Multiple sequence alignment - TraesCS4D01G275900

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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 TraesCS4D01G275900 chr4D 100.000 3873 0 0 1 3873 446908202 446912074 0.000000e+00 7153.0
1 TraesCS4D01G275900 chr4B 91.652 2791 151 44 635 3393 559280186 559282926 0.000000e+00 3788.0
2 TraesCS4D01G275900 chr4B 91.304 414 27 4 3458 3867 559283258 559283666 1.220000e-154 556.0
3 TraesCS4D01G275900 chr4B 97.436 39 1 0 3408 3446 559283258 559283296 2.500000e-07 67.6
4 TraesCS4D01G275900 chr4A 93.483 1688 83 18 1584 3252 20266353 20264674 0.000000e+00 2483.0
5 TraesCS4D01G275900 chr4A 92.407 1554 74 23 1 1522 20267895 20266354 0.000000e+00 2176.0
6 TraesCS4D01G275900 chr4A 87.260 416 23 8 3458 3868 20264610 20264220 7.630000e-122 448.0
7 TraesCS4D01G275900 chr4A 89.423 104 8 2 3344 3446 20264673 20264572 1.130000e-25 128.0
8 TraesCS4D01G275900 chr5B 86.058 208 19 8 3248 3446 387956305 387956099 8.430000e-52 215.0
9 TraesCS4D01G275900 chr6D 87.097 62 8 0 196 257 42558773 42558712 1.930000e-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 TraesCS4D01G275900 chr4D 446908202 446912074 3872 False 7153.000000 7153 100.00000 1 3873 1 chr4D.!!$F1 3872
1 TraesCS4D01G275900 chr4B 559280186 559283666 3480 False 1470.533333 3788 93.46400 635 3867 3 chr4B.!!$F1 3232
2 TraesCS4D01G275900 chr4A 20264220 20267895 3675 True 1308.750000 2483 90.64325 1 3868 4 chr4A.!!$R1 3867

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
84 85 0.179181 TATCAGTTCGCGGACACGTC 60.179 55.0 21.79 0.0 43.45 4.34 F
1393 1440 0.175989 CTCCTTCTTGCGTACCTCCC 59.824 60.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1583 0.321564 TCCGATGACCAAACTGCAGG 60.322 55.0 19.93 2.94 0.0 4.85 R
3320 3394 0.034960 TAGGCCGCCATGTTTTGCTA 60.035 50.0 13.15 0.00 0.0 3.49 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
20 21 2.483876 CGGCCGAAATGTGATACATCT 58.516 47.619 24.07 0.00 37.97 2.90
42 43 0.463833 GGGTTAGGGCATCTCCAACG 60.464 60.000 0.00 0.00 36.21 4.10
44 45 1.653151 GTTAGGGCATCTCCAACGAC 58.347 55.000 0.00 0.00 36.21 4.34
50 51 0.442699 GCATCTCCAACGACGTTTCC 59.557 55.000 11.24 0.00 0.00 3.13
57 58 1.292061 CAACGACGTTTCCCAAGTCA 58.708 50.000 11.24 0.00 34.80 3.41
59 60 0.748450 ACGACGTTTCCCAAGTCAGA 59.252 50.000 0.00 0.00 34.80 3.27
63 64 1.760613 ACGTTTCCCAAGTCAGACTCA 59.239 47.619 2.72 0.00 0.00 3.41
84 85 0.179181 TATCAGTTCGCGGACACGTC 60.179 55.000 21.79 0.00 43.45 4.34
87 88 2.127270 GTTCGCGGACACGTCGTA 60.127 61.111 14.01 0.00 43.45 3.43
88 89 1.725625 GTTCGCGGACACGTCGTAA 60.726 57.895 14.01 0.00 43.45 3.18
133 134 4.081198 GCCATCCAACCATGTCCATTAAAA 60.081 41.667 0.00 0.00 0.00 1.52
134 135 5.396660 GCCATCCAACCATGTCCATTAAAAT 60.397 40.000 0.00 0.00 0.00 1.82
135 136 6.050432 CCATCCAACCATGTCCATTAAAATG 58.950 40.000 0.00 0.00 36.17 2.32
136 137 6.352051 CCATCCAACCATGTCCATTAAAATGT 60.352 38.462 2.25 0.00 34.60 2.71
137 138 7.147759 CCATCCAACCATGTCCATTAAAATGTA 60.148 37.037 2.25 0.00 34.60 2.29
138 139 7.969690 TCCAACCATGTCCATTAAAATGTAT 57.030 32.000 2.25 0.00 34.60 2.29
139 140 7.780064 TCCAACCATGTCCATTAAAATGTATG 58.220 34.615 2.25 4.21 34.60 2.39
140 141 6.479660 CCAACCATGTCCATTAAAATGTATGC 59.520 38.462 2.25 0.00 34.60 3.14
141 142 6.788598 ACCATGTCCATTAAAATGTATGCA 57.211 33.333 0.00 0.00 34.60 3.96
142 143 6.572519 ACCATGTCCATTAAAATGTATGCAC 58.427 36.000 0.00 0.00 34.60 4.57
143 144 5.984926 CCATGTCCATTAAAATGTATGCACC 59.015 40.000 0.00 0.00 34.60 5.01
144 145 6.183360 CCATGTCCATTAAAATGTATGCACCT 60.183 38.462 0.00 0.00 34.60 4.00
145 146 7.014134 CCATGTCCATTAAAATGTATGCACCTA 59.986 37.037 0.00 0.00 34.60 3.08
146 147 8.579006 CATGTCCATTAAAATGTATGCACCTAT 58.421 33.333 0.00 0.00 34.60 2.57
211 213 5.221891 TCGACTTTGCATATTTCTCTTGC 57.778 39.130 0.00 0.00 36.91 4.01
256 258 1.467342 CATCTCATGCTGGTGTGTGTG 59.533 52.381 0.00 0.00 0.00 3.82
257 259 0.469494 TCTCATGCTGGTGTGTGTGT 59.531 50.000 0.00 0.00 0.00 3.72
268 270 3.629855 TGGTGTGTGTGTTTGACTATTGG 59.370 43.478 0.00 0.00 0.00 3.16
269 271 3.630312 GGTGTGTGTGTTTGACTATTGGT 59.370 43.478 0.00 0.00 0.00 3.67
277 279 6.203915 GTGTGTTTGACTATTGGTATGTGTCA 59.796 38.462 0.00 0.00 36.10 3.58
278 280 6.203915 TGTGTTTGACTATTGGTATGTGTCAC 59.796 38.462 0.00 0.00 37.38 3.67
279 281 6.426937 GTGTTTGACTATTGGTATGTGTCACT 59.573 38.462 4.27 0.00 37.38 3.41
284 286 5.724328 ACTATTGGTATGTGTCACTGTCAG 58.276 41.667 4.27 0.00 0.00 3.51
300 302 3.096852 TGTCAGGATCCATGTAGTTCGT 58.903 45.455 15.82 0.00 0.00 3.85
306 308 6.097696 TCAGGATCCATGTAGTTCGTGAATAA 59.902 38.462 15.82 0.00 35.23 1.40
330 332 3.253188 GCTTTTGTTGATGGTGCTCTACA 59.747 43.478 0.00 0.00 0.00 2.74
357 359 3.744238 TGAATTTGGAGTGAGACGACA 57.256 42.857 0.00 0.00 0.00 4.35
363 365 1.754803 TGGAGTGAGACGACAACACTT 59.245 47.619 15.28 4.19 43.49 3.16
375 377 3.121944 CGACAACACTTGTATGCACTCTC 59.878 47.826 0.00 0.00 45.52 3.20
392 394 2.870411 CTCTCGACGGGTGTTTTTCTTT 59.130 45.455 0.00 0.00 0.00 2.52
393 395 2.867975 TCTCGACGGGTGTTTTTCTTTC 59.132 45.455 0.00 0.00 0.00 2.62
394 396 2.610374 CTCGACGGGTGTTTTTCTTTCA 59.390 45.455 0.00 0.00 0.00 2.69
401 404 4.201841 CGGGTGTTTTTCTTTCAGTAACGT 60.202 41.667 0.00 0.00 0.00 3.99
410 413 2.642139 TTCAGTAACGTCGGGACATC 57.358 50.000 0.00 0.00 0.00 3.06
418 421 1.444917 CGTCGGGACATCCTCATCGA 61.445 60.000 0.00 0.00 35.95 3.59
428 431 1.621992 TCCTCATCGATAGCCAGGTC 58.378 55.000 0.00 0.00 0.00 3.85
439 442 2.113139 CCAGGTCGGCCAAAGTGT 59.887 61.111 9.71 0.00 37.19 3.55
464 467 1.202639 TGCTGTCAATGTGGACGAGTT 60.203 47.619 0.00 0.00 40.72 3.01
491 494 8.577939 GGTCCGTTTTTCGCTAATTAAATAAAC 58.422 33.333 0.00 0.00 38.35 2.01
600 605 3.203716 GGACATTCCTAACCGTTGGATC 58.796 50.000 0.00 0.00 32.53 3.36
674 696 6.365970 ACTATTTCCATATCCATCGAGCTT 57.634 37.500 0.00 0.00 0.00 3.74
688 710 7.103641 TCCATCGAGCTTTAGTCACTAATTTT 58.896 34.615 0.00 0.00 0.00 1.82
731 753 9.468532 AAACAGAAGACAATAGATTTGAAAAGC 57.531 29.630 0.00 0.00 0.00 3.51
798 822 0.391661 TCCTCGCTGCCAAGTCAATC 60.392 55.000 0.00 0.00 0.00 2.67
845 869 4.466370 TCATCTCCCTACCAACTAACTGTG 59.534 45.833 0.00 0.00 0.00 3.66
904 928 2.972505 CACACACACACGGGAGCC 60.973 66.667 0.00 0.00 0.00 4.70
924 952 1.512926 CAGAGACCGGAAACACCAAG 58.487 55.000 9.46 0.00 38.90 3.61
1131 1162 0.337082 TCATGGGTAAGTCTCCCCGA 59.663 55.000 0.00 0.00 44.44 5.14
1189 1235 4.974438 TGGCCGGGGTTCCTGACT 62.974 66.667 2.18 0.00 29.82 3.41
1207 1253 3.783362 TTGGGGTTGTGTGGCCGAG 62.783 63.158 0.00 0.00 0.00 4.63
1393 1440 0.175989 CTCCTTCTTGCGTACCTCCC 59.824 60.000 0.00 0.00 0.00 4.30
1532 1579 3.844943 GCAACTTTTCTGTAGTCGTGTGC 60.845 47.826 0.00 0.00 0.00 4.57
1533 1580 3.173668 ACTTTTCTGTAGTCGTGTGCA 57.826 42.857 0.00 0.00 0.00 4.57
1534 1581 2.864343 ACTTTTCTGTAGTCGTGTGCAC 59.136 45.455 10.75 10.75 0.00 4.57
1535 1582 2.588027 TTTCTGTAGTCGTGTGCACA 57.412 45.000 17.42 17.42 0.00 4.57
1536 1583 1.847818 TTCTGTAGTCGTGTGCACAC 58.152 50.000 35.04 35.04 43.15 3.82
1537 1584 0.031585 TCTGTAGTCGTGTGCACACC 59.968 55.000 37.23 26.54 43.66 4.16
1538 1585 0.032130 CTGTAGTCGTGTGCACACCT 59.968 55.000 37.23 30.89 43.66 4.00
1539 1586 0.249280 TGTAGTCGTGTGCACACCTG 60.249 55.000 37.23 26.64 43.66 4.00
1540 1587 1.300620 TAGTCGTGTGCACACCTGC 60.301 57.895 37.23 27.47 43.66 4.85
1548 1595 3.525221 GCACACCTGCAGTTTGGT 58.475 55.556 13.81 0.35 43.62 3.67
1549 1596 1.360192 GCACACCTGCAGTTTGGTC 59.640 57.895 13.81 2.29 43.62 4.02
1550 1597 1.383456 GCACACCTGCAGTTTGGTCA 61.383 55.000 13.81 0.00 43.62 4.02
1551 1598 1.321474 CACACCTGCAGTTTGGTCAT 58.679 50.000 13.81 0.00 33.75 3.06
1552 1599 1.267806 CACACCTGCAGTTTGGTCATC 59.732 52.381 13.81 0.00 33.75 2.92
1554 1601 0.606401 ACCTGCAGTTTGGTCATCGG 60.606 55.000 13.81 0.00 29.18 4.18
1555 1602 0.321564 CCTGCAGTTTGGTCATCGGA 60.322 55.000 13.81 0.00 0.00 4.55
1556 1603 1.679944 CCTGCAGTTTGGTCATCGGAT 60.680 52.381 13.81 0.00 0.00 4.18
1557 1604 2.419990 CCTGCAGTTTGGTCATCGGATA 60.420 50.000 13.81 0.00 0.00 2.59
1558 1605 2.609459 CTGCAGTTTGGTCATCGGATAC 59.391 50.000 5.25 0.00 0.00 2.24
1559 1606 2.236146 TGCAGTTTGGTCATCGGATACT 59.764 45.455 0.00 0.00 0.00 2.12
1560 1607 2.609459 GCAGTTTGGTCATCGGATACTG 59.391 50.000 10.54 10.54 0.00 2.74
1561 1608 2.609459 CAGTTTGGTCATCGGATACTGC 59.391 50.000 4.03 0.00 0.00 4.40
1562 1609 2.501723 AGTTTGGTCATCGGATACTGCT 59.498 45.455 0.00 0.00 0.00 4.24
1563 1610 3.055094 AGTTTGGTCATCGGATACTGCTT 60.055 43.478 0.00 0.00 0.00 3.91
1565 1612 2.388735 TGGTCATCGGATACTGCTTCT 58.611 47.619 0.00 0.00 0.00 2.85
1567 1614 3.318275 TGGTCATCGGATACTGCTTCTAC 59.682 47.826 0.00 0.00 0.00 2.59
1576 1624 4.890581 GGATACTGCTTCTACCTTCAGAGA 59.109 45.833 0.00 0.00 0.00 3.10
1578 1626 4.529109 ACTGCTTCTACCTTCAGAGAAC 57.471 45.455 0.00 0.00 0.00 3.01
1580 1628 3.154710 TGCTTCTACCTTCAGAGAACGA 58.845 45.455 0.00 0.00 0.00 3.85
1595 1643 4.158764 AGAGAACGAGTAATTCTGACCCAG 59.841 45.833 0.00 0.00 36.53 4.45
1596 1644 4.087182 AGAACGAGTAATTCTGACCCAGA 58.913 43.478 0.00 0.00 38.87 3.86
1627 1678 8.547069 GCTTCTGAATAGACATATCAGTGTTTC 58.453 37.037 0.00 0.00 31.21 2.78
1631 1682 8.407457 TGAATAGACATATCAGTGTTTCGTTC 57.593 34.615 0.00 0.00 31.16 3.95
1639 1690 8.873830 ACATATCAGTGTTTCGTTCTAAGATTG 58.126 33.333 0.00 0.00 0.00 2.67
1640 1691 9.087424 CATATCAGTGTTTCGTTCTAAGATTGA 57.913 33.333 0.00 0.00 0.00 2.57
1643 1694 8.378172 TCAGTGTTTCGTTCTAAGATTGATTT 57.622 30.769 0.00 0.00 0.00 2.17
1654 1705 9.617975 GTTCTAAGATTGATTTTCAGGAAAGTG 57.382 33.333 0.00 0.00 0.00 3.16
1663 1714 8.477419 TGATTTTCAGGAAAGTGGAATAGTTT 57.523 30.769 0.00 0.00 34.65 2.66
1679 1730 6.094048 GGAATAGTTTAGCAATCTGAACTGCA 59.906 38.462 14.99 0.00 45.26 4.41
1797 1848 7.284351 CACTTTTCAGTCTGAATAAAGTCGAC 58.716 38.462 21.86 7.70 36.08 4.20
1871 1923 4.574527 CGTAGCAATCACAGTTTCTCAG 57.425 45.455 0.00 0.00 0.00 3.35
1897 1949 5.466728 TCTGTTTGCTGTCTCTATTGTTGAC 59.533 40.000 0.00 0.00 0.00 3.18
1972 2030 8.967918 AGGGATAAGTTACTTTTAAATGCTTCC 58.032 33.333 1.94 0.00 0.00 3.46
2187 2248 1.806496 AGCATATCCCTGCAGGTACA 58.194 50.000 30.63 14.96 44.77 2.90
2229 2290 1.903404 CACTTCAGCCCCAACACCC 60.903 63.158 0.00 0.00 0.00 4.61
2277 2338 1.579429 GGCAAACCGTAACTGCTGG 59.421 57.895 0.00 0.00 36.32 4.85
2283 2344 1.636148 ACCGTAACTGCTGGACCTTA 58.364 50.000 0.00 0.00 0.00 2.69
2284 2345 1.274447 ACCGTAACTGCTGGACCTTAC 59.726 52.381 0.00 0.00 0.00 2.34
2286 2347 1.274167 CGTAACTGCTGGACCTTACCA 59.726 52.381 0.00 0.00 38.33 3.25
2330 2395 8.552865 ACATTTTGTGATCATGTTGTTTTCATG 58.447 29.630 0.00 0.00 42.53 3.07
2531 2596 7.343057 AGACTGTAAGATCATATGGACACAAGA 59.657 37.037 2.13 0.00 37.43 3.02
2540 2605 2.358322 TGGACACAAGAAACTTCCCC 57.642 50.000 0.00 0.00 0.00 4.81
2680 2746 0.397941 AGCTGGCTCTGCAAGTGTTA 59.602 50.000 0.00 0.00 31.11 2.41
2755 2821 2.600420 CTCGACATCTGAATCGGTTGTG 59.400 50.000 10.23 4.15 38.86 3.33
2761 2827 3.326836 TCTGAATCGGTTGTGCATACA 57.673 42.857 0.00 0.00 34.31 2.29
2779 2845 8.458843 GTGCATACAGGTTAATTTACTGTCATT 58.541 33.333 11.19 0.00 43.78 2.57
2826 2894 2.986479 CTGTTTTGCGGCAAATTCTACC 59.014 45.455 26.87 12.16 33.19 3.18
3020 3090 4.750098 CACTTGTTGATTCTTCTACGGTGT 59.250 41.667 0.00 0.00 33.73 4.16
3116 3189 4.156008 GTCTATTTGATCGTTGGTTGGCTT 59.844 41.667 0.00 0.00 0.00 4.35
3188 3261 9.344309 GAATCCTACGCTCTATAAATAGAACAC 57.656 37.037 1.58 0.00 38.80 3.32
3190 3263 8.405418 TCCTACGCTCTATAAATAGAACACAT 57.595 34.615 1.58 0.00 38.80 3.21
3284 3358 6.433093 GGAAAACACCTGAGCTTTATTAAGGA 59.567 38.462 0.00 0.00 31.76 3.36
3288 3362 5.119694 CACCTGAGCTTTATTAAGGAGGTC 58.880 45.833 0.00 7.42 38.16 3.85
3289 3363 4.783227 ACCTGAGCTTTATTAAGGAGGTCA 59.217 41.667 13.39 13.39 43.31 4.02
3305 3379 4.101741 GGAGGTCAGGTAGCAGATACAAAT 59.898 45.833 0.00 0.00 35.96 2.32
3314 3388 0.537371 CAGATACAAATCCCGGGGGC 60.537 60.000 23.50 1.12 31.98 5.80
3315 3389 0.697854 AGATACAAATCCCGGGGGCT 60.698 55.000 23.50 2.40 31.98 5.19
3316 3390 0.250770 GATACAAATCCCGGGGGCTC 60.251 60.000 23.50 4.53 34.68 4.70
3318 3392 3.738481 CAAATCCCGGGGGCTCCA 61.738 66.667 23.50 0.00 34.36 3.86
3319 3393 3.420482 AAATCCCGGGGGCTCCAG 61.420 66.667 23.50 0.00 34.36 3.86
3320 3394 4.760220 AATCCCGGGGGCTCCAGT 62.760 66.667 23.50 0.00 34.36 4.00
3321 3395 2.850851 AAATCCCGGGGGCTCCAGTA 62.851 60.000 23.50 0.00 34.36 2.74
3322 3396 3.776016 ATCCCGGGGGCTCCAGTAG 62.776 68.421 23.50 0.00 34.36 2.57
3339 3414 0.034960 TAGCAAAACATGGCGGCCTA 60.035 50.000 21.46 7.11 34.54 3.93
3356 3431 5.279056 GCGGCCTAGACATAAAACTAGAGAT 60.279 44.000 0.00 0.00 38.53 2.75
3374 3450 8.925161 CTAGAGATATTCTAGCAGTTTATGGC 57.075 38.462 8.21 0.00 46.54 4.40
3378 3454 7.465116 AGATATTCTAGCAGTTTATGGCCATT 58.535 34.615 26.37 6.27 0.00 3.16
3406 3524 7.068839 ACATTGTACACCCTTGTTTCATGTTTA 59.931 33.333 0.00 0.00 37.15 2.01
3457 3850 4.314440 GCGACTCCAGGGTGTGCA 62.314 66.667 0.00 0.00 0.00 4.57
3458 3851 2.425592 CGACTCCAGGGTGTGCAA 59.574 61.111 0.00 0.00 0.00 4.08
3459 3852 1.669115 CGACTCCAGGGTGTGCAAG 60.669 63.158 0.00 0.00 0.00 4.01
3460 3853 1.302832 GACTCCAGGGTGTGCAAGG 60.303 63.158 0.00 0.00 0.00 3.61
3461 3854 1.768684 GACTCCAGGGTGTGCAAGGA 61.769 60.000 0.00 0.00 0.00 3.36
3462 3855 1.352622 ACTCCAGGGTGTGCAAGGAA 61.353 55.000 0.00 0.00 0.00 3.36
3463 3856 0.178992 CTCCAGGGTGTGCAAGGAAA 60.179 55.000 0.00 0.00 0.00 3.13
3464 3857 0.467290 TCCAGGGTGTGCAAGGAAAC 60.467 55.000 0.00 0.00 0.00 2.78
3465 3858 0.754957 CCAGGGTGTGCAAGGAAACA 60.755 55.000 0.00 0.00 0.00 2.83
3466 3859 1.331214 CAGGGTGTGCAAGGAAACAT 58.669 50.000 0.00 0.00 0.00 2.71
3467 3860 1.270550 CAGGGTGTGCAAGGAAACATC 59.729 52.381 0.00 0.00 0.00 3.06
3468 3861 1.145738 AGGGTGTGCAAGGAAACATCT 59.854 47.619 0.00 0.00 0.00 2.90
3469 3862 1.541588 GGGTGTGCAAGGAAACATCTC 59.458 52.381 0.00 0.00 0.00 2.75
3470 3863 1.197721 GGTGTGCAAGGAAACATCTCG 59.802 52.381 0.00 0.00 0.00 4.04
3471 3864 1.873591 GTGTGCAAGGAAACATCTCGT 59.126 47.619 0.00 0.00 0.00 4.18
3472 3865 3.064207 GTGTGCAAGGAAACATCTCGTA 58.936 45.455 0.00 0.00 0.00 3.43
3473 3866 3.123621 GTGTGCAAGGAAACATCTCGTAG 59.876 47.826 0.00 0.00 0.00 3.51
3474 3867 3.006430 TGTGCAAGGAAACATCTCGTAGA 59.994 43.478 0.00 0.00 0.00 2.59
3475 3868 3.994392 GTGCAAGGAAACATCTCGTAGAA 59.006 43.478 0.00 0.00 34.09 2.10
3476 3869 3.994392 TGCAAGGAAACATCTCGTAGAAC 59.006 43.478 0.00 0.00 34.09 3.01
3477 3870 3.371285 GCAAGGAAACATCTCGTAGAACC 59.629 47.826 0.00 0.00 34.09 3.62
3478 3871 4.822026 CAAGGAAACATCTCGTAGAACCT 58.178 43.478 0.00 0.00 34.09 3.50
3479 3872 5.623824 GCAAGGAAACATCTCGTAGAACCTA 60.624 44.000 0.00 0.00 34.09 3.08
3480 3873 5.579564 AGGAAACATCTCGTAGAACCTAC 57.420 43.478 0.00 0.00 34.09 3.18
3481 3874 5.014858 AGGAAACATCTCGTAGAACCTACA 58.985 41.667 5.17 0.00 34.09 2.74
3482 3875 5.657302 AGGAAACATCTCGTAGAACCTACAT 59.343 40.000 5.17 0.00 34.09 2.29
3483 3876 6.154706 AGGAAACATCTCGTAGAACCTACATT 59.845 38.462 5.17 0.00 34.09 2.71
3484 3877 6.255887 GGAAACATCTCGTAGAACCTACATTG 59.744 42.308 5.17 0.00 34.09 2.82
3485 3878 5.916661 ACATCTCGTAGAACCTACATTGT 57.083 39.130 5.17 0.00 34.09 2.71
3486 3879 7.400599 AACATCTCGTAGAACCTACATTGTA 57.599 36.000 5.17 0.00 34.09 2.41
3487 3880 6.793349 ACATCTCGTAGAACCTACATTGTAC 58.207 40.000 5.17 0.00 34.09 2.90
3488 3881 6.376299 ACATCTCGTAGAACCTACATTGTACA 59.624 38.462 0.00 0.00 34.09 2.90
3489 3882 6.187125 TCTCGTAGAACCTACATTGTACAC 57.813 41.667 0.00 0.00 34.09 2.90
3490 3883 5.124457 TCTCGTAGAACCTACATTGTACACC 59.876 44.000 0.00 0.00 34.09 4.16
3491 3884 4.100529 CGTAGAACCTACATTGTACACCG 58.899 47.826 0.00 0.00 29.78 4.94
3492 3885 4.379813 CGTAGAACCTACATTGTACACCGT 60.380 45.833 0.00 0.00 29.78 4.83
3493 3886 4.612264 AGAACCTACATTGTACACCGTT 57.388 40.909 0.00 0.00 0.00 4.44
3508 3901 2.682856 CACCGTTGGTTAAGATCATGGG 59.317 50.000 0.00 0.00 31.02 4.00
3533 3926 3.069443 CCTCTCCTCTGCTTCCTTCATAC 59.931 52.174 0.00 0.00 0.00 2.39
3534 3927 3.034635 TCTCCTCTGCTTCCTTCATACC 58.965 50.000 0.00 0.00 0.00 2.73
3535 3928 1.757118 TCCTCTGCTTCCTTCATACCG 59.243 52.381 0.00 0.00 0.00 4.02
3536 3929 1.482593 CCTCTGCTTCCTTCATACCGT 59.517 52.381 0.00 0.00 0.00 4.83
3537 3930 2.693591 CCTCTGCTTCCTTCATACCGTA 59.306 50.000 0.00 0.00 0.00 4.02
3557 3950 2.915869 AGATACTTCTGACAACCCCCA 58.084 47.619 0.00 0.00 0.00 4.96
3620 4013 0.674581 CATCAAGCACAGCCCTTCGA 60.675 55.000 0.00 0.00 0.00 3.71
3642 4035 2.176546 CGCCATTGCCTCAACACG 59.823 61.111 0.00 0.00 0.00 4.49
3742 4135 2.031012 CAGCCGAGCACCTGTTGA 59.969 61.111 0.00 0.00 0.00 3.18
3778 4171 5.794687 TGTAGCATCAACATTACCTTTCG 57.205 39.130 0.00 0.00 0.00 3.46
3867 4260 1.272807 AGCCCAGCTCATGCAAAAAT 58.727 45.000 0.00 0.00 42.74 1.82
3869 4262 1.735571 GCCCAGCTCATGCAAAAATTG 59.264 47.619 0.00 0.00 42.74 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.696314 GGAGATGCCCTAACCCCCA 60.696 63.158 0.00 0.00 0.00 4.96
42 43 2.223971 TGAGTCTGACTTGGGAAACGTC 60.224 50.000 12.27 0.00 0.00 4.34
44 45 2.135933 GTGAGTCTGACTTGGGAAACG 58.864 52.381 12.27 0.00 0.00 3.60
50 51 5.398603 AACTGATAGTGAGTCTGACTTGG 57.601 43.478 12.27 0.00 0.00 3.61
57 58 1.402259 CCGCGAACTGATAGTGAGTCT 59.598 52.381 8.23 0.00 0.00 3.24
59 60 1.132643 GTCCGCGAACTGATAGTGAGT 59.867 52.381 8.23 0.00 0.00 3.41
63 64 0.179171 CGTGTCCGCGAACTGATAGT 60.179 55.000 8.23 0.00 0.00 2.12
84 85 6.436261 ACTTACGTATCCATCATGTCTTACG 58.564 40.000 0.00 8.80 38.59 3.18
87 88 5.523916 GCAACTTACGTATCCATCATGTCTT 59.476 40.000 0.00 0.00 0.00 3.01
88 89 5.050490 GCAACTTACGTATCCATCATGTCT 58.950 41.667 0.00 0.00 0.00 3.41
92 93 4.415881 TGGCAACTTACGTATCCATCAT 57.584 40.909 0.00 0.00 37.61 2.45
93 94 3.897141 TGGCAACTTACGTATCCATCA 57.103 42.857 0.00 0.00 37.61 3.07
94 95 3.746492 GGATGGCAACTTACGTATCCATC 59.254 47.826 20.82 20.82 43.80 3.51
109 110 0.335705 ATGGACATGGTTGGATGGCA 59.664 50.000 0.00 0.00 32.34 4.92
156 157 4.339247 AGTTCTTCACAAATGACCACCAAG 59.661 41.667 0.00 0.00 33.38 3.61
211 213 0.371645 GACTTTGATGGCGAGCTTCG 59.628 55.000 0.00 0.00 43.89 3.79
219 221 0.749454 ATGGCTCCGACTTTGATGGC 60.749 55.000 0.00 0.00 0.00 4.40
256 258 6.426937 ACAGTGACACATACCAATAGTCAAAC 59.573 38.462 8.59 0.00 40.47 2.93
257 259 6.530120 ACAGTGACACATACCAATAGTCAAA 58.470 36.000 8.59 0.00 40.47 2.69
268 270 3.195610 TGGATCCTGACAGTGACACATAC 59.804 47.826 14.23 0.00 0.00 2.39
269 271 3.440127 TGGATCCTGACAGTGACACATA 58.560 45.455 14.23 0.00 0.00 2.29
277 279 3.131223 CGAACTACATGGATCCTGACAGT 59.869 47.826 14.23 13.17 0.00 3.55
278 280 3.131223 ACGAACTACATGGATCCTGACAG 59.869 47.826 14.23 12.64 0.00 3.51
279 281 3.096852 ACGAACTACATGGATCCTGACA 58.903 45.455 14.23 0.00 0.00 3.58
284 286 6.526566 GTTATTCACGAACTACATGGATCC 57.473 41.667 4.20 4.20 0.00 3.36
300 302 5.218885 CACCATCAACAAAAGCGTTATTCA 58.781 37.500 0.00 0.00 0.00 2.57
306 308 1.001378 GAGCACCATCAACAAAAGCGT 60.001 47.619 0.00 0.00 0.00 5.07
309 311 4.516698 ACTGTAGAGCACCATCAACAAAAG 59.483 41.667 0.00 0.00 0.00 2.27
310 312 4.460263 ACTGTAGAGCACCATCAACAAAA 58.540 39.130 0.00 0.00 0.00 2.44
330 332 6.934645 TCGTCTCACTCCAAATTCAATTTACT 59.065 34.615 0.00 0.00 0.00 2.24
357 359 3.318017 GTCGAGAGTGCATACAAGTGTT 58.682 45.455 0.00 0.00 0.00 3.32
363 365 0.963856 ACCCGTCGAGAGTGCATACA 60.964 55.000 0.00 0.00 0.00 2.29
375 377 2.353579 ACTGAAAGAAAAACACCCGTCG 59.646 45.455 0.00 0.00 37.43 5.12
392 394 0.813184 GGATGTCCCGACGTTACTGA 59.187 55.000 0.00 0.00 0.00 3.41
393 395 0.815734 AGGATGTCCCGACGTTACTG 59.184 55.000 0.00 0.00 40.87 2.74
394 396 1.101331 GAGGATGTCCCGACGTTACT 58.899 55.000 0.00 0.00 40.87 2.24
401 404 2.437413 CTATCGATGAGGATGTCCCGA 58.563 52.381 8.54 0.00 40.87 5.14
410 413 0.242286 CGACCTGGCTATCGATGAGG 59.758 60.000 8.54 10.20 40.86 3.86
428 431 1.131126 CAGCATAGAACACTTTGGCCG 59.869 52.381 0.00 0.00 0.00 6.13
439 442 3.056179 TCGTCCACATTGACAGCATAGAA 60.056 43.478 0.00 0.00 34.88 2.10
464 467 5.686159 TTTAATTAGCGAAAAACGGACCA 57.314 34.783 0.00 0.00 42.83 4.02
512 515 4.024809 GGCGGATGCTGTTTTACTATTCTC 60.025 45.833 0.00 0.00 42.25 2.87
600 605 4.766404 ATTTAGCCCAGTTCAAACGAAG 57.234 40.909 0.00 0.00 0.00 3.79
688 710 8.735315 TCTTCTGTTTTTCACAAACTATTGTCA 58.265 29.630 0.00 0.00 46.78 3.58
731 753 3.933722 AGATGGCGCTCCCGGATG 61.934 66.667 7.64 0.00 35.87 3.51
798 822 1.831106 GGTTTTATGGGGGCTTCCAAG 59.169 52.381 4.42 0.00 40.62 3.61
845 869 0.749454 AAAGAGGCGGATGGATGTGC 60.749 55.000 0.00 0.00 0.00 4.57
904 928 0.107831 TTGGTGTTTCCGGTCTCTGG 59.892 55.000 0.00 0.00 39.52 3.86
924 952 4.065281 CTGCTTTGCTGCTGCCCC 62.065 66.667 13.47 0.00 38.71 5.80
1183 1229 0.823356 CCACACAACCCCAAGTCAGG 60.823 60.000 0.00 0.00 0.00 3.86
1189 1235 3.783362 CTCGGCCACACAACCCCAA 62.783 63.158 2.24 0.00 0.00 4.12
1393 1440 3.631227 GCCCATTGATGAAGGAAGAGAAG 59.369 47.826 0.00 0.00 0.00 2.85
1532 1579 1.267806 GATGACCAAACTGCAGGTGTG 59.732 52.381 19.93 12.31 38.50 3.82
1533 1580 1.609208 GATGACCAAACTGCAGGTGT 58.391 50.000 19.93 6.55 38.50 4.16
1534 1581 0.518636 CGATGACCAAACTGCAGGTG 59.481 55.000 19.93 15.20 38.50 4.00
1535 1582 0.606401 CCGATGACCAAACTGCAGGT 60.606 55.000 19.93 9.19 41.83 4.00
1536 1583 0.321564 TCCGATGACCAAACTGCAGG 60.322 55.000 19.93 2.94 0.00 4.85
1537 1584 1.742761 ATCCGATGACCAAACTGCAG 58.257 50.000 13.48 13.48 0.00 4.41
1538 1585 2.236146 AGTATCCGATGACCAAACTGCA 59.764 45.455 0.00 0.00 0.00 4.41
1539 1586 2.609459 CAGTATCCGATGACCAAACTGC 59.391 50.000 0.00 0.00 0.00 4.40
1540 1587 2.609459 GCAGTATCCGATGACCAAACTG 59.391 50.000 3.32 3.32 36.74 3.16
1541 1588 2.501723 AGCAGTATCCGATGACCAAACT 59.498 45.455 0.00 0.00 0.00 2.66
1543 1590 3.197766 AGAAGCAGTATCCGATGACCAAA 59.802 43.478 0.00 0.00 0.00 3.28
1544 1591 2.766263 AGAAGCAGTATCCGATGACCAA 59.234 45.455 0.00 0.00 0.00 3.67
1545 1592 2.388735 AGAAGCAGTATCCGATGACCA 58.611 47.619 0.00 0.00 0.00 4.02
1546 1593 3.305471 GGTAGAAGCAGTATCCGATGACC 60.305 52.174 0.00 0.00 0.00 4.02
1547 1594 3.570550 AGGTAGAAGCAGTATCCGATGAC 59.429 47.826 0.00 0.00 0.00 3.06
1548 1595 3.833732 AGGTAGAAGCAGTATCCGATGA 58.166 45.455 0.00 0.00 0.00 2.92
1549 1596 4.038042 TGAAGGTAGAAGCAGTATCCGATG 59.962 45.833 0.00 0.00 0.00 3.84
1550 1597 4.215908 TGAAGGTAGAAGCAGTATCCGAT 58.784 43.478 0.00 0.00 0.00 4.18
1551 1598 3.628008 TGAAGGTAGAAGCAGTATCCGA 58.372 45.455 0.00 0.00 0.00 4.55
1552 1599 3.632604 TCTGAAGGTAGAAGCAGTATCCG 59.367 47.826 0.00 0.00 0.00 4.18
1554 1601 6.270064 GTTCTCTGAAGGTAGAAGCAGTATC 58.730 44.000 0.00 0.00 32.56 2.24
1555 1602 5.163602 CGTTCTCTGAAGGTAGAAGCAGTAT 60.164 44.000 0.00 0.00 32.56 2.12
1556 1603 4.156190 CGTTCTCTGAAGGTAGAAGCAGTA 59.844 45.833 0.00 0.00 32.56 2.74
1557 1604 3.057174 CGTTCTCTGAAGGTAGAAGCAGT 60.057 47.826 0.00 0.00 32.56 4.40
1558 1605 3.191581 TCGTTCTCTGAAGGTAGAAGCAG 59.808 47.826 0.00 0.00 32.56 4.24
1559 1606 3.154710 TCGTTCTCTGAAGGTAGAAGCA 58.845 45.455 0.00 0.00 32.56 3.91
1560 1607 3.191791 ACTCGTTCTCTGAAGGTAGAAGC 59.808 47.826 0.00 0.00 32.56 3.86
1561 1608 6.497785 TTACTCGTTCTCTGAAGGTAGAAG 57.502 41.667 0.00 0.00 32.56 2.85
1562 1609 7.393796 AGAATTACTCGTTCTCTGAAGGTAGAA 59.606 37.037 0.00 0.00 30.34 2.10
1563 1610 6.885376 AGAATTACTCGTTCTCTGAAGGTAGA 59.115 38.462 0.00 0.00 30.34 2.59
1565 1612 6.657966 TCAGAATTACTCGTTCTCTGAAGGTA 59.342 38.462 0.00 0.00 39.55 3.08
1567 1614 5.802956 GTCAGAATTACTCGTTCTCTGAAGG 59.197 44.000 1.86 0.00 42.97 3.46
1576 1624 4.884668 TTCTGGGTCAGAATTACTCGTT 57.115 40.909 6.28 0.00 44.27 3.85
1612 1663 8.635877 ATCTTAGAACGAAACACTGATATGTC 57.364 34.615 0.00 0.00 30.55 3.06
1613 1664 8.873830 CAATCTTAGAACGAAACACTGATATGT 58.126 33.333 0.00 0.00 0.00 2.29
1621 1672 9.107367 CTGAAAATCAATCTTAGAACGAAACAC 57.893 33.333 0.00 0.00 0.00 3.32
1627 1678 8.507249 ACTTTCCTGAAAATCAATCTTAGAACG 58.493 33.333 0.00 0.00 0.00 3.95
1631 1682 8.340618 TCCACTTTCCTGAAAATCAATCTTAG 57.659 34.615 0.00 0.00 0.00 2.18
1640 1691 8.523658 GCTAAACTATTCCACTTTCCTGAAAAT 58.476 33.333 0.00 0.00 0.00 1.82
1643 1694 6.539173 TGCTAAACTATTCCACTTTCCTGAA 58.461 36.000 0.00 0.00 0.00 3.02
1654 1705 6.094048 TGCAGTTCAGATTGCTAAACTATTCC 59.906 38.462 8.44 0.00 39.10 3.01
1663 1714 2.302733 TCTGGTGCAGTTCAGATTGCTA 59.697 45.455 9.47 0.00 39.10 3.49
1797 1848 3.476552 TGTGGACTTTCAGTGCCTAAAG 58.523 45.455 2.17 2.17 35.52 1.85
1855 1907 5.998454 ACAGAACTGAGAAACTGTGATTG 57.002 39.130 8.87 0.00 41.16 2.67
1871 1923 5.931441 ACAATAGAGACAGCAAACAGAAC 57.069 39.130 0.00 0.00 0.00 3.01
1897 1949 4.806640 AAATTTAAGACCCATGCCTGTG 57.193 40.909 0.00 0.00 0.00 3.66
1913 1969 8.362639 ACTGACAGAGATGCATGTTAAAAATTT 58.637 29.630 10.08 0.00 0.00 1.82
1934 1991 8.240267 AGTAACTTATCCCTATTCTGACTGAC 57.760 38.462 0.00 0.00 0.00 3.51
1972 2030 0.994995 CTGAAGATGACACGAAGGCG 59.005 55.000 0.00 0.00 44.79 5.52
2013 2072 2.370189 ACACAAGAACTCTGAAGAGGGG 59.630 50.000 11.87 0.00 46.13 4.79
2114 2173 3.058224 GCAACTCTGTGTTATTTTCCGCT 60.058 43.478 0.00 0.00 37.07 5.52
2117 2176 9.937175 GATATAAGCAACTCTGTGTTATTTTCC 57.063 33.333 0.00 0.00 37.07 3.13
2126 2185 9.632807 GGATAGTTAGATATAAGCAACTCTGTG 57.367 37.037 0.00 0.00 33.47 3.66
2144 2205 7.094118 GCTTTTGTTGGTTATGTGGGATAGTTA 60.094 37.037 0.00 0.00 0.00 2.24
2145 2206 6.295067 GCTTTTGTTGGTTATGTGGGATAGTT 60.295 38.462 0.00 0.00 0.00 2.24
2146 2207 5.185056 GCTTTTGTTGGTTATGTGGGATAGT 59.815 40.000 0.00 0.00 0.00 2.12
2147 2208 5.184864 TGCTTTTGTTGGTTATGTGGGATAG 59.815 40.000 0.00 0.00 0.00 2.08
2148 2209 5.080337 TGCTTTTGTTGGTTATGTGGGATA 58.920 37.500 0.00 0.00 0.00 2.59
2187 2248 6.426633 TGTCGTTAGAACATGTGTGATCAATT 59.573 34.615 0.00 0.00 30.17 2.32
2229 2290 1.008361 CATTTTTGGGTGAAGGCGCG 61.008 55.000 0.00 0.00 0.00 6.86
2273 2334 2.271944 AACAAGTGGTAAGGTCCAGC 57.728 50.000 0.00 0.00 38.23 4.85
2277 2338 3.558033 TGGGAAAACAAGTGGTAAGGTC 58.442 45.455 0.00 0.00 0.00 3.85
2283 2344 4.712337 TGTACAAATGGGAAAACAAGTGGT 59.288 37.500 0.00 0.00 0.00 4.16
2284 2345 5.269505 TGTACAAATGGGAAAACAAGTGG 57.730 39.130 0.00 0.00 0.00 4.00
2286 2347 7.826744 ACAAAATGTACAAATGGGAAAACAAGT 59.173 29.630 0.00 0.00 0.00 3.16
2531 2596 1.493022 TGCTGTACACAGGGGAAGTTT 59.507 47.619 11.18 0.00 43.94 2.66
2540 2605 1.596954 GCGTGGTTTTGCTGTACACAG 60.597 52.381 4.96 4.96 46.40 3.66
2680 2746 1.417145 AGGTGCATGGCAATTGTTTGT 59.583 42.857 7.40 0.00 41.47 2.83
2745 2811 2.489938 ACCTGTATGCACAACCGATT 57.510 45.000 0.00 0.00 33.22 3.34
2755 2821 7.432252 GCAATGACAGTAAATTAACCTGTATGC 59.568 37.037 14.23 14.23 39.43 3.14
2761 2827 7.015195 ACAAAGGCAATGACAGTAAATTAACCT 59.985 33.333 0.00 0.00 0.00 3.50
2779 2845 4.558178 CTGCAAATGATGTAACAAAGGCA 58.442 39.130 0.00 0.00 0.00 4.75
2826 2894 1.698532 AGGCCAATATCAGCAGAGGAG 59.301 52.381 5.01 0.00 0.00 3.69
2898 2967 6.369065 GTGAACAAATACTCCCTCTAGTGTTG 59.631 42.308 0.00 0.00 31.98 3.33
3020 3090 7.665145 TCCATTTTCACACTACATCAATTCTCA 59.335 33.333 0.00 0.00 0.00 3.27
3248 3322 7.454694 AGCTCAGGTGTTTTCCCTAAAAATAAT 59.545 33.333 0.00 0.00 39.01 1.28
3269 3343 4.783227 ACCTGACCTCCTTAATAAAGCTCA 59.217 41.667 0.00 0.00 0.00 4.26
3271 3345 5.163290 GCTACCTGACCTCCTTAATAAAGCT 60.163 44.000 0.00 0.00 0.00 3.74
3284 3358 4.101741 GGATTTGTATCTGCTACCTGACCT 59.898 45.833 0.00 0.00 0.00 3.85
3288 3362 3.393800 CGGGATTTGTATCTGCTACCTG 58.606 50.000 0.00 0.00 0.00 4.00
3289 3363 2.368875 CCGGGATTTGTATCTGCTACCT 59.631 50.000 0.00 0.00 0.00 3.08
3290 3364 2.550208 CCCGGGATTTGTATCTGCTACC 60.550 54.545 18.48 0.00 0.00 3.18
3305 3379 4.475444 CTACTGGAGCCCCCGGGA 62.475 72.222 26.32 0.00 45.98 5.14
3314 3388 1.131126 CGCCATGTTTTGCTACTGGAG 59.869 52.381 0.00 0.00 0.00 3.86
3315 3389 1.164411 CGCCATGTTTTGCTACTGGA 58.836 50.000 0.00 0.00 0.00 3.86
3316 3390 0.171007 CCGCCATGTTTTGCTACTGG 59.829 55.000 0.00 0.00 0.00 4.00
3318 3392 1.595093 GGCCGCCATGTTTTGCTACT 61.595 55.000 3.91 0.00 0.00 2.57
3319 3393 1.153842 GGCCGCCATGTTTTGCTAC 60.154 57.895 3.91 0.00 0.00 3.58
3320 3394 0.034960 TAGGCCGCCATGTTTTGCTA 60.035 50.000 13.15 0.00 0.00 3.49
3321 3395 1.304052 TAGGCCGCCATGTTTTGCT 60.304 52.632 13.15 0.00 0.00 3.91
3322 3396 1.139520 CTAGGCCGCCATGTTTTGC 59.860 57.895 13.15 0.00 0.00 3.68
3323 3397 0.451783 GTCTAGGCCGCCATGTTTTG 59.548 55.000 13.15 0.00 0.00 2.44
3324 3398 0.037590 TGTCTAGGCCGCCATGTTTT 59.962 50.000 13.15 0.00 0.00 2.43
3356 3431 7.996066 TGTAAATGGCCATAAACTGCTAGAATA 59.004 33.333 21.15 0.00 0.00 1.75
3366 3441 6.754675 GGTGTACAATGTAAATGGCCATAAAC 59.245 38.462 21.15 19.81 0.00 2.01
3373 3449 4.219725 ACAAGGGTGTACAATGTAAATGGC 59.780 41.667 0.00 0.00 35.72 4.40
3374 3450 5.975693 ACAAGGGTGTACAATGTAAATGG 57.024 39.130 0.00 0.00 35.72 3.16
3378 3454 6.547880 ACATGAAACAAGGGTGTACAATGTAA 59.452 34.615 0.00 0.00 36.80 2.41
3406 3524 5.480205 GAGGTTCTACGAGATGTTTCCTTT 58.520 41.667 0.00 0.00 0.00 3.11
3441 3834 1.669115 CTTGCACACCCTGGAGTCG 60.669 63.158 0.00 0.00 0.00 4.18
3446 3839 0.754957 TGTTTCCTTGCACACCCTGG 60.755 55.000 0.00 0.00 0.00 4.45
3448 3841 1.145738 AGATGTTTCCTTGCACACCCT 59.854 47.619 0.00 0.00 0.00 4.34
3449 3842 1.541588 GAGATGTTTCCTTGCACACCC 59.458 52.381 0.00 0.00 0.00 4.61
3450 3843 1.197721 CGAGATGTTTCCTTGCACACC 59.802 52.381 0.00 0.00 0.00 4.16
3451 3844 1.873591 ACGAGATGTTTCCTTGCACAC 59.126 47.619 0.00 0.00 0.00 3.82
3452 3845 2.254546 ACGAGATGTTTCCTTGCACA 57.745 45.000 0.00 0.00 0.00 4.57
3453 3846 3.585862 TCTACGAGATGTTTCCTTGCAC 58.414 45.455 0.00 0.00 0.00 4.57
3454 3847 3.953712 TCTACGAGATGTTTCCTTGCA 57.046 42.857 0.00 0.00 0.00 4.08
3455 3848 3.371285 GGTTCTACGAGATGTTTCCTTGC 59.629 47.826 0.00 0.00 0.00 4.01
3456 3849 4.822026 AGGTTCTACGAGATGTTTCCTTG 58.178 43.478 0.00 0.00 0.00 3.61
3457 3850 5.479375 TGTAGGTTCTACGAGATGTTTCCTT 59.521 40.000 0.00 0.00 0.00 3.36
3458 3851 5.014858 TGTAGGTTCTACGAGATGTTTCCT 58.985 41.667 0.00 0.00 0.00 3.36
3459 3852 5.320549 TGTAGGTTCTACGAGATGTTTCC 57.679 43.478 0.00 0.00 0.00 3.13
3460 3853 6.812160 ACAATGTAGGTTCTACGAGATGTTTC 59.188 38.462 0.00 0.00 0.00 2.78
3461 3854 6.698380 ACAATGTAGGTTCTACGAGATGTTT 58.302 36.000 0.00 0.00 0.00 2.83
3462 3855 6.282199 ACAATGTAGGTTCTACGAGATGTT 57.718 37.500 0.00 0.00 0.00 2.71
3463 3856 5.916661 ACAATGTAGGTTCTACGAGATGT 57.083 39.130 0.00 1.59 0.00 3.06
3464 3857 6.691818 GTGTACAATGTAGGTTCTACGAGATG 59.308 42.308 0.00 1.10 0.00 2.90
3465 3858 6.183360 GGTGTACAATGTAGGTTCTACGAGAT 60.183 42.308 0.00 0.00 0.00 2.75
3466 3859 5.124457 GGTGTACAATGTAGGTTCTACGAGA 59.876 44.000 0.00 0.00 0.00 4.04
3467 3860 5.338365 GGTGTACAATGTAGGTTCTACGAG 58.662 45.833 0.00 0.00 0.00 4.18
3468 3861 4.142622 CGGTGTACAATGTAGGTTCTACGA 60.143 45.833 0.00 0.00 0.00 3.43
3469 3862 4.100529 CGGTGTACAATGTAGGTTCTACG 58.899 47.826 0.00 0.00 0.00 3.51
3470 3863 5.064441 ACGGTGTACAATGTAGGTTCTAC 57.936 43.478 0.00 0.00 0.00 2.59
3471 3864 5.472148 CAACGGTGTACAATGTAGGTTCTA 58.528 41.667 0.00 0.00 0.00 2.10
3472 3865 4.312443 CAACGGTGTACAATGTAGGTTCT 58.688 43.478 0.00 0.00 0.00 3.01
3473 3866 3.434299 CCAACGGTGTACAATGTAGGTTC 59.566 47.826 0.00 0.00 0.00 3.62
3474 3867 3.181452 ACCAACGGTGTACAATGTAGGTT 60.181 43.478 0.00 0.00 32.98 3.50
3475 3868 2.369532 ACCAACGGTGTACAATGTAGGT 59.630 45.455 0.00 0.59 32.98 3.08
3476 3869 3.048337 ACCAACGGTGTACAATGTAGG 57.952 47.619 0.00 0.00 32.98 3.18
3477 3870 5.927689 TCTTAACCAACGGTGTACAATGTAG 59.072 40.000 0.00 0.00 35.34 2.74
3478 3871 5.851720 TCTTAACCAACGGTGTACAATGTA 58.148 37.500 0.00 0.00 35.34 2.29
3479 3872 4.706035 TCTTAACCAACGGTGTACAATGT 58.294 39.130 0.00 0.00 35.34 2.71
3480 3873 5.410132 TGATCTTAACCAACGGTGTACAATG 59.590 40.000 0.00 0.00 35.34 2.82
3481 3874 5.553123 TGATCTTAACCAACGGTGTACAAT 58.447 37.500 0.00 0.00 35.34 2.71
3482 3875 4.958509 TGATCTTAACCAACGGTGTACAA 58.041 39.130 0.00 0.00 35.34 2.41
3483 3876 4.603989 TGATCTTAACCAACGGTGTACA 57.396 40.909 0.00 0.00 35.34 2.90
3484 3877 4.331717 CCATGATCTTAACCAACGGTGTAC 59.668 45.833 0.00 0.00 35.34 2.90
3485 3878 4.509616 CCATGATCTTAACCAACGGTGTA 58.490 43.478 0.00 0.00 35.34 2.90
3486 3879 3.343617 CCATGATCTTAACCAACGGTGT 58.656 45.455 0.00 0.00 35.34 4.16
3487 3880 2.682856 CCCATGATCTTAACCAACGGTG 59.317 50.000 0.00 0.00 35.34 4.94
3488 3881 2.307686 ACCCATGATCTTAACCAACGGT 59.692 45.455 0.00 0.00 37.65 4.83
3489 3882 2.999331 ACCCATGATCTTAACCAACGG 58.001 47.619 0.00 0.00 0.00 4.44
3490 3883 3.377172 GGAACCCATGATCTTAACCAACG 59.623 47.826 0.00 0.00 0.00 4.10
3491 3884 4.600062 AGGAACCCATGATCTTAACCAAC 58.400 43.478 0.00 0.00 0.00 3.77
3492 3885 4.540099 AGAGGAACCCATGATCTTAACCAA 59.460 41.667 0.00 0.00 0.00 3.67
3493 3886 4.111577 AGAGGAACCCATGATCTTAACCA 58.888 43.478 0.00 0.00 0.00 3.67
3508 3901 1.567357 AGGAAGCAGAGGAGAGGAAC 58.433 55.000 0.00 0.00 0.00 3.62
3533 3926 3.181478 GGGGTTGTCAGAAGTATCTACGG 60.181 52.174 0.00 0.00 33.50 4.02
3534 3927 3.181478 GGGGGTTGTCAGAAGTATCTACG 60.181 52.174 0.00 0.00 33.50 3.51
3535 3928 3.773119 TGGGGGTTGTCAGAAGTATCTAC 59.227 47.826 0.00 0.00 33.50 2.59
3536 3929 4.069312 TGGGGGTTGTCAGAAGTATCTA 57.931 45.455 0.00 0.00 33.50 1.98
3537 3930 2.915869 TGGGGGTTGTCAGAAGTATCT 58.084 47.619 0.00 0.00 35.88 1.98
3620 4013 1.902918 TTGAGGCAATGGCGTGCTT 60.903 52.632 12.07 5.20 44.31 3.91
3642 4035 4.174762 GGAGACTGTTTACGATCCAGTTC 58.825 47.826 3.51 4.00 39.43 3.01
3742 4135 7.935210 TGTTGATGCTACATTGTCATATGAGAT 59.065 33.333 5.42 0.56 0.00 2.75
3778 4171 1.973812 GTCCTCCAAAGGGTGCTGC 60.974 63.158 0.00 0.00 43.56 5.25


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

AutoCloner maintained by Alex Coulton.