Multiple sequence alignment - TraesCS4D01G181200

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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 TraesCS4D01G181200 chr4D 100.000 8154 0 0 1 8154 316525633 316533786 0.000000e+00 15058.0
1 TraesCS4D01G181200 chr4D 98.462 65 1 0 6495 6559 316532063 316532127 1.860000e-21 115.0
2 TraesCS4D01G181200 chr4D 98.462 65 1 0 6431 6495 316532127 316532191 1.860000e-21 115.0
3 TraesCS4D01G181200 chr4B 97.139 6291 112 38 1888 8154 394104979 394111225 0.000000e+00 10558.0
4 TraesCS4D01G181200 chr4B 96.599 1088 27 6 648 1726 394103894 394104980 0.000000e+00 1796.0
5 TraesCS4D01G181200 chr4B 98.462 65 1 0 6495 6559 394109524 394109588 1.860000e-21 115.0
6 TraesCS4D01G181200 chr4B 98.462 65 1 0 6431 6495 394109588 394109652 1.860000e-21 115.0
7 TraesCS4D01G181200 chr4B 85.135 74 8 3 528 599 98700795 98700867 1.140000e-08 73.1
8 TraesCS4D01G181200 chr4A 97.537 3248 61 10 4916 8154 158185687 158182450 0.000000e+00 5537.0
9 TraesCS4D01G181200 chr4A 96.419 3044 71 16 1888 4917 158188831 158185812 0.000000e+00 4983.0
10 TraesCS4D01G181200 chr4A 94.206 1260 49 8 482 1726 158190080 158188830 0.000000e+00 1901.0
11 TraesCS4D01G181200 chr4A 90.023 441 34 6 1 437 158190525 158190091 5.530000e-156 562.0
12 TraesCS4D01G181200 chr4A 78.512 363 66 9 62 417 729107398 729107755 2.290000e-55 228.0
13 TraesCS4D01G181200 chr4A 96.923 65 2 0 6495 6559 158184169 158184105 8.650000e-20 110.0
14 TraesCS4D01G181200 chr4A 95.385 65 3 0 6431 6495 158184105 158184041 4.030000e-18 104.0
15 TraesCS4D01G181200 chr4A 81.982 111 18 2 4043 4152 542605670 542605779 8.710000e-15 93.5
16 TraesCS4D01G181200 chr7D 98.690 458 5 1 3719 4175 112768764 112769221 0.000000e+00 811.0
17 TraesCS4D01G181200 chr7D 75.740 338 68 13 16 347 594146614 594146285 3.050000e-34 158.0
18 TraesCS4D01G181200 chr7D 96.970 33 1 0 2171 2203 8604073 8604105 1.000000e-03 56.5
19 TraesCS4D01G181200 chr5D 96.491 171 6 0 1725 1895 60139909 60139739 4.820000e-72 283.0
20 TraesCS4D01G181200 chr3D 96.471 170 6 0 1724 1893 410304661 410304830 1.730000e-71 281.0
21 TraesCS4D01G181200 chr3D 96.450 169 5 1 1722 1889 95568345 95568177 2.240000e-70 278.0
22 TraesCS4D01G181200 chr3D 94.915 177 8 1 1718 1894 396430337 396430162 8.060000e-70 276.0
23 TraesCS4D01G181200 chr3D 91.623 191 14 2 1702 1892 6669738 6669550 6.280000e-66 263.0
24 TraesCS4D01G181200 chr2D 96.450 169 6 0 1724 1892 8930268 8930100 6.230000e-71 279.0
25 TraesCS4D01G181200 chr2D 75.000 408 72 25 16 417 87830014 87830397 2.360000e-35 161.0
26 TraesCS4D01G181200 chr3A 95.858 169 7 0 1725 1893 40915054 40914886 2.900000e-69 274.0
27 TraesCS4D01G181200 chr3A 90.984 122 5 2 8033 8154 543727213 543727098 8.470000e-35 159.0
28 TraesCS4D01G181200 chr3A 75.375 333 73 9 18 347 436455362 436455688 1.420000e-32 152.0
29 TraesCS4D01G181200 chr3A 74.474 333 80 5 8 336 743383941 743384272 1.100000e-28 139.0
30 TraesCS4D01G181200 chr2A 94.857 175 7 2 1715 1889 38600806 38600978 1.040000e-68 272.0
31 TraesCS4D01G181200 chr6D 87.500 216 22 5 1690 1905 218407179 218407389 2.270000e-60 244.0
32 TraesCS4D01G181200 chr6D 77.240 413 81 9 8 414 362869675 362870080 6.370000e-56 230.0
33 TraesCS4D01G181200 chr2B 77.163 416 65 19 9 417 67211184 67211576 1.780000e-51 215.0
34 TraesCS4D01G181200 chr2B 91.111 45 4 0 534 578 182018447 182018491 2.460000e-05 62.1
35 TraesCS4D01G181200 chr3B 78.198 344 65 9 8 347 43564467 43564804 2.310000e-50 211.0
36 TraesCS4D01G181200 chr3B 79.545 308 49 12 130 430 738756759 738756459 2.980000e-49 207.0
37 TraesCS4D01G181200 chr3B 77.907 344 66 9 8 347 43570740 43571077 1.070000e-48 206.0
38 TraesCS4D01G181200 chr1A 79.832 238 37 8 185 417 490780530 490780761 6.550000e-36 163.0
39 TraesCS4D01G181200 chr1B 88.462 52 4 2 552 603 668763933 668763884 2.460000e-05 62.1
40 TraesCS4D01G181200 chr7A 96.970 33 1 0 2159 2191 156565693 156565661 1.000000e-03 56.5


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 TraesCS4D01G181200 chr4D 316525633 316533786 8153 False 5096.0 15058 98.974667 1 8154 3 chr4D.!!$F1 8153
1 TraesCS4D01G181200 chr4B 394103894 394111225 7331 False 3146.0 10558 97.665500 648 8154 4 chr4B.!!$F2 7506
2 TraesCS4D01G181200 chr4A 158182450 158190525 8075 True 2199.5 5537 95.082167 1 8154 6 chr4A.!!$R1 8153

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
121 125 0.175073 ATCCCAACGGTTCGTCTAGC 59.825 55.000 0.00 0.0 39.99 3.42 F
474 478 0.249398 AAAGTAGCTACCCTGCCACG 59.751 55.000 20.31 0.0 30.24 4.94 F
516 520 0.252197 GCCTCATACCGTGTCCCTTT 59.748 55.000 0.00 0.0 0.00 3.11 F
652 656 0.445436 CTTGCTCAGCGAACATCACC 59.555 55.000 0.00 0.0 0.00 4.02 F
937 958 0.898326 AAACCCAGCACGAAATCCCC 60.898 55.000 0.00 0.0 0.00 4.81 F
1739 1760 3.181426 TGCTATATACTCCCTCCGTTCCA 60.181 47.826 0.00 0.0 0.00 3.53 F
2557 2582 0.183492 TTTGGGCTTGAGTGCAGTCT 59.817 50.000 21.79 0.0 34.04 3.24 F
3354 3379 0.951558 AAATGTCACGGAAGGCACAC 59.048 50.000 0.00 0.0 30.81 3.82 F
4073 4107 0.667993 CCGTGCCTGAAAAGAAAGCA 59.332 50.000 0.00 0.0 0.00 3.91 F
4265 4304 2.490903 GCACAGAGGGAGTACGAAGTTA 59.509 50.000 0.00 0.0 37.78 2.24 F
5098 5268 3.733224 CGAGCGATTTCTGGAAGTATCTG 59.267 47.826 0.00 0.0 33.76 2.90 F
6119 6291 2.644798 AGGAAACCTACAACCAGCTCAT 59.355 45.455 0.00 0.0 28.47 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1590 0.097150 TCTTCACGATGTCGCTCTCG 59.903 55.000 1.77 0.00 44.43 4.04 R
1871 1892 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30 R
1872 1893 0.549950 ATCTACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55 R
1873 1894 0.669077 CATCTACTCCCTCCGTTCCG 59.331 60.000 0.00 0.00 0.00 4.30 R
1874 1895 1.777941 ACATCTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62 R
3232 3257 0.178068 TCGGCAGCTACAGGGAATTC 59.822 55.000 0.00 0.00 0.00 2.17 R
4042 4076 0.556747 AGGCACGGAGGGAGTACTAT 59.443 55.000 0.00 0.00 0.00 2.12 R
4265 4304 0.820871 GCTCCGAATCTCAGTGACCT 59.179 55.000 0.00 0.00 0.00 3.85 R
5632 5802 4.202567 CCCATAAGGCCATAACTACCACAT 60.203 45.833 5.01 0.00 0.00 3.21 R
5723 5895 7.359595 GCATATACAAAGTGAAGTGTCAAACA 58.640 34.615 0.00 0.00 34.87 2.83 R
6657 6836 5.527951 TGCAAGCAACAACGAAAATCTTAT 58.472 33.333 0.00 0.00 0.00 1.73 R
7443 7623 1.006571 TGTCAGAGTCCGCGGTTTC 60.007 57.895 27.15 22.49 0.00 2.78 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
38 42 5.901552 AGTTTGTTTATGGTTTGTGTCCTG 58.098 37.500 0.00 0.00 0.00 3.86
88 92 7.635971 GCTCCCTGAGATGAAATAAGGTTCTTA 60.636 40.741 0.00 0.00 0.00 2.10
102 106 0.252974 TTCTTACAGCCTAGCCCCCA 60.253 55.000 0.00 0.00 0.00 4.96
106 110 2.983706 TACAGCCTAGCCCCCATCCC 62.984 65.000 0.00 0.00 0.00 3.85
110 114 2.510906 CTAGCCCCCATCCCAACG 59.489 66.667 0.00 0.00 0.00 4.10
111 115 3.093835 TAGCCCCCATCCCAACGG 61.094 66.667 0.00 0.00 0.00 4.44
113 117 4.376170 GCCCCCATCCCAACGGTT 62.376 66.667 0.00 0.00 0.00 4.44
121 125 0.175073 ATCCCAACGGTTCGTCTAGC 59.825 55.000 0.00 0.00 39.99 3.42
164 168 4.162690 GCCTCCGGCGGATCTTGT 62.163 66.667 31.23 0.00 39.62 3.16
183 187 2.227194 GTGGGATTCAGTCGGTGTTTT 58.773 47.619 0.00 0.00 0.00 2.43
196 200 1.335810 GGTGTTTTTCTTCGGTGGACC 59.664 52.381 0.00 0.00 0.00 4.46
202 206 0.250295 TTCTTCGGTGGACCTGCTTG 60.250 55.000 0.00 0.00 0.00 4.01
210 214 1.299976 GGACCTGCTTGGATTCGGT 59.700 57.895 3.40 0.00 39.71 4.69
212 216 1.079127 ACCTGCTTGGATTCGGTCG 60.079 57.895 3.40 0.00 39.71 4.79
213 217 1.079127 CCTGCTTGGATTCGGTCGT 60.079 57.895 0.00 0.00 38.35 4.34
214 218 1.084370 CCTGCTTGGATTCGGTCGTC 61.084 60.000 0.00 0.00 38.35 4.20
222 226 0.632241 GATTCGGTCGTCGTTCGTTC 59.368 55.000 9.04 5.48 40.80 3.95
241 245 4.442705 GTTCGTGTTCGTGTTTCTACATG 58.557 43.478 0.00 0.00 41.69 3.21
246 250 4.271533 GTGTTCGTGTTTCTACATGTTGGA 59.728 41.667 2.30 0.00 41.20 3.53
247 251 5.049680 GTGTTCGTGTTTCTACATGTTGGAT 60.050 40.000 2.30 0.00 41.20 3.41
248 252 5.178623 TGTTCGTGTTTCTACATGTTGGATC 59.821 40.000 2.30 0.00 41.20 3.36
249 253 4.250464 TCGTGTTTCTACATGTTGGATCC 58.750 43.478 2.30 4.20 41.20 3.36
250 254 4.020573 TCGTGTTTCTACATGTTGGATCCT 60.021 41.667 14.23 0.00 41.20 3.24
257 261 5.601662 TCTACATGTTGGATCCTTTCGATC 58.398 41.667 14.23 0.00 45.91 3.69
267 271 5.044558 GGATCCTTTCGATCTACACTTCAC 58.955 45.833 3.84 0.00 45.90 3.18
272 276 6.071334 TCCTTTCGATCTACACTTCACTTCAT 60.071 38.462 0.00 0.00 0.00 2.57
312 316 1.832167 TGTGCTGGTCTTTTGGGGC 60.832 57.895 0.00 0.00 0.00 5.80
329 333 1.019805 GGCCTTAGCACGGTGACTTC 61.020 60.000 13.29 0.00 42.56 3.01
332 336 1.673033 CCTTAGCACGGTGACTTCCTG 60.673 57.143 13.29 1.05 0.00 3.86
355 359 5.926542 TGACTGTCTACTACAATGTTTGCTC 59.073 40.000 9.51 0.00 37.74 4.26
362 366 3.990469 ACTACAATGTTTGCTCGACTCTG 59.010 43.478 0.00 0.00 0.00 3.35
369 373 3.190874 GTTTGCTCGACTCTGATAAGGG 58.809 50.000 0.00 0.00 0.00 3.95
382 386 4.755629 TCTGATAAGGGAGAGACGATAACG 59.244 45.833 0.00 0.00 45.75 3.18
384 388 4.514441 TGATAAGGGAGAGACGATAACGAC 59.486 45.833 0.00 0.00 42.66 4.34
406 410 2.126463 CGACTTCGGCTCGCTCAA 60.126 61.111 0.00 0.00 35.37 3.02
443 447 2.042095 TAGGCAGGGCTGGGCTAA 59.958 61.111 5.52 0.00 40.03 3.09
444 448 2.375345 TAGGCAGGGCTGGGCTAAC 61.375 63.158 5.52 0.00 40.03 2.34
445 449 4.047125 GGCAGGGCTGGGCTAACA 62.047 66.667 0.00 0.00 0.00 2.41
446 450 2.035626 GCAGGGCTGGGCTAACAA 59.964 61.111 0.00 0.00 0.00 2.83
447 451 2.343426 GCAGGGCTGGGCTAACAAC 61.343 63.158 0.00 0.00 0.00 3.32
448 452 1.678970 CAGGGCTGGGCTAACAACC 60.679 63.158 0.00 0.00 0.00 3.77
449 453 1.852626 AGGGCTGGGCTAACAACCT 60.853 57.895 0.00 0.00 0.00 3.50
450 454 1.378646 GGGCTGGGCTAACAACCTC 60.379 63.158 0.00 0.00 0.00 3.85
451 455 1.685820 GGCTGGGCTAACAACCTCT 59.314 57.895 0.00 0.00 0.00 3.69
452 456 0.678048 GGCTGGGCTAACAACCTCTG 60.678 60.000 0.00 0.00 0.00 3.35
453 457 1.308783 GCTGGGCTAACAACCTCTGC 61.309 60.000 0.00 0.00 0.00 4.26
454 458 0.326264 CTGGGCTAACAACCTCTGCT 59.674 55.000 0.00 0.00 0.00 4.24
455 459 1.555075 CTGGGCTAACAACCTCTGCTA 59.445 52.381 0.00 0.00 0.00 3.49
456 460 1.982226 TGGGCTAACAACCTCTGCTAA 59.018 47.619 0.00 0.00 0.00 3.09
457 461 2.373836 TGGGCTAACAACCTCTGCTAAA 59.626 45.455 0.00 0.00 0.00 1.85
458 462 3.010420 GGGCTAACAACCTCTGCTAAAG 58.990 50.000 0.00 0.00 0.00 1.85
459 463 3.559384 GGGCTAACAACCTCTGCTAAAGT 60.559 47.826 0.00 0.00 0.00 2.66
460 464 4.323257 GGGCTAACAACCTCTGCTAAAGTA 60.323 45.833 0.00 0.00 0.00 2.24
461 465 4.870991 GGCTAACAACCTCTGCTAAAGTAG 59.129 45.833 0.00 0.00 0.00 2.57
473 477 3.180891 CTAAAGTAGCTACCCTGCCAC 57.819 52.381 20.31 0.00 0.00 5.01
474 478 0.249398 AAAGTAGCTACCCTGCCACG 59.751 55.000 20.31 0.00 30.24 4.94
475 479 1.614241 AAGTAGCTACCCTGCCACGG 61.614 60.000 20.31 0.00 30.24 4.94
476 480 2.038329 TAGCTACCCTGCCACGGT 59.962 61.111 0.00 0.00 37.40 4.83
477 481 2.056223 TAGCTACCCTGCCACGGTC 61.056 63.158 0.00 0.00 34.66 4.79
478 482 2.791613 TAGCTACCCTGCCACGGTCA 62.792 60.000 0.00 0.00 34.66 4.02
479 483 3.065306 CTACCCTGCCACGGTCAA 58.935 61.111 0.00 0.00 34.66 3.18
480 484 1.375523 CTACCCTGCCACGGTCAAC 60.376 63.158 0.00 0.00 34.66 3.18
507 511 2.502213 TTGTCATACGCCTCATACCG 57.498 50.000 0.00 0.00 0.00 4.02
516 520 0.252197 GCCTCATACCGTGTCCCTTT 59.748 55.000 0.00 0.00 0.00 3.11
517 521 1.742750 GCCTCATACCGTGTCCCTTTC 60.743 57.143 0.00 0.00 0.00 2.62
524 528 1.308069 CCGTGTCCCTTTCTGCATGG 61.308 60.000 0.00 0.00 0.00 3.66
528 532 2.473768 TCCCTTTCTGCATGGGACA 58.526 52.632 11.38 0.00 42.85 4.02
544 548 5.554437 TGGGACACTGTTTGTAGTTATCA 57.446 39.130 0.00 0.00 39.17 2.15
545 549 5.302360 TGGGACACTGTTTGTAGTTATCAC 58.698 41.667 0.00 0.00 39.17 3.06
546 550 5.071250 TGGGACACTGTTTGTAGTTATCACT 59.929 40.000 0.00 0.00 39.17 3.41
549 553 7.309621 GGGACACTGTTTGTAGTTATCACTAGA 60.310 40.741 0.00 0.00 39.17 2.43
552 556 8.035394 ACACTGTTTGTAGTTATCACTAGATGG 58.965 37.037 0.00 0.00 36.09 3.51
570 574 5.406163 AGATGGTCTATGGACATGGATGTA 58.594 41.667 11.67 0.00 43.77 2.29
584 588 9.382275 GGACATGGATGTAATTTTTATTGCTTT 57.618 29.630 0.00 0.00 41.95 3.51
643 647 2.030893 TGAATTTTGTCCTTGCTCAGCG 60.031 45.455 0.00 0.00 0.00 5.18
652 656 0.445436 CTTGCTCAGCGAACATCACC 59.555 55.000 0.00 0.00 0.00 4.02
664 675 6.306356 CAGCGAACATCACCAAATAGAAAAAG 59.694 38.462 0.00 0.00 0.00 2.27
746 758 1.451387 ACGAATTGGATCCGTGGCC 60.451 57.895 7.39 0.00 35.02 5.36
747 759 2.534019 CGAATTGGATCCGTGGCCG 61.534 63.158 7.39 3.21 0.00 6.13
761 773 2.497138 GTGGCCGGTGTTAAAGTTACT 58.503 47.619 1.90 0.00 0.00 2.24
802 818 3.939939 TGCCTGCTTCTGCACCGA 61.940 61.111 0.00 0.00 45.31 4.69
838 857 7.704899 GCGCCTATATTTTACACTTTCCAAAAT 59.295 33.333 0.00 0.00 36.25 1.82
937 958 0.898326 AAACCCAGCACGAAATCCCC 60.898 55.000 0.00 0.00 0.00 4.81
974 995 3.677424 CGATCGAAGCTTTTCTTCCTCCT 60.677 47.826 10.26 0.00 46.60 3.69
1726 1747 7.485913 GCCATAATGTTGCAATGTGCTATATAC 59.514 37.037 0.59 0.00 45.31 1.47
1727 1748 8.733458 CCATAATGTTGCAATGTGCTATATACT 58.267 33.333 0.59 0.00 45.31 2.12
1728 1749 9.764870 CATAATGTTGCAATGTGCTATATACTC 57.235 33.333 0.59 0.00 45.31 2.59
1729 1750 6.808008 ATGTTGCAATGTGCTATATACTCC 57.192 37.500 0.59 0.00 45.31 3.85
1730 1751 5.063204 TGTTGCAATGTGCTATATACTCCC 58.937 41.667 0.59 0.00 45.31 4.30
1731 1752 5.163205 TGTTGCAATGTGCTATATACTCCCT 60.163 40.000 0.59 0.00 45.31 4.20
1732 1753 5.152623 TGCAATGTGCTATATACTCCCTC 57.847 43.478 1.43 0.00 45.31 4.30
1733 1754 4.020218 TGCAATGTGCTATATACTCCCTCC 60.020 45.833 1.43 0.00 45.31 4.30
1734 1755 4.748892 CAATGTGCTATATACTCCCTCCG 58.251 47.826 0.00 0.00 0.00 4.63
1735 1756 3.520691 TGTGCTATATACTCCCTCCGT 57.479 47.619 0.00 0.00 0.00 4.69
1736 1757 3.840991 TGTGCTATATACTCCCTCCGTT 58.159 45.455 0.00 0.00 0.00 4.44
1737 1758 3.825014 TGTGCTATATACTCCCTCCGTTC 59.175 47.826 0.00 0.00 0.00 3.95
1738 1759 3.193056 GTGCTATATACTCCCTCCGTTCC 59.807 52.174 0.00 0.00 0.00 3.62
1739 1760 3.181426 TGCTATATACTCCCTCCGTTCCA 60.181 47.826 0.00 0.00 0.00 3.53
1740 1761 3.830755 GCTATATACTCCCTCCGTTCCAA 59.169 47.826 0.00 0.00 0.00 3.53
1741 1762 4.282703 GCTATATACTCCCTCCGTTCCAAA 59.717 45.833 0.00 0.00 0.00 3.28
1742 1763 5.221581 GCTATATACTCCCTCCGTTCCAAAA 60.222 44.000 0.00 0.00 0.00 2.44
1743 1764 5.906772 ATATACTCCCTCCGTTCCAAAAT 57.093 39.130 0.00 0.00 0.00 1.82
1744 1765 7.310237 GCTATATACTCCCTCCGTTCCAAAATA 60.310 40.741 0.00 0.00 0.00 1.40
1745 1766 5.906772 ATACTCCCTCCGTTCCAAAATAT 57.093 39.130 0.00 0.00 0.00 1.28
1746 1767 8.674925 ATATACTCCCTCCGTTCCAAAATATA 57.325 34.615 0.00 0.00 0.00 0.86
1747 1768 5.703730 ACTCCCTCCGTTCCAAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
1748 1769 5.681639 ACTCCCTCCGTTCCAAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
1749 1770 5.191124 ACTCCCTCCGTTCCAAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
1750 1771 5.677567 TCCCTCCGTTCCAAAATATAAGTC 58.322 41.667 0.00 0.00 0.00 3.01
1751 1772 5.427481 TCCCTCCGTTCCAAAATATAAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
1752 1773 6.069847 TCCCTCCGTTCCAAAATATAAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
1753 1774 6.602009 CCCTCCGTTCCAAAATATAAGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
1754 1775 7.201705 CCCTCCGTTCCAAAATATAAGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
1755 1776 7.553044 CCTCCGTTCCAAAATATAAGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
1756 1777 9.595823 CTCCGTTCCAAAATATAAGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
1757 1778 9.595823 TCCGTTCCAAAATATAAGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
1758 1779 9.595823 CCGTTCCAAAATATAAGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
1787 1808 9.665719 TTTCAATAGATGACTACATACAAAGCA 57.334 29.630 0.00 0.00 37.92 3.91
1788 1809 9.665719 TTCAATAGATGACTACATACAAAGCAA 57.334 29.630 0.00 0.00 37.92 3.91
1789 1810 9.665719 TCAATAGATGACTACATACAAAGCAAA 57.334 29.630 0.00 0.00 36.82 3.68
1793 1814 8.565896 AGATGACTACATACAAAGCAAAATGA 57.434 30.769 0.00 0.00 36.82 2.57
1794 1815 8.671921 AGATGACTACATACAAAGCAAAATGAG 58.328 33.333 0.00 0.00 36.82 2.90
1795 1816 7.744087 TGACTACATACAAAGCAAAATGAGT 57.256 32.000 0.00 0.00 0.00 3.41
1796 1817 7.584108 TGACTACATACAAAGCAAAATGAGTG 58.416 34.615 0.00 0.00 0.00 3.51
1797 1818 7.443879 TGACTACATACAAAGCAAAATGAGTGA 59.556 33.333 0.00 0.00 0.00 3.41
1798 1819 8.165239 ACTACATACAAAGCAAAATGAGTGAA 57.835 30.769 0.00 0.00 0.00 3.18
1799 1820 8.796475 ACTACATACAAAGCAAAATGAGTGAAT 58.204 29.630 0.00 0.00 0.00 2.57
1800 1821 9.282247 CTACATACAAAGCAAAATGAGTGAATC 57.718 33.333 0.00 0.00 0.00 2.52
1801 1822 7.889469 ACATACAAAGCAAAATGAGTGAATCT 58.111 30.769 0.00 0.00 0.00 2.40
1802 1823 9.013229 ACATACAAAGCAAAATGAGTGAATCTA 57.987 29.630 0.00 0.00 0.00 1.98
1803 1824 9.282247 CATACAAAGCAAAATGAGTGAATCTAC 57.718 33.333 0.00 0.00 0.00 2.59
1804 1825 7.275888 ACAAAGCAAAATGAGTGAATCTACA 57.724 32.000 0.00 0.00 0.00 2.74
1805 1826 7.141363 ACAAAGCAAAATGAGTGAATCTACAC 58.859 34.615 0.00 0.00 40.60 2.90
1850 1871 9.607988 ACATTCGTATGTTATAGTCCATTTGAA 57.392 29.630 1.31 0.00 42.29 2.69
1854 1875 9.607988 TCGTATGTTATAGTCCATTTGAAATGT 57.392 29.630 15.93 1.43 0.00 2.71
1855 1876 9.864034 CGTATGTTATAGTCCATTTGAAATGTC 57.136 33.333 15.93 9.10 0.00 3.06
1865 1886 9.136323 AGTCCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 14.21 39.41 3.24
1866 1887 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
1879 1900 9.897349 GTCTAAAAAGACTTATATTTCGGAACG 57.103 33.333 0.00 0.00 44.07 3.95
2319 2343 7.643764 ACACATGTTTCAAAAACTCGAGTATTG 59.356 33.333 26.36 26.36 0.00 1.90
2401 2426 7.609056 ACTCTGCAAGCATTCATTTAAGAATT 58.391 30.769 0.00 0.00 36.13 2.17
2456 2481 2.673043 CGTCTGCTACCGGTGTATGTTT 60.673 50.000 19.93 0.00 0.00 2.83
2463 2488 3.149005 ACCGGTGTATGTTTTCCATGT 57.851 42.857 6.12 0.00 34.86 3.21
2468 2493 4.589908 GGTGTATGTTTTCCATGTCTCCT 58.410 43.478 0.00 0.00 34.86 3.69
2523 2548 2.655090 TTGGAAGTTCACCATGCAGA 57.345 45.000 5.01 0.00 37.26 4.26
2557 2582 0.183492 TTTGGGCTTGAGTGCAGTCT 59.817 50.000 21.79 0.00 34.04 3.24
2832 2857 8.540388 AGTGAGCACTGAGGTATAAGAAAAATA 58.460 33.333 1.71 0.00 40.75 1.40
2885 2910 6.482835 TGCGGATCAACAACTAAATAAATCG 58.517 36.000 0.00 0.00 0.00 3.34
2946 2971 4.576053 GGTATGTACTCAAATCTGCATGCA 59.424 41.667 21.29 21.29 0.00 3.96
2981 3006 2.420687 GCTAGAGGTACATTGGCAAGCT 60.421 50.000 5.96 0.00 0.00 3.74
2996 3021 3.558109 GGCAAGCTAAGAAACTGACCTCT 60.558 47.826 0.00 0.00 0.00 3.69
3232 3257 6.688637 ATGTGATGTCATAGAACACATTGG 57.311 37.500 10.57 0.00 45.66 3.16
3354 3379 0.951558 AAATGTCACGGAAGGCACAC 59.048 50.000 0.00 0.00 30.81 3.82
3566 3591 2.813908 CAGCTTGGCGTACGTCCC 60.814 66.667 18.57 11.24 0.00 4.46
3679 3704 3.941188 CTCACACTGGTGGGCGGT 61.941 66.667 5.70 0.00 45.32 5.68
3794 3820 3.986817 TCCCTACCAGATCAGAGAGAGAT 59.013 47.826 0.00 0.00 0.00 2.75
3818 3850 2.986728 GGGAGAGAGAGAGAGGAGGTAT 59.013 54.545 0.00 0.00 0.00 2.73
3968 4000 1.519408 TGAGGCCTGTTTAAGAACGC 58.481 50.000 12.00 0.00 38.65 4.84
4042 4076 3.230134 ACTTTTGCAAGGCTACATTCCA 58.770 40.909 0.00 0.00 33.82 3.53
4073 4107 0.667993 CCGTGCCTGAAAAGAAAGCA 59.332 50.000 0.00 0.00 0.00 3.91
4109 4143 4.422840 TGATGTCAAACTGTGCAAAGTTG 58.577 39.130 22.92 15.97 40.28 3.16
4215 4249 5.526846 TCAAATTTTGCACCATTTGACTTCC 59.473 36.000 21.03 0.00 42.06 3.46
4217 4251 4.478206 TTTTGCACCATTTGACTTCCAA 57.522 36.364 0.00 0.00 0.00 3.53
4218 4252 4.686191 TTTGCACCATTTGACTTCCAAT 57.314 36.364 0.00 0.00 34.23 3.16
4219 4253 4.686191 TTGCACCATTTGACTTCCAATT 57.314 36.364 0.00 0.00 34.23 2.32
4265 4304 2.490903 GCACAGAGGGAGTACGAAGTTA 59.509 50.000 0.00 0.00 37.78 2.24
4553 4592 6.145048 CAGCTTCTCCAATCAATCAAAACAAC 59.855 38.462 0.00 0.00 0.00 3.32
4674 4715 3.838565 TGTGGGGAAAAGTCTATGCAAA 58.161 40.909 0.00 0.00 0.00 3.68
4792 4834 6.039616 GTGCGAGTCTGAATTTCTAGAGATT 58.960 40.000 8.18 8.18 0.00 2.40
5098 5268 3.733224 CGAGCGATTTCTGGAAGTATCTG 59.267 47.826 0.00 0.00 33.76 2.90
5780 5952 7.970061 TCACAAATACGTAGGAATACACTGTAC 59.030 37.037 0.08 0.00 0.00 2.90
5790 5962 8.954350 GTAGGAATACACTGTACAAAGAGAGTA 58.046 37.037 0.00 0.00 0.00 2.59
6017 6189 3.104843 GAGGAGTACTCACATGATGCC 57.895 52.381 23.91 4.33 45.85 4.40
6119 6291 2.644798 AGGAAACCTACAACCAGCTCAT 59.355 45.455 0.00 0.00 28.47 2.90
6410 6582 6.532657 GTGCTTATTATGCTTTGCACAAGAAT 59.467 34.615 10.44 9.16 46.64 2.40
7479 7659 1.340991 ACAGTTGTGTTCCTGTTGCCT 60.341 47.619 0.00 0.00 38.76 4.75
7527 7707 1.571919 GTGAGTCAAACTGTCAGCGT 58.428 50.000 0.00 0.00 0.00 5.07
7768 7948 6.927381 TGGTTCTAGTTTCTACTGTAACTTGC 59.073 38.462 0.26 0.00 35.78 4.01
7935 8118 7.322699 CAGTTGCACAGGTTTTTACTTATTACG 59.677 37.037 0.00 0.00 0.00 3.18
7936 8119 6.864360 TGCACAGGTTTTTACTTATTACGT 57.136 33.333 0.00 0.00 0.00 3.57
7937 8120 7.959689 TGCACAGGTTTTTACTTATTACGTA 57.040 32.000 0.00 0.00 0.00 3.57
7938 8121 8.020861 TGCACAGGTTTTTACTTATTACGTAG 57.979 34.615 0.00 0.00 0.00 3.51
7939 8122 7.871973 TGCACAGGTTTTTACTTATTACGTAGA 59.128 33.333 0.00 0.00 0.00 2.59
8030 8213 2.033801 CACTGCCTTGTCTTTCAACCTG 59.966 50.000 0.00 0.00 32.18 4.00
8031 8214 1.000938 CTGCCTTGTCTTTCAACCTGC 60.001 52.381 0.00 0.00 32.18 4.85
8059 8242 2.899838 GGCACAGACGCAACCACA 60.900 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 28 1.227823 CCGAGCAGGACACAAACCA 60.228 57.895 0.00 0.00 45.00 3.67
38 42 2.279784 CGCCTCATCTTCCCGAGC 60.280 66.667 0.00 0.00 0.00 5.03
88 92 2.774351 GGATGGGGGCTAGGCTGT 60.774 66.667 16.80 0.00 0.00 4.40
102 106 0.175073 GCTAGACGAACCGTTGGGAT 59.825 55.000 0.00 0.00 41.37 3.85
121 125 1.497278 CACACGCCCTCAAATGACG 59.503 57.895 0.00 0.00 0.00 4.35
153 157 0.107214 TGAATCCCACAAGATCCGCC 60.107 55.000 0.00 0.00 0.00 6.13
155 159 2.555199 GACTGAATCCCACAAGATCCG 58.445 52.381 0.00 0.00 0.00 4.18
164 168 2.649531 AAAACACCGACTGAATCCCA 57.350 45.000 0.00 0.00 0.00 4.37
183 187 0.250295 CAAGCAGGTCCACCGAAGAA 60.250 55.000 0.00 0.00 42.08 2.52
196 200 1.413767 CGACGACCGAATCCAAGCAG 61.414 60.000 0.00 0.00 41.76 4.24
202 206 0.730494 AACGAACGACGACCGAATCC 60.730 55.000 17.20 0.00 45.77 3.01
210 214 1.254986 CGAACACGAACGAACGACGA 61.255 55.000 18.82 0.00 45.77 4.20
212 216 0.112437 CACGAACACGAACGAACGAC 60.112 55.000 11.97 0.00 37.03 4.34
213 217 0.523125 ACACGAACACGAACGAACGA 60.523 50.000 11.97 0.00 37.03 3.85
214 218 0.295470 AACACGAACACGAACGAACG 59.705 50.000 0.14 0.00 39.31 3.95
222 226 4.200827 CAACATGTAGAAACACGAACACG 58.799 43.478 0.00 0.00 38.78 4.49
246 250 5.923733 AGTGAAGTGTAGATCGAAAGGAT 57.076 39.130 0.00 0.00 38.35 3.24
247 251 5.243060 TGAAGTGAAGTGTAGATCGAAAGGA 59.757 40.000 0.00 0.00 0.00 3.36
248 252 5.470368 TGAAGTGAAGTGTAGATCGAAAGG 58.530 41.667 0.00 0.00 0.00 3.11
249 253 6.021074 CGATGAAGTGAAGTGTAGATCGAAAG 60.021 42.308 0.00 0.00 34.75 2.62
250 254 5.800438 CGATGAAGTGAAGTGTAGATCGAAA 59.200 40.000 0.00 0.00 34.75 3.46
257 261 1.920574 CGCCGATGAAGTGAAGTGTAG 59.079 52.381 0.00 0.00 0.00 2.74
267 271 0.179145 AGTAACCGTCGCCGATGAAG 60.179 55.000 8.12 0.00 35.63 3.02
272 276 1.081242 GAACAGTAACCGTCGCCGA 60.081 57.895 0.00 0.00 35.63 5.54
290 294 0.670162 CCAAAAGACCAGCACACCAG 59.330 55.000 0.00 0.00 0.00 4.00
312 316 0.608640 AGGAAGTCACCGTGCTAAGG 59.391 55.000 0.00 0.00 34.73 2.69
329 333 5.120830 GCAAACATTGTAGTAGACAGTCAGG 59.879 44.000 2.66 0.00 39.88 3.86
332 336 5.061064 CGAGCAAACATTGTAGTAGACAGTC 59.939 44.000 0.00 0.00 39.88 3.51
355 359 2.546368 CGTCTCTCCCTTATCAGAGTCG 59.454 54.545 2.15 2.15 40.29 4.18
362 366 4.377226 CGTCGTTATCGTCTCTCCCTTATC 60.377 50.000 0.00 0.00 38.33 1.75
369 373 1.910863 GCGTCGTCGTTATCGTCTCTC 60.911 57.143 3.66 0.00 39.49 3.20
382 386 4.755614 AGCCGAAGTCGCGTCGTC 62.756 66.667 15.16 12.20 36.77 4.20
406 410 1.302832 GCCACTGGCTACAAGCACT 60.303 57.895 13.28 0.00 46.69 4.40
425 429 2.375345 TTAGCCCAGCCCTGCCTAC 61.375 63.158 0.00 0.00 0.00 3.18
428 432 3.583882 TTGTTAGCCCAGCCCTGCC 62.584 63.158 0.00 0.00 0.00 4.85
437 441 2.781681 TTAGCAGAGGTTGTTAGCCC 57.218 50.000 0.00 0.00 0.00 5.19
438 442 3.676093 ACTTTAGCAGAGGTTGTTAGCC 58.324 45.455 0.00 0.00 0.00 3.93
453 457 2.481449 CGTGGCAGGGTAGCTACTTTAG 60.481 54.545 22.74 11.73 42.97 1.85
454 458 1.479323 CGTGGCAGGGTAGCTACTTTA 59.521 52.381 22.74 2.35 42.97 1.85
455 459 0.249398 CGTGGCAGGGTAGCTACTTT 59.751 55.000 22.74 9.10 42.97 2.66
456 460 1.614241 CCGTGGCAGGGTAGCTACTT 61.614 60.000 22.74 9.46 42.97 2.24
457 461 2.058595 CCGTGGCAGGGTAGCTACT 61.059 63.158 22.74 1.53 42.97 2.57
458 462 2.294132 GACCGTGGCAGGGTAGCTAC 62.294 65.000 30.01 15.88 41.89 3.58
459 463 2.038329 ACCGTGGCAGGGTAGCTA 59.962 61.111 29.05 0.00 34.08 3.32
460 464 3.391382 GACCGTGGCAGGGTAGCT 61.391 66.667 30.01 9.35 36.34 3.32
461 465 3.248446 TTGACCGTGGCAGGGTAGC 62.248 63.158 30.01 19.43 36.34 3.58
462 466 1.375523 GTTGACCGTGGCAGGGTAG 60.376 63.158 30.01 6.13 36.34 3.18
463 467 1.697082 TTGTTGACCGTGGCAGGGTA 61.697 55.000 30.01 14.46 36.34 3.69
464 468 2.559922 TTTGTTGACCGTGGCAGGGT 62.560 55.000 30.33 30.33 39.39 4.34
465 469 1.795170 CTTTGTTGACCGTGGCAGGG 61.795 60.000 23.87 23.87 35.02 4.45
466 470 1.654220 CTTTGTTGACCGTGGCAGG 59.346 57.895 0.00 0.00 37.30 4.85
467 471 0.817634 TCCTTTGTTGACCGTGGCAG 60.818 55.000 0.00 0.00 0.00 4.85
468 472 0.179004 ATCCTTTGTTGACCGTGGCA 60.179 50.000 0.00 0.00 0.00 4.92
469 473 0.958822 AATCCTTTGTTGACCGTGGC 59.041 50.000 0.00 0.00 0.00 5.01
470 474 3.011949 CAAATCCTTTGTTGACCGTGG 57.988 47.619 0.00 0.00 35.94 4.94
480 484 3.689161 TGAGGCGTATGACAAATCCTTTG 59.311 43.478 0.00 0.00 45.95 2.77
495 499 2.718073 GGGACACGGTATGAGGCGT 61.718 63.158 0.00 0.00 0.00 5.68
500 504 1.066430 GCAGAAAGGGACACGGTATGA 60.066 52.381 0.00 0.00 0.00 2.15
507 511 0.038166 TCCCATGCAGAAAGGGACAC 59.962 55.000 13.28 0.00 46.42 3.67
516 520 1.133823 ACAAACAGTGTCCCATGCAGA 60.134 47.619 0.00 0.00 34.38 4.26
517 521 1.321474 ACAAACAGTGTCCCATGCAG 58.679 50.000 0.00 0.00 34.38 4.41
524 528 7.600065 TCTAGTGATAACTACAAACAGTGTCC 58.400 38.462 0.00 0.00 41.98 4.02
528 532 8.135382 ACCATCTAGTGATAACTACAAACAGT 57.865 34.615 0.00 0.00 0.00 3.55
544 548 5.079998 TCCATGTCCATAGACCATCTAGT 57.920 43.478 0.00 0.00 42.81 2.57
545 549 5.483231 ACATCCATGTCCATAGACCATCTAG 59.517 44.000 0.00 0.00 42.81 2.43
546 550 5.406163 ACATCCATGTCCATAGACCATCTA 58.594 41.667 0.00 0.00 42.81 1.98
549 553 6.708885 ATTACATCCATGTCCATAGACCAT 57.291 37.500 0.00 0.00 42.81 3.55
558 562 8.947055 AAGCAATAAAAATTACATCCATGTCC 57.053 30.769 0.00 0.00 41.97 4.02
606 610 9.755804 GACAAAATTCAGAAAATTTTCTCCTCT 57.244 29.630 26.87 11.97 45.23 3.69
609 613 8.893219 AGGACAAAATTCAGAAAATTTTCTCC 57.107 30.769 26.87 20.96 45.23 3.71
615 619 7.274447 TGAGCAAGGACAAAATTCAGAAAATT 58.726 30.769 0.00 0.00 0.00 1.82
616 620 6.819284 TGAGCAAGGACAAAATTCAGAAAAT 58.181 32.000 0.00 0.00 0.00 1.82
621 625 3.572584 GCTGAGCAAGGACAAAATTCAG 58.427 45.455 0.00 0.00 35.03 3.02
652 656 9.450807 CACCACAACTTACTCTTTTTCTATTTG 57.549 33.333 0.00 0.00 0.00 2.32
664 675 0.875059 GCCAGCACCACAACTTACTC 59.125 55.000 0.00 0.00 0.00 2.59
672 683 1.907807 GGGATTTGCCAGCACCACA 60.908 57.895 0.00 0.00 38.95 4.17
747 759 3.069289 CCGGGTGAGTAACTTTAACACC 58.931 50.000 0.00 0.00 46.79 4.16
761 773 0.528924 CGTGACAGTTATCCGGGTGA 59.471 55.000 0.00 0.00 0.00 4.02
802 818 1.544825 ATATAGGCGCTGGCATCGGT 61.545 55.000 13.03 0.00 42.47 4.69
937 958 2.227089 GATCGGATTCGGGGGATCGG 62.227 65.000 0.00 0.00 36.95 4.18
974 995 2.005995 CGCGCGAGATTTGGATTGA 58.994 52.632 28.94 0.00 0.00 2.57
1152 1173 3.966026 CTTCGAGGACGTGCCGGAC 62.966 68.421 5.05 0.00 43.43 4.79
1569 1590 0.097150 TCTTCACGATGTCGCTCTCG 59.903 55.000 1.77 0.00 44.43 4.04
1726 1747 5.681639 ACTTATATTTTGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1727 1748 5.427481 AGACTTATATTTTGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1728 1749 5.681639 AGACTTATATTTTGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1729 1750 7.553044 AGAAAGACTTATATTTTGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
1730 1751 8.494016 AGAAAGACTTATATTTTGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
1731 1752 9.595823 CTAGAAAGACTTATATTTTGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
1732 1753 9.595823 TCTAGAAAGACTTATATTTTGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
1761 1782 9.665719 TGCTTTGTATGTAGTCATCTATTGAAA 57.334 29.630 0.00 0.00 35.70 2.69
1762 1783 9.665719 TTGCTTTGTATGTAGTCATCTATTGAA 57.334 29.630 0.00 0.00 35.70 2.69
1763 1784 9.665719 TTTGCTTTGTATGTAGTCATCTATTGA 57.334 29.630 0.00 0.00 35.70 2.57
1767 1788 9.665719 TCATTTTGCTTTGTATGTAGTCATCTA 57.334 29.630 0.00 0.00 35.70 1.98
1768 1789 8.565896 TCATTTTGCTTTGTATGTAGTCATCT 57.434 30.769 0.00 0.00 35.70 2.90
1769 1790 8.454106 ACTCATTTTGCTTTGTATGTAGTCATC 58.546 33.333 0.00 0.00 35.70 2.92
1770 1791 8.239314 CACTCATTTTGCTTTGTATGTAGTCAT 58.761 33.333 0.00 0.00 38.00 3.06
1771 1792 7.443879 TCACTCATTTTGCTTTGTATGTAGTCA 59.556 33.333 0.00 0.00 0.00 3.41
1772 1793 7.806690 TCACTCATTTTGCTTTGTATGTAGTC 58.193 34.615 0.00 0.00 0.00 2.59
1773 1794 7.744087 TCACTCATTTTGCTTTGTATGTAGT 57.256 32.000 0.00 0.00 0.00 2.73
1774 1795 9.282247 GATTCACTCATTTTGCTTTGTATGTAG 57.718 33.333 0.00 0.00 0.00 2.74
1775 1796 9.013229 AGATTCACTCATTTTGCTTTGTATGTA 57.987 29.630 0.00 0.00 0.00 2.29
1776 1797 7.889469 AGATTCACTCATTTTGCTTTGTATGT 58.111 30.769 0.00 0.00 0.00 2.29
1777 1798 9.282247 GTAGATTCACTCATTTTGCTTTGTATG 57.718 33.333 0.00 0.00 0.00 2.39
1778 1799 9.013229 TGTAGATTCACTCATTTTGCTTTGTAT 57.987 29.630 0.00 0.00 0.00 2.29
1779 1800 8.289618 GTGTAGATTCACTCATTTTGCTTTGTA 58.710 33.333 0.00 0.00 35.68 2.41
1780 1801 7.013655 AGTGTAGATTCACTCATTTTGCTTTGT 59.986 33.333 0.00 0.00 44.07 2.83
1781 1802 7.365741 AGTGTAGATTCACTCATTTTGCTTTG 58.634 34.615 0.00 0.00 44.07 2.77
1782 1803 7.516198 AGTGTAGATTCACTCATTTTGCTTT 57.484 32.000 0.00 0.00 44.07 3.51
1828 1849 9.607988 ACATTTCAAATGGACTATAACATACGA 57.392 29.630 14.70 0.00 0.00 3.43
1829 1850 9.864034 GACATTTCAAATGGACTATAACATACG 57.136 33.333 14.70 0.00 0.00 3.06
1839 1860 9.136323 AGTCTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 41.02 3.85
1840 1861 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
1853 1874 9.897349 CGTTCCGAAATATAAGTCTTTTTAGAC 57.103 33.333 0.00 0.00 39.00 2.59
1854 1875 9.090692 CCGTTCCGAAATATAAGTCTTTTTAGA 57.909 33.333 0.00 0.00 0.00 2.10
1855 1876 9.090692 TCCGTTCCGAAATATAAGTCTTTTTAG 57.909 33.333 0.00 0.00 0.00 1.85
1856 1877 9.090692 CTCCGTTCCGAAATATAAGTCTTTTTA 57.909 33.333 0.00 0.00 0.00 1.52
1857 1878 7.065443 CCTCCGTTCCGAAATATAAGTCTTTTT 59.935 37.037 0.00 0.00 0.00 1.94
1858 1879 6.537660 CCTCCGTTCCGAAATATAAGTCTTTT 59.462 38.462 0.00 0.00 0.00 2.27
1859 1880 6.047231 CCTCCGTTCCGAAATATAAGTCTTT 58.953 40.000 0.00 0.00 0.00 2.52
1860 1881 5.452917 CCCTCCGTTCCGAAATATAAGTCTT 60.453 44.000 0.00 0.00 0.00 3.01
1861 1882 4.038883 CCCTCCGTTCCGAAATATAAGTCT 59.961 45.833 0.00 0.00 0.00 3.24
1862 1883 4.038402 TCCCTCCGTTCCGAAATATAAGTC 59.962 45.833 0.00 0.00 0.00 3.01
1863 1884 3.962718 TCCCTCCGTTCCGAAATATAAGT 59.037 43.478 0.00 0.00 0.00 2.24
1864 1885 4.038883 ACTCCCTCCGTTCCGAAATATAAG 59.961 45.833 0.00 0.00 0.00 1.73
1865 1886 3.962718 ACTCCCTCCGTTCCGAAATATAA 59.037 43.478 0.00 0.00 0.00 0.98
1866 1887 3.569491 ACTCCCTCCGTTCCGAAATATA 58.431 45.455 0.00 0.00 0.00 0.86
1867 1888 2.395619 ACTCCCTCCGTTCCGAAATAT 58.604 47.619 0.00 0.00 0.00 1.28
1868 1889 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1869 1890 1.755380 CTACTCCCTCCGTTCCGAAAT 59.245 52.381 0.00 0.00 0.00 2.17
1870 1891 1.180029 CTACTCCCTCCGTTCCGAAA 58.820 55.000 0.00 0.00 0.00 3.46
1871 1892 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
1872 1893 0.549950 ATCTACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
1873 1894 0.669077 CATCTACTCCCTCCGTTCCG 59.331 60.000 0.00 0.00 0.00 4.30
1874 1895 1.777941 ACATCTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
1875 1896 5.163437 ACAATAACATCTACTCCCTCCGTTC 60.163 44.000 0.00 0.00 0.00 3.95
1876 1897 4.715297 ACAATAACATCTACTCCCTCCGTT 59.285 41.667 0.00 0.00 0.00 4.44
1877 1898 4.099573 CACAATAACATCTACTCCCTCCGT 59.900 45.833 0.00 0.00 0.00 4.69
1878 1899 4.501571 CCACAATAACATCTACTCCCTCCG 60.502 50.000 0.00 0.00 0.00 4.63
1879 1900 4.654262 TCCACAATAACATCTACTCCCTCC 59.346 45.833 0.00 0.00 0.00 4.30
1880 1901 5.871396 TCCACAATAACATCTACTCCCTC 57.129 43.478 0.00 0.00 0.00 4.30
1881 1902 6.831664 ATTCCACAATAACATCTACTCCCT 57.168 37.500 0.00 0.00 0.00 4.20
2319 2343 5.105716 TGCTAGTCACTATGTTCTGTTCTCC 60.106 44.000 0.00 0.00 0.00 3.71
2456 2481 6.612863 TCAGATTATGAAGAGGAGACATGGAA 59.387 38.462 0.00 0.00 34.02 3.53
2463 2488 8.981659 TGTTACAATCAGATTATGAAGAGGAGA 58.018 33.333 0.00 0.00 42.53 3.71
2523 2548 4.159557 AGCCCAAAACAGAAACACCATAT 58.840 39.130 0.00 0.00 0.00 1.78
2557 2582 8.964772 GGTAAACTCACTCTAACCTAAGTCATA 58.035 37.037 0.00 0.00 0.00 2.15
2946 2971 3.245052 ACCTCTAGCAAATTTGTGCCTCT 60.245 43.478 19.03 9.76 46.14 3.69
2981 3006 4.021016 GGCAGAGAAGAGGTCAGTTTCTTA 60.021 45.833 0.00 0.00 33.97 2.10
2996 3021 1.770658 CCATGGTGGATAGGCAGAGAA 59.229 52.381 2.57 0.00 40.96 2.87
3232 3257 0.178068 TCGGCAGCTACAGGGAATTC 59.822 55.000 0.00 0.00 0.00 2.17
3354 3379 2.039405 GCTCTTGGCTCCACTGCTG 61.039 63.158 0.00 0.00 38.06 4.41
3584 3609 9.656323 AACTATGACATACTATTTAGAGGGTGA 57.344 33.333 0.00 0.00 0.00 4.02
3794 3820 2.126882 CTCCTCTCTCTCTCTCCCTGA 58.873 57.143 0.00 0.00 0.00 3.86
3818 3850 1.489481 CACCTATCCTCCTCACTGCA 58.511 55.000 0.00 0.00 0.00 4.41
4042 4076 0.556747 AGGCACGGAGGGAGTACTAT 59.443 55.000 0.00 0.00 0.00 2.12
4109 4143 5.847111 AGTTTTTCCTACAAACTTGGTCC 57.153 39.130 0.00 0.00 40.83 4.46
4265 4304 0.820871 GCTCCGAATCTCAGTGACCT 59.179 55.000 0.00 0.00 0.00 3.85
4362 4401 6.591834 GGTAACATGATATCTTGCTCGCTTAT 59.408 38.462 16.39 0.00 0.00 1.73
4553 4592 7.148641 AGATGTAACTATAGGACAGCATTTCG 58.851 38.462 20.68 0.00 31.97 3.46
4771 4813 7.254137 TGTCAATCTCTAGAAATTCAGACTCG 58.746 38.462 9.46 0.00 0.00 4.18
4792 4834 3.664107 AGCACTAAAATCGCTTCTGTCA 58.336 40.909 0.00 0.00 29.87 3.58
5372 5542 6.139679 AGAATTATCCACCAAAGTCCTGAA 57.860 37.500 0.00 0.00 0.00 3.02
5632 5802 4.202567 CCCATAAGGCCATAACTACCACAT 60.203 45.833 5.01 0.00 0.00 3.21
5723 5895 7.359595 GCATATACAAAGTGAAGTGTCAAACA 58.640 34.615 0.00 0.00 34.87 2.83
5790 5962 9.927081 AAATCCTGTTAGGTTCAATATGAGAAT 57.073 29.630 0.00 0.00 36.53 2.40
6017 6189 7.770433 TCTGGGTAGATGTTGAACTTATTGATG 59.230 37.037 0.00 0.00 0.00 3.07
6657 6836 5.527951 TGCAAGCAACAACGAAAATCTTAT 58.472 33.333 0.00 0.00 0.00 1.73
7123 7302 4.687215 TGAGACCTGGCTGCACGC 62.687 66.667 0.50 0.11 38.13 5.34
7443 7623 1.006571 TGTCAGAGTCCGCGGTTTC 60.007 57.895 27.15 22.49 0.00 2.78
7479 7659 2.414750 TGCGAGACAGCATATCGGA 58.585 52.632 7.07 1.59 42.92 4.55
7527 7707 4.643953 GCAAATGCAGTACGAATTTACGA 58.356 39.130 0.00 0.00 41.59 3.43
7737 7917 6.313324 ACAGTAGAAACTAGAACCAGGTACT 58.687 40.000 0.00 0.00 33.78 2.73
7768 7948 2.223537 GGGTTTGTTCAAAGCCACAG 57.776 50.000 29.52 0.00 46.57 3.66
7935 8118 8.429493 AAACAGTAACAAAACACCTACTCTAC 57.571 34.615 0.00 0.00 0.00 2.59
7936 8119 8.480501 AGAAACAGTAACAAAACACCTACTCTA 58.519 33.333 0.00 0.00 0.00 2.43
7937 8120 7.336396 AGAAACAGTAACAAAACACCTACTCT 58.664 34.615 0.00 0.00 0.00 3.24
7938 8121 7.549615 AGAAACAGTAACAAAACACCTACTC 57.450 36.000 0.00 0.00 0.00 2.59
7939 8122 7.608761 TCAAGAAACAGTAACAAAACACCTACT 59.391 33.333 0.00 0.00 0.00 2.57
8059 8242 1.118838 GGCAGACTAGATGAGCAGGT 58.881 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.