Multiple sequence alignment - TraesCS1B01G195500

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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 TraesCS1B01G195500 chr1B 100.000 2351 0 0 1 2351 350632254 350629904 0.000000e+00 4342
1 TraesCS1B01G195500 chr1B 89.737 419 34 7 1641 2056 669802665 669803077 5.750000e-146 527
2 TraesCS1B01G195500 chr1B 89.474 209 20 1 576 782 643042824 643043032 1.790000e-66 263
3 TraesCS1B01G195500 chr1B 88.517 209 21 3 576 782 593563261 593563468 1.390000e-62 250
4 TraesCS1B01G195500 chr1D 95.491 865 31 4 781 1639 261373340 261374202 0.000000e+00 1375
5 TraesCS1B01G195500 chr1D 89.952 418 36 4 1641 2056 458743046 458743459 3.440000e-148 534
6 TraesCS1B01G195500 chr1D 97.386 306 6 1 2047 2350 458744136 458744441 9.630000e-144 520
7 TraesCS1B01G195500 chr1D 93.510 339 9 3 1 336 261372822 261373150 2.100000e-135 492
8 TraesCS1B01G195500 chr1D 89.806 206 19 1 579 782 71764667 71764462 1.790000e-66 263
9 TraesCS1B01G195500 chr1D 89.552 201 19 2 378 577 261373148 261373347 1.080000e-63 254
10 TraesCS1B01G195500 chr1D 88.835 206 21 1 579 782 18864558 18864763 3.880000e-63 252
11 TraesCS1B01G195500 chr1D 88.462 130 14 1 575 703 486996012 486996141 3.130000e-34 156
12 TraesCS1B01G195500 chr1A 91.985 811 46 8 781 1578 338601039 338600235 0.000000e+00 1120
13 TraesCS1B01G195500 chr1A 90.777 206 17 1 579 782 566517100 566517305 8.280000e-70 274
14 TraesCS1B01G195500 chr1A 92.126 127 6 2 224 347 338601352 338601227 2.400000e-40 176
15 TraesCS1B01G195500 chr6D 90.670 418 32 5 1641 2056 148621808 148622220 1.230000e-152 549
16 TraesCS1B01G195500 chr6D 89.387 424 39 4 1635 2056 467362922 467363341 1.600000e-146 529
17 TraesCS1B01G195500 chr6D 97.394 307 6 1 2047 2351 310007841 310007535 2.680000e-144 521
18 TraesCS1B01G195500 chr6D 97.068 307 7 1 2047 2351 467364018 467364324 1.250000e-142 516
19 TraesCS1B01G195500 chr2D 90.670 418 32 5 1641 2056 527886473 527886885 1.230000e-152 549
20 TraesCS1B01G195500 chr2D 90.094 424 33 7 1636 2056 566728577 566728160 2.060000e-150 542
21 TraesCS1B01G195500 chr2D 97.068 307 7 1 2047 2351 618544866 618545172 1.250000e-142 516
22 TraesCS1B01G195500 chr2D 96.743 307 8 1 2047 2351 516844877 516845183 5.800000e-141 510
23 TraesCS1B01G195500 chr2D 96.743 307 8 1 2047 2351 565161138 565160832 5.800000e-141 510
24 TraesCS1B01G195500 chr3D 90.191 418 35 4 1641 2056 413947441 413947028 7.390000e-150 540
25 TraesCS1B01G195500 chr3D 89.524 420 36 6 1641 2058 92379868 92380281 2.070000e-145 525
26 TraesCS1B01G195500 chr3D 97.068 307 7 1 2047 2351 26669407 26669101 1.250000e-142 516
27 TraesCS1B01G195500 chr6B 89.362 423 38 5 1636 2056 572077086 572077503 2.070000e-145 525
28 TraesCS1B01G195500 chr6B 90.196 204 16 3 582 782 542504077 542503875 1.790000e-66 263
29 TraesCS1B01G195500 chr6B 88.626 211 21 2 575 782 87674524 87674314 1.080000e-63 254
30 TraesCS1B01G195500 chr4D 97.068 307 7 1 2047 2351 450521385 450521691 1.250000e-142 516
31 TraesCS1B01G195500 chr4D 96.743 307 8 1 2047 2351 508427857 508428163 5.800000e-141 510
32 TraesCS1B01G195500 chr4D 82.781 302 26 21 1026 1323 501234114 501233835 1.800000e-61 246
33 TraesCS1B01G195500 chr4D 90.419 167 15 1 1158 1323 501161638 501161472 3.930000e-53 219
34 TraesCS1B01G195500 chr5A 84.641 306 27 15 1022 1323 683125619 683125908 1.060000e-73 287
35 TraesCS1B01G195500 chr5A 88.479 217 22 1 576 789 560808246 560808462 2.320000e-65 259
36 TraesCS1B01G195500 chr3B 91.748 206 14 2 579 782 61546135 61546339 1.380000e-72 283
37 TraesCS1B01G195500 chr3B 90.291 206 18 1 579 782 62672649 62672444 3.850000e-68 268
38 TraesCS1B01G195500 chr7B 89.498 219 18 3 579 794 645396204 645395988 2.980000e-69 272
39 TraesCS1B01G195500 chr7B 90.047 211 19 1 574 782 714779749 714779959 2.980000e-69 272
40 TraesCS1B01G195500 chr5B 90.732 205 17 2 579 782 586274534 586274331 2.980000e-69 272
41 TraesCS1B01G195500 chr5B 89.320 206 19 2 579 782 387765921 387765717 3.000000e-64 255
42 TraesCS1B01G195500 chr2B 90.338 207 17 1 579 782 27548138 27547932 3.850000e-68 268
43 TraesCS1B01G195500 chrUn 89.524 210 18 3 576 782 74802855 74803063 1.790000e-66 263
44 TraesCS1B01G195500 chrUn 88.350 206 21 3 579 782 138415666 138415870 6.490000e-61 244
45 TraesCS1B01G195500 chrUn 87.923 207 21 3 579 782 138271934 138272139 8.400000e-60 241
46 TraesCS1B01G195500 chrUn 87.981 208 20 4 579 782 171112601 171112395 8.400000e-60 241
47 TraesCS1B01G195500 chrUn 87.864 206 22 3 579 782 138345952 138346156 3.020000e-59 239
48 TraesCS1B01G195500 chrUn 87.864 206 22 3 579 782 312018740 312018944 3.020000e-59 239
49 TraesCS1B01G195500 chrUn 87.379 206 24 1 579 782 73675783 73675578 3.910000e-58 235
50 TraesCS1B01G195500 chr4B 88.942 208 17 5 579 782 560238409 560238614 3.880000e-63 252
51 TraesCS1B01G195500 chr4B 82.353 306 31 16 1022 1323 645084442 645084156 6.490000e-61 244
52 TraesCS1B01G195500 chr6A 87.923 207 21 3 579 782 558457705 558457500 8.400000e-60 241
53 TraesCS1B01G195500 chr6A 87.923 207 21 3 579 782 558461025 558460820 8.400000e-60 241
54 TraesCS1B01G195500 chr4A 86.916 214 24 3 578 788 733355899 733355687 1.090000e-58 237


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 TraesCS1B01G195500 chr1B 350629904 350632254 2350 True 4342.0 4342 100.0000 1 2351 1 chr1B.!!$R1 2350
1 TraesCS1B01G195500 chr1D 261372822 261374202 1380 False 707.0 1375 92.8510 1 1639 3 chr1D.!!$F3 1638
2 TraesCS1B01G195500 chr1D 458743046 458744441 1395 False 527.0 534 93.6690 1641 2350 2 chr1D.!!$F4 709
3 TraesCS1B01G195500 chr1A 338600235 338601352 1117 True 648.0 1120 92.0555 224 1578 2 chr1A.!!$R1 1354
4 TraesCS1B01G195500 chr6D 467362922 467364324 1402 False 522.5 529 93.2275 1635 2351 2 chr6D.!!$F2 716
5 TraesCS1B01G195500 chr6A 558457500 558461025 3525 True 241.0 241 87.9230 579 782 2 chr6A.!!$R1 203

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
570 579 0.955428 TCTCGTGGCCACAAAGCATC 60.955 55.0 34.16 6.15 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 1807 0.109412 AATCGACGACTGGGACGAAC 60.109 55.0 0.0 0.0 38.22 3.95 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
101 102 1.240256 GTCTCGTGACTGTCTGGAGT 58.760 55.000 20.24 0.00 39.94 3.85
122 123 0.968901 TGGACCGCTATGTCGACCTT 60.969 55.000 14.12 3.01 36.07 3.50
123 124 1.027357 GGACCGCTATGTCGACCTTA 58.973 55.000 14.12 4.14 36.07 2.69
213 214 6.604735 CATGTAATGCAGGTAAGTCCTTAC 57.395 41.667 8.39 8.39 39.97 2.34
214 215 6.349300 CATGTAATGCAGGTAAGTCCTTACT 58.651 40.000 14.89 1.64 39.97 2.24
215 216 7.497595 CATGTAATGCAGGTAAGTCCTTACTA 58.502 38.462 14.89 3.08 39.97 1.82
218 219 7.835682 TGTAATGCAGGTAAGTCCTTACTAGTA 59.164 37.037 14.89 0.00 45.67 1.82
221 222 6.962182 TGCAGGTAAGTCCTTACTAGTACTA 58.038 40.000 14.89 1.89 45.67 1.82
222 223 7.580910 TGCAGGTAAGTCCTTACTAGTACTAT 58.419 38.462 14.89 0.00 45.67 2.12
237 238 7.163441 ACTAGTACTATCTAGCTAACAGCCTC 58.837 42.308 2.33 0.00 43.77 4.70
304 311 1.732259 GTCCACCGTGTTGCTCTTATG 59.268 52.381 0.00 0.00 0.00 1.90
336 343 2.505118 GCTCTGACACCGAGCGAC 60.505 66.667 1.35 0.00 43.69 5.19
337 344 2.983930 GCTCTGACACCGAGCGACT 61.984 63.158 1.35 0.00 43.69 4.18
338 345 1.154131 CTCTGACACCGAGCGACTG 60.154 63.158 0.00 0.00 0.00 3.51
339 346 1.578206 CTCTGACACCGAGCGACTGA 61.578 60.000 0.00 0.00 0.00 3.41
340 347 1.442857 CTGACACCGAGCGACTGAC 60.443 63.158 0.00 0.00 0.00 3.51
341 348 2.502080 GACACCGAGCGACTGACG 60.502 66.667 0.00 0.00 45.66 4.35
342 349 2.962827 GACACCGAGCGACTGACGA 61.963 63.158 3.29 0.00 45.77 4.20
343 350 2.254703 GACACCGAGCGACTGACGAT 62.255 60.000 3.29 0.00 45.46 3.73
344 351 1.869574 CACCGAGCGACTGACGATG 60.870 63.158 3.29 0.00 41.91 3.84
345 352 2.951745 CCGAGCGACTGACGATGC 60.952 66.667 3.29 0.00 41.91 3.91
346 353 2.101185 CGAGCGACTGACGATGCT 59.899 61.111 3.29 0.00 41.91 3.79
347 354 1.515088 CGAGCGACTGACGATGCTT 60.515 57.895 3.29 0.00 41.91 3.91
348 355 1.073216 CGAGCGACTGACGATGCTTT 61.073 55.000 3.29 0.00 41.91 3.51
349 356 1.071605 GAGCGACTGACGATGCTTTT 58.928 50.000 3.29 0.00 41.91 2.27
350 357 1.461127 GAGCGACTGACGATGCTTTTT 59.539 47.619 3.29 0.00 41.91 1.94
390 397 2.297597 GGAACTGACGATGCTATAGCCT 59.702 50.000 21.84 12.45 41.18 4.58
392 399 4.022242 GGAACTGACGATGCTATAGCCTAA 60.022 45.833 21.84 3.87 41.18 2.69
435 442 2.868583 CAAGATGTGCTCGACCCATAAG 59.131 50.000 0.00 0.00 0.00 1.73
458 465 3.435601 CCTTCCATCAATTCCCTACCCAG 60.436 52.174 0.00 0.00 0.00 4.45
558 567 1.005340 GATTCAGCTTGCTCTCGTGG 58.995 55.000 0.00 0.00 0.00 4.94
560 569 3.123620 CAGCTTGCTCTCGTGGCC 61.124 66.667 0.00 0.00 0.00 5.36
569 578 0.957395 CTCTCGTGGCCACAAAGCAT 60.957 55.000 34.16 0.00 0.00 3.79
570 579 0.955428 TCTCGTGGCCACAAAGCATC 60.955 55.000 34.16 6.15 0.00 3.91
571 580 1.926511 CTCGTGGCCACAAAGCATCC 61.927 60.000 34.16 5.35 0.00 3.51
572 581 2.267351 CGTGGCCACAAAGCATCCA 61.267 57.895 34.16 0.00 0.00 3.41
573 582 1.290009 GTGGCCACAAAGCATCCAC 59.710 57.895 31.23 0.00 40.13 4.02
574 583 1.907807 TGGCCACAAAGCATCCACC 60.908 57.895 0.00 0.00 0.00 4.61
575 584 2.649129 GGCCACAAAGCATCCACCC 61.649 63.158 0.00 0.00 0.00 4.61
576 585 1.907807 GCCACAAAGCATCCACCCA 60.908 57.895 0.00 0.00 0.00 4.51
577 586 1.966762 CCACAAAGCATCCACCCAC 59.033 57.895 0.00 0.00 0.00 4.61
594 603 4.473520 CGGATCCGGCTTGCCTGT 62.474 66.667 26.95 0.00 35.56 4.00
597 606 1.078143 GATCCGGCTTGCCTGTTCT 60.078 57.895 10.12 0.00 0.00 3.01
600 609 1.302832 CCGGCTTGCCTGTTCTCTT 60.303 57.895 10.12 0.00 0.00 2.85
606 615 2.356125 GCTTGCCTGTTCTCTTCCCATA 60.356 50.000 0.00 0.00 0.00 2.74
615 624 3.970640 GTTCTCTTCCCATACTCCCATCT 59.029 47.826 0.00 0.00 0.00 2.90
631 640 2.619849 CCATCTGTGCTCCCACTTCATT 60.620 50.000 0.00 0.00 42.54 2.57
642 651 3.071892 TCCCACTTCATTCTACGGTTGTT 59.928 43.478 0.00 0.00 0.00 2.83
643 652 3.435671 CCCACTTCATTCTACGGTTGTTC 59.564 47.826 0.00 0.00 0.00 3.18
650 659 7.282450 ACTTCATTCTACGGTTGTTCTTTTTCT 59.718 33.333 0.00 0.00 0.00 2.52
652 661 7.992008 TCATTCTACGGTTGTTCTTTTTCTTT 58.008 30.769 0.00 0.00 0.00 2.52
655 664 8.677871 TTCTACGGTTGTTCTTTTTCTTTTTC 57.322 30.769 0.00 0.00 0.00 2.29
656 665 7.252708 TCTACGGTTGTTCTTTTTCTTTTTCC 58.747 34.615 0.00 0.00 0.00 3.13
713 724 1.203758 GTGGGGCCGGACTTTATTTTG 59.796 52.381 7.57 0.00 0.00 2.44
731 742 9.504708 TTTATTTTGTTCCAATCAAATCATGCT 57.495 25.926 0.00 0.00 35.25 3.79
734 745 6.587206 TTGTTCCAATCAAATCATGCTACA 57.413 33.333 0.00 0.00 0.00 2.74
737 748 8.467963 TGTTCCAATCAAATCATGCTACATAT 57.532 30.769 0.00 0.00 0.00 1.78
739 750 8.355169 GTTCCAATCAAATCATGCTACATATGT 58.645 33.333 13.93 13.93 0.00 2.29
748 759 1.836802 TGCTACATATGTGGGAGCACA 59.163 47.619 22.22 9.33 41.00 4.57
762 773 2.969806 GCACAGATGGGCACACACG 61.970 63.158 1.27 0.00 45.57 4.49
763 774 2.669569 ACAGATGGGCACACACGC 60.670 61.111 0.00 0.00 0.00 5.34
834 845 1.306141 ACCTTCCCCTCTCGCATCA 60.306 57.895 0.00 0.00 0.00 3.07
849 860 1.474077 GCATCAAACTCCACCATGGAC 59.526 52.381 21.47 0.00 42.67 4.02
884 928 6.667414 CAGTCTCTATATAAATCCCCTCTGCT 59.333 42.308 0.00 0.00 0.00 4.24
904 948 5.129634 TGCTTCCAAGATTACTCAAACACA 58.870 37.500 0.00 0.00 0.00 3.72
939 983 4.154195 AGAACTCACAAGTCACAACAACAC 59.846 41.667 0.00 0.00 33.48 3.32
971 1015 2.526304 TCTTGAACTCTCGTGGTTGG 57.474 50.000 0.00 0.00 0.00 3.77
986 1030 4.618693 CGTGGTTGGTTTTAGTTGGTTTGT 60.619 41.667 0.00 0.00 0.00 2.83
1393 1450 2.356313 CCGTCTTCAGCGCTGTGT 60.356 61.111 34.70 0.00 0.00 3.72
1472 1529 1.461127 CGAGCTGTAGCCAAGTGAAAC 59.539 52.381 0.00 0.00 43.38 2.78
1546 1603 7.484641 GTGAATAGAAATAAAATGTTGCTCGCA 59.515 33.333 0.00 0.00 0.00 5.10
1601 1658 4.096231 TCTGTATTGGAATTTCGGTGCATG 59.904 41.667 0.00 0.00 0.00 4.06
1604 1661 2.721274 TGGAATTTCGGTGCATGTTG 57.279 45.000 0.00 0.00 0.00 3.33
1646 1703 3.330267 GGAACGATTCCTCATAGCATCC 58.670 50.000 8.87 0.00 46.57 3.51
1651 1708 2.196742 TTCCTCATAGCATCCCCAGT 57.803 50.000 0.00 0.00 0.00 4.00
1652 1709 2.196742 TCCTCATAGCATCCCCAGTT 57.803 50.000 0.00 0.00 0.00 3.16
1656 1713 3.209410 CTCATAGCATCCCCAGTTGTTC 58.791 50.000 0.00 0.00 0.00 3.18
1658 1715 0.251916 TAGCATCCCCAGTTGTTCGG 59.748 55.000 0.00 0.00 0.00 4.30
1663 1720 3.966543 CCCAGTTGTTCGGCCCCT 61.967 66.667 0.00 0.00 0.00 4.79
1682 1739 1.670811 CTCAGGGCGCATAAAAATCGT 59.329 47.619 10.83 0.00 0.00 3.73
1684 1741 1.670811 CAGGGCGCATAAAAATCGTCT 59.329 47.619 10.83 0.00 0.00 4.18
1686 1743 1.668751 GGGCGCATAAAAATCGTCTCA 59.331 47.619 10.83 0.00 0.00 3.27
1689 1746 3.002246 GGCGCATAAAAATCGTCTCATGA 59.998 43.478 10.83 0.00 0.00 3.07
1690 1747 4.495679 GGCGCATAAAAATCGTCTCATGAA 60.496 41.667 10.83 0.00 0.00 2.57
1732 1789 2.275380 GCTGGGGTCGGTTTTGCAT 61.275 57.895 0.00 0.00 0.00 3.96
1764 1821 2.571216 CCCAGTTCGTCCCAGTCGT 61.571 63.158 0.00 0.00 0.00 4.34
1791 1848 2.931068 GCCCACTTTTGAAGCCCCG 61.931 63.158 0.00 0.00 0.00 5.73
1805 1862 0.038618 GCCCCGTTTCAGCGAAAAAT 60.039 50.000 5.51 0.00 33.14 1.82
1816 1873 2.361757 CAGCGAAAAATGCCCATATGGA 59.638 45.455 24.00 4.24 37.39 3.41
2004 2062 6.662414 AAATCATATTTCATCACACGTCGT 57.338 33.333 0.00 0.00 0.00 4.34
2008 2066 0.249699 TTTCATCACACGTCGTGCCT 60.250 50.000 24.80 7.17 45.92 4.75
2157 4253 6.087522 CCGACAGAACTTAGAAACACTCTAG 58.912 44.000 0.00 0.00 37.93 2.43
2160 4256 5.172205 CAGAACTTAGAAACACTCTAGGCC 58.828 45.833 0.00 0.00 37.26 5.19
2205 4301 2.265904 CGTCCTGTGAGTCACCGGA 61.266 63.158 27.14 27.14 43.52 5.14
2317 5148 1.843368 AGTTGTCGAACTCCCGGATA 58.157 50.000 0.73 0.00 38.01 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.340076 CAAACTTGCAATGCGCCA 57.660 50.000 4.18 0.00 41.33 5.69
101 102 1.381928 GGTCGACATAGCGGTCCAGA 61.382 60.000 18.91 0.00 34.24 3.86
122 123 4.963373 TCCTTGAAACGTGGAACTTCATA 58.037 39.130 0.75 0.00 32.11 2.15
123 124 3.815809 TCCTTGAAACGTGGAACTTCAT 58.184 40.909 0.75 0.00 32.11 2.57
165 166 9.573166 TGTAATAATCAGTGATTCTATTTGGGG 57.427 33.333 21.49 0.00 33.95 4.96
206 207 9.995003 TGTTAGCTAGATAGTACTAGTAAGGAC 57.005 37.037 8.85 0.00 41.10 3.85
208 209 8.938906 GCTGTTAGCTAGATAGTACTAGTAAGG 58.061 40.741 8.85 0.00 41.10 2.69
209 210 8.938906 GGCTGTTAGCTAGATAGTACTAGTAAG 58.061 40.741 8.85 6.32 41.99 2.34
210 211 8.658619 AGGCTGTTAGCTAGATAGTACTAGTAA 58.341 37.037 8.85 0.00 41.99 2.24
211 212 8.204903 AGGCTGTTAGCTAGATAGTACTAGTA 57.795 38.462 8.85 0.00 41.99 1.82
212 213 7.081857 AGGCTGTTAGCTAGATAGTACTAGT 57.918 40.000 8.85 0.00 41.99 2.57
213 214 6.596497 GGAGGCTGTTAGCTAGATAGTACTAG 59.404 46.154 8.85 0.00 41.99 2.57
214 215 6.272792 AGGAGGCTGTTAGCTAGATAGTACTA 59.727 42.308 4.77 4.77 41.99 1.82
215 216 5.073965 AGGAGGCTGTTAGCTAGATAGTACT 59.926 44.000 0.00 0.00 41.99 2.73
218 219 4.148838 CAGGAGGCTGTTAGCTAGATAGT 58.851 47.826 0.00 0.00 41.99 2.12
221 222 2.962421 GACAGGAGGCTGTTAGCTAGAT 59.038 50.000 0.00 0.00 41.99 1.98
222 223 2.291605 TGACAGGAGGCTGTTAGCTAGA 60.292 50.000 0.00 0.00 41.99 2.43
291 295 3.555956 CGACCCATACATAAGAGCAACAC 59.444 47.826 0.00 0.00 0.00 3.32
304 311 1.732259 CAGAGCAAACACGACCCATAC 59.268 52.381 0.00 0.00 0.00 2.39
360 367 0.464013 TCGTCAGTTCCCCGCAAAAA 60.464 50.000 0.00 0.00 0.00 1.94
361 368 0.250553 ATCGTCAGTTCCCCGCAAAA 60.251 50.000 0.00 0.00 0.00 2.44
362 369 0.953471 CATCGTCAGTTCCCCGCAAA 60.953 55.000 0.00 0.00 0.00 3.68
363 370 1.375396 CATCGTCAGTTCCCCGCAA 60.375 57.895 0.00 0.00 0.00 4.85
364 371 2.264480 CATCGTCAGTTCCCCGCA 59.736 61.111 0.00 0.00 0.00 5.69
365 372 2.292794 TAGCATCGTCAGTTCCCCGC 62.293 60.000 0.00 0.00 0.00 6.13
366 373 0.389391 ATAGCATCGTCAGTTCCCCG 59.611 55.000 0.00 0.00 0.00 5.73
367 374 2.610727 GCTATAGCATCGTCAGTTCCCC 60.611 54.545 20.01 0.00 41.59 4.81
368 375 2.610727 GGCTATAGCATCGTCAGTTCCC 60.611 54.545 25.53 0.23 44.36 3.97
369 376 2.297597 AGGCTATAGCATCGTCAGTTCC 59.702 50.000 25.53 4.25 44.36 3.62
370 377 3.651803 AGGCTATAGCATCGTCAGTTC 57.348 47.619 25.53 4.75 44.36 3.01
371 378 5.290386 GTTTAGGCTATAGCATCGTCAGTT 58.710 41.667 25.53 2.87 44.36 3.16
390 397 7.810658 TGTAACGTGTTGTTTTTACAGGTTTA 58.189 30.769 16.06 6.70 46.44 2.01
435 442 2.587522 GGTAGGGAATTGATGGAAGGC 58.412 52.381 0.00 0.00 0.00 4.35
458 465 9.129209 GCTGGACAAAGATAAAACTAACATTTC 57.871 33.333 0.00 0.00 0.00 2.17
558 567 1.907807 TGGGTGGATGCTTTGTGGC 60.908 57.895 0.00 0.00 0.00 5.01
560 569 1.580942 CGTGGGTGGATGCTTTGTG 59.419 57.895 0.00 0.00 0.00 3.33
571 580 4.096003 AAGCCGGATCCGTGGGTG 62.096 66.667 31.22 17.27 35.82 4.61
572 581 4.096003 CAAGCCGGATCCGTGGGT 62.096 66.667 31.22 19.97 37.64 4.51
575 584 4.473520 AGGCAAGCCGGATCCGTG 62.474 66.667 31.22 23.53 41.95 4.94
576 585 4.473520 CAGGCAAGCCGGATCCGT 62.474 66.667 31.22 12.64 41.95 4.69
577 586 3.976701 AACAGGCAAGCCGGATCCG 62.977 63.158 27.65 27.65 41.95 4.18
594 603 3.969976 CAGATGGGAGTATGGGAAGAGAA 59.030 47.826 0.00 0.00 0.00 2.87
597 606 3.041211 CACAGATGGGAGTATGGGAAGA 58.959 50.000 0.00 0.00 0.00 2.87
600 609 1.131638 GCACAGATGGGAGTATGGGA 58.868 55.000 0.00 0.00 0.00 4.37
606 615 1.229625 TGGGAGCACAGATGGGAGT 60.230 57.895 0.00 0.00 0.00 3.85
615 624 2.353704 CGTAGAATGAAGTGGGAGCACA 60.354 50.000 0.00 0.00 0.00 4.57
631 640 7.252708 GGAAAAAGAAAAAGAACAACCGTAGA 58.747 34.615 0.00 0.00 0.00 2.59
652 661 8.440771 GGGAGATGATTAGATTAGAAAGGGAAA 58.559 37.037 0.00 0.00 0.00 3.13
655 664 6.503570 AGGGGAGATGATTAGATTAGAAAGGG 59.496 42.308 0.00 0.00 0.00 3.95
656 665 7.236432 TCAGGGGAGATGATTAGATTAGAAAGG 59.764 40.741 0.00 0.00 0.00 3.11
713 724 8.355169 ACATATGTAGCATGATTTGATTGGAAC 58.645 33.333 6.56 0.00 0.00 3.62
728 739 1.836802 TGTGCTCCCACATATGTAGCA 59.163 47.619 22.22 22.22 46.51 3.49
739 750 2.934932 TGCCCATCTGTGCTCCCA 60.935 61.111 0.00 0.00 0.00 4.37
763 774 3.672295 GAGACTTGCCTGCTCCCCG 62.672 68.421 0.00 0.00 0.00 5.73
884 928 5.470098 GCTCTGTGTTTGAGTAATCTTGGAA 59.530 40.000 0.00 0.00 34.30 3.53
904 948 2.225467 GTGAGTTCTTGGCTTTGCTCT 58.775 47.619 0.00 0.00 0.00 4.09
939 983 2.032030 AGTTCAAGAACGAATTGTGCGG 60.032 45.455 7.25 0.00 45.50 5.69
971 1015 7.974243 ACGATTACAACAAACCAACTAAAAC 57.026 32.000 0.00 0.00 0.00 2.43
986 1030 2.198406 GCGCCATCACTACGATTACAA 58.802 47.619 0.00 0.00 29.21 2.41
1347 1394 2.785105 GCGTCGTTAGCGCGTTCAT 61.785 57.895 8.43 0.00 45.36 2.57
1358 1408 2.430921 CGAGGAAGCTGCGTCGTT 60.431 61.111 25.35 1.96 40.21 3.85
1546 1603 4.284746 ACCGACTGAAAAAGGAGATCTTCT 59.715 41.667 0.00 0.00 33.94 2.85
1601 1658 4.464112 GAGTTATGAGCGTCCAAAACAAC 58.536 43.478 0.00 0.00 0.00 3.32
1604 1661 2.093783 CCGAGTTATGAGCGTCCAAAAC 59.906 50.000 0.00 0.00 0.00 2.43
1639 1696 0.251916 CCGAACAACTGGGGATGCTA 59.748 55.000 0.00 0.00 0.00 3.49
1646 1703 3.920093 GAGGGGCCGAACAACTGGG 62.920 68.421 0.00 0.00 0.00 4.45
1663 1720 1.668751 GACGATTTTTATGCGCCCTGA 59.331 47.619 4.18 0.00 0.00 3.86
1668 1725 4.195744 TCATGAGACGATTTTTATGCGC 57.804 40.909 0.00 0.00 0.00 6.09
1682 1739 1.809869 CCGTCTCGCCTTCATGAGA 59.190 57.895 0.00 0.00 38.85 3.27
1684 1741 2.184322 GCCGTCTCGCCTTCATGA 59.816 61.111 0.00 0.00 0.00 3.07
1686 1743 3.449227 TCGCCGTCTCGCCTTCAT 61.449 61.111 0.00 0.00 0.00 2.57
1689 1746 4.117661 GAGTCGCCGTCTCGCCTT 62.118 66.667 0.00 0.00 0.00 4.35
1721 1778 0.250124 ACGACTGGATGCAAAACCGA 60.250 50.000 0.00 0.00 0.00 4.69
1748 1805 1.442184 CGACGACTGGGACGAACTG 60.442 63.158 0.00 0.00 34.70 3.16
1749 1806 0.959372 ATCGACGACTGGGACGAACT 60.959 55.000 0.00 0.00 38.22 3.01
1750 1807 0.109412 AATCGACGACTGGGACGAAC 60.109 55.000 0.00 0.00 38.22 3.95
1752 1809 0.599558 AAAATCGACGACTGGGACGA 59.400 50.000 0.00 0.00 39.01 4.20
1753 1810 0.713883 CAAAATCGACGACTGGGACG 59.286 55.000 0.00 0.00 0.00 4.79
1754 1811 1.076332 CCAAAATCGACGACTGGGAC 58.924 55.000 0.00 0.00 0.00 4.46
1755 1812 0.672401 GCCAAAATCGACGACTGGGA 60.672 55.000 18.88 0.00 0.00 4.37
1764 1821 2.311463 TCAAAAGTGGGCCAAAATCGA 58.689 42.857 8.40 0.00 0.00 3.59
1791 1848 2.147436 TGGGCATTTTTCGCTGAAAC 57.853 45.000 3.71 0.00 30.83 2.78
1805 1862 2.567169 CCTATTCTCGTCCATATGGGCA 59.433 50.000 25.58 11.97 40.62 5.36
1816 1873 2.233922 CCGAATATGGGCCTATTCTCGT 59.766 50.000 22.48 3.70 36.42 4.18
1915 1973 7.414436 TGTTGTTGTACTATTTTGCTGAAGTC 58.586 34.615 0.00 0.00 0.00 3.01
2004 2062 4.641645 CAAGGGCGACACCAGGCA 62.642 66.667 0.00 0.00 42.05 4.75
2008 2066 2.112297 GGTTCAAGGGCGACACCA 59.888 61.111 0.00 0.00 42.05 4.17
2205 4301 1.303309 GATGCTTGCATACGGAGCTT 58.697 50.000 8.17 2.45 37.32 3.74
2317 5148 4.301072 TTTCCTCCGGATTGTGAATTCT 57.699 40.909 3.57 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.