Multiple sequence alignment - TraesCS7D01G327900

Loading Multiple Alignment...

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 TraesCS7D01G327900 chr7D 100.000 4328 0 0 1 4328 419143617 419147944 0.000000e+00 7993.0
1 TraesCS7D01G327900 chr7A 92.133 3610 164 53 506 4064 514437886 514434346 0.000000e+00 4983.0
2 TraesCS7D01G327900 chr7B 90.095 2423 130 42 610 2977 435000786 435003153 0.000000e+00 3044.0
3 TraesCS7D01G327900 chr7B 90.484 599 37 9 3197 3780 435003510 435004103 0.000000e+00 773.0
4 TraesCS7D01G327900 chr7B 88.470 451 42 9 3883 4326 435005890 435006337 1.770000e-148 536.0
5 TraesCS7D01G327900 chr7B 79.359 562 77 24 63 606 435000204 435000744 4.120000e-95 359.0
6 TraesCS7D01G327900 chr7B 89.583 96 9 1 2991 3086 435003137 435003231 2.110000e-23 121.0
7 TraesCS7D01G327900 chr7B 93.243 74 5 0 3810 3883 435004253 435004326 4.580000e-20 110.0
8 TraesCS7D01G327900 chr7B 78.947 133 21 4 331 461 251309372 251309245 2.770000e-12 84.2
9 TraesCS7D01G327900 chr6D 72.330 412 78 27 113 509 252953236 252952846 3.560000e-16 97.1
10 TraesCS7D01G327900 chr4D 72.105 380 76 22 143 509 194544406 194544044 2.140000e-13 87.9


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 TraesCS7D01G327900 chr7D 419143617 419147944 4327 False 7993.000000 7993 100.000 1 4328 1 chr7D.!!$F1 4327
1 TraesCS7D01G327900 chr7A 514434346 514437886 3540 True 4983.000000 4983 92.133 506 4064 1 chr7A.!!$R1 3558
2 TraesCS7D01G327900 chr7B 435000204 435006337 6133 False 823.833333 3044 88.539 63 4326 6 chr7B.!!$F1 4263

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
46 47 0.109532 TTTGATGGCAGACCGGAACA 59.890 50.0 9.46 0.00 39.70 3.18 F
730 796 0.320073 TAAGGTCGACCAAACAGGCG 60.320 55.0 35.00 0.00 43.14 5.52 F
1014 1090 0.471191 TGATCATGGGAGATGCGCTT 59.529 50.0 9.73 0.55 0.00 4.68 F
1791 1898 0.531753 GAGAGAGAAGAATGGCCCGC 60.532 60.0 0.00 0.00 0.00 6.13 F
2264 2377 0.896019 CGATCTCCGGCTCCACCTAT 60.896 60.0 0.00 0.00 35.61 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1324 0.108615 GCGAGCACTTCTGCCTCTTA 60.109 55.000 0.00 0.00 45.53 2.10 R
2682 2805 0.106268 TGCAGTGTTTGGTCCCATGT 60.106 50.000 0.00 0.00 0.00 3.21 R
2818 2953 0.462047 CTAGCCATCCAACCCACGTC 60.462 60.000 0.00 0.00 0.00 4.34 R
3297 3604 2.225019 CGTTTGCTGAATCTCTTGCACT 59.775 45.455 0.00 0.00 35.01 4.40 R
4015 6025 0.178068 AGATACGTGCATGTGTCCCC 59.822 55.000 26.54 8.25 31.04 4.81 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 3.598019 GGTCAAATTGGCATCATGTGT 57.402 42.857 0.00 0.00 0.00 3.72
21 22 3.255725 GGTCAAATTGGCATCATGTGTG 58.744 45.455 0.00 0.00 0.00 3.82
22 23 3.056678 GGTCAAATTGGCATCATGTGTGA 60.057 43.478 0.00 0.00 39.04 3.58
23 24 3.922240 GTCAAATTGGCATCATGTGTGAC 59.078 43.478 0.00 2.95 37.14 3.67
24 25 3.827876 TCAAATTGGCATCATGTGTGACT 59.172 39.130 7.92 0.00 37.14 3.41
25 26 3.861276 AATTGGCATCATGTGTGACTG 57.139 42.857 7.92 0.00 37.14 3.51
26 27 2.565046 TTGGCATCATGTGTGACTGA 57.435 45.000 7.92 0.00 37.14 3.41
27 28 2.793288 TGGCATCATGTGTGACTGAT 57.207 45.000 7.92 0.00 37.14 2.90
28 29 3.076079 TGGCATCATGTGTGACTGATT 57.924 42.857 7.92 0.00 37.14 2.57
29 30 3.423749 TGGCATCATGTGTGACTGATTT 58.576 40.909 7.92 0.00 37.14 2.17
30 31 3.191791 TGGCATCATGTGTGACTGATTTG 59.808 43.478 7.92 0.00 37.14 2.32
31 32 3.441222 GGCATCATGTGTGACTGATTTGA 59.559 43.478 5.27 0.00 37.14 2.69
32 33 4.097437 GGCATCATGTGTGACTGATTTGAT 59.903 41.667 5.27 0.00 37.14 2.57
33 34 5.034797 GCATCATGTGTGACTGATTTGATG 58.965 41.667 0.00 0.00 41.03 3.07
34 35 5.578776 CATCATGTGTGACTGATTTGATGG 58.421 41.667 0.00 0.00 37.14 3.51
35 36 3.441222 TCATGTGTGACTGATTTGATGGC 59.559 43.478 0.00 0.00 0.00 4.40
36 37 2.861274 TGTGTGACTGATTTGATGGCA 58.139 42.857 0.00 0.00 0.00 4.92
37 38 2.815503 TGTGTGACTGATTTGATGGCAG 59.184 45.455 0.00 0.00 35.81 4.85
38 39 3.076621 GTGTGACTGATTTGATGGCAGA 58.923 45.455 0.00 0.00 33.94 4.26
39 40 3.076621 TGTGACTGATTTGATGGCAGAC 58.923 45.455 0.00 0.00 33.94 3.51
40 41 2.421424 GTGACTGATTTGATGGCAGACC 59.579 50.000 0.00 0.00 33.94 3.85
41 42 1.667724 GACTGATTTGATGGCAGACCG 59.332 52.381 0.00 0.00 39.70 4.79
42 43 1.019673 CTGATTTGATGGCAGACCGG 58.980 55.000 0.00 0.00 39.70 5.28
43 44 0.617935 TGATTTGATGGCAGACCGGA 59.382 50.000 9.46 0.00 39.70 5.14
44 45 1.004161 TGATTTGATGGCAGACCGGAA 59.996 47.619 9.46 0.00 39.70 4.30
45 46 1.401905 GATTTGATGGCAGACCGGAAC 59.598 52.381 9.46 0.99 39.70 3.62
46 47 0.109532 TTTGATGGCAGACCGGAACA 59.890 50.000 9.46 0.00 39.70 3.18
47 48 0.605319 TTGATGGCAGACCGGAACAC 60.605 55.000 9.46 0.00 39.70 3.32
48 49 1.745489 GATGGCAGACCGGAACACC 60.745 63.158 9.46 4.73 39.70 4.16
49 50 3.268103 ATGGCAGACCGGAACACCC 62.268 63.158 9.46 6.91 39.70 4.61
72 73 4.787598 GCTTGAGCGAATTACAATATGGG 58.212 43.478 0.00 0.00 0.00 4.00
85 86 8.725606 ATTACAATATGGGTTAATGGCTCATT 57.274 30.769 5.84 5.84 37.80 2.57
88 89 6.183360 ACAATATGGGTTAATGGCTCATTTGG 60.183 38.462 5.85 0.00 35.54 3.28
90 91 4.323569 TGGGTTAATGGCTCATTTGGTA 57.676 40.909 5.85 0.00 35.54 3.25
112 113 8.696374 TGGTACAAATTAAAGGAATGTTGACAA 58.304 29.630 0.00 0.00 31.92 3.18
182 183 3.719173 TTTGGTTCAACGGAATTGGAC 57.281 42.857 0.00 0.00 45.15 4.02
201 202 6.684897 TGGACAAATGAAAAATGGAGGAAT 57.315 33.333 0.00 0.00 0.00 3.01
205 206 8.506437 GGACAAATGAAAAATGGAGGAATTTTC 58.494 33.333 0.00 0.00 38.49 2.29
220 221 6.894339 GGAATTTTCCCTTAACTGAACTCA 57.106 37.500 0.00 0.00 41.62 3.41
221 222 7.284919 GGAATTTTCCCTTAACTGAACTCAA 57.715 36.000 0.00 0.00 41.62 3.02
226 227 7.889873 TTTCCCTTAACTGAACTCAATTTCA 57.110 32.000 0.00 0.00 34.30 2.69
233 234 9.971922 CTTAACTGAACTCAATTTCAAAAGGAT 57.028 29.630 0.00 0.00 35.07 3.24
244 247 9.265901 TCAATTTCAAAAGGATAAAAATGCGAA 57.734 25.926 0.00 0.00 0.00 4.70
263 266 5.095490 GCGAAAATTCTAACATCCACTTGG 58.905 41.667 0.00 0.00 0.00 3.61
277 280 3.909995 TCCACTTGGATCTCCTTCTCAAA 59.090 43.478 0.00 0.00 39.78 2.69
279 282 5.014544 TCCACTTGGATCTCCTTCTCAAATT 59.985 40.000 0.00 0.00 39.78 1.82
280 283 5.713861 CCACTTGGATCTCCTTCTCAAATTT 59.286 40.000 0.00 0.00 37.39 1.82
285 295 4.337836 GGATCTCCTTCTCAAATTTGGAGC 59.662 45.833 17.90 7.98 42.77 4.70
294 304 4.393062 TCTCAAATTTGGAGCACGAGATTC 59.607 41.667 17.90 0.00 32.38 2.52
296 306 4.154737 TCAAATTTGGAGCACGAGATTCAG 59.845 41.667 17.90 0.00 0.00 3.02
300 310 3.170791 TGGAGCACGAGATTCAGATTC 57.829 47.619 0.00 0.00 0.00 2.52
301 311 2.762887 TGGAGCACGAGATTCAGATTCT 59.237 45.455 0.00 0.00 0.00 2.40
310 320 7.148573 GCACGAGATTCAGATTCTTAGTGAAAA 60.149 37.037 22.65 0.00 38.29 2.29
409 421 9.956720 CAATTCTTATGAACCAAACATCTATCC 57.043 33.333 0.00 0.00 34.71 2.59
410 422 9.699410 AATTCTTATGAACCAAACATCTATCCA 57.301 29.630 0.00 0.00 34.71 3.41
423 435 9.559958 CAAACATCTATCCAAAGTTGACATAAC 57.440 33.333 0.00 0.00 0.00 1.89
451 464 9.846248 CCTATGTTTGCTAATCCTATATTTTGC 57.154 33.333 0.00 0.00 0.00 3.68
455 468 6.573664 TTGCTAATCCTATATTTTGCGCAT 57.426 33.333 12.75 0.00 0.00 4.73
540 554 6.413783 AAGGAGCCTAAGAGCTTACTAATC 57.586 41.667 0.00 0.00 45.15 1.75
549 563 1.768870 AGCTTACTAATCCCGCCATGT 59.231 47.619 0.00 0.00 0.00 3.21
550 564 2.172717 AGCTTACTAATCCCGCCATGTT 59.827 45.455 0.00 0.00 0.00 2.71
560 574 3.436243 TCCCGCCATGTTTTAAAAGGAT 58.564 40.909 0.00 0.00 0.00 3.24
694 760 6.210078 GCTGTAGATTAGTATTTCAGCGTCT 58.790 40.000 0.00 0.00 37.62 4.18
699 765 6.217294 AGATTAGTATTTCAGCGTCTTAGCC 58.783 40.000 0.00 0.00 38.01 3.93
722 788 4.499188 CGATTAGCTCATTAAGGTCGACCA 60.499 45.833 35.00 16.57 38.89 4.02
730 796 0.320073 TAAGGTCGACCAAACAGGCG 60.320 55.000 35.00 0.00 43.14 5.52
734 800 3.353836 CGACCAAACAGGCGGGTG 61.354 66.667 0.00 0.00 43.14 4.61
782 851 2.029743 CCGAAGTGTTGTTGGTGGG 58.970 57.895 0.00 0.00 0.00 4.61
1014 1090 0.471191 TGATCATGGGAGATGCGCTT 59.529 50.000 9.73 0.55 0.00 4.68
1036 1112 1.657751 CGATCAGCTCCTCGTGGACA 61.658 60.000 1.10 0.00 37.46 4.02
1095 1171 2.351253 CCTATTCAGCATCCTCGAGACG 60.351 54.545 15.71 2.45 0.00 4.18
1101 1177 1.433879 CATCCTCGAGACGTGGGAC 59.566 63.158 15.71 0.00 40.35 4.46
1224 1300 4.498520 CGAGCACGGCAGGACGAT 62.499 66.667 0.00 0.00 37.61 3.73
1235 1311 1.374252 AGGACGATTGTGACGGCAC 60.374 57.895 16.50 16.50 45.35 5.01
1311 1387 1.003839 GAAGACGGCCCACATCACA 60.004 57.895 0.00 0.00 0.00 3.58
1448 1524 0.595095 CAACCTGCAGAGCTTTCCAC 59.405 55.000 17.39 0.00 0.00 4.02
1486 1562 7.751047 TCTCTACATTAATTTGAGTACGCAC 57.249 36.000 0.00 0.00 0.00 5.34
1487 1563 6.471198 TCTCTACATTAATTTGAGTACGCACG 59.529 38.462 0.00 0.00 0.00 5.34
1488 1564 6.094719 TCTACATTAATTTGAGTACGCACGT 58.905 36.000 0.00 0.00 0.00 4.49
1489 1565 4.953269 ACATTAATTTGAGTACGCACGTG 58.047 39.130 12.28 12.28 0.00 4.49
1518 1594 9.140286 CTCGATCTTTACTTGTTTAGATGTTGA 57.860 33.333 0.00 0.00 0.00 3.18
1561 1637 4.088638 CGAACTAGCCGATGATTCATTACG 59.911 45.833 0.00 0.91 0.00 3.18
1589 1679 9.999009 CACGTTCTGTAGTAGATTATCACTTAA 57.001 33.333 0.00 0.00 34.80 1.85
1607 1697 5.469760 CACTTAATGACAGTGACATCAACCA 59.530 40.000 8.54 0.00 43.90 3.67
1686 1776 4.341487 TGGTGTACTACATGTCTACAGCT 58.659 43.478 28.49 9.13 36.87 4.24
1687 1777 4.398358 TGGTGTACTACATGTCTACAGCTC 59.602 45.833 28.49 17.22 36.87 4.09
1690 1780 4.640647 TGTACTACATGTCTACAGCTCCAG 59.359 45.833 0.00 0.00 0.00 3.86
1791 1898 0.531753 GAGAGAGAAGAATGGCCCGC 60.532 60.000 0.00 0.00 0.00 6.13
1793 1900 2.897350 GAGAAGAATGGCCCGCCG 60.897 66.667 0.00 0.00 39.42 6.46
1794 1901 3.682292 GAGAAGAATGGCCCGCCGT 62.682 63.158 0.00 0.00 39.42 5.68
1843 1950 4.610333 ACTTTCTTTCTTGGAAACCCTGT 58.390 39.130 0.00 0.00 0.00 4.00
1931 2044 5.409826 GGCACTGACATATACTATGCCTTTC 59.590 44.000 5.11 0.00 46.13 2.62
1989 2102 2.567615 GTGGTGGACTACATCAAGGAGT 59.432 50.000 0.00 0.00 43.03 3.85
2192 2305 3.474570 GTCCCGATCAGCCCTGCT 61.475 66.667 0.00 0.00 40.77 4.24
2264 2377 0.896019 CGATCTCCGGCTCCACCTAT 60.896 60.000 0.00 0.00 35.61 2.57
2589 2702 3.587797 CCGTCAAGGTGTGTACATACT 57.412 47.619 20.38 6.87 34.51 2.12
2590 2703 4.707030 CCGTCAAGGTGTGTACATACTA 57.293 45.455 20.38 3.72 34.51 1.82
2591 2704 5.258456 CCGTCAAGGTGTGTACATACTAT 57.742 43.478 20.38 8.58 34.51 2.12
2592 2705 6.381481 CCGTCAAGGTGTGTACATACTATA 57.619 41.667 20.38 3.71 34.51 1.31
2593 2706 6.204359 CCGTCAAGGTGTGTACATACTATAC 58.796 44.000 20.38 12.93 34.51 1.47
2682 2805 4.760878 TGAACGTAGTAAAGGCATGCATA 58.239 39.130 21.36 6.51 45.00 3.14
2708 2833 1.888512 GACCAAACACTGCATGGACAT 59.111 47.619 10.25 0.00 37.66 3.06
2709 2834 3.081061 GACCAAACACTGCATGGACATA 58.919 45.455 10.25 0.00 37.66 2.29
2710 2835 3.696051 GACCAAACACTGCATGGACATAT 59.304 43.478 10.25 0.00 37.66 1.78
2711 2836 4.854173 ACCAAACACTGCATGGACATATA 58.146 39.130 10.25 0.00 37.66 0.86
2712 2837 4.640201 ACCAAACACTGCATGGACATATAC 59.360 41.667 10.25 0.00 37.66 1.47
2847 2982 1.348775 GGATGGCTAGCTTGGACCCT 61.349 60.000 15.72 0.00 0.00 4.34
2984 3119 9.346725 GACTAAACTGATGAAAAATGTTCCATC 57.653 33.333 0.00 0.00 36.77 3.51
3409 3729 6.822667 ATTGAACAGTGAAGATGCATGTAA 57.177 33.333 2.46 0.00 0.00 2.41
3435 3755 1.135315 CGCATGCTTAGGTTTGTGCAT 60.135 47.619 17.13 0.00 45.57 3.96
3476 3798 2.094494 TCGAAACTGAGGATGAGCTGAC 60.094 50.000 0.00 0.00 0.00 3.51
3659 3981 3.829886 TTCGTTTGGAATGCTTGCTAG 57.170 42.857 0.00 0.00 0.00 3.42
3705 4029 1.716826 CGAGTAGGTCCGACAGCTCC 61.717 65.000 4.82 0.00 33.71 4.70
3750 4074 6.790285 AATTGAAGTGAATTTTGGTGCATC 57.210 33.333 0.00 0.00 0.00 3.91
3765 4089 6.154203 TGGTGCATCAAACTCAATTGTTTA 57.846 33.333 0.00 0.00 37.98 2.01
3799 4123 4.408596 TGCCATATGGTGAACTAGTCATGA 59.591 41.667 22.79 0.00 38.90 3.07
3816 4260 0.675837 TGATTGCTGCAGAGACTGGC 60.676 55.000 20.43 0.39 31.21 4.85
3863 4307 2.423373 CCATTACCTGGCTTATGCACCT 60.423 50.000 2.72 0.00 38.47 4.00
3942 5950 2.801679 TCGGACCGTTGTTGTAAATCAC 59.198 45.455 14.79 0.00 0.00 3.06
4005 6015 5.415701 TGGACTTTGAATGCATCCTACTTTC 59.584 40.000 0.00 0.00 0.00 2.62
4028 6038 0.178068 ATACGAGGGGACACATGCAC 59.822 55.000 0.00 0.00 0.00 4.57
4079 6089 8.523658 ACCATAACAAGGAAGAAAATAGAAAGC 58.476 33.333 0.00 0.00 0.00 3.51
4094 6104 8.572855 AAATAGAAAGCTGTGCTAGAAATTCT 57.427 30.769 0.00 0.00 38.25 2.40
4104 6114 8.186821 GCTGTGCTAGAAATTCTGATAAAATGT 58.813 33.333 5.64 0.00 0.00 2.71
4117 6127 4.693566 TGATAAAATGTCCAACCAGTCGTC 59.306 41.667 0.00 0.00 0.00 4.20
4122 6132 0.458025 GTCCAACCAGTCGTCGATCC 60.458 60.000 0.00 0.00 0.00 3.36
4132 6142 3.912907 GTCGATCCGGCGGACCAT 61.913 66.667 33.71 16.84 32.98 3.55
4137 6147 0.173708 GATCCGGCGGACCATATCTC 59.826 60.000 33.71 19.28 32.98 2.75
4145 6155 3.997021 GGCGGACCATATCTCTGTTAATG 59.003 47.826 0.00 0.00 35.26 1.90
4171 6182 9.926751 GCATCATACTATCAAATCCAATAATCG 57.073 33.333 0.00 0.00 0.00 3.34
4209 6220 9.645059 ATTGTACTCATTGGATCTACATAATCG 57.355 33.333 0.00 0.00 0.00 3.34
4270 6282 7.713764 AAATGTTTAAGAGTGATTTGTTGGC 57.286 32.000 0.00 0.00 0.00 4.52
4289 6301 0.036448 CAACATGCATGGGGCCAAAA 59.964 50.000 29.41 0.00 43.89 2.44
4326 6340 4.519540 TTCTTGCCCACTATTGCTTTTC 57.480 40.909 0.00 0.00 0.00 2.29
4327 6341 2.825532 TCTTGCCCACTATTGCTTTTCC 59.174 45.455 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.056678 TCACACATGATGCCAATTTGACC 60.057 43.478 0.00 0.00 0.00 4.02
1 2 3.922240 GTCACACATGATGCCAATTTGAC 59.078 43.478 0.00 0.00 37.14 3.18
2 3 3.827876 AGTCACACATGATGCCAATTTGA 59.172 39.130 0.00 0.00 37.14 2.69
3 4 3.924073 CAGTCACACATGATGCCAATTTG 59.076 43.478 0.00 0.00 37.14 2.32
4 5 3.827876 TCAGTCACACATGATGCCAATTT 59.172 39.130 0.00 0.00 37.14 1.82
5 6 3.423749 TCAGTCACACATGATGCCAATT 58.576 40.909 0.00 0.00 37.14 2.32
6 7 3.076079 TCAGTCACACATGATGCCAAT 57.924 42.857 0.00 0.00 37.14 3.16
7 8 2.565046 TCAGTCACACATGATGCCAA 57.435 45.000 0.00 0.00 37.14 4.52
8 9 2.793288 ATCAGTCACACATGATGCCA 57.207 45.000 0.00 0.00 37.14 4.92
9 10 3.441222 TCAAATCAGTCACACATGATGCC 59.559 43.478 0.00 0.00 37.14 4.40
10 11 4.690184 TCAAATCAGTCACACATGATGC 57.310 40.909 0.00 0.00 37.14 3.91
11 12 5.578776 CCATCAAATCAGTCACACATGATG 58.421 41.667 0.00 0.00 41.28 3.07
12 13 4.097437 GCCATCAAATCAGTCACACATGAT 59.903 41.667 0.00 0.00 37.14 2.45
13 14 3.441222 GCCATCAAATCAGTCACACATGA 59.559 43.478 0.00 0.00 0.00 3.07
14 15 3.191791 TGCCATCAAATCAGTCACACATG 59.808 43.478 0.00 0.00 0.00 3.21
15 16 3.423749 TGCCATCAAATCAGTCACACAT 58.576 40.909 0.00 0.00 0.00 3.21
16 17 2.815503 CTGCCATCAAATCAGTCACACA 59.184 45.455 0.00 0.00 0.00 3.72
17 18 3.076621 TCTGCCATCAAATCAGTCACAC 58.923 45.455 0.00 0.00 0.00 3.82
18 19 3.076621 GTCTGCCATCAAATCAGTCACA 58.923 45.455 0.00 0.00 0.00 3.58
19 20 2.421424 GGTCTGCCATCAAATCAGTCAC 59.579 50.000 0.00 0.00 34.09 3.67
20 21 2.715046 GGTCTGCCATCAAATCAGTCA 58.285 47.619 0.00 0.00 34.09 3.41
21 22 1.667724 CGGTCTGCCATCAAATCAGTC 59.332 52.381 0.00 0.00 34.09 3.51
22 23 1.679944 CCGGTCTGCCATCAAATCAGT 60.680 52.381 0.00 0.00 34.09 3.41
23 24 1.019673 CCGGTCTGCCATCAAATCAG 58.980 55.000 0.00 0.00 34.09 2.90
24 25 0.617935 TCCGGTCTGCCATCAAATCA 59.382 50.000 0.00 0.00 34.09 2.57
25 26 1.401905 GTTCCGGTCTGCCATCAAATC 59.598 52.381 0.00 0.00 34.09 2.17
26 27 1.271871 TGTTCCGGTCTGCCATCAAAT 60.272 47.619 0.00 0.00 34.09 2.32
27 28 0.109532 TGTTCCGGTCTGCCATCAAA 59.890 50.000 0.00 0.00 34.09 2.69
28 29 0.605319 GTGTTCCGGTCTGCCATCAA 60.605 55.000 0.00 0.00 34.09 2.57
29 30 1.003839 GTGTTCCGGTCTGCCATCA 60.004 57.895 0.00 0.00 34.09 3.07
30 31 1.745489 GGTGTTCCGGTCTGCCATC 60.745 63.158 0.00 0.00 34.09 3.51
31 32 2.351276 GGTGTTCCGGTCTGCCAT 59.649 61.111 0.00 0.00 34.09 4.40
32 33 3.948719 GGGTGTTCCGGTCTGCCA 61.949 66.667 0.00 0.00 34.09 4.92
50 51 4.275936 ACCCATATTGTAATTCGCTCAAGC 59.724 41.667 0.00 0.00 37.78 4.01
51 52 6.377327 AACCCATATTGTAATTCGCTCAAG 57.623 37.500 0.00 0.00 0.00 3.02
52 53 7.867305 TTAACCCATATTGTAATTCGCTCAA 57.133 32.000 0.00 0.00 0.00 3.02
53 54 7.040755 CCATTAACCCATATTGTAATTCGCTCA 60.041 37.037 0.00 0.00 0.00 4.26
54 55 7.305474 CCATTAACCCATATTGTAATTCGCTC 58.695 38.462 0.00 0.00 0.00 5.03
55 56 6.294508 GCCATTAACCCATATTGTAATTCGCT 60.295 38.462 0.00 0.00 0.00 4.93
56 57 5.861787 GCCATTAACCCATATTGTAATTCGC 59.138 40.000 0.00 0.00 0.00 4.70
57 58 7.040755 TGAGCCATTAACCCATATTGTAATTCG 60.041 37.037 0.00 0.00 0.00 3.34
58 59 8.177119 TGAGCCATTAACCCATATTGTAATTC 57.823 34.615 0.00 0.00 0.00 2.17
59 60 8.725606 ATGAGCCATTAACCCATATTGTAATT 57.274 30.769 0.00 0.00 0.00 1.40
60 61 8.725606 AATGAGCCATTAACCCATATTGTAAT 57.274 30.769 0.00 0.00 31.77 1.89
61 62 8.420222 CAAATGAGCCATTAACCCATATTGTAA 58.580 33.333 1.52 0.00 32.43 2.41
72 73 9.646427 TTAATTTGTACCAAATGAGCCATTAAC 57.354 29.630 3.17 0.70 32.43 2.01
85 86 8.696374 TGTCAACATTCCTTTAATTTGTACCAA 58.304 29.630 0.00 0.00 0.00 3.67
152 153 6.392625 TCCGTTGAACCAAAAACATGAATA 57.607 33.333 0.00 0.00 0.00 1.75
153 154 5.269505 TCCGTTGAACCAAAAACATGAAT 57.730 34.783 0.00 0.00 0.00 2.57
154 155 4.720649 TCCGTTGAACCAAAAACATGAA 57.279 36.364 0.00 0.00 0.00 2.57
156 157 5.277250 CCAATTCCGTTGAACCAAAAACATG 60.277 40.000 0.00 0.00 40.37 3.21
157 158 4.813697 CCAATTCCGTTGAACCAAAAACAT 59.186 37.500 0.00 0.00 40.37 2.71
158 159 4.081642 TCCAATTCCGTTGAACCAAAAACA 60.082 37.500 0.00 0.00 40.37 2.83
159 160 4.269123 GTCCAATTCCGTTGAACCAAAAAC 59.731 41.667 0.00 0.00 40.37 2.43
171 172 5.700373 CCATTTTTCATTTGTCCAATTCCGT 59.300 36.000 0.00 0.00 0.00 4.69
172 173 5.931146 TCCATTTTTCATTTGTCCAATTCCG 59.069 36.000 0.00 0.00 0.00 4.30
173 174 6.372381 CCTCCATTTTTCATTTGTCCAATTCC 59.628 38.462 0.00 0.00 0.00 3.01
182 183 7.666804 AGGGAAAATTCCTCCATTTTTCATTTG 59.333 33.333 11.75 0.00 46.72 2.32
186 187 6.762077 AAGGGAAAATTCCTCCATTTTTCA 57.238 33.333 11.75 0.00 46.72 2.69
187 188 8.375506 AGTTAAGGGAAAATTCCTCCATTTTTC 58.624 33.333 11.75 0.00 46.72 2.29
201 202 8.299990 TGAAATTGAGTTCAGTTAAGGGAAAA 57.700 30.769 0.00 0.00 32.56 2.29
205 206 7.653311 CCTTTTGAAATTGAGTTCAGTTAAGGG 59.347 37.037 15.92 7.09 38.69 3.95
216 217 8.711457 CGCATTTTTATCCTTTTGAAATTGAGT 58.289 29.630 0.00 0.00 0.00 3.41
217 218 8.924691 TCGCATTTTTATCCTTTTGAAATTGAG 58.075 29.630 0.00 0.00 0.00 3.02
219 220 9.875675 TTTCGCATTTTTATCCTTTTGAAATTG 57.124 25.926 0.00 0.00 0.00 2.32
233 234 9.134734 GTGGATGTTAGAATTTTCGCATTTTTA 57.865 29.630 0.00 0.00 0.00 1.52
239 242 5.335583 CCAAGTGGATGTTAGAATTTTCGCA 60.336 40.000 0.00 0.00 37.39 5.10
263 266 4.946157 TGCTCCAAATTTGAGAAGGAGATC 59.054 41.667 19.86 6.08 46.89 2.75
264 267 4.704057 GTGCTCCAAATTTGAGAAGGAGAT 59.296 41.667 19.86 0.00 46.89 2.75
265 268 4.074970 GTGCTCCAAATTTGAGAAGGAGA 58.925 43.478 19.86 5.43 46.89 3.71
267 270 2.813754 CGTGCTCCAAATTTGAGAAGGA 59.186 45.455 19.86 11.59 0.00 3.36
269 272 3.748048 TCTCGTGCTCCAAATTTGAGAAG 59.252 43.478 19.86 13.72 0.00 2.85
271 274 3.401033 TCTCGTGCTCCAAATTTGAGA 57.599 42.857 19.86 13.23 0.00 3.27
272 275 4.154737 TGAATCTCGTGCTCCAAATTTGAG 59.845 41.667 19.86 14.70 0.00 3.02
273 276 4.071423 TGAATCTCGTGCTCCAAATTTGA 58.929 39.130 19.86 5.10 0.00 2.69
274 277 4.154737 TCTGAATCTCGTGCTCCAAATTTG 59.845 41.667 11.40 11.40 0.00 2.32
277 280 3.616956 TCTGAATCTCGTGCTCCAAAT 57.383 42.857 0.00 0.00 0.00 2.32
279 282 3.196469 AGAATCTGAATCTCGTGCTCCAA 59.804 43.478 0.00 0.00 0.00 3.53
280 283 2.762887 AGAATCTGAATCTCGTGCTCCA 59.237 45.455 0.00 0.00 0.00 3.86
285 295 7.818493 TTTCACTAAGAATCTGAATCTCGTG 57.182 36.000 14.23 14.23 35.83 4.35
388 398 8.960591 ACTTTGGATAGATGTTTGGTTCATAAG 58.039 33.333 0.00 0.00 0.00 1.73
389 399 8.877864 ACTTTGGATAGATGTTTGGTTCATAA 57.122 30.769 0.00 0.00 0.00 1.90
392 404 6.775142 TCAACTTTGGATAGATGTTTGGTTCA 59.225 34.615 0.00 0.00 0.00 3.18
434 446 6.611381 TGAATGCGCAAAATATAGGATTAGC 58.389 36.000 17.11 0.00 0.00 3.09
481 494 7.173047 GGATTCTAAAAATGCCTGAAAAGCAAA 59.827 33.333 0.00 0.00 44.83 3.68
482 495 6.650390 GGATTCTAAAAATGCCTGAAAAGCAA 59.350 34.615 0.00 0.00 44.83 3.91
483 496 6.014327 AGGATTCTAAAAATGCCTGAAAAGCA 60.014 34.615 0.00 0.00 45.94 3.91
484 497 6.312180 CAGGATTCTAAAAATGCCTGAAAAGC 59.688 38.462 0.00 0.00 44.27 3.51
485 498 7.330208 CACAGGATTCTAAAAATGCCTGAAAAG 59.670 37.037 13.09 0.00 44.27 2.27
487 500 6.493115 TCACAGGATTCTAAAAATGCCTGAAA 59.507 34.615 13.09 0.00 44.27 2.69
488 501 6.009589 TCACAGGATTCTAAAAATGCCTGAA 58.990 36.000 13.09 0.00 44.27 3.02
491 504 5.185828 GGTTCACAGGATTCTAAAAATGCCT 59.814 40.000 0.00 0.00 0.00 4.75
492 505 5.047377 TGGTTCACAGGATTCTAAAAATGCC 60.047 40.000 0.00 0.00 0.00 4.40
494 507 7.599998 CCTTTGGTTCACAGGATTCTAAAAATG 59.400 37.037 0.00 0.00 33.52 2.32
495 508 7.508977 TCCTTTGGTTCACAGGATTCTAAAAAT 59.491 33.333 0.00 0.00 35.68 1.82
540 554 3.885724 ATCCTTTTAAAACATGGCGGG 57.114 42.857 0.00 0.00 0.00 6.13
608 622 8.023706 GGTCAAATGAAAATCACTAGAGGTTTC 58.976 37.037 0.00 3.78 34.60 2.78
617 669 7.439056 GTGTTGATTGGTCAAATGAAAATCACT 59.561 33.333 16.43 0.00 45.38 3.41
618 670 7.224362 TGTGTTGATTGGTCAAATGAAAATCAC 59.776 33.333 16.43 13.39 45.38 3.06
619 671 7.224362 GTGTGTTGATTGGTCAAATGAAAATCA 59.776 33.333 14.25 14.25 45.38 2.57
620 672 7.439056 AGTGTGTTGATTGGTCAAATGAAAATC 59.561 33.333 10.80 10.80 45.38 2.17
673 735 7.326547 GGCTAAGACGCTGAAATACTAATCTAC 59.673 40.741 0.00 0.00 0.00 2.59
674 736 7.368833 GGCTAAGACGCTGAAATACTAATCTA 58.631 38.462 0.00 0.00 0.00 1.98
675 737 6.217294 GGCTAAGACGCTGAAATACTAATCT 58.783 40.000 0.00 0.00 0.00 2.40
676 738 5.117287 CGGCTAAGACGCTGAAATACTAATC 59.883 44.000 0.00 0.00 38.57 1.75
681 743 2.805845 TCGGCTAAGACGCTGAAATAC 58.194 47.619 0.00 0.00 42.01 1.89
694 760 5.539048 GACCTTAATGAGCTAATCGGCTAA 58.461 41.667 0.00 0.00 43.20 3.09
699 765 3.982058 GGTCGACCTTAATGAGCTAATCG 59.018 47.826 27.64 0.00 0.00 3.34
730 796 1.445582 CAACTCGAGGCGTACACCC 60.446 63.158 18.41 0.00 0.00 4.61
734 800 1.660560 TAGGGCAACTCGAGGCGTAC 61.661 60.000 18.41 3.99 0.00 3.67
903 975 1.742831 TGTTGTGTGCAAGTGGAAGAC 59.257 47.619 0.00 0.00 34.94 3.01
994 1070 0.035036 AGCGCATCTCCCATGATCAG 59.965 55.000 11.47 0.00 0.00 2.90
1014 1090 1.153765 CACGAGGAGCTGATCGCAA 60.154 57.895 15.19 0.00 42.61 4.85
1036 1112 2.490217 CTGGAACTCGCCGTCGAT 59.510 61.111 0.00 0.00 44.56 3.59
1176 1252 1.291877 CTTTGTTCCCCGACGCAGAG 61.292 60.000 0.00 0.00 0.00 3.35
1183 1259 2.282180 GCTGCCTTTGTTCCCCGA 60.282 61.111 0.00 0.00 0.00 5.14
1212 1288 1.374252 GTCACAATCGTCCTGCCGT 60.374 57.895 0.00 0.00 0.00 5.68
1248 1324 0.108615 GCGAGCACTTCTGCCTCTTA 60.109 55.000 0.00 0.00 45.53 2.10
1431 1507 0.475906 AAGTGGAAAGCTCTGCAGGT 59.524 50.000 15.13 0.00 0.00 4.00
1438 1514 8.425703 AGATAAATAGGTAGAAGTGGAAAGCTC 58.574 37.037 0.00 0.00 0.00 4.09
1484 1560 5.152097 ACAAGTAAAGATCGAGTACACGTG 58.848 41.667 15.48 15.48 34.70 4.49
1485 1561 5.368256 ACAAGTAAAGATCGAGTACACGT 57.632 39.130 12.42 0.40 34.70 4.49
1486 1562 6.686130 AAACAAGTAAAGATCGAGTACACG 57.314 37.500 6.34 6.34 0.00 4.49
1487 1563 8.961294 TCTAAACAAGTAAAGATCGAGTACAC 57.039 34.615 0.00 0.00 0.00 2.90
1488 1564 9.569167 CATCTAAACAAGTAAAGATCGAGTACA 57.431 33.333 0.00 0.00 0.00 2.90
1489 1565 9.570488 ACATCTAAACAAGTAAAGATCGAGTAC 57.430 33.333 0.00 0.00 0.00 2.73
1518 1594 6.320418 AGTTCGTTAGTTGACCCAAAAAGAAT 59.680 34.615 0.00 0.00 0.00 2.40
1561 1637 5.686397 GTGATAATCTACTACAGAACGTGGC 59.314 44.000 0.00 0.00 36.67 5.01
1589 1679 2.106338 TGGTGGTTGATGTCACTGTCAT 59.894 45.455 0.00 0.00 34.57 3.06
1607 1697 1.210478 CCAACGAGGAAGATCCATGGT 59.790 52.381 12.58 0.00 39.61 3.55
1768 1873 3.133003 CGGGCCATTCTTCTCTCTCTAAA 59.867 47.826 4.39 0.00 0.00 1.85
1769 1874 2.695666 CGGGCCATTCTTCTCTCTCTAA 59.304 50.000 4.39 0.00 0.00 2.10
1770 1875 2.311463 CGGGCCATTCTTCTCTCTCTA 58.689 52.381 4.39 0.00 0.00 2.43
1791 1898 1.948145 ACTCATCGGTTAGCTAGACGG 59.052 52.381 16.01 11.29 0.00 4.79
1793 1900 3.564644 TGCTACTCATCGGTTAGCTAGAC 59.435 47.826 0.00 0.00 35.05 2.59
1794 1901 3.816994 TGCTACTCATCGGTTAGCTAGA 58.183 45.455 0.00 0.00 35.05 2.43
1931 2044 1.952367 GCTTGGTCACCCTGATCCAAG 60.952 57.143 19.12 19.12 46.44 3.61
1989 2102 0.664761 GACTGCTTCACTTGCTGCAA 59.335 50.000 15.16 15.16 34.90 4.08
2018 2131 2.177778 GCCTTGCGCTGCTTCTTC 59.822 61.111 9.73 0.00 0.00 2.87
2264 2377 4.077184 GTCATCGCCGGGGACACA 62.077 66.667 25.09 7.60 0.00 3.72
2626 2748 2.039084 AGGGGAAGTAAGACAACTGCTG 59.961 50.000 0.00 0.00 0.00 4.41
2682 2805 0.106268 TGCAGTGTTTGGTCCCATGT 60.106 50.000 0.00 0.00 0.00 3.21
2708 2833 9.578576 TCCTCTTCGGCTTTAATTAGTAGTATA 57.421 33.333 0.00 0.00 0.00 1.47
2709 2834 8.358895 GTCCTCTTCGGCTTTAATTAGTAGTAT 58.641 37.037 0.00 0.00 0.00 2.12
2710 2835 7.201857 GGTCCTCTTCGGCTTTAATTAGTAGTA 60.202 40.741 0.00 0.00 0.00 1.82
2711 2836 6.406737 GGTCCTCTTCGGCTTTAATTAGTAGT 60.407 42.308 0.00 0.00 0.00 2.73
2712 2837 5.984323 GGTCCTCTTCGGCTTTAATTAGTAG 59.016 44.000 0.00 0.00 0.00 2.57
2818 2953 0.462047 CTAGCCATCCAACCCACGTC 60.462 60.000 0.00 0.00 0.00 4.34
2847 2982 4.380843 TCCCTATTTTGAAGCTTGGTCA 57.619 40.909 2.10 0.00 0.00 4.02
2988 3123 9.199982 CTGCTCACATTTTTCATCAGTTTTTAT 57.800 29.630 0.00 0.00 0.00 1.40
2989 3124 7.169645 GCTGCTCACATTTTTCATCAGTTTTTA 59.830 33.333 0.00 0.00 0.00 1.52
3124 3393 4.880120 TCGAGGGTGTATATATAGCTTCCG 59.120 45.833 12.90 11.07 0.00 4.30
3131 3400 6.096423 GCTGTGGAATCGAGGGTGTATATATA 59.904 42.308 0.00 0.00 0.00 0.86
3171 3443 2.283839 CGAGCAATGCATTTTAAACGCG 60.284 45.455 9.83 3.53 0.00 6.01
3297 3604 2.225019 CGTTTGCTGAATCTCTTGCACT 59.775 45.455 0.00 0.00 35.01 4.40
3409 3729 3.756434 ACAAACCTAAGCATGCGTAACAT 59.244 39.130 13.01 0.00 40.66 2.71
3422 3742 3.020274 ACACACACATGCACAAACCTAA 58.980 40.909 0.00 0.00 0.00 2.69
3435 3755 4.758165 TCGATCTTACTAGACACACACACA 59.242 41.667 0.00 0.00 31.99 3.72
3436 3756 5.292671 TCGATCTTACTAGACACACACAC 57.707 43.478 0.00 0.00 31.99 3.82
3476 3798 2.436646 ATTCAAGTGCCCGGCTCG 60.437 61.111 11.61 0.00 0.00 5.03
3659 3981 5.807011 CCATACAAGGCAAAATTCAAGCTAC 59.193 40.000 0.00 0.00 0.00 3.58
3705 4029 3.341823 AGATGTTACCTGCAAGCTGAAG 58.658 45.455 0.16 0.00 0.00 3.02
3750 4074 9.586435 AAAAGAAGAGGTAAACAATTGAGTTTG 57.414 29.630 13.59 0.00 41.48 2.93
3765 4089 4.019174 CACCATATGGCAAAAGAAGAGGT 58.981 43.478 22.18 0.00 39.32 3.85
3799 4123 0.392729 GAGCCAGTCTCTGCAGCAAT 60.393 55.000 9.47 0.00 38.78 3.56
3863 4307 5.479306 GCAGGAAATTAGTCAGTCTGTACA 58.521 41.667 0.00 0.00 0.00 2.90
3942 5950 6.369890 CGATCTATTCTACAACCCATCCATTG 59.630 42.308 0.00 0.00 0.00 2.82
4005 6015 2.671351 GCATGTGTCCCCTCGTATATCG 60.671 54.545 0.00 0.00 41.41 2.92
4015 6025 0.178068 AGATACGTGCATGTGTCCCC 59.822 55.000 26.54 8.25 31.04 4.81
4017 6027 3.983988 CAGATAGATACGTGCATGTGTCC 59.016 47.826 26.54 14.86 31.04 4.02
4054 6064 8.743714 AGCTTTCTATTTTCTTCCTTGTTATGG 58.256 33.333 0.00 0.00 0.00 2.74
4067 6077 9.283420 GAATTTCTAGCACAGCTTTCTATTTTC 57.717 33.333 0.00 0.00 40.44 2.29
4071 6081 7.334090 TCAGAATTTCTAGCACAGCTTTCTAT 58.666 34.615 0.00 0.00 40.44 1.98
4079 6089 9.713740 GACATTTTATCAGAATTTCTAGCACAG 57.286 33.333 0.00 0.00 0.00 3.66
4094 6104 4.647611 ACGACTGGTTGGACATTTTATCA 58.352 39.130 0.00 0.00 0.00 2.15
4104 6114 1.888018 GGATCGACGACTGGTTGGA 59.112 57.895 0.00 0.00 0.00 3.53
4117 6127 1.153823 GATATGGTCCGCCGGATCG 60.154 63.158 10.04 0.00 35.15 3.69
4122 6132 0.389391 AACAGAGATATGGTCCGCCG 59.611 55.000 0.00 0.00 37.67 6.46
4145 6155 9.926751 CGATTATTGGATTTGATAGTATGATGC 57.073 33.333 0.00 0.00 0.00 3.91
4184 6195 8.638873 ACGATTATGTAGATCCAATGAGTACAA 58.361 33.333 0.00 0.00 31.30 2.41
4185 6196 8.178313 ACGATTATGTAGATCCAATGAGTACA 57.822 34.615 0.00 0.00 31.78 2.90
4245 6256 7.768120 TGCCAACAAATCACTCTTAAACATTTT 59.232 29.630 0.00 0.00 0.00 1.82
4267 6279 3.392243 GCCCCATGCATGTTGCCA 61.392 61.111 24.58 0.00 44.23 4.92
4268 6280 4.165486 GGCCCCATGCATGTTGCC 62.165 66.667 29.78 29.78 44.23 4.52
4270 6282 0.036448 TTTTGGCCCCATGCATGTTG 59.964 50.000 24.58 15.80 43.89 3.33
4289 6301 6.183361 TGGGCAAGAATGAGAATTTTCCTTTT 60.183 34.615 0.00 0.00 0.00 2.27
4296 6308 6.628844 GCAATAGTGGGCAAGAATGAGAATTT 60.629 38.462 0.00 0.00 0.00 1.82
4303 6315 4.460948 AAAGCAATAGTGGGCAAGAATG 57.539 40.909 0.00 0.00 0.00 2.67
4304 6316 4.081476 GGAAAAGCAATAGTGGGCAAGAAT 60.081 41.667 0.00 0.00 0.00 2.40
4305 6317 3.258123 GGAAAAGCAATAGTGGGCAAGAA 59.742 43.478 0.00 0.00 0.00 2.52
4306 6318 2.825532 GGAAAAGCAATAGTGGGCAAGA 59.174 45.455 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.