Multiple sequence alignment - TraesCS5B01G366700

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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 TraesCS5B01G366700 chr5B 100.000 4594 0 0 1 4594 545410250 545405657 0.000000e+00 8484.0
1 TraesCS5B01G366700 chr5B 82.942 1149 134 35 1707 2812 545429437 545428308 0.000000e+00 979.0
2 TraesCS5B01G366700 chr5B 86.836 433 20 18 999 1405 545430049 545429628 2.520000e-122 449.0
3 TraesCS5B01G366700 chr5B 82.710 428 56 12 3197 3620 545428198 545427785 9.390000e-97 364.0
4 TraesCS5B01G366700 chr5D 88.733 1429 87 29 55 1451 447235704 447237090 0.000000e+00 1679.0
5 TraesCS5B01G366700 chr5D 87.830 1479 106 41 3162 4590 447238832 447240286 0.000000e+00 1666.0
6 TraesCS5B01G366700 chr5D 91.800 1000 66 11 1967 2959 447237613 447238603 0.000000e+00 1378.0
7 TraesCS5B01G366700 chr5D 91.494 1011 65 19 1967 2959 230638869 230639876 0.000000e+00 1371.0
8 TraesCS5B01G366700 chr5D 86.207 870 103 10 1966 2820 447205876 447206743 0.000000e+00 926.0
9 TraesCS5B01G366700 chr5D 84.325 504 54 16 1469 1963 447237075 447237562 1.940000e-128 470.0
10 TraesCS5B01G366700 chr5D 87.376 404 32 15 2572 2959 442366886 442367286 3.260000e-121 446.0
11 TraesCS5B01G366700 chr5D 82.992 488 38 19 927 1405 447205119 447205570 2.570000e-107 399.0
12 TraesCS5B01G366700 chr5D 85.455 385 51 3 3236 3620 447206925 447207304 3.330000e-106 396.0
13 TraesCS5B01G366700 chr5D 90.426 282 17 3 1176 1451 230638085 230638362 3.380000e-96 363.0
14 TraesCS5B01G366700 chr5D 83.123 397 30 9 1469 1836 230638347 230638735 1.230000e-85 327.0
15 TraesCS5B01G366700 chr5D 88.462 52 6 0 245 296 14135013 14134962 3.840000e-06 63.9
16 TraesCS5B01G366700 chr1B 91.031 1048 85 5 1967 3010 159410026 159408984 0.000000e+00 1406.0
17 TraesCS5B01G366700 chr1B 86.822 258 30 4 1707 1963 159410327 159410073 7.520000e-73 285.0
18 TraesCS5B01G366700 chr1B 91.765 85 7 0 1624 1708 159410436 159410352 8.070000e-23 119.0
19 TraesCS5B01G366700 chr6D 91.098 1011 69 17 1967 2959 15852517 15851510 0.000000e+00 1349.0
20 TraesCS5B01G366700 chr6D 90.681 279 16 5 1179 1451 15853298 15853024 3.380000e-96 363.0
21 TraesCS5B01G366700 chr6D 83.417 398 27 15 1469 1836 15853039 15852651 2.650000e-87 333.0
22 TraesCS5B01G366700 chr5A 92.035 791 27 11 3798 4588 565395823 565395069 0.000000e+00 1079.0
23 TraesCS5B01G366700 chr5A 91.961 709 41 6 1967 2661 565397705 565396999 0.000000e+00 979.0
24 TraesCS5B01G366700 chr5A 88.193 830 33 23 658 1451 565399038 565398238 0.000000e+00 929.0
25 TraesCS5B01G366700 chr5A 85.912 866 108 9 1967 2820 565404388 565403525 0.000000e+00 911.0
26 TraesCS5B01G366700 chr5A 84.631 488 48 14 3236 3711 565396326 565395854 1.160000e-125 460.0
27 TraesCS5B01G366700 chr5A 86.199 442 27 24 995 1405 565405172 565404734 9.070000e-122 448.0
28 TraesCS5B01G366700 chr5A 84.797 467 43 14 3165 3620 565403411 565402962 1.170000e-120 444.0
29 TraesCS5B01G366700 chr5A 85.274 292 29 11 2673 2959 565396956 565396674 5.820000e-74 289.0
30 TraesCS5B01G366700 chr5A 87.137 241 21 7 1469 1709 565398253 565398023 9.800000e-67 265.0
31 TraesCS5B01G366700 chr5A 95.946 74 2 1 1762 1835 565397914 565397842 8.070000e-23 119.0
32 TraesCS5B01G366700 chr4D 87.129 404 33 15 2572 2959 3464961 3465361 1.520000e-119 440.0
33 TraesCS5B01G366700 chr4D 87.719 57 7 0 4251 4307 506216783 506216839 2.970000e-07 67.6
34 TraesCS5B01G366700 chr4D 96.970 33 1 0 245 277 433351606 433351638 6.420000e-04 56.5
35 TraesCS5B01G366700 chr2D 83.333 252 36 6 4250 4498 536153648 536153400 1.290000e-55 228.0
36 TraesCS5B01G366700 chr2D 85.294 68 9 1 245 312 601977435 601977369 8.250000e-08 69.4
37 TraesCS5B01G366700 chr2B 82.171 258 40 6 4248 4502 637576821 637576567 2.780000e-52 217.0
38 TraesCS5B01G366700 chr2A 82.540 252 38 6 4250 4498 678965612 678965364 2.780000e-52 217.0
39 TraesCS5B01G366700 chr3D 96.000 75 2 1 1762 1836 156838838 156838765 2.240000e-23 121.0
40 TraesCS5B01G366700 chr3D 94.667 75 3 1 1762 1836 26880644 26880571 1.040000e-21 115.0
41 TraesCS5B01G366700 chr3D 94.595 74 0 2 1378 1451 26881019 26880950 1.350000e-20 111.0
42 TraesCS5B01G366700 chr3D 91.892 74 2 2 1378 1451 156839213 156839144 2.920000e-17 100.0
43 TraesCS5B01G366700 chr3D 79.412 102 16 3 4252 4349 414637551 414637651 2.970000e-07 67.6
44 TraesCS5B01G366700 chr3D 100.000 28 0 0 245 272 275639142 275639115 8.000000e-03 52.8
45 TraesCS5B01G366700 chr1D 96.000 75 2 1 1762 1836 398337712 398337785 2.240000e-23 121.0
46 TraesCS5B01G366700 chr7D 91.765 85 5 2 1762 1845 546441730 546441813 2.900000e-22 117.0
47 TraesCS5B01G366700 chrUn 91.892 74 2 2 1378 1451 154694413 154694482 2.920000e-17 100.0
48 TraesCS5B01G366700 chrUn 97.436 39 0 1 3232 3270 53041169 53041206 1.070000e-06 65.8
49 TraesCS5B01G366700 chr3A 85.897 78 6 3 4276 4349 535727801 535727725 1.370000e-10 78.7
50 TraesCS5B01G366700 chr7B 97.619 42 1 0 1 42 379202733 379202692 6.380000e-09 73.1
51 TraesCS5B01G366700 chr7B 97.436 39 0 1 3232 3270 182139797 182139760 1.070000e-06 65.8
52 TraesCS5B01G366700 chr4A 97.436 39 0 1 3232 3270 546447090 546447127 1.070000e-06 65.8
53 TraesCS5B01G366700 chr3B 83.117 77 8 3 4276 4348 540476474 540476549 1.070000e-06 65.8
54 TraesCS5B01G366700 chr6B 100.000 33 0 0 259 291 123378581 123378613 1.380000e-05 62.1
55 TraesCS5B01G366700 chr6B 100.000 31 0 0 245 275 144274521 144274551 1.790000e-04 58.4
56 TraesCS5B01G366700 chr6B 94.595 37 2 0 241 277 274980720 274980756 1.790000e-04 58.4


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 TraesCS5B01G366700 chr5B 545405657 545410250 4593 True 8484.000000 8484 100.000000 1 4594 1 chr5B.!!$R1 4593
1 TraesCS5B01G366700 chr5B 545427785 545430049 2264 True 597.333333 979 84.162667 999 3620 3 chr5B.!!$R2 2621
2 TraesCS5B01G366700 chr5D 447235704 447240286 4582 False 1298.250000 1679 88.172000 55 4590 4 chr5D.!!$F4 4535
3 TraesCS5B01G366700 chr5D 230638085 230639876 1791 False 687.000000 1371 88.347667 1176 2959 3 chr5D.!!$F2 1783
4 TraesCS5B01G366700 chr5D 447205119 447207304 2185 False 573.666667 926 84.884667 927 3620 3 chr5D.!!$F3 2693
5 TraesCS5B01G366700 chr1B 159408984 159410436 1452 True 603.333333 1406 89.872667 1624 3010 3 chr1B.!!$R1 1386
6 TraesCS5B01G366700 chr6D 15851510 15853298 1788 True 681.666667 1349 88.398667 1179 2959 3 chr6D.!!$R1 1780
7 TraesCS5B01G366700 chr5A 565395069 565405172 10103 True 592.300000 1079 88.208500 658 4588 10 chr5A.!!$R1 3930

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
26 27 0.109597 GTCCAAGCAAACCGCATCAG 60.110 55.000 0.00 0.0 46.13 2.90 F
27 28 0.250684 TCCAAGCAAACCGCATCAGA 60.251 50.000 0.00 0.0 46.13 3.27 F
1697 7252 0.105862 ACCCCAATGGAGCATCATGG 60.106 55.000 0.00 0.0 36.25 3.66 F
2482 8226 2.162208 GCTATGTGCACTGCTGCTAAAA 59.838 45.455 19.41 0.0 44.57 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 7081 1.272092 TGCAACCCATCTTCTCCTTGG 60.272 52.381 0.00 0.0 0.00 3.61 R
1987 7709 2.450476 ACAATCAGCAGGGGATCAAAC 58.550 47.619 0.00 0.0 0.00 2.93 R
3102 8912 0.376152 GCGCATCACTCAATCTGGTG 59.624 55.000 0.30 0.0 35.06 4.17 R
3602 9495 0.390603 TGTATGGTACGTGCTGCCAC 60.391 55.000 3.01 0.0 37.49 5.01 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
23 24 3.365535 GGTCCAAGCAAACCGCAT 58.634 55.556 0.00 0.00 46.13 4.73
24 25 1.212751 GGTCCAAGCAAACCGCATC 59.787 57.895 0.00 0.00 46.13 3.91
25 26 1.523154 GGTCCAAGCAAACCGCATCA 61.523 55.000 0.00 0.00 46.13 3.07
26 27 0.109597 GTCCAAGCAAACCGCATCAG 60.110 55.000 0.00 0.00 46.13 2.90
27 28 0.250684 TCCAAGCAAACCGCATCAGA 60.251 50.000 0.00 0.00 46.13 3.27
28 29 0.109597 CCAAGCAAACCGCATCAGAC 60.110 55.000 0.00 0.00 46.13 3.51
29 30 0.453282 CAAGCAAACCGCATCAGACG 60.453 55.000 0.00 0.00 46.13 4.18
46 47 2.110006 GGCTGGGCCTCGAAGATC 59.890 66.667 4.53 0.00 46.69 2.75
47 48 2.279784 GCTGGGCCTCGAAGATCG 60.280 66.667 4.53 0.00 42.10 3.69
48 49 2.279784 CTGGGCCTCGAAGATCGC 60.280 66.667 4.53 0.00 40.21 4.58
49 50 2.759973 TGGGCCTCGAAGATCGCT 60.760 61.111 4.53 0.00 40.21 4.93
50 51 2.279784 GGGCCTCGAAGATCGCTG 60.280 66.667 0.84 0.00 40.21 5.18
51 52 2.964389 GGCCTCGAAGATCGCTGC 60.964 66.667 0.00 0.00 40.21 5.25
52 53 2.964389 GCCTCGAAGATCGCTGCC 60.964 66.667 0.00 0.00 40.21 4.85
102 103 5.295787 ACATACTTAACATGTACATTGGCCG 59.704 40.000 5.37 0.00 34.88 6.13
143 144 9.083080 CATCACACTAACAAGTTAATCGTATCA 57.917 33.333 0.00 0.00 0.00 2.15
165 166 7.030234 TCAAGTACTCCTAACTAGAGGAAGT 57.970 40.000 0.00 2.78 45.20 3.01
173 174 3.955650 AACTAGAGGAAGTTTAGCGCA 57.044 42.857 11.47 0.00 36.26 6.09
231 232 2.036475 ACGACAGATCTTGCAAGTGACT 59.964 45.455 25.19 18.46 0.00 3.41
235 236 3.999663 ACAGATCTTGCAAGTGACTAAGC 59.000 43.478 25.19 8.46 0.00 3.09
285 286 9.924650 AAATAAGTGTCTCAACTTCGTACTAAT 57.075 29.630 0.00 0.00 40.77 1.73
290 291 9.754382 AGTGTCTCAACTTCGTACTAATTTTAA 57.246 29.630 0.00 0.00 0.00 1.52
319 320 9.646427 CAATAGAAAAAGTACTAAGCAGTCTCT 57.354 33.333 0.00 0.00 36.14 3.10
329 330 6.664428 ACTAAGCAGTCTCTCTTTCTCTTT 57.336 37.500 0.00 0.00 0.00 2.52
331 332 4.535526 AGCAGTCTCTCTTTCTCTTTCC 57.464 45.455 0.00 0.00 0.00 3.13
351 352 2.030457 CCAGCCGATAACGTGTGAAATC 59.970 50.000 0.00 0.00 37.88 2.17
361 362 1.735018 CGTGTGAAATCGGCCAATGTA 59.265 47.619 2.24 0.00 0.00 2.29
400 401 1.391729 CCAACATCCCCACCCCAAT 59.608 57.895 0.00 0.00 0.00 3.16
406 407 3.350163 CCCCACCCCAATGCCTCT 61.350 66.667 0.00 0.00 0.00 3.69
425 426 1.153549 CTTTCCCTTCCTCTCGCGG 60.154 63.158 6.13 0.00 0.00 6.46
455 456 4.899239 CCGCTCCCTCATCACCGC 62.899 72.222 0.00 0.00 0.00 5.68
465 466 2.124151 ATCACCGCCTTCCCATGC 60.124 61.111 0.00 0.00 0.00 4.06
496 497 1.074775 CTAGTTGTTGCCCCTGCCA 59.925 57.895 0.00 0.00 36.33 4.92
545 546 2.025418 CCACCGTACTTGCACCGTC 61.025 63.158 0.00 0.00 0.00 4.79
551 552 2.214216 TACTTGCACCGTCAGCCCT 61.214 57.895 0.00 0.00 0.00 5.19
563 564 1.078567 CAGCCCTCTTGCTCACCTC 60.079 63.158 0.00 0.00 40.32 3.85
564 565 2.125350 GCCCTCTTGCTCACCTCG 60.125 66.667 0.00 0.00 0.00 4.63
568 569 1.536073 CCTCTTGCTCACCTCGGTCA 61.536 60.000 0.00 0.00 0.00 4.02
651 657 8.352942 CGAAGAATAGCAAATTTTAGGGCTTAT 58.647 33.333 6.11 0.00 37.79 1.73
652 658 9.684448 GAAGAATAGCAAATTTTAGGGCTTATC 57.316 33.333 6.11 5.76 37.79 1.75
653 659 8.766994 AGAATAGCAAATTTTAGGGCTTATCA 57.233 30.769 6.11 0.00 37.79 2.15
655 661 9.987272 GAATAGCAAATTTTAGGGCTTATCAAT 57.013 29.630 6.11 0.00 37.79 2.57
659 665 7.765819 AGCAAATTTTAGGGCTTATCAATCAAC 59.234 33.333 0.00 0.00 31.34 3.18
668 6146 8.401490 AGGGCTTATCAATCAACATCTATTTC 57.599 34.615 0.00 0.00 0.00 2.17
720 6201 4.686972 ACATCATGTATTGAGTCGTCTGG 58.313 43.478 0.00 0.00 37.89 3.86
754 6235 1.669795 CCGTGGCAAGAAATGGAAAGC 60.670 52.381 0.76 0.00 0.00 3.51
796 6277 1.961180 CTCAGCTCGTCCGGGGAAAT 61.961 60.000 0.00 0.00 0.00 2.17
798 6279 2.203029 GCTCGTCCGGGGAAATCC 60.203 66.667 0.00 0.00 0.00 3.01
819 6300 3.941483 CCACAGCTCGTTTCTTTCCATAT 59.059 43.478 0.00 0.00 0.00 1.78
823 6304 6.961554 CACAGCTCGTTTCTTTCCATATAAAC 59.038 38.462 0.00 0.00 0.00 2.01
957 6464 2.041405 CCTCCCTCACTCCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
958 6465 2.641746 CCTCCCTCACTCCCTCCCT 61.642 68.421 0.00 0.00 0.00 4.20
959 6466 1.075600 CTCCCTCACTCCCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
960 6467 2.041405 CCCTCACTCCCTCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
961 6468 2.041405 CCTCACTCCCTCCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
962 6469 2.641746 CCTCACTCCCTCCCTCCCT 61.642 68.421 0.00 0.00 0.00 4.20
963 6470 1.075600 CTCACTCCCTCCCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
1159 6675 1.101331 CACCTCCACCGGTACTACTC 58.899 60.000 6.87 0.00 34.94 2.59
1205 6742 3.302365 AACCAATCATTTTCCTGCGTG 57.698 42.857 0.00 0.00 0.00 5.34
1206 6743 2.513753 ACCAATCATTTTCCTGCGTGA 58.486 42.857 0.00 0.00 0.00 4.35
1451 6997 9.806203 TTTCTTGATCATTTACATTAGGCATTG 57.194 29.630 0.00 0.00 0.00 2.82
1452 6998 8.523915 TCTTGATCATTTACATTAGGCATTGT 57.476 30.769 0.00 0.00 0.00 2.71
1453 6999 8.407832 TCTTGATCATTTACATTAGGCATTGTG 58.592 33.333 0.00 0.00 0.00 3.33
1454 7000 7.643569 TGATCATTTACATTAGGCATTGTGT 57.356 32.000 0.00 0.00 0.00 3.72
1455 7001 8.065473 TGATCATTTACATTAGGCATTGTGTT 57.935 30.769 0.00 0.00 0.00 3.32
1456 7002 8.190122 TGATCATTTACATTAGGCATTGTGTTC 58.810 33.333 0.00 0.00 0.00 3.18
1457 7003 7.459795 TCATTTACATTAGGCATTGTGTTCA 57.540 32.000 0.00 0.00 0.00 3.18
1458 7004 7.890515 TCATTTACATTAGGCATTGTGTTCAA 58.109 30.769 0.00 0.00 37.98 2.69
1459 7005 8.363390 TCATTTACATTAGGCATTGTGTTCAAA 58.637 29.630 0.00 0.00 37.11 2.69
1460 7006 8.986847 CATTTACATTAGGCATTGTGTTCAAAA 58.013 29.630 0.00 0.00 37.11 2.44
1461 7007 8.948631 TTTACATTAGGCATTGTGTTCAAAAA 57.051 26.923 0.00 0.00 37.11 1.94
1531 7077 5.428457 ACTGGAGTATGATATGTTGAACCCA 59.572 40.000 0.00 0.00 0.00 4.51
1532 7078 5.680619 TGGAGTATGATATGTTGAACCCAC 58.319 41.667 0.00 0.00 0.00 4.61
1533 7079 5.190726 TGGAGTATGATATGTTGAACCCACA 59.809 40.000 0.00 0.00 0.00 4.17
1534 7080 6.119536 GGAGTATGATATGTTGAACCCACAA 58.880 40.000 0.00 0.00 0.00 3.33
1535 7081 6.038271 GGAGTATGATATGTTGAACCCACAAC 59.962 42.308 0.00 0.00 46.83 3.32
1589 7135 4.167554 TGACCAACAGTTGTTTGTTCAC 57.832 40.909 12.42 0.00 39.17 3.18
1653 7204 8.950210 TGTGCTCTAATTTTCTTCCTGATTAAG 58.050 33.333 0.00 0.00 0.00 1.85
1696 7251 1.784358 AACCCCAATGGAGCATCATG 58.216 50.000 0.00 0.00 36.25 3.07
1697 7252 0.105862 ACCCCAATGGAGCATCATGG 60.106 55.000 0.00 0.00 36.25 3.66
1709 7265 4.202441 GAGCATCATGGGAGAAAGCTTAA 58.798 43.478 0.00 0.00 34.46 1.85
1711 7267 3.696051 GCATCATGGGAGAAAGCTTAACA 59.304 43.478 0.00 0.00 0.00 2.41
1712 7268 4.201990 GCATCATGGGAGAAAGCTTAACAG 60.202 45.833 0.00 0.00 0.00 3.16
1713 7269 4.908601 TCATGGGAGAAAGCTTAACAGA 57.091 40.909 0.00 0.00 0.00 3.41
1716 7272 4.431416 TGGGAGAAAGCTTAACAGACAA 57.569 40.909 0.00 0.00 0.00 3.18
1719 7306 5.833131 TGGGAGAAAGCTTAACAGACAATTT 59.167 36.000 0.00 0.00 0.00 1.82
1784 7401 4.097741 TGTGTTGCTGAATACTGCTTGTTT 59.902 37.500 0.00 0.00 40.71 2.83
1796 7413 5.581126 ACTGCTTGTTTGTTTGATCAAGA 57.419 34.783 8.41 0.00 39.39 3.02
1846 7512 7.648112 GGTCAGAAGTAATTGTGTTTTTCTTCC 59.352 37.037 0.00 0.00 32.89 3.46
1964 7634 5.006165 GCTAACTGCAGTTATAAGAGCACTG 59.994 44.000 31.99 21.32 39.49 3.66
1996 7718 8.093927 TCCTAAACATCAATTTTGTTTGATCCC 58.906 33.333 19.46 0.00 44.63 3.85
2007 7729 2.225091 TGTTTGATCCCCTGCTGATTGT 60.225 45.455 0.00 0.00 0.00 2.71
2125 7849 2.367894 TGCCTATGATGAAGGAGCTGAG 59.632 50.000 0.00 0.00 36.08 3.35
2252 7988 6.095860 TGGATGCCTGTCAAAAATATTCAGAG 59.904 38.462 3.33 0.00 0.00 3.35
2455 8199 3.565482 ACTGTTTGCCTGTGTATGAACTG 59.435 43.478 0.00 0.00 0.00 3.16
2457 8201 3.563808 TGTTTGCCTGTGTATGAACTGTC 59.436 43.478 0.00 0.00 0.00 3.51
2482 8226 2.162208 GCTATGTGCACTGCTGCTAAAA 59.838 45.455 19.41 0.00 44.57 1.52
2691 8469 4.398319 ACCTTCTTACAGACATGGTTTGG 58.602 43.478 0.00 0.00 0.00 3.28
2881 8670 7.718272 TTTCTGCAATCATTTTCTGAAAAGG 57.282 32.000 18.50 18.50 37.44 3.11
2938 8730 4.627284 TTTGTCCCAATCTTTCCGTAGA 57.373 40.909 0.00 0.00 0.00 2.59
2939 8731 4.627284 TTGTCCCAATCTTTCCGTAGAA 57.373 40.909 0.00 0.00 0.00 2.10
3002 8810 7.387948 TCTTGAACAGCCTTCTAGTTATTTGAC 59.612 37.037 0.00 0.00 0.00 3.18
3012 8820 5.234752 TCTAGTTATTTGACTGCAAGCGAA 58.765 37.500 0.00 0.00 37.60 4.70
3016 8824 7.088589 AGTTATTTGACTGCAAGCGAATAAT 57.911 32.000 17.34 8.98 37.96 1.28
3023 8831 6.661669 TGACTGCAAGCGAATAATTGATATG 58.338 36.000 0.00 0.00 37.60 1.78
3025 8833 6.432936 ACTGCAAGCGAATAATTGATATGTG 58.567 36.000 0.00 0.00 37.60 3.21
3030 8838 7.645340 GCAAGCGAATAATTGATATGTGAGTTT 59.355 33.333 0.00 0.00 0.00 2.66
3032 8840 7.134815 AGCGAATAATTGATATGTGAGTTTGC 58.865 34.615 0.00 0.00 0.00 3.68
3034 8842 7.416817 CGAATAATTGATATGTGAGTTTGCCA 58.583 34.615 0.00 0.00 0.00 4.92
3043 8851 4.299586 TGTGAGTTTGCCATAATCCTGA 57.700 40.909 0.00 0.00 0.00 3.86
3050 8858 2.492025 TGCCATAATCCTGACCTCCTT 58.508 47.619 0.00 0.00 0.00 3.36
3070 8879 7.663493 CCTCCTTAGGTAATCTTGATGAAATCC 59.337 40.741 0.00 0.00 39.43 3.01
3075 8884 9.618890 TTAGGTAATCTTGATGAAATCCAGAAG 57.381 33.333 0.00 0.00 46.58 2.85
3080 8889 6.627087 TCTTGATGAAATCCAGAAGTACCT 57.373 37.500 0.00 0.00 41.58 3.08
3084 8893 5.250543 TGATGAAATCCAGAAGTACCTCCAA 59.749 40.000 0.00 0.00 44.73 3.53
3085 8894 5.779241 TGAAATCCAGAAGTACCTCCAAT 57.221 39.130 0.00 0.00 0.00 3.16
3086 8895 6.139679 TGAAATCCAGAAGTACCTCCAATT 57.860 37.500 0.00 0.00 0.00 2.32
3088 8897 3.350219 TCCAGAAGTACCTCCAATTGC 57.650 47.619 0.00 0.00 0.00 3.56
3105 8915 0.941542 TGCGCAAGTAACTCAACACC 59.058 50.000 8.16 0.00 41.68 4.16
3107 8917 1.069906 GCGCAAGTAACTCAACACCAG 60.070 52.381 0.30 0.00 41.68 4.00
3108 8918 2.479837 CGCAAGTAACTCAACACCAGA 58.520 47.619 0.00 0.00 0.00 3.86
3109 8919 3.067106 CGCAAGTAACTCAACACCAGAT 58.933 45.455 0.00 0.00 0.00 2.90
3110 8920 3.498397 CGCAAGTAACTCAACACCAGATT 59.502 43.478 0.00 0.00 0.00 2.40
3111 8921 4.611355 CGCAAGTAACTCAACACCAGATTG 60.611 45.833 0.00 0.00 0.00 2.67
3112 8922 4.515191 GCAAGTAACTCAACACCAGATTGA 59.485 41.667 0.00 0.00 34.89 2.57
3118 8928 4.941325 CTCAACACCAGATTGAGTGATG 57.059 45.455 6.58 0.00 45.32 3.07
3119 8929 3.076621 TCAACACCAGATTGAGTGATGC 58.923 45.455 0.00 0.00 36.89 3.91
3121 8931 0.376152 CACCAGATTGAGTGATGCGC 59.624 55.000 0.00 0.00 36.01 6.09
3122 8932 0.036105 ACCAGATTGAGTGATGCGCA 60.036 50.000 14.96 14.96 0.00 6.09
3124 8934 2.158914 ACCAGATTGAGTGATGCGCATA 60.159 45.455 25.40 6.84 0.00 3.14
3125 8935 2.479275 CCAGATTGAGTGATGCGCATAG 59.521 50.000 25.40 3.23 0.00 2.23
3126 8936 2.479275 CAGATTGAGTGATGCGCATAGG 59.521 50.000 25.40 0.00 0.00 2.57
3127 8937 2.103771 AGATTGAGTGATGCGCATAGGT 59.896 45.455 25.40 10.43 0.00 3.08
3128 8938 2.401583 TTGAGTGATGCGCATAGGTT 57.598 45.000 25.40 9.43 0.00 3.50
3129 8939 2.401583 TGAGTGATGCGCATAGGTTT 57.598 45.000 25.40 7.48 0.00 3.27
3130 8940 2.279741 TGAGTGATGCGCATAGGTTTC 58.720 47.619 25.40 16.30 0.00 2.78
3131 8941 2.279741 GAGTGATGCGCATAGGTTTCA 58.720 47.619 25.40 14.38 0.00 2.69
3132 8942 2.009774 AGTGATGCGCATAGGTTTCAC 58.990 47.619 25.40 25.06 34.99 3.18
3133 8943 1.737236 GTGATGCGCATAGGTTTCACA 59.263 47.619 26.42 15.23 34.92 3.58
3134 8944 2.161410 GTGATGCGCATAGGTTTCACAA 59.839 45.455 26.42 0.00 34.92 3.33
3135 8945 3.016031 TGATGCGCATAGGTTTCACAAT 58.984 40.909 25.40 0.00 0.00 2.71
3136 8946 4.035091 GTGATGCGCATAGGTTTCACAATA 59.965 41.667 26.42 0.00 34.92 1.90
3143 8953 6.018262 GCGCATAGGTTTCACAATACTGATAA 60.018 38.462 0.30 0.00 0.00 1.75
3163 8992 9.619727 CTGATAATTATGAACTTGTTCGTTACG 57.380 33.333 12.61 0.00 0.00 3.18
3168 8997 3.117794 TGAACTTGTTCGTTACGACCAG 58.882 45.455 7.06 6.23 34.89 4.00
3175 9004 4.370049 TGTTCGTTACGACCAGAATTCAA 58.630 39.130 7.06 0.00 34.89 2.69
3179 9008 4.802039 TCGTTACGACCAGAATTCAATAGC 59.198 41.667 2.33 0.00 0.00 2.97
3183 9012 3.313526 ACGACCAGAATTCAATAGCATGC 59.686 43.478 10.51 10.51 0.00 4.06
3273 9156 1.279496 TGCTGATTCAGGTGCCTACT 58.721 50.000 15.28 0.00 31.21 2.57
3279 9162 4.575885 TGATTCAGGTGCCTACTGTTAAC 58.424 43.478 0.00 0.00 37.25 2.01
3294 9177 4.755123 ACTGTTAACCAAGAGAACGGAATG 59.245 41.667 2.48 0.00 34.27 2.67
3391 9277 3.772572 ACACAAGGTAATTAATTGCCCCC 59.227 43.478 26.17 13.49 42.66 5.40
3401 9287 2.231716 AATTGCCCCCTTCAACCTAC 57.768 50.000 0.00 0.00 0.00 3.18
3411 9297 4.160626 CCCCTTCAACCTACTCTACTCTTG 59.839 50.000 0.00 0.00 0.00 3.02
3412 9298 4.382147 CCCTTCAACCTACTCTACTCTTGC 60.382 50.000 0.00 0.00 0.00 4.01
3413 9299 4.464597 CCTTCAACCTACTCTACTCTTGCT 59.535 45.833 0.00 0.00 0.00 3.91
3414 9300 5.652891 CCTTCAACCTACTCTACTCTTGCTA 59.347 44.000 0.00 0.00 0.00 3.49
3415 9301 6.404954 CCTTCAACCTACTCTACTCTTGCTAC 60.405 46.154 0.00 0.00 0.00 3.58
3416 9302 4.948621 TCAACCTACTCTACTCTTGCTACC 59.051 45.833 0.00 0.00 0.00 3.18
3417 9303 4.866327 ACCTACTCTACTCTTGCTACCT 57.134 45.455 0.00 0.00 0.00 3.08
3418 9304 5.195848 ACCTACTCTACTCTTGCTACCTT 57.804 43.478 0.00 0.00 0.00 3.50
3419 9305 5.195185 ACCTACTCTACTCTTGCTACCTTC 58.805 45.833 0.00 0.00 0.00 3.46
3420 9306 5.194432 CCTACTCTACTCTTGCTACCTTCA 58.806 45.833 0.00 0.00 0.00 3.02
3421 9307 5.652891 CCTACTCTACTCTTGCTACCTTCAA 59.347 44.000 0.00 0.00 0.00 2.69
3422 9308 5.652994 ACTCTACTCTTGCTACCTTCAAG 57.347 43.478 0.00 0.00 41.57 3.02
3438 9324 5.071115 ACCTTCAAGAGTAGAAGAACAAGCT 59.929 40.000 4.61 0.00 44.00 3.74
3442 9328 7.050970 TCAAGAGTAGAAGAACAAGCTGTTA 57.949 36.000 0.00 0.00 41.28 2.41
3443 9329 7.148641 TCAAGAGTAGAAGAACAAGCTGTTAG 58.851 38.462 0.00 0.00 41.28 2.34
3444 9330 6.658188 AGAGTAGAAGAACAAGCTGTTAGT 57.342 37.500 0.00 0.00 41.28 2.24
3447 9333 8.639761 AGAGTAGAAGAACAAGCTGTTAGTTAA 58.360 33.333 0.00 0.00 41.28 2.01
3448 9334 8.590719 AGTAGAAGAACAAGCTGTTAGTTAAC 57.409 34.615 0.00 0.00 41.28 2.01
3450 9336 6.592870 AGAAGAACAAGCTGTTAGTTAACCT 58.407 36.000 0.88 0.00 41.28 3.50
3456 9349 7.299246 ACAAGCTGTTAGTTAACCTCTCTTA 57.701 36.000 0.88 0.00 35.37 2.10
3467 9360 6.655425 AGTTAACCTCTCTTATTTTGCAGGTC 59.345 38.462 0.88 0.00 32.90 3.85
3525 9418 2.285773 GCAAAGGGCAAAGGGAGGG 61.286 63.158 0.00 0.00 43.97 4.30
3530 9423 2.359975 GGCAAAGGGAGGGTCGTG 60.360 66.667 0.00 0.00 0.00 4.35
3533 9426 0.536460 GCAAAGGGAGGGTCGTGAAA 60.536 55.000 0.00 0.00 0.00 2.69
3574 9467 3.616956 TCTGCAGACATACCCTTCTTG 57.383 47.619 13.74 0.00 0.00 3.02
3620 9513 1.418342 CGTGGCAGCACGTACCATAC 61.418 60.000 7.27 0.00 42.91 2.39
3621 9514 0.390603 GTGGCAGCACGTACCATACA 60.391 55.000 0.00 0.00 35.53 2.29
3669 9564 2.043411 CTGTTCGGTTGATTTTGTGCG 58.957 47.619 0.00 0.00 0.00 5.34
3718 9613 2.801421 GCTCGAGGAGCGTGATCA 59.199 61.111 15.58 0.00 45.85 2.92
3736 9640 6.788930 CGTGATCATCATGTCAAACAATATCG 59.211 38.462 0.00 0.00 0.00 2.92
3739 9643 9.492973 TGATCATCATGTCAAACAATATCGTAT 57.507 29.630 0.00 0.00 0.00 3.06
3763 9667 5.419155 TCATCTGGTTCTTTAGTCTGTCGAT 59.581 40.000 0.00 0.00 0.00 3.59
3768 9672 4.097012 GTTCTTTAGTCTGTCGATCGGTC 58.903 47.826 16.41 9.60 0.00 4.79
3769 9673 3.340928 TCTTTAGTCTGTCGATCGGTCA 58.659 45.455 16.41 13.64 0.00 4.02
3780 9686 3.724751 GTCGATCGGTCAAATAGTTCTCG 59.275 47.826 16.41 0.00 0.00 4.04
3784 9690 2.821378 TCGGTCAAATAGTTCTCGGTGA 59.179 45.455 0.00 0.00 0.00 4.02
3790 9696 5.869888 GTCAAATAGTTCTCGGTGATCACTT 59.130 40.000 24.50 5.65 0.00 3.16
3791 9697 6.035112 GTCAAATAGTTCTCGGTGATCACTTC 59.965 42.308 24.50 8.80 0.00 3.01
3797 9703 2.890945 TCTCGGTGATCACTTCTGTTCA 59.109 45.455 24.50 0.00 0.00 3.18
3798 9704 3.511540 TCTCGGTGATCACTTCTGTTCAT 59.488 43.478 24.50 0.00 30.49 2.57
3799 9705 3.588955 TCGGTGATCACTTCTGTTCATG 58.411 45.455 24.50 3.55 30.49 3.07
3800 9706 3.006859 TCGGTGATCACTTCTGTTCATGT 59.993 43.478 24.50 0.00 30.49 3.21
3801 9707 3.748048 CGGTGATCACTTCTGTTCATGTT 59.252 43.478 24.50 0.00 30.49 2.71
3802 9708 4.143030 CGGTGATCACTTCTGTTCATGTTC 60.143 45.833 24.50 2.67 30.49 3.18
3803 9709 4.756642 GGTGATCACTTCTGTTCATGTTCA 59.243 41.667 24.50 0.00 30.49 3.18
3833 9739 4.328440 CGAAGCCTTTGTCAGAGACTTATG 59.672 45.833 0.00 0.00 33.15 1.90
3853 9759 3.458579 CTGACGAACGTGGTCGCG 61.459 66.667 7.30 0.00 45.00 5.87
4032 9942 8.691661 TCTGTATGTATATCTGCACTACTTCA 57.308 34.615 0.00 0.00 0.00 3.02
4068 9978 1.915141 AAATGGTGTCCAGCTTCCAG 58.085 50.000 0.00 0.00 36.75 3.86
4077 9987 1.207089 TCCAGCTTCCAGAACCATACG 59.793 52.381 0.00 0.00 0.00 3.06
4083 9993 0.249120 TCCAGAACCATACGCCACTG 59.751 55.000 0.00 0.00 0.00 3.66
4097 10007 1.100510 CCACTGATGGCATCTGTTGG 58.899 55.000 30.11 27.52 39.82 3.77
4098 10008 1.100510 CACTGATGGCATCTGTTGGG 58.899 55.000 30.11 18.87 39.09 4.12
4099 10009 0.994247 ACTGATGGCATCTGTTGGGA 59.006 50.000 27.91 7.58 38.11 4.37
4100 10010 1.064906 ACTGATGGCATCTGTTGGGAG 60.065 52.381 27.91 17.63 38.11 4.30
4101 10011 0.256752 TGATGGCATCTGTTGGGAGG 59.743 55.000 26.49 0.00 0.00 4.30
4102 10012 1.076485 ATGGCATCTGTTGGGAGGC 60.076 57.895 0.00 0.00 41.52 4.70
4105 10015 1.001641 GCATCTGTTGGGAGGCTGT 60.002 57.895 0.00 0.00 39.52 4.40
4106 10016 0.610232 GCATCTGTTGGGAGGCTGTT 60.610 55.000 0.00 0.00 39.52 3.16
4107 10017 1.457346 CATCTGTTGGGAGGCTGTTC 58.543 55.000 0.00 0.00 0.00 3.18
4108 10018 1.004044 CATCTGTTGGGAGGCTGTTCT 59.996 52.381 0.00 0.00 0.00 3.01
4110 10020 0.109342 CTGTTGGGAGGCTGTTCTGT 59.891 55.000 0.00 0.00 0.00 3.41
4181 10111 5.627499 TCAAGAAATGGTTACAGCATCAC 57.373 39.130 0.00 0.00 34.88 3.06
4255 10185 2.350522 GTGAGGTGATGTGGCTTACTG 58.649 52.381 0.00 0.00 0.00 2.74
4357 10287 4.208686 GCGTAGGAGGCGTGGGAG 62.209 72.222 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.886886 GGTTTGCTTGGACCGTTAGA 58.113 50.000 0.00 0.00 0.00 2.10
6 7 1.212751 GATGCGGTTTGCTTGGACC 59.787 57.895 0.00 0.00 46.63 4.46
7 8 0.109597 CTGATGCGGTTTGCTTGGAC 60.110 55.000 0.00 0.00 46.63 4.02
8 9 0.250684 TCTGATGCGGTTTGCTTGGA 60.251 50.000 0.00 0.00 46.63 3.53
9 10 0.109597 GTCTGATGCGGTTTGCTTGG 60.110 55.000 0.00 0.00 46.63 3.61
10 11 0.453282 CGTCTGATGCGGTTTGCTTG 60.453 55.000 0.00 0.00 46.63 4.01
11 12 1.577328 CCGTCTGATGCGGTTTGCTT 61.577 55.000 0.00 0.00 46.63 3.91
13 14 2.480555 CCGTCTGATGCGGTTTGC 59.519 61.111 0.00 0.00 43.84 3.68
30 31 2.279784 CGATCTTCGAGGCCCAGC 60.280 66.667 0.00 0.00 43.74 4.85
32 33 2.759973 AGCGATCTTCGAGGCCCA 60.760 61.111 0.00 0.00 43.74 5.36
33 34 2.279784 CAGCGATCTTCGAGGCCC 60.280 66.667 0.00 0.00 43.74 5.80
34 35 2.964389 GCAGCGATCTTCGAGGCC 60.964 66.667 0.00 0.00 43.74 5.19
35 36 2.964389 GGCAGCGATCTTCGAGGC 60.964 66.667 0.32 3.20 43.74 4.70
37 38 0.531532 ATTGGGCAGCGATCTTCGAG 60.532 55.000 0.32 0.00 43.74 4.04
38 39 0.750249 TATTGGGCAGCGATCTTCGA 59.250 50.000 0.32 0.00 43.74 3.71
40 41 4.370364 TTTTTATTGGGCAGCGATCTTC 57.630 40.909 0.00 0.00 0.00 2.87
74 75 9.104965 GCCAATGTACATGTTAAGTATGTAAGA 57.895 33.333 9.63 5.31 41.26 2.10
102 103 2.730672 GATGCGAGGTGTCACGTGC 61.731 63.158 11.67 6.86 0.00 5.34
116 117 6.165659 ACGATTAACTTGTTAGTGTGATGC 57.834 37.500 0.00 0.00 34.01 3.91
143 144 9.465199 CTAAACTTCCTCTAGTTAGGAGTACTT 57.535 37.037 0.00 0.00 46.29 2.24
165 166 1.404035 TCTACTCGATGCTGCGCTAAA 59.596 47.619 9.73 0.00 0.00 1.85
178 179 8.424899 GTGTCATCCACATAGAGCTCTACTCG 62.425 50.000 25.52 18.15 45.98 4.18
205 206 2.014335 TGCAAGATCTGTCGTGGATG 57.986 50.000 0.00 0.00 34.85 3.51
210 211 2.036475 AGTCACTTGCAAGATCTGTCGT 59.964 45.455 32.50 5.62 0.00 4.34
211 212 2.681706 AGTCACTTGCAAGATCTGTCG 58.318 47.619 32.50 11.10 0.00 4.35
213 214 3.999663 GCTTAGTCACTTGCAAGATCTGT 59.000 43.478 32.50 14.47 0.00 3.41
231 232 4.917385 TGAAGGGAGTGCTTATTTGCTTA 58.083 39.130 0.00 0.00 0.00 3.09
235 236 9.487790 TTTTAAAATGAAGGGAGTGCTTATTTG 57.512 29.630 0.00 0.00 0.00 2.32
297 298 7.533289 AGAGAGACTGCTTAGTACTTTTTCT 57.467 36.000 0.00 0.00 0.00 2.52
298 299 8.596271 AAAGAGAGACTGCTTAGTACTTTTTC 57.404 34.615 0.00 0.00 0.00 2.29
300 301 7.958088 AGAAAGAGAGACTGCTTAGTACTTTT 58.042 34.615 0.00 0.00 0.00 2.27
302 303 6.946009 AGAGAAAGAGAGACTGCTTAGTACTT 59.054 38.462 0.00 0.00 0.00 2.24
303 304 6.481643 AGAGAAAGAGAGACTGCTTAGTACT 58.518 40.000 0.00 0.00 0.00 2.73
317 318 2.248248 TCGGCTGGAAAGAGAAAGAGA 58.752 47.619 0.00 0.00 0.00 3.10
319 320 4.504858 GTTATCGGCTGGAAAGAGAAAGA 58.495 43.478 0.00 0.00 0.00 2.52
329 330 0.604073 TTCACACGTTATCGGCTGGA 59.396 50.000 0.00 0.00 41.85 3.86
331 332 2.285026 CGATTTCACACGTTATCGGCTG 60.285 50.000 0.00 0.00 41.85 4.85
361 362 2.042569 GGGTAGGGGACTTGAAAATGGT 59.957 50.000 0.00 0.00 43.67 3.55
400 401 1.203364 AGAGGAAGGGAAAGAGAGGCA 60.203 52.381 0.00 0.00 0.00 4.75
406 407 1.605058 CCGCGAGAGGAAGGGAAAGA 61.605 60.000 8.23 0.00 0.00 2.52
446 447 1.224315 CATGGGAAGGCGGTGATGA 59.776 57.895 0.00 0.00 0.00 2.92
496 497 2.399580 CGGAGAAGGAGGGTTTAGGAT 58.600 52.381 0.00 0.00 0.00 3.24
522 523 2.032071 GCAAGTACGGTGGTGGCT 59.968 61.111 0.00 0.00 0.00 4.75
545 546 1.078567 GAGGTGAGCAAGAGGGCTG 60.079 63.158 0.00 0.00 45.99 4.85
551 552 1.967535 CTGACCGAGGTGAGCAAGA 59.032 57.895 0.00 0.00 0.00 3.02
651 657 4.940654 TGGCACGAAATAGATGTTGATTGA 59.059 37.500 0.00 0.00 0.00 2.57
652 658 5.233957 TGGCACGAAATAGATGTTGATTG 57.766 39.130 0.00 0.00 0.00 2.67
653 659 5.895636 TTGGCACGAAATAGATGTTGATT 57.104 34.783 0.00 0.00 0.00 2.57
655 661 5.895636 ATTTGGCACGAAATAGATGTTGA 57.104 34.783 0.00 0.00 0.00 3.18
659 665 8.900511 CCATTATATTTGGCACGAAATAGATG 57.099 34.615 0.00 12.35 32.60 2.90
720 6201 1.433837 CCACGGTAGTAATTGCGGGC 61.434 60.000 0.00 0.00 0.00 6.13
796 6277 1.140052 TGGAAAGAAACGAGCTGTGGA 59.860 47.619 0.00 0.00 0.00 4.02
798 6279 6.662414 TTATATGGAAAGAAACGAGCTGTG 57.338 37.500 0.00 0.00 0.00 3.66
819 6300 2.735478 CACGCAGCGTCCGGTTTA 60.735 61.111 19.98 0.00 38.32 2.01
849 6330 1.789078 TTATCTCGCCGCCTACGTCC 61.789 60.000 0.00 0.00 37.70 4.79
850 6331 0.385723 CTTATCTCGCCGCCTACGTC 60.386 60.000 0.00 0.00 37.70 4.34
851 6332 0.816825 TCTTATCTCGCCGCCTACGT 60.817 55.000 0.00 0.00 37.70 3.57
852 6333 0.385723 GTCTTATCTCGCCGCCTACG 60.386 60.000 0.00 0.00 39.67 3.51
854 6335 1.947013 CGTCTTATCTCGCCGCCTA 59.053 57.895 0.00 0.00 0.00 3.93
1205 6742 3.322369 CATCAGATCAGAGCTCAGCATC 58.678 50.000 17.77 13.22 0.00 3.91
1206 6743 2.037902 CCATCAGATCAGAGCTCAGCAT 59.962 50.000 17.77 4.01 0.00 3.79
1238 6781 2.847234 AACCCTGCAGTCCGTCCA 60.847 61.111 13.81 0.00 0.00 4.02
1239 6782 2.047179 GAACCCTGCAGTCCGTCC 60.047 66.667 13.81 0.00 0.00 4.79
1241 6784 2.743718 CTGAACCCTGCAGTCCGT 59.256 61.111 13.81 2.57 0.00 4.69
1334 6877 2.432628 GGCAACTCCACCTCGACG 60.433 66.667 0.00 0.00 34.01 5.12
1467 7013 9.807649 GAACAGATCAAATGCCTAATGTAAATT 57.192 29.630 0.00 0.00 0.00 1.82
1468 7014 8.416329 GGAACAGATCAAATGCCTAATGTAAAT 58.584 33.333 0.00 0.00 0.00 1.40
1469 7015 7.395772 TGGAACAGATCAAATGCCTAATGTAAA 59.604 33.333 0.00 0.00 0.00 2.01
1470 7016 6.889177 TGGAACAGATCAAATGCCTAATGTAA 59.111 34.615 0.00 0.00 0.00 2.41
1471 7017 6.422333 TGGAACAGATCAAATGCCTAATGTA 58.578 36.000 0.00 0.00 0.00 2.29
1472 7018 5.263599 TGGAACAGATCAAATGCCTAATGT 58.736 37.500 0.00 0.00 0.00 2.71
1473 7019 5.840243 TGGAACAGATCAAATGCCTAATG 57.160 39.130 0.00 0.00 0.00 1.90
1474 7020 5.954150 AGTTGGAACAGATCAAATGCCTAAT 59.046 36.000 0.00 0.00 42.39 1.73
1475 7021 5.183713 CAGTTGGAACAGATCAAATGCCTAA 59.816 40.000 0.00 0.00 42.39 2.69
1476 7022 4.701651 CAGTTGGAACAGATCAAATGCCTA 59.298 41.667 0.00 0.00 42.39 3.93
1477 7023 3.508793 CAGTTGGAACAGATCAAATGCCT 59.491 43.478 0.00 0.00 42.39 4.75
1478 7024 3.507233 TCAGTTGGAACAGATCAAATGCC 59.493 43.478 0.00 0.00 42.39 4.40
1479 7025 4.771590 TCAGTTGGAACAGATCAAATGC 57.228 40.909 0.00 0.00 42.39 3.56
1480 7026 8.517878 ACTAAATCAGTTGGAACAGATCAAATG 58.482 33.333 0.00 0.00 42.39 2.32
1481 7027 8.641498 ACTAAATCAGTTGGAACAGATCAAAT 57.359 30.769 0.00 0.00 42.39 2.32
1482 7028 8.999431 GTACTAAATCAGTTGGAACAGATCAAA 58.001 33.333 0.00 0.00 42.39 2.69
1483 7029 8.375506 AGTACTAAATCAGTTGGAACAGATCAA 58.624 33.333 0.00 0.00 42.39 2.57
1525 7071 2.158667 TCTTCTCCTTGGTTGTGGGTTC 60.159 50.000 0.00 0.00 0.00 3.62
1531 7077 2.065799 ACCCATCTTCTCCTTGGTTGT 58.934 47.619 0.00 0.00 0.00 3.32
1532 7078 2.821969 CAACCCATCTTCTCCTTGGTTG 59.178 50.000 4.98 4.98 44.54 3.77
1533 7079 2.819348 GCAACCCATCTTCTCCTTGGTT 60.819 50.000 0.00 0.00 36.56 3.67
1534 7080 1.272147 GCAACCCATCTTCTCCTTGGT 60.272 52.381 0.00 0.00 0.00 3.67
1535 7081 1.272092 TGCAACCCATCTTCTCCTTGG 60.272 52.381 0.00 0.00 0.00 3.61
1589 7135 9.498176 ACCAAAATTACTAGTAGTACAACTTGG 57.502 33.333 23.10 23.10 28.93 3.61
1696 7251 5.966742 AATTGTCTGTTAAGCTTTCTCCC 57.033 39.130 3.20 0.00 0.00 4.30
1697 7252 7.920682 TGAAAAATTGTCTGTTAAGCTTTCTCC 59.079 33.333 3.20 0.00 0.00 3.71
1738 7325 3.149196 GGGAGACAGAACATTTTGCTGA 58.851 45.455 0.00 0.00 33.94 4.26
1784 7401 9.337396 AGTGTTAGTGTATTTCTTGATCAAACA 57.663 29.630 9.88 7.66 0.00 2.83
1925 7595 4.424626 CAGTTAGCGTCTCTGAAGCATAA 58.575 43.478 8.04 2.28 39.36 1.90
1987 7709 2.450476 ACAATCAGCAGGGGATCAAAC 58.550 47.619 0.00 0.00 0.00 2.93
1996 7718 6.201806 GTGCTCTTATAACTACAATCAGCAGG 59.798 42.308 0.00 0.00 35.13 4.85
2007 7729 3.317455 TCCCGGGTGCTCTTATAACTA 57.683 47.619 22.86 0.00 0.00 2.24
2125 7849 1.823041 GGAGAGCCATTCAGCTGCC 60.823 63.158 9.47 0.00 45.15 4.85
2252 7988 5.866633 AGACGATCTCACTGAGAAAACATTC 59.133 40.000 12.83 4.24 42.27 2.67
2455 8199 0.449388 GCAGTGCACATAGCCTTGAC 59.551 55.000 21.04 0.00 44.83 3.18
2457 8201 0.450583 CAGCAGTGCACATAGCCTTG 59.549 55.000 21.04 11.01 44.83 3.61
2691 8469 5.697633 TCCGTCCACTAAAATACTGTCAAAC 59.302 40.000 0.00 0.00 0.00 2.93
2893 8685 3.216800 AGAAGCAAGCAATTCACTGTCA 58.783 40.909 0.00 0.00 0.00 3.58
2896 8688 5.978934 AAAAAGAAGCAAGCAATTCACTG 57.021 34.783 0.00 0.00 0.00 3.66
2926 8718 7.148239 CCTGTGCTAATTTTTCTACGGAAAGAT 60.148 37.037 0.00 0.00 41.66 2.40
2959 8751 4.906618 TCAAGAAGTAAGCCAACTTAGGG 58.093 43.478 1.51 0.00 39.78 3.53
2974 8766 7.913674 AATAACTAGAAGGCTGTTCAAGAAG 57.086 36.000 0.00 0.00 0.00 2.85
3002 8810 6.661669 TCACATATCAATTATTCGCTTGCAG 58.338 36.000 0.00 0.00 0.00 4.41
3016 8824 7.013559 CAGGATTATGGCAAACTCACATATCAA 59.986 37.037 0.00 0.00 0.00 2.57
3023 8831 3.378427 GGTCAGGATTATGGCAAACTCAC 59.622 47.826 0.00 0.00 0.00 3.51
3025 8833 3.879892 GAGGTCAGGATTATGGCAAACTC 59.120 47.826 0.00 0.00 0.00 3.01
3030 8838 2.196742 AGGAGGTCAGGATTATGGCA 57.803 50.000 0.00 0.00 0.00 4.92
3032 8840 4.899352 CCTAAGGAGGTCAGGATTATGG 57.101 50.000 0.00 0.00 38.16 2.74
3050 8858 8.772250 ACTTCTGGATTTCATCAAGATTACCTA 58.228 33.333 0.00 0.00 39.05 3.08
3061 8870 5.359194 TGGAGGTACTTCTGGATTTCATC 57.641 43.478 4.85 0.00 41.55 2.92
3066 8875 4.273318 GCAATTGGAGGTACTTCTGGATT 58.727 43.478 7.72 1.04 41.55 3.01
3070 8879 1.398390 GCGCAATTGGAGGTACTTCTG 59.602 52.381 0.30 0.00 41.55 3.02
3073 8882 1.812571 CTTGCGCAATTGGAGGTACTT 59.187 47.619 25.26 0.00 41.55 2.24
3075 8884 1.165270 ACTTGCGCAATTGGAGGTAC 58.835 50.000 25.26 0.00 0.00 3.34
3080 8889 2.499197 TGAGTTACTTGCGCAATTGGA 58.501 42.857 25.26 6.77 0.00 3.53
3084 8893 2.031157 GGTGTTGAGTTACTTGCGCAAT 60.031 45.455 25.26 15.90 0.00 3.56
3085 8894 1.332375 GGTGTTGAGTTACTTGCGCAA 59.668 47.619 23.48 23.48 0.00 4.85
3086 8895 0.941542 GGTGTTGAGTTACTTGCGCA 59.058 50.000 5.66 5.66 0.00 6.09
3088 8897 2.479837 TCTGGTGTTGAGTTACTTGCG 58.520 47.619 0.00 0.00 0.00 4.85
3098 8908 3.076621 GCATCACTCAATCTGGTGTTGA 58.923 45.455 0.00 0.00 36.07 3.18
3099 8909 2.159612 CGCATCACTCAATCTGGTGTTG 60.160 50.000 0.00 0.00 36.68 3.33
3100 8910 2.079158 CGCATCACTCAATCTGGTGTT 58.921 47.619 0.00 0.00 35.26 3.32
3101 8911 1.730501 CGCATCACTCAATCTGGTGT 58.269 50.000 0.00 0.00 35.26 4.16
3102 8912 0.376152 GCGCATCACTCAATCTGGTG 59.624 55.000 0.30 0.00 35.06 4.17
3105 8915 2.479275 CCTATGCGCATCACTCAATCTG 59.521 50.000 29.11 5.21 0.00 2.90
3107 8917 2.487934 ACCTATGCGCATCACTCAATC 58.512 47.619 29.11 0.00 0.00 2.67
3108 8918 2.627515 ACCTATGCGCATCACTCAAT 57.372 45.000 29.11 3.07 0.00 2.57
3109 8919 2.401583 AACCTATGCGCATCACTCAA 57.598 45.000 29.11 7.20 0.00 3.02
3110 8920 2.279741 GAAACCTATGCGCATCACTCA 58.720 47.619 29.11 8.05 0.00 3.41
3111 8921 2.030946 GTGAAACCTATGCGCATCACTC 59.969 50.000 29.11 16.97 35.49 3.51
3112 8922 2.009774 GTGAAACCTATGCGCATCACT 58.990 47.619 29.11 6.25 35.49 3.41
3114 8924 2.106477 TGTGAAACCTATGCGCATCA 57.894 45.000 29.11 16.10 34.36 3.07
3118 8928 3.621268 TCAGTATTGTGAAACCTATGCGC 59.379 43.478 0.00 0.00 34.36 6.09
3119 8929 5.991328 ATCAGTATTGTGAAACCTATGCG 57.009 39.130 0.00 0.00 34.36 4.73
3143 8953 6.399204 GGTCGTAACGAACAAGTTCATAAT 57.601 37.500 12.86 0.00 43.67 1.28
3163 8992 4.337555 ACAGCATGCTATTGAATTCTGGTC 59.662 41.667 22.19 0.00 42.53 4.02
3179 9008 3.916172 GTGAATAAAGTGTGCACAGCATG 59.084 43.478 22.40 0.00 41.91 4.06
3183 9012 4.539870 CCTTGTGAATAAAGTGTGCACAG 58.460 43.478 22.40 3.15 40.16 3.66
3247 9130 3.382546 GGCACCTGAATCAGCAAATACAT 59.617 43.478 4.40 0.00 0.00 2.29
3249 9132 3.019564 AGGCACCTGAATCAGCAAATAC 58.980 45.455 4.40 0.00 0.00 1.89
3251 9134 2.226962 AGGCACCTGAATCAGCAAAT 57.773 45.000 4.40 0.00 0.00 2.32
3273 9156 3.500680 GCATTCCGTTCTCTTGGTTAACA 59.499 43.478 8.10 0.00 0.00 2.41
3279 9162 1.470098 CCAAGCATTCCGTTCTCTTGG 59.530 52.381 5.12 5.12 45.07 3.61
3294 9177 2.335011 GTTGGTTCGGTGCCAAGC 59.665 61.111 6.52 0.00 45.50 4.01
3346 9232 4.180946 CTCGTGGCTCGGACGGAG 62.181 72.222 9.26 5.68 46.06 4.63
3391 9277 5.652994 AGCAAGAGTAGAGTAGGTTGAAG 57.347 43.478 0.00 0.00 0.00 3.02
3401 9287 5.906113 TCTTGAAGGTAGCAAGAGTAGAG 57.094 43.478 0.00 0.00 44.81 2.43
3411 9297 6.026947 TGTTCTTCTACTCTTGAAGGTAGC 57.973 41.667 12.89 0.00 40.73 3.58
3412 9298 6.588373 GCTTGTTCTTCTACTCTTGAAGGTAG 59.412 42.308 11.99 11.99 40.73 3.18
3413 9299 6.267928 AGCTTGTTCTTCTACTCTTGAAGGTA 59.732 38.462 0.00 0.00 40.73 3.08
3414 9300 5.071115 AGCTTGTTCTTCTACTCTTGAAGGT 59.929 40.000 0.00 0.00 40.73 3.50
3415 9301 5.407995 CAGCTTGTTCTTCTACTCTTGAAGG 59.592 44.000 0.00 0.00 40.73 3.46
3416 9302 5.988561 ACAGCTTGTTCTTCTACTCTTGAAG 59.011 40.000 0.00 0.00 41.46 3.02
3417 9303 5.918608 ACAGCTTGTTCTTCTACTCTTGAA 58.081 37.500 0.00 0.00 0.00 2.69
3418 9304 5.537300 ACAGCTTGTTCTTCTACTCTTGA 57.463 39.130 0.00 0.00 0.00 3.02
3419 9305 6.926272 ACTAACAGCTTGTTCTTCTACTCTTG 59.074 38.462 5.04 0.00 40.22 3.02
3420 9306 7.056844 ACTAACAGCTTGTTCTTCTACTCTT 57.943 36.000 5.04 0.00 40.22 2.85
3421 9307 6.658188 ACTAACAGCTTGTTCTTCTACTCT 57.342 37.500 5.04 0.00 40.22 3.24
3422 9308 8.701540 GTTAACTAACAGCTTGTTCTTCTACTC 58.298 37.037 0.00 0.00 40.22 2.59
3428 9314 6.592870 AGAGGTTAACTAACAGCTTGTTCTT 58.407 36.000 5.42 2.54 40.22 2.52
3438 9324 8.911918 TGCAAAATAAGAGAGGTTAACTAACA 57.088 30.769 5.42 0.00 37.92 2.41
3442 9328 6.543735 ACCTGCAAAATAAGAGAGGTTAACT 58.456 36.000 5.42 0.00 29.17 2.24
3443 9329 6.655425 AGACCTGCAAAATAAGAGAGGTTAAC 59.345 38.462 0.00 0.00 33.89 2.01
3444 9330 6.779860 AGACCTGCAAAATAAGAGAGGTTAA 58.220 36.000 0.00 0.00 33.89 2.01
3447 9333 4.917906 AGACCTGCAAAATAAGAGAGGT 57.082 40.909 0.00 0.00 36.51 3.85
3448 9334 5.983540 AGTAGACCTGCAAAATAAGAGAGG 58.016 41.667 0.00 0.00 0.00 3.69
3450 9336 6.655003 CCAAAGTAGACCTGCAAAATAAGAGA 59.345 38.462 0.00 0.00 0.00 3.10
3456 9349 2.562738 GCCCAAAGTAGACCTGCAAAAT 59.437 45.455 0.00 0.00 0.00 1.82
3467 9360 4.082125 AGACCAGATTTTGCCCAAAGTAG 58.918 43.478 0.00 0.00 0.00 2.57
3525 9418 3.144605 GTCGCCGACTTTCACGAC 58.855 61.111 10.56 0.00 46.64 4.34
3530 9423 3.871248 AACCGGGTCGCCGACTTTC 62.871 63.158 17.76 6.47 34.88 2.62
3533 9426 2.990967 TAAACCGGGTCGCCGACT 60.991 61.111 17.76 0.00 34.88 4.18
3574 9467 2.048127 AGGCTGGAACTTCGTCGC 60.048 61.111 0.00 0.00 0.00 5.19
3602 9495 0.390603 TGTATGGTACGTGCTGCCAC 60.391 55.000 3.01 0.00 37.49 5.01
3606 9499 4.678509 AAAACATGTATGGTACGTGCTG 57.321 40.909 0.00 0.00 46.93 4.41
3612 9505 7.812648 ACACACACATAAAACATGTATGGTAC 58.187 34.615 10.95 0.00 31.24 3.34
3620 9513 5.984627 TCTTCGACACACACATAAAACATG 58.015 37.500 0.00 0.00 0.00 3.21
3621 9514 5.989168 TCTCTTCGACACACACATAAAACAT 59.011 36.000 0.00 0.00 0.00 2.71
3650 9545 1.862008 GCGCACAAAATCAACCGAACA 60.862 47.619 0.30 0.00 0.00 3.18
3652 9547 0.658829 CGCGCACAAAATCAACCGAA 60.659 50.000 8.75 0.00 0.00 4.30
3669 9564 5.169032 GCTAAGTTCAATTTACGTAATGCGC 59.831 40.000 9.18 0.00 46.11 6.09
3718 9613 9.716531 AGATGATACGATATTGTTTGACATGAT 57.283 29.630 0.00 0.00 0.00 2.45
3736 9640 6.693545 CGACAGACTAAAGAACCAGATGATAC 59.306 42.308 0.00 0.00 0.00 2.24
3739 9643 4.765339 TCGACAGACTAAAGAACCAGATGA 59.235 41.667 0.00 0.00 0.00 2.92
3763 9667 2.821378 TCACCGAGAACTATTTGACCGA 59.179 45.455 0.00 0.00 0.00 4.69
3768 9672 6.035435 CAGAAGTGATCACCGAGAACTATTTG 59.965 42.308 22.21 4.88 0.00 2.32
3769 9673 6.102663 CAGAAGTGATCACCGAGAACTATTT 58.897 40.000 22.21 5.82 0.00 1.40
3780 9686 4.756642 TGAACATGAACAGAAGTGATCACC 59.243 41.667 22.21 8.10 38.21 4.02
3784 9690 6.949352 AACTTGAACATGAACAGAAGTGAT 57.051 33.333 0.00 0.00 0.00 3.06
3790 9696 4.627058 TCGCTAACTTGAACATGAACAGA 58.373 39.130 0.00 0.00 0.00 3.41
3791 9697 4.990543 TCGCTAACTTGAACATGAACAG 57.009 40.909 0.00 0.00 0.00 3.16
3797 9703 3.059352 AGGCTTCGCTAACTTGAACAT 57.941 42.857 0.00 0.00 0.00 2.71
3798 9704 2.543777 AGGCTTCGCTAACTTGAACA 57.456 45.000 0.00 0.00 0.00 3.18
3799 9705 3.003378 ACAAAGGCTTCGCTAACTTGAAC 59.997 43.478 0.00 0.00 0.00 3.18
3800 9706 3.211045 ACAAAGGCTTCGCTAACTTGAA 58.789 40.909 0.00 0.00 0.00 2.69
3801 9707 2.806244 GACAAAGGCTTCGCTAACTTGA 59.194 45.455 0.00 0.00 0.00 3.02
3802 9708 2.548057 TGACAAAGGCTTCGCTAACTTG 59.452 45.455 0.00 0.00 0.00 3.16
3803 9709 2.808543 CTGACAAAGGCTTCGCTAACTT 59.191 45.455 0.00 0.00 0.00 2.66
3833 9739 1.873355 GCGACCACGTTCGTCAGTTC 61.873 60.000 10.99 0.00 41.26 3.01
3919 9825 8.806146 ACTTTTGCTTCCTTTTGACACATATAT 58.194 29.630 0.00 0.00 0.00 0.86
3920 9826 8.177119 ACTTTTGCTTCCTTTTGACACATATA 57.823 30.769 0.00 0.00 0.00 0.86
4032 9942 5.048224 CACCATTTTCTGCTCAAGTTCAGAT 60.048 40.000 0.00 0.00 38.90 2.90
4068 9978 1.299541 CCATCAGTGGCGTATGGTTC 58.700 55.000 1.24 0.00 39.01 3.62
4083 9993 1.105759 GCCTCCCAACAGATGCCATC 61.106 60.000 0.00 0.00 0.00 3.51
4097 10007 2.147150 GTGAAGAACAGAACAGCCTCC 58.853 52.381 0.00 0.00 0.00 4.30
4098 10008 2.838736 TGTGAAGAACAGAACAGCCTC 58.161 47.619 0.00 0.00 33.78 4.70
4099 10009 3.181451 TGATGTGAAGAACAGAACAGCCT 60.181 43.478 0.00 0.00 43.64 4.58
4100 10010 3.058639 GTGATGTGAAGAACAGAACAGCC 60.059 47.826 0.00 0.00 43.64 4.85
4101 10011 3.561310 TGTGATGTGAAGAACAGAACAGC 59.439 43.478 0.00 0.00 43.64 4.40
4102 10012 4.813161 AGTGTGATGTGAAGAACAGAACAG 59.187 41.667 0.00 0.00 43.64 3.16
4105 10015 4.769688 ACAGTGTGATGTGAAGAACAGAA 58.230 39.130 0.00 0.00 43.64 3.02
4106 10016 4.406648 ACAGTGTGATGTGAAGAACAGA 57.593 40.909 0.00 0.00 43.64 3.41
4107 10017 6.347969 CCATTACAGTGTGATGTGAAGAACAG 60.348 42.308 22.35 4.55 43.64 3.16
4108 10018 5.469760 CCATTACAGTGTGATGTGAAGAACA 59.530 40.000 22.35 0.00 44.79 3.18
4110 10020 4.455533 GCCATTACAGTGTGATGTGAAGAA 59.544 41.667 22.35 0.08 34.56 2.52
4181 10111 5.936686 TCTTTGCTCTTCTTGTGATTGAG 57.063 39.130 0.00 0.00 0.00 3.02
4255 10185 1.077429 GCTCATCACCAAGGACCCC 60.077 63.158 0.00 0.00 0.00 4.95
4357 10287 2.040544 CAAGCCGGACACCATGACC 61.041 63.158 5.05 0.00 0.00 4.02
4420 10350 4.129737 ATGGACTACGCGTGCGCT 62.130 61.111 24.59 0.00 44.19 5.92


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

AutoCloner maintained by Alex Coulton.