Multiple sequence alignment - TraesCS2D01G563000

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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 TraesCS2D01G563000 chr2D 100.000 2749 0 0 1 2749 634483439 634480691 0.000000e+00 5077.0
1 TraesCS2D01G563000 chr2D 89.150 682 44 10 1192 1867 634556415 634555758 0.000000e+00 822.0
2 TraesCS2D01G563000 chr2D 80.727 1183 119 61 681 1820 634575819 634574703 0.000000e+00 821.0
3 TraesCS2D01G563000 chr2D 81.327 1130 95 63 731 1822 634659086 634658035 0.000000e+00 811.0
4 TraesCS2D01G563000 chr2D 81.716 536 62 17 2246 2747 627647574 627647041 5.480000e-112 414.0
5 TraesCS2D01G563000 chr2D 77.000 900 61 66 60 866 634557618 634556772 5.560000e-102 381.0
6 TraesCS2D01G563000 chr2D 87.234 235 27 1 2516 2747 95280908 95280674 5.840000e-67 265.0
7 TraesCS2D01G563000 chr2D 79.211 380 30 25 296 646 634576182 634575823 4.610000e-53 219.0
8 TraesCS2D01G563000 chr2D 80.876 251 19 13 886 1136 634556654 634556433 1.310000e-38 171.0
9 TraesCS2D01G563000 chr2D 90.123 81 6 1 60 138 634659661 634659581 1.350000e-18 104.0
10 TraesCS2D01G563000 chr2A 84.075 2179 151 91 1 2070 778913724 778915815 0.000000e+00 1921.0
11 TraesCS2D01G563000 chr2A 87.570 1070 81 24 761 1822 778876134 778877159 0.000000e+00 1192.0
12 TraesCS2D01G563000 chr2A 89.260 689 37 11 1192 1867 778827458 778828122 0.000000e+00 828.0
13 TraesCS2D01G563000 chr2A 78.643 1489 142 99 404 1803 778788294 778789695 0.000000e+00 826.0
14 TraesCS2D01G563000 chr2A 81.752 1107 87 57 731 1822 778759802 778760808 0.000000e+00 819.0
15 TraesCS2D01G563000 chr2A 80.560 1142 120 59 57 1136 778826339 778827440 0.000000e+00 785.0
16 TraesCS2D01G563000 chr2A 88.085 235 25 1 2516 2747 758238500 758238734 2.700000e-70 276.0
17 TraesCS2D01G563000 chr2A 84.279 229 11 7 621 837 778875809 778876024 1.670000e-47 200.0
18 TraesCS2D01G563000 chr2A 84.500 200 19 7 240 428 778869853 778870051 1.300000e-43 187.0
19 TraesCS2D01G563000 chr2A 88.489 139 15 1 658 796 778814181 778814318 1.690000e-37 167.0
20 TraesCS2D01G563000 chr2A 74.336 339 41 22 291 617 778759438 778759742 4.840000e-18 102.0
21 TraesCS2D01G563000 chr2A 85.263 95 4 2 538 623 778870144 778870237 3.770000e-14 89.8
22 TraesCS2D01G563000 chr2A 97.368 38 1 0 1 38 778826307 778826344 6.350000e-07 65.8
23 TraesCS2D01G563000 chr2B 82.744 1669 114 74 1 1584 777522966 777521387 0.000000e+00 1327.0
24 TraesCS2D01G563000 chr2B 83.938 1351 103 48 509 1822 777549974 777548701 0.000000e+00 1188.0
25 TraesCS2D01G563000 chr2B 82.043 1175 107 51 681 1822 777619221 777618118 0.000000e+00 905.0
26 TraesCS2D01G563000 chr2B 83.229 954 71 49 886 1822 777659053 777658172 0.000000e+00 793.0
27 TraesCS2D01G563000 chr2B 81.867 739 45 41 731 1465 777635415 777634762 8.660000e-150 540.0
28 TraesCS2D01G563000 chr2B 83.240 358 28 17 2418 2743 23268837 23269194 1.600000e-77 300.0
29 TraesCS2D01G563000 chr2B 76.607 389 33 27 353 718 777607878 777607525 7.880000e-36 161.0
30 TraesCS2D01G563000 chr2B 77.199 307 26 21 353 646 777619500 777619225 3.690000e-29 139.0
31 TraesCS2D01G563000 chr2B 79.688 192 19 9 505 682 777659358 777659173 1.340000e-23 121.0
32 TraesCS2D01G563000 chr2B 94.915 59 3 0 60 118 777608285 777608227 2.910000e-15 93.5
33 TraesCS2D01G563000 chr3B 81.034 406 39 14 2366 2741 431054308 431053911 3.460000e-74 289.0
34 TraesCS2D01G563000 chr7B 88.412 233 24 1 2518 2747 156952955 156953187 7.500000e-71 278.0
35 TraesCS2D01G563000 chr7B 80.548 365 37 8 2416 2747 134209803 134210166 1.630000e-62 250.0
36 TraesCS2D01G563000 chr7A 81.967 366 31 9 2416 2747 171249685 171250049 7.500000e-71 278.0
37 TraesCS2D01G563000 chr6B 87.815 238 23 4 2516 2747 333514818 333515055 9.700000e-70 274.0
38 TraesCS2D01G563000 chr5B 87.660 235 25 3 2516 2747 24772194 24771961 1.250000e-68 270.0
39 TraesCS2D01G563000 chr5B 87.712 236 23 4 2516 2747 487452985 487453218 1.250000e-68 270.0
40 TraesCS2D01G563000 chr5B 77.679 224 39 7 2268 2482 487452674 487452895 2.870000e-25 126.0
41 TraesCS2D01G563000 chr4A 81.667 360 33 11 2416 2743 182918355 182918713 4.510000e-68 268.0
42 TraesCS2D01G563000 chr3D 86.864 236 27 2 2516 2747 523638262 523638027 7.550000e-66 261.0
43 TraesCS2D01G563000 chr3D 80.242 248 39 9 2243 2482 313973698 313973453 7.820000e-41 178.0
44 TraesCS2D01G563000 chr5D 80.495 364 34 10 2416 2743 556392458 556392820 7.600000e-61 244.0
45 TraesCS2D01G563000 chr5A 79.666 359 41 13 2416 2743 139508853 139509210 2.130000e-56 230.0
46 TraesCS2D01G563000 chr5A 88.095 84 9 1 2308 2390 129623003 129623086 6.270000e-17 99.0
47 TraesCS2D01G563000 chr3A 89.320 103 5 5 2416 2515 460863187 460863088 1.030000e-24 124.0
48 TraesCS2D01G563000 chr6D 79.710 138 20 7 2242 2372 437926541 437926677 2.910000e-15 93.5


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 TraesCS2D01G563000 chr2D 634480691 634483439 2748 True 5077.0 5077 100.000000 1 2749 1 chr2D.!!$R3 2748
1 TraesCS2D01G563000 chr2D 634574703 634576182 1479 True 520.0 821 79.969000 296 1820 2 chr2D.!!$R5 1524
2 TraesCS2D01G563000 chr2D 634555758 634557618 1860 True 458.0 822 82.342000 60 1867 3 chr2D.!!$R4 1807
3 TraesCS2D01G563000 chr2D 634658035 634659661 1626 True 457.5 811 85.725000 60 1822 2 chr2D.!!$R6 1762
4 TraesCS2D01G563000 chr2D 627647041 627647574 533 True 414.0 414 81.716000 2246 2747 1 chr2D.!!$R2 501
5 TraesCS2D01G563000 chr2A 778913724 778915815 2091 False 1921.0 1921 84.075000 1 2070 1 chr2A.!!$F4 2069
6 TraesCS2D01G563000 chr2A 778788294 778789695 1401 False 826.0 826 78.643000 404 1803 1 chr2A.!!$F2 1399
7 TraesCS2D01G563000 chr2A 778875809 778877159 1350 False 696.0 1192 85.924500 621 1822 2 chr2A.!!$F8 1201
8 TraesCS2D01G563000 chr2A 778826307 778828122 1815 False 559.6 828 89.062667 1 1867 3 chr2A.!!$F6 1866
9 TraesCS2D01G563000 chr2A 778759438 778760808 1370 False 460.5 819 78.044000 291 1822 2 chr2A.!!$F5 1531
10 TraesCS2D01G563000 chr2B 777521387 777522966 1579 True 1327.0 1327 82.744000 1 1584 1 chr2B.!!$R1 1583
11 TraesCS2D01G563000 chr2B 777548701 777549974 1273 True 1188.0 1188 83.938000 509 1822 1 chr2B.!!$R2 1313
12 TraesCS2D01G563000 chr2B 777634762 777635415 653 True 540.0 540 81.867000 731 1465 1 chr2B.!!$R3 734
13 TraesCS2D01G563000 chr2B 777618118 777619500 1382 True 522.0 905 79.621000 353 1822 2 chr2B.!!$R5 1469
14 TraesCS2D01G563000 chr2B 777658172 777659358 1186 True 457.0 793 81.458500 505 1822 2 chr2B.!!$R6 1317

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
867 1451 0.396556 GTCCTCAGGTCCTCCCTCTC 60.397 65.0 0.0 0.0 43.86 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 3052 0.034767 CTGGTGATGTGGCTCATGGT 60.035 55.0 6.8 0.0 36.83 3.55 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
346 474 0.946221 CGTGCTTGTCTGGACTGGAC 60.946 60.000 2.38 5.82 0.00 4.02
386 533 4.914983 TGCAAGATTCCATCCATCTATCC 58.085 43.478 0.00 0.00 30.35 2.59
395 542 1.665916 CCATCTATCCAGCACGGCG 60.666 63.158 4.80 4.80 33.14 6.46
463 667 2.348779 CGTTCGGTTTCCTTGGTAAACG 60.349 50.000 9.65 9.65 37.64 3.60
678 994 2.261671 CCGCGCCGGCTTCTATAT 59.738 61.111 26.68 0.00 41.17 0.86
679 995 1.509463 CCGCGCCGGCTTCTATATA 59.491 57.895 26.68 0.00 41.17 0.86
848 1432 1.092921 CGTCTCACTCTCTCCTCCCG 61.093 65.000 0.00 0.00 0.00 5.14
851 1435 0.750182 CTCACTCTCTCCTCCCGTCC 60.750 65.000 0.00 0.00 0.00 4.79
852 1436 1.208844 TCACTCTCTCCTCCCGTCCT 61.209 60.000 0.00 0.00 0.00 3.85
853 1437 0.750182 CACTCTCTCCTCCCGTCCTC 60.750 65.000 0.00 0.00 0.00 3.71
854 1438 1.208844 ACTCTCTCCTCCCGTCCTCA 61.209 60.000 0.00 0.00 0.00 3.86
855 1439 0.465460 CTCTCTCCTCCCGTCCTCAG 60.465 65.000 0.00 0.00 0.00 3.35
856 1440 1.454847 CTCTCCTCCCGTCCTCAGG 60.455 68.421 0.00 0.00 0.00 3.86
857 1441 2.218115 CTCTCCTCCCGTCCTCAGGT 62.218 65.000 0.00 0.00 0.00 4.00
858 1442 1.755008 CTCCTCCCGTCCTCAGGTC 60.755 68.421 0.00 0.00 0.00 3.85
859 1443 2.760385 CCTCCCGTCCTCAGGTCC 60.760 72.222 0.00 0.00 0.00 4.46
860 1444 2.360980 CTCCCGTCCTCAGGTCCT 59.639 66.667 0.00 0.00 0.00 3.85
861 1445 1.755008 CTCCCGTCCTCAGGTCCTC 60.755 68.421 0.00 0.00 0.00 3.71
862 1446 2.760385 CCCGTCCTCAGGTCCTCC 60.760 72.222 0.00 0.00 0.00 4.30
863 1447 2.760385 CCGTCCTCAGGTCCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
865 1449 1.755008 CGTCCTCAGGTCCTCCCTC 60.755 68.421 0.00 0.00 43.86 4.30
866 1450 1.700985 GTCCTCAGGTCCTCCCTCT 59.299 63.158 0.00 0.00 43.86 3.69
867 1451 0.396556 GTCCTCAGGTCCTCCCTCTC 60.397 65.000 0.00 0.00 43.86 3.20
868 1452 1.075600 CCTCAGGTCCTCCCTCTCC 60.076 68.421 0.00 0.00 43.86 3.71
869 1453 1.589399 CCTCAGGTCCTCCCTCTCCT 61.589 65.000 0.00 0.00 43.86 3.69
870 1454 1.227249 CTCAGGTCCTCCCTCTCCTA 58.773 60.000 0.00 0.00 43.86 2.94
871 1455 1.144913 CTCAGGTCCTCCCTCTCCTAG 59.855 61.905 0.00 0.00 43.86 3.02
1079 1834 4.069232 CCAAGCCTCCGACGCTGA 62.069 66.667 0.00 0.00 36.47 4.26
1158 1949 3.509137 TTCTCCGGCAAGCGACGTT 62.509 57.895 0.00 0.00 44.52 3.99
1174 1965 1.751536 CGTTCATACTGATGCGCGCA 61.752 55.000 38.27 38.27 32.62 6.09
1175 1966 0.042708 GTTCATACTGATGCGCGCAG 60.043 55.000 38.44 27.03 39.26 5.18
1206 2010 1.831652 CTGTGGTGACCAGGAGGGAC 61.832 65.000 3.58 0.00 41.15 4.46
1227 2031 1.566018 GGTGACCAAGAAGAACGGCG 61.566 60.000 4.80 4.80 0.00 6.46
1509 2328 4.379243 AGCCGGAACAGCAGGACG 62.379 66.667 5.05 0.00 33.08 4.79
1772 2626 2.152699 GGCGTCGTCATGTCAGTCG 61.153 63.158 0.00 0.00 0.00 4.18
1822 2676 2.140065 TTTATCATCGCAGCCTCGAG 57.860 50.000 5.13 5.13 42.14 4.04
1823 2677 0.315251 TTATCATCGCAGCCTCGAGG 59.685 55.000 27.83 27.83 42.14 4.63
1824 2678 1.527433 TATCATCGCAGCCTCGAGGG 61.527 60.000 32.06 17.85 42.14 4.30
1825 2679 3.531207 CATCGCAGCCTCGAGGGA 61.531 66.667 32.06 20.69 42.14 4.20
1830 2684 2.725008 CAGCCTCGAGGGATCGAC 59.275 66.667 32.06 14.63 37.20 4.20
1867 2722 1.344763 ACCTTACCAGTCTGCAGTGTC 59.655 52.381 14.67 5.94 0.00 3.67
1868 2723 1.344438 CCTTACCAGTCTGCAGTGTCA 59.656 52.381 14.67 0.00 0.00 3.58
1869 2724 2.408050 CTTACCAGTCTGCAGTGTCAC 58.592 52.381 14.67 4.21 0.00 3.67
1870 2725 0.679505 TACCAGTCTGCAGTGTCACC 59.320 55.000 14.67 0.00 0.00 4.02
1871 2726 1.337384 ACCAGTCTGCAGTGTCACCA 61.337 55.000 14.67 0.00 0.00 4.17
1874 2729 0.105593 AGTCTGCAGTGTCACCAGTG 59.894 55.000 14.67 0.00 43.62 3.66
1877 2732 0.462581 CTGCAGTGTCACCAGTGTGT 60.463 55.000 5.25 0.00 42.87 3.72
1883 2738 0.752658 TGTCACCAGTGTGTCTCCTG 59.247 55.000 0.00 0.00 43.26 3.86
1884 2739 1.040646 GTCACCAGTGTGTCTCCTGA 58.959 55.000 0.00 0.00 43.26 3.86
1912 2771 5.480073 AGGAATGTACTCATAGAGCTCCATC 59.520 44.000 10.93 0.00 31.79 3.51
1917 2776 3.088532 ACTCATAGAGCTCCATCGATCC 58.911 50.000 10.93 0.00 32.04 3.36
1920 2779 2.208132 TAGAGCTCCATCGATCCTCC 57.792 55.000 10.93 0.00 0.00 4.30
1922 2781 0.829602 GAGCTCCATCGATCCTCCCA 60.830 60.000 0.87 0.00 0.00 4.37
1940 2806 5.435291 CTCCCATTTCTTCTCATGCTTAGT 58.565 41.667 0.00 0.00 0.00 2.24
1958 2828 6.710295 TGCTTAGTTATAAATGATGTGGCGAT 59.290 34.615 0.00 0.00 0.00 4.58
1967 2837 3.724508 TGATGTGGCGATTGTTGTTTT 57.275 38.095 0.00 0.00 0.00 2.43
1970 2840 5.777802 TGATGTGGCGATTGTTGTTTTAAT 58.222 33.333 0.00 0.00 0.00 1.40
1982 2852 7.959689 TTGTTGTTTTAATCAATGGACCATG 57.040 32.000 8.02 2.69 0.00 3.66
1997 2867 2.099921 GACCATGATCAGTCGTGTAGCT 59.900 50.000 0.09 0.00 39.29 3.32
2005 2875 1.185618 AGTCGTGTAGCTGCAGGGAA 61.186 55.000 21.75 3.49 0.00 3.97
2011 2881 1.127343 GTAGCTGCAGGGAAGAGGAT 58.873 55.000 17.12 0.00 0.00 3.24
2022 2892 4.469945 CAGGGAAGAGGATGTAACTTGGTA 59.530 45.833 0.00 0.00 0.00 3.25
2023 2893 5.131142 CAGGGAAGAGGATGTAACTTGGTAT 59.869 44.000 0.00 0.00 0.00 2.73
2037 2907 8.428852 TGTAACTTGGTATGTGCAGTGATATAT 58.571 33.333 0.00 0.00 0.00 0.86
2049 2919 9.282569 TGTGCAGTGATATATTATATGTTTGCA 57.717 29.630 15.00 15.00 34.67 4.08
2070 2947 6.281405 TGCAATAAAATGGTTAAACGGTGTT 58.719 32.000 0.00 0.00 0.00 3.32
2071 2948 6.201044 TGCAATAAAATGGTTAAACGGTGTTG 59.799 34.615 0.00 0.00 0.00 3.33
2072 2949 6.585852 CAATAAAATGGTTAAACGGTGTTGC 58.414 36.000 0.00 0.00 0.00 4.17
2073 2950 4.394439 AAAATGGTTAAACGGTGTTGCT 57.606 36.364 0.00 0.00 0.00 3.91
2074 2951 3.636282 AATGGTTAAACGGTGTTGCTC 57.364 42.857 0.00 0.00 0.00 4.26
2075 2952 1.310904 TGGTTAAACGGTGTTGCTCC 58.689 50.000 0.00 0.00 0.00 4.70
2076 2953 1.310904 GGTTAAACGGTGTTGCTCCA 58.689 50.000 0.00 0.00 0.00 3.86
2077 2954 1.265905 GGTTAAACGGTGTTGCTCCAG 59.734 52.381 0.00 0.00 0.00 3.86
2078 2955 0.948678 TTAAACGGTGTTGCTCCAGC 59.051 50.000 0.00 0.00 42.50 4.85
2092 2969 4.419522 GCTCCAGCAAGAAAAATTACGA 57.580 40.909 0.00 0.00 41.59 3.43
2093 2970 4.794169 GCTCCAGCAAGAAAAATTACGAA 58.206 39.130 0.00 0.00 41.59 3.85
2094 2971 4.853743 GCTCCAGCAAGAAAAATTACGAAG 59.146 41.667 0.00 0.00 41.59 3.79
2095 2972 5.371115 TCCAGCAAGAAAAATTACGAAGG 57.629 39.130 0.00 0.00 0.00 3.46
2096 2973 5.067273 TCCAGCAAGAAAAATTACGAAGGA 58.933 37.500 0.00 0.00 0.00 3.36
2097 2974 5.533154 TCCAGCAAGAAAAATTACGAAGGAA 59.467 36.000 0.00 0.00 0.00 3.36
2098 2975 6.039941 TCCAGCAAGAAAAATTACGAAGGAAA 59.960 34.615 0.00 0.00 0.00 3.13
2099 2976 6.699642 CCAGCAAGAAAAATTACGAAGGAAAA 59.300 34.615 0.00 0.00 0.00 2.29
2100 2977 7.096065 CCAGCAAGAAAAATTACGAAGGAAAAG 60.096 37.037 0.00 0.00 0.00 2.27
2101 2978 7.647715 CAGCAAGAAAAATTACGAAGGAAAAGA 59.352 33.333 0.00 0.00 0.00 2.52
2102 2979 7.648112 AGCAAGAAAAATTACGAAGGAAAAGAC 59.352 33.333 0.00 0.00 0.00 3.01
2103 2980 7.434013 GCAAGAAAAATTACGAAGGAAAAGACA 59.566 33.333 0.00 0.00 0.00 3.41
2104 2981 9.463443 CAAGAAAAATTACGAAGGAAAAGACAT 57.537 29.630 0.00 0.00 0.00 3.06
2112 2989 9.751542 ATTACGAAGGAAAAGACATACTAGATG 57.248 33.333 0.00 0.00 0.00 2.90
2113 2990 7.171630 ACGAAGGAAAAGACATACTAGATGT 57.828 36.000 0.00 1.94 34.52 3.06
2114 2991 8.289939 ACGAAGGAAAAGACATACTAGATGTA 57.710 34.615 0.00 0.00 35.37 2.29
2115 2992 8.746530 ACGAAGGAAAAGACATACTAGATGTAA 58.253 33.333 0.00 0.00 34.45 2.41
2116 2993 9.582431 CGAAGGAAAAGACATACTAGATGTAAA 57.418 33.333 0.00 0.00 34.45 2.01
2134 3011 9.099454 AGATGTAAATTTATCTTGAACCGAGTC 57.901 33.333 0.31 0.00 29.64 3.36
2135 3012 7.605410 TGTAAATTTATCTTGAACCGAGTCC 57.395 36.000 0.31 0.00 0.00 3.85
2136 3013 5.796350 AAATTTATCTTGAACCGAGTCCG 57.204 39.130 0.00 0.00 0.00 4.79
2137 3014 3.947910 TTTATCTTGAACCGAGTCCGT 57.052 42.857 0.00 0.00 0.00 4.69
2138 3015 2.933495 TATCTTGAACCGAGTCCGTG 57.067 50.000 0.00 0.00 0.00 4.94
2139 3016 1.254026 ATCTTGAACCGAGTCCGTGA 58.746 50.000 0.00 0.00 0.00 4.35
2140 3017 1.254026 TCTTGAACCGAGTCCGTGAT 58.746 50.000 0.00 0.00 0.00 3.06
2141 3018 1.067846 TCTTGAACCGAGTCCGTGATG 60.068 52.381 0.00 0.00 0.00 3.07
2142 3019 0.669318 TTGAACCGAGTCCGTGATGC 60.669 55.000 0.00 0.00 0.00 3.91
2143 3020 1.080093 GAACCGAGTCCGTGATGCA 60.080 57.895 0.00 0.00 0.00 3.96
2144 3021 1.352156 GAACCGAGTCCGTGATGCAC 61.352 60.000 0.00 0.00 0.00 4.57
2145 3022 2.094757 AACCGAGTCCGTGATGCACA 62.095 55.000 0.00 0.00 33.40 4.57
2146 3023 2.094659 CCGAGTCCGTGATGCACAC 61.095 63.158 8.75 8.75 45.11 3.82
2154 3031 4.172625 TGATGCACACAACCCACC 57.827 55.556 0.00 0.00 0.00 4.61
2155 3032 1.530419 TGATGCACACAACCCACCC 60.530 57.895 0.00 0.00 0.00 4.61
2156 3033 2.203625 ATGCACACAACCCACCCC 60.204 61.111 0.00 0.00 0.00 4.95
2157 3034 2.992817 GATGCACACAACCCACCCCA 62.993 60.000 0.00 0.00 0.00 4.96
2158 3035 3.223589 GCACACAACCCACCCCAC 61.224 66.667 0.00 0.00 0.00 4.61
2159 3036 2.277072 CACACAACCCACCCCACA 59.723 61.111 0.00 0.00 0.00 4.17
2160 3037 2.124693 CACACAACCCACCCCACAC 61.125 63.158 0.00 0.00 0.00 3.82
2161 3038 2.277072 CACAACCCACCCCACACA 59.723 61.111 0.00 0.00 0.00 3.72
2162 3039 2.124693 CACAACCCACCCCACACAC 61.125 63.158 0.00 0.00 0.00 3.82
2163 3040 2.277072 CAACCCACCCCACACACA 59.723 61.111 0.00 0.00 0.00 3.72
2164 3041 2.124693 CAACCCACCCCACACACAC 61.125 63.158 0.00 0.00 0.00 3.82
2165 3042 3.707640 AACCCACCCCACACACACG 62.708 63.158 0.00 0.00 0.00 4.49
2168 3045 4.866224 CACCCCACACACACGCCA 62.866 66.667 0.00 0.00 0.00 5.69
2169 3046 4.868116 ACCCCACACACACGCCAC 62.868 66.667 0.00 0.00 0.00 5.01
2170 3047 4.866224 CCCCACACACACGCCACA 62.866 66.667 0.00 0.00 0.00 4.17
2171 3048 2.826287 CCCACACACACGCCACAA 60.826 61.111 0.00 0.00 0.00 3.33
2172 3049 2.715005 CCACACACACGCCACAAG 59.285 61.111 0.00 0.00 0.00 3.16
2173 3050 2.024588 CACACACACGCCACAAGC 59.975 61.111 0.00 0.00 38.52 4.01
2174 3051 2.437537 ACACACACGCCACAAGCA 60.438 55.556 0.00 0.00 44.04 3.91
2175 3052 2.043405 ACACACACGCCACAAGCAA 61.043 52.632 0.00 0.00 44.04 3.91
2176 3053 1.586042 CACACACGCCACAAGCAAC 60.586 57.895 0.00 0.00 44.04 4.17
2177 3054 2.026014 CACACGCCACAAGCAACC 59.974 61.111 0.00 0.00 44.04 3.77
2178 3055 2.439338 ACACGCCACAAGCAACCA 60.439 55.556 0.00 0.00 44.04 3.67
2179 3056 1.827789 ACACGCCACAAGCAACCAT 60.828 52.632 0.00 0.00 44.04 3.55
2180 3057 1.372004 CACGCCACAAGCAACCATG 60.372 57.895 0.00 0.00 44.04 3.66
2181 3058 1.528076 ACGCCACAAGCAACCATGA 60.528 52.632 0.00 0.00 44.04 3.07
2182 3059 1.210931 CGCCACAAGCAACCATGAG 59.789 57.895 0.00 0.00 44.04 2.90
2183 3060 1.080298 GCCACAAGCAACCATGAGC 60.080 57.895 0.00 0.00 42.97 4.26
2184 3061 1.588082 CCACAAGCAACCATGAGCC 59.412 57.895 0.00 0.00 0.00 4.70
2185 3062 1.180456 CCACAAGCAACCATGAGCCA 61.180 55.000 0.00 0.00 0.00 4.75
2186 3063 0.038892 CACAAGCAACCATGAGCCAC 60.039 55.000 0.00 0.00 0.00 5.01
2187 3064 0.467844 ACAAGCAACCATGAGCCACA 60.468 50.000 0.00 0.00 0.00 4.17
2188 3065 0.892755 CAAGCAACCATGAGCCACAT 59.107 50.000 0.00 0.00 40.17 3.21
2189 3066 1.135199 CAAGCAACCATGAGCCACATC 60.135 52.381 0.00 0.00 37.07 3.06
2190 3067 0.038599 AGCAACCATGAGCCACATCA 59.961 50.000 0.00 0.00 37.07 3.07
2191 3068 0.171903 GCAACCATGAGCCACATCAC 59.828 55.000 0.00 0.00 37.07 3.06
2192 3069 0.813184 CAACCATGAGCCACATCACC 59.187 55.000 0.00 0.00 37.07 4.02
2193 3070 0.405198 AACCATGAGCCACATCACCA 59.595 50.000 0.00 0.00 37.07 4.17
2194 3071 0.034767 ACCATGAGCCACATCACCAG 60.035 55.000 0.00 0.00 37.07 4.00
2195 3072 1.381928 CCATGAGCCACATCACCAGC 61.382 60.000 0.00 0.00 37.07 4.85
2196 3073 1.450848 ATGAGCCACATCACCAGCG 60.451 57.895 0.00 0.00 33.46 5.18
2197 3074 2.046892 GAGCCACATCACCAGCGT 60.047 61.111 0.00 0.00 0.00 5.07
2198 3075 1.672356 GAGCCACATCACCAGCGTT 60.672 57.895 0.00 0.00 0.00 4.84
2199 3076 1.639298 GAGCCACATCACCAGCGTTC 61.639 60.000 0.00 0.00 0.00 3.95
2200 3077 2.690778 GCCACATCACCAGCGTTCC 61.691 63.158 0.00 0.00 0.00 3.62
2201 3078 1.003355 CCACATCACCAGCGTTCCT 60.003 57.895 0.00 0.00 0.00 3.36
2202 3079 1.021390 CCACATCACCAGCGTTCCTC 61.021 60.000 0.00 0.00 0.00 3.71
2203 3080 1.021390 CACATCACCAGCGTTCCTCC 61.021 60.000 0.00 0.00 0.00 4.30
2204 3081 1.450312 CATCACCAGCGTTCCTCCC 60.450 63.158 0.00 0.00 0.00 4.30
2205 3082 1.918293 ATCACCAGCGTTCCTCCCA 60.918 57.895 0.00 0.00 0.00 4.37
2206 3083 2.185310 ATCACCAGCGTTCCTCCCAC 62.185 60.000 0.00 0.00 0.00 4.61
2207 3084 2.526873 ACCAGCGTTCCTCCCACT 60.527 61.111 0.00 0.00 0.00 4.00
2208 3085 2.046892 CCAGCGTTCCTCCCACTG 60.047 66.667 0.00 0.00 0.00 3.66
2209 3086 2.583441 CCAGCGTTCCTCCCACTGA 61.583 63.158 0.00 0.00 0.00 3.41
2210 3087 1.371183 CAGCGTTCCTCCCACTGAA 59.629 57.895 0.00 0.00 0.00 3.02
2211 3088 0.036010 CAGCGTTCCTCCCACTGAAT 60.036 55.000 0.00 0.00 0.00 2.57
2212 3089 0.036010 AGCGTTCCTCCCACTGAATG 60.036 55.000 0.00 0.00 0.00 2.67
2230 3107 1.405872 TGGAATGCCAGGATCATTGC 58.594 50.000 0.00 0.00 39.92 3.56
2231 3108 1.063492 TGGAATGCCAGGATCATTGCT 60.063 47.619 4.99 0.00 41.11 3.91
2232 3109 2.037144 GGAATGCCAGGATCATTGCTT 58.963 47.619 4.99 0.00 38.63 3.91
2233 3110 2.035576 GGAATGCCAGGATCATTGCTTC 59.964 50.000 4.99 6.16 38.63 3.86
2234 3111 2.750141 ATGCCAGGATCATTGCTTCT 57.250 45.000 4.99 0.00 0.00 2.85
2235 3112 2.519771 TGCCAGGATCATTGCTTCTT 57.480 45.000 4.99 0.00 0.00 2.52
2236 3113 2.372264 TGCCAGGATCATTGCTTCTTC 58.628 47.619 4.99 0.00 0.00 2.87
2237 3114 1.332997 GCCAGGATCATTGCTTCTTCG 59.667 52.381 0.00 0.00 0.00 3.79
2238 3115 2.910199 CCAGGATCATTGCTTCTTCGA 58.090 47.619 0.00 0.00 0.00 3.71
2239 3116 3.474600 CCAGGATCATTGCTTCTTCGAT 58.525 45.455 0.00 0.00 0.00 3.59
2240 3117 3.881688 CCAGGATCATTGCTTCTTCGATT 59.118 43.478 0.00 0.00 0.00 3.34
2241 3118 5.059161 CCAGGATCATTGCTTCTTCGATTA 58.941 41.667 0.00 0.00 0.00 1.75
2242 3119 5.704515 CCAGGATCATTGCTTCTTCGATTAT 59.295 40.000 0.00 0.00 0.00 1.28
2243 3120 6.206243 CCAGGATCATTGCTTCTTCGATTATT 59.794 38.462 0.00 0.00 0.00 1.40
2244 3121 7.296660 CAGGATCATTGCTTCTTCGATTATTC 58.703 38.462 0.00 0.00 0.00 1.75
2245 3122 6.146837 AGGATCATTGCTTCTTCGATTATTCG 59.853 38.462 0.57 0.57 46.87 3.34
2258 3135 0.800012 TTATTCGAGCAACCCAACGC 59.200 50.000 0.00 0.00 0.00 4.84
2262 3139 3.723348 GAGCAACCCAACGCGTCC 61.723 66.667 14.44 0.00 0.00 4.79
2265 3142 2.590575 CAACCCAACGCGTCCACT 60.591 61.111 14.44 0.00 0.00 4.00
2266 3143 2.184167 CAACCCAACGCGTCCACTT 61.184 57.895 14.44 0.00 0.00 3.16
2270 3147 0.236449 CCCAACGCGTCCACTTAAAC 59.764 55.000 14.44 0.00 0.00 2.01
2272 3149 0.111001 CAACGCGTCCACTTAAACGG 60.111 55.000 14.44 0.00 39.24 4.44
2278 3155 2.023223 TCCACTTAAACGGACGCGC 61.023 57.895 5.73 0.00 0.00 6.86
2279 3156 2.025418 CCACTTAAACGGACGCGCT 61.025 57.895 5.73 0.00 0.00 5.92
2280 3157 1.562575 CCACTTAAACGGACGCGCTT 61.563 55.000 5.73 0.00 0.00 4.68
2282 3159 0.233848 ACTTAAACGGACGCGCTTTG 59.766 50.000 5.73 0.00 0.00 2.77
2284 3161 0.656785 TTAAACGGACGCGCTTTGTT 59.343 45.000 5.73 3.03 0.00 2.83
2285 3162 0.232816 TAAACGGACGCGCTTTGTTC 59.767 50.000 5.73 0.00 0.00 3.18
2286 3163 2.689575 AAACGGACGCGCTTTGTTCG 62.690 55.000 5.73 12.28 43.92 3.95
2294 3171 3.234368 CGCTTTGTTCGCTTTGTGT 57.766 47.368 0.00 0.00 0.00 3.72
2295 3172 2.376915 CGCTTTGTTCGCTTTGTGTA 57.623 45.000 0.00 0.00 0.00 2.90
2296 3173 2.916111 CGCTTTGTTCGCTTTGTGTAT 58.084 42.857 0.00 0.00 0.00 2.29
2301 3179 5.683743 GCTTTGTTCGCTTTGTGTATGTTTA 59.316 36.000 0.00 0.00 0.00 2.01
2305 3183 5.049954 TGTTCGCTTTGTGTATGTTTAGGTC 60.050 40.000 0.00 0.00 0.00 3.85
2308 3186 3.425758 GCTTTGTGTATGTTTAGGTCGGC 60.426 47.826 0.00 0.00 0.00 5.54
2313 3191 1.615165 TATGTTTAGGTCGGCCGCCA 61.615 55.000 31.19 18.81 40.50 5.69
2320 3198 4.103103 GTCGGCCGCCAGCTTTTC 62.103 66.667 23.51 0.00 43.05 2.29
2323 3201 3.670377 GGCCGCCAGCTTTTCGTT 61.670 61.111 3.91 0.00 43.05 3.85
2352 3231 2.010582 TTTGTTTGGGTCGGCAGTGC 62.011 55.000 6.55 6.55 0.00 4.40
2373 3252 0.825840 CCCAACACACGGACCCATTT 60.826 55.000 0.00 0.00 0.00 2.32
2375 3254 1.000717 CCAACACACGGACCCATTTTC 60.001 52.381 0.00 0.00 0.00 2.29
2376 3255 1.678627 CAACACACGGACCCATTTTCA 59.321 47.619 0.00 0.00 0.00 2.69
2377 3256 1.314730 ACACACGGACCCATTTTCAC 58.685 50.000 0.00 0.00 0.00 3.18
2381 3260 1.302993 CGGACCCATTTTCACCCGT 60.303 57.895 0.00 0.00 33.02 5.28
2417 3296 6.535150 TGCCGTCATTTTTCAAACAAAATACA 59.465 30.769 0.00 0.00 35.09 2.29
2422 3301 9.424659 GTCATTTTTCAAACAAAATACAAGCAG 57.575 29.630 0.00 0.00 35.09 4.24
2439 3318 9.784531 ATACAAGCAGACAAATATAGCATAGTT 57.215 29.630 0.00 0.00 0.00 2.24
2447 3326 7.227512 AGACAAATATAGCATAGTTCACAAGCC 59.772 37.037 0.00 0.00 0.00 4.35
2545 3451 5.717119 CTTAACCAAATCATCTTGCAGCTT 58.283 37.500 0.00 0.00 0.00 3.74
2555 3461 5.005740 TCATCTTGCAGCTTAATGTGAGTT 58.994 37.500 0.00 0.00 0.00 3.01
2557 3463 5.362556 TCTTGCAGCTTAATGTGAGTTTC 57.637 39.130 0.00 0.00 0.00 2.78
2558 3464 5.065914 TCTTGCAGCTTAATGTGAGTTTCT 58.934 37.500 0.00 0.00 0.00 2.52
2585 3491 8.825745 CAATCATGCATTTGATGATGAAATTGA 58.174 29.630 5.34 0.00 39.21 2.57
2591 3497 9.389755 TGCATTTGATGATGAAATTGAATGAAT 57.610 25.926 0.00 0.00 0.00 2.57
2603 3509 6.601741 AATTGAATGAATTGTGCAAACGTT 57.398 29.167 0.00 0.00 32.69 3.99
2621 3527 3.797353 GCGGCCCCTCCATTCTCA 61.797 66.667 0.00 0.00 34.01 3.27
2636 3545 4.945543 CCATTCTCAGGAACATTGTCATCA 59.054 41.667 0.00 0.00 33.96 3.07
2658 3567 2.291930 TGGAACTGAAACCCTTGGTTGT 60.292 45.455 0.00 0.00 46.20 3.32
2668 3577 4.198028 ACCCTTGGTTGTAGATACGTTC 57.802 45.455 0.00 0.00 27.29 3.95
2674 3583 0.101040 TTGTAGATACGTTCCGGGCG 59.899 55.000 15.75 15.75 0.00 6.13
2677 3586 1.789078 TAGATACGTTCCGGGCGCTC 61.789 60.000 16.94 0.06 0.00 5.03
2680 3589 1.457823 ATACGTTCCGGGCGCTCATA 61.458 55.000 8.62 0.00 0.00 2.15
2681 3590 1.665264 TACGTTCCGGGCGCTCATAA 61.665 55.000 8.62 0.00 0.00 1.90
2683 3592 1.157870 CGTTCCGGGCGCTCATAATT 61.158 55.000 8.62 0.00 0.00 1.40
2726 3635 1.696336 ACACAAGCAGTCATCACCTCT 59.304 47.619 0.00 0.00 0.00 3.69
2735 3644 4.384056 CAGTCATCACCTCTCACAACTTT 58.616 43.478 0.00 0.00 0.00 2.66
2743 3652 2.223805 CCTCTCACAACTTTTTGGTGCC 60.224 50.000 0.00 0.00 36.69 5.01
2747 3656 0.829990 ACAACTTTTTGGTGCCCCAG 59.170 50.000 0.00 0.00 43.15 4.45
2748 3657 0.106521 CAACTTTTTGGTGCCCCAGG 59.893 55.000 0.00 0.00 43.15 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 182 0.944311 CGGATCGGCGTTAATGGAGG 60.944 60.000 6.85 0.00 0.00 4.30
145 184 1.593209 GCGGATCGGCGTTAATGGA 60.593 57.895 9.70 0.00 0.00 3.41
395 542 4.144703 GTTCTCGGTCCGCCCTCC 62.145 72.222 6.34 0.00 0.00 4.30
463 667 0.600057 AGTGTAGGACCGTTCGTTCC 59.400 55.000 0.61 0.61 0.00 3.62
677 993 7.724506 CGTCCAGTGGGTGTCCTATATATATAT 59.275 40.741 9.92 10.10 34.93 0.86
678 994 7.058525 CGTCCAGTGGGTGTCCTATATATATA 58.941 42.308 9.92 2.49 34.93 0.86
679 995 5.892119 CGTCCAGTGGGTGTCCTATATATAT 59.108 44.000 9.92 0.00 34.93 0.86
718 1035 1.202222 CGTGGCCTACTAGTGGTAACG 60.202 57.143 5.39 13.79 42.51 3.18
855 1439 1.074889 CTAGCTAGGAGAGGGAGGACC 59.925 61.905 13.32 0.00 40.67 4.46
856 1440 1.074889 CCTAGCTAGGAGAGGGAGGAC 59.925 61.905 32.79 0.00 46.63 3.85
857 1441 1.346675 ACCTAGCTAGGAGAGGGAGGA 60.347 57.143 40.40 0.00 46.63 3.71
858 1442 1.154430 ACCTAGCTAGGAGAGGGAGG 58.846 60.000 40.40 18.38 46.63 4.30
859 1443 4.668138 ATTACCTAGCTAGGAGAGGGAG 57.332 50.000 40.40 15.99 46.63 4.30
860 1444 4.742012 CAATTACCTAGCTAGGAGAGGGA 58.258 47.826 40.40 20.78 46.63 4.20
861 1445 3.259625 GCAATTACCTAGCTAGGAGAGGG 59.740 52.174 40.40 26.66 46.63 4.30
862 1446 3.259625 GGCAATTACCTAGCTAGGAGAGG 59.740 52.174 40.40 25.76 46.63 3.69
863 1447 4.156477 AGGCAATTACCTAGCTAGGAGAG 58.844 47.826 40.40 25.38 46.63 3.20
864 1448 4.200447 AGGCAATTACCTAGCTAGGAGA 57.800 45.455 40.40 28.24 46.63 3.71
1063 1818 2.169789 CATCAGCGTCGGAGGCTTG 61.170 63.158 21.47 14.80 37.20 4.01
1064 1819 2.185350 CATCAGCGTCGGAGGCTT 59.815 61.111 21.47 6.76 37.20 4.35
1065 1820 2.755876 TCATCAGCGTCGGAGGCT 60.756 61.111 18.69 18.69 40.34 4.58
1079 1834 0.392729 GAGTGGCTGCTCTTGCTCAT 60.393 55.000 0.00 0.00 40.48 2.90
1175 1966 2.180204 ACCACAGTTCAGCACACGC 61.180 57.895 0.00 0.00 38.99 5.34
1177 1968 0.657840 GTCACCACAGTTCAGCACAC 59.342 55.000 0.00 0.00 0.00 3.82
1178 1969 0.463654 GGTCACCACAGTTCAGCACA 60.464 55.000 0.00 0.00 0.00 4.57
1182 1980 0.758734 TCCTGGTCACCACAGTTCAG 59.241 55.000 0.00 0.00 34.16 3.02
1183 1981 0.758734 CTCCTGGTCACCACAGTTCA 59.241 55.000 0.00 0.00 34.16 3.18
1184 1982 0.035458 CCTCCTGGTCACCACAGTTC 59.965 60.000 0.00 0.00 34.16 3.01
1206 2010 0.949105 CCGTTCTTCTTGGTCACCGG 60.949 60.000 0.00 0.00 0.00 5.28
1227 2031 2.125753 CTGCTGACTCTGGCCGTC 60.126 66.667 0.00 0.00 0.00 4.79
1238 2048 4.318949 TTCGGCTGCTGCTGCTGA 62.319 61.111 31.10 31.10 44.83 4.26
1822 2676 0.824759 ACAACTAGCTGGTCGATCCC 59.175 55.000 2.06 0.00 34.77 3.85
1823 2677 2.271800 CAACAACTAGCTGGTCGATCC 58.728 52.381 2.06 0.00 0.00 3.36
1824 2678 1.661112 GCAACAACTAGCTGGTCGATC 59.339 52.381 2.06 0.00 0.00 3.69
1825 2679 1.276421 AGCAACAACTAGCTGGTCGAT 59.724 47.619 2.06 0.00 40.13 3.59
1830 2684 3.059352 AGGTAAGCAACAACTAGCTGG 57.941 47.619 0.00 0.00 41.70 4.85
1868 2723 0.470833 AGCTCAGGAGACACACTGGT 60.471 55.000 0.00 0.00 35.47 4.00
1869 2724 1.476085 CTAGCTCAGGAGACACACTGG 59.524 57.143 0.00 0.00 35.47 4.00
1870 2725 2.937469 CTAGCTCAGGAGACACACTG 57.063 55.000 0.00 0.00 36.07 3.66
1883 2738 5.710099 AGCTCTATGAGTACATTCCTAGCTC 59.290 44.000 0.00 0.00 37.87 4.09
1884 2739 5.640147 AGCTCTATGAGTACATTCCTAGCT 58.360 41.667 0.00 0.00 37.87 3.32
1902 2761 0.541764 GGGAGGATCGATGGAGCTCT 60.542 60.000 14.64 0.00 34.37 4.09
1903 2762 0.829602 TGGGAGGATCGATGGAGCTC 60.830 60.000 0.54 4.71 34.37 4.09
1912 2771 3.827008 TGAGAAGAAATGGGAGGATCG 57.173 47.619 0.00 0.00 34.37 3.69
1917 2776 5.435291 ACTAAGCATGAGAAGAAATGGGAG 58.565 41.667 0.00 0.00 0.00 4.30
1940 2806 7.094508 ACAACAATCGCCACATCATTTATAA 57.905 32.000 0.00 0.00 0.00 0.98
1958 2828 7.730084 TCATGGTCCATTGATTAAAACAACAA 58.270 30.769 0.00 0.00 0.00 2.83
1967 2837 5.163311 ACGACTGATCATGGTCCATTGATTA 60.163 40.000 0.00 5.33 0.00 1.75
1970 2840 2.501316 ACGACTGATCATGGTCCATTGA 59.499 45.455 0.00 4.12 0.00 2.57
1982 2852 1.554392 CTGCAGCTACACGACTGATC 58.446 55.000 0.00 0.00 35.90 2.92
1997 2867 2.551270 AGTTACATCCTCTTCCCTGCA 58.449 47.619 0.00 0.00 0.00 4.41
2005 2875 4.225042 TGCACATACCAAGTTACATCCTCT 59.775 41.667 0.00 0.00 0.00 3.69
2011 2881 4.344359 TCACTGCACATACCAAGTTACA 57.656 40.909 0.00 0.00 0.00 2.41
2023 2893 9.282569 TGCAAACATATAATATATCACTGCACA 57.717 29.630 12.16 0.00 30.52 4.57
2041 2911 7.442666 ACCGTTTAACCATTTTATTGCAAACAT 59.557 29.630 1.71 0.00 0.00 2.71
2042 2912 6.761714 ACCGTTTAACCATTTTATTGCAAACA 59.238 30.769 1.71 0.00 0.00 2.83
2043 2913 7.066505 CACCGTTTAACCATTTTATTGCAAAC 58.933 34.615 1.71 0.00 0.00 2.93
2044 2914 6.761714 ACACCGTTTAACCATTTTATTGCAAA 59.238 30.769 1.71 0.00 0.00 3.68
2046 2916 5.844004 ACACCGTTTAACCATTTTATTGCA 58.156 33.333 0.00 0.00 0.00 4.08
2047 2917 6.585852 CAACACCGTTTAACCATTTTATTGC 58.414 36.000 0.00 0.00 0.00 3.56
2048 2918 6.422400 AGCAACACCGTTTAACCATTTTATTG 59.578 34.615 0.00 0.00 0.00 1.90
2049 2919 6.517605 AGCAACACCGTTTAACCATTTTATT 58.482 32.000 0.00 0.00 0.00 1.40
2050 2920 6.091718 AGCAACACCGTTTAACCATTTTAT 57.908 33.333 0.00 0.00 0.00 1.40
2071 2948 4.419522 TCGTAATTTTTCTTGCTGGAGC 57.580 40.909 0.00 0.00 42.50 4.70
2072 2949 5.181245 TCCTTCGTAATTTTTCTTGCTGGAG 59.819 40.000 0.00 0.00 0.00 3.86
2073 2950 5.067273 TCCTTCGTAATTTTTCTTGCTGGA 58.933 37.500 0.00 0.00 0.00 3.86
2074 2951 5.371115 TCCTTCGTAATTTTTCTTGCTGG 57.629 39.130 0.00 0.00 0.00 4.85
2075 2952 7.647715 TCTTTTCCTTCGTAATTTTTCTTGCTG 59.352 33.333 0.00 0.00 0.00 4.41
2076 2953 7.648112 GTCTTTTCCTTCGTAATTTTTCTTGCT 59.352 33.333 0.00 0.00 0.00 3.91
2077 2954 7.434013 TGTCTTTTCCTTCGTAATTTTTCTTGC 59.566 33.333 0.00 0.00 0.00 4.01
2078 2955 8.850454 TGTCTTTTCCTTCGTAATTTTTCTTG 57.150 30.769 0.00 0.00 0.00 3.02
2086 2963 9.751542 CATCTAGTATGTCTTTTCCTTCGTAAT 57.248 33.333 0.00 0.00 0.00 1.89
2087 2964 8.746530 ACATCTAGTATGTCTTTTCCTTCGTAA 58.253 33.333 2.97 0.00 0.00 3.18
2088 2965 8.289939 ACATCTAGTATGTCTTTTCCTTCGTA 57.710 34.615 2.97 0.00 0.00 3.43
2089 2966 7.171630 ACATCTAGTATGTCTTTTCCTTCGT 57.828 36.000 2.97 0.00 0.00 3.85
2090 2967 9.582431 TTTACATCTAGTATGTCTTTTCCTTCG 57.418 33.333 10.02 0.00 33.76 3.79
2108 2985 9.099454 GACTCGGTTCAAGATAAATTTACATCT 57.901 33.333 0.00 0.00 32.85 2.90
2109 2986 8.336080 GGACTCGGTTCAAGATAAATTTACATC 58.664 37.037 0.00 0.00 0.00 3.06
2110 2987 7.011109 CGGACTCGGTTCAAGATAAATTTACAT 59.989 37.037 0.00 0.00 0.00 2.29
2111 2988 6.311935 CGGACTCGGTTCAAGATAAATTTACA 59.688 38.462 0.00 0.00 0.00 2.41
2112 2989 6.312180 ACGGACTCGGTTCAAGATAAATTTAC 59.688 38.462 0.00 0.00 41.39 2.01
2113 2990 6.311935 CACGGACTCGGTTCAAGATAAATTTA 59.688 38.462 0.00 0.00 41.39 1.40
2114 2991 5.121768 CACGGACTCGGTTCAAGATAAATTT 59.878 40.000 0.00 0.00 41.39 1.82
2115 2992 4.630069 CACGGACTCGGTTCAAGATAAATT 59.370 41.667 0.00 0.00 41.39 1.82
2116 2993 4.081862 TCACGGACTCGGTTCAAGATAAAT 60.082 41.667 0.00 0.00 41.39 1.40
2117 2994 3.256383 TCACGGACTCGGTTCAAGATAAA 59.744 43.478 0.00 0.00 41.39 1.40
2118 2995 2.821378 TCACGGACTCGGTTCAAGATAA 59.179 45.455 0.00 0.00 41.39 1.75
2119 2996 2.439409 TCACGGACTCGGTTCAAGATA 58.561 47.619 0.00 0.00 41.39 1.98
2120 2997 1.254026 TCACGGACTCGGTTCAAGAT 58.746 50.000 0.00 0.00 41.39 2.40
2121 2998 1.067846 CATCACGGACTCGGTTCAAGA 60.068 52.381 0.00 0.00 41.39 3.02
2122 2999 1.350193 CATCACGGACTCGGTTCAAG 58.650 55.000 0.00 0.00 41.39 3.02
2123 3000 0.669318 GCATCACGGACTCGGTTCAA 60.669 55.000 0.00 0.00 41.39 2.69
2124 3001 1.080093 GCATCACGGACTCGGTTCA 60.080 57.895 0.00 0.00 41.39 3.18
2125 3002 1.080093 TGCATCACGGACTCGGTTC 60.080 57.895 0.00 0.00 41.39 3.62
2126 3003 1.374252 GTGCATCACGGACTCGGTT 60.374 57.895 0.00 0.00 41.39 4.44
2127 3004 2.261671 GTGCATCACGGACTCGGT 59.738 61.111 0.00 0.00 41.39 4.69
2128 3005 2.094659 GTGTGCATCACGGACTCGG 61.095 63.158 0.00 0.00 41.39 4.63
2129 3006 3.463505 GTGTGCATCACGGACTCG 58.536 61.111 0.00 0.00 37.14 4.18
2136 3013 1.659794 GGTGGGTTGTGTGCATCAC 59.340 57.895 11.13 11.13 46.31 3.06
2137 3014 1.530419 GGGTGGGTTGTGTGCATCA 60.530 57.895 0.00 0.00 0.00 3.07
2138 3015 2.275380 GGGGTGGGTTGTGTGCATC 61.275 63.158 0.00 0.00 0.00 3.91
2139 3016 2.203625 GGGGTGGGTTGTGTGCAT 60.204 61.111 0.00 0.00 0.00 3.96
2140 3017 3.744155 TGGGGTGGGTTGTGTGCA 61.744 61.111 0.00 0.00 0.00 4.57
2141 3018 3.223589 GTGGGGTGGGTTGTGTGC 61.224 66.667 0.00 0.00 0.00 4.57
2142 3019 2.124693 GTGTGGGGTGGGTTGTGTG 61.125 63.158 0.00 0.00 0.00 3.82
2143 3020 2.277404 GTGTGGGGTGGGTTGTGT 59.723 61.111 0.00 0.00 0.00 3.72
2144 3021 2.124693 GTGTGTGGGGTGGGTTGTG 61.125 63.158 0.00 0.00 0.00 3.33
2145 3022 2.277404 GTGTGTGGGGTGGGTTGT 59.723 61.111 0.00 0.00 0.00 3.32
2146 3023 2.124693 GTGTGTGTGGGGTGGGTTG 61.125 63.158 0.00 0.00 0.00 3.77
2147 3024 2.277404 GTGTGTGTGGGGTGGGTT 59.723 61.111 0.00 0.00 0.00 4.11
2148 3025 4.183858 CGTGTGTGTGGGGTGGGT 62.184 66.667 0.00 0.00 0.00 4.51
2151 3028 4.866224 TGGCGTGTGTGTGGGGTG 62.866 66.667 0.00 0.00 0.00 4.61
2152 3029 4.868116 GTGGCGTGTGTGTGGGGT 62.868 66.667 0.00 0.00 0.00 4.95
2153 3030 4.866224 TGTGGCGTGTGTGTGGGG 62.866 66.667 0.00 0.00 0.00 4.96
2154 3031 2.826287 TTGTGGCGTGTGTGTGGG 60.826 61.111 0.00 0.00 0.00 4.61
2155 3032 2.715005 CTTGTGGCGTGTGTGTGG 59.285 61.111 0.00 0.00 0.00 4.17
2156 3033 2.024588 GCTTGTGGCGTGTGTGTG 59.975 61.111 0.00 0.00 0.00 3.82
2157 3034 2.043405 TTGCTTGTGGCGTGTGTGT 61.043 52.632 0.00 0.00 45.43 3.72
2158 3035 1.586042 GTTGCTTGTGGCGTGTGTG 60.586 57.895 0.00 0.00 45.43 3.82
2159 3036 2.770589 GGTTGCTTGTGGCGTGTGT 61.771 57.895 0.00 0.00 45.43 3.72
2160 3037 2.026014 GGTTGCTTGTGGCGTGTG 59.974 61.111 0.00 0.00 45.43 3.82
2161 3038 1.827789 ATGGTTGCTTGTGGCGTGT 60.828 52.632 0.00 0.00 45.43 4.49
2162 3039 1.372004 CATGGTTGCTTGTGGCGTG 60.372 57.895 0.00 0.00 45.43 5.34
2163 3040 1.518056 CTCATGGTTGCTTGTGGCGT 61.518 55.000 0.00 0.00 45.43 5.68
2164 3041 1.210931 CTCATGGTTGCTTGTGGCG 59.789 57.895 0.00 0.00 45.43 5.69
2165 3042 1.080298 GCTCATGGTTGCTTGTGGC 60.080 57.895 0.00 0.00 42.22 5.01
2166 3043 1.180456 TGGCTCATGGTTGCTTGTGG 61.180 55.000 0.00 0.00 0.00 4.17
2167 3044 0.038892 GTGGCTCATGGTTGCTTGTG 60.039 55.000 0.00 0.00 0.00 3.33
2168 3045 0.467844 TGTGGCTCATGGTTGCTTGT 60.468 50.000 0.00 0.00 0.00 3.16
2169 3046 0.892755 ATGTGGCTCATGGTTGCTTG 59.107 50.000 0.47 0.00 35.19 4.01
2170 3047 1.180029 GATGTGGCTCATGGTTGCTT 58.820 50.000 6.80 0.00 36.83 3.91
2171 3048 0.038599 TGATGTGGCTCATGGTTGCT 59.961 50.000 6.80 0.00 36.83 3.91
2172 3049 0.171903 GTGATGTGGCTCATGGTTGC 59.828 55.000 6.80 0.00 36.83 4.17
2173 3050 0.813184 GGTGATGTGGCTCATGGTTG 59.187 55.000 6.80 0.00 36.83 3.77
2174 3051 0.405198 TGGTGATGTGGCTCATGGTT 59.595 50.000 6.80 0.00 36.83 3.67
2175 3052 0.034767 CTGGTGATGTGGCTCATGGT 60.035 55.000 6.80 0.00 36.83 3.55
2176 3053 1.381928 GCTGGTGATGTGGCTCATGG 61.382 60.000 6.80 0.00 36.83 3.66
2177 3054 1.712018 CGCTGGTGATGTGGCTCATG 61.712 60.000 6.80 0.00 36.83 3.07
2178 3055 1.450848 CGCTGGTGATGTGGCTCAT 60.451 57.895 0.94 0.94 39.77 2.90
2179 3056 2.046988 CGCTGGTGATGTGGCTCA 60.047 61.111 0.00 0.00 0.00 4.26
2180 3057 1.639298 GAACGCTGGTGATGTGGCTC 61.639 60.000 0.00 0.00 0.00 4.70
2181 3058 1.672356 GAACGCTGGTGATGTGGCT 60.672 57.895 0.00 0.00 0.00 4.75
2182 3059 2.690778 GGAACGCTGGTGATGTGGC 61.691 63.158 0.00 0.00 0.00 5.01
2183 3060 1.003355 AGGAACGCTGGTGATGTGG 60.003 57.895 0.00 0.00 0.00 4.17
2184 3061 1.021390 GGAGGAACGCTGGTGATGTG 61.021 60.000 0.00 0.00 0.00 3.21
2185 3062 1.296715 GGAGGAACGCTGGTGATGT 59.703 57.895 0.00 0.00 0.00 3.06
2186 3063 1.450312 GGGAGGAACGCTGGTGATG 60.450 63.158 0.00 0.00 0.00 3.07
2187 3064 1.918293 TGGGAGGAACGCTGGTGAT 60.918 57.895 0.00 0.00 0.00 3.06
2188 3065 2.525629 TGGGAGGAACGCTGGTGA 60.526 61.111 0.00 0.00 0.00 4.02
2189 3066 2.358737 GTGGGAGGAACGCTGGTG 60.359 66.667 0.00 0.00 0.00 4.17
2190 3067 2.526873 AGTGGGAGGAACGCTGGT 60.527 61.111 0.00 0.00 0.00 4.00
2191 3068 2.046892 CAGTGGGAGGAACGCTGG 60.047 66.667 0.00 0.00 41.48 4.85
2192 3069 0.036010 ATTCAGTGGGAGGAACGCTG 60.036 55.000 0.00 0.00 45.34 5.18
2193 3070 0.036010 CATTCAGTGGGAGGAACGCT 60.036 55.000 0.00 0.00 0.00 5.07
2194 3071 1.026718 CCATTCAGTGGGAGGAACGC 61.027 60.000 0.00 0.00 44.79 4.84
2195 3072 3.159298 CCATTCAGTGGGAGGAACG 57.841 57.895 0.00 0.00 44.79 3.95
2204 3081 2.133281 TCCTGGCATTCCATTCAGTG 57.867 50.000 0.00 0.00 42.51 3.66
2205 3082 2.242965 TGATCCTGGCATTCCATTCAGT 59.757 45.455 0.00 0.00 42.51 3.41
2206 3083 2.940158 TGATCCTGGCATTCCATTCAG 58.060 47.619 0.00 0.00 42.51 3.02
2207 3084 3.605726 ATGATCCTGGCATTCCATTCA 57.394 42.857 0.00 0.00 42.51 2.57
2208 3085 3.554337 GCAATGATCCTGGCATTCCATTC 60.554 47.826 0.00 0.00 42.51 2.67
2209 3086 2.367567 GCAATGATCCTGGCATTCCATT 59.632 45.455 0.00 0.00 42.51 3.16
2210 3087 1.968493 GCAATGATCCTGGCATTCCAT 59.032 47.619 0.00 0.00 42.51 3.41
2211 3088 1.063492 AGCAATGATCCTGGCATTCCA 60.063 47.619 0.00 0.00 40.85 3.53
2212 3089 1.700955 AGCAATGATCCTGGCATTCC 58.299 50.000 0.00 0.00 33.93 3.01
2213 3090 2.957006 AGAAGCAATGATCCTGGCATTC 59.043 45.455 0.00 1.86 33.93 2.67
2214 3091 3.028094 AGAAGCAATGATCCTGGCATT 57.972 42.857 0.00 0.00 36.45 3.56
2215 3092 2.750141 AGAAGCAATGATCCTGGCAT 57.250 45.000 0.00 0.00 0.00 4.40
2216 3093 2.372264 GAAGAAGCAATGATCCTGGCA 58.628 47.619 0.00 0.00 0.00 4.92
2217 3094 1.332997 CGAAGAAGCAATGATCCTGGC 59.667 52.381 0.00 0.00 0.00 4.85
2218 3095 2.910199 TCGAAGAAGCAATGATCCTGG 58.090 47.619 0.00 0.00 0.00 4.45
2219 3096 6.798315 ATAATCGAAGAAGCAATGATCCTG 57.202 37.500 0.00 0.00 43.58 3.86
2220 3097 7.432350 GAATAATCGAAGAAGCAATGATCCT 57.568 36.000 0.00 0.00 43.58 3.24
2237 3114 2.538939 GCGTTGGGTTGCTCGAATAATC 60.539 50.000 0.00 0.00 0.00 1.75
2238 3115 1.400494 GCGTTGGGTTGCTCGAATAAT 59.600 47.619 0.00 0.00 0.00 1.28
2239 3116 0.800012 GCGTTGGGTTGCTCGAATAA 59.200 50.000 0.00 0.00 0.00 1.40
2240 3117 1.355796 CGCGTTGGGTTGCTCGAATA 61.356 55.000 0.00 0.00 0.00 1.75
2241 3118 2.677003 CGCGTTGGGTTGCTCGAAT 61.677 57.895 0.00 0.00 0.00 3.34
2242 3119 3.342627 CGCGTTGGGTTGCTCGAA 61.343 61.111 0.00 0.00 0.00 3.71
2243 3120 4.595538 ACGCGTTGGGTTGCTCGA 62.596 61.111 5.58 0.00 0.00 4.04
2244 3121 4.072088 GACGCGTTGGGTTGCTCG 62.072 66.667 15.53 0.00 0.00 5.03
2245 3122 3.723348 GGACGCGTTGGGTTGCTC 61.723 66.667 15.53 0.00 0.00 4.26
2246 3123 4.555709 TGGACGCGTTGGGTTGCT 62.556 61.111 15.53 0.00 0.00 3.91
2247 3124 4.322385 GTGGACGCGTTGGGTTGC 62.322 66.667 15.53 0.00 0.00 4.17
2248 3125 0.881159 TAAGTGGACGCGTTGGGTTG 60.881 55.000 15.53 0.00 0.00 3.77
2249 3126 0.179051 TTAAGTGGACGCGTTGGGTT 60.179 50.000 15.53 8.15 0.00 4.11
2250 3127 0.179051 TTTAAGTGGACGCGTTGGGT 60.179 50.000 15.53 0.40 0.00 4.51
2251 3128 0.236449 GTTTAAGTGGACGCGTTGGG 59.764 55.000 15.53 0.00 0.00 4.12
2253 3130 0.111001 CCGTTTAAGTGGACGCGTTG 60.111 55.000 15.53 0.00 37.91 4.10
2256 3133 1.777199 GTCCGTTTAAGTGGACGCG 59.223 57.895 3.53 3.53 44.68 6.01
2262 3139 0.233848 AAAGCGCGTCCGTTTAAGTG 59.766 50.000 8.43 0.00 36.88 3.16
2265 3142 0.656785 AACAAAGCGCGTCCGTTTAA 59.343 45.000 8.43 0.00 36.88 1.52
2266 3143 0.232816 GAACAAAGCGCGTCCGTTTA 59.767 50.000 8.43 0.00 36.88 2.01
2278 3155 6.359617 CCTAAACATACACAAAGCGAACAAAG 59.640 38.462 0.00 0.00 0.00 2.77
2279 3156 6.183360 ACCTAAACATACACAAAGCGAACAAA 60.183 34.615 0.00 0.00 0.00 2.83
2280 3157 5.297278 ACCTAAACATACACAAAGCGAACAA 59.703 36.000 0.00 0.00 0.00 2.83
2282 3159 5.352643 ACCTAAACATACACAAAGCGAAC 57.647 39.130 0.00 0.00 0.00 3.95
2284 3161 3.676172 CGACCTAAACATACACAAAGCGA 59.324 43.478 0.00 0.00 0.00 4.93
2285 3162 3.181524 CCGACCTAAACATACACAAAGCG 60.182 47.826 0.00 0.00 0.00 4.68
2286 3163 3.425758 GCCGACCTAAACATACACAAAGC 60.426 47.826 0.00 0.00 0.00 3.51
2287 3164 3.126343 GGCCGACCTAAACATACACAAAG 59.874 47.826 0.00 0.00 0.00 2.77
2291 3168 1.283736 CGGCCGACCTAAACATACAC 58.716 55.000 24.07 0.00 0.00 2.90
2293 3170 1.156034 GGCGGCCGACCTAAACATAC 61.156 60.000 33.48 5.78 0.00 2.39
2294 3171 1.144496 GGCGGCCGACCTAAACATA 59.856 57.895 33.48 0.00 0.00 2.29
2295 3172 2.124860 GGCGGCCGACCTAAACAT 60.125 61.111 33.48 0.00 0.00 2.71
2296 3173 3.599285 CTGGCGGCCGACCTAAACA 62.599 63.158 32.09 7.58 0.00 2.83
2308 3186 2.173382 CGAACGAAAAGCTGGCGG 59.827 61.111 7.82 0.00 0.00 6.13
2313 3191 0.818040 AACAGGGCGAACGAAAAGCT 60.818 50.000 0.00 0.00 0.00 3.74
2317 3195 1.473278 ACAAAAACAGGGCGAACGAAA 59.527 42.857 0.00 0.00 0.00 3.46
2318 3196 1.096416 ACAAAAACAGGGCGAACGAA 58.904 45.000 0.00 0.00 0.00 3.85
2320 3198 1.586123 CAAACAAAAACAGGGCGAACG 59.414 47.619 0.00 0.00 0.00 3.95
2323 3201 0.461961 CCCAAACAAAAACAGGGCGA 59.538 50.000 0.00 0.00 31.81 5.54
2360 3239 0.538746 GGGTGAAAATGGGTCCGTGT 60.539 55.000 0.00 0.00 0.00 4.49
2362 3241 1.302993 CGGGTGAAAATGGGTCCGT 60.303 57.895 0.00 0.00 33.63 4.69
2399 3278 9.160496 TGTCTGCTTGTATTTTGTTTGAAAAAT 57.840 25.926 1.08 1.08 41.45 1.82
2401 3280 8.539770 TTGTCTGCTTGTATTTTGTTTGAAAA 57.460 26.923 0.00 0.00 0.00 2.29
2417 3296 7.770433 TGTGAACTATGCTATATTTGTCTGCTT 59.230 33.333 0.00 0.00 0.00 3.91
2422 3301 7.012327 TGGCTTGTGAACTATGCTATATTTGTC 59.988 37.037 0.00 0.00 0.00 3.18
2432 3311 8.971321 CATATTTATTTGGCTTGTGAACTATGC 58.029 33.333 0.00 0.00 0.00 3.14
2439 3318 9.407380 ACTATGACATATTTATTTGGCTTGTGA 57.593 29.630 0.00 0.00 0.00 3.58
2524 3430 6.832520 TTAAGCTGCAAGATGATTTGGTTA 57.167 33.333 1.02 0.00 34.07 2.85
2527 3433 5.518847 CACATTAAGCTGCAAGATGATTTGG 59.481 40.000 1.02 0.00 34.07 3.28
2545 3451 7.634671 ATGCATGATTGAGAAACTCACATTA 57.365 32.000 0.00 0.00 40.46 1.90
2555 3461 7.341445 TCATCATCAAATGCATGATTGAGAA 57.659 32.000 16.64 9.29 38.67 2.87
2557 3463 8.593492 ATTTCATCATCAAATGCATGATTGAG 57.407 30.769 16.64 10.36 38.67 3.02
2558 3464 8.825745 CAATTTCATCATCAAATGCATGATTGA 58.174 29.630 14.53 14.53 38.67 2.57
2603 3509 3.797353 GAGAATGGAGGGGCCGCA 61.797 66.667 23.39 0.86 40.66 5.69
2606 3512 1.281925 TTCCTGAGAATGGAGGGGCC 61.282 60.000 0.00 0.00 34.76 5.80
2609 3515 3.285484 CAATGTTCCTGAGAATGGAGGG 58.715 50.000 0.00 0.00 34.76 4.30
2617 3523 4.225717 TCCATGATGACAATGTTCCTGAGA 59.774 41.667 0.00 0.00 0.00 3.27
2621 3527 4.703575 CAGTTCCATGATGACAATGTTCCT 59.296 41.667 0.00 0.00 0.00 3.36
2636 3545 2.965147 CAACCAAGGGTTTCAGTTCCAT 59.035 45.455 0.00 0.00 44.33 3.41
2668 3577 0.511221 CGTAAATTATGAGCGCCCGG 59.489 55.000 2.29 0.00 0.00 5.73
2674 3583 8.229811 TGCACAATATGATCGTAAATTATGAGC 58.770 33.333 3.72 3.72 0.00 4.26


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

AutoCloner maintained by Alex Coulton.