Multiple sequence alignment - TraesCS6B01G348000

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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 TraesCS6B01G348000 chr6B 100.000 3511 0 0 1 3511 612856363 612859873 0.000000e+00 6484
1 TraesCS6B01G348000 chr6B 80.287 1461 244 34 1010 2435 612847990 612849441 0.000000e+00 1062
2 TraesCS6B01G348000 chr6D 91.259 2780 173 31 761 3511 408213188 408215926 0.000000e+00 3723
3 TraesCS6B01G348000 chr6D 80.596 1443 226 34 1010 2418 408183262 408184684 0.000000e+00 1064
4 TraesCS6B01G348000 chr6D 83.084 668 75 14 123 768 408212500 408213151 1.090000e-159 573
5 TraesCS6B01G348000 chr6D 76.233 446 96 10 1881 2321 408156102 408155662 9.800000e-56 228
6 TraesCS6B01G348000 chr6D 75.342 438 98 10 1878 2310 420560253 420560685 5.940000e-48 202
7 TraesCS6B01G348000 chr6A 90.804 2501 159 40 773 3231 554302650 554305121 0.000000e+00 3278
8 TraesCS6B01G348000 chr6A 79.454 1465 246 36 1010 2441 553925990 553927432 0.000000e+00 987
9 TraesCS6B01G348000 chr6A 91.040 346 28 3 3166 3511 554305113 554305455 6.860000e-127 464
10 TraesCS6B01G348000 chr6A 86.986 146 6 5 773 917 553943136 553943269 6.070000e-33 152
11 TraesCS6B01G348000 chr6A 95.714 70 3 0 699 768 553942956 553943025 2.860000e-21 113
12 TraesCS6B01G348000 chr2A 77.350 468 92 13 1878 2338 448293937 448293477 7.470000e-67 265
13 TraesCS6B01G348000 chr3B 75.484 465 98 14 1880 2336 224956709 224956253 2.750000e-51 213


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 TraesCS6B01G348000 chr6B 612856363 612859873 3510 False 6484 6484 100.0000 1 3511 1 chr6B.!!$F2 3510
1 TraesCS6B01G348000 chr6B 612847990 612849441 1451 False 1062 1062 80.2870 1010 2435 1 chr6B.!!$F1 1425
2 TraesCS6B01G348000 chr6D 408212500 408215926 3426 False 2148 3723 87.1715 123 3511 2 chr6D.!!$F3 3388
3 TraesCS6B01G348000 chr6D 408183262 408184684 1422 False 1064 1064 80.5960 1010 2418 1 chr6D.!!$F1 1408
4 TraesCS6B01G348000 chr6A 554302650 554305455 2805 False 1871 3278 90.9220 773 3511 2 chr6A.!!$F3 2738
5 TraesCS6B01G348000 chr6A 553925990 553927432 1442 False 987 987 79.4540 1010 2441 1 chr6A.!!$F1 1431

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
93 94 0.179004 ACACGGCACATCCCTTTGAA 60.179 50.0 0.00 0.0 0.00 2.69 F
1500 1597 0.109723 TGCCACTCAAAGGTACCACC 59.890 55.0 15.94 0.0 38.99 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2218 0.322636 TCTCGGCGAGAAACTCCTCT 60.323 55.0 35.09 0.00 35.59 3.69 R
3118 3288 1.078759 CGAGGCTGAGGCTACAAACG 61.079 60.0 9.08 3.87 38.98 3.60 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
25 26 7.674564 GTGCACATGCGAAAATATTTAAATGT 58.325 30.769 13.17 0.84 45.83 2.71
26 27 8.802856 GTGCACATGCGAAAATATTTAAATGTA 58.197 29.630 13.17 0.00 45.83 2.29
27 28 9.526713 TGCACATGCGAAAATATTTAAATGTAT 57.473 25.926 11.05 0.00 45.83 2.29
28 29 9.782028 GCACATGCGAAAATATTTAAATGTATG 57.218 29.630 11.05 9.89 0.00 2.39
48 49 8.074613 TGTATGGTAAAGCTAGTCATACAAGT 57.925 34.615 20.15 0.00 43.74 3.16
49 50 8.195436 TGTATGGTAAAGCTAGTCATACAAGTC 58.805 37.037 20.15 4.53 43.74 3.01
50 51 6.599356 TGGTAAAGCTAGTCATACAAGTCA 57.401 37.500 0.00 0.00 0.00 3.41
51 52 6.395629 TGGTAAAGCTAGTCATACAAGTCAC 58.604 40.000 0.00 0.00 0.00 3.67
52 53 6.014925 TGGTAAAGCTAGTCATACAAGTCACA 60.015 38.462 0.00 0.00 0.00 3.58
53 54 6.310711 GGTAAAGCTAGTCATACAAGTCACAC 59.689 42.308 0.00 0.00 0.00 3.82
54 55 5.730296 AAGCTAGTCATACAAGTCACACT 57.270 39.130 0.00 0.00 0.00 3.55
55 56 5.317733 AGCTAGTCATACAAGTCACACTC 57.682 43.478 0.00 0.00 0.00 3.51
56 57 4.099120 GCTAGTCATACAAGTCACACTCG 58.901 47.826 0.00 0.00 0.00 4.18
57 58 2.947852 AGTCATACAAGTCACACTCGC 58.052 47.619 0.00 0.00 0.00 5.03
58 59 1.993370 GTCATACAAGTCACACTCGCC 59.007 52.381 0.00 0.00 0.00 5.54
59 60 1.616374 TCATACAAGTCACACTCGCCA 59.384 47.619 0.00 0.00 0.00 5.69
60 61 2.233676 TCATACAAGTCACACTCGCCAT 59.766 45.455 0.00 0.00 0.00 4.40
61 62 3.445805 TCATACAAGTCACACTCGCCATA 59.554 43.478 0.00 0.00 0.00 2.74
62 63 2.831685 ACAAGTCACACTCGCCATAA 57.168 45.000 0.00 0.00 0.00 1.90
63 64 3.120321 ACAAGTCACACTCGCCATAAA 57.880 42.857 0.00 0.00 0.00 1.40
64 65 3.472652 ACAAGTCACACTCGCCATAAAA 58.527 40.909 0.00 0.00 0.00 1.52
65 66 4.072131 ACAAGTCACACTCGCCATAAAAT 58.928 39.130 0.00 0.00 0.00 1.82
66 67 4.154195 ACAAGTCACACTCGCCATAAAATC 59.846 41.667 0.00 0.00 0.00 2.17
67 68 3.937814 AGTCACACTCGCCATAAAATCA 58.062 40.909 0.00 0.00 0.00 2.57
68 69 3.935203 AGTCACACTCGCCATAAAATCAG 59.065 43.478 0.00 0.00 0.00 2.90
69 70 2.677836 TCACACTCGCCATAAAATCAGC 59.322 45.455 0.00 0.00 0.00 4.26
70 71 2.419673 CACACTCGCCATAAAATCAGCA 59.580 45.455 0.00 0.00 0.00 4.41
71 72 3.065786 CACACTCGCCATAAAATCAGCAT 59.934 43.478 0.00 0.00 0.00 3.79
72 73 4.273235 CACACTCGCCATAAAATCAGCATA 59.727 41.667 0.00 0.00 0.00 3.14
73 74 5.049198 CACACTCGCCATAAAATCAGCATAT 60.049 40.000 0.00 0.00 0.00 1.78
74 75 6.147656 CACACTCGCCATAAAATCAGCATATA 59.852 38.462 0.00 0.00 0.00 0.86
75 76 6.147821 ACACTCGCCATAAAATCAGCATATAC 59.852 38.462 0.00 0.00 0.00 1.47
76 77 6.147656 CACTCGCCATAAAATCAGCATATACA 59.852 38.462 0.00 0.00 0.00 2.29
77 78 6.147821 ACTCGCCATAAAATCAGCATATACAC 59.852 38.462 0.00 0.00 0.00 2.90
78 79 5.120053 TCGCCATAAAATCAGCATATACACG 59.880 40.000 0.00 0.00 0.00 4.49
79 80 5.631026 GCCATAAAATCAGCATATACACGG 58.369 41.667 0.00 0.00 0.00 4.94
80 81 5.631026 CCATAAAATCAGCATATACACGGC 58.369 41.667 0.00 0.00 0.00 5.68
81 82 5.181056 CCATAAAATCAGCATATACACGGCA 59.819 40.000 0.00 0.00 0.00 5.69
82 83 4.552166 AAAATCAGCATATACACGGCAC 57.448 40.909 0.00 0.00 0.00 5.01
83 84 2.908688 ATCAGCATATACACGGCACA 57.091 45.000 0.00 0.00 0.00 4.57
84 85 2.908688 TCAGCATATACACGGCACAT 57.091 45.000 0.00 0.00 0.00 3.21
85 86 2.754472 TCAGCATATACACGGCACATC 58.246 47.619 0.00 0.00 0.00 3.06
86 87 1.800586 CAGCATATACACGGCACATCC 59.199 52.381 0.00 0.00 0.00 3.51
87 88 1.156736 GCATATACACGGCACATCCC 58.843 55.000 0.00 0.00 0.00 3.85
88 89 1.270839 GCATATACACGGCACATCCCT 60.271 52.381 0.00 0.00 0.00 4.20
89 90 2.810400 GCATATACACGGCACATCCCTT 60.810 50.000 0.00 0.00 0.00 3.95
90 91 3.476552 CATATACACGGCACATCCCTTT 58.523 45.455 0.00 0.00 0.00 3.11
91 92 1.750193 ATACACGGCACATCCCTTTG 58.250 50.000 0.00 0.00 0.00 2.77
92 93 0.687920 TACACGGCACATCCCTTTGA 59.312 50.000 0.00 0.00 0.00 2.69
93 94 0.179004 ACACGGCACATCCCTTTGAA 60.179 50.000 0.00 0.00 0.00 2.69
94 95 1.176527 CACGGCACATCCCTTTGAAT 58.823 50.000 0.00 0.00 0.00 2.57
95 96 1.135315 CACGGCACATCCCTTTGAATG 60.135 52.381 0.00 0.00 0.00 2.67
96 97 1.176527 CGGCACATCCCTTTGAATGT 58.823 50.000 0.00 0.00 0.00 2.71
97 98 1.545582 CGGCACATCCCTTTGAATGTT 59.454 47.619 0.00 0.00 0.00 2.71
98 99 2.029110 CGGCACATCCCTTTGAATGTTT 60.029 45.455 0.00 0.00 0.00 2.83
99 100 3.554752 CGGCACATCCCTTTGAATGTTTT 60.555 43.478 0.00 0.00 0.00 2.43
100 101 4.321601 CGGCACATCCCTTTGAATGTTTTA 60.322 41.667 0.00 0.00 0.00 1.52
101 102 4.929211 GGCACATCCCTTTGAATGTTTTAC 59.071 41.667 0.00 0.00 0.00 2.01
102 103 5.279456 GGCACATCCCTTTGAATGTTTTACT 60.279 40.000 0.00 0.00 0.00 2.24
103 104 6.223120 GCACATCCCTTTGAATGTTTTACTT 58.777 36.000 0.00 0.00 0.00 2.24
104 105 6.705825 GCACATCCCTTTGAATGTTTTACTTT 59.294 34.615 0.00 0.00 0.00 2.66
105 106 7.226523 GCACATCCCTTTGAATGTTTTACTTTT 59.773 33.333 0.00 0.00 0.00 2.27
106 107 9.108284 CACATCCCTTTGAATGTTTTACTTTTT 57.892 29.630 0.00 0.00 0.00 1.94
130 131 6.867519 TGTTACATTCCCTCTAATCTCACA 57.132 37.500 0.00 0.00 0.00 3.58
133 134 8.160765 TGTTACATTCCCTCTAATCTCACAAAA 58.839 33.333 0.00 0.00 0.00 2.44
167 168 9.126151 TGGTGTTTAAGATATTGTTTCAGTGAA 57.874 29.630 0.08 0.08 0.00 3.18
189 190 7.920682 GTGAAAATTTTGTACTTGGACTGTGAT 59.079 33.333 8.47 0.00 0.00 3.06
194 195 4.110036 TGTACTTGGACTGTGATCATCG 57.890 45.455 0.00 0.00 0.00 3.84
197 198 1.931841 CTTGGACTGTGATCATCGCTG 59.068 52.381 0.00 3.66 32.98 5.18
198 199 0.897621 TGGACTGTGATCATCGCTGT 59.102 50.000 10.27 10.27 40.84 4.40
324 325 9.678260 AAAGAGTCATTTATCAAAGCTACATCT 57.322 29.630 0.00 0.00 0.00 2.90
326 327 9.107177 AGAGTCATTTATCAAAGCTACATCTTG 57.893 33.333 0.00 0.00 0.00 3.02
327 328 9.102757 GAGTCATTTATCAAAGCTACATCTTGA 57.897 33.333 0.47 0.47 0.00 3.02
328 329 9.453572 AGTCATTTATCAAAGCTACATCTTGAA 57.546 29.630 2.08 0.00 0.00 2.69
365 369 5.163834 GCCCAAAACATGCATCACTTATTTG 60.164 40.000 0.00 2.72 0.00 2.32
384 388 6.635030 ATTTGTGAACTGGGAAGTAACTTC 57.365 37.500 0.00 0.00 39.52 3.01
405 416 5.779241 TCCCATTAATCTCTCCTTTGTGT 57.221 39.130 0.00 0.00 0.00 3.72
406 417 6.139679 TCCCATTAATCTCTCCTTTGTGTT 57.860 37.500 0.00 0.00 0.00 3.32
411 422 7.255942 CCATTAATCTCTCCTTTGTGTTGGTTT 60.256 37.037 0.00 0.00 0.00 3.27
419 430 3.307059 CCTTTGTGTTGGTTTTTCCCACA 60.307 43.478 0.00 0.00 39.16 4.17
432 443 6.349363 GGTTTTTCCCACATGTCTAGCTTAAG 60.349 42.308 0.00 0.00 0.00 1.85
433 444 5.755409 TTTCCCACATGTCTAGCTTAAGA 57.245 39.130 6.67 0.00 0.00 2.10
451 462 9.746457 AGCTTAAGAAGAAGATAAATCTGGTTT 57.254 29.630 6.67 0.00 37.19 3.27
458 469 7.020827 AGAAGATAAATCTGGTTTCACAGGA 57.979 36.000 0.00 0.00 38.98 3.86
463 476 8.743714 AGATAAATCTGGTTTCACAGGATTTTC 58.256 33.333 0.00 0.00 38.98 2.29
473 486 4.792068 TCACAGGATTTTCTTTGTCAGGT 58.208 39.130 0.00 0.00 0.00 4.00
474 487 5.200483 TCACAGGATTTTCTTTGTCAGGTT 58.800 37.500 0.00 0.00 0.00 3.50
476 489 4.275936 ACAGGATTTTCTTTGTCAGGTTCG 59.724 41.667 0.00 0.00 0.00 3.95
487 500 6.488683 TCTTTGTCAGGTTCGTAATTGGAAAT 59.511 34.615 0.00 0.00 0.00 2.17
494 507 6.370442 CAGGTTCGTAATTGGAAATGTGAGTA 59.630 38.462 0.00 0.00 0.00 2.59
510 525 8.615360 AATGTGAGTAGTATATATGCTCCCAT 57.385 34.615 6.60 4.23 35.44 4.00
514 529 7.124298 GTGAGTAGTATATATGCTCCCATGGAA 59.876 40.741 15.22 0.00 32.85 3.53
521 536 9.717942 GTATATATGCTCCCATGGAATATCTTC 57.282 37.037 15.22 0.00 32.85 2.87
526 541 5.846164 TGCTCCCATGGAATATCTTCTTAGA 59.154 40.000 15.22 0.00 34.21 2.10
530 545 9.228949 CTCCCATGGAATATCTTCTTAGATTTG 57.771 37.037 15.22 0.00 41.38 2.32
531 546 8.948362 TCCCATGGAATATCTTCTTAGATTTGA 58.052 33.333 15.22 0.00 41.38 2.69
557 572 6.018588 TCCAACTTATATATTTTCACGTGGCG 60.019 38.462 17.00 0.00 0.00 5.69
558 573 5.917541 ACTTATATATTTTCACGTGGCGG 57.082 39.130 17.00 0.00 0.00 6.13
573 588 4.738998 CGGGCAGATGGCACCCAA 62.739 66.667 11.10 0.00 45.76 4.12
588 603 5.535753 GCACCCAAGCCATTAATTAATCT 57.464 39.130 7.76 1.05 0.00 2.40
589 604 5.291971 GCACCCAAGCCATTAATTAATCTG 58.708 41.667 7.76 4.16 0.00 2.90
590 605 5.068987 GCACCCAAGCCATTAATTAATCTGA 59.931 40.000 7.76 0.00 0.00 3.27
591 606 6.239402 GCACCCAAGCCATTAATTAATCTGAT 60.239 38.462 7.76 0.00 0.00 2.90
592 607 7.687592 GCACCCAAGCCATTAATTAATCTGATT 60.688 37.037 7.76 8.14 0.00 2.57
593 608 7.654520 CACCCAAGCCATTAATTAATCTGATTG 59.345 37.037 19.12 19.12 0.00 2.67
594 609 7.345392 ACCCAAGCCATTAATTAATCTGATTGT 59.655 33.333 21.74 10.63 0.00 2.71
595 610 8.206189 CCCAAGCCATTAATTAATCTGATTGTT 58.794 33.333 21.74 9.85 0.00 2.83
617 632 7.686519 TGTTAAATGAAATTTATGCATGCTGC 58.313 30.769 20.33 0.00 46.47 5.25
623 638 7.951703 AATGAAATTTATGCATGCTGCGGAATA 60.952 33.333 20.33 4.09 39.19 1.75
633 648 3.088532 TGCTGCGGAATAACCTGAAATT 58.911 40.909 0.00 0.00 36.31 1.82
644 659 3.928727 ACCTGAAATTGCAGACACATG 57.071 42.857 15.61 0.00 38.14 3.21
645 660 3.225104 ACCTGAAATTGCAGACACATGT 58.775 40.909 15.61 0.00 38.14 3.21
646 661 3.005050 ACCTGAAATTGCAGACACATGTG 59.995 43.478 24.25 24.25 38.14 3.21
662 677 3.067883 ACATGTGCAGCAACAACACAATA 59.932 39.130 0.00 0.00 46.47 1.90
689 712 9.933723 AAAAAGGAAATGATTAGTTCAATCCAG 57.066 29.630 0.00 0.00 42.61 3.86
698 721 6.947733 TGATTAGTTCAATCCAGGTGACAATT 59.052 34.615 0.00 0.00 42.17 2.32
699 722 6.573664 TTAGTTCAATCCAGGTGACAATTG 57.426 37.500 3.24 3.24 0.00 2.32
739 762 3.424703 TCCAGCTTCCCTTTTCTTGATG 58.575 45.455 0.00 0.00 0.00 3.07
802 869 0.458669 GAAGGGCGTATCAGGTTCGA 59.541 55.000 0.00 0.00 0.00 3.71
806 873 2.696707 AGGGCGTATCAGGTTCGAATTA 59.303 45.455 0.00 0.00 0.00 1.40
807 874 3.133362 AGGGCGTATCAGGTTCGAATTAA 59.867 43.478 0.00 0.00 0.00 1.40
808 875 3.872771 GGGCGTATCAGGTTCGAATTAAA 59.127 43.478 0.00 0.00 0.00 1.52
907 986 2.851195 ACAACAATCAAGAACGGCTCT 58.149 42.857 0.00 0.00 35.13 4.09
908 987 2.808543 ACAACAATCAAGAACGGCTCTC 59.191 45.455 0.00 0.00 31.02 3.20
993 1075 1.216710 GTCACCAGGCGGAGAGAAG 59.783 63.158 2.43 0.00 31.91 2.85
1083 1165 2.749044 CTCGCCAAGGTGCTGCAT 60.749 61.111 5.27 0.00 0.00 3.96
1310 1398 3.474570 GGACCTGCTGGCGAGGAT 61.475 66.667 9.95 0.00 36.63 3.24
1311 1399 2.202987 GACCTGCTGGCGAGGATG 60.203 66.667 9.95 0.00 36.63 3.51
1312 1400 2.685017 ACCTGCTGGCGAGGATGA 60.685 61.111 9.95 0.00 36.63 2.92
1372 1466 2.892425 GGGTGATGAGCTTCGCGG 60.892 66.667 6.13 0.00 0.00 6.46
1500 1597 0.109723 TGCCACTCAAAGGTACCACC 59.890 55.000 15.94 0.00 38.99 4.61
1519 1644 3.648067 CACCCCATGGAGTATGACAGTAT 59.352 47.826 15.22 0.00 39.21 2.12
1978 2115 1.811266 GCATCACCGTCATGTCGCT 60.811 57.895 6.84 0.00 0.00 4.93
2264 2401 4.753877 TTCGCCGAGCAGACGACG 62.754 66.667 0.00 0.00 40.10 5.12
2273 2410 2.254350 CAGACGACGAACTGCCGA 59.746 61.111 0.00 0.00 0.00 5.54
2348 2485 2.435059 GAGGTGGCAAGGCTCGTC 60.435 66.667 0.00 3.34 0.00 4.20
2514 2651 5.888161 ACCGATGATCCTAAAAGCTGAAAAT 59.112 36.000 0.00 0.00 0.00 1.82
2544 2684 4.456911 GTCTTGTTGAATCAGCCTGATCAA 59.543 41.667 7.84 10.83 35.76 2.57
2556 2696 3.202818 AGCCTGATCAATGTGATGGGTAA 59.797 43.478 0.00 0.00 37.20 2.85
2559 2699 5.278660 GCCTGATCAATGTGATGGGTAAATC 60.279 44.000 0.00 0.00 37.20 2.17
2561 2701 5.679601 TGATCAATGTGATGGGTAAATCGA 58.320 37.500 0.00 0.00 37.20 3.59
2562 2702 6.118852 TGATCAATGTGATGGGTAAATCGAA 58.881 36.000 0.00 0.00 37.20 3.71
2564 2704 7.936301 TGATCAATGTGATGGGTAAATCGAATA 59.064 33.333 0.00 0.00 37.20 1.75
2565 2705 8.690203 ATCAATGTGATGGGTAAATCGAATAA 57.310 30.769 0.00 0.00 35.43 1.40
2567 2707 7.228507 TCAATGTGATGGGTAAATCGAATAAGG 59.771 37.037 0.00 0.00 0.00 2.69
2568 2708 4.819630 TGTGATGGGTAAATCGAATAAGGC 59.180 41.667 0.00 0.00 0.00 4.35
2569 2709 4.062293 TGATGGGTAAATCGAATAAGGCG 58.938 43.478 0.00 0.00 0.00 5.52
2570 2710 3.547054 TGGGTAAATCGAATAAGGCGT 57.453 42.857 0.00 0.00 0.00 5.68
2572 2712 4.263435 TGGGTAAATCGAATAAGGCGTTT 58.737 39.130 0.00 0.00 0.00 3.60
2583 2745 7.290118 TCGAATAAGGCGTTTACTGTTTAAAC 58.710 34.615 11.54 11.54 34.91 2.01
2597 2759 0.179051 TTAAACCCGTTGTGCGTCCT 60.179 50.000 0.00 0.00 39.32 3.85
2604 2766 2.006888 CCGTTGTGCGTCCTTATCAAT 58.993 47.619 0.00 0.00 39.32 2.57
2605 2767 2.418628 CCGTTGTGCGTCCTTATCAATT 59.581 45.455 0.00 0.00 39.32 2.32
2606 2768 3.485216 CCGTTGTGCGTCCTTATCAATTC 60.485 47.826 0.00 0.00 39.32 2.17
2608 2770 4.651994 GTTGTGCGTCCTTATCAATTCTG 58.348 43.478 0.00 0.00 0.00 3.02
2609 2771 3.270027 TGTGCGTCCTTATCAATTCTGG 58.730 45.455 0.00 0.00 0.00 3.86
2610 2772 3.055458 TGTGCGTCCTTATCAATTCTGGA 60.055 43.478 0.00 0.00 0.00 3.86
2612 2774 3.197766 TGCGTCCTTATCAATTCTGGACT 59.802 43.478 0.00 0.00 43.45 3.85
2613 2775 3.557595 GCGTCCTTATCAATTCTGGACTG 59.442 47.826 0.00 0.00 43.45 3.51
2614 2776 4.122776 CGTCCTTATCAATTCTGGACTGG 58.877 47.826 0.00 0.00 43.45 4.00
2615 2777 4.383118 CGTCCTTATCAATTCTGGACTGGT 60.383 45.833 0.00 0.00 43.45 4.00
2616 2778 4.878397 GTCCTTATCAATTCTGGACTGGTG 59.122 45.833 0.00 0.00 42.63 4.17
2617 2779 4.782691 TCCTTATCAATTCTGGACTGGTGA 59.217 41.667 0.00 0.00 0.00 4.02
2618 2780 5.250543 TCCTTATCAATTCTGGACTGGTGAA 59.749 40.000 0.00 0.00 0.00 3.18
2619 2781 5.587844 CCTTATCAATTCTGGACTGGTGAAG 59.412 44.000 0.00 0.00 0.00 3.02
2620 2782 4.916041 ATCAATTCTGGACTGGTGAAGA 57.084 40.909 0.00 0.00 0.00 2.87
2621 2783 4.705110 TCAATTCTGGACTGGTGAAGAA 57.295 40.909 0.00 0.00 33.45 2.52
2622 2784 5.047566 TCAATTCTGGACTGGTGAAGAAA 57.952 39.130 0.00 0.00 32.72 2.52
2623 2785 5.445069 TCAATTCTGGACTGGTGAAGAAAA 58.555 37.500 0.00 0.00 32.72 2.29
2624 2786 6.070656 TCAATTCTGGACTGGTGAAGAAAAT 58.929 36.000 0.00 0.00 32.72 1.82
2625 2787 5.972107 ATTCTGGACTGGTGAAGAAAATG 57.028 39.130 0.00 0.00 32.72 2.32
2626 2788 4.705110 TCTGGACTGGTGAAGAAAATGA 57.295 40.909 0.00 0.00 0.00 2.57
2627 2789 5.246981 TCTGGACTGGTGAAGAAAATGAT 57.753 39.130 0.00 0.00 0.00 2.45
2628 2790 5.248640 TCTGGACTGGTGAAGAAAATGATC 58.751 41.667 0.00 0.00 0.00 2.92
2629 2791 4.335416 TGGACTGGTGAAGAAAATGATCC 58.665 43.478 0.00 0.00 0.00 3.36
2630 2792 4.202556 TGGACTGGTGAAGAAAATGATCCA 60.203 41.667 0.00 0.00 0.00 3.41
2631 2793 4.766891 GGACTGGTGAAGAAAATGATCCAA 59.233 41.667 0.00 0.00 0.00 3.53
2632 2794 5.335976 GGACTGGTGAAGAAAATGATCCAAC 60.336 44.000 0.00 0.00 0.00 3.77
2633 2795 5.139727 ACTGGTGAAGAAAATGATCCAACA 58.860 37.500 0.00 0.00 0.00 3.33
2634 2796 5.242393 ACTGGTGAAGAAAATGATCCAACAG 59.758 40.000 0.00 0.00 42.96 3.16
2635 2797 5.139727 TGGTGAAGAAAATGATCCAACAGT 58.860 37.500 0.00 0.00 0.00 3.55
2636 2798 6.303054 TGGTGAAGAAAATGATCCAACAGTA 58.697 36.000 0.00 0.00 0.00 2.74
2637 2799 6.947733 TGGTGAAGAAAATGATCCAACAGTAT 59.052 34.615 0.00 0.00 0.00 2.12
2638 2800 7.094248 TGGTGAAGAAAATGATCCAACAGTATG 60.094 37.037 0.00 0.00 46.00 2.39
2639 2801 6.749118 GTGAAGAAAATGATCCAACAGTATGC 59.251 38.462 0.00 0.00 42.53 3.14
2640 2802 6.660521 TGAAGAAAATGATCCAACAGTATGCT 59.339 34.615 0.00 0.00 42.53 3.79
2658 2820 5.663795 ATGCTAAGACAAACTATGCATCG 57.336 39.130 0.19 0.00 40.69 3.84
2680 2842 3.412981 CGATGTCGTTCTCTCAGTGAT 57.587 47.619 0.00 0.00 34.11 3.06
2681 2843 3.104470 CGATGTCGTTCTCTCAGTGATG 58.896 50.000 0.00 0.00 34.11 3.07
2724 2886 9.041354 AGTCCTACTGAAGAACATTTCTCTATT 57.959 33.333 0.00 0.00 39.61 1.73
2742 2912 7.827701 TCTCTATTCTGTAACAATCGAGTGTT 58.172 34.615 30.86 30.86 43.95 3.32
2796 2966 6.074729 CGTAGACATAGAGAAGACGACTACTG 60.075 46.154 0.00 0.00 0.00 2.74
2838 3008 6.262273 GGACTTATTCTGGCGAATTCCATTTA 59.738 38.462 9.24 0.00 40.28 1.40
2849 3019 2.851263 TTCCATTTACTGGCGTGAGT 57.149 45.000 0.00 0.00 45.52 3.41
2916 3086 9.028284 TGCAGAAATAGGAAAAGAATCAGAAAT 57.972 29.630 0.00 0.00 0.00 2.17
2975 3145 7.562454 TTCCAGTCAAGAAACGAGTATTTTT 57.438 32.000 0.00 0.00 0.00 1.94
2979 3149 8.504005 CCAGTCAAGAAACGAGTATTTTTGTAT 58.496 33.333 0.00 0.00 0.00 2.29
2989 3159 5.737290 CGAGTATTTTTGTATTCCTTTGCGG 59.263 40.000 0.00 0.00 0.00 5.69
2990 3160 5.961272 AGTATTTTTGTATTCCTTTGCGGG 58.039 37.500 0.00 0.00 0.00 6.13
2992 3162 1.917872 TTTGTATTCCTTTGCGGGCT 58.082 45.000 0.00 0.00 0.00 5.19
3101 3271 1.806542 GATCTTTCAACAGGCGCTGAA 59.193 47.619 7.64 6.53 35.18 3.02
3118 3288 3.181502 GCTGAAGCTTCTTGGTTATCTGC 60.182 47.826 26.09 9.80 36.40 4.26
3137 3307 1.078759 CGTTTGTAGCCTCAGCCTCG 61.079 60.000 0.00 0.00 41.25 4.63
3186 3411 3.441222 TGCAACATATGTCAGCAGAAAGG 59.559 43.478 24.06 2.73 35.19 3.11
3199 3424 3.755378 AGCAGAAAGGCATGAGTTTACTG 59.245 43.478 0.00 6.20 35.83 2.74
3207 3432 4.342092 AGGCATGAGTTTACTGCAAAGTTT 59.658 37.500 0.00 0.00 37.64 2.66
3215 3440 8.031864 TGAGTTTACTGCAAAGTTTGATCAAAA 58.968 29.630 22.07 10.31 29.58 2.44
3418 3643 1.117142 TGGAAAGAACCCTCGGTCGT 61.117 55.000 0.00 0.00 33.12 4.34
3498 3723 2.618816 GGATTCTGGCCACTTGTCATGA 60.619 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.674564 ACATTTAAATATTTTCGCATGTGCAC 58.325 30.769 10.75 10.75 42.21 4.57
1 2 7.824704 ACATTTAAATATTTTCGCATGTGCA 57.175 28.000 5.91 0.00 42.21 4.57
2 3 9.782028 CATACATTTAAATATTTTCGCATGTGC 57.218 29.630 5.91 0.00 37.78 4.57
20 21 9.899661 TTGTATGACTAGCTTTACCATACATTT 57.100 29.630 20.97 0.00 44.83 2.32
21 22 9.547753 CTTGTATGACTAGCTTTACCATACATT 57.452 33.333 20.97 0.00 44.83 2.71
22 23 8.705594 ACTTGTATGACTAGCTTTACCATACAT 58.294 33.333 20.97 11.60 44.83 2.29
23 24 8.074613 ACTTGTATGACTAGCTTTACCATACA 57.925 34.615 18.53 18.53 44.23 2.29
24 25 8.195436 TGACTTGTATGACTAGCTTTACCATAC 58.805 37.037 15.38 15.38 39.71 2.39
25 26 8.195436 GTGACTTGTATGACTAGCTTTACCATA 58.805 37.037 0.00 0.00 0.00 2.74
26 27 7.042335 GTGACTTGTATGACTAGCTTTACCAT 58.958 38.462 0.00 0.00 0.00 3.55
27 28 6.014925 TGTGACTTGTATGACTAGCTTTACCA 60.015 38.462 0.00 0.00 0.00 3.25
28 29 6.310711 GTGTGACTTGTATGACTAGCTTTACC 59.689 42.308 0.00 0.00 0.00 2.85
29 30 7.091443 AGTGTGACTTGTATGACTAGCTTTAC 58.909 38.462 0.00 0.00 0.00 2.01
30 31 7.228314 AGTGTGACTTGTATGACTAGCTTTA 57.772 36.000 0.00 0.00 0.00 1.85
31 32 6.102897 AGTGTGACTTGTATGACTAGCTTT 57.897 37.500 0.00 0.00 0.00 3.51
32 33 5.620205 CGAGTGTGACTTGTATGACTAGCTT 60.620 44.000 0.00 0.00 0.00 3.74
33 34 4.142578 CGAGTGTGACTTGTATGACTAGCT 60.143 45.833 0.00 0.00 0.00 3.32
34 35 4.099120 CGAGTGTGACTTGTATGACTAGC 58.901 47.826 0.00 0.00 0.00 3.42
35 36 4.099120 GCGAGTGTGACTTGTATGACTAG 58.901 47.826 0.00 0.00 32.12 2.57
36 37 3.119602 GGCGAGTGTGACTTGTATGACTA 60.120 47.826 0.00 0.00 32.12 2.59
37 38 2.352814 GGCGAGTGTGACTTGTATGACT 60.353 50.000 0.00 0.00 32.12 3.41
38 39 1.993370 GGCGAGTGTGACTTGTATGAC 59.007 52.381 0.00 0.00 32.12 3.06
39 40 1.616374 TGGCGAGTGTGACTTGTATGA 59.384 47.619 0.00 0.00 32.12 2.15
40 41 2.078849 TGGCGAGTGTGACTTGTATG 57.921 50.000 0.00 0.00 32.12 2.39
41 42 4.465632 TTATGGCGAGTGTGACTTGTAT 57.534 40.909 0.00 0.00 32.12 2.29
42 43 3.945981 TTATGGCGAGTGTGACTTGTA 57.054 42.857 0.00 0.00 32.12 2.41
43 44 2.831685 TTATGGCGAGTGTGACTTGT 57.168 45.000 0.00 0.00 32.12 3.16
44 45 4.154015 TGATTTTATGGCGAGTGTGACTTG 59.846 41.667 0.00 0.00 32.67 3.16
45 46 4.323417 TGATTTTATGGCGAGTGTGACTT 58.677 39.130 0.00 0.00 0.00 3.01
46 47 3.935203 CTGATTTTATGGCGAGTGTGACT 59.065 43.478 0.00 0.00 0.00 3.41
47 48 3.485877 GCTGATTTTATGGCGAGTGTGAC 60.486 47.826 0.00 0.00 0.00 3.67
48 49 2.677836 GCTGATTTTATGGCGAGTGTGA 59.322 45.455 0.00 0.00 0.00 3.58
49 50 2.419673 TGCTGATTTTATGGCGAGTGTG 59.580 45.455 0.00 0.00 0.00 3.82
50 51 2.710377 TGCTGATTTTATGGCGAGTGT 58.290 42.857 0.00 0.00 0.00 3.55
51 52 3.976793 ATGCTGATTTTATGGCGAGTG 57.023 42.857 0.00 0.00 0.00 3.51
52 53 6.147821 GTGTATATGCTGATTTTATGGCGAGT 59.852 38.462 0.00 0.00 0.00 4.18
53 54 6.537566 GTGTATATGCTGATTTTATGGCGAG 58.462 40.000 0.00 0.00 0.00 5.03
54 55 5.120053 CGTGTATATGCTGATTTTATGGCGA 59.880 40.000 0.00 0.00 0.00 5.54
55 56 5.315982 CGTGTATATGCTGATTTTATGGCG 58.684 41.667 0.00 0.00 0.00 5.69
56 57 5.631026 CCGTGTATATGCTGATTTTATGGC 58.369 41.667 0.00 0.00 0.00 4.40
57 58 5.181056 TGCCGTGTATATGCTGATTTTATGG 59.819 40.000 0.00 0.00 0.00 2.74
58 59 6.079763 GTGCCGTGTATATGCTGATTTTATG 58.920 40.000 0.00 0.00 0.00 1.90
59 60 5.762711 TGTGCCGTGTATATGCTGATTTTAT 59.237 36.000 0.00 0.00 0.00 1.40
60 61 5.119694 TGTGCCGTGTATATGCTGATTTTA 58.880 37.500 0.00 0.00 0.00 1.52
61 62 3.944650 TGTGCCGTGTATATGCTGATTTT 59.055 39.130 0.00 0.00 0.00 1.82
62 63 3.540617 TGTGCCGTGTATATGCTGATTT 58.459 40.909 0.00 0.00 0.00 2.17
63 64 3.192541 TGTGCCGTGTATATGCTGATT 57.807 42.857 0.00 0.00 0.00 2.57
64 65 2.908688 TGTGCCGTGTATATGCTGAT 57.091 45.000 0.00 0.00 0.00 2.90
65 66 2.547855 GGATGTGCCGTGTATATGCTGA 60.548 50.000 0.00 0.00 0.00 4.26
66 67 1.800586 GGATGTGCCGTGTATATGCTG 59.199 52.381 0.00 0.00 0.00 4.41
67 68 1.270839 GGGATGTGCCGTGTATATGCT 60.271 52.381 0.00 0.00 37.63 3.79
68 69 1.156736 GGGATGTGCCGTGTATATGC 58.843 55.000 0.00 0.00 37.63 3.14
69 70 2.839486 AGGGATGTGCCGTGTATATG 57.161 50.000 0.00 0.00 37.63 1.78
70 71 3.135712 TCAAAGGGATGTGCCGTGTATAT 59.864 43.478 0.00 0.00 37.63 0.86
71 72 2.502130 TCAAAGGGATGTGCCGTGTATA 59.498 45.455 0.00 0.00 37.63 1.47
72 73 1.280710 TCAAAGGGATGTGCCGTGTAT 59.719 47.619 0.00 0.00 37.63 2.29
73 74 0.687920 TCAAAGGGATGTGCCGTGTA 59.312 50.000 0.00 0.00 37.63 2.90
74 75 0.179004 TTCAAAGGGATGTGCCGTGT 60.179 50.000 0.00 0.00 37.63 4.49
75 76 1.135315 CATTCAAAGGGATGTGCCGTG 60.135 52.381 0.00 0.00 37.63 4.94
76 77 1.176527 CATTCAAAGGGATGTGCCGT 58.823 50.000 0.00 0.00 37.63 5.68
77 78 1.176527 ACATTCAAAGGGATGTGCCG 58.823 50.000 0.00 0.00 37.63 5.69
78 79 3.683365 AAACATTCAAAGGGATGTGCC 57.317 42.857 0.00 0.00 0.00 5.01
79 80 5.783111 AGTAAAACATTCAAAGGGATGTGC 58.217 37.500 0.00 0.00 0.00 4.57
80 81 8.661352 AAAAGTAAAACATTCAAAGGGATGTG 57.339 30.769 0.00 0.00 0.00 3.21
103 104 9.010029 GTGAGATTAGAGGGAATGTAACAAAAA 57.990 33.333 0.00 0.00 0.00 1.94
104 105 8.160765 TGTGAGATTAGAGGGAATGTAACAAAA 58.839 33.333 0.00 0.00 0.00 2.44
105 106 7.685481 TGTGAGATTAGAGGGAATGTAACAAA 58.315 34.615 0.00 0.00 0.00 2.83
106 107 7.252612 TGTGAGATTAGAGGGAATGTAACAA 57.747 36.000 0.00 0.00 0.00 2.83
107 108 6.867519 TGTGAGATTAGAGGGAATGTAACA 57.132 37.500 0.00 0.00 0.00 2.41
108 109 8.561738 TTTTGTGAGATTAGAGGGAATGTAAC 57.438 34.615 0.00 0.00 0.00 2.50
141 142 8.684386 TCACTGAAACAATATCTTAAACACCA 57.316 30.769 0.00 0.00 0.00 4.17
156 157 8.307483 TCCAAGTACAAAATTTTCACTGAAACA 58.693 29.630 13.03 0.00 30.83 2.83
167 168 7.581213 TGATCACAGTCCAAGTACAAAATTT 57.419 32.000 0.00 0.00 0.00 1.82
169 170 6.092670 CGATGATCACAGTCCAAGTACAAAAT 59.907 38.462 0.00 0.00 0.00 1.82
180 181 2.015736 AACAGCGATGATCACAGTCC 57.984 50.000 8.12 0.00 0.00 3.85
189 190 7.667043 AACAATAAAACTCTAACAGCGATGA 57.333 32.000 8.12 0.00 0.00 2.92
298 299 9.678260 AGATGTAGCTTTGATAAATGACTCTTT 57.322 29.630 0.00 0.00 0.00 2.52
299 300 9.678260 AAGATGTAGCTTTGATAAATGACTCTT 57.322 29.630 0.00 0.00 0.00 2.85
320 321 5.121142 GGGCAATGACACAATTTTCAAGATG 59.879 40.000 0.00 0.00 0.00 2.90
321 322 5.221682 TGGGCAATGACACAATTTTCAAGAT 60.222 36.000 0.00 0.00 0.00 2.40
322 323 4.100653 TGGGCAATGACACAATTTTCAAGA 59.899 37.500 0.00 0.00 0.00 3.02
324 325 4.412796 TGGGCAATGACACAATTTTCAA 57.587 36.364 0.00 0.00 0.00 2.69
326 327 5.065731 TGTTTTGGGCAATGACACAATTTTC 59.934 36.000 0.00 0.00 0.00 2.29
327 328 4.946157 TGTTTTGGGCAATGACACAATTTT 59.054 33.333 0.00 0.00 0.00 1.82
328 329 4.521146 TGTTTTGGGCAATGACACAATTT 58.479 34.783 0.00 0.00 0.00 1.82
376 380 7.757242 AAGGAGAGATTAATGGGAAGTTACT 57.243 36.000 0.00 0.00 0.00 2.24
384 388 5.126061 CCAACACAAAGGAGAGATTAATGGG 59.874 44.000 0.00 0.00 0.00 4.00
405 416 3.572255 GCTAGACATGTGGGAAAAACCAA 59.428 43.478 1.15 0.00 43.34 3.67
406 417 3.153919 GCTAGACATGTGGGAAAAACCA 58.846 45.455 1.15 0.00 41.20 3.67
411 422 5.755409 TCTTAAGCTAGACATGTGGGAAA 57.245 39.130 1.15 0.00 0.00 3.13
432 443 7.607991 TCCTGTGAAACCAGATTTATCTTCTTC 59.392 37.037 0.00 0.00 34.36 2.87
433 444 7.461749 TCCTGTGAAACCAGATTTATCTTCTT 58.538 34.615 0.00 0.00 34.36 2.52
444 455 5.656416 ACAAAGAAAATCCTGTGAAACCAGA 59.344 36.000 0.00 0.00 34.36 3.86
450 461 5.200483 ACCTGACAAAGAAAATCCTGTGAA 58.800 37.500 0.00 0.00 0.00 3.18
451 462 4.792068 ACCTGACAAAGAAAATCCTGTGA 58.208 39.130 0.00 0.00 0.00 3.58
453 464 4.275936 CGAACCTGACAAAGAAAATCCTGT 59.724 41.667 0.00 0.00 0.00 4.00
454 465 4.275936 ACGAACCTGACAAAGAAAATCCTG 59.724 41.667 0.00 0.00 0.00 3.86
458 469 7.013846 TCCAATTACGAACCTGACAAAGAAAAT 59.986 33.333 0.00 0.00 0.00 1.82
463 476 5.682943 TTCCAATTACGAACCTGACAAAG 57.317 39.130 0.00 0.00 0.00 2.77
487 500 6.381133 CCATGGGAGCATATATACTACTCACA 59.619 42.308 2.85 13.10 44.32 3.58
494 507 9.457776 AAGATATTCCATGGGAGCATATATACT 57.542 33.333 13.02 1.18 31.21 2.12
530 545 8.015658 GCCACGTGAAAATATATAAGTTGGATC 58.984 37.037 19.30 0.00 0.00 3.36
531 546 7.307751 CGCCACGTGAAAATATATAAGTTGGAT 60.308 37.037 19.30 0.00 0.00 3.41
543 558 1.302383 CTGCCCGCCACGTGAAAATA 61.302 55.000 19.30 0.00 0.00 1.40
544 559 2.596046 TGCCCGCCACGTGAAAAT 60.596 55.556 19.30 0.00 0.00 1.82
557 572 2.757099 CTTGGGTGCCATCTGCCC 60.757 66.667 0.00 0.00 42.64 5.36
558 573 3.455469 GCTTGGGTGCCATCTGCC 61.455 66.667 0.00 0.00 40.16 4.85
569 584 7.729116 ACAATCAGATTAATTAATGGCTTGGG 58.271 34.615 15.39 2.87 0.00 4.12
617 632 4.155826 TGTCTGCAATTTCAGGTTATTCCG 59.844 41.667 5.23 0.00 41.99 4.30
623 638 3.638160 ACATGTGTCTGCAATTTCAGGTT 59.362 39.130 5.23 0.00 34.91 3.50
625 640 3.571571 CACATGTGTCTGCAATTTCAGG 58.428 45.455 18.03 0.00 34.91 3.86
633 648 1.102222 TTGCTGCACATGTGTCTGCA 61.102 50.000 31.06 31.06 38.56 4.41
644 659 5.462034 TTTTTATTGTGTTGTTGCTGCAC 57.538 34.783 0.00 0.00 0.00 4.57
669 684 7.121168 TGTCACCTGGATTGAACTAATCATTTC 59.879 37.037 0.00 0.00 45.70 2.17
675 690 6.721208 ACAATTGTCACCTGGATTGAACTAAT 59.279 34.615 4.92 0.00 34.47 1.73
677 692 5.473162 CACAATTGTCACCTGGATTGAACTA 59.527 40.000 8.48 0.00 34.47 2.24
679 694 4.549458 CACAATTGTCACCTGGATTGAAC 58.451 43.478 8.48 0.00 34.47 3.18
681 696 3.156293 CCACAATTGTCACCTGGATTGA 58.844 45.455 8.48 0.00 34.47 2.57
689 712 1.039856 ACCTTGCCACAATTGTCACC 58.960 50.000 8.48 0.41 0.00 4.02
739 762 2.295909 TGCAATTGCCACCAAGAACTAC 59.704 45.455 26.94 0.00 41.18 2.73
882 959 6.480320 AGAGCCGTTCTTGATTGTTGTATATC 59.520 38.462 0.00 0.00 29.61 1.63
889 966 3.409026 AGAGAGCCGTTCTTGATTGTT 57.591 42.857 0.00 0.00 35.87 2.83
890 967 4.744795 ATAGAGAGCCGTTCTTGATTGT 57.255 40.909 0.00 0.00 35.87 2.71
907 986 7.061054 CGGGACAAGAGGGTGATATATATAGA 58.939 42.308 0.00 0.00 0.00 1.98
908 987 6.265649 CCGGGACAAGAGGGTGATATATATAG 59.734 46.154 0.00 0.00 0.00 1.31
936 1015 1.781025 ATGTGTCGTGGCACCAAACG 61.781 55.000 12.86 0.00 41.11 3.60
983 1062 0.809241 CATGGCTGTCTTCTCTCCGC 60.809 60.000 0.00 0.00 0.00 5.54
986 1065 1.473080 GGCTCATGGCTGTCTTCTCTC 60.473 57.143 6.20 0.00 41.46 3.20
1056 1138 1.004560 CTTGGCGAGGTTCAGCAGA 60.005 57.895 0.00 0.00 34.54 4.26
1290 1378 4.154347 CTCGCCAGCAGGTCCCTC 62.154 72.222 0.00 0.00 37.19 4.30
1310 1398 3.515286 GCCTCCCGTCGTCGATCA 61.515 66.667 2.98 0.00 39.71 2.92
1311 1399 4.267503 GGCCTCCCGTCGTCGATC 62.268 72.222 2.98 0.00 39.71 3.69
1372 1466 4.436998 CTCGTCGGCCACCTCCAC 62.437 72.222 2.24 0.00 0.00 4.02
1500 1597 4.344968 TCACATACTGTCATACTCCATGGG 59.655 45.833 13.02 5.22 35.16 4.00
1510 1635 4.835678 TGCAGTCAATCACATACTGTCAT 58.164 39.130 0.00 0.00 42.10 3.06
1519 1644 8.022550 CACAGTTATAATTTGCAGTCAATCACA 58.977 33.333 0.00 0.00 31.33 3.58
1676 1807 1.418373 CGTCGAAGTTGAGCATGACA 58.582 50.000 0.00 0.00 0.00 3.58
1937 2074 1.334419 CCGAAGTTGACGTACACGACT 60.334 52.381 9.04 0.00 43.02 4.18
2081 2218 0.322636 TCTCGGCGAGAAACTCCTCT 60.323 55.000 35.09 0.00 35.59 3.69
2360 2497 2.730672 CTTGCCTTTCTCGCCGTCG 61.731 63.158 0.00 0.00 0.00 5.12
2514 2651 4.439974 GGCTGATTCAACAAGACAACAACA 60.440 41.667 0.00 0.00 0.00 3.33
2544 2684 5.473504 GCCTTATTCGATTTACCCATCACAT 59.526 40.000 0.00 0.00 0.00 3.21
2556 2696 6.490566 AAACAGTAAACGCCTTATTCGATT 57.509 33.333 0.00 0.00 0.00 3.34
2559 2699 6.520790 GGTTTAAACAGTAAACGCCTTATTCG 59.479 38.462 19.57 0.00 38.06 3.34
2561 2701 6.568271 CGGGTTTAAACAGTAAACGCCTTATT 60.568 38.462 19.57 0.00 43.19 1.40
2562 2702 5.106594 CGGGTTTAAACAGTAAACGCCTTAT 60.107 40.000 19.57 0.00 43.19 1.73
2564 2704 3.003585 CGGGTTTAAACAGTAAACGCCTT 59.996 43.478 19.57 0.00 43.19 4.35
2565 2705 2.549329 CGGGTTTAAACAGTAAACGCCT 59.451 45.455 19.57 0.00 43.19 5.52
2567 2707 3.607422 ACGGGTTTAAACAGTAAACGC 57.393 42.857 19.57 13.18 42.90 4.84
2568 2708 4.729564 CACAACGGGTTTAAACAGTAAACG 59.270 41.667 19.57 14.36 38.06 3.60
2569 2709 4.500117 GCACAACGGGTTTAAACAGTAAAC 59.500 41.667 19.57 1.42 36.86 2.01
2570 2710 4.670347 GCACAACGGGTTTAAACAGTAAA 58.330 39.130 19.57 0.00 0.00 2.01
2572 2712 2.287373 CGCACAACGGGTTTAAACAGTA 59.713 45.455 19.57 0.00 38.44 2.74
2597 2759 6.373005 TCTTCACCAGTCCAGAATTGATAA 57.627 37.500 0.00 0.00 0.00 1.75
2604 2766 5.047566 TCATTTTCTTCACCAGTCCAGAA 57.952 39.130 0.00 0.00 0.00 3.02
2605 2767 4.705110 TCATTTTCTTCACCAGTCCAGA 57.295 40.909 0.00 0.00 0.00 3.86
2606 2768 4.397417 GGATCATTTTCTTCACCAGTCCAG 59.603 45.833 0.00 0.00 0.00 3.86
2608 2770 4.335416 TGGATCATTTTCTTCACCAGTCC 58.665 43.478 0.00 0.00 0.00 3.85
2609 2771 5.241506 TGTTGGATCATTTTCTTCACCAGTC 59.758 40.000 0.00 0.00 0.00 3.51
2610 2772 5.139727 TGTTGGATCATTTTCTTCACCAGT 58.860 37.500 0.00 0.00 0.00 4.00
2612 2774 5.139727 ACTGTTGGATCATTTTCTTCACCA 58.860 37.500 0.00 0.00 0.00 4.17
2613 2775 5.712152 ACTGTTGGATCATTTTCTTCACC 57.288 39.130 0.00 0.00 0.00 4.02
2614 2776 6.749118 GCATACTGTTGGATCATTTTCTTCAC 59.251 38.462 0.00 0.00 0.00 3.18
2615 2777 6.660521 AGCATACTGTTGGATCATTTTCTTCA 59.339 34.615 0.00 0.00 0.00 3.02
2616 2778 7.093322 AGCATACTGTTGGATCATTTTCTTC 57.907 36.000 0.00 0.00 0.00 2.87
2617 2779 8.579850 TTAGCATACTGTTGGATCATTTTCTT 57.420 30.769 0.00 0.00 0.00 2.52
2618 2780 8.049117 TCTTAGCATACTGTTGGATCATTTTCT 58.951 33.333 0.00 0.00 0.00 2.52
2619 2781 8.125448 GTCTTAGCATACTGTTGGATCATTTTC 58.875 37.037 0.00 0.00 0.00 2.29
2620 2782 7.611467 TGTCTTAGCATACTGTTGGATCATTTT 59.389 33.333 0.00 0.00 0.00 1.82
2621 2783 7.112122 TGTCTTAGCATACTGTTGGATCATTT 58.888 34.615 0.00 0.00 0.00 2.32
2622 2784 6.653020 TGTCTTAGCATACTGTTGGATCATT 58.347 36.000 0.00 0.00 0.00 2.57
2623 2785 6.239217 TGTCTTAGCATACTGTTGGATCAT 57.761 37.500 0.00 0.00 0.00 2.45
2624 2786 5.675684 TGTCTTAGCATACTGTTGGATCA 57.324 39.130 0.00 0.00 0.00 2.92
2625 2787 6.595716 AGTTTGTCTTAGCATACTGTTGGATC 59.404 38.462 0.00 0.00 31.29 3.36
2626 2788 6.476378 AGTTTGTCTTAGCATACTGTTGGAT 58.524 36.000 0.00 0.00 31.29 3.41
2627 2789 5.865085 AGTTTGTCTTAGCATACTGTTGGA 58.135 37.500 0.00 0.00 31.29 3.53
2628 2790 7.677276 GCATAGTTTGTCTTAGCATACTGTTGG 60.677 40.741 8.84 0.00 33.79 3.77
2629 2791 7.148423 TGCATAGTTTGTCTTAGCATACTGTTG 60.148 37.037 8.84 7.89 33.79 3.33
2630 2792 6.878923 TGCATAGTTTGTCTTAGCATACTGTT 59.121 34.615 8.84 0.00 33.79 3.16
2631 2793 6.406370 TGCATAGTTTGTCTTAGCATACTGT 58.594 36.000 8.84 0.00 33.79 3.55
2632 2794 6.908870 TGCATAGTTTGTCTTAGCATACTG 57.091 37.500 8.84 0.00 33.79 2.74
2633 2795 6.422100 CGATGCATAGTTTGTCTTAGCATACT 59.578 38.462 0.00 5.53 41.76 2.12
2634 2796 6.420903 TCGATGCATAGTTTGTCTTAGCATAC 59.579 38.462 0.00 0.00 41.76 2.39
2635 2797 6.420903 GTCGATGCATAGTTTGTCTTAGCATA 59.579 38.462 0.00 0.00 41.76 3.14
2636 2798 5.235186 GTCGATGCATAGTTTGTCTTAGCAT 59.765 40.000 0.00 0.00 43.16 3.79
2637 2799 4.566759 GTCGATGCATAGTTTGTCTTAGCA 59.433 41.667 0.00 0.00 38.42 3.49
2638 2800 4.317418 CGTCGATGCATAGTTTGTCTTAGC 60.317 45.833 0.00 0.00 0.00 3.09
2639 2801 5.034797 TCGTCGATGCATAGTTTGTCTTAG 58.965 41.667 0.00 0.00 0.00 2.18
2640 2802 4.989044 TCGTCGATGCATAGTTTGTCTTA 58.011 39.130 0.00 0.00 0.00 2.10
2670 2832 4.948608 ACTACGTACACATCACTGAGAG 57.051 45.455 0.00 0.00 0.00 3.20
2675 2837 4.038282 TGGTGAAACTACGTACACATCACT 59.962 41.667 18.06 0.00 36.74 3.41
2680 2842 3.243501 GGACTGGTGAAACTACGTACACA 60.244 47.826 13.92 0.71 36.74 3.72
2681 2843 3.005155 AGGACTGGTGAAACTACGTACAC 59.995 47.826 5.69 5.69 36.74 2.90
2718 2880 7.542477 ACAACACTCGATTGTTACAGAATAGAG 59.458 37.037 19.26 7.16 37.62 2.43
2724 2886 5.242171 TCCTACAACACTCGATTGTTACAGA 59.758 40.000 19.26 11.68 40.68 3.41
2838 3008 1.940613 GAAACTGAAACTCACGCCAGT 59.059 47.619 0.00 0.00 41.14 4.00
2849 3019 3.252215 CCCATTGTACTGCGAAACTGAAA 59.748 43.478 0.00 0.00 0.00 2.69
2952 3122 6.540914 ACAAAAATACTCGTTTCTTGACTGGA 59.459 34.615 0.00 0.00 0.00 3.86
2975 3145 1.557832 AGTAGCCCGCAAAGGAATACA 59.442 47.619 0.00 0.00 45.00 2.29
2979 3149 3.453353 ACTATTAGTAGCCCGCAAAGGAA 59.547 43.478 0.00 0.00 45.00 3.36
2989 3159 4.471548 TCTGGACAGGACTATTAGTAGCC 58.528 47.826 0.00 0.00 0.00 3.93
2990 3160 5.106475 CGATCTGGACAGGACTATTAGTAGC 60.106 48.000 0.00 0.00 0.00 3.58
2992 3162 5.314529 CCGATCTGGACAGGACTATTAGTA 58.685 45.833 0.00 0.00 42.00 1.82
3004 3174 2.093021 TGATTTGATGCCGATCTGGACA 60.093 45.455 7.64 5.75 42.00 4.02
3101 3271 2.770164 ACGCAGATAACCAAGAAGCT 57.230 45.000 0.00 0.00 0.00 3.74
3118 3288 1.078759 CGAGGCTGAGGCTACAAACG 61.079 60.000 9.08 3.87 38.98 3.60
3137 3307 3.997021 CACAACCAACTCAGACAGTATCC 59.003 47.826 0.00 0.00 32.30 2.59
3186 3411 5.280945 TCAAACTTTGCAGTAAACTCATGC 58.719 37.500 0.00 0.00 40.40 4.06
3215 3440 3.914426 AGCGACTATGTTCCCATCTTT 57.086 42.857 0.00 0.00 32.29 2.52
3284 3509 6.209391 CCTCAGTTTTCAGACCACCAAAATAT 59.791 38.462 0.00 0.00 0.00 1.28
3418 3643 1.667830 CCGCCGTTCTTTCAGCAGA 60.668 57.895 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.