Multiple sequence alignment - TraesCS3A01G057700

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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 TraesCS3A01G057700 chr3A 100.000 4902 0 0 1 4902 33586337 33581436 0.000000e+00 9053.0
1 TraesCS3A01G057700 chr3A 83.298 1407 185 37 310 1696 193611274 193609898 0.000000e+00 1251.0
2 TraesCS3A01G057700 chr3A 82.806 1390 180 35 310 1663 33287650 33289016 0.000000e+00 1188.0
3 TraesCS3A01G057700 chr3A 80.000 915 143 22 3069 3975 193607951 193607069 1.490000e-179 640.0
4 TraesCS3A01G057700 chr3A 79.286 980 147 29 3006 3975 33289887 33290820 6.920000e-178 634.0
5 TraesCS3A01G057700 chr3A 72.600 1281 276 53 402 1655 33427218 33425986 7.810000e-93 351.0
6 TraesCS3A01G057700 chr3A 72.274 1284 275 51 402 1655 193602988 193601756 1.700000e-84 324.0
7 TraesCS3A01G057700 chr3D 94.416 4459 166 26 139 4557 24103960 24099545 0.000000e+00 6778.0
8 TraesCS3A01G057700 chr3D 90.813 283 19 2 2799 3081 24063310 24063035 5.990000e-99 372.0
9 TraesCS3A01G057700 chr3D 86.567 134 2 5 1 134 24104167 24104050 3.080000e-27 134.0
10 TraesCS3A01G057700 chr3B 95.160 2066 70 12 2293 4342 41353395 41351344 0.000000e+00 3234.0
11 TraesCS3A01G057700 chr3B 93.895 2162 79 11 171 2302 41356820 41354682 0.000000e+00 3212.0
12 TraesCS3A01G057700 chr3B 82.581 1395 190 38 286 1654 41430438 41429071 0.000000e+00 1181.0
13 TraesCS3A01G057700 chr3B 78.896 924 146 36 3070 3978 41428403 41427514 9.150000e-162 580.0
14 TraesCS3A01G057700 chr3B 73.110 1283 260 61 402 1652 41251496 41252725 3.580000e-101 379.0
15 TraesCS3A01G057700 chr3B 93.827 81 3 1 54 134 41357000 41356922 2.400000e-23 121.0
16 TraesCS3A01G057700 chr6D 88.794 1401 109 19 1936 3328 411497231 411495871 0.000000e+00 1674.0
17 TraesCS3A01G057700 chr6D 83.669 1690 208 35 176 1827 411498913 411497254 0.000000e+00 1530.0
18 TraesCS3A01G057700 chr6D 88.975 771 73 4 3398 4161 411495866 411495101 0.000000e+00 942.0
19 TraesCS3A01G057700 chr6D 88.000 375 31 9 4175 4549 411495049 411494689 9.750000e-117 431.0
20 TraesCS3A01G057700 chr6A 87.836 1414 113 24 1936 3334 556100601 556099232 0.000000e+00 1604.0
21 TraesCS3A01G057700 chr6A 83.254 1690 215 36 176 1827 556102283 556100624 0.000000e+00 1491.0
22 TraesCS3A01G057700 chr6A 88.586 771 76 4 3398 4161 556099232 556098467 0.000000e+00 926.0
23 TraesCS3A01G057700 chr6A 84.646 254 23 11 4175 4418 556098415 556098168 6.340000e-59 239.0
24 TraesCS3A01G057700 chr6A 90.441 136 10 1 4414 4549 556096561 556096429 5.040000e-40 176.0
25 TraesCS3A01G057700 chr6A 78.656 253 48 5 403 655 556094348 556094102 3.930000e-36 163.0
26 TraesCS3A01G057700 chr1B 73.036 560 122 25 1280 1832 624503210 624503747 2.350000e-38 171.0
27 TraesCS3A01G057700 chr1B 76.324 321 65 10 1270 1586 624088105 624088418 1.410000e-35 161.0
28 TraesCS3A01G057700 chr1B 75.000 216 49 5 3551 3764 624501772 624501984 1.450000e-15 95.3
29 TraesCS3A01G057700 chr1A 74.766 321 70 10 1270 1586 548531943 548532256 3.080000e-27 134.0
30 TraesCS3A01G057700 chr6B 90.244 82 7 1 4822 4902 5679980 5679899 6.710000e-19 106.0
31 TraesCS3A01G057700 chr1D 75.115 217 47 7 3551 3764 453964743 453964955 1.450000e-15 95.3


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 TraesCS3A01G057700 chr3A 33581436 33586337 4901 True 9053.00 9053 100.000000 1 4902 1 chr3A.!!$R2 4901
1 TraesCS3A01G057700 chr3A 193607069 193611274 4205 True 945.50 1251 81.649000 310 3975 2 chr3A.!!$R4 3665
2 TraesCS3A01G057700 chr3A 33287650 33290820 3170 False 911.00 1188 81.046000 310 3975 2 chr3A.!!$F1 3665
3 TraesCS3A01G057700 chr3A 33425986 33427218 1232 True 351.00 351 72.600000 402 1655 1 chr3A.!!$R1 1253
4 TraesCS3A01G057700 chr3A 193601756 193602988 1232 True 324.00 324 72.274000 402 1655 1 chr3A.!!$R3 1253
5 TraesCS3A01G057700 chr3D 24099545 24104167 4622 True 3456.00 6778 90.491500 1 4557 2 chr3D.!!$R2 4556
6 TraesCS3A01G057700 chr3B 41351344 41357000 5656 True 2189.00 3234 94.294000 54 4342 3 chr3B.!!$R1 4288
7 TraesCS3A01G057700 chr3B 41427514 41430438 2924 True 880.50 1181 80.738500 286 3978 2 chr3B.!!$R2 3692
8 TraesCS3A01G057700 chr3B 41251496 41252725 1229 False 379.00 379 73.110000 402 1652 1 chr3B.!!$F1 1250
9 TraesCS3A01G057700 chr6D 411494689 411498913 4224 True 1144.25 1674 87.359500 176 4549 4 chr6D.!!$R1 4373
10 TraesCS3A01G057700 chr6A 556094102 556102283 8181 True 766.50 1604 85.569833 176 4549 6 chr6A.!!$R1 4373

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
228 317 0.398696 TGAAGTAACACCGCCACCAT 59.601 50.0 0.00 0.00 0.00 3.55 F
250 342 0.683179 CCAACCTTTCCCCGGATTCC 60.683 60.0 0.73 0.00 0.00 3.01 F
953 1097 0.873721 CATGTGTTGTCGACATGGCA 59.126 50.0 20.80 17.46 44.68 4.92 F
2275 2760 0.324943 TGCTAGGGCCAGTGTCTTTC 59.675 55.0 6.18 0.00 37.74 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 1400 0.104672 TCCCACTTGTCCCAGGAGAA 60.105 55.0 0.00 0.0 0.00 2.87 R
1484 1644 0.883833 CTGGACCATTGCTTCCACAC 59.116 55.0 0.00 0.0 36.96 3.82 R
2734 4532 1.032657 GCCAGTCTAGAGTCCGCAGA 61.033 60.0 10.15 0.0 0.00 4.26 R
4161 7372 0.179045 ATATCAGGTCCGTTGCTGCC 60.179 55.0 0.00 0.0 0.00 4.85 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
26 27 0.878416 TAGCCGTTGGATTTGTGTGC 59.122 50.000 0.00 0.00 0.00 4.57
51 52 4.639171 TGCGCTCGCTTGACACGA 62.639 61.111 9.73 0.00 42.51 4.35
72 73 4.274700 GCCGCGCCGTAGTGGATA 62.275 66.667 0.00 0.00 44.18 2.59
151 179 3.767806 GGGTTCCCCGTCCTCGAC 61.768 72.222 0.00 0.00 39.71 4.20
216 305 2.490903 GTCGCCTCTGTACCTGAAGTAA 59.509 50.000 0.00 0.00 31.05 2.24
221 310 3.367087 CCTCTGTACCTGAAGTAACACCG 60.367 52.174 0.00 0.00 31.05 4.94
228 317 0.398696 TGAAGTAACACCGCCACCAT 59.601 50.000 0.00 0.00 0.00 3.55
250 342 0.683179 CCAACCTTTCCCCGGATTCC 60.683 60.000 0.73 0.00 0.00 3.01
917 1061 4.440181 TGTCGTTGCGGCACTTAA 57.560 50.000 0.05 0.00 36.25 1.85
928 1072 2.699954 CGGCACTTAACCAAGTCTGAT 58.300 47.619 0.00 0.00 43.30 2.90
953 1097 0.873721 CATGTGTTGTCGACATGGCA 59.126 50.000 20.80 17.46 44.68 4.92
967 1114 1.749063 CATGGCATGTCACAGCAGATT 59.251 47.619 19.32 0.00 0.00 2.40
996 1144 1.002868 CTCACTGGGCTGGGTTGAG 60.003 63.158 0.00 0.00 0.00 3.02
1240 1400 1.051812 CACTGTGTGGGAGAGGAAGT 58.948 55.000 0.00 0.00 0.00 3.01
1484 1644 0.890683 GTTGACATGGAAAGGGCAGG 59.109 55.000 0.00 0.00 0.00 4.85
1499 1659 1.181098 GCAGGTGTGGAAGCAATGGT 61.181 55.000 0.00 0.00 0.00 3.55
1523 1686 2.557490 AGTTCTCTCTTGGACGGTACAC 59.443 50.000 0.00 0.00 0.00 2.90
1593 1756 0.768221 TGACCCCAGGTGCTTCTTCT 60.768 55.000 0.00 0.00 35.25 2.85
1595 1758 0.984995 ACCCCAGGTGCTTCTTCTAC 59.015 55.000 0.00 0.00 32.98 2.59
1610 1774 6.569127 TTCTTCTACCTTTATGCCCATGTA 57.431 37.500 0.00 0.00 0.00 2.29
1611 1775 6.569127 TCTTCTACCTTTATGCCCATGTAA 57.431 37.500 0.00 0.00 0.00 2.41
1612 1776 7.149202 TCTTCTACCTTTATGCCCATGTAAT 57.851 36.000 0.00 0.00 0.00 1.89
1613 1777 8.270137 TCTTCTACCTTTATGCCCATGTAATA 57.730 34.615 0.00 0.00 0.00 0.98
1684 2135 4.685169 ATGTGCTTAGGACAATGTTTCG 57.315 40.909 11.14 0.00 0.00 3.46
1848 2314 1.671979 CAGCATGGACCCTGTGTATG 58.328 55.000 0.00 0.00 0.00 2.39
1849 2315 0.548031 AGCATGGACCCTGTGTATGG 59.452 55.000 0.00 0.00 0.00 2.74
1850 2316 0.546122 GCATGGACCCTGTGTATGGA 59.454 55.000 0.00 0.00 0.00 3.41
1851 2317 1.747206 GCATGGACCCTGTGTATGGAC 60.747 57.143 0.00 0.00 0.00 4.02
1852 2318 1.839994 CATGGACCCTGTGTATGGACT 59.160 52.381 0.00 0.00 0.00 3.85
1853 2319 2.932184 TGGACCCTGTGTATGGACTA 57.068 50.000 0.00 0.00 0.00 2.59
1854 2320 3.414759 TGGACCCTGTGTATGGACTAT 57.585 47.619 0.00 0.00 0.00 2.12
1921 2387 9.905713 AACACACATCATATATTCTGTAACCTT 57.094 29.630 0.00 0.00 0.00 3.50
1965 2439 3.125146 TGCACGATGAAATAGCTGTTGAC 59.875 43.478 0.00 0.00 0.00 3.18
2046 2529 5.969423 TCCCATACCTAGTTAACTTGTTCG 58.031 41.667 14.49 2.06 0.00 3.95
2112 2595 3.019564 CTCATCCATTCCTCCAACCAAC 58.980 50.000 0.00 0.00 0.00 3.77
2178 2663 6.096705 TCCATGAACCGAATTAAAGCATCAAT 59.903 34.615 0.00 0.00 0.00 2.57
2275 2760 0.324943 TGCTAGGGCCAGTGTCTTTC 59.675 55.000 6.18 0.00 37.74 2.62
2488 4273 3.357203 TGCTGACGGGGCAATAAAATTA 58.643 40.909 0.00 0.00 36.71 1.40
2550 4336 8.557029 CCTTTTTATCTAACTGTTTCGTTGTCT 58.443 33.333 0.00 0.00 0.00 3.41
2557 4343 7.259882 TCTAACTGTTTCGTTGTCTCAAACTA 58.740 34.615 0.00 0.00 32.28 2.24
2734 4532 0.680921 AGCAGTGTGTGGTGCAAGTT 60.681 50.000 0.00 0.00 42.47 2.66
2874 6022 3.684788 GCATGTTTAGACCGTTGATCTGT 59.315 43.478 0.00 0.00 0.00 3.41
2993 6145 8.579682 AAATTTTATGTGCTTTCACTCTTCAC 57.420 30.769 0.00 0.00 43.49 3.18
2994 6146 6.691754 TTTTATGTGCTTTCACTCTTCACA 57.308 33.333 0.00 0.00 43.49 3.58
3034 6186 4.216257 TCTTGGTGAACATCTTAAGCAAGC 59.784 41.667 5.39 0.00 44.06 4.01
3486 6690 8.895737 AGCATTCTTGGGCAATTATTTAAATTG 58.104 29.630 5.91 0.84 39.84 2.32
3520 6724 5.715439 TCCCATTGTGACTGAATCCTAAT 57.285 39.130 0.00 0.00 0.00 1.73
3555 6765 8.640063 ATGCAGATGGTAAAATATGCTAATGA 57.360 30.769 5.51 0.00 43.56 2.57
3851 7062 6.751888 CGGAGCCCTTAGTGATTTTAATTTTG 59.248 38.462 0.00 0.00 0.00 2.44
4008 7219 5.185056 GGCAAAGAATACAGTTTATGGGTGT 59.815 40.000 0.00 0.00 0.00 4.16
4009 7220 6.092748 GCAAAGAATACAGTTTATGGGTGTG 58.907 40.000 0.00 0.00 0.00 3.82
4038 7249 6.541641 GCTACTGAGATTGATGTCCTTTCATT 59.458 38.462 0.00 0.00 0.00 2.57
4057 7268 4.288366 TCATTGGGACTGGTATCAAGTTCA 59.712 41.667 0.00 0.00 0.00 3.18
4072 7283 4.081254 TCAAGTTCACAGGAGATGGATGAG 60.081 45.833 0.00 0.00 0.00 2.90
4078 7289 3.005684 CACAGGAGATGGATGAGAGCTAC 59.994 52.174 0.00 0.00 0.00 3.58
4161 7372 5.654497 GGAAATTCAAGCCCAGTAATTCTG 58.346 41.667 0.00 0.00 43.27 3.02
4188 7437 0.891373 CGGACCTGATATCGATGCCT 59.109 55.000 8.54 0.00 0.00 4.75
4321 7575 0.953727 CCGTGGTTATGGGCATGATG 59.046 55.000 0.00 0.00 0.00 3.07
4322 7576 0.311790 CGTGGTTATGGGCATGATGC 59.688 55.000 9.33 9.33 44.08 3.91
4323 7577 1.696063 GTGGTTATGGGCATGATGCT 58.304 50.000 17.84 0.00 44.28 3.79
4324 7578 2.810032 CGTGGTTATGGGCATGATGCTA 60.810 50.000 17.84 7.35 44.28 3.49
4402 7665 9.186837 AGTACTACATATGTTGTTGCTACTACT 57.813 33.333 24.46 17.29 39.87 2.57
4405 7668 6.422776 ACATATGTTGTTGCTACTACTTGC 57.577 37.500 13.01 0.00 33.74 4.01
4406 7669 6.173339 ACATATGTTGTTGCTACTACTTGCT 58.827 36.000 13.01 0.67 33.74 3.91
4407 7670 7.327975 ACATATGTTGTTGCTACTACTTGCTA 58.672 34.615 13.01 2.48 33.74 3.49
4408 7671 7.492669 ACATATGTTGTTGCTACTACTTGCTAG 59.507 37.037 13.01 0.00 33.74 3.42
4448 9322 0.109597 GCATGAAGAAACTGGTGGCG 60.110 55.000 0.00 0.00 0.00 5.69
4467 9341 2.353406 GCGGGTTGTGCTCTTCTAAGTA 60.353 50.000 0.00 0.00 0.00 2.24
4514 9388 5.586877 TCAATCCTGGTTGTACCTAGTAGT 58.413 41.667 0.00 0.00 39.58 2.73
4515 9389 6.734532 TCAATCCTGGTTGTACCTAGTAGTA 58.265 40.000 0.00 0.00 39.58 1.82
4516 9390 6.832384 TCAATCCTGGTTGTACCTAGTAGTAG 59.168 42.308 0.00 0.00 39.58 2.57
4552 9447 7.924103 ATCGGTTGTTTTACTCAATTGTTTC 57.076 32.000 5.13 0.00 0.00 2.78
4576 9471 9.494271 TTCTTGTATCATAAGATTGTATCTGCC 57.506 33.333 0.00 0.00 40.13 4.85
4577 9472 8.650490 TCTTGTATCATAAGATTGTATCTGCCA 58.350 33.333 0.00 0.00 40.13 4.92
4578 9473 9.445878 CTTGTATCATAAGATTGTATCTGCCAT 57.554 33.333 0.00 0.00 40.13 4.40
4579 9474 8.782339 TGTATCATAAGATTGTATCTGCCATG 57.218 34.615 0.00 0.00 40.13 3.66
4580 9475 6.754702 ATCATAAGATTGTATCTGCCATGC 57.245 37.500 0.00 0.00 40.13 4.06
4581 9476 4.692155 TCATAAGATTGTATCTGCCATGCG 59.308 41.667 0.00 0.00 40.13 4.73
4582 9477 1.888215 AGATTGTATCTGCCATGCGG 58.112 50.000 0.00 0.00 38.44 5.69
4583 9478 0.877071 GATTGTATCTGCCATGCGGG 59.123 55.000 0.00 0.00 35.34 6.13
4599 9494 3.741476 GGCAACTGAAGGCGCCAG 61.741 66.667 31.54 20.31 44.25 4.85
4601 9496 2.684843 GCAACTGAAGGCGCCAGAG 61.685 63.158 31.54 22.31 35.69 3.35
4602 9497 1.302033 CAACTGAAGGCGCCAGAGT 60.302 57.895 31.54 23.01 35.69 3.24
4603 9498 1.004440 AACTGAAGGCGCCAGAGTC 60.004 57.895 31.54 19.76 35.69 3.36
4604 9499 2.125350 CTGAAGGCGCCAGAGTCC 60.125 66.667 31.54 10.83 33.65 3.85
4605 9500 2.922503 TGAAGGCGCCAGAGTCCA 60.923 61.111 31.54 13.41 0.00 4.02
4606 9501 2.249413 CTGAAGGCGCCAGAGTCCAT 62.249 60.000 31.54 0.76 33.65 3.41
4607 9502 1.522580 GAAGGCGCCAGAGTCCATC 60.523 63.158 31.54 9.30 0.00 3.51
4608 9503 2.244117 GAAGGCGCCAGAGTCCATCA 62.244 60.000 31.54 0.00 0.00 3.07
4610 9505 1.890979 GGCGCCAGAGTCCATCATG 60.891 63.158 24.80 0.00 0.00 3.07
4611 9506 1.153289 GCGCCAGAGTCCATCATGT 60.153 57.895 0.00 0.00 0.00 3.21
4612 9507 1.156645 GCGCCAGAGTCCATCATGTC 61.157 60.000 0.00 0.00 0.00 3.06
4616 9511 1.472201 CCAGAGTCCATCATGTCGGTG 60.472 57.143 0.00 0.00 0.00 4.94
4617 9512 0.826715 AGAGTCCATCATGTCGGTGG 59.173 55.000 0.00 0.00 0.00 4.61
4619 9514 1.754803 GAGTCCATCATGTCGGTGGTA 59.245 52.381 0.00 0.00 34.61 3.25
4620 9515 1.480954 AGTCCATCATGTCGGTGGTAC 59.519 52.381 0.00 0.00 34.61 3.34
4621 9516 0.828022 TCCATCATGTCGGTGGTACC 59.172 55.000 4.43 4.43 34.61 3.34
4623 9518 1.473257 CCATCATGTCGGTGGTACCAG 60.473 57.143 16.93 4.58 38.47 4.00
4625 9520 1.449601 CATGTCGGTGGTACCAGGC 60.450 63.158 16.93 6.85 38.47 4.85
4626 9521 1.612442 ATGTCGGTGGTACCAGGCT 60.612 57.895 16.93 0.00 38.47 4.58
4627 9522 1.899437 ATGTCGGTGGTACCAGGCTG 61.899 60.000 16.93 10.05 38.47 4.85
4628 9523 2.118732 TCGGTGGTACCAGGCTGA 59.881 61.111 16.93 12.48 38.47 4.26
4630 9525 1.153369 CGGTGGTACCAGGCTGATG 60.153 63.158 16.93 2.11 38.47 3.07
4632 9527 0.839946 GGTGGTACCAGGCTGATGAT 59.160 55.000 16.93 0.72 38.42 2.45
4633 9528 1.475751 GGTGGTACCAGGCTGATGATG 60.476 57.143 16.93 0.41 38.42 3.07
4634 9529 1.210478 GTGGTACCAGGCTGATGATGT 59.790 52.381 16.93 7.35 0.00 3.06
4635 9530 1.915489 TGGTACCAGGCTGATGATGTT 59.085 47.619 17.94 0.00 0.00 2.71
4637 9532 2.092968 GGTACCAGGCTGATGATGTTCA 60.093 50.000 17.94 0.00 0.00 3.18
4640 9535 0.376152 CAGGCTGATGATGTTCACGC 59.624 55.000 9.42 0.00 0.00 5.34
4642 9537 1.349627 GCTGATGATGTTCACGCGG 59.650 57.895 12.47 0.00 0.00 6.46
4644 9539 0.371301 CTGATGATGTTCACGCGGTG 59.629 55.000 12.47 6.71 34.45 4.94
4645 9540 1.018752 TGATGATGTTCACGCGGTGG 61.019 55.000 12.47 0.00 33.87 4.61
4646 9541 1.003839 ATGATGTTCACGCGGTGGT 60.004 52.632 12.47 0.00 33.87 4.16
4647 9542 1.298157 ATGATGTTCACGCGGTGGTG 61.298 55.000 12.47 0.00 39.29 4.17
4648 9543 1.959226 GATGTTCACGCGGTGGTGT 60.959 57.895 12.47 0.00 39.00 4.16
4650 9545 2.279918 GTTCACGCGGTGGTGTCT 60.280 61.111 12.47 0.00 39.00 3.41
4653 9548 0.389296 TTCACGCGGTGGTGTCTATG 60.389 55.000 12.47 0.00 39.00 2.23
4654 9549 1.214325 CACGCGGTGGTGTCTATGA 59.786 57.895 12.47 0.00 33.82 2.15
4655 9550 0.802222 CACGCGGTGGTGTCTATGAG 60.802 60.000 12.47 0.00 33.82 2.90
4658 9553 1.103803 GCGGTGGTGTCTATGAGAGA 58.896 55.000 0.00 0.00 0.00 3.10
4669 9564 3.887352 TCTATGAGAGACAAGGTAGCGT 58.113 45.455 0.00 0.00 0.00 5.07
4671 9566 2.201921 TGAGAGACAAGGTAGCGTCT 57.798 50.000 2.60 2.60 45.07 4.18
4672 9567 1.813178 TGAGAGACAAGGTAGCGTCTG 59.187 52.381 7.14 0.00 42.48 3.51
4673 9568 1.813786 GAGAGACAAGGTAGCGTCTGT 59.186 52.381 7.14 3.69 42.48 3.41
4674 9569 1.542030 AGAGACAAGGTAGCGTCTGTG 59.458 52.381 7.14 0.00 42.48 3.66
4675 9570 0.603569 AGACAAGGTAGCGTCTGTGG 59.396 55.000 2.21 0.00 40.92 4.17
4677 9572 1.204941 GACAAGGTAGCGTCTGTGGAT 59.795 52.381 2.69 0.00 0.00 3.41
4678 9573 1.066858 ACAAGGTAGCGTCTGTGGATG 60.067 52.381 0.00 0.00 0.00 3.51
4683 9578 2.887568 GCGTCTGTGGATGCCGAG 60.888 66.667 0.00 0.00 45.79 4.63
4684 9579 2.202797 CGTCTGTGGATGCCGAGG 60.203 66.667 0.00 0.00 0.00 4.63
4685 9580 2.982130 GTCTGTGGATGCCGAGGT 59.018 61.111 0.00 0.00 0.00 3.85
4686 9581 1.296715 GTCTGTGGATGCCGAGGTT 59.703 57.895 0.00 0.00 0.00 3.50
4687 9582 1.021390 GTCTGTGGATGCCGAGGTTG 61.021 60.000 0.00 0.00 0.00 3.77
4688 9583 1.191489 TCTGTGGATGCCGAGGTTGA 61.191 55.000 0.00 0.00 0.00 3.18
4690 9585 0.392863 TGTGGATGCCGAGGTTGATG 60.393 55.000 0.00 0.00 0.00 3.07
4691 9586 0.107703 GTGGATGCCGAGGTTGATGA 60.108 55.000 0.00 0.00 0.00 2.92
4692 9587 0.178767 TGGATGCCGAGGTTGATGAG 59.821 55.000 0.00 0.00 0.00 2.90
4693 9588 0.533755 GGATGCCGAGGTTGATGAGG 60.534 60.000 0.00 0.00 0.00 3.86
4695 9590 1.412710 GATGCCGAGGTTGATGAGGTA 59.587 52.381 0.00 0.00 0.00 3.08
4696 9591 0.824109 TGCCGAGGTTGATGAGGTAG 59.176 55.000 0.00 0.00 0.00 3.18
4697 9592 0.105039 GCCGAGGTTGATGAGGTAGG 59.895 60.000 0.00 0.00 0.00 3.18
4699 9594 0.753262 CGAGGTTGATGAGGTAGGGG 59.247 60.000 0.00 0.00 0.00 4.79
4701 9596 0.044855 AGGTTGATGAGGTAGGGGCT 59.955 55.000 0.00 0.00 0.00 5.19
4702 9597 0.919710 GGTTGATGAGGTAGGGGCTT 59.080 55.000 0.00 0.00 0.00 4.35
4703 9598 1.285078 GGTTGATGAGGTAGGGGCTTT 59.715 52.381 0.00 0.00 0.00 3.51
4704 9599 2.369394 GTTGATGAGGTAGGGGCTTTG 58.631 52.381 0.00 0.00 0.00 2.77
4705 9600 0.918983 TGATGAGGTAGGGGCTTTGG 59.081 55.000 0.00 0.00 0.00 3.28
4706 9601 0.466372 GATGAGGTAGGGGCTTTGGC 60.466 60.000 0.00 0.00 37.82 4.52
4708 9603 1.378646 GAGGTAGGGGCTTTGGCAC 60.379 63.158 0.00 0.00 42.01 5.01
4714 9609 4.118584 GGGCTTTGGCACCTCAAT 57.881 55.556 0.00 0.00 40.87 2.57
4715 9610 1.893062 GGGCTTTGGCACCTCAATC 59.107 57.895 0.00 0.00 40.87 2.67
4716 9611 0.613012 GGGCTTTGGCACCTCAATCT 60.613 55.000 0.00 0.00 40.87 2.40
4717 9612 0.529378 GGCTTTGGCACCTCAATCTG 59.471 55.000 0.00 0.00 40.87 2.90
4719 9614 1.471684 GCTTTGGCACCTCAATCTGAG 59.528 52.381 0.00 0.00 40.10 3.35
4727 9622 3.448267 CTCAATCTGAGGCGCTGAA 57.552 52.632 7.64 0.00 40.71 3.02
4729 9624 0.610174 TCAATCTGAGGCGCTGAAGT 59.390 50.000 7.64 0.00 0.00 3.01
4731 9626 0.107945 AATCTGAGGCGCTGAAGTCC 60.108 55.000 7.64 0.00 0.00 3.85
4732 9627 1.260538 ATCTGAGGCGCTGAAGTCCA 61.261 55.000 7.64 0.00 0.00 4.02
4733 9628 1.220206 CTGAGGCGCTGAAGTCCAT 59.780 57.895 7.64 0.00 0.00 3.41
4735 9630 1.522580 GAGGCGCTGAAGTCCATCC 60.523 63.158 7.64 0.00 0.00 3.51
4737 9632 2.184322 GCGCTGAAGTCCATCCGA 59.816 61.111 0.00 0.00 0.00 4.55
4738 9633 1.227380 GCGCTGAAGTCCATCCGAT 60.227 57.895 0.00 0.00 0.00 4.18
4740 9635 0.936764 CGCTGAAGTCCATCCGATCG 60.937 60.000 8.51 8.51 0.00 3.69
4741 9636 0.103208 GCTGAAGTCCATCCGATCGT 59.897 55.000 15.09 0.00 0.00 3.73
4742 9637 1.866063 GCTGAAGTCCATCCGATCGTC 60.866 57.143 15.09 2.71 0.00 4.20
4743 9638 0.744874 TGAAGTCCATCCGATCGTCC 59.255 55.000 15.09 0.00 0.00 4.79
4744 9639 0.317938 GAAGTCCATCCGATCGTCCG 60.318 60.000 15.09 0.00 0.00 4.79
4746 9641 1.008767 GTCCATCCGATCGTCCGAC 60.009 63.158 15.09 9.84 0.00 4.79
4747 9642 1.153025 TCCATCCGATCGTCCGACT 60.153 57.895 15.09 0.00 0.00 4.18
4748 9643 0.750546 TCCATCCGATCGTCCGACTT 60.751 55.000 15.09 0.00 0.00 3.01
4751 9646 1.100510 ATCCGATCGTCCGACTTTGA 58.899 50.000 15.09 0.66 0.00 2.69
4753 9648 0.801067 CCGATCGTCCGACTTTGACC 60.801 60.000 15.09 0.00 0.00 4.02
4754 9649 1.132199 CGATCGTCCGACTTTGACCG 61.132 60.000 7.03 0.00 0.00 4.79
4755 9650 0.801067 GATCGTCCGACTTTGACCGG 60.801 60.000 0.00 0.00 46.57 5.28
4756 9651 2.221906 ATCGTCCGACTTTGACCGGG 62.222 60.000 6.32 0.00 45.36 5.73
4758 9653 1.368579 GTCCGACTTTGACCGGGAA 59.631 57.895 6.32 0.00 45.36 3.97
4759 9654 0.669625 GTCCGACTTTGACCGGGAAG 60.670 60.000 6.32 9.67 45.36 3.46
4760 9655 0.828762 TCCGACTTTGACCGGGAAGA 60.829 55.000 17.84 0.00 45.36 2.87
4761 9656 0.249398 CCGACTTTGACCGGGAAGAT 59.751 55.000 17.84 5.72 41.89 2.40
4762 9657 1.479323 CCGACTTTGACCGGGAAGATA 59.521 52.381 17.84 0.00 41.89 1.98
4763 9658 2.102588 CCGACTTTGACCGGGAAGATAT 59.897 50.000 17.84 0.13 41.89 1.63
4764 9659 3.123804 CGACTTTGACCGGGAAGATATG 58.876 50.000 17.84 4.50 0.00 1.78
4765 9660 3.430374 CGACTTTGACCGGGAAGATATGT 60.430 47.826 17.84 2.18 0.00 2.29
4766 9661 4.514401 GACTTTGACCGGGAAGATATGTT 58.486 43.478 17.84 0.00 0.00 2.71
4767 9662 4.261801 ACTTTGACCGGGAAGATATGTTG 58.738 43.478 17.84 0.00 0.00 3.33
4768 9663 3.275617 TTGACCGGGAAGATATGTTGG 57.724 47.619 6.32 0.00 0.00 3.77
4769 9664 1.134220 TGACCGGGAAGATATGTTGGC 60.134 52.381 6.32 0.00 0.00 4.52
4770 9665 0.916086 ACCGGGAAGATATGTTGGCA 59.084 50.000 6.32 0.00 0.00 4.92
4771 9666 1.494721 ACCGGGAAGATATGTTGGCAT 59.505 47.619 6.32 0.00 39.03 4.40
4772 9667 1.881973 CCGGGAAGATATGTTGGCATG 59.118 52.381 0.00 0.00 36.58 4.06
4773 9668 2.575532 CGGGAAGATATGTTGGCATGT 58.424 47.619 0.00 0.00 36.58 3.21
4779 9674 6.294176 GGGAAGATATGTTGGCATGTATTGAC 60.294 42.308 0.00 0.00 36.58 3.18
4781 9676 5.610398 AGATATGTTGGCATGTATTGACGA 58.390 37.500 0.00 0.00 35.37 4.20
4782 9677 5.698089 AGATATGTTGGCATGTATTGACGAG 59.302 40.000 0.00 0.00 35.37 4.18
4783 9678 2.355197 TGTTGGCATGTATTGACGAGG 58.645 47.619 0.00 0.00 35.37 4.63
4784 9679 1.064060 GTTGGCATGTATTGACGAGGC 59.936 52.381 0.00 0.00 35.37 4.70
4785 9680 0.809636 TGGCATGTATTGACGAGGCG 60.810 55.000 0.00 0.00 35.37 5.52
4786 9681 1.498865 GGCATGTATTGACGAGGCGG 61.499 60.000 0.00 0.00 0.00 6.13
4787 9682 0.810031 GCATGTATTGACGAGGCGGT 60.810 55.000 0.00 0.00 0.00 5.68
4788 9683 0.930310 CATGTATTGACGAGGCGGTG 59.070 55.000 0.00 0.00 0.00 4.94
4789 9684 0.535335 ATGTATTGACGAGGCGGTGT 59.465 50.000 0.00 0.00 0.00 4.16
4790 9685 0.319083 TGTATTGACGAGGCGGTGTT 59.681 50.000 0.00 0.00 0.00 3.32
4791 9686 0.997196 GTATTGACGAGGCGGTGTTC 59.003 55.000 0.00 0.00 0.00 3.18
4793 9688 0.250124 ATTGACGAGGCGGTGTTCAA 60.250 50.000 0.00 0.00 0.00 2.69
4794 9689 0.878523 TTGACGAGGCGGTGTTCAAG 60.879 55.000 0.00 0.00 0.00 3.02
4795 9690 1.006571 GACGAGGCGGTGTTCAAGA 60.007 57.895 0.00 0.00 0.00 3.02
4796 9691 1.006102 ACGAGGCGGTGTTCAAGAG 60.006 57.895 0.00 0.00 0.00 2.85
4798 9693 0.319555 CGAGGCGGTGTTCAAGAGAA 60.320 55.000 0.00 0.00 0.00 2.87
4799 9694 1.872237 CGAGGCGGTGTTCAAGAGAAA 60.872 52.381 0.00 0.00 35.08 2.52
4800 9695 1.801178 GAGGCGGTGTTCAAGAGAAAG 59.199 52.381 0.00 0.00 35.08 2.62
4801 9696 0.238553 GGCGGTGTTCAAGAGAAAGC 59.761 55.000 0.00 0.00 35.08 3.51
4802 9697 1.230324 GCGGTGTTCAAGAGAAAGCT 58.770 50.000 0.00 0.00 35.08 3.74
4803 9698 1.604278 GCGGTGTTCAAGAGAAAGCTT 59.396 47.619 0.00 0.00 35.08 3.74
4805 9700 3.621794 CGGTGTTCAAGAGAAAGCTTTG 58.378 45.455 18.30 2.07 35.08 2.77
4806 9701 3.065371 CGGTGTTCAAGAGAAAGCTTTGT 59.935 43.478 18.30 13.50 35.08 2.83
4807 9702 4.354587 GGTGTTCAAGAGAAAGCTTTGTG 58.645 43.478 18.30 9.19 35.08 3.33
4808 9703 4.354587 GTGTTCAAGAGAAAGCTTTGTGG 58.645 43.478 18.30 4.73 35.08 4.17
4809 9704 3.181487 TGTTCAAGAGAAAGCTTTGTGGC 60.181 43.478 18.30 1.49 35.08 5.01
4817 9712 1.068585 AGCTTTGTGGCTTGCTTGC 59.931 52.632 0.00 0.00 39.86 4.01
4825 9720 2.968206 GCTTGCTTGCCTTCCTGG 59.032 61.111 0.00 0.00 39.35 4.45
4826 9721 1.604593 GCTTGCTTGCCTTCCTGGA 60.605 57.895 0.00 0.00 38.35 3.86
4827 9722 1.593296 GCTTGCTTGCCTTCCTGGAG 61.593 60.000 0.00 0.00 38.35 3.86
4828 9723 0.964358 CTTGCTTGCCTTCCTGGAGG 60.964 60.000 0.00 0.00 39.93 4.30
4834 9729 4.056805 CCTTCCTGGAGGCAGCTA 57.943 61.111 0.00 0.00 38.35 3.32
4835 9730 1.828768 CCTTCCTGGAGGCAGCTAG 59.171 63.158 0.00 0.00 38.35 3.42
4845 9740 2.985456 GCAGCTAGCCCTGTGTCT 59.015 61.111 12.13 0.00 37.23 3.41
4846 9741 1.449246 GCAGCTAGCCCTGTGTCTG 60.449 63.158 12.13 1.13 37.23 3.51
4847 9742 1.220206 CAGCTAGCCCTGTGTCTGG 59.780 63.158 12.13 0.00 0.00 3.86
4853 9748 2.674380 CCCTGTGTCTGGCAAGGC 60.674 66.667 0.00 0.00 0.00 4.35
4854 9749 2.113774 CCTGTGTCTGGCAAGGCA 59.886 61.111 0.00 0.00 35.02 4.75
4856 9751 0.896940 CCTGTGTCTGGCAAGGCAAT 60.897 55.000 0.00 0.00 40.47 3.56
4857 9752 0.963962 CTGTGTCTGGCAAGGCAATT 59.036 50.000 0.00 0.00 40.47 2.32
4858 9753 0.675083 TGTGTCTGGCAAGGCAATTG 59.325 50.000 0.00 0.00 40.47 2.32
4873 9768 1.098050 AATTGCTTGCCTTCTAGCGG 58.902 50.000 0.00 0.00 42.66 5.52
4874 9769 0.253044 ATTGCTTGCCTTCTAGCGGA 59.747 50.000 2.44 0.00 42.66 5.54
4875 9770 0.391661 TTGCTTGCCTTCTAGCGGAG 60.392 55.000 2.44 0.00 42.66 4.63
4876 9771 1.522580 GCTTGCCTTCTAGCGGAGG 60.523 63.158 2.44 2.81 31.96 4.30
4877 9772 1.961180 GCTTGCCTTCTAGCGGAGGA 61.961 60.000 9.90 0.00 31.96 3.71
4878 9773 0.103937 CTTGCCTTCTAGCGGAGGAG 59.896 60.000 9.90 0.00 34.65 3.69
4879 9774 1.961180 TTGCCTTCTAGCGGAGGAGC 61.961 60.000 9.90 1.80 34.65 4.70
4880 9775 3.133946 CCTTCTAGCGGAGGAGCC 58.866 66.667 1.61 0.00 38.01 4.70
4881 9776 1.456705 CCTTCTAGCGGAGGAGCCT 60.457 63.158 0.00 0.00 38.01 4.58
4882 9777 1.045911 CCTTCTAGCGGAGGAGCCTT 61.046 60.000 0.00 0.00 38.01 4.35
4884 9779 0.033011 TTCTAGCGGAGGAGCCTTCT 60.033 55.000 0.00 0.00 38.01 2.85
4886 9781 1.202830 TCTAGCGGAGGAGCCTTCTAG 60.203 57.143 11.77 11.77 38.13 2.43
4888 9783 2.503382 GCGGAGGAGCCTTCTAGGG 61.503 68.421 0.00 0.00 35.37 3.53
4900 9795 3.968265 CCTTCTAGGGGCAAAATCAAGA 58.032 45.455 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.659794 GCACACAAATCCAACGGCT 59.340 52.632 0.00 0.00 0.00 5.52
61 62 2.361438 GGACTCCACTTATCCACTACGG 59.639 54.545 0.00 0.00 32.35 4.02
70 71 3.782656 ACCAAAACGGACTCCACTTAT 57.217 42.857 0.00 0.00 38.63 1.73
71 72 3.564053 AACCAAAACGGACTCCACTTA 57.436 42.857 0.00 0.00 38.63 2.24
72 73 2.430248 AACCAAAACGGACTCCACTT 57.570 45.000 0.00 0.00 38.63 3.16
203 292 1.001181 GGCGGTGTTACTTCAGGTACA 59.999 52.381 0.00 0.00 0.00 2.90
216 305 3.126703 TTGGTGATGGTGGCGGTGT 62.127 57.895 0.00 0.00 0.00 4.16
221 310 0.603065 GAAAGGTTGGTGATGGTGGC 59.397 55.000 0.00 0.00 0.00 5.01
228 317 1.137594 ATCCGGGGAAAGGTTGGTGA 61.138 55.000 0.00 0.00 0.00 4.02
250 342 2.686816 GCCGAACACGGGATTGGTG 61.687 63.158 2.77 0.00 45.94 4.17
802 946 4.201679 TGGCGGTCGATGTAGGCG 62.202 66.667 0.00 0.00 0.00 5.52
917 1061 3.110705 ACATGAGCCTATCAGACTTGGT 58.889 45.455 0.00 0.00 42.53 3.67
928 1072 1.616374 TGTCGACAACACATGAGCCTA 59.384 47.619 17.62 0.00 31.20 3.93
967 1114 1.071987 CCAGTGAGCCTGCAACAGA 59.928 57.895 0.00 0.00 40.06 3.41
1240 1400 0.104672 TCCCACTTGTCCCAGGAGAA 60.105 55.000 0.00 0.00 0.00 2.87
1368 1528 2.289195 CGGCAGCGGGGTATAGAAAATA 60.289 50.000 0.00 0.00 0.00 1.40
1484 1644 0.883833 CTGGACCATTGCTTCCACAC 59.116 55.000 0.00 0.00 36.96 3.82
1499 1659 1.257743 CCGTCCAAGAGAGAACTGGA 58.742 55.000 0.00 0.00 0.00 3.86
1613 1777 8.999431 TCAAAAGATAAGACTGCGAGTTAAATT 58.001 29.630 0.00 0.00 0.00 1.82
1684 2135 5.527582 GTCCAATGTCCATAGTGTCAATACC 59.472 44.000 0.00 0.00 0.00 2.73
1757 2208 6.019762 CGCATCAACATGTATGAATCATAGC 58.980 40.000 11.95 0.00 31.86 2.97
1763 2214 7.552458 TTCTAACGCATCAACATGTATGAAT 57.448 32.000 11.95 1.14 31.86 2.57
1848 2314 6.069331 TGTATAAGTGAGGTCTCCATAGTCC 58.931 44.000 0.00 0.00 0.00 3.85
1849 2315 6.207810 CCTGTATAAGTGAGGTCTCCATAGTC 59.792 46.154 0.00 0.00 0.00 2.59
1850 2316 6.071984 CCTGTATAAGTGAGGTCTCCATAGT 58.928 44.000 0.00 0.00 0.00 2.12
1851 2317 5.047660 GCCTGTATAAGTGAGGTCTCCATAG 60.048 48.000 0.00 0.00 0.00 2.23
1852 2318 4.833380 GCCTGTATAAGTGAGGTCTCCATA 59.167 45.833 0.00 0.00 0.00 2.74
1853 2319 3.643792 GCCTGTATAAGTGAGGTCTCCAT 59.356 47.826 0.00 0.00 0.00 3.41
1854 2320 3.031736 GCCTGTATAAGTGAGGTCTCCA 58.968 50.000 0.00 0.00 0.00 3.86
1947 2421 5.872635 ACAATGTCAACAGCTATTTCATCG 58.127 37.500 0.00 0.00 0.00 3.84
1965 2439 5.248640 ACACCTGGACTATCTTTGACAATG 58.751 41.667 0.00 0.00 0.00 2.82
1982 2456 2.945080 ATGGCCTCATGATACACCTG 57.055 50.000 3.32 0.00 31.34 4.00
2098 2581 1.455822 TCCTGGTTGGTTGGAGGAAT 58.544 50.000 0.00 0.00 37.07 3.01
2178 2663 4.141711 GCCACTTGAGGTTGTCTATATCCA 60.142 45.833 0.00 0.00 0.00 3.41
2275 2760 2.719739 AGGACAAGCAACATGAGATGG 58.280 47.619 0.00 0.00 33.60 3.51
2361 4142 4.037089 CCATAAACAGCATGCATAGCAAGA 59.963 41.667 21.98 0.00 43.62 3.02
2502 4287 6.617879 AGGACGGCAAAAGAAAAATGTATAC 58.382 36.000 0.00 0.00 0.00 1.47
2667 4465 3.064545 CCTACAGAAGCAGCAGCATAAAC 59.935 47.826 3.17 0.00 45.49 2.01
2734 4532 1.032657 GCCAGTCTAGAGTCCGCAGA 61.033 60.000 10.15 0.00 0.00 4.26
2993 6145 7.387673 TCACCAAGAAAGTTACAGACATACATG 59.612 37.037 0.00 0.00 0.00 3.21
2994 6146 7.450074 TCACCAAGAAAGTTACAGACATACAT 58.550 34.615 0.00 0.00 0.00 2.29
3034 6186 0.887836 ATGCTATCACATGGGCTGCG 60.888 55.000 0.00 0.00 0.00 5.18
3042 6194 4.936411 GCAGAGCTAATGATGCTATCACAT 59.064 41.667 2.62 0.00 43.01 3.21
3486 6690 7.067372 TCAGTCACAATGGGAATTCATAACATC 59.933 37.037 7.93 0.00 0.00 3.06
3503 6707 8.664798 CACGATTTTATTAGGATTCAGTCACAA 58.335 33.333 0.00 0.00 0.00 3.33
3520 6724 6.993786 TTTACCATCTGCATCACGATTTTA 57.006 33.333 0.00 0.00 0.00 1.52
3555 6765 1.065926 TCGATGCAGCTTCACCTTGAT 60.066 47.619 0.00 0.00 0.00 2.57
3851 7062 4.037446 TGCTGAAACAATTGAACCAGGTAC 59.963 41.667 13.59 4.27 0.00 3.34
4008 7219 2.502947 ACATCAATCTCAGTAGCAGCCA 59.497 45.455 0.00 0.00 0.00 4.75
4009 7220 3.129871 GACATCAATCTCAGTAGCAGCC 58.870 50.000 0.00 0.00 0.00 4.85
4038 7249 2.976185 TGTGAACTTGATACCAGTCCCA 59.024 45.455 0.00 0.00 0.00 4.37
4043 7254 4.808414 TCTCCTGTGAACTTGATACCAG 57.192 45.455 0.00 0.00 0.00 4.00
4057 7268 2.475339 AGCTCTCATCCATCTCCTGT 57.525 50.000 0.00 0.00 0.00 4.00
4072 7283 2.442084 CGTTGTTCACGGGTAGCTC 58.558 57.895 0.00 0.00 45.89 4.09
4094 7305 1.087771 CCTTTGTATCGACCACGGCC 61.088 60.000 0.00 0.00 40.21 6.13
4161 7372 0.179045 ATATCAGGTCCGTTGCTGCC 60.179 55.000 0.00 0.00 0.00 4.85
4163 7374 1.067060 TCGATATCAGGTCCGTTGCTG 59.933 52.381 3.12 0.00 0.00 4.41
4166 7381 2.061773 GCATCGATATCAGGTCCGTTG 58.938 52.381 0.00 0.00 0.00 4.10
4169 7384 0.891373 AGGCATCGATATCAGGTCCG 59.109 55.000 0.00 0.00 0.00 4.79
4188 7437 1.492599 TGGGAAGATGACACAACCACA 59.507 47.619 0.00 0.00 0.00 4.17
4321 7575 2.611292 CAGCACCTTCACATAAGCTAGC 59.389 50.000 6.62 6.62 0.00 3.42
4322 7576 3.201290 CCAGCACCTTCACATAAGCTAG 58.799 50.000 0.00 0.00 0.00 3.42
4323 7577 2.571653 ACCAGCACCTTCACATAAGCTA 59.428 45.455 0.00 0.00 0.00 3.32
4324 7578 1.352352 ACCAGCACCTTCACATAAGCT 59.648 47.619 0.00 0.00 0.00 3.74
4401 7664 3.196685 AGCAGGAAGAAGGTACTAGCAAG 59.803 47.826 0.00 0.00 38.49 4.01
4402 7665 3.173965 AGCAGGAAGAAGGTACTAGCAA 58.826 45.455 0.00 0.00 38.49 3.91
4405 7668 3.526534 GCAAGCAGGAAGAAGGTACTAG 58.473 50.000 0.00 0.00 38.49 2.57
4406 7669 2.094182 CGCAAGCAGGAAGAAGGTACTA 60.094 50.000 0.00 0.00 38.49 1.82
4407 7670 3.931747 ACGCAAGCAGGAAGAAGGTACT 61.932 50.000 0.00 0.00 42.68 2.73
4408 7671 1.079503 CGCAAGCAGGAAGAAGGTAC 58.920 55.000 0.00 0.00 0.00 3.34
4448 9322 5.306394 AGTTTACTTAGAAGAGCACAACCC 58.694 41.667 0.00 0.00 0.00 4.11
4467 9341 5.254032 AGATCTGGGGTTCTAATTGGAGTTT 59.746 40.000 0.00 0.00 0.00 2.66
4514 9388 8.851541 AAAACAACCGATACTTCATTTACCTA 57.148 30.769 0.00 0.00 0.00 3.08
4515 9389 7.754851 AAAACAACCGATACTTCATTTACCT 57.245 32.000 0.00 0.00 0.00 3.08
4516 9390 8.724229 AGTAAAACAACCGATACTTCATTTACC 58.276 33.333 0.00 0.00 33.45 2.85
4519 9393 8.385898 TGAGTAAAACAACCGATACTTCATTT 57.614 30.769 0.00 0.00 0.00 2.32
4552 9447 8.837788 TGGCAGATACAATCTTATGATACAAG 57.162 34.615 0.00 0.00 37.58 3.16
4576 9471 2.879907 CCTTCAGTTGCCCGCATG 59.120 61.111 0.00 0.00 0.00 4.06
4577 9472 3.064324 GCCTTCAGTTGCCCGCAT 61.064 61.111 0.00 0.00 0.00 4.73
4583 9478 2.669569 TCTGGCGCCTTCAGTTGC 60.670 61.111 29.70 0.00 34.15 4.17
4584 9479 1.294659 GACTCTGGCGCCTTCAGTTG 61.295 60.000 29.70 15.49 34.15 3.16
4585 9480 1.004440 GACTCTGGCGCCTTCAGTT 60.004 57.895 29.70 8.36 34.15 3.16
4586 9481 2.659610 GACTCTGGCGCCTTCAGT 59.340 61.111 29.70 24.62 34.15 3.41
4587 9482 2.125350 GGACTCTGGCGCCTTCAG 60.125 66.667 29.70 21.55 0.00 3.02
4589 9484 1.522580 GATGGACTCTGGCGCCTTC 60.523 63.158 29.70 17.63 0.00 3.46
4590 9485 1.630126 ATGATGGACTCTGGCGCCTT 61.630 55.000 29.70 9.25 0.00 4.35
4591 9486 2.068821 ATGATGGACTCTGGCGCCT 61.069 57.895 29.70 6.86 0.00 5.52
4592 9487 1.890979 CATGATGGACTCTGGCGCC 60.891 63.158 22.73 22.73 0.00 6.53
4593 9488 1.153289 ACATGATGGACTCTGGCGC 60.153 57.895 0.00 0.00 0.00 6.53
4594 9489 0.873312 CGACATGATGGACTCTGGCG 60.873 60.000 0.00 0.00 0.00 5.69
4597 9492 1.472201 CCACCGACATGATGGACTCTG 60.472 57.143 13.66 3.10 29.36 3.35
4598 9493 0.826715 CCACCGACATGATGGACTCT 59.173 55.000 13.66 0.00 29.36 3.24
4599 9494 0.537188 ACCACCGACATGATGGACTC 59.463 55.000 13.66 0.00 29.36 3.36
4601 9496 1.472728 GGTACCACCGACATGATGGAC 60.473 57.143 7.15 8.58 29.36 4.02
4602 9497 0.828022 GGTACCACCGACATGATGGA 59.172 55.000 7.15 0.00 29.36 3.41
4603 9498 0.539518 TGGTACCACCGACATGATGG 59.460 55.000 11.60 2.68 42.58 3.51
4604 9499 1.473257 CCTGGTACCACCGACATGATG 60.473 57.143 11.60 0.00 42.58 3.07
4605 9500 0.830648 CCTGGTACCACCGACATGAT 59.169 55.000 11.60 0.00 42.58 2.45
4606 9501 1.895020 GCCTGGTACCACCGACATGA 61.895 60.000 11.60 0.00 42.58 3.07
4607 9502 1.449601 GCCTGGTACCACCGACATG 60.450 63.158 11.60 0.00 42.58 3.21
4608 9503 1.612442 AGCCTGGTACCACCGACAT 60.612 57.895 11.60 0.00 42.58 3.06
4610 9505 1.614241 ATCAGCCTGGTACCACCGAC 61.614 60.000 11.60 0.26 42.58 4.79
4611 9506 1.305802 ATCAGCCTGGTACCACCGA 60.306 57.895 11.60 5.39 42.58 4.69
4612 9507 1.153369 CATCAGCCTGGTACCACCG 60.153 63.158 11.60 5.10 42.58 4.94
4616 9511 2.092968 TGAACATCATCAGCCTGGTACC 60.093 50.000 4.43 4.43 0.00 3.34
4617 9512 2.939103 GTGAACATCATCAGCCTGGTAC 59.061 50.000 0.00 0.00 0.00 3.34
4619 9514 1.676916 CGTGAACATCATCAGCCTGGT 60.677 52.381 0.00 0.00 0.00 4.00
4620 9515 1.012086 CGTGAACATCATCAGCCTGG 58.988 55.000 0.00 0.00 0.00 4.45
4621 9516 0.376152 GCGTGAACATCATCAGCCTG 59.624 55.000 0.00 0.00 0.00 4.85
4623 9518 1.349627 CGCGTGAACATCATCAGCC 59.650 57.895 0.00 0.00 0.00 4.85
4625 9520 0.371301 CACCGCGTGAACATCATCAG 59.629 55.000 4.92 0.00 35.23 2.90
4626 9521 1.018752 CCACCGCGTGAACATCATCA 61.019 55.000 4.92 0.00 35.23 3.07
4627 9522 1.019278 ACCACCGCGTGAACATCATC 61.019 55.000 4.92 0.00 35.23 2.92
4628 9523 1.003839 ACCACCGCGTGAACATCAT 60.004 52.632 4.92 0.00 35.23 2.45
4630 9525 1.897398 GACACCACCGCGTGAACATC 61.897 60.000 4.92 0.00 37.20 3.06
4632 9527 1.736365 TAGACACCACCGCGTGAACA 61.736 55.000 4.92 0.00 37.20 3.18
4633 9528 0.389426 ATAGACACCACCGCGTGAAC 60.389 55.000 4.92 0.00 37.20 3.18
4634 9529 0.389296 CATAGACACCACCGCGTGAA 60.389 55.000 4.92 0.00 37.20 3.18
4635 9530 1.214325 CATAGACACCACCGCGTGA 59.786 57.895 4.92 0.00 37.20 4.35
4637 9532 0.963856 TCTCATAGACACCACCGCGT 60.964 55.000 4.92 0.00 0.00 6.01
4648 9543 3.878103 GACGCTACCTTGTCTCTCATAGA 59.122 47.826 0.00 0.00 32.37 1.98
4650 9545 3.628032 CAGACGCTACCTTGTCTCTCATA 59.372 47.826 0.00 0.00 43.33 2.15
4653 9548 1.813786 ACAGACGCTACCTTGTCTCTC 59.186 52.381 0.00 0.00 43.33 3.20
4654 9549 1.542030 CACAGACGCTACCTTGTCTCT 59.458 52.381 0.00 0.00 43.33 3.10
4655 9550 1.402984 CCACAGACGCTACCTTGTCTC 60.403 57.143 0.00 0.00 43.33 3.36
4658 9553 1.066858 CATCCACAGACGCTACCTTGT 60.067 52.381 0.00 0.00 0.00 3.16
4660 9555 0.108138 GCATCCACAGACGCTACCTT 60.108 55.000 0.00 0.00 0.00 3.50
4662 9557 1.521681 GGCATCCACAGACGCTACC 60.522 63.158 0.00 0.00 30.12 3.18
4663 9558 1.878522 CGGCATCCACAGACGCTAC 60.879 63.158 0.00 0.00 30.12 3.58
4666 9561 2.887568 CTCGGCATCCACAGACGC 60.888 66.667 0.00 0.00 0.00 5.19
4667 9562 2.202797 CCTCGGCATCCACAGACG 60.203 66.667 0.00 0.00 0.00 4.18
4669 9564 1.191489 TCAACCTCGGCATCCACAGA 61.191 55.000 0.00 0.00 0.00 3.41
4671 9566 0.392863 CATCAACCTCGGCATCCACA 60.393 55.000 0.00 0.00 0.00 4.17
4672 9567 0.107703 TCATCAACCTCGGCATCCAC 60.108 55.000 0.00 0.00 0.00 4.02
4673 9568 0.178767 CTCATCAACCTCGGCATCCA 59.821 55.000 0.00 0.00 0.00 3.41
4674 9569 0.533755 CCTCATCAACCTCGGCATCC 60.534 60.000 0.00 0.00 0.00 3.51
4675 9570 0.179000 ACCTCATCAACCTCGGCATC 59.821 55.000 0.00 0.00 0.00 3.91
4677 9572 0.824109 CTACCTCATCAACCTCGGCA 59.176 55.000 0.00 0.00 0.00 5.69
4678 9573 0.105039 CCTACCTCATCAACCTCGGC 59.895 60.000 0.00 0.00 0.00 5.54
4679 9574 0.753262 CCCTACCTCATCAACCTCGG 59.247 60.000 0.00 0.00 0.00 4.63
4680 9575 0.753262 CCCCTACCTCATCAACCTCG 59.247 60.000 0.00 0.00 0.00 4.63
4681 9576 0.470341 GCCCCTACCTCATCAACCTC 59.530 60.000 0.00 0.00 0.00 3.85
4683 9578 0.919710 AAGCCCCTACCTCATCAACC 59.080 55.000 0.00 0.00 0.00 3.77
4684 9579 2.369394 CAAAGCCCCTACCTCATCAAC 58.631 52.381 0.00 0.00 0.00 3.18
4685 9580 1.284785 CCAAAGCCCCTACCTCATCAA 59.715 52.381 0.00 0.00 0.00 2.57
4686 9581 0.918983 CCAAAGCCCCTACCTCATCA 59.081 55.000 0.00 0.00 0.00 3.07
4687 9582 0.466372 GCCAAAGCCCCTACCTCATC 60.466 60.000 0.00 0.00 0.00 2.92
4688 9583 1.214305 TGCCAAAGCCCCTACCTCAT 61.214 55.000 0.00 0.00 38.69 2.90
4690 9585 1.378646 GTGCCAAAGCCCCTACCTC 60.379 63.158 0.00 0.00 38.69 3.85
4691 9586 2.763902 GTGCCAAAGCCCCTACCT 59.236 61.111 0.00 0.00 38.69 3.08
4692 9587 2.362503 GGTGCCAAAGCCCCTACC 60.363 66.667 0.00 0.00 38.69 3.18
4693 9588 2.763902 AGGTGCCAAAGCCCCTAC 59.236 61.111 0.00 0.00 46.20 3.18
4696 9591 1.607801 GATTGAGGTGCCAAAGCCCC 61.608 60.000 0.00 0.00 36.65 5.80
4697 9592 0.613012 AGATTGAGGTGCCAAAGCCC 60.613 55.000 0.00 0.00 38.69 5.19
4699 9594 1.471684 CTCAGATTGAGGTGCCAAAGC 59.528 52.381 0.00 0.00 40.71 3.51
4711 9606 1.005340 GACTTCAGCGCCTCAGATTG 58.995 55.000 2.29 0.00 0.00 2.67
4712 9607 0.107945 GGACTTCAGCGCCTCAGATT 60.108 55.000 2.29 0.00 0.00 2.40
4713 9608 1.260538 TGGACTTCAGCGCCTCAGAT 61.261 55.000 2.29 0.00 0.00 2.90
4714 9609 1.260538 ATGGACTTCAGCGCCTCAGA 61.261 55.000 2.29 0.00 0.00 3.27
4715 9610 0.809241 GATGGACTTCAGCGCCTCAG 60.809 60.000 2.29 0.00 0.00 3.35
4716 9611 1.219124 GATGGACTTCAGCGCCTCA 59.781 57.895 2.29 0.00 0.00 3.86
4717 9612 1.522580 GGATGGACTTCAGCGCCTC 60.523 63.158 2.29 0.00 31.40 4.70
4719 9614 2.650813 ATCGGATGGACTTCAGCGCC 62.651 60.000 2.29 0.00 31.40 6.53
4720 9615 1.218230 GATCGGATGGACTTCAGCGC 61.218 60.000 0.00 0.00 31.40 5.92
4721 9616 0.936764 CGATCGGATGGACTTCAGCG 60.937 60.000 7.38 0.00 31.40 5.18
4722 9617 0.103208 ACGATCGGATGGACTTCAGC 59.897 55.000 20.98 0.00 0.00 4.26
4723 9618 1.269309 GGACGATCGGATGGACTTCAG 60.269 57.143 20.98 0.00 0.00 3.02
4724 9619 0.744874 GGACGATCGGATGGACTTCA 59.255 55.000 20.98 0.00 0.00 3.02
4725 9620 0.317938 CGGACGATCGGATGGACTTC 60.318 60.000 20.98 4.78 0.00 3.01
4726 9621 0.750546 TCGGACGATCGGATGGACTT 60.751 55.000 20.98 0.00 0.00 3.01
4727 9622 1.153025 TCGGACGATCGGATGGACT 60.153 57.895 20.98 0.00 0.00 3.85
4729 9624 0.750546 AAGTCGGACGATCGGATGGA 60.751 55.000 20.98 8.13 0.00 3.41
4731 9626 1.200483 CAAAGTCGGACGATCGGATG 58.800 55.000 20.98 8.21 0.00 3.51
4732 9627 1.100510 TCAAAGTCGGACGATCGGAT 58.899 50.000 20.98 0.00 0.00 4.18
4733 9628 0.169672 GTCAAAGTCGGACGATCGGA 59.830 55.000 20.98 4.08 0.00 4.55
4735 9630 1.132199 CGGTCAAAGTCGGACGATCG 61.132 60.000 14.88 14.88 36.12 3.69
4737 9632 4.883026 CGGTCAAAGTCGGACGAT 57.117 55.556 1.89 0.00 36.12 3.73
4742 9637 0.249398 ATCTTCCCGGTCAAAGTCGG 59.751 55.000 0.00 0.00 45.29 4.79
4743 9638 2.953466 TATCTTCCCGGTCAAAGTCG 57.047 50.000 0.00 0.00 0.00 4.18
4744 9639 4.138487 ACATATCTTCCCGGTCAAAGTC 57.862 45.455 0.00 0.00 0.00 3.01
4746 9641 3.627577 CCAACATATCTTCCCGGTCAAAG 59.372 47.826 0.00 1.07 0.00 2.77
4747 9642 3.616219 CCAACATATCTTCCCGGTCAAA 58.384 45.455 0.00 0.00 0.00 2.69
4748 9643 2.682563 GCCAACATATCTTCCCGGTCAA 60.683 50.000 0.00 0.00 0.00 3.18
4751 9646 0.916086 TGCCAACATATCTTCCCGGT 59.084 50.000 0.00 0.00 0.00 5.28
4753 9648 2.575532 ACATGCCAACATATCTTCCCG 58.424 47.619 0.00 0.00 33.67 5.14
4754 9649 5.769662 TCAATACATGCCAACATATCTTCCC 59.230 40.000 0.00 0.00 33.67 3.97
4755 9650 6.566564 CGTCAATACATGCCAACATATCTTCC 60.567 42.308 0.00 0.00 33.67 3.46
4756 9651 6.202762 TCGTCAATACATGCCAACATATCTTC 59.797 38.462 0.00 0.00 33.67 2.87
4758 9653 5.610398 TCGTCAATACATGCCAACATATCT 58.390 37.500 0.00 0.00 33.67 1.98
4759 9654 5.106948 CCTCGTCAATACATGCCAACATATC 60.107 44.000 0.00 0.00 33.67 1.63
4760 9655 4.756642 CCTCGTCAATACATGCCAACATAT 59.243 41.667 0.00 0.00 33.67 1.78
4761 9656 4.126437 CCTCGTCAATACATGCCAACATA 58.874 43.478 0.00 0.00 33.67 2.29
4762 9657 2.945008 CCTCGTCAATACATGCCAACAT 59.055 45.455 0.00 0.00 36.79 2.71
4763 9658 2.355197 CCTCGTCAATACATGCCAACA 58.645 47.619 0.00 0.00 0.00 3.33
4764 9659 1.064060 GCCTCGTCAATACATGCCAAC 59.936 52.381 0.00 0.00 0.00 3.77
4765 9660 1.378531 GCCTCGTCAATACATGCCAA 58.621 50.000 0.00 0.00 0.00 4.52
4766 9661 0.809636 CGCCTCGTCAATACATGCCA 60.810 55.000 0.00 0.00 0.00 4.92
4767 9662 1.498865 CCGCCTCGTCAATACATGCC 61.499 60.000 0.00 0.00 0.00 4.40
4768 9663 0.810031 ACCGCCTCGTCAATACATGC 60.810 55.000 0.00 0.00 0.00 4.06
4769 9664 0.930310 CACCGCCTCGTCAATACATG 59.070 55.000 0.00 0.00 0.00 3.21
4770 9665 0.535335 ACACCGCCTCGTCAATACAT 59.465 50.000 0.00 0.00 0.00 2.29
4771 9666 0.319083 AACACCGCCTCGTCAATACA 59.681 50.000 0.00 0.00 0.00 2.29
4772 9667 0.997196 GAACACCGCCTCGTCAATAC 59.003 55.000 0.00 0.00 0.00 1.89
4773 9668 0.604073 TGAACACCGCCTCGTCAATA 59.396 50.000 0.00 0.00 0.00 1.90
4779 9674 0.319555 TTCTCTTGAACACCGCCTCG 60.320 55.000 0.00 0.00 0.00 4.63
4781 9676 1.884235 CTTTCTCTTGAACACCGCCT 58.116 50.000 0.00 0.00 31.02 5.52
4782 9677 0.238553 GCTTTCTCTTGAACACCGCC 59.761 55.000 0.00 0.00 31.02 6.13
4783 9678 1.230324 AGCTTTCTCTTGAACACCGC 58.770 50.000 0.00 0.00 31.02 5.68
4784 9679 3.065371 ACAAAGCTTTCTCTTGAACACCG 59.935 43.478 9.23 0.00 31.02 4.94
4785 9680 4.354587 CACAAAGCTTTCTCTTGAACACC 58.645 43.478 9.23 0.00 31.02 4.16
4786 9681 4.354587 CCACAAAGCTTTCTCTTGAACAC 58.645 43.478 9.23 0.00 31.02 3.32
4787 9682 3.181487 GCCACAAAGCTTTCTCTTGAACA 60.181 43.478 9.23 0.00 31.02 3.18
4788 9683 3.067320 AGCCACAAAGCTTTCTCTTGAAC 59.933 43.478 9.23 1.17 41.41 3.18
4789 9684 3.290710 AGCCACAAAGCTTTCTCTTGAA 58.709 40.909 9.23 0.00 41.41 2.69
4790 9685 2.936202 AGCCACAAAGCTTTCTCTTGA 58.064 42.857 9.23 0.00 41.41 3.02
4800 9695 3.633951 GCAAGCAAGCCACAAAGC 58.366 55.556 0.00 0.00 0.00 3.51
4808 9703 1.593296 CTCCAGGAAGGCAAGCAAGC 61.593 60.000 0.00 0.00 37.29 4.01
4809 9704 0.964358 CCTCCAGGAAGGCAAGCAAG 60.964 60.000 0.00 0.00 37.39 4.01
4811 9706 2.759114 CCTCCAGGAAGGCAAGCA 59.241 61.111 0.00 0.00 37.39 3.91
4817 9712 1.828768 CTAGCTGCCTCCAGGAAGG 59.171 63.158 2.52 0.00 41.45 3.46
4818 9713 1.145819 GCTAGCTGCCTCCAGGAAG 59.854 63.158 7.70 0.00 44.16 3.46
4819 9714 3.313874 GCTAGCTGCCTCCAGGAA 58.686 61.111 7.70 0.00 39.54 3.36
4828 9723 1.449246 CAGACACAGGGCTAGCTGC 60.449 63.158 15.72 0.00 41.94 5.25
4831 9726 2.124942 GCCAGACACAGGGCTAGC 60.125 66.667 6.04 6.04 46.74 3.42
4838 9733 0.963962 AATTGCCTTGCCAGACACAG 59.036 50.000 0.00 0.00 0.00 3.66
4839 9734 0.675083 CAATTGCCTTGCCAGACACA 59.325 50.000 0.00 0.00 0.00 3.72
4840 9735 3.502237 CAATTGCCTTGCCAGACAC 57.498 52.632 0.00 0.00 0.00 3.67
4852 9747 1.796617 CGCTAGAAGGCAAGCAATTGC 60.797 52.381 23.05 23.05 46.64 3.56
4853 9748 1.202222 CCGCTAGAAGGCAAGCAATTG 60.202 52.381 0.00 0.00 38.70 2.32
4854 9749 1.098050 CCGCTAGAAGGCAAGCAATT 58.902 50.000 0.00 0.00 38.70 2.32
4856 9751 0.391661 CTCCGCTAGAAGGCAAGCAA 60.392 55.000 0.00 0.00 38.70 3.91
4857 9752 1.219124 CTCCGCTAGAAGGCAAGCA 59.781 57.895 0.00 0.00 38.70 3.91
4858 9753 1.522580 CCTCCGCTAGAAGGCAAGC 60.523 63.158 0.00 0.00 35.33 4.01
4859 9754 0.103937 CTCCTCCGCTAGAAGGCAAG 59.896 60.000 0.00 0.00 0.00 4.01
4860 9755 1.961180 GCTCCTCCGCTAGAAGGCAA 61.961 60.000 0.00 0.00 0.00 4.52
4861 9756 2.427245 GCTCCTCCGCTAGAAGGCA 61.427 63.158 0.00 0.00 0.00 4.75
4862 9757 2.419620 GCTCCTCCGCTAGAAGGC 59.580 66.667 0.00 0.00 0.00 4.35
4863 9758 1.045911 AAGGCTCCTCCGCTAGAAGG 61.046 60.000 0.00 0.00 40.77 3.46
4864 9759 0.387565 GAAGGCTCCTCCGCTAGAAG 59.612 60.000 0.00 0.00 40.77 2.85
4865 9760 0.033011 AGAAGGCTCCTCCGCTAGAA 60.033 55.000 0.00 0.00 40.77 2.10
4870 9765 2.503382 CCCTAGAAGGCTCCTCCGC 61.503 68.421 0.00 0.00 40.77 5.54
4879 9774 3.968265 TCTTGATTTTGCCCCTAGAAGG 58.032 45.455 0.00 0.00 34.30 3.46


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

AutoCloner maintained by Alex Coulton.