Multiple sequence alignment - TraesCS6A01G419900

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 TraesCS6A01G419900 chr6A 100.000 5705 0 0 1 5705 617034923 617040627 0.000000e+00 10536.0
1 TraesCS6A01G419900 chr6A 97.707 567 10 3 2 565 74105382 74105948 0.000000e+00 972.0
2 TraesCS6A01G419900 chr6A 82.418 819 94 22 2440 3221 616975422 616976227 0.000000e+00 669.0
3 TraesCS6A01G419900 chr6A 81.981 616 75 27 4199 4809 616981818 616982402 1.850000e-134 490.0
4 TraesCS6A01G419900 chr6A 100.000 28 0 0 1383 1410 509559410 509559437 1.000000e-02 52.8
5 TraesCS6A01G419900 chr6B 91.030 2263 153 20 2610 4848 717908698 717906462 0.000000e+00 3009.0
6 TraesCS6A01G419900 chr6B 90.350 829 34 17 1797 2622 717909520 717908735 0.000000e+00 1046.0
7 TraesCS6A01G419900 chr6B 97.552 572 11 3 1 569 70698361 70697790 0.000000e+00 976.0
8 TraesCS6A01G419900 chr6B 97.373 571 12 3 1 569 716423471 716424040 0.000000e+00 968.0
9 TraesCS6A01G419900 chr6B 82.051 1092 143 38 3733 4809 717917391 717916338 0.000000e+00 881.0
10 TraesCS6A01G419900 chr6B 88.446 753 38 15 694 1409 717910765 717910025 0.000000e+00 863.0
11 TraesCS6A01G419900 chr6B 83.314 881 99 22 2372 3223 717919165 717918304 0.000000e+00 769.0
12 TraesCS6A01G419900 chr6B 83.568 639 64 15 3374 4002 717918376 717917769 1.390000e-155 560.0
13 TraesCS6A01G419900 chr6B 89.639 415 22 6 5071 5479 717905935 717905536 5.100000e-140 508.0
14 TraesCS6A01G419900 chr6B 86.632 389 39 11 1416 1796 717909945 717909562 8.840000e-113 418.0
15 TraesCS6A01G419900 chr6B 92.121 165 7 3 4883 5045 717906153 717905993 1.600000e-55 228.0
16 TraesCS6A01G419900 chr6B 76.908 498 51 31 689 1154 717920879 717920414 2.070000e-54 224.0
17 TraesCS6A01G419900 chr6B 87.500 96 2 2 568 663 717910854 717910769 1.010000e-17 102.0
18 TraesCS6A01G419900 chr6B 90.000 60 6 0 878 937 717921105 717921046 1.700000e-10 78.7
19 TraesCS6A01G419900 chr6D 95.088 1649 59 12 1604 3234 472793160 472791516 0.000000e+00 2577.0
20 TraesCS6A01G419900 chr6D 90.578 1263 86 19 3292 4530 472791513 472790260 0.000000e+00 1642.0
21 TraesCS6A01G419900 chr6D 97.412 657 14 1 884 1540 472793807 472793154 0.000000e+00 1116.0
22 TraesCS6A01G419900 chr6D 86.754 921 79 17 2440 3340 472801303 472800406 0.000000e+00 985.0
23 TraesCS6A01G419900 chr6D 83.134 1002 119 28 3770 4746 472800481 472799505 0.000000e+00 869.0
24 TraesCS6A01G419900 chr6D 95.497 533 24 0 2689 3221 472689673 472690205 0.000000e+00 852.0
25 TraesCS6A01G419900 chr6D 92.283 311 15 4 568 869 472794177 472793867 3.160000e-117 433.0
26 TraesCS6A01G419900 chr6D 88.500 200 16 1 3374 3566 472690135 472690334 9.560000e-58 235.0
27 TraesCS6A01G419900 chr6D 89.552 134 9 2 569 697 472689340 472689473 1.270000e-36 165.0
28 TraesCS6A01G419900 chr5B 97.400 577 11 4 1 574 127860075 127860650 0.000000e+00 979.0
29 TraesCS6A01G419900 chr4A 97.561 574 11 3 1 572 701553033 701553605 0.000000e+00 979.0
30 TraesCS6A01G419900 chr4A 97.703 566 11 2 1 564 718594637 718595202 0.000000e+00 972.0
31 TraesCS6A01G419900 chr7A 98.046 563 9 2 1 561 724224564 724225126 0.000000e+00 977.0
32 TraesCS6A01G419900 chr5A 98.043 562 10 1 1 561 1840285 1839724 0.000000e+00 976.0
33 TraesCS6A01G419900 chr1A 97.382 573 11 4 1 569 4558560 4557988 0.000000e+00 972.0
34 TraesCS6A01G419900 chr1D 77.063 715 120 27 4960 5636 26269786 26269078 6.980000e-99 372.0
35 TraesCS6A01G419900 chr7D 79.459 370 57 11 5279 5630 41601101 41600733 1.590000e-60 244.0
36 TraesCS6A01G419900 chr7D 86.607 112 15 0 1040 1151 106414916 106415027 2.160000e-24 124.0
37 TraesCS6A01G419900 chr3B 72.609 460 103 14 5190 5630 685394193 685394648 4.640000e-26 130.0
38 TraesCS6A01G419900 chr7B 88.525 61 7 0 2543 2603 734272714 734272654 2.200000e-09 75.0
39 TraesCS6A01G419900 chr4D 100.000 32 0 0 1380 1411 140896481 140896512 6.170000e-05 60.2
40 TraesCS6A01G419900 chr5D 100.000 28 0 0 1383 1410 547518573 547518600 1.000000e-02 52.8
41 TraesCS6A01G419900 chr5D 100.000 28 0 0 1383 1410 547799012 547799039 1.000000e-02 52.8
42 TraesCS6A01G419900 chr4B 100.000 28 0 0 1383 1410 42939387 42939360 1.000000e-02 52.8
43 TraesCS6A01G419900 chr4B 100.000 28 0 0 1383 1410 119340235 119340208 1.000000e-02 52.8
44 TraesCS6A01G419900 chr4B 100.000 28 0 0 1383 1410 579402828 579402801 1.000000e-02 52.8


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 TraesCS6A01G419900 chr6A 617034923 617040627 5704 False 10536.000000 10536 100.000000 1 5705 1 chr6A.!!$F5 5704
1 TraesCS6A01G419900 chr6A 74105382 74105948 566 False 972.000000 972 97.707000 2 565 1 chr6A.!!$F1 563
2 TraesCS6A01G419900 chr6A 616975422 616976227 805 False 669.000000 669 82.418000 2440 3221 1 chr6A.!!$F3 781
3 TraesCS6A01G419900 chr6A 616981818 616982402 584 False 490.000000 490 81.981000 4199 4809 1 chr6A.!!$F4 610
4 TraesCS6A01G419900 chr6B 70697790 70698361 571 True 976.000000 976 97.552000 1 569 1 chr6B.!!$R1 568
5 TraesCS6A01G419900 chr6B 716423471 716424040 569 False 968.000000 968 97.373000 1 569 1 chr6B.!!$F1 568
6 TraesCS6A01G419900 chr6B 717905536 717910854 5318 True 882.000000 3009 89.388286 568 5479 7 chr6B.!!$R2 4911
7 TraesCS6A01G419900 chr6B 717916338 717921105 4767 True 502.540000 881 83.168200 689 4809 5 chr6B.!!$R3 4120
8 TraesCS6A01G419900 chr6D 472790260 472794177 3917 True 1442.000000 2577 93.840250 568 4530 4 chr6D.!!$R1 3962
9 TraesCS6A01G419900 chr6D 472799505 472801303 1798 True 927.000000 985 84.944000 2440 4746 2 chr6D.!!$R2 2306
10 TraesCS6A01G419900 chr6D 472689340 472690334 994 False 417.333333 852 91.183000 569 3566 3 chr6D.!!$F1 2997
11 TraesCS6A01G419900 chr5B 127860075 127860650 575 False 979.000000 979 97.400000 1 574 1 chr5B.!!$F1 573
12 TraesCS6A01G419900 chr4A 701553033 701553605 572 False 979.000000 979 97.561000 1 572 1 chr4A.!!$F1 571
13 TraesCS6A01G419900 chr4A 718594637 718595202 565 False 972.000000 972 97.703000 1 564 1 chr4A.!!$F2 563
14 TraesCS6A01G419900 chr7A 724224564 724225126 562 False 977.000000 977 98.046000 1 561 1 chr7A.!!$F1 560
15 TraesCS6A01G419900 chr5A 1839724 1840285 561 True 976.000000 976 98.043000 1 561 1 chr5A.!!$R1 560
16 TraesCS6A01G419900 chr1A 4557988 4558560 572 True 972.000000 972 97.382000 1 569 1 chr1A.!!$R1 568
17 TraesCS6A01G419900 chr1D 26269078 26269786 708 True 372.000000 372 77.063000 4960 5636 1 chr1D.!!$R1 676

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
808 841 0.034756 AGGCAGCAACATACGTGTCA 59.965 50.000 0.00 0.0 37.67 3.58 F
1552 1841 0.901580 CCTTCAGGCTGGCCAACAAT 60.902 55.000 15.73 0.0 38.92 2.71 F
1621 1910 2.230750 GCTCCTGCAGAAGCTTGAAATT 59.769 45.455 18.89 0.0 42.74 1.82 F
2989 3517 1.705186 AGATGGTGCAAGTACCTTGGT 59.295 47.619 8.76 0.0 41.31 3.67 F
4100 5332 0.736053 GTGTTGGCTGGAAACGTGAA 59.264 50.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2739 0.547075 TCCCCGACTTGGTTGTTTGA 59.453 50.000 0.00 0.0 35.15 2.69 R
2539 2978 2.737679 GCATCAGCCTTCTTTTCATGGC 60.738 50.000 0.00 0.0 45.21 4.40 R
3124 3652 4.025040 TGAGCAGATAAAGGCCCATATG 57.975 45.455 0.00 0.0 0.00 1.78 R
4498 5737 0.027979 CACAACTCACACAGGTTGCG 59.972 55.000 5.85 0.0 44.41 4.85 R
5661 7229 0.039035 AACCGGGCATAAAAGGCTCA 59.961 50.000 6.32 0.0 0.00 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
107 108 1.677217 GGCCAAGAGAACGAGCAGAAT 60.677 52.381 0.00 0.00 0.00 2.40
393 396 1.275291 TCCTCAGGTGATCGGTTCAAC 59.725 52.381 0.00 0.00 42.84 3.18
565 569 5.408604 CAGTCACCGTAAAACAGCTCTAATT 59.591 40.000 0.00 0.00 0.00 1.40
566 570 6.588756 CAGTCACCGTAAAACAGCTCTAATTA 59.411 38.462 0.00 0.00 0.00 1.40
663 676 6.128309 CCCAAACAAAGGAAGAAACAACAAAG 60.128 38.462 0.00 0.00 0.00 2.77
805 838 2.584791 GAAAAGGCAGCAACATACGTG 58.415 47.619 0.00 0.00 0.00 4.49
806 839 1.604604 AAAGGCAGCAACATACGTGT 58.395 45.000 0.00 0.00 41.28 4.49
807 840 1.156736 AAGGCAGCAACATACGTGTC 58.843 50.000 0.00 0.00 37.67 3.67
808 841 0.034756 AGGCAGCAACATACGTGTCA 59.965 50.000 0.00 0.00 37.67 3.58
809 842 1.086696 GGCAGCAACATACGTGTCAT 58.913 50.000 0.00 0.00 37.67 3.06
810 843 1.062587 GGCAGCAACATACGTGTCATC 59.937 52.381 0.00 0.00 37.67 2.92
811 844 1.267038 GCAGCAACATACGTGTCATCG 60.267 52.381 0.00 0.00 37.67 3.84
812 845 0.999406 AGCAACATACGTGTCATCGC 59.001 50.000 0.00 0.00 37.67 4.58
820 853 5.593968 ACATACGTGTCATCGCCTTTATTA 58.406 37.500 0.00 0.00 31.41 0.98
965 1051 2.370189 CCTATTACTTCTGGCCTCCTGG 59.630 54.545 3.32 0.00 0.00 4.45
1210 1299 4.722194 TCATTCATTCGCTGCTTGTTAAC 58.278 39.130 0.00 0.00 0.00 2.01
1344 1549 5.020795 TCCTCAAGTACAACTAGTGCCATA 58.979 41.667 0.00 0.00 32.67 2.74
1379 1584 2.684881 CACTCCATGGCCTGTGTTAATC 59.315 50.000 6.96 0.00 0.00 1.75
1552 1841 0.901580 CCTTCAGGCTGGCCAACAAT 60.902 55.000 15.73 0.00 38.92 2.71
1588 1877 2.359850 GGCTGCGGTGTCCATGAA 60.360 61.111 0.00 0.00 0.00 2.57
1621 1910 2.230750 GCTCCTGCAGAAGCTTGAAATT 59.769 45.455 18.89 0.00 42.74 1.82
1725 2015 5.727434 TCTGTTCCCTCCGTAAAGAAATAC 58.273 41.667 0.00 0.00 0.00 1.89
1730 2020 5.727434 TCCCTCCGTAAAGAAATACAAGAC 58.273 41.667 0.00 0.00 0.00 3.01
1732 2022 4.874396 CCTCCGTAAAGAAATACAAGACCC 59.126 45.833 0.00 0.00 0.00 4.46
1733 2023 4.835678 TCCGTAAAGAAATACAAGACCCC 58.164 43.478 0.00 0.00 0.00 4.95
1734 2024 4.286549 TCCGTAAAGAAATACAAGACCCCA 59.713 41.667 0.00 0.00 0.00 4.96
1735 2025 5.045432 TCCGTAAAGAAATACAAGACCCCAT 60.045 40.000 0.00 0.00 0.00 4.00
1736 2026 5.296035 CCGTAAAGAAATACAAGACCCCATC 59.704 44.000 0.00 0.00 0.00 3.51
1737 2027 5.878116 CGTAAAGAAATACAAGACCCCATCA 59.122 40.000 0.00 0.00 0.00 3.07
1740 2030 9.574516 GTAAAGAAATACAAGACCCCATCATAT 57.425 33.333 0.00 0.00 0.00 1.78
1831 2176 5.713025 TCCAGCAATGAAACTAATTGCTTC 58.287 37.500 18.32 0.00 0.00 3.86
2215 2595 7.504911 CCTCTAGCTAGTACCCAACATTAACTA 59.495 40.741 20.10 0.00 0.00 2.24
2219 2599 7.668492 AGCTAGTACCCAACATTAACTATAGC 58.332 38.462 0.00 0.00 0.00 2.97
2313 2739 7.949690 TGATTGATGTTTCAGATTCTGGAAT 57.050 32.000 10.57 0.00 31.09 3.01
2329 2755 2.621055 TGGAATCAAACAACCAAGTCGG 59.379 45.455 0.00 0.00 42.50 4.79
2422 2860 5.907662 TCCATCCTGATTTCTTCCAGAGTAT 59.092 40.000 0.00 0.00 32.37 2.12
2458 2896 7.112122 TGTTGAGATGATTACAGTATGGCTTT 58.888 34.615 0.00 0.00 43.62 3.51
2539 2978 4.064768 TCTGCCATGGCCCAAGGG 62.065 66.667 33.44 15.72 41.09 3.95
2705 3210 7.148154 TGCTCTCTAACTTCAACTATCACTCTC 60.148 40.741 0.00 0.00 0.00 3.20
2726 3231 6.778821 TCTCCAGAAAGATAATGTGTCCAAA 58.221 36.000 0.00 0.00 0.00 3.28
2860 3388 2.413677 GTGTGTGCACATTGACCCA 58.586 52.632 24.69 12.28 43.97 4.51
2989 3517 1.705186 AGATGGTGCAAGTACCTTGGT 59.295 47.619 8.76 0.00 41.31 3.67
3032 3560 5.762179 TGATGATTAACCTTGAGTGGTCT 57.238 39.130 0.00 0.00 39.83 3.85
3150 3678 2.751806 GGGCCTTTATCTGCTCATATGC 59.248 50.000 0.84 0.00 0.00 3.14
3227 3755 7.502226 TCATCATGTATGGTCAATTCCTAAACC 59.498 37.037 0.00 0.00 36.15 3.27
3240 3768 6.642733 ATTCCTAAACCCTGATCAAGAGAA 57.357 37.500 0.00 0.00 0.00 2.87
3244 3772 6.445139 TCCTAAACCCTGATCAAGAGAAATCT 59.555 38.462 0.00 0.00 0.00 2.40
3335 3863 4.113354 CGAAAGCTTGAGGATAGTACACC 58.887 47.826 0.00 0.00 0.00 4.16
3397 3925 2.479198 GCGGCTAACTTGCGGTTC 59.521 61.111 0.00 0.00 39.17 3.62
3445 3988 8.578448 TCATGTATGGTCAATTCATTTCTTCA 57.422 30.769 0.00 0.00 0.00 3.02
3462 4005 7.922505 TTTCTTCATCAAATTAAACACACGG 57.077 32.000 0.00 0.00 0.00 4.94
3484 4027 7.980099 CACGGTCTATTTACTAAACTGGAGAAT 59.020 37.037 0.00 0.00 0.00 2.40
3501 4044 7.344612 ACTGGAGAATTGGGTTTTAAACTCTTT 59.655 33.333 9.25 3.10 31.48 2.52
3715 4258 5.047660 CAGATATAAGTTCTTCCCGAGGAGG 60.048 48.000 0.00 0.00 40.63 4.30
3736 4279 5.192176 AGGTCCCGTAAACACTAACAAAAA 58.808 37.500 0.00 0.00 0.00 1.94
3756 4304 3.832615 AAATCTAACGCGGTCCCTATT 57.167 42.857 12.47 0.00 0.00 1.73
3793 4342 7.066645 TCCTTTTCTTCTATTGATGCTCACATG 59.933 37.037 0.00 0.00 36.35 3.21
3951 4504 4.513692 TGTGTTTGTGGACATGCTAGTTAC 59.486 41.667 0.00 0.00 0.00 2.50
3992 4545 2.865551 GCTGTTGTTGTTGGTTGATTGG 59.134 45.455 0.00 0.00 0.00 3.16
4100 5332 0.736053 GTGTTGGCTGGAAACGTGAA 59.264 50.000 0.00 0.00 0.00 3.18
4117 5349 3.756434 CGTGAACCCAATAACTGGTGAAT 59.244 43.478 0.00 0.00 44.76 2.57
4130 5362 9.920946 AATAACTGGTGAATATGTTAGACCATT 57.079 29.630 6.15 0.00 36.14 3.16
4148 5380 0.830648 TTCTATGGTGGCGAAGAGGG 59.169 55.000 0.00 0.00 0.00 4.30
4189 5421 4.002982 CGTGACTCCAATTTCCAGAATCA 58.997 43.478 0.00 0.00 0.00 2.57
4190 5422 4.142816 CGTGACTCCAATTTCCAGAATCAC 60.143 45.833 0.00 0.00 0.00 3.06
4367 5601 7.281324 TGCGTACTTTTGGTAAATACAGCATAT 59.719 33.333 0.00 0.00 31.56 1.78
4368 5602 8.767085 GCGTACTTTTGGTAAATACAGCATATA 58.233 33.333 0.00 0.00 31.56 0.86
4479 5717 1.820906 GCCAATGAGAGCCGATGCA 60.821 57.895 0.00 0.00 41.13 3.96
4638 5877 0.107945 GAGGCTCGCCAGAGTTCATT 60.108 55.000 11.02 0.00 46.03 2.57
4719 5959 8.129211 GGCAACAAATGACTATCACCTATTAAC 58.871 37.037 0.00 0.00 32.61 2.01
4859 6117 0.256464 ACGTGTTTCCCCCACAAGAA 59.744 50.000 0.00 0.00 33.00 2.52
4862 6120 2.166664 CGTGTTTCCCCCACAAGAAAAA 59.833 45.455 0.00 0.00 33.98 1.94
4865 6123 3.841255 TGTTTCCCCCACAAGAAAAAGTT 59.159 39.130 0.00 0.00 33.98 2.66
4866 6124 4.081365 TGTTTCCCCCACAAGAAAAAGTTC 60.081 41.667 0.00 0.00 33.98 3.01
4867 6125 3.390175 TCCCCCACAAGAAAAAGTTCA 57.610 42.857 0.00 0.00 36.09 3.18
4869 6127 4.294347 TCCCCCACAAGAAAAAGTTCAAT 58.706 39.130 0.00 0.00 36.09 2.57
4871 6129 4.100808 CCCCCACAAGAAAAAGTTCAATCA 59.899 41.667 0.00 0.00 36.09 2.57
4872 6130 5.396213 CCCCCACAAGAAAAAGTTCAATCAA 60.396 40.000 0.00 0.00 36.09 2.57
4875 6133 6.818142 CCCACAAGAAAAAGTTCAATCAAGTT 59.182 34.615 0.00 0.00 36.09 2.66
4876 6134 7.978975 CCCACAAGAAAAAGTTCAATCAAGTTA 59.021 33.333 0.00 0.00 36.09 2.24
4877 6135 9.533253 CCACAAGAAAAAGTTCAATCAAGTTAT 57.467 29.630 0.00 0.00 36.09 1.89
5026 6544 1.604378 CTTCGTGGATTCAGGCCCT 59.396 57.895 0.00 0.00 0.00 5.19
5045 6563 1.278985 CTTGCAGATGTACCCTCACCA 59.721 52.381 0.00 0.00 0.00 4.17
5046 6564 0.904649 TGCAGATGTACCCTCACCAG 59.095 55.000 0.00 0.00 0.00 4.00
5049 6567 2.179427 CAGATGTACCCTCACCAGTCA 58.821 52.381 0.00 0.00 0.00 3.41
5050 6568 2.093973 CAGATGTACCCTCACCAGTCAC 60.094 54.545 0.00 0.00 0.00 3.67
5053 6571 1.229400 TACCCTCACCAGTCACCCC 60.229 63.158 0.00 0.00 0.00 4.95
5091 6641 6.483974 TGTTGTACCATCTACGTTTTCACAAT 59.516 34.615 0.00 0.00 0.00 2.71
5092 6642 7.656542 TGTTGTACCATCTACGTTTTCACAATA 59.343 33.333 0.00 0.00 0.00 1.90
5093 6643 8.662141 GTTGTACCATCTACGTTTTCACAATAT 58.338 33.333 0.00 0.00 0.00 1.28
5094 6644 9.872721 TTGTACCATCTACGTTTTCACAATATA 57.127 29.630 0.00 0.00 0.00 0.86
5139 6690 5.066593 GGAAAATAGGTTGCCTGATCCTAG 58.933 45.833 0.00 0.00 37.27 3.02
5175 6726 2.356125 GCCTCCAACTGCTATTCCAAGA 60.356 50.000 0.00 0.00 0.00 3.02
5196 6747 8.244802 CCAAGATAGCATATACTACTGGTACAC 58.755 40.741 0.00 0.00 32.72 2.90
5198 6749 8.935614 AGATAGCATATACTACTGGTACACAA 57.064 34.615 0.00 0.00 32.72 3.33
5219 6770 6.266103 CACAAGCAATGGGATATTGGTATTCT 59.734 38.462 4.96 0.00 38.60 2.40
5220 6771 6.491403 ACAAGCAATGGGATATTGGTATTCTC 59.509 38.462 4.96 0.00 38.60 2.87
5229 6780 5.221461 GGATATTGGTATTCTCGACACCACT 60.221 44.000 3.57 2.25 41.95 4.00
5242 6793 1.686587 ACACCACTGATGAGTCGTTCA 59.313 47.619 0.00 0.00 40.85 3.18
5244 6795 1.337260 ACCACTGATGAGTCGTTCAGC 60.337 52.381 18.12 1.90 42.51 4.26
5360 6916 1.198713 CTGGGTGATGCAGGACTACT 58.801 55.000 0.00 0.00 0.00 2.57
5370 6926 0.386113 CAGGACTACTAAGCCGAGGC 59.614 60.000 5.89 5.89 42.33 4.70
5389 6945 1.610624 GCCTGGGATTTCAAGTGTCGA 60.611 52.381 0.00 0.00 0.00 4.20
5406 6962 0.591170 CGAGTTGAATTGCCGGTTGT 59.409 50.000 1.90 0.00 0.00 3.32
5447 7003 1.588239 ATGCCCTCTCCATCAACAGA 58.412 50.000 0.00 0.00 0.00 3.41
5448 7004 0.907486 TGCCCTCTCCATCAACAGAG 59.093 55.000 0.00 0.00 36.63 3.35
5486 7054 1.506493 GGACAGTGAGCTCAGTTGTG 58.494 55.000 28.92 20.52 0.00 3.33
5490 7058 2.366590 ACAGTGAGCTCAGTTGTGATGA 59.633 45.455 25.23 0.00 30.18 2.92
5512 7080 2.624838 CTGGCTGTTTCAGGTTGATGTT 59.375 45.455 0.00 0.00 31.21 2.71
5513 7081 2.361757 TGGCTGTTTCAGGTTGATGTTG 59.638 45.455 0.00 0.00 31.21 3.33
5517 7085 4.261741 GCTGTTTCAGGTTGATGTTGATGT 60.262 41.667 0.00 0.00 31.21 3.06
5530 7098 4.241590 TGTTGATGTCAAGTTGATTGCC 57.758 40.909 9.18 0.00 38.89 4.52
5539 7107 3.896888 TCAAGTTGATTGCCAGTTTCCAT 59.103 39.130 0.08 0.00 38.89 3.41
5542 7110 1.462616 TGATTGCCAGTTTCCATCCG 58.537 50.000 0.00 0.00 0.00 4.18
5562 7130 3.849911 CGAGAGGCAACAATTCTACTCA 58.150 45.455 0.00 0.00 41.41 3.41
5563 7131 4.437239 CGAGAGGCAACAATTCTACTCAT 58.563 43.478 0.00 0.00 41.41 2.90
5564 7132 4.872691 CGAGAGGCAACAATTCTACTCATT 59.127 41.667 0.00 0.00 41.41 2.57
5565 7133 5.352569 CGAGAGGCAACAATTCTACTCATTT 59.647 40.000 0.00 0.00 41.41 2.32
5567 7135 7.150783 AGAGGCAACAATTCTACTCATTTTC 57.849 36.000 0.00 0.00 41.41 2.29
5593 7161 5.384063 TCAAGCAAACTCTTGTTCAACAA 57.616 34.783 2.24 2.24 42.90 2.83
5599 7167 5.062183 GCAAACTCTTGTTCAACAAACCTTC 59.938 40.000 4.13 0.00 37.69 3.46
5604 7172 5.961272 TCTTGTTCAACAAACCTTCTTTCC 58.039 37.500 4.13 0.00 37.69 3.13
5606 7174 4.011023 TGTTCAACAAACCTTCTTTCCGA 58.989 39.130 0.00 0.00 37.03 4.55
5617 7185 1.183549 TCTTTCCGACACTAGAGGGC 58.816 55.000 0.00 0.00 0.00 5.19
5629 7197 4.184629 CACTAGAGGGCTATGTTGTGAAC 58.815 47.826 0.00 0.00 0.00 3.18
5630 7198 2.789409 AGAGGGCTATGTTGTGAACC 57.211 50.000 0.00 0.00 0.00 3.62
5636 7204 2.012051 GCTATGTTGTGAACCCCTCGG 61.012 57.143 0.00 0.00 0.00 4.63
5637 7205 1.553248 CTATGTTGTGAACCCCTCGGA 59.447 52.381 0.00 0.00 0.00 4.55
5638 7206 0.768622 ATGTTGTGAACCCCTCGGAA 59.231 50.000 0.00 0.00 0.00 4.30
5639 7207 0.107831 TGTTGTGAACCCCTCGGAAG 59.892 55.000 0.00 0.00 0.00 3.46
5640 7208 0.395312 GTTGTGAACCCCTCGGAAGA 59.605 55.000 0.00 0.00 39.12 2.87
5641 7209 1.003233 GTTGTGAACCCCTCGGAAGAT 59.997 52.381 0.00 0.00 40.84 2.40
5642 7210 1.358152 TGTGAACCCCTCGGAAGATT 58.642 50.000 0.00 0.00 40.84 2.40
5643 7211 2.542550 TGTGAACCCCTCGGAAGATTA 58.457 47.619 0.00 0.00 40.84 1.75
5644 7212 3.112263 TGTGAACCCCTCGGAAGATTAT 58.888 45.455 0.00 0.00 40.84 1.28
5645 7213 3.118408 TGTGAACCCCTCGGAAGATTATG 60.118 47.826 0.00 0.00 40.84 1.90
5646 7214 3.112263 TGAACCCCTCGGAAGATTATGT 58.888 45.455 0.00 0.00 40.84 2.29
5647 7215 3.521937 TGAACCCCTCGGAAGATTATGTT 59.478 43.478 0.00 0.00 40.84 2.71
5648 7216 3.560636 ACCCCTCGGAAGATTATGTTG 57.439 47.619 0.00 0.00 40.84 3.33
5649 7217 2.844348 ACCCCTCGGAAGATTATGTTGT 59.156 45.455 0.00 0.00 40.84 3.32
5650 7218 3.118371 ACCCCTCGGAAGATTATGTTGTC 60.118 47.826 0.00 0.00 40.84 3.18
5651 7219 3.118408 CCCCTCGGAAGATTATGTTGTCA 60.118 47.826 0.00 0.00 40.84 3.58
5652 7220 4.513442 CCCTCGGAAGATTATGTTGTCAA 58.487 43.478 0.00 0.00 40.84 3.18
5653 7221 4.941263 CCCTCGGAAGATTATGTTGTCAAA 59.059 41.667 0.00 0.00 40.84 2.69
5654 7222 5.163754 CCCTCGGAAGATTATGTTGTCAAAC 60.164 44.000 0.00 0.00 40.84 2.93
5655 7223 5.163754 CCTCGGAAGATTATGTTGTCAAACC 60.164 44.000 0.00 0.00 40.84 3.27
5656 7224 5.556915 TCGGAAGATTATGTTGTCAAACCT 58.443 37.500 0.00 0.00 32.73 3.50
5657 7225 6.001460 TCGGAAGATTATGTTGTCAAACCTT 58.999 36.000 0.00 0.00 32.73 3.50
5658 7226 6.148811 TCGGAAGATTATGTTGTCAAACCTTC 59.851 38.462 0.00 0.00 32.73 3.46
5659 7227 6.314784 GGAAGATTATGTTGTCAAACCTTCG 58.685 40.000 0.00 0.00 35.25 3.79
5660 7228 6.148811 GGAAGATTATGTTGTCAAACCTTCGA 59.851 38.462 0.00 0.00 35.25 3.71
5661 7229 7.148239 GGAAGATTATGTTGTCAAACCTTCGAT 60.148 37.037 0.00 0.00 35.25 3.59
5662 7230 7.076842 AGATTATGTTGTCAAACCTTCGATG 57.923 36.000 0.00 0.00 35.25 3.84
5663 7231 6.878923 AGATTATGTTGTCAAACCTTCGATGA 59.121 34.615 0.00 0.00 35.25 2.92
5664 7232 6.480524 TTATGTTGTCAAACCTTCGATGAG 57.519 37.500 0.00 0.00 35.25 2.90
5665 7233 2.548057 TGTTGTCAAACCTTCGATGAGC 59.452 45.455 0.00 0.00 35.25 4.26
5666 7234 1.808411 TGTCAAACCTTCGATGAGCC 58.192 50.000 0.00 0.00 0.00 4.70
5667 7235 1.347707 TGTCAAACCTTCGATGAGCCT 59.652 47.619 0.00 0.00 0.00 4.58
5668 7236 2.224523 TGTCAAACCTTCGATGAGCCTT 60.225 45.455 0.00 0.00 0.00 4.35
5669 7237 2.814336 GTCAAACCTTCGATGAGCCTTT 59.186 45.455 0.00 0.00 0.00 3.11
5670 7238 3.253432 GTCAAACCTTCGATGAGCCTTTT 59.747 43.478 0.00 0.00 0.00 2.27
5671 7239 4.454504 GTCAAACCTTCGATGAGCCTTTTA 59.545 41.667 0.00 0.00 0.00 1.52
5672 7240 5.123979 GTCAAACCTTCGATGAGCCTTTTAT 59.876 40.000 0.00 0.00 0.00 1.40
5673 7241 5.123820 TCAAACCTTCGATGAGCCTTTTATG 59.876 40.000 0.00 0.00 0.00 1.90
5674 7242 2.945668 ACCTTCGATGAGCCTTTTATGC 59.054 45.455 0.00 0.00 0.00 3.14
5675 7243 2.291741 CCTTCGATGAGCCTTTTATGCC 59.708 50.000 0.00 0.00 0.00 4.40
5676 7244 1.967319 TCGATGAGCCTTTTATGCCC 58.033 50.000 0.00 0.00 0.00 5.36
5677 7245 0.588252 CGATGAGCCTTTTATGCCCG 59.412 55.000 0.00 0.00 0.00 6.13
5678 7246 0.954452 GATGAGCCTTTTATGCCCGG 59.046 55.000 0.00 0.00 0.00 5.73
5679 7247 0.258774 ATGAGCCTTTTATGCCCGGT 59.741 50.000 0.00 0.00 0.00 5.28
5680 7248 0.039035 TGAGCCTTTTATGCCCGGTT 59.961 50.000 0.00 0.00 0.00 4.44
5681 7249 1.282447 TGAGCCTTTTATGCCCGGTTA 59.718 47.619 0.00 0.00 0.00 2.85
5682 7250 2.092103 TGAGCCTTTTATGCCCGGTTAT 60.092 45.455 0.00 0.00 0.00 1.89
5683 7251 2.293399 GAGCCTTTTATGCCCGGTTATG 59.707 50.000 0.00 0.00 0.00 1.90
5684 7252 2.028876 GCCTTTTATGCCCGGTTATGT 58.971 47.619 0.00 0.00 0.00 2.29
5685 7253 3.117813 AGCCTTTTATGCCCGGTTATGTA 60.118 43.478 0.00 0.00 0.00 2.29
5686 7254 3.824443 GCCTTTTATGCCCGGTTATGTAT 59.176 43.478 0.00 0.00 0.00 2.29
5687 7255 4.279922 GCCTTTTATGCCCGGTTATGTATT 59.720 41.667 0.00 0.00 0.00 1.89
5688 7256 5.474189 GCCTTTTATGCCCGGTTATGTATTA 59.526 40.000 0.00 0.00 0.00 0.98
5689 7257 6.016108 GCCTTTTATGCCCGGTTATGTATTAA 60.016 38.462 0.00 0.00 0.00 1.40
5690 7258 7.364970 CCTTTTATGCCCGGTTATGTATTAAC 58.635 38.462 0.00 0.00 39.64 2.01
5691 7259 7.013464 CCTTTTATGCCCGGTTATGTATTAACA 59.987 37.037 0.00 0.00 41.74 2.41
5692 7260 6.864360 TTATGCCCGGTTATGTATTAACAC 57.136 37.500 0.00 0.00 41.74 3.32
5693 7261 4.490899 TGCCCGGTTATGTATTAACACT 57.509 40.909 0.00 0.00 41.74 3.55
5694 7262 4.846040 TGCCCGGTTATGTATTAACACTT 58.154 39.130 0.00 0.00 41.74 3.16
5695 7263 5.987098 TGCCCGGTTATGTATTAACACTTA 58.013 37.500 0.00 0.00 41.74 2.24
5696 7264 6.050432 TGCCCGGTTATGTATTAACACTTAG 58.950 40.000 0.00 0.00 41.74 2.18
5697 7265 5.049886 GCCCGGTTATGTATTAACACTTAGC 60.050 44.000 0.00 0.00 41.74 3.09
5698 7266 5.467735 CCCGGTTATGTATTAACACTTAGCC 59.532 44.000 0.00 3.45 41.74 3.93
5699 7267 6.285990 CCGGTTATGTATTAACACTTAGCCT 58.714 40.000 9.83 0.00 41.74 4.58
5700 7268 6.764560 CCGGTTATGTATTAACACTTAGCCTT 59.235 38.462 9.83 0.00 41.74 4.35
5701 7269 7.281549 CCGGTTATGTATTAACACTTAGCCTTT 59.718 37.037 9.83 0.00 41.74 3.11
5702 7270 8.671028 CGGTTATGTATTAACACTTAGCCTTTT 58.329 33.333 9.83 0.00 41.74 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 2.818921 AGGTATGAATTTGGCTTGGCA 58.181 42.857 0.00 0.00 0.00 4.92
116 117 6.485648 GCGTACCATCCTTAAGGTATGAATTT 59.514 38.462 24.22 13.66 45.88 1.82
543 547 5.857822 AATTAGAGCTGTTTTACGGTGAC 57.142 39.130 0.00 0.00 0.00 3.67
663 676 2.557056 GGGAAAGTAGTCTTTTGTGCCC 59.443 50.000 0.00 0.00 42.99 5.36
805 838 8.682128 TTTCACAAAATAATAAAGGCGATGAC 57.318 30.769 0.00 0.00 0.00 3.06
806 839 7.487829 GCTTTCACAAAATAATAAAGGCGATGA 59.512 33.333 0.00 0.00 0.00 2.92
807 840 7.513505 CGCTTTCACAAAATAATAAAGGCGATG 60.514 37.037 3.75 0.00 33.07 3.84
808 841 6.472163 CGCTTTCACAAAATAATAAAGGCGAT 59.528 34.615 3.75 0.00 33.07 4.58
809 842 5.797934 CGCTTTCACAAAATAATAAAGGCGA 59.202 36.000 3.75 0.00 33.07 5.54
810 843 5.004345 CCGCTTTCACAAAATAATAAAGGCG 59.996 40.000 0.00 0.00 32.11 5.52
811 844 5.220397 GCCGCTTTCACAAAATAATAAAGGC 60.220 40.000 0.00 0.00 0.00 4.35
812 845 6.099341 AGCCGCTTTCACAAAATAATAAAGG 58.901 36.000 0.00 0.00 0.00 3.11
820 853 3.451141 TCAAAGCCGCTTTCACAAAAT 57.549 38.095 15.60 0.00 30.60 1.82
1210 1299 6.280643 TGCTATACTGCATTGGTAACAGTAG 58.719 40.000 7.97 0.00 46.74 2.57
1286 1382 4.973168 ACAGGTGTGAGCAATAGAAAGAA 58.027 39.130 0.00 0.00 0.00 2.52
1344 1549 1.977854 TGGAGTGTCACTGGCAGTAAT 59.022 47.619 21.59 3.84 0.00 1.89
1379 1584 7.998753 ATATTTCTTTACGGAAGGAGTAACG 57.001 36.000 0.00 0.00 35.98 3.18
1541 1827 1.026718 GGGTCGAGATTGTTGGCCAG 61.027 60.000 5.11 0.00 35.70 4.85
1574 1863 1.811965 CTTGAATTCATGGACACCGCA 59.188 47.619 9.40 0.00 0.00 5.69
1576 1865 2.420022 GGTCTTGAATTCATGGACACCG 59.580 50.000 27.75 7.70 33.64 4.94
1588 1877 1.448540 CAGGAGCGCGGTCTTGAAT 60.449 57.895 37.47 17.15 0.00 2.57
1621 1910 6.402222 TGCATGTATACAGAACACACATACA 58.598 36.000 11.91 0.00 36.73 2.29
1705 1995 6.091849 GTCTTGTATTTCTTTACGGAGGGAAC 59.908 42.308 0.00 0.00 0.00 3.62
1725 2015 7.835822 TGTAAACAAAATATGATGGGGTCTTG 58.164 34.615 0.00 0.00 0.00 3.02
1730 2020 6.040842 CCCTCTGTAAACAAAATATGATGGGG 59.959 42.308 0.00 0.00 0.00 4.96
1732 2022 7.557719 ACTCCCTCTGTAAACAAAATATGATGG 59.442 37.037 0.00 0.00 0.00 3.51
1733 2023 8.511604 ACTCCCTCTGTAAACAAAATATGATG 57.488 34.615 0.00 0.00 0.00 3.07
1734 2024 9.614792 GTACTCCCTCTGTAAACAAAATATGAT 57.385 33.333 0.00 0.00 0.00 2.45
1735 2025 8.822805 AGTACTCCCTCTGTAAACAAAATATGA 58.177 33.333 0.00 0.00 0.00 2.15
1736 2026 9.449719 AAGTACTCCCTCTGTAAACAAAATATG 57.550 33.333 0.00 0.00 0.00 1.78
1831 2176 1.595982 CGTGCGTTGCAATGAAACCG 61.596 55.000 22.81 11.49 41.47 4.44
2215 2595 5.362430 TGTGACAAAAGAAACAAAGGGCTAT 59.638 36.000 0.00 0.00 0.00 2.97
2219 2599 4.864247 CAGTGTGACAAAAGAAACAAAGGG 59.136 41.667 0.00 0.00 0.00 3.95
2313 2739 0.547075 TCCCCGACTTGGTTGTTTGA 59.453 50.000 0.00 0.00 35.15 2.69
2329 2755 6.493802 AGGAAGATACACCTTTTTCTTTTCCC 59.506 38.462 0.00 0.00 31.95 3.97
2422 2860 5.988310 ATCATCTCAACATCTTGCCAAAA 57.012 34.783 0.00 0.00 0.00 2.44
2458 2896 5.960113 ACATGTAATAATGAAAAGCGGCAA 58.040 33.333 1.45 0.00 0.00 4.52
2539 2978 2.737679 GCATCAGCCTTCTTTTCATGGC 60.738 50.000 0.00 0.00 45.21 4.40
2705 3210 6.430925 TCTGTTTGGACACATTATCTTTCTGG 59.569 38.462 0.00 0.00 0.00 3.86
3032 3560 4.842531 TTGAGCAAGGGATCAATCAGTA 57.157 40.909 0.00 0.00 43.94 2.74
3124 3652 4.025040 TGAGCAGATAAAGGCCCATATG 57.975 45.455 0.00 0.00 0.00 1.78
3150 3678 4.814294 AAGTTAGCCGCCTCGCCG 62.814 66.667 0.00 0.00 0.00 6.46
3227 3755 9.781633 AATTAGATCAGATTTCTCTTGATCAGG 57.218 33.333 14.07 0.00 37.89 3.86
3240 3768 7.081526 GTGAGCACACAAATTAGATCAGATT 57.918 36.000 9.58 0.00 45.32 2.40
3335 3863 8.136057 AGACGTAGCAAAGAATCTGAAATATG 57.864 34.615 0.00 0.00 0.00 1.78
3462 4005 9.110502 CCCAATTCTCCAGTTTAGTAAATAGAC 57.889 37.037 0.00 0.00 0.00 2.59
3501 4044 9.901172 GAATAAGGACCTTGAACTCCTTTAATA 57.099 33.333 17.47 0.00 43.24 0.98
3527 4070 9.865321 ATCATTTTCATTGTAATCAGGAAACAG 57.135 29.630 0.00 0.00 32.57 3.16
3652 4195 0.977108 AACAATTGGCGGCCATCCAT 60.977 50.000 24.49 10.96 31.53 3.41
3674 4217 2.436417 TCTGGAGTTAAGTTGGCATGC 58.564 47.619 9.90 9.90 0.00 4.06
3736 4279 3.832615 AATAGGGACCGCGTTAGATTT 57.167 42.857 4.92 0.00 0.00 2.17
3756 4304 9.480053 CAATAGAAGAAAAGGAATCAAGCAAAA 57.520 29.630 0.00 0.00 0.00 2.44
3793 4342 6.509418 TGATTTGCAATGGTCTAAACTACC 57.491 37.500 0.00 0.00 37.53 3.18
3810 4363 4.326504 ACCTCAACCTTTTGCTGATTTG 57.673 40.909 0.00 0.00 32.17 2.32
3886 4439 3.056821 GGGAACAAGTATGAAAGGGCAAC 60.057 47.826 0.00 0.00 0.00 4.17
3934 4487 5.584649 GCATTTAGTAACTAGCATGTCCACA 59.415 40.000 0.00 0.00 0.00 4.17
3977 4530 1.501169 GCAGCCAATCAACCAACAAC 58.499 50.000 0.00 0.00 0.00 3.32
3992 4545 7.534400 ATCTCATCAGAAGAGCTATGGCAGC 62.534 48.000 3.10 0.00 40.68 5.25
4007 5237 6.485648 TCACTTGCCAATAATCATCTCATCAG 59.514 38.462 0.00 0.00 0.00 2.90
4053 5285 4.901868 ACAATTCAAAAGCCATCTGCAAT 58.098 34.783 0.00 0.00 44.83 3.56
4130 5362 0.032515 TCCCTCTTCGCCACCATAGA 60.033 55.000 0.00 0.00 0.00 1.98
4148 5380 3.185391 CACGACTTTCTTCAAGAAGGCTC 59.815 47.826 9.13 5.70 35.01 4.70
4384 5621 3.008813 TGCATGGGCCACAAAATTGTAAT 59.991 39.130 9.28 0.00 38.40 1.89
4498 5737 0.027979 CACAACTCACACAGGTTGCG 59.972 55.000 5.85 0.00 44.41 4.85
4549 5788 0.524862 GTGGCCAAGATGAAGCACAG 59.475 55.000 7.24 0.00 0.00 3.66
4638 5877 3.804786 TCACTAACTGTTGACGACCAA 57.195 42.857 2.69 0.00 0.00 3.67
4719 5959 6.536582 ACAAGCTCTATTACACACAGCAATAG 59.463 38.462 0.00 0.00 34.81 1.73
4725 5965 7.863375 GGACTATACAAGCTCTATTACACACAG 59.137 40.741 0.00 0.00 0.00 3.66
4812 6054 3.194116 TCCGTCGCTGGTATTTTTCTACT 59.806 43.478 0.00 0.00 0.00 2.57
4862 6120 8.095452 AGGGATAGTGATAACTTGATTGAACT 57.905 34.615 0.00 0.00 0.00 3.01
4865 6123 8.816894 GGATAGGGATAGTGATAACTTGATTGA 58.183 37.037 0.00 0.00 0.00 2.57
4866 6124 8.043710 GGGATAGGGATAGTGATAACTTGATTG 58.956 40.741 0.00 0.00 0.00 2.67
4867 6125 7.964293 AGGGATAGGGATAGTGATAACTTGATT 59.036 37.037 0.00 0.00 0.00 2.57
4869 6127 6.875469 AGGGATAGGGATAGTGATAACTTGA 58.125 40.000 0.00 0.00 0.00 3.02
4871 6129 9.684702 TTTAAGGGATAGGGATAGTGATAACTT 57.315 33.333 0.00 0.00 0.00 2.66
4872 6130 9.684702 TTTTAAGGGATAGGGATAGTGATAACT 57.315 33.333 0.00 0.00 0.00 2.24
4906 6422 1.303309 GTGCCAGCGAGCTATCATTT 58.697 50.000 0.00 0.00 0.00 2.32
4938 6454 2.677337 GGTGCGCAAAATATTGGCATTT 59.323 40.909 14.00 0.00 41.48 2.32
4939 6455 2.278854 GGTGCGCAAAATATTGGCATT 58.721 42.857 14.00 0.00 41.48 3.56
4940 6456 1.206610 TGGTGCGCAAAATATTGGCAT 59.793 42.857 14.00 0.00 41.48 4.40
5026 6544 1.278985 CTGGTGAGGGTACATCTGCAA 59.721 52.381 0.00 0.00 0.00 4.08
5045 6563 0.898789 CAGTCGGTAGTGGGGTGACT 60.899 60.000 0.00 0.00 40.35 3.41
5046 6564 1.183676 ACAGTCGGTAGTGGGGTGAC 61.184 60.000 0.00 0.00 0.00 3.67
5049 6567 0.761702 ACAACAGTCGGTAGTGGGGT 60.762 55.000 0.00 0.00 0.00 4.95
5050 6568 0.395312 AACAACAGTCGGTAGTGGGG 59.605 55.000 0.00 0.00 0.00 4.96
5053 6571 3.054878 GGTACAACAACAGTCGGTAGTG 58.945 50.000 0.00 0.00 0.00 2.74
5139 6690 0.376502 GAGGCAATCTTGAAGAGCGC 59.623 55.000 0.00 0.00 0.00 5.92
5175 6726 7.232737 TGCTTGTGTACCAGTAGTATATGCTAT 59.767 37.037 3.71 0.00 32.28 2.97
5183 6734 4.323180 CCCATTGCTTGTGTACCAGTAGTA 60.323 45.833 0.00 0.00 0.00 1.82
5184 6735 3.559171 CCCATTGCTTGTGTACCAGTAGT 60.559 47.826 0.00 0.00 0.00 2.73
5185 6736 3.009723 CCCATTGCTTGTGTACCAGTAG 58.990 50.000 0.00 0.00 0.00 2.57
5196 6747 6.348786 CGAGAATACCAATATCCCATTGCTTG 60.349 42.308 0.00 0.00 0.00 4.01
5198 6749 5.013079 TCGAGAATACCAATATCCCATTGCT 59.987 40.000 0.00 0.00 0.00 3.91
5219 6770 0.521735 CGACTCATCAGTGGTGTCGA 59.478 55.000 10.09 0.00 45.80 4.20
5220 6771 0.241213 ACGACTCATCAGTGGTGTCG 59.759 55.000 13.23 13.23 46.93 4.35
5229 6780 3.515630 GATCTTGCTGAACGACTCATCA 58.484 45.455 0.00 0.00 32.14 3.07
5242 6793 2.109799 CGGGATGCGGATCTTGCT 59.890 61.111 16.91 0.00 0.00 3.91
5244 6795 1.064060 GAAAACGGGATGCGGATCTTG 59.936 52.381 16.91 11.50 0.00 3.02
5360 6916 1.279025 AAATCCCAGGCCTCGGCTTA 61.279 55.000 12.35 0.00 41.60 3.09
5370 6926 2.289694 ACTCGACACTTGAAATCCCAGG 60.290 50.000 0.00 0.00 0.00 4.45
5389 6945 0.591170 CGACAACCGGCAATTCAACT 59.409 50.000 0.00 0.00 33.91 3.16
5406 6962 1.079612 CACTGCTGCATGGTCTCGA 60.080 57.895 1.31 0.00 0.00 4.04
5447 7003 0.538057 CCAGGCACAACCATCACACT 60.538 55.000 0.00 0.00 43.14 3.55
5448 7004 1.526575 CCCAGGCACAACCATCACAC 61.527 60.000 0.00 0.00 43.14 3.82
5479 7035 1.888215 ACAGCCAGTCATCACAACTG 58.112 50.000 0.00 0.00 43.04 3.16
5480 7036 2.645838 AACAGCCAGTCATCACAACT 57.354 45.000 0.00 0.00 0.00 3.16
5486 7054 2.191128 ACCTGAAACAGCCAGTCATC 57.809 50.000 0.00 0.00 0.00 2.92
5490 7058 2.233271 CATCAACCTGAAACAGCCAGT 58.767 47.619 0.00 0.00 0.00 4.00
5517 7085 3.295093 TGGAAACTGGCAATCAACTTGA 58.705 40.909 0.00 0.00 36.97 3.02
5530 7098 0.250234 TGCCTCTCGGATGGAAACTG 59.750 55.000 1.96 0.00 0.00 3.16
5539 7107 2.832129 AGTAGAATTGTTGCCTCTCGGA 59.168 45.455 0.00 0.00 0.00 4.55
5542 7110 6.749923 AAATGAGTAGAATTGTTGCCTCTC 57.250 37.500 0.00 0.00 0.00 3.20
5549 7117 7.750229 TGAGCAGAAAATGAGTAGAATTGTT 57.250 32.000 0.00 0.00 0.00 2.83
5550 7118 7.574592 GCTTGAGCAGAAAATGAGTAGAATTGT 60.575 37.037 0.00 0.00 41.59 2.71
5578 7146 6.590234 AAGAAGGTTTGTTGAACAAGAGTT 57.410 33.333 10.91 5.82 39.53 3.01
5593 7161 3.258622 CCTCTAGTGTCGGAAAGAAGGTT 59.741 47.826 0.00 0.00 0.00 3.50
5599 7167 1.187087 AGCCCTCTAGTGTCGGAAAG 58.813 55.000 0.00 0.00 0.00 2.62
5604 7172 2.427453 ACAACATAGCCCTCTAGTGTCG 59.573 50.000 0.00 0.00 0.00 4.35
5606 7174 3.441101 TCACAACATAGCCCTCTAGTGT 58.559 45.455 0.00 0.00 0.00 3.55
5617 7185 1.553248 TCCGAGGGGTTCACAACATAG 59.447 52.381 0.00 0.00 33.83 2.23
5629 7197 3.118408 TGACAACATAATCTTCCGAGGGG 60.118 47.826 0.00 0.00 0.00 4.79
5630 7198 4.137116 TGACAACATAATCTTCCGAGGG 57.863 45.455 0.00 0.00 0.00 4.30
5636 7204 7.129109 TCGAAGGTTTGACAACATAATCTTC 57.871 36.000 0.00 0.00 34.68 2.87
5637 7205 7.390440 TCATCGAAGGTTTGACAACATAATCTT 59.610 33.333 0.00 0.00 34.15 2.40
5638 7206 6.878923 TCATCGAAGGTTTGACAACATAATCT 59.121 34.615 0.00 0.00 34.15 2.40
5639 7207 7.072177 TCATCGAAGGTTTGACAACATAATC 57.928 36.000 0.00 0.00 34.15 1.75
5640 7208 6.403636 GCTCATCGAAGGTTTGACAACATAAT 60.404 38.462 0.00 0.00 34.15 1.28
5641 7209 5.106712 GCTCATCGAAGGTTTGACAACATAA 60.107 40.000 0.00 0.00 34.15 1.90
5642 7210 4.391830 GCTCATCGAAGGTTTGACAACATA 59.608 41.667 0.00 0.00 34.15 2.29
5643 7211 3.189287 GCTCATCGAAGGTTTGACAACAT 59.811 43.478 0.00 0.00 34.15 2.71
5644 7212 2.548057 GCTCATCGAAGGTTTGACAACA 59.452 45.455 0.00 0.00 34.15 3.33
5645 7213 2.095718 GGCTCATCGAAGGTTTGACAAC 60.096 50.000 0.00 0.00 0.00 3.32
5646 7214 2.151202 GGCTCATCGAAGGTTTGACAA 58.849 47.619 0.00 0.00 0.00 3.18
5647 7215 1.347707 AGGCTCATCGAAGGTTTGACA 59.652 47.619 0.00 0.00 0.00 3.58
5648 7216 2.100605 AGGCTCATCGAAGGTTTGAC 57.899 50.000 0.00 0.00 0.00 3.18
5649 7217 2.859165 AAGGCTCATCGAAGGTTTGA 57.141 45.000 0.00 0.00 0.00 2.69
5650 7218 3.923017 AAAAGGCTCATCGAAGGTTTG 57.077 42.857 0.00 0.00 0.00 2.93
5651 7219 4.142381 GCATAAAAGGCTCATCGAAGGTTT 60.142 41.667 0.00 0.00 0.00 3.27
5652 7220 3.378427 GCATAAAAGGCTCATCGAAGGTT 59.622 43.478 0.00 0.00 0.00 3.50
5653 7221 2.945668 GCATAAAAGGCTCATCGAAGGT 59.054 45.455 0.00 0.00 0.00 3.50
5654 7222 2.291741 GGCATAAAAGGCTCATCGAAGG 59.708 50.000 0.00 0.00 0.00 3.46
5655 7223 2.291741 GGGCATAAAAGGCTCATCGAAG 59.708 50.000 0.00 0.00 0.00 3.79
5656 7224 2.297701 GGGCATAAAAGGCTCATCGAA 58.702 47.619 0.00 0.00 0.00 3.71
5657 7225 1.810031 CGGGCATAAAAGGCTCATCGA 60.810 52.381 0.00 0.00 0.00 3.59
5658 7226 0.588252 CGGGCATAAAAGGCTCATCG 59.412 55.000 0.00 0.00 0.00 3.84
5659 7227 0.954452 CCGGGCATAAAAGGCTCATC 59.046 55.000 0.00 0.00 0.00 2.92
5660 7228 0.258774 ACCGGGCATAAAAGGCTCAT 59.741 50.000 6.32 0.00 0.00 2.90
5661 7229 0.039035 AACCGGGCATAAAAGGCTCA 59.961 50.000 6.32 0.00 0.00 4.26
5662 7230 2.047002 TAACCGGGCATAAAAGGCTC 57.953 50.000 6.32 0.00 0.00 4.70
5663 7231 2.306847 CATAACCGGGCATAAAAGGCT 58.693 47.619 6.32 0.00 0.00 4.58
5664 7232 2.028876 ACATAACCGGGCATAAAAGGC 58.971 47.619 6.32 0.00 0.00 4.35
5665 7233 7.013464 TGTTAATACATAACCGGGCATAAAAGG 59.987 37.037 6.32 0.00 42.74 3.11
5666 7234 7.858879 GTGTTAATACATAACCGGGCATAAAAG 59.141 37.037 6.32 0.00 42.74 2.27
5667 7235 7.556996 AGTGTTAATACATAACCGGGCATAAAA 59.443 33.333 6.32 0.00 42.74 1.52
5668 7236 7.055378 AGTGTTAATACATAACCGGGCATAAA 58.945 34.615 6.32 0.00 42.74 1.40
5669 7237 6.593807 AGTGTTAATACATAACCGGGCATAA 58.406 36.000 6.32 0.00 42.74 1.90
5670 7238 6.177310 AGTGTTAATACATAACCGGGCATA 57.823 37.500 6.32 0.00 42.74 3.14
5671 7239 5.043737 AGTGTTAATACATAACCGGGCAT 57.956 39.130 6.32 0.00 42.74 4.40
5672 7240 4.490899 AGTGTTAATACATAACCGGGCA 57.509 40.909 6.32 0.00 42.74 5.36
5673 7241 5.049886 GCTAAGTGTTAATACATAACCGGGC 60.050 44.000 6.32 0.00 42.74 6.13
5674 7242 5.467735 GGCTAAGTGTTAATACATAACCGGG 59.532 44.000 6.32 0.00 42.74 5.73
5675 7243 6.285990 AGGCTAAGTGTTAATACATAACCGG 58.714 40.000 0.00 0.00 42.74 5.28
5676 7244 7.781548 AAGGCTAAGTGTTAATACATAACCG 57.218 36.000 5.08 0.00 42.74 4.44


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

AutoCloner maintained by Alex Coulton.