Multiple sequence alignment - TraesCS2B01G395300

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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 TraesCS2B01G395300 chr2B 100.000 3331 0 0 1 3331 560434169 560437499 0.000000e+00 6152.0
1 TraesCS2B01G395300 chr2B 92.982 2465 99 26 886 3331 106494842 106492433 0.000000e+00 3526.0
2 TraesCS2B01G395300 chr2B 81.469 286 33 15 1650 1923 89557312 89557589 2.010000e-52 217.0
3 TraesCS2B01G395300 chr2B 95.455 66 2 1 2131 2195 253732821 253732886 1.630000e-18 104.0
4 TraesCS2B01G395300 chr2B 93.939 66 3 1 2131 2195 253782717 253782782 7.610000e-17 99.0
5 TraesCS2B01G395300 chr5A 90.412 1554 90 29 1474 2996 181420565 181419040 0.000000e+00 1989.0
6 TraesCS2B01G395300 chr5A 89.538 1558 94 23 1476 2996 578114556 578113031 0.000000e+00 1910.0
7 TraesCS2B01G395300 chr5A 89.300 514 45 6 678 1187 181421501 181420994 1.300000e-178 636.0
8 TraesCS2B01G395300 chr5A 94.444 72 4 0 1328 1399 181420659 181420588 9.770000e-21 111.0
9 TraesCS2B01G395300 chr5A 93.220 59 4 0 620 678 671960798 671960856 1.650000e-13 87.9
10 TraesCS2B01G395300 chr7B 89.389 1555 98 25 1479 2996 256181334 256179810 0.000000e+00 1895.0
11 TraesCS2B01G395300 chr7B 83.173 624 61 12 678 1284 256182440 256181844 6.330000e-147 531.0
12 TraesCS2B01G395300 chr7B 87.179 78 10 0 601 678 484625618 484625541 4.580000e-14 89.8
13 TraesCS2B01G395300 chr5D 89.247 1553 93 29 1479 2996 543489206 543487693 0.000000e+00 1875.0
14 TraesCS2B01G395300 chr5D 86.650 412 25 7 888 1284 543490827 543490431 2.370000e-116 429.0
15 TraesCS2B01G395300 chr5D 92.105 114 8 1 1282 1395 543489348 543489236 3.440000e-35 159.0
16 TraesCS2B01G395300 chr4D 92.711 1317 50 24 1768 3075 71380917 71379638 0.000000e+00 1858.0
17 TraesCS2B01G395300 chr4D 90.113 617 41 4 680 1281 71382673 71382062 0.000000e+00 784.0
18 TraesCS2B01G395300 chr4D 83.369 463 39 21 2878 3331 71379766 71379333 8.660000e-106 394.0
19 TraesCS2B01G395300 chr4D 85.897 390 19 10 1395 1770 71381374 71381007 1.870000e-102 383.0
20 TraesCS2B01G395300 chr4D 95.726 117 5 0 1279 1395 71381458 71381342 4.390000e-44 189.0
21 TraesCS2B01G395300 chr3D 92.770 1314 50 24 1768 3072 600658265 600659542 0.000000e+00 1858.0
22 TraesCS2B01G395300 chr3D 90.675 622 40 2 674 1281 600656657 600657274 0.000000e+00 811.0
23 TraesCS2B01G395300 chr3D 83.369 463 39 21 2878 3331 600659417 600659850 8.660000e-106 394.0
24 TraesCS2B01G395300 chr3D 91.716 169 4 1 1612 1770 600657974 600658142 3.340000e-55 226.0
25 TraesCS2B01G395300 chr3D 97.000 100 3 0 1279 1378 600657876 600657975 5.720000e-38 169.0
26 TraesCS2B01G395300 chr3D 90.000 60 6 0 616 675 469492060 469492119 9.910000e-11 78.7
27 TraesCS2B01G395300 chr2A 93.348 451 23 2 132 576 621193131 621193580 0.000000e+00 660.0
28 TraesCS2B01G395300 chr2A 94.915 59 3 0 620 678 37100757 37100815 3.540000e-15 93.5
29 TraesCS2B01G395300 chr2A 94.828 58 3 0 566 623 621194965 621195022 1.270000e-14 91.6
30 TraesCS2B01G395300 chr2A 92.188 64 4 1 612 675 655753995 655754057 4.580000e-14 89.8
31 TraesCS2B01G395300 chr2D 78.038 469 46 25 101 521 478110676 478111135 3.320000e-60 243.0
32 TraesCS2B01G395300 chr2D 87.302 63 8 0 616 678 478122963 478122901 4.610000e-09 73.1
33 TraesCS2B01G395300 chr7D 90.230 174 15 1 1773 1944 619000836 619000663 3.340000e-55 226.0
34 TraesCS2B01G395300 chr1D 89.655 174 16 1 1773 1944 170103495 170103668 1.560000e-53 220.0
35 TraesCS2B01G395300 chr1D 91.228 57 5 0 619 675 350155519 350155575 9.910000e-11 78.7
36 TraesCS2B01G395300 chr3B 80.303 264 35 12 2631 2878 44280441 44280703 2.040000e-42 183.0
37 TraesCS2B01G395300 chrUn 91.525 59 5 0 620 678 71515184 71515126 7.660000e-12 82.4
38 TraesCS2B01G395300 chr6A 89.655 58 6 0 620 677 577862032 577862089 1.280000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G395300 chr2B 560434169 560437499 3330 False 6152.0 6152 100.000000 1 3331 1 chr2B.!!$F4 3330
1 TraesCS2B01G395300 chr2B 106492433 106494842 2409 True 3526.0 3526 92.982000 886 3331 1 chr2B.!!$R1 2445
2 TraesCS2B01G395300 chr5A 578113031 578114556 1525 True 1910.0 1910 89.538000 1476 2996 1 chr5A.!!$R1 1520
3 TraesCS2B01G395300 chr5A 181419040 181421501 2461 True 912.0 1989 91.385333 678 2996 3 chr5A.!!$R2 2318
4 TraesCS2B01G395300 chr7B 256179810 256182440 2630 True 1213.0 1895 86.281000 678 2996 2 chr7B.!!$R2 2318
5 TraesCS2B01G395300 chr5D 543487693 543490827 3134 True 821.0 1875 89.334000 888 2996 3 chr5D.!!$R1 2108
6 TraesCS2B01G395300 chr4D 71379333 71382673 3340 True 721.6 1858 89.563200 680 3331 5 chr4D.!!$R1 2651
7 TraesCS2B01G395300 chr3D 600656657 600659850 3193 False 691.6 1858 91.106000 674 3331 5 chr3D.!!$F2 2657
8 TraesCS2B01G395300 chr2A 621193131 621195022 1891 False 375.8 660 94.088000 132 623 2 chr2A.!!$F3 491

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
49 50 0.037975 GGCTCGTGGTTACCGAAGAA 60.038 55.0 0.00 0.00 33.34 2.52 F
582 589 0.318107 CTTGCTTGCTTCAACCGGTG 60.318 55.0 8.52 2.16 0.00 4.94 F
588 595 0.394488 TGCTTCAACCGGTGGTTTCA 60.394 50.0 8.52 1.37 44.33 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 2746 1.002366 CTGATAAGAGGTGCGTGTGC 58.998 55.000 0.00 0.0 43.2 4.57 R
1684 3010 2.363306 TCCAGCAGTGTCCATTGTTT 57.637 45.000 0.00 0.0 0.0 2.83 R
2491 4283 3.393426 AAATGGTCCATGAATCTGCCT 57.607 42.857 4.74 0.0 0.0 4.75 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
22 23 5.673337 CCGAGTCAGATTCTCAAACAAAA 57.327 39.130 0.00 0.00 32.79 2.44
23 24 5.683859 CCGAGTCAGATTCTCAAACAAAAG 58.316 41.667 0.00 0.00 32.79 2.27
24 25 5.237344 CCGAGTCAGATTCTCAAACAAAAGT 59.763 40.000 0.00 0.00 32.79 2.66
25 26 6.423905 CCGAGTCAGATTCTCAAACAAAAGTA 59.576 38.462 0.00 0.00 32.79 2.24
26 27 7.042051 CCGAGTCAGATTCTCAAACAAAAGTAA 60.042 37.037 0.00 0.00 32.79 2.24
27 28 8.335356 CGAGTCAGATTCTCAAACAAAAGTAAA 58.665 33.333 0.00 0.00 32.79 2.01
31 32 9.748708 TCAGATTCTCAAACAAAAGTAAAATGG 57.251 29.630 0.00 0.00 0.00 3.16
32 33 8.490355 CAGATTCTCAAACAAAAGTAAAATGGC 58.510 33.333 0.00 0.00 0.00 4.40
33 34 8.424133 AGATTCTCAAACAAAAGTAAAATGGCT 58.576 29.630 0.00 0.00 0.00 4.75
34 35 8.593492 ATTCTCAAACAAAAGTAAAATGGCTC 57.407 30.769 0.00 0.00 0.00 4.70
35 36 6.205784 TCTCAAACAAAAGTAAAATGGCTCG 58.794 36.000 0.00 0.00 0.00 5.03
36 37 5.897050 TCAAACAAAAGTAAAATGGCTCGT 58.103 33.333 0.00 0.00 0.00 4.18
37 38 5.746245 TCAAACAAAAGTAAAATGGCTCGTG 59.254 36.000 0.00 0.00 0.00 4.35
38 39 4.237349 ACAAAAGTAAAATGGCTCGTGG 57.763 40.909 0.00 0.00 0.00 4.94
39 40 3.634910 ACAAAAGTAAAATGGCTCGTGGT 59.365 39.130 0.00 0.00 0.00 4.16
40 41 4.098807 ACAAAAGTAAAATGGCTCGTGGTT 59.901 37.500 0.00 0.00 0.00 3.67
41 42 5.299782 ACAAAAGTAAAATGGCTCGTGGTTA 59.700 36.000 0.00 0.00 0.00 2.85
42 43 5.366829 AAAGTAAAATGGCTCGTGGTTAC 57.633 39.130 0.00 0.00 0.00 2.50
43 44 3.340928 AGTAAAATGGCTCGTGGTTACC 58.659 45.455 0.00 0.00 0.00 2.85
44 45 1.161843 AAAATGGCTCGTGGTTACCG 58.838 50.000 0.00 0.00 0.00 4.02
45 46 0.322322 AAATGGCTCGTGGTTACCGA 59.678 50.000 0.00 0.00 0.00 4.69
46 47 0.322322 AATGGCTCGTGGTTACCGAA 59.678 50.000 0.00 0.00 33.34 4.30
47 48 0.108329 ATGGCTCGTGGTTACCGAAG 60.108 55.000 0.00 0.00 33.34 3.79
48 49 1.180456 TGGCTCGTGGTTACCGAAGA 61.180 55.000 0.00 0.00 33.34 2.87
49 50 0.037975 GGCTCGTGGTTACCGAAGAA 60.038 55.000 0.00 0.00 33.34 2.52
50 51 1.347320 GCTCGTGGTTACCGAAGAAG 58.653 55.000 0.00 0.00 33.34 2.85
51 52 1.068055 GCTCGTGGTTACCGAAGAAGA 60.068 52.381 0.00 0.00 33.34 2.87
52 53 2.416972 GCTCGTGGTTACCGAAGAAGAT 60.417 50.000 0.00 0.00 33.34 2.40
53 54 3.179830 CTCGTGGTTACCGAAGAAGATG 58.820 50.000 0.00 0.00 33.34 2.90
54 55 2.094390 TCGTGGTTACCGAAGAAGATGG 60.094 50.000 0.00 0.00 0.00 3.51
55 56 2.094390 CGTGGTTACCGAAGAAGATGGA 60.094 50.000 0.00 0.00 0.00 3.41
56 57 3.522553 GTGGTTACCGAAGAAGATGGAG 58.477 50.000 0.00 0.00 0.00 3.86
57 58 3.056035 GTGGTTACCGAAGAAGATGGAGT 60.056 47.826 0.00 0.00 0.00 3.85
58 59 4.159135 GTGGTTACCGAAGAAGATGGAGTA 59.841 45.833 0.00 0.00 0.00 2.59
59 60 4.159135 TGGTTACCGAAGAAGATGGAGTAC 59.841 45.833 0.00 0.00 0.00 2.73
60 61 4.441217 GGTTACCGAAGAAGATGGAGTACC 60.441 50.000 0.00 0.00 0.00 3.34
61 62 3.103080 ACCGAAGAAGATGGAGTACCT 57.897 47.619 0.00 0.00 37.04 3.08
62 63 2.761208 ACCGAAGAAGATGGAGTACCTG 59.239 50.000 0.00 0.00 37.04 4.00
63 64 3.024547 CCGAAGAAGATGGAGTACCTGA 58.975 50.000 0.00 0.00 37.04 3.86
64 65 3.067461 CCGAAGAAGATGGAGTACCTGAG 59.933 52.174 0.00 0.00 37.04 3.35
65 66 3.490078 CGAAGAAGATGGAGTACCTGAGC 60.490 52.174 0.00 0.00 37.04 4.26
66 67 2.028130 AGAAGATGGAGTACCTGAGCG 58.972 52.381 0.00 0.00 37.04 5.03
67 68 1.067821 GAAGATGGAGTACCTGAGCGG 59.932 57.143 0.00 0.00 37.04 5.52
68 69 1.068250 GATGGAGTACCTGAGCGGC 59.932 63.158 0.00 0.00 37.04 6.53
69 70 2.370647 GATGGAGTACCTGAGCGGCC 62.371 65.000 0.00 0.00 37.04 6.13
70 71 3.075005 GGAGTACCTGAGCGGCCA 61.075 66.667 2.24 0.00 35.61 5.36
71 72 2.184579 GAGTACCTGAGCGGCCAC 59.815 66.667 2.24 0.00 35.61 5.01
72 73 2.603473 AGTACCTGAGCGGCCACA 60.603 61.111 2.24 0.00 35.61 4.17
73 74 2.125512 GTACCTGAGCGGCCACAG 60.126 66.667 2.24 14.88 35.61 3.66
74 75 2.603473 TACCTGAGCGGCCACAGT 60.603 61.111 18.51 11.70 35.61 3.55
75 76 1.304630 TACCTGAGCGGCCACAGTA 60.305 57.895 18.51 11.00 35.61 2.74
76 77 0.686441 TACCTGAGCGGCCACAGTAT 60.686 55.000 18.51 11.52 35.61 2.12
77 78 1.522355 CCTGAGCGGCCACAGTATG 60.522 63.158 18.51 5.16 46.00 2.39
103 104 2.704725 TTTTTCCTCGCATGCAACTC 57.295 45.000 19.57 0.00 0.00 3.01
104 105 0.516877 TTTTCCTCGCATGCAACTCG 59.483 50.000 19.57 0.14 0.00 4.18
105 106 0.320334 TTTCCTCGCATGCAACTCGA 60.320 50.000 19.57 5.23 0.00 4.04
106 107 1.014044 TTCCTCGCATGCAACTCGAC 61.014 55.000 19.57 0.00 0.00 4.20
107 108 2.691522 CTCGCATGCAACTCGACG 59.308 61.111 19.57 0.00 0.00 5.12
108 109 2.049526 TCGCATGCAACTCGACGT 60.050 55.556 19.57 0.00 0.00 4.34
109 110 2.094539 CGCATGCAACTCGACGTG 59.905 61.111 19.57 0.00 0.00 4.49
110 111 2.476051 GCATGCAACTCGACGTGG 59.524 61.111 14.21 0.00 0.00 4.94
111 112 3.027170 GCATGCAACTCGACGTGGG 62.027 63.158 14.21 0.00 0.00 4.61
112 113 2.742372 ATGCAACTCGACGTGGGC 60.742 61.111 0.00 5.52 0.00 5.36
113 114 4.980805 TGCAACTCGACGTGGGCC 62.981 66.667 0.00 0.00 0.00 5.80
114 115 4.681978 GCAACTCGACGTGGGCCT 62.682 66.667 4.53 0.00 0.00 5.19
115 116 2.738521 CAACTCGACGTGGGCCTG 60.739 66.667 4.53 0.00 0.00 4.85
116 117 4.681978 AACTCGACGTGGGCCTGC 62.682 66.667 4.53 0.00 0.00 4.85
137 138 2.923854 GCGTCCGCGATCTGATTG 59.076 61.111 8.23 0.24 41.33 2.67
147 148 1.572085 GATCTGATTGGCGCCATCGG 61.572 60.000 33.25 29.82 35.95 4.18
206 207 2.978010 CGACCCTTTGCTGCCGTT 60.978 61.111 0.00 0.00 0.00 4.44
211 212 3.964875 CTTTGCTGCCGTTGCCGT 61.965 61.111 0.00 0.00 36.33 5.68
292 293 2.535984 GCTCGAACCAACTATCATCACG 59.464 50.000 0.00 0.00 0.00 4.35
324 325 2.829003 TCCCTCGCTACTCTGCCG 60.829 66.667 0.00 0.00 0.00 5.69
381 382 0.318441 CCCTCTTCGCTGAGTTGTCA 59.682 55.000 4.33 0.00 32.50 3.58
383 384 2.166459 CCCTCTTCGCTGAGTTGTCATA 59.834 50.000 4.33 0.00 32.50 2.15
391 392 7.763985 TCTTCGCTGAGTTGTCATATTATTTCA 59.236 33.333 0.00 0.00 30.18 2.69
393 394 7.041721 TCGCTGAGTTGTCATATTATTTCAGT 58.958 34.615 0.00 0.00 34.72 3.41
395 396 7.010460 CGCTGAGTTGTCATATTATTTCAGTCA 59.990 37.037 0.00 0.00 34.72 3.41
513 520 2.069273 GCATGTGGAGTATGCGTATCC 58.931 52.381 0.00 7.21 41.16 2.59
576 583 2.563798 CCCGGCTTGCTTGCTTCAA 61.564 57.895 0.00 0.00 0.00 2.69
577 584 1.372128 CCGGCTTGCTTGCTTCAAC 60.372 57.895 0.00 0.00 0.00 3.18
578 585 1.372128 CGGCTTGCTTGCTTCAACC 60.372 57.895 1.96 0.00 0.00 3.77
579 586 1.372128 GGCTTGCTTGCTTCAACCG 60.372 57.895 1.96 0.00 0.00 4.44
580 587 1.372128 GCTTGCTTGCTTCAACCGG 60.372 57.895 0.00 0.00 0.00 5.28
581 588 2.032981 CTTGCTTGCTTCAACCGGT 58.967 52.632 0.00 0.00 0.00 5.28
582 589 0.318107 CTTGCTTGCTTCAACCGGTG 60.318 55.000 8.52 2.16 0.00 4.94
583 590 1.733402 TTGCTTGCTTCAACCGGTGG 61.733 55.000 8.52 4.63 0.00 4.61
584 591 2.193536 GCTTGCTTCAACCGGTGGT 61.194 57.895 8.52 0.00 37.65 4.16
588 595 0.394488 TGCTTCAACCGGTGGTTTCA 60.394 50.000 8.52 1.37 44.33 2.69
589 596 0.958822 GCTTCAACCGGTGGTTTCAT 59.041 50.000 8.52 0.00 44.33 2.57
590 597 1.335872 GCTTCAACCGGTGGTTTCATG 60.336 52.381 8.52 0.00 44.33 3.07
592 599 0.466372 TCAACCGGTGGTTTCATGCA 60.466 50.000 8.52 0.00 44.33 3.96
595 602 2.560861 CGGTGGTTTCATGCACGG 59.439 61.111 0.00 0.00 0.00 4.94
596 603 1.963855 CGGTGGTTTCATGCACGGA 60.964 57.895 0.00 0.00 0.00 4.69
597 604 1.875963 GGTGGTTTCATGCACGGAG 59.124 57.895 0.00 0.00 0.00 4.63
598 605 0.605319 GGTGGTTTCATGCACGGAGA 60.605 55.000 0.00 0.00 0.00 3.71
599 606 1.234821 GTGGTTTCATGCACGGAGAA 58.765 50.000 0.00 0.00 0.00 2.87
600 607 1.812571 GTGGTTTCATGCACGGAGAAT 59.187 47.619 0.00 0.00 0.00 2.40
601 608 3.006940 GTGGTTTCATGCACGGAGAATA 58.993 45.455 0.00 0.00 0.00 1.75
604 611 3.309954 GGTTTCATGCACGGAGAATACTC 59.690 47.826 0.00 0.00 41.94 2.59
621 628 9.327628 GAGAATACTCCCTTTGTTCCTAAATAC 57.672 37.037 0.00 0.00 37.19 1.89
622 629 9.059023 AGAATACTCCCTTTGTTCCTAAATACT 57.941 33.333 0.00 0.00 0.00 2.12
623 630 9.682465 GAATACTCCCTTTGTTCCTAAATACTT 57.318 33.333 0.00 0.00 0.00 2.24
624 631 9.682465 AATACTCCCTTTGTTCCTAAATACTTC 57.318 33.333 0.00 0.00 0.00 3.01
625 632 6.482524 ACTCCCTTTGTTCCTAAATACTTCC 58.517 40.000 0.00 0.00 0.00 3.46
626 633 6.274908 ACTCCCTTTGTTCCTAAATACTTCCT 59.725 38.462 0.00 0.00 0.00 3.36
627 634 6.718294 TCCCTTTGTTCCTAAATACTTCCTC 58.282 40.000 0.00 0.00 0.00 3.71
628 635 5.886474 CCCTTTGTTCCTAAATACTTCCTCC 59.114 44.000 0.00 0.00 0.00 4.30
629 636 5.585047 CCTTTGTTCCTAAATACTTCCTCCG 59.415 44.000 0.00 0.00 0.00 4.63
630 637 5.750352 TTGTTCCTAAATACTTCCTCCGT 57.250 39.130 0.00 0.00 0.00 4.69
631 638 6.855763 TTGTTCCTAAATACTTCCTCCGTA 57.144 37.500 0.00 0.00 0.00 4.02
632 639 6.855763 TGTTCCTAAATACTTCCTCCGTAA 57.144 37.500 0.00 0.00 0.00 3.18
633 640 7.243604 TGTTCCTAAATACTTCCTCCGTAAA 57.756 36.000 0.00 0.00 0.00 2.01
634 641 7.099120 TGTTCCTAAATACTTCCTCCGTAAAC 58.901 38.462 0.00 0.00 0.00 2.01
635 642 7.038799 TGTTCCTAAATACTTCCTCCGTAAACT 60.039 37.037 0.00 0.00 0.00 2.66
636 643 8.470002 GTTCCTAAATACTTCCTCCGTAAACTA 58.530 37.037 0.00 0.00 0.00 2.24
637 644 8.593945 TCCTAAATACTTCCTCCGTAAACTAA 57.406 34.615 0.00 0.00 0.00 2.24
638 645 9.205513 TCCTAAATACTTCCTCCGTAAACTAAT 57.794 33.333 0.00 0.00 0.00 1.73
754 761 5.751509 CGTTTGTTTCGGGATATGAGATGTA 59.248 40.000 0.00 0.00 0.00 2.29
761 768 2.093973 GGGATATGAGATGTAGCCGGTG 60.094 54.545 1.90 0.00 0.00 4.94
840 847 4.124351 GGATCGTGGCGACGGACA 62.124 66.667 21.31 2.21 46.11 4.02
865 873 2.897972 GACGTTCGGTAGGCCCAT 59.102 61.111 0.00 0.00 0.00 4.00
890 898 1.643286 TCCATTTAACCCAGCCCATCA 59.357 47.619 0.00 0.00 0.00 3.07
937 945 2.642154 TTCGCTCCAACAAACCCTAA 57.358 45.000 0.00 0.00 0.00 2.69
969 978 3.290710 CATCTCAATCGACCCCCAAATT 58.709 45.455 0.00 0.00 0.00 1.82
1016 1025 2.211250 AAGATGGCAGATGCAGTTGT 57.789 45.000 7.19 0.00 44.36 3.32
1027 1036 1.960417 TGCAGTTGTTGATTCGGTCA 58.040 45.000 0.00 0.00 34.25 4.02
1036 1045 0.535335 TGATTCGGTCACCCTGCTAC 59.465 55.000 0.00 0.00 0.00 3.58
1082 1091 3.693085 AGGAACGTCGTGACATATGTAGT 59.307 43.478 8.71 0.02 0.00 2.73
1086 1095 2.462927 CGTCGTGACATATGTAGTTCGC 59.537 50.000 8.71 2.07 0.00 4.70
1357 2628 0.824759 AGAGGAAATTCGACTCCCCG 59.175 55.000 4.18 0.00 31.50 5.73
1391 2666 4.202121 GGATGGCAATTACAGTCGACTAGA 60.202 45.833 19.57 6.08 0.00 2.43
1392 2667 4.794278 TGGCAATTACAGTCGACTAGAA 57.206 40.909 19.57 15.24 0.00 2.10
1393 2668 4.491676 TGGCAATTACAGTCGACTAGAAC 58.508 43.478 19.57 4.26 0.00 3.01
1394 2669 4.219944 TGGCAATTACAGTCGACTAGAACT 59.780 41.667 19.57 2.03 0.00 3.01
1395 2670 4.563184 GGCAATTACAGTCGACTAGAACTG 59.437 45.833 19.57 15.51 35.54 3.16
1396 2671 5.162075 GCAATTACAGTCGACTAGAACTGT 58.838 41.667 19.57 23.56 41.06 3.55
1397 2672 5.286558 GCAATTACAGTCGACTAGAACTGTC 59.713 44.000 19.57 7.93 39.80 3.51
1398 2673 6.613233 CAATTACAGTCGACTAGAACTGTCT 58.387 40.000 19.57 14.84 39.80 3.41
1399 2674 6.821031 ATTACAGTCGACTAGAACTGTCTT 57.179 37.500 19.57 14.71 39.80 3.01
1400 2675 4.491234 ACAGTCGACTAGAACTGTCTTG 57.509 45.455 19.57 4.57 36.93 3.02
1401 2676 3.253677 ACAGTCGACTAGAACTGTCTTGG 59.746 47.826 19.57 3.36 36.93 3.61
1402 2677 3.502595 CAGTCGACTAGAACTGTCTTGGA 59.497 47.826 19.57 0.00 35.12 3.53
1403 2678 4.156922 CAGTCGACTAGAACTGTCTTGGAT 59.843 45.833 19.57 0.00 35.12 3.41
1404 2679 4.156922 AGTCGACTAGAACTGTCTTGGATG 59.843 45.833 18.46 0.00 35.12 3.51
1405 2680 3.444034 TCGACTAGAACTGTCTTGGATGG 59.556 47.826 0.00 0.00 35.12 3.51
1406 2681 3.526534 GACTAGAACTGTCTTGGATGGC 58.473 50.000 0.00 0.00 35.12 4.40
1407 2682 2.906389 ACTAGAACTGTCTTGGATGGCA 59.094 45.455 0.00 0.00 35.12 4.92
1408 2683 2.957402 AGAACTGTCTTGGATGGCAA 57.043 45.000 0.00 0.00 0.00 4.52
1409 2684 3.446442 AGAACTGTCTTGGATGGCAAT 57.554 42.857 0.00 0.00 0.00 3.56
1410 2685 3.771216 AGAACTGTCTTGGATGGCAATT 58.229 40.909 0.00 0.00 0.00 2.32
1411 2686 4.922206 AGAACTGTCTTGGATGGCAATTA 58.078 39.130 0.00 0.00 0.00 1.40
1412 2687 4.702131 AGAACTGTCTTGGATGGCAATTAC 59.298 41.667 0.00 0.00 0.00 1.89
1413 2688 4.032960 ACTGTCTTGGATGGCAATTACA 57.967 40.909 0.00 0.00 0.00 2.41
1414 2689 4.012374 ACTGTCTTGGATGGCAATTACAG 58.988 43.478 0.00 2.84 39.14 2.74
1415 2690 4.012374 CTGTCTTGGATGGCAATTACAGT 58.988 43.478 0.00 0.00 0.00 3.55
1416 2691 4.009675 TGTCTTGGATGGCAATTACAGTC 58.990 43.478 0.00 0.00 0.00 3.51
1417 2692 3.063997 GTCTTGGATGGCAATTACAGTCG 59.936 47.826 0.00 0.00 0.00 4.18
1418 2693 3.055458 TCTTGGATGGCAATTACAGTCGA 60.055 43.478 0.00 0.00 0.00 4.20
1419 2694 2.627945 TGGATGGCAATTACAGTCGAC 58.372 47.619 7.70 7.70 0.00 4.20
1420 2695 2.236146 TGGATGGCAATTACAGTCGACT 59.764 45.455 13.58 13.58 0.00 4.18
1421 2696 3.449377 TGGATGGCAATTACAGTCGACTA 59.551 43.478 19.57 2.81 0.00 2.59
1422 2697 4.081365 TGGATGGCAATTACAGTCGACTAA 60.081 41.667 19.57 10.71 0.00 2.24
1448 2723 2.280183 CGCTCTGTCTTATCTGAAACGC 59.720 50.000 0.00 0.00 0.00 4.84
1453 2728 4.686091 TCTGTCTTATCTGAAACGCACAAG 59.314 41.667 0.00 0.00 0.00 3.16
1459 2734 0.925267 CTGAAACGCACAAGCACACG 60.925 55.000 0.00 0.00 42.27 4.49
1460 2735 2.277884 AAACGCACAAGCACACGC 60.278 55.556 0.00 0.00 42.27 5.34
1461 2736 2.911439 GAAACGCACAAGCACACGCA 62.911 55.000 0.00 0.00 42.27 5.24
1462 2737 3.733190 AACGCACAAGCACACGCAC 62.733 57.895 0.00 0.00 42.27 5.34
1471 2746 4.918060 CACACGCACACGCACACG 62.918 66.667 0.00 0.00 45.53 4.49
1498 2773 4.202264 ACGCACCTCTTATCAGGGAAATAG 60.202 45.833 0.00 0.00 37.96 1.73
1578 2853 0.955919 GGCGGCTCTACAAGTTTGCT 60.956 55.000 0.00 0.00 0.00 3.91
1593 2868 4.993905 AGTTTGCTTTCGGTAAATATGCC 58.006 39.130 0.00 0.00 32.58 4.40
1684 3010 2.027653 TCTGGTGTTGGTCGATGCAATA 60.028 45.455 0.00 0.00 0.00 1.90
2180 3958 7.610865 TGAACTCTGAAATTTGGTTTTGACTT 58.389 30.769 0.00 0.00 0.00 3.01
2445 4227 6.767902 AGTACTGTCACAGTTCACATGAAAAT 59.232 34.615 17.55 0.00 42.59 1.82
2448 4230 5.590145 TGTCACAGTTCACATGAAAATTGG 58.410 37.500 0.00 0.00 35.58 3.16
2488 4280 5.627499 TGGCACTCTGAATGTAAATTCAC 57.373 39.130 4.07 0.00 35.80 3.18
2489 4281 5.069318 TGGCACTCTGAATGTAAATTCACA 58.931 37.500 4.07 0.00 35.80 3.58
2490 4282 5.711506 TGGCACTCTGAATGTAAATTCACAT 59.288 36.000 4.07 0.00 40.90 3.21
2491 4283 6.883756 TGGCACTCTGAATGTAAATTCACATA 59.116 34.615 4.07 0.00 38.19 2.29
2492 4284 7.066163 TGGCACTCTGAATGTAAATTCACATAG 59.934 37.037 4.07 5.52 38.19 2.23
2493 4285 7.412853 GCACTCTGAATGTAAATTCACATAGG 58.587 38.462 4.07 0.00 38.19 2.57
2494 4286 7.412853 CACTCTGAATGTAAATTCACATAGGC 58.587 38.462 4.07 0.00 38.19 3.93
2495 4287 7.066163 CACTCTGAATGTAAATTCACATAGGCA 59.934 37.037 4.07 0.00 38.19 4.75
2496 4288 7.281774 ACTCTGAATGTAAATTCACATAGGCAG 59.718 37.037 4.07 10.64 38.19 4.85
2497 4289 7.337938 TCTGAATGTAAATTCACATAGGCAGA 58.662 34.615 13.65 13.65 38.19 4.26
2650 4466 7.279615 TCACATGGAAGAGTAAGTCTTTTTGA 58.720 34.615 0.00 0.00 46.21 2.69
2654 4470 6.299141 TGGAAGAGTAAGTCTTTTTGATGCT 58.701 36.000 0.00 0.00 46.21 3.79
2779 4600 7.199541 CTCCCATAGAGCAAATGTGAAATAG 57.800 40.000 0.00 0.00 35.31 1.73
2861 4686 7.559897 TGGTGTTTTTCTTCCACTTTCTCTATT 59.440 33.333 0.00 0.00 0.00 1.73
2994 4963 6.232581 TCCAAAAACTCATTGGTTGATTGT 57.767 33.333 5.31 0.00 46.05 2.71
2998 4967 8.242739 CCAAAAACTCATTGGTTGATTGTTTTT 58.757 29.630 0.00 0.00 44.81 1.94
3039 5012 9.826574 TGTATCCAAACACTATATTGGTAGTTC 57.173 33.333 4.62 0.00 45.12 3.01
3109 5082 0.474660 AGGGTGAGGAAGGAGCAACT 60.475 55.000 0.00 0.00 0.00 3.16
3132 5105 5.189928 TGTTGGAGTCACAATAACAACAGT 58.810 37.500 0.00 0.00 41.99 3.55
3152 5125 1.227973 GCGATGGTGGGGAAGGATC 60.228 63.158 0.00 0.00 0.00 3.36
3153 5126 1.069765 CGATGGTGGGGAAGGATCG 59.930 63.158 0.00 0.00 0.00 3.69
3154 5127 1.399744 CGATGGTGGGGAAGGATCGA 61.400 60.000 0.00 0.00 38.53 3.59
3155 5128 1.059913 GATGGTGGGGAAGGATCGAT 58.940 55.000 0.00 0.00 0.00 3.59
3156 5129 1.421646 GATGGTGGGGAAGGATCGATT 59.578 52.381 0.00 0.00 0.00 3.34
3157 5130 0.837272 TGGTGGGGAAGGATCGATTC 59.163 55.000 0.00 0.00 0.00 2.52
3158 5131 0.108774 GGTGGGGAAGGATCGATTCC 59.891 60.000 16.40 16.40 44.65 3.01
3165 5138 4.345337 GGATCGATTCCGCCACTC 57.655 61.111 0.00 0.00 33.93 3.51
3166 5139 1.441729 GGATCGATTCCGCCACTCA 59.558 57.895 0.00 0.00 33.93 3.41
3167 5140 0.598680 GGATCGATTCCGCCACTCAG 60.599 60.000 0.00 0.00 33.93 3.35
3168 5141 0.598680 GATCGATTCCGCCACTCAGG 60.599 60.000 0.00 0.00 41.84 3.86
3169 5142 1.330655 ATCGATTCCGCCACTCAGGT 61.331 55.000 0.00 0.00 40.61 4.00
3213 5186 3.859650 GATTCCATCGGCAATGCTG 57.140 52.632 7.93 7.93 33.71 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.237344 ACTTTTGTTTGAGAATCTGACTCGG 59.763 40.000 0.00 0.00 37.22 4.63
1 2 6.292389 ACTTTTGTTTGAGAATCTGACTCG 57.708 37.500 0.00 0.00 37.22 4.18
6 7 8.490355 GCCATTTTACTTTTGTTTGAGAATCTG 58.510 33.333 0.00 0.00 34.92 2.90
7 8 8.424133 AGCCATTTTACTTTTGTTTGAGAATCT 58.576 29.630 0.00 0.00 34.92 2.40
8 9 8.593492 AGCCATTTTACTTTTGTTTGAGAATC 57.407 30.769 0.00 0.00 0.00 2.52
9 10 7.382218 CGAGCCATTTTACTTTTGTTTGAGAAT 59.618 33.333 0.00 0.00 0.00 2.40
10 11 6.695278 CGAGCCATTTTACTTTTGTTTGAGAA 59.305 34.615 0.00 0.00 0.00 2.87
11 12 6.183360 ACGAGCCATTTTACTTTTGTTTGAGA 60.183 34.615 0.00 0.00 0.00 3.27
12 13 5.977129 ACGAGCCATTTTACTTTTGTTTGAG 59.023 36.000 0.00 0.00 0.00 3.02
13 14 5.746245 CACGAGCCATTTTACTTTTGTTTGA 59.254 36.000 0.00 0.00 0.00 2.69
14 15 5.051106 CCACGAGCCATTTTACTTTTGTTTG 60.051 40.000 0.00 0.00 0.00 2.93
15 16 5.047188 CCACGAGCCATTTTACTTTTGTTT 58.953 37.500 0.00 0.00 0.00 2.83
16 17 4.098807 ACCACGAGCCATTTTACTTTTGTT 59.901 37.500 0.00 0.00 0.00 2.83
17 18 3.634910 ACCACGAGCCATTTTACTTTTGT 59.365 39.130 0.00 0.00 0.00 2.83
18 19 4.237349 ACCACGAGCCATTTTACTTTTG 57.763 40.909 0.00 0.00 0.00 2.44
19 20 4.929819 AACCACGAGCCATTTTACTTTT 57.070 36.364 0.00 0.00 0.00 2.27
20 21 4.216902 GGTAACCACGAGCCATTTTACTTT 59.783 41.667 0.00 0.00 0.00 2.66
21 22 3.754850 GGTAACCACGAGCCATTTTACTT 59.245 43.478 0.00 0.00 0.00 2.24
22 23 3.340928 GGTAACCACGAGCCATTTTACT 58.659 45.455 0.00 0.00 0.00 2.24
23 24 2.094734 CGGTAACCACGAGCCATTTTAC 59.905 50.000 0.00 0.00 0.00 2.01
24 25 2.028294 TCGGTAACCACGAGCCATTTTA 60.028 45.455 0.00 0.00 35.12 1.52
25 26 1.161843 CGGTAACCACGAGCCATTTT 58.838 50.000 0.00 0.00 0.00 1.82
26 27 0.322322 TCGGTAACCACGAGCCATTT 59.678 50.000 0.00 0.00 35.12 2.32
27 28 0.322322 TTCGGTAACCACGAGCCATT 59.678 50.000 0.00 0.00 41.81 3.16
28 29 0.108329 CTTCGGTAACCACGAGCCAT 60.108 55.000 0.00 0.00 41.81 4.40
29 30 1.180456 TCTTCGGTAACCACGAGCCA 61.180 55.000 0.00 0.00 41.81 4.75
30 31 0.037975 TTCTTCGGTAACCACGAGCC 60.038 55.000 0.00 0.00 41.81 4.70
31 32 1.068055 TCTTCTTCGGTAACCACGAGC 60.068 52.381 0.00 0.00 41.81 5.03
32 33 3.179830 CATCTTCTTCGGTAACCACGAG 58.820 50.000 0.00 0.00 41.81 4.18
33 34 2.094390 CCATCTTCTTCGGTAACCACGA 60.094 50.000 0.00 0.00 38.78 4.35
34 35 2.094390 TCCATCTTCTTCGGTAACCACG 60.094 50.000 0.00 0.00 0.00 4.94
35 36 3.056035 ACTCCATCTTCTTCGGTAACCAC 60.056 47.826 0.00 0.00 0.00 4.16
36 37 3.170717 ACTCCATCTTCTTCGGTAACCA 58.829 45.455 0.00 0.00 0.00 3.67
37 38 3.889520 ACTCCATCTTCTTCGGTAACC 57.110 47.619 0.00 0.00 0.00 2.85
38 39 4.401837 AGGTACTCCATCTTCTTCGGTAAC 59.598 45.833 0.00 0.00 35.89 2.50
39 40 4.401519 CAGGTACTCCATCTTCTTCGGTAA 59.598 45.833 0.00 0.00 34.60 2.85
40 41 3.952323 CAGGTACTCCATCTTCTTCGGTA 59.048 47.826 0.00 0.00 34.60 4.02
41 42 2.761208 CAGGTACTCCATCTTCTTCGGT 59.239 50.000 0.00 0.00 34.60 4.69
42 43 3.024547 TCAGGTACTCCATCTTCTTCGG 58.975 50.000 0.00 0.00 34.60 4.30
43 44 3.490078 GCTCAGGTACTCCATCTTCTTCG 60.490 52.174 0.00 0.00 34.60 3.79
44 45 3.490078 CGCTCAGGTACTCCATCTTCTTC 60.490 52.174 0.00 0.00 34.60 2.87
45 46 2.428890 CGCTCAGGTACTCCATCTTCTT 59.571 50.000 0.00 0.00 34.60 2.52
46 47 2.028130 CGCTCAGGTACTCCATCTTCT 58.972 52.381 0.00 0.00 34.60 2.85
47 48 1.067821 CCGCTCAGGTACTCCATCTTC 59.932 57.143 0.00 0.00 34.60 2.87
48 49 1.115467 CCGCTCAGGTACTCCATCTT 58.885 55.000 0.00 0.00 34.60 2.40
49 50 1.395826 GCCGCTCAGGTACTCCATCT 61.396 60.000 0.00 0.00 43.70 2.90
50 51 1.068250 GCCGCTCAGGTACTCCATC 59.932 63.158 0.00 0.00 43.70 3.51
51 52 2.435693 GGCCGCTCAGGTACTCCAT 61.436 63.158 0.00 0.00 43.70 3.41
52 53 3.075005 GGCCGCTCAGGTACTCCA 61.075 66.667 0.00 0.00 43.70 3.86
53 54 3.075005 TGGCCGCTCAGGTACTCC 61.075 66.667 0.00 0.00 43.70 3.85
54 55 2.184579 GTGGCCGCTCAGGTACTC 59.815 66.667 9.68 0.00 43.70 2.59
55 56 2.603473 TGTGGCCGCTCAGGTACT 60.603 61.111 18.96 0.00 43.70 2.73
56 57 1.601419 TACTGTGGCCGCTCAGGTAC 61.601 60.000 18.96 0.00 43.70 3.34
57 58 0.686441 ATACTGTGGCCGCTCAGGTA 60.686 55.000 18.96 14.55 43.70 3.08
58 59 1.990060 ATACTGTGGCCGCTCAGGT 60.990 57.895 18.96 12.91 43.70 4.00
59 60 1.522355 CATACTGTGGCCGCTCAGG 60.522 63.158 18.96 7.64 44.97 3.86
60 61 0.391661 AACATACTGTGGCCGCTCAG 60.392 55.000 18.96 17.83 37.65 3.35
61 62 0.391130 GAACATACTGTGGCCGCTCA 60.391 55.000 18.96 6.39 0.00 4.26
62 63 0.108138 AGAACATACTGTGGCCGCTC 60.108 55.000 18.96 4.50 0.00 5.03
63 64 0.324943 AAGAACATACTGTGGCCGCT 59.675 50.000 18.96 0.00 0.00 5.52
64 65 1.165270 AAAGAACATACTGTGGCCGC 58.835 50.000 10.11 10.11 0.00 6.53
65 66 3.915437 AAAAAGAACATACTGTGGCCG 57.085 42.857 0.00 0.00 0.00 6.13
84 85 1.069296 CGAGTTGCATGCGAGGAAAAA 60.069 47.619 14.09 0.00 0.00 1.94
85 86 0.516877 CGAGTTGCATGCGAGGAAAA 59.483 50.000 14.09 0.00 0.00 2.29
86 87 0.320334 TCGAGTTGCATGCGAGGAAA 60.320 50.000 14.09 0.00 0.00 3.13
87 88 1.014044 GTCGAGTTGCATGCGAGGAA 61.014 55.000 14.09 0.00 34.41 3.36
88 89 1.446099 GTCGAGTTGCATGCGAGGA 60.446 57.895 14.09 6.20 34.41 3.71
89 90 2.792290 CGTCGAGTTGCATGCGAGG 61.792 63.158 14.09 5.55 34.41 4.63
90 91 2.088763 ACGTCGAGTTGCATGCGAG 61.089 57.895 14.09 0.00 34.41 5.03
91 92 2.049526 ACGTCGAGTTGCATGCGA 60.050 55.556 14.09 8.74 0.00 5.10
92 93 2.094539 CACGTCGAGTTGCATGCG 59.905 61.111 14.09 0.00 0.00 4.73
93 94 2.476051 CCACGTCGAGTTGCATGC 59.524 61.111 11.82 11.82 0.00 4.06
94 95 3.027170 GCCCACGTCGAGTTGCATG 62.027 63.158 0.00 0.00 0.00 4.06
95 96 2.742372 GCCCACGTCGAGTTGCAT 60.742 61.111 0.00 0.00 0.00 3.96
96 97 4.980805 GGCCCACGTCGAGTTGCA 62.981 66.667 0.00 0.00 31.57 4.08
97 98 4.681978 AGGCCCACGTCGAGTTGC 62.682 66.667 0.00 0.00 0.00 4.17
98 99 2.738521 CAGGCCCACGTCGAGTTG 60.739 66.667 0.00 0.00 0.00 3.16
99 100 4.681978 GCAGGCCCACGTCGAGTT 62.682 66.667 0.00 0.00 0.00 3.01
120 121 2.589492 CCAATCAGATCGCGGACGC 61.589 63.158 6.13 6.63 39.84 5.19
121 122 2.589492 GCCAATCAGATCGCGGACG 61.589 63.158 6.13 0.00 42.01 4.79
122 123 2.589492 CGCCAATCAGATCGCGGAC 61.589 63.158 6.13 0.00 40.91 4.79
123 124 2.279451 CGCCAATCAGATCGCGGA 60.279 61.111 6.13 0.00 40.91 5.54
124 125 4.005472 GCGCCAATCAGATCGCGG 62.005 66.667 20.61 7.72 44.60 6.46
126 127 2.180131 GATGGCGCCAATCAGATCGC 62.180 60.000 36.33 10.28 45.99 4.58
127 128 1.864862 GATGGCGCCAATCAGATCG 59.135 57.895 36.33 0.00 0.00 3.69
128 129 1.572085 CCGATGGCGCCAATCAGATC 61.572 60.000 36.33 23.84 35.83 2.75
129 130 1.598962 CCGATGGCGCCAATCAGAT 60.599 57.895 36.33 16.92 35.83 2.90
130 131 2.203056 CCGATGGCGCCAATCAGA 60.203 61.111 36.33 9.29 35.83 3.27
147 148 2.122167 AGACACCTCCGATCGAGCC 61.122 63.158 18.66 0.00 37.27 4.70
254 255 4.988598 CTTCGCACTGGGCACGGT 62.989 66.667 1.50 0.00 45.17 4.83
274 275 1.593006 GCCGTGATGATAGTTGGTTCG 59.407 52.381 0.00 0.00 0.00 3.95
282 283 3.119291 GACAGTTCAGCCGTGATGATAG 58.881 50.000 0.00 0.00 30.85 2.08
292 293 0.326264 AGGGACATGACAGTTCAGCC 59.674 55.000 0.00 0.00 34.35 4.85
369 370 7.010460 TGACTGAAATAATATGACAACTCAGCG 59.990 37.037 0.00 0.00 33.86 5.18
391 392 8.915036 CACAGGTTTAATAGTAGGACTATGACT 58.085 37.037 0.00 0.00 40.32 3.41
393 394 9.132923 CTCACAGGTTTAATAGTAGGACTATGA 57.867 37.037 0.00 0.00 40.32 2.15
395 396 7.563924 TGCTCACAGGTTTAATAGTAGGACTAT 59.436 37.037 0.00 0.00 42.86 2.12
398 399 5.974108 TGCTCACAGGTTTAATAGTAGGAC 58.026 41.667 0.00 0.00 0.00 3.85
434 441 1.083657 CAGCAACGCACGTGTACAC 60.084 57.895 18.38 16.32 0.00 2.90
488 495 0.378257 GCATACTCCACATGCAACGG 59.622 55.000 0.00 0.00 46.47 4.44
528 535 0.379669 GCTCTGGACCGCAATGAATG 59.620 55.000 0.00 0.00 0.00 2.67
531 538 2.125552 CGCTCTGGACCGCAATGA 60.126 61.111 0.00 0.00 0.00 2.57
561 568 1.372128 CGGTTGAAGCAAGCAAGCC 60.372 57.895 9.60 3.66 41.25 4.35
576 583 2.258013 CGTGCATGAAACCACCGGT 61.258 57.895 0.00 0.00 37.65 5.28
577 584 2.560861 CGTGCATGAAACCACCGG 59.439 61.111 0.00 0.00 0.00 5.28
578 585 1.911293 CTCCGTGCATGAAACCACCG 61.911 60.000 7.72 0.00 0.00 4.94
579 586 0.605319 TCTCCGTGCATGAAACCACC 60.605 55.000 7.72 0.00 0.00 4.61
580 587 1.234821 TTCTCCGTGCATGAAACCAC 58.765 50.000 7.72 0.00 0.00 4.16
581 588 2.198827 ATTCTCCGTGCATGAAACCA 57.801 45.000 7.72 0.00 0.00 3.67
582 589 3.270877 AGTATTCTCCGTGCATGAAACC 58.729 45.455 7.72 0.00 0.00 3.27
583 590 4.522297 GAGTATTCTCCGTGCATGAAAC 57.478 45.455 7.72 0.00 34.87 2.78
595 602 9.327628 GTATTTAGGAACAAAGGGAGTATTCTC 57.672 37.037 0.00 0.00 39.76 2.87
596 603 9.059023 AGTATTTAGGAACAAAGGGAGTATTCT 57.941 33.333 0.00 0.00 0.00 2.40
597 604 9.682465 AAGTATTTAGGAACAAAGGGAGTATTC 57.318 33.333 0.00 0.00 0.00 1.75
598 605 9.682465 GAAGTATTTAGGAACAAAGGGAGTATT 57.318 33.333 0.00 0.00 0.00 1.89
599 606 8.272889 GGAAGTATTTAGGAACAAAGGGAGTAT 58.727 37.037 0.00 0.00 0.00 2.12
600 607 7.460082 AGGAAGTATTTAGGAACAAAGGGAGTA 59.540 37.037 0.00 0.00 0.00 2.59
601 608 6.274908 AGGAAGTATTTAGGAACAAAGGGAGT 59.725 38.462 0.00 0.00 0.00 3.85
604 611 5.886474 GGAGGAAGTATTTAGGAACAAAGGG 59.114 44.000 0.00 0.00 0.00 3.95
605 612 5.585047 CGGAGGAAGTATTTAGGAACAAAGG 59.415 44.000 0.00 0.00 0.00 3.11
606 613 6.171213 ACGGAGGAAGTATTTAGGAACAAAG 58.829 40.000 0.00 0.00 0.00 2.77
607 614 6.117975 ACGGAGGAAGTATTTAGGAACAAA 57.882 37.500 0.00 0.00 0.00 2.83
608 615 5.750352 ACGGAGGAAGTATTTAGGAACAA 57.250 39.130 0.00 0.00 0.00 2.83
609 616 6.855763 TTACGGAGGAAGTATTTAGGAACA 57.144 37.500 0.00 0.00 0.00 3.18
610 617 7.326454 AGTTTACGGAGGAAGTATTTAGGAAC 58.674 38.462 0.00 0.00 0.00 3.62
611 618 7.486407 AGTTTACGGAGGAAGTATTTAGGAA 57.514 36.000 0.00 0.00 0.00 3.36
656 663 8.942338 TTTCGCATTTAGATCACTACATTAGT 57.058 30.769 0.00 0.00 40.28 2.24
659 666 9.722056 GATTTTTCGCATTTAGATCACTACATT 57.278 29.630 0.00 0.00 0.00 2.71
660 667 8.892723 TGATTTTTCGCATTTAGATCACTACAT 58.107 29.630 0.00 0.00 0.00 2.29
661 668 8.262715 TGATTTTTCGCATTTAGATCACTACA 57.737 30.769 0.00 0.00 0.00 2.74
662 669 9.722056 AATGATTTTTCGCATTTAGATCACTAC 57.278 29.630 0.00 0.00 31.02 2.73
663 670 9.720667 CAATGATTTTTCGCATTTAGATCACTA 57.279 29.630 0.00 0.00 32.74 2.74
664 671 7.703621 CCAATGATTTTTCGCATTTAGATCACT 59.296 33.333 0.00 0.00 32.74 3.41
665 672 7.515684 GCCAATGATTTTTCGCATTTAGATCAC 60.516 37.037 0.00 0.00 32.74 3.06
666 673 6.476380 GCCAATGATTTTTCGCATTTAGATCA 59.524 34.615 0.00 0.00 32.74 2.92
667 674 6.345250 CGCCAATGATTTTTCGCATTTAGATC 60.345 38.462 0.00 0.00 32.74 2.75
668 675 5.459762 CGCCAATGATTTTTCGCATTTAGAT 59.540 36.000 0.00 0.00 32.74 1.98
669 676 4.797868 CGCCAATGATTTTTCGCATTTAGA 59.202 37.500 0.00 0.00 32.74 2.10
670 677 4.548726 GCGCCAATGATTTTTCGCATTTAG 60.549 41.667 0.00 0.00 41.84 1.85
671 678 3.305629 GCGCCAATGATTTTTCGCATTTA 59.694 39.130 0.00 0.00 41.84 1.40
672 679 2.094099 GCGCCAATGATTTTTCGCATTT 59.906 40.909 0.00 0.00 41.84 2.32
683 690 2.586079 CTCGTCCGCGCCAATGAT 60.586 61.111 0.00 0.00 38.14 2.45
754 761 1.613630 ATCTCCTGGAACACCGGCT 60.614 57.895 0.00 0.00 0.00 5.52
802 809 1.219522 AAACGCCGTCTCTTTCCGTG 61.220 55.000 0.00 0.00 31.92 4.94
807 814 0.036306 ATCCCAAACGCCGTCTCTTT 59.964 50.000 0.00 0.00 0.00 2.52
840 847 0.179145 CTACCGAACGTCGCTTGGAT 60.179 55.000 8.95 0.00 38.82 3.41
865 873 2.622977 GGGCTGGGTTAAATGGATGTGA 60.623 50.000 0.00 0.00 0.00 3.58
890 898 0.175760 CGAATGAGGACCACACCGAT 59.824 55.000 9.03 0.00 34.73 4.18
969 978 1.729586 AGCTAGGGTGTCTTGGTTCA 58.270 50.000 0.00 0.00 0.00 3.18
1027 1036 1.913762 AAGGCACGAGTAGCAGGGT 60.914 57.895 0.00 0.00 0.00 4.34
1326 2531 4.321899 CGAATTTCCTCTGCAAAATCCCAA 60.322 41.667 0.00 0.00 0.00 4.12
1357 2628 4.525912 AATTGCCATCCAAGACAAAGAC 57.474 40.909 0.00 0.00 36.76 3.01
1391 2666 4.406456 TGTAATTGCCATCCAAGACAGTT 58.594 39.130 0.00 0.00 36.76 3.16
1392 2667 4.012374 CTGTAATTGCCATCCAAGACAGT 58.988 43.478 10.41 0.00 41.67 3.55
1393 2668 4.012374 ACTGTAATTGCCATCCAAGACAG 58.988 43.478 14.36 14.36 46.54 3.51
1394 2669 4.009675 GACTGTAATTGCCATCCAAGACA 58.990 43.478 0.00 0.00 36.76 3.41
1395 2670 3.063997 CGACTGTAATTGCCATCCAAGAC 59.936 47.826 0.00 0.00 36.76 3.01
1396 2671 3.055458 TCGACTGTAATTGCCATCCAAGA 60.055 43.478 0.00 0.00 36.76 3.02
1397 2672 3.063997 GTCGACTGTAATTGCCATCCAAG 59.936 47.826 8.70 0.00 36.76 3.61
1398 2673 3.006940 GTCGACTGTAATTGCCATCCAA 58.993 45.455 8.70 0.00 37.94 3.53
1399 2674 2.236146 AGTCGACTGTAATTGCCATCCA 59.764 45.455 19.30 0.00 0.00 3.41
1400 2675 2.906354 AGTCGACTGTAATTGCCATCC 58.094 47.619 19.30 0.00 0.00 3.51
1401 2676 6.092259 AGTTTTAGTCGACTGTAATTGCCATC 59.908 38.462 28.12 7.83 0.00 3.51
1402 2677 5.938125 AGTTTTAGTCGACTGTAATTGCCAT 59.062 36.000 28.12 0.00 0.00 4.40
1403 2678 5.302360 AGTTTTAGTCGACTGTAATTGCCA 58.698 37.500 28.12 1.06 0.00 4.92
1404 2679 5.444218 CGAGTTTTAGTCGACTGTAATTGCC 60.444 44.000 28.12 9.39 43.33 4.52
1405 2680 5.539207 CGAGTTTTAGTCGACTGTAATTGC 58.461 41.667 28.12 13.56 43.33 3.56
1406 2681 5.345202 AGCGAGTTTTAGTCGACTGTAATTG 59.655 40.000 28.12 15.42 43.33 2.32
1407 2682 5.467705 AGCGAGTTTTAGTCGACTGTAATT 58.532 37.500 28.12 16.90 43.33 1.40
1408 2683 5.056894 AGCGAGTTTTAGTCGACTGTAAT 57.943 39.130 28.12 11.77 43.33 1.89
1409 2684 4.214971 AGAGCGAGTTTTAGTCGACTGTAA 59.785 41.667 28.12 18.00 43.33 2.41
1410 2685 3.750130 AGAGCGAGTTTTAGTCGACTGTA 59.250 43.478 28.12 12.95 43.33 2.74
1411 2686 2.553172 AGAGCGAGTTTTAGTCGACTGT 59.447 45.455 28.12 5.33 43.33 3.55
1412 2687 2.911723 CAGAGCGAGTTTTAGTCGACTG 59.088 50.000 28.12 10.31 43.33 3.51
1413 2688 2.553172 ACAGAGCGAGTTTTAGTCGACT 59.447 45.455 23.66 23.66 43.33 4.18
1414 2689 2.909863 GACAGAGCGAGTTTTAGTCGAC 59.090 50.000 7.70 7.70 43.33 4.20
1415 2690 2.812591 AGACAGAGCGAGTTTTAGTCGA 59.187 45.455 8.01 0.00 43.33 4.20
1416 2691 3.204597 AGACAGAGCGAGTTTTAGTCG 57.795 47.619 0.00 0.00 43.49 4.18
1417 2692 6.470877 CAGATAAGACAGAGCGAGTTTTAGTC 59.529 42.308 0.00 0.00 0.00 2.59
1418 2693 6.151312 TCAGATAAGACAGAGCGAGTTTTAGT 59.849 38.462 0.00 0.00 0.00 2.24
1419 2694 6.556212 TCAGATAAGACAGAGCGAGTTTTAG 58.444 40.000 0.00 0.00 0.00 1.85
1420 2695 6.510879 TCAGATAAGACAGAGCGAGTTTTA 57.489 37.500 0.00 0.00 0.00 1.52
1421 2696 5.392767 TCAGATAAGACAGAGCGAGTTTT 57.607 39.130 0.00 0.00 0.00 2.43
1422 2697 5.392767 TTCAGATAAGACAGAGCGAGTTT 57.607 39.130 0.00 0.00 0.00 2.66
1448 2723 2.351097 CGTGTGCGTGTGCTTGTG 60.351 61.111 0.00 0.00 43.34 3.33
1471 2746 1.002366 CTGATAAGAGGTGCGTGTGC 58.998 55.000 0.00 0.00 43.20 4.57
1498 2773 5.011023 AGCCTTGCACCTAAATTAATATGGC 59.989 40.000 0.00 0.00 34.90 4.40
1568 2843 5.861787 GCATATTTACCGAAAGCAAACTTGT 59.138 36.000 0.00 0.00 35.85 3.16
1578 2853 4.764050 TCAGAGGGCATATTTACCGAAA 57.236 40.909 0.00 0.00 0.00 3.46
1593 2868 7.864108 TCACCATATGTGTAAATTTCAGAGG 57.136 36.000 1.24 0.00 45.61 3.69
1625 2905 5.248477 AGTGCAGACTTGGTTTCCTATTCTA 59.752 40.000 0.00 0.00 0.00 2.10
1684 3010 2.363306 TCCAGCAGTGTCCATTGTTT 57.637 45.000 0.00 0.00 0.00 2.83
2270 4049 7.609760 TGCCTACATAGTGAAACAAACATAG 57.390 36.000 0.00 0.00 41.43 2.23
2288 4067 5.484173 TCATGAAAATTCGTGATGCCTAC 57.516 39.130 12.78 0.00 45.50 3.18
2411 4190 5.468540 ACTGTGACAGTACTGAAAGCATA 57.531 39.130 29.30 16.36 43.46 3.14
2445 4227 5.722263 CCATGTGAATTTACATTCTGCCAA 58.278 37.500 12.81 0.00 39.17 4.52
2448 4230 4.563976 GTGCCATGTGAATTTACATTCTGC 59.436 41.667 12.81 14.92 39.17 4.26
2488 4280 3.497103 TGGTCCATGAATCTGCCTATG 57.503 47.619 0.00 0.00 0.00 2.23
2489 4281 4.736611 AATGGTCCATGAATCTGCCTAT 57.263 40.909 4.74 0.00 0.00 2.57
2490 4282 4.524802 AAATGGTCCATGAATCTGCCTA 57.475 40.909 4.74 0.00 0.00 3.93
2491 4283 3.393426 AAATGGTCCATGAATCTGCCT 57.607 42.857 4.74 0.00 0.00 4.75
2492 4284 5.302568 TGATTAAATGGTCCATGAATCTGCC 59.697 40.000 25.86 11.83 32.69 4.85
2493 4285 6.395426 TGATTAAATGGTCCATGAATCTGC 57.605 37.500 25.86 12.06 32.69 4.26
2494 4286 9.472361 GAAATGATTAAATGGTCCATGAATCTG 57.528 33.333 25.86 0.00 32.69 2.90
2495 4287 9.204337 TGAAATGATTAAATGGTCCATGAATCT 57.796 29.630 25.86 14.91 32.69 2.40
2496 4288 9.991906 ATGAAATGATTAAATGGTCCATGAATC 57.008 29.630 22.25 22.25 32.38 2.52
2497 4289 9.991906 GATGAAATGATTAAATGGTCCATGAAT 57.008 29.630 4.74 8.44 0.00 2.57
2650 4466 9.866655 TTCCATCTGAAGGTTTAAATATAGCAT 57.133 29.630 0.00 0.00 0.00 3.79
2654 4470 9.120538 GCTGTTCCATCTGAAGGTTTAAATATA 57.879 33.333 0.00 0.00 32.37 0.86
2661 4477 3.152341 CAGCTGTTCCATCTGAAGGTTT 58.848 45.455 5.25 0.00 30.23 3.27
2779 4600 0.249868 GTTTTCCTTGGCCCTTGCAC 60.250 55.000 0.00 0.00 40.13 4.57
3039 5012 4.065088 TCAATCAGTGAGGAGTTTTTCGG 58.935 43.478 0.00 0.00 0.00 4.30
3109 5082 5.065859 CACTGTTGTTATTGTGACTCCAACA 59.934 40.000 0.00 0.00 39.65 3.33
3132 5105 3.727258 CCTTCCCCACCATCGCCA 61.727 66.667 0.00 0.00 0.00 5.69
3152 5125 1.811266 CACCTGAGTGGCGGAATCG 60.811 63.158 0.00 0.00 40.55 3.34
3153 5126 4.208632 CACCTGAGTGGCGGAATC 57.791 61.111 0.00 0.00 40.55 2.52
3161 5134 2.434884 AATCGCGCCACCTGAGTG 60.435 61.111 0.00 0.00 44.12 3.51
3162 5135 2.125512 GAATCGCGCCACCTGAGT 60.126 61.111 0.00 0.00 0.00 3.41
3163 5136 2.169789 CAGAATCGCGCCACCTGAG 61.170 63.158 0.00 0.00 0.00 3.35
3164 5137 2.125552 CAGAATCGCGCCACCTGA 60.126 61.111 0.00 0.00 0.00 3.86
3165 5138 3.869272 GCAGAATCGCGCCACCTG 61.869 66.667 0.00 7.24 0.00 4.00
3171 5144 2.815211 TGAGTGGCAGAATCGCGC 60.815 61.111 0.00 0.00 0.00 6.86
3208 5181 1.198867 CGTAGATCGAGCTAGCAGCAT 59.801 52.381 18.83 4.67 45.56 3.79
3213 5186 0.890090 ACCCCGTAGATCGAGCTAGC 60.890 60.000 11.35 6.62 42.86 3.42
3266 5239 1.327690 TTCTAGTTCCATCGCCCGCT 61.328 55.000 0.00 0.00 0.00 5.52
3274 5247 4.202161 ACGCGATCAATCTTCTAGTTCCAT 60.202 41.667 15.93 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.