Multiple sequence alignment - TraesCS2A01G280000

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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 TraesCS2A01G280000 chr2A 100.000 5977 0 0 1 5977 467690609 467696585 0.000000e+00 11038.0
1 TraesCS2A01G280000 chr2A 94.737 285 15 0 4170 4454 57993225 57992941 1.530000e-120 444.0
2 TraesCS2A01G280000 chr2A 96.000 50 1 1 3465 3514 467694029 467694077 4.970000e-11 80.5
3 TraesCS2A01G280000 chr2A 96.000 50 1 1 3421 3469 467694073 467694122 4.970000e-11 80.5
4 TraesCS2A01G280000 chr2D 94.063 2594 90 25 906 3469 350599487 350602046 0.000000e+00 3879.0
5 TraesCS2A01G280000 chr2D 95.750 1247 37 14 4454 5691 350602591 350603830 0.000000e+00 1995.0
6 TraesCS2A01G280000 chr2D 96.500 600 19 2 3465 4063 350601998 350602596 0.000000e+00 990.0
7 TraesCS2A01G280000 chr2D 90.390 385 23 10 193 566 63727412 63727031 1.500000e-135 494.0
8 TraesCS2A01G280000 chr2D 93.793 290 17 1 4170 4459 115585898 115586186 9.200000e-118 435.0
9 TraesCS2A01G280000 chr2D 95.327 214 6 4 5768 5977 350617149 350617362 2.670000e-88 337.0
10 TraesCS2A01G280000 chr2D 97.500 120 3 0 4057 4176 115583421 115583540 7.850000e-49 206.0
11 TraesCS2A01G280000 chr2D 97.674 86 0 1 5698 5783 350603984 350604067 4.830000e-31 147.0
12 TraesCS2A01G280000 chr2B 93.282 2590 99 36 906 3469 416503153 416505693 0.000000e+00 3749.0
13 TraesCS2A01G280000 chr2B 95.767 945 29 10 4454 5392 416506235 416507174 0.000000e+00 1513.0
14 TraesCS2A01G280000 chr2B 96.167 600 18 3 3465 4063 416505645 416506240 0.000000e+00 976.0
15 TraesCS2A01G280000 chr2B 89.226 297 13 9 5698 5977 416507481 416507775 2.650000e-93 353.0
16 TraesCS2A01G280000 chr2B 86.452 310 30 9 232 534 342233596 342233292 4.470000e-86 329.0
17 TraesCS2A01G280000 chr2B 94.872 156 8 0 5470 5625 416507185 416507340 1.660000e-60 244.0
18 TraesCS2A01G280000 chr4D 84.196 715 76 24 193 888 395197663 395196967 0.000000e+00 660.0
19 TraesCS2A01G280000 chr4D 96.694 121 4 0 4056 4176 27571230 27571350 1.020000e-47 202.0
20 TraesCS2A01G280000 chr4D 87.571 177 15 5 4 178 395197984 395197813 1.310000e-46 198.0
21 TraesCS2A01G280000 chr4D 84.884 86 10 2 2949 3031 9998417 9998502 3.840000e-12 84.2
22 TraesCS2A01G280000 chr3A 82.968 775 84 24 180 915 507652699 507653464 0.000000e+00 656.0
23 TraesCS2A01G280000 chr3A 89.305 187 13 4 4 189 507652482 507652662 1.680000e-55 228.0
24 TraesCS2A01G280000 chr3A 85.417 192 22 4 4 194 62572672 62572858 1.700000e-45 195.0
25 TraesCS2A01G280000 chr5D 86.348 564 59 17 232 782 354906880 354906322 3.080000e-167 599.0
26 TraesCS2A01G280000 chr5D 98.261 115 2 0 4062 4176 382355254 382355140 1.020000e-47 202.0
27 TraesCS2A01G280000 chr5D 94.444 126 6 1 4051 4176 111606853 111606729 6.110000e-45 193.0
28 TraesCS2A01G280000 chr7D 87.571 531 42 13 193 710 423659145 423659664 1.430000e-165 593.0
29 TraesCS2A01G280000 chr7D 87.280 511 45 9 193 691 604860601 604861103 3.130000e-157 566.0
30 TraesCS2A01G280000 chr7D 85.876 531 54 13 193 710 52793568 52794090 4.070000e-151 545.0
31 TraesCS2A01G280000 chr7D 89.614 414 36 6 3653 4062 279735908 279735498 2.470000e-143 520.0
32 TraesCS2A01G280000 chr7A 88.072 503 54 5 3557 4058 33511843 33512340 5.160000e-165 592.0
33 TraesCS2A01G280000 chr7A 89.130 414 38 6 3653 4062 316026825 316027235 5.340000e-140 508.0
34 TraesCS2A01G280000 chr7A 88.592 412 43 3 3653 4062 130083288 130082879 1.160000e-136 497.0
35 TraesCS2A01G280000 chr7A 86.280 379 42 8 4472 4847 33512350 33512721 2.590000e-108 403.0
36 TraesCS2A01G280000 chr7B 82.016 734 86 21 185 888 219449094 219448377 3.100000e-162 582.0
37 TraesCS2A01G280000 chr7B 87.216 485 49 12 232 710 662936682 662936205 1.900000e-149 540.0
38 TraesCS2A01G280000 chr7B 89.623 212 15 6 183 394 219449500 219449296 4.590000e-66 263.0
39 TraesCS2A01G280000 chr7B 88.442 199 16 5 4 201 219449724 219449532 3.600000e-57 233.0
40 TraesCS2A01G280000 chr7B 91.837 147 8 3 40 185 219449284 219449141 1.020000e-47 202.0
41 TraesCS2A01G280000 chr5A 86.704 534 46 15 192 710 643373030 643372507 2.420000e-158 569.0
42 TraesCS2A01G280000 chr5A 89.346 413 39 4 3653 4062 353160942 353160532 1.150000e-141 514.0
43 TraesCS2A01G280000 chr5A 96.140 285 11 0 4170 4454 345359241 345358957 3.260000e-127 466.0
44 TraesCS2A01G280000 chr5A 99.123 114 1 0 4063 4176 484441613 484441726 7.850000e-49 206.0
45 TraesCS2A01G280000 chr5A 98.261 115 2 0 4062 4176 345359311 345359197 1.020000e-47 202.0
46 TraesCS2A01G280000 chr5B 88.036 443 45 6 3557 3996 123206140 123206577 8.880000e-143 518.0
47 TraesCS2A01G280000 chr5B 87.133 443 48 7 3557 3996 123406475 123406911 1.500000e-135 494.0
48 TraesCS2A01G280000 chr5B 83.377 379 48 9 4472 4847 123406970 123407336 2.670000e-88 337.0
49 TraesCS2A01G280000 chr5B 83.113 379 49 9 4472 4847 123206636 123207002 1.240000e-86 331.0
50 TraesCS2A01G280000 chr1A 96.491 285 9 1 4170 4454 13778959 13779242 2.520000e-128 470.0
51 TraesCS2A01G280000 chr1A 94.700 283 15 0 4170 4452 13781059 13781341 1.980000e-119 440.0
52 TraesCS2A01G280000 chr1A 92.667 300 18 3 4170 4465 394147161 394146862 4.280000e-116 429.0
53 TraesCS2A01G280000 chr6D 84.394 487 56 12 235 710 184419581 184420058 1.520000e-125 460.0
54 TraesCS2A01G280000 chr6D 94.035 285 17 0 4170 4454 21990296 21990012 3.310000e-117 433.0
55 TraesCS2A01G280000 chr6D 96.774 124 4 0 4053 4176 11351918 11351795 2.180000e-49 207.0
56 TraesCS2A01G280000 chr6A 94.774 287 15 0 4170 4456 511418152 511418438 1.180000e-121 448.0
57 TraesCS2A01G280000 chr6A 94.737 285 15 0 4170 4454 23395380 23395664 1.530000e-120 444.0
58 TraesCS2A01G280000 chr3D 97.479 119 3 0 4058 4176 178656022 178655904 2.820000e-48 204.0
59 TraesCS2A01G280000 chr1D 99.115 113 1 0 4064 4176 112172017 112171905 2.820000e-48 204.0
60 TraesCS2A01G280000 chr1D 87.500 112 10 4 90 201 378864031 378864138 6.290000e-25 126.0


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 TraesCS2A01G280000 chr2A 467690609 467696585 5976 False 3733.00 11038 97.333333 1 5977 3 chr2A.!!$F1 5976
1 TraesCS2A01G280000 chr2D 350599487 350604067 4580 False 1752.75 3879 95.996750 906 5783 4 chr2D.!!$F3 4877
2 TraesCS2A01G280000 chr2D 115583421 115586186 2765 False 320.50 435 95.646500 4057 4459 2 chr2D.!!$F2 402
3 TraesCS2A01G280000 chr2B 416503153 416507775 4622 False 1367.00 3749 93.862800 906 5977 5 chr2B.!!$F1 5071
4 TraesCS2A01G280000 chr4D 395196967 395197984 1017 True 429.00 660 85.883500 4 888 2 chr4D.!!$R1 884
5 TraesCS2A01G280000 chr3A 507652482 507653464 982 False 442.00 656 86.136500 4 915 2 chr3A.!!$F2 911
6 TraesCS2A01G280000 chr5D 354906322 354906880 558 True 599.00 599 86.348000 232 782 1 chr5D.!!$R2 550
7 TraesCS2A01G280000 chr7D 423659145 423659664 519 False 593.00 593 87.571000 193 710 1 chr7D.!!$F2 517
8 TraesCS2A01G280000 chr7D 604860601 604861103 502 False 566.00 566 87.280000 193 691 1 chr7D.!!$F3 498
9 TraesCS2A01G280000 chr7D 52793568 52794090 522 False 545.00 545 85.876000 193 710 1 chr7D.!!$F1 517
10 TraesCS2A01G280000 chr7A 33511843 33512721 878 False 497.50 592 87.176000 3557 4847 2 chr7A.!!$F2 1290
11 TraesCS2A01G280000 chr7B 219448377 219449724 1347 True 320.00 582 87.979500 4 888 4 chr7B.!!$R2 884
12 TraesCS2A01G280000 chr5A 643372507 643373030 523 True 569.00 569 86.704000 192 710 1 chr5A.!!$R2 518
13 TraesCS2A01G280000 chr5B 123206140 123207002 862 False 424.50 518 85.574500 3557 4847 2 chr5B.!!$F1 1290
14 TraesCS2A01G280000 chr5B 123406475 123407336 861 False 415.50 494 85.255000 3557 4847 2 chr5B.!!$F2 1290
15 TraesCS2A01G280000 chr1A 13778959 13781341 2382 False 455.00 470 95.595500 4170 4454 2 chr1A.!!$F1 284

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
744 1392 0.032267 GGGATAGTAGTGGAGCGTGC 59.968 60.0 0.0 0.0 0.00 5.34 F
1029 1687 0.030705 CTTCCCTCCCTCATCCCTCA 60.031 60.0 0.0 0.0 0.00 3.86 F
1544 2202 0.521735 GAATTGGTCTGTTGGACGCC 59.478 55.0 0.0 0.0 45.35 5.68 F
3402 4092 0.110486 AGTTGTCCCTTGGCGACATT 59.890 50.0 0.0 2.8 39.86 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 2395 1.337447 ACCGTGTCCAAGGTTACATCG 60.337 52.381 0.00 0.0 40.26 3.84 R
2900 3587 0.884514 GGAAGAGGGCTGTTCTTTGC 59.115 55.000 0.00 0.0 35.14 3.68 R
3461 4151 0.107831 ACACTCCCAAGCGCAAACTA 59.892 50.000 11.47 0.0 0.00 2.24 R
5276 8349 0.250424 CACACATGTGGACTCTGCCA 60.250 55.000 28.64 0.0 42.10 4.92 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
67 69 6.646267 ACCCGCTTCTAACATGAGTTTTATA 58.354 36.000 0.00 0.00 39.15 0.98
68 70 7.280356 ACCCGCTTCTAACATGAGTTTTATAT 58.720 34.615 0.00 0.00 39.15 0.86
69 71 7.773690 ACCCGCTTCTAACATGAGTTTTATATT 59.226 33.333 0.00 0.00 39.15 1.28
127 131 7.931948 AGTTGCATGTGTTTAGTACTAGAGTTT 59.068 33.333 2.23 0.00 0.00 2.66
135 139 7.930325 GTGTTTAGTACTAGAGTTTCCCTGTTT 59.070 37.037 2.23 0.00 0.00 2.83
145 149 4.212716 AGTTTCCCTGTTTTTACACCTCC 58.787 43.478 0.00 0.00 0.00 4.30
178 182 4.315803 TCTAGACTTTTTGCACAGCTACC 58.684 43.478 0.00 0.00 0.00 3.18
181 233 3.503748 AGACTTTTTGCACAGCTACCATC 59.496 43.478 0.00 0.00 0.00 3.51
185 237 1.298157 TTGCACAGCTACCATCGCAC 61.298 55.000 0.00 0.00 0.00 5.34
207 394 5.854866 CACAGAGTTGTTTCAATGCATACAG 59.145 40.000 0.00 0.00 34.62 2.74
353 543 4.398358 GCTCAAGATGCATGCCATACATAT 59.602 41.667 16.68 0.00 36.64 1.78
443 1049 4.098914 AGTTGATGTTCAAGTAGGGCAA 57.901 40.909 0.00 0.00 38.19 4.52
481 1112 1.265454 GGGAAGAGAGAAAGCCGGGA 61.265 60.000 2.18 0.00 0.00 5.14
560 1195 1.620822 TTTTTGGAGCAAGGAGGAGC 58.379 50.000 0.00 0.00 0.00 4.70
563 1198 0.478072 TTGGAGCAAGGAGGAGCAAA 59.522 50.000 0.00 0.00 0.00 3.68
567 1202 1.277557 GAGCAAGGAGGAGCAAAGAGA 59.722 52.381 0.00 0.00 0.00 3.10
633 1270 8.749354 GGGCAAATCTATTTTAGAGGAAGAAAA 58.251 33.333 0.00 0.00 38.38 2.29
676 1314 4.379243 CCCTGCGCGGACTTGTCT 62.379 66.667 20.25 0.00 33.16 3.41
682 1320 0.306533 GCGCGGACTTGTCTTTCAAA 59.693 50.000 8.83 0.00 35.48 2.69
693 1331 6.699575 CTTGTCTTTCAAAGAAAAGGGAGA 57.300 37.500 19.15 0.00 45.27 3.71
695 1333 7.475137 TTGTCTTTCAAAGAAAAGGGAGAAA 57.525 32.000 0.00 0.00 39.67 2.52
697 1335 6.663523 TGTCTTTCAAAGAAAAGGGAGAAAGT 59.336 34.615 0.00 0.00 41.42 2.66
710 1348 1.300697 GAAAGTGGTCGCGTGAGGT 60.301 57.895 5.77 0.00 0.00 3.85
732 1375 2.844839 GAGGGCGCTGGGGATAGT 60.845 66.667 8.56 0.00 0.00 2.12
735 1378 1.837499 GGGCGCTGGGGATAGTAGT 60.837 63.158 7.64 0.00 0.00 2.73
744 1392 0.032267 GGGATAGTAGTGGAGCGTGC 59.968 60.000 0.00 0.00 0.00 5.34
813 1463 0.171231 CTCGATCAGGTGAAGCGACA 59.829 55.000 4.72 0.00 33.55 4.35
816 1466 1.402852 CGATCAGGTGAAGCGACAAGA 60.403 52.381 0.00 0.00 0.00 3.02
826 1476 1.750399 GCGACAAGACATGGGGCAT 60.750 57.895 0.00 0.00 33.19 4.40
835 1486 2.668612 CATGGGGCATGTGGTTTCA 58.331 52.632 0.00 0.00 37.12 2.69
869 1526 2.554272 CGGCGTGGTTTCTTTCCG 59.446 61.111 0.00 0.00 0.00 4.30
883 1540 1.697432 CTTTCCGTATATGGGAGGGCA 59.303 52.381 11.19 0.00 34.45 5.36
890 1547 2.621672 ATATGGGAGGGCACTCGGGT 62.622 60.000 10.51 0.02 44.93 5.28
900 1557 2.283966 ACTCGGGTGCCAGCTAGT 60.284 61.111 0.00 0.00 0.00 2.57
901 1558 2.352032 ACTCGGGTGCCAGCTAGTC 61.352 63.158 0.00 0.00 0.00 2.59
902 1559 3.417275 CTCGGGTGCCAGCTAGTCG 62.417 68.421 0.00 0.00 0.00 4.18
903 1560 4.514577 CGGGTGCCAGCTAGTCGG 62.515 72.222 0.00 0.00 0.00 4.79
904 1561 4.162690 GGGTGCCAGCTAGTCGGG 62.163 72.222 0.00 0.00 0.00 5.14
905 1562 3.391382 GGTGCCAGCTAGTCGGGT 61.391 66.667 0.00 0.00 32.16 5.28
906 1563 2.184579 GTGCCAGCTAGTCGGGTC 59.815 66.667 0.00 0.00 32.16 4.46
907 1564 3.075005 TGCCAGCTAGTCGGGTCC 61.075 66.667 0.00 0.00 32.16 4.46
908 1565 3.075005 GCCAGCTAGTCGGGTCCA 61.075 66.667 0.00 0.00 32.16 4.02
909 1566 2.435693 GCCAGCTAGTCGGGTCCAT 61.436 63.158 0.00 0.00 32.16 3.41
910 1567 1.113517 GCCAGCTAGTCGGGTCCATA 61.114 60.000 0.00 0.00 32.16 2.74
911 1568 1.633774 CCAGCTAGTCGGGTCCATAT 58.366 55.000 0.00 0.00 0.00 1.78
912 1569 2.803956 CCAGCTAGTCGGGTCCATATA 58.196 52.381 0.00 0.00 0.00 0.86
915 1572 4.223032 CCAGCTAGTCGGGTCCATATAAAT 59.777 45.833 0.00 0.00 0.00 1.40
929 1586 7.493320 GGTCCATATAAATTCGTGTACAGACAA 59.507 37.037 0.00 0.00 37.31 3.18
973 1631 0.250553 TGCCATTTTCCTCCGTTCGT 60.251 50.000 0.00 0.00 0.00 3.85
983 1641 1.204941 CCTCCGTTCGTTCATCTCCTT 59.795 52.381 0.00 0.00 0.00 3.36
1025 1683 1.715785 CTCTCTTCCCTCCCTCATCC 58.284 60.000 0.00 0.00 0.00 3.51
1026 1684 0.266152 TCTCTTCCCTCCCTCATCCC 59.734 60.000 0.00 0.00 0.00 3.85
1027 1685 0.267356 CTCTTCCCTCCCTCATCCCT 59.733 60.000 0.00 0.00 0.00 4.20
1028 1686 0.266152 TCTTCCCTCCCTCATCCCTC 59.734 60.000 0.00 0.00 0.00 4.30
1029 1687 0.030705 CTTCCCTCCCTCATCCCTCA 60.031 60.000 0.00 0.00 0.00 3.86
1030 1688 0.649992 TTCCCTCCCTCATCCCTCAT 59.350 55.000 0.00 0.00 0.00 2.90
1031 1689 1.557681 TCCCTCCCTCATCCCTCATA 58.442 55.000 0.00 0.00 0.00 2.15
1078 1736 1.229723 GACCAACCACCCTCCCCTA 60.230 63.158 0.00 0.00 0.00 3.53
1109 1767 2.470990 ACAGGGACAGAGATGTATGCA 58.529 47.619 0.00 0.00 0.00 3.96
1237 1895 2.972713 TGTCCAAGAGGTCAGCTTAAGT 59.027 45.455 4.02 0.00 35.89 2.24
1269 1927 1.869767 CTGCTCCTTCCATATCGTTGC 59.130 52.381 0.00 0.00 0.00 4.17
1368 2026 1.607148 GCCTTGTTTTAGGTTGCTCGT 59.393 47.619 0.00 0.00 37.63 4.18
1402 2060 1.776667 CCCCTAGATTCCATGCCTTCA 59.223 52.381 0.00 0.00 0.00 3.02
1423 2081 7.972277 CCTTCATTCATGTTAGAATTGAGGTTG 59.028 37.037 0.00 0.00 36.13 3.77
1508 2166 5.563592 TGTGGTGTCAGATTCAATGATTCT 58.436 37.500 2.13 2.13 0.00 2.40
1514 2172 5.883673 TGTCAGATTCAATGATTCTGCATGA 59.116 36.000 23.09 9.44 38.88 3.07
1544 2202 0.521735 GAATTGGTCTGTTGGACGCC 59.478 55.000 0.00 0.00 45.35 5.68
1546 2204 0.889186 ATTGGTCTGTTGGACGCCAC 60.889 55.000 0.00 0.00 45.35 5.01
1689 2352 4.284490 TGGTATGGACTATGGAATGAGCTC 59.716 45.833 6.82 6.82 0.00 4.09
1708 2371 8.270080 TGAGCTCGGATAATACTAGTTGATAG 57.730 38.462 9.64 0.00 37.53 2.08
1712 2375 5.035443 CGGATAATACTAGTTGATAGCGCC 58.965 45.833 2.29 0.00 34.56 6.53
1750 2413 0.719465 GCGATGTAACCTTGGACACG 59.281 55.000 0.00 0.00 0.00 4.49
2007 2675 7.373493 CCTGCTTGTAAAAGAAAGATCAATGT 58.627 34.615 0.00 0.00 0.00 2.71
2018 2686 7.992754 AGAAAGATCAATGTTCTTTGCTAGT 57.007 32.000 20.19 0.00 42.08 2.57
2043 2714 5.358725 ACGCATGGTTTAAGTTATTAAGGGG 59.641 40.000 0.00 0.00 32.58 4.79
2070 2742 4.188247 AGTTCTTGCGAGCATTGTACTA 57.812 40.909 0.00 0.00 0.00 1.82
2125 2798 5.794687 TTCACGCGTATTGATTTCTTGAT 57.205 34.783 13.44 0.00 0.00 2.57
2130 2803 6.571154 CACGCGTATTGATTTCTTGATGTATG 59.429 38.462 13.44 0.00 0.00 2.39
2243 2916 9.937175 GATGTATCTTAAATGAAGTAAGGCAAC 57.063 33.333 0.00 0.00 36.45 4.17
2271 2944 6.044989 ACCTTTTATTTTGGCCCCATTTAACT 59.955 34.615 0.00 0.00 0.00 2.24
2273 2946 6.943899 TTTATTTTGGCCCCATTTAACTCT 57.056 33.333 0.00 0.00 0.00 3.24
2617 3290 4.278170 CCAGTTTCTTGCTTTCCACATGTA 59.722 41.667 0.00 0.00 0.00 2.29
2624 3297 3.146066 TGCTTTCCACATGTACCAGAAC 58.854 45.455 0.00 0.00 0.00 3.01
2625 3298 2.159627 GCTTTCCACATGTACCAGAACG 59.840 50.000 0.00 0.00 0.00 3.95
2626 3299 1.803334 TTCCACATGTACCAGAACGC 58.197 50.000 0.00 0.00 0.00 4.84
2627 3300 0.973632 TCCACATGTACCAGAACGCT 59.026 50.000 0.00 0.00 0.00 5.07
2628 3301 2.172679 TCCACATGTACCAGAACGCTA 58.827 47.619 0.00 0.00 0.00 4.26
2629 3302 2.165641 TCCACATGTACCAGAACGCTAG 59.834 50.000 0.00 0.00 0.00 3.42
2639 3324 7.829725 TGTACCAGAACGCTAGACTTTATTTA 58.170 34.615 0.00 0.00 0.00 1.40
2669 3354 9.798994 GTTGATGAATAGCTTGAAAGATCAATT 57.201 29.630 0.00 0.00 44.29 2.32
2745 3430 6.682423 TTTGGATAATGCTGTGACACTATG 57.318 37.500 7.20 0.00 0.00 2.23
2776 3461 8.574251 TTAGCTTGCTATGTTTTTCTATTCCA 57.426 30.769 2.99 0.00 0.00 3.53
2809 3494 2.483014 TTAACACTTGATCCCGGTGG 57.517 50.000 0.00 0.00 35.53 4.61
2825 3510 4.994852 CCCGGTGGTATATTTGTCTACATG 59.005 45.833 0.00 0.00 0.00 3.21
2900 3587 7.028926 AGCTCTCTCATTAGCATTTCATTTG 57.971 36.000 0.00 0.00 41.32 2.32
2912 3599 4.612033 GCATTTCATTTGCAAAGAACAGCC 60.612 41.667 18.19 0.62 39.90 4.85
2913 3600 2.818130 TCATTTGCAAAGAACAGCCC 57.182 45.000 18.19 0.00 0.00 5.19
2946 3633 8.438676 ACAAAGATTACTAGGATAACATGTGC 57.561 34.615 0.00 0.00 0.00 4.57
2947 3634 7.224753 ACAAAGATTACTAGGATAACATGTGCG 59.775 37.037 0.00 0.00 0.00 5.34
2948 3635 6.406692 AGATTACTAGGATAACATGTGCGT 57.593 37.500 0.00 0.00 0.00 5.24
2949 3636 6.817184 AGATTACTAGGATAACATGTGCGTT 58.183 36.000 0.00 0.00 0.00 4.84
3052 3742 1.705873 ACTTCTATAGCTGGACCCCG 58.294 55.000 0.00 0.00 0.00 5.73
3102 3792 7.534723 AGGATTTACTATAGGCGAATGTGTA 57.465 36.000 4.43 0.00 0.00 2.90
3111 3801 2.000447 GGCGAATGTGTACCTGAACTC 59.000 52.381 0.00 0.00 0.00 3.01
3203 3893 7.575414 TGTTATACTTCCAAGAAAGCAACAA 57.425 32.000 0.00 0.00 29.84 2.83
3219 3909 6.857777 AGCAACAATCACATTAGCTCTATC 57.142 37.500 0.00 0.00 0.00 2.08
3275 3965 4.823276 CTCGTGATGAGGGTCTGC 57.177 61.111 0.00 0.00 41.29 4.26
3281 3971 2.679059 CGTGATGAGGGTCTGCTGAATT 60.679 50.000 0.00 0.00 0.00 2.17
3334 4024 3.389925 ACAATGGGTTGCTGAATGTTG 57.610 42.857 0.00 0.00 38.96 3.33
3335 4025 2.037511 ACAATGGGTTGCTGAATGTTGG 59.962 45.455 0.00 0.00 38.96 3.77
3336 4026 2.299582 CAATGGGTTGCTGAATGTTGGA 59.700 45.455 0.00 0.00 0.00 3.53
3337 4027 2.307496 TGGGTTGCTGAATGTTGGAT 57.693 45.000 0.00 0.00 0.00 3.41
3338 4028 1.894466 TGGGTTGCTGAATGTTGGATG 59.106 47.619 0.00 0.00 0.00 3.51
3339 4029 1.895131 GGGTTGCTGAATGTTGGATGT 59.105 47.619 0.00 0.00 0.00 3.06
3340 4030 2.299867 GGGTTGCTGAATGTTGGATGTT 59.700 45.455 0.00 0.00 0.00 2.71
3341 4031 3.319755 GGTTGCTGAATGTTGGATGTTG 58.680 45.455 0.00 0.00 0.00 3.33
3342 4032 2.728690 TGCTGAATGTTGGATGTTGC 57.271 45.000 0.00 0.00 0.00 4.17
3343 4033 1.273048 TGCTGAATGTTGGATGTTGCC 59.727 47.619 0.00 0.00 0.00 4.52
3344 4034 1.547372 GCTGAATGTTGGATGTTGCCT 59.453 47.619 0.00 0.00 0.00 4.75
3345 4035 2.028748 GCTGAATGTTGGATGTTGCCTT 60.029 45.455 0.00 0.00 0.00 4.35
3346 4036 3.581755 CTGAATGTTGGATGTTGCCTTG 58.418 45.455 0.00 0.00 0.00 3.61
3347 4037 2.299582 TGAATGTTGGATGTTGCCTTGG 59.700 45.455 0.00 0.00 0.00 3.61
3348 4038 2.014010 ATGTTGGATGTTGCCTTGGT 57.986 45.000 0.00 0.00 0.00 3.67
3349 4039 2.666272 TGTTGGATGTTGCCTTGGTA 57.334 45.000 0.00 0.00 0.00 3.25
3350 4040 2.513753 TGTTGGATGTTGCCTTGGTAG 58.486 47.619 0.00 0.00 0.00 3.18
3351 4041 2.158534 TGTTGGATGTTGCCTTGGTAGT 60.159 45.455 0.00 0.00 0.00 2.73
3402 4092 0.110486 AGTTGTCCCTTGGCGACATT 59.890 50.000 0.00 2.80 39.86 2.71
3432 4122 2.503895 ACTCATCTTTGGCTTGGGAG 57.496 50.000 0.00 0.00 0.00 4.30
3433 4123 1.707427 ACTCATCTTTGGCTTGGGAGT 59.293 47.619 0.00 0.00 0.00 3.85
3434 4124 2.089980 CTCATCTTTGGCTTGGGAGTG 58.910 52.381 0.00 0.00 0.00 3.51
3435 4125 1.425066 TCATCTTTGGCTTGGGAGTGT 59.575 47.619 0.00 0.00 0.00 3.55
3436 4126 1.542915 CATCTTTGGCTTGGGAGTGTG 59.457 52.381 0.00 0.00 0.00 3.82
3437 4127 0.550914 TCTTTGGCTTGGGAGTGTGT 59.449 50.000 0.00 0.00 0.00 3.72
3438 4128 1.771854 TCTTTGGCTTGGGAGTGTGTA 59.228 47.619 0.00 0.00 0.00 2.90
3439 4129 2.154462 CTTTGGCTTGGGAGTGTGTAG 58.846 52.381 0.00 0.00 0.00 2.74
3440 4130 1.429930 TTGGCTTGGGAGTGTGTAGA 58.570 50.000 0.00 0.00 0.00 2.59
3441 4131 1.429930 TGGCTTGGGAGTGTGTAGAA 58.570 50.000 0.00 0.00 0.00 2.10
3442 4132 1.985159 TGGCTTGGGAGTGTGTAGAAT 59.015 47.619 0.00 0.00 0.00 2.40
3443 4133 2.375174 TGGCTTGGGAGTGTGTAGAATT 59.625 45.455 0.00 0.00 0.00 2.17
3444 4134 3.585289 TGGCTTGGGAGTGTGTAGAATTA 59.415 43.478 0.00 0.00 0.00 1.40
3445 4135 4.042311 TGGCTTGGGAGTGTGTAGAATTAA 59.958 41.667 0.00 0.00 0.00 1.40
3446 4136 4.395231 GGCTTGGGAGTGTGTAGAATTAAC 59.605 45.833 0.00 0.00 0.00 2.01
3447 4137 5.246307 GCTTGGGAGTGTGTAGAATTAACT 58.754 41.667 0.00 0.00 0.00 2.24
3448 4138 6.403878 GCTTGGGAGTGTGTAGAATTAACTA 58.596 40.000 0.00 0.00 0.00 2.24
3449 4139 7.048512 GCTTGGGAGTGTGTAGAATTAACTAT 58.951 38.462 0.00 0.00 0.00 2.12
3450 4140 7.553044 GCTTGGGAGTGTGTAGAATTAACTATT 59.447 37.037 0.00 0.00 0.00 1.73
3452 4142 9.880157 TTGGGAGTGTGTAGAATTAACTATTAC 57.120 33.333 0.00 0.00 0.00 1.89
3453 4143 8.480501 TGGGAGTGTGTAGAATTAACTATTACC 58.519 37.037 0.00 0.00 0.00 2.85
3454 4144 8.480501 GGGAGTGTGTAGAATTAACTATTACCA 58.519 37.037 0.00 0.00 0.00 3.25
3468 4158 9.595823 TTAACTATTACCATGTCTCTAGTTTGC 57.404 33.333 11.07 0.00 33.05 3.68
3469 4159 6.273825 ACTATTACCATGTCTCTAGTTTGCG 58.726 40.000 0.00 0.00 0.00 4.85
3470 4160 1.726853 ACCATGTCTCTAGTTTGCGC 58.273 50.000 0.00 0.00 0.00 6.09
3471 4161 1.276421 ACCATGTCTCTAGTTTGCGCT 59.724 47.619 9.73 0.00 0.00 5.92
3472 4162 2.289694 ACCATGTCTCTAGTTTGCGCTT 60.290 45.455 9.73 0.00 0.00 4.68
3473 4163 2.094894 CCATGTCTCTAGTTTGCGCTTG 59.905 50.000 9.73 0.00 0.00 4.01
3474 4164 1.795768 TGTCTCTAGTTTGCGCTTGG 58.204 50.000 9.73 0.00 0.00 3.61
3475 4165 1.079503 GTCTCTAGTTTGCGCTTGGG 58.920 55.000 9.73 0.00 0.00 4.12
3476 4166 0.973632 TCTCTAGTTTGCGCTTGGGA 59.026 50.000 9.73 0.00 0.00 4.37
3477 4167 1.066858 TCTCTAGTTTGCGCTTGGGAG 60.067 52.381 9.73 8.93 0.00 4.30
3482 4172 1.453015 TTTGCGCTTGGGAGTGTGT 60.453 52.632 9.73 0.00 35.79 3.72
3525 4218 5.703130 GTCTCTAGTTTGCTTCAATTCTGGT 59.297 40.000 0.00 0.00 0.00 4.00
3526 4219 5.702670 TCTCTAGTTTGCTTCAATTCTGGTG 59.297 40.000 0.00 0.00 0.00 4.17
3527 4220 5.376625 TCTAGTTTGCTTCAATTCTGGTGT 58.623 37.500 0.00 0.00 0.00 4.16
3546 4239 5.998981 TGGTGTTGTTGTATGTAGGTTAAGG 59.001 40.000 0.00 0.00 0.00 2.69
3555 4249 5.360144 TGTATGTAGGTTAAGGCAGAGAGTC 59.640 44.000 0.00 0.00 0.00 3.36
3605 4299 1.224075 ATGTGCATGATGTAGCTCGC 58.776 50.000 0.00 0.00 0.00 5.03
3650 4344 8.061920 TGGGGAATGTGTGATATACCATTTTTA 58.938 33.333 0.00 0.00 33.31 1.52
3651 4345 8.576442 GGGGAATGTGTGATATACCATTTTTAG 58.424 37.037 0.00 0.00 33.31 1.85
3931 4626 1.871080 CATCCCGATGGTAAGAGCAC 58.129 55.000 0.00 0.00 35.24 4.40
3961 4658 4.241681 TGCCGGATCTTTAATTTTGCAAC 58.758 39.130 5.05 0.00 0.00 4.17
3999 4696 5.055812 GGCTTCTCACATCCTTCATCTAAG 58.944 45.833 0.00 0.00 34.73 2.18
4181 7246 9.740710 ATTTGCTTAGGAGTCAAGTAACTTATT 57.259 29.630 0.00 0.00 29.02 1.40
4397 7463 4.351054 CACCAGCCCTCGCCCTTT 62.351 66.667 0.00 0.00 34.57 3.11
4405 7471 3.798511 CTCGCCCTTTCCCCTCCC 61.799 72.222 0.00 0.00 0.00 4.30
4407 7473 3.798511 CGCCCTTTCCCCTCCCTC 61.799 72.222 0.00 0.00 0.00 4.30
4454 7520 1.569653 AGGGTACAAGCTCCTACCAC 58.430 55.000 17.51 9.65 35.03 4.16
4492 7558 9.162764 AGTACGTAGTTAGAATGCATCATTTTT 57.837 29.630 0.00 0.00 37.78 1.94
4541 7608 2.996621 CAGAACTACTGCCTGCACTTAC 59.003 50.000 0.00 0.00 39.86 2.34
4569 7636 0.543410 TCCGGGGATATGGCACGTAT 60.543 55.000 0.00 0.00 0.00 3.06
4646 7714 2.213499 GCATGCGTATACTTTGCCTCT 58.787 47.619 0.00 0.00 0.00 3.69
4927 7998 1.769665 TGGCCAGACCAGCTGATTT 59.230 52.632 17.39 0.00 46.36 2.17
5026 8097 8.271458 TCATTGGAAACTGGCATTATTAGAGTA 58.729 33.333 0.00 0.00 0.00 2.59
5088 8160 5.907391 CGTTGCTCAGTGTAAAGGTTTTAAG 59.093 40.000 0.00 0.00 0.00 1.85
5174 8246 7.569240 AGGAATCTATTTACAAGAGAGGTTGG 58.431 38.462 0.00 0.00 0.00 3.77
5264 8337 6.873605 CACTGTCTTGTGTTATGGTGATCTAA 59.126 38.462 0.00 0.00 33.61 2.10
5276 8349 2.158696 GGTGATCTAAGGGATGCAAGCT 60.159 50.000 0.00 0.00 34.33 3.74
5278 8351 2.158711 TGATCTAAGGGATGCAAGCTGG 60.159 50.000 0.00 0.00 34.33 4.85
5296 8369 0.250467 GGCAGAGTCCACATGTGTGT 60.250 55.000 23.79 8.24 44.21 3.72
5365 8440 1.965935 AATTTTGCTTTGTGGGTGGC 58.034 45.000 0.00 0.00 0.00 5.01
5368 8443 0.975040 TTTGCTTTGTGGGTGGCAGT 60.975 50.000 0.00 0.00 36.06 4.40
5392 8467 2.892425 GCCGTCTGCTTCATCCCG 60.892 66.667 0.00 0.00 36.87 5.14
5394 8469 2.721167 CCGTCTGCTTCATCCCGGA 61.721 63.158 0.73 0.00 37.66 5.14
5395 8470 1.218047 CGTCTGCTTCATCCCGGAA 59.782 57.895 0.73 0.00 0.00 4.30
5396 8471 0.807667 CGTCTGCTTCATCCCGGAAG 60.808 60.000 0.73 0.00 45.58 3.46
5402 8483 1.740718 GCTTCATCCCGGAAGTGTCTC 60.741 57.143 0.73 0.00 44.81 3.36
5515 8597 5.991933 TGGCTGCTTTATTGAATTGGTAA 57.008 34.783 0.00 0.00 0.00 2.85
5633 8715 4.442893 CGAGTGGGATGCCTCATTAGTTTA 60.443 45.833 4.35 0.00 0.00 2.01
5639 8721 5.220796 GGGATGCCTCATTAGTTTAACGAAC 60.221 44.000 0.00 0.00 38.58 3.95
5677 8759 7.584396 TCTATAGATCCTACCATACCAGTCA 57.416 40.000 0.00 0.00 0.00 3.41
5691 8773 6.094048 CCATACCAGTCAGGATAAAAACAGTG 59.906 42.308 0.00 0.00 41.22 3.66
5694 8776 4.821805 CCAGTCAGGATAAAAACAGTGTGT 59.178 41.667 0.00 0.00 41.22 3.72
5695 8777 5.995282 CCAGTCAGGATAAAAACAGTGTGTA 59.005 40.000 0.00 0.00 41.22 2.90
5696 8778 6.147821 CCAGTCAGGATAAAAACAGTGTGTAG 59.852 42.308 0.00 0.00 41.22 2.74
5717 8946 8.141909 GTGTAGATGCATCACTAATGTAAGGTA 58.858 37.037 27.81 4.55 37.71 3.08
5718 8947 8.870116 TGTAGATGCATCACTAATGTAAGGTAT 58.130 33.333 27.81 4.45 37.71 2.73
5794 9026 2.210013 TGGCGCCTCTGTTCTCAGT 61.210 57.895 29.70 0.00 41.91 3.41
5805 9037 5.299531 CCTCTGTTCTCAGTATGGAACGATA 59.700 44.000 0.00 0.00 44.12 2.92
5821 9053 3.921677 ACGATACATCCACGTTCACTTT 58.078 40.909 0.00 0.00 36.91 2.66
5832 9064 4.495184 CCACGTTCACTTTAACTGAACCAC 60.495 45.833 15.12 0.00 43.10 4.16
5835 9067 4.260620 CGTTCACTTTAACTGAACCACCTG 60.261 45.833 15.12 2.95 43.10 4.00
5862 9094 5.461526 GTTTCTTTCATGTTAACCCAGCTC 58.538 41.667 2.48 0.00 0.00 4.09
5876 9108 1.933853 CCAGCTCGTTTTATTCCTCCG 59.066 52.381 0.00 0.00 0.00 4.63
5877 9109 2.418197 CCAGCTCGTTTTATTCCTCCGA 60.418 50.000 0.00 0.00 0.00 4.55
5879 9111 3.871594 CAGCTCGTTTTATTCCTCCGAAT 59.128 43.478 0.00 0.00 41.67 3.34
5893 9126 3.740832 CCTCCGAATTGAAAGTTTTTGCC 59.259 43.478 0.00 0.00 0.00 4.52
5894 9127 4.367450 CTCCGAATTGAAAGTTTTTGCCA 58.633 39.130 0.00 0.00 0.00 4.92
5896 9129 6.090483 TCCGAATTGAAAGTTTTTGCCATA 57.910 33.333 0.00 0.00 0.00 2.74
5898 9131 7.158021 TCCGAATTGAAAGTTTTTGCCATATT 58.842 30.769 0.00 0.00 0.00 1.28
5899 9132 7.659390 TCCGAATTGAAAGTTTTTGCCATATTT 59.341 29.630 0.00 0.00 0.00 1.40
5900 9133 7.956943 CCGAATTGAAAGTTTTTGCCATATTTC 59.043 33.333 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.767673 ACTCATGTTAGAAGCGGGTAGAA 59.232 43.478 0.00 0.00 0.00 2.10
40 41 3.362706 ACTCATGTTAGAAGCGGGTAGA 58.637 45.455 0.00 0.00 0.00 2.59
127 131 4.495565 TCTAGGAGGTGTAAAAACAGGGA 58.504 43.478 0.00 0.00 0.00 4.20
178 182 3.607422 TTGAAACAACTCTGTGCGATG 57.393 42.857 0.00 0.00 35.37 3.84
181 233 2.046313 GCATTGAAACAACTCTGTGCG 58.954 47.619 0.00 0.00 35.37 5.34
185 237 6.005583 ACTGTATGCATTGAAACAACTCTG 57.994 37.500 3.54 0.00 0.00 3.35
207 394 8.182227 GCAACACCAAAACCTAATTCTCTATAC 58.818 37.037 0.00 0.00 0.00 1.47
353 543 1.999648 AGATTGCTTTGAGCCAACCA 58.000 45.000 0.00 0.00 41.51 3.67
443 1049 1.151899 TACTCAACCACCCCAGCCT 60.152 57.895 0.00 0.00 0.00 4.58
515 1146 4.222588 AGATCTGGAGACAACAAAGGAGAG 59.777 45.833 0.00 0.00 42.06 3.20
517 1148 4.020751 TCAGATCTGGAGACAACAAAGGAG 60.021 45.833 22.42 0.00 42.06 3.69
524 1155 5.707298 TCCAAAAATCAGATCTGGAGACAAC 59.293 40.000 22.42 0.00 42.06 3.32
560 1195 1.457303 CGACGCAAGAACCTCTCTTTG 59.543 52.381 0.00 0.00 41.97 2.77
563 1198 1.587054 CCGACGCAAGAACCTCTCT 59.413 57.895 0.00 0.00 43.62 3.10
567 1202 1.961277 CAAGCCGACGCAAGAACCT 60.961 57.895 0.00 0.00 43.62 3.50
633 1270 4.302930 CCCTTCTTCCTCCTTATTCCTCT 58.697 47.826 0.00 0.00 0.00 3.69
639 1277 2.632634 GGGTCCCCTTCTTCCTCCTTAT 60.633 54.545 0.00 0.00 0.00 1.73
666 1304 5.273944 CCTTTTCTTTGAAAGACAAGTCCG 58.726 41.667 24.17 11.47 41.50 4.79
669 1307 6.187682 TCTCCCTTTTCTTTGAAAGACAAGT 58.812 36.000 24.17 0.00 41.50 3.16
676 1314 5.719563 ACCACTTTCTCCCTTTTCTTTGAAA 59.280 36.000 0.00 0.00 0.00 2.69
682 1320 2.810767 GCGACCACTTTCTCCCTTTTCT 60.811 50.000 0.00 0.00 0.00 2.52
693 1331 1.594293 CACCTCACGCGACCACTTT 60.594 57.895 15.93 0.00 0.00 2.66
695 1333 4.664677 GCACCTCACGCGACCACT 62.665 66.667 15.93 0.00 0.00 4.00
732 1375 4.476410 CTCGCGCACGCTCCACTA 62.476 66.667 13.70 0.00 39.84 2.74
744 1392 2.587194 CCTCCTTGCATCCTCGCG 60.587 66.667 0.00 0.00 33.35 5.87
751 1399 2.697644 CCCTCCCCCTCCTTGCAT 60.698 66.667 0.00 0.00 0.00 3.96
755 1403 4.416601 CGGTCCCTCCCCCTCCTT 62.417 72.222 0.00 0.00 0.00 3.36
826 1476 3.182967 GACACGCAAAAATGAAACCACA 58.817 40.909 0.00 0.00 0.00 4.17
828 1478 2.796383 CGGACACGCAAAAATGAAACCA 60.796 45.455 0.00 0.00 0.00 3.67
854 1505 3.001939 CCATATACGGAAAGAAACCACGC 59.998 47.826 0.00 0.00 0.00 5.34
869 1526 0.608640 CCGAGTGCCCTCCCATATAC 59.391 60.000 0.00 0.00 33.93 1.47
883 1540 2.283966 ACTAGCTGGCACCCGAGT 60.284 61.111 0.00 0.00 0.00 4.18
890 1547 3.075005 GGACCCGACTAGCTGGCA 61.075 66.667 0.00 0.00 0.00 4.92
892 1549 1.633774 ATATGGACCCGACTAGCTGG 58.366 55.000 0.00 0.00 0.00 4.85
893 1550 4.866508 TTTATATGGACCCGACTAGCTG 57.133 45.455 0.00 0.00 0.00 4.24
900 1557 4.675976 ACACGAATTTATATGGACCCGA 57.324 40.909 0.00 0.00 0.00 5.14
901 1558 5.291178 TGTACACGAATTTATATGGACCCG 58.709 41.667 0.00 0.00 0.00 5.28
902 1559 6.423001 GTCTGTACACGAATTTATATGGACCC 59.577 42.308 0.00 0.00 0.00 4.46
903 1560 6.982141 TGTCTGTACACGAATTTATATGGACC 59.018 38.462 0.00 0.00 0.00 4.46
904 1561 7.997107 TGTCTGTACACGAATTTATATGGAC 57.003 36.000 0.00 0.00 0.00 4.02
905 1562 8.255206 AGTTGTCTGTACACGAATTTATATGGA 58.745 33.333 0.00 0.00 34.61 3.41
906 1563 8.328146 CAGTTGTCTGTACACGAATTTATATGG 58.672 37.037 0.00 0.00 34.61 2.74
907 1564 8.328146 CCAGTTGTCTGTACACGAATTTATATG 58.672 37.037 0.00 0.00 39.82 1.78
908 1565 7.494625 CCCAGTTGTCTGTACACGAATTTATAT 59.505 37.037 0.00 0.00 39.82 0.86
909 1566 6.814644 CCCAGTTGTCTGTACACGAATTTATA 59.185 38.462 0.00 0.00 39.82 0.98
910 1567 5.642063 CCCAGTTGTCTGTACACGAATTTAT 59.358 40.000 0.00 0.00 39.82 1.40
911 1568 4.992319 CCCAGTTGTCTGTACACGAATTTA 59.008 41.667 0.00 0.00 39.82 1.40
912 1569 3.813166 CCCAGTTGTCTGTACACGAATTT 59.187 43.478 0.00 0.00 39.82 1.82
915 1572 1.539496 GCCCAGTTGTCTGTACACGAA 60.539 52.381 0.00 0.00 39.82 3.85
950 1608 0.988832 ACGGAGGAAAATGGCAGGTA 59.011 50.000 0.00 0.00 0.00 3.08
973 1631 1.141881 GCGAGGCGAAGGAGATGAA 59.858 57.895 0.00 0.00 0.00 2.57
1025 1683 0.386100 CGAGCCGACACGATATGAGG 60.386 60.000 0.00 0.00 34.29 3.86
1026 1684 0.586802 TCGAGCCGACACGATATGAG 59.413 55.000 0.00 0.00 33.83 2.90
1027 1685 1.018910 TTCGAGCCGACACGATATGA 58.981 50.000 0.00 0.00 38.69 2.15
1028 1686 1.781429 CTTTCGAGCCGACACGATATG 59.219 52.381 0.00 0.00 38.69 1.78
1029 1687 1.404391 ACTTTCGAGCCGACACGATAT 59.596 47.619 0.00 0.00 38.69 1.63
1030 1688 0.806868 ACTTTCGAGCCGACACGATA 59.193 50.000 0.00 0.00 38.69 2.92
1031 1689 0.456312 GACTTTCGAGCCGACACGAT 60.456 55.000 0.00 0.00 38.69 3.73
1078 1736 2.040813 TCTGTCCCTGTTCCTACGTACT 59.959 50.000 0.00 0.00 0.00 2.73
1109 1767 2.060980 GCCGGTGGAGATCTGGTCT 61.061 63.158 0.00 0.00 40.81 3.85
1237 1895 3.706373 GAGCAGGTGGGAGCGGAA 61.706 66.667 0.00 0.00 35.48 4.30
1269 1927 1.218316 GTTACAGAGGGAGCCGTGG 59.782 63.158 0.00 0.00 0.00 4.94
1316 1974 3.136443 CACCATCCCTAAGCACATAGGAA 59.864 47.826 10.79 0.00 44.46 3.36
1402 2060 6.947733 TCCACAACCTCAATTCTAACATGAAT 59.052 34.615 0.00 0.00 38.19 2.57
1423 2081 1.465794 AGCTCGTCCTTACTCTCCAC 58.534 55.000 0.00 0.00 0.00 4.02
1514 2172 7.396907 TCCAACAGACCAATTCATGATATTTGT 59.603 33.333 0.00 2.05 0.00 2.83
1544 2202 4.534794 TGTTATGCTGCATAATGACGTG 57.465 40.909 30.96 0.00 38.37 4.49
1546 2204 4.469552 CCATGTTATGCTGCATAATGACG 58.530 43.478 30.96 20.86 38.37 4.35
1689 2352 5.035443 GGCGCTATCAACTAGTATTATCCG 58.965 45.833 7.64 0.00 0.00 4.18
1708 2371 2.914777 CTTCTAGCTCCCACAGGCGC 62.915 65.000 0.00 0.00 44.74 6.53
1732 2395 1.337447 ACCGTGTCCAAGGTTACATCG 60.337 52.381 0.00 0.00 40.26 3.84
1750 2413 7.603024 AGTTACTGCTAGATTGAGTAAAACACC 59.397 37.037 0.00 0.00 34.73 4.16
1779 2442 4.994852 GCAACAGTTCATACCTCAGTTACA 59.005 41.667 0.00 0.00 0.00 2.41
1862 2525 7.324178 TCAGACTAGAAAGCAGGACTATTTTC 58.676 38.462 0.00 0.00 0.00 2.29
1879 2542 4.036971 CCACCCTCGATACTTTCAGACTAG 59.963 50.000 0.00 0.00 0.00 2.57
1938 2605 6.128661 CGTGTCAGCAAGCTTTACAAAGTATA 60.129 38.462 0.00 0.00 38.28 1.47
2018 2686 6.543100 CCCCTTAATAACTTAAACCATGCGTA 59.457 38.462 0.00 0.00 0.00 4.42
2070 2742 3.814504 AGTGAAGTGGGGAAACATGAT 57.185 42.857 0.00 0.00 0.00 2.45
2125 2798 3.634910 TCGTTGCCTACAGATAGCATACA 59.365 43.478 0.00 0.00 0.00 2.29
2130 2803 2.579207 TGTCGTTGCCTACAGATAGC 57.421 50.000 0.00 0.00 0.00 2.97
2243 2916 3.445987 TGGGGCCAAAATAAAAGGTAGG 58.554 45.455 4.39 0.00 0.00 3.18
2271 2944 6.381133 TGATCCTTAAGTGCAGACAGATAAGA 59.619 38.462 0.97 0.00 31.37 2.10
2273 2946 6.155221 ACTGATCCTTAAGTGCAGACAGATAA 59.845 38.462 17.93 0.00 0.00 1.75
2487 3160 2.811431 CGTACAGGCCTTTCATCAACAA 59.189 45.455 0.00 0.00 0.00 2.83
2617 3290 6.812160 CACTAAATAAAGTCTAGCGTTCTGGT 59.188 38.462 0.00 0.00 0.00 4.00
2624 3297 7.491372 TCATCAACCACTAAATAAAGTCTAGCG 59.509 37.037 0.00 0.00 0.00 4.26
2625 3298 8.718102 TCATCAACCACTAAATAAAGTCTAGC 57.282 34.615 0.00 0.00 0.00 3.42
2629 3302 9.937175 GCTATTCATCAACCACTAAATAAAGTC 57.063 33.333 0.00 0.00 0.00 3.01
2639 3324 6.240894 TCTTTCAAGCTATTCATCAACCACT 58.759 36.000 0.00 0.00 0.00 4.00
2669 3354 6.475504 TCATTTAGAAAGATCAGTTCCAGCA 58.524 36.000 0.00 0.00 0.00 4.41
2711 3396 8.391106 CACAGCATTATCCAAAAGAGTTACTAC 58.609 37.037 0.00 0.00 0.00 2.73
2733 3418 4.692625 AGCTAAGCAAACATAGTGTCACAG 59.307 41.667 5.62 0.00 0.00 3.66
2745 3430 6.642540 AGAAAAACATAGCAAGCTAAGCAAAC 59.357 34.615 12.91 0.00 31.73 2.93
2788 3473 3.520317 ACCACCGGGATCAAGTGTTAATA 59.480 43.478 6.32 0.00 38.05 0.98
2804 3489 6.764877 GTCATGTAGACAAATATACCACCG 57.235 41.667 0.00 0.00 46.77 4.94
2825 3510 9.736023 CAATAAATAAAGGCTCAAACCTATGTC 57.264 33.333 0.00 0.00 39.93 3.06
2877 3564 5.686397 GCAAATGAAATGCTAATGAGAGAGC 59.314 40.000 0.00 0.00 40.64 4.09
2900 3587 0.884514 GGAAGAGGGCTGTTCTTTGC 59.115 55.000 0.00 0.00 35.14 3.68
2912 3599 7.899648 TCCTAGTAATCTTTGTAGGAAGAGG 57.100 40.000 0.00 0.00 38.48 3.69
2945 3632 2.061028 CAAGGGAAATGCTGAAAACGC 58.939 47.619 0.00 0.00 0.00 4.84
2946 3633 2.295909 TCCAAGGGAAATGCTGAAAACG 59.704 45.455 0.00 0.00 0.00 3.60
2947 3634 4.021192 TGATCCAAGGGAAATGCTGAAAAC 60.021 41.667 0.00 0.00 34.34 2.43
2948 3635 4.021192 GTGATCCAAGGGAAATGCTGAAAA 60.021 41.667 0.00 0.00 34.34 2.29
2949 3636 3.511146 GTGATCCAAGGGAAATGCTGAAA 59.489 43.478 0.00 0.00 34.34 2.69
3077 3767 7.534723 ACACATTCGCCTATAGTAAATCCTA 57.465 36.000 0.00 0.00 0.00 2.94
3085 3775 4.212716 TCAGGTACACATTCGCCTATAGT 58.787 43.478 0.00 0.00 0.00 2.12
3102 3792 7.937942 AGACTATATATACACACGAGTTCAGGT 59.062 37.037 0.00 0.00 0.00 4.00
3111 3801 7.654568 TGGAAACCAGACTATATATACACACG 58.345 38.462 0.00 0.00 0.00 4.49
3203 3893 7.536159 TGACAGATGATAGAGCTAATGTGAT 57.464 36.000 0.00 0.00 0.00 3.06
3219 3909 2.708051 AGCATGACCACTTGACAGATG 58.292 47.619 0.00 0.00 0.00 2.90
3275 3965 6.694411 CAGAGGTTTTGAACAGAACAATTCAG 59.306 38.462 9.68 0.34 36.26 3.02
3281 3971 2.687935 GGCAGAGGTTTTGAACAGAACA 59.312 45.455 9.68 0.00 0.00 3.18
3333 4023 2.238646 CCTACTACCAAGGCAACATCCA 59.761 50.000 0.00 0.00 41.41 3.41
3334 4024 2.238898 ACCTACTACCAAGGCAACATCC 59.761 50.000 0.00 0.00 37.67 3.51
3335 4025 3.629142 ACCTACTACCAAGGCAACATC 57.371 47.619 0.00 0.00 37.67 3.06
3336 4026 3.199289 GGTACCTACTACCAAGGCAACAT 59.801 47.826 4.06 0.00 44.32 2.71
3337 4027 2.568509 GGTACCTACTACCAAGGCAACA 59.431 50.000 4.06 0.00 44.32 3.33
3338 4028 3.257469 GGTACCTACTACCAAGGCAAC 57.743 52.381 4.06 0.00 44.32 4.17
3346 4036 3.512724 TGTGCTGAAAGGTACCTACTACC 59.487 47.826 16.67 4.88 45.19 3.18
3347 4037 4.381718 CCTGTGCTGAAAGGTACCTACTAC 60.382 50.000 16.67 9.41 0.00 2.73
3348 4038 3.767673 CCTGTGCTGAAAGGTACCTACTA 59.232 47.826 16.67 3.23 0.00 1.82
3349 4039 2.567615 CCTGTGCTGAAAGGTACCTACT 59.432 50.000 16.67 5.36 0.00 2.57
3350 4040 2.302157 ACCTGTGCTGAAAGGTACCTAC 59.698 50.000 16.67 13.12 45.15 3.18
3351 4041 2.616524 ACCTGTGCTGAAAGGTACCTA 58.383 47.619 16.67 0.00 45.15 3.08
3365 4055 6.287589 ACAACTAGAGGAGATAAACCTGTG 57.712 41.667 0.00 0.00 37.93 3.66
3402 4092 9.859427 CAAGCCAAAGATGAGTAATTTCAATAA 57.141 29.630 0.00 0.00 0.00 1.40
3442 4132 9.595823 GCAAACTAGAGACATGGTAATAGTTAA 57.404 33.333 12.92 0.00 33.54 2.01
3443 4133 7.919091 CGCAAACTAGAGACATGGTAATAGTTA 59.081 37.037 12.92 0.00 33.54 2.24
3444 4134 6.757010 CGCAAACTAGAGACATGGTAATAGTT 59.243 38.462 0.00 3.95 35.55 2.24
3445 4135 6.273825 CGCAAACTAGAGACATGGTAATAGT 58.726 40.000 0.00 0.00 0.00 2.12
3446 4136 5.175856 GCGCAAACTAGAGACATGGTAATAG 59.824 44.000 0.30 0.00 0.00 1.73
3447 4137 5.047847 GCGCAAACTAGAGACATGGTAATA 58.952 41.667 0.30 0.00 0.00 0.98
3448 4138 3.871594 GCGCAAACTAGAGACATGGTAAT 59.128 43.478 0.30 0.00 0.00 1.89
3449 4139 3.056107 AGCGCAAACTAGAGACATGGTAA 60.056 43.478 11.47 0.00 0.00 2.85
3450 4140 2.496070 AGCGCAAACTAGAGACATGGTA 59.504 45.455 11.47 0.00 0.00 3.25
3451 4141 1.276421 AGCGCAAACTAGAGACATGGT 59.724 47.619 11.47 0.00 0.00 3.55
3452 4142 2.015736 AGCGCAAACTAGAGACATGG 57.984 50.000 11.47 0.00 0.00 3.66
3453 4143 2.094894 CCAAGCGCAAACTAGAGACATG 59.905 50.000 11.47 0.00 0.00 3.21
3454 4144 2.350522 CCAAGCGCAAACTAGAGACAT 58.649 47.619 11.47 0.00 0.00 3.06
3455 4145 1.608025 CCCAAGCGCAAACTAGAGACA 60.608 52.381 11.47 0.00 0.00 3.41
3456 4146 1.079503 CCCAAGCGCAAACTAGAGAC 58.920 55.000 11.47 0.00 0.00 3.36
3457 4147 0.973632 TCCCAAGCGCAAACTAGAGA 59.026 50.000 11.47 0.00 0.00 3.10
3458 4148 1.338200 ACTCCCAAGCGCAAACTAGAG 60.338 52.381 11.47 10.30 0.00 2.43
3459 4149 0.685097 ACTCCCAAGCGCAAACTAGA 59.315 50.000 11.47 0.00 0.00 2.43
3460 4150 0.798776 CACTCCCAAGCGCAAACTAG 59.201 55.000 11.47 3.64 0.00 2.57
3461 4151 0.107831 ACACTCCCAAGCGCAAACTA 59.892 50.000 11.47 0.00 0.00 2.24
3462 4152 1.152963 ACACTCCCAAGCGCAAACT 60.153 52.632 11.47 0.00 0.00 2.66
3463 4153 1.008538 CACACTCCCAAGCGCAAAC 60.009 57.895 11.47 0.00 0.00 2.93
3464 4154 0.179043 TACACACTCCCAAGCGCAAA 60.179 50.000 11.47 0.00 0.00 3.68
3465 4155 0.602638 CTACACACTCCCAAGCGCAA 60.603 55.000 11.47 0.00 0.00 4.85
3466 4156 1.005037 CTACACACTCCCAAGCGCA 60.005 57.895 11.47 0.00 0.00 6.09
3467 4157 0.320421 TTCTACACACTCCCAAGCGC 60.320 55.000 0.00 0.00 0.00 5.92
3468 4158 2.386661 ATTCTACACACTCCCAAGCG 57.613 50.000 0.00 0.00 0.00 4.68
3469 4159 5.246307 AGTTAATTCTACACACTCCCAAGC 58.754 41.667 0.00 0.00 0.00 4.01
3471 4161 9.880157 GTAATAGTTAATTCTACACACTCCCAA 57.120 33.333 0.00 0.00 0.00 4.12
3472 4162 8.480501 GGTAATAGTTAATTCTACACACTCCCA 58.519 37.037 0.00 0.00 0.00 4.37
3473 4163 8.480501 TGGTAATAGTTAATTCTACACACTCCC 58.519 37.037 0.00 0.00 0.00 4.30
3474 4164 9.310716 GTGGTAATAGTTAATTCTACACACTCC 57.689 37.037 0.00 0.00 31.29 3.85
3475 4165 9.017669 CGTGGTAATAGTTAATTCTACACACTC 57.982 37.037 0.00 0.00 31.29 3.51
3476 4166 8.526147 ACGTGGTAATAGTTAATTCTACACACT 58.474 33.333 0.00 0.00 31.29 3.55
3477 4167 8.693542 ACGTGGTAATAGTTAATTCTACACAC 57.306 34.615 0.00 0.00 31.29 3.82
3525 4218 5.622180 TGCCTTAACCTACATACAACAACA 58.378 37.500 0.00 0.00 0.00 3.33
3526 4219 5.935789 TCTGCCTTAACCTACATACAACAAC 59.064 40.000 0.00 0.00 0.00 3.32
3527 4220 6.014070 TCTCTGCCTTAACCTACATACAACAA 60.014 38.462 0.00 0.00 0.00 2.83
3555 4249 8.966868 AGTTTTATATAAGGTGTTCCACATTGG 58.033 33.333 4.68 0.00 38.78 3.16
3590 4284 2.430546 ACTAGCGAGCTACATCATGC 57.569 50.000 0.00 0.00 0.00 4.06
3605 4299 5.885912 TCCCCAAAATAAGCAAGCTTACTAG 59.114 40.000 16.01 7.34 40.76 2.57
3650 4344 7.814587 GCAAAACAAGCCAGAAAGTATATTTCT 59.185 33.333 0.00 0.00 39.16 2.52
3651 4345 7.814587 AGCAAAACAAGCCAGAAAGTATATTTC 59.185 33.333 0.00 0.00 0.00 2.17
3931 4626 1.683943 AAAGATCCGGCATGATGTGG 58.316 50.000 0.00 0.00 0.00 4.17
3961 4658 4.400251 TGAGAAGCCAAGAAATGCCTATTG 59.600 41.667 0.00 0.00 0.00 1.90
3999 4696 5.652452 AGCCAAACCATACTGAAATTACTCC 59.348 40.000 0.00 0.00 0.00 3.85
4143 4840 8.034313 ACTCCTAAGCAAATGATCCTAATACA 57.966 34.615 0.00 0.00 0.00 2.29
4155 4852 9.740710 AATAAGTTACTTGACTCCTAAGCAAAT 57.259 29.630 8.00 0.00 0.00 2.32
4181 7246 8.034313 ACTCCTAAGCAAATGATCCTAATACA 57.966 34.615 0.00 0.00 0.00 2.29
4193 7258 6.543735 AGGTTTACTTGACTCCTAAGCAAAT 58.456 36.000 0.00 0.00 0.00 2.32
4306 7371 2.285442 AGGAGGCGGCTAGGGTTT 60.285 61.111 13.24 0.00 0.00 3.27
4397 7463 1.869946 TTGTAGGGGAGGGAGGGGA 60.870 63.158 0.00 0.00 0.00 4.81
4405 7471 1.683418 GGGCGTAGGTTGTAGGGGAG 61.683 65.000 0.00 0.00 0.00 4.30
4407 7473 2.738938 GGGGCGTAGGTTGTAGGGG 61.739 68.421 0.00 0.00 0.00 4.79
4440 7506 1.348036 GTCCTTGTGGTAGGAGCTTGT 59.652 52.381 0.00 0.00 44.81 3.16
4454 7520 7.755591 TCTAACTACGTACTTATGTGTCCTTG 58.244 38.462 0.00 0.00 0.00 3.61
4492 7558 1.971357 GGTTCAGTCCAGTTCCTCAGA 59.029 52.381 0.00 0.00 0.00 3.27
4646 7714 2.543777 AAGCTTGACCTTTGCGACTA 57.456 45.000 0.00 0.00 0.00 2.59
4927 7998 3.068165 CAGCACGGATACCTCATCAGTTA 59.932 47.826 0.00 0.00 39.69 2.24
5046 8117 4.611366 GCAACGCAACACTGAAATACTAAC 59.389 41.667 0.00 0.00 0.00 2.34
5088 8160 4.620184 GCTGAGCATGAAAACAGATGAAAC 59.380 41.667 0.00 0.00 32.90 2.78
5174 8246 7.226720 TCAACACCTTGTTTCTTTCTCTATGAC 59.773 37.037 0.00 0.00 38.77 3.06
5241 8314 6.536582 CCTTAGATCACCATAACACAAGACAG 59.463 42.308 0.00 0.00 0.00 3.51
5242 8315 6.406370 CCTTAGATCACCATAACACAAGACA 58.594 40.000 0.00 0.00 0.00 3.41
5252 8325 4.505566 GCTTGCATCCCTTAGATCACCATA 60.506 45.833 0.00 0.00 30.59 2.74
5264 8337 2.044252 CTGCCAGCTTGCATCCCT 60.044 61.111 13.56 0.00 41.16 4.20
5276 8349 0.250424 CACACATGTGGACTCTGCCA 60.250 55.000 28.64 0.00 42.10 4.92
5296 8369 6.936279 TCATGTTGGTTTAACTTTTGGTTCA 58.064 32.000 0.00 0.00 40.05 3.18
5365 8440 2.609825 GCAGACGGCATATCCACTG 58.390 57.895 0.00 0.00 43.97 3.66
5377 8452 0.807667 CTTCCGGGATGAAGCAGACG 60.808 60.000 0.00 0.00 35.72 4.18
5392 8467 1.569479 GGCAACGCAGAGACACTTCC 61.569 60.000 0.00 0.00 0.00 3.46
5394 8469 1.598130 GGGCAACGCAGAGACACTT 60.598 57.895 0.00 0.00 37.60 3.16
5395 8470 2.031163 GGGCAACGCAGAGACACT 59.969 61.111 0.00 0.00 37.60 3.55
5396 8471 2.031163 AGGGCAACGCAGAGACAC 59.969 61.111 0.00 0.00 37.60 3.67
5402 8483 3.346631 GATTGGCAGGGCAACGCAG 62.347 63.158 10.62 0.00 37.60 5.18
5441 8522 0.842635 ACAATCATCCAGGAGCTCCC 59.157 55.000 29.54 11.59 36.42 4.30
5515 8597 6.468333 TGCCATTGCAAATGATGTAACTAT 57.532 33.333 1.71 0.00 46.66 2.12
5544 8626 3.976654 TCAATGAACCCCCAAATTTTCCA 59.023 39.130 0.00 0.00 0.00 3.53
5545 8627 4.323417 GTCAATGAACCCCCAAATTTTCC 58.677 43.478 0.00 0.00 0.00 3.13
5633 8715 9.935682 CTATAGAATTTATGCATTGTGTTCGTT 57.064 29.630 3.54 1.69 0.00 3.85
5677 8759 6.237901 TGCATCTACACACTGTTTTTATCCT 58.762 36.000 0.00 0.00 0.00 3.24
5691 8773 6.986817 ACCTTACATTAGTGATGCATCTACAC 59.013 38.462 26.32 17.16 39.47 2.90
5717 8946 2.567615 GGAGCGTCATGTTCCCCTATAT 59.432 50.000 0.00 0.00 41.86 0.86
5718 8947 1.968493 GGAGCGTCATGTTCCCCTATA 59.032 52.381 0.00 0.00 41.86 1.31
5786 9015 5.921408 GGATGTATCGTTCCATACTGAGAAC 59.079 44.000 0.00 0.00 39.19 3.01
5794 9026 4.659111 AACGTGGATGTATCGTTCCATA 57.341 40.909 0.00 0.00 43.61 2.74
5805 9037 4.699637 TCAGTTAAAGTGAACGTGGATGT 58.300 39.130 0.00 0.00 34.36 3.06
5832 9064 5.983118 GGTTAACATGAAAGAAACCAACAGG 59.017 40.000 8.10 0.00 39.51 4.00
5835 9067 5.908341 TGGGTTAACATGAAAGAAACCAAC 58.092 37.500 8.10 0.00 41.12 3.77
5862 9094 6.608610 ACTTTCAATTCGGAGGAATAAAACG 58.391 36.000 0.00 0.00 41.99 3.60
5879 9111 8.674263 ACATGAAATATGGCAAAAACTTTCAA 57.326 26.923 0.00 3.35 36.52 2.69
5937 9183 2.028294 ACAGCAGACTCACCAGAATCAG 60.028 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.