Multiple sequence alignment - TraesCS6B01G097800

Loading Multiple Alignment...

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 TraesCS6B01G097800 chr6B 100.000 4446 0 0 1 4446 75424503 75420058 0.000000e+00 8211.0
1 TraesCS6B01G097800 chr6B 81.957 2167 259 66 2279 4359 75045498 75043378 0.000000e+00 1714.0
2 TraesCS6B01G097800 chr6B 84.922 1532 190 28 1020 2527 75526311 75524797 0.000000e+00 1511.0
3 TraesCS6B01G097800 chr6B 91.737 835 54 10 3620 4446 75405874 75405047 0.000000e+00 1146.0
4 TraesCS6B01G097800 chr6B 82.784 1243 142 36 3110 4302 75524587 75523367 0.000000e+00 1044.0
5 TraesCS6B01G097800 chr6B 72.599 354 82 14 1823 2165 51435025 51434676 7.870000e-18 102.0
6 TraesCS6B01G097800 chr6D 94.794 1748 47 16 2723 4446 35716313 35714586 0.000000e+00 2684.0
7 TraesCS6B01G097800 chr6D 91.279 1720 130 13 707 2414 35718332 35716621 0.000000e+00 2327.0
8 TraesCS6B01G097800 chr6D 79.170 2338 334 76 1012 3293 35642079 35639839 0.000000e+00 1478.0
9 TraesCS6B01G097800 chr6D 84.948 1156 142 21 1399 2534 36084578 36083435 0.000000e+00 1142.0
10 TraesCS6B01G097800 chr6D 81.344 1399 199 31 1019 2372 35667512 35666131 0.000000e+00 1081.0
11 TraesCS6B01G097800 chr6D 82.470 1255 150 37 3081 4276 36083438 36082195 0.000000e+00 1035.0
12 TraesCS6B01G097800 chr6D 76.912 1412 247 54 1414 2781 35885890 35884514 0.000000e+00 728.0
13 TraesCS6B01G097800 chr6D 84.211 627 78 7 3330 3939 35639839 35639217 1.380000e-164 590.0
14 TraesCS6B01G097800 chr6D 83.411 645 91 9 996 1629 36106123 36105484 6.410000e-163 584.0
15 TraesCS6B01G097800 chr6D 96.764 309 10 0 2450 2758 35716621 35716313 2.370000e-142 516.0
16 TraesCS6B01G097800 chr6D 81.056 644 86 22 3045 3655 36073550 36072910 8.650000e-132 481.0
17 TraesCS6B01G097800 chr6D 78.117 754 129 19 1632 2357 36105451 36104706 3.160000e-121 446.0
18 TraesCS6B01G097800 chr6D 87.467 383 43 4 1020 1401 36090453 36090075 1.900000e-118 436.0
19 TraesCS6B01G097800 chr6D 91.429 280 24 0 1021 1300 36074173 36073894 6.980000e-103 385.0
20 TraesCS6B01G097800 chr6D 76.678 596 107 24 1729 2303 36324593 36325177 7.230000e-78 302.0
21 TraesCS6B01G097800 chr6D 72.022 361 86 14 1823 2172 27682974 27682618 4.740000e-15 93.5
22 TraesCS6B01G097800 chr6A 85.000 1540 196 23 1019 2534 39670766 39669238 0.000000e+00 1531.0
23 TraesCS6B01G097800 chr6A 84.211 1539 208 22 1020 2534 39628973 39627446 0.000000e+00 1463.0
24 TraesCS6B01G097800 chr6A 84.016 1539 208 26 1022 2534 39581183 39579657 0.000000e+00 1445.0
25 TraesCS6B01G097800 chr6A 81.461 1780 231 54 1562 3293 39590484 39588756 0.000000e+00 1367.0
26 TraesCS6B01G097800 chr6A 82.544 1604 199 43 1731 3293 39548202 39546639 0.000000e+00 1336.0
27 TraesCS6B01G097800 chr6A 82.243 1605 200 42 1731 3293 39638109 39636548 0.000000e+00 1306.0
28 TraesCS6B01G097800 chr6A 81.723 1242 164 30 3110 4302 39579642 39578415 0.000000e+00 977.0
29 TraesCS6B01G097800 chr6A 79.344 1433 209 45 996 2357 39878026 39876610 0.000000e+00 926.0
30 TraesCS6B01G097800 chr6A 85.008 627 72 8 3330 3939 39588756 39588135 6.320000e-173 617.0
31 TraesCS6B01G097800 chr6A 86.871 556 65 6 3388 3939 39546568 39546017 2.270000e-172 616.0
32 TraesCS6B01G097800 chr6A 84.689 627 74 11 3330 3939 39636548 39635927 1.370000e-169 606.0
33 TraesCS6B01G097800 chr6A 74.363 589 126 17 1732 2303 40622821 40622241 1.240000e-55 228.0
34 TraesCS6B01G097800 chr6A 71.910 356 81 16 1823 2165 30423378 30423727 7.920000e-13 86.1
35 TraesCS6B01G097800 chr1B 82.249 1859 238 52 1995 3795 57616191 57618015 0.000000e+00 1520.0
36 TraesCS6B01G097800 chr1B 81.753 1118 143 35 889 1966 57615021 57616117 0.000000e+00 878.0
37 TraesCS6B01G097800 chr5B 90.407 688 63 3 1 687 648024761 648025446 0.000000e+00 902.0
38 TraesCS6B01G097800 chr1D 82.622 961 113 24 2870 3795 37882864 37883805 0.000000e+00 800.0
39 TraesCS6B01G097800 chr1D 81.350 933 134 25 1995 2908 37881021 37881932 0.000000e+00 723.0
40 TraesCS6B01G097800 chr1A 85.519 366 36 5 1000 1361 36785354 36785706 2.530000e-97 366.0
41 TraesCS6B01G097800 chr1A 76.495 485 109 5 3 485 15094961 15095442 4.410000e-65 259.0
42 TraesCS6B01G097800 chr1A 76.240 484 112 3 3 485 15051584 15052065 2.050000e-63 254.0
43 TraesCS6B01G097800 chr1A 76.289 485 110 5 3 485 15139194 15139675 2.050000e-63 254.0
44 TraesCS6B01G097800 chr1A 81.013 158 28 2 1991 2147 36789948 36790104 1.680000e-24 124.0
45 TraesCS6B01G097800 chr4A 77.391 460 99 4 1 458 476124082 476123626 7.330000e-68 268.0
46 TraesCS6B01G097800 chr4A 76.240 484 112 3 3 485 694688103 694687622 2.050000e-63 254.0
47 TraesCS6B01G097800 chr4A 75.926 486 110 7 3 485 694702087 694701606 4.440000e-60 243.0
48 TraesCS6B01G097800 chr7B 76.653 484 110 3 3 485 89890510 89890991 9.480000e-67 265.0
49 TraesCS6B01G097800 chr3A 76.446 484 111 3 3 485 657518321 657518802 4.410000e-65 259.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G097800 chr6B 75420058 75424503 4445 True 8211.000000 8211 100.0000 1 4446 1 chr6B.!!$R4 4445
1 TraesCS6B01G097800 chr6B 75043378 75045498 2120 True 1714.000000 1714 81.9570 2279 4359 1 chr6B.!!$R2 2080
2 TraesCS6B01G097800 chr6B 75523367 75526311 2944 True 1277.500000 1511 83.8530 1020 4302 2 chr6B.!!$R5 3282
3 TraesCS6B01G097800 chr6B 75405047 75405874 827 True 1146.000000 1146 91.7370 3620 4446 1 chr6B.!!$R3 826
4 TraesCS6B01G097800 chr6D 35714586 35718332 3746 True 1842.333333 2684 94.2790 707 4446 3 chr6D.!!$R6 3739
5 TraesCS6B01G097800 chr6D 36082195 36084578 2383 True 1088.500000 1142 83.7090 1399 4276 2 chr6D.!!$R8 2877
6 TraesCS6B01G097800 chr6D 35666131 35667512 1381 True 1081.000000 1081 81.3440 1019 2372 1 chr6D.!!$R2 1353
7 TraesCS6B01G097800 chr6D 35639217 35642079 2862 True 1034.000000 1478 81.6905 1012 3939 2 chr6D.!!$R5 2927
8 TraesCS6B01G097800 chr6D 35884514 35885890 1376 True 728.000000 728 76.9120 1414 2781 1 chr6D.!!$R3 1367
9 TraesCS6B01G097800 chr6D 36104706 36106123 1417 True 515.000000 584 80.7640 996 2357 2 chr6D.!!$R9 1361
10 TraesCS6B01G097800 chr6D 36072910 36074173 1263 True 433.000000 481 86.2425 1021 3655 2 chr6D.!!$R7 2634
11 TraesCS6B01G097800 chr6D 36324593 36325177 584 False 302.000000 302 76.6780 1729 2303 1 chr6D.!!$F1 574
12 TraesCS6B01G097800 chr6A 39669238 39670766 1528 True 1531.000000 1531 85.0000 1019 2534 1 chr6A.!!$R2 1515
13 TraesCS6B01G097800 chr6A 39627446 39628973 1527 True 1463.000000 1463 84.2110 1020 2534 1 chr6A.!!$R1 1514
14 TraesCS6B01G097800 chr6A 39578415 39581183 2768 True 1211.000000 1445 82.8695 1022 4302 2 chr6A.!!$R6 3280
15 TraesCS6B01G097800 chr6A 39588135 39590484 2349 True 992.000000 1367 83.2345 1562 3939 2 chr6A.!!$R7 2377
16 TraesCS6B01G097800 chr6A 39546017 39548202 2185 True 976.000000 1336 84.7075 1731 3939 2 chr6A.!!$R5 2208
17 TraesCS6B01G097800 chr6A 39635927 39638109 2182 True 956.000000 1306 83.4660 1731 3939 2 chr6A.!!$R8 2208
18 TraesCS6B01G097800 chr6A 39876610 39878026 1416 True 926.000000 926 79.3440 996 2357 1 chr6A.!!$R3 1361
19 TraesCS6B01G097800 chr6A 40622241 40622821 580 True 228.000000 228 74.3630 1732 2303 1 chr6A.!!$R4 571
20 TraesCS6B01G097800 chr1B 57615021 57618015 2994 False 1199.000000 1520 82.0010 889 3795 2 chr1B.!!$F1 2906
21 TraesCS6B01G097800 chr5B 648024761 648025446 685 False 902.000000 902 90.4070 1 687 1 chr5B.!!$F1 686
22 TraesCS6B01G097800 chr1D 37881021 37883805 2784 False 761.500000 800 81.9860 1995 3795 2 chr1D.!!$F1 1800

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
677 678 0.104304 ATAGAAACCCTAGCCGCACG 59.896 55.000 0.00 0.0 0.00 5.34 F
1555 1626 0.247460 AGACGAGCAGCAGCATACAA 59.753 50.000 3.17 0.0 45.49 2.41 F
1934 2068 1.146774 TGCTTCATGGGTTCTGGGAAA 59.853 47.619 0.00 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1691 0.856982 TGGTGGGAAGTTTGGATGGT 59.143 50.000 0.00 0.00 0.0 3.55 R
2435 2695 1.268625 CAACCGGTTTCAACTAAGGGC 59.731 52.381 19.55 0.00 0.0 5.19 R
3564 5142 5.344743 TGGAATGTTGCAACCAGTAAAAA 57.655 34.783 26.14 5.77 0.0 1.94 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
20 21 3.645975 CACCACGTGTGTTCCCGC 61.646 66.667 15.65 0.00 40.26 6.13
36 37 1.067749 CGCTCAGCCTCATCTCCAG 59.932 63.158 0.00 0.00 0.00 3.86
55 56 5.982356 TCCAGAATATCACCTGAGTTTCTG 58.018 41.667 16.21 16.21 41.59 3.02
74 75 4.991760 GCAGATGCTCGACAATGC 57.008 55.556 0.00 10.43 37.73 3.56
103 104 2.223572 GCAAAAGCCATCCGGTATCTTG 60.224 50.000 0.00 0.00 33.28 3.02
136 137 2.485302 CCAGATCGGCATGAACACCATA 60.485 50.000 0.00 0.00 33.31 2.74
138 139 2.700371 AGATCGGCATGAACACCATAGA 59.300 45.455 0.00 0.00 33.31 1.98
141 142 2.170397 TCGGCATGAACACCATAGACAT 59.830 45.455 0.00 0.00 33.31 3.06
150 151 5.105187 TGAACACCATAGACATCTCTTCAGG 60.105 44.000 0.00 0.00 0.00 3.86
186 187 2.785562 GTATGGGCACAGTAACACCAA 58.214 47.619 0.00 0.00 34.45 3.67
193 194 3.550030 GGCACAGTAACACCAACATGTTC 60.550 47.826 8.48 0.00 41.89 3.18
199 200 4.578928 AGTAACACCAACATGTTCCTGAAC 59.421 41.667 8.48 10.09 41.89 3.18
217 218 2.204059 AGCCAAGGACCCTGCTCT 60.204 61.111 0.00 0.00 0.00 4.09
232 233 0.178068 GCTCTAGCATCCGTTCCCAA 59.822 55.000 0.00 0.00 41.59 4.12
295 296 2.396157 CGGCCGAAACCTAACTGGC 61.396 63.158 24.07 0.00 44.98 4.85
351 352 2.301870 AGAAGGCAGTATGGTTGAACGA 59.698 45.455 0.00 0.00 35.86 3.85
355 356 4.079253 AGGCAGTATGGTTGAACGATTTT 58.921 39.130 0.00 0.00 35.86 1.82
356 357 4.082787 AGGCAGTATGGTTGAACGATTTTG 60.083 41.667 0.00 0.00 35.86 2.44
357 358 4.320935 GGCAGTATGGTTGAACGATTTTGT 60.321 41.667 0.00 0.00 35.86 2.83
359 360 5.390613 CAGTATGGTTGAACGATTTTGTCC 58.609 41.667 0.00 0.00 0.00 4.02
360 361 3.552604 ATGGTTGAACGATTTTGTCCG 57.447 42.857 0.00 0.00 0.00 4.79
361 362 2.290464 TGGTTGAACGATTTTGTCCGT 58.710 42.857 0.00 0.00 41.14 4.69
362 363 2.032302 TGGTTGAACGATTTTGTCCGTG 59.968 45.455 0.00 0.00 39.14 4.94
363 364 2.032426 GGTTGAACGATTTTGTCCGTGT 59.968 45.455 0.00 0.00 39.14 4.49
364 365 3.033185 GTTGAACGATTTTGTCCGTGTG 58.967 45.455 0.00 0.00 39.14 3.82
365 366 2.552031 TGAACGATTTTGTCCGTGTGA 58.448 42.857 0.00 0.00 39.14 3.58
398 399 2.001812 CCAACCATCTCACACTCTCG 57.998 55.000 0.00 0.00 0.00 4.04
404 405 3.259374 ACCATCTCACACTCTCGTTGATT 59.741 43.478 0.00 0.00 0.00 2.57
405 406 3.615937 CCATCTCACACTCTCGTTGATTG 59.384 47.826 0.00 0.00 0.00 2.67
408 409 2.407090 TCACACTCTCGTTGATTGCAG 58.593 47.619 0.00 0.00 0.00 4.41
410 411 1.081892 CACTCTCGTTGATTGCAGGG 58.918 55.000 0.00 0.00 0.00 4.45
425 426 2.242965 TGCAGGGTCATCCTCATCAATT 59.757 45.455 0.00 0.00 46.12 2.32
440 441 7.439356 TCCTCATCAATTACAAGATCATCGAAC 59.561 37.037 0.00 0.00 0.00 3.95
498 499 1.403814 CAGATCAGGAACCCTAGCGA 58.596 55.000 0.00 0.00 29.64 4.93
503 504 2.280186 GGAACCCTAGCGATGCCG 60.280 66.667 0.00 0.00 39.16 5.69
504 505 2.792947 GGAACCCTAGCGATGCCGA 61.793 63.158 0.00 0.00 38.22 5.54
508 509 2.279517 CCTAGCGATGCCGACACC 60.280 66.667 0.00 0.00 38.22 4.16
520 521 2.642254 CGACACCCCCGCTAGTTCA 61.642 63.158 0.00 0.00 0.00 3.18
524 525 2.183555 CCCCCGCTAGTTCACGAC 59.816 66.667 0.00 0.00 0.00 4.34
525 526 2.348888 CCCCCGCTAGTTCACGACT 61.349 63.158 0.00 0.00 42.55 4.18
526 527 1.153823 CCCCGCTAGTTCACGACTG 60.154 63.158 0.00 0.00 39.48 3.51
527 528 1.153823 CCCGCTAGTTCACGACTGG 60.154 63.158 0.00 0.00 39.48 4.00
528 529 1.153823 CCGCTAGTTCACGACTGGG 60.154 63.158 0.00 0.00 39.48 4.45
529 530 1.805945 CGCTAGTTCACGACTGGGC 60.806 63.158 0.00 0.00 39.48 5.36
530 531 1.292223 GCTAGTTCACGACTGGGCA 59.708 57.895 0.00 0.00 39.48 5.36
531 532 0.108138 GCTAGTTCACGACTGGGCAT 60.108 55.000 0.00 0.00 39.48 4.40
532 533 1.927895 CTAGTTCACGACTGGGCATC 58.072 55.000 0.00 0.00 39.48 3.91
533 534 0.535335 TAGTTCACGACTGGGCATCC 59.465 55.000 0.00 0.00 39.48 3.51
534 535 1.194781 AGTTCACGACTGGGCATCCT 61.195 55.000 0.00 0.00 37.17 3.24
535 536 1.021390 GTTCACGACTGGGCATCCTG 61.021 60.000 0.00 0.00 37.91 3.86
536 537 2.124983 CACGACTGGGCATCCTGG 60.125 66.667 0.00 0.00 36.44 4.45
537 538 3.402681 ACGACTGGGCATCCTGGG 61.403 66.667 0.00 0.00 36.44 4.45
538 539 3.402681 CGACTGGGCATCCTGGGT 61.403 66.667 0.00 0.00 36.44 4.51
539 540 2.592308 GACTGGGCATCCTGGGTC 59.408 66.667 0.00 0.00 36.44 4.46
540 541 3.391665 GACTGGGCATCCTGGGTCG 62.392 68.421 0.00 0.00 36.44 4.79
541 542 4.181010 CTGGGCATCCTGGGTCGG 62.181 72.222 0.00 0.00 0.00 4.79
542 543 4.731853 TGGGCATCCTGGGTCGGA 62.732 66.667 0.00 0.00 37.50 4.55
543 544 4.176752 GGGCATCCTGGGTCGGAC 62.177 72.222 0.00 0.00 35.52 4.79
544 545 4.530857 GGCATCCTGGGTCGGACG 62.531 72.222 1.43 0.00 35.52 4.79
545 546 3.458163 GCATCCTGGGTCGGACGA 61.458 66.667 1.43 0.00 35.52 4.20
546 547 2.797278 GCATCCTGGGTCGGACGAT 61.797 63.158 1.43 0.00 35.52 3.73
547 548 1.364171 CATCCTGGGTCGGACGATC 59.636 63.158 1.43 0.00 35.52 3.69
548 549 1.833049 ATCCTGGGTCGGACGATCC 60.833 63.158 16.71 16.71 45.36 3.36
560 561 4.462394 CGATCCATCGCCACCAAT 57.538 55.556 0.00 0.00 43.84 3.16
561 562 1.944035 CGATCCATCGCCACCAATG 59.056 57.895 0.00 0.00 43.84 2.82
562 563 1.656441 GATCCATCGCCACCAATGC 59.344 57.895 0.00 0.00 0.00 3.56
563 564 0.820891 GATCCATCGCCACCAATGCT 60.821 55.000 0.00 0.00 0.00 3.79
564 565 1.105167 ATCCATCGCCACCAATGCTG 61.105 55.000 0.00 0.00 0.00 4.41
573 574 3.266964 CCAATGCTGGGTGACACG 58.733 61.111 0.00 0.00 39.30 4.49
574 575 2.334946 CCAATGCTGGGTGACACGG 61.335 63.158 0.00 0.00 39.30 4.94
575 576 1.302431 CAATGCTGGGTGACACGGA 60.302 57.895 0.00 0.00 0.00 4.69
576 577 1.003355 AATGCTGGGTGACACGGAG 60.003 57.895 0.00 0.00 0.00 4.63
578 579 0.902984 ATGCTGGGTGACACGGAGTA 60.903 55.000 0.00 0.00 41.61 2.59
579 580 1.215647 GCTGGGTGACACGGAGTAG 59.784 63.158 0.00 0.00 41.61 2.57
580 581 1.215647 CTGGGTGACACGGAGTAGC 59.784 63.158 0.00 0.00 41.61 3.58
581 582 2.181021 GGGTGACACGGAGTAGCG 59.819 66.667 0.00 0.00 41.61 4.26
582 583 2.506438 GGTGACACGGAGTAGCGC 60.506 66.667 0.00 0.00 41.61 5.92
583 584 2.874780 GTGACACGGAGTAGCGCG 60.875 66.667 0.00 0.00 41.61 6.86
584 585 3.051479 TGACACGGAGTAGCGCGA 61.051 61.111 12.10 0.00 41.61 5.87
585 586 2.404186 TGACACGGAGTAGCGCGAT 61.404 57.895 12.10 5.99 41.61 4.58
586 587 1.654743 GACACGGAGTAGCGCGATC 60.655 63.158 12.10 0.69 41.61 3.69
587 588 2.319011 GACACGGAGTAGCGCGATCA 62.319 60.000 12.10 0.00 41.61 2.92
588 589 1.655654 CACGGAGTAGCGCGATCAG 60.656 63.158 12.10 4.93 41.61 2.90
589 590 2.727647 CGGAGTAGCGCGATCAGC 60.728 66.667 12.10 0.00 43.95 4.26
613 614 2.732016 CCGCGACGGGATGGAATA 59.268 61.111 8.23 0.00 44.15 1.75
614 615 1.663702 CCGCGACGGGATGGAATAC 60.664 63.158 8.23 0.00 44.15 1.89
615 616 1.362717 CGCGACGGGATGGAATACT 59.637 57.895 0.00 0.00 0.00 2.12
616 617 0.939577 CGCGACGGGATGGAATACTG 60.940 60.000 0.00 0.00 40.35 2.74
617 618 0.387929 GCGACGGGATGGAATACTGA 59.612 55.000 0.00 0.00 34.53 3.41
618 619 1.000955 GCGACGGGATGGAATACTGAT 59.999 52.381 0.00 0.00 34.53 2.90
619 620 2.927014 GCGACGGGATGGAATACTGATC 60.927 54.545 0.00 0.00 34.53 2.92
620 621 2.352814 CGACGGGATGGAATACTGATCC 60.353 54.545 0.00 0.00 34.53 3.36
621 622 1.618837 ACGGGATGGAATACTGATCCG 59.381 52.381 0.00 0.00 34.53 4.18
622 623 1.893137 CGGGATGGAATACTGATCCGA 59.107 52.381 0.00 0.00 34.53 4.55
623 624 2.497675 CGGGATGGAATACTGATCCGAT 59.502 50.000 0.00 0.00 34.53 4.18
624 625 3.429547 CGGGATGGAATACTGATCCGATC 60.430 52.174 1.01 1.01 34.53 3.69
625 626 3.429547 GGGATGGAATACTGATCCGATCG 60.430 52.174 8.51 8.51 39.98 3.69
626 627 3.444034 GGATGGAATACTGATCCGATCGA 59.556 47.826 18.66 2.91 39.98 3.59
627 628 4.082190 GGATGGAATACTGATCCGATCGAA 60.082 45.833 18.66 0.00 39.98 3.71
628 629 4.505313 TGGAATACTGATCCGATCGAAG 57.495 45.455 18.66 10.76 39.98 3.79
629 630 4.142038 TGGAATACTGATCCGATCGAAGA 58.858 43.478 18.66 6.61 39.88 2.87
630 631 4.023107 TGGAATACTGATCCGATCGAAGAC 60.023 45.833 18.66 5.69 38.75 3.01
631 632 4.216687 GGAATACTGATCCGATCGAAGACT 59.783 45.833 18.66 0.00 42.51 3.24
632 633 5.365403 AATACTGATCCGATCGAAGACTC 57.635 43.478 18.66 6.09 42.51 3.36
633 634 1.600013 ACTGATCCGATCGAAGACTCG 59.400 52.381 18.66 0.00 46.87 4.18
634 635 0.308068 TGATCCGATCGAAGACTCGC 59.692 55.000 18.66 0.00 45.04 5.03
635 636 0.589223 GATCCGATCGAAGACTCGCT 59.411 55.000 18.66 0.00 45.04 4.93
636 637 0.309302 ATCCGATCGAAGACTCGCTG 59.691 55.000 18.66 0.00 45.04 5.18
637 638 1.298713 CCGATCGAAGACTCGCTGG 60.299 63.158 18.66 0.00 45.04 4.85
638 639 1.941734 CGATCGAAGACTCGCTGGC 60.942 63.158 10.26 0.00 45.04 4.85
639 640 1.941734 GATCGAAGACTCGCTGGCG 60.942 63.158 8.80 8.80 45.04 5.69
640 641 2.600122 GATCGAAGACTCGCTGGCGT 62.600 60.000 14.55 0.00 45.04 5.68
641 642 2.874010 ATCGAAGACTCGCTGGCGTG 62.874 60.000 14.55 14.29 45.04 5.34
642 643 2.811317 GAAGACTCGCTGGCGTGG 60.811 66.667 18.56 13.24 40.74 4.94
643 644 4.379243 AAGACTCGCTGGCGTGGG 62.379 66.667 18.56 11.23 40.74 4.61
647 648 4.803426 CTCGCTGGCGTGGGAGTC 62.803 72.222 14.55 0.00 40.64 3.36
651 652 3.625897 CTGGCGTGGGAGTCACCA 61.626 66.667 0.00 0.00 43.23 4.17
652 653 3.596066 CTGGCGTGGGAGTCACCAG 62.596 68.421 0.98 0.00 42.20 4.00
653 654 3.311110 GGCGTGGGAGTCACCAGA 61.311 66.667 0.98 0.00 42.20 3.86
654 655 2.262915 GCGTGGGAGTCACCAGAG 59.737 66.667 0.98 1.14 42.20 3.35
655 656 2.276116 GCGTGGGAGTCACCAGAGA 61.276 63.158 0.98 0.00 42.20 3.10
656 657 1.886585 CGTGGGAGTCACCAGAGAG 59.113 63.158 0.98 0.00 42.20 3.20
657 658 1.599606 CGTGGGAGTCACCAGAGAGG 61.600 65.000 0.98 0.00 42.20 3.69
658 659 0.251832 GTGGGAGTCACCAGAGAGGA 60.252 60.000 0.98 0.00 42.20 3.71
659 660 0.712979 TGGGAGTCACCAGAGAGGAT 59.287 55.000 0.00 0.00 41.22 3.24
660 661 1.930204 TGGGAGTCACCAGAGAGGATA 59.070 52.381 0.00 0.00 41.22 2.59
661 662 2.091610 TGGGAGTCACCAGAGAGGATAG 60.092 54.545 0.00 0.00 41.22 2.08
662 663 2.175931 GGGAGTCACCAGAGAGGATAGA 59.824 54.545 0.00 0.00 41.22 1.98
663 664 3.373220 GGGAGTCACCAGAGAGGATAGAA 60.373 52.174 0.00 0.00 41.22 2.10
664 665 4.282496 GGAGTCACCAGAGAGGATAGAAA 58.718 47.826 0.00 0.00 41.22 2.52
665 666 4.098807 GGAGTCACCAGAGAGGATAGAAAC 59.901 50.000 0.00 0.00 41.22 2.78
666 667 4.027437 AGTCACCAGAGAGGATAGAAACC 58.973 47.826 0.00 0.00 41.22 3.27
667 668 3.133183 GTCACCAGAGAGGATAGAAACCC 59.867 52.174 0.00 0.00 41.22 4.11
668 669 3.012959 TCACCAGAGAGGATAGAAACCCT 59.987 47.826 0.00 0.00 41.22 4.34
669 670 4.232122 TCACCAGAGAGGATAGAAACCCTA 59.768 45.833 0.00 0.00 41.22 3.53
670 671 4.586841 CACCAGAGAGGATAGAAACCCTAG 59.413 50.000 0.00 0.00 41.22 3.02
671 672 3.576550 CCAGAGAGGATAGAAACCCTAGC 59.423 52.174 0.00 0.00 41.22 3.42
674 675 3.608760 GGATAGAAACCCTAGCCGC 57.391 57.895 0.00 0.00 43.26 6.53
675 676 0.756903 GGATAGAAACCCTAGCCGCA 59.243 55.000 0.00 0.00 43.26 5.69
676 677 1.540580 GGATAGAAACCCTAGCCGCAC 60.541 57.143 0.00 0.00 43.26 5.34
677 678 0.104304 ATAGAAACCCTAGCCGCACG 59.896 55.000 0.00 0.00 0.00 5.34
678 679 1.952102 TAGAAACCCTAGCCGCACGG 61.952 60.000 4.30 4.30 38.57 4.94
679 680 4.404098 AAACCCTAGCCGCACGGG 62.404 66.667 11.65 13.79 43.79 5.28
689 690 3.834799 CGCACGGGTAGGGGAGAC 61.835 72.222 0.00 0.00 0.00 3.36
703 704 2.651135 GGAGACCACGTAGGACTTTC 57.349 55.000 10.46 4.06 42.62 2.62
704 705 1.135460 GGAGACCACGTAGGACTTTCG 60.135 57.143 10.46 0.00 42.62 3.46
705 706 0.886563 AGACCACGTAGGACTTTCGG 59.113 55.000 10.46 0.00 39.46 4.30
706 707 0.600057 GACCACGTAGGACTTTCGGT 59.400 55.000 10.46 0.00 41.22 4.69
707 708 0.316204 ACCACGTAGGACTTTCGGTG 59.684 55.000 10.46 0.00 41.22 4.94
708 709 0.316204 CCACGTAGGACTTTCGGTGT 59.684 55.000 0.00 0.00 41.22 4.16
709 710 1.415374 CACGTAGGACTTTCGGTGTG 58.585 55.000 0.00 0.00 0.00 3.82
710 711 1.035139 ACGTAGGACTTTCGGTGTGT 58.965 50.000 0.00 0.00 0.00 3.72
711 712 1.000938 ACGTAGGACTTTCGGTGTGTC 60.001 52.381 0.00 0.00 0.00 3.67
736 737 0.248843 TGTGATGACGTGGCTATGCA 59.751 50.000 0.00 0.00 0.00 3.96
745 746 0.394565 GTGGCTATGCAGGTCTAGGG 59.605 60.000 0.00 0.00 0.00 3.53
809 810 4.280929 GCACATTTTTAGGGGAGTTGTTCT 59.719 41.667 0.00 0.00 0.00 3.01
810 811 5.772521 CACATTTTTAGGGGAGTTGTTCTG 58.227 41.667 0.00 0.00 0.00 3.02
816 817 2.690840 AGGGGAGTTGTTCTGTACAGT 58.309 47.619 21.99 1.69 38.19 3.55
823 824 6.456501 GGAGTTGTTCTGTACAGTAGTTGAT 58.543 40.000 21.99 5.00 38.19 2.57
864 865 9.773328 CTGCGTAAGAAAATCAATCATAAAAGA 57.227 29.630 0.00 0.00 43.02 2.52
907 908 0.889186 CTGGTTGTGTGTAGTGGGCC 60.889 60.000 0.00 0.00 0.00 5.80
922 925 3.138468 AGTGGGCCTTCTTTTACTTGAGT 59.862 43.478 4.53 0.00 0.00 3.41
941 944 0.329931 TTCTCGTGGGCTCTCTCTCT 59.670 55.000 0.00 0.00 0.00 3.10
957 963 5.758784 TCTCTCTCTCCCGAAAAAGAAAAAC 59.241 40.000 0.00 0.00 0.00 2.43
980 986 1.629043 GAGTAGGTCACTCCACCACA 58.371 55.000 0.00 0.00 46.94 4.17
981 987 1.968493 GAGTAGGTCACTCCACCACAA 59.032 52.381 0.00 0.00 46.94 3.33
982 988 2.567615 GAGTAGGTCACTCCACCACAAT 59.432 50.000 0.00 0.00 46.94 2.71
986 1011 1.202879 GGTCACTCCACCACAATCCAA 60.203 52.381 0.00 0.00 36.32 3.53
991 1016 0.850100 TCCACCACAATCCAACACCT 59.150 50.000 0.00 0.00 0.00 4.00
1101 1144 3.758133 GATCCTCCTCCGCCTCCCA 62.758 68.421 0.00 0.00 0.00 4.37
1363 1422 2.423446 GCCATGGCCTCCTACTCG 59.577 66.667 27.24 0.00 34.56 4.18
1450 1509 1.386525 CGTTCCCCCGGAGTTCGATA 61.387 60.000 0.73 0.00 42.43 2.92
1456 1515 1.329256 CCCGGAGTTCGATATGGAGT 58.671 55.000 0.73 0.00 42.43 3.85
1457 1516 1.269998 CCCGGAGTTCGATATGGAGTC 59.730 57.143 0.73 0.00 42.43 3.36
1502 1570 3.461773 CGCCACCGGAGACATCCT 61.462 66.667 9.46 0.00 44.22 3.24
1555 1626 0.247460 AGACGAGCAGCAGCATACAA 59.753 50.000 3.17 0.00 45.49 2.41
1620 1691 2.479560 CGATCGCATCTCAACACCACTA 60.480 50.000 0.26 0.00 0.00 2.74
1677 1802 2.266279 ACTATGGGTGTGCTAGTTGGT 58.734 47.619 0.00 0.00 0.00 3.67
1693 1818 2.492088 GTTGGTCATTCCCTTTACTGGC 59.508 50.000 0.00 0.00 34.77 4.85
1809 1934 8.186821 CCAGTGGATATTCTCAAGAAAAACATC 58.813 37.037 1.68 0.00 37.61 3.06
1934 2068 1.146774 TGCTTCATGGGTTCTGGGAAA 59.853 47.619 0.00 0.00 0.00 3.13
1952 2086 4.099419 GGGAAAAACTGTTGAACTGGACAT 59.901 41.667 7.13 0.00 0.00 3.06
1977 2117 7.918076 TGTTACTTTCCCTGAATACAGAAGAT 58.082 34.615 0.00 0.00 46.03 2.40
2247 2494 6.145048 GCGTTAAGCTAACAAGTTGAAGTAGA 59.855 38.462 10.54 0.00 44.04 2.59
2362 2621 5.936187 TGTGATGGTTATGATTTGGCAAT 57.064 34.783 0.00 0.00 0.00 3.56
2435 2695 8.864069 ATTCTACTCTATCGTGATTTTGAGTG 57.136 34.615 16.14 10.20 36.39 3.51
2475 2735 4.836125 TGAGCATCTCCTTTGTCAAAAC 57.164 40.909 0.00 0.00 34.92 2.43
2537 2988 4.039703 CGCATGCTCTTGTTATGGAATTG 58.960 43.478 17.13 0.00 0.00 2.32
2553 3004 4.458989 TGGAATTGTATGGTTTGAGTCAGC 59.541 41.667 0.00 0.00 0.00 4.26
2869 3371 6.135290 TCATTCAGCAGTGTTATTATTGGC 57.865 37.500 0.00 0.00 0.00 4.52
2870 3372 5.651576 TCATTCAGCAGTGTTATTATTGGCA 59.348 36.000 0.00 0.00 0.00 4.92
2961 4432 8.474025 TGGCAAGGTAGAACAATAATAAATTGG 58.526 33.333 3.07 0.00 33.56 3.16
2986 4457 9.850628 GGGTTTATTTCATCTTTACTGGTTAAC 57.149 33.333 0.00 0.00 0.00 2.01
3138 4620 5.358442 TCACTTCAGGTCAGCTAATAGTCTC 59.642 44.000 0.00 0.00 0.00 3.36
3158 4644 7.983307 AGTCTCTGTGCATATTCTTCATTTTC 58.017 34.615 0.00 0.00 0.00 2.29
3161 4647 8.963725 TCTCTGTGCATATTCTTCATTTTCATT 58.036 29.630 0.00 0.00 0.00 2.57
3584 5163 8.821894 TGTTTATTTTTACTGGTTGCAACATTC 58.178 29.630 29.55 13.98 0.00 2.67
3680 5261 8.642935 TGAATTGATACCCAACAATAACTGAA 57.357 30.769 0.00 0.00 37.63 3.02
3946 5533 6.709018 TGTATGATCGAAGAGTCCACATTA 57.291 37.500 0.00 0.00 43.63 1.90
4151 5764 1.905637 TACTTCTGCTCGTCCTCACA 58.094 50.000 0.00 0.00 0.00 3.58
4153 5766 1.000283 ACTTCTGCTCGTCCTCACAAG 60.000 52.381 0.00 0.00 0.00 3.16
4175 5794 9.480053 ACAAGTTATTTGAGATTGAAAACATGG 57.520 29.630 0.00 0.00 39.21 3.66
4311 5955 5.475909 TCCAAAGTGAGAACTACTACGTGAT 59.524 40.000 0.00 0.00 0.00 3.06
4334 5979 8.991026 TGATGGTTTTATGCTTTCATTTTTCAG 58.009 29.630 0.00 0.00 34.22 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.240134 GAGGCTGAGCGGGAACACA 62.240 63.158 0.00 0.00 0.00 3.72
20 21 4.527427 TGATATTCTGGAGATGAGGCTGAG 59.473 45.833 0.00 0.00 0.00 3.35
36 37 5.423015 TGCTCAGAAACTCAGGTGATATTC 58.577 41.667 0.00 0.00 0.00 1.75
67 68 3.427863 GCTTTTGCAAGAAGAGCATTGTC 59.572 43.478 19.18 2.55 46.58 3.18
103 104 1.303309 CGATCTGGCTCCAAATCCAC 58.697 55.000 0.00 0.00 0.00 4.02
136 137 3.648067 TCACCAAACCTGAAGAGATGTCT 59.352 43.478 0.00 0.00 32.81 3.41
138 139 4.437682 TTCACCAAACCTGAAGAGATGT 57.562 40.909 0.00 0.00 0.00 3.06
141 142 3.394274 TGGATTCACCAAACCTGAAGAGA 59.606 43.478 0.00 0.00 46.75 3.10
177 178 4.336993 TGTTCAGGAACATGTTGGTGTTAC 59.663 41.667 17.58 14.17 45.42 2.50
193 194 1.303643 GGGTCCTTGGCTGTTCAGG 60.304 63.158 1.97 0.00 0.00 3.86
199 200 1.267574 TAGAGCAGGGTCCTTGGCTG 61.268 60.000 6.58 0.00 36.59 4.85
217 218 1.416401 GGAGATTGGGAACGGATGCTA 59.584 52.381 0.00 0.00 0.00 3.49
232 233 2.107141 GCGGCGTGCTTAGGAGAT 59.893 61.111 9.37 0.00 41.73 2.75
351 352 2.358322 AGGGTTCACACGGACAAAAT 57.642 45.000 0.00 0.00 0.00 1.82
355 356 1.525077 GCAAGGGTTCACACGGACA 60.525 57.895 0.00 0.00 0.00 4.02
356 357 1.098712 TTGCAAGGGTTCACACGGAC 61.099 55.000 0.00 0.00 0.00 4.79
357 358 0.817634 CTTGCAAGGGTTCACACGGA 60.818 55.000 19.14 0.00 0.00 4.69
359 360 1.654220 CCTTGCAAGGGTTCACACG 59.346 57.895 34.08 8.29 42.66 4.49
398 399 2.134789 AGGATGACCCTGCAATCAAC 57.865 50.000 0.00 0.00 45.61 3.18
408 409 5.684704 TCTTGTAATTGATGAGGATGACCC 58.315 41.667 0.00 0.00 36.73 4.46
410 411 8.618702 ATGATCTTGTAATTGATGAGGATGAC 57.381 34.615 0.00 0.00 0.00 3.06
425 426 6.867550 AGATGAAGTGTTCGATGATCTTGTA 58.132 36.000 0.00 0.00 0.00 2.41
440 441 5.121454 GCAACTCAACCTAGAAGATGAAGTG 59.879 44.000 0.00 0.00 0.00 3.16
476 477 1.972207 GCTAGGGTTCCTGATCTGGGT 60.972 57.143 17.73 2.15 34.61 4.51
503 504 1.079336 GTGAACTAGCGGGGGTGTC 60.079 63.158 0.00 0.00 0.00 3.67
504 505 2.939261 CGTGAACTAGCGGGGGTGT 61.939 63.158 0.00 0.00 0.00 4.16
508 509 1.153823 CAGTCGTGAACTAGCGGGG 60.154 63.158 0.00 0.00 36.07 5.73
515 516 1.194781 AGGATGCCCAGTCGTGAACT 61.195 55.000 0.00 0.00 39.44 3.01
520 521 3.402681 CCCAGGATGCCCAGTCGT 61.403 66.667 0.00 0.00 33.88 4.34
524 525 4.181010 CCGACCCAGGATGCCCAG 62.181 72.222 0.00 0.00 33.88 4.45
525 526 4.731853 TCCGACCCAGGATGCCCA 62.732 66.667 0.00 0.00 34.92 5.36
526 527 4.176752 GTCCGACCCAGGATGCCC 62.177 72.222 0.00 0.00 43.04 5.36
527 528 4.530857 CGTCCGACCCAGGATGCC 62.531 72.222 0.00 0.00 43.04 4.40
528 529 2.701163 GATCGTCCGACCCAGGATGC 62.701 65.000 0.60 0.00 44.81 3.91
529 530 1.364171 GATCGTCCGACCCAGGATG 59.636 63.158 0.00 0.00 46.16 3.51
530 531 1.833049 GGATCGTCCGACCCAGGAT 60.833 63.158 0.00 0.00 43.04 3.24
531 532 2.441532 GGATCGTCCGACCCAGGA 60.442 66.667 0.00 0.00 38.11 3.86
532 533 2.088674 GATGGATCGTCCGACCCAGG 62.089 65.000 8.99 0.00 41.90 4.45
533 534 1.364171 GATGGATCGTCCGACCCAG 59.636 63.158 8.99 0.00 41.90 4.45
534 535 2.486663 CGATGGATCGTCCGACCCA 61.487 63.158 5.03 5.03 42.97 4.51
535 536 2.335369 CGATGGATCGTCCGACCC 59.665 66.667 0.70 0.00 44.74 4.46
544 545 0.820891 AGCATTGGTGGCGATGGATC 60.821 55.000 0.00 0.00 36.08 3.36
545 546 1.105167 CAGCATTGGTGGCGATGGAT 61.105 55.000 7.98 0.00 36.08 3.41
546 547 1.750018 CAGCATTGGTGGCGATGGA 60.750 57.895 7.98 0.00 36.08 3.41
547 548 2.777972 CCAGCATTGGTGGCGATGG 61.778 63.158 21.05 0.00 44.28 3.51
548 549 2.802792 CCAGCATTGGTGGCGATG 59.197 61.111 21.05 0.00 44.28 3.84
555 556 1.600636 CGTGTCACCCAGCATTGGT 60.601 57.895 0.00 0.00 43.40 3.67
556 557 2.334946 CCGTGTCACCCAGCATTGG 61.335 63.158 0.00 0.00 44.60 3.16
557 558 1.300971 CTCCGTGTCACCCAGCATTG 61.301 60.000 0.00 0.00 0.00 2.82
558 559 1.003355 CTCCGTGTCACCCAGCATT 60.003 57.895 0.00 0.00 0.00 3.56
559 560 0.902984 TACTCCGTGTCACCCAGCAT 60.903 55.000 0.00 0.00 0.00 3.79
560 561 1.532078 TACTCCGTGTCACCCAGCA 60.532 57.895 0.00 0.00 0.00 4.41
561 562 1.215647 CTACTCCGTGTCACCCAGC 59.784 63.158 0.00 0.00 0.00 4.85
562 563 1.215647 GCTACTCCGTGTCACCCAG 59.784 63.158 0.00 0.00 0.00 4.45
563 564 2.632544 CGCTACTCCGTGTCACCCA 61.633 63.158 0.00 0.00 0.00 4.51
564 565 2.181021 CGCTACTCCGTGTCACCC 59.819 66.667 0.00 0.00 0.00 4.61
565 566 2.506438 GCGCTACTCCGTGTCACC 60.506 66.667 0.00 0.00 0.00 4.02
566 567 2.594119 ATCGCGCTACTCCGTGTCAC 62.594 60.000 5.56 0.00 39.54 3.67
567 568 2.319011 GATCGCGCTACTCCGTGTCA 62.319 60.000 5.56 0.00 39.54 3.58
568 569 1.654743 GATCGCGCTACTCCGTGTC 60.655 63.158 5.56 0.00 39.54 3.67
569 570 2.324332 CTGATCGCGCTACTCCGTGT 62.324 60.000 5.56 0.00 39.54 4.49
570 571 1.655654 CTGATCGCGCTACTCCGTG 60.656 63.158 5.56 0.00 39.87 4.94
571 572 2.716244 CTGATCGCGCTACTCCGT 59.284 61.111 5.56 0.00 0.00 4.69
572 573 2.727647 GCTGATCGCGCTACTCCG 60.728 66.667 5.56 0.00 0.00 4.63
597 598 0.939577 CAGTATTCCATCCCGTCGCG 60.940 60.000 0.00 0.00 0.00 5.87
598 599 0.387929 TCAGTATTCCATCCCGTCGC 59.612 55.000 0.00 0.00 0.00 5.19
599 600 2.352814 GGATCAGTATTCCATCCCGTCG 60.353 54.545 0.00 0.00 31.31 5.12
600 601 2.352814 CGGATCAGTATTCCATCCCGTC 60.353 54.545 0.00 0.00 33.65 4.79
601 602 1.618837 CGGATCAGTATTCCATCCCGT 59.381 52.381 0.00 0.00 33.65 5.28
602 603 1.893137 TCGGATCAGTATTCCATCCCG 59.107 52.381 0.00 0.00 33.65 5.14
603 604 3.429547 CGATCGGATCAGTATTCCATCCC 60.430 52.174 17.53 0.00 33.65 3.85
604 605 3.444034 TCGATCGGATCAGTATTCCATCC 59.556 47.826 16.41 0.00 32.45 3.51
605 606 4.703645 TCGATCGGATCAGTATTCCATC 57.296 45.455 16.41 0.00 32.45 3.51
606 607 4.767409 TCTTCGATCGGATCAGTATTCCAT 59.233 41.667 16.41 0.00 32.45 3.41
607 608 4.023107 GTCTTCGATCGGATCAGTATTCCA 60.023 45.833 16.41 0.00 32.45 3.53
608 609 4.216687 AGTCTTCGATCGGATCAGTATTCC 59.783 45.833 16.41 0.05 0.00 3.01
609 610 5.365403 AGTCTTCGATCGGATCAGTATTC 57.635 43.478 16.41 3.98 0.00 1.75
610 611 5.365403 GAGTCTTCGATCGGATCAGTATT 57.635 43.478 16.41 0.00 0.00 1.89
625 626 2.811317 CCACGCCAGCGAGTCTTC 60.811 66.667 20.32 0.00 42.83 2.87
626 627 4.379243 CCCACGCCAGCGAGTCTT 62.379 66.667 20.32 0.00 42.83 3.01
628 629 4.803426 CTCCCACGCCAGCGAGTC 62.803 72.222 20.32 0.00 42.83 3.36
630 631 4.803426 GACTCCCACGCCAGCGAG 62.803 72.222 20.32 11.06 42.83 5.03
634 635 3.625897 TGGTGACTCCCACGCCAG 61.626 66.667 0.00 0.00 46.62 4.85
635 636 3.625897 CTGGTGACTCCCACGCCA 61.626 66.667 0.00 0.00 46.62 5.69
636 637 3.302347 CTCTGGTGACTCCCACGCC 62.302 68.421 0.00 0.00 46.62 5.68
637 638 2.219325 CTCTCTGGTGACTCCCACGC 62.219 65.000 0.00 0.00 46.62 5.34
638 639 1.599606 CCTCTCTGGTGACTCCCACG 61.600 65.000 0.00 0.00 46.62 4.94
639 640 0.251832 TCCTCTCTGGTGACTCCCAC 60.252 60.000 0.00 0.00 44.95 4.61
640 641 0.712979 ATCCTCTCTGGTGACTCCCA 59.287 55.000 0.00 0.00 37.07 4.37
641 642 2.175931 TCTATCCTCTCTGGTGACTCCC 59.824 54.545 0.00 0.00 37.07 4.30
642 643 3.586470 TCTATCCTCTCTGGTGACTCC 57.414 52.381 0.00 0.00 37.07 3.85
643 644 4.098807 GGTTTCTATCCTCTCTGGTGACTC 59.901 50.000 0.00 0.00 37.07 3.36
644 645 4.027437 GGTTTCTATCCTCTCTGGTGACT 58.973 47.826 0.00 0.00 37.07 3.41
645 646 3.133183 GGGTTTCTATCCTCTCTGGTGAC 59.867 52.174 0.00 0.00 37.07 3.67
646 647 3.012959 AGGGTTTCTATCCTCTCTGGTGA 59.987 47.826 0.00 0.00 37.07 4.02
647 648 3.379452 AGGGTTTCTATCCTCTCTGGTG 58.621 50.000 0.00 0.00 37.07 4.17
648 649 3.786213 AGGGTTTCTATCCTCTCTGGT 57.214 47.619 0.00 0.00 37.07 4.00
649 650 3.576550 GCTAGGGTTTCTATCCTCTCTGG 59.423 52.174 0.00 0.00 34.75 3.86
650 651 3.576550 GGCTAGGGTTTCTATCCTCTCTG 59.423 52.174 0.00 0.00 32.81 3.35
651 652 3.752542 CGGCTAGGGTTTCTATCCTCTCT 60.753 52.174 0.00 0.00 33.26 3.10
652 653 2.559231 CGGCTAGGGTTTCTATCCTCTC 59.441 54.545 0.00 0.00 33.26 3.20
653 654 2.599677 CGGCTAGGGTTTCTATCCTCT 58.400 52.381 0.00 0.00 33.26 3.69
654 655 1.001068 GCGGCTAGGGTTTCTATCCTC 59.999 57.143 0.00 0.00 33.26 3.71
655 656 1.049402 GCGGCTAGGGTTTCTATCCT 58.951 55.000 0.00 0.00 33.26 3.24
656 657 0.756903 TGCGGCTAGGGTTTCTATCC 59.243 55.000 0.00 0.00 32.35 2.59
657 658 1.867166 GTGCGGCTAGGGTTTCTATC 58.133 55.000 0.00 0.00 0.00 2.08
658 659 0.104304 CGTGCGGCTAGGGTTTCTAT 59.896 55.000 0.00 0.00 0.00 1.98
659 660 1.514087 CGTGCGGCTAGGGTTTCTA 59.486 57.895 0.00 0.00 0.00 2.10
660 661 2.264794 CGTGCGGCTAGGGTTTCT 59.735 61.111 0.00 0.00 0.00 2.52
661 662 2.818274 CCGTGCGGCTAGGGTTTC 60.818 66.667 0.00 0.00 0.00 2.78
662 663 4.404098 CCCGTGCGGCTAGGGTTT 62.404 66.667 20.26 0.00 40.27 3.27
666 667 3.912907 CCTACCCGTGCGGCTAGG 61.913 72.222 15.15 15.15 32.46 3.02
667 668 3.912907 CCCTACCCGTGCGGCTAG 61.913 72.222 4.91 5.60 33.26 3.42
672 673 3.834799 GTCTCCCCTACCCGTGCG 61.835 72.222 0.00 0.00 0.00 5.34
673 674 3.468140 GGTCTCCCCTACCCGTGC 61.468 72.222 0.00 0.00 0.00 5.34
674 675 2.038329 TGGTCTCCCCTACCCGTG 59.962 66.667 0.00 0.00 36.06 4.94
675 676 2.038490 GTGGTCTCCCCTACCCGT 59.962 66.667 0.00 0.00 36.06 5.28
676 677 2.556840 TACGTGGTCTCCCCTACCCG 62.557 65.000 0.00 0.00 36.06 5.28
677 678 0.754587 CTACGTGGTCTCCCCTACCC 60.755 65.000 0.00 0.00 36.06 3.69
678 679 0.754587 CCTACGTGGTCTCCCCTACC 60.755 65.000 0.00 0.00 37.53 3.18
679 680 0.257039 TCCTACGTGGTCTCCCCTAC 59.743 60.000 0.00 0.00 37.07 3.18
680 681 0.257039 GTCCTACGTGGTCTCCCCTA 59.743 60.000 0.00 0.00 37.07 3.53
681 682 1.000107 GTCCTACGTGGTCTCCCCT 60.000 63.158 0.00 0.00 37.07 4.79
682 683 0.614134 AAGTCCTACGTGGTCTCCCC 60.614 60.000 0.00 0.00 33.12 4.81
683 684 1.204231 GAAAGTCCTACGTGGTCTCCC 59.796 57.143 0.00 0.00 33.12 4.30
684 685 1.135460 CGAAAGTCCTACGTGGTCTCC 60.135 57.143 0.00 0.00 33.12 3.71
685 686 1.135460 CCGAAAGTCCTACGTGGTCTC 60.135 57.143 0.00 0.00 33.12 3.36
686 687 0.886563 CCGAAAGTCCTACGTGGTCT 59.113 55.000 0.00 0.00 35.75 3.85
687 688 0.600057 ACCGAAAGTCCTACGTGGTC 59.400 55.000 0.00 0.00 37.07 4.02
688 689 0.316204 CACCGAAAGTCCTACGTGGT 59.684 55.000 0.00 0.00 37.07 4.16
689 690 0.316204 ACACCGAAAGTCCTACGTGG 59.684 55.000 0.00 0.00 37.10 4.94
690 691 1.269413 ACACACCGAAAGTCCTACGTG 60.269 52.381 0.00 0.00 0.00 4.49
691 692 1.000938 GACACACCGAAAGTCCTACGT 60.001 52.381 0.00 0.00 0.00 3.57
692 693 1.694639 GACACACCGAAAGTCCTACG 58.305 55.000 0.00 0.00 0.00 3.51
693 694 1.267806 TCGACACACCGAAAGTCCTAC 59.732 52.381 0.00 0.00 35.42 3.18
694 695 1.267806 GTCGACACACCGAAAGTCCTA 59.732 52.381 11.55 0.00 40.51 2.94
695 696 0.031721 GTCGACACACCGAAAGTCCT 59.968 55.000 11.55 0.00 40.51 3.85
696 697 0.031721 AGTCGACACACCGAAAGTCC 59.968 55.000 19.50 0.00 40.51 3.85
697 698 1.849097 AAGTCGACACACCGAAAGTC 58.151 50.000 19.50 0.00 40.51 3.01
698 699 1.931172 CAAAGTCGACACACCGAAAGT 59.069 47.619 19.50 0.00 40.51 2.66
699 700 1.931172 ACAAAGTCGACACACCGAAAG 59.069 47.619 19.50 0.00 40.51 2.62
700 701 1.661617 CACAAAGTCGACACACCGAAA 59.338 47.619 19.50 0.00 40.51 3.46
701 702 1.135053 TCACAAAGTCGACACACCGAA 60.135 47.619 19.50 0.00 40.51 4.30
702 703 0.456628 TCACAAAGTCGACACACCGA 59.543 50.000 19.50 5.62 36.06 4.69
703 704 1.192312 CATCACAAAGTCGACACACCG 59.808 52.381 19.50 3.09 0.00 4.94
704 705 2.221055 GTCATCACAAAGTCGACACACC 59.779 50.000 19.50 0.00 0.00 4.16
705 706 2.097396 CGTCATCACAAAGTCGACACAC 60.097 50.000 19.50 0.00 0.00 3.82
706 707 2.124122 CGTCATCACAAAGTCGACACA 58.876 47.619 19.50 0.00 0.00 3.72
707 708 2.097396 CACGTCATCACAAAGTCGACAC 60.097 50.000 19.50 2.46 0.00 3.67
708 709 2.124122 CACGTCATCACAAAGTCGACA 58.876 47.619 19.50 0.00 0.00 4.35
709 710 1.455786 CCACGTCATCACAAAGTCGAC 59.544 52.381 7.70 7.70 0.00 4.20
710 711 1.778334 CCACGTCATCACAAAGTCGA 58.222 50.000 0.00 0.00 0.00 4.20
711 712 0.163788 GCCACGTCATCACAAAGTCG 59.836 55.000 0.00 0.00 0.00 4.18
768 769 4.681244 ATGTGCACATAACCATTCAATGGC 60.681 41.667 30.50 0.89 43.83 4.40
770 771 6.971527 AAATGTGCACATAACCATTCAATG 57.028 33.333 31.55 0.00 35.10 2.82
782 783 3.778265 ACTCCCCTAAAAATGTGCACAT 58.222 40.909 26.61 26.61 38.41 3.21
785 786 3.571590 ACAACTCCCCTAAAAATGTGCA 58.428 40.909 0.00 0.00 0.00 4.57
787 788 5.301805 ACAGAACAACTCCCCTAAAAATGTG 59.698 40.000 0.00 0.00 0.00 3.21
830 831 8.641499 ATTGATTTTCTTACGCAGTTTCAAAA 57.359 26.923 0.00 0.00 37.78 2.44
832 833 7.421599 TGATTGATTTTCTTACGCAGTTTCAA 58.578 30.769 0.00 0.00 37.78 2.69
873 874 4.021192 CACAACCAGCATACCCAGATTTTT 60.021 41.667 0.00 0.00 0.00 1.94
874 875 3.511146 CACAACCAGCATACCCAGATTTT 59.489 43.478 0.00 0.00 0.00 1.82
875 876 3.091545 CACAACCAGCATACCCAGATTT 58.908 45.455 0.00 0.00 0.00 2.17
907 908 5.177696 CCCACGAGAACTCAAGTAAAAGAAG 59.822 44.000 0.00 0.00 0.00 2.85
922 925 0.329931 AGAGAGAGAGCCCACGAGAA 59.670 55.000 0.00 0.00 0.00 2.87
941 944 4.707934 ACTCCTTGTTTTTCTTTTTCGGGA 59.292 37.500 0.00 0.00 0.00 5.14
977 983 1.618343 GGGGAAAGGTGTTGGATTGTG 59.382 52.381 0.00 0.00 0.00 3.33
978 984 1.219213 TGGGGAAAGGTGTTGGATTGT 59.781 47.619 0.00 0.00 0.00 2.71
980 986 1.219213 TGTGGGGAAAGGTGTTGGATT 59.781 47.619 0.00 0.00 0.00 3.01
981 987 0.856982 TGTGGGGAAAGGTGTTGGAT 59.143 50.000 0.00 0.00 0.00 3.41
982 988 0.856982 ATGTGGGGAAAGGTGTTGGA 59.143 50.000 0.00 0.00 0.00 3.53
986 1011 0.251341 GCTCATGTGGGGAAAGGTGT 60.251 55.000 0.00 0.00 0.00 4.16
1101 1144 1.075896 GAGGGAGGACGGATCTGGT 60.076 63.158 6.47 0.00 0.00 4.00
1450 1509 3.782443 GAACCGGGCCGACTCCAT 61.782 66.667 30.79 6.12 0.00 3.41
1502 1570 1.142060 CCAACACCACCTGGAAGTGTA 59.858 52.381 20.95 0.00 43.69 2.90
1620 1691 0.856982 TGGTGGGAAGTTTGGATGGT 59.143 50.000 0.00 0.00 0.00 3.55
1677 1802 3.073798 TGAACAGCCAGTAAAGGGAATGA 59.926 43.478 0.00 0.00 0.00 2.57
1693 1818 6.673154 TGTTGCTGATCTATCATTGAACAG 57.327 37.500 2.57 2.57 37.39 3.16
1809 1934 2.878406 CCGCATAACCTGGAATTGGTAG 59.122 50.000 0.00 0.00 36.69 3.18
1811 1936 1.684869 CCCGCATAACCTGGAATTGGT 60.685 52.381 0.00 0.00 39.91 3.67
1934 2068 5.885912 AGTAACATGTCCAGTTCAACAGTTT 59.114 36.000 0.00 0.00 0.00 2.66
1952 2086 7.311092 TCTTCTGTATTCAGGGAAAGTAACA 57.689 36.000 0.00 0.00 41.59 2.41
1989 2174 5.904362 ATTCAGCAAACCCTTGTAGAATC 57.096 39.130 0.00 0.00 35.28 2.52
1993 2178 5.957842 TTGTATTCAGCAAACCCTTGTAG 57.042 39.130 0.00 0.00 34.79 2.74
2406 2665 8.466798 TCAAAATCACGATAGAGTAGAATCACA 58.533 33.333 0.00 0.00 41.38 3.58
2435 2695 1.268625 CAACCGGTTTCAACTAAGGGC 59.731 52.381 19.55 0.00 0.00 5.19
2475 2735 9.881529 AACAGCAATGCTAAATTTTATTTTGTG 57.118 25.926 7.70 0.00 36.40 3.33
2537 2988 1.732259 CACCGCTGACTCAAACCATAC 59.268 52.381 0.00 0.00 0.00 2.39
2553 3004 8.450964 AGTAAACAGATAATGAATTTGACACCG 58.549 33.333 0.00 0.00 0.00 4.94
2600 3051 4.202050 ACTGCTGACCTTTTTGACATGTTC 60.202 41.667 0.00 0.00 0.00 3.18
2783 3284 6.015519 TGACATTTCATTTGGTTCAAGGTAGG 60.016 38.462 0.00 0.00 0.00 3.18
3138 4620 7.276878 TGCAATGAAAATGAAGAATATGCACAG 59.723 33.333 0.00 0.00 35.39 3.66
3158 4644 7.734924 ACAATATATACTCACTGGTGCAATG 57.265 36.000 0.00 0.00 0.00 2.82
3161 4647 6.986231 CAGAACAATATATACTCACTGGTGCA 59.014 38.462 0.00 0.00 0.00 4.57
3564 5142 5.344743 TGGAATGTTGCAACCAGTAAAAA 57.655 34.783 26.14 5.77 0.00 1.94
3584 5163 6.616947 TCGTAGCCACAAAAATAGAAAATGG 58.383 36.000 0.00 0.00 0.00 3.16
3647 5226 7.767250 TGTTGGGTATCAATTCATTGTGTAA 57.233 32.000 0.00 0.00 38.84 2.41
3974 5561 0.179000 CAGATGACCACACTAGCCCC 59.821 60.000 0.00 0.00 0.00 5.80
4137 5750 2.724977 TAACTTGTGAGGACGAGCAG 57.275 50.000 0.00 0.00 37.12 4.24
4302 5936 6.374333 ATGAAAGCATAAAACCATCACGTAGT 59.626 34.615 0.00 0.00 34.43 2.73
4311 5955 8.954950 TTCTGAAAAATGAAAGCATAAAACCA 57.045 26.923 0.00 0.00 33.44 3.67
4424 6069 1.599542 GCTCCGGATTTGAAAGGATCG 59.400 52.381 3.57 0.00 31.66 3.69


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

AutoCloner maintained by Alex Coulton.