Multiple sequence alignment - TraesCS5D01G553800

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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 TraesCS5D01G553800 chr5D 100.000 4769 0 0 1 4769 558310298 558305530 0.000000e+00 8807.0
1 TraesCS5D01G553800 chr5D 82.129 1315 208 15 1084 2388 545766119 545764822 0.000000e+00 1101.0
2 TraesCS5D01G553800 chr5D 84.150 694 97 7 2401 3092 545764779 545764097 0.000000e+00 660.0
3 TraesCS5D01G553800 chr5D 84.322 472 57 13 1767 2227 545665530 545665065 3.390000e-121 446.0
4 TraesCS5D01G553800 chr5D 83.887 391 57 3 2222 2609 545664549 545664162 7.540000e-98 368.0
5 TraesCS5D01G553800 chr5D 88.360 189 19 3 4274 4461 543589094 543589280 1.730000e-54 224.0
6 TraesCS5D01G553800 chr5D 76.111 360 63 17 1368 1716 11308760 11308413 2.950000e-37 167.0
7 TraesCS5D01G553800 chr5D 84.286 140 22 0 1651 1790 545665737 545665598 2.310000e-28 137.0
8 TraesCS5D01G553800 chr5D 84.211 76 11 1 3013 3087 545649365 545649290 6.620000e-09 73.1
9 TraesCS5D01G553800 chr5B 94.481 3153 105 23 494 3641 704442096 704445184 0.000000e+00 4795.0
10 TraesCS5D01G553800 chr5B 90.881 954 59 10 3823 4769 704445681 704446613 0.000000e+00 1254.0
11 TraesCS5D01G553800 chr5B 82.460 1374 202 21 1755 3104 688552651 688551293 0.000000e+00 1166.0
12 TraesCS5D01G553800 chr5B 83.970 1204 148 25 1022 2204 571029495 571030674 0.000000e+00 1112.0
13 TraesCS5D01G553800 chr5B 96.400 500 16 2 1 499 704441560 704442058 0.000000e+00 822.0
14 TraesCS5D01G553800 chr5B 87.831 189 22 1 4274 4461 347932535 347932723 2.230000e-53 220.0
15 TraesCS5D01G553800 chr5B 93.694 111 6 1 4457 4566 704320074 704320184 1.060000e-36 165.0
16 TraesCS5D01G553800 chr5B 72.165 291 68 10 1939 2219 36554151 36553864 5.120000e-10 76.8
17 TraesCS5D01G553800 chr1A 73.905 1575 324 52 1236 2792 558502386 558500881 6.980000e-153 551.0
18 TraesCS5D01G553800 chr1A 79.720 143 27 2 2905 3046 558500768 558500627 8.440000e-18 102.0
19 TraesCS5D01G553800 chr1A 79.130 115 13 6 727 831 35946995 35946882 8.560000e-08 69.4
20 TraesCS5D01G553800 chr7A 90.576 191 16 1 4274 4462 260000837 260001027 7.920000e-63 252.0
21 TraesCS5D01G553800 chr7B 89.418 189 19 1 4275 4462 747608518 747608706 2.220000e-58 237.0
22 TraesCS5D01G553800 chr4A 89.005 191 21 0 4274 4464 737319486 737319296 2.220000e-58 237.0
23 TraesCS5D01G553800 chr4A 88.312 154 16 2 4617 4769 615110201 615110353 2.930000e-42 183.0
24 TraesCS5D01G553800 chr4A 91.892 111 8 1 4457 4566 610816698 610816808 2.300000e-33 154.0
25 TraesCS5D01G553800 chr4A 88.235 85 9 1 379 463 492156985 492157068 3.040000e-17 100.0
26 TraesCS5D01G553800 chr7D 87.895 190 22 1 4275 4463 171013123 171013312 6.210000e-54 222.0
27 TraesCS5D01G553800 chr2D 87.129 202 18 4 4572 4769 24267991 24267794 6.210000e-54 222.0
28 TraesCS5D01G553800 chr2D 97.143 35 1 0 793 827 468861071 468861105 5.150000e-05 60.2
29 TraesCS5D01G553800 chr4D 87.831 189 20 3 4274 4460 323997739 323997552 8.040000e-53 219.0
30 TraesCS5D01G553800 chr1D 86.634 202 18 7 4274 4471 315545845 315545649 1.040000e-51 215.0
31 TraesCS5D01G553800 chr6B 87.586 145 18 0 327 471 94128266 94128410 8.210000e-38 169.0
32 TraesCS5D01G553800 chr6B 95.349 43 2 0 2165 2207 641404132 641404090 8.560000e-08 69.4
33 TraesCS5D01G553800 chr1B 86.620 142 19 0 322 463 57067904 57068045 1.780000e-34 158.0
34 TraesCS5D01G553800 chr1B 97.143 35 1 0 794 828 159911082 159911048 5.150000e-05 60.2
35 TraesCS5D01G553800 chr6A 88.430 121 12 2 4651 4769 198184801 198184681 1.380000e-30 145.0
36 TraesCS5D01G553800 chr2B 86.408 103 6 2 371 473 136624500 136624594 6.530000e-19 106.0
37 TraesCS5D01G553800 chr2B 72.694 271 70 4 1929 2197 785983868 785983600 2.360000e-13 87.9
38 TraesCS5D01G553800 chr2B 89.796 49 2 3 775 821 716054815 716054862 5.150000e-05 60.2
39 TraesCS5D01G553800 chr4B 86.047 86 9 2 3449 3531 656641224 656641139 6.570000e-14 89.8
40 TraesCS5D01G553800 chr4B 94.595 37 2 0 791 827 89357657 89357693 1.850000e-04 58.4
41 TraesCS5D01G553800 chr6D 95.349 43 2 0 2165 2207 426108861 426108819 8.560000e-08 69.4
42 TraesCS5D01G553800 chr6D 90.196 51 4 1 3959 4009 147691841 147691792 1.110000e-06 65.8
43 TraesCS5D01G553800 chr6D 97.143 35 1 0 794 828 277340757 277340723 5.150000e-05 60.2
44 TraesCS5D01G553800 chr3D 90.385 52 2 3 778 828 519317306 519317355 1.110000e-06 65.8
45 TraesCS5D01G553800 chr3B 88.462 52 4 2 778 828 756831321 756831271 1.430000e-05 62.1


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 TraesCS5D01G553800 chr5D 558305530 558310298 4768 True 8807.000000 8807 100.000000 1 4769 1 chr5D.!!$R3 4768
1 TraesCS5D01G553800 chr5D 545764097 545766119 2022 True 880.500000 1101 83.139500 1084 3092 2 chr5D.!!$R5 2008
2 TraesCS5D01G553800 chr5D 545664162 545665737 1575 True 317.000000 446 84.165000 1651 2609 3 chr5D.!!$R4 958
3 TraesCS5D01G553800 chr5B 704441560 704446613 5053 False 2290.333333 4795 93.920667 1 4769 3 chr5B.!!$F4 4768
4 TraesCS5D01G553800 chr5B 688551293 688552651 1358 True 1166.000000 1166 82.460000 1755 3104 1 chr5B.!!$R2 1349
5 TraesCS5D01G553800 chr5B 571029495 571030674 1179 False 1112.000000 1112 83.970000 1022 2204 1 chr5B.!!$F2 1182
6 TraesCS5D01G553800 chr1A 558500627 558502386 1759 True 326.500000 551 76.812500 1236 3046 2 chr1A.!!$R2 1810

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
472 473 1.078848 CGAACAAGCTCTCAGGGGG 60.079 63.158 0.00 0.0 0.00 5.40 F
1069 1113 0.398239 AGCAGATGCAGAGGCTAGGA 60.398 55.000 7.68 0.0 45.16 2.94 F
2369 3047 0.868406 GGCTGGTGAAGAAAGTGACG 59.132 55.000 0.00 0.0 0.00 4.35 F
3065 3787 0.033796 AACTAGGGGATGTCGGTCGA 60.034 55.000 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2148 0.248866 CGCACCGGAATAAAATGCCC 60.249 55.0 9.46 0.00 32.55 5.36 R
2750 3464 0.898789 CTGGAGTACCACTGACCGGT 60.899 60.0 6.92 6.92 41.77 5.28 R
3252 3974 0.030195 TCATAGGATGGCTGGGTGGA 60.030 55.0 0.00 0.00 0.00 4.02 R
4421 5525 0.034767 CCTTTGGCCTCTGCATCTGA 60.035 55.0 3.32 0.00 40.13 3.27 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
148 149 6.424812 TCAAGTACAAGGATGAATATGCATCG 59.575 38.462 16.16 6.57 44.35 3.84
154 155 7.642669 ACAAGGATGAATATGCATCGTAAAAG 58.357 34.615 17.36 11.12 44.35 2.27
155 156 7.283127 ACAAGGATGAATATGCATCGTAAAAGT 59.717 33.333 17.36 11.62 44.35 2.66
202 203 3.058914 GTGGTTCCTGAATGTTGAAGACG 60.059 47.826 0.00 0.00 0.00 4.18
203 204 3.181459 TGGTTCCTGAATGTTGAAGACGA 60.181 43.478 0.00 0.00 0.00 4.20
250 251 5.154932 GCATATCTACGAACGTCTAGCATT 58.845 41.667 2.45 0.00 0.00 3.56
278 279 2.325082 ACGTCGATTGGCCTGCAAC 61.325 57.895 3.32 0.00 0.00 4.17
346 347 2.027469 CAGGCCTAGTTCGGTTAAACCT 60.027 50.000 3.98 0.00 35.66 3.50
467 468 3.462483 TTGTAACCGAACAAGCTCTCA 57.538 42.857 0.00 0.00 34.50 3.27
472 473 1.078848 CGAACAAGCTCTCAGGGGG 60.079 63.158 0.00 0.00 0.00 5.40
473 474 1.544825 CGAACAAGCTCTCAGGGGGA 61.545 60.000 0.00 0.00 0.00 4.81
509 553 1.679680 GATGGTGGTCTGCATCAATGG 59.320 52.381 0.00 0.00 0.00 3.16
545 589 3.387947 GGTCCTTCGCCTTCCGGA 61.388 66.667 0.00 0.00 37.59 5.14
546 590 2.184579 GTCCTTCGCCTTCCGGAG 59.815 66.667 3.34 0.00 42.42 4.63
581 625 2.358003 AGCTCAAGTGCTCCGTGC 60.358 61.111 0.00 0.00 39.34 5.34
595 639 3.682858 GCTCCGTGCTGAACAGTAAAATA 59.317 43.478 3.77 0.00 38.95 1.40
596 640 4.153475 GCTCCGTGCTGAACAGTAAAATAA 59.847 41.667 3.77 0.00 38.95 1.40
723 767 7.581213 TTTAAAGATGAAGTTTCTCAGGCAA 57.419 32.000 0.00 0.00 0.00 4.52
737 781 8.611757 GTTTCTCAGGCAATTAAAACATTTGTT 58.388 29.630 0.00 0.00 40.50 2.83
750 794 7.913674 AAAACATTTGTTAAAGTTTGCCAGA 57.086 28.000 0.00 0.00 37.25 3.86
751 795 7.913674 AAACATTTGTTAAAGTTTGCCAGAA 57.086 28.000 0.00 0.00 37.25 3.02
752 796 7.913674 AACATTTGTTAAAGTTTGCCAGAAA 57.086 28.000 0.00 0.00 36.32 2.52
753 797 7.913674 ACATTTGTTAAAGTTTGCCAGAAAA 57.086 28.000 0.00 0.00 0.00 2.29
754 798 8.504812 ACATTTGTTAAAGTTTGCCAGAAAAT 57.495 26.923 0.00 0.00 0.00 1.82
755 799 8.397148 ACATTTGTTAAAGTTTGCCAGAAAATG 58.603 29.630 0.00 8.35 37.33 2.32
756 800 7.913674 TTTGTTAAAGTTTGCCAGAAAATGT 57.086 28.000 0.00 0.00 0.00 2.71
757 801 7.913674 TTGTTAAAGTTTGCCAGAAAATGTT 57.086 28.000 0.00 0.00 0.00 2.71
758 802 7.913674 TGTTAAAGTTTGCCAGAAAATGTTT 57.086 28.000 0.00 0.00 0.00 2.83
759 803 7.746929 TGTTAAAGTTTGCCAGAAAATGTTTG 58.253 30.769 0.00 0.00 0.00 2.93
760 804 7.389053 TGTTAAAGTTTGCCAGAAAATGTTTGT 59.611 29.630 0.00 0.00 0.00 2.83
761 805 8.874816 GTTAAAGTTTGCCAGAAAATGTTTGTA 58.125 29.630 0.00 0.00 0.00 2.41
762 806 7.538303 AAAGTTTGCCAGAAAATGTTTGTAG 57.462 32.000 0.00 0.00 0.00 2.74
763 807 6.463995 AGTTTGCCAGAAAATGTTTGTAGA 57.536 33.333 0.00 0.00 0.00 2.59
764 808 6.872920 AGTTTGCCAGAAAATGTTTGTAGAA 58.127 32.000 0.00 0.00 0.00 2.10
765 809 6.756542 AGTTTGCCAGAAAATGTTTGTAGAAC 59.243 34.615 0.00 0.00 0.00 3.01
766 810 6.463995 TTGCCAGAAAATGTTTGTAGAACT 57.536 33.333 0.00 0.00 0.00 3.01
840 884 1.545651 GGACTTTCACCCTTGGTCCTG 60.546 57.143 0.00 0.00 42.04 3.86
897 941 4.899352 AGAGCTGTTGTTGATTAGGAGT 57.101 40.909 0.00 0.00 0.00 3.85
933 977 6.906848 TGGGGTCCCATCTTAATTAGTTAAG 58.093 40.000 10.98 10.64 42.94 1.85
935 979 5.469084 GGGTCCCATCTTAATTAGTTAAGCG 59.531 44.000 11.78 6.48 44.15 4.68
938 982 6.202379 GTCCCATCTTAATTAGTTAAGCGGAC 59.798 42.308 21.64 21.64 44.15 4.79
1049 1093 2.680913 CCACGTGGCTGCTTGTAGC 61.681 63.158 24.02 2.09 42.82 3.58
1069 1113 0.398239 AGCAGATGCAGAGGCTAGGA 60.398 55.000 7.68 0.00 45.16 2.94
1271 1324 5.707764 GGAAATCCAGTTGCTAGTTCTTCTT 59.292 40.000 0.00 0.00 35.64 2.52
1312 1365 2.170607 TCCTCTTCTTTAATGGCGGAGG 59.829 50.000 13.58 13.58 39.88 4.30
1359 1412 5.202004 TGCTTAGGTTTTCTTTGTGGGTAA 58.798 37.500 0.00 0.00 0.00 2.85
1618 1671 2.054021 TGTGTTCTGGGAGTCCATGAA 58.946 47.619 12.30 11.39 43.11 2.57
1636 1689 4.476752 GGGTCGCCGCCACCATAA 62.477 66.667 9.54 0.00 35.35 1.90
1887 2032 1.774254 ACCAGATGGAAGTTCACCACA 59.226 47.619 5.72 0.00 40.36 4.17
1910 2055 7.663493 CACAGAGAGGTAGTGACATCAGATATA 59.337 40.741 0.00 0.00 38.88 0.86
1997 2142 0.978146 AGGCTATGGTGCTTCGGACT 60.978 55.000 0.00 0.00 0.00 3.85
2003 2148 0.895530 TGGTGCTTCGGACTAAGAGG 59.104 55.000 0.00 0.00 0.00 3.69
2285 2963 1.398692 TCAGGCCTTTGTGGTCAAAC 58.601 50.000 0.00 0.00 44.59 2.93
2369 3047 0.868406 GGCTGGTGAAGAAAGTGACG 59.132 55.000 0.00 0.00 0.00 4.35
2750 3464 6.136155 TCTGGTCACATATCCTGAGATGTTA 58.864 40.000 4.74 0.00 40.85 2.41
2865 3587 3.670091 GCCTATGGTCGACGAGCTATTAC 60.670 52.174 25.62 10.58 0.00 1.89
2882 3604 6.014156 AGCTATTACTAGAGTTGGGGCTAATG 60.014 42.308 0.00 0.00 0.00 1.90
2903 3625 2.093783 GGAAGTCGATTTAAGTGGCACG 59.906 50.000 12.71 0.00 0.00 5.34
3003 3725 1.741032 GCACAGCTGAGCAGAGGAC 60.741 63.158 28.20 0.00 0.00 3.85
3065 3787 0.033796 AACTAGGGGATGTCGGTCGA 60.034 55.000 0.00 0.00 0.00 4.20
3137 3859 3.636231 TTGCTCCCACCCCGTCTG 61.636 66.667 0.00 0.00 0.00 3.51
3157 3879 2.506472 GAATCCGCCTCTCCCACC 59.494 66.667 0.00 0.00 0.00 4.61
3218 3940 1.154205 CGACCATCAAGCCGGATGAC 61.154 60.000 5.05 8.67 46.00 3.06
3230 3952 1.153349 GGATGACGGAACAGCTCCC 60.153 63.158 0.00 0.00 41.87 4.30
3238 3960 1.920835 GAACAGCTCCCTCCACCCT 60.921 63.158 0.00 0.00 0.00 4.34
3239 3961 2.190488 GAACAGCTCCCTCCACCCTG 62.190 65.000 0.00 0.00 0.00 4.45
3240 3962 4.106925 CAGCTCCCTCCACCCTGC 62.107 72.222 0.00 0.00 0.00 4.85
3241 3963 4.664267 AGCTCCCTCCACCCTGCA 62.664 66.667 0.00 0.00 0.00 4.41
3242 3964 4.106925 GCTCCCTCCACCCTGCAG 62.107 72.222 6.78 6.78 0.00 4.41
3243 3965 4.106925 CTCCCTCCACCCTGCAGC 62.107 72.222 8.66 0.00 0.00 5.25
3246 3968 4.421515 CCTCCACCCTGCAGCCAG 62.422 72.222 8.66 1.22 38.85 4.85
3253 3975 4.486503 CCTGCAGCCAGCTCCCTC 62.487 72.222 8.66 0.00 45.94 4.30
3254 3976 4.486503 CTGCAGCCAGCTCCCTCC 62.487 72.222 0.00 0.00 45.94 4.30
3256 3978 4.792804 GCAGCCAGCTCCCTCCAC 62.793 72.222 0.00 0.00 41.15 4.02
3257 3979 4.106925 CAGCCAGCTCCCTCCACC 62.107 72.222 0.00 0.00 0.00 4.61
3279 4001 0.403271 GCCATCCTATGAGCCATGGT 59.597 55.000 14.67 0.00 38.49 3.55
3341 4063 4.943705 AGTCGTTAGATGCACAATCCATTT 59.056 37.500 0.00 0.00 35.72 2.32
3344 4066 5.589855 TCGTTAGATGCACAATCCATTTGAT 59.410 36.000 0.00 0.00 38.76 2.57
3347 4069 7.431249 GTTAGATGCACAATCCATTTGATGAT 58.569 34.615 0.00 0.00 38.76 2.45
3348 4070 6.085555 AGATGCACAATCCATTTGATGATC 57.914 37.500 0.00 0.00 38.76 2.92
3352 4074 6.103330 TGCACAATCCATTTGATGATCTTTG 58.897 36.000 0.00 0.00 38.76 2.77
3353 4075 6.103997 GCACAATCCATTTGATGATCTTTGT 58.896 36.000 0.00 0.00 38.76 2.83
3354 4076 7.093858 TGCACAATCCATTTGATGATCTTTGTA 60.094 33.333 0.00 0.00 38.76 2.41
3355 4077 7.221452 GCACAATCCATTTGATGATCTTTGTAC 59.779 37.037 0.00 0.00 38.76 2.90
3356 4078 7.703621 CACAATCCATTTGATGATCTTTGTACC 59.296 37.037 0.00 0.00 38.76 3.34
3357 4079 7.396907 ACAATCCATTTGATGATCTTTGTACCA 59.603 33.333 0.00 0.00 38.76 3.25
3358 4080 7.578310 ATCCATTTGATGATCTTTGTACCAG 57.422 36.000 0.00 0.00 30.54 4.00
3392 4117 0.249120 TGTGTGTAAGCCTCGATGGG 59.751 55.000 3.56 0.00 36.00 4.00
3437 4162 7.054491 AGTGAAATGTGAATTTGGTTTAGCT 57.946 32.000 0.00 0.00 0.00 3.32
3438 4163 6.925165 AGTGAAATGTGAATTTGGTTTAGCTG 59.075 34.615 0.00 0.00 0.00 4.24
3439 4164 6.146021 GTGAAATGTGAATTTGGTTTAGCTGG 59.854 38.462 0.00 0.00 0.00 4.85
3548 4273 5.360429 TCATCATATGGAATTTGGTGGTGTG 59.640 40.000 2.13 0.00 37.07 3.82
3595 4320 4.023536 TGGTTCAAAGAAATAAGCGTCACC 60.024 41.667 0.00 0.00 0.00 4.02
3617 4342 0.588980 GGCTTAAATACGCAGCGTGC 60.589 55.000 30.67 22.28 41.39 5.34
3641 4366 2.033801 AGCTAGCTAAATTTGCATGCGG 59.966 45.455 17.69 0.00 36.55 5.69
3642 4367 2.388121 CTAGCTAAATTTGCATGCGGC 58.612 47.619 14.09 8.21 45.13 6.53
3656 4381 3.455152 CGGCATCCGTCCCTCATA 58.545 61.111 0.00 0.00 42.73 2.15
3657 4382 1.975327 CGGCATCCGTCCCTCATAT 59.025 57.895 0.00 0.00 42.73 1.78
3658 4383 0.390340 CGGCATCCGTCCCTCATATG 60.390 60.000 0.00 0.00 42.73 1.78
3659 4384 0.674895 GGCATCCGTCCCTCATATGC 60.675 60.000 0.00 0.00 41.69 3.14
3660 4385 0.035317 GCATCCGTCCCTCATATGCA 59.965 55.000 0.00 0.00 41.94 3.96
3661 4386 1.943046 GCATCCGTCCCTCATATGCAG 60.943 57.143 0.00 0.00 41.94 4.41
3662 4387 1.620323 CATCCGTCCCTCATATGCAGA 59.380 52.381 0.00 0.00 0.00 4.26
3663 4388 2.015456 TCCGTCCCTCATATGCAGAT 57.985 50.000 0.00 0.00 0.00 2.90
3664 4389 1.620323 TCCGTCCCTCATATGCAGATG 59.380 52.381 15.24 15.24 0.00 2.90
3665 4390 1.338484 CCGTCCCTCATATGCAGATGG 60.338 57.143 20.58 11.36 0.00 3.51
3666 4391 1.345741 CGTCCCTCATATGCAGATGGT 59.654 52.381 20.58 0.00 0.00 3.55
3667 4392 2.775890 GTCCCTCATATGCAGATGGTG 58.224 52.381 20.58 13.42 0.00 4.17
3679 4404 1.466167 CAGATGGTGCCAAAGACTTCG 59.534 52.381 0.00 0.00 0.00 3.79
3680 4405 1.072331 AGATGGTGCCAAAGACTTCGT 59.928 47.619 0.00 0.00 0.00 3.85
3681 4406 1.464997 GATGGTGCCAAAGACTTCGTC 59.535 52.381 0.00 0.00 0.00 4.20
3682 4407 0.179234 TGGTGCCAAAGACTTCGTCA 59.821 50.000 0.00 0.00 34.60 4.35
3683 4408 0.868406 GGTGCCAAAGACTTCGTCAG 59.132 55.000 0.00 0.00 34.60 3.51
3684 4409 0.868406 GTGCCAAAGACTTCGTCAGG 59.132 55.000 0.00 0.00 34.60 3.86
3685 4410 0.756294 TGCCAAAGACTTCGTCAGGA 59.244 50.000 0.00 0.00 34.60 3.86
3686 4411 1.270305 TGCCAAAGACTTCGTCAGGAG 60.270 52.381 0.00 0.00 34.60 3.69
3687 4412 1.941668 GCCAAAGACTTCGTCAGGAGG 60.942 57.143 0.00 0.00 34.60 4.30
3688 4413 1.344763 CCAAAGACTTCGTCAGGAGGT 59.655 52.381 0.00 0.00 37.73 3.85
3689 4414 2.224305 CCAAAGACTTCGTCAGGAGGTT 60.224 50.000 0.00 0.00 34.71 3.50
3690 4415 2.802816 CAAAGACTTCGTCAGGAGGTTG 59.197 50.000 0.00 0.00 34.71 3.77
3691 4416 0.318762 AGACTTCGTCAGGAGGTTGC 59.681 55.000 0.00 0.00 34.71 4.17
3692 4417 0.033504 GACTTCGTCAGGAGGTTGCA 59.966 55.000 0.00 0.00 34.71 4.08
3693 4418 0.249911 ACTTCGTCAGGAGGTTGCAC 60.250 55.000 0.00 0.00 29.31 4.57
3694 4419 0.249868 CTTCGTCAGGAGGTTGCACA 60.250 55.000 0.00 0.00 0.00 4.57
3695 4420 0.396435 TTCGTCAGGAGGTTGCACAT 59.604 50.000 0.00 0.00 0.00 3.21
3696 4421 0.320683 TCGTCAGGAGGTTGCACATG 60.321 55.000 0.00 0.00 0.00 3.21
3697 4422 0.320683 CGTCAGGAGGTTGCACATGA 60.321 55.000 0.00 0.00 0.00 3.07
3698 4423 1.877680 CGTCAGGAGGTTGCACATGAA 60.878 52.381 0.00 0.00 0.00 2.57
3699 4424 2.229792 GTCAGGAGGTTGCACATGAAA 58.770 47.619 0.00 0.00 0.00 2.69
3700 4425 2.821969 GTCAGGAGGTTGCACATGAAAT 59.178 45.455 0.00 0.00 0.00 2.17
3701 4426 3.256631 GTCAGGAGGTTGCACATGAAATT 59.743 43.478 0.00 0.00 0.00 1.82
3702 4427 3.256383 TCAGGAGGTTGCACATGAAATTG 59.744 43.478 0.00 0.00 0.00 2.32
3703 4428 2.564062 AGGAGGTTGCACATGAAATTGG 59.436 45.455 0.00 0.00 0.00 3.16
3704 4429 2.299867 GGAGGTTGCACATGAAATTGGT 59.700 45.455 0.00 0.00 0.00 3.67
3705 4430 3.319755 GAGGTTGCACATGAAATTGGTG 58.680 45.455 0.00 0.00 35.68 4.17
3717 4442 2.496899 AATTGGTGTCTCTTCGCCAT 57.503 45.000 0.00 0.00 45.56 4.40
3742 4467 3.810941 GTGTGGTGTGATCTCGGTAAAAA 59.189 43.478 0.00 0.00 0.00 1.94
3750 4475 3.122278 TGATCTCGGTAAAAAGCGAAACG 59.878 43.478 1.19 0.00 0.00 3.60
3762 4487 0.247537 GCGAAACGTGGCCTTTATCG 60.248 55.000 3.32 9.15 0.00 2.92
3770 4495 4.007659 ACGTGGCCTTTATCGAAAAGAAT 58.992 39.130 16.62 0.00 0.00 2.40
3775 4500 7.218204 CGTGGCCTTTATCGAAAAGAATAAAAG 59.782 37.037 16.62 1.54 32.01 2.27
3778 4503 7.665080 CCTTTATCGAAAAGAATAAAAGGCG 57.335 36.000 16.62 0.00 38.88 5.52
3779 4504 7.469260 CCTTTATCGAAAAGAATAAAAGGCGA 58.531 34.615 16.62 0.00 38.88 5.54
3780 4505 7.966204 CCTTTATCGAAAAGAATAAAAGGCGAA 59.034 33.333 16.62 0.00 38.88 4.70
3781 4506 9.337091 CTTTATCGAAAAGAATAAAAGGCGAAA 57.663 29.630 12.07 0.00 0.00 3.46
3782 4507 8.663771 TTATCGAAAAGAATAAAAGGCGAAAC 57.336 30.769 0.00 0.00 0.00 2.78
3783 4508 5.141568 TCGAAAAGAATAAAAGGCGAAACG 58.858 37.500 0.00 0.00 0.00 3.60
3784 4509 4.907582 CGAAAAGAATAAAAGGCGAAACGT 59.092 37.500 0.00 0.00 0.00 3.99
3786 4511 5.427036 AAAGAATAAAAGGCGAAACGTCA 57.573 34.783 0.00 0.00 32.13 4.35
3787 4512 4.663636 AGAATAAAAGGCGAAACGTCAG 57.336 40.909 0.00 0.00 32.13 3.51
3788 4513 4.312443 AGAATAAAAGGCGAAACGTCAGA 58.688 39.130 0.00 0.00 32.13 3.27
3789 4514 4.753107 AGAATAAAAGGCGAAACGTCAGAA 59.247 37.500 0.00 0.00 32.13 3.02
3790 4515 2.750301 AAAAGGCGAAACGTCAGAAC 57.250 45.000 0.00 0.00 32.13 3.01
3791 4516 1.658994 AAAGGCGAAACGTCAGAACA 58.341 45.000 0.00 0.00 32.13 3.18
3813 4538 6.357367 ACAATGAAATCACTAGATGGTACCC 58.643 40.000 10.07 0.00 33.90 3.69
3839 4942 3.487544 GCAAAGGTCACACACACTTTCTC 60.488 47.826 0.00 0.00 31.31 2.87
3846 4949 4.065088 TCACACACACTTTCTCTAATGGC 58.935 43.478 0.00 0.00 0.00 4.40
3892 4995 8.119226 GTGCTACATTTTGTCATAATCTGAGTC 58.881 37.037 0.00 0.00 33.51 3.36
3978 5082 3.701241 TGTTTTCACCATTGCGTTTCTC 58.299 40.909 0.00 0.00 0.00 2.87
4073 5177 1.273606 CAAGAAAGGCTGGAGACGAGA 59.726 52.381 0.00 0.00 0.00 4.04
4145 5249 9.646427 ACACAAACACTTAAAAAGCTGAAATAA 57.354 25.926 0.00 0.00 0.00 1.40
4177 5281 8.558700 CAAAAACCCAAGAAAATTGAATACCAG 58.441 33.333 0.00 0.00 0.00 4.00
4206 5310 3.502191 TGTGCTTCACTTTTCACAACC 57.498 42.857 0.00 0.00 36.62 3.77
4270 5374 2.350676 GCACATTGCGATGTCTGTTTGA 60.351 45.455 17.05 0.00 44.55 2.69
4285 5389 7.936584 TGTCTGTTTGAAAGTTTGGTATTAGG 58.063 34.615 0.00 0.00 0.00 2.69
4296 5400 5.010820 AGTTTGGTATTAGGCTCGGACTATC 59.989 44.000 0.00 0.00 0.00 2.08
4298 5402 3.080319 GGTATTAGGCTCGGACTATCGT 58.920 50.000 0.00 0.00 0.00 3.73
4321 5425 3.455910 CACCCCTTCATCAAGTGGATAGA 59.544 47.826 0.00 0.00 31.72 1.98
4328 5432 6.407412 CCTTCATCAAGTGGATAGAAGTAGCA 60.407 42.308 13.90 0.00 38.31 3.49
4358 5462 9.102757 GATGTTGCTAAGATAATGACTTCAGAA 57.897 33.333 0.00 0.00 0.00 3.02
4421 5525 9.826574 ATTAATAAAATTGTTGCATGCATCTCT 57.173 25.926 23.37 9.31 0.00 3.10
4424 5528 4.371855 AATTGTTGCATGCATCTCTCAG 57.628 40.909 23.37 0.00 0.00 3.35
4436 5540 0.325016 TCTCTCAGATGCAGAGGCCA 60.325 55.000 5.01 0.00 38.39 5.36
4440 5544 0.034767 TCAGATGCAGAGGCCAAAGG 60.035 55.000 5.01 0.00 40.13 3.11
4446 5550 0.034670 GCAGAGGCCAAAGGTCATCT 60.035 55.000 5.01 0.00 0.00 2.90
4521 5630 2.634815 ATGAGATGCCTAGTGCCTTG 57.365 50.000 1.42 0.00 40.16 3.61
4534 5643 3.406764 AGTGCCTTGAAAGAAGCTGTAG 58.593 45.455 0.00 0.00 0.00 2.74
4597 5706 8.818622 AAAAGGTTTCTCCCCACTTTATATAC 57.181 34.615 0.00 0.00 36.75 1.47
4598 5707 7.519347 AAGGTTTCTCCCCACTTTATATACA 57.481 36.000 0.00 0.00 36.75 2.29
4599 5708 7.519347 AGGTTTCTCCCCACTTTATATACAA 57.481 36.000 0.00 0.00 36.75 2.41
4600 5709 7.935405 AGGTTTCTCCCCACTTTATATACAAA 58.065 34.615 0.00 0.00 36.75 2.83
4601 5710 8.053355 AGGTTTCTCCCCACTTTATATACAAAG 58.947 37.037 1.87 1.87 37.93 2.77
4602 5711 7.201794 GGTTTCTCCCCACTTTATATACAAAGC 60.202 40.741 3.35 0.00 38.79 3.51
4603 5712 6.569127 TCTCCCCACTTTATATACAAAGCA 57.431 37.500 3.35 0.00 38.79 3.91
4604 5713 6.964464 TCTCCCCACTTTATATACAAAGCAA 58.036 36.000 3.35 0.00 38.79 3.91
4605 5714 6.826741 TCTCCCCACTTTATATACAAAGCAAC 59.173 38.462 3.35 0.00 38.79 4.17
4606 5715 5.889289 TCCCCACTTTATATACAAAGCAACC 59.111 40.000 3.35 0.00 38.79 3.77
4607 5716 5.654650 CCCCACTTTATATACAAAGCAACCA 59.345 40.000 3.35 0.00 38.79 3.67
4608 5717 6.323739 CCCCACTTTATATACAAAGCAACCAT 59.676 38.462 3.35 0.00 38.79 3.55
4609 5718 7.425606 CCCACTTTATATACAAAGCAACCATC 58.574 38.462 3.35 0.00 38.79 3.51
4610 5719 7.068103 CCCACTTTATATACAAAGCAACCATCA 59.932 37.037 3.35 0.00 38.79 3.07
4611 5720 7.915397 CCACTTTATATACAAAGCAACCATCAC 59.085 37.037 3.35 0.00 38.79 3.06
4612 5721 7.915397 CACTTTATATACAAAGCAACCATCACC 59.085 37.037 3.35 0.00 38.79 4.02
4618 5727 1.238439 AAGCAACCATCACCGAACAG 58.762 50.000 0.00 0.00 0.00 3.16
4631 5740 1.566018 CGAACAGACCGAAACCTGCC 61.566 60.000 0.00 0.00 33.90 4.85
4648 5757 2.139917 TGCCGATACAAACACACACTC 58.860 47.619 0.00 0.00 0.00 3.51
4662 5771 0.392461 ACACTCCACACCACACACAC 60.392 55.000 0.00 0.00 0.00 3.82
4691 5800 3.424433 CGGGATACAAAGACGCTGAAAAC 60.424 47.826 0.00 0.00 39.74 2.43
4692 5801 3.119955 GGGATACAAAGACGCTGAAAACC 60.120 47.826 0.00 0.00 39.74 3.27
4734 5844 7.765695 AATCCTAGCAAACATCAGAAGAAAA 57.234 32.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 7.807977 ACTTTTACGATGCATATTCATCCTT 57.192 32.000 9.39 0.68 39.64 3.36
148 149 4.578928 TGTCAGAAGGGAAGCAACTTTTAC 59.421 41.667 0.00 0.00 0.00 2.01
154 155 4.301628 CATTTTGTCAGAAGGGAAGCAAC 58.698 43.478 0.00 0.00 0.00 4.17
155 156 3.243839 GCATTTTGTCAGAAGGGAAGCAA 60.244 43.478 0.00 0.00 0.00 3.91
202 203 3.891049 ACCAAGCAAATAGGTGATCCTC 58.109 45.455 0.00 0.00 43.94 3.71
250 251 1.740585 CCAATCGACGTGGCCAATTAA 59.259 47.619 7.24 0.00 0.00 1.40
304 305 4.570926 TGAAGGAGATTACATGGGAGGAT 58.429 43.478 0.00 0.00 0.00 3.24
346 347 3.563261 CCTCTTCAGTCCTCTCCAAGAGA 60.563 52.174 5.54 0.00 45.07 3.10
360 361 0.321671 TCGCCTCCAAACCTCTTCAG 59.678 55.000 0.00 0.00 0.00 3.02
421 422 4.322725 GGTTTGAAGGGGATTGAAATGGAC 60.323 45.833 0.00 0.00 0.00 4.02
463 464 0.712979 ATGTCTCACTCCCCCTGAGA 59.287 55.000 0.00 0.00 44.42 3.27
467 468 1.630878 GAACAATGTCTCACTCCCCCT 59.369 52.381 0.00 0.00 0.00 4.79
472 473 4.391216 CACCATCTGAACAATGTCTCACTC 59.609 45.833 0.00 0.00 0.00 3.51
473 474 4.321718 CACCATCTGAACAATGTCTCACT 58.678 43.478 0.00 0.00 0.00 3.41
509 553 2.945668 ACCTCTTCCGCTATCAAATTGC 59.054 45.455 0.00 0.00 0.00 3.56
545 589 2.196925 CGGGAGCAGATAGTCCGCT 61.197 63.158 0.00 0.00 39.12 5.52
546 590 2.136196 CTCGGGAGCAGATAGTCCGC 62.136 65.000 0.00 0.00 40.42 5.54
627 671 9.670719 TTTGTCAAAGTTTTCCAAACAAAAATC 57.329 25.926 0.00 0.00 33.60 2.17
737 781 8.470805 TCTACAAACATTTTCTGGCAAACTTTA 58.529 29.630 0.00 0.00 0.00 1.85
840 884 1.929836 GATGTTGACGTCTGAGATGGC 59.070 52.381 17.92 3.16 0.00 4.40
897 941 0.040499 GGACCCCAATTGGTTAGGCA 59.960 55.000 22.91 0.00 39.24 4.75
935 979 1.070786 TGTTCCTTCGGTGCAGTCC 59.929 57.895 0.00 0.00 0.00 3.85
938 982 0.034059 AGAGTGTTCCTTCGGTGCAG 59.966 55.000 0.00 0.00 0.00 4.41
983 1027 7.678194 ATTTGTACAAAACATGTTGTTCTCG 57.322 32.000 23.97 0.00 40.14 4.04
986 1030 8.868916 AGTCAATTTGTACAAAACATGTTGTTC 58.131 29.630 23.97 17.61 40.14 3.18
1049 1093 0.249953 CCTAGCCTCTGCATCTGCTG 60.250 60.000 12.65 3.22 42.66 4.41
1188 1241 8.616076 GGTTGTTCACTGGATTAATTCTCTATG 58.384 37.037 0.00 0.00 0.00 2.23
1312 1365 1.258982 CATCAGTGCTATTTCGCCGAC 59.741 52.381 0.00 0.00 0.00 4.79
1636 1689 6.319658 CACAAATATACCTGGAAGAAGCACAT 59.680 38.462 0.00 0.00 34.07 3.21
1887 2032 7.750655 TGTATATCTGATGTCACTACCTCTCT 58.249 38.462 0.00 0.00 0.00 3.10
1997 2142 3.203487 ACCGGAATAAAATGCCCCTCTTA 59.797 43.478 9.46 0.00 0.00 2.10
2003 2148 0.248866 CGCACCGGAATAAAATGCCC 60.249 55.000 9.46 0.00 32.55 5.36
2285 2963 2.442236 AGTTGTATTGCCCCATGGAG 57.558 50.000 15.22 0.00 0.00 3.86
2369 3047 5.537188 CTGACCACTAGGCTTGATATCTTC 58.463 45.833 2.20 0.00 39.06 2.87
2543 3257 1.250328 TCAGCAATGGACCAAGCTTG 58.750 50.000 19.93 19.93 34.61 4.01
2647 3361 1.538419 CCGAAAGATCCGGGAGTAAGC 60.538 57.143 0.00 0.00 43.05 3.09
2723 3437 4.871822 TCTCAGGATATGTGACCAGAAGA 58.128 43.478 0.00 0.00 0.00 2.87
2750 3464 0.898789 CTGGAGTACCACTGACCGGT 60.899 60.000 6.92 6.92 41.77 5.28
2865 3587 3.456277 ACTTCCATTAGCCCCAACTCTAG 59.544 47.826 0.00 0.00 0.00 2.43
2882 3604 2.093783 CGTGCCACTTAAATCGACTTCC 59.906 50.000 0.00 0.00 0.00 3.46
2903 3625 8.729805 AGTCTCTCATCTCATTTAATGTTTCC 57.270 34.615 4.77 0.00 0.00 3.13
3003 3725 2.154462 AGCAAATGTGAGAAACTCCCG 58.846 47.619 0.00 0.00 0.00 5.14
3065 3787 6.427853 GGCTTGTAAAATTGAAATTGAAGGCT 59.572 34.615 0.00 0.00 31.49 4.58
3119 3841 3.637273 AGACGGGGTGGGAGCAAC 61.637 66.667 0.00 0.00 0.00 4.17
3120 3842 3.636231 CAGACGGGGTGGGAGCAA 61.636 66.667 0.00 0.00 0.00 3.91
3142 3864 2.444895 GAGGTGGGAGAGGCGGAT 60.445 66.667 0.00 0.00 0.00 4.18
3160 3882 1.796749 GTCGTCGTTCTCGGCTGAC 60.797 63.158 0.00 0.00 39.73 3.51
3239 3961 4.792804 GTGGAGGGAGCTGGCTGC 62.793 72.222 8.47 8.47 43.29 5.25
3240 3962 4.106925 GGTGGAGGGAGCTGGCTG 62.107 72.222 0.00 0.00 0.00 4.85
3243 3965 3.406200 CTGGGTGGAGGGAGCTGG 61.406 72.222 0.00 0.00 0.00 4.85
3244 3966 4.106925 GCTGGGTGGAGGGAGCTG 62.107 72.222 0.00 0.00 0.00 4.24
3247 3969 2.693864 ATGGCTGGGTGGAGGGAG 60.694 66.667 0.00 0.00 0.00 4.30
3248 3970 2.692368 GATGGCTGGGTGGAGGGA 60.692 66.667 0.00 0.00 0.00 4.20
3249 3971 2.914734 TAGGATGGCTGGGTGGAGGG 62.915 65.000 0.00 0.00 0.00 4.30
3250 3972 0.769776 ATAGGATGGCTGGGTGGAGG 60.770 60.000 0.00 0.00 0.00 4.30
3251 3973 0.399454 CATAGGATGGCTGGGTGGAG 59.601 60.000 0.00 0.00 0.00 3.86
3252 3974 0.030195 TCATAGGATGGCTGGGTGGA 60.030 55.000 0.00 0.00 0.00 4.02
3253 3975 0.399454 CTCATAGGATGGCTGGGTGG 59.601 60.000 0.00 0.00 0.00 4.61
3254 3976 0.250640 GCTCATAGGATGGCTGGGTG 60.251 60.000 0.00 0.00 0.00 4.61
3255 3977 1.422161 GGCTCATAGGATGGCTGGGT 61.422 60.000 0.00 0.00 0.00 4.51
3256 3978 1.377994 GGCTCATAGGATGGCTGGG 59.622 63.158 0.00 0.00 0.00 4.45
3257 3979 0.697079 ATGGCTCATAGGATGGCTGG 59.303 55.000 0.00 0.00 0.00 4.85
3258 3980 1.613520 CCATGGCTCATAGGATGGCTG 60.614 57.143 0.00 0.00 0.00 4.85
3329 4051 6.103997 ACAAAGATCATCAAATGGATTGTGC 58.896 36.000 0.00 0.00 40.11 4.57
3364 4089 5.069119 TCGAGGCTTACACACATAATCTGAT 59.931 40.000 0.00 0.00 0.00 2.90
3373 4098 0.249120 CCCATCGAGGCTTACACACA 59.751 55.000 0.00 0.00 35.39 3.72
3400 4125 7.160547 TCACATTTCACTCATATGCATTTGT 57.839 32.000 15.51 2.98 0.00 2.83
3437 4162 2.700371 CACATGTCATAGAGTAGCCCCA 59.300 50.000 0.00 0.00 0.00 4.96
3438 4163 2.037772 CCACATGTCATAGAGTAGCCCC 59.962 54.545 0.00 0.00 0.00 5.80
3439 4164 2.037772 CCCACATGTCATAGAGTAGCCC 59.962 54.545 0.00 0.00 0.00 5.19
3520 4245 6.322201 ACCACCAAATTCCATATGATGAACTC 59.678 38.462 3.65 0.00 0.00 3.01
3527 4252 4.928263 TCACACCACCAAATTCCATATGA 58.072 39.130 3.65 0.00 0.00 2.15
3539 4264 2.208132 ACACTTTGTTCACACCACCA 57.792 45.000 0.00 0.00 0.00 4.17
3548 4273 8.063630 CCAAAGCATCAAAATAACACTTTGTTC 58.936 33.333 10.58 0.00 40.22 3.18
3595 4320 1.396996 ACGCTGCGTATTTAAGCCTTG 59.603 47.619 27.89 0.00 38.73 3.61
3617 4342 3.800506 GCATGCAAATTTAGCTAGCTTGG 59.199 43.478 24.88 2.96 32.85 3.61
3641 4366 0.035317 TGCATATGAGGGACGGATGC 59.965 55.000 6.97 0.00 42.57 3.91
3642 4367 1.620323 TCTGCATATGAGGGACGGATG 59.380 52.381 6.97 0.00 0.00 3.51
3643 4368 2.015456 TCTGCATATGAGGGACGGAT 57.985 50.000 6.97 0.00 0.00 4.18
3644 4369 1.620323 CATCTGCATATGAGGGACGGA 59.380 52.381 6.97 0.00 0.00 4.69
3645 4370 1.338484 CCATCTGCATATGAGGGACGG 60.338 57.143 13.31 0.00 37.55 4.79
3646 4371 1.345741 ACCATCTGCATATGAGGGACG 59.654 52.381 13.31 0.00 37.55 4.79
3647 4372 2.775890 CACCATCTGCATATGAGGGAC 58.224 52.381 13.31 0.00 37.55 4.46
3648 4373 1.072806 GCACCATCTGCATATGAGGGA 59.927 52.381 13.31 1.09 46.29 4.20
3649 4374 1.531423 GCACCATCTGCATATGAGGG 58.469 55.000 13.31 8.50 46.29 4.30
3658 4383 1.200948 GAAGTCTTTGGCACCATCTGC 59.799 52.381 0.00 0.00 46.31 4.26
3659 4384 1.466167 CGAAGTCTTTGGCACCATCTG 59.534 52.381 0.00 0.00 0.00 2.90
3660 4385 1.072331 ACGAAGTCTTTGGCACCATCT 59.928 47.619 4.81 0.00 29.74 2.90
3661 4386 1.523758 ACGAAGTCTTTGGCACCATC 58.476 50.000 4.81 0.00 29.74 3.51
3662 4387 3.725754 ACGAAGTCTTTGGCACCAT 57.274 47.368 4.81 0.00 29.74 3.55
3674 4399 2.913631 TGTGCAACCTCCTGACGAAGT 61.914 52.381 0.00 0.00 40.07 3.01
3675 4400 0.249868 TGTGCAACCTCCTGACGAAG 60.250 55.000 0.00 0.00 34.36 3.79
3676 4401 0.396435 ATGTGCAACCTCCTGACGAA 59.604 50.000 0.00 0.00 34.36 3.85
3677 4402 0.320683 CATGTGCAACCTCCTGACGA 60.321 55.000 0.00 0.00 34.36 4.20
3678 4403 0.320683 TCATGTGCAACCTCCTGACG 60.321 55.000 0.00 0.00 34.36 4.35
3679 4404 1.896220 TTCATGTGCAACCTCCTGAC 58.104 50.000 0.00 0.00 34.36 3.51
3680 4405 2.655090 TTTCATGTGCAACCTCCTGA 57.345 45.000 0.00 0.00 34.36 3.86
3681 4406 3.581755 CAATTTCATGTGCAACCTCCTG 58.418 45.455 0.00 0.00 34.36 3.86
3682 4407 2.564062 CCAATTTCATGTGCAACCTCCT 59.436 45.455 0.00 0.00 34.36 3.69
3683 4408 2.299867 ACCAATTTCATGTGCAACCTCC 59.700 45.455 0.00 0.00 34.36 4.30
3684 4409 3.243839 ACACCAATTTCATGTGCAACCTC 60.244 43.478 0.00 0.00 34.36 3.85
3685 4410 2.699846 ACACCAATTTCATGTGCAACCT 59.300 40.909 0.00 0.00 34.36 3.50
3686 4411 3.059166 GACACCAATTTCATGTGCAACC 58.941 45.455 0.00 0.00 34.36 3.77
3687 4412 3.981211 AGACACCAATTTCATGTGCAAC 58.019 40.909 0.00 0.00 33.30 4.17
3688 4413 3.890756 AGAGACACCAATTTCATGTGCAA 59.109 39.130 0.00 0.00 33.30 4.08
3689 4414 3.489355 AGAGACACCAATTTCATGTGCA 58.511 40.909 0.00 0.00 33.30 4.57
3690 4415 4.479619 GAAGAGACACCAATTTCATGTGC 58.520 43.478 0.00 0.00 33.30 4.57
3691 4416 4.715896 CGAAGAGACACCAATTTCATGTG 58.284 43.478 0.00 0.00 36.11 3.21
3692 4417 3.189287 GCGAAGAGACACCAATTTCATGT 59.811 43.478 0.00 0.00 0.00 3.21
3693 4418 3.426695 GGCGAAGAGACACCAATTTCATG 60.427 47.826 0.00 0.00 0.00 3.07
3694 4419 2.749621 GGCGAAGAGACACCAATTTCAT 59.250 45.455 0.00 0.00 0.00 2.57
3695 4420 2.151202 GGCGAAGAGACACCAATTTCA 58.849 47.619 0.00 0.00 0.00 2.69
3696 4421 2.151202 TGGCGAAGAGACACCAATTTC 58.849 47.619 0.00 0.00 28.76 2.17
3697 4422 2.270352 TGGCGAAGAGACACCAATTT 57.730 45.000 0.00 0.00 28.76 1.82
3698 4423 2.086869 CATGGCGAAGAGACACCAATT 58.913 47.619 0.00 0.00 43.31 2.32
3699 4424 1.003580 ACATGGCGAAGAGACACCAAT 59.996 47.619 0.00 0.00 43.31 3.16
3700 4425 0.396435 ACATGGCGAAGAGACACCAA 59.604 50.000 0.00 0.00 43.31 3.67
3701 4426 0.320683 CACATGGCGAAGAGACACCA 60.321 55.000 0.00 0.00 43.31 4.17
3702 4427 0.320771 ACACATGGCGAAGAGACACC 60.321 55.000 0.00 0.00 43.31 4.16
3703 4428 0.792640 CACACATGGCGAAGAGACAC 59.207 55.000 0.00 0.00 43.31 3.67
3704 4429 0.392706 ACACACATGGCGAAGAGACA 59.607 50.000 0.00 0.00 45.56 3.41
3705 4430 0.792640 CACACACATGGCGAAGAGAC 59.207 55.000 0.00 0.00 0.00 3.36
3717 4442 0.033366 CCGAGATCACACCACACACA 59.967 55.000 0.00 0.00 0.00 3.72
3742 4467 1.084289 GATAAAGGCCACGTTTCGCT 58.916 50.000 5.01 0.00 0.00 4.93
3750 4475 7.488150 CCTTTTATTCTTTTCGATAAAGGCCAC 59.512 37.037 5.01 0.00 0.00 5.01
3762 4487 5.910723 TGACGTTTCGCCTTTTATTCTTTTC 59.089 36.000 0.00 0.00 0.00 2.29
3770 4495 3.196463 TGTTCTGACGTTTCGCCTTTTA 58.804 40.909 0.00 0.00 0.00 1.52
3775 4500 1.529438 TCATTGTTCTGACGTTTCGCC 59.471 47.619 0.00 0.00 0.00 5.54
3777 4502 5.336990 GTGATTTCATTGTTCTGACGTTTCG 59.663 40.000 0.00 0.00 0.00 3.46
3778 4503 6.430451 AGTGATTTCATTGTTCTGACGTTTC 58.570 36.000 0.00 0.00 0.00 2.78
3779 4504 6.377327 AGTGATTTCATTGTTCTGACGTTT 57.623 33.333 0.00 0.00 0.00 3.60
3780 4505 6.929049 TCTAGTGATTTCATTGTTCTGACGTT 59.071 34.615 0.00 0.00 0.00 3.99
3781 4506 6.455647 TCTAGTGATTTCATTGTTCTGACGT 58.544 36.000 0.00 0.00 0.00 4.34
3782 4507 6.951256 TCTAGTGATTTCATTGTTCTGACG 57.049 37.500 0.00 0.00 0.00 4.35
3783 4508 7.335422 ACCATCTAGTGATTTCATTGTTCTGAC 59.665 37.037 0.00 0.00 0.00 3.51
3784 4509 7.397221 ACCATCTAGTGATTTCATTGTTCTGA 58.603 34.615 0.00 0.00 0.00 3.27
3786 4511 7.770897 GGTACCATCTAGTGATTTCATTGTTCT 59.229 37.037 7.15 0.00 0.00 3.01
3787 4512 7.920738 GGTACCATCTAGTGATTTCATTGTTC 58.079 38.462 7.15 0.00 0.00 3.18
3788 4513 7.865706 GGTACCATCTAGTGATTTCATTGTT 57.134 36.000 7.15 0.00 0.00 2.83
3789 4514 8.744296 AGGGGTACCATCTAGTGATTTCATTGT 61.744 40.741 15.35 0.00 40.34 2.71
3790 4515 6.409695 AGGGGTACCATCTAGTGATTTCATTG 60.410 42.308 15.35 0.00 40.34 2.82
3791 4516 5.672194 AGGGGTACCATCTAGTGATTTCATT 59.328 40.000 15.35 0.00 40.34 2.57
3839 4942 1.715585 CGCCACTTGTCGCCATTAG 59.284 57.895 0.00 0.00 0.00 1.73
3846 4949 4.374702 GCAGTGCGCCACTTGTCG 62.375 66.667 4.18 0.00 42.59 4.35
3927 5031 6.404734 GGACGCATGGTTCAAGAGATAATTTT 60.405 38.462 0.00 0.00 0.00 1.82
3928 5032 5.066505 GGACGCATGGTTCAAGAGATAATTT 59.933 40.000 0.00 0.00 0.00 1.82
3929 5033 4.576463 GGACGCATGGTTCAAGAGATAATT 59.424 41.667 0.00 0.00 0.00 1.40
3930 5034 4.130118 GGACGCATGGTTCAAGAGATAAT 58.870 43.478 0.00 0.00 0.00 1.28
3948 5052 0.309302 TGGTGAAAACATTGCGGACG 59.691 50.000 0.00 0.00 0.00 4.79
3949 5053 2.723124 ATGGTGAAAACATTGCGGAC 57.277 45.000 0.00 0.00 0.00 4.79
3978 5082 6.516478 TCTTATTTCGAAGATCTCAATGCG 57.484 37.500 0.00 0.00 35.04 4.73
3999 5103 6.365520 GTCCAAACCTATTTACATGGGATCT 58.634 40.000 0.00 0.00 34.53 2.75
4040 5144 3.257375 GCCTTTCTTGGTATCCGGTTTTT 59.743 43.478 0.00 0.00 0.00 1.94
4045 5149 1.668419 CAGCCTTTCTTGGTATCCGG 58.332 55.000 0.00 0.00 0.00 5.14
4046 5150 1.209504 TCCAGCCTTTCTTGGTATCCG 59.790 52.381 0.00 0.00 0.00 4.18
4160 5264 7.288810 TGTGCTTCTGGTATTCAATTTTCTT 57.711 32.000 0.00 0.00 0.00 2.52
4218 5322 7.698130 GGTATGAAAAATCACAGTTGTGCTATC 59.302 37.037 7.38 2.91 45.25 2.08
4270 5374 4.019591 AGTCCGAGCCTAATACCAAACTTT 60.020 41.667 0.00 0.00 0.00 2.66
4296 5400 1.442769 CACTTGATGAAGGGGTGACG 58.557 55.000 0.00 0.00 32.95 4.35
4328 5432 8.798859 AAGTCATTATCTTAGCAACATCTGTT 57.201 30.769 0.00 0.00 39.12 3.16
4420 5524 1.380524 CTTTGGCCTCTGCATCTGAG 58.619 55.000 3.32 0.00 40.13 3.35
4421 5525 0.034767 CCTTTGGCCTCTGCATCTGA 60.035 55.000 3.32 0.00 40.13 3.27
4424 5528 0.322816 TGACCTTTGGCCTCTGCATC 60.323 55.000 3.32 0.00 40.13 3.91
4521 5630 4.600012 TTATTGCGCTACAGCTTCTTTC 57.400 40.909 9.73 0.00 39.32 2.62
4585 5694 7.915397 GTGATGGTTGCTTTGTATATAAAGTGG 59.085 37.037 19.42 0.81 39.33 4.00
4589 5698 6.824196 TCGGTGATGGTTGCTTTGTATATAAA 59.176 34.615 0.00 0.00 0.00 1.40
4590 5699 6.350103 TCGGTGATGGTTGCTTTGTATATAA 58.650 36.000 0.00 0.00 0.00 0.98
4591 5700 5.919755 TCGGTGATGGTTGCTTTGTATATA 58.080 37.500 0.00 0.00 0.00 0.86
4592 5701 4.776349 TCGGTGATGGTTGCTTTGTATAT 58.224 39.130 0.00 0.00 0.00 0.86
4594 5703 3.066291 TCGGTGATGGTTGCTTTGTAT 57.934 42.857 0.00 0.00 0.00 2.29
4595 5704 2.550606 GTTCGGTGATGGTTGCTTTGTA 59.449 45.455 0.00 0.00 0.00 2.41
4596 5705 1.336755 GTTCGGTGATGGTTGCTTTGT 59.663 47.619 0.00 0.00 0.00 2.83
4597 5706 1.336440 TGTTCGGTGATGGTTGCTTTG 59.664 47.619 0.00 0.00 0.00 2.77
4598 5707 1.608590 CTGTTCGGTGATGGTTGCTTT 59.391 47.619 0.00 0.00 0.00 3.51
4599 5708 1.202758 TCTGTTCGGTGATGGTTGCTT 60.203 47.619 0.00 0.00 0.00 3.91
4600 5709 0.396435 TCTGTTCGGTGATGGTTGCT 59.604 50.000 0.00 0.00 0.00 3.91
4601 5710 0.517316 GTCTGTTCGGTGATGGTTGC 59.483 55.000 0.00 0.00 0.00 4.17
4602 5711 1.156736 GGTCTGTTCGGTGATGGTTG 58.843 55.000 0.00 0.00 0.00 3.77
4603 5712 0.320421 CGGTCTGTTCGGTGATGGTT 60.320 55.000 0.00 0.00 0.00 3.67
4604 5713 1.183030 TCGGTCTGTTCGGTGATGGT 61.183 55.000 0.00 0.00 0.00 3.55
4605 5714 0.037697 TTCGGTCTGTTCGGTGATGG 60.038 55.000 0.00 0.00 0.00 3.51
4606 5715 1.459592 GTTTCGGTCTGTTCGGTGATG 59.540 52.381 0.00 0.00 0.00 3.07
4607 5716 1.607251 GGTTTCGGTCTGTTCGGTGAT 60.607 52.381 0.00 0.00 0.00 3.06
4608 5717 0.249573 GGTTTCGGTCTGTTCGGTGA 60.250 55.000 0.00 0.00 0.00 4.02
4609 5718 0.249741 AGGTTTCGGTCTGTTCGGTG 60.250 55.000 0.00 0.00 0.00 4.94
4610 5719 0.249741 CAGGTTTCGGTCTGTTCGGT 60.250 55.000 0.00 0.00 0.00 4.69
4611 5720 1.566018 GCAGGTTTCGGTCTGTTCGG 61.566 60.000 0.00 0.00 33.81 4.30
4612 5721 1.566018 GGCAGGTTTCGGTCTGTTCG 61.566 60.000 0.00 0.00 33.81 3.95
4618 5727 0.108520 TGTATCGGCAGGTTTCGGTC 60.109 55.000 0.00 0.00 0.00 4.79
4631 5740 3.059868 GTGTGGAGTGTGTGTTTGTATCG 60.060 47.826 0.00 0.00 0.00 2.92
4648 5757 1.379176 TTGGGTGTGTGTGGTGTGG 60.379 57.895 0.00 0.00 0.00 4.17
4691 5800 1.970092 TTTGTTGGGGTAGTGTTCGG 58.030 50.000 0.00 0.00 0.00 4.30
4692 5801 3.057806 GGATTTTGTTGGGGTAGTGTTCG 60.058 47.826 0.00 0.00 0.00 3.95
4734 5844 5.181245 ACAACTTCGTAGCAATGCTTATTGT 59.819 36.000 14.85 11.92 40.44 2.71


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

AutoCloner maintained by Alex Coulton.