Multiple sequence alignment - TraesCS2B01G559600

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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 TraesCS2B01G559600 chr2B 100.000 4389 0 0 1 4389 753747003 753751391 0.000000e+00 8106.0
1 TraesCS2B01G559600 chr2B 94.924 1182 44 10 960 2140 753830030 753828864 0.000000e+00 1836.0
2 TraesCS2B01G559600 chr2B 87.952 1494 130 21 2176 3632 753765566 753767046 0.000000e+00 1716.0
3 TraesCS2B01G559600 chr2B 87.508 1489 137 20 2180 3632 753828760 753827285 0.000000e+00 1674.0
4 TraesCS2B01G559600 chr2B 90.449 869 80 3 2714 3581 753843285 753842419 0.000000e+00 1142.0
5 TraesCS2B01G559600 chr2B 88.677 892 96 3 1011 1898 765594804 765593914 0.000000e+00 1083.0
6 TraesCS2B01G559600 chr2B 79.498 478 69 20 3350 3806 753705286 753705755 3.300000e-81 313.0
7 TraesCS2B01G559600 chr2B 95.161 124 3 2 1 124 753731578 753731698 4.480000e-45 193.0
8 TraesCS2B01G559600 chr2B 92.029 138 8 2 1 138 753716892 753717026 1.610000e-44 191.0
9 TraesCS2B01G559600 chr2B 91.852 135 11 0 775 909 753830178 753830044 5.790000e-44 189.0
10 TraesCS2B01G559600 chr2B 91.304 138 9 2 1 138 753718086 753718220 7.500000e-43 185.0
11 TraesCS2B01G559600 chr2B 89.437 142 13 2 3709 3848 753842408 753842267 1.250000e-40 178.0
12 TraesCS2B01G559600 chr2B 92.742 124 5 3 1 124 753715711 753715830 4.510000e-40 176.0
13 TraesCS2B01G559600 chr2B 77.224 281 52 9 3856 4127 753826100 753825823 2.110000e-33 154.0
14 TraesCS2B01G559600 chr2D 93.261 2686 108 30 1738 4389 617510676 617513322 0.000000e+00 3890.0
15 TraesCS2B01G559600 chr2D 83.653 1823 232 38 2237 4009 617463420 617465226 0.000000e+00 1655.0
16 TraesCS2B01G559600 chr2D 89.357 902 93 3 1000 1898 623958499 623957598 0.000000e+00 1131.0
17 TraesCS2B01G559600 chr2D 87.472 902 113 0 997 1898 623895267 623896168 0.000000e+00 1040.0
18 TraesCS2B01G559600 chr2D 88.312 462 36 3 127 572 617509776 617510235 4.990000e-149 538.0
19 TraesCS2B01G559600 chr2D 82.203 118 18 3 136 251 600439259 600439143 1.000000e-16 99.0
20 TraesCS2B01G559600 chr2D 100.000 29 0 0 4361 4389 105673734 105673706 2.000000e-03 54.7
21 TraesCS2B01G559600 chr2D 100.000 29 0 0 4361 4389 137571945 137571917 2.000000e-03 54.7
22 TraesCS2B01G559600 chr2D 100.000 28 0 0 4362 4389 598558913 598558940 8.000000e-03 52.8
23 TraesCS2B01G559600 chr2A 92.415 1437 63 23 717 2133 748088312 748089722 0.000000e+00 2008.0
24 TraesCS2B01G559600 chr2A 84.354 1828 217 37 2237 4012 748079740 748081550 0.000000e+00 1727.0
25 TraesCS2B01G559600 chr2A 88.889 1296 99 20 2585 3848 748165835 748167117 0.000000e+00 1554.0
26 TraesCS2B01G559600 chr2A 88.580 1296 104 19 2585 3848 748124842 748126125 0.000000e+00 1533.0
27 TraesCS2B01G559600 chr2A 88.503 1296 107 17 2585 3848 748190195 748191480 0.000000e+00 1530.0
28 TraesCS2B01G559600 chr2A 94.182 911 53 0 997 1907 748078215 748079125 0.000000e+00 1389.0
29 TraesCS2B01G559600 chr2A 88.827 904 94 6 1000 1898 755335701 755336602 0.000000e+00 1103.0
30 TraesCS2B01G559600 chr2A 88.717 904 95 3 1000 1898 755177510 755176609 0.000000e+00 1098.0
31 TraesCS2B01G559600 chr2A 87.090 914 115 3 997 1908 755251675 755250763 0.000000e+00 1031.0
32 TraesCS2B01G559600 chr2A 88.565 446 49 1 1458 1903 755086151 755086594 1.390000e-149 540.0
33 TraesCS2B01G559600 chr2A 83.612 299 35 6 2191 2477 748165523 748165819 7.240000e-68 268.0
34 TraesCS2B01G559600 chr2A 83.390 295 35 6 2195 2477 748189887 748190179 1.210000e-65 261.0
35 TraesCS2B01G559600 chr2A 83.333 288 34 5 2195 2470 748124533 748124818 2.030000e-63 254.0
36 TraesCS2B01G559600 chr2A 97.087 103 3 0 589 691 748082852 748082954 1.620000e-39 174.0
37 TraesCS2B01G559600 chr2A 78.092 283 34 12 3856 4129 748126417 748126680 2.110000e-33 154.0
38 TraesCS2B01G559600 chr2A 78.014 282 34 15 3856 4129 748191772 748192033 7.600000e-33 152.0
39 TraesCS2B01G559600 chr2A 95.556 45 2 0 1983 2027 755113324 755113368 6.090000e-09 73.1
40 TraesCS2B01G559600 chr5B 81.250 144 25 2 126 267 134533045 134533188 9.980000e-22 115.0
41 TraesCS2B01G559600 chr3D 78.626 131 25 3 126 254 148333063 148332934 2.810000e-12 84.2
42 TraesCS2B01G559600 chr3D 100.000 28 0 0 4362 4389 354528166 354528139 8.000000e-03 52.8
43 TraesCS2B01G559600 chr3D 100.000 28 0 0 4362 4389 566545870 566545897 8.000000e-03 52.8
44 TraesCS2B01G559600 chr6D 78.400 125 24 3 126 248 12986133 12986256 1.310000e-10 78.7
45 TraesCS2B01G559600 chr7D 93.333 45 3 0 1983 2027 534472093 534472049 2.830000e-07 67.6
46 TraesCS2B01G559600 chr4D 100.000 33 0 0 333 365 416792875 416792907 1.320000e-05 62.1
47 TraesCS2B01G559600 chr3B 96.970 33 1 0 4357 4389 815882263 815882295 6.130000e-04 56.5
48 TraesCS2B01G559600 chr7B 100.000 29 0 0 4361 4389 499486972 499486944 2.000000e-03 54.7
49 TraesCS2B01G559600 chr7A 100.000 29 0 0 4361 4389 511592784 511592812 2.000000e-03 54.7


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 TraesCS2B01G559600 chr2B 753747003 753751391 4388 False 8106.000000 8106 100.000000 1 4389 1 chr2B.!!$F3 4388
1 TraesCS2B01G559600 chr2B 753765566 753767046 1480 False 1716.000000 1716 87.952000 2176 3632 1 chr2B.!!$F4 1456
2 TraesCS2B01G559600 chr2B 765593914 765594804 890 True 1083.000000 1083 88.677000 1011 1898 1 chr2B.!!$R1 887
3 TraesCS2B01G559600 chr2B 753825823 753830178 4355 True 963.250000 1836 87.877000 775 4127 4 chr2B.!!$R2 3352
4 TraesCS2B01G559600 chr2B 753842267 753843285 1018 True 660.000000 1142 89.943000 2714 3848 2 chr2B.!!$R3 1134
5 TraesCS2B01G559600 chr2D 617509776 617513322 3546 False 2214.000000 3890 90.786500 127 4389 2 chr2D.!!$F4 4262
6 TraesCS2B01G559600 chr2D 617463420 617465226 1806 False 1655.000000 1655 83.653000 2237 4009 1 chr2D.!!$F2 1772
7 TraesCS2B01G559600 chr2D 623957598 623958499 901 True 1131.000000 1131 89.357000 1000 1898 1 chr2D.!!$R4 898
8 TraesCS2B01G559600 chr2D 623895267 623896168 901 False 1040.000000 1040 87.472000 997 1898 1 chr2D.!!$F3 901
9 TraesCS2B01G559600 chr2A 748088312 748089722 1410 False 2008.000000 2008 92.415000 717 2133 1 chr2A.!!$F1 1416
10 TraesCS2B01G559600 chr2A 755335701 755336602 901 False 1103.000000 1103 88.827000 1000 1898 1 chr2A.!!$F4 898
11 TraesCS2B01G559600 chr2A 755176609 755177510 901 True 1098.000000 1098 88.717000 1000 1898 1 chr2A.!!$R1 898
12 TraesCS2B01G559600 chr2A 748078215 748082954 4739 False 1096.666667 1727 91.874333 589 4012 3 chr2A.!!$F5 3423
13 TraesCS2B01G559600 chr2A 755250763 755251675 912 True 1031.000000 1031 87.090000 997 1908 1 chr2A.!!$R2 911
14 TraesCS2B01G559600 chr2A 748165523 748167117 1594 False 911.000000 1554 86.250500 2191 3848 2 chr2A.!!$F7 1657
15 TraesCS2B01G559600 chr2A 748189887 748192033 2146 False 647.666667 1530 83.302333 2195 4129 3 chr2A.!!$F8 1934
16 TraesCS2B01G559600 chr2A 748124533 748126680 2147 False 647.000000 1533 83.335000 2195 4129 3 chr2A.!!$F6 1934

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
520 537 0.031721 CGTAGGGGTGTCGGCTAATC 59.968 60.0 0.00 0.00 0.00 1.75 F
581 598 0.178068 CCAAGGTCGATCCACGGATT 59.822 55.0 0.00 0.00 42.82 3.01 F
601 618 0.179134 CTCTGGCGTAGTACTGCACC 60.179 60.0 10.77 10.77 0.00 5.01 F
691 708 0.529773 GCGCACCTACGGATTGATCA 60.530 55.0 0.30 0.00 0.00 2.92 F
2027 2309 0.896923 GGCCAGCCATGTTGATTGAA 59.103 50.0 3.12 0.00 35.81 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2454 1.517361 GGCAAAATGGCAGCCCTAC 59.483 57.895 9.64 0.0 43.14 3.18 R
2533 3133 1.144969 TCTTCACGCGTTGGATGAAC 58.855 50.000 10.22 0.0 0.00 3.18 R
2561 3162 4.200092 GGAAGCTATTGTTCCTAACCCAG 58.800 47.826 0.00 0.0 40.46 4.45 R
3028 3656 5.947566 AGGTATTGTGTAACCGGCTATTTTT 59.052 36.000 0.00 0.0 40.88 1.94 R
4133 6349 3.317711 TCATCAATGCTTTTGGTTCGTGT 59.682 39.130 1.03 0.0 0.00 4.49 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
62 63 9.667107 TTTTGCTGGGCTATACTAATGATATAC 57.333 33.333 0.00 0.00 0.00 1.47
63 64 8.609617 TTGCTGGGCTATACTAATGATATACT 57.390 34.615 0.00 0.00 0.00 2.12
64 65 8.609617 TGCTGGGCTATACTAATGATATACTT 57.390 34.615 0.00 0.00 0.00 2.24
65 66 8.478066 TGCTGGGCTATACTAATGATATACTTG 58.522 37.037 0.00 0.00 0.00 3.16
66 67 7.439655 GCTGGGCTATACTAATGATATACTTGC 59.560 40.741 0.00 0.00 0.00 4.01
67 68 8.374184 TGGGCTATACTAATGATATACTTGCA 57.626 34.615 0.00 0.00 0.00 4.08
68 69 8.992349 TGGGCTATACTAATGATATACTTGCAT 58.008 33.333 0.00 0.00 0.00 3.96
79 80 8.959705 ATGATATACTTGCATACCAGATCATG 57.040 34.615 0.00 0.00 31.92 3.07
87 88 2.519441 CCAGATCATGGGCCCCTG 59.481 66.667 22.27 21.26 46.36 4.45
88 89 2.203451 CAGATCATGGGCCCCTGC 60.203 66.667 22.27 8.01 0.00 4.85
104 105 4.512914 GCCTAGCCTGGGCCCTTG 62.513 72.222 25.70 15.30 43.49 3.61
105 106 3.813724 CCTAGCCTGGGCCCTTGG 61.814 72.222 25.70 24.95 43.17 3.61
122 123 3.423154 GCCGTTGCCTCTCGTTGG 61.423 66.667 0.00 0.00 0.00 3.77
131 132 0.108615 CCTCTCGTTGGCAAGACGAT 60.109 55.000 14.12 0.00 46.93 3.73
133 134 0.389817 TCTCGTTGGCAAGACGATGG 60.390 55.000 14.12 5.01 46.93 3.51
184 185 6.042781 TGTTTCATGTCCTACTTTACCTCACT 59.957 38.462 0.00 0.00 0.00 3.41
205 206 1.231958 GCGACCGGACCAACATTTGA 61.232 55.000 9.46 0.00 0.00 2.69
211 212 1.324383 GGACCAACATTTGAACGGGT 58.676 50.000 0.00 0.00 0.00 5.28
276 277 5.808050 GCTCCTCTTTAGATTTTGAGGGGTT 60.808 44.000 9.18 0.00 46.12 4.11
295 296 4.086457 GGTTGGATTTGTTGTATCTGGGT 58.914 43.478 0.00 0.00 0.00 4.51
314 315 4.202419 TGGGTTGTAGTTGCTCTTATGTGT 60.202 41.667 0.00 0.00 0.00 3.72
315 316 4.760204 GGGTTGTAGTTGCTCTTATGTGTT 59.240 41.667 0.00 0.00 0.00 3.32
316 317 5.240844 GGGTTGTAGTTGCTCTTATGTGTTT 59.759 40.000 0.00 0.00 0.00 2.83
351 352 9.715123 CAAATGCAATATATTAATATCGCGGAA 57.285 29.630 11.28 0.00 0.00 4.30
368 369 3.810941 GCGGAAATATCAATTACACCCGA 59.189 43.478 0.00 0.00 0.00 5.14
369 370 4.454504 GCGGAAATATCAATTACACCCGAT 59.545 41.667 0.00 0.00 0.00 4.18
372 373 6.426937 CGGAAATATCAATTACACCCGATCTT 59.573 38.462 0.00 0.00 0.00 2.40
472 489 1.909700 AGATGGAAAAGCCTTTCGCA 58.090 45.000 1.79 2.30 41.70 5.10
483 500 1.429148 CCTTTCGCATGCCTACCGTC 61.429 60.000 13.15 0.00 0.00 4.79
486 503 0.101759 TTCGCATGCCTACCGTCTAC 59.898 55.000 13.15 0.00 0.00 2.59
491 508 0.394762 ATGCCTACCGTCTACCGTCA 60.395 55.000 0.00 0.00 33.66 4.35
511 528 3.692424 GTGTTCAACGTAGGGGTGT 57.308 52.632 0.00 0.00 0.00 4.16
512 529 1.505425 GTGTTCAACGTAGGGGTGTC 58.495 55.000 0.00 0.00 0.00 3.67
513 530 0.032403 TGTTCAACGTAGGGGTGTCG 59.968 55.000 0.00 0.00 0.00 4.35
514 531 0.668401 GTTCAACGTAGGGGTGTCGG 60.668 60.000 0.00 0.00 0.00 4.79
515 532 2.433664 CAACGTAGGGGTGTCGGC 60.434 66.667 0.00 0.00 0.00 5.54
516 533 2.602568 AACGTAGGGGTGTCGGCT 60.603 61.111 0.00 0.00 0.00 5.52
517 534 1.304381 AACGTAGGGGTGTCGGCTA 60.304 57.895 0.00 0.00 0.00 3.93
518 535 0.899717 AACGTAGGGGTGTCGGCTAA 60.900 55.000 0.00 0.00 0.00 3.09
519 536 0.685458 ACGTAGGGGTGTCGGCTAAT 60.685 55.000 0.00 0.00 0.00 1.73
520 537 0.031721 CGTAGGGGTGTCGGCTAATC 59.968 60.000 0.00 0.00 0.00 1.75
521 538 0.031721 GTAGGGGTGTCGGCTAATCG 59.968 60.000 0.00 0.00 0.00 3.34
522 539 1.111116 TAGGGGTGTCGGCTAATCGG 61.111 60.000 0.00 0.00 0.00 4.18
523 540 2.588034 GGGTGTCGGCTAATCGGC 60.588 66.667 0.00 0.00 35.05 5.54
524 541 2.499685 GGTGTCGGCTAATCGGCT 59.500 61.111 0.00 0.00 35.57 5.52
525 542 1.153429 GGTGTCGGCTAATCGGCTT 60.153 57.895 0.00 0.00 35.57 4.35
526 543 1.429148 GGTGTCGGCTAATCGGCTTG 61.429 60.000 0.00 0.00 35.57 4.01
527 544 1.813753 TGTCGGCTAATCGGCTTGC 60.814 57.895 0.00 0.00 35.57 4.01
528 545 1.813753 GTCGGCTAATCGGCTTGCA 60.814 57.895 0.00 0.00 35.72 4.08
529 546 1.813753 TCGGCTAATCGGCTTGCAC 60.814 57.895 0.00 0.00 35.72 4.57
530 547 2.823829 CGGCTAATCGGCTTGCACC 61.824 63.158 0.00 0.00 35.72 5.01
531 548 1.748879 GGCTAATCGGCTTGCACCA 60.749 57.895 0.00 0.00 34.85 4.17
532 549 1.429423 GCTAATCGGCTTGCACCAC 59.571 57.895 0.00 0.00 0.00 4.16
533 550 1.993369 GCTAATCGGCTTGCACCACC 61.993 60.000 0.00 0.00 0.00 4.61
534 551 0.392998 CTAATCGGCTTGCACCACCT 60.393 55.000 0.00 0.00 0.00 4.00
535 552 0.676466 TAATCGGCTTGCACCACCTG 60.676 55.000 0.00 0.00 0.00 4.00
543 560 4.269523 GCACCACCTGCACCTGGA 62.270 66.667 11.24 0.00 46.29 3.86
544 561 2.033141 CACCACCTGCACCTGGAG 59.967 66.667 11.24 0.00 0.00 3.86
545 562 3.958860 ACCACCTGCACCTGGAGC 61.959 66.667 9.32 9.32 31.63 4.70
546 563 3.644606 CCACCTGCACCTGGAGCT 61.645 66.667 16.96 0.00 31.63 4.09
547 564 2.293318 CCACCTGCACCTGGAGCTA 61.293 63.158 16.96 3.29 31.63 3.32
548 565 1.220206 CACCTGCACCTGGAGCTAG 59.780 63.158 16.96 11.84 31.63 3.42
549 566 1.229336 ACCTGCACCTGGAGCTAGT 60.229 57.895 16.96 11.00 31.63 2.57
550 567 1.220206 CCTGCACCTGGAGCTAGTG 59.780 63.158 16.96 5.15 31.63 2.74
551 568 1.548357 CCTGCACCTGGAGCTAGTGT 61.548 60.000 16.96 0.00 33.96 3.55
552 569 1.186200 CTGCACCTGGAGCTAGTGTA 58.814 55.000 16.96 2.97 33.96 2.90
553 570 1.550524 CTGCACCTGGAGCTAGTGTAA 59.449 52.381 16.96 0.00 33.96 2.41
554 571 1.550524 TGCACCTGGAGCTAGTGTAAG 59.449 52.381 16.96 0.00 33.96 2.34
555 572 1.134670 GCACCTGGAGCTAGTGTAAGG 60.135 57.143 8.98 0.00 33.96 2.69
556 573 1.482593 CACCTGGAGCTAGTGTAAGGG 59.517 57.143 0.00 0.00 0.00 3.95
557 574 0.466124 CCTGGAGCTAGTGTAAGGGC 59.534 60.000 0.00 0.00 0.00 5.19
558 575 1.195115 CTGGAGCTAGTGTAAGGGCA 58.805 55.000 0.00 0.00 0.00 5.36
559 576 1.765314 CTGGAGCTAGTGTAAGGGCAT 59.235 52.381 0.00 0.00 0.00 4.40
560 577 1.762957 TGGAGCTAGTGTAAGGGCATC 59.237 52.381 0.00 0.00 0.00 3.91
561 578 2.043227 GGAGCTAGTGTAAGGGCATCT 58.957 52.381 0.00 0.00 0.00 2.90
562 579 2.036604 GGAGCTAGTGTAAGGGCATCTC 59.963 54.545 0.00 0.00 0.00 2.75
563 580 2.036604 GAGCTAGTGTAAGGGCATCTCC 59.963 54.545 0.00 0.00 0.00 3.71
564 581 1.762957 GCTAGTGTAAGGGCATCTCCA 59.237 52.381 0.00 0.00 36.21 3.86
565 582 2.170607 GCTAGTGTAAGGGCATCTCCAA 59.829 50.000 0.00 0.00 36.21 3.53
566 583 3.742640 GCTAGTGTAAGGGCATCTCCAAG 60.743 52.174 0.00 0.00 36.21 3.61
567 584 1.561542 AGTGTAAGGGCATCTCCAAGG 59.438 52.381 0.00 0.00 36.21 3.61
568 585 1.282157 GTGTAAGGGCATCTCCAAGGT 59.718 52.381 0.00 0.00 36.21 3.50
569 586 1.559682 TGTAAGGGCATCTCCAAGGTC 59.440 52.381 0.00 0.00 36.21 3.85
570 587 0.830648 TAAGGGCATCTCCAAGGTCG 59.169 55.000 0.00 0.00 36.21 4.79
571 588 0.909610 AAGGGCATCTCCAAGGTCGA 60.910 55.000 0.00 0.00 36.21 4.20
572 589 0.692419 AGGGCATCTCCAAGGTCGAT 60.692 55.000 0.00 0.00 36.21 3.59
573 590 0.250081 GGGCATCTCCAAGGTCGATC 60.250 60.000 0.00 0.00 36.21 3.69
574 591 0.250081 GGCATCTCCAAGGTCGATCC 60.250 60.000 0.00 0.00 34.01 3.36
575 592 0.465705 GCATCTCCAAGGTCGATCCA 59.534 55.000 0.00 0.00 39.02 3.41
576 593 1.808133 GCATCTCCAAGGTCGATCCAC 60.808 57.143 0.00 0.00 39.02 4.02
577 594 0.747255 ATCTCCAAGGTCGATCCACG 59.253 55.000 0.00 0.00 44.09 4.94
578 595 1.141881 CTCCAAGGTCGATCCACGG 59.858 63.158 0.00 0.00 42.82 4.94
579 596 1.304630 TCCAAGGTCGATCCACGGA 60.305 57.895 0.00 1.58 42.82 4.69
580 597 0.686441 TCCAAGGTCGATCCACGGAT 60.686 55.000 0.00 0.00 42.82 4.18
581 598 0.178068 CCAAGGTCGATCCACGGATT 59.822 55.000 0.00 0.00 42.82 3.01
582 599 1.571919 CAAGGTCGATCCACGGATTC 58.428 55.000 0.00 0.00 42.82 2.52
583 600 1.137086 CAAGGTCGATCCACGGATTCT 59.863 52.381 0.00 0.00 42.82 2.40
584 601 1.033574 AGGTCGATCCACGGATTCTC 58.966 55.000 0.00 0.00 42.82 2.87
585 602 1.033574 GGTCGATCCACGGATTCTCT 58.966 55.000 0.00 0.00 42.82 3.10
586 603 1.269309 GGTCGATCCACGGATTCTCTG 60.269 57.143 0.00 0.00 42.82 3.35
587 604 1.032794 TCGATCCACGGATTCTCTGG 58.967 55.000 0.00 0.00 42.82 3.86
588 605 0.598680 CGATCCACGGATTCTCTGGC 60.599 60.000 0.00 0.00 38.46 4.85
589 606 0.598680 GATCCACGGATTCTCTGGCG 60.599 60.000 0.00 0.00 34.60 5.69
590 607 1.330655 ATCCACGGATTCTCTGGCGT 61.331 55.000 0.00 0.00 0.00 5.68
591 608 0.681887 TCCACGGATTCTCTGGCGTA 60.682 55.000 0.00 0.00 0.00 4.42
592 609 0.249073 CCACGGATTCTCTGGCGTAG 60.249 60.000 0.00 0.00 0.00 3.51
593 610 0.456221 CACGGATTCTCTGGCGTAGT 59.544 55.000 0.00 0.00 0.00 2.73
594 611 1.674441 CACGGATTCTCTGGCGTAGTA 59.326 52.381 0.00 0.00 0.00 1.82
595 612 1.674962 ACGGATTCTCTGGCGTAGTAC 59.325 52.381 0.00 0.00 0.00 2.73
596 613 1.948145 CGGATTCTCTGGCGTAGTACT 59.052 52.381 0.00 0.00 0.00 2.73
597 614 2.287069 CGGATTCTCTGGCGTAGTACTG 60.287 54.545 5.39 0.00 0.00 2.74
598 615 2.544069 GGATTCTCTGGCGTAGTACTGC 60.544 54.545 5.39 2.60 0.00 4.40
599 616 1.541379 TTCTCTGGCGTAGTACTGCA 58.459 50.000 11.70 0.00 0.00 4.41
600 617 0.809385 TCTCTGGCGTAGTACTGCAC 59.191 55.000 11.70 0.78 0.00 4.57
601 618 0.179134 CTCTGGCGTAGTACTGCACC 60.179 60.000 10.77 10.77 0.00 5.01
602 619 1.516386 CTGGCGTAGTACTGCACCG 60.516 63.158 12.58 7.43 0.00 4.94
603 620 2.884207 GGCGTAGTACTGCACCGC 60.884 66.667 11.70 15.04 43.35 5.68
604 621 2.126228 GCGTAGTACTGCACCGCA 60.126 61.111 19.38 0.00 43.53 5.69
605 622 2.442188 GCGTAGTACTGCACCGCAC 61.442 63.158 19.38 3.61 43.53 5.34
606 623 1.804326 CGTAGTACTGCACCGCACC 60.804 63.158 11.70 0.00 33.79 5.01
607 624 1.804326 GTAGTACTGCACCGCACCG 60.804 63.158 5.39 0.00 33.79 4.94
608 625 1.972752 TAGTACTGCACCGCACCGA 60.973 57.895 5.39 0.00 33.79 4.69
609 626 1.929806 TAGTACTGCACCGCACCGAG 61.930 60.000 5.39 0.00 33.79 4.63
610 627 3.299977 TACTGCACCGCACCGAGT 61.300 61.111 0.00 0.00 33.79 4.18
611 628 3.567478 TACTGCACCGCACCGAGTG 62.567 63.158 0.25 0.25 33.79 3.51
639 656 2.774439 GGCCGACGATAATGCAAATT 57.226 45.000 0.00 0.00 0.00 1.82
640 657 3.889196 GGCCGACGATAATGCAAATTA 57.111 42.857 0.00 0.00 0.00 1.40
641 658 4.419522 GGCCGACGATAATGCAAATTAT 57.580 40.909 0.00 0.00 0.00 1.28
642 659 4.158384 GGCCGACGATAATGCAAATTATG 58.842 43.478 0.00 0.00 0.00 1.90
643 660 4.083537 GGCCGACGATAATGCAAATTATGA 60.084 41.667 0.00 0.00 0.00 2.15
644 661 5.391950 GGCCGACGATAATGCAAATTATGAT 60.392 40.000 0.00 0.00 0.00 2.45
645 662 6.086222 GCCGACGATAATGCAAATTATGATT 58.914 36.000 0.00 0.00 0.00 2.57
646 663 6.582295 GCCGACGATAATGCAAATTATGATTT 59.418 34.615 0.00 0.00 35.90 2.17
655 672 3.519579 CAAATTATGATTTGGCCACGCA 58.480 40.909 3.88 3.99 45.37 5.24
656 673 2.869233 ATTATGATTTGGCCACGCAC 57.131 45.000 3.88 0.00 0.00 5.34
657 674 0.814457 TTATGATTTGGCCACGCACC 59.186 50.000 3.88 0.00 0.00 5.01
658 675 1.372838 TATGATTTGGCCACGCACCG 61.373 55.000 3.88 0.00 0.00 4.94
659 676 4.776647 GATTTGGCCACGCACCGC 62.777 66.667 3.88 0.00 0.00 5.68
671 688 2.809601 CACCGCACTACCGCAGTC 60.810 66.667 0.00 0.00 34.26 3.51
672 689 4.415332 ACCGCACTACCGCAGTCG 62.415 66.667 0.00 0.00 34.26 4.18
684 701 4.111016 CAGTCGCGCACCTACGGA 62.111 66.667 8.75 0.00 0.00 4.69
685 702 3.138798 AGTCGCGCACCTACGGAT 61.139 61.111 8.75 0.00 0.00 4.18
686 703 2.202703 GTCGCGCACCTACGGATT 60.203 61.111 8.75 0.00 0.00 3.01
687 704 2.202690 TCGCGCACCTACGGATTG 60.203 61.111 8.75 0.00 0.00 2.67
688 705 2.202690 CGCGCACCTACGGATTGA 60.203 61.111 8.75 0.00 0.00 2.57
689 706 1.591594 CGCGCACCTACGGATTGAT 60.592 57.895 8.75 0.00 0.00 2.57
690 707 1.548973 CGCGCACCTACGGATTGATC 61.549 60.000 8.75 0.00 0.00 2.92
691 708 0.529773 GCGCACCTACGGATTGATCA 60.530 55.000 0.30 0.00 0.00 2.92
692 709 1.934589 CGCACCTACGGATTGATCAA 58.065 50.000 11.26 11.26 0.00 2.57
693 710 2.276201 CGCACCTACGGATTGATCAAA 58.724 47.619 13.09 0.00 0.00 2.69
694 711 2.030457 CGCACCTACGGATTGATCAAAC 59.970 50.000 13.09 9.88 0.00 2.93
695 712 3.006940 GCACCTACGGATTGATCAAACA 58.993 45.455 13.09 0.00 0.00 2.83
696 713 3.438781 GCACCTACGGATTGATCAAACAA 59.561 43.478 13.09 0.00 0.00 2.83
697 714 4.083003 GCACCTACGGATTGATCAAACAAA 60.083 41.667 13.09 0.00 33.44 2.83
698 715 5.393027 GCACCTACGGATTGATCAAACAAAT 60.393 40.000 13.09 0.00 33.44 2.32
699 716 6.183360 GCACCTACGGATTGATCAAACAAATA 60.183 38.462 13.09 2.93 33.44 1.40
700 717 7.186804 CACCTACGGATTGATCAAACAAATAC 58.813 38.462 13.09 0.00 33.44 1.89
701 718 7.065803 CACCTACGGATTGATCAAACAAATACT 59.934 37.037 13.09 0.00 33.44 2.12
702 719 8.262227 ACCTACGGATTGATCAAACAAATACTA 58.738 33.333 13.09 0.00 33.44 1.82
703 720 8.548721 CCTACGGATTGATCAAACAAATACTAC 58.451 37.037 13.09 0.00 33.44 2.73
704 721 7.316544 ACGGATTGATCAAACAAATACTACC 57.683 36.000 13.09 3.18 33.44 3.18
705 722 6.882140 ACGGATTGATCAAACAAATACTACCA 59.118 34.615 13.09 0.00 33.44 3.25
706 723 7.148306 ACGGATTGATCAAACAAATACTACCAC 60.148 37.037 13.09 0.00 33.44 4.16
707 724 7.480810 GGATTGATCAAACAAATACTACCACC 58.519 38.462 13.09 0.00 33.44 4.61
708 725 6.827586 TTGATCAAACAAATACTACCACCC 57.172 37.500 5.45 0.00 0.00 4.61
709 726 5.882040 TGATCAAACAAATACTACCACCCA 58.118 37.500 0.00 0.00 0.00 4.51
710 727 5.943416 TGATCAAACAAATACTACCACCCAG 59.057 40.000 0.00 0.00 0.00 4.45
711 728 5.313280 TCAAACAAATACTACCACCCAGT 57.687 39.130 0.00 0.00 0.00 4.00
712 729 6.436738 TCAAACAAATACTACCACCCAGTA 57.563 37.500 0.00 0.00 33.22 2.74
713 730 6.839454 TCAAACAAATACTACCACCCAGTAA 58.161 36.000 0.00 0.00 32.47 2.24
714 731 6.938030 TCAAACAAATACTACCACCCAGTAAG 59.062 38.462 0.00 0.00 32.47 2.34
715 732 5.431179 ACAAATACTACCACCCAGTAAGG 57.569 43.478 0.00 0.00 32.47 2.69
824 848 4.035278 TGTCAATATGTCACGCGTGATA 57.965 40.909 40.84 37.99 42.18 2.15
859 883 5.188434 ACTGATATGGATTTGGTCACACAG 58.812 41.667 0.00 0.00 0.00 3.66
868 892 5.880332 GGATTTGGTCACACAGCTTTAGATA 59.120 40.000 0.00 0.00 0.00 1.98
873 897 5.186198 GGTCACACAGCTTTAGATATGGTT 58.814 41.667 0.00 0.00 0.00 3.67
914 938 9.011095 CCCGAACAGTACAAAGATCTCTATATA 57.989 37.037 0.00 0.00 0.00 0.86
976 1012 1.964373 AGTTCCGTGCGCCGATTTT 60.964 52.632 17.96 0.98 39.56 1.82
1080 1116 3.181442 CCGTCTATCTCCTCAACCTCCTA 60.181 52.174 0.00 0.00 0.00 2.94
1961 2243 2.470801 AAAATTCCGCGCGCACATGT 62.471 50.000 32.61 11.53 0.00 3.21
1962 2244 1.640210 AAATTCCGCGCGCACATGTA 61.640 50.000 32.61 10.19 0.00 2.29
1963 2245 1.436195 AATTCCGCGCGCACATGTAT 61.436 50.000 32.61 12.09 0.00 2.29
2027 2309 0.896923 GGCCAGCCATGTTGATTGAA 59.103 50.000 3.12 0.00 35.81 2.69
2060 2370 9.764363 ATTTCTAGAAATGTTAGCATCGACATA 57.236 29.630 26.26 0.00 39.36 2.29
2062 2372 8.972262 TCTAGAAATGTTAGCATCGACATATC 57.028 34.615 0.00 0.00 35.55 1.63
2066 2376 9.197694 AGAAATGTTAGCATCGACATATCTAAC 57.802 33.333 12.94 12.94 39.43 2.34
2091 2403 9.233649 ACATGCCACAAATTTCATATTCATTTT 57.766 25.926 0.00 0.00 0.00 1.82
2159 2472 1.257055 TGTAGGGCTGCCATTTTGCC 61.257 55.000 22.05 0.33 45.42 4.52
2162 2475 1.986210 GGGCTGCCATTTTGCCTCT 60.986 57.895 22.05 0.00 45.45 3.69
2346 2940 5.968387 AAAATTCCTACAGAATAGTCGCG 57.032 39.130 0.00 0.00 44.75 5.87
2392 2988 6.536224 TGCATGACAGATTACTCATGTGTTAG 59.464 38.462 5.63 0.00 39.49 2.34
2401 2997 8.589338 AGATTACTCATGTGTTAGAAAGAGTGT 58.411 33.333 5.63 0.00 37.00 3.55
2405 3001 5.297547 TCATGTGTTAGAAAGAGTGTCACC 58.702 41.667 0.00 0.00 0.00 4.02
2470 3068 9.764363 GAATTCCTATGTTTTTCCTTTGTTTCT 57.236 29.630 0.00 0.00 0.00 2.52
2515 3114 3.685756 GCATTTCCAACAATTCCACCATG 59.314 43.478 0.00 0.00 0.00 3.66
2517 3116 2.988636 TCCAACAATTCCACCATGGA 57.011 45.000 21.47 0.00 46.61 3.41
2533 3133 2.807045 GACCTCGCACGACTGCAG 60.807 66.667 13.48 13.48 44.50 4.41
2555 3156 2.422597 TCATCCAACGCGTGAAGAATT 58.577 42.857 14.98 0.00 0.00 2.17
2561 3162 4.971220 TCCAACGCGTGAAGAATTAAAAAC 59.029 37.500 14.98 0.00 0.00 2.43
2637 3238 6.473131 TCTTATGTCGCAAATCAATGAATTGC 59.527 34.615 22.22 22.22 42.80 3.56
2638 3239 3.252400 TGTCGCAAATCAATGAATTGCC 58.748 40.909 24.91 15.15 43.15 4.52
2677 3283 8.570488 CATCCAAACAGTACATATATGTGCAAT 58.430 33.333 28.53 16.88 44.40 3.56
2678 3284 8.518430 TCCAAACAGTACATATATGTGCAATT 57.482 30.769 28.53 20.61 44.40 2.32
2679 3285 8.620416 TCCAAACAGTACATATATGTGCAATTC 58.380 33.333 28.53 12.89 44.40 2.17
2680 3286 8.404765 CCAAACAGTACATATATGTGCAATTCA 58.595 33.333 28.53 7.31 44.40 2.57
2681 3287 9.786105 CAAACAGTACATATATGTGCAATTCAA 57.214 29.630 28.53 6.65 44.40 2.69
2720 3345 4.854399 TCTATCAAAAACAACGTGCTTGG 58.146 39.130 0.00 0.00 33.66 3.61
2926 3554 6.419116 GCTCCAAAAGAAACATTGAAGAAGAC 59.581 38.462 0.00 0.00 0.00 3.01
3028 3656 2.289195 ACGCAAACCCGAGAGAACATTA 60.289 45.455 0.00 0.00 0.00 1.90
3410 4039 7.353414 TGAATTAGAAACAAAATGTGTCCCA 57.647 32.000 0.00 0.00 40.60 4.37
3411 4040 7.786030 TGAATTAGAAACAAAATGTGTCCCAA 58.214 30.769 0.00 0.00 40.60 4.12
3747 5079 5.188327 TCCAATGAGTACTATTGAGAGCG 57.812 43.478 18.71 8.20 37.65 5.03
3781 5114 7.582667 AGACAAATGGTTAACTTATATGGCC 57.417 36.000 5.42 0.00 0.00 5.36
3787 5120 6.969993 TGGTTAACTTATATGGCCATTTCC 57.030 37.500 26.37 11.84 0.00 3.13
3853 5482 8.878769 GTTCTCAGAGGAAGAAAATAAGACATC 58.121 37.037 0.00 0.00 0.00 3.06
3884 5514 7.652300 TTCACAACAGAATATATACGCCATC 57.348 36.000 0.00 0.00 0.00 3.51
3895 5525 9.167311 GAATATATACGCCATCCAAAGATTCTT 57.833 33.333 0.00 0.00 0.00 2.52
3935 5565 4.322080 TTCGTCGCCATGAGAATTATCT 57.678 40.909 1.19 0.00 39.10 1.98
4251 6801 8.717717 TGGAGATCTAATGTGGATAGAACAATT 58.282 33.333 0.00 0.00 33.37 2.32
4286 6836 6.975772 TGACCAAGGAAATAAAGAAACAAACG 59.024 34.615 0.00 0.00 0.00 3.60
4366 6916 1.286248 TGGCCCTTCTTTCCTACTCC 58.714 55.000 0.00 0.00 0.00 3.85
4377 6927 0.033405 TCCTACTCCCTCCGTTCCTG 60.033 60.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.667107 GTATATCATTAGTATAGCCCAGCAAAA 57.333 33.333 0.00 0.00 0.00 2.44
37 38 9.046846 AGTATATCATTAGTATAGCCCAGCAAA 57.953 33.333 0.00 0.00 0.00 3.68
38 39 8.609617 AGTATATCATTAGTATAGCCCAGCAA 57.390 34.615 0.00 0.00 0.00 3.91
39 40 8.478066 CAAGTATATCATTAGTATAGCCCAGCA 58.522 37.037 0.00 0.00 0.00 4.41
40 41 7.439655 GCAAGTATATCATTAGTATAGCCCAGC 59.560 40.741 0.00 0.00 0.00 4.85
41 42 8.478066 TGCAAGTATATCATTAGTATAGCCCAG 58.522 37.037 0.00 0.00 0.00 4.45
42 43 8.374184 TGCAAGTATATCATTAGTATAGCCCA 57.626 34.615 0.00 0.00 0.00 5.36
53 54 9.392259 CATGATCTGGTATGCAAGTATATCATT 57.608 33.333 9.67 0.00 0.00 2.57
54 55 7.991460 CCATGATCTGGTATGCAAGTATATCAT 59.009 37.037 0.00 0.00 40.49 2.45
55 56 7.333323 CCATGATCTGGTATGCAAGTATATCA 58.667 38.462 0.00 0.00 40.49 2.15
56 57 6.765036 CCCATGATCTGGTATGCAAGTATATC 59.235 42.308 0.00 0.00 44.30 1.63
57 58 6.656902 CCCATGATCTGGTATGCAAGTATAT 58.343 40.000 0.00 0.00 44.30 0.86
58 59 5.571454 GCCCATGATCTGGTATGCAAGTATA 60.571 44.000 0.00 0.00 44.30 1.47
59 60 4.808665 GCCCATGATCTGGTATGCAAGTAT 60.809 45.833 0.00 0.00 44.30 2.12
60 61 3.496692 GCCCATGATCTGGTATGCAAGTA 60.497 47.826 0.00 0.00 44.30 2.24
61 62 2.750807 GCCCATGATCTGGTATGCAAGT 60.751 50.000 0.00 0.00 44.30 3.16
62 63 1.884579 GCCCATGATCTGGTATGCAAG 59.115 52.381 0.00 0.00 44.30 4.01
63 64 1.479205 GGCCCATGATCTGGTATGCAA 60.479 52.381 0.00 0.00 44.30 4.08
64 65 0.111061 GGCCCATGATCTGGTATGCA 59.889 55.000 0.00 0.00 44.30 3.96
65 66 0.610232 GGGCCCATGATCTGGTATGC 60.610 60.000 19.95 6.47 44.30 3.14
66 67 0.038744 GGGGCCCATGATCTGGTATG 59.961 60.000 26.86 0.00 44.30 2.39
67 68 0.103715 AGGGGCCCATGATCTGGTAT 60.104 55.000 27.72 0.00 44.30 2.73
68 69 1.061905 CAGGGGCCCATGATCTGGTA 61.062 60.000 33.03 0.00 44.30 3.25
69 70 2.045132 AGGGGCCCATGATCTGGT 59.955 61.111 27.72 0.00 44.30 4.00
70 71 2.519441 CAGGGGCCCATGATCTGG 59.481 66.667 33.03 1.80 45.51 3.86
71 72 2.203451 GCAGGGGCCCATGATCTG 60.203 66.667 39.75 27.91 0.00 2.90
88 89 3.813724 CCAAGGGCCCAGGCTAGG 61.814 72.222 27.56 12.13 41.60 3.02
89 90 4.512914 GCCAAGGGCCCAGGCTAG 62.513 72.222 37.70 17.76 44.06 3.42
105 106 3.423154 CCAACGAGAGGCAACGGC 61.423 66.667 0.00 0.00 46.39 5.68
112 113 1.289066 TCGTCTTGCCAACGAGAGG 59.711 57.895 0.00 0.00 43.65 3.69
113 114 4.966005 TCGTCTTGCCAACGAGAG 57.034 55.556 0.00 0.00 43.65 3.20
117 118 2.398554 CCCCATCGTCTTGCCAACG 61.399 63.158 0.00 0.00 41.39 4.10
118 119 2.700773 GCCCCATCGTCTTGCCAAC 61.701 63.158 0.00 0.00 0.00 3.77
119 120 2.361104 GCCCCATCGTCTTGCCAA 60.361 61.111 0.00 0.00 0.00 4.52
120 121 4.424711 GGCCCCATCGTCTTGCCA 62.425 66.667 0.00 0.00 41.76 4.92
121 122 4.115199 AGGCCCCATCGTCTTGCC 62.115 66.667 0.00 0.00 42.48 4.52
122 123 2.514824 GAGGCCCCATCGTCTTGC 60.515 66.667 0.00 0.00 0.00 4.01
123 124 2.202932 CGAGGCCCCATCGTCTTG 60.203 66.667 0.00 0.00 35.48 3.02
124 125 2.363795 TCGAGGCCCCATCGTCTT 60.364 61.111 12.10 0.00 40.95 3.01
125 126 3.148279 GTCGAGGCCCCATCGTCT 61.148 66.667 12.10 0.00 40.95 4.18
184 185 2.684192 AAATGTTGGTCCGGTCGCCA 62.684 55.000 0.00 6.18 0.00 5.69
276 277 4.735369 ACAACCCAGATACAACAAATCCA 58.265 39.130 0.00 0.00 0.00 3.41
351 352 6.545666 TGCAAAGATCGGGTGTAATTGATATT 59.454 34.615 0.00 0.00 0.00 1.28
355 356 3.680490 TGCAAAGATCGGGTGTAATTGA 58.320 40.909 0.00 0.00 0.00 2.57
453 470 1.909700 TGCGAAAGGCTTTTCCATCT 58.090 45.000 14.66 0.00 44.05 2.90
455 472 1.404583 GCATGCGAAAGGCTTTTCCAT 60.405 47.619 14.66 15.48 44.05 3.41
456 473 0.038343 GCATGCGAAAGGCTTTTCCA 60.038 50.000 14.66 13.94 44.05 3.53
483 500 0.774098 CGTTGAACACGTGACGGTAG 59.226 55.000 25.01 5.49 44.49 3.18
503 520 1.111116 CCGATTAGCCGACACCCCTA 61.111 60.000 0.00 0.00 0.00 3.53
508 525 2.006772 CAAGCCGATTAGCCGACAC 58.993 57.895 0.00 0.00 0.00 3.67
509 526 1.813753 GCAAGCCGATTAGCCGACA 60.814 57.895 0.00 0.00 0.00 4.35
510 527 1.813753 TGCAAGCCGATTAGCCGAC 60.814 57.895 0.00 0.00 0.00 4.79
511 528 1.813753 GTGCAAGCCGATTAGCCGA 60.814 57.895 0.00 0.00 0.00 5.54
512 529 2.709475 GTGCAAGCCGATTAGCCG 59.291 61.111 0.00 0.00 0.00 5.52
513 530 1.748879 TGGTGCAAGCCGATTAGCC 60.749 57.895 0.00 0.00 0.00 3.93
514 531 1.429423 GTGGTGCAAGCCGATTAGC 59.571 57.895 0.00 0.00 0.00 3.09
515 532 0.392998 AGGTGGTGCAAGCCGATTAG 60.393 55.000 0.00 0.00 0.00 1.73
516 533 0.676466 CAGGTGGTGCAAGCCGATTA 60.676 55.000 0.00 0.00 0.00 1.75
517 534 1.973281 CAGGTGGTGCAAGCCGATT 60.973 57.895 0.00 0.00 0.00 3.34
518 535 2.360350 CAGGTGGTGCAAGCCGAT 60.360 61.111 0.00 0.00 0.00 4.18
527 544 2.033141 CTCCAGGTGCAGGTGGTG 59.967 66.667 12.92 7.81 35.14 4.17
528 545 3.958860 GCTCCAGGTGCAGGTGGT 61.959 66.667 8.73 0.00 35.14 4.16
529 546 2.249413 CTAGCTCCAGGTGCAGGTGG 62.249 65.000 15.92 7.82 34.87 4.61
530 547 1.220206 CTAGCTCCAGGTGCAGGTG 59.780 63.158 15.92 0.00 0.00 4.00
531 548 1.229336 ACTAGCTCCAGGTGCAGGT 60.229 57.895 15.92 10.29 0.00 4.00
532 549 1.220206 CACTAGCTCCAGGTGCAGG 59.780 63.158 15.92 9.69 0.00 4.85
533 550 1.186200 TACACTAGCTCCAGGTGCAG 58.814 55.000 15.92 12.42 34.70 4.41
534 551 1.550524 CTTACACTAGCTCCAGGTGCA 59.449 52.381 15.92 1.41 34.70 4.57
535 552 1.134670 CCTTACACTAGCTCCAGGTGC 60.135 57.143 5.25 5.25 34.70 5.01
536 553 1.482593 CCCTTACACTAGCTCCAGGTG 59.517 57.143 0.00 0.00 37.05 4.00
537 554 1.867363 CCCTTACACTAGCTCCAGGT 58.133 55.000 0.00 0.00 0.00 4.00
538 555 0.466124 GCCCTTACACTAGCTCCAGG 59.534 60.000 0.00 0.00 0.00 4.45
539 556 1.195115 TGCCCTTACACTAGCTCCAG 58.805 55.000 0.00 0.00 0.00 3.86
540 557 1.762957 GATGCCCTTACACTAGCTCCA 59.237 52.381 0.00 0.00 0.00 3.86
541 558 2.036604 GAGATGCCCTTACACTAGCTCC 59.963 54.545 0.00 0.00 0.00 4.70
542 559 2.036604 GGAGATGCCCTTACACTAGCTC 59.963 54.545 0.00 0.00 0.00 4.09
543 560 2.043227 GGAGATGCCCTTACACTAGCT 58.957 52.381 0.00 0.00 0.00 3.32
544 561 1.762957 TGGAGATGCCCTTACACTAGC 59.237 52.381 0.00 0.00 34.97 3.42
545 562 3.181461 CCTTGGAGATGCCCTTACACTAG 60.181 52.174 0.00 0.00 34.97 2.57
546 563 2.771943 CCTTGGAGATGCCCTTACACTA 59.228 50.000 0.00 0.00 34.97 2.74
547 564 1.561542 CCTTGGAGATGCCCTTACACT 59.438 52.381 0.00 0.00 34.97 3.55
548 565 1.282157 ACCTTGGAGATGCCCTTACAC 59.718 52.381 0.00 0.00 34.97 2.90
549 566 1.559682 GACCTTGGAGATGCCCTTACA 59.440 52.381 0.00 0.00 34.97 2.41
550 567 1.473434 CGACCTTGGAGATGCCCTTAC 60.473 57.143 0.00 0.00 34.97 2.34
551 568 0.830648 CGACCTTGGAGATGCCCTTA 59.169 55.000 0.00 0.00 34.97 2.69
552 569 0.909610 TCGACCTTGGAGATGCCCTT 60.910 55.000 0.00 0.00 34.97 3.95
553 570 0.692419 ATCGACCTTGGAGATGCCCT 60.692 55.000 0.00 0.00 34.97 5.19
554 571 0.250081 GATCGACCTTGGAGATGCCC 60.250 60.000 0.00 0.00 34.97 5.36
555 572 0.250081 GGATCGACCTTGGAGATGCC 60.250 60.000 0.00 0.00 35.41 4.40
556 573 0.465705 TGGATCGACCTTGGAGATGC 59.534 55.000 11.61 11.61 39.86 3.91
557 574 1.536922 CGTGGATCGACCTTGGAGATG 60.537 57.143 1.93 0.00 42.86 2.90
558 575 0.747255 CGTGGATCGACCTTGGAGAT 59.253 55.000 1.93 0.00 42.86 2.75
559 576 1.320344 CCGTGGATCGACCTTGGAGA 61.320 60.000 1.93 0.00 42.86 3.71
560 577 1.141881 CCGTGGATCGACCTTGGAG 59.858 63.158 1.93 0.00 42.86 3.86
561 578 0.686441 ATCCGTGGATCGACCTTGGA 60.686 55.000 14.82 14.82 43.10 3.53
562 579 0.178068 AATCCGTGGATCGACCTTGG 59.822 55.000 1.04 0.00 42.86 3.61
563 580 1.137086 AGAATCCGTGGATCGACCTTG 59.863 52.381 1.04 0.00 42.86 3.61
564 581 1.409427 GAGAATCCGTGGATCGACCTT 59.591 52.381 1.04 0.00 42.86 3.50
565 582 1.033574 GAGAATCCGTGGATCGACCT 58.966 55.000 1.04 0.00 42.86 3.85
566 583 1.033574 AGAGAATCCGTGGATCGACC 58.966 55.000 1.04 0.00 42.86 4.79
567 584 1.269309 CCAGAGAATCCGTGGATCGAC 60.269 57.143 1.04 0.00 42.86 4.20
568 585 1.032794 CCAGAGAATCCGTGGATCGA 58.967 55.000 1.04 0.00 42.86 3.59
569 586 0.598680 GCCAGAGAATCCGTGGATCG 60.599 60.000 1.04 0.00 33.66 3.69
570 587 0.598680 CGCCAGAGAATCCGTGGATC 60.599 60.000 1.04 0.00 33.66 3.36
571 588 1.330655 ACGCCAGAGAATCCGTGGAT 61.331 55.000 2.87 0.00 33.66 3.41
572 589 0.681887 TACGCCAGAGAATCCGTGGA 60.682 55.000 2.87 0.00 32.93 4.02
573 590 0.249073 CTACGCCAGAGAATCCGTGG 60.249 60.000 0.00 0.00 32.93 4.94
574 591 0.456221 ACTACGCCAGAGAATCCGTG 59.544 55.000 0.00 0.00 32.93 4.94
575 592 1.674962 GTACTACGCCAGAGAATCCGT 59.325 52.381 0.00 0.00 34.95 4.69
576 593 1.948145 AGTACTACGCCAGAGAATCCG 59.052 52.381 0.00 0.00 33.66 4.18
577 594 2.544069 GCAGTACTACGCCAGAGAATCC 60.544 54.545 0.00 0.00 33.66 3.01
578 595 2.099263 TGCAGTACTACGCCAGAGAATC 59.901 50.000 0.00 0.00 0.00 2.52
579 596 2.100197 TGCAGTACTACGCCAGAGAAT 58.900 47.619 0.00 0.00 0.00 2.40
580 597 1.201647 GTGCAGTACTACGCCAGAGAA 59.798 52.381 0.00 0.00 0.00 2.87
581 598 0.809385 GTGCAGTACTACGCCAGAGA 59.191 55.000 0.00 0.00 0.00 3.10
582 599 0.179134 GGTGCAGTACTACGCCAGAG 60.179 60.000 19.04 0.00 36.44 3.35
583 600 1.888018 GGTGCAGTACTACGCCAGA 59.112 57.895 19.04 0.00 36.44 3.86
584 601 1.516386 CGGTGCAGTACTACGCCAG 60.516 63.158 22.61 12.95 36.18 4.85
585 602 2.569657 CGGTGCAGTACTACGCCA 59.430 61.111 22.61 3.97 36.18 5.69
586 603 2.884207 GCGGTGCAGTACTACGCC 60.884 66.667 14.78 14.78 44.01 5.68
588 605 1.804326 GGTGCGGTGCAGTACTACG 60.804 63.158 0.00 0.00 40.08 3.51
589 606 1.804326 CGGTGCGGTGCAGTACTAC 60.804 63.158 0.00 0.00 40.08 2.73
590 607 1.929806 CTCGGTGCGGTGCAGTACTA 61.930 60.000 0.00 0.00 40.08 1.82
591 608 3.282745 CTCGGTGCGGTGCAGTACT 62.283 63.158 0.00 0.00 40.08 2.73
592 609 2.809601 CTCGGTGCGGTGCAGTAC 60.810 66.667 0.00 0.00 40.08 2.73
593 610 3.299977 ACTCGGTGCGGTGCAGTA 61.300 61.111 0.00 0.00 40.08 2.74
594 611 4.969196 CACTCGGTGCGGTGCAGT 62.969 66.667 0.00 0.00 40.08 4.40
613 630 1.727511 ATTATCGTCGGCCGGTTCGA 61.728 55.000 30.16 30.16 37.11 3.71
614 631 1.299620 ATTATCGTCGGCCGGTTCG 60.300 57.895 27.83 25.45 37.11 3.95
615 632 1.828331 GCATTATCGTCGGCCGGTTC 61.828 60.000 27.83 15.10 37.11 3.62
616 633 1.885850 GCATTATCGTCGGCCGGTT 60.886 57.895 27.83 10.26 37.11 4.44
617 634 2.279918 GCATTATCGTCGGCCGGT 60.280 61.111 27.83 11.80 37.11 5.28
618 635 1.433053 TTTGCATTATCGTCGGCCGG 61.433 55.000 27.83 10.69 37.11 6.13
619 636 0.586319 ATTTGCATTATCGTCGGCCG 59.414 50.000 22.12 22.12 38.13 6.13
620 637 2.774439 AATTTGCATTATCGTCGGCC 57.226 45.000 0.00 0.00 0.00 6.13
621 638 5.029650 TCATAATTTGCATTATCGTCGGC 57.970 39.130 0.00 0.00 33.88 5.54
622 639 7.060979 CCAAATCATAATTTGCATTATCGTCGG 59.939 37.037 0.00 0.00 46.90 4.79
623 640 7.409661 GCCAAATCATAATTTGCATTATCGTCG 60.410 37.037 0.00 0.00 46.90 5.12
624 641 7.148755 GGCCAAATCATAATTTGCATTATCGTC 60.149 37.037 0.00 0.00 46.90 4.20
625 642 6.646240 GGCCAAATCATAATTTGCATTATCGT 59.354 34.615 0.00 0.00 46.90 3.73
626 643 6.645827 TGGCCAAATCATAATTTGCATTATCG 59.354 34.615 0.61 0.00 46.90 2.92
627 644 7.359431 CGTGGCCAAATCATAATTTGCATTATC 60.359 37.037 7.24 0.00 46.90 1.75
628 645 6.424509 CGTGGCCAAATCATAATTTGCATTAT 59.575 34.615 7.24 0.00 46.90 1.28
629 646 5.752472 CGTGGCCAAATCATAATTTGCATTA 59.248 36.000 7.24 0.00 46.90 1.90
630 647 4.571580 CGTGGCCAAATCATAATTTGCATT 59.428 37.500 7.24 0.00 46.90 3.56
631 648 4.121317 CGTGGCCAAATCATAATTTGCAT 58.879 39.130 7.24 0.00 46.90 3.96
632 649 3.519579 CGTGGCCAAATCATAATTTGCA 58.480 40.909 7.24 0.00 46.90 4.08
633 650 2.284952 GCGTGGCCAAATCATAATTTGC 59.715 45.455 7.24 0.00 46.90 3.68
635 652 3.520569 GTGCGTGGCCAAATCATAATTT 58.479 40.909 7.24 0.00 35.43 1.82
636 653 2.159114 GGTGCGTGGCCAAATCATAATT 60.159 45.455 7.24 0.00 0.00 1.40
637 654 1.408702 GGTGCGTGGCCAAATCATAAT 59.591 47.619 7.24 0.00 0.00 1.28
638 655 0.814457 GGTGCGTGGCCAAATCATAA 59.186 50.000 7.24 0.00 0.00 1.90
639 656 1.372838 CGGTGCGTGGCCAAATCATA 61.373 55.000 7.24 0.00 0.00 2.15
640 657 2.699768 CGGTGCGTGGCCAAATCAT 61.700 57.895 7.24 0.00 0.00 2.45
641 658 3.361158 CGGTGCGTGGCCAAATCA 61.361 61.111 7.24 2.23 0.00 2.57
642 659 4.776647 GCGGTGCGTGGCCAAATC 62.777 66.667 7.24 0.00 0.00 2.17
678 695 8.548721 GGTAGTATTTGTTTGATCAATCCGTAG 58.451 37.037 9.40 0.00 0.00 3.51
679 696 8.041919 TGGTAGTATTTGTTTGATCAATCCGTA 58.958 33.333 9.40 0.00 0.00 4.02
680 697 6.882140 TGGTAGTATTTGTTTGATCAATCCGT 59.118 34.615 9.40 0.56 0.00 4.69
681 698 7.186804 GTGGTAGTATTTGTTTGATCAATCCG 58.813 38.462 9.40 0.00 0.00 4.18
682 699 7.416326 GGGTGGTAGTATTTGTTTGATCAATCC 60.416 40.741 9.40 3.88 0.00 3.01
683 700 7.122055 TGGGTGGTAGTATTTGTTTGATCAATC 59.878 37.037 9.40 9.29 0.00 2.67
684 701 6.951198 TGGGTGGTAGTATTTGTTTGATCAAT 59.049 34.615 9.40 0.00 0.00 2.57
685 702 6.307776 TGGGTGGTAGTATTTGTTTGATCAA 58.692 36.000 3.38 3.38 0.00 2.57
686 703 5.882040 TGGGTGGTAGTATTTGTTTGATCA 58.118 37.500 0.00 0.00 0.00 2.92
687 704 5.944007 ACTGGGTGGTAGTATTTGTTTGATC 59.056 40.000 0.00 0.00 0.00 2.92
688 705 5.887754 ACTGGGTGGTAGTATTTGTTTGAT 58.112 37.500 0.00 0.00 0.00 2.57
689 706 5.313280 ACTGGGTGGTAGTATTTGTTTGA 57.687 39.130 0.00 0.00 0.00 2.69
690 707 6.150474 CCTTACTGGGTGGTAGTATTTGTTTG 59.850 42.308 0.00 0.00 31.27 2.93
691 708 6.243148 CCTTACTGGGTGGTAGTATTTGTTT 58.757 40.000 0.00 0.00 31.27 2.83
692 709 5.805424 GCCTTACTGGGTGGTAGTATTTGTT 60.805 44.000 0.00 0.00 36.00 2.83
693 710 4.324022 GCCTTACTGGGTGGTAGTATTTGT 60.324 45.833 0.00 0.00 36.00 2.83
694 711 4.196971 GCCTTACTGGGTGGTAGTATTTG 58.803 47.826 0.00 0.00 36.00 2.32
695 712 3.847780 TGCCTTACTGGGTGGTAGTATTT 59.152 43.478 0.00 0.00 36.00 1.40
696 713 3.199289 GTGCCTTACTGGGTGGTAGTATT 59.801 47.826 0.00 0.00 36.00 1.89
697 714 2.770232 GTGCCTTACTGGGTGGTAGTAT 59.230 50.000 0.00 0.00 36.00 2.12
698 715 2.181975 GTGCCTTACTGGGTGGTAGTA 58.818 52.381 0.00 0.00 36.00 1.82
699 716 0.981943 GTGCCTTACTGGGTGGTAGT 59.018 55.000 0.00 0.00 36.00 2.73
700 717 0.252197 GGTGCCTTACTGGGTGGTAG 59.748 60.000 0.00 0.00 36.00 3.18
701 718 1.546589 CGGTGCCTTACTGGGTGGTA 61.547 60.000 0.00 0.00 36.00 3.25
702 719 2.890766 CGGTGCCTTACTGGGTGGT 61.891 63.158 0.00 0.00 36.00 4.16
703 720 2.046314 CGGTGCCTTACTGGGTGG 60.046 66.667 0.00 0.00 36.00 4.61
704 721 1.375523 GTCGGTGCCTTACTGGGTG 60.376 63.158 0.00 0.00 36.28 4.61
705 722 2.939261 CGTCGGTGCCTTACTGGGT 61.939 63.158 0.00 0.00 36.28 4.51
706 723 2.125673 CGTCGGTGCCTTACTGGG 60.126 66.667 0.00 0.00 36.28 4.45
707 724 2.125673 CCGTCGGTGCCTTACTGG 60.126 66.667 2.08 0.00 36.28 4.00
708 725 1.012486 GTTCCGTCGGTGCCTTACTG 61.012 60.000 11.88 0.00 36.99 2.74
709 726 1.291272 GTTCCGTCGGTGCCTTACT 59.709 57.895 11.88 0.00 0.00 2.24
710 727 1.005867 TGTTCCGTCGGTGCCTTAC 60.006 57.895 11.88 2.38 0.00 2.34
711 728 1.180456 TCTGTTCCGTCGGTGCCTTA 61.180 55.000 11.88 0.00 0.00 2.69
712 729 2.030562 CTGTTCCGTCGGTGCCTT 59.969 61.111 11.88 0.00 0.00 4.35
713 730 2.915659 TCTGTTCCGTCGGTGCCT 60.916 61.111 11.88 0.00 0.00 4.75
714 731 2.432628 CTCTGTTCCGTCGGTGCC 60.433 66.667 11.88 0.94 0.00 5.01
715 732 3.112709 GCTCTGTTCCGTCGGTGC 61.113 66.667 11.88 6.05 0.00 5.01
753 770 0.179045 CGTAGGCTCCTTTCCCATGG 60.179 60.000 4.14 4.14 0.00 3.66
759 776 3.259902 CAAAGGTACGTAGGCTCCTTTC 58.740 50.000 19.64 0.00 44.97 2.62
796 813 3.294102 CGTGACATATTGACATGCATGC 58.706 45.455 26.53 18.59 0.00 4.06
838 862 3.947196 GCTGTGTGACCAAATCCATATCA 59.053 43.478 0.00 0.00 0.00 2.15
859 883 7.013942 ACCGGGAATAAAAACCATATCTAAAGC 59.986 37.037 6.32 0.00 0.00 3.51
868 892 3.101437 GGGAACCGGGAATAAAAACCAT 58.899 45.455 6.32 0.00 40.86 3.55
915 939 9.281075 CGCACAACGCTATTTATATATAGTGTA 57.719 33.333 21.99 0.00 46.00 2.90
918 942 8.242053 ACTCGCACAACGCTATTTATATATAGT 58.758 33.333 10.68 0.00 43.23 2.12
919 943 8.524267 CACTCGCACAACGCTATTTATATATAG 58.476 37.037 5.98 5.98 43.23 1.31
920 944 8.238631 TCACTCGCACAACGCTATTTATATATA 58.761 33.333 0.00 0.00 43.23 0.86
921 945 7.061905 GTCACTCGCACAACGCTATTTATATAT 59.938 37.037 0.00 0.00 43.23 0.86
976 1012 6.299805 TGCTAAGATGCTTCCTCTCTTTTA 57.700 37.500 0.00 0.00 31.89 1.52
1017 1053 3.127533 GCTAGCCACGGCACAAGG 61.128 66.667 11.35 0.00 44.88 3.61
1623 1783 2.203195 GCCTGCATGATGGCCGTA 60.203 61.111 15.79 0.00 43.11 4.02
1961 2243 4.533311 TCAGATGGCAAGGCTGATCATATA 59.467 41.667 12.24 0.00 34.02 0.86
1962 2244 3.329814 TCAGATGGCAAGGCTGATCATAT 59.670 43.478 12.24 0.00 34.02 1.78
1963 2245 2.707257 TCAGATGGCAAGGCTGATCATA 59.293 45.455 12.24 0.00 34.02 2.15
2038 2320 8.978564 AGATATGTCGATGCTAACATTTCTAG 57.021 34.615 6.65 0.00 40.26 2.43
2041 2323 8.978539 TGTTAGATATGTCGATGCTAACATTTC 58.021 33.333 17.00 8.68 43.27 2.17
2046 2328 6.183360 GGCATGTTAGATATGTCGATGCTAAC 60.183 42.308 13.96 0.00 40.59 2.34
2047 2329 5.869344 GGCATGTTAGATATGTCGATGCTAA 59.131 40.000 13.96 0.00 33.51 3.09
2048 2330 5.047377 TGGCATGTTAGATATGTCGATGCTA 60.047 40.000 13.96 8.63 32.96 3.49
2049 2331 4.248859 GGCATGTTAGATATGTCGATGCT 58.751 43.478 13.96 0.00 33.51 3.79
2060 2370 9.754382 GAATATGAAATTTGTGGCATGTTAGAT 57.246 29.630 0.00 0.00 0.00 1.98
2062 2372 8.929827 TGAATATGAAATTTGTGGCATGTTAG 57.070 30.769 0.00 0.00 0.00 2.34
2065 2375 8.795842 AAATGAATATGAAATTTGTGGCATGT 57.204 26.923 0.00 0.00 0.00 3.21
2133 2446 5.582950 AAATGGCAGCCCTACAATCTATA 57.417 39.130 9.64 0.00 0.00 1.31
2134 2447 4.459852 AAATGGCAGCCCTACAATCTAT 57.540 40.909 9.64 0.00 0.00 1.98
2135 2448 3.951563 AAATGGCAGCCCTACAATCTA 57.048 42.857 9.64 0.00 0.00 1.98
2141 2454 1.517361 GGCAAAATGGCAGCCCTAC 59.483 57.895 9.64 0.00 43.14 3.18
2189 2569 4.911522 TCCGGACATAGGGAAATAAGGAAT 59.088 41.667 0.00 0.00 0.00 3.01
2264 2850 3.623960 TGTTTTCACTGTTAGTGGTTCCG 59.376 43.478 8.91 0.00 45.94 4.30
2346 2940 8.537223 CATGCATGATTTCTGTAAAAGTTATGC 58.463 33.333 22.59 0.00 34.55 3.14
2392 2988 4.320275 GGAAAATTCCGGTGACACTCTTTC 60.320 45.833 0.00 5.97 37.65 2.62
2470 3068 3.838317 AGTGAAATACAGTCAGCCTGGTA 59.162 43.478 0.00 0.00 46.06 3.25
2533 3133 1.144969 TCTTCACGCGTTGGATGAAC 58.855 50.000 10.22 0.00 0.00 3.18
2555 3156 7.235804 AGCTATTGTTCCTAACCCAGTTTTTA 58.764 34.615 0.00 0.00 0.00 1.52
2561 3162 4.200092 GGAAGCTATTGTTCCTAACCCAG 58.800 47.826 0.00 0.00 40.46 4.45
3028 3656 5.947566 AGGTATTGTGTAACCGGCTATTTTT 59.052 36.000 0.00 0.00 40.88 1.94
3679 5005 7.423314 GCATGCGAATGAAATGTTGTATTTTTC 59.577 33.333 7.84 0.00 0.00 2.29
3781 5114 8.466798 CAATACTTAAGGTGTAAAGGGGAAATG 58.533 37.037 7.53 0.00 0.00 2.32
3787 5120 7.308951 CCAACACAATACTTAAGGTGTAAAGGG 60.309 40.741 13.45 10.06 43.16 3.95
3895 5525 9.005180 GCGACGAATTATGAACAATGAAATTTA 57.995 29.630 0.00 0.00 31.22 1.40
3935 5565 8.073768 GGACAAATATTTCTGAACGTTGAAGAA 58.926 33.333 5.00 12.11 0.00 2.52
3987 5621 9.825972 GAAAGATTTATGAACTTTCGAATGTGA 57.174 29.630 16.47 7.80 39.59 3.58
4133 6349 3.317711 TCATCAATGCTTTTGGTTCGTGT 59.682 39.130 1.03 0.00 0.00 4.49
4366 6916 4.770795 AGACAAATATTCAGGAACGGAGG 58.229 43.478 0.00 0.00 31.97 4.30


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

AutoCloner maintained by Alex Coulton.