Multiple sequence alignment - TraesCS6B01G239000

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 TraesCS6B01G239000 chr6B 100.000 4717 0 0 1 4717 415874015 415869299 0.000000e+00 8711.0
1 TraesCS6B01G239000 chr6B 84.637 358 43 7 38 386 281336550 281336904 3.490000e-91 346.0
2 TraesCS6B01G239000 chr6D 90.033 3612 203 69 1 3537 267528376 267524847 0.000000e+00 4530.0
3 TraesCS6B01G239000 chr6D 91.414 396 31 2 4062 4457 267520707 267520315 1.490000e-149 540.0
4 TraesCS6B01G239000 chr6D 96.029 277 11 0 4441 4717 267520294 267520018 7.200000e-123 451.0
5 TraesCS6B01G239000 chr6D 88.272 324 22 5 3569 3876 267524851 267524528 1.600000e-99 374.0
6 TraesCS6B01G239000 chr6D 93.506 154 6 3 3896 4049 267524542 267524393 4.750000e-55 226.0
7 TraesCS6B01G239000 chr6A 89.737 3001 186 53 608 3537 381083439 381080490 0.000000e+00 3723.0
8 TraesCS6B01G239000 chr6A 93.791 612 34 3 1 608 381084131 381083520 0.000000e+00 917.0
9 TraesCS6B01G239000 chr6A 90.885 373 23 5 4093 4457 381035486 381035117 1.530000e-134 490.0
10 TraesCS6B01G239000 chr6A 94.585 277 15 0 4441 4717 381035096 381034820 3.370000e-116 429.0
11 TraesCS6B01G239000 chr6A 87.307 323 26 8 3569 3876 381080494 381080172 5.810000e-94 355.0
12 TraesCS6B01G239000 chr6A 93.197 147 7 2 3896 4042 381080186 381080043 3.700000e-51 213.0
13 TraesCS6B01G239000 chr6A 92.517 147 8 2 3896 4042 381035766 381035623 1.720000e-49 207.0
14 TraesCS6B01G239000 chr1A 85.043 468 58 11 2 465 30193024 30193483 2.570000e-127 466.0
15 TraesCS6B01G239000 chr1A 91.304 46 2 2 3519 3562 400957594 400957549 1.420000e-05 62.1
16 TraesCS6B01G239000 chr1D 84.829 468 57 11 2 465 30103575 30104032 4.300000e-125 459.0
17 TraesCS6B01G239000 chr1D 95.122 41 2 0 3522 3562 405374234 405374274 1.100000e-06 65.8
18 TraesCS6B01G239000 chr1B 84.188 468 60 11 2 465 48279506 48279963 4.330000e-120 442.0
19 TraesCS6B01G239000 chr1B 89.583 48 3 2 3515 3562 15438514 15438559 5.100000e-05 60.2
20 TraesCS6B01G239000 chr7A 92.672 232 17 0 3578 3809 7136682 7136451 7.560000e-88 335.0
21 TraesCS6B01G239000 chr7A 90.441 136 9 2 3406 3537 7136824 7136689 4.850000e-40 176.0
22 TraesCS6B01G239000 chr5A 97.500 40 1 0 3523 3562 24414757 24414718 8.470000e-08 69.4
23 TraesCS6B01G239000 chr5B 97.436 39 0 1 3524 3562 531281771 531281808 1.100000e-06 65.8
24 TraesCS6B01G239000 chr5D 95.122 41 1 1 3522 3562 543829405 543829366 3.940000e-06 63.9
25 TraesCS6B01G239000 chr2B 95.122 41 1 1 3522 3562 738486650 738486689 3.940000e-06 63.9
26 TraesCS6B01G239000 chr2B 93.023 43 1 1 3534 3574 638267413 638267371 1.420000e-05 62.1
27 TraesCS6B01G239000 chr4D 84.746 59 5 3 3508 3562 371792505 371792563 6.590000e-04 56.5


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 TraesCS6B01G239000 chr6B 415869299 415874015 4716 True 8711.000000 8711 100.000000 1 4717 1 chr6B.!!$R1 4716
1 TraesCS6B01G239000 chr6D 267520018 267528376 8358 True 1224.200000 4530 91.850800 1 4717 5 chr6D.!!$R1 4716
2 TraesCS6B01G239000 chr6A 381080043 381084131 4088 True 1302.000000 3723 91.008000 1 4042 4 chr6A.!!$R2 4041
3 TraesCS6B01G239000 chr6A 381034820 381035766 946 True 375.333333 490 92.662333 3896 4717 3 chr6A.!!$R1 821

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
897 989 1.341531 CAACGTCAGTCCAGTTCTCCT 59.658 52.381 0.00 0.00 0.00 3.69 F
1437 1555 0.037605 ACGGCGCTGTTAGCTTAAGT 60.038 50.000 18.16 0.00 39.60 2.24 F
1800 1935 1.274447 GGCCTCAGCAAGAAAGCATTT 59.726 47.619 0.00 0.00 41.04 2.32 F
3192 3377 0.104671 AAATGTGTGCACCAAGCCAC 59.895 50.000 15.69 5.07 44.83 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2455 2598 0.311790 GTGTTGTCAGTGTGCCATGG 59.688 55.0 7.63 7.63 0.00 3.66 R
2497 2640 0.389948 AACTTCGACTAAGGCCAGCG 60.390 55.0 5.01 3.05 39.73 5.18 R
3558 3743 0.039911 AGTGAAGTACTCCCTCCGCT 59.960 55.0 0.00 0.00 33.17 5.52 R
4334 8234 0.039074 ACGAGAGGAAGCAGTTCACG 60.039 55.0 0.00 0.00 33.93 4.35 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
144 145 4.207891 TCATGCTTTCCTCAAGGTAGAC 57.792 45.455 0.00 0.00 36.34 2.59
148 149 3.840666 TGCTTTCCTCAAGGTAGACATCT 59.159 43.478 0.00 0.00 36.34 2.90
220 221 1.912043 AGCTAACCAGGATTGTGCTCT 59.088 47.619 0.00 0.00 0.00 4.09
239 240 4.442893 GCTCTTTTTAGGTGGCTGGTTTTT 60.443 41.667 0.00 0.00 0.00 1.94
262 263 4.507756 TCGCTTCACAAGAAATATGGATCG 59.492 41.667 0.00 0.00 32.35 3.69
298 299 3.990092 TCTAGATGTAATTTCGCGGCAT 58.010 40.909 6.13 1.59 0.00 4.40
361 362 6.467677 GCCAGAGGCTATCAATAATCTACAA 58.532 40.000 0.00 0.00 46.69 2.41
458 459 7.905604 ATGTTCTTGTGAAGATTAACATCGA 57.094 32.000 0.00 0.00 37.38 3.59
544 548 1.610554 GGGAGTAAGCTGCGTGGGTA 61.611 60.000 0.00 0.00 33.52 3.69
596 600 8.689061 TCTTGAAGATTATGTTGGATGGATTTG 58.311 33.333 0.00 0.00 0.00 2.32
606 692 7.099266 TGTTGGATGGATTTGATCATGTTAC 57.901 36.000 0.00 0.00 0.00 2.50
678 764 5.055642 TGTACTGTGTGTCTGTACTATGC 57.944 43.478 13.17 0.00 45.42 3.14
750 836 9.590451 AATTCATCTGCGTTGATCAAATTATTT 57.410 25.926 10.35 0.00 0.00 1.40
820 908 7.406553 TGCTTATGAATTATTGTTAGTCGCAC 58.593 34.615 0.00 0.00 0.00 5.34
826 914 2.489938 ATTGTTAGTCGCACCACCAT 57.510 45.000 0.00 0.00 0.00 3.55
881 973 2.005451 CATCTCTTTCAGGCCTCAACG 58.995 52.381 0.00 0.00 0.00 4.10
897 989 1.341531 CAACGTCAGTCCAGTTCTCCT 59.658 52.381 0.00 0.00 0.00 3.69
948 1040 2.486966 GCCAATTGCAGAGCCGAC 59.513 61.111 0.00 0.00 40.77 4.79
1088 1198 2.577593 CTCCTCCCGTTCCCGTTC 59.422 66.667 0.00 0.00 0.00 3.95
1126 1236 1.017701 CCCTTCAAAGGTACGCGGTC 61.018 60.000 12.47 2.10 44.98 4.79
1183 1293 3.216292 GCTGCCGGTGGTTGTGTT 61.216 61.111 1.90 0.00 0.00 3.32
1332 1442 1.132262 GCTCACCTCTCTCAACTCTCG 59.868 57.143 0.00 0.00 0.00 4.04
1346 1456 0.248702 CTCTCGCGCCTTTCTACTCC 60.249 60.000 0.00 0.00 0.00 3.85
1376 1488 3.460362 TTACACTACGCGTCTACAGTG 57.540 47.619 29.07 29.07 43.21 3.66
1377 1489 1.233019 ACACTACGCGTCTACAGTGT 58.767 50.000 30.17 30.17 45.08 3.55
1437 1555 0.037605 ACGGCGCTGTTAGCTTAAGT 60.038 50.000 18.16 0.00 39.60 2.24
1440 1558 2.474032 CGGCGCTGTTAGCTTAAGTTTC 60.474 50.000 8.45 0.00 39.60 2.78
1443 1561 3.363673 GCGCTGTTAGCTTAAGTTTCGTT 60.364 43.478 0.00 0.00 39.60 3.85
1489 1611 7.749570 GTGATGCATGTATGAATCTCTAAATGC 59.250 37.037 2.46 9.92 42.31 3.56
1490 1612 6.564709 TGCATGTATGAATCTCTAAATGCC 57.435 37.500 12.64 1.58 38.67 4.40
1494 1616 7.361542 GCATGTATGAATCTCTAAATGCCGAAT 60.362 37.037 7.08 0.00 34.51 3.34
1509 1631 4.728534 TGCCGAATTGCTGTTATTTGTAC 58.271 39.130 0.00 0.00 0.00 2.90
1518 1650 1.807742 TGTTATTTGTACGGCTGTGCC 59.192 47.619 8.92 0.00 46.75 5.01
1661 1796 7.336176 GGTAGGACTAAAAACCATTTCTAGTGG 59.664 40.741 0.00 0.00 42.55 4.00
1662 1797 7.086685 AGGACTAAAAACCATTTCTAGTGGA 57.913 36.000 4.93 0.00 39.12 4.02
1663 1798 7.168905 AGGACTAAAAACCATTTCTAGTGGAG 58.831 38.462 4.93 0.00 39.12 3.86
1664 1799 6.374613 GGACTAAAAACCATTTCTAGTGGAGG 59.625 42.308 4.93 0.00 39.12 4.30
1665 1800 6.849151 ACTAAAAACCATTTCTAGTGGAGGT 58.151 36.000 4.93 0.05 39.12 3.85
1666 1801 6.940867 ACTAAAAACCATTTCTAGTGGAGGTC 59.059 38.462 4.93 0.00 39.12 3.85
1688 1823 2.905075 TGGTTAATCGTGGATGCTCAG 58.095 47.619 0.00 0.00 0.00 3.35
1693 1828 5.277538 GGTTAATCGTGGATGCTCAGATTTC 60.278 44.000 9.94 6.22 34.02 2.17
1708 1843 2.095461 GATTTCCCTGTCCTTTGCTCC 58.905 52.381 0.00 0.00 0.00 4.70
1764 1899 4.499037 TCCTGTATTCGATGTGGATACG 57.501 45.455 0.00 0.00 42.51 3.06
1800 1935 1.274447 GGCCTCAGCAAGAAAGCATTT 59.726 47.619 0.00 0.00 41.04 2.32
1812 1947 9.578439 AGCAAGAAAGCATTTAACTTTATGATC 57.422 29.630 0.00 0.00 39.27 2.92
1820 1955 7.445402 AGCATTTAACTTTATGATCGGTATGCT 59.555 33.333 0.00 0.00 39.02 3.79
1844 1979 1.534175 CGGAGTTCTGGCTACATCGTC 60.534 57.143 0.00 0.00 0.00 4.20
1911 2046 6.370593 TCAACTTTGTTCGCACTATTTCATC 58.629 36.000 0.00 0.00 0.00 2.92
1915 2050 8.213518 ACTTTGTTCGCACTATTTCATCATAT 57.786 30.769 0.00 0.00 0.00 1.78
1947 2083 7.390027 CCATAGAAGATTATAACCTGGAGTGG 58.610 42.308 0.00 0.00 0.00 4.00
1949 2085 6.487299 AGAAGATTATAACCTGGAGTGGTC 57.513 41.667 0.00 0.00 39.83 4.02
1968 2104 5.364157 GTGGTCCTTCAGTATAGACAATCCT 59.636 44.000 0.00 0.00 0.00 3.24
2008 2144 5.352569 AGCTAATAGTGCATCAAACACAGTC 59.647 40.000 0.00 0.00 40.59 3.51
2022 2158 6.481976 TCAAACACAGTCACGAGATGTAAAAT 59.518 34.615 0.00 0.00 0.00 1.82
2024 2160 8.443160 CAAACACAGTCACGAGATGTAAAATAT 58.557 33.333 0.00 0.00 0.00 1.28
2115 2251 6.322969 TCGACTCATATAGTACCACCATTTGT 59.677 38.462 0.00 0.00 39.07 2.83
2120 2256 9.261180 CTCATATAGTACCACCATTTGTAGTTG 57.739 37.037 0.00 0.00 0.00 3.16
2139 2275 5.352284 AGTTGTAGACTTCAAGTGTGACTG 58.648 41.667 0.00 0.00 33.92 3.51
2205 2344 8.454106 AGCTCAACAATGTCATTCAATAAGTAC 58.546 33.333 0.00 0.00 0.00 2.73
2214 2353 6.090763 TGTCATTCAATAAGTACGCTTGACAG 59.909 38.462 7.13 4.50 36.22 3.51
2232 2375 2.076863 CAGTTAAACTTGGGCCTCTCG 58.923 52.381 4.53 0.00 0.00 4.04
2274 2417 7.092716 ACCAATTAGATTGAATGACTTTGCAC 58.907 34.615 2.37 0.00 42.83 4.57
2298 2441 7.013846 CACCAAATTCCTAGGAACTTTGTACAA 59.986 37.037 31.32 3.59 41.75 2.41
2302 2445 5.223449 TCCTAGGAACTTTGTACAACAGG 57.777 43.478 9.71 6.60 41.75 4.00
2303 2446 4.657039 TCCTAGGAACTTTGTACAACAGGT 59.343 41.667 9.71 7.85 41.75 4.00
2396 2539 7.438459 TGTTAGCTTACTTTCTCAGTTTCTGAC 59.562 37.037 4.27 0.00 35.39 3.51
2407 2550 3.003275 TCAGTTTCTGACGTTGGATTTGC 59.997 43.478 0.00 0.00 35.39 3.68
2409 2552 3.569701 AGTTTCTGACGTTGGATTTGCAT 59.430 39.130 0.00 0.00 0.00 3.96
2411 2554 4.582701 TTCTGACGTTGGATTTGCATTT 57.417 36.364 0.00 0.00 0.00 2.32
2415 2558 4.297510 TGACGTTGGATTTGCATTTCTTG 58.702 39.130 0.00 0.00 0.00 3.02
2424 2567 5.574443 GGATTTGCATTTCTTGTTAGCTCAC 59.426 40.000 0.00 0.00 0.00 3.51
2436 2579 6.823689 TCTTGTTAGCTCACTTTCTGACTTTT 59.176 34.615 0.00 0.00 0.00 2.27
2447 2590 4.836125 TTCTGACTTTTTGATGCTGGAC 57.164 40.909 0.00 0.00 0.00 4.02
2451 2594 3.953612 TGACTTTTTGATGCTGGACTTGT 59.046 39.130 0.00 0.00 0.00 3.16
2453 2596 5.769662 TGACTTTTTGATGCTGGACTTGTAT 59.230 36.000 0.00 0.00 0.00 2.29
2455 2598 6.681777 ACTTTTTGATGCTGGACTTGTATTC 58.318 36.000 0.00 0.00 0.00 1.75
2460 2603 3.003394 TGCTGGACTTGTATTCCATGG 57.997 47.619 4.97 4.97 42.43 3.66
2478 2621 3.138884 TGGCACACTGACAACACATAT 57.861 42.857 0.00 0.00 28.38 1.78
2479 2622 3.485394 TGGCACACTGACAACACATATT 58.515 40.909 0.00 0.00 28.38 1.28
2480 2623 3.888323 TGGCACACTGACAACACATATTT 59.112 39.130 0.00 0.00 28.38 1.40
2485 2628 6.642131 GCACACTGACAACACATATTTTCATT 59.358 34.615 0.00 0.00 0.00 2.57
2497 2640 8.306761 ACACATATTTTCATTCCTTTTCACCTC 58.693 33.333 0.00 0.00 0.00 3.85
2507 2650 0.398696 TTTTCACCTCGCTGGCCTTA 59.601 50.000 3.32 0.00 40.22 2.69
2510 2653 1.153549 CACCTCGCTGGCCTTAGTC 60.154 63.158 3.32 0.00 40.22 2.59
2606 2758 2.723273 GGTGTCTACCATTTTCCTGGG 58.277 52.381 0.00 0.00 46.71 4.45
2607 2759 2.092323 GTGTCTACCATTTTCCTGGGC 58.908 52.381 0.00 0.00 40.85 5.36
2608 2760 1.707989 TGTCTACCATTTTCCTGGGCA 59.292 47.619 0.00 0.00 40.85 5.36
2609 2761 2.290896 TGTCTACCATTTTCCTGGGCAG 60.291 50.000 0.00 0.00 40.85 4.85
2610 2762 1.106285 CTACCATTTTCCTGGGCAGC 58.894 55.000 0.00 0.00 40.85 5.25
2611 2763 0.407528 TACCATTTTCCTGGGCAGCA 59.592 50.000 0.00 0.00 40.85 4.41
2612 2764 0.901580 ACCATTTTCCTGGGCAGCAG 60.902 55.000 0.00 0.00 40.85 4.24
2613 2765 0.901580 CCATTTTCCTGGGCAGCAGT 60.902 55.000 0.00 0.00 32.28 4.40
2658 2810 1.798234 TTGTGTGGCATGCTGCTCAC 61.798 55.000 18.92 16.85 44.28 3.51
2681 2833 5.299028 ACACACACAAGATGCTATTTCAACA 59.701 36.000 0.00 0.00 0.00 3.33
2709 2886 9.793252 CCTAAATCTTGGACAAAAATATCACTG 57.207 33.333 0.00 0.00 0.00 3.66
2722 2899 9.467258 CAAAAATATCACTGTTTCAGTCATTGT 57.533 29.630 0.00 0.00 43.43 2.71
2726 2903 6.791887 ATCACTGTTTCAGTCATTGTACTG 57.208 37.500 0.00 8.90 43.43 2.74
2727 2904 5.056480 TCACTGTTTCAGTCATTGTACTGG 58.944 41.667 12.99 3.76 43.43 4.00
2728 2905 5.056480 CACTGTTTCAGTCATTGTACTGGA 58.944 41.667 12.99 5.29 43.43 3.86
2729 2906 5.527214 CACTGTTTCAGTCATTGTACTGGAA 59.473 40.000 12.99 9.65 43.43 3.53
2730 2907 6.038161 CACTGTTTCAGTCATTGTACTGGAAA 59.962 38.462 9.93 8.94 44.62 3.13
2731 2908 6.260936 ACTGTTTCAGTCATTGTACTGGAAAG 59.739 38.462 9.93 11.09 44.62 2.62
2732 2909 5.008613 TGTTTCAGTCATTGTACTGGAAAGC 59.991 40.000 9.93 5.36 44.62 3.51
2733 2910 3.674997 TCAGTCATTGTACTGGAAAGCC 58.325 45.455 12.99 0.00 45.69 4.35
2734 2911 2.416547 CAGTCATTGTACTGGAAAGCCG 59.583 50.000 0.00 0.00 42.63 5.52
2735 2912 1.130561 GTCATTGTACTGGAAAGCCGC 59.869 52.381 0.00 0.00 36.79 6.53
2736 2913 1.003118 TCATTGTACTGGAAAGCCGCT 59.997 47.619 0.00 0.00 36.79 5.52
2737 2914 2.235155 TCATTGTACTGGAAAGCCGCTA 59.765 45.455 0.00 0.00 36.79 4.26
2738 2915 2.088950 TTGTACTGGAAAGCCGCTAC 57.911 50.000 0.00 0.00 36.79 3.58
2739 2916 1.263356 TGTACTGGAAAGCCGCTACT 58.737 50.000 0.00 0.00 36.79 2.57
2740 2917 1.621814 TGTACTGGAAAGCCGCTACTT 59.378 47.619 0.00 0.00 36.79 2.24
2741 2918 2.000447 GTACTGGAAAGCCGCTACTTG 59.000 52.381 0.00 0.00 36.79 3.16
2742 2919 0.955919 ACTGGAAAGCCGCTACTTGC 60.956 55.000 0.00 0.00 36.79 4.01
2743 2920 0.955428 CTGGAAAGCCGCTACTTGCA 60.955 55.000 0.00 0.00 43.06 4.08
2744 2921 0.955428 TGGAAAGCCGCTACTTGCAG 60.955 55.000 0.00 0.00 43.06 4.41
2745 2922 0.955919 GGAAAGCCGCTACTTGCAGT 60.956 55.000 0.00 0.00 43.06 4.40
2746 2923 0.166814 GAAAGCCGCTACTTGCAGTG 59.833 55.000 0.00 0.00 43.06 3.66
2758 2935 6.508088 CGCTACTTGCAGTGCTAGTAATTTAC 60.508 42.308 30.26 19.44 43.51 2.01
2773 2950 1.857318 TTTACGGTTGCATGTGCCCG 61.857 55.000 17.30 17.30 46.50 6.13
2776 2953 2.983030 GGTTGCATGTGCCCGTCA 60.983 61.111 2.07 0.00 41.18 4.35
2799 2976 3.981071 TTGGTGCTACTGCTACATCTT 57.019 42.857 0.00 0.00 40.48 2.40
2813 2990 2.540515 ACATCTTTGTAGCGTCCATCG 58.459 47.619 0.00 0.00 37.13 3.84
2822 2999 2.209838 AGCGTCCATCGTAGAACATG 57.790 50.000 0.00 0.00 43.58 3.21
2837 3014 1.795768 ACATGTGCGATTCAACGTCT 58.204 45.000 0.00 0.00 35.59 4.18
2839 3016 1.460743 CATGTGCGATTCAACGTCTGT 59.539 47.619 0.00 0.00 35.59 3.41
2852 3029 4.974368 AACGTCTGTTGTGGATTTTTGA 57.026 36.364 0.00 0.00 36.81 2.69
2873 3050 4.200092 GACTGACAGTTTTGATATCCCCC 58.800 47.826 10.01 0.00 0.00 5.40
2877 3054 4.770010 TGACAGTTTTGATATCCCCCAAAC 59.230 41.667 0.00 4.84 32.67 2.93
2879 3056 5.402630 ACAGTTTTGATATCCCCCAAACTT 58.597 37.500 13.00 6.40 32.67 2.66
2933 3110 5.746721 ACTTTACAATGCTGGTTTCGAAAAC 59.253 36.000 19.09 19.09 0.00 2.43
2997 3180 5.007034 AGGTAGGAGTCATCGTATGATCTG 58.993 45.833 0.00 0.00 42.04 2.90
3004 3187 6.309980 GGAGTCATCGTATGATCTGCTATTTG 59.690 42.308 0.00 0.00 42.04 2.32
3168 3353 3.813166 AGTGTGACGGTGTTATTTTCCTG 59.187 43.478 0.00 0.00 0.00 3.86
3188 3373 2.159128 TGACCAAAATGTGTGCACCAAG 60.159 45.455 15.69 4.39 0.00 3.61
3189 3374 1.219646 CCAAAATGTGTGCACCAAGC 58.780 50.000 15.69 2.61 45.96 4.01
3190 3375 1.219646 CAAAATGTGTGCACCAAGCC 58.780 50.000 15.69 0.00 44.83 4.35
3191 3376 0.829333 AAAATGTGTGCACCAAGCCA 59.171 45.000 15.69 3.59 44.83 4.75
3192 3377 0.104671 AAATGTGTGCACCAAGCCAC 59.895 50.000 15.69 5.07 44.83 5.01
3193 3378 1.747325 AATGTGTGCACCAAGCCACC 61.747 55.000 15.69 0.00 44.83 4.61
3194 3379 2.832661 GTGTGCACCAAGCCACCA 60.833 61.111 15.69 0.00 44.83 4.17
3195 3380 2.043551 TGTGCACCAAGCCACCAA 60.044 55.556 15.69 0.00 44.83 3.67
3215 3400 4.339247 CCAAGGCCTTGTATTATGGTTGAG 59.661 45.833 37.09 17.66 38.85 3.02
3262 3447 1.710809 ACCTTGCCACCAACCTAAGAT 59.289 47.619 0.00 0.00 0.00 2.40
3266 3451 2.524306 TGCCACCAACCTAAGATTTGG 58.476 47.619 0.00 0.00 46.72 3.28
3305 3490 9.696917 CAGTACACATGTAGATAAGCATGATAA 57.303 33.333 10.90 0.00 43.60 1.75
3346 3531 8.455903 TTCTGAGATGATCCAAATATGTTTCC 57.544 34.615 0.00 0.00 0.00 3.13
3361 3546 2.428890 TGTTTCCGCATTCCACAAAAGT 59.571 40.909 0.00 0.00 0.00 2.66
3537 3722 9.834628 TTCGTTTTGAAAAATATCCATGTACTC 57.165 29.630 0.00 0.00 32.37 2.59
3538 3723 8.455682 TCGTTTTGAAAAATATCCATGTACTCC 58.544 33.333 0.00 0.00 0.00 3.85
3539 3724 7.700656 CGTTTTGAAAAATATCCATGTACTCCC 59.299 37.037 0.00 0.00 0.00 4.30
3540 3725 8.749354 GTTTTGAAAAATATCCATGTACTCCCT 58.251 33.333 0.00 0.00 0.00 4.20
3541 3726 8.519799 TTTGAAAAATATCCATGTACTCCCTC 57.480 34.615 0.00 0.00 0.00 4.30
3542 3727 6.601332 TGAAAAATATCCATGTACTCCCTCC 58.399 40.000 0.00 0.00 0.00 4.30
3543 3728 4.891992 AAATATCCATGTACTCCCTCCG 57.108 45.455 0.00 0.00 0.00 4.63
3544 3729 3.544698 ATATCCATGTACTCCCTCCGT 57.455 47.619 0.00 0.00 0.00 4.69
3545 3730 4.669866 ATATCCATGTACTCCCTCCGTA 57.330 45.455 0.00 0.00 0.00 4.02
3546 3731 2.832643 TCCATGTACTCCCTCCGTAA 57.167 50.000 0.00 0.00 0.00 3.18
3547 3732 3.104519 TCCATGTACTCCCTCCGTAAA 57.895 47.619 0.00 0.00 0.00 2.01
3548 3733 2.762327 TCCATGTACTCCCTCCGTAAAC 59.238 50.000 0.00 0.00 0.00 2.01
3549 3734 2.764572 CCATGTACTCCCTCCGTAAACT 59.235 50.000 0.00 0.00 0.00 2.66
3550 3735 3.956199 CCATGTACTCCCTCCGTAAACTA 59.044 47.826 0.00 0.00 0.00 2.24
3551 3736 4.403432 CCATGTACTCCCTCCGTAAACTAA 59.597 45.833 0.00 0.00 0.00 2.24
3552 3737 5.070047 CCATGTACTCCCTCCGTAAACTAAT 59.930 44.000 0.00 0.00 0.00 1.73
3553 3738 6.266103 CCATGTACTCCCTCCGTAAACTAATA 59.734 42.308 0.00 0.00 0.00 0.98
3554 3739 7.039223 CCATGTACTCCCTCCGTAAACTAATAT 60.039 40.741 0.00 0.00 0.00 1.28
3555 3740 9.017509 CATGTACTCCCTCCGTAAACTAATATA 57.982 37.037 0.00 0.00 0.00 0.86
3556 3741 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
3557 3742 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
3558 3743 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
3559 3744 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3560 3745 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3561 3746 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3562 3747 6.091437 CCTCCGTAAACTAATATAAGAGCGG 58.909 44.000 0.00 0.00 37.15 5.52
3563 3748 6.072286 CCTCCGTAAACTAATATAAGAGCGGA 60.072 42.308 0.00 0.00 41.57 5.54
3564 3749 6.906659 TCCGTAAACTAATATAAGAGCGGAG 58.093 40.000 0.00 0.00 39.42 4.63
3565 3750 6.072286 TCCGTAAACTAATATAAGAGCGGAGG 60.072 42.308 0.00 0.00 39.42 4.30
3566 3751 6.091437 CGTAAACTAATATAAGAGCGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3567 3752 6.072286 CGTAAACTAATATAAGAGCGGAGGGA 60.072 42.308 0.00 0.00 0.00 4.20
3574 3759 1.476477 AAGAGCGGAGGGAGTACTTC 58.524 55.000 0.00 0.00 0.00 3.01
3601 3786 5.381174 TTGTCTGCAATGGAAAGATCTTG 57.619 39.130 9.17 0.00 0.00 3.02
3623 3808 4.997395 TGAAACATTCTTCTTCTTCCTCGG 59.003 41.667 0.00 0.00 0.00 4.63
3723 3908 7.112122 ACAATTACAGCCTCATTAACTGATCA 58.888 34.615 0.00 0.00 35.38 2.92
3727 3912 9.851686 ATTACAGCCTCATTAACTGATCAATTA 57.148 29.630 0.00 0.00 35.38 1.40
3729 3914 7.112122 ACAGCCTCATTAACTGATCAATTACA 58.888 34.615 0.00 0.00 35.38 2.41
3739 3924 9.739276 TTAACTGATCAATTACAAGGAAGATGT 57.261 29.630 0.00 0.00 34.81 3.06
3754 3939 2.653726 AGATGTTGTGGTGTTCAAGCA 58.346 42.857 0.00 0.00 0.00 3.91
3770 3955 1.484038 AGCAAACTTGAAGGTGGCAA 58.516 45.000 12.85 0.00 0.00 4.52
3785 3970 1.064134 GCAATTCGGGCGTTCATCC 59.936 57.895 0.00 0.00 0.00 3.51
3799 3984 3.037549 GTTCATCCTGAGAGAGACCCAT 58.962 50.000 0.00 0.00 0.00 4.00
3800 3985 3.411454 TCATCCTGAGAGAGACCCATT 57.589 47.619 0.00 0.00 0.00 3.16
3809 4010 3.879892 GAGAGAGACCCATTACAATTGCC 59.120 47.826 5.05 0.00 0.00 4.52
3822 4023 2.463589 AATTGCCGCCGTTCCTCAGA 62.464 55.000 0.00 0.00 0.00 3.27
3858 4059 3.430218 CACACAGAGACGGAATGTTCTTC 59.570 47.826 0.00 0.00 0.00 2.87
3935 4136 7.002250 TGAATATCTAGAGCCTCATTTCTGG 57.998 40.000 0.00 0.00 0.00 3.86
3982 4183 5.278957 GGCCGCACAGGATAATTATGATTTT 60.279 40.000 1.78 0.00 45.00 1.82
4050 7890 6.375174 TCTCAAAAATATCACATGTGTGGAGG 59.625 38.462 24.63 8.92 45.65 4.30
4051 7891 6.009589 TCAAAAATATCACATGTGTGGAGGT 58.990 36.000 24.63 5.93 45.65 3.85
4080 7955 3.741476 CTCTTGCTGGCGGTTGGC 61.741 66.667 0.00 0.00 42.51 4.52
4112 8004 1.285280 TCCGATAATATGCCCTGGGG 58.715 55.000 16.03 4.75 38.57 4.96
4123 8015 1.152963 CCCTGGGGATTTAGGTGCG 60.153 63.158 4.27 0.00 37.50 5.34
4146 8038 6.734871 GCGGAATATTCCTTTTCATAACCCAC 60.735 42.308 27.86 0.92 45.33 4.61
4226 8118 5.184671 CCGTAACTCAACTAGGGTTAGAAGT 59.815 44.000 0.00 0.00 33.88 3.01
4238 8130 1.068055 GTTAGAAGTCCGAACCGCAGA 60.068 52.381 0.00 0.00 0.00 4.26
4259 8151 5.877012 CAGATATATGTTCCCAATTCCTCCG 59.123 44.000 0.00 0.00 0.00 4.63
4267 8159 0.036010 CCAATTCCTCCGCAGAGTGT 60.036 55.000 0.00 0.00 38.58 3.55
4334 8234 2.196749 CCACATGTCATACTCACGAGC 58.803 52.381 0.00 0.00 0.00 5.03
4356 8256 0.603569 GAACTGCTTCCTCTCGTGGA 59.396 55.000 0.00 0.00 0.00 4.02
4395 8295 4.724602 TGCAGAGGACGAGCGTGC 62.725 66.667 6.41 6.41 36.69 5.34
4410 8310 1.659794 GTGCGGCTCATGGTTTTGT 59.340 52.632 0.00 0.00 0.00 2.83
4428 8328 5.930837 TTTGTCCTTCAATTGTTTGGTCT 57.069 34.783 5.13 0.00 35.84 3.85
4431 8331 5.690865 TGTCCTTCAATTGTTTGGTCTACT 58.309 37.500 5.13 0.00 33.44 2.57
4433 8333 6.708949 TGTCCTTCAATTGTTTGGTCTACTAC 59.291 38.462 5.13 1.22 33.44 2.73
4452 8386 2.945456 ACCAAACCAAGAAGGAAGGAC 58.055 47.619 0.00 0.00 41.22 3.85
4466 8400 2.508526 GAAGGACACAGCACAAGGATT 58.491 47.619 0.00 0.00 0.00 3.01
4486 8420 2.052468 TGATCCATCTGACATCTGGGG 58.948 52.381 4.16 0.00 0.00 4.96
4636 8570 3.379445 CGTCTACCACGCCCACCT 61.379 66.667 0.00 0.00 42.87 4.00
4638 8572 1.597797 CGTCTACCACGCCCACCTAA 61.598 60.000 0.00 0.00 42.87 2.69
4639 8573 0.609662 GTCTACCACGCCCACCTAAA 59.390 55.000 0.00 0.00 0.00 1.85
4643 8577 1.125711 ACCACGCCCACCTAAACTCT 61.126 55.000 0.00 0.00 0.00 3.24
4651 8585 2.640826 CCCACCTAAACTCTTACCCACA 59.359 50.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 2.418976 CACACAAGTCCTGATGCAGATG 59.581 50.000 0.00 0.00 32.44 2.90
148 149 0.890542 GGCACACAAGTCCTGATGCA 60.891 55.000 0.00 0.00 40.37 3.96
220 221 3.738590 GCGAAAAACCAGCCACCTAAAAA 60.739 43.478 0.00 0.00 0.00 1.94
239 240 4.507756 CGATCCATATTTCTTGTGAAGCGA 59.492 41.667 0.00 0.00 33.28 4.93
325 326 1.538950 GCCTCTGGCTGAACTTTTGAG 59.461 52.381 0.73 0.00 46.69 3.02
458 459 1.210478 AGTTGTAGCTCCATGCCGATT 59.790 47.619 0.00 0.00 44.23 3.34
518 522 0.898320 GCAGCTTACTCCCTCAGACA 59.102 55.000 0.00 0.00 0.00 3.41
569 573 8.827832 AATCCATCCAACATAATCTTCAAGAA 57.172 30.769 0.00 0.00 0.00 2.52
583 587 7.338800 AGTAACATGATCAAATCCATCCAAC 57.661 36.000 0.00 0.00 0.00 3.77
606 692 4.641989 AGTGGCACTTGCATCCTAATTTAG 59.358 41.667 15.88 0.00 44.36 1.85
820 908 1.471287 CTGCACTGAACATCATGGTGG 59.529 52.381 11.45 0.00 0.00 4.61
897 989 2.055689 CTGCAGACCTTGTGGGGACA 62.056 60.000 8.42 0.00 40.03 4.02
948 1040 4.379603 CGTAGCTTTATCCCCATCTCGTAG 60.380 50.000 0.00 0.00 0.00 3.51
980 1076 5.739935 GCCATTTTCTTGCTTTCCTCTCAAA 60.740 40.000 0.00 0.00 0.00 2.69
981 1077 4.262164 GCCATTTTCTTGCTTTCCTCTCAA 60.262 41.667 0.00 0.00 0.00 3.02
1088 1198 2.815647 GCAGGCGAGGACGAAAGG 60.816 66.667 0.00 0.00 42.66 3.11
1126 1236 1.532868 CAGGAAAACGCAGGAGACAAG 59.467 52.381 0.00 0.00 0.00 3.16
1193 1303 0.475632 TCTTCACCACCCCACTCCAT 60.476 55.000 0.00 0.00 0.00 3.41
1332 1442 2.317530 AATGAGGAGTAGAAAGGCGC 57.682 50.000 0.00 0.00 0.00 6.53
1346 1456 3.896238 CGCGTAGTGTAAACGAAATGAG 58.104 45.455 0.00 0.00 42.90 2.90
1426 1544 7.958112 TTCAAACAACGAAACTTAAGCTAAC 57.042 32.000 1.29 0.00 0.00 2.34
1437 1555 3.422417 TGCCGAATTCAAACAACGAAA 57.578 38.095 6.22 0.00 0.00 3.46
1440 1558 2.250188 GGATGCCGAATTCAAACAACG 58.750 47.619 6.22 0.00 0.00 4.10
1443 1561 2.824936 ACATGGATGCCGAATTCAAACA 59.175 40.909 6.22 0.34 0.00 2.83
1489 1611 4.339429 CCGTACAAATAACAGCAATTCGG 58.661 43.478 0.00 0.00 0.00 4.30
1490 1612 3.783943 GCCGTACAAATAACAGCAATTCG 59.216 43.478 0.00 0.00 0.00 3.34
1494 1616 3.058570 CACAGCCGTACAAATAACAGCAA 60.059 43.478 0.00 0.00 0.00 3.91
1518 1650 2.765135 TCTTCTGCTCCCTGATCTTCAG 59.235 50.000 0.00 0.00 43.91 3.02
1661 1796 3.604875 TCCACGATTAACCAAGACCTC 57.395 47.619 0.00 0.00 0.00 3.85
1662 1797 3.873910 CATCCACGATTAACCAAGACCT 58.126 45.455 0.00 0.00 0.00 3.85
1663 1798 2.354821 GCATCCACGATTAACCAAGACC 59.645 50.000 0.00 0.00 0.00 3.85
1664 1799 3.270877 AGCATCCACGATTAACCAAGAC 58.729 45.455 0.00 0.00 0.00 3.01
1665 1800 3.055458 TGAGCATCCACGATTAACCAAGA 60.055 43.478 0.00 0.00 0.00 3.02
1666 1801 3.270027 TGAGCATCCACGATTAACCAAG 58.730 45.455 0.00 0.00 0.00 3.61
1688 1823 2.095461 GGAGCAAAGGACAGGGAAATC 58.905 52.381 0.00 0.00 0.00 2.17
1693 1828 1.202580 CGATAGGAGCAAAGGACAGGG 60.203 57.143 0.00 0.00 0.00 4.45
1708 1843 1.971505 TTCACCCAGGCCTGCGATAG 61.972 60.000 28.39 13.14 0.00 2.08
1741 1876 4.680110 CGTATCCACATCGAATACAGGAAC 59.320 45.833 0.00 0.00 0.00 3.62
1746 1881 3.313249 ACGACGTATCCACATCGAATACA 59.687 43.478 0.00 0.00 37.97 2.29
1764 1899 2.352960 GAGGCCATTCAAATCAGACGAC 59.647 50.000 5.01 0.00 0.00 4.34
1800 1935 7.383029 CCGTTTAGCATACCGATCATAAAGTTA 59.617 37.037 0.00 0.00 0.00 2.24
1812 1947 2.858344 CAGAACTCCGTTTAGCATACCG 59.142 50.000 0.00 0.00 0.00 4.02
1820 1955 3.428452 CGATGTAGCCAGAACTCCGTTTA 60.428 47.826 0.00 0.00 0.00 2.01
1824 1959 0.456221 ACGATGTAGCCAGAACTCCG 59.544 55.000 0.00 0.00 0.00 4.63
1844 1979 0.445436 GCAAGCAACAGTCAGATCCG 59.555 55.000 0.00 0.00 0.00 4.18
1915 2050 9.778741 CAGGTTATAATCTTCTATGGCAACTTA 57.221 33.333 0.00 0.00 37.61 2.24
1931 2066 5.036916 TGAAGGACCACTCCAGGTTATAAT 58.963 41.667 0.00 0.00 43.38 1.28
1932 2067 4.431378 TGAAGGACCACTCCAGGTTATAA 58.569 43.478 0.00 0.00 43.38 0.98
1933 2068 4.030913 CTGAAGGACCACTCCAGGTTATA 58.969 47.826 0.00 0.00 43.38 0.98
1939 2075 4.339814 GTCTATACTGAAGGACCACTCCAG 59.660 50.000 0.00 0.00 39.39 3.86
1968 2104 6.663953 ACTATTAGCTTGTTAGTCTCCAGTCA 59.336 38.462 0.00 0.00 0.00 3.41
1982 2118 5.941733 TGTGTTTGATGCACTATTAGCTTG 58.058 37.500 0.00 0.00 37.70 4.01
2008 2144 7.697691 AGAAAAGGCATATTTTACATCTCGTG 58.302 34.615 0.00 0.00 32.62 4.35
2022 2158 9.685276 TCAATCTATCTTGAAAGAAAAGGCATA 57.315 29.630 0.00 0.00 38.77 3.14
2024 2160 7.667219 AGTCAATCTATCTTGAAAGAAAAGGCA 59.333 33.333 0.00 0.00 38.77 4.75
2083 2219 9.339850 GGTGGTACTATATGAGTCGACATATAT 57.660 37.037 19.50 20.40 41.65 0.86
2084 2220 8.323567 TGGTGGTACTATATGAGTCGACATATA 58.676 37.037 19.50 15.21 41.67 0.86
2092 2228 8.639761 ACTACAAATGGTGGTACTATATGAGTC 58.360 37.037 0.00 0.00 39.72 3.36
2101 2237 6.269307 AGTCTACAACTACAAATGGTGGTACT 59.731 38.462 0.00 0.00 40.75 2.73
2115 2251 6.320418 TCAGTCACACTTGAAGTCTACAACTA 59.680 38.462 0.00 0.00 37.17 2.24
2120 2256 5.593010 AGTTCAGTCACACTTGAAGTCTAC 58.407 41.667 0.00 0.00 31.90 2.59
2139 2275 5.049167 CCTATGCAAGAGTGATGAGAGTTC 58.951 45.833 0.00 0.00 0.00 3.01
2205 2344 2.604614 GCCCAAGTTTAACTGTCAAGCG 60.605 50.000 0.00 0.00 0.00 4.68
2214 2353 1.804748 CACGAGAGGCCCAAGTTTAAC 59.195 52.381 0.00 0.00 0.00 2.01
2256 2399 5.534207 TTTGGTGCAAAGTCATTCAATCT 57.466 34.783 0.00 0.00 0.00 2.40
2263 2406 4.463891 CCTAGGAATTTGGTGCAAAGTCAT 59.536 41.667 1.05 0.00 46.05 3.06
2271 2414 4.280929 ACAAAGTTCCTAGGAATTTGGTGC 59.719 41.667 33.74 21.58 36.87 5.01
2274 2417 7.013846 TGTTGTACAAAGTTCCTAGGAATTTGG 59.986 37.037 33.74 30.44 37.18 3.28
2298 2441 2.164338 GAGAACTTCTCCTCGACCTGT 58.836 52.381 7.49 0.00 37.55 4.00
2302 2445 4.872664 TCTTTTGAGAACTTCTCCTCGAC 58.127 43.478 14.98 0.00 42.73 4.20
2303 2446 5.730296 ATCTTTTGAGAACTTCTCCTCGA 57.270 39.130 14.98 7.65 42.73 4.04
2378 2521 5.047847 CCAACGTCAGAAACTGAGAAAGTA 58.952 41.667 1.53 0.00 41.46 2.24
2386 2529 3.243035 TGCAAATCCAACGTCAGAAACTG 60.243 43.478 0.00 0.00 0.00 3.16
2396 2539 5.164061 GCTAACAAGAAATGCAAATCCAACG 60.164 40.000 0.00 0.00 0.00 4.10
2407 2550 7.041508 AGTCAGAAAGTGAGCTAACAAGAAATG 60.042 37.037 3.43 0.00 35.13 2.32
2409 2552 6.349300 AGTCAGAAAGTGAGCTAACAAGAAA 58.651 36.000 3.43 0.00 35.13 2.52
2411 2554 5.537300 AGTCAGAAAGTGAGCTAACAAGA 57.463 39.130 3.43 0.00 35.13 3.02
2415 2558 7.016361 TCAAAAAGTCAGAAAGTGAGCTAAC 57.984 36.000 0.00 0.00 35.13 2.34
2424 2567 5.009410 AGTCCAGCATCAAAAAGTCAGAAAG 59.991 40.000 0.00 0.00 0.00 2.62
2436 2579 4.299586 TGGAATACAAGTCCAGCATCAA 57.700 40.909 0.00 0.00 40.33 2.57
2447 2590 3.127548 GTCAGTGTGCCATGGAATACAAG 59.872 47.826 20.94 12.95 0.00 3.16
2451 2594 3.081061 GTTGTCAGTGTGCCATGGAATA 58.919 45.455 18.40 0.00 0.00 1.75
2453 2596 1.317613 GTTGTCAGTGTGCCATGGAA 58.682 50.000 18.40 0.00 0.00 3.53
2455 2598 0.311790 GTGTTGTCAGTGTGCCATGG 59.688 55.000 7.63 7.63 0.00 3.66
2460 2603 5.518812 TGAAAATATGTGTTGTCAGTGTGC 58.481 37.500 0.00 0.00 0.00 4.57
2478 2621 3.888930 AGCGAGGTGAAAAGGAATGAAAA 59.111 39.130 0.00 0.00 0.00 2.29
2479 2622 3.253188 CAGCGAGGTGAAAAGGAATGAAA 59.747 43.478 0.00 0.00 0.00 2.69
2480 2623 2.813754 CAGCGAGGTGAAAAGGAATGAA 59.186 45.455 0.00 0.00 0.00 2.57
2485 2628 1.302511 GCCAGCGAGGTGAAAAGGA 60.303 57.895 3.61 0.00 40.61 3.36
2497 2640 0.389948 AACTTCGACTAAGGCCAGCG 60.390 55.000 5.01 3.05 39.73 5.18
2589 2741 2.369394 CTGCCCAGGAAAATGGTAGAC 58.631 52.381 0.00 0.00 38.81 2.59
2596 2748 1.538687 GCACTGCTGCCCAGGAAAAT 61.539 55.000 0.00 0.00 46.14 1.82
2600 2752 2.300197 TATGCACTGCTGCCCAGGA 61.300 57.895 1.98 0.00 46.14 3.86
2603 2755 2.045045 GGTATGCACTGCTGCCCA 60.045 61.111 1.98 0.00 43.51 5.36
2605 2757 0.962356 AAGTGGTATGCACTGCTGCC 60.962 55.000 1.98 2.73 43.51 4.85
2606 2758 0.449388 GAAGTGGTATGCACTGCTGC 59.551 55.000 1.98 0.00 44.52 5.25
2607 2759 2.105006 AGAAGTGGTATGCACTGCTG 57.895 50.000 1.98 0.00 37.19 4.41
2608 2760 2.867109 AAGAAGTGGTATGCACTGCT 57.133 45.000 1.98 0.00 40.14 4.24
2609 2761 4.455877 AGTTTAAGAAGTGGTATGCACTGC 59.544 41.667 0.00 0.00 32.56 4.40
2610 2762 6.204688 TCAAGTTTAAGAAGTGGTATGCACTG 59.795 38.462 0.00 0.00 32.56 3.66
2611 2763 6.296026 TCAAGTTTAAGAAGTGGTATGCACT 58.704 36.000 0.00 0.00 33.80 4.40
2612 2764 6.554334 TCAAGTTTAAGAAGTGGTATGCAC 57.446 37.500 0.00 0.00 0.00 4.57
2613 2765 5.181245 GCTCAAGTTTAAGAAGTGGTATGCA 59.819 40.000 0.00 0.00 0.00 3.96
2658 2810 5.761003 TGTTGAAATAGCATCTTGTGTGTG 58.239 37.500 0.00 0.00 0.00 3.82
2722 2899 1.674817 GCAAGTAGCGGCTTTCCAGTA 60.675 52.381 8.26 0.00 0.00 2.74
2738 2915 4.630069 ACCGTAAATTACTAGCACTGCAAG 59.370 41.667 3.30 0.00 42.29 4.01
2739 2916 4.571919 ACCGTAAATTACTAGCACTGCAA 58.428 39.130 3.30 0.00 0.00 4.08
2740 2917 4.196626 ACCGTAAATTACTAGCACTGCA 57.803 40.909 3.30 0.00 0.00 4.41
2741 2918 4.726876 GCAACCGTAAATTACTAGCACTGC 60.727 45.833 1.42 0.00 0.00 4.40
2742 2919 4.390603 TGCAACCGTAAATTACTAGCACTG 59.609 41.667 1.42 0.00 0.00 3.66
2743 2920 4.571919 TGCAACCGTAAATTACTAGCACT 58.428 39.130 1.42 0.00 0.00 4.40
2744 2921 4.932268 TGCAACCGTAAATTACTAGCAC 57.068 40.909 1.42 0.00 0.00 4.40
2745 2922 4.938832 ACATGCAACCGTAAATTACTAGCA 59.061 37.500 1.42 6.40 0.00 3.49
2746 2923 5.263185 CACATGCAACCGTAAATTACTAGC 58.737 41.667 1.42 1.27 0.00 3.42
2758 2935 4.101790 GACGGGCACATGCAACCG 62.102 66.667 16.82 16.82 46.50 4.44
2773 2950 4.693283 TGTAGCAGTAGCACCAATATGAC 58.307 43.478 0.00 0.00 45.49 3.06
2776 2953 5.815233 AGATGTAGCAGTAGCACCAATAT 57.185 39.130 0.00 0.00 45.49 1.28
2799 2976 2.488937 TGTTCTACGATGGACGCTACAA 59.511 45.455 0.00 0.00 46.94 2.41
2813 2990 3.122948 ACGTTGAATCGCACATGTTCTAC 59.877 43.478 0.00 0.00 0.00 2.59
2837 3014 4.704540 ACTGTCAGTCAAAAATCCACAACA 59.295 37.500 0.00 0.00 0.00 3.33
2839 3016 5.913137 AACTGTCAGTCAAAAATCCACAA 57.087 34.783 5.82 0.00 0.00 3.33
2852 3029 3.591527 TGGGGGATATCAAAACTGTCAGT 59.408 43.478 4.83 0.00 0.00 3.41
2873 3050 5.237779 AGCAATTGATCTGCCAAAAAGTTTG 59.762 36.000 10.34 0.00 40.86 2.93
2877 3054 4.921470 CAGCAATTGATCTGCCAAAAAG 57.079 40.909 10.34 0.00 40.86 2.27
2924 3101 7.040961 CCTTGTACCCAGAATAAGTTTTCGAAA 60.041 37.037 6.47 6.47 0.00 3.46
2933 3110 5.896073 ATCCTCCTTGTACCCAGAATAAG 57.104 43.478 0.00 0.00 0.00 1.73
3168 3353 2.472816 CTTGGTGCACACATTTTGGTC 58.527 47.619 20.43 0.00 0.00 4.02
3189 3374 2.958355 CCATAATACAAGGCCTTGGTGG 59.042 50.000 41.04 32.81 44.45 4.61
3190 3375 3.631250 ACCATAATACAAGGCCTTGGTG 58.369 45.455 41.04 29.47 44.45 4.17
3191 3376 4.023291 CAACCATAATACAAGGCCTTGGT 58.977 43.478 41.04 29.16 44.45 3.67
3192 3377 4.277476 TCAACCATAATACAAGGCCTTGG 58.723 43.478 41.04 28.52 44.45 3.61
3193 3378 4.339247 CCTCAACCATAATACAAGGCCTTG 59.661 45.833 38.30 38.30 45.58 3.61
3194 3379 4.229582 TCCTCAACCATAATACAAGGCCTT 59.770 41.667 13.78 13.78 0.00 4.35
3195 3380 3.785887 TCCTCAACCATAATACAAGGCCT 59.214 43.478 0.00 0.00 0.00 5.19
3208 3393 3.394274 TCTCACAGGAAAATCCTCAACCA 59.606 43.478 0.00 0.00 45.66 3.67
3215 3400 5.189180 AGCTTGTATCTCACAGGAAAATCC 58.811 41.667 0.00 0.00 38.72 3.01
3262 3447 3.627395 ACTGTAATCTGATCGCCCAAA 57.373 42.857 0.00 0.00 0.00 3.28
3266 3451 4.041740 TGTGTACTGTAATCTGATCGCC 57.958 45.455 0.00 0.00 0.00 5.54
3346 3531 3.853671 GCTGAATACTTTTGTGGAATGCG 59.146 43.478 0.00 0.00 0.00 4.73
3361 3546 8.334263 TGTCATTTCACTAACAATGCTGAATA 57.666 30.769 0.00 0.00 31.47 1.75
3528 3713 2.764572 AGTTTACGGAGGGAGTACATGG 59.235 50.000 0.00 0.00 0.00 3.66
3532 3717 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
3533 3718 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
3534 3719 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
3535 3720 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
3536 3721 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3537 3722 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3538 3723 6.072286 TCCGCTCTTATATTAGTTTACGGAGG 60.072 42.308 0.00 0.00 40.70 4.30
3539 3724 6.906659 TCCGCTCTTATATTAGTTTACGGAG 58.093 40.000 0.00 0.00 40.70 4.63
3540 3725 6.072286 CCTCCGCTCTTATATTAGTTTACGGA 60.072 42.308 12.72 12.72 43.08 4.69
3541 3726 6.091437 CCTCCGCTCTTATATTAGTTTACGG 58.909 44.000 0.00 0.00 38.27 4.02
3542 3727 6.072286 TCCCTCCGCTCTTATATTAGTTTACG 60.072 42.308 0.00 0.00 0.00 3.18
3543 3728 7.039853 ACTCCCTCCGCTCTTATATTAGTTTAC 60.040 40.741 0.00 0.00 0.00 2.01
3544 3729 7.008941 ACTCCCTCCGCTCTTATATTAGTTTA 58.991 38.462 0.00 0.00 0.00 2.01
3545 3730 5.839606 ACTCCCTCCGCTCTTATATTAGTTT 59.160 40.000 0.00 0.00 0.00 2.66
3546 3731 5.395611 ACTCCCTCCGCTCTTATATTAGTT 58.604 41.667 0.00 0.00 0.00 2.24
3547 3732 5.000570 ACTCCCTCCGCTCTTATATTAGT 57.999 43.478 0.00 0.00 0.00 2.24
3548 3733 6.181908 AGTACTCCCTCCGCTCTTATATTAG 58.818 44.000 0.00 0.00 0.00 1.73
3549 3734 6.137104 AGTACTCCCTCCGCTCTTATATTA 57.863 41.667 0.00 0.00 0.00 0.98
3550 3735 5.000570 AGTACTCCCTCCGCTCTTATATT 57.999 43.478 0.00 0.00 0.00 1.28
3551 3736 4.661247 AGTACTCCCTCCGCTCTTATAT 57.339 45.455 0.00 0.00 0.00 0.86
3552 3737 4.141321 TGAAGTACTCCCTCCGCTCTTATA 60.141 45.833 0.00 0.00 0.00 0.98
3553 3738 3.224269 GAAGTACTCCCTCCGCTCTTAT 58.776 50.000 0.00 0.00 0.00 1.73
3554 3739 2.025605 TGAAGTACTCCCTCCGCTCTTA 60.026 50.000 0.00 0.00 0.00 2.10
3555 3740 1.272536 TGAAGTACTCCCTCCGCTCTT 60.273 52.381 0.00 0.00 0.00 2.85
3556 3741 0.331954 TGAAGTACTCCCTCCGCTCT 59.668 55.000 0.00 0.00 0.00 4.09
3557 3742 0.456628 GTGAAGTACTCCCTCCGCTC 59.543 60.000 0.00 0.00 0.00 5.03
3558 3743 0.039911 AGTGAAGTACTCCCTCCGCT 59.960 55.000 0.00 0.00 33.17 5.52
3559 3744 0.896226 AAGTGAAGTACTCCCTCCGC 59.104 55.000 0.00 0.00 39.18 5.54
3560 3745 3.244112 ACAAAAGTGAAGTACTCCCTCCG 60.244 47.826 0.00 0.00 39.18 4.63
3561 3746 4.040584 AGACAAAAGTGAAGTACTCCCTCC 59.959 45.833 0.00 0.00 39.18 4.30
3562 3747 4.991687 CAGACAAAAGTGAAGTACTCCCTC 59.008 45.833 0.00 0.00 39.18 4.30
3563 3748 4.743955 GCAGACAAAAGTGAAGTACTCCCT 60.744 45.833 0.00 0.00 39.18 4.20
3564 3749 3.498777 GCAGACAAAAGTGAAGTACTCCC 59.501 47.826 0.00 0.00 39.18 4.30
3565 3750 4.127171 TGCAGACAAAAGTGAAGTACTCC 58.873 43.478 0.00 0.00 39.18 3.85
3566 3751 5.734855 TTGCAGACAAAAGTGAAGTACTC 57.265 39.130 0.00 0.00 39.18 2.59
3567 3752 5.009010 CCATTGCAGACAAAAGTGAAGTACT 59.991 40.000 0.00 0.00 39.77 2.73
3574 3759 4.935702 TCTTTCCATTGCAGACAAAAGTG 58.064 39.130 11.20 0.00 39.77 3.16
3601 3786 5.120986 GTCCGAGGAAGAAGAAGAATGTTTC 59.879 44.000 0.00 0.00 0.00 2.78
3723 3908 5.833131 ACACCACAACATCTTCCTTGTAATT 59.167 36.000 0.00 0.00 0.00 1.40
3727 3912 3.297134 ACACCACAACATCTTCCTTGT 57.703 42.857 0.00 0.00 0.00 3.16
3729 3914 3.897239 TGAACACCACAACATCTTCCTT 58.103 40.909 0.00 0.00 0.00 3.36
3739 3924 3.951775 AAGTTTGCTTGAACACCACAA 57.048 38.095 0.00 0.00 32.92 3.33
3754 3939 2.035832 CCGAATTGCCACCTTCAAGTTT 59.964 45.455 0.00 0.00 0.00 2.66
3765 3950 1.653094 GATGAACGCCCGAATTGCCA 61.653 55.000 0.00 0.00 0.00 4.92
3770 3955 1.904771 TCAGGATGAACGCCCGAAT 59.095 52.632 0.00 0.00 45.97 3.34
3785 3970 4.574013 GCAATTGTAATGGGTCTCTCTCAG 59.426 45.833 7.40 0.00 0.00 3.35
3799 3984 0.606944 AGGAACGGCGGCAATTGTAA 60.607 50.000 13.24 0.00 0.00 2.41
3800 3985 1.003112 AGGAACGGCGGCAATTGTA 60.003 52.632 13.24 0.00 0.00 2.41
3809 4010 2.125912 CAGGTCTGAGGAACGGCG 60.126 66.667 4.80 4.80 33.70 6.46
3881 4082 7.538678 GTAGATACTTCTACGGTGAACGAAAAA 59.461 37.037 0.00 0.00 43.59 1.94
3882 4083 7.023575 GTAGATACTTCTACGGTGAACGAAAA 58.976 38.462 0.00 0.00 43.59 2.29
3883 4084 6.546395 GTAGATACTTCTACGGTGAACGAAA 58.454 40.000 0.00 0.00 43.59 3.46
3884 4085 6.111768 GTAGATACTTCTACGGTGAACGAA 57.888 41.667 0.00 0.00 43.59 3.85
3885 4086 5.725110 GTAGATACTTCTACGGTGAACGA 57.275 43.478 0.00 0.00 43.59 3.85
3935 4136 6.549952 CCTGAACTTCTGTAATTCATTGAGC 58.450 40.000 0.00 0.00 32.16 4.26
3995 4196 9.657419 AAGATTTTCTCAACACAATTTTCAACT 57.343 25.926 0.00 0.00 0.00 3.16
4006 4207 6.851222 TGAGACTCAAGATTTTCTCAACAC 57.149 37.500 1.64 0.00 41.16 3.32
4037 4238 4.336433 GGAAATATCACCTCCACACATGTG 59.664 45.833 24.25 24.25 45.23 3.21
4038 4239 4.526970 GGAAATATCACCTCCACACATGT 58.473 43.478 0.00 0.00 0.00 3.21
4039 4240 3.561310 CGGAAATATCACCTCCACACATG 59.439 47.826 0.00 0.00 0.00 3.21
4040 4241 3.199946 ACGGAAATATCACCTCCACACAT 59.800 43.478 0.00 0.00 0.00 3.21
4050 7890 3.557595 CCAGCAAGAGACGGAAATATCAC 59.442 47.826 0.00 0.00 0.00 3.06
4051 7891 3.797039 CCAGCAAGAGACGGAAATATCA 58.203 45.455 0.00 0.00 0.00 2.15
4080 7955 6.260936 GCATATTATCGGATTCCCCAATACAG 59.739 42.308 0.00 0.00 34.14 2.74
4146 8038 3.072211 GTTTTCTAACCCGAGTTGGAGG 58.928 50.000 0.00 0.00 43.41 4.30
4226 8118 3.305813 GGAACATATATCTGCGGTTCGGA 60.306 47.826 0.00 0.00 38.90 4.55
4238 8130 4.042809 TGCGGAGGAATTGGGAACATATAT 59.957 41.667 0.00 0.00 42.32 0.86
4259 8151 1.202698 ACCTTCCAGAACACACTCTGC 60.203 52.381 0.00 0.00 41.36 4.26
4267 8159 3.572642 TCTGTGACTACCTTCCAGAACA 58.427 45.455 0.00 0.00 0.00 3.18
4309 8201 1.632920 TGAGTATGACATGTGGGCCAA 59.367 47.619 8.40 0.00 0.00 4.52
4334 8234 0.039074 ACGAGAGGAAGCAGTTCACG 60.039 55.000 0.00 0.00 33.93 4.35
4338 8238 1.270907 ATCCACGAGAGGAAGCAGTT 58.729 50.000 0.00 0.00 41.92 3.16
4356 8256 7.227156 TGCAATTGGTTGGGTGTTTATTAAAT 58.773 30.769 7.72 0.00 35.83 1.40
4395 8295 1.200020 GAAGGACAAAACCATGAGCCG 59.800 52.381 0.00 0.00 0.00 5.52
4428 8328 4.909088 TCCTTCCTTCTTGGTTTGGTAGTA 59.091 41.667 0.00 0.00 37.07 1.82
4431 8331 3.460340 TGTCCTTCCTTCTTGGTTTGGTA 59.540 43.478 0.00 0.00 37.07 3.25
4433 8333 2.623416 GTGTCCTTCCTTCTTGGTTTGG 59.377 50.000 0.00 0.00 37.07 3.28
4434 8334 3.287222 TGTGTCCTTCCTTCTTGGTTTG 58.713 45.455 0.00 0.00 37.07 2.93
4438 8372 1.202806 TGCTGTGTCCTTCCTTCTTGG 60.203 52.381 0.00 0.00 37.10 3.61
4439 8373 1.876156 GTGCTGTGTCCTTCCTTCTTG 59.124 52.381 0.00 0.00 0.00 3.02
4444 8378 0.109342 CCTTGTGCTGTGTCCTTCCT 59.891 55.000 0.00 0.00 0.00 3.36
4466 8400 2.052468 CCCCAGATGTCAGATGGATCA 58.948 52.381 7.52 0.00 36.09 2.92
4486 8420 1.000843 GTGGGACCAAATTCAGGTTGC 59.999 52.381 4.24 0.00 40.09 4.17
4494 8428 1.228003 TGACGCGTGGGACCAAATT 60.228 52.632 20.70 0.00 0.00 1.82
4629 8563 1.631898 TGGGTAAGAGTTTAGGTGGGC 59.368 52.381 0.00 0.00 0.00 5.36
4636 8570 2.564062 CGGAGGTGTGGGTAAGAGTTTA 59.436 50.000 0.00 0.00 0.00 2.01
4638 8572 0.974383 CGGAGGTGTGGGTAAGAGTT 59.026 55.000 0.00 0.00 0.00 3.01
4639 8573 1.542187 GCGGAGGTGTGGGTAAGAGT 61.542 60.000 0.00 0.00 0.00 3.24
4643 8577 3.697747 CGGCGGAGGTGTGGGTAA 61.698 66.667 0.00 0.00 0.00 2.85
4651 8585 3.039988 CGATGTATCGGCGGAGGT 58.960 61.111 7.21 0.00 45.93 3.85


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

AutoCloner maintained by Alex Coulton.