Multiple sequence alignment - TraesCS3D01G079300

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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 TraesCS3D01G079300 chr3D 100.000 6052 0 0 1 6052 39395065 39389014 0.000000e+00 11177.0
1 TraesCS3D01G079300 chr3D 93.182 44 3 0 2554 2597 39392476 39392433 1.410000e-06 65.8
2 TraesCS3D01G079300 chr3D 93.182 44 3 0 2590 2633 39392512 39392469 1.410000e-06 65.8
3 TraesCS3D01G079300 chr3B 92.575 3515 167 40 2587 6052 62951323 62947854 0.000000e+00 4959.0
4 TraesCS3D01G079300 chr3B 92.691 602 44 0 1996 2597 62951878 62951277 0.000000e+00 869.0
5 TraesCS3D01G079300 chr3B 84.734 845 45 31 482 1287 62953975 62953176 0.000000e+00 769.0
6 TraesCS3D01G079300 chr3B 89.931 437 21 4 1 426 62954406 62953982 5.340000e-150 542.0
7 TraesCS3D01G079300 chr3B 83.768 499 39 25 1317 1806 62952640 62952175 9.320000e-118 435.0
8 TraesCS3D01G079300 chr3B 90.106 283 14 6 1795 2076 62952141 62951872 7.460000e-94 355.0
9 TraesCS3D01G079300 chr3A 90.318 2675 128 46 2593 5192 50894700 50892082 0.000000e+00 3384.0
10 TraesCS3D01G079300 chr3A 93.455 932 49 6 5123 6052 50891945 50891024 0.000000e+00 1373.0
11 TraesCS3D01G079300 chr3A 93.289 894 49 7 1709 2597 50895547 50894660 0.000000e+00 1308.0
12 TraesCS3D01G079300 chr3A 86.997 1069 65 29 651 1676 50896585 50895548 0.000000e+00 1136.0
13 TraesCS3D01G079300 chr3A 92.637 584 30 4 1 581 50897264 50896691 0.000000e+00 828.0


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 TraesCS3D01G079300 chr3D 39389014 39395065 6051 True 3769.533333 11177 95.454667 1 6052 3 chr3D.!!$R1 6051
1 TraesCS3D01G079300 chr3B 62947854 62954406 6552 True 1321.500000 4959 88.967500 1 6052 6 chr3B.!!$R1 6051
2 TraesCS3D01G079300 chr3A 50891024 50897264 6240 True 1605.800000 3384 91.339200 1 6052 5 chr3A.!!$R1 6051

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
335 339 0.114364 TCCAGTAGCCCTGACTGACA 59.886 55.0 4.38 0.0 46.01 3.58 F
1709 2340 0.041839 GCGCTGAATCATGTTAGCCG 60.042 55.0 0.00 0.0 32.70 5.52 F
3236 3990 0.107017 GTATGCAGGTGCCATGGTCT 60.107 55.0 14.67 6.1 41.18 3.85 F
4140 4895 0.322098 CCATTGGACCGCAACAGGTA 60.322 55.0 0.00 0.0 46.09 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2347 0.039437 AGCGGTGTAACAGTCGACAG 60.039 55.0 19.50 12.96 39.98 3.51 R
3414 4168 0.025898 CAGTGCGCTCAATCACATCG 59.974 55.0 9.73 0.00 35.76 3.84 R
4144 4899 0.032403 CAACCACACCATGCAACCAG 59.968 55.0 0.00 0.00 0.00 4.00 R
5198 6245 0.521735 GTTCGTGGCACATCCTTTCC 59.478 55.0 19.09 0.00 44.52 3.13 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
57 58 1.686110 ACCACCTCCGAGATGGTCC 60.686 63.158 8.87 0.00 37.70 4.46
122 126 1.366319 AGACCAGCCACAAGGAGAAT 58.634 50.000 0.00 0.00 36.89 2.40
236 240 2.353607 CGCGGCGAGTACCAGATC 60.354 66.667 19.16 0.00 0.00 2.75
267 271 2.355837 GCTGCGTGGACGAGAACA 60.356 61.111 2.73 0.00 43.02 3.18
335 339 0.114364 TCCAGTAGCCCTGACTGACA 59.886 55.000 4.38 0.00 46.01 3.58
375 379 2.292267 AGCTCAAGAGTGTTGGTTGTG 58.708 47.619 0.00 0.00 0.00 3.33
436 448 0.324275 TTGCTGGGTAATCCTTGGCC 60.324 55.000 0.00 0.00 36.20 5.36
459 471 3.778954 ATATGCTTTACAGAGGCTCCC 57.221 47.619 11.71 0.00 0.00 4.30
470 482 1.840635 AGAGGCTCCCAACTGTTATCC 59.159 52.381 11.71 0.00 0.00 2.59
476 488 2.305927 CTCCCAACTGTTATCCTGTGGT 59.694 50.000 0.00 0.00 0.00 4.16
477 489 2.714250 TCCCAACTGTTATCCTGTGGTT 59.286 45.455 0.00 0.00 0.00 3.67
478 490 3.911260 TCCCAACTGTTATCCTGTGGTTA 59.089 43.478 0.00 0.00 0.00 2.85
479 491 4.007659 CCCAACTGTTATCCTGTGGTTAC 58.992 47.826 0.00 0.00 0.00 2.50
480 492 4.263331 CCCAACTGTTATCCTGTGGTTACT 60.263 45.833 0.00 0.00 0.00 2.24
533 545 3.245371 TGGATGTGAGGAATTCAGGCTTT 60.245 43.478 7.93 0.00 36.21 3.51
538 550 4.761739 TGTGAGGAATTCAGGCTTTTAGTG 59.238 41.667 7.93 0.00 36.21 2.74
547 559 5.298989 TCAGGCTTTTAGTGTAGTTTGGA 57.701 39.130 0.00 0.00 0.00 3.53
550 562 3.190744 GGCTTTTAGTGTAGTTTGGAGCC 59.809 47.826 0.00 0.00 40.15 4.70
610 671 5.604758 TGATGCTAACTGCTCTAACTGAT 57.395 39.130 0.00 0.00 43.37 2.90
611 672 5.354767 TGATGCTAACTGCTCTAACTGATG 58.645 41.667 0.00 0.00 43.37 3.07
612 673 5.127682 TGATGCTAACTGCTCTAACTGATGA 59.872 40.000 0.00 0.00 43.37 2.92
620 681 3.567585 TGCTCTAACTGATGAGATCTCCG 59.432 47.826 20.03 8.32 32.44 4.63
629 690 4.464947 TGATGAGATCTCCGTATGTGACT 58.535 43.478 20.03 0.00 0.00 3.41
631 692 4.639135 TGAGATCTCCGTATGTGACTTG 57.361 45.455 20.03 0.00 0.00 3.16
634 695 0.535335 TCTCCGTATGTGACTTGGGC 59.465 55.000 0.00 0.00 0.00 5.36
689 756 4.520111 TGGATATGATGAATTCCGGCTTTG 59.480 41.667 2.27 0.00 0.00 2.77
691 758 2.505650 TGATGAATTCCGGCTTTGGA 57.494 45.000 2.27 0.00 35.83 3.53
693 760 3.364549 TGATGAATTCCGGCTTTGGATT 58.635 40.909 2.27 0.00 38.00 3.01
724 791 3.999001 TGATCTGATGTGTCTGTCTTTGC 59.001 43.478 0.00 0.00 0.00 3.68
729 796 2.017138 TGTGTCTGTCTTTGCGTTCA 57.983 45.000 0.00 0.00 0.00 3.18
735 802 2.100749 TCTGTCTTTGCGTTCACTCAGA 59.899 45.455 0.00 0.00 0.00 3.27
749 816 7.300320 CGTTCACTCAGATGAATTCAAATCAA 58.700 34.615 13.09 0.00 40.60 2.57
755 822 8.733458 ACTCAGATGAATTCAAATCAAATCGAA 58.267 29.630 13.09 0.00 0.00 3.71
757 824 8.513774 TCAGATGAATTCAAATCAAATCGAACA 58.486 29.630 13.09 0.00 0.00 3.18
763 830 4.393834 TCAAATCAAATCGAACACTCCCA 58.606 39.130 0.00 0.00 0.00 4.37
790 858 2.354188 GAAACCGGGCACGCAAAC 60.354 61.111 0.58 0.00 39.22 2.93
824 892 7.770366 AGCAATGCTGGATATATGAATTCAA 57.230 32.000 13.09 2.57 37.57 2.69
836 904 0.598065 GAATTCAAGCTTGCCGTGGT 59.402 50.000 21.99 3.26 0.00 4.16
847 915 4.767255 CCGTGGTGCTCCTCTGCC 62.767 72.222 6.34 0.00 34.23 4.85
895 977 2.176273 CAGATTTGCCGCTCGGGAG 61.176 63.158 10.57 0.00 36.83 4.30
945 1035 4.012895 CACGCACACGCCAGGTTC 62.013 66.667 0.00 0.00 45.53 3.62
967 1057 4.605967 CTCGCTCGCTCGCTCCTC 62.606 72.222 0.00 0.00 0.00 3.71
1326 1948 2.180204 CCCTACCCGCTGCATTTCG 61.180 63.158 0.00 0.00 0.00 3.46
1367 1989 0.793861 GTTATTTCGGTGCTGCGTGA 59.206 50.000 0.00 0.00 0.00 4.35
1393 2015 2.268298 TGCTTAGCTTCGAATCGAACC 58.732 47.619 14.59 8.32 41.05 3.62
1398 2020 2.096248 AGCTTCGAATCGAACCTCTCT 58.904 47.619 14.59 4.15 41.05 3.10
1399 2021 2.159310 AGCTTCGAATCGAACCTCTCTG 60.159 50.000 14.59 4.18 41.05 3.35
1402 2024 1.544246 TCGAATCGAACCTCTCTGCAA 59.456 47.619 1.57 0.00 31.06 4.08
1403 2025 1.656095 CGAATCGAACCTCTCTGCAAC 59.344 52.381 0.00 0.00 0.00 4.17
1404 2026 2.672478 CGAATCGAACCTCTCTGCAACT 60.672 50.000 0.00 0.00 0.00 3.16
1406 2028 4.495422 GAATCGAACCTCTCTGCAACTAA 58.505 43.478 0.00 0.00 0.00 2.24
1408 2030 4.537135 TCGAACCTCTCTGCAACTAATT 57.463 40.909 0.00 0.00 0.00 1.40
1409 2031 4.495422 TCGAACCTCTCTGCAACTAATTC 58.505 43.478 0.00 0.00 0.00 2.17
1410 2032 4.021456 TCGAACCTCTCTGCAACTAATTCA 60.021 41.667 0.00 0.00 0.00 2.57
1411 2033 4.872691 CGAACCTCTCTGCAACTAATTCAT 59.127 41.667 0.00 0.00 0.00 2.57
1413 2035 4.775236 ACCTCTCTGCAACTAATTCATCC 58.225 43.478 0.00 0.00 0.00 3.51
1414 2036 4.225942 ACCTCTCTGCAACTAATTCATCCA 59.774 41.667 0.00 0.00 0.00 3.41
1415 2037 5.188434 CCTCTCTGCAACTAATTCATCCAA 58.812 41.667 0.00 0.00 0.00 3.53
1416 2038 5.826737 CCTCTCTGCAACTAATTCATCCAAT 59.173 40.000 0.00 0.00 0.00 3.16
1417 2039 6.320672 CCTCTCTGCAACTAATTCATCCAATT 59.679 38.462 0.00 0.00 38.35 2.32
1418 2040 7.092137 TCTCTGCAACTAATTCATCCAATTG 57.908 36.000 0.00 0.00 35.34 2.32
1419 2041 5.653507 TCTGCAACTAATTCATCCAATTGC 58.346 37.500 0.00 0.00 40.99 3.56
1420 2042 5.185442 TCTGCAACTAATTCATCCAATTGCA 59.815 36.000 8.31 8.31 46.23 4.08
1421 2043 5.791666 TGCAACTAATTCATCCAATTGCAA 58.208 33.333 0.00 0.00 45.64 4.08
1422 2044 6.408035 TGCAACTAATTCATCCAATTGCAAT 58.592 32.000 5.99 5.99 45.64 3.56
1423 2045 6.879993 TGCAACTAATTCATCCAATTGCAATT 59.120 30.769 18.99 18.99 45.64 2.32
1444 2066 7.591165 CAATTATCGCATCCTGAATTTCTGAT 58.409 34.615 4.98 1.44 0.00 2.90
1458 2080 1.659954 CTGATACGCGAGCTCTGCC 60.660 63.158 15.93 9.93 0.00 4.85
1525 2156 2.504032 CCGGTGTGTGGTGTCTGT 59.496 61.111 0.00 0.00 0.00 3.41
1611 2242 2.037620 GCCATGATCCTCTGACGCCT 62.038 60.000 0.00 0.00 0.00 5.52
1647 2278 2.012673 CCTAACAGCCTGCACTGAATC 58.987 52.381 11.03 0.00 40.25 2.52
1648 2279 2.616256 CCTAACAGCCTGCACTGAATCA 60.616 50.000 11.03 0.00 40.25 2.57
1651 2282 1.003928 ACAGCCTGCACTGAATCATGA 59.996 47.619 11.03 0.00 40.25 3.07
1657 2288 4.700700 CCTGCACTGAATCATGATCACTA 58.299 43.478 9.06 0.00 0.00 2.74
1660 2291 4.877823 TGCACTGAATCATGATCACTAACC 59.122 41.667 9.06 0.00 0.00 2.85
1688 2319 2.407616 GCGAATTGCGTTAGGCCC 59.592 61.111 0.00 0.00 43.41 5.80
1689 2320 2.112815 GCGAATTGCGTTAGGCCCT 61.113 57.895 0.00 0.00 43.41 5.19
1690 2321 1.721487 CGAATTGCGTTAGGCCCTG 59.279 57.895 0.00 0.00 42.61 4.45
1691 2322 1.433471 GAATTGCGTTAGGCCCTGC 59.567 57.895 0.00 0.00 42.61 4.85
1692 2323 2.322999 GAATTGCGTTAGGCCCTGCG 62.323 60.000 0.00 1.98 42.61 5.18
1696 2327 4.451150 CGTTAGGCCCTGCGCTGA 62.451 66.667 16.65 0.00 37.74 4.26
1697 2328 2.046314 GTTAGGCCCTGCGCTGAA 60.046 61.111 16.65 0.00 37.74 3.02
1701 2332 1.699054 TAGGCCCTGCGCTGAATCAT 61.699 55.000 16.65 4.54 37.74 2.45
1702 2333 2.719979 GCCCTGCGCTGAATCATG 59.280 61.111 16.65 0.00 0.00 3.07
1703 2334 2.117156 GCCCTGCGCTGAATCATGT 61.117 57.895 16.65 0.00 0.00 3.21
1704 2335 1.660560 GCCCTGCGCTGAATCATGTT 61.661 55.000 16.65 0.00 0.00 2.71
1705 2336 1.667236 CCCTGCGCTGAATCATGTTA 58.333 50.000 16.65 0.00 0.00 2.41
1706 2337 1.600957 CCCTGCGCTGAATCATGTTAG 59.399 52.381 16.65 0.00 0.00 2.34
1707 2338 1.003116 CCTGCGCTGAATCATGTTAGC 60.003 52.381 16.65 0.00 0.00 3.09
1708 2339 1.003116 CTGCGCTGAATCATGTTAGCC 60.003 52.381 9.73 0.00 32.70 3.93
1709 2340 0.041839 GCGCTGAATCATGTTAGCCG 60.042 55.000 0.00 0.00 32.70 5.52
1710 2341 0.041839 CGCTGAATCATGTTAGCCGC 60.042 55.000 0.00 0.00 32.70 6.53
1711 2342 1.303309 GCTGAATCATGTTAGCCGCT 58.697 50.000 0.00 0.00 0.00 5.52
1712 2343 1.003116 GCTGAATCATGTTAGCCGCTG 60.003 52.381 2.16 0.00 0.00 5.18
1713 2344 2.554142 CTGAATCATGTTAGCCGCTGA 58.446 47.619 2.16 0.00 0.00 4.26
1714 2345 2.279741 TGAATCATGTTAGCCGCTGAC 58.720 47.619 8.32 8.32 0.00 3.51
1715 2346 1.258982 GAATCATGTTAGCCGCTGACG 59.741 52.381 10.42 0.00 39.67 4.35
1716 2347 1.154205 ATCATGTTAGCCGCTGACGC 61.154 55.000 10.42 0.00 38.22 5.19
1717 2348 1.811266 CATGTTAGCCGCTGACGCT 60.811 57.895 10.42 0.00 38.22 5.07
1718 2349 1.811266 ATGTTAGCCGCTGACGCTG 60.811 57.895 10.42 0.00 38.22 5.18
1719 2350 2.432628 GTTAGCCGCTGACGCTGT 60.433 61.111 2.16 0.00 38.22 4.40
1720 2351 2.126071 TTAGCCGCTGACGCTGTC 60.126 61.111 2.16 2.32 38.22 3.51
1721 2352 3.964221 TTAGCCGCTGACGCTGTCG 62.964 63.158 2.16 0.00 42.43 4.35
1733 2369 1.334992 CGCTGTCGACTGTTACACCG 61.335 60.000 21.51 12.48 38.10 4.94
1740 2376 2.488937 TCGACTGTTACACCGCTGATTA 59.511 45.455 0.00 0.00 0.00 1.75
1746 2382 3.106672 GTTACACCGCTGATTAGTCTCG 58.893 50.000 0.00 0.00 0.00 4.04
1765 2404 2.149578 CGATCCCAGATGCATTCCTTC 58.850 52.381 0.00 0.00 0.00 3.46
1768 2407 1.030457 CCCAGATGCATTCCTTCTGC 58.970 55.000 0.00 0.00 41.80 4.26
1781 2420 0.940126 CTTCTGCACGCTTGTTCTGT 59.060 50.000 0.00 0.00 0.00 3.41
1790 2429 3.003689 CACGCTTGTTCTGTTCCTTTCAT 59.996 43.478 0.00 0.00 0.00 2.57
1913 2594 0.620556 TGGATGGCTTCCTTCCTGAC 59.379 55.000 19.03 0.00 44.99 3.51
1967 2648 4.555511 GCTTGGATGATCTTTATGTTCGGC 60.556 45.833 0.00 0.00 0.00 5.54
1985 2667 1.479205 GGCATATGATGGTTCTGCCCA 60.479 52.381 6.97 0.00 45.26 5.36
2029 2773 4.622740 GCATAAACACAGTCAATTTGCCTC 59.377 41.667 0.00 0.00 0.00 4.70
2036 2780 5.471456 ACACAGTCAATTTGCCTCTTCTTAG 59.529 40.000 0.00 0.00 0.00 2.18
2044 2788 2.467880 TGCCTCTTCTTAGTACAGGGG 58.532 52.381 0.00 0.00 0.00 4.79
2264 3008 6.796705 TTTCTTTCGAAAGGGATTGAGTAC 57.203 37.500 31.82 0.00 34.35 2.73
2464 3208 1.940613 AGTGACCTTGAAAACTGCGTC 59.059 47.619 0.00 0.00 0.00 5.19
2557 3301 9.661563 TTCATGTTTATCTTTAGACAATACGGT 57.338 29.630 0.00 0.00 0.00 4.83
2558 3302 9.309516 TCATGTTTATCTTTAGACAATACGGTC 57.690 33.333 0.00 0.00 38.08 4.79
2559 3303 9.093970 CATGTTTATCTTTAGACAATACGGTCA 57.906 33.333 0.00 0.00 40.29 4.02
2560 3304 9.832445 ATGTTTATCTTTAGACAATACGGTCAT 57.168 29.630 0.00 0.00 40.29 3.06
2561 3305 9.309516 TGTTTATCTTTAGACAATACGGTCATC 57.690 33.333 0.00 0.00 40.29 2.92
2562 3306 9.530633 GTTTATCTTTAGACAATACGGTCATCT 57.469 33.333 0.00 0.00 40.29 2.90
2565 3309 8.649973 ATCTTTAGACAATACGGTCATCTTTC 57.350 34.615 0.00 0.00 40.29 2.62
2566 3310 7.837863 TCTTTAGACAATACGGTCATCTTTCT 58.162 34.615 0.00 0.00 40.29 2.52
2567 3311 8.311836 TCTTTAGACAATACGGTCATCTTTCTT 58.688 33.333 0.00 0.00 40.29 2.52
2568 3312 7.827819 TTAGACAATACGGTCATCTTTCTTG 57.172 36.000 0.00 0.00 40.29 3.02
2569 3313 5.178797 AGACAATACGGTCATCTTTCTTGG 58.821 41.667 0.00 0.00 40.29 3.61
2570 3314 3.689649 ACAATACGGTCATCTTTCTTGGC 59.310 43.478 0.00 0.00 0.00 4.52
2571 3315 2.396590 TACGGTCATCTTTCTTGGCC 57.603 50.000 0.00 0.00 35.45 5.36
2572 3316 0.400213 ACGGTCATCTTTCTTGGCCA 59.600 50.000 0.00 0.00 38.85 5.36
2573 3317 1.004745 ACGGTCATCTTTCTTGGCCAT 59.995 47.619 6.09 0.00 38.85 4.40
2574 3318 1.402968 CGGTCATCTTTCTTGGCCATG 59.597 52.381 6.09 9.88 38.85 3.66
2575 3319 2.450476 GGTCATCTTTCTTGGCCATGT 58.550 47.619 17.54 0.00 38.76 3.21
2576 3320 2.827921 GGTCATCTTTCTTGGCCATGTT 59.172 45.455 17.54 0.00 38.76 2.71
2577 3321 3.367703 GGTCATCTTTCTTGGCCATGTTG 60.368 47.826 17.54 9.49 38.76 3.33
2578 3322 3.507233 GTCATCTTTCTTGGCCATGTTGA 59.493 43.478 17.54 13.75 0.00 3.18
2579 3323 4.159135 GTCATCTTTCTTGGCCATGTTGAT 59.841 41.667 17.54 15.11 0.00 2.57
2580 3324 5.357878 GTCATCTTTCTTGGCCATGTTGATA 59.642 40.000 17.54 4.08 0.00 2.15
2581 3325 5.357878 TCATCTTTCTTGGCCATGTTGATAC 59.642 40.000 17.54 0.00 0.00 2.24
2582 3326 4.661222 TCTTTCTTGGCCATGTTGATACA 58.339 39.130 17.54 0.00 38.95 2.29
2583 3327 4.458989 TCTTTCTTGGCCATGTTGATACAC 59.541 41.667 17.54 0.00 37.03 2.90
2584 3328 3.431673 TCTTGGCCATGTTGATACACA 57.568 42.857 17.54 0.00 37.03 3.72
2585 3329 3.966979 TCTTGGCCATGTTGATACACAT 58.033 40.909 17.54 0.00 37.93 3.21
2758 3502 6.625873 AACTTTTCACACTTCTTCCATCTC 57.374 37.500 0.00 0.00 0.00 2.75
2788 3532 7.553504 AAGACCCCTAAAAGCATAAATGTTT 57.446 32.000 0.00 0.00 32.40 2.83
2891 3635 2.704572 AGCTGTATTGGTGTTCAGAGC 58.295 47.619 0.00 0.00 0.00 4.09
3001 3745 8.662141 AGGTAATATAATTATTTAAGCACGCCG 58.338 33.333 2.68 0.00 30.64 6.46
3051 3805 4.107622 GCATACAACAGAATGAATGTGGC 58.892 43.478 0.00 0.00 39.69 5.01
3236 3990 0.107017 GTATGCAGGTGCCATGGTCT 60.107 55.000 14.67 6.10 41.18 3.85
3414 4168 4.509600 CGAGCCTCTACATCCATTTCTTTC 59.490 45.833 0.00 0.00 0.00 2.62
3776 4531 2.805671 TGTCGTGCAGTTTTCTATGGTG 59.194 45.455 0.00 0.00 0.00 4.17
3823 4578 0.472734 AGGGACTTGTGTGCTCCTCT 60.473 55.000 0.00 0.00 27.25 3.69
3895 4650 3.985410 TCAGCCATCTGAAAAGGGG 57.015 52.632 0.00 0.00 45.69 4.79
3907 4662 1.625315 GAAAAGGGGCCAATGCTTCTT 59.375 47.619 4.39 0.00 37.74 2.52
3947 4702 4.439563 CCCCTGTTTTATCGCAATGTAACC 60.440 45.833 0.00 0.00 0.00 2.85
4077 4832 4.099573 ACCTCGCAACTATACTGTTAGCAT 59.900 41.667 0.00 0.00 0.00 3.79
4082 4837 4.209288 GCAACTATACTGTTAGCATGGACG 59.791 45.833 0.00 0.00 0.00 4.79
4121 4876 4.338379 ACCTCTTTATCGAAGGTATGGC 57.662 45.455 3.87 0.00 35.98 4.40
4124 4879 4.263068 CCTCTTTATCGAAGGTATGGCCAT 60.263 45.833 24.45 24.45 40.61 4.40
4125 4880 5.304686 TCTTTATCGAAGGTATGGCCATT 57.695 39.130 26.37 6.21 40.61 3.16
4133 4888 1.453015 GTATGGCCATTGGACCGCA 60.453 57.895 26.37 0.00 0.00 5.69
4134 4889 1.034838 GTATGGCCATTGGACCGCAA 61.035 55.000 26.37 0.00 0.00 4.85
4137 4892 2.568090 GCCATTGGACCGCAACAG 59.432 61.111 6.95 0.00 0.00 3.16
4140 4895 0.322098 CCATTGGACCGCAACAGGTA 60.322 55.000 0.00 0.00 46.09 3.08
4144 4899 0.535335 TGGACCGCAACAGGTATCTC 59.465 55.000 0.00 0.00 46.09 2.75
4146 4901 1.471676 GGACCGCAACAGGTATCTCTG 60.472 57.143 0.00 0.00 46.09 3.35
4171 4926 0.471591 ATGGTGTGGTTGCCATTGGT 60.472 50.000 4.26 0.00 42.34 3.67
4180 4935 2.365293 GGTTGCCATTGGTTTCTCAAGT 59.635 45.455 4.26 0.00 0.00 3.16
4181 4936 3.572255 GGTTGCCATTGGTTTCTCAAGTA 59.428 43.478 4.26 0.00 0.00 2.24
4182 4937 4.546570 GTTGCCATTGGTTTCTCAAGTAC 58.453 43.478 4.26 0.00 0.00 2.73
4183 4938 4.098914 TGCCATTGGTTTCTCAAGTACT 57.901 40.909 4.26 0.00 0.00 2.73
4214 4969 1.896220 TGCCTGCTAACAACTTGGAG 58.104 50.000 0.00 0.00 0.00 3.86
4292 5047 3.186119 CTCGAAGCTGAATTCTCTGGTC 58.814 50.000 7.05 0.00 31.59 4.02
4345 5108 9.565213 CATTCTCAGTCATTACTTCAAATTTCC 57.435 33.333 0.00 0.00 31.97 3.13
4364 5127 4.502105 TCCTAATGCTTCACTTGGCATA 57.498 40.909 0.00 0.00 46.70 3.14
4386 5178 7.542130 GCATACCATTTTTGAGTTCTTACTTGG 59.458 37.037 0.00 0.00 33.84 3.61
4387 5179 8.576442 CATACCATTTTTGAGTTCTTACTTGGT 58.424 33.333 0.00 0.00 39.86 3.67
4388 5180 7.418337 ACCATTTTTGAGTTCTTACTTGGTT 57.582 32.000 0.00 0.00 35.49 3.67
4389 5181 7.847096 ACCATTTTTGAGTTCTTACTTGGTTT 58.153 30.769 0.00 0.00 35.49 3.27
4390 5182 8.318412 ACCATTTTTGAGTTCTTACTTGGTTTT 58.682 29.630 0.00 0.00 35.49 2.43
4391 5183 8.603181 CCATTTTTGAGTTCTTACTTGGTTTTG 58.397 33.333 0.00 0.00 33.84 2.44
4406 5198 0.895100 TTTTGCTACCTGGCTGGCTG 60.895 55.000 10.71 1.43 40.22 4.85
4418 5210 1.202475 GGCTGGCTGCTAAGAGACTAC 60.202 57.143 16.14 0.00 42.39 2.73
4466 5259 6.124088 GTTGTGATTGACTCAACTTCAACT 57.876 37.500 17.89 0.00 44.48 3.16
4473 5266 6.422776 TTGACTCAACTTCAACTTCACTTC 57.577 37.500 0.00 0.00 0.00 3.01
4523 5319 2.034221 GCCACCCACCTTGACTCC 59.966 66.667 0.00 0.00 0.00 3.85
4589 5385 1.909700 TGTTCATGAGCCAAAGGGAC 58.090 50.000 7.13 0.00 35.59 4.46
4657 5453 3.774702 GACGCCGTTGTTCCGAGC 61.775 66.667 0.00 0.00 0.00 5.03
4748 5601 3.055591 GCTCATCATCATCGACGACAAT 58.944 45.455 0.00 0.00 0.00 2.71
4754 5607 2.844122 TCATCGACGACAATGACGAT 57.156 45.000 12.41 7.64 45.03 3.73
4763 5616 2.413112 CGACAATGACGATTTCTGCACT 59.587 45.455 0.00 0.00 0.00 4.40
4905 5758 4.737177 AGCAGAGGGCCAGCAAGC 62.737 66.667 6.18 6.05 46.50 4.01
5012 5865 1.812922 CGCTAGCCAGCCACTGAAG 60.813 63.158 9.66 0.00 45.64 3.02
5118 6165 7.085116 ACTTCACTAGTTACTTCATGAGTTCG 58.915 38.462 0.00 0.00 39.86 3.95
5134 6181 1.755380 GTTCGTCCAGTGTAGCCCTAT 59.245 52.381 0.00 0.00 0.00 2.57
5163 6210 9.681692 TGATATTCTCAACATGTTTTTGTTCTG 57.318 29.630 8.77 0.00 37.73 3.02
5168 6215 8.410030 TCTCAACATGTTTTTGTTCTGAATTG 57.590 30.769 8.77 0.00 37.73 2.32
5169 6216 8.034215 TCTCAACATGTTTTTGTTCTGAATTGT 58.966 29.630 8.77 0.00 37.73 2.71
5170 6217 9.299963 CTCAACATGTTTTTGTTCTGAATTGTA 57.700 29.630 8.77 0.00 37.73 2.41
5189 6236 9.151471 GAATTGTAGTAACTATGAAGCTCAACA 57.849 33.333 0.00 0.00 0.00 3.33
5209 6256 5.982890 ACAATAAGTTGGGAAAGGATGTG 57.017 39.130 0.00 0.00 39.70 3.21
5238 6285 4.321718 ACCACTGACATCAACATTCAGAG 58.678 43.478 4.88 0.00 39.36 3.35
5274 6323 5.766150 ACAGCATCTACTGAGTAGACATC 57.234 43.478 23.37 14.87 46.06 3.06
5367 6416 2.506217 TCGACGACGATGGCAAGC 60.506 61.111 5.75 0.00 43.81 4.01
5437 6487 2.806244 ACAAGAAAGTCGTTGCGCTTAT 59.194 40.909 9.73 0.00 0.00 1.73
5497 6547 0.179084 TGCGCTACCTAATGGCTGAC 60.179 55.000 9.73 0.00 36.63 3.51
5511 6561 2.266554 GGCTGACGATGAGAAGAACAG 58.733 52.381 0.00 0.00 0.00 3.16
5512 6562 1.658095 GCTGACGATGAGAAGAACAGC 59.342 52.381 0.00 0.00 41.33 4.40
5513 6563 2.928301 GCTGACGATGAGAAGAACAGCA 60.928 50.000 0.00 0.00 45.33 4.41
5514 6564 2.665537 CTGACGATGAGAAGAACAGCAC 59.334 50.000 0.00 0.00 0.00 4.40
5515 6565 2.035832 TGACGATGAGAAGAACAGCACA 59.964 45.455 0.00 0.00 0.00 4.57
5575 6625 1.153107 CTCCAATGGCAGCATCGGA 60.153 57.895 0.00 0.00 0.00 4.55
5578 6628 1.164662 CCAATGGCAGCATCGGAGAG 61.165 60.000 0.00 0.00 43.63 3.20
5629 6679 1.373497 CTCAGACGCCGCTGACTTT 60.373 57.895 7.06 0.00 39.84 2.66
5659 6709 1.079612 CTGCAGCTGATGGACGACA 60.080 57.895 20.43 1.68 0.00 4.35
5748 6798 2.175202 GATCACTCCTATCTCCGGCAT 58.825 52.381 0.00 0.00 0.00 4.40
5800 6850 2.040544 CCGGTGTGATTGGACCAGC 61.041 63.158 0.00 0.00 31.97 4.85
5821 6871 0.865769 GCGTCGCCCATTCGAATATT 59.134 50.000 10.97 0.00 40.43 1.28
5845 6895 0.743097 GCCATCCAGCAGATTCAACC 59.257 55.000 0.00 0.00 30.59 3.77
5857 6907 4.680237 TCAACCGACTGCGCTGGG 62.680 66.667 18.98 12.98 35.83 4.45
5905 6955 1.080772 CACGCCGAAGCTGTAGACA 60.081 57.895 0.00 0.00 36.60 3.41
6022 7072 1.654220 CACAAACTTGGACAGCCCG 59.346 57.895 0.00 0.00 37.93 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.979197 GCAGCTTGGAGTGCAGCAG 61.979 63.158 0.00 2.61 41.54 4.24
84 85 0.320771 TTCCTCAGGTCGCTCTTTGC 60.321 55.000 0.00 0.00 38.57 3.68
85 86 1.273606 TCTTCCTCAGGTCGCTCTTTG 59.726 52.381 0.00 0.00 0.00 2.77
94 98 1.152030 TGGCTGGTCTTCCTCAGGT 60.152 57.895 0.00 0.00 34.23 4.00
141 145 2.791331 GAAACACGCGAACGCTGC 60.791 61.111 15.93 0.00 45.53 5.25
375 379 2.289694 ACAGACCACACACATAGCTTCC 60.290 50.000 0.00 0.00 0.00 3.46
436 448 5.181748 GGGAGCCTCTGTAAAGCATATATG 58.818 45.833 8.45 8.45 0.00 1.78
459 471 5.995282 TGAAGTAACCACAGGATAACAGTTG 59.005 40.000 0.00 0.00 0.00 3.16
470 482 7.387673 TGATGATGTTAAGTGAAGTAACCACAG 59.612 37.037 0.00 0.00 37.01 3.66
476 488 5.880332 GGCCTGATGATGTTAAGTGAAGTAA 59.120 40.000 0.00 0.00 0.00 2.24
477 489 5.045942 TGGCCTGATGATGTTAAGTGAAGTA 60.046 40.000 3.32 0.00 0.00 2.24
478 490 4.263462 TGGCCTGATGATGTTAAGTGAAGT 60.263 41.667 3.32 0.00 0.00 3.01
479 491 4.264253 TGGCCTGATGATGTTAAGTGAAG 58.736 43.478 3.32 0.00 0.00 3.02
480 492 4.299586 TGGCCTGATGATGTTAAGTGAA 57.700 40.909 3.32 0.00 0.00 3.18
510 522 2.512896 AGCCTGAATTCCTCACATCCAT 59.487 45.455 2.27 0.00 0.00 3.41
520 532 6.819397 AACTACACTAAAAGCCTGAATTCC 57.181 37.500 2.27 0.00 0.00 3.01
533 545 2.290071 GGCTGGCTCCAAACTACACTAA 60.290 50.000 0.00 0.00 0.00 2.24
538 550 1.098050 CATGGCTGGCTCCAAACTAC 58.902 55.000 2.00 0.00 39.96 2.73
547 559 1.341679 ACATCAATCACATGGCTGGCT 60.342 47.619 2.00 0.00 0.00 4.75
550 562 4.193865 TCTGTACATCAATCACATGGCTG 58.806 43.478 0.00 0.00 0.00 4.85
602 663 6.205658 TCACATACGGAGATCTCATCAGTTAG 59.794 42.308 23.85 14.12 0.00 2.34
610 671 3.381590 CCAAGTCACATACGGAGATCTCA 59.618 47.826 23.85 4.32 0.00 3.27
611 672 3.243569 CCCAAGTCACATACGGAGATCTC 60.244 52.174 14.75 14.75 0.00 2.75
612 673 2.695666 CCCAAGTCACATACGGAGATCT 59.304 50.000 0.00 0.00 0.00 2.75
620 681 1.089920 CAGCAGCCCAAGTCACATAC 58.910 55.000 0.00 0.00 0.00 2.39
634 695 8.547965 TATGGATTCATATATGGCAAGCAGCAG 61.548 40.741 12.78 0.00 38.77 4.24
689 756 2.311463 TCAGATCAGAGGGACGAATCC 58.689 52.381 0.00 0.00 45.42 3.01
691 758 3.069300 CACATCAGATCAGAGGGACGAAT 59.931 47.826 4.75 0.00 0.00 3.34
693 760 2.027385 CACATCAGATCAGAGGGACGA 58.973 52.381 4.75 0.00 0.00 4.20
724 791 6.834876 TGATTTGAATTCATCTGAGTGAACG 58.165 36.000 9.40 0.00 40.60 3.95
729 796 8.272545 TCGATTTGATTTGAATTCATCTGAGT 57.727 30.769 9.40 0.00 0.00 3.41
735 802 7.756722 GGAGTGTTCGATTTGATTTGAATTCAT 59.243 33.333 9.40 0.00 0.00 2.57
755 822 1.191535 TCGGATTCGAATGGGAGTGT 58.808 50.000 16.96 0.00 43.03 3.55
813 881 3.067180 CCACGGCAAGCTTGAATTCATAT 59.933 43.478 30.39 2.83 0.00 1.78
836 904 3.695606 GGACACGGCAGAGGAGCA 61.696 66.667 0.00 0.00 35.83 4.26
847 915 4.916943 AGTACCTACTGAAACGGGACACG 61.917 52.174 0.00 0.00 41.22 4.49
895 977 4.489679 AATTTTGAACGAAGCAGAGACC 57.510 40.909 0.00 0.00 0.00 3.85
1307 1423 1.823899 GAAATGCAGCGGGTAGGGG 60.824 63.158 0.00 0.00 0.00 4.79
1315 1937 2.176546 CACCACCGAAATGCAGCG 59.823 61.111 0.00 0.00 0.00 5.18
1326 1948 2.100631 CAGGATCGAACGCACCACC 61.101 63.158 0.00 0.00 0.00 4.61
1330 1952 2.456119 CCAGCAGGATCGAACGCAC 61.456 63.158 0.00 0.00 36.89 5.34
1367 1989 4.811024 TCGATTCGAAGCTAAGCAATCATT 59.189 37.500 12.15 0.00 31.06 2.57
1393 2015 6.939132 ATTGGATGAATTAGTTGCAGAGAG 57.061 37.500 0.00 0.00 0.00 3.20
1398 2020 5.402997 TGCAATTGGATGAATTAGTTGCA 57.597 34.783 7.72 5.84 45.44 4.08
1399 2021 6.913873 ATTGCAATTGGATGAATTAGTTGC 57.086 33.333 5.99 0.00 40.45 4.17
1402 2024 7.596248 GCGATAATTGCAATTGGATGAATTAGT 59.404 33.333 30.43 5.85 32.65 2.24
1403 2025 7.595875 TGCGATAATTGCAATTGGATGAATTAG 59.404 33.333 30.43 15.12 39.87 1.73
1404 2026 7.432059 TGCGATAATTGCAATTGGATGAATTA 58.568 30.769 30.43 10.91 39.87 1.40
1406 2028 5.845103 TGCGATAATTGCAATTGGATGAAT 58.155 33.333 30.43 16.92 39.87 2.57
1408 2030 4.915158 TGCGATAATTGCAATTGGATGA 57.085 36.364 30.43 13.70 39.87 2.92
1409 2031 4.624024 GGATGCGATAATTGCAATTGGATG 59.376 41.667 30.43 18.97 46.87 3.51
1410 2032 4.525487 AGGATGCGATAATTGCAATTGGAT 59.475 37.500 30.43 21.11 46.87 3.41
1411 2033 3.890756 AGGATGCGATAATTGCAATTGGA 59.109 39.130 30.43 17.67 46.87 3.53
1413 2035 4.862350 TCAGGATGCGATAATTGCAATTG 58.138 39.130 30.43 17.22 46.87 2.32
1414 2036 5.518848 TTCAGGATGCGATAATTGCAATT 57.481 34.783 26.72 26.72 46.87 2.32
1415 2037 5.717078 ATTCAGGATGCGATAATTGCAAT 57.283 34.783 5.99 5.99 46.87 3.56
1416 2038 5.518848 AATTCAGGATGCGATAATTGCAA 57.481 34.783 0.00 0.00 46.87 4.08
1418 2040 5.628193 CAGAAATTCAGGATGCGATAATTGC 59.372 40.000 0.00 0.00 34.76 3.56
1419 2041 6.962686 TCAGAAATTCAGGATGCGATAATTG 58.037 36.000 0.00 0.00 34.76 2.32
1420 2042 7.756395 ATCAGAAATTCAGGATGCGATAATT 57.244 32.000 0.00 0.00 34.76 1.40
1421 2043 7.063898 CGTATCAGAAATTCAGGATGCGATAAT 59.936 37.037 22.75 0.00 44.81 1.28
1422 2044 6.366061 CGTATCAGAAATTCAGGATGCGATAA 59.634 38.462 22.75 0.00 44.81 1.75
1423 2045 5.863935 CGTATCAGAAATTCAGGATGCGATA 59.136 40.000 22.75 5.41 44.81 2.92
1426 2048 3.363378 GCGTATCAGAAATTCAGGATGCG 60.363 47.826 22.81 22.81 44.82 4.73
1525 2156 4.022155 GGGTGGTTAATTCGCCAGTTTTTA 60.022 41.667 11.69 0.00 36.56 1.52
1634 2265 2.033049 GTGATCATGATTCAGTGCAGGC 59.967 50.000 10.14 0.00 0.00 4.85
1647 2278 3.931907 TTCCAGGGGTTAGTGATCATG 57.068 47.619 0.00 0.00 0.00 3.07
1648 2279 4.325344 CCTTTTCCAGGGGTTAGTGATCAT 60.325 45.833 0.00 0.00 39.39 2.45
1651 2282 2.291605 GCCTTTTCCAGGGGTTAGTGAT 60.292 50.000 0.00 0.00 44.16 3.06
1660 2291 0.108662 GCAATTCGCCTTTTCCAGGG 60.109 55.000 0.00 0.00 44.16 4.45
1688 2319 1.003116 GGCTAACATGATTCAGCGCAG 60.003 52.381 11.47 0.00 34.80 5.18
1689 2320 1.016627 GGCTAACATGATTCAGCGCA 58.983 50.000 11.47 0.00 34.80 6.09
1690 2321 0.041839 CGGCTAACATGATTCAGCGC 60.042 55.000 0.00 0.00 34.80 5.92
1691 2322 0.041839 GCGGCTAACATGATTCAGCG 60.042 55.000 0.00 0.90 34.80 5.18
1692 2323 1.003116 CAGCGGCTAACATGATTCAGC 60.003 52.381 0.26 1.83 0.00 4.26
1693 2324 2.286294 GTCAGCGGCTAACATGATTCAG 59.714 50.000 0.26 0.00 0.00 3.02
1694 2325 2.279741 GTCAGCGGCTAACATGATTCA 58.720 47.619 0.26 0.00 0.00 2.57
1695 2326 1.258982 CGTCAGCGGCTAACATGATTC 59.741 52.381 0.26 0.00 0.00 2.52
1696 2327 1.290203 CGTCAGCGGCTAACATGATT 58.710 50.000 0.26 0.00 0.00 2.57
1697 2328 1.154205 GCGTCAGCGGCTAACATGAT 61.154 55.000 0.26 0.00 38.78 2.45
1709 2340 0.386858 TAACAGTCGACAGCGTCAGC 60.387 55.000 19.50 0.00 45.58 4.26
1710 2341 1.328439 GTAACAGTCGACAGCGTCAG 58.672 55.000 19.50 0.86 38.98 3.51
1711 2342 0.664224 TGTAACAGTCGACAGCGTCA 59.336 50.000 19.50 8.37 38.98 4.35
1712 2343 1.050767 GTGTAACAGTCGACAGCGTC 58.949 55.000 19.50 5.78 36.18 5.19
1713 2344 0.318445 GGTGTAACAGTCGACAGCGT 60.318 55.000 19.50 8.91 39.98 5.07
1714 2345 2.431539 GGTGTAACAGTCGACAGCG 58.568 57.895 19.50 8.22 39.98 5.18
1715 2346 1.615107 GCGGTGTAACAGTCGACAGC 61.615 60.000 19.50 5.03 39.98 4.40
1716 2347 0.039437 AGCGGTGTAACAGTCGACAG 60.039 55.000 19.50 12.96 39.98 3.51
1717 2348 0.318360 CAGCGGTGTAACAGTCGACA 60.318 55.000 19.50 0.00 39.98 4.35
1718 2349 0.039798 TCAGCGGTGTAACAGTCGAC 60.040 55.000 15.22 7.70 39.98 4.20
1719 2350 0.885879 ATCAGCGGTGTAACAGTCGA 59.114 50.000 15.22 0.00 39.98 4.20
1720 2351 1.710013 AATCAGCGGTGTAACAGTCG 58.290 50.000 15.22 0.00 39.98 4.18
1721 2352 3.846360 ACTAATCAGCGGTGTAACAGTC 58.154 45.455 15.22 0.00 39.98 3.51
1733 2369 2.887783 TCTGGGATCGAGACTAATCAGC 59.112 50.000 0.00 0.00 0.00 4.26
1740 2376 1.714541 ATGCATCTGGGATCGAGACT 58.285 50.000 0.00 0.00 0.00 3.24
1746 2382 3.147629 CAGAAGGAATGCATCTGGGATC 58.852 50.000 0.00 0.00 37.51 3.36
1765 2404 0.040958 GGAACAGAACAAGCGTGCAG 60.041 55.000 0.00 0.00 0.00 4.41
1768 2407 2.354510 TGAAAGGAACAGAACAAGCGTG 59.645 45.455 0.00 0.00 0.00 5.34
1807 2488 5.623824 GCAATCTTGAGCTGATGGAATTTGT 60.624 40.000 0.00 0.00 0.00 2.83
1811 2492 2.617308 CGCAATCTTGAGCTGATGGAAT 59.383 45.455 0.00 0.00 0.00 3.01
1913 2594 0.827089 TTGGCACAGACCCATGTTGG 60.827 55.000 0.00 0.00 42.39 3.77
2029 2773 8.251383 TCAAGATAATCCCCTGTACTAAGAAG 57.749 38.462 0.00 0.00 0.00 2.85
2036 2780 6.954684 TCCTATCTCAAGATAATCCCCTGTAC 59.045 42.308 1.64 0.00 36.66 2.90
2264 3008 6.619173 GAGAATCAATTTGTGCACGAAGCAG 61.619 44.000 23.36 15.38 45.91 4.24
2464 3208 2.163815 ACCAGGACTGTATCTTCGAACG 59.836 50.000 0.00 0.00 0.00 3.95
2494 3238 7.581076 GCAATAGATGATCCCTACACTCATGAT 60.581 40.741 0.00 0.00 30.00 2.45
2550 3294 3.279434 GGCCAAGAAAGATGACCGTATT 58.721 45.455 0.00 0.00 0.00 1.89
2551 3295 2.238646 TGGCCAAGAAAGATGACCGTAT 59.761 45.455 0.61 0.00 0.00 3.06
2552 3296 1.626321 TGGCCAAGAAAGATGACCGTA 59.374 47.619 0.61 0.00 0.00 4.02
2553 3297 0.400213 TGGCCAAGAAAGATGACCGT 59.600 50.000 0.61 0.00 0.00 4.83
2554 3298 1.402968 CATGGCCAAGAAAGATGACCG 59.597 52.381 10.96 0.00 0.00 4.79
2555 3299 2.450476 ACATGGCCAAGAAAGATGACC 58.550 47.619 16.33 0.00 0.00 4.02
2556 3300 3.507233 TCAACATGGCCAAGAAAGATGAC 59.493 43.478 16.33 0.00 0.00 3.06
2557 3301 3.765381 TCAACATGGCCAAGAAAGATGA 58.235 40.909 16.33 7.72 0.00 2.92
2558 3302 4.730949 ATCAACATGGCCAAGAAAGATG 57.269 40.909 16.33 6.86 0.00 2.90
2559 3303 5.126061 GTGTATCAACATGGCCAAGAAAGAT 59.874 40.000 16.33 15.48 38.08 2.40
2560 3304 4.458989 GTGTATCAACATGGCCAAGAAAGA 59.541 41.667 16.33 9.40 38.08 2.52
2561 3305 4.218200 TGTGTATCAACATGGCCAAGAAAG 59.782 41.667 16.33 3.91 38.08 2.62
2562 3306 4.148079 TGTGTATCAACATGGCCAAGAAA 58.852 39.130 16.33 0.00 38.08 2.52
2563 3307 3.760738 TGTGTATCAACATGGCCAAGAA 58.239 40.909 16.33 0.00 38.08 2.52
2564 3308 3.431673 TGTGTATCAACATGGCCAAGA 57.568 42.857 16.33 8.98 38.08 3.02
2565 3309 5.125257 TGTTATGTGTATCAACATGGCCAAG 59.875 40.000 10.96 8.43 40.93 3.61
2566 3310 5.012893 TGTTATGTGTATCAACATGGCCAA 58.987 37.500 10.96 0.00 40.93 4.52
2567 3311 4.397730 GTGTTATGTGTATCAACATGGCCA 59.602 41.667 8.56 8.56 40.93 5.36
2568 3312 4.495679 CGTGTTATGTGTATCAACATGGCC 60.496 45.833 0.00 0.00 40.93 5.36
2569 3313 4.495679 CCGTGTTATGTGTATCAACATGGC 60.496 45.833 10.93 0.00 46.63 4.40
2570 3314 5.155509 CCGTGTTATGTGTATCAACATGG 57.844 43.478 9.76 9.76 46.97 3.66
2571 3315 5.350091 TGACCGTGTTATGTGTATCAACATG 59.650 40.000 0.17 0.00 40.93 3.21
2572 3316 5.483811 TGACCGTGTTATGTGTATCAACAT 58.516 37.500 0.00 0.00 43.21 2.71
2573 3317 4.884247 TGACCGTGTTATGTGTATCAACA 58.116 39.130 0.00 0.00 0.00 3.33
2574 3318 5.810587 AGATGACCGTGTTATGTGTATCAAC 59.189 40.000 0.00 0.00 0.00 3.18
2575 3319 5.972935 AGATGACCGTGTTATGTGTATCAA 58.027 37.500 0.00 0.00 0.00 2.57
2576 3320 5.592104 AGATGACCGTGTTATGTGTATCA 57.408 39.130 0.00 0.00 0.00 2.15
2577 3321 6.757010 AGAAAGATGACCGTGTTATGTGTATC 59.243 38.462 0.00 0.00 0.00 2.24
2578 3322 6.640518 AGAAAGATGACCGTGTTATGTGTAT 58.359 36.000 0.00 0.00 0.00 2.29
2579 3323 6.032956 AGAAAGATGACCGTGTTATGTGTA 57.967 37.500 0.00 0.00 0.00 2.90
2580 3324 4.894784 AGAAAGATGACCGTGTTATGTGT 58.105 39.130 0.00 0.00 0.00 3.72
2581 3325 5.390885 CCAAGAAAGATGACCGTGTTATGTG 60.391 44.000 0.00 0.00 0.00 3.21
2582 3326 4.695455 CCAAGAAAGATGACCGTGTTATGT 59.305 41.667 0.00 0.00 0.00 2.29
2583 3327 4.437390 GCCAAGAAAGATGACCGTGTTATG 60.437 45.833 0.00 0.00 0.00 1.90
2584 3328 3.689649 GCCAAGAAAGATGACCGTGTTAT 59.310 43.478 0.00 0.00 0.00 1.89
2585 3329 3.071479 GCCAAGAAAGATGACCGTGTTA 58.929 45.455 0.00 0.00 0.00 2.41
2758 3502 4.015872 TGCTTTTAGGGGTCTTAGTGTG 57.984 45.455 0.00 0.00 0.00 3.82
2788 3532 1.067295 ACTTGGGTCTCTGCATTCCA 58.933 50.000 0.00 0.00 0.00 3.53
2993 3737 3.234630 TAGTCAAAGGCGGCGTGCT 62.235 57.895 9.37 9.95 45.43 4.40
3001 3745 6.535508 AGAACTGAATATTCGTAGTCAAAGGC 59.464 38.462 10.80 0.00 0.00 4.35
3051 3805 6.253298 TGAAATGAAACAGTCAAAAGAAAGCG 59.747 34.615 0.00 0.00 40.50 4.68
3217 3971 0.107017 AGACCATGGCACCTGCATAC 60.107 55.000 13.04 0.00 44.36 2.39
3236 3990 2.696707 GTGGTAACGTCATCTATGGGGA 59.303 50.000 0.00 0.00 42.51 4.81
3379 4133 1.970917 GAGGCTCGTCGCATGTTTGG 61.971 60.000 0.00 0.00 41.67 3.28
3414 4168 0.025898 CAGTGCGCTCAATCACATCG 59.974 55.000 9.73 0.00 35.76 3.84
3527 4282 3.084039 CCTGCCAACACACATTATCACT 58.916 45.455 0.00 0.00 0.00 3.41
3823 4578 0.523519 TTGTTTCAGTGTTGCACGCA 59.476 45.000 0.00 0.00 39.64 5.24
3895 4650 4.974399 ACTATACCCTAAGAAGCATTGGC 58.026 43.478 0.00 0.00 41.61 4.52
3907 4662 3.117246 CAGGGGACACTGACTATACCCTA 60.117 52.174 0.00 0.00 44.87 3.53
3947 4702 5.405269 GCAATAACAAAGCACAAACCCTTAG 59.595 40.000 0.00 0.00 0.00 2.18
4077 4832 3.153130 TCAATTGAATTCTTGGCGTCCA 58.847 40.909 5.45 0.00 0.00 4.02
4082 4837 5.787380 AGAGGTTTCAATTGAATTCTTGGC 58.213 37.500 21.10 9.91 33.54 4.52
4121 4876 0.322098 TACCTGTTGCGGTCCAATGG 60.322 55.000 0.00 0.00 38.49 3.16
4124 4879 0.981183 AGATACCTGTTGCGGTCCAA 59.019 50.000 0.00 0.00 38.49 3.53
4125 4880 0.535335 GAGATACCTGTTGCGGTCCA 59.465 55.000 0.00 0.00 38.49 4.02
4133 4888 3.614092 CATGCAACCAGAGATACCTGTT 58.386 45.455 0.00 0.00 32.43 3.16
4134 4889 2.092753 CCATGCAACCAGAGATACCTGT 60.093 50.000 0.00 0.00 32.43 4.00
4137 4892 2.292267 CACCATGCAACCAGAGATACC 58.708 52.381 0.00 0.00 0.00 2.73
4140 4895 1.615116 CCACACCATGCAACCAGAGAT 60.615 52.381 0.00 0.00 0.00 2.75
4144 4899 0.032403 CAACCACACCATGCAACCAG 59.968 55.000 0.00 0.00 0.00 4.00
4146 4901 1.300853 GCAACCACACCATGCAACC 60.301 57.895 0.00 0.00 39.81 3.77
4171 4926 9.582431 GCATGTAGTAACATAGTACTTGAGAAA 57.418 33.333 0.00 0.00 44.70 2.52
4180 4935 7.068962 TGTTAGCAGGCATGTAGTAACATAGTA 59.931 37.037 14.79 0.00 44.70 1.82
4181 4936 6.127168 TGTTAGCAGGCATGTAGTAACATAGT 60.127 38.462 14.79 0.00 44.70 2.12
4182 4937 6.280643 TGTTAGCAGGCATGTAGTAACATAG 58.719 40.000 14.79 0.00 44.70 2.23
4183 4938 6.228616 TGTTAGCAGGCATGTAGTAACATA 57.771 37.500 14.79 0.36 44.70 2.29
4214 4969 3.304928 CCTTCACAGCAATCTGAAACACC 60.305 47.826 0.00 0.00 42.95 4.16
4292 5047 1.605710 CCGAATTGCAGGCTATCCTTG 59.394 52.381 0.00 0.00 41.93 3.61
4364 5127 7.418337 AACCAAGTAAGAACTCAAAAATGGT 57.582 32.000 0.00 0.00 39.81 3.55
4386 5178 0.895559 AGCCAGCCAGGTAGCAAAAC 60.896 55.000 0.00 0.00 40.61 2.43
4387 5179 0.895100 CAGCCAGCCAGGTAGCAAAA 60.895 55.000 0.00 0.00 40.61 2.44
4388 5180 1.303561 CAGCCAGCCAGGTAGCAAA 60.304 57.895 0.00 0.00 40.61 3.68
4389 5181 2.352422 CAGCCAGCCAGGTAGCAA 59.648 61.111 0.00 0.00 40.61 3.91
4390 5182 4.415150 GCAGCCAGCCAGGTAGCA 62.415 66.667 0.00 0.00 40.61 3.49
4406 5198 6.415280 CGTGTCAACATATGTAGTCTCTTAGC 59.585 42.308 9.21 0.00 0.00 3.09
4466 5259 1.266718 GCAATTGACCTGCGAAGTGAA 59.733 47.619 10.34 0.00 0.00 3.18
4473 5266 2.676121 TGGGGCAATTGACCTGCG 60.676 61.111 29.39 0.00 44.77 5.18
4501 5294 0.251341 GTCAAGGTGGGTGGCATCTT 60.251 55.000 0.00 0.00 0.00 2.40
4502 5295 1.136329 AGTCAAGGTGGGTGGCATCT 61.136 55.000 0.00 0.00 0.00 2.90
4523 5319 3.411446 TGGTATTTGTGGCTCACTGAAG 58.589 45.455 6.83 0.00 35.11 3.02
4640 5436 3.774702 GCTCGGAACAACGGCGTC 61.775 66.667 15.17 0.00 0.00 5.19
4641 5437 4.295119 AGCTCGGAACAACGGCGT 62.295 61.111 6.77 6.77 0.00 5.68
4643 5439 3.119096 GGAGCTCGGAACAACGGC 61.119 66.667 7.83 0.00 0.00 5.68
4644 5440 2.758770 TTCGGAGCTCGGAACAACGG 62.759 60.000 27.34 0.00 39.77 4.44
4647 5443 0.677288 TCTTTCGGAGCTCGGAACAA 59.323 50.000 29.94 20.09 39.77 2.83
4648 5444 0.038526 GTCTTTCGGAGCTCGGAACA 60.039 55.000 29.94 19.34 39.77 3.18
4649 5445 0.038526 TGTCTTTCGGAGCTCGGAAC 60.039 55.000 29.94 21.81 39.77 3.62
4657 5453 1.219393 GGGAGCCTGTCTTTCGGAG 59.781 63.158 0.00 0.00 0.00 4.63
4712 5565 0.616111 TGAGCTTCTCCCACTCCTCC 60.616 60.000 0.00 0.00 0.00 4.30
4748 5601 0.389817 CCGGAGTGCAGAAATCGTCA 60.390 55.000 0.00 0.00 0.00 4.35
4754 5607 0.832135 AGGAGACCGGAGTGCAGAAA 60.832 55.000 9.46 0.00 0.00 2.52
4763 5616 1.000486 CCTGGAAGAGGAGACCGGA 60.000 63.158 9.46 0.00 46.33 5.14
4850 5703 2.841988 AGCCGCTCCAGGATCCTC 60.842 66.667 12.69 0.00 0.00 3.71
5012 5865 1.405121 CGTACCCTGTTGAAGGTAGGC 60.405 57.143 0.00 0.00 45.78 3.93
5118 6165 5.746990 ATCATTATAGGGCTACACTGGAC 57.253 43.478 0.00 0.00 0.00 4.02
5157 6204 9.151471 GCTTCATAGTTACTACAATTCAGAACA 57.849 33.333 0.00 0.00 0.00 3.18
5163 6210 9.151471 TGTTGAGCTTCATAGTTACTACAATTC 57.849 33.333 0.00 0.00 0.00 2.17
5170 6217 9.726438 AACTTATTGTTGAGCTTCATAGTTACT 57.274 29.630 0.00 0.00 37.52 2.24
5189 6236 3.769300 GGCACATCCTTTCCCAACTTATT 59.231 43.478 0.00 0.00 0.00 1.40
5198 6245 0.521735 GTTCGTGGCACATCCTTTCC 59.478 55.000 19.09 0.00 44.52 3.13
5207 6254 0.884704 ATGTCAGTGGTTCGTGGCAC 60.885 55.000 7.79 7.79 29.31 5.01
5209 6256 0.602638 TGATGTCAGTGGTTCGTGGC 60.603 55.000 0.00 0.00 0.00 5.01
5257 6304 7.575414 ATTGTTCGATGTCTACTCAGTAGAT 57.425 36.000 17.76 2.56 45.21 1.98
5274 6323 3.311106 AGCAAGCAACATGAATTGTTCG 58.689 40.909 0.00 0.00 45.55 3.95
5437 6487 0.984230 CCAAGAGCCTCCTGTAACCA 59.016 55.000 0.00 0.00 0.00 3.67
5497 6547 1.392853 GCTGTGCTGTTCTTCTCATCG 59.607 52.381 0.00 0.00 0.00 3.84
5511 6561 0.790814 GTCTAGAAACACCGCTGTGC 59.209 55.000 8.32 0.00 46.86 4.57
5513 6563 3.908737 GGTCTAGAAACACCGCTGT 57.091 52.632 0.00 0.00 0.00 4.40
5659 6709 1.153086 GCGGCCAAGGATGTCTCAT 60.153 57.895 2.24 0.00 0.00 2.90
5748 6798 1.080093 GACCCGCTCATCAACGACA 60.080 57.895 0.00 0.00 0.00 4.35
5857 6907 1.369091 AAATCATCAGTGGCCGTCGC 61.369 55.000 0.00 0.00 0.00 5.19
5859 6909 2.029838 AGAAATCATCAGTGGCCGTC 57.970 50.000 0.00 0.00 0.00 4.79
5905 6955 2.072298 GAGCTGACAACAAAGAGCGAT 58.928 47.619 0.00 0.00 0.00 4.58
5982 7032 0.727398 GTGGGAAGTAATGCACGAGC 59.273 55.000 0.00 0.00 42.57 5.03


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

AutoCloner maintained by Alex Coulton.