Multiple sequence alignment - TraesCS7D01G149800

Loading Multiple Alignment...

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 TraesCS7D01G149800 chr7D 100.000 8288 0 0 1 8288 98645179 98636892 0.000000e+00 15306.0
1 TraesCS7D01G149800 chr7B 94.647 4054 145 35 507 4521 53652965 53648945 0.000000e+00 6218.0
2 TraesCS7D01G149800 chr7B 93.769 3354 177 18 4587 7915 53648946 53645600 0.000000e+00 5007.0
3 TraesCS7D01G149800 chr7B 94.347 513 22 3 1 508 53653553 53653043 0.000000e+00 780.0
4 TraesCS7D01G149800 chr7B 91.005 378 20 5 7914 8288 53645373 53645007 1.610000e-136 497.0
5 TraesCS7D01G149800 chr7A 94.650 3738 147 32 2930 6655 100764296 100760600 0.000000e+00 5746.0
6 TraesCS7D01G149800 chr7A 88.635 2534 162 68 308 2796 100766898 100764446 0.000000e+00 2968.0
7 TraesCS7D01G149800 chr7A 88.484 1563 107 42 6688 8221 100760606 100759088 0.000000e+00 1821.0
8 TraesCS7D01G149800 chr7A 100.000 33 0 0 8256 8288 100759082 100759050 2.500000e-05 62.1
9 TraesCS7D01G149800 chr2A 85.333 75 9 2 4912 4985 20623428 20623501 8.920000e-10 76.8


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 TraesCS7D01G149800 chr7D 98636892 98645179 8287 True 15306.000 15306 100.00000 1 8288 1 chr7D.!!$R1 8287
1 TraesCS7D01G149800 chr7B 53645007 53653553 8546 True 3125.500 6218 93.44200 1 8288 4 chr7B.!!$R1 8287
2 TraesCS7D01G149800 chr7A 100759050 100766898 7848 True 2649.275 5746 92.94225 308 8288 4 chr7A.!!$R1 7980

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
663 754 0.030638 GAACAAAGCACGTGCCACAT 59.969 50.000 35.51 18.99 43.38 3.21 F
1413 1513 0.250124 TCGGGTTTGTAGCACCACAG 60.250 55.000 0.00 0.00 35.80 3.66 F
1861 1967 0.039798 CGCTGTATCAATGCCCATGC 60.040 55.000 0.00 0.00 38.26 4.06 F
1934 2043 2.239654 CTCAAGCCTCAAGGGTATTCCA 59.760 50.000 0.31 0.00 46.73 3.53 F
2893 3057 2.360600 TGGGGACGAATTTGGGCG 60.361 61.111 0.00 0.00 0.00 6.13 F
3960 4147 0.322187 TCATCACTGCTGTGCTGCAT 60.322 50.000 19.22 6.31 43.49 3.96 F
4585 4839 0.613260 ATCTTTACCACGCTGGCTCA 59.387 50.000 4.23 0.00 42.67 4.26 F
5095 5356 0.251916 CCGTACTGATTCCCAAGGCA 59.748 55.000 0.00 0.00 0.00 4.75 F
6417 6681 0.312729 ACCAAAAAGCGCGTTAAGGG 59.687 50.000 23.31 19.46 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1737 0.034756 TCTGCAAGTAGGCTGCGAAA 59.965 50.000 0.00 0.00 33.76 3.46 R
2660 2796 0.511221 CCACCTAACAAGACGTTGCG 59.489 55.000 0.00 0.00 38.63 4.85 R
2940 3122 0.741221 CTTGAAGCCACTCGGTAGCC 60.741 60.000 0.00 0.00 33.28 3.93 R
2945 3127 1.002087 AGTTACCTTGAAGCCACTCGG 59.998 52.381 0.00 0.00 0.00 4.63 R
4569 4823 0.036164 ACATGAGCCAGCGTGGTAAA 59.964 50.000 0.00 0.00 40.46 2.01 R
4796 5050 1.112916 TGACCACCGAGCTCTGAACA 61.113 55.000 12.54 5.29 0.00 3.18 R
5449 5710 1.600636 CAAGGGCTTTCTGTGCGGA 60.601 57.895 0.00 0.00 0.00 5.54 R
6994 7265 0.652592 CTTATGGACAGGCGCGAAAG 59.347 55.000 12.10 0.00 0.00 2.62 R
7749 8060 0.593263 CCGTCGTACGCCCTGATAAC 60.593 60.000 11.24 0.00 40.91 1.89 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
37 38 6.475727 ACAAGGATATTTTCACTACGACATCG 59.524 38.462 0.00 0.00 46.33 3.84
43 44 9.229784 GATATTTTCACTACGACATCGAAGTTA 57.770 33.333 8.54 0.00 43.02 2.24
98 99 2.042464 TGGCCACCTAAAATGCACAAA 58.958 42.857 0.00 0.00 0.00 2.83
110 111 7.327032 CCTAAAATGCACAAAACTAAGCTCTTC 59.673 37.037 0.00 0.00 0.00 2.87
220 221 6.633500 TTGATATTGGCTTTACTGGCATAC 57.367 37.500 0.00 0.00 42.07 2.39
221 222 4.754618 TGATATTGGCTTTACTGGCATACG 59.245 41.667 0.00 0.00 42.07 3.06
223 224 2.018542 TGGCTTTACTGGCATACGAC 57.981 50.000 0.00 0.00 37.59 4.34
235 236 1.403249 GCATACGACGTGGGTTGTACT 60.403 52.381 11.56 0.00 43.93 2.73
236 237 2.256174 CATACGACGTGGGTTGTACTG 58.744 52.381 11.56 0.00 43.93 2.74
260 261 6.485313 TGACACTTGGACCTTGTGTTTTATAG 59.515 38.462 19.04 0.00 43.81 1.31
262 263 7.057894 ACACTTGGACCTTGTGTTTTATAGAA 58.942 34.615 14.45 0.00 41.45 2.10
268 269 7.236019 TGGACCTTGTGTTTTATAGAAGTCCTA 59.764 37.037 0.00 0.00 0.00 2.94
332 338 0.673644 CCAAAGAGGCACCGACGAAT 60.674 55.000 0.00 0.00 0.00 3.34
396 402 8.596293 TCATTTAAATGAAAGGAGCTCCAATTT 58.404 29.630 33.90 28.80 42.11 1.82
597 685 1.303317 AAAGCCCAAGTAGCCACCG 60.303 57.895 0.00 0.00 0.00 4.94
601 689 1.740296 CCCAAGTAGCCACCGTTCG 60.740 63.158 0.00 0.00 0.00 3.95
663 754 0.030638 GAACAAAGCACGTGCCACAT 59.969 50.000 35.51 18.99 43.38 3.21
1069 1167 2.099921 CACAGGAGGATAGAGTTCCACG 59.900 54.545 0.00 0.00 38.32 4.94
1070 1168 1.067821 CAGGAGGATAGAGTTCCACGC 59.932 57.143 0.00 0.00 38.32 5.34
1071 1169 1.063567 AGGAGGATAGAGTTCCACGCT 60.064 52.381 0.00 0.00 38.32 5.07
1303 1401 2.850647 GCAAATTCGCAGCTCTGATTTC 59.149 45.455 0.29 0.00 0.00 2.17
1340 1440 8.908786 TCTTAAAGCTGTGATATTTGATAGGG 57.091 34.615 0.00 0.00 0.00 3.53
1341 1441 7.939039 TCTTAAAGCTGTGATATTTGATAGGGG 59.061 37.037 0.00 0.00 0.00 4.79
1342 1442 4.647564 AGCTGTGATATTTGATAGGGGG 57.352 45.455 0.00 0.00 0.00 5.40
1343 1443 3.983410 AGCTGTGATATTTGATAGGGGGT 59.017 43.478 0.00 0.00 0.00 4.95
1344 1444 4.416848 AGCTGTGATATTTGATAGGGGGTT 59.583 41.667 0.00 0.00 0.00 4.11
1345 1445 5.103515 AGCTGTGATATTTGATAGGGGGTTT 60.104 40.000 0.00 0.00 0.00 3.27
1388 1488 1.153127 TGTTTGGACGCCGGAGTTT 60.153 52.632 13.57 0.00 0.00 2.66
1390 1490 0.382873 GTTTGGACGCCGGAGTTTTT 59.617 50.000 13.57 0.00 0.00 1.94
1402 1502 4.231439 CCGGAGTTTTTAATTCGGGTTTG 58.769 43.478 0.00 0.00 34.54 2.93
1405 1505 6.081693 CGGAGTTTTTAATTCGGGTTTGTAG 58.918 40.000 0.00 0.00 0.00 2.74
1408 1508 6.210796 AGTTTTTAATTCGGGTTTGTAGCAC 58.789 36.000 0.00 0.00 0.00 4.40
1413 1513 0.250124 TCGGGTTTGTAGCACCACAG 60.250 55.000 0.00 0.00 35.80 3.66
1450 1554 6.971184 GCTCGTACTAGTTAGTAAAAGATGCA 59.029 38.462 0.00 0.00 40.20 3.96
1465 1569 4.859304 AGATGCACAGAATTTGCTTCAA 57.141 36.364 15.08 0.00 43.31 2.69
1528 1632 1.538047 TTCAGCTTGTGATGCCCTTC 58.462 50.000 0.00 0.00 34.17 3.46
1529 1633 0.401356 TCAGCTTGTGATGCCCTTCA 59.599 50.000 0.00 0.00 0.00 3.02
1530 1634 1.202915 TCAGCTTGTGATGCCCTTCAA 60.203 47.619 0.00 0.00 0.00 2.69
1532 1636 2.232941 CAGCTTGTGATGCCCTTCAAAT 59.767 45.455 0.00 0.00 0.00 2.32
1536 1641 1.820519 TGTGATGCCCTTCAAATGCTC 59.179 47.619 0.00 0.00 0.00 4.26
1541 1646 3.598019 TGCCCTTCAAATGCTCAAATC 57.402 42.857 0.00 0.00 0.00 2.17
1632 1737 1.585006 CTTGACGTACACGGAGCCT 59.415 57.895 6.72 0.00 44.95 4.58
1757 1862 2.754552 GTTGCATCAGGCTTGTGGATTA 59.245 45.455 0.00 0.00 45.15 1.75
1842 1948 7.771826 TGTAAAAGGTATATGGCTTGGTTCTAC 59.228 37.037 0.00 0.00 0.00 2.59
1861 1967 0.039798 CGCTGTATCAATGCCCATGC 60.040 55.000 0.00 0.00 38.26 4.06
1865 1971 3.748083 CTGTATCAATGCCCATGCTACT 58.252 45.455 0.00 0.00 38.71 2.57
1878 1984 6.270000 TGCCCATGCTACTACTACTTGAATAT 59.730 38.462 0.00 0.00 38.71 1.28
1907 2016 5.305585 TCACTTCCAAAGACAACCATACTC 58.694 41.667 0.00 0.00 0.00 2.59
1934 2043 2.239654 CTCAAGCCTCAAGGGTATTCCA 59.760 50.000 0.31 0.00 46.73 3.53
1992 2104 3.540359 GCTTGAATCACGTTCGAATCGAG 60.540 47.826 21.26 14.34 39.80 4.04
1993 2105 3.481112 TGAATCACGTTCGAATCGAGA 57.519 42.857 21.26 19.04 39.80 4.04
1994 2106 3.828786 TGAATCACGTTCGAATCGAGAA 58.171 40.909 21.26 10.02 39.80 2.87
2056 2168 5.624509 CGTTTATCATCCACTGGAGAAGTCA 60.625 44.000 3.62 0.00 36.83 3.41
2186 2299 4.691216 GGAACAGGTATCAAGTCAGTTGTC 59.309 45.833 0.00 0.00 37.43 3.18
2217 2330 5.912892 TCTTATCACTGCATCGAATAACCA 58.087 37.500 0.00 0.00 0.00 3.67
2379 2501 7.637511 ACTCCCTCTATTTGAAAGATGTGAAT 58.362 34.615 0.00 0.00 0.00 2.57
2394 2516 8.969260 AAGATGTGAATCTACAATCAGCATTA 57.031 30.769 0.00 0.00 33.69 1.90
2583 2719 3.895232 TCACTCTTGTATCCTTCTGGC 57.105 47.619 0.00 0.00 0.00 4.85
2590 2726 2.421725 TGTATCCTTCTGGCCCATGAT 58.578 47.619 0.00 0.00 0.00 2.45
2660 2796 5.462398 CGAGGGAGTAAATTGCACTACATAC 59.538 44.000 5.33 0.00 0.00 2.39
2673 2809 3.427528 CACTACATACGCAACGTCTTGTT 59.572 43.478 12.01 0.00 41.54 2.83
2753 2889 3.818961 AAATGTTGCGTGTCTGATCAG 57.181 42.857 17.07 17.07 0.00 2.90
2783 2919 5.381174 TTGAGTGGCAAGAAATGAGAATG 57.619 39.130 0.00 0.00 31.55 2.67
2893 3057 2.360600 TGGGGACGAATTTGGGCG 60.361 61.111 0.00 0.00 0.00 6.13
2940 3122 7.290842 GGTGCATTCACTTGTATAATATGTCG 58.709 38.462 0.00 0.00 42.72 4.35
2945 3127 8.648097 CATTCACTTGTATAATATGTCGGCTAC 58.352 37.037 0.00 0.00 0.00 3.58
2962 3144 1.822990 CTACCGAGTGGCTTCAAGGTA 59.177 52.381 0.00 0.00 39.70 3.08
3055 3239 7.573469 GCACACACTTTTACGGTTTTATCCATA 60.573 37.037 0.00 0.00 0.00 2.74
3083 3267 3.710209 AGAAGCTGATACTGCCAACTT 57.290 42.857 0.00 0.00 0.00 2.66
3104 3289 1.901464 CACTCCAAAACCCACCCCG 60.901 63.158 0.00 0.00 0.00 5.73
3139 3324 1.895131 CACCAGGGCTGCTTTACATTT 59.105 47.619 0.00 0.00 0.00 2.32
3159 3344 8.133024 ACATTTATAACTGAAAATGGAAGCCA 57.867 30.769 9.59 0.00 43.96 4.75
3160 3345 8.253113 ACATTTATAACTGAAAATGGAAGCCAG 58.747 33.333 9.59 0.00 43.96 4.85
3227 3412 2.285756 TCACGAAACTGTGCCTTTTACG 59.714 45.455 0.00 0.00 39.73 3.18
3231 3416 3.124636 CGAAACTGTGCCTTTTACGCTAT 59.875 43.478 0.00 0.00 0.00 2.97
3232 3417 4.327898 CGAAACTGTGCCTTTTACGCTATA 59.672 41.667 0.00 0.00 0.00 1.31
3233 3418 5.541098 AAACTGTGCCTTTTACGCTATAC 57.459 39.130 0.00 0.00 0.00 1.47
3234 3419 4.467198 ACTGTGCCTTTTACGCTATACT 57.533 40.909 0.00 0.00 0.00 2.12
3235 3420 4.828829 ACTGTGCCTTTTACGCTATACTT 58.171 39.130 0.00 0.00 0.00 2.24
3236 3421 4.630069 ACTGTGCCTTTTACGCTATACTTG 59.370 41.667 0.00 0.00 0.00 3.16
3237 3422 4.823157 TGTGCCTTTTACGCTATACTTGA 58.177 39.130 0.00 0.00 0.00 3.02
3336 3523 7.445096 TCTGCATTTGTTCTATTCTTCTGTTGA 59.555 33.333 0.00 0.00 0.00 3.18
3362 3549 8.644318 AGCTAACAGTAATTTCAATACCTACG 57.356 34.615 0.00 0.00 0.00 3.51
3367 3554 9.709495 AACAGTAATTTCAATACCTACGTACAA 57.291 29.630 0.00 0.00 0.00 2.41
3424 3611 5.241728 ACATACTCCCTGTTTTCAGCTTTTC 59.758 40.000 0.00 0.00 45.76 2.29
3508 3695 1.734465 GTACTGCTGGATTCTGTGCAC 59.266 52.381 10.75 10.75 0.00 4.57
3732 3919 3.329743 TCTCGTAGCTTCCGTAATTCG 57.670 47.619 0.00 0.00 39.52 3.34
3861 4048 6.317391 AGAGCTTAGTTCACAGAATATTTGGC 59.683 38.462 0.00 0.00 0.00 4.52
3952 4139 4.473199 CATTTCTGTTGTCATCACTGCTG 58.527 43.478 0.00 0.00 0.00 4.41
3959 4146 1.071814 TCATCACTGCTGTGCTGCA 59.928 52.632 19.22 0.00 43.49 4.41
3960 4147 0.322187 TCATCACTGCTGTGCTGCAT 60.322 50.000 19.22 6.31 43.49 3.96
4178 4365 9.696917 AGCAAAGAAAAGGTTTACAATTGATAG 57.303 29.630 13.59 0.00 0.00 2.08
4506 4693 2.291735 TGGGATGTGGCACAATCTTGAT 60.292 45.455 25.95 5.79 44.16 2.57
4521 4775 6.996879 ACAATCTTGATGATAATCAGGTCTGG 59.003 38.462 2.25 0.00 34.45 3.86
4522 4776 6.760440 ATCTTGATGATAATCAGGTCTGGT 57.240 37.500 2.25 0.00 32.79 4.00
4523 4777 7.862274 ATCTTGATGATAATCAGGTCTGGTA 57.138 36.000 2.25 0.00 32.79 3.25
4524 4778 7.862274 TCTTGATGATAATCAGGTCTGGTAT 57.138 36.000 2.25 0.00 31.46 2.73
4525 4779 8.956446 TCTTGATGATAATCAGGTCTGGTATA 57.044 34.615 2.25 0.00 31.46 1.47
4526 4780 9.379770 TCTTGATGATAATCAGGTCTGGTATAA 57.620 33.333 2.25 0.00 31.46 0.98
4527 4781 9.650539 CTTGATGATAATCAGGTCTGGTATAAG 57.349 37.037 0.00 0.00 31.46 1.73
4528 4782 8.956446 TGATGATAATCAGGTCTGGTATAAGA 57.044 34.615 0.00 0.00 0.00 2.10
4529 4783 9.552695 TGATGATAATCAGGTCTGGTATAAGAT 57.447 33.333 0.00 0.00 0.00 2.40
4531 4785 8.956446 TGATAATCAGGTCTGGTATAAGATCA 57.044 34.615 0.00 0.00 28.97 2.92
4532 4786 9.029368 TGATAATCAGGTCTGGTATAAGATCAG 57.971 37.037 0.00 0.00 28.97 2.90
4533 4787 9.249053 GATAATCAGGTCTGGTATAAGATCAGA 57.751 37.037 0.00 0.00 35.45 3.27
4534 4788 7.921041 AATCAGGTCTGGTATAAGATCAGAA 57.079 36.000 0.00 0.00 38.97 3.02
4535 4789 8.503428 AATCAGGTCTGGTATAAGATCAGAAT 57.497 34.615 0.00 0.00 38.97 2.40
4536 4790 7.921041 TCAGGTCTGGTATAAGATCAGAATT 57.079 36.000 0.00 0.00 38.97 2.17
4537 4791 8.324191 TCAGGTCTGGTATAAGATCAGAATTT 57.676 34.615 0.00 0.00 38.97 1.82
4538 4792 8.772250 TCAGGTCTGGTATAAGATCAGAATTTT 58.228 33.333 0.00 0.00 38.97 1.82
4552 4806 9.566432 AGATCAGAATTTTACTCTTCTTTGTGT 57.434 29.630 0.00 0.00 29.34 3.72
4553 4807 9.604626 GATCAGAATTTTACTCTTCTTTGTGTG 57.395 33.333 0.00 0.00 29.34 3.82
4554 4808 7.930217 TCAGAATTTTACTCTTCTTTGTGTGG 58.070 34.615 0.00 0.00 29.34 4.17
4555 4809 7.556275 TCAGAATTTTACTCTTCTTTGTGTGGT 59.444 33.333 0.00 0.00 29.34 4.16
4556 4810 8.190784 CAGAATTTTACTCTTCTTTGTGTGGTT 58.809 33.333 0.00 0.00 29.34 3.67
4557 4811 8.749354 AGAATTTTACTCTTCTTTGTGTGGTTT 58.251 29.630 0.00 0.00 0.00 3.27
4563 4817 9.616156 TTACTCTTCTTTGTGTGGTTTATAACA 57.384 29.630 0.00 0.00 0.00 2.41
4564 4818 7.927048 ACTCTTCTTTGTGTGGTTTATAACAC 58.073 34.615 0.00 0.00 45.55 3.32
4565 4819 7.773690 ACTCTTCTTTGTGTGGTTTATAACACT 59.226 33.333 2.97 0.00 45.55 3.55
4566 4820 9.268268 CTCTTCTTTGTGTGGTTTATAACACTA 57.732 33.333 2.97 0.00 45.55 2.74
4567 4821 9.787435 TCTTCTTTGTGTGGTTTATAACACTAT 57.213 29.630 2.97 0.00 45.55 2.12
4569 4823 9.787435 TTCTTTGTGTGGTTTATAACACTATCT 57.213 29.630 2.97 0.00 45.55 1.98
4570 4824 9.787435 TCTTTGTGTGGTTTATAACACTATCTT 57.213 29.630 2.97 0.00 45.55 2.40
4574 4828 9.439500 TGTGTGGTTTATAACACTATCTTTACC 57.561 33.333 2.97 0.00 45.55 2.85
4575 4829 9.439500 GTGTGGTTTATAACACTATCTTTACCA 57.561 33.333 2.97 0.00 42.72 3.25
4577 4831 8.598075 GTGGTTTATAACACTATCTTTACCACG 58.402 37.037 11.14 0.00 41.39 4.94
4578 4832 7.278424 TGGTTTATAACACTATCTTTACCACGC 59.722 37.037 0.00 0.00 0.00 5.34
4579 4833 7.493645 GGTTTATAACACTATCTTTACCACGCT 59.506 37.037 0.00 0.00 0.00 5.07
4580 4834 7.997107 TTATAACACTATCTTTACCACGCTG 57.003 36.000 0.00 0.00 0.00 5.18
4581 4835 3.247006 ACACTATCTTTACCACGCTGG 57.753 47.619 2.92 2.92 45.02 4.85
4582 4836 1.933853 CACTATCTTTACCACGCTGGC 59.066 52.381 4.23 0.00 42.67 4.85
4583 4837 1.831736 ACTATCTTTACCACGCTGGCT 59.168 47.619 4.23 0.00 42.67 4.75
4584 4838 2.159085 ACTATCTTTACCACGCTGGCTC 60.159 50.000 4.23 0.00 42.67 4.70
4585 4839 0.613260 ATCTTTACCACGCTGGCTCA 59.387 50.000 4.23 0.00 42.67 4.26
4586 4840 0.613260 TCTTTACCACGCTGGCTCAT 59.387 50.000 4.23 0.00 42.67 2.90
4587 4841 0.729116 CTTTACCACGCTGGCTCATG 59.271 55.000 4.23 0.00 42.67 3.07
4796 5050 7.573710 TGTTATGGCATCCTTAATTCTACAGT 58.426 34.615 1.65 0.00 0.00 3.55
4854 5115 8.519492 TTTTTGCTTGTTCTAATTAGTGATGC 57.481 30.769 12.19 11.28 0.00 3.91
5095 5356 0.251916 CCGTACTGATTCCCAAGGCA 59.748 55.000 0.00 0.00 0.00 4.75
5250 5511 5.732331 ACAAAATGATCCCTGGGAAGATA 57.268 39.130 21.42 6.78 34.34 1.98
5314 5575 4.543590 AAATCGAGTGGTCTGACATCTT 57.456 40.909 10.38 0.00 0.00 2.40
5449 5710 0.550914 TCAAAACAGTGTCCTGCCCT 59.449 50.000 0.00 0.00 42.81 5.19
5536 5797 6.876257 AGTTGCTTCAAGTAGTCATAAAGAGG 59.124 38.462 0.00 0.00 0.00 3.69
5605 5866 1.340889 TGTCATTGCAGGAACCAAAGC 59.659 47.619 0.00 0.00 0.00 3.51
5971 6232 1.998315 CTCTCAAGCAAGATGACCACG 59.002 52.381 0.00 0.00 0.00 4.94
5990 6251 2.029290 ACGTAGTGAAGGCTTTGACGAT 60.029 45.455 22.29 10.17 42.51 3.73
6047 6308 6.390048 TCTCTCTCCCTTGTTAGAGAAGTA 57.610 41.667 3.85 0.00 45.69 2.24
6193 6454 4.646492 ACATTTGTGCAGAAGGAGAAAACT 59.354 37.500 0.00 0.00 32.38 2.66
6389 6650 8.748380 ATTATCACTAAAGCAACAAAAGAAGC 57.252 30.769 0.00 0.00 0.00 3.86
6390 6651 4.597079 TCACTAAAGCAACAAAAGAAGCG 58.403 39.130 0.00 0.00 0.00 4.68
6417 6681 0.312729 ACCAAAAAGCGCGTTAAGGG 59.687 50.000 23.31 19.46 0.00 3.95
6635 6902 4.576463 GTGATGATAACATGACCAGGAACC 59.424 45.833 0.00 0.00 35.24 3.62
6638 6905 3.118775 TGATAACATGACCAGGAACCGAG 60.119 47.826 0.00 0.00 0.00 4.63
6698 6965 7.400339 AGTTGGGTTCAATCTCTTCTACAGATA 59.600 37.037 0.00 0.00 35.10 1.98
6781 7048 1.298014 CACAGAGGACTTGAGGGCC 59.702 63.158 0.00 0.00 45.71 5.80
6794 7061 1.188863 GAGGGCCGAAGTTACTGGTA 58.811 55.000 0.00 0.00 0.00 3.25
6808 7075 8.465273 AAGTTACTGGTAAGCAATTCTCTTTT 57.535 30.769 0.00 0.00 0.00 2.27
6994 7265 1.002430 TGCTGGATGAGTGGTGAGTTC 59.998 52.381 0.00 0.00 0.00 3.01
7006 7277 1.069090 TGAGTTCTTTCGCGCCTGT 59.931 52.632 0.00 0.00 0.00 4.00
7051 7322 4.982241 TCTGAATCCTGGTCTTTTCTGT 57.018 40.909 0.00 0.00 0.00 3.41
7057 7328 0.955919 CTGGTCTTTTCTGTCCGGGC 60.956 60.000 0.00 0.00 0.00 6.13
7101 7372 5.180271 TGAACTTACCATCCATTCGGTTAC 58.820 41.667 0.00 0.00 36.69 2.50
7149 7420 1.001378 CGTGGAAAGGCAAAGAAGGTG 60.001 52.381 0.00 0.00 0.00 4.00
7170 7441 1.067495 AGGAAAGCGAAGGAAGACGAG 60.067 52.381 0.00 0.00 0.00 4.18
7288 7559 3.111939 CCAGACCGAGTCGCTAGG 58.888 66.667 7.12 2.04 37.67 3.02
7303 7575 1.646189 CTAGGCTTGCCGAAAGAGAC 58.354 55.000 5.95 0.00 38.24 3.36
7335 7607 3.018149 GGCTCCGTAGAAAGAGAAGAGA 58.982 50.000 0.00 0.00 0.00 3.10
7367 7639 4.915704 TGTATCGCCCATTTTTCGAAATC 58.084 39.130 12.12 0.00 35.77 2.17
7557 7835 4.637483 TTTGTTCTTGTTTCTCCAGCAG 57.363 40.909 0.00 0.00 0.00 4.24
7572 7850 7.066307 TCTCCAGCAGCATAGTTATGATTTA 57.934 36.000 3.38 0.00 35.75 1.40
7609 7887 9.979578 ATATGAGTTCTATTTTCTCTAGCAGTG 57.020 33.333 0.00 0.00 0.00 3.66
7615 7893 8.883731 GTTCTATTTTCTCTAGCAGTGCAATTA 58.116 33.333 19.20 0.00 0.00 1.40
7621 7899 8.560355 TTTCTCTAGCAGTGCAATTATTTGTA 57.440 30.769 19.20 0.00 35.17 2.41
7624 7902 4.019919 AGCAGTGCAATTATTTGTAGCG 57.980 40.909 19.20 0.00 35.17 4.26
7631 7909 5.459762 GTGCAATTATTTGTAGCGATGCAAT 59.540 36.000 4.72 0.00 43.30 3.56
7632 7910 6.019640 GTGCAATTATTTGTAGCGATGCAATT 60.020 34.615 4.72 4.56 43.30 2.32
7637 7918 9.748708 AATTATTTGTAGCGATGCAATTGTATT 57.251 25.926 10.53 4.39 0.00 1.89
7641 7922 5.809464 TGTAGCGATGCAATTGTATTTCTG 58.191 37.500 10.53 3.18 0.00 3.02
7642 7923 4.297299 AGCGATGCAATTGTATTTCTGG 57.703 40.909 10.53 0.48 0.00 3.86
7645 7953 4.970003 GCGATGCAATTGTATTTCTGGTAC 59.030 41.667 10.53 0.00 0.00 3.34
7664 7972 4.508124 GGTACGGTAGAAATGCAGAATCAG 59.492 45.833 0.00 0.00 0.00 2.90
7674 7982 7.588512 AGAAATGCAGAATCAGTCTTGTAAAC 58.411 34.615 0.00 0.00 32.70 2.01
7677 7988 5.368145 TGCAGAATCAGTCTTGTAAACTGT 58.632 37.500 3.45 0.00 43.68 3.55
7683 7994 5.229921 TCAGTCTTGTAAACTGTTTGCAC 57.770 39.130 21.03 11.66 43.68 4.57
7749 8060 3.820467 TCTTGTCTGCTGTGTTTAATGGG 59.180 43.478 0.00 0.00 0.00 4.00
7754 8065 5.414454 TGTCTGCTGTGTTTAATGGGTTATC 59.586 40.000 0.00 0.00 0.00 1.75
7769 8080 0.747644 TTATCAGGGCGTACGACGGA 60.748 55.000 21.65 17.98 42.82 4.69
7872 8186 2.596452 GATAGTGGTATGATCGTGCGG 58.404 52.381 0.00 0.00 0.00 5.69
7874 8188 0.535335 AGTGGTATGATCGTGCGGTT 59.465 50.000 0.00 0.00 0.00 4.44
7921 8463 1.427435 GCGCTATCTCTTCCATCTGC 58.573 55.000 0.00 0.00 0.00 4.26
7997 8539 4.024048 TGAAGAGAAGTTCAAACCGAATGC 60.024 41.667 5.50 0.00 35.63 3.56
8000 8542 5.305585 AGAGAAGTTCAAACCGAATGCTTA 58.694 37.500 5.50 0.00 35.63 3.09
8001 8543 5.409826 AGAGAAGTTCAAACCGAATGCTTAG 59.590 40.000 5.50 0.00 35.63 2.18
8002 8544 3.831715 AGTTCAAACCGAATGCTTAGC 57.168 42.857 0.00 0.00 35.63 3.09
8006 8549 0.035820 AAACCGAATGCTTAGCCCGA 60.036 50.000 0.29 0.00 0.00 5.14
8011 8554 1.002468 CGAATGCTTAGCCCGAAATGG 60.002 52.381 0.29 0.00 37.55 3.16
8029 8572 5.413309 AATGGAATTTACGGCCAATTTCA 57.587 34.783 9.76 9.76 34.30 2.69
8056 8599 6.353323 TGAATTTCGGTGGAATATAGCTTCA 58.647 36.000 0.00 0.00 30.88 3.02
8064 8609 5.348986 GTGGAATATAGCTTCACTTCGACA 58.651 41.667 0.00 0.00 0.00 4.35
8075 8620 3.804036 TCACTTCGACACAAATTCAGGT 58.196 40.909 0.00 0.00 0.00 4.00
8126 8671 1.852626 AGGCCTAGCAAACCCAGGT 60.853 57.895 1.29 0.00 0.00 4.00
8189 8735 1.987770 CGAATTCACAACCATGCAAGC 59.012 47.619 6.22 0.00 0.00 4.01
8196 8743 1.542915 ACAACCATGCAAGCTGATGAC 59.457 47.619 0.00 0.00 0.00 3.06
8213 8760 5.190677 TGATGACATCTGAGCACATTTCAT 58.809 37.500 16.25 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 7.837202 TTCGGTTGAATCGTGAAATATAGTT 57.163 32.000 0.00 0.00 0.00 2.24
91 92 5.574891 TTTGAAGAGCTTAGTTTTGTGCA 57.425 34.783 0.00 0.00 0.00 4.57
98 99 4.823989 ACACATGCTTTGAAGAGCTTAGTT 59.176 37.500 0.00 0.00 43.11 2.24
220 221 0.031043 TGTCAGTACAACCCACGTCG 59.969 55.000 0.00 0.00 30.91 5.12
221 222 1.068127 AGTGTCAGTACAACCCACGTC 59.932 52.381 0.00 0.00 37.36 4.34
223 224 1.864711 CAAGTGTCAGTACAACCCACG 59.135 52.381 0.00 0.00 37.36 4.94
235 236 2.799126 AACACAAGGTCCAAGTGTCA 57.201 45.000 16.77 0.00 44.99 3.58
236 237 5.767816 ATAAAACACAAGGTCCAAGTGTC 57.232 39.130 16.77 0.00 44.99 3.67
260 261 8.857098 TGGTACTTCATGTGTATATAGGACTTC 58.143 37.037 0.00 0.00 0.00 3.01
262 263 8.958060 ATGGTACTTCATGTGTATATAGGACT 57.042 34.615 0.00 0.00 0.00 3.85
396 402 3.215151 TCAACCGGCTATTTGTTTGACA 58.785 40.909 0.00 0.00 0.00 3.58
409 416 0.099436 GACTGCATTGATCAACCGGC 59.901 55.000 11.07 14.95 0.00 6.13
597 685 4.804496 GAGGAGAGCTGCTCGAAC 57.196 61.111 22.77 16.53 44.91 3.95
601 689 0.687427 AAGGAGGAGGAGAGCTGCTC 60.687 60.000 21.72 21.72 45.76 4.26
663 754 2.237143 GGTGATCTGGAGTGTTGGATCA 59.763 50.000 0.00 0.00 41.16 2.92
705 796 1.595382 CGAATGGACGGCTGGGATC 60.595 63.158 0.00 0.00 0.00 3.36
865 962 2.159819 ATCCGGGGCTTCGATCGATG 62.160 60.000 20.18 21.69 0.00 3.84
1303 1401 2.989422 CTTTAAGAGCACAAACCCCG 57.011 50.000 0.00 0.00 0.00 5.73
1330 1430 1.687996 CGCCCAAACCCCCTATCAAAT 60.688 52.381 0.00 0.00 0.00 2.32
1333 1433 0.991355 ATCGCCCAAACCCCCTATCA 60.991 55.000 0.00 0.00 0.00 2.15
1334 1434 1.003233 CTATCGCCCAAACCCCCTATC 59.997 57.143 0.00 0.00 0.00 2.08
1335 1435 1.064825 CTATCGCCCAAACCCCCTAT 58.935 55.000 0.00 0.00 0.00 2.57
1336 1436 0.030909 TCTATCGCCCAAACCCCCTA 60.031 55.000 0.00 0.00 0.00 3.53
1337 1437 1.307517 TCTATCGCCCAAACCCCCT 60.308 57.895 0.00 0.00 0.00 4.79
1338 1438 1.148498 CTCTATCGCCCAAACCCCC 59.852 63.158 0.00 0.00 0.00 5.40
1339 1439 1.526225 GCTCTATCGCCCAAACCCC 60.526 63.158 0.00 0.00 0.00 4.95
1340 1440 0.815615 CAGCTCTATCGCCCAAACCC 60.816 60.000 0.00 0.00 0.00 4.11
1341 1441 1.440145 GCAGCTCTATCGCCCAAACC 61.440 60.000 0.00 0.00 0.00 3.27
1342 1442 0.462759 AGCAGCTCTATCGCCCAAAC 60.463 55.000 0.00 0.00 0.00 2.93
1343 1443 1.119684 TAGCAGCTCTATCGCCCAAA 58.880 50.000 0.00 0.00 0.00 3.28
1344 1444 1.001293 CATAGCAGCTCTATCGCCCAA 59.999 52.381 0.00 0.00 35.86 4.12
1345 1445 0.605083 CATAGCAGCTCTATCGCCCA 59.395 55.000 0.00 0.00 35.86 5.36
1388 1488 4.023021 GTGGTGCTACAAACCCGAATTAAA 60.023 41.667 0.00 0.00 36.83 1.52
1390 1490 3.075884 GTGGTGCTACAAACCCGAATTA 58.924 45.455 0.00 0.00 36.83 1.40
1402 1502 4.154195 CCTAAAATCACACTGTGGTGCTAC 59.846 45.833 13.09 0.00 46.57 3.58
1405 1505 2.351738 GCCTAAAATCACACTGTGGTGC 60.352 50.000 13.09 0.00 46.57 5.01
1408 1508 2.416547 CGAGCCTAAAATCACACTGTGG 59.583 50.000 13.09 1.42 33.87 4.17
1413 1513 5.648572 ACTAGTACGAGCCTAAAATCACAC 58.351 41.667 2.52 0.00 0.00 3.82
1450 1554 5.467735 GGCAATTCTTTGAAGCAAATTCTGT 59.532 36.000 0.00 0.00 38.83 3.41
1465 1569 7.628769 AAAACACAAAGAAATGGCAATTCTT 57.371 28.000 21.76 21.76 46.30 2.52
1482 1586 6.655848 GTCATTACCCACCATACTAAAACACA 59.344 38.462 0.00 0.00 0.00 3.72
1484 1588 6.780901 TGTCATTACCCACCATACTAAAACA 58.219 36.000 0.00 0.00 0.00 2.83
1528 1632 2.095110 TGCAGTCCGATTTGAGCATTTG 60.095 45.455 0.00 0.00 0.00 2.32
1529 1633 2.161855 TGCAGTCCGATTTGAGCATTT 58.838 42.857 0.00 0.00 0.00 2.32
1530 1634 1.825090 TGCAGTCCGATTTGAGCATT 58.175 45.000 0.00 0.00 0.00 3.56
1532 1636 1.825090 AATGCAGTCCGATTTGAGCA 58.175 45.000 0.00 0.00 36.34 4.26
1563 1668 1.533625 TCCCAAGATTTTGCAGACCG 58.466 50.000 0.00 0.00 32.79 4.79
1632 1737 0.034756 TCTGCAAGTAGGCTGCGAAA 59.965 50.000 0.00 0.00 33.76 3.46
1727 1832 1.542915 GCCTGATGCAACACTGTCAAT 59.457 47.619 0.00 0.00 40.77 2.57
1757 1862 5.587844 CAGATCAATTTACTGCTAGCTTGGT 59.412 40.000 17.23 13.92 0.00 3.67
1834 1939 3.194861 GCATTGATACAGCGTAGAACCA 58.805 45.455 0.00 0.00 0.00 3.67
1842 1948 0.039798 GCATGGGCATTGATACAGCG 60.040 55.000 0.00 0.00 40.72 5.18
1861 1967 9.619316 GTGATGCTCATATTCAAGTAGTAGTAG 57.381 37.037 0.00 0.00 0.00 2.57
1865 1971 8.144478 GGAAGTGATGCTCATATTCAAGTAGTA 58.856 37.037 12.00 0.00 30.94 1.82
1878 1984 3.490439 TGTCTTTGGAAGTGATGCTCA 57.510 42.857 0.00 0.00 0.00 4.26
1889 1998 2.037902 TGCGAGTATGGTTGTCTTTGGA 59.962 45.455 0.00 0.00 0.00 3.53
1907 2016 0.731417 CCTTGAGGCTTGAGAATGCG 59.269 55.000 0.00 0.00 0.00 4.73
1934 2043 6.294508 GGTGAAAACTTGCCAATAGTGTGTAT 60.295 38.462 0.00 0.00 0.00 2.29
2186 2299 7.412137 TCGATGCAGTGATAAGATTGTATTG 57.588 36.000 0.00 0.00 0.00 1.90
2289 2410 2.561478 AATGGAAGCACCGTACTTGT 57.439 45.000 0.00 0.00 42.61 3.16
2379 2501 8.791327 TTCAAACAGATAATGCTGATTGTAGA 57.209 30.769 12.09 1.39 44.30 2.59
2394 2516 8.621532 TGTAGCTTTACATCTTTCAAACAGAT 57.378 30.769 0.00 0.00 0.00 2.90
2583 2719 3.228453 CAGGGATTGAGGAAATCATGGG 58.772 50.000 0.00 0.00 45.69 4.00
2590 2726 4.141482 GGTATAGCACAGGGATTGAGGAAA 60.141 45.833 0.00 0.00 0.00 3.13
2660 2796 0.511221 CCACCTAACAAGACGTTGCG 59.489 55.000 0.00 0.00 38.63 4.85
2673 2809 5.834460 TCTGTGACCTAGATTTACCACCTA 58.166 41.667 0.00 0.00 0.00 3.08
2753 2889 7.709947 TCATTTCTTGCCACTCAATATGATTC 58.290 34.615 0.00 0.00 33.57 2.52
2783 2919 3.531538 TGACAGAAACACAGTCCACTTC 58.468 45.455 0.00 0.00 34.74 3.01
2913 3077 6.490040 ACATATTATACAAGTGAATGCACCCC 59.510 38.462 0.00 0.00 46.32 4.95
2916 3080 7.290842 CCGACATATTATACAAGTGAATGCAC 58.709 38.462 0.00 0.00 45.49 4.57
2940 3122 0.741221 CTTGAAGCCACTCGGTAGCC 60.741 60.000 0.00 0.00 33.28 3.93
2945 3127 1.002087 AGTTACCTTGAAGCCACTCGG 59.998 52.381 0.00 0.00 0.00 4.63
2986 3168 2.699321 CTGGCTAACTACCCTCCCTTAC 59.301 54.545 0.00 0.00 0.00 2.34
3055 3239 5.104776 TGGCAGTATCAGCTTCTTTCAGTAT 60.105 40.000 0.00 0.00 0.00 2.12
3083 3267 1.456705 GGTGGGTTTTGGAGTGCCA 60.457 57.895 0.00 0.00 44.17 4.92
3104 3289 3.328505 CCTGGTGACAAAAATGCCATTC 58.671 45.455 0.00 0.00 42.06 2.67
3139 3324 5.885912 GGACTGGCTTCCATTTTCAGTTATA 59.114 40.000 0.00 0.00 38.60 0.98
3235 3420 8.795842 TTACTAGTGGAAGTTTGAAGTTTTCA 57.204 30.769 5.39 0.00 38.04 2.69
3336 3523 9.095065 CGTAGGTATTGAAATTACTGTTAGCTT 57.905 33.333 0.00 0.00 0.00 3.74
3508 3695 2.245159 TGGTTCTGAAGAGCACACAG 57.755 50.000 0.00 0.00 0.00 3.66
3699 3886 4.770795 AGCTACGAGAAATGCCTATTTGT 58.229 39.130 0.00 0.00 36.66 2.83
3732 3919 1.140452 TCATGAGCATCTTCCTGCCTC 59.860 52.381 0.00 0.00 43.33 4.70
3783 3970 4.520492 ACTCCAGAAGGTAAACAGCATTTG 59.480 41.667 0.00 0.00 35.89 2.32
3861 4048 1.519455 CTGACTTCTTAGGCGGCCG 60.519 63.158 24.05 24.05 29.01 6.13
3952 4139 7.011763 CACCTGGAACATATATATATGCAGCAC 59.988 40.741 26.04 15.38 42.98 4.40
3960 4147 9.448438 GTGCATTTCACCTGGAACATATATATA 57.552 33.333 0.00 0.00 39.79 0.86
4178 4365 2.365293 ACTGTCAAAACATTTGGAGCCC 59.635 45.455 3.25 0.00 34.13 5.19
4506 4693 8.956446 TGATCTTATACCAGACCTGATTATCA 57.044 34.615 0.00 0.00 0.00 2.15
4526 4780 9.566432 ACACAAAGAAGAGTAAAATTCTGATCT 57.434 29.630 0.00 0.00 35.95 2.75
4527 4781 9.604626 CACACAAAGAAGAGTAAAATTCTGATC 57.395 33.333 0.00 0.00 35.95 2.92
4528 4782 8.571336 CCACACAAAGAAGAGTAAAATTCTGAT 58.429 33.333 0.00 0.00 35.95 2.90
4529 4783 7.556275 ACCACACAAAGAAGAGTAAAATTCTGA 59.444 33.333 0.00 0.00 35.95 3.27
4530 4784 7.707104 ACCACACAAAGAAGAGTAAAATTCTG 58.293 34.615 0.00 0.00 35.95 3.02
4531 4785 7.881775 ACCACACAAAGAAGAGTAAAATTCT 57.118 32.000 0.00 0.00 37.36 2.40
4532 4786 8.926715 AAACCACACAAAGAAGAGTAAAATTC 57.073 30.769 0.00 0.00 0.00 2.17
4537 4791 9.616156 TGTTATAAACCACACAAAGAAGAGTAA 57.384 29.630 0.00 0.00 0.00 2.24
4538 4792 9.048446 GTGTTATAAACCACACAAAGAAGAGTA 57.952 33.333 1.37 0.00 42.51 2.59
4539 4793 7.773690 AGTGTTATAAACCACACAAAGAAGAGT 59.226 33.333 7.88 0.00 44.94 3.24
4540 4794 8.154649 AGTGTTATAAACCACACAAAGAAGAG 57.845 34.615 7.88 0.00 44.94 2.85
4541 4795 9.787435 ATAGTGTTATAAACCACACAAAGAAGA 57.213 29.630 7.88 0.00 44.94 2.87
4543 4797 9.787435 AGATAGTGTTATAAACCACACAAAGAA 57.213 29.630 7.88 0.00 44.94 2.52
4544 4798 9.787435 AAGATAGTGTTATAAACCACACAAAGA 57.213 29.630 7.88 0.00 44.94 2.52
4548 4802 9.439500 GGTAAAGATAGTGTTATAAACCACACA 57.561 33.333 7.88 0.00 44.94 3.72
4549 4803 9.439500 TGGTAAAGATAGTGTTATAAACCACAC 57.561 33.333 8.45 3.72 43.17 3.82
4551 4805 8.598075 CGTGGTAAAGATAGTGTTATAAACCAC 58.402 37.037 14.59 14.59 46.07 4.16
4552 4806 7.278424 GCGTGGTAAAGATAGTGTTATAAACCA 59.722 37.037 0.00 0.00 0.00 3.67
4553 4807 7.493645 AGCGTGGTAAAGATAGTGTTATAAACC 59.506 37.037 0.00 0.00 0.00 3.27
4554 4808 8.325997 CAGCGTGGTAAAGATAGTGTTATAAAC 58.674 37.037 0.00 0.00 0.00 2.01
4555 4809 7.493320 CCAGCGTGGTAAAGATAGTGTTATAAA 59.507 37.037 0.00 0.00 31.35 1.40
4556 4810 6.982141 CCAGCGTGGTAAAGATAGTGTTATAA 59.018 38.462 0.00 0.00 31.35 0.98
4557 4811 6.509656 CCAGCGTGGTAAAGATAGTGTTATA 58.490 40.000 0.00 0.00 31.35 0.98
4558 4812 5.357257 CCAGCGTGGTAAAGATAGTGTTAT 58.643 41.667 0.00 0.00 31.35 1.89
4559 4813 4.751060 CCAGCGTGGTAAAGATAGTGTTA 58.249 43.478 0.00 0.00 31.35 2.41
4560 4814 3.596214 CCAGCGTGGTAAAGATAGTGTT 58.404 45.455 0.00 0.00 31.35 3.32
4561 4815 2.677037 GCCAGCGTGGTAAAGATAGTGT 60.677 50.000 6.02 0.00 40.46 3.55
4562 4816 1.933853 GCCAGCGTGGTAAAGATAGTG 59.066 52.381 6.02 0.00 40.46 2.74
4563 4817 1.831736 AGCCAGCGTGGTAAAGATAGT 59.168 47.619 6.02 0.00 40.46 2.12
4564 4818 2.159099 TGAGCCAGCGTGGTAAAGATAG 60.159 50.000 6.02 0.00 40.46 2.08
4565 4819 1.828595 TGAGCCAGCGTGGTAAAGATA 59.171 47.619 6.02 0.00 40.46 1.98
4566 4820 0.613260 TGAGCCAGCGTGGTAAAGAT 59.387 50.000 6.02 0.00 40.46 2.40
4567 4821 0.613260 ATGAGCCAGCGTGGTAAAGA 59.387 50.000 6.02 0.00 40.46 2.52
4568 4822 0.729116 CATGAGCCAGCGTGGTAAAG 59.271 55.000 6.02 0.00 40.46 1.85
4569 4823 0.036164 ACATGAGCCAGCGTGGTAAA 59.964 50.000 0.00 0.00 40.46 2.01
4570 4824 0.899019 TACATGAGCCAGCGTGGTAA 59.101 50.000 0.00 0.00 40.46 2.85
4571 4825 0.174845 GTACATGAGCCAGCGTGGTA 59.825 55.000 0.00 0.00 40.46 3.25
4572 4826 1.079127 GTACATGAGCCAGCGTGGT 60.079 57.895 0.00 0.00 40.46 4.16
4573 4827 1.815421 GGTACATGAGCCAGCGTGG 60.815 63.158 0.00 0.25 41.55 4.94
4574 4828 1.079197 TGGTACATGAGCCAGCGTG 60.079 57.895 0.00 0.00 0.00 5.34
4575 4829 3.387716 TGGTACATGAGCCAGCGT 58.612 55.556 0.00 0.00 0.00 5.07
4790 5044 1.542030 ACCGAGCTCTGAACACTGTAG 59.458 52.381 12.54 0.00 0.00 2.74
4796 5050 1.112916 TGACCACCGAGCTCTGAACA 61.113 55.000 12.54 5.29 0.00 3.18
4966 5227 2.352323 GCCATAAACAGAACCCAAACCG 60.352 50.000 0.00 0.00 0.00 4.44
5095 5356 4.079253 ACTTGGCGTACCTGAAATTGATT 58.921 39.130 0.00 0.00 36.63 2.57
5250 5511 7.244886 TCCGATTACACCATTGATAGATGAT 57.755 36.000 0.00 0.00 0.00 2.45
5449 5710 1.600636 CAAGGGCTTTCTGTGCGGA 60.601 57.895 0.00 0.00 0.00 5.54
5536 5797 2.681848 CCAGTTGACCTGATGAAGATGC 59.318 50.000 0.00 0.00 44.49 3.91
5605 5866 3.384532 GGCCAATGCACCACCAGG 61.385 66.667 0.00 0.00 40.13 4.45
5971 6232 3.585862 TCATCGTCAAAGCCTTCACTAC 58.414 45.455 0.00 0.00 0.00 2.73
6060 6321 5.487433 TCACGATTTGACTGGTTCATATGT 58.513 37.500 1.90 0.00 32.84 2.29
6074 6335 2.286294 GGAGCAGCATAGTCACGATTTG 59.714 50.000 0.00 0.00 0.00 2.32
6193 6454 5.854010 CTTGCTCAAGTCCTGGTAGTATA 57.146 43.478 1.61 0.00 33.87 1.47
6389 6650 2.150424 CGCGCTTTTTGGTTTTCTTACG 59.850 45.455 5.56 0.00 0.00 3.18
6390 6651 3.110358 ACGCGCTTTTTGGTTTTCTTAC 58.890 40.909 5.73 0.00 0.00 2.34
6501 6765 3.898517 TCCGCTTACGAGATGTAGATG 57.101 47.619 0.00 0.00 43.93 2.90
6600 6864 2.274948 ATCATCACCGGCACCAGCAT 62.275 55.000 0.00 0.00 44.61 3.79
6635 6902 1.543802 AGCAGAAGTTCCACTCTCTCG 59.456 52.381 0.00 0.00 0.00 4.04
6638 6905 2.167487 CCCTAGCAGAAGTTCCACTCTC 59.833 54.545 0.00 0.00 0.00 3.20
6698 6965 4.743493 ACGTTGTTTCTTGAATGTGCTTT 58.257 34.783 0.00 0.00 0.00 3.51
6781 7048 5.869888 AGAGAATTGCTTACCAGTAACTTCG 59.130 40.000 0.00 0.00 0.00 3.79
6794 7061 5.467705 GTGCATCTGAAAAGAGAATTGCTT 58.532 37.500 0.00 0.00 31.78 3.91
6808 7075 1.478105 ACATAGTGAGCGTGCATCTGA 59.522 47.619 0.00 0.00 0.00 3.27
6994 7265 0.652592 CTTATGGACAGGCGCGAAAG 59.347 55.000 12.10 0.00 0.00 2.62
7036 7307 0.685097 CCGGACAGAAAAGACCAGGA 59.315 55.000 0.00 0.00 0.00 3.86
7051 7322 4.269523 AAGCAGTTGCAGCCCGGA 62.270 61.111 0.73 0.00 45.16 5.14
7057 7328 1.534595 GGTCTCTTGAAGCAGTTGCAG 59.465 52.381 6.90 0.00 45.16 4.41
7101 7372 1.153086 CTCATCCCTGGAAAGCCGG 60.153 63.158 0.00 0.00 40.49 6.13
7103 7374 0.182299 CTCCTCATCCCTGGAAAGCC 59.818 60.000 0.00 0.00 31.23 4.35
7149 7420 1.067776 TCGTCTTCCTTCGCTTTCCTC 60.068 52.381 0.00 0.00 0.00 3.71
7170 7441 2.126228 TTCATGCCGTCGTCGTCC 60.126 61.111 0.71 0.00 35.01 4.79
7288 7559 1.782181 GTCGTCTCTTTCGGCAAGC 59.218 57.895 0.00 0.00 32.96 4.01
7335 7607 2.577700 TGGGCGATACAACAACACTTT 58.422 42.857 0.00 0.00 0.00 2.66
7537 7815 2.358898 GCTGCTGGAGAAACAAGAACAA 59.641 45.455 0.00 0.00 0.00 2.83
7538 7816 1.949525 GCTGCTGGAGAAACAAGAACA 59.050 47.619 0.00 0.00 0.00 3.18
7584 7862 7.923344 GCACTGCTAGAGAAAATAGAACTCATA 59.077 37.037 0.00 0.00 33.69 2.15
7588 7866 6.042638 TGCACTGCTAGAGAAAATAGAACT 57.957 37.500 1.98 0.00 0.00 3.01
7594 7872 8.526147 ACAAATAATTGCACTGCTAGAGAAAAT 58.474 29.630 1.98 0.00 40.34 1.82
7595 7873 7.885297 ACAAATAATTGCACTGCTAGAGAAAA 58.115 30.769 1.98 0.00 40.34 2.29
7609 7887 6.019640 ACAATTGCATCGCTACAAATAATTGC 60.020 34.615 5.05 0.00 40.34 3.56
7615 7893 7.433131 CAGAAATACAATTGCATCGCTACAAAT 59.567 33.333 5.05 0.00 0.00 2.32
7618 7896 5.220835 CCAGAAATACAATTGCATCGCTACA 60.221 40.000 5.05 0.00 0.00 2.74
7621 7899 3.696051 ACCAGAAATACAATTGCATCGCT 59.304 39.130 5.05 0.00 0.00 4.93
7624 7902 5.065988 ACCGTACCAGAAATACAATTGCATC 59.934 40.000 5.05 0.00 0.00 3.91
7631 7909 6.314400 GCATTTCTACCGTACCAGAAATACAA 59.686 38.462 17.65 0.13 45.33 2.41
7632 7910 5.813672 GCATTTCTACCGTACCAGAAATACA 59.186 40.000 17.65 0.39 45.33 2.29
7637 7918 3.512329 TCTGCATTTCTACCGTACCAGAA 59.488 43.478 0.00 0.00 0.00 3.02
7641 7922 4.439057 TGATTCTGCATTTCTACCGTACC 58.561 43.478 0.00 0.00 0.00 3.34
7642 7923 5.109903 ACTGATTCTGCATTTCTACCGTAC 58.890 41.667 0.00 0.00 0.00 3.67
7645 7953 4.437239 AGACTGATTCTGCATTTCTACCG 58.563 43.478 0.00 0.00 31.12 4.02
7664 7972 6.944557 AAAAGTGCAAACAGTTTACAAGAC 57.055 33.333 0.17 0.00 46.42 3.01
7674 7982 6.074676 GCAACTGAGATAAAAAGTGCAAACAG 60.075 38.462 0.00 0.00 0.00 3.16
7677 7988 5.288804 GGCAACTGAGATAAAAAGTGCAAA 58.711 37.500 0.00 0.00 0.00 3.68
7683 7994 4.023193 ACCAACGGCAACTGAGATAAAAAG 60.023 41.667 0.00 0.00 0.00 2.27
7749 8060 0.593263 CCGTCGTACGCCCTGATAAC 60.593 60.000 11.24 0.00 40.91 1.89
7754 8065 2.505557 GTTCCGTCGTACGCCCTG 60.506 66.667 11.24 0.08 40.91 4.45
7769 8080 0.755327 GGTTGTGAACTGGGCCTGTT 60.755 55.000 26.41 26.41 0.00 3.16
7872 8186 1.000163 TGAGACGCTCCAACTCAGAAC 60.000 52.381 0.00 0.00 36.04 3.01
7874 8188 1.203287 CATGAGACGCTCCAACTCAGA 59.797 52.381 0.00 0.00 42.55 3.27
7921 8463 1.340308 TGGACATCACCATGAAGCCTG 60.340 52.381 0.00 0.00 34.77 4.85
7953 8495 3.855853 GCTCCCGCCTTCTCCCTC 61.856 72.222 0.00 0.00 0.00 4.30
7954 8496 4.406763 AGCTCCCGCCTTCTCCCT 62.407 66.667 0.00 0.00 36.60 4.20
7955 8497 3.855853 GAGCTCCCGCCTTCTCCC 61.856 72.222 0.87 0.00 36.60 4.30
7956 8498 3.855853 GGAGCTCCCGCCTTCTCC 61.856 72.222 23.19 0.00 38.40 3.71
7997 8539 4.261031 CCGTAAATTCCATTTCGGGCTAAG 60.261 45.833 10.05 0.00 38.29 2.18
8000 8542 2.021457 CCGTAAATTCCATTTCGGGCT 58.979 47.619 10.05 0.00 38.29 5.19
8001 8543 1.535226 GCCGTAAATTCCATTTCGGGC 60.535 52.381 15.57 11.85 40.83 6.13
8002 8544 1.066454 GGCCGTAAATTCCATTTCGGG 59.934 52.381 15.57 7.61 40.25 5.14
8006 8549 5.641636 GTGAAATTGGCCGTAAATTCCATTT 59.358 36.000 0.00 0.00 36.29 2.32
8011 8554 5.465935 TCAAGTGAAATTGGCCGTAAATTC 58.534 37.500 0.00 0.00 0.00 2.17
8029 8572 6.357367 AGCTATATTCCACCGAAATTCAAGT 58.643 36.000 0.00 0.00 0.00 3.16
8056 8599 3.804036 TCACCTGAATTTGTGTCGAAGT 58.196 40.909 0.00 0.00 34.14 3.01
8064 8609 4.152402 CGAGACGATTTCACCTGAATTTGT 59.848 41.667 0.00 3.48 35.74 2.83
8075 8620 2.863739 CTGTGTAGCGAGACGATTTCA 58.136 47.619 0.00 0.00 0.00 2.69
8126 8671 1.512230 CGTACGATCCCCGGTTTCA 59.488 57.895 10.44 0.00 43.93 2.69
8189 8735 4.634443 TGAAATGTGCTCAGATGTCATCAG 59.366 41.667 15.20 7.23 0.00 2.90
8196 8743 5.122711 TGTGTGTATGAAATGTGCTCAGATG 59.877 40.000 0.00 0.00 0.00 2.90
8213 8760 4.729458 GCTTTCTTTCTTTGCGTGTGTGTA 60.729 41.667 0.00 0.00 0.00 2.90
8241 8790 1.420138 AGTTACTCAACTGTGGGGGTG 59.580 52.381 0.00 0.00 43.50 4.61
8242 8791 1.815757 AGTTACTCAACTGTGGGGGT 58.184 50.000 0.00 0.00 43.50 4.95


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

AutoCloner maintained by Alex Coulton.