Multiple sequence alignment - TraesCS1D01G205600

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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 TraesCS1D01G205600 chr1D 100.000 4405 0 0 1 4405 291082291 291086695 0.000000e+00 8135.0
1 TraesCS1D01G205600 chr1D 88.904 730 59 11 814 1537 291588421 291587708 0.000000e+00 880.0
2 TraesCS1D01G205600 chr1D 84.346 428 34 15 2981 3406 291586205 291585809 5.340000e-104 388.0
3 TraesCS1D01G205600 chr1D 86.648 352 21 11 1614 1963 291587684 291587357 2.500000e-97 366.0
4 TraesCS1D01G205600 chr1D 79.211 558 87 18 2252 2798 291587011 291586472 1.160000e-95 361.0
5 TraesCS1D01G205600 chr1D 100.000 65 0 0 4169 4233 291086393 291086457 2.150000e-23 121.0
6 TraesCS1D01G205600 chr1D 100.000 65 0 0 4103 4167 291086459 291086523 2.150000e-23 121.0
7 TraesCS1D01G205600 chr1B 87.137 1135 88 22 833 1957 392530320 392529234 0.000000e+00 1234.0
8 TraesCS1D01G205600 chr1B 90.859 733 52 6 814 1537 392150433 392151159 0.000000e+00 968.0
9 TraesCS1D01G205600 chr1B 93.939 462 20 5 1997 2456 392151504 392151959 0.000000e+00 691.0
10 TraesCS1D01G205600 chr1B 90.737 475 36 7 2981 3449 392528177 392527705 1.040000e-175 627.0
11 TraesCS1D01G205600 chr1B 81.609 783 120 19 42 814 522724569 522723801 1.040000e-175 627.0
12 TraesCS1D01G205600 chr1B 81.600 750 103 15 85 810 12922331 12921593 4.910000e-164 588.0
13 TraesCS1D01G205600 chr1B 94.253 348 18 2 1618 1965 392151184 392151529 8.390000e-147 531.0
14 TraesCS1D01G205600 chr1B 78.784 740 105 31 2248 2983 392528965 392528274 2.420000e-122 449.0
15 TraesCS1D01G205600 chr1A 90.868 876 28 21 2252 3094 363421488 363422344 0.000000e+00 1127.0
16 TraesCS1D01G205600 chr1A 92.297 714 47 5 814 1521 363420122 363420833 0.000000e+00 1007.0
17 TraesCS1D01G205600 chr1A 89.689 708 57 7 833 1537 363656042 363655348 0.000000e+00 889.0
18 TraesCS1D01G205600 chr1A 85.606 792 86 17 35 814 449814840 449814065 0.000000e+00 806.0
19 TraesCS1D01G205600 chr1A 85.510 628 60 16 3482 4103 363422803 363423405 1.040000e-175 627.0
20 TraesCS1D01G205600 chr1A 94.220 346 20 0 1618 1963 363420878 363421223 3.020000e-146 529.0
21 TraesCS1D01G205600 chr1A 78.934 788 122 28 2033 2798 363654945 363654180 3.060000e-136 496.0
22 TraesCS1D01G205600 chr1A 92.241 348 25 1 1618 1963 363655319 363654972 3.960000e-135 492.0
23 TraesCS1D01G205600 chr1A 94.444 288 16 0 3128 3415 363422515 363422802 1.120000e-120 444.0
24 TraesCS1D01G205600 chr1A 79.647 624 79 22 2981 3589 363653899 363653309 5.310000e-109 405.0
25 TraesCS1D01G205600 chr1A 96.000 150 5 1 2031 2179 363421256 363421405 4.400000e-60 243.0
26 TraesCS1D01G205600 chr1A 85.965 228 13 3 4177 4385 363423450 363423677 4.430000e-55 226.0
27 TraesCS1D01G205600 chr7A 88.150 827 54 10 31 816 533572770 533571947 0.000000e+00 944.0
28 TraesCS1D01G205600 chr7B 87.271 817 42 13 31 816 157212902 157213687 0.000000e+00 876.0
29 TraesCS1D01G205600 chr4D 83.627 794 98 20 33 816 34131738 34130967 0.000000e+00 717.0
30 TraesCS1D01G205600 chr4D 83.069 756 77 17 35 757 386367718 386368455 1.340000e-179 640.0
31 TraesCS1D01G205600 chr7D 84.097 742 99 13 85 816 603159541 603160273 0.000000e+00 699.0
32 TraesCS1D01G205600 chr7D 100.000 35 0 0 1 35 583084844 583084878 1.020000e-06 65.8
33 TraesCS1D01G205600 chr5D 81.807 797 120 17 31 814 352819783 352820567 0.000000e+00 645.0
34 TraesCS1D01G205600 chr3D 81.853 788 116 14 42 817 39185932 39186704 4.800000e-179 638.0
35 TraesCS1D01G205600 chr3B 82.058 797 98 27 29 816 792855698 792854938 4.800000e-179 638.0
36 TraesCS1D01G205600 chr3B 97.222 72 2 0 746 817 22257166 22257095 5.980000e-24 122.0
37 TraesCS1D01G205600 chr3B 92.593 81 6 0 746 826 172327362 172327282 2.780000e-22 117.0


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 TraesCS1D01G205600 chr1D 291082291 291086695 4404 False 2792.333333 8135 100.000000 1 4405 3 chr1D.!!$F1 4404
1 TraesCS1D01G205600 chr1D 291585809 291588421 2612 True 498.750000 880 84.777250 814 3406 4 chr1D.!!$R1 2592
2 TraesCS1D01G205600 chr1B 392527705 392530320 2615 True 770.000000 1234 85.552667 833 3449 3 chr1B.!!$R3 2616
3 TraesCS1D01G205600 chr1B 392150433 392151959 1526 False 730.000000 968 93.017000 814 2456 3 chr1B.!!$F1 1642
4 TraesCS1D01G205600 chr1B 522723801 522724569 768 True 627.000000 627 81.609000 42 814 1 chr1B.!!$R2 772
5 TraesCS1D01G205600 chr1B 12921593 12922331 738 True 588.000000 588 81.600000 85 810 1 chr1B.!!$R1 725
6 TraesCS1D01G205600 chr1A 449814065 449814840 775 True 806.000000 806 85.606000 35 814 1 chr1A.!!$R1 779
7 TraesCS1D01G205600 chr1A 363420122 363423677 3555 False 600.428571 1127 91.329143 814 4385 7 chr1A.!!$F1 3571
8 TraesCS1D01G205600 chr1A 363653309 363656042 2733 True 570.500000 889 85.127750 833 3589 4 chr1A.!!$R2 2756
9 TraesCS1D01G205600 chr7A 533571947 533572770 823 True 944.000000 944 88.150000 31 816 1 chr7A.!!$R1 785
10 TraesCS1D01G205600 chr7B 157212902 157213687 785 False 876.000000 876 87.271000 31 816 1 chr7B.!!$F1 785
11 TraesCS1D01G205600 chr4D 34130967 34131738 771 True 717.000000 717 83.627000 33 816 1 chr4D.!!$R1 783
12 TraesCS1D01G205600 chr4D 386367718 386368455 737 False 640.000000 640 83.069000 35 757 1 chr4D.!!$F1 722
13 TraesCS1D01G205600 chr7D 603159541 603160273 732 False 699.000000 699 84.097000 85 816 1 chr7D.!!$F2 731
14 TraesCS1D01G205600 chr5D 352819783 352820567 784 False 645.000000 645 81.807000 31 814 1 chr5D.!!$F1 783
15 TraesCS1D01G205600 chr3D 39185932 39186704 772 False 638.000000 638 81.853000 42 817 1 chr3D.!!$F1 775
16 TraesCS1D01G205600 chr3B 792854938 792855698 760 True 638.000000 638 82.058000 29 816 1 chr3B.!!$R3 787

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
918 1024 0.104855 TCTCTGCACTCCACACACAC 59.895 55.0 0.00 0.0 0.00 3.82 F
1523 1645 0.032540 GGAACCAAGGCAAGTGCAAG 59.967 55.0 5.52 0.0 44.36 4.01 F
1766 1888 0.388649 CACAGGTACGCAGGACAGAC 60.389 60.0 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2892 3192 0.110056 CTTCCACACAGCGTTGATGC 60.110 55.0 6.16 0.0 0.00 3.91 R
2997 3411 0.029035 CGACGTCGTAGGGATCCTTG 59.971 60.0 29.08 0.0 34.61 3.61 R
3472 4066 0.034896 GAGCAAAGGAGACGGGTTGA 59.965 55.0 0.00 0.0 0.00 3.18 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
17 18 3.719121 ACAGCGAGATGGGCTTCT 58.281 55.556 0.00 0.00 39.08 2.85
18 19 1.986413 ACAGCGAGATGGGCTTCTT 59.014 52.632 0.00 0.00 39.08 2.52
19 20 0.107945 ACAGCGAGATGGGCTTCTTC 60.108 55.000 0.00 0.00 39.08 2.87
20 21 0.177604 CAGCGAGATGGGCTTCTTCT 59.822 55.000 0.00 0.00 39.08 2.85
21 22 0.463620 AGCGAGATGGGCTTCTTCTC 59.536 55.000 10.93 10.93 40.96 2.87
22 23 0.531753 GCGAGATGGGCTTCTTCTCC 60.532 60.000 13.49 6.88 41.17 3.71
23 24 0.249238 CGAGATGGGCTTCTTCTCCG 60.249 60.000 13.49 8.24 41.17 4.63
24 25 0.105778 GAGATGGGCTTCTTCTCCGG 59.894 60.000 0.00 0.00 39.44 5.14
25 26 1.524849 GATGGGCTTCTTCTCCGGC 60.525 63.158 0.00 0.00 0.00 6.13
26 27 3.391665 ATGGGCTTCTTCTCCGGCG 62.392 63.158 0.00 0.00 0.00 6.46
29 30 4.760047 GCTTCTTCTCCGGCGCCA 62.760 66.667 28.98 6.80 0.00 5.69
507 596 3.808656 GACCCCGAGGACGACGAC 61.809 72.222 0.00 0.00 42.66 4.34
751 856 2.561956 CCGTATCCGTCTGGCCGAT 61.562 63.158 0.00 0.00 34.14 4.18
918 1024 0.104855 TCTCTGCACTCCACACACAC 59.895 55.000 0.00 0.00 0.00 3.82
1084 1200 2.656646 CAGCACGGCCTGACAGTA 59.343 61.111 0.00 0.00 34.77 2.74
1206 1322 2.176792 GGGTACGTCACGACCGAC 59.823 66.667 2.91 0.00 36.51 4.79
1233 1349 0.320421 TCGGCAAGGCACTGTTCTAC 60.320 55.000 0.00 0.00 40.86 2.59
1250 1366 3.015327 TCTACTGGTTCTTCGAGGCTAC 58.985 50.000 0.00 0.00 0.00 3.58
1257 1373 1.830279 TCTTCGAGGCTACGGAGAAA 58.170 50.000 12.84 0.00 43.60 2.52
1263 1379 1.757699 GAGGCTACGGAGAAACCTGAT 59.242 52.381 0.00 0.00 36.31 2.90
1266 1382 2.103263 GGCTACGGAGAAACCTGATGAT 59.897 50.000 0.00 0.00 36.31 2.45
1275 1391 5.184892 AGAAACCTGATGATAAGCCACTT 57.815 39.130 0.00 0.00 0.00 3.16
1354 1473 1.961793 TCAGAAAACTTCGTGGGTGG 58.038 50.000 0.00 0.00 34.02 4.61
1374 1495 5.701290 GGTGGAAGATGTATGTAATGTAGCC 59.299 44.000 0.00 0.00 0.00 3.93
1387 1509 0.457166 TGTAGCCGTACATCGTGTGC 60.457 55.000 0.00 0.00 34.02 4.57
1389 1511 0.099968 TAGCCGTACATCGTGTGCTC 59.900 55.000 0.00 0.00 36.39 4.26
1523 1645 0.032540 GGAACCAAGGCAAGTGCAAG 59.967 55.000 5.52 0.00 44.36 4.01
1524 1646 0.746659 GAACCAAGGCAAGTGCAAGT 59.253 50.000 5.52 0.00 44.36 3.16
1528 1650 1.342174 CCAAGGCAAGTGCAAGTCAAT 59.658 47.619 5.52 0.00 44.36 2.57
1530 1652 3.005684 CCAAGGCAAGTGCAAGTCAATAA 59.994 43.478 5.52 0.00 44.36 1.40
1532 1654 5.105797 CCAAGGCAAGTGCAAGTCAATAATA 60.106 40.000 5.52 0.00 44.36 0.98
1533 1655 6.389091 CAAGGCAAGTGCAAGTCAATAATAA 58.611 36.000 5.52 0.00 44.36 1.40
1534 1656 5.954335 AGGCAAGTGCAAGTCAATAATAAC 58.046 37.500 5.52 0.00 44.36 1.89
1535 1657 5.476599 AGGCAAGTGCAAGTCAATAATAACA 59.523 36.000 5.52 0.00 44.36 2.41
1536 1658 6.153340 AGGCAAGTGCAAGTCAATAATAACAT 59.847 34.615 5.52 0.00 44.36 2.71
1537 1659 6.254157 GGCAAGTGCAAGTCAATAATAACATG 59.746 38.462 5.52 0.00 44.36 3.21
1538 1660 6.237648 GCAAGTGCAAGTCAATAATAACATGC 60.238 38.462 0.00 0.00 39.76 4.06
1539 1661 5.894807 AGTGCAAGTCAATAATAACATGCC 58.105 37.500 0.00 0.00 38.86 4.40
1540 1662 5.418524 AGTGCAAGTCAATAATAACATGCCA 59.581 36.000 0.00 0.00 38.86 4.92
1541 1663 6.097270 AGTGCAAGTCAATAATAACATGCCAT 59.903 34.615 0.00 0.00 38.86 4.40
1542 1664 7.285172 AGTGCAAGTCAATAATAACATGCCATA 59.715 33.333 0.00 0.00 38.86 2.74
1543 1665 8.084073 GTGCAAGTCAATAATAACATGCCATAT 58.916 33.333 0.00 0.00 38.86 1.78
1544 1666 8.083462 TGCAAGTCAATAATAACATGCCATATG 58.917 33.333 0.00 0.00 38.86 1.78
1545 1667 8.084073 GCAAGTCAATAATAACATGCCATATGT 58.916 33.333 1.24 0.00 34.85 2.29
1546 1668 9.616634 CAAGTCAATAATAACATGCCATATGTC 57.383 33.333 1.24 0.00 0.00 3.06
1547 1669 8.340618 AGTCAATAATAACATGCCATATGTCC 57.659 34.615 1.24 0.00 0.00 4.02
1548 1670 7.394359 AGTCAATAATAACATGCCATATGTCCC 59.606 37.037 1.24 0.00 0.00 4.46
1549 1671 6.663093 TCAATAATAACATGCCATATGTCCCC 59.337 38.462 1.24 0.00 0.00 4.81
1550 1672 4.467861 AATAACATGCCATATGTCCCCA 57.532 40.909 1.24 0.00 0.00 4.96
1551 1673 2.071778 AACATGCCATATGTCCCCAC 57.928 50.000 1.24 0.00 0.00 4.61
1552 1674 0.925558 ACATGCCATATGTCCCCACA 59.074 50.000 1.24 0.00 36.78 4.17
1553 1675 1.287442 ACATGCCATATGTCCCCACAA 59.713 47.619 1.24 0.00 35.64 3.33
1554 1676 2.292126 ACATGCCATATGTCCCCACAAA 60.292 45.455 1.24 0.00 35.64 2.83
1555 1677 2.612285 TGCCATATGTCCCCACAAAA 57.388 45.000 1.24 0.00 35.64 2.44
1556 1678 2.894731 TGCCATATGTCCCCACAAAAA 58.105 42.857 1.24 0.00 35.64 1.94
1589 1711 6.051717 CCATATGCAGTAATCATAGTAGGCC 58.948 44.000 0.00 0.00 30.84 5.19
1594 1716 8.789767 ATGCAGTAATCATAGTAGGCCTATAT 57.210 34.615 17.38 10.69 34.49 0.86
1595 1717 8.609617 TGCAGTAATCATAGTAGGCCTATATT 57.390 34.615 17.38 12.74 34.49 1.28
1755 1877 2.677037 CGGGAGACAATTCCACAGGTAC 60.677 54.545 0.00 0.00 39.09 3.34
1759 1881 1.732259 GACAATTCCACAGGTACGCAG 59.268 52.381 0.00 0.00 0.00 5.18
1766 1888 0.388649 CACAGGTACGCAGGACAGAC 60.389 60.000 0.00 0.00 0.00 3.51
1963 2088 6.853720 TGCCGACTTATTCATAGATAGCTAC 58.146 40.000 0.00 0.00 0.00 3.58
1964 2089 6.659668 TGCCGACTTATTCATAGATAGCTACT 59.340 38.462 0.00 0.00 0.00 2.57
1965 2090 7.148222 TGCCGACTTATTCATAGATAGCTACTC 60.148 40.741 0.00 0.00 0.00 2.59
1966 2091 7.680113 GCCGACTTATTCATAGATAGCTACTCC 60.680 44.444 0.00 0.00 0.00 3.85
1967 2092 7.337184 CCGACTTATTCATAGATAGCTACTCCA 59.663 40.741 0.00 0.00 0.00 3.86
1968 2093 8.394877 CGACTTATTCATAGATAGCTACTCCAG 58.605 40.741 0.00 0.00 0.00 3.86
1971 2096 8.815565 TTATTCATAGATAGCTACTCCAGAGG 57.184 38.462 0.00 0.00 0.00 3.69
1973 2098 5.811190 TCATAGATAGCTACTCCAGAGGAC 58.189 45.833 0.00 0.00 0.00 3.85
1975 2100 4.806952 AGATAGCTACTCCAGAGGACTT 57.193 45.455 0.00 0.00 0.00 3.01
1976 2101 4.725490 AGATAGCTACTCCAGAGGACTTC 58.275 47.826 0.00 0.00 0.00 3.01
1977 2102 4.415512 AGATAGCTACTCCAGAGGACTTCT 59.584 45.833 0.00 0.00 36.25 2.85
1980 2105 5.915744 AGCTACTCCAGAGGACTTCTATA 57.084 43.478 0.00 0.00 33.83 1.31
1984 2109 6.206048 GCTACTCCAGAGGACTTCTATAACTC 59.794 46.154 0.00 0.00 33.83 3.01
1985 2110 6.080969 ACTCCAGAGGACTTCTATAACTCA 57.919 41.667 0.00 0.00 33.83 3.41
1986 2111 5.889289 ACTCCAGAGGACTTCTATAACTCAC 59.111 44.000 0.00 0.00 33.83 3.51
1988 2113 6.253758 TCCAGAGGACTTCTATAACTCACAA 58.746 40.000 0.00 0.00 33.83 3.33
1989 2114 6.724441 TCCAGAGGACTTCTATAACTCACAAA 59.276 38.462 0.00 0.00 33.83 2.83
1990 2115 7.234782 TCCAGAGGACTTCTATAACTCACAAAA 59.765 37.037 0.00 0.00 33.83 2.44
1991 2116 8.043710 CCAGAGGACTTCTATAACTCACAAAAT 58.956 37.037 0.00 0.00 33.83 1.82
1992 2117 9.442047 CAGAGGACTTCTATAACTCACAAAATT 57.558 33.333 0.00 0.00 33.83 1.82
1996 2121 9.989869 GGACTTCTATAACTCACAAAATTAAGC 57.010 33.333 0.00 0.00 0.00 3.09
2000 2165 7.985476 TCTATAACTCACAAAATTAAGCTGCC 58.015 34.615 0.00 0.00 0.00 4.85
2002 2167 4.935352 ACTCACAAAATTAAGCTGCCAA 57.065 36.364 0.00 0.00 0.00 4.52
2008 2173 7.441017 TCACAAAATTAAGCTGCCAACTTATT 58.559 30.769 0.00 0.00 30.07 1.40
2012 2177 9.585099 CAAAATTAAGCTGCCAACTTATTCATA 57.415 29.630 0.00 0.00 30.07 2.15
2013 2178 9.807649 AAAATTAAGCTGCCAACTTATTCATAG 57.192 29.630 0.00 0.00 30.07 2.23
2015 2180 7.938140 TTAAGCTGCCAACTTATTCATAGTT 57.062 32.000 0.00 0.00 36.31 2.24
2020 2185 6.093495 GCTGCCAACTTATTCATAGTTGTACA 59.907 38.462 12.97 0.00 46.98 2.90
2021 2186 7.201732 GCTGCCAACTTATTCATAGTTGTACAT 60.202 37.037 12.97 0.00 46.98 2.29
2023 2188 9.674068 TGCCAACTTATTCATAGTTGTACATTA 57.326 29.630 12.97 0.00 46.98 1.90
2056 2228 6.037940 GCTCATGATCTGACTTTTGCTCATTA 59.962 38.462 0.00 0.00 0.00 1.90
2156 2329 6.387465 GCCTCCAAAGAAAACTACATAAACC 58.613 40.000 0.00 0.00 0.00 3.27
2218 2395 9.042450 TCACTCCCTCAAAATTTCACTAGTATA 57.958 33.333 0.00 0.00 0.00 1.47
2498 2745 2.668212 CCGGCTTTGAACGCCTCA 60.668 61.111 11.07 0.00 45.37 3.86
2512 2759 1.443407 CCTCATCCTCGGCGAACAT 59.557 57.895 12.13 2.35 0.00 2.71
2513 2760 0.598680 CCTCATCCTCGGCGAACATC 60.599 60.000 12.13 0.00 0.00 3.06
2514 2761 0.936764 CTCATCCTCGGCGAACATCG 60.937 60.000 12.13 0.00 43.89 3.84
2515 2762 1.951130 CATCCTCGGCGAACATCGG 60.951 63.158 12.13 8.56 40.84 4.18
2516 2763 2.125326 ATCCTCGGCGAACATCGGA 61.125 57.895 15.85 15.85 40.84 4.55
2517 2764 2.076622 ATCCTCGGCGAACATCGGAG 62.077 60.000 17.95 1.67 40.84 4.63
2560 2807 0.407139 AGCAAAGCATCCTCCTTGGT 59.593 50.000 0.00 0.00 37.07 3.67
2574 2821 4.039609 CCTCCTTGGTTTCAGCTTCAAAAT 59.960 41.667 0.00 0.00 0.00 1.82
2610 2878 1.756950 CCCCCTCGGTCTGATCGAA 60.757 63.158 14.59 0.00 36.15 3.71
2617 2885 1.068541 TCGGTCTGATCGAACAGTGTG 60.069 52.381 20.52 12.00 38.79 3.82
2625 2893 5.934043 TCTGATCGAACAGTGTGATTGATTT 59.066 36.000 20.52 0.00 38.79 2.17
2629 2897 6.370433 TCGAACAGTGTGATTGATTTTTCA 57.630 33.333 0.00 0.00 0.00 2.69
2631 2899 6.857451 TCGAACAGTGTGATTGATTTTTCATG 59.143 34.615 0.00 0.00 0.00 3.07
2634 2902 5.693104 ACAGTGTGATTGATTTTTCATGCAC 59.307 36.000 0.00 0.00 0.00 4.57
2750 3035 1.900981 CATGCCAACACCACGGGAA 60.901 57.895 0.00 0.00 0.00 3.97
2758 3043 1.153249 CACCACGGGAATGCCGTAT 60.153 57.895 20.26 7.54 42.19 3.06
2784 3069 2.297033 ACGTTCTCTGCCGGTAAGTTTA 59.703 45.455 1.90 0.00 0.00 2.01
2785 3070 3.056322 ACGTTCTCTGCCGGTAAGTTTAT 60.056 43.478 1.90 0.00 0.00 1.40
2788 3076 4.811969 TCTCTGCCGGTAAGTTTATTCA 57.188 40.909 1.90 0.00 0.00 2.57
2804 3092 2.185004 TTCACCTAGCTGAGTTTGCC 57.815 50.000 0.00 0.00 0.00 4.52
2807 3095 1.059913 ACCTAGCTGAGTTTGCCTGT 58.940 50.000 0.00 0.00 0.00 4.00
2829 3117 4.057406 TGGGCTCAGAATTGTGTTTTTG 57.943 40.909 2.11 0.00 0.00 2.44
2830 3118 3.450457 TGGGCTCAGAATTGTGTTTTTGT 59.550 39.130 2.11 0.00 0.00 2.83
2831 3119 3.803778 GGGCTCAGAATTGTGTTTTTGTG 59.196 43.478 2.11 0.00 0.00 3.33
2832 3120 4.432712 GGCTCAGAATTGTGTTTTTGTGT 58.567 39.130 2.11 0.00 0.00 3.72
2833 3121 5.451242 GGGCTCAGAATTGTGTTTTTGTGTA 60.451 40.000 2.11 0.00 0.00 2.90
2834 3122 5.458779 GGCTCAGAATTGTGTTTTTGTGTAC 59.541 40.000 2.11 0.00 0.00 2.90
2835 3123 5.458779 GCTCAGAATTGTGTTTTTGTGTACC 59.541 40.000 2.11 0.00 0.00 3.34
2836 3124 5.897050 TCAGAATTGTGTTTTTGTGTACCC 58.103 37.500 2.11 0.00 0.00 3.69
2837 3125 5.419155 TCAGAATTGTGTTTTTGTGTACCCA 59.581 36.000 2.11 0.00 0.00 4.51
2852 3152 6.186957 TGTGTACCCATTTCATAGCTGAATT 58.813 36.000 0.00 0.00 40.95 2.17
2858 3158 8.995027 ACCCATTTCATAGCTGAATTTATACA 57.005 30.769 0.00 0.00 40.95 2.29
2865 3165 9.787532 TTCATAGCTGAATTTATACAGTTTTGC 57.212 29.630 0.00 0.00 36.46 3.68
2892 3192 5.687285 GTGTGGTGTTTCTTTTCAGCAATAG 59.313 40.000 0.00 0.00 42.27 1.73
2901 3201 2.830772 TTCAGCAATAGCATCAACGC 57.169 45.000 0.00 0.00 45.49 4.84
3107 3684 6.123045 AGCAGGTACCACTACTGTTTTAAT 57.877 37.500 15.94 0.00 34.79 1.40
3132 3709 9.860898 ATTAATTGGATAACTGAACAAAAGAGC 57.139 29.630 0.00 0.00 0.00 4.09
3133 3710 6.899393 ATTGGATAACTGAACAAAAGAGCA 57.101 33.333 0.00 0.00 0.00 4.26
3134 3711 5.947228 TGGATAACTGAACAAAAGAGCAG 57.053 39.130 0.00 0.00 34.65 4.24
3135 3712 4.761739 TGGATAACTGAACAAAAGAGCAGG 59.238 41.667 0.00 0.00 32.82 4.85
3136 3713 5.003804 GGATAACTGAACAAAAGAGCAGGA 58.996 41.667 0.00 0.00 32.82 3.86
3137 3714 5.123027 GGATAACTGAACAAAAGAGCAGGAG 59.877 44.000 0.00 0.00 32.82 3.69
3138 3715 3.845781 ACTGAACAAAAGAGCAGGAGA 57.154 42.857 0.00 0.00 32.82 3.71
3139 3716 4.156455 ACTGAACAAAAGAGCAGGAGAA 57.844 40.909 0.00 0.00 32.82 2.87
3158 3735 0.759346 ATCCCATCGACAAGTAGCCC 59.241 55.000 0.00 0.00 0.00 5.19
3160 3737 1.338136 CCCATCGACAAGTAGCCCCT 61.338 60.000 0.00 0.00 0.00 4.79
3167 3744 2.298610 GACAAGTAGCCCCTAATTGGC 58.701 52.381 14.44 9.29 43.47 4.52
3181 3758 6.151817 CCCCTAATTGGCTGCTAATTAATCTC 59.848 42.308 24.85 0.00 31.67 2.75
3334 3922 3.049674 CATGGTGCCAACGTCGCT 61.050 61.111 8.80 0.00 0.00 4.93
3440 4034 0.589223 TCACAATTCGCACGTTTCCC 59.411 50.000 0.00 0.00 0.00 3.97
3449 4043 2.014128 CGCACGTTTCCCCAATAAGAT 58.986 47.619 0.00 0.00 0.00 2.40
3451 4045 3.013921 GCACGTTTCCCCAATAAGATCA 58.986 45.455 0.00 0.00 0.00 2.92
3452 4046 3.442273 GCACGTTTCCCCAATAAGATCAA 59.558 43.478 0.00 0.00 0.00 2.57
3454 4048 4.096382 CACGTTTCCCCAATAAGATCAAGG 59.904 45.833 0.00 0.00 0.00 3.61
3455 4049 3.632145 CGTTTCCCCAATAAGATCAAGGG 59.368 47.826 0.00 0.00 39.29 3.95
3460 4054 2.785857 CCCAATAAGATCAAGGGGGTCT 59.214 50.000 0.00 0.00 35.83 3.85
3461 4055 3.181439 CCCAATAAGATCAAGGGGGTCTC 60.181 52.174 0.00 0.00 35.83 3.36
3462 4056 3.181439 CCAATAAGATCAAGGGGGTCTCC 60.181 52.174 0.00 0.00 0.00 3.71
3463 4057 2.961536 TAAGATCAAGGGGGTCTCCA 57.038 50.000 0.00 0.00 37.22 3.86
3466 4060 2.131023 AGATCAAGGGGGTCTCCATTC 58.869 52.381 0.00 0.00 37.44 2.67
3469 4063 1.565759 TCAAGGGGGTCTCCATTCATG 59.434 52.381 0.00 0.00 37.44 3.07
3499 4105 2.095161 CGTCTCCTTTGCTCTTCTACGT 60.095 50.000 0.00 0.00 0.00 3.57
3500 4106 3.503891 GTCTCCTTTGCTCTTCTACGTC 58.496 50.000 0.00 0.00 0.00 4.34
3520 4126 4.246458 GTCACCTGTAGTTCCTGATCAAC 58.754 47.826 0.00 0.00 0.00 3.18
3528 4135 2.982488 AGTTCCTGATCAACCTGGTCTT 59.018 45.455 0.00 0.00 0.00 3.01
3600 4207 5.348986 TGCCGAGATCAGTTGTCTAAATAC 58.651 41.667 0.00 0.00 0.00 1.89
3614 4221 9.017669 GTTGTCTAAATACGATTTCTACGTCAT 57.982 33.333 0.00 0.00 43.62 3.06
3660 4267 9.994432 AATATCTCTTTTGCTATTTTTCAGTCG 57.006 29.630 0.00 0.00 0.00 4.18
3678 4285 5.475220 TCAGTCGCCTGAAAATTTATTTGGA 59.525 36.000 0.00 0.00 44.67 3.53
3679 4286 6.015856 TCAGTCGCCTGAAAATTTATTTGGAA 60.016 34.615 0.00 0.00 44.67 3.53
3680 4287 6.644592 CAGTCGCCTGAAAATTTATTTGGAAA 59.355 34.615 0.00 0.00 41.50 3.13
3681 4288 7.170658 CAGTCGCCTGAAAATTTATTTGGAAAA 59.829 33.333 0.00 0.00 41.50 2.29
3682 4289 7.170828 AGTCGCCTGAAAATTTATTTGGAAAAC 59.829 33.333 0.00 0.00 0.00 2.43
3683 4290 6.144724 TCGCCTGAAAATTTATTTGGAAAACG 59.855 34.615 0.00 0.00 0.00 3.60
3684 4291 6.074034 CGCCTGAAAATTTATTTGGAAAACGT 60.074 34.615 0.00 0.00 0.00 3.99
3685 4292 7.517575 CGCCTGAAAATTTATTTGGAAAACGTT 60.518 33.333 0.00 0.00 0.00 3.99
3686 4293 8.126074 GCCTGAAAATTTATTTGGAAAACGTTT 58.874 29.630 7.96 7.96 0.00 3.60
3687 4294 9.432077 CCTGAAAATTTATTTGGAAAACGTTTG 57.568 29.630 15.46 0.00 0.00 2.93
3696 4303 9.810545 TTATTTGGAAAACGTTTGAAATCTTCT 57.189 25.926 15.46 0.00 0.00 2.85
3697 4304 8.716646 ATTTGGAAAACGTTTGAAATCTTCTT 57.283 26.923 15.46 0.00 0.00 2.52
3698 4305 8.541133 TTTGGAAAACGTTTGAAATCTTCTTT 57.459 26.923 15.46 0.00 0.00 2.52
3699 4306 8.541133 TTGGAAAACGTTTGAAATCTTCTTTT 57.459 26.923 15.46 0.00 0.00 2.27
3700 4307 8.541133 TGGAAAACGTTTGAAATCTTCTTTTT 57.459 26.923 15.46 0.00 0.00 1.94
3748 4355 3.867055 CGGATGATTTCTGGAACATCG 57.133 47.619 0.00 0.00 39.66 3.84
3749 4356 3.198068 CGGATGATTTCTGGAACATCGT 58.802 45.455 0.00 4.87 39.66 3.73
3750 4357 3.623060 CGGATGATTTCTGGAACATCGTT 59.377 43.478 0.00 0.00 39.66 3.85
3752 4359 5.391950 CGGATGATTTCTGGAACATCGTTTT 60.392 40.000 0.00 0.00 39.66 2.43
3753 4360 6.183360 CGGATGATTTCTGGAACATCGTTTTA 60.183 38.462 0.00 0.00 39.66 1.52
3757 4379 5.682943 TTTCTGGAACATCGTTTTAGTGG 57.317 39.130 0.00 0.00 38.20 4.00
3779 4401 0.610232 ACCATGCACTGCTTCCTTCC 60.610 55.000 1.98 0.00 0.00 3.46
3783 4405 2.394563 GCACTGCTTCCTTCCGAGC 61.395 63.158 0.00 0.00 39.33 5.03
3812 4435 3.404869 TCCTGCCTTATCTCTTGAGGA 57.595 47.619 0.00 0.00 32.11 3.71
3815 4438 2.690497 CTGCCTTATCTCTTGAGGACGA 59.310 50.000 0.00 0.00 32.11 4.20
3837 4460 1.611491 CGTCCCCTAGCTCTCTCATTC 59.389 57.143 0.00 0.00 0.00 2.67
3841 4465 3.964031 TCCCCTAGCTCTCTCATTCTTTC 59.036 47.826 0.00 0.00 0.00 2.62
3843 4467 3.243704 CCCTAGCTCTCTCATTCTTTCCG 60.244 52.174 0.00 0.00 0.00 4.30
3851 4475 4.397730 TCTCTCATTCTTTCCGTCTCTCTG 59.602 45.833 0.00 0.00 0.00 3.35
3859 4483 0.324738 TCCGTCTCTCTGCCCAGAAT 60.325 55.000 0.00 0.00 36.94 2.40
3860 4484 1.063942 TCCGTCTCTCTGCCCAGAATA 60.064 52.381 0.00 0.00 36.94 1.75
3861 4485 1.967066 CCGTCTCTCTGCCCAGAATAT 59.033 52.381 0.00 0.00 36.94 1.28
3863 4487 3.192422 CCGTCTCTCTGCCCAGAATATAG 59.808 52.174 0.00 0.00 36.94 1.31
3876 4500 9.532494 TGCCCAGAATATAGCATAACAATATTT 57.468 29.630 0.00 0.00 0.00 1.40
3974 4601 5.407084 GGGTTAATGGTTCCAAATTTTGACG 59.593 40.000 10.72 0.00 0.00 4.35
4011 4638 7.980742 AAAAACGTCACTTTCTTTGGAATAC 57.019 32.000 0.00 0.00 0.00 1.89
4032 4659 3.825014 ACTTCCGCTAGACAAGAGTAACA 59.175 43.478 0.00 0.00 0.00 2.41
4034 4661 4.436242 TCCGCTAGACAAGAGTAACAAG 57.564 45.455 0.00 0.00 0.00 3.16
4039 4666 5.163602 CGCTAGACAAGAGTAACAAGGATCT 60.164 44.000 0.00 0.00 0.00 2.75
4085 4712 3.840666 GCAGGGTAGAGGATCCATGAATA 59.159 47.826 15.82 0.00 37.66 1.75
4103 4730 7.362660 CCATGAATAGTTGCATAGCAGCATATT 60.363 37.037 8.48 8.69 45.19 1.28
4104 4731 7.514784 TGAATAGTTGCATAGCAGCATATTT 57.485 32.000 8.48 0.00 45.19 1.40
4141 4805 9.217223 GTAACACCATTTATTATACAAGCAACG 57.783 33.333 0.00 0.00 0.00 4.10
4142 4806 7.385778 ACACCATTTATTATACAAGCAACGT 57.614 32.000 0.00 0.00 0.00 3.99
4143 4807 8.495361 ACACCATTTATTATACAAGCAACGTA 57.505 30.769 0.00 0.00 0.00 3.57
4144 4808 9.116067 ACACCATTTATTATACAAGCAACGTAT 57.884 29.630 0.00 0.00 34.08 3.06
4145 4809 9.381027 CACCATTTATTATACAAGCAACGTATG 57.619 33.333 0.00 0.00 32.01 2.39
4146 4810 9.332502 ACCATTTATTATACAAGCAACGTATGA 57.667 29.630 0.00 0.00 32.01 2.15
4152 4816 8.896320 ATTATACAAGCAACGTATGAATACCA 57.104 30.769 0.00 0.00 32.01 3.25
4153 4817 8.719560 TTATACAAGCAACGTATGAATACCAA 57.280 30.769 0.00 0.00 32.01 3.67
4154 4818 5.950758 ACAAGCAACGTATGAATACCAAA 57.049 34.783 0.00 0.00 0.00 3.28
4155 4819 6.320494 ACAAGCAACGTATGAATACCAAAA 57.680 33.333 0.00 0.00 0.00 2.44
4156 4820 6.378582 ACAAGCAACGTATGAATACCAAAAG 58.621 36.000 0.00 0.00 0.00 2.27
4157 4821 6.016610 ACAAGCAACGTATGAATACCAAAAGT 60.017 34.615 0.00 0.00 0.00 2.66
4158 4822 7.173562 ACAAGCAACGTATGAATACCAAAAGTA 59.826 33.333 0.00 0.00 34.76 2.24
4159 4823 7.303634 AGCAACGTATGAATACCAAAAGTAG 57.696 36.000 0.00 0.00 33.42 2.57
4160 4824 6.877322 AGCAACGTATGAATACCAAAAGTAGT 59.123 34.615 0.00 0.00 33.42 2.73
4161 4825 8.036575 AGCAACGTATGAATACCAAAAGTAGTA 58.963 33.333 0.00 0.00 33.42 1.82
4162 4826 8.823818 GCAACGTATGAATACCAAAAGTAGTAT 58.176 33.333 0.00 0.00 33.42 2.12
4164 4828 9.538508 AACGTATGAATACCAAAAGTAGTATCC 57.461 33.333 0.00 0.00 33.42 2.59
4165 4829 8.921205 ACGTATGAATACCAAAAGTAGTATCCT 58.079 33.333 0.00 0.00 33.42 3.24
4166 4830 9.760077 CGTATGAATACCAAAAGTAGTATCCTT 57.240 33.333 0.00 0.00 33.42 3.36
4225 4889 7.303634 AGCAACGTATGAATACCAAAAGTAG 57.696 36.000 0.00 0.00 33.42 2.57
4227 4891 8.036575 AGCAACGTATGAATACCAAAAGTAGTA 58.963 33.333 0.00 0.00 33.42 1.82
4228 4892 8.823818 GCAACGTATGAATACCAAAAGTAGTAT 58.176 33.333 0.00 0.00 33.42 2.12
4249 4925 1.203928 CTTGACAGGAGATTAGCGCG 58.796 55.000 0.00 0.00 0.00 6.86
4327 5003 2.679132 GATCACACCCCGATCGGACG 62.679 65.000 35.42 25.04 37.50 4.79
4353 5034 2.031012 CCCAGTCACGCTGCAAGA 59.969 61.111 0.00 0.00 43.71 3.02
4385 5066 4.454504 AGAACGTTCGTGCCTTATGAATTT 59.545 37.500 21.87 0.00 36.72 1.82
4386 5067 4.078363 ACGTTCGTGCCTTATGAATTTG 57.922 40.909 0.00 0.00 36.72 2.32
4387 5068 3.119990 ACGTTCGTGCCTTATGAATTTGG 60.120 43.478 0.00 0.00 36.72 3.28
4388 5069 3.126171 CGTTCGTGCCTTATGAATTTGGA 59.874 43.478 0.00 0.00 36.72 3.53
4389 5070 4.378978 CGTTCGTGCCTTATGAATTTGGAA 60.379 41.667 0.00 0.00 36.72 3.53
4390 5071 5.650543 GTTCGTGCCTTATGAATTTGGAAT 58.349 37.500 0.00 0.00 36.72 3.01
4391 5072 5.913137 TCGTGCCTTATGAATTTGGAATT 57.087 34.783 0.00 0.00 0.00 2.17
4392 5073 6.279513 TCGTGCCTTATGAATTTGGAATTT 57.720 33.333 0.00 0.00 0.00 1.82
4393 5074 6.098679 TCGTGCCTTATGAATTTGGAATTTG 58.901 36.000 0.00 0.00 0.00 2.32
4394 5075 5.291614 CGTGCCTTATGAATTTGGAATTTGG 59.708 40.000 0.00 0.00 0.00 3.28
4395 5076 6.405538 GTGCCTTATGAATTTGGAATTTGGA 58.594 36.000 0.00 0.00 0.00 3.53
4396 5077 6.878389 GTGCCTTATGAATTTGGAATTTGGAA 59.122 34.615 0.00 0.00 0.00 3.53
4397 5078 7.064966 GTGCCTTATGAATTTGGAATTTGGAAG 59.935 37.037 0.00 0.00 0.00 3.46
4398 5079 7.105588 GCCTTATGAATTTGGAATTTGGAAGT 58.894 34.615 0.00 0.00 0.00 3.01
4399 5080 8.257306 GCCTTATGAATTTGGAATTTGGAAGTA 58.743 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.177604 AGAAGAAGCCCATCTCGCTG 59.822 55.000 0.00 0.00 36.47 5.18
2 3 0.463620 GAGAAGAAGCCCATCTCGCT 59.536 55.000 0.00 0.00 38.53 4.93
3 4 0.531753 GGAGAAGAAGCCCATCTCGC 60.532 60.000 0.00 0.00 40.37 5.03
4 5 0.249238 CGGAGAAGAAGCCCATCTCG 60.249 60.000 0.00 0.00 40.37 4.04
6 7 1.977293 GCCGGAGAAGAAGCCCATCT 61.977 60.000 5.05 0.00 0.00 2.90
7 8 1.524849 GCCGGAGAAGAAGCCCATC 60.525 63.158 5.05 0.00 0.00 3.51
8 9 2.592308 GCCGGAGAAGAAGCCCAT 59.408 61.111 5.05 0.00 0.00 4.00
9 10 4.082523 CGCCGGAGAAGAAGCCCA 62.083 66.667 5.05 0.00 0.00 5.36
12 13 4.760047 TGGCGCCGGAGAAGAAGC 62.760 66.667 23.90 0.00 0.00 3.86
13 14 2.510238 CTGGCGCCGGAGAAGAAG 60.510 66.667 32.31 11.01 0.00 2.85
14 15 4.760047 GCTGGCGCCGGAGAAGAA 62.760 66.667 39.24 9.34 0.00 2.52
307 344 0.589223 CATCTCCTCGTACTCTCCGC 59.411 60.000 0.00 0.00 0.00 5.54
563 659 1.269517 ACGCGTCCACATTTGCATTTT 60.270 42.857 5.58 0.00 0.00 1.82
665 770 3.336715 GACCCATTTTGACGGCGCC 62.337 63.158 19.07 19.07 0.00 6.53
710 815 1.288752 CCGCTTCCGCATTTGGTTT 59.711 52.632 0.00 0.00 35.30 3.27
712 817 3.061848 CCCGCTTCCGCATTTGGT 61.062 61.111 0.00 0.00 35.30 3.67
737 842 2.443952 TGGATCGGCCAGACGGAT 60.444 61.111 2.24 0.00 43.33 4.18
751 856 0.382515 CCGCTTTTTGTCCGTTTGGA 59.617 50.000 0.00 0.00 43.88 3.53
1084 1200 0.316204 GCATCAAGGCTTGCTGTTGT 59.684 50.000 26.42 6.21 35.95 3.32
1233 1349 0.179134 CCGTAGCCTCGAAGAACCAG 60.179 60.000 0.00 0.00 34.09 4.00
1250 1366 3.134458 GGCTTATCATCAGGTTTCTCCG 58.866 50.000 0.00 0.00 41.99 4.63
1257 1373 3.370953 GGACAAGTGGCTTATCATCAGGT 60.371 47.826 0.00 0.00 0.00 4.00
1263 1379 3.780294 ACCATAGGACAAGTGGCTTATCA 59.220 43.478 0.00 0.00 36.47 2.15
1266 1382 5.765576 TTAACCATAGGACAAGTGGCTTA 57.234 39.130 0.00 0.00 36.47 3.09
1275 1391 5.505780 CAACCTCCATTTAACCATAGGACA 58.494 41.667 0.00 0.00 0.00 4.02
1324 1443 5.748630 ACGAAGTTTTCTGAATTTTCAAGGC 59.251 36.000 0.00 0.00 37.78 4.35
1354 1473 7.143340 TGTACGGCTACATTACATACATCTTC 58.857 38.462 0.00 0.00 0.00 2.87
1374 1495 0.366871 GCAAGAGCACACGATGTACG 59.633 55.000 0.00 0.00 43.83 3.67
1493 1615 0.748005 CTTGGTTCCAGGCATACGGG 60.748 60.000 0.00 0.00 35.52 5.28
1523 1645 7.362920 GGGGACATATGGCATGTTATTATTGAC 60.363 40.741 11.56 0.00 31.52 3.18
1524 1646 6.663093 GGGGACATATGGCATGTTATTATTGA 59.337 38.462 11.56 0.00 31.52 2.57
1528 1650 5.163045 TGTGGGGACATATGGCATGTTATTA 60.163 40.000 11.56 0.00 46.14 0.98
1530 1652 3.139957 TGTGGGGACATATGGCATGTTAT 59.860 43.478 11.56 0.00 46.14 1.89
1532 1654 1.287442 TGTGGGGACATATGGCATGTT 59.713 47.619 11.56 0.00 46.14 2.71
1533 1655 0.925558 TGTGGGGACATATGGCATGT 59.074 50.000 11.56 0.87 46.14 3.21
1534 1656 2.070305 TTGTGGGGACATATGGCATG 57.930 50.000 11.56 0.00 46.14 4.06
1535 1657 2.844654 TTTGTGGGGACATATGGCAT 57.155 45.000 11.56 4.88 46.14 4.40
1536 1658 2.612285 TTTTGTGGGGACATATGGCA 57.388 45.000 11.56 0.00 46.14 4.92
1607 1729 9.831737 GCTATACATGCTTCCATAGTTTTATTG 57.168 33.333 0.00 0.00 0.00 1.90
1608 1730 9.799106 AGCTATACATGCTTCCATAGTTTTATT 57.201 29.630 0.00 0.00 37.52 1.40
1609 1731 9.799106 AAGCTATACATGCTTCCATAGTTTTAT 57.201 29.630 0.00 0.00 46.39 1.40
1611 1733 9.057089 GTAAGCTATACATGCTTCCATAGTTTT 57.943 33.333 4.18 0.00 46.39 2.43
1612 1734 8.432805 AGTAAGCTATACATGCTTCCATAGTTT 58.567 33.333 4.18 0.35 46.39 2.66
1616 1738 7.303182 ACAGTAAGCTATACATGCTTCCATA 57.697 36.000 4.18 0.00 46.39 2.74
1641 1763 1.032014 GGCAGCTGAAAGTTCACCAA 58.968 50.000 20.43 0.00 35.30 3.67
1759 1881 1.079503 GAGGAAACGCATGTCTGTCC 58.920 55.000 0.00 0.00 0.00 4.02
1766 1888 3.797039 TGGATAGAAGAGGAAACGCATG 58.203 45.455 0.00 0.00 0.00 4.06
1770 1892 6.371548 TCATTGTTTGGATAGAAGAGGAAACG 59.628 38.462 0.00 0.00 0.00 3.60
1943 2068 9.456147 TCTGGAGTAGCTATCTATGAATAAGTC 57.544 37.037 0.00 0.00 0.00 3.01
1963 2088 5.888724 TGTGAGTTATAGAAGTCCTCTGGAG 59.111 44.000 2.57 0.00 34.54 3.86
1964 2089 5.827756 TGTGAGTTATAGAAGTCCTCTGGA 58.172 41.667 2.57 0.00 34.54 3.86
1965 2090 6.531503 TTGTGAGTTATAGAAGTCCTCTGG 57.468 41.667 2.57 0.00 34.54 3.86
1966 2091 9.442047 AATTTTGTGAGTTATAGAAGTCCTCTG 57.558 33.333 2.57 0.00 34.54 3.35
1973 2098 9.495754 GCAGCTTAATTTTGTGAGTTATAGAAG 57.504 33.333 0.00 0.00 0.00 2.85
1975 2100 7.609918 TGGCAGCTTAATTTTGTGAGTTATAGA 59.390 33.333 0.00 0.00 0.00 1.98
1976 2101 7.761409 TGGCAGCTTAATTTTGTGAGTTATAG 58.239 34.615 0.00 0.00 0.00 1.31
1977 2102 7.695480 TGGCAGCTTAATTTTGTGAGTTATA 57.305 32.000 0.00 0.00 0.00 0.98
1980 2105 4.935352 TGGCAGCTTAATTTTGTGAGTT 57.065 36.364 0.00 0.00 0.00 3.01
1984 2109 7.384660 TGAATAAGTTGGCAGCTTAATTTTGTG 59.615 33.333 24.45 0.00 32.92 3.33
1985 2110 7.441017 TGAATAAGTTGGCAGCTTAATTTTGT 58.559 30.769 24.45 7.26 32.92 2.83
1986 2111 7.887996 TGAATAAGTTGGCAGCTTAATTTTG 57.112 32.000 24.45 0.00 32.92 2.44
1988 2113 8.971073 ACTATGAATAAGTTGGCAGCTTAATTT 58.029 29.630 24.45 16.39 32.92 1.82
1989 2114 8.525290 ACTATGAATAAGTTGGCAGCTTAATT 57.475 30.769 24.45 18.42 32.92 1.40
1990 2115 8.408601 CAACTATGAATAAGTTGGCAGCTTAAT 58.591 33.333 24.45 17.93 46.52 1.40
1991 2116 7.761409 CAACTATGAATAAGTTGGCAGCTTAA 58.239 34.615 24.45 11.34 46.52 1.85
1992 2117 7.320443 CAACTATGAATAAGTTGGCAGCTTA 57.680 36.000 23.22 23.22 46.52 3.09
1993 2118 6.199937 CAACTATGAATAAGTTGGCAGCTT 57.800 37.500 20.41 20.41 46.52 3.74
1994 2119 5.824904 CAACTATGAATAAGTTGGCAGCT 57.175 39.130 0.00 0.00 46.52 4.24
2023 2188 9.582431 CAAAAGTCAGATCATGAGCAAAATTAT 57.418 29.630 14.38 0.00 39.07 1.28
2027 2192 5.010314 AGCAAAAGTCAGATCATGAGCAAAA 59.990 36.000 14.38 0.00 39.07 2.44
2056 2228 3.248602 GCGATCGAGTGGCAAGAAATTAT 59.751 43.478 21.57 0.00 0.00 1.28
2156 2329 2.787473 TGTACCAGGATGCCTTTGAG 57.213 50.000 0.00 0.00 31.97 3.02
2234 2481 6.264292 TCCCGATCTAGAATCAGAAGAAGAAG 59.736 42.308 0.00 0.00 0.00 2.85
2244 2491 1.001706 CGCGTTCCCGATCTAGAATCA 60.002 52.381 0.00 0.00 35.63 2.57
2498 2745 2.076622 CTCCGATGTTCGCCGAGGAT 62.077 60.000 0.00 0.00 38.82 3.24
2512 2759 1.228337 TTGGTCTGTCCGACTCCGA 60.228 57.895 0.00 0.00 42.44 4.55
2513 2760 1.080705 GTTGGTCTGTCCGACTCCG 60.081 63.158 4.32 0.00 44.97 4.63
2514 2761 1.080705 CGTTGGTCTGTCCGACTCC 60.081 63.158 9.21 1.20 45.93 3.85
2515 2762 1.080705 CCGTTGGTCTGTCCGACTC 60.081 63.158 9.21 0.00 45.93 3.36
2516 2763 3.048602 CCGTTGGTCTGTCCGACT 58.951 61.111 9.21 0.00 45.93 4.18
2517 2764 2.737376 GCCGTTGGTCTGTCCGAC 60.737 66.667 1.66 1.66 44.95 4.79
2560 2807 5.294060 GTGGCTGAAAATTTTGAAGCTGAAA 59.706 36.000 24.05 12.07 34.29 2.69
2574 2821 3.169908 GGGGGAAATAAGTGGCTGAAAA 58.830 45.455 0.00 0.00 0.00 2.29
2610 2878 5.693104 GTGCATGAAAAATCAATCACACTGT 59.307 36.000 0.00 0.00 0.00 3.55
2617 2885 6.774354 AACTGTGTGCATGAAAAATCAATC 57.226 33.333 0.00 0.00 0.00 2.67
2625 2893 4.022935 GGAGATCAAACTGTGTGCATGAAA 60.023 41.667 0.00 0.00 0.00 2.69
2629 2897 3.244665 TGAGGAGATCAAACTGTGTGCAT 60.245 43.478 0.00 0.00 34.02 3.96
2631 2899 2.771089 TGAGGAGATCAAACTGTGTGC 58.229 47.619 0.00 0.00 34.02 4.57
2750 3035 1.612463 GAGAACGTAGGGATACGGCAT 59.388 52.381 11.94 0.00 46.68 4.40
2758 3043 2.050350 CCGGCAGAGAACGTAGGGA 61.050 63.158 0.00 0.00 0.00 4.20
2784 3069 2.307098 AGGCAAACTCAGCTAGGTGAAT 59.693 45.455 23.89 13.15 0.00 2.57
2785 3070 1.699634 AGGCAAACTCAGCTAGGTGAA 59.300 47.619 23.89 9.49 0.00 3.18
2788 3076 1.059913 ACAGGCAAACTCAGCTAGGT 58.940 50.000 0.00 0.00 0.00 3.08
2804 3092 2.233271 ACACAATTCTGAGCCCAACAG 58.767 47.619 0.00 0.00 36.80 3.16
2807 3095 4.081198 ACAAAAACACAATTCTGAGCCCAA 60.081 37.500 0.00 0.00 0.00 4.12
2821 3109 6.364976 GCTATGAAATGGGTACACAAAAACAC 59.635 38.462 0.00 0.00 0.00 3.32
2852 3152 5.358442 ACACCACACAAGCAAAACTGTATAA 59.642 36.000 0.00 0.00 0.00 0.98
2857 3157 2.652941 ACACCACACAAGCAAAACTG 57.347 45.000 0.00 0.00 0.00 3.16
2858 3158 3.258123 AGAAACACCACACAAGCAAAACT 59.742 39.130 0.00 0.00 0.00 2.66
2865 3165 3.859386 GCTGAAAAGAAACACCACACAAG 59.141 43.478 0.00 0.00 0.00 3.16
2892 3192 0.110056 CTTCCACACAGCGTTGATGC 60.110 55.000 6.16 0.00 0.00 3.91
2997 3411 0.029035 CGACGTCGTAGGGATCCTTG 59.971 60.000 29.08 0.00 34.61 3.61
3107 3684 8.855110 TGCTCTTTTGTTCAGTTATCCAATTAA 58.145 29.630 0.00 0.00 0.00 1.40
3116 3693 5.290493 TCTCCTGCTCTTTTGTTCAGTTA 57.710 39.130 0.00 0.00 0.00 2.24
3119 3696 4.155644 GGATTCTCCTGCTCTTTTGTTCAG 59.844 45.833 0.00 0.00 32.53 3.02
3120 3697 4.074970 GGATTCTCCTGCTCTTTTGTTCA 58.925 43.478 0.00 0.00 32.53 3.18
3121 3698 3.441922 GGGATTCTCCTGCTCTTTTGTTC 59.558 47.826 0.00 0.00 36.57 3.18
3122 3699 3.181429 TGGGATTCTCCTGCTCTTTTGTT 60.181 43.478 0.00 0.00 36.57 2.83
3123 3700 2.376518 TGGGATTCTCCTGCTCTTTTGT 59.623 45.455 0.00 0.00 36.57 2.83
3124 3701 3.077484 TGGGATTCTCCTGCTCTTTTG 57.923 47.619 0.00 0.00 36.57 2.44
3125 3702 3.683847 CGATGGGATTCTCCTGCTCTTTT 60.684 47.826 0.00 0.00 36.57 2.27
3126 3703 2.158842 CGATGGGATTCTCCTGCTCTTT 60.159 50.000 0.00 0.00 36.57 2.52
3127 3704 1.415659 CGATGGGATTCTCCTGCTCTT 59.584 52.381 0.00 0.00 36.57 2.85
3128 3705 1.047002 CGATGGGATTCTCCTGCTCT 58.953 55.000 0.00 0.00 36.57 4.09
3129 3706 1.043816 TCGATGGGATTCTCCTGCTC 58.956 55.000 0.00 0.00 36.57 4.26
3130 3707 0.755686 GTCGATGGGATTCTCCTGCT 59.244 55.000 0.00 0.00 36.57 4.24
3131 3708 0.465705 TGTCGATGGGATTCTCCTGC 59.534 55.000 0.00 0.00 36.57 4.85
3132 3709 2.169352 ACTTGTCGATGGGATTCTCCTG 59.831 50.000 0.00 0.00 36.57 3.86
3133 3710 2.472029 ACTTGTCGATGGGATTCTCCT 58.528 47.619 0.00 0.00 36.57 3.69
3134 3711 2.990066 ACTTGTCGATGGGATTCTCC 57.010 50.000 0.00 0.00 35.23 3.71
3135 3712 3.385577 GCTACTTGTCGATGGGATTCTC 58.614 50.000 0.00 0.00 0.00 2.87
3136 3713 2.103263 GGCTACTTGTCGATGGGATTCT 59.897 50.000 0.00 0.00 0.00 2.40
3137 3714 2.484889 GGCTACTTGTCGATGGGATTC 58.515 52.381 0.00 0.00 0.00 2.52
3138 3715 1.141053 GGGCTACTTGTCGATGGGATT 59.859 52.381 0.00 0.00 0.00 3.01
3139 3716 0.759346 GGGCTACTTGTCGATGGGAT 59.241 55.000 0.00 0.00 0.00 3.85
3158 3735 7.750229 TGAGATTAATTAGCAGCCAATTAGG 57.250 36.000 6.19 0.00 41.84 2.69
3160 3737 8.922931 TGATGAGATTAATTAGCAGCCAATTA 57.077 30.769 2.20 2.20 0.00 1.40
3181 3758 8.574737 TGTGAGATAGTGTCATAAGATCTGATG 58.425 37.037 13.39 13.39 0.00 3.07
3417 4011 0.653636 AACGTGCGAATTGTGACGTT 59.346 45.000 10.68 10.68 46.99 3.99
3421 4015 0.589223 GGGAAACGTGCGAATTGTGA 59.411 50.000 0.00 0.00 0.00 3.58
3425 4019 1.253100 ATTGGGGAAACGTGCGAATT 58.747 45.000 0.00 0.00 0.00 2.17
3440 4034 3.181439 GGAGACCCCCTTGATCTTATTGG 60.181 52.174 0.00 0.00 0.00 3.16
3449 4043 1.565759 CATGAATGGAGACCCCCTTGA 59.434 52.381 0.00 0.00 0.00 3.02
3462 4056 2.874701 GAGACGGGTTGATCCATGAATG 59.125 50.000 0.00 0.00 38.11 2.67
3463 4057 2.158755 GGAGACGGGTTGATCCATGAAT 60.159 50.000 0.00 0.00 38.11 2.57
3466 4060 0.833287 AGGAGACGGGTTGATCCATG 59.167 55.000 0.00 0.00 38.11 3.66
3469 4063 1.739067 CAAAGGAGACGGGTTGATCC 58.261 55.000 0.00 0.00 0.00 3.36
3470 4064 1.087501 GCAAAGGAGACGGGTTGATC 58.912 55.000 0.00 0.00 0.00 2.92
3471 4065 0.693049 AGCAAAGGAGACGGGTTGAT 59.307 50.000 0.00 0.00 0.00 2.57
3472 4066 0.034896 GAGCAAAGGAGACGGGTTGA 59.965 55.000 0.00 0.00 0.00 3.18
3473 4067 0.035458 AGAGCAAAGGAGACGGGTTG 59.965 55.000 0.00 0.00 0.00 3.77
3474 4068 0.765510 AAGAGCAAAGGAGACGGGTT 59.234 50.000 0.00 0.00 0.00 4.11
3475 4069 0.321996 GAAGAGCAAAGGAGACGGGT 59.678 55.000 0.00 0.00 0.00 5.28
3476 4070 0.610687 AGAAGAGCAAAGGAGACGGG 59.389 55.000 0.00 0.00 0.00 5.28
3477 4071 2.732597 CGTAGAAGAGCAAAGGAGACGG 60.733 54.545 0.00 0.00 0.00 4.79
3478 4072 2.095161 ACGTAGAAGAGCAAAGGAGACG 60.095 50.000 0.00 0.00 0.00 4.18
3479 4073 3.057456 TGACGTAGAAGAGCAAAGGAGAC 60.057 47.826 0.00 0.00 0.00 3.36
3480 4074 3.057456 GTGACGTAGAAGAGCAAAGGAGA 60.057 47.826 0.00 0.00 0.00 3.71
3499 4105 3.260884 GGTTGATCAGGAACTACAGGTGA 59.739 47.826 0.00 0.00 36.02 4.02
3500 4106 3.261897 AGGTTGATCAGGAACTACAGGTG 59.738 47.826 0.00 0.00 36.02 4.00
3520 4126 3.370840 TGAAATCCATCCAAGACCAGG 57.629 47.619 0.00 0.00 0.00 4.45
3528 4135 4.996122 GTGTTTTGCAATGAAATCCATCCA 59.004 37.500 0.00 0.00 33.53 3.41
3639 4246 4.853743 GGCGACTGAAAAATAGCAAAAGAG 59.146 41.667 0.00 0.00 0.00 2.85
3640 4247 4.518970 AGGCGACTGAAAAATAGCAAAAGA 59.481 37.500 0.00 0.00 41.13 2.52
3660 4267 7.184800 ACGTTTTCCAAATAAATTTTCAGGC 57.815 32.000 0.00 0.00 0.00 4.85
3698 4305 4.240096 TCAAACGTTTTTACCCGCAAAAA 58.760 34.783 11.66 0.00 35.56 1.94
3699 4306 3.841643 TCAAACGTTTTTACCCGCAAAA 58.158 36.364 11.66 0.00 0.00 2.44
3700 4307 3.498927 TCAAACGTTTTTACCCGCAAA 57.501 38.095 11.66 0.00 0.00 3.68
3701 4308 3.498927 TTCAAACGTTTTTACCCGCAA 57.501 38.095 11.66 0.00 0.00 4.85
3702 4309 3.498927 TTTCAAACGTTTTTACCCGCA 57.501 38.095 11.66 0.00 0.00 5.69
3703 4310 4.043073 TGATTTCAAACGTTTTTACCCGC 58.957 39.130 11.66 0.00 0.00 6.13
3704 4311 4.441744 GGTGATTTCAAACGTTTTTACCCG 59.558 41.667 11.66 0.00 0.00 5.28
3705 4312 4.746115 GGGTGATTTCAAACGTTTTTACCC 59.254 41.667 21.00 21.00 37.46 3.69
3706 4313 4.441744 CGGGTGATTTCAAACGTTTTTACC 59.558 41.667 11.66 12.68 0.00 2.85
3707 4314 4.441744 CCGGGTGATTTCAAACGTTTTTAC 59.558 41.667 11.66 3.86 0.00 2.01
3708 4315 4.337555 TCCGGGTGATTTCAAACGTTTTTA 59.662 37.500 11.66 0.00 0.00 1.52
3709 4316 3.130693 TCCGGGTGATTTCAAACGTTTTT 59.869 39.130 11.66 0.00 0.00 1.94
3745 4352 2.944094 GCATGGTCCCCACTAAAACGAT 60.944 50.000 0.00 0.00 35.80 3.73
3748 4355 1.544246 GTGCATGGTCCCCACTAAAAC 59.456 52.381 0.00 0.00 35.80 2.43
3749 4356 1.427368 AGTGCATGGTCCCCACTAAAA 59.573 47.619 1.57 0.00 38.00 1.52
3750 4357 1.072266 AGTGCATGGTCCCCACTAAA 58.928 50.000 1.57 0.00 38.00 1.85
3752 4359 1.990424 CAGTGCATGGTCCCCACTA 59.010 57.895 3.06 0.00 37.70 2.74
3753 4360 2.759114 CAGTGCATGGTCCCCACT 59.241 61.111 0.00 0.00 40.22 4.00
3757 4379 2.048603 GGAAGCAGTGCATGGTCCC 61.049 63.158 19.20 4.89 39.18 4.46
3769 4391 2.172483 GAGTGGCTCGGAAGGAAGCA 62.172 60.000 0.00 0.00 0.00 3.91
3783 4405 2.093447 AGATAAGGCAGGAAACGAGTGG 60.093 50.000 0.00 0.00 0.00 4.00
3792 4414 3.034635 GTCCTCAAGAGATAAGGCAGGA 58.965 50.000 0.00 0.00 0.00 3.86
3812 4435 0.535553 GAGAGCTAGGGGACGATCGT 60.536 60.000 22.97 22.97 0.00 3.73
3815 4438 0.847373 TGAGAGAGCTAGGGGACGAT 59.153 55.000 0.00 0.00 0.00 3.73
3821 4444 3.243704 CGGAAAGAATGAGAGAGCTAGGG 60.244 52.174 0.00 0.00 0.00 3.53
3826 4449 3.130340 AGAGACGGAAAGAATGAGAGAGC 59.870 47.826 0.00 0.00 0.00 4.09
3837 4460 0.108424 CTGGGCAGAGAGACGGAAAG 60.108 60.000 0.00 0.00 0.00 2.62
3841 4465 1.403814 TATTCTGGGCAGAGAGACGG 58.596 55.000 0.00 0.00 38.88 4.79
3843 4467 3.576118 TGCTATATTCTGGGCAGAGAGAC 59.424 47.826 0.00 0.00 38.88 3.36
3885 4509 6.936335 TCAGATGCATAGTTTGTCTTGAGAAA 59.064 34.615 0.00 0.00 0.00 2.52
3907 4532 9.844790 TGTTTGCACTTGAGATTTATAAATCAG 57.155 29.630 30.52 23.30 45.59 2.90
3949 4576 5.407084 GTCAAAATTTGGAACCATTAACCCG 59.593 40.000 5.83 0.00 0.00 5.28
3961 4588 4.202101 ACATGTCTTGCGTCAAAATTTGGA 60.202 37.500 5.83 0.00 0.00 3.53
3974 4601 4.904154 GTGACGTTTTTAGACATGTCTTGC 59.096 41.667 32.14 16.43 40.93 4.01
4011 4638 4.436242 TGTTACTCTTGTCTAGCGGAAG 57.564 45.455 0.00 0.00 0.00 3.46
4018 4645 9.475620 TTCATAGATCCTTGTTACTCTTGTCTA 57.524 33.333 0.00 0.00 0.00 2.59
4057 4684 3.017442 GGATCCTCTACCCTGCAAAAAC 58.983 50.000 3.84 0.00 0.00 2.43
4058 4685 2.647299 TGGATCCTCTACCCTGCAAAAA 59.353 45.455 14.23 0.00 0.00 1.94
4059 4686 2.274542 TGGATCCTCTACCCTGCAAAA 58.725 47.619 14.23 0.00 0.00 2.44
4065 4692 5.361630 ACTATTCATGGATCCTCTACCCT 57.638 43.478 14.23 0.00 0.00 4.34
4135 4799 6.877322 ACTACTTTTGGTATTCATACGTTGCT 59.123 34.615 0.00 0.00 34.11 3.91
4136 4800 7.068692 ACTACTTTTGGTATTCATACGTTGC 57.931 36.000 0.00 0.00 34.11 4.17
4138 4802 9.538508 GGATACTACTTTTGGTATTCATACGTT 57.461 33.333 0.00 0.00 34.11 3.99
4181 4845 9.217223 CGTTGCTTGTATAATAAATGGTGTTAC 57.783 33.333 0.00 0.00 0.00 2.50
4182 4846 8.948145 ACGTTGCTTGTATAATAAATGGTGTTA 58.052 29.630 0.00 0.00 0.00 2.41
4183 4847 7.822658 ACGTTGCTTGTATAATAAATGGTGTT 58.177 30.769 0.00 0.00 0.00 3.32
4184 4848 7.385778 ACGTTGCTTGTATAATAAATGGTGT 57.614 32.000 0.00 0.00 0.00 4.16
4185 4849 9.381027 CATACGTTGCTTGTATAATAAATGGTG 57.619 33.333 0.00 0.00 31.52 4.17
4186 4850 9.332502 TCATACGTTGCTTGTATAATAAATGGT 57.667 29.630 0.00 0.00 31.52 3.55
4192 4856 9.984190 TGGTATTCATACGTTGCTTGTATAATA 57.016 29.630 0.00 0.00 34.11 0.98
4193 4857 8.896320 TGGTATTCATACGTTGCTTGTATAAT 57.104 30.769 0.00 0.00 34.11 1.28
4194 4858 8.719560 TTGGTATTCATACGTTGCTTGTATAA 57.280 30.769 0.00 0.00 34.11 0.98
4195 4859 8.719560 TTTGGTATTCATACGTTGCTTGTATA 57.280 30.769 0.00 0.00 34.11 1.47
4196 4860 7.618502 TTTGGTATTCATACGTTGCTTGTAT 57.381 32.000 0.00 0.00 34.11 2.29
4197 4861 7.173562 ACTTTTGGTATTCATACGTTGCTTGTA 59.826 33.333 0.00 0.00 34.11 2.41
4198 4862 5.950758 TTTGGTATTCATACGTTGCTTGT 57.049 34.783 0.00 0.00 34.11 3.16
4229 4893 1.576356 GCGCTAATCTCCTGTCAAGG 58.424 55.000 0.00 0.00 46.06 3.61
4241 4917 0.178068 ATTGACTGGGTCGCGCTAAT 59.822 50.000 5.56 0.00 34.95 1.73
4274 4950 2.094906 TGATTGGGACGTGACGAGTTAG 60.095 50.000 13.70 0.00 0.00 2.34
4320 4996 4.760047 GGCTGCACACCGTCCGAT 62.760 66.667 0.50 0.00 0.00 4.18
4324 5000 4.626081 ACTGGGCTGCACACCGTC 62.626 66.667 0.00 0.00 0.00 4.79
4327 5003 2.980233 GTGACTGGGCTGCACACC 60.980 66.667 0.00 0.00 32.96 4.16
4353 5034 2.922758 GCACGAACGTTCTCTCATCTGT 60.923 50.000 24.80 10.59 0.00 3.41
4366 5047 3.126171 TCCAAATTCATAAGGCACGAACG 59.874 43.478 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.