Multiple sequence alignment - TraesCS7A01G440700

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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 TraesCS7A01G440700 chr7A 100.000 5254 0 0 1 5254 635048947 635054200 0.000000e+00 9703.0
1 TraesCS7A01G440700 chr7A 84.105 1749 221 25 2515 4230 635241190 635242914 0.000000e+00 1637.0
2 TraesCS7A01G440700 chr7A 81.494 1740 265 39 2568 4274 635270704 635272419 0.000000e+00 1376.0
3 TraesCS7A01G440700 chr7A 89.609 1049 76 12 1489 2513 736488993 736490032 0.000000e+00 1303.0
4 TraesCS7A01G440700 chr7A 81.468 1662 233 48 2543 4178 635094128 635095740 0.000000e+00 1293.0
5 TraesCS7A01G440700 chr7A 81.626 898 113 21 3422 4284 635238807 635239687 0.000000e+00 697.0
6 TraesCS7A01G440700 chr4A 93.931 1104 35 8 320 1423 311740863 311739792 0.000000e+00 1639.0
7 TraesCS7A01G440700 chr4A 85.475 179 20 3 1218 1396 211390076 211390248 1.160000e-41 182.0
8 TraesCS7A01G440700 chr7D 84.039 1748 225 30 2515 4230 549770519 549772244 0.000000e+00 1633.0
9 TraesCS7A01G440700 chr7D 83.402 1687 216 37 2515 4174 549697341 549698990 0.000000e+00 1506.0
10 TraesCS7A01G440700 chr7D 81.115 1811 280 35 2511 4283 549783251 549785037 0.000000e+00 1393.0
11 TraesCS7A01G440700 chr7D 82.041 1676 236 42 2523 4174 549705402 549707036 0.000000e+00 1367.0
12 TraesCS7A01G440700 chr7D 87.085 1053 102 18 1489 2512 572313635 572314682 0.000000e+00 1160.0
13 TraesCS7A01G440700 chr7D 87.343 1035 95 15 1488 2492 381004840 381003812 0.000000e+00 1153.0
14 TraesCS7A01G440700 chr7D 90.407 761 49 9 1779 2516 141566711 141565952 0.000000e+00 979.0
15 TraesCS7A01G440700 chr7D 80.702 1140 175 27 2798 3916 549685221 549686336 0.000000e+00 845.0
16 TraesCS7A01G440700 chr7D 79.641 334 41 14 437 750 165477851 165478177 1.150000e-51 215.0
17 TraesCS7A01G440700 chr7D 82.773 238 21 8 3903 4121 549746163 549746399 1.490000e-45 195.0
18 TraesCS7A01G440700 chr7D 91.453 117 9 1 4355 4470 549548555 549548671 5.450000e-35 159.0
19 TraesCS7A01G440700 chr7B 83.190 1749 236 33 2515 4230 594063603 594065326 0.000000e+00 1548.0
20 TraesCS7A01G440700 chr7B 80.762 1679 249 49 2523 4178 594048338 594049965 0.000000e+00 1243.0
21 TraesCS7A01G440700 chr7B 94.730 778 41 0 2977 3754 594015313 594016090 0.000000e+00 1210.0
22 TraesCS7A01G440700 chr7B 81.935 1395 204 23 2912 4274 594116195 594117573 0.000000e+00 1136.0
23 TraesCS7A01G440700 chr7B 85.558 1094 136 11 2543 3624 594035402 594036485 0.000000e+00 1125.0
24 TraesCS7A01G440700 chr7B 95.596 545 18 1 4716 5254 594020189 594020733 0.000000e+00 869.0
25 TraesCS7A01G440700 chr7B 82.014 1023 134 26 3232 4230 594055752 594056748 0.000000e+00 824.0
26 TraesCS7A01G440700 chr7B 83.206 524 83 5 679 1198 576676021 576675499 4.760000e-130 475.0
27 TraesCS7A01G440700 chr7B 85.971 278 31 3 2205 2476 742342885 742342610 1.850000e-74 291.0
28 TraesCS7A01G440700 chr7B 89.051 137 10 3 4352 4483 593925113 593925249 1.170000e-36 165.0
29 TraesCS7A01G440700 chr7B 93.939 66 3 1 90 154 594062761 594062826 1.200000e-16 99.0
30 TraesCS7A01G440700 chrUn 91.242 1119 89 7 314 1426 320716604 320717719 0.000000e+00 1515.0
31 TraesCS7A01G440700 chrUn 90.885 1119 93 7 314 1426 267641496 267642611 0.000000e+00 1493.0
32 TraesCS7A01G440700 chrUn 86.729 1070 102 20 1478 2513 228914596 228913533 0.000000e+00 1153.0
33 TraesCS7A01G440700 chrUn 86.717 1069 103 20 1478 2513 266698954 266697892 0.000000e+00 1151.0
34 TraesCS7A01G440700 chrUn 97.059 34 1 0 851 884 342689171 342689138 2.040000e-04 58.4
35 TraesCS7A01G440700 chrUn 97.059 34 1 0 851 884 342690962 342690995 2.040000e-04 58.4
36 TraesCS7A01G440700 chrUn 97.059 34 1 0 851 884 459813845 459813812 2.040000e-04 58.4
37 TraesCS7A01G440700 chrUn 97.059 34 0 1 851 884 342689056 342689024 7.350000e-04 56.5
38 TraesCS7A01G440700 chrUn 97.059 34 0 1 851 884 342691077 342691109 7.350000e-04 56.5
39 TraesCS7A01G440700 chr2D 90.404 1115 97 7 317 1424 620479382 620480493 0.000000e+00 1458.0
40 TraesCS7A01G440700 chr2D 88.962 1069 72 19 1490 2513 445183732 445184799 0.000000e+00 1279.0
41 TraesCS7A01G440700 chr2D 89.583 1008 79 8 1495 2477 151470210 151469204 0.000000e+00 1256.0
42 TraesCS7A01G440700 chr2D 82.407 432 65 9 785 1210 642238070 642237644 2.990000e-97 366.0
43 TraesCS7A01G440700 chr5D 90.840 1048 69 11 1489 2513 5692149 5691106 0.000000e+00 1378.0
44 TraesCS7A01G440700 chr5D 81.851 551 82 9 679 1225 361569235 361568699 1.040000e-121 448.0
45 TraesCS7A01G440700 chr5D 78.632 468 56 22 509 941 170324243 170323785 2.410000e-68 270.0
46 TraesCS7A01G440700 chr5D 87.770 139 15 2 4341 4477 17506414 17506276 1.510000e-35 161.0
47 TraesCS7A01G440700 chr3A 87.726 1051 102 10 1488 2512 46987347 46986298 0.000000e+00 1201.0
48 TraesCS7A01G440700 chr6D 87.559 1061 90 21 1489 2514 464696088 464697141 0.000000e+00 1190.0
49 TraesCS7A01G440700 chr6D 81.667 120 18 3 994 1109 131025764 131025645 4.330000e-16 97.1
50 TraesCS7A01G440700 chr2A 86.794 1045 110 13 1491 2511 21995552 21994512 0.000000e+00 1140.0
51 TraesCS7A01G440700 chr2A 88.663 591 45 5 1945 2513 238371328 238370738 0.000000e+00 701.0
52 TraesCS7A01G440700 chr5A 86.393 1073 98 15 1488 2513 488997016 488998087 0.000000e+00 1129.0
53 TraesCS7A01G440700 chr5A 83.099 213 30 6 1214 1424 606697727 606697935 6.950000e-44 189.0
54 TraesCS7A01G440700 chr5B 86.053 1054 88 28 1489 2513 17578008 17579031 0.000000e+00 1077.0
55 TraesCS7A01G440700 chr5B 86.842 798 67 10 607 1398 141907079 141906314 0.000000e+00 857.0
56 TraesCS7A01G440700 chr5B 87.385 650 78 4 320 967 382780884 382780237 0.000000e+00 743.0
57 TraesCS7A01G440700 chr5B 86.449 642 75 9 785 1421 382780362 382779728 0.000000e+00 693.0
58 TraesCS7A01G440700 chr5B 87.329 292 32 2 320 611 141944718 141944432 3.920000e-86 329.0
59 TraesCS7A01G440700 chr5B 83.168 202 32 2 4308 4509 30846759 30846560 3.230000e-42 183.0
60 TraesCS7A01G440700 chr5B 87.586 145 16 2 4335 4477 13842514 13842658 3.250000e-37 167.0
61 TraesCS7A01G440700 chr5B 85.075 134 16 2 669 798 17964890 17965023 3.300000e-27 134.0
62 TraesCS7A01G440700 chr1D 83.696 552 80 9 679 1225 440868569 440868023 3.630000e-141 512.0
63 TraesCS7A01G440700 chr1D 80.696 316 47 10 4354 4661 436721564 436721255 3.160000e-57 233.0
64 TraesCS7A01G440700 chr1D 82.126 207 28 7 787 992 52679309 52679111 9.050000e-38 169.0
65 TraesCS7A01G440700 chr1D 83.051 118 15 4 790 907 270618709 270618597 9.310000e-18 102.0
66 TraesCS7A01G440700 chr1A 81.798 445 70 7 785 1222 14148827 14149267 3.870000e-96 363.0
67 TraesCS7A01G440700 chr1A 81.798 445 70 7 785 1222 14156816 14157256 3.870000e-96 363.0
68 TraesCS7A01G440700 chr1A 85.928 334 39 4 4336 4661 566416054 566416387 3.010000e-92 350.0
69 TraesCS7A01G440700 chr1A 85.629 334 40 4 4336 4661 566410414 566410747 1.400000e-90 344.0
70 TraesCS7A01G440700 chr1A 85.294 340 40 7 4331 4661 566413194 566413532 5.040000e-90 342.0
71 TraesCS7A01G440700 chr1A 87.000 200 22 4 1224 1422 574300523 574300327 6.850000e-54 222.0
72 TraesCS7A01G440700 chr6A 83.807 352 48 8 806 1153 131440175 131439829 5.070000e-85 326.0
73 TraesCS7A01G440700 chr3D 86.469 303 20 4 2230 2511 556989378 556989076 3.950000e-81 313.0
74 TraesCS7A01G440700 chr6B 81.433 307 39 12 4370 4661 118041488 118041185 8.800000e-58 235.0
75 TraesCS7A01G440700 chr4B 78.554 401 46 17 787 1153 29695963 29696357 1.470000e-55 228.0
76 TraesCS7A01G440700 chr4B 84.530 181 25 3 794 973 417220360 417220182 5.410000e-40 176.0
77 TraesCS7A01G440700 chr4B 83.077 195 27 5 794 986 82414686 82414496 7.000000e-39 172.0
78 TraesCS7A01G440700 chr4B 85.246 122 13 4 992 1108 662379047 662379168 2.570000e-23 121.0
79 TraesCS7A01G440700 chr4D 87.113 194 19 3 1229 1422 15773127 15773314 1.150000e-51 215.0
80 TraesCS7A01G440700 chr4D 77.971 345 51 17 785 1109 364037933 364038272 5.370000e-45 193.0
81 TraesCS7A01G440700 chr4D 84.416 154 22 2 1005 1157 52830272 52830424 3.280000e-32 150.0
82 TraesCS7A01G440700 chr4D 81.905 105 13 6 783 884 47524904 47525005 3.370000e-12 84.2
83 TraesCS7A01G440700 chr1B 85.507 207 23 6 787 990 453819782 453819580 5.330000e-50 209.0


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 TraesCS7A01G440700 chr7A 635048947 635054200 5253 False 9703.000000 9703 100.0000 1 5254 1 chr7A.!!$F1 5253
1 TraesCS7A01G440700 chr7A 635270704 635272419 1715 False 1376.000000 1376 81.4940 2568 4274 1 chr7A.!!$F3 1706
2 TraesCS7A01G440700 chr7A 736488993 736490032 1039 False 1303.000000 1303 89.6090 1489 2513 1 chr7A.!!$F4 1024
3 TraesCS7A01G440700 chr7A 635094128 635095740 1612 False 1293.000000 1293 81.4680 2543 4178 1 chr7A.!!$F2 1635
4 TraesCS7A01G440700 chr7A 635238807 635242914 4107 False 1167.000000 1637 82.8655 2515 4284 2 chr7A.!!$F5 1769
5 TraesCS7A01G440700 chr4A 311739792 311740863 1071 True 1639.000000 1639 93.9310 320 1423 1 chr4A.!!$R1 1103
6 TraesCS7A01G440700 chr7D 549770519 549772244 1725 False 1633.000000 1633 84.0390 2515 4230 1 chr7D.!!$F7 1715
7 TraesCS7A01G440700 chr7D 549697341 549698990 1649 False 1506.000000 1506 83.4020 2515 4174 1 chr7D.!!$F4 1659
8 TraesCS7A01G440700 chr7D 549783251 549785037 1786 False 1393.000000 1393 81.1150 2511 4283 1 chr7D.!!$F8 1772
9 TraesCS7A01G440700 chr7D 549705402 549707036 1634 False 1367.000000 1367 82.0410 2523 4174 1 chr7D.!!$F5 1651
10 TraesCS7A01G440700 chr7D 572313635 572314682 1047 False 1160.000000 1160 87.0850 1489 2512 1 chr7D.!!$F9 1023
11 TraesCS7A01G440700 chr7D 381003812 381004840 1028 True 1153.000000 1153 87.3430 1488 2492 1 chr7D.!!$R2 1004
12 TraesCS7A01G440700 chr7D 141565952 141566711 759 True 979.000000 979 90.4070 1779 2516 1 chr7D.!!$R1 737
13 TraesCS7A01G440700 chr7D 549685221 549686336 1115 False 845.000000 845 80.7020 2798 3916 1 chr7D.!!$F3 1118
14 TraesCS7A01G440700 chr7B 594048338 594049965 1627 False 1243.000000 1243 80.7620 2523 4178 1 chr7B.!!$F5 1655
15 TraesCS7A01G440700 chr7B 594015313 594016090 777 False 1210.000000 1210 94.7300 2977 3754 1 chr7B.!!$F2 777
16 TraesCS7A01G440700 chr7B 594116195 594117573 1378 False 1136.000000 1136 81.9350 2912 4274 1 chr7B.!!$F7 1362
17 TraesCS7A01G440700 chr7B 594035402 594036485 1083 False 1125.000000 1125 85.5580 2543 3624 1 chr7B.!!$F4 1081
18 TraesCS7A01G440700 chr7B 594020189 594020733 544 False 869.000000 869 95.5960 4716 5254 1 chr7B.!!$F3 538
19 TraesCS7A01G440700 chr7B 594055752 594056748 996 False 824.000000 824 82.0140 3232 4230 1 chr7B.!!$F6 998
20 TraesCS7A01G440700 chr7B 594062761 594065326 2565 False 823.500000 1548 88.5645 90 4230 2 chr7B.!!$F8 4140
21 TraesCS7A01G440700 chr7B 576675499 576676021 522 True 475.000000 475 83.2060 679 1198 1 chr7B.!!$R1 519
22 TraesCS7A01G440700 chrUn 320716604 320717719 1115 False 1515.000000 1515 91.2420 314 1426 1 chrUn.!!$F2 1112
23 TraesCS7A01G440700 chrUn 267641496 267642611 1115 False 1493.000000 1493 90.8850 314 1426 1 chrUn.!!$F1 1112
24 TraesCS7A01G440700 chrUn 228913533 228914596 1063 True 1153.000000 1153 86.7290 1478 2513 1 chrUn.!!$R1 1035
25 TraesCS7A01G440700 chrUn 266697892 266698954 1062 True 1151.000000 1151 86.7170 1478 2513 1 chrUn.!!$R2 1035
26 TraesCS7A01G440700 chr2D 620479382 620480493 1111 False 1458.000000 1458 90.4040 317 1424 1 chr2D.!!$F2 1107
27 TraesCS7A01G440700 chr2D 445183732 445184799 1067 False 1279.000000 1279 88.9620 1490 2513 1 chr2D.!!$F1 1023
28 TraesCS7A01G440700 chr2D 151469204 151470210 1006 True 1256.000000 1256 89.5830 1495 2477 1 chr2D.!!$R1 982
29 TraesCS7A01G440700 chr5D 5691106 5692149 1043 True 1378.000000 1378 90.8400 1489 2513 1 chr5D.!!$R1 1024
30 TraesCS7A01G440700 chr5D 361568699 361569235 536 True 448.000000 448 81.8510 679 1225 1 chr5D.!!$R4 546
31 TraesCS7A01G440700 chr3A 46986298 46987347 1049 True 1201.000000 1201 87.7260 1488 2512 1 chr3A.!!$R1 1024
32 TraesCS7A01G440700 chr6D 464696088 464697141 1053 False 1190.000000 1190 87.5590 1489 2514 1 chr6D.!!$F1 1025
33 TraesCS7A01G440700 chr2A 21994512 21995552 1040 True 1140.000000 1140 86.7940 1491 2511 1 chr2A.!!$R1 1020
34 TraesCS7A01G440700 chr2A 238370738 238371328 590 True 701.000000 701 88.6630 1945 2513 1 chr2A.!!$R2 568
35 TraesCS7A01G440700 chr5A 488997016 488998087 1071 False 1129.000000 1129 86.3930 1488 2513 1 chr5A.!!$F1 1025
36 TraesCS7A01G440700 chr5B 17578008 17579031 1023 False 1077.000000 1077 86.0530 1489 2513 1 chr5B.!!$F2 1024
37 TraesCS7A01G440700 chr5B 141906314 141907079 765 True 857.000000 857 86.8420 607 1398 1 chr5B.!!$R2 791
38 TraesCS7A01G440700 chr5B 382779728 382780884 1156 True 718.000000 743 86.9170 320 1421 2 chr5B.!!$R4 1101
39 TraesCS7A01G440700 chr1D 440868023 440868569 546 True 512.000000 512 83.6960 679 1225 1 chr1D.!!$R4 546
40 TraesCS7A01G440700 chr1A 566410414 566416387 5973 False 345.333333 350 85.6170 4331 4661 3 chr1A.!!$F3 330

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
137 139 1.063070 TGCACTTGGAACCCCCACTA 61.063 55.000 0.00 0.0 46.62 2.74 F
196 683 1.089481 TTCGATGGCATCTCAACCGC 61.089 55.000 23.97 0.0 0.00 5.68 F
1432 2051 2.210116 AGCGTCGCCCTTATTACATTG 58.790 47.619 14.86 0.0 0.00 2.82 F
2368 3060 1.134877 TGTGGTGAAAACGGACGTGTA 60.135 47.619 0.00 0.0 0.00 2.90 F
4069 4838 0.642291 GAGCGTCATCGTGATGTGTG 59.358 55.000 9.51 2.9 39.72 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 1863 0.375106 GCAATTACTCGAGCCTGCAC 59.625 55.000 13.61 0.0 0.00 4.57 R
1575 2196 0.382515 TACTTGTTTTGCCCACACGC 59.617 50.000 0.00 0.0 0.00 5.34 R
2724 3440 1.200020 GGCTTCTTTTCGTCATGGTGG 59.800 52.381 0.00 0.0 0.00 4.61 R
4136 4905 0.251474 ACAGCCAGCACCATTCACAT 60.251 50.000 0.00 0.0 0.00 3.21 R
5097 6411 1.344763 AGGTAGATGGATGCTAACCGC 59.655 52.381 0.00 0.0 39.77 5.68 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.356793 CGAGCCCTCGCATCATCC 60.357 66.667 4.63 0.00 46.50 3.51
19 20 4.615815 AGCCCTCGCATCATCCGC 62.616 66.667 0.00 0.00 37.52 5.54
20 21 4.615815 GCCCTCGCATCATCCGCT 62.616 66.667 0.00 0.00 34.03 5.52
21 22 2.356793 CCCTCGCATCATCCGCTC 60.357 66.667 0.00 0.00 0.00 5.03
23 24 2.356793 CTCGCATCATCCGCTCCC 60.357 66.667 0.00 0.00 0.00 4.30
136 138 2.357593 CTGCACTTGGAACCCCCACT 62.358 60.000 0.00 0.00 46.62 4.00
137 139 1.063070 TGCACTTGGAACCCCCACTA 61.063 55.000 0.00 0.00 46.62 2.74
194 681 1.737838 TGTTCGATGGCATCTCAACC 58.262 50.000 23.97 11.72 0.00 3.77
196 683 1.089481 TTCGATGGCATCTCAACCGC 61.089 55.000 23.97 0.00 0.00 5.68
240 773 4.445452 TTAGTCACTACCGACATGTTCC 57.555 45.455 0.00 0.00 38.43 3.62
254 787 6.194463 CGACATGTTCCTGCAGTAATTATTG 58.806 40.000 13.81 3.70 0.00 1.90
258 791 8.458843 ACATGTTCCTGCAGTAATTATTGTTAC 58.541 33.333 13.81 0.00 35.33 2.50
265 798 9.853555 CCTGCAGTAATTATTGTTACATTGAAA 57.146 29.630 13.81 0.00 37.10 2.69
276 809 7.892778 TTGTTACATTGAAATAGTACGCTGA 57.107 32.000 0.00 0.00 0.00 4.26
277 810 7.892778 TGTTACATTGAAATAGTACGCTGAA 57.107 32.000 0.00 0.00 0.00 3.02
278 811 8.487313 TGTTACATTGAAATAGTACGCTGAAT 57.513 30.769 0.00 0.00 0.00 2.57
281 814 7.609760 ACATTGAAATAGTACGCTGAATGAA 57.390 32.000 0.00 0.00 0.00 2.57
285 818 7.234187 TGAAATAGTACGCTGAATGAATGTC 57.766 36.000 0.00 0.00 0.00 3.06
286 819 6.257849 TGAAATAGTACGCTGAATGAATGTCC 59.742 38.462 0.00 0.00 0.00 4.02
289 822 4.122776 AGTACGCTGAATGAATGTCCATC 58.877 43.478 0.00 0.00 0.00 3.51
291 824 3.201290 ACGCTGAATGAATGTCCATCTC 58.799 45.455 0.00 0.00 0.00 2.75
292 825 3.200483 CGCTGAATGAATGTCCATCTCA 58.800 45.455 0.00 0.00 0.00 3.27
296 829 5.466058 GCTGAATGAATGTCCATCTCAGTAG 59.534 44.000 0.46 0.00 35.95 2.57
299 832 8.078060 TGAATGAATGTCCATCTCAGTAGTTA 57.922 34.615 0.00 0.00 0.00 2.24
302 835 7.660030 TGAATGTCCATCTCAGTAGTTATGA 57.340 36.000 0.00 0.00 0.00 2.15
303 836 8.255111 TGAATGTCCATCTCAGTAGTTATGAT 57.745 34.615 0.00 0.00 0.00 2.45
306 839 8.899427 ATGTCCATCTCAGTAGTTATGATTTG 57.101 34.615 0.00 0.00 0.00 2.32
309 842 6.057533 CCATCTCAGTAGTTATGATTTGCCA 58.942 40.000 0.00 0.00 0.00 4.92
313 846 8.579850 TCTCAGTAGTTATGATTTGCCAATTT 57.420 30.769 0.00 0.00 0.00 1.82
442 975 5.426504 CTTCTTATCTTCACTGTGAGCCAT 58.573 41.667 10.77 6.95 0.00 4.40
827 1380 8.734386 CAAAGGTCTTGCTGTAGAAAATTAGAT 58.266 33.333 0.00 0.00 0.00 1.98
1048 1664 6.248433 AGAAGAAGAGGTTTTGCAATATGGA 58.752 36.000 0.00 0.00 0.00 3.41
1285 1903 2.485426 GCAACAAGCAGACTATTGCAGA 59.515 45.455 2.54 0.00 46.47 4.26
1427 2046 3.851620 CGTAGCGTCGCCCTTATTA 57.148 52.632 14.86 0.00 0.00 0.98
1430 2049 2.606308 CGTAGCGTCGCCCTTATTACAT 60.606 50.000 14.86 0.00 0.00 2.29
1431 2050 2.614829 AGCGTCGCCCTTATTACATT 57.385 45.000 14.86 0.00 0.00 2.71
1432 2051 2.210116 AGCGTCGCCCTTATTACATTG 58.790 47.619 14.86 0.00 0.00 2.82
1435 2054 3.399330 CGTCGCCCTTATTACATTGGAT 58.601 45.455 0.00 0.00 0.00 3.41
1437 2056 4.319477 CGTCGCCCTTATTACATTGGATTG 60.319 45.833 0.00 0.00 0.00 2.67
1438 2057 4.023193 GTCGCCCTTATTACATTGGATTGG 60.023 45.833 0.00 0.00 0.00 3.16
1441 2060 4.280929 GCCCTTATTACATTGGATTGGGAC 59.719 45.833 0.00 0.00 34.34 4.46
1468 2089 5.578727 GTGGACAACAATTGCAAAACTAACA 59.421 36.000 1.71 0.00 0.00 2.41
1473 2094 9.209297 GACAACAATTGCAAAACTAACAAATTC 57.791 29.630 1.71 0.00 0.00 2.17
1556 2177 2.940410 ACGTTTTGTGTGGTGTCTAAGG 59.060 45.455 0.00 0.00 0.00 2.69
1575 2196 2.821366 GATCAGCCCACACGCCTG 60.821 66.667 0.00 0.00 0.00 4.85
1637 2264 3.681835 GCGGTCCCTCTCACACGT 61.682 66.667 0.00 0.00 0.00 4.49
1820 2470 1.274167 CAGTTGCCATGGTTGCTCAAT 59.726 47.619 14.67 0.00 0.00 2.57
1869 2521 3.642848 AGATGCCATTTTTGGACAACTGT 59.357 39.130 0.00 0.00 0.00 3.55
1872 2524 4.211125 TGCCATTTTTGGACAACTGTAGA 58.789 39.130 0.00 0.00 0.00 2.59
2153 2813 1.219646 GCAAAACACATGGCAACTGG 58.780 50.000 0.00 0.00 37.61 4.00
2170 2830 2.556622 ACTGGCATGTTCGGGTAAAAAG 59.443 45.455 0.00 0.00 0.00 2.27
2236 2906 1.474677 CCCTGCAAAACACATGGCAAA 60.475 47.619 0.00 0.00 35.59 3.68
2295 2967 2.017049 GCGAACTGATAAATGCCCACT 58.983 47.619 0.00 0.00 0.00 4.00
2304 2976 2.085343 AAATGCCCACTCACCAGCCT 62.085 55.000 0.00 0.00 0.00 4.58
2368 3060 1.134877 TGTGGTGAAAACGGACGTGTA 60.135 47.619 0.00 0.00 0.00 2.90
2389 3081 1.447317 GCGACCGAATGAATGCCCAT 61.447 55.000 0.00 0.00 0.00 4.00
2405 3097 1.224592 CATACACCAGCCCAGTCCC 59.775 63.158 0.00 0.00 0.00 4.46
2483 3176 1.270412 TGTGTGGGCGAGATAAAACGT 60.270 47.619 0.00 0.00 0.00 3.99
2541 3234 7.231519 GGATTTAGGGTGCTCTTTTATATGCTT 59.768 37.037 0.00 0.00 0.00 3.91
2655 3358 4.157840 GCAAGTTGAATTTAGGGGTACAGG 59.842 45.833 7.16 0.00 0.00 4.00
2659 3362 7.093965 AGTTGAATTTAGGGGTACAGGTAAA 57.906 36.000 0.00 0.00 0.00 2.01
2669 3372 4.881850 GGGGTACAGGTAAACTCAATCATG 59.118 45.833 0.00 0.00 0.00 3.07
2724 3440 4.922026 ACACCGGTGGCGGTCAAC 62.922 66.667 36.47 0.00 40.77 3.18
2774 3491 1.592400 CCTTGACGACCTGCCGAGTA 61.592 60.000 0.00 0.00 0.00 2.59
2796 3513 8.774546 AGTAGATTGTCATTGAAGAGATCCTA 57.225 34.615 0.00 0.00 0.00 2.94
2878 3595 0.944386 CACCTCCACCAACAAGTTCG 59.056 55.000 0.00 0.00 0.00 3.95
2891 3608 1.792367 CAAGTTCGTGCTCGACAATCA 59.208 47.619 10.88 0.00 46.03 2.57
3003 3720 2.440409 GCCTCCAATCAAAAGCTCTCA 58.560 47.619 0.00 0.00 0.00 3.27
3478 4209 3.965539 ATGCGCAGTCCTGACCAGC 62.966 63.158 18.32 0.00 0.00 4.85
3750 4481 4.863491 ACTTTCTGTTGCATTGTGACATC 58.137 39.130 0.00 0.00 0.00 3.06
3822 4553 9.900710 CCAGTATACTTCACTAATCAGTACATC 57.099 37.037 1.56 0.00 32.21 3.06
3832 4563 1.781786 TCAGTACATCCAGGAGAGCC 58.218 55.000 0.00 0.00 0.00 4.70
3868 4599 4.212004 CGTTCAGTGAGATGCAAGAAGAAA 59.788 41.667 0.00 0.00 0.00 2.52
3870 4601 5.219343 TCAGTGAGATGCAAGAAGAAAGA 57.781 39.130 0.00 0.00 0.00 2.52
3881 4612 9.495754 GATGCAAGAAGAAAGATTTGTGTATAC 57.504 33.333 0.00 0.00 0.00 1.47
3894 4625 2.102420 TGTGTATACGGAGCCTCCATTG 59.898 50.000 12.13 0.00 35.91 2.82
3896 4627 2.364324 TGTATACGGAGCCTCCATTGTC 59.636 50.000 12.13 0.00 35.91 3.18
3898 4629 2.202932 CGGAGCCTCCATTGTCCG 60.203 66.667 12.13 0.00 45.48 4.79
3967 4713 4.164796 AGTGTCCATCCTTTATGAGCATGA 59.835 41.667 0.00 0.00 37.86 3.07
4018 4770 9.686683 AGTAGAACTGAACAATTTATATGGCTT 57.313 29.630 0.00 0.00 0.00 4.35
4046 4815 0.877213 CTTGGTGCCTTTTGTGCTGC 60.877 55.000 0.00 0.00 0.00 5.25
4069 4838 0.642291 GAGCGTCATCGTGATGTGTG 59.358 55.000 9.51 2.90 39.72 3.82
4125 4894 3.311106 TCCTGTTTACTTTCACTACGCG 58.689 45.455 3.53 3.53 0.00 6.01
4136 4905 5.748152 ACTTTCACTACGCGTTGTTAAGTAA 59.252 36.000 30.73 18.37 0.00 2.24
4147 4916 5.567534 GCGTTGTTAAGTAATGTGAATGGTG 59.432 40.000 0.00 0.00 0.00 4.17
4157 4929 0.804989 GTGAATGGTGCTGGCTGTAC 59.195 55.000 4.06 4.06 0.00 2.90
4164 4936 1.537202 GGTGCTGGCTGTACTTTGAAG 59.463 52.381 11.90 0.00 0.00 3.02
4230 5003 3.523606 AGTAGAGAATCAGTGCAGCAG 57.476 47.619 0.00 0.00 37.82 4.24
4237 5018 2.376808 ATCAGTGCAGCAGTGTCTAC 57.623 50.000 26.30 0.00 36.33 2.59
4242 5023 2.768527 AGTGCAGCAGTGTCTACCATAT 59.231 45.455 0.50 0.00 0.00 1.78
4267 5048 6.748333 TGCTAAGAAATCAGTTCCATCAAG 57.252 37.500 0.00 0.00 36.86 3.02
4276 5057 9.525409 GAAATCAGTTCCATCAAGAAAATATGG 57.475 33.333 0.00 0.00 41.33 2.74
4283 5064 5.771666 TCCATCAAGAAAATATGGGAGATGC 59.228 40.000 0.00 0.00 40.53 3.91
4284 5065 5.537295 CCATCAAGAAAATATGGGAGATGCA 59.463 40.000 0.00 0.00 37.17 3.96
4286 5067 5.759059 TCAAGAAAATATGGGAGATGCAGT 58.241 37.500 0.00 0.00 0.00 4.40
4288 5069 5.643421 AGAAAATATGGGAGATGCAGTCT 57.357 39.130 0.00 0.00 40.81 3.24
4300 5081 5.163281 AGATGCAGTCTCTGTCATTTTCT 57.837 39.130 0.00 0.00 31.95 2.52
4301 5082 5.558818 AGATGCAGTCTCTGTCATTTTCTT 58.441 37.500 0.00 0.00 31.95 2.52
4302 5083 5.642919 AGATGCAGTCTCTGTCATTTTCTTC 59.357 40.000 0.00 0.00 31.95 2.87
4303 5084 3.742882 TGCAGTCTCTGTCATTTTCTTCG 59.257 43.478 0.00 0.00 33.43 3.79
4304 5085 3.124297 GCAGTCTCTGTCATTTTCTTCGG 59.876 47.826 0.00 0.00 33.43 4.30
4305 5086 3.681897 CAGTCTCTGTCATTTTCTTCGGG 59.318 47.826 0.00 0.00 0.00 5.14
4308 5089 4.515567 GTCTCTGTCATTTTCTTCGGGTTT 59.484 41.667 0.00 0.00 0.00 3.27
4309 5090 5.008712 GTCTCTGTCATTTTCTTCGGGTTTT 59.991 40.000 0.00 0.00 0.00 2.43
4310 5091 5.592688 TCTCTGTCATTTTCTTCGGGTTTTT 59.407 36.000 0.00 0.00 0.00 1.94
4337 5643 2.851263 ACGATTGTTGGGCAGTCTTA 57.149 45.000 0.00 0.00 32.40 2.10
4346 5652 6.121776 TGTTGGGCAGTCTTATCTTCTAAA 57.878 37.500 0.00 0.00 0.00 1.85
4372 5678 9.804977 ATTAGATCTAGAATGCAATTTAAGCCT 57.195 29.630 2.02 0.00 36.07 4.58
4382 5688 9.485206 GAATGCAATTTAAGCCTATGATGATTT 57.515 29.630 0.00 0.00 36.07 2.17
4409 5715 7.415206 GCTTTATGTTGGAATTACCGTCAGATT 60.415 37.037 0.00 0.00 42.61 2.40
4450 5756 1.468914 GGCTTTCTGAGGCTTAAACCG 59.531 52.381 0.00 0.00 46.86 4.44
4451 5757 1.135660 GCTTTCTGAGGCTTAAACCGC 60.136 52.381 0.00 0.00 33.69 5.68
4452 5758 2.427506 CTTTCTGAGGCTTAAACCGCT 58.572 47.619 0.24 0.00 33.69 5.52
4454 5760 3.688694 TTCTGAGGCTTAAACCGCTTA 57.311 42.857 0.24 0.00 33.69 3.09
4455 5761 3.688694 TCTGAGGCTTAAACCGCTTAA 57.311 42.857 0.24 0.00 33.69 1.85
4456 5762 3.596214 TCTGAGGCTTAAACCGCTTAAG 58.404 45.455 0.00 0.00 46.44 1.85
4461 5767 4.337985 GGCTTAAACCGCTTAAGTCTTC 57.662 45.455 4.02 0.00 45.19 2.87
4462 5768 4.001652 GGCTTAAACCGCTTAAGTCTTCT 58.998 43.478 4.02 0.00 45.19 2.85
4463 5769 5.173664 GGCTTAAACCGCTTAAGTCTTCTA 58.826 41.667 4.02 0.00 45.19 2.10
4470 5784 8.667076 AAACCGCTTAAGTCTTCTACTTTTTA 57.333 30.769 4.02 0.00 46.61 1.52
4471 5785 8.843885 AACCGCTTAAGTCTTCTACTTTTTAT 57.156 30.769 4.02 0.00 46.61 1.40
4503 5817 8.792830 AACTTGGTTCATATTATATCATCCCG 57.207 34.615 0.00 0.00 0.00 5.14
4511 5825 8.374184 TCATATTATATCATCCCGGTGAAGAA 57.626 34.615 0.00 0.00 0.00 2.52
4516 5830 1.762957 TCATCCCGGTGAAGAATCTCC 59.237 52.381 0.00 0.00 36.15 3.71
4517 5831 1.486310 CATCCCGGTGAAGAATCTCCA 59.514 52.381 0.00 0.00 38.82 3.86
4524 5838 4.444876 CCGGTGAAGAATCTCCAACCATAT 60.445 45.833 0.00 0.00 38.82 1.78
4531 5845 6.319048 AGAATCTCCAACCATATGAAGTGT 57.681 37.500 3.65 0.00 0.00 3.55
4573 5887 1.335689 GCTGCTTTTCTCCACTGCAAG 60.336 52.381 0.00 0.00 42.29 4.01
4574 5888 0.670162 TGCTTTTCTCCACTGCAAGC 59.330 50.000 0.00 0.00 40.29 4.01
4584 5898 1.302033 ACTGCAAGCGTCCTCCTTG 60.302 57.895 0.00 0.00 41.93 3.61
4586 5900 2.747855 GCAAGCGTCCTCCTTGGG 60.748 66.667 3.66 0.00 39.95 4.12
4587 5901 2.747855 CAAGCGTCCTCCTTGGGC 60.748 66.667 0.00 0.00 36.82 5.36
4592 5906 1.912220 CGTCCTCCTTGGGCCATAA 59.088 57.895 7.26 0.00 37.05 1.90
4618 5932 0.179020 TGGTTTGGTCTGTGCTGGAG 60.179 55.000 0.00 0.00 0.00 3.86
4650 5964 1.341976 ACCTGGTTTGGTTCAGCTGTT 60.342 47.619 14.67 0.00 36.89 3.16
4653 5967 2.166254 CTGGTTTGGTTCAGCTGTTTGT 59.834 45.455 14.67 0.00 0.00 2.83
4661 5975 4.044426 GGTTCAGCTGTTTGTGTGATTTC 58.956 43.478 14.67 0.00 0.00 2.17
4662 5976 4.202050 GGTTCAGCTGTTTGTGTGATTTCT 60.202 41.667 14.67 0.00 0.00 2.52
4663 5977 4.818534 TCAGCTGTTTGTGTGATTTCTC 57.181 40.909 14.67 0.00 0.00 2.87
4664 5978 4.454678 TCAGCTGTTTGTGTGATTTCTCT 58.545 39.130 14.67 0.00 0.00 3.10
4665 5979 4.883585 TCAGCTGTTTGTGTGATTTCTCTT 59.116 37.500 14.67 0.00 0.00 2.85
4666 5980 5.357878 TCAGCTGTTTGTGTGATTTCTCTTT 59.642 36.000 14.67 0.00 0.00 2.52
4667 5981 6.542005 TCAGCTGTTTGTGTGATTTCTCTTTA 59.458 34.615 14.67 0.00 0.00 1.85
4668 5982 7.066887 TCAGCTGTTTGTGTGATTTCTCTTTAA 59.933 33.333 14.67 0.00 0.00 1.52
4669 5983 7.864379 CAGCTGTTTGTGTGATTTCTCTTTAAT 59.136 33.333 5.25 0.00 0.00 1.40
4670 5984 8.078596 AGCTGTTTGTGTGATTTCTCTTTAATC 58.921 33.333 0.00 0.00 33.58 1.75
4671 5985 8.078596 GCTGTTTGTGTGATTTCTCTTTAATCT 58.921 33.333 0.00 0.00 34.00 2.40
4672 5986 9.956720 CTGTTTGTGTGATTTCTCTTTAATCTT 57.043 29.630 0.00 0.00 34.00 2.40
4673 5987 9.734620 TGTTTGTGTGATTTCTCTTTAATCTTG 57.265 29.630 0.00 0.00 34.00 3.02
4674 5988 8.694394 GTTTGTGTGATTTCTCTTTAATCTTGC 58.306 33.333 0.00 0.00 34.00 4.01
4675 5989 7.750229 TGTGTGATTTCTCTTTAATCTTGCT 57.250 32.000 0.00 0.00 34.00 3.91
4676 5990 8.169977 TGTGTGATTTCTCTTTAATCTTGCTT 57.830 30.769 0.00 0.00 34.00 3.91
4677 5991 8.077991 TGTGTGATTTCTCTTTAATCTTGCTTG 58.922 33.333 0.00 0.00 34.00 4.01
4678 5992 7.061557 GTGTGATTTCTCTTTAATCTTGCTTGC 59.938 37.037 0.00 0.00 34.00 4.01
4679 5993 7.040201 TGTGATTTCTCTTTAATCTTGCTTGCT 60.040 33.333 0.00 0.00 34.00 3.91
4680 5994 7.484324 GTGATTTCTCTTTAATCTTGCTTGCTC 59.516 37.037 0.00 0.00 34.00 4.26
4681 5995 7.392673 TGATTTCTCTTTAATCTTGCTTGCTCT 59.607 33.333 0.00 0.00 34.00 4.09
4682 5996 6.492007 TTCTCTTTAATCTTGCTTGCTCTG 57.508 37.500 0.00 0.00 0.00 3.35
4683 5997 5.555017 TCTCTTTAATCTTGCTTGCTCTGT 58.445 37.500 0.00 0.00 0.00 3.41
4684 5998 6.000219 TCTCTTTAATCTTGCTTGCTCTGTT 59.000 36.000 0.00 0.00 0.00 3.16
4685 5999 6.488006 TCTCTTTAATCTTGCTTGCTCTGTTT 59.512 34.615 0.00 0.00 0.00 2.83
4686 6000 7.013655 TCTCTTTAATCTTGCTTGCTCTGTTTT 59.986 33.333 0.00 0.00 0.00 2.43
4687 6001 7.491682 TCTTTAATCTTGCTTGCTCTGTTTTT 58.508 30.769 0.00 0.00 0.00 1.94
4734 6048 6.486253 TCTTGTCTGTAAATGTGAATCTGC 57.514 37.500 0.00 0.00 0.00 4.26
4742 6056 2.134789 ATGTGAATCTGCCTGGGAAC 57.865 50.000 0.00 0.00 0.00 3.62
4744 6058 1.355381 TGTGAATCTGCCTGGGAACAT 59.645 47.619 0.00 0.00 41.51 2.71
4933 6247 2.697229 TGAGATACAGGCCTGTGATGAG 59.303 50.000 42.35 15.51 44.63 2.90
4941 6255 2.644798 AGGCCTGTGATGAGTTTAAGGT 59.355 45.455 3.11 0.00 0.00 3.50
4948 6262 4.518970 TGTGATGAGTTTAAGGTTCCAAGC 59.481 41.667 0.00 0.00 0.00 4.01
5072 6386 1.404391 CATTGCAGAAGGCCACTCATC 59.596 52.381 5.01 0.00 43.89 2.92
5074 6388 0.321919 TGCAGAAGGCCACTCATCAC 60.322 55.000 5.01 0.00 43.89 3.06
5097 6411 6.094048 CACCTCATTTCCTGTATTACCTGTTG 59.906 42.308 0.00 0.00 0.00 3.33
5098 6412 5.066505 CCTCATTTCCTGTATTACCTGTTGC 59.933 44.000 0.00 0.00 0.00 4.17
5133 6447 8.281531 TCCATCTACCTGATTTTTACCATGAAT 58.718 33.333 0.00 0.00 32.05 2.57
5230 6550 2.219674 GTGTGTTTCTTGTCTGAGCTCG 59.780 50.000 9.64 4.19 0.00 5.03
5245 6565 2.733552 GAGCTCGTATGCACATGGTATG 59.266 50.000 0.00 0.00 34.99 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.356793 CGGATGATGCGAGGGCTC 60.357 66.667 0.00 0.00 40.82 4.70
3 4 4.615815 AGCGGATGATGCGAGGGC 62.616 66.667 11.36 0.00 37.44 5.19
5 6 2.356793 GGAGCGGATGATGCGAGG 60.357 66.667 11.36 0.00 37.44 4.63
6 7 2.356793 GGGAGCGGATGATGCGAG 60.357 66.667 11.36 0.00 37.44 5.03
9 10 4.996434 CCCGGGAGCGGATGATGC 62.996 72.222 18.48 0.00 0.00 3.91
10 11 3.231889 CTCCCGGGAGCGGATGATG 62.232 68.421 36.90 12.11 35.31 3.07
11 12 2.919856 CTCCCGGGAGCGGATGAT 60.920 66.667 36.90 0.00 35.31 2.45
86 87 2.125512 GTACCAGAGCAGCGGGTG 60.126 66.667 14.54 2.14 45.16 4.61
88 89 2.185350 CAGTACCAGAGCAGCGGG 59.815 66.667 0.00 0.00 37.91 6.13
157 624 5.983118 TCGAACATAGTCATGCATAATTCGT 59.017 36.000 0.00 0.00 37.15 3.85
158 625 6.452244 TCGAACATAGTCATGCATAATTCG 57.548 37.500 0.00 7.67 37.16 3.34
160 627 6.348786 GCCATCGAACATAGTCATGCATAATT 60.349 38.462 0.00 0.00 35.39 1.40
194 681 0.526662 AGAAGGTTCTAGTGACCGCG 59.473 55.000 0.00 0.00 35.34 6.46
196 683 5.578005 TGAATAGAAGGTTCTAGTGACCG 57.422 43.478 4.51 0.00 42.55 4.79
254 787 8.600625 TCATTCAGCGTACTATTTCAATGTAAC 58.399 33.333 0.00 0.00 0.00 2.50
258 791 8.124823 ACATTCATTCAGCGTACTATTTCAATG 58.875 33.333 0.00 0.00 0.00 2.82
265 798 5.276461 TGGACATTCATTCAGCGTACTAT 57.724 39.130 0.00 0.00 0.00 2.12
267 800 3.610040 TGGACATTCATTCAGCGTACT 57.390 42.857 0.00 0.00 0.00 2.73
268 801 4.122776 AGATGGACATTCATTCAGCGTAC 58.877 43.478 0.00 0.00 0.00 3.67
269 802 4.141959 TGAGATGGACATTCATTCAGCGTA 60.142 41.667 0.00 0.00 0.00 4.42
271 804 3.200483 TGAGATGGACATTCATTCAGCG 58.800 45.455 0.00 0.00 0.00 5.18
272 805 4.197750 ACTGAGATGGACATTCATTCAGC 58.802 43.478 12.64 0.00 36.68 4.26
273 806 6.580788 ACTACTGAGATGGACATTCATTCAG 58.419 40.000 11.79 11.79 37.75 3.02
274 807 6.550938 ACTACTGAGATGGACATTCATTCA 57.449 37.500 0.00 0.00 0.00 2.57
275 808 8.986847 CATAACTACTGAGATGGACATTCATTC 58.013 37.037 0.00 0.00 0.00 2.67
276 809 8.708378 TCATAACTACTGAGATGGACATTCATT 58.292 33.333 0.00 0.00 0.00 2.57
277 810 8.255111 TCATAACTACTGAGATGGACATTCAT 57.745 34.615 0.00 0.00 0.00 2.57
278 811 7.660030 TCATAACTACTGAGATGGACATTCA 57.340 36.000 0.00 0.00 0.00 2.57
281 814 7.443575 GCAAATCATAACTACTGAGATGGACAT 59.556 37.037 0.00 0.00 0.00 3.06
285 818 6.057533 TGGCAAATCATAACTACTGAGATGG 58.942 40.000 0.00 0.00 0.00 3.51
286 819 7.558161 TTGGCAAATCATAACTACTGAGATG 57.442 36.000 0.00 0.00 0.00 2.90
299 832 9.432982 TTTCCCTAGTATAAATTGGCAAATCAT 57.567 29.630 3.01 0.00 0.00 2.45
302 835 7.683463 GCGTTTCCCTAGTATAAATTGGCAAAT 60.683 37.037 3.01 0.00 0.00 2.32
303 836 6.404954 GCGTTTCCCTAGTATAAATTGGCAAA 60.405 38.462 3.01 0.00 0.00 3.68
306 839 4.820173 AGCGTTTCCCTAGTATAAATTGGC 59.180 41.667 0.00 0.00 0.00 4.52
313 846 7.175641 GGTGATAGTTAGCGTTTCCCTAGTATA 59.824 40.741 0.00 0.00 0.00 1.47
317 850 4.501058 GGGTGATAGTTAGCGTTTCCCTAG 60.501 50.000 0.00 0.00 0.00 3.02
318 851 3.385755 GGGTGATAGTTAGCGTTTCCCTA 59.614 47.826 0.00 0.00 0.00 3.53
827 1380 1.371183 CAACAAGACCTCCTCCGCA 59.629 57.895 0.00 0.00 0.00 5.69
943 1556 0.250684 TTCTGCAACATCTTCCGCCA 60.251 50.000 0.00 0.00 0.00 5.69
1048 1664 9.638176 ATCTTCTATAATTTCCTGCAACAAGAT 57.362 29.630 0.00 0.00 0.00 2.40
1173 1789 2.918600 CCGTTCGATTGTGTGATACGAA 59.081 45.455 2.33 0.00 39.89 3.85
1246 1863 0.375106 GCAATTACTCGAGCCTGCAC 59.625 55.000 13.61 0.00 0.00 4.57
1285 1903 3.951775 TTGCAACAAGAGTGGTGTTTT 57.048 38.095 0.00 0.00 44.95 2.43
1427 2046 2.109834 TCCACTTGTCCCAATCCAATGT 59.890 45.455 0.00 0.00 0.00 2.71
1430 2049 1.496857 TGTCCACTTGTCCCAATCCAA 59.503 47.619 0.00 0.00 0.00 3.53
1431 2050 1.144691 TGTCCACTTGTCCCAATCCA 58.855 50.000 0.00 0.00 0.00 3.41
1432 2051 1.886542 GTTGTCCACTTGTCCCAATCC 59.113 52.381 0.00 0.00 0.00 3.01
1435 2054 2.516227 TTGTTGTCCACTTGTCCCAA 57.484 45.000 0.00 0.00 0.00 4.12
1437 2056 2.545742 GCAATTGTTGTCCACTTGTCCC 60.546 50.000 7.40 0.00 36.41 4.46
1438 2057 2.100584 TGCAATTGTTGTCCACTTGTCC 59.899 45.455 7.40 0.00 36.41 4.02
1441 2060 4.630940 AGTTTTGCAATTGTTGTCCACTTG 59.369 37.500 7.40 0.00 36.93 3.16
1444 2063 5.578727 TGTTAGTTTTGCAATTGTTGTCCAC 59.421 36.000 7.40 0.00 0.00 4.02
1445 2064 5.724328 TGTTAGTTTTGCAATTGTTGTCCA 58.276 33.333 7.40 0.00 0.00 4.02
1448 2067 8.725148 TGAATTTGTTAGTTTTGCAATTGTTGT 58.275 25.926 7.40 0.00 0.00 3.32
1575 2196 0.382515 TACTTGTTTTGCCCACACGC 59.617 50.000 0.00 0.00 0.00 5.34
1637 2264 7.384115 GCATTATCTATTTTGCCTACACGTAGA 59.616 37.037 5.77 0.00 35.21 2.59
1869 2521 5.425217 ACCAGACCATACATGACAACATCTA 59.575 40.000 0.00 0.00 34.15 1.98
1872 2524 4.574674 ACCAGACCATACATGACAACAT 57.425 40.909 0.00 0.00 37.19 2.71
2127 2787 2.632028 TGCCATGTGTTTTGCAAGGTAT 59.368 40.909 0.00 0.00 0.00 2.73
2153 2813 3.751698 ACTCTCTTTTTACCCGAACATGC 59.248 43.478 0.00 0.00 0.00 4.06
2236 2906 1.909781 CCACACCCAAAGCTGCCAT 60.910 57.895 0.00 0.00 0.00 4.40
2295 2967 2.519622 CCCACACAGAGGCTGGTGA 61.520 63.158 19.40 0.00 35.92 4.02
2304 2976 1.468506 TAGCAGTTCGCCCACACAGA 61.469 55.000 0.00 0.00 44.04 3.41
2368 3060 1.819632 GGCATTCATTCGGTCGCCT 60.820 57.895 0.00 0.00 36.58 5.52
2389 3081 2.205749 TGGGACTGGGCTGGTGTA 59.794 61.111 0.00 0.00 0.00 2.90
2405 3097 1.732077 GCATGTTTATGGTGCCACGTG 60.732 52.381 9.08 9.08 34.79 4.49
2521 3214 5.116084 TCAAGCATATAAAAGAGCACCCT 57.884 39.130 0.00 0.00 0.00 4.34
2524 3217 8.400947 TGAAGAATCAAGCATATAAAAGAGCAC 58.599 33.333 0.00 0.00 30.99 4.40
2600 3299 7.255590 GCATAACAGTATTTGGCATAGGTCAAT 60.256 37.037 0.00 0.00 38.64 2.57
2632 3335 4.157840 CCTGTACCCCTAAATTCAACTTGC 59.842 45.833 0.00 0.00 0.00 4.01
2724 3440 1.200020 GGCTTCTTTTCGTCATGGTGG 59.800 52.381 0.00 0.00 0.00 4.61
2774 3491 7.201992 GGACTAGGATCTCTTCAATGACAATCT 60.202 40.741 0.00 0.00 0.00 2.40
2878 3595 3.611433 GGCAATGATTGTCGAGCAC 57.389 52.632 7.05 0.00 0.00 4.40
3003 3720 5.407407 ACTTAGAGTGTCGAATGATTGGT 57.593 39.130 0.00 0.00 0.00 3.67
3478 4209 1.157870 AACGACAAACGACAGCCCAG 61.158 55.000 0.00 0.00 45.77 4.45
3750 4481 5.719173 ACATAACCCAAAAACATTCCATCG 58.281 37.500 0.00 0.00 0.00 3.84
3868 4599 3.069729 GGAGGCTCCGTATACACAAATCT 59.930 47.826 19.53 0.00 0.00 2.40
3870 4601 2.769663 TGGAGGCTCCGTATACACAAAT 59.230 45.455 27.58 0.00 40.17 2.32
3881 4612 2.202932 CGGACAATGGAGGCTCCG 60.203 66.667 27.58 16.38 40.17 4.63
3894 4625 1.617357 CCACCTTATAGCCCTACGGAC 59.383 57.143 0.00 0.00 0.00 4.79
3896 4627 1.713297 ACCACCTTATAGCCCTACGG 58.287 55.000 0.00 0.00 0.00 4.02
3898 4629 5.146298 AGAAGTACCACCTTATAGCCCTAC 58.854 45.833 0.00 0.00 0.00 3.18
4018 4770 2.584835 AAGGCACCAAGTGATAGCAA 57.415 45.000 0.00 0.00 35.23 3.91
4046 4815 0.926155 CATCACGATGACGCTCAAGG 59.074 55.000 0.47 0.00 43.96 3.61
4069 4838 8.085296 GCACAGATGTATAGCATATATACTCCC 58.915 40.741 6.60 0.00 38.06 4.30
4121 4890 5.379003 CATTCACATTACTTAACAACGCGT 58.621 37.500 5.58 5.58 0.00 6.01
4125 4894 6.582295 CAGCACCATTCACATTACTTAACAAC 59.418 38.462 0.00 0.00 0.00 3.32
4136 4905 0.251474 ACAGCCAGCACCATTCACAT 60.251 50.000 0.00 0.00 0.00 3.21
4147 4916 1.068954 GCACTTCAAAGTACAGCCAGC 60.069 52.381 0.00 0.00 37.08 4.85
4230 5003 9.109393 TGATTTCTTAGCAAATATGGTAGACAC 57.891 33.333 0.00 0.00 40.38 3.67
4237 5018 7.999679 TGGAACTGATTTCTTAGCAAATATGG 58.000 34.615 0.00 0.00 34.26 2.74
4242 5023 7.448161 TCTTGATGGAACTGATTTCTTAGCAAA 59.552 33.333 0.00 0.00 31.26 3.68
4283 5064 3.681897 CCCGAAGAAAATGACAGAGACTG 59.318 47.826 0.00 0.00 37.52 3.51
4284 5065 3.325135 ACCCGAAGAAAATGACAGAGACT 59.675 43.478 0.00 0.00 0.00 3.24
4286 5067 4.351874 AACCCGAAGAAAATGACAGAGA 57.648 40.909 0.00 0.00 0.00 3.10
4288 5069 5.845391 AAAAACCCGAAGAAAATGACAGA 57.155 34.783 0.00 0.00 0.00 3.41
4317 5098 1.981256 AAGACTGCCCAACAATCGTT 58.019 45.000 0.00 0.00 35.01 3.85
4319 5100 3.535561 AGATAAGACTGCCCAACAATCG 58.464 45.455 0.00 0.00 27.16 3.34
4320 5101 5.189180 AGAAGATAAGACTGCCCAACAATC 58.811 41.667 0.00 0.00 0.00 2.67
4321 5102 5.184892 AGAAGATAAGACTGCCCAACAAT 57.815 39.130 0.00 0.00 0.00 2.71
4322 5103 4.640771 AGAAGATAAGACTGCCCAACAA 57.359 40.909 0.00 0.00 0.00 2.83
4323 5104 5.755409 TTAGAAGATAAGACTGCCCAACA 57.245 39.130 0.00 0.00 0.00 3.33
4324 5105 7.631717 AATTTAGAAGATAAGACTGCCCAAC 57.368 36.000 0.00 0.00 0.00 3.77
4325 5106 8.768397 TCTAATTTAGAAGATAAGACTGCCCAA 58.232 33.333 3.60 0.00 0.00 4.12
4327 5108 9.430623 GATCTAATTTAGAAGATAAGACTGCCC 57.569 37.037 10.07 0.00 38.50 5.36
4346 5652 9.804977 AGGCTTAAATTGCATTCTAGATCTAAT 57.195 29.630 3.57 0.00 0.00 1.73
4356 5662 9.485206 AAATCATCATAGGCTTAAATTGCATTC 57.515 29.630 0.00 0.00 0.00 2.67
4361 5667 8.882415 AAGCAAATCATCATAGGCTTAAATTG 57.118 30.769 0.00 0.00 39.57 2.32
4366 5672 8.696043 ACATAAAGCAAATCATCATAGGCTTA 57.304 30.769 0.00 0.00 40.38 3.09
4382 5688 5.004448 TGACGGTAATTCCAACATAAAGCA 58.996 37.500 0.00 0.00 35.57 3.91
4409 5715 7.185318 AGCCACAAAAATATCATCATTTGGA 57.815 32.000 0.00 0.00 37.15 3.53
4412 5718 9.158233 CAGAAAGCCACAAAAATATCATCATTT 57.842 29.630 0.00 0.00 0.00 2.32
4429 5735 2.514803 GGTTTAAGCCTCAGAAAGCCA 58.485 47.619 0.26 0.00 0.00 4.75
4480 5794 7.280876 CACCGGGATGATATAATATGAACCAAG 59.719 40.741 6.32 0.00 0.00 3.61
4483 5797 6.884832 TCACCGGGATGATATAATATGAACC 58.115 40.000 6.32 0.00 0.00 3.62
4490 5804 7.365117 GGAGATTCTTCACCGGGATGATATAAT 60.365 40.741 6.32 1.94 30.61 1.28
4494 5808 3.578716 GGAGATTCTTCACCGGGATGATA 59.421 47.826 6.32 0.90 30.61 2.15
4503 5817 5.684704 TCATATGGTTGGAGATTCTTCACC 58.315 41.667 2.13 0.88 33.55 4.02
4511 5825 4.162320 ACGACACTTCATATGGTTGGAGAT 59.838 41.667 2.13 0.00 0.00 2.75
4516 5830 6.274001 GTCATACGACACTTCATATGGTTG 57.726 41.667 2.13 0.00 42.13 3.77
4560 5874 1.301716 GGACGCTTGCAGTGGAGAA 60.302 57.895 0.00 0.00 0.00 2.87
4573 5887 2.265467 TTATGGCCCAAGGAGGACGC 62.265 60.000 0.00 0.00 38.01 5.19
4574 5888 0.463833 GTTATGGCCCAAGGAGGACG 60.464 60.000 0.00 0.00 38.01 4.79
4625 5939 2.034179 GCTGAACCAAACCAGGTACAAC 59.966 50.000 0.00 0.00 42.25 3.32
4629 5943 1.493022 ACAGCTGAACCAAACCAGGTA 59.507 47.619 23.35 0.00 42.25 3.08
4631 5945 1.402787 AACAGCTGAACCAAACCAGG 58.597 50.000 23.35 0.00 0.00 4.45
4650 5964 8.169977 AGCAAGATTAAAGAGAAATCACACAA 57.830 30.769 0.00 0.00 36.09 3.33
4653 5967 7.040201 AGCAAGCAAGATTAAAGAGAAATCACA 60.040 33.333 0.00 0.00 36.09 3.58
4661 5975 5.876612 ACAGAGCAAGCAAGATTAAAGAG 57.123 39.130 0.00 0.00 0.00 2.85
4662 5976 6.639632 AAACAGAGCAAGCAAGATTAAAGA 57.360 33.333 0.00 0.00 0.00 2.52
4663 5977 7.704789 AAAAACAGAGCAAGCAAGATTAAAG 57.295 32.000 0.00 0.00 0.00 1.85
4708 6022 8.668353 GCAGATTCACATTTACAGACAAGAATA 58.332 33.333 0.00 0.00 0.00 1.75
4709 6023 7.362401 GGCAGATTCACATTTACAGACAAGAAT 60.362 37.037 0.00 0.00 0.00 2.40
4710 6024 6.072508 GGCAGATTCACATTTACAGACAAGAA 60.073 38.462 0.00 0.00 0.00 2.52
4711 6025 5.412594 GGCAGATTCACATTTACAGACAAGA 59.587 40.000 0.00 0.00 0.00 3.02
4712 6026 5.413833 AGGCAGATTCACATTTACAGACAAG 59.586 40.000 0.00 0.00 0.00 3.16
4713 6027 5.181811 CAGGCAGATTCACATTTACAGACAA 59.818 40.000 0.00 0.00 0.00 3.18
4714 6028 4.696877 CAGGCAGATTCACATTTACAGACA 59.303 41.667 0.00 0.00 0.00 3.41
4742 6056 5.237996 CAGGTACCTATCAACATGCAGAATG 59.762 44.000 15.80 0.00 42.48 2.67
4744 6058 4.469586 TCAGGTACCTATCAACATGCAGAA 59.530 41.667 15.80 0.00 0.00 3.02
4824 6138 2.171341 AAGAAAGGCTTGTCTCCGAC 57.829 50.000 0.00 0.00 34.93 4.79
4837 6151 6.145048 GTCAATTCAATTGCTGGACAAGAAAG 59.855 38.462 5.12 0.00 42.87 2.62
4933 6247 4.142381 CCATGCTAGCTTGGAACCTTAAAC 60.142 45.833 35.16 0.00 41.96 2.01
4948 6262 5.465056 GCTACTAAGAAAGAAGCCATGCTAG 59.535 44.000 0.00 0.00 38.25 3.42
5022 6336 6.436843 AAGGAGTAGTGTCAACAAAGTTTG 57.563 37.500 14.13 14.13 0.00 2.93
5023 6337 7.312899 CAAAAGGAGTAGTGTCAACAAAGTTT 58.687 34.615 0.00 0.00 0.00 2.66
5072 6386 5.745227 ACAGGTAATACAGGAAATGAGGTG 58.255 41.667 0.00 0.00 0.00 4.00
5074 6388 5.066505 GCAACAGGTAATACAGGAAATGAGG 59.933 44.000 0.00 0.00 0.00 3.86
5097 6411 1.344763 AGGTAGATGGATGCTAACCGC 59.655 52.381 0.00 0.00 39.77 5.68
5098 6412 2.628178 TCAGGTAGATGGATGCTAACCG 59.372 50.000 0.00 0.00 0.00 4.44
5133 6447 4.162698 AGGGGTCGCAGTGTTTACAATATA 59.837 41.667 0.00 0.00 0.00 0.86
5187 6507 6.039941 ACACTTTCGAACATTTTGGTCCAATA 59.960 34.615 4.80 0.39 27.88 1.90
5230 6550 6.918892 TTACTGTTCATACCATGTGCATAC 57.081 37.500 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.