Multiple sequence alignment - TraesCS5D01G368400

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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 TraesCS5D01G368400 chr5D 100.000 4699 0 0 1 4699 444473549 444478247 0.000000e+00 8678.0
1 TraesCS5D01G368400 chr5D 89.988 829 65 5 2519 3335 511590618 511591440 0.000000e+00 1055.0
2 TraesCS5D01G368400 chr5D 88.193 830 80 8 2519 3336 511525797 511526620 0.000000e+00 974.0
3 TraesCS5D01G368400 chr5D 90.133 527 40 2 2519 3037 511626995 511627517 0.000000e+00 675.0
4 TraesCS5D01G368400 chr5D 87.426 509 39 3 1984 2492 511525172 511525655 3.170000e-156 562.0
5 TraesCS5D01G368400 chr5D 86.275 306 30 5 3043 3336 511627756 511628061 5.870000e-84 322.0
6 TraesCS5D01G368400 chr5D 88.538 253 26 3 4258 4509 46332548 46332298 2.120000e-78 303.0
7 TraesCS5D01G368400 chr5D 79.310 377 70 6 2015 2388 444301487 444301858 1.680000e-64 257.0
8 TraesCS5D01G368400 chr5D 77.644 416 69 15 2003 2409 444354777 444355177 1.020000e-56 231.0
9 TraesCS5D01G368400 chr5D 81.188 303 43 6 2098 2390 444531122 444531420 1.020000e-56 231.0
10 TraesCS5D01G368400 chr5D 78.674 347 63 9 4351 4690 489894008 489893666 2.200000e-53 220.0
11 TraesCS5D01G368400 chr5D 92.800 125 9 0 2368 2492 511590353 511590477 1.040000e-41 182.0
12 TraesCS5D01G368400 chr5D 80.620 129 23 2 3898 4024 417623078 417622950 1.080000e-16 99.0
13 TraesCS5D01G368400 chr5D 79.832 119 18 3 1158 1270 444353259 444353377 1.080000e-11 82.4
14 TraesCS5D01G368400 chr5D 100.000 30 0 0 2490 2519 511525749 511525778 6.570000e-04 56.5
15 TraesCS5D01G368400 chr5D 100.000 28 0 0 2489 2516 511590569 511590596 8.000000e-03 52.8
16 TraesCS5D01G368400 chr5B 92.035 1582 107 7 2519 4086 541285849 541287425 0.000000e+00 2206.0
17 TraesCS5D01G368400 chr5B 87.044 1343 130 22 1 1330 541283185 541284496 0.000000e+00 1476.0
18 TraesCS5D01G368400 chr5B 95.866 508 20 1 1984 2491 541285226 541285732 0.000000e+00 821.0
19 TraesCS5D01G368400 chr5B 85.519 511 42 4 1984 2492 642745348 642745828 5.430000e-139 505.0
20 TraesCS5D01G368400 chr5B 91.436 362 26 4 1984 2343 642574130 642574488 4.220000e-135 492.0
21 TraesCS5D01G368400 chr5B 86.577 447 53 5 4258 4699 47329084 47329528 1.970000e-133 486.0
22 TraesCS5D01G368400 chr5B 84.736 511 46 5 1984 2492 642721055 642721535 2.540000e-132 483.0
23 TraesCS5D01G368400 chr5B 90.083 363 30 4 1984 2343 642489176 642489535 2.560000e-127 466.0
24 TraesCS5D01G368400 chr5B 80.135 594 72 22 2538 3104 541302449 541303023 7.320000e-108 401.0
25 TraesCS5D01G368400 chr5B 89.000 300 33 0 2044 2343 642480058 642480357 5.740000e-99 372.0
26 TraesCS5D01G368400 chr5B 77.726 642 109 28 1 634 231754161 231753546 3.460000e-96 363.0
27 TraesCS5D01G368400 chr5B 77.812 649 100 18 2515 3136 541305542 541306173 1.240000e-95 361.0
28 TraesCS5D01G368400 chr5B 85.345 348 27 4 1326 1656 541284789 541285129 5.820000e-89 339.0
29 TraesCS5D01G368400 chr5B 79.874 477 82 9 1984 2448 541099622 541100096 2.090000e-88 337.0
30 TraesCS5D01G368400 chr5B 80.275 436 79 6 4267 4699 70918387 70917956 5.870000e-84 322.0
31 TraesCS5D01G368400 chr5B 81.058 359 51 10 2098 2448 541300665 541301014 2.150000e-68 270.0
32 TraesCS5D01G368400 chr5B 74.522 628 105 37 1 612 89316604 89317192 6.120000e-54 222.0
33 TraesCS5D01G368400 chr5B 79.928 279 33 11 990 1263 541156321 541156581 2.890000e-42 183.0
34 TraesCS5D01G368400 chr5B 77.895 285 51 11 345 622 207068429 207068150 2.910000e-37 167.0
35 TraesCS5D01G368400 chr5B 76.531 294 58 10 344 631 361012398 361012110 2.930000e-32 150.0
36 TraesCS5D01G368400 chr5B 76.094 297 60 10 344 634 421453201 421452910 1.360000e-30 145.0
37 TraesCS5D01G368400 chr5B 81.579 114 15 5 1158 1266 541956004 541955892 6.480000e-14 89.8
38 TraesCS5D01G368400 chr5B 76.471 153 29 5 3898 4049 504811595 504811449 5.040000e-10 76.8
39 TraesCS5D01G368400 chr5B 90.476 42 4 0 1931 1972 434427721 434427680 6.570000e-04 56.5
40 TraesCS5D01G368400 chr5A 91.140 1377 95 14 2519 3877 561267948 561269315 0.000000e+00 1842.0
41 TraesCS5D01G368400 chr5A 95.481 509 23 0 1984 2492 561267241 561267749 0.000000e+00 813.0
42 TraesCS5D01G368400 chr5A 88.276 580 46 11 895 1462 561264647 561265216 0.000000e+00 675.0
43 TraesCS5D01G368400 chr5A 85.102 443 46 6 4258 4696 561270115 561270541 7.220000e-118 435.0
44 TraesCS5D01G368400 chr5A 79.353 649 102 19 2516 3142 561978698 561978060 1.210000e-115 427.0
45 TraesCS5D01G368400 chr5A 79.669 605 85 13 2525 3104 561517160 561517751 7.320000e-108 401.0
46 TraesCS5D01G368400 chr5A 85.759 323 39 3 2538 2853 561453036 561453358 7.530000e-88 335.0
47 TraesCS5D01G368400 chr5A 75.900 639 102 32 1 633 19655192 19654600 3.580000e-71 279.0
48 TraesCS5D01G368400 chr5A 80.672 357 56 8 2100 2448 561451910 561452261 1.000000e-66 265.0
49 TraesCS5D01G368400 chr5A 90.374 187 13 4 3898 4084 561269370 561269551 1.690000e-59 241.0
50 TraesCS5D01G368400 chr5A 85.437 103 12 2 1158 1260 561980393 561980294 2.310000e-18 104.0
51 TraesCS5D01G368400 chr5A 78.344 157 20 9 3899 4049 531079123 531078975 6.480000e-14 89.8
52 TraesCS5D01G368400 chr3D 98.881 268 3 0 1665 1932 338306843 338307110 3.290000e-131 479.0
53 TraesCS5D01G368400 chr3D 98.134 268 5 0 1665 1932 276509703 276509436 7.120000e-128 468.0
54 TraesCS5D01G368400 chr3D 97.770 269 6 0 1664 1932 276513246 276512978 9.210000e-127 464.0
55 TraesCS5D01G368400 chr3D 97.015 268 7 1 1665 1932 338303296 338303562 2.580000e-122 449.0
56 TraesCS5D01G368400 chr3D 82.353 357 55 5 1 357 14073753 14074101 2.120000e-78 303.0
57 TraesCS5D01G368400 chr3D 86.555 119 13 3 401 518 330906221 330906105 1.370000e-25 128.0
58 TraesCS5D01G368400 chr1D 81.157 605 104 8 1 602 229409421 229408824 1.180000e-130 477.0
59 TraesCS5D01G368400 chr1D 80.836 287 47 6 1 285 463989539 463989819 7.920000e-53 219.0
60 TraesCS5D01G368400 chr1D 76.792 293 58 9 345 631 383179109 383178821 6.300000e-34 156.0
61 TraesCS5D01G368400 chr2D 82.913 515 71 10 1 514 71776804 71776306 9.280000e-122 448.0
62 TraesCS5D01G368400 chr2D 78.652 356 63 10 4351 4698 5432700 5432350 1.700000e-54 224.0
63 TraesCS5D01G368400 chr2D 77.663 291 40 12 1 290 513018167 513017901 2.260000e-33 154.0
64 TraesCS5D01G368400 chr7A 80.195 616 101 16 1 609 726492289 726491688 4.320000e-120 442.0
65 TraesCS5D01G368400 chr2A 80.822 438 75 9 4256 4690 669631120 669631551 7.530000e-88 335.0
66 TraesCS5D01G368400 chrUn 95.431 197 6 3 1665 1860 319434515 319434321 1.270000e-80 311.0
67 TraesCS5D01G368400 chrUn 100.000 165 0 0 1665 1829 458245368 458245204 5.910000e-79 305.0
68 TraesCS5D01G368400 chr4A 79.540 435 84 5 4267 4699 36804407 36803976 5.910000e-79 305.0
69 TraesCS5D01G368400 chr3A 94.924 197 7 3 1665 1860 217980161 217979967 5.910000e-79 305.0
70 TraesCS5D01G368400 chr3A 75.158 632 123 21 4 631 536931909 536931308 2.790000e-67 267.0
71 TraesCS5D01G368400 chr3A 83.200 125 21 0 3895 4019 9342793 9342917 1.070000e-21 115.0
72 TraesCS5D01G368400 chr4B 76.499 617 94 35 1 610 633770687 633771259 5.950000e-74 289.0
73 TraesCS5D01G368400 chr4B 89.796 49 5 0 1931 1979 589799430 589799382 3.930000e-06 63.9
74 TraesCS5D01G368400 chr1A 93.434 198 7 4 1664 1860 363009046 363009238 5.950000e-74 289.0
75 TraesCS5D01G368400 chr1A 93.434 198 7 4 1664 1860 363009944 363010136 5.950000e-74 289.0
76 TraesCS5D01G368400 chr1A 78.788 198 39 3 419 615 576541582 576541387 3.820000e-26 130.0
77 TraesCS5D01G368400 chr1A 81.102 127 22 2 3895 4019 9244651 9244525 2.990000e-17 100.0
78 TraesCS5D01G368400 chr1A 97.222 36 1 0 1944 1979 542002581 542002616 1.410000e-05 62.1
79 TraesCS5D01G368400 chr7D 80.811 370 66 5 4323 4689 39140745 39141112 7.700000e-73 285.0
80 TraesCS5D01G368400 chr4D 73.773 652 124 35 1 631 22230566 22231191 3.680000e-51 213.0
81 TraesCS5D01G368400 chr6A 75.732 239 48 10 399 633 562673019 562673251 1.380000e-20 111.0
82 TraesCS5D01G368400 chr3B 79.612 103 20 1 3894 3996 9913681 9913580 6.520000e-09 73.1
83 TraesCS5D01G368400 chr6B 97.222 36 1 0 1944 1979 184013752 184013717 1.410000e-05 62.1
84 TraesCS5D01G368400 chr1B 97.222 36 1 0 1944 1979 41091053 41091088 1.410000e-05 62.1
85 TraesCS5D01G368400 chr1B 97.222 36 1 0 1944 1979 502103085 502103050 1.410000e-05 62.1
86 TraesCS5D01G368400 chr1B 97.222 36 1 0 1944 1979 610173756 610173791 1.410000e-05 62.1
87 TraesCS5D01G368400 chr1B 90.476 42 4 0 1931 1972 378400620 378400661 6.570000e-04 56.5
88 TraesCS5D01G368400 chr7B 90.698 43 4 0 1938 1980 457403393 457403435 1.830000e-04 58.4


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 TraesCS5D01G368400 chr5D 444473549 444478247 4698 False 8678.000000 8678 100.000000 1 4699 1 chr5D.!!$F2 4698
1 TraesCS5D01G368400 chr5D 511525172 511526620 1448 False 530.833333 974 91.873000 1984 3336 3 chr5D.!!$F5 1352
2 TraesCS5D01G368400 chr5D 511626995 511628061 1066 False 498.500000 675 88.204000 2519 3336 2 chr5D.!!$F7 817
3 TraesCS5D01G368400 chr5D 511590353 511591440 1087 False 429.933333 1055 94.262667 2368 3335 3 chr5D.!!$F6 967
4 TraesCS5D01G368400 chr5B 541283185 541287425 4240 False 1210.500000 2206 90.072500 1 4086 4 chr5B.!!$F10 4085
5 TraesCS5D01G368400 chr5B 231753546 231754161 615 True 363.000000 363 77.726000 1 634 1 chr5B.!!$R3 633
6 TraesCS5D01G368400 chr5B 541300665 541306173 5508 False 344.000000 401 79.668333 2098 3136 3 chr5B.!!$F11 1038
7 TraesCS5D01G368400 chr5B 89316604 89317192 588 False 222.000000 222 74.522000 1 612 1 chr5B.!!$F2 611
8 TraesCS5D01G368400 chr5A 561264647 561270541 5894 False 801.200000 1842 90.074600 895 4696 5 chr5A.!!$F2 3801
9 TraesCS5D01G368400 chr5A 561517160 561517751 591 False 401.000000 401 79.669000 2525 3104 1 chr5A.!!$F1 579
10 TraesCS5D01G368400 chr5A 561451910 561453358 1448 False 300.000000 335 83.215500 2100 2853 2 chr5A.!!$F3 753
11 TraesCS5D01G368400 chr5A 19654600 19655192 592 True 279.000000 279 75.900000 1 633 1 chr5A.!!$R1 632
12 TraesCS5D01G368400 chr5A 561978060 561980393 2333 True 265.500000 427 82.395000 1158 3142 2 chr5A.!!$R3 1984
13 TraesCS5D01G368400 chr3D 276509436 276513246 3810 True 466.000000 468 97.952000 1664 1932 2 chr3D.!!$R2 268
14 TraesCS5D01G368400 chr3D 338303296 338307110 3814 False 464.000000 479 97.948000 1665 1932 2 chr3D.!!$F2 267
15 TraesCS5D01G368400 chr1D 229408824 229409421 597 True 477.000000 477 81.157000 1 602 1 chr1D.!!$R1 601
16 TraesCS5D01G368400 chr7A 726491688 726492289 601 True 442.000000 442 80.195000 1 609 1 chr7A.!!$R1 608
17 TraesCS5D01G368400 chr3A 536931308 536931909 601 True 267.000000 267 75.158000 4 631 1 chr3A.!!$R2 627
18 TraesCS5D01G368400 chr4B 633770687 633771259 572 False 289.000000 289 76.499000 1 610 1 chr4B.!!$F1 609
19 TraesCS5D01G368400 chr1A 363009046 363010136 1090 False 289.000000 289 93.434000 1664 1860 2 chr1A.!!$F2 196
20 TraesCS5D01G368400 chr4D 22230566 22231191 625 False 213.000000 213 73.773000 1 631 1 chr4D.!!$F1 630

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
585 662 0.402504 TTGTGTCGGTTTAGCCCCAT 59.597 50.0 0.0 0.0 0.0 4.00 F
1382 1806 0.102481 ACGTACATCCTCCATCGCAC 59.898 55.0 0.0 0.0 0.0 5.34 F
3038 13929 0.322546 ATGACTTCGGGGTTGCTTCC 60.323 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 8192 0.239347 AAACCGGTCTACTCGTCACG 59.761 55.000 8.04 0.0 0.00 4.35 R
3076 14200 1.068333 CAGAATTTGGGCACGGTGAAG 60.068 52.381 13.29 0.0 0.00 3.02 R
4546 16120 0.179048 CCAGCATGCGGAGGAACATA 60.179 55.000 20.02 0.0 31.97 2.29 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
49 50 3.041940 CTTGCGGTCGTGGTGGAC 61.042 66.667 0.00 0.00 36.18 4.02
52 53 1.817911 TTGCGGTCGTGGTGGACATA 61.818 55.000 0.00 0.00 38.70 2.29
61 62 2.497770 GTGGACATACGACCGGGG 59.502 66.667 6.32 0.00 0.00 5.73
63 64 2.442643 GGACATACGACCGGGGGA 60.443 66.667 6.32 0.00 0.00 4.81
222 236 1.712018 GGACCAAATAGCCGCGAACC 61.712 60.000 8.23 0.00 0.00 3.62
300 332 1.149854 GTTTTGGGGGACGGACTGT 59.850 57.895 0.00 0.00 0.00 3.55
377 438 3.684628 AGGGGCGAAGGGAGAGGA 61.685 66.667 0.00 0.00 0.00 3.71
378 439 3.157949 GGGGCGAAGGGAGAGGAG 61.158 72.222 0.00 0.00 0.00 3.69
476 552 4.357947 GCTGTCCACCTCGACGCA 62.358 66.667 0.00 0.00 35.40 5.24
515 591 0.958876 GCCGGAAATGGGTCGAAAGT 60.959 55.000 5.05 0.00 0.00 2.66
548 625 2.344025 GACGTTTATCCGTTTGCTCCT 58.656 47.619 0.00 0.00 41.98 3.69
560 637 4.452733 GCTCCTACGCGTTGGGCT 62.453 66.667 33.69 4.80 40.44 5.19
573 650 2.051345 GGGCTGCGTTTTGTGTCG 60.051 61.111 0.00 0.00 0.00 4.35
585 662 0.402504 TTGTGTCGGTTTAGCCCCAT 59.597 50.000 0.00 0.00 0.00 4.00
638 715 1.651737 TGGAGTTGGCCTTAGTGCTA 58.348 50.000 3.32 0.00 0.00 3.49
641 718 2.622436 GAGTTGGCCTTAGTGCTAGTG 58.378 52.381 3.32 0.00 0.00 2.74
650 727 4.755123 GCCTTAGTGCTAGTGTTTTTCTGA 59.245 41.667 0.00 0.00 0.00 3.27
671 748 9.581099 TTCTGAATTTAATTTAGGATTTTCGGC 57.419 29.630 9.14 0.00 0.00 5.54
700 777 5.914635 TGCATTCAATGAGAGAAAACGTTTC 59.085 36.000 15.01 8.08 0.00 2.78
702 779 7.041440 TGCATTCAATGAGAGAAAACGTTTCTA 60.041 33.333 15.01 0.00 0.00 2.10
703 780 7.269297 GCATTCAATGAGAGAAAACGTTTCTAC 59.731 37.037 15.01 9.09 0.00 2.59
705 782 9.706691 ATTCAATGAGAGAAAACGTTTCTACTA 57.293 29.630 15.01 0.34 0.00 1.82
707 784 8.975439 TCAATGAGAGAAAACGTTTCTACTAAC 58.025 33.333 15.01 11.16 0.00 2.34
716 793 6.545504 AACGTTTCTACTAACTACGAGACA 57.454 37.500 0.00 0.00 36.21 3.41
724 801 8.502105 TCTACTAACTACGAGACAATGATGAA 57.498 34.615 0.00 0.00 0.00 2.57
725 802 8.396390 TCTACTAACTACGAGACAATGATGAAC 58.604 37.037 0.00 0.00 0.00 3.18
726 803 6.028368 ACTAACTACGAGACAATGATGAACG 58.972 40.000 0.00 0.00 0.00 3.95
727 804 4.436242 ACTACGAGACAATGATGAACGT 57.564 40.909 0.00 0.00 37.13 3.99
729 806 4.857588 ACTACGAGACAATGATGAACGTTC 59.142 41.667 21.42 21.42 35.89 3.95
732 809 3.181530 CGAGACAATGATGAACGTTCCAC 60.182 47.826 24.78 17.99 0.00 4.02
735 812 4.929808 AGACAATGATGAACGTTCCACTAC 59.070 41.667 24.78 11.86 0.00 2.73
736 813 3.678072 ACAATGATGAACGTTCCACTACG 59.322 43.478 24.78 12.10 46.52 3.51
737 814 3.861276 ATGATGAACGTTCCACTACGA 57.139 42.857 24.78 5.26 43.99 3.43
738 815 3.211803 TGATGAACGTTCCACTACGAG 57.788 47.619 24.78 0.00 43.99 4.18
739 816 1.918609 GATGAACGTTCCACTACGAGC 59.081 52.381 24.78 3.96 43.99 5.03
740 817 0.669619 TGAACGTTCCACTACGAGCA 59.330 50.000 24.78 0.19 43.99 4.26
741 818 1.271379 TGAACGTTCCACTACGAGCAT 59.729 47.619 24.78 0.00 43.99 3.79
742 819 1.918609 GAACGTTCCACTACGAGCATC 59.081 52.381 17.68 0.00 43.99 3.91
755 832 8.438513 CCACTACGAGCATCTTAAAATGATATG 58.561 37.037 0.00 0.00 0.00 1.78
757 834 5.920312 ACGAGCATCTTAAAATGATATGCG 58.080 37.500 0.00 0.00 45.84 4.73
762 839 6.020372 GCATCTTAAAATGATATGCGAGCTC 58.980 40.000 2.73 2.73 34.25 4.09
768 845 8.786937 TTAAAATGATATGCGAGCTCAATTTC 57.213 30.769 15.40 11.35 0.00 2.17
785 862 3.422417 TTTCTCGAAGATGCTCGTAGG 57.578 47.619 0.00 0.00 39.84 3.18
806 883 1.645455 CAGGATGCACGCTGTATGC 59.355 57.895 0.00 0.00 43.68 3.14
825 902 3.026431 ATTCGTAGCGGTGGGTGGG 62.026 63.158 0.00 0.00 0.00 4.61
826 903 4.682334 TCGTAGCGGTGGGTGGGA 62.682 66.667 0.00 0.00 0.00 4.37
827 904 4.143333 CGTAGCGGTGGGTGGGAG 62.143 72.222 0.00 0.00 0.00 4.30
828 905 3.001406 GTAGCGGTGGGTGGGAGT 61.001 66.667 0.00 0.00 0.00 3.85
829 906 1.683365 GTAGCGGTGGGTGGGAGTA 60.683 63.158 0.00 0.00 0.00 2.59
830 907 1.683365 TAGCGGTGGGTGGGAGTAC 60.683 63.158 0.00 0.00 0.00 2.73
831 908 4.446413 GCGGTGGGTGGGAGTACG 62.446 72.222 0.00 0.00 0.00 3.67
832 909 4.446413 CGGTGGGTGGGAGTACGC 62.446 72.222 0.00 0.00 0.00 4.42
833 910 3.315949 GGTGGGTGGGAGTACGCA 61.316 66.667 0.00 0.00 40.61 5.24
838 915 3.852316 GTGGGAGTACGCACGAAC 58.148 61.111 0.00 0.00 46.56 3.95
839 916 2.084681 GTGGGAGTACGCACGAACG 61.085 63.158 0.00 0.00 46.56 3.95
840 917 2.260154 TGGGAGTACGCACGAACGA 61.260 57.895 8.71 0.00 36.70 3.85
841 918 1.138247 GGGAGTACGCACGAACGAT 59.862 57.895 8.71 0.00 36.70 3.73
842 919 0.457337 GGGAGTACGCACGAACGATT 60.457 55.000 8.71 0.00 36.70 3.34
843 920 1.343506 GGAGTACGCACGAACGATTT 58.656 50.000 8.71 0.00 36.70 2.17
844 921 1.319669 GGAGTACGCACGAACGATTTC 59.680 52.381 8.71 3.30 36.70 2.17
845 922 2.248487 GAGTACGCACGAACGATTTCT 58.752 47.619 8.71 2.06 36.70 2.52
848 925 0.782384 ACGCACGAACGATTTCTGTC 59.218 50.000 8.71 0.00 36.70 3.51
850 927 1.201704 CGCACGAACGATTTCTGTCTG 60.202 52.381 0.14 0.00 34.06 3.51
851 928 1.126846 GCACGAACGATTTCTGTCTGG 59.873 52.381 0.14 0.00 0.00 3.86
856 933 3.985279 CGAACGATTTCTGTCTGGTGTTA 59.015 43.478 0.00 0.00 0.00 2.41
864 941 2.875933 TCTGTCTGGTGTTAAAAAGGCG 59.124 45.455 0.00 0.00 0.00 5.52
872 949 1.868498 TGTTAAAAAGGCGTCCGAGTG 59.132 47.619 0.00 0.00 0.00 3.51
882 959 2.050714 TCCGAGTGACGACAACGC 60.051 61.111 9.30 0.00 45.77 4.84
884 961 2.645510 CCGAGTGACGACAACGCAC 61.646 63.158 9.30 0.00 45.77 5.34
924 1009 3.792047 CACGTGGACGGCATGCAG 61.792 66.667 21.36 18.97 44.95 4.41
964 1052 2.305858 AGTCGGAGTGTATATCCCCC 57.694 55.000 0.00 0.00 32.86 5.40
1022 1110 1.448013 GTCGCCTTTTCCTCCTCCG 60.448 63.158 0.00 0.00 0.00 4.63
1382 1806 0.102481 ACGTACATCCTCCATCGCAC 59.898 55.000 0.00 0.00 0.00 5.34
1396 1820 3.184379 CCATCGCACATTACTAACATCCG 59.816 47.826 0.00 0.00 0.00 4.18
1417 1841 4.163552 CGCGTCTAGACAAATCTAACACA 58.836 43.478 22.37 0.00 36.98 3.72
1442 1866 7.520451 AAAGTAATTTGACAAGGAGGGTTAC 57.480 36.000 0.00 0.00 0.00 2.50
1458 1882 5.602628 AGGGTTACGATTCTTCATTAGCTC 58.397 41.667 0.00 0.00 0.00 4.09
1462 1886 6.694411 GGTTACGATTCTTCATTAGCTCGTAA 59.306 38.462 10.28 10.28 43.68 3.18
1464 1888 9.390795 GTTACGATTCTTCATTAGCTCGTAATA 57.609 33.333 15.55 0.00 45.28 0.98
1465 1889 9.955208 TTACGATTCTTCATTAGCTCGTAATAA 57.045 29.630 10.28 0.00 42.54 1.40
1466 1890 8.867112 ACGATTCTTCATTAGCTCGTAATAAA 57.133 30.769 0.00 0.00 38.98 1.40
1532 3316 5.055642 GAAATTAGTTTTCCCCAAGTCCG 57.944 43.478 0.00 0.00 38.22 4.79
1533 3317 3.801307 ATTAGTTTTCCCCAAGTCCGT 57.199 42.857 0.00 0.00 0.00 4.69
1553 3341 5.184287 TCCGTATGCGTATCTGATTTATCCA 59.816 40.000 1.69 0.00 36.15 3.41
1554 3342 6.042777 CCGTATGCGTATCTGATTTATCCAT 58.957 40.000 1.69 0.00 36.15 3.41
1575 3363 5.569059 CCATACGAAGCAATCAACAAACTTC 59.431 40.000 0.00 0.00 34.71 3.01
1576 3364 3.964909 ACGAAGCAATCAACAAACTTCC 58.035 40.909 0.00 0.00 34.58 3.46
1581 3369 5.130292 AGCAATCAACAAACTTCCATCTG 57.870 39.130 0.00 0.00 0.00 2.90
1608 3396 0.812811 ATCCGCTGCACTGCACATAG 60.813 55.000 0.00 0.00 33.79 2.23
1613 3401 1.129998 GCTGCACTGCACATAGTTGAG 59.870 52.381 0.00 0.00 33.79 3.02
1624 3412 3.688185 CACATAGTTGAGTGCAGCAGAAT 59.312 43.478 0.00 0.00 0.00 2.40
1658 3446 8.952278 AGCATAATTTGTATTACTTCCGTTTCA 58.048 29.630 0.00 0.00 0.00 2.69
1659 3447 9.562583 GCATAATTTGTATTACTTCCGTTTCAA 57.437 29.630 0.00 0.00 0.00 2.69
1833 7231 2.966516 CCACTGGATACCCTCCTTAGTC 59.033 54.545 0.00 0.00 45.21 2.59
1946 7547 6.420903 GGCTGCTAACAAAAAGGTTCTTTTAG 59.579 38.462 0.00 2.35 32.29 1.85
1975 7607 8.095937 TGTCTACATACGGATGTATCTAACAG 57.904 38.462 20.64 9.35 45.42 3.16
2016 8118 3.006967 TGTGCCTTCTTCTCCTAGTGTTC 59.993 47.826 0.00 0.00 0.00 3.18
2090 8192 7.870445 GGAGAAGATATTGACTCATCTTGTACC 59.130 40.741 1.76 0.00 40.68 3.34
2101 8212 3.373130 TCATCTTGTACCGTGACGAGTAG 59.627 47.826 6.54 0.00 33.21 2.57
2136 8247 5.172232 CGAGTTGAGACTATTTATGTCAGCG 59.828 44.000 0.00 0.00 35.88 5.18
2209 8320 5.967674 CGATCTACTGAAATGCATTTGTTCC 59.032 40.000 28.67 14.59 0.00 3.62
2307 8419 1.615392 GGCAGGCAACAGTCAGAATTT 59.385 47.619 0.00 0.00 41.41 1.82
2328 8445 5.670792 TTCTGATTCAGGTAACGGTGTAT 57.329 39.130 13.59 0.00 46.39 2.29
2544 10267 5.490139 ACTGTTTCATCAATCCTTATGCG 57.510 39.130 0.00 0.00 0.00 4.73
2568 10298 6.042143 GTCCTTGCTTTCATTTTCAACAGAA 58.958 36.000 0.00 0.00 0.00 3.02
2841 10579 4.408182 AAGGTACATGGAATTCCTCTCG 57.592 45.455 24.73 12.61 36.82 4.04
2845 10583 3.252974 ACATGGAATTCCTCTCGACAC 57.747 47.619 24.73 0.00 36.82 3.67
3038 13929 0.322546 ATGACTTCGGGGTTGCTTCC 60.323 55.000 0.00 0.00 0.00 3.46
3076 14200 4.767255 CGTGCTCAGGTGGGCCTC 62.767 72.222 4.53 0.00 44.97 4.70
3106 14230 4.221482 GTGCCCAAATTCTGAAGAAAGGAT 59.779 41.667 9.75 0.00 37.61 3.24
3108 14232 4.382362 GCCCAAATTCTGAAGAAAGGATGG 60.382 45.833 9.75 9.14 37.61 3.51
3161 14285 2.605818 GCGTCTTCGTATAACCAATGCA 59.394 45.455 0.00 0.00 39.49 3.96
3163 14287 4.109766 CGTCTTCGTATAACCAATGCAGA 58.890 43.478 0.00 0.00 0.00 4.26
3178 14302 5.875910 CCAATGCAGATTTTTATTCTTGCCA 59.124 36.000 0.00 0.00 0.00 4.92
3226 14352 2.202810 GTGCCGCTCTCTGCCTAC 60.203 66.667 0.00 0.00 38.78 3.18
3231 14357 1.140589 CGCTCTCTGCCTACACTGG 59.859 63.158 0.00 0.00 38.78 4.00
3234 14360 0.820871 CTCTCTGCCTACACTGGGAC 59.179 60.000 0.00 0.00 0.00 4.46
3296 14434 0.405585 ACTGGGTTGGTCATCTTGGG 59.594 55.000 0.00 0.00 0.00 4.12
3344 14482 1.232621 GGCCAACAAGGACGGTACAC 61.233 60.000 0.00 0.00 41.22 2.90
3354 14492 3.725490 AGGACGGTACACTTTGAGTTTC 58.275 45.455 0.00 0.00 0.00 2.78
3364 14502 4.142381 ACACTTTGAGTTTCAGGCAAAGAC 60.142 41.667 18.10 0.00 46.98 3.01
3392 14530 2.095059 GCTATTGCAGTTTGTGACCTGG 60.095 50.000 0.00 0.00 39.41 4.45
3432 14570 2.116125 GCTGTGAGGGGGCTGTTT 59.884 61.111 0.00 0.00 0.00 2.83
3434 14572 2.203480 TGTGAGGGGGCTGTTTGC 60.203 61.111 0.00 0.00 41.94 3.68
3445 14583 1.251251 GCTGTTTGCTCCATGGAACT 58.749 50.000 17.00 0.00 38.95 3.01
3470 14608 0.898326 GCATTCCTTGGTCGGGGTTT 60.898 55.000 0.00 0.00 0.00 3.27
3505 14643 1.630148 CCCTTCTTCATCGACGACAC 58.370 55.000 0.00 0.00 0.00 3.67
3602 14740 2.636412 GCCCGAGTCCCTTTTTGCC 61.636 63.158 0.00 0.00 0.00 4.52
3603 14741 1.074951 CCCGAGTCCCTTTTTGCCT 59.925 57.895 0.00 0.00 0.00 4.75
3678 14816 4.338400 TCACCATCTCACATACTCTTACCG 59.662 45.833 0.00 0.00 0.00 4.02
3706 14844 3.837213 AACTGTTATGTCTGCATGTGC 57.163 42.857 0.00 0.00 42.50 4.57
3913 15087 2.732366 CAACTAGATGATACGCTGCGT 58.268 47.619 31.22 31.22 44.35 5.24
4086 15260 2.726373 CGACTACAGTGAGAGACAAGCG 60.726 54.545 0.00 0.00 0.00 4.68
4089 15263 1.739562 CAGTGAGAGACAAGCGGGC 60.740 63.158 0.00 0.00 0.00 6.13
4090 15264 2.811317 GTGAGAGACAAGCGGGCG 60.811 66.667 0.00 0.00 0.00 6.13
4091 15265 2.989253 TGAGAGACAAGCGGGCGA 60.989 61.111 0.00 0.00 0.00 5.54
4092 15266 2.507324 GAGAGACAAGCGGGCGAC 60.507 66.667 0.00 0.00 0.00 5.19
4143 15360 2.456840 CTCCTCCACCCCCTTCCT 59.543 66.667 0.00 0.00 0.00 3.36
4152 15369 1.862138 CCCCCTTCCTTTCCCCCTT 60.862 63.158 0.00 0.00 0.00 3.95
4154 15371 0.851332 CCCCTTCCTTTCCCCCTTCT 60.851 60.000 0.00 0.00 0.00 2.85
4155 15372 0.332972 CCCTTCCTTTCCCCCTTCTG 59.667 60.000 0.00 0.00 0.00 3.02
4156 15373 1.076438 CCTTCCTTTCCCCCTTCTGT 58.924 55.000 0.00 0.00 0.00 3.41
4157 15374 1.429299 CCTTCCTTTCCCCCTTCTGTT 59.571 52.381 0.00 0.00 0.00 3.16
4161 15378 1.425448 CCTTTCCCCCTTCTGTTGTCT 59.575 52.381 0.00 0.00 0.00 3.41
4172 15390 2.964925 GTTGTCTCGGCGTGCACA 60.965 61.111 18.64 8.33 0.00 4.57
4191 15409 4.087892 CTGAGCCTGTCCCGGGTG 62.088 72.222 22.86 12.04 34.32 4.61
4221 15439 3.752339 GCGGCCCCTGCTTTTCTG 61.752 66.667 0.00 0.00 37.74 3.02
4224 15442 1.910276 GGCCCCTGCTTTTCTGCTT 60.910 57.895 0.00 0.00 37.74 3.91
4227 15445 0.540365 CCCCTGCTTTTCTGCTTCCA 60.540 55.000 0.00 0.00 0.00 3.53
4228 15446 0.600057 CCCTGCTTTTCTGCTTCCAC 59.400 55.000 0.00 0.00 0.00 4.02
4229 15447 0.239347 CCTGCTTTTCTGCTTCCACG 59.761 55.000 0.00 0.00 0.00 4.94
4230 15448 0.947244 CTGCTTTTCTGCTTCCACGT 59.053 50.000 0.00 0.00 0.00 4.49
4231 15449 0.944386 TGCTTTTCTGCTTCCACGTC 59.056 50.000 0.00 0.00 0.00 4.34
4234 15452 1.946768 CTTTTCTGCTTCCACGTCCAA 59.053 47.619 0.00 0.00 0.00 3.53
4296 15866 4.112341 CTCGGTGTCGTCGTCCCC 62.112 72.222 0.00 0.00 37.69 4.81
4297 15867 4.953010 TCGGTGTCGTCGTCCCCA 62.953 66.667 0.00 0.00 37.69 4.96
4307 15877 0.322546 GTCGTCCCCAATTCCTTGCT 60.323 55.000 0.00 0.00 0.00 3.91
4314 15884 2.158264 CCCCAATTCCTTGCTATCCCAT 60.158 50.000 0.00 0.00 0.00 4.00
4315 15885 3.580039 CCCAATTCCTTGCTATCCCATT 58.420 45.455 0.00 0.00 0.00 3.16
4316 15886 3.969312 CCCAATTCCTTGCTATCCCATTT 59.031 43.478 0.00 0.00 0.00 2.32
4348 15918 0.257039 GGCCTCATGATGGTGACCTT 59.743 55.000 2.11 0.00 0.00 3.50
4404 15974 3.301554 CATGTTGGTGGGCCGCAA 61.302 61.111 20.39 4.17 37.67 4.85
4421 15991 2.673368 CGCAAGTTGGATGGAAGACTAC 59.327 50.000 4.75 0.00 0.00 2.73
4422 15992 2.673368 GCAAGTTGGATGGAAGACTACG 59.327 50.000 4.75 0.00 0.00 3.51
4425 15995 3.375699 AGTTGGATGGAAGACTACGGAT 58.624 45.455 0.00 0.00 0.00 4.18
4441 16011 1.520666 GATCGGGTGGGTAGTGGTG 59.479 63.158 0.00 0.00 0.00 4.17
4475 16049 3.682292 AAATCCCTGTCGGCTCGCC 62.682 63.158 0.00 0.00 0.00 5.54
4522 16096 1.378514 GCCGCCATTCCTTCCTGAA 60.379 57.895 0.00 0.00 0.00 3.02
4546 16120 1.129058 GTCGGATGTACCCATTCCCT 58.871 55.000 0.00 0.00 34.64 4.20
4547 16121 2.322658 GTCGGATGTACCCATTCCCTA 58.677 52.381 0.00 0.00 34.64 3.53
4559 16133 1.140852 CATTCCCTATGTTCCTCCGCA 59.859 52.381 0.00 0.00 0.00 5.69
4563 16137 0.107456 CCTATGTTCCTCCGCATGCT 59.893 55.000 17.13 0.00 0.00 3.79
4567 16141 3.008517 TTCCTCCGCATGCTGGGA 61.009 61.111 22.59 18.17 31.21 4.37
4598 16172 2.047274 ATGTCCGGACAACAGCGG 60.047 61.111 39.04 0.00 45.41 5.52
4599 16173 2.879233 ATGTCCGGACAACAGCGGT 61.879 57.895 39.04 19.69 45.41 5.68
4600 16174 3.041940 GTCCGGACAACAGCGGTG 61.042 66.667 29.75 14.13 0.00 4.94
4601 16175 3.542676 TCCGGACAACAGCGGTGT 61.543 61.111 15.81 15.81 39.19 4.16
4608 16182 4.211986 AACAGCGGTGTTGTCGTT 57.788 50.000 30.41 6.88 45.58 3.85
4609 16183 1.719117 AACAGCGGTGTTGTCGTTG 59.281 52.632 30.41 0.00 45.58 4.10
4616 16190 1.433837 GGTGTTGTCGTTGCGTTCCT 61.434 55.000 0.00 0.00 0.00 3.36
4638 16212 3.211045 TCTTGAAGGTGTTGCTTGGTAC 58.789 45.455 0.00 0.00 0.00 3.34
4639 16213 2.719531 TGAAGGTGTTGCTTGGTACA 57.280 45.000 0.00 0.00 0.00 2.90
4644 16218 1.153147 TGTTGCTTGGTACACGGCA 60.153 52.632 0.00 0.00 43.40 5.69
4647 16221 0.464735 TTGCTTGGTACACGGCAGTT 60.465 50.000 0.00 0.00 45.06 3.16
4648 16222 0.464735 TGCTTGGTACACGGCAGTTT 60.465 50.000 0.00 0.00 41.08 2.66
4649 16223 0.040425 GCTTGGTACACGGCAGTTTG 60.040 55.000 0.00 0.00 39.29 2.93
4650 16224 1.588674 CTTGGTACACGGCAGTTTGA 58.411 50.000 0.00 0.00 39.29 2.69
4657 16231 1.225855 CACGGCAGTTTGAAGCACTA 58.774 50.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.108362 GCTTCCCCCGGTCGTATG 59.892 66.667 0.00 0.00 0.00 2.39
61 62 2.185608 GGAGCTCGAGGTGCTTCC 59.814 66.667 26.34 15.57 41.30 3.46
63 64 3.394836 GGGGAGCTCGAGGTGCTT 61.395 66.667 30.75 1.92 41.30 3.91
262 277 3.069946 CCACCACGCCATGCCATT 61.070 61.111 0.00 0.00 0.00 3.16
300 332 0.179084 CGCCTTCCTCGCTTTCCATA 60.179 55.000 0.00 0.00 0.00 2.74
367 428 0.341609 CTTCCCCTCTCCTCTCCCTT 59.658 60.000 0.00 0.00 0.00 3.95
368 429 0.556380 TCTTCCCCTCTCCTCTCCCT 60.556 60.000 0.00 0.00 0.00 4.20
372 433 3.449918 CTTTTCTCTTCCCCTCTCCTCT 58.550 50.000 0.00 0.00 0.00 3.69
377 438 1.132036 ACCCCTTTTCTCTTCCCCTCT 60.132 52.381 0.00 0.00 0.00 3.69
378 439 1.004862 CACCCCTTTTCTCTTCCCCTC 59.995 57.143 0.00 0.00 0.00 4.30
456 521 4.357947 GTCGAGGTGGACAGCGCA 62.358 66.667 11.47 0.00 36.91 6.09
489 565 1.264045 ACCCATTTCCGGCCCAAATG 61.264 55.000 20.91 20.91 39.84 2.32
515 591 4.218852 GGATAAACGTCCATTTTTCACCCA 59.781 41.667 0.00 0.00 38.20 4.51
560 637 1.268133 GCTAAACCGACACAAAACGCA 60.268 47.619 0.00 0.00 0.00 5.24
573 650 1.949465 CGTCAGTATGGGGCTAAACC 58.051 55.000 0.00 0.00 36.16 3.27
616 693 2.576191 AGCACTAAGGCCAACTCCAATA 59.424 45.455 5.01 0.00 0.00 1.90
650 727 8.194769 ACATCGCCGAAAATCCTAAATTAAATT 58.805 29.630 0.00 0.00 0.00 1.82
661 738 0.381801 ATGCACATCGCCGAAAATCC 59.618 50.000 0.00 0.00 41.33 3.01
668 745 0.377905 TCATTGAATGCACATCGCCG 59.622 50.000 0.00 0.00 41.33 6.46
670 747 2.610833 TCTCTCATTGAATGCACATCGC 59.389 45.455 0.00 0.00 42.89 4.58
671 748 4.870221 TTCTCTCATTGAATGCACATCG 57.130 40.909 0.00 0.00 0.00 3.84
687 764 7.865707 TCGTAGTTAGTAGAAACGTTTTCTCT 58.134 34.615 15.89 10.51 35.21 3.10
700 777 7.373703 CGTTCATCATTGTCTCGTAGTTAGTAG 59.626 40.741 0.00 0.00 0.00 2.57
702 779 6.028368 CGTTCATCATTGTCTCGTAGTTAGT 58.972 40.000 0.00 0.00 0.00 2.24
703 780 6.028368 ACGTTCATCATTGTCTCGTAGTTAG 58.972 40.000 0.00 0.00 0.00 2.34
705 782 4.806330 ACGTTCATCATTGTCTCGTAGTT 58.194 39.130 0.00 0.00 0.00 2.24
707 784 4.265556 GGAACGTTCATCATTGTCTCGTAG 59.734 45.833 28.24 0.00 0.00 3.51
716 793 4.174009 CTCGTAGTGGAACGTTCATCATT 58.826 43.478 28.24 16.89 45.86 2.57
724 801 1.174783 AGATGCTCGTAGTGGAACGT 58.825 50.000 0.00 0.00 45.86 3.99
725 802 2.279582 AAGATGCTCGTAGTGGAACG 57.720 50.000 0.00 0.00 45.86 3.95
726 803 6.312918 TCATTTTAAGATGCTCGTAGTGGAAC 59.687 38.462 1.10 0.00 0.00 3.62
727 804 6.403049 TCATTTTAAGATGCTCGTAGTGGAA 58.597 36.000 1.10 0.00 0.00 3.53
729 806 6.851222 ATCATTTTAAGATGCTCGTAGTGG 57.149 37.500 1.10 0.00 0.00 4.00
732 809 7.062255 TCGCATATCATTTTAAGATGCTCGTAG 59.938 37.037 1.10 0.00 40.58 3.51
735 812 6.156932 TCGCATATCATTTTAAGATGCTCG 57.843 37.500 1.10 1.49 40.58 5.03
736 813 6.020372 GCTCGCATATCATTTTAAGATGCTC 58.980 40.000 1.10 0.00 40.58 4.26
737 814 5.704515 AGCTCGCATATCATTTTAAGATGCT 59.295 36.000 1.10 0.00 40.58 3.79
738 815 5.936054 AGCTCGCATATCATTTTAAGATGC 58.064 37.500 1.10 0.00 39.59 3.91
739 816 7.125536 TGAGCTCGCATATCATTTTAAGATG 57.874 36.000 9.64 0.00 0.00 2.90
740 817 7.734924 TTGAGCTCGCATATCATTTTAAGAT 57.265 32.000 9.64 0.00 0.00 2.40
741 818 7.734924 ATTGAGCTCGCATATCATTTTAAGA 57.265 32.000 9.64 0.00 0.00 2.10
742 819 8.792831 AAATTGAGCTCGCATATCATTTTAAG 57.207 30.769 9.64 0.00 29.51 1.85
757 834 3.870419 AGCATCTTCGAGAAATTGAGCTC 59.130 43.478 6.82 6.82 0.00 4.09
762 839 4.208047 CCTACGAGCATCTTCGAGAAATTG 59.792 45.833 2.12 0.00 43.03 2.32
768 845 2.679355 CTCCTACGAGCATCTTCGAG 57.321 55.000 2.12 0.00 43.03 4.04
785 862 0.531532 ATACAGCGTGCATCCTGCTC 60.532 55.000 14.31 0.00 45.31 4.26
788 865 1.091197 TGCATACAGCGTGCATCCTG 61.091 55.000 13.18 13.18 46.76 3.86
806 883 1.813753 CCACCCACCGCTACGAATG 60.814 63.158 0.00 0.00 0.00 2.67
807 884 2.582436 CCACCCACCGCTACGAAT 59.418 61.111 0.00 0.00 0.00 3.34
825 902 2.026507 CAGAAATCGTTCGTGCGTACTC 59.973 50.000 1.24 0.00 38.90 2.59
826 903 1.983605 CAGAAATCGTTCGTGCGTACT 59.016 47.619 1.24 0.00 38.90 2.73
827 904 1.717645 ACAGAAATCGTTCGTGCGTAC 59.282 47.619 0.00 0.00 38.90 3.67
828 905 1.980844 GACAGAAATCGTTCGTGCGTA 59.019 47.619 1.99 0.00 38.90 4.42
829 906 0.782384 GACAGAAATCGTTCGTGCGT 59.218 50.000 1.99 0.00 38.90 5.24
830 907 1.060713 AGACAGAAATCGTTCGTGCG 58.939 50.000 0.00 0.00 38.90 5.34
831 908 1.126846 CCAGACAGAAATCGTTCGTGC 59.873 52.381 0.00 0.00 38.90 5.34
832 909 2.155732 CACCAGACAGAAATCGTTCGTG 59.844 50.000 0.00 0.00 38.90 4.35
833 910 2.223971 ACACCAGACAGAAATCGTTCGT 60.224 45.455 0.00 0.00 38.90 3.85
834 911 2.404215 ACACCAGACAGAAATCGTTCG 58.596 47.619 0.00 0.00 38.90 3.95
835 912 5.917541 TTAACACCAGACAGAAATCGTTC 57.082 39.130 0.00 0.00 0.00 3.95
837 914 6.238648 CCTTTTTAACACCAGACAGAAATCGT 60.239 38.462 0.00 0.00 0.00 3.73
838 915 6.142817 CCTTTTTAACACCAGACAGAAATCG 58.857 40.000 0.00 0.00 0.00 3.34
839 916 5.920840 GCCTTTTTAACACCAGACAGAAATC 59.079 40.000 0.00 0.00 0.00 2.17
840 917 5.507315 CGCCTTTTTAACACCAGACAGAAAT 60.507 40.000 0.00 0.00 0.00 2.17
841 918 4.201970 CGCCTTTTTAACACCAGACAGAAA 60.202 41.667 0.00 0.00 0.00 2.52
842 919 3.314080 CGCCTTTTTAACACCAGACAGAA 59.686 43.478 0.00 0.00 0.00 3.02
843 920 2.875933 CGCCTTTTTAACACCAGACAGA 59.124 45.455 0.00 0.00 0.00 3.41
844 921 2.616842 ACGCCTTTTTAACACCAGACAG 59.383 45.455 0.00 0.00 0.00 3.51
845 922 2.614983 GACGCCTTTTTAACACCAGACA 59.385 45.455 0.00 0.00 0.00 3.41
848 925 1.069500 CGGACGCCTTTTTAACACCAG 60.069 52.381 0.00 0.00 0.00 4.00
850 927 1.196127 CTCGGACGCCTTTTTAACACC 59.804 52.381 0.00 0.00 0.00 4.16
851 928 1.869132 ACTCGGACGCCTTTTTAACAC 59.131 47.619 0.00 0.00 0.00 3.32
856 933 2.613390 GTCACTCGGACGCCTTTTT 58.387 52.632 0.00 0.00 36.65 1.94
864 941 2.362800 GCGTTGTCGTCACTCGGAC 61.363 63.158 8.02 0.00 43.36 4.79
896 973 3.478394 CCACGTGCGACATCACCG 61.478 66.667 10.91 0.00 33.57 4.94
897 974 2.048597 TCCACGTGCGACATCACC 60.049 61.111 10.91 0.00 33.57 4.02
899 976 2.430075 CGTCCACGTGCGACATCA 60.430 61.111 26.19 0.00 34.11 3.07
924 1009 1.200948 ACTAGTAACAGCCGACGGAAC 59.799 52.381 20.50 6.85 0.00 3.62
964 1052 4.729918 GGGAGTGCTGTGGCCTGG 62.730 72.222 3.32 0.00 37.74 4.45
1001 1089 2.436115 GGAGGAAAAGGCGACGGG 60.436 66.667 0.00 0.00 0.00 5.28
1039 1130 4.821589 CTCGCTGGCTCGAACCCC 62.822 72.222 1.61 0.00 38.08 4.95
1073 1164 2.579787 CGCTCCCGTCGACATCAC 60.580 66.667 17.16 0.00 0.00 3.06
1382 1806 4.910456 GTCTAGACGCGGATGTTAGTAATG 59.090 45.833 12.47 0.00 0.00 1.90
1396 1820 6.462073 TTTGTGTTAGATTTGTCTAGACGC 57.538 37.500 17.85 7.45 0.00 5.19
1417 1841 7.255346 CGTAACCCTCCTTGTCAAATTACTTTT 60.255 37.037 0.00 0.00 0.00 2.27
1429 1853 3.581332 TGAAGAATCGTAACCCTCCTTGT 59.419 43.478 0.00 0.00 0.00 3.16
1525 3309 3.349488 TCAGATACGCATACGGACTTG 57.651 47.619 0.00 0.00 46.04 3.16
1528 3312 5.515626 GGATAAATCAGATACGCATACGGAC 59.484 44.000 0.00 0.00 46.04 4.79
1529 3313 5.184287 TGGATAAATCAGATACGCATACGGA 59.816 40.000 0.00 0.00 46.04 4.69
1530 3314 5.407502 TGGATAAATCAGATACGCATACGG 58.592 41.667 0.00 0.00 46.04 4.02
1532 3316 7.913821 TCGTATGGATAAATCAGATACGCATAC 59.086 37.037 19.19 12.18 41.70 2.39
1533 3317 7.992008 TCGTATGGATAAATCAGATACGCATA 58.008 34.615 19.19 8.15 41.70 3.14
1553 3341 5.240623 TGGAAGTTTGTTGATTGCTTCGTAT 59.759 36.000 0.00 0.00 37.14 3.06
1554 3342 4.576873 TGGAAGTTTGTTGATTGCTTCGTA 59.423 37.500 0.00 0.00 37.14 3.43
1575 3363 1.202463 AGCGGATCGAAGAACAGATGG 60.202 52.381 0.00 0.00 43.58 3.51
1576 3364 1.857217 CAGCGGATCGAAGAACAGATG 59.143 52.381 0.00 0.00 43.58 2.90
1581 3369 0.737715 AGTGCAGCGGATCGAAGAAC 60.738 55.000 0.00 0.00 43.58 3.01
1608 3396 5.464168 ACATAAAATTCTGCTGCACTCAAC 58.536 37.500 0.00 0.00 0.00 3.18
1613 3401 4.985413 TGCTACATAAAATTCTGCTGCAC 58.015 39.130 0.00 0.00 0.00 4.57
1649 3437 4.705991 ACCCTAACACTTTTTGAAACGGAA 59.294 37.500 0.00 0.00 0.00 4.30
1656 3444 5.376756 ACCAGTACCCTAACACTTTTTGA 57.623 39.130 0.00 0.00 0.00 2.69
1658 3446 6.752285 TCTACCAGTACCCTAACACTTTTT 57.248 37.500 0.00 0.00 0.00 1.94
1659 3447 6.947376 ATCTACCAGTACCCTAACACTTTT 57.053 37.500 0.00 0.00 0.00 2.27
1660 3448 7.187676 AGTATCTACCAGTACCCTAACACTTT 58.812 38.462 0.00 0.00 0.00 2.66
1661 3449 6.739664 AGTATCTACCAGTACCCTAACACTT 58.260 40.000 0.00 0.00 0.00 3.16
1662 3450 6.338591 AGTATCTACCAGTACCCTAACACT 57.661 41.667 0.00 0.00 0.00 3.55
1914 7312 1.327303 TTTGTTAGCAGCCCACCTTG 58.673 50.000 0.00 0.00 0.00 3.61
1959 7560 5.587844 AGTCGTTACTGTTAGATACATCCGT 59.412 40.000 0.00 0.00 35.85 4.69
1972 7604 8.013378 GCACATAACAAAATTAGTCGTTACTGT 58.987 33.333 0.00 0.00 36.36 3.55
1975 7607 7.524065 AGGCACATAACAAAATTAGTCGTTAC 58.476 34.615 0.00 0.00 0.00 2.50
1988 8081 4.640771 AGGAGAAGAAGGCACATAACAA 57.359 40.909 0.00 0.00 0.00 2.83
2090 8192 0.239347 AAACCGGTCTACTCGTCACG 59.761 55.000 8.04 0.00 0.00 4.35
2101 8212 2.728318 GTCTCAACTCGTAAAACCGGTC 59.272 50.000 8.04 0.00 0.00 4.79
2136 8247 2.801113 TTTGCAGCAAGAATCGCCGC 62.801 55.000 8.12 0.00 33.31 6.53
2307 8419 5.046878 ACAATACACCGTTACCTGAATCAGA 60.047 40.000 12.53 0.00 32.44 3.27
2513 10217 7.729116 AGGATTGATGAAACAGTTCAAACAAT 58.271 30.769 17.08 17.08 46.66 2.71
2516 10220 9.132521 CATAAGGATTGATGAAACAGTTCAAAC 57.867 33.333 0.00 0.00 46.66 2.93
2544 10267 5.591099 TCTGTTGAAAATGAAAGCAAGGAC 58.409 37.500 0.00 0.00 0.00 3.85
2568 10298 1.914798 AGCTCCATGAAGGCTTTCTCT 59.085 47.619 10.19 0.00 37.29 3.10
2784 10522 2.267324 GCTGCCTCTGTCAGGTCC 59.733 66.667 0.00 0.00 45.61 4.46
2838 10576 2.492088 TGGGATCACTTACTGTGTCGAG 59.508 50.000 0.00 0.00 46.27 4.04
2845 10583 8.267183 TGGCAATATATATGGGATCACTTACTG 58.733 37.037 0.00 0.00 0.00 2.74
2863 10602 5.075493 GGTCTCTCAATCCAATGGCAATAT 58.925 41.667 0.00 0.00 0.00 1.28
2864 10603 4.166725 AGGTCTCTCAATCCAATGGCAATA 59.833 41.667 0.00 0.00 0.00 1.90
2865 10604 3.053095 AGGTCTCTCAATCCAATGGCAAT 60.053 43.478 0.00 0.00 0.00 3.56
2868 10607 2.172293 AGAGGTCTCTCAATCCAATGGC 59.828 50.000 0.00 0.00 42.34 4.40
2932 10673 3.059461 GTGCAGCAAAACCATGTGATTTG 60.059 43.478 0.00 10.51 37.17 2.32
3038 13929 3.303461 CGAAGTCATAGACAGCTACCTCG 60.303 52.174 0.00 0.00 34.60 4.63
3076 14200 1.068333 CAGAATTTGGGCACGGTGAAG 60.068 52.381 13.29 0.00 0.00 3.02
3178 14302 4.579869 CTTCACAGCCCAGTTAACAGTAT 58.420 43.478 8.61 0.00 0.00 2.12
3223 14349 5.359194 ACTGAATATTGGTCCCAGTGTAG 57.641 43.478 6.07 0.00 36.80 2.74
3226 14352 3.696051 CCAACTGAATATTGGTCCCAGTG 59.304 47.826 7.33 3.52 41.55 3.66
3231 14357 4.855340 TCTTCCCAACTGAATATTGGTCC 58.145 43.478 0.00 0.00 44.46 4.46
3234 14360 7.056635 ACATACTCTTCCCAACTGAATATTGG 58.943 38.462 0.00 0.00 45.36 3.16
3315 14453 2.169561 TCCTTGTTGGCCCTTTGTTTTC 59.830 45.455 0.00 0.00 35.26 2.29
3338 14476 3.211045 TGCCTGAAACTCAAAGTGTACC 58.789 45.455 0.00 0.00 0.00 3.34
3344 14482 4.637483 TGTCTTTGCCTGAAACTCAAAG 57.363 40.909 7.42 7.42 44.69 2.77
3354 14492 1.372128 GCGGCTTTGTCTTTGCCTG 60.372 57.895 0.00 0.00 44.09 4.85
3372 14510 2.095059 GCCAGGTCACAAACTGCAATAG 60.095 50.000 0.00 0.00 33.43 1.73
3392 14530 4.043200 GCGAAGGTGCCCTTGTGC 62.043 66.667 10.77 10.41 44.82 4.57
3412 14550 4.421515 CAGCCCCCTCACAGCCAG 62.422 72.222 0.00 0.00 0.00 4.85
3415 14553 2.116125 AAACAGCCCCCTCACAGC 59.884 61.111 0.00 0.00 0.00 4.40
3420 14558 2.505364 ATGGAGCAAACAGCCCCCTC 62.505 60.000 0.00 0.00 41.18 4.30
3421 14559 2.551413 ATGGAGCAAACAGCCCCCT 61.551 57.895 0.00 0.00 41.18 4.79
3427 14565 1.815003 GGAGTTCCATGGAGCAAACAG 59.185 52.381 27.96 0.00 35.64 3.16
3432 14570 3.963733 CAAGGAGTTCCATGGAGCA 57.036 52.632 27.96 6.70 38.89 4.26
3445 14583 0.322456 CGACCAAGGAATGCCAAGGA 60.322 55.000 7.45 0.00 35.18 3.36
3602 14740 2.169832 TTCCTCCTCGCTCACAAAAG 57.830 50.000 0.00 0.00 0.00 2.27
3603 14741 2.218603 GTTTCCTCCTCGCTCACAAAA 58.781 47.619 0.00 0.00 0.00 2.44
3678 14816 4.868171 TGCAGACATAACAGTTTCGATACC 59.132 41.667 2.13 0.00 0.00 2.73
3706 14844 0.380733 TCGGTGTATAGCAGAGCACG 59.619 55.000 0.00 0.00 33.09 5.34
4143 15360 1.071699 CGAGACAACAGAAGGGGGAAA 59.928 52.381 0.00 0.00 0.00 3.13
4152 15369 2.355837 GCACGCCGAGACAACAGA 60.356 61.111 0.00 0.00 0.00 3.41
4154 15371 2.964925 GTGCACGCCGAGACAACA 60.965 61.111 0.00 0.00 0.00 3.33
4155 15372 2.943345 CTGTGCACGCCGAGACAAC 61.943 63.158 13.13 0.00 0.00 3.32
4156 15373 2.661537 CTGTGCACGCCGAGACAA 60.662 61.111 13.13 0.00 0.00 3.18
4220 15438 1.375396 CCGATTGGACGTGGAAGCA 60.375 57.895 0.00 0.00 37.49 3.91
4221 15439 2.750888 GCCGATTGGACGTGGAAGC 61.751 63.158 1.98 0.00 37.49 3.86
4224 15442 1.514087 GTAGCCGATTGGACGTGGA 59.486 57.895 1.98 0.00 37.49 4.02
4287 15857 1.644786 GCAAGGAATTGGGGACGACG 61.645 60.000 0.00 0.00 0.00 5.12
4289 15859 1.281419 TAGCAAGGAATTGGGGACGA 58.719 50.000 0.00 0.00 0.00 4.20
4316 15886 5.241403 TCATGAGGCCTAGAAGACAAAAA 57.759 39.130 4.42 0.00 0.00 1.94
4332 15902 4.403752 TCTCACTAAGGTCACCATCATGAG 59.596 45.833 10.52 10.52 33.84 2.90
4348 15918 2.044555 CACCCTCGCCGTCTCACTA 61.045 63.158 0.00 0.00 0.00 2.74
4368 15938 2.310233 CGCCACCACAGTCTTGACG 61.310 63.158 0.00 0.00 0.00 4.35
4400 15970 1.813513 AGTCTTCCATCCAACTTGCG 58.186 50.000 0.00 0.00 0.00 4.85
4401 15971 2.673368 CGTAGTCTTCCATCCAACTTGC 59.327 50.000 0.00 0.00 0.00 4.01
4404 15974 2.816411 TCCGTAGTCTTCCATCCAACT 58.184 47.619 0.00 0.00 0.00 3.16
4421 15991 2.792947 CCACTACCCACCCGATCCG 61.793 68.421 0.00 0.00 0.00 4.18
4422 15992 1.688187 ACCACTACCCACCCGATCC 60.688 63.158 0.00 0.00 0.00 3.36
4425 15995 1.055551 AAACACCACTACCCACCCGA 61.056 55.000 0.00 0.00 0.00 5.14
4441 16011 2.301870 GGATTTCTCCCAACCCCAAAAC 59.698 50.000 0.00 0.00 35.28 2.43
4501 16075 3.140814 GGAAGGAATGGCGGCACC 61.141 66.667 16.34 12.81 39.84 5.01
4502 16076 2.044946 AGGAAGGAATGGCGGCAC 60.045 61.111 16.34 1.46 0.00 5.01
4503 16077 2.045045 CAGGAAGGAATGGCGGCA 60.045 61.111 16.34 16.34 0.00 5.69
4504 16078 1.378514 TTCAGGAAGGAATGGCGGC 60.379 57.895 0.00 0.00 0.00 6.53
4505 16079 2.785868 CTTCAGGAAGGAATGGCGG 58.214 57.895 1.01 0.00 34.87 6.13
4522 16096 3.152400 GGGTACATCCGACGCCCT 61.152 66.667 0.00 0.00 36.49 5.19
4546 16120 0.179048 CCAGCATGCGGAGGAACATA 60.179 55.000 20.02 0.00 31.97 2.29
4547 16121 1.452651 CCAGCATGCGGAGGAACAT 60.453 57.895 20.02 0.00 31.97 2.71
4598 16172 0.375803 AAGGAACGCAACGACAACAC 59.624 50.000 0.00 0.00 0.00 3.32
4599 16173 0.653636 GAAGGAACGCAACGACAACA 59.346 50.000 0.00 0.00 0.00 3.33
4600 16174 0.935196 AGAAGGAACGCAACGACAAC 59.065 50.000 0.00 0.00 0.00 3.32
4601 16175 1.329292 CAAGAAGGAACGCAACGACAA 59.671 47.619 0.00 0.00 0.00 3.18
4602 16176 0.934496 CAAGAAGGAACGCAACGACA 59.066 50.000 0.00 0.00 0.00 4.35
4603 16177 1.214367 TCAAGAAGGAACGCAACGAC 58.786 50.000 0.00 0.00 0.00 4.34
4616 16190 2.733956 ACCAAGCAACACCTTCAAGAA 58.266 42.857 0.00 0.00 0.00 2.52
4638 16212 1.195448 CTAGTGCTTCAAACTGCCGTG 59.805 52.381 0.00 0.00 0.00 4.94
4639 16213 1.512926 CTAGTGCTTCAAACTGCCGT 58.487 50.000 0.00 0.00 0.00 5.68
4657 16231 0.836400 ATTCGACCCACCACACTCCT 60.836 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.