Multiple sequence alignment - TraesCS6A01G269200

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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 TraesCS6A01G269200 chr6A 100.000 4216 0 0 1 4216 495476434 495472219 0.000000e+00 7786.0
1 TraesCS6A01G269200 chr6A 91.118 304 27 0 1 304 410230283 410230586 3.030000e-111 412.0
2 TraesCS6A01G269200 chr6A 89.935 308 31 0 1 308 108080799 108080492 8.490000e-107 398.0
3 TraesCS6A01G269200 chr6A 89.677 310 28 3 1 308 464139971 464139664 3.950000e-105 392.0
4 TraesCS6A01G269200 chr6A 89.355 310 29 3 1 308 305474386 305474079 1.840000e-103 387.0
5 TraesCS6A01G269200 chr6A 89.286 308 33 0 1 308 538405594 538405901 1.840000e-103 387.0
6 TraesCS6A01G269200 chr6D 92.161 2934 119 33 473 3376 347994976 347997828 0.000000e+00 4041.0
7 TraesCS6A01G269200 chr6D 93.831 308 19 0 1 308 347994569 347994876 8.260000e-127 464.0
8 TraesCS6A01G269200 chr6D 90.032 311 25 5 1 308 114810602 114810909 8.490000e-107 398.0
9 TraesCS6A01G269200 chr6D 89.677 310 27 4 1 308 363053957 363054263 1.420000e-104 390.0
10 TraesCS6A01G269200 chr6D 88.710 310 31 3 1 308 389617856 389617549 3.980000e-100 375.0
11 TraesCS6A01G269200 chr6D 87.611 226 28 0 88 313 389625996 389625771 3.230000e-66 263.0
12 TraesCS6A01G269200 chr6D 91.608 143 5 6 321 458 347994853 347994993 1.550000e-44 191.0
13 TraesCS6A01G269200 chr6B 91.382 2866 150 47 563 3376 532198041 532195221 0.000000e+00 3834.0
14 TraesCS6A01G269200 chr6B 86.985 461 34 9 1 458 532199185 532198748 2.930000e-136 496.0
15 TraesCS6A01G269200 chr6B 89.677 310 28 3 1 308 631206493 631206186 3.950000e-105 392.0
16 TraesCS6A01G269200 chr7D 90.848 743 65 3 3475 4216 364625317 364624577 0.000000e+00 992.0
17 TraesCS6A01G269200 chr7D 90.283 741 68 4 3477 4216 19571761 19572498 0.000000e+00 966.0
18 TraesCS6A01G269200 chr7D 89.879 741 72 3 3477 4216 141565958 141566696 0.000000e+00 950.0
19 TraesCS6A01G269200 chr7D 89.879 741 71 4 3477 4216 446354806 446355543 0.000000e+00 950.0
20 TraesCS6A01G269200 chr7D 90.909 297 26 1 13 309 45841334 45841039 8.490000e-107 398.0
21 TraesCS6A01G269200 chr3D 90.726 744 65 4 3475 4216 9327201 9326460 0.000000e+00 989.0
22 TraesCS6A01G269200 chr5D 90.296 742 68 4 3477 4216 14646467 14647206 0.000000e+00 968.0
23 TraesCS6A01G269200 chr5D 89.757 742 72 4 3477 4216 565334722 565335461 0.000000e+00 946.0
24 TraesCS6A01G269200 chr4D 89.879 741 71 4 3477 4216 405710427 405709690 0.000000e+00 950.0
25 TraesCS6A01G269200 chr2D 89.919 744 66 8 3477 4216 593187952 593188690 0.000000e+00 950.0
26 TraesCS6A01G269200 chr2D 89.935 308 30 1 1 308 499912094 499912400 3.050000e-106 396.0
27 TraesCS6A01G269200 chr3A 90.968 310 24 3 1 308 742912164 742912471 8.430000e-112 414.0
28 TraesCS6A01G269200 chr3B 90.645 310 25 3 1 308 792182460 792182153 3.920000e-110 409.0
29 TraesCS6A01G269200 chr1B 90.879 307 24 3 1 305 554144906 554145210 3.920000e-110 409.0
30 TraesCS6A01G269200 chr7A 90.789 304 28 0 1 304 65482662 65482965 1.410000e-109 407.0
31 TraesCS6A01G269200 chr1A 90.000 310 27 3 1 308 23148010 23148317 8.490000e-107 398.0
32 TraesCS6A01G269200 chr1A 89.474 304 31 1 1 304 118282404 118282102 2.380000e-102 383.0
33 TraesCS6A01G269200 chr1A 88.673 309 32 2 1 308 559620582 559620888 1.430000e-99 374.0
34 TraesCS6A01G269200 chr1A 88.387 310 32 3 1 308 498720558 498720251 1.850000e-98 370.0
35 TraesCS6A01G269200 chr1D 88.387 310 32 3 1 308 175906021 175905714 1.850000e-98 370.0
36 TraesCS6A01G269200 chr1D 88.026 309 29 6 2 308 292548253 292547951 4.010000e-95 359.0
37 TraesCS6A01G269200 chr1D 86.645 307 39 1 2 308 449647582 449647886 5.220000e-89 339.0
38 TraesCS6A01G269200 chr1D 84.740 308 32 7 1 308 454552451 454552743 1.150000e-75 294.0
39 TraesCS6A01G269200 chr1D 86.441 236 28 3 75 308 449642335 449642568 5.410000e-64 255.0
40 TraesCS6A01G269200 chr5A 89.655 58 4 2 2419 2475 680735427 680735371 5.850000e-09 73.1


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 TraesCS6A01G269200 chr6A 495472219 495476434 4215 True 7786.000000 7786 100.000000 1 4216 1 chr6A.!!$R4 4215
1 TraesCS6A01G269200 chr6D 347994569 347997828 3259 False 1565.333333 4041 92.533333 1 3376 3 chr6D.!!$F3 3375
2 TraesCS6A01G269200 chr6B 532195221 532199185 3964 True 2165.000000 3834 89.183500 1 3376 2 chr6B.!!$R2 3375
3 TraesCS6A01G269200 chr7D 364624577 364625317 740 True 992.000000 992 90.848000 3475 4216 1 chr7D.!!$R2 741
4 TraesCS6A01G269200 chr7D 19571761 19572498 737 False 966.000000 966 90.283000 3477 4216 1 chr7D.!!$F1 739
5 TraesCS6A01G269200 chr7D 141565958 141566696 738 False 950.000000 950 89.879000 3477 4216 1 chr7D.!!$F2 739
6 TraesCS6A01G269200 chr7D 446354806 446355543 737 False 950.000000 950 89.879000 3477 4216 1 chr7D.!!$F3 739
7 TraesCS6A01G269200 chr3D 9326460 9327201 741 True 989.000000 989 90.726000 3475 4216 1 chr3D.!!$R1 741
8 TraesCS6A01G269200 chr5D 14646467 14647206 739 False 968.000000 968 90.296000 3477 4216 1 chr5D.!!$F1 739
9 TraesCS6A01G269200 chr5D 565334722 565335461 739 False 946.000000 946 89.757000 3477 4216 1 chr5D.!!$F2 739
10 TraesCS6A01G269200 chr4D 405709690 405710427 737 True 950.000000 950 89.879000 3477 4216 1 chr4D.!!$R1 739
11 TraesCS6A01G269200 chr2D 593187952 593188690 738 False 950.000000 950 89.919000 3477 4216 1 chr2D.!!$F2 739

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
462 495 0.677731 ATCAGTTGGCATGTGTCCCG 60.678 55.0 0.0 0.0 0.0 5.14 F
1571 2309 0.098200 CTCGTCGTAACTCCATCGCA 59.902 55.0 0.0 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 3059 0.322456 CCCATGACGAGGAAAGGCAA 60.322 55.0 0.0 0.0 0.0 4.52 R
3228 3971 0.030908 CCTGAGGTCTACGCCGATTC 59.969 60.0 0.0 0.0 0.0 2.52 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
90 91 6.253946 AGGGGGAGTGTTAAGAATAGAATG 57.746 41.667 0.00 0.00 0.00 2.67
95 96 6.884836 GGGAGTGTTAAGAATAGAATGGTTGT 59.115 38.462 0.00 0.00 0.00 3.32
191 192 2.017138 GCCTCTCAAGACAACTAGGC 57.983 55.000 0.00 0.00 42.40 3.93
268 269 2.908351 ACTTCCGCCCGGGTATAAATAT 59.092 45.455 24.63 0.00 37.00 1.28
276 277 4.507869 GCCCGGGTATAAATATCCCACTTT 60.508 45.833 24.63 0.00 41.12 2.66
293 323 8.519799 TCCCACTTTTATCATCAATAAAGACC 57.480 34.615 0.00 0.00 40.15 3.85
309 339 9.880157 CAATAAAGACCAATGGATCATCTTTTT 57.120 29.630 17.13 9.50 39.62 1.94
354 384 7.621428 TGAATCATCTTTCATTCAACTCCTC 57.379 36.000 0.00 0.00 36.33 3.71
355 385 7.170277 TGAATCATCTTTCATTCAACTCCTCA 58.830 34.615 0.00 0.00 36.33 3.86
356 386 7.832685 TGAATCATCTTTCATTCAACTCCTCAT 59.167 33.333 0.00 0.00 36.33 2.90
357 387 8.591114 AATCATCTTTCATTCAACTCCTCATT 57.409 30.769 0.00 0.00 0.00 2.57
409 442 0.818296 CGAAGGAGGTGAATCGGTCT 59.182 55.000 0.00 0.00 0.00 3.85
416 449 1.276421 AGGTGAATCGGTCTGAGGTTG 59.724 52.381 0.00 0.00 0.00 3.77
445 478 6.718522 AGGAACACTAGGCTAGTTAAGATC 57.281 41.667 24.19 16.10 36.76 2.75
448 481 6.097129 GGAACACTAGGCTAGTTAAGATCAGT 59.903 42.308 24.19 13.41 36.76 3.41
457 490 5.220739 GCTAGTTAAGATCAGTTGGCATGTG 60.221 44.000 0.00 0.00 0.00 3.21
458 491 4.655963 AGTTAAGATCAGTTGGCATGTGT 58.344 39.130 0.00 0.00 0.00 3.72
459 492 4.697352 AGTTAAGATCAGTTGGCATGTGTC 59.303 41.667 0.00 0.00 0.00 3.67
460 493 2.119801 AGATCAGTTGGCATGTGTCC 57.880 50.000 0.00 0.00 0.00 4.02
461 494 1.098050 GATCAGTTGGCATGTGTCCC 58.902 55.000 0.00 0.00 0.00 4.46
462 495 0.677731 ATCAGTTGGCATGTGTCCCG 60.678 55.000 0.00 0.00 0.00 5.14
463 496 2.672996 AGTTGGCATGTGTCCCGC 60.673 61.111 0.00 0.00 0.00 6.13
464 497 2.983030 GTTGGCATGTGTCCCGCA 60.983 61.111 0.00 0.00 0.00 5.69
465 498 2.203408 TTGGCATGTGTCCCGCAA 60.203 55.556 0.00 0.00 0.00 4.85
466 499 1.829970 TTGGCATGTGTCCCGCAAA 60.830 52.632 0.00 0.00 0.00 3.68
467 500 1.395045 TTGGCATGTGTCCCGCAAAA 61.395 50.000 0.00 0.00 0.00 2.44
468 501 1.365633 GGCATGTGTCCCGCAAAAA 59.634 52.632 0.00 0.00 0.00 1.94
492 525 4.778534 AAAGATCAGTTGGCATGTGAAG 57.221 40.909 3.67 0.00 0.00 3.02
493 526 2.719739 AGATCAGTTGGCATGTGAAGG 58.280 47.619 3.67 0.00 0.00 3.46
546 1229 3.360340 AGCGCACTTGCTGGCTTC 61.360 61.111 11.47 0.00 45.28 3.86
547 1230 3.663176 GCGCACTTGCTGGCTTCA 61.663 61.111 0.30 0.00 39.32 3.02
548 1231 2.986306 GCGCACTTGCTGGCTTCAT 61.986 57.895 0.30 0.00 39.32 2.57
549 1232 1.647545 GCGCACTTGCTGGCTTCATA 61.648 55.000 0.30 0.00 39.32 2.15
550 1233 0.804364 CGCACTTGCTGGCTTCATAA 59.196 50.000 0.00 0.00 39.32 1.90
552 1235 2.159338 CGCACTTGCTGGCTTCATAATT 60.159 45.455 0.00 0.00 39.32 1.40
556 1239 5.163622 GCACTTGCTGGCTTCATAATTCTTA 60.164 40.000 0.00 0.00 38.21 2.10
557 1240 6.460676 GCACTTGCTGGCTTCATAATTCTTAT 60.461 38.462 0.00 0.00 38.21 1.73
558 1241 7.255242 GCACTTGCTGGCTTCATAATTCTTATA 60.255 37.037 0.00 0.00 38.21 0.98
568 1251 8.026607 GCTTCATAATTCTTATACGAGAGAGCT 58.973 37.037 0.00 0.00 0.00 4.09
578 1261 8.591940 TCTTATACGAGAGAGCTACCATAGTTA 58.408 37.037 0.00 0.00 0.00 2.24
584 1267 6.546428 AGAGAGCTACCATAGTTAAAAGCA 57.454 37.500 0.00 0.00 32.42 3.91
736 1420 2.035442 GGGCTCAGAAGACAACGGC 61.035 63.158 0.00 0.00 28.86 5.68
760 1444 4.344968 CCAAACAAATCTGGTCCTTTTCCT 59.655 41.667 0.00 0.00 0.00 3.36
784 1468 4.021104 CAGAAAAGGAAGGAATGAAACCCC 60.021 45.833 0.00 0.00 0.00 4.95
789 1473 2.023984 GGAAGGAATGAAACCCCATCCT 60.024 50.000 0.00 0.00 0.00 3.24
793 1477 2.017049 GAATGAAACCCCATCCTGTCG 58.983 52.381 0.00 0.00 0.00 4.35
794 1478 0.991920 ATGAAACCCCATCCTGTCGT 59.008 50.000 0.00 0.00 0.00 4.34
803 1487 0.742281 CATCCTGTCGTCCCTTGCTG 60.742 60.000 0.00 0.00 0.00 4.41
851 1535 2.887360 CGCTTGATTTGGGGGCTG 59.113 61.111 0.00 0.00 0.00 4.85
852 1536 2.713967 CGCTTGATTTGGGGGCTGG 61.714 63.158 0.00 0.00 0.00 4.85
853 1537 2.361567 GCTTGATTTGGGGGCTGGG 61.362 63.158 0.00 0.00 0.00 4.45
854 1538 2.284552 TTGATTTGGGGGCTGGGC 60.285 61.111 0.00 0.00 0.00 5.36
855 1539 2.810488 CTTGATTTGGGGGCTGGGCT 62.810 60.000 0.00 0.00 0.00 5.19
856 1540 2.761213 GATTTGGGGGCTGGGCTG 60.761 66.667 0.00 0.00 0.00 4.85
891 1575 1.078143 AATCACTCCGCCAAGCTCC 60.078 57.895 0.00 0.00 0.00 4.70
972 1661 3.522731 CGAGAGGAGCCGTGGGAG 61.523 72.222 0.00 0.00 0.00 4.30
973 1662 3.844090 GAGAGGAGCCGTGGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
1140 1844 0.912486 CCCGATCTCCTTTCCACCTT 59.088 55.000 0.00 0.00 0.00 3.50
1154 1858 3.647636 TCCACCTTATCTTCTCCCTCTG 58.352 50.000 0.00 0.00 0.00 3.35
1243 1976 3.469008 TTCTTTCTGGAGCAGACGAAA 57.531 42.857 0.00 0.00 40.46 3.46
1257 1990 1.801178 GACGAAACTTGAAGCAGAGGG 59.199 52.381 0.00 0.00 0.00 4.30
1311 2046 2.202946 GCCTCCTAGAGCGTTGCC 60.203 66.667 0.00 0.00 0.00 4.52
1312 2047 2.105128 CCTCCTAGAGCGTTGCCG 59.895 66.667 0.00 0.00 37.07 5.69
1345 2080 1.671328 CTGCAATCTCATCCAGCAGTG 59.329 52.381 0.00 0.00 45.57 3.66
1349 2084 2.871022 CAATCTCATCCAGCAGTGCTAC 59.129 50.000 19.26 0.00 36.40 3.58
1353 2088 2.735772 ATCCAGCAGTGCTACGGGG 61.736 63.158 19.26 15.09 36.40 5.73
1355 2090 3.706373 CAGCAGTGCTACGGGGGT 61.706 66.667 19.26 0.00 36.40 4.95
1356 2091 3.706373 AGCAGTGCTACGGGGGTG 61.706 66.667 18.11 0.00 36.99 4.61
1384 2119 1.746991 GGCCTTGTGGAGCTGTAGC 60.747 63.158 0.00 0.00 42.49 3.58
1444 2179 1.918609 GAGCGACAGATGTTACCGAAC 59.081 52.381 0.00 0.00 36.00 3.95
1521 2259 2.621055 CAAAATGTCCAACTCCACCGAA 59.379 45.455 0.00 0.00 0.00 4.30
1559 2297 5.403766 GCAAATATGATTCAGATCTCGTCGT 59.596 40.000 0.00 0.00 33.28 4.34
1560 2298 6.582672 GCAAATATGATTCAGATCTCGTCGTA 59.417 38.462 0.00 0.00 33.28 3.43
1561 2299 7.114953 GCAAATATGATTCAGATCTCGTCGTAA 59.885 37.037 0.00 0.00 33.28 3.18
1571 2309 0.098200 CTCGTCGTAACTCCATCGCA 59.902 55.000 0.00 0.00 0.00 5.10
1576 2314 0.855349 CGTAACTCCATCGCAGCATC 59.145 55.000 0.00 0.00 0.00 3.91
1585 2323 2.286831 CCATCGCAGCATCTGAATTGAC 60.287 50.000 0.00 0.00 32.44 3.18
1587 2325 2.635714 TCGCAGCATCTGAATTGACAT 58.364 42.857 0.00 0.00 32.44 3.06
1590 2328 3.181504 CGCAGCATCTGAATTGACATTGA 60.182 43.478 0.00 0.00 32.44 2.57
1627 2366 2.349817 CCGCGAATGAGCATTTGATACC 60.350 50.000 8.23 0.00 34.78 2.73
1650 2389 4.461405 GCATCTGCGTTTGATATCATGTC 58.539 43.478 6.17 0.00 0.00 3.06
1668 2407 1.532868 GTCAGTTGATCGCTTGTTGCT 59.467 47.619 0.00 0.00 40.11 3.91
1670 2409 2.995939 TCAGTTGATCGCTTGTTGCTAG 59.004 45.455 0.00 0.00 40.11 3.42
1671 2410 2.738846 CAGTTGATCGCTTGTTGCTAGT 59.261 45.455 0.00 0.00 40.11 2.57
1674 2413 3.586100 TGATCGCTTGTTGCTAGTACA 57.414 42.857 0.00 0.00 40.11 2.90
1675 2414 3.920446 TGATCGCTTGTTGCTAGTACAA 58.080 40.909 10.72 10.72 40.11 2.41
1676 2415 4.503910 TGATCGCTTGTTGCTAGTACAAT 58.496 39.130 11.36 0.24 40.11 2.71
1677 2416 4.935205 TGATCGCTTGTTGCTAGTACAATT 59.065 37.500 11.36 1.20 40.11 2.32
1678 2417 4.921470 TCGCTTGTTGCTAGTACAATTC 57.079 40.909 11.36 7.26 40.11 2.17
1679 2418 4.311606 TCGCTTGTTGCTAGTACAATTCA 58.688 39.130 11.36 0.00 40.11 2.57
1681 2420 4.846137 CGCTTGTTGCTAGTACAATTCAAC 59.154 41.667 11.36 4.69 40.11 3.18
1682 2421 4.846137 GCTTGTTGCTAGTACAATTCAACG 59.154 41.667 11.36 3.11 39.68 4.10
1729 2469 6.274157 TCTGAAGAACTGTATGTCTTCTCC 57.726 41.667 17.11 0.00 39.28 3.71
1730 2470 5.775195 TCTGAAGAACTGTATGTCTTCTCCA 59.225 40.000 17.11 2.89 39.28 3.86
1731 2471 6.267699 TCTGAAGAACTGTATGTCTTCTCCAA 59.732 38.462 17.11 2.14 39.28 3.53
1733 2473 6.875726 TGAAGAACTGTATGTCTTCTCCAATG 59.124 38.462 17.11 0.00 39.28 2.82
2072 2812 2.126189 GGCTACGTCGTGTGGGTC 60.126 66.667 8.47 0.00 0.00 4.46
2144 2884 2.809601 AGCGGCGTCATCGACAAC 60.810 61.111 9.37 0.00 46.73 3.32
2319 3059 1.308326 CTCGGGGTCTTCTCCCTCT 59.692 63.158 1.72 0.00 46.27 3.69
2399 3139 0.243907 AGGTCGATCTCCACAACGTG 59.756 55.000 0.00 0.00 0.00 4.49
2462 3202 1.142748 CTGGGACTCGATCAGCACC 59.857 63.158 0.00 0.00 0.00 5.01
2928 3668 2.355837 TGTCGTTCGTCCTGCTGC 60.356 61.111 0.00 0.00 0.00 5.25
3245 3988 1.471119 AAGAATCGGCGTAGACCTCA 58.529 50.000 6.85 0.00 0.00 3.86
3377 4120 3.479006 GTGTTTCATTCACGATTGTCCG 58.521 45.455 0.00 0.00 0.00 4.79
3378 4121 3.185594 GTGTTTCATTCACGATTGTCCGA 59.814 43.478 0.00 0.00 0.00 4.55
3379 4122 3.810386 TGTTTCATTCACGATTGTCCGAA 59.190 39.130 0.00 0.00 0.00 4.30
3380 4123 4.273724 TGTTTCATTCACGATTGTCCGAAA 59.726 37.500 0.00 0.00 0.00 3.46
3381 4124 5.209240 GTTTCATTCACGATTGTCCGAAAA 58.791 37.500 0.00 0.00 0.00 2.29
3382 4125 4.398549 TCATTCACGATTGTCCGAAAAC 57.601 40.909 0.00 0.00 0.00 2.43
3383 4126 3.810386 TCATTCACGATTGTCCGAAAACA 59.190 39.130 0.00 0.00 0.00 2.83
3384 4127 4.454161 TCATTCACGATTGTCCGAAAACAT 59.546 37.500 0.00 0.00 0.00 2.71
3385 4128 3.804518 TCACGATTGTCCGAAAACATG 57.195 42.857 0.00 0.00 0.00 3.21
3386 4129 3.135225 TCACGATTGTCCGAAAACATGT 58.865 40.909 0.00 0.00 0.00 3.21
3387 4130 3.562141 TCACGATTGTCCGAAAACATGTT 59.438 39.130 4.92 4.92 0.00 2.71
3388 4131 4.035792 TCACGATTGTCCGAAAACATGTTT 59.964 37.500 18.13 18.13 0.00 2.83
3389 4132 4.737765 CACGATTGTCCGAAAACATGTTTT 59.262 37.500 31.40 31.40 44.59 2.43
3390 4133 5.910166 CACGATTGTCCGAAAACATGTTTTA 59.090 36.000 31.09 17.91 42.26 1.52
3391 4134 6.086241 CACGATTGTCCGAAAACATGTTTTAG 59.914 38.462 31.09 29.17 42.26 1.85
3392 4135 6.017770 ACGATTGTCCGAAAACATGTTTTAGA 60.018 34.615 32.83 27.74 42.26 2.10
3393 4136 6.519761 CGATTGTCCGAAAACATGTTTTAGAG 59.480 38.462 32.83 25.51 42.26 2.43
3394 4137 5.103290 TGTCCGAAAACATGTTTTAGAGC 57.897 39.130 32.83 25.74 42.26 4.09
3395 4138 4.819630 TGTCCGAAAACATGTTTTAGAGCT 59.180 37.500 32.83 15.95 42.26 4.09
3396 4139 5.049680 TGTCCGAAAACATGTTTTAGAGCTC 60.050 40.000 32.83 21.11 42.26 4.09
3397 4140 5.049680 GTCCGAAAACATGTTTTAGAGCTCA 60.050 40.000 32.83 15.77 42.26 4.26
3398 4141 5.705441 TCCGAAAACATGTTTTAGAGCTCAT 59.295 36.000 32.83 14.06 42.26 2.90
3399 4142 5.796935 CCGAAAACATGTTTTAGAGCTCATG 59.203 40.000 32.83 17.61 42.26 3.07
3400 4143 5.284660 CGAAAACATGTTTTAGAGCTCATGC 59.715 40.000 31.09 16.24 42.26 4.06
3401 4144 5.710513 AAACATGTTTTAGAGCTCATGCA 57.289 34.783 18.13 7.65 40.57 3.96
3402 4145 4.691860 ACATGTTTTAGAGCTCATGCAC 57.308 40.909 17.77 7.78 40.57 4.57
3403 4146 3.441572 ACATGTTTTAGAGCTCATGCACC 59.558 43.478 17.77 0.00 40.57 5.01
3404 4147 3.423539 TGTTTTAGAGCTCATGCACCT 57.576 42.857 17.77 0.00 42.74 4.00
3405 4148 3.338249 TGTTTTAGAGCTCATGCACCTC 58.662 45.455 17.77 0.00 42.74 3.85
3406 4149 2.299993 TTTAGAGCTCATGCACCTCG 57.700 50.000 17.77 0.00 42.74 4.63
3407 4150 0.461548 TTAGAGCTCATGCACCTCGG 59.538 55.000 17.77 0.00 42.74 4.63
3408 4151 2.021068 TAGAGCTCATGCACCTCGGC 62.021 60.000 17.77 0.00 42.74 5.54
3409 4152 4.479993 AGCTCATGCACCTCGGCC 62.480 66.667 0.00 0.00 42.74 6.13
3411 4154 4.864334 CTCATGCACCTCGGCCCC 62.864 72.222 0.00 0.00 0.00 5.80
3417 4160 2.365105 CACCTCGGCCCCCTCTTA 60.365 66.667 0.00 0.00 0.00 2.10
3418 4161 1.766461 CACCTCGGCCCCCTCTTAT 60.766 63.158 0.00 0.00 0.00 1.73
3419 4162 1.459730 ACCTCGGCCCCCTCTTATC 60.460 63.158 0.00 0.00 0.00 1.75
3420 4163 1.152226 CCTCGGCCCCCTCTTATCT 60.152 63.158 0.00 0.00 0.00 1.98
3421 4164 0.114560 CCTCGGCCCCCTCTTATCTA 59.885 60.000 0.00 0.00 0.00 1.98
3422 4165 1.551452 CTCGGCCCCCTCTTATCTAG 58.449 60.000 0.00 0.00 0.00 2.43
3423 4166 0.542232 TCGGCCCCCTCTTATCTAGC 60.542 60.000 0.00 0.00 0.00 3.42
3424 4167 1.545706 CGGCCCCCTCTTATCTAGCC 61.546 65.000 0.00 0.00 35.55 3.93
3425 4168 0.473886 GGCCCCCTCTTATCTAGCCA 60.474 60.000 0.00 0.00 38.79 4.75
3426 4169 1.662686 GCCCCCTCTTATCTAGCCAT 58.337 55.000 0.00 0.00 0.00 4.40
3427 4170 1.557371 GCCCCCTCTTATCTAGCCATC 59.443 57.143 0.00 0.00 0.00 3.51
3428 4171 2.192263 CCCCCTCTTATCTAGCCATCC 58.808 57.143 0.00 0.00 0.00 3.51
3429 4172 2.495383 CCCCCTCTTATCTAGCCATCCA 60.495 54.545 0.00 0.00 0.00 3.41
3430 4173 3.458831 CCCCTCTTATCTAGCCATCCAT 58.541 50.000 0.00 0.00 0.00 3.41
3431 4174 3.848975 CCCCTCTTATCTAGCCATCCATT 59.151 47.826 0.00 0.00 0.00 3.16
3432 4175 4.080638 CCCCTCTTATCTAGCCATCCATTC 60.081 50.000 0.00 0.00 0.00 2.67
3433 4176 4.782156 CCCTCTTATCTAGCCATCCATTCT 59.218 45.833 0.00 0.00 0.00 2.40
3434 4177 5.104982 CCCTCTTATCTAGCCATCCATTCTC 60.105 48.000 0.00 0.00 0.00 2.87
3435 4178 5.721000 CCTCTTATCTAGCCATCCATTCTCT 59.279 44.000 0.00 0.00 0.00 3.10
3436 4179 6.894654 CCTCTTATCTAGCCATCCATTCTCTA 59.105 42.308 0.00 0.00 0.00 2.43
3437 4180 7.564660 CCTCTTATCTAGCCATCCATTCTCTAT 59.435 40.741 0.00 0.00 0.00 1.98
3438 4181 8.907829 TCTTATCTAGCCATCCATTCTCTATT 57.092 34.615 0.00 0.00 0.00 1.73
3439 4182 9.331466 TCTTATCTAGCCATCCATTCTCTATTT 57.669 33.333 0.00 0.00 0.00 1.40
3440 4183 9.598517 CTTATCTAGCCATCCATTCTCTATTTC 57.401 37.037 0.00 0.00 0.00 2.17
3441 4184 7.811482 ATCTAGCCATCCATTCTCTATTTCT 57.189 36.000 0.00 0.00 0.00 2.52
3442 4185 7.238486 TCTAGCCATCCATTCTCTATTTCTC 57.762 40.000 0.00 0.00 0.00 2.87
3443 4186 7.015680 TCTAGCCATCCATTCTCTATTTCTCT 58.984 38.462 0.00 0.00 0.00 3.10
3444 4187 6.512514 AGCCATCCATTCTCTATTTCTCTT 57.487 37.500 0.00 0.00 0.00 2.85
3445 4188 6.532826 AGCCATCCATTCTCTATTTCTCTTC 58.467 40.000 0.00 0.00 0.00 2.87
3446 4189 6.100859 AGCCATCCATTCTCTATTTCTCTTCA 59.899 38.462 0.00 0.00 0.00 3.02
3447 4190 6.941436 GCCATCCATTCTCTATTTCTCTTCAT 59.059 38.462 0.00 0.00 0.00 2.57
3448 4191 7.447853 GCCATCCATTCTCTATTTCTCTTCATT 59.552 37.037 0.00 0.00 0.00 2.57
3449 4192 8.784994 CCATCCATTCTCTATTTCTCTTCATTG 58.215 37.037 0.00 0.00 0.00 2.82
3450 4193 7.798596 TCCATTCTCTATTTCTCTTCATTGC 57.201 36.000 0.00 0.00 0.00 3.56
3451 4194 6.481313 TCCATTCTCTATTTCTCTTCATTGCG 59.519 38.462 0.00 0.00 0.00 4.85
3452 4195 6.481313 CCATTCTCTATTTCTCTTCATTGCGA 59.519 38.462 0.00 0.00 0.00 5.10
3453 4196 7.172875 CCATTCTCTATTTCTCTTCATTGCGAT 59.827 37.037 0.00 0.00 0.00 4.58
3454 4197 8.557864 CATTCTCTATTTCTCTTCATTGCGATT 58.442 33.333 0.00 0.00 0.00 3.34
3455 4198 8.498054 TTCTCTATTTCTCTTCATTGCGATTT 57.502 30.769 0.00 0.00 0.00 2.17
3456 4199 7.913423 TCTCTATTTCTCTTCATTGCGATTTG 58.087 34.615 0.00 0.00 0.00 2.32
3457 4200 7.550551 TCTCTATTTCTCTTCATTGCGATTTGT 59.449 33.333 0.00 0.00 0.00 2.83
3458 4201 7.466805 TCTATTTCTCTTCATTGCGATTTGTG 58.533 34.615 0.00 0.00 0.00 3.33
3459 4202 5.437289 TTTCTCTTCATTGCGATTTGTGT 57.563 34.783 0.00 0.00 0.00 3.72
3460 4203 6.552859 TTTCTCTTCATTGCGATTTGTGTA 57.447 33.333 0.00 0.00 0.00 2.90
3461 4204 6.552859 TTCTCTTCATTGCGATTTGTGTAA 57.447 33.333 0.00 0.00 0.00 2.41
3462 4205 6.169419 TCTCTTCATTGCGATTTGTGTAAG 57.831 37.500 0.00 0.00 0.00 2.34
3463 4206 5.700832 TCTCTTCATTGCGATTTGTGTAAGT 59.299 36.000 0.00 0.00 0.00 2.24
3464 4207 6.871492 TCTCTTCATTGCGATTTGTGTAAGTA 59.129 34.615 0.00 0.00 0.00 2.24
3465 4208 6.827641 TCTTCATTGCGATTTGTGTAAGTAC 58.172 36.000 0.00 0.00 0.00 2.73
3466 4209 5.539582 TCATTGCGATTTGTGTAAGTACC 57.460 39.130 0.00 0.00 0.00 3.34
3467 4210 5.242434 TCATTGCGATTTGTGTAAGTACCT 58.758 37.500 0.00 0.00 0.00 3.08
3468 4211 5.703592 TCATTGCGATTTGTGTAAGTACCTT 59.296 36.000 0.00 0.00 0.00 3.50
3469 4212 6.205853 TCATTGCGATTTGTGTAAGTACCTTT 59.794 34.615 0.00 0.00 0.00 3.11
3470 4213 5.600908 TGCGATTTGTGTAAGTACCTTTC 57.399 39.130 0.00 0.00 0.00 2.62
3471 4214 4.150980 TGCGATTTGTGTAAGTACCTTTCG 59.849 41.667 0.00 0.00 0.00 3.46
3472 4215 4.634991 CGATTTGTGTAAGTACCTTTCGC 58.365 43.478 0.00 0.00 0.00 4.70
3473 4216 4.435121 CGATTTGTGTAAGTACCTTTCGCC 60.435 45.833 0.00 0.00 0.00 5.54
3487 4230 2.623878 TTCGCCCAGAAACACTAACA 57.376 45.000 0.00 0.00 35.61 2.41
3511 4254 0.319727 CACGTGTGGGCATTTGCATT 60.320 50.000 7.58 0.00 44.36 3.56
3522 4265 2.663808 CATTTGCATTTCGCTCACACA 58.336 42.857 0.00 0.00 43.06 3.72
3551 4294 1.098712 ACGTCCGTTTGTGGTTGCAT 61.099 50.000 0.00 0.00 0.00 3.96
3571 4314 8.449397 GTTGCATAAATTTTGGCATATTTGTGA 58.551 29.630 23.70 13.20 35.90 3.58
3610 4354 0.881118 GTGTGTGGGCATTCATTCGT 59.119 50.000 0.00 0.00 0.00 3.85
3615 4360 1.199097 GTGGGCATTCATTCGTTCGTT 59.801 47.619 0.00 0.00 0.00 3.85
3632 4378 1.259507 CGTTCACACGTCCGTTTTCAT 59.740 47.619 0.00 0.00 41.84 2.57
3633 4379 2.285950 CGTTCACACGTCCGTTTTCATT 60.286 45.455 0.00 0.00 41.84 2.57
3637 4383 4.059511 TCACACGTCCGTTTTCATTACAT 58.940 39.130 0.00 0.00 0.00 2.29
3641 4387 4.094294 CACGTCCGTTTTCATTACATGGAT 59.906 41.667 0.00 0.00 0.00 3.41
3652 4400 2.908688 TACATGGATGGATCGGTGTG 57.091 50.000 0.00 0.00 0.00 3.82
3664 4412 1.892862 CGGTGTGGTGGGCGTTTAA 60.893 57.895 0.00 0.00 0.00 1.52
3676 4424 0.308376 GCGTTTAACAGTTCGCCCAA 59.692 50.000 6.59 0.00 42.33 4.12
3719 4467 2.439156 GGCTGGTCTGTGGGCATC 60.439 66.667 0.00 0.00 0.00 3.91
3730 4478 1.831106 TGTGGGCATCTATCAGTTCGT 59.169 47.619 0.00 0.00 0.00 3.85
3737 4485 3.676049 GCATCTATCAGTTCGTCCACACA 60.676 47.826 0.00 0.00 0.00 3.72
3738 4486 4.686972 CATCTATCAGTTCGTCCACACAT 58.313 43.478 0.00 0.00 0.00 3.21
3816 4564 1.610624 GCAACTGCCCTAGTGTGCTTA 60.611 52.381 0.00 0.00 40.26 3.09
3820 4568 4.837093 ACTGCCCTAGTGTGCTTATAAA 57.163 40.909 0.00 0.00 38.49 1.40
3903 4651 1.160137 CAACTGCCCTAGTGTGCTTC 58.840 55.000 0.00 0.00 40.26 3.86
3979 4729 2.149803 TAGCGCTACACGGCAACTGT 62.150 55.000 14.45 0.00 43.93 3.55
4000 4750 4.775780 TGTCTAGTGTTAGTAGGTGGCAAT 59.224 41.667 0.00 0.00 0.00 3.56
4001 4751 5.105473 TGTCTAGTGTTAGTAGGTGGCAATC 60.105 44.000 0.00 0.00 0.00 2.67
4008 4758 5.014333 TGTTAGTAGGTGGCAATCCCTAAAA 59.986 40.000 4.09 0.69 35.16 1.52
4018 4768 7.361971 GGTGGCAATCCCTAAAATTTTCAAATG 60.362 37.037 6.72 2.41 0.00 2.32
4028 4778 9.434420 CCTAAAATTTTCAAATGATGGCAACTA 57.566 29.630 6.72 0.00 37.61 2.24
4072 4822 2.062971 TCCGCCTAGTGTTAGTAGGG 57.937 55.000 10.79 2.83 40.81 3.53
4119 4869 5.680619 TCATGGCAACTATAGTAAACCAGG 58.319 41.667 19.58 19.58 31.05 4.45
4123 4873 4.266714 GCAACTATAGTAAACCAGGCCAA 58.733 43.478 5.01 0.00 0.00 4.52
4206 4957 2.610976 GCAGTTGAGCAATCATGGCAAA 60.611 45.455 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.082313 GGGTATATCCATCATCTTCACAAATTT 57.918 33.333 0.00 0.00 38.11 1.82
157 158 0.322816 GAGGCAAGGAAGTGCATGGA 60.323 55.000 0.00 0.00 46.81 3.41
173 174 3.685139 TTGCCTAGTTGTCTTGAGAGG 57.315 47.619 0.00 0.00 0.00 3.69
268 269 8.112822 TGGTCTTTATTGATGATAAAAGTGGGA 58.887 33.333 0.00 0.00 39.17 4.37
276 277 9.865152 TGATCCATTGGTCTTTATTGATGATAA 57.135 29.630 1.86 0.00 0.00 1.75
330 360 7.170277 TGAGGAGTTGAATGAAAGATGATTCA 58.830 34.615 0.00 0.00 43.03 2.57
331 361 7.621428 TGAGGAGTTGAATGAAAGATGATTC 57.379 36.000 0.00 0.00 0.00 2.52
332 362 8.591114 AATGAGGAGTTGAATGAAAGATGATT 57.409 30.769 0.00 0.00 0.00 2.57
333 363 8.591114 AAATGAGGAGTTGAATGAAAGATGAT 57.409 30.769 0.00 0.00 0.00 2.45
334 364 8.413309 AAAATGAGGAGTTGAATGAAAGATGA 57.587 30.769 0.00 0.00 0.00 2.92
375 408 0.318107 CTTCGCTTGCACCTGTTTGG 60.318 55.000 0.00 0.00 42.93 3.28
409 442 4.437682 AGTGTTCCTTTCATCAACCTCA 57.562 40.909 0.00 0.00 0.00 3.86
416 449 5.346181 ACTAGCCTAGTGTTCCTTTCATC 57.654 43.478 2.96 0.00 37.69 2.92
445 478 2.981560 GCGGGACACATGCCAACTG 61.982 63.158 0.00 0.00 35.61 3.16
448 481 1.395045 TTTTGCGGGACACATGCCAA 61.395 50.000 0.00 0.00 35.61 4.52
469 502 5.510179 CCTTCACATGCCAACTGATCTTTTT 60.510 40.000 0.00 0.00 0.00 1.94
470 503 4.021719 CCTTCACATGCCAACTGATCTTTT 60.022 41.667 0.00 0.00 0.00 2.27
471 504 3.508793 CCTTCACATGCCAACTGATCTTT 59.491 43.478 0.00 0.00 0.00 2.52
472 505 3.087031 CCTTCACATGCCAACTGATCTT 58.913 45.455 0.00 0.00 0.00 2.40
473 506 2.619849 CCCTTCACATGCCAACTGATCT 60.620 50.000 0.00 0.00 0.00 2.75
474 507 1.747355 CCCTTCACATGCCAACTGATC 59.253 52.381 0.00 0.00 0.00 2.92
475 508 1.355381 TCCCTTCACATGCCAACTGAT 59.645 47.619 0.00 0.00 0.00 2.90
476 509 0.770499 TCCCTTCACATGCCAACTGA 59.230 50.000 0.00 0.00 0.00 3.41
477 510 1.171308 CTCCCTTCACATGCCAACTG 58.829 55.000 0.00 0.00 0.00 3.16
478 511 0.773644 ACTCCCTTCACATGCCAACT 59.226 50.000 0.00 0.00 0.00 3.16
479 512 1.620822 AACTCCCTTCACATGCCAAC 58.379 50.000 0.00 0.00 0.00 3.77
480 513 3.737559 ATAACTCCCTTCACATGCCAA 57.262 42.857 0.00 0.00 0.00 4.52
481 514 3.118038 GGTATAACTCCCTTCACATGCCA 60.118 47.826 0.00 0.00 0.00 4.92
482 515 3.477530 GGTATAACTCCCTTCACATGCC 58.522 50.000 0.00 0.00 0.00 4.40
483 516 3.131396 CGGTATAACTCCCTTCACATGC 58.869 50.000 0.00 0.00 0.00 4.06
484 517 4.402056 ACGGTATAACTCCCTTCACATG 57.598 45.455 0.00 0.00 0.00 3.21
485 518 4.766375 CAACGGTATAACTCCCTTCACAT 58.234 43.478 0.00 0.00 0.00 3.21
486 519 3.618019 GCAACGGTATAACTCCCTTCACA 60.618 47.826 0.00 0.00 0.00 3.58
487 520 2.934553 GCAACGGTATAACTCCCTTCAC 59.065 50.000 0.00 0.00 0.00 3.18
488 521 2.093341 GGCAACGGTATAACTCCCTTCA 60.093 50.000 0.00 0.00 0.00 3.02
492 525 1.761198 AGAGGCAACGGTATAACTCCC 59.239 52.381 0.00 0.00 46.39 4.30
493 526 4.280174 TCATAGAGGCAACGGTATAACTCC 59.720 45.833 0.00 0.00 46.39 3.85
532 1210 3.129988 AGAATTATGAAGCCAGCAAGTGC 59.870 43.478 0.00 0.00 42.49 4.40
546 1229 8.731605 TGGTAGCTCTCTCGTATAAGAATTATG 58.268 37.037 0.00 0.00 42.24 1.90
547 1230 8.865420 TGGTAGCTCTCTCGTATAAGAATTAT 57.135 34.615 0.00 0.00 44.82 1.28
548 1231 8.865420 ATGGTAGCTCTCTCGTATAAGAATTA 57.135 34.615 0.00 0.00 33.48 1.40
549 1232 7.768807 ATGGTAGCTCTCTCGTATAAGAATT 57.231 36.000 0.00 0.00 0.00 2.17
550 1233 8.104566 ACTATGGTAGCTCTCTCGTATAAGAAT 58.895 37.037 0.00 0.00 0.00 2.40
552 1235 7.006865 ACTATGGTAGCTCTCTCGTATAAGA 57.993 40.000 0.00 0.00 0.00 2.10
556 1239 8.461249 TTTTAACTATGGTAGCTCTCTCGTAT 57.539 34.615 0.00 0.00 0.00 3.06
557 1240 7.468357 GCTTTTAACTATGGTAGCTCTCTCGTA 60.468 40.741 0.00 0.00 0.00 3.43
558 1241 6.680872 GCTTTTAACTATGGTAGCTCTCTCGT 60.681 42.308 0.00 0.00 0.00 4.18
568 1251 5.592688 GGGCATTCTGCTTTTAACTATGGTA 59.407 40.000 0.00 0.00 44.28 3.25
570 1253 4.498009 CGGGCATTCTGCTTTTAACTATGG 60.498 45.833 0.00 0.00 44.28 2.74
578 1261 4.402155 TCATTAATCGGGCATTCTGCTTTT 59.598 37.500 0.00 0.00 44.28 2.27
584 1267 5.440610 AGACTTTCATTAATCGGGCATTCT 58.559 37.500 0.00 0.00 0.00 2.40
591 1274 5.005779 CGGACAAGAGACTTTCATTAATCGG 59.994 44.000 0.00 0.00 0.00 4.18
699 1382 2.039746 CCCCTGCGGATATGTGGAATAA 59.960 50.000 0.00 0.00 0.00 1.40
704 1387 2.281761 GCCCCTGCGGATATGTGG 60.282 66.667 0.00 0.00 0.00 4.17
736 1420 4.503123 GGAAAAGGACCAGATTTGTTTGGG 60.503 45.833 0.00 0.00 38.82 4.12
760 1444 4.832823 GGGTTTCATTCCTTCCTTTTCTGA 59.167 41.667 0.00 0.00 0.00 3.27
772 1456 2.379005 GACAGGATGGGGTTTCATTCC 58.621 52.381 0.00 0.00 43.62 3.01
773 1457 2.017049 CGACAGGATGGGGTTTCATTC 58.983 52.381 0.00 0.00 43.62 2.67
774 1458 1.354368 ACGACAGGATGGGGTTTCATT 59.646 47.619 0.00 0.00 43.62 2.57
775 1459 0.991920 ACGACAGGATGGGGTTTCAT 59.008 50.000 0.00 0.00 43.62 2.57
784 1468 0.742281 CAGCAAGGGACGACAGGATG 60.742 60.000 0.00 0.00 46.00 3.51
789 1473 2.280797 GTGCAGCAAGGGACGACA 60.281 61.111 0.00 0.00 0.00 4.35
803 1487 2.497107 AATAATGGAATGCAGCGTGC 57.503 45.000 0.00 3.44 45.29 5.34
851 1535 0.470341 GTGAAGTATCCTCCCAGCCC 59.530 60.000 0.00 0.00 0.00 5.19
852 1536 1.414550 GAGTGAAGTATCCTCCCAGCC 59.585 57.143 0.00 0.00 0.00 4.85
853 1537 2.111384 TGAGTGAAGTATCCTCCCAGC 58.889 52.381 0.00 0.00 0.00 4.85
854 1538 4.406972 TGATTGAGTGAAGTATCCTCCCAG 59.593 45.833 0.00 0.00 0.00 4.45
855 1539 4.162320 GTGATTGAGTGAAGTATCCTCCCA 59.838 45.833 0.00 0.00 0.00 4.37
856 1540 4.407296 AGTGATTGAGTGAAGTATCCTCCC 59.593 45.833 0.00 0.00 0.00 4.30
1104 1808 2.183046 GCGAGCTCACTCACCTCC 59.817 66.667 15.40 0.00 43.66 4.30
1109 1813 2.755876 ATCGGGCGAGCTCACTCA 60.756 61.111 15.40 0.00 43.66 3.41
1140 1844 4.883021 ACTGTACCAGAGGGAGAAGATA 57.117 45.455 0.00 0.00 38.05 1.98
1154 1858 0.739813 ATCGAAGCGCCAACTGTACC 60.740 55.000 2.29 0.00 0.00 3.34
1221 1954 3.469008 TCGTCTGCTCCAGAAAGAAAA 57.531 42.857 0.00 0.00 42.46 2.29
1222 1955 3.469008 TTCGTCTGCTCCAGAAAGAAA 57.531 42.857 10.12 0.00 42.46 2.52
1223 1956 3.131396 GTTTCGTCTGCTCCAGAAAGAA 58.869 45.455 9.06 9.06 42.46 2.52
1224 1957 2.365617 AGTTTCGTCTGCTCCAGAAAGA 59.634 45.455 0.00 0.00 42.46 2.52
1225 1958 2.760374 AGTTTCGTCTGCTCCAGAAAG 58.240 47.619 0.00 0.00 42.46 2.62
1257 1990 2.832201 GCTGAATGGGCCCTGAGC 60.832 66.667 25.70 19.84 42.60 4.26
1343 2078 4.404098 CACCCACCCCCGTAGCAC 62.404 72.222 0.00 0.00 0.00 4.40
1345 2080 3.087906 ATCACCCACCCCCGTAGC 61.088 66.667 0.00 0.00 0.00 3.58
1349 2084 4.802051 CAGCATCACCCACCCCCG 62.802 72.222 0.00 0.00 0.00 5.73
1353 2088 3.590466 AAGGCCAGCATCACCCACC 62.590 63.158 5.01 0.00 0.00 4.61
1355 2090 2.036098 CAAGGCCAGCATCACCCA 59.964 61.111 5.01 0.00 0.00 4.51
1356 2091 2.036256 ACAAGGCCAGCATCACCC 59.964 61.111 5.01 0.00 0.00 4.61
1384 2119 1.268625 TGCTCCGCCTATACACGTATG 59.731 52.381 0.00 0.00 0.00 2.39
1424 2159 1.918609 GTTCGGTAACATCTGTCGCTC 59.081 52.381 0.00 0.00 35.56 5.03
1450 2185 2.202797 CTGTCCATGTCCGGCTCG 60.203 66.667 0.00 0.00 0.00 5.03
1499 2237 1.335872 CGGTGGAGTTGGACATTTTGC 60.336 52.381 0.00 0.00 0.00 3.68
1500 2238 2.226330 TCGGTGGAGTTGGACATTTTG 58.774 47.619 0.00 0.00 0.00 2.44
1501 2239 2.649531 TCGGTGGAGTTGGACATTTT 57.350 45.000 0.00 0.00 0.00 1.82
1532 2270 4.435253 CGAGATCTGAATCATATTTGCCGC 60.435 45.833 0.00 0.00 34.07 6.53
1533 2271 4.687948 ACGAGATCTGAATCATATTTGCCG 59.312 41.667 0.00 0.00 34.07 5.69
1534 2272 5.164012 CGACGAGATCTGAATCATATTTGCC 60.164 44.000 0.00 0.00 34.07 4.52
1535 2273 5.403766 ACGACGAGATCTGAATCATATTTGC 59.596 40.000 0.00 0.00 34.07 3.68
1536 2274 6.999956 ACGACGAGATCTGAATCATATTTG 57.000 37.500 0.00 0.00 34.07 2.32
1559 2297 1.756538 TCAGATGCTGCGATGGAGTTA 59.243 47.619 0.00 0.00 0.00 2.24
1560 2298 0.538584 TCAGATGCTGCGATGGAGTT 59.461 50.000 0.00 0.00 0.00 3.01
1561 2299 0.538584 TTCAGATGCTGCGATGGAGT 59.461 50.000 0.00 0.00 0.00 3.85
1571 2309 5.892119 AGGATTCAATGTCAATTCAGATGCT 59.108 36.000 0.00 0.00 0.00 3.79
1590 2328 3.343617 TCGCGGAAATGAAAGAAGGATT 58.656 40.909 6.13 0.00 0.00 3.01
1641 2380 5.363101 ACAAGCGATCAACTGACATGATAT 58.637 37.500 0.00 0.00 37.64 1.63
1646 2385 2.095567 GCAACAAGCGATCAACTGACAT 60.096 45.455 0.00 0.00 0.00 3.06
1668 2407 5.063438 GCATGAGAAGCGTTGAATTGTACTA 59.937 40.000 0.00 0.00 0.00 1.82
1670 2409 4.091424 GCATGAGAAGCGTTGAATTGTAC 58.909 43.478 0.00 0.00 0.00 2.90
1671 2410 4.002982 AGCATGAGAAGCGTTGAATTGTA 58.997 39.130 0.00 0.00 37.01 2.41
1674 2413 3.341823 AGAGCATGAGAAGCGTTGAATT 58.658 40.909 0.00 0.00 37.01 2.17
1675 2414 2.983229 AGAGCATGAGAAGCGTTGAAT 58.017 42.857 0.00 0.00 37.01 2.57
1676 2415 2.462456 AGAGCATGAGAAGCGTTGAA 57.538 45.000 0.00 0.00 37.01 2.69
1677 2416 3.592898 TTAGAGCATGAGAAGCGTTGA 57.407 42.857 0.00 0.00 37.01 3.18
1678 2417 3.545624 GCATTAGAGCATGAGAAGCGTTG 60.546 47.826 0.00 0.00 37.01 4.10
1679 2418 2.611292 GCATTAGAGCATGAGAAGCGTT 59.389 45.455 0.00 0.00 37.01 4.84
1681 2420 1.530293 GGCATTAGAGCATGAGAAGCG 59.470 52.381 0.00 0.00 37.01 4.68
1682 2421 1.530293 CGGCATTAGAGCATGAGAAGC 59.470 52.381 0.00 0.00 35.83 3.86
1729 2469 2.488355 CGGGCTTCTGCTGCATTG 59.512 61.111 1.31 0.00 39.59 2.82
1730 2470 3.446570 GCGGGCTTCTGCTGCATT 61.447 61.111 1.31 0.00 39.59 3.56
2144 2884 2.124236 AGGACGGGGTAGAGAGCG 60.124 66.667 0.00 0.00 0.00 5.03
2319 3059 0.322456 CCCATGACGAGGAAAGGCAA 60.322 55.000 0.00 0.00 0.00 4.52
2378 3118 0.526211 CGTTGTGGAGATCGACCTCA 59.474 55.000 9.53 0.00 34.94 3.86
2399 3139 1.640917 TCAGGTACAGGTTCCAGTCC 58.359 55.000 0.00 0.00 0.00 3.85
2462 3202 1.227089 CCTGATCTCGCCGGACAAG 60.227 63.158 5.05 0.00 0.00 3.16
2840 3580 0.820226 TCTCCTGGAAGCTCATCGTG 59.180 55.000 0.00 0.00 0.00 4.35
3228 3971 0.030908 CCTGAGGTCTACGCCGATTC 59.969 60.000 0.00 0.00 0.00 2.52
3245 3988 6.071728 CCATAACTTTCAGCAATTCAGAACCT 60.072 38.462 0.00 0.00 0.00 3.50
3376 4119 5.284660 GCATGAGCTCTAAAACATGTTTTCG 59.715 40.000 33.71 28.00 41.14 3.46
3377 4120 6.088616 GTGCATGAGCTCTAAAACATGTTTTC 59.911 38.462 33.71 21.68 41.21 2.29
3378 4121 5.922544 GTGCATGAGCTCTAAAACATGTTTT 59.077 36.000 32.63 32.63 42.42 2.43
3379 4122 5.464168 GTGCATGAGCTCTAAAACATGTTT 58.536 37.500 18.13 18.13 41.14 2.83
3380 4123 4.082571 GGTGCATGAGCTCTAAAACATGTT 60.083 41.667 16.19 4.92 41.14 2.71
3381 4124 3.441572 GGTGCATGAGCTCTAAAACATGT 59.558 43.478 16.19 0.00 41.14 3.21
3382 4125 3.693085 AGGTGCATGAGCTCTAAAACATG 59.307 43.478 16.19 10.65 42.74 3.21
3383 4126 3.944015 GAGGTGCATGAGCTCTAAAACAT 59.056 43.478 16.19 6.18 44.54 2.71
3384 4127 3.338249 GAGGTGCATGAGCTCTAAAACA 58.662 45.455 16.19 3.43 44.54 2.83
3385 4128 2.349886 CGAGGTGCATGAGCTCTAAAAC 59.650 50.000 16.19 8.30 45.58 2.43
3386 4129 2.621338 CGAGGTGCATGAGCTCTAAAA 58.379 47.619 16.19 0.00 45.58 1.52
3387 4130 1.134699 CCGAGGTGCATGAGCTCTAAA 60.135 52.381 16.19 0.00 45.58 1.85
3388 4131 0.461548 CCGAGGTGCATGAGCTCTAA 59.538 55.000 16.19 0.00 45.58 2.10
3389 4132 2.021068 GCCGAGGTGCATGAGCTCTA 62.021 60.000 16.19 1.49 45.58 2.43
3390 4133 2.898738 CCGAGGTGCATGAGCTCT 59.101 61.111 16.19 0.00 45.58 4.09
3391 4134 2.894387 GCCGAGGTGCATGAGCTC 60.894 66.667 6.82 6.82 44.51 4.09
3392 4135 4.479993 GGCCGAGGTGCATGAGCT 62.480 66.667 0.00 0.00 42.74 4.09
3394 4137 4.864334 GGGGCCGAGGTGCATGAG 62.864 72.222 0.00 0.00 0.00 2.90
3400 4143 1.759459 GATAAGAGGGGGCCGAGGTG 61.759 65.000 0.00 0.00 0.00 4.00
3401 4144 1.459730 GATAAGAGGGGGCCGAGGT 60.460 63.158 0.00 0.00 0.00 3.85
3402 4145 0.114560 TAGATAAGAGGGGGCCGAGG 59.885 60.000 0.00 0.00 0.00 4.63
3403 4146 1.551452 CTAGATAAGAGGGGGCCGAG 58.449 60.000 0.00 0.00 0.00 4.63
3404 4147 0.542232 GCTAGATAAGAGGGGGCCGA 60.542 60.000 0.00 0.00 0.00 5.54
3405 4148 1.545706 GGCTAGATAAGAGGGGGCCG 61.546 65.000 0.00 0.00 0.00 6.13
3406 4149 0.473886 TGGCTAGATAAGAGGGGGCC 60.474 60.000 0.00 0.00 38.67 5.80
3407 4150 1.557371 GATGGCTAGATAAGAGGGGGC 59.443 57.143 0.00 0.00 0.00 5.80
3408 4151 2.192263 GGATGGCTAGATAAGAGGGGG 58.808 57.143 0.00 0.00 0.00 5.40
3409 4152 2.907892 TGGATGGCTAGATAAGAGGGG 58.092 52.381 0.00 0.00 0.00 4.79
3410 4153 4.782156 AGAATGGATGGCTAGATAAGAGGG 59.218 45.833 0.00 0.00 0.00 4.30
3411 4154 5.721000 AGAGAATGGATGGCTAGATAAGAGG 59.279 44.000 0.00 0.00 0.00 3.69
3412 4155 6.855763 AGAGAATGGATGGCTAGATAAGAG 57.144 41.667 0.00 0.00 0.00 2.85
3413 4156 8.907829 AATAGAGAATGGATGGCTAGATAAGA 57.092 34.615 0.00 0.00 0.00 2.10
3414 4157 9.598517 GAAATAGAGAATGGATGGCTAGATAAG 57.401 37.037 0.00 0.00 0.00 1.73
3415 4158 9.331466 AGAAATAGAGAATGGATGGCTAGATAA 57.669 33.333 0.00 0.00 0.00 1.75
3416 4159 8.907829 AGAAATAGAGAATGGATGGCTAGATA 57.092 34.615 0.00 0.00 0.00 1.98
3417 4160 7.679453 AGAGAAATAGAGAATGGATGGCTAGAT 59.321 37.037 0.00 0.00 0.00 1.98
3418 4161 7.015680 AGAGAAATAGAGAATGGATGGCTAGA 58.984 38.462 0.00 0.00 0.00 2.43
3419 4162 7.243604 AGAGAAATAGAGAATGGATGGCTAG 57.756 40.000 0.00 0.00 0.00 3.42
3420 4163 7.290948 TGAAGAGAAATAGAGAATGGATGGCTA 59.709 37.037 0.00 0.00 0.00 3.93
3421 4164 6.100859 TGAAGAGAAATAGAGAATGGATGGCT 59.899 38.462 0.00 0.00 0.00 4.75
3422 4165 6.294473 TGAAGAGAAATAGAGAATGGATGGC 58.706 40.000 0.00 0.00 0.00 4.40
3423 4166 8.784994 CAATGAAGAGAAATAGAGAATGGATGG 58.215 37.037 0.00 0.00 0.00 3.51
3424 4167 8.291032 GCAATGAAGAGAAATAGAGAATGGATG 58.709 37.037 0.00 0.00 0.00 3.51
3425 4168 7.172875 CGCAATGAAGAGAAATAGAGAATGGAT 59.827 37.037 0.00 0.00 0.00 3.41
3426 4169 6.481313 CGCAATGAAGAGAAATAGAGAATGGA 59.519 38.462 0.00 0.00 0.00 3.41
3427 4170 6.481313 TCGCAATGAAGAGAAATAGAGAATGG 59.519 38.462 0.00 0.00 0.00 3.16
3428 4171 7.474398 TCGCAATGAAGAGAAATAGAGAATG 57.526 36.000 0.00 0.00 0.00 2.67
3429 4172 8.674263 AATCGCAATGAAGAGAAATAGAGAAT 57.326 30.769 0.00 0.00 0.00 2.40
3430 4173 8.393366 CAAATCGCAATGAAGAGAAATAGAGAA 58.607 33.333 0.00 0.00 0.00 2.87
3431 4174 7.550551 ACAAATCGCAATGAAGAGAAATAGAGA 59.449 33.333 0.00 0.00 0.00 3.10
3432 4175 7.639072 CACAAATCGCAATGAAGAGAAATAGAG 59.361 37.037 0.00 0.00 0.00 2.43
3433 4176 7.119699 ACACAAATCGCAATGAAGAGAAATAGA 59.880 33.333 0.00 0.00 0.00 1.98
3434 4177 7.246311 ACACAAATCGCAATGAAGAGAAATAG 58.754 34.615 0.00 0.00 0.00 1.73
3435 4178 7.144722 ACACAAATCGCAATGAAGAGAAATA 57.855 32.000 0.00 0.00 0.00 1.40
3436 4179 6.017400 ACACAAATCGCAATGAAGAGAAAT 57.983 33.333 0.00 0.00 0.00 2.17
3437 4180 5.437289 ACACAAATCGCAATGAAGAGAAA 57.563 34.783 0.00 0.00 0.00 2.52
3438 4181 6.204688 ACTTACACAAATCGCAATGAAGAGAA 59.795 34.615 0.00 0.00 0.00 2.87
3439 4182 5.700832 ACTTACACAAATCGCAATGAAGAGA 59.299 36.000 0.00 0.00 0.00 3.10
3440 4183 5.931532 ACTTACACAAATCGCAATGAAGAG 58.068 37.500 0.00 0.00 0.00 2.85
3441 4184 5.940192 ACTTACACAAATCGCAATGAAGA 57.060 34.783 0.00 0.00 0.00 2.87
3442 4185 6.021596 GGTACTTACACAAATCGCAATGAAG 58.978 40.000 0.00 0.00 0.00 3.02
3443 4186 5.703592 AGGTACTTACACAAATCGCAATGAA 59.296 36.000 0.00 0.00 27.25 2.57
3444 4187 5.242434 AGGTACTTACACAAATCGCAATGA 58.758 37.500 0.00 0.00 27.25 2.57
3445 4188 5.545658 AGGTACTTACACAAATCGCAATG 57.454 39.130 0.00 0.00 27.25 2.82
3461 4204 1.418637 TGTTTCTGGGCGAAAGGTACT 59.581 47.619 0.00 0.00 42.01 2.73
3462 4205 1.534163 GTGTTTCTGGGCGAAAGGTAC 59.466 52.381 0.00 0.00 42.01 3.34
3463 4206 1.418637 AGTGTTTCTGGGCGAAAGGTA 59.581 47.619 0.00 0.00 42.01 3.08
3464 4207 0.182775 AGTGTTTCTGGGCGAAAGGT 59.817 50.000 0.00 0.00 42.01 3.50
3465 4208 2.178912 TAGTGTTTCTGGGCGAAAGG 57.821 50.000 0.00 0.00 42.01 3.11
3466 4209 2.875933 TGTTAGTGTTTCTGGGCGAAAG 59.124 45.455 0.00 0.00 42.01 2.62
3467 4210 2.614983 GTGTTAGTGTTTCTGGGCGAAA 59.385 45.455 0.00 0.00 39.23 3.46
3468 4211 2.215196 GTGTTAGTGTTTCTGGGCGAA 58.785 47.619 0.00 0.00 0.00 4.70
3469 4212 1.541670 GGTGTTAGTGTTTCTGGGCGA 60.542 52.381 0.00 0.00 0.00 5.54
3470 4213 0.872388 GGTGTTAGTGTTTCTGGGCG 59.128 55.000 0.00 0.00 0.00 6.13
3471 4214 2.271944 AGGTGTTAGTGTTTCTGGGC 57.728 50.000 0.00 0.00 0.00 5.36
3472 4215 4.062991 GTGTAGGTGTTAGTGTTTCTGGG 58.937 47.826 0.00 0.00 0.00 4.45
3473 4216 3.739300 CGTGTAGGTGTTAGTGTTTCTGG 59.261 47.826 0.00 0.00 0.00 3.86
3487 4230 0.109723 AAATGCCCACACGTGTAGGT 59.890 50.000 29.69 12.18 0.00 3.08
3522 4265 0.323629 AAACGGACGTGGATCCACAT 59.676 50.000 37.42 28.32 46.47 3.21
3610 4354 1.324134 GAAAACGGACGTGTGAACGAA 59.676 47.619 5.12 0.00 36.85 3.85
3615 4360 3.455327 TGTAATGAAAACGGACGTGTGA 58.545 40.909 0.00 0.00 0.00 3.58
3632 4378 2.158827 CCACACCGATCCATCCATGTAA 60.159 50.000 0.00 0.00 0.00 2.41
3633 4379 1.416030 CCACACCGATCCATCCATGTA 59.584 52.381 0.00 0.00 0.00 2.29
3637 4383 1.601703 CACCACACCGATCCATCCA 59.398 57.895 0.00 0.00 0.00 3.41
3641 4387 4.028490 GCCCACCACACCGATCCA 62.028 66.667 0.00 0.00 0.00 3.41
3652 4400 0.236449 CGAACTGTTAAACGCCCACC 59.764 55.000 0.00 0.00 0.00 4.61
3664 4412 1.153329 TGACGTTTGGGCGAACTGT 60.153 52.632 0.00 1.78 35.59 3.55
3676 4424 2.353269 TGCGTGATTGAAAACTGACGTT 59.647 40.909 0.00 0.00 34.03 3.99
3690 4438 4.415150 CCAGCCCCTGTGCGTGAT 62.415 66.667 0.00 0.00 36.02 3.06
3719 4467 3.448686 GGATGTGTGGACGAACTGATAG 58.551 50.000 0.00 0.00 0.00 2.08
3730 4478 0.039764 AGAGGAGACGGATGTGTGGA 59.960 55.000 0.00 0.00 0.00 4.02
3737 4485 0.684805 GTGTGGGAGAGGAGACGGAT 60.685 60.000 0.00 0.00 0.00 4.18
3738 4486 1.304217 GTGTGGGAGAGGAGACGGA 60.304 63.158 0.00 0.00 0.00 4.69
3816 4564 5.690464 AGAGAGAGTTGCCATCTGTTTAT 57.310 39.130 0.00 0.00 0.00 1.40
3820 4568 4.363991 AAAAGAGAGAGTTGCCATCTGT 57.636 40.909 0.00 0.00 0.00 3.41
3903 4651 3.132646 AGAGAGAGTTGCCATCTGCTTAG 59.867 47.826 0.00 0.00 42.00 2.18
3979 4729 4.404715 GGATTGCCACCTACTAACACTAGA 59.595 45.833 0.00 0.00 0.00 2.43
4000 4750 7.013823 TGCCATCATTTGAAAATTTTAGGGA 57.986 32.000 2.75 0.00 0.00 4.20
4001 4751 7.391275 AGTTGCCATCATTTGAAAATTTTAGGG 59.609 33.333 2.75 0.00 0.00 3.53
4018 4768 7.217200 TGGTCTGATTTACTATAGTTGCCATC 58.783 38.462 11.40 8.20 0.00 3.51
4053 4803 1.410648 CCCCTACTAACACTAGGCGGA 60.411 57.143 0.00 0.00 30.78 5.54
4055 4805 1.038280 CCCCCTACTAACACTAGGCG 58.962 60.000 0.00 0.00 30.78 5.52
4072 4822 2.701423 TGAAAAACTTTAGGGGTTGCCC 59.299 45.455 0.00 0.00 44.51 5.36


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

AutoCloner maintained by Alex Coulton.