Multiple sequence alignment - TraesCS6D01G141900

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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 TraesCS6D01G141900 chr6D 100.000 5091 0 0 1 5091 111434928 111440018 0.000000e+00 9402.0
1 TraesCS6D01G141900 chr6D 98.113 53 1 0 159 211 429815841 429815789 5.430000e-15 93.5
2 TraesCS6D01G141900 chr6B 96.411 2229 53 12 2882 5091 200312797 200315017 0.000000e+00 3648.0
3 TraesCS6D01G141900 chr6B 93.818 2378 80 25 497 2850 200310465 200312799 0.000000e+00 3515.0
4 TraesCS6D01G141900 chr6B 80.488 164 20 8 4 162 200310061 200310217 1.160000e-21 115.0
5 TraesCS6D01G141900 chr6B 94.444 36 2 0 4844 4879 200314805 200314840 7.120000e-04 56.5
6 TraesCS6D01G141900 chr6A 94.238 1753 82 7 2916 4667 136992739 136991005 0.000000e+00 2660.0
7 TraesCS6D01G141900 chr6A 97.018 1509 39 5 1415 2920 136994967 136993462 0.000000e+00 2532.0
8 TraesCS6D01G141900 chr6A 98.113 53 1 0 159 211 457378213 457378161 5.430000e-15 93.5
9 TraesCS6D01G141900 chr5D 88.670 203 18 3 3463 3661 468172029 468172230 5.090000e-60 243.0
10 TraesCS6D01G141900 chr5D 82.166 157 21 4 248 400 476465813 476465966 1.490000e-25 128.0
11 TraesCS6D01G141900 chr5D 96.226 53 2 0 159 211 6262305 6262253 2.530000e-13 87.9
12 TraesCS6D01G141900 chr5D 100.000 35 0 0 4678 4712 464527912 464527878 1.180000e-06 65.8
13 TraesCS6D01G141900 chr1D 88.725 204 16 4 3466 3664 481697813 481698014 5.090000e-60 243.0
14 TraesCS6D01G141900 chr1D 87.192 203 21 2 3465 3663 447360023 447360224 5.130000e-55 226.0
15 TraesCS6D01G141900 chr1D 86.087 115 12 4 236 348 462306362 462306250 2.490000e-23 121.0
16 TraesCS6D01G141900 chr1D 98.113 53 1 0 159 211 254447637 254447689 5.430000e-15 93.5
17 TraesCS6D01G141900 chr5B 88.177 203 19 3 3463 3661 574957884 574958085 2.370000e-58 237.0
18 TraesCS6D01G141900 chr5B 100.000 35 0 0 4678 4712 280589042 280589008 1.180000e-06 65.8
19 TraesCS6D01G141900 chr7D 87.685 203 20 2 3465 3663 622026780 622026981 1.100000e-56 231.0
20 TraesCS6D01G141900 chr7D 100.000 35 0 0 4678 4712 381895366 381895332 1.180000e-06 65.8
21 TraesCS6D01G141900 chrUn 87.192 203 21 2 3465 3663 27663857 27664058 5.130000e-55 226.0
22 TraesCS6D01G141900 chrUn 96.296 54 1 1 159 211 414538443 414538390 2.530000e-13 87.9
23 TraesCS6D01G141900 chrUn 100.000 35 0 0 4678 4712 237093983 237093949 1.180000e-06 65.8
24 TraesCS6D01G141900 chr3D 87.192 203 21 2 3465 3663 546378943 546379144 5.130000e-55 226.0
25 TraesCS6D01G141900 chr3D 85.714 112 13 3 236 346 477227895 477227786 1.160000e-21 115.0
26 TraesCS6D01G141900 chr3D 96.226 53 2 0 159 211 147096043 147095991 2.530000e-13 87.9
27 TraesCS6D01G141900 chr4B 83.824 136 15 4 211 345 661197401 661197272 6.920000e-24 122.0
28 TraesCS6D01G141900 chr2D 82.734 139 15 5 267 399 8470720 8470855 1.160000e-21 115.0
29 TraesCS6D01G141900 chr2D 84.746 118 10 7 233 346 43802030 43802143 1.500000e-20 111.0
30 TraesCS6D01G141900 chr2D 86.047 86 11 1 396 481 14968515 14968599 1.950000e-14 91.6
31 TraesCS6D01G141900 chr2D 98.039 51 1 0 161 211 135988129 135988179 7.020000e-14 89.8
32 TraesCS6D01G141900 chr2D 81.651 109 17 3 224 330 425996480 425996373 2.530000e-13 87.9
33 TraesCS6D01G141900 chr7B 86.869 99 11 2 252 349 94701610 94701513 5.390000e-20 110.0
34 TraesCS6D01G141900 chr7B 100.000 35 0 0 4678 4712 703561752 703561718 1.180000e-06 65.8
35 TraesCS6D01G141900 chr1B 83.929 112 13 5 237 348 488648821 488648715 9.020000e-18 102.0
36 TraesCS6D01G141900 chr1B 90.385 52 4 1 407 458 134450109 134450059 3.290000e-07 67.6
37 TraesCS6D01G141900 chr3B 98.113 53 1 0 159 211 101907545 101907493 5.430000e-15 93.5
38 TraesCS6D01G141900 chr3B 98.113 53 1 0 159 211 419793881 419793829 5.430000e-15 93.5
39 TraesCS6D01G141900 chr2B 84.146 82 12 1 400 481 531108884 531108964 1.520000e-10 78.7
40 TraesCS6D01G141900 chr4D 100.000 35 0 0 4678 4712 123476870 123476904 1.180000e-06 65.8
41 TraesCS6D01G141900 chr4D 100.000 35 0 0 4678 4712 450990625 450990591 1.180000e-06 65.8
42 TraesCS6D01G141900 chr4D 100.000 35 0 0 4678 4712 451011269 451011303 1.180000e-06 65.8


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 TraesCS6D01G141900 chr6D 111434928 111440018 5090 False 9402.000 9402 100.00000 1 5091 1 chr6D.!!$F1 5090
1 TraesCS6D01G141900 chr6B 200310061 200315017 4956 False 1833.625 3648 91.29025 4 5091 4 chr6B.!!$F1 5087
2 TraesCS6D01G141900 chr6A 136991005 136994967 3962 True 2596.000 2660 95.62800 1415 4667 2 chr6A.!!$R2 3252

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
178 181 0.035056 TCTCTTTTGCTAGGCCCAGC 60.035 55.0 17.13 17.13 42.15 4.85 F
225 228 0.389948 CAAGGGCACAGTCGTACCTC 60.390 60.0 0.00 0.00 32.16 3.85 F
1168 1196 0.179032 AGGTGTTCGTGTCCATGCAA 60.179 50.0 0.00 0.00 0.00 4.08 F
1174 1202 0.950555 TCGTGTCCATGCAACAGAGC 60.951 55.0 0.00 0.00 0.00 4.09 F
2955 3715 0.472471 ATCCCGGGCGTACAATCATT 59.528 50.0 18.49 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1017 1044 0.319083 AGTAAATGTGACCGTCGGCA 59.681 50.000 12.28 7.78 0.00 5.69 R
1529 1558 0.591170 CAACGTGGGTCAACATGGAC 59.409 55.000 0.00 0.00 37.06 4.02 R
2936 3696 0.472471 AATGATTGTACGCCCGGGAT 59.528 50.000 29.31 14.70 0.00 3.85 R
3044 3804 1.342496 CTCATAGCCTTCTCGCCATCA 59.658 52.381 0.00 0.00 0.00 3.07 R
4931 5707 1.209383 CGAGGCAACGACGAGAGAA 59.791 57.895 0.00 0.00 46.39 2.87 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
21 22 1.396996 CAAGGCACGGATTTACTTCGG 59.603 52.381 0.00 0.00 0.00 4.30
25 26 1.352114 CACGGATTTACTTCGGCGAA 58.648 50.000 22.33 22.33 0.00 4.70
47 48 2.034104 GCACAATCATGCCTCTCAGA 57.966 50.000 0.00 0.00 39.86 3.27
48 49 2.362736 GCACAATCATGCCTCTCAGAA 58.637 47.619 0.00 0.00 39.86 3.02
49 50 2.751259 GCACAATCATGCCTCTCAGAAA 59.249 45.455 0.00 0.00 39.86 2.52
50 51 3.181499 GCACAATCATGCCTCTCAGAAAG 60.181 47.826 0.00 0.00 39.86 2.62
51 52 3.377485 CACAATCATGCCTCTCAGAAAGG 59.623 47.826 0.00 0.00 36.95 3.11
53 54 1.956869 TCATGCCTCTCAGAAAGGGA 58.043 50.000 0.00 0.00 38.73 4.20
55 56 2.644299 TCATGCCTCTCAGAAAGGGAAA 59.356 45.455 0.00 0.00 37.81 3.13
56 57 3.074390 TCATGCCTCTCAGAAAGGGAAAA 59.926 43.478 0.00 0.00 37.81 2.29
60 61 3.424703 CCTCTCAGAAAGGGAAAATGCA 58.575 45.455 0.00 0.00 0.00 3.96
62 63 4.142227 CCTCTCAGAAAGGGAAAATGCATG 60.142 45.833 0.00 0.00 0.00 4.06
63 64 3.194116 TCTCAGAAAGGGAAAATGCATGC 59.806 43.478 11.82 11.82 0.00 4.06
98 101 3.814504 TGCCTCTCAGAAAGGGAAAAT 57.185 42.857 0.00 0.00 34.26 1.82
99 102 3.424703 TGCCTCTCAGAAAGGGAAAATG 58.575 45.455 0.00 0.00 34.26 2.32
100 103 2.165234 GCCTCTCAGAAAGGGAAAATGC 59.835 50.000 0.00 0.00 34.26 3.56
101 104 2.421424 CCTCTCAGAAAGGGAAAATGCG 59.579 50.000 0.00 0.00 0.00 4.73
102 105 3.077359 CTCTCAGAAAGGGAAAATGCGT 58.923 45.455 0.00 0.00 0.00 5.24
103 106 3.486383 TCTCAGAAAGGGAAAATGCGTT 58.514 40.909 0.00 0.00 0.00 4.84
104 107 3.888930 TCTCAGAAAGGGAAAATGCGTTT 59.111 39.130 0.00 0.00 0.00 3.60
105 108 4.340950 TCTCAGAAAGGGAAAATGCGTTTT 59.659 37.500 16.39 16.39 40.13 2.43
121 124 6.312645 TGCGTTTTCTTTTTCTTTCTTTCG 57.687 33.333 0.00 0.00 0.00 3.46
147 150 4.820894 AGCCACGAATTTACTTCTAGGT 57.179 40.909 0.00 0.00 31.58 3.08
149 152 6.481434 AGCCACGAATTTACTTCTAGGTAT 57.519 37.500 0.00 0.00 31.58 2.73
162 165 6.587273 ACTTCTAGGTATGGATTTGCTTCTC 58.413 40.000 0.00 0.00 0.00 2.87
163 166 6.385467 ACTTCTAGGTATGGATTTGCTTCTCT 59.615 38.462 0.00 0.00 0.00 3.10
164 167 6.814954 TCTAGGTATGGATTTGCTTCTCTT 57.185 37.500 0.00 0.00 0.00 2.85
165 168 7.200434 TCTAGGTATGGATTTGCTTCTCTTT 57.800 36.000 0.00 0.00 0.00 2.52
166 169 7.633789 TCTAGGTATGGATTTGCTTCTCTTTT 58.366 34.615 0.00 0.00 0.00 2.27
167 170 6.521151 AGGTATGGATTTGCTTCTCTTTTG 57.479 37.500 0.00 0.00 0.00 2.44
168 171 5.105063 GGTATGGATTTGCTTCTCTTTTGC 58.895 41.667 0.00 0.00 0.00 3.68
169 172 5.105595 GGTATGGATTTGCTTCTCTTTTGCT 60.106 40.000 0.00 0.00 0.00 3.91
170 173 6.095440 GGTATGGATTTGCTTCTCTTTTGCTA 59.905 38.462 0.00 0.00 0.00 3.49
171 174 5.633830 TGGATTTGCTTCTCTTTTGCTAG 57.366 39.130 0.00 0.00 0.00 3.42
172 175 4.460382 TGGATTTGCTTCTCTTTTGCTAGG 59.540 41.667 0.00 0.00 0.00 3.02
173 176 3.923017 TTTGCTTCTCTTTTGCTAGGC 57.077 42.857 0.00 0.00 0.00 3.93
174 177 1.826385 TGCTTCTCTTTTGCTAGGCC 58.174 50.000 0.00 0.00 0.00 5.19
175 178 1.098869 GCTTCTCTTTTGCTAGGCCC 58.901 55.000 0.00 0.00 0.00 5.80
176 179 1.614317 GCTTCTCTTTTGCTAGGCCCA 60.614 52.381 0.00 0.00 0.00 5.36
177 180 2.363683 CTTCTCTTTTGCTAGGCCCAG 58.636 52.381 0.00 0.00 0.00 4.45
178 181 0.035056 TCTCTTTTGCTAGGCCCAGC 60.035 55.000 17.13 17.13 42.15 4.85
183 186 4.145436 TGCTAGGCCCAGCACTAA 57.855 55.556 22.80 0.00 46.41 2.24
184 187 2.382526 TGCTAGGCCCAGCACTAAA 58.617 52.632 22.80 0.00 46.41 1.85
185 188 0.695924 TGCTAGGCCCAGCACTAAAA 59.304 50.000 22.80 0.00 46.41 1.52
186 189 1.074727 TGCTAGGCCCAGCACTAAAAA 59.925 47.619 22.80 0.00 46.41 1.94
225 228 0.389948 CAAGGGCACAGTCGTACCTC 60.390 60.000 0.00 0.00 32.16 3.85
274 277 5.673337 TTTTTCCTTTCATGAGAGACACG 57.327 39.130 14.63 0.00 0.00 4.49
286 290 5.312120 TGAGAGACACGGATTTACTTCTC 57.688 43.478 0.00 0.00 0.00 2.87
293 297 2.165845 ACGGATTTACTTCTCGTGGAGG 59.834 50.000 0.00 0.00 32.60 4.30
296 300 3.432326 GGATTTACTTCTCGTGGAGGCAT 60.432 47.826 0.00 0.00 0.00 4.40
298 302 1.847328 TACTTCTCGTGGAGGCATGA 58.153 50.000 0.00 0.00 0.00 3.07
326 330 1.133253 CGCAAGAGGCACAATCGTG 59.867 57.895 0.00 0.00 45.17 4.35
341 345 1.301401 CGTGCCTGTTCGGAAAGGA 60.301 57.895 3.19 0.00 35.40 3.36
366 370 3.921257 CCGTACTCCCGGTTCTTTT 57.079 52.632 0.00 0.00 43.07 2.27
401 405 5.713822 AGTTTATCGAAACCTATCAACGC 57.286 39.130 0.00 0.00 45.21 4.84
404 408 1.621107 TCGAAACCTATCAACGCGAC 58.379 50.000 15.93 0.00 0.00 5.19
428 432 3.341857 TCCAACAATGAAAACGGTTCG 57.658 42.857 0.00 0.00 0.00 3.95
437 441 4.634184 TGAAAACGGTTCGAAATTTGGA 57.366 36.364 0.00 0.00 0.00 3.53
441 445 1.149987 CGGTTCGAAATTTGGACGGA 58.850 50.000 0.00 0.00 0.00 4.69
442 446 1.735571 CGGTTCGAAATTTGGACGGAT 59.264 47.619 0.00 0.00 0.00 4.18
443 447 2.475519 CGGTTCGAAATTTGGACGGATG 60.476 50.000 0.00 0.00 0.00 3.51
445 449 2.483014 TCGAAATTTGGACGGATGGT 57.517 45.000 0.00 0.00 0.00 3.55
447 451 2.486203 TCGAAATTTGGACGGATGGTTG 59.514 45.455 0.00 0.00 0.00 3.77
448 452 2.486203 CGAAATTTGGACGGATGGTTGA 59.514 45.455 0.00 0.00 0.00 3.18
449 453 3.057876 CGAAATTTGGACGGATGGTTGAA 60.058 43.478 0.00 0.00 0.00 2.69
450 454 4.485163 GAAATTTGGACGGATGGTTGAAG 58.515 43.478 0.00 0.00 0.00 3.02
451 455 2.940994 TTTGGACGGATGGTTGAAGA 57.059 45.000 0.00 0.00 0.00 2.87
452 456 2.940994 TTGGACGGATGGTTGAAGAA 57.059 45.000 0.00 0.00 0.00 2.52
454 458 2.778299 TGGACGGATGGTTGAAGAAAG 58.222 47.619 0.00 0.00 0.00 2.62
455 459 2.370519 TGGACGGATGGTTGAAGAAAGA 59.629 45.455 0.00 0.00 0.00 2.52
456 460 3.181449 TGGACGGATGGTTGAAGAAAGAA 60.181 43.478 0.00 0.00 0.00 2.52
457 461 3.818773 GGACGGATGGTTGAAGAAAGAAA 59.181 43.478 0.00 0.00 0.00 2.52
458 462 4.277423 GGACGGATGGTTGAAGAAAGAAAA 59.723 41.667 0.00 0.00 0.00 2.29
459 463 5.048013 GGACGGATGGTTGAAGAAAGAAAAT 60.048 40.000 0.00 0.00 0.00 1.82
460 464 5.772521 ACGGATGGTTGAAGAAAGAAAATG 58.227 37.500 0.00 0.00 0.00 2.32
461 465 5.301805 ACGGATGGTTGAAGAAAGAAAATGT 59.698 36.000 0.00 0.00 0.00 2.71
462 466 6.183360 ACGGATGGTTGAAGAAAGAAAATGTT 60.183 34.615 0.00 0.00 0.00 2.71
463 467 6.701400 CGGATGGTTGAAGAAAGAAAATGTTT 59.299 34.615 0.00 0.00 0.00 2.83
464 468 7.224557 CGGATGGTTGAAGAAAGAAAATGTTTT 59.775 33.333 0.00 0.00 0.00 2.43
465 469 8.337532 GGATGGTTGAAGAAAGAAAATGTTTTG 58.662 33.333 0.00 0.00 0.00 2.44
466 470 9.097257 GATGGTTGAAGAAAGAAAATGTTTTGA 57.903 29.630 0.00 0.00 0.00 2.69
467 471 8.839310 TGGTTGAAGAAAGAAAATGTTTTGAA 57.161 26.923 0.00 0.00 0.00 2.69
468 472 9.447157 TGGTTGAAGAAAGAAAATGTTTTGAAT 57.553 25.926 0.00 0.00 0.00 2.57
488 492 8.710749 TTGAATAAAATGAATCTATGGGAGGG 57.289 34.615 0.00 0.00 0.00 4.30
489 493 7.825709 TGAATAAAATGAATCTATGGGAGGGT 58.174 34.615 0.00 0.00 0.00 4.34
490 494 7.725397 TGAATAAAATGAATCTATGGGAGGGTG 59.275 37.037 0.00 0.00 0.00 4.61
491 495 5.732331 AAAATGAATCTATGGGAGGGTGA 57.268 39.130 0.00 0.00 0.00 4.02
492 496 5.937492 AAATGAATCTATGGGAGGGTGAT 57.063 39.130 0.00 0.00 0.00 3.06
493 497 5.511386 AATGAATCTATGGGAGGGTGATC 57.489 43.478 0.00 0.00 0.00 2.92
494 498 4.219392 TGAATCTATGGGAGGGTGATCT 57.781 45.455 0.00 0.00 0.00 2.75
495 499 4.163427 TGAATCTATGGGAGGGTGATCTC 58.837 47.826 0.00 0.00 0.00 2.75
505 509 2.235898 GAGGGTGATCTCTGCAAAGAGT 59.764 50.000 0.00 0.00 37.23 3.24
510 514 5.241662 GGTGATCTCTGCAAAGAGTACTTT 58.758 41.667 0.00 0.00 45.75 2.66
593 607 3.072476 TGGCCCATAATAAGCTAGTCCAC 59.928 47.826 0.00 0.00 0.00 4.02
594 608 3.559384 GGCCCATAATAAGCTAGTCCACC 60.559 52.174 0.00 0.00 0.00 4.61
595 609 3.072476 GCCCATAATAAGCTAGTCCACCA 59.928 47.826 0.00 0.00 0.00 4.17
600 614 1.327690 TAAGCTAGTCCACCAGGGCG 61.328 60.000 0.00 0.00 46.92 6.13
620 634 2.460669 GGAAGACATCAAAAGGCCCAT 58.539 47.619 0.00 0.00 0.00 4.00
621 635 2.167075 GGAAGACATCAAAAGGCCCATG 59.833 50.000 0.00 0.00 0.00 3.66
622 636 2.905415 AGACATCAAAAGGCCCATGA 57.095 45.000 0.00 1.37 0.00 3.07
623 637 3.173953 AGACATCAAAAGGCCCATGAA 57.826 42.857 0.00 0.00 0.00 2.57
624 638 2.827921 AGACATCAAAAGGCCCATGAAC 59.172 45.455 0.00 0.00 0.00 3.18
625 639 1.901833 ACATCAAAAGGCCCATGAACC 59.098 47.619 0.00 0.00 0.00 3.62
626 640 2.181975 CATCAAAAGGCCCATGAACCT 58.818 47.619 0.00 0.00 38.14 3.50
627 641 3.245586 ACATCAAAAGGCCCATGAACCTA 60.246 43.478 0.00 0.00 34.31 3.08
628 642 2.802719 TCAAAAGGCCCATGAACCTAC 58.197 47.619 0.00 0.00 34.31 3.18
654 668 2.662596 CCTTGTCAGTAGCCGGCA 59.337 61.111 31.54 12.31 0.00 5.69
754 781 1.478837 CCGTCTCTACCAGATAGGCCA 60.479 57.143 5.01 0.00 43.14 5.36
775 802 1.460305 ACCGCATCCTCCTAGCCAT 60.460 57.895 0.00 0.00 0.00 4.40
779 806 0.839853 GCATCCTCCTAGCCATCCCT 60.840 60.000 0.00 0.00 0.00 4.20
859 886 1.376037 GGTGAGTTCCTTGCCCTCG 60.376 63.158 0.00 0.00 0.00 4.63
907 934 1.972795 ACCCGCTTGAACACTAGGTTA 59.027 47.619 0.00 0.00 40.63 2.85
930 957 3.840666 TCCTGCTGTAGATTGGAGAAGTT 59.159 43.478 0.00 0.00 0.00 2.66
934 961 3.935828 GCTGTAGATTGGAGAAGTTGGTC 59.064 47.826 0.00 0.00 0.00 4.02
943 970 2.612972 GGAGAAGTTGGTCGATTGCAGA 60.613 50.000 0.00 0.00 0.00 4.26
944 971 3.265791 GAGAAGTTGGTCGATTGCAGAT 58.734 45.455 0.00 0.00 0.00 2.90
971 998 7.942341 TGGACAAGTTGGTTGATATTTTACTCT 59.058 33.333 7.96 0.00 38.60 3.24
972 999 8.793592 GGACAAGTTGGTTGATATTTTACTCTT 58.206 33.333 7.96 0.00 38.60 2.85
1017 1044 8.275040 AGCCTTTTCATGGACTATACATTTACT 58.725 33.333 0.00 0.00 0.00 2.24
1061 1089 3.441222 TCACTTCCATGTTTGCAGCTATG 59.559 43.478 0.00 0.00 0.00 2.23
1135 1163 6.258507 CCTTGTTGCCAATTATTCTAAATGCC 59.741 38.462 0.00 0.00 0.00 4.40
1168 1196 0.179032 AGGTGTTCGTGTCCATGCAA 60.179 50.000 0.00 0.00 0.00 4.08
1174 1202 0.950555 TCGTGTCCATGCAACAGAGC 60.951 55.000 0.00 0.00 0.00 4.09
1184 1212 4.409570 CATGCAACAGAGCTTGTAATGTC 58.590 43.478 0.00 0.00 39.73 3.06
1197 1225 2.175931 TGTAATGTCCCCAACACCACTT 59.824 45.455 0.00 0.00 41.75 3.16
1202 1230 1.697982 GTCCCCAACACCACTTCTAGT 59.302 52.381 0.00 0.00 0.00 2.57
1207 1235 3.555168 CCCAACACCACTTCTAGTCACTC 60.555 52.174 0.00 0.00 0.00 3.51
1236 1264 2.430465 TGAAGCTTCTTCACATCCAGC 58.570 47.619 26.09 0.00 0.00 4.85
1251 1279 3.627395 TCCAGCGTTTGATATGAACCT 57.373 42.857 0.00 0.00 0.00 3.50
1252 1280 3.531538 TCCAGCGTTTGATATGAACCTC 58.468 45.455 0.00 0.00 0.00 3.85
1253 1281 3.197766 TCCAGCGTTTGATATGAACCTCT 59.802 43.478 0.00 0.00 0.00 3.69
1304 1332 8.713737 ATAGAAATCTTAAGTTCGTACAACCC 57.286 34.615 1.63 0.00 34.72 4.11
1315 1343 1.339342 CGTACAACCCGGGAAAGGAAT 60.339 52.381 32.02 0.00 0.00 3.01
1319 1347 2.024414 CAACCCGGGAAAGGAATGATC 58.976 52.381 32.02 0.00 0.00 2.92
1529 1558 5.444663 TGATCTCGATCATCACTACCTTG 57.555 43.478 5.53 0.00 42.42 3.61
1544 1573 1.247567 CCTTGTCCATGTTGACCCAC 58.752 55.000 0.00 0.00 34.25 4.61
1669 1699 3.882888 AGAGTGTTCGCTCCAAATTTTGA 59.117 39.130 10.72 0.00 36.20 2.69
1676 1706 6.695278 TGTTCGCTCCAAATTTTGAACTTAAG 59.305 34.615 10.72 0.00 37.27 1.85
1710 1740 6.983906 TCTAGTGATCTTGATATTCAGGCA 57.016 37.500 0.00 0.00 0.00 4.75
1711 1741 6.753180 TCTAGTGATCTTGATATTCAGGCAC 58.247 40.000 0.00 0.00 0.00 5.01
2021 2051 7.118060 TCCATCAACAATGAAATATGACCTCA 58.882 34.615 0.00 0.00 39.49 3.86
2307 2337 5.665459 ACTCTTACATGAATCTGCAGGTAC 58.335 41.667 15.13 5.96 35.12 3.34
2562 2594 5.898120 AGTCCTGTACTAGAGGATATGCAT 58.102 41.667 3.79 3.79 41.75 3.96
2798 2830 5.401531 AACAACTATCGCCAGAGTAGAAA 57.598 39.130 0.00 0.00 0.00 2.52
2936 3696 4.680237 CACCAAGCGAGGCCGTCA 62.680 66.667 0.00 0.00 38.24 4.35
2955 3715 0.472471 ATCCCGGGCGTACAATCATT 59.528 50.000 18.49 0.00 0.00 2.57
2982 3742 2.191513 GCGGCATCATGACCAGCAT 61.192 57.895 15.78 0.00 37.85 3.79
3044 3804 1.202903 ACTAGTCTCGGTGGTGTGAGT 60.203 52.381 0.00 0.00 33.88 3.41
3047 3807 0.603569 GTCTCGGTGGTGTGAGTGAT 59.396 55.000 0.00 0.00 33.88 3.06
3188 3956 3.487711 GCGTGGTAATTGTGTGAACAACA 60.488 43.478 0.00 0.00 36.04 3.33
3216 3984 2.498167 CTTGAGGTCTTGACCCAACAG 58.502 52.381 15.44 6.06 0.00 3.16
3362 4130 5.458041 AATGACCCAGTCAAAATCAACAG 57.542 39.130 0.91 0.00 45.96 3.16
3595 4363 2.808906 ACCCTCTCCAAATAAGCACC 57.191 50.000 0.00 0.00 0.00 5.01
3788 4561 9.851686 AGCTTAAACTAATAATGTGATGGATGA 57.148 29.630 0.00 0.00 0.00 2.92
3830 4603 4.826274 AAGATCGGACCAGAATTTCTCA 57.174 40.909 0.00 0.00 0.00 3.27
4145 4918 3.262420 GACATGAACGTGCCAATCTAGT 58.738 45.455 0.00 0.00 0.00 2.57
4167 4940 2.996621 CCCGTTTCAGATGTTGTCTCTC 59.003 50.000 0.00 0.00 34.00 3.20
4225 4998 7.254898 CCATGCTATCTACATGTTTGGTTGTAG 60.255 40.741 2.30 4.16 44.28 2.74
4305 5078 9.477484 TGAGTGTTAGAAGTACTGAATTTCTTC 57.523 33.333 0.00 0.00 37.24 2.87
4323 5096 5.981088 TCTTCAGCAATTCTATTTTGGCA 57.019 34.783 0.00 0.00 0.00 4.92
4374 5147 0.338814 ACCCTCCGTTCCTACCTCAT 59.661 55.000 0.00 0.00 0.00 2.90
4721 5494 4.099881 TGCACCTTTCTTTGAGCAATTCTT 59.900 37.500 0.00 0.00 0.00 2.52
4791 5564 7.942990 TGTATTTAAAACGAAAATGGTGACCT 58.057 30.769 2.11 0.00 0.00 3.85
4854 5629 7.422746 CGATAAATTCTTTTAGTGCAAGTCGAC 59.577 37.037 7.70 7.70 31.07 4.20
4875 5650 9.993454 GTCGACTATATATAAGAACCCCTTTTT 57.007 33.333 8.70 0.00 36.34 1.94
4898 5673 9.926751 TTTTCTCGTGTAAGTCGACTATATAAG 57.073 33.333 20.39 12.21 33.71 1.73
4900 5675 8.877808 TCTCGTGTAAGTCGACTATATAAGAA 57.122 34.615 20.39 0.00 33.71 2.52
4901 5676 8.759641 TCTCGTGTAAGTCGACTATATAAGAAC 58.240 37.037 20.39 8.01 33.71 3.01
4902 5677 7.855545 TCGTGTAAGTCGACTATATAAGAACC 58.144 38.462 20.39 0.00 32.30 3.62
4904 5679 7.041508 CGTGTAAGTCGACTATATAAGAACCCT 60.042 40.741 20.39 0.17 0.00 4.34
4905 5680 8.628280 GTGTAAGTCGACTATATAAGAACCCTT 58.372 37.037 20.39 0.00 36.43 3.95
4931 5707 2.282462 CTCCAGCCGCCCAACTTT 60.282 61.111 0.00 0.00 0.00 2.66
4948 5724 1.721926 CTTTTCTCTCGTCGTTGCCTC 59.278 52.381 0.00 0.00 0.00 4.70
4996 5772 1.817099 CCGACAATGCCTCCTCTGC 60.817 63.158 0.00 0.00 0.00 4.26
5026 5802 4.908601 TCCTCTCTGCAAAATCAAGGTA 57.091 40.909 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.073816 CGAAGTAAATCCGTGCCTTGT 58.926 47.619 0.00 0.00 0.00 3.16
1 2 1.396996 CCGAAGTAAATCCGTGCCTTG 59.603 52.381 0.00 0.00 0.00 3.61
2 3 1.734163 CCGAAGTAAATCCGTGCCTT 58.266 50.000 0.00 0.00 0.00 4.35
15 16 0.889186 ATTGTGCCTTTCGCCGAAGT 60.889 50.000 0.00 0.00 36.24 3.01
21 22 2.657336 GCATGATTGTGCCTTTCGC 58.343 52.632 0.00 0.00 39.18 4.70
33 34 2.485659 TCCCTTTCTGAGAGGCATGAT 58.514 47.619 8.69 0.00 32.74 2.45
34 35 1.956869 TCCCTTTCTGAGAGGCATGA 58.043 50.000 8.69 0.00 32.74 3.07
35 36 2.795231 TTCCCTTTCTGAGAGGCATG 57.205 50.000 8.69 0.00 32.74 4.06
36 37 3.814504 TTTTCCCTTTCTGAGAGGCAT 57.185 42.857 8.69 0.00 32.74 4.40
38 39 2.165234 GCATTTTCCCTTTCTGAGAGGC 59.835 50.000 8.69 0.00 32.74 4.70
40 41 4.677250 GCATGCATTTTCCCTTTCTGAGAG 60.677 45.833 14.21 0.00 0.00 3.20
42 43 3.518590 GCATGCATTTTCCCTTTCTGAG 58.481 45.455 14.21 0.00 0.00 3.35
44 45 2.094597 TCGCATGCATTTTCCCTTTCTG 60.095 45.455 19.57 0.00 0.00 3.02
45 46 2.170166 TCGCATGCATTTTCCCTTTCT 58.830 42.857 19.57 0.00 0.00 2.52
46 47 2.652941 TCGCATGCATTTTCCCTTTC 57.347 45.000 19.57 0.00 0.00 2.62
47 48 3.328505 CTTTCGCATGCATTTTCCCTTT 58.671 40.909 19.57 0.00 0.00 3.11
48 49 2.354003 CCTTTCGCATGCATTTTCCCTT 60.354 45.455 19.57 0.00 0.00 3.95
49 50 1.205417 CCTTTCGCATGCATTTTCCCT 59.795 47.619 19.57 0.00 0.00 4.20
50 51 1.643880 CCTTTCGCATGCATTTTCCC 58.356 50.000 19.57 0.00 0.00 3.97
51 52 1.001624 GCCTTTCGCATGCATTTTCC 58.998 50.000 19.57 0.00 37.47 3.13
53 54 3.910817 TGCCTTTCGCATGCATTTT 57.089 42.105 19.57 0.00 44.64 1.82
62 63 1.154150 GCATGACTGTGCCTTTCGC 60.154 57.895 0.00 0.00 39.18 4.70
98 101 5.220135 GCGAAAGAAAGAAAAAGAAAACGCA 60.220 36.000 0.00 0.00 39.63 5.24
99 102 5.181084 GCGAAAGAAAGAAAAAGAAAACGC 58.819 37.500 0.00 0.00 0.00 4.84
100 103 5.226360 TCGCGAAAGAAAGAAAAAGAAAACG 59.774 36.000 6.20 0.00 0.00 3.60
101 104 6.548931 TCGCGAAAGAAAGAAAAAGAAAAC 57.451 33.333 6.20 0.00 0.00 2.43
102 105 7.569677 TTTCGCGAAAGAAAGAAAAAGAAAA 57.430 28.000 29.22 1.80 35.44 2.29
121 124 2.894307 AGTAAATTCGTGGCTTTCGC 57.106 45.000 0.00 0.00 0.00 4.70
132 135 9.343539 AGCAAATCCATACCTAGAAGTAAATTC 57.656 33.333 0.00 0.00 38.28 2.17
147 150 6.319658 CCTAGCAAAAGAGAAGCAAATCCATA 59.680 38.462 0.00 0.00 0.00 2.74
149 152 4.460382 CCTAGCAAAAGAGAAGCAAATCCA 59.540 41.667 0.00 0.00 0.00 3.41
167 170 1.834188 TTTTTAGTGCTGGGCCTAGC 58.166 50.000 32.63 32.63 43.95 3.42
194 197 4.822896 ACTGTGCCCTTGTAATCGTAAAAA 59.177 37.500 0.00 0.00 0.00 1.94
195 198 4.391155 ACTGTGCCCTTGTAATCGTAAAA 58.609 39.130 0.00 0.00 0.00 1.52
196 199 3.998341 GACTGTGCCCTTGTAATCGTAAA 59.002 43.478 0.00 0.00 0.00 2.01
197 200 3.592059 GACTGTGCCCTTGTAATCGTAA 58.408 45.455 0.00 0.00 0.00 3.18
198 201 2.416296 CGACTGTGCCCTTGTAATCGTA 60.416 50.000 0.00 0.00 0.00 3.43
199 202 1.671850 CGACTGTGCCCTTGTAATCGT 60.672 52.381 0.00 0.00 0.00 3.73
200 203 0.999406 CGACTGTGCCCTTGTAATCG 59.001 55.000 0.00 0.00 0.00 3.34
201 204 2.094762 ACGACTGTGCCCTTGTAATC 57.905 50.000 0.00 0.00 0.00 1.75
202 205 2.354403 GGTACGACTGTGCCCTTGTAAT 60.354 50.000 0.00 0.00 44.38 1.89
203 206 1.001181 GGTACGACTGTGCCCTTGTAA 59.999 52.381 0.00 0.00 44.38 2.41
204 207 0.604578 GGTACGACTGTGCCCTTGTA 59.395 55.000 0.00 0.00 44.38 2.41
205 208 1.370064 GGTACGACTGTGCCCTTGT 59.630 57.895 0.00 0.00 44.38 3.16
206 209 4.278956 GGTACGACTGTGCCCTTG 57.721 61.111 0.00 0.00 44.38 3.61
257 260 3.533606 ATCCGTGTCTCTCATGAAAGG 57.466 47.619 0.00 0.00 35.23 3.11
259 262 6.037786 AGTAAATCCGTGTCTCTCATGAAA 57.962 37.500 0.00 0.00 35.23 2.69
262 265 5.655488 AGAAGTAAATCCGTGTCTCTCATG 58.345 41.667 0.00 0.00 0.00 3.07
263 266 5.449314 CGAGAAGTAAATCCGTGTCTCTCAT 60.449 44.000 0.00 0.00 31.37 2.90
264 267 4.142665 CGAGAAGTAAATCCGTGTCTCTCA 60.143 45.833 0.00 0.00 31.37 3.27
265 268 4.142643 ACGAGAAGTAAATCCGTGTCTCTC 60.143 45.833 0.00 0.00 31.37 3.20
266 269 3.757493 ACGAGAAGTAAATCCGTGTCTCT 59.243 43.478 0.00 0.00 31.37 3.10
268 271 3.367087 CCACGAGAAGTAAATCCGTGTCT 60.367 47.826 0.00 0.00 46.13 3.41
269 272 2.921754 CCACGAGAAGTAAATCCGTGTC 59.078 50.000 0.00 0.00 46.13 3.67
270 273 2.559668 TCCACGAGAAGTAAATCCGTGT 59.440 45.455 0.00 0.00 46.13 4.49
271 274 3.179830 CTCCACGAGAAGTAAATCCGTG 58.820 50.000 0.00 0.00 46.83 4.94
272 275 2.165845 CCTCCACGAGAAGTAAATCCGT 59.834 50.000 0.00 0.00 0.00 4.69
273 276 2.810650 CCTCCACGAGAAGTAAATCCG 58.189 52.381 0.00 0.00 0.00 4.18
274 277 2.093658 TGCCTCCACGAGAAGTAAATCC 60.094 50.000 0.00 0.00 0.00 3.01
286 290 3.334078 GCAAATTCATGCCTCCACG 57.666 52.632 0.00 0.00 40.49 4.94
321 325 0.673644 CCTTTCCGAACAGGCACGAT 60.674 55.000 0.00 0.00 40.77 3.73
377 381 6.540205 GCGTTGATAGGTTTCGATAAACTTT 58.460 36.000 3.75 0.00 43.76 2.66
378 382 5.220340 CGCGTTGATAGGTTTCGATAAACTT 60.220 40.000 0.00 0.00 43.76 2.66
401 405 3.597825 CGTTTTCATTGTTGGATTCGTCG 59.402 43.478 0.00 0.00 0.00 5.12
404 408 3.896122 ACCGTTTTCATTGTTGGATTCG 58.104 40.909 0.00 0.00 0.00 3.34
428 432 4.217550 TCTTCAACCATCCGTCCAAATTTC 59.782 41.667 0.00 0.00 0.00 2.17
437 441 5.301805 ACATTTTCTTTCTTCAACCATCCGT 59.698 36.000 0.00 0.00 0.00 4.69
441 445 9.447157 TTCAAAACATTTTCTTTCTTCAACCAT 57.553 25.926 0.00 0.00 0.00 3.55
442 446 8.839310 TTCAAAACATTTTCTTTCTTCAACCA 57.161 26.923 0.00 0.00 0.00 3.67
462 466 9.146586 CCCTCCCATAGATTCATTTTATTCAAA 57.853 33.333 0.00 0.00 0.00 2.69
463 467 8.288812 ACCCTCCCATAGATTCATTTTATTCAA 58.711 33.333 0.00 0.00 0.00 2.69
464 468 7.725397 CACCCTCCCATAGATTCATTTTATTCA 59.275 37.037 0.00 0.00 0.00 2.57
465 469 7.944554 TCACCCTCCCATAGATTCATTTTATTC 59.055 37.037 0.00 0.00 0.00 1.75
466 470 7.825709 TCACCCTCCCATAGATTCATTTTATT 58.174 34.615 0.00 0.00 0.00 1.40
467 471 7.406620 TCACCCTCCCATAGATTCATTTTAT 57.593 36.000 0.00 0.00 0.00 1.40
468 472 6.840090 TCACCCTCCCATAGATTCATTTTA 57.160 37.500 0.00 0.00 0.00 1.52
469 473 5.732331 TCACCCTCCCATAGATTCATTTT 57.268 39.130 0.00 0.00 0.00 1.82
470 474 5.614402 AGATCACCCTCCCATAGATTCATTT 59.386 40.000 0.00 0.00 0.00 2.32
471 475 5.168679 AGATCACCCTCCCATAGATTCATT 58.831 41.667 0.00 0.00 0.00 2.57
472 476 4.772483 AGATCACCCTCCCATAGATTCAT 58.228 43.478 0.00 0.00 0.00 2.57
473 477 4.140591 AGAGATCACCCTCCCATAGATTCA 60.141 45.833 0.00 0.00 33.76 2.57
474 478 4.222588 CAGAGATCACCCTCCCATAGATTC 59.777 50.000 0.00 0.00 33.76 2.52
475 479 4.166539 CAGAGATCACCCTCCCATAGATT 58.833 47.826 0.00 0.00 33.76 2.40
476 480 3.788933 CAGAGATCACCCTCCCATAGAT 58.211 50.000 0.00 0.00 33.76 1.98
477 481 2.757950 GCAGAGATCACCCTCCCATAGA 60.758 54.545 0.00 0.00 33.76 1.98
478 482 1.622811 GCAGAGATCACCCTCCCATAG 59.377 57.143 0.00 0.00 33.76 2.23
479 483 1.062198 TGCAGAGATCACCCTCCCATA 60.062 52.381 0.00 0.00 33.76 2.74
480 484 0.326904 TGCAGAGATCACCCTCCCAT 60.327 55.000 0.00 0.00 33.76 4.00
481 485 0.547471 TTGCAGAGATCACCCTCCCA 60.547 55.000 0.00 0.00 33.76 4.37
482 486 0.620556 TTTGCAGAGATCACCCTCCC 59.379 55.000 0.00 0.00 33.76 4.30
483 487 1.556911 TCTTTGCAGAGATCACCCTCC 59.443 52.381 2.15 0.00 33.76 4.30
518 522 8.770438 TGAAGCCAAAATTTAAGCGAAATTAT 57.230 26.923 11.33 2.53 45.21 1.28
555 559 2.023461 CAGGTCGAGTCTAGCGCG 59.977 66.667 0.00 0.00 41.76 6.86
593 607 0.322456 TTTGATGTCTTCCGCCCTGG 60.322 55.000 0.00 0.00 40.09 4.45
594 608 1.470098 CTTTTGATGTCTTCCGCCCTG 59.530 52.381 0.00 0.00 0.00 4.45
595 609 1.614317 CCTTTTGATGTCTTCCGCCCT 60.614 52.381 0.00 0.00 0.00 5.19
600 614 1.923356 TGGGCCTTTTGATGTCTTCC 58.077 50.000 4.53 0.00 0.00 3.46
620 634 2.637872 CAAGGGAGGTTCAGTAGGTTCA 59.362 50.000 0.00 0.00 0.00 3.18
621 635 2.638363 ACAAGGGAGGTTCAGTAGGTTC 59.362 50.000 0.00 0.00 0.00 3.62
622 636 2.638363 GACAAGGGAGGTTCAGTAGGTT 59.362 50.000 0.00 0.00 0.00 3.50
623 637 2.258109 GACAAGGGAGGTTCAGTAGGT 58.742 52.381 0.00 0.00 0.00 3.08
624 638 2.234908 CTGACAAGGGAGGTTCAGTAGG 59.765 54.545 0.00 0.00 0.00 3.18
625 639 2.900546 ACTGACAAGGGAGGTTCAGTAG 59.099 50.000 1.27 0.00 36.77 2.57
626 640 2.972348 ACTGACAAGGGAGGTTCAGTA 58.028 47.619 1.27 0.00 36.77 2.74
627 641 1.807814 ACTGACAAGGGAGGTTCAGT 58.192 50.000 0.00 0.00 34.12 3.41
628 642 2.354203 GCTACTGACAAGGGAGGTTCAG 60.354 54.545 0.00 0.00 0.00 3.02
654 668 1.375268 GAGCAGCGGCAGAGAAAGT 60.375 57.895 12.44 0.00 44.61 2.66
754 781 2.435693 GCTAGGAGGATGCGGTGGT 61.436 63.158 0.00 0.00 0.00 4.16
775 802 2.470990 TCTGCTGATGCTTAAGAGGGA 58.529 47.619 6.67 0.00 40.48 4.20
779 806 4.261783 CCGTAGATCTGCTGATGCTTAAGA 60.262 45.833 11.21 0.00 40.48 2.10
820 847 3.617735 GCTAGGGAGGGCCGCTAC 61.618 72.222 7.35 0.47 39.04 3.58
834 861 1.340017 GCAAGGAACTCACCATGGCTA 60.340 52.381 13.04 0.00 38.49 3.93
859 886 3.321968 ACTTTCAATTTGGTGAGGAAGGC 59.678 43.478 0.00 0.00 0.00 4.35
907 934 4.036518 ACTTCTCCAATCTACAGCAGGAT 58.963 43.478 0.00 0.00 0.00 3.24
930 957 1.003003 TGTCCAATCTGCAATCGACCA 59.997 47.619 0.00 0.00 0.00 4.02
934 961 3.495193 CAACTTGTCCAATCTGCAATCG 58.505 45.455 0.00 0.00 0.00 3.34
943 970 9.088987 AGTAAAATATCAACCAACTTGTCCAAT 57.911 29.630 0.00 0.00 0.00 3.16
944 971 8.472007 AGTAAAATATCAACCAACTTGTCCAA 57.528 30.769 0.00 0.00 0.00 3.53
971 998 4.141779 GGCTAGGGTTTCGGAGAAGATTAA 60.142 45.833 0.00 0.00 45.90 1.40
972 999 3.387050 GGCTAGGGTTTCGGAGAAGATTA 59.613 47.826 0.00 0.00 45.90 1.75
983 1010 3.444034 GTCCATGAAAAGGCTAGGGTTTC 59.556 47.826 0.00 3.06 32.92 2.78
1017 1044 0.319083 AGTAAATGTGACCGTCGGCA 59.681 50.000 12.28 7.78 0.00 5.69
1092 1120 8.919661 GCAACAAGGGTATAATACGTAATCTAC 58.080 37.037 0.00 0.00 0.00 2.59
1168 1196 1.985159 TGGGGACATTACAAGCTCTGT 59.015 47.619 6.74 6.74 37.48 3.41
1174 1202 2.556622 GTGGTGTTGGGGACATTACAAG 59.443 50.000 0.00 0.00 41.10 3.16
1184 1212 1.697432 TGACTAGAAGTGGTGTTGGGG 59.303 52.381 0.00 0.00 0.00 4.96
1197 1225 6.605194 AGCTTCATCATACTTGAGTGACTAGA 59.395 38.462 0.00 0.00 34.73 2.43
1202 1230 6.291648 AGAAGCTTCATCATACTTGAGTGA 57.708 37.500 27.57 0.00 34.73 3.41
1207 1235 6.732531 TGTGAAGAAGCTTCATCATACTTG 57.267 37.500 30.60 0.00 37.27 3.16
1262 1290 8.787852 AGATTTCTATTCTTCTTTTGCGAGTTT 58.212 29.630 0.00 0.00 0.00 2.66
1291 1319 0.758123 TTTCCCGGGTTGTACGAACT 59.242 50.000 22.86 0.00 0.00 3.01
1296 1324 2.089201 CATTCCTTTCCCGGGTTGTAC 58.911 52.381 22.86 0.00 0.00 2.90
1304 1332 3.006967 ACGGATAGATCATTCCTTTCCCG 59.993 47.826 11.03 0.00 30.92 5.14
1315 1343 3.006217 CCATTCAGAGCACGGATAGATCA 59.994 47.826 0.00 0.00 0.00 2.92
1319 1347 3.257873 AGATCCATTCAGAGCACGGATAG 59.742 47.826 0.00 0.00 36.60 2.08
1402 1431 2.354510 TGTTGCCGCTACTTCATAATGC 59.645 45.455 6.52 0.00 0.00 3.56
1409 1438 1.726853 AGATGTGTTGCCGCTACTTC 58.273 50.000 6.52 4.29 0.00 3.01
1440 1469 3.064207 GTGCAACAAGATCACTAACGGA 58.936 45.455 0.00 0.00 36.32 4.69
1529 1558 0.591170 CAACGTGGGTCAACATGGAC 59.409 55.000 0.00 0.00 37.06 4.02
1544 1573 4.508124 GCTAAGGATATCACTTGGTCAACG 59.492 45.833 4.83 0.00 0.00 4.10
1858 1888 4.663636 ACATGGAAGATTTTCGACGTTC 57.336 40.909 0.00 0.00 33.98 3.95
2021 2051 1.982958 ACCCGTTAGGAAGTGAACCAT 59.017 47.619 0.00 0.00 41.02 3.55
2324 2355 6.121590 TCCATCACAGCTTTAATAATGCAGA 58.878 36.000 12.41 7.94 34.29 4.26
2562 2594 3.149196 GAGTTGTTCTGATTCAAGGCCA 58.851 45.455 5.01 0.00 0.00 5.36
2798 2830 1.152830 ACTCCGTTGTTGCCCCAAT 59.847 52.632 0.00 0.00 0.00 3.16
2936 3696 0.472471 AATGATTGTACGCCCGGGAT 59.528 50.000 29.31 14.70 0.00 3.85
2955 3715 3.333899 ATGATGCCGCACTGCCAGA 62.334 57.895 0.00 0.00 0.00 3.86
2982 3742 3.536917 CGGTATCGCTGGCCTCCA 61.537 66.667 3.32 0.00 0.00 3.86
3044 3804 1.342496 CTCATAGCCTTCTCGCCATCA 59.658 52.381 0.00 0.00 0.00 3.07
3047 3807 1.342496 CATCTCATAGCCTTCTCGCCA 59.658 52.381 0.00 0.00 0.00 5.69
3188 3956 1.072930 AAGACCTCAAGGGGGTGGT 60.073 57.895 0.00 0.00 40.27 4.16
3216 3984 2.965831 AGAAGGGAAAAGCTTTGGGAAC 59.034 45.455 13.54 3.70 0.00 3.62
3362 4130 5.772521 AGGTGTACAATTTTCTGATTGTGC 58.227 37.500 12.16 11.32 46.60 4.57
3595 4363 2.616842 ACCAGTGTTTCTTTAAGCACCG 59.383 45.455 2.10 0.00 45.12 4.94
3720 4491 4.491676 TGTACAAGCATCCGACTCTAAAC 58.508 43.478 0.00 0.00 0.00 2.01
3730 4501 4.434725 CGATCGCATATTGTACAAGCATCC 60.435 45.833 14.65 0.00 0.00 3.51
3788 4561 2.799017 TGTACGACACCTACCATCAGT 58.201 47.619 0.00 0.00 0.00 3.41
3830 4603 5.713792 AACATGAGAGCTGCTATACGTAT 57.286 39.130 13.54 13.54 0.00 3.06
4145 4918 2.632996 AGAGACAACATCTGAAACGGGA 59.367 45.455 0.00 0.00 38.00 5.14
4167 4940 2.837498 TCGTACATCCTGCATCAATGG 58.163 47.619 7.69 0.00 0.00 3.16
4225 4998 4.918810 AACTGAAAAATCTGGTCACCAC 57.081 40.909 0.00 0.00 0.00 4.16
4305 5078 3.558418 GGCATGCCAAAATAGAATTGCTG 59.442 43.478 32.08 0.00 35.81 4.41
4323 5096 5.163416 GCATATAGTTTCCAAAACCAGGCAT 60.163 40.000 0.00 0.00 0.00 4.40
4374 5147 8.429237 AAATGATATACCTCAAACCAAACCAA 57.571 30.769 0.00 0.00 0.00 3.67
4680 5453 6.042143 AGGTGCAAATAAGCCATTTTATTCG 58.958 36.000 0.00 0.00 34.49 3.34
4721 5494 3.121019 CCGTTTTGTTTCCGGCCA 58.879 55.556 2.24 0.00 34.62 5.36
4791 5564 1.351017 CAACCTCTTAGGCCCTGTTCA 59.649 52.381 0.00 0.00 39.63 3.18
4875 5650 8.759641 GTTCTTATATAGTCGACTTACACGAGA 58.240 37.037 25.44 16.37 40.37 4.04
4905 5680 1.303317 GCGGCTGGAGGAGGAAAAA 60.303 57.895 0.00 0.00 0.00 1.94
4931 5707 1.209383 CGAGGCAACGACGAGAGAA 59.791 57.895 0.00 0.00 46.39 2.87
4968 5744 2.011222 GGCATTGTCGGTCGGATTAAA 58.989 47.619 0.00 0.00 0.00 1.52
4996 5772 3.623906 TTGCAGAGAGGAAGATGAAGG 57.376 47.619 0.00 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.