Multiple sequence alignment - TraesCS7B01G162000

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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 TraesCS7B01G162000 chr7B 100.000 3329 0 0 1 3329 222303827 222307155 0.000000e+00 6148
1 TraesCS7B01G162000 chr7B 100.000 2701 0 0 3640 6340 222307466 222310166 0.000000e+00 4988
2 TraesCS7B01G162000 chr7B 87.725 334 36 2 2972 3305 387155705 387156033 9.970000e-103 385
3 TraesCS7B01G162000 chr7D 95.185 3344 96 26 1 3305 246028121 246031438 0.000000e+00 5223
4 TraesCS7B01G162000 chr7D 98.017 1715 25 2 3640 5354 246031439 246033144 0.000000e+00 2970
5 TraesCS7B01G162000 chr7D 96.374 910 22 8 5433 6340 246033145 246034045 0.000000e+00 1487
6 TraesCS7B01G162000 chr7D 87.463 335 40 2 2972 3305 390684916 390685249 9.970000e-103 385
7 TraesCS7B01G162000 chr7A 94.531 2322 86 20 1 2300 262463447 262465749 0.000000e+00 3546
8 TraesCS7B01G162000 chr7A 96.676 1113 37 0 3992 5104 262467088 262468200 0.000000e+00 1851
9 TraesCS7B01G162000 chr7A 90.861 1127 45 24 5227 6340 262468195 262469276 0.000000e+00 1458
10 TraesCS7B01G162000 chr7A 88.716 257 17 5 3673 3917 262466699 262466955 2.870000e-78 303
11 TraesCS7B01G162000 chr7A 87.975 158 11 5 2394 2548 262465951 262466103 5.050000e-41 180
12 TraesCS7B01G162000 chr7A 94.000 100 6 0 2296 2395 262465785 262465884 1.100000e-32 152
13 TraesCS7B01G162000 chr5A 90.774 336 26 3 2972 3303 365931081 365930747 1.620000e-120 444
14 TraesCS7B01G162000 chr1B 89.971 339 30 2 2975 3310 440279960 440280297 9.760000e-118 435
15 TraesCS7B01G162000 chr3D 89.150 341 30 4 2972 3306 263812253 263812592 9.830000e-113 418
16 TraesCS7B01G162000 chr5D 89.086 339 32 3 2972 3306 485614830 485615167 3.540000e-112 416
17 TraesCS7B01G162000 chr3A 87.834 337 36 4 2972 3306 299560303 299559970 2.140000e-104 390
18 TraesCS7B01G162000 chr4B 87.353 340 36 5 2972 3306 169595828 169595491 3.590000e-102 383


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 TraesCS7B01G162000 chr7B 222303827 222310166 6339 False 5568.000000 6148 100.000000 1 6340 2 chr7B.!!$F2 6339
1 TraesCS7B01G162000 chr7D 246028121 246034045 5924 False 3226.666667 5223 96.525333 1 6340 3 chr7D.!!$F2 6339
2 TraesCS7B01G162000 chr7A 262463447 262469276 5829 False 1248.333333 3546 92.126500 1 6340 6 chr7A.!!$F1 6339

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
266 268 0.249322 CCGGCCAAGTATACCACGAG 60.249 60.000 2.24 0.0 0.00 4.18 F
267 269 0.249322 CGGCCAAGTATACCACGAGG 60.249 60.000 2.24 0.0 42.21 4.63 F
1013 1018 0.912486 GTGGGACCTACATTCTGGCT 59.088 55.000 2.55 0.0 0.00 4.75 F
1785 1805 1.163420 TGTGCGTTGTCGATTGGCTT 61.163 50.000 0.00 0.0 39.71 4.35 F
3092 3445 0.108138 CGGACTCCTCCCATGTCAAC 60.108 60.000 0.00 0.0 31.93 3.18 F
3312 3665 0.107654 GCACCTCTCCGCCTATGTTT 60.108 55.000 0.00 0.0 0.00 2.83 F
3313 3666 1.679032 GCACCTCTCCGCCTATGTTTT 60.679 52.381 0.00 0.0 0.00 2.43 F
4428 4848 0.600255 ACTTGACGGCTTCACTTCGG 60.600 55.000 0.00 0.0 32.26 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1470 1476 0.035317 TCATCACCGCAACTCAAGCT 59.965 50.000 0.00 0.0 0.00 3.74 R
1879 1899 1.331214 ACTTGGGCAGAACCATTGTG 58.669 50.000 0.00 0.0 40.91 3.33 R
2952 3305 2.887337 CGGAAAAGGCTTTGTTGTTGT 58.113 42.857 14.19 0.0 0.00 3.32 R
3157 3510 1.824230 GGTTTGGGCATATTCAGTGCA 59.176 47.619 0.29 0.0 44.25 4.57 R
4235 4655 0.676466 CCCCACGTGCAGCTTCAATA 60.676 55.000 10.91 0.0 0.00 1.90 R
4412 4832 1.006571 GACCGAAGTGAAGCCGTCA 60.007 57.895 0.00 0.0 0.00 4.35 R
4590 5010 1.131126 CTGTAGCCCTTGCATTGTTCG 59.869 52.381 0.00 0.0 41.13 3.95 R
5378 5798 0.472471 AACAACTCCCGAGCCAAAGA 59.528 50.000 0.00 0.0 0.00 2.52 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
106 108 3.652274 AGCCATTTCAAACGACAATTGG 58.348 40.909 10.83 0.00 0.00 3.16
127 129 3.366985 GGCCAACGAAACTAAATTCCAGG 60.367 47.826 0.00 0.00 0.00 4.45
132 134 6.294508 CCAACGAAACTAAATTCCAGGACAAT 60.295 38.462 0.00 0.00 0.00 2.71
136 138 7.664318 ACGAAACTAAATTCCAGGACAATAGTT 59.336 33.333 11.67 11.67 34.55 2.24
166 168 1.656652 ACATTCGCATACTGCTGGAC 58.343 50.000 0.00 0.00 42.25 4.02
190 192 6.095440 ACCAATAGGATCGAATCAACAAAAGG 59.905 38.462 0.00 0.00 38.69 3.11
191 193 6.095440 CCAATAGGATCGAATCAACAAAAGGT 59.905 38.462 0.00 0.00 36.89 3.50
255 257 1.097547 GTGTGATGATCCCGGCCAAG 61.098 60.000 2.24 0.00 0.00 3.61
257 259 0.468226 GTGATGATCCCGGCCAAGTA 59.532 55.000 2.24 0.00 0.00 2.24
264 266 1.227438 CCCGGCCAAGTATACCACG 60.227 63.158 2.24 0.00 0.00 4.94
265 267 1.678598 CCCGGCCAAGTATACCACGA 61.679 60.000 2.24 0.00 0.00 4.35
266 268 0.249322 CCGGCCAAGTATACCACGAG 60.249 60.000 2.24 0.00 0.00 4.18
267 269 0.249322 CGGCCAAGTATACCACGAGG 60.249 60.000 2.24 0.00 42.21 4.63
282 284 2.155732 CACGAGGATGAACAAACGACAG 59.844 50.000 0.00 0.00 0.00 3.51
283 285 2.035449 ACGAGGATGAACAAACGACAGA 59.965 45.455 0.00 0.00 0.00 3.41
295 297 0.935898 ACGACAGACCTATAGCGACG 59.064 55.000 0.00 0.00 0.00 5.12
296 298 0.935898 CGACAGACCTATAGCGACGT 59.064 55.000 0.00 0.00 0.00 4.34
297 299 2.130395 CGACAGACCTATAGCGACGTA 58.870 52.381 0.00 0.00 0.00 3.57
299 301 3.388308 GACAGACCTATAGCGACGTAGA 58.612 50.000 0.00 0.00 0.00 2.59
300 302 3.391965 ACAGACCTATAGCGACGTAGAG 58.608 50.000 0.00 0.00 0.00 2.43
301 303 3.181467 ACAGACCTATAGCGACGTAGAGT 60.181 47.826 0.00 0.00 0.00 3.24
302 304 3.184783 CAGACCTATAGCGACGTAGAGTG 59.815 52.174 0.00 0.00 0.00 3.51
303 305 3.069300 AGACCTATAGCGACGTAGAGTGA 59.931 47.826 0.00 0.00 0.00 3.41
306 308 3.676172 CCTATAGCGACGTAGAGTGAGAG 59.324 52.174 0.00 0.00 0.00 3.20
850 855 2.167693 TCATGATGTACTTCGTGACCCC 59.832 50.000 23.02 0.00 36.87 4.95
1013 1018 0.912486 GTGGGACCTACATTCTGGCT 59.088 55.000 2.55 0.00 0.00 4.75
1348 1354 3.390521 AGGGAGCATTCGCCGTCA 61.391 61.111 0.00 0.00 39.83 4.35
1368 1374 2.734591 GTCGCGGCTCATATGGGA 59.265 61.111 6.82 0.00 0.00 4.37
1470 1476 6.168389 GGTTTTCGGTCAGAGTTTAGGATTA 58.832 40.000 0.00 0.00 0.00 1.75
1481 1487 5.877564 AGAGTTTAGGATTAGCTTGAGTTGC 59.122 40.000 0.00 0.00 0.00 4.17
1646 1655 9.589111 GGAGTAAGACTTCCTTTTCTTATGTAG 57.411 37.037 0.00 0.00 36.84 2.74
1673 1682 1.483415 ACTTGGATCATTTGGCCATGC 59.517 47.619 6.09 0.00 31.96 4.06
1730 1739 7.884877 GTGGAGTCAATAATGGGATCATATGAA 59.115 37.037 9.99 0.00 32.44 2.57
1731 1740 8.105197 TGGAGTCAATAATGGGATCATATGAAG 58.895 37.037 9.99 0.00 32.44 3.02
1732 1741 7.066766 GGAGTCAATAATGGGATCATATGAAGC 59.933 40.741 9.99 4.99 32.44 3.86
1733 1742 7.696981 AGTCAATAATGGGATCATATGAAGCT 58.303 34.615 9.99 0.00 32.44 3.74
1739 1759 5.489792 TGGGATCATATGAAGCTTAGGTC 57.510 43.478 9.99 0.00 0.00 3.85
1785 1805 1.163420 TGTGCGTTGTCGATTGGCTT 61.163 50.000 0.00 0.00 39.71 4.35
1879 1899 1.495584 TTGCACGTCTTCTGAACGCC 61.496 55.000 2.04 0.00 0.00 5.68
2381 2443 5.874093 AGGATCTTAGCATAATGTGAAGGG 58.126 41.667 0.00 0.00 0.00 3.95
2452 2585 1.518325 TGTGTCTTTGGGCACGTATG 58.482 50.000 0.00 0.00 38.36 2.39
2563 2730 8.427902 AAGCAGATTCCATGAGACATAGTATA 57.572 34.615 0.00 0.00 0.00 1.47
2595 2762 7.536622 GCAGTGTAGAAAATCATATGCATTAGC 59.463 37.037 3.54 0.00 42.57 3.09
2952 3305 9.616156 TGACTAAATTACTAACTCCAACAACAA 57.384 29.630 0.00 0.00 0.00 2.83
2970 3323 5.049749 ACAACAACAACAACAAAGCCTTTTC 60.050 36.000 0.00 0.00 0.00 2.29
3024 3377 2.556840 TAGCTTCCATGCACCCCTGC 62.557 60.000 0.00 0.00 44.52 4.85
3047 3400 3.125316 CCATGGCTAGTTCTTTCGTGAAC 59.875 47.826 0.00 9.45 44.67 3.18
3092 3445 0.108138 CGGACTCCTCCCATGTCAAC 60.108 60.000 0.00 0.00 31.93 3.18
3102 3455 4.003648 CTCCCATGTCAACTTTGGTCTAC 58.996 47.826 0.00 0.00 0.00 2.59
3129 3482 5.861251 CGACCTCTCTTGATATAATCAGCAC 59.139 44.000 0.00 0.00 40.94 4.40
3157 3510 3.083349 TCCGCTATGCACTGGCCT 61.083 61.111 3.32 0.00 40.13 5.19
3191 3544 2.621998 CCCAAACCATCTCAGATGATGC 59.378 50.000 16.90 0.00 41.65 3.91
3287 3640 2.485677 GTGGCCACACATCCATCTG 58.514 57.895 31.23 0.00 46.90 2.90
3305 3658 2.045926 AACATGCACCTCTCCGCC 60.046 61.111 0.00 0.00 0.00 6.13
3306 3659 2.527951 GAACATGCACCTCTCCGCCT 62.528 60.000 0.00 0.00 0.00 5.52
3307 3660 1.264749 AACATGCACCTCTCCGCCTA 61.265 55.000 0.00 0.00 0.00 3.93
3308 3661 1.050988 ACATGCACCTCTCCGCCTAT 61.051 55.000 0.00 0.00 0.00 2.57
3309 3662 0.602106 CATGCACCTCTCCGCCTATG 60.602 60.000 0.00 0.00 0.00 2.23
3310 3663 1.050988 ATGCACCTCTCCGCCTATGT 61.051 55.000 0.00 0.00 0.00 2.29
3311 3664 1.264749 TGCACCTCTCCGCCTATGTT 61.265 55.000 0.00 0.00 0.00 2.71
3312 3665 0.107654 GCACCTCTCCGCCTATGTTT 60.108 55.000 0.00 0.00 0.00 2.83
3313 3666 1.679032 GCACCTCTCCGCCTATGTTTT 60.679 52.381 0.00 0.00 0.00 2.43
3314 3667 2.711542 CACCTCTCCGCCTATGTTTTT 58.288 47.619 0.00 0.00 0.00 1.94
3315 3668 3.869065 CACCTCTCCGCCTATGTTTTTA 58.131 45.455 0.00 0.00 0.00 1.52
3316 3669 4.258543 CACCTCTCCGCCTATGTTTTTAA 58.741 43.478 0.00 0.00 0.00 1.52
3317 3670 4.332819 CACCTCTCCGCCTATGTTTTTAAG 59.667 45.833 0.00 0.00 0.00 1.85
3318 3671 3.877508 CCTCTCCGCCTATGTTTTTAAGG 59.122 47.826 0.00 0.00 0.00 2.69
3324 3677 4.016113 GCCTATGTTTTTAAGGCGTCTG 57.984 45.455 0.00 0.00 45.82 3.51
3325 3678 3.439129 GCCTATGTTTTTAAGGCGTCTGT 59.561 43.478 0.00 0.00 45.82 3.41
3326 3679 4.632688 GCCTATGTTTTTAAGGCGTCTGTA 59.367 41.667 0.00 0.00 45.82 2.74
3327 3680 5.122711 GCCTATGTTTTTAAGGCGTCTGTAA 59.877 40.000 0.00 0.00 45.82 2.41
3328 3681 6.674760 GCCTATGTTTTTAAGGCGTCTGTAAG 60.675 42.308 0.00 0.00 45.82 2.34
3668 4021 1.872952 CTGTTGAACATGTCGCCTTCA 59.127 47.619 0.00 0.00 0.00 3.02
3711 4064 7.891498 ACAACTTCAAATTACCTAAACCTGT 57.109 32.000 0.00 0.00 0.00 4.00
3759 4112 7.438160 CGATGACCTACTGATAAATTTGTGCTA 59.562 37.037 0.00 0.00 0.00 3.49
3823 4184 9.559732 TGTATAATCCACAAGATGTAGATTTGG 57.440 33.333 8.93 0.00 35.70 3.28
4235 4655 3.726557 TCTTCCAAATCACTGGATGCT 57.273 42.857 0.00 0.00 45.03 3.79
4326 4746 2.427506 GAAAGTGCCCTCTAACACCAG 58.572 52.381 0.00 0.00 37.51 4.00
4375 4795 5.008811 CACTAGGTATTCCTACGGAGACAAG 59.991 48.000 0.00 0.00 44.58 3.16
4401 4821 2.572333 TTTAGCTGCTGGGGATGGGC 62.572 60.000 13.43 0.00 0.00 5.36
4412 4832 1.217942 GGGGATGGGCTAATGGAACTT 59.782 52.381 0.00 0.00 0.00 2.66
4428 4848 0.600255 ACTTGACGGCTTCACTTCGG 60.600 55.000 0.00 0.00 32.26 4.30
4546 4966 1.667724 AGTCAACAGCGATGCTTATGC 59.332 47.619 0.00 0.00 36.40 3.14
4590 5010 4.580167 TGGATAAGATGGTAACTGCAATGC 59.420 41.667 0.00 0.00 37.61 3.56
5328 5748 0.923358 ATTGGGCTCCATAACCGGAA 59.077 50.000 9.46 0.00 33.65 4.30
5344 5764 3.190535 ACCGGAATTCTTATTGTGTGCAC 59.809 43.478 9.46 10.75 0.00 4.57
5362 5782 2.926159 GCACCGCAATGTTTACATGCTT 60.926 45.455 0.00 0.00 36.56 3.91
5387 5807 5.958955 ACTGCTTATTCATTTCTTTGGCTC 58.041 37.500 0.00 0.00 0.00 4.70
5392 5812 2.113860 TCATTTCTTTGGCTCGGGAG 57.886 50.000 0.00 0.00 0.00 4.30
5399 5819 1.681264 CTTTGGCTCGGGAGTTGTTTT 59.319 47.619 0.00 0.00 0.00 2.43
5401 5821 1.285950 GGCTCGGGAGTTGTTTTGC 59.714 57.895 0.00 0.00 0.00 3.68
5419 5839 0.322816 GCTCTTGATGCCCTGGTCAA 60.323 55.000 0.00 0.00 33.63 3.18
5588 6015 5.106317 ACTGGCGGTTGATACATTAAACAAG 60.106 40.000 0.00 0.00 0.00 3.16
5641 6068 1.972795 ACTCCGTGTTTGGGCTAGTAA 59.027 47.619 0.00 0.00 0.00 2.24
5661 6088 4.689612 AATCTATGCGACCAGTGGTTAT 57.310 40.909 17.93 13.65 35.25 1.89
5676 6103 7.971722 ACCAGTGGTTATTTTCATATTTTACGC 59.028 33.333 9.70 0.00 27.29 4.42
5686 6113 2.861462 TATTTTACGCCATGGCAAGC 57.139 45.000 34.93 9.63 42.06 4.01
5707 6134 6.041423 AGCAAGCTTAAATAAATTGGTGCT 57.959 33.333 0.00 0.00 31.00 4.40
5769 6196 1.113788 AGTTTGGCAGCTGAAGCAAA 58.886 45.000 20.43 0.00 45.16 3.68
5828 6255 4.323569 TCATACTCTCCAGTCTCCAGTT 57.676 45.455 0.00 0.00 33.62 3.16
5831 6258 5.652891 TCATACTCTCCAGTCTCCAGTTTAC 59.347 44.000 0.00 0.00 33.62 2.01
5857 6285 4.722194 TCTTTTTCATCATCGCCTTTTCG 58.278 39.130 0.00 0.00 0.00 3.46
5938 6369 2.552315 ACTAGTGGCCATCGTTTTGTTG 59.448 45.455 9.72 0.00 0.00 3.33
5939 6370 0.031994 AGTGGCCATCGTTTTGTTGC 59.968 50.000 9.72 0.00 0.00 4.17
5940 6371 0.031994 GTGGCCATCGTTTTGTTGCT 59.968 50.000 9.72 0.00 0.00 3.91
5952 6383 0.310543 TTGTTGCTGCAATGTCGACC 59.689 50.000 19.11 4.18 0.00 4.79
6147 6585 7.148623 CCTGAGTTCCGTACTTTCTGTATTTTC 60.149 40.741 0.00 0.00 37.17 2.29
6186 6624 5.581126 TCTGAGTTTGTTTTTGATGCACT 57.419 34.783 0.00 0.00 0.00 4.40
6196 6634 1.527034 TTGATGCACTGGCTTCTGTC 58.473 50.000 0.00 0.00 42.84 3.51
6197 6635 0.689055 TGATGCACTGGCTTCTGTCT 59.311 50.000 0.00 0.00 42.84 3.41
6198 6636 1.072806 TGATGCACTGGCTTCTGTCTT 59.927 47.619 0.00 0.00 42.84 3.01
6199 6637 1.736681 GATGCACTGGCTTCTGTCTTC 59.263 52.381 0.00 0.00 40.15 2.87
6200 6638 0.761187 TGCACTGGCTTCTGTCTTCT 59.239 50.000 0.00 0.00 41.91 2.85
6201 6639 1.155042 GCACTGGCTTCTGTCTTCTG 58.845 55.000 0.00 0.00 36.96 3.02
6202 6640 1.542108 GCACTGGCTTCTGTCTTCTGT 60.542 52.381 0.00 0.00 36.96 3.41
6203 6641 2.141517 CACTGGCTTCTGTCTTCTGTG 58.858 52.381 0.00 0.00 0.00 3.66
6204 6642 2.042464 ACTGGCTTCTGTCTTCTGTGA 58.958 47.619 0.00 0.00 0.00 3.58
6205 6643 2.224161 ACTGGCTTCTGTCTTCTGTGAC 60.224 50.000 0.00 0.00 37.47 3.67
6235 6674 7.075851 TCTCATATCTGCTCCAATCAGAAAT 57.924 36.000 0.00 0.00 43.01 2.17
6287 6726 3.825014 AGTTCAAAGTGCATCATTGAGCT 59.175 39.130 16.85 16.85 39.28 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 108 3.504520 TCCTGGAATTTAGTTTCGTTGGC 59.495 43.478 0.00 0.00 0.00 4.52
127 129 7.448748 AATGTTGGTTCTGGTAACTATTGTC 57.551 36.000 0.00 0.00 37.61 3.18
132 134 3.998341 GCGAATGTTGGTTCTGGTAACTA 59.002 43.478 0.00 0.00 37.61 2.24
136 138 2.552599 TGCGAATGTTGGTTCTGGTA 57.447 45.000 0.00 0.00 0.00 3.25
166 168 6.095440 ACCTTTTGTTGATTCGATCCTATTGG 59.905 38.462 0.00 0.00 0.00 3.16
190 192 1.215382 GCCCATTTTTGGCCGAGAC 59.785 57.895 0.00 0.00 43.33 3.36
191 193 3.693411 GCCCATTTTTGGCCGAGA 58.307 55.556 0.00 0.00 43.33 4.04
216 218 1.408340 CATTCACACTTGGTGTTGCCA 59.592 47.619 0.19 0.00 45.08 4.92
217 219 1.408702 ACATTCACACTTGGTGTTGCC 59.591 47.619 0.19 0.00 45.08 4.52
218 220 2.159254 ACACATTCACACTTGGTGTTGC 60.159 45.455 0.19 0.00 45.08 4.17
219 221 3.128415 TCACACATTCACACTTGGTGTTG 59.872 43.478 0.19 0.72 45.08 3.33
220 222 3.351740 TCACACATTCACACTTGGTGTT 58.648 40.909 0.19 0.00 45.08 3.32
223 225 3.819368 TCATCACACATTCACACTTGGT 58.181 40.909 0.00 0.00 0.00 3.67
224 226 4.142534 GGATCATCACACATTCACACTTGG 60.143 45.833 0.00 0.00 0.00 3.61
226 228 4.012374 GGGATCATCACACATTCACACTT 58.988 43.478 0.00 0.00 0.00 3.16
229 231 2.631267 CGGGATCATCACACATTCACA 58.369 47.619 0.00 0.00 0.00 3.58
230 232 1.942657 CCGGGATCATCACACATTCAC 59.057 52.381 0.00 0.00 0.00 3.18
231 233 1.746861 GCCGGGATCATCACACATTCA 60.747 52.381 2.18 0.00 0.00 2.57
232 234 0.947244 GCCGGGATCATCACACATTC 59.053 55.000 2.18 0.00 0.00 2.67
233 235 0.466189 GGCCGGGATCATCACACATT 60.466 55.000 2.18 0.00 0.00 2.71
234 236 1.149174 GGCCGGGATCATCACACAT 59.851 57.895 2.18 0.00 0.00 3.21
235 237 1.846712 TTGGCCGGGATCATCACACA 61.847 55.000 2.18 0.00 0.00 3.72
255 257 4.266976 CGTTTGTTCATCCTCGTGGTATAC 59.733 45.833 2.99 0.00 34.23 1.47
257 259 3.056393 TCGTTTGTTCATCCTCGTGGTAT 60.056 43.478 2.99 0.00 34.23 2.73
264 266 2.737252 GGTCTGTCGTTTGTTCATCCTC 59.263 50.000 0.00 0.00 0.00 3.71
265 267 2.368875 AGGTCTGTCGTTTGTTCATCCT 59.631 45.455 0.00 0.00 0.00 3.24
266 268 2.767505 AGGTCTGTCGTTTGTTCATCC 58.232 47.619 0.00 0.00 0.00 3.51
267 269 5.232414 GCTATAGGTCTGTCGTTTGTTCATC 59.768 44.000 1.04 0.00 0.00 2.92
282 284 3.388308 TCACTCTACGTCGCTATAGGTC 58.612 50.000 1.04 0.00 0.00 3.85
283 285 3.069300 TCTCACTCTACGTCGCTATAGGT 59.931 47.826 1.04 0.00 0.00 3.08
295 297 4.081087 ACTCCTCTCTCACTCTCACTCTAC 60.081 50.000 0.00 0.00 0.00 2.59
296 298 4.081142 CACTCCTCTCTCACTCTCACTCTA 60.081 50.000 0.00 0.00 0.00 2.43
297 299 2.912956 ACTCCTCTCTCACTCTCACTCT 59.087 50.000 0.00 0.00 0.00 3.24
299 301 2.290896 CCACTCCTCTCTCACTCTCACT 60.291 54.545 0.00 0.00 0.00 3.41
300 302 2.091541 CCACTCCTCTCTCACTCTCAC 58.908 57.143 0.00 0.00 0.00 3.51
301 303 1.988846 TCCACTCCTCTCTCACTCTCA 59.011 52.381 0.00 0.00 0.00 3.27
302 304 2.238646 TCTCCACTCCTCTCTCACTCTC 59.761 54.545 0.00 0.00 0.00 3.20
303 305 2.274542 TCTCCACTCCTCTCTCACTCT 58.725 52.381 0.00 0.00 0.00 3.24
306 308 1.408702 GCATCTCCACTCCTCTCTCAC 59.591 57.143 0.00 0.00 0.00 3.51
350 352 4.084147 CCCGAGGGACCCCAGGTA 62.084 72.222 17.86 0.00 35.25 3.08
479 481 4.570874 GGAGGAAGCGATGGGGCC 62.571 72.222 0.00 0.00 0.00 5.80
662 664 2.438434 CAACCTGACGCCCATCCC 60.438 66.667 0.00 0.00 0.00 3.85
665 667 2.034066 CCACAACCTGACGCCCAT 59.966 61.111 0.00 0.00 0.00 4.00
670 674 1.891919 CCACACCCACAACCTGACG 60.892 63.158 0.00 0.00 0.00 4.35
850 855 2.815211 CGTCAGCCCCACATGTCG 60.815 66.667 0.00 0.00 0.00 4.35
877 882 2.582052 ACTTCCTGAAAATGGAACGCA 58.418 42.857 0.00 0.00 38.53 5.24
1002 1007 1.204704 CGACCTGTCAGCCAGAATGTA 59.795 52.381 0.00 0.00 44.49 2.29
1003 1008 0.036952 CGACCTGTCAGCCAGAATGT 60.037 55.000 0.00 0.00 44.49 2.71
1013 1018 3.025924 ACGGAAGTACGACCTGTCA 57.974 52.632 9.08 0.00 46.88 3.58
1213 1218 1.709994 GGGCGAAGAAGGATGGGGAT 61.710 60.000 0.00 0.00 0.00 3.85
1268 1273 4.100808 AGAGTCCAGAAGAACCTGATATGC 59.899 45.833 0.00 0.00 36.29 3.14
1273 1278 2.900546 GGAAGAGTCCAGAAGAACCTGA 59.099 50.000 0.00 0.00 44.26 3.86
1348 1354 2.737180 CATATGAGCCGCGACCCT 59.263 61.111 8.23 0.00 0.00 4.34
1470 1476 0.035317 TCATCACCGCAACTCAAGCT 59.965 50.000 0.00 0.00 0.00 3.74
1481 1487 3.815401 GGGATAGAAACCAATCATCACCG 59.185 47.826 0.00 0.00 0.00 4.94
1646 1655 4.929211 GGCCAAATGATCCAAGTTTAACAC 59.071 41.667 0.00 0.00 0.00 3.32
1673 1682 1.596603 TGTCACTTGTGCATCCAGTG 58.403 50.000 13.90 13.90 0.00 3.66
1730 1739 5.531122 TTCTATACAATGCGACCTAAGCT 57.469 39.130 0.00 0.00 35.28 3.74
1731 1740 5.696724 ACATTCTATACAATGCGACCTAAGC 59.303 40.000 1.04 0.00 37.28 3.09
1732 1741 7.224753 ACAACATTCTATACAATGCGACCTAAG 59.775 37.037 1.04 0.00 37.28 2.18
1733 1742 7.011016 CACAACATTCTATACAATGCGACCTAA 59.989 37.037 1.04 0.00 37.28 2.69
1739 1759 4.907579 TGCACAACATTCTATACAATGCG 58.092 39.130 1.04 0.00 37.28 4.73
1879 1899 1.331214 ACTTGGGCAGAACCATTGTG 58.669 50.000 0.00 0.00 40.91 3.33
2381 2443 8.148351 TCGCCAGCCTTATTATTATATATCCAC 58.852 37.037 0.00 0.00 0.00 4.02
2505 2638 6.128138 AGGAACTCCTACTACTGCAATTTT 57.872 37.500 0.00 0.00 46.48 1.82
2506 2639 5.763876 AGGAACTCCTACTACTGCAATTT 57.236 39.130 0.00 0.00 46.48 1.82
2563 2730 8.133627 GCATATGATTTTCTACACTGCTTGATT 58.866 33.333 6.97 0.00 0.00 2.57
2646 2814 6.421801 GCACTGAGCAACAAAAAGATAAACAT 59.578 34.615 0.00 0.00 44.79 2.71
2711 3059 3.301794 TTGGATATCAAGGCAGCATGT 57.698 42.857 4.83 0.00 39.31 3.21
2789 3137 3.072944 GAGCTCAAGATGAGTGCAAAGT 58.927 45.455 9.40 0.00 45.94 2.66
2952 3305 2.887337 CGGAAAAGGCTTTGTTGTTGT 58.113 42.857 14.19 0.00 0.00 3.32
3024 3377 2.009774 CACGAAAGAACTAGCCATGGG 58.990 52.381 15.13 0.00 0.00 4.00
3047 3400 4.280819 AGAGAGATCTGAAGGACTGGAAG 58.719 47.826 0.00 0.00 42.29 3.46
3102 3455 4.772624 TGATTATATCAAGAGAGGTCGGGG 59.227 45.833 0.00 0.00 36.11 5.73
3157 3510 1.824230 GGTTTGGGCATATTCAGTGCA 59.176 47.619 0.29 0.00 44.25 4.57
3160 3513 4.210331 GAGATGGTTTGGGCATATTCAGT 58.790 43.478 0.00 0.00 0.00 3.41
3191 3544 4.082895 CCAATTGAAGAGAAGCTTGTCCAG 60.083 45.833 19.26 2.97 36.83 3.86
3287 3640 2.109126 GGCGGAGAGGTGCATGTTC 61.109 63.158 0.00 0.00 0.00 3.18
3641 3994 3.120649 GCGACATGTTCAACAGTAAGGTC 60.121 47.826 0.00 0.00 0.00 3.85
3668 4021 4.497291 TGTTGGAGTTGGTAAAGAGTGT 57.503 40.909 0.00 0.00 0.00 3.55
3711 4064 5.065346 TCGTATCACAAAGCAGACAACAAAA 59.935 36.000 0.00 0.00 0.00 2.44
3759 4112 9.334947 CTGATGACAATCATTATAACAGAACCT 57.665 33.333 0.00 0.00 41.97 3.50
3867 4228 7.974501 GCAAAGAGCTAACTATAGAGTAACACA 59.025 37.037 6.78 0.00 41.15 3.72
4235 4655 0.676466 CCCCACGTGCAGCTTCAATA 60.676 55.000 10.91 0.00 0.00 1.90
4326 4746 4.016444 TGGAGGATAAATGCTGTTTCACC 58.984 43.478 0.00 0.00 0.00 4.02
4375 4795 2.958355 TCCCCAGCAGCTAAATAAATGC 59.042 45.455 0.00 0.00 38.97 3.56
4401 4821 3.125316 GTGAAGCCGTCAAGTTCCATTAG 59.875 47.826 0.00 0.00 38.23 1.73
4412 4832 1.006571 GACCGAAGTGAAGCCGTCA 60.007 57.895 0.00 0.00 0.00 4.35
4546 4966 5.878116 TCCATATTTCCAAAGAACGTGGTAG 59.122 40.000 0.00 0.00 37.43 3.18
4590 5010 1.131126 CTGTAGCCCTTGCATTGTTCG 59.869 52.381 0.00 0.00 41.13 3.95
5199 5619 1.202076 GCTAGTTTCCGAGCAATGCAC 60.202 52.381 8.35 0.00 38.97 4.57
5328 5748 2.158559 TGCGGTGCACACAATAAGAAT 58.841 42.857 20.43 0.00 31.71 2.40
5344 5764 4.558470 CAGTTAAGCATGTAAACATTGCGG 59.442 41.667 0.00 0.00 36.34 5.69
5362 5782 7.466746 AGCCAAAGAAATGAATAAGCAGTTA 57.533 32.000 0.00 0.00 0.00 2.24
5378 5798 0.472471 AACAACTCCCGAGCCAAAGA 59.528 50.000 0.00 0.00 0.00 2.52
5387 5807 1.946768 TCAAGAGCAAAACAACTCCCG 59.053 47.619 0.00 0.00 33.18 5.14
5392 5812 2.036346 AGGGCATCAAGAGCAAAACAAC 59.964 45.455 0.00 0.00 0.00 3.32
5399 5819 1.300963 GACCAGGGCATCAAGAGCA 59.699 57.895 0.00 0.00 0.00 4.26
5401 5821 2.431954 ATTGACCAGGGCATCAAGAG 57.568 50.000 0.00 0.00 38.19 2.85
5531 5958 4.681978 ACTCCACTCGTTGGCGCC 62.682 66.667 22.73 22.73 46.47 6.53
5641 6068 4.689612 AATAACCACTGGTCGCATAGAT 57.310 40.909 0.00 0.00 33.12 1.98
5661 6088 5.330455 TGCCATGGCGTAAAATATGAAAA 57.670 34.783 30.87 5.86 45.51 2.29
5676 6103 2.747396 TTTAAGCTTGCTTGCCATGG 57.253 45.000 17.04 7.63 0.00 3.66
5707 6134 8.565896 AATACAGTTAAAGATCACATGCTCAA 57.434 30.769 0.00 0.00 0.00 3.02
5769 6196 3.525199 AGGTTATCCTTCCATCTGTTGCT 59.475 43.478 0.00 0.00 42.12 3.91
5828 6255 4.394920 GGCGATGATGAAAAAGAGGTGTAA 59.605 41.667 0.00 0.00 0.00 2.41
5831 6258 3.012518 AGGCGATGATGAAAAAGAGGTG 58.987 45.455 0.00 0.00 0.00 4.00
5857 6285 2.932614 ACTTGCATCAGTCTGCGTATTC 59.067 45.455 0.00 0.00 45.30 1.75
5938 6369 4.505217 CGCGGTCGACATTGCAGC 62.505 66.667 18.91 10.94 38.10 5.25
5939 6370 2.667318 AACGCGGTCGACATTGCAG 61.667 57.895 18.91 14.99 39.41 4.41
5940 6371 2.663520 AACGCGGTCGACATTGCA 60.664 55.556 18.91 0.00 39.41 4.08
5952 6383 3.836348 CGTTTTATAACTTGTCCAACGCG 59.164 43.478 3.53 3.53 31.89 6.01
6147 6585 0.890996 AGAAAGCAACCGCCTTCAGG 60.891 55.000 0.00 0.00 40.46 3.86
6186 6624 2.042464 AGTCACAGAAGACAGAAGCCA 58.958 47.619 0.00 0.00 40.98 4.75
6196 6634 7.364970 CAGATATGAGATCTCAGTCACAGAAG 58.635 42.308 28.26 9.87 43.61 2.85
6197 6635 6.238981 GCAGATATGAGATCTCAGTCACAGAA 60.239 42.308 28.26 3.89 43.61 3.02
6198 6636 5.241285 GCAGATATGAGATCTCAGTCACAGA 59.759 44.000 28.26 4.17 43.61 3.41
6199 6637 5.242171 AGCAGATATGAGATCTCAGTCACAG 59.758 44.000 28.26 20.46 43.61 3.66
6200 6638 5.139001 AGCAGATATGAGATCTCAGTCACA 58.861 41.667 28.26 12.55 43.61 3.58
6201 6639 5.335897 GGAGCAGATATGAGATCTCAGTCAC 60.336 48.000 28.26 21.59 43.61 3.67
6202 6640 4.766373 GGAGCAGATATGAGATCTCAGTCA 59.234 45.833 28.26 17.07 43.61 3.41
6203 6641 4.766373 TGGAGCAGATATGAGATCTCAGTC 59.234 45.833 28.26 25.57 43.61 3.51
6204 6642 4.738685 TGGAGCAGATATGAGATCTCAGT 58.261 43.478 28.26 19.86 43.61 3.41
6205 6643 5.725325 TTGGAGCAGATATGAGATCTCAG 57.275 43.478 28.26 16.38 43.61 3.35
6287 6726 6.228995 TGATATTGCAATTTGCTCAACCAAA 58.771 32.000 18.75 6.71 45.31 3.28


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

AutoCloner maintained by Alex Coulton.