455 9.754382 TGTAAAGAAACGTAAGAGTGTTTAGAT 57.246 29.630 0.00 0.00 38.35 1.98
2179 2457 8.882415 AAAGAAACGTAAGAGTGTTTAGATCA 57.118 30.769 0.00 0.00 38.35 2.92
2180 2458 7.870588 AGAAACGTAAGAGTGTTTAGATCAC 57.129 36.000 0.00 0.00 38.35 3.06
2181 2459 7.659186 AGAAACGTAAGAGTGTTTAGATCACT 58.341 34.615 0.00 0.00 46.86 3.41
2182 2460 8.790718 AGAAACGTAAGAGTGTTTAGATCACTA 58.209 33.333 0.00 0.00 44.68 2.74
2183 2461 8.967552 AAACGTAAGAGTGTTTAGATCACTAG 57.032 34.615 0.00 0.00 44.68 2.57
2184 2462 7.684937 ACGTAAGAGTGTTTAGATCACTAGT 57.315 36.000 0.00 0.00 44.68 2.57
2185 2463 8.783833 ACGTAAGAGTGTTTAGATCACTAGTA 57.216 34.615 0.00 0.00 44.68 1.82
2186 2464 8.663911 ACGTAAGAGTGTTTAGATCACTAGTAC 58.336 37.037 0.00 0.00 44.68 2.73
2187 2465 8.881743 CGTAAGAGTGTTTAGATCACTAGTACT 58.118 37.037 0.00 0.00 44.68 2.73
2224 2502 9.813446 AAACACTCTTATATTACTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
2225 2503 7.949434 ACACTCTTATATTACTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
2226 2504 7.781693 ACACTCTTATATTACTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
2227 2505 8.298140 CACTCTTATATTACTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
2228 2506 8.003629 ACTCTTATATTACTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
2229 2507 9.512588 CTCTTATATTACTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2299 2577 0.237498 GGACTGCAAACTACCGTTGC 59.763 55.000 2.24 2.24 32.65 4.17
2320 2598 4.098349 TGCTTATCCATTTGGTTCATCTGC 59.902 41.667 0.00 0.00 36.34 4.26
2369 2647 9.425577 GTTAGTCTTATTCTAGGTGATAATGGC 57.574 37.037 0.00 0.00 0.00 4.40
2743 3353 5.480073 TGTTTTGCCCATTAGCTTAATGTCT 59.520 36.000 0.00 0.00 43.05 3.41
2744 3354 6.014669 TGTTTTGCCCATTAGCTTAATGTCTT 60.015 34.615 0.00 0.00 43.05 3.01
2745 3355 5.581126 TTGCCCATTAGCTTAATGTCTTG 57.419 39.130 0.00 0.00 43.05 3.02
2746 3356 4.599041 TGCCCATTAGCTTAATGTCTTGT 58.401 39.130 0.00 0.00 43.05 3.16
2747 3357 5.016173 TGCCCATTAGCTTAATGTCTTGTT 58.984 37.500 0.00 0.00 43.05 2.83
2748 3358 5.105797 TGCCCATTAGCTTAATGTCTTGTTG 60.106 40.000 0.00 0.00 43.05 3.33
2749 3359 5.125417 GCCCATTAGCTTAATGTCTTGTTGA 59.875 40.000 0.00 0.00 43.05 3.18
2750 3360 6.183360 GCCCATTAGCTTAATGTCTTGTTGAT 60.183 38.462 0.00 0.00 43.05 2.57
2751 3361 7.198390 CCCATTAGCTTAATGTCTTGTTGATG 58.802 38.462 0.00 0.00 43.05 3.07
2752 3362 7.148018 CCCATTAGCTTAATGTCTTGTTGATGT 60.148 37.037 0.00 0.00 43.05 3.06
2753 3363 7.912250 CCATTAGCTTAATGTCTTGTTGATGTC 59.088 37.037 0.00 0.00 43.05 3.06
2784 3394 1.215423 AGTGCTGGAGGGAGTTTGTTT 59.785 47.619 0.00 0.00 0.00 2.83
2877 3529 7.838884 ACATTAGTTTACAGAGGGAGTAGAAC 58.161 38.462 0.00 0.00 0.00 3.01
2878 3530 7.674772 ACATTAGTTTACAGAGGGAGTAGAACT 59.325 37.037 0.00 0.00 32.70 3.01
2879 3531 5.986501 AGTTTACAGAGGGAGTAGAACTG 57.013 43.478 0.00 0.00 35.14 3.16
3247 3929 6.700960 TGTTTGTGCAAATGTCTAAAGGATTG 59.299 34.615 0.46 0.00 32.36 2.67
3507 4202 4.439305 TTGTCCATGTGCTTTATCTTGC 57.561 40.909 0.00 0.00 0.00 4.01
3600 4298 2.238144 ACTAGGTGCTGATGATGCAGTT 59.762 45.455 0.00 0.00 41.41 3.16
3791 4504 8.699130 TCAGTAGCTGAGAATTCTTTGATCATA 58.301 33.333 9.87 0.00 35.39 2.15
3801 4514 9.570468 AGAATTCTTTGATCATATATGTGCTGT 57.430 29.630 12.42 0.00 0.00 4.40
4087 4925 9.588774 CTGCTTGTTTGTGATTTTTATGAATTG 57.411 29.630 0.00 0.00 0.00 2.32
4242 5133 6.483974 AGAGAAGATACTCTGTACATACCACG 59.516 42.308 0.00 0.00 44.29 4.94
4401 5325 2.743928 GTCCTGCAACCCAGCTCG 60.744 66.667 0.00 0.00 40.36 5.03
4500 5424 7.707624 AATGGCATTGTTCAAGATTCTTCTA 57.292 32.000 12.82 0.00 0.00 2.10
4660 5588 9.155975 GGATTCGATGTAGAAATGTTATGCTAT 57.844 33.333 0.00 0.00 33.43 2.97
4679 5607 8.972262 ATGCTATAAATACATACACAGAGTCG 57.028 34.615 0.00 0.00 0.00 4.18
4900 5832 3.538591 TGATTGCTAGCAAGGTGATGAG 58.461 45.455 31.88 0.00 39.47 2.90
4901 5833 3.198417 TGATTGCTAGCAAGGTGATGAGA 59.802 43.478 31.88 8.54 39.47 3.27
4972 5908 4.336433 ACACATTTGCCTTATCTTCCATCG 59.664 41.667 0.00 0.00 0.00 3.84
5080 6061 2.026356 CCTGTCCATCACCACCAATACA 60.026 50.000 0.00 0.00 0.00 2.29
5226 6207 9.082313 AGTTGAGTTCCTAAATCATTTCATTGT 57.918 29.630 0.00 0.00 0.00 2.71
5421 6407 8.798859 ATGTAGCAAGTGTTTTCTAATCTCAT 57.201 30.769 0.00 0.00 0.00 2.90
5505 10543 3.554934 TCATTAGTAGGCATGGGCTTTG 58.445 45.455 0.00 0.00 39.70 2.77
5782 10835 5.444218 CGGTTCTGCTTTTAGTTCGATGTAC 60.444 44.000 0.00 0.00 0.00 2.90
6121 11189 7.676004 TCTATGACATTCAACCAGAGTTTGTA 58.324 34.615 0.00 0.00 32.45 2.41
6142 11210 6.607689 TGTAGATTCCAAGTATTTTTGTGCG 58.392 36.000 0.00 0.00 0.00 5.34
6211 11279 1.630878 GAAGCTCTTCTCCCTTTCCCA 59.369 52.381 2.55 0.00 36.69 4.37
6319 11387 1.134946 AGTGTGGCAACTGCAAAGTTC 59.865 47.619 3.76 0.00 44.36 3.01
6325 11393 2.035066 GGCAACTGCAAAGTTCACAGAT 59.965 45.455 11.04 0.00 44.36 2.90
6424 11501 3.922375 TCTTGTCTGGGTTGGGAAAAAT 58.078 40.909 0.00 0.00 0.00 1.82
6494 11571 0.996762 AAGGGACCACACAAGGGGAA 60.997 55.000 0.00 0.00 0.00 3.97
6516 11593 3.075148 TCGTCAAGACAGAGAGGTACAG 58.925 50.000 0.00 0.00 0.00 2.74
6633 11710 0.252742 ACCGGAATTGGAGGAGGAGT 60.253 55.000 9.46 0.00 0.00 3.85
6637 11714 1.065126 GGAATTGGAGGAGGAGTGGTG 60.065 57.143 0.00 0.00 0.00 4.17
6707 11784 3.840124 AAGGCGAAACTAATAGGAGGG 57.160 47.619 0.00 0.00 0.00 4.30
6715 11792 7.067859 GGCGAAACTAATAGGAGGGTTTTTAAT 59.932 37.037 0.00 0.00 32.95 1.40
6827 11904 2.007608 GTAGATTTGGTGGCTTCGACC 58.992 52.381 0.00 0.00 0.00 4.79
6861 11938 0.323178 AGCCAAGGTGAGCAATCTGG 60.323 55.000 0.00 0.00 0.00 3.86
6984 12061 1.899437 CTAGGAACCGCAGCTTCCCA 61.899 60.000 9.36 0.00 38.42 4.37
7138 12215 4.701956 AATGCCCTTGTTTTCAGTATCG 57.298 40.909 0.00 0.00 0.00 2.92
7174 12263 0.249953 TTTTGCCATGCACTGCCTTG 60.250 50.000 6.81 0.00 38.71 3.61
7253 12343 4.718961 ACACACTGCTAAGACTGGAATTT 58.281 39.130 0.00 0.00 0.00 1.82
7287 12378 5.299782 ACGTAGAGACAGAGACTTCTTTTGT 59.700 40.000 0.00 0.00 0.00 2.83
7311 12402 9.023962 TGTTTAGTTGCTTCATATCATTTCCTT 57.976 29.630 0.00 0.00 0.00 3.36
7317 12408 6.334989 TGCTTCATATCATTTCCTTTGCTTG 58.665 36.000 0.00 0.00 0.00 4.01
7451 12547 2.977914 TGTAACCTGATCTTCTGCTGC 58.022 47.619 0.00 0.00 0.00 5.25
7474 12570 0.674895 CCTGTAGACAAGCAGGGTGC 60.675 60.000 2.86 0.00 46.27 5.01
7514 12610 4.006319 ACAGCATCTTTCCTCTAGCAAAC 58.994 43.478 0.00 0.00 0.00 2.93
7578 12674 4.776349 TGACTGGTACATTCACACAAACT 58.224 39.130 0.00 0.00 43.06 2.66
7640 12736 8.484214 AGCTGATACAAATCCAGAGATAGTTA 57.516 34.615 0.00 0.00 30.42 2.24
7742 12838 5.127519 TGGGGATAGAACTTGAAATGCATTG 59.872 40.000 13.82 2.58 0.00 2.82
7793 12889 9.739276 TCTTTGGTAGTGATGAAAAGAATGTAT 57.261 29.630 0.00 0.00 34.75 2.29
7829 12925 4.439057 TCACTCAGGGCATACGTATTTTC 58.561 43.478 5.03 0.00 0.00 2.29
7849 12946 3.431856 TCGGAAAATACATCGTGTCTCG 58.568 45.455 0.00 0.00 41.41 4.04
7885 12982 5.721480 TCCTGTATGATCTTCAAAGTCTGGA 59.279 40.000 0.00 0.00 0.00 3.86
7889 12986 8.868522 TGTATGATCTTCAAAGTCTGGAAAAT 57.131 30.769 0.00 0.00 0.00 1.82
7890 12987 9.958180 TGTATGATCTTCAAAGTCTGGAAAATA 57.042 29.630 0.00 0.00 0.00 1.40
7894 12991 9.354673 TGATCTTCAAAGTCTGGAAAATAAAGT 57.645 29.630 0.00 0.00 0.00 2.66
7921 13018 1.066071 GGCTACCAGGTTCTCAGGTTC 60.066 57.143 0.00 0.00 36.87 3.62
7922 13019 1.066071 GCTACCAGGTTCTCAGGTTCC 60.066 57.143 0.00 0.00 36.87 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.153369 CTCGCGGAACCATGTCCAT 60.153 57.895 6.13 0.00 37.56 3.41
86 87 8.194769 AGTTTTTAATTTACTATTCATGCGGGG 58.805 33.333 0.00 0.00 0.00 5.73
218 219 7.697691 AGACGCCAATTATATTTTCTTCACTG 58.302 34.615 0.00 0.00 0.00 3.66
263 264 9.033481 TGACAAAATCAAAGCTACATTGAAAAG 57.967 29.630 3.54 0.00 39.98 2.27
542 556 9.793252 ACCGATCTTTTCATTTAAATCAATGAG 57.207 29.630 0.00 0.00 42.73 2.90
564 578 3.807622 GTCATCTTGACAGTTTTGACCGA 59.192 43.478 2.85 0.00 46.22 4.69
582 596 4.162888 TGGTCATAGCTGTCAATCAGTCAT 59.837 41.667 0.00 0.00 45.23 3.06
585 599 4.558226 TTGGTCATAGCTGTCAATCAGT 57.442 40.909 0.00 0.00 45.23 3.41
586 600 4.095483 GGTTTGGTCATAGCTGTCAATCAG 59.905 45.833 0.00 0.00 46.12 2.90
587 601 4.009675 GGTTTGGTCATAGCTGTCAATCA 58.990 43.478 0.00 0.00 0.00 2.57
588 602 4.009675 TGGTTTGGTCATAGCTGTCAATC 58.990 43.478 0.00 0.00 0.00 2.67
589 603 3.758554 GTGGTTTGGTCATAGCTGTCAAT 59.241 43.478 0.00 0.00 0.00 2.57
605 619 7.784073 TGATGGTGATAATAATGATGGTGGTTT 59.216 33.333 0.00 0.00 0.00 3.27
606 620 7.296856 TGATGGTGATAATAATGATGGTGGTT 58.703 34.615 0.00 0.00 0.00 3.67
607 621 6.851318 TGATGGTGATAATAATGATGGTGGT 58.149 36.000 0.00 0.00 0.00 4.16
649 664 4.443394 GCAGAAGAAAAGACGAGACGTAAA 59.557 41.667 0.00 0.00 41.37 2.01
651 666 3.562505 GCAGAAGAAAAGACGAGACGTA 58.437 45.455 0.00 0.00 41.37 3.57
655 670 3.827302 AGTAGGCAGAAGAAAAGACGAGA 59.173 43.478 0.00 0.00 0.00 4.04
659 674 7.819900 TCTCAATAAGTAGGCAGAAGAAAAGAC 59.180 37.037 0.00 0.00 0.00 3.01
660 675 7.907389 TCTCAATAAGTAGGCAGAAGAAAAGA 58.093 34.615 0.00 0.00 0.00 2.52
661 676 8.610896 CATCTCAATAAGTAGGCAGAAGAAAAG 58.389 37.037 0.00 0.00 0.00 2.27
662 677 8.103305 ACATCTCAATAAGTAGGCAGAAGAAAA 58.897 33.333 0.00 0.00 0.00 2.29
666 681 5.236047 GCACATCTCAATAAGTAGGCAGAAG 59.764 44.000 0.00 0.00 0.00 2.85
667 682 5.118990 GCACATCTCAATAAGTAGGCAGAA 58.881 41.667 0.00 0.00 0.00 3.02
668 683 4.697514 GCACATCTCAATAAGTAGGCAGA 58.302 43.478 0.00 0.00 0.00 4.26
669 684 3.492383 CGCACATCTCAATAAGTAGGCAG 59.508 47.826 0.00 0.00 0.00 4.85
670 685 3.457234 CGCACATCTCAATAAGTAGGCA 58.543 45.455 0.00 0.00 0.00 4.75
671 686 2.221981 GCGCACATCTCAATAAGTAGGC 59.778 50.000 0.30 0.00 0.00 3.93
672 687 3.492383 CAGCGCACATCTCAATAAGTAGG 59.508 47.826 11.47 0.00 0.00 3.18
673 688 3.060003 GCAGCGCACATCTCAATAAGTAG 60.060 47.826 11.47 0.00 0.00 2.57
674 689 2.866156 GCAGCGCACATCTCAATAAGTA 59.134 45.455 11.47 0.00 0.00 2.24
675 690 1.667724 GCAGCGCACATCTCAATAAGT 59.332 47.619 11.47 0.00 0.00 2.24
678 693 2.300533 CGCAGCGCACATCTCAATA 58.699 52.632 11.47 0.00 0.00 1.90
954 981 1.347062 CTTCCCTCTATCTCCCTGCC 58.653 60.000 0.00 0.00 0.00 4.85
958 985 2.615391 CTTCCCTTCCCTCTATCTCCC 58.385 57.143 0.00 0.00 0.00 4.30
976 1003 1.918262 TGATGTCAGAAGATGCCCCTT 59.082 47.619 0.00 0.00 0.00 3.95
977 1004 1.489649 CTGATGTCAGAAGATGCCCCT 59.510 52.381 3.96 0.00 46.59 4.79
1341 1369 9.781633 GATGAGTCCTCTAGTATAACTTGTAGA 57.218 37.037 0.00 0.00 0.00 2.59
1417 1445 2.061028 GTGCAAAGGAATCGCAAAAGG 58.939 47.619 0.00 0.00 37.41 3.11
1498 1527 3.190744 AGAGTTTGCATGATTGAGCAGTG 59.809 43.478 0.00 0.00 42.39 3.66
1512 1541 1.303309 CATCGGGATGGAGAGTTTGC 58.697 55.000 0.62 0.00 35.24 3.68
1517 1546 2.341543 CCGCATCGGGATGGAGAG 59.658 66.667 10.44 0.00 44.15 3.20
1552 1581 9.478019 CAGACTGATACGTCAATCAAAAATAAC 57.522 33.333 0.00 0.00 33.16 1.89
1678 1789 1.754226 ACAAACTCGCCACAAAACCAT 59.246 42.857 0.00 0.00 0.00 3.55
1679 1790 1.178276 ACAAACTCGCCACAAAACCA 58.822 45.000 0.00 0.00 0.00 3.67
1690 1801 4.725556 TTTTCCTCATCGAACAAACTCG 57.274 40.909 0.00 0.00 40.25 4.18
1768 2009 3.885297 ACCAATGCAACATAGATGCCTAC 59.115 43.478 0.00 0.00 43.16 3.18
1769 2010 4.169059 ACCAATGCAACATAGATGCCTA 57.831 40.909 0.00 0.00 43.16 3.93
1971 2214 8.087750 AGAATGCATCACCGAAAATTTAAAAGA 58.912 29.630 0.00 0.00 0.00 2.52
1973 2216 7.117523 CCAGAATGCATCACCGAAAATTTAAAA 59.882 33.333 0.00 0.00 31.97 1.52
1976 2219 5.394005 CCCAGAATGCATCACCGAAAATTTA 60.394 40.000 0.00 0.00 31.97 1.40
1977 2220 4.497300 CCAGAATGCATCACCGAAAATTT 58.503 39.130 0.00 0.00 31.97 1.82
1978 2221 3.119029 CCCAGAATGCATCACCGAAAATT 60.119 43.478 0.00 0.00 31.97 1.82
1979 2222 2.428171 CCCAGAATGCATCACCGAAAAT 59.572 45.455 0.00 0.00 31.97 1.82
1981 2224 1.462616 CCCAGAATGCATCACCGAAA 58.537 50.000 0.00 0.00 31.97 3.46
1982 2225 1.031571 GCCCAGAATGCATCACCGAA 61.032 55.000 0.00 0.00 31.97 4.30
1985 2228 0.682209 AGTGCCCAGAATGCATCACC 60.682 55.000 0.00 0.00 41.46 4.02
1986 2229 1.945394 CTAGTGCCCAGAATGCATCAC 59.055 52.381 0.00 2.42 41.46 3.06
2016 2263 3.056313 GCCGAAATCCCAGCAGTGC 62.056 63.158 7.13 7.13 0.00 4.40
2146 2424 5.634020 CACTCTTACGTTTCTTTACAGAGGG 59.366 44.000 0.00 0.00 32.21 4.30
2147 2425 6.214399 ACACTCTTACGTTTCTTTACAGAGG 58.786 40.000 0.00 0.00 32.21 3.69
2148 2426 7.695869 AACACTCTTACGTTTCTTTACAGAG 57.304 36.000 0.00 0.00 33.83 3.35
2149 2427 9.241317 CTAAACACTCTTACGTTTCTTTACAGA 57.759 33.333 0.00 0.00 36.72 3.41
2150 2428 9.241317 TCTAAACACTCTTACGTTTCTTTACAG 57.759 33.333 0.00 0.00 36.72 2.74
2151 2429 9.754382 ATCTAAACACTCTTACGTTTCTTTACA 57.246 29.630 0.00 0.00 36.72 2.41
2153 2431 9.970395 TGATCTAAACACTCTTACGTTTCTTTA 57.030 29.630 0.00 0.00 36.72 1.85
2154 2432 8.762426 GTGATCTAAACACTCTTACGTTTCTTT 58.238 33.333 0.00 0.00 36.72 2.52
2155 2433 8.142551 AGTGATCTAAACACTCTTACGTTTCTT 58.857 33.333 0.00 0.00 43.84 2.52
2156 2434 7.659186 AGTGATCTAAACACTCTTACGTTTCT 58.341 34.615 0.00 0.00 43.84 2.52
2157 2435 7.870588 AGTGATCTAAACACTCTTACGTTTC 57.129 36.000 0.00 0.00 43.84 2.78
2158 2436 8.574737 ACTAGTGATCTAAACACTCTTACGTTT 58.425 33.333 0.00 0.00 45.58 3.60
2159 2437 8.108551 ACTAGTGATCTAAACACTCTTACGTT 57.891 34.615 0.00 0.00 45.58 3.99
2160 2438 7.684937 ACTAGTGATCTAAACACTCTTACGT 57.315 36.000 0.00 0.00 45.58 3.57
2161 2439 8.881743 AGTACTAGTGATCTAAACACTCTTACG 58.118 37.037 5.39 0.00 45.58 3.18
2198 2476 9.813446 CCTCCGTAAAGTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
2199 2477 8.419442 CCCTCCGTAAAGTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
2200 2478 7.781693 TCCCTCCGTAAAGTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
2201 2479 8.174733 TCCCTCCGTAAAGTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
2202 2480 8.003629 ACTCCCTCCGTAAAGTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
2203 2481 8.406730 ACTCCCTCCGTAAAGTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2204 2482 9.289782 GTACTCCCTCCGTAAAGTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2205 2483 9.294614 AGTACTCCCTCCGTAAAGTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
2206 2484 9.646522 AAGTACTCCCTCCGTAAAGTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
2207 2485 9.646522 AAAGTACTCCCTCCGTAAAGTAATATA 57.353 33.333 0.00 0.00 0.00 0.86
2208 2486 8.544687 AAAGTACTCCCTCCGTAAAGTAATAT 57.455 34.615 0.00 0.00 0.00 1.28
2209 2487 7.961326 AAAGTACTCCCTCCGTAAAGTAATA 57.039 36.000 0.00 0.00 0.00 0.98
2210 2488 6.864151 AAAGTACTCCCTCCGTAAAGTAAT 57.136 37.500 0.00 0.00 0.00 1.89
2211 2489 6.670695 AAAAGTACTCCCTCCGTAAAGTAA 57.329 37.500 0.00 0.00 0.00 2.24
2212 2490 6.670695 AAAAAGTACTCCCTCCGTAAAGTA 57.329 37.500 0.00 0.00 0.00 2.24
2213 2491 5.557576 AAAAAGTACTCCCTCCGTAAAGT 57.442 39.130 0.00 0.00 0.00 2.66
2299 2577 4.646040 TGGCAGATGAACCAAATGGATAAG 59.354 41.667 6.42 0.00 38.94 1.73
2336 2614 8.092687 TCACCTAGAATAAGACTAACCAAACAC 58.907 37.037 0.00 0.00 0.00 3.32
2743 3353 4.699735 ACTGTCACAACAAGACATCAACAA 59.300 37.500 0.00 0.00 44.27 2.83
2744 3354 4.094739 CACTGTCACAACAAGACATCAACA 59.905 41.667 0.00 0.00 44.27 3.33
2745 3355 4.591202 CACTGTCACAACAAGACATCAAC 58.409 43.478 0.00 0.00 44.27 3.18
2746 3356 3.065233 GCACTGTCACAACAAGACATCAA 59.935 43.478 0.00 0.00 44.27 2.57
2747 3357 2.613595 GCACTGTCACAACAAGACATCA 59.386 45.455 0.00 0.00 44.27 3.07
2748 3358 2.874701 AGCACTGTCACAACAAGACATC 59.125 45.455 0.00 0.00 44.27 3.06
2749 3359 2.615447 CAGCACTGTCACAACAAGACAT 59.385 45.455 0.00 0.00 44.27 3.06
2750 3360 2.009051 CAGCACTGTCACAACAAGACA 58.991 47.619 0.00 0.00 43.23 3.41
2751 3361 1.331756 CCAGCACTGTCACAACAAGAC 59.668 52.381 0.00 0.00 34.24 3.01
2752 3362 1.209261 TCCAGCACTGTCACAACAAGA 59.791 47.619 0.00 0.00 34.24 3.02
2753 3363 1.600957 CTCCAGCACTGTCACAACAAG 59.399 52.381 0.00 0.00 34.24 3.16
2877 3529 9.464714 AGCGTAAATCAGTACAACTATATTCAG 57.535 33.333 0.00 0.00 0.00 3.02
2977 3635 7.121315 ACCACCAGAAAAGCAATAATAGAGAAC 59.879 37.037 0.00 0.00 0.00 3.01
3247 3929 3.514362 CGTTGGCCCGCCCATTAC 61.514 66.667 0.00 0.00 44.89 1.89
3407 4093 2.159296 ACAAAAGCCTCGGTTGAAACAC 60.159 45.455 0.00 0.00 0.00 3.32
3507 4202 8.122330 TGTAGCAAAAGCATCATAGAATAAACG 58.878 33.333 0.00 0.00 0.00 3.60
3600 4298 2.233922 GCCAGAAGTAGAGCAGTTACCA 59.766 50.000 0.00 0.00 0.00 3.25
3791 4504 9.618890 AAAGACTTCACATATAACAGCACATAT 57.381 29.630 0.00 0.00 0.00 1.78
3793 4506 7.627088 GCAAAGACTTCACATATAACAGCACAT 60.627 37.037 0.00 0.00 0.00 3.21
3795 4508 6.024049 GCAAAGACTTCACATATAACAGCAC 58.976 40.000 0.00 0.00 0.00 4.40
3801 4514 5.651576 TGCATGGCAAAGACTTCACATATAA 59.348 36.000 0.00 0.00 34.76 0.98
3992 4828 0.395311 TGCGGGAGGTACTGGTCTAG 60.395 60.000 0.00 0.00 41.55 2.43
4087 4925 9.406828 GTGGTGTCTAACAGAAATAAATTTTCC 57.593 33.333 0.00 0.00 0.00 3.13
4199 5047 7.099764 TCTTCTCTTGGTTAAAGCATCTGTAG 58.900 38.462 0.00 0.00 35.69 2.74
4242 5133 7.147976 AGTCAACCAAAGAGCATAATTGTTTC 58.852 34.615 0.00 0.00 0.00 2.78
4401 5325 5.415701 TCCTTGCATTCTATGGAAAAGTGAC 59.584 40.000 0.00 0.00 40.14 3.67
4500 5424 7.624360 TCACTTTGTGTAACTGAAAGTCAAT 57.376 32.000 0.00 0.00 39.96 2.57
4660 5588 9.811995 AAATTAGCGACTCTGTGTATGTATTTA 57.188 29.630 0.00 0.00 0.00 1.40
4900 5832 3.932710 TCGCATTCCACACTATTTCAGTC 59.067 43.478 0.00 0.00 34.26 3.51
4901 5833 3.937814 TCGCATTCCACACTATTTCAGT 58.062 40.909 0.00 0.00 38.32 3.41
4972 5908 3.075148 GCAGTGGAAGAAAGTTAGGACC 58.925 50.000 0.00 0.00 0.00 4.46
5080 6061 8.049117 ACCCACATTAGCAAATATCGATATGAT 58.951 33.333 18.42 10.04 41.30 2.45
5103 6084 7.708998 TCATTTTACACTTGAAACAACTACCC 58.291 34.615 0.00 0.00 0.00 3.69
5369 6354 6.939730 TCACTGACTTATTAATGCCAACTGAA 59.060 34.615 0.00 0.00 0.00 3.02
5533 10571 2.139118 GAAAGAGCATACCGCATCTCC 58.861 52.381 0.00 0.00 46.13 3.71
5782 10835 3.756434 ACCAAATGTACACGGATTTCAGG 59.244 43.478 13.34 5.10 0.00 3.86
6121 11189 4.618227 GCCGCACAAAAATACTTGGAATCT 60.618 41.667 0.00 0.00 0.00 2.40
6142 11210 0.178961 ACCCACTTTCCCTTGAAGCC 60.179 55.000 0.00 0.00 0.00 4.35
6211 11279 3.417101 TGCATCAAATACGGTCTTTGGT 58.583 40.909 16.04 8.63 34.95 3.67
6319 11387 1.202110 GCACGCTGGATTTGATCTGTG 60.202 52.381 0.00 0.00 0.00 3.66
6325 11393 1.159285 CAAGAGCACGCTGGATTTGA 58.841 50.000 0.00 0.00 0.00 2.69
6494 11571 3.687125 TGTACCTCTCTGTCTTGACGAT 58.313 45.455 0.00 0.00 0.00 3.73
6633 11710 3.225798 GCCTGTGCAAAGCCACCA 61.226 61.111 0.00 0.00 37.47 4.17
6637 11714 2.341176 CCAAGCCTGTGCAAAGCC 59.659 61.111 0.00 0.00 41.13 4.35
6707 11784 5.245075 TCTGATCCCACCAACCATTAAAAAC 59.755 40.000 0.00 0.00 0.00 2.43
6715 11792 1.497309 GGGTCTGATCCCACCAACCA 61.497 60.000 11.35 0.00 46.30 3.67
6737 11814 0.535780 TCAACCAGCTTGCCTGTCTG 60.536 55.000 0.00 0.00 40.06 3.51
6738 11815 0.250640 CTCAACCAGCTTGCCTGTCT 60.251 55.000 0.00 0.00 40.06 3.41
6827 11904 2.757099 GCTGCCCCCAATCACCAG 60.757 66.667 0.00 0.00 0.00 4.00
6861 11938 3.062042 CTGGGGTAGTCGTACAACAAAC 58.938 50.000 0.00 0.00 0.00 2.93
6984 12061 6.491714 ACATCCTTACATAGATGAAGCTGT 57.508 37.500 6.98 1.34 42.04 4.40
7123 12200 8.895845 CAACAGAATTTCGATACTGAAAACAAG 58.104 33.333 12.92 0.00 40.90 3.16
7138 12215 4.152938 GGCAAAATCCAGCAACAGAATTTC 59.847 41.667 0.00 0.00 0.00 2.17
7174 12263 4.197750 ACCAGACAAGAAGATCATCATGC 58.802 43.478 3.26 0.00 0.00 4.06
7253 12343 5.300034 TCTCTGTCTCTACGTAAAACACCAA 59.700 40.000 0.00 0.00 0.00 3.67
7287 12378 9.859427 CAAAGGAAATGATATGAAGCAACTAAA 57.141 29.630 0.00 0.00 0.00 1.85
7354 12445 3.568007 GTGTTCACTGTTTTCATGGCCTA 59.432 43.478 3.32 0.00 0.00 3.93
7434 12529 3.604582 GTTAGCAGCAGAAGATCAGGTT 58.395 45.455 0.00 0.00 0.00 3.50
7435 12530 2.093235 GGTTAGCAGCAGAAGATCAGGT 60.093 50.000 0.00 0.00 0.00 4.00
7514 12610 9.203421 TGTACAATATCGTCTATGCTAAAATGG 57.797 33.333 0.00 0.00 0.00 3.16
7578 12674 7.202130 CCCATCCCAGAATAGAAGATGTCTTTA 60.202 40.741 0.00 0.00 37.84 1.85
7640 12736 9.434420 CAATCTAACAAGAGAAAGAACAGAGAT 57.566 33.333 0.00 0.00 0.00 2.75
7670 12766 1.002900 GCAAGCTTAGTGTGCGAAACA 60.003 47.619 0.00 0.00 36.04 2.83
7742 12838 2.417097 GTGCTGTGGGTGCCAAAC 59.583 61.111 0.00 0.00 34.18 2.93
7793 12889 5.556915 CCCTGAGTGAAAATACCAGTTACA 58.443 41.667 0.00 0.00 0.00 2.41
7807 12903 4.439057 GAAAATACGTATGCCCTGAGTGA 58.561 43.478 9.24 0.00 0.00 3.41
7829 12925 3.001070 CACGAGACACGATGTATTTTCCG 60.001 47.826 0.00 0.00 45.77 4.30
7845 12942 0.888619 AGGATGAAAGCGACACGAGA 59.111 50.000 0.00 0.00 0.00 4.04
7849 12946 3.521560 TCATACAGGATGAAAGCGACAC 58.478 45.455 0.00 0.00 41.80 3.67
7885 12982 7.092399 ACCTGGTAGCCTGATAGACTTTATTTT 60.092 37.037 0.00 0.00 0.00 1.82
7889 12986 4.880164 ACCTGGTAGCCTGATAGACTTTA 58.120 43.478 0.00 0.00 0.00 1.85
7890 12987 3.725634 ACCTGGTAGCCTGATAGACTTT 58.274 45.455 0.00 0.00 0.00 2.66
7894 12991 3.052869 TGAGAACCTGGTAGCCTGATAGA 60.053 47.826 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.