Multiple sequence alignment - TraesCS2B01G256200

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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 TraesCS2B01G256200 chr2B 100.000 3198 0 0 1 3198 297993540 297990343 0.000000e+00 5906.0
1 TraesCS2B01G256200 chr2B 84.929 564 73 7 2640 3198 643861219 643860663 7.750000e-156 560.0
2 TraesCS2B01G256200 chr2B 94.792 96 5 0 531 626 436926472 436926377 1.990000e-32 150.0
3 TraesCS2B01G256200 chr2B 95.652 92 4 0 531 622 401410403 401410312 7.150000e-32 148.0
4 TraesCS2B01G256200 chr5B 93.223 1505 70 17 1702 3198 144728224 144726744 0.000000e+00 2185.0
5 TraesCS2B01G256200 chr5B 94.426 610 30 2 1104 1709 144738005 144737396 0.000000e+00 935.0
6 TraesCS2B01G256200 chr5B 85.530 387 38 9 253 623 375708511 375708895 3.870000e-104 388.0
7 TraesCS2B01G256200 chr5B 93.522 247 14 2 796 1040 144738585 144738339 1.810000e-97 366.0
8 TraesCS2B01G256200 chr5B 94.527 201 11 0 782 982 633881070 633880870 8.610000e-81 311.0
9 TraesCS2B01G256200 chr5B 86.525 141 16 3 655 792 164755098 164755238 5.530000e-33 152.0
10 TraesCS2B01G256200 chr5B 95.699 93 4 0 528 620 601222293 601222201 1.990000e-32 150.0
11 TraesCS2B01G256200 chr5B 95.556 90 4 0 530 619 203732987 203733076 9.250000e-31 145.0
12 TraesCS2B01G256200 chr5B 95.506 89 4 0 531 619 116787716 116787804 3.330000e-30 143.0
13 TraesCS2B01G256200 chr6D 91.947 1577 90 18 1158 2701 286410772 286409200 0.000000e+00 2174.0
14 TraesCS2B01G256200 chr6D 89.982 549 50 3 2654 3198 286409200 286408653 0.000000e+00 704.0
15 TraesCS2B01G256200 chr6D 83.096 633 82 13 2261 2875 234406610 234405985 1.300000e-153 553.0
16 TraesCS2B01G256200 chr6D 92.893 197 14 0 58 254 261117393 261117589 1.450000e-73 287.0
17 TraesCS2B01G256200 chr6D 92.893 197 14 0 58 254 414904372 414904568 1.450000e-73 287.0
18 TraesCS2B01G256200 chr6D 93.750 96 3 3 531 624 308270365 308270459 1.200000e-29 141.0
19 TraesCS2B01G256200 chr5A 89.550 1110 93 15 1088 2190 180656303 180655210 0.000000e+00 1386.0
20 TraesCS2B01G256200 chr5A 88.942 1040 83 9 2186 3198 180630553 180629519 0.000000e+00 1254.0
21 TraesCS2B01G256200 chr5A 88.412 233 24 3 1224 1455 687287776 687287546 8.740000e-71 278.0
22 TraesCS2B01G256200 chr5A 91.579 95 6 2 2186 2280 180643871 180643779 2.590000e-26 130.0
23 TraesCS2B01G256200 chr5A 91.579 95 6 2 2186 2280 180647335 180647243 2.590000e-26 130.0
24 TraesCS2B01G256200 chr5A 100.000 29 0 0 1375 1403 58419187 58419159 2.000000e-03 54.7
25 TraesCS2B01G256200 chr5A 100.000 29 0 0 1375 1403 150662128 150662156 2.000000e-03 54.7
26 TraesCS2B01G256200 chr3B 89.493 1066 95 10 1106 2157 286881651 286880589 0.000000e+00 1332.0
27 TraesCS2B01G256200 chr3B 88.075 587 66 3 2615 3198 710427236 710426651 0.000000e+00 693.0
28 TraesCS2B01G256200 chr3B 89.510 286 28 2 253 536 111667787 111668072 8.430000e-96 361.0
29 TraesCS2B01G256200 chr3B 77.609 527 65 25 2382 2877 537684875 537684371 1.460000e-68 270.0
30 TraesCS2B01G256200 chr3B 96.629 89 3 0 531 619 248242731 248242819 7.150000e-32 148.0
31 TraesCS2B01G256200 chr3B 96.629 89 3 0 531 619 409099713 409099625 7.150000e-32 148.0
32 TraesCS2B01G256200 chr1A 84.050 1210 143 28 1702 2875 108667616 108668811 0.000000e+00 1120.0
33 TraesCS2B01G256200 chr1A 93.103 116 8 0 811 926 414784786 414784901 1.530000e-38 171.0
34 TraesCS2B01G256200 chr4D 85.414 953 98 20 2277 3198 23103248 23102306 0.000000e+00 952.0
35 TraesCS2B01G256200 chr4D 85.996 507 43 4 58 536 313913628 313914134 4.730000e-143 518.0
36 TraesCS2B01G256200 chr4D 90.370 135 12 1 655 788 208187559 208187693 3.280000e-40 176.0
37 TraesCS2B01G256200 chr4D 88.235 136 14 2 655 788 153494925 153495060 9.180000e-36 161.0
38 TraesCS2B01G256200 chr4D 85.000 140 19 2 655 792 254105664 254105803 1.200000e-29 141.0
39 TraesCS2B01G256200 chr7B 89.078 586 61 2 2615 3198 527439157 527439741 0.000000e+00 725.0
40 TraesCS2B01G256200 chr7B 85.996 507 43 10 58 536 483505257 483504751 4.730000e-143 518.0
41 TraesCS2B01G256200 chr7B 84.086 509 49 7 58 536 513037949 513037443 2.250000e-126 462.0
42 TraesCS2B01G256200 chr7B 90.036 281 25 3 256 534 529369827 529369548 8.430000e-96 361.0
43 TraesCS2B01G256200 chr7B 86.036 222 17 8 1302 1522 733905133 733904925 3.210000e-55 226.0
44 TraesCS2B01G256200 chr5D 88.756 587 62 3 2615 3198 317734708 317734123 0.000000e+00 715.0
45 TraesCS2B01G256200 chr6B 89.214 547 56 2 2655 3198 407932090 407932636 0.000000e+00 680.0
46 TraesCS2B01G256200 chr6B 84.520 562 77 6 2640 3198 356578594 356579148 6.030000e-152 547.0
47 TraesCS2B01G256200 chr2D 78.560 653 92 25 2261 2875 163856461 163855819 1.390000e-103 387.0
48 TraesCS2B01G256200 chr2D 90.559 286 25 2 253 536 615820333 615820618 8.370000e-101 377.0
49 TraesCS2B01G256200 chr2D 93.401 197 13 0 58 254 249170685 249170881 3.120000e-75 292.0
50 TraesCS2B01G256200 chr2D 94.595 185 10 0 58 242 313793676 313793860 1.450000e-73 287.0
51 TraesCS2B01G256200 chr2D 88.235 136 14 2 655 788 257244485 257244620 9.180000e-36 161.0
52 TraesCS2B01G256200 chr1B 91.197 284 21 4 256 536 582508382 582508100 1.800000e-102 383.0
53 TraesCS2B01G256200 chr1B 89.161 286 29 2 253 536 323914469 323914754 3.920000e-94 355.0
54 TraesCS2B01G256200 chr1B 89.085 284 29 2 253 534 235222871 235223154 5.080000e-93 351.0
55 TraesCS2B01G256200 chr4B 85.635 362 33 9 56 398 540604321 540604682 2.340000e-96 363.0
56 TraesCS2B01G256200 chr7D 87.261 314 30 7 256 561 104191816 104191505 1.830000e-92 350.0
57 TraesCS2B01G256200 chr6A 92.893 197 14 0 58 254 381741317 381741121 1.450000e-73 287.0
58 TraesCS2B01G256200 chr6A 96.667 90 3 0 530 619 441039054 441038965 1.990000e-32 150.0
59 TraesCS2B01G256200 chr4A 86.765 136 16 2 655 788 317642030 317642165 1.990000e-32 150.0
60 TraesCS2B01G256200 chr4A 94.737 38 1 1 1375 1411 296864747 296864784 1.240000e-04 58.4
61 TraesCS2B01G256200 chr7A 85.714 140 18 2 655 792 415792719 415792580 2.570000e-31 147.0
62 TraesCS2B01G256200 chr7A 84.507 142 18 4 655 793 415390911 415390771 1.550000e-28 137.0
63 TraesCS2B01G256200 chr7A 94.118 51 2 1 1317 1367 236643019 236642970 3.420000e-10 76.8
64 TraesCS2B01G256200 chr3A 94.737 38 1 1 1375 1411 364351004 364351041 1.240000e-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 TraesCS2B01G256200 chr2B 297990343 297993540 3197 True 5906.0 5906 100.0000 1 3198 1 chr2B.!!$R1 3197
1 TraesCS2B01G256200 chr2B 643860663 643861219 556 True 560.0 560 84.9290 2640 3198 1 chr2B.!!$R4 558
2 TraesCS2B01G256200 chr5B 144726744 144728224 1480 True 2185.0 2185 93.2230 1702 3198 1 chr5B.!!$R1 1496
3 TraesCS2B01G256200 chr5B 144737396 144738585 1189 True 650.5 935 93.9740 796 1709 2 chr5B.!!$R4 913
4 TraesCS2B01G256200 chr6D 286408653 286410772 2119 True 1439.0 2174 90.9645 1158 3198 2 chr6D.!!$R2 2040
5 TraesCS2B01G256200 chr6D 234405985 234406610 625 True 553.0 553 83.0960 2261 2875 1 chr6D.!!$R1 614
6 TraesCS2B01G256200 chr5A 180655210 180656303 1093 True 1386.0 1386 89.5500 1088 2190 1 chr5A.!!$R3 1102
7 TraesCS2B01G256200 chr5A 180629519 180630553 1034 True 1254.0 1254 88.9420 2186 3198 1 chr5A.!!$R2 1012
8 TraesCS2B01G256200 chr3B 286880589 286881651 1062 True 1332.0 1332 89.4930 1106 2157 1 chr3B.!!$R1 1051
9 TraesCS2B01G256200 chr3B 710426651 710427236 585 True 693.0 693 88.0750 2615 3198 1 chr3B.!!$R4 583
10 TraesCS2B01G256200 chr3B 537684371 537684875 504 True 270.0 270 77.6090 2382 2877 1 chr3B.!!$R3 495
11 TraesCS2B01G256200 chr1A 108667616 108668811 1195 False 1120.0 1120 84.0500 1702 2875 1 chr1A.!!$F1 1173
12 TraesCS2B01G256200 chr4D 23102306 23103248 942 True 952.0 952 85.4140 2277 3198 1 chr4D.!!$R1 921
13 TraesCS2B01G256200 chr4D 313913628 313914134 506 False 518.0 518 85.9960 58 536 1 chr4D.!!$F4 478
14 TraesCS2B01G256200 chr7B 527439157 527439741 584 False 725.0 725 89.0780 2615 3198 1 chr7B.!!$F1 583
15 TraesCS2B01G256200 chr7B 483504751 483505257 506 True 518.0 518 85.9960 58 536 1 chr7B.!!$R1 478
16 TraesCS2B01G256200 chr7B 513037443 513037949 506 True 462.0 462 84.0860 58 536 1 chr7B.!!$R2 478
17 TraesCS2B01G256200 chr5D 317734123 317734708 585 True 715.0 715 88.7560 2615 3198 1 chr5D.!!$R1 583
18 TraesCS2B01G256200 chr6B 407932090 407932636 546 False 680.0 680 89.2140 2655 3198 1 chr6B.!!$F2 543
19 TraesCS2B01G256200 chr6B 356578594 356579148 554 False 547.0 547 84.5200 2640 3198 1 chr6B.!!$F1 558
20 TraesCS2B01G256200 chr2D 163855819 163856461 642 True 387.0 387 78.5600 2261 2875 1 chr2D.!!$R1 614

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
539 570 0.038801 GAAGGCTTTTGCTGGCTGAC 60.039 55.0 0.0 0.0 46.54 3.51 F
1048 1081 0.098728 CGTCACCATCCGCCAAATTC 59.901 55.0 0.0 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1794 0.689080 GGCCATGGACAGAGAGGAGA 60.689 60.0 18.40 0.0 0.00 3.71 R
2750 3181 0.107897 CTGCACACCGGGCATAAGTA 60.108 55.0 6.32 0.0 41.06 2.24 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
24 25 6.353404 TCTTCTTCTTCTTCTTCCTCTTCC 57.647 41.667 0.00 0.00 0.00 3.46
25 26 6.081356 TCTTCTTCTTCTTCTTCCTCTTCCT 58.919 40.000 0.00 0.00 0.00 3.36
26 27 5.993748 TCTTCTTCTTCTTCCTCTTCCTC 57.006 43.478 0.00 0.00 0.00 3.71
27 28 5.650283 TCTTCTTCTTCTTCCTCTTCCTCT 58.350 41.667 0.00 0.00 0.00 3.69
28 29 6.081356 TCTTCTTCTTCTTCCTCTTCCTCTT 58.919 40.000 0.00 0.00 0.00 2.85
29 30 5.993748 TCTTCTTCTTCCTCTTCCTCTTC 57.006 43.478 0.00 0.00 0.00 2.87
30 31 4.775253 TCTTCTTCTTCCTCTTCCTCTTCC 59.225 45.833 0.00 0.00 0.00 3.46
31 32 4.412060 TCTTCTTCCTCTTCCTCTTCCT 57.588 45.455 0.00 0.00 0.00 3.36
32 33 4.349365 TCTTCTTCCTCTTCCTCTTCCTC 58.651 47.826 0.00 0.00 0.00 3.71
33 34 4.045334 TCTTCTTCCTCTTCCTCTTCCTCT 59.955 45.833 0.00 0.00 0.00 3.69
34 35 4.412060 TCTTCCTCTTCCTCTTCCTCTT 57.588 45.455 0.00 0.00 0.00 2.85
35 36 4.349365 TCTTCCTCTTCCTCTTCCTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
36 37 3.108847 TCCTCTTCCTCTTCCTCTTCC 57.891 52.381 0.00 0.00 0.00 3.46
37 38 2.657459 TCCTCTTCCTCTTCCTCTTCCT 59.343 50.000 0.00 0.00 0.00 3.36
38 39 3.031013 CCTCTTCCTCTTCCTCTTCCTC 58.969 54.545 0.00 0.00 0.00 3.71
39 40 3.309848 CCTCTTCCTCTTCCTCTTCCTCT 60.310 52.174 0.00 0.00 0.00 3.69
40 41 4.352893 CTCTTCCTCTTCCTCTTCCTCTT 58.647 47.826 0.00 0.00 0.00 2.85
41 42 4.349365 TCTTCCTCTTCCTCTTCCTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
42 43 3.108847 TCCTCTTCCTCTTCCTCTTCC 57.891 52.381 0.00 0.00 0.00 3.46
43 44 2.657459 TCCTCTTCCTCTTCCTCTTCCT 59.343 50.000 0.00 0.00 0.00 3.36
44 45 3.031013 CCTCTTCCTCTTCCTCTTCCTC 58.969 54.545 0.00 0.00 0.00 3.71
45 46 3.309848 CCTCTTCCTCTTCCTCTTCCTCT 60.310 52.174 0.00 0.00 0.00 3.69
46 47 4.352893 CTCTTCCTCTTCCTCTTCCTCTT 58.647 47.826 0.00 0.00 0.00 2.85
47 48 4.349365 TCTTCCTCTTCCTCTTCCTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
48 49 3.108847 TCCTCTTCCTCTTCCTCTTCC 57.891 52.381 0.00 0.00 0.00 3.46
49 50 2.657459 TCCTCTTCCTCTTCCTCTTCCT 59.343 50.000 0.00 0.00 0.00 3.36
50 51 3.031013 CCTCTTCCTCTTCCTCTTCCTC 58.969 54.545 0.00 0.00 0.00 3.71
51 52 3.309848 CCTCTTCCTCTTCCTCTTCCTCT 60.310 52.174 0.00 0.00 0.00 3.69
52 53 4.352893 CTCTTCCTCTTCCTCTTCCTCTT 58.647 47.826 0.00 0.00 0.00 2.85
53 54 4.349365 TCTTCCTCTTCCTCTTCCTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
54 55 3.108847 TCCTCTTCCTCTTCCTCTTCC 57.891 52.381 0.00 0.00 0.00 3.46
55 56 2.657459 TCCTCTTCCTCTTCCTCTTCCT 59.343 50.000 0.00 0.00 0.00 3.36
56 57 3.031013 CCTCTTCCTCTTCCTCTTCCTC 58.969 54.545 0.00 0.00 0.00 3.71
68 69 6.272324 TCTTCCTCTTCCTCTTGTTGGATTTA 59.728 38.462 0.00 0.00 33.09 1.40
254 256 0.385974 GCAAACTAGCAACACTGGCG 60.386 55.000 0.00 0.00 36.08 5.69
292 321 1.066929 CCAAATAGGCCTGGCAAACAC 60.067 52.381 22.05 1.96 0.00 3.32
303 333 1.094785 GGCAAACACGGCATCTATGT 58.905 50.000 0.00 0.00 0.00 2.29
374 404 1.210478 CCCTAGCTAAGCTCTTTGCCA 59.790 52.381 11.33 0.00 44.23 4.92
425 455 1.686110 CCCCTAACGGCTCTCACCT 60.686 63.158 0.00 0.00 0.00 4.00
433 463 2.574955 GGCTCTCACCTCACACCGT 61.575 63.158 0.00 0.00 0.00 4.83
457 487 4.986587 CCGTCGTCGTTGCCGTCA 62.987 66.667 0.71 0.00 35.01 4.35
479 509 2.741092 GCCTCGGATGGCGGATAA 59.259 61.111 3.32 0.00 43.74 1.75
490 520 4.498009 GGATGGCGGATAACACAATCTTTG 60.498 45.833 0.00 0.00 0.00 2.77
491 521 3.417101 TGGCGGATAACACAATCTTTGT 58.583 40.909 0.00 0.00 46.75 2.83
501 532 3.242608 ACACAATCTTTGTCGTCCGTTTG 60.243 43.478 0.00 0.00 43.23 2.93
526 557 1.668151 GCGGACGACAAAGAAGGCT 60.668 57.895 0.00 0.00 0.00 4.58
536 567 1.069668 CAAAGAAGGCTTTTGCTGGCT 59.930 47.619 0.00 0.00 42.27 4.75
537 568 0.677842 AAGAAGGCTTTTGCTGGCTG 59.322 50.000 0.00 0.00 46.54 4.85
538 569 0.178981 AGAAGGCTTTTGCTGGCTGA 60.179 50.000 0.00 0.00 46.54 4.26
539 570 0.038801 GAAGGCTTTTGCTGGCTGAC 60.039 55.000 0.00 0.00 46.54 3.51
540 571 1.799258 AAGGCTTTTGCTGGCTGACG 61.799 55.000 0.00 0.00 46.54 4.35
541 572 2.256461 GCTTTTGCTGGCTGACGG 59.744 61.111 0.00 0.00 43.35 4.79
548 579 2.032528 CTGGCTGACGGCAAAGGA 59.967 61.111 8.86 0.00 45.84 3.36
549 580 2.281484 TGGCTGACGGCAAAGGAC 60.281 61.111 8.86 0.00 43.40 3.85
550 581 2.032681 GGCTGACGGCAAAGGACT 59.967 61.111 8.86 0.00 44.01 3.85
551 582 1.600916 GGCTGACGGCAAAGGACTT 60.601 57.895 8.86 0.00 44.01 3.01
552 583 1.172812 GGCTGACGGCAAAGGACTTT 61.173 55.000 8.86 0.00 44.01 2.66
563 594 2.031465 GGACTTTGCCGTCCGGAA 59.969 61.111 5.23 0.00 43.56 4.30
564 595 1.376812 GGACTTTGCCGTCCGGAAT 60.377 57.895 5.23 0.00 43.56 3.01
565 596 1.366854 GGACTTTGCCGTCCGGAATC 61.367 60.000 5.23 0.00 43.56 2.52
566 597 0.391263 GACTTTGCCGTCCGGAATCT 60.391 55.000 5.23 0.00 37.50 2.40
567 598 0.673644 ACTTTGCCGTCCGGAATCTG 60.674 55.000 5.23 0.00 37.50 2.90
568 599 0.673644 CTTTGCCGTCCGGAATCTGT 60.674 55.000 5.23 0.00 37.50 3.41
569 600 0.953471 TTTGCCGTCCGGAATCTGTG 60.953 55.000 5.23 0.00 37.50 3.66
570 601 3.195698 GCCGTCCGGAATCTGTGC 61.196 66.667 5.23 0.00 37.50 4.57
571 602 2.511600 CCGTCCGGAATCTGTGCC 60.512 66.667 5.23 0.00 37.50 5.01
572 603 2.579201 CGTCCGGAATCTGTGCCT 59.421 61.111 5.23 0.00 0.00 4.75
573 604 1.079127 CGTCCGGAATCTGTGCCTT 60.079 57.895 5.23 0.00 0.00 4.35
574 605 0.673644 CGTCCGGAATCTGTGCCTTT 60.674 55.000 5.23 0.00 0.00 3.11
575 606 0.804989 GTCCGGAATCTGTGCCTTTG 59.195 55.000 5.23 0.00 0.00 2.77
576 607 0.960364 TCCGGAATCTGTGCCTTTGC 60.960 55.000 0.00 0.00 38.26 3.68
577 608 1.508088 CGGAATCTGTGCCTTTGCC 59.492 57.895 0.00 0.00 36.33 4.52
578 609 1.508088 GGAATCTGTGCCTTTGCCG 59.492 57.895 0.00 0.00 36.33 5.69
579 610 1.244019 GGAATCTGTGCCTTTGCCGT 61.244 55.000 0.00 0.00 36.33 5.68
580 611 0.169009 GAATCTGTGCCTTTGCCGTC 59.831 55.000 0.00 0.00 36.33 4.79
581 612 1.244019 AATCTGTGCCTTTGCCGTCC 61.244 55.000 0.00 0.00 36.33 4.79
582 613 3.726517 CTGTGCCTTTGCCGTCCG 61.727 66.667 0.00 0.00 36.33 4.79
587 618 3.814268 CCTTTGCCGTCCGCCATG 61.814 66.667 0.00 0.00 36.24 3.66
588 619 3.814268 CTTTGCCGTCCGCCATGG 61.814 66.667 7.63 7.63 36.24 3.66
599 630 3.053291 GCCATGGCGGACGACAAA 61.053 61.111 23.48 0.00 36.35 2.83
600 631 3.039202 GCCATGGCGGACGACAAAG 62.039 63.158 23.48 0.00 36.35 2.77
601 632 1.375396 CCATGGCGGACGACAAAGA 60.375 57.895 3.64 0.00 36.35 2.52
602 633 0.953471 CCATGGCGGACGACAAAGAA 60.953 55.000 3.64 0.00 36.35 2.52
603 634 0.443869 CATGGCGGACGACAAAGAAG 59.556 55.000 3.64 0.00 36.35 2.85
604 635 0.320374 ATGGCGGACGACAAAGAAGA 59.680 50.000 3.64 0.00 36.35 2.87
605 636 0.320374 TGGCGGACGACAAAGAAGAT 59.680 50.000 0.00 0.00 0.00 2.40
606 637 0.721718 GGCGGACGACAAAGAAGATG 59.278 55.000 0.00 0.00 0.00 2.90
607 638 1.671850 GGCGGACGACAAAGAAGATGA 60.672 52.381 0.00 0.00 0.00 2.92
608 639 2.271800 GCGGACGACAAAGAAGATGAT 58.728 47.619 0.00 0.00 0.00 2.45
609 640 2.673368 GCGGACGACAAAGAAGATGATT 59.327 45.455 0.00 0.00 0.00 2.57
610 641 3.242123 GCGGACGACAAAGAAGATGATTC 60.242 47.826 0.00 0.00 0.00 2.52
611 642 3.307242 CGGACGACAAAGAAGATGATTCC 59.693 47.826 0.00 0.00 0.00 3.01
612 643 4.253685 GGACGACAAAGAAGATGATTCCA 58.746 43.478 0.00 0.00 0.00 3.53
613 644 4.331168 GGACGACAAAGAAGATGATTCCAG 59.669 45.833 0.00 0.00 0.00 3.86
614 645 4.899502 ACGACAAAGAAGATGATTCCAGT 58.100 39.130 0.00 0.00 0.00 4.00
615 646 6.037786 ACGACAAAGAAGATGATTCCAGTA 57.962 37.500 0.00 0.00 0.00 2.74
616 647 6.102663 ACGACAAAGAAGATGATTCCAGTAG 58.897 40.000 0.00 0.00 0.00 2.57
617 648 6.102663 CGACAAAGAAGATGATTCCAGTAGT 58.897 40.000 0.00 0.00 0.00 2.73
618 649 6.035435 CGACAAAGAAGATGATTCCAGTAGTG 59.965 42.308 0.00 0.00 0.00 2.74
619 650 6.773638 ACAAAGAAGATGATTCCAGTAGTGT 58.226 36.000 0.00 0.00 0.00 3.55
620 651 6.652481 ACAAAGAAGATGATTCCAGTAGTGTG 59.348 38.462 0.00 0.00 0.00 3.82
621 652 6.365970 AAGAAGATGATTCCAGTAGTGTGT 57.634 37.500 0.00 0.00 0.00 3.72
622 653 5.728471 AGAAGATGATTCCAGTAGTGTGTG 58.272 41.667 0.00 0.00 0.00 3.82
623 654 5.247110 AGAAGATGATTCCAGTAGTGTGTGT 59.753 40.000 0.00 0.00 0.00 3.72
624 655 4.825422 AGATGATTCCAGTAGTGTGTGTG 58.175 43.478 0.00 0.00 0.00 3.82
625 656 4.284490 AGATGATTCCAGTAGTGTGTGTGT 59.716 41.667 0.00 0.00 0.00 3.72
626 657 3.727726 TGATTCCAGTAGTGTGTGTGTG 58.272 45.455 0.00 0.00 0.00 3.82
627 658 1.948104 TTCCAGTAGTGTGTGTGTGC 58.052 50.000 0.00 0.00 0.00 4.57
628 659 0.249280 TCCAGTAGTGTGTGTGTGCG 60.249 55.000 0.00 0.00 0.00 5.34
629 660 1.564622 CAGTAGTGTGTGTGTGCGC 59.435 57.895 0.00 0.00 0.00 6.09
630 661 1.949133 AGTAGTGTGTGTGTGCGCG 60.949 57.895 0.00 0.00 0.00 6.86
631 662 3.334751 TAGTGTGTGTGTGCGCGC 61.335 61.111 27.26 27.26 36.27 6.86
645 676 3.871574 GCGCGCGTCTCTCTCTCT 61.872 66.667 32.35 0.00 0.00 3.10
646 677 2.323105 CGCGCGTCTCTCTCTCTC 59.677 66.667 24.19 0.00 0.00 3.20
647 678 2.171079 CGCGCGTCTCTCTCTCTCT 61.171 63.158 24.19 0.00 0.00 3.10
648 679 1.641677 GCGCGTCTCTCTCTCTCTC 59.358 63.158 8.43 0.00 0.00 3.20
649 680 0.810031 GCGCGTCTCTCTCTCTCTCT 60.810 60.000 8.43 0.00 0.00 3.10
650 681 1.537348 GCGCGTCTCTCTCTCTCTCTA 60.537 57.143 8.43 0.00 0.00 2.43
651 682 2.866460 GCGCGTCTCTCTCTCTCTCTAT 60.866 54.545 8.43 0.00 0.00 1.98
652 683 3.613193 GCGCGTCTCTCTCTCTCTCTATA 60.613 52.174 8.43 0.00 0.00 1.31
653 684 4.744570 CGCGTCTCTCTCTCTCTCTATAT 58.255 47.826 0.00 0.00 0.00 0.86
654 685 5.677852 GCGCGTCTCTCTCTCTCTCTATATA 60.678 48.000 8.43 0.00 0.00 0.86
655 686 6.504398 CGCGTCTCTCTCTCTCTCTATATAT 58.496 44.000 0.00 0.00 0.00 0.86
656 687 7.645402 CGCGTCTCTCTCTCTCTCTATATATA 58.355 42.308 0.00 0.00 0.00 0.86
657 688 8.297426 CGCGTCTCTCTCTCTCTCTATATATAT 58.703 40.741 0.00 0.00 0.00 0.86
727 758 5.888412 GTGTAAACACAAATTTCCTGCTG 57.112 39.130 8.35 0.00 45.75 4.41
728 759 5.587289 GTGTAAACACAAATTTCCTGCTGA 58.413 37.500 8.35 0.00 45.75 4.26
729 760 5.458779 GTGTAAACACAAATTTCCTGCTGAC 59.541 40.000 8.35 0.00 45.75 3.51
730 761 5.359576 TGTAAACACAAATTTCCTGCTGACT 59.640 36.000 0.00 0.00 0.00 3.41
731 762 5.343307 AAACACAAATTTCCTGCTGACTT 57.657 34.783 0.00 0.00 0.00 3.01
732 763 5.343307 AACACAAATTTCCTGCTGACTTT 57.657 34.783 0.00 0.00 0.00 2.66
733 764 4.685924 ACACAAATTTCCTGCTGACTTTG 58.314 39.130 0.00 1.76 34.38 2.77
734 765 4.402155 ACACAAATTTCCTGCTGACTTTGA 59.598 37.500 13.25 0.00 33.29 2.69
735 766 4.980434 CACAAATTTCCTGCTGACTTTGAG 59.020 41.667 13.25 6.29 33.29 3.02
736 767 4.646492 ACAAATTTCCTGCTGACTTTGAGT 59.354 37.500 13.25 0.00 33.29 3.41
737 768 5.127682 ACAAATTTCCTGCTGACTTTGAGTT 59.872 36.000 13.25 0.00 33.29 3.01
738 769 6.321181 ACAAATTTCCTGCTGACTTTGAGTTA 59.679 34.615 13.25 0.00 33.29 2.24
739 770 7.014615 ACAAATTTCCTGCTGACTTTGAGTTAT 59.985 33.333 13.25 0.00 33.29 1.89
740 771 7.530426 AATTTCCTGCTGACTTTGAGTTATT 57.470 32.000 0.00 0.00 0.00 1.40
741 772 6.560253 TTTCCTGCTGACTTTGAGTTATTC 57.440 37.500 0.00 0.00 0.00 1.75
742 773 4.579869 TCCTGCTGACTTTGAGTTATTCC 58.420 43.478 0.00 0.00 0.00 3.01
743 774 4.041567 TCCTGCTGACTTTGAGTTATTCCA 59.958 41.667 0.00 0.00 0.00 3.53
744 775 4.154918 CCTGCTGACTTTGAGTTATTCCAC 59.845 45.833 0.00 0.00 0.00 4.02
745 776 4.973168 TGCTGACTTTGAGTTATTCCACT 58.027 39.130 0.00 0.00 0.00 4.00
746 777 6.109156 TGCTGACTTTGAGTTATTCCACTA 57.891 37.500 0.00 0.00 0.00 2.74
747 778 6.530120 TGCTGACTTTGAGTTATTCCACTAA 58.470 36.000 0.00 0.00 0.00 2.24
748 779 6.995686 TGCTGACTTTGAGTTATTCCACTAAA 59.004 34.615 0.00 0.00 0.00 1.85
749 780 7.041372 TGCTGACTTTGAGTTATTCCACTAAAC 60.041 37.037 0.00 0.00 0.00 2.01
750 781 7.573283 GCTGACTTTGAGTTATTCCACTAAACC 60.573 40.741 0.00 0.00 0.00 3.27
751 782 7.284074 TGACTTTGAGTTATTCCACTAAACCA 58.716 34.615 0.00 0.00 0.00 3.67
752 783 7.942341 TGACTTTGAGTTATTCCACTAAACCAT 59.058 33.333 0.00 0.00 0.00 3.55
753 784 9.444600 GACTTTGAGTTATTCCACTAAACCATA 57.555 33.333 0.00 0.00 0.00 2.74
754 785 9.975218 ACTTTGAGTTATTCCACTAAACCATAT 57.025 29.630 0.00 0.00 0.00 1.78
756 787 9.967451 TTTGAGTTATTCCACTAAACCATATGA 57.033 29.630 3.65 0.00 0.00 2.15
757 788 9.613428 TTGAGTTATTCCACTAAACCATATGAG 57.387 33.333 3.65 0.00 0.00 2.90
758 789 8.988060 TGAGTTATTCCACTAAACCATATGAGA 58.012 33.333 3.65 0.00 0.00 3.27
759 790 9.482627 GAGTTATTCCACTAAACCATATGAGAG 57.517 37.037 3.65 0.00 0.00 3.20
760 791 9.213777 AGTTATTCCACTAAACCATATGAGAGA 57.786 33.333 3.65 0.00 0.00 3.10
761 792 9.832445 GTTATTCCACTAAACCATATGAGAGAA 57.168 33.333 3.65 3.64 0.00 2.87
763 794 8.970859 ATTCCACTAAACCATATGAGAGAAAG 57.029 34.615 3.65 0.00 0.00 2.62
764 795 6.889198 TCCACTAAACCATATGAGAGAAAGG 58.111 40.000 3.65 0.00 0.00 3.11
765 796 6.058183 CCACTAAACCATATGAGAGAAAGGG 58.942 44.000 3.65 0.00 0.00 3.95
766 797 6.353082 CCACTAAACCATATGAGAGAAAGGGT 60.353 42.308 3.65 0.00 0.00 4.34
767 798 6.540189 CACTAAACCATATGAGAGAAAGGGTG 59.460 42.308 3.65 0.00 0.00 4.61
768 799 5.520748 AAACCATATGAGAGAAAGGGTGT 57.479 39.130 3.65 0.00 0.00 4.16
769 800 6.636454 AAACCATATGAGAGAAAGGGTGTA 57.364 37.500 3.65 0.00 0.00 2.90
770 801 6.831664 AACCATATGAGAGAAAGGGTGTAT 57.168 37.500 3.65 0.00 0.00 2.29
771 802 7.931015 AACCATATGAGAGAAAGGGTGTATA 57.069 36.000 3.65 0.00 0.00 1.47
772 803 7.546250 ACCATATGAGAGAAAGGGTGTATAG 57.454 40.000 3.65 0.00 0.00 1.31
773 804 7.306013 ACCATATGAGAGAAAGGGTGTATAGA 58.694 38.462 3.65 0.00 0.00 1.98
774 805 7.453126 ACCATATGAGAGAAAGGGTGTATAGAG 59.547 40.741 3.65 0.00 0.00 2.43
775 806 7.671819 CCATATGAGAGAAAGGGTGTATAGAGA 59.328 40.741 3.65 0.00 0.00 3.10
776 807 9.083422 CATATGAGAGAAAGGGTGTATAGAGAA 57.917 37.037 0.00 0.00 0.00 2.87
777 808 7.979786 ATGAGAGAAAGGGTGTATAGAGAAA 57.020 36.000 0.00 0.00 0.00 2.52
778 809 7.792364 TGAGAGAAAGGGTGTATAGAGAAAA 57.208 36.000 0.00 0.00 0.00 2.29
779 810 7.612677 TGAGAGAAAGGGTGTATAGAGAAAAC 58.387 38.462 0.00 0.00 0.00 2.43
780 811 6.948589 AGAGAAAGGGTGTATAGAGAAAACC 58.051 40.000 0.00 0.00 0.00 3.27
781 812 6.500751 AGAGAAAGGGTGTATAGAGAAAACCA 59.499 38.462 0.00 0.00 32.28 3.67
782 813 7.182930 AGAGAAAGGGTGTATAGAGAAAACCAT 59.817 37.037 0.00 0.00 32.28 3.55
783 814 8.388656 AGAAAGGGTGTATAGAGAAAACCATA 57.611 34.615 0.00 0.00 32.28 2.74
784 815 9.004231 AGAAAGGGTGTATAGAGAAAACCATAT 57.996 33.333 0.00 0.00 32.28 1.78
845 876 7.446106 AGGGTGGTTCTATTATGATAACACA 57.554 36.000 0.00 0.00 0.00 3.72
901 932 4.657436 ATTCTGATAACACCTCTCCGAC 57.343 45.455 0.00 0.00 0.00 4.79
907 938 2.702592 AACACCTCTCCGACAAAACA 57.297 45.000 0.00 0.00 0.00 2.83
963 994 3.503839 TTCCCCACCACCACCACC 61.504 66.667 0.00 0.00 0.00 4.61
1001 1033 2.603008 CTTCGCCCCCATTCCCAT 59.397 61.111 0.00 0.00 0.00 4.00
1025 1058 2.230653 CCACCACTCCACCCATCCA 61.231 63.158 0.00 0.00 0.00 3.41
1045 1078 3.053291 GCGTCACCATCCGCCAAA 61.053 61.111 0.00 0.00 43.96 3.28
1046 1079 2.406616 GCGTCACCATCCGCCAAAT 61.407 57.895 0.00 0.00 43.96 2.32
1047 1080 1.933115 GCGTCACCATCCGCCAAATT 61.933 55.000 0.00 0.00 43.96 1.82
1048 1081 0.098728 CGTCACCATCCGCCAAATTC 59.901 55.000 0.00 0.00 0.00 2.17
1049 1082 1.173043 GTCACCATCCGCCAAATTCA 58.827 50.000 0.00 0.00 0.00 2.57
1050 1083 1.750778 GTCACCATCCGCCAAATTCAT 59.249 47.619 0.00 0.00 0.00 2.57
1051 1084 2.023673 TCACCATCCGCCAAATTCATC 58.976 47.619 0.00 0.00 0.00 2.92
1052 1085 1.067516 CACCATCCGCCAAATTCATCC 59.932 52.381 0.00 0.00 0.00 3.51
1053 1086 0.311790 CCATCCGCCAAATTCATCCG 59.688 55.000 0.00 0.00 0.00 4.18
1054 1087 0.311790 CATCCGCCAAATTCATCCGG 59.688 55.000 0.00 0.00 40.25 5.14
1055 1088 1.455383 ATCCGCCAAATTCATCCGGC 61.455 55.000 0.00 0.00 41.30 6.13
1057 1090 2.278792 GCCAAATTCATCCGGCGC 60.279 61.111 0.00 0.00 34.26 6.53
1058 1091 2.024588 CCAAATTCATCCGGCGCG 59.975 61.111 0.00 0.00 0.00 6.86
1059 1092 2.651863 CAAATTCATCCGGCGCGC 60.652 61.111 25.94 25.94 0.00 6.86
1060 1093 3.887868 AAATTCATCCGGCGCGCC 61.888 61.111 39.82 39.82 0.00 6.53
1074 1107 4.767255 CGCCACCACCTCCTGCTC 62.767 72.222 0.00 0.00 0.00 4.26
1075 1108 4.416738 GCCACCACCTCCTGCTCC 62.417 72.222 0.00 0.00 0.00 4.70
1076 1109 3.721706 CCACCACCTCCTGCTCCC 61.722 72.222 0.00 0.00 0.00 4.30
1077 1110 4.087892 CACCACCTCCTGCTCCCG 62.088 72.222 0.00 0.00 0.00 5.14
1121 1424 0.981943 CGTACCACCTTCTTCCCCTT 59.018 55.000 0.00 0.00 0.00 3.95
1128 1431 1.685820 CTTCTTCCCCTTCCCGCTT 59.314 57.895 0.00 0.00 0.00 4.68
1418 1729 4.528039 CCCCCATCCCGCTGCATT 62.528 66.667 0.00 0.00 0.00 3.56
1421 1732 1.152984 CCCATCCCGCTGCATTGTA 60.153 57.895 0.00 0.00 0.00 2.41
1457 1768 3.361174 CGACCACGGCCCAAAATT 58.639 55.556 0.00 0.00 35.72 1.82
1561 1872 1.084084 CCCTTACCTTCCCCCTCCA 59.916 63.158 0.00 0.00 0.00 3.86
1602 1913 1.361668 CCATCAACGGCGAGGTCAAG 61.362 60.000 16.62 0.00 0.00 3.02
1609 1920 4.388499 GCGAGGTCAAGGGCCGAA 62.388 66.667 0.00 0.00 0.00 4.30
1737 2063 3.201494 CCATCGACGGCAGACTCT 58.799 61.111 0.00 0.00 0.00 3.24
1746 2072 2.125753 GCAGACTCTGGCGACCTG 60.126 66.667 8.17 0.00 31.21 4.00
1749 2075 0.179116 CAGACTCTGGCGACCTGATG 60.179 60.000 0.00 4.37 31.33 3.07
1787 2113 3.560251 ACTTCCAGCGGTGCCACT 61.560 61.111 9.63 0.00 0.00 4.00
2013 2341 1.003839 GTTGCAGTCCATCCCACGA 60.004 57.895 0.00 0.00 0.00 4.35
2080 2409 2.398588 CCCTGGATCTAACTGCCACTA 58.601 52.381 0.00 0.00 0.00 2.74
2174 2505 3.243704 GCTTGCATTTTACTTGGTGTGGA 60.244 43.478 0.00 0.00 0.00 4.02
2301 2642 6.144241 TGTTTGTGTGTGTCGTGTGTATATAC 59.856 38.462 5.89 5.89 0.00 1.47
2518 2868 0.379316 GTTTGTCAACCCCACACGTC 59.621 55.000 0.00 0.00 0.00 4.34
2519 2869 0.253610 TTTGTCAACCCCACACGTCT 59.746 50.000 0.00 0.00 0.00 4.18
2529 2879 2.268298 CCCACACGTCTAGTACATTGC 58.732 52.381 0.00 0.00 0.00 3.56
2686 3064 8.386606 TGTTGTTCATTTCATAAGTGCAAAAAC 58.613 29.630 0.00 0.00 0.00 2.43
2732 3163 8.891928 CGACAAAATAGTAATGTTGTTCACTTG 58.108 33.333 0.00 0.00 42.51 3.16
2750 3181 2.676632 TGTCCATACGTTTGCGGTAT 57.323 45.000 0.00 0.00 43.45 2.73
2844 3276 4.812476 CGCTTGCCCGTCCGATGA 62.812 66.667 0.00 0.00 0.00 2.92
2910 3342 3.417101 TGTTCATCCCGTAAGTGCAAAT 58.583 40.909 0.00 0.00 0.00 2.32
2938 3372 6.854496 TGTTACAGAAGCGAAACAAAGTAT 57.146 33.333 0.00 0.00 0.00 2.12
3011 3445 3.321111 TGCACTCTACTTTCTCGTCCTTT 59.679 43.478 0.00 0.00 0.00 3.11
3115 3552 4.999950 CAGTTTTCAGCCAGATGAAGTACT 59.000 41.667 8.69 8.69 40.16 2.73
3134 3571 3.831323 ACTCATGTTGATTTGGGTGTCA 58.169 40.909 0.00 0.00 0.00 3.58
3149 3588 2.676342 GGTGTCACGAAAAACAGTGTCT 59.324 45.455 0.00 0.00 39.25 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.650283 AGAGGAAGAGGAAGAAGAAGAAGA 58.350 41.667 0.00 0.00 0.00 2.87
5 6 6.358974 AAGAGGAAGAGGAAGAAGAAGAAG 57.641 41.667 0.00 0.00 0.00 2.85
6 7 5.247337 GGAAGAGGAAGAGGAAGAAGAAGAA 59.753 44.000 0.00 0.00 0.00 2.52
8 9 4.777366 AGGAAGAGGAAGAGGAAGAAGAAG 59.223 45.833 0.00 0.00 0.00 2.85
11 12 4.352893 AGAGGAAGAGGAAGAGGAAGAAG 58.647 47.826 0.00 0.00 0.00 2.85
12 13 4.412060 AGAGGAAGAGGAAGAGGAAGAA 57.588 45.455 0.00 0.00 0.00 2.52
13 14 4.349365 GAAGAGGAAGAGGAAGAGGAAGA 58.651 47.826 0.00 0.00 0.00 2.87
14 15 3.450817 GGAAGAGGAAGAGGAAGAGGAAG 59.549 52.174 0.00 0.00 0.00 3.46
15 16 3.078305 AGGAAGAGGAAGAGGAAGAGGAA 59.922 47.826 0.00 0.00 0.00 3.36
16 17 2.657459 AGGAAGAGGAAGAGGAAGAGGA 59.343 50.000 0.00 0.00 0.00 3.71
17 18 3.031013 GAGGAAGAGGAAGAGGAAGAGG 58.969 54.545 0.00 0.00 0.00 3.69
18 19 3.981212 AGAGGAAGAGGAAGAGGAAGAG 58.019 50.000 0.00 0.00 0.00 2.85
19 20 4.349365 GAAGAGGAAGAGGAAGAGGAAGA 58.651 47.826 0.00 0.00 0.00 2.87
20 21 3.450817 GGAAGAGGAAGAGGAAGAGGAAG 59.549 52.174 0.00 0.00 0.00 3.46
21 22 3.078305 AGGAAGAGGAAGAGGAAGAGGAA 59.922 47.826 0.00 0.00 0.00 3.36
22 23 2.657459 AGGAAGAGGAAGAGGAAGAGGA 59.343 50.000 0.00 0.00 0.00 3.71
23 24 3.031013 GAGGAAGAGGAAGAGGAAGAGG 58.969 54.545 0.00 0.00 0.00 3.69
24 25 3.981212 AGAGGAAGAGGAAGAGGAAGAG 58.019 50.000 0.00 0.00 0.00 2.85
25 26 4.349365 GAAGAGGAAGAGGAAGAGGAAGA 58.651 47.826 0.00 0.00 0.00 2.87
26 27 3.450817 GGAAGAGGAAGAGGAAGAGGAAG 59.549 52.174 0.00 0.00 0.00 3.46
27 28 3.078305 AGGAAGAGGAAGAGGAAGAGGAA 59.922 47.826 0.00 0.00 0.00 3.36
28 29 2.657459 AGGAAGAGGAAGAGGAAGAGGA 59.343 50.000 0.00 0.00 0.00 3.71
29 30 3.031013 GAGGAAGAGGAAGAGGAAGAGG 58.969 54.545 0.00 0.00 0.00 3.69
30 31 3.981212 AGAGGAAGAGGAAGAGGAAGAG 58.019 50.000 0.00 0.00 0.00 2.85
31 32 4.349365 GAAGAGGAAGAGGAAGAGGAAGA 58.651 47.826 0.00 0.00 0.00 2.87
32 33 3.450817 GGAAGAGGAAGAGGAAGAGGAAG 59.549 52.174 0.00 0.00 0.00 3.46
33 34 3.078305 AGGAAGAGGAAGAGGAAGAGGAA 59.922 47.826 0.00 0.00 0.00 3.36
34 35 2.657459 AGGAAGAGGAAGAGGAAGAGGA 59.343 50.000 0.00 0.00 0.00 3.71
35 36 3.031013 GAGGAAGAGGAAGAGGAAGAGG 58.969 54.545 0.00 0.00 0.00 3.69
36 37 3.981212 AGAGGAAGAGGAAGAGGAAGAG 58.019 50.000 0.00 0.00 0.00 2.85
37 38 4.093011 CAAGAGGAAGAGGAAGAGGAAGA 58.907 47.826 0.00 0.00 0.00 2.87
38 39 3.837731 ACAAGAGGAAGAGGAAGAGGAAG 59.162 47.826 0.00 0.00 0.00 3.46
39 40 3.863086 ACAAGAGGAAGAGGAAGAGGAA 58.137 45.455 0.00 0.00 0.00 3.36
40 41 3.551635 ACAAGAGGAAGAGGAAGAGGA 57.448 47.619 0.00 0.00 0.00 3.71
41 42 3.307339 CCAACAAGAGGAAGAGGAAGAGG 60.307 52.174 0.00 0.00 0.00 3.69
42 43 3.580458 TCCAACAAGAGGAAGAGGAAGAG 59.420 47.826 0.00 0.00 30.71 2.85
43 44 3.587498 TCCAACAAGAGGAAGAGGAAGA 58.413 45.455 0.00 0.00 30.71 2.87
44 45 4.566426 ATCCAACAAGAGGAAGAGGAAG 57.434 45.455 0.00 0.00 38.93 3.46
45 46 5.324832 AAATCCAACAAGAGGAAGAGGAA 57.675 39.130 0.00 0.00 38.93 3.36
46 47 6.448369 TTAAATCCAACAAGAGGAAGAGGA 57.552 37.500 0.00 0.00 38.93 3.71
47 48 6.886459 TGATTAAATCCAACAAGAGGAAGAGG 59.114 38.462 0.00 0.00 38.93 3.69
48 49 7.928307 TGATTAAATCCAACAAGAGGAAGAG 57.072 36.000 0.00 0.00 38.93 2.85
49 50 8.704849 TTTGATTAAATCCAACAAGAGGAAGA 57.295 30.769 0.00 0.00 38.93 2.87
168 170 2.771943 CAAAGAGGCTACACATCCCCTA 59.228 50.000 0.00 0.00 0.00 3.53
254 256 1.282930 GGTCACTTTGTCGTCCGCTC 61.283 60.000 0.00 0.00 0.00 5.03
292 321 0.031314 AGCAGACGACATAGATGCCG 59.969 55.000 0.00 0.00 39.61 5.69
312 342 1.742768 GCCAGCTATACCGTCTGCT 59.257 57.895 0.00 0.00 36.04 4.24
374 404 2.449031 TTTGCCGTCCGCTGACTGAT 62.449 55.000 6.71 0.00 39.47 2.90
394 424 1.840224 TTAGGGGGTTAACGGCGCTT 61.840 55.000 6.90 3.13 0.00 4.68
477 507 3.719924 ACGGACGACAAAGATTGTGTTA 58.280 40.909 0.00 0.00 45.52 2.41
478 508 2.557317 ACGGACGACAAAGATTGTGTT 58.443 42.857 0.00 0.00 45.52 3.32
479 509 2.234300 ACGGACGACAAAGATTGTGT 57.766 45.000 0.00 0.00 45.52 3.72
490 520 0.432361 GCTTCGTACAAACGGACGAC 59.568 55.000 0.00 0.00 46.96 4.34
501 532 0.706729 CTTTGTCGTCCGCTTCGTAC 59.293 55.000 0.00 0.00 0.00 3.67
526 557 2.124060 TTGCCGTCAGCCAGCAAAA 61.124 52.632 0.00 0.00 43.14 2.44
547 578 0.391263 AGATTCCGGACGGCAAAGTC 60.391 55.000 1.83 0.00 40.25 3.01
548 579 0.673644 CAGATTCCGGACGGCAAAGT 60.674 55.000 1.83 0.00 34.68 2.66
549 580 0.673644 ACAGATTCCGGACGGCAAAG 60.674 55.000 1.83 0.00 34.68 2.77
550 581 0.953471 CACAGATTCCGGACGGCAAA 60.953 55.000 1.83 0.00 34.68 3.68
551 582 1.375396 CACAGATTCCGGACGGCAA 60.375 57.895 1.83 2.18 34.68 4.52
552 583 2.264480 CACAGATTCCGGACGGCA 59.736 61.111 1.83 0.00 34.68 5.69
553 584 3.195698 GCACAGATTCCGGACGGC 61.196 66.667 1.83 0.00 34.68 5.68
554 585 2.511600 GGCACAGATTCCGGACGG 60.512 66.667 1.83 3.96 0.00 4.79
555 586 0.673644 AAAGGCACAGATTCCGGACG 60.674 55.000 1.83 0.00 0.00 4.79
556 587 0.804989 CAAAGGCACAGATTCCGGAC 59.195 55.000 1.83 0.00 0.00 4.79
557 588 0.960364 GCAAAGGCACAGATTCCGGA 60.960 55.000 0.00 0.00 40.72 5.14
558 589 1.508088 GCAAAGGCACAGATTCCGG 59.492 57.895 0.00 0.00 40.72 5.14
559 590 1.508088 GGCAAAGGCACAGATTCCG 59.492 57.895 0.00 0.00 43.71 4.30
560 591 1.244019 ACGGCAAAGGCACAGATTCC 61.244 55.000 0.00 0.00 43.71 3.01
561 592 0.169009 GACGGCAAAGGCACAGATTC 59.831 55.000 0.00 0.00 43.71 2.52
562 593 1.244019 GGACGGCAAAGGCACAGATT 61.244 55.000 0.00 0.00 43.71 2.40
563 594 1.675641 GGACGGCAAAGGCACAGAT 60.676 57.895 0.00 0.00 43.71 2.90
564 595 2.281484 GGACGGCAAAGGCACAGA 60.281 61.111 0.00 0.00 43.71 3.41
565 596 3.726517 CGGACGGCAAAGGCACAG 61.727 66.667 0.00 0.00 43.71 3.66
582 613 3.039202 CTTTGTCGTCCGCCATGGC 62.039 63.158 27.67 27.67 37.80 4.40
583 614 0.953471 TTCTTTGTCGTCCGCCATGG 60.953 55.000 7.63 7.63 40.09 3.66
584 615 0.443869 CTTCTTTGTCGTCCGCCATG 59.556 55.000 0.00 0.00 0.00 3.66
585 616 0.320374 TCTTCTTTGTCGTCCGCCAT 59.680 50.000 0.00 0.00 0.00 4.40
586 617 0.320374 ATCTTCTTTGTCGTCCGCCA 59.680 50.000 0.00 0.00 0.00 5.69
587 618 0.721718 CATCTTCTTTGTCGTCCGCC 59.278 55.000 0.00 0.00 0.00 6.13
588 619 1.710013 TCATCTTCTTTGTCGTCCGC 58.290 50.000 0.00 0.00 0.00 5.54
589 620 3.307242 GGAATCATCTTCTTTGTCGTCCG 59.693 47.826 0.00 0.00 0.00 4.79
590 621 4.253685 TGGAATCATCTTCTTTGTCGTCC 58.746 43.478 0.00 0.00 0.00 4.79
591 622 4.932200 ACTGGAATCATCTTCTTTGTCGTC 59.068 41.667 0.00 0.00 0.00 4.20
592 623 4.899502 ACTGGAATCATCTTCTTTGTCGT 58.100 39.130 0.00 0.00 0.00 4.34
593 624 6.035435 CACTACTGGAATCATCTTCTTTGTCG 59.965 42.308 0.00 0.00 0.00 4.35
594 625 6.876257 ACACTACTGGAATCATCTTCTTTGTC 59.124 38.462 0.00 0.00 0.00 3.18
595 626 6.652481 CACACTACTGGAATCATCTTCTTTGT 59.348 38.462 0.00 0.00 0.00 2.83
596 627 6.652481 ACACACTACTGGAATCATCTTCTTTG 59.348 38.462 0.00 0.00 0.00 2.77
597 628 6.652481 CACACACTACTGGAATCATCTTCTTT 59.348 38.462 0.00 0.00 0.00 2.52
598 629 6.169094 CACACACTACTGGAATCATCTTCTT 58.831 40.000 0.00 0.00 0.00 2.52
599 630 5.247110 ACACACACTACTGGAATCATCTTCT 59.753 40.000 0.00 0.00 0.00 2.85
600 631 5.349817 CACACACACTACTGGAATCATCTTC 59.650 44.000 0.00 0.00 0.00 2.87
601 632 5.221722 ACACACACACTACTGGAATCATCTT 60.222 40.000 0.00 0.00 0.00 2.40
602 633 4.284490 ACACACACACTACTGGAATCATCT 59.716 41.667 0.00 0.00 0.00 2.90
603 634 4.389992 CACACACACACTACTGGAATCATC 59.610 45.833 0.00 0.00 0.00 2.92
604 635 4.318332 CACACACACACTACTGGAATCAT 58.682 43.478 0.00 0.00 0.00 2.45
605 636 3.727726 CACACACACACTACTGGAATCA 58.272 45.455 0.00 0.00 0.00 2.57
606 637 2.480419 GCACACACACACTACTGGAATC 59.520 50.000 0.00 0.00 0.00 2.52
607 638 2.494059 GCACACACACACTACTGGAAT 58.506 47.619 0.00 0.00 0.00 3.01
608 639 1.804746 CGCACACACACACTACTGGAA 60.805 52.381 0.00 0.00 0.00 3.53
609 640 0.249280 CGCACACACACACTACTGGA 60.249 55.000 0.00 0.00 0.00 3.86
610 641 1.831389 GCGCACACACACACTACTGG 61.831 60.000 0.30 0.00 0.00 4.00
611 642 1.564622 GCGCACACACACACTACTG 59.435 57.895 0.30 0.00 0.00 2.74
612 643 1.949133 CGCGCACACACACACTACT 60.949 57.895 8.75 0.00 0.00 2.57
613 644 2.544359 CGCGCACACACACACTAC 59.456 61.111 8.75 0.00 0.00 2.73
614 645 3.334751 GCGCGCACACACACACTA 61.335 61.111 29.10 0.00 0.00 2.74
628 659 3.783588 GAGAGAGAGAGACGCGCGC 62.784 68.421 32.58 23.91 0.00 6.86
629 660 2.089433 GAGAGAGAGAGAGACGCGCG 62.089 65.000 30.96 30.96 0.00 6.86
630 661 0.810031 AGAGAGAGAGAGAGACGCGC 60.810 60.000 5.73 0.00 0.00 6.86
631 662 2.502213 TAGAGAGAGAGAGAGACGCG 57.498 55.000 3.53 3.53 0.00 6.01
705 736 5.458779 GTCAGCAGGAAATTTGTGTTTACAC 59.541 40.000 6.07 6.07 46.59 2.90
706 737 5.359576 AGTCAGCAGGAAATTTGTGTTTACA 59.640 36.000 0.00 0.00 34.31 2.41
707 738 5.831997 AGTCAGCAGGAAATTTGTGTTTAC 58.168 37.500 0.00 0.00 0.00 2.01
708 739 6.463995 AAGTCAGCAGGAAATTTGTGTTTA 57.536 33.333 0.00 0.00 0.00 2.01
709 740 5.343307 AAGTCAGCAGGAAATTTGTGTTT 57.657 34.783 0.00 0.00 0.00 2.83
710 741 5.105392 TCAAAGTCAGCAGGAAATTTGTGTT 60.105 36.000 0.00 0.00 36.53 3.32
711 742 4.402155 TCAAAGTCAGCAGGAAATTTGTGT 59.598 37.500 0.00 0.00 36.53 3.72
712 743 4.935702 TCAAAGTCAGCAGGAAATTTGTG 58.064 39.130 0.00 0.00 36.53 3.33
713 744 4.646492 ACTCAAAGTCAGCAGGAAATTTGT 59.354 37.500 0.00 0.00 36.53 2.83
714 745 5.192327 ACTCAAAGTCAGCAGGAAATTTG 57.808 39.130 0.00 9.33 36.50 2.32
715 746 5.859205 AACTCAAAGTCAGCAGGAAATTT 57.141 34.783 0.00 0.00 0.00 1.82
716 747 7.309438 GGAATAACTCAAAGTCAGCAGGAAATT 60.309 37.037 0.00 0.00 0.00 1.82
717 748 6.151817 GGAATAACTCAAAGTCAGCAGGAAAT 59.848 38.462 0.00 0.00 0.00 2.17
718 749 5.473504 GGAATAACTCAAAGTCAGCAGGAAA 59.526 40.000 0.00 0.00 0.00 3.13
719 750 5.003804 GGAATAACTCAAAGTCAGCAGGAA 58.996 41.667 0.00 0.00 0.00 3.36
720 751 4.041567 TGGAATAACTCAAAGTCAGCAGGA 59.958 41.667 0.00 0.00 0.00 3.86
721 752 4.154918 GTGGAATAACTCAAAGTCAGCAGG 59.845 45.833 0.00 0.00 0.00 4.85
722 753 4.999950 AGTGGAATAACTCAAAGTCAGCAG 59.000 41.667 0.00 0.00 0.00 4.24
723 754 4.973168 AGTGGAATAACTCAAAGTCAGCA 58.027 39.130 0.00 0.00 0.00 4.41
724 755 7.298854 GTTTAGTGGAATAACTCAAAGTCAGC 58.701 38.462 0.00 0.00 0.00 4.26
725 756 7.444183 TGGTTTAGTGGAATAACTCAAAGTCAG 59.556 37.037 0.00 0.00 0.00 3.51
726 757 7.284074 TGGTTTAGTGGAATAACTCAAAGTCA 58.716 34.615 0.00 0.00 0.00 3.41
727 758 7.739498 TGGTTTAGTGGAATAACTCAAAGTC 57.261 36.000 0.00 0.00 0.00 3.01
728 759 9.975218 ATATGGTTTAGTGGAATAACTCAAAGT 57.025 29.630 0.00 0.00 0.00 2.66
730 761 9.967451 TCATATGGTTTAGTGGAATAACTCAAA 57.033 29.630 2.13 0.00 0.00 2.69
731 762 9.613428 CTCATATGGTTTAGTGGAATAACTCAA 57.387 33.333 2.13 0.00 0.00 3.02
732 763 8.988060 TCTCATATGGTTTAGTGGAATAACTCA 58.012 33.333 2.13 0.00 0.00 3.41
733 764 9.482627 CTCTCATATGGTTTAGTGGAATAACTC 57.517 37.037 2.13 0.00 0.00 3.01
734 765 9.213777 TCTCTCATATGGTTTAGTGGAATAACT 57.786 33.333 2.13 0.00 0.00 2.24
735 766 9.832445 TTCTCTCATATGGTTTAGTGGAATAAC 57.168 33.333 2.13 0.00 0.00 1.89
738 769 7.995488 CCTTTCTCTCATATGGTTTAGTGGAAT 59.005 37.037 2.13 0.00 0.00 3.01
739 770 7.338710 CCTTTCTCTCATATGGTTTAGTGGAA 58.661 38.462 2.13 0.88 0.00 3.53
740 771 6.126768 CCCTTTCTCTCATATGGTTTAGTGGA 60.127 42.308 2.13 0.00 0.00 4.02
741 772 6.058183 CCCTTTCTCTCATATGGTTTAGTGG 58.942 44.000 2.13 0.00 0.00 4.00
742 773 6.540189 CACCCTTTCTCTCATATGGTTTAGTG 59.460 42.308 2.13 0.00 0.00 2.74
743 774 6.215636 ACACCCTTTCTCTCATATGGTTTAGT 59.784 38.462 2.13 0.00 0.00 2.24
744 775 6.653989 ACACCCTTTCTCTCATATGGTTTAG 58.346 40.000 2.13 0.00 0.00 1.85
745 776 6.636454 ACACCCTTTCTCTCATATGGTTTA 57.364 37.500 2.13 0.00 0.00 2.01
746 777 5.520748 ACACCCTTTCTCTCATATGGTTT 57.479 39.130 2.13 0.00 0.00 3.27
747 778 6.831664 ATACACCCTTTCTCTCATATGGTT 57.168 37.500 2.13 0.00 0.00 3.67
748 779 7.306013 TCTATACACCCTTTCTCTCATATGGT 58.694 38.462 2.13 0.00 0.00 3.55
749 780 7.671819 TCTCTATACACCCTTTCTCTCATATGG 59.328 40.741 2.13 0.00 0.00 2.74
750 781 8.642935 TCTCTATACACCCTTTCTCTCATATG 57.357 38.462 0.00 0.00 0.00 1.78
751 782 9.661954 TTTCTCTATACACCCTTTCTCTCATAT 57.338 33.333 0.00 0.00 0.00 1.78
752 783 9.488762 TTTTCTCTATACACCCTTTCTCTCATA 57.511 33.333 0.00 0.00 0.00 2.15
753 784 7.979786 TTTCTCTATACACCCTTTCTCTCAT 57.020 36.000 0.00 0.00 0.00 2.90
754 785 7.310485 GGTTTTCTCTATACACCCTTTCTCTCA 60.310 40.741 0.00 0.00 0.00 3.27
755 786 7.042950 GGTTTTCTCTATACACCCTTTCTCTC 58.957 42.308 0.00 0.00 0.00 3.20
756 787 6.500751 TGGTTTTCTCTATACACCCTTTCTCT 59.499 38.462 0.00 0.00 0.00 3.10
757 788 6.708285 TGGTTTTCTCTATACACCCTTTCTC 58.292 40.000 0.00 0.00 0.00 2.87
758 789 6.697641 TGGTTTTCTCTATACACCCTTTCT 57.302 37.500 0.00 0.00 0.00 2.52
867 898 9.075678 GGTGTTATCAGAATAAGCTACCTAGTA 57.924 37.037 0.00 0.00 31.08 1.82
901 932 1.554595 CTGCGCGCAGTTTGTTTTG 59.445 52.632 44.44 23.10 39.10 2.44
975 1006 2.271173 GGGGCGAAGGGGTAGTTG 59.729 66.667 0.00 0.00 0.00 3.16
979 1010 2.286578 AATGGGGGCGAAGGGGTA 60.287 61.111 0.00 0.00 0.00 3.69
1021 1054 2.202932 GATGGTGACGCGCTGGAT 60.203 61.111 5.73 0.00 0.00 3.41
1040 1073 2.278792 GCGCCGGATGAATTTGGC 60.279 61.111 5.05 0.00 44.09 4.52
1041 1074 2.024588 CGCGCCGGATGAATTTGG 59.975 61.111 5.05 0.00 0.00 3.28
1042 1075 2.651863 GCGCGCCGGATGAATTTG 60.652 61.111 23.24 0.00 0.00 2.32
1043 1076 3.887868 GGCGCGCCGGATGAATTT 61.888 61.111 37.24 0.00 0.00 1.82
1057 1090 4.767255 GAGCAGGAGGTGGTGGCG 62.767 72.222 0.00 0.00 36.87 5.69
1058 1091 4.416738 GGAGCAGGAGGTGGTGGC 62.417 72.222 0.00 0.00 36.87 5.01
1059 1092 3.721706 GGGAGCAGGAGGTGGTGG 61.722 72.222 0.00 0.00 36.87 4.61
1060 1093 4.087892 CGGGAGCAGGAGGTGGTG 62.088 72.222 0.00 0.00 36.87 4.17
1208 1517 1.067416 GCGTGTGAGGATGGCGATA 59.933 57.895 0.00 0.00 0.00 2.92
1418 1729 1.203313 AGAGGAAGAAGCCCAGGTACA 60.203 52.381 0.00 0.00 0.00 2.90
1421 1732 0.912006 GGAGAGGAAGAAGCCCAGGT 60.912 60.000 0.00 0.00 0.00 4.00
1483 1794 0.689080 GGCCATGGACAGAGAGGAGA 60.689 60.000 18.40 0.00 0.00 3.71
1602 1913 3.373565 CAACCCAAGCTTCGGCCC 61.374 66.667 10.36 0.00 43.01 5.80
1609 1920 1.425066 TGATGAACTCCAACCCAAGCT 59.575 47.619 0.00 0.00 0.00 3.74
1904 2231 0.693767 CATGGGGGAGGAGAGAGCTT 60.694 60.000 0.00 0.00 0.00 3.74
2013 2341 0.736325 GCGATGCGTACTGAAGGTGT 60.736 55.000 0.00 0.00 0.00 4.16
2174 2505 1.203523 CGCAGCTAGAGAACCTTCTGT 59.796 52.381 0.00 0.00 37.73 3.41
2233 2564 2.693591 TCTCCCAGCCGAAGTGTATTAG 59.306 50.000 0.00 0.00 0.00 1.73
2301 2642 9.086336 TGCACATTAAAACAGAGAAAAAGAAAG 57.914 29.630 0.00 0.00 0.00 2.62
2387 2730 1.656587 TGGGGAGATAAGTGCACTGT 58.343 50.000 22.49 12.74 0.00 3.55
2518 2868 7.672351 TTTTCAACAAAACGCAATGTACTAG 57.328 32.000 0.00 0.00 0.00 2.57
2580 2932 6.936279 TGTGAAACAGGTATTTTTCCAAACA 58.064 32.000 0.00 0.00 45.67 2.83
2714 3144 7.329962 CGTATGGACAAGTGAACAACATTACTA 59.670 37.037 0.00 0.00 0.00 1.82
2716 3146 6.073440 ACGTATGGACAAGTGAACAACATTAC 60.073 38.462 0.00 0.00 0.00 1.89
2732 3163 3.709987 AGTATACCGCAAACGTATGGAC 58.290 45.455 0.00 0.00 37.70 4.02
2750 3181 0.107897 CTGCACACCGGGCATAAGTA 60.108 55.000 6.32 0.00 41.06 2.24
2822 3254 4.143333 GGACGGGCAAGCGAGCTA 62.143 66.667 0.00 0.00 34.17 3.32
2931 3365 4.749245 AGAAGTGAACCGCAATACTTTG 57.251 40.909 0.00 0.00 33.83 2.77
2938 3372 3.745975 CACTATCAAGAAGTGAACCGCAA 59.254 43.478 0.00 0.00 45.89 4.85
3115 3552 2.551887 CGTGACACCCAAATCAACATGA 59.448 45.455 0.00 0.00 0.00 3.07
3118 3555 2.333688 TCGTGACACCCAAATCAACA 57.666 45.000 0.00 0.00 0.00 3.33
3134 3571 4.351192 GAAATGCAGACACTGTTTTTCGT 58.649 39.130 0.00 0.00 33.43 3.85
3149 3588 7.158021 AGGAATTTTGAATTTACCGAAATGCA 58.842 30.769 0.00 0.00 38.60 3.96


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

AutoCloner maintained by Alex Coulton.