Multiple sequence alignment - TraesCS6D01G135600

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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 TraesCS6D01G135600 chr6D 100.000 7922 0 0 1 7922 104055924 104063845 0.000000e+00 14630.0
1 TraesCS6D01G135600 chr6D 82.230 287 35 11 183 456 254961856 254962139 4.780000e-57 233.0
2 TraesCS6D01G135600 chr6D 84.946 186 22 5 239 419 81921301 81921117 4.880000e-42 183.0
3 TraesCS6D01G135600 chr6D 83.636 165 24 3 12 173 450356058 450356222 1.380000e-32 152.0
4 TraesCS6D01G135600 chr6D 95.122 41 1 1 7559 7598 156809573 156809613 6.640000e-06 63.9
5 TraesCS6D01G135600 chr6B 95.888 3356 83 17 693 4015 189124616 189127949 0.000000e+00 5382.0
6 TraesCS6D01G135600 chr6B 94.711 3214 119 22 4061 7246 189128227 189131417 0.000000e+00 4946.0
7 TraesCS6D01G135600 chr6B 93.717 191 12 0 7319 7509 189131457 189131647 3.620000e-73 287.0
8 TraesCS6D01G135600 chr6B 96.667 60 2 0 7502 7561 189138372 189138431 5.060000e-17 100.0
9 TraesCS6D01G135600 chr6A 97.845 2784 47 10 1858 4631 125480625 125483405 0.000000e+00 4796.0
10 TraesCS6D01G135600 chr6A 95.299 2957 74 29 4631 7558 125483454 125486374 0.000000e+00 4630.0
11 TraesCS6D01G135600 chr6A 93.954 1836 61 14 1 1827 125478830 125480624 0.000000e+00 2730.0
12 TraesCS6D01G135600 chr7D 95.294 340 14 2 7585 7922 202027797 202028136 9.050000e-149 538.0
13 TraesCS6D01G135600 chr7D 81.375 349 49 6 248 583 1295146 1295491 3.640000e-68 270.0
14 TraesCS6D01G135600 chr7D 79.894 189 20 14 7362 7538 168488709 168488891 1.080000e-23 122.0
15 TraesCS6D01G135600 chr7D 78.392 199 23 12 182 366 93051762 93051570 2.340000e-20 111.0
16 TraesCS6D01G135600 chr7D 95.000 40 1 1 7558 7596 162189050 162189011 2.390000e-05 62.1
17 TraesCS6D01G135600 chr7D 95.000 40 1 1 7558 7596 511631846 511631807 2.390000e-05 62.1
18 TraesCS6D01G135600 chr5D 92.722 371 17 8 7559 7922 445095999 445095632 1.960000e-145 527.0
19 TraesCS6D01G135600 chr5D 83.662 355 50 7 235 583 531657293 531657645 2.130000e-85 327.0
20 TraesCS6D01G135600 chr5D 84.337 166 21 4 12 173 488876943 488877107 2.960000e-34 158.0
21 TraesCS6D01G135600 chr5D 95.000 40 1 1 7558 7596 437094312 437094351 2.390000e-05 62.1
22 TraesCS6D01G135600 chrUn 87.097 341 17 10 7585 7922 92586306 92585990 2.100000e-95 361.0
23 TraesCS6D01G135600 chrUn 94.118 51 3 0 7505 7555 372351908 372351958 2.370000e-10 78.7
24 TraesCS6D01G135600 chr2A 86.510 341 27 7 7586 7922 650611361 650611686 2.720000e-94 357.0
25 TraesCS6D01G135600 chr2A 87.248 149 11 8 7602 7746 777208712 777208568 6.360000e-36 163.0
26 TraesCS6D01G135600 chr2B 86.431 339 28 13 7585 7922 528465941 528466262 9.780000e-94 355.0
27 TraesCS6D01G135600 chr2B 95.536 112 5 0 7450 7561 546823808 546823919 6.320000e-41 180.0
28 TraesCS6D01G135600 chr4A 92.593 243 17 1 7319 7561 597663577 597663336 1.640000e-91 348.0
29 TraesCS6D01G135600 chr4A 96.098 205 8 0 7718 7922 615512324 615512528 1.270000e-87 335.0
30 TraesCS6D01G135600 chr2D 84.636 371 32 15 7559 7922 547209865 547210217 5.880000e-91 346.0
31 TraesCS6D01G135600 chr2D 84.906 159 23 1 16 173 64628250 64628092 8.230000e-35 159.0
32 TraesCS6D01G135600 chr2D 77.586 290 47 9 169 445 371244602 371244318 8.230000e-35 159.0
33 TraesCS6D01G135600 chr1A 81.425 393 61 9 202 583 56099316 56098925 2.150000e-80 311.0
34 TraesCS6D01G135600 chr1A 86.081 273 33 5 311 580 7081532 7081802 1.010000e-73 289.0
35 TraesCS6D01G135600 chr1A 85.145 276 36 5 311 583 7064711 7064984 2.180000e-70 278.0
36 TraesCS6D01G135600 chr1A 85.535 159 21 2 16 173 536364036 536363879 1.770000e-36 165.0
37 TraesCS6D01G135600 chr1A 93.103 58 2 2 7479 7535 364997515 364997459 5.090000e-12 84.2
38 TraesCS6D01G135600 chr3A 82.759 348 41 14 234 567 738042489 738042831 7.780000e-75 292.0
39 TraesCS6D01G135600 chr3A 79.335 421 57 18 182 583 595757977 595757568 1.310000e-67 268.0
40 TraesCS6D01G135600 chr3A 90.960 177 16 0 7744 7920 10142422 10142246 1.030000e-58 239.0
41 TraesCS6D01G135600 chr7A 84.112 321 29 12 7623 7922 671523928 671523609 2.800000e-74 291.0
42 TraesCS6D01G135600 chr5B 82.353 323 30 5 237 552 608216263 608215961 1.020000e-63 255.0
43 TraesCS6D01G135600 chr5B 79.297 256 29 9 7319 7555 548863673 548863923 2.960000e-34 158.0
44 TraesCS6D01G135600 chr5B 95.000 40 1 1 7559 7597 521783047 521783086 2.390000e-05 62.1
45 TraesCS6D01G135600 chr4D 78.818 406 44 19 183 570 65466501 65466120 1.330000e-57 235.0
46 TraesCS6D01G135600 chr3B 90.055 181 18 0 7742 7922 402456943 402457123 1.330000e-57 235.0
47 TraesCS6D01G135600 chr3B 86.164 159 19 3 12 168 258169700 258169543 1.370000e-37 169.0
48 TraesCS6D01G135600 chr1D 81.752 274 46 4 311 583 220918662 220918932 8.000000e-55 226.0
49 TraesCS6D01G135600 chr1D 86.164 159 18 4 16 172 238651284 238651440 1.370000e-37 169.0
50 TraesCS6D01G135600 chr1D 84.906 159 21 3 16 173 442153685 442153841 2.960000e-34 158.0
51 TraesCS6D01G135600 chr1D 76.761 284 49 14 181 457 204005030 204004757 8.290000e-30 143.0
52 TraesCS6D01G135600 chr1D 97.368 38 1 0 7559 7596 375766186 375766223 1.850000e-06 65.8
53 TraesCS6D01G135600 chr3D 86.310 168 11 1 7646 7801 265482178 265482011 1.060000e-38 172.0
54 TraesCS6D01G135600 chr3D 88.679 53 3 2 7547 7598 54330852 54330902 2.390000e-05 62.1
55 TraesCS6D01G135600 chr3D 93.023 43 2 1 7555 7596 134599602 134599560 2.390000e-05 62.1
56 TraesCS6D01G135600 chr5A 85.535 159 22 1 16 173 42693156 42693314 1.770000e-36 165.0


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 TraesCS6D01G135600 chr6D 104055924 104063845 7921 False 14630.000000 14630 100.000000 1 7922 1 chr6D.!!$F1 7921
1 TraesCS6D01G135600 chr6B 189124616 189131647 7031 False 3538.333333 5382 94.772000 693 7509 3 chr6B.!!$F2 6816
2 TraesCS6D01G135600 chr6A 125478830 125486374 7544 False 4052.000000 4796 95.699333 1 7558 3 chr6A.!!$F1 7557

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
574 583 0.672401 CCGTTGTAATGCACGGGTCT 60.672 55.000 3.38 0.0 37.78 3.85 F
1316 1336 0.729140 GTGCCGTTCGATTTTGCCTG 60.729 55.000 0.00 0.0 0.00 4.85 F
1644 1668 0.877743 TGGTGTTGTGTGTGTGTGTG 59.122 50.000 0.00 0.0 0.00 3.82 F
1645 1669 0.878416 GGTGTTGTGTGTGTGTGTGT 59.122 50.000 0.00 0.0 0.00 3.72 F
1654 1678 1.063912 GTGTGTGTGTGTGTGATGTGG 59.936 52.381 0.00 0.0 0.00 4.17 F
1655 1679 1.065854 TGTGTGTGTGTGTGATGTGGA 60.066 47.619 0.00 0.0 0.00 4.02 F
3877 3920 0.258774 AGGTGGTGTTCCTGCAAGTT 59.741 50.000 0.00 0.0 33.62 2.66 F
4714 5043 2.754552 TGATGCTGCATAAGTTCCAACC 59.245 45.455 16.23 0.0 0.00 3.77 F
6552 6886 5.918011 TGTATTTCATTGTTTGGCTTTCGTC 59.082 36.000 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1836 0.963856 ACGAGAGTGCACGGTCCATA 60.964 55.000 12.01 0.00 46.97 2.74 R
2633 2661 2.121564 CTGAAACCACTGCACTGCCG 62.122 60.000 0.00 0.00 0.00 5.69 R
2657 2685 2.938428 AGTTTATTCCCATGCCCCAA 57.062 45.000 0.00 0.00 0.00 4.12 R
3517 3545 4.670621 CGTTGCAAACTACACATTCTGAAC 59.329 41.667 0.00 0.00 46.99 3.18 R
3856 3899 0.670162 CTTGCAGGAACACCACCTTG 59.330 55.000 0.00 0.00 35.35 3.61 R
4082 4361 7.999679 TGGAATTAGATGAACAGCCAATTTAG 58.000 34.615 0.00 0.00 0.00 1.85 R
5253 5585 0.526211 TGTCGACCTCATCCAACTCG 59.474 55.000 14.12 0.00 0.00 4.18 R
6702 7036 0.615331 GCTGGATCACCCTCTTGACA 59.385 55.000 0.00 0.00 35.38 3.58 R
7419 7806 0.037326 TAGATCAATCCATCCGCGGC 60.037 55.000 23.51 1.36 0.00 6.53 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
133 135 4.934602 TGATTGTGTATCTCGTTGATGCAA 59.065 37.500 11.57 9.83 46.47 4.08
147 149 7.311408 TCGTTGATGCAACAAAATATGATCAA 58.689 30.769 11.32 0.00 43.70 2.57
170 172 6.460103 AGGCCATAGGAGATTATGATTTGT 57.540 37.500 5.01 0.00 33.75 2.83
229 231 8.532977 AAATTGGTGGATTTTAGAAATGTTCG 57.467 30.769 0.00 0.00 34.02 3.95
230 232 5.054390 TGGTGGATTTTAGAAATGTTCGC 57.946 39.130 0.00 0.00 34.02 4.70
231 233 4.082463 TGGTGGATTTTAGAAATGTTCGCC 60.082 41.667 0.00 0.00 34.02 5.54
232 234 4.095610 GTGGATTTTAGAAATGTTCGCCG 58.904 43.478 0.00 0.00 34.02 6.46
233 235 4.004314 TGGATTTTAGAAATGTTCGCCGA 58.996 39.130 0.00 0.00 34.02 5.54
234 236 4.638421 TGGATTTTAGAAATGTTCGCCGAT 59.362 37.500 0.00 0.00 34.02 4.18
235 237 5.124776 TGGATTTTAGAAATGTTCGCCGATT 59.875 36.000 0.00 0.00 34.02 3.34
236 238 5.681543 GGATTTTAGAAATGTTCGCCGATTC 59.318 40.000 0.00 0.00 34.02 2.52
237 239 4.609691 TTTAGAAATGTTCGCCGATTCC 57.390 40.909 0.00 0.00 34.02 3.01
238 240 2.107950 AGAAATGTTCGCCGATTCCA 57.892 45.000 0.00 0.00 34.02 3.53
239 241 2.432444 AGAAATGTTCGCCGATTCCAA 58.568 42.857 0.00 0.00 34.02 3.53
240 242 2.817258 AGAAATGTTCGCCGATTCCAAA 59.183 40.909 0.00 0.00 34.02 3.28
512 521 5.949952 TGATAGTGTATATAGGTGATGCGGT 59.050 40.000 0.00 0.00 0.00 5.68
569 578 1.434555 TTCTCCCGTTGTAATGCACG 58.565 50.000 0.00 0.00 0.00 5.34
574 583 0.672401 CCGTTGTAATGCACGGGTCT 60.672 55.000 3.38 0.00 37.78 3.85
585 594 2.223618 TGCACGGGTCTTTTTGCTAAAC 60.224 45.455 0.00 0.00 35.91 2.01
597 606 9.011095 GTCTTTTTGCTAAACTAATACTCCCTT 57.989 33.333 0.00 0.00 0.00 3.95
598 607 9.582648 TCTTTTTGCTAAACTAATACTCCCTTT 57.417 29.630 0.00 0.00 0.00 3.11
604 613 7.288389 TGCTAAACTAATACTCCCTTTATCCGA 59.712 37.037 0.00 0.00 0.00 4.55
617 626 6.821665 TCCCTTTATCCGAAAATACTTGTGAG 59.178 38.462 0.00 0.00 0.00 3.51
682 691 6.726490 AGGAGTATAAGGCGTTTTAGATCA 57.274 37.500 0.00 0.00 0.00 2.92
683 692 6.750148 AGGAGTATAAGGCGTTTTAGATCAG 58.250 40.000 0.00 0.00 0.00 2.90
684 693 6.550108 AGGAGTATAAGGCGTTTTAGATCAGA 59.450 38.462 0.00 0.00 0.00 3.27
865 877 1.486310 TCCAACATCTTCCTCCATCCG 59.514 52.381 0.00 0.00 0.00 4.18
973 993 1.728490 GCACCCGAATCCTCATTGGC 61.728 60.000 0.00 0.00 35.26 4.52
1288 1308 3.024547 TCCTCGTCTCAGGTTGGAATAG 58.975 50.000 0.00 0.00 34.76 1.73
1315 1335 1.579429 GTGCCGTTCGATTTTGCCT 59.421 52.632 0.00 0.00 0.00 4.75
1316 1336 0.729140 GTGCCGTTCGATTTTGCCTG 60.729 55.000 0.00 0.00 0.00 4.85
1371 1394 1.208052 AGTCGGCTATGCAGATGTGTT 59.792 47.619 0.00 0.00 35.03 3.32
1400 1423 3.313526 AGCACACTGATATTGCCGAATTC 59.686 43.478 0.00 0.00 36.91 2.17
1423 1446 4.734398 ACTTTGTTTTCTCCATTGTGCA 57.266 36.364 0.00 0.00 0.00 4.57
1561 1585 4.141620 GGCATTCCCTCTCTAGTTCATGAA 60.142 45.833 3.38 3.38 0.00 2.57
1643 1667 1.610363 TTGGTGTTGTGTGTGTGTGT 58.390 45.000 0.00 0.00 0.00 3.72
1644 1668 0.877743 TGGTGTTGTGTGTGTGTGTG 59.122 50.000 0.00 0.00 0.00 3.82
1645 1669 0.878416 GGTGTTGTGTGTGTGTGTGT 59.122 50.000 0.00 0.00 0.00 3.72
1646 1670 1.400888 GGTGTTGTGTGTGTGTGTGTG 60.401 52.381 0.00 0.00 0.00 3.82
1647 1671 1.265635 GTGTTGTGTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
1650 1674 2.106477 TGTGTGTGTGTGTGTGTGAT 57.894 45.000 0.00 0.00 0.00 3.06
1651 1675 1.736681 TGTGTGTGTGTGTGTGTGATG 59.263 47.619 0.00 0.00 0.00 3.07
1652 1676 1.737236 GTGTGTGTGTGTGTGTGATGT 59.263 47.619 0.00 0.00 0.00 3.06
1653 1677 1.736681 TGTGTGTGTGTGTGTGATGTG 59.263 47.619 0.00 0.00 0.00 3.21
1654 1678 1.063912 GTGTGTGTGTGTGTGATGTGG 59.936 52.381 0.00 0.00 0.00 4.17
1655 1679 1.065854 TGTGTGTGTGTGTGATGTGGA 60.066 47.619 0.00 0.00 0.00 4.02
1656 1680 1.599071 GTGTGTGTGTGTGATGTGGAG 59.401 52.381 0.00 0.00 0.00 3.86
1657 1681 1.484240 TGTGTGTGTGTGATGTGGAGA 59.516 47.619 0.00 0.00 0.00 3.71
1658 1682 2.104622 TGTGTGTGTGTGATGTGGAGAT 59.895 45.455 0.00 0.00 0.00 2.75
1659 1683 3.323403 TGTGTGTGTGTGATGTGGAGATA 59.677 43.478 0.00 0.00 0.00 1.98
1677 1701 8.125448 GTGGAGATAATTTGAAGCATAACAGTC 58.875 37.037 0.00 0.00 0.00 3.51
1700 1724 7.040755 AGTCGTGTCATGAAAATTAATTGACCA 60.041 33.333 12.48 7.13 36.68 4.02
1749 1773 6.757010 AGCATTATCAGTTTACTACGAGTTGG 59.243 38.462 0.00 0.00 0.00 3.77
1754 1778 6.216801 TCAGTTTACTACGAGTTGGCATAT 57.783 37.500 0.00 0.00 0.00 1.78
1795 1819 2.408704 GCATGGTAATCGCGTAGATCAC 59.591 50.000 5.77 0.00 38.98 3.06
1796 1820 3.638484 CATGGTAATCGCGTAGATCACA 58.362 45.455 5.77 0.00 38.98 3.58
1812 1836 4.943705 AGATCACATGTTTTGCTTCGGTAT 59.056 37.500 0.00 0.00 0.00 2.73
1818 1842 5.065988 ACATGTTTTGCTTCGGTATATGGAC 59.934 40.000 0.00 0.00 0.00 4.02
2657 2685 2.620115 CAGTGCAGTGGTTTCAGTCAAT 59.380 45.455 14.08 0.00 0.00 2.57
3035 3063 6.830324 TGCCATCTTGCCATATCTTTATATCC 59.170 38.462 0.00 0.00 0.00 2.59
3248 3276 4.418013 TCTGTTGTAATTTGGCGTGATG 57.582 40.909 0.00 0.00 0.00 3.07
3856 3899 3.733443 AGCAAACAACCAATCAGTTCC 57.267 42.857 0.00 0.00 0.00 3.62
3877 3920 0.258774 AGGTGGTGTTCCTGCAAGTT 59.741 50.000 0.00 0.00 33.62 2.66
3885 3928 2.948979 TGTTCCTGCAAGTTGTAACCAG 59.051 45.455 4.48 3.18 0.00 4.00
4065 4344 5.178061 AGTTTTGCAAGGAAAGTTGGAAAG 58.822 37.500 0.00 0.00 45.06 2.62
4082 4361 9.606631 AGTTGGAAAGTAATCATATCAAGAGAC 57.393 33.333 0.00 0.00 0.00 3.36
4136 4416 6.998258 ATGCAATATTTCAGCTTATTTCGC 57.002 33.333 0.00 0.00 0.00 4.70
4445 4725 3.365364 GCCTGAAACACTGATACTTGCAC 60.365 47.826 0.00 0.00 0.00 4.57
4476 4756 7.201974 GGGTATATGCGGTATGGTATCAATACT 60.202 40.741 0.53 0.00 33.81 2.12
4497 4777 6.716934 ACTGTATCTGAACAAGTATCGGAT 57.283 37.500 0.00 0.00 43.54 4.18
4597 4877 3.686016 TGTACTGATTCTTTTGCTCCCC 58.314 45.455 0.00 0.00 0.00 4.81
4599 4879 2.800250 ACTGATTCTTTTGCTCCCCTG 58.200 47.619 0.00 0.00 0.00 4.45
4619 4899 2.852449 TGGCACTCCTCTTATTCCCATT 59.148 45.455 0.00 0.00 0.00 3.16
4641 4970 3.617284 TCAGCATGTCAATTCATCAGCT 58.383 40.909 0.00 0.00 37.40 4.24
4708 5037 8.727910 CATATCTGTATTGATGCTGCATAAGTT 58.272 33.333 16.23 2.56 0.00 2.66
4714 5043 2.754552 TGATGCTGCATAAGTTCCAACC 59.245 45.455 16.23 0.00 0.00 3.77
6519 6852 6.506500 AATTTGCTTGAGTCATGGAACTAG 57.493 37.500 11.73 0.00 0.00 2.57
6537 6871 8.822805 TGGAACTAGGTTCTAGTTGTATTTCAT 58.177 33.333 20.77 0.00 41.70 2.57
6552 6886 5.918011 TGTATTTCATTGTTTGGCTTTCGTC 59.082 36.000 0.00 0.00 0.00 4.20
6702 7036 1.611261 TAACTACGGTGCCAGGCCT 60.611 57.895 9.64 0.00 0.00 5.19
6744 7078 0.738975 TGGTGGAGAACGAGATAGCG 59.261 55.000 0.00 0.00 37.29 4.26
6856 7190 1.835927 GCAGCTGGTCCTTCAGAGGT 61.836 60.000 17.12 0.00 43.97 3.85
6937 7271 3.069016 TGACTGAGGCGTGAGAACTTTAA 59.931 43.478 0.00 0.00 0.00 1.52
6938 7272 4.246458 GACTGAGGCGTGAGAACTTTAAT 58.754 43.478 0.00 0.00 0.00 1.40
6939 7273 5.047590 TGACTGAGGCGTGAGAACTTTAATA 60.048 40.000 0.00 0.00 0.00 0.98
7032 7366 2.436417 GCACATCAGCTTGTTCCCTTA 58.564 47.619 0.00 0.00 0.00 2.69
7076 7412 2.211250 ATTGTGTCTTGCATGGCTCT 57.789 45.000 5.73 0.00 0.00 4.09
7078 7414 0.109153 TGTGTCTTGCATGGCTCTGT 59.891 50.000 5.73 0.00 0.00 3.41
7086 7436 0.681175 GCATGGCTCTGTTTTGGGTT 59.319 50.000 0.00 0.00 0.00 4.11
7124 7475 0.648958 GCCCAACGCGACTATACAAC 59.351 55.000 15.93 0.00 0.00 3.32
7135 7486 3.366679 CGACTATACAACTGGACACGGTT 60.367 47.826 0.00 0.00 46.91 4.44
7315 7686 6.321821 AGGTGCAATAAATAACTGAGGGTA 57.678 37.500 0.00 0.00 0.00 3.69
7319 7690 6.094881 GTGCAATAAATAACTGAGGGTAGCAA 59.905 38.462 0.00 0.00 0.00 3.91
7320 7691 6.318648 TGCAATAAATAACTGAGGGTAGCAAG 59.681 38.462 0.00 0.00 0.00 4.01
7340 7727 1.378762 GGCACCTTCTGGTTGCCTA 59.621 57.895 15.99 0.00 46.05 3.93
7360 7747 1.337260 ACGATGGCGCTTCAGATATCC 60.337 52.381 7.64 0.00 42.48 2.59
7419 7806 5.175126 GGACGTGATACAACTATCAAATCCG 59.825 44.000 0.00 3.06 40.42 4.18
7473 7860 2.858768 ACCATTACTCAATCCCACCCAT 59.141 45.455 0.00 0.00 0.00 4.00
7549 7936 9.923143 CCACTATCAAATCCAACTATACGAATA 57.077 33.333 0.00 0.00 0.00 1.75
7558 7945 7.591421 TCCAACTATACGAATATGACTGGAA 57.409 36.000 0.00 0.00 0.00 3.53
7559 7946 8.190326 TCCAACTATACGAATATGACTGGAAT 57.810 34.615 0.00 0.00 0.00 3.01
7560 7947 8.304596 TCCAACTATACGAATATGACTGGAATC 58.695 37.037 0.00 0.00 0.00 2.52
7561 7948 8.307483 CCAACTATACGAATATGACTGGAATCT 58.693 37.037 0.00 0.00 0.00 2.40
7562 7949 9.347934 CAACTATACGAATATGACTGGAATCTC 57.652 37.037 0.00 0.00 0.00 2.75
7563 7950 8.871629 ACTATACGAATATGACTGGAATCTCT 57.128 34.615 0.00 0.00 0.00 3.10
7564 7951 9.961264 ACTATACGAATATGACTGGAATCTCTA 57.039 33.333 0.00 0.00 0.00 2.43
7566 7953 8.871629 ATACGAATATGACTGGAATCTCTACT 57.128 34.615 0.00 0.00 0.00 2.57
7567 7954 7.209471 ACGAATATGACTGGAATCTCTACTC 57.791 40.000 0.00 0.00 0.00 2.59
7568 7955 6.207810 ACGAATATGACTGGAATCTCTACTCC 59.792 42.308 0.00 0.00 0.00 3.85
7569 7956 6.432783 CGAATATGACTGGAATCTCTACTCCT 59.567 42.308 0.00 0.00 32.51 3.69
7570 7957 7.608376 CGAATATGACTGGAATCTCTACTCCTA 59.392 40.741 0.00 0.00 32.51 2.94
7571 7958 9.303116 GAATATGACTGGAATCTCTACTCCTAA 57.697 37.037 0.00 0.00 32.51 2.69
7572 7959 9.836179 AATATGACTGGAATCTCTACTCCTAAT 57.164 33.333 0.00 0.00 32.51 1.73
7573 7960 6.968263 TGACTGGAATCTCTACTCCTAATG 57.032 41.667 0.00 0.00 32.51 1.90
7574 7961 6.436027 TGACTGGAATCTCTACTCCTAATGT 58.564 40.000 0.00 0.00 32.51 2.71
7575 7962 6.547880 TGACTGGAATCTCTACTCCTAATGTC 59.452 42.308 0.00 0.00 32.51 3.06
7576 7963 6.678547 ACTGGAATCTCTACTCCTAATGTCT 58.321 40.000 0.00 0.00 32.51 3.41
7577 7964 6.775629 ACTGGAATCTCTACTCCTAATGTCTC 59.224 42.308 0.00 0.00 32.51 3.36
7578 7965 6.673583 TGGAATCTCTACTCCTAATGTCTCA 58.326 40.000 0.00 0.00 32.51 3.27
7579 7966 6.775142 TGGAATCTCTACTCCTAATGTCTCAG 59.225 42.308 0.00 0.00 32.51 3.35
7580 7967 6.775629 GGAATCTCTACTCCTAATGTCTCAGT 59.224 42.308 0.00 0.00 0.00 3.41
7581 7968 7.286775 GGAATCTCTACTCCTAATGTCTCAGTT 59.713 40.741 0.00 0.00 0.00 3.16
7582 7969 7.581213 ATCTCTACTCCTAATGTCTCAGTTG 57.419 40.000 0.00 0.00 0.00 3.16
7583 7970 5.888724 TCTCTACTCCTAATGTCTCAGTTGG 59.111 44.000 0.00 0.00 0.00 3.77
7584 7971 5.580998 TCTACTCCTAATGTCTCAGTTGGT 58.419 41.667 0.00 0.00 0.00 3.67
7585 7972 6.728411 TCTACTCCTAATGTCTCAGTTGGTA 58.272 40.000 0.00 0.00 0.00 3.25
7586 7973 7.355101 TCTACTCCTAATGTCTCAGTTGGTAT 58.645 38.462 0.00 0.00 0.00 2.73
7587 7974 6.875972 ACTCCTAATGTCTCAGTTGGTATT 57.124 37.500 0.00 0.00 0.00 1.89
7588 7975 7.259088 ACTCCTAATGTCTCAGTTGGTATTT 57.741 36.000 0.00 0.00 0.00 1.40
7589 7976 7.690256 ACTCCTAATGTCTCAGTTGGTATTTT 58.310 34.615 0.00 0.00 0.00 1.82
7590 7977 7.824779 ACTCCTAATGTCTCAGTTGGTATTTTC 59.175 37.037 0.00 0.00 0.00 2.29
7591 7978 6.816640 TCCTAATGTCTCAGTTGGTATTTTCG 59.183 38.462 0.00 0.00 0.00 3.46
7592 7979 6.594159 CCTAATGTCTCAGTTGGTATTTTCGT 59.406 38.462 0.00 0.00 0.00 3.85
7593 7980 6.877611 AATGTCTCAGTTGGTATTTTCGTT 57.122 33.333 0.00 0.00 0.00 3.85
7594 7981 5.917541 TGTCTCAGTTGGTATTTTCGTTC 57.082 39.130 0.00 0.00 0.00 3.95
7595 7982 4.753107 TGTCTCAGTTGGTATTTTCGTTCC 59.247 41.667 0.00 0.00 0.00 3.62
7596 7983 4.753107 GTCTCAGTTGGTATTTTCGTTCCA 59.247 41.667 0.00 0.00 0.00 3.53
7597 7984 4.753107 TCTCAGTTGGTATTTTCGTTCCAC 59.247 41.667 0.00 0.00 0.00 4.02
7598 7985 3.816523 TCAGTTGGTATTTTCGTTCCACC 59.183 43.478 0.00 0.00 0.00 4.61
7599 7986 3.566322 CAGTTGGTATTTTCGTTCCACCA 59.434 43.478 0.00 0.00 37.50 4.17
7600 7987 3.566742 AGTTGGTATTTTCGTTCCACCAC 59.433 43.478 0.00 0.00 38.95 4.16
7601 7988 3.495434 TGGTATTTTCGTTCCACCACT 57.505 42.857 0.00 0.00 34.40 4.00
7602 7989 3.822940 TGGTATTTTCGTTCCACCACTT 58.177 40.909 0.00 0.00 34.40 3.16
7603 7990 4.208746 TGGTATTTTCGTTCCACCACTTT 58.791 39.130 0.00 0.00 34.40 2.66
7604 7991 4.276431 TGGTATTTTCGTTCCACCACTTTC 59.724 41.667 0.00 0.00 34.40 2.62
7605 7992 3.619233 ATTTTCGTTCCACCACTTTCG 57.381 42.857 0.00 0.00 0.00 3.46
7606 7993 2.027003 TTTCGTTCCACCACTTTCGT 57.973 45.000 0.00 0.00 0.00 3.85
7607 7994 1.574134 TTCGTTCCACCACTTTCGTC 58.426 50.000 0.00 0.00 0.00 4.20
7608 7995 0.249573 TCGTTCCACCACTTTCGTCC 60.250 55.000 0.00 0.00 0.00 4.79
7609 7996 1.554042 CGTTCCACCACTTTCGTCCG 61.554 60.000 0.00 0.00 0.00 4.79
7610 7997 0.531311 GTTCCACCACTTTCGTCCGT 60.531 55.000 0.00 0.00 0.00 4.69
7611 7998 0.178533 TTCCACCACTTTCGTCCGTT 59.821 50.000 0.00 0.00 0.00 4.44
7612 7999 0.178533 TCCACCACTTTCGTCCGTTT 59.821 50.000 0.00 0.00 0.00 3.60
7613 8000 1.018910 CCACCACTTTCGTCCGTTTT 58.981 50.000 0.00 0.00 0.00 2.43
7614 8001 1.402613 CCACCACTTTCGTCCGTTTTT 59.597 47.619 0.00 0.00 0.00 1.94
7646 8033 2.930826 TTTGTCCTCTTCTCACACCC 57.069 50.000 0.00 0.00 0.00 4.61
7647 8034 1.056660 TTGTCCTCTTCTCACACCCC 58.943 55.000 0.00 0.00 0.00 4.95
7648 8035 1.185618 TGTCCTCTTCTCACACCCCG 61.186 60.000 0.00 0.00 0.00 5.73
7649 8036 1.609501 TCCTCTTCTCACACCCCGG 60.610 63.158 0.00 0.00 0.00 5.73
7650 8037 1.609501 CCTCTTCTCACACCCCGGA 60.610 63.158 0.73 0.00 0.00 5.14
7651 8038 0.978146 CCTCTTCTCACACCCCGGAT 60.978 60.000 0.73 0.00 0.00 4.18
7652 8039 0.905357 CTCTTCTCACACCCCGGATT 59.095 55.000 0.73 0.00 0.00 3.01
7653 8040 0.613260 TCTTCTCACACCCCGGATTG 59.387 55.000 0.73 0.89 0.00 2.67
7654 8041 1.002624 TTCTCACACCCCGGATTGC 60.003 57.895 0.73 0.00 0.00 3.56
7655 8042 2.438434 CTCACACCCCGGATTGCC 60.438 66.667 0.73 0.00 0.00 4.52
7656 8043 3.995506 CTCACACCCCGGATTGCCC 62.996 68.421 0.73 0.00 0.00 5.36
7665 8052 3.857038 GGATTGCCCGACCCGCTA 61.857 66.667 0.00 0.00 0.00 4.26
7666 8053 2.188469 GATTGCCCGACCCGCTAA 59.812 61.111 0.00 0.00 0.00 3.09
7667 8054 1.450669 GATTGCCCGACCCGCTAAA 60.451 57.895 0.00 0.00 0.00 1.85
7668 8055 1.001887 ATTGCCCGACCCGCTAAAA 60.002 52.632 0.00 0.00 0.00 1.52
7669 8056 0.609681 ATTGCCCGACCCGCTAAAAA 60.610 50.000 0.00 0.00 0.00 1.94
7687 8074 2.327200 AAAAATCCCCTCGTCCGATC 57.673 50.000 0.00 0.00 0.00 3.69
7688 8075 0.468648 AAAATCCCCTCGTCCGATCC 59.531 55.000 0.00 0.00 0.00 3.36
7689 8076 1.408453 AAATCCCCTCGTCCGATCCC 61.408 60.000 0.00 0.00 0.00 3.85
7690 8077 3.829904 ATCCCCTCGTCCGATCCCC 62.830 68.421 0.00 0.00 0.00 4.81
7691 8078 4.853142 CCCCTCGTCCGATCCCCA 62.853 72.222 0.00 0.00 0.00 4.96
7692 8079 2.762459 CCCTCGTCCGATCCCCAA 60.762 66.667 0.00 0.00 0.00 4.12
7693 8080 2.499685 CCTCGTCCGATCCCCAAC 59.500 66.667 0.00 0.00 0.00 3.77
7694 8081 2.499685 CTCGTCCGATCCCCAACC 59.500 66.667 0.00 0.00 0.00 3.77
7695 8082 2.038329 TCGTCCGATCCCCAACCT 59.962 61.111 0.00 0.00 0.00 3.50
7696 8083 2.017559 CTCGTCCGATCCCCAACCTC 62.018 65.000 0.00 0.00 0.00 3.85
7697 8084 2.908796 GTCCGATCCCCAACCTCC 59.091 66.667 0.00 0.00 0.00 4.30
7698 8085 2.366435 TCCGATCCCCAACCTCCC 60.366 66.667 0.00 0.00 0.00 4.30
7699 8086 3.489513 CCGATCCCCAACCTCCCC 61.490 72.222 0.00 0.00 0.00 4.81
7700 8087 3.489513 CGATCCCCAACCTCCCCC 61.490 72.222 0.00 0.00 0.00 5.40
7725 8112 4.874977 GTCGCCGCTGCCTCCTAC 62.875 72.222 0.00 0.00 0.00 3.18
7730 8117 4.514577 CGCTGCCTCCTACCGGTG 62.515 72.222 19.93 7.24 0.00 4.94
7731 8118 4.840005 GCTGCCTCCTACCGGTGC 62.840 72.222 19.93 12.61 0.00 5.01
7732 8119 4.514577 CTGCCTCCTACCGGTGCG 62.515 72.222 19.93 8.16 33.68 5.34
7736 8123 4.814294 CTCCTACCGGTGCGCCAC 62.814 72.222 19.93 2.79 34.09 5.01
7751 8138 3.322466 CACCACTCCCGCCTCCTT 61.322 66.667 0.00 0.00 0.00 3.36
7752 8139 3.003763 ACCACTCCCGCCTCCTTC 61.004 66.667 0.00 0.00 0.00 3.46
7753 8140 3.787001 CCACTCCCGCCTCCTTCC 61.787 72.222 0.00 0.00 0.00 3.46
7754 8141 4.148825 CACTCCCGCCTCCTTCCG 62.149 72.222 0.00 0.00 0.00 4.30
7778 8165 3.470888 CGTCATCCCCGCCTCCTT 61.471 66.667 0.00 0.00 0.00 3.36
7779 8166 2.998949 GTCATCCCCGCCTCCTTT 59.001 61.111 0.00 0.00 0.00 3.11
7780 8167 1.153147 GTCATCCCCGCCTCCTTTC 60.153 63.158 0.00 0.00 0.00 2.62
7781 8168 2.203070 CATCCCCGCCTCCTTTCG 60.203 66.667 0.00 0.00 0.00 3.46
7782 8169 3.480133 ATCCCCGCCTCCTTTCGG 61.480 66.667 0.00 0.00 44.89 4.30
7805 8192 2.520982 CGTCATCCCCGCCTCCTA 60.521 66.667 0.00 0.00 0.00 2.94
7806 8193 2.857744 CGTCATCCCCGCCTCCTAC 61.858 68.421 0.00 0.00 0.00 3.18
7807 8194 2.122989 TCATCCCCGCCTCCTACC 60.123 66.667 0.00 0.00 0.00 3.18
7808 8195 3.616721 CATCCCCGCCTCCTACCG 61.617 72.222 0.00 0.00 0.00 4.02
7809 8196 4.936081 ATCCCCGCCTCCTACCGG 62.936 72.222 0.00 0.00 43.97 5.28
7832 8219 3.391382 CGCCGGACCCTCCTTCTT 61.391 66.667 5.05 0.00 33.30 2.52
7833 8220 2.585153 GCCGGACCCTCCTTCTTC 59.415 66.667 5.05 0.00 33.30 2.87
7834 8221 3.032667 GCCGGACCCTCCTTCTTCC 62.033 68.421 5.05 0.00 33.30 3.46
7835 8222 2.368011 CCGGACCCTCCTTCTTCCC 61.368 68.421 0.00 0.00 33.30 3.97
7836 8223 1.306226 CGGACCCTCCTTCTTCCCT 60.306 63.158 0.00 0.00 33.30 4.20
7837 8224 1.617947 CGGACCCTCCTTCTTCCCTG 61.618 65.000 0.00 0.00 33.30 4.45
7838 8225 1.275421 GGACCCTCCTTCTTCCCTGG 61.275 65.000 0.00 0.00 32.53 4.45
7839 8226 0.252742 GACCCTCCTTCTTCCCTGGA 60.253 60.000 0.00 0.00 0.00 3.86
7840 8227 0.252927 ACCCTCCTTCTTCCCTGGAG 60.253 60.000 0.00 0.00 45.02 3.86
7841 8228 1.631071 CCCTCCTTCTTCCCTGGAGC 61.631 65.000 0.00 0.00 44.32 4.70
7842 8229 1.519719 CTCCTTCTTCCCTGGAGCG 59.480 63.158 0.00 0.00 40.52 5.03
7843 8230 2.124942 CCTTCTTCCCTGGAGCGC 60.125 66.667 0.00 0.00 0.00 5.92
7844 8231 2.124942 CTTCTTCCCTGGAGCGCC 60.125 66.667 2.29 0.00 0.00 6.53
7845 8232 2.927856 TTCTTCCCTGGAGCGCCA 60.928 61.111 9.48 9.48 43.47 5.69
7846 8233 3.254024 TTCTTCCCTGGAGCGCCAC 62.254 63.158 4.49 0.00 39.92 5.01
7847 8234 4.785453 CTTCCCTGGAGCGCCACC 62.785 72.222 4.49 9.31 39.92 4.61
7903 8290 4.148825 CCGCCGTCTTCCCCAGAG 62.149 72.222 0.00 0.00 29.34 3.35
7904 8291 4.821589 CGCCGTCTTCCCCAGAGC 62.822 72.222 0.00 0.00 29.34 4.09
7905 8292 4.821589 GCCGTCTTCCCCAGAGCG 62.822 72.222 0.00 0.00 29.34 5.03
7906 8293 4.821589 CCGTCTTCCCCAGAGCGC 62.822 72.222 0.00 0.00 29.34 5.92
7907 8294 4.821589 CGTCTTCCCCAGAGCGCC 62.822 72.222 2.29 0.00 29.34 6.53
7908 8295 3.706373 GTCTTCCCCAGAGCGCCA 61.706 66.667 2.29 0.00 29.34 5.69
7909 8296 3.706373 TCTTCCCCAGAGCGCCAC 61.706 66.667 2.29 0.00 0.00 5.01
7910 8297 4.785453 CTTCCCCAGAGCGCCACC 62.785 72.222 2.29 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.360681 CCTGAACGTTTCTCAAATTCATGAAC 59.639 38.462 11.07 0.00 0.00 3.18
133 135 6.613699 TCCTATGGCCTTGATCATATTTTGT 58.386 36.000 3.32 0.00 0.00 2.83
147 149 6.460103 ACAAATCATAATCTCCTATGGCCT 57.540 37.500 3.32 0.00 31.33 5.19
203 205 8.987890 CGAACATTTCTAAAATCCACCAATTTT 58.012 29.630 0.00 0.00 40.82 1.82
217 219 3.601435 TGGAATCGGCGAACATTTCTAA 58.399 40.909 15.93 3.43 0.00 2.10
221 223 3.651803 TTTTGGAATCGGCGAACATTT 57.348 38.095 15.93 2.70 0.00 2.32
222 224 3.651803 TTTTTGGAATCGGCGAACATT 57.348 38.095 15.93 3.16 0.00 2.71
239 241 8.504005 ACATTTCTAGAATCGACGAACATTTTT 58.496 29.630 5.89 0.00 0.00 1.94
240 242 8.029642 ACATTTCTAGAATCGACGAACATTTT 57.970 30.769 5.89 0.00 0.00 1.82
248 250 4.862574 TGGTGAACATTTCTAGAATCGACG 59.137 41.667 5.89 0.00 0.00 5.12
263 265 8.558973 AAACAATTTTCTTGAATTGGTGAACA 57.441 26.923 13.10 0.00 44.01 3.18
501 510 0.035439 CCCACTTTACCGCATCACCT 60.035 55.000 0.00 0.00 0.00 4.00
512 521 6.774673 TCTACAATGACAATGACCCACTTTA 58.225 36.000 0.00 0.00 0.00 1.85
546 555 3.978855 GTGCATTACAACGGGAGAAAAAC 59.021 43.478 0.00 0.00 0.00 2.43
569 578 7.148120 GGGAGTATTAGTTTAGCAAAAAGACCC 60.148 40.741 0.00 0.00 0.00 4.46
597 606 9.667107 ATTTCTCTCACAAGTATTTTCGGATAA 57.333 29.630 0.00 0.00 0.00 1.75
598 607 9.098355 CATTTCTCTCACAAGTATTTTCGGATA 57.902 33.333 0.00 0.00 0.00 2.59
638 647 3.207265 TCCATCCGGAAATACATGTGG 57.793 47.619 9.01 9.46 38.83 4.17
682 691 5.916661 TCCAAAGCTCGTAGTATTCTTCT 57.083 39.130 0.00 0.00 0.00 2.85
683 692 6.183360 GGTTTCCAAAGCTCGTAGTATTCTTC 60.183 42.308 0.00 0.00 33.81 2.87
684 693 5.642491 GGTTTCCAAAGCTCGTAGTATTCTT 59.358 40.000 0.00 0.00 33.81 2.52
865 877 1.972027 GAAAAGAGAGAAGCGGCGGC 61.972 60.000 9.78 8.43 40.37 6.53
973 993 3.344515 GAGGGTTTAGGGTTTAGCTGTG 58.655 50.000 0.00 0.00 0.00 3.66
1162 1182 4.247380 GGCCATGGGAGGAGCGAG 62.247 72.222 15.13 0.00 0.00 5.03
1400 1423 5.687285 GTGCACAATGGAGAAAACAAAGTAG 59.313 40.000 13.17 0.00 0.00 2.57
1423 1446 9.427821 ACTATCAATCTGTAACTGGAGAATAGT 57.572 33.333 0.00 0.00 0.00 2.12
1497 1521 9.439500 AGTTTATGATCACCAATTTGGAAAATG 57.561 29.630 22.19 9.66 40.96 2.32
1561 1585 8.887393 TCTAATTTTAAGGGTAAAGGTGAGAGT 58.113 33.333 0.00 0.00 30.92 3.24
1643 1667 6.127925 GCTTCAAATTATCTCCACATCACACA 60.128 38.462 0.00 0.00 0.00 3.72
1644 1668 6.127925 TGCTTCAAATTATCTCCACATCACAC 60.128 38.462 0.00 0.00 0.00 3.82
1645 1669 5.945191 TGCTTCAAATTATCTCCACATCACA 59.055 36.000 0.00 0.00 0.00 3.58
1646 1670 6.441093 TGCTTCAAATTATCTCCACATCAC 57.559 37.500 0.00 0.00 0.00 3.06
1647 1671 8.623903 GTTATGCTTCAAATTATCTCCACATCA 58.376 33.333 0.00 0.00 0.00 3.07
1650 1674 7.611467 ACTGTTATGCTTCAAATTATCTCCACA 59.389 33.333 0.00 0.00 0.00 4.17
1651 1675 7.989826 ACTGTTATGCTTCAAATTATCTCCAC 58.010 34.615 0.00 0.00 0.00 4.02
1652 1676 7.011389 CGACTGTTATGCTTCAAATTATCTCCA 59.989 37.037 0.00 0.00 0.00 3.86
1653 1677 7.011482 ACGACTGTTATGCTTCAAATTATCTCC 59.989 37.037 0.00 0.00 0.00 3.71
1654 1678 7.848051 CACGACTGTTATGCTTCAAATTATCTC 59.152 37.037 0.00 0.00 0.00 2.75
1655 1679 7.334421 ACACGACTGTTATGCTTCAAATTATCT 59.666 33.333 0.00 0.00 0.00 1.98
1656 1680 7.464358 ACACGACTGTTATGCTTCAAATTATC 58.536 34.615 0.00 0.00 0.00 1.75
1657 1681 7.119116 TGACACGACTGTTATGCTTCAAATTAT 59.881 33.333 0.00 0.00 0.00 1.28
1658 1682 6.425417 TGACACGACTGTTATGCTTCAAATTA 59.575 34.615 0.00 0.00 0.00 1.40
1659 1683 5.238432 TGACACGACTGTTATGCTTCAAATT 59.762 36.000 0.00 0.00 0.00 1.82
1677 1701 8.464770 AATGGTCAATTAATTTTCATGACACG 57.535 30.769 15.59 0.00 41.60 4.49
1700 1724 4.305539 TCACCATGTCTGTCCAATGAAT 57.694 40.909 0.00 0.00 0.00 2.57
1782 1806 3.242413 GCAAAACATGTGATCTACGCGAT 60.242 43.478 15.93 0.00 34.25 4.58
1795 1819 5.505654 GGTCCATATACCGAAGCAAAACATG 60.506 44.000 0.00 0.00 0.00 3.21
1796 1820 4.578928 GGTCCATATACCGAAGCAAAACAT 59.421 41.667 0.00 0.00 0.00 2.71
1812 1836 0.963856 ACGAGAGTGCACGGTCCATA 60.964 55.000 12.01 0.00 46.97 2.74
1835 1859 3.186409 TCGAACACATAAGCAAACTCAGC 59.814 43.478 0.00 0.00 0.00 4.26
2633 2661 2.121564 CTGAAACCACTGCACTGCCG 62.122 60.000 0.00 0.00 0.00 5.69
2657 2685 2.938428 AGTTTATTCCCATGCCCCAA 57.062 45.000 0.00 0.00 0.00 4.12
3035 3063 7.916977 TGAAATTTGAGACAGAACTCACAATTG 59.083 33.333 3.24 3.24 44.94 2.32
3122 3150 7.946381 TCATGACTAGTCTACTTGAACATCT 57.054 36.000 23.01 0.00 0.00 2.90
3223 3251 5.277825 TCACGCCAAATTACAACAGAAAAG 58.722 37.500 0.00 0.00 0.00 2.27
3248 3276 5.772521 ACAGAAATAACCAACTGCATTGTC 58.227 37.500 0.00 0.00 36.47 3.18
3517 3545 4.670621 CGTTGCAAACTACACATTCTGAAC 59.329 41.667 0.00 0.00 46.99 3.18
3856 3899 0.670162 CTTGCAGGAACACCACCTTG 59.330 55.000 0.00 0.00 35.35 3.61
4082 4361 7.999679 TGGAATTAGATGAACAGCCAATTTAG 58.000 34.615 0.00 0.00 0.00 1.85
4136 4416 2.947652 CAAGTAATGCTCCCATGTCCAG 59.052 50.000 0.00 0.00 0.00 3.86
4445 4725 2.621338 CATACCGCATATACCCAGCTG 58.379 52.381 6.78 6.78 0.00 4.24
4597 4877 1.839994 TGGGAATAAGAGGAGTGCCAG 59.160 52.381 0.00 0.00 29.24 4.85
4599 4879 3.584733 AATGGGAATAAGAGGAGTGCC 57.415 47.619 0.00 0.00 0.00 5.01
4619 4899 4.014406 AGCTGATGAATTGACATGCTGAA 58.986 39.130 0.00 0.00 31.52 3.02
4708 5037 1.896660 GAAGGTTGCGCTGGTTGGA 60.897 57.895 9.73 0.00 0.00 3.53
4714 5043 4.997395 ACATAATATAGGAAGGTTGCGCTG 59.003 41.667 9.73 0.00 0.00 5.18
4807 5136 2.308570 ACAGGTTACCAGCATCCATTGA 59.691 45.455 3.51 0.00 0.00 2.57
5184 5516 5.922053 TCAACTAGATCAATAGCTGCACAT 58.078 37.500 1.02 0.00 0.00 3.21
5253 5585 0.526211 TGTCGACCTCATCCAACTCG 59.474 55.000 14.12 0.00 0.00 4.18
5529 5862 5.638234 GGTTAACTCTGTCAATCTACCACAC 59.362 44.000 5.42 0.00 0.00 3.82
6002 6335 4.938080 ACTCACTCATGTCAATCCGTATC 58.062 43.478 0.00 0.00 0.00 2.24
6350 6683 1.067283 CGAGCAATCTCAGTCACCTGT 60.067 52.381 0.00 0.00 39.30 4.00
6511 6844 8.197592 TGAAATACAACTAGAACCTAGTTCCA 57.802 34.615 14.44 7.56 42.85 3.53
6519 6852 7.328493 GCCAAACAATGAAATACAACTAGAACC 59.672 37.037 0.00 0.00 0.00 3.62
6537 6871 0.658897 GGTCGACGAAAGCCAAACAA 59.341 50.000 9.92 0.00 0.00 2.83
6702 7036 0.615331 GCTGGATCACCCTCTTGACA 59.385 55.000 0.00 0.00 35.38 3.58
6744 7078 2.266055 CCCTTGAGGACACCGAGC 59.734 66.667 0.00 0.00 38.24 5.03
6856 7190 4.067972 ACTCTGTGCTTCCGTTTTCTAA 57.932 40.909 0.00 0.00 0.00 2.10
6937 7271 6.140303 TGAACCTAACGAAAGATACGCTAT 57.860 37.500 0.00 0.00 0.00 2.97
6938 7272 5.565592 TGAACCTAACGAAAGATACGCTA 57.434 39.130 0.00 0.00 0.00 4.26
6939 7273 4.445452 TGAACCTAACGAAAGATACGCT 57.555 40.909 0.00 0.00 0.00 5.07
7032 7366 3.081804 GTGGATTCCACGAAACCAGAAT 58.918 45.455 19.65 0.00 43.32 2.40
7076 7412 0.671251 GTCCATGCGAACCCAAAACA 59.329 50.000 0.00 0.00 0.00 2.83
7078 7414 1.403814 TTGTCCATGCGAACCCAAAA 58.596 45.000 0.00 0.00 0.00 2.44
7143 7494 7.228507 GCTCAAATTTGGACCAAAAATAGGTTT 59.771 33.333 23.11 14.47 40.09 3.27
7145 7496 6.230472 GCTCAAATTTGGACCAAAAATAGGT 58.770 36.000 23.11 3.18 43.46 3.08
7148 7499 6.432403 AGGCTCAAATTTGGACCAAAAATA 57.568 33.333 23.11 8.72 36.90 1.40
7214 7585 1.985622 TGGGGAGAGATGGGAAATGT 58.014 50.000 0.00 0.00 0.00 2.71
7268 7639 2.203538 AGGCAGTGGCAAGGTTGG 60.204 61.111 20.04 0.00 43.71 3.77
7340 7727 1.337260 GGATATCTGAAGCGCCATCGT 60.337 52.381 2.29 0.00 38.14 3.73
7360 7747 0.677098 AGCAAGCTCCAGTGCAGATG 60.677 55.000 10.57 0.00 43.42 2.90
7419 7806 0.037326 TAGATCAATCCATCCGCGGC 60.037 55.000 23.51 1.36 0.00 6.53
7473 7860 2.620048 TAGCTAGGAGCCATGCCCCA 62.620 60.000 0.00 0.00 43.77 4.96
7543 7930 6.207810 GGAGTAGAGATTCCAGTCATATTCGT 59.792 42.308 0.00 0.00 31.70 3.85
7549 7936 7.072562 ACATTAGGAGTAGAGATTCCAGTCAT 58.927 38.462 0.00 0.00 33.85 3.06
7558 7945 6.549364 CCAACTGAGACATTAGGAGTAGAGAT 59.451 42.308 0.00 0.00 0.00 2.75
7559 7946 5.888724 CCAACTGAGACATTAGGAGTAGAGA 59.111 44.000 0.00 0.00 0.00 3.10
7560 7947 5.654650 ACCAACTGAGACATTAGGAGTAGAG 59.345 44.000 0.00 0.00 0.00 2.43
7561 7948 5.580998 ACCAACTGAGACATTAGGAGTAGA 58.419 41.667 0.00 0.00 0.00 2.59
7562 7949 5.923733 ACCAACTGAGACATTAGGAGTAG 57.076 43.478 0.00 0.00 0.00 2.57
7563 7950 7.973048 AATACCAACTGAGACATTAGGAGTA 57.027 36.000 0.00 0.00 0.00 2.59
7564 7951 6.875972 AATACCAACTGAGACATTAGGAGT 57.124 37.500 0.00 0.00 0.00 3.85
7565 7952 7.010552 CGAAAATACCAACTGAGACATTAGGAG 59.989 40.741 0.00 0.00 0.00 3.69
7566 7953 6.816640 CGAAAATACCAACTGAGACATTAGGA 59.183 38.462 0.00 0.00 0.00 2.94
7567 7954 6.594159 ACGAAAATACCAACTGAGACATTAGG 59.406 38.462 0.00 0.00 0.00 2.69
7568 7955 7.596749 ACGAAAATACCAACTGAGACATTAG 57.403 36.000 0.00 0.00 0.00 1.73
7569 7956 7.118680 GGAACGAAAATACCAACTGAGACATTA 59.881 37.037 0.00 0.00 0.00 1.90
7570 7957 6.072673 GGAACGAAAATACCAACTGAGACATT 60.073 38.462 0.00 0.00 0.00 2.71
7571 7958 5.411669 GGAACGAAAATACCAACTGAGACAT 59.588 40.000 0.00 0.00 0.00 3.06
7572 7959 4.753107 GGAACGAAAATACCAACTGAGACA 59.247 41.667 0.00 0.00 0.00 3.41
7573 7960 4.753107 TGGAACGAAAATACCAACTGAGAC 59.247 41.667 0.00 0.00 0.00 3.36
7574 7961 4.753107 GTGGAACGAAAATACCAACTGAGA 59.247 41.667 0.00 0.00 34.11 3.27
7575 7962 4.083484 GGTGGAACGAAAATACCAACTGAG 60.083 45.833 0.00 0.00 38.12 3.35
7576 7963 3.816523 GGTGGAACGAAAATACCAACTGA 59.183 43.478 0.00 0.00 38.12 3.41
7577 7964 3.566322 TGGTGGAACGAAAATACCAACTG 59.434 43.478 0.00 0.00 40.35 3.16
7578 7965 3.566742 GTGGTGGAACGAAAATACCAACT 59.433 43.478 0.00 0.00 42.51 3.16
7579 7966 3.566742 AGTGGTGGAACGAAAATACCAAC 59.433 43.478 0.00 0.00 42.51 3.77
7580 7967 3.822940 AGTGGTGGAACGAAAATACCAA 58.177 40.909 0.00 0.00 42.51 3.67
7581 7968 3.495434 AGTGGTGGAACGAAAATACCA 57.505 42.857 0.00 0.00 38.98 3.25
7582 7969 4.612033 CGAAAGTGGTGGAACGAAAATACC 60.612 45.833 0.00 0.00 38.12 2.73
7583 7970 4.024641 ACGAAAGTGGTGGAACGAAAATAC 60.025 41.667 0.00 0.00 46.97 1.89
7584 7971 4.128643 ACGAAAGTGGTGGAACGAAAATA 58.871 39.130 0.00 0.00 46.97 1.40
7585 7972 2.946990 ACGAAAGTGGTGGAACGAAAAT 59.053 40.909 0.00 0.00 46.97 1.82
7586 7973 2.358015 ACGAAAGTGGTGGAACGAAAA 58.642 42.857 0.00 0.00 46.97 2.29
7587 7974 2.027003 ACGAAAGTGGTGGAACGAAA 57.973 45.000 0.00 0.00 46.97 3.46
7588 7975 3.764658 ACGAAAGTGGTGGAACGAA 57.235 47.368 0.00 0.00 46.97 3.85
7625 8012 3.551846 GGGTGTGAGAAGAGGACAAAAA 58.448 45.455 0.00 0.00 0.00 1.94
7626 8013 2.158667 GGGGTGTGAGAAGAGGACAAAA 60.159 50.000 0.00 0.00 0.00 2.44
7627 8014 1.420138 GGGGTGTGAGAAGAGGACAAA 59.580 52.381 0.00 0.00 0.00 2.83
7628 8015 1.056660 GGGGTGTGAGAAGAGGACAA 58.943 55.000 0.00 0.00 0.00 3.18
7629 8016 1.185618 CGGGGTGTGAGAAGAGGACA 61.186 60.000 0.00 0.00 0.00 4.02
7630 8017 1.592223 CGGGGTGTGAGAAGAGGAC 59.408 63.158 0.00 0.00 0.00 3.85
7631 8018 1.609501 CCGGGGTGTGAGAAGAGGA 60.610 63.158 0.00 0.00 0.00 3.71
7632 8019 0.978146 ATCCGGGGTGTGAGAAGAGG 60.978 60.000 0.00 0.00 0.00 3.69
7633 8020 0.905357 AATCCGGGGTGTGAGAAGAG 59.095 55.000 0.00 0.00 0.00 2.85
7634 8021 0.613260 CAATCCGGGGTGTGAGAAGA 59.387 55.000 0.00 0.00 0.00 2.87
7635 8022 1.026718 GCAATCCGGGGTGTGAGAAG 61.027 60.000 0.00 0.00 0.00 2.85
7636 8023 1.002624 GCAATCCGGGGTGTGAGAA 60.003 57.895 0.00 0.00 0.00 2.87
7637 8024 2.668632 GCAATCCGGGGTGTGAGA 59.331 61.111 0.00 0.00 0.00 3.27
7638 8025 2.438434 GGCAATCCGGGGTGTGAG 60.438 66.667 0.00 0.00 0.00 3.51
7639 8026 4.041762 GGGCAATCCGGGGTGTGA 62.042 66.667 0.00 0.00 0.00 3.58
7648 8035 2.879813 TTTAGCGGGTCGGGCAATCC 62.880 60.000 0.00 0.00 0.00 3.01
7649 8036 1.027792 TTTTAGCGGGTCGGGCAATC 61.028 55.000 0.00 0.00 0.00 2.67
7650 8037 0.609681 TTTTTAGCGGGTCGGGCAAT 60.610 50.000 0.00 0.00 0.00 3.56
7651 8038 1.228184 TTTTTAGCGGGTCGGGCAA 60.228 52.632 0.00 0.00 0.00 4.52
7652 8039 2.430805 TTTTTAGCGGGTCGGGCA 59.569 55.556 0.00 0.00 0.00 5.36
7668 8055 1.134189 GGATCGGACGAGGGGATTTTT 60.134 52.381 0.00 0.00 0.00 1.94
7669 8056 0.468648 GGATCGGACGAGGGGATTTT 59.531 55.000 0.00 0.00 0.00 1.82
7670 8057 1.408453 GGGATCGGACGAGGGGATTT 61.408 60.000 0.00 0.00 0.00 2.17
7671 8058 1.837499 GGGATCGGACGAGGGGATT 60.837 63.158 0.00 0.00 0.00 3.01
7672 8059 2.203655 GGGATCGGACGAGGGGAT 60.204 66.667 0.00 0.00 0.00 3.85
7673 8060 4.534824 GGGGATCGGACGAGGGGA 62.535 72.222 0.00 0.00 0.00 4.81
7674 8061 4.853142 TGGGGATCGGACGAGGGG 62.853 72.222 0.00 0.00 0.00 4.79
7675 8062 2.762459 TTGGGGATCGGACGAGGG 60.762 66.667 0.00 0.00 0.00 4.30
7676 8063 2.499685 GTTGGGGATCGGACGAGG 59.500 66.667 0.00 0.00 0.00 4.63
7677 8064 2.017559 GAGGTTGGGGATCGGACGAG 62.018 65.000 0.00 0.00 0.00 4.18
7678 8065 2.038329 AGGTTGGGGATCGGACGA 59.962 61.111 0.00 0.00 0.00 4.20
7679 8066 2.499685 GAGGTTGGGGATCGGACG 59.500 66.667 0.00 0.00 0.00 4.79
7680 8067 2.743179 GGGAGGTTGGGGATCGGAC 61.743 68.421 0.00 0.00 0.00 4.79
7681 8068 2.366435 GGGAGGTTGGGGATCGGA 60.366 66.667 0.00 0.00 0.00 4.55
7682 8069 3.489513 GGGGAGGTTGGGGATCGG 61.490 72.222 0.00 0.00 0.00 4.18
7683 8070 3.489513 GGGGGAGGTTGGGGATCG 61.490 72.222 0.00 0.00 0.00 3.69
7708 8095 4.874977 GTAGGAGGCAGCGGCGAC 62.875 72.222 12.98 1.23 42.47 5.19
7713 8100 4.514577 CACCGGTAGGAGGCAGCG 62.515 72.222 6.87 0.00 41.02 5.18
7714 8101 4.840005 GCACCGGTAGGAGGCAGC 62.840 72.222 6.87 0.00 41.02 5.25
7715 8102 4.514577 CGCACCGGTAGGAGGCAG 62.515 72.222 6.87 0.00 41.02 4.85
7719 8106 4.814294 GTGGCGCACCGGTAGGAG 62.814 72.222 6.87 0.00 41.02 3.69
7734 8121 3.316573 GAAGGAGGCGGGAGTGGTG 62.317 68.421 0.00 0.00 0.00 4.17
7735 8122 3.003763 GAAGGAGGCGGGAGTGGT 61.004 66.667 0.00 0.00 0.00 4.16
7736 8123 3.787001 GGAAGGAGGCGGGAGTGG 61.787 72.222 0.00 0.00 0.00 4.00
7737 8124 4.148825 CGGAAGGAGGCGGGAGTG 62.149 72.222 0.00 0.00 0.00 3.51
7761 8148 2.925162 GAAAGGAGGCGGGGATGACG 62.925 65.000 0.00 0.00 0.00 4.35
7762 8149 1.153147 GAAAGGAGGCGGGGATGAC 60.153 63.158 0.00 0.00 0.00 3.06
7763 8150 2.731571 CGAAAGGAGGCGGGGATGA 61.732 63.158 0.00 0.00 0.00 2.92
7764 8151 2.203070 CGAAAGGAGGCGGGGATG 60.203 66.667 0.00 0.00 0.00 3.51
7788 8175 2.520982 TAGGAGGCGGGGATGACG 60.521 66.667 0.00 0.00 0.00 4.35
7789 8176 2.508751 GGTAGGAGGCGGGGATGAC 61.509 68.421 0.00 0.00 0.00 3.06
7790 8177 2.122989 GGTAGGAGGCGGGGATGA 60.123 66.667 0.00 0.00 0.00 2.92
7791 8178 3.616721 CGGTAGGAGGCGGGGATG 61.617 72.222 0.00 0.00 0.00 3.51
7792 8179 4.936081 CCGGTAGGAGGCGGGGAT 62.936 72.222 0.00 0.00 41.02 3.85
7815 8202 3.372554 GAAGAAGGAGGGTCCGGCG 62.373 68.421 0.00 0.00 42.75 6.46
7816 8203 2.585153 GAAGAAGGAGGGTCCGGC 59.415 66.667 0.00 0.00 42.75 6.13
7817 8204 2.368011 GGGAAGAAGGAGGGTCCGG 61.368 68.421 0.00 0.00 42.75 5.14
7818 8205 1.306226 AGGGAAGAAGGAGGGTCCG 60.306 63.158 0.00 0.00 42.75 4.79
7819 8206 1.275421 CCAGGGAAGAAGGAGGGTCC 61.275 65.000 0.00 0.00 36.58 4.46
7820 8207 0.252742 TCCAGGGAAGAAGGAGGGTC 60.253 60.000 0.00 0.00 0.00 4.46
7821 8208 0.252927 CTCCAGGGAAGAAGGAGGGT 60.253 60.000 0.00 0.00 44.10 4.34
7822 8209 2.614001 CTCCAGGGAAGAAGGAGGG 58.386 63.158 0.00 0.00 44.10 4.30
7825 8212 2.660064 GCGCTCCAGGGAAGAAGGA 61.660 63.158 0.00 0.00 0.00 3.36
7826 8213 2.124942 GCGCTCCAGGGAAGAAGG 60.125 66.667 0.00 0.00 0.00 3.46
7827 8214 2.124942 GGCGCTCCAGGGAAGAAG 60.125 66.667 7.64 0.00 0.00 2.85
7828 8215 2.927856 TGGCGCTCCAGGGAAGAA 60.928 61.111 7.64 0.00 37.47 2.52
7829 8216 3.706373 GTGGCGCTCCAGGGAAGA 61.706 66.667 7.64 0.00 44.48 2.87
7830 8217 4.785453 GGTGGCGCTCCAGGGAAG 62.785 72.222 7.64 0.00 44.48 3.46
7886 8273 4.148825 CTCTGGGGAAGACGGCGG 62.149 72.222 13.24 0.00 0.00 6.13
7887 8274 4.821589 GCTCTGGGGAAGACGGCG 62.822 72.222 4.80 4.80 0.00 6.46
7888 8275 4.821589 CGCTCTGGGGAAGACGGC 62.822 72.222 0.00 0.00 0.00 5.68
7889 8276 4.821589 GCGCTCTGGGGAAGACGG 62.822 72.222 0.00 0.00 33.06 4.79
7890 8277 4.821589 GGCGCTCTGGGGAAGACG 62.822 72.222 7.64 0.00 34.54 4.18
7891 8278 3.706373 TGGCGCTCTGGGGAAGAC 61.706 66.667 7.64 0.00 0.00 3.01
7892 8279 3.706373 GTGGCGCTCTGGGGAAGA 61.706 66.667 7.64 0.00 0.00 2.87
7893 8280 4.785453 GGTGGCGCTCTGGGGAAG 62.785 72.222 7.64 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.