Multiple sequence alignment - TraesCS7B01G047500

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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 TraesCS7B01G047500 chr7B 100.000 4221 0 0 1 4221 46996623 47000843 0.000000e+00 7795.0
1 TraesCS7B01G047500 chr7B 87.069 116 15 0 4106 4221 690752651 690752766 9.520000e-27 132.0
2 TraesCS7B01G047500 chr7B 100.000 37 0 0 1699 1735 290959649 290959685 7.570000e-08 69.4
3 TraesCS7B01G047500 chr7D 92.475 1701 77 17 2537 4221 93787231 93788896 0.000000e+00 2385.0
4 TraesCS7B01G047500 chr7D 91.319 887 40 14 818 1693 93785434 93786294 0.000000e+00 1177.0
5 TraesCS7B01G047500 chr7D 90.177 621 53 6 1699 2318 93786362 93786975 0.000000e+00 802.0
6 TraesCS7B01G047500 chr7D 87.160 662 50 15 1 636 93784697 93785349 0.000000e+00 719.0
7 TraesCS7B01G047500 chr7D 86.607 112 15 0 4110 4221 606638404 606638293 1.590000e-24 124.0
8 TraesCS7B01G047500 chr7A 95.046 969 40 6 2537 3502 96564755 96565718 0.000000e+00 1517.0
9 TraesCS7B01G047500 chr7A 90.433 878 37 18 830 1693 96562907 96563751 0.000000e+00 1112.0
10 TraesCS7B01G047500 chr7A 89.116 588 47 10 1738 2318 96563920 96564497 0.000000e+00 715.0
11 TraesCS7B01G047500 chr7A 90.155 386 18 8 3843 4221 96567357 96567729 6.350000e-133 484.0
12 TraesCS7B01G047500 chr7A 88.571 315 10 5 3538 3847 96566230 96566523 4.010000e-95 359.0
13 TraesCS7B01G047500 chr7A 94.488 127 5 2 38 163 96560499 96560624 1.200000e-45 195.0
14 TraesCS7B01G047500 chr7A 92.135 89 5 2 257 344 96562192 96562279 1.590000e-24 124.0
15 TraesCS7B01G047500 chr7A 86.607 112 15 0 4110 4221 698677123 698677234 1.590000e-24 124.0
16 TraesCS7B01G047500 chr7A 91.935 62 3 2 153 213 96561775 96561835 7.520000e-13 86.1
17 TraesCS7B01G047500 chr7A 100.000 36 0 0 1 36 96560260 96560295 2.720000e-07 67.6
18 TraesCS7B01G047500 chr7A 84.746 59 5 4 1699 1754 20100275 20100218 5.900000e-04 56.5
19 TraesCS7B01G047500 chr4B 96.939 98 2 1 2537 2633 77297395 77297492 3.380000e-36 163.0
20 TraesCS7B01G047500 chr6D 85.841 113 16 0 4109 4221 443846995 443847107 2.060000e-23 121.0
21 TraesCS7B01G047500 chr2D 90.909 88 7 1 3770 3856 208540231 208540144 2.670000e-22 117.0
22 TraesCS7B01G047500 chr2D 89.796 49 3 2 1699 1746 340262140 340262187 1.270000e-05 62.1
23 TraesCS7B01G047500 chr6A 86.538 104 14 0 4109 4212 591437049 591437152 9.590000e-22 115.0
24 TraesCS7B01G047500 chr6A 85.577 104 15 0 4109 4212 591436032 591436135 4.460000e-20 110.0
25 TraesCS7B01G047500 chr6B 91.566 83 6 1 3775 3856 642350318 642350236 3.450000e-21 113.0
26 TraesCS7B01G047500 chr6B 85.577 104 15 0 4109 4212 668247617 668247720 4.460000e-20 110.0
27 TraesCS7B01G047500 chr3B 89.130 92 8 2 3767 3856 429973520 429973611 3.450000e-21 113.0
28 TraesCS7B01G047500 chr3B 88.889 90 9 1 3771 3859 44742114 44742025 4.460000e-20 110.0
29 TraesCS7B01G047500 chr3B 89.655 87 8 1 3771 3856 62394194 62394280 4.460000e-20 110.0
30 TraesCS7B01G047500 chr3B 100.000 37 0 0 1699 1735 578595766 578595730 7.570000e-08 69.4
31 TraesCS7B01G047500 chr5B 89.011 91 9 1 3768 3857 604056463 604056373 1.240000e-20 111.0
32 TraesCS7B01G047500 chr4A 89.773 88 5 3 3770 3855 149042766 149042851 4.460000e-20 110.0
33 TraesCS7B01G047500 chr5D 83.168 101 9 3 1943 2043 86759659 86759567 7.520000e-13 86.1
34 TraesCS7B01G047500 chr1D 95.349 43 2 0 1699 1741 305589085 305589043 7.570000e-08 69.4
35 TraesCS7B01G047500 chr1A 95.349 43 2 0 1699 1741 384334634 384334592 7.570000e-08 69.4
36 TraesCS7B01G047500 chr4D 93.333 45 3 0 1699 1743 119751885 119751929 2.720000e-07 67.6
37 TraesCS7B01G047500 chr3A 90.000 50 4 1 1699 1747 539706 539755 3.520000e-06 63.9


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 TraesCS7B01G047500 chr7B 46996623 47000843 4220 False 7795.000000 7795 100.00000 1 4221 1 chr7B.!!$F1 4220
1 TraesCS7B01G047500 chr7D 93784697 93788896 4199 False 1270.750000 2385 90.28275 1 4221 4 chr7D.!!$F1 4220
2 TraesCS7B01G047500 chr7A 96560260 96567729 7469 False 517.744444 1517 92.43100 1 4221 9 chr7A.!!$F2 4220

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
791 2529 0.619255 TTTGAGGGGGTGAGCGGATA 60.619 55.0 0.00 0.0 0.00 2.59 F
1656 3864 0.249868 GCGATGGTCGGGATGATGAA 60.250 55.0 1.29 0.0 40.84 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 3901 0.370273 GCTCAAACGGATGTAGCGTG 59.630 55.0 0.00 0.00 0.00 5.34 R
3378 5775 0.248621 GACTATTTGCCGTGCATGCC 60.249 55.0 16.68 5.63 38.76 4.40 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
46 249 1.127397 GACGCTTACTAACGGGCAAAC 59.873 52.381 0.00 0.00 0.00 2.93
209 1740 2.307496 TTGCCATGGTGGATGTTCTT 57.693 45.000 14.67 0.00 40.96 2.52
231 1762 7.079700 TCTTAGATAACCTCATCCCAACCATA 58.920 38.462 0.00 0.00 0.00 2.74
232 1763 5.568620 AGATAACCTCATCCCAACCATAC 57.431 43.478 0.00 0.00 0.00 2.39
257 1788 5.888161 GTGGATGCCCCCATTTATATTCTAG 59.112 44.000 0.00 0.00 38.66 2.43
259 1790 6.738086 TGGATGCCCCCATTTATATTCTAGTA 59.262 38.462 0.00 0.00 0.00 1.82
300 1979 7.789273 TTGCTCACAAAATGATCATGTTTTT 57.211 28.000 9.46 4.31 36.48 1.94
351 2030 9.941664 CATTATATCTTGTTCTCAATGGTGTTC 57.058 33.333 0.00 0.00 32.82 3.18
356 2035 3.750371 TGTTCTCAATGGTGTTCCGAAT 58.250 40.909 0.00 0.00 36.30 3.34
369 2048 3.127376 TGTTCCGAATGATTGTGCTCATG 59.873 43.478 0.00 0.00 36.03 3.07
379 2058 4.590222 TGATTGTGCTCATGAGGCTCTATA 59.410 41.667 23.89 0.00 0.00 1.31
388 2067 6.398234 TCATGAGGCTCTATACAGTTCTTC 57.602 41.667 16.72 0.00 0.00 2.87
416 2096 1.994074 GCATTTGCGTGCATCAATGAA 59.006 42.857 18.58 1.00 44.43 2.57
423 2108 1.068402 CGTGCATCAATGAACAGGCAA 60.068 47.619 2.15 0.00 36.04 4.52
454 2139 5.823045 TGTGTTTTTCTCCCTCTTCTTCTTC 59.177 40.000 0.00 0.00 0.00 2.87
455 2140 6.058833 GTGTTTTTCTCCCTCTTCTTCTTCT 58.941 40.000 0.00 0.00 0.00 2.85
456 2141 6.544197 GTGTTTTTCTCCCTCTTCTTCTTCTT 59.456 38.462 0.00 0.00 0.00 2.52
457 2142 6.768381 TGTTTTTCTCCCTCTTCTTCTTCTTC 59.232 38.462 0.00 0.00 0.00 2.87
470 2155 4.223700 TCTTCTTCTTCAGCTAGATTGCCA 59.776 41.667 0.00 0.00 0.00 4.92
477 2162 4.142609 TCAGCTAGATTGCCAAGGTTAG 57.857 45.455 0.00 0.00 0.00 2.34
502 2200 7.399191 AGGTACATGTACTTGAGACCTGATTAA 59.601 37.037 29.89 0.00 36.10 1.40
514 2212 8.099364 TGAGACCTGATTAAAATGAAGTTGTC 57.901 34.615 0.00 0.00 0.00 3.18
520 2218 5.240623 TGATTAAAATGAAGTTGTCGGTGCT 59.759 36.000 0.00 0.00 0.00 4.40
535 2233 2.985847 GCTTTGTGCGCCTTCCCT 60.986 61.111 4.18 0.00 0.00 4.20
643 2381 4.944962 TGGCATAATGAGTTGTCTTTCG 57.055 40.909 0.00 0.00 0.00 3.46
670 2408 2.353323 CCCTTTTTGTAGGCGTAGTCC 58.647 52.381 0.00 0.00 33.73 3.85
676 2414 3.756933 TTGTAGGCGTAGTCCACTTTT 57.243 42.857 0.00 0.00 0.00 2.27
677 2415 3.756933 TGTAGGCGTAGTCCACTTTTT 57.243 42.857 0.00 0.00 0.00 1.94
702 2440 7.979444 TTTAAGGAACAGACAGAAATAGTGG 57.021 36.000 0.00 0.00 0.00 4.00
703 2441 3.944087 AGGAACAGACAGAAATAGTGGC 58.056 45.455 0.00 0.00 0.00 5.01
704 2442 3.584848 AGGAACAGACAGAAATAGTGGCT 59.415 43.478 0.00 0.00 31.38 4.75
705 2443 4.777896 AGGAACAGACAGAAATAGTGGCTA 59.222 41.667 0.00 0.00 29.58 3.93
706 2444 5.426833 AGGAACAGACAGAAATAGTGGCTAT 59.573 40.000 0.00 0.00 29.58 2.97
707 2445 6.069963 AGGAACAGACAGAAATAGTGGCTATT 60.070 38.462 0.00 0.00 38.17 1.73
708 2446 6.599638 GGAACAGACAGAAATAGTGGCTATTT 59.400 38.462 12.31 12.31 45.66 1.40
709 2447 7.121315 GGAACAGACAGAAATAGTGGCTATTTT 59.879 37.037 13.32 1.32 43.84 1.82
710 2448 8.409358 AACAGACAGAAATAGTGGCTATTTTT 57.591 30.769 13.32 7.07 43.84 1.94
787 2525 4.492604 TTTTTGAGGGGGTGAGCG 57.507 55.556 0.00 0.00 0.00 5.03
788 2526 1.228429 TTTTTGAGGGGGTGAGCGG 60.228 57.895 0.00 0.00 0.00 5.52
791 2529 0.619255 TTTGAGGGGGTGAGCGGATA 60.619 55.000 0.00 0.00 0.00 2.59
792 2530 1.335132 TTGAGGGGGTGAGCGGATAC 61.335 60.000 0.00 0.00 0.00 2.24
798 2540 2.014857 GGGGTGAGCGGATACTTTTTC 58.985 52.381 0.00 0.00 0.00 2.29
799 2541 2.355818 GGGGTGAGCGGATACTTTTTCT 60.356 50.000 0.00 0.00 0.00 2.52
816 2558 2.479566 TCTGTGTCTTGGATTCCAGC 57.520 50.000 5.36 1.71 33.81 4.85
903 3095 1.132689 CCCTACCCCTCTATTCCTGCT 60.133 57.143 0.00 0.00 0.00 4.24
1027 3224 1.681666 CCTCACAGCACACATCCCT 59.318 57.895 0.00 0.00 0.00 4.20
1048 3245 4.416601 CTCCCCTTCCTCCCCGGT 62.417 72.222 0.00 0.00 0.00 5.28
1084 3281 3.408501 CTCGGCTCGTGCTCCAGAG 62.409 68.421 9.61 9.29 39.59 3.35
1216 3413 1.394151 CTCCTCAAGGTCCCCTCCT 59.606 63.158 0.00 0.00 39.84 3.69
1219 3416 0.689412 CCTCAAGGTCCCCTCCTCTC 60.689 65.000 0.00 0.00 36.74 3.20
1220 3417 0.689412 CTCAAGGTCCCCTCCTCTCC 60.689 65.000 0.00 0.00 36.74 3.71
1221 3418 1.156322 TCAAGGTCCCCTCCTCTCCT 61.156 60.000 0.00 0.00 36.74 3.69
1222 3419 0.689412 CAAGGTCCCCTCCTCTCCTC 60.689 65.000 0.00 0.00 36.74 3.71
1223 3420 0.858139 AAGGTCCCCTCCTCTCCTCT 60.858 60.000 0.00 0.00 36.74 3.69
1224 3421 0.858139 AGGTCCCCTCCTCTCCTCTT 60.858 60.000 0.00 0.00 31.32 2.85
1225 3422 0.397957 GGTCCCCTCCTCTCCTCTTC 60.398 65.000 0.00 0.00 0.00 2.87
1226 3423 0.634465 GTCCCCTCCTCTCCTCTTCT 59.366 60.000 0.00 0.00 0.00 2.85
1227 3424 1.854280 GTCCCCTCCTCTCCTCTTCTA 59.146 57.143 0.00 0.00 0.00 2.10
1228 3425 1.854280 TCCCCTCCTCTCCTCTTCTAC 59.146 57.143 0.00 0.00 0.00 2.59
1229 3426 1.856920 CCCCTCCTCTCCTCTTCTACT 59.143 57.143 0.00 0.00 0.00 2.57
1230 3427 2.158519 CCCCTCCTCTCCTCTTCTACTC 60.159 59.091 0.00 0.00 0.00 2.59
1231 3428 2.158519 CCCTCCTCTCCTCTTCTACTCC 60.159 59.091 0.00 0.00 0.00 3.85
1252 3449 2.666317 CCCCCTGGCCTTATTTACTTG 58.334 52.381 3.32 0.00 0.00 3.16
1327 3528 2.203337 TGCAGCAAAGCCCGAAGT 60.203 55.556 0.00 0.00 0.00 3.01
1416 3617 1.112113 GGCTTCTCCATCCGTACTCA 58.888 55.000 0.00 0.00 34.01 3.41
1419 3620 2.100197 CTTCTCCATCCGTACTCACCA 58.900 52.381 0.00 0.00 0.00 4.17
1427 3628 1.345415 TCCGTACTCACCAAAAGGTCC 59.655 52.381 0.00 0.00 0.00 4.46
1476 3677 6.867550 TCTGTCTTCCACTCACTATATTGTG 58.132 40.000 10.61 10.61 39.15 3.33
1477 3678 6.663523 TCTGTCTTCCACTCACTATATTGTGA 59.336 38.462 17.27 17.27 43.72 3.58
1513 3721 4.568760 GTCCAGCTCTAGCATAAGTTTGAC 59.431 45.833 4.54 0.00 45.16 3.18
1528 3736 5.443185 AGTTTGACAGACACATGGATTTG 57.557 39.130 0.00 0.00 0.00 2.32
1560 3768 0.612229 CAGCCAAGCTTCTCTGGAGA 59.388 55.000 6.34 0.00 36.40 3.71
1638 3846 1.155042 GAATCGCTGGATCAGATGGC 58.845 55.000 0.00 0.00 32.44 4.40
1656 3864 0.249868 GCGATGGTCGGGATGATGAA 60.250 55.000 1.29 0.00 40.84 2.57
1693 3901 4.590850 AGGCAATCAGTTTTTCCTTGTC 57.409 40.909 0.00 0.00 0.00 3.18
1694 3902 3.960102 AGGCAATCAGTTTTTCCTTGTCA 59.040 39.130 0.00 0.00 0.00 3.58
1696 3904 3.730715 GCAATCAGTTTTTCCTTGTCACG 59.269 43.478 0.00 0.00 0.00 4.35
1697 3905 3.626028 ATCAGTTTTTCCTTGTCACGC 57.374 42.857 0.00 0.00 0.00 5.34
1714 4010 2.750815 GCTACATCCGTTTGAGCGT 58.249 52.632 0.00 0.00 0.00 5.07
1727 4056 5.204833 CGTTTGAGCGTCAATTAATATGGG 58.795 41.667 0.00 0.00 36.11 4.00
1729 4058 6.293407 CGTTTGAGCGTCAATTAATATGGGAT 60.293 38.462 0.00 0.00 36.11 3.85
1792 4127 9.000486 GTTTGGCCTATTGATAAGTATACCTTC 58.000 37.037 3.32 0.00 34.46 3.46
2016 4352 1.532523 TGATTCGGATGCTGCACAAA 58.467 45.000 3.57 0.00 0.00 2.83
2089 4425 3.788227 AGCACTGAACATCAACCCTAA 57.212 42.857 0.00 0.00 0.00 2.69
2099 4435 9.793252 CTGAACATCAACCCTAAGAAATATTTG 57.207 33.333 5.17 0.00 0.00 2.32
2117 4453 2.941333 CAGGTGCTGCACGAGTTG 59.059 61.111 24.86 16.28 34.83 3.16
2138 4474 2.975851 GCTGCTTTTGTTTCATCGTCAG 59.024 45.455 0.00 0.00 0.00 3.51
2139 4475 3.548818 GCTGCTTTTGTTTCATCGTCAGT 60.549 43.478 0.00 0.00 0.00 3.41
2146 4482 4.955925 TGTTTCATCGTCAGTTGTTTGT 57.044 36.364 0.00 0.00 0.00 2.83
2150 4486 7.129622 TGTTTCATCGTCAGTTGTTTGTTATC 58.870 34.615 0.00 0.00 0.00 1.75
2155 4491 9.214957 TCATCGTCAGTTGTTTGTTATCTTATT 57.785 29.630 0.00 0.00 0.00 1.40
2156 4492 9.265938 CATCGTCAGTTGTTTGTTATCTTATTG 57.734 33.333 0.00 0.00 0.00 1.90
2158 4494 8.832521 TCGTCAGTTGTTTGTTATCTTATTGTT 58.167 29.630 0.00 0.00 0.00 2.83
2159 4495 8.891928 CGTCAGTTGTTTGTTATCTTATTGTTG 58.108 33.333 0.00 0.00 0.00 3.33
2160 4496 9.180678 GTCAGTTGTTTGTTATCTTATTGTTGG 57.819 33.333 0.00 0.00 0.00 3.77
2161 4497 8.908903 TCAGTTGTTTGTTATCTTATTGTTGGT 58.091 29.630 0.00 0.00 0.00 3.67
2178 4514 7.389803 TTGTTGGTATGTTCATATGTTGAGG 57.610 36.000 1.90 0.00 35.27 3.86
2188 4524 6.127925 TGTTCATATGTTGAGGCACTTCATTC 60.128 38.462 1.90 0.00 41.55 2.67
2212 4548 2.162408 GTGCTTCTGTAGGCATTGTTCC 59.838 50.000 0.00 0.00 40.66 3.62
2213 4549 2.040278 TGCTTCTGTAGGCATTGTTCCT 59.960 45.455 0.00 0.00 37.72 3.36
2217 4553 1.131126 CTGTAGGCATTGTTCCTTGCG 59.869 52.381 0.00 0.00 39.78 4.85
2227 4563 1.957177 TGTTCCTTGCGTGCCAAAATA 59.043 42.857 0.00 0.00 31.94 1.40
2246 4582 2.610438 ATGGCCAAGGAAACATCTGT 57.390 45.000 10.96 0.00 0.00 3.41
2247 4583 3.737559 ATGGCCAAGGAAACATCTGTA 57.262 42.857 10.96 0.00 0.00 2.74
2250 4586 3.010027 TGGCCAAGGAAACATCTGTATCA 59.990 43.478 0.61 0.00 0.00 2.15
2251 4587 3.378427 GGCCAAGGAAACATCTGTATCAC 59.622 47.826 0.00 0.00 0.00 3.06
2261 4597 3.840666 ACATCTGTATCACCCAGTGAACT 59.159 43.478 0.91 0.00 45.96 3.01
2318 4654 9.146984 CGATAATCTACAACAACTTTCAGGTAA 57.853 33.333 0.00 0.00 0.00 2.85
2322 4658 7.781548 TCTACAACAACTTTCAGGTAAACTC 57.218 36.000 0.00 0.00 0.00 3.01
2323 4659 7.332557 TCTACAACAACTTTCAGGTAAACTCA 58.667 34.615 0.00 0.00 0.00 3.41
2324 4660 6.190954 ACAACAACTTTCAGGTAAACTCAC 57.809 37.500 0.00 0.00 0.00 3.51
2325 4661 5.163794 ACAACAACTTTCAGGTAAACTCACG 60.164 40.000 0.00 0.00 0.00 4.35
2326 4662 4.510571 ACAACTTTCAGGTAAACTCACGT 58.489 39.130 0.00 0.00 0.00 4.49
2327 4663 4.331717 ACAACTTTCAGGTAAACTCACGTG 59.668 41.667 9.94 9.94 36.00 4.49
2328 4664 2.870411 ACTTTCAGGTAAACTCACGTGC 59.130 45.455 11.67 0.00 34.95 5.34
2329 4665 2.605837 TTCAGGTAAACTCACGTGCA 57.394 45.000 11.67 0.00 34.95 4.57
2331 4667 3.120321 TCAGGTAAACTCACGTGCAAT 57.880 42.857 11.67 0.00 34.95 3.56
2333 4669 3.880490 TCAGGTAAACTCACGTGCAATTT 59.120 39.130 11.67 12.89 34.95 1.82
2334 4670 4.336993 TCAGGTAAACTCACGTGCAATTTT 59.663 37.500 11.67 9.35 34.95 1.82
2336 4672 3.662186 GGTAAACTCACGTGCAATTTTCG 59.338 43.478 11.67 0.00 0.00 3.46
2338 4674 3.684103 AACTCACGTGCAATTTTCGAA 57.316 38.095 11.67 0.00 0.00 3.71
2343 4679 4.416620 TCACGTGCAATTTTCGAAAAAGT 58.583 34.783 25.77 14.67 0.00 2.66
2344 4680 4.859798 TCACGTGCAATTTTCGAAAAAGTT 59.140 33.333 25.77 14.51 0.00 2.66
2345 4681 5.003967 TCACGTGCAATTTTCGAAAAAGTTC 59.996 36.000 25.77 15.40 0.00 3.01
2346 4682 5.004345 CACGTGCAATTTTCGAAAAAGTTCT 59.996 36.000 25.77 7.60 0.00 3.01
2347 4683 5.575218 ACGTGCAATTTTCGAAAAAGTTCTT 59.425 32.000 25.77 13.12 0.00 2.52
2350 4686 6.894517 GTGCAATTTTCGAAAAAGTTCTTGAC 59.105 34.615 26.38 19.93 0.00 3.18
2351 4687 6.811170 TGCAATTTTCGAAAAAGTTCTTGACT 59.189 30.769 26.38 8.56 41.47 3.41
2352 4688 7.009174 TGCAATTTTCGAAAAAGTTCTTGACTC 59.991 33.333 26.38 15.23 37.72 3.36
2354 4690 9.716507 CAATTTTCGAAAAAGTTCTTGACTCTA 57.283 29.630 25.77 0.00 37.72 2.43
2356 4692 7.837202 TTTCGAAAAAGTTCTTGACTCTACA 57.163 32.000 8.44 0.00 37.72 2.74
2357 4693 7.837202 TTCGAAAAAGTTCTTGACTCTACAA 57.163 32.000 0.00 0.00 37.72 2.41
2360 4696 9.706691 TCGAAAAAGTTCTTGACTCTACAATAT 57.293 29.630 0.00 0.00 37.72 1.28
2386 4748 4.813027 ACTCTACATTTTGGCTTTGCATG 58.187 39.130 0.00 0.00 0.00 4.06
2390 4752 2.147958 CATTTTGGCTTTGCATGCACT 58.852 42.857 22.58 0.00 0.00 4.40
2397 4759 3.181467 TGGCTTTGCATGCACTTTAAACT 60.181 39.130 22.58 0.00 0.00 2.66
2398 4760 3.184986 GGCTTTGCATGCACTTTAAACTG 59.815 43.478 22.58 1.97 0.00 3.16
2399 4761 4.050553 GCTTTGCATGCACTTTAAACTGA 58.949 39.130 22.58 0.00 0.00 3.41
2400 4762 4.507388 GCTTTGCATGCACTTTAAACTGAA 59.493 37.500 22.58 6.92 0.00 3.02
2401 4763 5.006552 GCTTTGCATGCACTTTAAACTGAAA 59.993 36.000 22.58 6.36 0.00 2.69
2402 4764 6.293027 GCTTTGCATGCACTTTAAACTGAAAT 60.293 34.615 22.58 0.00 0.00 2.17
2403 4765 7.551035 TTTGCATGCACTTTAAACTGAAATT 57.449 28.000 22.58 0.00 0.00 1.82
2405 4767 8.830201 TTGCATGCACTTTAAACTGAAATTAT 57.170 26.923 22.58 0.00 0.00 1.28
2406 4768 9.920133 TTGCATGCACTTTAAACTGAAATTATA 57.080 25.926 22.58 0.00 0.00 0.98
2407 4769 9.571810 TGCATGCACTTTAAACTGAAATTATAG 57.428 29.630 18.46 0.00 0.00 1.31
2408 4770 9.573133 GCATGCACTTTAAACTGAAATTATAGT 57.427 29.630 14.21 0.00 0.00 2.12
2422 4784 8.506168 TGAAATTATAGTTGATGAACCACCTC 57.494 34.615 0.00 0.00 31.81 3.85
2424 4786 9.125026 GAAATTATAGTTGATGAACCACCTCAT 57.875 33.333 0.00 0.00 38.79 2.90
2425 4787 8.455903 AATTATAGTTGATGAACCACCTCATG 57.544 34.615 0.00 0.00 36.15 3.07
2426 4788 2.440409 AGTTGATGAACCACCTCATGC 58.560 47.619 0.00 0.00 36.15 4.06
2427 4789 2.040813 AGTTGATGAACCACCTCATGCT 59.959 45.455 0.00 0.00 36.15 3.79
2428 4790 3.264193 AGTTGATGAACCACCTCATGCTA 59.736 43.478 0.00 0.00 36.15 3.49
2429 4791 3.998913 TGATGAACCACCTCATGCTAA 57.001 42.857 0.00 0.00 36.15 3.09
2430 4792 4.299586 TGATGAACCACCTCATGCTAAA 57.700 40.909 0.00 0.00 36.15 1.85
2431 4793 4.264253 TGATGAACCACCTCATGCTAAAG 58.736 43.478 0.00 0.00 36.15 1.85
2432 4794 4.019411 TGATGAACCACCTCATGCTAAAGA 60.019 41.667 0.00 0.00 36.15 2.52
2433 4795 3.942829 TGAACCACCTCATGCTAAAGAG 58.057 45.455 0.00 0.00 0.00 2.85
2434 4796 3.582647 TGAACCACCTCATGCTAAAGAGA 59.417 43.478 0.00 0.00 33.74 3.10
2435 4797 4.041567 TGAACCACCTCATGCTAAAGAGAA 59.958 41.667 0.00 0.00 33.74 2.87
2436 4798 4.213564 ACCACCTCATGCTAAAGAGAAG 57.786 45.455 0.00 0.00 33.74 2.85
2437 4799 2.941720 CCACCTCATGCTAAAGAGAAGC 59.058 50.000 0.00 0.00 40.50 3.86
2438 4800 2.606725 CACCTCATGCTAAAGAGAAGCG 59.393 50.000 0.00 0.00 43.11 4.68
2439 4801 2.234908 ACCTCATGCTAAAGAGAAGCGT 59.765 45.455 0.00 0.00 43.11 5.07
2440 4802 2.863137 CCTCATGCTAAAGAGAAGCGTC 59.137 50.000 0.00 0.00 43.11 5.19
2441 4803 3.515630 CTCATGCTAAAGAGAAGCGTCA 58.484 45.455 1.61 0.00 43.11 4.35
2442 4804 3.925379 TCATGCTAAAGAGAAGCGTCAA 58.075 40.909 1.61 0.00 43.11 3.18
2443 4805 4.507710 TCATGCTAAAGAGAAGCGTCAAT 58.492 39.130 1.61 0.00 43.11 2.57
2533 4913 9.528018 AAATTGTGTTAAGAGTACCAACATTTG 57.472 29.630 0.00 0.00 34.89 2.32
2535 4915 7.633193 TGTGTTAAGAGTACCAACATTTGTT 57.367 32.000 0.00 0.00 39.12 2.83
2541 4921 9.575868 TTAAGAGTACCAACATTTGTTTATCCA 57.424 29.630 0.00 0.00 35.83 3.41
2542 4922 8.472007 AAGAGTACCAACATTTGTTTATCCAA 57.528 30.769 0.00 0.00 35.83 3.53
2543 4923 7.882179 AGAGTACCAACATTTGTTTATCCAAC 58.118 34.615 0.00 0.00 35.83 3.77
2545 4925 8.189119 AGTACCAACATTTGTTTATCCAACAT 57.811 30.769 0.00 0.00 45.17 2.71
2636 5032 5.763876 ATAAGTTGCCTCTTAGAACCTGT 57.236 39.130 4.51 0.00 34.12 4.00
2658 5054 6.946340 TGTAGAGGAGTTATTGCTGAATTCA 58.054 36.000 8.12 8.12 0.00 2.57
2672 5068 4.142227 GCTGAATTCAAACTGCCATCAGAT 60.142 41.667 9.88 0.00 42.95 2.90
2677 5073 3.273434 TCAAACTGCCATCAGATACAGC 58.727 45.455 11.07 3.20 42.95 4.40
2683 5079 2.224042 TGCCATCAGATACAGCGTAAGG 60.224 50.000 0.00 0.00 38.28 2.69
2721 5117 7.841956 AGTTGAGCTTACAGTCATTACAGTAT 58.158 34.615 0.00 0.00 28.94 2.12
2724 5120 8.011844 TGAGCTTACAGTCATTACAGTATCAT 57.988 34.615 0.00 0.00 28.94 2.45
2725 5121 9.131791 TGAGCTTACAGTCATTACAGTATCATA 57.868 33.333 0.00 0.00 28.94 2.15
2745 5141 5.545335 TCATATGGAACTATCTGATGGCTGT 59.455 40.000 2.13 0.00 0.00 4.40
2923 5319 0.750911 CAATGGAAGAGCTGCTCCCC 60.751 60.000 25.09 24.33 0.00 4.81
3070 5466 3.550437 ATAGGCGAGAGAAGCAATTGT 57.450 42.857 7.40 0.00 36.08 2.71
3124 5520 2.553904 GGGCCTCCTGTATCATGGATTG 60.554 54.545 0.84 0.00 0.00 2.67
3166 5562 3.607741 AGCTGTGATTTCCAGTGATGAG 58.392 45.455 0.00 0.00 32.41 2.90
3242 5638 6.419710 GTGAATACCGTATCGTGATTCATTCA 59.580 38.462 14.25 0.00 38.43 2.57
3254 5650 5.007921 CGTGATTCATTCAACCATGCTATCA 59.992 40.000 0.00 0.00 35.70 2.15
3282 5679 4.271807 TGTATCAGGGAGTTGGAGAGAT 57.728 45.455 0.00 0.00 0.00 2.75
3289 5686 3.012274 AGGGAGTTGGAGAGATCAAGAGA 59.988 47.826 0.00 0.00 0.00 3.10
3292 5689 5.358922 GGAGTTGGAGAGATCAAGAGAATG 58.641 45.833 0.00 0.00 0.00 2.67
3300 5697 5.231702 AGAGATCAAGAGAATGATGCGATG 58.768 41.667 0.00 0.00 40.08 3.84
3312 5709 1.374343 ATGCGATGCCTTCAGTGCAG 61.374 55.000 0.00 0.00 42.92 4.41
3331 5728 4.141505 TGCAGTTGCTTATATGAAGGGCTA 60.142 41.667 5.62 0.00 42.66 3.93
3359 5756 6.204688 GCATCATATCGAAACCTGAAACCATA 59.795 38.462 0.00 0.00 0.00 2.74
3362 5759 6.984474 TCATATCGAAACCTGAAACCATACTC 59.016 38.462 0.00 0.00 0.00 2.59
3401 5798 1.819928 TGCACGGCAAATAGTCACAT 58.180 45.000 0.00 0.00 34.76 3.21
3402 5799 1.468127 TGCACGGCAAATAGTCACATG 59.532 47.619 0.00 0.00 34.76 3.21
3428 5825 0.301687 GCTATGGATGTCGTGTTGCG 59.698 55.000 0.00 0.00 43.01 4.85
3473 5870 2.084546 GGAAGCTTGGTTAAGACGCAT 58.915 47.619 2.10 0.00 35.92 4.73
3590 6463 4.039973 TCGTGTTTCTGTAAACCTGAGGAT 59.960 41.667 4.99 0.00 43.66 3.24
3740 6615 1.131638 TAGGAGGTGCATTAGCCAGG 58.868 55.000 0.00 0.00 41.13 4.45
3741 6616 0.621571 AGGAGGTGCATTAGCCAGGA 60.622 55.000 0.00 0.00 41.13 3.86
3742 6617 0.475906 GGAGGTGCATTAGCCAGGAT 59.524 55.000 0.00 0.00 41.13 3.24
3743 6618 1.699634 GGAGGTGCATTAGCCAGGATA 59.300 52.381 0.00 0.00 41.13 2.59
3744 6619 2.551071 GGAGGTGCATTAGCCAGGATAC 60.551 54.545 0.00 0.00 41.13 2.24
3745 6620 2.104792 GAGGTGCATTAGCCAGGATACA 59.895 50.000 0.00 0.00 41.13 2.29
3746 6621 2.158755 AGGTGCATTAGCCAGGATACAC 60.159 50.000 0.00 0.00 41.13 2.90
3747 6622 2.421388 GGTGCATTAGCCAGGATACACA 60.421 50.000 6.36 0.00 41.13 3.72
3748 6623 2.614057 GTGCATTAGCCAGGATACACAC 59.386 50.000 0.00 0.00 41.13 3.82
3749 6624 2.238395 TGCATTAGCCAGGATACACACA 59.762 45.455 0.00 0.00 41.13 3.72
3750 6625 2.614057 GCATTAGCCAGGATACACACAC 59.386 50.000 0.00 0.00 34.22 3.82
3751 6626 3.872696 CATTAGCCAGGATACACACACA 58.127 45.455 0.00 0.00 41.41 3.72
3752 6627 3.328382 TTAGCCAGGATACACACACAC 57.672 47.619 0.00 0.00 41.41 3.82
3753 6628 0.037326 AGCCAGGATACACACACACG 60.037 55.000 0.00 0.00 41.41 4.49
3754 6629 1.635663 GCCAGGATACACACACACGC 61.636 60.000 0.00 0.00 41.41 5.34
3755 6630 0.320334 CCAGGATACACACACACGCA 60.320 55.000 0.00 0.00 41.41 5.24
3756 6631 0.790207 CAGGATACACACACACGCAC 59.210 55.000 0.00 0.00 41.41 5.34
3757 6632 0.666274 AGGATACACACACACGCACG 60.666 55.000 0.00 0.00 41.41 5.34
3758 6633 1.129809 GATACACACACACGCACGC 59.870 57.895 0.00 0.00 0.00 5.34
3759 6634 1.553195 GATACACACACACGCACGCA 61.553 55.000 0.00 0.00 0.00 5.24
3760 6635 1.556591 ATACACACACACGCACGCAG 61.557 55.000 0.00 0.00 0.00 5.18
3794 6670 4.596212 ACCCCCTCCGTAAAGAATATAAGG 59.404 45.833 0.00 0.00 0.00 2.69
3860 7579 1.763545 GTTTAGGGAGGGAGTAGCAGG 59.236 57.143 0.00 0.00 0.00 4.85
3876 7595 1.274712 CAGGGAGAGAAGCAAGAGGT 58.725 55.000 0.00 0.00 0.00 3.85
3878 7597 2.039613 CAGGGAGAGAAGCAAGAGGTTT 59.960 50.000 0.00 0.00 35.19 3.27
3941 7660 6.873997 TCCCACACACTTGTATTACAGATAG 58.126 40.000 0.00 0.00 33.30 2.08
3981 7700 4.559862 AGAAAACCTATGCAGCAGTAGT 57.440 40.909 0.00 0.00 0.00 2.73
3982 7701 5.677319 AGAAAACCTATGCAGCAGTAGTA 57.323 39.130 0.00 0.00 0.00 1.82
3988 7707 4.582656 ACCTATGCAGCAGTAGTAAGAGAG 59.417 45.833 0.00 0.00 0.00 3.20
4004 7723 8.445275 AGTAAGAGAGATGTATACACACAGAG 57.555 38.462 7.96 0.00 37.54 3.35
4029 7748 5.474876 AGGTATACCGGCATAGTTGTAGTAC 59.525 44.000 16.31 0.00 42.08 2.73
4030 7749 5.241506 GGTATACCGGCATAGTTGTAGTACA 59.758 44.000 6.06 0.00 0.00 2.90
4031 7750 5.857471 ATACCGGCATAGTTGTAGTACAA 57.143 39.130 11.75 11.75 35.42 2.41
4032 7751 4.119442 ACCGGCATAGTTGTAGTACAAG 57.881 45.455 16.03 5.87 39.00 3.16
4033 7752 2.864343 CCGGCATAGTTGTAGTACAAGC 59.136 50.000 16.03 14.72 39.00 4.01
4034 7753 3.517602 CGGCATAGTTGTAGTACAAGCA 58.482 45.455 16.03 7.38 39.00 3.91
4035 7754 4.119862 CGGCATAGTTGTAGTACAAGCAT 58.880 43.478 16.03 9.29 39.00 3.79
4036 7755 4.570772 CGGCATAGTTGTAGTACAAGCATT 59.429 41.667 16.03 5.45 39.00 3.56
4049 7768 1.062294 CAAGCATTGCTCTTCTCGCTC 59.938 52.381 12.39 0.00 40.39 5.03
4062 7781 0.238289 CTCGCTCAAAACCACGCAAT 59.762 50.000 0.00 0.00 0.00 3.56
4068 7787 2.979813 CTCAAAACCACGCAATACAAGC 59.020 45.455 0.00 0.00 0.00 4.01
4104 7831 3.197790 CACCGGAGCAGCAATCGG 61.198 66.667 9.46 16.32 46.95 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 316 3.118811 CCCCACAACACTTCAACAACAAT 60.119 43.478 0.00 0.00 0.00 2.71
209 1740 5.245301 CGTATGGTTGGGATGAGGTTATCTA 59.755 44.000 0.00 0.00 0.00 1.98
231 1762 0.555769 ATAAATGGGGGCATCCACGT 59.444 50.000 0.83 0.00 40.06 4.49
232 1763 2.577606 TATAAATGGGGGCATCCACG 57.422 50.000 0.83 0.00 40.06 4.94
259 1790 9.461312 TTGTGAGCAATAAACATCCTAGTTATT 57.539 29.630 0.00 0.00 0.00 1.40
300 1979 7.391833 TGTGTACACATGCATAAACTATGGAAA 59.608 33.333 24.62 0.00 39.96 3.13
351 2030 2.289820 CCTCATGAGCACAATCATTCGG 59.710 50.000 17.76 0.00 37.84 4.30
356 2035 1.558294 AGAGCCTCATGAGCACAATCA 59.442 47.619 17.76 0.00 0.00 2.57
379 2058 2.665008 TGCAGGCGCAGAAGAACTGT 62.665 55.000 10.83 0.00 45.36 3.55
402 2082 0.799534 GCCTGTTCATTGATGCACGC 60.800 55.000 0.00 0.00 0.00 5.34
414 2094 5.438761 AAACACAAGTAGATTGCCTGTTC 57.561 39.130 0.00 0.00 43.15 3.18
416 2096 5.594317 AGAAAAACACAAGTAGATTGCCTGT 59.406 36.000 0.00 0.00 43.15 4.00
423 2108 6.441088 AGAGGGAGAAAAACACAAGTAGAT 57.559 37.500 0.00 0.00 0.00 1.98
454 2139 2.996631 ACCTTGGCAATCTAGCTGAAG 58.003 47.619 0.00 0.00 34.17 3.02
455 2140 3.439857 AACCTTGGCAATCTAGCTGAA 57.560 42.857 0.00 0.00 34.17 3.02
456 2141 3.118261 CCTAACCTTGGCAATCTAGCTGA 60.118 47.826 0.00 0.00 34.17 4.26
457 2142 3.209410 CCTAACCTTGGCAATCTAGCTG 58.791 50.000 0.00 0.00 34.17 4.24
470 2155 6.070938 GGTCTCAAGTACATGTACCTAACCTT 60.071 42.308 28.29 14.61 36.75 3.50
477 2162 5.599999 ATCAGGTCTCAAGTACATGTACC 57.400 43.478 28.29 16.54 36.75 3.34
502 2200 3.130340 ACAAAGCACCGACAACTTCATTT 59.870 39.130 0.00 0.00 0.00 2.32
520 2218 1.693627 TTAAAGGGAAGGCGCACAAA 58.306 45.000 10.83 0.00 0.00 2.83
629 2365 1.523758 GGCCACGAAAGACAACTCAT 58.476 50.000 0.00 0.00 0.00 2.90
643 2381 1.584495 CTACAAAAAGGGCGGCCAC 59.416 57.895 31.59 10.38 0.00 5.01
676 2414 8.846211 CCACTATTTCTGTCTGTTCCTTAAAAA 58.154 33.333 0.00 0.00 0.00 1.94
677 2415 7.040686 GCCACTATTTCTGTCTGTTCCTTAAAA 60.041 37.037 0.00 0.00 0.00 1.52
678 2416 6.430000 GCCACTATTTCTGTCTGTTCCTTAAA 59.570 38.462 0.00 0.00 0.00 1.52
679 2417 5.938125 GCCACTATTTCTGTCTGTTCCTTAA 59.062 40.000 0.00 0.00 0.00 1.85
680 2418 5.248477 AGCCACTATTTCTGTCTGTTCCTTA 59.752 40.000 0.00 0.00 0.00 2.69
681 2419 4.042187 AGCCACTATTTCTGTCTGTTCCTT 59.958 41.667 0.00 0.00 0.00 3.36
682 2420 3.584848 AGCCACTATTTCTGTCTGTTCCT 59.415 43.478 0.00 0.00 0.00 3.36
683 2421 3.944087 AGCCACTATTTCTGTCTGTTCC 58.056 45.455 0.00 0.00 0.00 3.62
684 2422 7.617041 AAATAGCCACTATTTCTGTCTGTTC 57.383 36.000 6.74 0.00 41.14 3.18
685 2423 8.409358 AAAAATAGCCACTATTTCTGTCTGTT 57.591 30.769 11.82 0.81 43.27 3.16
773 2511 1.002403 TATCCGCTCACCCCCTCAA 59.998 57.895 0.00 0.00 0.00 3.02
779 2517 2.678336 CAGAAAAAGTATCCGCTCACCC 59.322 50.000 0.00 0.00 0.00 4.61
780 2518 3.125316 CACAGAAAAAGTATCCGCTCACC 59.875 47.826 0.00 0.00 0.00 4.02
781 2519 3.746492 ACACAGAAAAAGTATCCGCTCAC 59.254 43.478 0.00 0.00 0.00 3.51
782 2520 3.994392 GACACAGAAAAAGTATCCGCTCA 59.006 43.478 0.00 0.00 0.00 4.26
783 2521 4.246458 AGACACAGAAAAAGTATCCGCTC 58.754 43.478 0.00 0.00 0.00 5.03
784 2522 4.273148 AGACACAGAAAAAGTATCCGCT 57.727 40.909 0.00 0.00 0.00 5.52
785 2523 4.378459 CCAAGACACAGAAAAAGTATCCGC 60.378 45.833 0.00 0.00 0.00 5.54
786 2524 4.994852 TCCAAGACACAGAAAAAGTATCCG 59.005 41.667 0.00 0.00 0.00 4.18
787 2525 7.362142 GGAATCCAAGACACAGAAAAAGTATCC 60.362 40.741 0.00 0.00 0.00 2.59
788 2526 7.174946 TGGAATCCAAGACACAGAAAAAGTATC 59.825 37.037 0.00 0.00 0.00 2.24
791 2529 5.200483 TGGAATCCAAGACACAGAAAAAGT 58.800 37.500 0.00 0.00 0.00 2.66
792 2530 5.766222 CTGGAATCCAAGACACAGAAAAAG 58.234 41.667 2.61 0.00 30.80 2.27
798 2540 2.486472 AGCTGGAATCCAAGACACAG 57.514 50.000 2.61 0.00 30.80 3.66
799 2541 2.553028 GGAAGCTGGAATCCAAGACACA 60.553 50.000 2.61 0.00 35.71 3.72
868 3056 2.465010 TAGGGCCCACCGGAAAGAGA 62.465 60.000 27.56 0.00 46.96 3.10
894 3086 2.289072 GGCGCTATTCTCAGCAGGAATA 60.289 50.000 7.64 0.00 41.88 1.75
903 3095 2.586079 GCAGCGGCGCTATTCTCA 60.586 61.111 35.90 0.00 36.40 3.27
1027 3224 1.318380 GGGGAGGAAGGGGAGATGA 59.682 63.158 0.00 0.00 0.00 2.92
1246 3443 1.308047 CCAGCTGTGTGTGCAAGTAA 58.692 50.000 13.81 0.00 0.00 2.24
1248 3445 1.825191 CCCAGCTGTGTGTGCAAGT 60.825 57.895 13.81 0.00 0.00 3.16
1249 3446 1.526686 TCCCAGCTGTGTGTGCAAG 60.527 57.895 13.81 0.00 0.00 4.01
1250 3447 1.823470 GTCCCAGCTGTGTGTGCAA 60.823 57.895 13.81 0.00 0.00 4.08
1251 3448 2.203195 GTCCCAGCTGTGTGTGCA 60.203 61.111 13.81 0.00 0.00 4.57
1252 3449 2.111878 AGTCCCAGCTGTGTGTGC 59.888 61.111 13.81 0.00 0.00 4.57
1327 3528 2.877113 CACCGACACGCGCGAATA 60.877 61.111 39.36 0.00 39.11 1.75
1427 3628 3.209410 GAATGCTTGTAGTGATGGAGGG 58.791 50.000 0.00 0.00 0.00 4.30
1476 3677 3.991121 GAGCTGGACTCAAAACTGTACTC 59.009 47.826 0.00 0.00 45.49 2.59
1477 3678 3.996480 GAGCTGGACTCAAAACTGTACT 58.004 45.455 0.00 0.00 45.49 2.73
1513 3721 2.230508 AGCAAGCAAATCCATGTGTCTG 59.769 45.455 0.00 0.00 0.00 3.51
1528 3736 0.314935 TTGGCTGCAGTTAAGCAAGC 59.685 50.000 16.64 0.00 45.13 4.01
1560 3768 1.909302 TCTTTCCAGAATTCGCCTCCT 59.091 47.619 0.00 0.00 0.00 3.69
1620 3828 3.319135 GCCATCTGATCCAGCGATT 57.681 52.632 0.00 0.00 0.00 3.34
1638 3846 1.788258 CTTCATCATCCCGACCATCG 58.212 55.000 0.00 0.00 40.07 3.84
1656 3864 1.135960 GCCTTCTCCAGATAAGGGCT 58.864 55.000 12.30 0.00 42.19 5.19
1693 3901 0.370273 GCTCAAACGGATGTAGCGTG 59.630 55.000 0.00 0.00 0.00 5.34
1694 3902 2.750815 GCTCAAACGGATGTAGCGT 58.249 52.632 0.00 0.00 0.00 5.07
1696 3904 0.645868 GACGCTCAAACGGATGTAGC 59.354 55.000 0.00 0.00 37.37 3.58
1697 3905 1.990799 TGACGCTCAAACGGATGTAG 58.009 50.000 0.00 0.00 37.37 2.74
1714 4010 5.375354 ACACCCTCCATCCCATATTAATTGA 59.625 40.000 0.00 0.00 0.00 2.57
1727 4056 6.293698 ACGGTTAAAATATACACCCTCCATC 58.706 40.000 0.00 0.00 0.00 3.51
1729 4058 5.697082 ACGGTTAAAATATACACCCTCCA 57.303 39.130 0.00 0.00 0.00 3.86
1763 4095 9.953565 GGTATACTTATCAATAGGCCAAACATA 57.046 33.333 5.01 0.00 0.00 2.29
1792 4127 2.755103 GCAAAATTCCCCTACTCAGTGG 59.245 50.000 0.00 0.00 0.00 4.00
2016 4352 1.273098 ACGTAACCCAGGGATCAGTCT 60.273 52.381 14.54 0.00 0.00 3.24
2113 4449 3.181487 ACGATGAAACAAAAGCAGCAACT 60.181 39.130 0.00 0.00 0.00 3.16
2114 4450 3.115554 ACGATGAAACAAAAGCAGCAAC 58.884 40.909 0.00 0.00 0.00 4.17
2117 4453 2.975851 CTGACGATGAAACAAAAGCAGC 59.024 45.455 0.00 0.00 0.00 5.25
2125 4461 4.955925 ACAAACAACTGACGATGAAACA 57.044 36.364 0.00 0.00 0.00 2.83
2155 4491 5.356751 GCCTCAACATATGAACATACCAACA 59.643 40.000 10.38 0.00 37.67 3.33
2156 4492 5.356751 TGCCTCAACATATGAACATACCAAC 59.643 40.000 10.38 0.00 37.67 3.77
2158 4494 4.881273 GTGCCTCAACATATGAACATACCA 59.119 41.667 10.38 0.00 37.67 3.25
2159 4495 5.126067 AGTGCCTCAACATATGAACATACC 58.874 41.667 10.38 0.00 37.67 2.73
2160 4496 6.316140 TGAAGTGCCTCAACATATGAACATAC 59.684 38.462 10.38 0.09 37.67 2.39
2161 4497 6.413892 TGAAGTGCCTCAACATATGAACATA 58.586 36.000 10.38 0.00 37.67 2.29
2162 4498 5.255687 TGAAGTGCCTCAACATATGAACAT 58.744 37.500 10.38 0.00 37.67 2.71
2164 4500 5.824904 ATGAAGTGCCTCAACATATGAAC 57.175 39.130 10.38 0.00 37.67 3.18
2166 4502 5.748402 AGAATGAAGTGCCTCAACATATGA 58.252 37.500 10.38 0.00 36.38 2.15
2168 4504 5.948162 ACAAGAATGAAGTGCCTCAACATAT 59.052 36.000 0.00 0.00 0.00 1.78
2169 4505 5.181811 CACAAGAATGAAGTGCCTCAACATA 59.818 40.000 0.00 0.00 0.00 2.29
2171 4507 3.316029 CACAAGAATGAAGTGCCTCAACA 59.684 43.478 0.00 0.00 0.00 3.33
2172 4508 3.893720 CACAAGAATGAAGTGCCTCAAC 58.106 45.455 0.00 0.00 0.00 3.18
2188 4524 2.816087 ACAATGCCTACAGAAGCACAAG 59.184 45.455 0.00 0.00 42.84 3.16
2194 4530 3.119708 GCAAGGAACAATGCCTACAGAAG 60.120 47.826 0.00 0.00 37.45 2.85
2227 4563 2.610438 ACAGATGTTTCCTTGGCCAT 57.390 45.000 6.09 0.00 0.00 4.40
2232 4568 4.588899 TGGGTGATACAGATGTTTCCTTG 58.411 43.478 0.00 0.00 0.00 3.61
2235 4571 3.941483 CACTGGGTGATACAGATGTTTCC 59.059 47.826 0.00 0.00 39.24 3.13
2239 4575 3.840666 AGTTCACTGGGTGATACAGATGT 59.159 43.478 1.10 0.00 42.40 3.06
2246 4582 4.593206 ACTCTTTCAGTTCACTGGGTGATA 59.407 41.667 7.11 0.00 42.40 2.15
2247 4583 3.392616 ACTCTTTCAGTTCACTGGGTGAT 59.607 43.478 7.11 0.00 42.40 3.06
2250 4586 3.933861 AACTCTTTCAGTTCACTGGGT 57.066 42.857 7.11 0.00 42.07 4.51
2261 4597 7.441890 TTGTTGTACAAACTGAACTCTTTCA 57.558 32.000 10.51 0.00 35.82 2.69
2292 4628 7.596749 ACCTGAAAGTTGTTGTAGATTATCG 57.403 36.000 0.00 0.00 0.00 2.92
2304 4640 4.331717 CACGTGAGTTTACCTGAAAGTTGT 59.668 41.667 10.90 0.00 46.40 3.32
2308 4644 2.869801 TGCACGTGAGTTTACCTGAAAG 59.130 45.455 22.23 0.00 46.40 2.62
2318 4654 3.684103 TTCGAAAATTGCACGTGAGTT 57.316 38.095 22.23 7.22 46.40 3.01
2320 4656 4.499040 ACTTTTTCGAAAATTGCACGTGAG 59.501 37.500 23.05 15.76 0.00 3.51
2322 4658 4.753516 ACTTTTTCGAAAATTGCACGTG 57.246 36.364 23.05 12.28 0.00 4.49
2323 4659 5.099575 AGAACTTTTTCGAAAATTGCACGT 58.900 33.333 23.05 10.98 36.78 4.49
2324 4660 5.620098 AGAACTTTTTCGAAAATTGCACG 57.380 34.783 23.05 10.44 36.78 5.34
2325 4661 6.894517 GTCAAGAACTTTTTCGAAAATTGCAC 59.105 34.615 23.05 17.15 36.78 4.57
2326 4662 6.811170 AGTCAAGAACTTTTTCGAAAATTGCA 59.189 30.769 23.05 8.23 36.78 4.08
2327 4663 7.220875 AGAGTCAAGAACTTTTTCGAAAATTGC 59.779 33.333 23.05 17.30 38.74 3.56
2328 4664 8.620533 AGAGTCAAGAACTTTTTCGAAAATTG 57.379 30.769 23.05 21.42 38.74 2.32
2329 4665 9.717892 GTAGAGTCAAGAACTTTTTCGAAAATT 57.282 29.630 23.05 15.53 38.74 1.82
2331 4667 8.259049 TGTAGAGTCAAGAACTTTTTCGAAAA 57.741 30.769 19.08 19.08 38.74 2.29
2333 4669 7.837202 TTGTAGAGTCAAGAACTTTTTCGAA 57.163 32.000 0.00 0.00 38.74 3.71
2334 4670 9.706691 ATATTGTAGAGTCAAGAACTTTTTCGA 57.293 29.630 0.00 0.00 38.74 3.71
2354 4690 8.807948 AGCCAAAATGTAGAGTACAATATTGT 57.192 30.769 23.80 23.80 42.76 2.71
2357 4693 8.190784 GCAAAGCCAAAATGTAGAGTACAATAT 58.809 33.333 0.00 0.00 42.76 1.28
2360 4696 5.300539 TGCAAAGCCAAAATGTAGAGTACAA 59.699 36.000 0.00 0.00 42.76 2.41
2361 4697 4.824537 TGCAAAGCCAAAATGTAGAGTACA 59.175 37.500 0.00 0.00 43.80 2.90
2362 4698 5.371115 TGCAAAGCCAAAATGTAGAGTAC 57.629 39.130 0.00 0.00 0.00 2.73
2363 4699 5.622007 GCATGCAAAGCCAAAATGTAGAGTA 60.622 40.000 14.21 0.00 0.00 2.59
2365 4701 3.615496 GCATGCAAAGCCAAAATGTAGAG 59.385 43.478 14.21 0.00 0.00 2.43
2366 4702 3.006644 TGCATGCAAAGCCAAAATGTAGA 59.993 39.130 20.30 0.00 0.00 2.59
2367 4703 3.123959 GTGCATGCAAAGCCAAAATGTAG 59.876 43.478 24.58 0.00 0.00 2.74
2370 4732 2.147958 AGTGCATGCAAAGCCAAAATG 58.852 42.857 24.58 0.00 0.00 2.32
2373 4735 2.328819 AAAGTGCATGCAAAGCCAAA 57.671 40.000 24.58 0.00 0.00 3.28
2382 4744 9.573133 ACTATAATTTCAGTTTAAAGTGCATGC 57.427 29.630 16.77 11.82 0.00 4.06
2397 4759 8.106462 TGAGGTGGTTCATCAACTATAATTTCA 58.894 33.333 0.00 0.00 34.38 2.69
2398 4760 8.506168 TGAGGTGGTTCATCAACTATAATTTC 57.494 34.615 0.00 0.00 34.38 2.17
2399 4761 8.906867 CATGAGGTGGTTCATCAACTATAATTT 58.093 33.333 0.00 0.00 40.25 1.82
2400 4762 7.013655 GCATGAGGTGGTTCATCAACTATAATT 59.986 37.037 0.00 0.00 40.25 1.40
2401 4763 6.488006 GCATGAGGTGGTTCATCAACTATAAT 59.512 38.462 0.00 0.00 40.25 1.28
2402 4764 5.822519 GCATGAGGTGGTTCATCAACTATAA 59.177 40.000 0.00 0.00 40.25 0.98
2403 4765 5.130975 AGCATGAGGTGGTTCATCAACTATA 59.869 40.000 0.00 0.00 40.25 1.31
2405 4767 3.264193 AGCATGAGGTGGTTCATCAACTA 59.736 43.478 0.00 0.00 40.25 2.24
2406 4768 2.040813 AGCATGAGGTGGTTCATCAACT 59.959 45.455 0.00 0.00 40.25 3.16
2407 4769 2.440409 AGCATGAGGTGGTTCATCAAC 58.560 47.619 0.00 0.00 40.25 3.18
2408 4770 2.885135 AGCATGAGGTGGTTCATCAA 57.115 45.000 0.00 0.00 40.25 2.57
2409 4771 3.998913 TTAGCATGAGGTGGTTCATCA 57.001 42.857 0.00 0.00 41.11 3.07
2410 4772 4.517285 TCTTTAGCATGAGGTGGTTCATC 58.483 43.478 0.00 0.00 39.69 2.92
2412 4774 3.582647 TCTCTTTAGCATGAGGTGGTTCA 59.417 43.478 0.00 0.00 39.69 3.18
2413 4775 4.207891 TCTCTTTAGCATGAGGTGGTTC 57.792 45.455 0.00 0.00 39.69 3.62
2414 4776 4.583871 CTTCTCTTTAGCATGAGGTGGTT 58.416 43.478 0.00 0.00 39.69 3.67
2416 4778 2.941720 GCTTCTCTTTAGCATGAGGTGG 59.058 50.000 0.00 0.00 38.51 4.61
2417 4779 2.606725 CGCTTCTCTTTAGCATGAGGTG 59.393 50.000 0.00 0.00 38.55 4.00
2418 4780 2.234908 ACGCTTCTCTTTAGCATGAGGT 59.765 45.455 0.00 0.00 38.55 3.85
2419 4781 2.863137 GACGCTTCTCTTTAGCATGAGG 59.137 50.000 0.00 0.00 38.55 3.86
2422 4784 4.871993 ATTGACGCTTCTCTTTAGCATG 57.128 40.909 0.00 0.00 38.55 4.06
2424 4786 5.689383 AAAATTGACGCTTCTCTTTAGCA 57.311 34.783 0.00 0.00 38.55 3.49
2453 4815 9.846248 GAGCTGTTCAACTGATAAATTGTAAAT 57.154 29.630 0.00 0.00 0.00 1.40
2455 4817 7.665559 AGGAGCTGTTCAACTGATAAATTGTAA 59.334 33.333 0.00 0.00 0.00 2.41
2461 4823 4.973168 ACAGGAGCTGTTCAACTGATAAA 58.027 39.130 0.00 0.00 42.59 1.40
2499 4861 9.485206 GGTACTCTTAACACAATTTCTTCAGTA 57.515 33.333 0.00 0.00 0.00 2.74
2507 4887 9.528018 CAAATGTTGGTACTCTTAACACAATTT 57.472 29.630 0.00 0.00 37.17 1.82
2508 4888 8.691797 ACAAATGTTGGTACTCTTAACACAATT 58.308 29.630 0.00 0.00 37.17 2.32
2516 4896 9.575868 TTGGATAAACAAATGTTGGTACTCTTA 57.424 29.630 0.00 0.00 38.44 2.10
2517 4897 8.357402 GTTGGATAAACAAATGTTGGTACTCTT 58.643 33.333 0.00 0.00 38.44 2.85
2518 4898 7.504238 TGTTGGATAAACAAATGTTGGTACTCT 59.496 33.333 0.00 0.00 45.85 3.24
2520 4900 7.589958 TGTTGGATAAACAAATGTTGGTACT 57.410 32.000 0.00 0.00 45.85 2.73
2533 4913 3.620488 TCTCCTGCCATGTTGGATAAAC 58.380 45.455 0.00 0.00 40.96 2.01
2535 4915 4.524802 AATCTCCTGCCATGTTGGATAA 57.475 40.909 0.00 0.00 40.96 1.75
2539 4919 3.824133 TCATAATCTCCTGCCATGTTGG 58.176 45.455 0.00 0.00 41.55 3.77
2541 4921 3.825014 GCATCATAATCTCCTGCCATGTT 59.175 43.478 0.00 0.00 0.00 2.71
2542 4922 3.181437 TGCATCATAATCTCCTGCCATGT 60.181 43.478 0.00 0.00 31.89 3.21
2543 4923 3.418047 TGCATCATAATCTCCTGCCATG 58.582 45.455 0.00 0.00 31.89 3.66
2545 4925 2.440627 ACTGCATCATAATCTCCTGCCA 59.559 45.455 0.00 0.00 31.89 4.92
2636 5032 8.103305 AGTTTGAATTCAGCAATAACTCCTCTA 58.897 33.333 14.07 0.00 0.00 2.43
2658 5054 2.283298 CGCTGTATCTGATGGCAGTTT 58.717 47.619 18.50 0.00 42.84 2.66
2683 5079 8.231304 TGTAAGCTCAACTTATACGTAAACAC 57.769 34.615 0.00 0.00 42.75 3.32
2690 5086 7.757097 AATGACTGTAAGCTCAACTTATACG 57.243 36.000 0.00 0.00 42.75 3.06
2692 5088 9.803315 CTGTAATGACTGTAAGCTCAACTTATA 57.197 33.333 0.00 0.00 42.75 0.98
2693 5089 8.314751 ACTGTAATGACTGTAAGCTCAACTTAT 58.685 33.333 0.00 0.00 42.75 1.73
2721 5117 5.545335 ACAGCCATCAGATAGTTCCATATGA 59.455 40.000 3.65 0.00 31.19 2.15
2724 5120 7.559335 AATACAGCCATCAGATAGTTCCATA 57.441 36.000 0.00 0.00 0.00 2.74
2725 5121 6.445451 AATACAGCCATCAGATAGTTCCAT 57.555 37.500 0.00 0.00 0.00 3.41
2745 5141 7.123997 TGCCATATTTTTCTCTGCAAGGAAATA 59.876 33.333 12.49 13.13 34.61 1.40
3070 5466 0.605319 CACCGACTAGCCAAAAGGCA 60.605 55.000 9.42 0.00 37.35 4.75
3124 5520 1.616159 TGGCAGTTAGTTTTCCAGCC 58.384 50.000 0.00 0.00 40.93 4.85
3166 5562 6.825721 AGGTGAATTCAGAAGGTATCATGTTC 59.174 38.462 8.80 0.00 0.00 3.18
3242 5638 7.921304 TGATACAATCCTATGATAGCATGGTT 58.079 34.615 1.12 0.00 35.94 3.67
3254 5650 5.476983 TCCAACTCCCTGATACAATCCTAT 58.523 41.667 0.00 0.00 0.00 2.57
3282 5679 2.158856 AGGCATCGCATCATTCTCTTGA 60.159 45.455 0.00 0.00 0.00 3.02
3289 5686 1.674441 CACTGAAGGCATCGCATCATT 59.326 47.619 0.00 0.00 0.00 2.57
3292 5689 1.354506 GCACTGAAGGCATCGCATC 59.645 57.895 0.00 0.00 0.00 3.91
3300 5697 1.238439 TAAGCAACTGCACTGAAGGC 58.762 50.000 4.22 0.00 45.16 4.35
3312 5709 4.214332 GCAGTAGCCCTTCATATAAGCAAC 59.786 45.833 0.00 0.00 33.58 4.17
3331 5728 4.406648 TCAGGTTTCGATATGATGCAGT 57.593 40.909 0.00 0.00 0.00 4.40
3378 5775 0.248621 GACTATTTGCCGTGCATGCC 60.249 55.000 16.68 5.63 38.76 4.40
3401 5798 4.457949 ACACGACATCCATAGCGATATACA 59.542 41.667 0.00 0.00 0.00 2.29
3402 5799 4.982999 ACACGACATCCATAGCGATATAC 58.017 43.478 0.00 0.00 0.00 1.47
3428 5825 3.294214 AGAGGGCATCAAAATGGTCATC 58.706 45.455 0.58 0.00 33.19 2.92
3473 5870 9.452287 GGGTTTAGTAGATGTAAACATGGTTTA 57.548 33.333 0.00 0.00 40.64 2.01
3590 6463 8.918202 ACACAAAAACTCATAAACCTCATCTA 57.082 30.769 0.00 0.00 0.00 1.98
3701 6575 7.125792 TCCTACATCCAAAATCTCTTCTACC 57.874 40.000 0.00 0.00 0.00 3.18
3740 6615 1.129809 GCGTGCGTGTGTGTGTATC 59.870 57.895 0.00 0.00 0.00 2.24
3741 6616 1.556591 CTGCGTGCGTGTGTGTGTAT 61.557 55.000 0.00 0.00 0.00 2.29
3742 6617 2.202756 TGCGTGCGTGTGTGTGTA 60.203 55.556 0.00 0.00 0.00 2.90
3743 6618 3.563088 CTGCGTGCGTGTGTGTGT 61.563 61.111 0.00 0.00 0.00 3.72
3744 6619 2.576287 AAACTGCGTGCGTGTGTGTG 62.576 55.000 0.00 0.00 0.00 3.82
3745 6620 1.917782 AAAACTGCGTGCGTGTGTGT 61.918 50.000 0.00 0.00 0.00 3.72
3746 6621 1.193665 GAAAACTGCGTGCGTGTGTG 61.194 55.000 0.00 0.00 0.00 3.82
3747 6622 1.061887 GAAAACTGCGTGCGTGTGT 59.938 52.632 0.00 0.00 0.00 3.72
3748 6623 0.316937 ATGAAAACTGCGTGCGTGTG 60.317 50.000 0.00 0.00 0.00 3.82
3749 6624 1.194547 CTATGAAAACTGCGTGCGTGT 59.805 47.619 0.00 0.00 0.00 4.49
3750 6625 1.194547 ACTATGAAAACTGCGTGCGTG 59.805 47.619 0.00 0.00 0.00 5.34
3751 6626 1.508632 ACTATGAAAACTGCGTGCGT 58.491 45.000 0.00 0.00 0.00 5.24
3752 6627 2.222729 GGTACTATGAAAACTGCGTGCG 60.223 50.000 0.00 0.00 0.00 5.34
3753 6628 2.095372 GGGTACTATGAAAACTGCGTGC 59.905 50.000 0.00 0.00 0.00 5.34
3754 6629 2.676342 GGGGTACTATGAAAACTGCGTG 59.324 50.000 0.00 0.00 0.00 5.34
3755 6630 2.355412 GGGGGTACTATGAAAACTGCGT 60.355 50.000 0.00 0.00 0.00 5.24
3756 6631 2.093128 AGGGGGTACTATGAAAACTGCG 60.093 50.000 0.00 0.00 0.00 5.18
3757 6632 3.542648 GAGGGGGTACTATGAAAACTGC 58.457 50.000 0.00 0.00 0.00 4.40
3758 6633 3.431766 CGGAGGGGGTACTATGAAAACTG 60.432 52.174 0.00 0.00 0.00 3.16
3759 6634 2.770232 CGGAGGGGGTACTATGAAAACT 59.230 50.000 0.00 0.00 0.00 2.66
3760 6635 2.502947 ACGGAGGGGGTACTATGAAAAC 59.497 50.000 0.00 0.00 0.00 2.43
3827 6706 6.388689 TCCCTCCCTAAACAAATATAAGAGCA 59.611 38.462 0.00 0.00 0.00 4.26
3860 7579 2.810852 CACAAACCTCTTGCTTCTCTCC 59.189 50.000 0.00 0.00 0.00 3.71
3876 7595 6.757897 ACATTTTGTCTCTCTTGTCACAAA 57.242 33.333 0.00 0.00 37.04 2.83
3878 7597 5.879777 TCAACATTTTGTCTCTCTTGTCACA 59.120 36.000 0.00 0.00 34.02 3.58
3941 7660 4.710423 TCTTGTGCTCTCTATCTGACAC 57.290 45.455 0.00 0.00 0.00 3.67
3981 7700 7.717436 CCTCTCTGTGTGTATACATCTCTCTTA 59.283 40.741 9.18 0.00 39.39 2.10
3982 7701 6.545666 CCTCTCTGTGTGTATACATCTCTCTT 59.454 42.308 9.18 0.00 39.39 2.85
3988 7707 7.361031 CGGTATACCTCTCTGTGTGTATACATC 60.361 44.444 19.68 6.47 43.79 3.06
4004 7723 4.522022 ACTACAACTATGCCGGTATACCTC 59.478 45.833 19.68 11.49 0.00 3.85
4029 7748 1.062294 GAGCGAGAAGAGCAATGCTTG 59.938 52.381 9.91 0.00 39.88 4.01
4030 7749 1.338484 TGAGCGAGAAGAGCAATGCTT 60.338 47.619 9.91 0.00 39.88 3.91
4031 7750 0.248565 TGAGCGAGAAGAGCAATGCT 59.751 50.000 7.79 7.79 43.88 3.79
4032 7751 1.081892 TTGAGCGAGAAGAGCAATGC 58.918 50.000 0.00 0.00 37.01 3.56
4033 7752 3.486584 GTTTTGAGCGAGAAGAGCAATG 58.513 45.455 0.00 0.00 37.01 2.82
4034 7753 2.485814 GGTTTTGAGCGAGAAGAGCAAT 59.514 45.455 0.00 0.00 37.01 3.56
4035 7754 1.873591 GGTTTTGAGCGAGAAGAGCAA 59.126 47.619 0.00 0.00 37.01 3.91
4036 7755 1.202639 TGGTTTTGAGCGAGAAGAGCA 60.203 47.619 0.00 0.00 37.01 4.26
4037 7756 1.195674 GTGGTTTTGAGCGAGAAGAGC 59.804 52.381 0.00 0.00 0.00 4.09
4044 7763 1.195900 GTATTGCGTGGTTTTGAGCGA 59.804 47.619 0.00 0.00 0.00 4.93
4062 7781 2.050350 CCGGAGAGGGTCGCTTGTA 61.050 63.158 0.00 0.00 35.97 2.41
4104 7831 3.440872 AGAACTACACCGTCTGATCTGAC 59.559 47.826 19.73 19.73 0.00 3.51


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

AutoCloner maintained by Alex Coulton.