Multiple sequence alignment - TraesCS2D01G226100

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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 TraesCS2D01G226100 chr2D 100.000 3532 0 0 1 3532 194193792 194190261 0.000000e+00 6523.0
1 TraesCS2D01G226100 chr2B 91.939 2109 87 26 1125 3198 250071199 250069139 0.000000e+00 2876.0
2 TraesCS2D01G226100 chr2B 90.076 393 10 3 713 1100 250071640 250071272 1.910000e-132 483.0
3 TraesCS2D01G226100 chr2B 91.798 317 23 2 380 696 250072008 250071695 4.190000e-119 438.0
4 TraesCS2D01G226100 chr2B 90.850 306 23 4 5 310 250072524 250072224 4.250000e-109 405.0
5 TraesCS2D01G226100 chr2B 97.368 76 2 0 3455 3530 250069103 250069028 2.860000e-26 130.0
6 TraesCS2D01G226100 chr2B 92.063 63 1 3 3127 3186 250069154 250069093 6.280000e-13 86.1
7 TraesCS2D01G226100 chr2A 92.523 1110 60 16 1 1100 208153022 208151926 0.000000e+00 1568.0
8 TraesCS2D01G226100 chr2A 90.702 968 57 4 1125 2073 208151846 208150893 0.000000e+00 1258.0
9 TraesCS2D01G226100 chr2A 89.794 921 75 5 2070 2977 208142356 208141442 0.000000e+00 1162.0
10 TraesCS2D01G226100 chr2A 94.030 268 10 3 3198 3459 717765862 717765595 5.490000e-108 401.0
11 TraesCS2D01G226100 chr2A 89.121 239 13 4 2970 3198 208112169 208111934 5.770000e-73 285.0
12 TraesCS2D01G226100 chr2A 96.154 78 3 0 3453 3530 208111938 208111861 1.030000e-25 128.0
13 TraesCS2D01G226100 chr5A 87.091 550 62 8 1617 2161 606050722 606050177 6.480000e-172 614.0
14 TraesCS2D01G226100 chr5A 95.506 267 6 3 3196 3456 465260195 465259929 4.220000e-114 422.0
15 TraesCS2D01G226100 chr5A 80.688 523 63 24 2193 2707 606050181 606049689 4.310000e-99 372.0
16 TraesCS2D01G226100 chr5A 90.052 191 19 0 1940 2130 533281201 533281391 7.570000e-62 248.0
17 TraesCS2D01G226100 chr5A 76.033 242 38 14 2305 2531 533281480 533281716 1.340000e-19 108.0
18 TraesCS2D01G226100 chr5D 86.182 550 67 8 1617 2161 484414200 484413655 1.410000e-163 586.0
19 TraesCS2D01G226100 chr5D 81.905 525 70 17 2193 2707 484413659 484413150 1.520000e-113 420.0
20 TraesCS2D01G226100 chr5D 90.576 191 18 0 1940 2130 418430210 418430400 1.630000e-63 254.0
21 TraesCS2D01G226100 chr5B 86.322 541 64 8 1617 2151 595623176 595622640 6.570000e-162 580.0
22 TraesCS2D01G226100 chr5B 94.052 269 10 3 3195 3457 711285253 711285521 1.530000e-108 403.0
23 TraesCS2D01G226100 chr5B 93.431 274 11 4 3196 3462 94680689 94680416 1.980000e-107 399.0
24 TraesCS2D01G226100 chr5B 80.344 524 66 25 2193 2707 595622634 595622139 2.590000e-96 363.0
25 TraesCS2D01G226100 chr5B 89.529 191 20 0 1940 2130 505770386 505770576 3.520000e-60 243.0
26 TraesCS2D01G226100 chr1B 95.076 264 7 3 3196 3453 368956380 368956117 9.130000e-111 411.0
27 TraesCS2D01G226100 chr6A 93.190 279 13 3 3184 3456 601864807 601864529 4.250000e-109 405.0
28 TraesCS2D01G226100 chr6D 94.318 264 9 3 3196 3453 947888 948151 1.980000e-107 399.0
29 TraesCS2D01G226100 chr3A 93.704 270 11 3 3196 3459 505743743 505743474 1.980000e-107 399.0
30 TraesCS2D01G226100 chr7B 93.680 269 11 3 3196 3458 677059090 677059358 7.100000e-107 398.0
31 TraesCS2D01G226100 chr7A 91.489 188 16 0 1940 2127 649799742 649799555 3.500000e-65 259.0
32 TraesCS2D01G226100 chr7A 90.426 188 18 0 1940 2127 649478011 649477824 7.570000e-62 248.0


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 TraesCS2D01G226100 chr2D 194190261 194193792 3531 True 6523.00 6523 100.0000 1 3532 1 chr2D.!!$R1 3531
1 TraesCS2D01G226100 chr2B 250069028 250072524 3496 True 736.35 2876 92.3490 5 3530 6 chr2B.!!$R1 3525
2 TraesCS2D01G226100 chr2A 208150893 208153022 2129 True 1413.00 1568 91.6125 1 2073 2 chr2A.!!$R4 2072
3 TraesCS2D01G226100 chr2A 208141442 208142356 914 True 1162.00 1162 89.7940 2070 2977 1 chr2A.!!$R1 907
4 TraesCS2D01G226100 chr5A 606049689 606050722 1033 True 493.00 614 83.8895 1617 2707 2 chr5A.!!$R2 1090
5 TraesCS2D01G226100 chr5D 484413150 484414200 1050 True 503.00 586 84.0435 1617 2707 2 chr5D.!!$R1 1090
6 TraesCS2D01G226100 chr5B 595622139 595623176 1037 True 471.50 580 83.3330 1617 2707 2 chr5B.!!$R2 1090

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
497 644 0.609662 AAACTAGGCCCGTTAAGCGA 59.390 50.0 8.31 0.00 44.77 4.93 F
1560 1825 0.252375 AACTGGGCATGCATTCCCTT 60.252 50.0 30.94 17.69 43.04 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1878 1.534595 CACTTGGCAAGAGAGAAGCAC 59.465 52.381 32.50 0.0 0.00 4.40 R
3444 3747 0.035915 GAAACCTCCTCAGGCTGGTC 60.036 60.000 15.73 0.0 45.05 4.02 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
75 76 2.364002 CACCCGGTTTTCCATGTTTCTT 59.636 45.455 0.00 0.00 40.70 2.52
181 182 5.141182 AGATCCTTTAGCATCGAGTTAGGA 58.859 41.667 0.00 0.00 35.03 2.94
243 244 5.562298 GGAGTGACTCCTCTCTAGTAGAT 57.438 47.826 23.97 0.00 46.41 1.98
262 263 7.445945 AGTAGATGCTACATGGGAAGAATTAC 58.554 38.462 7.29 0.00 0.00 1.89
265 266 4.199310 TGCTACATGGGAAGAATTACAGC 58.801 43.478 0.00 0.00 0.00 4.40
269 270 2.107950 TGGGAAGAATTACAGCCACG 57.892 50.000 0.00 0.00 0.00 4.94
275 276 3.328382 AGAATTACAGCCACGTAAGCA 57.672 42.857 11.84 0.00 45.62 3.91
276 277 3.670625 AGAATTACAGCCACGTAAGCAA 58.329 40.909 11.84 0.00 45.62 3.91
317 318 4.762825 TGGGGACAAGTCGTTTCG 57.237 55.556 0.00 0.00 37.44 3.46
320 321 1.368579 GGGACAAGTCGTTTCGGGA 59.631 57.895 0.00 0.00 0.00 5.14
321 322 0.669625 GGGACAAGTCGTTTCGGGAG 60.670 60.000 0.00 0.00 0.00 4.30
323 324 1.289800 GACAAGTCGTTTCGGGAGGC 61.290 60.000 0.00 0.00 0.00 4.70
385 532 1.219646 GGCGTTTGTACAAGAACCGA 58.780 50.000 8.56 0.00 0.00 4.69
386 533 1.193874 GGCGTTTGTACAAGAACCGAG 59.806 52.381 8.56 0.00 0.00 4.63
415 562 4.097437 TCGACAAGAGCCAAACGTCTATAT 59.903 41.667 0.00 0.00 0.00 0.86
416 563 5.297527 TCGACAAGAGCCAAACGTCTATATA 59.702 40.000 0.00 0.00 0.00 0.86
457 604 1.600636 CGTCAAGGCCCAAGAAGCA 60.601 57.895 0.00 0.00 0.00 3.91
463 610 1.755783 GGCCCAAGAAGCATCCCAG 60.756 63.158 0.00 0.00 0.00 4.45
497 644 0.609662 AAACTAGGCCCGTTAAGCGA 59.390 50.000 8.31 0.00 44.77 4.93
543 690 7.242914 ACTTATAGCCGTTGTATAGTTTTGC 57.757 36.000 0.00 0.00 0.00 3.68
544 691 4.789095 ATAGCCGTTGTATAGTTTTGCG 57.211 40.909 0.00 0.00 0.00 4.85
593 740 1.293267 ACCAATCGGTTGTAACGCGG 61.293 55.000 12.47 0.00 46.31 6.46
742 927 5.046878 ACAGTTCAACCCATTCGTCATACTA 60.047 40.000 0.00 0.00 0.00 1.82
816 1002 4.430423 GACCAACAGAAGCGCGCG 62.430 66.667 28.44 28.44 0.00 6.86
926 1112 1.427072 AAACCACACCCCTCTCCCTG 61.427 60.000 0.00 0.00 0.00 4.45
1100 1291 0.948678 GCTTTGCTTGTTACGTGGGA 59.051 50.000 0.00 0.00 0.00 4.37
1102 1293 2.414161 GCTTTGCTTGTTACGTGGGATC 60.414 50.000 0.00 0.00 0.00 3.36
1103 1294 1.434555 TTGCTTGTTACGTGGGATCG 58.565 50.000 0.00 0.00 0.00 3.69
1104 1295 0.604073 TGCTTGTTACGTGGGATCGA 59.396 50.000 0.00 0.00 34.70 3.59
1123 1337 2.406691 CGATAGCTGCTAGATTTCGTGC 59.593 50.000 15.41 0.00 32.07 5.34
1130 1376 2.496070 TGCTAGATTTCGTGCTGTAGGT 59.504 45.455 0.00 0.00 0.00 3.08
1142 1388 1.594862 GCTGTAGGTTTGATGCTAGCG 59.405 52.381 10.77 0.00 0.00 4.26
1145 1391 4.430007 CTGTAGGTTTGATGCTAGCGTAA 58.570 43.478 10.03 0.00 0.00 3.18
1149 1395 3.933332 AGGTTTGATGCTAGCGTAAGAAC 59.067 43.478 10.03 13.80 43.02 3.01
1153 1399 3.024547 TGATGCTAGCGTAAGAACCTCT 58.975 45.455 10.03 0.00 43.02 3.69
1167 1413 5.346181 AGAACCTCTAGCTTTGGTGTATC 57.654 43.478 0.00 0.00 33.89 2.24
1259 1506 6.455647 TCTGAACCATGTACACTAGTTCTTG 58.544 40.000 23.96 18.89 38.10 3.02
1279 1526 9.669353 GTTCTTGATTACTGTATATTTGCATGG 57.331 33.333 0.00 0.00 0.00 3.66
1283 1530 8.565896 TGATTACTGTATATTTGCATGGGATC 57.434 34.615 0.00 0.00 0.00 3.36
1316 1563 6.035758 GCTTCACGTTCCTAATTACCAAGTAG 59.964 42.308 0.00 0.00 0.00 2.57
1560 1825 0.252375 AACTGGGCATGCATTCCCTT 60.252 50.000 30.94 17.69 43.04 3.95
1561 1826 0.974010 ACTGGGCATGCATTCCCTTG 60.974 55.000 30.94 24.82 43.04 3.61
1564 1829 2.105528 GCATGCATTCCCTTGGCG 59.894 61.111 14.21 0.00 0.00 5.69
1613 1878 6.007703 TCTAATGTTTCACCTTAACTTGGGG 58.992 40.000 0.00 0.00 0.00 4.96
1848 2117 5.769662 TGAACATTCCTGCACTTGTTTCTAT 59.230 36.000 0.00 0.00 32.73 1.98
1947 2219 6.934056 TGTTGCAAATGCTATTTAGGTGAAT 58.066 32.000 0.00 0.00 42.66 2.57
2153 2425 4.641954 CATCGTTGCTTGTGATTGTCTAC 58.358 43.478 0.00 0.00 0.00 2.59
2167 2439 0.249398 GTCTACCGACCTGCCAACAT 59.751 55.000 0.00 0.00 33.98 2.71
2183 2455 9.842775 CCTGCCAACATGATATATATAGTTCAT 57.157 33.333 0.00 3.84 0.00 2.57
2221 2493 2.502130 TGTCTACCAATTCACCGCCATA 59.498 45.455 0.00 0.00 0.00 2.74
2259 2531 6.071051 TGCCTGTGTAGTGTATTTGTCTGATA 60.071 38.462 0.00 0.00 0.00 2.15
2260 2532 6.816640 GCCTGTGTAGTGTATTTGTCTGATAA 59.183 38.462 0.00 0.00 0.00 1.75
2648 2932 4.537135 TGTATCCAAACTCCTGTGTCTC 57.463 45.455 0.00 0.00 0.00 3.36
2771 3060 4.280425 TGACATGGTAATTTGAGCTTTGCA 59.720 37.500 0.00 0.00 0.00 4.08
2772 3061 5.047164 TGACATGGTAATTTGAGCTTTGCAT 60.047 36.000 0.00 0.00 0.00 3.96
2775 3064 7.558604 ACATGGTAATTTGAGCTTTGCATATT 58.441 30.769 0.00 0.00 0.00 1.28
2791 3080 9.100554 CTTTGCATATTCTTTTTGGCATATGAA 57.899 29.630 6.97 4.24 33.20 2.57
2799 3088 7.225784 TCTTTTTGGCATATGAAAGCTGTTA 57.774 32.000 6.97 0.00 0.00 2.41
2837 3126 1.826385 ATTGCGAAGGGTTCTTCCTG 58.174 50.000 0.00 0.00 44.88 3.86
2963 3263 6.596497 TCCGTTTCTTATTTAGTCATTCCCAC 59.404 38.462 0.00 0.00 0.00 4.61
2981 3281 3.064820 CCCACGAATCAAAACGGAATAGG 59.935 47.826 0.00 0.00 0.00 2.57
2996 3296 5.415077 ACGGAATAGGTTCTACATATCCTCG 59.585 44.000 0.00 0.00 34.68 4.63
3002 3302 5.077564 AGGTTCTACATATCCTCGCACATA 58.922 41.667 0.00 0.00 0.00 2.29
3021 3321 8.017373 CGCACATAATTCCCATCTTAATACAAG 58.983 37.037 0.00 0.00 0.00 3.16
3033 3333 8.956426 CCATCTTAATACAAGTTCCTGCTTTAA 58.044 33.333 0.00 0.00 0.00 1.52
3039 3339 3.230976 CAAGTTCCTGCTTTAAACCCCT 58.769 45.455 0.00 0.00 0.00 4.79
3042 3342 5.270979 AGTTCCTGCTTTAAACCCCTATT 57.729 39.130 0.00 0.00 0.00 1.73
3050 3350 5.949952 TGCTTTAAACCCCTATTCCTCTTTC 59.050 40.000 0.00 0.00 0.00 2.62
3174 3477 3.897325 TCGCATTGTAGATTACGCCTAG 58.103 45.455 0.00 0.00 0.00 3.02
3177 3480 4.743151 CGCATTGTAGATTACGCCTAGAAA 59.257 41.667 0.00 0.00 0.00 2.52
3179 3482 5.177696 GCATTGTAGATTACGCCTAGAAAGG 59.822 44.000 0.00 0.00 46.76 3.11
3180 3483 5.927281 TTGTAGATTACGCCTAGAAAGGT 57.073 39.130 0.00 0.00 45.64 3.50
3193 3496 5.684030 GCCTAGAAAGGTGTTCCATCGATAA 60.684 44.000 0.00 0.00 45.64 1.75
3198 3501 2.103263 AGGTGTTCCATCGATAAGAGGC 59.897 50.000 0.00 0.00 35.89 4.70
3200 3503 3.321111 GGTGTTCCATCGATAAGAGGCTA 59.679 47.826 0.00 0.00 0.00 3.93
3201 3504 4.551388 GTGTTCCATCGATAAGAGGCTAG 58.449 47.826 0.00 0.00 0.00 3.42
3202 3505 4.038162 GTGTTCCATCGATAAGAGGCTAGT 59.962 45.833 0.00 0.00 0.00 2.57
3203 3506 4.278669 TGTTCCATCGATAAGAGGCTAGTC 59.721 45.833 0.00 0.00 0.00 2.59
3205 3508 4.667573 TCCATCGATAAGAGGCTAGTCAT 58.332 43.478 0.00 0.00 0.00 3.06
3206 3509 5.816682 TCCATCGATAAGAGGCTAGTCATA 58.183 41.667 0.00 0.00 0.00 2.15
3207 3510 5.883115 TCCATCGATAAGAGGCTAGTCATAG 59.117 44.000 0.00 0.00 0.00 2.23
3209 3512 6.404184 CCATCGATAAGAGGCTAGTCATAGTG 60.404 46.154 0.00 0.00 0.00 2.74
3210 3513 5.004448 TCGATAAGAGGCTAGTCATAGTGG 58.996 45.833 0.00 0.00 0.00 4.00
3211 3514 5.004448 CGATAAGAGGCTAGTCATAGTGGA 58.996 45.833 0.00 0.00 0.00 4.02
3212 3515 5.473846 CGATAAGAGGCTAGTCATAGTGGAA 59.526 44.000 0.00 0.00 0.00 3.53
3213 3516 6.568844 CGATAAGAGGCTAGTCATAGTGGAAC 60.569 46.154 0.00 0.00 0.00 3.62
3239 3542 5.088141 GCTAGTAACATAGCGTACTTCGA 57.912 43.478 0.00 0.00 42.86 3.71
3240 3543 5.138788 GCTAGTAACATAGCGTACTTCGAG 58.861 45.833 0.00 0.00 42.86 4.04
3241 3544 5.050499 GCTAGTAACATAGCGTACTTCGAGA 60.050 44.000 0.00 0.00 42.86 4.04
3242 3545 5.808042 AGTAACATAGCGTACTTCGAGAA 57.192 39.130 0.00 0.00 42.86 2.87
3243 3546 6.187125 AGTAACATAGCGTACTTCGAGAAA 57.813 37.500 0.00 0.00 42.86 2.52
3244 3547 6.615088 AGTAACATAGCGTACTTCGAGAAAA 58.385 36.000 0.00 0.00 42.86 2.29
3245 3548 7.256286 AGTAACATAGCGTACTTCGAGAAAAT 58.744 34.615 0.00 0.00 42.86 1.82
3246 3549 6.963049 AACATAGCGTACTTCGAGAAAATT 57.037 33.333 0.00 0.00 42.86 1.82
3247 3550 6.570690 ACATAGCGTACTTCGAGAAAATTC 57.429 37.500 0.00 0.00 42.86 2.17
3248 3551 6.331061 ACATAGCGTACTTCGAGAAAATTCT 58.669 36.000 0.00 0.00 42.86 2.40
3249 3552 6.253727 ACATAGCGTACTTCGAGAAAATTCTG 59.746 38.462 0.00 0.00 42.86 3.02
3250 3553 3.368236 AGCGTACTTCGAGAAAATTCTGC 59.632 43.478 0.00 0.00 42.86 4.26
3251 3554 3.368236 GCGTACTTCGAGAAAATTCTGCT 59.632 43.478 0.00 0.00 42.86 4.24
3252 3555 4.143094 GCGTACTTCGAGAAAATTCTGCTT 60.143 41.667 0.00 0.00 42.86 3.91
3253 3556 5.061808 GCGTACTTCGAGAAAATTCTGCTTA 59.938 40.000 0.00 0.00 42.86 3.09
3254 3557 6.237861 GCGTACTTCGAGAAAATTCTGCTTAT 60.238 38.462 0.00 0.00 42.86 1.73
3255 3558 7.113658 CGTACTTCGAGAAAATTCTGCTTATG 58.886 38.462 0.00 0.00 42.86 1.90
3256 3559 7.201444 CGTACTTCGAGAAAATTCTGCTTATGT 60.201 37.037 0.00 0.00 42.86 2.29
3257 3560 6.835914 ACTTCGAGAAAATTCTGCTTATGTG 58.164 36.000 0.00 0.00 37.73 3.21
3258 3561 5.221891 TCGAGAAAATTCTGCTTATGTGC 57.778 39.130 0.00 0.00 37.73 4.57
3259 3562 4.694982 TCGAGAAAATTCTGCTTATGTGCA 59.305 37.500 0.00 0.00 37.73 4.57
3260 3563 5.181056 TCGAGAAAATTCTGCTTATGTGCAA 59.819 36.000 0.00 0.00 42.83 4.08
3261 3564 5.510674 CGAGAAAATTCTGCTTATGTGCAAG 59.489 40.000 0.00 0.00 42.83 4.01
3262 3565 6.336842 AGAAAATTCTGCTTATGTGCAAGT 57.663 33.333 0.00 0.00 42.83 3.16
3263 3566 7.452880 AGAAAATTCTGCTTATGTGCAAGTA 57.547 32.000 0.00 0.00 42.83 2.24
3264 3567 7.885297 AGAAAATTCTGCTTATGTGCAAGTAA 58.115 30.769 0.00 0.00 42.83 2.24
3265 3568 8.526147 AGAAAATTCTGCTTATGTGCAAGTAAT 58.474 29.630 0.00 0.00 42.83 1.89
3266 3569 9.143631 GAAAATTCTGCTTATGTGCAAGTAATT 57.856 29.630 0.00 0.00 42.83 1.40
3270 3573 9.740239 ATTCTGCTTATGTGCAAGTAATTAATG 57.260 29.630 0.00 0.00 42.83 1.90
3271 3574 8.504812 TCTGCTTATGTGCAAGTAATTAATGA 57.495 30.769 0.00 0.00 42.83 2.57
3272 3575 8.615211 TCTGCTTATGTGCAAGTAATTAATGAG 58.385 33.333 0.00 0.00 42.83 2.90
3273 3576 8.504812 TGCTTATGTGCAAGTAATTAATGAGA 57.495 30.769 0.00 0.00 40.29 3.27
3274 3577 8.615211 TGCTTATGTGCAAGTAATTAATGAGAG 58.385 33.333 0.00 0.00 40.29 3.20
3275 3578 8.830580 GCTTATGTGCAAGTAATTAATGAGAGA 58.169 33.333 0.00 0.00 0.00 3.10
3278 3581 7.558161 TGTGCAAGTAATTAATGAGAGATGG 57.442 36.000 0.00 0.00 0.00 3.51
3279 3582 7.112122 TGTGCAAGTAATTAATGAGAGATGGT 58.888 34.615 0.00 0.00 0.00 3.55
3280 3583 8.264347 TGTGCAAGTAATTAATGAGAGATGGTA 58.736 33.333 0.00 0.00 0.00 3.25
3281 3584 9.109393 GTGCAAGTAATTAATGAGAGATGGTAA 57.891 33.333 0.00 0.00 0.00 2.85
3282 3585 9.109393 TGCAAGTAATTAATGAGAGATGGTAAC 57.891 33.333 4.19 0.00 0.00 2.50
3312 3615 6.160664 TGTTACTGTAACATAGCGCTTTTC 57.839 37.500 25.14 2.12 43.23 2.29
3313 3616 5.697178 TGTTACTGTAACATAGCGCTTTTCA 59.303 36.000 25.14 7.38 43.23 2.69
3314 3617 6.203145 TGTTACTGTAACATAGCGCTTTTCAA 59.797 34.615 25.14 0.00 43.23 2.69
3315 3618 5.283060 ACTGTAACATAGCGCTTTTCAAG 57.717 39.130 18.68 7.94 0.00 3.02
3316 3619 4.994852 ACTGTAACATAGCGCTTTTCAAGA 59.005 37.500 18.68 0.00 0.00 3.02
3317 3620 5.107065 ACTGTAACATAGCGCTTTTCAAGAC 60.107 40.000 18.68 6.42 0.00 3.01
3318 3621 4.752604 TGTAACATAGCGCTTTTCAAGACA 59.247 37.500 18.68 9.17 0.00 3.41
3319 3622 4.829064 AACATAGCGCTTTTCAAGACAA 57.171 36.364 18.68 0.00 0.00 3.18
3320 3623 4.410492 ACATAGCGCTTTTCAAGACAAG 57.590 40.909 18.68 0.00 0.00 3.16
3321 3624 4.065088 ACATAGCGCTTTTCAAGACAAGA 58.935 39.130 18.68 0.00 0.00 3.02
3322 3625 4.697352 ACATAGCGCTTTTCAAGACAAGAT 59.303 37.500 18.68 0.00 0.00 2.40
3323 3626 3.549299 AGCGCTTTTCAAGACAAGATG 57.451 42.857 2.64 0.00 0.00 2.90
3324 3627 3.141398 AGCGCTTTTCAAGACAAGATGA 58.859 40.909 2.64 0.00 0.00 2.92
3325 3628 3.188048 AGCGCTTTTCAAGACAAGATGAG 59.812 43.478 2.64 0.00 0.00 2.90
3326 3629 3.058639 GCGCTTTTCAAGACAAGATGAGT 60.059 43.478 0.00 0.00 0.00 3.41
3327 3630 4.706527 CGCTTTTCAAGACAAGATGAGTC 58.293 43.478 0.41 0.00 36.26 3.36
3329 3632 5.635280 CGCTTTTCAAGACAAGATGAGTCTA 59.365 40.000 0.41 0.00 45.11 2.59
3330 3633 6.400515 CGCTTTTCAAGACAAGATGAGTCTAC 60.401 42.308 0.41 0.00 45.11 2.59
3331 3634 6.400515 GCTTTTCAAGACAAGATGAGTCTACG 60.401 42.308 0.41 0.00 45.11 3.51
3332 3635 4.703645 TCAAGACAAGATGAGTCTACGG 57.296 45.455 0.00 0.00 45.11 4.02
3333 3636 3.444034 TCAAGACAAGATGAGTCTACGGG 59.556 47.826 0.00 0.00 45.11 5.28
3334 3637 1.751924 AGACAAGATGAGTCTACGGGC 59.248 52.381 0.00 0.00 44.10 6.13
3335 3638 1.751924 GACAAGATGAGTCTACGGGCT 59.248 52.381 0.00 0.00 33.30 5.19
3336 3639 2.950309 GACAAGATGAGTCTACGGGCTA 59.050 50.000 0.00 0.00 33.30 3.93
3337 3640 3.362706 ACAAGATGAGTCTACGGGCTAA 58.637 45.455 0.00 0.00 33.30 3.09
3338 3641 3.961408 ACAAGATGAGTCTACGGGCTAAT 59.039 43.478 0.00 0.00 33.30 1.73
3339 3642 5.138276 ACAAGATGAGTCTACGGGCTAATA 58.862 41.667 0.00 0.00 33.30 0.98
3340 3643 5.597182 ACAAGATGAGTCTACGGGCTAATAA 59.403 40.000 0.00 0.00 33.30 1.40
3341 3644 6.097839 ACAAGATGAGTCTACGGGCTAATAAA 59.902 38.462 0.00 0.00 33.30 1.40
3342 3645 6.919775 AGATGAGTCTACGGGCTAATAAAT 57.080 37.500 0.00 0.00 31.36 1.40
3343 3646 6.692486 AGATGAGTCTACGGGCTAATAAATG 58.308 40.000 0.00 0.00 31.36 2.32
3344 3647 6.493802 AGATGAGTCTACGGGCTAATAAATGA 59.506 38.462 0.00 0.00 31.36 2.57
3345 3648 6.474140 TGAGTCTACGGGCTAATAAATGAA 57.526 37.500 0.00 0.00 0.00 2.57
3346 3649 6.513180 TGAGTCTACGGGCTAATAAATGAAG 58.487 40.000 0.00 0.00 0.00 3.02
3347 3650 5.298347 AGTCTACGGGCTAATAAATGAAGC 58.702 41.667 0.00 0.00 35.47 3.86
3396 3699 9.953565 TTACTTTGCATTATGAAGGTAGTAACT 57.046 29.630 0.00 0.00 0.00 2.24
3397 3700 8.863872 ACTTTGCATTATGAAGGTAGTAACTT 57.136 30.769 0.00 0.00 0.00 2.66
3398 3701 9.953565 ACTTTGCATTATGAAGGTAGTAACTTA 57.046 29.630 0.00 0.00 0.00 2.24
3401 3704 9.595823 TTGCATTATGAAGGTAGTAACTTAGAC 57.404 33.333 0.00 0.00 0.00 2.59
3402 3705 8.978472 TGCATTATGAAGGTAGTAACTTAGACT 58.022 33.333 0.00 0.00 0.00 3.24
3408 3711 8.558973 TGAAGGTAGTAACTTAGACTAGTGTC 57.441 38.462 0.00 0.00 43.22 3.67
3409 3712 8.159447 TGAAGGTAGTAACTTAGACTAGTGTCA 58.841 37.037 0.00 0.00 45.20 3.58
3410 3713 9.176460 GAAGGTAGTAACTTAGACTAGTGTCAT 57.824 37.037 0.00 0.00 45.20 3.06
3414 3717 9.881529 GTAGTAACTTAGACTAGTGTCATATGC 57.118 37.037 0.00 0.00 45.20 3.14
3415 3718 8.521170 AGTAACTTAGACTAGTGTCATATGCA 57.479 34.615 0.00 0.00 45.20 3.96
3416 3719 9.137459 AGTAACTTAGACTAGTGTCATATGCAT 57.863 33.333 3.79 3.79 45.20 3.96
3417 3720 9.186323 GTAACTTAGACTAGTGTCATATGCATG 57.814 37.037 10.16 0.00 45.20 4.06
3418 3721 7.588497 ACTTAGACTAGTGTCATATGCATGA 57.412 36.000 10.16 0.00 45.20 3.07
3431 3734 7.588497 TCATATGCATGACACTAGTCTAAGT 57.412 36.000 10.16 0.00 45.20 2.24
3432 3735 8.011844 TCATATGCATGACACTAGTCTAAGTT 57.988 34.615 10.16 0.00 45.20 2.66
3433 3736 9.131791 TCATATGCATGACACTAGTCTAAGTTA 57.868 33.333 10.16 0.00 45.20 2.24
3434 3737 9.186323 CATATGCATGACACTAGTCTAAGTTAC 57.814 37.037 10.16 0.00 45.20 2.50
3435 3738 6.835819 TGCATGACACTAGTCTAAGTTACT 57.164 37.500 0.00 0.00 45.20 2.24
3436 3739 6.853720 TGCATGACACTAGTCTAAGTTACTC 58.146 40.000 0.00 0.00 45.20 2.59
3437 3740 6.127703 TGCATGACACTAGTCTAAGTTACTCC 60.128 42.308 0.00 0.00 45.20 3.85
3438 3741 6.680872 GCATGACACTAGTCTAAGTTACTCCC 60.681 46.154 0.00 0.00 45.20 4.30
3439 3742 5.884322 TGACACTAGTCTAAGTTACTCCCA 58.116 41.667 0.00 0.00 45.20 4.37
3440 3743 5.709164 TGACACTAGTCTAAGTTACTCCCAC 59.291 44.000 0.00 0.00 45.20 4.61
3441 3744 5.890049 ACACTAGTCTAAGTTACTCCCACT 58.110 41.667 0.00 0.00 0.00 4.00
3442 3745 7.025520 ACACTAGTCTAAGTTACTCCCACTA 57.974 40.000 0.00 0.00 0.00 2.74
3443 3746 7.641249 ACACTAGTCTAAGTTACTCCCACTAT 58.359 38.462 0.00 0.00 0.00 2.12
3444 3747 7.556996 ACACTAGTCTAAGTTACTCCCACTATG 59.443 40.741 0.00 0.00 0.00 2.23
3445 3748 7.774157 CACTAGTCTAAGTTACTCCCACTATGA 59.226 40.741 0.00 0.00 0.00 2.15
3446 3749 7.774625 ACTAGTCTAAGTTACTCCCACTATGAC 59.225 40.741 0.00 0.00 31.77 3.06
3447 3750 5.892686 AGTCTAAGTTACTCCCACTATGACC 59.107 44.000 0.00 0.00 31.89 4.02
3448 3751 5.655532 GTCTAAGTTACTCCCACTATGACCA 59.344 44.000 0.00 0.00 0.00 4.02
3449 3752 5.892119 TCTAAGTTACTCCCACTATGACCAG 59.108 44.000 0.00 0.00 0.00 4.00
3450 3753 2.766828 AGTTACTCCCACTATGACCAGC 59.233 50.000 0.00 0.00 0.00 4.85
3451 3754 1.789523 TACTCCCACTATGACCAGCC 58.210 55.000 0.00 0.00 0.00 4.85
3452 3755 0.043334 ACTCCCACTATGACCAGCCT 59.957 55.000 0.00 0.00 0.00 4.58
3453 3756 0.467384 CTCCCACTATGACCAGCCTG 59.533 60.000 0.00 0.00 0.00 4.85
3475 3778 1.480498 GGAGGTTTCCTGCTCCCAAAA 60.480 52.381 0.00 0.00 38.98 2.44
3530 3833 2.044946 ATCGCCCCTTTGAGCACC 60.045 61.111 0.00 0.00 0.00 5.01
3531 3834 3.976701 ATCGCCCCTTTGAGCACCG 62.977 63.158 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 182 2.146342 CACAGTGCTTCGACCAGATTT 58.854 47.619 0.00 0.00 0.00 2.17
243 244 4.199310 GCTGTAATTCTTCCCATGTAGCA 58.801 43.478 0.00 0.00 0.00 3.49
312 313 4.772687 GACCCCGCCTCCCGAAAC 62.773 72.222 0.00 0.00 40.02 2.78
321 322 4.864334 CAGGATGCTGACCCCGCC 62.864 72.222 8.85 0.00 0.00 6.13
347 348 3.031736 GCCCTCTTCAGTAGTGGATGTA 58.968 50.000 0.00 0.00 39.43 2.29
385 532 1.371558 GGCTCTTGTCGACAACCCT 59.628 57.895 26.53 0.00 0.00 4.34
386 533 0.534203 TTGGCTCTTGTCGACAACCC 60.534 55.000 26.53 23.77 0.00 4.11
415 562 6.869913 CGATTTGGGTTGTAGTTCTGTAACTA 59.130 38.462 0.00 0.00 44.26 2.24
457 604 3.577389 GCTTACAAGCCACTGGGAT 57.423 52.632 2.40 0.00 46.20 3.85
497 644 7.223472 AGTACTAAGTAGAATCAGGTACCCT 57.777 40.000 8.74 0.00 31.52 4.34
543 690 4.023707 GTCCAAATCCTAGCCAAATGATCG 60.024 45.833 0.00 0.00 0.00 3.69
544 691 4.023707 CGTCCAAATCCTAGCCAAATGATC 60.024 45.833 0.00 0.00 0.00 2.92
593 740 1.549950 CCTCCCTCCCTCTCAGCTATC 60.550 61.905 0.00 0.00 0.00 2.08
813 999 3.119990 ACTTTTATGATCAACCAACCGCG 60.120 43.478 0.00 0.00 0.00 6.46
816 1002 4.021544 TGCCACTTTTATGATCAACCAACC 60.022 41.667 0.00 0.00 0.00 3.77
870 1056 0.246635 GAGCTAGGGTTTGCGAGTCA 59.753 55.000 0.00 0.00 0.00 3.41
1100 1291 4.480541 CACGAAATCTAGCAGCTATCGAT 58.519 43.478 23.66 12.68 33.42 3.59
1102 1293 2.406691 GCACGAAATCTAGCAGCTATCG 59.593 50.000 17.74 17.74 35.16 2.92
1103 1294 3.428198 CAGCACGAAATCTAGCAGCTATC 59.572 47.826 1.54 0.00 0.00 2.08
1104 1295 3.181471 ACAGCACGAAATCTAGCAGCTAT 60.181 43.478 1.54 0.00 0.00 2.97
1123 1337 2.893637 ACGCTAGCATCAAACCTACAG 58.106 47.619 16.45 0.00 0.00 2.74
1130 1376 4.081642 AGAGGTTCTTACGCTAGCATCAAA 60.082 41.667 16.45 1.85 0.00 2.69
1142 1388 4.895961 ACACCAAAGCTAGAGGTTCTTAC 58.104 43.478 0.00 0.00 34.26 2.34
1145 1391 4.162509 GGATACACCAAAGCTAGAGGTTCT 59.837 45.833 0.00 0.00 38.79 3.01
1167 1413 1.850441 CTAATCGTTTAGTCCGCGTGG 59.150 52.381 9.28 9.28 31.85 4.94
1259 1506 8.798859 AGATCCCATGCAAATATACAGTAATC 57.201 34.615 0.00 0.00 0.00 1.75
1279 1526 1.278238 CGTGAAGCGGTACAAGATCC 58.722 55.000 0.00 0.00 36.85 3.36
1283 1530 0.788391 GGAACGTGAAGCGGTACAAG 59.212 55.000 0.00 0.00 42.72 3.16
1340 1587 4.069304 GCCTGACATAACCAGTACAACAA 58.931 43.478 0.00 0.00 0.00 2.83
1343 1590 2.354303 CCGCCTGACATAACCAGTACAA 60.354 50.000 0.00 0.00 0.00 2.41
1348 1595 1.819632 GCCCGCCTGACATAACCAG 60.820 63.158 0.00 0.00 0.00 4.00
1375 1622 9.388506 GAAGATCTATTGATTCCTTCTCAAACA 57.611 33.333 0.00 0.00 36.30 2.83
1498 1763 6.199937 AGTATCATGAAATGTGAAGTTGCC 57.800 37.500 0.00 0.00 46.80 4.52
1560 1825 2.498644 TGACAAATGGTTATCCGCCA 57.501 45.000 0.00 0.00 40.68 5.69
1561 1826 5.508200 TTAATGACAAATGGTTATCCGCC 57.492 39.130 0.00 0.00 36.30 6.13
1564 1829 9.696917 GATGGAATTAATGACAAATGGTTATCC 57.303 33.333 0.00 0.00 0.00 2.59
1613 1878 1.534595 CACTTGGCAAGAGAGAAGCAC 59.465 52.381 32.50 0.00 0.00 4.40
1741 2009 8.675705 ATGGTTGTCATCATAACGATAATCAA 57.324 30.769 0.00 0.00 28.91 2.57
1750 2018 7.031226 ACATGCTTATGGTTGTCATCATAAC 57.969 36.000 0.00 0.00 37.30 1.89
1947 2219 2.224209 GGTCTTCTTGGTCTTCGGAACA 60.224 50.000 0.00 0.00 40.30 3.18
2007 2279 4.527038 CCCTTCTTGTACTGAGTGACCTTA 59.473 45.833 0.00 0.00 0.00 2.69
2153 2425 2.260844 ATATCATGTTGGCAGGTCGG 57.739 50.000 0.00 0.00 0.00 4.79
2221 2493 2.637872 ACACAGGCACACCATAAGTACT 59.362 45.455 0.00 0.00 39.06 2.73
2280 2552 3.191162 ACGTCACAACATTAGCATTGCAT 59.809 39.130 11.91 0.00 0.00 3.96
2321 2596 3.305199 GCAGCTTCAGCACAATCTTCTTT 60.305 43.478 0.75 0.00 45.16 2.52
2648 2932 0.726827 TCGCCTCTTGCTTAAATGCG 59.273 50.000 0.00 0.00 41.68 4.73
2734 3018 3.021695 CCATGTCAATCAACTCCATGCT 58.978 45.455 0.00 0.00 33.29 3.79
2771 3060 8.480501 ACAGCTTTCATATGCCAAAAAGAATAT 58.519 29.630 15.29 0.30 31.81 1.28
2772 3061 7.839907 ACAGCTTTCATATGCCAAAAAGAATA 58.160 30.769 15.29 0.00 31.81 1.75
2775 3064 5.726980 ACAGCTTTCATATGCCAAAAAGA 57.273 34.783 15.29 0.00 31.81 2.52
2791 3080 3.332919 CAGCAGTCACTGATAACAGCTT 58.667 45.455 9.70 0.00 46.95 3.74
2799 3088 1.067295 TTTCCCCAGCAGTCACTGAT 58.933 50.000 9.70 0.00 40.25 2.90
2837 3126 0.865769 CACAACTAGACACGTTGGGC 59.134 55.000 0.00 0.00 44.49 5.36
2963 3263 5.796350 AGAACCTATTCCGTTTTGATTCG 57.204 39.130 0.00 0.00 35.18 3.34
2981 3281 7.063544 GGAATTATGTGCGAGGATATGTAGAAC 59.936 40.741 0.00 0.00 0.00 3.01
2996 3296 8.850156 ACTTGTATTAAGATGGGAATTATGTGC 58.150 33.333 0.00 0.00 0.00 4.57
3002 3302 7.068716 GCAGGAACTTGTATTAAGATGGGAATT 59.931 37.037 0.00 0.00 34.60 2.17
3021 3321 4.401519 GGAATAGGGGTTTAAAGCAGGAAC 59.598 45.833 18.43 1.35 0.00 3.62
3033 3333 4.921644 TTTCGAAAGAGGAATAGGGGTT 57.078 40.909 6.47 0.00 43.69 4.11
3184 3487 5.650266 ACTATGACTAGCCTCTTATCGATGG 59.350 44.000 8.54 1.12 0.00 3.51
3193 3496 4.258457 AGTTCCACTATGACTAGCCTCT 57.742 45.455 0.00 0.00 0.00 3.69
3198 3501 7.811117 ACTAGCTAAGTTCCACTATGACTAG 57.189 40.000 0.00 0.00 33.35 2.57
3200 3503 7.614583 TGTTACTAGCTAAGTTCCACTATGACT 59.385 37.037 0.00 0.00 39.80 3.41
3201 3504 7.769220 TGTTACTAGCTAAGTTCCACTATGAC 58.231 38.462 0.00 0.00 39.80 3.06
3202 3505 7.949690 TGTTACTAGCTAAGTTCCACTATGA 57.050 36.000 0.00 0.00 39.80 2.15
3203 3506 9.900710 CTATGTTACTAGCTAAGTTCCACTATG 57.099 37.037 0.00 0.00 39.80 2.23
3205 3508 7.255035 CGCTATGTTACTAGCTAAGTTCCACTA 60.255 40.741 0.00 0.00 41.61 2.74
3206 3509 6.459848 CGCTATGTTACTAGCTAAGTTCCACT 60.460 42.308 0.00 0.00 41.61 4.00
3207 3510 5.686397 CGCTATGTTACTAGCTAAGTTCCAC 59.314 44.000 0.00 0.00 41.61 4.02
3209 3512 5.829829 ACGCTATGTTACTAGCTAAGTTCC 58.170 41.667 0.00 0.00 41.61 3.62
3210 3513 7.638134 AGTACGCTATGTTACTAGCTAAGTTC 58.362 38.462 0.00 0.00 41.61 3.01
3211 3514 7.565323 AGTACGCTATGTTACTAGCTAAGTT 57.435 36.000 0.00 0.00 41.61 2.66
3212 3515 7.518052 CGAAGTACGCTATGTTACTAGCTAAGT 60.518 40.741 0.00 0.00 41.61 2.24
3213 3516 6.791299 CGAAGTACGCTATGTTACTAGCTAAG 59.209 42.308 0.00 0.00 41.61 2.18
3216 3519 4.813161 TCGAAGTACGCTATGTTACTAGCT 59.187 41.667 10.40 0.00 41.61 3.32
3217 3520 5.050499 TCTCGAAGTACGCTATGTTACTAGC 60.050 44.000 0.00 4.52 42.26 3.42
3218 3521 6.522233 TCTCGAAGTACGCTATGTTACTAG 57.478 41.667 0.00 0.00 42.26 2.57
3219 3522 6.908870 TTCTCGAAGTACGCTATGTTACTA 57.091 37.500 0.00 0.00 42.26 1.82
3221 3524 6.859715 TTTTCTCGAAGTACGCTATGTTAC 57.140 37.500 0.00 0.00 42.26 2.50
3224 3527 6.253727 CAGAATTTTCTCGAAGTACGCTATGT 59.746 38.462 0.00 0.00 42.26 2.29
3225 3528 6.631847 CAGAATTTTCTCGAAGTACGCTATG 58.368 40.000 0.00 0.00 42.26 2.23
3226 3529 5.232414 GCAGAATTTTCTCGAAGTACGCTAT 59.768 40.000 0.00 0.00 42.26 2.97
3227 3530 4.561606 GCAGAATTTTCTCGAAGTACGCTA 59.438 41.667 0.00 0.00 42.26 4.26
3229 3532 3.368236 AGCAGAATTTTCTCGAAGTACGC 59.632 43.478 0.00 0.00 42.26 4.42
3230 3533 5.517037 AAGCAGAATTTTCTCGAAGTACG 57.483 39.130 0.00 0.00 44.09 3.67
3231 3534 7.900352 CACATAAGCAGAATTTTCTCGAAGTAC 59.100 37.037 0.00 0.00 34.74 2.73
3232 3535 7.413000 GCACATAAGCAGAATTTTCTCGAAGTA 60.413 37.037 0.00 0.00 34.74 2.24
3233 3536 6.621596 GCACATAAGCAGAATTTTCTCGAAGT 60.622 38.462 0.00 0.00 34.74 3.01
3234 3537 5.736358 GCACATAAGCAGAATTTTCTCGAAG 59.264 40.000 0.00 0.00 34.74 3.79
3235 3538 5.181056 TGCACATAAGCAGAATTTTCTCGAA 59.819 36.000 0.00 0.00 40.11 3.71
3236 3539 4.694982 TGCACATAAGCAGAATTTTCTCGA 59.305 37.500 0.00 0.00 40.11 4.04
3237 3540 4.973396 TGCACATAAGCAGAATTTTCTCG 58.027 39.130 0.00 0.00 40.11 4.04
3238 3541 6.385033 ACTTGCACATAAGCAGAATTTTCTC 58.615 36.000 0.00 0.00 46.54 2.87
3239 3542 6.336842 ACTTGCACATAAGCAGAATTTTCT 57.663 33.333 0.00 0.00 46.54 2.52
3240 3543 8.693542 ATTACTTGCACATAAGCAGAATTTTC 57.306 30.769 0.00 0.00 46.54 2.29
3244 3547 9.740239 CATTAATTACTTGCACATAAGCAGAAT 57.260 29.630 0.00 0.00 46.54 2.40
3245 3548 8.955388 TCATTAATTACTTGCACATAAGCAGAA 58.045 29.630 0.00 0.00 46.54 3.02
3246 3549 8.504812 TCATTAATTACTTGCACATAAGCAGA 57.495 30.769 0.00 0.00 46.54 4.26
3247 3550 8.615211 TCTCATTAATTACTTGCACATAAGCAG 58.385 33.333 0.00 0.00 46.54 4.24
3248 3551 8.504812 TCTCATTAATTACTTGCACATAAGCA 57.495 30.769 0.00 0.00 43.99 3.91
3249 3552 8.830580 TCTCTCATTAATTACTTGCACATAAGC 58.169 33.333 0.00 0.00 0.00 3.09
3252 3555 9.276590 CCATCTCTCATTAATTACTTGCACATA 57.723 33.333 0.00 0.00 0.00 2.29
3253 3556 7.776969 ACCATCTCTCATTAATTACTTGCACAT 59.223 33.333 0.00 0.00 0.00 3.21
3254 3557 7.112122 ACCATCTCTCATTAATTACTTGCACA 58.888 34.615 0.00 0.00 0.00 4.57
3255 3558 7.559590 ACCATCTCTCATTAATTACTTGCAC 57.440 36.000 0.00 0.00 0.00 4.57
3256 3559 9.109393 GTTACCATCTCTCATTAATTACTTGCA 57.891 33.333 0.00 0.00 0.00 4.08
3257 3560 9.109393 TGTTACCATCTCTCATTAATTACTTGC 57.891 33.333 0.00 0.00 0.00 4.01
3289 3592 7.570507 CTTGAAAAGCGCTATGTTACAGTAACA 60.571 37.037 25.09 25.09 44.55 2.41
3290 3593 6.160664 TGAAAAGCGCTATGTTACAGTAAC 57.839 37.500 12.05 15.58 39.11 2.50
3291 3594 6.647481 TCTTGAAAAGCGCTATGTTACAGTAA 59.353 34.615 12.05 0.00 45.70 2.24
3292 3595 6.090358 GTCTTGAAAAGCGCTATGTTACAGTA 59.910 38.462 12.05 0.00 45.70 2.74
3293 3596 4.994852 TCTTGAAAAGCGCTATGTTACAGT 59.005 37.500 12.05 0.00 45.70 3.55
3294 3597 5.107104 TGTCTTGAAAAGCGCTATGTTACAG 60.107 40.000 12.05 5.30 45.70 2.74
3295 3598 4.752604 TGTCTTGAAAAGCGCTATGTTACA 59.247 37.500 12.05 7.09 45.70 2.41
3296 3599 5.277601 TGTCTTGAAAAGCGCTATGTTAC 57.722 39.130 12.05 4.27 45.70 2.50
3297 3600 5.699001 TCTTGTCTTGAAAAGCGCTATGTTA 59.301 36.000 12.05 0.00 45.70 2.41
3298 3601 4.515191 TCTTGTCTTGAAAAGCGCTATGTT 59.485 37.500 12.05 5.31 45.70 2.71
3299 3602 4.065088 TCTTGTCTTGAAAAGCGCTATGT 58.935 39.130 12.05 0.00 45.70 2.29
3300 3603 4.668576 TCTTGTCTTGAAAAGCGCTATG 57.331 40.909 12.05 0.00 45.70 2.23
3301 3604 4.937620 TCATCTTGTCTTGAAAAGCGCTAT 59.062 37.500 12.05 1.76 45.70 2.97
3302 3605 4.314961 TCATCTTGTCTTGAAAAGCGCTA 58.685 39.130 12.05 0.00 45.70 4.26
3303 3606 3.141398 TCATCTTGTCTTGAAAAGCGCT 58.859 40.909 2.64 2.64 45.70 5.92
3304 3607 3.058639 ACTCATCTTGTCTTGAAAAGCGC 60.059 43.478 0.00 0.00 45.70 5.92
3305 3608 4.450419 AGACTCATCTTGTCTTGAAAAGCG 59.550 41.667 0.00 0.00 45.70 4.68
3306 3609 5.938438 AGACTCATCTTGTCTTGAAAAGC 57.062 39.130 0.00 0.00 45.70 3.51
3307 3610 6.090088 CCGTAGACTCATCTTGTCTTGAAAAG 59.910 42.308 1.67 0.00 41.45 2.27
3308 3611 5.926542 CCGTAGACTCATCTTGTCTTGAAAA 59.073 40.000 1.67 0.00 41.45 2.29
3309 3612 5.470368 CCGTAGACTCATCTTGTCTTGAAA 58.530 41.667 1.67 0.00 41.45 2.69
3310 3613 4.082190 CCCGTAGACTCATCTTGTCTTGAA 60.082 45.833 1.67 0.00 41.45 2.69
3311 3614 3.444034 CCCGTAGACTCATCTTGTCTTGA 59.556 47.826 1.67 0.00 41.45 3.02
3312 3615 3.775202 CCCGTAGACTCATCTTGTCTTG 58.225 50.000 1.67 0.00 41.45 3.02
3313 3616 2.166664 GCCCGTAGACTCATCTTGTCTT 59.833 50.000 1.67 0.00 41.45 3.01
3314 3617 1.751924 GCCCGTAGACTCATCTTGTCT 59.248 52.381 0.00 0.00 45.48 3.41
3315 3618 1.751924 AGCCCGTAGACTCATCTTGTC 59.248 52.381 0.00 0.00 36.29 3.18
3316 3619 1.853963 AGCCCGTAGACTCATCTTGT 58.146 50.000 0.00 0.00 36.29 3.16
3317 3620 4.592485 ATTAGCCCGTAGACTCATCTTG 57.408 45.455 0.00 0.00 36.29 3.02
3318 3621 6.726490 TTTATTAGCCCGTAGACTCATCTT 57.274 37.500 0.00 0.00 36.29 2.40
3319 3622 6.493802 TCATTTATTAGCCCGTAGACTCATCT 59.506 38.462 0.00 0.00 39.15 2.90
3320 3623 6.688578 TCATTTATTAGCCCGTAGACTCATC 58.311 40.000 0.00 0.00 0.00 2.92
3321 3624 6.665992 TCATTTATTAGCCCGTAGACTCAT 57.334 37.500 0.00 0.00 0.00 2.90
3322 3625 6.474140 TTCATTTATTAGCCCGTAGACTCA 57.526 37.500 0.00 0.00 0.00 3.41
3323 3626 5.405873 GCTTCATTTATTAGCCCGTAGACTC 59.594 44.000 0.00 0.00 0.00 3.36
3324 3627 5.298347 GCTTCATTTATTAGCCCGTAGACT 58.702 41.667 0.00 0.00 0.00 3.24
3325 3628 4.451435 GGCTTCATTTATTAGCCCGTAGAC 59.549 45.833 0.00 0.00 46.94 2.59
3326 3629 4.638304 GGCTTCATTTATTAGCCCGTAGA 58.362 43.478 0.00 0.00 46.94 2.59
3370 3673 9.953565 AGTTACTACCTTCATAATGCAAAGTAA 57.046 29.630 0.00 0.00 0.00 2.24
3371 3674 9.953565 AAGTTACTACCTTCATAATGCAAAGTA 57.046 29.630 0.00 0.00 0.00 2.24
3372 3675 8.863872 AAGTTACTACCTTCATAATGCAAAGT 57.136 30.769 0.00 0.00 0.00 2.66
3375 3678 9.595823 GTCTAAGTTACTACCTTCATAATGCAA 57.404 33.333 0.00 0.00 0.00 4.08
3376 3679 8.978472 AGTCTAAGTTACTACCTTCATAATGCA 58.022 33.333 0.00 0.00 0.00 3.96
3382 3685 9.176460 GACACTAGTCTAAGTTACTACCTTCAT 57.824 37.037 0.00 0.00 41.64 2.57
3383 3686 8.159447 TGACACTAGTCTAAGTTACTACCTTCA 58.841 37.037 0.00 0.00 45.20 3.02
3384 3687 8.558973 TGACACTAGTCTAAGTTACTACCTTC 57.441 38.462 0.00 0.00 45.20 3.46
3388 3691 9.881529 GCATATGACACTAGTCTAAGTTACTAC 57.118 37.037 6.97 0.00 45.20 2.73
3389 3692 9.623000 TGCATATGACACTAGTCTAAGTTACTA 57.377 33.333 6.97 0.00 45.20 1.82
3390 3693 8.521170 TGCATATGACACTAGTCTAAGTTACT 57.479 34.615 6.97 0.00 45.20 2.24
3391 3694 9.186323 CATGCATATGACACTAGTCTAAGTTAC 57.814 37.037 6.97 0.00 45.20 2.50
3392 3695 9.131791 TCATGCATATGACACTAGTCTAAGTTA 57.868 33.333 6.97 0.00 45.20 2.24
3393 3696 8.011844 TCATGCATATGACACTAGTCTAAGTT 57.988 34.615 6.97 0.00 45.20 2.66
3394 3697 7.588497 TCATGCATATGACACTAGTCTAAGT 57.412 36.000 6.97 0.00 45.20 2.24
3407 3710 7.588497 ACTTAGACTAGTGTCATGCATATGA 57.412 36.000 6.97 0.00 45.20 2.15
3408 3711 9.186323 GTAACTTAGACTAGTGTCATGCATATG 57.814 37.037 0.00 0.00 45.20 1.78
3409 3712 9.137459 AGTAACTTAGACTAGTGTCATGCATAT 57.863 33.333 0.00 0.00 45.20 1.78
3410 3713 8.521170 AGTAACTTAGACTAGTGTCATGCATA 57.479 34.615 0.00 0.00 45.20 3.14
3411 3714 7.411486 AGTAACTTAGACTAGTGTCATGCAT 57.589 36.000 0.00 0.00 45.20 3.96
3412 3715 6.127703 GGAGTAACTTAGACTAGTGTCATGCA 60.128 42.308 0.00 0.00 45.20 3.96
3413 3716 6.267070 GGAGTAACTTAGACTAGTGTCATGC 58.733 44.000 0.00 0.00 45.20 4.06
3414 3717 6.377429 TGGGAGTAACTTAGACTAGTGTCATG 59.623 42.308 0.00 0.00 45.20 3.07
3415 3718 6.377712 GTGGGAGTAACTTAGACTAGTGTCAT 59.622 42.308 0.00 0.00 45.20 3.06
3416 3719 5.709164 GTGGGAGTAACTTAGACTAGTGTCA 59.291 44.000 0.00 0.00 45.20 3.58
3417 3720 5.945191 AGTGGGAGTAACTTAGACTAGTGTC 59.055 44.000 0.00 0.00 43.22 3.67
3418 3721 5.890049 AGTGGGAGTAACTTAGACTAGTGT 58.110 41.667 0.00 0.00 0.00 3.55
3419 3722 7.774157 TCATAGTGGGAGTAACTTAGACTAGTG 59.226 40.741 0.00 0.00 0.00 2.74
3420 3723 7.774625 GTCATAGTGGGAGTAACTTAGACTAGT 59.225 40.741 0.00 0.00 32.20 2.57
3421 3724 7.229106 GGTCATAGTGGGAGTAACTTAGACTAG 59.771 44.444 0.00 0.00 33.88 2.57
3422 3725 7.059156 GGTCATAGTGGGAGTAACTTAGACTA 58.941 42.308 0.00 0.00 33.88 2.59
3423 3726 5.892686 GGTCATAGTGGGAGTAACTTAGACT 59.107 44.000 0.00 0.00 33.88 3.24
3424 3727 5.655532 TGGTCATAGTGGGAGTAACTTAGAC 59.344 44.000 0.00 0.00 33.22 2.59
3425 3728 5.834460 TGGTCATAGTGGGAGTAACTTAGA 58.166 41.667 0.00 0.00 0.00 2.10
3426 3729 5.452077 GCTGGTCATAGTGGGAGTAACTTAG 60.452 48.000 0.00 0.00 0.00 2.18
3427 3730 4.404715 GCTGGTCATAGTGGGAGTAACTTA 59.595 45.833 0.00 0.00 0.00 2.24
3428 3731 3.197983 GCTGGTCATAGTGGGAGTAACTT 59.802 47.826 0.00 0.00 0.00 2.66
3429 3732 2.766828 GCTGGTCATAGTGGGAGTAACT 59.233 50.000 0.00 0.00 0.00 2.24
3430 3733 2.158943 GGCTGGTCATAGTGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
3431 3734 2.116238 GGCTGGTCATAGTGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
3432 3735 1.291033 AGGCTGGTCATAGTGGGAGTA 59.709 52.381 0.00 0.00 0.00 2.59
3433 3736 0.043334 AGGCTGGTCATAGTGGGAGT 59.957 55.000 0.00 0.00 0.00 3.85
3434 3737 0.467384 CAGGCTGGTCATAGTGGGAG 59.533 60.000 6.61 0.00 0.00 4.30
3435 3738 0.042581 TCAGGCTGGTCATAGTGGGA 59.957 55.000 15.73 0.00 0.00 4.37
3436 3739 0.467384 CTCAGGCTGGTCATAGTGGG 59.533 60.000 15.73 0.00 0.00 4.61
3437 3740 0.467384 CCTCAGGCTGGTCATAGTGG 59.533 60.000 15.73 1.12 0.00 4.00
3438 3741 1.411977 CTCCTCAGGCTGGTCATAGTG 59.588 57.143 15.73 0.00 0.00 2.74
3439 3742 1.690845 CCTCCTCAGGCTGGTCATAGT 60.691 57.143 15.73 0.00 30.98 2.12
3440 3743 1.047002 CCTCCTCAGGCTGGTCATAG 58.953 60.000 15.73 3.79 30.98 2.23
3441 3744 0.339859 ACCTCCTCAGGCTGGTCATA 59.660 55.000 15.73 0.00 45.05 2.15
3442 3745 0.548682 AACCTCCTCAGGCTGGTCAT 60.549 55.000 15.73 0.00 45.05 3.06
3443 3746 0.768221 AAACCTCCTCAGGCTGGTCA 60.768 55.000 15.73 0.00 45.05 4.02
3444 3747 0.035915 GAAACCTCCTCAGGCTGGTC 60.036 60.000 15.73 0.00 45.05 4.02
3445 3748 1.492993 GGAAACCTCCTCAGGCTGGT 61.493 60.000 15.73 0.30 45.05 4.00
3446 3749 1.301293 GGAAACCTCCTCAGGCTGG 59.699 63.158 15.73 5.31 45.05 4.85
3466 3769 0.387565 TTTCGGTGCTTTTTGGGAGC 59.612 50.000 0.00 0.00 40.53 4.70
3475 3778 0.580104 CGACGTTTCTTTCGGTGCTT 59.420 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.