Multiple sequence alignment - TraesCS3D01G265100

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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 TraesCS3D01G265100 chr3D 100.000 3629 0 0 1 3629 367238141 367234513 0.000000e+00 6702.0
1 TraesCS3D01G265100 chr3B 89.134 2770 146 76 551 3228 478324052 478321346 0.000000e+00 3304.0
2 TraesCS3D01G265100 chr3B 80.741 540 30 32 10 533 478330795 478330314 1.600000e-93 353.0
3 TraesCS3D01G265100 chr3B 81.271 299 19 14 3346 3628 478321298 478321021 1.320000e-49 207.0
4 TraesCS3D01G265100 chr3A 89.597 2653 139 72 1 2576 489313142 489310550 0.000000e+00 3243.0
5 TraesCS3D01G265100 chr3A 88.906 649 49 10 2586 3226 489310297 489309664 0.000000e+00 778.0
6 TraesCS3D01G265100 chr3A 98.077 104 2 0 3317 3420 489309654 489309551 8.000000e-42 182.0
7 TraesCS3D01G265100 chr3A 91.667 84 2 2 3454 3532 489309562 489309479 1.070000e-20 111.0
8 TraesCS3D01G265100 chr3A 86.250 80 9 2 3551 3629 489309490 489309412 6.460000e-13 86.1
9 TraesCS3D01G265100 chr1D 90.476 147 13 1 1178 1324 459880642 459880497 3.700000e-45 193.0
10 TraesCS3D01G265100 chr1D 92.553 94 7 0 1769 1862 459880277 459880184 6.320000e-28 135.0
11 TraesCS3D01G265100 chr1A 90.541 148 11 3 1178 1324 551593136 551592991 3.700000e-45 193.0
12 TraesCS3D01G265100 chr1A 91.837 98 7 1 1769 1866 551592780 551592684 6.320000e-28 135.0
13 TraesCS3D01G265100 chr1B 88.514 148 14 3 1178 1324 631967718 631967573 3.720000e-40 176.0
14 TraesCS3D01G265100 chr1B 92.553 94 7 0 1769 1862 631967367 631967274 6.320000e-28 135.0
15 TraesCS3D01G265100 chr5B 80.473 169 27 6 1156 1321 391144709 391144874 1.370000e-24 124.0
16 TraesCS3D01G265100 chr5B 81.752 137 15 9 1177 1308 585835966 585835835 4.960000e-19 106.0
17 TraesCS3D01G265100 chr7B 91.860 86 7 0 1764 1849 561280494 561280409 1.770000e-23 121.0
18 TraesCS3D01G265100 chr5A 81.944 144 21 5 1181 1321 436089153 436089294 2.290000e-22 117.0
19 TraesCS3D01G265100 chr7D 90.698 86 8 0 1764 1849 524915755 524915670 8.230000e-22 115.0
20 TraesCS3D01G265100 chr7A 90.698 86 8 0 1764 1849 604853602 604853517 8.230000e-22 115.0
21 TraesCS3D01G265100 chr6B 90.588 85 8 0 1765 1849 652629938 652629854 2.960000e-21 113.0
22 TraesCS3D01G265100 chr2D 86.458 96 9 4 3223 3316 495785960 495786053 6.410000e-18 102.0
23 TraesCS3D01G265100 chr5D 81.022 137 16 9 1177 1308 478222935 478222804 2.310000e-17 100.0


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 TraesCS3D01G265100 chr3D 367234513 367238141 3628 True 6702.00 6702 100.0000 1 3629 1 chr3D.!!$R1 3628
1 TraesCS3D01G265100 chr3B 478321021 478324052 3031 True 1755.50 3304 85.2025 551 3628 2 chr3B.!!$R2 3077
2 TraesCS3D01G265100 chr3A 489309412 489313142 3730 True 880.02 3243 90.8994 1 3629 5 chr3A.!!$R1 3628

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
470 485 0.103208 ACGCGTCTTCCATCTGATCC 59.897 55.0 5.58 0.0 0.0 3.36 F
1039 1112 0.178961 AGGTCCGATCCGATCATCCA 60.179 55.0 9.07 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 2546 0.301687 GATGCGGTGACATTAGTGCG 59.698 55.0 0.00 0.0 0.0 5.34 R
2674 3043 0.104855 AACTCAAGCTCGCACAGTGA 59.895 50.0 4.15 0.0 0.0 3.41 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
39 40 6.694447 TCTTTGTTTAGTACGGTGCTTATCT 58.306 36.000 3.56 0.00 0.00 1.98
69 70 0.503117 GCACGAGTTTGACAGACGAC 59.497 55.000 0.00 0.00 0.00 4.34
102 103 0.743345 GTTTTCGTGGATCGGGGAGG 60.743 60.000 0.00 0.00 40.32 4.30
106 107 2.764128 GTGGATCGGGGAGGAGCA 60.764 66.667 0.00 0.00 0.00 4.26
117 118 3.670637 GAGGAGCAGCATCACCGCA 62.671 63.158 0.00 0.00 0.00 5.69
126 127 1.083806 GCATCACCGCATTCGTCTGA 61.084 55.000 0.00 0.00 0.00 3.27
127 128 0.647410 CATCACCGCATTCGTCTGAC 59.353 55.000 0.00 0.00 0.00 3.51
128 129 0.532573 ATCACCGCATTCGTCTGACT 59.467 50.000 6.21 0.00 0.00 3.41
129 130 0.109272 TCACCGCATTCGTCTGACTC 60.109 55.000 6.21 0.00 0.00 3.36
130 131 0.388520 CACCGCATTCGTCTGACTCA 60.389 55.000 6.21 0.00 0.00 3.41
131 132 0.317160 ACCGCATTCGTCTGACTCAA 59.683 50.000 6.21 0.00 0.00 3.02
157 159 2.553268 GCACTCGTCACAAGCAGC 59.447 61.111 0.00 0.00 0.00 5.25
161 163 2.661537 TCGTCACAAGCAGCCACG 60.662 61.111 0.00 0.00 0.00 4.94
201 206 6.744175 AGATTTCAGAGATCCATCAGCTTA 57.256 37.500 0.00 0.00 0.00 3.09
211 216 6.015918 AGATCCATCAGCTTAGCTATACTGT 58.984 40.000 6.35 7.62 36.40 3.55
212 217 6.496565 AGATCCATCAGCTTAGCTATACTGTT 59.503 38.462 6.35 10.68 36.40 3.16
214 219 5.363868 TCCATCAGCTTAGCTATACTGTTGT 59.636 40.000 21.42 10.60 36.40 3.32
224 229 3.871594 GCTATACTGTTGTGGCGAGAATT 59.128 43.478 0.00 0.00 0.00 2.17
225 230 5.047847 GCTATACTGTTGTGGCGAGAATTA 58.952 41.667 0.00 0.00 0.00 1.40
227 232 6.202954 GCTATACTGTTGTGGCGAGAATTATT 59.797 38.462 0.00 0.00 0.00 1.40
228 233 7.254795 GCTATACTGTTGTGGCGAGAATTATTT 60.255 37.037 0.00 0.00 0.00 1.40
230 235 6.084326 ACTGTTGTGGCGAGAATTATTTTT 57.916 33.333 0.00 0.00 0.00 1.94
250 255 2.498077 CAGCTCGGGAGATCTGTGA 58.502 57.895 0.00 0.00 45.41 3.58
251 256 1.039068 CAGCTCGGGAGATCTGTGAT 58.961 55.000 0.00 0.00 45.41 3.06
252 257 1.039068 AGCTCGGGAGATCTGTGATG 58.961 55.000 0.00 0.00 38.80 3.07
253 258 1.035923 GCTCGGGAGATCTGTGATGA 58.964 55.000 0.00 0.00 38.80 2.92
254 259 1.617850 GCTCGGGAGATCTGTGATGAT 59.382 52.381 0.00 0.00 38.80 2.45
255 260 2.352617 GCTCGGGAGATCTGTGATGATC 60.353 54.545 0.00 0.00 42.18 2.92
256 261 1.882623 TCGGGAGATCTGTGATGATCG 59.117 52.381 0.00 0.00 45.35 3.69
257 262 1.668337 CGGGAGATCTGTGATGATCGC 60.668 57.143 0.00 0.00 45.35 4.58
258 263 1.617850 GGGAGATCTGTGATGATCGCT 59.382 52.381 0.00 0.00 45.35 4.93
259 264 2.352617 GGGAGATCTGTGATGATCGCTC 60.353 54.545 0.00 0.00 45.35 5.03
260 265 2.352617 GGAGATCTGTGATGATCGCTCC 60.353 54.545 0.00 1.78 45.35 4.70
261 266 2.557924 GAGATCTGTGATGATCGCTCCT 59.442 50.000 0.00 0.00 45.35 3.69
262 267 2.557924 AGATCTGTGATGATCGCTCCTC 59.442 50.000 7.57 1.61 45.35 3.71
263 268 0.665298 TCTGTGATGATCGCTCCTCG 59.335 55.000 7.57 0.00 40.15 4.63
264 269 0.938637 CTGTGATGATCGCTCCTCGC 60.939 60.000 7.57 0.00 38.27 5.03
265 270 1.066422 GTGATGATCGCTCCTCGCA 59.934 57.895 0.00 0.00 39.08 5.10
266 271 0.319383 GTGATGATCGCTCCTCGCAT 60.319 55.000 0.00 0.00 39.08 4.73
267 272 0.319297 TGATGATCGCTCCTCGCATG 60.319 55.000 0.00 0.00 39.08 4.06
268 273 1.624865 GATGATCGCTCCTCGCATGC 61.625 60.000 7.91 7.91 39.08 4.06
269 274 2.028778 GATCGCTCCTCGCATGCT 59.971 61.111 17.13 0.00 39.08 3.79
270 275 2.021039 GATCGCTCCTCGCATGCTC 61.021 63.158 17.13 0.00 39.08 4.26
271 276 2.690099 GATCGCTCCTCGCATGCTCA 62.690 60.000 17.13 0.58 39.08 4.26
272 277 2.302199 ATCGCTCCTCGCATGCTCAA 62.302 55.000 17.13 0.00 39.08 3.02
277 282 0.321346 TCCTCGCATGCTCAACTCAA 59.679 50.000 17.13 0.00 0.00 3.02
287 292 0.689623 CTCAACTCAACTGCTCCCCT 59.310 55.000 0.00 0.00 0.00 4.79
290 295 1.610522 CAACTCAACTGCTCCCCTTTG 59.389 52.381 0.00 0.00 0.00 2.77
292 297 0.401738 CTCAACTGCTCCCCTTTGGA 59.598 55.000 0.00 0.00 42.41 3.53
316 321 1.148273 TTTCAGCCCTGCGTCAGTT 59.852 52.632 6.19 0.00 0.00 3.16
363 372 2.083774 GGGTGCGACATTTCATCAGAA 58.916 47.619 0.00 0.00 0.00 3.02
381 390 1.680735 GAATTTCAGTGCCACCACACA 59.319 47.619 0.00 0.00 44.53 3.72
389 398 3.068881 CCACCACACACGGGATCT 58.931 61.111 0.00 0.00 0.00 2.75
390 399 1.375908 CCACCACACACGGGATCTG 60.376 63.158 0.00 0.00 0.00 2.90
391 400 1.375908 CACCACACACGGGATCTGG 60.376 63.158 0.00 0.00 0.00 3.86
392 401 1.535444 ACCACACACGGGATCTGGA 60.535 57.895 0.00 0.00 0.00 3.86
394 403 1.448540 CACACACGGGATCTGGAGC 60.449 63.158 0.00 0.00 0.00 4.70
395 404 1.610673 ACACACGGGATCTGGAGCT 60.611 57.895 0.00 0.00 0.00 4.09
396 405 0.324368 ACACACGGGATCTGGAGCTA 60.324 55.000 0.00 0.00 0.00 3.32
403 412 0.316841 GGATCTGGAGCTAGCGAAGG 59.683 60.000 9.55 1.83 0.00 3.46
426 435 3.342627 CGTCCGCCAAGAAACGCA 61.343 61.111 0.00 0.00 0.00 5.24
428 437 2.668212 TCCGCCAAGAAACGCAGG 60.668 61.111 0.00 0.00 0.00 4.85
470 485 0.103208 ACGCGTCTTCCATCTGATCC 59.897 55.000 5.58 0.00 0.00 3.36
481 496 3.781965 TCCATCTGATCCATCCACTGAAA 59.218 43.478 0.00 0.00 0.00 2.69
483 498 4.141551 CCATCTGATCCATCCACTGAAAGA 60.142 45.833 0.00 0.00 37.43 2.52
485 500 4.836825 TCTGATCCATCCACTGAAAGAAC 58.163 43.478 0.00 0.00 37.43 3.01
522 537 0.317770 ACATTTGGCACGAAACGCAG 60.318 50.000 0.00 0.00 0.00 5.18
562 577 5.068329 GCTTCCCAGATGGATTTTTCTAAGG 59.932 44.000 0.00 0.00 44.66 2.69
563 578 5.129368 TCCCAGATGGATTTTTCTAAGGG 57.871 43.478 0.00 0.00 38.61 3.95
586 601 3.129502 CCTCCGCGTGACCGACTA 61.130 66.667 4.92 0.00 35.63 2.59
587 602 2.693762 CCTCCGCGTGACCGACTAA 61.694 63.158 4.92 0.00 35.63 2.24
588 603 1.210931 CTCCGCGTGACCGACTAAA 59.789 57.895 4.92 0.00 35.63 1.85
589 604 0.797249 CTCCGCGTGACCGACTAAAG 60.797 60.000 4.92 0.00 35.63 1.85
590 605 2.442188 CCGCGTGACCGACTAAAGC 61.442 63.158 4.92 0.00 35.63 3.51
591 606 2.442188 CGCGTGACCGACTAAAGCC 61.442 63.158 0.00 0.00 35.63 4.35
592 607 2.442188 GCGTGACCGACTAAAGCCG 61.442 63.158 0.00 0.00 35.63 5.52
593 608 1.210931 CGTGACCGACTAAAGCCGA 59.789 57.895 0.00 0.00 35.63 5.54
631 654 0.386858 TCTCGCGCACAAGTACAGAC 60.387 55.000 8.75 0.00 0.00 3.51
649 687 8.162085 AGTACAGACGGAGGAATTATAGTATGA 58.838 37.037 0.00 0.00 0.00 2.15
743 781 2.714530 GCGCGCGAAACCAAATTTA 58.285 47.368 37.18 0.00 0.00 1.40
744 782 1.264672 GCGCGCGAAACCAAATTTAT 58.735 45.000 37.18 0.00 0.00 1.40
747 785 3.776478 GCGCGCGAAACCAAATTTATTTC 60.776 43.478 37.18 4.99 0.00 2.17
748 786 3.362237 CGCGCGAAACCAAATTTATTTCA 59.638 39.130 28.94 0.00 32.89 2.69
749 787 4.031201 CGCGCGAAACCAAATTTATTTCAT 59.969 37.500 28.94 0.00 32.89 2.57
750 788 5.443955 CGCGCGAAACCAAATTTATTTCATT 60.444 36.000 28.94 1.22 32.89 2.57
751 789 6.303370 GCGCGAAACCAAATTTATTTCATTT 58.697 32.000 12.10 4.85 32.89 2.32
752 790 6.794636 GCGCGAAACCAAATTTATTTCATTTT 59.205 30.769 12.10 2.88 32.89 1.82
753 791 7.322461 GCGCGAAACCAAATTTATTTCATTTTT 59.678 29.630 12.10 2.10 32.89 1.94
772 810 1.259142 TTGGAATACGGCCACGGAGA 61.259 55.000 2.24 0.00 46.48 3.71
796 834 2.432300 AATGCTACGGTCGAGGGGG 61.432 63.158 0.00 0.00 0.00 5.40
855 896 2.813179 CGTAGGTACGTACGCGGCT 61.813 63.158 28.59 12.60 44.13 5.52
1030 1103 2.107141 CGCAGGAAGGTCCGATCC 59.893 66.667 8.34 8.34 42.75 3.36
1031 1104 2.107141 GCAGGAAGGTCCGATCCG 59.893 66.667 10.16 7.36 42.75 4.18
1032 1105 2.423898 GCAGGAAGGTCCGATCCGA 61.424 63.158 10.16 0.00 42.75 4.55
1033 1106 1.749334 GCAGGAAGGTCCGATCCGAT 61.749 60.000 10.16 0.00 42.75 4.18
1038 1111 0.969894 AAGGTCCGATCCGATCATCC 59.030 55.000 9.07 7.16 0.00 3.51
1039 1112 0.178961 AGGTCCGATCCGATCATCCA 60.179 55.000 9.07 0.00 0.00 3.41
1040 1113 0.898320 GGTCCGATCCGATCATCCAT 59.102 55.000 9.07 0.00 0.00 3.41
1051 1124 2.427095 CGATCATCCATCATACGCCCTA 59.573 50.000 0.00 0.00 0.00 3.53
1060 1136 1.900016 ATACGCCCTATCGTGCCGA 60.900 57.895 0.00 0.00 43.21 5.54
1061 1137 1.457823 ATACGCCCTATCGTGCCGAA 61.458 55.000 1.44 0.00 43.21 4.30
1175 1253 3.456365 GCGAGAGGGAGCAGCAGA 61.456 66.667 0.00 0.00 0.00 4.26
1221 1299 4.821589 GCGAGCGTGAAGAGGGGG 62.822 72.222 0.00 0.00 0.00 5.40
1325 1407 1.717645 GAAAGCAGGTACGTACGTGTG 59.282 52.381 35.42 25.09 42.33 3.82
1351 1433 2.158330 CGCGTGCTGCAGTAATCGA 61.158 57.895 16.64 0.00 46.97 3.59
1354 1439 0.458543 CGTGCTGCAGTAATCGACCT 60.459 55.000 16.64 0.00 0.00 3.85
1356 1441 0.740868 TGCTGCAGTAATCGACCTGC 60.741 55.000 20.71 20.71 42.54 4.85
1435 1532 4.084888 CCGGCGTCGTCCTTTTGC 62.085 66.667 9.28 0.00 33.95 3.68
1472 1591 7.546250 TTCCTAATTTTCCATGGTTGCTAAA 57.454 32.000 12.58 1.13 0.00 1.85
1473 1592 7.169158 TCCTAATTTTCCATGGTTGCTAAAG 57.831 36.000 12.58 2.95 0.00 1.85
1474 1593 5.812127 CCTAATTTTCCATGGTTGCTAAAGC 59.188 40.000 12.58 0.00 42.50 3.51
1477 1596 4.953940 TTTCCATGGTTGCTAAAGCTTT 57.046 36.364 17.30 17.30 42.66 3.51
1478 1597 3.940209 TCCATGGTTGCTAAAGCTTTG 57.060 42.857 22.02 12.32 42.66 2.77
1479 1598 3.495331 TCCATGGTTGCTAAAGCTTTGA 58.505 40.909 22.02 3.28 42.66 2.69
1539 1659 0.543749 GGCTGAGGTGGCTCAACTAT 59.456 55.000 0.00 0.00 28.17 2.12
1628 1748 2.304761 ACTCCATCGGAAGCAGGTAAAA 59.695 45.455 0.00 0.00 0.00 1.52
1672 1792 1.165907 TGAATCGCATGCGGATTCCC 61.166 55.000 35.26 24.64 40.25 3.97
1738 1859 4.163552 TGTCACGTAATTGACTGATCGTC 58.836 43.478 9.77 9.77 45.34 4.20
1751 1873 1.470494 TGATCGTCTCTCTCTGTGTGC 59.530 52.381 0.00 0.00 0.00 4.57
1758 1880 3.519973 CTCTCTGTGTGCGTGCCCA 62.520 63.158 0.00 0.00 0.00 5.36
1893 2015 1.002134 GCAGCACTACCACCACCAT 60.002 57.895 0.00 0.00 0.00 3.55
2058 2180 3.792736 GGCGCCATGTACTCCCCA 61.793 66.667 24.80 0.00 0.00 4.96
2098 2220 1.404748 TCGGTCACTACAACGTCAACA 59.595 47.619 0.00 0.00 0.00 3.33
2100 2222 1.862827 GGTCACTACAACGTCAACACC 59.137 52.381 0.00 0.00 0.00 4.16
2422 2544 4.051237 GACATGAGAAACAAAACCAAGCC 58.949 43.478 0.00 0.00 0.00 4.35
2423 2545 3.450457 ACATGAGAAACAAAACCAAGCCA 59.550 39.130 0.00 0.00 0.00 4.75
2424 2546 3.518634 TGAGAAACAAAACCAAGCCAC 57.481 42.857 0.00 0.00 0.00 5.01
2425 2547 2.159310 TGAGAAACAAAACCAAGCCACG 60.159 45.455 0.00 0.00 0.00 4.94
2465 2587 1.584483 GCGCAAGATGTTCATGCCG 60.584 57.895 0.30 0.00 37.78 5.69
2466 2588 1.980951 GCGCAAGATGTTCATGCCGA 61.981 55.000 0.30 0.00 37.78 5.54
2467 2589 0.027194 CGCAAGATGTTCATGCCGAG 59.973 55.000 0.00 0.00 37.78 4.63
2468 2590 0.248377 GCAAGATGTTCATGCCGAGC 60.248 55.000 0.00 0.00 35.28 5.03
2481 2603 3.797008 CGAGCTAGTCGTCGGTCT 58.203 61.111 0.00 0.00 44.20 3.85
2673 3042 0.036765 GTACCAACCATGCAGTCCGA 60.037 55.000 0.00 0.00 0.00 4.55
2674 3043 0.908910 TACCAACCATGCAGTCCGAT 59.091 50.000 0.00 0.00 0.00 4.18
2675 3044 0.392998 ACCAACCATGCAGTCCGATC 60.393 55.000 0.00 0.00 0.00 3.69
2881 3275 6.936900 ACACACACTGCTGAGAATAAATACTT 59.063 34.615 0.00 0.00 0.00 2.24
2882 3276 8.094548 ACACACACTGCTGAGAATAAATACTTA 58.905 33.333 0.00 0.00 0.00 2.24
2883 3277 8.598924 CACACACTGCTGAGAATAAATACTTAG 58.401 37.037 0.00 0.00 0.00 2.18
2884 3278 7.766278 ACACACTGCTGAGAATAAATACTTAGG 59.234 37.037 0.00 0.00 0.00 2.69
2885 3279 7.981789 CACACTGCTGAGAATAAATACTTAGGA 59.018 37.037 0.00 0.00 0.00 2.94
2886 3280 8.540388 ACACTGCTGAGAATAAATACTTAGGAA 58.460 33.333 0.00 0.00 0.00 3.36
2887 3281 8.821894 CACTGCTGAGAATAAATACTTAGGAAC 58.178 37.037 0.00 0.00 0.00 3.62
2888 3282 7.707035 ACTGCTGAGAATAAATACTTAGGAACG 59.293 37.037 0.00 0.00 0.00 3.95
2890 3284 7.147794 TGCTGAGAATAAATACTTAGGAACGGA 60.148 37.037 0.00 0.00 0.00 4.69
2891 3285 7.382759 GCTGAGAATAAATACTTAGGAACGGAG 59.617 40.741 0.00 0.00 0.00 4.63
2892 3286 7.723324 TGAGAATAAATACTTAGGAACGGAGG 58.277 38.462 0.00 0.00 0.00 4.30
2893 3287 7.063934 AGAATAAATACTTAGGAACGGAGGG 57.936 40.000 0.00 0.00 0.00 4.30
2895 3289 6.667558 ATAAATACTTAGGAACGGAGGGAG 57.332 41.667 0.00 0.00 0.00 4.30
2896 3290 3.684408 ATACTTAGGAACGGAGGGAGT 57.316 47.619 0.00 0.00 0.00 3.85
2897 3291 4.803329 ATACTTAGGAACGGAGGGAGTA 57.197 45.455 0.00 0.00 0.00 2.59
2898 3292 3.684408 ACTTAGGAACGGAGGGAGTAT 57.316 47.619 0.00 0.00 0.00 2.12
2899 3293 3.297736 ACTTAGGAACGGAGGGAGTATG 58.702 50.000 0.00 0.00 0.00 2.39
2903 3297 1.553704 GGAACGGAGGGAGTATGTGTT 59.446 52.381 0.00 0.00 0.00 3.32
2904 3298 2.027469 GGAACGGAGGGAGTATGTGTTT 60.027 50.000 0.00 0.00 0.00 2.83
2906 3300 2.253610 ACGGAGGGAGTATGTGTTTGA 58.746 47.619 0.00 0.00 0.00 2.69
2907 3301 2.838202 ACGGAGGGAGTATGTGTTTGAT 59.162 45.455 0.00 0.00 0.00 2.57
2909 3303 3.741388 CGGAGGGAGTATGTGTTTGATCC 60.741 52.174 0.00 0.00 0.00 3.36
2910 3304 3.458189 GAGGGAGTATGTGTTTGATCCG 58.542 50.000 0.00 0.00 0.00 4.18
2911 3305 2.838202 AGGGAGTATGTGTTTGATCCGT 59.162 45.455 0.00 0.00 0.00 4.69
2912 3306 4.028131 AGGGAGTATGTGTTTGATCCGTA 58.972 43.478 0.00 0.00 0.00 4.02
2913 3307 4.654262 AGGGAGTATGTGTTTGATCCGTAT 59.346 41.667 0.00 0.00 0.00 3.06
2914 3308 4.750098 GGGAGTATGTGTTTGATCCGTATG 59.250 45.833 0.00 0.00 0.00 2.39
2915 3309 5.357257 GGAGTATGTGTTTGATCCGTATGT 58.643 41.667 0.00 0.00 0.00 2.29
2916 3310 6.461927 GGGAGTATGTGTTTGATCCGTATGTA 60.462 42.308 0.00 0.00 0.00 2.29
2917 3311 6.641314 GGAGTATGTGTTTGATCCGTATGTAG 59.359 42.308 0.00 0.00 0.00 2.74
2918 3312 7.108841 AGTATGTGTTTGATCCGTATGTAGT 57.891 36.000 0.00 0.00 0.00 2.73
2919 3313 7.201145 AGTATGTGTTTGATCCGTATGTAGTC 58.799 38.462 0.00 0.00 0.00 2.59
2920 3314 5.394224 TGTGTTTGATCCGTATGTAGTCA 57.606 39.130 0.00 0.00 0.00 3.41
2921 3315 5.165676 TGTGTTTGATCCGTATGTAGTCAC 58.834 41.667 0.00 0.00 0.00 3.67
2922 3316 5.047590 TGTGTTTGATCCGTATGTAGTCACT 60.048 40.000 0.00 0.00 0.00 3.41
2940 3334 6.888430 AGTCACTTGTTTGATCAATTCGTAC 58.112 36.000 9.40 4.61 0.00 3.67
2941 3335 6.481976 AGTCACTTGTTTGATCAATTCGTACA 59.518 34.615 9.40 7.39 0.00 2.90
2984 3381 1.285078 CTAAAAAGCTAGGCAGGGGGT 59.715 52.381 0.00 0.00 0.00 4.95
3017 3414 2.807906 CGCATGATGTACCGCGCAA 61.808 57.895 8.75 0.00 41.38 4.85
3023 3420 0.645868 GATGTACCGCGCAAGTTCTC 59.354 55.000 8.75 0.00 41.68 2.87
3043 3440 2.027073 GTGTGACGCGCTGGATGAA 61.027 57.895 5.73 0.00 0.00 2.57
3054 3451 1.079405 TGGATGAAGGCGACGAACC 60.079 57.895 0.00 0.00 0.00 3.62
3110 3521 1.364171 GATGGACCAGGTCGATCGG 59.636 63.158 24.30 0.47 37.84 4.18
3146 3557 4.807039 CTTTGCATGGGCGGCAGC 62.807 66.667 12.47 12.35 45.35 5.25
3211 3622 1.798813 GAGCGAGGCGAAGAAAGAAAA 59.201 47.619 0.00 0.00 0.00 2.29
3228 3639 2.806945 AAAATGCACCCAGCTAGCTA 57.193 45.000 18.86 0.00 45.94 3.32
3229 3640 2.044123 AAATGCACCCAGCTAGCTAC 57.956 50.000 18.86 5.47 45.94 3.58
3231 3642 0.755686 ATGCACCCAGCTAGCTACTC 59.244 55.000 18.86 5.85 45.94 2.59
3232 3643 1.330655 TGCACCCAGCTAGCTACTCC 61.331 60.000 18.86 5.81 45.94 3.85
3233 3644 2.034048 GCACCCAGCTAGCTACTCCC 62.034 65.000 18.86 2.46 41.15 4.30
3234 3645 0.397816 CACCCAGCTAGCTACTCCCT 60.398 60.000 18.86 0.00 0.00 4.20
3235 3646 0.105913 ACCCAGCTAGCTACTCCCTC 60.106 60.000 18.86 0.00 0.00 4.30
3236 3647 0.187361 CCCAGCTAGCTACTCCCTCT 59.813 60.000 18.86 0.00 0.00 3.69
3237 3648 1.616159 CCAGCTAGCTACTCCCTCTC 58.384 60.000 18.86 0.00 0.00 3.20
3238 3649 1.616159 CAGCTAGCTACTCCCTCTCC 58.384 60.000 18.86 0.00 0.00 3.71
3239 3650 0.481128 AGCTAGCTACTCCCTCTCCC 59.519 60.000 17.69 0.00 0.00 4.30
3240 3651 0.186386 GCTAGCTACTCCCTCTCCCA 59.814 60.000 7.70 0.00 0.00 4.37
3241 3652 1.203125 GCTAGCTACTCCCTCTCCCAT 60.203 57.143 7.70 0.00 0.00 4.00
3242 3653 2.041891 GCTAGCTACTCCCTCTCCCATA 59.958 54.545 7.70 0.00 0.00 2.74
3243 3654 3.500654 GCTAGCTACTCCCTCTCCCATAA 60.501 52.174 7.70 0.00 0.00 1.90
3244 3655 3.933239 AGCTACTCCCTCTCCCATAAT 57.067 47.619 0.00 0.00 0.00 1.28
3245 3656 5.575987 GCTAGCTACTCCCTCTCCCATAATA 60.576 48.000 7.70 0.00 0.00 0.98
3246 3657 5.560467 AGCTACTCCCTCTCCCATAATAT 57.440 43.478 0.00 0.00 0.00 1.28
3247 3658 6.676164 AGCTACTCCCTCTCCCATAATATA 57.324 41.667 0.00 0.00 0.00 0.86
3248 3659 7.057732 AGCTACTCCCTCTCCCATAATATAA 57.942 40.000 0.00 0.00 0.00 0.98
3249 3660 7.129425 AGCTACTCCCTCTCCCATAATATAAG 58.871 42.308 0.00 0.00 0.00 1.73
3250 3661 7.035764 AGCTACTCCCTCTCCCATAATATAAGA 60.036 40.741 0.00 0.00 0.00 2.10
3251 3662 7.286775 GCTACTCCCTCTCCCATAATATAAGAG 59.713 44.444 0.00 0.00 34.55 2.85
3252 3663 7.122311 ACTCCCTCTCCCATAATATAAGAGT 57.878 40.000 0.00 0.00 33.23 3.24
3253 3664 7.549141 ACTCCCTCTCCCATAATATAAGAGTT 58.451 38.462 0.00 0.00 33.23 3.01
3254 3665 8.019652 ACTCCCTCTCCCATAATATAAGAGTTT 58.980 37.037 0.00 0.00 33.23 2.66
3255 3666 8.814448 TCCCTCTCCCATAATATAAGAGTTTT 57.186 34.615 0.00 0.00 33.23 2.43
3256 3667 9.237706 TCCCTCTCCCATAATATAAGAGTTTTT 57.762 33.333 0.00 0.00 33.23 1.94
3287 3698 9.578439 ACACTACACTAGTATAAAAATCGTTCC 57.422 33.333 0.00 0.00 37.23 3.62
3288 3699 9.798994 CACTACACTAGTATAAAAATCGTTCCT 57.201 33.333 0.00 0.00 37.23 3.36
3305 3716 7.621428 TCGTTCCTATATTATAAGACGGAGG 57.379 40.000 10.60 0.00 0.00 4.30
3306 3717 6.600822 TCGTTCCTATATTATAAGACGGAGGG 59.399 42.308 10.60 0.00 0.00 4.30
3307 3718 6.600822 CGTTCCTATATTATAAGACGGAGGGA 59.399 42.308 5.24 0.00 0.00 4.20
3308 3719 7.201714 CGTTCCTATATTATAAGACGGAGGGAG 60.202 44.444 5.24 0.00 0.00 4.30
3309 3720 7.281366 TCCTATATTATAAGACGGAGGGAGT 57.719 40.000 5.24 0.00 0.00 3.85
3310 3721 8.397951 TCCTATATTATAAGACGGAGGGAGTA 57.602 38.462 5.24 0.00 0.00 2.59
3311 3722 8.839745 TCCTATATTATAAGACGGAGGGAGTAA 58.160 37.037 5.24 0.00 0.00 2.24
3312 3723 9.643735 CCTATATTATAAGACGGAGGGAGTAAT 57.356 37.037 0.00 0.00 0.00 1.89
3532 3967 0.746659 GGCAATGGATTAAGGCGCTT 59.253 50.000 7.64 0.00 0.00 4.68
3533 3968 1.953686 GGCAATGGATTAAGGCGCTTA 59.046 47.619 7.64 0.85 0.00 3.09
3534 3969 2.360801 GGCAATGGATTAAGGCGCTTAA 59.639 45.455 7.64 10.71 39.73 1.85
3535 3970 3.372060 GCAATGGATTAAGGCGCTTAAC 58.628 45.455 7.64 5.62 38.51 2.01
3536 3971 3.066760 GCAATGGATTAAGGCGCTTAACT 59.933 43.478 7.64 0.00 38.51 2.24
3537 3972 4.440112 GCAATGGATTAAGGCGCTTAACTT 60.440 41.667 7.64 4.41 38.51 2.66
3538 3973 5.650543 CAATGGATTAAGGCGCTTAACTTT 58.349 37.500 7.64 2.36 38.51 2.66
3560 3995 2.038387 TTTGAGGGAGATTAAGGCGC 57.962 50.000 0.00 0.00 0.00 6.53
3583 4018 5.605534 CTTAACTAGCATGTGGAGTAGCAT 58.394 41.667 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 0.933509 GCGTCGTCTGTCAAACTCGT 60.934 55.000 0.00 0.00 0.00 4.18
106 107 1.086067 CAGACGAATGCGGTGATGCT 61.086 55.000 0.00 0.00 43.17 3.79
117 118 4.551388 GTCAGTTCTTGAGTCAGACGAAT 58.449 43.478 0.00 0.00 36.21 3.34
126 127 1.600663 CGAGTGCGTCAGTTCTTGAGT 60.601 52.381 0.00 0.00 36.21 3.41
127 128 1.056103 CGAGTGCGTCAGTTCTTGAG 58.944 55.000 0.00 0.00 36.21 3.02
128 129 3.179433 CGAGTGCGTCAGTTCTTGA 57.821 52.632 0.00 0.00 0.00 3.02
150 152 0.813184 AATCCAATCGTGGCTGCTTG 59.187 50.000 0.00 0.00 45.54 4.01
151 153 1.549203 AAATCCAATCGTGGCTGCTT 58.451 45.000 0.00 0.00 45.54 3.91
153 155 2.423538 AGTAAAATCCAATCGTGGCTGC 59.576 45.455 0.00 0.00 45.54 5.25
154 156 5.116180 TCTAGTAAAATCCAATCGTGGCTG 58.884 41.667 0.00 0.00 45.54 4.85
170 172 9.426534 TGATGGATCTCTGAAATCTTCTAGTAA 57.573 33.333 0.00 0.00 0.00 2.24
177 182 5.633655 AGCTGATGGATCTCTGAAATCTT 57.366 39.130 0.00 0.00 0.00 2.40
191 196 5.464722 CACAACAGTATAGCTAAGCTGATGG 59.535 44.000 26.31 19.09 40.10 3.51
192 197 5.464722 CCACAACAGTATAGCTAAGCTGATG 59.535 44.000 25.25 24.41 40.10 3.07
201 206 2.100197 TCTCGCCACAACAGTATAGCT 58.900 47.619 0.00 0.00 0.00 3.32
233 238 1.039068 CATCACAGATCTCCCGAGCT 58.961 55.000 0.00 0.00 36.03 4.09
234 239 1.035923 TCATCACAGATCTCCCGAGC 58.964 55.000 0.00 0.00 0.00 5.03
235 240 2.095314 CGATCATCACAGATCTCCCGAG 60.095 54.545 0.00 0.00 41.74 4.63
236 241 1.882623 CGATCATCACAGATCTCCCGA 59.117 52.381 0.00 0.00 41.74 5.14
237 242 1.668337 GCGATCATCACAGATCTCCCG 60.668 57.143 0.00 0.00 41.74 5.14
241 246 2.557924 GAGGAGCGATCATCACAGATCT 59.442 50.000 10.88 0.00 41.74 2.75
243 248 1.269174 CGAGGAGCGATCATCACAGAT 59.731 52.381 16.13 0.00 44.57 2.90
244 249 0.665298 CGAGGAGCGATCATCACAGA 59.335 55.000 16.13 0.00 44.57 3.41
246 251 1.066422 GCGAGGAGCGATCATCACA 59.934 57.895 16.13 0.00 44.57 3.58
247 252 3.929389 GCGAGGAGCGATCATCAC 58.071 61.111 16.13 1.25 44.57 3.06
257 262 0.108472 TGAGTTGAGCATGCGAGGAG 60.108 55.000 13.01 0.00 0.00 3.69
258 263 0.321346 TTGAGTTGAGCATGCGAGGA 59.679 50.000 13.01 0.00 0.00 3.71
259 264 0.445436 GTTGAGTTGAGCATGCGAGG 59.555 55.000 13.01 0.00 0.00 4.63
260 265 1.128136 CAGTTGAGTTGAGCATGCGAG 59.872 52.381 13.01 0.00 0.00 5.03
261 266 1.150827 CAGTTGAGTTGAGCATGCGA 58.849 50.000 13.01 0.00 0.00 5.10
262 267 0.453950 GCAGTTGAGTTGAGCATGCG 60.454 55.000 13.01 0.00 0.00 4.73
263 268 0.879765 AGCAGTTGAGTTGAGCATGC 59.120 50.000 10.51 10.51 0.00 4.06
264 269 1.467734 GGAGCAGTTGAGTTGAGCATG 59.532 52.381 0.00 0.00 0.00 4.06
265 270 1.612726 GGGAGCAGTTGAGTTGAGCAT 60.613 52.381 0.00 0.00 0.00 3.79
266 271 0.250467 GGGAGCAGTTGAGTTGAGCA 60.250 55.000 0.00 0.00 0.00 4.26
267 272 0.957888 GGGGAGCAGTTGAGTTGAGC 60.958 60.000 0.00 0.00 0.00 4.26
268 273 0.689623 AGGGGAGCAGTTGAGTTGAG 59.310 55.000 0.00 0.00 0.00 3.02
269 274 1.140312 AAGGGGAGCAGTTGAGTTGA 58.860 50.000 0.00 0.00 0.00 3.18
270 275 1.610522 CAAAGGGGAGCAGTTGAGTTG 59.389 52.381 0.00 0.00 0.00 3.16
271 276 1.479389 CCAAAGGGGAGCAGTTGAGTT 60.479 52.381 0.00 0.00 40.01 3.01
272 277 0.111253 CCAAAGGGGAGCAGTTGAGT 59.889 55.000 0.00 0.00 40.01 3.41
287 292 1.203001 AGGGCTGAAACCGATTCCAAA 60.203 47.619 0.00 0.00 37.22 3.28
290 295 1.657751 GCAGGGCTGAAACCGATTCC 61.658 60.000 0.00 0.00 37.22 3.01
292 297 2.040544 CGCAGGGCTGAAACCGATT 61.041 57.895 0.00 0.00 0.00 3.34
316 321 3.071023 ACGGATTCCAGTTTCAGAGTCAA 59.929 43.478 3.09 0.00 0.00 3.18
363 372 1.032014 GTGTGTGGTGGCACTGAAAT 58.968 50.000 18.45 0.00 39.89 2.17
381 390 2.196925 CGCTAGCTCCAGATCCCGT 61.197 63.158 13.93 0.00 0.00 5.28
389 398 1.144716 CATGCCTTCGCTAGCTCCA 59.855 57.895 13.93 2.82 35.36 3.86
390 399 0.878086 GTCATGCCTTCGCTAGCTCC 60.878 60.000 13.93 0.00 35.36 4.70
391 400 1.211818 CGTCATGCCTTCGCTAGCTC 61.212 60.000 13.93 0.00 35.36 4.09
392 401 1.227089 CGTCATGCCTTCGCTAGCT 60.227 57.895 13.93 0.00 35.36 3.32
394 403 0.872021 GGACGTCATGCCTTCGCTAG 60.872 60.000 18.91 0.00 35.36 3.42
395 404 1.141019 GGACGTCATGCCTTCGCTA 59.859 57.895 18.91 0.00 35.36 4.26
396 405 2.125512 GGACGTCATGCCTTCGCT 60.126 61.111 18.91 0.00 35.36 4.93
403 412 1.573829 TTTCTTGGCGGACGTCATGC 61.574 55.000 18.91 19.61 0.00 4.06
448 460 1.079819 CAGATGGAAGACGCGTGGT 60.080 57.895 20.70 2.86 0.00 4.16
470 485 2.162681 GGGGTGTTCTTTCAGTGGATG 58.837 52.381 0.00 0.00 0.00 3.51
481 496 0.768622 TCCACATTTCGGGGTGTTCT 59.231 50.000 0.00 0.00 33.19 3.01
483 498 0.893727 GCTCCACATTTCGGGGTGTT 60.894 55.000 0.00 0.00 33.19 3.32
485 500 1.303236 TGCTCCACATTTCGGGGTG 60.303 57.895 0.00 0.00 34.82 4.61
533 548 3.322501 TCCATCTGGGAAGCTGCTA 57.677 52.632 0.90 0.00 44.80 3.49
534 549 4.159099 TCCATCTGGGAAGCTGCT 57.841 55.556 0.00 0.00 44.80 4.24
562 577 3.838271 TCACGCGGAGGAGATGCC 61.838 66.667 12.47 0.00 0.00 4.40
563 578 2.583593 GTCACGCGGAGGAGATGC 60.584 66.667 12.47 0.00 0.00 3.91
585 600 1.234821 CCACTTGTTGCTCGGCTTTA 58.765 50.000 0.00 0.00 0.00 1.85
586 601 0.751643 ACCACTTGTTGCTCGGCTTT 60.752 50.000 0.00 0.00 0.00 3.51
587 602 1.152963 ACCACTTGTTGCTCGGCTT 60.153 52.632 0.00 0.00 0.00 4.35
588 603 1.598130 GACCACTTGTTGCTCGGCT 60.598 57.895 0.00 0.00 0.00 5.52
589 604 2.946762 GACCACTTGTTGCTCGGC 59.053 61.111 0.00 0.00 0.00 5.54
590 605 0.670546 ATCGACCACTTGTTGCTCGG 60.671 55.000 0.00 0.00 0.00 4.63
591 606 0.716108 GATCGACCACTTGTTGCTCG 59.284 55.000 0.00 0.00 0.00 5.03
592 607 0.716108 CGATCGACCACTTGTTGCTC 59.284 55.000 10.26 0.00 0.00 4.26
593 608 0.033504 ACGATCGACCACTTGTTGCT 59.966 50.000 24.34 0.00 0.00 3.91
631 654 6.208797 TCAGTGGTCATACTATAATTCCTCCG 59.791 42.308 0.00 0.00 0.00 4.63
649 687 0.830444 TACTTCTGGGCGTCAGTGGT 60.830 55.000 7.56 9.34 43.76 4.16
750 788 0.882474 CCGTGGCCGTATTCCAAAAA 59.118 50.000 0.00 0.00 35.01 1.94
751 789 0.036448 TCCGTGGCCGTATTCCAAAA 59.964 50.000 0.00 0.00 35.01 2.44
752 790 0.391927 CTCCGTGGCCGTATTCCAAA 60.392 55.000 0.00 0.00 35.01 3.28
753 791 1.219664 CTCCGTGGCCGTATTCCAA 59.780 57.895 0.00 0.00 35.01 3.53
754 792 1.672854 CTCTCCGTGGCCGTATTCCA 61.673 60.000 0.00 0.00 0.00 3.53
755 793 1.067582 CTCTCCGTGGCCGTATTCC 59.932 63.158 0.00 0.00 0.00 3.01
756 794 1.067582 CCTCTCCGTGGCCGTATTC 59.932 63.158 0.00 0.00 0.00 1.75
772 810 0.968901 TCGACCGTAGCATTGTCCCT 60.969 55.000 0.00 0.00 0.00 4.20
796 834 1.984321 GACGCCGTCTCTGTCTCTCC 61.984 65.000 10.56 0.00 0.00 3.71
1012 1085 2.586357 GATCGGACCTTCCTGCGC 60.586 66.667 0.00 0.00 33.30 6.09
1013 1086 2.107141 GGATCGGACCTTCCTGCG 59.893 66.667 3.62 0.00 33.30 5.18
1014 1087 1.749334 ATCGGATCGGACCTTCCTGC 61.749 60.000 4.94 0.00 33.30 4.85
1015 1088 0.315568 GATCGGATCGGACCTTCCTG 59.684 60.000 4.94 3.50 33.30 3.86
1024 1097 2.975732 ATGATGGATGATCGGATCGG 57.024 50.000 12.99 0.00 33.17 4.18
1025 1098 3.366719 CGTATGATGGATGATCGGATCG 58.633 50.000 12.99 0.00 33.17 3.69
1030 1103 1.205655 AGGGCGTATGATGGATGATCG 59.794 52.381 0.00 0.00 33.17 3.69
1031 1104 4.626042 GATAGGGCGTATGATGGATGATC 58.374 47.826 4.14 0.00 0.00 2.92
1032 1105 3.068732 CGATAGGGCGTATGATGGATGAT 59.931 47.826 4.14 0.00 0.00 2.45
1033 1106 2.427095 CGATAGGGCGTATGATGGATGA 59.573 50.000 4.14 0.00 0.00 2.92
1060 1136 2.827383 GAAGCCTCTCGTCGCTGCTT 62.827 60.000 9.16 9.16 44.38 3.91
1061 1137 3.349481 GAAGCCTCTCGTCGCTGCT 62.349 63.158 0.00 0.00 34.94 4.24
1091 1167 1.724582 AAACACACGCCCTCTGTTGC 61.725 55.000 0.00 0.00 0.00 4.17
1096 1172 0.738389 CAAACAAACACACGCCCTCT 59.262 50.000 0.00 0.00 0.00 3.69
1098 1174 1.671901 CCCAAACAAACACACGCCCT 61.672 55.000 0.00 0.00 0.00 5.19
1099 1175 1.227118 CCCAAACAAACACACGCCC 60.227 57.895 0.00 0.00 0.00 6.13
1103 1180 0.387565 ATCCGCCCAAACAAACACAC 59.612 50.000 0.00 0.00 0.00 3.82
1284 1362 2.812499 GGGAGCGCGATCCAGTTA 59.188 61.111 40.53 0.00 41.52 2.24
1354 1439 2.521950 CTAGGCTAGCTCCGGGCA 60.522 66.667 15.72 3.17 44.79 5.36
1435 1532 3.810310 ATTAGGAAGCTCCTCGAACTG 57.190 47.619 7.85 0.00 45.66 3.16
1539 1659 2.682136 TTGATGTCCGGCCGGAGA 60.682 61.111 46.28 44.09 46.16 3.71
1738 1859 1.735920 GGCACGCACACAGAGAGAG 60.736 63.158 0.00 0.00 0.00 3.20
2307 2429 2.100631 CGCGTTGGGGAAGTAGCAG 61.101 63.158 0.00 0.00 0.00 4.24
2422 2544 1.288419 TGCGGTGACATTAGTGCGTG 61.288 55.000 0.00 0.00 0.00 5.34
2423 2545 0.391130 ATGCGGTGACATTAGTGCGT 60.391 50.000 0.00 0.00 0.00 5.24
2424 2546 0.301687 GATGCGGTGACATTAGTGCG 59.698 55.000 0.00 0.00 0.00 5.34
2425 2547 0.657840 GGATGCGGTGACATTAGTGC 59.342 55.000 0.00 0.00 0.00 4.40
2465 2587 2.016171 GGAGACCGACGACTAGCTC 58.984 63.158 0.00 0.00 0.00 4.09
2466 2588 4.222105 GGAGACCGACGACTAGCT 57.778 61.111 0.00 0.00 0.00 3.32
2478 2600 0.737715 CAGCCTGCAACTACGGAGAC 60.738 60.000 0.00 0.00 0.00 3.36
2481 2603 2.662596 CCAGCCTGCAACTACGGA 59.337 61.111 0.00 0.00 0.00 4.69
2518 2644 6.552629 CATCTCATGGACACAGAAAATGAAG 58.447 40.000 0.00 0.00 0.00 3.02
2673 3042 0.319728 ACTCAAGCTCGCACAGTGAT 59.680 50.000 4.15 0.00 0.00 3.06
2674 3043 0.104855 AACTCAAGCTCGCACAGTGA 59.895 50.000 4.15 0.00 0.00 3.41
2675 3044 1.723542 CTAACTCAAGCTCGCACAGTG 59.276 52.381 0.00 0.00 0.00 3.66
2881 3275 2.024655 ACACATACTCCCTCCGTTCCTA 60.025 50.000 0.00 0.00 0.00 2.94
2882 3276 1.273098 ACACATACTCCCTCCGTTCCT 60.273 52.381 0.00 0.00 0.00 3.36
2883 3277 1.192428 ACACATACTCCCTCCGTTCC 58.808 55.000 0.00 0.00 0.00 3.62
2884 3278 3.000727 CAAACACATACTCCCTCCGTTC 58.999 50.000 0.00 0.00 0.00 3.95
2885 3279 2.635915 TCAAACACATACTCCCTCCGTT 59.364 45.455 0.00 0.00 0.00 4.44
2886 3280 2.253610 TCAAACACATACTCCCTCCGT 58.746 47.619 0.00 0.00 0.00 4.69
2887 3281 3.458189 GATCAAACACATACTCCCTCCG 58.542 50.000 0.00 0.00 0.00 4.63
2888 3282 3.741388 CGGATCAAACACATACTCCCTCC 60.741 52.174 0.00 0.00 0.00 4.30
2890 3284 2.838202 ACGGATCAAACACATACTCCCT 59.162 45.455 0.00 0.00 0.00 4.20
2891 3285 3.261981 ACGGATCAAACACATACTCCC 57.738 47.619 0.00 0.00 0.00 4.30
2892 3286 5.357257 ACATACGGATCAAACACATACTCC 58.643 41.667 0.00 0.00 0.00 3.85
2893 3287 7.201145 ACTACATACGGATCAAACACATACTC 58.799 38.462 0.00 0.00 0.00 2.59
2895 3289 6.976349 TGACTACATACGGATCAAACACATAC 59.024 38.462 0.00 0.00 0.00 2.39
2896 3290 6.976349 GTGACTACATACGGATCAAACACATA 59.024 38.462 0.00 0.00 0.00 2.29
2897 3291 5.810587 GTGACTACATACGGATCAAACACAT 59.189 40.000 0.00 0.00 0.00 3.21
2898 3292 5.047590 AGTGACTACATACGGATCAAACACA 60.048 40.000 0.00 0.00 0.00 3.72
2899 3293 5.408356 AGTGACTACATACGGATCAAACAC 58.592 41.667 0.00 0.00 0.00 3.32
2903 3297 5.654603 ACAAGTGACTACATACGGATCAA 57.345 39.130 0.00 0.00 0.00 2.57
2904 3298 5.654603 AACAAGTGACTACATACGGATCA 57.345 39.130 0.00 0.00 0.00 2.92
2906 3300 6.032956 TCAAACAAGTGACTACATACGGAT 57.967 37.500 0.00 0.00 0.00 4.18
2907 3301 5.456548 TCAAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 0.00 4.69
2909 3303 6.944557 TGATCAAACAAGTGACTACATACG 57.055 37.500 0.00 0.00 0.00 3.06
2910 3304 9.760660 GAATTGATCAAACAAGTGACTACATAC 57.239 33.333 13.09 0.00 33.22 2.39
2911 3305 8.655970 CGAATTGATCAAACAAGTGACTACATA 58.344 33.333 13.09 0.00 33.22 2.29
2912 3306 7.173218 ACGAATTGATCAAACAAGTGACTACAT 59.827 33.333 13.09 0.00 33.22 2.29
2913 3307 6.481976 ACGAATTGATCAAACAAGTGACTACA 59.518 34.615 13.09 0.00 33.22 2.74
2914 3308 6.888430 ACGAATTGATCAAACAAGTGACTAC 58.112 36.000 13.09 0.00 33.22 2.73
2915 3309 7.654116 TGTACGAATTGATCAAACAAGTGACTA 59.346 33.333 13.09 0.00 33.22 2.59
2916 3310 6.481976 TGTACGAATTGATCAAACAAGTGACT 59.518 34.615 13.09 0.00 33.22 3.41
2917 3311 6.655062 TGTACGAATTGATCAAACAAGTGAC 58.345 36.000 13.09 5.89 33.22 3.67
2918 3312 6.565811 GCTGTACGAATTGATCAAACAAGTGA 60.566 38.462 13.09 2.28 33.22 3.41
2919 3313 5.565259 GCTGTACGAATTGATCAAACAAGTG 59.435 40.000 13.09 1.97 33.22 3.16
2920 3314 5.470098 AGCTGTACGAATTGATCAAACAAGT 59.530 36.000 13.09 12.31 33.22 3.16
2921 3315 5.791974 CAGCTGTACGAATTGATCAAACAAG 59.208 40.000 13.09 7.08 33.22 3.16
2922 3316 5.238432 ACAGCTGTACGAATTGATCAAACAA 59.762 36.000 20.16 0.00 0.00 2.83
2940 3334 0.957395 ATCGGACCAAGCAACAGCTG 60.957 55.000 13.48 13.48 38.93 4.24
2941 3335 0.957395 CATCGGACCAAGCAACAGCT 60.957 55.000 0.00 0.00 41.23 4.24
3017 3414 2.050351 CGCGTCACACCGAGAACT 60.050 61.111 0.00 0.00 0.00 3.01
3043 3440 3.681835 AGCTTCGGTTCGTCGCCT 61.682 61.111 0.00 0.00 0.00 5.52
3110 3521 1.580845 GCATATGCGAGCCCCATGAC 61.581 60.000 12.82 0.00 0.00 3.06
3141 3552 2.674033 TGCATGACACTGGCTGCC 60.674 61.111 12.87 12.87 33.70 4.85
3175 3586 1.177256 GCTCCATGTCCATGATGGGC 61.177 60.000 9.60 9.60 43.98 5.36
3178 3589 1.509703 CTCGCTCCATGTCCATGATG 58.490 55.000 8.82 2.69 41.20 3.07
3211 3622 1.139853 GAGTAGCTAGCTGGGTGCATT 59.860 52.381 27.68 2.24 45.94 3.56
3228 3639 7.122311 ACTCTTATATTATGGGAGAGGGAGT 57.878 40.000 11.87 0.00 38.48 3.85
3229 3640 8.442660 AAACTCTTATATTATGGGAGAGGGAG 57.557 38.462 11.87 0.00 38.48 4.30
3261 3672 9.578439 GGAACGATTTTTATACTAGTGTAGTGT 57.422 33.333 5.39 0.00 39.81 3.55
3262 3673 9.798994 AGGAACGATTTTTATACTAGTGTAGTG 57.201 33.333 5.39 0.00 39.81 2.74
3279 3690 8.684520 CCTCCGTCTTATAATATAGGAACGATT 58.315 37.037 12.25 0.00 0.00 3.34
3280 3691 7.284944 CCCTCCGTCTTATAATATAGGAACGAT 59.715 40.741 12.25 0.00 0.00 3.73
3281 3692 6.600822 CCCTCCGTCTTATAATATAGGAACGA 59.399 42.308 12.25 4.08 0.00 3.85
3282 3693 6.600822 TCCCTCCGTCTTATAATATAGGAACG 59.399 42.308 0.00 1.90 0.00 3.95
3283 3694 7.614974 ACTCCCTCCGTCTTATAATATAGGAAC 59.385 40.741 0.00 0.00 0.00 3.62
3284 3695 7.706674 ACTCCCTCCGTCTTATAATATAGGAA 58.293 38.462 0.00 0.00 0.00 3.36
3285 3696 7.281366 ACTCCCTCCGTCTTATAATATAGGA 57.719 40.000 0.00 0.00 0.00 2.94
3286 3697 9.643735 ATTACTCCCTCCGTCTTATAATATAGG 57.356 37.037 0.00 0.00 0.00 2.57
3291 3702 9.151177 TGTTAATTACTCCCTCCGTCTTATAAT 57.849 33.333 0.00 0.00 0.00 1.28
3292 3703 8.537728 TGTTAATTACTCCCTCCGTCTTATAA 57.462 34.615 0.00 0.00 0.00 0.98
3293 3704 7.232127 CCTGTTAATTACTCCCTCCGTCTTATA 59.768 40.741 0.00 0.00 0.00 0.98
3294 3705 6.041751 CCTGTTAATTACTCCCTCCGTCTTAT 59.958 42.308 0.00 0.00 0.00 1.73
3295 3706 5.361857 CCTGTTAATTACTCCCTCCGTCTTA 59.638 44.000 0.00 0.00 0.00 2.10
3296 3707 4.161754 CCTGTTAATTACTCCCTCCGTCTT 59.838 45.833 0.00 0.00 0.00 3.01
3297 3708 3.705072 CCTGTTAATTACTCCCTCCGTCT 59.295 47.826 0.00 0.00 0.00 4.18
3298 3709 3.740452 GCCTGTTAATTACTCCCTCCGTC 60.740 52.174 0.00 0.00 0.00 4.79
3299 3710 2.169978 GCCTGTTAATTACTCCCTCCGT 59.830 50.000 0.00 0.00 0.00 4.69
3300 3711 2.802057 CGCCTGTTAATTACTCCCTCCG 60.802 54.545 0.00 0.00 0.00 4.63
3301 3712 2.169978 ACGCCTGTTAATTACTCCCTCC 59.830 50.000 0.00 0.00 0.00 4.30
3302 3713 3.195661 CACGCCTGTTAATTACTCCCTC 58.804 50.000 0.00 0.00 0.00 4.30
3303 3714 2.570302 ACACGCCTGTTAATTACTCCCT 59.430 45.455 0.00 0.00 0.00 4.20
3304 3715 2.676342 CACACGCCTGTTAATTACTCCC 59.324 50.000 0.00 0.00 0.00 4.30
3305 3716 2.676342 CCACACGCCTGTTAATTACTCC 59.324 50.000 0.00 0.00 0.00 3.85
3306 3717 3.592059 TCCACACGCCTGTTAATTACTC 58.408 45.455 0.00 0.00 0.00 2.59
3307 3718 3.688694 TCCACACGCCTGTTAATTACT 57.311 42.857 0.00 0.00 0.00 2.24
3308 3719 3.486875 GCATCCACACGCCTGTTAATTAC 60.487 47.826 0.00 0.00 0.00 1.89
3309 3720 2.680841 GCATCCACACGCCTGTTAATTA 59.319 45.455 0.00 0.00 0.00 1.40
3310 3721 1.472480 GCATCCACACGCCTGTTAATT 59.528 47.619 0.00 0.00 0.00 1.40
3311 3722 1.094785 GCATCCACACGCCTGTTAAT 58.905 50.000 0.00 0.00 0.00 1.40
3312 3723 0.250510 TGCATCCACACGCCTGTTAA 60.251 50.000 0.00 0.00 0.00 2.01
3315 3726 1.968017 CTTGCATCCACACGCCTGT 60.968 57.895 0.00 0.00 0.00 4.00
3443 3864 6.144078 TCGAGTAATCAAATAGTGCTAGCA 57.856 37.500 14.93 14.93 0.00 3.49
3444 3865 7.087639 AGATCGAGTAATCAAATAGTGCTAGC 58.912 38.462 8.10 8.10 0.00 3.42
3461 3882 9.529823 TGGACATAGGTTAATATAAGATCGAGT 57.470 33.333 0.00 0.00 0.00 4.18
3474 3895 2.104111 CAGGCCGATGGACATAGGTTAA 59.896 50.000 12.11 0.00 36.18 2.01
3477 3898 1.410850 CCAGGCCGATGGACATAGGT 61.411 60.000 5.01 0.00 43.57 3.08
3542 3977 1.204146 AGCGCCTTAATCTCCCTCAA 58.796 50.000 2.29 0.00 0.00 3.02
3543 3978 1.204146 AAGCGCCTTAATCTCCCTCA 58.796 50.000 2.29 0.00 0.00 3.86
3544 3979 3.132160 GTTAAGCGCCTTAATCTCCCTC 58.868 50.000 2.29 0.00 38.07 4.30
3545 3980 2.772515 AGTTAAGCGCCTTAATCTCCCT 59.227 45.455 2.29 0.00 38.07 4.20
3546 3981 3.195471 AGTTAAGCGCCTTAATCTCCC 57.805 47.619 2.29 0.00 38.07 4.30
3547 3982 3.741856 GCTAGTTAAGCGCCTTAATCTCC 59.258 47.826 2.29 0.00 42.53 3.71
3548 3983 4.975921 GCTAGTTAAGCGCCTTAATCTC 57.024 45.455 2.29 0.00 42.53 2.75
3560 3995 5.011090 TGCTACTCCACATGCTAGTTAAG 57.989 43.478 0.00 0.00 0.00 1.85
3583 4018 3.671008 ACTAAACGTGACCACTATGCA 57.329 42.857 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.