Multiple sequence alignment - TraesCS1A01G031100

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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 TraesCS1A01G031100 chr1A 100.000 3298 0 0 1 3298 14466963 14470260 0.000000e+00 6091.0
1 TraesCS1A01G031100 chr1A 92.946 482 31 3 2444 2923 443205764 443206244 0.000000e+00 699.0
2 TraesCS1A01G031100 chr1B 92.299 1766 103 17 676 2421 18678249 18676497 0.000000e+00 2477.0
3 TraesCS1A01G031100 chr1B 92.312 1756 99 18 676 2416 18572079 18570345 0.000000e+00 2462.0
4 TraesCS1A01G031100 chr1B 81.490 859 94 29 1 807 18681402 18680557 0.000000e+00 645.0
5 TraesCS1A01G031100 chr1B 81.128 869 89 27 1 807 18573483 18572628 7.770000e-176 627.0
6 TraesCS1A01G031100 chr1B 89.041 438 47 1 1799 2236 18675855 18675419 2.890000e-150 542.0
7 TraesCS1A01G031100 chr1B 89.041 438 44 2 1799 2236 18569702 18569269 1.040000e-149 540.0
8 TraesCS1A01G031100 chr1B 88.525 183 20 1 2240 2421 18675157 18674975 1.540000e-53 220.0
9 TraesCS1A01G031100 chr1B 81.522 92 8 6 3212 3298 18568744 18568657 2.120000e-07 67.6
10 TraesCS1A01G031100 chr1B 81.111 90 12 4 3212 3298 18674894 18674807 2.120000e-07 67.6
11 TraesCS1A01G031100 chr1D 92.009 1752 126 7 676 2418 12821874 12823620 0.000000e+00 2447.0
12 TraesCS1A01G031100 chr1D 81.928 498 54 12 13 485 12821315 12821801 3.990000e-104 388.0
13 TraesCS1A01G031100 chr1D 89.474 57 3 3 346 401 64216441 64216495 5.910000e-08 69.4
14 TraesCS1A01G031100 chr1D 92.000 50 3 1 352 401 230515555 230515507 5.910000e-08 69.4
15 TraesCS1A01G031100 chr1D 92.000 50 1 3 352 400 339160394 339160347 2.120000e-07 67.6
16 TraesCS1A01G031100 chr4A 95.882 510 18 3 2414 2923 396424565 396424059 0.000000e+00 822.0
17 TraesCS1A01G031100 chr4A 93.790 467 28 1 2443 2908 527166496 527166962 0.000000e+00 701.0
18 TraesCS1A01G031100 chr4A 77.907 172 34 4 251 420 46132538 46132369 1.620000e-18 104.0
19 TraesCS1A01G031100 chr7A 93.908 476 26 3 2450 2923 644704538 644704064 0.000000e+00 715.0
20 TraesCS1A01G031100 chr7A 93.096 478 31 2 2447 2923 173865852 173866328 0.000000e+00 699.0
21 TraesCS1A01G031100 chr6A 93.388 484 27 5 2443 2923 327885582 327885101 0.000000e+00 712.0
22 TraesCS1A01G031100 chr6A 92.739 482 33 2 2443 2923 204419590 204419110 0.000000e+00 695.0
23 TraesCS1A01G031100 chr6A 85.652 230 28 5 2968 3194 229083022 229083249 1.530000e-58 237.0
24 TraesCS1A01G031100 chr2A 93.843 471 27 2 2443 2912 730146441 730145972 0.000000e+00 708.0
25 TraesCS1A01G031100 chr2A 93.590 468 29 1 2443 2909 114247769 114248236 0.000000e+00 697.0
26 TraesCS1A01G031100 chr2A 85.020 247 28 3 2968 3212 72690992 72691231 3.290000e-60 243.0
27 TraesCS1A01G031100 chr2A 73.438 192 47 4 280 469 236078752 236078941 5.910000e-08 69.4
28 TraesCS1A01G031100 chr2A 84.211 57 9 0 2097 2153 15030964 15030908 4.600000e-04 56.5
29 TraesCS1A01G031100 chr6B 91.020 245 21 1 2968 3212 98990603 98990846 2.450000e-86 329.0
30 TraesCS1A01G031100 chr6B 80.180 222 36 8 241 459 481042807 481043023 3.410000e-35 159.0
31 TraesCS1A01G031100 chr7B 89.879 247 23 2 2968 3214 92051421 92051177 1.910000e-82 316.0
32 TraesCS1A01G031100 chr7B 82.105 95 16 1 348 442 204057699 204057606 2.730000e-11 80.5
33 TraesCS1A01G031100 chr2B 88.571 245 23 4 2968 3212 161202381 161202142 3.220000e-75 292.0
34 TraesCS1A01G031100 chr2B 87.449 247 26 4 2968 3212 672527237 672526994 2.510000e-71 279.0
35 TraesCS1A01G031100 chr5A 87.649 251 22 8 2968 3212 79268087 79268334 1.940000e-72 283.0
36 TraesCS1A01G031100 chr5A 85.593 236 33 1 2973 3208 708315260 708315494 2.540000e-61 246.0
37 TraesCS1A01G031100 chr7D 90.521 211 17 3 3005 3214 211643461 211643669 3.240000e-70 276.0
38 TraesCS1A01G031100 chr6D 75.000 232 47 10 245 469 469972900 469973127 2.710000e-16 97.1
39 TraesCS1A01G031100 chr4B 79.365 126 22 4 281 405 650851863 650851741 5.860000e-13 86.1
40 TraesCS1A01G031100 chr4B 82.895 76 10 3 352 426 541189001 541188928 7.640000e-07 65.8
41 TraesCS1A01G031100 chrUn 82.105 95 16 1 348 442 217712050 217712143 2.730000e-11 80.5
42 TraesCS1A01G031100 chr3D 91.071 56 5 0 346 401 53842921 53842976 3.530000e-10 76.8
43 TraesCS1A01G031100 chr3D 92.593 54 3 1 352 405 221358260 221358208 3.530000e-10 76.8
44 TraesCS1A01G031100 chr3D 76.923 143 26 7 266 405 483687538 483687400 1.270000e-09 75.0
45 TraesCS1A01G031100 chr3A 80.198 101 20 0 1637 1737 707616207 707616107 3.530000e-10 76.8
46 TraesCS1A01G031100 chr4D 78.462 130 16 9 346 469 352060226 352060349 1.270000e-09 75.0
47 TraesCS1A01G031100 chr4D 77.519 129 25 3 293 420 418625982 418625857 1.270000e-09 75.0
48 TraesCS1A01G031100 chr5D 90.741 54 4 1 352 405 68621658 68621606 1.640000e-08 71.3
49 TraesCS1A01G031100 chr2D 85.965 57 8 0 2097 2153 12920622 12920566 9.880000e-06 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 TraesCS1A01G031100 chr1A 14466963 14470260 3297 False 6091.00 6091 100.00000 1 3298 1 chr1A.!!$F1 3297
1 TraesCS1A01G031100 chr1B 18568657 18573483 4826 True 924.15 2462 86.00075 1 3298 4 chr1B.!!$R1 3297
2 TraesCS1A01G031100 chr1B 18674807 18681402 6595 True 790.32 2477 86.49320 1 3298 5 chr1B.!!$R2 3297
3 TraesCS1A01G031100 chr1D 12821315 12823620 2305 False 1417.50 2447 86.96850 13 2418 2 chr1D.!!$F2 2405
4 TraesCS1A01G031100 chr4A 396424059 396424565 506 True 822.00 822 95.88200 2414 2923 1 chr4A.!!$R2 509

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
654 719 0.030369 GGTGGCCGTAGATAGACACG 59.97 60.0 0.0 0.0 37.89 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 6409 0.179084 CAGGTATCCGTGGCATCGTT 60.179 55.0 0.0 0.0 0.0 3.85 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
42 43 3.423154 GCACCGCTTGGAACCTCG 61.423 66.667 0.00 0.00 36.26 4.63
43 44 2.342279 CACCGCTTGGAACCTCGA 59.658 61.111 0.00 0.00 36.26 4.04
44 45 1.301401 CACCGCTTGGAACCTCGAA 60.301 57.895 0.00 0.00 36.26 3.71
45 46 1.004918 ACCGCTTGGAACCTCGAAG 60.005 57.895 0.00 0.00 35.64 3.79
46 47 1.741770 CCGCTTGGAACCTCGAAGG 60.742 63.158 1.40 0.00 36.65 3.46
47 48 1.741770 CGCTTGGAACCTCGAAGGG 60.742 63.158 5.98 2.08 40.58 3.95
48 49 1.377333 GCTTGGAACCTCGAAGGGG 60.377 63.158 5.98 0.00 40.58 4.79
49 50 1.377333 CTTGGAACCTCGAAGGGGC 60.377 63.158 5.98 0.00 40.58 5.80
50 51 2.124507 CTTGGAACCTCGAAGGGGCA 62.125 60.000 5.98 0.00 40.58 5.36
51 52 1.497309 TTGGAACCTCGAAGGGGCAT 61.497 55.000 5.98 0.00 40.58 4.40
52 53 1.153147 GGAACCTCGAAGGGGCATC 60.153 63.158 5.98 0.00 40.58 3.91
53 54 1.602237 GAACCTCGAAGGGGCATCA 59.398 57.895 5.98 0.00 40.58 3.07
54 55 0.035439 GAACCTCGAAGGGGCATCAA 60.035 55.000 5.98 0.00 40.58 2.57
55 56 0.625849 AACCTCGAAGGGGCATCAAT 59.374 50.000 5.98 0.00 40.58 2.57
56 57 0.107017 ACCTCGAAGGGGCATCAATG 60.107 55.000 5.98 0.00 40.58 2.82
57 58 0.181114 CCTCGAAGGGGCATCAATGA 59.819 55.000 0.00 0.00 0.00 2.57
58 59 1.202855 CCTCGAAGGGGCATCAATGAT 60.203 52.381 0.00 0.00 0.00 2.45
59 60 2.579873 CTCGAAGGGGCATCAATGATT 58.420 47.619 0.00 0.00 0.00 2.57
60 61 2.954318 CTCGAAGGGGCATCAATGATTT 59.046 45.455 0.00 0.00 0.00 2.17
61 62 3.364549 TCGAAGGGGCATCAATGATTTT 58.635 40.909 0.00 0.00 0.00 1.82
62 63 3.768757 TCGAAGGGGCATCAATGATTTTT 59.231 39.130 0.00 0.00 0.00 1.94
113 114 5.757886 TGGAGACACGTCAAATGAAAAATC 58.242 37.500 0.00 0.00 33.40 2.17
114 115 5.154222 GGAGACACGTCAAATGAAAAATCC 58.846 41.667 0.00 0.00 0.00 3.01
115 116 5.278266 GGAGACACGTCAAATGAAAAATCCA 60.278 40.000 0.00 0.00 0.00 3.41
138 161 9.368416 TCCAGTATATCTTAGCTTAATCAGTGT 57.632 33.333 0.00 0.00 0.00 3.55
174 197 0.899717 AATGCATGGGTCCGCTTGTT 60.900 50.000 0.00 0.00 0.00 2.83
185 208 1.597797 CCGCTTGTTCATGGGCATGT 61.598 55.000 0.00 0.00 39.72 3.21
190 213 2.234896 TGTTCATGGGCATGTTCCAT 57.765 45.000 14.35 14.35 45.14 3.41
229 254 8.871686 AAAAAGAAAACCATGTTTGCTACTAG 57.128 30.769 0.75 0.00 0.00 2.57
262 311 3.053095 TCCATCCGGGTTTACTAGTCTCT 60.053 47.826 0.00 0.00 38.11 3.10
265 314 4.313020 TCCGGGTTTACTAGTCTCTTCT 57.687 45.455 0.00 0.00 0.00 2.85
266 315 5.441718 TCCGGGTTTACTAGTCTCTTCTA 57.558 43.478 0.00 0.00 0.00 2.10
418 469 6.322201 ACATTTTGCTAGCCTAATATGTGCTT 59.678 34.615 17.30 0.76 36.57 3.91
419 470 7.502226 ACATTTTGCTAGCCTAATATGTGCTTA 59.498 33.333 17.30 0.00 36.57 3.09
426 477 9.052759 GCTAGCCTAATATGTGCTTAAAGTTTA 57.947 33.333 2.29 0.00 36.57 2.01
450 501 6.435164 AGCCCAAAATACAATGAGGACTAAT 58.565 36.000 0.00 0.00 0.00 1.73
469 520 3.538634 ATAAAACCAGACGGAGGTAGC 57.461 47.619 0.00 0.00 38.76 3.58
485 536 5.091261 AGGTAGCACGATTGAGAATTCTT 57.909 39.130 9.87 0.00 0.00 2.52
496 547 5.443185 TTGAGAATTCTTTGGAGTGCAAG 57.557 39.130 9.87 0.00 0.00 4.01
498 549 2.560105 AGAATTCTTTGGAGTGCAAGCC 59.440 45.455 0.88 0.00 0.00 4.35
505 556 1.246056 TGGAGTGCAAGCCATTCAGC 61.246 55.000 4.75 0.00 32.24 4.26
510 561 1.401552 GTGCAAGCCATTCAGCGAATA 59.598 47.619 0.00 0.00 38.01 1.75
511 562 1.672363 TGCAAGCCATTCAGCGAATAG 59.328 47.619 3.96 0.00 38.01 1.73
518 569 3.812053 GCCATTCAGCGAATAGTCAATCT 59.188 43.478 3.96 0.00 30.44 2.40
531 582 7.307989 CGAATAGTCAATCTGGTGTTGAGTTTT 60.308 37.037 2.01 1.47 39.34 2.43
538 589 3.446873 TCTGGTGTTGAGTTTTGTGCAAT 59.553 39.130 0.00 0.00 0.00 3.56
540 591 5.301551 TCTGGTGTTGAGTTTTGTGCAATAT 59.698 36.000 0.00 0.00 0.00 1.28
547 598 7.924947 TGTTGAGTTTTGTGCAATATTTCATCA 59.075 29.630 0.00 0.00 0.00 3.07
654 719 0.030369 GGTGGCCGTAGATAGACACG 59.970 60.000 0.00 0.00 37.89 4.49
660 725 4.225208 GGCCGTAGATAGACACGAATAAC 58.775 47.826 0.00 0.00 40.56 1.89
695 782 1.607628 GCCATGGAGAGCAATCATCAC 59.392 52.381 18.40 0.00 0.00 3.06
711 798 7.325338 GCAATCATCACATACTAACATCATTGC 59.675 37.037 0.00 0.00 35.79 3.56
717 804 5.237996 CACATACTAACATCATTGCCTCCTG 59.762 44.000 0.00 0.00 0.00 3.86
723 810 4.996788 ACATCATTGCCTCCTGATTTTC 57.003 40.909 0.00 0.00 29.74 2.29
727 814 3.010472 TCATTGCCTCCTGATTTTCCTCA 59.990 43.478 0.00 0.00 0.00 3.86
730 817 3.359033 TGCCTCCTGATTTTCCTCAATG 58.641 45.455 0.00 0.00 0.00 2.82
862 3388 9.146586 ACATAATTAATGACACCAATGCCTAAT 57.853 29.630 0.00 0.00 39.07 1.73
922 3452 3.082698 TGCATGCCGAGCAAATAATTC 57.917 42.857 16.68 0.00 43.62 2.17
975 3506 7.713942 GCTTAATATCCCCCACTATATAAACGG 59.286 40.741 0.00 0.00 0.00 4.44
1065 3596 2.125512 CCCTCTTCCGCTCGTTGG 60.126 66.667 0.00 0.00 0.00 3.77
1109 3640 2.283101 TCCAGCACCACATTGCCC 60.283 61.111 0.00 0.00 44.14 5.36
1138 3669 3.825833 CTACGTCCGGCGATGGAGC 62.826 68.421 22.10 0.00 44.77 4.70
1214 3746 1.436336 GACGTACCATAGTGCCGCT 59.564 57.895 0.00 0.00 0.00 5.52
1307 3839 2.049618 CTCGGCTATGAGCTCGGC 60.050 66.667 9.64 12.83 41.99 5.54
1412 3944 4.160626 GGTGGTCTCATCACTACTTTAGCT 59.839 45.833 0.00 0.00 35.61 3.32
1424 3956 2.716217 ACTTTAGCTGGAGATGTTGCC 58.284 47.619 0.00 0.00 0.00 4.52
1452 3984 1.031571 GGCATCATCCAAGAACGCCA 61.032 55.000 0.00 0.00 39.00 5.69
1550 4082 0.955428 CGCCTGCTAAGCAACAAGGA 60.955 55.000 0.00 0.00 38.41 3.36
1565 4097 1.741706 CAAGGAGCATGTGGTAAGCAG 59.258 52.381 0.00 0.00 0.00 4.24
1582 4114 6.150976 GGTAAGCAGTTTATATGGCATGCATA 59.849 38.462 21.36 15.05 36.15 3.14
1614 4153 7.575343 GGTTACACAACTGAAACAACCTTGTTA 60.575 37.037 3.87 0.00 41.15 2.41
1806 4345 3.130869 TCGCATGGATCAAATCAAAAGGG 59.869 43.478 0.00 0.00 0.00 3.95
1837 4376 1.076485 GAGGCCGAGTACCCCTACA 60.076 63.158 0.00 0.00 0.00 2.74
2024 4564 0.241749 TACAAGTCCGGCGTGTACAG 59.758 55.000 16.24 1.17 40.21 2.74
2124 4664 2.747686 GCCAAGAACTCGTGGGGA 59.252 61.111 12.72 0.00 44.16 4.81
2130 4670 1.186267 AGAACTCGTGGGGACAGACC 61.186 60.000 0.00 0.00 44.46 3.85
2331 6401 3.126879 GCACGCACATGCTGGCTA 61.127 61.111 1.82 0.00 42.62 3.93
2339 6409 0.392863 ACATGCTGGCTATGCGAACA 60.393 50.000 0.00 0.00 0.00 3.18
2341 6411 0.734889 ATGCTGGCTATGCGAACAAC 59.265 50.000 0.00 0.00 0.00 3.32
2354 6424 1.647346 GAACAACGATGCCACGGATA 58.353 50.000 0.00 0.00 37.61 2.59
2355 6425 1.326548 GAACAACGATGCCACGGATAC 59.673 52.381 0.00 0.00 37.61 2.24
2356 6426 0.461339 ACAACGATGCCACGGATACC 60.461 55.000 0.00 0.00 37.61 2.73
2359 6429 1.300931 CGATGCCACGGATACCTGG 60.301 63.158 0.00 0.00 0.00 4.45
2374 6444 1.414181 ACCTGGATTGCTGGATCTACG 59.586 52.381 8.09 0.00 0.00 3.51
2393 6463 3.150767 ACGCTAAATTACTTTGGCACCA 58.849 40.909 13.06 0.00 46.03 4.17
2400 6470 9.014297 GCTAAATTACTTTGGCACCATATCTAT 57.986 33.333 8.70 0.00 45.31 1.98
2532 6602 1.079750 GTCACCCTGAGCGAGGAAC 60.080 63.158 6.40 0.00 46.33 3.62
2548 6618 4.322801 CGAGGAACAGTTATTCTTCACCCT 60.323 45.833 0.00 0.00 35.08 4.34
2582 6652 6.463995 ACCATCAATGCACCGTAATTTTAT 57.536 33.333 0.00 0.00 0.00 1.40
2584 6654 5.691305 CCATCAATGCACCGTAATTTTATGG 59.309 40.000 6.97 6.97 43.87 2.74
2608 6678 7.147949 TGGTCCGTAAGTTTTGTTTTATTTCCA 60.148 33.333 0.00 0.00 0.00 3.53
2620 6690 8.511604 TTGTTTTATTTCCAATGCAAAAAGGA 57.488 26.923 0.00 0.00 0.00 3.36
2622 6692 8.401709 TGTTTTATTTCCAATGCAAAAAGGAAC 58.598 29.630 10.78 5.30 39.69 3.62
2948 7018 2.030540 GTGTCTGGTTCTACGTGTGCTA 60.031 50.000 0.00 0.00 0.00 3.49
2965 7035 6.402011 CGTGTGCTATGATGTGTATGTTTTGA 60.402 38.462 0.00 0.00 0.00 2.69
2966 7036 6.742718 GTGTGCTATGATGTGTATGTTTTGAC 59.257 38.462 0.00 0.00 0.00 3.18
2970 7040 5.902613 ATGATGTGTATGTTTTGACAGGG 57.097 39.130 0.00 0.00 0.00 4.45
2971 7041 3.505680 TGATGTGTATGTTTTGACAGGGC 59.494 43.478 0.00 0.00 0.00 5.19
2972 7042 2.937519 TGTGTATGTTTTGACAGGGCA 58.062 42.857 0.00 0.00 0.00 5.36
2973 7043 3.495331 TGTGTATGTTTTGACAGGGCAT 58.505 40.909 0.00 0.00 0.00 4.40
2974 7044 3.255395 TGTGTATGTTTTGACAGGGCATG 59.745 43.478 0.00 0.00 0.00 4.06
2976 7046 4.457603 GTGTATGTTTTGACAGGGCATGTA 59.542 41.667 4.11 0.00 44.17 2.29
2977 7047 4.457603 TGTATGTTTTGACAGGGCATGTAC 59.542 41.667 4.11 0.00 44.17 2.90
2978 7048 2.937519 TGTTTTGACAGGGCATGTACA 58.062 42.857 4.11 2.76 44.17 2.90
2979 7049 3.291584 TGTTTTGACAGGGCATGTACAA 58.708 40.909 4.11 8.79 44.17 2.41
2982 7052 2.127271 TGACAGGGCATGTACAATGG 57.873 50.000 4.11 0.00 44.17 3.16
2983 7053 1.354031 TGACAGGGCATGTACAATGGT 59.646 47.619 4.11 0.00 44.17 3.55
2984 7054 2.224992 TGACAGGGCATGTACAATGGTT 60.225 45.455 4.11 0.00 44.17 3.67
2985 7055 2.164219 GACAGGGCATGTACAATGGTTG 59.836 50.000 4.11 0.00 44.17 3.77
2986 7056 2.224992 ACAGGGCATGTACAATGGTTGA 60.225 45.455 1.47 0.00 41.60 3.18
2991 7061 4.887071 GGGCATGTACAATGGTTGATAAGA 59.113 41.667 0.00 0.00 0.00 2.10
2992 7062 5.536161 GGGCATGTACAATGGTTGATAAGAT 59.464 40.000 0.00 0.00 0.00 2.40
2993 7063 6.714810 GGGCATGTACAATGGTTGATAAGATA 59.285 38.462 0.00 0.00 0.00 1.98
2994 7064 7.094634 GGGCATGTACAATGGTTGATAAGATAG 60.095 40.741 0.00 0.00 0.00 2.08
2995 7065 7.445402 GGCATGTACAATGGTTGATAAGATAGT 59.555 37.037 0.00 0.00 0.00 2.12
2996 7066 8.840321 GCATGTACAATGGTTGATAAGATAGTT 58.160 33.333 0.00 0.00 0.00 2.24
3063 7133 9.311916 GATGTCTACAATGGATCATCTATTAGC 57.688 37.037 0.00 0.00 31.99 3.09
3064 7134 7.615403 TGTCTACAATGGATCATCTATTAGCC 58.385 38.462 0.00 0.00 0.00 3.93
3065 7135 7.455953 TGTCTACAATGGATCATCTATTAGCCT 59.544 37.037 0.00 0.00 0.00 4.58
3066 7136 8.317679 GTCTACAATGGATCATCTATTAGCCTT 58.682 37.037 0.00 0.00 0.00 4.35
3067 7137 9.547279 TCTACAATGGATCATCTATTAGCCTTA 57.453 33.333 0.00 0.00 0.00 2.69
3070 7140 9.055689 ACAATGGATCATCTATTAGCCTTATCT 57.944 33.333 0.00 0.00 0.00 1.98
3071 7141 9.902684 CAATGGATCATCTATTAGCCTTATCTT 57.097 33.333 0.00 0.00 0.00 2.40
3073 7143 8.670521 TGGATCATCTATTAGCCTTATCTTCA 57.329 34.615 0.00 0.00 0.00 3.02
3074 7144 9.104713 TGGATCATCTATTAGCCTTATCTTCAA 57.895 33.333 0.00 0.00 0.00 2.69
3087 7157 9.343539 AGCCTTATCTTCAATAACTGGTTATTC 57.656 33.333 13.71 2.51 42.11 1.75
3088 7158 9.120538 GCCTTATCTTCAATAACTGGTTATTCA 57.879 33.333 13.71 1.48 42.11 2.57
3102 7172 8.415950 ACTGGTTATTCATAAAAATGTGGTGA 57.584 30.769 0.00 0.00 0.00 4.02
3103 7173 8.522830 ACTGGTTATTCATAAAAATGTGGTGAG 58.477 33.333 0.00 0.00 0.00 3.51
3104 7174 8.642935 TGGTTATTCATAAAAATGTGGTGAGA 57.357 30.769 0.00 0.00 0.00 3.27
3105 7175 8.519526 TGGTTATTCATAAAAATGTGGTGAGAC 58.480 33.333 0.00 0.00 0.00 3.36
3106 7176 8.519526 GGTTATTCATAAAAATGTGGTGAGACA 58.480 33.333 0.00 0.00 0.00 3.41
3112 7182 9.241919 TCATAAAAATGTGGTGAGACATATTGT 57.758 29.630 0.00 0.00 35.43 2.71
3113 7183 9.292846 CATAAAAATGTGGTGAGACATATTGTG 57.707 33.333 0.00 0.00 35.43 3.33
3114 7184 4.970662 AATGTGGTGAGACATATTGTGC 57.029 40.909 0.00 0.00 35.43 4.57
3115 7185 3.701205 TGTGGTGAGACATATTGTGCT 57.299 42.857 0.00 0.00 0.00 4.40
3116 7186 4.817318 TGTGGTGAGACATATTGTGCTA 57.183 40.909 0.00 0.00 0.00 3.49
3117 7187 5.159273 TGTGGTGAGACATATTGTGCTAA 57.841 39.130 0.00 0.00 0.00 3.09
3118 7188 5.178061 TGTGGTGAGACATATTGTGCTAAG 58.822 41.667 0.00 0.00 0.00 2.18
3119 7189 5.046663 TGTGGTGAGACATATTGTGCTAAGA 60.047 40.000 0.00 0.00 0.00 2.10
3120 7190 5.521735 GTGGTGAGACATATTGTGCTAAGAG 59.478 44.000 0.00 0.00 0.00 2.85
3121 7191 5.422012 TGGTGAGACATATTGTGCTAAGAGA 59.578 40.000 0.00 0.00 0.00 3.10
3122 7192 6.070824 TGGTGAGACATATTGTGCTAAGAGAA 60.071 38.462 0.00 0.00 0.00 2.87
3123 7193 6.478344 GGTGAGACATATTGTGCTAAGAGAAG 59.522 42.308 0.00 0.00 0.00 2.85
3124 7194 7.261325 GTGAGACATATTGTGCTAAGAGAAGA 58.739 38.462 0.00 0.00 0.00 2.87
3125 7195 7.221838 GTGAGACATATTGTGCTAAGAGAAGAC 59.778 40.741 0.00 0.00 0.00 3.01
3126 7196 7.093771 TGAGACATATTGTGCTAAGAGAAGACA 60.094 37.037 0.00 0.00 0.00 3.41
3127 7197 7.615403 AGACATATTGTGCTAAGAGAAGACAA 58.385 34.615 0.00 0.00 0.00 3.18
3128 7198 7.763528 AGACATATTGTGCTAAGAGAAGACAAG 59.236 37.037 0.00 0.00 30.49 3.16
3129 7199 6.314896 ACATATTGTGCTAAGAGAAGACAAGC 59.685 38.462 0.00 0.00 30.49 4.01
3130 7200 3.045601 TGTGCTAAGAGAAGACAAGCC 57.954 47.619 0.00 0.00 32.14 4.35
3131 7201 2.634940 TGTGCTAAGAGAAGACAAGCCT 59.365 45.455 0.00 0.00 32.14 4.58
3132 7202 3.071602 TGTGCTAAGAGAAGACAAGCCTT 59.928 43.478 0.00 0.00 32.14 4.35
3133 7203 4.068599 GTGCTAAGAGAAGACAAGCCTTT 58.931 43.478 0.00 0.00 32.14 3.11
3134 7204 4.517075 GTGCTAAGAGAAGACAAGCCTTTT 59.483 41.667 0.00 0.00 32.14 2.27
3135 7205 5.009110 GTGCTAAGAGAAGACAAGCCTTTTT 59.991 40.000 0.00 0.00 32.14 1.94
3136 7206 5.239525 TGCTAAGAGAAGACAAGCCTTTTTC 59.760 40.000 0.00 0.00 32.14 2.29
3137 7207 5.471797 GCTAAGAGAAGACAAGCCTTTTTCT 59.528 40.000 0.00 0.00 0.00 2.52
3138 7208 6.016693 GCTAAGAGAAGACAAGCCTTTTTCTT 60.017 38.462 0.00 0.00 36.34 2.52
3139 7209 7.173390 GCTAAGAGAAGACAAGCCTTTTTCTTA 59.827 37.037 0.00 0.00 34.37 2.10
3140 7210 9.225436 CTAAGAGAAGACAAGCCTTTTTCTTAT 57.775 33.333 0.00 0.00 34.37 1.73
3141 7211 7.446001 AGAGAAGACAAGCCTTTTTCTTATG 57.554 36.000 0.00 0.00 34.37 1.90
3142 7212 7.227156 AGAGAAGACAAGCCTTTTTCTTATGA 58.773 34.615 0.00 0.00 34.37 2.15
3143 7213 7.887495 AGAGAAGACAAGCCTTTTTCTTATGAT 59.113 33.333 0.00 0.00 34.37 2.45
3144 7214 8.414629 AGAAGACAAGCCTTTTTCTTATGATT 57.585 30.769 0.00 0.00 34.37 2.57
3145 7215 8.864087 AGAAGACAAGCCTTTTTCTTATGATTT 58.136 29.630 0.00 0.00 34.37 2.17
3146 7216 9.133627 GAAGACAAGCCTTTTTCTTATGATTTC 57.866 33.333 0.00 0.00 34.37 2.17
3147 7217 8.414629 AGACAAGCCTTTTTCTTATGATTTCT 57.585 30.769 0.00 0.00 0.00 2.52
3148 7218 8.518702 AGACAAGCCTTTTTCTTATGATTTCTC 58.481 33.333 0.00 0.00 0.00 2.87
3149 7219 8.414629 ACAAGCCTTTTTCTTATGATTTCTCT 57.585 30.769 0.00 0.00 0.00 3.10
3150 7220 8.518702 ACAAGCCTTTTTCTTATGATTTCTCTC 58.481 33.333 0.00 0.00 0.00 3.20
3151 7221 8.738106 CAAGCCTTTTTCTTATGATTTCTCTCT 58.262 33.333 0.00 0.00 0.00 3.10
3152 7222 8.504812 AGCCTTTTTCTTATGATTTCTCTCTC 57.495 34.615 0.00 0.00 0.00 3.20
3153 7223 7.555914 AGCCTTTTTCTTATGATTTCTCTCTCC 59.444 37.037 0.00 0.00 0.00 3.71
3154 7224 7.555914 GCCTTTTTCTTATGATTTCTCTCTCCT 59.444 37.037 0.00 0.00 0.00 3.69
3155 7225 9.108284 CCTTTTTCTTATGATTTCTCTCTCCTC 57.892 37.037 0.00 0.00 0.00 3.71
3156 7226 9.108284 CTTTTTCTTATGATTTCTCTCTCCTCC 57.892 37.037 0.00 0.00 0.00 4.30
3157 7227 7.739995 TTTCTTATGATTTCTCTCTCCTCCA 57.260 36.000 0.00 0.00 0.00 3.86
3158 7228 6.723298 TCTTATGATTTCTCTCTCCTCCAC 57.277 41.667 0.00 0.00 0.00 4.02
3159 7229 5.600484 TCTTATGATTTCTCTCTCCTCCACC 59.400 44.000 0.00 0.00 0.00 4.61
3160 7230 3.481559 TGATTTCTCTCTCCTCCACCT 57.518 47.619 0.00 0.00 0.00 4.00
3161 7231 3.370104 TGATTTCTCTCTCCTCCACCTC 58.630 50.000 0.00 0.00 0.00 3.85
3162 7232 3.245766 TGATTTCTCTCTCCTCCACCTCA 60.246 47.826 0.00 0.00 0.00 3.86
3163 7233 3.481559 TTTCTCTCTCCTCCACCTCAT 57.518 47.619 0.00 0.00 0.00 2.90
3164 7234 2.746279 TCTCTCTCCTCCACCTCATC 57.254 55.000 0.00 0.00 0.00 2.92
3165 7235 1.925959 TCTCTCTCCTCCACCTCATCA 59.074 52.381 0.00 0.00 0.00 3.07
3166 7236 2.517553 TCTCTCTCCTCCACCTCATCAT 59.482 50.000 0.00 0.00 0.00 2.45
3167 7237 3.052262 TCTCTCTCCTCCACCTCATCATT 60.052 47.826 0.00 0.00 0.00 2.57
3168 7238 3.710677 CTCTCTCCTCCACCTCATCATTT 59.289 47.826 0.00 0.00 0.00 2.32
3169 7239 4.883759 TCTCTCCTCCACCTCATCATTTA 58.116 43.478 0.00 0.00 0.00 1.40
3170 7240 5.471424 TCTCTCCTCCACCTCATCATTTAT 58.529 41.667 0.00 0.00 0.00 1.40
3171 7241 5.541868 TCTCTCCTCCACCTCATCATTTATC 59.458 44.000 0.00 0.00 0.00 1.75
3172 7242 4.594920 TCTCCTCCACCTCATCATTTATCC 59.405 45.833 0.00 0.00 0.00 2.59
3173 7243 4.570926 TCCTCCACCTCATCATTTATCCT 58.429 43.478 0.00 0.00 0.00 3.24
3174 7244 5.726560 TCCTCCACCTCATCATTTATCCTA 58.273 41.667 0.00 0.00 0.00 2.94
3175 7245 5.544176 TCCTCCACCTCATCATTTATCCTAC 59.456 44.000 0.00 0.00 0.00 3.18
3176 7246 5.468540 TCCACCTCATCATTTATCCTACG 57.531 43.478 0.00 0.00 0.00 3.51
3177 7247 4.899457 TCCACCTCATCATTTATCCTACGT 59.101 41.667 0.00 0.00 0.00 3.57
3178 7248 4.991056 CCACCTCATCATTTATCCTACGTG 59.009 45.833 0.00 0.00 0.00 4.49
3179 7249 4.991056 CACCTCATCATTTATCCTACGTGG 59.009 45.833 0.00 0.00 37.10 4.94
3180 7250 3.997021 CCTCATCATTTATCCTACGTGGC 59.003 47.826 0.00 0.00 35.26 5.01
3181 7251 4.503123 CCTCATCATTTATCCTACGTGGCA 60.503 45.833 0.00 0.00 35.26 4.92
3182 7252 5.227569 TCATCATTTATCCTACGTGGCAT 57.772 39.130 0.00 0.00 35.26 4.40
3183 7253 5.620206 TCATCATTTATCCTACGTGGCATT 58.380 37.500 0.00 0.00 35.26 3.56
3184 7254 5.700832 TCATCATTTATCCTACGTGGCATTC 59.299 40.000 0.00 0.00 35.26 2.67
3185 7255 4.385825 TCATTTATCCTACGTGGCATTCC 58.614 43.478 0.00 0.00 35.26 3.01
3186 7256 4.102524 TCATTTATCCTACGTGGCATTCCT 59.897 41.667 0.00 0.00 35.26 3.36
3187 7257 5.305902 TCATTTATCCTACGTGGCATTCCTA 59.694 40.000 0.00 0.00 35.26 2.94
3188 7258 5.617528 TTTATCCTACGTGGCATTCCTAA 57.382 39.130 0.00 0.00 35.26 2.69
3189 7259 3.753294 ATCCTACGTGGCATTCCTAAG 57.247 47.619 0.00 0.00 35.26 2.18
3190 7260 2.742348 TCCTACGTGGCATTCCTAAGA 58.258 47.619 0.00 0.00 35.26 2.10
3191 7261 3.305720 TCCTACGTGGCATTCCTAAGAT 58.694 45.455 0.00 0.00 35.26 2.40
3192 7262 4.476297 TCCTACGTGGCATTCCTAAGATA 58.524 43.478 0.00 0.00 35.26 1.98
3193 7263 4.523173 TCCTACGTGGCATTCCTAAGATAG 59.477 45.833 0.00 0.00 35.26 2.08
3194 7264 4.523173 CCTACGTGGCATTCCTAAGATAGA 59.477 45.833 0.00 0.00 0.00 1.98
3195 7265 5.010719 CCTACGTGGCATTCCTAAGATAGAA 59.989 44.000 0.00 0.00 0.00 2.10
3196 7266 5.552870 ACGTGGCATTCCTAAGATAGAAT 57.447 39.130 0.00 0.00 0.00 2.40
3197 7267 5.542779 ACGTGGCATTCCTAAGATAGAATC 58.457 41.667 0.00 0.00 0.00 2.52
3198 7268 5.070446 ACGTGGCATTCCTAAGATAGAATCA 59.930 40.000 0.00 0.00 0.00 2.57
3199 7269 6.169094 CGTGGCATTCCTAAGATAGAATCAT 58.831 40.000 0.00 0.00 0.00 2.45
3200 7270 6.652481 CGTGGCATTCCTAAGATAGAATCATT 59.348 38.462 0.00 0.00 0.00 2.57
3201 7271 7.360691 CGTGGCATTCCTAAGATAGAATCATTG 60.361 40.741 0.00 0.00 0.00 2.82
3202 7272 7.446625 GTGGCATTCCTAAGATAGAATCATTGT 59.553 37.037 0.00 0.00 0.00 2.71
3203 7273 8.659527 TGGCATTCCTAAGATAGAATCATTGTA 58.340 33.333 0.00 0.00 0.00 2.41
3204 7274 8.940952 GGCATTCCTAAGATAGAATCATTGTAC 58.059 37.037 0.00 0.00 0.00 2.90
3205 7275 9.494271 GCATTCCTAAGATAGAATCATTGTACA 57.506 33.333 0.00 0.00 0.00 2.90
3208 7278 9.494271 TTCCTAAGATAGAATCATTGTACATGC 57.506 33.333 0.00 0.00 0.00 4.06
3209 7279 8.097038 TCCTAAGATAGAATCATTGTACATGCC 58.903 37.037 0.00 0.00 0.00 4.40
3210 7280 7.335422 CCTAAGATAGAATCATTGTACATGCCC 59.665 40.741 0.00 0.00 0.00 5.36
3214 7284 7.880195 AGATAGAATCATTGTACATGCCCTAAC 59.120 37.037 0.00 0.00 0.00 2.34
3261 7332 6.202570 TGAAACATGAAGCAATTAAACAAGCC 59.797 34.615 0.00 0.00 0.00 4.35
3262 7333 4.236935 ACATGAAGCAATTAAACAAGCCG 58.763 39.130 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.531122 AGCGGTGCCATATATATAATCGT 57.469 39.130 0.00 0.00 0.00 3.73
63 64 0.113385 TGCCCCTTCCCGATCAAAAA 59.887 50.000 0.00 0.00 0.00 1.94
64 65 0.610785 GTGCCCCTTCCCGATCAAAA 60.611 55.000 0.00 0.00 0.00 2.44
65 66 1.001393 GTGCCCCTTCCCGATCAAA 60.001 57.895 0.00 0.00 0.00 2.69
66 67 2.674754 GTGCCCCTTCCCGATCAA 59.325 61.111 0.00 0.00 0.00 2.57
67 68 3.407967 GGTGCCCCTTCCCGATCA 61.408 66.667 0.00 0.00 0.00 2.92
68 69 2.284515 ATTGGTGCCCCTTCCCGATC 62.285 60.000 0.00 0.00 0.00 3.69
69 70 2.316586 ATTGGTGCCCCTTCCCGAT 61.317 57.895 0.00 0.00 0.00 4.18
70 71 2.938798 ATTGGTGCCCCTTCCCGA 60.939 61.111 0.00 0.00 0.00 5.14
71 72 2.572333 ATCATTGGTGCCCCTTCCCG 62.572 60.000 0.00 0.00 0.00 5.14
72 73 1.044790 CATCATTGGTGCCCCTTCCC 61.045 60.000 0.00 0.00 0.00 3.97
73 74 1.044790 CCATCATTGGTGCCCCTTCC 61.045 60.000 0.00 0.00 38.30 3.46
113 114 9.416794 CACACTGATTAAGCTAAGATATACTGG 57.583 37.037 0.00 0.00 0.00 4.00
138 161 7.092079 CCATGCATTTGAAAGAAACTGTATCA 58.908 34.615 0.00 0.00 0.00 2.15
226 251 4.021894 CCCGGATGGAGTGAGAATTACTAG 60.022 50.000 0.73 0.00 37.49 2.57
229 254 2.434702 ACCCGGATGGAGTGAGAATTAC 59.565 50.000 0.73 0.00 37.49 1.89
377 428 7.377398 AGCAAAATGTTAATGCATGTCACTAA 58.623 30.769 0.00 0.00 42.45 2.24
418 469 8.527810 CCTCATTGTATTTTGGGCTAAACTTTA 58.472 33.333 0.00 0.00 0.00 1.85
419 470 7.234577 TCCTCATTGTATTTTGGGCTAAACTTT 59.765 33.333 0.00 0.00 0.00 2.66
426 477 4.322057 AGTCCTCATTGTATTTTGGGCT 57.678 40.909 0.00 0.00 0.00 5.19
450 501 2.028748 GTGCTACCTCCGTCTGGTTTTA 60.029 50.000 0.00 0.00 38.88 1.52
469 520 5.625251 CACTCCAAAGAATTCTCAATCGTG 58.375 41.667 8.78 9.99 0.00 4.35
485 536 1.250328 CTGAATGGCTTGCACTCCAA 58.750 50.000 9.87 0.00 35.75 3.53
496 547 3.812053 AGATTGACTATTCGCTGAATGGC 59.188 43.478 12.17 6.76 34.57 4.40
498 549 4.813161 ACCAGATTGACTATTCGCTGAATG 59.187 41.667 12.17 6.61 33.95 2.67
505 556 5.171476 ACTCAACACCAGATTGACTATTCG 58.829 41.667 0.00 0.00 32.67 3.34
510 561 4.949856 ACAAAACTCAACACCAGATTGACT 59.050 37.500 0.00 0.00 32.67 3.41
511 562 5.036737 CACAAAACTCAACACCAGATTGAC 58.963 41.667 0.00 0.00 32.67 3.18
518 569 3.883830 ATTGCACAAAACTCAACACCA 57.116 38.095 0.00 0.00 0.00 4.17
576 631 3.822940 AGAAAATGTCCGTGGGTTGTAA 58.177 40.909 0.00 0.00 0.00 2.41
654 719 5.009911 TGGCATGGCTATGTGATTGTTATTC 59.990 40.000 21.08 0.00 36.65 1.75
660 725 2.029380 CCATGGCATGGCTATGTGATTG 60.029 50.000 31.96 5.61 44.21 2.67
695 782 5.614308 TCAGGAGGCAATGATGTTAGTATG 58.386 41.667 0.00 0.00 0.00 2.39
711 798 4.338879 ACACATTGAGGAAAATCAGGAGG 58.661 43.478 0.00 0.00 0.00 4.30
808 3334 2.159114 TGCTCACATGCTATGCTCGTAA 60.159 45.455 0.00 0.00 0.00 3.18
862 3388 4.038042 GCTACACCTCACATCATGCTACTA 59.962 45.833 0.00 0.00 0.00 1.82
975 3506 1.671379 GGTTCTCAGTTCCGTGGGC 60.671 63.158 0.00 0.00 0.00 5.36
1065 3596 0.181824 ACTAGGAGGACGAGGAGAGC 59.818 60.000 0.00 0.00 0.00 4.09
1138 3669 0.812811 CATCAGCAGGTCATGGTCGG 60.813 60.000 0.00 0.00 37.60 4.79
1214 3746 3.825160 AAACCGCCGCAGCTTCTCA 62.825 57.895 0.00 0.00 36.60 3.27
1267 3799 3.691342 CGGCGTCCCTGTTGGAGA 61.691 66.667 0.00 0.00 46.38 3.71
1307 3839 0.728466 GGTCGGTGAACTCGTTCTCG 60.728 60.000 10.75 13.11 40.14 4.04
1412 3944 2.669133 CCCCTCGGCAACATCTCCA 61.669 63.158 0.00 0.00 0.00 3.86
1424 3956 4.996434 GATGATGCCGCCCCCTCG 62.996 72.222 0.00 0.00 0.00 4.63
1435 3967 1.262417 CGATGGCGTTCTTGGATGATG 59.738 52.381 0.00 0.00 0.00 3.07
1452 3984 4.556898 CGTCAAATTACGATCCTCCTCGAT 60.557 45.833 0.00 0.00 45.68 3.59
1550 4082 5.532406 CCATATAAACTGCTTACCACATGCT 59.468 40.000 0.00 0.00 0.00 3.79
1565 4097 5.146460 CACACGTATGCATGCCATATAAAC 58.854 41.667 16.68 3.42 38.60 2.01
1614 4153 2.489329 GCATCCTACAGCAATGTTGTGT 59.511 45.455 12.98 1.96 0.00 3.72
1620 4159 1.333931 CAGCAGCATCCTACAGCAATG 59.666 52.381 0.00 0.00 0.00 2.82
1740 4279 2.780643 CATGGCGAGCTGAACACG 59.219 61.111 0.00 0.00 35.25 4.49
1787 4326 3.432608 GCCCCCTTTTGATTTGATCCATG 60.433 47.826 0.00 0.00 0.00 3.66
2130 4670 1.301293 GAAGCCCTTCTGACCCCAG 59.699 63.158 0.88 0.00 41.74 4.45
2331 6401 1.501741 GTGGCATCGTTGTTCGCAT 59.498 52.632 0.00 0.00 39.67 4.73
2339 6409 0.179084 CAGGTATCCGTGGCATCGTT 60.179 55.000 0.00 0.00 0.00 3.85
2341 6411 1.300931 CCAGGTATCCGTGGCATCG 60.301 63.158 0.00 0.00 39.57 3.84
2354 6424 1.414181 CGTAGATCCAGCAATCCAGGT 59.586 52.381 0.00 0.00 0.00 4.00
2355 6425 1.875576 GCGTAGATCCAGCAATCCAGG 60.876 57.143 0.00 0.00 0.00 4.45
2356 6426 1.069823 AGCGTAGATCCAGCAATCCAG 59.930 52.381 7.29 0.00 0.00 3.86
2359 6429 5.931441 AATTTAGCGTAGATCCAGCAATC 57.069 39.130 7.29 0.00 0.00 2.67
2374 6444 7.277174 AGATATGGTGCCAAAGTAATTTAGC 57.723 36.000 0.00 0.00 0.00 3.09
2509 6579 0.738975 CTCGCTCAGGGTGACGAATA 59.261 55.000 0.00 0.00 32.66 1.75
2532 6602 6.739331 ATAGAGGAGGGTGAAGAATAACTG 57.261 41.667 0.00 0.00 0.00 3.16
2548 6618 5.827797 GGTGCATTGATGGTAAAATAGAGGA 59.172 40.000 0.00 0.00 0.00 3.71
2582 6652 7.147949 TGGAAATAAAACAAAACTTACGGACCA 60.148 33.333 0.00 0.00 0.00 4.02
2584 6654 8.631676 TTGGAAATAAAACAAAACTTACGGAC 57.368 30.769 0.00 0.00 0.00 4.79
2587 6657 8.543774 TGCATTGGAAATAAAACAAAACTTACG 58.456 29.630 0.00 0.00 0.00 3.18
2608 6678 5.523438 TTCTTACCGTTCCTTTTTGCATT 57.477 34.783 0.00 0.00 0.00 3.56
2620 6690 7.599998 ACGGCGATTATATATTTTCTTACCGTT 59.400 33.333 16.62 0.00 44.46 4.44
2622 6692 7.515957 ACGGCGATTATATATTTTCTTACCG 57.484 36.000 16.62 0.00 40.13 4.02
2923 6993 0.318445 ACGTAGAACCAGACACACGC 60.318 55.000 0.00 0.00 32.90 5.34
2924 6994 1.268896 ACACGTAGAACCAGACACACG 60.269 52.381 0.00 0.00 35.62 4.49
2925 6995 2.124903 CACACGTAGAACCAGACACAC 58.875 52.381 0.00 0.00 0.00 3.82
2931 7001 3.503827 TCATAGCACACGTAGAACCAG 57.496 47.619 0.00 0.00 0.00 4.00
2933 7003 3.551890 CACATCATAGCACACGTAGAACC 59.448 47.826 0.00 0.00 0.00 3.62
2936 7006 5.067283 ACATACACATCATAGCACACGTAGA 59.933 40.000 0.00 0.00 0.00 2.59
2948 7018 4.158394 GCCCTGTCAAAACATACACATCAT 59.842 41.667 0.00 0.00 34.13 2.45
2965 7035 2.170166 CAACCATTGTACATGCCCTGT 58.830 47.619 0.00 0.00 42.13 4.00
2966 7036 2.445427 TCAACCATTGTACATGCCCTG 58.555 47.619 0.00 0.00 0.00 4.45
2970 7040 8.383318 ACTATCTTATCAACCATTGTACATGC 57.617 34.615 0.00 0.00 0.00 4.06
3037 7107 9.311916 GCTAATAGATGATCCATTGTAGACATC 57.688 37.037 0.00 0.00 35.74 3.06
3038 7108 8.263640 GGCTAATAGATGATCCATTGTAGACAT 58.736 37.037 0.00 0.00 0.00 3.06
3039 7109 7.455953 AGGCTAATAGATGATCCATTGTAGACA 59.544 37.037 0.00 0.00 0.00 3.41
3040 7110 7.846066 AGGCTAATAGATGATCCATTGTAGAC 58.154 38.462 0.00 0.00 0.00 2.59
3041 7111 8.441311 AAGGCTAATAGATGATCCATTGTAGA 57.559 34.615 0.00 0.00 0.00 2.59
3044 7114 9.055689 AGATAAGGCTAATAGATGATCCATTGT 57.944 33.333 0.00 0.00 0.00 2.71
3045 7115 9.902684 AAGATAAGGCTAATAGATGATCCATTG 57.097 33.333 0.00 0.00 0.00 2.82
3047 7117 9.276791 TGAAGATAAGGCTAATAGATGATCCAT 57.723 33.333 0.00 0.00 0.00 3.41
3048 7118 8.670521 TGAAGATAAGGCTAATAGATGATCCA 57.329 34.615 0.00 0.00 0.00 3.41
3061 7131 9.343539 GAATAACCAGTTATTGAAGATAAGGCT 57.656 33.333 18.07 0.00 43.52 4.58
3062 7132 9.120538 TGAATAACCAGTTATTGAAGATAAGGC 57.879 33.333 18.07 3.42 43.52 4.35
3076 7146 8.865090 TCACCACATTTTTATGAATAACCAGTT 58.135 29.630 0.00 0.00 0.00 3.16
3077 7147 8.415950 TCACCACATTTTTATGAATAACCAGT 57.584 30.769 0.00 0.00 0.00 4.00
3078 7148 8.739039 TCTCACCACATTTTTATGAATAACCAG 58.261 33.333 0.00 0.00 0.00 4.00
3079 7149 8.519526 GTCTCACCACATTTTTATGAATAACCA 58.480 33.333 0.00 0.00 0.00 3.67
3080 7150 8.519526 TGTCTCACCACATTTTTATGAATAACC 58.480 33.333 0.00 0.00 0.00 2.85
3086 7156 9.241919 ACAATATGTCTCACCACATTTTTATGA 57.758 29.630 0.00 0.00 38.07 2.15
3087 7157 9.292846 CACAATATGTCTCACCACATTTTTATG 57.707 33.333 0.00 0.00 38.07 1.90
3088 7158 7.975616 GCACAATATGTCTCACCACATTTTTAT 59.024 33.333 0.00 0.00 38.07 1.40
3089 7159 7.176515 AGCACAATATGTCTCACCACATTTTTA 59.823 33.333 0.00 0.00 38.07 1.52
3090 7160 6.015180 AGCACAATATGTCTCACCACATTTTT 60.015 34.615 0.00 0.00 38.07 1.94
3091 7161 5.477984 AGCACAATATGTCTCACCACATTTT 59.522 36.000 0.00 0.00 38.07 1.82
3092 7162 5.012239 AGCACAATATGTCTCACCACATTT 58.988 37.500 0.00 0.00 38.07 2.32
3093 7163 4.592942 AGCACAATATGTCTCACCACATT 58.407 39.130 0.00 0.00 38.07 2.71
3094 7164 4.226427 AGCACAATATGTCTCACCACAT 57.774 40.909 0.00 0.00 40.28 3.21
3095 7165 3.701205 AGCACAATATGTCTCACCACA 57.299 42.857 0.00 0.00 0.00 4.17
3096 7166 5.419542 TCTTAGCACAATATGTCTCACCAC 58.580 41.667 0.00 0.00 0.00 4.16
3097 7167 5.422012 TCTCTTAGCACAATATGTCTCACCA 59.578 40.000 0.00 0.00 0.00 4.17
3098 7168 5.907207 TCTCTTAGCACAATATGTCTCACC 58.093 41.667 0.00 0.00 0.00 4.02
3099 7169 7.221838 GTCTTCTCTTAGCACAATATGTCTCAC 59.778 40.741 0.00 0.00 0.00 3.51
3100 7170 7.093771 TGTCTTCTCTTAGCACAATATGTCTCA 60.094 37.037 0.00 0.00 0.00 3.27
3101 7171 7.261325 TGTCTTCTCTTAGCACAATATGTCTC 58.739 38.462 0.00 0.00 0.00 3.36
3102 7172 7.175347 TGTCTTCTCTTAGCACAATATGTCT 57.825 36.000 0.00 0.00 0.00 3.41
3103 7173 7.465245 GCTTGTCTTCTCTTAGCACAATATGTC 60.465 40.741 0.00 0.00 0.00 3.06
3104 7174 6.314896 GCTTGTCTTCTCTTAGCACAATATGT 59.685 38.462 0.00 0.00 0.00 2.29
3105 7175 6.238320 GGCTTGTCTTCTCTTAGCACAATATG 60.238 42.308 0.00 0.00 33.60 1.78
3106 7176 5.819901 GGCTTGTCTTCTCTTAGCACAATAT 59.180 40.000 0.00 0.00 33.60 1.28
3107 7177 5.046304 AGGCTTGTCTTCTCTTAGCACAATA 60.046 40.000 0.00 0.00 33.60 1.90
3108 7178 4.006319 GGCTTGTCTTCTCTTAGCACAAT 58.994 43.478 0.00 0.00 33.60 2.71
3109 7179 3.071602 AGGCTTGTCTTCTCTTAGCACAA 59.928 43.478 0.00 0.00 33.60 3.33
3110 7180 2.634940 AGGCTTGTCTTCTCTTAGCACA 59.365 45.455 0.00 0.00 33.60 4.57
3111 7181 3.326836 AGGCTTGTCTTCTCTTAGCAC 57.673 47.619 0.00 0.00 33.60 4.40
3112 7182 4.357918 AAAGGCTTGTCTTCTCTTAGCA 57.642 40.909 0.00 0.00 33.60 3.49
3113 7183 5.471797 AGAAAAAGGCTTGTCTTCTCTTAGC 59.528 40.000 0.00 0.00 0.00 3.09
3114 7184 7.503521 AAGAAAAAGGCTTGTCTTCTCTTAG 57.496 36.000 16.68 0.00 34.51 2.18
3115 7185 9.003658 CATAAGAAAAAGGCTTGTCTTCTCTTA 57.996 33.333 22.71 16.60 38.27 2.10
3116 7186 7.721399 TCATAAGAAAAAGGCTTGTCTTCTCTT 59.279 33.333 22.71 15.28 38.27 2.85
3117 7187 7.227156 TCATAAGAAAAAGGCTTGTCTTCTCT 58.773 34.615 22.71 6.62 38.27 3.10
3118 7188 7.440523 TCATAAGAAAAAGGCTTGTCTTCTC 57.559 36.000 22.71 4.57 38.27 2.87
3119 7189 8.414629 AATCATAAGAAAAAGGCTTGTCTTCT 57.585 30.769 22.71 17.23 38.27 2.85
3120 7190 9.133627 GAAATCATAAGAAAAAGGCTTGTCTTC 57.866 33.333 22.71 15.66 38.27 2.87
3121 7191 8.864087 AGAAATCATAAGAAAAAGGCTTGTCTT 58.136 29.630 22.67 22.67 41.27 3.01
3122 7192 8.414629 AGAAATCATAAGAAAAAGGCTTGTCT 57.585 30.769 0.00 4.05 29.58 3.41
3123 7193 8.518702 AGAGAAATCATAAGAAAAAGGCTTGTC 58.481 33.333 0.00 1.38 0.00 3.18
3124 7194 8.414629 AGAGAAATCATAAGAAAAAGGCTTGT 57.585 30.769 0.00 0.00 0.00 3.16
3125 7195 8.738106 AGAGAGAAATCATAAGAAAAAGGCTTG 58.262 33.333 0.00 0.00 0.00 4.01
3126 7196 8.876303 AGAGAGAAATCATAAGAAAAAGGCTT 57.124 30.769 0.00 0.00 0.00 4.35
3127 7197 7.555914 GGAGAGAGAAATCATAAGAAAAAGGCT 59.444 37.037 0.00 0.00 0.00 4.58
3128 7198 7.555914 AGGAGAGAGAAATCATAAGAAAAAGGC 59.444 37.037 0.00 0.00 0.00 4.35
3129 7199 9.108284 GAGGAGAGAGAAATCATAAGAAAAAGG 57.892 37.037 0.00 0.00 0.00 3.11
3130 7200 9.108284 GGAGGAGAGAGAAATCATAAGAAAAAG 57.892 37.037 0.00 0.00 0.00 2.27
3131 7201 8.605947 TGGAGGAGAGAGAAATCATAAGAAAAA 58.394 33.333 0.00 0.00 0.00 1.94
3132 7202 8.043710 GTGGAGGAGAGAGAAATCATAAGAAAA 58.956 37.037 0.00 0.00 0.00 2.29
3133 7203 7.365117 GGTGGAGGAGAGAGAAATCATAAGAAA 60.365 40.741 0.00 0.00 0.00 2.52
3134 7204 6.098982 GGTGGAGGAGAGAGAAATCATAAGAA 59.901 42.308 0.00 0.00 0.00 2.52
3135 7205 5.600484 GGTGGAGGAGAGAGAAATCATAAGA 59.400 44.000 0.00 0.00 0.00 2.10
3136 7206 5.602145 AGGTGGAGGAGAGAGAAATCATAAG 59.398 44.000 0.00 0.00 0.00 1.73
3137 7207 5.533112 AGGTGGAGGAGAGAGAAATCATAA 58.467 41.667 0.00 0.00 0.00 1.90
3138 7208 5.144100 GAGGTGGAGGAGAGAGAAATCATA 58.856 45.833 0.00 0.00 0.00 2.15
3139 7209 3.966665 GAGGTGGAGGAGAGAGAAATCAT 59.033 47.826 0.00 0.00 0.00 2.45
3140 7210 3.245766 TGAGGTGGAGGAGAGAGAAATCA 60.246 47.826 0.00 0.00 0.00 2.57
3141 7211 3.370104 TGAGGTGGAGGAGAGAGAAATC 58.630 50.000 0.00 0.00 0.00 2.17
3142 7212 3.481559 TGAGGTGGAGGAGAGAGAAAT 57.518 47.619 0.00 0.00 0.00 2.17
3143 7213 3.245766 TGATGAGGTGGAGGAGAGAGAAA 60.246 47.826 0.00 0.00 0.00 2.52
3144 7214 2.313041 TGATGAGGTGGAGGAGAGAGAA 59.687 50.000 0.00 0.00 0.00 2.87
3145 7215 1.925959 TGATGAGGTGGAGGAGAGAGA 59.074 52.381 0.00 0.00 0.00 3.10
3146 7216 2.450867 TGATGAGGTGGAGGAGAGAG 57.549 55.000 0.00 0.00 0.00 3.20
3147 7217 3.411454 AATGATGAGGTGGAGGAGAGA 57.589 47.619 0.00 0.00 0.00 3.10
3148 7218 5.279910 GGATAAATGATGAGGTGGAGGAGAG 60.280 48.000 0.00 0.00 0.00 3.20
3149 7219 4.594920 GGATAAATGATGAGGTGGAGGAGA 59.405 45.833 0.00 0.00 0.00 3.71
3150 7220 4.596643 AGGATAAATGATGAGGTGGAGGAG 59.403 45.833 0.00 0.00 0.00 3.69
3151 7221 4.570926 AGGATAAATGATGAGGTGGAGGA 58.429 43.478 0.00 0.00 0.00 3.71
3152 7222 4.989875 AGGATAAATGATGAGGTGGAGG 57.010 45.455 0.00 0.00 0.00 4.30
3153 7223 5.011125 ACGTAGGATAAATGATGAGGTGGAG 59.989 44.000 0.00 0.00 0.00 3.86
3154 7224 4.899457 ACGTAGGATAAATGATGAGGTGGA 59.101 41.667 0.00 0.00 0.00 4.02
3155 7225 4.991056 CACGTAGGATAAATGATGAGGTGG 59.009 45.833 0.00 0.00 0.00 4.61
3156 7226 4.991056 CCACGTAGGATAAATGATGAGGTG 59.009 45.833 0.00 0.00 41.22 4.00
3157 7227 4.503296 GCCACGTAGGATAAATGATGAGGT 60.503 45.833 8.04 0.00 41.22 3.85
3158 7228 3.997021 GCCACGTAGGATAAATGATGAGG 59.003 47.826 8.04 0.00 41.22 3.86
3159 7229 4.631131 TGCCACGTAGGATAAATGATGAG 58.369 43.478 8.04 0.00 41.22 2.90
3160 7230 4.681074 TGCCACGTAGGATAAATGATGA 57.319 40.909 8.04 0.00 41.22 2.92
3161 7231 5.106555 GGAATGCCACGTAGGATAAATGATG 60.107 44.000 8.04 0.00 41.22 3.07
3162 7232 5.003804 GGAATGCCACGTAGGATAAATGAT 58.996 41.667 8.04 0.00 41.22 2.45
3163 7233 4.102524 AGGAATGCCACGTAGGATAAATGA 59.897 41.667 8.04 0.00 41.22 2.57
3164 7234 4.389374 AGGAATGCCACGTAGGATAAATG 58.611 43.478 8.04 0.00 41.22 2.32
3165 7235 4.706842 AGGAATGCCACGTAGGATAAAT 57.293 40.909 8.04 0.00 41.22 1.40
3166 7236 5.364446 TCTTAGGAATGCCACGTAGGATAAA 59.636 40.000 8.04 0.00 41.22 1.40
3167 7237 4.897076 TCTTAGGAATGCCACGTAGGATAA 59.103 41.667 8.04 0.00 41.22 1.75
3168 7238 4.476297 TCTTAGGAATGCCACGTAGGATA 58.524 43.478 8.04 0.00 41.22 2.59
3169 7239 3.305720 TCTTAGGAATGCCACGTAGGAT 58.694 45.455 8.04 0.00 41.22 3.24
3170 7240 2.742348 TCTTAGGAATGCCACGTAGGA 58.258 47.619 8.04 0.00 41.22 2.94
3171 7241 3.753294 ATCTTAGGAATGCCACGTAGG 57.247 47.619 0.00 0.00 41.84 3.18
3172 7242 5.707242 TCTATCTTAGGAATGCCACGTAG 57.293 43.478 0.00 0.00 36.29 3.51
3173 7243 6.266786 TGATTCTATCTTAGGAATGCCACGTA 59.733 38.462 0.00 0.00 36.29 3.57
3174 7244 5.070446 TGATTCTATCTTAGGAATGCCACGT 59.930 40.000 0.00 0.00 36.29 4.49
3175 7245 5.541845 TGATTCTATCTTAGGAATGCCACG 58.458 41.667 0.00 0.00 36.29 4.94
3176 7246 7.446625 ACAATGATTCTATCTTAGGAATGCCAC 59.553 37.037 0.00 0.00 36.29 5.01
3177 7247 7.520798 ACAATGATTCTATCTTAGGAATGCCA 58.479 34.615 0.00 0.00 36.29 4.92
3178 7248 7.992754 ACAATGATTCTATCTTAGGAATGCC 57.007 36.000 0.00 0.00 33.05 4.40
3179 7249 9.494271 TGTACAATGATTCTATCTTAGGAATGC 57.506 33.333 0.00 0.00 33.05 3.56
3182 7252 9.494271 GCATGTACAATGATTCTATCTTAGGAA 57.506 33.333 0.00 0.00 0.00 3.36
3183 7253 8.097038 GGCATGTACAATGATTCTATCTTAGGA 58.903 37.037 0.00 0.00 0.00 2.94
3184 7254 7.335422 GGGCATGTACAATGATTCTATCTTAGG 59.665 40.741 0.00 0.00 0.00 2.69
3185 7255 8.099537 AGGGCATGTACAATGATTCTATCTTAG 58.900 37.037 0.00 0.00 0.00 2.18
3186 7256 7.977818 AGGGCATGTACAATGATTCTATCTTA 58.022 34.615 0.00 0.00 0.00 2.10
3187 7257 6.845908 AGGGCATGTACAATGATTCTATCTT 58.154 36.000 0.00 0.00 0.00 2.40
3188 7258 6.445451 AGGGCATGTACAATGATTCTATCT 57.555 37.500 0.00 0.00 0.00 1.98
3189 7259 7.661437 TGTTAGGGCATGTACAATGATTCTATC 59.339 37.037 0.00 0.00 0.00 2.08
3190 7260 7.517320 TGTTAGGGCATGTACAATGATTCTAT 58.483 34.615 0.00 0.00 0.00 1.98
3191 7261 6.894682 TGTTAGGGCATGTACAATGATTCTA 58.105 36.000 0.00 0.00 0.00 2.10
3192 7262 5.754782 TGTTAGGGCATGTACAATGATTCT 58.245 37.500 0.00 0.00 0.00 2.40
3193 7263 6.449635 TTGTTAGGGCATGTACAATGATTC 57.550 37.500 0.00 0.00 0.00 2.52
3194 7264 8.532186 TTATTGTTAGGGCATGTACAATGATT 57.468 30.769 18.44 2.91 40.38 2.57
3195 7265 7.779798 ACTTATTGTTAGGGCATGTACAATGAT 59.220 33.333 18.44 6.65 40.38 2.45
3196 7266 7.116075 ACTTATTGTTAGGGCATGTACAATGA 58.884 34.615 18.44 12.46 40.38 2.57
3197 7267 7.333528 ACTTATTGTTAGGGCATGTACAATG 57.666 36.000 18.44 0.12 40.38 2.82
3198 7268 7.954666 AACTTATTGTTAGGGCATGTACAAT 57.045 32.000 15.33 15.33 42.20 2.71
3199 7269 9.116067 GATAACTTATTGTTAGGGCATGTACAA 57.884 33.333 0.00 4.57 43.46 2.41
3200 7270 8.491134 AGATAACTTATTGTTAGGGCATGTACA 58.509 33.333 0.00 0.00 43.46 2.90
3201 7271 8.904099 AGATAACTTATTGTTAGGGCATGTAC 57.096 34.615 0.00 0.00 43.46 2.90
3202 7272 9.991906 GTAGATAACTTATTGTTAGGGCATGTA 57.008 33.333 0.00 0.00 43.46 2.29
3203 7273 8.714906 AGTAGATAACTTATTGTTAGGGCATGT 58.285 33.333 0.00 0.00 43.46 3.21
3232 7302 9.979578 TTGTTTAATTGCTTCATGTTTCAGTAT 57.020 25.926 0.00 0.00 0.00 2.12
3235 7305 7.285788 GCTTGTTTAATTGCTTCATGTTTCAG 58.714 34.615 0.00 0.00 0.00 3.02
3236 7306 6.202570 GGCTTGTTTAATTGCTTCATGTTTCA 59.797 34.615 0.00 0.00 0.00 2.69
3237 7307 6.593072 GGCTTGTTTAATTGCTTCATGTTTC 58.407 36.000 0.00 0.00 0.00 2.78
3238 7308 5.177327 CGGCTTGTTTAATTGCTTCATGTTT 59.823 36.000 0.00 0.00 0.00 2.83
3240 7310 4.236935 CGGCTTGTTTAATTGCTTCATGT 58.763 39.130 0.00 0.00 0.00 3.21
3241 7311 3.061161 GCGGCTTGTTTAATTGCTTCATG 59.939 43.478 0.00 0.00 0.00 3.07
3243 7313 2.609244 GGCGGCTTGTTTAATTGCTTCA 60.609 45.455 0.00 0.00 0.00 3.02
3244 7314 1.992667 GGCGGCTTGTTTAATTGCTTC 59.007 47.619 0.00 0.00 0.00 3.86
3246 7316 0.965439 TGGCGGCTTGTTTAATTGCT 59.035 45.000 11.43 0.00 0.00 3.91
3247 7317 1.726248 CTTGGCGGCTTGTTTAATTGC 59.274 47.619 11.43 0.00 0.00 3.56
3248 7318 3.025287 ACTTGGCGGCTTGTTTAATTG 57.975 42.857 11.43 0.00 0.00 2.32
3251 7321 1.002251 CGAACTTGGCGGCTTGTTTAA 60.002 47.619 11.43 0.00 0.00 1.52
3252 7322 0.589223 CGAACTTGGCGGCTTGTTTA 59.411 50.000 11.43 0.00 0.00 2.01
3261 7332 2.787723 GCATATGTGAACGAACTTGGCG 60.788 50.000 4.29 0.00 0.00 5.69
3262 7333 2.420022 AGCATATGTGAACGAACTTGGC 59.580 45.455 4.29 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.