Multiple sequence alignment - TraesCS4B01G011200

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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 TraesCS4B01G011200 chr4B 100.000 4720 0 0 1 4720 7374685 7379404 0.000000e+00 8717.0
1 TraesCS4B01G011200 chr4B 82.122 2036 242 46 1980 3922 7171381 7173387 0.000000e+00 1631.0
2 TraesCS4B01G011200 chr4B 82.289 2010 238 43 2004 3922 7309471 7311453 0.000000e+00 1631.0
3 TraesCS4B01G011200 chr4B 82.906 1872 223 51 2133 3922 7354507 7356363 0.000000e+00 1594.0
4 TraesCS4B01G011200 chr4B 86.182 1129 92 31 713 1785 7170329 7171449 0.000000e+00 1162.0
5 TraesCS4B01G011200 chr4B 85.324 1172 106 25 667 1785 7308357 7309515 0.000000e+00 1151.0
6 TraesCS4B01G011200 chr4B 85.778 1125 104 20 713 1785 7217288 7218408 0.000000e+00 1140.0
7 TraesCS4B01G011200 chr4B 85.714 1127 101 25 713 1785 7262904 7264024 0.000000e+00 1134.0
8 TraesCS4B01G011200 chr4B 85.913 1079 95 26 754 1779 7353355 7354429 0.000000e+00 1098.0
9 TraesCS4B01G011200 chr4B 76.844 1749 287 61 1878 3577 7457431 7459110 0.000000e+00 878.0
10 TraesCS4B01G011200 chr4B 94.716 511 27 0 2 512 7159392 7159902 0.000000e+00 795.0
11 TraesCS4B01G011200 chr4B 94.716 511 26 1 2 512 7253719 7254228 0.000000e+00 793.0
12 TraesCS4B01G011200 chr4B 94.716 511 25 2 2 512 7297944 7298452 0.000000e+00 793.0
13 TraesCS4B01G011200 chr4B 94.521 511 27 1 2 512 7344561 7345070 0.000000e+00 787.0
14 TraesCS4B01G011200 chr4B 94.325 511 28 1 2 512 7206655 7207164 0.000000e+00 782.0
15 TraesCS4B01G011200 chr4B 93.738 511 32 0 2 512 7192340 7192850 0.000000e+00 767.0
16 TraesCS4B01G011200 chr4B 93.346 511 34 0 2 512 7238775 7239285 0.000000e+00 756.0
17 TraesCS4B01G011200 chr4B 88.596 342 33 5 3581 3921 7220011 7220347 1.220000e-110 411.0
18 TraesCS4B01G011200 chr4B 88.047 343 35 5 3581 3922 7265626 7265963 7.360000e-108 401.0
19 TraesCS4B01G011200 chr4B 79.866 447 70 16 1807 2241 7382154 7382592 4.590000e-80 309.0
20 TraesCS4B01G011200 chr4B 74.178 213 36 9 1782 1991 7376168 7376364 2.360000e-08 71.3
21 TraesCS4B01G011200 chr4A 91.667 4056 243 35 679 4657 598816175 598812138 0.000000e+00 5529.0
22 TraesCS4B01G011200 chr4A 83.944 1638 191 37 2327 3925 599246791 599245187 0.000000e+00 1502.0
23 TraesCS4B01G011200 chr4A 81.115 1991 263 58 2004 3925 599101533 599099587 0.000000e+00 1489.0
24 TraesCS4B01G011200 chr4A 83.812 1637 194 37 2327 3925 599124753 599123150 0.000000e+00 1489.0
25 TraesCS4B01G011200 chr4A 83.771 1639 192 39 2327 3925 599157712 599156108 0.000000e+00 1485.0
26 TraesCS4B01G011200 chr4A 80.983 1993 262 61 2004 3925 599222339 599220393 0.000000e+00 1472.0
27 TraesCS4B01G011200 chr4A 86.527 1336 100 29 515 1788 599102803 599101486 0.000000e+00 1397.0
28 TraesCS4B01G011200 chr4A 86.377 1336 102 28 515 1788 599180182 599178865 0.000000e+00 1386.0
29 TraesCS4B01G011200 chr4A 86.302 1336 103 28 515 1788 599223609 599222292 0.000000e+00 1380.0
30 TraesCS4B01G011200 chr4A 86.235 1344 98 29 515 1788 599126294 599124968 0.000000e+00 1376.0
31 TraesCS4B01G011200 chr4A 86.097 1345 99 32 515 1788 599248334 599247007 0.000000e+00 1367.0
32 TraesCS4B01G011200 chr4A 86.078 1336 105 27 515 1788 599147022 599145706 0.000000e+00 1362.0
33 TraesCS4B01G011200 chr4A 85.961 1332 115 29 515 1788 599085080 599083763 0.000000e+00 1358.0
34 TraesCS4B01G011200 chr4A 85.884 1346 100 31 515 1788 599159255 599157928 0.000000e+00 1351.0
35 TraesCS4B01G011200 chr4A 83.173 1456 170 37 2510 3925 599144526 599143106 0.000000e+00 1262.0
36 TraesCS4B01G011200 chr4A 83.468 1361 153 39 2604 3925 599083254 599081927 0.000000e+00 1201.0
37 TraesCS4B01G011200 chr4A 91.781 511 38 3 5 512 599159814 599159305 0.000000e+00 708.0
38 TraesCS4B01G011200 chr4A 91.781 511 38 3 5 512 599248893 599248384 0.000000e+00 708.0
39 TraesCS4B01G011200 chr4A 87.196 453 56 2 3961 4412 598957933 598957482 9.060000e-142 514.0
40 TraesCS4B01G011200 chr4A 86.534 453 59 2 3961 4412 598907566 598907115 9.120000e-137 497.0
41 TraesCS4B01G011200 chr4A 85.874 446 60 3 3961 4405 599099583 599099140 5.530000e-129 472.0
42 TraesCS4B01G011200 chr4A 85.650 446 61 3 3961 4405 599220389 599219946 2.570000e-127 466.0
43 TraesCS4B01G011200 chr4A 85.426 446 62 3 3961 4405 599176961 599176518 1.200000e-125 460.0
44 TraesCS4B01G011200 chr4A 85.756 344 41 7 3581 3922 598907910 598907573 1.620000e-94 357.0
45 TraesCS4B01G011200 chr4A 85.756 344 41 7 3581 3922 598958277 598957940 1.620000e-94 357.0
46 TraesCS4B01G011200 chr4D 91.667 1452 108 8 2131 3578 4459651 4461093 0.000000e+00 1999.0
47 TraesCS4B01G011200 chr4D 82.530 1992 231 76 2021 3922 4417928 4419892 0.000000e+00 1642.0
48 TraesCS4B01G011200 chr4D 85.266 1595 127 41 277 1785 4416383 4417955 0.000000e+00 1544.0
49 TraesCS4B01G011200 chr4D 90.359 1141 101 8 3583 4720 4461127 4462261 0.000000e+00 1489.0
50 TraesCS4B01G011200 chr4D 88.927 578 33 11 560 1122 4458568 4459129 0.000000e+00 684.0
51 TraesCS4B01G011200 chr4D 85.540 491 64 4 3961 4449 4419899 4420384 1.520000e-139 507.0
52 TraesCS4B01G011200 chrUn 83.944 1638 191 37 2327 3925 216674910 216673306 0.000000e+00 1502.0
53 TraesCS4B01G011200 chrUn 86.153 1336 104 31 515 1788 360633419 360632103 0.000000e+00 1367.0
54 TraesCS4B01G011200 chrUn 87.336 687 63 13 1117 1788 216675803 216675126 0.000000e+00 765.0
55 TraesCS4B01G011200 chrUn 85.694 720 43 17 515 1182 216652490 216651779 0.000000e+00 704.0
56 TraesCS4B01G011200 chrUn 87.723 448 24 6 515 935 385952857 385952414 1.180000e-135 494.0
57 TraesCS4B01G011200 chr6A 85.877 1140 91 30 690 1788 593027288 593026178 0.000000e+00 1149.0
58 TraesCS4B01G011200 chr6A 83.034 1338 156 35 2021 3302 593026208 593024886 0.000000e+00 1147.0
59 TraesCS4B01G011200 chr6A 86.323 446 59 2 3961 4405 593024322 593023878 7.100000e-133 484.0
60 TraesCS4B01G011200 chr6D 89.591 269 21 3 4453 4720 84938547 84938809 7.570000e-88 335.0


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 TraesCS4B01G011200 chr4B 7374685 7379404 4719 False 4394.150000 8717 87.089000 1 4720 2 chr4B.!!$F15 4719
1 TraesCS4B01G011200 chr4B 7170329 7173387 3058 False 1396.500000 1631 84.152000 713 3922 2 chr4B.!!$F10 3209
2 TraesCS4B01G011200 chr4B 7308357 7311453 3096 False 1391.000000 1631 83.806500 667 3922 2 chr4B.!!$F13 3255
3 TraesCS4B01G011200 chr4B 7353355 7356363 3008 False 1346.000000 1594 84.409500 754 3922 2 chr4B.!!$F14 3168
4 TraesCS4B01G011200 chr4B 7457431 7459110 1679 False 878.000000 878 76.844000 1878 3577 1 chr4B.!!$F9 1699
5 TraesCS4B01G011200 chr4B 7159392 7159902 510 False 795.000000 795 94.716000 2 512 1 chr4B.!!$F1 510
6 TraesCS4B01G011200 chr4B 7253719 7254228 509 False 793.000000 793 94.716000 2 512 1 chr4B.!!$F5 510
7 TraesCS4B01G011200 chr4B 7297944 7298452 508 False 793.000000 793 94.716000 2 512 1 chr4B.!!$F6 510
8 TraesCS4B01G011200 chr4B 7344561 7345070 509 False 787.000000 787 94.521000 2 512 1 chr4B.!!$F7 510
9 TraesCS4B01G011200 chr4B 7206655 7207164 509 False 782.000000 782 94.325000 2 512 1 chr4B.!!$F3 510
10 TraesCS4B01G011200 chr4B 7217288 7220347 3059 False 775.500000 1140 87.187000 713 3921 2 chr4B.!!$F11 3208
11 TraesCS4B01G011200 chr4B 7262904 7265963 3059 False 767.500000 1134 86.880500 713 3922 2 chr4B.!!$F12 3209
12 TraesCS4B01G011200 chr4B 7192340 7192850 510 False 767.000000 767 93.738000 2 512 1 chr4B.!!$F2 510
13 TraesCS4B01G011200 chr4B 7238775 7239285 510 False 756.000000 756 93.346000 2 512 1 chr4B.!!$F4 510
14 TraesCS4B01G011200 chr4A 598812138 598816175 4037 True 5529.000000 5529 91.667000 679 4657 1 chr4A.!!$R1 3978
15 TraesCS4B01G011200 chr4A 599123150 599126294 3144 True 1432.500000 1489 85.023500 515 3925 2 chr4A.!!$R6 3410
16 TraesCS4B01G011200 chr4A 599143106 599147022 3916 True 1312.000000 1362 84.625500 515 3925 2 chr4A.!!$R7 3410
17 TraesCS4B01G011200 chr4A 599081927 599085080 3153 True 1279.500000 1358 84.714500 515 3925 2 chr4A.!!$R4 3410
18 TraesCS4B01G011200 chr4A 599245187 599248893 3706 True 1192.333333 1502 87.274000 5 3925 3 chr4A.!!$R11 3920
19 TraesCS4B01G011200 chr4A 599156108 599159814 3706 True 1181.333333 1485 87.145333 5 3925 3 chr4A.!!$R8 3920
20 TraesCS4B01G011200 chr4A 599099140 599102803 3663 True 1119.333333 1489 84.505333 515 4405 3 chr4A.!!$R5 3890
21 TraesCS4B01G011200 chr4A 599219946 599223609 3663 True 1106.000000 1472 84.311667 515 4405 3 chr4A.!!$R10 3890
22 TraesCS4B01G011200 chr4A 599176518 599180182 3664 True 923.000000 1386 85.901500 515 4405 2 chr4A.!!$R9 3890
23 TraesCS4B01G011200 chr4A 598957482 598958277 795 True 435.500000 514 86.476000 3581 4412 2 chr4A.!!$R3 831
24 TraesCS4B01G011200 chr4A 598907115 598907910 795 True 427.000000 497 86.145000 3581 4412 2 chr4A.!!$R2 831
25 TraesCS4B01G011200 chr4D 4458568 4462261 3693 False 1390.666667 1999 90.317667 560 4720 3 chr4D.!!$F2 4160
26 TraesCS4B01G011200 chr4D 4416383 4420384 4001 False 1231.000000 1642 84.445333 277 4449 3 chr4D.!!$F1 4172
27 TraesCS4B01G011200 chrUn 360632103 360633419 1316 True 1367.000000 1367 86.153000 515 1788 1 chrUn.!!$R2 1273
28 TraesCS4B01G011200 chrUn 216673306 216675803 2497 True 1133.500000 1502 85.640000 1117 3925 2 chrUn.!!$R4 2808
29 TraesCS4B01G011200 chrUn 216651779 216652490 711 True 704.000000 704 85.694000 515 1182 1 chrUn.!!$R1 667
30 TraesCS4B01G011200 chr6A 593023878 593027288 3410 True 926.666667 1149 85.078000 690 4405 3 chr6A.!!$R1 3715

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
220 223 0.254462 TAATGCGTGGGAATCTGCCA 59.746 50.000 0.0 0.0 34.62 4.92 F
563 624 0.621609 AAAGGGCATGTAGGCGGTTA 59.378 50.000 0.0 0.0 45.36 2.85 F
1231 1371 1.153369 ATCAATGACGCCCACGAGG 60.153 57.895 0.0 0.0 43.93 4.63 F
1867 2058 0.095935 CGCTTGCACTGTCATGTAGC 59.904 55.000 0.0 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 2039 0.095935 GCTACATGACAGTGCAAGCG 59.904 55.000 0.0 0.0 0.00 4.68 R
1849 2040 0.449388 GGCTACATGACAGTGCAAGC 59.551 55.000 0.0 0.0 33.19 4.01 R
2420 2919 1.295423 GCCCATGACGTACACACCT 59.705 57.895 0.0 0.0 0.00 4.00 R
3826 5189 0.733729 TTTTACACACACACACCGCC 59.266 50.000 0.0 0.0 0.00 6.13 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
92 93 5.791303 AGGTAACCCCATAGCTAAAGTTT 57.209 39.130 0.00 0.00 32.12 2.66
167 168 5.505819 GGCCTCCGTTTGCTAGAATTAATTC 60.506 44.000 18.70 18.70 37.06 2.17
220 223 0.254462 TAATGCGTGGGAATCTGCCA 59.746 50.000 0.00 0.00 34.62 4.92
262 265 3.242739 TGAAGAAAGTTCAAAGCGCTGTC 60.243 43.478 12.58 0.00 0.00 3.51
304 307 6.999705 TTAGTTAGTTGGTCAGGTAAAGGA 57.000 37.500 0.00 0.00 0.00 3.36
331 335 1.066605 GCCAATGATGCTTAGCTGGTG 59.933 52.381 5.60 0.00 0.00 4.17
365 370 1.674057 CCACACTGGGACTGAGACC 59.326 63.158 0.00 0.00 32.67 3.85
385 390 2.823758 GGCCTAGACTCCCATGGGC 61.824 68.421 27.41 12.59 38.92 5.36
418 423 1.672881 GAATCTTGGACAATGGGCGAG 59.327 52.381 0.00 0.00 0.00 5.03
463 468 3.326006 TGAGTGAAGAAGGTCAATGCTCT 59.674 43.478 0.00 0.00 0.00 4.09
480 485 3.994392 TGCTCTTTGTAAAGCTCTTACGG 59.006 43.478 11.58 6.91 39.31 4.02
512 517 5.092105 CGATCATGACATATCTCGAGGAAC 58.908 45.833 13.56 0.00 0.00 3.62
514 519 5.444663 TCATGACATATCTCGAGGAACTG 57.555 43.478 13.56 7.98 41.55 3.16
516 521 2.959030 TGACATATCTCGAGGAACTGGG 59.041 50.000 13.56 0.00 41.55 4.45
517 522 2.959707 GACATATCTCGAGGAACTGGGT 59.040 50.000 13.56 2.28 41.55 4.51
541 593 1.064825 ACTCTTTGGAATGACCGGGT 58.935 50.000 6.32 0.00 42.61 5.28
542 594 2.262637 ACTCTTTGGAATGACCGGGTA 58.737 47.619 6.32 0.00 42.61 3.69
563 624 0.621609 AAAGGGCATGTAGGCGGTTA 59.378 50.000 0.00 0.00 45.36 2.85
662 724 2.698797 GGATGGTCTTCTATTCGTCCCA 59.301 50.000 0.00 0.00 31.07 4.37
681 743 3.447229 CCCAATAAACATTGTGAGGGACC 59.553 47.826 0.00 0.00 0.00 4.46
685 747 5.982890 ATAAACATTGTGAGGGACCAAAG 57.017 39.130 0.00 0.00 0.00 2.77
686 748 3.312736 AACATTGTGAGGGACCAAAGT 57.687 42.857 0.00 0.00 0.00 2.66
824 899 2.106683 CGGGCCGTTTCCAAGCTAG 61.107 63.158 19.97 0.00 0.00 3.42
913 1002 2.294791 CAGCTATACAACCTCCTCTCCG 59.705 54.545 0.00 0.00 0.00 4.63
915 1008 1.614413 CTATACAACCTCCTCTCCGCC 59.386 57.143 0.00 0.00 0.00 6.13
959 1064 1.895020 CGAATTCCCCCGTCTCCACA 61.895 60.000 0.00 0.00 0.00 4.17
969 1074 1.247419 CGTCTCCACAGCTCAGTCCT 61.247 60.000 0.00 0.00 0.00 3.85
1102 1212 2.224209 CCCTTCTAGTCGTGTGGTTGTT 60.224 50.000 0.00 0.00 0.00 2.83
1134 1274 2.047655 TTGGCATGGTCGACGTCC 60.048 61.111 10.58 4.02 0.00 4.79
1231 1371 1.153369 ATCAATGACGCCCACGAGG 60.153 57.895 0.00 0.00 43.93 4.63
1346 1494 4.845580 AATCGCAGGGAGCAGCCG 62.846 66.667 0.00 0.00 46.13 5.52
1388 1536 1.881903 AAGCTCTGACGCAGCAGCTA 61.882 55.000 21.33 1.90 40.87 3.32
1433 1589 5.500234 TGACCATCATAAACCCTTTCTCTG 58.500 41.667 0.00 0.00 0.00 3.35
1439 1595 6.688073 TCATAAACCCTTTCTCTGTCTTCT 57.312 37.500 0.00 0.00 0.00 2.85
1455 1611 7.562135 TCTGTCTTCTACCCGCTTATTTTTAT 58.438 34.615 0.00 0.00 0.00 1.40
1460 1620 7.926555 TCTTCTACCCGCTTATTTTTATCTCTG 59.073 37.037 0.00 0.00 0.00 3.35
1510 1677 6.849811 GTCATGCGATTCAGATCTGTTTATTG 59.150 38.462 21.92 16.76 0.00 1.90
1526 1696 6.486056 TGTTTATTGTACTGGGCAAAGGATA 58.514 36.000 0.00 0.00 0.00 2.59
1698 1887 9.702494 TTAATGATCTGCTATTCTGTGTATCAG 57.298 33.333 0.00 0.00 44.85 2.90
1713 1902 8.467598 TCTGTGTATCAGTAATAGTGGTTCTTC 58.532 37.037 0.00 0.00 43.97 2.87
1756 1947 9.712305 GCTATTCTATGTATCACTAATGGTGTT 57.288 33.333 0.00 0.00 45.50 3.32
1775 1966 1.243902 TTTTTCTAGCTTGCCCACGG 58.756 50.000 0.00 0.00 0.00 4.94
1793 1984 2.282701 GGCATTGATGTCGTGCAATT 57.717 45.000 10.83 0.00 40.53 2.32
1794 1985 2.609350 GGCATTGATGTCGTGCAATTT 58.391 42.857 10.83 0.00 40.53 1.82
1795 1986 3.768406 GGCATTGATGTCGTGCAATTTA 58.232 40.909 10.83 0.00 40.53 1.40
1796 1987 3.792956 GGCATTGATGTCGTGCAATTTAG 59.207 43.478 10.83 0.00 40.53 1.85
1797 1988 4.438608 GGCATTGATGTCGTGCAATTTAGA 60.439 41.667 10.83 0.00 40.53 2.10
1798 1989 5.276270 GCATTGATGTCGTGCAATTTAGAT 58.724 37.500 0.00 0.00 38.68 1.98
1799 1990 5.397534 GCATTGATGTCGTGCAATTTAGATC 59.602 40.000 0.00 0.00 38.68 2.75
1800 1991 6.722301 CATTGATGTCGTGCAATTTAGATCT 58.278 36.000 0.00 0.00 32.74 2.75
1801 1992 5.723492 TGATGTCGTGCAATTTAGATCTG 57.277 39.130 5.18 0.00 0.00 2.90
1802 1993 5.178061 TGATGTCGTGCAATTTAGATCTGT 58.822 37.500 5.18 0.00 0.00 3.41
1803 1994 5.643348 TGATGTCGTGCAATTTAGATCTGTT 59.357 36.000 5.18 0.00 0.00 3.16
1804 1995 5.940192 TGTCGTGCAATTTAGATCTGTTT 57.060 34.783 5.18 0.00 0.00 2.83
1805 1996 7.333174 TGATGTCGTGCAATTTAGATCTGTTTA 59.667 33.333 5.18 0.00 0.00 2.01
1806 1997 7.609760 TGTCGTGCAATTTAGATCTGTTTAT 57.390 32.000 5.18 0.00 0.00 1.40
1807 1998 8.039603 TGTCGTGCAATTTAGATCTGTTTATT 57.960 30.769 5.18 0.00 0.00 1.40
1808 1999 7.962373 TGTCGTGCAATTTAGATCTGTTTATTG 59.038 33.333 5.18 10.25 0.00 1.90
1809 2000 7.962918 GTCGTGCAATTTAGATCTGTTTATTGT 59.037 33.333 5.18 0.00 0.00 2.71
1810 2001 9.157104 TCGTGCAATTTAGATCTGTTTATTGTA 57.843 29.630 5.18 6.56 0.00 2.41
1811 2002 9.210426 CGTGCAATTTAGATCTGTTTATTGTAC 57.790 33.333 19.73 19.73 36.16 2.90
1814 2005 9.722056 GCAATTTAGATCTGTTTATTGTACTGG 57.278 33.333 5.18 0.00 0.00 4.00
1816 2007 7.859325 TTTAGATCTGTTTATTGTACTGGGC 57.141 36.000 5.18 0.00 0.00 5.36
1817 2008 5.435686 AGATCTGTTTATTGTACTGGGCA 57.564 39.130 0.00 0.00 0.00 5.36
1818 2009 5.815581 AGATCTGTTTATTGTACTGGGCAA 58.184 37.500 0.00 0.00 0.00 4.52
1819 2010 6.245408 AGATCTGTTTATTGTACTGGGCAAA 58.755 36.000 0.00 0.00 0.00 3.68
1820 2011 5.957842 TCTGTTTATTGTACTGGGCAAAG 57.042 39.130 0.00 0.00 0.00 2.77
1821 2012 4.764823 TCTGTTTATTGTACTGGGCAAAGG 59.235 41.667 0.00 0.00 0.00 3.11
1822 2013 4.730966 TGTTTATTGTACTGGGCAAAGGA 58.269 39.130 0.00 0.00 0.00 3.36
1823 2014 5.329399 TGTTTATTGTACTGGGCAAAGGAT 58.671 37.500 0.00 0.00 0.00 3.24
1824 2015 5.777732 TGTTTATTGTACTGGGCAAAGGATT 59.222 36.000 0.00 0.00 0.00 3.01
1825 2016 6.071616 TGTTTATTGTACTGGGCAAAGGATTC 60.072 38.462 0.00 0.00 0.00 2.52
1826 2017 3.806949 TTGTACTGGGCAAAGGATTCT 57.193 42.857 0.00 0.00 0.00 2.40
1827 2018 4.919774 TTGTACTGGGCAAAGGATTCTA 57.080 40.909 0.00 0.00 0.00 2.10
1828 2019 5.450818 TTGTACTGGGCAAAGGATTCTAT 57.549 39.130 0.00 0.00 0.00 1.98
1829 2020 5.450818 TGTACTGGGCAAAGGATTCTATT 57.549 39.130 0.00 0.00 0.00 1.73
1830 2021 5.826643 TGTACTGGGCAAAGGATTCTATTT 58.173 37.500 0.00 0.00 0.00 1.40
1831 2022 5.652014 TGTACTGGGCAAAGGATTCTATTTG 59.348 40.000 0.00 9.26 39.01 2.32
1832 2023 4.677182 ACTGGGCAAAGGATTCTATTTGT 58.323 39.130 12.99 0.00 38.41 2.83
1833 2024 4.706962 ACTGGGCAAAGGATTCTATTTGTC 59.293 41.667 12.99 11.34 39.67 3.18
1834 2025 4.671831 TGGGCAAAGGATTCTATTTGTCA 58.328 39.130 16.04 11.65 41.63 3.58
1835 2026 4.462483 TGGGCAAAGGATTCTATTTGTCAC 59.538 41.667 16.04 10.49 41.63 3.67
1836 2027 4.462483 GGGCAAAGGATTCTATTTGTCACA 59.538 41.667 16.04 0.00 41.63 3.58
1837 2028 5.047377 GGGCAAAGGATTCTATTTGTCACAA 60.047 40.000 16.04 0.00 41.63 3.33
1838 2029 6.454795 GGCAAAGGATTCTATTTGTCACAAA 58.545 36.000 5.18 5.18 40.04 2.83
1839 2030 6.928492 GGCAAAGGATTCTATTTGTCACAAAA 59.072 34.615 7.14 0.00 40.04 2.44
1840 2031 7.440856 GGCAAAGGATTCTATTTGTCACAAAAA 59.559 33.333 7.14 0.00 40.04 1.94
1857 2048 3.715628 AAAAAGAATGTCGCTTGCACT 57.284 38.095 0.00 0.00 0.00 4.40
1858 2049 2.693797 AAAGAATGTCGCTTGCACTG 57.306 45.000 0.00 0.00 0.00 3.66
1859 2050 1.597742 AAGAATGTCGCTTGCACTGT 58.402 45.000 0.00 0.00 0.00 3.55
1860 2051 1.151668 AGAATGTCGCTTGCACTGTC 58.848 50.000 0.00 0.00 0.00 3.51
1861 2052 0.867746 GAATGTCGCTTGCACTGTCA 59.132 50.000 0.00 0.00 0.00 3.58
1862 2053 1.466167 GAATGTCGCTTGCACTGTCAT 59.534 47.619 0.00 0.00 0.00 3.06
1863 2054 0.800631 ATGTCGCTTGCACTGTCATG 59.199 50.000 0.00 0.00 0.00 3.07
1864 2055 0.532640 TGTCGCTTGCACTGTCATGT 60.533 50.000 0.00 0.00 0.00 3.21
1865 2056 1.270041 TGTCGCTTGCACTGTCATGTA 60.270 47.619 0.00 0.00 0.00 2.29
1866 2057 1.391485 GTCGCTTGCACTGTCATGTAG 59.609 52.381 0.00 0.00 0.00 2.74
1867 2058 0.095935 CGCTTGCACTGTCATGTAGC 59.904 55.000 0.00 0.00 0.00 3.58
1868 2059 0.449388 GCTTGCACTGTCATGTAGCC 59.551 55.000 0.00 0.00 0.00 3.93
1869 2060 1.812235 CTTGCACTGTCATGTAGCCA 58.188 50.000 0.00 0.00 0.00 4.75
1870 2061 2.362736 CTTGCACTGTCATGTAGCCAT 58.637 47.619 0.00 0.00 0.00 4.40
1871 2062 3.534554 CTTGCACTGTCATGTAGCCATA 58.465 45.455 0.00 0.00 0.00 2.74
1872 2063 3.625649 TGCACTGTCATGTAGCCATAA 57.374 42.857 0.00 0.00 0.00 1.90
1873 2064 4.155063 TGCACTGTCATGTAGCCATAAT 57.845 40.909 0.00 0.00 0.00 1.28
1874 2065 4.525996 TGCACTGTCATGTAGCCATAATT 58.474 39.130 0.00 0.00 0.00 1.40
1875 2066 4.949238 TGCACTGTCATGTAGCCATAATTT 59.051 37.500 0.00 0.00 0.00 1.82
1876 2067 5.163632 TGCACTGTCATGTAGCCATAATTTG 60.164 40.000 0.00 0.00 0.00 2.32
1883 2074 8.623903 TGTCATGTAGCCATAATTTGAAGAATC 58.376 33.333 0.00 0.00 0.00 2.52
1901 2092 6.541111 AGAATCGAGTTTAGTTGTGTTTCC 57.459 37.500 0.00 0.00 0.00 3.13
1906 2097 5.981315 TCGAGTTTAGTTGTGTTTCCTGTAG 59.019 40.000 0.00 0.00 0.00 2.74
1908 2099 4.820173 AGTTTAGTTGTGTTTCCTGTAGCC 59.180 41.667 0.00 0.00 0.00 3.93
1916 2107 2.028748 TGTTTCCTGTAGCCGAGTTACC 60.029 50.000 0.00 0.00 0.00 2.85
1931 2122 4.686972 GAGTTACCGGTATCCCAGTTAAC 58.313 47.826 16.67 9.08 0.00 2.01
1936 2127 2.480759 CCGGTATCCCAGTTAACGTCAG 60.481 54.545 0.00 0.00 0.00 3.51
1937 2128 2.547826 GGTATCCCAGTTAACGTCAGC 58.452 52.381 0.00 0.00 0.00 4.26
1938 2129 2.093869 GGTATCCCAGTTAACGTCAGCA 60.094 50.000 0.00 0.00 0.00 4.41
1943 2134 1.129251 CCAGTTAACGTCAGCAGCATG 59.871 52.381 0.00 0.00 40.87 4.06
1958 2149 6.615264 AGCAGCATGATGAGTATAAAGTTG 57.385 37.500 16.67 0.00 39.69 3.16
1961 2152 6.643845 CAGCATGATGAGTATAAAGTTGTCG 58.356 40.000 4.56 0.00 39.69 4.35
1962 2153 6.256539 CAGCATGATGAGTATAAAGTTGTCGT 59.743 38.462 4.56 0.00 39.69 4.34
1963 2154 6.818644 AGCATGATGAGTATAAAGTTGTCGTT 59.181 34.615 0.00 0.00 0.00 3.85
1965 2156 7.962918 GCATGATGAGTATAAAGTTGTCGTTTT 59.037 33.333 0.00 0.00 0.00 2.43
1966 2157 9.825972 CATGATGAGTATAAAGTTGTCGTTTTT 57.174 29.630 0.00 0.00 0.00 1.94
1967 2158 9.825972 ATGATGAGTATAAAGTTGTCGTTTTTG 57.174 29.630 0.00 0.00 0.00 2.44
1968 2159 8.832521 TGATGAGTATAAAGTTGTCGTTTTTGT 58.167 29.630 0.00 0.00 0.00 2.83
1969 2160 9.103048 GATGAGTATAAAGTTGTCGTTTTTGTG 57.897 33.333 0.00 0.00 0.00 3.33
1970 2161 8.199176 TGAGTATAAAGTTGTCGTTTTTGTGA 57.801 30.769 0.00 0.00 0.00 3.58
1971 2162 8.666573 TGAGTATAAAGTTGTCGTTTTTGTGAA 58.333 29.630 0.00 0.00 0.00 3.18
1972 2163 8.831000 AGTATAAAGTTGTCGTTTTTGTGAAC 57.169 30.769 0.00 0.00 0.00 3.18
1973 2164 8.452534 AGTATAAAGTTGTCGTTTTTGTGAACA 58.547 29.630 0.00 0.00 0.00 3.18
1979 2170 5.769967 TGTCGTTTTTGTGAACATTTTGG 57.230 34.783 0.00 0.00 0.00 3.28
1984 2175 6.697892 TCGTTTTTGTGAACATTTTGGGTATC 59.302 34.615 0.00 0.00 0.00 2.24
2001 2192 9.671279 TTTGGGTATCAATGATATACAGCTATG 57.329 33.333 6.21 0.00 34.98 2.23
2015 2208 2.980476 CAGCTATGCGTATCACTAACGG 59.020 50.000 0.00 0.00 40.64 4.44
2016 2209 2.621998 AGCTATGCGTATCACTAACGGT 59.378 45.455 0.00 0.00 40.64 4.83
2070 2531 2.547299 TTTTATTCGGGTGTGTCGGT 57.453 45.000 0.00 0.00 0.00 4.69
2157 2621 5.991933 TTAGCCATAGATAGAAGAGCTGG 57.008 43.478 0.00 0.00 0.00 4.85
2246 2716 4.507756 GTGAGGGCAACTTTTGTCATTTTC 59.492 41.667 0.00 0.00 36.88 2.29
2263 2733 7.227711 TGTCATTTTCCGAATGTTTCTTCTACA 59.772 33.333 0.00 0.00 0.00 2.74
2324 2812 4.759693 TCGACAATGAACAAAGTATGGCTT 59.240 37.500 0.00 0.00 39.52 4.35
2341 2829 6.570672 ATGGCTTGTATTAATGATCTGCAG 57.429 37.500 7.63 7.63 0.00 4.41
2361 2849 4.809426 GCAGTTCTACATAACGCTAATGGT 59.191 41.667 0.00 0.00 34.46 3.55
2420 2919 0.678950 TTCAGATGTGTCAGACGGCA 59.321 50.000 0.00 0.00 0.00 5.69
2439 2938 1.004320 GGTGTGTACGTCATGGGCA 60.004 57.895 0.00 0.00 0.00 5.36
2546 3747 0.400213 ATGGTCCGGCAAGAAAGACA 59.600 50.000 0.00 0.00 0.00 3.41
2595 3799 5.648572 ACTACTGGTCTGCTATTTTACGTC 58.351 41.667 0.00 0.00 0.00 4.34
2602 3806 3.991773 TCTGCTATTTTACGTCACACCAC 59.008 43.478 0.00 0.00 0.00 4.16
2661 3869 7.464577 CGAGTTGACAATCATGATACGAAATGT 60.465 37.037 9.04 8.39 0.00 2.71
2674 3884 4.559862 ACGAAATGTCTCCTTGAGGATT 57.440 40.909 0.00 0.00 44.46 3.01
2698 3908 6.764877 TTATTGAGTTGACGTCTCAGTTTC 57.235 37.500 17.92 6.62 41.87 2.78
2701 3911 5.707242 TGAGTTGACGTCTCAGTTTCTAT 57.293 39.130 17.92 0.00 37.07 1.98
2709 3928 7.883217 TGACGTCTCAGTTTCTATTAAGTTCT 58.117 34.615 17.92 0.00 0.00 3.01
2756 3982 2.734670 CATGTTTCAGTGTTGGTGCAG 58.265 47.619 0.00 0.00 0.00 4.41
3016 4248 6.918892 TTCACATTGTTGATATTACTCGGG 57.081 37.500 0.00 0.00 0.00 5.14
3182 4431 4.058124 CTCTTCAGAATTTGACCGTGTGA 58.942 43.478 0.00 0.00 34.94 3.58
3338 4593 6.270231 ACTTCTCACTAGTTTCATAACCCACT 59.730 38.462 0.00 0.00 34.71 4.00
3340 4595 5.542635 TCTCACTAGTTTCATAACCCACTGT 59.457 40.000 0.00 0.00 34.71 3.55
3565 4836 2.979401 TTAAGCTTCGCGAAATGCAA 57.021 40.000 27.95 15.71 46.97 4.08
3578 4849 6.419413 TCGCGAAATGCAAAAATAAGAAACTT 59.581 30.769 6.20 0.00 46.97 2.66
3579 4850 7.043059 TCGCGAAATGCAAAAATAAGAAACTTT 60.043 29.630 6.20 0.00 46.97 2.66
3617 4917 6.545504 CACCATTATGTGCCATAGACTTAC 57.454 41.667 0.00 0.00 0.00 2.34
3746 5074 0.401738 CAAGTGAAGGGGGAAGAGCA 59.598 55.000 0.00 0.00 0.00 4.26
3797 5126 3.869832 GTCCATGTGTCTCTGATGATGTG 59.130 47.826 0.00 0.00 0.00 3.21
3800 5129 1.624813 TGTGTCTCTGATGATGTGGCA 59.375 47.619 0.00 0.00 0.00 4.92
3808 5154 3.189080 TCTGATGATGTGGCACTTTTTCG 59.811 43.478 19.83 9.55 0.00 3.46
3812 5175 2.287547 TGATGTGGCACTTTTTCGAAGC 60.288 45.455 19.83 0.00 0.00 3.86
3826 5189 1.067565 TCGAAGCTTGTCTGGCACTAG 60.068 52.381 2.10 0.00 0.00 2.57
3827 5190 1.731720 GAAGCTTGTCTGGCACTAGG 58.268 55.000 2.10 0.00 0.00 3.02
3830 5193 1.448540 CTTGTCTGGCACTAGGCGG 60.449 63.158 0.00 0.00 46.16 6.13
3831 5194 2.172483 CTTGTCTGGCACTAGGCGGT 62.172 60.000 0.00 0.00 46.23 5.68
3917 5280 5.901552 ACTAAAATTGTTGTCCTGTGTTGG 58.098 37.500 0.00 0.00 0.00 3.77
3927 5290 2.354821 GTCCTGTGTTGGTGTCTGTTTC 59.645 50.000 0.00 0.00 0.00 2.78
3934 5297 4.508124 GTGTTGGTGTCTGTTTCTCTAGTG 59.492 45.833 0.00 0.00 0.00 2.74
3994 5357 0.179059 TGTGTCGTGGATGTGTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
4047 5410 1.916181 CCTGGTTGGTTGGTCCTCTAT 59.084 52.381 0.00 0.00 37.07 1.98
4093 5456 7.667043 TGTGTTCGTTTTTCTCTATAAGCAT 57.333 32.000 0.00 0.00 0.00 3.79
4128 5491 2.232399 TGTTGTACCGAGAGTGTAGCA 58.768 47.619 0.00 0.00 0.00 3.49
4175 5538 5.245531 AGCATGTCTTTTCGGTCTGAAATA 58.754 37.500 7.67 0.00 45.62 1.40
4178 5541 7.552687 AGCATGTCTTTTCGGTCTGAAATATTA 59.447 33.333 7.67 0.00 45.62 0.98
4244 5607 0.332972 GGAGGAGGGGCAAAACAGAT 59.667 55.000 0.00 0.00 0.00 2.90
4283 5646 0.967380 CATCCAGGGACCACAAAGCC 60.967 60.000 0.00 0.00 0.00 4.35
4362 5726 7.506261 TGGTACAAAAAGTCTGGGCTAATTAAA 59.494 33.333 0.00 0.00 31.92 1.52
4383 5748 3.552132 TCGCCAATTATAGCTCCAACA 57.448 42.857 0.00 0.00 0.00 3.33
4421 5786 4.557705 ACATACTACTCCTAGGCCACAAT 58.442 43.478 5.01 0.00 0.00 2.71
4450 5816 3.576982 AGACTACCCTGAATCACGAACAA 59.423 43.478 0.00 0.00 0.00 2.83
4451 5817 4.223032 AGACTACCCTGAATCACGAACAAT 59.777 41.667 0.00 0.00 0.00 2.71
4501 5867 1.053424 GTGGTGGTTCAGACCTGGTA 58.947 55.000 0.00 0.00 46.66 3.25
4507 5873 1.763545 GGTTCAGACCTGGTAGATCCC 59.236 57.143 0.00 1.24 42.99 3.85
4555 5921 6.529829 GTCACATCGGATTATCTCTATCAAGC 59.470 42.308 0.00 0.00 0.00 4.01
4573 5939 3.753294 AGCGCAATAGTAGCAATACCT 57.247 42.857 11.47 0.00 0.00 3.08
4585 5951 1.477558 GCAATACCTGGGCATAGCTGT 60.478 52.381 0.00 0.00 0.00 4.40
4606 5972 8.258007 AGCTGTAGTATGTAAAATGCTTGTAGA 58.742 33.333 0.00 0.00 0.00 2.59
4648 6014 2.190538 TCATCATTGAGTGGCCTCTGA 58.809 47.619 13.11 0.00 38.61 3.27
4657 6023 3.327757 TGAGTGGCCTCTGAACATAGTTT 59.672 43.478 13.11 0.00 38.61 2.66
4662 6028 6.212791 AGTGGCCTCTGAACATAGTTTAGTTA 59.787 38.462 6.51 0.00 0.00 2.24
4665 6031 7.552687 TGGCCTCTGAACATAGTTTAGTTATTG 59.447 37.037 3.32 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.291377 AGTTTGTGAGCTTCAACATTCTAGA 58.709 36.000 5.06 0.00 0.00 2.43
1 2 6.551385 AGTTTGTGAGCTTCAACATTCTAG 57.449 37.500 5.06 0.00 0.00 2.43
3 4 4.024556 CGAGTTTGTGAGCTTCAACATTCT 60.025 41.667 5.06 4.39 0.00 2.40
92 93 2.297701 AGTTTTGAAGCAAGGCGAGAA 58.702 42.857 0.00 0.00 0.00 2.87
167 168 5.856986 TCGTCACTTTCTTCTCAACTATTCG 59.143 40.000 0.00 0.00 0.00 3.34
262 265 6.804770 ACTAATACTACGTAGGCTCATCAG 57.195 41.667 25.63 14.50 0.00 2.90
304 307 2.910579 AGCATCATTGGCTTGCCAT 58.089 47.368 15.58 3.20 38.81 4.40
331 335 5.634859 CCAGTGTGGCTAATCATTCAAAAAC 59.365 40.000 0.00 0.00 0.00 2.43
365 370 1.414061 CCCATGGGAGTCTAGGCCAG 61.414 65.000 28.27 0.00 37.50 4.85
385 390 2.203126 GATTCCCCTCTGCTGCCG 60.203 66.667 0.00 0.00 0.00 5.69
418 423 1.731720 GATATTGCTGGATCGGGCTC 58.268 55.000 9.37 0.00 0.00 4.70
463 468 4.748102 CACTCACCGTAAGAGCTTTACAAA 59.252 41.667 14.80 0.00 43.02 2.83
480 485 1.078201 TGTCATGATCGCGCACTCAC 61.078 55.000 8.75 0.00 0.00 3.51
512 517 5.875359 GTCATTCCAAAGAGTACTTACCCAG 59.125 44.000 0.00 0.00 35.05 4.45
513 518 5.280317 GGTCATTCCAAAGAGTACTTACCCA 60.280 44.000 0.00 0.00 35.05 4.51
514 519 5.183969 GGTCATTCCAAAGAGTACTTACCC 58.816 45.833 0.00 0.00 35.05 3.69
516 521 4.868734 CCGGTCATTCCAAAGAGTACTTAC 59.131 45.833 0.00 0.00 35.05 2.34
517 522 4.081309 CCCGGTCATTCCAAAGAGTACTTA 60.081 45.833 0.00 0.00 35.05 2.24
541 593 2.051692 ACCGCCTACATGCCCTTTATA 58.948 47.619 0.00 0.00 0.00 0.98
542 594 0.843984 ACCGCCTACATGCCCTTTAT 59.156 50.000 0.00 0.00 0.00 1.40
578 639 5.449862 GCATTCCGCCACTTTGTATGATTTA 60.450 40.000 0.00 0.00 32.94 1.40
587 648 0.449388 GAGAGCATTCCGCCACTTTG 59.551 55.000 0.00 0.00 44.04 2.77
662 724 5.838521 ACTTTGGTCCCTCACAATGTTTATT 59.161 36.000 0.00 0.00 33.00 1.40
824 899 1.927895 AGCTGTACTGCGTCATTAGC 58.072 50.000 17.71 3.70 38.13 3.09
874 963 2.716017 GGGCTCACGAGGGTCTCTG 61.716 68.421 0.00 0.00 0.00 3.35
915 1008 3.343788 GAGTGCACGAGGACGGGAG 62.344 68.421 12.01 0.00 46.86 4.30
928 1021 3.100862 GAATTCGGCTGCGGAGTGC 62.101 63.158 5.62 2.57 46.70 4.40
938 1031 2.203029 GAGACGGGGGAATTCGGC 60.203 66.667 0.00 0.00 34.07 5.54
986 1096 2.194056 CCATGGCAAGGCGAGGAT 59.806 61.111 0.00 0.00 0.00 3.24
1035 1145 0.948623 TGTACATGCCGGCGATATGC 60.949 55.000 23.90 11.31 45.38 3.14
1134 1274 1.002134 GTCCACCACACCCTGGATG 60.002 63.158 0.00 0.00 43.95 3.51
1346 1494 1.070289 ACCTCGTCAAAGTCCACTTCC 59.930 52.381 0.00 0.00 34.61 3.46
1373 1521 3.055144 CATTAGCTGCTGCGTCAGA 57.945 52.632 13.43 0.00 45.42 3.27
1388 1536 1.221840 CCTAGAGGTGCACCGCATT 59.778 57.895 36.38 22.06 41.91 3.56
1433 1589 7.927092 AGAGATAAAAATAAGCGGGTAGAAGAC 59.073 37.037 0.00 0.00 0.00 3.01
1439 1595 6.646267 ACACAGAGATAAAAATAAGCGGGTA 58.354 36.000 0.00 0.00 0.00 3.69
1455 1611 1.405105 GCAGGCAAACAAACACAGAGA 59.595 47.619 0.00 0.00 0.00 3.10
1460 1620 1.481819 CGCAGCAGGCAAACAAACAC 61.482 55.000 0.00 0.00 45.17 3.32
1510 1677 7.450903 ACATATAAGTATCCTTTGCCCAGTAC 58.549 38.462 0.00 0.00 31.89 2.73
1655 1844 9.877178 AGATCATTAATACCAGGAATATTCGAC 57.123 33.333 9.32 0.00 0.00 4.20
1703 1892 6.636454 TCATTAATACCAGGAAGAACCACT 57.364 37.500 0.00 0.00 42.04 4.00
1710 1899 9.160496 GAATAGCAGATCATTAATACCAGGAAG 57.840 37.037 0.00 0.00 0.00 3.46
1756 1947 1.243902 CCGTGGGCAAGCTAGAAAAA 58.756 50.000 0.00 0.00 0.00 1.94
1757 1948 2.941210 CCGTGGGCAAGCTAGAAAA 58.059 52.632 0.00 0.00 0.00 2.29
1758 1949 4.713946 CCGTGGGCAAGCTAGAAA 57.286 55.556 0.00 0.00 0.00 2.52
1769 1960 1.745115 ACGACATCAATGCCGTGGG 60.745 57.895 3.50 0.00 44.93 4.61
1770 1961 3.889227 ACGACATCAATGCCGTGG 58.111 55.556 3.50 0.00 44.93 4.94
1773 1964 0.099259 ATTGCACGACATCAATGCCG 59.901 50.000 0.00 0.00 39.61 5.69
1774 1965 2.282701 AATTGCACGACATCAATGCC 57.717 45.000 0.00 0.00 38.63 4.40
1775 1966 4.661125 TCTAAATTGCACGACATCAATGC 58.339 39.130 0.00 0.00 39.88 3.56
1776 1967 6.631636 CAGATCTAAATTGCACGACATCAATG 59.368 38.462 0.00 0.00 33.61 2.82
1777 1968 6.317140 ACAGATCTAAATTGCACGACATCAAT 59.683 34.615 0.00 0.00 34.66 2.57
1778 1969 5.643348 ACAGATCTAAATTGCACGACATCAA 59.357 36.000 0.00 0.00 0.00 2.57
1779 1970 5.178061 ACAGATCTAAATTGCACGACATCA 58.822 37.500 0.00 0.00 0.00 3.07
1780 1971 5.725110 ACAGATCTAAATTGCACGACATC 57.275 39.130 0.00 0.00 0.00 3.06
1781 1972 6.500684 AAACAGATCTAAATTGCACGACAT 57.499 33.333 0.00 0.00 0.00 3.06
1782 1973 5.940192 AAACAGATCTAAATTGCACGACA 57.060 34.783 0.00 0.00 0.00 4.35
1783 1974 7.962918 ACAATAAACAGATCTAAATTGCACGAC 59.037 33.333 13.96 0.00 0.00 4.34
1784 1975 8.039603 ACAATAAACAGATCTAAATTGCACGA 57.960 30.769 13.96 0.00 0.00 4.35
1785 1976 9.210426 GTACAATAAACAGATCTAAATTGCACG 57.790 33.333 13.96 0.00 0.00 5.34
1788 1979 9.722056 CCAGTACAATAAACAGATCTAAATTGC 57.278 33.333 13.96 4.51 0.00 3.56
1790 1981 8.903820 GCCCAGTACAATAAACAGATCTAAATT 58.096 33.333 0.00 0.00 0.00 1.82
1791 1982 8.052748 TGCCCAGTACAATAAACAGATCTAAAT 58.947 33.333 0.00 0.00 0.00 1.40
1792 1983 7.398829 TGCCCAGTACAATAAACAGATCTAAA 58.601 34.615 0.00 0.00 0.00 1.85
1793 1984 6.953101 TGCCCAGTACAATAAACAGATCTAA 58.047 36.000 0.00 0.00 0.00 2.10
1794 1985 6.553953 TGCCCAGTACAATAAACAGATCTA 57.446 37.500 0.00 0.00 0.00 1.98
1795 1986 5.435686 TGCCCAGTACAATAAACAGATCT 57.564 39.130 0.00 0.00 0.00 2.75
1796 1987 6.404734 CCTTTGCCCAGTACAATAAACAGATC 60.405 42.308 0.00 0.00 0.00 2.75
1797 1988 5.418840 CCTTTGCCCAGTACAATAAACAGAT 59.581 40.000 0.00 0.00 0.00 2.90
1798 1989 4.764823 CCTTTGCCCAGTACAATAAACAGA 59.235 41.667 0.00 0.00 0.00 3.41
1799 1990 4.764823 TCCTTTGCCCAGTACAATAAACAG 59.235 41.667 0.00 0.00 0.00 3.16
1800 1991 4.730966 TCCTTTGCCCAGTACAATAAACA 58.269 39.130 0.00 0.00 0.00 2.83
1801 1992 5.914898 ATCCTTTGCCCAGTACAATAAAC 57.085 39.130 0.00 0.00 0.00 2.01
1802 1993 6.252995 AGAATCCTTTGCCCAGTACAATAAA 58.747 36.000 0.00 0.00 0.00 1.40
1803 1994 5.826643 AGAATCCTTTGCCCAGTACAATAA 58.173 37.500 0.00 0.00 0.00 1.40
1804 1995 5.450818 AGAATCCTTTGCCCAGTACAATA 57.549 39.130 0.00 0.00 0.00 1.90
1805 1996 4.322057 AGAATCCTTTGCCCAGTACAAT 57.678 40.909 0.00 0.00 0.00 2.71
1806 1997 3.806949 AGAATCCTTTGCCCAGTACAA 57.193 42.857 0.00 0.00 0.00 2.41
1807 1998 5.450818 AATAGAATCCTTTGCCCAGTACA 57.549 39.130 0.00 0.00 0.00 2.90
1808 1999 5.652452 ACAAATAGAATCCTTTGCCCAGTAC 59.348 40.000 5.99 0.00 36.12 2.73
1809 2000 5.826643 ACAAATAGAATCCTTTGCCCAGTA 58.173 37.500 5.99 0.00 36.12 2.74
1810 2001 4.677182 ACAAATAGAATCCTTTGCCCAGT 58.323 39.130 5.99 0.00 36.12 4.00
1811 2002 4.706476 TGACAAATAGAATCCTTTGCCCAG 59.294 41.667 5.99 0.00 36.12 4.45
1812 2003 4.462483 GTGACAAATAGAATCCTTTGCCCA 59.538 41.667 5.99 3.14 36.12 5.36
1813 2004 4.462483 TGTGACAAATAGAATCCTTTGCCC 59.538 41.667 5.99 1.16 36.12 5.36
1814 2005 5.643379 TGTGACAAATAGAATCCTTTGCC 57.357 39.130 5.99 0.00 36.12 4.52
1815 2006 7.945033 TTTTGTGACAAATAGAATCCTTTGC 57.055 32.000 11.97 1.74 36.12 3.68
1837 2028 3.181487 ACAGTGCAAGCGACATTCTTTTT 60.181 39.130 0.00 0.00 0.00 1.94
1838 2029 2.358898 ACAGTGCAAGCGACATTCTTTT 59.641 40.909 0.00 0.00 0.00 2.27
1839 2030 1.949525 ACAGTGCAAGCGACATTCTTT 59.050 42.857 0.00 0.00 0.00 2.52
1840 2031 1.532868 GACAGTGCAAGCGACATTCTT 59.467 47.619 0.00 0.00 0.00 2.52
1841 2032 1.151668 GACAGTGCAAGCGACATTCT 58.848 50.000 0.00 0.00 0.00 2.40
1842 2033 0.867746 TGACAGTGCAAGCGACATTC 59.132 50.000 0.00 0.00 0.00 2.67
1843 2034 1.198408 CATGACAGTGCAAGCGACATT 59.802 47.619 0.00 0.00 0.00 2.71
1844 2035 0.800631 CATGACAGTGCAAGCGACAT 59.199 50.000 0.00 0.00 0.00 3.06
1845 2036 0.532640 ACATGACAGTGCAAGCGACA 60.533 50.000 0.00 0.00 0.00 4.35
1846 2037 1.391485 CTACATGACAGTGCAAGCGAC 59.609 52.381 0.00 0.00 0.00 5.19
1847 2038 1.713597 CTACATGACAGTGCAAGCGA 58.286 50.000 0.00 0.00 0.00 4.93
1848 2039 0.095935 GCTACATGACAGTGCAAGCG 59.904 55.000 0.00 0.00 0.00 4.68
1849 2040 0.449388 GGCTACATGACAGTGCAAGC 59.551 55.000 0.00 0.00 33.19 4.01
1850 2041 1.812235 TGGCTACATGACAGTGCAAG 58.188 50.000 0.00 0.00 0.00 4.01
1851 2042 2.495155 ATGGCTACATGACAGTGCAA 57.505 45.000 0.00 0.00 36.95 4.08
1852 2043 3.625649 TTATGGCTACATGACAGTGCA 57.374 42.857 0.00 0.00 36.95 4.57
1853 2044 5.066375 TCAAATTATGGCTACATGACAGTGC 59.934 40.000 0.00 0.00 36.95 4.40
1854 2045 6.682423 TCAAATTATGGCTACATGACAGTG 57.318 37.500 0.00 0.00 36.95 3.66
1855 2046 7.112122 TCTTCAAATTATGGCTACATGACAGT 58.888 34.615 0.00 0.00 36.95 3.55
1856 2047 7.558161 TCTTCAAATTATGGCTACATGACAG 57.442 36.000 0.00 0.00 36.95 3.51
1857 2048 7.936496 TTCTTCAAATTATGGCTACATGACA 57.064 32.000 0.00 0.00 37.97 3.58
1858 2049 7.800380 CGATTCTTCAAATTATGGCTACATGAC 59.200 37.037 0.00 0.00 37.97 3.06
1859 2050 7.714813 TCGATTCTTCAAATTATGGCTACATGA 59.285 33.333 0.00 0.00 37.97 3.07
1860 2051 7.864686 TCGATTCTTCAAATTATGGCTACATG 58.135 34.615 0.00 0.00 37.97 3.21
1861 2052 7.716998 ACTCGATTCTTCAAATTATGGCTACAT 59.283 33.333 0.00 0.00 41.13 2.29
1862 2053 7.047891 ACTCGATTCTTCAAATTATGGCTACA 58.952 34.615 0.00 0.00 0.00 2.74
1863 2054 7.484035 ACTCGATTCTTCAAATTATGGCTAC 57.516 36.000 0.00 0.00 0.00 3.58
1864 2055 8.506168 AAACTCGATTCTTCAAATTATGGCTA 57.494 30.769 0.00 0.00 0.00 3.93
1865 2056 7.396540 AAACTCGATTCTTCAAATTATGGCT 57.603 32.000 0.00 0.00 0.00 4.75
1866 2057 8.398665 ACTAAACTCGATTCTTCAAATTATGGC 58.601 33.333 0.00 0.00 0.00 4.40
1871 2062 8.621286 ACACAACTAAACTCGATTCTTCAAATT 58.379 29.630 0.00 0.00 0.00 1.82
1872 2063 8.154649 ACACAACTAAACTCGATTCTTCAAAT 57.845 30.769 0.00 0.00 0.00 2.32
1873 2064 7.548196 ACACAACTAAACTCGATTCTTCAAA 57.452 32.000 0.00 0.00 0.00 2.69
1874 2065 7.548196 AACACAACTAAACTCGATTCTTCAA 57.452 32.000 0.00 0.00 0.00 2.69
1875 2066 7.254658 GGAAACACAACTAAACTCGATTCTTCA 60.255 37.037 0.00 0.00 0.00 3.02
1876 2067 7.041984 AGGAAACACAACTAAACTCGATTCTTC 60.042 37.037 0.00 0.00 0.00 2.87
1883 2074 5.333111 GCTACAGGAAACACAACTAAACTCG 60.333 44.000 0.00 0.00 0.00 4.18
1893 2084 1.045407 ACTCGGCTACAGGAAACACA 58.955 50.000 0.00 0.00 0.00 3.72
1894 2085 2.165319 AACTCGGCTACAGGAAACAC 57.835 50.000 0.00 0.00 0.00 3.32
1896 2087 2.614779 GGTAACTCGGCTACAGGAAAC 58.385 52.381 0.00 0.00 0.00 2.78
1919 2110 2.418197 GCTGCTGACGTTAACTGGGATA 60.418 50.000 3.71 0.00 0.00 2.59
1931 2122 2.214387 TACTCATCATGCTGCTGACG 57.786 50.000 0.00 0.00 0.00 4.35
1936 2127 6.369059 ACAACTTTATACTCATCATGCTGC 57.631 37.500 0.00 0.00 0.00 5.25
1937 2128 6.256539 ACGACAACTTTATACTCATCATGCTG 59.743 38.462 0.00 0.00 0.00 4.41
1938 2129 6.341316 ACGACAACTTTATACTCATCATGCT 58.659 36.000 0.00 0.00 0.00 3.79
1943 2134 9.103048 CACAAAAACGACAACTTTATACTCATC 57.897 33.333 0.00 0.00 0.00 2.92
1953 2144 7.287229 CAAAATGTTCACAAAAACGACAACTT 58.713 30.769 0.00 0.00 31.58 2.66
1955 2146 6.012482 CCAAAATGTTCACAAAAACGACAAC 58.988 36.000 0.00 0.00 31.58 3.32
1956 2147 5.120830 CCCAAAATGTTCACAAAAACGACAA 59.879 36.000 0.00 0.00 31.58 3.18
1957 2148 4.627467 CCCAAAATGTTCACAAAAACGACA 59.373 37.500 0.00 0.00 31.58 4.35
1958 2149 4.627900 ACCCAAAATGTTCACAAAAACGAC 59.372 37.500 0.00 0.00 31.58 4.34
1961 2152 7.778470 TGATACCCAAAATGTTCACAAAAAC 57.222 32.000 0.00 0.00 0.00 2.43
1962 2153 8.834465 CATTGATACCCAAAATGTTCACAAAAA 58.166 29.630 0.00 0.00 38.43 1.94
1963 2154 8.206867 TCATTGATACCCAAAATGTTCACAAAA 58.793 29.630 0.00 0.00 38.43 2.44
1965 2156 7.295322 TCATTGATACCCAAAATGTTCACAA 57.705 32.000 0.00 0.00 38.43 3.33
1966 2157 6.907853 TCATTGATACCCAAAATGTTCACA 57.092 33.333 0.00 0.00 38.43 3.58
1971 2162 8.796475 GCTGTATATCATTGATACCCAAAATGT 58.204 33.333 8.51 0.00 38.43 2.71
1972 2163 9.017509 AGCTGTATATCATTGATACCCAAAATG 57.982 33.333 8.51 0.00 38.43 2.32
1979 2170 6.980978 ACGCATAGCTGTATATCATTGATACC 59.019 38.462 8.51 3.85 0.00 2.73
1984 2175 7.704047 AGTGATACGCATAGCTGTATATCATTG 59.296 37.037 11.76 0.00 35.57 2.82
1993 2184 3.550233 CCGTTAGTGATACGCATAGCTGT 60.550 47.826 0.00 0.00 37.67 4.40
1995 2186 2.621998 ACCGTTAGTGATACGCATAGCT 59.378 45.455 0.00 0.00 37.67 3.32
1996 2187 3.009301 ACCGTTAGTGATACGCATAGC 57.991 47.619 0.00 0.00 37.67 2.97
2015 2208 4.095610 CGTGGACAAACAAGAAAACTCAC 58.904 43.478 0.00 0.00 0.00 3.51
2016 2209 4.004314 TCGTGGACAAACAAGAAAACTCA 58.996 39.130 0.00 0.00 0.00 3.41
2018 2211 3.754323 TGTCGTGGACAAACAAGAAAACT 59.246 39.130 0.00 0.00 39.78 2.66
2019 2212 4.086199 TGTCGTGGACAAACAAGAAAAC 57.914 40.909 0.00 0.00 39.78 2.43
2026 2221 2.065512 CATCGATGTCGTGGACAAACA 58.934 47.619 17.50 0.00 45.96 2.83
2246 2716 8.454106 AGATTCAATTGTAGAAGAAACATTCGG 58.546 33.333 5.13 0.00 34.27 4.30
2263 2733 7.899973 ACATTGCCTAAACAGAAGATTCAATT 58.100 30.769 0.00 0.00 0.00 2.32
2341 2829 7.478520 AATGACCATTAGCGTTATGTAGAAC 57.521 36.000 0.00 0.00 0.00 3.01
2370 2868 6.549364 ACAACAACATTCAGGTGGAGAAATAA 59.451 34.615 0.00 0.00 40.07 1.40
2420 2919 1.295423 GCCCATGACGTACACACCT 59.705 57.895 0.00 0.00 0.00 4.00
2579 3783 3.991773 TGGTGTGACGTAAAATAGCAGAC 59.008 43.478 0.00 0.00 0.00 3.51
2602 3806 5.710513 TGATGAACCTGAAAAATCACCAG 57.289 39.130 0.00 0.00 0.00 4.00
2615 3823 8.830580 CAACTCGACATATTATTTGATGAACCT 58.169 33.333 0.00 0.00 0.00 3.50
2635 3843 5.949233 TTCGTATCATGATTGTCAACTCG 57.051 39.130 14.65 6.69 0.00 4.18
2674 3884 6.984474 AGAAACTGAGACGTCAACTCAATAAA 59.016 34.615 19.50 0.00 42.58 1.40
2701 3911 6.882140 TGCGGATCAGGAAATTAAGAACTTAA 59.118 34.615 9.03 9.03 39.12 1.85
2876 4105 5.652014 TGGCAGGTTTAAATAGAGACATTGG 59.348 40.000 0.00 0.00 0.00 3.16
3064 4296 4.280929 TGCTGTAAACAGAAGTCTAGAGCA 59.719 41.667 14.21 0.00 46.59 4.26
3133 4365 2.686915 CAGAACTGAGATGAAATGCCCC 59.313 50.000 0.00 0.00 0.00 5.80
3401 4664 4.020543 ACTAAGTGCTCCAAAACCAAACA 58.979 39.130 0.00 0.00 0.00 2.83
3525 4789 8.748380 CTTAATTTAAGCTGGGAAACAAGAAG 57.252 34.615 3.33 0.00 0.00 2.85
3565 4836 9.533253 CAAGTCACATGGAAAGTTTCTTATTTT 57.467 29.630 15.05 0.00 0.00 1.82
3578 4849 1.142667 TGGTGCTCAAGTCACATGGAA 59.857 47.619 0.00 0.00 36.22 3.53
3579 4850 0.764271 TGGTGCTCAAGTCACATGGA 59.236 50.000 0.00 0.00 36.22 3.41
3617 4917 7.625828 AGTACCTTCCGAAAAATGATTAAGG 57.374 36.000 0.00 0.00 38.36 2.69
3653 4981 8.843262 TGCATCAAAAGATGAATAATAGGTCAG 58.157 33.333 9.49 0.00 42.54 3.51
3746 5074 1.052124 CAAGGATTGCATGGGGCCAT 61.052 55.000 4.39 0.00 40.39 4.40
3797 5126 2.033424 AGACAAGCTTCGAAAAAGTGCC 59.967 45.455 0.00 0.00 0.00 5.01
3800 5129 2.033424 GCCAGACAAGCTTCGAAAAAGT 59.967 45.455 0.00 0.00 0.00 2.66
3808 5154 1.731720 CCTAGTGCCAGACAAGCTTC 58.268 55.000 0.00 0.00 0.00 3.86
3812 5175 1.448540 CCGCCTAGTGCCAGACAAG 60.449 63.158 0.00 0.00 36.24 3.16
3826 5189 0.733729 TTTTACACACACACACCGCC 59.266 50.000 0.00 0.00 0.00 6.13
3827 5190 1.399089 AGTTTTACACACACACACCGC 59.601 47.619 0.00 0.00 0.00 5.68
3830 5193 8.676454 TTCATTTAAGTTTTACACACACACAC 57.324 30.769 0.00 0.00 0.00 3.82
3917 5280 6.813649 TGAATATGCACTAGAGAAACAGACAC 59.186 38.462 0.00 0.00 0.00 3.67
3950 5313 8.428063 CACTAGAATATGGACTTGATTCCTCTT 58.572 37.037 0.00 0.00 36.51 2.85
4047 5410 7.138081 CACAACATACAGCAAAACATAGTCAA 58.862 34.615 0.00 0.00 0.00 3.18
4093 5456 4.082679 GGTACAACAACCAACAACAAGACA 60.083 41.667 0.00 0.00 39.50 3.41
4128 5491 5.499139 AACATGTCGAAATATGGCGATTT 57.501 34.783 0.00 0.00 38.91 2.17
4217 5580 2.522193 CCCCTCCTCCGGCTACTC 60.522 72.222 0.00 0.00 0.00 2.59
4244 5607 3.161450 GCCCCGCAGACTATCCCA 61.161 66.667 0.00 0.00 0.00 4.37
4283 5646 2.967076 CCGCCCCATGAATCGACG 60.967 66.667 0.00 0.00 0.00 5.12
4362 5726 4.085357 TGTTGGAGCTATAATTGGCGAT 57.915 40.909 0.00 0.00 33.93 4.58
4383 5748 9.113838 GAGTAGTATGTTGTTCCATCAATCATT 57.886 33.333 0.00 0.00 0.00 2.57
4421 5786 8.070034 TCGTGATTCAGGGTAGTCTAAATAAA 57.930 34.615 6.52 0.00 0.00 1.40
4450 5816 4.168014 CAGTAACAACAATCGCAATGCAT 58.832 39.130 5.91 0.00 0.00 3.96
4451 5817 3.563508 CAGTAACAACAATCGCAATGCA 58.436 40.909 5.91 0.00 0.00 3.96
4501 5867 1.995626 CAACCTGTCCCCGGGATCT 60.996 63.158 26.32 0.00 39.78 2.75
4507 5873 1.269448 CAATCAAACAACCTGTCCCCG 59.731 52.381 0.00 0.00 0.00 5.73
4555 5921 3.067106 CCCAGGTATTGCTACTATTGCG 58.933 50.000 0.00 0.00 0.00 4.85
4573 5939 5.880164 TTTACATACTACAGCTATGCCCA 57.120 39.130 0.00 0.00 0.00 5.36
4681 6047 9.349713 TCTCACAGAAAACCATGTATTTAACTT 57.650 29.630 0.00 0.00 0.00 2.66
4685 6051 8.918202 AGTTCTCACAGAAAACCATGTATTTA 57.082 30.769 0.00 0.00 35.75 1.40


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

AutoCloner maintained by Alex Coulton.