Multiple sequence alignment - TraesCS2A01G348600

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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 TraesCS2A01G348600 chr2A 100.000 3911 0 0 1 3911 587403638 587407548 0.000000e+00 7223
1 TraesCS2A01G348600 chr2A 81.627 332 44 8 1357 1680 586901580 586901258 3.880000e-65 259
2 TraesCS2A01G348600 chr2D 95.109 2985 76 35 490 3427 445059041 445062002 0.000000e+00 4639
3 TraesCS2A01G348600 chr2D 86.430 958 84 25 1091 2039 443485876 443484956 0.000000e+00 1007
4 TraesCS2A01G348600 chr2D 90.541 740 62 4 2063 2801 443484450 443483718 0.000000e+00 972
5 TraesCS2A01G348600 chr2D 95.067 446 17 3 44 484 445058524 445058969 0.000000e+00 697
6 TraesCS2A01G348600 chr2D 91.057 123 8 2 3776 3896 445062400 445062521 3.130000e-36 163
7 TraesCS2A01G348600 chr2B 93.809 2988 86 28 490 3423 523232480 523235422 0.000000e+00 4401
8 TraesCS2A01G348600 chr2B 82.218 478 66 11 1975 2450 522541351 522540891 1.020000e-105 394
9 TraesCS2A01G348600 chr2B 80.155 388 58 9 1344 1721 522214300 522213922 4.980000e-69 272
10 TraesCS2A01G348600 chr2B 91.975 162 10 3 227 386 523232039 523232199 1.410000e-54 224
11 TraesCS2A01G348600 chr2B 89.103 156 17 0 3584 3739 523237048 523237203 1.110000e-45 195
12 TraesCS2A01G348600 chr2B 78.135 311 50 11 1344 1646 522213195 522212895 8.630000e-42 182
13 TraesCS2A01G348600 chr2B 91.111 135 9 2 3765 3896 523239887 523240021 3.100000e-41 180
14 TraesCS2A01G348600 chr2B 74.558 452 90 21 2260 2694 359133989 359134432 1.440000e-39 174
15 TraesCS2A01G348600 chr2B 89.552 134 14 0 136 269 523231905 523232038 1.870000e-38 171
16 TraesCS2A01G348600 chr2B 93.069 101 7 0 384 484 523232303 523232403 8.760000e-32 148
17 TraesCS2A01G348600 chr2B 90.625 96 9 0 45 140 523225227 523225322 1.140000e-25 128
18 TraesCS2A01G348600 chr4D 80.915 634 100 15 2175 2805 74159238 74158623 7.600000e-132 481
19 TraesCS2A01G348600 chr4D 86.087 115 14 2 1652 1765 74159604 74159491 5.310000e-24 122
20 TraesCS2A01G348600 chr4B 80.915 634 100 15 2175 2805 106491961 106491346 7.600000e-132 481
21 TraesCS2A01G348600 chr4B 88.793 116 10 3 3466 3578 120529740 120529855 5.270000e-29 139
22 TraesCS2A01G348600 chr4B 88.696 115 7 5 3466 3578 427019300 427019410 6.820000e-28 135
23 TraesCS2A01G348600 chr4B 80.925 173 28 4 1594 1765 106492385 106492217 8.820000e-27 132
24 TraesCS2A01G348600 chr4B 87.719 114 10 4 3466 3576 270860297 270860409 3.170000e-26 130
25 TraesCS2A01G348600 chr4A 80.284 634 104 16 2175 2805 513805335 513805950 3.560000e-125 459
26 TraesCS2A01G348600 chr4A 87.069 116 11 4 3466 3578 38673086 38673200 1.140000e-25 128
27 TraesCS2A01G348600 chr4A 85.593 118 15 2 1649 1765 513804965 513805081 5.310000e-24 122
28 TraesCS2A01G348600 chr5A 78.435 626 111 16 2169 2789 230454334 230454940 1.700000e-103 387
29 TraesCS2A01G348600 chr5A 78.866 582 106 10 2175 2755 225243112 225243677 1.030000e-100 377
30 TraesCS2A01G348600 chr5D 78.352 619 111 15 2175 2789 192538786 192539385 2.850000e-101 379
31 TraesCS2A01G348600 chr5D 88.889 117 9 4 3465 3578 304160218 304160333 1.470000e-29 141
32 TraesCS2A01G348600 chr5B 77.607 585 105 12 2175 2758 212635546 212634987 8.100000e-87 331
33 TraesCS2A01G348600 chr1A 74.943 435 86 17 2260 2684 460281920 460282341 1.120000e-40 178
34 TraesCS2A01G348600 chr1A 90.517 116 7 4 3466 3578 583582398 583582512 2.430000e-32 150
35 TraesCS2A01G348600 chr1A 87.179 117 11 4 3465 3578 10586583 10586468 3.170000e-26 130
36 TraesCS2A01G348600 chr1A 82.734 139 21 3 1622 1759 460281549 460281685 1.910000e-23 121
37 TraesCS2A01G348600 chr1B 89.720 107 8 3 3480 3584 470293684 470293579 2.450000e-27 134
38 TraesCS2A01G348600 chr7A 86.957 115 13 2 3465 3578 594887695 594887582 1.140000e-25 128
39 TraesCS2A01G348600 chr1D 82.734 139 21 3 1622 1759 360467798 360467934 1.910000e-23 121


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 TraesCS2A01G348600 chr2A 587403638 587407548 3910 False 7223.0 7223 100.000000 1 3911 1 chr2A.!!$F1 3910
1 TraesCS2A01G348600 chr2D 445058524 445062521 3997 False 1833.0 4639 93.744333 44 3896 3 chr2D.!!$F1 3852
2 TraesCS2A01G348600 chr2D 443483718 443485876 2158 True 989.5 1007 88.485500 1091 2801 2 chr2D.!!$R1 1710
3 TraesCS2A01G348600 chr2B 523231905 523240021 8116 False 886.5 4401 91.436500 136 3896 6 chr2B.!!$F3 3760
4 TraesCS2A01G348600 chr2B 522212895 522214300 1405 True 227.0 272 79.145000 1344 1721 2 chr2B.!!$R2 377
5 TraesCS2A01G348600 chr4D 74158623 74159604 981 True 301.5 481 83.501000 1652 2805 2 chr4D.!!$R1 1153
6 TraesCS2A01G348600 chr4B 106491346 106492385 1039 True 306.5 481 80.920000 1594 2805 2 chr4B.!!$R1 1211
7 TraesCS2A01G348600 chr4A 513804965 513805950 985 False 290.5 459 82.938500 1649 2805 2 chr4A.!!$F2 1156
8 TraesCS2A01G348600 chr5A 230454334 230454940 606 False 387.0 387 78.435000 2169 2789 1 chr5A.!!$F2 620
9 TraesCS2A01G348600 chr5A 225243112 225243677 565 False 377.0 377 78.866000 2175 2755 1 chr5A.!!$F1 580
10 TraesCS2A01G348600 chr5D 192538786 192539385 599 False 379.0 379 78.352000 2175 2789 1 chr5D.!!$F1 614
11 TraesCS2A01G348600 chr5B 212634987 212635546 559 True 331.0 331 77.607000 2175 2758 1 chr5B.!!$R1 583

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
488 714 1.847328 TTGAGGTCTACATCTGCGGA 58.153 50.0 0.00 0.00 0.00 5.54 F
1455 1700 0.608130 TCAGCATGCTGTACGGAACT 59.392 50.0 39.08 5.22 43.96 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 2145 0.178947 ATTCCCCCGTTGGCTGAAAA 60.179 50.0 0.00 0.0 0.0 2.29 R
3086 4272 0.680061 AGACAGAAGGACACCGGAAC 59.320 55.0 9.46 0.0 0.0 3.62 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
23 24 6.169557 TCCATATGACACACCTATGGTTAC 57.830 41.667 3.65 0.00 43.22 2.50
24 25 5.663556 TCCATATGACACACCTATGGTTACA 59.336 40.000 3.65 0.00 43.22 2.41
25 26 6.157123 TCCATATGACACACCTATGGTTACAA 59.843 38.462 3.65 0.00 43.22 2.41
26 27 6.826231 CCATATGACACACCTATGGTTACAAA 59.174 38.462 3.65 0.00 40.20 2.83
27 28 7.338196 CCATATGACACACCTATGGTTACAAAA 59.662 37.037 3.65 0.00 40.20 2.44
28 29 8.902806 CATATGACACACCTATGGTTACAAAAT 58.097 33.333 0.00 0.00 31.02 1.82
29 30 7.775053 ATGACACACCTATGGTTACAAAATT 57.225 32.000 0.00 0.00 31.02 1.82
30 31 7.209471 TGACACACCTATGGTTACAAAATTC 57.791 36.000 0.00 0.00 31.02 2.17
31 32 6.207810 TGACACACCTATGGTTACAAAATTCC 59.792 38.462 0.00 0.00 31.02 3.01
32 33 6.311735 ACACACCTATGGTTACAAAATTCCT 58.688 36.000 0.00 0.00 31.02 3.36
33 34 6.780522 ACACACCTATGGTTACAAAATTCCTT 59.219 34.615 0.00 0.00 31.02 3.36
34 35 7.289084 ACACACCTATGGTTACAAAATTCCTTT 59.711 33.333 0.00 0.00 31.02 3.11
35 36 8.147704 CACACCTATGGTTACAAAATTCCTTTT 58.852 33.333 0.00 0.00 31.77 2.27
36 37 8.710239 ACACCTATGGTTACAAAATTCCTTTTT 58.290 29.630 0.00 0.00 33.72 1.94
42 43 8.132604 TGGTTACAAAATTCCTTTTTAAAGCG 57.867 30.769 0.00 0.00 35.75 4.68
96 97 5.470098 GGATTGGTACATCGAACTGCATTAT 59.530 40.000 0.00 0.00 39.30 1.28
195 196 8.433126 CACTAACTAAATTGGTTCGACAAGTAG 58.567 37.037 0.00 0.00 33.23 2.57
205 206 4.143389 GGTTCGACAAGTAGAACGTTGATG 60.143 45.833 5.00 0.00 43.23 3.07
239 240 9.744468 ATTTTGTAGTGACATTTTAAGTTCCAC 57.256 29.630 0.00 0.00 34.86 4.02
255 299 5.327732 AGTTCCACAGTCATTTTCATCCAT 58.672 37.500 0.00 0.00 0.00 3.41
302 346 4.806892 TCATAGTGGATTCCATGCCATTT 58.193 39.130 9.01 0.00 35.28 2.32
367 412 2.359900 GTTAGATGAGCACCCAGTTGG 58.640 52.381 0.00 0.00 41.37 3.77
435 590 7.624360 TGTGCCCAACTCTTAAAATACATAG 57.376 36.000 0.00 0.00 0.00 2.23
487 713 2.672961 TTTGAGGTCTACATCTGCGG 57.327 50.000 0.00 0.00 0.00 5.69
488 714 1.847328 TTGAGGTCTACATCTGCGGA 58.153 50.000 0.00 0.00 0.00 5.54
499 725 7.145985 GTCTACATCTGCGGAACTTATTATGA 58.854 38.462 0.00 0.00 0.00 2.15
576 802 4.350520 AGAAAATCCAAAATTTGAGGCCCA 59.649 37.500 7.37 0.00 0.00 5.36
579 805 3.534357 TCCAAAATTTGAGGCCCAGTA 57.466 42.857 7.37 0.00 0.00 2.74
581 807 4.424842 TCCAAAATTTGAGGCCCAGTATT 58.575 39.130 7.37 0.00 0.00 1.89
1077 1322 2.751688 GGGTTGTCCAAGCGGGTA 59.248 61.111 3.41 0.00 39.53 3.69
1452 1697 1.153842 CGTCAGCATGCTGTACGGA 60.154 57.895 37.42 24.90 43.96 4.69
1453 1698 0.735978 CGTCAGCATGCTGTACGGAA 60.736 55.000 37.42 24.35 43.96 4.30
1454 1699 0.721718 GTCAGCATGCTGTACGGAAC 59.278 55.000 39.08 27.55 43.96 3.62
1455 1700 0.608130 TCAGCATGCTGTACGGAACT 59.392 50.000 39.08 5.22 43.96 3.01
1516 1762 7.820872 ACCATTTTTCATCTTGTCAATCAATCC 59.179 33.333 0.00 0.00 35.35 3.01
1852 2122 5.440610 ACATGTTGAATCAAGGGGATCTAC 58.559 41.667 0.00 0.00 34.28 2.59
1857 2127 3.711704 TGAATCAAGGGGATCTACTGACC 59.288 47.826 0.00 0.00 34.28 4.02
1875 2145 3.818210 TGACCACGACATTGCTACAAAAT 59.182 39.130 0.00 0.00 0.00 1.82
1952 2581 3.869272 GCCGGCAAGAGCATCACG 61.869 66.667 24.80 0.00 44.61 4.35
2150 3262 3.077229 TGTGTTTGCTGATTTGTTCCG 57.923 42.857 0.00 0.00 0.00 4.30
2152 3264 3.042887 GTGTTTGCTGATTTGTTCCGTC 58.957 45.455 0.00 0.00 0.00 4.79
2153 3265 2.034053 TGTTTGCTGATTTGTTCCGTCC 59.966 45.455 0.00 0.00 0.00 4.79
2169 3281 3.814842 TCCGTCCTTGCATGCTAATTATG 59.185 43.478 20.33 6.11 0.00 1.90
2731 3900 1.817099 GATGTTCCTCCAGGCGCTG 60.817 63.158 7.64 3.34 34.44 5.18
2935 4113 1.865865 GTGTACTGTGTGTGGTCAGG 58.134 55.000 0.00 0.00 36.17 3.86
3011 4197 1.414919 TGGAAAAGTCGTGTGGCTAGT 59.585 47.619 0.00 0.00 0.00 2.57
3086 4272 3.176867 GCATGTGTAAACGTGTGTTTTCG 59.823 43.478 7.10 0.00 45.89 3.46
3100 4286 1.262417 GTTTTCGTTCCGGTGTCCTTC 59.738 52.381 0.00 0.00 0.00 3.46
3152 4339 0.841289 TTTTCCACAGACCGGGAAGT 59.159 50.000 6.32 0.00 43.59 3.01
3241 4432 1.399714 AACACACTCGAGTCCACTGA 58.600 50.000 16.96 0.00 0.00 3.41
3434 4638 2.964978 CCTTTTTGGGCGAGCCAG 59.035 61.111 16.65 4.01 37.98 4.85
3461 6233 7.865889 CCAAAACTTTATTACAAACAGTCCCTC 59.134 37.037 0.00 0.00 0.00 4.30
3462 6234 6.796705 AACTTTATTACAAACAGTCCCTCG 57.203 37.500 0.00 0.00 0.00 4.63
3464 6236 5.012354 ACTTTATTACAAACAGTCCCTCGGA 59.988 40.000 0.00 0.00 0.00 4.55
3465 6237 5.687166 TTATTACAAACAGTCCCTCGGAT 57.313 39.130 0.00 0.00 32.73 4.18
3466 6238 6.795144 TTATTACAAACAGTCCCTCGGATA 57.205 37.500 0.00 0.00 32.73 2.59
3467 6239 4.460948 TTACAAACAGTCCCTCGGATAC 57.539 45.455 0.00 0.00 32.73 2.24
3469 6241 2.496470 ACAAACAGTCCCTCGGATACTC 59.504 50.000 0.00 0.00 32.73 2.59
3470 6242 1.777941 AACAGTCCCTCGGATACTCC 58.222 55.000 0.00 0.00 32.73 3.85
3472 6244 0.186386 CAGTCCCTCGGATACTCCCT 59.814 60.000 0.00 0.00 32.73 4.20
3473 6245 0.935194 AGTCCCTCGGATACTCCCTT 59.065 55.000 0.00 0.00 32.73 3.95
3474 6246 1.133419 AGTCCCTCGGATACTCCCTTC 60.133 57.143 0.00 0.00 32.73 3.46
3475 6247 0.178998 TCCCTCGGATACTCCCTTCG 60.179 60.000 0.00 0.00 31.13 3.79
3476 6248 0.467659 CCCTCGGATACTCCCTTCGT 60.468 60.000 0.00 0.00 31.13 3.85
3477 6249 1.400737 CCTCGGATACTCCCTTCGTT 58.599 55.000 0.00 0.00 31.13 3.85
3478 6250 1.337387 CCTCGGATACTCCCTTCGTTC 59.663 57.143 0.00 0.00 31.13 3.95
3479 6251 2.299521 CTCGGATACTCCCTTCGTTCT 58.700 52.381 0.00 0.00 31.13 3.01
3480 6252 2.688958 CTCGGATACTCCCTTCGTTCTT 59.311 50.000 0.00 0.00 31.13 2.52
3481 6253 3.094572 TCGGATACTCCCTTCGTTCTTT 58.905 45.455 0.00 0.00 31.13 2.52
3482 6254 3.512724 TCGGATACTCCCTTCGTTCTTTT 59.487 43.478 0.00 0.00 31.13 2.27
3483 6255 4.706476 TCGGATACTCCCTTCGTTCTTTTA 59.294 41.667 0.00 0.00 31.13 1.52
3484 6256 5.041940 CGGATACTCCCTTCGTTCTTTTAG 58.958 45.833 0.00 0.00 31.13 1.85
3485 6257 5.393896 CGGATACTCCCTTCGTTCTTTTAGT 60.394 44.000 0.00 0.00 31.13 2.24
3486 6258 6.183360 CGGATACTCCCTTCGTTCTTTTAGTA 60.183 42.308 0.00 0.00 31.13 1.82
3487 6259 7.469732 CGGATACTCCCTTCGTTCTTTTAGTAT 60.470 40.741 0.00 0.00 31.13 2.12
3488 6260 7.652507 GGATACTCCCTTCGTTCTTTTAGTATG 59.347 40.741 0.00 0.00 31.02 2.39
3489 6261 5.176592 ACTCCCTTCGTTCTTTTAGTATGC 58.823 41.667 0.00 0.00 0.00 3.14
3490 6262 5.155278 TCCCTTCGTTCTTTTAGTATGCA 57.845 39.130 0.00 0.00 0.00 3.96
3491 6263 5.741011 TCCCTTCGTTCTTTTAGTATGCAT 58.259 37.500 3.79 3.79 0.00 3.96
3492 6264 6.880484 TCCCTTCGTTCTTTTAGTATGCATA 58.120 36.000 1.16 1.16 0.00 3.14
3493 6265 7.506114 TCCCTTCGTTCTTTTAGTATGCATAT 58.494 34.615 10.16 2.05 0.00 1.78
3494 6266 8.644216 TCCCTTCGTTCTTTTAGTATGCATATA 58.356 33.333 10.16 1.09 0.00 0.86
3495 6267 9.268268 CCCTTCGTTCTTTTAGTATGCATATAA 57.732 33.333 10.16 7.03 0.00 0.98
3523 6295 7.928908 TTGATCAAAGTCAAACATTGCTAAC 57.071 32.000 5.45 0.00 35.31 2.34
3524 6296 7.275888 TGATCAAAGTCAAACATTGCTAACT 57.724 32.000 0.00 0.00 27.93 2.24
3525 6297 7.715657 TGATCAAAGTCAAACATTGCTAACTT 58.284 30.769 0.00 0.00 27.93 2.66
3526 6298 8.196771 TGATCAAAGTCAAACATTGCTAACTTT 58.803 29.630 0.00 0.00 37.41 2.66
3529 6301 7.755582 AAAGTCAAACATTGCTAACTTTGAC 57.244 32.000 18.19 18.19 46.84 3.18
3533 6305 8.494236 GTCAAACATTGCTAACTTTGACTAAG 57.506 34.615 18.40 0.00 44.69 2.18
3604 6376 8.399425 TGACATTTATTACAAACAAACAGACGT 58.601 29.630 0.00 0.00 0.00 4.34
3605 6377 8.555166 ACATTTATTACAAACAAACAGACGTG 57.445 30.769 0.00 0.00 0.00 4.49
3628 6400 7.519002 GTGATCTCCAACTTAACACACAATAC 58.481 38.462 0.00 0.00 0.00 1.89
3630 6402 7.387673 TGATCTCCAACTTAACACACAATACTG 59.612 37.037 0.00 0.00 0.00 2.74
3657 6436 3.066064 CGAAACACTCCATCCACACAAAA 59.934 43.478 0.00 0.00 0.00 2.44
3663 6442 5.596361 ACACTCCATCCACACAAAACATAAA 59.404 36.000 0.00 0.00 0.00 1.40
3664 6443 5.920273 CACTCCATCCACACAAAACATAAAC 59.080 40.000 0.00 0.00 0.00 2.01
3676 6455 9.320352 ACACAAAACATAAACAAGATAAAACCC 57.680 29.630 0.00 0.00 0.00 4.11
3681 6460 7.513371 ACATAAACAAGATAAAACCCGTTGA 57.487 32.000 0.00 0.00 0.00 3.18
3683 6462 8.581578 ACATAAACAAGATAAAACCCGTTGAAT 58.418 29.630 0.00 0.00 0.00 2.57
3720 6499 2.961526 ATCAACTAAGCATCGACGGT 57.038 45.000 0.00 0.00 0.00 4.83
3753 9191 8.747538 AACAACTTTAACCAATAGTCAGACTT 57.252 30.769 8.80 0.00 0.00 3.01
3799 9269 7.639113 AAAAGAAAGTGGTCTGTTGTATTGA 57.361 32.000 0.00 0.00 0.00 2.57
3802 9272 7.027778 AGAAAGTGGTCTGTTGTATTGAAAC 57.972 36.000 0.00 0.00 0.00 2.78
3862 9332 8.864069 AGATAAATAGTGAGACATCTGAAACG 57.136 34.615 0.00 0.00 0.00 3.60
3896 9368 8.859090 TCACTAGAATCATGTGGATTTTGTTTT 58.141 29.630 0.00 0.00 46.17 2.43
3897 9369 9.480053 CACTAGAATCATGTGGATTTTGTTTTT 57.520 29.630 0.00 0.00 46.17 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.857734 TTTGTAACCATAGGTGTGTCATATG 57.142 36.000 0.00 0.00 39.57 1.78
3 4 9.474313 AATTTTGTAACCATAGGTGTGTCATAT 57.526 29.630 0.00 0.00 35.34 1.78
4 5 8.871629 AATTTTGTAACCATAGGTGTGTCATA 57.128 30.769 0.00 0.00 35.34 2.15
5 6 7.093945 GGAATTTTGTAACCATAGGTGTGTCAT 60.094 37.037 0.00 0.00 35.34 3.06
6 7 6.207810 GGAATTTTGTAACCATAGGTGTGTCA 59.792 38.462 0.00 0.00 35.34 3.58
7 8 6.433093 AGGAATTTTGTAACCATAGGTGTGTC 59.567 38.462 0.00 0.00 35.34 3.67
8 9 6.311735 AGGAATTTTGTAACCATAGGTGTGT 58.688 36.000 0.00 0.00 35.34 3.72
9 10 6.834168 AGGAATTTTGTAACCATAGGTGTG 57.166 37.500 0.00 0.00 35.34 3.82
10 11 7.849322 AAAGGAATTTTGTAACCATAGGTGT 57.151 32.000 0.00 0.00 35.34 4.16
16 17 8.769891 CGCTTTAAAAAGGAATTTTGTAACCAT 58.230 29.630 4.71 0.00 41.29 3.55
17 18 7.224949 CCGCTTTAAAAAGGAATTTTGTAACCA 59.775 33.333 4.71 0.00 41.29 3.67
18 19 7.307514 CCCGCTTTAAAAAGGAATTTTGTAACC 60.308 37.037 9.49 0.00 41.29 2.85
19 20 7.438757 TCCCGCTTTAAAAAGGAATTTTGTAAC 59.561 33.333 9.49 0.00 41.29 2.50
20 21 7.498443 TCCCGCTTTAAAAAGGAATTTTGTAA 58.502 30.769 9.49 0.00 41.29 2.41
21 22 7.052142 TCCCGCTTTAAAAAGGAATTTTGTA 57.948 32.000 9.49 0.00 41.29 2.41
22 23 5.919755 TCCCGCTTTAAAAAGGAATTTTGT 58.080 33.333 9.49 0.00 41.29 2.83
23 24 6.852858 TTCCCGCTTTAAAAAGGAATTTTG 57.147 33.333 9.49 0.00 41.29 2.44
24 25 8.458573 AAATTCCCGCTTTAAAAAGGAATTTT 57.541 26.923 26.81 18.58 39.07 1.82
25 26 8.458573 AAAATTCCCGCTTTAAAAAGGAATTT 57.541 26.923 26.81 26.81 41.15 1.82
26 27 8.458573 AAAAATTCCCGCTTTAAAAAGGAATT 57.541 26.923 21.75 21.75 36.68 2.17
27 28 9.214957 CTAAAAATTCCCGCTTTAAAAAGGAAT 57.785 29.630 15.41 15.41 36.53 3.01
28 29 8.205512 ACTAAAAATTCCCGCTTTAAAAAGGAA 58.794 29.630 12.96 12.96 36.53 3.36
29 30 7.728148 ACTAAAAATTCCCGCTTTAAAAAGGA 58.272 30.769 9.49 3.87 36.53 3.36
30 31 7.956420 ACTAAAAATTCCCGCTTTAAAAAGG 57.044 32.000 4.71 2.49 36.53 3.11
31 32 9.858247 GAAACTAAAAATTCCCGCTTTAAAAAG 57.142 29.630 0.00 0.00 39.03 2.27
32 33 8.828644 GGAAACTAAAAATTCCCGCTTTAAAAA 58.171 29.630 0.00 0.00 39.36 1.94
33 34 7.985752 TGGAAACTAAAAATTCCCGCTTTAAAA 59.014 29.630 2.36 0.00 43.66 1.52
34 35 7.498443 TGGAAACTAAAAATTCCCGCTTTAAA 58.502 30.769 2.36 0.00 43.66 1.52
35 36 7.052142 TGGAAACTAAAAATTCCCGCTTTAA 57.948 32.000 2.36 0.00 43.66 1.52
36 37 6.651975 TGGAAACTAAAAATTCCCGCTTTA 57.348 33.333 2.36 0.00 43.66 1.85
37 38 5.538849 TGGAAACTAAAAATTCCCGCTTT 57.461 34.783 2.36 0.00 43.66 3.51
38 39 5.738619 ATGGAAACTAAAAATTCCCGCTT 57.261 34.783 2.36 0.00 43.66 4.68
39 40 6.844097 TTATGGAAACTAAAAATTCCCGCT 57.156 33.333 2.36 0.00 43.66 5.52
40 41 7.465379 GCAATTATGGAAACTAAAAATTCCCGC 60.465 37.037 2.36 0.00 43.66 6.13
41 42 7.547370 TGCAATTATGGAAACTAAAAATTCCCG 59.453 33.333 2.36 0.00 43.66 5.14
42 43 8.785329 TGCAATTATGGAAACTAAAAATTCCC 57.215 30.769 2.36 0.00 43.66 3.97
51 52 9.381033 CAATCCAAAATGCAATTATGGAAACTA 57.619 29.630 16.96 1.72 33.67 2.24
96 97 4.129878 GTCGAATCGATGTATGAGACGA 57.870 45.455 9.10 0.00 38.42 4.20
195 196 3.698029 AATGGCATAGCATCAACGTTC 57.302 42.857 0.00 0.00 0.00 3.95
205 206 4.963276 TGTCACTACAAAATGGCATAGC 57.037 40.909 0.00 0.00 30.91 2.97
255 299 8.579850 AGCTCATTGAACCAATATTCAGTTAA 57.420 30.769 1.31 0.00 39.68 2.01
367 412 4.089923 GTCGCTACAAAATTGGCATTGAAC 59.910 41.667 6.33 0.00 0.00 3.18
371 420 3.932545 TGTCGCTACAAAATTGGCATT 57.067 38.095 0.00 0.00 30.91 3.56
470 625 1.476891 GTTCCGCAGATGTAGACCTCA 59.523 52.381 0.00 0.00 0.00 3.86
487 713 6.772716 TGCTCCCTCCAATTCATAATAAGTTC 59.227 38.462 0.00 0.00 0.00 3.01
488 714 6.672593 TGCTCCCTCCAATTCATAATAAGTT 58.327 36.000 0.00 0.00 0.00 2.66
499 725 4.228210 TGAAGAATACTGCTCCCTCCAATT 59.772 41.667 0.00 0.00 0.00 2.32
553 779 4.350520 TGGGCCTCAAATTTTGGATTTTCT 59.649 37.500 4.53 0.00 0.00 2.52
554 780 4.650734 TGGGCCTCAAATTTTGGATTTTC 58.349 39.130 4.53 0.00 0.00 2.29
555 781 4.104579 ACTGGGCCTCAAATTTTGGATTTT 59.895 37.500 4.53 0.00 0.00 1.82
579 805 9.171877 GGATCATCTCTTCACTAGAAAACAAAT 57.828 33.333 0.00 0.00 32.35 2.32
581 807 7.911651 AGGATCATCTCTTCACTAGAAAACAA 58.088 34.615 0.00 0.00 32.35 2.83
601 827 2.906354 ACGGTCAATGCAAGTAGGATC 58.094 47.619 0.00 0.00 0.00 3.36
602 828 3.704566 TCTACGGTCAATGCAAGTAGGAT 59.295 43.478 0.00 0.00 36.41 3.24
865 1098 3.281727 TTGGTGCTGTCACTCTTCTTT 57.718 42.857 0.00 0.00 42.72 2.52
873 1106 3.058914 GTGTACAGATTTGGTGCTGTCAC 60.059 47.826 0.00 0.00 43.75 3.67
876 1109 3.207265 TGTGTACAGATTTGGTGCTGT 57.793 42.857 0.00 0.00 46.31 4.40
1047 1292 1.813753 CAACCCCATGGCGTCGTAG 60.814 63.158 6.09 0.00 33.59 3.51
1452 1697 6.152323 TGGAGTGCGATTTAGTCTAGTTAGTT 59.848 38.462 0.00 0.00 0.00 2.24
1453 1698 5.651139 TGGAGTGCGATTTAGTCTAGTTAGT 59.349 40.000 0.00 0.00 0.00 2.24
1454 1699 5.972382 GTGGAGTGCGATTTAGTCTAGTTAG 59.028 44.000 0.00 0.00 0.00 2.34
1455 1700 5.163581 GGTGGAGTGCGATTTAGTCTAGTTA 60.164 44.000 0.00 0.00 0.00 2.24
1543 1795 1.413767 CTTGATCGCCCTGTTCGTCG 61.414 60.000 0.00 0.00 0.00 5.12
1852 2122 2.078849 TGTAGCAATGTCGTGGTCAG 57.921 50.000 0.00 0.00 0.00 3.51
1857 2127 6.614162 GCTGAAAATTTTGTAGCAATGTCGTG 60.614 38.462 22.44 1.27 34.64 4.35
1875 2145 0.178947 ATTCCCCCGTTGGCTGAAAA 60.179 50.000 0.00 0.00 0.00 2.29
1952 2581 1.743996 GCCAGACTTTCTCCATCACC 58.256 55.000 0.00 0.00 0.00 4.02
2150 3262 5.284079 CAACCATAATTAGCATGCAAGGAC 58.716 41.667 21.98 0.00 0.00 3.85
2152 3264 4.053295 GCAACCATAATTAGCATGCAAGG 58.947 43.478 21.98 12.24 32.80 3.61
2153 3265 4.684877 TGCAACCATAATTAGCATGCAAG 58.315 39.130 21.98 1.25 39.15 4.01
2169 3281 1.845809 CTTCAGCGTGTCCTGCAACC 61.846 60.000 0.00 0.00 32.87 3.77
2395 3564 1.153429 GATGACCTGGTACGTGCCC 60.153 63.158 20.66 9.67 0.00 5.36
2886 4055 9.517609 AATTAGTAGTACATCGAAGCAGTAAAG 57.482 33.333 2.52 0.00 0.00 1.85
2935 4113 1.373873 GACCACCGGACGAAACCTC 60.374 63.158 9.46 0.00 0.00 3.85
3011 4197 1.749063 CACGACCACTATGCCAGTAGA 59.251 52.381 0.00 0.00 34.98 2.59
3057 4243 1.065031 CGTTTACACATGCCAAGCGC 61.065 55.000 0.00 0.00 38.31 5.92
3086 4272 0.680061 AGACAGAAGGACACCGGAAC 59.320 55.000 9.46 0.00 0.00 3.62
3100 4286 1.531149 CAAACCCAGCACGTTAGACAG 59.469 52.381 0.00 0.00 0.00 3.51
3152 4339 3.410631 TCGCCACTCCATTGACTTAAA 57.589 42.857 0.00 0.00 0.00 1.52
3241 4432 2.635443 CGACCGGGCCATGCTTTTT 61.635 57.895 6.32 0.00 0.00 1.94
3280 4482 1.254954 AACGAAACGCTAGAGGAGGT 58.745 50.000 0.00 0.00 0.00 3.85
3348 4550 2.049767 TCCTAGCGATGGCGTGACA 61.050 57.895 0.00 0.00 46.35 3.58
3427 4631 3.575965 AATAAAGTTTTGGCTGGCTCG 57.424 42.857 2.00 0.00 0.00 5.03
3430 4634 5.755861 TGTTTGTAATAAAGTTTTGGCTGGC 59.244 36.000 0.00 0.00 0.00 4.85
3431 4635 6.983890 ACTGTTTGTAATAAAGTTTTGGCTGG 59.016 34.615 0.00 0.00 0.00 4.85
3434 4638 6.422701 GGGACTGTTTGTAATAAAGTTTTGGC 59.577 38.462 0.00 0.00 0.00 4.52
3464 6236 6.985059 GCATACTAAAAGAACGAAGGGAGTAT 59.015 38.462 0.00 0.00 30.82 2.12
3465 6237 6.071221 TGCATACTAAAAGAACGAAGGGAGTA 60.071 38.462 0.00 0.00 0.00 2.59
3466 6238 5.176592 GCATACTAAAAGAACGAAGGGAGT 58.823 41.667 0.00 0.00 0.00 3.85
3467 6239 5.175859 TGCATACTAAAAGAACGAAGGGAG 58.824 41.667 0.00 0.00 0.00 4.30
3469 6241 7.730364 ATATGCATACTAAAAGAACGAAGGG 57.270 36.000 8.99 0.00 0.00 3.95
3498 6270 8.196771 AGTTAGCAATGTTTGACTTTGATCAAA 58.803 29.630 19.45 19.45 44.40 2.69
3499 6271 7.715657 AGTTAGCAATGTTTGACTTTGATCAA 58.284 30.769 3.38 3.38 35.88 2.57
3500 6272 7.275888 AGTTAGCAATGTTTGACTTTGATCA 57.724 32.000 9.91 0.00 35.88 2.92
3501 6273 8.482429 CAAAGTTAGCAATGTTTGACTTTGATC 58.518 33.333 21.88 0.00 45.80 2.92
3502 6274 8.196771 TCAAAGTTAGCAATGTTTGACTTTGAT 58.803 29.630 23.46 10.58 46.09 2.57
3503 6275 7.754069 CAAAGTTAGCAATGTTTGACTTTGA 57.246 32.000 21.88 0.00 45.80 2.69
3504 6276 7.754069 TCAAAGTTAGCAATGTTTGACTTTG 57.246 32.000 21.10 21.10 45.12 2.77
3509 6281 8.220755 ACTTAGTCAAAGTTAGCAATGTTTGA 57.779 30.769 0.00 0.00 46.61 2.69
3577 6349 9.227490 CGTCTGTTTGTTTGTAATAAATGTCAA 57.773 29.630 0.00 0.00 0.00 3.18
3578 6350 8.399425 ACGTCTGTTTGTTTGTAATAAATGTCA 58.601 29.630 0.00 0.00 0.00 3.58
3579 6351 8.678510 CACGTCTGTTTGTTTGTAATAAATGTC 58.321 33.333 0.00 0.00 0.00 3.06
3580 6352 8.399425 TCACGTCTGTTTGTTTGTAATAAATGT 58.601 29.630 0.00 0.00 0.00 2.71
3581 6353 8.775220 TCACGTCTGTTTGTTTGTAATAAATG 57.225 30.769 0.00 0.00 0.00 2.32
3582 6354 9.607285 GATCACGTCTGTTTGTTTGTAATAAAT 57.393 29.630 0.00 0.00 0.00 1.40
3604 6376 7.387673 CAGTATTGTGTGTTAAGTTGGAGATCA 59.612 37.037 0.00 0.00 0.00 2.92
3605 6377 7.148407 CCAGTATTGTGTGTTAAGTTGGAGATC 60.148 40.741 0.00 0.00 0.00 2.75
3657 6436 7.513371 TCAACGGGTTTTATCTTGTTTATGT 57.487 32.000 0.00 0.00 0.00 2.29
3663 6442 6.399639 ACAATTCAACGGGTTTTATCTTGT 57.600 33.333 0.00 0.00 0.00 3.16
3664 6443 7.651704 AGAAACAATTCAACGGGTTTTATCTTG 59.348 33.333 0.00 0.00 38.06 3.02
3673 6452 5.533154 TGTTATGAGAAACAATTCAACGGGT 59.467 36.000 0.00 0.00 36.45 5.28
3720 6499 9.509956 ACTATTGGTTAAAGTTGTTAGTATGCA 57.490 29.630 0.00 0.00 0.00 3.96
3757 9195 8.882415 TTTCTTTTAGTCACGACTATTGTCTT 57.118 30.769 7.71 0.00 42.83 3.01
3759 9197 8.215132 CACTTTCTTTTAGTCACGACTATTGTC 58.785 37.037 7.71 0.00 42.83 3.18
3862 9332 4.093998 CACATGATTCTAGTGAGTGTTGGC 59.906 45.833 0.00 0.00 35.33 4.52


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

AutoCloner maintained by Alex Coulton.