Multiple sequence alignment - TraesCS3A01G414100

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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 TraesCS3A01G414100 chr3A 100.000 6473 0 0 1 6473 657922783 657929255 0.000000e+00 11954.0
1 TraesCS3A01G414100 chr3A 87.059 85 11 0 3822 3906 550415739 550415655 5.340000e-16 97.1
2 TraesCS3A01G414100 chr3A 90.909 55 3 2 4767 4819 657927518 657927572 9.000000e-09 73.1
3 TraesCS3A01G414100 chr3A 90.909 55 3 2 4736 4790 657927549 657927601 9.000000e-09 73.1
4 TraesCS3A01G414100 chr3D 94.387 5095 185 40 701 5743 523154279 523159324 0.000000e+00 7731.0
5 TraesCS3A01G414100 chr3D 93.165 556 29 6 1 554 523153591 523154139 0.000000e+00 808.0
6 TraesCS3A01G414100 chr3D 91.765 425 19 5 6063 6473 523159636 523160058 1.560000e-160 577.0
7 TraesCS3A01G414100 chr3D 96.053 76 3 0 577 652 523154134 523154209 2.450000e-24 124.0
8 TraesCS3A01G414100 chr3D 90.909 55 3 2 4767 4819 523158301 523158355 9.000000e-09 73.1
9 TraesCS3A01G414100 chr3D 90.909 55 3 2 4736 4790 523158362 523158414 9.000000e-09 73.1
10 TraesCS3A01G414100 chr3D 100.000 33 0 0 651 683 523154246 523154278 1.950000e-05 62.1
11 TraesCS3A01G414100 chr3B 96.209 1688 38 8 1958 3634 689511314 689512986 0.000000e+00 2739.0
12 TraesCS3A01G414100 chr3B 94.348 1380 59 8 4302 5673 689514068 689515436 0.000000e+00 2098.0
13 TraesCS3A01G414100 chr3B 94.432 1311 35 17 651 1960 689509920 689511193 0.000000e+00 1982.0
14 TraesCS3A01G414100 chr3B 93.103 493 33 1 3821 4312 689513459 689513951 0.000000e+00 721.0
15 TraesCS3A01G414100 chr3B 85.414 665 28 27 1 652 689509275 689509883 1.530000e-175 627.0
16 TraesCS3A01G414100 chr3B 88.471 425 17 6 6074 6473 689515796 689516213 9.760000e-133 484.0
17 TraesCS3A01G414100 chr3B 94.397 232 8 3 3615 3842 689513162 689513392 1.030000e-92 351.0
18 TraesCS3A01G414100 chr3B 85.263 95 12 1 3814 3906 157247083 157247177 5.340000e-16 97.1
19 TraesCS3A01G414100 chr3B 90.909 55 3 2 4736 4790 689514533 689514585 9.000000e-09 73.1
20 TraesCS3A01G414100 chr3B 89.091 55 4 2 4767 4819 689514502 689514556 4.190000e-07 67.6
21 TraesCS3A01G414100 chr7A 91.549 71 6 0 3831 3901 205123831 205123901 1.490000e-16 99.0
22 TraesCS3A01G414100 chr5D 86.250 80 11 0 3822 3901 309047472 309047393 3.220000e-13 87.9
23 TraesCS3A01G414100 chr5D 86.667 75 10 0 3827 3901 60477049 60476975 4.160000e-12 84.2
24 TraesCS3A01G414100 chr1A 87.179 78 7 3 3827 3901 236718478 236718401 1.160000e-12 86.1
25 TraesCS3A01G414100 chr4B 86.667 75 10 0 3827 3901 270831750 270831676 4.160000e-12 84.2


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 TraesCS3A01G414100 chr3A 657922783 657929255 6472 False 4033.400000 11954 93.939333 1 6473 3 chr3A.!!$F1 6472
1 TraesCS3A01G414100 chr3D 523153591 523160058 6467 False 1349.757143 7731 93.884000 1 6473 7 chr3D.!!$F1 6472
2 TraesCS3A01G414100 chr3B 689509275 689516213 6938 False 1015.855556 2739 91.819333 1 6473 9 chr3B.!!$F2 6472

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
121 122 0.109132 ACCATTTTTGCGCTGCTAGC 60.109 50.0 9.73 8.1 38.02 3.42 F
122 123 0.171903 CCATTTTTGCGCTGCTAGCT 59.828 50.0 17.23 0.0 39.60 3.32 F
131 132 0.319383 CGCTGCTAGCTGTATCCTGG 60.319 60.0 21.03 0.0 39.60 4.45 F
132 133 0.755686 GCTGCTAGCTGTATCCTGGT 59.244 55.0 21.03 0.0 38.45 4.00 F
495 522 0.912487 AATGGGGTCTCGGCTAACCA 60.912 55.0 0.00 0.0 37.28 3.67 F
3253 3475 1.035932 AGGCGCCGCTAAGAGACTTA 61.036 55.0 23.20 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2258 1.673033 GCGCTGCTTGAGTAGGAAAGA 60.673 52.381 0.00 0.00 0.00 2.52 R
2099 2312 7.669304 TCTTCCACACATATTTGAGAATTCCAA 59.331 33.333 0.65 3.65 0.00 3.53 R
2538 2751 4.037803 ACCTGCGCAATTTATATGCATCAA 59.962 37.500 13.05 0.00 44.01 2.57 R
3028 3250 3.635373 CCTCCAATTGTAGGTAGCTCGTA 59.365 47.826 8.88 0.00 0.00 3.43 R
3341 3563 2.158682 AGTAACACCTCACCATGTGCAA 60.159 45.455 0.00 0.00 35.90 4.08 R
5579 6252 0.246360 ACATGGAGAACGCGATCACA 59.754 50.000 15.93 14.77 0.00 3.58 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
20 21 3.813529 CTAGTTTTGAGTTTGAGGCCG 57.186 47.619 0.00 0.00 0.00 6.13
21 22 0.668535 AGTTTTGAGTTTGAGGCCGC 59.331 50.000 0.00 0.00 0.00 6.53
110 111 6.657541 TCTGGTAGCTTTAATCGACCATTTTT 59.342 34.615 2.80 0.00 38.29 1.94
121 122 0.109132 ACCATTTTTGCGCTGCTAGC 60.109 50.000 9.73 8.10 38.02 3.42
122 123 0.171903 CCATTTTTGCGCTGCTAGCT 59.828 50.000 17.23 0.00 39.60 3.32
123 124 1.265568 CATTTTTGCGCTGCTAGCTG 58.734 50.000 17.23 16.92 39.60 4.24
124 125 0.883833 ATTTTTGCGCTGCTAGCTGT 59.116 45.000 21.03 0.00 39.60 4.40
125 126 1.518325 TTTTTGCGCTGCTAGCTGTA 58.482 45.000 21.03 6.22 39.60 2.74
126 127 1.737838 TTTTGCGCTGCTAGCTGTAT 58.262 45.000 21.03 0.00 39.60 2.29
127 128 1.290203 TTTGCGCTGCTAGCTGTATC 58.710 50.000 21.03 11.68 39.60 2.24
128 129 0.530650 TTGCGCTGCTAGCTGTATCC 60.531 55.000 21.03 9.02 39.60 2.59
129 130 1.365633 GCGCTGCTAGCTGTATCCT 59.634 57.895 21.03 0.00 39.60 3.24
130 131 0.943359 GCGCTGCTAGCTGTATCCTG 60.943 60.000 21.03 7.37 39.60 3.86
131 132 0.319383 CGCTGCTAGCTGTATCCTGG 60.319 60.000 21.03 0.00 39.60 4.45
132 133 0.755686 GCTGCTAGCTGTATCCTGGT 59.244 55.000 21.03 0.00 38.45 4.00
133 134 1.139853 GCTGCTAGCTGTATCCTGGTT 59.860 52.381 21.03 0.00 38.45 3.67
134 135 2.420687 GCTGCTAGCTGTATCCTGGTTT 60.421 50.000 21.03 0.00 38.45 3.27
135 136 3.878778 CTGCTAGCTGTATCCTGGTTTT 58.121 45.455 17.23 0.00 0.00 2.43
136 137 3.609853 TGCTAGCTGTATCCTGGTTTTG 58.390 45.455 17.23 0.00 0.00 2.44
137 138 3.009033 TGCTAGCTGTATCCTGGTTTTGT 59.991 43.478 17.23 0.00 0.00 2.83
138 139 4.010349 GCTAGCTGTATCCTGGTTTTGTT 58.990 43.478 7.70 0.00 0.00 2.83
139 140 4.142600 GCTAGCTGTATCCTGGTTTTGTTG 60.143 45.833 7.70 0.00 0.00 3.33
140 141 4.098914 AGCTGTATCCTGGTTTTGTTGA 57.901 40.909 0.00 0.00 0.00 3.18
141 142 4.666512 AGCTGTATCCTGGTTTTGTTGAT 58.333 39.130 0.00 0.00 0.00 2.57
146 147 6.744112 TGTATCCTGGTTTTGTTGATTGTTC 58.256 36.000 0.00 0.00 0.00 3.18
151 171 5.048364 CCTGGTTTTGTTGATTGTTCCGATA 60.048 40.000 0.00 0.00 0.00 2.92
152 172 6.392625 TGGTTTTGTTGATTGTTCCGATAA 57.607 33.333 0.00 0.00 0.00 1.75
153 173 6.987386 TGGTTTTGTTGATTGTTCCGATAAT 58.013 32.000 0.00 0.00 0.00 1.28
154 174 7.437748 TGGTTTTGTTGATTGTTCCGATAATT 58.562 30.769 0.00 0.00 0.00 1.40
165 185 6.403333 TGTTCCGATAATTTATATCAGCGC 57.597 37.500 0.00 0.00 0.00 5.92
185 205 7.767198 TCAGCGCATATTTAGGTAGTTTTTAGT 59.233 33.333 11.47 0.00 0.00 2.24
187 207 8.395633 AGCGCATATTTAGGTAGTTTTTAGTTG 58.604 33.333 11.47 0.00 0.00 3.16
290 315 5.104900 AGTCACCGTATCCTTAAGCTGATTT 60.105 40.000 0.00 0.00 0.00 2.17
398 425 9.829507 ATTTAGTAGATTCTTGAATGTCTCCTG 57.170 33.333 0.09 0.00 0.00 3.86
408 435 6.875726 TCTTGAATGTCTCCTGTTGATGTTAG 59.124 38.462 0.00 0.00 0.00 2.34
440 467 3.154710 AGTTTTTCTGGGGACGATTTCC 58.845 45.455 0.00 0.00 45.00 3.13
495 522 0.912487 AATGGGGTCTCGGCTAACCA 60.912 55.000 0.00 0.00 37.28 3.67
517 544 7.932335 ACCATACGAAGAACTAGATACTTCTG 58.068 38.462 18.08 15.13 38.16 3.02
554 602 5.593010 CATAGCTGAAGTCAGTTACTACCC 58.407 45.833 9.94 0.00 45.45 3.69
555 603 2.832733 AGCTGAAGTCAGTTACTACCCC 59.167 50.000 9.94 0.00 45.45 4.95
556 604 2.832733 GCTGAAGTCAGTTACTACCCCT 59.167 50.000 9.94 0.00 45.45 4.79
557 605 3.261137 GCTGAAGTCAGTTACTACCCCTT 59.739 47.826 9.94 0.00 45.45 3.95
558 606 4.262938 GCTGAAGTCAGTTACTACCCCTTT 60.263 45.833 9.94 0.00 45.45 3.11
559 607 5.046807 GCTGAAGTCAGTTACTACCCCTTTA 60.047 44.000 9.94 0.00 45.45 1.85
560 608 6.519551 GCTGAAGTCAGTTACTACCCCTTTAA 60.520 42.308 9.94 0.00 45.45 1.52
561 609 7.563724 TGAAGTCAGTTACTACCCCTTTAAT 57.436 36.000 0.00 0.00 37.50 1.40
562 610 7.618137 TGAAGTCAGTTACTACCCCTTTAATC 58.382 38.462 0.00 0.00 37.50 1.75
563 611 7.236019 TGAAGTCAGTTACTACCCCTTTAATCA 59.764 37.037 0.00 0.00 37.50 2.57
564 612 7.184067 AGTCAGTTACTACCCCTTTAATCAG 57.816 40.000 0.00 0.00 36.36 2.90
565 613 6.729569 AGTCAGTTACTACCCCTTTAATCAGT 59.270 38.462 0.00 0.00 36.36 3.41
566 614 7.897565 AGTCAGTTACTACCCCTTTAATCAGTA 59.102 37.037 0.00 0.00 36.36 2.74
567 615 8.534496 GTCAGTTACTACCCCTTTAATCAGTAA 58.466 37.037 0.00 0.00 0.00 2.24
568 616 9.275572 TCAGTTACTACCCCTTTAATCAGTAAT 57.724 33.333 0.00 0.00 32.77 1.89
569 617 9.326413 CAGTTACTACCCCTTTAATCAGTAATG 57.674 37.037 0.00 0.00 32.77 1.90
570 618 8.491958 AGTTACTACCCCTTTAATCAGTAATGG 58.508 37.037 0.00 0.00 36.95 3.16
575 623 5.646692 CCCTTTAATCAGTAATGGGGAGA 57.353 43.478 7.77 0.00 46.64 3.71
576 624 6.013554 CCCTTTAATCAGTAATGGGGAGAA 57.986 41.667 7.77 0.00 46.64 2.87
577 625 5.828328 CCCTTTAATCAGTAATGGGGAGAAC 59.172 44.000 7.77 0.00 46.64 3.01
578 626 6.353951 CCCTTTAATCAGTAATGGGGAGAACT 60.354 42.308 7.77 0.00 46.64 3.01
579 627 7.147373 CCCTTTAATCAGTAATGGGGAGAACTA 60.147 40.741 7.77 0.00 46.64 2.24
580 628 7.715686 CCTTTAATCAGTAATGGGGAGAACTAC 59.284 40.741 0.00 0.00 34.66 2.73
581 629 5.632034 AATCAGTAATGGGGAGAACTACC 57.368 43.478 0.00 0.00 0.00 3.18
594 642 6.464607 GGGGAGAACTACCTGGAGAAAATATC 60.465 46.154 0.00 0.00 32.79 1.63
611 659 7.558807 AGAAAATATCAGTGGCTTCATTGATGA 59.441 33.333 12.52 0.00 44.20 2.92
823 909 4.988540 TCACTACGACATGTTTTCCTCTTG 59.011 41.667 0.00 0.00 0.00 3.02
849 935 5.468409 TGACTTTGTTCGATCAGCATTAACA 59.532 36.000 0.00 0.00 0.00 2.41
852 938 7.370383 ACTTTGTTCGATCAGCATTAACAATT 58.630 30.769 0.00 0.00 39.15 2.32
880 966 6.779117 TCTGCTGTGTTACTATTACGTACTC 58.221 40.000 0.00 0.00 0.00 2.59
1011 1097 6.867519 TTGTACTGATCTATGGAAGTGGAA 57.132 37.500 0.00 0.00 0.00 3.53
1027 1113 4.573900 AGTGGAAACTCTACAAGATGCTG 58.426 43.478 0.00 0.00 29.47 4.41
1165 1251 8.989980 GGCTATATTTGAAGGTACATAACTCAC 58.010 37.037 0.00 0.00 0.00 3.51
1195 1281 5.483583 TGTTTCCATTTGCTTATAGCCCTTT 59.516 36.000 0.00 0.00 41.51 3.11
1493 1581 5.415701 ACAGTATTTAAGCTGTGATGTTGGG 59.584 40.000 8.10 0.00 43.45 4.12
1533 1621 6.460781 ACAAAGTTCATGTTTCATGCATCAT 58.539 32.000 0.00 0.00 0.00 2.45
1536 1624 9.093970 CAAAGTTCATGTTTCATGCATCATATT 57.906 29.630 0.00 0.00 0.00 1.28
1537 1625 8.642908 AAGTTCATGTTTCATGCATCATATTG 57.357 30.769 0.00 0.00 0.00 1.90
1538 1626 8.002984 AGTTCATGTTTCATGCATCATATTGA 57.997 30.769 0.00 0.00 0.00 2.57
1539 1627 8.638873 AGTTCATGTTTCATGCATCATATTGAT 58.361 29.630 0.00 0.00 37.65 2.57
1540 1628 9.902196 GTTCATGTTTCATGCATCATATTGATA 57.098 29.630 0.00 0.00 34.28 2.15
1542 1630 9.292195 TCATGTTTCATGCATCATATTGATAGT 57.708 29.630 0.00 0.00 34.28 2.12
1543 1631 9.556030 CATGTTTCATGCATCATATTGATAGTC 57.444 33.333 0.00 0.00 34.28 2.59
1544 1632 8.102800 TGTTTCATGCATCATATTGATAGTCC 57.897 34.615 0.00 0.00 34.28 3.85
1545 1633 7.720515 TGTTTCATGCATCATATTGATAGTCCA 59.279 33.333 0.00 0.00 34.28 4.02
1546 1634 8.737175 GTTTCATGCATCATATTGATAGTCCAT 58.263 33.333 0.00 0.00 34.28 3.41
1547 1635 9.962809 TTTCATGCATCATATTGATAGTCCATA 57.037 29.630 0.00 0.00 34.28 2.74
1548 1636 8.953368 TCATGCATCATATTGATAGTCCATAC 57.047 34.615 0.00 0.00 34.28 2.39
1549 1637 8.542080 TCATGCATCATATTGATAGTCCATACA 58.458 33.333 0.00 0.00 34.28 2.29
1550 1638 9.169592 CATGCATCATATTGATAGTCCATACAA 57.830 33.333 0.00 0.00 34.28 2.41
1551 1639 9.743581 ATGCATCATATTGATAGTCCATACAAA 57.256 29.630 0.00 0.00 34.28 2.83
1552 1640 9.223099 TGCATCATATTGATAGTCCATACAAAG 57.777 33.333 0.00 0.00 34.28 2.77
1553 1641 9.224267 GCATCATATTGATAGTCCATACAAAGT 57.776 33.333 0.00 0.00 34.28 2.66
1863 1951 6.356556 GGGCTGCCCAATTTCTATAAAATTT 58.643 36.000 32.46 0.00 44.65 1.82
2045 2258 5.890985 AGTATTGTCATCTAGTCAGCTCTGT 59.109 40.000 0.00 0.00 0.00 3.41
2099 2312 7.886629 TCATGCTTAAGCTTTCCTTCATATT 57.113 32.000 26.90 0.00 42.66 1.28
2111 2324 8.253113 GCTTTCCTTCATATTTGGAATTCTCAA 58.747 33.333 5.23 5.42 39.30 3.02
2176 2389 4.129380 TGGAGAAATGGAAGCATGTATCG 58.871 43.478 0.00 0.00 0.00 2.92
2184 2397 4.717877 TGGAAGCATGTATCGGAATTGAT 58.282 39.130 0.00 0.00 0.00 2.57
2185 2398 5.863965 TGGAAGCATGTATCGGAATTGATA 58.136 37.500 0.00 0.00 0.00 2.15
2234 2447 7.775053 AATCAAGTTTCCATGCCTAAACTAA 57.225 32.000 15.26 9.82 43.35 2.24
3047 3269 5.236478 CCAAATACGAGCTACCTACAATTGG 59.764 44.000 10.83 0.00 0.00 3.16
3072 3294 4.443598 GGAATACCTAAGGCTGAGGTTGAG 60.444 50.000 28.63 0.00 45.40 3.02
3253 3475 1.035932 AGGCGCCGCTAAGAGACTTA 61.036 55.000 23.20 0.00 0.00 2.24
3270 3492 7.772166 AGAGACTTAGAAAACCAACAAAAAGG 58.228 34.615 0.00 0.00 0.00 3.11
3341 3563 3.680777 TTCTTCACCAGGAAAAAGGGT 57.319 42.857 0.00 0.00 34.44 4.34
3659 4074 9.189156 TCTTGAAGATGGATTTTGTTTATAGGG 57.811 33.333 0.00 0.00 0.00 3.53
3688 4103 3.057946 GCCCTTTGTAGCTTTGTTCTCAG 60.058 47.826 0.00 0.00 0.00 3.35
3784 4199 7.176515 AGGATAGAATCACTATACACTCAGCTG 59.823 40.741 7.63 7.63 43.08 4.24
3844 4351 9.359653 TGGTACTACCTCTGTTCCTAAATATAC 57.640 37.037 6.79 0.00 39.58 1.47
3848 4355 7.776969 ACTACCTCTGTTCCTAAATATACGACA 59.223 37.037 0.00 0.00 0.00 4.35
3855 4362 9.104965 CTGTTCCTAAATATACGACATTTTGGA 57.895 33.333 14.67 14.67 42.00 3.53
3860 4367 9.716507 CCTAAATATACGACATTTTGGAAGTTG 57.283 33.333 12.39 0.00 39.28 3.16
3861 4368 9.221775 CTAAATATACGACATTTTGGAAGTTGC 57.778 33.333 0.00 0.00 0.00 4.17
3976 4483 8.956426 TGTTCATTGAACTCATTACCCTATTTC 58.044 33.333 25.49 0.00 42.39 2.17
3991 4498 3.129287 CCTATTTCGCTGCCTTGTCAATT 59.871 43.478 0.00 0.00 0.00 2.32
4051 4558 5.818336 TCTGAACCTTCATTACAACGTTTGA 59.182 36.000 0.00 0.00 36.46 2.69
4093 4600 3.366374 GCTTAACATGTTGGCCTCACTTC 60.366 47.826 21.42 0.00 0.00 3.01
4229 4736 6.280855 ACAATTTAGACCAATTAGCCAACC 57.719 37.500 0.00 0.00 0.00 3.77
4249 4756 0.252239 GGTCCAAATGGGGAAAGCCT 60.252 55.000 0.00 0.00 39.05 4.58
4336 4971 4.784079 GCCGTTATTAGTAATTGTGGCGTG 60.784 45.833 13.07 3.99 0.00 5.34
4412 5047 7.499563 GGATGTCTCACTAGATGTCACTAAGTA 59.500 40.741 0.00 0.00 33.30 2.24
4421 5056 9.409918 ACTAGATGTCACTAAGTATGCTCTTTA 57.590 33.333 0.00 0.00 0.00 1.85
4833 5498 9.434420 GATAACAAGGAGATTCATTCCATAGAG 57.566 37.037 0.00 0.00 37.18 2.43
4834 5499 5.619220 ACAAGGAGATTCATTCCATAGAGC 58.381 41.667 0.00 0.00 37.18 4.09
4839 5504 5.481105 GAGATTCATTCCATAGAGCCAGAG 58.519 45.833 0.00 0.00 0.00 3.35
5095 5760 0.829990 TCTAATGGATCACGCTGCCA 59.170 50.000 0.00 0.00 35.91 4.92
5166 5833 4.974368 TTCGCCGGAAAATGATGTAATT 57.026 36.364 5.05 0.00 0.00 1.40
5170 5840 5.587043 TCGCCGGAAAATGATGTAATTACTT 59.413 36.000 16.33 10.23 0.00 2.24
5195 5865 6.057321 TCCCTTTTCAACTTATACGGATGT 57.943 37.500 0.00 0.00 0.00 3.06
5331 6004 3.193479 GGAAAAGCAACCCTTCGATCATT 59.807 43.478 0.00 0.00 31.99 2.57
5438 6111 4.737177 AGGGCAGAGCAGCAAGGC 62.737 66.667 0.00 0.00 35.83 4.35
5468 6141 1.223763 GAGGTTCATCGGGGTTCCC 59.776 63.158 0.00 0.00 41.09 3.97
5478 6151 1.613061 GGGGTTCCCGTGATCCATT 59.387 57.895 1.48 0.00 32.13 3.16
5499 6172 1.003464 TGCTGCAAGGCAAGTAGATGA 59.997 47.619 0.00 0.00 38.41 2.92
5500 6173 2.086869 GCTGCAAGGCAAGTAGATGAA 58.913 47.619 0.00 0.00 38.41 2.57
5501 6174 2.489329 GCTGCAAGGCAAGTAGATGAAA 59.511 45.455 0.00 0.00 38.41 2.69
5558 6231 0.173935 TTGTGGACGACGAACACACT 59.826 50.000 22.09 0.00 43.99 3.55
5677 6350 6.090129 GGTTTCTTTCGCAGCATGTATTTTA 58.910 36.000 0.00 0.00 39.31 1.52
5757 6436 9.862371 GTATGCCTATAAGGATGAATATATCGG 57.138 37.037 0.00 0.00 37.67 4.18
5758 6437 8.727100 ATGCCTATAAGGATGAATATATCGGA 57.273 34.615 0.00 0.00 37.67 4.55
5759 6438 8.547481 TGCCTATAAGGATGAATATATCGGAA 57.453 34.615 0.00 0.00 37.67 4.30
5760 6439 8.642432 TGCCTATAAGGATGAATATATCGGAAG 58.358 37.037 0.00 0.00 37.67 3.46
5761 6440 8.643324 GCCTATAAGGATGAATATATCGGAAGT 58.357 37.037 0.00 0.00 37.67 3.01
5767 6446 9.853177 AAGGATGAATATATCGGAAGTTTTCTT 57.147 29.630 0.00 0.00 43.55 2.52
5768 6447 9.277783 AGGATGAATATATCGGAAGTTTTCTTG 57.722 33.333 0.00 0.00 40.61 3.02
5769 6448 8.017946 GGATGAATATATCGGAAGTTTTCTTGC 58.982 37.037 0.00 0.00 43.33 4.01
5770 6449 7.857734 TGAATATATCGGAAGTTTTCTTGCA 57.142 32.000 0.00 0.00 46.34 4.08
5771 6450 8.275015 TGAATATATCGGAAGTTTTCTTGCAA 57.725 30.769 0.00 0.00 46.34 4.08
5772 6451 8.735315 TGAATATATCGGAAGTTTTCTTGCAAA 58.265 29.630 0.00 0.00 46.34 3.68
5773 6452 9.567848 GAATATATCGGAAGTTTTCTTGCAAAA 57.432 29.630 0.00 0.00 46.34 2.44
5774 6453 9.921637 AATATATCGGAAGTTTTCTTGCAAAAA 57.078 25.926 0.00 1.75 46.34 1.94
5775 6454 7.873739 ATATCGGAAGTTTTCTTGCAAAAAG 57.126 32.000 0.00 0.00 46.34 2.27
5776 6455 5.317733 TCGGAAGTTTTCTTGCAAAAAGA 57.682 34.783 0.00 0.00 46.34 2.52
5788 6467 7.499321 TCTTGCAAAAAGAAAAATGATGCAT 57.501 28.000 0.00 0.00 41.38 3.96
5817 6496 3.184178 CGGCAATGGAATGAAAACACAAC 59.816 43.478 0.00 0.00 0.00 3.32
5822 6501 2.099921 TGGAATGAAAACACAACACCGG 59.900 45.455 0.00 0.00 0.00 5.28
5827 6514 1.995646 AAAACACAACACCGGGCGAC 61.996 55.000 6.32 0.00 0.00 5.19
5837 6524 0.899720 ACCGGGCGACTTTGAATCTA 59.100 50.000 6.32 0.00 0.00 1.98
5838 6525 1.287425 CCGGGCGACTTTGAATCTAC 58.713 55.000 0.00 0.00 0.00 2.59
5842 6531 2.159282 GGGCGACTTTGAATCTACTCGA 60.159 50.000 0.00 0.00 0.00 4.04
5854 6543 9.574458 TTTGAATCTACTCGAAGAAGATTACTG 57.426 33.333 13.55 0.00 42.20 2.74
5855 6544 8.282455 TGAATCTACTCGAAGAAGATTACTGT 57.718 34.615 13.55 0.00 42.20 3.55
5864 6553 6.879993 TCGAAGAAGATTACTGTCTGTACTCT 59.120 38.462 4.52 4.52 41.15 3.24
5865 6554 6.964370 CGAAGAAGATTACTGTCTGTACTCTG 59.036 42.308 9.55 0.00 39.33 3.35
5875 6564 6.297582 ACTGTCTGTACTCTGTACTGTAGTT 58.702 40.000 8.94 2.67 0.00 2.24
5885 6574 5.067954 TCTGTACTGTAGTTGCACTCTGTA 58.932 41.667 0.00 0.00 0.00 2.74
5900 6589 4.623167 CACTCTGTAAAAGATGACACGGAG 59.377 45.833 7.65 7.65 45.73 4.63
5909 6598 7.745620 AAAAGATGACACGGAGATTACTTTT 57.254 32.000 0.00 0.00 32.67 2.27
5943 6632 5.880054 ACATGGAAATTACTCGACCTTTG 57.120 39.130 0.00 0.00 0.00 2.77
5946 6635 4.710324 TGGAAATTACTCGACCTTTGTGT 58.290 39.130 0.00 0.00 0.00 3.72
5976 6665 2.095263 CACGACAAATTGGCCCAGTTAG 60.095 50.000 0.00 0.00 0.00 2.34
6007 6696 3.758023 CTCAGCCCATTTGTTACACATGA 59.242 43.478 12.47 0.00 0.00 3.07
6010 6699 3.894427 AGCCCATTTGTTACACATGACAA 59.106 39.130 12.47 0.00 32.82 3.18
6043 6732 4.590647 TGAAAACAATTAGCCCATCCAACA 59.409 37.500 0.00 0.00 0.00 3.33
6044 6733 5.248020 TGAAAACAATTAGCCCATCCAACAT 59.752 36.000 0.00 0.00 0.00 2.71
6045 6734 5.760484 AAACAATTAGCCCATCCAACATT 57.240 34.783 0.00 0.00 0.00 2.71
6046 6735 5.760484 AACAATTAGCCCATCCAACATTT 57.240 34.783 0.00 0.00 0.00 2.32
6047 6736 5.760484 ACAATTAGCCCATCCAACATTTT 57.240 34.783 0.00 0.00 0.00 1.82
6048 6737 6.125589 ACAATTAGCCCATCCAACATTTTT 57.874 33.333 0.00 0.00 0.00 1.94
6166 6928 3.244457 CGGGGGCTATAAAACCTAGGAAG 60.244 52.174 17.98 3.92 0.00 3.46
6326 7111 5.639082 GCCGACTTTTGATTTTGAAATGGAT 59.361 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 6.331369 ACAATCAACAAAACCAGGATACAG 57.669 37.500 0.00 0.00 41.41 2.74
122 123 6.239176 GGAACAATCAACAAAACCAGGATACA 60.239 38.462 0.00 0.00 41.41 2.29
123 124 6.156519 GGAACAATCAACAAAACCAGGATAC 58.843 40.000 0.00 0.00 0.00 2.24
124 125 5.048364 CGGAACAATCAACAAAACCAGGATA 60.048 40.000 0.00 0.00 0.00 2.59
125 126 4.261994 CGGAACAATCAACAAAACCAGGAT 60.262 41.667 0.00 0.00 0.00 3.24
126 127 3.067461 CGGAACAATCAACAAAACCAGGA 59.933 43.478 0.00 0.00 0.00 3.86
127 128 3.067461 TCGGAACAATCAACAAAACCAGG 59.933 43.478 0.00 0.00 0.00 4.45
128 129 4.300189 TCGGAACAATCAACAAAACCAG 57.700 40.909 0.00 0.00 0.00 4.00
129 130 4.927978 ATCGGAACAATCAACAAAACCA 57.072 36.364 0.00 0.00 0.00 3.67
130 131 7.883229 AATTATCGGAACAATCAACAAAACC 57.117 32.000 0.00 0.00 0.00 3.27
138 139 8.655970 CGCTGATATAAATTATCGGAACAATCA 58.344 33.333 5.78 0.00 33.30 2.57
139 140 7.636359 GCGCTGATATAAATTATCGGAACAATC 59.364 37.037 0.00 0.00 33.30 2.67
140 141 7.119116 TGCGCTGATATAAATTATCGGAACAAT 59.881 33.333 9.73 0.00 33.30 2.71
141 142 6.425417 TGCGCTGATATAAATTATCGGAACAA 59.575 34.615 9.73 0.00 33.30 2.83
153 173 9.938280 AACTACCTAAATATGCGCTGATATAAA 57.062 29.630 9.73 0.00 0.00 1.40
154 174 9.938280 AAACTACCTAAATATGCGCTGATATAA 57.062 29.630 9.73 0.00 0.00 0.98
194 214 4.157656 AGTTAAGCAAACAGAGCAACAACA 59.842 37.500 4.96 0.00 40.83 3.33
195 215 4.500477 CAGTTAAGCAAACAGAGCAACAAC 59.500 41.667 4.96 0.00 40.83 3.32
196 216 4.439974 CCAGTTAAGCAAACAGAGCAACAA 60.440 41.667 4.96 0.00 40.83 2.83
197 217 3.066621 CCAGTTAAGCAAACAGAGCAACA 59.933 43.478 4.96 0.00 40.83 3.33
198 218 3.315191 TCCAGTTAAGCAAACAGAGCAAC 59.685 43.478 4.96 0.00 40.83 4.17
290 315 1.887854 TCGACCGTCAATTCCACTGTA 59.112 47.619 0.00 0.00 0.00 2.74
398 425 6.327279 ACTAACAAAAGGGCTAACATCAAC 57.673 37.500 0.00 0.00 0.00 3.18
408 435 4.377021 CCCAGAAAAACTAACAAAAGGGC 58.623 43.478 0.00 0.00 0.00 5.19
440 467 7.041721 TGAACAATAGCACTTCCTACATACAG 58.958 38.462 0.00 0.00 0.00 2.74
517 544 4.708177 TCAGCTATGCCTCCAAGATTAAC 58.292 43.478 0.00 0.00 0.00 2.01
554 602 6.663734 AGTTCTCCCCATTACTGATTAAAGG 58.336 40.000 0.00 0.00 0.00 3.11
555 603 7.715686 GGTAGTTCTCCCCATTACTGATTAAAG 59.284 40.741 0.00 0.00 0.00 1.85
556 604 7.404980 AGGTAGTTCTCCCCATTACTGATTAAA 59.595 37.037 0.00 0.00 0.00 1.52
557 605 6.906901 AGGTAGTTCTCCCCATTACTGATTAA 59.093 38.462 0.00 0.00 0.00 1.40
558 606 6.326583 CAGGTAGTTCTCCCCATTACTGATTA 59.673 42.308 0.00 0.00 0.00 1.75
559 607 5.131142 CAGGTAGTTCTCCCCATTACTGATT 59.869 44.000 0.00 0.00 0.00 2.57
560 608 4.656112 CAGGTAGTTCTCCCCATTACTGAT 59.344 45.833 0.00 0.00 0.00 2.90
561 609 4.030913 CAGGTAGTTCTCCCCATTACTGA 58.969 47.826 0.00 0.00 0.00 3.41
562 610 3.134804 CCAGGTAGTTCTCCCCATTACTG 59.865 52.174 0.00 0.00 0.00 2.74
563 611 3.013648 TCCAGGTAGTTCTCCCCATTACT 59.986 47.826 0.00 0.00 0.00 2.24
564 612 3.381335 TCCAGGTAGTTCTCCCCATTAC 58.619 50.000 0.00 0.00 0.00 1.89
565 613 3.273886 TCTCCAGGTAGTTCTCCCCATTA 59.726 47.826 0.00 0.00 0.00 1.90
566 614 2.045885 TCTCCAGGTAGTTCTCCCCATT 59.954 50.000 0.00 0.00 0.00 3.16
567 615 1.651770 TCTCCAGGTAGTTCTCCCCAT 59.348 52.381 0.00 0.00 0.00 4.00
568 616 1.089978 TCTCCAGGTAGTTCTCCCCA 58.910 55.000 0.00 0.00 0.00 4.96
569 617 2.249309 TTCTCCAGGTAGTTCTCCCC 57.751 55.000 0.00 0.00 0.00 4.81
570 618 4.846168 ATTTTCTCCAGGTAGTTCTCCC 57.154 45.455 0.00 0.00 0.00 4.30
571 619 7.125792 TGATATTTTCTCCAGGTAGTTCTCC 57.874 40.000 0.00 0.00 0.00 3.71
572 620 7.708752 CACTGATATTTTCTCCAGGTAGTTCTC 59.291 40.741 0.00 0.00 0.00 2.87
573 621 7.365117 CCACTGATATTTTCTCCAGGTAGTTCT 60.365 40.741 0.00 0.00 0.00 3.01
574 622 6.763610 CCACTGATATTTTCTCCAGGTAGTTC 59.236 42.308 0.00 0.00 0.00 3.01
575 623 6.653989 CCACTGATATTTTCTCCAGGTAGTT 58.346 40.000 0.00 0.00 0.00 2.24
576 624 5.396884 GCCACTGATATTTTCTCCAGGTAGT 60.397 44.000 0.00 0.00 0.00 2.73
577 625 5.059833 GCCACTGATATTTTCTCCAGGTAG 58.940 45.833 0.00 0.00 0.00 3.18
578 626 4.721776 AGCCACTGATATTTTCTCCAGGTA 59.278 41.667 0.00 0.00 0.00 3.08
579 627 3.525199 AGCCACTGATATTTTCTCCAGGT 59.475 43.478 0.00 0.00 0.00 4.00
580 628 4.162040 AGCCACTGATATTTTCTCCAGG 57.838 45.455 0.00 0.00 0.00 4.45
581 629 5.188434 TGAAGCCACTGATATTTTCTCCAG 58.812 41.667 0.00 0.00 0.00 3.86
594 642 3.079960 GCATCATCAATGAAGCCACTG 57.920 47.619 8.62 0.00 43.50 3.66
762 848 9.374838 GCAAACAAAAGGATTCAGATGATAATT 57.625 29.630 0.00 0.00 0.00 1.40
823 909 2.143122 TGCTGATCGAACAAAGTCACC 58.857 47.619 0.00 0.00 0.00 4.02
849 935 6.824305 AATAGTAACACAGCAGAAGCAATT 57.176 33.333 0.00 0.00 45.49 2.32
852 938 4.862574 CGTAATAGTAACACAGCAGAAGCA 59.137 41.667 0.00 0.00 45.49 3.91
955 1041 7.279981 TCCAATGTTCGTACTAATCAAATCCTG 59.720 37.037 0.00 0.00 0.00 3.86
1011 1097 4.159506 GTCTCCTCAGCATCTTGTAGAGTT 59.840 45.833 0.00 0.00 0.00 3.01
1027 1113 3.917300 TCCCTCCATTCTTAGTCTCCTC 58.083 50.000 0.00 0.00 0.00 3.71
1165 1251 6.694411 GCTATAAGCAAATGGAAACATCACAG 59.306 38.462 0.00 0.00 46.21 3.66
1493 1581 5.567138 ACTTTGTATGGCTAAACTGCATC 57.433 39.130 0.00 0.00 34.04 3.91
1541 1629 9.353999 GGTTGAATTAATGAACTTTGTATGGAC 57.646 33.333 9.39 0.00 0.00 4.02
1542 1630 8.527810 GGGTTGAATTAATGAACTTTGTATGGA 58.472 33.333 9.39 0.00 0.00 3.41
1543 1631 7.763985 GGGGTTGAATTAATGAACTTTGTATGG 59.236 37.037 9.39 0.00 0.00 2.74
1544 1632 8.531146 AGGGGTTGAATTAATGAACTTTGTATG 58.469 33.333 9.39 0.00 0.00 2.39
1545 1633 8.664669 AGGGGTTGAATTAATGAACTTTGTAT 57.335 30.769 9.39 0.00 0.00 2.29
1546 1634 8.485578 AAGGGGTTGAATTAATGAACTTTGTA 57.514 30.769 9.39 0.00 0.00 2.41
1547 1635 6.994421 AGGGGTTGAATTAATGAACTTTGT 57.006 33.333 9.39 0.00 0.00 2.83
1548 1636 7.930865 TCAAAGGGGTTGAATTAATGAACTTTG 59.069 33.333 0.00 0.00 43.43 2.77
1549 1637 8.028652 TCAAAGGGGTTGAATTAATGAACTTT 57.971 30.769 9.39 0.00 43.43 2.66
1550 1638 7.610580 TCAAAGGGGTTGAATTAATGAACTT 57.389 32.000 9.39 0.00 43.43 2.66
1790 1878 4.393834 TCAAACATGACCCGAAAGAATCA 58.606 39.130 0.00 0.00 0.00 2.57
1799 1887 6.072728 TCAGATTTAGTTTCAAACATGACCCG 60.073 38.462 2.41 0.00 0.00 5.28
1887 1975 9.412460 TCATATAGGAAACAAAATCATGCTTCT 57.588 29.630 0.00 0.00 0.00 2.85
2045 2258 1.673033 GCGCTGCTTGAGTAGGAAAGA 60.673 52.381 0.00 0.00 0.00 2.52
2099 2312 7.669304 TCTTCCACACATATTTGAGAATTCCAA 59.331 33.333 0.65 3.65 0.00 3.53
2538 2751 4.037803 ACCTGCGCAATTTATATGCATCAA 59.962 37.500 13.05 0.00 44.01 2.57
3028 3250 3.635373 CCTCCAATTGTAGGTAGCTCGTA 59.365 47.826 8.88 0.00 0.00 3.43
3047 3269 3.310193 ACCTCAGCCTTAGGTATTCCTC 58.690 50.000 0.00 0.00 45.69 3.71
3072 3294 5.985911 TGATACCTAACCAAAGAAGTAGCC 58.014 41.667 0.00 0.00 0.00 3.93
3253 3475 7.616313 TCAATGTACCTTTTTGTTGGTTTTCT 58.384 30.769 0.00 0.00 37.74 2.52
3341 3563 2.158682 AGTAACACCTCACCATGTGCAA 60.159 45.455 0.00 0.00 35.90 4.08
3600 3822 6.899089 AGAATGACATGTACCATCATTACCA 58.101 36.000 13.38 0.00 41.89 3.25
3659 4074 4.022329 ACAAAGCTACAAAGGGCACAATAC 60.022 41.667 0.00 0.00 0.00 1.89
3688 4103 7.806014 TGTGTTTTGTTTAAGTCTCAACTGTTC 59.194 33.333 0.00 0.00 35.36 3.18
3737 4152 6.327781 TCCTACTTGGGCCATACTGATAATA 58.672 40.000 7.26 0.00 36.20 0.98
3844 4351 6.761731 TTAAATGCAACTTCCAAAATGTCG 57.238 33.333 0.00 0.00 0.00 4.35
3848 4355 6.017192 GGCAGTTTAAATGCAACTTCCAAAAT 60.017 34.615 18.82 0.00 45.68 1.82
3855 4362 5.220567 CGTTTTGGCAGTTTAAATGCAACTT 60.221 36.000 18.82 0.00 45.68 2.66
3860 4367 4.048504 AGACGTTTTGGCAGTTTAAATGC 58.951 39.130 9.00 9.00 43.09 3.56
3861 4368 6.693545 TGTAAGACGTTTTGGCAGTTTAAATG 59.306 34.615 0.83 1.12 0.00 2.32
3964 4471 3.214328 CAAGGCAGCGAAATAGGGTAAT 58.786 45.455 0.00 0.00 0.00 1.89
3976 4483 0.883833 AAGGAATTGACAAGGCAGCG 59.116 50.000 0.00 0.00 0.00 5.18
3991 4498 7.595819 TTTTTCTAAGAAAATGGCAGAAGGA 57.404 32.000 0.00 0.00 0.00 3.36
4043 4550 1.873591 GAGACAGCATGGTCAAACGTT 59.126 47.619 0.00 0.00 43.62 3.99
4051 4558 3.262915 AGCTCTTTAAGAGACAGCATGGT 59.737 43.478 24.40 0.00 45.07 3.55
4229 4736 1.604147 GGCTTTCCCCATTTGGACCG 61.604 60.000 0.00 0.00 37.39 4.79
4364 4999 9.112725 CATCCAAGAAATAATGTGTGACATCTA 57.887 33.333 0.00 0.00 37.97 1.98
4456 5091 2.038952 CTGAACCTCAGGACATTCCACA 59.961 50.000 0.00 0.00 40.71 4.17
4527 5162 1.447317 AACTTCCACGGCACTGCTTG 61.447 55.000 0.00 0.00 0.00 4.01
4672 5307 3.751246 GGCCGCATTTGCAGCTCA 61.751 61.111 10.32 0.00 43.56 4.26
4833 5498 3.314635 CAGTTCTGCAAATATCCTCTGGC 59.685 47.826 0.00 0.00 0.00 4.85
4834 5499 4.774124 TCAGTTCTGCAAATATCCTCTGG 58.226 43.478 0.00 0.00 0.00 3.86
4839 5504 3.633525 TGGCATCAGTTCTGCAAATATCC 59.366 43.478 0.00 0.00 41.47 2.59
5095 5760 3.616219 TGCGCCACTTATCCTAAACAAT 58.384 40.909 4.18 0.00 0.00 2.71
5166 5833 7.178983 TCCGTATAAGTTGAAAAGGGAGAAGTA 59.821 37.037 0.00 0.00 0.00 2.24
5170 5840 6.070424 ACATCCGTATAAGTTGAAAAGGGAGA 60.070 38.462 0.00 0.00 0.00 3.71
5331 6004 0.333312 AAATGGCCGGTGGTATTGGA 59.667 50.000 1.90 0.00 0.00 3.53
5438 6111 3.316573 GAACCTCTCCCCTGTGCCG 62.317 68.421 0.00 0.00 0.00 5.69
5468 6141 1.468565 CCTTGCAGCAAATGGATCACG 60.469 52.381 9.65 0.00 0.00 4.35
5500 6173 7.162082 ACTATCTCTCTCGGATGTTTGTTTTT 58.838 34.615 0.00 0.00 0.00 1.94
5501 6174 6.702329 ACTATCTCTCTCGGATGTTTGTTTT 58.298 36.000 0.00 0.00 0.00 2.43
5505 6178 5.533154 ACCTACTATCTCTCTCGGATGTTTG 59.467 44.000 0.00 0.00 0.00 2.93
5558 6231 4.622313 ACAACAACTTCGTCGCGATAATAA 59.378 37.500 14.06 3.60 35.23 1.40
5579 6252 0.246360 ACATGGAGAACGCGATCACA 59.754 50.000 15.93 14.77 0.00 3.58
5580 6253 0.647410 CACATGGAGAACGCGATCAC 59.353 55.000 15.93 9.64 0.00 3.06
5581 6254 1.083806 GCACATGGAGAACGCGATCA 61.084 55.000 15.93 3.44 0.00 2.92
5677 6350 6.703607 GCAAGCTCTATGAACATACTGTACAT 59.296 38.462 0.00 0.00 0.00 2.29
5698 6371 2.460918 CTACCTCGAACGTATGGCAAG 58.539 52.381 0.00 0.00 0.00 4.01
5741 6420 9.853177 AAGAAAACTTCCGATATATTCATCCTT 57.147 29.630 0.00 0.00 0.00 3.36
5742 6421 9.277783 CAAGAAAACTTCCGATATATTCATCCT 57.722 33.333 0.00 0.00 0.00 3.24
5743 6422 8.017946 GCAAGAAAACTTCCGATATATTCATCC 58.982 37.037 0.00 0.00 0.00 3.51
5744 6423 8.559536 TGCAAGAAAACTTCCGATATATTCATC 58.440 33.333 0.00 0.00 0.00 2.92
5745 6424 8.450578 TGCAAGAAAACTTCCGATATATTCAT 57.549 30.769 0.00 0.00 0.00 2.57
5746 6425 7.857734 TGCAAGAAAACTTCCGATATATTCA 57.142 32.000 0.00 0.00 0.00 2.57
5747 6426 9.567848 TTTTGCAAGAAAACTTCCGATATATTC 57.432 29.630 0.00 0.00 0.00 1.75
5748 6427 9.921637 TTTTTGCAAGAAAACTTCCGATATATT 57.078 25.926 0.00 0.00 0.00 1.28
5749 6428 9.573133 CTTTTTGCAAGAAAACTTCCGATATAT 57.427 29.630 3.79 0.00 0.00 0.86
5750 6429 8.788806 TCTTTTTGCAAGAAAACTTCCGATATA 58.211 29.630 3.79 0.00 0.00 0.86
5751 6430 7.657336 TCTTTTTGCAAGAAAACTTCCGATAT 58.343 30.769 3.79 0.00 0.00 1.63
5752 6431 7.033530 TCTTTTTGCAAGAAAACTTCCGATA 57.966 32.000 3.79 0.00 0.00 2.92
5753 6432 5.901552 TCTTTTTGCAAGAAAACTTCCGAT 58.098 33.333 3.79 0.00 0.00 4.18
5754 6433 5.317733 TCTTTTTGCAAGAAAACTTCCGA 57.682 34.783 3.79 0.00 0.00 4.55
5755 6434 6.401955 TTTCTTTTTGCAAGAAAACTTCCG 57.598 33.333 9.16 0.00 41.64 4.30
5762 6441 7.759465 TGCATCATTTTTCTTTTTGCAAGAAA 58.241 26.923 7.77 7.77 42.53 2.52
5763 6442 7.317842 TGCATCATTTTTCTTTTTGCAAGAA 57.682 28.000 0.00 0.00 35.85 2.52
5764 6443 6.922247 TGCATCATTTTTCTTTTTGCAAGA 57.078 29.167 0.00 0.00 35.85 3.02
5765 6444 7.112844 CACATGCATCATTTTTCTTTTTGCAAG 59.887 33.333 0.00 0.00 41.38 4.01
5766 6445 6.913132 CACATGCATCATTTTTCTTTTTGCAA 59.087 30.769 0.00 0.00 41.38 4.08
5767 6446 6.431278 CACATGCATCATTTTTCTTTTTGCA 58.569 32.000 0.00 0.00 42.15 4.08
5768 6447 5.341196 GCACATGCATCATTTTTCTTTTTGC 59.659 36.000 0.00 0.00 41.59 3.68
5769 6448 6.904954 GCACATGCATCATTTTTCTTTTTG 57.095 33.333 0.00 0.00 41.59 2.44
5807 6486 1.298788 CGCCCGGTGTTGTGTTTTC 60.299 57.895 0.00 0.00 0.00 2.29
5817 6496 0.673644 AGATTCAAAGTCGCCCGGTG 60.674 55.000 0.00 0.00 0.00 4.94
5822 6501 3.146618 TCGAGTAGATTCAAAGTCGCC 57.853 47.619 9.98 0.00 38.22 5.54
5827 6514 9.796120 AGTAATCTTCTTCGAGTAGATTCAAAG 57.204 33.333 16.91 0.89 40.17 2.77
5837 6524 5.968528 ACAGACAGTAATCTTCTTCGAGT 57.031 39.130 0.00 0.00 0.00 4.18
5838 6525 7.079182 AGTACAGACAGTAATCTTCTTCGAG 57.921 40.000 0.00 0.00 33.72 4.04
5854 6543 5.048921 TGCAACTACAGTACAGAGTACAGAC 60.049 44.000 9.68 0.00 0.00 3.51
5855 6544 5.048921 GTGCAACTACAGTACAGAGTACAGA 60.049 44.000 9.68 0.00 0.00 3.41
5875 6564 3.740832 CGTGTCATCTTTTACAGAGTGCA 59.259 43.478 0.00 0.00 33.87 4.57
5885 6574 7.745620 AAAAGTAATCTCCGTGTCATCTTTT 57.254 32.000 0.00 0.00 0.00 2.27
5915 6604 4.035112 TCGAGTAATTTCCATGTACCCCT 58.965 43.478 0.00 0.00 0.00 4.79
5916 6605 4.124970 GTCGAGTAATTTCCATGTACCCC 58.875 47.826 0.00 0.00 0.00 4.95
5919 6608 6.370718 ACAAAGGTCGAGTAATTTCCATGTAC 59.629 38.462 0.00 0.00 0.00 2.90
5920 6609 6.370442 CACAAAGGTCGAGTAATTTCCATGTA 59.630 38.462 0.00 0.00 0.00 2.29
5922 6611 5.181245 ACACAAAGGTCGAGTAATTTCCATG 59.819 40.000 0.00 0.00 0.00 3.66
5924 6613 4.710324 ACACAAAGGTCGAGTAATTTCCA 58.290 39.130 0.00 0.00 0.00 3.53
5957 6646 1.135402 GCTAACTGGGCCAATTTGTCG 60.135 52.381 5.18 0.00 0.00 4.35
5960 6649 2.660189 CAGCTAACTGGGCCAATTTG 57.340 50.000 5.18 4.95 40.48 2.32
6007 6696 2.953020 TGTTTTCAGCGCTGTTTTTGT 58.047 38.095 34.70 0.00 0.00 2.83
6010 6699 4.209080 GCTAATTGTTTTCAGCGCTGTTTT 59.791 37.500 34.70 19.75 0.00 2.43
6058 6747 1.110442 CAAAAGTTGGACTGGGCACA 58.890 50.000 0.00 0.00 0.00 4.57
6059 6748 1.111277 ACAAAAGTTGGACTGGGCAC 58.889 50.000 0.00 0.00 34.12 5.01
6060 6749 2.691011 GTTACAAAAGTTGGACTGGGCA 59.309 45.455 0.00 0.00 34.12 5.36
6367 7153 9.739276 ATGACCTAAAACAAAACAGATCTATGA 57.261 29.630 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.