Multiple sequence alignment - TraesCS6A01G057000

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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 TraesCS6A01G057000 chr6A 100.000 4032 0 0 1 4032 29970435 29966404 0.000000e+00 7446.0
1 TraesCS6A01G057000 chr6A 85.227 880 98 19 1901 2770 29603909 29604766 0.000000e+00 876.0
2 TraesCS6A01G057000 chr6A 86.639 711 76 12 2092 2793 29887377 29886677 0.000000e+00 769.0
3 TraesCS6A01G057000 chr6A 88.778 401 44 1 2834 3233 29886376 29885976 1.300000e-134 490.0
4 TraesCS6A01G057000 chr6A 87.349 332 32 9 3346 3673 29885977 29885652 4.920000e-99 372.0
5 TraesCS6A01G057000 chr6A 82.009 428 49 16 1020 1435 30137002 30136591 4.990000e-89 339.0
6 TraesCS6A01G057000 chr6A 79.583 480 65 18 1006 1467 29495961 29496425 3.030000e-81 313.0
7 TraesCS6A01G057000 chr6A 75.948 686 117 34 1634 2298 30040869 30040211 3.910000e-80 309.0
8 TraesCS6A01G057000 chr6A 79.245 477 63 16 1018 1476 30041689 30041231 2.360000e-77 300.0
9 TraesCS6A01G057000 chr6A 83.533 334 39 11 3660 3990 29884940 29884620 8.470000e-77 298.0
10 TraesCS6A01G057000 chr6A 75.291 688 123 37 1630 2298 30136192 30135533 6.600000e-73 285.0
11 TraesCS6A01G057000 chr6A 87.342 79 6 3 1962 2036 30212212 30212134 2.000000e-13 87.9
12 TraesCS6A01G057000 chr6A 81.443 97 17 1 2206 2302 34030808 34030903 1.200000e-10 78.7
13 TraesCS6A01G057000 chr6D 94.646 1326 62 5 1629 2949 27860947 27862268 0.000000e+00 2047.0
14 TraesCS6A01G057000 chr6D 93.725 1004 54 5 2997 3998 27862269 27863265 0.000000e+00 1496.0
15 TraesCS6A01G057000 chr6D 89.914 813 40 17 831 1607 27859903 27860709 0.000000e+00 1009.0
16 TraesCS6A01G057000 chr6D 86.041 874 100 16 1901 2770 28303029 28302174 0.000000e+00 918.0
17 TraesCS6A01G057000 chr6D 85.692 643 67 18 3350 3987 27973993 27974615 0.000000e+00 654.0
18 TraesCS6A01G057000 chr6D 81.833 611 77 15 1016 1607 28305143 28304548 2.180000e-132 483.0
19 TraesCS6A01G057000 chr6D 87.531 401 49 1 2834 3233 27973592 27973992 2.840000e-126 462.0
20 TraesCS6A01G057000 chr6D 82.618 466 69 11 1630 2089 28304312 28303853 6.280000e-108 401.0
21 TraesCS6A01G057000 chr6D 80.591 474 62 13 1018 1476 27815757 27815299 4.990000e-89 339.0
22 TraesCS6A01G057000 chr6D 83.029 383 39 11 964 1340 27729316 27729678 1.400000e-84 324.0
23 TraesCS6A01G057000 chr6D 79.388 490 64 19 1006 1475 28411446 28410974 1.090000e-80 311.0
24 TraesCS6A01G057000 chr6D 80.126 317 40 10 2773 3087 28302068 28301773 8.780000e-52 215.0
25 TraesCS6A01G057000 chr6D 82.474 97 16 1 2206 2302 28656702 28656607 2.580000e-12 84.2
26 TraesCS6A01G057000 chr7D 95.208 793 13 8 1 768 65755980 65756772 0.000000e+00 1230.0
27 TraesCS6A01G057000 chr7D 96.000 75 3 0 32 106 7939469 7939395 5.470000e-24 122.0
28 TraesCS6A01G057000 chr2A 93.687 792 11 9 1 768 764305097 764304321 0.000000e+00 1149.0
29 TraesCS6A01G057000 chr2A 95.745 47 2 0 757 803 764304298 764304252 4.320000e-10 76.8
30 TraesCS6A01G057000 chr6B 82.055 613 70 17 1014 1607 52361273 52360682 1.680000e-133 486.0
31 TraesCS6A01G057000 chr6B 85.575 409 50 9 1630 2035 52360446 52360044 1.730000e-113 420.0
32 TraesCS6A01G057000 chr6B 80.442 588 81 19 1029 1601 51912421 51912989 6.230000e-113 418.0
33 TraesCS6A01G057000 chr6B 80.162 494 61 19 1005 1476 51611983 51612461 6.460000e-88 335.0
34 TraesCS6A01G057000 chr6B 76.462 684 117 30 1634 2298 51576842 51576184 8.350000e-87 331.0
35 TraesCS6A01G057000 chr6B 83.881 335 50 4 2773 3104 52358126 52357793 2.340000e-82 316.0
36 TraesCS6A01G057000 chr6B 81.766 351 56 6 3474 3822 52357675 52357331 1.830000e-73 287.0
37 TraesCS6A01G057000 chr6B 74.964 691 115 40 1630 2298 51612807 51613461 8.590000e-67 265.0
38 TraesCS6A01G057000 chr6B 88.776 196 20 2 1017 1211 76153341 76153147 5.210000e-59 239.0
39 TraesCS6A01G057000 chr6B 86.634 202 19 7 1901 2098 52359193 52358996 2.440000e-52 217.0
40 TraesCS6A01G057000 chr6B 80.000 125 19 6 2176 2299 62109325 62109444 2.000000e-13 87.9
41 TraesCS6A01G057000 chr6B 82.022 89 15 1 2214 2302 62127243 62127330 1.550000e-09 75.0
42 TraesCS6A01G057000 chrUn 77.388 513 79 21 1006 1498 286651815 286651320 1.850000e-68 270.0
43 TraesCS6A01G057000 chr3D 79.525 337 61 6 289 619 553237744 553238078 2.420000e-57 233.0
44 TraesCS6A01G057000 chr3D 96.396 111 3 1 1 111 22171274 22171165 8.900000e-42 182.0
45 TraesCS6A01G057000 chr3D 100.000 62 0 0 707 768 22171170 22171109 9.160000e-22 115.0
46 TraesCS6A01G057000 chr2D 79.228 337 62 6 289 619 378906760 378907094 1.130000e-55 228.0
47 TraesCS6A01G057000 chr2B 94.059 101 6 0 6 106 138659575 138659675 1.940000e-33 154.0
48 TraesCS6A01G057000 chr3A 96.296 54 2 0 1 54 68361312 68361259 5.550000e-14 89.8
49 TraesCS6A01G057000 chr5D 86.842 76 7 3 2708 2782 553770350 553770423 9.290000e-12 82.4
50 TraesCS6A01G057000 chr3B 87.931 58 6 1 746 803 52182989 52182933 2.600000e-07 67.6
51 TraesCS6A01G057000 chr5B 86.667 60 5 2 2736 2793 697028167 697028109 3.360000e-06 63.9
52 TraesCS6A01G057000 chr1B 100.000 32 0 0 4001 4032 502834441 502834410 4.350000e-05 60.2


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 TraesCS6A01G057000 chr6A 29966404 29970435 4031 True 7446.000000 7446 100.000000 1 4032 1 chr6A.!!$R1 4031
1 TraesCS6A01G057000 chr6A 29603909 29604766 857 False 876.000000 876 85.227000 1901 2770 1 chr6A.!!$F2 869
2 TraesCS6A01G057000 chr6A 29884620 29887377 2757 True 482.250000 769 86.574750 2092 3990 4 chr6A.!!$R3 1898
3 TraesCS6A01G057000 chr6A 30135533 30137002 1469 True 312.000000 339 78.650000 1020 2298 2 chr6A.!!$R5 1278
4 TraesCS6A01G057000 chr6A 30040211 30041689 1478 True 304.500000 309 77.596500 1018 2298 2 chr6A.!!$R4 1280
5 TraesCS6A01G057000 chr6D 27859903 27863265 3362 False 1517.333333 2047 92.761667 831 3998 3 chr6D.!!$F2 3167
6 TraesCS6A01G057000 chr6D 27973592 27974615 1023 False 558.000000 654 86.611500 2834 3987 2 chr6D.!!$F3 1153
7 TraesCS6A01G057000 chr6D 28301773 28305143 3370 True 504.250000 918 82.654500 1016 3087 4 chr6D.!!$R4 2071
8 TraesCS6A01G057000 chr7D 65755980 65756772 792 False 1230.000000 1230 95.208000 1 768 1 chr7D.!!$F1 767
9 TraesCS6A01G057000 chr2A 764304252 764305097 845 True 612.900000 1149 94.716000 1 803 2 chr2A.!!$R1 802
10 TraesCS6A01G057000 chr6B 51912421 51912989 568 False 418.000000 418 80.442000 1029 1601 1 chr6B.!!$F1 572
11 TraesCS6A01G057000 chr6B 52357331 52361273 3942 True 345.200000 486 83.982200 1014 3822 5 chr6B.!!$R3 2808
12 TraesCS6A01G057000 chr6B 51576184 51576842 658 True 331.000000 331 76.462000 1634 2298 1 chr6B.!!$R1 664
13 TraesCS6A01G057000 chr6B 51611983 51613461 1478 False 300.000000 335 77.563000 1005 2298 2 chr6B.!!$F4 1293

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
914 974 0.776810 TCCAATGGGCCTGACTTCAA 59.223 50.0 4.53 0.0 0.0 2.69 F
1611 1752 0.321996 GGAACTCCCCTGACAGTGAC 59.678 60.0 0.00 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2595 0.321564 ACTTACAGAGCGCCATTGCA 60.322 50.0 2.29 0.0 37.32 4.08 R
3320 6123 0.034756 ACGCACATGACAGTAAGCCA 59.965 50.0 0.00 0.0 0.00 4.75 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
243 245 1.133790 GTCGTATCGTACCTGGTTGCT 59.866 52.381 3.84 0.00 0.00 3.91
803 863 2.608090 GTGCACTACGAAGGATTTAGGC 59.392 50.000 10.32 0.00 0.00 3.93
804 864 2.500098 TGCACTACGAAGGATTTAGGCT 59.500 45.455 0.00 0.00 0.00 4.58
805 865 3.124560 GCACTACGAAGGATTTAGGCTC 58.875 50.000 0.00 0.00 0.00 4.70
806 866 3.181474 GCACTACGAAGGATTTAGGCTCT 60.181 47.826 0.00 0.00 0.00 4.09
807 867 4.680975 GCACTACGAAGGATTTAGGCTCTT 60.681 45.833 0.00 0.00 0.00 2.85
808 868 5.420409 CACTACGAAGGATTTAGGCTCTTT 58.580 41.667 0.00 0.00 0.00 2.52
809 869 5.875359 CACTACGAAGGATTTAGGCTCTTTT 59.125 40.000 0.00 0.00 0.00 2.27
810 870 6.371825 CACTACGAAGGATTTAGGCTCTTTTT 59.628 38.462 0.00 0.00 0.00 1.94
871 931 7.164230 TGAGAAAAAGGAAGCAAACAAGTAA 57.836 32.000 0.00 0.00 0.00 2.24
877 937 4.270008 AGGAAGCAAACAAGTAAGTGTGT 58.730 39.130 0.00 0.00 0.00 3.72
880 940 4.273005 AGCAAACAAGTAAGTGTGTTCG 57.727 40.909 0.00 0.00 36.97 3.95
889 949 1.101049 AAGTGTGTTCGTGGGCCTTG 61.101 55.000 4.53 0.00 0.00 3.61
895 955 1.029681 GTTCGTGGGCCTTGTTTCTT 58.970 50.000 4.53 0.00 0.00 2.52
905 965 1.276138 CCTTGTTTCTTCCAATGGGCC 59.724 52.381 0.00 0.00 0.00 5.80
914 974 0.776810 TCCAATGGGCCTGACTTCAA 59.223 50.000 4.53 0.00 0.00 2.69
923 983 3.465871 GGCCTGACTTCAATCTCATCTC 58.534 50.000 0.00 0.00 0.00 2.75
947 1017 4.753662 TCGCCTAGGTCACCCGCT 62.754 66.667 11.31 0.00 35.12 5.52
948 1018 3.771160 CGCCTAGGTCACCCGCTT 61.771 66.667 11.31 0.00 35.12 4.68
956 1026 1.527380 GTCACCCGCTTTCCAACCA 60.527 57.895 0.00 0.00 0.00 3.67
958 1028 1.826054 CACCCGCTTTCCAACCACA 60.826 57.895 0.00 0.00 0.00 4.17
959 1029 1.528309 ACCCGCTTTCCAACCACAG 60.528 57.895 0.00 0.00 0.00 3.66
960 1030 2.644992 CCGCTTTCCAACCACAGC 59.355 61.111 0.00 0.00 0.00 4.40
962 1032 3.432186 GCTTTCCAACCACAGCGT 58.568 55.556 0.00 0.00 0.00 5.07
987 1057 3.064324 GCGGCTGCTTCACCCATT 61.064 61.111 11.21 0.00 38.39 3.16
988 1058 2.879907 CGGCTGCTTCACCCATTG 59.120 61.111 0.00 0.00 0.00 2.82
992 1062 2.283821 TGCTTCACCCATTGCCCC 60.284 61.111 0.00 0.00 0.00 5.80
1001 1071 4.528039 CATTGCCCCCTCCCGCAT 62.528 66.667 0.00 0.00 34.35 4.73
1002 1072 4.528039 ATTGCCCCCTCCCGCATG 62.528 66.667 0.00 0.00 34.35 4.06
1156 1245 4.148825 CCTCCGACCCAGCCTTCG 62.149 72.222 0.00 0.00 34.93 3.79
1203 1292 3.189770 AAACCCTCCCCTCCTCGGT 62.190 63.158 0.00 0.00 0.00 4.69
1239 1328 3.387947 GACGGGCTCCCCTTCGAA 61.388 66.667 0.00 0.00 42.67 3.71
1243 1332 2.269241 GGCTCCCCTTCGAACCTG 59.731 66.667 0.00 0.00 0.00 4.00
1498 1615 1.371558 GGCGAGGTTCACTTCCAGT 59.628 57.895 0.00 0.00 0.00 4.00
1501 1618 1.797025 CGAGGTTCACTTCCAGTTCC 58.203 55.000 0.00 0.00 0.00 3.62
1502 1619 1.070134 CGAGGTTCACTTCCAGTTCCA 59.930 52.381 0.00 0.00 0.00 3.53
1503 1620 2.772287 GAGGTTCACTTCCAGTTCCAG 58.228 52.381 0.00 0.00 0.00 3.86
1504 1621 1.421646 AGGTTCACTTCCAGTTCCAGG 59.578 52.381 0.00 0.00 0.00 4.45
1506 1623 2.495084 GTTCACTTCCAGTTCCAGGTC 58.505 52.381 0.00 0.00 0.00 3.85
1522 1642 3.428999 CCAGGTCGTCGTGTCAGATTATT 60.429 47.826 1.95 0.00 0.00 1.40
1578 1719 3.679083 CGTGGGGTTCTCTAATCTCAACC 60.679 52.174 0.00 0.00 38.07 3.77
1611 1752 0.321996 GGAACTCCCCTGACAGTGAC 59.678 60.000 0.00 0.00 0.00 3.67
1612 1753 1.048601 GAACTCCCCTGACAGTGACA 58.951 55.000 0.00 0.00 0.00 3.58
1614 1755 1.122019 ACTCCCCTGACAGTGACACC 61.122 60.000 0.84 0.00 0.00 4.16
1615 1756 1.074850 TCCCCTGACAGTGACACCA 60.075 57.895 0.84 0.00 0.00 4.17
1619 1760 1.410850 CCTGACAGTGACACCAGGGT 61.411 60.000 17.24 5.71 41.76 4.34
1620 1761 0.469917 CTGACAGTGACACCAGGGTT 59.530 55.000 0.84 0.00 0.00 4.11
1621 1762 0.468226 TGACAGTGACACCAGGGTTC 59.532 55.000 0.84 0.00 0.00 3.62
1622 1763 0.600255 GACAGTGACACCAGGGTTCG 60.600 60.000 0.84 0.00 0.00 3.95
1624 1765 2.032071 GTGACACCAGGGTTCGGG 59.968 66.667 0.00 0.00 0.00 5.14
1626 1767 1.766864 TGACACCAGGGTTCGGGAA 60.767 57.895 0.00 0.00 32.37 3.97
1627 1768 1.302271 GACACCAGGGTTCGGGAAC 60.302 63.158 2.95 2.95 40.45 3.62
1700 2063 2.230660 GGGAAGAACTGTTGAACTGGG 58.769 52.381 7.13 0.00 0.00 4.45
1708 2071 1.410153 CTGTTGAACTGGGCAAGCTTT 59.590 47.619 0.00 0.00 0.00 3.51
1725 2088 6.183360 GCAAGCTTTTCTCTATGGATTCACAT 60.183 38.462 0.00 0.00 34.90 3.21
1749 2112 6.177610 TGATTTCTTGACCATACAAGGGTAC 58.822 40.000 0.00 0.00 44.84 3.34
1893 2259 5.047164 TGAAACCGTCTATGCTACAGGTAAA 60.047 40.000 0.00 0.00 0.00 2.01
1894 2260 5.410355 AACCGTCTATGCTACAGGTAAAA 57.590 39.130 0.00 0.00 0.00 1.52
1919 2285 1.172180 TGCCTTTGCACTGCTGGTAC 61.172 55.000 1.98 0.00 44.23 3.34
1954 2494 9.965824 CAAGTTACTTTTGATAATTGGTTCTGT 57.034 29.630 0.00 0.00 0.00 3.41
2249 3706 5.475909 CCTGCCTATTGACATATGCAAGAAT 59.524 40.000 14.81 6.55 36.44 2.40
2462 4762 8.682936 AAGACTAGATTTGTCATTGAAACTGT 57.317 30.769 0.00 0.00 36.94 3.55
2522 4822 4.024218 GTGACATGATATGCTTGAAGGAGC 60.024 45.833 0.00 0.00 43.00 4.70
2544 4845 3.250762 CACTCCGAGCTTTGTTTTGATGA 59.749 43.478 0.00 0.00 0.00 2.92
2662 4964 9.787435 TGTTAAATTCAAGTAGTTGGTGACTAT 57.213 29.630 10.39 0.00 42.57 2.12
2687 4989 8.754230 TCGAGCTCATATATTTCTGAAAGATG 57.246 34.615 17.87 14.95 46.36 2.90
2706 5008 3.194005 TGTGCCTATTAGCTAACCTGC 57.806 47.619 8.70 11.60 0.00 4.85
2822 5330 4.021894 GTGCCATTACACCACAAATTACCA 60.022 41.667 0.00 0.00 34.35 3.25
2828 5336 2.884639 ACACCACAAATTACCAGCTGAC 59.115 45.455 17.39 0.00 0.00 3.51
2887 5562 4.556233 CGAGATGACTGAACTTTGGTGTA 58.444 43.478 0.00 0.00 0.00 2.90
2979 5654 1.734465 CTTCAGCGTCTTTCCATGGAC 59.266 52.381 15.91 2.03 0.00 4.02
2989 5664 5.903810 GTCTTTCCATGGACGAATAGTACT 58.096 41.667 15.91 0.00 33.83 2.73
3003 5698 7.039882 ACGAATAGTACTAATGGTTTGACTGG 58.960 38.462 6.70 0.00 0.00 4.00
3006 5701 5.562298 AGTACTAATGGTTTGACTGGTGT 57.438 39.130 0.00 0.00 0.00 4.16
3008 5703 3.399330 ACTAATGGTTTGACTGGTGTCG 58.601 45.455 0.00 0.00 45.70 4.35
3015 5710 3.303791 GGTTTGACTGGTGTCGTTGATTC 60.304 47.826 0.00 0.00 45.70 2.52
3045 5740 5.992217 CAGGTACCTAGATTTGTATTCTGGC 59.008 44.000 15.80 0.00 0.00 4.85
3174 5869 5.453339 GGAAGTGGAATCGTAGGATTGATCA 60.453 44.000 15.07 8.01 42.86 2.92
3194 5889 6.772716 TGATCATTAATTGCTAACTTCCCTCC 59.227 38.462 0.00 0.00 0.00 4.30
3195 5890 6.073447 TCATTAATTGCTAACTTCCCTCCA 57.927 37.500 0.00 0.00 0.00 3.86
3242 6045 4.889832 CCAACTGGCTTGATGAAGATAC 57.110 45.455 0.00 0.00 30.42 2.24
3243 6046 4.264253 CCAACTGGCTTGATGAAGATACA 58.736 43.478 0.00 0.00 30.42 2.29
3244 6047 4.334759 CCAACTGGCTTGATGAAGATACAG 59.665 45.833 0.00 3.40 35.13 2.74
3245 6048 5.181009 CAACTGGCTTGATGAAGATACAGA 58.819 41.667 14.90 0.00 34.08 3.41
3246 6049 4.764172 ACTGGCTTGATGAAGATACAGAC 58.236 43.478 14.90 0.00 34.08 3.51
3247 6050 4.469227 ACTGGCTTGATGAAGATACAGACT 59.531 41.667 14.90 0.00 34.08 3.24
3248 6051 5.046014 ACTGGCTTGATGAAGATACAGACTT 60.046 40.000 14.90 0.00 34.08 3.01
3249 6052 5.181009 TGGCTTGATGAAGATACAGACTTG 58.819 41.667 0.00 0.00 0.00 3.16
3250 6053 4.034975 GGCTTGATGAAGATACAGACTTGC 59.965 45.833 0.00 0.00 0.00 4.01
3251 6054 4.874966 GCTTGATGAAGATACAGACTTGCT 59.125 41.667 0.00 0.00 0.00 3.91
3252 6055 5.353678 GCTTGATGAAGATACAGACTTGCTT 59.646 40.000 0.00 0.00 0.00 3.91
3253 6056 6.675002 GCTTGATGAAGATACAGACTTGCTTG 60.675 42.308 0.00 0.00 0.00 4.01
3254 6057 5.181009 TGATGAAGATACAGACTTGCTTGG 58.819 41.667 0.00 0.00 0.00 3.61
3255 6058 3.942829 TGAAGATACAGACTTGCTTGGG 58.057 45.455 0.00 0.00 0.00 4.12
3256 6059 3.327757 TGAAGATACAGACTTGCTTGGGT 59.672 43.478 0.00 0.00 0.00 4.51
3257 6060 4.202461 TGAAGATACAGACTTGCTTGGGTT 60.202 41.667 0.00 0.00 0.00 4.11
3258 6061 5.012664 TGAAGATACAGACTTGCTTGGGTTA 59.987 40.000 0.00 0.00 0.00 2.85
3259 6062 5.499004 AGATACAGACTTGCTTGGGTTAA 57.501 39.130 0.00 0.00 0.00 2.01
3260 6063 6.067217 AGATACAGACTTGCTTGGGTTAAT 57.933 37.500 0.00 0.00 0.00 1.40
3261 6064 6.485171 AGATACAGACTTGCTTGGGTTAATT 58.515 36.000 0.00 0.00 0.00 1.40
3262 6065 7.630082 AGATACAGACTTGCTTGGGTTAATTA 58.370 34.615 0.00 0.00 0.00 1.40
3263 6066 7.770897 AGATACAGACTTGCTTGGGTTAATTAG 59.229 37.037 0.00 0.00 0.00 1.73
3264 6067 4.459337 ACAGACTTGCTTGGGTTAATTAGC 59.541 41.667 0.00 0.00 0.00 3.09
3265 6068 4.458989 CAGACTTGCTTGGGTTAATTAGCA 59.541 41.667 1.55 0.00 41.51 3.49
3266 6069 5.126061 CAGACTTGCTTGGGTTAATTAGCAT 59.874 40.000 1.55 0.00 42.60 3.79
3267 6070 5.716703 AGACTTGCTTGGGTTAATTAGCATT 59.283 36.000 1.55 0.00 42.60 3.56
3268 6071 6.211384 AGACTTGCTTGGGTTAATTAGCATTT 59.789 34.615 1.55 0.00 42.60 2.32
3269 6072 6.165577 ACTTGCTTGGGTTAATTAGCATTTG 58.834 36.000 1.55 0.00 42.60 2.32
3270 6073 5.736951 TGCTTGGGTTAATTAGCATTTGT 57.263 34.783 1.55 0.00 38.61 2.83
3271 6074 5.477510 TGCTTGGGTTAATTAGCATTTGTG 58.522 37.500 1.55 0.00 38.61 3.33
3272 6075 4.869861 GCTTGGGTTAATTAGCATTTGTGG 59.130 41.667 1.55 0.00 33.88 4.17
3273 6076 5.568624 GCTTGGGTTAATTAGCATTTGTGGT 60.569 40.000 1.55 0.00 33.88 4.16
3274 6077 6.350612 GCTTGGGTTAATTAGCATTTGTGGTA 60.351 38.462 1.55 0.00 33.88 3.25
3275 6078 6.518208 TGGGTTAATTAGCATTTGTGGTAC 57.482 37.500 1.55 0.00 0.00 3.34
3276 6079 6.010850 TGGGTTAATTAGCATTTGTGGTACA 58.989 36.000 1.55 0.00 0.00 2.90
3277 6080 6.665680 TGGGTTAATTAGCATTTGTGGTACAT 59.334 34.615 1.55 0.00 44.52 2.29
3278 6081 7.179338 TGGGTTAATTAGCATTTGTGGTACATT 59.821 33.333 1.55 0.00 44.52 2.71
3279 6082 8.038351 GGGTTAATTAGCATTTGTGGTACATTT 58.962 33.333 1.55 0.00 44.52 2.32
3280 6083 8.868916 GGTTAATTAGCATTTGTGGTACATTTG 58.131 33.333 1.55 0.00 44.52 2.32
3281 6084 6.966435 AATTAGCATTTGTGGTACATTTGC 57.034 33.333 0.00 7.94 44.52 3.68
3282 6085 5.720371 TTAGCATTTGTGGTACATTTGCT 57.280 34.783 17.43 17.43 43.98 3.91
3283 6086 4.605640 AGCATTTGTGGTACATTTGCTT 57.394 36.364 11.17 1.00 41.11 3.91
3284 6087 4.959723 AGCATTTGTGGTACATTTGCTTT 58.040 34.783 11.17 0.00 41.11 3.51
3285 6088 6.095432 AGCATTTGTGGTACATTTGCTTTA 57.905 33.333 11.17 0.00 41.11 1.85
3286 6089 6.700352 AGCATTTGTGGTACATTTGCTTTAT 58.300 32.000 11.17 0.00 41.11 1.40
3287 6090 6.591062 AGCATTTGTGGTACATTTGCTTTATG 59.409 34.615 11.17 0.00 41.11 1.90
3288 6091 6.672836 GCATTTGTGGTACATTTGCTTTATGC 60.673 38.462 0.00 0.00 44.52 3.14
3289 6092 5.720371 TTGTGGTACATTTGCTTTATGCT 57.280 34.783 0.00 0.00 44.52 3.79
3290 6093 5.720371 TGTGGTACATTTGCTTTATGCTT 57.280 34.783 0.00 0.00 44.52 3.91
3291 6094 6.095432 TGTGGTACATTTGCTTTATGCTTT 57.905 33.333 0.00 0.00 44.52 3.51
3292 6095 6.155827 TGTGGTACATTTGCTTTATGCTTTC 58.844 36.000 0.00 0.00 44.52 2.62
3293 6096 5.576774 GTGGTACATTTGCTTTATGCTTTCC 59.423 40.000 0.00 0.00 44.52 3.13
3294 6097 5.244851 TGGTACATTTGCTTTATGCTTTCCA 59.755 36.000 0.00 0.00 43.37 3.53
3295 6098 6.162777 GGTACATTTGCTTTATGCTTTCCAA 58.837 36.000 0.00 0.00 43.37 3.53
3296 6099 6.311200 GGTACATTTGCTTTATGCTTTCCAAG 59.689 38.462 0.00 0.00 43.37 3.61
3314 6117 3.795905 CAAGGTTGCCTGCCCAAT 58.204 55.556 0.00 0.00 32.13 3.16
3315 6118 1.294138 CAAGGTTGCCTGCCCAATG 59.706 57.895 0.00 0.00 32.13 2.82
3316 6119 1.155859 AAGGTTGCCTGCCCAATGA 59.844 52.632 0.00 0.00 32.13 2.57
3317 6120 0.252375 AAGGTTGCCTGCCCAATGAT 60.252 50.000 0.00 0.00 32.13 2.45
3318 6121 0.685458 AGGTTGCCTGCCCAATGATC 60.685 55.000 0.00 0.00 29.57 2.92
3319 6122 0.685458 GGTTGCCTGCCCAATGATCT 60.685 55.000 0.00 0.00 0.00 2.75
3320 6123 1.188863 GTTGCCTGCCCAATGATCTT 58.811 50.000 0.00 0.00 0.00 2.40
3321 6124 1.134907 GTTGCCTGCCCAATGATCTTG 60.135 52.381 0.00 0.00 0.00 3.02
3322 6125 0.685131 TGCCTGCCCAATGATCTTGG 60.685 55.000 13.87 13.87 39.25 3.61
3323 6126 2.024590 GCCTGCCCAATGATCTTGGC 62.025 60.000 14.89 11.57 44.27 4.52
3324 6127 0.396695 CCTGCCCAATGATCTTGGCT 60.397 55.000 14.89 0.00 44.32 4.75
3325 6128 1.481871 CTGCCCAATGATCTTGGCTT 58.518 50.000 14.89 0.00 44.32 4.35
3326 6129 2.658285 CTGCCCAATGATCTTGGCTTA 58.342 47.619 14.89 5.97 44.32 3.09
3327 6130 2.360165 CTGCCCAATGATCTTGGCTTAC 59.640 50.000 14.89 7.48 44.32 2.34
3328 6131 2.025037 TGCCCAATGATCTTGGCTTACT 60.025 45.455 14.89 0.00 44.32 2.24
3329 6132 2.360165 GCCCAATGATCTTGGCTTACTG 59.640 50.000 14.89 5.41 40.77 2.74
3330 6133 3.624777 CCCAATGATCTTGGCTTACTGT 58.375 45.455 14.89 0.00 38.23 3.55
3331 6134 3.629398 CCCAATGATCTTGGCTTACTGTC 59.371 47.826 14.89 0.00 38.23 3.51
3332 6135 4.264253 CCAATGATCTTGGCTTACTGTCA 58.736 43.478 9.94 0.00 32.18 3.58
3333 6136 4.885907 CCAATGATCTTGGCTTACTGTCAT 59.114 41.667 9.94 0.00 32.18 3.06
3334 6137 5.220989 CCAATGATCTTGGCTTACTGTCATG 60.221 44.000 9.94 0.00 32.18 3.07
3335 6138 4.558226 TGATCTTGGCTTACTGTCATGT 57.442 40.909 0.00 0.00 0.00 3.21
3336 6139 4.256110 TGATCTTGGCTTACTGTCATGTG 58.744 43.478 0.00 0.00 0.00 3.21
3337 6140 2.426522 TCTTGGCTTACTGTCATGTGC 58.573 47.619 0.00 0.00 0.00 4.57
3338 6141 1.129251 CTTGGCTTACTGTCATGTGCG 59.871 52.381 0.00 0.00 0.00 5.34
3339 6142 0.034756 TGGCTTACTGTCATGTGCGT 59.965 50.000 0.00 0.00 0.00 5.24
3340 6143 0.443869 GGCTTACTGTCATGTGCGTG 59.556 55.000 0.00 0.00 0.00 5.34
3341 6144 1.148310 GCTTACTGTCATGTGCGTGT 58.852 50.000 0.00 0.00 0.00 4.49
3342 6145 2.333926 GCTTACTGTCATGTGCGTGTA 58.666 47.619 0.00 0.00 0.00 2.90
3343 6146 2.930040 GCTTACTGTCATGTGCGTGTAT 59.070 45.455 0.00 0.00 0.00 2.29
3344 6147 3.000322 GCTTACTGTCATGTGCGTGTATC 60.000 47.826 0.00 0.00 0.00 2.24
3345 6148 4.424626 CTTACTGTCATGTGCGTGTATCT 58.575 43.478 0.00 0.00 0.00 1.98
3346 6149 2.610433 ACTGTCATGTGCGTGTATCTG 58.390 47.619 0.00 0.00 0.00 2.90
3347 6150 2.029020 ACTGTCATGTGCGTGTATCTGT 60.029 45.455 0.00 0.00 0.00 3.41
3348 6151 3.192633 ACTGTCATGTGCGTGTATCTGTA 59.807 43.478 0.00 0.00 0.00 2.74
3359 6162 4.860352 GCGTGTATCTGTATGTGTGTGTTA 59.140 41.667 0.00 0.00 0.00 2.41
3444 6257 7.011950 CGTTGTATTCCTGCTTATGTCCATTTA 59.988 37.037 0.00 0.00 0.00 1.40
3448 6261 5.435686 TCCTGCTTATGTCCATTTAGTGT 57.564 39.130 0.00 0.00 0.00 3.55
3450 6263 4.201950 CCTGCTTATGTCCATTTAGTGTGC 60.202 45.833 0.00 0.00 0.00 4.57
3456 6269 2.546368 TGTCCATTTAGTGTGCGTGTTC 59.454 45.455 0.00 0.00 0.00 3.18
3457 6270 2.806244 GTCCATTTAGTGTGCGTGTTCT 59.194 45.455 0.00 0.00 0.00 3.01
3458 6271 2.805671 TCCATTTAGTGTGCGTGTTCTG 59.194 45.455 0.00 0.00 0.00 3.02
3459 6272 2.548057 CCATTTAGTGTGCGTGTTCTGT 59.452 45.455 0.00 0.00 0.00 3.41
3461 6274 3.666883 TTTAGTGTGCGTGTTCTGTTG 57.333 42.857 0.00 0.00 0.00 3.33
3462 6275 2.588027 TAGTGTGCGTGTTCTGTTGA 57.412 45.000 0.00 0.00 0.00 3.18
3496 6311 5.177326 TGATTTTGGCTAATGAATGTTGGC 58.823 37.500 0.00 0.00 35.15 4.52
3686 7229 1.413082 CCATAGGGACCACTGGCTAGA 60.413 57.143 3.17 0.00 35.59 2.43
3718 7263 8.540507 TCTTCCTTGCATATTAGTCTAAGTCT 57.459 34.615 0.00 0.00 0.00 3.24
3796 7341 2.428171 CTGGCCAATTTCTGTATGGGTG 59.572 50.000 7.01 0.00 34.71 4.61
3797 7342 2.225242 TGGCCAATTTCTGTATGGGTGT 60.225 45.455 0.61 0.00 34.71 4.16
3839 7384 2.180131 GACGCAAAGCACCAGCAGAG 62.180 60.000 0.00 0.00 45.49 3.35
3840 7385 2.257676 GCAAAGCACCAGCAGAGC 59.742 61.111 0.00 0.00 45.49 4.09
3855 7400 3.731653 GAGCGAGCTTCCTCCCTGC 62.732 68.421 0.00 0.00 34.49 4.85
3866 7411 1.302285 CTCCCTGCCAGCATTCTGT 59.698 57.895 0.00 0.00 38.66 3.41
3886 7431 2.410053 GTCGCGATCAGGAGATTATTGC 59.590 50.000 14.06 0.00 33.72 3.56
3908 7453 1.123861 TGTCTCCAACTCAGCCAGCT 61.124 55.000 0.00 0.00 0.00 4.24
3959 7504 1.195442 TCTCCATTGGCCACACCGTA 61.195 55.000 3.88 0.00 43.94 4.02
3962 7507 0.962489 CCATTGGCCACACCGTAAAA 59.038 50.000 3.88 0.00 43.94 1.52
3967 7512 0.170339 GGCCACACCGTAAAAGATGC 59.830 55.000 0.00 0.00 0.00 3.91
4001 7546 2.906897 ACCAAGCGGTGCCTGTTG 60.907 61.111 0.00 0.00 46.79 3.33
4002 7547 3.673484 CCAAGCGGTGCCTGTTGG 61.673 66.667 0.00 4.68 33.85 3.77
4003 7548 2.594303 CAAGCGGTGCCTGTTGGA 60.594 61.111 0.00 0.00 34.57 3.53
4004 7549 1.973281 CAAGCGGTGCCTGTTGGAT 60.973 57.895 0.00 0.00 34.57 3.41
4005 7550 0.676466 CAAGCGGTGCCTGTTGGATA 60.676 55.000 0.00 0.00 34.57 2.59
4006 7551 0.037590 AAGCGGTGCCTGTTGGATAA 59.962 50.000 0.00 0.00 34.57 1.75
4007 7552 0.392998 AGCGGTGCCTGTTGGATAAG 60.393 55.000 0.00 0.00 34.57 1.73
4008 7553 0.676782 GCGGTGCCTGTTGGATAAGT 60.677 55.000 0.00 0.00 34.57 2.24
4009 7554 1.369625 CGGTGCCTGTTGGATAAGTC 58.630 55.000 0.00 0.00 34.57 3.01
4010 7555 1.066143 CGGTGCCTGTTGGATAAGTCT 60.066 52.381 0.00 0.00 34.57 3.24
4011 7556 2.359900 GGTGCCTGTTGGATAAGTCTG 58.640 52.381 0.00 0.00 34.57 3.51
4012 7557 2.290323 GGTGCCTGTTGGATAAGTCTGT 60.290 50.000 0.00 0.00 34.57 3.41
4013 7558 2.744202 GTGCCTGTTGGATAAGTCTGTG 59.256 50.000 0.00 0.00 34.57 3.66
4014 7559 2.371841 TGCCTGTTGGATAAGTCTGTGT 59.628 45.455 0.00 0.00 34.57 3.72
4015 7560 3.580895 TGCCTGTTGGATAAGTCTGTGTA 59.419 43.478 0.00 0.00 34.57 2.90
4016 7561 3.933332 GCCTGTTGGATAAGTCTGTGTAC 59.067 47.826 0.00 0.00 34.57 2.90
4017 7562 4.322801 GCCTGTTGGATAAGTCTGTGTACT 60.323 45.833 0.00 0.00 34.57 2.73
4018 7563 5.105473 GCCTGTTGGATAAGTCTGTGTACTA 60.105 44.000 0.00 0.00 34.57 1.82
4019 7564 6.565234 CCTGTTGGATAAGTCTGTGTACTAG 58.435 44.000 0.00 0.00 34.57 2.57
4020 7565 6.405953 CCTGTTGGATAAGTCTGTGTACTAGG 60.406 46.154 0.00 0.00 34.57 3.02
4021 7566 5.421056 TGTTGGATAAGTCTGTGTACTAGGG 59.579 44.000 0.00 0.00 0.00 3.53
4022 7567 5.202746 TGGATAAGTCTGTGTACTAGGGT 57.797 43.478 0.00 0.00 0.00 4.34
4023 7568 5.586877 TGGATAAGTCTGTGTACTAGGGTT 58.413 41.667 0.00 0.00 0.00 4.11
4024 7569 6.021030 TGGATAAGTCTGTGTACTAGGGTTT 58.979 40.000 0.00 0.00 0.00 3.27
4025 7570 6.499350 TGGATAAGTCTGTGTACTAGGGTTTT 59.501 38.462 0.00 0.00 0.00 2.43
4026 7571 7.016858 TGGATAAGTCTGTGTACTAGGGTTTTT 59.983 37.037 0.00 0.00 0.00 1.94
4027 7572 7.333672 GGATAAGTCTGTGTACTAGGGTTTTTG 59.666 40.741 0.00 0.00 0.00 2.44
4028 7573 5.625568 AGTCTGTGTACTAGGGTTTTTGT 57.374 39.130 0.00 0.00 0.00 2.83
4029 7574 5.365619 AGTCTGTGTACTAGGGTTTTTGTG 58.634 41.667 0.00 0.00 0.00 3.33
4030 7575 4.514066 GTCTGTGTACTAGGGTTTTTGTGG 59.486 45.833 0.00 0.00 0.00 4.17
4031 7576 3.818773 CTGTGTACTAGGGTTTTTGTGGG 59.181 47.826 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
662 664 0.393808 CAATACCCACCCTTGTCCCG 60.394 60.000 0.00 0.00 0.00 5.14
663 665 0.033503 CCAATACCCACCCTTGTCCC 60.034 60.000 0.00 0.00 0.00 4.46
669 695 1.056660 CGCTATCCAATACCCACCCT 58.943 55.000 0.00 0.00 0.00 4.34
816 876 9.613428 ACATTTCCTATCATATCGTTTTCTCAA 57.387 29.630 0.00 0.00 0.00 3.02
817 877 9.613428 AACATTTCCTATCATATCGTTTTCTCA 57.387 29.630 0.00 0.00 0.00 3.27
857 917 4.728608 CGAACACACTTACTTGTTTGCTTC 59.271 41.667 0.00 0.00 36.06 3.86
863 923 2.940410 CCCACGAACACACTTACTTGTT 59.060 45.455 0.00 0.00 38.67 2.83
865 925 1.263217 GCCCACGAACACACTTACTTG 59.737 52.381 0.00 0.00 0.00 3.16
871 931 1.525995 CAAGGCCCACGAACACACT 60.526 57.895 0.00 0.00 0.00 3.55
877 937 1.314730 GAAGAAACAAGGCCCACGAA 58.685 50.000 0.00 0.00 0.00 3.85
880 940 1.408969 TTGGAAGAAACAAGGCCCAC 58.591 50.000 0.00 0.00 0.00 4.61
889 949 1.546029 GTCAGGCCCATTGGAAGAAAC 59.454 52.381 3.62 0.00 0.00 2.78
895 955 0.776810 TTGAAGTCAGGCCCATTGGA 59.223 50.000 3.62 0.00 0.00 3.53
905 965 5.577554 CACAGTGAGATGAGATTGAAGTCAG 59.422 44.000 0.00 0.00 0.00 3.51
914 974 1.135915 GGCGACACAGTGAGATGAGAT 59.864 52.381 7.81 0.00 0.00 2.75
923 983 0.388649 GTGACCTAGGCGACACAGTG 60.389 60.000 21.53 0.00 34.05 3.66
947 1017 0.107410 ACTGACGCTGTGGTTGGAAA 60.107 50.000 0.00 0.00 0.00 3.13
948 1018 0.813610 CACTGACGCTGTGGTTGGAA 60.814 55.000 8.32 0.00 31.27 3.53
956 1026 4.969196 CCGCCACACTGACGCTGT 62.969 66.667 0.00 0.00 0.00 4.40
961 1031 4.996434 AGCAGCCGCCACACTGAC 62.996 66.667 0.00 0.00 39.83 3.51
962 1032 4.254709 AAGCAGCCGCCACACTGA 62.255 61.111 0.00 0.00 39.83 3.41
1185 1274 2.285442 CCGAGGAGGGGAGGGTTT 60.285 66.667 0.00 0.00 35.97 3.27
1203 1292 3.556775 CGTCAAAAACTCCGTGGAAGTAA 59.443 43.478 0.00 0.00 0.00 2.24
1239 1328 4.070552 GGCTCGAAGCGGACAGGT 62.071 66.667 0.00 0.00 43.62 4.00
1243 1332 1.064458 GAGTAGGCTCGAAGCGGAC 59.936 63.158 0.00 0.00 43.62 4.79
1306 1395 0.393077 ACACGGAGGTTGGAGTCAAG 59.607 55.000 0.00 0.00 32.92 3.02
1498 1615 0.820482 TCTGACACGACGACCTGGAA 60.820 55.000 0.00 0.00 0.00 3.53
1501 1618 2.913777 TAATCTGACACGACGACCTG 57.086 50.000 0.00 0.00 0.00 4.00
1502 1619 4.495349 CGTAATAATCTGACACGACGACCT 60.495 45.833 0.00 0.00 34.66 3.85
1503 1620 3.722780 CGTAATAATCTGACACGACGACC 59.277 47.826 0.00 0.00 34.66 4.79
1504 1621 4.581493 TCGTAATAATCTGACACGACGAC 58.419 43.478 0.00 0.00 36.77 4.34
1506 1623 4.665292 GTCTCGTAATAATCTGACACGACG 59.335 45.833 0.00 0.00 36.77 5.12
1522 1642 3.818961 CGAGTAAACACAGGTCTCGTA 57.181 47.619 0.00 0.00 41.64 3.43
1578 1719 1.077716 GTTCCCGGATGGAGTTGGG 60.078 63.158 0.73 0.00 46.24 4.12
1607 1748 2.032071 CCCGAACCCTGGTGTCAC 59.968 66.667 0.00 0.00 0.00 3.67
1611 1752 1.003718 GAGTTCCCGAACCCTGGTG 60.004 63.158 3.97 0.00 42.06 4.17
1612 1753 2.222013 GGAGTTCCCGAACCCTGGT 61.222 63.158 3.97 0.00 42.06 4.00
1614 1755 0.328258 ATTGGAGTTCCCGAACCCTG 59.672 55.000 3.97 0.00 42.06 4.45
1615 1756 1.073098 AATTGGAGTTCCCGAACCCT 58.927 50.000 3.97 0.00 42.06 4.34
1700 2063 5.124457 TGTGAATCCATAGAGAAAAGCTTGC 59.876 40.000 0.00 0.00 0.00 4.01
1708 2071 9.117183 CAAGAAATCATGTGAATCCATAGAGAA 57.883 33.333 0.00 0.00 0.00 2.87
1725 2088 5.255397 ACCCTTGTATGGTCAAGAAATCA 57.745 39.130 7.83 0.00 45.11 2.57
1749 2112 2.099405 ACCAAATTATTGTCCTGGGCG 58.901 47.619 0.00 0.00 34.60 6.13
1753 2116 5.713025 CAGGAACACCAAATTATTGTCCTG 58.287 41.667 9.93 9.93 43.68 3.86
1951 2491 3.367703 GGATGTGAAAGGCATTCCAACAG 60.368 47.826 0.00 0.00 37.22 3.16
1954 2494 3.173953 AGGATGTGAAAGGCATTCCAA 57.826 42.857 0.00 0.00 37.22 3.53
2007 2550 3.829948 AGCAGCAAAAGAACAATCGATG 58.170 40.909 0.00 0.00 0.00 3.84
2011 2554 4.805192 TCAACAAGCAGCAAAAGAACAATC 59.195 37.500 0.00 0.00 0.00 2.67
2046 2595 0.321564 ACTTACAGAGCGCCATTGCA 60.322 50.000 2.29 0.00 37.32 4.08
2348 4633 4.020218 ACACAACACATGTCTACAGCCTAT 60.020 41.667 0.00 0.00 41.46 2.57
2462 4762 6.642707 AAAGTGGGTAATTCGTGATGAAAA 57.357 33.333 0.00 0.00 40.71 2.29
2495 4795 7.512130 TCCTTCAAGCATATCATGTCACTAAT 58.488 34.615 0.00 0.00 0.00 1.73
2522 4822 3.250762 TCATCAAAACAAAGCTCGGAGTG 59.749 43.478 6.90 0.00 0.00 3.51
2523 4823 3.251004 GTCATCAAAACAAAGCTCGGAGT 59.749 43.478 6.90 0.00 0.00 3.85
2636 4938 9.787435 ATAGTCACCAACTACTTGAATTTAACA 57.213 29.630 0.00 0.00 43.21 2.41
2662 4964 8.363390 ACATCTTTCAGAAATATATGAGCTCGA 58.637 33.333 9.64 0.00 0.00 4.04
2687 4989 3.134458 CAGCAGGTTAGCTAATAGGCAC 58.866 50.000 20.85 5.89 44.54 5.01
2706 5008 3.434984 GTGGAGTAGAAAAGCAGAAGCAG 59.565 47.826 0.00 0.00 45.49 4.24
2822 5330 3.777106 TGGAAACAGAGATTGTCAGCT 57.223 42.857 0.00 0.00 39.73 4.24
2938 5613 5.438761 AGTTATGCAACCTCACAAGTTTC 57.561 39.130 0.00 0.00 35.05 2.78
2942 5617 4.614535 GCTGAAGTTATGCAACCTCACAAG 60.615 45.833 0.00 0.00 32.80 3.16
2979 5654 7.010183 CACCAGTCAAACCATTAGTACTATTCG 59.990 40.741 2.79 0.00 0.00 3.34
2989 5664 3.478857 ACGACACCAGTCAAACCATTA 57.521 42.857 0.00 0.00 45.23 1.90
3003 5698 2.480419 CCTGTGGAAGAATCAACGACAC 59.520 50.000 0.00 0.00 31.55 3.67
3006 5701 3.306502 GGTACCTGTGGAAGAATCAACGA 60.307 47.826 4.06 0.00 31.55 3.85
3008 5703 4.287766 AGGTACCTGTGGAAGAATCAAC 57.712 45.455 15.42 0.00 0.00 3.18
3015 5710 5.422214 ACAAATCTAGGTACCTGTGGAAG 57.578 43.478 25.33 13.34 0.00 3.46
3174 5869 9.301897 GATAATGGAGGGAAGTTAGCAATTAAT 57.698 33.333 0.00 0.00 0.00 1.40
3194 5889 9.888878 CTAATTGTGTCCAGCAATAAGATAATG 57.111 33.333 0.00 0.00 35.73 1.90
3195 5890 8.571336 GCTAATTGTGTCCAGCAATAAGATAAT 58.429 33.333 0.00 0.00 35.73 1.28
3233 6036 4.018960 ACCCAAGCAAGTCTGTATCTTCAT 60.019 41.667 0.00 0.00 0.00 2.57
3234 6037 3.327757 ACCCAAGCAAGTCTGTATCTTCA 59.672 43.478 0.00 0.00 0.00 3.02
3235 6038 3.944087 ACCCAAGCAAGTCTGTATCTTC 58.056 45.455 0.00 0.00 0.00 2.87
3236 6039 4.373156 AACCCAAGCAAGTCTGTATCTT 57.627 40.909 0.00 0.00 0.00 2.40
3237 6040 5.499004 TTAACCCAAGCAAGTCTGTATCT 57.501 39.130 0.00 0.00 0.00 1.98
3238 6041 6.759497 AATTAACCCAAGCAAGTCTGTATC 57.241 37.500 0.00 0.00 0.00 2.24
3239 6042 6.318900 GCTAATTAACCCAAGCAAGTCTGTAT 59.681 38.462 0.00 0.00 35.05 2.29
3240 6043 5.646360 GCTAATTAACCCAAGCAAGTCTGTA 59.354 40.000 0.00 0.00 35.05 2.74
3241 6044 4.459337 GCTAATTAACCCAAGCAAGTCTGT 59.541 41.667 0.00 0.00 35.05 3.41
3242 6045 4.458989 TGCTAATTAACCCAAGCAAGTCTG 59.541 41.667 0.00 0.00 41.74 3.51
3243 6046 4.662278 TGCTAATTAACCCAAGCAAGTCT 58.338 39.130 0.00 0.00 41.74 3.24
3249 6052 4.869861 CCACAAATGCTAATTAACCCAAGC 59.130 41.667 0.00 0.00 35.51 4.01
3250 6053 6.036577 ACCACAAATGCTAATTAACCCAAG 57.963 37.500 0.00 0.00 0.00 3.61
3251 6054 6.493802 TGTACCACAAATGCTAATTAACCCAA 59.506 34.615 0.00 0.00 0.00 4.12
3252 6055 6.010850 TGTACCACAAATGCTAATTAACCCA 58.989 36.000 0.00 0.00 0.00 4.51
3253 6056 6.518208 TGTACCACAAATGCTAATTAACCC 57.482 37.500 0.00 0.00 0.00 4.11
3254 6057 8.868916 CAAATGTACCACAAATGCTAATTAACC 58.131 33.333 0.00 0.00 0.00 2.85
3255 6058 8.379902 GCAAATGTACCACAAATGCTAATTAAC 58.620 33.333 10.60 0.00 39.29 2.01
3256 6059 8.310382 AGCAAATGTACCACAAATGCTAATTAA 58.690 29.630 16.05 0.00 45.76 1.40
3257 6060 7.835822 AGCAAATGTACCACAAATGCTAATTA 58.164 30.769 16.05 0.00 45.76 1.40
3258 6061 6.700352 AGCAAATGTACCACAAATGCTAATT 58.300 32.000 16.05 0.00 45.76 1.40
3259 6062 6.284891 AGCAAATGTACCACAAATGCTAAT 57.715 33.333 16.05 0.00 45.76 1.73
3260 6063 5.720371 AGCAAATGTACCACAAATGCTAA 57.280 34.783 16.05 0.00 45.76 3.09
3261 6064 5.720371 AAGCAAATGTACCACAAATGCTA 57.280 34.783 17.22 0.00 46.39 3.49
3263 6066 6.672836 GCATAAAGCAAATGTACCACAAATGC 60.673 38.462 10.11 10.11 44.79 3.56
3264 6067 6.764094 GCATAAAGCAAATGTACCACAAATG 58.236 36.000 0.00 0.00 44.79 2.32
3265 6068 6.966435 GCATAAAGCAAATGTACCACAAAT 57.034 33.333 0.00 0.00 44.79 2.32
3297 6100 1.186917 TCATTGGGCAGGCAACCTTG 61.187 55.000 0.00 0.00 37.17 3.61
3298 6101 0.252375 ATCATTGGGCAGGCAACCTT 60.252 50.000 0.00 0.00 37.17 3.50
3299 6102 0.685458 GATCATTGGGCAGGCAACCT 60.685 55.000 0.00 0.00 37.17 3.50
3300 6103 0.685458 AGATCATTGGGCAGGCAACC 60.685 55.000 0.00 0.00 37.17 3.77
3301 6104 1.134907 CAAGATCATTGGGCAGGCAAC 60.135 52.381 0.00 0.00 0.00 4.17
3302 6105 1.187974 CAAGATCATTGGGCAGGCAA 58.812 50.000 0.00 0.00 0.00 4.52
3303 6106 0.685131 CCAAGATCATTGGGCAGGCA 60.685 55.000 13.28 0.00 35.96 4.75
3304 6107 2.024590 GCCAAGATCATTGGGCAGGC 62.025 60.000 19.31 3.27 45.70 4.85
3305 6108 2.121645 GCCAAGATCATTGGGCAGG 58.878 57.895 19.31 0.00 45.70 4.85
3308 6111 2.360165 CAGTAAGCCAAGATCATTGGGC 59.640 50.000 19.31 14.42 46.77 5.36
3309 6112 3.624777 ACAGTAAGCCAAGATCATTGGG 58.375 45.455 19.31 6.78 39.90 4.12
3310 6113 4.264253 TGACAGTAAGCCAAGATCATTGG 58.736 43.478 15.63 15.63 42.37 3.16
3311 6114 5.356190 ACATGACAGTAAGCCAAGATCATTG 59.644 40.000 0.00 0.00 0.00 2.82
3312 6115 5.356190 CACATGACAGTAAGCCAAGATCATT 59.644 40.000 0.00 0.00 0.00 2.57
3313 6116 4.880120 CACATGACAGTAAGCCAAGATCAT 59.120 41.667 0.00 0.00 0.00 2.45
3314 6117 4.256110 CACATGACAGTAAGCCAAGATCA 58.744 43.478 0.00 0.00 0.00 2.92
3315 6118 3.064545 GCACATGACAGTAAGCCAAGATC 59.935 47.826 0.00 0.00 0.00 2.75
3316 6119 3.012518 GCACATGACAGTAAGCCAAGAT 58.987 45.455 0.00 0.00 0.00 2.40
3317 6120 2.426522 GCACATGACAGTAAGCCAAGA 58.573 47.619 0.00 0.00 0.00 3.02
3318 6121 1.129251 CGCACATGACAGTAAGCCAAG 59.871 52.381 0.00 0.00 0.00 3.61
3319 6122 1.155889 CGCACATGACAGTAAGCCAA 58.844 50.000 0.00 0.00 0.00 4.52
3320 6123 0.034756 ACGCACATGACAGTAAGCCA 59.965 50.000 0.00 0.00 0.00 4.75
3321 6124 0.443869 CACGCACATGACAGTAAGCC 59.556 55.000 0.00 0.00 0.00 4.35
3322 6125 1.148310 ACACGCACATGACAGTAAGC 58.852 50.000 0.00 0.00 0.00 3.09
3323 6126 4.266265 CAGATACACGCACATGACAGTAAG 59.734 45.833 0.00 0.00 0.00 2.34
3324 6127 4.173256 CAGATACACGCACATGACAGTAA 58.827 43.478 0.00 0.00 0.00 2.24
3325 6128 3.192633 ACAGATACACGCACATGACAGTA 59.807 43.478 0.00 0.00 0.00 2.74
3326 6129 2.029020 ACAGATACACGCACATGACAGT 60.029 45.455 0.00 0.00 0.00 3.55
3327 6130 2.610433 ACAGATACACGCACATGACAG 58.390 47.619 0.00 0.00 0.00 3.51
3328 6131 2.741759 ACAGATACACGCACATGACA 57.258 45.000 0.00 0.00 0.00 3.58
3329 6132 4.026558 CACATACAGATACACGCACATGAC 60.027 45.833 0.00 0.00 0.00 3.06
3330 6133 4.111916 CACATACAGATACACGCACATGA 58.888 43.478 0.00 0.00 0.00 3.07
3331 6134 3.865164 ACACATACAGATACACGCACATG 59.135 43.478 0.00 0.00 0.00 3.21
3332 6135 3.865164 CACACATACAGATACACGCACAT 59.135 43.478 0.00 0.00 0.00 3.21
3333 6136 3.249917 CACACATACAGATACACGCACA 58.750 45.455 0.00 0.00 0.00 4.57
3334 6137 3.060761 CACACACATACAGATACACGCAC 59.939 47.826 0.00 0.00 0.00 5.34
3335 6138 3.249917 CACACACATACAGATACACGCA 58.750 45.455 0.00 0.00 0.00 5.24
3336 6139 3.250744 ACACACACATACAGATACACGC 58.749 45.455 0.00 0.00 0.00 5.34
3337 6140 6.937886 TTAACACACACATACAGATACACG 57.062 37.500 0.00 0.00 0.00 4.49
3338 6141 8.703604 AGATTAACACACACATACAGATACAC 57.296 34.615 0.00 0.00 0.00 2.90
3339 6142 9.366216 GAAGATTAACACACACATACAGATACA 57.634 33.333 0.00 0.00 0.00 2.29
3340 6143 9.587772 AGAAGATTAACACACACATACAGATAC 57.412 33.333 0.00 0.00 0.00 2.24
3341 6144 9.803315 GAGAAGATTAACACACACATACAGATA 57.197 33.333 0.00 0.00 0.00 1.98
3342 6145 8.535335 AGAGAAGATTAACACACACATACAGAT 58.465 33.333 0.00 0.00 0.00 2.90
3343 6146 7.896811 AGAGAAGATTAACACACACATACAGA 58.103 34.615 0.00 0.00 0.00 3.41
3344 6147 8.031864 AGAGAGAAGATTAACACACACATACAG 58.968 37.037 0.00 0.00 0.00 2.74
3345 6148 7.814587 CAGAGAGAAGATTAACACACACATACA 59.185 37.037 0.00 0.00 0.00 2.29
3346 6149 7.815068 ACAGAGAGAAGATTAACACACACATAC 59.185 37.037 0.00 0.00 0.00 2.39
3347 6150 7.896811 ACAGAGAGAAGATTAACACACACATA 58.103 34.615 0.00 0.00 0.00 2.29
3348 6151 6.763355 ACAGAGAGAAGATTAACACACACAT 58.237 36.000 0.00 0.00 0.00 3.21
3359 6162 5.611374 TCAAACGGAAACAGAGAGAAGATT 58.389 37.500 0.00 0.00 0.00 2.40
3444 6257 1.953559 ATCAACAGAACACGCACACT 58.046 45.000 0.00 0.00 0.00 3.55
3496 6311 0.322816 ACCAGGCAGGCAAGTGTATG 60.323 55.000 0.00 0.00 43.14 2.39
3558 6375 2.303163 TGCATGATGAAAGCATTGCC 57.697 45.000 4.70 0.00 42.55 4.52
3686 7229 2.270434 TATGCAAGGAAGAGGAGGGT 57.730 50.000 0.00 0.00 0.00 4.34
3718 7263 9.312904 AGGAATAATTTGGAGAGAAAATCAACA 57.687 29.630 0.00 0.00 0.00 3.33
3839 7384 4.847444 GGCAGGGAGGAAGCTCGC 62.847 72.222 0.00 0.00 36.68 5.03
3840 7385 3.382803 CTGGCAGGGAGGAAGCTCG 62.383 68.421 6.61 0.00 0.00 5.03
3855 7400 0.807275 TGATCGCGACAGAATGCTGG 60.807 55.000 12.93 0.00 46.60 4.85
3866 7411 2.297315 AGCAATAATCTCCTGATCGCGA 59.703 45.455 13.09 13.09 31.51 5.87
3886 7431 0.394192 TGGCTGAGTTGGAGACACAG 59.606 55.000 0.00 0.00 46.06 3.66
3990 7535 1.066143 AGACTTATCCAACAGGCACCG 60.066 52.381 0.00 0.00 0.00 4.94
3998 7543 5.421374 ACCCTAGTACACAGACTTATCCAAC 59.579 44.000 0.00 0.00 0.00 3.77
3999 7544 5.586877 ACCCTAGTACACAGACTTATCCAA 58.413 41.667 0.00 0.00 0.00 3.53
4000 7545 5.202746 ACCCTAGTACACAGACTTATCCA 57.797 43.478 0.00 0.00 0.00 3.41
4001 7546 6.541934 AAACCCTAGTACACAGACTTATCC 57.458 41.667 0.00 0.00 0.00 2.59
4002 7547 7.876582 ACAAAAACCCTAGTACACAGACTTATC 59.123 37.037 0.00 0.00 0.00 1.75
4003 7548 7.660208 CACAAAAACCCTAGTACACAGACTTAT 59.340 37.037 0.00 0.00 0.00 1.73
4004 7549 6.987992 CACAAAAACCCTAGTACACAGACTTA 59.012 38.462 0.00 0.00 0.00 2.24
4005 7550 5.820947 CACAAAAACCCTAGTACACAGACTT 59.179 40.000 0.00 0.00 0.00 3.01
4006 7551 5.365619 CACAAAAACCCTAGTACACAGACT 58.634 41.667 0.00 0.00 0.00 3.24
4007 7552 4.514066 CCACAAAAACCCTAGTACACAGAC 59.486 45.833 0.00 0.00 0.00 3.51
4008 7553 4.445162 CCCACAAAAACCCTAGTACACAGA 60.445 45.833 0.00 0.00 0.00 3.41
4009 7554 3.818773 CCCACAAAAACCCTAGTACACAG 59.181 47.826 0.00 0.00 0.00 3.66
4010 7555 3.822940 CCCACAAAAACCCTAGTACACA 58.177 45.455 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.