Multiple sequence alignment - TraesCS3D01G472200

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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 TraesCS3D01G472200 chr3D 100.000 3356 0 0 1 3356 574237569 574240924 0.000000e+00 6198.0
1 TraesCS3D01G472200 chr3D 87.313 1474 169 9 928 2399 574228708 574230165 0.000000e+00 1670.0
2 TraesCS3D01G472200 chr3D 85.385 130 13 4 3221 3345 574264080 574264208 2.720000e-26 130.0
3 TraesCS3D01G472200 chrUn 90.491 3218 187 44 95 3252 41229375 41226217 0.000000e+00 4137.0
4 TraesCS3D01G472200 chrUn 87.216 1541 188 8 970 2508 183979784 183981317 0.000000e+00 1746.0
5 TraesCS3D01G472200 chrUn 86.857 350 26 7 270 599 41229173 41228824 1.140000e-99 374.0
6 TraesCS3D01G472200 chr3A 92.221 2944 133 39 95 2957 709189082 709192010 0.000000e+00 4080.0
7 TraesCS3D01G472200 chr3A 86.127 1557 195 9 928 2482 709162921 709164458 0.000000e+00 1659.0
8 TraesCS3D01G472200 chr7A 90.419 668 30 9 675 1336 728375820 728375181 0.000000e+00 848.0
9 TraesCS3D01G472200 chr7A 84.711 484 29 13 167 622 728376815 728376349 3.070000e-120 442.0
10 TraesCS3D01G472200 chr7A 91.429 105 5 2 167 271 576382729 576382629 1.260000e-29 141.0
11 TraesCS3D01G472200 chr7A 90.476 105 6 2 167 271 658723572 658723672 5.840000e-28 135.0
12 TraesCS3D01G472200 chr7A 88.889 99 9 1 3064 3162 661560336 661560432 1.640000e-23 121.0
13 TraesCS3D01G472200 chr7A 97.059 68 2 0 1269 1336 658723815 658723882 7.610000e-22 115.0
14 TraesCS3D01G472200 chr7A 95.588 68 3 0 1269 1336 576382486 576382419 3.540000e-20 110.0
15 TraesCS3D01G472200 chr2D 91.011 356 24 3 917 1267 348004054 348004406 1.090000e-129 473.0
16 TraesCS3D01G472200 chr2D 82.552 384 35 19 141 497 348003417 348003795 3.250000e-80 309.0
17 TraesCS3D01G472200 chr2D 94.175 103 5 1 433 534 635135973 635136075 4.480000e-34 156.0
18 TraesCS3D01G472200 chr2D 96.000 75 3 0 1262 1336 348066343 348066417 4.550000e-24 122.0
19 TraesCS3D01G472200 chr2A 85.227 440 51 6 2050 2482 526303190 526303622 1.110000e-119 440.0
20 TraesCS3D01G472200 chr2A 88.679 53 2 2 185 237 732303734 732303686 1.010000e-05 62.1
21 TraesCS3D01G472200 chr7B 79.038 291 40 15 497 775 540635420 540635139 2.660000e-41 180.0
22 TraesCS3D01G472200 chr6B 78.082 292 40 19 497 775 483730243 483729963 2.680000e-36 163.0
23 TraesCS3D01G472200 chr6B 77.055 292 43 17 497 775 152441951 152441671 2.700000e-31 147.0
24 TraesCS3D01G472200 chr3B 77.055 292 43 18 497 775 286476117 286476397 2.700000e-31 147.0
25 TraesCS3D01G472200 chr3B 84.783 138 15 5 3224 3356 764529474 764529338 2.100000e-27 134.0
26 TraesCS3D01G472200 chr3B 81.560 141 22 4 3220 3356 764459308 764459168 2.740000e-21 113.0
27 TraesCS3D01G472200 chr3B 85.714 56 8 0 3102 3157 764529591 764529536 3.620000e-05 60.2
28 TraesCS3D01G472200 chr7D 91.509 106 5 1 433 534 477179805 477179910 3.490000e-30 143.0
29 TraesCS3D01G472200 chr2B 87.879 99 10 1 3064 3162 750540122 750540218 7.610000e-22 115.0
30 TraesCS3D01G472200 chr2B 90.566 53 1 2 185 237 506806385 506806337 2.160000e-07 67.6


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 TraesCS3D01G472200 chr3D 574237569 574240924 3355 False 6198.0 6198 100.0000 1 3356 1 chr3D.!!$F2 3355
1 TraesCS3D01G472200 chr3D 574228708 574230165 1457 False 1670.0 1670 87.3130 928 2399 1 chr3D.!!$F1 1471
2 TraesCS3D01G472200 chrUn 41226217 41229375 3158 True 2255.5 4137 88.6740 95 3252 2 chrUn.!!$R1 3157
3 TraesCS3D01G472200 chrUn 183979784 183981317 1533 False 1746.0 1746 87.2160 970 2508 1 chrUn.!!$F1 1538
4 TraesCS3D01G472200 chr3A 709189082 709192010 2928 False 4080.0 4080 92.2210 95 2957 1 chr3A.!!$F2 2862
5 TraesCS3D01G472200 chr3A 709162921 709164458 1537 False 1659.0 1659 86.1270 928 2482 1 chr3A.!!$F1 1554
6 TraesCS3D01G472200 chr7A 728375181 728376815 1634 True 645.0 848 87.5650 167 1336 2 chr7A.!!$R2 1169
7 TraesCS3D01G472200 chr2D 348003417 348004406 989 False 391.0 473 86.7815 141 1267 2 chr2D.!!$F3 1126

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
51 52 0.099968 TCGAGGTCGATTTAGCGGTG 59.900 55.000 0.00 0.0 44.22 4.94 F
55 56 0.458669 GGTCGATTTAGCGGTGAGGA 59.541 55.000 0.00 0.0 0.00 3.71 F
56 57 1.068741 GGTCGATTTAGCGGTGAGGAT 59.931 52.381 0.00 0.0 0.00 3.24 F
2307 2857 1.066143 CGCTACCAGGTTGAGGTGAAT 60.066 52.381 5.05 0.0 40.26 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2590 2.373169 AGTGGCAGAATTCTTCAGGACA 59.627 45.455 4.86 0.0 0.00 4.02 R
2226 2776 2.039084 AGATCCTTCCTGCGACTTGTTT 59.961 45.455 0.00 0.0 0.00 2.83 R
2340 2890 9.017509 TCAATTGATTGCTATTCAAAGTCTTCT 57.982 29.630 3.38 0.0 38.34 2.85 R
3294 3856 0.034059 AGGACACGCTCAAGTGAAGG 59.966 55.000 4.00 0.0 44.43 3.46 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
34 35 3.460857 TTTTGTTTGGGGAATTGGTCG 57.539 42.857 0.00 0.00 0.00 4.79
35 36 2.366640 TTGTTTGGGGAATTGGTCGA 57.633 45.000 0.00 0.00 0.00 4.20
36 37 1.904287 TGTTTGGGGAATTGGTCGAG 58.096 50.000 0.00 0.00 0.00 4.04
37 38 1.173913 GTTTGGGGAATTGGTCGAGG 58.826 55.000 0.00 0.00 0.00 4.63
38 39 0.774908 TTTGGGGAATTGGTCGAGGT 59.225 50.000 0.00 0.00 0.00 3.85
39 40 0.326927 TTGGGGAATTGGTCGAGGTC 59.673 55.000 0.00 0.00 0.00 3.85
40 41 1.153429 GGGGAATTGGTCGAGGTCG 60.153 63.158 0.00 0.00 41.45 4.79
50 51 2.485677 TCGAGGTCGATTTAGCGGT 58.514 52.632 0.00 0.00 44.22 5.68
51 52 0.099968 TCGAGGTCGATTTAGCGGTG 59.900 55.000 0.00 0.00 44.22 4.94
52 53 0.099968 CGAGGTCGATTTAGCGGTGA 59.900 55.000 0.00 0.00 43.02 4.02
53 54 1.841450 GAGGTCGATTTAGCGGTGAG 58.159 55.000 0.00 0.00 0.00 3.51
54 55 0.460311 AGGTCGATTTAGCGGTGAGG 59.540 55.000 0.00 0.00 0.00 3.86
55 56 0.458669 GGTCGATTTAGCGGTGAGGA 59.541 55.000 0.00 0.00 0.00 3.71
56 57 1.068741 GGTCGATTTAGCGGTGAGGAT 59.931 52.381 0.00 0.00 0.00 3.24
57 58 2.483188 GGTCGATTTAGCGGTGAGGATT 60.483 50.000 0.00 0.00 0.00 3.01
58 59 2.540101 GTCGATTTAGCGGTGAGGATTG 59.460 50.000 0.00 0.00 0.00 2.67
59 60 1.867233 CGATTTAGCGGTGAGGATTGG 59.133 52.381 0.00 0.00 0.00 3.16
60 61 2.483013 CGATTTAGCGGTGAGGATTGGA 60.483 50.000 0.00 0.00 0.00 3.53
61 62 3.744660 GATTTAGCGGTGAGGATTGGAT 58.255 45.455 0.00 0.00 0.00 3.41
62 63 3.644966 TTTAGCGGTGAGGATTGGATT 57.355 42.857 0.00 0.00 0.00 3.01
63 64 4.764050 TTTAGCGGTGAGGATTGGATTA 57.236 40.909 0.00 0.00 0.00 1.75
64 65 2.918712 AGCGGTGAGGATTGGATTAG 57.081 50.000 0.00 0.00 0.00 1.73
65 66 1.202698 AGCGGTGAGGATTGGATTAGC 60.203 52.381 0.00 0.00 0.00 3.09
66 67 1.202698 GCGGTGAGGATTGGATTAGCT 60.203 52.381 0.00 0.00 0.00 3.32
67 68 2.037251 GCGGTGAGGATTGGATTAGCTA 59.963 50.000 0.00 0.00 0.00 3.32
68 69 3.654414 CGGTGAGGATTGGATTAGCTAC 58.346 50.000 0.00 0.00 0.00 3.58
69 70 3.654414 GGTGAGGATTGGATTAGCTACG 58.346 50.000 0.00 0.00 0.00 3.51
70 71 3.321111 GGTGAGGATTGGATTAGCTACGA 59.679 47.826 0.00 0.00 0.00 3.43
71 72 4.021016 GGTGAGGATTGGATTAGCTACGAT 60.021 45.833 0.00 0.00 0.00 3.73
72 73 5.511545 GGTGAGGATTGGATTAGCTACGATT 60.512 44.000 0.00 0.00 0.00 3.34
73 74 5.992217 GTGAGGATTGGATTAGCTACGATTT 59.008 40.000 0.00 0.00 0.00 2.17
74 75 5.991606 TGAGGATTGGATTAGCTACGATTTG 59.008 40.000 0.00 0.00 0.00 2.32
75 76 5.930135 AGGATTGGATTAGCTACGATTTGT 58.070 37.500 0.00 0.00 0.00 2.83
76 77 5.992217 AGGATTGGATTAGCTACGATTTGTC 59.008 40.000 0.00 0.00 0.00 3.18
77 78 5.992217 GGATTGGATTAGCTACGATTTGTCT 59.008 40.000 0.00 0.00 0.00 3.41
78 79 6.073548 GGATTGGATTAGCTACGATTTGTCTG 60.074 42.308 0.00 0.00 0.00 3.51
79 80 5.339008 TGGATTAGCTACGATTTGTCTGT 57.661 39.130 0.00 0.00 0.00 3.41
80 81 5.109210 TGGATTAGCTACGATTTGTCTGTG 58.891 41.667 0.00 0.00 0.00 3.66
81 82 4.025647 GGATTAGCTACGATTTGTCTGTGC 60.026 45.833 0.00 0.00 0.00 4.57
82 83 2.455674 AGCTACGATTTGTCTGTGCA 57.544 45.000 0.00 0.00 0.00 4.57
83 84 2.766313 AGCTACGATTTGTCTGTGCAA 58.234 42.857 0.00 0.00 0.00 4.08
84 85 3.138304 AGCTACGATTTGTCTGTGCAAA 58.862 40.909 0.00 0.00 41.77 3.68
86 87 4.216257 AGCTACGATTTGTCTGTGCAAATT 59.784 37.500 11.74 3.72 45.68 1.82
87 88 4.917415 GCTACGATTTGTCTGTGCAAATTT 59.083 37.500 11.74 0.00 45.68 1.82
88 89 5.164158 GCTACGATTTGTCTGTGCAAATTTG 60.164 40.000 14.03 14.03 45.68 2.32
89 90 4.681744 ACGATTTGTCTGTGCAAATTTGT 58.318 34.783 19.03 10.90 45.68 2.83
90 91 4.739716 ACGATTTGTCTGTGCAAATTTGTC 59.260 37.500 19.03 11.87 45.68 3.18
91 92 4.143762 CGATTTGTCTGTGCAAATTTGTCG 60.144 41.667 19.03 11.94 45.68 4.35
92 93 4.362932 TTTGTCTGTGCAAATTTGTCGA 57.637 36.364 19.03 8.08 33.91 4.20
93 94 3.332761 TGTCTGTGCAAATTTGTCGAC 57.667 42.857 19.03 9.11 0.00 4.20
134 135 3.947841 TGTTCGTTGTGCGGCTGC 61.948 61.111 11.65 11.65 41.72 5.25
139 140 4.030452 GTTGTGCGGCTGCTGGTC 62.030 66.667 20.27 7.30 43.34 4.02
143 144 4.383861 TGCGGCTGCTGGTCTCAG 62.384 66.667 20.27 0.00 43.34 3.35
205 210 2.756760 AGTTATGCATTTGAGTGCTGGG 59.243 45.455 3.54 0.00 45.27 4.45
284 316 1.575447 GCATCCCCTCCCCTGTTTCT 61.575 60.000 0.00 0.00 0.00 2.52
303 335 8.918202 TGTTTCTTGTTGTTGGTAGAATAGAT 57.082 30.769 0.00 0.00 0.00 1.98
332 368 1.131315 GCTTCGCTTTGATTGAGGTCC 59.869 52.381 0.00 0.00 0.00 4.46
484 538 9.515020 TTTAGATAGTTTTGTTTTGCACTTGAG 57.485 29.630 0.00 0.00 0.00 3.02
513 568 3.259625 GTCCCTAGGATCCTCAACTATGC 59.740 52.174 20.22 0.00 32.73 3.14
514 569 2.569404 CCCTAGGATCCTCAACTATGCC 59.431 54.545 20.22 0.00 0.00 4.40
557 620 5.197549 GCATTTGTACATACATGCGTACAG 58.802 41.667 17.65 11.15 46.26 2.74
570 633 1.937899 GCGTACAGCCGTAAATCCAAT 59.062 47.619 0.00 0.00 40.81 3.16
586 649 5.886960 ATCCAATTGTACTTGCTGTCTTC 57.113 39.130 4.43 0.00 0.00 2.87
593 656 5.722021 TGTACTTGCTGTCTTCTACATGA 57.278 39.130 0.00 0.00 37.50 3.07
594 657 6.286240 TGTACTTGCTGTCTTCTACATGAT 57.714 37.500 0.00 0.00 37.50 2.45
595 658 6.701340 TGTACTTGCTGTCTTCTACATGATT 58.299 36.000 0.00 0.00 37.50 2.57
596 659 7.836842 TGTACTTGCTGTCTTCTACATGATTA 58.163 34.615 0.00 0.00 37.50 1.75
622 685 2.796557 TCAGGTTGTGGTTGTTTGTCA 58.203 42.857 0.00 0.00 0.00 3.58
623 686 2.752354 TCAGGTTGTGGTTGTTTGTCAG 59.248 45.455 0.00 0.00 0.00 3.51
624 687 2.491693 CAGGTTGTGGTTGTTTGTCAGT 59.508 45.455 0.00 0.00 0.00 3.41
625 688 3.056891 CAGGTTGTGGTTGTTTGTCAGTT 60.057 43.478 0.00 0.00 0.00 3.16
626 689 3.576550 AGGTTGTGGTTGTTTGTCAGTTT 59.423 39.130 0.00 0.00 0.00 2.66
627 690 3.924073 GGTTGTGGTTGTTTGTCAGTTTC 59.076 43.478 0.00 0.00 0.00 2.78
673 1212 6.974965 TGATATATCTGCGCTATGTCCTATG 58.025 40.000 9.73 0.00 0.00 2.23
683 1222 5.406649 CGCTATGTCCTATGGAAGAAGATC 58.593 45.833 0.00 0.00 31.38 2.75
691 1230 7.038017 TGTCCTATGGAAGAAGATCCCATATTC 60.038 40.741 7.78 0.36 40.81 1.75
707 1246 2.307496 ATTCAGTGCCATTGGAACCA 57.693 45.000 10.43 0.00 29.51 3.67
710 1249 3.448093 TCAGTGCCATTGGAACCATTA 57.552 42.857 10.43 0.00 29.51 1.90
777 1320 5.559035 GCCATGCGTCTCTTTGATTATGTAC 60.559 44.000 0.00 0.00 0.00 2.90
780 1323 4.796830 TGCGTCTCTTTGATTATGTACGTC 59.203 41.667 0.00 0.00 0.00 4.34
881 1424 2.533266 ACTTGTCACGACTGCAAGAT 57.467 45.000 15.96 3.58 41.31 2.40
926 1469 8.797350 TTATATGATGCCTTGATGTATTCCTG 57.203 34.615 0.00 0.00 0.00 3.86
959 1503 8.327941 TCCTGCAATAATATGTTATTCAGCTC 57.672 34.615 18.32 5.55 38.21 4.09
964 1508 9.212641 GCAATAATATGTTATTCAGCTCTCTCA 57.787 33.333 4.60 0.00 38.21 3.27
1815 2365 4.836825 AGATACTCAAGGTGGTTGATGTG 58.163 43.478 0.00 0.00 44.44 3.21
1905 2455 5.956068 AGTTCATCCAAGAAAAGAAGCTC 57.044 39.130 0.00 0.00 0.00 4.09
2040 2590 5.357032 GGAAAATCTTGACATCAACCGGTAT 59.643 40.000 8.00 0.00 0.00 2.73
2121 2671 2.419324 GGCAGATCAGAGCAACTTCAAG 59.581 50.000 0.00 0.00 0.00 3.02
2196 2746 2.481185 GTGGTTTGCCGAAAACTATCGA 59.519 45.455 11.76 0.00 46.27 3.59
2226 2776 1.140652 TGCACACTGGAGTTCATCACA 59.859 47.619 0.00 0.00 0.00 3.58
2307 2857 1.066143 CGCTACCAGGTTGAGGTGAAT 60.066 52.381 5.05 0.00 40.26 2.57
2483 3034 6.548622 AGGAAAAGAACTTAAGGTTTGTACCC 59.451 38.462 7.53 0.00 46.28 3.69
2508 3059 0.248843 CGCCAGCTCCTCTTCTTCTT 59.751 55.000 0.00 0.00 0.00 2.52
2509 3060 1.738700 CGCCAGCTCCTCTTCTTCTTC 60.739 57.143 0.00 0.00 0.00 2.87
2511 3062 2.418609 GCCAGCTCCTCTTCTTCTTCTC 60.419 54.545 0.00 0.00 0.00 2.87
2519 3070 8.058847 AGCTCCTCTTCTTCTTCTCTCTTATAA 58.941 37.037 0.00 0.00 0.00 0.98
2548 3100 3.763897 GGAATGCCTTGTATTGTGTTCCT 59.236 43.478 0.00 0.00 33.00 3.36
2580 3132 8.728088 AATGTTTGATTCGATGTTGTTACTTC 57.272 30.769 0.00 0.00 0.00 3.01
2810 3362 5.298276 TCTGTTAAGTTTGTGGGTCATTGTC 59.702 40.000 0.00 0.00 0.00 3.18
2855 3414 4.036734 TCTGAACCAAAGTTGTGATGCTTC 59.963 41.667 0.00 0.00 35.94 3.86
2870 3429 4.458989 TGATGCTTCCACTACATTTGAACC 59.541 41.667 0.00 0.00 0.00 3.62
2951 3512 6.775629 TGTGCTATGTACTCTATCCACATGTA 59.224 38.462 0.00 0.00 34.78 2.29
2957 3518 7.654022 TGTACTCTATCCACATGTATGTTGA 57.346 36.000 0.00 1.85 39.39 3.18
2958 3519 8.250143 TGTACTCTATCCACATGTATGTTGAT 57.750 34.615 13.84 13.84 43.17 2.57
2959 3520 8.360390 TGTACTCTATCCACATGTATGTTGATC 58.640 37.037 13.02 2.19 40.85 2.92
2960 3521 7.609097 ACTCTATCCACATGTATGTTGATCT 57.391 36.000 13.02 0.00 40.85 2.75
2961 3522 8.027524 ACTCTATCCACATGTATGTTGATCTT 57.972 34.615 13.02 0.00 40.85 2.40
2962 3523 8.147058 ACTCTATCCACATGTATGTTGATCTTC 58.853 37.037 13.02 0.00 40.85 2.87
2963 3524 7.445121 TCTATCCACATGTATGTTGATCTTCC 58.555 38.462 13.02 0.00 40.85 3.46
2964 3525 5.698741 TCCACATGTATGTTGATCTTCCT 57.301 39.130 0.00 0.00 39.39 3.36
2965 3526 6.065976 TCCACATGTATGTTGATCTTCCTT 57.934 37.500 0.00 0.00 39.39 3.36
2966 3527 6.484288 TCCACATGTATGTTGATCTTCCTTT 58.516 36.000 0.00 0.00 39.39 3.11
2967 3528 7.629157 TCCACATGTATGTTGATCTTCCTTTA 58.371 34.615 0.00 0.00 39.39 1.85
2968 3529 8.274322 TCCACATGTATGTTGATCTTCCTTTAT 58.726 33.333 0.00 0.00 39.39 1.40
2978 3539 7.177216 TGTTGATCTTCCTTTATGTTTGCTCAT 59.823 33.333 0.00 0.00 0.00 2.90
2983 3544 3.616821 TCCTTTATGTTTGCTCATCGTCG 59.383 43.478 0.00 0.00 0.00 5.12
2985 3546 0.920664 TATGTTTGCTCATCGTCGCG 59.079 50.000 0.00 0.00 0.00 5.87
2986 3547 1.014044 ATGTTTGCTCATCGTCGCGT 61.014 50.000 5.77 0.00 0.00 6.01
2990 3551 3.906649 GCTCATCGTCGCGTGCAG 61.907 66.667 5.77 0.00 0.00 4.41
2992 3553 2.202479 TCATCGTCGCGTGCAGAG 60.202 61.111 5.77 0.00 0.00 3.35
2993 3554 2.504899 CATCGTCGCGTGCAGAGT 60.505 61.111 5.77 0.00 0.00 3.24
3022 3584 6.349973 TGCTAAAGATTTTACTGAGCATCG 57.650 37.500 0.00 0.00 38.61 3.84
3039 3601 3.121113 GCATCGGAATTTGTTTTGGTTCG 59.879 43.478 0.00 0.00 0.00 3.95
3055 3617 2.354203 GGTTCGAGATTCCTGAAGCACT 60.354 50.000 10.90 0.00 39.30 4.40
3056 3618 2.662006 TCGAGATTCCTGAAGCACTG 57.338 50.000 0.00 0.00 0.00 3.66
3088 3650 7.589958 TTTTTGTGGCTAAGATAAACCAGAA 57.410 32.000 0.00 0.00 34.01 3.02
3139 3701 5.511234 AGGATTCATTATGCTGAAGTTGC 57.489 39.130 0.00 0.00 38.47 4.17
3141 3703 5.067413 AGGATTCATTATGCTGAAGTTGCTG 59.933 40.000 0.00 0.00 38.47 4.41
3142 3704 3.770263 TCATTATGCTGAAGTTGCTGC 57.230 42.857 0.00 0.00 0.00 5.25
3143 3705 3.349927 TCATTATGCTGAAGTTGCTGCT 58.650 40.909 0.00 0.00 34.32 4.24
3144 3706 4.516323 TCATTATGCTGAAGTTGCTGCTA 58.484 39.130 0.00 0.00 34.32 3.49
3145 3707 4.943093 TCATTATGCTGAAGTTGCTGCTAA 59.057 37.500 0.00 0.00 34.32 3.09
3147 3709 6.767423 TCATTATGCTGAAGTTGCTGCTAATA 59.233 34.615 0.00 0.00 34.32 0.98
3148 3710 7.282901 TCATTATGCTGAAGTTGCTGCTAATAA 59.717 33.333 0.00 0.00 34.32 1.40
3152 3714 7.572523 TGCTGAAGTTGCTGCTAATAATAAT 57.427 32.000 0.00 0.00 34.32 1.28
3154 3716 6.860023 GCTGAAGTTGCTGCTAATAATAATGG 59.140 38.462 0.00 0.00 0.00 3.16
3155 3717 7.255242 GCTGAAGTTGCTGCTAATAATAATGGA 60.255 37.037 0.00 0.00 0.00 3.41
3156 3718 7.930217 TGAAGTTGCTGCTAATAATAATGGAC 58.070 34.615 0.00 0.00 0.00 4.02
3157 3719 7.775093 TGAAGTTGCTGCTAATAATAATGGACT 59.225 33.333 0.00 0.00 0.00 3.85
3174 3736 7.765695 AATGGACTGAACAAATGTCTACAAT 57.234 32.000 0.00 0.00 0.00 2.71
3201 3763 0.316204 GCTGCATGTTCAGTTTGCCT 59.684 50.000 0.00 0.00 36.49 4.75
3204 3766 2.030371 TGCATGTTCAGTTTGCCTTGA 58.970 42.857 0.00 0.00 35.51 3.02
3215 3777 5.407995 TCAGTTTGCCTTGAAAACAGTTTTG 59.592 36.000 16.21 2.96 39.49 2.44
3228 3790 4.470334 ACAGTTTTGTTGCCATCAGTTT 57.530 36.364 0.00 0.00 32.28 2.66
3242 3804 4.976116 CCATCAGTTTCAGAACGGAAAAAC 59.024 41.667 2.21 0.00 41.97 2.43
3243 3805 5.449862 CCATCAGTTTCAGAACGGAAAAACA 60.450 40.000 2.21 0.00 41.97 2.83
3248 3810 6.197096 CAGTTTCAGAACGGAAAAACATTCAG 59.803 38.462 2.21 0.00 40.75 3.02
3249 3811 4.223320 TCAGAACGGAAAAACATTCAGC 57.777 40.909 0.00 0.00 0.00 4.26
3251 3813 4.338118 TCAGAACGGAAAAACATTCAGCTT 59.662 37.500 0.00 0.00 0.00 3.74
3252 3814 5.529430 TCAGAACGGAAAAACATTCAGCTTA 59.471 36.000 0.00 0.00 0.00 3.09
3253 3815 6.206634 TCAGAACGGAAAAACATTCAGCTTAT 59.793 34.615 0.00 0.00 0.00 1.73
3254 3816 6.863126 CAGAACGGAAAAACATTCAGCTTATT 59.137 34.615 0.00 0.00 0.00 1.40
3255 3817 7.061094 CAGAACGGAAAAACATTCAGCTTATTC 59.939 37.037 0.00 0.00 0.00 1.75
3256 3818 6.575162 ACGGAAAAACATTCAGCTTATTCT 57.425 33.333 0.00 0.00 0.00 2.40
3257 3819 6.981722 ACGGAAAAACATTCAGCTTATTCTT 58.018 32.000 0.00 0.00 0.00 2.52
3258 3820 8.106247 ACGGAAAAACATTCAGCTTATTCTTA 57.894 30.769 0.00 0.00 0.00 2.10
3259 3821 8.021396 ACGGAAAAACATTCAGCTTATTCTTAC 58.979 33.333 0.00 0.00 0.00 2.34
3260 3822 7.216317 CGGAAAAACATTCAGCTTATTCTTACG 59.784 37.037 0.00 0.00 0.00 3.18
3261 3823 8.234546 GGAAAAACATTCAGCTTATTCTTACGA 58.765 33.333 0.00 0.00 0.00 3.43
3262 3824 9.607285 GAAAAACATTCAGCTTATTCTTACGAA 57.393 29.630 0.00 0.00 0.00 3.85
3263 3825 9.959749 AAAAACATTCAGCTTATTCTTACGAAA 57.040 25.926 0.00 0.00 31.91 3.46
3264 3826 9.612620 AAAACATTCAGCTTATTCTTACGAAAG 57.387 29.630 0.00 0.00 31.91 2.62
3266 3828 8.324163 ACATTCAGCTTATTCTTACGAAAGTT 57.676 30.769 0.00 0.00 46.40 2.66
3267 3829 8.230486 ACATTCAGCTTATTCTTACGAAAGTTG 58.770 33.333 0.00 0.00 46.40 3.16
3268 3830 7.956420 TTCAGCTTATTCTTACGAAAGTTGA 57.044 32.000 0.00 0.00 46.40 3.18
3269 3831 7.582435 TCAGCTTATTCTTACGAAAGTTGAG 57.418 36.000 0.00 0.00 46.40 3.02
3270 3832 6.590292 TCAGCTTATTCTTACGAAAGTTGAGG 59.410 38.462 0.00 0.00 46.40 3.86
3271 3833 6.369065 CAGCTTATTCTTACGAAAGTTGAGGT 59.631 38.462 0.00 0.00 46.40 3.85
3272 3834 6.935208 AGCTTATTCTTACGAAAGTTGAGGTT 59.065 34.615 0.00 0.00 46.40 3.50
3273 3835 7.015877 GCTTATTCTTACGAAAGTTGAGGTTG 58.984 38.462 0.00 0.00 46.40 3.77
3274 3836 4.806342 TTCTTACGAAAGTTGAGGTTGC 57.194 40.909 0.00 0.00 46.40 4.17
3275 3837 3.135994 TCTTACGAAAGTTGAGGTTGCC 58.864 45.455 0.00 0.00 46.40 4.52
3276 3838 1.886886 TACGAAAGTTGAGGTTGCCC 58.113 50.000 0.00 0.00 46.40 5.36
3277 3839 0.182775 ACGAAAGTTGAGGTTGCCCT 59.817 50.000 0.00 0.00 46.40 5.19
3278 3840 0.593128 CGAAAGTTGAGGTTGCCCTG 59.407 55.000 0.00 0.00 42.86 4.45
3279 3841 0.315251 GAAAGTTGAGGTTGCCCTGC 59.685 55.000 0.00 0.00 42.86 4.85
3280 3842 0.106015 AAAGTTGAGGTTGCCCTGCT 60.106 50.000 0.00 0.00 42.86 4.24
3281 3843 0.825010 AAGTTGAGGTTGCCCTGCTG 60.825 55.000 0.00 0.00 42.86 4.41
3282 3844 2.598394 TTGAGGTTGCCCTGCTGC 60.598 61.111 0.00 0.00 42.86 5.25
3283 3845 3.137385 TTGAGGTTGCCCTGCTGCT 62.137 57.895 0.00 0.00 42.86 4.24
3284 3846 2.749441 GAGGTTGCCCTGCTGCTC 60.749 66.667 0.00 0.00 42.86 4.26
3285 3847 3.557903 GAGGTTGCCCTGCTGCTCA 62.558 63.158 0.00 0.00 42.86 4.26
3286 3848 3.060615 GGTTGCCCTGCTGCTCAG 61.061 66.667 0.00 0.38 42.49 3.35
3297 3859 3.547567 CTGCTCAGCTTGTAGCCTT 57.452 52.632 0.00 0.00 43.77 4.35
3298 3860 1.367659 CTGCTCAGCTTGTAGCCTTC 58.632 55.000 0.00 0.00 43.77 3.46
3299 3861 0.686789 TGCTCAGCTTGTAGCCTTCA 59.313 50.000 0.00 0.00 43.77 3.02
3300 3862 1.082690 GCTCAGCTTGTAGCCTTCAC 58.917 55.000 0.00 0.00 43.77 3.18
3301 3863 1.338579 GCTCAGCTTGTAGCCTTCACT 60.339 52.381 0.00 0.00 43.77 3.41
3302 3864 2.873649 GCTCAGCTTGTAGCCTTCACTT 60.874 50.000 0.00 0.00 43.77 3.16
3303 3865 2.740981 CTCAGCTTGTAGCCTTCACTTG 59.259 50.000 0.00 0.00 43.77 3.16
3304 3866 2.368548 TCAGCTTGTAGCCTTCACTTGA 59.631 45.455 0.00 0.00 43.77 3.02
3305 3867 2.740981 CAGCTTGTAGCCTTCACTTGAG 59.259 50.000 0.00 0.00 43.77 3.02
3306 3868 1.466558 GCTTGTAGCCTTCACTTGAGC 59.533 52.381 0.00 0.00 34.48 4.26
3307 3869 1.728971 CTTGTAGCCTTCACTTGAGCG 59.271 52.381 0.00 0.00 0.00 5.03
3308 3870 0.679505 TGTAGCCTTCACTTGAGCGT 59.320 50.000 0.00 0.00 0.00 5.07
3309 3871 1.071605 GTAGCCTTCACTTGAGCGTG 58.928 55.000 0.00 0.00 36.25 5.34
3310 3872 0.679505 TAGCCTTCACTTGAGCGTGT 59.320 50.000 0.00 0.00 36.33 4.49
3311 3873 0.601311 AGCCTTCACTTGAGCGTGTC 60.601 55.000 0.00 0.00 36.33 3.67
3312 3874 1.569479 GCCTTCACTTGAGCGTGTCC 61.569 60.000 0.00 0.00 36.33 4.02
3313 3875 0.034059 CCTTCACTTGAGCGTGTCCT 59.966 55.000 0.00 0.00 36.33 3.85
3314 3876 1.143305 CTTCACTTGAGCGTGTCCTG 58.857 55.000 0.00 0.00 36.33 3.86
3315 3877 0.249868 TTCACTTGAGCGTGTCCTGG 60.250 55.000 0.00 0.00 36.33 4.45
3316 3878 1.112916 TCACTTGAGCGTGTCCTGGA 61.113 55.000 0.00 0.00 36.33 3.86
3317 3879 0.036952 CACTTGAGCGTGTCCTGGAT 60.037 55.000 0.00 0.00 0.00 3.41
3318 3880 0.036952 ACTTGAGCGTGTCCTGGATG 60.037 55.000 0.00 0.00 0.00 3.51
3319 3881 0.247460 CTTGAGCGTGTCCTGGATGA 59.753 55.000 0.00 0.00 0.00 2.92
3320 3882 0.037326 TTGAGCGTGTCCTGGATGAC 60.037 55.000 0.00 0.00 35.77 3.06
3321 3883 1.153549 GAGCGTGTCCTGGATGACC 60.154 63.158 0.00 0.00 34.25 4.02
3322 3884 2.509336 GCGTGTCCTGGATGACCG 60.509 66.667 0.00 1.36 39.42 4.79
3323 3885 2.970639 CGTGTCCTGGATGACCGT 59.029 61.111 0.00 0.00 39.42 4.83
3324 3886 1.153823 CGTGTCCTGGATGACCGTC 60.154 63.158 0.00 0.00 39.42 4.79
3325 3887 1.153823 GTGTCCTGGATGACCGTCG 60.154 63.158 0.00 0.00 39.42 5.12
3326 3888 2.202756 GTCCTGGATGACCGTCGC 60.203 66.667 0.00 0.00 39.42 5.19
3327 3889 3.458163 TCCTGGATGACCGTCGCC 61.458 66.667 0.00 3.83 39.42 5.54
3328 3890 3.770040 CCTGGATGACCGTCGCCA 61.770 66.667 11.25 11.25 39.42 5.69
3329 3891 2.509336 CTGGATGACCGTCGCCAC 60.509 66.667 8.44 0.00 39.42 5.01
3330 3892 2.994995 TGGATGACCGTCGCCACT 60.995 61.111 8.44 0.00 39.42 4.00
3331 3893 2.509336 GGATGACCGTCGCCACTG 60.509 66.667 5.59 0.00 0.00 3.66
3332 3894 3.188786 GATGACCGTCGCCACTGC 61.189 66.667 0.00 0.00 0.00 4.40
3333 3895 3.932580 GATGACCGTCGCCACTGCA 62.933 63.158 0.00 0.00 37.32 4.41
3334 3896 3.529341 ATGACCGTCGCCACTGCAA 62.529 57.895 0.00 0.00 37.32 4.08
3335 3897 2.970324 GACCGTCGCCACTGCAAA 60.970 61.111 0.00 0.00 37.32 3.68
3336 3898 2.281484 ACCGTCGCCACTGCAAAT 60.281 55.556 0.00 0.00 37.32 2.32
3337 3899 2.176546 CCGTCGCCACTGCAAATG 59.823 61.111 0.00 0.00 37.32 2.32
3338 3900 2.324330 CCGTCGCCACTGCAAATGA 61.324 57.895 0.00 0.00 37.32 2.57
3339 3901 1.154413 CGTCGCCACTGCAAATGAC 60.154 57.895 0.00 0.00 37.32 3.06
3340 3902 1.154413 GTCGCCACTGCAAATGACG 60.154 57.895 0.56 0.56 37.32 4.35
3341 3903 2.502510 CGCCACTGCAAATGACGC 60.503 61.111 0.00 0.00 37.32 5.19
3342 3904 2.126346 GCCACTGCAAATGACGCC 60.126 61.111 0.00 0.00 37.47 5.68
3343 3905 2.918345 GCCACTGCAAATGACGCCA 61.918 57.895 0.00 0.00 37.47 5.69
3344 3906 1.659233 CCACTGCAAATGACGCCAA 59.341 52.632 0.00 0.00 0.00 4.52
3345 3907 0.244450 CCACTGCAAATGACGCCAAT 59.756 50.000 0.00 0.00 0.00 3.16
3346 3908 1.337074 CCACTGCAAATGACGCCAATT 60.337 47.619 0.00 0.00 0.00 2.32
3347 3909 1.722464 CACTGCAAATGACGCCAATTG 59.278 47.619 0.00 0.00 36.51 2.32
3348 3910 1.337074 ACTGCAAATGACGCCAATTGG 60.337 47.619 20.81 20.81 34.56 3.16
3349 3911 0.037512 TGCAAATGACGCCAATTGGG 60.038 50.000 25.73 17.36 34.56 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.451178 TCGACCAATTCCCCAAACAAAAA 59.549 39.130 0.00 0.00 0.00 1.94
14 15 3.031736 TCGACCAATTCCCCAAACAAAA 58.968 40.909 0.00 0.00 0.00 2.44
15 16 2.625790 CTCGACCAATTCCCCAAACAAA 59.374 45.455 0.00 0.00 0.00 2.83
16 17 2.235016 CTCGACCAATTCCCCAAACAA 58.765 47.619 0.00 0.00 0.00 2.83
17 18 1.546773 CCTCGACCAATTCCCCAAACA 60.547 52.381 0.00 0.00 0.00 2.83
18 19 1.173913 CCTCGACCAATTCCCCAAAC 58.826 55.000 0.00 0.00 0.00 2.93
19 20 0.774908 ACCTCGACCAATTCCCCAAA 59.225 50.000 0.00 0.00 0.00 3.28
20 21 0.326927 GACCTCGACCAATTCCCCAA 59.673 55.000 0.00 0.00 0.00 4.12
21 22 1.895020 CGACCTCGACCAATTCCCCA 61.895 60.000 0.00 0.00 43.02 4.96
22 23 1.153429 CGACCTCGACCAATTCCCC 60.153 63.158 0.00 0.00 43.02 4.81
23 24 1.895238 TCGACCTCGACCAATTCCC 59.105 57.895 0.00 0.00 44.22 3.97
33 34 0.099968 TCACCGCTAAATCGACCTCG 59.900 55.000 0.00 0.00 41.45 4.63
34 35 1.536284 CCTCACCGCTAAATCGACCTC 60.536 57.143 0.00 0.00 0.00 3.85
35 36 0.460311 CCTCACCGCTAAATCGACCT 59.540 55.000 0.00 0.00 0.00 3.85
36 37 0.458669 TCCTCACCGCTAAATCGACC 59.541 55.000 0.00 0.00 0.00 4.79
37 38 2.510768 ATCCTCACCGCTAAATCGAC 57.489 50.000 0.00 0.00 0.00 4.20
38 39 2.483013 CCAATCCTCACCGCTAAATCGA 60.483 50.000 0.00 0.00 0.00 3.59
39 40 1.867233 CCAATCCTCACCGCTAAATCG 59.133 52.381 0.00 0.00 0.00 3.34
40 41 3.194005 TCCAATCCTCACCGCTAAATC 57.806 47.619 0.00 0.00 0.00 2.17
41 42 3.864789 ATCCAATCCTCACCGCTAAAT 57.135 42.857 0.00 0.00 0.00 1.40
42 43 3.644966 AATCCAATCCTCACCGCTAAA 57.355 42.857 0.00 0.00 0.00 1.85
43 44 3.494398 GCTAATCCAATCCTCACCGCTAA 60.494 47.826 0.00 0.00 0.00 3.09
44 45 2.037251 GCTAATCCAATCCTCACCGCTA 59.963 50.000 0.00 0.00 0.00 4.26
45 46 1.202698 GCTAATCCAATCCTCACCGCT 60.203 52.381 0.00 0.00 0.00 5.52
46 47 1.202698 AGCTAATCCAATCCTCACCGC 60.203 52.381 0.00 0.00 0.00 5.68
47 48 2.918712 AGCTAATCCAATCCTCACCG 57.081 50.000 0.00 0.00 0.00 4.94
48 49 3.321111 TCGTAGCTAATCCAATCCTCACC 59.679 47.826 0.00 0.00 0.00 4.02
49 50 4.585955 TCGTAGCTAATCCAATCCTCAC 57.414 45.455 0.00 0.00 0.00 3.51
50 51 5.808366 AATCGTAGCTAATCCAATCCTCA 57.192 39.130 0.00 0.00 0.00 3.86
51 52 5.992217 ACAAATCGTAGCTAATCCAATCCTC 59.008 40.000 0.00 0.00 0.00 3.71
52 53 5.930135 ACAAATCGTAGCTAATCCAATCCT 58.070 37.500 0.00 0.00 0.00 3.24
53 54 5.992217 AGACAAATCGTAGCTAATCCAATCC 59.008 40.000 0.00 0.00 0.00 3.01
54 55 6.480320 ACAGACAAATCGTAGCTAATCCAATC 59.520 38.462 0.00 0.00 0.00 2.67
55 56 6.258727 CACAGACAAATCGTAGCTAATCCAAT 59.741 38.462 0.00 0.00 0.00 3.16
56 57 5.580691 CACAGACAAATCGTAGCTAATCCAA 59.419 40.000 0.00 0.00 0.00 3.53
57 58 5.109210 CACAGACAAATCGTAGCTAATCCA 58.891 41.667 0.00 0.00 0.00 3.41
58 59 4.025647 GCACAGACAAATCGTAGCTAATCC 60.026 45.833 0.00 0.00 0.00 3.01
59 60 4.566759 TGCACAGACAAATCGTAGCTAATC 59.433 41.667 0.00 0.00 0.00 1.75
60 61 4.503910 TGCACAGACAAATCGTAGCTAAT 58.496 39.130 0.00 0.00 0.00 1.73
61 62 3.920446 TGCACAGACAAATCGTAGCTAA 58.080 40.909 0.00 0.00 0.00 3.09
62 63 3.586100 TGCACAGACAAATCGTAGCTA 57.414 42.857 0.00 0.00 0.00 3.32
63 64 2.455674 TGCACAGACAAATCGTAGCT 57.544 45.000 0.00 0.00 0.00 3.32
64 65 3.536158 TTTGCACAGACAAATCGTAGC 57.464 42.857 0.00 0.00 34.68 3.58
65 66 5.914635 ACAAATTTGCACAGACAAATCGTAG 59.085 36.000 18.12 0.00 46.80 3.51
66 67 5.826586 ACAAATTTGCACAGACAAATCGTA 58.173 33.333 18.12 0.00 46.80 3.43
67 68 4.681744 ACAAATTTGCACAGACAAATCGT 58.318 34.783 18.12 2.18 46.80 3.73
68 69 4.143762 CGACAAATTTGCACAGACAAATCG 60.144 41.667 18.12 11.30 46.80 3.34
69 70 4.975502 TCGACAAATTTGCACAGACAAATC 59.024 37.500 18.12 3.40 46.80 2.17
71 72 4.101942 GTCGACAAATTTGCACAGACAAA 58.898 39.130 18.12 0.00 43.27 2.83
72 73 3.690422 GTCGACAAATTTGCACAGACAA 58.310 40.909 18.12 0.00 0.00 3.18
73 74 2.286125 CGTCGACAAATTTGCACAGACA 60.286 45.455 18.12 0.00 0.00 3.41
74 75 2.286184 ACGTCGACAAATTTGCACAGAC 60.286 45.455 18.12 18.10 0.00 3.51
75 76 1.937223 ACGTCGACAAATTTGCACAGA 59.063 42.857 18.12 9.31 0.00 3.41
76 77 2.383298 ACGTCGACAAATTTGCACAG 57.617 45.000 18.12 8.58 0.00 3.66
77 78 2.834574 AACGTCGACAAATTTGCACA 57.165 40.000 18.12 0.00 0.00 4.57
78 79 3.102276 TCAAACGTCGACAAATTTGCAC 58.898 40.909 22.64 11.02 33.09 4.57
79 80 3.406728 TCAAACGTCGACAAATTTGCA 57.593 38.095 22.64 13.82 33.09 4.08
80 81 4.947077 ATTCAAACGTCGACAAATTTGC 57.053 36.364 22.64 9.87 33.09 3.68
81 82 7.387180 TGAAAATTCAAACGTCGACAAATTTG 58.613 30.769 21.94 21.94 33.55 2.32
82 83 7.513190 TGAAAATTCAAACGTCGACAAATTT 57.487 28.000 17.16 14.33 33.55 1.82
83 84 6.291585 GCTGAAAATTCAAACGTCGACAAATT 60.292 34.615 17.16 9.62 36.64 1.82
84 85 5.173131 GCTGAAAATTCAAACGTCGACAAAT 59.827 36.000 17.16 4.07 36.64 2.32
85 86 4.497608 GCTGAAAATTCAAACGTCGACAAA 59.502 37.500 17.16 1.76 36.64 2.83
86 87 4.032355 GCTGAAAATTCAAACGTCGACAA 58.968 39.130 17.16 1.67 36.64 3.18
87 88 3.311322 AGCTGAAAATTCAAACGTCGACA 59.689 39.130 17.16 0.00 36.64 4.35
88 89 3.873529 AGCTGAAAATTCAAACGTCGAC 58.126 40.909 5.18 5.18 36.64 4.20
89 90 4.545823 AAGCTGAAAATTCAAACGTCGA 57.454 36.364 0.00 0.00 36.64 4.20
90 91 4.085619 CCAAAGCTGAAAATTCAAACGTCG 60.086 41.667 0.00 0.00 36.64 5.12
91 92 4.209080 CCCAAAGCTGAAAATTCAAACGTC 59.791 41.667 0.00 0.00 36.64 4.34
92 93 4.119136 CCCAAAGCTGAAAATTCAAACGT 58.881 39.130 0.00 0.00 36.64 3.99
93 94 3.059665 GCCCAAAGCTGAAAATTCAAACG 60.060 43.478 0.00 0.00 36.64 3.60
143 144 2.432628 CACGACGTTCAGAGGGGC 60.433 66.667 0.00 0.00 0.00 5.80
205 210 5.944599 TGATCCTATTATCCTACAGACCGAC 59.055 44.000 0.00 0.00 0.00 4.79
361 403 9.713684 TCTTCCATGTTCCCATTAGAAAATTAT 57.286 29.630 0.00 0.00 0.00 1.28
370 412 7.690454 TCTAAGATCTTCCATGTTCCCATTA 57.310 36.000 12.24 0.00 0.00 1.90
405 459 7.255104 CCAGCTGCATAATAATTCGAAAAGGTA 60.255 37.037 8.66 0.00 0.00 3.08
484 538 1.411651 GGATCCTAGGGACCCAGCAC 61.412 65.000 14.60 0.00 32.98 4.40
513 568 3.305335 GCAGAACCAGTTAAACCATGTGG 60.305 47.826 0.00 0.00 42.17 4.17
514 569 3.317711 TGCAGAACCAGTTAAACCATGTG 59.682 43.478 0.00 0.00 0.00 3.21
557 620 4.102649 GCAAGTACAATTGGATTTACGGC 58.897 43.478 10.83 8.63 0.00 5.68
570 633 6.096673 TCATGTAGAAGACAGCAAGTACAA 57.903 37.500 0.00 0.00 42.79 2.41
593 656 9.487790 CAAACAACCACAACCTGAAATAATAAT 57.512 29.630 0.00 0.00 0.00 1.28
594 657 8.478877 ACAAACAACCACAACCTGAAATAATAA 58.521 29.630 0.00 0.00 0.00 1.40
595 658 8.012957 ACAAACAACCACAACCTGAAATAATA 57.987 30.769 0.00 0.00 0.00 0.98
596 659 6.883744 ACAAACAACCACAACCTGAAATAAT 58.116 32.000 0.00 0.00 0.00 1.28
606 669 4.805219 AGAAACTGACAAACAACCACAAC 58.195 39.130 0.00 0.00 0.00 3.32
622 685 7.441458 GTGGCGAGGATATATACAAAAGAAACT 59.559 37.037 0.00 0.00 0.00 2.66
623 686 7.441458 AGTGGCGAGGATATATACAAAAGAAAC 59.559 37.037 0.00 0.00 0.00 2.78
624 687 7.441157 CAGTGGCGAGGATATATACAAAAGAAA 59.559 37.037 0.00 0.00 0.00 2.52
625 688 6.929049 CAGTGGCGAGGATATATACAAAAGAA 59.071 38.462 0.00 0.00 0.00 2.52
626 689 6.266786 TCAGTGGCGAGGATATATACAAAAGA 59.733 38.462 0.00 0.00 0.00 2.52
627 690 6.455647 TCAGTGGCGAGGATATATACAAAAG 58.544 40.000 0.00 0.00 0.00 2.27
673 1212 4.759183 GCACTGAATATGGGATCTTCTTCC 59.241 45.833 0.00 0.00 34.83 3.46
683 1222 2.948115 TCCAATGGCACTGAATATGGG 58.052 47.619 0.00 0.00 0.00 4.00
691 1230 3.956199 AGATAATGGTTCCAATGGCACTG 59.044 43.478 1.55 0.00 0.00 3.66
707 1246 7.486407 AATCTTCAGGCCAAACAAAGATAAT 57.514 32.000 5.01 0.00 36.05 1.28
710 1249 5.813513 AAATCTTCAGGCCAAACAAAGAT 57.186 34.783 5.01 8.75 38.09 2.40
912 1455 5.065731 GGAACAGAAGCAGGAATACATCAAG 59.934 44.000 0.00 0.00 0.00 3.02
926 1469 6.382869 ACATATTATTGCAGGAACAGAAGC 57.617 37.500 0.00 0.00 0.00 3.86
1815 2365 2.760374 CCATTCTCTCCGCCATAAGAC 58.240 52.381 0.00 0.00 0.00 3.01
1905 2455 3.447586 TCTCCTCAAAGTACTTCCCGATG 59.552 47.826 8.95 3.17 0.00 3.84
2040 2590 2.373169 AGTGGCAGAATTCTTCAGGACA 59.627 45.455 4.86 0.00 0.00 4.02
2226 2776 2.039084 AGATCCTTCCTGCGACTTGTTT 59.961 45.455 0.00 0.00 0.00 2.83
2340 2890 9.017509 TCAATTGATTGCTATTCAAAGTCTTCT 57.982 29.630 3.38 0.00 38.34 2.85
2483 3034 3.267860 GAGGAGCTGGCGCGATTG 61.268 66.667 12.10 0.00 42.32 2.67
2508 3059 8.109634 AGGCATTCCTTTTGTTTATAAGAGAGA 58.890 33.333 0.00 0.00 40.66 3.10
2509 3060 8.286191 AGGCATTCCTTTTGTTTATAAGAGAG 57.714 34.615 0.00 0.00 40.66 3.20
2548 3100 7.651304 ACAACATCGAATCAAACATTAGCAAAA 59.349 29.630 0.00 0.00 0.00 2.44
2580 3132 3.379452 AGTCTTACTCTTCATCCCCCTG 58.621 50.000 0.00 0.00 0.00 4.45
2624 3176 6.162079 AGACTTCATACTTCATCACACAGTG 58.838 40.000 0.00 0.00 34.45 3.66
2639 3191 1.542472 TCACGCCGACAAGACTTCATA 59.458 47.619 0.00 0.00 0.00 2.15
2660 3212 1.407979 GAAATGCAGCCTTCCTCCATG 59.592 52.381 0.00 0.00 0.00 3.66
2762 3314 3.854666 AGTTCAAGACTCACATCGATGG 58.145 45.455 28.09 17.13 31.20 3.51
2855 3414 5.163622 CCAATAGCAGGTTCAAATGTAGTGG 60.164 44.000 0.00 0.00 0.00 4.00
2870 3429 4.333913 AGCTGTGTCTATCCAATAGCAG 57.666 45.455 0.00 0.00 32.31 4.24
2943 3504 6.764308 AAAGGAAGATCAACATACATGTGG 57.236 37.500 9.11 2.98 41.61 4.17
2951 3512 7.177216 TGAGCAAACATAAAGGAAGATCAACAT 59.823 33.333 0.00 0.00 0.00 2.71
2957 3518 5.882557 ACGATGAGCAAACATAAAGGAAGAT 59.117 36.000 0.00 0.00 0.00 2.40
2958 3519 5.245531 ACGATGAGCAAACATAAAGGAAGA 58.754 37.500 0.00 0.00 0.00 2.87
2959 3520 5.551760 ACGATGAGCAAACATAAAGGAAG 57.448 39.130 0.00 0.00 0.00 3.46
2960 3521 4.092821 CGACGATGAGCAAACATAAAGGAA 59.907 41.667 0.00 0.00 0.00 3.36
2961 3522 3.616821 CGACGATGAGCAAACATAAAGGA 59.383 43.478 0.00 0.00 0.00 3.36
2962 3523 3.785505 GCGACGATGAGCAAACATAAAGG 60.786 47.826 0.00 0.00 0.00 3.11
2963 3524 3.345714 GCGACGATGAGCAAACATAAAG 58.654 45.455 0.00 0.00 0.00 1.85
2964 3525 2.222707 CGCGACGATGAGCAAACATAAA 60.223 45.455 0.00 0.00 0.00 1.40
2965 3526 1.323235 CGCGACGATGAGCAAACATAA 59.677 47.619 0.00 0.00 0.00 1.90
2966 3527 0.920664 CGCGACGATGAGCAAACATA 59.079 50.000 0.00 0.00 0.00 2.29
2967 3528 1.014044 ACGCGACGATGAGCAAACAT 61.014 50.000 15.93 0.00 0.00 2.71
2968 3529 1.663388 ACGCGACGATGAGCAAACA 60.663 52.632 15.93 0.00 0.00 2.83
2978 3539 3.961197 ACACTCTGCACGCGACGA 61.961 61.111 15.93 5.76 0.00 4.20
2990 3551 6.744537 CAGTAAAATCTTTAGCATGCACACTC 59.255 38.462 21.98 0.00 0.00 3.51
2992 3553 6.611381 TCAGTAAAATCTTTAGCATGCACAC 58.389 36.000 21.98 2.20 0.00 3.82
2993 3554 6.623549 GCTCAGTAAAATCTTTAGCATGCACA 60.624 38.462 21.98 3.86 0.00 4.57
3022 3584 5.633601 GGAATCTCGAACCAAAACAAATTCC 59.366 40.000 0.00 0.00 34.63 3.01
3028 3590 4.079980 TCAGGAATCTCGAACCAAAACA 57.920 40.909 0.00 0.00 0.00 2.83
3039 3601 2.740981 CACACAGTGCTTCAGGAATCTC 59.259 50.000 0.00 0.00 0.00 2.75
3055 3617 4.824537 TCTTAGCCACAAAAATAGCACACA 59.175 37.500 0.00 0.00 0.00 3.72
3056 3618 5.371115 TCTTAGCCACAAAAATAGCACAC 57.629 39.130 0.00 0.00 0.00 3.82
3065 3627 6.208599 CCTTCTGGTTTATCTTAGCCACAAAA 59.791 38.462 0.00 0.00 0.00 2.44
3067 3629 5.013704 TCCTTCTGGTTTATCTTAGCCACAA 59.986 40.000 0.00 0.00 34.23 3.33
3072 3634 7.631717 AACAATCCTTCTGGTTTATCTTAGC 57.368 36.000 0.00 0.00 34.23 3.09
3088 3650 5.304101 TGCACATTTACCAGAAAACAATCCT 59.696 36.000 0.00 0.00 0.00 3.24
3123 3685 3.777465 AGCAGCAACTTCAGCATAATG 57.223 42.857 0.00 0.00 0.00 1.90
3124 3686 7.572523 TTATTAGCAGCAACTTCAGCATAAT 57.427 32.000 0.00 0.00 0.00 1.28
3126 3688 8.675705 TTATTATTAGCAGCAACTTCAGCATA 57.324 30.769 0.00 0.00 0.00 3.14
3127 3689 7.572523 TTATTATTAGCAGCAACTTCAGCAT 57.427 32.000 0.00 0.00 0.00 3.79
3129 3691 6.860023 CCATTATTATTAGCAGCAACTTCAGC 59.140 38.462 0.00 0.00 0.00 4.26
3130 3692 8.072567 GTCCATTATTATTAGCAGCAACTTCAG 58.927 37.037 0.00 0.00 0.00 3.02
3132 3694 8.072567 CAGTCCATTATTATTAGCAGCAACTTC 58.927 37.037 0.00 0.00 0.00 3.01
3133 3695 7.775093 TCAGTCCATTATTATTAGCAGCAACTT 59.225 33.333 0.00 0.00 0.00 2.66
3134 3696 7.282585 TCAGTCCATTATTATTAGCAGCAACT 58.717 34.615 0.00 0.00 0.00 3.16
3135 3697 7.496529 TCAGTCCATTATTATTAGCAGCAAC 57.503 36.000 0.00 0.00 0.00 4.17
3137 3699 7.053498 TGTTCAGTCCATTATTATTAGCAGCA 58.947 34.615 0.00 0.00 0.00 4.41
3138 3700 7.496529 TGTTCAGTCCATTATTATTAGCAGC 57.503 36.000 0.00 0.00 0.00 5.25
3147 3709 8.862325 TGTAGACATTTGTTCAGTCCATTATT 57.138 30.769 0.00 0.00 32.82 1.40
3148 3710 8.862325 TTGTAGACATTTGTTCAGTCCATTAT 57.138 30.769 0.00 0.00 32.82 1.28
3152 3714 6.371548 GCTATTGTAGACATTTGTTCAGTCCA 59.628 38.462 0.00 0.00 32.82 4.02
3154 3716 7.331934 TGAGCTATTGTAGACATTTGTTCAGTC 59.668 37.037 0.00 0.00 0.00 3.51
3155 3717 7.161404 TGAGCTATTGTAGACATTTGTTCAGT 58.839 34.615 0.00 0.00 0.00 3.41
3156 3718 7.201591 CCTGAGCTATTGTAGACATTTGTTCAG 60.202 40.741 17.39 17.39 38.54 3.02
3157 3719 6.595326 CCTGAGCTATTGTAGACATTTGTTCA 59.405 38.462 0.00 5.81 0.00 3.18
3187 3749 5.083533 TGTTTTCAAGGCAAACTGAACAT 57.916 34.783 0.75 0.00 35.50 2.71
3215 3777 2.350772 CCGTTCTGAAACTGATGGCAAC 60.351 50.000 0.00 0.00 32.95 4.17
3228 3790 3.882888 AGCTGAATGTTTTTCCGTTCTGA 59.117 39.130 0.00 0.00 33.54 3.27
3255 3817 3.537793 GGCAACCTCAACTTTCGTAAG 57.462 47.619 0.00 0.00 37.40 2.34
3279 3841 1.338484 TGAAGGCTACAAGCTGAGCAG 60.338 52.381 7.39 0.51 41.99 4.24
3280 3842 0.686789 TGAAGGCTACAAGCTGAGCA 59.313 50.000 7.39 0.00 41.99 4.26
3281 3843 1.082690 GTGAAGGCTACAAGCTGAGC 58.917 55.000 0.00 0.00 41.99 4.26
3282 3844 2.740981 CAAGTGAAGGCTACAAGCTGAG 59.259 50.000 0.00 0.00 41.99 3.35
3283 3845 2.368548 TCAAGTGAAGGCTACAAGCTGA 59.631 45.455 0.00 0.00 41.99 4.26
3284 3846 2.740981 CTCAAGTGAAGGCTACAAGCTG 59.259 50.000 0.00 0.00 41.99 4.24
3285 3847 2.873649 GCTCAAGTGAAGGCTACAAGCT 60.874 50.000 0.00 0.00 41.99 3.74
3286 3848 1.466558 GCTCAAGTGAAGGCTACAAGC 59.533 52.381 0.00 0.00 41.46 4.01
3287 3849 1.728971 CGCTCAAGTGAAGGCTACAAG 59.271 52.381 0.00 0.00 0.00 3.16
3288 3850 1.070134 ACGCTCAAGTGAAGGCTACAA 59.930 47.619 0.00 0.00 0.00 2.41
3289 3851 0.679505 ACGCTCAAGTGAAGGCTACA 59.320 50.000 0.00 0.00 0.00 2.74
3290 3852 1.071605 CACGCTCAAGTGAAGGCTAC 58.928 55.000 0.00 0.00 44.43 3.58
3291 3853 0.679505 ACACGCTCAAGTGAAGGCTA 59.320 50.000 4.00 0.00 44.43 3.93
3292 3854 0.601311 GACACGCTCAAGTGAAGGCT 60.601 55.000 4.00 0.00 44.43 4.58
3293 3855 1.569479 GGACACGCTCAAGTGAAGGC 61.569 60.000 4.00 0.00 44.43 4.35
3294 3856 0.034059 AGGACACGCTCAAGTGAAGG 59.966 55.000 4.00 0.00 44.43 3.46
3295 3857 1.143305 CAGGACACGCTCAAGTGAAG 58.857 55.000 4.00 0.00 44.43 3.02
3296 3858 0.249868 CCAGGACACGCTCAAGTGAA 60.250 55.000 4.00 0.00 44.43 3.18
3297 3859 1.112916 TCCAGGACACGCTCAAGTGA 61.113 55.000 4.00 0.00 44.43 3.41
3298 3860 0.036952 ATCCAGGACACGCTCAAGTG 60.037 55.000 0.00 0.00 46.83 3.16
3299 3861 0.036952 CATCCAGGACACGCTCAAGT 60.037 55.000 0.00 0.00 0.00 3.16
3300 3862 0.247460 TCATCCAGGACACGCTCAAG 59.753 55.000 0.00 0.00 0.00 3.02
3301 3863 0.037326 GTCATCCAGGACACGCTCAA 60.037 55.000 0.00 0.00 37.73 3.02
3302 3864 1.591703 GTCATCCAGGACACGCTCA 59.408 57.895 0.00 0.00 37.73 4.26
3303 3865 1.153549 GGTCATCCAGGACACGCTC 60.154 63.158 0.00 0.00 39.59 5.03
3304 3866 2.982130 GGTCATCCAGGACACGCT 59.018 61.111 0.00 0.00 39.59 5.07
3305 3867 2.509336 CGGTCATCCAGGACACGC 60.509 66.667 0.00 0.00 39.59 5.34
3306 3868 1.153823 GACGGTCATCCAGGACACG 60.154 63.158 2.62 0.00 39.59 4.49
3307 3869 1.153823 CGACGGTCATCCAGGACAC 60.154 63.158 9.10 0.00 39.59 3.67
3308 3870 3.001902 GCGACGGTCATCCAGGACA 62.002 63.158 9.10 0.00 39.59 4.02
3309 3871 2.202756 GCGACGGTCATCCAGGAC 60.203 66.667 9.10 0.00 37.06 3.85
3310 3872 3.458163 GGCGACGGTCATCCAGGA 61.458 66.667 9.10 0.00 0.00 3.86
3311 3873 3.770040 TGGCGACGGTCATCCAGG 61.770 66.667 13.19 0.00 0.00 4.45
3312 3874 2.509336 GTGGCGACGGTCATCCAG 60.509 66.667 16.45 0.00 0.00 3.86
3313 3875 2.994995 AGTGGCGACGGTCATCCA 60.995 61.111 13.19 13.19 0.00 3.41
3314 3876 2.509336 CAGTGGCGACGGTCATCC 60.509 66.667 9.10 8.98 0.00 3.51
3315 3877 3.188786 GCAGTGGCGACGGTCATC 61.189 66.667 9.10 0.00 0.00 2.92
3316 3878 3.529341 TTGCAGTGGCGACGGTCAT 62.529 57.895 9.10 0.00 45.35 3.06
3317 3879 3.741830 TTTGCAGTGGCGACGGTCA 62.742 57.895 9.10 0.00 45.35 4.02
3318 3880 2.325082 ATTTGCAGTGGCGACGGTC 61.325 57.895 0.00 0.00 45.35 4.79
3319 3881 2.281484 ATTTGCAGTGGCGACGGT 60.281 55.556 0.56 0.00 45.35 4.83
3320 3882 2.176546 CATTTGCAGTGGCGACGG 59.823 61.111 0.00 0.00 45.35 4.79
3321 3883 1.154413 GTCATTTGCAGTGGCGACG 60.154 57.895 0.00 0.00 45.35 5.12
3322 3884 1.154413 CGTCATTTGCAGTGGCGAC 60.154 57.895 19.44 7.77 46.80 5.19
3323 3885 2.965147 GCGTCATTTGCAGTGGCGA 61.965 57.895 25.77 1.43 46.80 5.54
3324 3886 2.502510 GCGTCATTTGCAGTGGCG 60.503 61.111 19.73 19.73 46.60 5.69
3325 3887 2.126346 GGCGTCATTTGCAGTGGC 60.126 61.111 0.00 0.00 41.68 5.01
3326 3888 0.244450 ATTGGCGTCATTTGCAGTGG 59.756 50.000 0.00 0.00 0.00 4.00
3327 3889 1.722464 CAATTGGCGTCATTTGCAGTG 59.278 47.619 11.26 0.00 30.69 3.66
3328 3890 1.337074 CCAATTGGCGTCATTTGCAGT 60.337 47.619 12.53 0.00 34.62 4.40
3329 3891 1.352114 CCAATTGGCGTCATTTGCAG 58.648 50.000 12.53 3.42 34.62 4.41
3330 3892 0.037512 CCCAATTGGCGTCATTTGCA 60.038 50.000 19.75 0.00 34.62 4.08
3331 3893 0.740516 CCCCAATTGGCGTCATTTGC 60.741 55.000 19.75 0.00 34.62 3.68
3332 3894 0.894141 TCCCCAATTGGCGTCATTTG 59.106 50.000 19.75 15.80 35.30 2.32
3333 3895 1.638529 TTCCCCAATTGGCGTCATTT 58.361 45.000 19.75 0.00 0.00 2.32
3334 3896 1.864669 ATTCCCCAATTGGCGTCATT 58.135 45.000 19.75 0.00 0.00 2.57
3335 3897 1.756538 GAATTCCCCAATTGGCGTCAT 59.243 47.619 19.75 4.51 31.94 3.06
3336 3898 1.181786 GAATTCCCCAATTGGCGTCA 58.818 50.000 19.75 2.72 31.94 4.35


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

AutoCloner maintained by Alex Coulton.