Multiple sequence alignment - TraesCS7D01G059100

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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 TraesCS7D01G059100 chr7D 100.000 3659 0 0 1 3659 31958173 31954515 0.000000e+00 6758
1 TraesCS7D01G059100 chr7A 89.570 1975 137 23 1 1928 32034591 32032639 0.000000e+00 2442
2 TraesCS7D01G059100 chr7A 96.909 1100 29 3 513 1607 32291846 32290747 0.000000e+00 1838
3 TraesCS7D01G059100 chr7A 92.505 934 54 8 1960 2879 32032639 32031708 0.000000e+00 1323
4 TraesCS7D01G059100 chr7A 97.872 517 11 0 1 517 32292790 32292274 0.000000e+00 894
5 TraesCS7D01G059100 chr7A 82.262 451 52 16 3082 3520 32031627 32031193 7.470000e-97 364
6 TraesCS7D01G059100 chr7A 81.818 440 40 18 1 414 32196276 32195851 2.110000e-87 333
7 TraesCS7D01G059100 chr7A 88.350 103 9 2 566 668 32034471 32034372 1.780000e-23 121
8 TraesCS7D01G059100 chr4A 94.207 1519 69 9 1369 2878 695997675 695999183 0.000000e+00 2300
9 TraesCS7D01G059100 chr4A 92.693 479 22 7 3026 3497 695999176 695999648 0.000000e+00 678
10 TraesCS7D01G059100 chr4A 82.659 173 19 9 249 414 695341298 695341466 3.810000e-30 143
11 TraesCS7D01G059100 chr6A 89.431 123 11 2 1572 1692 74652330 74652452 1.760000e-33 154
12 TraesCS7D01G059100 chrUn 88.462 104 9 2 565 668 298009137 298009037 4.960000e-24 122


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 TraesCS7D01G059100 chr7D 31954515 31958173 3658 True 6758.0 6758 100.00000 1 3659 1 chr7D.!!$R1 3658
1 TraesCS7D01G059100 chr7A 32290747 32292790 2043 True 1366.0 1838 97.39050 1 1607 2 chr7A.!!$R3 1606
2 TraesCS7D01G059100 chr7A 32031193 32034591 3398 True 1062.5 2442 88.17175 1 3520 4 chr7A.!!$R2 3519
3 TraesCS7D01G059100 chr4A 695997675 695999648 1973 False 1489.0 2300 93.45000 1369 3497 2 chr4A.!!$F2 2128

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
985 1463 0.037882 CTGCAGCTCGTCTCCAAAGA 60.038 55.0 0.0 0.0 0.0 2.52 F
2532 3017 0.110486 GGAAGTCAGGCAGGGTTTCA 59.890 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2575 3060 0.032678 CCGGAGCAAGCTATGACGAT 59.967 55.0 0.0 0.0 0.00 3.73 R
3521 4069 0.030504 TGATTGCTGGTGTGCGTTTG 59.969 50.0 0.0 0.0 35.36 2.93 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
108 124 4.532126 TCTCACCACTATTGTGTCTCCATT 59.468 41.667 6.55 0.00 42.34 3.16
416 449 8.995220 TCAATACTACACAATACCAACAAAGAC 58.005 33.333 0.00 0.00 0.00 3.01
759 1232 1.359848 CACACCATACGGAGCAAGTC 58.640 55.000 0.00 0.00 35.59 3.01
951 1428 2.012948 GCGTGCACTGCAAAGAAGC 61.013 57.895 22.75 9.71 41.47 3.86
961 1438 1.322442 GCAAAGAAGCCAACACCTCT 58.678 50.000 0.00 0.00 0.00 3.69
985 1463 0.037882 CTGCAGCTCGTCTCCAAAGA 60.038 55.000 0.00 0.00 0.00 2.52
1025 1506 2.398754 TCCTCCTCACAACTCCTCAA 57.601 50.000 0.00 0.00 0.00 3.02
1026 1507 1.971357 TCCTCCTCACAACTCCTCAAC 59.029 52.381 0.00 0.00 0.00 3.18
1035 1516 1.498865 AACTCCTCAACGCTGCAACG 61.499 55.000 8.18 8.18 39.50 4.10
1048 1529 3.055719 CAACGGCGGCCAACTCAT 61.056 61.111 20.71 0.00 0.00 2.90
1083 1564 4.883172 TCCCAATGGAGATCACAGGTGATA 60.883 45.833 14.45 0.35 42.23 2.15
1164 1646 0.254178 GCATCCTCTCCTTCTTGGCA 59.746 55.000 0.00 0.00 35.26 4.92
1215 1697 3.755628 GGCTCGCTGTACGTCCCA 61.756 66.667 0.00 0.00 44.19 4.37
1502 1986 3.436924 CGGGTTAAAGCGGTGGCC 61.437 66.667 0.00 0.00 41.24 5.36
1601 2085 3.077907 CCAGAAAGAAGGGGCCGA 58.922 61.111 0.00 0.00 0.00 5.54
1629 2113 1.656587 ATCACTGGGTGGACTTAGCA 58.343 50.000 0.00 0.00 33.87 3.49
1711 2195 5.012561 GGTGCCAAGGTATGATAATCTCTCT 59.987 44.000 0.00 0.00 0.00 3.10
1758 2242 5.064452 GTCCTGACTGTTCTTTATCATGCAG 59.936 44.000 0.00 0.00 0.00 4.41
1874 2358 3.763360 CCTTTGACATAAAGCCATGTGGA 59.237 43.478 2.55 0.00 39.25 4.02
1954 2438 3.823873 TGTATCGTGCACCAAAAAGGAAT 59.176 39.130 12.15 0.00 41.22 3.01
1997 2481 1.004918 GGTTGAGCTGGTACGCTGT 60.005 57.895 0.00 0.00 38.19 4.40
2027 2511 6.313519 TCATACTAGCCAGTCTCCAAAAAT 57.686 37.500 0.00 0.00 36.14 1.82
2285 2769 6.653989 TGGGTGTTAATGTTTTGTCCAAATT 58.346 32.000 0.00 0.00 0.00 1.82
2437 2922 1.522569 CTGGGAGTTGACGGGATCC 59.477 63.158 1.92 1.92 0.00 3.36
2442 2927 1.229529 AGTTGACGGGATCCTGGGT 60.230 57.895 24.68 13.76 0.00 4.51
2516 3001 2.057922 GATAGAAGGGGCCATCAGGAA 58.942 52.381 4.39 0.00 36.89 3.36
2520 3005 0.846427 AAGGGGCCATCAGGAAGTCA 60.846 55.000 4.39 0.00 36.89 3.41
2532 3017 0.110486 GGAAGTCAGGCAGGGTTTCA 59.890 55.000 0.00 0.00 0.00 2.69
2547 3032 4.225267 AGGGTTTCACTCATCGTCCTAATT 59.775 41.667 0.00 0.00 0.00 1.40
2689 3179 2.691409 AGATTAAGCACGCTTAGCCA 57.309 45.000 11.09 0.00 39.36 4.75
2696 3186 1.926511 GCACGCTTAGCCATGCAAGT 61.927 55.000 19.24 0.00 37.20 3.16
2697 3187 1.368641 CACGCTTAGCCATGCAAGTA 58.631 50.000 0.00 0.00 0.00 2.24
2716 3206 6.566753 GCAAGTAAGATCTGAGTTGTTCCAAC 60.567 42.308 23.34 7.08 0.00 3.77
2749 3240 2.280524 ACGCTTTGCCGCACTGTA 60.281 55.556 0.00 0.00 0.00 2.74
2751 3242 1.154413 CGCTTTGCCGCACTGTAAG 60.154 57.895 0.00 0.00 42.29 2.34
2753 3244 1.515521 GCTTTGCCGCACTGTAAGGT 61.516 55.000 0.00 0.00 39.30 3.50
2754 3245 0.951558 CTTTGCCGCACTGTAAGGTT 59.048 50.000 0.00 0.00 39.30 3.50
2927 3427 8.848474 ATAAAATAGCGAACCTATATTGCACT 57.152 30.769 0.00 0.00 35.70 4.40
2928 3428 9.938280 ATAAAATAGCGAACCTATATTGCACTA 57.062 29.630 0.00 0.00 35.70 2.74
2929 3429 8.848474 AAAATAGCGAACCTATATTGCACTAT 57.152 30.769 1.87 1.87 35.70 2.12
2930 3430 9.938280 AAAATAGCGAACCTATATTGCACTATA 57.062 29.630 3.98 3.98 35.70 1.31
2931 3431 9.587772 AAATAGCGAACCTATATTGCACTATAG 57.412 33.333 19.31 19.31 35.70 1.31
2932 3432 5.411781 AGCGAACCTATATTGCACTATAGC 58.588 41.667 20.36 12.50 32.55 2.97
2933 3433 5.047306 AGCGAACCTATATTGCACTATAGCA 60.047 40.000 20.36 0.00 43.99 3.49
2967 3467 4.610400 GCTATAGCGAACGATTGTACAC 57.390 45.455 9.40 0.00 0.00 2.90
2968 3468 4.288531 GCTATAGCGAACGATTGTACACT 58.711 43.478 9.40 0.00 0.00 3.55
2969 3469 4.146616 GCTATAGCGAACGATTGTACACTG 59.853 45.833 9.40 0.00 0.00 3.66
2970 3470 2.717580 AGCGAACGATTGTACACTGA 57.282 45.000 0.00 0.00 0.00 3.41
2971 3471 3.232213 AGCGAACGATTGTACACTGAT 57.768 42.857 0.00 0.00 0.00 2.90
2972 3472 3.585862 AGCGAACGATTGTACACTGATT 58.414 40.909 0.00 0.00 0.00 2.57
2973 3473 3.994392 AGCGAACGATTGTACACTGATTT 59.006 39.130 0.00 0.00 0.00 2.17
2974 3474 5.165676 AGCGAACGATTGTACACTGATTTA 58.834 37.500 0.00 0.00 0.00 1.40
2975 3475 5.810587 AGCGAACGATTGTACACTGATTTAT 59.189 36.000 0.00 0.00 0.00 1.40
2976 3476 6.312918 AGCGAACGATTGTACACTGATTTATT 59.687 34.615 0.00 0.00 0.00 1.40
2977 3477 6.959311 GCGAACGATTGTACACTGATTTATTT 59.041 34.615 0.00 0.00 0.00 1.40
2978 3478 7.045612 GCGAACGATTGTACACTGATTTATTTG 60.046 37.037 0.00 0.00 0.00 2.32
2979 3479 8.166066 CGAACGATTGTACACTGATTTATTTGA 58.834 33.333 0.00 0.00 0.00 2.69
2980 3480 9.478019 GAACGATTGTACACTGATTTATTTGAG 57.522 33.333 0.00 0.00 0.00 3.02
2981 3481 7.464358 ACGATTGTACACTGATTTATTTGAGC 58.536 34.615 0.00 0.00 0.00 4.26
2982 3482 6.624917 CGATTGTACACTGATTTATTTGAGCG 59.375 38.462 0.00 0.00 0.00 5.03
2983 3483 7.464045 CGATTGTACACTGATTTATTTGAGCGA 60.464 37.037 0.00 0.00 0.00 4.93
2984 3484 6.647212 TGTACACTGATTTATTTGAGCGAG 57.353 37.500 0.00 0.00 0.00 5.03
2985 3485 6.394809 TGTACACTGATTTATTTGAGCGAGA 58.605 36.000 0.00 0.00 0.00 4.04
2986 3486 5.786401 ACACTGATTTATTTGAGCGAGAC 57.214 39.130 0.00 0.00 0.00 3.36
2987 3487 5.237815 ACACTGATTTATTTGAGCGAGACA 58.762 37.500 0.00 0.00 0.00 3.41
2988 3488 5.877012 ACACTGATTTATTTGAGCGAGACAT 59.123 36.000 0.00 0.00 0.00 3.06
2989 3489 6.372659 ACACTGATTTATTTGAGCGAGACATT 59.627 34.615 0.00 0.00 0.00 2.71
2990 3490 6.685828 CACTGATTTATTTGAGCGAGACATTG 59.314 38.462 0.00 0.00 0.00 2.82
2991 3491 5.572211 TGATTTATTTGAGCGAGACATTGC 58.428 37.500 0.00 0.00 35.89 3.56
2993 3493 5.627499 TTTATTTGAGCGAGACATTGCTT 57.373 34.783 0.00 0.00 46.74 3.91
2994 3494 6.735678 TTTATTTGAGCGAGACATTGCTTA 57.264 33.333 0.00 0.00 46.74 3.09
2995 3495 4.871993 ATTTGAGCGAGACATTGCTTAG 57.128 40.909 0.00 0.00 46.74 2.18
2996 3496 3.592898 TTGAGCGAGACATTGCTTAGA 57.407 42.857 0.00 0.00 46.74 2.10
2997 3497 3.592898 TGAGCGAGACATTGCTTAGAA 57.407 42.857 0.00 0.00 46.74 2.10
2998 3498 4.128925 TGAGCGAGACATTGCTTAGAAT 57.871 40.909 0.00 0.00 46.74 2.40
2999 3499 3.867493 TGAGCGAGACATTGCTTAGAATG 59.133 43.478 0.00 0.00 46.74 2.67
3000 3500 2.611292 AGCGAGACATTGCTTAGAATGC 59.389 45.455 0.00 0.00 44.23 3.56
3001 3501 2.611292 GCGAGACATTGCTTAGAATGCT 59.389 45.455 0.00 0.00 36.89 3.79
3002 3502 3.804325 GCGAGACATTGCTTAGAATGCTA 59.196 43.478 0.00 0.00 36.89 3.49
3003 3503 4.450419 GCGAGACATTGCTTAGAATGCTAT 59.550 41.667 0.00 0.00 36.89 2.97
3004 3504 5.635280 GCGAGACATTGCTTAGAATGCTATA 59.365 40.000 0.00 0.00 36.89 1.31
3005 3505 6.183360 GCGAGACATTGCTTAGAATGCTATAG 60.183 42.308 0.00 0.00 36.89 1.31
3006 3506 6.183360 CGAGACATTGCTTAGAATGCTATAGC 60.183 42.308 18.18 18.18 36.89 2.97
3007 3507 5.636965 AGACATTGCTTAGAATGCTATAGCG 59.363 40.000 19.55 4.82 45.83 4.26
3008 3508 4.153117 ACATTGCTTAGAATGCTATAGCGC 59.847 41.667 19.55 14.56 45.83 5.92
3009 3509 2.328473 TGCTTAGAATGCTATAGCGCG 58.672 47.619 19.55 0.00 45.83 6.86
3010 3510 1.059835 GCTTAGAATGCTATAGCGCGC 59.940 52.381 26.66 26.66 45.83 6.86
3011 3511 2.600731 CTTAGAATGCTATAGCGCGCT 58.399 47.619 38.01 38.01 45.83 5.92
3012 3512 3.759418 CTTAGAATGCTATAGCGCGCTA 58.241 45.455 39.72 39.72 45.83 4.26
3013 3513 2.724977 AGAATGCTATAGCGCGCTAA 57.275 45.000 40.90 26.78 45.83 3.09
3014 3514 3.238108 AGAATGCTATAGCGCGCTAAT 57.762 42.857 40.90 29.53 45.83 1.73
3015 3515 3.589988 AGAATGCTATAGCGCGCTAATT 58.410 40.909 40.90 33.24 45.83 1.40
3016 3516 3.997021 AGAATGCTATAGCGCGCTAATTT 59.003 39.130 40.90 28.16 45.83 1.82
3017 3517 4.452455 AGAATGCTATAGCGCGCTAATTTT 59.548 37.500 40.90 27.06 45.83 1.82
3018 3518 4.749245 ATGCTATAGCGCGCTAATTTTT 57.251 36.364 40.90 27.45 45.83 1.94
3044 3544 2.956333 TGTATAGACACGACCCATGGAG 59.044 50.000 15.22 5.95 0.00 3.86
3065 3586 6.323996 TGGAGTGTAGTGTTATCCTAGGATTG 59.676 42.308 29.06 0.00 36.17 2.67
3277 3818 9.397280 TGTACATTGGTCGGATAAATGAAAATA 57.603 29.630 17.39 2.87 35.67 1.40
3363 3904 5.407407 ACAGAGGTGGTAATAAGTGTCAG 57.593 43.478 0.00 0.00 0.00 3.51
3366 3907 6.668283 ACAGAGGTGGTAATAAGTGTCAGTAT 59.332 38.462 0.00 0.00 0.00 2.12
3407 3951 2.666619 GCAGCAGCAAGTTCACACATAC 60.667 50.000 0.00 0.00 41.58 2.39
3459 4003 7.624360 TGCACTTTACAGAAAGAAAGAAAGA 57.376 32.000 4.50 0.00 44.23 2.52
3526 4074 8.732413 ATTTATATGCAGCATAATCACAAACG 57.268 30.769 19.12 0.00 29.74 3.60
3527 4075 2.261037 TGCAGCATAATCACAAACGC 57.739 45.000 0.00 0.00 0.00 4.84
3528 4076 1.538950 TGCAGCATAATCACAAACGCA 59.461 42.857 0.00 0.00 0.00 5.24
3529 4077 1.913403 GCAGCATAATCACAAACGCAC 59.087 47.619 0.00 0.00 0.00 5.34
3530 4078 2.668001 GCAGCATAATCACAAACGCACA 60.668 45.455 0.00 0.00 0.00 4.57
3531 4079 2.910482 CAGCATAATCACAAACGCACAC 59.090 45.455 0.00 0.00 0.00 3.82
3532 4080 2.095263 AGCATAATCACAAACGCACACC 60.095 45.455 0.00 0.00 0.00 4.16
3533 4081 2.351253 GCATAATCACAAACGCACACCA 60.351 45.455 0.00 0.00 0.00 4.17
3534 4082 3.491356 CATAATCACAAACGCACACCAG 58.509 45.455 0.00 0.00 0.00 4.00
3535 4083 0.030638 AATCACAAACGCACACCAGC 59.969 50.000 0.00 0.00 0.00 4.85
3536 4084 1.100463 ATCACAAACGCACACCAGCA 61.100 50.000 0.00 0.00 0.00 4.41
3537 4085 1.138459 CACAAACGCACACCAGCAA 59.862 52.632 0.00 0.00 0.00 3.91
3538 4086 0.248990 CACAAACGCACACCAGCAAT 60.249 50.000 0.00 0.00 0.00 3.56
3539 4087 0.030638 ACAAACGCACACCAGCAATC 59.969 50.000 0.00 0.00 0.00 2.67
3540 4088 0.030504 CAAACGCACACCAGCAATCA 59.969 50.000 0.00 0.00 0.00 2.57
3541 4089 0.311790 AAACGCACACCAGCAATCAG 59.688 50.000 0.00 0.00 0.00 2.90
3542 4090 2.133742 AACGCACACCAGCAATCAGC 62.134 55.000 0.00 0.00 46.19 4.26
3556 4104 5.808042 GCAATCAGCTCAAGAACTATGAA 57.192 39.130 0.00 0.00 41.15 2.57
3557 4105 5.808403 GCAATCAGCTCAAGAACTATGAAG 58.192 41.667 0.00 0.00 41.15 3.02
3558 4106 5.220815 GCAATCAGCTCAAGAACTATGAAGG 60.221 44.000 0.00 0.00 41.15 3.46
3559 4107 3.866651 TCAGCTCAAGAACTATGAAGGC 58.133 45.455 0.00 0.00 0.00 4.35
3560 4108 3.261643 TCAGCTCAAGAACTATGAAGGCA 59.738 43.478 0.00 0.00 0.00 4.75
3561 4109 3.373439 CAGCTCAAGAACTATGAAGGCAC 59.627 47.826 0.00 0.00 0.00 5.01
3562 4110 3.008375 AGCTCAAGAACTATGAAGGCACA 59.992 43.478 0.00 0.00 0.00 4.57
3563 4111 3.753272 GCTCAAGAACTATGAAGGCACAA 59.247 43.478 0.00 0.00 0.00 3.33
3564 4112 4.397417 GCTCAAGAACTATGAAGGCACAAT 59.603 41.667 0.00 0.00 0.00 2.71
3565 4113 5.448360 GCTCAAGAACTATGAAGGCACAATC 60.448 44.000 0.00 0.00 0.00 2.67
3566 4114 5.559770 TCAAGAACTATGAAGGCACAATCA 58.440 37.500 0.00 0.00 0.00 2.57
3567 4115 5.645067 TCAAGAACTATGAAGGCACAATCAG 59.355 40.000 0.00 0.00 30.46 2.90
3568 4116 4.521146 AGAACTATGAAGGCACAATCAGG 58.479 43.478 0.00 0.00 30.46 3.86
3569 4117 2.648059 ACTATGAAGGCACAATCAGGC 58.352 47.619 0.00 0.00 30.46 4.85
3570 4118 2.025981 ACTATGAAGGCACAATCAGGCA 60.026 45.455 0.00 0.00 30.46 4.75
3571 4119 1.471119 ATGAAGGCACAATCAGGCAG 58.529 50.000 0.00 0.00 30.46 4.85
3572 4120 0.401356 TGAAGGCACAATCAGGCAGA 59.599 50.000 0.00 0.00 0.00 4.26
3573 4121 1.202915 TGAAGGCACAATCAGGCAGAA 60.203 47.619 0.00 0.00 0.00 3.02
3574 4122 1.471684 GAAGGCACAATCAGGCAGAAG 59.528 52.381 0.00 0.00 0.00 2.85
3575 4123 0.323178 AGGCACAATCAGGCAGAAGG 60.323 55.000 0.00 0.00 0.00 3.46
3576 4124 0.322816 GGCACAATCAGGCAGAAGGA 60.323 55.000 0.00 0.00 0.00 3.36
3577 4125 1.538047 GCACAATCAGGCAGAAGGAA 58.462 50.000 0.00 0.00 0.00 3.36
3578 4126 1.200948 GCACAATCAGGCAGAAGGAAC 59.799 52.381 0.00 0.00 0.00 3.62
3579 4127 1.815003 CACAATCAGGCAGAAGGAACC 59.185 52.381 0.00 0.00 0.00 3.62
3580 4128 1.707427 ACAATCAGGCAGAAGGAACCT 59.293 47.619 0.00 0.00 0.00 3.50
3581 4129 2.912956 ACAATCAGGCAGAAGGAACCTA 59.087 45.455 0.00 0.00 30.84 3.08
3582 4130 3.330701 ACAATCAGGCAGAAGGAACCTAA 59.669 43.478 0.00 0.00 30.84 2.69
3583 4131 3.636153 ATCAGGCAGAAGGAACCTAAC 57.364 47.619 0.00 0.00 30.84 2.34
3584 4132 1.275291 TCAGGCAGAAGGAACCTAACG 59.725 52.381 0.00 0.00 30.84 3.18
3585 4133 0.036294 AGGCAGAAGGAACCTAACGC 60.036 55.000 0.00 0.00 29.98 4.84
3586 4134 1.025113 GGCAGAAGGAACCTAACGCC 61.025 60.000 10.18 10.18 0.00 5.68
3587 4135 0.036294 GCAGAAGGAACCTAACGCCT 60.036 55.000 0.00 0.00 0.00 5.52
3588 4136 1.206371 GCAGAAGGAACCTAACGCCTA 59.794 52.381 0.00 0.00 0.00 3.93
3589 4137 2.889852 CAGAAGGAACCTAACGCCTAC 58.110 52.381 0.00 0.00 0.00 3.18
3590 4138 1.829849 AGAAGGAACCTAACGCCTACC 59.170 52.381 0.00 0.00 0.00 3.18
3591 4139 1.551883 GAAGGAACCTAACGCCTACCA 59.448 52.381 0.00 0.00 0.00 3.25
3592 4140 1.875488 AGGAACCTAACGCCTACCAT 58.125 50.000 0.00 0.00 0.00 3.55
3593 4141 1.485066 AGGAACCTAACGCCTACCATG 59.515 52.381 0.00 0.00 0.00 3.66
3594 4142 1.483415 GGAACCTAACGCCTACCATGA 59.517 52.381 0.00 0.00 0.00 3.07
3595 4143 2.547826 GAACCTAACGCCTACCATGAC 58.452 52.381 0.00 0.00 0.00 3.06
3596 4144 0.828677 ACCTAACGCCTACCATGACC 59.171 55.000 0.00 0.00 0.00 4.02
3597 4145 0.106149 CCTAACGCCTACCATGACCC 59.894 60.000 0.00 0.00 0.00 4.46
3598 4146 0.828022 CTAACGCCTACCATGACCCA 59.172 55.000 0.00 0.00 0.00 4.51
3599 4147 1.416401 CTAACGCCTACCATGACCCAT 59.584 52.381 0.00 0.00 0.00 4.00
3600 4148 0.623723 AACGCCTACCATGACCCATT 59.376 50.000 0.00 0.00 0.00 3.16
3601 4149 0.107214 ACGCCTACCATGACCCATTG 60.107 55.000 0.00 0.00 0.00 2.82
3602 4150 0.180171 CGCCTACCATGACCCATTGA 59.820 55.000 0.00 0.00 0.00 2.57
3603 4151 1.811558 CGCCTACCATGACCCATTGAG 60.812 57.143 0.00 0.00 0.00 3.02
3604 4152 1.477558 GCCTACCATGACCCATTGAGG 60.478 57.143 0.00 0.00 37.03 3.86
3605 4153 2.126882 CCTACCATGACCCATTGAGGA 58.873 52.381 0.00 0.00 41.22 3.71
3606 4154 2.158755 CCTACCATGACCCATTGAGGAC 60.159 54.545 0.00 0.00 41.22 3.85
3607 4155 1.371467 ACCATGACCCATTGAGGACA 58.629 50.000 0.00 0.00 41.22 4.02
3608 4156 1.710244 ACCATGACCCATTGAGGACAA 59.290 47.619 0.00 0.00 41.22 3.18
3609 4157 2.109834 ACCATGACCCATTGAGGACAAA 59.890 45.455 0.00 0.00 41.22 2.83
3610 4158 3.164268 CCATGACCCATTGAGGACAAAA 58.836 45.455 0.00 0.00 41.22 2.44
3611 4159 3.194116 CCATGACCCATTGAGGACAAAAG 59.806 47.826 0.00 0.00 41.22 2.27
3612 4160 2.238521 TGACCCATTGAGGACAAAAGC 58.761 47.619 0.00 0.00 41.22 3.51
3613 4161 2.238521 GACCCATTGAGGACAAAAGCA 58.761 47.619 0.00 0.00 41.22 3.91
3614 4162 2.827921 GACCCATTGAGGACAAAAGCAT 59.172 45.455 0.00 0.00 41.22 3.79
3615 4163 2.827921 ACCCATTGAGGACAAAAGCATC 59.172 45.455 0.00 0.00 41.22 3.91
3616 4164 2.167075 CCCATTGAGGACAAAAGCATCC 59.833 50.000 0.00 0.00 41.22 3.51
3617 4165 2.827322 CCATTGAGGACAAAAGCATCCA 59.173 45.455 0.00 0.00 41.22 3.41
3618 4166 3.449737 CCATTGAGGACAAAAGCATCCAT 59.550 43.478 0.00 0.00 41.22 3.41
3619 4167 4.430007 CATTGAGGACAAAAGCATCCATG 58.570 43.478 0.00 0.00 39.54 3.66
3620 4168 3.159213 TGAGGACAAAAGCATCCATGT 57.841 42.857 0.00 0.00 37.47 3.21
3621 4169 2.821378 TGAGGACAAAAGCATCCATGTG 59.179 45.455 0.00 0.00 37.47 3.21
3622 4170 1.547372 AGGACAAAAGCATCCATGTGC 59.453 47.619 0.10 0.10 45.38 4.57
3628 4176 2.202650 GCATCCATGTGCGGTTGC 60.203 61.111 0.00 0.00 42.78 4.17
3629 4177 2.703798 GCATCCATGTGCGGTTGCT 61.704 57.895 5.89 0.00 44.82 3.91
3630 4178 1.430632 CATCCATGTGCGGTTGCTC 59.569 57.895 0.00 0.00 43.34 4.26
3631 4179 2.108514 ATCCATGTGCGGTTGCTCG 61.109 57.895 0.00 0.00 43.34 5.03
3632 4180 2.520465 ATCCATGTGCGGTTGCTCGA 62.520 55.000 0.00 0.00 43.34 4.04
3633 4181 2.108514 CCATGTGCGGTTGCTCGAT 61.109 57.895 0.00 0.00 43.34 3.59
3634 4182 1.349627 CATGTGCGGTTGCTCGATC 59.650 57.895 0.00 0.00 43.34 3.69
3635 4183 1.079197 ATGTGCGGTTGCTCGATCA 60.079 52.632 0.00 0.00 43.34 2.92
3636 4184 1.086067 ATGTGCGGTTGCTCGATCAG 61.086 55.000 0.00 0.00 43.34 2.90
3637 4185 1.446099 GTGCGGTTGCTCGATCAGA 60.446 57.895 0.00 0.00 43.34 3.27
3650 4198 8.412608 TTGCTCGATCAGAGTAAATTAAAGAG 57.587 34.615 12.82 0.00 46.18 2.85
3651 4199 7.492669 TTGCTCGATCAGAGTAAATTAAAGAGG 59.507 37.037 12.82 0.00 46.18 3.69
3652 4200 7.401484 CTCGATCAGAGTAAATTAAAGAGGC 57.599 40.000 6.45 0.00 41.99 4.70
3653 4201 6.281405 TCGATCAGAGTAAATTAAAGAGGCC 58.719 40.000 0.00 0.00 0.00 5.19
3654 4202 6.098409 TCGATCAGAGTAAATTAAAGAGGCCT 59.902 38.462 3.86 3.86 0.00 5.19
3655 4203 6.763610 CGATCAGAGTAAATTAAAGAGGCCTT 59.236 38.462 6.77 0.00 0.00 4.35
3656 4204 7.254590 CGATCAGAGTAAATTAAAGAGGCCTTG 60.255 40.741 6.77 0.00 31.91 3.61
3657 4205 6.779860 TCAGAGTAAATTAAAGAGGCCTTGT 58.220 36.000 6.77 0.00 31.91 3.16
3658 4206 6.655003 TCAGAGTAAATTAAAGAGGCCTTGTG 59.345 38.462 6.77 0.00 31.91 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 124 8.539544 TGTGATGAGATAAGAGTTGTGGAATTA 58.460 33.333 0.00 0.00 0.00 1.40
416 449 3.634397 TTTTACAGAGGGAGGCTGATG 57.366 47.619 0.00 0.00 36.86 3.07
599 1067 5.622914 GCTTTGCAGGTGTTTGATGTATCAT 60.623 40.000 0.00 0.00 36.56 2.45
759 1232 4.607955 TCTGCCTATCTTCAATAACGTCG 58.392 43.478 0.00 0.00 0.00 5.12
810 1283 1.648467 GCCCTTCTGACCGTGCATTC 61.648 60.000 0.00 0.00 0.00 2.67
951 1428 2.082231 CTGCAGATCAAGAGGTGTTGG 58.918 52.381 8.42 0.00 0.00 3.77
961 1438 0.174389 GGAGACGAGCTGCAGATCAA 59.826 55.000 29.71 0.00 34.66 2.57
985 1463 3.634397 ATCCATCGTTCTGGTCAATGT 57.366 42.857 2.29 0.00 37.57 2.71
1035 1516 2.044946 AAGGATGAGTTGGCCGCC 60.045 61.111 1.04 1.04 0.00 6.13
1038 1519 1.840635 AGGTAGAAGGATGAGTTGGCC 59.159 52.381 0.00 0.00 0.00 5.36
1048 1529 2.196595 CCATTGGGACAGGTAGAAGGA 58.803 52.381 0.00 0.00 42.39 3.36
1134 1615 1.596477 GAGGATGCATGCGAGGACC 60.596 63.158 14.09 11.21 0.00 4.46
1194 1676 4.415332 ACGTACAGCGAGCCACCG 62.415 66.667 0.00 0.00 44.77 4.94
1215 1697 0.744414 CGGCCACGATGTTGAGGATT 60.744 55.000 2.24 0.00 44.60 3.01
1341 1823 1.153978 GACCACGGCGACATCGTAA 60.154 57.895 16.62 0.00 42.22 3.18
1601 2085 0.918983 CACCCAGTGATACCCATGGT 59.081 55.000 11.73 1.30 36.21 3.55
1629 2113 0.603975 GCCAGACGGAGAAAAGCACT 60.604 55.000 0.00 0.00 0.00 4.40
1711 2195 6.436027 ACTCAGGAATCAGGATTCTGTAGTA 58.564 40.000 18.52 2.53 44.90 1.82
1758 2242 6.899114 AGACATGACGATGGAAAAAGTTAAC 58.101 36.000 0.00 0.00 33.39 2.01
1874 2358 2.026915 TGTGATGAGCCAGTATGCAACT 60.027 45.455 0.00 0.00 39.81 3.16
1954 2438 1.470979 GGCTTTTCCGAGTCTGCGATA 60.471 52.381 0.00 0.00 0.00 2.92
1997 2481 4.797743 AGACTGGCTAGTATGATCTGTCA 58.202 43.478 1.28 0.00 37.25 3.58
2044 2528 6.869421 AGGAAAAATTGTTATCGCAAATCG 57.131 33.333 0.00 0.00 40.15 3.34
2274 2758 5.978322 GCCGTTAGTTGTTAATTTGGACAAA 59.022 36.000 0.00 0.00 37.49 2.83
2279 2763 4.481463 CCTGCCGTTAGTTGTTAATTTGG 58.519 43.478 0.00 0.00 0.00 3.28
2285 2769 1.338389 GGAGCCTGCCGTTAGTTGTTA 60.338 52.381 0.00 0.00 0.00 2.41
2308 2792 3.130633 CAGAACCACGAACTCATCAACA 58.869 45.455 0.00 0.00 0.00 3.33
2437 2922 1.736645 CGTAGACCAACGCACCCAG 60.737 63.158 0.00 0.00 35.87 4.45
2516 3001 0.398318 GAGTGAAACCCTGCCTGACT 59.602 55.000 0.00 0.00 37.80 3.41
2520 3005 0.036010 CGATGAGTGAAACCCTGCCT 60.036 55.000 0.00 0.00 37.80 4.75
2532 3017 3.935203 CAGCAACAATTAGGACGATGAGT 59.065 43.478 0.00 0.00 0.00 3.41
2575 3060 0.032678 CCGGAGCAAGCTATGACGAT 59.967 55.000 0.00 0.00 0.00 3.73
2689 3179 5.645497 GGAACAACTCAGATCTTACTTGCAT 59.355 40.000 0.00 0.00 0.00 3.96
2749 3240 8.201242 ACAATTTATATCAAACCCACAACCTT 57.799 30.769 0.00 0.00 0.00 3.50
2751 3242 8.524487 TGTACAATTTATATCAAACCCACAACC 58.476 33.333 0.00 0.00 0.00 3.77
2753 3244 9.303116 AGTGTACAATTTATATCAAACCCACAA 57.697 29.630 0.00 0.00 0.00 3.33
2754 3245 8.871629 AGTGTACAATTTATATCAAACCCACA 57.128 30.769 0.00 0.00 0.00 4.17
2785 3277 5.263968 TCACTAGCTAAACATCCTAGCAC 57.736 43.478 0.00 0.00 43.55 4.40
2825 3317 9.382244 CAAACTTAGCAGTTGAAATAGTGTAAC 57.618 33.333 0.00 0.00 42.89 2.50
2901 3401 9.284968 AGTGCAATATAGGTTCGCTATTTTATT 57.715 29.630 0.00 0.00 0.00 1.40
2902 3402 8.848474 AGTGCAATATAGGTTCGCTATTTTAT 57.152 30.769 0.00 0.00 0.00 1.40
2903 3403 9.938280 ATAGTGCAATATAGGTTCGCTATTTTA 57.062 29.630 4.55 0.00 29.27 1.52
2904 3404 8.848474 ATAGTGCAATATAGGTTCGCTATTTT 57.152 30.769 4.55 0.00 29.27 1.82
2905 3405 9.587772 CTATAGTGCAATATAGGTTCGCTATTT 57.412 33.333 26.30 0.00 33.74 1.40
2906 3406 7.707035 GCTATAGTGCAATATAGGTTCGCTATT 59.293 37.037 31.52 2.46 36.60 1.73
2907 3407 7.147897 TGCTATAGTGCAATATAGGTTCGCTAT 60.148 37.037 31.52 14.22 40.29 2.97
2908 3408 6.152154 TGCTATAGTGCAATATAGGTTCGCTA 59.848 38.462 31.52 13.34 40.29 4.26
2909 3409 5.047306 TGCTATAGTGCAATATAGGTTCGCT 60.047 40.000 31.52 6.78 40.29 4.93
2910 3410 5.168569 TGCTATAGTGCAATATAGGTTCGC 58.831 41.667 31.52 22.21 40.29 4.70
2946 3446 4.146616 CAGTGTACAATCGTTCGCTATAGC 59.853 45.833 15.09 15.09 32.20 2.97
2947 3447 5.507974 TCAGTGTACAATCGTTCGCTATAG 58.492 41.667 0.00 0.00 32.20 1.31
2948 3448 5.488645 TCAGTGTACAATCGTTCGCTATA 57.511 39.130 0.00 0.00 32.20 1.31
2949 3449 4.365899 TCAGTGTACAATCGTTCGCTAT 57.634 40.909 0.00 0.00 32.20 2.97
2950 3450 3.835378 TCAGTGTACAATCGTTCGCTA 57.165 42.857 0.00 0.00 32.20 4.26
2951 3451 2.717580 TCAGTGTACAATCGTTCGCT 57.282 45.000 0.00 0.00 34.00 4.93
2952 3452 3.991605 AATCAGTGTACAATCGTTCGC 57.008 42.857 0.00 0.00 0.00 4.70
2953 3453 8.166066 TCAAATAAATCAGTGTACAATCGTTCG 58.834 33.333 0.00 0.00 0.00 3.95
2954 3454 9.478019 CTCAAATAAATCAGTGTACAATCGTTC 57.522 33.333 0.00 0.00 0.00 3.95
2955 3455 7.962918 GCTCAAATAAATCAGTGTACAATCGTT 59.037 33.333 0.00 0.00 0.00 3.85
2956 3456 7.464358 GCTCAAATAAATCAGTGTACAATCGT 58.536 34.615 0.00 0.00 0.00 3.73
2957 3457 6.624917 CGCTCAAATAAATCAGTGTACAATCG 59.375 38.462 0.00 0.00 0.00 3.34
2958 3458 7.684670 TCGCTCAAATAAATCAGTGTACAATC 58.315 34.615 0.00 0.00 0.00 2.67
2959 3459 7.549134 TCTCGCTCAAATAAATCAGTGTACAAT 59.451 33.333 0.00 0.00 0.00 2.71
2960 3460 6.871492 TCTCGCTCAAATAAATCAGTGTACAA 59.129 34.615 0.00 0.00 0.00 2.41
2961 3461 6.310467 GTCTCGCTCAAATAAATCAGTGTACA 59.690 38.462 0.00 0.00 0.00 2.90
2962 3462 6.310467 TGTCTCGCTCAAATAAATCAGTGTAC 59.690 38.462 0.00 0.00 0.00 2.90
2963 3463 6.394809 TGTCTCGCTCAAATAAATCAGTGTA 58.605 36.000 0.00 0.00 0.00 2.90
2964 3464 5.237815 TGTCTCGCTCAAATAAATCAGTGT 58.762 37.500 0.00 0.00 0.00 3.55
2965 3465 5.784750 TGTCTCGCTCAAATAAATCAGTG 57.215 39.130 0.00 0.00 0.00 3.66
2966 3466 6.676456 GCAATGTCTCGCTCAAATAAATCAGT 60.676 38.462 0.00 0.00 0.00 3.41
2967 3467 5.680229 GCAATGTCTCGCTCAAATAAATCAG 59.320 40.000 0.00 0.00 0.00 2.90
2968 3468 5.355071 AGCAATGTCTCGCTCAAATAAATCA 59.645 36.000 0.00 0.00 31.16 2.57
2969 3469 5.814783 AGCAATGTCTCGCTCAAATAAATC 58.185 37.500 0.00 0.00 31.16 2.17
2970 3470 5.824904 AGCAATGTCTCGCTCAAATAAAT 57.175 34.783 0.00 0.00 31.16 1.40
2971 3471 5.627499 AAGCAATGTCTCGCTCAAATAAA 57.373 34.783 0.00 0.00 37.54 1.40
2972 3472 6.106003 TCTAAGCAATGTCTCGCTCAAATAA 58.894 36.000 0.00 0.00 37.54 1.40
2973 3473 5.660460 TCTAAGCAATGTCTCGCTCAAATA 58.340 37.500 0.00 0.00 37.54 1.40
2974 3474 4.507710 TCTAAGCAATGTCTCGCTCAAAT 58.492 39.130 0.00 0.00 37.54 2.32
2975 3475 3.925379 TCTAAGCAATGTCTCGCTCAAA 58.075 40.909 0.00 0.00 37.54 2.69
2976 3476 3.592898 TCTAAGCAATGTCTCGCTCAA 57.407 42.857 0.00 0.00 37.54 3.02
2977 3477 3.592898 TTCTAAGCAATGTCTCGCTCA 57.407 42.857 0.00 0.00 37.54 4.26
2978 3478 3.303001 GCATTCTAAGCAATGTCTCGCTC 60.303 47.826 0.00 0.00 37.54 5.03
2979 3479 2.611292 GCATTCTAAGCAATGTCTCGCT 59.389 45.455 0.00 0.00 41.20 4.93
2980 3480 2.611292 AGCATTCTAAGCAATGTCTCGC 59.389 45.455 0.00 0.00 36.32 5.03
2981 3481 6.183360 GCTATAGCATTCTAAGCAATGTCTCG 60.183 42.308 20.01 0.00 41.59 4.04
2982 3482 6.183360 CGCTATAGCATTCTAAGCAATGTCTC 60.183 42.308 23.99 0.00 42.21 3.36
2983 3483 5.636965 CGCTATAGCATTCTAAGCAATGTCT 59.363 40.000 23.99 0.00 42.21 3.41
2984 3484 5.669848 GCGCTATAGCATTCTAAGCAATGTC 60.670 44.000 23.99 0.00 42.21 3.06
2985 3485 4.153117 GCGCTATAGCATTCTAAGCAATGT 59.847 41.667 23.99 0.00 42.21 2.71
2986 3486 4.645956 GCGCTATAGCATTCTAAGCAATG 58.354 43.478 23.99 4.49 42.21 2.82
2987 3487 3.369147 CGCGCTATAGCATTCTAAGCAAT 59.631 43.478 23.99 0.00 42.21 3.56
2988 3488 2.731451 CGCGCTATAGCATTCTAAGCAA 59.269 45.455 23.99 0.00 42.21 3.91
2989 3489 2.328473 CGCGCTATAGCATTCTAAGCA 58.672 47.619 23.99 0.00 42.21 3.91
2990 3490 1.059835 GCGCGCTATAGCATTCTAAGC 59.940 52.381 26.67 15.42 42.21 3.09
2991 3491 2.600731 AGCGCGCTATAGCATTCTAAG 58.399 47.619 35.79 7.30 42.21 2.18
2992 3492 2.724977 AGCGCGCTATAGCATTCTAA 57.275 45.000 35.79 0.00 42.21 2.10
2993 3493 3.842732 TTAGCGCGCTATAGCATTCTA 57.157 42.857 38.51 19.54 42.21 2.10
2994 3494 2.724977 TTAGCGCGCTATAGCATTCT 57.275 45.000 38.51 14.50 42.21 2.40
2995 3495 3.999229 AATTAGCGCGCTATAGCATTC 57.001 42.857 38.51 11.50 42.21 2.67
2996 3496 4.749245 AAAATTAGCGCGCTATAGCATT 57.251 36.364 38.51 30.06 42.21 3.56
2997 3497 4.749245 AAAAATTAGCGCGCTATAGCAT 57.251 36.364 38.51 26.49 42.21 3.79
3016 3516 7.281324 CCATGGGTCGTGTCTATACAATAAAAA 59.719 37.037 2.85 0.00 37.36 1.94
3017 3517 6.764085 CCATGGGTCGTGTCTATACAATAAAA 59.236 38.462 2.85 0.00 37.36 1.52
3018 3518 6.098552 TCCATGGGTCGTGTCTATACAATAAA 59.901 38.462 13.02 0.00 37.36 1.40
3019 3519 5.599242 TCCATGGGTCGTGTCTATACAATAA 59.401 40.000 13.02 0.00 37.36 1.40
3020 3520 5.141910 TCCATGGGTCGTGTCTATACAATA 58.858 41.667 13.02 0.00 37.36 1.90
3021 3521 3.964688 TCCATGGGTCGTGTCTATACAAT 59.035 43.478 13.02 0.00 37.36 2.71
3022 3522 3.367321 TCCATGGGTCGTGTCTATACAA 58.633 45.455 13.02 0.00 37.36 2.41
3023 3523 2.956333 CTCCATGGGTCGTGTCTATACA 59.044 50.000 13.02 0.00 0.00 2.29
3024 3524 2.957006 ACTCCATGGGTCGTGTCTATAC 59.043 50.000 13.02 0.00 0.00 1.47
3044 3544 6.514063 GGACAATCCTAGGATAACACTACAC 58.486 44.000 24.78 8.61 33.97 2.90
3065 3586 4.537135 TTAACTCAGGACATGTCAGGAC 57.463 45.455 26.47 9.77 0.00 3.85
3070 3591 5.940470 ACCTTTCATTAACTCAGGACATGTC 59.060 40.000 17.91 17.91 0.00 3.06
3074 3595 5.560722 TCACCTTTCATTAACTCAGGACA 57.439 39.130 0.00 0.00 0.00 4.02
3163 3700 5.257262 TGCATTGCTTACCCTTGTACATTA 58.743 37.500 10.49 0.00 0.00 1.90
3173 3710 4.432712 CCTTGTATTTGCATTGCTTACCC 58.567 43.478 10.49 0.00 0.00 3.69
3277 3818 8.321353 TGGTTGATTGTCTCTTATCTTACACAT 58.679 33.333 0.00 0.00 0.00 3.21
3332 3873 7.400915 ACTTATTACCACCTCTGTTATGTACCA 59.599 37.037 0.00 0.00 0.00 3.25
3333 3874 7.709613 CACTTATTACCACCTCTGTTATGTACC 59.290 40.741 0.00 0.00 0.00 3.34
3363 3904 9.221775 CTGCAAATCGTTCCAGTAAATTAATAC 57.778 33.333 0.00 0.00 0.00 1.89
3366 3907 6.090129 GCTGCAAATCGTTCCAGTAAATTAA 58.910 36.000 0.00 0.00 0.00 1.40
3407 3951 5.461032 TTTAGTAAACCCATTGTTGCTGG 57.539 39.130 0.00 0.00 37.23 4.85
3474 4018 9.461312 TTTATTAACTATGCAACTTCAGGTCAT 57.539 29.630 0.00 0.00 0.00 3.06
3502 4050 6.636447 GCGTTTGTGATTATGCTGCATATAAA 59.364 34.615 21.87 10.65 0.00 1.40
3517 4065 1.100463 TGCTGGTGTGCGTTTGTGAT 61.100 50.000 0.00 0.00 35.36 3.06
3520 4068 0.030638 GATTGCTGGTGTGCGTTTGT 59.969 50.000 0.00 0.00 35.36 2.83
3521 4069 0.030504 TGATTGCTGGTGTGCGTTTG 59.969 50.000 0.00 0.00 35.36 2.93
3522 4070 0.311790 CTGATTGCTGGTGTGCGTTT 59.688 50.000 0.00 0.00 35.36 3.60
3523 4071 1.951510 CTGATTGCTGGTGTGCGTT 59.048 52.632 0.00 0.00 35.36 4.84
3524 4072 2.620112 GCTGATTGCTGGTGTGCGT 61.620 57.895 0.00 0.00 38.95 5.24
3525 4073 2.177531 GCTGATTGCTGGTGTGCG 59.822 61.111 0.00 0.00 38.95 5.34
3534 4082 5.220815 CCTTCATAGTTCTTGAGCTGATTGC 60.221 44.000 0.00 0.00 43.29 3.56
3535 4083 5.220815 GCCTTCATAGTTCTTGAGCTGATTG 60.221 44.000 0.00 0.00 0.00 2.67
3536 4084 4.880696 GCCTTCATAGTTCTTGAGCTGATT 59.119 41.667 0.00 0.00 0.00 2.57
3537 4085 4.080695 TGCCTTCATAGTTCTTGAGCTGAT 60.081 41.667 0.00 0.00 0.00 2.90
3538 4086 3.261643 TGCCTTCATAGTTCTTGAGCTGA 59.738 43.478 0.00 0.00 0.00 4.26
3539 4087 3.373439 GTGCCTTCATAGTTCTTGAGCTG 59.627 47.826 0.00 0.00 0.00 4.24
3540 4088 3.008375 TGTGCCTTCATAGTTCTTGAGCT 59.992 43.478 0.00 0.00 0.00 4.09
3541 4089 3.338249 TGTGCCTTCATAGTTCTTGAGC 58.662 45.455 0.00 0.00 0.00 4.26
3542 4090 5.645067 TGATTGTGCCTTCATAGTTCTTGAG 59.355 40.000 0.00 0.00 0.00 3.02
3543 4091 5.559770 TGATTGTGCCTTCATAGTTCTTGA 58.440 37.500 0.00 0.00 0.00 3.02
3544 4092 5.163683 CCTGATTGTGCCTTCATAGTTCTTG 60.164 44.000 0.00 0.00 0.00 3.02
3545 4093 4.946157 CCTGATTGTGCCTTCATAGTTCTT 59.054 41.667 0.00 0.00 0.00 2.52
3546 4094 4.521146 CCTGATTGTGCCTTCATAGTTCT 58.479 43.478 0.00 0.00 0.00 3.01
3547 4095 3.065925 GCCTGATTGTGCCTTCATAGTTC 59.934 47.826 0.00 0.00 0.00 3.01
3548 4096 3.019564 GCCTGATTGTGCCTTCATAGTT 58.980 45.455 0.00 0.00 0.00 2.24
3549 4097 2.025981 TGCCTGATTGTGCCTTCATAGT 60.026 45.455 0.00 0.00 0.00 2.12
3550 4098 2.617308 CTGCCTGATTGTGCCTTCATAG 59.383 50.000 0.00 0.00 0.00 2.23
3551 4099 2.239402 TCTGCCTGATTGTGCCTTCATA 59.761 45.455 0.00 0.00 0.00 2.15
3552 4100 1.005097 TCTGCCTGATTGTGCCTTCAT 59.995 47.619 0.00 0.00 0.00 2.57
3553 4101 0.401356 TCTGCCTGATTGTGCCTTCA 59.599 50.000 0.00 0.00 0.00 3.02
3554 4102 1.471684 CTTCTGCCTGATTGTGCCTTC 59.528 52.381 0.00 0.00 0.00 3.46
3555 4103 1.542492 CTTCTGCCTGATTGTGCCTT 58.458 50.000 0.00 0.00 0.00 4.35
3556 4104 0.323178 CCTTCTGCCTGATTGTGCCT 60.323 55.000 0.00 0.00 0.00 4.75
3557 4105 0.322816 TCCTTCTGCCTGATTGTGCC 60.323 55.000 0.00 0.00 0.00 5.01
3558 4106 1.200948 GTTCCTTCTGCCTGATTGTGC 59.799 52.381 0.00 0.00 0.00 4.57
3559 4107 1.815003 GGTTCCTTCTGCCTGATTGTG 59.185 52.381 0.00 0.00 0.00 3.33
3560 4108 1.707427 AGGTTCCTTCTGCCTGATTGT 59.293 47.619 0.00 0.00 0.00 2.71
3561 4109 2.503895 AGGTTCCTTCTGCCTGATTG 57.496 50.000 0.00 0.00 0.00 2.67
3562 4110 3.619979 CGTTAGGTTCCTTCTGCCTGATT 60.620 47.826 0.00 0.00 34.07 2.57
3563 4111 2.093447 CGTTAGGTTCCTTCTGCCTGAT 60.093 50.000 0.00 0.00 34.07 2.90
3564 4112 1.275291 CGTTAGGTTCCTTCTGCCTGA 59.725 52.381 0.00 0.00 34.07 3.86
3565 4113 1.726853 CGTTAGGTTCCTTCTGCCTG 58.273 55.000 0.00 0.00 34.07 4.85
3566 4114 0.036294 GCGTTAGGTTCCTTCTGCCT 60.036 55.000 0.00 0.00 36.47 4.75
3567 4115 1.025113 GGCGTTAGGTTCCTTCTGCC 61.025 60.000 10.50 10.50 0.00 4.85
3568 4116 0.036294 AGGCGTTAGGTTCCTTCTGC 60.036 55.000 0.00 0.00 0.00 4.26
3569 4117 2.418334 GGTAGGCGTTAGGTTCCTTCTG 60.418 54.545 0.00 0.00 0.00 3.02
3570 4118 1.829849 GGTAGGCGTTAGGTTCCTTCT 59.170 52.381 0.00 0.00 0.00 2.85
3571 4119 1.551883 TGGTAGGCGTTAGGTTCCTTC 59.448 52.381 0.00 0.00 0.00 3.46
3572 4120 1.648116 TGGTAGGCGTTAGGTTCCTT 58.352 50.000 0.00 0.00 0.00 3.36
3573 4121 1.485066 CATGGTAGGCGTTAGGTTCCT 59.515 52.381 0.00 0.00 0.00 3.36
3574 4122 1.483415 TCATGGTAGGCGTTAGGTTCC 59.517 52.381 0.00 0.00 0.00 3.62
3575 4123 2.547826 GTCATGGTAGGCGTTAGGTTC 58.452 52.381 0.00 0.00 0.00 3.62
3576 4124 1.208776 GGTCATGGTAGGCGTTAGGTT 59.791 52.381 0.00 0.00 0.00 3.50
3577 4125 0.828677 GGTCATGGTAGGCGTTAGGT 59.171 55.000 0.00 0.00 0.00 3.08
3578 4126 0.106149 GGGTCATGGTAGGCGTTAGG 59.894 60.000 0.00 0.00 0.00 2.69
3579 4127 0.828022 TGGGTCATGGTAGGCGTTAG 59.172 55.000 0.00 0.00 0.00 2.34
3580 4128 1.502690 ATGGGTCATGGTAGGCGTTA 58.497 50.000 0.00 0.00 0.00 3.18
3581 4129 0.623723 AATGGGTCATGGTAGGCGTT 59.376 50.000 0.00 0.00 0.00 4.84
3582 4130 0.107214 CAATGGGTCATGGTAGGCGT 60.107 55.000 0.00 0.00 0.00 5.68
3583 4131 0.180171 TCAATGGGTCATGGTAGGCG 59.820 55.000 0.00 0.00 0.00 5.52
3584 4132 1.477558 CCTCAATGGGTCATGGTAGGC 60.478 57.143 0.00 0.00 0.00 3.93
3585 4133 2.126882 TCCTCAATGGGTCATGGTAGG 58.873 52.381 0.00 0.00 36.20 3.18
3586 4134 2.505407 TGTCCTCAATGGGTCATGGTAG 59.495 50.000 0.00 0.00 36.20 3.18
3587 4135 2.556766 TGTCCTCAATGGGTCATGGTA 58.443 47.619 0.00 0.00 36.20 3.25
3588 4136 1.371467 TGTCCTCAATGGGTCATGGT 58.629 50.000 0.00 0.00 36.20 3.55
3589 4137 2.512692 TTGTCCTCAATGGGTCATGG 57.487 50.000 0.00 0.00 36.20 3.66
3590 4138 3.367703 GCTTTTGTCCTCAATGGGTCATG 60.368 47.826 0.00 0.00 36.20 3.07
3591 4139 2.827921 GCTTTTGTCCTCAATGGGTCAT 59.172 45.455 0.00 0.00 36.20 3.06
3592 4140 2.238521 GCTTTTGTCCTCAATGGGTCA 58.761 47.619 0.00 0.00 36.20 4.02
3593 4141 2.238521 TGCTTTTGTCCTCAATGGGTC 58.761 47.619 0.00 0.00 36.20 4.46
3594 4142 2.380064 TGCTTTTGTCCTCAATGGGT 57.620 45.000 0.00 0.00 36.20 4.51
3595 4143 2.167075 GGATGCTTTTGTCCTCAATGGG 59.833 50.000 0.00 0.00 36.20 4.00
3596 4144 2.827322 TGGATGCTTTTGTCCTCAATGG 59.173 45.455 0.00 0.00 35.49 3.16
3597 4145 4.081862 ACATGGATGCTTTTGTCCTCAATG 60.082 41.667 0.00 0.00 35.49 2.82
3598 4146 4.081862 CACATGGATGCTTTTGTCCTCAAT 60.082 41.667 0.00 0.00 35.49 2.57
3599 4147 3.256383 CACATGGATGCTTTTGTCCTCAA 59.744 43.478 0.00 0.00 35.49 3.02
3600 4148 2.821378 CACATGGATGCTTTTGTCCTCA 59.179 45.455 0.00 0.00 35.49 3.86
3601 4149 2.416431 GCACATGGATGCTTTTGTCCTC 60.416 50.000 0.00 0.00 42.62 3.71
3602 4150 1.547372 GCACATGGATGCTTTTGTCCT 59.453 47.619 0.00 0.00 42.62 3.85
3603 4151 1.733389 CGCACATGGATGCTTTTGTCC 60.733 52.381 6.72 0.00 43.80 4.02
3604 4152 1.621107 CGCACATGGATGCTTTTGTC 58.379 50.000 6.72 0.00 43.80 3.18
3605 4153 0.244450 CCGCACATGGATGCTTTTGT 59.756 50.000 6.72 0.00 43.80 2.83
3606 4154 0.244450 ACCGCACATGGATGCTTTTG 59.756 50.000 6.72 0.00 43.80 2.44
3607 4155 0.968405 AACCGCACATGGATGCTTTT 59.032 45.000 6.72 0.00 43.80 2.27
3608 4156 0.244450 CAACCGCACATGGATGCTTT 59.756 50.000 6.72 0.00 43.80 3.51
3609 4157 1.885157 CAACCGCACATGGATGCTT 59.115 52.632 6.72 0.00 43.80 3.91
3610 4158 3.594568 CAACCGCACATGGATGCT 58.405 55.556 6.72 0.00 43.80 3.79
3612 4160 1.430632 GAGCAACCGCACATGGATG 59.569 57.895 0.00 0.00 42.27 3.51
3613 4161 2.108514 CGAGCAACCGCACATGGAT 61.109 57.895 0.00 0.00 42.27 3.41
3614 4162 2.520465 ATCGAGCAACCGCACATGGA 62.520 55.000 0.00 0.00 42.27 3.41
3615 4163 2.040213 GATCGAGCAACCGCACATGG 62.040 60.000 0.00 0.00 42.27 3.66
3616 4164 1.349627 GATCGAGCAACCGCACATG 59.650 57.895 0.00 0.00 42.27 3.21
3617 4165 1.079197 TGATCGAGCAACCGCACAT 60.079 52.632 0.00 0.00 42.27 3.21
3618 4166 1.737735 CTGATCGAGCAACCGCACA 60.738 57.895 4.32 0.00 42.27 4.57
3619 4167 1.416813 CTCTGATCGAGCAACCGCAC 61.417 60.000 4.32 0.00 42.27 5.34
3620 4168 1.153765 CTCTGATCGAGCAACCGCA 60.154 57.895 4.32 0.00 42.27 5.69
3621 4169 0.100682 TACTCTGATCGAGCAACCGC 59.899 55.000 4.32 0.00 43.85 5.68
3622 4170 2.561733 TTACTCTGATCGAGCAACCG 57.438 50.000 4.32 0.00 43.85 4.44
3623 4171 6.903883 TTAATTTACTCTGATCGAGCAACC 57.096 37.500 4.32 0.00 43.85 3.77
3624 4172 8.186178 TCTTTAATTTACTCTGATCGAGCAAC 57.814 34.615 4.32 0.00 43.85 4.17
3625 4173 7.492669 CCTCTTTAATTTACTCTGATCGAGCAA 59.507 37.037 4.32 5.61 43.85 3.91
3626 4174 6.980978 CCTCTTTAATTTACTCTGATCGAGCA 59.019 38.462 2.19 2.19 43.85 4.26
3627 4175 6.074034 GCCTCTTTAATTTACTCTGATCGAGC 60.074 42.308 12.53 0.00 43.85 5.03
3628 4176 6.422400 GGCCTCTTTAATTTACTCTGATCGAG 59.578 42.308 11.44 11.44 45.56 4.04
3629 4177 6.098409 AGGCCTCTTTAATTTACTCTGATCGA 59.902 38.462 0.00 0.00 0.00 3.59
3630 4178 6.284459 AGGCCTCTTTAATTTACTCTGATCG 58.716 40.000 0.00 0.00 0.00 3.69
3631 4179 7.554476 ACAAGGCCTCTTTAATTTACTCTGATC 59.446 37.037 5.23 0.00 0.00 2.92
3632 4180 7.337942 CACAAGGCCTCTTTAATTTACTCTGAT 59.662 37.037 5.23 0.00 0.00 2.90
3633 4181 6.655003 CACAAGGCCTCTTTAATTTACTCTGA 59.345 38.462 5.23 0.00 0.00 3.27
3634 4182 6.846350 CACAAGGCCTCTTTAATTTACTCTG 58.154 40.000 5.23 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.