Multiple sequence alignment - TraesCS2D01G402400

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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 TraesCS2D01G402400 chr2D 100.000 7549 0 0 1 7549 517097063 517089515 0.000000e+00 13941.0
1 TraesCS2D01G402400 chr2D 88.859 377 25 11 7116 7491 517056882 517056522 1.490000e-121 448.0
2 TraesCS2D01G402400 chr2D 88.400 250 17 7 6562 6802 517084345 517084099 2.660000e-74 291.0
3 TraesCS2D01G402400 chr2D 83.333 228 26 3 6797 7019 517083950 517083730 4.620000e-47 200.0
4 TraesCS2D01G402400 chr2B 91.239 4052 173 49 1 3957 608947022 608943058 0.000000e+00 5349.0
5 TraesCS2D01G402400 chr2B 93.719 1210 70 4 5480 6688 608943074 608941870 0.000000e+00 1808.0
6 TraesCS2D01G402400 chr2B 87.500 504 45 10 4981 5467 23377738 23378240 3.950000e-157 566.0
7 TraesCS2D01G402400 chr2B 86.219 283 33 3 6742 7019 608941870 608941589 1.230000e-77 302.0
8 TraesCS2D01G402400 chr2B 96.154 182 7 0 7088 7269 608940669 608940488 1.590000e-76 298.0
9 TraesCS2D01G402400 chr2A 90.394 2946 169 56 132 3040 661456850 661453982 0.000000e+00 3768.0
10 TraesCS2D01G402400 chr2A 94.671 1520 59 7 3961 5461 514815054 514816570 0.000000e+00 2338.0
11 TraesCS2D01G402400 chr2A 88.946 1556 123 13 5482 7019 661452912 661451388 0.000000e+00 1875.0
12 TraesCS2D01G402400 chr2A 91.932 942 49 7 3032 3963 661453816 661452892 0.000000e+00 1293.0
13 TraesCS2D01G402400 chr2A 88.548 489 23 12 7073 7549 661451087 661450620 5.110000e-156 562.0
14 TraesCS2D01G402400 chr2A 86.290 372 25 14 7180 7549 661406369 661406022 1.540000e-101 381.0
15 TraesCS2D01G402400 chr2A 90.541 148 5 2 1 143 661457300 661457157 3.600000e-43 187.0
16 TraesCS2D01G402400 chr6A 94.889 1526 56 8 3949 5455 558104358 558102836 0.000000e+00 2366.0
17 TraesCS2D01G402400 chr3D 94.612 1522 53 17 3965 5461 4350236 4348719 0.000000e+00 2329.0
18 TraesCS2D01G402400 chr3D 93.508 1525 72 15 3958 5458 454212824 454211303 0.000000e+00 2242.0
19 TraesCS2D01G402400 chr5D 95.041 1452 62 6 3961 5406 428380587 428379140 0.000000e+00 2274.0
20 TraesCS2D01G402400 chr3A 93.721 1513 74 5 3960 5452 208120071 208121582 0.000000e+00 2248.0
21 TraesCS2D01G402400 chr3A 92.622 1518 92 4 3960 5458 493859247 493857731 0.000000e+00 2165.0
22 TraesCS2D01G402400 chr7D 93.570 1524 61 12 3959 5461 69065077 69066584 0.000000e+00 2237.0
23 TraesCS2D01G402400 chr7A 93.602 1516 59 13 3959 5455 666011577 666013073 0.000000e+00 2228.0
24 TraesCS2D01G402400 chr1D 93.026 1520 73 9 3958 5461 490442946 490441444 0.000000e+00 2189.0
25 TraesCS2D01G402400 chr4D 91.924 1523 80 20 3959 5461 489335015 489333516 0.000000e+00 2091.0
26 TraesCS2D01G402400 chr4A 91.399 1523 95 13 3959 5462 708576914 708578419 0.000000e+00 2054.0
27 TraesCS2D01G402400 chr6D 94.874 1229 51 7 3942 5160 14595160 14596386 0.000000e+00 1910.0
28 TraesCS2D01G402400 chr7B 88.136 59 7 0 7425 7483 205387645 205387703 3.780000e-08 71.3


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 TraesCS2D01G402400 chr2D 517089515 517097063 7548 True 13941.00 13941 100.00000 1 7549 1 chr2D.!!$R2 7548
1 TraesCS2D01G402400 chr2D 517083730 517084345 615 True 245.50 291 85.86650 6562 7019 2 chr2D.!!$R3 457
2 TraesCS2D01G402400 chr2B 608940488 608947022 6534 True 1939.25 5349 91.83275 1 7269 4 chr2B.!!$R1 7268
3 TraesCS2D01G402400 chr2B 23377738 23378240 502 False 566.00 566 87.50000 4981 5467 1 chr2B.!!$F1 486
4 TraesCS2D01G402400 chr2A 514815054 514816570 1516 False 2338.00 2338 94.67100 3961 5461 1 chr2A.!!$F1 1500
5 TraesCS2D01G402400 chr2A 661450620 661457300 6680 True 1537.00 3768 90.07220 1 7549 5 chr2A.!!$R2 7548
6 TraesCS2D01G402400 chr6A 558102836 558104358 1522 True 2366.00 2366 94.88900 3949 5455 1 chr6A.!!$R1 1506
7 TraesCS2D01G402400 chr3D 4348719 4350236 1517 True 2329.00 2329 94.61200 3965 5461 1 chr3D.!!$R1 1496
8 TraesCS2D01G402400 chr3D 454211303 454212824 1521 True 2242.00 2242 93.50800 3958 5458 1 chr3D.!!$R2 1500
9 TraesCS2D01G402400 chr5D 428379140 428380587 1447 True 2274.00 2274 95.04100 3961 5406 1 chr5D.!!$R1 1445
10 TraesCS2D01G402400 chr3A 208120071 208121582 1511 False 2248.00 2248 93.72100 3960 5452 1 chr3A.!!$F1 1492
11 TraesCS2D01G402400 chr3A 493857731 493859247 1516 True 2165.00 2165 92.62200 3960 5458 1 chr3A.!!$R1 1498
12 TraesCS2D01G402400 chr7D 69065077 69066584 1507 False 2237.00 2237 93.57000 3959 5461 1 chr7D.!!$F1 1502
13 TraesCS2D01G402400 chr7A 666011577 666013073 1496 False 2228.00 2228 93.60200 3959 5455 1 chr7A.!!$F1 1496
14 TraesCS2D01G402400 chr1D 490441444 490442946 1502 True 2189.00 2189 93.02600 3958 5461 1 chr1D.!!$R1 1503
15 TraesCS2D01G402400 chr4D 489333516 489335015 1499 True 2091.00 2091 91.92400 3959 5461 1 chr4D.!!$R1 1502
16 TraesCS2D01G402400 chr4A 708576914 708578419 1505 False 2054.00 2054 91.39900 3959 5462 1 chr4A.!!$F1 1503
17 TraesCS2D01G402400 chr6D 14595160 14596386 1226 False 1910.00 1910 94.87400 3942 5160 1 chr6D.!!$F1 1218

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
427 754 0.111832 ACCTCACACCTGGTAGTCGA 59.888 55.0 0.0 1.3 34.36 4.20 F
2403 2816 0.166814 GTGCAAAGACGAGGACATGC 59.833 55.0 0.0 0.0 0.00 4.06 F
2420 2833 0.107214 TGCTGGGCATAGTAGTTGGC 60.107 55.0 0.0 0.0 38.82 4.52 F
3834 4456 0.318762 GGTCGGCCAGTCATAGGATC 59.681 60.0 0.0 0.0 34.09 3.36 F
5007 5645 0.251297 CCAAGCACCACCAGATCCAA 60.251 55.0 0.0 0.0 0.00 3.53 F
6035 6768 0.823356 TGTGGGAGCAGCAAAACCTC 60.823 55.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 2827 0.036875 CCTTCCCTTCTTCGCCAACT 59.963 55.0 0.0 0.00 0.00 3.16 R
3814 4436 0.398522 ATCCTATGACTGGCCGACCA 60.399 55.0 0.0 0.00 46.51 4.02 R
3873 4500 5.237815 TCGTTAGATTCAAATGTGTGCTCT 58.762 37.5 0.0 0.00 0.00 4.09 R
5466 6199 0.105593 AGAGTCGATACCGGCGAGTA 59.894 55.0 9.3 9.72 46.52 2.59 R
6378 7111 0.396435 TGGACTTGGTGCTCGAACAT 59.604 50.0 0.0 0.00 0.00 2.71 R
6992 7896 0.454196 ACGACCAACACAAAGCAACC 59.546 50.0 0.0 0.00 0.00 3.77 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
125 131 2.025793 TCCCGTCCCAAATTCAATGCTA 60.026 45.455 0.00 0.00 0.00 3.49
127 133 2.223572 CCGTCCCAAATTCAATGCTAGC 60.224 50.000 8.10 8.10 0.00 3.42
128 134 2.684881 CGTCCCAAATTCAATGCTAGCT 59.315 45.455 17.23 0.00 0.00 3.32
129 135 3.242870 CGTCCCAAATTCAATGCTAGCTC 60.243 47.826 17.23 0.00 0.00 4.09
130 136 3.067320 GTCCCAAATTCAATGCTAGCTCC 59.933 47.826 17.23 0.00 0.00 4.70
166 491 2.734175 CGTATCCAAGCTGCACTCGTAA 60.734 50.000 1.02 0.00 0.00 3.18
171 496 3.682858 TCCAAGCTGCACTCGTAAATAAC 59.317 43.478 1.02 0.00 0.00 1.89
176 501 3.621268 GCTGCACTCGTAAATAACCATCA 59.379 43.478 0.00 0.00 0.00 3.07
330 657 4.454319 AGAGCAGAGCAGCGGCAG 62.454 66.667 12.44 1.36 44.61 4.85
425 752 2.767505 CAAACCTCACACCTGGTAGTC 58.232 52.381 0.00 0.00 35.17 2.59
427 754 0.111832 ACCTCACACCTGGTAGTCGA 59.888 55.000 0.00 1.30 34.36 4.20
428 755 1.272536 ACCTCACACCTGGTAGTCGAT 60.273 52.381 0.00 0.00 34.36 3.59
429 756 1.405821 CCTCACACCTGGTAGTCGATC 59.594 57.143 0.00 0.00 0.00 3.69
430 757 1.405821 CTCACACCTGGTAGTCGATCC 59.594 57.143 0.00 0.00 0.00 3.36
431 758 1.182667 CACACCTGGTAGTCGATCCA 58.817 55.000 0.00 0.00 0.00 3.41
432 759 1.135083 CACACCTGGTAGTCGATCCAC 60.135 57.143 0.00 0.00 0.00 4.02
433 760 1.272536 ACACCTGGTAGTCGATCCACT 60.273 52.381 0.00 0.00 0.00 4.00
434 761 1.405821 CACCTGGTAGTCGATCCACTC 59.594 57.143 0.00 0.00 0.00 3.51
507 834 3.842206 ACAAAACCGTATACCCCCAAAA 58.158 40.909 0.00 0.00 0.00 2.44
516 843 2.590282 TACCCCCAAAACCAAGCTAC 57.410 50.000 0.00 0.00 0.00 3.58
517 844 0.178944 ACCCCCAAAACCAAGCTACC 60.179 55.000 0.00 0.00 0.00 3.18
518 845 0.902984 CCCCCAAAACCAAGCTACCC 60.903 60.000 0.00 0.00 0.00 3.69
592 919 1.581447 CCTCGGCCTTTGACAAAGC 59.419 57.895 20.47 15.50 37.18 3.51
593 920 1.207593 CTCGGCCTTTGACAAAGCG 59.792 57.895 20.47 18.52 37.18 4.68
599 926 1.244019 CCTTTGACAAAGCGAGGGGG 61.244 60.000 20.47 4.31 37.18 5.40
615 942 4.500826 GGTCCCCTCCCCTCCCTC 62.501 77.778 0.00 0.00 0.00 4.30
728 1056 2.497138 CACTGTGCTGATTCCACTTCA 58.503 47.619 0.00 0.00 34.38 3.02
817 1167 3.705604 GAAGATCCTTCTCTTCTCTGCG 58.294 50.000 6.58 0.00 45.04 5.18
912 1297 2.031120 CCTTCTGCTTGTTGTTCCCAA 58.969 47.619 0.00 0.00 0.00 4.12
1009 1398 1.369692 CCATAATGCGGGGCGAGTA 59.630 57.895 0.00 0.00 0.00 2.59
1402 1800 2.203167 TCGTCCTCCGGATCCGAG 60.203 66.667 35.42 26.46 42.83 4.63
1406 1804 2.203167 CCTCCGGATCCGAGTCGA 60.203 66.667 35.42 21.55 42.83 4.20
1410 1808 2.716244 CGGATCCGAGTCGACCTG 59.284 66.667 30.62 4.66 42.83 4.00
1918 2325 1.907739 CATTCCGGAGCTGGAGGAA 59.092 57.895 3.34 14.23 46.58 3.36
2020 2427 0.250793 TCGGTGCCGTCAATACCATT 59.749 50.000 10.60 0.00 40.74 3.16
2090 2503 1.075836 AATGTGGCCCCGCTAACAA 59.924 52.632 0.00 0.00 31.55 2.83
2095 2508 1.298667 GGCCCCGCTAACAAGAGAA 59.701 57.895 0.00 0.00 0.00 2.87
2152 2565 2.357760 GCCACCGCGGTTAAGACA 60.358 61.111 32.11 0.00 36.97 3.41
2170 2583 3.365265 CAGCTTGTTCGGGTGGCC 61.365 66.667 0.00 0.00 0.00 5.36
2263 2676 2.230508 CCACGGTGAGCTACTAGTTCAA 59.769 50.000 10.28 0.00 37.20 2.69
2403 2816 0.166814 GTGCAAAGACGAGGACATGC 59.833 55.000 0.00 0.00 0.00 4.06
2420 2833 0.107214 TGCTGGGCATAGTAGTTGGC 60.107 55.000 0.00 0.00 38.82 4.52
2429 2842 3.458189 CATAGTAGTTGGCGAAGAAGGG 58.542 50.000 0.00 0.00 0.00 3.95
2474 2887 2.889512 TCCTTGACACTGGAGAAGCTA 58.110 47.619 0.00 0.00 0.00 3.32
2501 2914 1.273838 TGGGAGAGGAAGCTGTATGGT 60.274 52.381 0.00 0.00 0.00 3.55
2514 2927 3.134804 GCTGTATGGTGAGGTCAAGGTAT 59.865 47.826 0.00 0.00 0.00 2.73
2516 2929 5.012148 GCTGTATGGTGAGGTCAAGGTATAT 59.988 44.000 0.00 0.00 0.00 0.86
2561 2975 2.094182 TGTGAGTAGAAATGGTCTCCGC 60.094 50.000 0.00 0.00 37.84 5.54
2563 2977 2.832129 TGAGTAGAAATGGTCTCCGCTT 59.168 45.455 0.00 0.00 37.84 4.68
2622 3036 5.047377 TGTGCAAGGGGATTTGAATAAGAAC 60.047 40.000 0.00 0.00 0.00 3.01
2691 3123 2.956132 TCTCATCATCTGGGTCCTCTC 58.044 52.381 0.00 0.00 0.00 3.20
2753 3185 4.187694 CTGTGGTCTTCTGGATCTTTAGC 58.812 47.826 0.00 0.00 0.00 3.09
2774 3206 9.886132 TTTAGCTAGACCTTTTATTTAGTCCAG 57.114 33.333 0.00 0.00 0.00 3.86
2886 3320 6.587608 GGGAAGATTTATGTCAAGCAAAAGTG 59.412 38.462 0.00 0.00 0.00 3.16
2889 3323 9.677567 GAAGATTTATGTCAAGCAAAAGTGTTA 57.322 29.630 0.00 0.00 0.00 2.41
2903 3337 6.510960 GCAAAAGTGTTACAATTTTTCGGCAT 60.511 34.615 18.79 0.00 39.13 4.40
2907 3341 5.047377 AGTGTTACAATTTTTCGGCATCCAT 60.047 36.000 0.00 0.00 0.00 3.41
2971 3413 2.242708 TGGTTGGTTGGTTCTGGTACTT 59.757 45.455 0.00 0.00 0.00 2.24
3011 3453 3.838244 TTGTGTGCACTTTAGGAGTCT 57.162 42.857 19.41 0.00 36.10 3.24
3073 3689 7.072263 AGATAAAGATCCACTATGGGAAGTG 57.928 40.000 0.00 0.00 45.33 3.16
3078 3694 4.407296 AGATCCACTATGGGAAGTGTCTTC 59.593 45.833 3.56 1.39 44.45 2.87
3114 3730 4.068599 GGCTGGATATAGAAGAACTTGCC 58.931 47.826 0.00 0.00 0.00 4.52
3121 3737 8.055181 TGGATATAGAAGAACTTGCCAGAAAAT 58.945 33.333 0.00 0.00 0.00 1.82
3145 3761 2.287909 GGTGCGGTTGCTTGAACAATTA 60.288 45.455 0.00 0.00 43.34 1.40
3211 3832 8.272173 AGGTATGCTAAGTTGGCTATTCTTAAA 58.728 33.333 12.78 0.00 0.00 1.52
3212 3833 8.899771 GGTATGCTAAGTTGGCTATTCTTAAAA 58.100 33.333 12.78 0.00 0.00 1.52
3334 3956 4.263462 TGACTGGATCTGCCACTTTATTGT 60.263 41.667 0.00 0.00 43.33 2.71
3446 4068 9.314133 ACTAGTTCAATAGATCATGGCTATACA 57.686 33.333 8.73 0.00 0.00 2.29
3449 4071 8.600668 AGTTCAATAGATCATGGCTATACATGT 58.399 33.333 2.69 2.69 46.39 3.21
3450 4072 8.663025 GTTCAATAGATCATGGCTATACATGTG 58.337 37.037 9.11 0.00 46.39 3.21
3451 4073 7.333323 TCAATAGATCATGGCTATACATGTGG 58.667 38.462 9.11 0.00 46.39 4.17
3452 4074 6.881067 ATAGATCATGGCTATACATGTGGT 57.119 37.500 9.11 0.00 46.39 4.16
3453 4075 5.157940 AGATCATGGCTATACATGTGGTC 57.842 43.478 9.11 0.69 46.39 4.02
3454 4076 4.594491 AGATCATGGCTATACATGTGGTCA 59.406 41.667 9.11 6.82 46.39 4.02
3455 4077 4.071961 TCATGGCTATACATGTGGTCAC 57.928 45.455 9.11 0.00 46.39 3.67
3456 4078 3.141398 CATGGCTATACATGTGGTCACC 58.859 50.000 9.11 4.26 42.48 4.02
3457 4079 2.192263 TGGCTATACATGTGGTCACCA 58.808 47.619 9.11 6.96 0.00 4.17
3458 4080 2.573915 TGGCTATACATGTGGTCACCAA 59.426 45.455 9.11 0.00 34.18 3.67
3459 4081 3.009584 TGGCTATACATGTGGTCACCAAA 59.990 43.478 9.11 0.00 34.18 3.28
3531 4153 3.909430 TGAAGAGAAGATGCGTTTACGT 58.091 40.909 4.05 0.00 42.22 3.57
3666 4288 0.950836 TTCGTGTCATTGCCAAGGTG 59.049 50.000 0.00 0.00 0.00 4.00
3747 4369 3.259123 TCCAAGGGTACGTCTCCTTTTAC 59.741 47.826 16.72 0.00 41.06 2.01
3814 4436 6.740411 TTCTTGCTGCAAAATGTTCTTTTT 57.260 29.167 16.74 0.00 0.00 1.94
3830 4452 2.107950 TTTTGGTCGGCCAGTCATAG 57.892 50.000 9.61 0.00 46.91 2.23
3834 4456 0.318762 GGTCGGCCAGTCATAGGATC 59.681 60.000 0.00 0.00 34.09 3.36
3835 4457 1.040646 GTCGGCCAGTCATAGGATCA 58.959 55.000 2.24 0.00 0.00 2.92
3864 4486 7.121759 ACTGTTAATTTCATCTTATGCACTGCT 59.878 33.333 1.98 0.00 0.00 4.24
3897 4524 5.349817 AGAGCACACATTTGAATCTAACGAG 59.650 40.000 0.00 0.00 0.00 4.18
3940 4567 4.593956 AGGATTGTTCCAAGAATCTGTCC 58.406 43.478 8.59 0.00 45.30 4.02
3941 4568 3.375299 GGATTGTTCCAAGAATCTGTCCG 59.625 47.826 8.59 0.00 42.12 4.79
3942 4569 3.762407 TTGTTCCAAGAATCTGTCCGA 57.238 42.857 0.00 0.00 0.00 4.55
3943 4570 3.040147 TGTTCCAAGAATCTGTCCGAC 57.960 47.619 0.00 0.00 0.00 4.79
3944 4571 2.632996 TGTTCCAAGAATCTGTCCGACT 59.367 45.455 0.00 0.00 0.00 4.18
3945 4572 3.254892 GTTCCAAGAATCTGTCCGACTC 58.745 50.000 0.00 0.00 0.00 3.36
3946 4573 2.808919 TCCAAGAATCTGTCCGACTCT 58.191 47.619 0.00 0.00 27.33 3.24
3947 4574 3.165875 TCCAAGAATCTGTCCGACTCTT 58.834 45.455 0.00 0.00 38.65 2.85
3949 4576 2.663826 AGAATCTGTCCGACTCTTGC 57.336 50.000 0.00 0.00 0.00 4.01
3950 4577 1.895798 AGAATCTGTCCGACTCTTGCA 59.104 47.619 0.00 0.00 0.00 4.08
3951 4578 2.499289 AGAATCTGTCCGACTCTTGCAT 59.501 45.455 0.00 0.00 0.00 3.96
3952 4579 3.701542 AGAATCTGTCCGACTCTTGCATA 59.298 43.478 0.00 0.00 0.00 3.14
3953 4580 4.160439 AGAATCTGTCCGACTCTTGCATAA 59.840 41.667 0.00 0.00 0.00 1.90
3954 4581 4.679373 ATCTGTCCGACTCTTGCATAAT 57.321 40.909 0.00 0.00 0.00 1.28
3955 4582 4.046938 TCTGTCCGACTCTTGCATAATC 57.953 45.455 0.00 0.00 0.00 1.75
3956 4583 3.701542 TCTGTCCGACTCTTGCATAATCT 59.298 43.478 0.00 0.00 0.00 2.40
4077 4707 2.005971 AAGTAAGACTAAAGCCGCCG 57.994 50.000 0.00 0.00 0.00 6.46
4457 5089 4.077822 CAGCTTGAAGTCCTTGGAAGATT 58.922 43.478 0.00 0.00 0.00 2.40
4512 5144 2.181021 CGTAGCACCTGTCGGTCC 59.819 66.667 0.00 0.00 43.24 4.46
4567 5200 2.244117 GATGAAGCCGCTCCACCTCA 62.244 60.000 0.00 0.00 0.00 3.86
4581 5215 1.554160 CACCTCATGCCTCTGACTTCT 59.446 52.381 0.00 0.00 0.00 2.85
4586 5220 0.749649 ATGCCTCTGACTTCTAGCGG 59.250 55.000 0.00 0.00 0.00 5.52
4733 5369 0.252197 GCCTCCATCAAGGTAACGGT 59.748 55.000 0.00 0.00 46.39 4.83
4749 5385 2.434185 GTGAGAACGCCGCCATCA 60.434 61.111 0.00 0.00 0.00 3.07
5007 5645 0.251297 CCAAGCACCACCAGATCCAA 60.251 55.000 0.00 0.00 0.00 3.53
5468 6201 3.557290 GGGGGTCGGGCCTGATAC 61.557 72.222 19.55 13.97 37.43 2.24
5469 6202 2.446036 GGGGTCGGGCCTGATACT 60.446 66.667 19.55 0.00 37.43 2.12
5470 6203 2.508751 GGGGTCGGGCCTGATACTC 61.509 68.421 19.55 10.58 37.43 2.59
5471 6204 2.728817 GGTCGGGCCTGATACTCG 59.271 66.667 19.55 2.76 0.00 4.18
5472 6205 2.027751 GTCGGGCCTGATACTCGC 59.972 66.667 19.55 0.00 0.00 5.03
5473 6206 3.224324 TCGGGCCTGATACTCGCC 61.224 66.667 11.27 0.00 42.23 5.54
5474 6207 4.647615 CGGGCCTGATACTCGCCG 62.648 72.222 5.28 0.00 43.99 6.46
5475 6208 4.301027 GGGCCTGATACTCGCCGG 62.301 72.222 0.84 0.00 43.99 6.13
5476 6209 3.537874 GGCCTGATACTCGCCGGT 61.538 66.667 1.90 0.00 31.92 5.28
5477 6210 2.198287 GGCCTGATACTCGCCGGTA 61.198 63.158 1.90 0.00 31.92 4.02
5478 6211 1.533469 GGCCTGATACTCGCCGGTAT 61.533 60.000 1.90 0.00 35.39 2.73
5497 6230 6.848335 CGGTATCGACTCTTGCATAATCTGC 61.848 48.000 0.00 0.00 44.70 4.26
5509 6242 2.917701 TAATCTGCGTTGCATTGTGG 57.082 45.000 0.00 0.00 38.13 4.17
5619 6352 5.149977 GCAAGCTGATTCTAACAAACTGAC 58.850 41.667 0.00 0.00 0.00 3.51
5681 6414 4.543590 ACACTCCTACCAGATTCAGTTG 57.456 45.455 0.00 0.00 0.00 3.16
5787 6520 7.882271 AGCTAGAACTGATTAAATGGATCATCC 59.118 37.037 0.00 0.00 36.96 3.51
5891 6624 4.020543 CTCAAGAGGCACCTACTTACTCT 58.979 47.826 0.00 0.00 40.02 3.24
5996 6729 3.064324 AACGCAATGCAGGCCCTC 61.064 61.111 5.91 0.00 0.00 4.30
5999 6732 3.818787 GCAATGCAGGCCCTCGTG 61.819 66.667 0.00 0.00 0.00 4.35
6035 6768 0.823356 TGTGGGAGCAGCAAAACCTC 60.823 55.000 0.00 0.00 0.00 3.85
6045 6778 2.030893 CAGCAAAACCTCGATCAAAGCA 60.031 45.455 0.00 0.00 0.00 3.91
6122 6855 1.745141 GCGCTGGAGATCAACAAGGAT 60.745 52.381 0.00 0.00 0.00 3.24
6132 6865 1.741770 AACAAGGATGCCGACGAGC 60.742 57.895 0.00 0.00 0.00 5.03
6148 6881 4.809070 GCTGAACAGGAAGCTGGT 57.191 55.556 3.99 0.00 36.47 4.00
6371 7104 3.883744 GAGGGTGCCACGGTGACTG 62.884 68.421 10.28 0.00 0.00 3.51
6373 7106 3.936203 GGTGCCACGGTGACTGGA 61.936 66.667 10.28 0.00 32.37 3.86
6377 7110 1.374758 GCCACGGTGACTGGAAGAG 60.375 63.158 10.28 0.00 37.43 2.85
6378 7111 1.816863 GCCACGGTGACTGGAAGAGA 61.817 60.000 10.28 0.00 37.43 3.10
6380 7113 1.404717 CCACGGTGACTGGAAGAGATG 60.405 57.143 10.28 0.00 37.43 2.90
6382 7115 1.971357 ACGGTGACTGGAAGAGATGTT 59.029 47.619 0.00 0.00 37.43 2.71
6383 7116 2.028930 ACGGTGACTGGAAGAGATGTTC 60.029 50.000 0.00 0.00 37.43 3.18
6427 7160 1.412079 TGTTGCCCAGAACTTGCAAT 58.588 45.000 0.00 0.00 45.66 3.56
6589 7326 7.286215 TGTGTAAGATAAGGCTATGGTAGAC 57.714 40.000 0.00 0.00 0.00 2.59
6608 7345 2.167900 GACTGGTGGTAGTATGGTGGTC 59.832 54.545 0.00 0.00 0.00 4.02
6646 7383 0.842030 AGGCTGGAACTGGGTGATCA 60.842 55.000 0.00 0.00 0.00 2.92
6661 7404 1.820519 TGATCATGCCCTGCTTTGTTC 59.179 47.619 0.00 0.00 0.00 3.18
6668 7411 2.295909 TGCCCTGCTTTGTTCATTACAC 59.704 45.455 0.00 0.00 36.21 2.90
6688 7432 0.320374 AAATGTCAACGCCTCCTCGA 59.680 50.000 0.00 0.00 0.00 4.04
6752 7496 2.034687 GAGGTGGCAGCATGGTGT 59.965 61.111 24.73 5.71 35.86 4.16
6799 7698 1.134551 GCTCCCAAGTCTTCAGGCTAG 60.135 57.143 0.00 0.00 0.00 3.42
6837 7736 0.174389 TCTGTGCCGAAGATCAGAGC 59.826 55.000 0.00 0.00 33.77 4.09
6866 7765 1.275657 GGCGTTGTGTCGTTGACAG 59.724 57.895 0.00 0.00 43.57 3.51
6904 7803 2.799126 TGGGCGAAACCATAATCACT 57.201 45.000 0.00 0.00 42.05 3.41
6906 7805 1.065551 GGGCGAAACCATAATCACTGC 59.934 52.381 0.00 0.00 42.05 4.40
6910 7809 2.365582 GAAACCATAATCACTGCCGGT 58.634 47.619 1.90 0.00 0.00 5.28
6913 7812 3.857157 ACCATAATCACTGCCGGTAAT 57.143 42.857 1.90 0.00 0.00 1.89
6924 7823 1.271102 TGCCGGTAATTTTTCAGCACC 59.729 47.619 1.90 0.00 0.00 5.01
6932 7831 6.280643 GGTAATTTTTCAGCACCAAGTTCTT 58.719 36.000 0.00 0.00 0.00 2.52
6941 7840 2.287248 GCACCAAGTTCTTGCTGAAGAC 60.287 50.000 10.78 0.00 37.97 3.01
6961 7860 1.423845 CTTGGTCCGCGTTGCATAC 59.576 57.895 4.92 0.00 0.00 2.39
6969 7868 1.280982 CGCGTTGCATACATCTGACT 58.719 50.000 0.00 0.00 0.00 3.41
6970 7869 1.660607 CGCGTTGCATACATCTGACTT 59.339 47.619 0.00 0.00 0.00 3.01
6971 7870 2.094258 CGCGTTGCATACATCTGACTTT 59.906 45.455 0.00 0.00 0.00 2.66
6974 7873 4.613622 GCGTTGCATACATCTGACTTTTGT 60.614 41.667 0.00 0.00 0.00 2.83
6975 7874 5.451908 CGTTGCATACATCTGACTTTTGTT 58.548 37.500 0.00 0.00 0.00 2.83
6982 7886 5.438761 ACATCTGACTTTTGTTTAGTGCC 57.561 39.130 0.00 0.00 0.00 5.01
7006 7914 0.823460 AGGGTGGTTGCTTTGTGTTG 59.177 50.000 0.00 0.00 0.00 3.33
7029 7997 7.731882 TGGTCGTTTTCAATGATTTAGTGTA 57.268 32.000 0.00 0.00 0.00 2.90
7030 7998 7.577979 TGGTCGTTTTCAATGATTTAGTGTAC 58.422 34.615 0.00 0.00 0.00 2.90
7065 8033 3.991051 CTGTGCTCCGTGGTCCGT 61.991 66.667 0.00 0.00 33.66 4.69
7066 8034 4.293648 TGTGCTCCGTGGTCCGTG 62.294 66.667 0.00 0.00 33.66 4.94
7086 8246 4.853196 CGTGGTTGCTTCTGTCATTAATTG 59.147 41.667 0.00 0.00 0.00 2.32
7129 8898 3.118038 TCATGGGCATGGAAGTTACCTAC 60.118 47.826 0.00 0.00 39.24 3.18
7175 8952 2.353610 CCCAAGTGCAATCCCCAGC 61.354 63.158 0.00 0.00 0.00 4.85
7274 9051 0.105593 CTGAGTGCTGGCGGATACAT 59.894 55.000 0.00 0.00 0.00 2.29
7281 9058 0.250038 CTGGCGGATACATGGGACTG 60.250 60.000 0.00 0.00 0.00 3.51
7286 9063 3.704566 GGCGGATACATGGGACTGATATA 59.295 47.826 0.00 0.00 0.00 0.86
7287 9064 4.345257 GGCGGATACATGGGACTGATATAT 59.655 45.833 0.00 0.00 0.00 0.86
7288 9065 5.538813 GGCGGATACATGGGACTGATATATA 59.461 44.000 0.00 0.00 0.00 0.86
7314 9093 6.442541 TTTTGAGTTCATACAGGGGACTAA 57.557 37.500 0.00 0.00 40.21 2.24
7323 9102 9.036980 GTTCATACAGGGGACTAATATGTATCT 57.963 37.037 0.00 0.00 40.21 1.98
7334 9113 7.283580 GGACTAATATGTATCTCCTGTAGCGAT 59.716 40.741 0.00 0.00 0.00 4.58
7349 9128 2.959071 GATCGCTCGCTCACAGGC 60.959 66.667 0.00 0.00 0.00 4.85
7353 9132 4.074526 GCTCGCTCACAGGCCTGA 62.075 66.667 39.19 17.43 0.00 3.86
7354 9133 2.183811 CTCGCTCACAGGCCTGAG 59.816 66.667 39.19 30.91 40.73 3.35
7402 9181 6.983890 TGCTCACCTTTTGTTTTAGAATTTCC 59.016 34.615 0.00 0.00 0.00 3.13
7409 9188 7.255486 CCTTTTGTTTTAGAATTTCCGGAGACT 60.255 37.037 3.34 5.67 0.00 3.24
7421 9200 1.334243 CCGGAGACTAACTAAGCCTCG 59.666 57.143 0.00 0.00 35.65 4.63
7480 9259 4.760047 GTCCAGCCGCCGTCACAT 62.760 66.667 0.00 0.00 0.00 3.21
7483 9262 3.490759 CAGCCGCCGTCACATGTC 61.491 66.667 0.00 0.00 0.00 3.06
7484 9263 4.760047 AGCCGCCGTCACATGTCC 62.760 66.667 0.00 0.00 0.00 4.02
7486 9265 4.735132 CCGCCGTCACATGTCCGT 62.735 66.667 12.09 0.00 0.00 4.69
7487 9266 2.179767 CGCCGTCACATGTCCGTA 59.820 61.111 12.09 0.00 0.00 4.02
7488 9267 2.156446 CGCCGTCACATGTCCGTAC 61.156 63.158 12.09 4.79 0.00 3.67
7489 9268 1.214589 GCCGTCACATGTCCGTACT 59.785 57.895 12.09 0.00 0.00 2.73
7490 9269 1.076533 GCCGTCACATGTCCGTACTG 61.077 60.000 12.09 0.64 0.00 2.74
7491 9270 0.457853 CCGTCACATGTCCGTACTGG 60.458 60.000 12.09 0.00 40.09 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 98 1.521141 GACGGGAAGTAAGGCCTCC 59.479 63.158 5.23 1.56 0.00 4.30
94 100 1.993948 GGGACGGGAAGTAAGGCCT 60.994 63.158 0.00 0.00 0.00 5.19
125 131 3.382832 CGTCCCAACGGAGGAGCT 61.383 66.667 0.00 0.00 45.32 4.09
166 491 5.715439 TCAAGGGTGAGATGATGGTTATT 57.285 39.130 0.00 0.00 0.00 1.40
330 657 0.387929 CATGCATTCCATGTCCTGCC 59.612 55.000 0.00 0.00 45.05 4.85
425 752 1.472201 CCTGTGTGGATGAGTGGATCG 60.472 57.143 0.00 0.00 38.35 3.69
427 754 0.254178 GCCTGTGTGGATGAGTGGAT 59.746 55.000 0.00 0.00 38.35 3.41
428 755 1.679311 GCCTGTGTGGATGAGTGGA 59.321 57.895 0.00 0.00 38.35 4.02
429 756 1.377725 GGCCTGTGTGGATGAGTGG 60.378 63.158 0.00 0.00 38.35 4.00
430 757 0.675837 CTGGCCTGTGTGGATGAGTG 60.676 60.000 3.32 0.00 38.35 3.51
431 758 1.681666 CTGGCCTGTGTGGATGAGT 59.318 57.895 3.32 0.00 38.35 3.41
432 759 1.077930 CCTGGCCTGTGTGGATGAG 60.078 63.158 3.32 0.00 38.35 2.90
433 760 3.080641 CCTGGCCTGTGTGGATGA 58.919 61.111 3.32 0.00 38.35 2.92
434 761 2.753043 GCCTGGCCTGTGTGGATG 60.753 66.667 7.66 0.00 38.35 3.51
507 834 0.112412 CTTTGGGTGGGTAGCTTGGT 59.888 55.000 0.00 0.00 0.00 3.67
599 926 4.500826 GGAGGGAGGGGAGGGGAC 62.501 77.778 0.00 0.00 0.00 4.46
614 941 2.849162 GCGAGGGATGGGATGGGA 60.849 66.667 0.00 0.00 0.00 4.37
615 942 2.851102 AGCGAGGGATGGGATGGG 60.851 66.667 0.00 0.00 0.00 4.00
618 945 3.564218 GGCAGCGAGGGATGGGAT 61.564 66.667 0.00 0.00 0.00 3.85
701 1029 1.728971 GAATCAGCACAGTGGAGAACG 59.271 52.381 1.84 0.00 0.00 3.95
709 1037 2.105477 ACTGAAGTGGAATCAGCACAGT 59.895 45.455 3.57 0.00 46.56 3.55
1009 1398 0.616111 ACCTACCTACTGCTGCTGCT 60.616 55.000 17.00 0.00 40.48 4.24
1219 1608 3.256716 CTCGTAGGATCCCGCGAGC 62.257 68.421 30.00 8.19 42.63 5.03
1225 1614 2.913060 AGCGCCTCGTAGGATCCC 60.913 66.667 8.55 0.00 37.67 3.85
1618 2016 3.570638 CCAGCTGCCGCATCGAAG 61.571 66.667 8.66 0.00 39.10 3.79
1918 2325 2.033755 CACGGTCTCCTCGTCGTCT 61.034 63.158 0.00 0.00 38.94 4.18
2008 2415 1.138266 ACCTCCGGAATGGTATTGACG 59.862 52.381 13.54 0.00 39.52 4.35
2020 2427 3.367743 CGGTTGTCGACCTCCGGA 61.368 66.667 28.68 2.93 46.92 5.14
2086 2499 2.668550 GCCGGCGGTTCTCTTGTT 60.669 61.111 28.82 0.00 0.00 2.83
2134 2547 2.357760 GTCTTAACCGCGGTGGCA 60.358 61.111 34.95 17.87 43.94 4.92
2143 2556 2.223377 CCGAACAAGCTGTGTCTTAACC 59.777 50.000 0.00 0.00 40.60 2.85
2152 2565 2.594592 GCCACCCGAACAAGCTGT 60.595 61.111 0.00 0.00 0.00 4.40
2170 2583 4.093291 AGCTCCCTTGCTGCCTCG 62.093 66.667 0.00 0.00 42.33 4.63
2263 2676 9.463902 AAAATGAATCAGATCATTCAGACTCTT 57.536 29.630 12.46 1.90 46.57 2.85
2300 2713 6.297080 ACAGTGAGTCAGATCATTCAGATT 57.703 37.500 0.00 0.00 37.00 2.40
2348 2761 2.697229 AGAGATTGCAGACATCATCCGA 59.303 45.455 0.00 0.00 0.00 4.55
2403 2816 0.464036 TCGCCAACTACTATGCCCAG 59.536 55.000 0.00 0.00 0.00 4.45
2411 2824 1.640917 TCCCTTCTTCGCCAACTACT 58.359 50.000 0.00 0.00 0.00 2.57
2414 2827 0.036875 CCTTCCCTTCTTCGCCAACT 59.963 55.000 0.00 0.00 0.00 3.16
2420 2833 0.321653 CCACCACCTTCCCTTCTTCG 60.322 60.000 0.00 0.00 0.00 3.79
2429 2842 1.379044 CCATGAGCCCACCACCTTC 60.379 63.158 0.00 0.00 0.00 3.46
2465 2878 5.046663 CCTCTCCCAGAAATATAGCTTCTCC 60.047 48.000 0.00 0.00 30.58 3.71
2474 2887 4.043596 ACAGCTTCCTCTCCCAGAAATAT 58.956 43.478 0.00 0.00 0.00 1.28
2501 2914 7.234782 ACGGAATATGAATATACCTTGACCTCA 59.765 37.037 0.00 0.00 0.00 3.86
2516 2929 7.827236 ACAGGAAAGTGATTAACGGAATATGAA 59.173 33.333 0.00 0.00 0.00 2.57
2531 2945 5.071788 ACCATTTCTACTCACAGGAAAGTGA 59.928 40.000 0.00 0.00 45.64 3.41
2538 2952 3.429547 CGGAGACCATTTCTACTCACAGG 60.430 52.174 0.00 0.00 31.97 4.00
2622 3036 3.067106 ACCTTTGTCATACTCACAAGCG 58.933 45.455 0.00 0.00 35.22 4.68
2691 3123 3.935203 AGATTAAGGTCAGACAACATGCG 59.065 43.478 2.17 0.00 0.00 4.73
2753 3185 6.539103 GCCACTGGACTAAATAAAAGGTCTAG 59.461 42.308 0.00 0.00 41.09 2.43
2774 3206 2.979240 TGGTTCAAACAAAAAGGCCAC 58.021 42.857 5.01 0.00 0.00 5.01
2837 3269 4.093556 CACAGAAAAGATCGTTTCCCTAGC 59.906 45.833 24.63 5.55 38.10 3.42
2848 3280 7.340487 ACATAAATCTTCCCCACAGAAAAGATC 59.660 37.037 0.00 0.00 37.46 2.75
2886 3320 7.820044 TTAATGGATGCCGAAAAATTGTAAC 57.180 32.000 0.00 0.00 0.00 2.50
2889 3323 9.442047 TTTATTTAATGGATGCCGAAAAATTGT 57.558 25.926 0.00 0.00 0.00 2.71
2903 3337 9.646427 GTAATGTTGTTGCCTTTATTTAATGGA 57.354 29.630 6.47 0.00 33.61 3.41
3011 3453 1.855295 TATCACGCCAAGACCACCTA 58.145 50.000 0.00 0.00 0.00 3.08
3114 3730 2.164219 AGCAACCGCACCATATTTTCTG 59.836 45.455 0.00 0.00 42.27 3.02
3121 3737 0.878416 GTTCAAGCAACCGCACCATA 59.122 50.000 0.00 0.00 42.27 2.74
3145 3761 7.182930 AGGATGAAAACCAGTAGACCTAATCTT 59.817 37.037 0.00 0.00 39.04 2.40
3168 3784 5.454755 GCATACCTAATCTTAGCAACCAGGA 60.455 44.000 0.00 0.00 0.00 3.86
3214 3835 9.755122 ACCTAGCTTACAAAATAGAAGGAATTT 57.245 29.630 0.00 0.00 0.00 1.82
3439 4061 4.261801 ACTTTGGTGACCACATGTATAGC 58.738 43.478 2.46 0.00 30.78 2.97
3519 4141 0.793861 TGGCAAGACGTAAACGCATC 59.206 50.000 1.74 0.00 44.43 3.91
3531 4153 4.835615 AGTCTCTTAGAGTTCTTGGCAAGA 59.164 41.667 25.38 25.38 35.26 3.02
3747 4369 7.814264 AAATTAGAGCAATTATCCTCCAGTG 57.186 36.000 0.00 0.00 35.74 3.66
3779 4401 4.613944 TGCAGCAAGAAATCAGAAAACAG 58.386 39.130 0.00 0.00 0.00 3.16
3814 4436 0.398522 ATCCTATGACTGGCCGACCA 60.399 55.000 0.00 0.00 46.51 4.02
3834 4456 9.282247 GTGCATAAGATGAAATTAACAGTTCTG 57.718 33.333 0.00 0.00 0.00 3.02
3835 4457 9.236006 AGTGCATAAGATGAAATTAACAGTTCT 57.764 29.630 0.00 0.00 0.00 3.01
3873 4500 5.237815 TCGTTAGATTCAAATGTGTGCTCT 58.762 37.500 0.00 0.00 0.00 4.09
3897 4524 9.490379 AATCCTAGATGTAAATGTACGATTTCC 57.510 33.333 6.56 0.00 32.40 3.13
3904 4531 8.958119 TGGAACAATCCTAGATGTAAATGTAC 57.042 34.615 0.00 0.00 46.70 2.90
4512 5144 1.129251 GTGGTGATGTCAAGTCATGCG 59.871 52.381 0.00 0.00 0.00 4.73
4567 5200 0.749649 CCGCTAGAAGTCAGAGGCAT 59.250 55.000 0.00 0.00 0.00 4.40
4700 5336 0.804933 GGAGGCATCGTCGTGTAACC 60.805 60.000 0.00 0.00 0.00 2.85
4733 5369 2.434185 GTGATGGCGGCGTTCTCA 60.434 61.111 9.37 6.04 0.00 3.27
4984 5622 2.142292 ATCTGGTGGTGCTTGGGTCC 62.142 60.000 0.00 0.00 0.00 4.46
5007 5645 0.753262 CCCTTGACTCCGATCCGATT 59.247 55.000 0.00 0.00 0.00 3.34
5018 5656 2.526110 GGTTTGGGGCCCTTGACT 59.474 61.111 25.93 0.00 0.00 3.41
5046 5684 3.957586 CCAGTGGTGCTGCCTCCA 61.958 66.667 0.00 9.09 43.71 3.86
5290 6023 2.436646 CTCCTCGCGGTTGGCATT 60.437 61.111 6.13 0.00 43.84 3.56
5463 6196 0.870393 GTCGATACCGGCGAGTATCA 59.130 55.000 29.98 20.99 45.96 2.15
5464 6197 1.128321 GAGTCGATACCGGCGAGTATC 59.872 57.143 25.47 25.47 46.52 2.24
5465 6198 1.155042 GAGTCGATACCGGCGAGTAT 58.845 55.000 9.30 14.45 46.52 2.12
5466 6199 0.105593 AGAGTCGATACCGGCGAGTA 59.894 55.000 9.30 9.72 46.52 2.59
5467 6200 0.747283 AAGAGTCGATACCGGCGAGT 60.747 55.000 9.30 9.66 46.52 4.18
5468 6201 0.317103 CAAGAGTCGATACCGGCGAG 60.317 60.000 9.30 0.06 46.52 5.03
5469 6202 1.725665 CAAGAGTCGATACCGGCGA 59.274 57.895 9.30 0.00 46.52 5.54
5470 6203 1.944676 GCAAGAGTCGATACCGGCG 60.945 63.158 0.00 0.00 46.52 6.46
5471 6204 0.249489 ATGCAAGAGTCGATACCGGC 60.249 55.000 0.00 0.00 41.44 6.13
5472 6205 3.364889 TTATGCAAGAGTCGATACCGG 57.635 47.619 0.00 0.00 36.24 5.28
5473 6206 4.618912 CAGATTATGCAAGAGTCGATACCG 59.381 45.833 0.00 0.00 37.07 4.02
5497 6230 2.741612 ACATGTTTCCACAATGCAACG 58.258 42.857 0.00 0.00 36.16 4.10
5498 6231 5.695816 ACATAACATGTTTCCACAATGCAAC 59.304 36.000 17.78 0.00 41.63 4.17
5509 6242 9.624697 TTTTATCTTCAGCACATAACATGTTTC 57.375 29.630 17.78 1.78 42.70 2.78
5588 6321 5.586243 TGTTAGAATCAGCTTGCACCTAATC 59.414 40.000 0.00 0.00 0.00 1.75
5619 6352 0.961753 GCAAACCTGGAAAGAGGTGG 59.038 55.000 0.00 0.00 46.29 4.61
5681 6414 4.864916 TTTCGCTTCTGATATCACTTGC 57.135 40.909 0.00 5.30 0.00 4.01
5787 6520 1.821136 GCTCACCCAGGAGGAAAAATG 59.179 52.381 0.00 0.00 39.89 2.32
5789 6522 0.250727 CGCTCACCCAGGAGGAAAAA 60.251 55.000 0.00 0.00 39.89 1.94
5837 6570 1.593750 GCAGAGTGCTAGCCATCCG 60.594 63.158 13.29 3.74 40.96 4.18
5882 6615 1.600058 TCCTCCCGGGAGAGTAAGTA 58.400 55.000 45.77 21.36 44.53 2.24
5906 6639 4.095334 CAGATGACGAAAATCAATGGAGCA 59.905 41.667 0.00 0.00 30.82 4.26
5913 6646 4.827304 TGTTGCAGATGACGAAAATCAA 57.173 36.364 0.00 0.00 30.82 2.57
5951 6684 1.285078 TCCTTCTCGGAGATCCTGTCA 59.715 52.381 8.81 0.00 36.69 3.58
6045 6778 1.349259 CGAACCGCGACGATCCTTTT 61.349 55.000 8.23 0.00 44.57 2.27
6122 6855 2.049156 CTGTTCAGCTCGTCGGCA 60.049 61.111 8.15 0.00 34.17 5.69
6132 6865 2.149578 CAAGACCAGCTTCCTGTTCAG 58.850 52.381 0.00 0.00 37.38 3.02
6191 6924 0.863119 GCGCCTCGTACGTTCGTATT 60.863 55.000 16.05 0.00 0.00 1.89
6224 6957 0.591170 AATTTACGTGCACGCTGCTT 59.409 45.000 37.35 22.66 45.31 3.91
6239 6972 4.696455 CTTGAACAACCAGCCTCAAATTT 58.304 39.130 0.00 0.00 0.00 1.82
6371 7104 1.066858 TGGTGCTCGAACATCTCTTCC 60.067 52.381 0.10 0.00 0.00 3.46
6372 7105 2.370281 TGGTGCTCGAACATCTCTTC 57.630 50.000 0.10 0.00 0.00 2.87
6373 7106 2.037772 ACTTGGTGCTCGAACATCTCTT 59.962 45.455 0.10 0.00 0.00 2.85
6377 7110 1.079503 GGACTTGGTGCTCGAACATC 58.920 55.000 0.00 0.00 0.00 3.06
6378 7111 0.396435 TGGACTTGGTGCTCGAACAT 59.604 50.000 0.00 0.00 0.00 2.71
6380 7113 1.569479 GCTGGACTTGGTGCTCGAAC 61.569 60.000 0.00 0.00 0.00 3.95
6382 7115 1.758440 AAGCTGGACTTGGTGCTCGA 61.758 55.000 0.00 0.00 37.17 4.04
6383 7116 1.302033 AAGCTGGACTTGGTGCTCG 60.302 57.895 0.00 0.00 37.17 5.03
6427 7160 7.397476 ACAGACTACTCATCCAAATCTACAGAA 59.603 37.037 0.00 0.00 0.00 3.02
6433 7166 7.726033 AACTACAGACTACTCATCCAAATCT 57.274 36.000 0.00 0.00 0.00 2.40
6503 7240 2.048127 GAGGATATCGGCACCGCC 60.048 66.667 3.66 0.00 46.75 6.13
6589 7326 2.431057 GAGACCACCATACTACCACCAG 59.569 54.545 0.00 0.00 0.00 4.00
6608 7345 5.356470 CAGCCTTCCCATTAGAAAAGAAGAG 59.644 44.000 0.00 0.00 36.83 2.85
6646 7383 3.056607 GTGTAATGAACAAAGCAGGGCAT 60.057 43.478 0.00 0.00 40.63 4.40
6668 7411 0.443869 CGAGGAGGCGTTGACATTTG 59.556 55.000 0.00 0.00 0.00 2.32
6688 7432 1.421268 TGGTCTCTGCTTTCCACACAT 59.579 47.619 0.00 0.00 0.00 3.21
6732 7476 2.353958 CCATGCTGCCACCTCTGT 59.646 61.111 0.00 0.00 0.00 3.41
6752 7496 0.847373 TTACAGTGCCCAACCAAGGA 59.153 50.000 0.00 0.00 0.00 3.36
6799 7698 4.137543 CAGAAGCCCATCCATAAACTACC 58.862 47.826 0.00 0.00 0.00 3.18
6895 7794 6.559810 TGAAAAATTACCGGCAGTGATTATG 58.440 36.000 0.00 0.00 33.78 1.90
6904 7803 1.271102 GGTGCTGAAAAATTACCGGCA 59.729 47.619 0.00 0.00 39.59 5.69
6906 7805 3.005367 ACTTGGTGCTGAAAAATTACCGG 59.995 43.478 0.00 0.00 34.16 5.28
6910 7809 5.752955 GCAAGAACTTGGTGCTGAAAAATTA 59.247 36.000 14.95 0.00 40.74 1.40
6913 7812 3.520569 GCAAGAACTTGGTGCTGAAAAA 58.479 40.909 14.95 0.00 40.74 1.94
6924 7823 2.856222 AGGGTCTTCAGCAAGAACTTG 58.144 47.619 9.82 9.82 44.80 3.16
6961 7860 4.520492 AGGGCACTAAACAAAAGTCAGATG 59.480 41.667 0.00 0.00 0.00 2.90
6969 7868 1.686052 CCTGCAGGGCACTAAACAAAA 59.314 47.619 26.14 0.00 33.79 2.44
6970 7869 1.327303 CCTGCAGGGCACTAAACAAA 58.673 50.000 26.14 0.00 33.79 2.83
6971 7870 3.034924 CCTGCAGGGCACTAAACAA 57.965 52.632 26.14 0.00 33.79 2.83
6982 7886 1.833934 AAAGCAACCACCCTGCAGG 60.834 57.895 26.87 26.87 42.48 4.85
6992 7896 0.454196 ACGACCAACACAAAGCAACC 59.546 50.000 0.00 0.00 0.00 3.77
7006 7914 7.803724 AGTACACTAAATCATTGAAAACGACC 58.196 34.615 0.00 0.00 0.00 4.79
7029 7997 1.214062 CGGCTCTTTCGCTCTGAGT 59.786 57.895 6.53 0.00 0.00 3.41
7030 7998 4.085302 CGGCTCTTTCGCTCTGAG 57.915 61.111 0.00 0.00 0.00 3.35
7059 8027 1.227853 ACAGAAGCAACCACGGACC 60.228 57.895 0.00 0.00 0.00 4.46
7063 8031 4.685169 ATTAATGACAGAAGCAACCACG 57.315 40.909 0.00 0.00 0.00 4.94
7065 8033 4.220382 CCCAATTAATGACAGAAGCAACCA 59.780 41.667 0.00 0.00 0.00 3.67
7066 8034 4.381932 CCCCAATTAATGACAGAAGCAACC 60.382 45.833 0.00 0.00 0.00 3.77
7067 8035 4.381932 CCCCCAATTAATGACAGAAGCAAC 60.382 45.833 0.00 0.00 0.00 4.17
7086 8246 7.201911 CCATGAAACTACATATTTTTCTCCCCC 60.202 40.741 0.00 0.00 31.68 5.40
7129 8898 2.389059 CGAAGGCGATCTATCACTGTG 58.611 52.381 0.17 0.17 40.82 3.66
7157 8934 2.353610 GCTGGGGATTGCACTTGGG 61.354 63.158 0.00 0.00 0.00 4.12
7175 8952 1.601903 TGAAAACTGCGGCAGTACTTG 59.398 47.619 33.53 9.58 44.62 3.16
7294 9071 6.844388 ACATATTAGTCCCCTGTATGAACTCA 59.156 38.462 0.00 0.00 30.90 3.41
7296 9073 8.974292 ATACATATTAGTCCCCTGTATGAACT 57.026 34.615 0.00 0.00 33.11 3.01
7297 9074 9.036980 AGATACATATTAGTCCCCTGTATGAAC 57.963 37.037 0.00 0.00 34.17 3.18
7298 9075 9.256228 GAGATACATATTAGTCCCCTGTATGAA 57.744 37.037 0.00 0.00 34.17 2.57
7299 9076 7.839705 GGAGATACATATTAGTCCCCTGTATGA 59.160 40.741 0.00 0.00 34.17 2.15
7300 9077 7.841729 AGGAGATACATATTAGTCCCCTGTATG 59.158 40.741 0.00 0.00 34.17 2.39
7314 9093 4.035792 GCGATCGCTACAGGAGATACATAT 59.964 45.833 31.94 0.00 34.68 1.78
7380 9159 6.321690 TCCGGAAATTCTAAAACAAAAGGTGA 59.678 34.615 0.00 0.00 0.00 4.02
7409 9188 1.206371 GACCCTTGCGAGGCTTAGTTA 59.794 52.381 15.36 0.00 42.09 2.24
7421 9200 0.759060 ACCACAAAAGGGACCCTTGC 60.759 55.000 26.95 0.00 43.92 4.01
7471 9250 1.076533 CAGTACGGACATGTGACGGC 61.077 60.000 19.78 13.36 0.00 5.68


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

AutoCloner maintained by Alex Coulton.