Multiple sequence alignment - TraesCS6B01G331500

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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 TraesCS6B01G331500 chr6B 100.000 4520 0 0 1 4520 582829221 582824702 0.000000e+00 8347.0
1 TraesCS6B01G331500 chr6B 80.788 406 50 10 328 720 482469785 482469395 4.420000e-75 292.0
2 TraesCS6B01G331500 chr6B 80.519 154 23 6 139 289 437841982 437842131 1.330000e-20 111.0
3 TraesCS6B01G331500 chr6D 90.787 4255 202 78 328 4520 389587411 389583285 0.000000e+00 5511.0
4 TraesCS6B01G331500 chr6D 82.857 385 45 6 328 701 337846903 337847277 4.360000e-85 326.0
5 TraesCS6B01G331500 chr6D 80.513 390 50 9 328 701 398237524 398237903 4.450000e-70 276.0
6 TraesCS6B01G331500 chr6D 78.233 317 34 16 330 634 11576029 11576322 2.160000e-38 171.0
7 TraesCS6B01G331500 chr6D 76.382 199 35 6 141 334 464167249 464167058 3.720000e-16 97.1
8 TraesCS6B01G331500 chr6A 92.409 3886 151 50 674 4520 535980410 535976630 0.000000e+00 5409.0
9 TraesCS6B01G331500 chr6A 80.665 331 45 8 25 338 535981164 535980836 5.840000e-59 239.0
10 TraesCS6B01G331500 chr6A 88.312 77 9 0 1881 1957 424798817 424798893 4.810000e-15 93.5
11 TraesCS6B01G331500 chr7D 80.247 567 78 21 174 717 386762540 386763095 3.280000e-106 396.0
12 TraesCS6B01G331500 chr7D 87.821 312 36 2 2374 2684 136471064 136470754 9.240000e-97 364.0
13 TraesCS6B01G331500 chr7D 79.006 362 66 6 328 689 258233467 258233818 5.840000e-59 239.0
14 TraesCS6B01G331500 chr7A 88.141 312 35 2 2374 2684 136172659 136172349 1.990000e-98 370.0
15 TraesCS6B01G331500 chr7B 87.619 315 37 2 2371 2684 99630433 99630746 9.240000e-97 364.0
16 TraesCS6B01G331500 chr4A 83.733 375 48 4 328 701 537537604 537537242 4.330000e-90 342.0
17 TraesCS6B01G331500 chr4A 77.397 146 29 4 177 321 136637650 136637508 2.900000e-12 84.2
18 TraesCS6B01G331500 chr3B 83.611 360 46 4 342 701 3265224 3264878 4.360000e-85 326.0
19 TraesCS6B01G331500 chr3B 88.889 45 5 0 2404 2448 117553110 117553066 6.320000e-04 56.5
20 TraesCS6B01G331500 chr2D 82.597 385 46 7 328 701 617956680 617956306 2.030000e-83 320.0
21 TraesCS6B01G331500 chr2D 80.000 225 23 6 489 702 609467797 609468010 3.640000e-31 147.0
22 TraesCS6B01G331500 chr2D 100.000 30 0 0 3660 3689 80684636 80684607 6.320000e-04 56.5
23 TraesCS6B01G331500 chr1B 85.266 319 31 12 330 634 431405233 431405549 9.440000e-82 315.0
24 TraesCS6B01G331500 chr1B 81.551 374 57 4 328 699 618552585 618552222 9.510000e-77 298.0
25 TraesCS6B01G331500 chr4D 82.480 371 42 8 342 701 58273964 58274322 2.040000e-78 303.0
26 TraesCS6B01G331500 chr4D 81.673 251 24 12 463 702 464851506 464851745 5.970000e-44 189.0
27 TraesCS6B01G331500 chr3D 80.519 385 54 6 328 701 374036362 374035988 4.450000e-70 276.0
28 TraesCS6B01G331500 chr3D 93.333 45 3 0 2404 2448 71495604 71495560 2.920000e-07 67.6
29 TraesCS6B01G331500 chr4B 77.180 539 70 20 139 634 125424399 125424927 9.640000e-67 265.0
30 TraesCS6B01G331500 chr4B 79.149 235 29 9 467 701 393402918 393402704 1.310000e-30 145.0
31 TraesCS6B01G331500 chr5A 77.528 267 37 10 447 701 513963265 513963520 6.100000e-29 139.0
32 TraesCS6B01G331500 chr5B 76.471 272 40 14 444 702 489471195 489471455 4.750000e-25 126.0
33 TraesCS6B01G331500 chrUn 85.246 61 8 1 2390 2449 9982666 9982726 1.360000e-05 62.1
34 TraesCS6B01G331500 chr2B 100.000 30 0 0 3660 3689 132331153 132331124 6.320000e-04 56.5


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 TraesCS6B01G331500 chr6B 582824702 582829221 4519 True 8347 8347 100.000 1 4520 1 chr6B.!!$R2 4519
1 TraesCS6B01G331500 chr6D 389583285 389587411 4126 True 5511 5511 90.787 328 4520 1 chr6D.!!$R1 4192
2 TraesCS6B01G331500 chr6A 535976630 535981164 4534 True 2824 5409 86.537 25 4520 2 chr6A.!!$R1 4495
3 TraesCS6B01G331500 chr7D 386762540 386763095 555 False 396 396 80.247 174 717 1 chr7D.!!$F2 543
4 TraesCS6B01G331500 chr4B 125424399 125424927 528 False 265 265 77.180 139 634 1 chr4B.!!$F1 495

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
558 613 0.038526 GTCAAGCCGACTCCGAAAGA 60.039 55.0 0.00 0.00 41.81 2.52 F
1221 1525 0.108329 GTGCGTTCCCTTGCTAGCTA 60.108 55.0 17.23 7.59 0.00 3.32 F
1422 1731 0.035820 GGGGGAGAAATGTGCACGTA 60.036 55.0 12.96 0.00 0.00 3.57 F
2727 3054 0.242825 TCGACCACGAGTAAGCCAAG 59.757 55.0 0.00 0.00 43.81 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1731 0.031585 ACGAGCACACACACATACGT 59.968 50.000 0.0 0.0 0.00 3.57 R
3000 3327 0.250467 TCTTGGTCAGCCAGCAGAAC 60.250 55.000 0.0 0.0 46.91 3.01 R
3206 3533 1.149148 GGTCCAGCGACAGTTCTTTC 58.851 55.000 0.0 0.0 41.13 2.62 R
3592 3925 1.070134 GTTGAAAAACCTTCAGCCCCC 59.930 52.381 0.0 0.0 0.00 5.40 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
110 111 1.152440 CATCGTAGGCTCCCTCCCT 60.152 63.158 0.00 0.00 34.61 4.20
113 114 1.381327 CGTAGGCTCCCTCCCTGAA 60.381 63.158 0.00 0.00 34.61 3.02
117 118 0.551131 AGGCTCCCTCCCTGAACAAT 60.551 55.000 0.00 0.00 0.00 2.71
118 119 0.106967 GGCTCCCTCCCTGAACAATC 60.107 60.000 0.00 0.00 0.00 2.67
119 120 0.462759 GCTCCCTCCCTGAACAATCG 60.463 60.000 0.00 0.00 0.00 3.34
126 131 1.351017 TCCCTGAACAATCGGCTTCTT 59.649 47.619 0.00 0.00 0.00 2.52
136 141 3.923017 ATCGGCTTCTTGTTTTCCTTG 57.077 42.857 0.00 0.00 0.00 3.61
161 176 1.478916 GCTAGGGCGAACTCTTCTCTT 59.521 52.381 0.00 0.00 0.00 2.85
170 185 4.375506 GCGAACTCTTCTCTTCAAACTTCG 60.376 45.833 0.00 0.00 0.00 3.79
193 208 2.202610 CGAGCTCGTGGATTCGCA 60.203 61.111 27.79 0.00 34.11 5.10
214 229 2.680913 CCCTCTGCTTGCCGTTTCG 61.681 63.158 0.00 0.00 0.00 3.46
237 254 4.426313 GGTGGCGGGGAGGGAAAG 62.426 72.222 0.00 0.00 0.00 2.62
274 291 7.034397 CACTCTGGTTAGTAGTTTAGGTTAGC 58.966 42.308 0.00 0.00 0.00 3.09
297 314 2.248280 TTTTAGTCCTCGCAAGTGCA 57.752 45.000 3.87 0.00 42.21 4.57
306 323 1.957695 CGCAAGTGCAGTGCTCAGA 60.958 57.895 17.60 0.00 42.21 3.27
309 326 1.302366 CAAGTGCAGTGCTCAGACAA 58.698 50.000 17.60 0.00 0.00 3.18
322 339 1.153168 AGACAAATGGCGGCGCTAT 60.153 52.632 32.30 28.90 0.00 2.97
379 426 0.575390 CTACGGCGTAAATTCCTGCG 59.425 55.000 21.32 1.95 0.00 5.18
383 430 1.712018 GGCGTAAATTCCTGCGGTCC 61.712 60.000 0.00 0.00 0.00 4.46
411 460 3.006644 GGACGGTGAGGTTAGAGTTTCTT 59.993 47.826 0.00 0.00 0.00 2.52
433 482 1.339610 TCTTGTGGCGAAATTTGGTGG 59.660 47.619 0.00 0.00 0.00 4.61
442 491 0.681175 AAATTTGGTGGCAGGTGCTC 59.319 50.000 1.26 0.00 41.70 4.26
535 584 0.537188 ACTTTCCGGCTGTCATCGAT 59.463 50.000 0.00 0.00 0.00 3.59
558 613 0.038526 GTCAAGCCGACTCCGAAAGA 60.039 55.000 0.00 0.00 41.81 2.52
568 634 4.129737 CCGAAAGAGGAGCGGCGA 62.130 66.667 12.98 0.00 38.46 5.54
570 636 2.261671 GAAAGAGGAGCGGCGACA 59.738 61.111 12.98 0.00 0.00 4.35
598 664 0.676466 TTCTGGCGGCAATAGTGGTG 60.676 55.000 14.48 0.00 0.00 4.17
671 959 4.388485 TCAAGATGCTTTGTACTTCTGCA 58.612 39.130 0.00 0.20 38.05 4.41
750 1047 3.679502 GCCCGTTCATTCATTTTTGAAGG 59.320 43.478 0.00 0.00 37.44 3.46
884 1181 2.923619 GGGGGAGGAAGAAGAGAGG 58.076 63.158 0.00 0.00 0.00 3.69
889 1186 3.330998 GGGGAGGAAGAAGAGAGGAAAAA 59.669 47.826 0.00 0.00 0.00 1.94
911 1208 0.796927 GGAGCTGCCTTTTACGACAC 59.203 55.000 0.00 0.00 0.00 3.67
1217 1521 2.047655 CGGTGCGTTCCCTTGCTA 60.048 61.111 0.00 0.00 0.00 3.49
1221 1525 0.108329 GTGCGTTCCCTTGCTAGCTA 60.108 55.000 17.23 7.59 0.00 3.32
1267 1576 0.868406 CTCTGTTTCTGACGGTTGCC 59.132 55.000 0.00 0.00 36.00 4.52
1268 1577 0.468226 TCTGTTTCTGACGGTTGCCT 59.532 50.000 0.00 0.00 36.00 4.75
1274 1583 1.071471 CTGACGGTTGCCTGGTCTT 59.929 57.895 0.00 0.00 0.00 3.01
1279 1588 1.237285 CGGTTGCCTGGTCTTCTTGG 61.237 60.000 0.00 0.00 0.00 3.61
1315 1624 0.597898 GAGAAATACGGCGAGAGGGC 60.598 60.000 16.62 0.00 37.98 5.19
1394 1703 1.590610 GCGTCTCAGGTGAGCTCTCA 61.591 60.000 16.19 0.00 41.80 3.27
1398 1707 1.102154 CTCAGGTGAGCTCTCATCGT 58.898 55.000 16.19 2.14 45.06 3.73
1402 1711 3.070018 CAGGTGAGCTCTCATCGTTTTT 58.930 45.455 16.19 0.00 45.06 1.94
1406 1715 1.740025 GAGCTCTCATCGTTTTTGGGG 59.260 52.381 6.43 0.00 0.00 4.96
1409 1718 2.359900 CTCTCATCGTTTTTGGGGGAG 58.640 52.381 0.00 0.00 0.00 4.30
1411 1720 2.373836 TCTCATCGTTTTTGGGGGAGAA 59.626 45.455 0.00 0.00 0.00 2.87
1412 1721 3.153919 CTCATCGTTTTTGGGGGAGAAA 58.846 45.455 0.00 0.00 0.00 2.52
1417 1726 2.766313 GTTTTTGGGGGAGAAATGTGC 58.234 47.619 0.00 0.00 0.00 4.57
1420 1729 0.893270 TTGGGGGAGAAATGTGCACG 60.893 55.000 13.13 0.00 0.00 5.34
1421 1730 1.303317 GGGGGAGAAATGTGCACGT 60.303 57.895 13.13 9.52 0.00 4.49
1422 1731 0.035820 GGGGGAGAAATGTGCACGTA 60.036 55.000 12.96 0.00 0.00 3.57
1423 1732 1.084289 GGGGAGAAATGTGCACGTAC 58.916 55.000 12.96 9.82 0.00 3.67
1424 1733 0.719465 GGGAGAAATGTGCACGTACG 59.281 55.000 12.96 15.01 0.00 3.67
1425 1734 1.425412 GGAGAAATGTGCACGTACGT 58.575 50.000 16.72 16.72 0.00 3.57
1426 1735 2.598589 GGAGAAATGTGCACGTACGTA 58.401 47.619 22.34 5.72 0.00 3.57
1427 1736 3.184541 GGAGAAATGTGCACGTACGTAT 58.815 45.455 22.34 8.17 0.00 3.06
1428 1737 3.000078 GGAGAAATGTGCACGTACGTATG 60.000 47.826 22.34 13.27 0.00 2.39
1429 1738 3.581755 AGAAATGTGCACGTACGTATGT 58.418 40.909 22.34 14.70 0.00 2.29
1430 1739 3.366724 AGAAATGTGCACGTACGTATGTG 59.633 43.478 33.70 33.70 44.10 3.21
1431 1740 2.357327 ATGTGCACGTACGTATGTGT 57.643 45.000 35.88 21.26 43.38 3.72
1432 1741 1.410402 TGTGCACGTACGTATGTGTG 58.590 50.000 35.88 26.26 43.38 3.82
1433 1742 1.269154 TGTGCACGTACGTATGTGTGT 60.269 47.619 35.88 13.57 43.38 3.72
1434 1743 1.123576 GTGCACGTACGTATGTGTGTG 59.876 52.381 35.88 22.41 43.38 3.82
1449 1758 1.442017 TGTGTGCTCGTCGTGATCG 60.442 57.895 0.00 0.00 38.55 3.69
1493 1802 0.528901 TCCTTTGGTGTCGTGTCGTG 60.529 55.000 0.00 0.00 0.00 4.35
1494 1803 1.495584 CCTTTGGTGTCGTGTCGTGG 61.496 60.000 0.00 0.00 0.00 4.94
1630 1939 7.141100 TCTTCAGTTTTCGTCTGAACTTTTT 57.859 32.000 4.56 0.00 43.88 1.94
1673 1982 2.728690 TGTCAAGTTGATGGCATTGC 57.271 45.000 9.18 0.00 28.02 3.56
1826 2135 5.990996 TCTCCCTGCAAATTTTCAATGAAAC 59.009 36.000 8.06 0.00 30.83 2.78
1851 2160 2.245795 TCGATGCTGCACATTTTTCG 57.754 45.000 3.57 9.72 39.84 3.46
1980 2289 1.593750 GCTCATCTACCAGGCGCTG 60.594 63.158 7.64 3.34 0.00 5.18
2302 2611 4.671590 TCGAGGCCTCCACGTCCA 62.672 66.667 27.20 0.00 38.64 4.02
2351 2663 2.556459 CCTCCTCGTCGGCGATGAT 61.556 63.158 29.77 0.00 46.80 2.45
2727 3054 0.242825 TCGACCACGAGTAAGCCAAG 59.757 55.000 0.00 0.00 43.81 3.61
2741 3068 2.362889 CAAGCCCATCACCCACCC 60.363 66.667 0.00 0.00 0.00 4.61
2742 3069 2.863484 AAGCCCATCACCCACCCA 60.863 61.111 0.00 0.00 0.00 4.51
2747 3074 1.152599 CCATCACCCACCCACACAA 59.847 57.895 0.00 0.00 0.00 3.33
2783 3110 3.423539 TCATAGGCTCTGTTTGTGCTT 57.576 42.857 0.00 0.00 35.67 3.91
2810 3137 8.642020 GCTGATGTTGATTTCATCTGTAAAAAC 58.358 33.333 11.95 0.00 41.30 2.43
2857 3184 4.078516 AACTACCGGGTGGCGCTC 62.079 66.667 10.66 0.23 39.70 5.03
2954 3281 4.998671 TGGTGAACTGCATTTTTCAGAA 57.001 36.364 5.93 0.00 32.40 3.02
2983 3310 2.359107 GCTACAGTGGCAGCAGCA 60.359 61.111 3.57 0.00 44.61 4.41
2984 3311 2.396955 GCTACAGTGGCAGCAGCAG 61.397 63.158 3.57 0.00 44.61 4.24
2985 3312 2.359107 TACAGTGGCAGCAGCAGC 60.359 61.111 2.65 0.00 44.61 5.25
3000 3327 0.939419 GCAGCCAAAACCAAGCAAAG 59.061 50.000 0.00 0.00 0.00 2.77
3065 3392 0.529555 GATCGAGAGGCAAGCAGGAC 60.530 60.000 0.00 0.00 0.00 3.85
3224 3551 2.156343 AGAAAGAACTGTCGCTGGAC 57.844 50.000 0.00 0.00 43.71 4.02
3235 3562 1.746615 CGCTGGACCTGAACCATGG 60.747 63.158 11.19 11.19 36.79 3.66
3237 3564 0.393537 GCTGGACCTGAACCATGGAG 60.394 60.000 21.47 5.19 36.79 3.86
3238 3565 0.254178 CTGGACCTGAACCATGGAGG 59.746 60.000 21.47 17.64 45.67 4.30
3272 3599 2.876550 GCCAAACTCTGACGTAAGGTTT 59.123 45.455 11.60 11.60 46.39 3.27
3554 3885 9.041354 AGTGATCCTCTTTTGTCTATACTTCTT 57.959 33.333 0.00 0.00 0.00 2.52
3555 3886 9.308318 GTGATCCTCTTTTGTCTATACTTCTTC 57.692 37.037 0.00 0.00 0.00 2.87
3556 3887 9.261035 TGATCCTCTTTTGTCTATACTTCTTCT 57.739 33.333 0.00 0.00 0.00 2.85
3592 3925 5.221422 GGATCAGAAATGTCTAGTGAGAGGG 60.221 48.000 0.00 0.00 30.85 4.30
3807 4143 1.135083 AGTCCGGTCAATGCGAAGTAG 60.135 52.381 0.00 0.00 0.00 2.57
3850 4186 3.763057 AGTTAAGAAATGGCGGAAAGGT 58.237 40.909 0.00 0.00 0.00 3.50
3867 4203 6.073765 CGGAAAGGTGATATTCAGATTTACCG 60.074 42.308 0.00 0.00 30.15 4.02
4047 4383 5.438761 ACAAAATAAGTCAGGCAACACTC 57.561 39.130 0.00 0.00 41.41 3.51
4131 4467 2.171237 TGTGGTGGGAGCTCATATCAAG 59.829 50.000 17.19 0.00 0.00 3.02
4182 4518 2.598045 CGGATCAGATGAACTGCCG 58.402 57.895 0.00 0.00 45.38 5.69
4288 4624 2.894126 TCAGACCCAGTCTCTGTTTCTC 59.106 50.000 0.00 0.00 41.37 2.87
4290 4626 1.276705 GACCCAGTCTCTGTTTCTCCC 59.723 57.143 0.00 0.00 0.00 4.30
4305 4641 6.451064 GTTTCTCCCTTCTTTTCAGAAACA 57.549 37.500 14.89 0.00 46.48 2.83
4309 4645 4.127171 TCCCTTCTTTTCAGAAACAGTCG 58.873 43.478 0.00 0.00 38.63 4.18
4342 4678 3.849911 TCCTTTACAGATTCAGTCGCAG 58.150 45.455 0.00 0.00 0.00 5.18
4357 4693 0.610687 CGCAGTTTCTCCCCTCTTCT 59.389 55.000 0.00 0.00 0.00 2.85
4359 4695 1.625818 GCAGTTTCTCCCCTCTTCTCA 59.374 52.381 0.00 0.00 0.00 3.27
4481 4817 3.301794 TTCCCCAATCATGTCAGATGG 57.698 47.619 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.242076 TCTTCTTGCCTTCTTGCTGC 58.758 50.000 0.00 0.00 0.00 5.25
52 53 2.319844 CCCTTTGGTTTCTTCTTGCCT 58.680 47.619 0.00 0.00 0.00 4.75
54 55 2.820059 CCCCTTTGGTTTCTTCTTGC 57.180 50.000 0.00 0.00 0.00 4.01
74 75 3.405831 GATGCTAGCTATGGATGCACAA 58.594 45.455 17.23 0.00 36.44 3.33
77 78 1.620323 ACGATGCTAGCTATGGATGCA 59.380 47.619 17.23 7.03 38.05 3.96
78 79 2.376808 ACGATGCTAGCTATGGATGC 57.623 50.000 17.23 0.00 0.00 3.91
110 111 4.499019 GGAAAACAAGAAGCCGATTGTTCA 60.499 41.667 10.18 0.00 46.16 3.18
113 114 3.222603 AGGAAAACAAGAAGCCGATTGT 58.777 40.909 0.00 0.00 41.28 2.71
117 118 1.336755 GCAAGGAAAACAAGAAGCCGA 59.663 47.619 0.00 0.00 0.00 5.54
118 119 1.770957 GCAAGGAAAACAAGAAGCCG 58.229 50.000 0.00 0.00 0.00 5.52
119 120 1.067060 ACGCAAGGAAAACAAGAAGCC 59.933 47.619 0.00 0.00 46.39 4.35
126 131 1.234821 CTAGCCACGCAAGGAAAACA 58.765 50.000 0.00 0.00 46.39 2.83
136 141 4.452733 AGTTCGCCCTAGCCACGC 62.453 66.667 0.00 0.00 34.57 5.34
149 164 4.084276 GCCGAAGTTTGAAGAGAAGAGTTC 60.084 45.833 0.00 0.00 0.00 3.01
161 176 4.302509 TCGCCGGCCGAAGTTTGA 62.303 61.111 30.73 11.71 44.21 2.69
193 208 2.142292 AAACGGCAAGCAGAGGGGAT 62.142 55.000 0.00 0.00 0.00 3.85
274 291 1.798813 ACTTGCGAGGACTAAAAAGCG 59.201 47.619 5.79 0.00 0.00 4.68
297 314 0.957395 CCGCCATTTGTCTGAGCACT 60.957 55.000 0.00 0.00 0.00 4.40
306 323 0.530288 AAAATAGCGCCGCCATTTGT 59.470 45.000 15.77 4.44 0.00 2.83
338 355 1.226046 CGTCGACTACGTCCAGCTG 60.226 63.158 14.70 6.78 46.72 4.24
339 356 3.175724 CGTCGACTACGTCCAGCT 58.824 61.111 14.70 0.00 46.72 4.24
362 409 3.481661 CGCAGGAATTTACGCCGT 58.518 55.556 0.00 0.00 0.00 5.68
383 430 0.688487 TAACCTCACCGTCCCAAAGG 59.312 55.000 0.00 0.00 0.00 3.11
391 439 3.387050 ACAAGAAACTCTAACCTCACCGT 59.613 43.478 0.00 0.00 0.00 4.83
411 460 2.028130 ACCAAATTTCGCCACAAGACA 58.972 42.857 0.00 0.00 0.00 3.41
433 482 1.877258 GCATAGATCTGGAGCACCTGC 60.877 57.143 5.18 0.00 42.49 4.85
442 491 3.565764 TGAACCCTTGCATAGATCTGG 57.434 47.619 5.18 0.00 0.00 3.86
576 642 2.106683 ACTATTGCCGCCAGAACGC 61.107 57.895 0.00 0.00 0.00 4.84
598 664 1.077169 AGATTCCAAGACCCCCAAACC 59.923 52.381 0.00 0.00 0.00 3.27
650 716 4.453478 TCTGCAGAAGTACAAAGCATCTTG 59.547 41.667 15.67 0.00 34.35 3.02
651 717 4.645535 TCTGCAGAAGTACAAAGCATCTT 58.354 39.130 15.67 0.00 34.35 2.40
701 989 5.788450 TGGTGTTCTTTTCTTTCTTGCAAA 58.212 33.333 0.00 0.00 0.00 3.68
702 990 5.398603 TGGTGTTCTTTTCTTTCTTGCAA 57.601 34.783 0.00 0.00 0.00 4.08
703 991 4.142182 CCTGGTGTTCTTTTCTTTCTTGCA 60.142 41.667 0.00 0.00 0.00 4.08
708 996 2.858646 GCGCCTGGTGTTCTTTTCTTTC 60.859 50.000 9.31 0.00 0.00 2.62
750 1047 2.261361 GAATTGTGTTGCCCGGGC 59.739 61.111 39.40 39.40 42.35 6.13
866 1163 0.340208 TCCTCTCTTCTTCCTCCCCC 59.660 60.000 0.00 0.00 0.00 5.40
1188 1492 1.179814 ACGCACCGAAGAGGAAGTCT 61.180 55.000 0.00 0.00 45.00 3.24
1267 1576 0.609957 TGCCATGCCAAGAAGACCAG 60.610 55.000 0.00 0.00 0.00 4.00
1268 1577 0.609957 CTGCCATGCCAAGAAGACCA 60.610 55.000 0.00 0.00 0.00 4.02
1274 1583 1.187974 CCAAATCTGCCATGCCAAGA 58.812 50.000 0.00 0.00 0.00 3.02
1279 1588 2.372264 TCTCTTCCAAATCTGCCATGC 58.628 47.619 0.00 0.00 0.00 4.06
1394 1703 3.258123 CACATTTCTCCCCCAAAAACGAT 59.742 43.478 0.00 0.00 0.00 3.73
1398 1707 2.103941 GTGCACATTTCTCCCCCAAAAA 59.896 45.455 13.17 0.00 0.00 1.94
1402 1711 1.303236 CGTGCACATTTCTCCCCCA 60.303 57.895 18.64 0.00 0.00 4.96
1406 1715 1.425412 ACGTACGTGCACATTTCTCC 58.575 50.000 22.14 0.00 0.00 3.71
1409 1718 3.122278 ACACATACGTACGTGCACATTTC 59.878 43.478 30.25 3.06 36.57 2.17
1411 1720 2.410392 CACACATACGTACGTGCACATT 59.590 45.455 30.25 7.72 36.57 2.71
1412 1721 1.989864 CACACATACGTACGTGCACAT 59.010 47.619 30.25 13.26 36.57 3.21
1417 1726 1.123576 GCACACACACATACGTACGTG 59.876 52.381 30.25 19.40 39.10 4.49
1420 1729 1.647213 CGAGCACACACACATACGTAC 59.353 52.381 0.00 0.00 0.00 3.67
1421 1730 1.267533 ACGAGCACACACACATACGTA 59.732 47.619 0.00 0.00 0.00 3.57
1422 1731 0.031585 ACGAGCACACACACATACGT 59.968 50.000 0.00 0.00 0.00 3.57
1423 1732 0.708370 GACGAGCACACACACATACG 59.292 55.000 0.00 0.00 0.00 3.06
1424 1733 0.708370 CGACGAGCACACACACATAC 59.292 55.000 0.00 0.00 0.00 2.39
1425 1734 0.312729 ACGACGAGCACACACACATA 59.687 50.000 0.00 0.00 0.00 2.29
1426 1735 1.067416 ACGACGAGCACACACACAT 59.933 52.632 0.00 0.00 0.00 3.21
1427 1736 1.876263 CACGACGAGCACACACACA 60.876 57.895 0.00 0.00 0.00 3.72
1428 1737 0.939577 ATCACGACGAGCACACACAC 60.940 55.000 0.00 0.00 0.00 3.82
1429 1738 0.663269 GATCACGACGAGCACACACA 60.663 55.000 0.00 0.00 0.00 3.72
1430 1739 1.665544 CGATCACGACGAGCACACAC 61.666 60.000 0.00 0.00 42.66 3.82
1431 1740 1.442017 CGATCACGACGAGCACACA 60.442 57.895 0.00 0.00 42.66 3.72
1432 1741 1.154282 TCGATCACGACGAGCACAC 60.154 57.895 0.00 0.00 43.81 3.82
1433 1742 3.259930 TCGATCACGACGAGCACA 58.740 55.556 0.00 0.00 43.81 4.57
1449 1758 4.361451 AAGAAACGCAATGTGATCCATC 57.639 40.909 0.00 0.00 31.75 3.51
1493 1802 4.619140 GCGCAATGCCGATCTGCC 62.619 66.667 0.30 0.00 37.76 4.85
1494 1803 4.950974 CGCGCAATGCCGATCTGC 62.951 66.667 8.75 1.59 42.08 4.26
1612 1921 6.311723 TCAGACAAAAAGTTCAGACGAAAAC 58.688 36.000 0.00 0.00 31.43 2.43
1630 1939 3.837146 AGATCAGCCTCTTCTTTCAGACA 59.163 43.478 0.00 0.00 0.00 3.41
1653 1962 2.607526 CGCAATGCCATCAACTTGACAA 60.608 45.455 0.00 0.00 0.00 3.18
1673 1982 2.631428 CACGAACACCCTGCAACG 59.369 61.111 0.00 0.00 0.00 4.10
1813 2122 8.627403 AGCATCGATCATAGTTTCATTGAAAAT 58.373 29.630 15.49 15.49 33.14 1.82
1826 2135 4.744136 AAATGTGCAGCATCGATCATAG 57.256 40.909 0.00 0.00 36.67 2.23
1851 2160 8.877779 GCGCCCATATAGATCATAATTCATATC 58.122 37.037 0.00 0.00 0.00 1.63
1980 2289 2.598394 TGCTGCTGGGGCTTGTTC 60.598 61.111 0.00 0.00 39.59 3.18
2152 2461 1.078848 CCTTGAGGGTCGGCTTCTG 60.079 63.158 0.00 0.00 0.00 3.02
2153 2462 2.960688 GCCTTGAGGGTCGGCTTCT 61.961 63.158 0.00 0.00 40.62 2.85
2154 2463 2.436824 GCCTTGAGGGTCGGCTTC 60.437 66.667 0.00 0.00 40.62 3.86
2322 2631 1.152567 CGAGGAGGAGGAGCAGGAT 60.153 63.158 0.00 0.00 0.00 3.24
2387 2714 1.730487 CTCGCGATCAGGCAGTAGT 59.270 57.895 10.36 0.00 0.00 2.73
2727 3054 3.978193 TGTGGGTGGGTGATGGGC 61.978 66.667 0.00 0.00 0.00 5.36
2747 3074 8.370182 AGAGCCTATGATTTTGTTTCATTTTGT 58.630 29.630 0.00 0.00 35.50 2.83
2810 3137 1.377725 GCCATATGATCCGGCTGGG 60.378 63.158 12.87 0.00 42.78 4.45
2857 3184 1.429825 CCTGGTCTCGTCGTAGCTG 59.570 63.158 0.00 0.00 0.00 4.24
2954 3281 5.439721 TGCCACTGTAGCATATCTGAAAAT 58.560 37.500 0.00 0.00 34.69 1.82
2983 3310 2.501316 AGAACTTTGCTTGGTTTTGGCT 59.499 40.909 0.00 0.00 0.00 4.75
2984 3311 2.609002 CAGAACTTTGCTTGGTTTTGGC 59.391 45.455 0.00 0.00 0.00 4.52
2985 3312 2.609002 GCAGAACTTTGCTTGGTTTTGG 59.391 45.455 0.00 0.00 40.89 3.28
3000 3327 0.250467 TCTTGGTCAGCCAGCAGAAC 60.250 55.000 0.00 0.00 46.91 3.01
3065 3392 2.282180 CCACCCCTTGAACACCCG 60.282 66.667 0.00 0.00 0.00 5.28
3154 3481 4.407365 TCCTTTTCCTCTTGGATTTGGTC 58.593 43.478 0.00 0.00 42.81 4.02
3160 3487 4.507512 GGTGTTCTCCTTTTCCTCTTGGAT 60.508 45.833 0.00 0.00 42.81 3.41
3206 3533 1.149148 GGTCCAGCGACAGTTCTTTC 58.851 55.000 0.00 0.00 41.13 2.62
3235 3562 1.981256 TGGCAAAGACCTGAAACCTC 58.019 50.000 0.00 0.00 0.00 3.85
3237 3564 2.430694 AGTTTGGCAAAGACCTGAAACC 59.569 45.455 13.94 0.00 29.88 3.27
3238 3565 3.381590 AGAGTTTGGCAAAGACCTGAAAC 59.618 43.478 13.94 0.00 0.00 2.78
3272 3599 3.181469 GCATCGACATGGAGGTAAAGGTA 60.181 47.826 0.00 0.00 0.00 3.08
3276 3603 2.905075 CTGCATCGACATGGAGGTAAA 58.095 47.619 0.00 0.00 43.17 2.01
3277 3604 2.602257 CTGCATCGACATGGAGGTAA 57.398 50.000 0.00 0.00 43.17 2.85
3281 3608 1.434622 GCACCTGCATCGACATGGAG 61.435 60.000 0.00 0.87 45.76 3.86
3282 3609 1.450134 GCACCTGCATCGACATGGA 60.450 57.895 0.00 0.00 41.59 3.41
3453 3784 1.026718 CGCAATGAACCCTGGAGTCC 61.027 60.000 0.73 0.73 0.00 3.85
3554 3885 9.213777 ACATTTCTGATCCTTGTAACCTATAGA 57.786 33.333 0.00 0.00 0.00 1.98
3555 3886 9.482627 GACATTTCTGATCCTTGTAACCTATAG 57.517 37.037 0.00 0.00 0.00 1.31
3556 3887 9.213777 AGACATTTCTGATCCTTGTAACCTATA 57.786 33.333 0.00 0.00 0.00 1.31
3557 3888 8.095452 AGACATTTCTGATCCTTGTAACCTAT 57.905 34.615 0.00 0.00 0.00 2.57
3558 3889 7.496346 AGACATTTCTGATCCTTGTAACCTA 57.504 36.000 0.00 0.00 0.00 3.08
3559 3890 6.380079 AGACATTTCTGATCCTTGTAACCT 57.620 37.500 0.00 0.00 0.00 3.50
3560 3891 7.278868 CACTAGACATTTCTGATCCTTGTAACC 59.721 40.741 0.00 0.00 32.75 2.85
3561 3892 8.035394 TCACTAGACATTTCTGATCCTTGTAAC 58.965 37.037 0.00 0.00 32.75 2.50
3562 3893 8.134202 TCACTAGACATTTCTGATCCTTGTAA 57.866 34.615 0.00 0.00 32.75 2.41
3563 3894 7.615757 TCTCACTAGACATTTCTGATCCTTGTA 59.384 37.037 0.00 0.00 32.75 2.41
3592 3925 1.070134 GTTGAAAAACCTTCAGCCCCC 59.930 52.381 0.00 0.00 0.00 5.40
3602 3935 4.686091 GCTAGGCATGAAAGTTGAAAAACC 59.314 41.667 0.00 0.00 0.00 3.27
3747 4083 9.403583 TCAACCTTTGACTGAAAAATACTACTT 57.596 29.630 0.00 0.00 34.08 2.24
3748 4084 8.974060 TCAACCTTTGACTGAAAAATACTACT 57.026 30.769 0.00 0.00 34.08 2.57
3850 4186 9.109393 CTCCTTTTTCGGTAAATCTGAATATCA 57.891 33.333 0.00 0.00 40.58 2.15
3867 4203 5.615289 TGCTATATCCTGCTCTCCTTTTTC 58.385 41.667 0.00 0.00 0.00 2.29
4019 4355 3.682858 TGCCTGACTTATTTTGTAGTCGC 59.317 43.478 0.00 0.00 42.88 5.19
4092 4428 2.892852 CACAGTGAATTCCCACCAACAT 59.107 45.455 2.27 0.00 37.76 2.71
4131 4467 4.033358 CAGCACGAGAAGTACATTCCAATC 59.967 45.833 0.00 0.00 38.84 2.67
4182 4518 4.180496 GCATCAGCAGGCAAAAGC 57.820 55.556 0.00 0.00 41.58 3.51
4288 4624 3.304057 GCGACTGTTTCTGAAAAGAAGGG 60.304 47.826 4.09 2.26 0.00 3.95
4290 4626 4.034510 ACTGCGACTGTTTCTGAAAAGAAG 59.965 41.667 4.09 5.91 0.00 2.85
4305 4641 1.343069 AGGAGGAAGAAACTGCGACT 58.657 50.000 0.00 0.00 0.00 4.18
4309 4645 4.642429 TCTGTAAAGGAGGAAGAAACTGC 58.358 43.478 0.00 0.00 0.00 4.40
4342 4678 3.772025 TCATCTGAGAAGAGGGGAGAAAC 59.228 47.826 0.00 0.00 0.00 2.78
4357 4693 3.358111 AGAGACCGAGACTTCATCTGA 57.642 47.619 0.00 0.00 38.00 3.27
4359 4695 3.020984 GGAAGAGACCGAGACTTCATCT 58.979 50.000 0.00 0.00 40.89 2.90
4481 4817 4.311606 GGGTTTGAAGACTGAAGAGACTC 58.688 47.826 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.