Multiple sequence alignment - TraesCS1D01G206500

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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 TraesCS1D01G206500 chr1D 100.000 6304 0 0 1 6304 292085279 292078976 0.000000e+00 11642
1 TraesCS1D01G206500 chr1A 93.801 4049 131 31 1 3979 364231484 364227486 0.000000e+00 5976
2 TraesCS1D01G206500 chr1A 91.699 1542 56 21 4011 5522 364227490 364225991 0.000000e+00 2073
3 TraesCS1D01G206500 chr1A 93.284 134 8 1 5729 5861 364225947 364225814 4.990000e-46 196
4 TraesCS1D01G206500 chr1B 93.702 2334 76 26 4011 6303 393077041 393074738 0.000000e+00 3430
5 TraesCS1D01G206500 chr1B 97.013 2042 26 10 1968 3979 393079073 393077037 0.000000e+00 3400
6 TraesCS1D01G206500 chr1B 90.788 2019 114 35 1 1978 393081195 393079208 0.000000e+00 2632
7 TraesCS1D01G206500 chr7D 91.198 409 34 2 5897 6303 84116243 84115835 7.140000e-154 555
8 TraesCS1D01G206500 chr7D 90.465 409 37 2 5897 6303 87336498 87336090 7.190000e-149 538
9 TraesCS1D01G206500 chr6D 91.337 404 33 2 5902 6303 343990376 343990779 9.240000e-153 551
10 TraesCS1D01G206500 chr6D 90.709 409 36 2 5897 6303 271002979 271002571 1.550000e-150 544
11 TraesCS1D01G206500 chr6D 90.488 410 35 4 5897 6303 145602309 145602717 7.190000e-149 538
12 TraesCS1D01G206500 chr5D 90.954 409 35 2 5897 6303 292759025 292759433 3.320000e-152 549
13 TraesCS1D01G206500 chr5A 90.465 409 37 2 5897 6303 140619418 140619826 7.190000e-149 538
14 TraesCS1D01G206500 chr3D 90.465 409 37 2 5897 6303 446004313 446003905 7.190000e-149 538


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 TraesCS1D01G206500 chr1D 292078976 292085279 6303 True 11642.000000 11642 100.000000 1 6304 1 chr1D.!!$R1 6303
1 TraesCS1D01G206500 chr1A 364225814 364231484 5670 True 2748.333333 5976 92.928000 1 5861 3 chr1A.!!$R1 5860
2 TraesCS1D01G206500 chr1B 393074738 393081195 6457 True 3154.000000 3430 93.834333 1 6303 3 chr1B.!!$R1 6302

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
510 536 0.107456 CGGTGAGGATTCTGATGGGG 59.893 60.000 0.00 0.00 0.00 4.96 F
928 991 0.107945 CGAGCAAGGGAAGGGAAGAG 60.108 60.000 0.00 0.00 0.00 2.85 F
1480 1547 0.600255 AGACAGTGCGGTGTGTTAGC 60.600 55.000 0.00 0.00 0.00 3.09 F
1557 1624 2.365617 TGAAGGAAGCTTCTCTTGTCGT 59.634 45.455 25.47 9.74 34.56 4.34 F
2349 2597 2.684001 TTCACGGTATGGTAGCAAGG 57.316 50.000 0.00 0.00 0.00 3.61 F
3388 3648 0.174617 GTCAGGTCCTGCTGCTAGTC 59.825 60.000 14.64 0.00 0.00 2.59 F
4155 4420 0.326238 TCAGGGCTGGTAACCTAGGG 60.326 60.000 14.81 0.00 34.71 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2333 2568 0.107848 GCACCTTGCTACCATACCGT 60.108 55.000 0.00 0.0 40.96 4.83 R
2426 2674 2.989909 TGACAGGTCAGCATTACCATG 58.010 47.619 0.00 0.0 39.64 3.66 R
3303 3563 2.022195 CACAGGCAATTATCAGCAGCT 58.978 47.619 0.00 0.0 0.00 4.24 R
3364 3624 2.524394 AGCAGGACCTGACCGTGT 60.524 61.111 26.25 0.0 32.44 4.49 R
4155 4420 1.134729 CAATTACCTGTGCCATTGCCC 60.135 52.381 0.00 0.0 36.33 5.36 R
5118 5431 0.106708 GTGCCCGGATATTCTCTGCA 59.893 55.000 0.73 0.0 0.00 4.41 R
6051 6367 1.879380 GCAGTGCCACAAGTATGTTGA 59.121 47.619 2.85 0.0 37.82 3.18 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
86 87 1.743252 CCCGCTTCAGAACCTCTGC 60.743 63.158 0.00 0.00 43.95 4.26
118 119 3.200593 CCGCAGCTGCTGTCATCC 61.201 66.667 34.22 12.16 39.32 3.51
119 120 2.435410 CGCAGCTGCTGTCATCCA 60.435 61.111 34.22 0.00 39.32 3.41
136 139 4.657824 AGGGTGACGCCGAACACG 62.658 66.667 11.26 0.00 37.82 4.49
138 141 3.103911 GGTGACGCCGAACACGAG 61.104 66.667 11.26 0.00 37.82 4.18
156 159 2.490991 GAGCCGACACAACCTAAAACT 58.509 47.619 0.00 0.00 0.00 2.66
161 164 2.356382 CGACACAACCTAAAACTGCCAA 59.644 45.455 0.00 0.00 0.00 4.52
164 167 5.351948 ACACAACCTAAAACTGCCAAATT 57.648 34.783 0.00 0.00 0.00 1.82
205 217 1.239968 GGCCACCTGCTTCTCAACAG 61.240 60.000 0.00 0.00 40.92 3.16
207 219 1.572085 CCACCTGCTTCTCAACAGCG 61.572 60.000 0.00 0.00 40.45 5.18
241 255 3.809832 ACTGTCGGTGAGAAAGAAACATG 59.190 43.478 0.00 0.00 36.24 3.21
261 275 1.268539 GGCCAAATTATTCTGACGCGG 60.269 52.381 12.47 0.00 0.00 6.46
262 276 1.400494 GCCAAATTATTCTGACGCGGT 59.600 47.619 12.47 0.00 0.00 5.68
263 277 2.791158 GCCAAATTATTCTGACGCGGTG 60.791 50.000 12.47 0.00 0.00 4.94
264 278 2.418628 CCAAATTATTCTGACGCGGTGT 59.581 45.455 12.47 0.00 0.00 4.16
384 410 0.974010 AGCGATTGTCGGAGGGGTAA 60.974 55.000 1.29 0.00 40.84 2.85
413 439 2.264480 CCACGCCAACGGAGATGA 59.736 61.111 0.00 0.00 46.04 2.92
427 453 0.904865 AGATGAGGGCAGAACGGTCA 60.905 55.000 1.87 0.00 0.00 4.02
466 492 0.253327 AAGGGATGAGAAGGGAACGC 59.747 55.000 0.00 0.00 0.00 4.84
510 536 0.107456 CGGTGAGGATTCTGATGGGG 59.893 60.000 0.00 0.00 0.00 4.96
782 845 1.262640 ACCCGGTATCACACCTCACC 61.263 60.000 0.00 0.00 46.19 4.02
783 846 1.520666 CCGGTATCACACCTCACCC 59.479 63.158 0.00 0.00 46.19 4.61
928 991 0.107945 CGAGCAAGGGAAGGGAAGAG 60.108 60.000 0.00 0.00 0.00 2.85
1422 1489 2.315925 ACAGTATGCTTATGCGCTGT 57.684 45.000 9.73 14.82 42.53 4.40
1480 1547 0.600255 AGACAGTGCGGTGTGTTAGC 60.600 55.000 0.00 0.00 0.00 3.09
1519 1586 7.306925 CGTTGGCGTAGATGTTTTATATAGCAA 60.307 37.037 0.00 0.00 0.00 3.91
1557 1624 2.365617 TGAAGGAAGCTTCTCTTGTCGT 59.634 45.455 25.47 9.74 34.56 4.34
1582 1649 3.906008 CACGAGTTTAATTCCAAGCGTTG 59.094 43.478 0.00 0.00 0.00 4.10
1583 1650 3.562557 ACGAGTTTAATTCCAAGCGTTGT 59.437 39.130 0.00 0.00 0.00 3.32
1622 1689 6.899771 CGTTACTTGTGCATGTATCATTACAC 59.100 38.462 0.00 0.00 41.02 2.90
1633 1700 5.902681 TGTATCATTACACAGCTACAGGTC 58.097 41.667 0.00 0.00 33.37 3.85
1636 1703 5.420725 TCATTACACAGCTACAGGTCAAT 57.579 39.130 0.00 0.00 0.00 2.57
1640 1707 4.357918 ACACAGCTACAGGTCAATTCTT 57.642 40.909 0.00 0.00 0.00 2.52
1721 1788 7.348274 AGGATCATCATAAGGAAGTTCCAGTAA 59.652 37.037 23.87 6.35 39.61 2.24
1725 1792 9.396022 TCATCATAAGGAAGTTCCAGTAATTTC 57.604 33.333 23.87 0.00 39.61 2.17
1735 1802 7.639113 AGTTCCAGTAATTTCTTGTGTGAAA 57.361 32.000 0.00 0.00 39.79 2.69
1896 1965 3.040147 TCTGGTAAACTGAGAAAGCCG 57.960 47.619 0.00 0.00 0.00 5.52
2276 2510 3.388024 TGAGTCTGTAACAGTTGGCTTCT 59.612 43.478 0.00 0.00 32.61 2.85
2277 2511 4.141711 TGAGTCTGTAACAGTTGGCTTCTT 60.142 41.667 0.00 0.00 32.61 2.52
2278 2512 5.069914 TGAGTCTGTAACAGTTGGCTTCTTA 59.930 40.000 0.00 0.00 32.61 2.10
2349 2597 2.684001 TTCACGGTATGGTAGCAAGG 57.316 50.000 0.00 0.00 0.00 3.61
2380 2628 9.250624 CTATCTTACTGTATTACAAACTCCTGC 57.749 37.037 0.00 0.00 0.00 4.85
2436 2684 5.521372 GCAATCTTTCTTTCCATGGTAATGC 59.479 40.000 12.58 9.50 31.93 3.56
3303 3563 9.733556 ACATGTGGTAGTATTTTTATTCTCACA 57.266 29.630 0.00 0.00 36.15 3.58
3332 3592 8.374743 TGCTGATAATTGCCTGTGATACTATTA 58.625 33.333 0.00 0.00 0.00 0.98
3388 3648 0.174617 GTCAGGTCCTGCTGCTAGTC 59.825 60.000 14.64 0.00 0.00 2.59
3843 4103 4.501400 GGCTTTGCAGGTAAAATCTGTTGT 60.501 41.667 0.00 0.00 34.89 3.32
3974 4234 5.499004 AAATCAACCTAGCCAGTGAGTAA 57.501 39.130 0.00 0.00 0.00 2.24
3975 4235 3.955650 TCAACCTAGCCAGTGAGTAAC 57.044 47.619 0.00 0.00 0.00 2.50
3976 4236 3.507411 TCAACCTAGCCAGTGAGTAACT 58.493 45.455 0.00 0.00 40.93 2.24
3977 4237 3.510360 TCAACCTAGCCAGTGAGTAACTC 59.490 47.826 0.00 0.00 36.83 3.01
3978 4238 3.459710 ACCTAGCCAGTGAGTAACTCT 57.540 47.619 0.00 0.00 36.83 3.24
3979 4239 3.780626 ACCTAGCCAGTGAGTAACTCTT 58.219 45.455 0.00 0.00 36.83 2.85
3980 4240 4.161102 ACCTAGCCAGTGAGTAACTCTTT 58.839 43.478 0.00 0.00 36.83 2.52
3981 4241 4.593634 ACCTAGCCAGTGAGTAACTCTTTT 59.406 41.667 0.00 0.00 36.83 2.27
3982 4242 5.071923 ACCTAGCCAGTGAGTAACTCTTTTT 59.928 40.000 0.00 0.00 36.83 1.94
4128 4388 3.426695 GCAATTATGCGTTTGCTGAGTCT 60.427 43.478 7.88 0.00 43.83 3.24
4130 4390 5.156355 CAATTATGCGTTTGCTGAGTCTTT 58.844 37.500 0.00 0.00 43.34 2.52
4132 4392 2.755836 TGCGTTTGCTGAGTCTTTTC 57.244 45.000 0.00 0.00 43.34 2.29
4155 4420 0.326238 TCAGGGCTGGTAACCTAGGG 60.326 60.000 14.81 0.00 34.71 3.53
4330 4596 1.661463 AGGATCTCCTGTGGCAAGAA 58.339 50.000 0.00 0.00 46.55 2.52
4445 4711 8.950210 CATTACAATCTGTTCATTGGTAACTCT 58.050 33.333 0.00 0.00 37.98 3.24
4458 4724 9.317827 TCATTGGTAACTCTAAACTACTAAGGT 57.682 33.333 0.00 0.00 37.61 3.50
4547 4813 6.000246 TGGCCTACAGTCAATTATTGATGA 58.000 37.500 11.01 0.00 42.47 2.92
4548 4814 6.604171 TGGCCTACAGTCAATTATTGATGAT 58.396 36.000 11.01 2.55 42.47 2.45
4573 4839 9.809395 ATTTCCTGATTCTGAATCATGTGATAT 57.191 29.630 27.87 20.70 46.10 1.63
4596 4863 5.062528 TGTTTCTTCAAAATGGAAATGGGC 58.937 37.500 0.00 0.00 32.71 5.36
4597 4864 3.979101 TCTTCAAAATGGAAATGGGCC 57.021 42.857 0.00 0.00 0.00 5.80
4666 4933 7.802738 TGAAAAACAGATTGTAGTTCCATACG 58.197 34.615 0.00 0.00 0.00 3.06
4685 4952 1.512926 GCCTTGATACCACCGCTATG 58.487 55.000 0.00 0.00 0.00 2.23
4692 4959 0.762842 TACCACCGCTATGGAGCCAT 60.763 55.000 9.91 7.25 46.86 4.40
4858 5165 9.912634 AACACATTTTATCATACCTTTGTTGAG 57.087 29.630 0.00 0.00 0.00 3.02
4859 5166 8.522830 ACACATTTTATCATACCTTTGTTGAGG 58.477 33.333 0.00 0.00 42.75 3.86
4860 5167 7.489113 CACATTTTATCATACCTTTGTTGAGGC 59.511 37.037 0.00 0.00 40.65 4.70
4861 5168 7.178274 ACATTTTATCATACCTTTGTTGAGGCA 59.822 33.333 0.00 0.00 40.65 4.75
4862 5169 6.757897 TTTATCATACCTTTGTTGAGGCAG 57.242 37.500 0.00 0.00 40.65 4.85
4863 5170 3.788227 TCATACCTTTGTTGAGGCAGT 57.212 42.857 0.00 0.00 40.65 4.40
4864 5171 3.411446 TCATACCTTTGTTGAGGCAGTG 58.589 45.455 0.00 0.00 40.65 3.66
4865 5172 3.149196 CATACCTTTGTTGAGGCAGTGT 58.851 45.455 0.00 0.00 40.65 3.55
4866 5173 1.680338 ACCTTTGTTGAGGCAGTGTC 58.320 50.000 0.00 0.00 40.65 3.67
4867 5174 1.212935 ACCTTTGTTGAGGCAGTGTCT 59.787 47.619 0.00 0.00 40.65 3.41
4868 5175 1.605710 CCTTTGTTGAGGCAGTGTCTG 59.394 52.381 0.00 0.00 34.12 3.51
4869 5176 2.564771 CTTTGTTGAGGCAGTGTCTGA 58.435 47.619 0.00 0.00 32.44 3.27
4983 5290 4.308526 TGCCTCCAATGGTTTGTATACA 57.691 40.909 0.08 0.08 0.00 2.29
5016 5323 5.012239 TGAGAATTTGCCTGCTCTTATTGT 58.988 37.500 0.00 0.00 0.00 2.71
5035 5342 1.859080 GTGTTCCGTCGGCTGATATTC 59.141 52.381 6.34 0.00 0.00 1.75
5047 5354 3.460103 GCTGATATTCGTTTCCCCGTTA 58.540 45.455 0.00 0.00 0.00 3.18
5118 5431 2.372172 AGAAATGGGGTTCTTCGACACT 59.628 45.455 0.00 0.00 34.03 3.55
5209 5522 5.656859 GGGAACTTTGGCCAGTAGATAAAAT 59.343 40.000 20.29 0.00 0.00 1.82
5529 5844 6.884280 TTTTCATCTTCTTTCCTCCTTGAC 57.116 37.500 0.00 0.00 0.00 3.18
5530 5845 5.567037 TTCATCTTCTTTCCTCCTTGACA 57.433 39.130 0.00 0.00 0.00 3.58
5531 5846 5.768980 TCATCTTCTTTCCTCCTTGACAT 57.231 39.130 0.00 0.00 0.00 3.06
5532 5847 6.131972 TCATCTTCTTTCCTCCTTGACATT 57.868 37.500 0.00 0.00 0.00 2.71
5533 5848 5.942236 TCATCTTCTTTCCTCCTTGACATTG 59.058 40.000 0.00 0.00 0.00 2.82
5534 5849 5.310409 TCTTCTTTCCTCCTTGACATTGT 57.690 39.130 0.00 0.00 0.00 2.71
5535 5850 5.694995 TCTTCTTTCCTCCTTGACATTGTT 58.305 37.500 0.00 0.00 0.00 2.83
5536 5851 6.837312 TCTTCTTTCCTCCTTGACATTGTTA 58.163 36.000 0.00 0.00 0.00 2.41
5537 5852 6.936900 TCTTCTTTCCTCCTTGACATTGTTAG 59.063 38.462 0.00 0.00 0.00 2.34
5639 5954 7.750458 ACAGCAGTACATTTTTGTCATATTTCG 59.250 33.333 0.00 0.00 0.00 3.46
5824 6139 4.799564 TGGGGTCAAATTTGCATAGAAC 57.200 40.909 13.54 5.20 0.00 3.01
5974 6290 5.753716 TGGTCATACATCCAATGTGAATGA 58.246 37.500 2.88 2.82 44.60 2.57
6101 6417 6.292923 AGGTTATATTGGTGTAAAGCGCATA 58.707 36.000 11.47 0.00 0.00 3.14
6110 6426 5.086727 GGTGTAAAGCGCATAAAGAAACTC 58.913 41.667 11.47 0.00 0.00 3.01
6113 6429 5.414454 TGTAAAGCGCATAAAGAAACTCCAT 59.586 36.000 11.47 0.00 0.00 3.41
6120 6436 4.640201 GCATAAAGAAACTCCATGCAGGTA 59.360 41.667 0.00 0.00 41.25 3.08
6127 6443 3.525800 ACTCCATGCAGGTAGGTTTTT 57.474 42.857 0.00 0.00 39.02 1.94
6135 6465 3.572255 TGCAGGTAGGTTTTTGGAATCAC 59.428 43.478 0.00 0.00 0.00 3.06
6150 6480 6.801539 TGGAATCACTTGATACTTGTGAAC 57.198 37.500 0.00 0.00 42.80 3.18
6187 6517 4.722361 AGATGACTAAACTCCGTTCTCC 57.278 45.455 0.00 0.00 0.00 3.71
6283 6613 4.088496 GCACGCGGCAATATCATTATTTTC 59.912 41.667 12.47 0.00 43.97 2.29
6292 6622 6.797033 GCAATATCATTATTTTCCGACCTTCG 59.203 38.462 0.00 0.00 40.07 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.279513 TCTTTTGTTCTTTGCTTTTCTCCA 57.720 33.333 0.00 0.00 0.00 3.86
19 20 5.456822 CCGCTCTTTCTTCTTTTGTTCTTTG 59.543 40.000 0.00 0.00 0.00 2.77
86 87 3.129502 CGGCCATGGCAGAGTGTG 61.130 66.667 36.56 13.62 44.11 3.82
111 112 2.662596 GCGTCACCCTGGATGACA 59.337 61.111 20.89 0.00 45.64 3.58
113 114 3.770040 CGGCGTCACCCTGGATGA 61.770 66.667 0.00 0.00 33.26 2.92
116 117 3.998672 GTTCGGCGTCACCCTGGA 61.999 66.667 6.85 0.00 33.26 3.86
118 119 3.041940 GTGTTCGGCGTCACCCTG 61.042 66.667 20.32 0.00 33.26 4.45
119 120 4.657824 CGTGTTCGGCGTCACCCT 62.658 66.667 23.06 0.00 33.26 4.34
136 139 2.223377 CAGTTTTAGGTTGTGTCGGCTC 59.777 50.000 0.00 0.00 0.00 4.70
138 141 1.334689 GCAGTTTTAGGTTGTGTCGGC 60.335 52.381 0.00 0.00 0.00 5.54
156 159 3.145286 TCGTCAGTCATCAAATTTGGCA 58.855 40.909 17.90 0.00 0.00 4.92
161 164 5.991606 TCTTTGTCTCGTCAGTCATCAAATT 59.008 36.000 0.00 0.00 0.00 1.82
164 167 4.550422 CTCTTTGTCTCGTCAGTCATCAA 58.450 43.478 0.00 0.00 0.00 2.57
199 203 1.144969 GTTCCAATCGACGCTGTTGA 58.855 50.000 8.41 1.91 0.00 3.18
205 217 0.438830 GACAGTGTTCCAATCGACGC 59.561 55.000 0.00 0.00 0.00 5.19
207 219 1.068474 CCGACAGTGTTCCAATCGAC 58.932 55.000 0.00 0.00 34.77 4.20
229 243 7.820872 CAGAATAATTTGGCCATGTTTCTTTCT 59.179 33.333 6.09 10.76 0.00 2.52
231 245 7.603784 GTCAGAATAATTTGGCCATGTTTCTTT 59.396 33.333 6.09 0.02 0.00 2.52
241 255 1.268539 CCGCGTCAGAATAATTTGGCC 60.269 52.381 4.92 0.00 0.00 5.36
281 295 2.903547 TTCTTCACAAAGGCGGCGC 61.904 57.895 26.17 26.17 33.03 6.53
283 297 0.383949 TTGTTCTTCACAAAGGCGGC 59.616 50.000 0.00 0.00 42.76 6.53
290 316 1.408702 GCTGGGCTTTGTTCTTCACAA 59.591 47.619 0.00 0.00 44.11 3.33
292 318 0.315251 GGCTGGGCTTTGTTCTTCAC 59.685 55.000 0.00 0.00 0.00 3.18
373 399 4.466898 GGTCCTTTACCCCTCCGA 57.533 61.111 0.00 0.00 43.16 4.55
413 439 2.526873 AGGTGACCGTTCTGCCCT 60.527 61.111 0.00 0.00 0.00 5.19
427 453 1.196012 GGAAAGGTGATCTCGGAGGT 58.804 55.000 4.96 0.00 0.00 3.85
466 492 3.419759 CTGAACCGTTTCGCCCCG 61.420 66.667 0.00 0.00 34.04 5.73
510 536 3.111853 TCGCACCCATTCATACTCATC 57.888 47.619 0.00 0.00 0.00 2.92
1274 1339 1.779221 TATTCCCCGTATCCGTGTGT 58.221 50.000 0.00 0.00 0.00 3.72
1422 1489 1.954382 CCCGTGTAGTATCAGCTAGCA 59.046 52.381 18.83 0.00 0.00 3.49
1429 1496 3.101437 ACCAATCACCCGTGTAGTATCA 58.899 45.455 0.00 0.00 0.00 2.15
1557 1624 2.227865 GCTTGGAATTAAACTCGTGCCA 59.772 45.455 0.00 0.00 0.00 4.92
1565 1632 4.231718 TCCACAACGCTTGGAATTAAAC 57.768 40.909 0.00 0.00 40.35 2.01
1582 1649 5.180680 ACAAGTAACGGAAGCTAAAATCCAC 59.819 40.000 3.16 0.00 35.34 4.02
1583 1650 5.180492 CACAAGTAACGGAAGCTAAAATCCA 59.820 40.000 3.16 0.00 35.34 3.41
1622 1689 6.634805 TCTCTTAAGAATTGACCTGTAGCTG 58.365 40.000 6.63 0.00 0.00 4.24
1636 1703 9.520515 AAGCAAATCCAGTAAATCTCTTAAGAA 57.479 29.630 6.63 0.00 34.49 2.52
1640 1707 7.554118 CCTCAAGCAAATCCAGTAAATCTCTTA 59.446 37.037 0.00 0.00 0.00 2.10
1725 1792 3.609373 CGCTATGCCAAATTTCACACAAG 59.391 43.478 0.00 0.00 0.00 3.16
1735 1802 4.454728 ACAATCAAACGCTATGCCAAAT 57.545 36.364 0.00 0.00 0.00 2.32
1870 1939 7.657761 CGGCTTTCTCAGTTTACCAGAATATAT 59.342 37.037 0.00 0.00 0.00 0.86
1896 1965 9.057089 CATTAGGATTCAACTATAAACTCCACC 57.943 37.037 0.00 0.00 0.00 4.61
2077 2295 1.047002 CCCTGCATTTTCCCAACACA 58.953 50.000 0.00 0.00 0.00 3.72
2330 2565 1.903860 ACCTTGCTACCATACCGTGAA 59.096 47.619 0.00 0.00 0.00 3.18
2331 2566 1.206132 CACCTTGCTACCATACCGTGA 59.794 52.381 0.00 0.00 0.00 4.35
2332 2567 1.651987 CACCTTGCTACCATACCGTG 58.348 55.000 0.00 0.00 0.00 4.94
2333 2568 0.107848 GCACCTTGCTACCATACCGT 60.108 55.000 0.00 0.00 40.96 4.83
2340 2588 2.990066 AGATAGTGCACCTTGCTACC 57.010 50.000 14.63 0.00 45.31 3.18
2349 2597 9.367444 AGTTTGTAATACAGTAAGATAGTGCAC 57.633 33.333 9.40 9.40 32.30 4.57
2380 2628 3.248495 TGCATGTGCCAAAACCATATG 57.752 42.857 2.07 0.00 41.18 1.78
2415 2663 6.096001 GTCAGCATTACCATGGAAAGAAAGAT 59.904 38.462 21.47 0.00 0.00 2.40
2426 2674 2.989909 TGACAGGTCAGCATTACCATG 58.010 47.619 0.00 0.00 39.64 3.66
2436 2684 5.518128 CACGAAGATCTAAATGACAGGTCAG 59.482 44.000 8.24 0.00 43.61 3.51
3303 3563 2.022195 CACAGGCAATTATCAGCAGCT 58.978 47.619 0.00 0.00 0.00 4.24
3364 3624 2.524394 AGCAGGACCTGACCGTGT 60.524 61.111 26.25 0.00 32.44 4.49
3843 4103 5.277297 CGAGAACAGTTGTTAACTTGCATCA 60.277 40.000 7.22 0.00 40.46 3.07
3879 4139 8.103924 GCGCAGAACAAATACAAATTTTATCAG 58.896 33.333 0.30 0.00 32.87 2.90
3884 4144 5.333263 GCTGCGCAGAACAAATACAAATTTT 60.333 36.000 40.21 0.00 32.87 1.82
3885 4145 4.150451 GCTGCGCAGAACAAATACAAATTT 59.850 37.500 40.21 0.00 35.65 1.82
3994 4254 9.416284 TGAATTAGAGTGTTACTTTTTCCCTTT 57.584 29.630 0.00 0.00 0.00 3.11
3995 4255 8.990163 TGAATTAGAGTGTTACTTTTTCCCTT 57.010 30.769 0.00 0.00 0.00 3.95
3996 4256 8.990163 TTGAATTAGAGTGTTACTTTTTCCCT 57.010 30.769 0.00 0.00 0.00 4.20
4003 4263 9.890629 TCATGCTATTGAATTAGAGTGTTACTT 57.109 29.630 0.00 0.00 0.00 2.24
4007 4267 9.182214 ACAATCATGCTATTGAATTAGAGTGTT 57.818 29.630 12.68 0.00 38.84 3.32
4008 4268 8.743085 ACAATCATGCTATTGAATTAGAGTGT 57.257 30.769 12.68 0.00 38.84 3.55
4067 4327 8.798859 AAACATAACTGCACTTCATAATCTCT 57.201 30.769 0.00 0.00 0.00 3.10
4128 4388 3.639561 GGTTACCAGCCCTGAAAAGAAAA 59.360 43.478 0.00 0.00 0.00 2.29
4130 4390 2.445525 AGGTTACCAGCCCTGAAAAGAA 59.554 45.455 3.51 0.00 0.00 2.52
4132 4392 2.586648 AGGTTACCAGCCCTGAAAAG 57.413 50.000 3.51 0.00 0.00 2.27
4155 4420 1.134729 CAATTACCTGTGCCATTGCCC 60.135 52.381 0.00 0.00 36.33 5.36
4312 4577 2.686915 CAATTCTTGCCACAGGAGATCC 59.313 50.000 0.00 0.00 0.00 3.36
4330 4596 4.034510 GCAGAGCGTGTATAGAAAAGCAAT 59.965 41.667 0.00 0.00 0.00 3.56
4427 4693 8.867097 AGTAGTTTAGAGTTACCAATGAACAGA 58.133 33.333 0.00 0.00 0.00 3.41
4509 4775 4.458989 TGTAGGCCAAATGATTCTGTGAAC 59.541 41.667 5.01 0.00 0.00 3.18
4573 4839 5.062528 GCCCATTTCCATTTTGAAGAAACA 58.937 37.500 0.00 0.00 32.67 2.83
4585 4852 2.123726 GAGGCGGCCCATTTCCAT 60.124 61.111 17.02 0.00 0.00 3.41
4596 4863 2.009774 CAGTATTTTGGTCAGAGGCGG 58.990 52.381 0.00 0.00 0.00 6.13
4597 4864 2.699954 ACAGTATTTTGGTCAGAGGCG 58.300 47.619 0.00 0.00 0.00 5.52
4648 4915 4.060038 AGGCGTATGGAACTACAATCTG 57.940 45.455 0.00 0.00 0.00 2.90
4666 4933 1.512926 CATAGCGGTGGTATCAAGGC 58.487 55.000 0.00 0.00 0.00 4.35
4846 5153 2.438021 AGACACTGCCTCAACAAAGGTA 59.562 45.455 0.00 0.00 38.79 3.08
4847 5154 1.212935 AGACACTGCCTCAACAAAGGT 59.787 47.619 0.00 0.00 38.79 3.50
4848 5155 1.605710 CAGACACTGCCTCAACAAAGG 59.394 52.381 0.00 0.00 39.62 3.11
4849 5156 2.564771 TCAGACACTGCCTCAACAAAG 58.435 47.619 0.00 0.00 0.00 2.77
4850 5157 2.682856 GTTCAGACACTGCCTCAACAAA 59.317 45.455 0.00 0.00 0.00 2.83
4851 5158 2.288666 GTTCAGACACTGCCTCAACAA 58.711 47.619 0.00 0.00 0.00 2.83
4852 5159 1.209261 TGTTCAGACACTGCCTCAACA 59.791 47.619 0.00 0.00 0.00 3.33
4853 5160 1.953559 TGTTCAGACACTGCCTCAAC 58.046 50.000 0.00 0.00 0.00 3.18
4854 5161 2.708216 TTGTTCAGACACTGCCTCAA 57.292 45.000 0.00 0.00 34.98 3.02
4855 5162 2.708216 TTTGTTCAGACACTGCCTCA 57.292 45.000 0.00 0.00 34.98 3.86
4856 5163 4.065088 TGTATTTGTTCAGACACTGCCTC 58.935 43.478 0.00 0.00 34.98 4.70
4857 5164 4.067896 CTGTATTTGTTCAGACACTGCCT 58.932 43.478 0.00 0.00 34.98 4.75
4858 5165 3.189287 CCTGTATTTGTTCAGACACTGCC 59.811 47.826 0.00 0.00 34.98 4.85
4859 5166 3.365364 GCCTGTATTTGTTCAGACACTGC 60.365 47.826 0.00 0.00 34.98 4.40
4860 5167 3.814842 TGCCTGTATTTGTTCAGACACTG 59.185 43.478 0.00 0.00 34.98 3.66
4861 5168 3.815401 GTGCCTGTATTTGTTCAGACACT 59.185 43.478 4.82 0.00 40.23 3.55
4862 5169 3.363970 CGTGCCTGTATTTGTTCAGACAC 60.364 47.826 0.00 0.00 40.08 3.67
4863 5170 2.805671 CGTGCCTGTATTTGTTCAGACA 59.194 45.455 0.00 0.00 34.02 3.41
4864 5171 2.412847 GCGTGCCTGTATTTGTTCAGAC 60.413 50.000 0.00 0.00 34.02 3.51
4865 5172 1.804151 GCGTGCCTGTATTTGTTCAGA 59.196 47.619 0.00 0.00 34.02 3.27
4866 5173 1.464023 CGCGTGCCTGTATTTGTTCAG 60.464 52.381 0.00 0.00 0.00 3.02
4867 5174 0.515127 CGCGTGCCTGTATTTGTTCA 59.485 50.000 0.00 0.00 0.00 3.18
4868 5175 0.179200 CCGCGTGCCTGTATTTGTTC 60.179 55.000 4.92 0.00 0.00 3.18
4869 5176 1.582610 CCCGCGTGCCTGTATTTGTT 61.583 55.000 4.92 0.00 0.00 2.83
4983 5290 1.537202 GCAAATTCTCAAGACGGCAGT 59.463 47.619 0.00 0.00 0.00 4.40
5016 5323 1.535226 CGAATATCAGCCGACGGAACA 60.535 52.381 20.50 0.00 0.00 3.18
5035 5342 2.268298 CACTGAGATAACGGGGAAACG 58.732 52.381 0.00 0.00 40.31 3.60
5047 5354 2.362369 CCTCCGGTGGCACTGAGAT 61.362 63.158 27.61 0.00 0.00 2.75
5118 5431 0.106708 GTGCCCGGATATTCTCTGCA 59.893 55.000 0.73 0.00 0.00 4.41
5455 5768 5.280945 ACATTGTTTGTGTCTATTGTGTGC 58.719 37.500 0.00 0.00 37.11 4.57
5508 5823 5.567037 TGTCAAGGAGGAAAGAAGATGAA 57.433 39.130 0.00 0.00 0.00 2.57
5524 5839 6.207417 ACCTTTCATGGTCTAACAATGTCAAG 59.793 38.462 0.00 0.00 34.86 3.02
5525 5840 6.068010 ACCTTTCATGGTCTAACAATGTCAA 58.932 36.000 0.00 0.00 34.86 3.18
5526 5841 5.630121 ACCTTTCATGGTCTAACAATGTCA 58.370 37.500 0.00 0.00 34.86 3.58
5527 5842 6.381801 CAACCTTTCATGGTCTAACAATGTC 58.618 40.000 0.00 0.00 39.83 3.06
5528 5843 5.278957 GCAACCTTTCATGGTCTAACAATGT 60.279 40.000 0.00 0.00 39.83 2.71
5529 5844 5.047802 AGCAACCTTTCATGGTCTAACAATG 60.048 40.000 0.00 0.00 39.83 2.82
5530 5845 5.079643 AGCAACCTTTCATGGTCTAACAAT 58.920 37.500 0.00 0.00 39.83 2.71
5531 5846 4.469657 AGCAACCTTTCATGGTCTAACAA 58.530 39.130 0.00 0.00 39.83 2.83
5532 5847 4.098914 AGCAACCTTTCATGGTCTAACA 57.901 40.909 0.00 0.00 39.83 2.41
5533 5848 6.599638 AGATTAGCAACCTTTCATGGTCTAAC 59.400 38.462 0.00 0.00 39.83 2.34
5534 5849 6.721318 AGATTAGCAACCTTTCATGGTCTAA 58.279 36.000 0.00 0.00 39.83 2.10
5535 5850 6.313519 AGATTAGCAACCTTTCATGGTCTA 57.686 37.500 0.00 0.00 39.83 2.59
5536 5851 5.184892 AGATTAGCAACCTTTCATGGTCT 57.815 39.130 0.00 0.00 39.83 3.85
5537 5852 5.415701 TCAAGATTAGCAACCTTTCATGGTC 59.584 40.000 0.00 0.00 39.83 4.02
5824 6139 3.320541 TGCAACAAACCCAAGAATAGGTG 59.679 43.478 0.00 0.00 36.19 4.00
5942 6258 6.575244 TTGGATGTATGACCATAGAAGGTT 57.425 37.500 0.00 0.00 43.38 3.50
5943 6259 6.101734 ACATTGGATGTATGACCATAGAAGGT 59.898 38.462 0.00 0.00 43.07 3.50
6051 6367 1.879380 GCAGTGCCACAAGTATGTTGA 59.121 47.619 2.85 0.00 37.82 3.18
6101 6417 3.074538 ACCTACCTGCATGGAGTTTCTTT 59.925 43.478 13.65 0.00 39.71 2.52
6110 6426 2.524306 TCCAAAAACCTACCTGCATGG 58.476 47.619 0.00 0.00 42.93 3.66
6113 6429 3.572255 GTGATTCCAAAAACCTACCTGCA 59.428 43.478 0.00 0.00 0.00 4.41
6120 6436 7.287696 ACAAGTATCAAGTGATTCCAAAAACCT 59.712 33.333 0.00 0.00 36.05 3.50
6127 6443 5.705441 GGTTCACAAGTATCAAGTGATTCCA 59.295 40.000 0.00 0.00 41.42 3.53
6135 6465 4.012374 AGGCATGGTTCACAAGTATCAAG 58.988 43.478 0.00 0.00 0.00 3.02
6162 6492 2.973945 ACGGAGTTTAGTCATCTTGCC 58.026 47.619 0.00 0.00 37.78 4.52
6187 6517 0.179111 TAGCTCGCTCCATTGTTCCG 60.179 55.000 0.00 0.00 0.00 4.30
6189 6519 3.001736 GTCATTAGCTCGCTCCATTGTTC 59.998 47.826 0.00 0.00 0.00 3.18
6192 6522 2.831333 AGTCATTAGCTCGCTCCATTG 58.169 47.619 0.00 0.00 0.00 2.82
6231 6561 3.068732 ACTCATCAGACCACATACATCGG 59.931 47.826 0.00 0.00 0.00 4.18
6246 6576 1.926510 CGCGTGCTTCAATACTCATCA 59.073 47.619 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.