Multiple sequence alignment - TraesCS2A01G111000

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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 TraesCS2A01G111000 chr2A 100.000 4414 0 0 1 4414 62372726 62368313 0.000000e+00 8152.0
1 TraesCS2A01G111000 chr2A 74.479 576 125 15 6 576 693153818 693154376 3.430000e-56 230.0
2 TraesCS2A01G111000 chr2A 90.769 130 10 2 4036 4163 630098141 630098270 5.870000e-39 172.0
3 TraesCS2A01G111000 chr2B 91.073 1053 52 20 674 1699 97397487 97396450 0.000000e+00 1386.0
4 TraesCS2A01G111000 chr2B 83.237 1378 104 56 1697 3007 97396413 97395096 0.000000e+00 1147.0
5 TraesCS2A01G111000 chr2B 88.484 686 44 10 3154 3821 97394735 97394067 0.000000e+00 797.0
6 TraesCS2A01G111000 chr2B 95.019 261 9 4 4156 4414 97393823 97393565 1.480000e-109 407.0
7 TraesCS2A01G111000 chr2B 75.130 575 121 16 6 576 569537888 569538444 2.640000e-62 250.0
8 TraesCS2A01G111000 chr2B 77.488 422 76 14 6 423 710279549 710279143 7.380000e-58 235.0
9 TraesCS2A01G111000 chr2B 89.510 143 14 1 3431 3572 97371222 97371080 3.510000e-41 180.0
10 TraesCS2A01G111000 chr2B 93.966 116 7 0 4043 4158 653603252 653603137 4.540000e-40 176.0
11 TraesCS2A01G111000 chr2D 89.128 1067 58 17 1997 3007 62033422 62032358 0.000000e+00 1275.0
12 TraesCS2A01G111000 chr2D 91.730 786 45 9 900 1677 62034572 62033799 0.000000e+00 1074.0
13 TraesCS2A01G111000 chr2D 91.206 796 59 8 1 790 62035775 62034985 0.000000e+00 1072.0
14 TraesCS2A01G111000 chr2D 85.989 935 52 35 3004 3891 62032269 62031367 0.000000e+00 928.0
15 TraesCS2A01G111000 chr2D 96.503 286 9 1 1697 1982 165661897 165662181 5.170000e-129 472.0
16 TraesCS2A01G111000 chr2D 95.804 286 11 1 1697 1982 104548749 104548465 1.120000e-125 460.0
17 TraesCS2A01G111000 chr2D 86.312 263 24 10 4156 4414 62030862 62030608 4.350000e-70 276.0
18 TraesCS2A01G111000 chr2D 73.793 580 111 20 11 576 178698001 178698553 1.620000e-44 191.0
19 TraesCS2A01G111000 chr2D 76.571 350 68 10 109 457 79779573 79779909 3.510000e-41 180.0
20 TraesCS2A01G111000 chr5D 96.503 286 9 1 1697 1982 437730518 437730234 5.170000e-129 472.0
21 TraesCS2A01G111000 chr5D 95.804 286 11 1 1697 1982 51587891 51587607 1.120000e-125 460.0
22 TraesCS2A01G111000 chr5D 77.098 572 111 14 7 574 455809487 455810042 3.310000e-81 313.0
23 TraesCS2A01G111000 chr5A 96.154 286 10 1 1697 1982 685424306 685424022 2.400000e-127 466.0
24 TraesCS2A01G111000 chr5A 74.350 577 125 18 7 576 575675326 575674766 1.600000e-54 224.0
25 TraesCS2A01G111000 chr5A 77.994 359 59 14 117 472 562544294 562543953 1.610000e-49 207.0
26 TraesCS2A01G111000 chr5A 78.014 282 55 7 14 292 578452360 578452083 2.110000e-38 171.0
27 TraesCS2A01G111000 chr5A 73.711 388 92 9 193 576 440674879 440675260 4.600000e-30 143.0
28 TraesCS2A01G111000 chr1A 96.154 286 10 1 1697 1982 29638947 29639231 2.400000e-127 466.0
29 TraesCS2A01G111000 chr1A 79.249 453 48 30 1070 1500 26548101 26547673 1.560000e-69 274.0
30 TraesCS2A01G111000 chr1A 86.538 52 7 0 11 62 543633036 543633087 1.710000e-04 58.4
31 TraesCS2A01G111000 chr7A 95.804 286 11 1 1697 1982 91596714 91596998 1.120000e-125 460.0
32 TraesCS2A01G111000 chr7A 95.798 119 5 0 4038 4156 17475386 17475504 4.510000e-45 193.0
33 TraesCS2A01G111000 chr7A 92.623 122 9 0 4037 4158 8523481 8523602 4.540000e-40 176.0
34 TraesCS2A01G111000 chr7A 79.096 177 36 1 400 576 54726492 54726667 2.160000e-23 121.0
35 TraesCS2A01G111000 chr4A 95.804 286 11 1 1697 1982 741933401 741933117 1.120000e-125 460.0
36 TraesCS2A01G111000 chr7D 95.502 289 9 2 1697 1982 592035565 592035852 4.020000e-125 459.0
37 TraesCS2A01G111000 chr7D 90.625 128 12 0 4038 4165 48534426 48534299 2.110000e-38 171.0
38 TraesCS2A01G111000 chr7D 80.000 215 32 10 4164 4373 623022645 623022853 9.890000e-32 148.0
39 TraesCS2A01G111000 chr3B 85.167 418 41 10 939 1356 80351142 80351538 4.110000e-110 409.0
40 TraesCS2A01G111000 chr3B 85.609 271 23 9 1070 1337 350050154 350050411 2.020000e-68 270.0
41 TraesCS2A01G111000 chr3B 87.243 243 20 8 1070 1310 773211824 773212057 2.620000e-67 267.0
42 TraesCS2A01G111000 chr3B 81.759 307 28 10 1411 1699 80369143 80369439 9.550000e-57 231.0
43 TraesCS2A01G111000 chr3B 80.315 254 40 8 4154 4402 694179223 694179471 2.710000e-42 183.0
44 TraesCS2A01G111000 chr3B 92.683 123 9 0 4037 4159 667390122 667390000 1.260000e-40 178.0
45 TraesCS2A01G111000 chr3B 93.277 119 8 0 4039 4157 526689436 526689554 4.540000e-40 176.0
46 TraesCS2A01G111000 chr3B 76.286 350 63 13 179 523 686426623 686426289 7.590000e-38 169.0
47 TraesCS2A01G111000 chr3B 74.803 381 77 14 132 508 384908163 384908528 2.130000e-33 154.0
48 TraesCS2A01G111000 chr3B 78.947 152 25 7 6 154 85338583 85338730 3.630000e-16 97.1
49 TraesCS2A01G111000 chr6D 78.299 576 106 13 6 576 337846676 337847237 1.950000e-93 353.0
50 TraesCS2A01G111000 chr5B 79.956 454 45 31 1070 1500 711381015 711381445 4.320000e-75 292.0
51 TraesCS2A01G111000 chr5B 79.907 214 34 9 4154 4363 510385203 510384995 9.890000e-32 148.0
52 TraesCS2A01G111000 chr6B 84.589 292 26 11 1070 1357 553748456 553748732 5.630000e-69 272.0
53 TraesCS2A01G111000 chr3A 86.831 243 23 7 1070 1310 622458915 622459150 3.390000e-66 263.0
54 TraesCS2A01G111000 chr3A 78.543 247 38 12 4154 4393 545907907 545908145 9.890000e-32 148.0
55 TraesCS2A01G111000 chr6A 76.173 533 98 19 1 522 594943353 594942839 2.040000e-63 254.0
56 TraesCS2A01G111000 chr4D 76.231 467 89 17 12 473 87927191 87927640 1.240000e-55 228.0
57 TraesCS2A01G111000 chr4D 81.159 207 28 9 4189 4391 74349106 74348907 5.910000e-34 156.0
58 TraesCS2A01G111000 chr4D 75.000 276 47 14 262 531 121472617 121472876 1.680000e-19 108.0
59 TraesCS2A01G111000 chr4B 94.017 117 7 0 4043 4159 527282632 527282516 1.260000e-40 178.0
60 TraesCS2A01G111000 chr4B 82.243 214 25 11 4192 4402 465007362 465007565 5.870000e-39 172.0
61 TraesCS2A01G111000 chr1B 90.076 131 12 1 4035 4165 481708565 481708436 7.590000e-38 169.0
62 TraesCS2A01G111000 chr1B 79.915 234 32 12 4145 4370 667972035 667971809 1.640000e-34 158.0
63 TraesCS2A01G111000 chr1D 74.830 294 60 8 286 577 223753991 223753710 2.160000e-23 121.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G111000 chr2A 62368313 62372726 4413 True 8152.00 8152 100.00000 1 4414 1 chr2A.!!$R1 4413
1 TraesCS2A01G111000 chr2A 693153818 693154376 558 False 230.00 230 74.47900 6 576 1 chr2A.!!$F2 570
2 TraesCS2A01G111000 chr2B 97393565 97397487 3922 True 934.25 1386 89.45325 674 4414 4 chr2B.!!$R4 3740
3 TraesCS2A01G111000 chr2B 569537888 569538444 556 False 250.00 250 75.13000 6 576 1 chr2B.!!$F1 570
4 TraesCS2A01G111000 chr2D 62030608 62035775 5167 True 925.00 1275 88.87300 1 4414 5 chr2D.!!$R2 4413
5 TraesCS2A01G111000 chr5D 455809487 455810042 555 False 313.00 313 77.09800 7 574 1 chr5D.!!$F1 567
6 TraesCS2A01G111000 chr5A 575674766 575675326 560 True 224.00 224 74.35000 7 576 1 chr5A.!!$R2 569
7 TraesCS2A01G111000 chr6D 337846676 337847237 561 False 353.00 353 78.29900 6 576 1 chr6D.!!$F1 570
8 TraesCS2A01G111000 chr6A 594942839 594943353 514 True 254.00 254 76.17300 1 522 1 chr6A.!!$R1 521

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
281 296 0.102481 GAGCTCCGCCGTAGATTTCA 59.898 55.0 0.87 0.0 0.00 2.69 F
317 332 0.651031 GCGATGTTAGGGTTTCTCGC 59.349 55.0 0.00 0.0 43.61 5.03 F
1144 1469 0.176910 TGTCGTTCCTTGCTGTGTGA 59.823 50.0 0.00 0.0 0.00 3.58 F
1941 2389 0.461339 GTCCACACGGTGTCAGTTGT 60.461 55.0 11.54 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1450 0.176910 TCACACAGCAAGGAACGACA 59.823 50.0 0.0 0.0 0.0 4.35 R
1175 1500 0.534412 CCTGCAAAACCCACACAACA 59.466 50.0 0.0 0.0 0.0 3.33 R
2601 3077 0.035056 ATGTGGCTGCTTAGTGGACC 60.035 55.0 0.0 0.0 0.0 4.46 R
3603 4358 0.109597 CATGCACGGTTCAGGAAAGC 60.110 55.0 0.0 0.0 0.0 3.51 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
64 68 4.778143 GGCGAGCCCGTGGATTGT 62.778 66.667 1.97 0.00 38.24 2.71
65 69 2.746277 GCGAGCCCGTGGATTGTT 60.746 61.111 0.00 0.00 38.24 2.83
66 70 2.750888 GCGAGCCCGTGGATTGTTC 61.751 63.158 0.00 0.00 38.24 3.18
70 74 2.760477 CCCGTGGATTGTTCCCCA 59.240 61.111 0.00 0.00 41.83 4.96
107 118 2.217038 GGCTGGTGTCAGGGAGTGA 61.217 63.158 0.00 0.00 41.19 3.41
230 243 2.028112 TGTCTTCTGGGTTCCGATTCTG 60.028 50.000 0.00 0.00 0.00 3.02
281 296 0.102481 GAGCTCCGCCGTAGATTTCA 59.898 55.000 0.87 0.00 0.00 2.69
317 332 0.651031 GCGATGTTAGGGTTTCTCGC 59.349 55.000 0.00 0.00 43.61 5.03
365 380 4.367450 GTGTCAGGTGCTTCAGATCTATC 58.633 47.826 0.00 0.00 0.00 2.08
370 385 4.100653 CAGGTGCTTCAGATCTATCCAAGA 59.899 45.833 0.00 0.00 39.02 3.02
398 413 1.666054 ACGACGGCCACAAACTTTAA 58.334 45.000 2.24 0.00 0.00 1.52
423 438 2.267961 GTCCTTAGGGGCACGTGG 59.732 66.667 18.88 0.00 37.14 4.94
433 448 1.448540 GGCACGTGGATGGAGACTG 60.449 63.158 18.88 0.00 0.00 3.51
546 566 7.040271 GGTCATTCAGTAGACTAGGGATCTAAC 60.040 44.444 0.00 0.00 35.18 2.34
562 582 9.474313 AGGGATCTAACTGCAATTTTTATTACA 57.526 29.630 0.00 0.00 0.00 2.41
665 685 3.119884 TGAATGTTGGATGAACGATGTGC 60.120 43.478 0.00 0.00 37.38 4.57
745 765 2.049802 GTTCCGCCACGAAGACGA 60.050 61.111 0.00 0.00 42.66 4.20
793 813 4.864334 CAGCCTCCACCGCCCATC 62.864 72.222 0.00 0.00 0.00 3.51
860 898 2.283173 CCACAGAGCCCCAAACCC 60.283 66.667 0.00 0.00 0.00 4.11
861 899 2.845345 CCACAGAGCCCCAAACCCT 61.845 63.158 0.00 0.00 0.00 4.34
876 914 4.079970 CAAACCCTTTTCCCCTCTACTTC 58.920 47.826 0.00 0.00 0.00 3.01
877 915 3.293215 ACCCTTTTCCCCTCTACTTCT 57.707 47.619 0.00 0.00 0.00 2.85
878 916 4.431158 ACCCTTTTCCCCTCTACTTCTA 57.569 45.455 0.00 0.00 0.00 2.10
881 919 4.406326 CCCTTTTCCCCTCTACTTCTACTC 59.594 50.000 0.00 0.00 0.00 2.59
970 1293 2.095263 GGAGAGCTCGATCTGATAGCAC 60.095 54.545 8.37 8.07 38.75 4.40
1118 1443 1.222113 CCGGGGCTTCTCCTCTTTC 59.778 63.158 0.00 0.00 31.12 2.62
1125 1450 3.403968 GGCTTCTCCTCTTTCTTTTCGT 58.596 45.455 0.00 0.00 0.00 3.85
1138 1463 1.597663 CTTTTCGTGTCGTTCCTTGCT 59.402 47.619 0.00 0.00 0.00 3.91
1144 1469 0.176910 TGTCGTTCCTTGCTGTGTGA 59.823 50.000 0.00 0.00 0.00 3.58
1350 1678 2.170187 TGCATTTCAACCTGCCTTGTTT 59.830 40.909 0.00 0.00 37.59 2.83
1351 1679 2.545106 GCATTTCAACCTGCCTTGTTTG 59.455 45.455 0.00 0.00 32.15 2.93
1352 1680 3.795877 CATTTCAACCTGCCTTGTTTGT 58.204 40.909 0.00 0.00 0.00 2.83
1353 1681 3.518634 TTTCAACCTGCCTTGTTTGTC 57.481 42.857 0.00 0.00 0.00 3.18
1355 1683 2.297701 TCAACCTGCCTTGTTTGTCTC 58.702 47.619 0.00 0.00 0.00 3.36
1449 1777 2.732282 GCCAAGTTGAAATCGGCTTAGC 60.732 50.000 3.87 0.00 39.73 3.09
1506 1838 3.133542 GTGGGTACTGGACTAATGGGTAC 59.866 52.174 0.00 0.00 34.00 3.34
1539 1871 4.324267 CCCCTCTACTGTTGGTAAACAAG 58.676 47.826 0.00 0.00 45.50 3.16
1650 1986 4.207019 CGGAATGCAGAAACAAAGAAACAC 59.793 41.667 0.00 0.00 0.00 3.32
1651 1987 4.207019 GGAATGCAGAAACAAAGAAACACG 59.793 41.667 0.00 0.00 0.00 4.49
1653 1989 4.427096 TGCAGAAACAAAGAAACACGAA 57.573 36.364 0.00 0.00 0.00 3.85
1776 2224 9.520204 CAACAATATCCCAAAACTGATAATGAC 57.480 33.333 0.00 0.00 0.00 3.06
1821 2269 4.197750 CTGCTTTTATGTGATCAGAGGCT 58.802 43.478 0.00 0.00 0.00 4.58
1839 2287 5.239525 AGAGGCTTAAACAGTGCAGTTTTAG 59.760 40.000 9.10 10.31 41.58 1.85
1925 2373 6.159988 GCTTAGTATACTCACATCATGGTCC 58.840 44.000 9.12 0.00 0.00 4.46
1941 2389 0.461339 GTCCACACGGTGTCAGTTGT 60.461 55.000 11.54 0.00 0.00 3.32
1971 2419 6.525629 AGCTGTAACCCATATTAGTGCTTAG 58.474 40.000 0.00 0.00 0.00 2.18
1972 2420 6.099845 AGCTGTAACCCATATTAGTGCTTAGT 59.900 38.462 0.00 0.00 0.00 2.24
1973 2421 7.289317 AGCTGTAACCCATATTAGTGCTTAGTA 59.711 37.037 0.00 0.00 0.00 1.82
1977 2425 9.866798 GTAACCCATATTAGTGCTTAGTATACC 57.133 37.037 0.00 0.00 0.00 2.73
1978 2426 8.737601 AACCCATATTAGTGCTTAGTATACCT 57.262 34.615 0.00 0.00 0.00 3.08
1979 2427 8.363761 ACCCATATTAGTGCTTAGTATACCTC 57.636 38.462 0.00 0.00 0.00 3.85
1980 2428 7.954056 ACCCATATTAGTGCTTAGTATACCTCA 59.046 37.037 0.00 0.00 0.00 3.86
1981 2429 8.982723 CCCATATTAGTGCTTAGTATACCTCAT 58.017 37.037 0.00 0.00 0.00 2.90
1986 2434 9.935241 ATTAGTGCTTAGTATACCTCATCATTG 57.065 33.333 0.00 0.00 0.00 2.82
1987 2435 7.366847 AGTGCTTAGTATACCTCATCATTGT 57.633 36.000 0.00 0.00 0.00 2.71
1988 2436 7.212976 AGTGCTTAGTATACCTCATCATTGTG 58.787 38.462 0.00 0.00 0.00 3.33
1989 2437 7.069950 AGTGCTTAGTATACCTCATCATTGTGA 59.930 37.037 0.00 0.00 0.00 3.58
1990 2438 7.169982 GTGCTTAGTATACCTCATCATTGTGAC 59.830 40.741 0.00 0.00 0.00 3.67
1991 2439 6.647067 GCTTAGTATACCTCATCATTGTGACC 59.353 42.308 0.00 0.00 0.00 4.02
1992 2440 5.201713 AGTATACCTCATCATTGTGACCG 57.798 43.478 0.00 0.00 0.00 4.79
1993 2441 4.893524 AGTATACCTCATCATTGTGACCGA 59.106 41.667 0.00 0.00 0.00 4.69
1994 2442 4.753516 ATACCTCATCATTGTGACCGAA 57.246 40.909 0.00 0.00 0.00 4.30
1995 2443 3.417069 ACCTCATCATTGTGACCGAAA 57.583 42.857 0.00 0.00 0.00 3.46
2001 2449 2.938838 TCATTGTGACCGAAAAAGGGT 58.061 42.857 0.00 0.00 41.48 4.34
2026 2474 2.093764 AGCTAGTCAACCTCATCACTGC 60.094 50.000 0.00 0.00 0.00 4.40
2106 2554 2.609459 CACATTTCTCGTGATAGCACCC 59.391 50.000 5.36 0.00 42.09 4.61
2120 2568 1.777272 AGCACCCTTCTCCTCAGTTTT 59.223 47.619 0.00 0.00 0.00 2.43
2172 2621 8.926710 CGTTATATGTAGGGAAAGATTAGCTTG 58.073 37.037 0.00 0.00 36.80 4.01
2202 2653 3.917329 TCTTTCTAGGTGTCAGTGACG 57.083 47.619 18.17 3.90 34.95 4.35
2213 2664 2.163613 TGTCAGTGACGATTCTGCGTAT 59.836 45.455 18.17 0.00 45.72 3.06
2214 2665 3.179830 GTCAGTGACGATTCTGCGTATT 58.820 45.455 7.68 0.00 45.72 1.89
2293 2758 5.319043 AGGAACTCACCAAGAATTTACCA 57.681 39.130 0.00 0.00 0.00 3.25
2303 2768 7.622081 TCACCAAGAATTTACCATACCTCTAGA 59.378 37.037 0.00 0.00 0.00 2.43
2385 2861 0.747255 TCTGATAGGCAGGTCGAAGC 59.253 55.000 0.00 0.00 44.98 3.86
2395 2871 1.303317 GGTCGAAGCCAACCCATGT 60.303 57.895 0.00 0.00 0.00 3.21
2445 2921 4.848357 CCTAATTGGTCTGGTGATGAACT 58.152 43.478 0.00 0.00 0.00 3.01
2448 2924 6.209391 CCTAATTGGTCTGGTGATGAACTTTT 59.791 38.462 0.00 0.00 0.00 2.27
2530 3006 7.675161 TGAACATAAGATCTATCCTCACCAA 57.325 36.000 0.00 0.00 0.00 3.67
2601 3077 2.579873 CCCAAGATTACCTGATGCTGG 58.420 52.381 0.00 0.00 0.00 4.85
2641 3119 8.624776 CCACATAGATCCCTCTAAACAAAAATC 58.375 37.037 0.00 0.00 37.52 2.17
2645 3123 9.981460 ATAGATCCCTCTAAACAAAAATCAGTT 57.019 29.630 0.00 0.00 37.52 3.16
2668 3146 1.668047 GCATTCTGCTTCAACTGCACC 60.668 52.381 0.00 0.00 40.96 5.01
2725 3208 5.974158 CCAGTTAGTCTCTTATCATGACACG 59.026 44.000 0.00 0.00 33.56 4.49
2791 3278 4.982241 ATCTTAAGCCAGCCAGCTATAA 57.018 40.909 0.00 0.74 44.11 0.98
2793 3280 4.645535 TCTTAAGCCAGCCAGCTATAATG 58.354 43.478 0.00 0.00 44.11 1.90
2864 3353 2.560105 GCTTGAGCACCTCTGGATTTTT 59.440 45.455 0.00 0.00 41.59 1.94
2883 3382 0.400213 TGTTTTGCCCTCTCGTGGAT 59.600 50.000 0.00 0.00 0.00 3.41
2893 3392 1.256812 TCTCGTGGATGAGAGTTGCA 58.743 50.000 0.00 0.00 40.01 4.08
2898 3404 1.225704 GGATGAGAGTTGCAGGGGG 59.774 63.158 0.00 0.00 0.00 5.40
3010 3621 8.121305 ACTGATCTTATAGATGTCCTGCTAAG 57.879 38.462 0.00 0.00 34.53 2.18
3106 3717 8.684386 TTTGTTTGTCTACATCCTTGTTATCA 57.316 30.769 0.00 0.00 37.28 2.15
3120 3731 3.495331 TGTTATCACTGGTGGCATTGTT 58.505 40.909 0.00 0.00 0.00 2.83
3162 3915 0.320683 TGTCCTTGTGCATCTCCACG 60.321 55.000 0.00 0.00 38.55 4.94
3191 3944 7.102993 AGTTTGCATTGTTTACTTGACCTTTT 58.897 30.769 0.00 0.00 0.00 2.27
3221 3974 7.759489 AGTCAAATCTAACATGTTTTGGCTA 57.241 32.000 20.75 1.82 38.79 3.93
3284 4037 3.699894 CACGCTCAGGCCCTCACT 61.700 66.667 0.00 0.00 34.44 3.41
3311 4064 1.455383 CCTTGGGTTGTTCTGCGCTT 61.455 55.000 9.73 0.00 0.00 4.68
3350 4103 3.341823 CCAGTCAGGTTCAGGATCAAAG 58.658 50.000 0.00 0.00 0.00 2.77
3380 4133 1.999648 ATGCAAAGCAGTTCCTTCCA 58.000 45.000 0.00 0.00 43.65 3.53
3407 4160 1.954382 AGAAACGCCAAAAAGGACTCC 59.046 47.619 0.00 0.00 41.22 3.85
3426 4179 1.354040 CGTGTAGAAGAGGCAGCAAG 58.646 55.000 0.00 0.00 0.00 4.01
3431 4184 5.661458 GTGTAGAAGAGGCAGCAAGTTATA 58.339 41.667 0.00 0.00 0.00 0.98
3501 4256 3.656559 AGCAAACAATCTGGCATTTCAC 58.343 40.909 0.00 0.00 0.00 3.18
3550 4305 6.466885 TTCCTGTTCTCTGTATAAGCTACC 57.533 41.667 0.00 0.00 0.00 3.18
3561 4316 3.560636 ATAAGCTACCGAACCAGCATT 57.439 42.857 0.00 0.00 40.36 3.56
3589 4344 2.021722 CCGTATGCAAATCCGTGGG 58.978 57.895 0.00 0.00 0.00 4.61
3603 4358 2.158682 TCCGTGGGGATGGAAATATGTG 60.159 50.000 0.00 0.00 37.43 3.21
3655 4418 8.908786 TGAATGAAATGTTTCTCTCTTACAGT 57.091 30.769 6.99 0.00 38.02 3.55
3656 4419 9.996554 TGAATGAAATGTTTCTCTCTTACAGTA 57.003 29.630 6.99 0.00 38.02 2.74
3660 4423 9.909644 TGAAATGTTTCTCTCTTACAGTACTAC 57.090 33.333 0.00 0.00 38.02 2.73
3678 4441 5.717078 ACTACTGATGAAGTAAACCGACA 57.283 39.130 0.00 0.00 40.92 4.35
3681 4444 4.315803 ACTGATGAAGTAAACCGACAAGG 58.684 43.478 0.00 0.00 41.46 3.61
3691 4454 2.517598 CCGACAAGGTGAGTTCGTG 58.482 57.895 0.00 0.00 34.51 4.35
3692 4455 1.557443 CCGACAAGGTGAGTTCGTGC 61.557 60.000 0.00 0.00 34.51 5.34
3739 4502 8.817100 CAAAAGAAAAACCTTATGGAGTGTTTC 58.183 33.333 0.81 5.61 37.04 2.78
3751 4515 6.877611 ATGGAGTGTTTCATTTCTAAACGT 57.122 33.333 0.00 0.00 39.23 3.99
3756 4520 6.715464 AGTGTTTCATTTCTAAACGTGACAG 58.285 36.000 0.00 0.00 39.23 3.51
3788 4552 2.450160 CGTGTTGTGTTGGCTTTTCTC 58.550 47.619 0.00 0.00 0.00 2.87
3789 4553 2.097466 CGTGTTGTGTTGGCTTTTCTCT 59.903 45.455 0.00 0.00 0.00 3.10
3791 4555 4.494484 GTGTTGTGTTGGCTTTTCTCTTT 58.506 39.130 0.00 0.00 0.00 2.52
3796 4560 5.890334 TGTGTTGGCTTTTCTCTTTTACTG 58.110 37.500 0.00 0.00 0.00 2.74
3797 4561 4.740205 GTGTTGGCTTTTCTCTTTTACTGC 59.260 41.667 0.00 0.00 0.00 4.40
3826 4597 1.243902 TTGAGGGCGTTTTGATGGAC 58.756 50.000 0.00 0.00 0.00 4.02
3827 4598 0.109532 TGAGGGCGTTTTGATGGACA 59.890 50.000 0.00 0.00 0.00 4.02
3828 4599 0.804989 GAGGGCGTTTTGATGGACAG 59.195 55.000 0.00 0.00 0.00 3.51
3829 4600 0.400213 AGGGCGTTTTGATGGACAGA 59.600 50.000 0.00 0.00 0.00 3.41
3830 4601 1.004745 AGGGCGTTTTGATGGACAGAT 59.995 47.619 0.00 0.00 0.00 2.90
3831 4602 2.238646 AGGGCGTTTTGATGGACAGATA 59.761 45.455 0.00 0.00 0.00 1.98
3832 4603 3.117888 AGGGCGTTTTGATGGACAGATAT 60.118 43.478 0.00 0.00 0.00 1.63
3833 4604 4.102524 AGGGCGTTTTGATGGACAGATATA 59.897 41.667 0.00 0.00 0.00 0.86
3834 4605 4.452455 GGGCGTTTTGATGGACAGATATAG 59.548 45.833 0.00 0.00 0.00 1.31
3835 4606 5.057149 GGCGTTTTGATGGACAGATATAGT 58.943 41.667 0.00 0.00 0.00 2.12
3836 4607 5.177696 GGCGTTTTGATGGACAGATATAGTC 59.822 44.000 0.27 0.27 35.29 2.59
3843 4614 2.630098 TGGACAGATATAGTCAGCAGCC 59.370 50.000 9.30 0.00 37.74 4.85
3851 4622 1.704641 TAGTCAGCAGCCGGTCATAT 58.295 50.000 1.90 0.00 0.00 1.78
3863 4634 4.835615 AGCCGGTCATATTCTGAAGTCTAT 59.164 41.667 1.90 0.00 35.07 1.98
3866 4637 7.015292 AGCCGGTCATATTCTGAAGTCTATTTA 59.985 37.037 1.90 0.00 35.07 1.40
3867 4638 7.656137 GCCGGTCATATTCTGAAGTCTATTTAA 59.344 37.037 1.90 0.00 35.07 1.52
3878 4654 9.462606 TCTGAAGTCTATTTAATTTCTTTCCCC 57.537 33.333 0.00 0.00 0.00 4.81
3885 4661 8.116026 TCTATTTAATTTCTTTCCCCTGAGCTT 58.884 33.333 0.00 0.00 0.00 3.74
3897 4673 1.278985 CCTGAGCTTGTGTGGTATCCA 59.721 52.381 0.00 0.00 0.00 3.41
3906 4682 4.579354 TGGTATCCACTGCCCAGT 57.421 55.556 0.00 0.00 43.61 4.00
3949 5077 2.087009 CGCGGACGTCTGGTTTCTC 61.087 63.158 25.20 6.92 33.53 2.87
3950 5078 2.087009 GCGGACGTCTGGTTTCTCG 61.087 63.158 25.20 13.59 0.00 4.04
4045 5177 5.993748 TTTTGACCTTCCATTGTATTCCC 57.006 39.130 0.00 0.00 0.00 3.97
4046 5178 4.946160 TTGACCTTCCATTGTATTCCCT 57.054 40.909 0.00 0.00 0.00 4.20
4047 5179 4.503714 TGACCTTCCATTGTATTCCCTC 57.496 45.455 0.00 0.00 0.00 4.30
4048 5180 3.202151 TGACCTTCCATTGTATTCCCTCC 59.798 47.826 0.00 0.00 0.00 4.30
4049 5181 2.172717 ACCTTCCATTGTATTCCCTCCG 59.827 50.000 0.00 0.00 0.00 4.63
4050 5182 2.172717 CCTTCCATTGTATTCCCTCCGT 59.827 50.000 0.00 0.00 0.00 4.69
4051 5183 3.467803 CTTCCATTGTATTCCCTCCGTC 58.532 50.000 0.00 0.00 0.00 4.79
4052 5184 1.766496 TCCATTGTATTCCCTCCGTCC 59.234 52.381 0.00 0.00 0.00 4.79
4053 5185 1.540363 CCATTGTATTCCCTCCGTCCG 60.540 57.143 0.00 0.00 0.00 4.79
4054 5186 0.756903 ATTGTATTCCCTCCGTCCGG 59.243 55.000 0.00 0.00 0.00 5.14
4055 5187 0.324552 TTGTATTCCCTCCGTCCGGA 60.325 55.000 0.00 0.00 42.90 5.14
4056 5188 0.324552 TGTATTCCCTCCGTCCGGAA 60.325 55.000 5.23 0.00 44.66 4.30
4057 5189 0.826062 GTATTCCCTCCGTCCGGAAA 59.174 55.000 5.23 1.92 44.66 3.13
4058 5190 1.415289 GTATTCCCTCCGTCCGGAAAT 59.585 52.381 5.23 9.21 44.66 2.17
4059 5191 1.797320 ATTCCCTCCGTCCGGAAATA 58.203 50.000 5.23 0.00 44.66 1.40
4060 5192 0.826062 TTCCCTCCGTCCGGAAATAC 59.174 55.000 5.23 0.00 44.66 1.89
4061 5193 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4062 5194 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4063 5195 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4064 5196 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4065 5197 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4066 5198 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4067 5199 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4068 5200 3.700539 TCCGTCCGGAAATACTTGTCATA 59.299 43.478 5.23 0.00 42.05 2.15
4069 5201 4.049186 CCGTCCGGAAATACTTGTCATAG 58.951 47.826 5.23 0.00 37.50 2.23
4070 5202 4.202080 CCGTCCGGAAATACTTGTCATAGA 60.202 45.833 5.23 0.00 37.50 1.98
4071 5203 5.345702 CGTCCGGAAATACTTGTCATAGAA 58.654 41.667 5.23 0.00 0.00 2.10
4072 5204 5.808540 CGTCCGGAAATACTTGTCATAGAAA 59.191 40.000 5.23 0.00 0.00 2.52
4073 5205 6.479001 CGTCCGGAAATACTTGTCATAGAAAT 59.521 38.462 5.23 0.00 0.00 2.17
4074 5206 7.516785 CGTCCGGAAATACTTGTCATAGAAATG 60.517 40.741 5.23 0.00 0.00 2.32
4075 5207 6.765989 TCCGGAAATACTTGTCATAGAAATGG 59.234 38.462 0.00 0.00 33.61 3.16
4076 5208 6.765989 CCGGAAATACTTGTCATAGAAATGGA 59.234 38.462 0.00 0.00 33.61 3.41
4077 5209 7.445402 CCGGAAATACTTGTCATAGAAATGGAT 59.555 37.037 0.00 0.00 33.61 3.41
4078 5210 8.285394 CGGAAATACTTGTCATAGAAATGGATG 58.715 37.037 0.00 0.00 33.61 3.51
4079 5211 9.125026 GGAAATACTTGTCATAGAAATGGATGT 57.875 33.333 0.00 0.00 33.61 3.06
4088 5220 8.515414 TGTCATAGAAATGGATGTATCTAGACG 58.485 37.037 0.00 0.00 31.98 4.18
4089 5221 8.516234 GTCATAGAAATGGATGTATCTAGACGT 58.484 37.037 0.00 0.00 33.61 4.34
4090 5222 9.734984 TCATAGAAATGGATGTATCTAGACGTA 57.265 33.333 0.00 0.00 33.61 3.57
4127 5259 7.826252 AGATACATCTATTTCCATCCATTTCCG 59.174 37.037 0.00 0.00 34.85 4.30
4128 5260 5.694995 ACATCTATTTCCATCCATTTCCGT 58.305 37.500 0.00 0.00 0.00 4.69
4129 5261 5.532406 ACATCTATTTCCATCCATTTCCGTG 59.468 40.000 0.00 0.00 0.00 4.94
4130 5262 5.366482 TCTATTTCCATCCATTTCCGTGA 57.634 39.130 0.00 0.00 0.00 4.35
4131 5263 5.123227 TCTATTTCCATCCATTTCCGTGAC 58.877 41.667 0.00 0.00 0.00 3.67
4132 5264 2.869101 TTCCATCCATTTCCGTGACA 57.131 45.000 0.00 0.00 0.00 3.58
4133 5265 2.869101 TCCATCCATTTCCGTGACAA 57.131 45.000 0.00 0.00 0.00 3.18
4134 5266 2.710377 TCCATCCATTTCCGTGACAAG 58.290 47.619 0.00 0.00 0.00 3.16
4135 5267 2.039746 TCCATCCATTTCCGTGACAAGT 59.960 45.455 0.00 0.00 0.00 3.16
4136 5268 3.262151 TCCATCCATTTCCGTGACAAGTA 59.738 43.478 0.00 0.00 0.00 2.24
4137 5269 4.006989 CCATCCATTTCCGTGACAAGTAA 58.993 43.478 0.00 0.00 0.00 2.24
4138 5270 4.640201 CCATCCATTTCCGTGACAAGTAAT 59.360 41.667 0.00 0.00 0.00 1.89
4139 5271 5.125417 CCATCCATTTCCGTGACAAGTAATT 59.875 40.000 0.00 0.00 0.00 1.40
4140 5272 5.873179 TCCATTTCCGTGACAAGTAATTC 57.127 39.130 0.00 0.00 0.00 2.17
4141 5273 4.698304 TCCATTTCCGTGACAAGTAATTCC 59.302 41.667 0.00 0.00 0.00 3.01
4142 5274 4.436852 CCATTTCCGTGACAAGTAATTCCG 60.437 45.833 0.00 0.00 0.00 4.30
4143 5275 2.373540 TCCGTGACAAGTAATTCCGG 57.626 50.000 0.00 0.00 35.41 5.14
4144 5276 1.894466 TCCGTGACAAGTAATTCCGGA 59.106 47.619 0.00 0.00 40.37 5.14
4145 5277 1.997606 CCGTGACAAGTAATTCCGGAC 59.002 52.381 1.83 0.00 36.12 4.79
4146 5278 1.652124 CGTGACAAGTAATTCCGGACG 59.348 52.381 1.83 0.00 0.00 4.79
4147 5279 1.997606 GTGACAAGTAATTCCGGACGG 59.002 52.381 1.83 3.96 0.00 4.79
4148 5280 1.894466 TGACAAGTAATTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4149 5281 2.094390 TGACAAGTAATTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4150 5282 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4151 5283 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4152 5284 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
4153 5285 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4154 5286 0.032813 TAATTCCGGACGGAGGGAGT 60.033 55.000 13.64 1.45 46.06 3.85
4155 5287 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4156 5288 0.754587 ATTCCGGACGGAGGGAGTAC 60.755 60.000 13.64 0.00 46.06 2.73
4157 5289 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
4158 5290 1.379576 CCGGACGGAGGGAGTACTT 60.380 63.158 4.40 0.00 37.50 2.24
4159 5291 1.664321 CCGGACGGAGGGAGTACTTG 61.664 65.000 4.40 0.00 37.50 3.16
4160 5292 0.964358 CGGACGGAGGGAGTACTTGT 60.964 60.000 0.00 0.00 0.00 3.16
4161 5293 0.531200 GGACGGAGGGAGTACTTGTG 59.469 60.000 0.00 0.00 0.00 3.33
4240 5374 6.183360 CGGCCAAAAATAGTGTGAATAGTCAT 60.183 38.462 2.24 0.00 35.80 3.06
4242 5376 7.196331 GCCAAAAATAGTGTGAATAGTCATCC 58.804 38.462 0.00 0.00 35.80 3.51
4405 5539 9.976776 TTCCTCATATAGGGTGTAGATACTAAG 57.023 37.037 0.00 0.00 46.55 2.18
4406 5540 9.347777 TCCTCATATAGGGTGTAGATACTAAGA 57.652 37.037 0.00 0.00 46.55 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 68 4.113815 CGGCAGGCAGATGGGGAA 62.114 66.667 0.00 0.00 0.00 3.97
107 118 1.408822 GGAGTGGAGGCATCGGAATTT 60.409 52.381 0.00 0.00 0.00 1.82
230 243 2.987821 GTCTAGACGGACAAACTCAAGC 59.012 50.000 7.22 0.00 36.35 4.01
270 283 1.749634 AGGAGACGGTGAAATCTACGG 59.250 52.381 0.00 0.00 30.38 4.02
281 296 3.382832 CCGCCTGAAGGAGACGGT 61.383 66.667 0.00 0.00 39.05 4.83
333 348 1.442769 CACCTGACACCAAATCTCGG 58.557 55.000 0.00 0.00 0.00 4.63
365 380 1.260561 CCGTCGTTGTTGAACTCTTGG 59.739 52.381 0.00 0.00 0.00 3.61
370 385 1.153329 TGGCCGTCGTTGTTGAACT 60.153 52.632 0.00 0.00 0.00 3.01
398 413 3.083997 CCCTAAGGACCAGCGCCT 61.084 66.667 2.29 0.00 37.35 5.52
423 438 2.822561 TGACAGTCAGACAGTCTCCATC 59.177 50.000 22.61 1.38 35.88 3.51
433 448 2.029828 ACCTTGTCGATGACAGTCAGAC 60.030 50.000 9.64 12.01 43.69 3.51
546 566 8.170553 GCACCTCAAATGTAATAAAAATTGCAG 58.829 33.333 0.00 0.00 30.14 4.41
561 581 5.382618 AAGAGCTAAAAGCACCTCAAATG 57.617 39.130 1.22 0.00 45.56 2.32
562 582 8.807948 TTATAAGAGCTAAAAGCACCTCAAAT 57.192 30.769 1.22 0.00 45.56 2.32
648 668 1.164411 TGGCACATCGTTCATCCAAC 58.836 50.000 0.00 0.00 0.00 3.77
665 685 0.325933 TCTCCTGTGGTTGCTGATGG 59.674 55.000 0.00 0.00 0.00 3.51
745 765 2.241880 CGTGGCTCGTGGTTTTCGT 61.242 57.895 0.00 0.00 34.52 3.85
815 841 1.473434 CGGGGGAAATGAGTCTACTGC 60.473 57.143 0.00 0.00 0.00 4.40
818 844 0.179054 GGCGGGGGAAATGAGTCTAC 60.179 60.000 0.00 0.00 0.00 2.59
843 881 2.283173 GGGTTTGGGGCTCTGTGG 60.283 66.667 0.00 0.00 0.00 4.17
844 882 0.469892 AAAGGGTTTGGGGCTCTGTG 60.470 55.000 0.00 0.00 0.00 3.66
860 898 5.274015 AGGAGTAGAAGTAGAGGGGAAAAG 58.726 45.833 0.00 0.00 0.00 2.27
861 899 5.270794 GAGGAGTAGAAGTAGAGGGGAAAA 58.729 45.833 0.00 0.00 0.00 2.29
918 1241 3.037833 CTGCGCGTGTGCTTCTGA 61.038 61.111 8.43 0.00 39.65 3.27
1118 1443 1.597663 AGCAAGGAACGACACGAAAAG 59.402 47.619 0.00 0.00 0.00 2.27
1125 1450 0.176910 TCACACAGCAAGGAACGACA 59.823 50.000 0.00 0.00 0.00 4.35
1138 1463 8.578151 TCAGATTCAATTCAATTCAATCACACA 58.422 29.630 9.18 0.00 0.00 3.72
1144 1469 7.567622 AGGGGATCAGATTCAATTCAATTCAAT 59.432 33.333 0.00 0.00 0.00 2.57
1175 1500 0.534412 CCTGCAAAACCCACACAACA 59.466 50.000 0.00 0.00 0.00 3.33
1178 1503 1.040339 GTCCCTGCAAAACCCACACA 61.040 55.000 0.00 0.00 0.00 3.72
1180 1505 1.826054 CGTCCCTGCAAAACCCACA 60.826 57.895 0.00 0.00 0.00 4.17
1181 1506 3.039134 CGTCCCTGCAAAACCCAC 58.961 61.111 0.00 0.00 0.00 4.61
1350 1678 7.009179 ACATAGAAATTCAACTCAGGAGACA 57.991 36.000 2.79 0.00 0.00 3.41
1351 1679 7.604164 TCAACATAGAAATTCAACTCAGGAGAC 59.396 37.037 2.79 0.00 0.00 3.36
1352 1680 7.679783 TCAACATAGAAATTCAACTCAGGAGA 58.320 34.615 2.79 0.00 0.00 3.71
1353 1681 7.912056 TCAACATAGAAATTCAACTCAGGAG 57.088 36.000 0.00 0.00 0.00 3.69
1355 1683 8.103948 ACTTCAACATAGAAATTCAACTCAGG 57.896 34.615 0.00 0.00 0.00 3.86
1449 1777 2.191513 CGGGCATTGCTGATGGGAG 61.192 63.158 8.82 0.00 36.21 4.30
1506 1838 1.918293 TAGAGGGGCACACCACAGG 60.918 63.158 0.00 0.00 44.59 4.00
1539 1871 4.380531 TCCAGAATTGAATACTCGCATCC 58.619 43.478 0.00 0.00 0.00 3.51
1776 2224 4.094442 GCTACCTCCCTTAACAAATTCACG 59.906 45.833 0.00 0.00 0.00 4.35
1821 2269 7.603651 TGGAAAACTAAAACTGCACTGTTTAA 58.396 30.769 4.67 0.00 38.98 1.52
1839 2287 4.149598 ACCCCAAAGACATACTGGAAAAC 58.850 43.478 0.00 0.00 31.38 2.43
1925 2373 1.062002 GTTGACAACTGACACCGTGTG 59.938 52.381 9.42 0.00 39.75 3.82
1941 2389 7.497595 CACTAATATGGGTTACAGCTAGTTGA 58.502 38.462 14.09 0.00 0.00 3.18
1971 2419 5.196341 TCGGTCACAATGATGAGGTATAC 57.804 43.478 0.00 0.00 0.00 1.47
1972 2420 5.862678 TTCGGTCACAATGATGAGGTATA 57.137 39.130 0.00 0.00 0.00 1.47
1973 2421 4.753516 TTCGGTCACAATGATGAGGTAT 57.246 40.909 0.00 0.00 0.00 2.73
1976 2424 4.379813 CCTTTTTCGGTCACAATGATGAGG 60.380 45.833 0.00 0.00 0.00 3.86
1977 2425 4.379813 CCCTTTTTCGGTCACAATGATGAG 60.380 45.833 0.00 0.00 0.00 2.90
1978 2426 3.505680 CCCTTTTTCGGTCACAATGATGA 59.494 43.478 0.00 0.00 0.00 2.92
1979 2427 3.255642 ACCCTTTTTCGGTCACAATGATG 59.744 43.478 0.00 0.00 0.00 3.07
1980 2428 3.496331 ACCCTTTTTCGGTCACAATGAT 58.504 40.909 0.00 0.00 0.00 2.45
1981 2429 2.938838 ACCCTTTTTCGGTCACAATGA 58.061 42.857 0.00 0.00 0.00 2.57
1982 2430 3.317993 AGAACCCTTTTTCGGTCACAATG 59.682 43.478 0.00 0.00 31.48 2.82
1983 2431 3.562182 AGAACCCTTTTTCGGTCACAAT 58.438 40.909 0.00 0.00 31.48 2.71
1984 2432 3.007473 AGAACCCTTTTTCGGTCACAA 57.993 42.857 0.00 0.00 31.48 3.33
1985 2433 2.721425 AGAACCCTTTTTCGGTCACA 57.279 45.000 0.00 0.00 31.48 3.58
1986 2434 2.483106 GCTAGAACCCTTTTTCGGTCAC 59.517 50.000 0.00 0.00 31.48 3.67
1987 2435 2.370849 AGCTAGAACCCTTTTTCGGTCA 59.629 45.455 0.00 0.00 31.48 4.02
1988 2436 3.055209 AGCTAGAACCCTTTTTCGGTC 57.945 47.619 0.00 0.00 31.48 4.79
1989 2437 3.581770 ACTAGCTAGAACCCTTTTTCGGT 59.418 43.478 27.45 0.00 34.07 4.69
1990 2438 4.182339 GACTAGCTAGAACCCTTTTTCGG 58.818 47.826 27.45 0.00 0.00 4.30
1991 2439 4.817517 TGACTAGCTAGAACCCTTTTTCG 58.182 43.478 27.45 0.00 0.00 3.46
1992 2440 5.411977 GGTTGACTAGCTAGAACCCTTTTTC 59.588 44.000 27.45 11.02 33.11 2.29
1993 2441 5.073280 AGGTTGACTAGCTAGAACCCTTTTT 59.927 40.000 28.29 14.92 38.98 1.94
1994 2442 4.597940 AGGTTGACTAGCTAGAACCCTTTT 59.402 41.667 28.29 15.19 38.98 2.27
1995 2443 4.168883 AGGTTGACTAGCTAGAACCCTTT 58.831 43.478 28.29 15.45 38.98 3.11
2001 2449 5.126222 CAGTGATGAGGTTGACTAGCTAGAA 59.874 44.000 27.45 11.92 33.94 2.10
2026 2474 8.504005 ACTATTTCTGACCTTTTACATTGAACG 58.496 33.333 0.00 0.00 0.00 3.95
2060 2508 7.822334 TGTTCATTACAGTTTATAGGTCTGGTG 59.178 37.037 0.00 0.00 34.02 4.17
2061 2509 7.822822 GTGTTCATTACAGTTTATAGGTCTGGT 59.177 37.037 0.00 0.00 37.45 4.00
2063 2511 8.771920 TGTGTTCATTACAGTTTATAGGTCTG 57.228 34.615 0.00 0.00 37.45 3.51
2064 2512 9.959721 AATGTGTTCATTACAGTTTATAGGTCT 57.040 29.630 0.00 0.00 41.76 3.85
2172 2621 8.251721 ACTGACACCTAGAAAGATATGTACAAC 58.748 37.037 0.00 0.00 0.00 3.32
2213 2664 8.004801 TGAGGGATAGTAGAGATTATGTGTCAA 58.995 37.037 0.00 0.00 0.00 3.18
2214 2665 7.526918 TGAGGGATAGTAGAGATTATGTGTCA 58.473 38.462 0.00 0.00 0.00 3.58
2303 2768 8.956446 TCCCTCCTTTAAAAGAAAATCATCTT 57.044 30.769 0.00 0.00 41.34 2.40
2414 2890 1.017387 GACCAATTAGGCAAGAGGCG 58.983 55.000 0.00 0.00 46.16 5.52
2445 2921 7.389803 TCTTGCGGATTCAAGAATCATAAAA 57.610 32.000 20.73 10.46 46.56 1.52
2527 3003 8.786898 TGTTCTGTCTCTTTTTCAATCTATTGG 58.213 33.333 3.00 0.00 38.30 3.16
2530 3006 8.787852 GGTTGTTCTGTCTCTTTTTCAATCTAT 58.212 33.333 0.00 0.00 0.00 1.98
2601 3077 0.035056 ATGTGGCTGCTTAGTGGACC 60.035 55.000 0.00 0.00 0.00 4.46
2668 3146 2.874701 CTGTCACAGTGGAAGTTTCTGG 59.125 50.000 0.00 0.00 34.02 3.86
2725 3208 3.823304 AGTCATTCTGCCAAGGAAGTTTC 59.177 43.478 0.00 0.00 0.00 2.78
2791 3278 4.168675 AGATGTGTGTTATTGGGATCCCAT 59.831 41.667 34.21 24.06 46.64 4.00
2793 3280 3.885297 CAGATGTGTGTTATTGGGATCCC 59.115 47.826 25.22 25.22 0.00 3.85
2864 3353 0.400213 ATCCACGAGAGGGCAAAACA 59.600 50.000 0.00 0.00 0.00 2.83
2898 3404 8.652290 AGGTCTGATAAGTATTCAGAATAACCC 58.348 37.037 4.31 2.87 41.44 4.11
2916 3422 7.827729 ACCTAAAGCGTTAATAAAAGGTCTGAT 59.172 33.333 0.00 0.00 30.31 2.90
3010 3621 6.651086 AGATTAACAGTAGGAACCTAAAGGC 58.349 40.000 1.88 0.00 39.32 4.35
3094 3705 2.308570 TGCCACCAGTGATAACAAGGAT 59.691 45.455 0.00 0.00 0.00 3.24
3162 3915 8.082242 AGGTCAAGTAAACAATGCAAACTAATC 58.918 33.333 0.00 0.00 0.00 1.75
3191 3944 9.729023 CAAAACATGTTAGATTTGACTACACAA 57.271 29.630 12.39 0.00 34.39 3.33
3238 3991 6.071165 CCTGCCAAGGTAGAAGAATTCAAATT 60.071 38.462 8.44 0.00 42.79 1.82
3284 4037 2.115910 CAACCCAAGGCAGCCAGA 59.884 61.111 15.80 0.00 0.00 3.86
3311 4064 4.610333 ACTGGTGATCATAGTACTCCACA 58.390 43.478 12.33 0.00 0.00 4.17
3344 4097 3.937814 TGCATAGTCGTGAACCTTTGAT 58.062 40.909 0.00 0.00 0.00 2.57
3350 4103 1.804151 TGCTTTGCATAGTCGTGAACC 59.196 47.619 6.03 0.00 31.71 3.62
3380 4133 1.600023 TTTTGGCGTTTCTGTCCGAT 58.400 45.000 0.00 0.00 0.00 4.18
3407 4160 1.337260 ACTTGCTGCCTCTTCTACACG 60.337 52.381 0.00 0.00 0.00 4.49
3431 4184 8.216423 CCATATCAGCTAATGGAAGCCTATATT 58.784 37.037 14.03 0.00 44.62 1.28
3501 4256 2.223340 GCAGAACTTGGATAACGGCATG 60.223 50.000 0.00 0.00 0.00 4.06
3603 4358 0.109597 CATGCACGGTTCAGGAAAGC 60.110 55.000 0.00 0.00 0.00 3.51
3648 4411 9.570488 GGTTTACTTCATCAGTAGTACTGTAAG 57.430 37.037 25.83 25.24 46.03 2.34
3649 4412 8.239314 CGGTTTACTTCATCAGTAGTACTGTAA 58.761 37.037 25.83 17.94 46.03 2.41
3650 4413 7.607607 TCGGTTTACTTCATCAGTAGTACTGTA 59.392 37.037 25.83 15.16 46.03 2.74
3651 4414 6.432162 TCGGTTTACTTCATCAGTAGTACTGT 59.568 38.462 25.83 13.23 46.03 3.55
3653 4416 6.432162 TGTCGGTTTACTTCATCAGTAGTACT 59.568 38.462 0.00 0.00 39.28 2.73
3654 4417 6.615088 TGTCGGTTTACTTCATCAGTAGTAC 58.385 40.000 0.00 0.00 39.28 2.73
3655 4418 6.822667 TGTCGGTTTACTTCATCAGTAGTA 57.177 37.500 0.00 0.00 39.28 1.82
3656 4419 5.717078 TGTCGGTTTACTTCATCAGTAGT 57.283 39.130 0.00 0.00 39.28 2.73
3657 4420 5.577164 CCTTGTCGGTTTACTTCATCAGTAG 59.423 44.000 0.00 0.00 39.28 2.57
3658 4421 5.011329 ACCTTGTCGGTTTACTTCATCAGTA 59.989 40.000 0.00 0.00 46.37 2.74
3659 4422 4.202326 ACCTTGTCGGTTTACTTCATCAGT 60.202 41.667 0.00 0.00 46.37 3.41
3660 4423 4.152402 CACCTTGTCGGTTTACTTCATCAG 59.848 45.833 0.00 0.00 46.37 2.90
3661 4424 4.062293 CACCTTGTCGGTTTACTTCATCA 58.938 43.478 0.00 0.00 46.37 3.07
3662 4425 4.312443 TCACCTTGTCGGTTTACTTCATC 58.688 43.478 0.00 0.00 46.37 2.92
3675 4438 1.853319 CGCACGAACTCACCTTGTC 59.147 57.895 0.00 0.00 0.00 3.18
3678 4441 1.956170 CTGCGCACGAACTCACCTT 60.956 57.895 5.66 0.00 0.00 3.50
3681 4444 1.488957 CTTCTGCGCACGAACTCAC 59.511 57.895 5.66 0.00 0.00 3.51
3682 4445 2.310233 GCTTCTGCGCACGAACTCA 61.310 57.895 5.66 0.00 0.00 3.41
3688 4451 2.473378 CAGAAGCTTCTGCGCACG 59.527 61.111 36.46 17.46 46.97 5.34
3710 4473 5.602561 ACTCCATAAGGTTTTTCTTTTGCCT 59.397 36.000 0.00 0.00 35.89 4.75
3718 4481 8.887036 AAATGAAACACTCCATAAGGTTTTTC 57.113 30.769 0.00 0.00 32.15 2.29
3719 4482 8.704668 AGAAATGAAACACTCCATAAGGTTTTT 58.295 29.630 0.00 0.00 32.15 1.94
3724 4487 7.962918 CGTTTAGAAATGAAACACTCCATAAGG 59.037 37.037 0.00 0.00 36.74 2.69
3739 4502 6.223138 TGCTTACTGTCACGTTTAGAAATG 57.777 37.500 0.00 0.00 0.00 2.32
3751 4515 2.001872 CACGCATCATGCTTACTGTCA 58.998 47.619 8.30 0.00 42.25 3.58
3756 4520 2.095768 ACACAACACGCATCATGCTTAC 60.096 45.455 8.30 0.00 42.25 2.34
3773 4537 5.678616 GCAGTAAAAGAGAAAAGCCAACACA 60.679 40.000 0.00 0.00 0.00 3.72
3788 4552 4.653535 CAAACGTCGTTTGCAGTAAAAG 57.346 40.909 31.27 10.50 44.59 2.27
3826 4597 1.615883 ACCGGCTGCTGACTATATCTG 59.384 52.381 10.70 0.00 0.00 2.90
3827 4598 1.889829 GACCGGCTGCTGACTATATCT 59.110 52.381 10.70 0.00 0.00 1.98
3828 4599 1.613925 TGACCGGCTGCTGACTATATC 59.386 52.381 10.70 0.00 0.00 1.63
3829 4600 1.704641 TGACCGGCTGCTGACTATAT 58.295 50.000 10.70 0.00 0.00 0.86
3830 4601 1.704641 ATGACCGGCTGCTGACTATA 58.295 50.000 10.70 0.00 0.00 1.31
3831 4602 1.704641 TATGACCGGCTGCTGACTAT 58.295 50.000 10.70 3.54 0.00 2.12
3832 4603 1.704641 ATATGACCGGCTGCTGACTA 58.295 50.000 10.70 0.00 0.00 2.59
3833 4604 0.833287 AATATGACCGGCTGCTGACT 59.167 50.000 10.70 0.00 0.00 3.41
3834 4605 1.202580 AGAATATGACCGGCTGCTGAC 60.203 52.381 10.70 4.43 0.00 3.51
3835 4606 1.123077 AGAATATGACCGGCTGCTGA 58.877 50.000 10.70 0.00 0.00 4.26
3836 4607 1.202568 TCAGAATATGACCGGCTGCTG 60.203 52.381 0.00 0.26 31.12 4.41
3863 4634 5.838521 ACAAGCTCAGGGGAAAGAAATTAAA 59.161 36.000 0.00 0.00 0.00 1.52
3866 4637 3.575687 CACAAGCTCAGGGGAAAGAAATT 59.424 43.478 0.00 0.00 0.00 1.82
3867 4638 3.160269 CACAAGCTCAGGGGAAAGAAAT 58.840 45.455 0.00 0.00 0.00 2.17
3870 4641 1.140312 ACACAAGCTCAGGGGAAAGA 58.860 50.000 0.00 0.00 0.00 2.52
3871 4642 1.242076 CACACAAGCTCAGGGGAAAG 58.758 55.000 0.00 0.00 0.00 2.62
3874 4650 0.472925 TACCACACAAGCTCAGGGGA 60.473 55.000 8.16 0.00 0.00 4.81
3878 4654 2.768253 TGGATACCACACAAGCTCAG 57.232 50.000 0.00 0.00 0.00 3.35
3900 4676 4.256180 CCCTATCCGGCACTGGGC 62.256 72.222 0.00 0.00 43.74 5.36
3904 4680 0.469518 GAGGTACCCTATCCGGCACT 60.470 60.000 8.74 0.00 31.76 4.40
3905 4681 0.469518 AGAGGTACCCTATCCGGCAC 60.470 60.000 8.74 0.00 31.76 5.01
3906 4682 0.263765 AAGAGGTACCCTATCCGGCA 59.736 55.000 8.74 0.00 31.76 5.69
3907 4683 0.680061 CAAGAGGTACCCTATCCGGC 59.320 60.000 8.74 0.00 31.76 6.13
3910 4686 3.232662 GTCTCCAAGAGGTACCCTATCC 58.767 54.545 8.74 0.00 31.76 2.59
3911 4687 2.885894 CGTCTCCAAGAGGTACCCTATC 59.114 54.545 8.74 0.00 31.76 2.08
3913 4689 1.684248 GCGTCTCCAAGAGGTACCCTA 60.684 57.143 8.74 0.00 31.76 3.53
3940 5068 5.278858 GGGTATAGATACACCGAGAAACCAG 60.279 48.000 2.28 0.00 35.53 4.00
4023 5155 5.650283 AGGGAATACAATGGAAGGTCAAAA 58.350 37.500 0.00 0.00 0.00 2.44
4039 5171 1.797320 ATTTCCGGACGGAGGGAATA 58.203 50.000 13.64 0.00 46.06 1.75
4041 5173 0.826062 GTATTTCCGGACGGAGGGAA 59.174 55.000 13.64 6.20 46.06 3.97
4043 5175 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4044 5176 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4045 5177 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4046 5178 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4047 5179 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4048 5180 4.928601 TCTATGACAAGTATTTCCGGACG 58.071 43.478 1.83 0.00 0.00 4.79
4049 5181 7.254795 CCATTTCTATGACAAGTATTTCCGGAC 60.255 40.741 1.83 0.00 33.37 4.79
4050 5182 6.765989 CCATTTCTATGACAAGTATTTCCGGA 59.234 38.462 0.00 0.00 33.37 5.14
4051 5183 6.765989 TCCATTTCTATGACAAGTATTTCCGG 59.234 38.462 0.00 0.00 33.37 5.14
4052 5184 7.786178 TCCATTTCTATGACAAGTATTTCCG 57.214 36.000 0.00 0.00 33.37 4.30
4053 5185 9.125026 ACATCCATTTCTATGACAAGTATTTCC 57.875 33.333 0.00 0.00 33.37 3.13
4062 5194 8.515414 CGTCTAGATACATCCATTTCTATGACA 58.485 37.037 0.00 0.00 33.37 3.58
4063 5195 8.516234 ACGTCTAGATACATCCATTTCTATGAC 58.484 37.037 0.00 0.00 33.37 3.06
4064 5196 8.637196 ACGTCTAGATACATCCATTTCTATGA 57.363 34.615 0.00 0.00 33.37 2.15
4101 5233 7.826252 CGGAAATGGATGGAAATAGATGTATCT 59.174 37.037 0.00 0.00 40.86 1.98
4102 5234 7.607991 ACGGAAATGGATGGAAATAGATGTATC 59.392 37.037 0.00 0.00 0.00 2.24
4103 5235 7.391554 CACGGAAATGGATGGAAATAGATGTAT 59.608 37.037 0.00 0.00 0.00 2.29
4104 5236 6.710295 CACGGAAATGGATGGAAATAGATGTA 59.290 38.462 0.00 0.00 0.00 2.29
4105 5237 5.532406 CACGGAAATGGATGGAAATAGATGT 59.468 40.000 0.00 0.00 0.00 3.06
4106 5238 5.764686 TCACGGAAATGGATGGAAATAGATG 59.235 40.000 0.00 0.00 0.00 2.90
4107 5239 5.765182 GTCACGGAAATGGATGGAAATAGAT 59.235 40.000 0.00 0.00 0.00 1.98
4108 5240 5.123227 GTCACGGAAATGGATGGAAATAGA 58.877 41.667 0.00 0.00 0.00 1.98
4109 5241 4.881273 TGTCACGGAAATGGATGGAAATAG 59.119 41.667 0.00 0.00 0.00 1.73
4110 5242 4.849518 TGTCACGGAAATGGATGGAAATA 58.150 39.130 0.00 0.00 0.00 1.40
4111 5243 3.696045 TGTCACGGAAATGGATGGAAAT 58.304 40.909 0.00 0.00 0.00 2.17
4112 5244 3.147553 TGTCACGGAAATGGATGGAAA 57.852 42.857 0.00 0.00 0.00 3.13
4113 5245 2.869101 TGTCACGGAAATGGATGGAA 57.131 45.000 0.00 0.00 0.00 3.53
4114 5246 2.039746 ACTTGTCACGGAAATGGATGGA 59.960 45.455 0.00 0.00 0.00 3.41
4115 5247 2.436417 ACTTGTCACGGAAATGGATGG 58.564 47.619 0.00 0.00 0.00 3.51
4116 5248 5.818136 ATTACTTGTCACGGAAATGGATG 57.182 39.130 0.00 0.00 0.00 3.51
4117 5249 5.357032 GGAATTACTTGTCACGGAAATGGAT 59.643 40.000 0.00 0.00 0.00 3.41
4118 5250 4.698304 GGAATTACTTGTCACGGAAATGGA 59.302 41.667 0.00 0.00 0.00 3.41
4119 5251 4.436852 CGGAATTACTTGTCACGGAAATGG 60.437 45.833 0.00 0.00 0.00 3.16
4120 5252 4.436852 CCGGAATTACTTGTCACGGAAATG 60.437 45.833 0.00 0.00 42.19 2.32
4121 5253 3.687698 CCGGAATTACTTGTCACGGAAAT 59.312 43.478 0.00 0.00 42.19 2.17
4122 5254 3.068560 CCGGAATTACTTGTCACGGAAA 58.931 45.455 0.00 0.00 42.19 3.13
4123 5255 2.299582 TCCGGAATTACTTGTCACGGAA 59.700 45.455 0.00 0.00 44.85 4.30
4124 5256 1.894466 TCCGGAATTACTTGTCACGGA 59.106 47.619 0.00 0.00 45.52 4.69
4125 5257 1.997606 GTCCGGAATTACTTGTCACGG 59.002 52.381 5.23 0.00 41.06 4.94
4126 5258 1.652124 CGTCCGGAATTACTTGTCACG 59.348 52.381 5.23 0.00 0.00 4.35
4127 5259 1.997606 CCGTCCGGAATTACTTGTCAC 59.002 52.381 5.23 0.00 37.50 3.67
4128 5260 1.894466 TCCGTCCGGAATTACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4129 5261 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4130 5262 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4131 5263 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4132 5264 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
4133 5265 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
4134 5266 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
4135 5267 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
4136 5268 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
4137 5269 0.754587 GTACTCCCTCCGTCCGGAAT 60.755 60.000 5.23 0.00 44.66 3.01
4138 5270 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
4139 5271 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
4140 5272 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
4141 5273 0.964358 ACAAGTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
4142 5274 0.531200 CACAAGTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
4143 5275 1.542492 TCACAAGTACTCCCTCCGTC 58.458 55.000 0.00 0.00 0.00 4.79
4144 5276 2.005370 TTCACAAGTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
4145 5277 3.396260 TTTTCACAAGTACTCCCTCCG 57.604 47.619 0.00 0.00 0.00 4.63
4146 5278 4.457466 TGTTTTTCACAAGTACTCCCTCC 58.543 43.478 0.00 0.00 29.87 4.30
4147 5279 6.294010 GGAATGTTTTTCACAAGTACTCCCTC 60.294 42.308 0.00 0.00 39.50 4.30
4148 5280 5.535030 GGAATGTTTTTCACAAGTACTCCCT 59.465 40.000 0.00 0.00 39.50 4.20
4149 5281 5.300792 TGGAATGTTTTTCACAAGTACTCCC 59.699 40.000 0.00 0.00 39.50 4.30
4150 5282 6.183360 TGTGGAATGTTTTTCACAAGTACTCC 60.183 38.462 0.00 0.00 46.18 3.85
4151 5283 6.791303 TGTGGAATGTTTTTCACAAGTACTC 58.209 36.000 0.00 0.00 46.18 2.59
4152 5284 6.767524 TGTGGAATGTTTTTCACAAGTACT 57.232 33.333 0.00 0.00 46.18 2.73
4159 5291 6.976636 TTCCTTTTGTGGAATGTTTTTCAC 57.023 33.333 0.00 0.00 40.80 3.18
4160 5292 7.094592 GGTTTTCCTTTTGTGGAATGTTTTTCA 60.095 33.333 0.00 0.00 44.55 2.69
4161 5293 7.247728 GGTTTTCCTTTTGTGGAATGTTTTTC 58.752 34.615 0.00 0.00 44.55 2.29
4294 5428 8.800370 TTTGCACTAGTATATGAATTTCCACA 57.200 30.769 0.00 0.00 0.00 4.17
4295 5429 9.722056 CTTTTGCACTAGTATATGAATTTCCAC 57.278 33.333 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.