Multiple sequence alignment - TraesCS7D01G235800

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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 TraesCS7D01G235800 chr7D 100.000 4131 0 0 1 4131 198717633 198713503 0.000000e+00 7629.0
1 TraesCS7D01G235800 chr7D 86.667 240 28 4 3293 3529 610799096 610798858 3.170000e-66 263.0
2 TraesCS7D01G235800 chr7D 87.281 228 25 3 3305 3528 474009681 474009908 1.470000e-64 257.0
3 TraesCS7D01G235800 chr7A 93.430 3318 153 36 1 3297 208129818 208126545 0.000000e+00 4859.0
4 TraesCS7D01G235800 chr7A 91.077 325 18 9 3696 4012 208126151 208125830 2.950000e-116 429.0
5 TraesCS7D01G235800 chr7A 89.076 119 8 3 3525 3638 208126552 208126434 4.300000e-30 143.0
6 TraesCS7D01G235800 chr7B 96.546 1274 36 4 1870 3143 162587544 162588809 0.000000e+00 2102.0
7 TraesCS7D01G235800 chr7B 85.735 1374 124 39 488 1832 162571973 162573303 0.000000e+00 1386.0
8 TraesCS7D01G235800 chr7B 86.820 478 16 27 3525 3987 162588911 162589356 1.330000e-134 490.0
9 TraesCS7D01G235800 chr7B 87.013 231 25 4 3305 3530 498088909 498089139 5.300000e-64 255.0
10 TraesCS7D01G235800 chr7B 85.185 243 28 8 3292 3529 717161969 717162208 4.130000e-60 243.0
11 TraesCS7D01G235800 chr7B 94.872 117 4 2 3183 3297 162588802 162588918 9.120000e-42 182.0
12 TraesCS7D01G235800 chr6A 87.295 244 26 5 3290 3529 578513078 578513320 1.460000e-69 274.0
13 TraesCS7D01G235800 chr6A 85.714 245 31 4 3290 3531 514704871 514705114 5.300000e-64 255.0
14 TraesCS7D01G235800 chr4D 85.484 248 29 7 3293 3534 503627236 503626990 6.860000e-63 252.0
15 TraesCS7D01G235800 chr1D 86.842 228 27 3 3305 3529 465990807 465991034 6.860000e-63 252.0
16 TraesCS7D01G235800 chr5B 85.366 246 31 4 3290 3532 516403919 516404162 2.470000e-62 250.0
17 TraesCS7D01G235800 chr1B 100.000 28 0 0 2682 2709 342086264 342086237 7.000000e-03 52.8


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 TraesCS7D01G235800 chr7D 198713503 198717633 4130 True 7629.000000 7629 100.000000 1 4131 1 chr7D.!!$R1 4130
1 TraesCS7D01G235800 chr7A 208125830 208129818 3988 True 1810.333333 4859 91.194333 1 4012 3 chr7A.!!$R1 4011
2 TraesCS7D01G235800 chr7B 162571973 162573303 1330 False 1386.000000 1386 85.735000 488 1832 1 chr7B.!!$F1 1344
3 TraesCS7D01G235800 chr7B 162587544 162589356 1812 False 924.666667 2102 92.746000 1870 3987 3 chr7B.!!$F4 2117

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
346 347 0.039618 TCCAATTTGGGAGGCTCCAC 59.960 55.000 33.27 22.57 38.64 4.02 F
423 424 0.109365 CCATCACCATTGCGCGAAAA 60.109 50.000 12.10 3.06 0.00 2.29 F
1463 1488 0.620556 TGGAGGAATTCAGCAGGGAC 59.379 55.000 7.93 0.00 0.00 4.46 F
2140 2172 2.202570 CGCAAGTACCTCGACGGG 60.203 66.667 0.00 0.00 36.97 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 1942 0.165727 TCGCACGCAAACATGATGAC 59.834 50.000 0.00 0.0 0.0 3.06 R
2326 2358 1.444553 CAGGAGGTTGACGACGAGC 60.445 63.158 0.00 0.0 0.0 5.03 R
2539 2571 0.246635 AGTACGCGTGCCTCAAGAAT 59.753 50.000 24.59 0.0 0.0 2.40 R
4023 4318 0.380733 CGCTGGCTAGACGTGTCATA 59.619 55.000 0.00 0.0 0.0 2.15 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
91 92 1.133869 GGTGTCGCGGTAATGTTGC 59.866 57.895 6.13 0.00 0.00 4.17
196 197 5.030147 TGAGCTTGGGAGTTTCTATTCCTA 58.970 41.667 0.00 0.00 33.85 2.94
212 213 1.407618 TCCTATCGGTGTTCATGGACG 59.592 52.381 0.00 0.00 0.00 4.79
227 228 4.952262 ATGGACGACATGTTGATTCTTG 57.048 40.909 20.26 0.00 38.70 3.02
244 245 6.257849 TGATTCTTGATACTTTACATCGGTGC 59.742 38.462 0.00 0.00 0.00 5.01
271 272 1.364721 TGGCATCGTCAACGGTATTG 58.635 50.000 2.31 0.00 40.29 1.90
279 280 3.676172 TCGTCAACGGTATTGTCATGTTC 59.324 43.478 2.31 0.00 40.29 3.18
285 286 4.843728 ACGGTATTGTCATGTTCTCCAAT 58.156 39.130 0.00 0.00 0.00 3.16
309 310 2.507484 TGAGTCTTTGTGGGCAAGATG 58.493 47.619 0.00 0.00 35.82 2.90
324 325 1.194781 AGATGGTTGCCTGTCCGTCT 61.195 55.000 0.00 0.00 42.95 4.18
346 347 0.039618 TCCAATTTGGGAGGCTCCAC 59.960 55.000 33.27 22.57 38.64 4.02
347 348 1.315257 CCAATTTGGGAGGCTCCACG 61.315 60.000 33.27 14.53 38.64 4.94
348 349 1.678970 AATTTGGGAGGCTCCACGC 60.679 57.895 33.27 17.66 38.64 5.34
349 350 2.424842 AATTTGGGAGGCTCCACGCA 62.425 55.000 33.27 20.08 38.64 5.24
350 351 3.842925 TTTGGGAGGCTCCACGCAC 62.843 63.158 33.27 16.93 38.64 5.34
360 361 2.434884 CCACGCACGCAATCCTCT 60.435 61.111 0.00 0.00 0.00 3.69
374 375 5.704515 CGCAATCCTCTCCTAATCAATCATT 59.295 40.000 0.00 0.00 0.00 2.57
376 377 6.072064 GCAATCCTCTCCTAATCAATCATTGG 60.072 42.308 0.00 0.00 0.00 3.16
377 378 7.229308 CAATCCTCTCCTAATCAATCATTGGA 58.771 38.462 0.00 0.00 0.00 3.53
392 393 9.806203 TCAATCATTGGATGAAAAATACATGTC 57.194 29.630 0.00 0.00 43.50 3.06
393 394 9.811995 CAATCATTGGATGAAAAATACATGTCT 57.188 29.630 0.00 0.00 43.50 3.41
399 400 8.492673 TGGATGAAAAATACATGTCTAGACAC 57.507 34.615 27.41 11.94 45.05 3.67
408 409 1.568504 TGTCTAGACACCCCACCATC 58.431 55.000 21.74 0.00 36.21 3.51
409 410 1.203250 TGTCTAGACACCCCACCATCA 60.203 52.381 21.74 0.00 36.21 3.07
421 422 1.673993 ACCATCACCATTGCGCGAA 60.674 52.632 12.10 0.00 0.00 4.70
422 423 1.240641 ACCATCACCATTGCGCGAAA 61.241 50.000 12.10 5.91 0.00 3.46
423 424 0.109365 CCATCACCATTGCGCGAAAA 60.109 50.000 12.10 3.06 0.00 2.29
424 425 1.668337 CCATCACCATTGCGCGAAAAA 60.668 47.619 12.10 0.00 0.00 1.94
451 452 2.428890 CTCTTCCTGAAGTAGATGCGGT 59.571 50.000 6.78 0.00 39.38 5.68
457 458 1.893137 TGAAGTAGATGCGGTGACACT 59.107 47.619 5.39 0.00 0.00 3.55
570 571 9.692749 TCGCTCTAAGTTCCATAATTATAACAG 57.307 33.333 11.78 4.11 0.00 3.16
587 588 8.770850 TTATAACAGTTTTACAAGAAACGTGC 57.229 30.769 0.00 0.00 42.78 5.34
589 590 3.033185 CAGTTTTACAAGAAACGTGCGG 58.967 45.455 0.00 0.00 42.78 5.69
774 777 2.182516 AGGGAGAAGGATCCACGATT 57.817 50.000 15.82 0.00 41.52 3.34
784 787 3.142174 GGATCCACGATTCCATTCCTTC 58.858 50.000 6.95 0.00 0.00 3.46
846 849 6.127703 CGGAAGTCCAAGTGTCTCTCTTATTA 60.128 42.308 0.00 0.00 35.14 0.98
847 850 7.262048 GGAAGTCCAAGTGTCTCTCTTATTAG 58.738 42.308 0.00 0.00 35.64 1.73
1065 1076 1.811679 GCCGTGGAAGAGCAGCTAC 60.812 63.158 0.00 0.00 0.00 3.58
1071 1082 0.670546 GGAAGAGCAGCTACGTTGCA 60.671 55.000 23.41 0.00 42.09 4.08
1098 1109 4.087892 TTGCTCGGCTCCCTGCTC 62.088 66.667 0.00 0.00 42.39 4.26
1107 1118 2.604686 TCCCTGCTCGTGCTCCTT 60.605 61.111 11.19 0.00 40.48 3.36
1178 1189 7.118496 TGATCAATCCTCCTCTTCTTCTAAC 57.882 40.000 0.00 0.00 0.00 2.34
1180 1191 6.783708 TCAATCCTCCTCTTCTTCTAACTC 57.216 41.667 0.00 0.00 0.00 3.01
1184 1195 5.505780 TCCTCCTCTTCTTCTAACTCTCAG 58.494 45.833 0.00 0.00 0.00 3.35
1185 1196 4.644685 CCTCCTCTTCTTCTAACTCTCAGG 59.355 50.000 0.00 0.00 0.00 3.86
1191 1204 5.478679 TCTTCTTCTAACTCTCAGGGTGAAG 59.521 44.000 0.00 0.00 0.00 3.02
1192 1205 4.999310 TCTTCTAACTCTCAGGGTGAAGA 58.001 43.478 3.76 3.76 36.94 2.87
1299 1319 1.645455 CGGCAATCGATTCAGCTGG 59.355 57.895 15.13 8.69 42.43 4.85
1301 1321 1.382522 GGCAATCGATTCAGCTGGAA 58.617 50.000 15.13 7.46 40.46 3.53
1333 1353 1.937391 GCATCGAAGAAGCCATCCG 59.063 57.895 0.00 0.00 46.44 4.18
1366 1390 4.323602 ACGCACGCAGAATCAATATATACG 59.676 41.667 0.00 0.00 0.00 3.06
1374 1398 7.921214 CGCAGAATCAATATATACGTAGGGATT 59.079 37.037 0.08 4.02 0.00 3.01
1409 1433 7.692908 TTTTGTGTAGCTAAATTTGCTGAAC 57.307 32.000 19.13 16.79 41.32 3.18
1463 1488 0.620556 TGGAGGAATTCAGCAGGGAC 59.379 55.000 7.93 0.00 0.00 4.46
1598 1624 3.988517 ACAAGTCTCGATTTCGACCTTTC 59.011 43.478 0.00 0.00 44.22 2.62
1694 1720 7.668052 ACAACTAGGTGCCATTTCTGTTTATTA 59.332 33.333 7.97 0.00 0.00 0.98
1697 1723 9.914834 ACTAGGTGCCATTTCTGTTTATTATTA 57.085 29.630 0.00 0.00 0.00 0.98
1721 1750 7.840342 ATTGTTGTTGTTGTTCAATTAGCAA 57.160 28.000 0.00 0.00 38.38 3.91
1736 1765 5.919272 ATTAGCAATCATCGTGTCATCAG 57.081 39.130 0.00 0.00 0.00 2.90
1847 1879 5.984233 CGAATCAAAGGAATTCGGTATGA 57.016 39.130 9.70 2.22 42.18 2.15
1848 1880 6.545504 CGAATCAAAGGAATTCGGTATGAT 57.454 37.500 9.70 4.41 42.18 2.45
1910 1942 2.408704 GTCAAGTTCGATCTGGTGAACG 59.591 50.000 0.00 0.00 46.94 3.95
2140 2172 2.202570 CGCAAGTACCTCGACGGG 60.203 66.667 0.00 0.00 36.97 5.28
2326 2358 3.322466 AACGGGGAGGTCCAGCTG 61.322 66.667 6.78 6.78 37.91 4.24
2525 2557 2.513897 GCGGGGACTACACCATGC 60.514 66.667 0.00 0.00 40.12 4.06
2539 2571 1.421268 ACCATGCTTGACTTCACCAGA 59.579 47.619 0.22 0.00 0.00 3.86
2668 2700 1.089920 CAAACAGCCGGAAGATCCTG 58.910 55.000 5.05 3.92 33.30 3.86
2718 2750 2.671963 GGCGGGGTTCAAGGTGAC 60.672 66.667 0.00 0.00 0.00 3.67
3058 3090 3.066814 GCGGAGTGGTACCTCGGT 61.067 66.667 14.36 0.00 35.06 4.69
3082 3114 2.726691 GGACGTGCGGATCAACGTG 61.727 63.158 20.65 0.00 39.02 4.49
3132 3164 0.321671 TTGGAGCACCTGCAGTAGAC 59.678 55.000 13.81 0.00 45.16 2.59
3151 3183 8.562892 CAGTAGACAGTTTGATTGAACAAAGAT 58.437 33.333 0.00 0.00 39.83 2.40
3155 3187 9.288576 AGACAGTTTGATTGAACAAAGATGATA 57.711 29.630 0.00 0.00 39.83 2.15
3270 3302 9.787435 AATGTACACGGATGGTAATTAATATGT 57.213 29.630 0.00 0.00 0.00 2.29
3271 3303 8.596271 TGTACACGGATGGTAATTAATATGTG 57.404 34.615 0.00 0.00 0.00 3.21
3298 3332 9.811995 TCAATGTACAACAATCATAGTACTACC 57.188 33.333 4.31 0.00 38.09 3.18
3299 3333 9.817809 CAATGTACAACAATCATAGTACTACCT 57.182 33.333 4.31 0.00 38.09 3.08
3302 3336 8.615211 TGTACAACAATCATAGTACTACCTACG 58.385 37.037 4.31 0.00 38.09 3.51
3303 3337 7.870509 ACAACAATCATAGTACTACCTACGA 57.129 36.000 4.31 0.00 0.00 3.43
3304 3338 8.461249 ACAACAATCATAGTACTACCTACGAT 57.539 34.615 4.31 0.38 0.00 3.73
3305 3339 8.566260 ACAACAATCATAGTACTACCTACGATC 58.434 37.037 4.31 0.00 0.00 3.69
3306 3340 7.684937 ACAATCATAGTACTACCTACGATCC 57.315 40.000 4.31 0.00 0.00 3.36
3307 3341 7.460071 ACAATCATAGTACTACCTACGATCCT 58.540 38.462 4.31 0.00 0.00 3.24
3308 3342 7.390996 ACAATCATAGTACTACCTACGATCCTG 59.609 40.741 4.31 0.00 0.00 3.86
3309 3343 6.676990 TCATAGTACTACCTACGATCCTGA 57.323 41.667 4.31 0.00 0.00 3.86
3310 3344 7.255199 TCATAGTACTACCTACGATCCTGAT 57.745 40.000 4.31 0.00 0.00 2.90
3311 3345 7.687388 TCATAGTACTACCTACGATCCTGATT 58.313 38.462 4.31 0.00 0.00 2.57
3312 3346 8.162085 TCATAGTACTACCTACGATCCTGATTT 58.838 37.037 4.31 0.00 0.00 2.17
3313 3347 9.445878 CATAGTACTACCTACGATCCTGATTTA 57.554 37.037 4.31 0.00 0.00 1.40
3314 3348 7.742556 AGTACTACCTACGATCCTGATTTAC 57.257 40.000 0.00 0.00 0.00 2.01
3315 3349 6.714356 AGTACTACCTACGATCCTGATTTACC 59.286 42.308 0.00 0.00 0.00 2.85
3316 3350 4.518211 ACTACCTACGATCCTGATTTACCG 59.482 45.833 0.00 0.00 0.00 4.02
3317 3351 2.626743 ACCTACGATCCTGATTTACCGG 59.373 50.000 0.00 0.00 0.00 5.28
3318 3352 2.626743 CCTACGATCCTGATTTACCGGT 59.373 50.000 13.98 13.98 0.00 5.28
3319 3353 2.884894 ACGATCCTGATTTACCGGTC 57.115 50.000 12.40 0.00 0.00 4.79
3320 3354 1.411612 ACGATCCTGATTTACCGGTCC 59.588 52.381 12.40 0.00 0.00 4.46
3321 3355 1.270147 CGATCCTGATTTACCGGTCCC 60.270 57.143 12.40 0.00 0.00 4.46
3322 3356 2.047830 GATCCTGATTTACCGGTCCCT 58.952 52.381 12.40 0.00 0.00 4.20
3323 3357 1.961133 TCCTGATTTACCGGTCCCTT 58.039 50.000 12.40 0.00 0.00 3.95
3324 3358 2.271777 TCCTGATTTACCGGTCCCTTT 58.728 47.619 12.40 0.00 0.00 3.11
3325 3359 2.026636 TCCTGATTTACCGGTCCCTTTG 60.027 50.000 12.40 0.00 0.00 2.77
3326 3360 1.743394 CTGATTTACCGGTCCCTTTGC 59.257 52.381 12.40 0.00 0.00 3.68
3327 3361 1.074084 TGATTTACCGGTCCCTTTGCA 59.926 47.619 12.40 0.00 0.00 4.08
3328 3362 2.291282 TGATTTACCGGTCCCTTTGCAT 60.291 45.455 12.40 0.00 0.00 3.96
3329 3363 2.296073 TTTACCGGTCCCTTTGCATT 57.704 45.000 12.40 0.00 0.00 3.56
3330 3364 2.296073 TTACCGGTCCCTTTGCATTT 57.704 45.000 12.40 0.00 0.00 2.32
3331 3365 2.296073 TACCGGTCCCTTTGCATTTT 57.704 45.000 12.40 0.00 0.00 1.82
3332 3366 0.678950 ACCGGTCCCTTTGCATTTTG 59.321 50.000 0.00 0.00 0.00 2.44
3333 3367 0.678950 CCGGTCCCTTTGCATTTTGT 59.321 50.000 0.00 0.00 0.00 2.83
3334 3368 1.605202 CCGGTCCCTTTGCATTTTGTG 60.605 52.381 0.00 0.00 0.00 3.33
3349 3383 6.607735 CATTTTGTGCCAAACTTTGATCTT 57.392 33.333 2.87 0.00 0.00 2.40
3350 3384 7.712264 CATTTTGTGCCAAACTTTGATCTTA 57.288 32.000 2.87 0.00 0.00 2.10
3351 3385 7.790000 CATTTTGTGCCAAACTTTGATCTTAG 58.210 34.615 2.87 0.00 0.00 2.18
3352 3386 6.707440 TTTGTGCCAAACTTTGATCTTAGA 57.293 33.333 2.87 0.00 0.00 2.10
3353 3387 6.899393 TTGTGCCAAACTTTGATCTTAGAT 57.101 33.333 2.87 0.00 0.00 1.98
3354 3388 6.899393 TGTGCCAAACTTTGATCTTAGATT 57.101 33.333 2.87 0.00 0.00 2.40
3355 3389 7.288810 TGTGCCAAACTTTGATCTTAGATTT 57.711 32.000 2.87 0.00 0.00 2.17
3356 3390 8.402798 TGTGCCAAACTTTGATCTTAGATTTA 57.597 30.769 2.87 0.00 0.00 1.40
3357 3391 8.855110 TGTGCCAAACTTTGATCTTAGATTTAA 58.145 29.630 2.87 0.00 0.00 1.52
3358 3392 9.129209 GTGCCAAACTTTGATCTTAGATTTAAC 57.871 33.333 2.87 0.00 0.00 2.01
3359 3393 9.077885 TGCCAAACTTTGATCTTAGATTTAACT 57.922 29.630 2.87 0.00 0.00 2.24
3383 3417 9.973450 ACTAACAAAATGTTAATGCATGTAACA 57.027 25.926 24.01 24.01 41.70 2.41
3505 3539 8.777578 ATTTAGGACAAAATATTAAGGGGTCC 57.222 34.615 12.43 12.43 42.75 4.46
3506 3540 5.806955 AGGACAAAATATTAAGGGGTCCA 57.193 39.130 18.28 0.00 44.38 4.02
3507 3541 6.160483 AGGACAAAATATTAAGGGGTCCAA 57.840 37.500 18.28 0.00 44.38 3.53
3508 3542 6.752091 AGGACAAAATATTAAGGGGTCCAAT 58.248 36.000 18.28 4.51 44.38 3.16
3509 3543 7.889178 AGGACAAAATATTAAGGGGTCCAATA 58.111 34.615 18.28 0.00 44.38 1.90
3510 3544 8.348354 AGGACAAAATATTAAGGGGTCCAATAA 58.652 33.333 18.28 0.00 44.38 1.40
3511 3545 8.983789 GGACAAAATATTAAGGGGTCCAATAAA 58.016 33.333 14.21 0.00 42.17 1.40
3516 3550 8.956446 AATATTAAGGGGTCCAATAAATCAGG 57.044 34.615 0.00 0.00 0.00 3.86
3517 3551 6.606241 ATTAAGGGGTCCAATAAATCAGGA 57.394 37.500 0.00 0.00 0.00 3.86
3523 3557 3.467803 GTCCAATAAATCAGGACGGAGG 58.532 50.000 0.00 0.00 42.02 4.30
3524 3558 3.112263 TCCAATAAATCAGGACGGAGGT 58.888 45.455 0.00 0.00 0.00 3.85
3525 3559 4.100498 GTCCAATAAATCAGGACGGAGGTA 59.900 45.833 0.00 0.00 42.02 3.08
3526 3560 4.344102 TCCAATAAATCAGGACGGAGGTAG 59.656 45.833 0.00 0.00 0.00 3.18
3527 3561 4.101119 CCAATAAATCAGGACGGAGGTAGT 59.899 45.833 0.00 0.00 0.00 2.73
3528 3562 5.303589 CCAATAAATCAGGACGGAGGTAGTA 59.696 44.000 0.00 0.00 0.00 1.82
3529 3563 6.214399 CAATAAATCAGGACGGAGGTAGTAC 58.786 44.000 0.00 0.00 0.00 2.73
3530 3564 3.666345 AATCAGGACGGAGGTAGTACT 57.334 47.619 0.00 0.00 31.85 2.73
3531 3565 4.785346 AATCAGGACGGAGGTAGTACTA 57.215 45.455 0.00 0.00 30.29 1.82
3640 3680 6.627395 AACCAAGAAATGTTTACACGATCA 57.373 33.333 0.00 0.00 0.00 2.92
3641 3681 6.817765 ACCAAGAAATGTTTACACGATCAT 57.182 33.333 0.00 0.00 0.00 2.45
3642 3682 6.842163 ACCAAGAAATGTTTACACGATCATC 58.158 36.000 0.00 0.00 0.00 2.92
3643 3683 6.429692 ACCAAGAAATGTTTACACGATCATCA 59.570 34.615 0.00 0.00 0.00 3.07
3646 3686 8.393366 CAAGAAATGTTTACACGATCATCATCT 58.607 33.333 0.00 0.00 0.00 2.90
3649 3689 8.716646 AAATGTTTACACGATCATCATCTACA 57.283 30.769 0.00 0.00 0.00 2.74
3650 3690 7.936950 ATGTTTACACGATCATCATCTACAG 57.063 36.000 0.00 0.00 0.00 2.74
3651 3691 6.863275 TGTTTACACGATCATCATCTACAGT 58.137 36.000 0.00 0.00 0.00 3.55
3652 3692 7.992008 TGTTTACACGATCATCATCTACAGTA 58.008 34.615 0.00 0.00 0.00 2.74
3653 3693 7.913821 TGTTTACACGATCATCATCTACAGTAC 59.086 37.037 0.00 0.00 0.00 2.73
3654 3694 5.440234 ACACGATCATCATCTACAGTACC 57.560 43.478 0.00 0.00 0.00 3.34
3655 3695 4.278669 ACACGATCATCATCTACAGTACCC 59.721 45.833 0.00 0.00 0.00 3.69
3656 3696 4.278419 CACGATCATCATCTACAGTACCCA 59.722 45.833 0.00 0.00 0.00 4.51
3657 3697 4.893524 ACGATCATCATCTACAGTACCCAA 59.106 41.667 0.00 0.00 0.00 4.12
3660 3700 6.294731 CGATCATCATCTACAGTACCCAATCA 60.295 42.308 0.00 0.00 0.00 2.57
3665 3705 2.094390 TCTACAGTACCCAATCACGCAC 60.094 50.000 0.00 0.00 0.00 5.34
3685 3725 1.997606 CGACGGAACTCCACCAATAAC 59.002 52.381 0.00 0.00 35.14 1.89
3909 4198 3.457380 TGGCTGCTAAGAGATTCTTGGAT 59.543 43.478 6.39 0.00 37.16 3.41
3978 4273 7.726033 AAAAATATGGCCAGTGTACCATTTA 57.274 32.000 13.05 4.33 44.37 1.40
4012 4307 4.283722 CAGTAGTAACCTTGTTGGAGTCCT 59.716 45.833 11.33 0.00 39.71 3.85
4013 4308 4.527427 AGTAGTAACCTTGTTGGAGTCCTC 59.473 45.833 11.33 4.40 39.71 3.71
4041 4336 2.802787 ATATGACACGTCTAGCCAGC 57.197 50.000 0.00 0.00 0.00 4.85
4042 4337 0.380733 TATGACACGTCTAGCCAGCG 59.619 55.000 0.00 0.00 0.00 5.18
4043 4338 2.881352 GACACGTCTAGCCAGCGC 60.881 66.667 0.00 0.00 0.00 5.92
4045 4340 2.125912 CACGTCTAGCCAGCGCTT 60.126 61.111 7.50 0.00 45.55 4.68
4046 4341 2.125912 ACGTCTAGCCAGCGCTTG 60.126 61.111 7.50 5.33 45.55 4.01
4047 4342 2.887568 CGTCTAGCCAGCGCTTGG 60.888 66.667 7.50 14.61 45.55 3.61
4058 4353 3.053291 CGCTTGGCCGCTTGGTTA 61.053 61.111 0.00 0.00 34.16 2.85
4059 4354 2.877691 GCTTGGCCGCTTGGTTAG 59.122 61.111 0.00 0.00 34.16 2.34
4060 4355 2.877691 CTTGGCCGCTTGGTTAGC 59.122 61.111 0.00 0.00 46.83 3.09
4068 4363 2.877691 CTTGGTTAGCAAGCGGCC 59.122 61.111 11.28 0.00 46.50 6.13
4069 4364 3.039202 CTTGGTTAGCAAGCGGCCG 62.039 63.158 24.05 24.05 46.50 6.13
4080 4375 4.449391 GCGGCCGGCTATTTTAGA 57.551 55.556 29.38 0.00 39.11 2.10
4081 4376 2.697819 GCGGCCGGCTATTTTAGAA 58.302 52.632 29.38 0.00 39.11 2.10
4082 4377 1.235724 GCGGCCGGCTATTTTAGAAT 58.764 50.000 29.38 0.00 39.11 2.40
4083 4378 2.419667 GCGGCCGGCTATTTTAGAATA 58.580 47.619 29.38 0.00 39.11 1.75
4084 4379 2.159037 GCGGCCGGCTATTTTAGAATAC 59.841 50.000 29.38 3.07 39.11 1.89
4085 4380 3.660865 CGGCCGGCTATTTTAGAATACT 58.339 45.455 28.56 0.00 0.00 2.12
4086 4381 4.062991 CGGCCGGCTATTTTAGAATACTT 58.937 43.478 28.56 0.00 0.00 2.24
4087 4382 4.151867 CGGCCGGCTATTTTAGAATACTTC 59.848 45.833 28.56 1.39 0.00 3.01
4088 4383 5.306394 GGCCGGCTATTTTAGAATACTTCT 58.694 41.667 28.56 0.00 43.72 2.85
4089 4384 5.763698 GGCCGGCTATTTTAGAATACTTCTT 59.236 40.000 28.56 0.00 41.14 2.52
4090 4385 6.293462 GGCCGGCTATTTTAGAATACTTCTTG 60.293 42.308 28.56 0.00 41.14 3.02
4091 4386 6.260271 GCCGGCTATTTTAGAATACTTCTTGT 59.740 38.462 22.15 0.00 41.14 3.16
4092 4387 7.518529 GCCGGCTATTTTAGAATACTTCTTGTC 60.519 40.741 22.15 0.00 41.14 3.18
4093 4388 7.041984 CCGGCTATTTTAGAATACTTCTTGTCC 60.042 40.741 0.00 0.00 41.14 4.02
4094 4389 7.041984 CGGCTATTTTAGAATACTTCTTGTCCC 60.042 40.741 0.00 0.00 41.14 4.46
4095 4390 7.993758 GGCTATTTTAGAATACTTCTTGTCCCT 59.006 37.037 0.00 0.00 41.14 4.20
4096 4391 9.047371 GCTATTTTAGAATACTTCTTGTCCCTC 57.953 37.037 0.00 0.00 41.14 4.30
4097 4392 9.549078 CTATTTTAGAATACTTCTTGTCCCTCC 57.451 37.037 0.00 0.00 41.14 4.30
4098 4393 7.569599 TTTTAGAATACTTCTTGTCCCTCCT 57.430 36.000 0.00 0.00 41.14 3.69
4099 4394 6.793505 TTAGAATACTTCTTGTCCCTCCTC 57.206 41.667 0.00 0.00 41.14 3.71
4100 4395 4.954089 AGAATACTTCTTGTCCCTCCTCT 58.046 43.478 0.00 0.00 36.36 3.69
4101 4396 6.093617 AGAATACTTCTTGTCCCTCCTCTA 57.906 41.667 0.00 0.00 36.36 2.43
4102 4397 6.503944 AGAATACTTCTTGTCCCTCCTCTAA 58.496 40.000 0.00 0.00 36.36 2.10
4103 4398 7.136203 AGAATACTTCTTGTCCCTCCTCTAAT 58.864 38.462 0.00 0.00 36.36 1.73
4104 4399 7.625682 AGAATACTTCTTGTCCCTCCTCTAATT 59.374 37.037 0.00 0.00 36.36 1.40
4105 4400 8.855804 AATACTTCTTGTCCCTCCTCTAATTA 57.144 34.615 0.00 0.00 0.00 1.40
4106 4401 6.800072 ACTTCTTGTCCCTCCTCTAATTAG 57.200 41.667 6.11 6.11 0.00 1.73
4107 4402 6.503944 ACTTCTTGTCCCTCCTCTAATTAGA 58.496 40.000 14.42 14.42 0.00 2.10
4108 4403 6.960542 ACTTCTTGTCCCTCCTCTAATTAGAA 59.039 38.462 15.85 1.96 0.00 2.10
4109 4404 7.458170 ACTTCTTGTCCCTCCTCTAATTAGAAA 59.542 37.037 15.85 6.81 0.00 2.52
4110 4405 7.808279 TCTTGTCCCTCCTCTAATTAGAAAA 57.192 36.000 15.85 6.49 0.00 2.29
4111 4406 8.214721 TCTTGTCCCTCCTCTAATTAGAAAAA 57.785 34.615 15.85 4.24 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.369983 AGTTCCCCTACCCTCCATCTT 59.630 52.381 0.00 0.00 0.00 2.40
6 7 1.027815 AGTTCCCCTACCCTCCATCT 58.972 55.000 0.00 0.00 0.00 2.90
91 92 4.261801 CAATACCCCTACCACTGTTGAAG 58.738 47.826 0.00 0.00 0.00 3.02
102 103 8.803397 ACTTTTATTTGAGACAATACCCCTAC 57.197 34.615 0.00 0.00 0.00 3.18
196 197 0.606096 TGTCGTCCATGAACACCGAT 59.394 50.000 0.00 0.00 0.00 4.18
221 222 6.112734 TGCACCGATGTAAAGTATCAAGAAT 58.887 36.000 0.00 0.00 0.00 2.40
227 228 4.630069 AGTGTTGCACCGATGTAAAGTATC 59.370 41.667 0.00 0.00 34.49 2.24
244 245 2.222796 CGTTGACGATGCCATAGTGTTG 60.223 50.000 0.00 0.00 43.02 3.33
271 272 6.402222 AGACTCAACTATTGGAGAACATGAC 58.598 40.000 0.00 0.00 35.17 3.06
279 280 4.697352 CCCACAAAGACTCAACTATTGGAG 59.303 45.833 0.00 0.00 37.18 3.86
285 286 3.135712 TCTTGCCCACAAAGACTCAACTA 59.864 43.478 0.00 0.00 34.74 2.24
309 310 1.653151 GATAAGACGGACAGGCAACC 58.347 55.000 0.00 0.00 37.17 3.77
318 319 3.118038 CCTCCCAAATTGGATAAGACGGA 60.118 47.826 14.62 0.00 40.96 4.69
324 325 2.584965 TGGAGCCTCCCAAATTGGATAA 59.415 45.455 14.62 0.00 40.96 1.75
346 347 0.179111 TTAGGAGAGGATTGCGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
347 348 2.139118 GATTAGGAGAGGATTGCGTGC 58.861 52.381 0.00 0.00 0.00 5.34
348 349 3.459232 TGATTAGGAGAGGATTGCGTG 57.541 47.619 0.00 0.00 0.00 5.34
349 350 4.101585 TGATTGATTAGGAGAGGATTGCGT 59.898 41.667 0.00 0.00 0.00 5.24
350 351 4.635223 TGATTGATTAGGAGAGGATTGCG 58.365 43.478 0.00 0.00 0.00 4.85
374 375 7.552687 GGTGTCTAGACATGTATTTTTCATCCA 59.447 37.037 27.54 0.00 43.97 3.41
376 377 7.012421 GGGGTGTCTAGACATGTATTTTTCATC 59.988 40.741 27.54 10.30 43.97 2.92
377 378 6.828785 GGGGTGTCTAGACATGTATTTTTCAT 59.171 38.462 27.54 0.00 43.97 2.57
392 393 0.541863 GGTGATGGTGGGGTGTCTAG 59.458 60.000 0.00 0.00 0.00 2.43
393 394 0.178888 TGGTGATGGTGGGGTGTCTA 60.179 55.000 0.00 0.00 0.00 2.59
399 400 2.417257 CGCAATGGTGATGGTGGGG 61.417 63.158 0.00 0.00 0.00 4.96
422 423 3.973472 ACTTCAGGAAGAGGGGTTTTT 57.027 42.857 15.51 0.00 40.79 1.94
423 424 4.240323 TCTACTTCAGGAAGAGGGGTTTT 58.760 43.478 15.51 0.00 40.79 2.43
424 425 3.870559 TCTACTTCAGGAAGAGGGGTTT 58.129 45.455 15.51 0.00 40.79 3.27
436 437 2.094494 AGTGTCACCGCATCTACTTCAG 60.094 50.000 0.00 0.00 0.00 3.02
443 444 0.319900 GTGTCAGTGTCACCGCATCT 60.320 55.000 9.09 0.00 0.00 2.90
451 452 1.688735 CCTTCTCTGGTGTCAGTGTCA 59.311 52.381 0.00 0.00 41.59 3.58
457 458 0.191064 ACCTCCCTTCTCTGGTGTCA 59.809 55.000 0.00 0.00 0.00 3.58
497 498 0.904865 CCCTGTCACTCCACTAGGCA 60.905 60.000 0.00 0.00 33.74 4.75
501 502 0.041238 CCTCCCCTGTCACTCCACTA 59.959 60.000 0.00 0.00 0.00 2.74
570 571 3.055613 ACCGCACGTTTCTTGTAAAAC 57.944 42.857 0.00 0.00 36.09 2.43
625 627 7.205297 AGATGTCACCAAAAGAATGTTTTGAG 58.795 34.615 15.87 9.13 0.00 3.02
632 634 7.829725 TCCATAAAGATGTCACCAAAAGAATG 58.170 34.615 0.00 0.00 0.00 2.67
784 787 4.988540 TGGTTCTTTGTACTTCATCGTGAG 59.011 41.667 0.00 0.00 0.00 3.51
846 849 6.862090 GGATTAGTTCGTTGCGAGAATATACT 59.138 38.462 0.00 0.00 37.14 2.12
847 850 6.862090 AGGATTAGTTCGTTGCGAGAATATAC 59.138 38.462 0.00 0.00 37.14 1.47
1024 1035 3.296709 ATCGGTTTGCGCTCCTCGT 62.297 57.895 9.73 0.00 41.07 4.18
1044 1055 2.185350 CTGCTCTTCCACGGCGAT 59.815 61.111 16.62 0.00 0.00 4.58
1071 1082 2.186903 CCGAGCAACAGGCCGTAT 59.813 61.111 0.00 0.00 46.50 3.06
1098 1109 1.656652 CCATCAGGTAAAGGAGCACG 58.343 55.000 0.00 0.00 0.00 5.34
1178 1189 6.467677 TCATAAAGTTTCTTCACCCTGAGAG 58.532 40.000 0.00 0.00 0.00 3.20
1180 1191 5.123027 GCTCATAAAGTTTCTTCACCCTGAG 59.877 44.000 0.00 0.00 0.00 3.35
1184 1195 7.362142 CCTTTAGCTCATAAAGTTTCTTCACCC 60.362 40.741 6.69 0.00 46.10 4.61
1185 1196 7.390718 TCCTTTAGCTCATAAAGTTTCTTCACC 59.609 37.037 6.69 0.00 46.10 4.02
1218 1237 9.846248 AAGCTTGTAAGATTGATCATAAAACAC 57.154 29.630 0.00 0.00 32.66 3.32
1245 1265 1.596260 CTGCGTATGAGCACCAAGATG 59.404 52.381 0.00 0.00 42.92 2.90
1299 1319 1.064654 GATGCTTCGCAGGGATTGTTC 59.935 52.381 0.00 0.00 43.65 3.18
1301 1321 1.091771 CGATGCTTCGCAGGGATTGT 61.092 55.000 9.21 0.00 43.65 2.71
1409 1433 5.051173 CGCATCATCTACAGTAGCTTCAAAG 60.051 44.000 2.26 0.00 0.00 2.77
1463 1488 1.398692 CCTTCTCCTCTTCCTCCTCG 58.601 60.000 0.00 0.00 0.00 4.63
1598 1624 2.977578 TCTGAAGAAGAGGGGACGG 58.022 57.895 0.00 0.00 0.00 4.79
1620 1646 2.734673 CTGCTCGCTTTCGTCCTGC 61.735 63.158 0.00 0.00 36.96 4.85
1694 1720 9.539825 TGCTAATTGAACAACAACAACAATAAT 57.460 25.926 0.00 0.00 41.52 1.28
1697 1723 7.840342 TTGCTAATTGAACAACAACAACAAT 57.160 28.000 0.00 0.00 41.52 2.71
1703 1729 6.582295 ACGATGATTGCTAATTGAACAACAAC 59.418 34.615 0.00 0.00 41.52 3.32
1712 1738 6.018507 TCTGATGACACGATGATTGCTAATTG 60.019 38.462 0.00 0.00 0.00 2.32
1713 1739 6.051074 TCTGATGACACGATGATTGCTAATT 58.949 36.000 0.00 0.00 0.00 1.40
1721 1750 6.820152 TCAGAAAAATCTGATGACACGATGAT 59.180 34.615 4.49 0.00 41.34 2.45
1736 1765 7.652909 TGATTGAAACCACACATCAGAAAAATC 59.347 33.333 0.00 0.00 0.00 2.17
1755 1784 4.844998 TTCATTTCGTTGCCTGATTGAA 57.155 36.364 0.00 0.00 0.00 2.69
1856 1888 5.779529 AAGCAATTGAAAGTCAGTCACAT 57.220 34.783 10.34 0.00 0.00 3.21
1910 1942 0.165727 TCGCACGCAAACATGATGAC 59.834 50.000 0.00 0.00 0.00 3.06
2140 2172 4.681978 ACCGTGACCGCCTTCAGC 62.682 66.667 0.00 0.00 38.52 4.26
2326 2358 1.444553 CAGGAGGTTGACGACGAGC 60.445 63.158 0.00 0.00 0.00 5.03
2525 2557 4.694509 CCTCAAGAATCTGGTGAAGTCAAG 59.305 45.833 0.00 0.00 0.00 3.02
2539 2571 0.246635 AGTACGCGTGCCTCAAGAAT 59.753 50.000 24.59 0.00 0.00 2.40
3058 3090 1.141019 GATCCGCACGTCCTGCTTA 59.859 57.895 0.00 0.00 44.64 3.09
3172 3204 2.885894 TGCACAACAATCATCAGCAAGA 59.114 40.909 0.00 0.00 0.00 3.02
3173 3205 2.984471 GTGCACAACAATCATCAGCAAG 59.016 45.455 13.17 0.00 31.78 4.01
3176 3208 3.240069 GAAGTGCACAACAATCATCAGC 58.760 45.455 21.04 0.00 0.00 4.26
3177 3209 3.504906 AGGAAGTGCACAACAATCATCAG 59.495 43.478 21.04 0.00 0.00 2.90
3179 3211 3.755378 AGAGGAAGTGCACAACAATCATC 59.245 43.478 21.04 14.72 31.58 2.92
3180 3212 3.504906 CAGAGGAAGTGCACAACAATCAT 59.495 43.478 21.04 6.55 0.00 2.45
3230 3262 7.778083 TCCGTGTACATTGAACACTATTCTAT 58.222 34.615 0.00 0.00 44.05 1.98
3269 3301 9.151471 AGTACTATGATTGTTGTACATTGACAC 57.849 33.333 0.00 0.00 38.09 3.67
3297 3331 2.626743 ACCGGTAAATCAGGATCGTAGG 59.373 50.000 4.49 0.00 35.40 3.18
3298 3332 3.305199 GGACCGGTAAATCAGGATCGTAG 60.305 52.174 7.34 0.00 35.40 3.51
3299 3333 2.624838 GGACCGGTAAATCAGGATCGTA 59.375 50.000 7.34 0.00 35.40 3.43
3300 3334 1.411612 GGACCGGTAAATCAGGATCGT 59.588 52.381 7.34 0.00 35.40 3.73
3301 3335 1.270147 GGGACCGGTAAATCAGGATCG 60.270 57.143 7.34 0.00 35.40 3.69
3302 3336 2.047830 AGGGACCGGTAAATCAGGATC 58.952 52.381 7.34 0.00 35.40 3.36
3303 3337 2.191981 AGGGACCGGTAAATCAGGAT 57.808 50.000 7.34 0.00 35.40 3.24
3304 3338 1.961133 AAGGGACCGGTAAATCAGGA 58.039 50.000 7.34 0.00 35.40 3.86
3305 3339 2.365582 CAAAGGGACCGGTAAATCAGG 58.634 52.381 7.34 0.00 37.42 3.86
3306 3340 1.743394 GCAAAGGGACCGGTAAATCAG 59.257 52.381 7.34 0.00 0.00 2.90
3307 3341 1.074084 TGCAAAGGGACCGGTAAATCA 59.926 47.619 7.34 0.00 0.00 2.57
3308 3342 1.828979 TGCAAAGGGACCGGTAAATC 58.171 50.000 7.34 0.00 0.00 2.17
3309 3343 2.525105 ATGCAAAGGGACCGGTAAAT 57.475 45.000 7.34 0.00 0.00 1.40
3310 3344 2.296073 AATGCAAAGGGACCGGTAAA 57.704 45.000 7.34 0.00 0.00 2.01
3311 3345 2.296073 AAATGCAAAGGGACCGGTAA 57.704 45.000 7.34 0.00 0.00 2.85
3312 3346 1.889829 CAAAATGCAAAGGGACCGGTA 59.110 47.619 7.34 0.00 0.00 4.02
3313 3347 0.678950 CAAAATGCAAAGGGACCGGT 59.321 50.000 6.92 6.92 0.00 5.28
3314 3348 0.678950 ACAAAATGCAAAGGGACCGG 59.321 50.000 0.00 0.00 0.00 5.28
3315 3349 1.782044 CACAAAATGCAAAGGGACCG 58.218 50.000 0.00 0.00 0.00 4.79
3331 3365 6.899393 AATCTAAGATCAAAGTTTGGCACA 57.101 33.333 15.47 0.00 0.00 4.57
3332 3366 9.129209 GTTAAATCTAAGATCAAAGTTTGGCAC 57.871 33.333 15.47 7.45 0.00 5.01
3333 3367 9.077885 AGTTAAATCTAAGATCAAAGTTTGGCA 57.922 29.630 15.47 0.00 0.00 4.92
3357 3391 9.973450 TGTTACATGCATTAACATTTTGTTAGT 57.027 25.926 20.77 6.21 42.93 2.24
3479 3513 9.209048 GGACCCCTTAATATTTTGTCCTAAATT 57.791 33.333 0.00 0.00 38.18 1.82
3480 3514 8.348354 TGGACCCCTTAATATTTTGTCCTAAAT 58.652 33.333 16.04 0.00 41.04 1.40
3481 3515 7.710579 TGGACCCCTTAATATTTTGTCCTAAA 58.289 34.615 16.04 0.00 41.04 1.85
3482 3516 7.286667 TGGACCCCTTAATATTTTGTCCTAA 57.713 36.000 16.04 2.69 41.04 2.69
3483 3517 6.911993 TGGACCCCTTAATATTTTGTCCTA 57.088 37.500 16.04 6.46 41.04 2.94
3484 3518 5.806955 TGGACCCCTTAATATTTTGTCCT 57.193 39.130 16.04 0.00 41.04 3.85
3485 3519 8.541899 TTATTGGACCCCTTAATATTTTGTCC 57.458 34.615 0.00 4.27 40.88 4.02
3490 3524 9.379770 CCTGATTTATTGGACCCCTTAATATTT 57.620 33.333 0.00 0.00 0.00 1.40
3491 3525 8.742437 TCCTGATTTATTGGACCCCTTAATATT 58.258 33.333 0.00 0.00 0.00 1.28
3492 3526 8.170730 GTCCTGATTTATTGGACCCCTTAATAT 58.829 37.037 0.00 0.00 43.10 1.28
3493 3527 7.523415 GTCCTGATTTATTGGACCCCTTAATA 58.477 38.462 0.00 0.00 43.10 0.98
3494 3528 6.373759 GTCCTGATTTATTGGACCCCTTAAT 58.626 40.000 0.00 0.00 43.10 1.40
3495 3529 5.630539 CGTCCTGATTTATTGGACCCCTTAA 60.631 44.000 0.00 0.00 45.31 1.85
3496 3530 4.141574 CGTCCTGATTTATTGGACCCCTTA 60.142 45.833 0.00 0.00 45.31 2.69
3497 3531 3.371595 CGTCCTGATTTATTGGACCCCTT 60.372 47.826 0.00 0.00 45.31 3.95
3498 3532 2.172717 CGTCCTGATTTATTGGACCCCT 59.827 50.000 0.00 0.00 45.31 4.79
3499 3533 2.572290 CGTCCTGATTTATTGGACCCC 58.428 52.381 0.00 0.00 45.31 4.95
3500 3534 2.171870 TCCGTCCTGATTTATTGGACCC 59.828 50.000 0.00 0.00 45.31 4.46
3501 3535 3.467803 CTCCGTCCTGATTTATTGGACC 58.532 50.000 0.00 0.00 45.31 4.46
3502 3536 3.118371 ACCTCCGTCCTGATTTATTGGAC 60.118 47.826 0.00 0.00 44.82 4.02
3503 3537 3.112263 ACCTCCGTCCTGATTTATTGGA 58.888 45.455 0.00 0.00 0.00 3.53
3504 3538 3.560636 ACCTCCGTCCTGATTTATTGG 57.439 47.619 0.00 0.00 0.00 3.16
3505 3539 5.277857 ACTACCTCCGTCCTGATTTATTG 57.722 43.478 0.00 0.00 0.00 1.90
3506 3540 6.134754 AGTACTACCTCCGTCCTGATTTATT 58.865 40.000 0.00 0.00 0.00 1.40
3507 3541 5.703310 AGTACTACCTCCGTCCTGATTTAT 58.297 41.667 0.00 0.00 0.00 1.40
3508 3542 5.121380 AGTACTACCTCCGTCCTGATTTA 57.879 43.478 0.00 0.00 0.00 1.40
3509 3543 3.978610 AGTACTACCTCCGTCCTGATTT 58.021 45.455 0.00 0.00 0.00 2.17
3510 3544 3.666345 AGTACTACCTCCGTCCTGATT 57.334 47.619 0.00 0.00 0.00 2.57
3511 3545 4.997545 ATAGTACTACCTCCGTCCTGAT 57.002 45.455 4.31 0.00 0.00 2.90
3512 3546 4.785346 AATAGTACTACCTCCGTCCTGA 57.215 45.455 4.31 0.00 0.00 3.86
3513 3547 5.221204 GGAAAATAGTACTACCTCCGTCCTG 60.221 48.000 4.31 0.00 0.00 3.86
3514 3548 4.892345 GGAAAATAGTACTACCTCCGTCCT 59.108 45.833 4.31 0.00 0.00 3.85
3515 3549 4.646492 TGGAAAATAGTACTACCTCCGTCC 59.354 45.833 4.31 7.23 0.00 4.79
3516 3550 5.841957 TGGAAAATAGTACTACCTCCGTC 57.158 43.478 4.31 0.00 0.00 4.79
3517 3551 7.727186 TCATATGGAAAATAGTACTACCTCCGT 59.273 37.037 18.58 18.58 0.00 4.69
3518 3552 8.118976 TCATATGGAAAATAGTACTACCTCCG 57.881 38.462 4.31 0.14 0.00 4.63
3601 3641 8.410673 TTTCTTGGTTAATATGTGTGGCTTTA 57.589 30.769 0.00 0.00 0.00 1.85
3638 3678 5.221244 CGTGATTGGGTACTGTAGATGATGA 60.221 44.000 0.00 0.00 0.00 2.92
3640 3680 4.501571 GCGTGATTGGGTACTGTAGATGAT 60.502 45.833 0.00 0.00 0.00 2.45
3641 3681 3.181479 GCGTGATTGGGTACTGTAGATGA 60.181 47.826 0.00 0.00 0.00 2.92
3642 3682 3.123804 GCGTGATTGGGTACTGTAGATG 58.876 50.000 0.00 0.00 0.00 2.90
3643 3683 2.764010 TGCGTGATTGGGTACTGTAGAT 59.236 45.455 0.00 0.00 0.00 1.98
3646 3686 1.403116 CGTGCGTGATTGGGTACTGTA 60.403 52.381 0.00 0.00 0.00 2.74
3649 3689 0.389426 GTCGTGCGTGATTGGGTACT 60.389 55.000 0.00 0.00 0.00 2.73
3650 3690 1.680105 CGTCGTGCGTGATTGGGTAC 61.680 60.000 0.00 0.00 35.54 3.34
3651 3691 1.444724 CGTCGTGCGTGATTGGGTA 60.445 57.895 0.00 0.00 35.54 3.69
3652 3692 2.736995 CGTCGTGCGTGATTGGGT 60.737 61.111 0.00 0.00 35.54 4.51
3653 3693 3.487202 CCGTCGTGCGTGATTGGG 61.487 66.667 0.00 0.00 39.32 4.12
3654 3694 2.024868 TTCCGTCGTGCGTGATTGG 61.025 57.895 0.00 0.00 39.32 3.16
3655 3695 1.129809 GTTCCGTCGTGCGTGATTG 59.870 57.895 0.00 0.00 39.32 2.67
3656 3696 1.006571 AGTTCCGTCGTGCGTGATT 60.007 52.632 0.00 0.00 39.32 2.57
3657 3697 1.443872 GAGTTCCGTCGTGCGTGAT 60.444 57.895 0.00 0.00 39.32 3.06
3660 3700 3.598715 TGGAGTTCCGTCGTGCGT 61.599 61.111 0.00 0.00 39.43 5.24
3665 3705 1.997606 GTTATTGGTGGAGTTCCGTCG 59.002 52.381 0.00 0.00 39.43 5.12
3669 3709 2.443416 GTGGGTTATTGGTGGAGTTCC 58.557 52.381 0.00 0.00 0.00 3.62
3670 3710 2.443416 GGTGGGTTATTGGTGGAGTTC 58.557 52.381 0.00 0.00 0.00 3.01
3685 3725 4.922471 TTCTTCTTTTAAAACGGGTGGG 57.078 40.909 0.00 0.00 0.00 4.61
3780 4068 7.805163 TCTGCCCTAGATGAAGAAATTATCAA 58.195 34.615 0.00 0.00 0.00 2.57
3922 4211 9.784531 TTTTGGCCATTAATTAAGTGATTTTGA 57.215 25.926 6.09 0.00 0.00 2.69
3978 4273 6.323225 ACAAGGTTACTACTGTATCCGCTATT 59.677 38.462 0.00 0.00 41.23 1.73
4018 4313 4.332819 GCTGGCTAGACGTGTCATATTTTT 59.667 41.667 0.00 0.00 0.00 1.94
4019 4314 3.871594 GCTGGCTAGACGTGTCATATTTT 59.128 43.478 0.00 0.00 0.00 1.82
4020 4315 3.458189 GCTGGCTAGACGTGTCATATTT 58.542 45.455 0.00 0.00 0.00 1.40
4021 4316 2.543861 CGCTGGCTAGACGTGTCATATT 60.544 50.000 0.00 0.00 0.00 1.28
4022 4317 1.001268 CGCTGGCTAGACGTGTCATAT 60.001 52.381 0.00 0.00 0.00 1.78
4023 4318 0.380733 CGCTGGCTAGACGTGTCATA 59.619 55.000 0.00 0.00 0.00 2.15
4024 4319 1.139734 CGCTGGCTAGACGTGTCAT 59.860 57.895 0.00 0.00 0.00 3.06
4025 4320 2.566529 CGCTGGCTAGACGTGTCA 59.433 61.111 0.00 0.00 0.00 3.58
4026 4321 2.881352 GCGCTGGCTAGACGTGTC 60.881 66.667 0.00 0.00 35.83 3.67
4041 4336 3.039202 CTAACCAAGCGGCCAAGCG 62.039 63.158 2.24 0.00 43.00 4.68
4042 4337 2.877691 CTAACCAAGCGGCCAAGC 59.122 61.111 2.24 0.00 34.57 4.01
4043 4338 2.877691 GCTAACCAAGCGGCCAAG 59.122 61.111 2.24 0.00 42.53 3.61
4052 4347 3.053291 CGGCCGCTTGCTAACCAA 61.053 61.111 14.67 0.00 40.92 3.67
4063 4358 1.235724 ATTCTAAAATAGCCGGCCGC 58.764 50.000 26.15 16.01 37.98 6.53
4064 4359 3.660865 AGTATTCTAAAATAGCCGGCCG 58.339 45.455 26.15 21.04 0.00 6.13
4065 4360 5.608676 GAAGTATTCTAAAATAGCCGGCC 57.391 43.478 26.15 5.07 43.23 6.13
4080 4375 7.757242 AATTAGAGGAGGGACAAGAAGTATT 57.243 36.000 0.00 0.00 0.00 1.89
4081 4376 8.290277 TCTAATTAGAGGAGGGACAAGAAGTAT 58.710 37.037 11.24 0.00 0.00 2.12
4082 4377 7.649715 TCTAATTAGAGGAGGGACAAGAAGTA 58.350 38.462 11.24 0.00 0.00 2.24
4083 4378 6.503944 TCTAATTAGAGGAGGGACAAGAAGT 58.496 40.000 11.24 0.00 0.00 3.01
4084 4379 7.425224 TTCTAATTAGAGGAGGGACAAGAAG 57.575 40.000 14.63 0.00 33.21 2.85
4085 4380 7.808279 TTTCTAATTAGAGGAGGGACAAGAA 57.192 36.000 14.63 0.29 33.21 2.52
4086 4381 7.808279 TTTTCTAATTAGAGGAGGGACAAGA 57.192 36.000 14.63 0.00 33.21 3.02


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

AutoCloner maintained by Alex Coulton.