Multiple sequence alignment - TraesCS2D01G087600

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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 TraesCS2D01G087600 chr2D 100.000 6988 0 0 1 6988 37773192 37766205 0.000000e+00 12905.0
1 TraesCS2D01G087600 chr2D 93.529 170 7 2 532 697 445189825 445189994 4.180000e-62 250.0
2 TraesCS2D01G087600 chr2A 94.486 6239 306 21 772 6988 42709255 42703033 0.000000e+00 9581.0
3 TraesCS2D01G087600 chr2A 82.143 308 31 10 234 534 42709936 42709646 7.000000e-60 243.0
4 TraesCS2D01G087600 chr2A 94.737 76 4 0 162 237 42710034 42709959 1.230000e-22 119.0
5 TraesCS2D01G087600 chr2A 89.412 85 8 1 6905 6988 42702630 42702546 9.590000e-19 106.0
6 TraesCS2D01G087600 chr2B 95.310 3390 145 7 3609 6988 66022283 66018898 0.000000e+00 5367.0
7 TraesCS2D01G087600 chr2B 93.872 1795 97 4 1738 3523 66024069 66022279 0.000000e+00 2693.0
8 TraesCS2D01G087600 chr2B 85.763 2037 225 29 1336 3328 66201899 66199884 0.000000e+00 2095.0
9 TraesCS2D01G087600 chr2B 88.170 1361 133 7 4737 6080 66197126 66195777 0.000000e+00 1596.0
10 TraesCS2D01G087600 chr2B 86.146 1256 146 18 3447 4692 66198364 66197127 0.000000e+00 1330.0
11 TraesCS2D01G087600 chr2B 88.877 962 93 10 695 1648 66025025 66024070 0.000000e+00 1171.0
12 TraesCS2D01G087600 chr2B 86.916 214 23 4 692 903 66027989 66027779 1.170000e-57 235.0
13 TraesCS2D01G087600 chr2B 90.909 165 15 0 1 165 66026351 66026187 9.120000e-54 222.0
14 TraesCS2D01G087600 chr2B 86.061 165 21 2 1 165 66037934 66037772 7.200000e-40 176.0
15 TraesCS2D01G087600 chr2B 93.421 76 5 0 162 237 66026136 66026061 5.730000e-21 113.0
16 TraesCS2D01G087600 chr2B 90.476 84 6 2 6907 6988 66018531 66018448 7.410000e-20 110.0
17 TraesCS2D01G087600 chr6D 95.494 466 19 1 1718 2183 473208334 473207871 0.000000e+00 743.0
18 TraesCS2D01G087600 chr1D 95.307 277 11 1 1907 2183 270372038 270371764 8.320000e-119 438.0
19 TraesCS2D01G087600 chr1D 93.064 173 7 3 529 696 422051589 422051417 1.510000e-61 248.0
20 TraesCS2D01G087600 chr1D 100.000 28 0 0 1955 1982 270372066 270372039 1.300000e-02 52.8
21 TraesCS2D01G087600 chr1A 93.818 275 15 1 1909 2183 582320615 582320343 5.040000e-111 412.0
22 TraesCS2D01G087600 chr1A 100.000 28 0 0 1955 1982 582320645 582320618 1.300000e-02 52.8
23 TraesCS2D01G087600 chr5D 95.266 169 4 2 529 693 408752471 408752639 1.490000e-66 265.0
24 TraesCS2D01G087600 chr5D 95.238 168 4 2 530 693 48668963 48669130 5.380000e-66 263.0
25 TraesCS2D01G087600 chr5D 95.152 165 4 2 533 693 340690755 340690591 2.500000e-64 257.0
26 TraesCS2D01G087600 chr5D 94.545 165 5 2 533 693 276657796 276657960 1.160000e-62 252.0
27 TraesCS2D01G087600 chr5D 92.529 174 7 4 532 699 524486266 524486439 1.950000e-60 244.0
28 TraesCS2D01G087600 chr5B 94.220 173 6 2 525 693 457962017 457961845 1.930000e-65 261.0
29 TraesCS2D01G087600 chr7D 94.545 165 5 2 533 693 237158773 237158609 1.160000e-62 252.0


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 TraesCS2D01G087600 chr2D 37766205 37773192 6987 True 12905.000000 12905 100.000000 1 6988 1 chr2D.!!$R1 6987
1 TraesCS2D01G087600 chr2A 42702546 42710034 7488 True 2512.250000 9581 90.194500 162 6988 4 chr2A.!!$R1 6826
2 TraesCS2D01G087600 chr2B 66195777 66201899 6122 True 1673.666667 2095 86.693000 1336 6080 3 chr2B.!!$R3 4744
3 TraesCS2D01G087600 chr2B 66018448 66027989 9541 True 1415.857143 5367 91.397286 1 6988 7 chr2B.!!$R2 6987

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
68 1707 0.870307 CCCCGTCGCTAGATTCGTTG 60.870 60.000 0.00 0.00 0.00 4.10 F
821 3610 1.061131 CGATGGTGAGAACATGCGAAC 59.939 52.381 0.00 0.00 0.00 3.95 F
1358 4155 1.300971 GCTCGCATGTTCTCAAGCCA 61.301 55.000 0.00 0.00 35.23 4.75 F
2314 5141 0.368227 GCGCAATCTCACAGAAGACG 59.632 55.000 0.30 0.00 0.00 4.18 F
2315 5142 0.368227 CGCAATCTCACAGAAGACGC 59.632 55.000 0.00 0.00 0.00 5.19 F
2317 5144 0.994995 CAATCTCACAGAAGACGCGG 59.005 55.000 12.47 0.00 0.00 6.46 F
3722 7967 0.388006 AAATTTGTTAGCACGCCCGC 60.388 50.000 0.00 0.00 0.00 6.13 F
4135 8385 0.031178 GGATGCCGCAATTGTGATCC 59.969 55.000 20.47 19.41 0.00 3.36 F
5705 9972 0.734889 GGTTGGTCATGCTGGATTCG 59.265 55.000 0.00 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1026 3820 0.527169 GACTACGGCGACCTTTAGGC 60.527 60.000 16.62 1.98 39.32 3.93 R
1630 4434 0.593128 ACACAAGAGGCACGCATTTC 59.407 50.000 0.00 0.00 0.00 2.17 R
3051 5890 0.809385 CAGAAGAAGCTGGCCATGTG 59.191 55.000 5.51 0.00 32.26 3.21 R
3720 7965 1.603678 GGCATTATGATTGCAAGGGCG 60.604 52.381 4.94 0.00 45.35 6.13 R
3722 7967 1.682854 ACGGCATTATGATTGCAAGGG 59.317 47.619 4.94 0.00 41.95 3.95 R
4103 8353 1.794714 GGCATCCAGGTCTCTCCTTA 58.205 55.000 0.00 0.00 45.67 2.69 R
4793 9043 0.257328 TGTTGCTCCTTGGGTTGTGA 59.743 50.000 0.00 0.00 0.00 3.58 R
5786 10053 0.107017 ATGTACCAGATGCCACCAGC 60.107 55.000 0.00 0.00 44.14 4.85 R
6590 10865 1.078143 GCTGATGGAAAGCGAGGGT 60.078 57.895 0.00 0.00 0.00 4.34 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
32 1671 1.204941 GTTCCTCTCTTTAGCTCCGCA 59.795 52.381 0.00 0.00 0.00 5.69
68 1707 0.870307 CCCCGTCGCTAGATTCGTTG 60.870 60.000 0.00 0.00 0.00 4.10
109 1748 1.344763 CTCCTCCCATTCCATCGGTAC 59.655 57.143 0.00 0.00 0.00 3.34
122 1761 4.981415 GGTACGTCTGTGGTGGAC 57.019 61.111 0.00 0.00 0.00 4.02
171 1864 2.171725 GTGTATGGGGCGCTTCGAC 61.172 63.158 7.64 0.00 0.00 4.20
184 1877 1.865340 GCTTCGACTTTGTTCCGTTCT 59.135 47.619 0.00 0.00 0.00 3.01
262 1981 4.877823 TGGATAAGCAGCACTAGACAATTG 59.122 41.667 3.24 3.24 0.00 2.32
319 2760 4.159693 TCGGCACTAGTACATGAATCTTGT 59.840 41.667 0.00 6.98 0.00 3.16
330 2771 9.088512 AGTACATGAATCTTGTATTTTCTCGAC 57.911 33.333 11.36 0.09 32.56 4.20
346 2787 8.433421 TTTTCTCGACAAAAATAGAGTGAACT 57.567 30.769 0.00 0.00 32.90 3.01
348 2789 8.744008 TTCTCGACAAAAATAGAGTGAACTAG 57.256 34.615 0.00 0.00 32.90 2.57
404 2845 2.993899 ACGTAGAAGAGTGCGGAATTTG 59.006 45.455 0.00 0.00 0.00 2.32
417 2858 5.295787 GTGCGGAATTTGTTCACCATAGATA 59.704 40.000 0.00 0.00 0.00 1.98
538 3325 4.817318 TTTGGCATTGGAAAATACTCCC 57.183 40.909 0.00 0.00 34.22 4.30
539 3326 3.756082 TGGCATTGGAAAATACTCCCT 57.244 42.857 0.00 0.00 34.22 4.20
540 3327 4.059773 TGGCATTGGAAAATACTCCCTT 57.940 40.909 0.00 0.00 34.22 3.95
541 3328 4.023291 TGGCATTGGAAAATACTCCCTTC 58.977 43.478 0.00 0.00 34.22 3.46
542 3329 3.066760 GGCATTGGAAAATACTCCCTTCG 59.933 47.826 0.00 0.00 34.22 3.79
543 3330 3.694566 GCATTGGAAAATACTCCCTTCGT 59.305 43.478 0.00 0.00 34.22 3.85
544 3331 4.157840 GCATTGGAAAATACTCCCTTCGTT 59.842 41.667 0.00 0.00 34.22 3.85
545 3332 5.676331 GCATTGGAAAATACTCCCTTCGTTC 60.676 44.000 0.00 0.00 34.22 3.95
546 3333 3.946606 TGGAAAATACTCCCTTCGTTCC 58.053 45.455 0.00 0.00 34.22 3.62
547 3334 3.585732 TGGAAAATACTCCCTTCGTTCCT 59.414 43.478 0.00 0.00 35.22 3.36
548 3335 4.778958 TGGAAAATACTCCCTTCGTTCCTA 59.221 41.667 0.00 0.00 35.22 2.94
549 3336 5.248934 TGGAAAATACTCCCTTCGTTCCTAA 59.751 40.000 0.00 0.00 35.22 2.69
550 3337 6.175471 GGAAAATACTCCCTTCGTTCCTAAA 58.825 40.000 0.00 0.00 32.14 1.85
551 3338 6.827251 GGAAAATACTCCCTTCGTTCCTAAAT 59.173 38.462 0.00 0.00 32.14 1.40
552 3339 7.989170 GGAAAATACTCCCTTCGTTCCTAAATA 59.011 37.037 0.00 0.00 32.14 1.40
553 3340 9.557061 GAAAATACTCCCTTCGTTCCTAAATAT 57.443 33.333 0.00 0.00 0.00 1.28
557 3344 7.672122 ACTCCCTTCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
558 3345 7.724287 ACTCCCTTCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
559 3346 7.564292 ACTCCCTTCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
560 3347 8.315220 TCCCTTCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
561 3348 8.765517 TCCCTTCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
562 3349 9.392259 CCCTTCGTTCCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
634 3421 8.900983 AGAGATAGATTCACTTATTTTGCTCC 57.099 34.615 0.00 0.00 0.00 4.70
635 3422 7.655328 AGAGATAGATTCACTTATTTTGCTCCG 59.345 37.037 0.00 0.00 0.00 4.63
636 3423 7.275920 AGATAGATTCACTTATTTTGCTCCGT 58.724 34.615 0.00 0.00 0.00 4.69
637 3424 8.421784 AGATAGATTCACTTATTTTGCTCCGTA 58.578 33.333 0.00 0.00 0.00 4.02
638 3425 9.209175 GATAGATTCACTTATTTTGCTCCGTAT 57.791 33.333 0.00 0.00 0.00 3.06
639 3426 7.251704 AGATTCACTTATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
640 3427 6.823689 AGATTCACTTATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
641 3428 7.985184 AGATTCACTTATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
642 3429 7.534085 TTCACTTATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
643 3430 6.636705 TCACTTATTTTGCTCCGTATGTAGT 58.363 36.000 0.00 0.00 0.00 2.73
644 3431 6.755141 TCACTTATTTTGCTCCGTATGTAGTC 59.245 38.462 0.00 0.00 0.00 2.59
645 3432 6.533723 CACTTATTTTGCTCCGTATGTAGTCA 59.466 38.462 0.00 0.00 0.00 3.41
646 3433 6.534079 ACTTATTTTGCTCCGTATGTAGTCAC 59.466 38.462 0.00 0.00 0.00 3.67
647 3434 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
648 3435 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
649 3436 5.648178 TTTGCTCCGTATGTAGTCACTTA 57.352 39.130 0.00 0.00 0.00 2.24
650 3437 5.847111 TTGCTCCGTATGTAGTCACTTAT 57.153 39.130 0.00 0.00 0.00 1.73
651 3438 5.847111 TGCTCCGTATGTAGTCACTTATT 57.153 39.130 0.00 0.00 0.00 1.40
652 3439 5.588240 TGCTCCGTATGTAGTCACTTATTG 58.412 41.667 0.00 0.00 0.00 1.90
653 3440 5.358725 TGCTCCGTATGTAGTCACTTATTGA 59.641 40.000 0.00 0.00 0.00 2.57
654 3441 6.127563 TGCTCCGTATGTAGTCACTTATTGAA 60.128 38.462 0.00 0.00 35.39 2.69
655 3442 6.755141 GCTCCGTATGTAGTCACTTATTGAAA 59.245 38.462 0.00 0.00 35.39 2.69
656 3443 7.438459 GCTCCGTATGTAGTCACTTATTGAAAT 59.562 37.037 0.00 0.00 35.39 2.17
657 3444 8.867112 TCCGTATGTAGTCACTTATTGAAATC 57.133 34.615 0.00 0.00 35.39 2.17
658 3445 8.692710 TCCGTATGTAGTCACTTATTGAAATCT 58.307 33.333 0.00 0.00 35.39 2.40
659 3446 8.969267 CCGTATGTAGTCACTTATTGAAATCTC 58.031 37.037 0.00 0.00 35.39 2.75
660 3447 9.737427 CGTATGTAGTCACTTATTGAAATCTCT 57.263 33.333 0.00 0.00 35.39 3.10
687 3474 7.625828 AAAGACTTATATTTTGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
688 3475 5.681639 AGACTTATATTTTGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
689 3476 5.427481 AGACTTATATTTTGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
690 3477 5.681639 ACTTATATTTTGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
691 3478 5.191124 ACTTATATTTTGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
692 3479 6.384886 ACTTATATTTTGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
693 3480 5.703730 ATATTTTGGAACGGAGGGAGTAA 57.296 39.130 0.00 0.00 0.00 2.24
702 3489 4.581077 ACGGAGGGAGTAATTAACGATC 57.419 45.455 0.00 0.00 0.00 3.69
708 3495 7.146648 GGAGGGAGTAATTAACGATCAAGTAG 58.853 42.308 0.00 0.00 0.00 2.57
737 3524 7.606858 TGAATCTAGATCTTGTTGCTCTTTG 57.393 36.000 5.51 0.00 0.00 2.77
753 3540 7.985634 TGCTCTTTGTTTTAGACATTTTGAC 57.014 32.000 0.00 0.00 38.26 3.18
762 3549 7.172532 TGTTTTAGACATTTTGACGCTGTAGAT 59.827 33.333 0.00 0.00 32.00 1.98
763 3550 7.667043 TTTAGACATTTTGACGCTGTAGATT 57.333 32.000 0.00 0.00 0.00 2.40
764 3551 8.766000 TTTAGACATTTTGACGCTGTAGATTA 57.234 30.769 0.00 0.00 0.00 1.75
769 3557 7.519002 ACATTTTGACGCTGTAGATTAACTTC 58.481 34.615 0.00 0.00 0.00 3.01
778 3566 8.472413 ACGCTGTAGATTAACTTCATTAAGGTA 58.528 33.333 0.00 0.00 36.20 3.08
807 3596 1.806542 GATGTGCTCAACAACGATGGT 59.193 47.619 0.00 0.00 43.61 3.55
821 3610 1.061131 CGATGGTGAGAACATGCGAAC 59.939 52.381 0.00 0.00 0.00 3.95
841 3630 2.086869 CCTCAAAGCATGAACCGATGT 58.913 47.619 0.00 0.00 37.67 3.06
899 3688 6.992715 ACAGCCATGTACTATCCATTTAGAAC 59.007 38.462 0.00 0.00 38.09 3.01
910 3700 8.830580 ACTATCCATTTAGAACATTGTTGATCG 58.169 33.333 6.80 1.13 30.44 3.69
925 3715 8.589629 CATTGTTGATCGAAAATTCAGATTTCC 58.410 33.333 0.00 0.00 34.44 3.13
994 3788 5.587443 TGAATTTCACATCATGAGGTGCTAG 59.413 40.000 30.58 11.81 42.26 3.42
1044 3838 1.514553 GCCTAAAGGTCGCCGTAGT 59.485 57.895 0.00 0.00 37.57 2.73
1121 3915 9.881649 ACATTGCTATGACCATATATCTACAAG 57.118 33.333 15.23 0.00 35.65 3.16
1225 4019 8.759481 TCATGGCATGGAGTTAATTGTATAAA 57.241 30.769 26.15 0.00 0.00 1.40
1252 4046 1.472728 GGATGGCGGTCTGTTCGTTAT 60.473 52.381 0.00 0.00 0.00 1.89
1255 4049 3.530265 TGGCGGTCTGTTCGTTATATT 57.470 42.857 0.00 0.00 0.00 1.28
1256 4050 3.864243 TGGCGGTCTGTTCGTTATATTT 58.136 40.909 0.00 0.00 0.00 1.40
1257 4051 5.008619 TGGCGGTCTGTTCGTTATATTTA 57.991 39.130 0.00 0.00 0.00 1.40
1298 4095 2.487086 CGAGCATAATGTGGATGGGGAA 60.487 50.000 0.00 0.00 0.00 3.97
1322 4119 3.197614 CGCCTACGCTCCAGAAGA 58.802 61.111 0.00 0.00 0.00 2.87
1334 4131 4.281525 CTCCAGAAGAGCTACGTACTTC 57.718 50.000 13.72 13.72 39.87 3.01
1358 4155 1.300971 GCTCGCATGTTCTCAAGCCA 61.301 55.000 0.00 0.00 35.23 4.75
1416 4213 1.760405 AGGAAGTCCAACTGGGGAAT 58.240 50.000 0.00 0.00 39.05 3.01
1426 4223 5.012046 GTCCAACTGGGGAATTGAAATCTTT 59.988 40.000 0.00 0.00 39.05 2.52
1486 4287 7.462571 AGGTTTACATACCCATTCTGTTTTC 57.537 36.000 0.00 0.00 39.08 2.29
1569 4370 6.543465 TGAATATGAAGAGTTGGATGCGAAAT 59.457 34.615 0.00 0.00 0.00 2.17
1571 4372 3.942829 TGAAGAGTTGGATGCGAAATCT 58.057 40.909 0.00 0.00 28.78 2.40
1587 4388 6.127403 GCGAAATCTATACCATCGTTTGTTC 58.873 40.000 0.00 0.00 36.01 3.18
1607 4408 3.263261 TCCGCACGTCATTTAATAGCAA 58.737 40.909 0.00 0.00 0.00 3.91
1609 4410 4.025229 TCCGCACGTCATTTAATAGCAATC 60.025 41.667 0.00 0.00 0.00 2.67
1648 4453 0.453282 CGAAATGCGTGCCTCTTGTG 60.453 55.000 0.00 0.00 34.64 3.33
1733 4560 9.074576 ACTACCAATAAACTGTTAAGGGAAAAG 57.925 33.333 0.00 0.00 0.00 2.27
1812 4639 2.892215 TGCAAGGCTCATCACAATCAAA 59.108 40.909 0.00 0.00 0.00 2.69
2003 4830 2.007608 GGGAAGCGTACAATGGAGTTC 58.992 52.381 0.00 0.00 0.00 3.01
2256 5083 1.402968 CTGCGCAATGAGGCTTTATGT 59.597 47.619 13.05 0.00 0.00 2.29
2314 5141 0.368227 GCGCAATCTCACAGAAGACG 59.632 55.000 0.30 0.00 0.00 4.18
2315 5142 0.368227 CGCAATCTCACAGAAGACGC 59.632 55.000 0.00 0.00 0.00 5.19
2317 5144 0.994995 CAATCTCACAGAAGACGCGG 59.005 55.000 12.47 0.00 0.00 6.46
2338 5165 3.879892 GGGATTCACTATGAAGGCTGAAC 59.120 47.826 0.00 0.00 40.05 3.18
2370 5197 6.655003 GTCAATTGGAAGACAGGAGATTTACA 59.345 38.462 5.42 0.00 34.93 2.41
2394 5221 3.648067 TCAAGACTGAGTTGGATGGTCTT 59.352 43.478 0.00 0.00 44.67 3.01
2493 5320 3.062234 GCTATGATACGCCTAATTTCGGC 59.938 47.826 8.07 8.07 44.11 5.54
2752 5579 3.198853 GGAAGTTAAGGAGGAGAGCACAT 59.801 47.826 0.00 0.00 0.00 3.21
2818 5645 7.227156 TGCAAAGAGTAAGGAGAAGAATCTTT 58.773 34.615 0.00 0.00 35.54 2.52
2863 5690 4.584029 AAGTCATTTACTTCATCACGCG 57.416 40.909 3.53 3.53 45.64 6.01
2916 5755 2.027929 TCGGAAAAGGAAGGAACGCATA 60.028 45.455 0.00 0.00 0.00 3.14
3051 5890 6.967135 AGGTTTTTACGGAGAAGTGAATTTC 58.033 36.000 0.00 0.00 0.00 2.17
3064 5903 2.028748 GTGAATTTCACATGGCCAGCTT 60.029 45.455 21.75 0.00 46.22 3.74
3065 5904 2.231964 TGAATTTCACATGGCCAGCTTC 59.768 45.455 13.05 6.65 0.00 3.86
3066 5905 2.226962 ATTTCACATGGCCAGCTTCT 57.773 45.000 13.05 0.00 0.00 2.85
3072 5911 1.379576 ATGGCCAGCTTCTTCTGCC 60.380 57.895 13.05 0.00 33.68 4.85
3118 5957 4.347607 AGATGGTCTTGAGGAATTTTGGG 58.652 43.478 0.00 0.00 0.00 4.12
3173 6012 4.436183 GCTTGAGAAAAATCAGGTACGCTC 60.436 45.833 0.00 0.00 0.00 5.03
3186 6025 9.614792 AATCAGGTACGCTCTATATTTCTTTTT 57.385 29.630 0.00 0.00 0.00 1.94
3468 7712 7.930217 TCCTTTTCGCTTGATATTTCCTTATG 58.070 34.615 0.00 0.00 0.00 1.90
3486 7731 5.829924 CCTTATGATCTGCCACTAAATTGGT 59.170 40.000 0.00 0.00 39.09 3.67
3505 7750 3.071023 TGGTCAATCAGGAAAGACGAACT 59.929 43.478 0.00 0.00 31.93 3.01
3510 7755 1.760613 TCAGGAAAGACGAACTGTGGT 59.239 47.619 0.00 0.00 32.92 4.16
3720 7965 1.544246 AGGAAATTTGTTAGCACGCCC 59.456 47.619 0.00 0.00 0.00 6.13
3721 7966 1.613270 GAAATTTGTTAGCACGCCCG 58.387 50.000 0.00 0.00 0.00 6.13
3722 7967 0.388006 AAATTTGTTAGCACGCCCGC 60.388 50.000 0.00 0.00 0.00 6.13
3723 7968 2.207788 AATTTGTTAGCACGCCCGCC 62.208 55.000 0.00 0.00 0.00 6.13
3794 8044 7.678947 AGTATGCCATGCTACTCATATTTTC 57.321 36.000 0.00 0.00 33.19 2.29
3803 8053 4.260784 GCTACTCATATTTTCCGGCACTTG 60.261 45.833 0.00 0.00 0.00 3.16
3818 8068 3.127721 GGCACTTGGAGAATAAGAACAGC 59.872 47.826 0.00 0.00 0.00 4.40
3819 8069 3.753272 GCACTTGGAGAATAAGAACAGCA 59.247 43.478 0.00 0.00 0.00 4.41
3948 8198 2.305635 TGGACTGGTGTGCAGATTATGT 59.694 45.455 0.00 0.00 39.59 2.29
4129 8379 1.033746 AGACCTGGATGCCGCAATTG 61.034 55.000 0.00 0.00 0.00 2.32
4135 8385 0.031178 GGATGCCGCAATTGTGATCC 59.969 55.000 20.47 19.41 0.00 3.36
4271 8521 3.091545 TCCTCACCAAAGGAATGCATTC 58.908 45.455 27.91 27.91 42.56 2.67
4531 8781 0.892358 CTGCATGTGCTTCACCAGGT 60.892 55.000 6.55 0.00 42.66 4.00
4601 8851 3.989705 ATTTTAAGCAATTTTCGCCGC 57.010 38.095 0.00 0.00 0.00 6.53
4615 8865 2.978018 GCCGCCCGAACTGGAAAAG 61.978 63.158 0.00 0.00 42.00 2.27
4667 8917 2.036256 AAGTGGCATGAGCACCCC 59.964 61.111 0.00 0.00 44.61 4.95
4713 8963 0.955905 TTTCTTACGGCTGGCCAAAC 59.044 50.000 7.01 0.92 35.37 2.93
5096 9346 1.819632 CCGGCAAGGTGGTATCAGC 60.820 63.158 0.00 0.00 41.37 4.26
5355 9605 5.057149 GCACTTACTTCACTCCAGAAGAAA 58.943 41.667 10.37 0.00 46.18 2.52
5407 9674 2.664851 TGTCGGTTGCAAGGCGAG 60.665 61.111 0.00 0.00 0.00 5.03
5594 9861 2.413351 CGCTCCGACGTCATGGAT 59.587 61.111 17.16 0.00 32.83 3.41
5600 9867 3.782046 CTCCGACGTCATGGATAAGTTT 58.218 45.455 17.16 0.00 32.83 2.66
5606 9873 5.220340 CGACGTCATGGATAAGTTTAACACC 60.220 44.000 17.16 0.00 0.00 4.16
5705 9972 0.734889 GGTTGGTCATGCTGGATTCG 59.265 55.000 0.00 0.00 0.00 3.34
5786 10053 2.358267 GAGGACCGTGTATGTCTACCTG 59.642 54.545 0.00 0.00 33.22 4.00
5884 10151 1.556564 CACGGACGCTATTTCGATGT 58.443 50.000 0.00 0.00 0.00 3.06
5912 10179 1.146358 GGAACGCGGTGACTGCTATC 61.146 60.000 15.19 11.69 0.00 2.08
6008 10275 5.305585 TGACTGACCAAAAGGATGTTCTAC 58.694 41.667 0.00 0.00 0.00 2.59
6024 10291 2.289467 TCTACCTCTCCTGTCCCTCTT 58.711 52.381 0.00 0.00 0.00 2.85
6040 10307 5.307196 GTCCCTCTTTCCTACATGGCTATTA 59.693 44.000 0.00 0.00 35.26 0.98
6050 10317 8.721133 TCCTACATGGCTATTATGTTCTTCTA 57.279 34.615 0.00 0.00 39.36 2.10
6073 10343 2.439701 TAGACCTGCGCCGTAGCT 60.440 61.111 4.18 0.00 38.13 3.32
6307 10582 4.877378 ACGTATGTGTAACTCCCTTTCA 57.123 40.909 0.00 0.00 38.04 2.69
6328 10603 3.685139 TTTGTTGCAACTGGAAAACCA 57.315 38.095 28.61 3.80 0.00 3.67
6357 10632 7.770433 TCAGTTTCTGTCTTTCAAGAATCTCAA 59.230 33.333 0.00 0.00 36.68 3.02
6358 10633 8.400947 CAGTTTCTGTCTTTCAAGAATCTCAAA 58.599 33.333 0.00 0.00 36.68 2.69
6367 10642 5.804944 TCAAGAATCTCAAAATTTGGGCA 57.195 34.783 5.83 0.00 0.00 5.36
6472 10747 0.723414 CGCGTCTCCTTCGTAGTACA 59.277 55.000 0.00 0.00 0.00 2.90
6528 10803 2.576191 CCCAACCTCAAGTCCCATCTTA 59.424 50.000 0.00 0.00 0.00 2.10
6569 10844 5.287226 AGTACCATTCGATCATTAACCGAC 58.713 41.667 0.00 0.00 31.60 4.79
6574 10849 3.060978 TCGATCATTAACCGACACTCG 57.939 47.619 0.00 0.00 40.07 4.18
6590 10865 3.204306 ACTCGGATAGTGATACGACCA 57.796 47.619 0.00 0.00 43.69 4.02
6596 10871 1.671979 TAGTGATACGACCACCCTCG 58.328 55.000 0.00 0.00 39.68 4.63
6607 10882 0.745845 CCACCCTCGCTTTCCATCAG 60.746 60.000 0.00 0.00 0.00 2.90
6643 10918 1.181098 ACCACCATTTCTGTGCAGCC 61.181 55.000 0.00 0.00 32.30 4.85
6656 10931 4.022935 TCTGTGCAGCCAGTTTAATTTCAG 60.023 41.667 9.83 0.00 34.02 3.02
6705 10980 0.322975 CCCTGGTTGGTGTGAGAGAG 59.677 60.000 0.00 0.00 0.00 3.20
6711 10986 3.945285 TGGTTGGTGTGAGAGAGAAAAAC 59.055 43.478 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.952978 AGAGAGGAACGTAGATTGCGAT 59.047 45.455 0.00 0.00 0.00 4.58
1 2 2.366533 AGAGAGGAACGTAGATTGCGA 58.633 47.619 0.00 0.00 0.00 5.10
2 3 2.853731 AGAGAGGAACGTAGATTGCG 57.146 50.000 0.00 0.00 0.00 4.85
3 4 4.504826 GCTAAAGAGAGGAACGTAGATTGC 59.495 45.833 0.00 0.00 0.00 3.56
4 5 5.897050 AGCTAAAGAGAGGAACGTAGATTG 58.103 41.667 0.00 0.00 0.00 2.67
32 1671 4.740822 GGGCAATGGTCACCGGCT 62.741 66.667 0.00 0.00 0.00 5.52
58 1697 2.202824 CCGGCCGCAACGAATCTA 60.203 61.111 22.85 0.00 0.00 1.98
86 1725 1.072159 GATGGAATGGGAGGAGGCG 59.928 63.158 0.00 0.00 0.00 5.52
115 1754 1.932156 AAACAGGGCAGTGTCCACCA 61.932 55.000 17.90 0.00 0.00 4.17
118 1757 1.150536 GGAAACAGGGCAGTGTCCA 59.849 57.895 17.90 0.00 44.02 4.02
122 1761 2.317609 CGACGGAAACAGGGCAGTG 61.318 63.158 0.00 0.00 0.00 3.66
124 1763 0.673644 AATCGACGGAAACAGGGCAG 60.674 55.000 0.00 0.00 0.00 4.85
171 1864 0.934496 TGCGACAGAACGGAACAAAG 59.066 50.000 0.00 0.00 0.00 2.77
330 2771 7.658179 TGCAGACTAGTTCACTCTATTTTTG 57.342 36.000 0.00 0.00 0.00 2.44
342 2783 4.635223 TCCATATGCATGCAGACTAGTTC 58.365 43.478 26.69 0.00 0.00 3.01
346 2787 5.718607 AGTATCTCCATATGCATGCAGACTA 59.281 40.000 26.69 14.12 31.66 2.59
348 2789 4.829968 AGTATCTCCATATGCATGCAGAC 58.170 43.478 26.69 6.86 31.66 3.51
371 2812 7.470900 GCACTCTTCTACGTTGTACTAGTATT 58.529 38.462 5.75 0.00 0.00 1.89
374 2815 4.142945 CGCACTCTTCTACGTTGTACTAGT 60.143 45.833 0.00 0.00 0.00 2.57
375 2816 4.332788 CGCACTCTTCTACGTTGTACTAG 58.667 47.826 0.00 0.00 0.00 2.57
379 2820 2.153645 TCCGCACTCTTCTACGTTGTA 58.846 47.619 0.00 0.00 0.00 2.41
380 2821 0.956633 TCCGCACTCTTCTACGTTGT 59.043 50.000 0.00 0.00 0.00 3.32
381 2822 2.060326 TTCCGCACTCTTCTACGTTG 57.940 50.000 0.00 0.00 0.00 4.10
382 2823 3.314541 AATTCCGCACTCTTCTACGTT 57.685 42.857 0.00 0.00 0.00 3.99
383 2824 2.993899 CAAATTCCGCACTCTTCTACGT 59.006 45.455 0.00 0.00 0.00 3.57
404 2845 6.341316 TCTCAAAGCACTATCTATGGTGAAC 58.659 40.000 10.29 0.00 41.19 3.18
417 2858 2.430465 ACATGCGAATCTCAAAGCACT 58.570 42.857 0.00 0.00 42.73 4.40
534 3321 7.953752 AGACTTATATTTAGGAACGAAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
536 3323 8.959705 AAAGACTTATATTTAGGAACGAAGGG 57.040 34.615 0.00 0.00 0.00 3.95
608 3395 9.988815 GGAGCAAAATAAGTGAATCTATCTCTA 57.011 33.333 0.00 0.00 31.77 2.43
609 3396 7.655328 CGGAGCAAAATAAGTGAATCTATCTCT 59.345 37.037 0.00 0.00 33.37 3.10
610 3397 7.439655 ACGGAGCAAAATAAGTGAATCTATCTC 59.560 37.037 0.00 0.00 0.00 2.75
611 3398 7.275920 ACGGAGCAAAATAAGTGAATCTATCT 58.724 34.615 0.00 0.00 0.00 1.98
612 3399 7.484035 ACGGAGCAAAATAAGTGAATCTATC 57.516 36.000 0.00 0.00 0.00 2.08
613 3400 8.993121 CATACGGAGCAAAATAAGTGAATCTAT 58.007 33.333 0.00 0.00 0.00 1.98
614 3401 7.985184 ACATACGGAGCAAAATAAGTGAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
615 3402 6.823689 ACATACGGAGCAAAATAAGTGAATCT 59.176 34.615 0.00 0.00 0.00 2.40
616 3403 7.016361 ACATACGGAGCAAAATAAGTGAATC 57.984 36.000 0.00 0.00 0.00 2.52
617 3404 7.769044 ACTACATACGGAGCAAAATAAGTGAAT 59.231 33.333 0.00 0.00 0.00 2.57
618 3405 7.101054 ACTACATACGGAGCAAAATAAGTGAA 58.899 34.615 0.00 0.00 0.00 3.18
619 3406 6.636705 ACTACATACGGAGCAAAATAAGTGA 58.363 36.000 0.00 0.00 0.00 3.41
620 3407 6.533723 TGACTACATACGGAGCAAAATAAGTG 59.466 38.462 0.00 0.00 0.00 3.16
621 3408 6.534079 GTGACTACATACGGAGCAAAATAAGT 59.466 38.462 0.00 0.00 0.00 2.24
622 3409 6.757010 AGTGACTACATACGGAGCAAAATAAG 59.243 38.462 0.00 0.00 0.00 1.73
623 3410 6.636705 AGTGACTACATACGGAGCAAAATAA 58.363 36.000 0.00 0.00 0.00 1.40
624 3411 6.216801 AGTGACTACATACGGAGCAAAATA 57.783 37.500 0.00 0.00 0.00 1.40
625 3412 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
626 3413 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
627 3414 4.530710 AAGTGACTACATACGGAGCAAA 57.469 40.909 0.00 0.00 0.00 3.68
628 3415 5.847111 ATAAGTGACTACATACGGAGCAA 57.153 39.130 0.00 0.00 0.00 3.91
629 3416 5.358725 TCAATAAGTGACTACATACGGAGCA 59.641 40.000 0.00 0.00 0.00 4.26
630 3417 5.828747 TCAATAAGTGACTACATACGGAGC 58.171 41.667 0.00 0.00 0.00 4.70
631 3418 8.873215 ATTTCAATAAGTGACTACATACGGAG 57.127 34.615 0.00 0.00 35.39 4.63
632 3419 8.692710 AGATTTCAATAAGTGACTACATACGGA 58.307 33.333 0.00 0.00 35.39 4.69
633 3420 8.873215 AGATTTCAATAAGTGACTACATACGG 57.127 34.615 0.00 0.00 35.39 4.02
634 3421 9.737427 AGAGATTTCAATAAGTGACTACATACG 57.263 33.333 0.00 0.00 35.39 3.06
661 3448 8.520351 CCTCCGTTCCAAAATATAAGTCTTTTT 58.480 33.333 0.00 0.00 0.00 1.94
662 3449 7.122204 CCCTCCGTTCCAAAATATAAGTCTTTT 59.878 37.037 0.00 0.00 0.00 2.27
663 3450 6.602009 CCCTCCGTTCCAAAATATAAGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
664 3451 6.069847 TCCCTCCGTTCCAAAATATAAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
665 3452 5.427481 TCCCTCCGTTCCAAAATATAAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
666 3453 5.677567 TCCCTCCGTTCCAAAATATAAGTC 58.322 41.667 0.00 0.00 0.00 3.01
667 3454 5.191124 ACTCCCTCCGTTCCAAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
668 3455 5.681639 ACTCCCTCCGTTCCAAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
669 3456 5.703730 ACTCCCTCCGTTCCAAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
670 3457 6.811634 TTACTCCCTCCGTTCCAAAATATA 57.188 37.500 0.00 0.00 0.00 0.86
671 3458 5.703730 TTACTCCCTCCGTTCCAAAATAT 57.296 39.130 0.00 0.00 0.00 1.28
672 3459 5.703730 ATTACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
673 3460 4.586306 ATTACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
674 3461 4.376225 AATTACTCCCTCCGTTCCAAAA 57.624 40.909 0.00 0.00 0.00 2.44
675 3462 5.247862 GTTAATTACTCCCTCCGTTCCAAA 58.752 41.667 0.00 0.00 0.00 3.28
676 3463 4.621274 CGTTAATTACTCCCTCCGTTCCAA 60.621 45.833 0.00 0.00 0.00 3.53
677 3464 3.119029 CGTTAATTACTCCCTCCGTTCCA 60.119 47.826 0.00 0.00 0.00 3.53
678 3465 3.131046 TCGTTAATTACTCCCTCCGTTCC 59.869 47.826 0.00 0.00 0.00 3.62
679 3466 4.376340 TCGTTAATTACTCCCTCCGTTC 57.624 45.455 0.00 0.00 0.00 3.95
680 3467 4.403432 TGATCGTTAATTACTCCCTCCGTT 59.597 41.667 0.00 0.00 0.00 4.44
681 3468 3.956199 TGATCGTTAATTACTCCCTCCGT 59.044 43.478 0.00 0.00 0.00 4.69
682 3469 4.579454 TGATCGTTAATTACTCCCTCCG 57.421 45.455 0.00 0.00 0.00 4.63
683 3470 5.915175 ACTTGATCGTTAATTACTCCCTCC 58.085 41.667 0.00 0.00 0.00 4.30
684 3471 7.714703 ACTACTTGATCGTTAATTACTCCCTC 58.285 38.462 0.00 0.00 0.00 4.30
685 3472 7.657023 ACTACTTGATCGTTAATTACTCCCT 57.343 36.000 0.00 0.00 0.00 4.20
686 3473 8.628280 ACTACTACTTGATCGTTAATTACTCCC 58.372 37.037 0.00 0.00 0.00 4.30
708 3495 7.978975 AGAGCAACAAGATCTAGATTCAACTAC 59.021 37.037 6.70 0.00 42.21 2.73
713 3500 7.164122 ACAAAGAGCAACAAGATCTAGATTCA 58.836 34.615 6.70 0.00 43.49 2.57
726 3513 8.031864 TCAAAATGTCTAAAACAAAGAGCAACA 58.968 29.630 0.00 0.00 42.37 3.33
737 3524 6.884187 TCTACAGCGTCAAAATGTCTAAAAC 58.116 36.000 0.00 0.00 0.00 2.43
753 3540 7.772332 ACCTTAATGAAGTTAATCTACAGCG 57.228 36.000 0.00 0.00 32.12 5.18
769 3557 8.162878 AGCACATCTCATTTCATACCTTAATG 57.837 34.615 0.00 0.00 0.00 1.90
801 3590 1.061131 GTTCGCATGTTCTCACCATCG 59.939 52.381 0.00 0.00 0.00 3.84
807 3596 2.542020 TTGAGGTTCGCATGTTCTCA 57.458 45.000 0.00 0.00 33.30 3.27
821 3610 2.086869 ACATCGGTTCATGCTTTGAGG 58.913 47.619 0.00 0.00 35.27 3.86
841 3630 5.390387 GCCATATACAACCCCTAAATCCAA 58.610 41.667 0.00 0.00 0.00 3.53
899 3688 8.589629 GGAAATCTGAATTTTCGATCAACAATG 58.410 33.333 0.00 0.00 35.21 2.82
925 3715 7.967854 TGTAATGGTTTGCTTCATATCGAAAAG 59.032 33.333 0.00 0.00 31.71 2.27
994 3788 2.408050 CGTATCTTCAGCCATGTAGCC 58.592 52.381 0.00 0.00 0.00 3.93
1026 3820 0.527169 GACTACGGCGACCTTTAGGC 60.527 60.000 16.62 1.98 39.32 3.93
1044 3838 2.567169 ACGAGTTTCACTGATGGGATGA 59.433 45.455 0.00 0.00 0.00 2.92
1069 3863 6.892658 AATGGATAATTGCCACGCTATTTA 57.107 33.333 4.23 0.00 38.44 1.40
1072 3866 6.264292 TGTTTAATGGATAATTGCCACGCTAT 59.736 34.615 4.23 0.00 38.44 2.97
1077 3871 6.762661 AGCAATGTTTAATGGATAATTGCCAC 59.237 34.615 13.00 0.00 37.57 5.01
1225 4019 3.083997 GACCGCCATCCCTGACCT 61.084 66.667 0.00 0.00 0.00 3.85
1252 4046 7.973048 ACTGTGGAACCAGAGTAGATAAATA 57.027 36.000 19.58 0.00 46.59 1.40
1322 4119 1.397692 GAGCAGTCGAAGTACGTAGCT 59.602 52.381 0.00 0.00 42.65 3.32
1358 4155 6.946340 TGATTGTACACAGATATCAACACCT 58.054 36.000 5.32 0.00 0.00 4.00
1416 4213 7.942341 AGTAGGTTGACATACCAAAGATTTCAA 59.058 33.333 2.65 0.00 40.82 2.69
1569 4370 3.119065 TGCGGAACAAACGATGGTATAGA 60.119 43.478 0.00 0.00 0.00 1.98
1571 4372 2.931325 GTGCGGAACAAACGATGGTATA 59.069 45.455 0.00 0.00 0.00 1.47
1587 4388 3.666883 TTGCTATTAAATGACGTGCGG 57.333 42.857 0.00 0.00 0.00 5.69
1630 4434 0.593128 ACACAAGAGGCACGCATTTC 59.407 50.000 0.00 0.00 0.00 2.17
1670 4475 8.496916 AGTTCCTTCTTTTGTAGTAGGGTTTTA 58.503 33.333 0.00 0.00 40.76 1.52
1762 4589 7.955918 TGAGACAGTAACATCTGCATGTATAT 58.044 34.615 0.00 0.00 42.89 0.86
1812 4639 9.902684 AGACACTGATCTTCAATATGATTTCTT 57.097 29.630 0.00 0.00 0.00 2.52
2172 4999 4.883585 GGTGTGCTCATGGAATCAAGATTA 59.116 41.667 0.00 0.00 0.00 1.75
2256 5083 7.939039 GTGACAGGGATATTTCTGATAATTGGA 59.061 37.037 11.61 0.00 35.20 3.53
2314 5141 1.202698 AGCCTTCATAGTGAATCCCGC 60.203 52.381 0.00 0.00 35.59 6.13
2315 5142 2.103094 TCAGCCTTCATAGTGAATCCCG 59.897 50.000 0.00 0.00 35.59 5.14
2317 5144 4.574013 CAGTTCAGCCTTCATAGTGAATCC 59.426 45.833 0.00 0.00 35.59 3.01
2338 5165 3.689347 TGTCTTCCAATTGACCATCCAG 58.311 45.455 7.12 0.00 32.67 3.86
2370 5197 2.975489 ACCATCCAACTCAGTCTTGACT 59.025 45.455 0.00 0.00 0.00 3.41
2394 5221 6.869315 TGTTCATACGAGAAAACATCCAAA 57.131 33.333 0.00 0.00 0.00 3.28
2493 5320 0.898320 ATCTCTTCCACCTGTCACGG 59.102 55.000 0.00 0.00 0.00 4.94
2752 5579 3.307480 GGACCCGGAGATCTTTCTTCAAA 60.307 47.826 0.73 0.00 30.30 2.69
2888 5715 4.644163 TCCTTCCTTTTCCGACCAAATA 57.356 40.909 0.00 0.00 0.00 1.40
2916 5755 8.044060 TCATTTTCTTGTATTCTCTTTCGCAT 57.956 30.769 0.00 0.00 0.00 4.73
3051 5890 0.809385 CAGAAGAAGCTGGCCATGTG 59.191 55.000 5.51 0.00 32.26 3.21
3064 5903 3.447229 TGACTGTCATTATCGGCAGAAGA 59.553 43.478 6.36 0.00 33.57 2.87
3065 5904 3.785486 TGACTGTCATTATCGGCAGAAG 58.215 45.455 6.36 0.00 33.57 2.85
3066 5905 3.885724 TGACTGTCATTATCGGCAGAA 57.114 42.857 6.36 0.00 33.57 3.02
3072 5911 7.757173 TCTTTCTCTTCTTGACTGTCATTATCG 59.243 37.037 11.86 0.38 0.00 2.92
3118 5957 4.156739 GGTCAATGAGTGGTCCATTTCTTC 59.843 45.833 0.00 0.00 32.40 2.87
3196 6035 8.713271 AGTTCTAAATCATTTCACGAGAAAGTC 58.287 33.333 13.37 0.00 46.13 3.01
3325 6167 2.964740 TCAGGAATTCAGAACGAGCAG 58.035 47.619 7.93 0.00 0.00 4.24
3331 6173 5.431765 TCAGGCTTATCAGGAATTCAGAAC 58.568 41.667 7.93 0.00 0.00 3.01
3390 7623 9.396022 CCAAAAAGTAGCTCATAATTCCTAAGA 57.604 33.333 0.00 0.00 0.00 2.10
3445 7689 9.604626 GATCATAAGGAAATATCAAGCGAAAAG 57.395 33.333 0.00 0.00 0.00 2.27
3450 7694 6.402983 GGCAGATCATAAGGAAATATCAAGCG 60.403 42.308 0.00 0.00 0.00 4.68
3468 7712 5.357878 TGATTGACCAATTTAGTGGCAGATC 59.642 40.000 0.00 0.00 43.00 2.75
3486 7731 4.058124 CACAGTTCGTCTTTCCTGATTGA 58.942 43.478 0.00 0.00 0.00 2.57
3505 7750 4.444536 ACAACTTTTAGCGAGTTACCACA 58.555 39.130 0.00 0.00 35.68 4.17
3510 7755 8.517878 AGTAGATGTACAACTTTTAGCGAGTTA 58.482 33.333 11.21 0.00 35.68 2.24
3720 7965 1.603678 GGCATTATGATTGCAAGGGCG 60.604 52.381 4.94 0.00 45.35 6.13
3721 7966 1.603678 CGGCATTATGATTGCAAGGGC 60.604 52.381 4.94 0.00 41.95 5.19
3722 7967 1.682854 ACGGCATTATGATTGCAAGGG 59.317 47.619 4.94 0.00 41.95 3.95
3723 7968 2.358582 TCACGGCATTATGATTGCAAGG 59.641 45.455 4.94 0.00 41.95 3.61
3789 8039 2.286365 TTCTCCAAGTGCCGGAAAAT 57.714 45.000 5.05 0.00 30.33 1.82
3794 8044 2.678336 GTTCTTATTCTCCAAGTGCCGG 59.322 50.000 0.00 0.00 0.00 6.13
3803 8053 8.593492 AAAATTTGTTGCTGTTCTTATTCTCC 57.407 30.769 0.00 0.00 0.00 3.71
3818 8068 6.979817 TGAATGTGAGTCCTGAAAATTTGTTG 59.020 34.615 0.00 0.00 0.00 3.33
3819 8069 7.068593 TCTGAATGTGAGTCCTGAAAATTTGTT 59.931 33.333 0.00 0.00 0.00 2.83
3948 8198 7.826744 TGCTTTATCTCCACACATACAACATTA 59.173 33.333 0.00 0.00 0.00 1.90
4001 8251 9.305925 AGTGAAAAGAAGTTGAAATTGCTTTAG 57.694 29.630 0.00 0.00 0.00 1.85
4103 8353 1.794714 GGCATCCAGGTCTCTCCTTA 58.205 55.000 0.00 0.00 45.67 2.69
4135 8385 7.499292 AGAAGGATCAAGTACAAGATCATCAG 58.501 38.462 21.64 0.00 41.84 2.90
4271 8521 5.612276 CGCCAAGTTTTTCCAAATGAATTCG 60.612 40.000 0.04 0.00 31.67 3.34
4439 8689 4.798574 CAGATTTTGGAGTAAGCACCAAC 58.201 43.478 0.00 0.00 43.32 3.77
4531 8781 1.774110 TGGCTTGCCTCTTTTGTCAA 58.226 45.000 13.18 0.00 0.00 3.18
4601 8851 3.366985 GGCAAATACTTTTCCAGTTCGGG 60.367 47.826 0.00 0.00 36.88 5.14
4664 8914 1.065854 GTCATGAGGAGAACACTGGGG 60.066 57.143 0.00 0.00 0.00 4.96
4667 8917 5.105595 TGAGTATGTCATGAGGAGAACACTG 60.106 44.000 0.00 0.00 0.00 3.66
4713 8963 1.129998 CTGCGGCATTCTTGAGTCTTG 59.870 52.381 1.75 0.00 0.00 3.02
4793 9043 0.257328 TGTTGCTCCTTGGGTTGTGA 59.743 50.000 0.00 0.00 0.00 3.58
4802 9052 4.326504 CAACTTGGATTTGTTGCTCCTT 57.673 40.909 0.00 0.00 37.36 3.36
4824 9074 1.153289 CCTTCATCAGCACCCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
5177 9427 5.599732 TCAGTGGGTTTCATGAAAATTGTG 58.400 37.500 22.07 15.07 31.33 3.33
5355 9605 7.607991 CCTCTTGTACCTGTCAACTTTATGAAT 59.392 37.037 0.00 0.00 0.00 2.57
5407 9674 0.798776 CAGCAGGTCGATGACAAACC 59.201 55.000 0.00 0.00 33.68 3.27
5420 9687 2.661566 CGACGACTTGTGCAGCAGG 61.662 63.158 0.00 0.00 0.00 4.85
5594 9861 5.051816 CCTTGACTGTCGGTGTTAAACTTA 58.948 41.667 2.98 0.00 0.00 2.24
5600 9867 3.890756 TCTTACCTTGACTGTCGGTGTTA 59.109 43.478 15.09 1.26 32.36 2.41
5606 9873 3.367498 CCTTCCTCTTACCTTGACTGTCG 60.367 52.174 2.98 0.00 0.00 4.35
5786 10053 0.107017 ATGTACCAGATGCCACCAGC 60.107 55.000 0.00 0.00 44.14 4.85
5912 10179 3.715495 CTCCTTGAGAAGACCATCATCG 58.285 50.000 0.00 0.00 0.00 3.84
6008 10275 1.199615 GGAAAGAGGGACAGGAGAGG 58.800 60.000 0.00 0.00 0.00 3.69
6024 10291 8.034313 AGAAGAACATAATAGCCATGTAGGAA 57.966 34.615 0.00 0.00 41.22 3.36
6040 10307 6.578023 GCAGGTCTACAGATTAGAAGAACAT 58.422 40.000 0.00 0.00 0.00 2.71
6050 10317 1.141881 CGGCGCAGGTCTACAGATT 59.858 57.895 10.83 0.00 0.00 2.40
6307 10582 4.213564 TGGTTTTCCAGTTGCAACAAAT 57.786 36.364 30.11 8.22 46.22 2.32
6328 10603 7.718753 AGATTCTTGAAAGACAGAAACTGACAT 59.281 33.333 5.76 0.00 34.13 3.06
6357 10632 6.408107 AGAATTTTGCAATTGCCCAAATTT 57.592 29.167 31.29 24.47 40.24 1.82
6358 10633 6.408107 AAGAATTTTGCAATTGCCCAAATT 57.592 29.167 31.27 31.27 41.56 1.82
6367 10642 7.274447 TCTTGTCTTGGAAGAATTTTGCAATT 58.726 30.769 0.00 0.00 36.68 2.32
6472 10747 2.176798 TGGTTTGACAGGGTGAAGGATT 59.823 45.455 0.00 0.00 0.00 3.01
6528 10803 6.775708 TGGTACTTCTAACTAAAAGGCACAT 58.224 36.000 0.00 0.00 0.00 3.21
6574 10849 2.557490 GAGGGTGGTCGTATCACTATCC 59.443 54.545 0.00 0.00 35.61 2.59
6590 10865 1.078143 GCTGATGGAAAGCGAGGGT 60.078 57.895 0.00 0.00 0.00 4.34
6643 10918 7.796838 TGTTCGAGATGACTGAAATTAAACTG 58.203 34.615 0.00 0.00 0.00 3.16
6656 10931 6.148811 TGGGAGTTAATTTTGTTCGAGATGAC 59.851 38.462 0.00 0.00 0.00 3.06
6705 10980 9.416284 TCTTTTACCTATCCCATATGGTTTTTC 57.584 33.333 20.46 0.00 34.33 2.29
6711 10986 8.760980 TTTGTTCTTTTACCTATCCCATATGG 57.239 34.615 15.41 15.41 0.00 2.74


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

AutoCloner maintained by Alex Coulton.