Multiple sequence alignment - TraesCS5D01G308300

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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 TraesCS5D01G308300 chr5D 100.000 3347 0 0 1 3347 405212820 405209474 0.000000e+00 6181
1 TraesCS5D01G308300 chr5B 95.554 1462 61 2 950 2407 486083887 486082426 0.000000e+00 2337
2 TraesCS5D01G308300 chr5B 87.006 177 11 6 3147 3321 486081495 486081329 4.410000e-44 189
3 TraesCS5D01G308300 chr5A 94.665 1462 69 3 950 2407 509105313 509106769 0.000000e+00 2259
4 TraesCS5D01G308300 chr5A 83.155 653 67 22 2687 3323 509107714 509108339 1.050000e-154 556
5 TraesCS5D01G308300 chr2D 88.321 959 89 19 1 952 29145463 29144521 0.000000e+00 1129
6 TraesCS5D01G308300 chr2D 86.085 963 114 15 1 953 641228511 641229463 0.000000e+00 1018
7 TraesCS5D01G308300 chr2D 79.107 1120 150 45 1312 2407 47423052 47421993 0.000000e+00 695
8 TraesCS5D01G308300 chr3A 88.330 934 99 8 1 929 175638329 175637401 0.000000e+00 1112
9 TraesCS5D01G308300 chr7D 86.812 963 105 14 1 951 567731558 567732510 0.000000e+00 1055
10 TraesCS5D01G308300 chr7D 86.938 957 99 15 1 952 552162994 552162059 0.000000e+00 1051
11 TraesCS5D01G308300 chr1D 86.653 959 108 14 1 949 476879077 476878129 0.000000e+00 1044
12 TraesCS5D01G308300 chr1D 85.106 611 59 18 1754 2355 102530176 102529589 2.220000e-166 595
13 TraesCS5D01G308300 chr3B 86.715 956 106 16 1 949 84903366 84902425 0.000000e+00 1042
14 TraesCS5D01G308300 chr3B 82.249 169 24 5 788 953 137135694 137135859 1.250000e-29 141
15 TraesCS5D01G308300 chr4D 85.938 960 115 14 1 951 294457809 294458757 0.000000e+00 1007
16 TraesCS5D01G308300 chr4D 85.923 959 115 15 1 949 393832404 393833352 0.000000e+00 1005
17 TraesCS5D01G308300 chr2B 79.931 1161 152 40 1286 2407 75617029 75615911 0.000000e+00 778
18 TraesCS5D01G308300 chr1A 86.507 667 69 9 1753 2407 102362337 102362994 0.000000e+00 713
19 TraesCS5D01G308300 chr2A 79.922 772 110 30 1313 2065 50960172 50959427 2.960000e-145 525
20 TraesCS5D01G308300 chr2A 85.279 197 27 2 2211 2406 50959381 50959186 5.660000e-48 202


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 TraesCS5D01G308300 chr5D 405209474 405212820 3346 True 6181.0 6181 100.0000 1 3347 1 chr5D.!!$R1 3346
1 TraesCS5D01G308300 chr5B 486081329 486083887 2558 True 1263.0 2337 91.2800 950 3321 2 chr5B.!!$R1 2371
2 TraesCS5D01G308300 chr5A 509105313 509108339 3026 False 1407.5 2259 88.9100 950 3323 2 chr5A.!!$F1 2373
3 TraesCS5D01G308300 chr2D 29144521 29145463 942 True 1129.0 1129 88.3210 1 952 1 chr2D.!!$R1 951
4 TraesCS5D01G308300 chr2D 641228511 641229463 952 False 1018.0 1018 86.0850 1 953 1 chr2D.!!$F1 952
5 TraesCS5D01G308300 chr2D 47421993 47423052 1059 True 695.0 695 79.1070 1312 2407 1 chr2D.!!$R2 1095
6 TraesCS5D01G308300 chr3A 175637401 175638329 928 True 1112.0 1112 88.3300 1 929 1 chr3A.!!$R1 928
7 TraesCS5D01G308300 chr7D 567731558 567732510 952 False 1055.0 1055 86.8120 1 951 1 chr7D.!!$F1 950
8 TraesCS5D01G308300 chr7D 552162059 552162994 935 True 1051.0 1051 86.9380 1 952 1 chr7D.!!$R1 951
9 TraesCS5D01G308300 chr1D 476878129 476879077 948 True 1044.0 1044 86.6530 1 949 1 chr1D.!!$R2 948
10 TraesCS5D01G308300 chr1D 102529589 102530176 587 True 595.0 595 85.1060 1754 2355 1 chr1D.!!$R1 601
11 TraesCS5D01G308300 chr3B 84902425 84903366 941 True 1042.0 1042 86.7150 1 949 1 chr3B.!!$R1 948
12 TraesCS5D01G308300 chr4D 294457809 294458757 948 False 1007.0 1007 85.9380 1 951 1 chr4D.!!$F1 950
13 TraesCS5D01G308300 chr4D 393832404 393833352 948 False 1005.0 1005 85.9230 1 949 1 chr4D.!!$F2 948
14 TraesCS5D01G308300 chr2B 75615911 75617029 1118 True 778.0 778 79.9310 1286 2407 1 chr2B.!!$R1 1121
15 TraesCS5D01G308300 chr1A 102362337 102362994 657 False 713.0 713 86.5070 1753 2407 1 chr1A.!!$F1 654
16 TraesCS5D01G308300 chr2A 50959186 50960172 986 True 363.5 525 82.6005 1313 2406 2 chr2A.!!$R1 1093

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
511 520 0.109504 GGAGAGTCTGTGCGTCTCAC 60.11 60.0 0.0 0.0 45.82 3.51 F
957 981 0.749649 CGAGATGCTCTTAGCCCACT 59.25 55.0 0.0 0.0 41.51 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 1912 0.387929 GCTCACCATGGCCATTCATG 59.612 55.0 17.92 14.59 42.92 3.07 R
2677 3547 0.108585 GCTTGTCTGACCACCAAGGA 59.891 55.0 5.17 0.00 41.22 3.36 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
127 129 4.828925 GTGGCCTCGAGCTGCTCC 62.829 72.222 22.97 10.52 43.05 4.70
157 159 2.992476 ACGGAAGTACTGCTCCCAT 58.008 52.632 7.84 0.00 46.88 4.00
174 176 4.853142 TAGCGGGCTGTCGGGGAT 62.853 66.667 2.86 0.00 0.00 3.85
237 240 2.214122 TACGGGTGATCTCCCCACGA 62.214 60.000 24.07 6.86 44.32 4.35
296 299 1.597302 CAGCGCTGATCCTCCATGG 60.597 63.158 33.66 4.97 37.10 3.66
297 300 2.281345 GCGCTGATCCTCCATGGG 60.281 66.667 13.02 2.26 36.20 4.00
343 348 1.202903 GGGTACTCGGCCTCATAGAGA 60.203 57.143 11.11 0.00 36.03 3.10
424 429 3.577313 GGAAAGCGCTCGGCCATC 61.577 66.667 12.06 2.49 45.17 3.51
463 470 0.705253 AGAAGAGAGGGAGGAACGGA 59.295 55.000 0.00 0.00 0.00 4.69
466 473 2.364448 AGAGGGAGGAACGGAGGC 60.364 66.667 0.00 0.00 0.00 4.70
508 517 1.528292 GGTGGAGAGTCTGTGCGTCT 61.528 60.000 0.00 0.00 0.00 4.18
510 519 0.537371 TGGAGAGTCTGTGCGTCTCA 60.537 55.000 0.00 0.00 38.83 3.27
511 520 0.109504 GGAGAGTCTGTGCGTCTCAC 60.110 60.000 0.00 0.00 45.82 3.51
512 521 0.109504 GAGAGTCTGTGCGTCTCACC 60.110 60.000 0.00 0.00 45.03 4.02
513 522 1.442857 GAGTCTGTGCGTCTCACCG 60.443 63.158 0.00 0.00 45.03 4.94
515 524 2.910479 TCTGTGCGTCTCACCGGT 60.910 61.111 0.00 0.00 45.03 5.28
648 662 0.767375 GGCATCAATGGAGGAGGCTA 59.233 55.000 0.00 0.00 41.46 3.93
655 669 3.081409 GGAGGAGGCTAACCGGCA 61.081 66.667 0.00 0.00 42.76 5.69
769 787 1.125270 ATTTTCGCGCCAAAAACGAC 58.875 45.000 16.69 0.00 35.20 4.34
845 865 1.376683 CCAATTTCGACCCGAGCCA 60.377 57.895 0.00 0.00 37.14 4.75
875 895 2.577059 CCTTTGGAGGCGCGACTA 59.423 61.111 18.29 0.00 35.94 2.59
957 981 0.749649 CGAGATGCTCTTAGCCCACT 59.250 55.000 0.00 0.00 41.51 4.00
966 990 2.366916 CTCTTAGCCCACTACCTCATGG 59.633 54.545 0.00 0.00 39.83 3.66
1001 1028 2.238084 TGTGGCTCTACCTCAGTGAT 57.762 50.000 0.00 0.00 37.01 3.06
1067 1094 3.432588 CCTCCGCAGACTCGTCGT 61.433 66.667 0.00 0.00 34.09 4.34
1078 1105 4.415332 TCGTCGTCGCTGCCTTCC 62.415 66.667 0.00 0.00 36.96 3.46
1209 1236 1.153823 CACCGCCTACACCTTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
1519 1564 1.375908 GTGTCTTGGAGCGCCATGA 60.376 57.895 19.12 19.12 45.46 3.07
1635 1693 4.609018 AGCGTGCTCAAGGCGTGT 62.609 61.111 0.00 0.00 44.54 4.49
1707 1773 1.464198 AGAGGGGTTTGCAGGGACT 60.464 57.895 0.00 0.00 43.88 3.85
1806 1873 3.482783 GACTCTGTTCGCTGCCGC 61.483 66.667 0.00 0.00 0.00 6.53
1833 1900 5.232463 GTTGTGCTGTGGAATTCAATGATT 58.768 37.500 7.93 0.00 0.00 2.57
1865 1932 0.032912 ATGAATGGCCATGGTGAGCA 60.033 50.000 21.63 11.15 0.00 4.26
1978 2052 2.060980 CGTCTGGAGGAAGGGAGGG 61.061 68.421 0.00 0.00 0.00 4.30
2088 2183 1.346068 GTTGAGGAGGCTGAGACTGTT 59.654 52.381 0.00 0.00 0.00 3.16
2244 2357 2.420022 GCGGTATGCTGTTCTGTTCAAT 59.580 45.455 0.00 0.00 41.73 2.57
2368 2486 2.489938 TGGTTGCTCCATGAGTTACC 57.510 50.000 0.00 8.77 41.93 2.85
2409 3251 3.334583 TGCACTGTTGGAAGATACCTC 57.665 47.619 0.00 0.00 0.00 3.85
2417 3259 3.033659 TGGAAGATACCTCCTCTGTCC 57.966 52.381 0.00 0.00 0.00 4.02
2418 3260 2.314852 TGGAAGATACCTCCTCTGTCCA 59.685 50.000 0.00 0.00 32.45 4.02
2419 3261 2.696187 GGAAGATACCTCCTCTGTCCAC 59.304 54.545 0.00 0.00 0.00 4.02
2422 3264 2.035632 GATACCTCCTCTGTCCACTGG 58.964 57.143 0.00 0.00 0.00 4.00
2427 3269 1.229336 CCTCTGTCCACTGGGAGGT 60.229 63.158 9.66 0.00 46.12 3.85
2428 3270 0.838122 CCTCTGTCCACTGGGAGGTT 60.838 60.000 9.66 0.00 46.12 3.50
2429 3271 1.552486 CCTCTGTCCACTGGGAGGTTA 60.552 57.143 9.66 0.00 46.12 2.85
2430 3272 1.827969 CTCTGTCCACTGGGAGGTTAG 59.172 57.143 0.00 0.00 46.12 2.34
2444 3286 3.835395 GGAGGTTAGCTATCTATGGCAGT 59.165 47.826 0.00 0.00 36.66 4.40
2452 3294 5.688807 AGCTATCTATGGCAGTTTCATGTT 58.311 37.500 1.00 0.00 36.66 2.71
2456 3298 5.426689 TCTATGGCAGTTTCATGTTCTCT 57.573 39.130 0.00 0.00 0.00 3.10
2462 3304 2.227388 CAGTTTCATGTTCTCTGGTGGC 59.773 50.000 0.00 0.00 0.00 5.01
2472 3314 0.947244 CTCTGGTGGCAAGAACACAC 59.053 55.000 0.00 0.00 40.54 3.82
2473 3315 0.254462 TCTGGTGGCAAGAACACACA 59.746 50.000 0.00 0.00 40.54 3.72
2475 3317 1.355210 GGTGGCAAGAACACACACG 59.645 57.895 0.00 0.00 40.54 4.49
2476 3318 1.298339 GTGGCAAGAACACACACGC 60.298 57.895 0.00 0.00 38.67 5.34
2477 3319 1.451207 TGGCAAGAACACACACGCT 60.451 52.632 0.00 0.00 0.00 5.07
2478 3320 0.179070 TGGCAAGAACACACACGCTA 60.179 50.000 0.00 0.00 0.00 4.26
2479 3321 1.156736 GGCAAGAACACACACGCTAT 58.843 50.000 0.00 0.00 0.00 2.97
2480 3322 1.535462 GGCAAGAACACACACGCTATT 59.465 47.619 0.00 0.00 0.00 1.73
2515 3383 7.387948 ACATGTTAACGTTTATTCTTCTGCTCT 59.612 33.333 5.91 0.00 0.00 4.09
2517 3385 8.236084 TGTTAACGTTTATTCTTCTGCTCTAC 57.764 34.615 5.91 0.00 0.00 2.59
2534 3402 3.552875 TCTACTTACTACCTGCAGCGAT 58.447 45.455 8.66 0.00 0.00 4.58
2550 3418 0.806868 CGATTGCTGGTGCTGTTCAT 59.193 50.000 0.00 0.00 40.48 2.57
2560 3428 2.388121 GTGCTGTTCATGTGCAACTTC 58.612 47.619 0.00 0.00 38.50 3.01
2563 3431 3.047796 GCTGTTCATGTGCAACTTCTTG 58.952 45.455 0.00 0.00 38.04 3.02
2573 3443 1.000060 GCAACTTCTTGCCATGAAGCA 60.000 47.619 17.52 0.00 46.27 3.91
2588 3458 2.439507 TGAAGCAAGAACCTGGAGAAGT 59.560 45.455 0.00 0.00 0.00 3.01
2593 3463 3.006967 GCAAGAACCTGGAGAAGTGAGTA 59.993 47.826 0.00 0.00 0.00 2.59
2594 3464 4.503296 GCAAGAACCTGGAGAAGTGAGTAA 60.503 45.833 0.00 0.00 0.00 2.24
2597 3467 4.282195 AGAACCTGGAGAAGTGAGTAACAG 59.718 45.833 0.00 0.00 0.00 3.16
2600 3470 4.841246 ACCTGGAGAAGTGAGTAACAGATT 59.159 41.667 0.00 0.00 0.00 2.40
2602 3472 5.407407 TGGAGAAGTGAGTAACAGATTCC 57.593 43.478 0.00 0.00 0.00 3.01
2603 3473 4.082190 TGGAGAAGTGAGTAACAGATTCCG 60.082 45.833 0.00 0.00 0.00 4.30
2605 3475 3.258372 AGAAGTGAGTAACAGATTCCGCA 59.742 43.478 0.00 0.00 0.00 5.69
2606 3476 3.678056 AGTGAGTAACAGATTCCGCAA 57.322 42.857 0.00 0.00 0.00 4.85
2607 3477 3.589988 AGTGAGTAACAGATTCCGCAAG 58.410 45.455 0.00 0.00 0.00 4.01
2622 3492 3.680642 CGCAAGGATTACCACATTCAG 57.319 47.619 0.00 0.00 38.94 3.02
2623 3493 3.009723 CGCAAGGATTACCACATTCAGT 58.990 45.455 0.00 0.00 38.94 3.41
2637 3507 6.785488 CACATTCAGTGCCGTACATATTAT 57.215 37.500 0.00 0.00 42.15 1.28
2638 3508 6.593072 CACATTCAGTGCCGTACATATTATG 58.407 40.000 2.03 2.03 42.15 1.90
2639 3509 5.179368 ACATTCAGTGCCGTACATATTATGC 59.821 40.000 3.52 0.00 0.00 3.14
2640 3510 3.659786 TCAGTGCCGTACATATTATGCC 58.340 45.455 3.52 0.00 0.00 4.40
2641 3511 3.323691 TCAGTGCCGTACATATTATGCCT 59.676 43.478 3.52 0.00 0.00 4.75
2642 3512 4.525100 TCAGTGCCGTACATATTATGCCTA 59.475 41.667 3.52 0.00 0.00 3.93
2643 3513 5.011227 TCAGTGCCGTACATATTATGCCTAA 59.989 40.000 3.52 0.00 0.00 2.69
2644 3514 5.348724 CAGTGCCGTACATATTATGCCTAAG 59.651 44.000 3.52 0.00 0.00 2.18
2645 3515 4.092968 GTGCCGTACATATTATGCCTAAGC 59.907 45.833 3.52 2.32 40.48 3.09
2646 3516 3.621715 GCCGTACATATTATGCCTAAGCC 59.378 47.826 3.52 0.00 38.69 4.35
2647 3517 4.623171 GCCGTACATATTATGCCTAAGCCT 60.623 45.833 3.52 0.00 38.69 4.58
2648 3518 5.109903 CCGTACATATTATGCCTAAGCCTC 58.890 45.833 3.52 0.00 38.69 4.70
2649 3519 5.337250 CCGTACATATTATGCCTAAGCCTCA 60.337 44.000 3.52 0.00 38.69 3.86
2650 3520 5.807520 CGTACATATTATGCCTAAGCCTCAG 59.192 44.000 3.52 0.00 38.69 3.35
2651 3521 6.350194 CGTACATATTATGCCTAAGCCTCAGA 60.350 42.308 3.52 0.00 38.69 3.27
2652 3522 6.633325 ACATATTATGCCTAAGCCTCAGAT 57.367 37.500 3.52 0.00 38.69 2.90
2653 3523 7.739995 ACATATTATGCCTAAGCCTCAGATA 57.260 36.000 3.52 0.00 38.69 1.98
2654 3524 7.790027 ACATATTATGCCTAAGCCTCAGATAG 58.210 38.462 3.52 0.00 38.69 2.08
2655 3525 7.401493 ACATATTATGCCTAAGCCTCAGATAGT 59.599 37.037 3.52 0.00 38.69 2.12
2656 3526 5.474578 TTATGCCTAAGCCTCAGATAGTG 57.525 43.478 0.00 0.00 38.69 2.74
2657 3527 3.032265 TGCCTAAGCCTCAGATAGTGA 57.968 47.619 0.00 0.00 38.69 3.41
2658 3528 3.374764 TGCCTAAGCCTCAGATAGTGAA 58.625 45.455 0.00 0.00 38.69 3.18
2659 3529 3.386078 TGCCTAAGCCTCAGATAGTGAAG 59.614 47.826 0.00 0.00 38.69 3.02
2660 3530 3.386402 GCCTAAGCCTCAGATAGTGAAGT 59.614 47.826 0.00 0.00 33.60 3.01
2661 3531 4.141824 GCCTAAGCCTCAGATAGTGAAGTT 60.142 45.833 0.00 0.00 33.60 2.66
2662 3532 5.627968 GCCTAAGCCTCAGATAGTGAAGTTT 60.628 44.000 0.00 0.00 33.60 2.66
2663 3533 6.045955 CCTAAGCCTCAGATAGTGAAGTTTC 58.954 44.000 0.00 0.00 33.60 2.78
2664 3534 5.753721 AAGCCTCAGATAGTGAAGTTTCT 57.246 39.130 0.00 0.00 33.60 2.52
2665 3535 5.753721 AGCCTCAGATAGTGAAGTTTCTT 57.246 39.130 0.00 0.00 33.60 2.52
2666 3536 6.120507 AGCCTCAGATAGTGAAGTTTCTTT 57.879 37.500 0.00 0.00 33.60 2.52
2667 3537 6.538263 AGCCTCAGATAGTGAAGTTTCTTTT 58.462 36.000 0.00 0.00 33.60 2.27
2668 3538 6.429385 AGCCTCAGATAGTGAAGTTTCTTTTG 59.571 38.462 0.00 0.00 33.60 2.44
2669 3539 6.606768 CCTCAGATAGTGAAGTTTCTTTTGC 58.393 40.000 0.00 0.00 33.60 3.68
2670 3540 6.429385 CCTCAGATAGTGAAGTTTCTTTTGCT 59.571 38.462 0.00 0.00 33.60 3.91
2671 3541 7.360776 CCTCAGATAGTGAAGTTTCTTTTGCTC 60.361 40.741 0.00 0.00 33.60 4.26
2672 3542 7.220030 TCAGATAGTGAAGTTTCTTTTGCTCT 58.780 34.615 0.00 0.00 29.64 4.09
2673 3543 7.716998 TCAGATAGTGAAGTTTCTTTTGCTCTT 59.283 33.333 0.00 0.00 29.64 2.85
2674 3544 8.348507 CAGATAGTGAAGTTTCTTTTGCTCTTT 58.651 33.333 0.00 0.00 0.00 2.52
2675 3545 8.563732 AGATAGTGAAGTTTCTTTTGCTCTTTC 58.436 33.333 0.00 0.00 0.00 2.62
2676 3546 6.765915 AGTGAAGTTTCTTTTGCTCTTTCT 57.234 33.333 0.00 0.00 0.00 2.52
2677 3547 7.163001 AGTGAAGTTTCTTTTGCTCTTTCTT 57.837 32.000 0.00 0.00 0.00 2.52
2678 3548 7.254137 AGTGAAGTTTCTTTTGCTCTTTCTTC 58.746 34.615 0.00 0.00 0.00 2.87
2679 3549 6.473778 GTGAAGTTTCTTTTGCTCTTTCTTCC 59.526 38.462 0.00 0.00 0.00 3.46
2680 3550 6.378280 TGAAGTTTCTTTTGCTCTTTCTTCCT 59.622 34.615 0.00 0.00 0.00 3.36
2683 3553 5.520376 TTCTTTTGCTCTTTCTTCCTTGG 57.480 39.130 0.00 0.00 0.00 3.61
2685 3555 4.339247 TCTTTTGCTCTTTCTTCCTTGGTG 59.661 41.667 0.00 0.00 0.00 4.17
2692 3562 2.930826 TTCTTCCTTGGTGGTCAGAC 57.069 50.000 0.00 0.00 37.07 3.51
2698 3568 1.233019 CTTGGTGGTCAGACAAGCTG 58.767 55.000 8.63 0.00 46.31 4.24
2700 3570 1.072159 GGTGGTCAGACAAGCTGCT 59.928 57.895 2.17 0.00 44.52 4.24
2733 3603 2.648059 CCAAGAGATGGTCATGTTCCC 58.352 52.381 0.00 0.00 44.85 3.97
2735 3605 2.240667 CAAGAGATGGTCATGTTCCCCT 59.759 50.000 0.00 0.00 0.00 4.79
2747 3617 3.995809 TTCCCCTAGCACCTCCCGG 62.996 68.421 0.00 0.00 0.00 5.73
2755 3625 3.411517 CACCTCCCGGCCAGGATT 61.412 66.667 21.58 0.00 45.00 3.01
2765 3635 3.451894 CCAGGATTTGGCCGCACC 61.452 66.667 0.00 0.00 40.87 5.01
2781 3654 2.279120 CCATGAGCTCGAGACGGC 60.279 66.667 18.75 0.33 0.00 5.68
2791 3664 2.363147 GAGACGGCCCTCTCCAGT 60.363 66.667 18.22 0.00 31.88 4.00
2804 3677 1.908619 TCTCCAGTGCATACATGTGGT 59.091 47.619 9.11 0.00 35.32 4.16
2864 3742 1.675641 GAGGACCATGCGGCTGTTT 60.676 57.895 0.00 0.00 34.57 2.83
2873 3751 1.360192 GCGGCTGTTTATCATGCCC 59.640 57.895 0.00 0.00 37.19 5.36
2880 3758 1.150536 TTTATCATGCCCGGGAGCC 59.849 57.895 29.31 7.28 0.00 4.70
2891 3769 2.747686 GGGAGCCGTCCAGTTTCA 59.252 61.111 0.00 0.00 46.07 2.69
2896 3774 1.166531 AGCCGTCCAGTTTCAGTTGC 61.167 55.000 0.00 0.00 0.00 4.17
2908 3786 2.706555 TCAGTTGCACTGTAGACTCG 57.293 50.000 13.59 0.00 46.03 4.18
2911 3789 1.273606 AGTTGCACTGTAGACTCGCAT 59.726 47.619 0.00 0.00 31.67 4.73
2917 3796 1.899814 ACTGTAGACTCGCATTTCCCA 59.100 47.619 0.00 0.00 0.00 4.37
2919 3798 3.704566 ACTGTAGACTCGCATTTCCCATA 59.295 43.478 0.00 0.00 0.00 2.74
2936 3815 3.524826 CCATAAGGGAGGGATCATGAGA 58.475 50.000 0.09 0.00 40.01 3.27
2942 3822 3.909364 AGGGAGGGATCATGAGAGATTTC 59.091 47.826 0.09 0.00 0.00 2.17
2960 3840 9.342308 AGAGATTTCTATGTTTGTTTTGAGTGA 57.658 29.630 0.00 0.00 0.00 3.41
2981 3862 9.277783 GAGTGATGTATTATTAACATTGCTCCT 57.722 33.333 0.00 0.00 37.69 3.69
3002 3883 7.442364 GCTCCTATTTGTATATCTTGCTGTGAA 59.558 37.037 0.00 0.00 0.00 3.18
3004 3885 9.109393 TCCTATTTGTATATCTTGCTGTGAAAC 57.891 33.333 0.00 0.00 37.35 2.78
3005 3886 8.345565 CCTATTTGTATATCTTGCTGTGAAACC 58.654 37.037 0.00 0.00 34.36 3.27
3006 3887 7.701539 ATTTGTATATCTTGCTGTGAAACCA 57.298 32.000 0.00 0.00 34.36 3.67
3007 3888 6.494893 TTGTATATCTTGCTGTGAAACCAC 57.505 37.500 0.00 0.00 34.36 4.16
3029 3910 7.782049 CCACAGTCTTGGTGATAGTAATTAGA 58.218 38.462 0.00 0.00 38.54 2.10
3030 3911 7.707035 CCACAGTCTTGGTGATAGTAATTAGAC 59.293 40.741 0.00 0.00 38.54 2.59
3036 3917 5.779922 TGGTGATAGTAATTAGACGGCATC 58.220 41.667 0.00 0.00 0.00 3.91
3039 3920 4.763279 TGATAGTAATTAGACGGCATCGGA 59.237 41.667 0.00 0.00 41.39 4.55
3072 3953 5.240623 TCTTCGTATTGCTCACAAATTTGGT 59.759 36.000 21.74 5.40 39.77 3.67
3103 3984 2.540101 CTGGTCGAGTTTGTGACAGTTC 59.460 50.000 0.00 0.00 36.83 3.01
3124 4009 4.842574 TCACAGCATAAACTGGCTTGATA 58.157 39.130 0.00 0.00 42.21 2.15
3125 4010 5.252547 TCACAGCATAAACTGGCTTGATAA 58.747 37.500 0.00 0.00 42.21 1.75
3126 4011 5.709631 TCACAGCATAAACTGGCTTGATAAA 59.290 36.000 0.00 0.00 42.21 1.40
3129 4014 6.153340 ACAGCATAAACTGGCTTGATAAACAT 59.847 34.615 0.00 0.00 42.21 2.71
3131 4016 6.377996 AGCATAAACTGGCTTGATAAACATCA 59.622 34.615 0.00 0.00 36.92 3.07
3177 4220 8.584157 TGCTTTTACTTTCCATGAACATGTATT 58.416 29.630 12.74 0.00 37.11 1.89
3242 4292 4.722700 ACCCGCATGCAGTCCCAC 62.723 66.667 19.57 0.00 0.00 4.61
3251 4301 2.737180 CAGTCCCACTGTCGCACT 59.263 61.111 0.00 0.00 41.19 4.40
3256 4306 0.613572 TCCCACTGTCGCACTATCCA 60.614 55.000 0.00 0.00 0.00 3.41
3258 4308 0.246360 CCACTGTCGCACTATCCACA 59.754 55.000 0.00 0.00 0.00 4.17
3294 4346 2.359900 GTCTTCATCCACGGCAAGAAT 58.640 47.619 0.00 0.00 0.00 2.40
3295 4347 3.531538 GTCTTCATCCACGGCAAGAATA 58.468 45.455 0.00 0.00 0.00 1.75
3296 4348 3.309954 GTCTTCATCCACGGCAAGAATAC 59.690 47.826 0.00 0.00 0.00 1.89
3319 4371 4.433615 GACTTCAGTGACTGTGTTCTTGA 58.566 43.478 12.93 0.00 32.61 3.02
3320 4372 5.028549 ACTTCAGTGACTGTGTTCTTGAT 57.971 39.130 12.93 0.00 32.61 2.57
3321 4373 5.053145 ACTTCAGTGACTGTGTTCTTGATC 58.947 41.667 12.93 0.00 32.61 2.92
3322 4374 4.944619 TCAGTGACTGTGTTCTTGATCT 57.055 40.909 12.93 0.00 32.61 2.75
3323 4375 5.282055 TCAGTGACTGTGTTCTTGATCTT 57.718 39.130 12.93 0.00 32.61 2.40
3324 4376 6.405278 TCAGTGACTGTGTTCTTGATCTTA 57.595 37.500 12.93 0.00 32.61 2.10
3325 4377 6.450545 TCAGTGACTGTGTTCTTGATCTTAG 58.549 40.000 12.93 0.00 32.61 2.18
3326 4378 6.265422 TCAGTGACTGTGTTCTTGATCTTAGA 59.735 38.462 12.93 0.00 32.61 2.10
3327 4379 6.585702 CAGTGACTGTGTTCTTGATCTTAGAG 59.414 42.308 4.01 0.00 0.00 2.43
3328 4380 5.347364 GTGACTGTGTTCTTGATCTTAGAGC 59.653 44.000 0.00 0.00 0.00 4.09
3329 4381 5.011023 TGACTGTGTTCTTGATCTTAGAGCA 59.989 40.000 0.00 0.00 31.58 4.26
3330 4382 5.858381 ACTGTGTTCTTGATCTTAGAGCAA 58.142 37.500 12.47 12.47 35.54 3.91
3331 4383 5.698545 ACTGTGTTCTTGATCTTAGAGCAAC 59.301 40.000 8.97 1.40 32.88 4.17
3332 4384 5.858381 TGTGTTCTTGATCTTAGAGCAACT 58.142 37.500 8.97 0.00 32.88 3.16
3333 4385 6.993079 TGTGTTCTTGATCTTAGAGCAACTA 58.007 36.000 8.97 0.00 32.88 2.24
3334 4386 7.615403 TGTGTTCTTGATCTTAGAGCAACTAT 58.385 34.615 8.97 0.00 32.88 2.12
3335 4387 8.749354 TGTGTTCTTGATCTTAGAGCAACTATA 58.251 33.333 8.97 0.00 32.88 1.31
3336 4388 9.243637 GTGTTCTTGATCTTAGAGCAACTATAG 57.756 37.037 8.97 0.00 32.88 1.31
3337 4389 7.923344 TGTTCTTGATCTTAGAGCAACTATAGC 59.077 37.037 8.97 0.00 32.88 2.97
3338 4390 7.588497 TCTTGATCTTAGAGCAACTATAGCA 57.412 36.000 8.97 0.00 32.88 3.49
3339 4391 7.656412 TCTTGATCTTAGAGCAACTATAGCAG 58.344 38.462 8.97 0.00 32.88 4.24
3340 4392 7.503902 TCTTGATCTTAGAGCAACTATAGCAGA 59.496 37.037 8.97 0.00 32.88 4.26
3341 4393 6.976088 TGATCTTAGAGCAACTATAGCAGAC 58.024 40.000 0.00 0.00 0.00 3.51
3342 4394 5.776173 TCTTAGAGCAACTATAGCAGACC 57.224 43.478 0.00 0.00 0.00 3.85
3343 4395 4.585162 TCTTAGAGCAACTATAGCAGACCC 59.415 45.833 0.00 0.00 0.00 4.46
3344 4396 2.043227 AGAGCAACTATAGCAGACCCC 58.957 52.381 0.00 0.00 0.00 4.95
3345 4397 0.753262 AGCAACTATAGCAGACCCCG 59.247 55.000 0.00 0.00 0.00 5.73
3346 4398 0.880718 GCAACTATAGCAGACCCCGC 60.881 60.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 132 3.682885 TACTTCCGTCGCCGCCAA 61.683 61.111 0.00 0.00 0.00 4.52
157 159 4.853142 ATCCCCGACAGCCCGCTA 62.853 66.667 0.00 0.00 0.00 4.26
174 176 1.615424 GAGGGAAGGGCCAGGTACA 60.615 63.158 6.18 0.00 38.95 2.90
222 225 2.494918 CGTCGTGGGGAGATCACC 59.505 66.667 0.00 0.00 40.76 4.02
224 227 3.822192 CGCGTCGTGGGGAGATCA 61.822 66.667 0.00 0.00 0.00 2.92
424 429 2.613506 GCCGTTTCCAGTTCACCCG 61.614 63.158 0.00 0.00 0.00 5.28
427 433 0.599204 TCTCGCCGTTTCCAGTTCAC 60.599 55.000 0.00 0.00 0.00 3.18
483 490 2.043852 AGACTCTCCACCGCCGAT 60.044 61.111 0.00 0.00 0.00 4.18
518 527 2.108970 CTATATAAGACGCCCCCTCCC 58.891 57.143 0.00 0.00 0.00 4.30
521 530 1.569653 GCCTATATAAGACGCCCCCT 58.430 55.000 0.00 0.00 0.00 4.79
655 669 1.252904 ATCAATGCCAAAGCTGCCGT 61.253 50.000 0.00 0.00 40.80 5.68
746 763 2.668250 GTTTTTGGCGCGAAAATAGGT 58.332 42.857 27.22 0.00 30.72 3.08
749 766 2.031857 AGTCGTTTTTGGCGCGAAAATA 60.032 40.909 27.22 16.63 36.37 1.40
845 865 0.321346 CCAAAGGCCCAATTTTCGCT 59.679 50.000 0.00 0.00 0.00 4.93
898 918 0.676782 CCCTCAGGCGATTTTTCGGT 60.677 55.000 0.00 0.00 0.00 4.69
957 981 0.546122 GTGGCACCATCCATGAGGTA 59.454 55.000 6.29 0.00 38.57 3.08
980 1007 2.540383 TCACTGAGGTAGAGCCACAAT 58.460 47.619 0.00 0.00 37.39 2.71
1001 1028 2.444696 CCATTTGGTCTGGGGGCA 59.555 61.111 0.00 0.00 0.00 5.36
1067 1094 2.283894 TGGAGAGGAAGGCAGCGA 60.284 61.111 0.00 0.00 0.00 4.93
1070 1097 1.078567 GCTGTGGAGAGGAAGGCAG 60.079 63.158 0.00 0.00 0.00 4.85
1071 1098 2.947532 CGCTGTGGAGAGGAAGGCA 61.948 63.158 0.00 0.00 0.00 4.75
1078 1105 4.154347 GGAGGGCGCTGTGGAGAG 62.154 72.222 8.56 0.00 0.00 3.20
1371 1402 2.432628 GAGTCGAACACCCTGCGG 60.433 66.667 0.00 0.00 0.00 5.69
1465 1507 1.201429 ATTCTGCCGAACACCTCCCT 61.201 55.000 0.00 0.00 30.67 4.20
1545 1602 4.435436 TGCAGCGCCTCGTCGAAT 62.435 61.111 2.29 0.00 0.00 3.34
1635 1693 1.073025 AACGGCACCAAGATGAGCA 59.927 52.632 0.00 0.00 0.00 4.26
1707 1773 1.004161 TCGGCCATGACATTCCTTTGA 59.996 47.619 2.24 0.00 0.00 2.69
1806 1873 0.586319 AATTCCACAGCACAACGTCG 59.414 50.000 0.00 0.00 0.00 5.12
1845 1912 0.387929 GCTCACCATGGCCATTCATG 59.612 55.000 17.92 14.59 42.92 3.07
1891 1958 1.370051 GCACAAAGCCGTTTCCGAC 60.370 57.895 0.00 0.00 37.23 4.79
1978 2052 1.594862 CCGCATCGACTGGAAAATCTC 59.405 52.381 0.00 0.00 0.00 2.75
2244 2357 3.669536 TCGACCATTGACTGCATACAAA 58.330 40.909 9.18 0.00 0.00 2.83
2373 2491 1.863454 GTGCATAGATCTGCCTTGTCG 59.137 52.381 5.18 0.00 41.58 4.35
2409 3251 3.719121 CCTCCCAGTGGACAGAGG 58.281 66.667 11.95 14.46 40.00 3.69
2417 3259 4.221703 CCATAGATAGCTAACCTCCCAGTG 59.778 50.000 0.00 0.00 0.00 3.66
2418 3260 4.421131 CCATAGATAGCTAACCTCCCAGT 58.579 47.826 0.00 0.00 0.00 4.00
2419 3261 3.196685 GCCATAGATAGCTAACCTCCCAG 59.803 52.174 0.00 0.00 0.00 4.45
2422 3264 3.835395 ACTGCCATAGATAGCTAACCTCC 59.165 47.826 0.00 0.00 0.00 4.30
2427 3269 6.830912 ACATGAAACTGCCATAGATAGCTAA 58.169 36.000 0.00 0.00 0.00 3.09
2428 3270 6.425210 ACATGAAACTGCCATAGATAGCTA 57.575 37.500 0.00 0.00 0.00 3.32
2429 3271 5.301835 ACATGAAACTGCCATAGATAGCT 57.698 39.130 0.00 0.00 0.00 3.32
2430 3272 5.762218 AGAACATGAAACTGCCATAGATAGC 59.238 40.000 0.00 0.00 0.00 2.97
2444 3286 2.655090 TGCCACCAGAGAACATGAAA 57.345 45.000 0.00 0.00 0.00 2.69
2452 3294 0.836606 TGTGTTCTTGCCACCAGAGA 59.163 50.000 0.00 0.00 31.71 3.10
2456 3298 1.372838 CGTGTGTGTTCTTGCCACCA 61.373 55.000 0.00 0.00 31.71 4.17
2485 3353 7.589587 CAGAAGAATAAACGTTAACATGTGCAA 59.410 33.333 0.00 0.00 0.00 4.08
2515 3383 4.041740 CAATCGCTGCAGGTAGTAAGTA 57.958 45.455 17.12 0.00 0.00 2.24
2534 3402 0.669619 CACATGAACAGCACCAGCAA 59.330 50.000 0.00 0.00 45.49 3.91
2541 3409 2.300433 AGAAGTTGCACATGAACAGCA 58.700 42.857 0.00 0.91 36.32 4.41
2563 3431 0.529378 CCAGGTTCTTGCTTCATGGC 59.471 55.000 0.00 0.00 0.00 4.40
2564 3432 2.089980 CTCCAGGTTCTTGCTTCATGG 58.910 52.381 0.00 0.00 34.85 3.66
2565 3433 3.063510 TCTCCAGGTTCTTGCTTCATG 57.936 47.619 0.00 0.00 0.00 3.07
2566 3434 3.073650 ACTTCTCCAGGTTCTTGCTTCAT 59.926 43.478 0.00 0.00 0.00 2.57
2567 3435 2.439507 ACTTCTCCAGGTTCTTGCTTCA 59.560 45.455 0.00 0.00 0.00 3.02
2569 3437 2.439507 TCACTTCTCCAGGTTCTTGCTT 59.560 45.455 0.00 0.00 0.00 3.91
2571 3441 2.224402 ACTCACTTCTCCAGGTTCTTGC 60.224 50.000 0.00 0.00 0.00 4.01
2573 3443 4.654262 TGTTACTCACTTCTCCAGGTTCTT 59.346 41.667 0.00 0.00 0.00 2.52
2577 3447 3.845860 TCTGTTACTCACTTCTCCAGGT 58.154 45.455 0.00 0.00 0.00 4.00
2588 3458 2.565391 TCCTTGCGGAATCTGTTACTCA 59.435 45.455 0.00 0.00 36.03 3.41
2593 3463 3.279434 GGTAATCCTTGCGGAATCTGTT 58.721 45.455 0.00 0.00 44.02 3.16
2594 3464 2.238646 TGGTAATCCTTGCGGAATCTGT 59.761 45.455 0.00 0.00 44.02 3.41
2597 3467 2.639065 TGTGGTAATCCTTGCGGAATC 58.361 47.619 0.00 0.00 44.02 2.52
2600 3470 2.026729 TGAATGTGGTAATCCTTGCGGA 60.027 45.455 0.00 0.00 45.16 5.54
2602 3472 3.009723 ACTGAATGTGGTAATCCTTGCG 58.990 45.455 0.00 0.00 34.23 4.85
2603 3473 3.428045 GCACTGAATGTGGTAATCCTTGC 60.428 47.826 0.00 0.00 46.27 4.01
2605 3475 3.356290 GGCACTGAATGTGGTAATCCTT 58.644 45.455 0.00 0.00 46.27 3.36
2606 3476 2.680805 CGGCACTGAATGTGGTAATCCT 60.681 50.000 0.00 0.00 46.27 3.24
2607 3477 1.670811 CGGCACTGAATGTGGTAATCC 59.329 52.381 0.00 0.00 46.27 3.01
2608 3478 2.356135 ACGGCACTGAATGTGGTAATC 58.644 47.619 0.00 0.00 46.27 1.75
2609 3479 2.489938 ACGGCACTGAATGTGGTAAT 57.510 45.000 0.00 0.00 46.27 1.89
2610 3480 2.037381 TGTACGGCACTGAATGTGGTAA 59.963 45.455 0.00 0.00 46.27 2.85
2611 3481 1.619332 TGTACGGCACTGAATGTGGTA 59.381 47.619 0.00 0.00 46.27 3.25
2612 3482 0.394938 TGTACGGCACTGAATGTGGT 59.605 50.000 0.00 0.00 46.27 4.16
2613 3483 1.737838 ATGTACGGCACTGAATGTGG 58.262 50.000 0.00 0.00 46.27 4.17
2615 3485 5.179368 GCATAATATGTACGGCACTGAATGT 59.821 40.000 1.92 0.00 0.00 2.71
2616 3486 5.390885 GGCATAATATGTACGGCACTGAATG 60.391 44.000 1.92 0.00 0.00 2.67
2617 3487 4.695455 GGCATAATATGTACGGCACTGAAT 59.305 41.667 1.92 0.00 0.00 2.57
2618 3488 4.062293 GGCATAATATGTACGGCACTGAA 58.938 43.478 1.92 0.00 0.00 3.02
2619 3489 3.323691 AGGCATAATATGTACGGCACTGA 59.676 43.478 1.92 0.00 0.00 3.41
2620 3490 3.664107 AGGCATAATATGTACGGCACTG 58.336 45.455 1.92 0.00 0.00 3.66
2621 3491 5.477607 TTAGGCATAATATGTACGGCACT 57.522 39.130 1.92 0.00 0.00 4.40
2622 3492 4.092968 GCTTAGGCATAATATGTACGGCAC 59.907 45.833 1.92 0.00 38.54 5.01
2623 3493 4.250464 GCTTAGGCATAATATGTACGGCA 58.750 43.478 1.92 0.00 38.54 5.69
2624 3494 3.621715 GGCTTAGGCATAATATGTACGGC 59.378 47.826 0.00 1.56 40.87 5.68
2625 3495 5.086104 AGGCTTAGGCATAATATGTACGG 57.914 43.478 8.84 0.00 40.87 4.02
2626 3496 5.720202 TGAGGCTTAGGCATAATATGTACG 58.280 41.667 8.84 0.00 40.87 3.67
2627 3497 6.936279 TCTGAGGCTTAGGCATAATATGTAC 58.064 40.000 8.84 0.00 40.87 2.90
2628 3498 7.739995 ATCTGAGGCTTAGGCATAATATGTA 57.260 36.000 8.84 0.00 40.87 2.29
2629 3499 6.633325 ATCTGAGGCTTAGGCATAATATGT 57.367 37.500 8.84 0.00 40.87 2.29
2630 3500 7.710044 CACTATCTGAGGCTTAGGCATAATATG 59.290 40.741 8.84 0.00 40.87 1.78
2631 3501 7.621285 TCACTATCTGAGGCTTAGGCATAATAT 59.379 37.037 8.84 0.00 40.87 1.28
2632 3502 6.954102 TCACTATCTGAGGCTTAGGCATAATA 59.046 38.462 8.84 0.04 40.87 0.98
2633 3503 5.782331 TCACTATCTGAGGCTTAGGCATAAT 59.218 40.000 8.84 0.00 40.87 1.28
2634 3504 5.147767 TCACTATCTGAGGCTTAGGCATAA 58.852 41.667 8.84 0.00 40.87 1.90
2635 3505 4.740902 TCACTATCTGAGGCTTAGGCATA 58.259 43.478 8.84 0.00 40.87 3.14
2636 3506 3.581101 TCACTATCTGAGGCTTAGGCAT 58.419 45.455 8.84 0.00 40.87 4.40
2637 3507 3.032265 TCACTATCTGAGGCTTAGGCA 57.968 47.619 8.84 0.00 40.87 4.75
2638 3508 3.386402 ACTTCACTATCTGAGGCTTAGGC 59.614 47.826 6.44 0.00 37.82 3.93
2639 3509 5.606348 AACTTCACTATCTGAGGCTTAGG 57.394 43.478 6.44 0.00 28.63 2.69
2640 3510 6.872920 AGAAACTTCACTATCTGAGGCTTAG 58.127 40.000 0.00 0.00 28.63 2.18
2641 3511 6.859112 AGAAACTTCACTATCTGAGGCTTA 57.141 37.500 0.00 0.00 28.63 3.09
2642 3512 5.753721 AGAAACTTCACTATCTGAGGCTT 57.246 39.130 0.00 0.00 28.63 4.35
2643 3513 5.753721 AAGAAACTTCACTATCTGAGGCT 57.246 39.130 0.00 0.00 28.63 4.58
2644 3514 6.606768 CAAAAGAAACTTCACTATCTGAGGC 58.393 40.000 0.00 0.00 28.63 4.70
2645 3515 6.429385 AGCAAAAGAAACTTCACTATCTGAGG 59.571 38.462 0.00 0.00 32.10 3.86
2646 3516 7.387397 AGAGCAAAAGAAACTTCACTATCTGAG 59.613 37.037 0.00 0.00 0.00 3.35
2647 3517 7.220030 AGAGCAAAAGAAACTTCACTATCTGA 58.780 34.615 0.00 0.00 0.00 3.27
2648 3518 7.432350 AGAGCAAAAGAAACTTCACTATCTG 57.568 36.000 0.00 0.00 0.00 2.90
2649 3519 8.457238 AAAGAGCAAAAGAAACTTCACTATCT 57.543 30.769 0.00 0.00 0.00 1.98
2650 3520 8.563732 AGAAAGAGCAAAAGAAACTTCACTATC 58.436 33.333 0.00 0.00 0.00 2.08
2651 3521 8.457238 AGAAAGAGCAAAAGAAACTTCACTAT 57.543 30.769 0.00 0.00 0.00 2.12
2652 3522 7.865706 AGAAAGAGCAAAAGAAACTTCACTA 57.134 32.000 0.00 0.00 0.00 2.74
2653 3523 6.765915 AGAAAGAGCAAAAGAAACTTCACT 57.234 33.333 0.00 0.00 0.00 3.41
2654 3524 6.473778 GGAAGAAAGAGCAAAAGAAACTTCAC 59.526 38.462 0.00 0.00 34.76 3.18
2655 3525 6.378280 AGGAAGAAAGAGCAAAAGAAACTTCA 59.622 34.615 0.00 0.00 34.76 3.02
2656 3526 6.800543 AGGAAGAAAGAGCAAAAGAAACTTC 58.199 36.000 0.00 0.00 0.00 3.01
2657 3527 6.782082 AGGAAGAAAGAGCAAAAGAAACTT 57.218 33.333 0.00 0.00 0.00 2.66
2658 3528 6.406288 CCAAGGAAGAAAGAGCAAAAGAAACT 60.406 38.462 0.00 0.00 0.00 2.66
2659 3529 5.750547 CCAAGGAAGAAAGAGCAAAAGAAAC 59.249 40.000 0.00 0.00 0.00 2.78
2660 3530 5.422012 ACCAAGGAAGAAAGAGCAAAAGAAA 59.578 36.000 0.00 0.00 0.00 2.52
2661 3531 4.956075 ACCAAGGAAGAAAGAGCAAAAGAA 59.044 37.500 0.00 0.00 0.00 2.52
2662 3532 4.339247 CACCAAGGAAGAAAGAGCAAAAGA 59.661 41.667 0.00 0.00 0.00 2.52
2663 3533 4.500375 CCACCAAGGAAGAAAGAGCAAAAG 60.500 45.833 0.00 0.00 41.22 2.27
2664 3534 3.384467 CCACCAAGGAAGAAAGAGCAAAA 59.616 43.478 0.00 0.00 41.22 2.44
2665 3535 2.958355 CCACCAAGGAAGAAAGAGCAAA 59.042 45.455 0.00 0.00 41.22 3.68
2666 3536 2.091885 ACCACCAAGGAAGAAAGAGCAA 60.092 45.455 0.00 0.00 41.22 3.91
2667 3537 1.494721 ACCACCAAGGAAGAAAGAGCA 59.505 47.619 0.00 0.00 41.22 4.26
2668 3538 2.155279 GACCACCAAGGAAGAAAGAGC 58.845 52.381 0.00 0.00 41.22 4.09
2669 3539 3.071602 TCTGACCACCAAGGAAGAAAGAG 59.928 47.826 0.00 0.00 41.22 2.85
2670 3540 3.045634 TCTGACCACCAAGGAAGAAAGA 58.954 45.455 0.00 0.00 41.22 2.52
2671 3541 3.142174 GTCTGACCACCAAGGAAGAAAG 58.858 50.000 0.00 0.00 41.22 2.62
2672 3542 2.507886 TGTCTGACCACCAAGGAAGAAA 59.492 45.455 5.17 0.00 41.22 2.52
2673 3543 2.123589 TGTCTGACCACCAAGGAAGAA 58.876 47.619 5.17 0.00 41.22 2.52
2674 3544 1.801242 TGTCTGACCACCAAGGAAGA 58.199 50.000 5.17 0.00 41.22 2.87
2675 3545 2.498167 CTTGTCTGACCACCAAGGAAG 58.502 52.381 5.17 0.00 41.22 3.46
2676 3546 1.476833 GCTTGTCTGACCACCAAGGAA 60.477 52.381 5.17 0.00 41.22 3.36
2677 3547 0.108585 GCTTGTCTGACCACCAAGGA 59.891 55.000 5.17 0.00 41.22 3.36
2678 3548 0.109342 AGCTTGTCTGACCACCAAGG 59.891 55.000 5.17 0.00 45.67 3.61
2679 3549 1.233019 CAGCTTGTCTGACCACCAAG 58.767 55.000 5.17 3.54 45.72 3.61
2680 3550 0.819259 GCAGCTTGTCTGACCACCAA 60.819 55.000 5.17 0.00 45.72 3.67
2683 3553 0.250038 TCAGCAGCTTGTCTGACCAC 60.250 55.000 5.17 0.00 45.72 4.16
2685 3555 1.155042 CTTCAGCAGCTTGTCTGACC 58.845 55.000 5.17 0.00 45.72 4.02
2759 3629 2.584418 CTCGAGCTCATGGTGCGG 60.584 66.667 15.40 0.00 35.28 5.69
2761 3631 1.875813 CGTCTCGAGCTCATGGTGC 60.876 63.158 15.40 0.00 0.00 5.01
2763 3633 3.069980 GCCGTCTCGAGCTCATGGT 62.070 63.158 15.40 0.00 0.00 3.55
2765 3635 2.279120 GGCCGTCTCGAGCTCATG 60.279 66.667 15.40 5.55 0.00 3.07
2766 3636 3.532155 GGGCCGTCTCGAGCTCAT 61.532 66.667 15.40 0.00 0.00 2.90
2767 3637 4.742649 AGGGCCGTCTCGAGCTCA 62.743 66.667 15.40 0.00 0.00 4.26
2768 3638 3.894947 GAGGGCCGTCTCGAGCTC 61.895 72.222 18.26 2.73 0.00 4.09
2769 3639 4.434354 AGAGGGCCGTCTCGAGCT 62.434 66.667 22.26 0.00 38.71 4.09
2771 3641 3.213402 GGAGAGGGCCGTCTCGAG 61.213 72.222 36.61 5.93 43.54 4.04
2772 3642 3.997400 CTGGAGAGGGCCGTCTCGA 62.997 68.421 36.61 33.55 43.54 4.04
2781 3654 1.487976 ACATGTATGCACTGGAGAGGG 59.512 52.381 0.00 0.00 0.00 4.30
2791 3664 3.194062 CATCGTGTACCACATGTATGCA 58.806 45.455 0.00 0.00 36.53 3.96
2804 3677 3.435566 GCGAGATCTTGAACATCGTGTA 58.564 45.455 14.59 0.00 35.87 2.90
2820 3694 3.531207 CGAGATGGCTGGGCGAGA 61.531 66.667 0.00 0.00 0.00 4.04
2864 3742 3.625897 CGGCTCCCGGGCATGATA 61.626 66.667 18.49 0.00 44.15 2.15
2880 3758 3.825812 GTGCAACTGAAACTGGACG 57.174 52.632 0.00 0.00 0.00 4.79
2896 3774 2.271800 GGGAAATGCGAGTCTACAGTG 58.728 52.381 0.00 0.00 0.00 3.66
2900 3778 4.058817 CCTTATGGGAAATGCGAGTCTAC 58.941 47.826 0.00 0.00 37.23 2.59
2917 3796 4.774243 TCTCTCATGATCCCTCCCTTAT 57.226 45.455 0.00 0.00 0.00 1.73
2919 3798 3.652323 ATCTCTCATGATCCCTCCCTT 57.348 47.619 0.00 0.00 0.00 3.95
2936 3815 9.903682 CATCACTCAAAACAAACATAGAAATCT 57.096 29.630 0.00 0.00 0.00 2.40
2981 3862 8.673711 GTGGTTTCACAGCAAGATATACAAATA 58.326 33.333 0.00 0.00 43.13 1.40
3004 3885 7.707035 GTCTAATTACTATCACCAAGACTGTGG 59.293 40.741 0.00 3.07 44.92 4.17
3005 3886 7.432545 CGTCTAATTACTATCACCAAGACTGTG 59.567 40.741 0.00 0.00 31.99 3.66
3006 3887 7.416438 CCGTCTAATTACTATCACCAAGACTGT 60.416 40.741 0.00 0.00 31.99 3.55
3007 3888 6.918569 CCGTCTAATTACTATCACCAAGACTG 59.081 42.308 0.00 0.00 31.99 3.51
3009 3890 5.690857 GCCGTCTAATTACTATCACCAAGAC 59.309 44.000 0.00 0.00 0.00 3.01
3010 3891 5.361571 TGCCGTCTAATTACTATCACCAAGA 59.638 40.000 0.00 0.00 0.00 3.02
3012 3893 5.601583 TGCCGTCTAATTACTATCACCAA 57.398 39.130 0.00 0.00 0.00 3.67
3016 3897 4.763279 TCCGATGCCGTCTAATTACTATCA 59.237 41.667 0.00 0.00 0.00 2.15
3017 3898 5.306532 TCCGATGCCGTCTAATTACTATC 57.693 43.478 0.00 0.00 0.00 2.08
3021 3902 4.167268 GAGATCCGATGCCGTCTAATTAC 58.833 47.826 0.00 0.00 0.00 1.89
3022 3903 3.119955 CGAGATCCGATGCCGTCTAATTA 60.120 47.826 0.00 0.00 41.76 1.40
3023 3904 2.351835 CGAGATCCGATGCCGTCTAATT 60.352 50.000 0.00 0.00 41.76 1.40
3024 3905 1.200252 CGAGATCCGATGCCGTCTAAT 59.800 52.381 0.00 0.00 41.76 1.73
3025 3906 0.591659 CGAGATCCGATGCCGTCTAA 59.408 55.000 0.00 0.00 41.76 2.10
3026 3907 0.250166 TCGAGATCCGATGCCGTCTA 60.250 55.000 2.65 0.00 43.23 2.59
3027 3908 1.526225 TCGAGATCCGATGCCGTCT 60.526 57.895 2.65 0.00 43.23 4.18
3028 3909 3.031495 TCGAGATCCGATGCCGTC 58.969 61.111 2.65 0.00 43.23 4.79
3072 3953 1.296392 CTCGACCAGGAACATGCCA 59.704 57.895 0.00 0.00 0.00 4.92
3103 3984 5.565592 TTATCAAGCCAGTTTATGCTGTG 57.434 39.130 0.00 0.00 38.00 3.66
3108 3989 6.974622 GGTGATGTTTATCAAGCCAGTTTATG 59.025 38.462 0.00 0.00 44.49 1.90
3116 4001 8.470002 AGAAATTAAGGTGATGTTTATCAAGCC 58.530 33.333 0.00 0.00 44.49 4.35
3126 4011 9.823647 CAGATACAGTAGAAATTAAGGTGATGT 57.176 33.333 0.00 0.00 0.00 3.06
3129 4014 8.079211 AGCAGATACAGTAGAAATTAAGGTGA 57.921 34.615 0.00 0.00 0.00 4.02
3131 4016 9.740710 AAAAGCAGATACAGTAGAAATTAAGGT 57.259 29.630 0.00 0.00 0.00 3.50
3177 4220 2.634639 TCCTTGGCCCAGTAGAGTAA 57.365 50.000 0.00 0.00 0.00 2.24
3242 4292 1.390123 CGTTTGTGGATAGTGCGACAG 59.610 52.381 0.00 0.00 0.00 3.51
3244 4294 1.126113 CACGTTTGTGGATAGTGCGAC 59.874 52.381 0.00 0.00 42.59 5.19
3256 4306 1.022451 ACGCACTGTTCCACGTTTGT 61.022 50.000 0.00 0.00 34.62 2.83
3258 4308 0.461339 AGACGCACTGTTCCACGTTT 60.461 50.000 0.00 0.00 39.16 3.60
3271 4321 2.434185 GCCGTGGATGAAGACGCA 60.434 61.111 0.00 0.00 34.18 5.24
3294 4346 3.630769 AGAACACAGTCACTGAAGTCGTA 59.369 43.478 13.14 0.00 35.18 3.43
3295 4347 2.427453 AGAACACAGTCACTGAAGTCGT 59.573 45.455 13.14 0.00 35.18 4.34
3296 4348 3.085443 AGAACACAGTCACTGAAGTCG 57.915 47.619 13.14 0.00 35.18 4.18
3319 4371 5.245075 GGGTCTGCTATAGTTGCTCTAAGAT 59.755 44.000 0.84 0.00 31.94 2.40
3320 4372 4.585162 GGGTCTGCTATAGTTGCTCTAAGA 59.415 45.833 0.84 0.00 31.94 2.10
3321 4373 4.262249 GGGGTCTGCTATAGTTGCTCTAAG 60.262 50.000 0.84 0.00 31.94 2.18
3322 4374 3.641906 GGGGTCTGCTATAGTTGCTCTAA 59.358 47.826 0.84 0.00 31.94 2.10
3323 4375 3.231818 GGGGTCTGCTATAGTTGCTCTA 58.768 50.000 0.84 0.00 0.00 2.43
3324 4376 2.043227 GGGGTCTGCTATAGTTGCTCT 58.957 52.381 0.84 0.00 0.00 4.09
3325 4377 1.269831 CGGGGTCTGCTATAGTTGCTC 60.270 57.143 0.84 0.00 0.00 4.26
3326 4378 0.753262 CGGGGTCTGCTATAGTTGCT 59.247 55.000 0.84 0.00 0.00 3.91
3327 4379 0.880718 GCGGGGTCTGCTATAGTTGC 60.881 60.000 0.84 0.00 0.00 4.17
3328 4380 3.290776 GCGGGGTCTGCTATAGTTG 57.709 57.895 0.84 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.