Multiple sequence alignment - TraesCS3D01G461800

Loading Multiple Alignment...

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 TraesCS3D01G461800 chr3D 100.000 2793 0 0 1 2793 566301444 566298652 0.000000e+00 5158.0
1 TraesCS3D01G461800 chr3D 87.773 1235 82 21 799 1982 566423160 566421944 0.000000e+00 1380.0
2 TraesCS3D01G461800 chr3D 91.615 644 26 14 669 1287 566131993 566131353 0.000000e+00 865.0
3 TraesCS3D01G461800 chr3D 92.093 430 24 5 1462 1889 566129640 566129219 5.150000e-167 597.0
4 TraesCS3D01G461800 chr3D 90.604 298 23 5 380 674 566132751 566132456 9.380000e-105 390.0
5 TraesCS3D01G461800 chr3D 79.482 463 57 23 986 1423 566101594 566101145 7.570000e-76 294.0
6 TraesCS3D01G461800 chr3D 87.967 241 18 5 2555 2790 566112529 566112295 9.860000e-70 274.0
7 TraesCS3D01G461800 chr3D 91.813 171 11 1 222 389 566137734 566137564 4.650000e-58 235.0
8 TraesCS3D01G461800 chr3D 80.800 250 22 10 2555 2792 566391868 566391633 3.700000e-39 172.0
9 TraesCS3D01G461800 chr3D 93.396 106 3 2 2595 2696 566409868 566409763 1.340000e-33 154.0
10 TraesCS3D01G461800 chr3D 87.156 109 9 2 277 381 566394253 566394146 4.890000e-23 119.0
11 TraesCS3D01G461800 chr3D 89.011 91 10 0 1892 1982 566100794 566100704 2.270000e-21 113.0
12 TraesCS3D01G461800 chr3D 97.222 36 1 0 1312 1347 566131317 566131282 8.350000e-06 62.1
13 TraesCS3D01G461800 chr3A 87.001 1354 87 34 669 1982 700953175 700954479 0.000000e+00 1443.0
14 TraesCS3D01G461800 chr3A 96.683 814 26 1 383 1196 701122988 701123800 0.000000e+00 1352.0
15 TraesCS3D01G461800 chr3A 96.942 556 14 1 1982 2537 77919593 77920145 0.000000e+00 929.0
16 TraesCS3D01G461800 chr3A 96.403 556 18 1 1982 2537 77918120 77918673 0.000000e+00 915.0
17 TraesCS3D01G461800 chr3A 84.852 845 67 20 1180 1982 700893457 700894282 0.000000e+00 795.0
18 TraesCS3D01G461800 chr3A 94.617 483 16 5 1315 1794 701123797 701124272 0.000000e+00 739.0
19 TraesCS3D01G461800 chr3A 77.490 1235 166 64 255 1423 701139289 701140477 3.030000e-179 638.0
20 TraesCS3D01G461800 chr3A 80.149 806 101 32 1200 1982 700945397 700946166 5.260000e-152 547.0
21 TraesCS3D01G461800 chr3A 82.576 660 67 20 936 1551 700908739 700909394 3.170000e-149 538.0
22 TraesCS3D01G461800 chr3A 84.375 512 46 17 701 1185 700960662 700961166 3.260000e-129 472.0
23 TraesCS3D01G461800 chr3A 83.436 489 62 12 699 1185 700944785 700945256 1.190000e-118 436.0
24 TraesCS3D01G461800 chr3A 82.061 524 54 22 1479 1977 701140482 701140990 7.200000e-111 411.0
25 TraesCS3D01G461800 chr3A 93.852 244 10 2 2555 2793 700954530 700954773 2.040000e-96 363.0
26 TraesCS3D01G461800 chr3A 80.000 430 49 17 256 674 700944035 700944438 1.640000e-72 283.0
27 TraesCS3D01G461800 chr3B 85.258 1221 91 42 808 1982 755575223 755576400 0.000000e+00 1175.0
28 TraesCS3D01G461800 chr3B 94.746 590 21 5 1315 1901 755771282 755771864 0.000000e+00 909.0
29 TraesCS3D01G461800 chr3B 90.373 644 31 15 669 1287 754720017 754720654 0.000000e+00 817.0
30 TraesCS3D01G461800 chr3B 87.926 646 51 4 1339 1982 754722096 754722716 0.000000e+00 736.0
31 TraesCS3D01G461800 chr3B 91.985 524 30 5 1462 1982 755606046 755606560 0.000000e+00 725.0
32 TraesCS3D01G461800 chr3B 86.923 650 32 22 669 1287 755605113 755605740 0.000000e+00 680.0
33 TraesCS3D01G461800 chr3B 91.485 458 33 4 222 674 754719095 754719551 2.360000e-175 625.0
34 TraesCS3D01G461800 chr3B 88.383 439 38 8 756 1185 754770975 754771409 1.480000e-142 516.0
35 TraesCS3D01G461800 chr3B 96.764 309 8 2 888 1196 755770979 755771285 5.330000e-142 514.0
36 TraesCS3D01G461800 chr3B 82.008 528 61 15 1479 1982 756082110 756081593 4.300000e-113 418.0
37 TraesCS3D01G461800 chr3B 95.951 247 4 3 2551 2793 755771922 755772166 2.020000e-106 396.0
38 TraesCS3D01G461800 chr3B 96.218 238 8 1 2557 2793 754722766 754723003 3.370000e-104 388.0
39 TraesCS3D01G461800 chr3B 79.181 586 63 24 1203 1762 755710576 755711128 4.430000e-93 351.0
40 TraesCS3D01G461800 chr3B 90.244 246 16 2 2555 2792 754772366 754772611 5.810000e-82 315.0
41 TraesCS3D01G461800 chr3B 90.244 246 16 2 2555 2793 755606611 755606855 5.810000e-82 315.0
42 TraesCS3D01G461800 chr3B 96.089 179 7 0 669 847 755770803 755770981 2.720000e-75 292.0
43 TraesCS3D01G461800 chr3B 84.109 258 22 8 256 507 755708703 755708947 6.020000e-57 231.0
44 TraesCS3D01G461800 chr3B 91.124 169 10 1 2555 2718 755660873 755661041 1.010000e-54 224.0
45 TraesCS3D01G461800 chr3B 81.503 173 19 7 504 674 755709264 755709425 2.260000e-26 130.0
46 TraesCS3D01G461800 chr3B 93.103 58 4 0 277 334 754770574 754770631 4.960000e-13 86.1
47 TraesCS3D01G461800 chr3B 97.778 45 1 0 277 321 755657430 755657474 8.290000e-11 78.7
48 TraesCS3D01G461800 chrUn 97.842 556 12 0 1982 2537 100679246 100679801 0.000000e+00 961.0
49 TraesCS3D01G461800 chrUn 96.959 559 17 0 1979 2537 100677777 100678335 0.000000e+00 939.0
50 TraesCS3D01G461800 chrUn 82.008 528 61 15 1479 1982 408040744 408041261 4.300000e-113 418.0
51 TraesCS3D01G461800 chr1A 96.763 556 18 0 1982 2537 56369272 56368717 0.000000e+00 928.0
52 TraesCS3D01G461800 chr2D 92.199 564 34 8 1978 2537 610713051 610713608 0.000000e+00 789.0
53 TraesCS3D01G461800 chr2B 89.279 569 44 14 1982 2538 30474977 30474414 0.000000e+00 697.0
54 TraesCS3D01G461800 chr1B 88.380 568 49 15 1982 2537 503071076 503071638 0.000000e+00 667.0
55 TraesCS3D01G461800 chr1B 88.070 570 48 18 1981 2537 503069594 503070156 0.000000e+00 658.0
56 TraesCS3D01G461800 chr4B 78.161 435 57 21 136 553 649490864 649491277 2.780000e-60 243.0


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 TraesCS3D01G461800 chr3D 566298652 566301444 2792 True 5158.000000 5158 100.000000 1 2793 1 chr3D.!!$R3 2792
1 TraesCS3D01G461800 chr3D 566421944 566423160 1216 True 1380.000000 1380 87.773000 799 1982 1 chr3D.!!$R5 1183
2 TraesCS3D01G461800 chr3D 566129219 566132751 3532 True 478.525000 865 92.883500 380 1889 4 chr3D.!!$R7 1509
3 TraesCS3D01G461800 chr3D 566100704 566101594 890 True 203.500000 294 84.246500 986 1982 2 chr3D.!!$R6 996
4 TraesCS3D01G461800 chr3A 701122988 701124272 1284 False 1045.500000 1352 95.650000 383 1794 2 chr3A.!!$F7 1411
5 TraesCS3D01G461800 chr3A 77918120 77920145 2025 False 922.000000 929 96.672500 1982 2537 2 chr3A.!!$F4 555
6 TraesCS3D01G461800 chr3A 700953175 700954773 1598 False 903.000000 1443 90.426500 669 2793 2 chr3A.!!$F6 2124
7 TraesCS3D01G461800 chr3A 700893457 700894282 825 False 795.000000 795 84.852000 1180 1982 1 chr3A.!!$F1 802
8 TraesCS3D01G461800 chr3A 700908739 700909394 655 False 538.000000 538 82.576000 936 1551 1 chr3A.!!$F2 615
9 TraesCS3D01G461800 chr3A 701139289 701140990 1701 False 524.500000 638 79.775500 255 1977 2 chr3A.!!$F8 1722
10 TraesCS3D01G461800 chr3A 700960662 700961166 504 False 472.000000 472 84.375000 701 1185 1 chr3A.!!$F3 484
11 TraesCS3D01G461800 chr3A 700944035 700946166 2131 False 422.000000 547 81.195000 256 1982 3 chr3A.!!$F5 1726
12 TraesCS3D01G461800 chr3B 755575223 755576400 1177 False 1175.000000 1175 85.258000 808 1982 1 chr3B.!!$F1 1174
13 TraesCS3D01G461800 chr3B 754719095 754723003 3908 False 641.500000 817 91.500500 222 2793 4 chr3B.!!$F2 2571
14 TraesCS3D01G461800 chr3B 755605113 755606855 1742 False 573.333333 725 89.717333 669 2793 3 chr3B.!!$F4 2124
15 TraesCS3D01G461800 chr3B 755770803 755772166 1363 False 527.750000 909 95.887500 669 2793 4 chr3B.!!$F7 2124
16 TraesCS3D01G461800 chr3B 756081593 756082110 517 True 418.000000 418 82.008000 1479 1982 1 chr3B.!!$R1 503
17 TraesCS3D01G461800 chr3B 754770574 754772611 2037 False 305.700000 516 90.576667 277 2792 3 chr3B.!!$F3 2515
18 TraesCS3D01G461800 chr3B 755708703 755711128 2425 False 237.333333 351 81.597667 256 1762 3 chr3B.!!$F6 1506
19 TraesCS3D01G461800 chrUn 100677777 100679801 2024 False 950.000000 961 97.400500 1979 2537 2 chrUn.!!$F2 558
20 TraesCS3D01G461800 chrUn 408040744 408041261 517 False 418.000000 418 82.008000 1479 1982 1 chrUn.!!$F1 503
21 TraesCS3D01G461800 chr1A 56368717 56369272 555 True 928.000000 928 96.763000 1982 2537 1 chr1A.!!$R1 555
22 TraesCS3D01G461800 chr2D 610713051 610713608 557 False 789.000000 789 92.199000 1978 2537 1 chr2D.!!$F1 559
23 TraesCS3D01G461800 chr2B 30474414 30474977 563 True 697.000000 697 89.279000 1982 2538 1 chr2B.!!$R1 556
24 TraesCS3D01G461800 chr1B 503069594 503071638 2044 False 662.500000 667 88.225000 1981 2537 2 chr1B.!!$F1 556

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
90 91 0.387239 GGCTTGATCGTGTTGTTGGC 60.387 55.0 0.0 0.0 0.0 4.52 F
91 92 0.725784 GCTTGATCGTGTTGTTGGCG 60.726 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1974 0.829182 AAGCAAGGCCCAAACTCCAG 60.829 55.0 0.0 0.0 0.0 3.86 R
1844 5946 2.755103 CAACCAATTTACCCTCCTGAGC 59.245 50.0 0.0 0.0 0.0 4.26 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
22 23 5.934402 TCTAGGCTTAACACTTAGAAGGG 57.066 43.478 0.00 0.00 34.93 3.95
23 24 5.586877 TCTAGGCTTAACACTTAGAAGGGA 58.413 41.667 0.00 0.00 32.48 4.20
24 25 6.021030 TCTAGGCTTAACACTTAGAAGGGAA 58.979 40.000 0.00 0.00 32.48 3.97
25 26 5.578157 AGGCTTAACACTTAGAAGGGAAA 57.422 39.130 0.00 0.00 32.48 3.13
26 27 6.140968 AGGCTTAACACTTAGAAGGGAAAT 57.859 37.500 0.00 0.00 32.48 2.17
27 28 6.181190 AGGCTTAACACTTAGAAGGGAAATC 58.819 40.000 0.00 0.00 32.48 2.17
28 29 5.357314 GGCTTAACACTTAGAAGGGAAATCC 59.643 44.000 0.00 0.00 32.48 3.01
40 41 4.576330 AGGGAAATCCTACACTTGGAAG 57.424 45.455 0.00 0.00 45.98 3.46
41 42 4.175962 AGGGAAATCCTACACTTGGAAGA 58.824 43.478 0.00 0.00 45.98 2.87
42 43 4.790790 AGGGAAATCCTACACTTGGAAGAT 59.209 41.667 0.00 0.00 45.98 2.40
43 44 4.884164 GGGAAATCCTACACTTGGAAGATG 59.116 45.833 0.00 0.00 37.13 2.90
44 45 4.884164 GGAAATCCTACACTTGGAAGATGG 59.116 45.833 0.00 0.00 37.13 3.51
45 46 5.339200 GGAAATCCTACACTTGGAAGATGGA 60.339 44.000 0.00 0.00 37.13 3.41
46 47 5.779241 AATCCTACACTTGGAAGATGGAA 57.221 39.130 0.00 0.00 37.13 3.53
47 48 4.553330 TCCTACACTTGGAAGATGGAAC 57.447 45.455 0.00 0.00 0.00 3.62
48 49 3.263425 TCCTACACTTGGAAGATGGAACC 59.737 47.826 0.00 0.00 0.00 3.62
49 50 3.009033 CCTACACTTGGAAGATGGAACCA 59.991 47.826 0.00 0.00 0.00 3.67
50 51 2.863809 ACACTTGGAAGATGGAACCAC 58.136 47.619 0.00 0.00 33.20 4.16
51 52 2.443255 ACACTTGGAAGATGGAACCACT 59.557 45.455 0.00 0.00 33.20 4.00
52 53 3.117512 ACACTTGGAAGATGGAACCACTT 60.118 43.478 0.00 2.44 33.20 3.16
53 54 3.503748 CACTTGGAAGATGGAACCACTTC 59.496 47.826 18.55 18.55 39.16 3.01
54 55 3.138283 ACTTGGAAGATGGAACCACTTCA 59.862 43.478 23.40 14.34 40.89 3.02
55 56 4.202609 ACTTGGAAGATGGAACCACTTCAT 60.203 41.667 23.40 5.62 40.89 2.57
56 57 5.014123 ACTTGGAAGATGGAACCACTTCATA 59.986 40.000 23.40 15.48 40.89 2.15
57 58 5.102953 TGGAAGATGGAACCACTTCATAG 57.897 43.478 23.40 0.00 40.89 2.23
58 59 4.536090 TGGAAGATGGAACCACTTCATAGT 59.464 41.667 23.40 0.67 40.89 2.12
59 60 5.014123 TGGAAGATGGAACCACTTCATAGTT 59.986 40.000 23.40 3.86 40.89 2.24
60 61 5.586643 GGAAGATGGAACCACTTCATAGTTC 59.413 44.000 23.40 9.85 40.89 3.01
61 62 5.762179 AGATGGAACCACTTCATAGTTCA 57.238 39.130 0.00 0.00 41.32 3.18
62 63 6.319048 AGATGGAACCACTTCATAGTTCAT 57.681 37.500 0.00 0.00 41.32 2.57
63 64 6.725364 AGATGGAACCACTTCATAGTTCATT 58.275 36.000 0.00 0.00 41.32 2.57
64 65 6.825721 AGATGGAACCACTTCATAGTTCATTC 59.174 38.462 0.00 1.35 41.32 2.67
65 66 5.875224 TGGAACCACTTCATAGTTCATTCA 58.125 37.500 4.69 0.00 41.32 2.57
66 67 5.705441 TGGAACCACTTCATAGTTCATTCAC 59.295 40.000 4.69 0.00 41.32 3.18
67 68 5.705441 GGAACCACTTCATAGTTCATTCACA 59.295 40.000 4.69 0.00 41.32 3.58
68 69 6.206634 GGAACCACTTCATAGTTCATTCACAA 59.793 38.462 4.69 0.00 41.32 3.33
69 70 7.255451 GGAACCACTTCATAGTTCATTCACAAA 60.255 37.037 4.69 0.00 41.32 2.83
70 71 7.581213 ACCACTTCATAGTTCATTCACAAAA 57.419 32.000 0.00 0.00 30.26 2.44
71 72 7.651808 ACCACTTCATAGTTCATTCACAAAAG 58.348 34.615 0.00 0.00 30.26 2.27
72 73 7.086376 CCACTTCATAGTTCATTCACAAAAGG 58.914 38.462 0.00 0.00 30.26 3.11
73 74 6.583806 CACTTCATAGTTCATTCACAAAAGGC 59.416 38.462 0.00 0.00 30.26 4.35
74 75 6.491403 ACTTCATAGTTCATTCACAAAAGGCT 59.509 34.615 0.00 0.00 0.00 4.58
75 76 6.899393 TCATAGTTCATTCACAAAAGGCTT 57.101 33.333 0.00 0.00 0.00 4.35
76 77 6.680810 TCATAGTTCATTCACAAAAGGCTTG 58.319 36.000 0.00 0.00 0.00 4.01
77 78 6.489700 TCATAGTTCATTCACAAAAGGCTTGA 59.510 34.615 0.00 0.00 0.00 3.02
78 79 5.796424 AGTTCATTCACAAAAGGCTTGAT 57.204 34.783 0.00 0.00 0.00 2.57
79 80 5.776744 AGTTCATTCACAAAAGGCTTGATC 58.223 37.500 0.00 0.00 0.00 2.92
80 81 4.424061 TCATTCACAAAAGGCTTGATCG 57.576 40.909 0.00 0.00 0.00 3.69
81 82 3.820467 TCATTCACAAAAGGCTTGATCGT 59.180 39.130 0.00 0.00 0.00 3.73
82 83 3.624326 TTCACAAAAGGCTTGATCGTG 57.376 42.857 0.00 6.40 0.00 4.35
83 84 2.571212 TCACAAAAGGCTTGATCGTGT 58.429 42.857 0.00 0.00 0.00 4.49
84 85 2.948979 TCACAAAAGGCTTGATCGTGTT 59.051 40.909 0.00 0.00 0.00 3.32
85 86 3.044986 CACAAAAGGCTTGATCGTGTTG 58.955 45.455 0.00 2.04 0.00 3.33
86 87 2.687935 ACAAAAGGCTTGATCGTGTTGT 59.312 40.909 0.00 2.75 30.10 3.32
87 88 3.130340 ACAAAAGGCTTGATCGTGTTGTT 59.870 39.130 0.00 0.00 30.62 2.83
88 89 3.354089 AAAGGCTTGATCGTGTTGTTG 57.646 42.857 0.00 0.00 0.00 3.33
89 90 1.238439 AGGCTTGATCGTGTTGTTGG 58.762 50.000 0.00 0.00 0.00 3.77
90 91 0.387239 GGCTTGATCGTGTTGTTGGC 60.387 55.000 0.00 0.00 0.00 4.52
91 92 0.725784 GCTTGATCGTGTTGTTGGCG 60.726 55.000 0.00 0.00 0.00 5.69
92 93 0.865111 CTTGATCGTGTTGTTGGCGA 59.135 50.000 0.00 0.00 39.02 5.54
93 94 1.262950 CTTGATCGTGTTGTTGGCGAA 59.737 47.619 0.00 0.00 38.17 4.70
94 95 1.518325 TGATCGTGTTGTTGGCGAAT 58.482 45.000 0.00 0.00 38.17 3.34
95 96 2.689646 TGATCGTGTTGTTGGCGAATA 58.310 42.857 0.00 0.00 38.17 1.75
96 97 2.413796 TGATCGTGTTGTTGGCGAATAC 59.586 45.455 0.00 0.00 38.17 1.89
97 98 1.867166 TCGTGTTGTTGGCGAATACA 58.133 45.000 0.00 0.00 0.00 2.29
98 99 2.210961 TCGTGTTGTTGGCGAATACAA 58.789 42.857 0.00 0.00 32.21 2.41
99 100 2.809119 TCGTGTTGTTGGCGAATACAAT 59.191 40.909 0.00 0.00 36.72 2.71
100 101 3.995048 TCGTGTTGTTGGCGAATACAATA 59.005 39.130 0.00 0.00 36.72 1.90
101 102 4.451435 TCGTGTTGTTGGCGAATACAATAA 59.549 37.500 0.00 0.00 36.72 1.40
102 103 5.049612 TCGTGTTGTTGGCGAATACAATAAA 60.050 36.000 0.00 0.00 36.72 1.40
103 104 5.797934 CGTGTTGTTGGCGAATACAATAAAT 59.202 36.000 0.00 0.00 36.72 1.40
104 105 6.306837 CGTGTTGTTGGCGAATACAATAAATT 59.693 34.615 0.00 0.00 36.72 1.82
105 106 7.148885 CGTGTTGTTGGCGAATACAATAAATTT 60.149 33.333 0.00 0.00 36.72 1.82
106 107 8.491950 GTGTTGTTGGCGAATACAATAAATTTT 58.508 29.630 0.00 0.00 36.72 1.82
107 108 8.704234 TGTTGTTGGCGAATACAATAAATTTTC 58.296 29.630 0.00 0.00 36.72 2.29
108 109 7.820044 TGTTGGCGAATACAATAAATTTTCC 57.180 32.000 0.00 0.00 0.00 3.13
109 110 7.607250 TGTTGGCGAATACAATAAATTTTCCT 58.393 30.769 0.00 0.00 0.00 3.36
110 111 8.091449 TGTTGGCGAATACAATAAATTTTCCTT 58.909 29.630 0.00 0.00 0.00 3.36
111 112 8.592155 GTTGGCGAATACAATAAATTTTCCTTC 58.408 33.333 0.00 0.00 0.00 3.46
112 113 7.831753 TGGCGAATACAATAAATTTTCCTTCA 58.168 30.769 0.00 0.00 0.00 3.02
113 114 7.973388 TGGCGAATACAATAAATTTTCCTTCAG 59.027 33.333 0.00 0.00 0.00 3.02
114 115 7.043391 GGCGAATACAATAAATTTTCCTTCAGC 60.043 37.037 0.00 1.60 0.00 4.26
115 116 7.487829 GCGAATACAATAAATTTTCCTTCAGCA 59.512 33.333 0.00 0.00 0.00 4.41
116 117 9.520204 CGAATACAATAAATTTTCCTTCAGCAT 57.480 29.630 0.00 0.00 0.00 3.79
120 121 8.712285 ACAATAAATTTTCCTTCAGCATCATG 57.288 30.769 0.00 0.00 0.00 3.07
121 122 8.533657 ACAATAAATTTTCCTTCAGCATCATGA 58.466 29.630 0.00 0.00 0.00 3.07
122 123 8.814235 CAATAAATTTTCCTTCAGCATCATGAC 58.186 33.333 0.00 0.00 0.00 3.06
123 124 5.988310 AATTTTCCTTCAGCATCATGACA 57.012 34.783 0.00 0.00 0.00 3.58
124 125 6.540438 AATTTTCCTTCAGCATCATGACAT 57.460 33.333 0.00 0.00 0.00 3.06
125 126 7.649533 AATTTTCCTTCAGCATCATGACATA 57.350 32.000 0.00 0.00 0.00 2.29
126 127 6.441093 TTTTCCTTCAGCATCATGACATAC 57.559 37.500 0.00 0.00 0.00 2.39
127 128 4.758773 TCCTTCAGCATCATGACATACA 57.241 40.909 0.00 0.00 0.00 2.29
128 129 5.101648 TCCTTCAGCATCATGACATACAA 57.898 39.130 0.00 0.00 0.00 2.41
129 130 5.499313 TCCTTCAGCATCATGACATACAAA 58.501 37.500 0.00 0.00 0.00 2.83
130 131 6.124340 TCCTTCAGCATCATGACATACAAAT 58.876 36.000 0.00 0.00 0.00 2.32
131 132 6.261603 TCCTTCAGCATCATGACATACAAATC 59.738 38.462 0.00 0.00 0.00 2.17
132 133 6.038936 CCTTCAGCATCATGACATACAAATCA 59.961 38.462 0.00 0.00 0.00 2.57
133 134 6.367686 TCAGCATCATGACATACAAATCAC 57.632 37.500 0.00 0.00 0.00 3.06
134 135 6.117488 TCAGCATCATGACATACAAATCACT 58.883 36.000 0.00 0.00 0.00 3.41
135 136 6.037830 TCAGCATCATGACATACAAATCACTG 59.962 38.462 0.00 0.00 0.00 3.66
136 137 4.974275 GCATCATGACATACAAATCACTGC 59.026 41.667 0.00 0.00 0.00 4.40
137 138 5.516996 CATCATGACATACAAATCACTGCC 58.483 41.667 0.00 0.00 0.00 4.85
138 139 3.947196 TCATGACATACAAATCACTGCCC 59.053 43.478 0.00 0.00 0.00 5.36
139 140 3.431673 TGACATACAAATCACTGCCCA 57.568 42.857 0.00 0.00 0.00 5.36
140 141 3.760738 TGACATACAAATCACTGCCCAA 58.239 40.909 0.00 0.00 0.00 4.12
141 142 4.343231 TGACATACAAATCACTGCCCAAT 58.657 39.130 0.00 0.00 0.00 3.16
142 143 4.771577 TGACATACAAATCACTGCCCAATT 59.228 37.500 0.00 0.00 0.00 2.32
143 144 5.245751 TGACATACAAATCACTGCCCAATTT 59.754 36.000 0.00 0.00 0.00 1.82
144 145 6.112927 ACATACAAATCACTGCCCAATTTT 57.887 33.333 0.00 0.00 0.00 1.82
145 146 6.532826 ACATACAAATCACTGCCCAATTTTT 58.467 32.000 0.00 0.00 0.00 1.94
166 167 7.663043 TTTTTGGGTAACACTTGGATTAACT 57.337 32.000 0.00 0.00 39.74 2.24
167 168 7.663043 TTTTGGGTAACACTTGGATTAACTT 57.337 32.000 0.00 0.00 39.74 2.66
168 169 6.887626 TTGGGTAACACTTGGATTAACTTC 57.112 37.500 0.00 0.00 39.74 3.01
169 170 6.195600 TGGGTAACACTTGGATTAACTTCT 57.804 37.500 0.00 0.00 39.74 2.85
170 171 6.607019 TGGGTAACACTTGGATTAACTTCTT 58.393 36.000 0.00 0.00 39.74 2.52
171 172 7.747690 TGGGTAACACTTGGATTAACTTCTTA 58.252 34.615 0.00 0.00 39.74 2.10
172 173 8.219178 TGGGTAACACTTGGATTAACTTCTTAA 58.781 33.333 0.00 0.00 39.74 1.85
173 174 9.070179 GGGTAACACTTGGATTAACTTCTTAAA 57.930 33.333 0.00 0.00 39.74 1.52
178 179 9.841295 ACACTTGGATTAACTTCTTAAAGTACA 57.159 29.630 0.00 0.00 45.07 2.90
189 190 8.685838 ACTTCTTAAAGTACATTTGCTAACCA 57.314 30.769 0.00 0.00 43.98 3.67
190 191 8.784043 ACTTCTTAAAGTACATTTGCTAACCAG 58.216 33.333 0.00 0.00 43.98 4.00
191 192 8.685838 TTCTTAAAGTACATTTGCTAACCAGT 57.314 30.769 0.00 0.00 32.01 4.00
192 193 9.781633 TTCTTAAAGTACATTTGCTAACCAGTA 57.218 29.630 0.00 0.00 32.01 2.74
193 194 9.211485 TCTTAAAGTACATTTGCTAACCAGTAC 57.789 33.333 0.00 10.13 33.80 2.73
194 195 8.905660 TTAAAGTACATTTGCTAACCAGTACA 57.094 30.769 16.33 1.51 35.51 2.90
195 196 7.996098 AAAGTACATTTGCTAACCAGTACAT 57.004 32.000 16.33 7.16 35.51 2.29
196 197 7.611213 AAGTACATTTGCTAACCAGTACATC 57.389 36.000 16.33 0.00 35.51 3.06
197 198 6.707290 AGTACATTTGCTAACCAGTACATCA 58.293 36.000 16.33 0.00 35.51 3.07
198 199 7.338710 AGTACATTTGCTAACCAGTACATCAT 58.661 34.615 16.33 1.27 35.51 2.45
199 200 6.441093 ACATTTGCTAACCAGTACATCATG 57.559 37.500 0.00 0.00 0.00 3.07
200 201 4.963276 TTTGCTAACCAGTACATCATGC 57.037 40.909 0.00 0.00 0.00 4.06
201 202 3.625649 TGCTAACCAGTACATCATGCA 57.374 42.857 0.00 0.00 0.00 3.96
202 203 4.155063 TGCTAACCAGTACATCATGCAT 57.845 40.909 0.00 0.00 0.00 3.96
203 204 5.289083 TGCTAACCAGTACATCATGCATA 57.711 39.130 0.00 0.00 0.00 3.14
204 205 5.056480 TGCTAACCAGTACATCATGCATAC 58.944 41.667 0.00 0.00 0.00 2.39
205 206 5.056480 GCTAACCAGTACATCATGCATACA 58.944 41.667 0.00 0.00 0.00 2.29
206 207 5.050091 GCTAACCAGTACATCATGCATACAC 60.050 44.000 0.00 0.00 0.00 2.90
207 208 4.486125 ACCAGTACATCATGCATACACA 57.514 40.909 0.00 0.00 0.00 3.72
208 209 4.842574 ACCAGTACATCATGCATACACAA 58.157 39.130 0.00 0.00 0.00 3.33
209 210 4.877823 ACCAGTACATCATGCATACACAAG 59.122 41.667 0.00 0.00 0.00 3.16
210 211 4.877823 CCAGTACATCATGCATACACAAGT 59.122 41.667 0.00 0.00 0.00 3.16
211 212 6.048509 CCAGTACATCATGCATACACAAGTA 58.951 40.000 0.00 0.00 34.10 2.24
212 213 6.707608 CCAGTACATCATGCATACACAAGTAT 59.292 38.462 0.00 0.00 41.57 2.12
213 214 7.095481 CCAGTACATCATGCATACACAAGTATC 60.095 40.741 0.00 0.00 38.88 2.24
214 215 7.654923 CAGTACATCATGCATACACAAGTATCT 59.345 37.037 0.00 0.00 38.88 1.98
215 216 8.860088 AGTACATCATGCATACACAAGTATCTA 58.140 33.333 0.00 0.00 38.88 1.98
216 217 9.645059 GTACATCATGCATACACAAGTATCTAT 57.355 33.333 0.00 0.00 38.88 1.98
217 218 8.768957 ACATCATGCATACACAAGTATCTATC 57.231 34.615 0.00 0.00 38.88 2.08
218 219 8.591940 ACATCATGCATACACAAGTATCTATCT 58.408 33.333 0.00 0.00 38.88 1.98
234 235 9.682465 AGTATCTATCTACATACGGCAGAATTA 57.318 33.333 0.00 0.00 31.74 1.40
241 242 0.756903 TACGGCAGAATTAGGAGGCC 59.243 55.000 0.00 0.00 41.20 5.19
350 360 1.066358 GTCACCCACCCAACTAGTAGC 60.066 57.143 0.00 0.00 0.00 3.58
358 371 6.331837 ACCCACCCAACTAGTAGCAAATATAT 59.668 38.462 0.00 0.00 0.00 0.86
367 393 5.832539 AGTAGCAAATATATGGCCTCACT 57.167 39.130 3.32 5.24 0.00 3.41
371 397 3.755378 GCAAATATATGGCCTCACTGGAG 59.245 47.826 3.32 0.00 41.02 3.86
381 412 1.882623 CCTCACTGGAGCAAAGGAAAC 59.117 52.381 0.00 0.00 39.96 2.78
403 434 3.366476 CGAGACTTCATTCGGTGACTTCT 60.366 47.826 0.00 0.00 36.32 2.85
470 508 3.689347 TGCAGAGTTCATGCCTGTTTAT 58.311 40.909 0.00 0.00 43.18 1.40
572 933 6.704512 TTTTTCATAAAAAGAGCCGATTGC 57.295 33.333 0.00 0.00 35.84 3.56
599 960 9.545105 TCTGTTACCGTCTTTTAATGTTTTCTA 57.455 29.630 0.00 0.00 0.00 2.10
734 1640 9.651913 AACGAAGCCATACATTTTTCATTTAAT 57.348 25.926 0.00 0.00 0.00 1.40
940 1876 1.600636 TGCTTGGGCAGGAAACTCG 60.601 57.895 0.00 0.00 44.28 4.18
1029 1974 3.397482 AGCGTTGATCCTGCAGATTATC 58.603 45.455 17.39 14.96 34.42 1.75
1164 2110 6.652481 CACTTTGTCTCTTCTATTGTCCATGT 59.348 38.462 0.00 0.00 0.00 3.21
1173 2119 5.006153 TCTATTGTCCATGTGGTACTTCG 57.994 43.478 0.00 0.00 36.34 3.79
1187 2155 5.585047 GTGGTACTTCGGAATTAATTGAGCT 59.415 40.000 5.17 0.00 0.00 4.09
1261 2347 3.778265 ACTCATGGTTTTGTATTGGCCT 58.222 40.909 3.32 0.00 0.00 5.19
1280 2367 2.303022 CCTAGTTCTTGTTCTGCCTCCA 59.697 50.000 0.00 0.00 0.00 3.86
1302 2390 6.495181 TCCATCTAAGAGAATAAGGTAGCCTG 59.505 42.308 0.00 0.00 32.13 4.85
1304 2392 7.180051 CCATCTAAGAGAATAAGGTAGCCTGAT 59.820 40.741 0.00 0.00 32.13 2.90
1344 2455 7.143340 CGATGAATTGTCCATTTGAGCAATAT 58.857 34.615 0.00 0.00 32.09 1.28
1347 2458 9.923143 ATGAATTGTCCATTTGAGCAATATATG 57.077 29.630 0.00 0.00 32.09 1.78
1368 3858 5.759506 TGTCAACAACCAATATGTTTCGT 57.240 34.783 0.00 0.00 38.90 3.85
1448 5501 5.809001 AGAACTAATGGCTGTCATTTCTCA 58.191 37.500 13.28 0.00 43.04 3.27
1449 5502 6.421485 AGAACTAATGGCTGTCATTTCTCAT 58.579 36.000 13.28 0.00 43.04 2.90
1555 5657 4.340950 AGCTAGCAAAGGTCTATCTGAGTC 59.659 45.833 18.83 0.00 0.00 3.36
1556 5658 4.340950 GCTAGCAAAGGTCTATCTGAGTCT 59.659 45.833 10.63 0.00 0.00 3.24
1557 5659 4.734398 AGCAAAGGTCTATCTGAGTCTG 57.266 45.455 0.00 0.00 0.00 3.51
1558 5660 4.348486 AGCAAAGGTCTATCTGAGTCTGA 58.652 43.478 1.83 1.83 0.00 3.27
1559 5661 4.402155 AGCAAAGGTCTATCTGAGTCTGAG 59.598 45.833 5.90 0.00 0.00 3.35
1560 5662 4.159506 GCAAAGGTCTATCTGAGTCTGAGT 59.840 45.833 5.90 0.00 0.00 3.41
1821 5923 1.286501 GTGCTCATAATCGCCGTCAA 58.713 50.000 0.00 0.00 0.00 3.18
1844 5946 2.237143 TCAGGCTAATTGTCAGTCAGGG 59.763 50.000 0.00 0.00 0.00 4.45
1901 6025 5.885912 GGACACTTGCTAATTTCATCCCTTA 59.114 40.000 0.00 0.00 0.00 2.69
2199 9301 2.584608 CTTCCTGGCGATCCGGTT 59.415 61.111 0.00 0.00 37.01 4.44
2324 9426 2.950172 CTCGAACGTGGCCAAACCG 61.950 63.158 7.24 10.42 43.94 4.44
2349 9451 2.702478 TCCGGACTCGATCTAGACCTTA 59.298 50.000 0.00 0.12 39.00 2.69
2538 9640 2.588620 ACCGTGGCTTATTCCAACAAA 58.411 42.857 0.00 0.00 37.96 2.83
2539 9641 3.161866 ACCGTGGCTTATTCCAACAAAT 58.838 40.909 0.00 0.00 37.96 2.32
2540 9642 4.337145 ACCGTGGCTTATTCCAACAAATA 58.663 39.130 0.00 0.00 37.96 1.40
2541 9643 4.398044 ACCGTGGCTTATTCCAACAAATAG 59.602 41.667 0.00 0.00 37.96 1.73
2542 9644 4.398044 CCGTGGCTTATTCCAACAAATAGT 59.602 41.667 0.00 0.00 37.96 2.12
2543 9645 5.105917 CCGTGGCTTATTCCAACAAATAGTT 60.106 40.000 0.00 0.00 42.42 2.24
2544 9646 6.094325 CCGTGGCTTATTCCAACAAATAGTTA 59.906 38.462 0.00 0.00 38.74 2.24
2545 9647 7.201785 CCGTGGCTTATTCCAACAAATAGTTAT 60.202 37.037 0.00 0.00 38.74 1.89
2546 9648 8.188139 CGTGGCTTATTCCAACAAATAGTTATT 58.812 33.333 0.00 0.00 38.74 1.40
2547 9649 9.301153 GTGGCTTATTCCAACAAATAGTTATTG 57.699 33.333 0.00 0.00 38.74 1.90
2548 9650 7.978975 TGGCTTATTCCAACAAATAGTTATTGC 59.021 33.333 0.00 0.00 38.74 3.56
2549 9651 8.197439 GGCTTATTCCAACAAATAGTTATTGCT 58.803 33.333 0.00 0.00 38.74 3.91
2550 9652 9.586435 GCTTATTCCAACAAATAGTTATTGCTT 57.414 29.630 0.00 0.00 38.74 3.91
2591 9693 2.110011 AGGTACCTGAAAAATGCCCTGT 59.890 45.455 15.42 0.00 0.00 4.00
2661 9771 5.660460 ACACATTTTTGGAAGGAAGTTCAC 58.340 37.500 5.01 0.00 36.82 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.934402 TCCCTTCTAAGTGTTAAGCCTAG 57.066 43.478 0.00 0.00 0.00 3.02
3 4 5.578157 TTTCCCTTCTAAGTGTTAAGCCT 57.422 39.130 0.00 0.00 0.00 4.58
5 6 6.181190 AGGATTTCCCTTCTAAGTGTTAAGC 58.819 40.000 0.00 0.00 44.85 3.09
6 7 8.319146 TGTAGGATTTCCCTTCTAAGTGTTAAG 58.681 37.037 0.00 0.00 44.85 1.85
7 8 8.098912 GTGTAGGATTTCCCTTCTAAGTGTTAA 58.901 37.037 0.00 0.00 44.85 2.01
8 9 7.456902 AGTGTAGGATTTCCCTTCTAAGTGTTA 59.543 37.037 0.00 0.00 44.85 2.41
9 10 6.272558 AGTGTAGGATTTCCCTTCTAAGTGTT 59.727 38.462 0.00 0.00 44.85 3.32
10 11 5.785940 AGTGTAGGATTTCCCTTCTAAGTGT 59.214 40.000 0.00 0.00 44.85 3.55
11 12 6.301169 AGTGTAGGATTTCCCTTCTAAGTG 57.699 41.667 0.00 0.00 44.85 3.16
12 13 6.296489 CCAAGTGTAGGATTTCCCTTCTAAGT 60.296 42.308 0.00 0.00 44.85 2.24
13 14 6.070194 TCCAAGTGTAGGATTTCCCTTCTAAG 60.070 42.308 0.00 0.00 44.85 2.18
14 15 5.788533 TCCAAGTGTAGGATTTCCCTTCTAA 59.211 40.000 0.00 0.00 44.85 2.10
15 16 5.347124 TCCAAGTGTAGGATTTCCCTTCTA 58.653 41.667 0.00 0.00 44.85 2.10
16 17 4.175962 TCCAAGTGTAGGATTTCCCTTCT 58.824 43.478 0.00 0.00 44.85 2.85
17 18 4.569719 TCCAAGTGTAGGATTTCCCTTC 57.430 45.455 0.00 0.00 44.85 3.46
18 19 4.601857 TCTTCCAAGTGTAGGATTTCCCTT 59.398 41.667 0.00 0.00 44.85 3.95
20 21 4.569719 TCTTCCAAGTGTAGGATTTCCC 57.430 45.455 0.00 0.00 34.56 3.97
21 22 4.884164 CCATCTTCCAAGTGTAGGATTTCC 59.116 45.833 0.00 0.00 34.56 3.13
22 23 5.745227 TCCATCTTCCAAGTGTAGGATTTC 58.255 41.667 0.00 0.00 34.56 2.17
23 24 5.779241 TCCATCTTCCAAGTGTAGGATTT 57.221 39.130 0.00 0.00 34.56 2.17
24 25 5.501156 GTTCCATCTTCCAAGTGTAGGATT 58.499 41.667 0.00 0.00 34.56 3.01
25 26 4.080299 GGTTCCATCTTCCAAGTGTAGGAT 60.080 45.833 0.00 0.00 34.56 3.24
26 27 3.263425 GGTTCCATCTTCCAAGTGTAGGA 59.737 47.826 0.00 0.00 0.00 2.94
27 28 3.009033 TGGTTCCATCTTCCAAGTGTAGG 59.991 47.826 0.00 0.00 0.00 3.18
28 29 4.003648 GTGGTTCCATCTTCCAAGTGTAG 58.996 47.826 0.00 0.00 32.82 2.74
29 30 3.650942 AGTGGTTCCATCTTCCAAGTGTA 59.349 43.478 0.00 0.00 32.82 2.90
30 31 2.443255 AGTGGTTCCATCTTCCAAGTGT 59.557 45.455 0.00 0.00 32.82 3.55
31 32 3.146104 AGTGGTTCCATCTTCCAAGTG 57.854 47.619 0.00 0.00 32.82 3.16
32 33 3.138283 TGAAGTGGTTCCATCTTCCAAGT 59.862 43.478 20.28 0.00 37.39 3.16
33 34 3.754965 TGAAGTGGTTCCATCTTCCAAG 58.245 45.455 20.28 0.00 37.39 3.61
34 35 3.874383 TGAAGTGGTTCCATCTTCCAA 57.126 42.857 20.28 9.09 37.39 3.53
35 36 4.536090 ACTATGAAGTGGTTCCATCTTCCA 59.464 41.667 20.28 13.77 37.39 3.53
36 37 5.104259 ACTATGAAGTGGTTCCATCTTCC 57.896 43.478 20.28 10.69 37.39 3.46
37 38 6.173339 TGAACTATGAAGTGGTTCCATCTTC 58.827 40.000 18.23 18.23 44.94 2.87
38 39 6.126863 TGAACTATGAAGTGGTTCCATCTT 57.873 37.500 0.00 1.20 44.94 2.40
39 40 5.762179 TGAACTATGAAGTGGTTCCATCT 57.238 39.130 0.00 0.00 44.94 2.90
40 41 6.599244 TGAATGAACTATGAAGTGGTTCCATC 59.401 38.462 0.00 0.00 44.94 3.51
41 42 6.375455 GTGAATGAACTATGAAGTGGTTCCAT 59.625 38.462 0.00 0.00 44.94 3.41
42 43 5.705441 GTGAATGAACTATGAAGTGGTTCCA 59.295 40.000 0.00 0.00 44.94 3.53
43 44 5.705441 TGTGAATGAACTATGAAGTGGTTCC 59.295 40.000 0.00 0.00 44.94 3.62
44 45 6.801539 TGTGAATGAACTATGAAGTGGTTC 57.198 37.500 0.00 0.00 45.53 3.62
45 46 7.581213 TTTGTGAATGAACTATGAAGTGGTT 57.419 32.000 0.00 0.00 35.62 3.67
46 47 7.255590 CCTTTTGTGAATGAACTATGAAGTGGT 60.256 37.037 0.00 0.00 35.62 4.16
47 48 7.086376 CCTTTTGTGAATGAACTATGAAGTGG 58.914 38.462 0.00 0.00 35.62 4.00
48 49 6.583806 GCCTTTTGTGAATGAACTATGAAGTG 59.416 38.462 0.00 0.00 35.62 3.16
49 50 6.491403 AGCCTTTTGTGAATGAACTATGAAGT 59.509 34.615 0.00 0.00 37.65 3.01
50 51 6.917533 AGCCTTTTGTGAATGAACTATGAAG 58.082 36.000 0.00 0.00 0.00 3.02
51 52 6.899393 AGCCTTTTGTGAATGAACTATGAA 57.101 33.333 0.00 0.00 0.00 2.57
52 53 6.489700 TCAAGCCTTTTGTGAATGAACTATGA 59.510 34.615 0.00 0.00 0.00 2.15
53 54 6.680810 TCAAGCCTTTTGTGAATGAACTATG 58.319 36.000 0.00 0.00 0.00 2.23
54 55 6.899393 TCAAGCCTTTTGTGAATGAACTAT 57.101 33.333 0.00 0.00 0.00 2.12
55 56 6.348458 CGATCAAGCCTTTTGTGAATGAACTA 60.348 38.462 0.00 0.00 0.00 2.24
56 57 5.563475 CGATCAAGCCTTTTGTGAATGAACT 60.563 40.000 0.00 0.00 0.00 3.01
57 58 4.618489 CGATCAAGCCTTTTGTGAATGAAC 59.382 41.667 0.00 0.00 0.00 3.18
58 59 4.278170 ACGATCAAGCCTTTTGTGAATGAA 59.722 37.500 0.00 0.00 0.00 2.57
59 60 3.820467 ACGATCAAGCCTTTTGTGAATGA 59.180 39.130 0.00 0.00 0.00 2.57
60 61 3.916172 CACGATCAAGCCTTTTGTGAATG 59.084 43.478 0.00 0.00 0.00 2.67
61 62 3.569701 ACACGATCAAGCCTTTTGTGAAT 59.430 39.130 3.97 0.00 0.00 2.57
62 63 2.948979 ACACGATCAAGCCTTTTGTGAA 59.051 40.909 3.97 0.00 0.00 3.18
63 64 2.571212 ACACGATCAAGCCTTTTGTGA 58.429 42.857 3.97 0.00 0.00 3.58
64 65 3.044986 CAACACGATCAAGCCTTTTGTG 58.955 45.455 0.00 0.00 0.00 3.33
65 66 2.687935 ACAACACGATCAAGCCTTTTGT 59.312 40.909 0.00 0.00 0.00 2.83
66 67 3.354089 ACAACACGATCAAGCCTTTTG 57.646 42.857 0.00 0.00 0.00 2.44
67 68 3.490761 CCAACAACACGATCAAGCCTTTT 60.491 43.478 0.00 0.00 0.00 2.27
68 69 2.034558 CCAACAACACGATCAAGCCTTT 59.965 45.455 0.00 0.00 0.00 3.11
69 70 1.608590 CCAACAACACGATCAAGCCTT 59.391 47.619 0.00 0.00 0.00 4.35
70 71 1.238439 CCAACAACACGATCAAGCCT 58.762 50.000 0.00 0.00 0.00 4.58
71 72 0.387239 GCCAACAACACGATCAAGCC 60.387 55.000 0.00 0.00 0.00 4.35
72 73 0.725784 CGCCAACAACACGATCAAGC 60.726 55.000 0.00 0.00 0.00 4.01
73 74 0.865111 TCGCCAACAACACGATCAAG 59.135 50.000 0.00 0.00 0.00 3.02
74 75 1.300481 TTCGCCAACAACACGATCAA 58.700 45.000 0.00 0.00 35.48 2.57
75 76 1.518325 ATTCGCCAACAACACGATCA 58.482 45.000 0.00 0.00 35.48 2.92
76 77 2.413796 TGTATTCGCCAACAACACGATC 59.586 45.455 0.00 0.00 35.48 3.69
77 78 2.418692 TGTATTCGCCAACAACACGAT 58.581 42.857 0.00 0.00 35.48 3.73
78 79 1.867166 TGTATTCGCCAACAACACGA 58.133 45.000 0.00 0.00 0.00 4.35
79 80 2.672188 TTGTATTCGCCAACAACACG 57.328 45.000 0.00 0.00 30.88 4.49
80 81 7.575332 AATTTATTGTATTCGCCAACAACAC 57.425 32.000 0.00 0.00 38.35 3.32
81 82 8.594881 AAAATTTATTGTATTCGCCAACAACA 57.405 26.923 0.00 0.00 38.35 3.33
82 83 8.166066 GGAAAATTTATTGTATTCGCCAACAAC 58.834 33.333 0.00 0.00 38.35 3.32
83 84 8.091449 AGGAAAATTTATTGTATTCGCCAACAA 58.909 29.630 0.00 0.00 39.73 2.83
84 85 7.607250 AGGAAAATTTATTGTATTCGCCAACA 58.393 30.769 0.00 0.00 0.00 3.33
85 86 8.474006 AAGGAAAATTTATTGTATTCGCCAAC 57.526 30.769 0.00 0.00 0.00 3.77
86 87 8.307483 TGAAGGAAAATTTATTGTATTCGCCAA 58.693 29.630 0.00 0.00 0.00 4.52
87 88 7.831753 TGAAGGAAAATTTATTGTATTCGCCA 58.168 30.769 0.00 0.00 0.00 5.69
88 89 7.043391 GCTGAAGGAAAATTTATTGTATTCGCC 60.043 37.037 0.00 0.00 0.00 5.54
89 90 7.487829 TGCTGAAGGAAAATTTATTGTATTCGC 59.512 33.333 0.00 1.39 0.00 4.70
90 91 8.909708 TGCTGAAGGAAAATTTATTGTATTCG 57.090 30.769 0.00 0.00 0.00 3.34
94 95 9.806203 CATGATGCTGAAGGAAAATTTATTGTA 57.194 29.630 0.00 0.00 0.00 2.41
95 96 8.533657 TCATGATGCTGAAGGAAAATTTATTGT 58.466 29.630 0.00 0.00 0.00 2.71
96 97 8.814235 GTCATGATGCTGAAGGAAAATTTATTG 58.186 33.333 0.00 0.00 0.00 1.90
97 98 8.533657 TGTCATGATGCTGAAGGAAAATTTATT 58.466 29.630 0.00 0.00 0.00 1.40
98 99 8.070034 TGTCATGATGCTGAAGGAAAATTTAT 57.930 30.769 0.00 0.00 0.00 1.40
99 100 7.465353 TGTCATGATGCTGAAGGAAAATTTA 57.535 32.000 0.00 0.00 0.00 1.40
100 101 6.349243 TGTCATGATGCTGAAGGAAAATTT 57.651 33.333 0.00 0.00 0.00 1.82
101 102 5.988310 TGTCATGATGCTGAAGGAAAATT 57.012 34.783 0.00 0.00 0.00 1.82
102 103 6.604396 TGTATGTCATGATGCTGAAGGAAAAT 59.396 34.615 0.00 0.00 0.00 1.82
103 104 5.945191 TGTATGTCATGATGCTGAAGGAAAA 59.055 36.000 0.00 0.00 0.00 2.29
104 105 5.499313 TGTATGTCATGATGCTGAAGGAAA 58.501 37.500 0.00 0.00 0.00 3.13
105 106 5.101648 TGTATGTCATGATGCTGAAGGAA 57.898 39.130 0.00 0.00 0.00 3.36
106 107 4.758773 TGTATGTCATGATGCTGAAGGA 57.241 40.909 0.00 0.00 0.00 3.36
107 108 5.823209 TTTGTATGTCATGATGCTGAAGG 57.177 39.130 0.00 0.00 0.00 3.46
108 109 6.910972 GTGATTTGTATGTCATGATGCTGAAG 59.089 38.462 0.00 0.00 0.00 3.02
109 110 6.600427 AGTGATTTGTATGTCATGATGCTGAA 59.400 34.615 0.00 0.00 0.00 3.02
110 111 6.037830 CAGTGATTTGTATGTCATGATGCTGA 59.962 38.462 0.00 0.00 0.00 4.26
111 112 6.199393 CAGTGATTTGTATGTCATGATGCTG 58.801 40.000 0.00 0.00 0.00 4.41
112 113 5.220989 GCAGTGATTTGTATGTCATGATGCT 60.221 40.000 0.00 0.00 32.84 3.79
113 114 4.974275 GCAGTGATTTGTATGTCATGATGC 59.026 41.667 0.00 0.00 0.00 3.91
114 115 5.506815 GGGCAGTGATTTGTATGTCATGATG 60.507 44.000 0.00 0.00 0.00 3.07
115 116 4.581824 GGGCAGTGATTTGTATGTCATGAT 59.418 41.667 0.00 0.00 0.00 2.45
116 117 3.947196 GGGCAGTGATTTGTATGTCATGA 59.053 43.478 0.00 0.00 0.00 3.07
117 118 3.695556 TGGGCAGTGATTTGTATGTCATG 59.304 43.478 0.00 0.00 0.00 3.07
118 119 3.966979 TGGGCAGTGATTTGTATGTCAT 58.033 40.909 0.00 0.00 0.00 3.06
119 120 3.431673 TGGGCAGTGATTTGTATGTCA 57.568 42.857 0.00 0.00 0.00 3.58
120 121 4.989279 ATTGGGCAGTGATTTGTATGTC 57.011 40.909 0.00 0.00 0.00 3.06
121 122 5.743636 AAATTGGGCAGTGATTTGTATGT 57.256 34.783 0.00 0.00 0.00 2.29
142 143 7.663043 AGTTAATCCAAGTGTTACCCAAAAA 57.337 32.000 0.00 0.00 0.00 1.94
143 144 7.562088 AGAAGTTAATCCAAGTGTTACCCAAAA 59.438 33.333 0.00 0.00 0.00 2.44
144 145 7.064229 AGAAGTTAATCCAAGTGTTACCCAAA 58.936 34.615 0.00 0.00 0.00 3.28
145 146 6.607019 AGAAGTTAATCCAAGTGTTACCCAA 58.393 36.000 0.00 0.00 0.00 4.12
146 147 6.195600 AGAAGTTAATCCAAGTGTTACCCA 57.804 37.500 0.00 0.00 0.00 4.51
147 148 8.625786 TTAAGAAGTTAATCCAAGTGTTACCC 57.374 34.615 0.00 0.00 0.00 3.69
152 153 9.841295 TGTACTTTAAGAAGTTAATCCAAGTGT 57.159 29.630 0.00 0.00 43.48 3.55
163 164 9.127277 TGGTTAGCAAATGTACTTTAAGAAGTT 57.873 29.630 0.00 0.00 43.48 2.66
165 166 8.784043 ACTGGTTAGCAAATGTACTTTAAGAAG 58.216 33.333 0.00 0.00 38.87 2.85
166 167 8.685838 ACTGGTTAGCAAATGTACTTTAAGAA 57.314 30.769 0.00 0.00 0.00 2.52
167 168 9.211485 GTACTGGTTAGCAAATGTACTTTAAGA 57.789 33.333 0.00 0.00 0.00 2.10
168 169 8.995220 TGTACTGGTTAGCAAATGTACTTTAAG 58.005 33.333 11.66 0.00 33.59 1.85
169 170 8.905660 TGTACTGGTTAGCAAATGTACTTTAA 57.094 30.769 11.66 0.00 33.59 1.52
170 171 9.158233 GATGTACTGGTTAGCAAATGTACTTTA 57.842 33.333 11.66 0.00 33.59 1.85
171 172 7.663905 TGATGTACTGGTTAGCAAATGTACTTT 59.336 33.333 11.66 0.00 33.59 2.66
172 173 7.165485 TGATGTACTGGTTAGCAAATGTACTT 58.835 34.615 11.66 7.07 33.59 2.24
173 174 6.707290 TGATGTACTGGTTAGCAAATGTACT 58.293 36.000 11.66 1.46 33.59 2.73
174 175 6.978343 TGATGTACTGGTTAGCAAATGTAC 57.022 37.500 5.78 5.78 0.00 2.90
175 176 6.038161 GCATGATGTACTGGTTAGCAAATGTA 59.962 38.462 0.00 0.00 0.00 2.29
176 177 5.163622 GCATGATGTACTGGTTAGCAAATGT 60.164 40.000 0.00 0.00 0.00 2.71
177 178 5.163632 TGCATGATGTACTGGTTAGCAAATG 60.164 40.000 0.00 0.00 0.00 2.32
178 179 4.949238 TGCATGATGTACTGGTTAGCAAAT 59.051 37.500 0.00 0.00 0.00 2.32
179 180 4.331108 TGCATGATGTACTGGTTAGCAAA 58.669 39.130 0.00 0.00 0.00 3.68
180 181 3.949132 TGCATGATGTACTGGTTAGCAA 58.051 40.909 0.00 0.00 0.00 3.91
181 182 3.625649 TGCATGATGTACTGGTTAGCA 57.374 42.857 0.00 0.00 0.00 3.49
182 183 5.050091 GTGTATGCATGATGTACTGGTTAGC 60.050 44.000 10.16 0.00 0.00 3.09
183 184 6.048509 TGTGTATGCATGATGTACTGGTTAG 58.951 40.000 10.16 0.00 0.00 2.34
184 185 5.983540 TGTGTATGCATGATGTACTGGTTA 58.016 37.500 10.16 0.00 0.00 2.85
185 186 4.842574 TGTGTATGCATGATGTACTGGTT 58.157 39.130 10.16 0.00 0.00 3.67
186 187 4.486125 TGTGTATGCATGATGTACTGGT 57.514 40.909 10.16 0.00 0.00 4.00
187 188 4.877823 ACTTGTGTATGCATGATGTACTGG 59.122 41.667 10.16 1.92 0.00 4.00
188 189 7.654923 AGATACTTGTGTATGCATGATGTACTG 59.345 37.037 10.16 0.00 39.29 2.74
189 190 7.730084 AGATACTTGTGTATGCATGATGTACT 58.270 34.615 10.16 2.72 39.29 2.73
190 191 7.953158 AGATACTTGTGTATGCATGATGTAC 57.047 36.000 10.16 0.00 39.29 2.90
191 192 9.860898 GATAGATACTTGTGTATGCATGATGTA 57.139 33.333 10.16 4.61 39.29 2.29
192 193 8.591940 AGATAGATACTTGTGTATGCATGATGT 58.408 33.333 10.16 2.48 39.29 3.06
193 194 8.999220 AGATAGATACTTGTGTATGCATGATG 57.001 34.615 10.16 0.00 39.29 3.07
195 196 9.077885 TGTAGATAGATACTTGTGTATGCATGA 57.922 33.333 10.16 0.00 39.29 3.07
196 197 9.866798 ATGTAGATAGATACTTGTGTATGCATG 57.133 33.333 10.16 0.00 39.29 4.06
199 200 9.491934 CGTATGTAGATAGATACTTGTGTATGC 57.508 37.037 5.83 0.00 39.29 3.14
200 201 9.989869 CCGTATGTAGATAGATACTTGTGTATG 57.010 37.037 5.83 0.00 39.29 2.39
201 202 8.675504 GCCGTATGTAGATAGATACTTGTGTAT 58.324 37.037 5.83 0.00 41.65 2.29
202 203 7.662669 TGCCGTATGTAGATAGATACTTGTGTA 59.337 37.037 5.83 0.00 32.16 2.90
203 204 6.489022 TGCCGTATGTAGATAGATACTTGTGT 59.511 38.462 5.83 0.00 32.16 3.72
204 205 6.909909 TGCCGTATGTAGATAGATACTTGTG 58.090 40.000 5.83 0.00 32.16 3.33
205 206 6.940867 TCTGCCGTATGTAGATAGATACTTGT 59.059 38.462 5.83 0.00 32.16 3.16
206 207 7.379098 TCTGCCGTATGTAGATAGATACTTG 57.621 40.000 5.83 0.00 32.16 3.16
207 208 7.997773 TTCTGCCGTATGTAGATAGATACTT 57.002 36.000 5.83 0.00 35.49 2.24
208 209 8.582657 AATTCTGCCGTATGTAGATAGATACT 57.417 34.615 5.83 0.00 35.49 2.12
209 210 9.938670 CTAATTCTGCCGTATGTAGATAGATAC 57.061 37.037 0.00 0.00 35.49 2.24
210 211 9.121658 CCTAATTCTGCCGTATGTAGATAGATA 57.878 37.037 0.00 0.00 35.49 1.98
211 212 7.834681 TCCTAATTCTGCCGTATGTAGATAGAT 59.165 37.037 0.00 0.00 35.49 1.98
212 213 7.173032 TCCTAATTCTGCCGTATGTAGATAGA 58.827 38.462 0.00 0.00 35.49 1.98
213 214 7.392494 TCCTAATTCTGCCGTATGTAGATAG 57.608 40.000 0.00 0.00 35.49 2.08
214 215 6.377429 CCTCCTAATTCTGCCGTATGTAGATA 59.623 42.308 0.00 0.00 35.49 1.98
215 216 5.186021 CCTCCTAATTCTGCCGTATGTAGAT 59.814 44.000 0.00 0.00 35.49 1.98
216 217 4.523173 CCTCCTAATTCTGCCGTATGTAGA 59.477 45.833 0.00 0.00 33.47 2.59
217 218 4.810790 CCTCCTAATTCTGCCGTATGTAG 58.189 47.826 0.00 0.00 0.00 2.74
218 219 3.006537 GCCTCCTAATTCTGCCGTATGTA 59.993 47.826 0.00 0.00 0.00 2.29
219 220 2.224305 GCCTCCTAATTCTGCCGTATGT 60.224 50.000 0.00 0.00 0.00 2.29
220 221 2.417719 GCCTCCTAATTCTGCCGTATG 58.582 52.381 0.00 0.00 0.00 2.39
241 242 4.188247 TCGAATGAGTAAGTTGGTGGAG 57.812 45.455 0.00 0.00 0.00 3.86
350 360 3.755378 GCTCCAGTGAGGCCATATATTTG 59.245 47.826 5.01 0.00 39.14 2.32
358 371 1.073722 CTTTGCTCCAGTGAGGCCA 59.926 57.895 5.01 0.00 39.14 5.36
367 393 1.416401 AGTCTCGTTTCCTTTGCTCCA 59.584 47.619 0.00 0.00 0.00 3.86
371 397 4.467735 GAATGAAGTCTCGTTTCCTTTGC 58.532 43.478 0.00 0.00 30.61 3.68
381 412 2.638556 AGTCACCGAATGAAGTCTCG 57.361 50.000 0.00 0.00 39.72 4.04
470 508 2.094906 CGATGTCGAGTTTGTGGTCCTA 60.095 50.000 0.00 0.00 43.02 2.94
566 927 2.279582 AGACGGTAACAGAGCAATCG 57.720 50.000 0.00 0.00 0.00 3.34
572 933 8.557029 AGAAAACATTAAAAGACGGTAACAGAG 58.443 33.333 0.00 0.00 0.00 3.35
734 1640 2.875296 CATGGGAGGAAAAACTGTGGA 58.125 47.619 0.00 0.00 0.00 4.02
934 1870 3.061697 GTCGACAAAACACACTCGAGTTT 59.938 43.478 17.26 6.93 37.50 2.66
940 1876 4.449068 AGATGATGTCGACAAAACACACTC 59.551 41.667 24.13 13.18 0.00 3.51
1029 1974 0.829182 AAGCAAGGCCCAAACTCCAG 60.829 55.000 0.00 0.00 0.00 3.86
1164 2110 5.741011 AGCTCAATTAATTCCGAAGTACCA 58.259 37.500 0.00 0.00 0.00 3.25
1219 2294 6.265196 TGAGTTGCACTTATCCTGAATTTTGT 59.735 34.615 0.00 0.00 0.00 2.83
1247 2333 6.327279 ACAAGAACTAGGCCAATACAAAAC 57.673 37.500 5.01 0.00 0.00 2.43
1261 2347 3.840666 AGATGGAGGCAGAACAAGAACTA 59.159 43.478 0.00 0.00 0.00 2.24
1302 2390 9.979270 CAATTCATCGGCAAAGTTCTATATATC 57.021 33.333 0.00 0.00 0.00 1.63
1304 2392 8.902540 ACAATTCATCGGCAAAGTTCTATATA 57.097 30.769 0.00 0.00 0.00 0.86
1306 2394 6.260050 GGACAATTCATCGGCAAAGTTCTATA 59.740 38.462 0.00 0.00 0.00 1.31
1309 2420 3.191371 GGACAATTCATCGGCAAAGTTCT 59.809 43.478 0.00 0.00 0.00 3.01
1344 2455 7.041030 ACACGAAACATATTGGTTGTTGACATA 60.041 33.333 0.00 0.00 37.38 2.29
1347 2458 5.398122 CACACGAAACATATTGGTTGTTGAC 59.602 40.000 0.00 0.00 37.38 3.18
1448 5501 6.237901 TGTGAGATGTAACAACTTTGGCTAT 58.762 36.000 0.00 0.00 0.00 2.97
1449 5502 5.616270 TGTGAGATGTAACAACTTTGGCTA 58.384 37.500 0.00 0.00 0.00 3.93
1555 5657 7.358931 GCATTCACAATTGATGTTTTCACTCAG 60.359 37.037 13.59 0.00 41.46 3.35
1556 5658 6.421501 GCATTCACAATTGATGTTTTCACTCA 59.578 34.615 13.59 0.00 41.46 3.41
1557 5659 6.421501 TGCATTCACAATTGATGTTTTCACTC 59.578 34.615 13.59 0.00 41.46 3.51
1558 5660 6.282167 TGCATTCACAATTGATGTTTTCACT 58.718 32.000 13.59 0.00 41.46 3.41
1559 5661 6.528014 TGCATTCACAATTGATGTTTTCAC 57.472 33.333 13.59 0.00 41.46 3.18
1560 5662 7.577107 CAATGCATTCACAATTGATGTTTTCA 58.423 30.769 13.59 2.28 41.46 2.69
1821 5923 3.055530 CCTGACTGACAATTAGCCTGACT 60.056 47.826 0.00 0.00 0.00 3.41
1844 5946 2.755103 CAACCAATTTACCCTCCTGAGC 59.245 50.000 0.00 0.00 0.00 4.26
1901 6025 7.348815 TCAAACAGACAATCCATCTATCCAAT 58.651 34.615 0.00 0.00 0.00 3.16
2199 9301 1.220749 GGGCAGCTCACGTTGGATA 59.779 57.895 0.00 0.00 0.00 2.59
2324 9426 0.860533 CTAGATCGAGTCCGGACGTC 59.139 60.000 28.26 22.63 36.20 4.34
2349 9451 0.727970 TACGTGCTTGTGTTTGCGTT 59.272 45.000 0.00 0.00 34.38 4.84
2538 9640 7.118390 GGCGAGTTATCATCAAGCAATAACTAT 59.882 37.037 6.91 0.00 43.03 2.12
2539 9641 6.423905 GGCGAGTTATCATCAAGCAATAACTA 59.576 38.462 6.91 0.00 43.03 2.24
2540 9642 5.237344 GGCGAGTTATCATCAAGCAATAACT 59.763 40.000 6.68 6.68 44.69 2.24
2541 9643 5.007626 TGGCGAGTTATCATCAAGCAATAAC 59.992 40.000 0.00 0.00 36.54 1.89
2542 9644 5.122519 TGGCGAGTTATCATCAAGCAATAA 58.877 37.500 0.00 0.00 0.00 1.40
2543 9645 4.702831 TGGCGAGTTATCATCAAGCAATA 58.297 39.130 0.00 0.00 0.00 1.90
2544 9646 3.544684 TGGCGAGTTATCATCAAGCAAT 58.455 40.909 0.00 0.00 0.00 3.56
2545 9647 2.984562 TGGCGAGTTATCATCAAGCAA 58.015 42.857 0.00 0.00 0.00 3.91
2546 9648 2.689553 TGGCGAGTTATCATCAAGCA 57.310 45.000 0.00 0.00 0.00 3.91
2547 9649 2.156504 CGATGGCGAGTTATCATCAAGC 59.843 50.000 0.00 0.00 40.82 4.01
2548 9650 3.642705 TCGATGGCGAGTTATCATCAAG 58.357 45.455 0.00 0.00 42.51 3.02
2549 9651 3.726291 TCGATGGCGAGTTATCATCAA 57.274 42.857 0.00 0.00 42.51 2.57
2661 9771 3.064900 AGAGCAGGGCAAAGACTAAAG 57.935 47.619 0.00 0.00 0.00 1.85
2728 9838 9.490379 ACTACGATCTAAACTTTTCTGTCAATT 57.510 29.630 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.