Multiple sequence alignment - TraesCS2D01G285800

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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 TraesCS2D01G285800 chr2D 100.000 4447 0 0 4022 8468 363979299 363974853 0.000000e+00 8213.0
1 TraesCS2D01G285800 chr2D 100.000 3760 0 0 1 3760 363983320 363979561 0.000000e+00 6944.0
2 TraesCS2D01G285800 chr2D 95.918 98 0 2 5385 5480 363977841 363977936 1.140000e-33 156.0
3 TraesCS2D01G285800 chr2B 93.313 3574 130 50 1 3519 432142925 432139406 0.000000e+00 5175.0
4 TraesCS2D01G285800 chr2B 96.016 2284 74 4 5504 7784 432137087 432134818 0.000000e+00 3698.0
5 TraesCS2D01G285800 chr2B 92.757 1146 44 18 4022 5143 432138586 432137456 0.000000e+00 1620.0
6 TraesCS2D01G285800 chr2B 93.750 560 16 7 7781 8334 432134657 432134111 0.000000e+00 822.0
7 TraesCS2D01G285800 chr2B 86.111 360 32 9 3403 3759 432139359 432139015 1.040000e-98 372.0
8 TraesCS2D01G285800 chr2B 91.770 243 20 0 5144 5386 432137339 432137097 1.050000e-88 339.0
9 TraesCS2D01G285800 chr2B 94.737 95 2 2 8374 8468 432133871 432133780 2.460000e-30 145.0
10 TraesCS2D01G285800 chr2A 95.570 2280 63 17 5517 7789 489963853 489961605 0.000000e+00 3616.0
11 TraesCS2D01G285800 chr2A 97.173 1733 37 10 1 1724 489970147 489968418 0.000000e+00 2918.0
12 TraesCS2D01G285800 chr2A 95.787 1804 56 7 1723 3519 489968321 489966531 0.000000e+00 2892.0
13 TraesCS2D01G285800 chr2A 95.864 677 18 8 7794 8468 489961346 489960678 0.000000e+00 1086.0
14 TraesCS2D01G285800 chr2A 93.040 704 29 6 4681 5369 489964645 489963947 0.000000e+00 1011.0
15 TraesCS2D01G285800 chr2A 92.125 673 37 5 4038 4695 489965680 489965009 0.000000e+00 935.0
16 TraesCS2D01G285800 chr2A 89.722 360 25 5 3403 3760 489966447 489966098 4.660000e-122 449.0
17 TraesCS2D01G285800 chr6B 86.040 1139 155 4 6283 7419 391095003 391096139 0.000000e+00 1219.0
18 TraesCS2D01G285800 chr6B 80.531 565 100 9 1001 1562 391071459 391072016 7.860000e-115 425.0
19 TraesCS2D01G285800 chr6B 83.171 410 51 12 2967 3374 391072612 391073005 8.080000e-95 359.0
20 TraesCS2D01G285800 chr6B 91.556 225 19 0 4418 4642 391073225 391073449 2.300000e-80 311.0
21 TraesCS2D01G285800 chr6B 89.583 96 9 1 5386 5480 548119001 548118906 4.150000e-23 121.0
22 TraesCS2D01G285800 chr6B 89.691 97 7 3 5385 5479 548118906 548119001 4.150000e-23 121.0
23 TraesCS2D01G285800 chr6D 85.953 1139 156 4 6283 7419 222734425 222735561 0.000000e+00 1214.0
24 TraesCS2D01G285800 chr6D 80.142 564 104 7 1001 1562 222721172 222721729 1.700000e-111 414.0
25 TraesCS2D01G285800 chr6D 83.698 411 47 14 2967 3374 222722325 222722718 3.730000e-98 370.0
26 TraesCS2D01G285800 chr6D 91.111 225 20 0 4418 4642 222722916 222723140 1.070000e-78 305.0
27 TraesCS2D01G285800 chr6D 91.579 95 8 0 5386 5480 324520774 324520680 1.920000e-26 132.0
28 TraesCS2D01G285800 chr6A 85.865 1139 157 4 6283 7419 278553320 278552184 0.000000e+00 1208.0
29 TraesCS2D01G285800 chr6A 80.462 563 104 6 1001 1562 278573826 278573269 7.860000e-115 425.0
30 TraesCS2D01G285800 chr6A 83.698 411 47 14 2967 3374 278572672 278572279 3.730000e-98 370.0
31 TraesCS2D01G285800 chr6A 91.556 225 19 0 4418 4642 278564196 278563972 2.300000e-80 311.0
32 TraesCS2D01G285800 chr5D 92.784 97 6 1 5385 5480 362056051 362056147 1.150000e-28 139.0
33 TraesCS2D01G285800 chr5D 90.099 101 7 3 5385 5483 362056147 362056048 2.480000e-25 128.0
34 TraesCS2D01G285800 chr5A 90.722 97 8 1 5385 5480 462862905 462863001 2.480000e-25 128.0
35 TraesCS2D01G285800 chr5A 88.119 101 9 3 5385 5483 462863001 462862902 5.370000e-22 117.0
36 TraesCS2D01G285800 chr5B 90.426 94 8 1 5385 5477 427929579 427929672 1.150000e-23 122.0
37 TraesCS2D01G285800 chr3D 97.368 38 1 0 8431 8468 277066532 277066569 1.970000e-06 65.8
38 TraesCS2D01G285800 chr3B 97.368 38 1 0 8431 8468 373285658 373285621 1.970000e-06 65.8
39 TraesCS2D01G285800 chr3A 97.368 38 1 0 8431 8468 362591466 362591429 1.970000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G285800 chr2D 363974853 363983320 8467 True 7578.500000 8213 100.000000 1 8468 2 chr2D.!!$R1 8467
1 TraesCS2D01G285800 chr2B 432133780 432142925 9145 True 1738.714286 5175 92.636286 1 8468 7 chr2B.!!$R1 8467
2 TraesCS2D01G285800 chr2A 489960678 489970147 9469 True 1843.857143 3616 94.183000 1 8468 7 chr2A.!!$R1 8467
3 TraesCS2D01G285800 chr6B 391095003 391096139 1136 False 1219.000000 1219 86.040000 6283 7419 1 chr6B.!!$F1 1136
4 TraesCS2D01G285800 chr6B 391071459 391073449 1990 False 365.000000 425 85.086000 1001 4642 3 chr6B.!!$F3 3641
5 TraesCS2D01G285800 chr6D 222734425 222735561 1136 False 1214.000000 1214 85.953000 6283 7419 1 chr6D.!!$F1 1136
6 TraesCS2D01G285800 chr6D 222721172 222723140 1968 False 363.000000 414 84.983667 1001 4642 3 chr6D.!!$F2 3641
7 TraesCS2D01G285800 chr6A 278552184 278553320 1136 True 1208.000000 1208 85.865000 6283 7419 1 chr6A.!!$R1 1136
8 TraesCS2D01G285800 chr6A 278572279 278573826 1547 True 397.500000 425 82.080000 1001 3374 2 chr6A.!!$R3 2373

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
726 741 0.670162 CTGTGTTGAAGTTGGCTGGG 59.330 55.0 0.00 0.0 0.00 4.45 F
1874 2017 0.035056 GGTGTTCTGCTAGGCATGGT 60.035 55.0 0.00 0.0 38.13 3.55 F
1916 2059 0.039798 GTGACGAGTGTGCGGAACTA 60.040 55.0 0.00 0.0 35.12 2.24 F
3251 3495 0.318120 CTCAAATTTTGGGCAGGCGT 59.682 50.0 9.18 0.0 0.00 5.68 F
4845 5853 0.318955 GCATTGGTGCCACAACACTC 60.319 55.0 0.00 0.0 45.76 3.51 F
5864 7053 0.465097 GCTCAGGCATGCACAGGTAT 60.465 55.0 21.36 0.0 38.54 2.73 F
6519 7708 0.179134 AAGAGACACTCCATACGCGC 60.179 55.0 5.73 0.0 0.00 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 2549 0.107017 AGATGGGCAATGAAGGTCGG 60.107 55.000 0.00 0.00 0.00 4.79 R
3634 4082 0.107312 CCTCCTCTGTCCCAATGCTG 60.107 60.000 0.00 0.00 0.00 4.41 R
3689 4138 6.435430 TGTGGCATATTTTATCATATCCGC 57.565 37.500 0.00 0.00 0.00 5.54 R
4911 5919 0.109342 CTTCAACAGTGGGCTCTGGT 59.891 55.000 12.85 5.36 39.48 4.00 R
5937 7126 0.532417 GCCTCATCAGGTAGCTGCAG 60.532 60.000 17.20 10.11 42.74 4.41 R
7233 8422 1.049402 CCCTATCCCGGAACTTCTCC 58.951 60.000 0.73 0.00 41.40 3.71 R
7962 9412 2.098298 CACGGCGCTTTCGGATTG 59.902 61.111 6.90 0.00 35.95 2.67 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
117 123 5.759059 TGAGGTAGTATTTCTTCGGTAGGA 58.241 41.667 0.00 0.00 0.00 2.94
124 130 7.287512 AGTATTTCTTCGGTAGGAGTATTCC 57.712 40.000 0.00 0.00 44.39 3.01
125 131 6.837568 AGTATTTCTTCGGTAGGAGTATTCCA 59.162 38.462 7.08 0.00 46.64 3.53
127 133 4.246712 TCTTCGGTAGGAGTATTCCACT 57.753 45.455 7.08 0.00 46.64 4.00
497 512 2.092323 GCTGGTTGGTTGGATAGTTCC 58.908 52.381 0.00 0.00 42.94 3.62
570 585 0.742990 AGCGCGCTATTTTGGTAGCA 60.743 50.000 35.79 0.00 45.78 3.49
726 741 0.670162 CTGTGTTGAAGTTGGCTGGG 59.330 55.000 0.00 0.00 0.00 4.45
1107 1126 0.945265 TGTTACGCAGTACGCCAACC 60.945 55.000 13.75 1.34 45.76 3.77
1558 1577 3.254892 GCTCGCCAGCTAGGTATTAATC 58.745 50.000 0.00 0.00 43.09 1.75
1874 2017 0.035056 GGTGTTCTGCTAGGCATGGT 60.035 55.000 0.00 0.00 38.13 3.55
1895 2038 2.062971 ATCGAGCTGCATTCCCATTT 57.937 45.000 1.02 0.00 0.00 2.32
1909 2052 0.238289 CCATTTGGTGACGAGTGTGC 59.762 55.000 0.00 0.00 29.70 4.57
1916 2059 0.039798 GTGACGAGTGTGCGGAACTA 60.040 55.000 0.00 0.00 35.12 2.24
1993 2136 1.141657 CATCCCCGATCATTGTCTGGT 59.858 52.381 0.00 0.00 0.00 4.00
2221 2376 9.555727 ACACTAAACATGTACAATTGTCTTAGT 57.444 29.630 15.85 18.82 34.17 2.24
2265 2420 9.399797 TGATACTTAAGCAAAAGTGATCATCAT 57.600 29.630 12.51 0.00 39.95 2.45
2282 2437 3.421919 TCATGTCCTGTGCAGAATGAA 57.578 42.857 0.02 0.00 39.69 2.57
2393 2549 3.662759 TGTTTTACCATCCCTCATCCC 57.337 47.619 0.00 0.00 0.00 3.85
2431 2587 3.090037 TCTAGCGAGCAGTTACCTTTCT 58.910 45.455 0.00 0.00 0.00 2.52
2525 2681 1.694693 GGCAGGGATGGGGACTTACTA 60.695 57.143 0.00 0.00 0.00 1.82
2534 2690 5.647225 GGATGGGGACTTACTACTATACTCG 59.353 48.000 0.00 0.00 0.00 4.18
2672 2831 3.404869 TCACATCAGTCTCAGGGGTAT 57.595 47.619 0.00 0.00 0.00 2.73
2719 2878 5.532406 TGCTGCTTCTTGAGACTATTGTTTT 59.468 36.000 0.00 0.00 0.00 2.43
2909 3144 6.064060 CCCAGGCAATTTCTTCACTGATATA 58.936 40.000 0.00 0.00 0.00 0.86
3159 3403 7.066284 TGGAGATATTTAGCAGCAAAGAGAAAC 59.934 37.037 0.00 0.00 0.00 2.78
3251 3495 0.318120 CTCAAATTTTGGGCAGGCGT 59.682 50.000 9.18 0.00 0.00 5.68
3266 3510 1.134037 AGGCGTACAAAGAACAACCCA 60.134 47.619 0.00 0.00 0.00 4.51
3457 3703 4.199432 TGAATTGCAATGCGGGTATTTT 57.801 36.364 13.82 0.00 0.00 1.82
3492 3743 3.736252 GCACTGATACCGATATGTGTGTC 59.264 47.826 0.00 0.00 0.00 3.67
3515 3962 4.709886 CAGTGTATCCATATCGGGGTGATA 59.290 45.833 0.00 0.00 43.54 2.15
3529 3976 1.623811 GGTGATACGGATACATGGGCT 59.376 52.381 0.00 0.00 0.00 5.19
3546 3994 5.041191 TGGGCTTGCCAATTTCTTTAAAA 57.959 34.783 14.04 0.00 0.00 1.52
3580 4028 7.215085 ACATCGATACATTTAACTACTTCCCC 58.785 38.462 0.00 0.00 0.00 4.81
3610 4058 1.583556 TGCATGGACATACTGGGACT 58.416 50.000 0.00 0.00 0.00 3.85
3611 4059 1.210234 TGCATGGACATACTGGGACTG 59.790 52.381 0.00 0.00 0.00 3.51
3617 4065 2.166664 GGACATACTGGGACTGTGAGTC 59.833 54.545 0.00 0.00 44.32 3.36
3618 4066 2.826128 GACATACTGGGACTGTGAGTCA 59.174 50.000 6.10 0.00 46.79 3.41
3627 4075 3.455328 CTGTGAGTCAGGGCAGATG 57.545 57.895 3.68 0.00 40.23 2.90
3634 4082 1.028868 GTCAGGGCAGATGGAGCAAC 61.029 60.000 0.00 0.00 0.00 4.17
3689 4138 7.072263 AGACATGGGAGAGTTTAGATAATGG 57.928 40.000 0.00 0.00 0.00 3.16
3712 4161 5.356751 GGCGGATATGATAAAATATGCCACA 59.643 40.000 0.00 0.00 34.21 4.17
3713 4162 6.039717 GGCGGATATGATAAAATATGCCACAT 59.960 38.462 0.00 0.00 34.21 3.21
3714 4163 7.228507 GGCGGATATGATAAAATATGCCACATA 59.771 37.037 0.00 0.00 34.21 2.29
4105 4720 3.766676 CGTCTATCGGACCATATCAGG 57.233 52.381 0.00 0.00 41.64 3.86
4198 4819 8.564574 TGTGATTTTACTTTGTCATTCTGTACC 58.435 33.333 0.00 0.00 0.00 3.34
4200 4821 6.548441 TTTTACTTTGTCATTCTGTACCGG 57.452 37.500 0.00 0.00 0.00 5.28
4201 4822 3.764237 ACTTTGTCATTCTGTACCGGT 57.236 42.857 13.98 13.98 0.00 5.28
4202 4823 3.399330 ACTTTGTCATTCTGTACCGGTG 58.601 45.455 19.93 0.00 0.00 4.94
4203 4824 3.181458 ACTTTGTCATTCTGTACCGGTGT 60.181 43.478 19.93 0.00 0.00 4.16
4205 4826 3.478857 TGTCATTCTGTACCGGTGTTT 57.521 42.857 19.93 0.00 0.00 2.83
4207 4828 4.958509 TGTCATTCTGTACCGGTGTTTTA 58.041 39.130 19.93 0.00 0.00 1.52
4208 4829 5.553123 TGTCATTCTGTACCGGTGTTTTAT 58.447 37.500 19.93 2.20 0.00 1.40
4209 4830 6.699366 TGTCATTCTGTACCGGTGTTTTATA 58.301 36.000 19.93 0.00 0.00 0.98
4210 4831 6.814644 TGTCATTCTGTACCGGTGTTTTATAG 59.185 38.462 19.93 4.33 0.00 1.31
4259 4880 6.375455 AGCCTTCAGTAATTAAGTGTTGATGG 59.625 38.462 13.96 13.96 34.68 3.51
4317 4938 1.064017 ACCCAAGGCTTTTGTCAGTCA 60.064 47.619 0.00 0.00 0.00 3.41
4679 5309 2.620115 CCATTGTTCTGTGTTGCTCACT 59.380 45.455 12.23 0.00 46.27 3.41
4786 5794 3.413846 TGACAAGAAAGATGAGCTGCT 57.586 42.857 0.00 0.00 0.00 4.24
4795 5803 3.817709 AGATGAGCTGCTCCTAGTTTC 57.182 47.619 25.61 12.73 0.00 2.78
4807 5815 5.470098 TGCTCCTAGTTTCAACATTTCTGAC 59.530 40.000 0.00 0.00 0.00 3.51
4845 5853 0.318955 GCATTGGTGCCACAACACTC 60.319 55.000 0.00 0.00 45.76 3.51
5013 6021 3.441572 ACACAGATGATGCTTTAGTTGCC 59.558 43.478 0.00 0.00 0.00 4.52
5192 6330 7.397892 TTTGACATCTCTTGTGGTTTTGTTA 57.602 32.000 0.00 0.00 39.18 2.41
5208 6346 9.126151 TGGTTTTGTTATCTGAATTGTTCACTA 57.874 29.630 0.00 0.00 35.46 2.74
5284 6422 3.243301 GGCTTGCATTGGTGTATCTCATG 60.243 47.826 0.00 0.00 0.00 3.07
5290 6428 5.887035 TGCATTGGTGTATCTCATGATTTGA 59.113 36.000 0.00 0.00 34.32 2.69
5327 6465 7.236640 TGAAAGGGTTAATTATCCTGGCTTTTT 59.763 33.333 11.51 1.59 0.00 1.94
5342 6480 5.144100 TGGCTTTTTCTGAAGTTCCCAATA 58.856 37.500 0.00 0.00 0.00 1.90
5350 6488 5.759059 TCTGAAGTTCCCAATATGCTTCAT 58.241 37.500 0.00 0.00 42.76 2.57
5352 6490 5.263599 TGAAGTTCCCAATATGCTTCATGT 58.736 37.500 0.00 0.00 40.07 3.21
5386 6524 6.840075 TCTAGACTTTCGCTAAGAGTGTTAC 58.160 40.000 4.43 0.00 37.30 2.50
5387 6525 5.708877 AGACTTTCGCTAAGAGTGTTACT 57.291 39.130 4.43 0.00 37.30 2.24
5388 6526 5.701855 AGACTTTCGCTAAGAGTGTTACTC 58.298 41.667 0.79 0.79 45.38 2.59
5389 6527 4.807443 ACTTTCGCTAAGAGTGTTACTCC 58.193 43.478 5.41 0.00 46.18 3.85
5390 6528 3.863142 TTCGCTAAGAGTGTTACTCCC 57.137 47.619 5.41 0.00 46.18 4.30
5391 6529 3.083122 TCGCTAAGAGTGTTACTCCCT 57.917 47.619 5.41 0.00 46.18 4.20
5392 6530 3.015327 TCGCTAAGAGTGTTACTCCCTC 58.985 50.000 5.41 0.00 46.18 4.30
5393 6531 2.099427 CGCTAAGAGTGTTACTCCCTCC 59.901 54.545 5.41 0.00 46.18 4.30
5394 6532 2.099427 GCTAAGAGTGTTACTCCCTCCG 59.901 54.545 5.41 0.00 46.18 4.63
5395 6533 2.599408 AAGAGTGTTACTCCCTCCGA 57.401 50.000 5.41 0.00 46.18 4.55
5396 6534 2.830651 AGAGTGTTACTCCCTCCGAT 57.169 50.000 5.41 0.00 46.18 4.18
5397 6535 2.657143 AGAGTGTTACTCCCTCCGATC 58.343 52.381 5.41 0.00 46.18 3.69
5398 6536 1.682323 GAGTGTTACTCCCTCCGATCC 59.318 57.143 0.00 0.00 39.28 3.36
5399 6537 1.006758 AGTGTTACTCCCTCCGATCCA 59.993 52.381 0.00 0.00 0.00 3.41
5400 6538 2.040178 GTGTTACTCCCTCCGATCCAT 58.960 52.381 0.00 0.00 0.00 3.41
5401 6539 3.117246 AGTGTTACTCCCTCCGATCCATA 60.117 47.826 0.00 0.00 0.00 2.74
5402 6540 3.833070 GTGTTACTCCCTCCGATCCATAT 59.167 47.826 0.00 0.00 0.00 1.78
5403 6541 4.283722 GTGTTACTCCCTCCGATCCATATT 59.716 45.833 0.00 0.00 0.00 1.28
5404 6542 5.479375 GTGTTACTCCCTCCGATCCATATTA 59.521 44.000 0.00 0.00 0.00 0.98
5405 6543 6.014840 GTGTTACTCCCTCCGATCCATATTAA 60.015 42.308 0.00 0.00 0.00 1.40
5406 6544 6.729100 TGTTACTCCCTCCGATCCATATTAAT 59.271 38.462 0.00 0.00 0.00 1.40
5407 6545 7.236847 TGTTACTCCCTCCGATCCATATTAATT 59.763 37.037 0.00 0.00 0.00 1.40
5408 6546 6.054860 ACTCCCTCCGATCCATATTAATTG 57.945 41.667 0.00 0.00 0.00 2.32
5409 6547 5.785423 ACTCCCTCCGATCCATATTAATTGA 59.215 40.000 0.00 0.00 0.00 2.57
5410 6548 6.049955 TCCCTCCGATCCATATTAATTGAC 57.950 41.667 0.00 0.00 0.00 3.18
5411 6549 4.870426 CCCTCCGATCCATATTAATTGACG 59.130 45.833 0.00 0.00 0.00 4.35
5412 6550 4.330074 CCTCCGATCCATATTAATTGACGC 59.670 45.833 0.00 0.00 0.00 5.19
5413 6551 5.147330 TCCGATCCATATTAATTGACGCT 57.853 39.130 0.00 0.00 0.00 5.07
5414 6552 4.929211 TCCGATCCATATTAATTGACGCTG 59.071 41.667 0.00 0.00 0.00 5.18
5415 6553 4.436050 CCGATCCATATTAATTGACGCTGC 60.436 45.833 0.00 0.00 0.00 5.25
5416 6554 4.389992 CGATCCATATTAATTGACGCTGCT 59.610 41.667 0.00 0.00 0.00 4.24
5417 6555 5.445142 CGATCCATATTAATTGACGCTGCTC 60.445 44.000 0.00 0.00 0.00 4.26
5418 6556 4.960938 TCCATATTAATTGACGCTGCTCT 58.039 39.130 0.00 0.00 0.00 4.09
5419 6557 6.096673 TCCATATTAATTGACGCTGCTCTA 57.903 37.500 0.00 0.00 0.00 2.43
5420 6558 6.159293 TCCATATTAATTGACGCTGCTCTAG 58.841 40.000 0.00 0.00 0.00 2.43
5421 6559 5.928839 CCATATTAATTGACGCTGCTCTAGT 59.071 40.000 0.00 0.00 0.00 2.57
5422 6560 7.039993 TCCATATTAATTGACGCTGCTCTAGTA 60.040 37.037 0.00 0.00 0.00 1.82
5423 6561 7.761704 CCATATTAATTGACGCTGCTCTAGTAT 59.238 37.037 0.00 0.00 0.00 2.12
5424 6562 9.788960 CATATTAATTGACGCTGCTCTAGTATA 57.211 33.333 0.00 0.00 0.00 1.47
5427 6565 9.712305 ATTAATTGACGCTGCTCTAGTATAATT 57.288 29.630 0.00 2.65 0.00 1.40
5428 6566 9.542462 TTAATTGACGCTGCTCTAGTATAATTT 57.458 29.630 0.00 0.00 0.00 1.82
5429 6567 7.644986 ATTGACGCTGCTCTAGTATAATTTC 57.355 36.000 0.00 0.00 0.00 2.17
5430 6568 6.144078 TGACGCTGCTCTAGTATAATTTCA 57.856 37.500 0.00 0.00 0.00 2.69
5431 6569 6.209361 TGACGCTGCTCTAGTATAATTTCAG 58.791 40.000 0.00 0.00 0.00 3.02
5432 6570 6.150396 ACGCTGCTCTAGTATAATTTCAGT 57.850 37.500 0.00 0.00 0.00 3.41
5433 6571 7.012989 TGACGCTGCTCTAGTATAATTTCAGTA 59.987 37.037 0.00 0.00 0.00 2.74
5434 6572 7.140048 ACGCTGCTCTAGTATAATTTCAGTAC 58.860 38.462 0.00 0.00 0.00 2.73
5435 6573 7.139392 CGCTGCTCTAGTATAATTTCAGTACA 58.861 38.462 0.00 0.00 0.00 2.90
5436 6574 7.648112 CGCTGCTCTAGTATAATTTCAGTACAA 59.352 37.037 0.00 0.00 0.00 2.41
5437 6575 9.314321 GCTGCTCTAGTATAATTTCAGTACAAA 57.686 33.333 0.00 0.00 0.00 2.83
5452 6590 8.873215 TTCAGTACAAATTATACTAGAGCAGC 57.127 34.615 0.00 0.00 31.53 5.25
5453 6591 7.139392 TCAGTACAAATTATACTAGAGCAGCG 58.861 38.462 0.00 0.00 31.53 5.18
5454 6592 6.918569 CAGTACAAATTATACTAGAGCAGCGT 59.081 38.462 0.00 0.00 31.53 5.07
5455 6593 7.113684 CAGTACAAATTATACTAGAGCAGCGTC 59.886 40.741 0.00 0.00 31.53 5.19
5456 6594 5.902681 ACAAATTATACTAGAGCAGCGTCA 58.097 37.500 0.00 0.00 0.00 4.35
5457 6595 6.338146 ACAAATTATACTAGAGCAGCGTCAA 58.662 36.000 0.00 0.00 0.00 3.18
5458 6596 6.986817 ACAAATTATACTAGAGCAGCGTCAAT 59.013 34.615 0.00 0.00 0.00 2.57
5459 6597 7.495934 ACAAATTATACTAGAGCAGCGTCAATT 59.504 33.333 0.00 0.00 0.00 2.32
5460 6598 8.978539 CAAATTATACTAGAGCAGCGTCAATTA 58.021 33.333 0.00 0.00 0.00 1.40
5461 6599 9.542462 AAATTATACTAGAGCAGCGTCAATTAA 57.458 29.630 0.00 0.00 0.00 1.40
5462 6600 9.712305 AATTATACTAGAGCAGCGTCAATTAAT 57.288 29.630 0.00 0.00 0.00 1.40
5465 6603 8.694975 ATACTAGAGCAGCGTCAATTAATATG 57.305 34.615 0.00 0.00 0.00 1.78
5466 6604 5.928839 ACTAGAGCAGCGTCAATTAATATGG 59.071 40.000 0.00 0.00 0.00 2.74
5467 6605 4.960938 AGAGCAGCGTCAATTAATATGGA 58.039 39.130 0.00 0.00 0.00 3.41
5468 6606 5.555017 AGAGCAGCGTCAATTAATATGGAT 58.445 37.500 0.00 0.00 0.00 3.41
5469 6607 5.641209 AGAGCAGCGTCAATTAATATGGATC 59.359 40.000 0.00 0.00 0.00 3.36
5470 6608 4.389992 AGCAGCGTCAATTAATATGGATCG 59.610 41.667 0.00 0.00 0.00 3.69
5471 6609 4.436050 GCAGCGTCAATTAATATGGATCGG 60.436 45.833 0.00 0.00 0.00 4.18
5472 6610 4.929211 CAGCGTCAATTAATATGGATCGGA 59.071 41.667 0.00 0.00 0.00 4.55
5473 6611 5.062683 CAGCGTCAATTAATATGGATCGGAG 59.937 44.000 0.00 0.00 0.00 4.63
5474 6612 4.330074 GCGTCAATTAATATGGATCGGAGG 59.670 45.833 0.00 0.00 0.00 4.30
5475 6613 4.870426 CGTCAATTAATATGGATCGGAGGG 59.130 45.833 0.00 0.00 0.00 4.30
5476 6614 5.337250 CGTCAATTAATATGGATCGGAGGGA 60.337 44.000 0.00 0.00 0.00 4.20
5477 6615 6.109359 GTCAATTAATATGGATCGGAGGGAG 58.891 44.000 0.00 0.00 0.00 4.30
5478 6616 5.785423 TCAATTAATATGGATCGGAGGGAGT 59.215 40.000 0.00 0.00 0.00 3.85
5479 6617 6.957606 TCAATTAATATGGATCGGAGGGAGTA 59.042 38.462 0.00 0.00 0.00 2.59
5480 6618 7.623677 TCAATTAATATGGATCGGAGGGAGTAT 59.376 37.037 0.00 0.00 0.00 2.12
5481 6619 8.924303 CAATTAATATGGATCGGAGGGAGTATA 58.076 37.037 0.00 0.00 0.00 1.47
5482 6620 9.502035 AATTAATATGGATCGGAGGGAGTATAA 57.498 33.333 0.00 0.00 0.00 0.98
5483 6621 9.676129 ATTAATATGGATCGGAGGGAGTATAAT 57.324 33.333 0.00 0.00 0.00 1.28
5486 6624 9.502035 AATATGGATCGGAGGGAGTATAATAAA 57.498 33.333 0.00 0.00 0.00 1.40
5487 6625 7.996758 ATGGATCGGAGGGAGTATAATAAAT 57.003 36.000 0.00 0.00 0.00 1.40
5488 6626 7.182817 TGGATCGGAGGGAGTATAATAAATG 57.817 40.000 0.00 0.00 0.00 2.32
5631 6819 2.296190 AGTTGACTCTACACATGCACGA 59.704 45.455 0.00 0.00 0.00 4.35
5632 6820 2.347697 TGACTCTACACATGCACGAC 57.652 50.000 0.00 0.00 0.00 4.34
5633 6821 1.886542 TGACTCTACACATGCACGACT 59.113 47.619 0.00 0.00 0.00 4.18
5668 6856 7.717436 CCCTCCTAGAATGAAAATCTTAGTTCC 59.283 40.741 0.00 0.00 0.00 3.62
5726 6914 8.776376 ATTTTCCACTTTATATTTTGGCAGTG 57.224 30.769 0.00 0.00 32.96 3.66
5768 6957 6.841119 TGCACTGTAATGAACATGTGTTATC 58.159 36.000 0.00 0.00 38.46 1.75
5864 7053 0.465097 GCTCAGGCATGCACAGGTAT 60.465 55.000 21.36 0.00 38.54 2.73
5904 7093 1.078567 CCAGAGAGCCTGCTTCACC 60.079 63.158 0.00 0.00 41.57 4.02
5926 7115 4.025313 CCGCCTTGTTTTTGTTTAACCATG 60.025 41.667 0.00 0.00 0.00 3.66
5937 7126 6.827586 TTGTTTAACCATGATCCCTTACAC 57.172 37.500 0.00 0.00 0.00 2.90
5939 7128 5.943416 TGTTTAACCATGATCCCTTACACTG 59.057 40.000 0.00 0.00 0.00 3.66
6055 7244 9.810545 GAAGGTATACATAGATTCTGGATAAGC 57.189 37.037 5.01 0.00 0.00 3.09
6056 7245 8.001881 AGGTATACATAGATTCTGGATAAGCG 57.998 38.462 5.01 0.00 0.00 4.68
6057 7246 6.697892 GGTATACATAGATTCTGGATAAGCGC 59.302 42.308 0.00 0.00 0.00 5.92
6058 7247 4.881019 ACATAGATTCTGGATAAGCGCT 57.119 40.909 2.64 2.64 0.00 5.92
6059 7248 4.815269 ACATAGATTCTGGATAAGCGCTC 58.185 43.478 12.06 0.00 0.00 5.03
6060 7249 4.526262 ACATAGATTCTGGATAAGCGCTCT 59.474 41.667 12.06 0.00 0.00 4.09
6061 7250 5.011533 ACATAGATTCTGGATAAGCGCTCTT 59.988 40.000 12.06 0.00 36.35 2.85
6062 7251 3.726607 AGATTCTGGATAAGCGCTCTTG 58.273 45.455 12.06 0.00 33.85 3.02
6063 7252 3.386078 AGATTCTGGATAAGCGCTCTTGA 59.614 43.478 12.06 0.54 33.85 3.02
6233 7422 6.321181 TCTTCCTTGTTCTGTTTATGCAACTT 59.679 34.615 0.00 0.00 36.21 2.66
6408 7597 2.495084 GAAGTTGGTCCTCTTGTCACC 58.505 52.381 4.97 0.00 0.00 4.02
6516 7705 3.634448 AGATGGAAGAGACACTCCATACG 59.366 47.826 3.63 0.00 42.43 3.06
6519 7708 0.179134 AAGAGACACTCCATACGCGC 60.179 55.000 5.73 0.00 0.00 6.86
6738 7927 5.019470 AGTGAGTTCATGGAGAGACATACA 58.981 41.667 0.00 0.00 0.00 2.29
6786 7975 4.323417 CAGGTTATGTTGGCTACACTGAA 58.677 43.478 3.38 0.00 40.19 3.02
7044 8233 5.954752 TGACTCTGATGAGAAAGATACCAGT 59.045 40.000 0.00 0.00 42.73 4.00
7149 8338 0.749818 TGTTCCGGCAGCTGACAAAA 60.750 50.000 22.03 10.13 0.00 2.44
7475 8664 3.034635 CTCTGAGTGCCTAGTTGGGTAT 58.965 50.000 0.00 0.00 36.00 2.73
7615 8806 6.106673 TCTCTTGAAGTTCGAAGTTTGAAGT 58.893 36.000 23.93 6.58 0.00 3.01
7635 8826 7.168219 TGAAGTGAGGCACTAGAAATTGTTAT 58.832 34.615 0.00 0.00 44.62 1.89
7753 8949 5.496556 TGTTTCTGAAGAACAGTTGAAGGA 58.503 37.500 0.00 0.00 45.86 3.36
7784 8980 3.363970 CCTGCAGTTACTTGCTTTGTACG 60.364 47.826 13.81 0.00 44.38 3.67
7785 8981 3.199677 TGCAGTTACTTGCTTTGTACGT 58.800 40.909 0.00 0.00 44.38 3.57
7786 8982 4.370049 TGCAGTTACTTGCTTTGTACGTA 58.630 39.130 0.00 0.00 44.38 3.57
7789 8985 5.611844 GCAGTTACTTGCTTTGTACGTACTG 60.612 44.000 25.12 13.50 40.89 2.74
7790 8986 5.461078 CAGTTACTTGCTTTGTACGTACTGT 59.539 40.000 25.12 14.03 29.08 3.55
7791 8987 6.638063 CAGTTACTTGCTTTGTACGTACTGTA 59.362 38.462 25.12 12.58 29.08 2.74
7962 9412 1.885871 GCAGGGGTGTTTGCTCATC 59.114 57.895 0.00 0.00 37.35 2.92
8000 9451 2.531206 GTTTAATCGCTCGCTCTCTGT 58.469 47.619 0.00 0.00 0.00 3.41
8001 9452 2.476873 TTAATCGCTCGCTCTCTGTC 57.523 50.000 0.00 0.00 0.00 3.51
8016 9467 1.406898 TCTGTCGCCTAGAAGCATCAG 59.593 52.381 0.00 0.00 35.68 2.90
8085 9537 9.956720 CAAGCGAAATTTATCCTCTGATATTTT 57.043 29.630 0.00 0.00 33.54 1.82
8390 10047 8.475331 TTTTGTTTGCCATTTCGTTTAAGTTA 57.525 26.923 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 123 8.522830 CCATGTTACAATGAAAAGTGGAATACT 58.477 33.333 0.00 0.00 42.89 2.12
124 130 7.161773 AGGATCCATGTTACAATGAAAAGTG 57.838 36.000 15.82 0.00 0.00 3.16
125 131 7.065803 CGTAGGATCCATGTTACAATGAAAAGT 59.934 37.037 15.82 0.00 0.00 2.66
127 133 7.315247 CGTAGGATCCATGTTACAATGAAAA 57.685 36.000 15.82 0.00 0.00 2.29
497 512 1.678101 GGATTCGCAGAATTTCCCCTG 59.322 52.381 5.48 0.00 45.90 4.45
570 585 2.551270 ACATATATCCACATCCCGGCT 58.449 47.619 0.00 0.00 0.00 5.52
726 741 7.145932 ACCAAGCTTGATAAGTTTCATGTAC 57.854 36.000 28.05 0.00 28.82 2.90
792 809 4.772100 ACACCTAATGACCCCAAATCAAAG 59.228 41.667 0.00 0.00 0.00 2.77
873 890 3.536075 TCCGATGGTAGATCCCACATA 57.464 47.619 0.00 0.00 37.31 2.29
925 942 8.025445 AGCATTACTCAAACAGAAAACATCATC 58.975 33.333 0.00 0.00 0.00 2.92
1107 1126 2.055042 CCCGAGAGTGAGGGTCCTG 61.055 68.421 0.00 0.00 42.67 3.86
1558 1577 9.450807 GATTTTCGTGGATAAATGAAGGTAATG 57.549 33.333 0.00 0.00 0.00 1.90
1874 2017 2.936919 ATGGGAATGCAGCTCGATTA 57.063 45.000 0.00 0.00 0.00 1.75
1895 2038 2.787567 TTCCGCACACTCGTCACCA 61.788 57.895 0.00 0.00 0.00 4.17
1909 2052 6.255887 GTGAGATGAATTAACCACTAGTTCCG 59.744 42.308 0.00 0.00 40.05 4.30
1916 2059 6.176183 CAGAAGGTGAGATGAATTAACCACT 58.824 40.000 0.00 0.00 33.13 4.00
2221 2376 7.904558 AGTATCATTCTGGATTAGTCACTGA 57.095 36.000 0.00 0.00 0.00 3.41
2265 2420 1.072806 AGCTTCATTCTGCACAGGACA 59.927 47.619 0.00 0.00 0.00 4.02
2282 2437 4.335594 ACAGCGTAAAAGAAGAACAAAGCT 59.664 37.500 0.00 0.00 0.00 3.74
2393 2549 0.107017 AGATGGGCAATGAAGGTCGG 60.107 55.000 0.00 0.00 0.00 4.79
2431 2587 1.070445 CATGGTTGGCTTGCCAAAGAA 59.930 47.619 26.12 15.74 38.38 2.52
2672 2831 8.413229 AGCAAAATAAGCAAGACTTGTTCTTAA 58.587 29.630 16.39 0.00 43.23 1.85
2964 3208 5.764686 CCATTCTTATAACCTGCACAGCATA 59.235 40.000 0.00 0.00 38.13 3.14
3251 3495 6.909550 ATTAAGCATGGGTTGTTCTTTGTA 57.090 33.333 0.00 0.00 0.00 2.41
3266 3510 2.243221 ACCAGGCTCTCCAATTAAGCAT 59.757 45.455 0.00 0.00 37.78 3.79
3405 3649 9.463443 ACTCATTTACAAGCACAAAATAAACTC 57.537 29.630 0.00 0.00 0.00 3.01
3468 3714 3.737774 CACACATATCGGTATCAGTGCTG 59.262 47.826 6.16 0.00 0.00 4.41
3492 3743 4.709886 TATCACCCCGATATGGATACACTG 59.290 45.833 0.00 0.00 42.60 3.66
3515 3962 1.152963 GGCAAGCCCATGTATCCGT 60.153 57.895 0.00 0.00 0.00 4.69
3546 3994 9.066892 AGTTAAATGTATCGATGTATTGGCAAT 57.933 29.630 18.01 18.01 0.00 3.56
3597 4045 2.826128 TGACTCACAGTCCCAGTATGTC 59.174 50.000 1.23 0.00 44.44 3.06
3599 4047 2.167281 CCTGACTCACAGTCCCAGTATG 59.833 54.545 1.23 0.00 44.44 2.39
3600 4048 2.461695 CCTGACTCACAGTCCCAGTAT 58.538 52.381 1.23 0.00 44.44 2.12
3602 4050 0.833834 CCCTGACTCACAGTCCCAGT 60.834 60.000 1.23 0.00 44.44 4.00
3610 4058 0.545071 TCCATCTGCCCTGACTCACA 60.545 55.000 0.00 0.00 0.00 3.58
3611 4059 0.177604 CTCCATCTGCCCTGACTCAC 59.822 60.000 0.00 0.00 0.00 3.51
3617 4065 1.001764 TGTTGCTCCATCTGCCCTG 60.002 57.895 0.00 0.00 0.00 4.45
3618 4066 1.302285 CTGTTGCTCCATCTGCCCT 59.698 57.895 0.00 0.00 0.00 5.19
3627 4075 0.895100 TGTCCCAATGCTGTTGCTCC 60.895 55.000 0.00 0.00 40.48 4.70
3634 4082 0.107312 CCTCCTCTGTCCCAATGCTG 60.107 60.000 0.00 0.00 0.00 4.41
3689 4138 6.435430 TGTGGCATATTTTATCATATCCGC 57.565 37.500 0.00 0.00 0.00 5.54
3713 4162 8.802267 GCATTTATCAAAGGCCAAATACCTATA 58.198 33.333 5.01 0.00 41.94 1.31
3714 4163 7.670364 GCATTTATCAAAGGCCAAATACCTAT 58.330 34.615 5.01 0.00 41.94 2.57
4157 4777 9.573166 AGTAAAATCACAATAATAGGCATGCTA 57.427 29.630 18.92 8.43 0.00 3.49
4158 4778 8.469309 AGTAAAATCACAATAATAGGCATGCT 57.531 30.769 18.92 6.26 0.00 3.79
4198 4819 7.024768 CCCAATAACAACACTATAAAACACCG 58.975 38.462 0.00 0.00 0.00 4.94
4200 4821 9.783256 GATCCCAATAACAACACTATAAAACAC 57.217 33.333 0.00 0.00 0.00 3.32
4201 4822 9.521841 TGATCCCAATAACAACACTATAAAACA 57.478 29.630 0.00 0.00 0.00 2.83
4207 4828 9.342308 CACTAATGATCCCAATAACAACACTAT 57.658 33.333 0.00 0.00 0.00 2.12
4208 4829 8.544622 TCACTAATGATCCCAATAACAACACTA 58.455 33.333 0.00 0.00 0.00 2.74
4209 4830 7.402054 TCACTAATGATCCCAATAACAACACT 58.598 34.615 0.00 0.00 0.00 3.55
4210 4831 7.624360 TCACTAATGATCCCAATAACAACAC 57.376 36.000 0.00 0.00 0.00 3.32
4291 4912 1.063266 ACAAAAGCCTTGGGTCCTCAA 60.063 47.619 1.60 0.00 0.00 3.02
4294 4915 0.555769 TGACAAAAGCCTTGGGTCCT 59.444 50.000 6.36 0.00 0.00 3.85
4317 4938 8.962884 ATTTTTAAACAAGCTTGATCCTTTGT 57.037 26.923 32.50 5.43 0.00 2.83
4390 5011 9.453572 AACAGAGCAGTCATGATTAATTTTCTA 57.546 29.630 0.00 0.00 0.00 2.10
4407 5028 5.990668 AGGGTAATAACCTAAACAGAGCAG 58.009 41.667 0.00 0.00 45.95 4.24
4679 5309 9.052759 GTGACTTTATCAGACTAAACCAGAAAA 57.947 33.333 0.00 0.00 38.28 2.29
4766 5774 3.332919 GAGCAGCTCATCTTTCTTGTCA 58.667 45.455 18.17 0.00 0.00 3.58
4767 5775 2.677337 GGAGCAGCTCATCTTTCTTGTC 59.323 50.000 24.09 0.00 31.08 3.18
4786 5794 6.483307 CAGTGTCAGAAATGTTGAAACTAGGA 59.517 38.462 0.00 0.00 40.34 2.94
4795 5803 7.664082 AGATAGAACAGTGTCAGAAATGTTG 57.336 36.000 0.00 0.00 36.08 3.33
4845 5853 5.758924 TCGATATGTTTCCTGTACTCATCG 58.241 41.667 0.00 0.00 34.35 3.84
4911 5919 0.109342 CTTCAACAGTGGGCTCTGGT 59.891 55.000 12.85 5.36 39.48 4.00
5013 6021 0.366871 GATATGATAACTGCGCCGCG 59.633 55.000 8.83 8.83 0.00 6.46
5112 6134 9.627123 ACAGCTAATACCTAAGAAATAATTGCA 57.373 29.630 0.00 0.00 0.00 4.08
5150 6288 8.746922 ATGTCAAAATCATACACATTCACAAC 57.253 30.769 0.00 0.00 0.00 3.32
5327 6465 5.178096 TGAAGCATATTGGGAACTTCAGA 57.822 39.130 0.00 0.00 41.20 3.27
5352 6490 3.861840 CGAAAGTCTAGAGCAATGGGAA 58.138 45.455 0.00 0.00 0.00 3.97
5386 6524 6.109359 GTCAATTAATATGGATCGGAGGGAG 58.891 44.000 0.00 0.00 0.00 4.30
5387 6525 5.337250 CGTCAATTAATATGGATCGGAGGGA 60.337 44.000 0.00 0.00 0.00 4.20
5388 6526 4.870426 CGTCAATTAATATGGATCGGAGGG 59.130 45.833 0.00 0.00 0.00 4.30
5389 6527 4.330074 GCGTCAATTAATATGGATCGGAGG 59.670 45.833 0.00 0.00 0.00 4.30
5390 6528 5.062683 CAGCGTCAATTAATATGGATCGGAG 59.937 44.000 0.00 0.00 0.00 4.63
5391 6529 4.929211 CAGCGTCAATTAATATGGATCGGA 59.071 41.667 0.00 0.00 0.00 4.55
5392 6530 4.436050 GCAGCGTCAATTAATATGGATCGG 60.436 45.833 0.00 0.00 0.00 4.18
5393 6531 4.389992 AGCAGCGTCAATTAATATGGATCG 59.610 41.667 0.00 0.00 0.00 3.69
5394 6532 5.641209 AGAGCAGCGTCAATTAATATGGATC 59.359 40.000 0.00 0.00 0.00 3.36
5395 6533 5.555017 AGAGCAGCGTCAATTAATATGGAT 58.445 37.500 0.00 0.00 0.00 3.41
5396 6534 4.960938 AGAGCAGCGTCAATTAATATGGA 58.039 39.130 0.00 0.00 0.00 3.41
5397 6535 5.928839 ACTAGAGCAGCGTCAATTAATATGG 59.071 40.000 0.00 0.00 0.00 2.74
5398 6536 8.694975 ATACTAGAGCAGCGTCAATTAATATG 57.305 34.615 0.00 0.00 0.00 1.78
5401 6539 9.712305 AATTATACTAGAGCAGCGTCAATTAAT 57.288 29.630 0.00 0.00 0.00 1.40
5402 6540 9.542462 AAATTATACTAGAGCAGCGTCAATTAA 57.458 29.630 0.00 0.00 0.00 1.40
5403 6541 9.193133 GAAATTATACTAGAGCAGCGTCAATTA 57.807 33.333 0.00 0.00 0.00 1.40
5404 6542 7.710907 TGAAATTATACTAGAGCAGCGTCAATT 59.289 33.333 0.00 0.00 0.00 2.32
5405 6543 7.210174 TGAAATTATACTAGAGCAGCGTCAAT 58.790 34.615 0.00 0.00 0.00 2.57
5406 6544 6.569780 TGAAATTATACTAGAGCAGCGTCAA 58.430 36.000 0.00 0.00 0.00 3.18
5407 6545 6.144078 TGAAATTATACTAGAGCAGCGTCA 57.856 37.500 0.00 0.00 0.00 4.35
5408 6546 6.210078 ACTGAAATTATACTAGAGCAGCGTC 58.790 40.000 0.00 0.00 0.00 5.19
5409 6547 6.150396 ACTGAAATTATACTAGAGCAGCGT 57.850 37.500 0.00 0.00 0.00 5.07
5410 6548 7.139392 TGTACTGAAATTATACTAGAGCAGCG 58.861 38.462 0.00 0.00 0.00 5.18
5411 6549 8.873215 TTGTACTGAAATTATACTAGAGCAGC 57.127 34.615 0.00 0.00 0.00 5.25
5426 6564 9.314321 GCTGCTCTAGTATAATTTGTACTGAAA 57.686 33.333 14.11 1.73 34.43 2.69
5427 6565 7.648112 CGCTGCTCTAGTATAATTTGTACTGAA 59.352 37.037 14.11 3.69 34.43 3.02
5428 6566 7.139392 CGCTGCTCTAGTATAATTTGTACTGA 58.861 38.462 14.11 9.39 34.43 3.41
5429 6567 6.918569 ACGCTGCTCTAGTATAATTTGTACTG 59.081 38.462 14.11 6.35 34.43 2.74
5430 6568 7.040473 ACGCTGCTCTAGTATAATTTGTACT 57.960 36.000 10.22 10.22 36.44 2.73
5431 6569 6.916387 TGACGCTGCTCTAGTATAATTTGTAC 59.084 38.462 0.00 0.00 0.00 2.90
5432 6570 7.034685 TGACGCTGCTCTAGTATAATTTGTA 57.965 36.000 0.00 0.00 0.00 2.41
5433 6571 5.902681 TGACGCTGCTCTAGTATAATTTGT 58.097 37.500 0.00 0.00 0.00 2.83
5434 6572 6.828502 TTGACGCTGCTCTAGTATAATTTG 57.171 37.500 0.00 0.00 0.00 2.32
5435 6573 9.542462 TTAATTGACGCTGCTCTAGTATAATTT 57.458 29.630 0.00 0.00 0.00 1.82
5436 6574 9.712305 ATTAATTGACGCTGCTCTAGTATAATT 57.288 29.630 0.00 2.65 0.00 1.40
5439 6577 9.788960 CATATTAATTGACGCTGCTCTAGTATA 57.211 33.333 0.00 0.00 0.00 1.47
5440 6578 7.761704 CCATATTAATTGACGCTGCTCTAGTAT 59.238 37.037 0.00 0.00 0.00 2.12
5441 6579 7.039993 TCCATATTAATTGACGCTGCTCTAGTA 60.040 37.037 0.00 0.00 0.00 1.82
5442 6580 5.928839 CCATATTAATTGACGCTGCTCTAGT 59.071 40.000 0.00 0.00 0.00 2.57
5443 6581 6.159293 TCCATATTAATTGACGCTGCTCTAG 58.841 40.000 0.00 0.00 0.00 2.43
5444 6582 6.096673 TCCATATTAATTGACGCTGCTCTA 57.903 37.500 0.00 0.00 0.00 2.43
5445 6583 4.960938 TCCATATTAATTGACGCTGCTCT 58.039 39.130 0.00 0.00 0.00 4.09
5446 6584 5.445142 CGATCCATATTAATTGACGCTGCTC 60.445 44.000 0.00 0.00 0.00 4.26
5447 6585 4.389992 CGATCCATATTAATTGACGCTGCT 59.610 41.667 0.00 0.00 0.00 4.24
5448 6586 4.436050 CCGATCCATATTAATTGACGCTGC 60.436 45.833 0.00 0.00 0.00 5.25
5449 6587 4.929211 TCCGATCCATATTAATTGACGCTG 59.071 41.667 0.00 0.00 0.00 5.18
5450 6588 5.147330 TCCGATCCATATTAATTGACGCT 57.853 39.130 0.00 0.00 0.00 5.07
5451 6589 4.330074 CCTCCGATCCATATTAATTGACGC 59.670 45.833 0.00 0.00 0.00 5.19
5452 6590 4.870426 CCCTCCGATCCATATTAATTGACG 59.130 45.833 0.00 0.00 0.00 4.35
5453 6591 6.049955 TCCCTCCGATCCATATTAATTGAC 57.950 41.667 0.00 0.00 0.00 3.18
5454 6592 5.785423 ACTCCCTCCGATCCATATTAATTGA 59.215 40.000 0.00 0.00 0.00 2.57
5455 6593 6.054860 ACTCCCTCCGATCCATATTAATTG 57.945 41.667 0.00 0.00 0.00 2.32
5456 6594 7.996758 ATACTCCCTCCGATCCATATTAATT 57.003 36.000 0.00 0.00 0.00 1.40
5457 6595 9.676129 ATTATACTCCCTCCGATCCATATTAAT 57.324 33.333 0.00 0.00 0.00 1.40
5460 6598 9.502035 TTTATTATACTCCCTCCGATCCATATT 57.498 33.333 0.00 0.00 0.00 1.28
5461 6599 9.676129 ATTTATTATACTCCCTCCGATCCATAT 57.324 33.333 0.00 0.00 0.00 1.78
5462 6600 8.924303 CATTTATTATACTCCCTCCGATCCATA 58.076 37.037 0.00 0.00 0.00 2.74
5463 6601 7.623677 TCATTTATTATACTCCCTCCGATCCAT 59.376 37.037 0.00 0.00 0.00 3.41
5464 6602 6.957606 TCATTTATTATACTCCCTCCGATCCA 59.042 38.462 0.00 0.00 0.00 3.41
5465 6603 7.419711 TCATTTATTATACTCCCTCCGATCC 57.580 40.000 0.00 0.00 0.00 3.36
5466 6604 9.892130 ATTTCATTTATTATACTCCCTCCGATC 57.108 33.333 0.00 0.00 0.00 3.69
5467 6605 9.672673 CATTTCATTTATTATACTCCCTCCGAT 57.327 33.333 0.00 0.00 0.00 4.18
5468 6606 8.876181 TCATTTCATTTATTATACTCCCTCCGA 58.124 33.333 0.00 0.00 0.00 4.55
5469 6607 9.672673 ATCATTTCATTTATTATACTCCCTCCG 57.327 33.333 0.00 0.00 0.00 4.63
5501 6639 5.763204 AGGGTGAAACGGCAATATTATACAG 59.237 40.000 0.00 0.00 38.12 2.74
5511 6649 2.817258 CAGATTAAGGGTGAAACGGCAA 59.183 45.455 0.00 0.00 38.12 4.52
5609 6797 2.409715 CGTGCATGTGTAGAGTCAACTG 59.590 50.000 0.00 0.00 0.00 3.16
5610 6798 2.296190 TCGTGCATGTGTAGAGTCAACT 59.704 45.455 5.68 0.00 0.00 3.16
5631 6819 8.974292 TTCATTCTAGGAGGGCTAATAATAGT 57.026 34.615 0.00 0.00 0.00 2.12
5722 6910 5.735354 GCAAATCAGATTATTGGCTCCACTG 60.735 44.000 0.00 0.00 33.68 3.66
5726 6914 4.340381 AGTGCAAATCAGATTATTGGCTCC 59.660 41.667 0.00 0.00 36.83 4.70
5768 6957 3.059597 CGGTCACTACAGAAACAGCAAAG 60.060 47.826 0.00 0.00 0.00 2.77
5864 7053 5.200483 GGGATCACAATTATTCAGGGTCAA 58.800 41.667 0.00 0.00 0.00 3.18
5869 7058 5.933617 TCTCTGGGATCACAATTATTCAGG 58.066 41.667 0.00 0.00 0.00 3.86
5904 7093 4.806247 TCATGGTTAAACAAAAACAAGGCG 59.194 37.500 0.00 0.00 27.97 5.52
5926 7115 2.483889 GGTAGCTGCAGTGTAAGGGATC 60.484 54.545 16.64 0.00 0.00 3.36
5937 7126 0.532417 GCCTCATCAGGTAGCTGCAG 60.532 60.000 17.20 10.11 42.74 4.41
5939 7128 1.227793 GGCCTCATCAGGTAGCTGC 60.228 63.158 17.20 4.10 42.74 5.25
6052 7241 2.017049 ACACAAAACTCAAGAGCGCTT 58.983 42.857 13.26 0.00 33.74 4.68
6053 7242 1.331756 CACACAAAACTCAAGAGCGCT 59.668 47.619 11.27 11.27 0.00 5.92
6054 7243 1.330521 TCACACAAAACTCAAGAGCGC 59.669 47.619 0.00 0.00 0.00 5.92
6055 7244 3.546815 CCTTCACACAAAACTCAAGAGCG 60.547 47.826 0.00 0.00 0.00 5.03
6056 7245 3.378427 ACCTTCACACAAAACTCAAGAGC 59.622 43.478 0.00 0.00 0.00 4.09
6057 7246 5.449177 GGAACCTTCACACAAAACTCAAGAG 60.449 44.000 0.00 0.00 0.00 2.85
6058 7247 4.398044 GGAACCTTCACACAAAACTCAAGA 59.602 41.667 0.00 0.00 0.00 3.02
6059 7248 4.399303 AGGAACCTTCACACAAAACTCAAG 59.601 41.667 0.00 0.00 0.00 3.02
6060 7249 4.340617 AGGAACCTTCACACAAAACTCAA 58.659 39.130 0.00 0.00 0.00 3.02
6061 7250 3.963129 AGGAACCTTCACACAAAACTCA 58.037 40.909 0.00 0.00 0.00 3.41
6062 7251 6.445357 TTTAGGAACCTTCACACAAAACTC 57.555 37.500 0.00 0.00 0.00 3.01
6063 7252 6.183360 CCATTTAGGAACCTTCACACAAAACT 60.183 38.462 0.00 0.00 41.22 2.66
6285 7474 2.505819 GTCTCTTAATTCCCCAGCCTGA 59.494 50.000 0.00 0.00 0.00 3.86
6408 7597 2.229675 TGTGCTGAATATCTGCCTCG 57.770 50.000 6.75 0.00 40.10 4.63
6516 7705 2.198287 ATCCTGCCCAATGATGCGC 61.198 57.895 0.00 0.00 0.00 6.09
6519 7708 1.340248 GCTTCATCCTGCCCAATGATG 59.660 52.381 0.00 0.00 37.75 3.07
6738 7927 2.567169 TGATCCGATGAGTTTGGACACT 59.433 45.455 0.00 0.00 40.94 3.55
6786 7975 2.972713 TGCTTCTGTTAGTTGACCTCCT 59.027 45.455 0.00 0.00 0.00 3.69
7044 8233 6.070251 TCACCAAGCTCTTGATCCTGTTATAA 60.070 38.462 10.94 0.00 42.93 0.98
7149 8338 2.641815 AGCAATCTCTTTCACCTCCAGT 59.358 45.455 0.00 0.00 0.00 4.00
7233 8422 1.049402 CCCTATCCCGGAACTTCTCC 58.951 60.000 0.73 0.00 41.40 3.71
7615 8806 8.856153 TTACAATAACAATTTCTAGTGCCTCA 57.144 30.769 0.00 0.00 0.00 3.86
7635 8826 7.418408 TGCATCTATGTTTGTTTCGTTTACAA 58.582 30.769 0.00 0.00 33.92 2.41
7753 8949 4.878397 GCAAGTAACTGCAGGTAGATGAAT 59.122 41.667 21.98 0.00 42.17 2.57
7784 8980 8.147642 TCTAGTCGCTACCTAAAATACAGTAC 57.852 38.462 0.00 0.00 0.00 2.73
7785 8981 8.206867 TCTCTAGTCGCTACCTAAAATACAGTA 58.793 37.037 0.00 0.00 0.00 2.74
7786 8982 7.052873 TCTCTAGTCGCTACCTAAAATACAGT 58.947 38.462 0.00 0.00 0.00 3.55
7789 8985 6.205270 AGCTCTCTAGTCGCTACCTAAAATAC 59.795 42.308 2.23 0.00 31.12 1.89
7790 8986 6.297582 AGCTCTCTAGTCGCTACCTAAAATA 58.702 40.000 2.23 0.00 31.12 1.40
7791 8987 5.134661 AGCTCTCTAGTCGCTACCTAAAAT 58.865 41.667 2.23 0.00 31.12 1.82
7869 9319 7.284944 AGCTGCTTCATAATTATCTCTTGCTTT 59.715 33.333 0.00 0.00 0.00 3.51
7872 9322 6.557291 AGCTGCTTCATAATTATCTCTTGC 57.443 37.500 0.00 0.00 0.00 4.01
7878 9328 6.484643 TGACAGGAAGCTGCTTCATAATTATC 59.515 38.462 35.27 22.81 41.77 1.75
7884 9334 3.701205 TTGACAGGAAGCTGCTTCATA 57.299 42.857 35.27 17.26 41.77 2.15
7962 9412 2.098298 CACGGCGCTTTCGGATTG 59.902 61.111 6.90 0.00 35.95 2.67
8000 9451 2.297315 CCATACTGATGCTTCTAGGCGA 59.703 50.000 0.88 0.00 34.52 5.54
8001 9452 2.297315 TCCATACTGATGCTTCTAGGCG 59.703 50.000 0.88 0.00 34.52 5.52
8085 9537 3.759618 GAGAGGAAAGAGGAACGAAGAGA 59.240 47.826 0.00 0.00 0.00 3.10
8086 9538 3.761752 AGAGAGGAAAGAGGAACGAAGAG 59.238 47.826 0.00 0.00 0.00 2.85
8299 9756 3.369385 CAAGCAAAACAAGAGAGCACAG 58.631 45.455 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.