Multiple sequence alignment - TraesCS1D01G365500

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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 TraesCS1D01G365500 chr1D 100.000 5418 0 0 1 5418 446262494 446267911 0.000000e+00 10006.0
1 TraesCS1D01G365500 chr1A 91.681 4496 177 84 444 4884 541988362 541992715 0.000000e+00 6048.0
2 TraesCS1D01G365500 chr1A 94.191 482 18 6 4875 5355 541993133 541993605 0.000000e+00 726.0
3 TraesCS1D01G365500 chr1A 89.333 75 7 1 63 136 391943484 391943410 5.780000e-15 93.5
4 TraesCS1D01G365500 chr1B 92.061 4144 184 53 764 4853 610160995 610165047 0.000000e+00 5696.0
5 TraesCS1D01G365500 chr1B 89.181 1368 95 18 1092 2428 634041062 634042407 0.000000e+00 1657.0
6 TraesCS1D01G365500 chr1B 90.261 575 39 8 1 564 610160299 610160867 0.000000e+00 736.0
7 TraesCS1D01G365500 chr1B 92.180 422 25 5 4940 5355 610165205 610165624 1.680000e-164 590.0
8 TraesCS1D01G365500 chr3B 89.327 1368 93 19 1092 2428 47624633 47623288 0.000000e+00 1668.0
9 TraesCS1D01G365500 chr3B 88.889 1368 98 19 1092 2428 702015723 702017067 0.000000e+00 1635.0
10 TraesCS1D01G365500 chr2B 89.108 1368 96 17 1092 2428 715698150 715699495 0.000000e+00 1652.0
11 TraesCS1D01G365500 chr2B 88.332 1397 112 24 1060 2428 792241052 792242425 0.000000e+00 1629.0
12 TraesCS1D01G365500 chr2B 88.386 1369 100 23 1092 2428 145166055 145167396 0.000000e+00 1592.0
13 TraesCS1D01G365500 chr2B 87.417 151 17 2 126 275 2645158 2645307 7.210000e-39 172.0
14 TraesCS1D01G365500 chr7B 89.150 1364 95 15 1096 2428 701833580 701834921 0.000000e+00 1650.0
15 TraesCS1D01G365500 chr7B 88.219 1061 77 15 1394 2428 97694159 97695197 0.000000e+00 1223.0
16 TraesCS1D01G365500 chr7B 87.219 845 69 15 1394 2215 66637302 66636474 0.000000e+00 926.0
17 TraesCS1D01G365500 chr4B 88.437 1401 104 23 1060 2428 499364970 499366344 0.000000e+00 1637.0
18 TraesCS1D01G365500 chr4B 88.091 1058 83 17 1394 2428 134178127 134179164 0.000000e+00 1216.0
19 TraesCS1D01G365500 chr6B 88.177 1404 105 27 1060 2428 100474947 100473570 0.000000e+00 1616.0
20 TraesCS1D01G365500 chr6B 92.500 80 6 0 196 275 19328896 19328975 1.230000e-21 115.0
21 TraesCS1D01G365500 chr6B 91.026 78 7 0 196 273 123736209 123736286 7.420000e-19 106.0
22 TraesCS1D01G365500 chr4A 87.633 752 45 16 1092 1813 693830822 693830089 0.000000e+00 830.0
23 TraesCS1D01G365500 chr6A 97.500 40 1 0 78 117 155093531 155093570 9.740000e-08 69.4


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 TraesCS1D01G365500 chr1D 446262494 446267911 5417 False 10006.000000 10006 100.000000 1 5418 1 chr1D.!!$F1 5417
1 TraesCS1D01G365500 chr1A 541988362 541993605 5243 False 3387.000000 6048 92.936000 444 5355 2 chr1A.!!$F1 4911
2 TraesCS1D01G365500 chr1B 610160299 610165624 5325 False 2340.666667 5696 91.500667 1 5355 3 chr1B.!!$F2 5354
3 TraesCS1D01G365500 chr1B 634041062 634042407 1345 False 1657.000000 1657 89.181000 1092 2428 1 chr1B.!!$F1 1336
4 TraesCS1D01G365500 chr3B 47623288 47624633 1345 True 1668.000000 1668 89.327000 1092 2428 1 chr3B.!!$R1 1336
5 TraesCS1D01G365500 chr3B 702015723 702017067 1344 False 1635.000000 1635 88.889000 1092 2428 1 chr3B.!!$F1 1336
6 TraesCS1D01G365500 chr2B 715698150 715699495 1345 False 1652.000000 1652 89.108000 1092 2428 1 chr2B.!!$F3 1336
7 TraesCS1D01G365500 chr2B 792241052 792242425 1373 False 1629.000000 1629 88.332000 1060 2428 1 chr2B.!!$F4 1368
8 TraesCS1D01G365500 chr2B 145166055 145167396 1341 False 1592.000000 1592 88.386000 1092 2428 1 chr2B.!!$F2 1336
9 TraesCS1D01G365500 chr7B 701833580 701834921 1341 False 1650.000000 1650 89.150000 1096 2428 1 chr7B.!!$F2 1332
10 TraesCS1D01G365500 chr7B 97694159 97695197 1038 False 1223.000000 1223 88.219000 1394 2428 1 chr7B.!!$F1 1034
11 TraesCS1D01G365500 chr7B 66636474 66637302 828 True 926.000000 926 87.219000 1394 2215 1 chr7B.!!$R1 821
12 TraesCS1D01G365500 chr4B 499364970 499366344 1374 False 1637.000000 1637 88.437000 1060 2428 1 chr4B.!!$F2 1368
13 TraesCS1D01G365500 chr4B 134178127 134179164 1037 False 1216.000000 1216 88.091000 1394 2428 1 chr4B.!!$F1 1034
14 TraesCS1D01G365500 chr6B 100473570 100474947 1377 True 1616.000000 1616 88.177000 1060 2428 1 chr6B.!!$R1 1368
15 TraesCS1D01G365500 chr4A 693830089 693830822 733 True 830.000000 830 87.633000 1092 1813 1 chr4A.!!$R1 721

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
595 620 0.174617 CCACAAACGCCCACAAAACT 59.825 50.0 0.00 0.0 0.00 2.66 F
1527 1580 0.104855 TCTGCGGAATTGCGCTCTAT 59.895 50.0 37.74 0.0 37.81 1.98 F
1717 1809 0.749454 AGGATTTGGGAGTGCGATGC 60.749 55.0 0.00 0.0 0.00 3.91 F
1844 1936 1.295357 TGGTGCGTACTGAATTGCCG 61.295 55.0 3.01 0.0 0.00 5.69 F
3565 3673 1.221414 ACAAGCTGTTCTTCTGCGTC 58.779 50.0 0.00 0.0 44.03 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1589 0.178068 GAGATGCCCGTACATGTGGT 59.822 55.000 9.11 0.0 0.00 4.16 R
3274 3382 0.320374 AATCGCCTGAAGGAACACGA 59.680 50.000 0.00 0.0 37.39 4.35 R
3565 3673 1.308069 CGGTCCCCAACAGAGCAATG 61.308 60.000 0.00 0.0 0.00 2.82 R
3574 3682 1.957695 GACGTTCACGGTCCCCAAC 60.958 63.158 4.07 0.0 44.95 3.77 R
5375 6026 0.178998 TCTAGACGATTCCCCCTCGG 60.179 60.000 0.00 0.0 40.37 4.63 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
169 171 1.990060 CTCCTTCCTCGCTTGGGGA 60.990 63.158 0.00 0.00 0.00 4.81
185 187 1.002624 GGATGGACACGGCTGGAAA 60.003 57.895 0.00 0.00 0.00 3.13
186 188 0.608035 GGATGGACACGGCTGGAAAA 60.608 55.000 0.00 0.00 0.00 2.29
187 189 1.243902 GATGGACACGGCTGGAAAAA 58.756 50.000 0.00 0.00 0.00 1.94
211 214 5.794767 AATTATCCCCAGGCCAAAAATTT 57.205 34.783 5.01 0.00 0.00 1.82
213 216 2.109229 TCCCCAGGCCAAAAATTTCA 57.891 45.000 5.01 0.00 0.00 2.69
225 228 2.730129 AAATTTCACCGGCAGCCCCT 62.730 55.000 5.63 0.00 0.00 4.79
296 301 1.447838 CCATTCGCTACCGCACACT 60.448 57.895 0.00 0.00 35.30 3.55
309 314 3.005261 ACCGCACACTATTTTTCATGCAA 59.995 39.130 0.00 0.00 33.27 4.08
336 341 5.418840 TCATAGCCCTTCCATTTCTGTTTTC 59.581 40.000 0.00 0.00 0.00 2.29
394 402 5.690464 AATGCAGAGACTTCTACTTCCAT 57.310 39.130 0.00 0.00 30.73 3.41
408 416 7.272037 TCTACTTCCATGAAGGTTTTGAAAC 57.728 36.000 8.56 0.00 43.25 2.78
439 447 7.095187 GCTTCGAGAAGGTTTGAAAAAGAGATA 60.095 37.037 13.92 0.00 38.80 1.98
470 481 2.660189 TAGTACGAAGCCCCGAAAAG 57.340 50.000 2.21 0.00 0.00 2.27
490 503 1.452108 CCGAGAAGGGGGAATGTGC 60.452 63.158 0.00 0.00 35.97 4.57
583 608 2.519780 TCCGGCCAACCCACAAAC 60.520 61.111 2.24 0.00 0.00 2.93
584 609 3.972276 CCGGCCAACCCACAAACG 61.972 66.667 2.24 0.00 0.00 3.60
585 610 4.639171 CGGCCAACCCACAAACGC 62.639 66.667 2.24 0.00 0.00 4.84
588 613 2.835431 CCAACCCACAAACGCCCA 60.835 61.111 0.00 0.00 0.00 5.36
589 614 2.415426 CAACCCACAAACGCCCAC 59.585 61.111 0.00 0.00 0.00 4.61
590 615 2.043852 AACCCACAAACGCCCACA 60.044 55.556 0.00 0.00 0.00 4.17
591 616 1.682684 AACCCACAAACGCCCACAA 60.683 52.632 0.00 0.00 0.00 3.33
592 617 1.258445 AACCCACAAACGCCCACAAA 61.258 50.000 0.00 0.00 0.00 2.83
593 618 1.258445 ACCCACAAACGCCCACAAAA 61.258 50.000 0.00 0.00 0.00 2.44
594 619 0.808060 CCCACAAACGCCCACAAAAC 60.808 55.000 0.00 0.00 0.00 2.43
595 620 0.174617 CCACAAACGCCCACAAAACT 59.825 50.000 0.00 0.00 0.00 2.66
596 621 1.555477 CACAAACGCCCACAAAACTC 58.445 50.000 0.00 0.00 0.00 3.01
597 622 0.458260 ACAAACGCCCACAAAACTCC 59.542 50.000 0.00 0.00 0.00 3.85
598 623 0.593773 CAAACGCCCACAAAACTCCG 60.594 55.000 0.00 0.00 0.00 4.63
599 624 2.344521 AAACGCCCACAAAACTCCGC 62.345 55.000 0.00 0.00 0.00 5.54
600 625 3.283684 CGCCCACAAAACTCCGCA 61.284 61.111 0.00 0.00 0.00 5.69
601 626 2.335011 GCCCACAAAACTCCGCAC 59.665 61.111 0.00 0.00 0.00 5.34
602 627 3.039134 CCCACAAAACTCCGCACC 58.961 61.111 0.00 0.00 0.00 5.01
603 628 1.826054 CCCACAAAACTCCGCACCA 60.826 57.895 0.00 0.00 0.00 4.17
604 629 1.654220 CCACAAAACTCCGCACCAG 59.346 57.895 0.00 0.00 0.00 4.00
605 630 1.008538 CACAAAACTCCGCACCAGC 60.009 57.895 0.00 0.00 37.42 4.85
606 631 1.152963 ACAAAACTCCGCACCAGCT 60.153 52.632 0.00 0.00 39.10 4.24
607 632 1.166531 ACAAAACTCCGCACCAGCTC 61.167 55.000 0.00 0.00 39.10 4.09
608 633 1.961277 AAAACTCCGCACCAGCTCG 60.961 57.895 0.00 0.00 39.10 5.03
658 683 3.636231 CTTCCCCCACACGGCAGA 61.636 66.667 0.00 0.00 0.00 4.26
659 684 3.901797 CTTCCCCCACACGGCAGAC 62.902 68.421 0.00 0.00 0.00 3.51
669 694 2.571757 CGGCAGACGGACAGCTTA 59.428 61.111 0.00 0.00 39.42 3.09
670 695 1.517257 CGGCAGACGGACAGCTTAG 60.517 63.158 0.00 0.00 39.42 2.18
671 696 1.811679 GGCAGACGGACAGCTTAGC 60.812 63.158 0.00 0.00 0.00 3.09
672 697 2.161486 GCAGACGGACAGCTTAGCG 61.161 63.158 0.00 0.00 0.00 4.26
673 698 2.161486 CAGACGGACAGCTTAGCGC 61.161 63.158 0.00 0.00 39.57 5.92
674 699 2.886124 GACGGACAGCTTAGCGCC 60.886 66.667 2.29 1.07 40.39 6.53
675 700 4.796231 ACGGACAGCTTAGCGCCG 62.796 66.667 25.44 25.44 46.83 6.46
705 730 3.441290 GAAGCAGCAGCAGCCCAG 61.441 66.667 6.10 0.00 45.49 4.45
752 777 2.319410 ATCCTTCCCTCCCTCCCTCG 62.319 65.000 0.00 0.00 0.00 4.63
757 782 4.896829 CCTCCCTCCCTCGCGCTA 62.897 72.222 5.56 0.00 0.00 4.26
758 783 3.291383 CTCCCTCCCTCGCGCTAG 61.291 72.222 5.56 3.19 0.00 3.42
761 786 2.594882 CCTCCCTCGCGCTAGCTA 60.595 66.667 13.93 0.00 42.32 3.32
762 787 2.622011 CCTCCCTCGCGCTAGCTAG 61.622 68.421 16.84 16.84 42.32 3.42
763 788 3.262142 CTCCCTCGCGCTAGCTAGC 62.262 68.421 31.88 31.88 45.62 3.42
764 789 3.291383 CCCTCGCGCTAGCTAGCT 61.291 66.667 36.02 23.12 46.85 3.32
765 790 1.966972 CCCTCGCGCTAGCTAGCTA 60.967 63.158 36.02 22.85 46.85 3.32
801 826 1.002684 ACTAAATACTCGCTCGCTCCG 60.003 52.381 0.00 0.00 0.00 4.63
871 901 3.311322 CGCTTTAACCCGCTATTGATTGA 59.689 43.478 0.00 0.00 0.00 2.57
922 952 0.462581 CTGCTCTAATTCCGCCAGCA 60.463 55.000 0.00 0.00 37.76 4.41
949 991 2.841988 GCGGCAGGAGGAGGATCT 60.842 66.667 0.00 0.00 33.73 2.75
950 992 2.866726 GCGGCAGGAGGAGGATCTC 61.867 68.421 0.00 0.00 33.73 2.75
959 1001 2.420890 GAGGATCTCCAGCCAGCG 59.579 66.667 0.00 0.00 38.89 5.18
960 1002 3.160047 AGGATCTCCAGCCAGCGG 61.160 66.667 0.00 0.00 38.89 5.52
961 1003 4.247380 GGATCTCCAGCCAGCGGG 62.247 72.222 2.00 2.00 35.64 6.13
962 1004 4.247380 GATCTCCAGCCAGCGGGG 62.247 72.222 9.00 3.12 40.85 5.73
963 1005 4.804420 ATCTCCAGCCAGCGGGGA 62.804 66.667 9.00 7.21 40.01 4.81
964 1006 4.804420 TCTCCAGCCAGCGGGGAT 62.804 66.667 9.00 0.00 40.01 3.85
965 1007 3.801997 CTCCAGCCAGCGGGGATT 61.802 66.667 9.00 0.00 40.01 3.01
1506 1559 1.945354 CTGCAGGTACGGTCCGTCAT 61.945 60.000 22.74 7.70 41.54 3.06
1527 1580 0.104855 TCTGCGGAATTGCGCTCTAT 59.895 50.000 37.74 0.00 37.81 1.98
1529 1582 0.937304 TGCGGAATTGCGCTCTATTC 59.063 50.000 37.74 13.86 37.81 1.75
1530 1583 0.937304 GCGGAATTGCGCTCTATTCA 59.063 50.000 33.23 0.00 36.56 2.57
1536 1589 4.511454 GGAATTGCGCTCTATTCATGTGTA 59.489 41.667 22.53 0.00 36.56 2.90
1537 1590 5.409643 AATTGCGCTCTATTCATGTGTAC 57.590 39.130 9.73 0.00 0.00 2.90
1538 1591 2.821546 TGCGCTCTATTCATGTGTACC 58.178 47.619 9.73 0.00 0.00 3.34
1618 1678 0.883833 ACAAGCGAAATTCAGGCTGG 59.116 50.000 15.73 0.00 37.06 4.85
1624 1685 1.953231 GAAATTCAGGCTGGCTGGGC 61.953 60.000 28.04 11.44 0.00 5.36
1717 1809 0.749454 AGGATTTGGGAGTGCGATGC 60.749 55.000 0.00 0.00 0.00 3.91
1719 1811 1.728490 GATTTGGGAGTGCGATGCCC 61.728 60.000 0.00 0.00 42.38 5.36
1754 1846 3.131577 GGATATGGTGTTCTGACGGTGTA 59.868 47.826 0.00 0.00 0.00 2.90
1844 1936 1.295357 TGGTGCGTACTGAATTGCCG 61.295 55.000 3.01 0.00 0.00 5.69
1909 2001 5.001232 GGACTGCAACCTTGTTTATACTGA 58.999 41.667 2.76 0.00 0.00 3.41
1910 2002 5.472137 GGACTGCAACCTTGTTTATACTGAA 59.528 40.000 2.76 0.00 0.00 3.02
1937 2030 6.151663 CATGTCTCCATGGCATAATTGAAA 57.848 37.500 6.96 0.00 43.95 2.69
2015 2118 6.236017 ACATGCTTGCATGAAAAAGAATTG 57.764 33.333 33.52 11.56 36.48 2.32
2090 2193 4.916983 TTTGGTTGATGGTTTCAGACTG 57.083 40.909 0.00 0.00 35.27 3.51
2137 2240 2.027688 GCACATCGTTAGCGTACTTGTC 59.972 50.000 0.00 0.00 39.49 3.18
2378 2482 7.426929 TTTATCAGTCTTGAGTTGAGAAAGC 57.573 36.000 0.00 0.00 36.61 3.51
2417 2521 7.326968 GCCTTCTGCATTCTTTTCTACTTAT 57.673 36.000 0.00 0.00 40.77 1.73
2644 2748 6.263617 TGTCCTACCCTTTTGTGTTCAAATAC 59.736 38.462 0.00 0.00 42.14 1.89
3274 3382 4.598807 TGGATAGCTGTAATGGATGGTGAT 59.401 41.667 0.00 0.00 0.00 3.06
3298 3406 2.151202 GTTCCTTCAGGCGATTCAACA 58.849 47.619 0.00 0.00 34.44 3.33
3307 3415 1.429463 GCGATTCAACACGAAGGTCT 58.571 50.000 0.00 0.00 36.95 3.85
3328 3436 5.045797 GTCTATCTCTGGTTACCTGGGTTTT 60.046 44.000 8.01 0.00 0.00 2.43
3565 3673 1.221414 ACAAGCTGTTCTTCTGCGTC 58.779 50.000 0.00 0.00 44.03 5.19
3574 3682 1.718396 TCTTCTGCGTCATTGCTCTG 58.282 50.000 0.00 0.00 35.36 3.35
3577 3685 1.150827 TCTGCGTCATTGCTCTGTTG 58.849 50.000 0.00 0.00 35.36 3.33
3674 3782 1.081175 CAGCGCTCTCAGTTCACGA 60.081 57.895 7.13 0.00 0.00 4.35
3703 3811 3.306294 CCATGACATATGAAGCTCGGCTA 60.306 47.826 10.38 0.00 38.25 3.93
3910 4018 3.532155 GCCGTCCTCGAGCTGGAT 61.532 66.667 17.01 0.00 39.71 3.41
3913 4021 1.459455 CCGTCCTCGAGCTGGATGAT 61.459 60.000 6.99 0.00 41.77 2.45
4078 4186 1.134371 GGCTACAACCTGATCCTCACC 60.134 57.143 0.00 0.00 0.00 4.02
4108 4216 1.896220 TCATGGACAGTGAGTTTGCC 58.104 50.000 0.00 0.00 0.00 4.52
4113 4221 1.876156 GGACAGTGAGTTTGCCTTCAG 59.124 52.381 0.00 0.00 0.00 3.02
4360 4468 4.242811 TGGCCAAGTTCTCCTCCATATAT 58.757 43.478 0.61 0.00 0.00 0.86
4397 4505 2.747855 GGGAGTTTGGCAGGCGAG 60.748 66.667 0.00 0.00 0.00 5.03
4448 4556 4.181010 CAGTGGGGGCGGGAGATG 62.181 72.222 0.00 0.00 0.00 2.90
4470 4578 4.300189 GTACACAACCAACAGATGCAAA 57.700 40.909 0.00 0.00 0.00 3.68
4471 4579 4.870363 GTACACAACCAACAGATGCAAAT 58.130 39.130 0.00 0.00 0.00 2.32
4603 4715 5.518848 AGAGTGCAGTAGATCAAGATCTG 57.481 43.478 20.01 7.85 46.80 2.90
4613 4725 5.083533 AGATCAAGATCTGTTCAGTGTCC 57.916 43.478 11.57 0.00 45.77 4.02
4615 4727 2.029020 TCAAGATCTGTTCAGTGTCCGG 60.029 50.000 0.00 0.00 0.00 5.14
4616 4728 1.633774 AGATCTGTTCAGTGTCCGGT 58.366 50.000 0.00 0.00 0.00 5.28
4618 4730 2.028930 AGATCTGTTCAGTGTCCGGTTC 60.029 50.000 0.00 0.00 0.00 3.62
4622 4737 0.391597 GTTCAGTGTCCGGTTCCTCA 59.608 55.000 0.00 0.00 0.00 3.86
4624 4739 1.124780 TCAGTGTCCGGTTCCTCAAA 58.875 50.000 0.00 0.00 0.00 2.69
4682 4799 4.734402 GCAATGCGCTAAGATTCAATTGGA 60.734 41.667 9.73 0.00 37.77 3.53
4691 4808 6.865205 GCTAAGATTCAATTGGATTGTATGCC 59.135 38.462 5.42 0.00 41.02 4.40
4696 4813 4.858850 TCAATTGGATTGTATGCCTGTCT 58.141 39.130 5.42 0.00 41.02 3.41
4697 4814 5.263599 TCAATTGGATTGTATGCCTGTCTT 58.736 37.500 5.42 0.00 41.02 3.01
4698 4815 5.716228 TCAATTGGATTGTATGCCTGTCTTT 59.284 36.000 5.42 0.00 41.02 2.52
4699 4816 6.211184 TCAATTGGATTGTATGCCTGTCTTTT 59.789 34.615 5.42 0.00 41.02 2.27
4739 4858 5.936956 TGTTCTTTTTGCACTTGTTTTCCAT 59.063 32.000 0.00 0.00 0.00 3.41
4740 4859 7.099764 TGTTCTTTTTGCACTTGTTTTCCATA 58.900 30.769 0.00 0.00 0.00 2.74
4771 4894 5.794687 TGGTGTGATTTTGCTTATCTACG 57.205 39.130 0.00 0.00 0.00 3.51
4772 4895 5.242434 TGGTGTGATTTTGCTTATCTACGT 58.758 37.500 0.00 0.00 0.00 3.57
4773 4896 5.121611 TGGTGTGATTTTGCTTATCTACGTG 59.878 40.000 0.00 0.00 0.00 4.49
4774 4897 5.022021 GTGTGATTTTGCTTATCTACGTGC 58.978 41.667 0.00 0.00 0.00 5.34
4775 4898 4.693095 TGTGATTTTGCTTATCTACGTGCA 59.307 37.500 0.00 0.00 0.00 4.57
4777 4900 5.734498 GTGATTTTGCTTATCTACGTGCAAG 59.266 40.000 8.47 0.00 44.52 4.01
4779 4902 3.603158 TTGCTTATCTACGTGCAAGGA 57.397 42.857 4.26 0.00 39.98 3.36
4780 4903 3.603158 TGCTTATCTACGTGCAAGGAA 57.397 42.857 4.26 0.00 32.12 3.36
4781 4904 4.137116 TGCTTATCTACGTGCAAGGAAT 57.863 40.909 4.26 0.00 32.12 3.01
4802 4925 8.834465 AGGAATGAATTCATCTTAGATGTTTCG 58.166 33.333 20.95 0.00 38.53 3.46
4826 4949 1.295792 TTTGTTCACGTCACTGGAGC 58.704 50.000 0.00 0.00 0.00 4.70
4898 5544 4.773209 GGCCTAGCCGATTGGTAC 57.227 61.111 0.00 0.00 39.62 3.34
4919 5565 2.114411 TCCAACCTTTGCCCGTCC 59.886 61.111 0.00 0.00 0.00 4.79
4936 5582 4.226761 CCGTCCAACTAAAATTTCACTGC 58.773 43.478 0.00 0.00 0.00 4.40
4994 5644 6.097412 ACCCTAAAATTGCTGAATTCTCCATC 59.903 38.462 7.05 0.00 30.02 3.51
5146 5796 4.497291 TTTGAGTTACACAACAGGAGGT 57.503 40.909 0.00 0.00 37.10 3.85
5197 5847 0.318275 TTTTGTTCGCGCATCCAACC 60.318 50.000 8.75 0.00 0.00 3.77
5260 5910 3.435186 GCGCTGGCTGGTTTCTCC 61.435 66.667 0.00 0.00 35.83 3.71
5262 5912 2.347490 GCTGGCTGGTTTCTCCGA 59.653 61.111 0.00 0.00 39.52 4.55
5314 5964 4.227512 TCATGTGCTGAAATGTTGTCAC 57.772 40.909 0.00 0.00 0.00 3.67
5331 5981 5.718649 TGTCACGCAGAAAAAGATATAGC 57.281 39.130 0.00 0.00 0.00 2.97
5358 6009 3.520187 CCAGCAGGGCAAATGAAAC 57.480 52.632 0.00 0.00 0.00 2.78
5359 6010 0.680618 CCAGCAGGGCAAATGAAACA 59.319 50.000 0.00 0.00 0.00 2.83
5360 6011 1.606224 CCAGCAGGGCAAATGAAACAC 60.606 52.381 0.00 0.00 0.00 3.32
5361 6012 1.068895 CAGCAGGGCAAATGAAACACA 59.931 47.619 0.00 0.00 0.00 3.72
5362 6013 1.761784 AGCAGGGCAAATGAAACACAA 59.238 42.857 0.00 0.00 0.00 3.33
5363 6014 2.369532 AGCAGGGCAAATGAAACACAAT 59.630 40.909 0.00 0.00 0.00 2.71
5364 6015 2.738314 GCAGGGCAAATGAAACACAATC 59.262 45.455 0.00 0.00 0.00 2.67
5365 6016 3.555586 GCAGGGCAAATGAAACACAATCT 60.556 43.478 0.00 0.00 0.00 2.40
5366 6017 4.321899 GCAGGGCAAATGAAACACAATCTA 60.322 41.667 0.00 0.00 0.00 1.98
5367 6018 5.625197 GCAGGGCAAATGAAACACAATCTAT 60.625 40.000 0.00 0.00 0.00 1.98
5368 6019 6.405731 GCAGGGCAAATGAAACACAATCTATA 60.406 38.462 0.00 0.00 0.00 1.31
5369 6020 7.198390 CAGGGCAAATGAAACACAATCTATAG 58.802 38.462 0.00 0.00 0.00 1.31
5370 6021 6.322201 AGGGCAAATGAAACACAATCTATAGG 59.678 38.462 0.00 0.00 0.00 2.57
5371 6022 6.096846 GGGCAAATGAAACACAATCTATAGGT 59.903 38.462 0.00 0.00 0.00 3.08
5372 6023 6.974622 GGCAAATGAAACACAATCTATAGGTG 59.025 38.462 0.00 3.14 38.47 4.00
5373 6024 7.362920 GGCAAATGAAACACAATCTATAGGTGT 60.363 37.037 7.27 7.27 46.92 4.16
5374 6025 7.698130 GCAAATGAAACACAATCTATAGGTGTC 59.302 37.037 12.02 2.57 44.40 3.67
5375 6026 7.865706 AATGAAACACAATCTATAGGTGTCC 57.134 36.000 12.02 8.81 44.40 4.02
5376 6027 5.741011 TGAAACACAATCTATAGGTGTCCC 58.259 41.667 12.02 8.56 44.40 4.46
5377 6028 4.402056 AACACAATCTATAGGTGTCCCG 57.598 45.455 12.02 3.84 44.40 5.14
5378 6029 3.638860 ACACAATCTATAGGTGTCCCGA 58.361 45.455 7.27 0.00 41.63 5.14
5379 6030 3.637229 ACACAATCTATAGGTGTCCCGAG 59.363 47.826 7.27 0.93 41.63 4.63
5380 6031 3.005897 CACAATCTATAGGTGTCCCGAGG 59.994 52.174 0.00 0.00 35.12 4.63
5381 6032 2.563179 CAATCTATAGGTGTCCCGAGGG 59.437 54.545 0.65 0.65 35.12 4.30
5382 6033 0.481567 TCTATAGGTGTCCCGAGGGG 59.518 60.000 8.53 0.00 46.11 4.79
5392 6043 4.593033 CCGAGGGGGAATCGTCTA 57.407 61.111 0.00 0.00 38.50 2.59
5393 6044 2.342478 CCGAGGGGGAATCGTCTAG 58.658 63.158 0.00 0.00 38.50 2.43
5394 6045 0.178998 CCGAGGGGGAATCGTCTAGA 60.179 60.000 0.00 0.00 38.50 2.43
5395 6046 1.688772 CGAGGGGGAATCGTCTAGAA 58.311 55.000 0.00 0.00 35.48 2.10
5396 6047 2.240279 CGAGGGGGAATCGTCTAGAAT 58.760 52.381 0.00 0.00 35.48 2.40
5397 6048 2.628657 CGAGGGGGAATCGTCTAGAATT 59.371 50.000 0.00 0.00 35.48 2.17
5398 6049 3.825014 CGAGGGGGAATCGTCTAGAATTA 59.175 47.826 0.00 0.00 35.48 1.40
5399 6050 4.321082 CGAGGGGGAATCGTCTAGAATTAC 60.321 50.000 0.00 0.00 35.48 1.89
5400 6051 4.817286 AGGGGGAATCGTCTAGAATTACT 58.183 43.478 0.00 0.00 0.00 2.24
5401 6052 5.961897 AGGGGGAATCGTCTAGAATTACTA 58.038 41.667 0.00 0.00 0.00 1.82
5402 6053 6.563163 AGGGGGAATCGTCTAGAATTACTAT 58.437 40.000 0.00 0.00 0.00 2.12
5403 6054 7.706674 AGGGGGAATCGTCTAGAATTACTATA 58.293 38.462 0.00 0.00 0.00 1.31
5404 6055 7.835181 AGGGGGAATCGTCTAGAATTACTATAG 59.165 40.741 0.00 0.00 0.00 1.31
5405 6056 7.416551 GGGGGAATCGTCTAGAATTACTATAGC 60.417 44.444 0.00 0.00 0.00 2.97
5406 6057 7.122353 GGGGAATCGTCTAGAATTACTATAGCA 59.878 40.741 0.00 0.00 0.00 3.49
5407 6058 7.969508 GGGAATCGTCTAGAATTACTATAGCAC 59.030 40.741 0.00 0.00 0.00 4.40
5408 6059 8.732531 GGAATCGTCTAGAATTACTATAGCACT 58.267 37.037 0.00 0.00 0.00 4.40
5411 6062 9.947433 ATCGTCTAGAATTACTATAGCACTAGT 57.053 33.333 0.00 0.00 36.04 2.57
5412 6063 9.775854 TCGTCTAGAATTACTATAGCACTAGTT 57.224 33.333 0.00 0.00 33.96 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.078848 GCACTCGGCCATCTTCTGT 60.079 57.895 2.24 0.00 36.11 3.41
82 83 3.461773 CCCGAGCTCCATGGACGT 61.462 66.667 11.44 0.00 0.00 4.34
138 140 3.591254 AAGGAGACAACGAGCCCGC 62.591 63.158 0.00 0.00 39.95 6.13
141 143 0.108567 GAGGAAGGAGACAACGAGCC 60.109 60.000 0.00 0.00 0.00 4.70
142 144 0.456995 CGAGGAAGGAGACAACGAGC 60.457 60.000 0.00 0.00 0.00 5.03
143 145 0.456995 GCGAGGAAGGAGACAACGAG 60.457 60.000 0.00 0.00 0.00 4.18
144 146 0.894184 AGCGAGGAAGGAGACAACGA 60.894 55.000 0.00 0.00 0.00 3.85
145 147 0.038159 AAGCGAGGAAGGAGACAACG 60.038 55.000 0.00 0.00 0.00 4.10
146 148 1.433534 CAAGCGAGGAAGGAGACAAC 58.566 55.000 0.00 0.00 0.00 3.32
147 149 0.321671 CCAAGCGAGGAAGGAGACAA 59.678 55.000 0.00 0.00 0.00 3.18
169 171 3.430473 TTTTTCCAGCCGTGTCCAT 57.570 47.368 0.00 0.00 0.00 3.41
186 188 5.590976 TTTTTGGCCTGGGGATAATTTTT 57.409 34.783 3.32 0.00 0.00 1.94
187 189 5.794767 ATTTTTGGCCTGGGGATAATTTT 57.205 34.783 3.32 0.00 0.00 1.82
188 190 5.794767 AATTTTTGGCCTGGGGATAATTT 57.205 34.783 3.32 0.00 0.00 1.82
189 191 5.252630 TGAAATTTTTGGCCTGGGGATAATT 59.747 36.000 3.32 0.00 0.00 1.40
190 192 4.787534 TGAAATTTTTGGCCTGGGGATAAT 59.212 37.500 3.32 0.00 0.00 1.28
192 194 3.517500 GTGAAATTTTTGGCCTGGGGATA 59.482 43.478 3.32 0.00 0.00 2.59
198 201 1.794512 CCGGTGAAATTTTTGGCCTG 58.205 50.000 3.32 0.00 0.00 4.85
201 204 1.147473 CTGCCGGTGAAATTTTTGGC 58.853 50.000 1.90 13.71 42.76 4.52
203 206 1.147473 GGCTGCCGGTGAAATTTTTG 58.853 50.000 1.35 0.00 0.00 2.44
296 301 5.221303 GGGCTATGAGCTTGCATGAAAAATA 60.221 40.000 3.33 0.00 41.99 1.40
309 314 2.782341 AGAAATGGAAGGGCTATGAGCT 59.218 45.455 0.00 0.00 41.99 4.09
336 341 6.575162 AAATGCAGTAGTTTTCCTAACTGG 57.425 37.500 0.00 0.00 31.20 4.00
374 379 4.089361 TCATGGAAGTAGAAGTCTCTGCA 58.911 43.478 0.00 0.00 36.79 4.41
375 380 4.727507 TCATGGAAGTAGAAGTCTCTGC 57.272 45.455 0.00 0.00 34.68 4.26
382 390 7.510549 TTCAAAACCTTCATGGAAGTAGAAG 57.489 36.000 5.37 0.00 37.92 2.85
394 402 3.013921 AGCAGACGTTTCAAAACCTTCA 58.986 40.909 0.00 0.00 35.51 3.02
408 416 1.457303 CAAACCTTCTCGAAGCAGACG 59.543 52.381 1.13 0.00 37.11 4.18
439 447 6.095021 GGGGCTTCGTACTATTTTTCAAAGAT 59.905 38.462 0.00 0.00 0.00 2.40
457 468 1.004200 TCGGACTTTTCGGGGCTTC 60.004 57.895 0.00 0.00 0.00 3.86
470 481 0.107654 CACATTCCCCCTTCTCGGAC 60.108 60.000 0.00 0.00 33.16 4.79
570 595 4.293648 GGGCGTTTGTGGGTTGGC 62.294 66.667 0.00 0.00 0.00 4.52
574 599 1.258445 TTTTGTGGGCGTTTGTGGGT 61.258 50.000 0.00 0.00 0.00 4.51
578 603 0.458260 GGAGTTTTGTGGGCGTTTGT 59.542 50.000 0.00 0.00 0.00 2.83
583 608 3.283684 TGCGGAGTTTTGTGGGCG 61.284 61.111 0.00 0.00 0.00 6.13
584 609 2.335011 GTGCGGAGTTTTGTGGGC 59.665 61.111 0.00 0.00 0.00 5.36
585 610 1.795170 CTGGTGCGGAGTTTTGTGGG 61.795 60.000 0.00 0.00 0.00 4.61
588 613 1.152963 AGCTGGTGCGGAGTTTTGT 60.153 52.632 0.00 0.00 45.42 2.83
589 614 1.576421 GAGCTGGTGCGGAGTTTTG 59.424 57.895 0.00 0.00 45.42 2.44
590 615 1.961277 CGAGCTGGTGCGGAGTTTT 60.961 57.895 0.00 0.00 45.42 2.43
591 616 2.357517 CGAGCTGGTGCGGAGTTT 60.358 61.111 0.00 0.00 45.42 2.66
628 653 4.678743 GGAAGGTGGTGGTGGGGC 62.679 72.222 0.00 0.00 0.00 5.80
629 654 3.979497 GGGAAGGTGGTGGTGGGG 61.979 72.222 0.00 0.00 0.00 4.96
630 655 3.979497 GGGGAAGGTGGTGGTGGG 61.979 72.222 0.00 0.00 0.00 4.61
631 656 3.979497 GGGGGAAGGTGGTGGTGG 61.979 72.222 0.00 0.00 0.00 4.61
658 683 4.796231 CGGCGCTAAGCTGTCCGT 62.796 66.667 7.64 0.00 46.91 4.69
680 705 3.497932 CTGCTGCTTCGCTGGCTC 61.498 66.667 0.00 0.00 0.00 4.70
763 788 6.406692 TTTAGTGGGTGATTAGCTAGCTAG 57.593 41.667 23.03 16.84 0.00 3.42
764 789 6.996180 ATTTAGTGGGTGATTAGCTAGCTA 57.004 37.500 20.67 20.67 0.00 3.32
765 790 5.896073 ATTTAGTGGGTGATTAGCTAGCT 57.104 39.130 23.12 23.12 0.00 3.32
839 864 3.424859 TTAAAGCGCGGGCGGAAC 61.425 61.111 19.46 0.00 46.35 3.62
871 901 8.357402 GTGGGCTCCGTTAATTAATTAATCAAT 58.643 33.333 20.60 0.00 35.02 2.57
930 972 3.160047 ATCCTCCTCCTGCCGCTG 61.160 66.667 0.00 0.00 0.00 5.18
933 975 2.206536 GGAGATCCTCCTCCTGCCG 61.207 68.421 5.78 0.00 46.41 5.69
934 976 3.884318 GGAGATCCTCCTCCTGCC 58.116 66.667 5.78 0.00 46.41 4.85
943 985 3.160047 CCGCTGGCTGGAGATCCT 61.160 66.667 0.00 0.00 36.82 3.24
949 991 4.113815 CAATCCCCGCTGGCTGGA 62.114 66.667 4.63 4.18 0.00 3.86
952 994 3.099170 ATCCAATCCCCGCTGGCT 61.099 61.111 0.00 0.00 32.33 4.75
953 995 2.595754 GATCCAATCCCCGCTGGC 60.596 66.667 0.00 0.00 32.33 4.85
954 996 2.281070 CGATCCAATCCCCGCTGG 60.281 66.667 0.00 0.00 0.00 4.85
955 997 2.281070 CCGATCCAATCCCCGCTG 60.281 66.667 0.00 0.00 0.00 5.18
956 998 3.560251 CCCGATCCAATCCCCGCT 61.560 66.667 0.00 0.00 0.00 5.52
958 1000 4.988598 CGCCCGATCCAATCCCCG 62.989 72.222 0.00 0.00 0.00 5.73
959 1001 4.643387 CCGCCCGATCCAATCCCC 62.643 72.222 0.00 0.00 0.00 4.81
1292 1335 1.656441 CCACACACAGCCTTGAAGC 59.344 57.895 0.00 0.00 0.00 3.86
1293 1336 0.466189 ACCCACACACAGCCTTGAAG 60.466 55.000 0.00 0.00 0.00 3.02
1294 1337 0.033601 AACCCACACACAGCCTTGAA 60.034 50.000 0.00 0.00 0.00 2.69
1295 1338 0.033601 AAACCCACACACAGCCTTGA 60.034 50.000 0.00 0.00 0.00 3.02
1296 1339 0.823460 AAAACCCACACACAGCCTTG 59.177 50.000 0.00 0.00 0.00 3.61
1345 1398 1.451651 GCGAACCAAATCAAAACAGCG 59.548 47.619 0.00 0.00 0.00 5.18
1536 1589 0.178068 GAGATGCCCGTACATGTGGT 59.822 55.000 9.11 0.00 0.00 4.16
1537 1590 0.875908 CGAGATGCCCGTACATGTGG 60.876 60.000 9.11 1.98 0.00 4.17
1538 1591 1.490693 GCGAGATGCCCGTACATGTG 61.491 60.000 9.11 0.00 37.76 3.21
1618 1678 2.573340 CACCAAAATCGGCCCAGC 59.427 61.111 0.00 0.00 0.00 4.85
1624 1685 1.080839 CAACCGCCACCAAAATCGG 60.081 57.895 0.00 0.00 46.61 4.18
1625 1686 1.732683 GCAACCGCCACCAAAATCG 60.733 57.895 0.00 0.00 0.00 3.34
1685 1771 3.117738 CCCAAATCCTGTCCTAAGCATCT 60.118 47.826 0.00 0.00 0.00 2.90
1777 1869 5.282510 CCGACTAGAACAGTTCATACCATC 58.717 45.833 15.85 3.60 37.72 3.51
1778 1870 4.099573 CCCGACTAGAACAGTTCATACCAT 59.900 45.833 15.85 0.00 37.72 3.55
1779 1871 3.446161 CCCGACTAGAACAGTTCATACCA 59.554 47.826 15.85 0.00 37.72 3.25
1780 1872 3.181478 CCCCGACTAGAACAGTTCATACC 60.181 52.174 15.85 1.56 37.72 2.73
1844 1936 4.813027 AGTCAAATTGTTCATGATGCACC 58.187 39.130 0.00 0.00 0.00 5.01
1964 2066 7.042254 CCAGTGGTAGTTAGTCTGTTTTACAAC 60.042 40.741 0.00 0.00 0.00 3.32
2039 2142 6.317140 CAGCATTTCAGAAGCTACATTTCCTA 59.683 38.462 0.00 0.00 36.73 2.94
2090 2193 3.067461 TGTTTGGTACTTTGGTGCATGAC 59.933 43.478 0.00 0.00 0.00 3.06
2137 2240 4.087510 CACTTATGTTGTCATGCAGTGG 57.912 45.455 0.00 0.00 39.89 4.00
2299 2403 8.806429 TCCATGAAAATTGCATTTCTAGACTA 57.194 30.769 12.67 0.00 39.51 2.59
2301 2405 8.937634 AATCCATGAAAATTGCATTTCTAGAC 57.062 30.769 12.67 0.00 39.51 2.59
2352 2456 8.345565 GCTTTCTCAACTCAAGACTGATAAAAA 58.654 33.333 0.00 0.00 0.00 1.94
2355 2459 6.425114 GTGCTTTCTCAACTCAAGACTGATAA 59.575 38.462 0.00 0.00 0.00 1.75
2357 2461 4.754114 GTGCTTTCTCAACTCAAGACTGAT 59.246 41.667 0.00 0.00 0.00 2.90
2358 2462 4.122776 GTGCTTTCTCAACTCAAGACTGA 58.877 43.478 0.00 0.00 0.00 3.41
2361 2465 4.572389 TGAAGTGCTTTCTCAACTCAAGAC 59.428 41.667 3.75 0.00 36.71 3.01
2378 2482 0.806868 AAGGCACATCGCATGAAGTG 59.193 50.000 0.00 0.00 44.54 3.16
2429 2533 7.280876 TGAGAATTCCAGAAAATATCAACGGAG 59.719 37.037 0.65 0.00 0.00 4.63
2433 2537 8.743714 AGGTTGAGAATTCCAGAAAATATCAAC 58.256 33.333 18.82 18.82 40.46 3.18
2476 2580 1.530655 TGTGTCGCCCTGAGAGACA 60.531 57.895 0.00 0.00 41.90 3.41
2525 2629 4.146564 CCAATATCACCATGCATTGAGGA 58.853 43.478 8.47 4.32 31.44 3.71
2644 2748 8.759641 CAGAGTGAAAAATATACCTCATTCTCG 58.240 37.037 4.05 0.00 33.95 4.04
3241 3349 6.393990 CATTACAGCTATCCATCTACCTGAC 58.606 44.000 0.00 0.00 0.00 3.51
3244 3352 5.655394 TCCATTACAGCTATCCATCTACCT 58.345 41.667 0.00 0.00 0.00 3.08
3274 3382 0.320374 AATCGCCTGAAGGAACACGA 59.680 50.000 0.00 0.00 37.39 4.35
3298 3406 3.952967 GGTAACCAGAGATAGACCTTCGT 59.047 47.826 0.00 0.00 0.00 3.85
3307 3415 5.853572 AAAAACCCAGGTAACCAGAGATA 57.146 39.130 0.00 0.00 37.17 1.98
3328 3436 3.263170 TGACCAGAACTATGGCTAGCAAA 59.737 43.478 18.24 4.19 44.80 3.68
3565 3673 1.308069 CGGTCCCCAACAGAGCAATG 61.308 60.000 0.00 0.00 0.00 2.82
3574 3682 1.957695 GACGTTCACGGTCCCCAAC 60.958 63.158 4.07 0.00 44.95 3.77
3577 3685 2.048503 CAGACGTTCACGGTCCCC 60.049 66.667 4.07 0.00 44.95 4.81
3607 3715 3.074687 TGCCATTACCACCAAGTAGGAAA 59.925 43.478 0.00 0.00 41.22 3.13
3674 3782 4.139786 GCTTCATATGTCATGGTGACCAT 58.860 43.478 12.20 12.20 46.40 3.55
3703 3811 4.513692 TCGACGAACATTTTCAAGTTCCAT 59.486 37.500 0.00 0.00 40.69 3.41
3910 4018 3.118186 TGCAGGTCATCATGATGTCATCA 60.118 43.478 30.01 17.70 44.55 3.07
3913 4021 2.914059 CTGCAGGTCATCATGATGTCA 58.086 47.619 30.01 19.90 39.72 3.58
4018 4126 1.153823 CTCGTTCCTGTACTGCGGG 60.154 63.158 0.00 0.00 45.18 6.13
4078 4186 2.823593 TCCATGAATGCGGCACCG 60.824 61.111 4.03 4.30 43.09 4.94
4108 4216 0.457851 CGCTCCAGTACCTCCTGAAG 59.542 60.000 0.00 0.00 34.23 3.02
4113 4221 1.076923 TCCTCGCTCCAGTACCTCC 60.077 63.158 0.00 0.00 0.00 4.30
4255 4363 2.746375 GGAGGTGTCGATGGCCCAT 61.746 63.158 0.00 0.00 0.00 4.00
4306 4414 0.386858 TGACGTCGTAGTGCTTCTGC 60.387 55.000 11.62 0.00 40.20 4.26
4397 4505 2.620585 GCTATTTGTCCCAGCCATCTTC 59.379 50.000 0.00 0.00 0.00 2.87
4490 4598 1.923006 TTCCCACGGGACCAACAACA 61.923 55.000 3.66 0.00 45.11 3.33
4603 4715 0.391597 TGAGGAACCGGACACTGAAC 59.608 55.000 9.46 0.00 0.00 3.18
4613 4725 2.290641 CCACAAGTTCTTTGAGGAACCG 59.709 50.000 2.79 0.00 46.80 4.44
4615 4727 3.551846 TCCCACAAGTTCTTTGAGGAAC 58.448 45.455 5.16 0.00 46.80 3.62
4616 4728 3.943671 TCCCACAAGTTCTTTGAGGAA 57.056 42.857 5.16 0.00 46.80 3.36
4618 4730 3.754965 TGATCCCACAAGTTCTTTGAGG 58.245 45.455 0.00 0.00 44.40 3.86
4622 4737 4.154942 AGCATTGATCCCACAAGTTCTTT 58.845 39.130 0.00 0.00 33.22 2.52
4624 4739 3.245016 TGAGCATTGATCCCACAAGTTCT 60.245 43.478 0.00 0.00 33.22 3.01
4740 4859 9.723601 ATAAGCAAAATCACACCATTTACAATT 57.276 25.926 0.00 0.00 0.00 2.32
4771 4894 7.325660 TCTAAGATGAATTCATTCCTTGCAC 57.674 36.000 21.57 6.86 36.57 4.57
4772 4895 7.558807 ACATCTAAGATGAATTCATTCCTTGCA 59.441 33.333 21.57 11.88 36.57 4.08
4773 4896 7.938715 ACATCTAAGATGAATTCATTCCTTGC 58.061 34.615 21.57 8.24 36.57 4.01
4777 4900 7.589221 GCGAAACATCTAAGATGAATTCATTCC 59.411 37.037 21.57 10.34 36.57 3.01
4779 4902 7.988737 TGCGAAACATCTAAGATGAATTCATT 58.011 30.769 21.57 10.60 36.57 2.57
4780 4903 7.558161 TGCGAAACATCTAAGATGAATTCAT 57.442 32.000 20.85 20.85 39.70 2.57
4781 4904 6.983474 TGCGAAACATCTAAGATGAATTCA 57.017 33.333 11.26 11.26 0.00 2.57
4802 4925 2.788786 CCAGTGACGTGAACAAAATTGC 59.211 45.455 0.00 0.00 0.00 3.56
4844 4967 5.206299 CACGCCACAAAACGTTAGAATTTA 58.794 37.500 0.00 0.00 41.32 1.40
4891 5537 3.320826 GCAAAGGTTGGACTTGTACCAAT 59.679 43.478 0.00 0.00 46.78 3.16
4898 5544 1.106944 ACGGGCAAAGGTTGGACTTG 61.107 55.000 0.00 0.00 0.00 3.16
4907 5553 1.611519 TTTAGTTGGACGGGCAAAGG 58.388 50.000 0.00 0.00 0.00 3.11
4919 5565 8.756376 CAATTTGTGCAGTGAAATTTTAGTTG 57.244 30.769 7.84 0.00 30.94 3.16
4936 5582 3.056678 TGGTAGCTTCCATGCAATTTGTG 60.057 43.478 8.18 0.00 34.99 3.33
4994 5644 2.559668 TGTAGGGTCGTACTTTCCTGTG 59.440 50.000 7.68 0.00 0.00 3.66
5146 5796 2.627221 GCATCCTCAGCTAGATCAGTCA 59.373 50.000 0.00 0.00 0.00 3.41
5197 5847 1.134491 ACCCGCGGAAGGAAGAAATAG 60.134 52.381 30.73 7.25 0.00 1.73
5245 5895 1.301677 CTTCGGAGAAACCAGCCAGC 61.302 60.000 0.00 0.00 45.90 4.85
5262 5912 3.950397 TGGTATGAATCGCAGGAAACTT 58.050 40.909 0.00 0.00 40.21 2.66
5314 5964 7.115095 GGTAGTACTGCTATATCTTTTTCTGCG 59.885 40.741 10.95 0.00 31.50 5.18
5355 6006 4.468510 TCGGGACACCTATAGATTGTGTTT 59.531 41.667 12.66 0.00 42.89 2.83
5356 6007 4.028131 TCGGGACACCTATAGATTGTGTT 58.972 43.478 12.66 0.69 42.89 3.32
5357 6008 3.637229 CTCGGGACACCTATAGATTGTGT 59.363 47.826 11.62 11.62 45.34 3.72
5358 6009 3.005897 CCTCGGGACACCTATAGATTGTG 59.994 52.174 10.68 8.42 36.11 3.33
5359 6010 3.231818 CCTCGGGACACCTATAGATTGT 58.768 50.000 0.00 3.98 33.28 2.71
5360 6011 2.563179 CCCTCGGGACACCTATAGATTG 59.437 54.545 0.00 0.51 37.50 2.67
5361 6012 2.890814 CCCTCGGGACACCTATAGATT 58.109 52.381 0.00 0.00 37.50 2.40
5362 6013 2.606751 CCCTCGGGACACCTATAGAT 57.393 55.000 0.00 0.00 37.50 1.98
5375 6026 0.178998 TCTAGACGATTCCCCCTCGG 60.179 60.000 0.00 0.00 40.37 4.63
5376 6027 1.688772 TTCTAGACGATTCCCCCTCG 58.311 55.000 0.00 0.00 41.77 4.63
5377 6028 4.833938 AGTAATTCTAGACGATTCCCCCTC 59.166 45.833 0.00 0.00 0.00 4.30
5378 6029 4.817286 AGTAATTCTAGACGATTCCCCCT 58.183 43.478 0.00 0.00 0.00 4.79
5379 6030 6.854091 ATAGTAATTCTAGACGATTCCCCC 57.146 41.667 0.00 0.00 31.67 5.40
5380 6031 7.122353 TGCTATAGTAATTCTAGACGATTCCCC 59.878 40.741 0.84 0.00 31.67 4.81
5381 6032 7.969508 GTGCTATAGTAATTCTAGACGATTCCC 59.030 40.741 0.84 0.00 31.67 3.97
5382 6033 8.732531 AGTGCTATAGTAATTCTAGACGATTCC 58.267 37.037 0.84 0.00 31.67 3.01
5385 6036 9.947433 ACTAGTGCTATAGTAATTCTAGACGAT 57.053 33.333 16.04 0.00 34.21 3.73
5386 6037 9.775854 AACTAGTGCTATAGTAATTCTAGACGA 57.224 33.333 16.04 0.00 34.90 4.20


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

AutoCloner maintained by Alex Coulton.