Multiple sequence alignment - TraesCS3B01G399800

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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 TraesCS3B01G399800 chr3B 100.000 2745 0 0 1 2745 631038573 631035829 0.000000e+00 5070.0
1 TraesCS3B01G399800 chr3D 93.742 2493 83 27 1 2453 474616675 474614216 0.000000e+00 3672.0
2 TraesCS3B01G399800 chr3D 85.417 240 17 12 2484 2713 614647743 614647974 1.640000e-57 233.0
3 TraesCS3B01G399800 chr3A 93.147 2510 86 35 1 2445 617062336 617059848 0.000000e+00 3603.0
4 TraesCS3B01G399800 chr5B 97.333 300 7 1 2446 2745 635612047 635612345 2.440000e-140 508.0
5 TraesCS3B01G399800 chr5B 78.107 169 35 2 1048 1215 288892876 288892709 3.740000e-19 106.0
6 TraesCS3B01G399800 chr5B 76.410 195 44 2 1036 1229 118452145 118452338 1.340000e-18 104.0
7 TraesCS3B01G399800 chr5D 86.942 291 18 14 2435 2713 536761671 536761389 2.650000e-80 309.0
8 TraesCS3B01G399800 chr5D 86.331 278 18 14 2445 2712 238080687 238080420 4.470000e-73 285.0
9 TraesCS3B01G399800 chr5D 78.698 169 34 2 1048 1215 254023410 254023577 8.040000e-21 111.0
10 TraesCS3B01G399800 chr5D 76.923 195 43 2 1036 1229 108103584 108103777 2.890000e-20 110.0
11 TraesCS3B01G399800 chr5D 97.222 36 1 0 2710 2745 536761377 536761342 8.210000e-06 62.1
12 TraesCS3B01G399800 chr2B 87.455 279 17 11 2446 2713 390950497 390950226 3.430000e-79 305.0
13 TraesCS3B01G399800 chr2B 97.222 36 1 0 2710 2745 390950214 390950179 8.210000e-06 62.1
14 TraesCS3B01G399800 chr1A 86.833 281 18 13 2445 2713 34557936 34557663 2.070000e-76 296.0
15 TraesCS3B01G399800 chr1A 79.330 179 33 4 1039 1215 33398703 33398527 3.710000e-24 122.0
16 TraesCS3B01G399800 chr1A 96.970 33 1 0 2713 2745 34557648 34557616 3.820000e-04 56.5
17 TraesCS3B01G399800 chr5A 86.643 277 19 12 2448 2713 606196919 606196650 9.620000e-75 291.0
18 TraesCS3B01G399800 chr5A 86.813 182 19 5 2446 2626 688371035 688371212 6.000000e-47 198.0
19 TraesCS3B01G399800 chr5A 78.698 169 34 2 1048 1215 336950101 336950268 8.040000e-21 111.0
20 TraesCS3B01G399800 chr5A 97.222 36 1 0 2710 2745 606196638 606196603 8.210000e-06 62.1
21 TraesCS3B01G399800 chr7A 86.029 272 24 11 2445 2713 43259842 43259582 2.080000e-71 279.0
22 TraesCS3B01G399800 chr7A 82.796 279 25 12 2446 2713 14510282 14510016 7.650000e-56 228.0
23 TraesCS3B01G399800 chr6A 82.462 325 25 25 2446 2745 526322438 526322121 3.510000e-64 255.0
24 TraesCS3B01G399800 chr7B 83.813 278 21 14 2449 2713 576431056 576430790 2.730000e-60 243.0
25 TraesCS3B01G399800 chr7B 97.222 36 1 0 2710 2745 576430778 576430743 8.210000e-06 62.1
26 TraesCS3B01G399800 chrUn 83.154 279 24 12 2446 2713 82062653 82062919 1.640000e-57 233.0
27 TraesCS3B01G399800 chr1D 78.771 179 34 4 1039 1215 35060885 35060709 1.730000e-22 117.0
28 TraesCS3B01G399800 chr1B 91.026 78 4 3 2436 2511 8030912 8030836 4.840000e-18 102.0


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 TraesCS3B01G399800 chr3B 631035829 631038573 2744 True 5070 5070 100.000 1 2745 1 chr3B.!!$R1 2744
1 TraesCS3B01G399800 chr3D 474614216 474616675 2459 True 3672 3672 93.742 1 2453 1 chr3D.!!$R1 2452
2 TraesCS3B01G399800 chr3A 617059848 617062336 2488 True 3603 3603 93.147 1 2445 1 chr3A.!!$R1 2444

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
202 203 0.323087 GCCGTTTAACCTGTCCCCAT 60.323 55.0 0.0 0.0 0.0 4.0 F
1280 1313 0.246086 AGCAGCAACGAGGAAGAGAG 59.754 55.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 1493 0.60813 CGGCCCGATGATCCAATCTA 59.392 55.0 0.0 0.0 0.00 1.98 R
2555 2635 0.03563 CTTCTCCTCACCCAGCAAGG 60.036 60.0 0.0 0.0 37.03 3.61 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
50 51 5.303971 CATTTCCATCCTCTGATCCAGTAC 58.696 45.833 0.00 0.00 32.61 2.73
141 142 1.621814 GTCTTGGTGGCAGGTGTACTA 59.378 52.381 0.00 0.00 0.00 1.82
147 148 3.007182 TGGTGGCAGGTGTACTACTTAAC 59.993 47.826 0.00 0.00 0.00 2.01
148 149 3.007182 GGTGGCAGGTGTACTACTTAACA 59.993 47.826 0.00 0.00 0.00 2.41
150 151 3.899360 TGGCAGGTGTACTACTTAACAGT 59.101 43.478 0.00 0.00 36.99 3.55
151 152 5.047802 GTGGCAGGTGTACTACTTAACAGTA 60.048 44.000 0.00 0.00 34.06 2.74
193 194 2.614983 TCTGTCTTGTTGCCGTTTAACC 59.385 45.455 0.00 0.00 0.00 2.85
197 198 2.614983 TCTTGTTGCCGTTTAACCTGTC 59.385 45.455 0.00 0.00 0.00 3.51
199 200 0.594602 GTTGCCGTTTAACCTGTCCC 59.405 55.000 0.00 0.00 0.00 4.46
200 201 0.537828 TTGCCGTTTAACCTGTCCCC 60.538 55.000 0.00 0.00 0.00 4.81
202 203 0.323087 GCCGTTTAACCTGTCCCCAT 60.323 55.000 0.00 0.00 0.00 4.00
203 204 1.065272 GCCGTTTAACCTGTCCCCATA 60.065 52.381 0.00 0.00 0.00 2.74
228 235 3.695830 ACTCAAGAAATCCACGCCTTA 57.304 42.857 0.00 0.00 0.00 2.69
275 290 6.802348 CACTTCGATTGGGTTATACTAGATCG 59.198 42.308 0.00 0.00 37.01 3.69
278 293 7.317842 TCGATTGGGTTATACTAGATCGATC 57.682 40.000 17.91 17.91 38.96 3.69
283 298 5.182570 TGGGTTATACTAGATCGATCAACGG 59.817 44.000 26.47 14.80 42.82 4.44
348 366 2.487532 CGTACGATTCCCCTCGGCT 61.488 63.158 10.44 0.00 42.88 5.52
381 399 2.202236 GACCCATGCAAGGAGCCAGA 62.202 60.000 10.18 0.00 44.83 3.86
386 404 1.134189 CATGCAAGGAGCCAGAGATCA 60.134 52.381 0.00 0.00 44.83 2.92
421 439 0.385390 CCCCAAATCAGCCGCATTAC 59.615 55.000 0.00 0.00 0.00 1.89
582 605 4.729458 GCGAGCTATGCTATCAGTAGTAGC 60.729 50.000 3.25 0.00 39.88 3.58
659 682 6.367374 AGGAAAACAAAAGGAAAGAAACCA 57.633 33.333 0.00 0.00 0.00 3.67
832 863 5.107824 GGAAGAAACAAGATCGGTAGTACC 58.892 45.833 9.50 9.50 34.05 3.34
834 865 5.069501 AGAAACAAGATCGGTAGTACCAC 57.930 43.478 19.41 9.62 38.47 4.16
882 915 3.501349 TGGGGTCAGATAGTAGAGCATC 58.499 50.000 0.00 0.00 34.11 3.91
898 931 4.502962 GAGCATCTTGAAGAAGTAGCTGT 58.497 43.478 15.85 0.00 39.12 4.40
917 950 5.123820 AGCTGTTAGATAGATCATCGAGCTC 59.876 44.000 2.73 2.73 38.81 4.09
1137 1170 3.133014 ATCCAGCGGATCTCCACG 58.867 61.111 4.51 0.00 38.09 4.94
1280 1313 0.246086 AGCAGCAACGAGGAAGAGAG 59.754 55.000 0.00 0.00 0.00 3.20
1365 1404 0.620556 CCAGAGGCTACAACCACCAT 59.379 55.000 0.00 0.00 0.00 3.55
1392 1431 4.148871 CGGATCATGACATGTAAGTTAGCG 59.851 45.833 14.98 0.00 0.00 4.26
1393 1432 5.050490 GGATCATGACATGTAAGTTAGCGT 58.950 41.667 14.98 0.00 0.00 5.07
1401 1446 1.068333 TGTAAGTTAGCGTCCACGTCC 60.068 52.381 0.36 0.00 42.22 4.79
1514 1559 0.339859 AGGCTATGTGAGGGAGGTGA 59.660 55.000 0.00 0.00 0.00 4.02
1609 1657 0.752009 CAGCCTACGACCTGGAGCTA 60.752 60.000 0.00 0.00 0.00 3.32
1687 1735 1.006102 CTTCTTCGACGTGGCCACT 60.006 57.895 32.28 19.76 0.00 4.00
1693 1741 3.986006 GACGTGGCCACTGGACGA 61.986 66.667 32.28 0.00 36.90 4.20
1744 1792 3.252701 GCTTCGATCGGTATCTGGTCTAA 59.747 47.826 16.41 0.00 0.00 2.10
1948 2022 2.159114 AGAGGATCAGAAAAGAGCTCGC 60.159 50.000 8.37 0.00 37.82 5.03
2023 2097 3.325135 TCTTTTTCTTCCTCCTCGCTTCT 59.675 43.478 0.00 0.00 0.00 2.85
2028 2102 4.521062 CCTCCTCGCTTCTGGCCG 62.521 72.222 0.00 0.00 37.74 6.13
2045 2119 1.935933 CCGGTTGCATGGTCTACTAC 58.064 55.000 0.00 0.00 0.00 2.73
2059 2133 6.258354 TGGTCTACTACAATTAACCTCTGGA 58.742 40.000 0.00 0.00 0.00 3.86
2063 2137 7.921745 GTCTACTACAATTAACCTCTGGATGAC 59.078 40.741 0.00 0.00 0.00 3.06
2160 2237 5.051816 ACCGTCGAAATCTACAGTCAAAAA 58.948 37.500 0.00 0.00 0.00 1.94
2161 2238 5.050567 ACCGTCGAAATCTACAGTCAAAAAC 60.051 40.000 0.00 0.00 0.00 2.43
2162 2239 5.050634 CCGTCGAAATCTACAGTCAAAAACA 60.051 40.000 0.00 0.00 0.00 2.83
2163 2240 6.347402 CCGTCGAAATCTACAGTCAAAAACAT 60.347 38.462 0.00 0.00 0.00 2.71
2251 2329 6.712095 AGTATGAACACATGATTTGACACAGT 59.288 34.615 0.00 0.00 0.00 3.55
2252 2330 7.877612 AGTATGAACACATGATTTGACACAGTA 59.122 33.333 0.00 0.00 0.00 2.74
2253 2331 7.692460 ATGAACACATGATTTGACACAGTAT 57.308 32.000 0.00 0.00 0.00 2.12
2422 2502 3.927142 GTGGTAGTCAACTGTGTATGCTC 59.073 47.826 0.00 0.00 0.00 4.26
2445 2525 2.046314 TAGGAAACTGCTGGGCGC 60.046 61.111 0.00 0.00 43.88 6.53
2503 2583 2.757077 GGGCCCCCGATATCTTGG 59.243 66.667 12.23 1.30 0.00 3.61
2504 2584 2.757077 GGCCCCCGATATCTTGGG 59.243 66.667 17.87 17.87 45.04 4.12
2508 2588 2.757077 CCCGATATCTTGGGGCCC 59.243 66.667 18.17 18.17 42.00 5.80
2509 2589 2.757077 CCGATATCTTGGGGCCCC 59.243 66.667 36.14 36.14 0.00 5.80
2510 2590 2.757077 CGATATCTTGGGGCCCCC 59.243 66.667 38.81 20.71 45.71 5.40
2511 2591 1.847968 CGATATCTTGGGGCCCCCT 60.848 63.158 38.81 21.71 45.70 4.79
2512 2592 1.842381 CGATATCTTGGGGCCCCCTC 61.842 65.000 38.81 21.60 45.70 4.30
2513 2593 0.476611 GATATCTTGGGGCCCCCTCT 60.477 60.000 38.81 21.70 45.70 3.69
2514 2594 0.027590 ATATCTTGGGGCCCCCTCTT 60.028 55.000 38.81 22.24 45.70 2.85
2515 2595 0.651124 TATCTTGGGGCCCCCTCTTA 59.349 55.000 38.81 21.15 45.70 2.10
2516 2596 0.027590 ATCTTGGGGCCCCCTCTTAT 60.028 55.000 38.81 20.58 45.70 1.73
2517 2597 0.697854 TCTTGGGGCCCCCTCTTATC 60.698 60.000 38.81 11.26 45.70 1.75
2518 2598 0.699231 CTTGGGGCCCCCTCTTATCT 60.699 60.000 38.81 0.00 45.70 1.98
2519 2599 0.993509 TTGGGGCCCCCTCTTATCTG 60.994 60.000 38.81 0.00 45.70 2.90
2520 2600 2.156774 GGGGCCCCCTCTTATCTGG 61.157 68.421 33.01 0.00 41.34 3.86
2521 2601 2.835049 GGGCCCCCTCTTATCTGGC 61.835 68.421 12.23 0.00 41.42 4.85
2522 2602 2.839836 GCCCCCTCTTATCTGGCC 59.160 66.667 0.00 0.00 36.07 5.36
2523 2603 2.078665 GCCCCCTCTTATCTGGCCA 61.079 63.158 4.71 4.71 36.07 5.36
2524 2604 1.645402 GCCCCCTCTTATCTGGCCAA 61.645 60.000 7.01 0.00 36.07 4.52
2525 2605 0.475906 CCCCCTCTTATCTGGCCAAG 59.524 60.000 7.01 0.15 0.00 3.61
2526 2606 1.216990 CCCCTCTTATCTGGCCAAGT 58.783 55.000 7.01 0.00 0.00 3.16
2527 2607 1.566231 CCCCTCTTATCTGGCCAAGTT 59.434 52.381 7.01 0.00 0.00 2.66
2528 2608 2.024941 CCCCTCTTATCTGGCCAAGTTT 60.025 50.000 7.01 0.00 0.00 2.66
2529 2609 3.202151 CCCCTCTTATCTGGCCAAGTTTA 59.798 47.826 7.01 0.00 0.00 2.01
2530 2610 4.325030 CCCCTCTTATCTGGCCAAGTTTAA 60.325 45.833 7.01 1.62 0.00 1.52
2531 2611 4.640647 CCCTCTTATCTGGCCAAGTTTAAC 59.359 45.833 7.01 0.00 0.00 2.01
2532 2612 5.253330 CCTCTTATCTGGCCAAGTTTAACA 58.747 41.667 7.01 0.00 0.00 2.41
2533 2613 5.888161 CCTCTTATCTGGCCAAGTTTAACAT 59.112 40.000 7.01 0.00 0.00 2.71
2534 2614 7.054124 CCTCTTATCTGGCCAAGTTTAACATA 58.946 38.462 7.01 0.00 0.00 2.29
2535 2615 7.012421 CCTCTTATCTGGCCAAGTTTAACATAC 59.988 40.741 7.01 0.00 0.00 2.39
2536 2616 6.537301 TCTTATCTGGCCAAGTTTAACATACG 59.463 38.462 7.01 0.00 0.00 3.06
2537 2617 4.010667 TCTGGCCAAGTTTAACATACGT 57.989 40.909 7.01 0.00 0.00 3.57
2538 2618 5.149973 TCTGGCCAAGTTTAACATACGTA 57.850 39.130 7.01 0.00 0.00 3.57
2539 2619 5.549347 TCTGGCCAAGTTTAACATACGTAA 58.451 37.500 7.01 0.00 0.00 3.18
2557 2637 5.019785 CGTAAGTTAAGTAATCTGGGCCT 57.980 43.478 4.53 0.00 0.00 5.19
2558 2638 5.425630 CGTAAGTTAAGTAATCTGGGCCTT 58.574 41.667 4.53 0.00 0.00 4.35
2559 2639 5.293569 CGTAAGTTAAGTAATCTGGGCCTTG 59.706 44.000 4.53 0.00 0.00 3.61
2560 2640 3.621558 AGTTAAGTAATCTGGGCCTTGC 58.378 45.455 4.53 0.00 0.00 4.01
2561 2641 3.267031 AGTTAAGTAATCTGGGCCTTGCT 59.733 43.478 4.53 0.00 0.00 3.91
2562 2642 2.134789 AAGTAATCTGGGCCTTGCTG 57.865 50.000 4.53 0.00 0.00 4.41
2563 2643 0.257039 AGTAATCTGGGCCTTGCTGG 59.743 55.000 4.53 0.00 39.35 4.85
2564 2644 0.753111 GTAATCTGGGCCTTGCTGGG 60.753 60.000 4.53 0.00 36.00 4.45
2565 2645 1.214305 TAATCTGGGCCTTGCTGGGT 61.214 55.000 4.53 0.00 36.00 4.51
2566 2646 2.793317 AATCTGGGCCTTGCTGGGTG 62.793 60.000 4.53 0.00 36.00 4.61
2567 2647 3.970410 CTGGGCCTTGCTGGGTGA 61.970 66.667 4.53 0.00 36.00 4.02
2568 2648 3.933048 CTGGGCCTTGCTGGGTGAG 62.933 68.421 4.53 0.00 36.00 3.51
2569 2649 4.748144 GGGCCTTGCTGGGTGAGG 62.748 72.222 0.84 0.00 36.00 3.86
2570 2650 3.650950 GGCCTTGCTGGGTGAGGA 61.651 66.667 0.00 0.00 36.00 3.71
2571 2651 2.045536 GCCTTGCTGGGTGAGGAG 60.046 66.667 0.00 0.00 36.00 3.69
2572 2652 2.596851 GCCTTGCTGGGTGAGGAGA 61.597 63.158 0.00 0.00 36.00 3.71
2573 2653 2.069776 CCTTGCTGGGTGAGGAGAA 58.930 57.895 0.00 0.00 32.11 2.87
2574 2654 0.035630 CCTTGCTGGGTGAGGAGAAG 60.036 60.000 0.00 0.00 32.11 2.85
2575 2655 0.979665 CTTGCTGGGTGAGGAGAAGA 59.020 55.000 0.00 0.00 0.00 2.87
2576 2656 1.349026 CTTGCTGGGTGAGGAGAAGAA 59.651 52.381 0.00 0.00 0.00 2.52
2577 2657 1.434188 TGCTGGGTGAGGAGAAGAAA 58.566 50.000 0.00 0.00 0.00 2.52
2578 2658 1.774254 TGCTGGGTGAGGAGAAGAAAA 59.226 47.619 0.00 0.00 0.00 2.29
2579 2659 2.174639 TGCTGGGTGAGGAGAAGAAAAA 59.825 45.455 0.00 0.00 0.00 1.94
2580 2660 2.816672 GCTGGGTGAGGAGAAGAAAAAG 59.183 50.000 0.00 0.00 0.00 2.27
2581 2661 3.416156 CTGGGTGAGGAGAAGAAAAAGG 58.584 50.000 0.00 0.00 0.00 3.11
2582 2662 2.163509 GGGTGAGGAGAAGAAAAAGGC 58.836 52.381 0.00 0.00 0.00 4.35
2583 2663 2.489073 GGGTGAGGAGAAGAAAAAGGCA 60.489 50.000 0.00 0.00 0.00 4.75
2584 2664 3.222603 GGTGAGGAGAAGAAAAAGGCAA 58.777 45.455 0.00 0.00 0.00 4.52
2585 2665 3.636764 GGTGAGGAGAAGAAAAAGGCAAA 59.363 43.478 0.00 0.00 0.00 3.68
2586 2666 4.499865 GGTGAGGAGAAGAAAAAGGCAAAC 60.500 45.833 0.00 0.00 0.00 2.93
2587 2667 4.339530 GTGAGGAGAAGAAAAAGGCAAACT 59.660 41.667 0.00 0.00 0.00 2.66
2588 2668 4.339247 TGAGGAGAAGAAAAAGGCAAACTG 59.661 41.667 0.00 0.00 0.00 3.16
2589 2669 3.638627 AGGAGAAGAAAAAGGCAAACTGG 59.361 43.478 0.00 0.00 0.00 4.00
2590 2670 3.243873 GGAGAAGAAAAAGGCAAACTGGG 60.244 47.826 0.00 0.00 0.00 4.45
2591 2671 2.103094 AGAAGAAAAAGGCAAACTGGGC 59.897 45.455 0.00 0.00 0.00 5.36
2592 2672 1.793414 AGAAAAAGGCAAACTGGGCT 58.207 45.000 0.00 0.00 46.88 5.19
2598 2678 2.789409 AGGCAAACTGGGCTTAGTAG 57.211 50.000 0.00 0.00 41.46 2.57
2599 2679 2.266279 AGGCAAACTGGGCTTAGTAGA 58.734 47.619 0.00 0.00 41.46 2.59
2600 2680 2.642807 AGGCAAACTGGGCTTAGTAGAA 59.357 45.455 0.00 0.00 41.46 2.10
2601 2681 2.747989 GGCAAACTGGGCTTAGTAGAAC 59.252 50.000 0.00 0.00 0.00 3.01
2602 2682 2.747989 GCAAACTGGGCTTAGTAGAACC 59.252 50.000 0.00 0.00 0.00 3.62
2603 2683 3.000727 CAAACTGGGCTTAGTAGAACCG 58.999 50.000 0.00 0.00 0.00 4.44
2604 2684 1.934410 ACTGGGCTTAGTAGAACCGT 58.066 50.000 0.00 0.00 0.00 4.83
2605 2685 1.549170 ACTGGGCTTAGTAGAACCGTG 59.451 52.381 0.00 0.00 0.00 4.94
2606 2686 0.248289 TGGGCTTAGTAGAACCGTGC 59.752 55.000 0.00 0.00 0.00 5.34
2607 2687 0.248289 GGGCTTAGTAGAACCGTGCA 59.752 55.000 0.00 0.00 0.00 4.57
2608 2688 1.338389 GGGCTTAGTAGAACCGTGCAA 60.338 52.381 0.00 0.00 0.00 4.08
2609 2689 2.000447 GGCTTAGTAGAACCGTGCAAG 59.000 52.381 0.00 0.00 0.00 4.01
2610 2690 2.612221 GGCTTAGTAGAACCGTGCAAGT 60.612 50.000 0.00 0.00 0.00 3.16
2611 2691 3.367703 GGCTTAGTAGAACCGTGCAAGTA 60.368 47.826 0.00 0.00 0.00 2.24
2612 2692 3.611549 GCTTAGTAGAACCGTGCAAGTAC 59.388 47.826 0.00 0.00 0.00 2.73
2613 2693 2.342910 AGTAGAACCGTGCAAGTACG 57.657 50.000 3.67 3.67 43.35 3.67
2614 2694 1.610522 AGTAGAACCGTGCAAGTACGT 59.389 47.619 9.66 0.00 42.24 3.57
2615 2695 1.717645 GTAGAACCGTGCAAGTACGTG 59.282 52.381 9.66 4.24 42.24 4.49
2616 2696 1.203313 GAACCGTGCAAGTACGTGC 59.797 57.895 24.50 24.50 45.15 5.34
2617 2697 1.219522 GAACCGTGCAAGTACGTGCT 61.220 55.000 29.46 12.93 45.17 4.40
2618 2698 0.812412 AACCGTGCAAGTACGTGCTT 60.812 50.000 29.46 13.53 45.17 3.91
2619 2699 0.812412 ACCGTGCAAGTACGTGCTTT 60.812 50.000 29.46 11.91 45.17 3.51
2620 2700 0.384230 CCGTGCAAGTACGTGCTTTG 60.384 55.000 29.46 19.71 45.17 2.77
2621 2701 0.384230 CGTGCAAGTACGTGCTTTGG 60.384 55.000 29.46 14.83 45.17 3.28
2622 2702 0.660300 GTGCAAGTACGTGCTTTGGC 60.660 55.000 29.46 17.39 45.17 4.52
2623 2703 1.098129 TGCAAGTACGTGCTTTGGCA 61.098 50.000 29.46 21.71 45.17 4.92
2633 2713 3.551259 GCTTTGGCAGCCTACTACA 57.449 52.632 14.15 0.00 43.65 2.74
2634 2714 1.087501 GCTTTGGCAGCCTACTACAC 58.912 55.000 14.15 0.00 43.65 2.90
2635 2715 1.359848 CTTTGGCAGCCTACTACACG 58.640 55.000 14.15 0.00 0.00 4.49
2636 2716 0.970640 TTTGGCAGCCTACTACACGA 59.029 50.000 14.15 0.00 0.00 4.35
2637 2717 0.530744 TTGGCAGCCTACTACACGAG 59.469 55.000 14.15 0.00 0.00 4.18
2638 2718 0.611062 TGGCAGCCTACTACACGAGT 60.611 55.000 14.15 0.00 42.69 4.18
2639 2719 1.340308 TGGCAGCCTACTACACGAGTA 60.340 52.381 14.15 0.00 39.81 2.59
2640 2720 1.065251 GGCAGCCTACTACACGAGTAC 59.935 57.143 3.29 0.00 39.81 2.73
2641 2721 2.015587 GCAGCCTACTACACGAGTACT 58.984 52.381 0.00 0.00 39.81 2.73
2642 2722 2.422832 GCAGCCTACTACACGAGTACTT 59.577 50.000 0.00 0.00 39.81 2.24
2643 2723 3.119566 GCAGCCTACTACACGAGTACTTT 60.120 47.826 0.00 0.00 39.81 2.66
2644 2724 4.413087 CAGCCTACTACACGAGTACTTTG 58.587 47.826 0.00 0.00 39.81 2.77
2645 2725 4.155462 CAGCCTACTACACGAGTACTTTGA 59.845 45.833 11.37 0.00 39.81 2.69
2646 2726 4.155644 AGCCTACTACACGAGTACTTTGAC 59.844 45.833 11.37 0.00 39.81 3.18
2647 2727 4.673841 GCCTACTACACGAGTACTTTGACC 60.674 50.000 11.37 0.00 39.81 4.02
2648 2728 4.456911 CCTACTACACGAGTACTTTGACCA 59.543 45.833 11.37 0.00 39.81 4.02
2649 2729 5.125097 CCTACTACACGAGTACTTTGACCAT 59.875 44.000 11.37 0.00 39.81 3.55
2650 2730 5.056894 ACTACACGAGTACTTTGACCATC 57.943 43.478 11.37 0.00 36.27 3.51
2651 2731 3.314541 ACACGAGTACTTTGACCATCC 57.685 47.619 11.37 0.00 0.00 3.51
2652 2732 2.259618 CACGAGTACTTTGACCATCCG 58.740 52.381 0.00 0.00 0.00 4.18
2653 2733 2.094906 CACGAGTACTTTGACCATCCGA 60.095 50.000 0.00 0.00 0.00 4.55
2654 2734 2.758979 ACGAGTACTTTGACCATCCGAT 59.241 45.455 0.00 0.00 0.00 4.18
2655 2735 3.116300 CGAGTACTTTGACCATCCGATG 58.884 50.000 0.00 0.93 0.00 3.84
2668 2748 2.910688 TCCGATGGATCTAGGTTTGC 57.089 50.000 0.00 0.00 0.00 3.68
2669 2749 1.068588 TCCGATGGATCTAGGTTTGCG 59.931 52.381 0.00 0.00 0.00 4.85
2670 2750 1.202533 CCGATGGATCTAGGTTTGCGT 60.203 52.381 0.00 0.00 0.00 5.24
2671 2751 2.035449 CCGATGGATCTAGGTTTGCGTA 59.965 50.000 0.00 0.00 0.00 4.42
2672 2752 3.306088 CCGATGGATCTAGGTTTGCGTAT 60.306 47.826 0.00 0.00 0.00 3.06
2673 2753 3.675225 CGATGGATCTAGGTTTGCGTATG 59.325 47.826 0.00 0.00 0.00 2.39
2674 2754 3.469008 TGGATCTAGGTTTGCGTATGG 57.531 47.619 0.00 0.00 0.00 2.74
2675 2755 3.035363 TGGATCTAGGTTTGCGTATGGA 58.965 45.455 0.00 0.00 0.00 3.41
2676 2756 3.646162 TGGATCTAGGTTTGCGTATGGAT 59.354 43.478 0.00 0.00 0.00 3.41
2677 2757 4.102524 TGGATCTAGGTTTGCGTATGGATT 59.897 41.667 0.00 0.00 0.00 3.01
2678 2758 4.452455 GGATCTAGGTTTGCGTATGGATTG 59.548 45.833 0.00 0.00 0.00 2.67
2679 2759 3.202906 TCTAGGTTTGCGTATGGATTGC 58.797 45.455 0.00 0.00 0.00 3.56
2680 2760 1.102978 AGGTTTGCGTATGGATTGCC 58.897 50.000 0.00 0.00 0.00 4.52
2681 2761 1.102978 GGTTTGCGTATGGATTGCCT 58.897 50.000 0.00 0.00 34.31 4.75
2682 2762 1.476488 GGTTTGCGTATGGATTGCCTT 59.524 47.619 0.00 0.00 34.31 4.35
2683 2763 2.529151 GTTTGCGTATGGATTGCCTTG 58.471 47.619 0.00 0.00 34.31 3.61
2684 2764 1.102154 TTGCGTATGGATTGCCTTGG 58.898 50.000 0.00 0.00 34.31 3.61
2685 2765 0.751277 TGCGTATGGATTGCCTTGGG 60.751 55.000 0.00 0.00 34.31 4.12
2686 2766 1.455383 GCGTATGGATTGCCTTGGGG 61.455 60.000 0.00 0.00 34.31 4.96
2696 2776 3.787001 CCTTGGGGCCCTCGTCTC 61.787 72.222 25.93 3.69 0.00 3.36
2697 2777 3.787001 CTTGGGGCCCTCGTCTCC 61.787 72.222 25.93 2.81 0.00 3.71
2698 2778 4.649705 TTGGGGCCCTCGTCTCCA 62.650 66.667 25.93 6.07 0.00 3.86
2699 2779 3.943137 TTGGGGCCCTCGTCTCCAT 62.943 63.158 25.93 0.00 0.00 3.41
2700 2780 3.551407 GGGGCCCTCGTCTCCATC 61.551 72.222 24.38 0.00 0.00 3.51
2701 2781 2.444895 GGGCCCTCGTCTCCATCT 60.445 66.667 17.04 0.00 0.00 2.90
2702 2782 2.066999 GGGCCCTCGTCTCCATCTT 61.067 63.158 17.04 0.00 0.00 2.40
2703 2783 1.443828 GGCCCTCGTCTCCATCTTC 59.556 63.158 0.00 0.00 0.00 2.87
2704 2784 1.330655 GGCCCTCGTCTCCATCTTCA 61.331 60.000 0.00 0.00 0.00 3.02
2705 2785 0.179097 GCCCTCGTCTCCATCTTCAC 60.179 60.000 0.00 0.00 0.00 3.18
2706 2786 1.479709 CCCTCGTCTCCATCTTCACT 58.520 55.000 0.00 0.00 0.00 3.41
2707 2787 2.656002 CCCTCGTCTCCATCTTCACTA 58.344 52.381 0.00 0.00 0.00 2.74
2708 2788 3.024547 CCCTCGTCTCCATCTTCACTAA 58.975 50.000 0.00 0.00 0.00 2.24
2709 2789 3.639094 CCCTCGTCTCCATCTTCACTAAT 59.361 47.826 0.00 0.00 0.00 1.73
2710 2790 4.261825 CCCTCGTCTCCATCTTCACTAATC 60.262 50.000 0.00 0.00 0.00 1.75
2711 2791 4.532276 CTCGTCTCCATCTTCACTAATCG 58.468 47.826 0.00 0.00 0.00 3.34
2712 2792 3.046390 CGTCTCCATCTTCACTAATCGC 58.954 50.000 0.00 0.00 0.00 4.58
2713 2793 3.385577 GTCTCCATCTTCACTAATCGCC 58.614 50.000 0.00 0.00 0.00 5.54
2714 2794 3.068873 GTCTCCATCTTCACTAATCGCCT 59.931 47.826 0.00 0.00 0.00 5.52
2715 2795 3.068732 TCTCCATCTTCACTAATCGCCTG 59.931 47.826 0.00 0.00 0.00 4.85
2716 2796 1.869767 CCATCTTCACTAATCGCCTGC 59.130 52.381 0.00 0.00 0.00 4.85
2717 2797 1.524355 CATCTTCACTAATCGCCTGCG 59.476 52.381 4.92 4.92 41.35 5.18
2718 2798 0.806102 TCTTCACTAATCGCCTGCGC 60.806 55.000 6.67 0.00 39.59 6.09
2719 2799 1.766143 CTTCACTAATCGCCTGCGCC 61.766 60.000 4.18 0.00 39.59 6.53
2720 2800 2.511373 CACTAATCGCCTGCGCCA 60.511 61.111 4.18 0.00 39.59 5.69
2721 2801 2.511600 ACTAATCGCCTGCGCCAC 60.512 61.111 4.18 0.00 39.59 5.01
2722 2802 3.272334 CTAATCGCCTGCGCCACC 61.272 66.667 4.18 0.00 39.59 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.725246 GCACTTGCATAACTTAATTATCGGT 58.275 36.000 0.00 0.00 41.59 4.69
50 51 4.237724 TCGCTCGCTCCATTATCTTAATG 58.762 43.478 1.14 1.14 0.00 1.90
197 198 5.066593 GGATTTCTTGAGTAGCTTATGGGG 58.933 45.833 0.00 0.00 0.00 4.96
199 200 5.235186 CGTGGATTTCTTGAGTAGCTTATGG 59.765 44.000 0.00 0.00 0.00 2.74
200 201 5.277058 GCGTGGATTTCTTGAGTAGCTTATG 60.277 44.000 0.00 0.00 0.00 1.90
202 203 4.181578 GCGTGGATTTCTTGAGTAGCTTA 58.818 43.478 0.00 0.00 0.00 3.09
203 204 3.003480 GCGTGGATTTCTTGAGTAGCTT 58.997 45.455 0.00 0.00 0.00 3.74
228 235 2.951642 CCGGCCTGTGAATTCAATATGT 59.048 45.455 10.35 0.00 0.00 2.29
275 290 4.817517 TCTAGTTTTGGAGTCCGTTGATC 58.182 43.478 4.30 0.00 0.00 2.92
278 293 4.755123 ACAATCTAGTTTTGGAGTCCGTTG 59.245 41.667 4.30 1.52 0.00 4.10
283 298 5.163713 GCATGGACAATCTAGTTTTGGAGTC 60.164 44.000 11.20 4.10 0.00 3.36
348 366 0.250424 TGGGTCGTGACTCGTGACTA 60.250 55.000 0.00 0.00 40.80 2.59
381 399 4.451900 GGTTCGTTATTCCATGGTGATCT 58.548 43.478 12.58 0.00 0.00 2.75
386 404 1.636519 TGGGGTTCGTTATTCCATGGT 59.363 47.619 12.58 0.00 0.00 3.55
421 439 2.672961 TGCCGAGTTGAGGATTACAG 57.327 50.000 0.00 0.00 0.00 2.74
582 605 1.210545 CTGCCACTGCTTGCAAAACG 61.211 55.000 0.00 0.00 36.98 3.60
861 894 3.141083 AGATGCTCTACTATCTGACCCCA 59.859 47.826 0.00 0.00 32.65 4.96
882 915 9.677567 GATCTATCTAACAGCTACTTCTTCAAG 57.322 37.037 0.00 0.00 35.50 3.02
889 922 7.361713 GCTCGATGATCTATCTAACAGCTACTT 60.362 40.741 0.00 0.00 33.44 2.24
890 923 6.093495 GCTCGATGATCTATCTAACAGCTACT 59.907 42.308 0.00 0.00 33.44 2.57
891 924 6.093495 AGCTCGATGATCTATCTAACAGCTAC 59.907 42.308 0.00 0.00 33.44 3.58
892 925 6.176896 AGCTCGATGATCTATCTAACAGCTA 58.823 40.000 0.00 0.00 33.44 3.32
893 926 5.009631 AGCTCGATGATCTATCTAACAGCT 58.990 41.667 0.00 3.92 33.44 4.24
894 927 5.309323 AGCTCGATGATCTATCTAACAGC 57.691 43.478 0.00 2.01 33.44 4.40
895 928 5.647658 AGGAGCTCGATGATCTATCTAACAG 59.352 44.000 7.83 0.00 33.44 3.16
896 929 5.565509 AGGAGCTCGATGATCTATCTAACA 58.434 41.667 7.83 0.00 33.44 2.41
897 930 6.119144 GAGGAGCTCGATGATCTATCTAAC 57.881 45.833 7.83 0.00 33.44 2.34
1365 1404 2.095604 TACATGTCATGATCCGGGGA 57.904 50.000 19.77 0.00 0.00 4.81
1392 1431 1.990563 CGTATGAACAAGGACGTGGAC 59.009 52.381 0.00 0.00 0.00 4.02
1393 1432 1.614903 ACGTATGAACAAGGACGTGGA 59.385 47.619 0.00 0.00 46.05 4.02
1401 1446 4.495422 ACCAAGCTCTACGTATGAACAAG 58.505 43.478 0.00 0.00 0.00 3.16
1447 1492 1.208052 CGGCCCGATGATCCAATCTAT 59.792 52.381 0.00 0.00 0.00 1.98
1448 1493 0.608130 CGGCCCGATGATCCAATCTA 59.392 55.000 0.00 0.00 0.00 1.98
1449 1494 1.372683 CGGCCCGATGATCCAATCT 59.627 57.895 0.00 0.00 0.00 2.40
1450 1495 1.672356 CCGGCCCGATGATCCAATC 60.672 63.158 3.71 0.00 0.00 2.67
1451 1496 2.431683 CCGGCCCGATGATCCAAT 59.568 61.111 3.71 0.00 0.00 3.16
1609 1657 2.948720 GCTGAACCTGTCCGCCTCT 61.949 63.158 0.00 0.00 30.63 3.69
1744 1792 2.549282 GTGCGTGCGACGTTGATT 59.451 55.556 7.08 0.00 44.73 2.57
1948 2022 3.629398 CGGAAAGGGATTGGAAATCTCTG 59.371 47.826 3.18 0.00 0.00 3.35
1996 2070 4.319839 GCGAGGAGGAAGAAAAAGAAACAG 60.320 45.833 0.00 0.00 0.00 3.16
1997 2071 3.564225 GCGAGGAGGAAGAAAAAGAAACA 59.436 43.478 0.00 0.00 0.00 2.83
1998 2072 3.815962 AGCGAGGAGGAAGAAAAAGAAAC 59.184 43.478 0.00 0.00 0.00 2.78
2001 2075 3.325135 AGAAGCGAGGAGGAAGAAAAAGA 59.675 43.478 0.00 0.00 0.00 2.52
2002 2076 3.434984 CAGAAGCGAGGAGGAAGAAAAAG 59.565 47.826 0.00 0.00 0.00 2.27
2003 2077 3.403038 CAGAAGCGAGGAGGAAGAAAAA 58.597 45.455 0.00 0.00 0.00 1.94
2023 2097 2.597818 TAGACCATGCAACCGGCCA 61.598 57.895 0.00 0.00 43.89 5.36
2028 2102 6.183360 GGTTAATTGTAGTAGACCATGCAACC 60.183 42.308 0.00 0.00 29.31 3.77
2045 2119 5.939883 TCAGTTGTCATCCAGAGGTTAATTG 59.060 40.000 0.00 0.00 0.00 2.32
2059 2133 5.221521 ACGGTCATATAGCATCAGTTGTCAT 60.222 40.000 0.00 0.00 0.00 3.06
2063 2137 8.932945 ATAATACGGTCATATAGCATCAGTTG 57.067 34.615 0.00 0.00 0.00 3.16
2096 2172 6.968131 TGACTGCAGATTTCATACTTGTAC 57.032 37.500 23.35 0.00 0.00 2.90
2163 2240 5.236047 GCCAAGTTAAAACATTGACATGCAA 59.764 36.000 0.00 5.27 41.53 4.08
2422 2502 0.460987 CCAGCAGTTTCCTAGAGCGG 60.461 60.000 0.00 0.00 0.00 5.52
2486 2566 2.757077 CCAAGATATCGGGGGCCC 59.243 66.667 15.76 15.76 0.00 5.80
2487 2567 2.757077 CCCAAGATATCGGGGGCC 59.243 66.667 21.61 0.00 38.95 5.80
2491 2571 2.757077 GGGCCCCAAGATATCGGG 59.243 66.667 12.23 9.27 42.67 5.14
2492 2572 2.757077 GGGGCCCCAAGATATCGG 59.243 66.667 37.61 0.00 35.81 4.18
2493 2573 2.757077 GGGGGCCCCAAGATATCG 59.243 66.667 41.80 0.00 44.65 2.92
2502 2582 2.156774 CCAGATAAGAGGGGGCCCC 61.157 68.421 35.78 35.78 45.90 5.80
2503 2583 2.835049 GCCAGATAAGAGGGGGCCC 61.835 68.421 15.76 15.76 38.70 5.80
2504 2584 2.839836 GCCAGATAAGAGGGGGCC 59.160 66.667 0.00 0.00 38.70 5.80
2505 2585 1.645402 TTGGCCAGATAAGAGGGGGC 61.645 60.000 5.11 0.00 45.45 5.80
2506 2586 0.475906 CTTGGCCAGATAAGAGGGGG 59.524 60.000 5.11 0.00 0.00 5.40
2507 2587 1.216990 ACTTGGCCAGATAAGAGGGG 58.783 55.000 5.11 0.00 0.00 4.79
2508 2588 3.372440 AAACTTGGCCAGATAAGAGGG 57.628 47.619 5.11 0.00 0.00 4.30
2509 2589 5.253330 TGTTAAACTTGGCCAGATAAGAGG 58.747 41.667 5.11 0.00 0.00 3.69
2510 2590 7.254455 CGTATGTTAAACTTGGCCAGATAAGAG 60.254 40.741 5.11 1.04 0.00 2.85
2511 2591 6.537301 CGTATGTTAAACTTGGCCAGATAAGA 59.463 38.462 5.11 3.52 0.00 2.10
2512 2592 6.315393 ACGTATGTTAAACTTGGCCAGATAAG 59.685 38.462 5.11 2.39 0.00 1.73
2513 2593 6.174760 ACGTATGTTAAACTTGGCCAGATAA 58.825 36.000 5.11 1.45 0.00 1.75
2514 2594 5.736813 ACGTATGTTAAACTTGGCCAGATA 58.263 37.500 5.11 0.00 0.00 1.98
2515 2595 4.585879 ACGTATGTTAAACTTGGCCAGAT 58.414 39.130 5.11 0.00 0.00 2.90
2516 2596 4.010667 ACGTATGTTAAACTTGGCCAGA 57.989 40.909 5.11 0.00 0.00 3.86
2517 2597 5.410439 ACTTACGTATGTTAAACTTGGCCAG 59.590 40.000 5.11 2.72 0.00 4.85
2518 2598 5.307204 ACTTACGTATGTTAAACTTGGCCA 58.693 37.500 0.00 0.00 0.00 5.36
2519 2599 5.868043 ACTTACGTATGTTAAACTTGGCC 57.132 39.130 8.22 0.00 0.00 5.36
2520 2600 8.498358 ACTTAACTTACGTATGTTAAACTTGGC 58.502 33.333 30.57 0.00 37.92 4.52
2529 2609 7.493645 GCCCAGATTACTTAACTTACGTATGTT 59.506 37.037 24.70 24.70 0.00 2.71
2530 2610 6.982724 GCCCAGATTACTTAACTTACGTATGT 59.017 38.462 8.22 8.22 0.00 2.29
2531 2611 6.423001 GGCCCAGATTACTTAACTTACGTATG 59.577 42.308 6.91 6.91 0.00 2.39
2532 2612 6.325804 AGGCCCAGATTACTTAACTTACGTAT 59.674 38.462 0.00 0.00 0.00 3.06
2533 2613 5.658190 AGGCCCAGATTACTTAACTTACGTA 59.342 40.000 0.00 0.00 0.00 3.57
2534 2614 4.468868 AGGCCCAGATTACTTAACTTACGT 59.531 41.667 0.00 0.00 0.00 3.57
2535 2615 5.019785 AGGCCCAGATTACTTAACTTACG 57.980 43.478 0.00 0.00 0.00 3.18
2536 2616 5.066117 GCAAGGCCCAGATTACTTAACTTAC 59.934 44.000 0.00 0.00 0.00 2.34
2537 2617 5.045140 AGCAAGGCCCAGATTACTTAACTTA 60.045 40.000 0.00 0.00 0.00 2.24
2538 2618 4.017126 GCAAGGCCCAGATTACTTAACTT 58.983 43.478 0.00 0.00 0.00 2.66
2539 2619 3.267031 AGCAAGGCCCAGATTACTTAACT 59.733 43.478 0.00 0.00 0.00 2.24
2540 2620 3.378427 CAGCAAGGCCCAGATTACTTAAC 59.622 47.826 0.00 0.00 0.00 2.01
2541 2621 3.620488 CAGCAAGGCCCAGATTACTTAA 58.380 45.455 0.00 0.00 0.00 1.85
2542 2622 2.092429 CCAGCAAGGCCCAGATTACTTA 60.092 50.000 0.00 0.00 0.00 2.24
2543 2623 1.341383 CCAGCAAGGCCCAGATTACTT 60.341 52.381 0.00 0.00 0.00 2.24
2544 2624 0.257039 CCAGCAAGGCCCAGATTACT 59.743 55.000 0.00 0.00 0.00 2.24
2545 2625 0.753111 CCCAGCAAGGCCCAGATTAC 60.753 60.000 0.00 0.00 35.39 1.89
2546 2626 1.214305 ACCCAGCAAGGCCCAGATTA 61.214 55.000 0.00 0.00 35.39 1.75
2547 2627 2.361771 CCCAGCAAGGCCCAGATT 59.638 61.111 0.00 0.00 35.39 2.40
2548 2628 2.943265 ACCCAGCAAGGCCCAGAT 60.943 61.111 0.00 0.00 35.39 2.90
2549 2629 3.970410 CACCCAGCAAGGCCCAGA 61.970 66.667 0.00 0.00 35.39 3.86
2550 2630 3.933048 CTCACCCAGCAAGGCCCAG 62.933 68.421 0.00 0.00 35.39 4.45
2551 2631 3.970410 CTCACCCAGCAAGGCCCA 61.970 66.667 0.00 0.00 35.39 5.36
2552 2632 4.748144 CCTCACCCAGCAAGGCCC 62.748 72.222 0.00 0.00 35.39 5.80
2553 2633 3.635268 CTCCTCACCCAGCAAGGCC 62.635 68.421 0.00 0.00 35.39 5.19
2554 2634 2.045536 CTCCTCACCCAGCAAGGC 60.046 66.667 0.00 0.00 35.39 4.35
2555 2635 0.035630 CTTCTCCTCACCCAGCAAGG 60.036 60.000 0.00 0.00 37.03 3.61
2556 2636 0.979665 TCTTCTCCTCACCCAGCAAG 59.020 55.000 0.00 0.00 0.00 4.01
2557 2637 1.434188 TTCTTCTCCTCACCCAGCAA 58.566 50.000 0.00 0.00 0.00 3.91
2558 2638 1.434188 TTTCTTCTCCTCACCCAGCA 58.566 50.000 0.00 0.00 0.00 4.41
2559 2639 2.568623 TTTTCTTCTCCTCACCCAGC 57.431 50.000 0.00 0.00 0.00 4.85
2560 2640 3.416156 CCTTTTTCTTCTCCTCACCCAG 58.584 50.000 0.00 0.00 0.00 4.45
2561 2641 2.489073 GCCTTTTTCTTCTCCTCACCCA 60.489 50.000 0.00 0.00 0.00 4.51
2562 2642 2.163509 GCCTTTTTCTTCTCCTCACCC 58.836 52.381 0.00 0.00 0.00 4.61
2563 2643 2.863809 TGCCTTTTTCTTCTCCTCACC 58.136 47.619 0.00 0.00 0.00 4.02
2564 2644 4.339530 AGTTTGCCTTTTTCTTCTCCTCAC 59.660 41.667 0.00 0.00 0.00 3.51
2565 2645 4.339247 CAGTTTGCCTTTTTCTTCTCCTCA 59.661 41.667 0.00 0.00 0.00 3.86
2566 2646 4.261783 CCAGTTTGCCTTTTTCTTCTCCTC 60.262 45.833 0.00 0.00 0.00 3.71
2567 2647 3.638627 CCAGTTTGCCTTTTTCTTCTCCT 59.361 43.478 0.00 0.00 0.00 3.69
2568 2648 3.243873 CCCAGTTTGCCTTTTTCTTCTCC 60.244 47.826 0.00 0.00 0.00 3.71
2569 2649 3.800261 GCCCAGTTTGCCTTTTTCTTCTC 60.800 47.826 0.00 0.00 0.00 2.87
2570 2650 2.103094 GCCCAGTTTGCCTTTTTCTTCT 59.897 45.455 0.00 0.00 0.00 2.85
2571 2651 2.103094 AGCCCAGTTTGCCTTTTTCTTC 59.897 45.455 0.00 0.00 0.00 2.87
2572 2652 2.118679 AGCCCAGTTTGCCTTTTTCTT 58.881 42.857 0.00 0.00 0.00 2.52
2573 2653 1.793414 AGCCCAGTTTGCCTTTTTCT 58.207 45.000 0.00 0.00 0.00 2.52
2574 2654 2.620251 AAGCCCAGTTTGCCTTTTTC 57.380 45.000 0.00 0.00 0.00 2.29
2575 2655 3.038280 ACTAAGCCCAGTTTGCCTTTTT 58.962 40.909 0.00 0.00 0.00 1.94
2576 2656 2.677914 ACTAAGCCCAGTTTGCCTTTT 58.322 42.857 0.00 0.00 0.00 2.27
2577 2657 2.381752 ACTAAGCCCAGTTTGCCTTT 57.618 45.000 0.00 0.00 0.00 3.11
2578 2658 2.642807 TCTACTAAGCCCAGTTTGCCTT 59.357 45.455 0.00 0.00 0.00 4.35
2579 2659 2.266279 TCTACTAAGCCCAGTTTGCCT 58.734 47.619 0.00 0.00 0.00 4.75
2580 2660 2.747989 GTTCTACTAAGCCCAGTTTGCC 59.252 50.000 0.00 0.00 0.00 4.52
2581 2661 2.747989 GGTTCTACTAAGCCCAGTTTGC 59.252 50.000 0.00 0.00 0.00 3.68
2582 2662 3.000727 CGGTTCTACTAAGCCCAGTTTG 58.999 50.000 0.00 0.00 0.00 2.93
2583 2663 2.636403 ACGGTTCTACTAAGCCCAGTTT 59.364 45.455 0.00 0.00 0.00 2.66
2584 2664 2.028385 CACGGTTCTACTAAGCCCAGTT 60.028 50.000 0.00 0.00 0.00 3.16
2585 2665 1.549170 CACGGTTCTACTAAGCCCAGT 59.451 52.381 0.00 0.00 0.00 4.00
2586 2666 1.739371 GCACGGTTCTACTAAGCCCAG 60.739 57.143 0.00 0.00 0.00 4.45
2587 2667 0.248289 GCACGGTTCTACTAAGCCCA 59.752 55.000 0.00 0.00 0.00 5.36
2588 2668 0.248289 TGCACGGTTCTACTAAGCCC 59.752 55.000 0.00 0.00 0.00 5.19
2589 2669 2.000447 CTTGCACGGTTCTACTAAGCC 59.000 52.381 0.00 0.00 0.00 4.35
2590 2670 2.685100 ACTTGCACGGTTCTACTAAGC 58.315 47.619 0.00 0.00 0.00 3.09
2591 2671 3.850273 CGTACTTGCACGGTTCTACTAAG 59.150 47.826 0.00 0.00 38.26 2.18
2592 2672 3.253188 ACGTACTTGCACGGTTCTACTAA 59.747 43.478 0.00 0.00 46.12 2.24
2593 2673 2.813754 ACGTACTTGCACGGTTCTACTA 59.186 45.455 0.00 0.00 46.12 1.82
2594 2674 1.610522 ACGTACTTGCACGGTTCTACT 59.389 47.619 0.00 0.00 46.12 2.57
2595 2675 1.717645 CACGTACTTGCACGGTTCTAC 59.282 52.381 0.00 0.00 46.12 2.59
2596 2676 1.931709 GCACGTACTTGCACGGTTCTA 60.932 52.381 18.60 0.00 46.12 2.10
2597 2677 1.219522 GCACGTACTTGCACGGTTCT 61.220 55.000 18.60 0.00 46.12 3.01
2598 2678 1.203313 GCACGTACTTGCACGGTTC 59.797 57.895 18.60 0.00 46.12 3.62
2599 2679 0.812412 AAGCACGTACTTGCACGGTT 60.812 50.000 24.34 8.66 45.62 4.44
2600 2680 0.812412 AAAGCACGTACTTGCACGGT 60.812 50.000 24.34 2.68 45.62 4.83
2601 2681 0.384230 CAAAGCACGTACTTGCACGG 60.384 55.000 24.34 10.23 45.62 4.94
2602 2682 0.384230 CCAAAGCACGTACTTGCACG 60.384 55.000 24.34 12.54 45.62 5.34
2603 2683 0.660300 GCCAAAGCACGTACTTGCAC 60.660 55.000 24.34 6.39 45.62 4.57
2604 2684 1.098129 TGCCAAAGCACGTACTTGCA 61.098 50.000 24.34 8.94 46.52 4.08
2605 2685 0.385974 CTGCCAAAGCACGTACTTGC 60.386 55.000 16.07 16.07 46.52 4.01
2606 2686 3.753774 CTGCCAAAGCACGTACTTG 57.246 52.632 0.80 0.00 46.52 3.16
2616 2696 1.067142 TCGTGTAGTAGGCTGCCAAAG 60.067 52.381 22.65 3.22 0.00 2.77
2617 2697 0.970640 TCGTGTAGTAGGCTGCCAAA 59.029 50.000 22.65 5.44 0.00 3.28
2618 2698 0.530744 CTCGTGTAGTAGGCTGCCAA 59.469 55.000 22.65 0.00 0.00 4.52
2619 2699 0.611062 ACTCGTGTAGTAGGCTGCCA 60.611 55.000 22.65 3.92 36.36 4.92
2620 2700 1.065251 GTACTCGTGTAGTAGGCTGCC 59.935 57.143 11.65 11.65 41.42 4.85
2621 2701 2.015587 AGTACTCGTGTAGTAGGCTGC 58.984 52.381 3.20 0.00 41.42 5.25
2622 2702 4.155462 TCAAAGTACTCGTGTAGTAGGCTG 59.845 45.833 5.47 2.66 41.42 4.85
2623 2703 4.155644 GTCAAAGTACTCGTGTAGTAGGCT 59.844 45.833 5.47 0.00 41.42 4.58
2624 2704 4.410448 GTCAAAGTACTCGTGTAGTAGGC 58.590 47.826 5.47 0.65 41.42 3.93
2625 2705 4.456911 TGGTCAAAGTACTCGTGTAGTAGG 59.543 45.833 5.47 2.15 41.42 3.18
2626 2706 5.618056 TGGTCAAAGTACTCGTGTAGTAG 57.382 43.478 5.47 2.80 41.42 2.57
2627 2707 5.124457 GGATGGTCAAAGTACTCGTGTAGTA 59.876 44.000 5.47 0.00 39.80 1.82
2628 2708 4.082354 GGATGGTCAAAGTACTCGTGTAGT 60.082 45.833 0.00 0.00 42.62 2.73
2629 2709 4.421948 GGATGGTCAAAGTACTCGTGTAG 58.578 47.826 0.00 0.00 0.00 2.74
2630 2710 3.119743 CGGATGGTCAAAGTACTCGTGTA 60.120 47.826 0.00 0.00 0.00 2.90
2631 2711 2.352421 CGGATGGTCAAAGTACTCGTGT 60.352 50.000 0.00 0.00 0.00 4.49
2632 2712 2.094906 TCGGATGGTCAAAGTACTCGTG 60.095 50.000 0.00 0.00 0.00 4.35
2633 2713 2.165167 TCGGATGGTCAAAGTACTCGT 58.835 47.619 0.00 0.00 0.00 4.18
2634 2714 2.933495 TCGGATGGTCAAAGTACTCG 57.067 50.000 0.00 0.00 0.00 4.18
2635 2715 3.458189 CCATCGGATGGTCAAAGTACTC 58.542 50.000 25.70 0.00 45.54 2.59
2636 2716 3.543680 CCATCGGATGGTCAAAGTACT 57.456 47.619 25.70 0.00 45.54 2.73
2647 2727 3.070018 GCAAACCTAGATCCATCGGATG 58.930 50.000 11.07 11.07 43.27 3.51
2648 2728 2.289072 CGCAAACCTAGATCCATCGGAT 60.289 50.000 0.00 0.00 46.28 4.18
2649 2729 1.068588 CGCAAACCTAGATCCATCGGA 59.931 52.381 0.00 0.00 35.55 4.55
2650 2730 1.202533 ACGCAAACCTAGATCCATCGG 60.203 52.381 0.00 0.00 0.00 4.18
2651 2731 2.225068 ACGCAAACCTAGATCCATCG 57.775 50.000 0.00 0.00 0.00 3.84
2652 2732 3.997021 CCATACGCAAACCTAGATCCATC 59.003 47.826 0.00 0.00 0.00 3.51
2653 2733 3.646162 TCCATACGCAAACCTAGATCCAT 59.354 43.478 0.00 0.00 0.00 3.41
2654 2734 3.035363 TCCATACGCAAACCTAGATCCA 58.965 45.455 0.00 0.00 0.00 3.41
2655 2735 3.746045 TCCATACGCAAACCTAGATCC 57.254 47.619 0.00 0.00 0.00 3.36
2656 2736 4.083802 GCAATCCATACGCAAACCTAGATC 60.084 45.833 0.00 0.00 0.00 2.75
2657 2737 3.815401 GCAATCCATACGCAAACCTAGAT 59.185 43.478 0.00 0.00 0.00 1.98
2658 2738 3.202906 GCAATCCATACGCAAACCTAGA 58.797 45.455 0.00 0.00 0.00 2.43
2659 2739 2.290641 GGCAATCCATACGCAAACCTAG 59.709 50.000 0.00 0.00 0.00 3.02
2660 2740 2.092646 AGGCAATCCATACGCAAACCTA 60.093 45.455 0.00 0.00 33.74 3.08
2661 2741 1.102978 GGCAATCCATACGCAAACCT 58.897 50.000 0.00 0.00 0.00 3.50
2662 2742 1.102978 AGGCAATCCATACGCAAACC 58.897 50.000 0.00 0.00 33.74 3.27
2663 2743 2.529151 CAAGGCAATCCATACGCAAAC 58.471 47.619 0.00 0.00 33.74 2.93
2664 2744 1.476085 CCAAGGCAATCCATACGCAAA 59.524 47.619 0.00 0.00 33.74 3.68
2665 2745 1.102154 CCAAGGCAATCCATACGCAA 58.898 50.000 0.00 0.00 33.74 4.85
2666 2746 0.751277 CCCAAGGCAATCCATACGCA 60.751 55.000 0.00 0.00 33.74 5.24
2667 2747 1.455383 CCCCAAGGCAATCCATACGC 61.455 60.000 0.00 0.00 33.74 4.42
2668 2748 2.719376 CCCCAAGGCAATCCATACG 58.281 57.895 0.00 0.00 33.74 3.06
2679 2759 3.787001 GAGACGAGGGCCCCAAGG 61.787 72.222 21.43 7.91 0.00 3.61
2680 2760 3.787001 GGAGACGAGGGCCCCAAG 61.787 72.222 21.43 13.13 0.00 3.61
2681 2761 3.943137 ATGGAGACGAGGGCCCCAA 62.943 63.158 21.43 0.00 0.00 4.12
2682 2762 4.414956 ATGGAGACGAGGGCCCCA 62.415 66.667 21.43 7.80 0.00 4.96
2683 2763 3.551407 GATGGAGACGAGGGCCCC 61.551 72.222 21.43 9.47 0.00 5.80
2684 2764 2.034048 GAAGATGGAGACGAGGGCCC 62.034 65.000 16.46 16.46 0.00 5.80
2685 2765 1.330655 TGAAGATGGAGACGAGGGCC 61.331 60.000 0.00 0.00 0.00 5.80
2686 2766 0.179097 GTGAAGATGGAGACGAGGGC 60.179 60.000 0.00 0.00 0.00 5.19
2687 2767 1.479709 AGTGAAGATGGAGACGAGGG 58.520 55.000 0.00 0.00 0.00 4.30
2688 2768 4.555708 CGATTAGTGAAGATGGAGACGAGG 60.556 50.000 0.00 0.00 0.00 4.63
2689 2769 4.532276 CGATTAGTGAAGATGGAGACGAG 58.468 47.826 0.00 0.00 0.00 4.18
2690 2770 3.243101 GCGATTAGTGAAGATGGAGACGA 60.243 47.826 0.00 0.00 0.00 4.20
2691 2771 3.046390 GCGATTAGTGAAGATGGAGACG 58.954 50.000 0.00 0.00 0.00 4.18
2692 2772 3.068873 AGGCGATTAGTGAAGATGGAGAC 59.931 47.826 0.00 0.00 0.00 3.36
2693 2773 3.068732 CAGGCGATTAGTGAAGATGGAGA 59.931 47.826 0.00 0.00 0.00 3.71
2694 2774 3.388308 CAGGCGATTAGTGAAGATGGAG 58.612 50.000 0.00 0.00 0.00 3.86
2695 2775 2.483714 GCAGGCGATTAGTGAAGATGGA 60.484 50.000 0.00 0.00 0.00 3.41
2696 2776 1.869767 GCAGGCGATTAGTGAAGATGG 59.130 52.381 0.00 0.00 0.00 3.51
2697 2777 1.524355 CGCAGGCGATTAGTGAAGATG 59.476 52.381 8.15 0.00 42.83 2.90
2698 2778 1.858091 CGCAGGCGATTAGTGAAGAT 58.142 50.000 8.15 0.00 42.83 2.40
2699 2779 0.806102 GCGCAGGCGATTAGTGAAGA 60.806 55.000 18.96 0.00 42.83 2.87
2700 2780 1.638467 GCGCAGGCGATTAGTGAAG 59.362 57.895 18.96 0.00 42.83 3.02
2701 2781 3.794270 GCGCAGGCGATTAGTGAA 58.206 55.556 18.96 0.00 42.83 3.18


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

AutoCloner maintained by Alex Coulton.