Multiple sequence alignment - TraesCS3A01G334100

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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 TraesCS3A01G334100 chr3A 100.000 6829 0 0 1 6829 579383502 579376674 0.000000e+00 12611
1 TraesCS3A01G334100 chr3A 90.146 274 26 1 1 274 571352924 571352652 8.420000e-94 355
2 TraesCS3A01G334100 chr3B 92.776 2450 116 32 4403 6829 576451457 576449046 0.000000e+00 3487
3 TraesCS3A01G334100 chr3B 92.817 1782 57 36 275 2022 576455655 576453911 0.000000e+00 2516
4 TraesCS3A01G334100 chr3B 92.643 1169 57 12 3150 4315 576452641 576451499 0.000000e+00 1655
5 TraesCS3A01G334100 chr3B 95.428 853 34 3 2140 2989 576453492 576452642 0.000000e+00 1354
6 TraesCS3A01G334100 chr3D 94.942 1799 42 18 275 2051 439683445 439681674 0.000000e+00 2772
7 TraesCS3A01G334100 chr3D 92.217 1773 121 11 2146 3912 439681673 439679912 0.000000e+00 2494
8 TraesCS3A01G334100 chr3D 90.353 1161 72 18 4403 5550 439679304 439678171 0.000000e+00 1487
9 TraesCS3A01G334100 chr3D 89.971 698 53 7 5551 6241 439678132 439677445 0.000000e+00 885
10 TraesCS3A01G334100 chr3D 90.116 344 21 7 6488 6829 439677278 439676946 1.050000e-117 435
11 TraesCS3A01G334100 chr3D 93.040 273 9 3 3900 4172 439679865 439679603 2.310000e-104 390
12 TraesCS3A01G334100 chr3D 95.172 145 6 1 4171 4315 439679489 439679346 1.920000e-55 228
13 TraesCS3A01G334100 chr1B 90.802 511 42 5 2159 2665 654383244 654383753 0.000000e+00 678
14 TraesCS3A01G334100 chr7B 90.467 514 41 3 2159 2665 703817111 703816599 0.000000e+00 671
15 TraesCS3A01G334100 chr7B 90.058 513 43 3 2160 2665 121028234 121027723 0.000000e+00 658
16 TraesCS3A01G334100 chr7B 89.608 510 44 6 2161 2663 26716632 26716125 2.080000e-179 640
17 TraesCS3A01G334100 chr7A 96.715 274 9 0 1 274 539742990 539743263 2.240000e-124 457
18 TraesCS3A01G334100 chr7A 93.333 180 12 0 1 180 54834309 54834130 4.060000e-67 267
19 TraesCS3A01G334100 chr7D 97.890 237 5 0 2561 2797 504424059 504423823 1.770000e-110 411
20 TraesCS3A01G334100 chr7D 88.218 331 30 5 2146 2469 504424389 504424061 2.990000e-103 387
21 TraesCS3A01G334100 chr7D 89.384 292 21 7 1761 2051 504424672 504424390 6.510000e-95 359
22 TraesCS3A01G334100 chr1A 93.066 274 19 0 1 274 259171568 259171841 1.070000e-107 401
23 TraesCS3A01G334100 chr4B 92.701 274 19 1 1 274 643600105 643600377 1.790000e-105 394
24 TraesCS3A01G334100 chr1D 91.241 274 24 0 1 274 260950248 260950521 2.330000e-99 374
25 TraesCS3A01G334100 chr5D 90.146 274 27 0 1 274 3986095 3985822 2.340000e-94 357
26 TraesCS3A01G334100 chr5D 90.146 274 27 0 1 274 3989723 3989450 2.340000e-94 357
27 TraesCS3A01G334100 chr5D 83.273 275 42 4 1 274 116251042 116251313 4.090000e-62 250


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 TraesCS3A01G334100 chr3A 579376674 579383502 6828 True 12611.000000 12611 100.000000 1 6829 1 chr3A.!!$R2 6828
1 TraesCS3A01G334100 chr3B 576449046 576455655 6609 True 2253.000000 3487 93.416000 275 6829 4 chr3B.!!$R1 6554
2 TraesCS3A01G334100 chr3D 439676946 439683445 6499 True 1241.571429 2772 92.258714 275 6829 7 chr3D.!!$R1 6554
3 TraesCS3A01G334100 chr1B 654383244 654383753 509 False 678.000000 678 90.802000 2159 2665 1 chr1B.!!$F1 506
4 TraesCS3A01G334100 chr7B 703816599 703817111 512 True 671.000000 671 90.467000 2159 2665 1 chr7B.!!$R3 506
5 TraesCS3A01G334100 chr7B 121027723 121028234 511 True 658.000000 658 90.058000 2160 2665 1 chr7B.!!$R2 505
6 TraesCS3A01G334100 chr7B 26716125 26716632 507 True 640.000000 640 89.608000 2161 2663 1 chr7B.!!$R1 502
7 TraesCS3A01G334100 chr7D 504423823 504424672 849 True 385.666667 411 91.830667 1761 2797 3 chr7D.!!$R1 1036
8 TraesCS3A01G334100 chr5D 3985822 3989723 3901 True 357.000000 357 90.146000 1 274 2 chr5D.!!$R1 273

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
785 793 0.108945 CGTCCCGTCAGGTTACTTCC 60.109 60.000 0.0 0.0 36.75 3.46 F
1364 2358 0.792640 CGATGTGGAGTGTCAAGTGC 59.207 55.000 0.0 0.0 0.00 4.40 F
2232 3803 0.960364 GAGTTGCTGATTTCGGGGCA 60.960 55.000 0.0 0.0 0.00 5.36 F
2331 3906 1.363744 CGCTAGAAACTTGCCTCCAG 58.636 55.000 0.0 0.0 0.00 3.86 F
4237 5991 2.489971 GGCTTTTGTTTGCCCTTTACC 58.510 47.619 0.0 0.0 43.11 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 3586 0.251077 CCTGCAACAAAGCTCCTCCT 60.251 55.000 0.00 0.00 34.99 3.69 R
3033 4612 1.460743 CTCAAGCCATGTGTACACGTG 59.539 52.381 32.46 32.46 45.43 4.49 R
4229 5983 1.280457 AGGAGCACTCAGGTAAAGGG 58.720 55.000 0.00 0.00 0.00 3.95 R
4322 6076 1.613437 CGGGTGCAGAAAAAGAATGGT 59.387 47.619 0.00 0.00 0.00 3.55 R
5875 7690 0.097674 GCTGGCTAATGCAACACTCG 59.902 55.000 0.00 0.00 41.91 4.18 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
30 31 0.820891 CAGGAATCAATGGCCGAGGG 60.821 60.000 0.00 0.00 0.00 4.30
49 50 2.283676 GGACGAGGGTGAGGGTGA 60.284 66.667 0.00 0.00 0.00 4.02
50 51 2.647158 GGACGAGGGTGAGGGTGAC 61.647 68.421 0.00 0.00 0.00 3.67
73 74 2.281484 GCCTCAACCCAACGAGCA 60.281 61.111 0.00 0.00 0.00 4.26
75 76 2.317609 CCTCAACCCAACGAGCACG 61.318 63.158 0.76 0.76 45.75 5.34
79 80 1.890510 AACCCAACGAGCACGAACC 60.891 57.895 11.40 0.00 42.66 3.62
131 132 2.080286 AGTCTCAAACCGGAATCGTG 57.920 50.000 9.46 0.00 33.95 4.35
138 139 0.984432 AACCGGAATCGTGGGGGTAT 60.984 55.000 9.46 0.00 33.95 2.73
166 167 1.883732 CTCGTCGGCAGAGGAAAGA 59.116 57.895 10.38 0.00 40.28 2.52
169 170 0.243907 CGTCGGCAGAGGAAAGAAGA 59.756 55.000 0.00 0.00 34.40 2.87
178 179 0.984995 AGGAAAGAAGAAGGGGGACG 59.015 55.000 0.00 0.00 0.00 4.79
184 185 1.152096 AAGAAGGGGGACGTGGTCT 60.152 57.895 0.00 0.00 32.47 3.85
193 194 0.321653 GGACGTGGTCTGAGCCAATT 60.322 55.000 4.17 0.00 40.68 2.32
226 227 2.203938 AGGGAGGCGAGGGAACAA 60.204 61.111 0.00 0.00 0.00 2.83
344 348 5.926542 GCAGGATAAAACCACCTTCTTTTTC 59.073 40.000 0.00 0.00 31.06 2.29
390 394 9.725019 TGATTCAACAGTATCTCAAATAGTTGT 57.275 29.630 2.43 0.00 36.97 3.32
407 411 4.032452 TCCTGAAGCGGCCATGCA 62.032 61.111 2.24 0.00 37.31 3.96
410 414 1.514087 CTGAAGCGGCCATGCAAAT 59.486 52.632 2.24 0.00 37.31 2.32
708 716 1.134670 CCACCGTTCCTCCTCTCATTC 60.135 57.143 0.00 0.00 0.00 2.67
783 791 1.538687 CCCGTCCCGTCAGGTTACTT 61.539 60.000 0.00 0.00 36.75 2.24
785 793 0.108945 CGTCCCGTCAGGTTACTTCC 60.109 60.000 0.00 0.00 36.75 3.46
786 794 0.971386 GTCCCGTCAGGTTACTTCCA 59.029 55.000 0.00 0.00 36.75 3.53
797 805 3.901844 AGGTTACTTCCACTACTTGCTCA 59.098 43.478 0.00 0.00 0.00 4.26
798 806 4.021016 AGGTTACTTCCACTACTTGCTCAG 60.021 45.833 0.00 0.00 0.00 3.35
799 807 2.464157 ACTTCCACTACTTGCTCAGC 57.536 50.000 0.00 0.00 0.00 4.26
800 808 1.694150 ACTTCCACTACTTGCTCAGCA 59.306 47.619 0.00 0.00 36.47 4.41
1109 2101 2.186903 CATGTAAGTCCCCGCGCT 59.813 61.111 5.56 0.00 0.00 5.92
1158 2152 2.795329 TCTTCCTTGTCCCATTTGCTC 58.205 47.619 0.00 0.00 0.00 4.26
1219 2213 3.435186 GCTTTCCTGCGCTCCACC 61.435 66.667 9.73 0.00 0.00 4.61
1296 2290 2.021208 GCTGATTGCTCCTCCTTTCCC 61.021 57.143 0.00 0.00 38.95 3.97
1364 2358 0.792640 CGATGTGGAGTGTCAAGTGC 59.207 55.000 0.00 0.00 0.00 4.40
1466 2468 1.655350 GTTGCTGCTGTTCGTGTGC 60.655 57.895 0.00 0.00 0.00 4.57
1727 2737 9.971922 ATTTGAACAAAGTACTACTACTTACGT 57.028 29.630 0.00 0.00 41.58 3.57
1728 2738 8.786937 TTGAACAAAGTACTACTACTTACGTG 57.213 34.615 0.00 0.00 41.58 4.49
1729 2739 7.930217 TGAACAAAGTACTACTACTTACGTGT 58.070 34.615 0.00 0.00 41.58 4.49
1730 2740 8.405531 TGAACAAAGTACTACTACTTACGTGTT 58.594 33.333 0.00 9.03 41.58 3.32
1731 2741 9.878599 GAACAAAGTACTACTACTTACGTGTTA 57.121 33.333 0.00 0.00 41.58 2.41
1803 2822 7.249147 GGTCTGTCATGATCTTCAGATTTTTG 58.751 38.462 14.69 0.00 38.80 2.44
1805 2824 8.295288 GTCTGTCATGATCTTCAGATTTTTGTT 58.705 33.333 14.69 0.00 38.80 2.83
1806 2825 8.853126 TCTGTCATGATCTTCAGATTTTTGTTT 58.147 29.630 9.13 0.00 34.37 2.83
1843 3107 2.002586 CTATGCGTTTGTGGACCAGAG 58.997 52.381 0.00 0.00 0.00 3.35
2022 3291 2.158019 TGGGATGGGCATAGGATGTAGA 60.158 50.000 0.00 0.00 0.00 2.59
2039 3573 6.933521 GGATGTAGAATGTGATATGCAAGACT 59.066 38.462 0.00 0.00 0.00 3.24
2055 3590 8.729805 ATGCAAGACTAGAATAAGAAAAGGAG 57.270 34.615 0.00 0.00 0.00 3.69
2056 3591 7.106239 TGCAAGACTAGAATAAGAAAAGGAGG 58.894 38.462 0.00 0.00 0.00 4.30
2057 3592 7.038302 TGCAAGACTAGAATAAGAAAAGGAGGA 60.038 37.037 0.00 0.00 0.00 3.71
2075 3611 2.811307 AGCTTTGTTGCAGGCTCAA 58.189 47.368 0.00 0.00 34.99 3.02
2079 3615 2.034558 GCTTTGTTGCAGGCTCAAACTA 59.965 45.455 9.52 0.89 0.00 2.24
2080 3616 3.305608 GCTTTGTTGCAGGCTCAAACTAT 60.306 43.478 9.52 0.00 0.00 2.12
2081 3617 4.797275 GCTTTGTTGCAGGCTCAAACTATT 60.797 41.667 9.52 0.00 0.00 1.73
2083 3619 4.935352 TGTTGCAGGCTCAAACTATTTT 57.065 36.364 9.52 0.00 0.00 1.82
2084 3620 4.870363 TGTTGCAGGCTCAAACTATTTTC 58.130 39.130 9.52 0.00 0.00 2.29
2085 3621 4.584325 TGTTGCAGGCTCAAACTATTTTCT 59.416 37.500 9.52 0.00 0.00 2.52
2086 3622 4.771590 TGCAGGCTCAAACTATTTTCTG 57.228 40.909 0.00 0.00 0.00 3.02
2087 3623 4.397420 TGCAGGCTCAAACTATTTTCTGA 58.603 39.130 0.00 0.00 0.00 3.27
2088 3624 4.456911 TGCAGGCTCAAACTATTTTCTGAG 59.543 41.667 0.00 0.00 38.66 3.35
2118 3654 6.655078 TTTTTGAGGGAAGGATTTTCTGAG 57.345 37.500 0.00 0.00 0.00 3.35
2119 3655 3.356529 TGAGGGAAGGATTTTCTGAGC 57.643 47.619 0.00 0.00 0.00 4.26
2121 3657 3.331889 TGAGGGAAGGATTTTCTGAGCTT 59.668 43.478 0.00 0.00 0.00 3.74
2123 3659 4.745351 AGGGAAGGATTTTCTGAGCTTTT 58.255 39.130 0.00 0.00 0.00 2.27
2124 3660 5.150715 AGGGAAGGATTTTCTGAGCTTTTT 58.849 37.500 0.00 0.00 0.00 1.94
2173 3744 7.064490 AGCTTTGTTTAACTGTGGTGAAAATTG 59.936 33.333 0.00 0.00 28.51 2.32
2232 3803 0.960364 GAGTTGCTGATTTCGGGGCA 60.960 55.000 0.00 0.00 0.00 5.36
2292 3863 8.840833 TTGCTAATTTCAGTACAAGTATGTCA 57.159 30.769 0.00 0.00 41.05 3.58
2324 3895 5.393124 TCAATCAATTGCGCTAGAAACTTG 58.607 37.500 9.73 2.09 37.68 3.16
2331 3906 1.363744 CGCTAGAAACTTGCCTCCAG 58.636 55.000 0.00 0.00 0.00 3.86
2341 3916 5.453567 AACTTGCCTCCAGTGATTTTAAC 57.546 39.130 0.00 0.00 0.00 2.01
2344 3919 5.705905 ACTTGCCTCCAGTGATTTTAACTAC 59.294 40.000 0.00 0.00 0.00 2.73
2370 3946 5.284861 TCCTGTACACTTTTCTGCTTGTA 57.715 39.130 0.00 0.00 0.00 2.41
2417 3996 4.767633 GTGAGTAGCACCGTCGAG 57.232 61.111 0.00 0.00 41.78 4.04
2994 4573 5.789643 TTCCTTGCAATTAAAGAGCTGTT 57.210 34.783 0.00 0.00 0.00 3.16
3010 4589 6.306987 AGAGCTGTTTGAATTCCCTAAAAGA 58.693 36.000 2.27 0.00 0.00 2.52
3016 4595 9.415544 CTGTTTGAATTCCCTAAAAGATCTTTG 57.584 33.333 21.15 9.72 32.36 2.77
3090 4669 6.497624 TGTTAGTGTTAAGGTCCTTTGGTA 57.502 37.500 10.04 0.00 0.00 3.25
3092 4671 6.100134 TGTTAGTGTTAAGGTCCTTTGGTAGT 59.900 38.462 10.04 0.57 0.00 2.73
3094 4673 3.501062 GTGTTAAGGTCCTTTGGTAGTGC 59.499 47.826 10.04 0.00 0.00 4.40
3095 4674 3.079578 GTTAAGGTCCTTTGGTAGTGCC 58.920 50.000 10.04 0.00 37.90 5.01
3120 4699 7.094762 CCAGTTAGATACCTTGTTCCTGTTTTC 60.095 40.741 0.00 0.00 0.00 2.29
3121 4700 7.444183 CAGTTAGATACCTTGTTCCTGTTTTCA 59.556 37.037 0.00 0.00 0.00 2.69
3191 4770 8.840833 TTCGCCATGCTTCTTAATAATATGTA 57.159 30.769 0.00 0.00 0.00 2.29
3248 4827 6.236409 CAGGATGGTGTCATATCTTAATGCT 58.764 40.000 0.00 0.00 32.98 3.79
3276 4855 6.817184 TCAAGTAGTAGCACCATTATCTTCC 58.183 40.000 0.00 0.00 0.00 3.46
3304 4883 4.674281 ACAGCCTAGTTGCCTATAACTC 57.326 45.455 0.00 0.00 41.01 3.01
3354 4933 3.815962 TGCTGAAAAATACTGTTGCGGTA 59.184 39.130 0.00 0.00 0.00 4.02
3355 4934 4.083537 TGCTGAAAAATACTGTTGCGGTAG 60.084 41.667 0.00 0.00 0.00 3.18
3360 4939 7.259161 TGAAAAATACTGTTGCGGTAGTTTTT 58.741 30.769 19.97 16.59 46.32 1.94
3504 5083 5.006165 GGCTTCTGATTCTAGTGACAAATCG 59.994 44.000 0.00 0.00 33.13 3.34
3535 5114 8.893727 ACAAATTAGATCATAAGGTACAGTTGC 58.106 33.333 0.00 0.00 0.00 4.17
3557 5136 5.059161 GCCACTACATATCTGATGCTTTGA 58.941 41.667 0.00 0.00 0.00 2.69
3594 5176 9.672086 TCCATTGTTTAAAGATAAGTTTCGTTG 57.328 29.630 0.00 0.00 0.00 4.10
3711 5293 9.330063 GTTCACTCATATCAGATTCCATTTGTA 57.670 33.333 0.00 0.00 0.00 2.41
3778 5360 7.448420 AGTGTATGAGGTATCATTTCATCCTG 58.552 38.462 0.00 0.00 43.92 3.86
4025 5666 8.880244 AGGTATATGCTCTACATTTCCATACAA 58.120 33.333 0.00 0.00 40.38 2.41
4038 5679 7.339212 ACATTTCCATACAAGATTCATCGGAAA 59.661 33.333 0.00 0.00 43.34 3.13
4046 5687 7.219484 ACAAGATTCATCGGAAATTTCTTGT 57.781 32.000 17.42 12.97 46.18 3.16
4047 5688 7.502177 CAAGATTCATCGGAAATTTCTTGTG 57.498 36.000 17.42 12.77 40.00 3.33
4048 5689 6.824305 AGATTCATCGGAAATTTCTTGTGT 57.176 33.333 17.42 6.91 36.43 3.72
4049 5690 7.219484 AGATTCATCGGAAATTTCTTGTGTT 57.781 32.000 17.42 6.64 36.43 3.32
4050 5691 8.335532 AGATTCATCGGAAATTTCTTGTGTTA 57.664 30.769 17.42 7.38 36.43 2.41
4051 5692 8.792633 AGATTCATCGGAAATTTCTTGTGTTAA 58.207 29.630 17.42 5.13 36.43 2.01
4052 5693 8.970691 ATTCATCGGAAATTTCTTGTGTTAAG 57.029 30.769 17.42 0.23 36.43 1.85
4053 5694 6.378582 TCATCGGAAATTTCTTGTGTTAAGC 58.621 36.000 17.42 0.00 0.00 3.09
4054 5695 5.116069 TCGGAAATTTCTTGTGTTAAGCC 57.884 39.130 17.42 0.00 0.00 4.35
4082 5723 4.482990 ACATCCATCCCTTTTGTTTGACT 58.517 39.130 0.00 0.00 0.00 3.41
4083 5724 4.281688 ACATCCATCCCTTTTGTTTGACTG 59.718 41.667 0.00 0.00 0.00 3.51
4105 5746 5.402630 TGATGTATACTTCTCCAGGGCATA 58.597 41.667 17.02 0.00 0.00 3.14
4108 5749 6.763715 TGTATACTTCTCCAGGGCATATTT 57.236 37.500 4.17 0.00 0.00 1.40
4162 5803 4.215613 GCGGGTGGAAATGGTAATATTCTC 59.784 45.833 0.00 0.00 0.00 2.87
4166 5807 7.883311 CGGGTGGAAATGGTAATATTCTCTAAT 59.117 37.037 0.00 0.00 0.00 1.73
4229 5983 3.118905 TGTTATGGGGCTTTTGTTTGC 57.881 42.857 0.00 0.00 0.00 3.68
4237 5991 2.489971 GGCTTTTGTTTGCCCTTTACC 58.510 47.619 0.00 0.00 43.11 2.85
4240 5994 3.181470 GCTTTTGTTTGCCCTTTACCTGA 60.181 43.478 0.00 0.00 0.00 3.86
4315 6069 5.220265 GCAATTATCAACTGATTTGTTGGCG 60.220 40.000 7.40 0.00 45.15 5.69
4316 6070 5.895636 ATTATCAACTGATTTGTTGGCGA 57.104 34.783 7.40 0.00 45.15 5.54
4317 6071 3.837213 ATCAACTGATTTGTTGGCGAG 57.163 42.857 7.40 0.00 45.15 5.03
4319 6073 3.734463 TCAACTGATTTGTTGGCGAGTA 58.266 40.909 7.40 0.00 45.15 2.59
4322 6076 4.530710 ACTGATTTGTTGGCGAGTAGTA 57.469 40.909 0.00 0.00 0.00 1.82
4323 6077 4.243270 ACTGATTTGTTGGCGAGTAGTAC 58.757 43.478 0.00 0.00 0.00 2.73
4324 6078 3.592059 TGATTTGTTGGCGAGTAGTACC 58.408 45.455 0.00 0.00 0.00 3.34
4325 6079 3.007074 TGATTTGTTGGCGAGTAGTACCA 59.993 43.478 0.00 0.00 0.00 3.25
4326 6080 3.688694 TTTGTTGGCGAGTAGTACCAT 57.311 42.857 0.00 0.00 32.39 3.55
4327 6081 3.688694 TTGTTGGCGAGTAGTACCATT 57.311 42.857 0.00 0.00 32.39 3.16
4328 6082 3.241067 TGTTGGCGAGTAGTACCATTC 57.759 47.619 0.00 0.00 32.39 2.67
4329 6083 2.829720 TGTTGGCGAGTAGTACCATTCT 59.170 45.455 0.00 0.00 32.39 2.40
4330 6084 3.259876 TGTTGGCGAGTAGTACCATTCTT 59.740 43.478 0.00 0.00 32.39 2.52
4336 6090 5.063564 GGCGAGTAGTACCATTCTTTTTCTG 59.936 44.000 0.00 0.00 0.00 3.02
4337 6091 5.446073 GCGAGTAGTACCATTCTTTTTCTGC 60.446 44.000 0.00 0.00 0.00 4.26
4338 6092 5.637810 CGAGTAGTACCATTCTTTTTCTGCA 59.362 40.000 0.00 0.00 0.00 4.41
4339 6093 6.401153 CGAGTAGTACCATTCTTTTTCTGCAC 60.401 42.308 0.00 0.00 0.00 4.57
4340 6094 5.705905 AGTAGTACCATTCTTTTTCTGCACC 59.294 40.000 0.00 0.00 0.00 5.01
4341 6095 3.826729 AGTACCATTCTTTTTCTGCACCC 59.173 43.478 0.00 0.00 0.00 4.61
4343 6097 1.613437 CCATTCTTTTTCTGCACCCGT 59.387 47.619 0.00 0.00 0.00 5.28
4344 6098 2.817258 CCATTCTTTTTCTGCACCCGTA 59.183 45.455 0.00 0.00 0.00 4.02
4345 6099 3.443681 CCATTCTTTTTCTGCACCCGTAT 59.556 43.478 0.00 0.00 0.00 3.06
4346 6100 4.082245 CCATTCTTTTTCTGCACCCGTATT 60.082 41.667 0.00 0.00 0.00 1.89
4348 6102 2.739913 TCTTTTTCTGCACCCGTATTCG 59.260 45.455 0.00 0.00 0.00 3.34
4364 6118 6.153212 CGTATTCGGGCTTTCAACATATAG 57.847 41.667 0.00 0.00 0.00 1.31
4365 6119 5.924254 CGTATTCGGGCTTTCAACATATAGA 59.076 40.000 0.00 0.00 0.00 1.98
4366 6120 6.590292 CGTATTCGGGCTTTCAACATATAGAT 59.410 38.462 0.00 0.00 0.00 1.98
4367 6121 7.758076 CGTATTCGGGCTTTCAACATATAGATA 59.242 37.037 0.00 0.00 0.00 1.98
4368 6122 7.907214 ATTCGGGCTTTCAACATATAGATAC 57.093 36.000 0.00 0.00 0.00 2.24
4369 6123 6.665992 TCGGGCTTTCAACATATAGATACT 57.334 37.500 0.00 0.00 0.00 2.12
4370 6124 7.062749 TCGGGCTTTCAACATATAGATACTT 57.937 36.000 0.00 0.00 0.00 2.24
4371 6125 7.152645 TCGGGCTTTCAACATATAGATACTTC 58.847 38.462 0.00 0.00 0.00 3.01
4372 6126 6.369065 CGGGCTTTCAACATATAGATACTTCC 59.631 42.308 0.00 0.00 0.00 3.46
4373 6127 6.369065 GGGCTTTCAACATATAGATACTTCCG 59.631 42.308 0.00 0.00 0.00 4.30
4374 6128 6.128526 GGCTTTCAACATATAGATACTTCCGC 60.129 42.308 0.00 0.00 0.00 5.54
4375 6129 6.647067 GCTTTCAACATATAGATACTTCCGCT 59.353 38.462 0.00 0.00 0.00 5.52
4376 6130 7.359598 GCTTTCAACATATAGATACTTCCGCTG 60.360 40.741 0.00 0.00 0.00 5.18
4377 6131 6.894339 TCAACATATAGATACTTCCGCTGA 57.106 37.500 0.00 0.00 0.00 4.26
4378 6132 7.468141 TCAACATATAGATACTTCCGCTGAT 57.532 36.000 0.00 0.00 0.00 2.90
4379 6133 7.315890 TCAACATATAGATACTTCCGCTGATG 58.684 38.462 0.00 0.00 0.00 3.07
4380 6134 5.655488 ACATATAGATACTTCCGCTGATGC 58.345 41.667 0.00 0.00 0.00 3.91
4381 6135 3.601443 ATAGATACTTCCGCTGATGCC 57.399 47.619 0.00 0.00 35.36 4.40
4382 6136 1.418334 AGATACTTCCGCTGATGCCT 58.582 50.000 0.00 0.00 35.36 4.75
4383 6137 2.598565 AGATACTTCCGCTGATGCCTA 58.401 47.619 0.00 0.00 35.36 3.93
4384 6138 2.560542 AGATACTTCCGCTGATGCCTAG 59.439 50.000 0.00 0.00 35.36 3.02
4385 6139 1.776662 TACTTCCGCTGATGCCTAGT 58.223 50.000 0.00 0.00 35.36 2.57
4386 6140 1.776662 ACTTCCGCTGATGCCTAGTA 58.223 50.000 0.00 0.00 35.36 1.82
4387 6141 1.409427 ACTTCCGCTGATGCCTAGTAC 59.591 52.381 0.00 0.00 35.36 2.73
4388 6142 1.683917 CTTCCGCTGATGCCTAGTACT 59.316 52.381 0.00 0.00 35.36 2.73
4389 6143 1.776662 TCCGCTGATGCCTAGTACTT 58.223 50.000 0.00 0.00 35.36 2.24
4390 6144 1.409064 TCCGCTGATGCCTAGTACTTG 59.591 52.381 0.00 0.00 35.36 3.16
4391 6145 1.137086 CCGCTGATGCCTAGTACTTGT 59.863 52.381 0.00 0.00 35.36 3.16
4392 6146 2.418746 CCGCTGATGCCTAGTACTTGTT 60.419 50.000 0.00 0.00 35.36 2.83
4393 6147 3.181479 CCGCTGATGCCTAGTACTTGTTA 60.181 47.826 0.00 0.00 35.36 2.41
4394 6148 4.045104 CGCTGATGCCTAGTACTTGTTAG 58.955 47.826 0.00 0.00 35.36 2.34
4395 6149 4.440250 CGCTGATGCCTAGTACTTGTTAGT 60.440 45.833 0.00 0.00 35.60 2.24
4396 6150 5.420409 GCTGATGCCTAGTACTTGTTAGTT 58.580 41.667 0.00 0.00 35.78 2.24
4397 6151 5.292101 GCTGATGCCTAGTACTTGTTAGTTG 59.708 44.000 0.00 0.00 35.78 3.16
4398 6152 6.354794 TGATGCCTAGTACTTGTTAGTTGT 57.645 37.500 0.00 0.00 35.78 3.32
4399 6153 6.765403 TGATGCCTAGTACTTGTTAGTTGTT 58.235 36.000 0.00 0.00 35.78 2.83
4400 6154 7.898918 TGATGCCTAGTACTTGTTAGTTGTTA 58.101 34.615 0.00 0.00 35.78 2.41
4401 6155 8.537016 TGATGCCTAGTACTTGTTAGTTGTTAT 58.463 33.333 0.00 0.00 35.78 1.89
4484 6238 0.829182 CCTTGGCCTTTGGTGAAGCT 60.829 55.000 3.32 0.00 33.84 3.74
4500 6254 3.005684 TGAAGCTCGATTTTTGTGCCATT 59.994 39.130 0.00 0.00 0.00 3.16
4532 6286 8.726988 GTCAGTGCCTTTTATGTTAATGTTCTA 58.273 33.333 0.00 0.00 0.00 2.10
4674 6428 5.688621 CGGAAAATTGTTGATAGCATCATGG 59.311 40.000 0.00 0.00 39.39 3.66
4676 6430 5.601583 AAATTGTTGATAGCATCATGGCA 57.398 34.783 0.00 0.00 39.39 4.92
4821 6575 1.409427 CCGAGCTCCTTAAGGTACCAG 59.591 57.143 21.04 12.00 35.33 4.00
4823 6577 2.159226 CGAGCTCCTTAAGGTACCAGTG 60.159 54.545 21.04 0.91 35.33 3.66
4862 6616 9.295825 TGTTACAGACACAATTAAATTCCTGAT 57.704 29.630 0.00 0.00 32.00 2.90
4884 6638 1.906574 CAGGGCCCAACTTAGTGAGTA 59.093 52.381 27.56 0.00 37.72 2.59
4973 6730 7.288389 ACCATGTCCGTCTATACTTTAATACCA 59.712 37.037 0.00 0.00 0.00 3.25
4975 6732 9.706691 CATGTCCGTCTATACTTTAATACCAAT 57.293 33.333 0.00 0.00 0.00 3.16
5048 6805 2.291741 GCTTACTGGCATATGCAACCTC 59.708 50.000 28.07 11.58 44.36 3.85
5054 6811 1.824230 GGCATATGCAACCTCCAACAA 59.176 47.619 28.07 0.00 44.36 2.83
5090 6847 2.909006 TGAGGATGCTCTTTCTCAAGGT 59.091 45.455 15.82 0.00 33.87 3.50
5127 6884 1.148273 TCGCTTGCAGAAACCCTGT 59.852 52.632 0.00 0.00 44.71 4.00
5284 7044 4.068599 GCTCTTTCCTCTGCTTAAGTTGT 58.931 43.478 4.02 0.00 0.00 3.32
5285 7045 4.517075 GCTCTTTCCTCTGCTTAAGTTGTT 59.483 41.667 4.02 0.00 0.00 2.83
5286 7046 5.561725 GCTCTTTCCTCTGCTTAAGTTGTTG 60.562 44.000 4.02 0.00 0.00 3.33
5334 7094 6.183361 GGCAGACTATTTGGGGAGTTAGAATA 60.183 42.308 0.00 0.00 0.00 1.75
5346 7110 6.599638 GGGGAGTTAGAATATTGTGATATGCC 59.400 42.308 0.00 0.00 0.00 4.40
5387 7153 1.799933 AGAATCTGAGCCTAGGGTGG 58.200 55.000 20.52 11.08 0.00 4.61
5388 7154 1.008938 AGAATCTGAGCCTAGGGTGGT 59.991 52.381 20.52 0.00 0.00 4.16
5389 7155 1.139853 GAATCTGAGCCTAGGGTGGTG 59.860 57.143 20.52 8.11 0.00 4.17
5390 7156 1.341156 ATCTGAGCCTAGGGTGGTGC 61.341 60.000 20.52 4.12 0.00 5.01
5409 7175 1.227853 GGGGTTGCGTGTTCTCACT 60.228 57.895 0.00 0.00 41.89 3.41
5447 7213 0.173481 GCTCGAATTGCCCCTTTTCC 59.827 55.000 0.00 0.00 0.00 3.13
5467 7233 8.810652 TTTTCCACTTCATTACTAAAACATGC 57.189 30.769 0.00 0.00 0.00 4.06
5469 7235 5.935206 TCCACTTCATTACTAAAACATGCGA 59.065 36.000 0.00 0.00 0.00 5.10
5493 7259 2.684881 CCTTCATAGCACGCTCCATTTT 59.315 45.455 0.00 0.00 0.00 1.82
5589 7400 4.957759 TCACTTGAACTGATGCATCATG 57.042 40.909 28.81 22.87 36.02 3.07
5623 7434 6.989759 GGGGAAAGCAAGAAAACATAGAAAAA 59.010 34.615 0.00 0.00 0.00 1.94
5625 7436 7.926018 GGGAAAGCAAGAAAACATAGAAAAAGA 59.074 33.333 0.00 0.00 0.00 2.52
5626 7437 9.313118 GGAAAGCAAGAAAACATAGAAAAAGAA 57.687 29.630 0.00 0.00 0.00 2.52
5699 7510 1.001293 CAGGCTGATAATCTGCGGCTA 59.999 52.381 9.42 0.00 41.49 3.93
5991 7806 8.564509 TCAGAATCATGTGATGAATGTTTACA 57.435 30.769 0.00 0.00 43.50 2.41
6111 7926 5.117584 ACTTGCAGAATAGCTTGAGATCTG 58.882 41.667 0.00 0.38 40.30 2.90
6144 7959 1.602377 GCTTGTGGACTTGTGGTGTAC 59.398 52.381 0.00 0.00 0.00 2.90
6179 7995 2.200081 ACCATACAGCCTGATGAGGTT 58.800 47.619 0.00 0.00 42.15 3.50
6299 8120 4.368391 CACTCACAGTGGACCAGC 57.632 61.111 0.00 0.00 42.35 4.85
6300 8121 1.447217 CACTCACAGTGGACCAGCA 59.553 57.895 0.00 0.00 42.35 4.41
6301 8122 0.035881 CACTCACAGTGGACCAGCAT 59.964 55.000 0.00 0.00 42.35 3.79
6302 8123 0.035881 ACTCACAGTGGACCAGCATG 59.964 55.000 0.00 0.00 0.00 4.06
6303 8124 0.322648 CTCACAGTGGACCAGCATGA 59.677 55.000 0.00 0.00 39.69 3.07
6304 8125 0.764271 TCACAGTGGACCAGCATGAA 59.236 50.000 0.00 0.00 39.69 2.57
6305 8126 1.352017 TCACAGTGGACCAGCATGAAT 59.648 47.619 0.00 0.00 39.69 2.57
6306 8127 1.471287 CACAGTGGACCAGCATGAATG 59.529 52.381 0.00 0.00 39.69 2.67
6316 8137 4.961637 CATGAATGCCGTCCAGGA 57.038 55.556 0.00 0.00 45.00 3.86
6317 8138 2.699073 CATGAATGCCGTCCAGGAG 58.301 57.895 0.00 0.00 45.00 3.69
6318 8139 0.107508 CATGAATGCCGTCCAGGAGT 60.108 55.000 0.00 0.00 45.00 3.85
6319 8140 1.138859 CATGAATGCCGTCCAGGAGTA 59.861 52.381 0.00 0.00 45.00 2.59
6320 8141 0.535335 TGAATGCCGTCCAGGAGTAC 59.465 55.000 0.00 0.00 45.00 2.73
6321 8142 0.179081 GAATGCCGTCCAGGAGTACC 60.179 60.000 0.00 0.00 45.00 3.34
6322 8143 1.623542 AATGCCGTCCAGGAGTACCC 61.624 60.000 0.00 0.00 45.00 3.69
6324 8145 1.988406 GCCGTCCAGGAGTACCCTT 60.988 63.158 0.00 0.00 44.85 3.95
6325 8146 0.685458 GCCGTCCAGGAGTACCCTTA 60.685 60.000 0.00 0.00 44.85 2.69
6326 8147 1.109609 CCGTCCAGGAGTACCCTTAC 58.890 60.000 0.00 2.62 44.85 2.34
6327 8148 1.617804 CCGTCCAGGAGTACCCTTACA 60.618 57.143 0.00 0.00 44.85 2.41
6374 8195 1.535685 GCCTGGGCTTCATGGATCT 59.464 57.895 4.12 0.00 38.26 2.75
6375 8196 0.822532 GCCTGGGCTTCATGGATCTG 60.823 60.000 4.12 0.00 38.26 2.90
6376 8197 0.841961 CCTGGGCTTCATGGATCTGA 59.158 55.000 0.00 0.00 0.00 3.27
6377 8198 1.213678 CCTGGGCTTCATGGATCTGAA 59.786 52.381 0.00 0.00 34.14 3.02
6378 8199 2.295885 CTGGGCTTCATGGATCTGAAC 58.704 52.381 0.00 0.00 31.98 3.18
6379 8200 1.634973 TGGGCTTCATGGATCTGAACA 59.365 47.619 0.00 0.00 31.98 3.18
6413 8264 1.141858 GTGTGATCCTCCTCATTCCCC 59.858 57.143 0.00 0.00 0.00 4.81
6466 8317 6.991938 TGGTAGAAAATTTGACCATTCAAGG 58.008 36.000 13.28 0.00 42.79 3.61
6515 8380 7.124599 TCCCAAAGCTTATTTGACATCATGATT 59.875 33.333 5.16 0.00 0.00 2.57
6531 8396 1.687660 TGATTTGGCAAAGCTTGAGCA 59.312 42.857 26.29 5.51 45.16 4.26
6569 8434 9.486123 TCCCCAATCAGAAATGTGATTTTTATA 57.514 29.630 3.28 0.00 43.29 0.98
6659 8525 6.174720 TCTGGATATAAACGAGGCAGATTT 57.825 37.500 0.00 0.00 0.00 2.17
6744 8610 2.690840 ACCAGATGGGATAGTGGTACC 58.309 52.381 4.43 4.43 41.65 3.34
6750 8616 1.006281 TGGGATAGTGGTACCGTCAGT 59.994 52.381 7.57 0.00 0.00 3.41
6756 8622 3.315949 GGTACCGTCAGTGGGGCA 61.316 66.667 0.00 0.00 0.00 5.36
6788 8654 3.388272 TGGAACACGCAGTTAAGCA 57.612 47.368 0.00 0.00 41.61 3.91
6789 8655 1.225855 TGGAACACGCAGTTAAGCAG 58.774 50.000 0.00 0.00 41.61 4.24
6790 8656 0.110192 GGAACACGCAGTTAAGCAGC 60.110 55.000 0.00 0.00 41.61 5.25
6813 8679 4.694233 CAGCAGCCTCACCACGCT 62.694 66.667 0.00 0.00 35.10 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.529244 CCCCTCGGCCATTGATTCC 60.529 63.158 2.24 0.00 0.00 3.01
30 31 4.716977 ACCCTCACCCTCGTCCCC 62.717 72.222 0.00 0.00 0.00 4.81
35 36 3.760035 CGGTCACCCTCACCCTCG 61.760 72.222 0.00 0.00 0.00 4.63
55 56 3.056328 GCTCGTTGGGTTGAGGCC 61.056 66.667 0.00 0.00 32.78 5.19
58 59 0.878523 TTCGTGCTCGTTGGGTTGAG 60.879 55.000 8.17 0.00 38.33 3.02
61 62 1.890510 GGTTCGTGCTCGTTGGGTT 60.891 57.895 8.17 0.00 38.33 4.11
73 74 3.569049 CTTCGTGGAGGCGGTTCGT 62.569 63.158 0.00 0.00 0.00 3.85
75 76 3.119096 GCTTCGTGGAGGCGGTTC 61.119 66.667 0.00 0.00 0.00 3.62
157 158 2.270858 GTCCCCCTTCTTCTTTCCTCT 58.729 52.381 0.00 0.00 0.00 3.69
166 167 1.152096 AGACCACGTCCCCCTTCTT 60.152 57.895 0.00 0.00 32.18 2.52
169 170 1.913762 CTCAGACCACGTCCCCCTT 60.914 63.158 0.00 0.00 32.18 3.95
178 179 3.055819 TCACTAGAATTGGCTCAGACCAC 60.056 47.826 0.00 0.00 40.19 4.16
184 185 4.261783 CGAGCTATCACTAGAATTGGCTCA 60.262 45.833 21.26 0.00 43.20 4.26
193 194 2.039216 CTCCCTCCGAGCTATCACTAGA 59.961 54.545 0.00 0.00 0.00 2.43
223 224 1.683441 GGAATGGGACCTCCGTTGT 59.317 57.895 0.00 0.00 44.41 3.32
322 325 6.041637 GGTGAAAAAGAAGGTGGTTTTATCCT 59.958 38.462 0.00 0.00 0.00 3.24
325 329 6.839134 AGAGGTGAAAAAGAAGGTGGTTTTAT 59.161 34.615 0.00 0.00 0.00 1.40
344 348 5.032327 TCATTTGAGGATGATGAGAGGTG 57.968 43.478 0.00 0.00 31.35 4.00
390 394 3.565961 TTGCATGGCCGCTTCAGGA 62.566 57.895 0.00 0.00 0.00 3.86
708 716 3.083997 CGTGAAGGGGGAGGAGGG 61.084 72.222 0.00 0.00 0.00 4.30
797 805 3.556633 CCTGACACTCTGATCAGTTTGCT 60.557 47.826 21.92 10.59 40.70 3.91
798 806 2.740981 CCTGACACTCTGATCAGTTTGC 59.259 50.000 21.92 14.83 40.70 3.68
799 807 3.993081 GTCCTGACACTCTGATCAGTTTG 59.007 47.826 21.92 20.13 40.70 2.93
800 808 3.643320 TGTCCTGACACTCTGATCAGTTT 59.357 43.478 21.92 7.74 40.70 2.66
1158 2152 0.315951 CATGCAGAAATGAGCGAGCG 60.316 55.000 0.00 0.00 0.00 5.03
1219 2213 2.104331 AGGGCTCGTAATCGCACG 59.896 61.111 0.00 0.00 43.28 5.34
1296 2290 2.388232 CGCTTTTCCTTCCCGTCCG 61.388 63.158 0.00 0.00 0.00 4.79
1324 2318 2.103941 GACAAGAGCTAATCAGAGGGGG 59.896 54.545 0.00 0.00 0.00 5.40
1722 2732 8.560355 TGTATTACACTCCTACTAACACGTAA 57.440 34.615 0.00 0.00 0.00 3.18
1724 2734 7.636150 ATGTATTACACTCCTACTAACACGT 57.364 36.000 0.00 0.00 0.00 4.49
1725 2735 7.972277 ACAATGTATTACACTCCTACTAACACG 59.028 37.037 0.00 0.00 0.00 4.49
1726 2736 9.084164 CACAATGTATTACACTCCTACTAACAC 57.916 37.037 0.00 0.00 0.00 3.32
1727 2737 7.762615 GCACAATGTATTACACTCCTACTAACA 59.237 37.037 0.00 0.00 0.00 2.41
1728 2738 7.043590 CGCACAATGTATTACACTCCTACTAAC 60.044 40.741 0.00 0.00 0.00 2.34
1729 2739 6.976349 CGCACAATGTATTACACTCCTACTAA 59.024 38.462 0.00 0.00 0.00 2.24
1730 2740 6.095860 ACGCACAATGTATTACACTCCTACTA 59.904 38.462 0.00 0.00 0.00 1.82
1731 2741 5.105473 ACGCACAATGTATTACACTCCTACT 60.105 40.000 0.00 0.00 0.00 2.57
1806 2825 4.975502 CGCATAGCACAGTTTCTTCAAAAA 59.024 37.500 0.00 0.00 0.00 1.94
1843 3107 6.146510 TCGGACGTGTGATAAATATATTTGGC 59.853 38.462 18.98 11.61 0.00 4.52
2039 3573 7.690256 ACAAAGCTCCTCCTTTTCTTATTCTA 58.310 34.615 0.00 0.00 32.97 2.10
2051 3586 0.251077 CCTGCAACAAAGCTCCTCCT 60.251 55.000 0.00 0.00 34.99 3.69
2053 3588 0.892814 AGCCTGCAACAAAGCTCCTC 60.893 55.000 0.00 0.00 34.99 3.71
2054 3589 0.892814 GAGCCTGCAACAAAGCTCCT 60.893 55.000 9.86 0.00 44.76 3.69
2055 3590 1.583477 GAGCCTGCAACAAAGCTCC 59.417 57.895 9.86 0.00 44.76 4.70
2057 3592 1.113788 TTTGAGCCTGCAACAAAGCT 58.886 45.000 9.29 0.00 38.56 3.74
2095 3631 5.011023 GCTCAGAAAATCCTTCCCTCAAAAA 59.989 40.000 0.00 0.00 0.00 1.94
2096 3632 4.524328 GCTCAGAAAATCCTTCCCTCAAAA 59.476 41.667 0.00 0.00 0.00 2.44
2097 3633 4.082125 GCTCAGAAAATCCTTCCCTCAAA 58.918 43.478 0.00 0.00 0.00 2.69
2099 3635 2.915604 AGCTCAGAAAATCCTTCCCTCA 59.084 45.455 0.00 0.00 0.00 3.86
2100 3636 3.643199 AGCTCAGAAAATCCTTCCCTC 57.357 47.619 0.00 0.00 0.00 4.30
2101 3637 4.394797 AAAGCTCAGAAAATCCTTCCCT 57.605 40.909 0.00 0.00 0.00 4.20
2102 3638 5.474578 AAAAAGCTCAGAAAATCCTTCCC 57.525 39.130 0.00 0.00 0.00 3.97
2126 3662 4.524328 GCTCAGAAAATCCTTCCCTCAAAA 59.476 41.667 0.00 0.00 0.00 2.44
2127 3663 4.082125 GCTCAGAAAATCCTTCCCTCAAA 58.918 43.478 0.00 0.00 0.00 2.69
2128 3664 3.331889 AGCTCAGAAAATCCTTCCCTCAA 59.668 43.478 0.00 0.00 0.00 3.02
2129 3665 2.915604 AGCTCAGAAAATCCTTCCCTCA 59.084 45.455 0.00 0.00 0.00 3.86
2130 3666 3.643199 AGCTCAGAAAATCCTTCCCTC 57.357 47.619 0.00 0.00 0.00 4.30
2131 3667 4.085009 CAAAGCTCAGAAAATCCTTCCCT 58.915 43.478 0.00 0.00 0.00 4.20
2132 3668 3.829026 ACAAAGCTCAGAAAATCCTTCCC 59.171 43.478 0.00 0.00 0.00 3.97
2134 3670 8.138074 AGTTAAACAAAGCTCAGAAAATCCTTC 58.862 33.333 0.00 0.00 0.00 3.46
2136 3672 7.068716 ACAGTTAAACAAAGCTCAGAAAATCCT 59.931 33.333 0.00 0.00 0.00 3.24
2137 3673 7.168135 CACAGTTAAACAAAGCTCAGAAAATCC 59.832 37.037 0.00 0.00 0.00 3.01
2138 3674 7.168135 CCACAGTTAAACAAAGCTCAGAAAATC 59.832 37.037 0.00 0.00 0.00 2.17
2292 3863 4.217118 AGCGCAATTGATTGAGAAAAGAGT 59.783 37.500 11.47 0.00 39.50 3.24
2324 3895 3.621715 CCGTAGTTAAAATCACTGGAGGC 59.378 47.826 0.00 0.00 0.00 4.70
2331 3906 7.009907 GTGTACAGGATCCGTAGTTAAAATCAC 59.990 40.741 14.25 12.23 0.00 3.06
2341 3916 5.103000 CAGAAAAGTGTACAGGATCCGTAG 58.897 45.833 14.25 8.18 0.00 3.51
2344 3919 2.673368 GCAGAAAAGTGTACAGGATCCG 59.327 50.000 5.98 3.99 0.00 4.18
2386 3962 6.870965 GGTGCTACTCACTGAAATCTATATGG 59.129 42.308 0.00 0.00 44.98 2.74
2417 3996 7.553044 ACCAGTAAGCTTTAGTAATCATGAACC 59.447 37.037 3.20 0.00 0.00 3.62
3016 4595 8.974408 TGTACACGTGCATAATACTGATATTTC 58.026 33.333 17.22 0.00 32.98 2.17
3033 4612 1.460743 CTCAAGCCATGTGTACACGTG 59.539 52.381 32.46 32.46 45.43 4.49
3090 4669 4.323562 GGAACAAGGTATCTAACTGGCACT 60.324 45.833 0.00 0.00 0.00 4.40
3092 4671 3.844211 AGGAACAAGGTATCTAACTGGCA 59.156 43.478 0.00 0.00 0.00 4.92
3094 4673 5.422214 ACAGGAACAAGGTATCTAACTGG 57.578 43.478 0.00 0.00 0.00 4.00
3095 4674 7.444183 TGAAAACAGGAACAAGGTATCTAACTG 59.556 37.037 0.00 0.00 0.00 3.16
3120 4699 7.229506 AGACTCAAACAAAAGGATAGGAAACTG 59.770 37.037 0.00 0.00 43.88 3.16
3191 4770 3.264450 AGGACCATTTTCCTCTGTCGAAT 59.736 43.478 0.00 0.00 42.98 3.34
3197 4776 5.256474 ACAACATAGGACCATTTTCCTCTG 58.744 41.667 0.00 0.00 42.98 3.35
3217 4796 5.846164 AGATATGACACCATCCTGGATACAA 59.154 40.000 9.27 0.00 40.96 2.41
3276 4855 2.017049 GGCAACTAGGCTGTTATGTGG 58.983 52.381 0.00 0.00 40.24 4.17
3359 4938 5.010282 GCATAAAGAGAACTGAGGGGAAAA 58.990 41.667 0.00 0.00 0.00 2.29
3360 4939 4.289672 AGCATAAAGAGAACTGAGGGGAAA 59.710 41.667 0.00 0.00 0.00 3.13
3362 4941 3.454858 AGCATAAAGAGAACTGAGGGGA 58.545 45.455 0.00 0.00 0.00 4.81
3363 4942 3.922171 AGCATAAAGAGAACTGAGGGG 57.078 47.619 0.00 0.00 0.00 4.79
3364 4943 6.825721 ACAATAAGCATAAAGAGAACTGAGGG 59.174 38.462 0.00 0.00 0.00 4.30
3365 4944 7.856145 ACAATAAGCATAAAGAGAACTGAGG 57.144 36.000 0.00 0.00 0.00 3.86
3480 5059 5.006165 CGATTTGTCACTAGAATCAGAAGCC 59.994 44.000 0.00 0.00 31.69 4.35
3504 5083 8.429641 TGTACCTTATGATCTAATTTGTCCCTC 58.570 37.037 0.00 0.00 0.00 4.30
3534 5113 5.059161 TCAAAGCATCAGATATGTAGTGGC 58.941 41.667 0.00 0.00 0.00 5.01
3535 5114 6.932960 TGATCAAAGCATCAGATATGTAGTGG 59.067 38.462 0.00 0.00 0.00 4.00
3594 5176 2.946762 GGCGAAGTGACTGTTGGC 59.053 61.111 0.00 0.00 0.00 4.52
3778 5360 6.697892 CCATGCTACAGTAGTACTAAAGCTTC 59.302 42.308 25.14 8.10 36.60 3.86
3834 5416 6.472016 TCTACCACTGAAGCAAAATCATGTA 58.528 36.000 0.00 0.00 0.00 2.29
4025 5666 6.824305 ACACAAGAAATTTCCGATGAATCT 57.176 33.333 14.61 0.00 0.00 2.40
4038 5679 6.797454 TGTTTAACGGCTTAACACAAGAAAT 58.203 32.000 0.00 0.00 0.00 2.17
4046 5687 4.396790 GGATGGATGTTTAACGGCTTAACA 59.603 41.667 0.00 0.00 0.00 2.41
4047 5688 4.201980 GGGATGGATGTTTAACGGCTTAAC 60.202 45.833 0.00 0.00 0.00 2.01
4048 5689 3.949113 GGGATGGATGTTTAACGGCTTAA 59.051 43.478 0.00 0.00 0.00 1.85
4049 5690 3.201266 AGGGATGGATGTTTAACGGCTTA 59.799 43.478 0.00 0.00 0.00 3.09
4050 5691 2.025321 AGGGATGGATGTTTAACGGCTT 60.025 45.455 0.00 0.00 0.00 4.35
4051 5692 1.564348 AGGGATGGATGTTTAACGGCT 59.436 47.619 0.00 0.00 0.00 5.52
4052 5693 2.052782 AGGGATGGATGTTTAACGGC 57.947 50.000 0.00 0.00 0.00 5.68
4053 5694 4.219725 ACAAAAGGGATGGATGTTTAACGG 59.780 41.667 0.00 0.00 0.00 4.44
4054 5695 5.385509 ACAAAAGGGATGGATGTTTAACG 57.614 39.130 0.00 0.00 0.00 3.18
4082 5723 3.653164 TGCCCTGGAGAAGTATACATCA 58.347 45.455 10.51 0.00 0.00 3.07
4083 5724 4.899352 ATGCCCTGGAGAAGTATACATC 57.101 45.455 5.50 2.46 0.00 3.06
4105 5746 7.589993 ACTGATCCCCTGAAGATGAAATAAAT 58.410 34.615 0.00 0.00 0.00 1.40
4108 5749 5.907662 AGACTGATCCCCTGAAGATGAAATA 59.092 40.000 0.00 0.00 0.00 1.40
4210 5964 2.422597 GGCAAACAAAAGCCCCATAAC 58.577 47.619 0.00 0.00 45.18 1.89
4229 5983 1.280457 AGGAGCACTCAGGTAAAGGG 58.720 55.000 0.00 0.00 0.00 3.95
4235 5989 3.055530 CACATTCTAAGGAGCACTCAGGT 60.056 47.826 0.00 0.00 0.00 4.00
4237 5991 3.055530 ACCACATTCTAAGGAGCACTCAG 60.056 47.826 0.00 0.00 0.00 3.35
4240 5994 4.353777 TCTACCACATTCTAAGGAGCACT 58.646 43.478 0.00 0.00 0.00 4.40
4315 6069 6.128254 GGTGCAGAAAAAGAATGGTACTACTC 60.128 42.308 0.00 0.00 0.00 2.59
4316 6070 5.705905 GGTGCAGAAAAAGAATGGTACTACT 59.294 40.000 0.00 0.00 0.00 2.57
4317 6071 5.106277 GGGTGCAGAAAAAGAATGGTACTAC 60.106 44.000 0.00 0.00 0.00 2.73
4319 6073 3.826729 GGGTGCAGAAAAAGAATGGTACT 59.173 43.478 0.00 0.00 0.00 2.73
4322 6076 1.613437 CGGGTGCAGAAAAAGAATGGT 59.387 47.619 0.00 0.00 0.00 3.55
4323 6077 1.613437 ACGGGTGCAGAAAAAGAATGG 59.387 47.619 0.00 0.00 0.00 3.16
4324 6078 4.701956 ATACGGGTGCAGAAAAAGAATG 57.298 40.909 0.00 0.00 0.00 2.67
4325 6079 4.142687 CGAATACGGGTGCAGAAAAAGAAT 60.143 41.667 0.00 0.00 35.72 2.40
4326 6080 3.187637 CGAATACGGGTGCAGAAAAAGAA 59.812 43.478 0.00 0.00 35.72 2.52
4327 6081 2.739913 CGAATACGGGTGCAGAAAAAGA 59.260 45.455 0.00 0.00 35.72 2.52
4328 6082 3.117434 CGAATACGGGTGCAGAAAAAG 57.883 47.619 0.00 0.00 35.72 2.27
4341 6095 5.924254 TCTATATGTTGAAAGCCCGAATACG 59.076 40.000 0.00 0.00 39.43 3.06
4343 6097 8.812972 AGTATCTATATGTTGAAAGCCCGAATA 58.187 33.333 0.00 0.00 0.00 1.75
4344 6098 7.680730 AGTATCTATATGTTGAAAGCCCGAAT 58.319 34.615 0.00 0.00 0.00 3.34
4345 6099 7.062749 AGTATCTATATGTTGAAAGCCCGAA 57.937 36.000 0.00 0.00 0.00 4.30
4346 6100 6.665992 AGTATCTATATGTTGAAAGCCCGA 57.334 37.500 0.00 0.00 0.00 5.14
4348 6102 6.369065 CGGAAGTATCTATATGTTGAAAGCCC 59.631 42.308 0.00 0.00 0.00 5.19
4349 6103 6.128526 GCGGAAGTATCTATATGTTGAAAGCC 60.129 42.308 0.00 0.00 0.00 4.35
4350 6104 6.647067 AGCGGAAGTATCTATATGTTGAAAGC 59.353 38.462 0.00 0.00 0.00 3.51
4351 6105 7.867909 TCAGCGGAAGTATCTATATGTTGAAAG 59.132 37.037 0.00 0.00 0.00 2.62
4352 6106 7.722363 TCAGCGGAAGTATCTATATGTTGAAA 58.278 34.615 0.00 0.00 0.00 2.69
4353 6107 7.284919 TCAGCGGAAGTATCTATATGTTGAA 57.715 36.000 0.00 0.00 0.00 2.69
4356 6110 6.102663 GCATCAGCGGAAGTATCTATATGTT 58.897 40.000 0.00 0.00 0.00 2.71
4357 6111 5.394663 GGCATCAGCGGAAGTATCTATATGT 60.395 44.000 0.00 0.00 43.41 2.29
4358 6112 5.046529 GGCATCAGCGGAAGTATCTATATG 58.953 45.833 0.00 0.00 43.41 1.78
4359 6113 4.959210 AGGCATCAGCGGAAGTATCTATAT 59.041 41.667 0.00 0.00 43.41 0.86
4360 6114 4.344978 AGGCATCAGCGGAAGTATCTATA 58.655 43.478 0.00 0.00 43.41 1.31
4361 6115 3.169099 AGGCATCAGCGGAAGTATCTAT 58.831 45.455 0.00 0.00 43.41 1.98
4362 6116 2.598565 AGGCATCAGCGGAAGTATCTA 58.401 47.619 0.00 0.00 43.41 1.98
4363 6117 1.418334 AGGCATCAGCGGAAGTATCT 58.582 50.000 0.00 0.00 43.41 1.98
4364 6118 2.297597 ACTAGGCATCAGCGGAAGTATC 59.702 50.000 0.00 0.00 43.41 2.24
4365 6119 2.320781 ACTAGGCATCAGCGGAAGTAT 58.679 47.619 0.00 0.00 43.41 2.12
4366 6120 1.776662 ACTAGGCATCAGCGGAAGTA 58.223 50.000 0.00 0.00 43.41 2.24
4367 6121 1.409427 GTACTAGGCATCAGCGGAAGT 59.591 52.381 0.00 0.00 43.41 3.01
4368 6122 1.683917 AGTACTAGGCATCAGCGGAAG 59.316 52.381 0.00 0.00 43.41 3.46
4369 6123 1.776662 AGTACTAGGCATCAGCGGAA 58.223 50.000 0.00 0.00 43.41 4.30
4370 6124 1.409064 CAAGTACTAGGCATCAGCGGA 59.591 52.381 0.00 0.00 43.41 5.54
4371 6125 1.137086 ACAAGTACTAGGCATCAGCGG 59.863 52.381 0.00 0.00 43.41 5.52
4372 6126 2.586258 ACAAGTACTAGGCATCAGCG 57.414 50.000 0.00 0.00 43.41 5.18
4373 6127 5.012328 ACTAACAAGTACTAGGCATCAGC 57.988 43.478 0.00 0.00 41.10 4.26
4374 6128 6.398918 ACAACTAACAAGTACTAGGCATCAG 58.601 40.000 0.00 0.00 0.00 2.90
4375 6129 6.354794 ACAACTAACAAGTACTAGGCATCA 57.645 37.500 0.00 0.00 0.00 3.07
4376 6130 8.943909 ATAACAACTAACAAGTACTAGGCATC 57.056 34.615 0.00 0.00 0.00 3.91
4500 6254 8.856153 TTAACATAAAAGGCACTGACAGAATA 57.144 30.769 10.08 0.00 40.86 1.75
4532 6286 4.235079 TGCCACAGCTCCTACAAATTAT 57.765 40.909 0.00 0.00 40.80 1.28
4674 6428 5.517770 GCCTGAAAAATTCATCATACTGTGC 59.482 40.000 0.00 0.00 39.30 4.57
4676 6430 6.660521 TGAGCCTGAAAAATTCATCATACTGT 59.339 34.615 0.00 0.00 39.30 3.55
4860 6614 0.919710 ACTAAGTTGGGCCCTGGATC 59.080 55.000 25.70 8.66 0.00 3.36
4862 6616 0.474854 TCACTAAGTTGGGCCCTGGA 60.475 55.000 25.70 6.11 0.00 3.86
4884 6638 0.178990 AGGGCTGCGGAAAGAAAACT 60.179 50.000 0.00 0.00 0.00 2.66
4941 6695 6.874288 AGTATAGACGGACATGGTAACTAC 57.126 41.667 0.00 0.00 37.61 2.73
4973 6730 5.476599 TGCCAGTAACTGCAACAGAAATATT 59.523 36.000 0.78 0.00 35.18 1.28
4975 6732 4.393834 TGCCAGTAACTGCAACAGAAATA 58.606 39.130 0.78 0.00 35.18 1.40
5048 6805 4.276678 TCAGCTTGTTGAGAAGATTGTTGG 59.723 41.667 0.00 0.00 0.00 3.77
5054 6811 4.515361 CATCCTCAGCTTGTTGAGAAGAT 58.485 43.478 14.54 7.84 45.95 2.40
5090 6847 2.165641 CGACTGTTGTAGTGCCTCCATA 59.834 50.000 0.00 0.00 40.53 2.74
5127 6884 1.771746 GGCCCAGGGATCCAGATGA 60.772 63.158 10.89 0.00 0.00 2.92
5204 6961 3.889538 AGTTTTCTAGGGTGCCAAGTTTC 59.110 43.478 0.00 0.00 0.00 2.78
5284 7044 1.005805 ACACCTCAGGCAATATGGCAA 59.994 47.619 4.05 0.00 46.46 4.52
5285 7045 0.625316 ACACCTCAGGCAATATGGCA 59.375 50.000 4.05 0.00 46.46 4.92
5286 7046 1.767759 AACACCTCAGGCAATATGGC 58.232 50.000 0.00 0.00 44.10 4.40
5334 7094 2.138542 AGGACCAGGGCATATCACAAT 58.861 47.619 0.00 0.00 0.00 2.71
5346 7110 6.900194 TCTATTCTCCAAAATAAGGACCAGG 58.100 40.000 0.00 0.00 0.00 4.45
5387 7153 4.322385 GAACACGCAACCCCGCAC 62.322 66.667 0.00 0.00 0.00 5.34
5388 7154 4.555709 AGAACACGCAACCCCGCA 62.556 61.111 0.00 0.00 0.00 5.69
5389 7155 3.723348 GAGAACACGCAACCCCGC 61.723 66.667 0.00 0.00 0.00 6.13
5390 7156 2.280524 TGAGAACACGCAACCCCG 60.281 61.111 0.00 0.00 0.00 5.73
5447 7213 7.429340 GGAATCGCATGTTTTAGTAATGAAGTG 59.571 37.037 0.00 0.00 0.00 3.16
5467 7233 1.789464 GAGCGTGCTATGAAGGAATCG 59.211 52.381 0.00 0.00 0.00 3.34
5469 7235 1.486310 TGGAGCGTGCTATGAAGGAAT 59.514 47.619 0.00 0.00 0.00 3.01
5657 7468 6.700960 CCTGCAGATAAAACATTGTTGAACAA 59.299 34.615 17.39 13.66 42.95 2.83
5699 7510 1.251251 GCATCTGCTGAAGGGTTTGT 58.749 50.000 0.00 0.00 38.21 2.83
5875 7690 0.097674 GCTGGCTAATGCAACACTCG 59.902 55.000 0.00 0.00 41.91 4.18
5991 7806 4.708421 AGCAATATCCACTGAACATTTGCT 59.292 37.500 0.00 0.00 42.53 3.91
6111 7926 3.011818 TCCACAAGCACATCACATCATC 58.988 45.455 0.00 0.00 0.00 2.92
6144 7959 6.142817 GCTGTATGGTTTATTTAGGCGATTG 58.857 40.000 0.00 0.00 0.00 2.67
6179 7995 9.034544 CGAGATGTTTATGAATCTGAACATGTA 57.965 33.333 0.00 0.00 41.37 2.29
6232 8050 7.716799 AAATGATCCATTAAGTAACTTGGCA 57.283 32.000 0.00 0.00 32.43 4.92
6299 8120 0.107508 ACTCCTGGACGGCATTCATG 60.108 55.000 0.00 0.00 0.00 3.07
6300 8121 1.139058 GTACTCCTGGACGGCATTCAT 59.861 52.381 0.00 0.00 0.00 2.57
6301 8122 0.535335 GTACTCCTGGACGGCATTCA 59.465 55.000 0.00 0.00 0.00 2.57
6302 8123 0.179081 GGTACTCCTGGACGGCATTC 60.179 60.000 0.00 0.00 0.00 2.67
6303 8124 1.623542 GGGTACTCCTGGACGGCATT 61.624 60.000 0.00 0.00 0.00 3.56
6304 8125 2.064581 GGGTACTCCTGGACGGCAT 61.065 63.158 0.00 0.00 0.00 4.40
6305 8126 2.682494 GGGTACTCCTGGACGGCA 60.682 66.667 0.00 0.00 0.00 5.69
6306 8127 2.363925 AGGGTACTCCTGGACGGC 60.364 66.667 0.00 0.00 46.07 5.68
6313 8134 6.129723 TCCTGATGGTGTAAGGGTACTCCT 62.130 50.000 0.00 0.00 42.19 3.69
6314 8135 2.434702 CCTGATGGTGTAAGGGTACTCC 59.565 54.545 0.00 0.00 42.08 3.85
6315 8136 3.371965 TCCTGATGGTGTAAGGGTACTC 58.628 50.000 0.00 0.00 34.23 2.59
6316 8137 3.484953 TCCTGATGGTGTAAGGGTACT 57.515 47.619 0.00 0.00 34.23 2.73
6317 8138 3.681874 GCTTCCTGATGGTGTAAGGGTAC 60.682 52.174 0.00 0.00 34.23 3.34
6318 8139 2.504175 GCTTCCTGATGGTGTAAGGGTA 59.496 50.000 0.00 0.00 34.23 3.69
6319 8140 1.282157 GCTTCCTGATGGTGTAAGGGT 59.718 52.381 0.00 0.00 34.23 4.34
6320 8141 1.408822 GGCTTCCTGATGGTGTAAGGG 60.409 57.143 0.00 0.00 34.23 3.95
6321 8142 1.408822 GGGCTTCCTGATGGTGTAAGG 60.409 57.143 0.00 0.00 34.23 2.69
6322 8143 1.561542 AGGGCTTCCTGATGGTGTAAG 59.438 52.381 0.00 0.00 39.96 2.34
6323 8144 1.668826 AGGGCTTCCTGATGGTGTAA 58.331 50.000 0.00 0.00 39.96 2.41
6324 8145 1.559682 GAAGGGCTTCCTGATGGTGTA 59.440 52.381 0.00 0.00 40.74 2.90
6325 8146 0.329596 GAAGGGCTTCCTGATGGTGT 59.670 55.000 0.00 0.00 40.74 4.16
6326 8147 0.329261 TGAAGGGCTTCCTGATGGTG 59.671 55.000 0.00 0.00 40.74 4.17
6327 8148 0.622665 CTGAAGGGCTTCCTGATGGT 59.377 55.000 0.00 0.00 40.74 3.55
6374 8195 9.515020 GATCACACTTCTTTTTAAACATGTTCA 57.485 29.630 12.39 0.00 0.00 3.18
6375 8196 8.968242 GGATCACACTTCTTTTTAAACATGTTC 58.032 33.333 12.39 0.00 0.00 3.18
6376 8197 8.695456 AGGATCACACTTCTTTTTAAACATGTT 58.305 29.630 4.92 4.92 0.00 2.71
6377 8198 8.237811 AGGATCACACTTCTTTTTAAACATGT 57.762 30.769 0.00 0.00 0.00 3.21
6378 8199 7.809806 GGAGGATCACACTTCTTTTTAAACATG 59.190 37.037 0.00 0.00 36.25 3.21
6379 8200 7.725844 AGGAGGATCACACTTCTTTTTAAACAT 59.274 33.333 0.00 0.00 36.25 2.71
6413 8264 3.713288 CATGATGCATGCCCACTAAAAG 58.287 45.455 16.68 0.00 35.02 2.27
6466 8317 2.347697 TCGCCATATCACGCTGATAC 57.652 50.000 9.05 0.00 41.62 2.24
6515 8380 2.914695 ATTTGCTCAAGCTTTGCCAA 57.085 40.000 15.89 12.48 42.66 4.52
6531 8396 5.878627 TCTGATTGGGGAAATTGCAAATTT 58.121 33.333 1.71 4.89 0.00 1.82
6569 8434 6.311200 GGCACTTCATTTATTTTCTTGCGAAT 59.689 34.615 0.00 0.00 0.00 3.34
6659 8525 5.731957 TGTGTAGCTTCCTTGTACATACA 57.268 39.130 0.00 0.00 0.00 2.29
6744 8610 1.021390 GTCTCATTGCCCCACTGACG 61.021 60.000 0.00 0.00 0.00 4.35
6750 8616 2.356278 GCTGGTCTCATTGCCCCA 59.644 61.111 0.00 0.00 0.00 4.96
6756 8622 0.321653 GTTCCACGGCTGGTCTCATT 60.322 55.000 0.00 0.00 38.90 2.57
6790 8656 3.432588 GTGAGGCTGCTGCTGCTG 61.433 66.667 26.79 16.73 40.48 4.41


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

AutoCloner maintained by Alex Coulton.