Multiple sequence alignment - TraesCS1B01G026200

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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 TraesCS1B01G026200 chr1B 100.000 4522 0 0 1 4522 12784194 12788715 0.000000e+00 8351.0
1 TraesCS1B01G026200 chr1B 89.890 1177 97 12 35 1198 13020450 13021617 0.000000e+00 1495.0
2 TraesCS1B01G026200 chr1B 88.748 1182 101 16 35 1198 13568908 13570075 0.000000e+00 1417.0
3 TraesCS1B01G026200 chr1B 84.553 1107 79 31 95 1198 12354145 12353128 0.000000e+00 1013.0
4 TraesCS1B01G026200 chr1B 89.943 348 25 2 1251 1597 12353117 12352779 1.490000e-119 440.0
5 TraesCS1B01G026200 chr1B 89.655 348 26 6 1251 1597 13021628 13021966 6.950000e-118 435.0
6 TraesCS1B01G026200 chr1B 88.793 348 29 4 1251 1597 13570086 13570424 7.000000e-113 418.0
7 TraesCS1B01G026200 chr1B 73.902 387 68 17 4146 4509 543513807 543513431 1.710000e-24 124.0
8 TraesCS1B01G026200 chr1A 93.259 3234 190 18 325 3538 10748135 10751360 0.000000e+00 4739.0
9 TraesCS1B01G026200 chr1A 82.775 209 16 11 92 296 10720185 10720377 7.780000e-38 169.0
10 TraesCS1B01G026200 chr1D 97.106 1624 44 3 1917 3538 9441707 9443329 0.000000e+00 2736.0
11 TraesCS1B01G026200 chr1D 93.605 1423 77 11 488 1906 9440316 9441728 0.000000e+00 2111.0
12 TraesCS1B01G026200 chr1D 88.441 372 29 7 23 390 9439958 9440319 1.930000e-118 436.0
13 TraesCS1B01G026200 chr1D 97.368 38 1 0 3699 3736 204855552 204855515 1.050000e-06 65.8
14 TraesCS1B01G026200 chr1D 97.368 38 1 0 3699 3736 311345337 311345374 1.050000e-06 65.8
15 TraesCS1B01G026200 chr7D 93.238 562 35 3 3537 4096 431033758 431034318 0.000000e+00 824.0
16 TraesCS1B01G026200 chr7D 92.260 323 23 1 4140 4462 431034954 431035274 1.480000e-124 457.0
17 TraesCS1B01G026200 chr7D 74.708 257 42 17 2168 2418 613323326 613323565 4.820000e-15 93.5
18 TraesCS1B01G026200 chr7D 74.409 254 42 18 2168 2418 613327571 613327804 2.240000e-13 87.9
19 TraesCS1B01G026200 chr7D 72.973 259 50 14 2181 2436 613135333 613135092 6.270000e-09 73.1
20 TraesCS1B01G026200 chr7D 97.368 38 1 0 3699 3736 119897072 119897035 1.050000e-06 65.8
21 TraesCS1B01G026200 chr7D 97.222 36 1 0 4487 4522 431035277 431035312 1.360000e-05 62.1
22 TraesCS1B01G026200 chr3A 92.254 426 30 3 3537 3959 604061639 604062064 6.470000e-168 601.0
23 TraesCS1B01G026200 chr3A 90.862 383 28 4 4145 4522 604069441 604069821 1.450000e-139 507.0
24 TraesCS1B01G026200 chr3A 93.750 160 4 3 3952 4111 604068644 604068797 7.560000e-58 235.0
25 TraesCS1B01G026200 chr6D 88.494 478 36 8 3531 4004 343405720 343406182 1.100000e-155 560.0
26 TraesCS1B01G026200 chr6D 90.501 379 32 3 4145 4522 343406868 343407243 8.740000e-137 497.0
27 TraesCS1B01G026200 chr6D 87.786 131 12 3 3982 4110 1519937 1520065 2.820000e-32 150.0
28 TraesCS1B01G026200 chr4A 88.462 130 11 2 3982 4110 478682712 478682838 2.180000e-33 154.0
29 TraesCS1B01G026200 chr3D 77.406 239 42 8 2181 2413 504013428 504013196 1.020000e-26 132.0
30 TraesCS1B01G026200 chr2B 74.160 387 67 17 4146 4509 205639764 205639388 3.670000e-26 130.0
31 TraesCS1B01G026200 chr6A 76.733 202 37 7 4140 4338 189774486 189774680 2.230000e-18 104.0
32 TraesCS1B01G026200 chr3B 75.566 221 34 13 2171 2385 665446926 665446720 1.730000e-14 91.6
33 TraesCS1B01G026200 chr3B 93.478 46 3 0 3530 3575 214555015 214554970 8.120000e-08 69.4
34 TraesCS1B01G026200 chr5B 75.882 170 32 8 2319 2484 367907830 367907994 1.350000e-10 78.7
35 TraesCS1B01G026200 chr6B 97.368 38 1 0 3700 3737 47865949 47865986 1.050000e-06 65.8
36 TraesCS1B01G026200 chr4D 97.368 38 1 0 3699 3736 450203786 450203749 1.050000e-06 65.8
37 TraesCS1B01G026200 chr5A 93.023 43 2 1 3704 3746 635948198 635948157 1.360000e-05 62.1


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 TraesCS1B01G026200 chr1B 12784194 12788715 4521 False 8351.0 8351 100.000000 1 4522 1 chr1B.!!$F1 4521
1 TraesCS1B01G026200 chr1B 13020450 13021966 1516 False 965.0 1495 89.772500 35 1597 2 chr1B.!!$F2 1562
2 TraesCS1B01G026200 chr1B 13568908 13570424 1516 False 917.5 1417 88.770500 35 1597 2 chr1B.!!$F3 1562
3 TraesCS1B01G026200 chr1B 12352779 12354145 1366 True 726.5 1013 87.248000 95 1597 2 chr1B.!!$R2 1502
4 TraesCS1B01G026200 chr1A 10748135 10751360 3225 False 4739.0 4739 93.259000 325 3538 1 chr1A.!!$F2 3213
5 TraesCS1B01G026200 chr1D 9439958 9443329 3371 False 1761.0 2736 93.050667 23 3538 3 chr1D.!!$F2 3515
6 TraesCS1B01G026200 chr7D 431033758 431035312 1554 False 447.7 824 94.240000 3537 4522 3 chr7D.!!$F3 985
7 TraesCS1B01G026200 chr3A 604068644 604069821 1177 False 371.0 507 92.306000 3952 4522 2 chr3A.!!$F2 570
8 TraesCS1B01G026200 chr6D 343405720 343407243 1523 False 528.5 560 89.497500 3531 4522 2 chr6D.!!$F2 991

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
677 734 0.664166 GCCGTTTGACAATGCCACAG 60.664 55.0 0.0 0.0 0.00 3.66 F
1347 1414 0.523966 CGTCTATGGCTCCGAGGATC 59.476 60.0 0.0 0.0 0.00 3.36 F
1348 1415 1.621992 GTCTATGGCTCCGAGGATCA 58.378 55.0 0.0 0.0 33.17 2.92 F
2336 2418 0.321671 AAGCTTGTTGCCGCTCTAGA 59.678 50.0 0.0 0.0 44.23 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1728 0.981183 TGCACTTAGGGACGGACAAT 59.019 50.000 0.0 0.0 0.00 2.71 R
2336 2418 1.260538 TTGCTCCGCTGAGATGAGGT 61.261 55.000 9.6 0.0 41.42 3.85 R
2341 2423 1.271054 ACAAGTTTGCTCCGCTGAGAT 60.271 47.619 9.6 0.0 41.42 2.75 R
4269 4990 0.035439 GATCCGAAACAGCTCCCCAA 60.035 55.000 0.0 0.0 0.00 4.12 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
77 78 5.066375 TCCTCTCAATGTTCAAACAACAGTG 59.934 40.000 8.28 8.28 44.64 3.66
81 82 1.550327 TGTTCAAACAACAGTGCCCA 58.450 45.000 0.00 0.00 35.67 5.36
84 85 5.469667 TGTTCAAACAACAGTGCCCACAC 62.470 47.826 0.82 0.00 40.64 3.82
194 199 1.047801 GCCTCCCCATCTCTCTCTTC 58.952 60.000 0.00 0.00 0.00 2.87
198 203 1.219213 TCCCCATCTCTCTCTTCCTCC 59.781 57.143 0.00 0.00 0.00 4.30
201 206 1.327303 CATCTCTCTCTTCCTCCCGG 58.673 60.000 0.00 0.00 0.00 5.73
247 264 1.557907 CGCGTACACACACACACAG 59.442 57.895 0.00 0.00 0.00 3.66
249 266 0.852777 GCGTACACACACACACAGAG 59.147 55.000 0.00 0.00 0.00 3.35
336 372 9.701098 AAATGAAGTGCATATGCTAATTAATGG 57.299 29.630 27.13 0.00 42.66 3.16
356 392 2.208431 GCTGATCGCTCTATGCAGTTT 58.792 47.619 0.00 0.00 43.06 2.66
363 399 2.286294 CGCTCTATGCAGTTTAGGCTTG 59.714 50.000 0.00 0.00 43.06 4.01
381 417 4.153475 GGCTTGTCACAAGAAACGCTTATA 59.847 41.667 22.30 0.00 34.31 0.98
402 438 0.989164 ACGAATGTGATGTGTACGCG 59.011 50.000 3.53 3.53 0.00 6.01
410 446 2.156891 GTGATGTGTACGCGTGTCAAAT 59.843 45.455 24.59 20.22 0.00 2.32
446 482 2.684927 GCCCACCTGATTGAGCTACATT 60.685 50.000 0.00 0.00 0.00 2.71
455 491 6.294120 CCTGATTGAGCTACATTCACAAAACA 60.294 38.462 0.00 0.00 35.77 2.83
458 494 4.843147 TGAGCTACATTCACAAAACAACG 58.157 39.130 0.00 0.00 0.00 4.10
484 537 2.877043 ACTTGCAAAACAGGCTGAAG 57.123 45.000 23.66 15.10 0.00 3.02
577 631 4.263572 CCTGTTGGCCGTGGGTGA 62.264 66.667 0.00 0.00 0.00 4.02
590 645 2.678336 CGTGGGTGATCTTTTTCTAGGC 59.322 50.000 0.00 0.00 0.00 3.93
599 654 3.472652 TCTTTTTCTAGGCGTTGCTTCA 58.527 40.909 0.00 0.00 0.00 3.02
676 733 1.106351 AGCCGTTTGACAATGCCACA 61.106 50.000 0.00 0.00 0.00 4.17
677 734 0.664166 GCCGTTTGACAATGCCACAG 60.664 55.000 0.00 0.00 0.00 3.66
681 738 2.030007 CGTTTGACAATGCCACAGGAAT 60.030 45.455 0.00 0.00 0.00 3.01
743 801 3.489355 TGCTAAGCATACATTCCCCATG 58.511 45.455 0.00 0.00 34.34 3.66
996 1061 3.316588 TCACCAATCAGCTAGAGATCGAC 59.683 47.826 0.00 0.00 0.00 4.20
1155 1220 1.220206 CGTGATCTGGCTTGCCTCT 59.780 57.895 13.18 0.00 0.00 3.69
1343 1410 2.336809 GGCGTCTATGGCTCCGAG 59.663 66.667 0.00 0.00 0.00 4.63
1344 1411 2.336809 GCGTCTATGGCTCCGAGG 59.663 66.667 0.00 0.00 0.00 4.63
1345 1412 2.194212 GCGTCTATGGCTCCGAGGA 61.194 63.158 0.00 0.00 0.00 3.71
1346 1413 1.528292 GCGTCTATGGCTCCGAGGAT 61.528 60.000 0.00 0.00 0.00 3.24
1347 1414 0.523966 CGTCTATGGCTCCGAGGATC 59.476 60.000 0.00 0.00 0.00 3.36
1348 1415 1.621992 GTCTATGGCTCCGAGGATCA 58.378 55.000 0.00 0.00 33.17 2.92
1349 1416 1.964223 GTCTATGGCTCCGAGGATCAA 59.036 52.381 0.00 0.00 33.17 2.57
1350 1417 2.365617 GTCTATGGCTCCGAGGATCAAA 59.634 50.000 0.00 0.00 33.17 2.69
1351 1418 2.630098 TCTATGGCTCCGAGGATCAAAG 59.370 50.000 0.00 0.00 33.17 2.77
1420 1496 4.334118 TGCGTGGTGAGCTGCCAT 62.334 61.111 9.53 0.00 38.40 4.40
1491 1567 2.203728 TACGTGCACCCTGACCCT 60.204 61.111 12.15 0.00 0.00 4.34
1652 1728 5.114081 GCGAGCTAGGACCTTTTTGTAATA 58.886 41.667 0.00 0.00 0.00 0.98
1679 1755 2.677037 CGTCCCTAAGTGCAACCCTTAG 60.677 54.545 13.19 13.19 40.59 2.18
1693 1769 5.690865 CAACCCTTAGCTATACCATCCAAA 58.309 41.667 0.00 0.00 0.00 3.28
1695 1771 6.530601 ACCCTTAGCTATACCATCCAAAAT 57.469 37.500 0.00 0.00 0.00 1.82
1702 1778 7.516198 AGCTATACCATCCAAAATGTCATTC 57.484 36.000 0.00 0.00 0.00 2.67
1786 1867 4.633565 GTGAGAGCATAGGGACTTCAAAAG 59.366 45.833 0.00 0.00 41.75 2.27
1803 1884 7.331687 ACTTCAAAAGTTTCCACATCAACAAAG 59.668 33.333 0.00 0.00 39.04 2.77
1813 1894 6.057533 TCCACATCAACAAAGCTATAGATGG 58.942 40.000 3.21 0.00 37.70 3.51
1828 1909 8.263640 AGCTATAGATGGGCAATCTGTTATTAG 58.736 37.037 14.86 3.48 45.64 1.73
1839 1920 9.860898 GGCAATCTGTTATTAGAAAACTTTCAT 57.139 29.630 5.07 0.00 39.61 2.57
1859 1940 8.531622 TTTCATATTTTTGTGTGCACCATTAG 57.468 30.769 15.69 0.00 0.00 1.73
2043 2125 5.965486 TCCAGTAGTGATGGGATGTACTAT 58.035 41.667 0.00 0.00 38.44 2.12
2051 2133 6.946583 AGTGATGGGATGTACTATGTACGTAT 59.053 38.462 0.00 0.00 0.00 3.06
2278 2360 2.675242 CCTTGGGGGTGCCGATGTA 61.675 63.158 0.00 0.00 0.00 2.29
2290 2372 4.448210 GTGCCGATGTATTTTTCCTCCTA 58.552 43.478 0.00 0.00 0.00 2.94
2336 2418 0.321671 AAGCTTGTTGCCGCTCTAGA 59.678 50.000 0.00 0.00 44.23 2.43
2341 2423 0.898326 TGTTGCCGCTCTAGACCTCA 60.898 55.000 0.00 0.00 0.00 3.86
2436 2522 1.153188 CACGCAGGTGGCCATGATA 60.153 57.895 9.72 0.00 40.58 2.15
2874 2961 6.290605 ACAAAAGGATGCAGTTTAATTGCTT 58.709 32.000 13.27 7.22 42.02 3.91
3028 3115 2.433239 ACAACTTCACCACGGTCTACTT 59.567 45.455 0.00 0.00 0.00 2.24
3043 3130 4.337555 GGTCTACTTCTACCTCACGCAATA 59.662 45.833 0.00 0.00 32.72 1.90
3070 3157 1.310933 GCTACCTCCTTCGTCGACCA 61.311 60.000 10.58 0.00 0.00 4.02
3167 3254 2.915659 TCCCAGTGGTTCGCGACT 60.916 61.111 9.15 0.00 36.58 4.18
3195 3282 1.153765 CTCGCGCTTGAGGTCATCA 60.154 57.895 5.56 0.00 35.62 3.07
3231 3318 2.482333 CCGGTTTTCCAACGCCACA 61.482 57.895 0.00 0.00 40.70 4.17
3551 3638 9.614792 CAAGTAATGAAAACTAGCTAATACCCT 57.385 33.333 0.00 0.00 0.00 4.34
3575 3662 3.430931 GCGTTGCTGCGGAAATTTATAA 58.569 40.909 0.00 0.00 0.00 0.98
3686 3774 7.004555 TCCAAACAATGTGTACATAGTCTCT 57.995 36.000 0.00 0.00 35.10 3.10
3690 3778 8.873830 CAAACAATGTGTACATAGTCTCTAAGG 58.126 37.037 0.00 0.00 35.10 2.69
3939 4040 8.225107 CCAAAAGACATGTTTTTATTCATGCAG 58.775 33.333 14.14 2.68 43.34 4.41
3940 4041 8.980610 CAAAAGACATGTTTTTATTCATGCAGA 58.019 29.630 14.14 0.00 43.34 4.26
3941 4042 9.715121 AAAAGACATGTTTTTATTCATGCAGAT 57.285 25.926 14.14 0.00 43.34 2.90
3942 4043 9.715121 AAAGACATGTTTTTATTCATGCAGATT 57.285 25.926 12.35 0.00 43.34 2.40
3943 4044 8.922058 AGACATGTTTTTATTCATGCAGATTC 57.078 30.769 0.00 0.00 43.34 2.52
3944 4045 8.525316 AGACATGTTTTTATTCATGCAGATTCA 58.475 29.630 0.00 0.00 43.34 2.57
3945 4046 9.309516 GACATGTTTTTATTCATGCAGATTCAT 57.690 29.630 0.00 0.00 43.34 2.57
3946 4047 9.093970 ACATGTTTTTATTCATGCAGATTCATG 57.906 29.630 0.00 0.00 43.34 3.07
3947 4048 9.093970 CATGTTTTTATTCATGCAGATTCATGT 57.906 29.630 0.00 0.00 43.18 3.21
3948 4049 8.468720 TGTTTTTATTCATGCAGATTCATGTG 57.531 30.769 0.00 0.00 43.18 3.21
3949 4050 8.089597 TGTTTTTATTCATGCAGATTCATGTGT 58.910 29.630 0.00 0.00 43.18 3.72
4008 4109 7.036220 ACTACAATCGAAGTTGATCAACCTAG 58.964 38.462 30.34 20.14 42.06 3.02
4051 4152 1.666189 GCAACCTCGCACCTAATTCTC 59.334 52.381 0.00 0.00 0.00 2.87
4096 4221 9.121517 CATGAGATTCTTTCATGTGTTGTTAAC 57.878 33.333 0.00 0.00 44.30 2.01
4097 4222 8.219546 TGAGATTCTTTCATGTGTTGTTAACA 57.780 30.769 3.59 3.59 39.52 2.41
4107 4232 2.992593 TGTTGTTAACACTGTCCTGCA 58.007 42.857 8.07 0.00 36.25 4.41
4108 4233 3.550820 TGTTGTTAACACTGTCCTGCAT 58.449 40.909 8.07 0.00 36.25 3.96
4109 4234 3.314913 TGTTGTTAACACTGTCCTGCATG 59.685 43.478 8.07 0.00 36.25 4.06
4110 4235 1.879380 TGTTAACACTGTCCTGCATGC 59.121 47.619 11.82 11.82 0.00 4.06
4127 4269 3.806380 CATGCTCAGCCTAGTGAGAAAT 58.194 45.455 13.18 4.51 46.02 2.17
4143 4860 1.325338 GAAATGAAACATGCGGCATGC 59.675 47.619 35.80 23.01 44.80 4.06
4156 4873 2.336667 CGGCATGCGTGATATACATGA 58.663 47.619 12.44 0.00 43.04 3.07
4194 4915 0.324738 TCCTCCTTCTCGTGGCTCAT 60.325 55.000 0.00 0.00 0.00 2.90
4269 4990 3.266772 TCTGCAGAGGGATTTAATGGTGT 59.733 43.478 13.74 0.00 0.00 4.16
4273 4994 3.701040 CAGAGGGATTTAATGGTGTTGGG 59.299 47.826 0.00 0.00 0.00 4.12
4276 4997 3.031013 GGGATTTAATGGTGTTGGGGAG 58.969 50.000 0.00 0.00 0.00 4.30
4292 5013 1.066143 GGGAGCTGTTTCGGATCAAGA 60.066 52.381 0.00 0.00 0.00 3.02
4293 5014 2.275318 GGAGCTGTTTCGGATCAAGAG 58.725 52.381 0.00 0.00 0.00 2.85
4311 5032 1.077429 GGTGGGAGGGAGACAATGC 60.077 63.158 0.00 0.00 0.00 3.56
4316 5037 1.373570 GGAGGGAGACAATGCGAAAG 58.626 55.000 0.00 0.00 0.00 2.62
4400 5121 2.478872 TCTAAGTGGGGGAGATGAGG 57.521 55.000 0.00 0.00 0.00 3.86
4423 5145 1.549203 GGGTGTAGGACGTACCAAGA 58.451 55.000 6.77 0.00 42.04 3.02
4437 5159 1.202698 ACCAAGAAGCACTGGAGACAC 60.203 52.381 0.00 0.00 35.60 3.67
4479 5202 4.191544 CCTTTTGGCTCAATCAGTCGATA 58.808 43.478 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.697654 AGTTCTCTGCAATCTCTGTGC 58.302 47.619 0.00 0.00 42.55 4.57
5 6 4.753610 TCAAAGTTCTCTGCAATCTCTGTG 59.246 41.667 0.00 0.00 0.00 3.66
6 7 4.965814 TCAAAGTTCTCTGCAATCTCTGT 58.034 39.130 0.00 0.00 0.00 3.41
7 8 5.674068 GCATCAAAGTTCTCTGCAATCTCTG 60.674 44.000 0.00 0.00 33.13 3.35
8 9 4.395542 GCATCAAAGTTCTCTGCAATCTCT 59.604 41.667 0.00 0.00 33.13 3.10
9 10 4.395542 AGCATCAAAGTTCTCTGCAATCTC 59.604 41.667 0.00 0.00 35.32 2.75
10 11 4.333690 AGCATCAAAGTTCTCTGCAATCT 58.666 39.130 0.00 0.00 35.32 2.40
11 12 4.395542 AGAGCATCAAAGTTCTCTGCAATC 59.604 41.667 0.00 0.00 37.82 2.67
12 13 4.333690 AGAGCATCAAAGTTCTCTGCAAT 58.666 39.130 0.00 0.00 37.82 3.56
13 14 3.748083 AGAGCATCAAAGTTCTCTGCAA 58.252 40.909 0.00 0.00 37.82 4.08
14 15 3.413846 AGAGCATCAAAGTTCTCTGCA 57.586 42.857 6.35 0.00 37.82 4.41
15 16 5.869753 TTTAGAGCATCAAAGTTCTCTGC 57.130 39.130 0.00 0.00 37.82 4.26
16 17 7.432350 AGTTTTAGAGCATCAAAGTTCTCTG 57.568 36.000 0.00 0.00 37.82 3.35
17 18 8.348507 CAAAGTTTTAGAGCATCAAAGTTCTCT 58.651 33.333 0.00 0.00 37.82 3.10
18 19 8.345565 TCAAAGTTTTAGAGCATCAAAGTTCTC 58.654 33.333 0.00 0.00 37.82 2.87
19 20 8.225603 TCAAAGTTTTAGAGCATCAAAGTTCT 57.774 30.769 0.00 0.00 37.82 3.01
20 21 8.909671 CATCAAAGTTTTAGAGCATCAAAGTTC 58.090 33.333 0.00 0.00 37.82 3.01
21 22 7.383300 GCATCAAAGTTTTAGAGCATCAAAGTT 59.617 33.333 0.00 0.00 37.82 2.66
56 57 4.439974 GGCACTGTTGTTTGAACATTGAGA 60.440 41.667 8.56 0.00 38.95 3.27
198 203 2.369629 CGTGTGCGTGTTAGACCGG 61.370 63.158 0.00 0.00 0.00 5.28
313 349 6.491062 AGCCATTAATTAGCATATGCACTTCA 59.509 34.615 28.62 10.98 45.16 3.02
356 392 1.871039 GCGTTTCTTGTGACAAGCCTA 59.129 47.619 19.99 5.59 0.00 3.93
363 399 5.908106 TCGTTTATAAGCGTTTCTTGTGAC 58.092 37.500 19.23 0.00 36.25 3.67
381 417 2.159894 CGCGTACACATCACATTCGTTT 60.160 45.455 0.00 0.00 0.00 3.60
402 438 5.916883 GCATGACAATATGCCTATTTGACAC 59.083 40.000 0.00 0.00 45.93 3.67
429 465 4.558226 TGTGAATGTAGCTCAATCAGGT 57.442 40.909 0.00 0.00 36.75 4.00
446 482 1.609555 GTATGGCCCGTTGTTTTGTGA 59.390 47.619 0.00 0.00 0.00 3.58
455 491 1.000394 GTTTTGCAAGTATGGCCCGTT 60.000 47.619 0.00 0.00 29.78 4.44
458 494 1.066929 CCTGTTTTGCAAGTATGGCCC 60.067 52.381 0.00 0.00 29.78 5.80
484 537 5.513849 CGCCCGTGGATTTTCTTTTATTTAC 59.486 40.000 0.00 0.00 0.00 2.01
577 631 4.072131 TGAAGCAACGCCTAGAAAAAGAT 58.928 39.130 0.00 0.00 0.00 2.40
590 645 2.741612 TGAGCCAAAATTGAAGCAACG 58.258 42.857 0.00 0.00 0.00 4.10
641 698 3.857052 ACGGCTTCTTTGTTATCGATCA 58.143 40.909 0.00 0.00 0.00 2.92
650 707 3.705604 CATTGTCAAACGGCTTCTTTGT 58.294 40.909 0.00 0.00 31.63 2.83
743 801 1.660167 GTACATAGGGGGCGTTGAAC 58.340 55.000 0.00 0.00 0.00 3.18
996 1061 4.738998 TGCGGCTTCCCCATGGTG 62.739 66.667 11.73 0.00 0.00 4.17
1155 1220 4.074526 GCCGCAGAGAGGTCAGCA 62.075 66.667 0.00 0.00 34.94 4.41
1242 1307 2.358737 CCGCCGCCACTCTCTTTT 60.359 61.111 0.00 0.00 0.00 2.27
1255 1320 3.524648 TTTCGTCTCCACCACCGCC 62.525 63.158 0.00 0.00 0.00 6.13
1332 1399 1.694150 CCTTTGATCCTCGGAGCCATA 59.306 52.381 0.00 0.00 0.00 2.74
1345 1412 2.376109 CAGCAAGCTGATCCCTTTGAT 58.624 47.619 16.75 0.00 46.30 2.57
1346 1413 1.615116 CCAGCAAGCTGATCCCTTTGA 60.615 52.381 22.76 0.00 46.30 2.69
1347 1414 0.815734 CCAGCAAGCTGATCCCTTTG 59.184 55.000 22.76 0.22 46.30 2.77
1348 1415 0.407139 ACCAGCAAGCTGATCCCTTT 59.593 50.000 22.76 0.00 46.30 3.11
1349 1416 0.323178 CACCAGCAAGCTGATCCCTT 60.323 55.000 22.76 0.00 46.30 3.95
1350 1417 1.302285 CACCAGCAAGCTGATCCCT 59.698 57.895 22.76 0.00 46.30 4.20
1351 1418 2.413142 GCACCAGCAAGCTGATCCC 61.413 63.158 22.76 5.15 46.30 3.85
1491 1567 1.064240 TCCGGTGAGCTGAGGTATGTA 60.064 52.381 0.00 0.00 0.00 2.29
1640 1716 5.650703 AGGGACGGACAATATTACAAAAAGG 59.349 40.000 0.00 0.00 0.00 3.11
1652 1728 0.981183 TGCACTTAGGGACGGACAAT 59.019 50.000 0.00 0.00 0.00 2.71
1679 1755 7.275888 TGAATGACATTTTGGATGGTATAGC 57.724 36.000 1.39 0.00 0.00 2.97
1767 1848 5.106118 GGAAACTTTTGAAGTCCCTATGCTC 60.106 44.000 0.00 0.00 41.91 4.26
1774 1855 4.340950 TGATGTGGAAACTTTTGAAGTCCC 59.659 41.667 0.00 0.61 41.91 4.46
1786 1867 7.377766 TCTATAGCTTTGTTGATGTGGAAAC 57.622 36.000 0.00 0.00 0.00 2.78
1803 1884 8.260818 TCTAATAACAGATTGCCCATCTATAGC 58.739 37.037 0.00 0.00 40.67 2.97
1813 1894 9.860898 ATGAAAGTTTTCTAATAACAGATTGCC 57.139 29.630 6.21 0.00 38.02 4.52
1828 1909 7.850492 GGTGCACACAAAAATATGAAAGTTTTC 59.150 33.333 20.43 0.00 37.69 2.29
1839 1920 7.753309 AGTACTAATGGTGCACACAAAAATA 57.247 32.000 20.43 0.00 32.88 1.40
2017 2099 5.667626 AGTACATCCCATCACTACTGGAATT 59.332 40.000 0.00 0.00 35.70 2.17
2043 2125 4.979815 CGATTGAACCTATGCATACGTACA 59.020 41.667 1.16 0.00 0.00 2.90
2051 2133 3.198409 AGATGCGATTGAACCTATGCA 57.802 42.857 0.00 0.00 36.69 3.96
2095 2177 8.774586 CAGAAATATAAGCGGCATTAAAGTACT 58.225 33.333 1.45 0.00 0.00 2.73
2278 2360 5.183140 CGTTGTTGGATGTAGGAGGAAAAAT 59.817 40.000 0.00 0.00 0.00 1.82
2290 2372 2.903547 GCACGCCGTTGTTGGATGT 61.904 57.895 0.00 0.00 0.00 3.06
2336 2418 1.260538 TTGCTCCGCTGAGATGAGGT 61.261 55.000 9.60 0.00 41.42 3.85
2341 2423 1.271054 ACAAGTTTGCTCCGCTGAGAT 60.271 47.619 9.60 0.00 41.42 2.75
2436 2522 3.641436 TCTCCGTGGTGATTGCTACATAT 59.359 43.478 0.00 0.00 0.00 1.78
2568 2654 6.218019 TCTTGATTCAAAGCTGGACAAAATG 58.782 36.000 0.01 0.00 0.00 2.32
2614 2701 5.411083 TTTTATATGTTTATGCTGCGCGA 57.589 34.783 12.10 0.00 0.00 5.87
2615 2702 5.850653 TCATTTTATATGTTTATGCTGCGCG 59.149 36.000 0.00 0.00 0.00 6.86
2616 2703 7.077605 TCTCATTTTATATGTTTATGCTGCGC 58.922 34.615 0.00 0.00 0.00 6.09
2617 2704 9.616634 AATCTCATTTTATATGTTTATGCTGCG 57.383 29.630 0.00 0.00 0.00 5.18
2707 2794 6.431234 AGATCAACAGTTCATTCCACCTAAAC 59.569 38.462 0.00 0.00 0.00 2.01
2784 2871 4.248859 CTGCACTGCTATCTAACACAACT 58.751 43.478 1.98 0.00 0.00 3.16
2874 2961 4.645136 ACGAGCTTCCTGTAGATCACAATA 59.355 41.667 0.00 0.00 36.48 1.90
3028 3115 3.635433 GCGTATTGCGTGAGGTAGA 57.365 52.632 0.00 0.00 43.66 2.59
3070 3157 3.231965 CGAGAACGTTGTGTATCGAAGT 58.768 45.455 5.00 0.00 40.48 3.01
3195 3282 1.593296 GGGAAGTAGGTCACGTCGCT 61.593 60.000 0.00 0.00 42.63 4.93
3231 3318 2.443390 GATGCAGGGGCCATTGCT 60.443 61.111 26.06 15.36 40.87 3.91
3631 3719 3.873361 CCACCACAGCTACAGTTCATATG 59.127 47.826 0.00 0.00 0.00 1.78
3686 3774 8.770010 TTTTGGAACAGAGGAAATAAACCTTA 57.230 30.769 0.00 0.00 42.39 2.69
3695 3783 6.017440 CGACACTTATTTTGGAACAGAGGAAA 60.017 38.462 0.00 0.00 42.39 3.13
3939 4040 7.092137 TCAAGATGATCCAAACACATGAATC 57.908 36.000 0.00 0.00 0.00 2.52
3940 4041 7.470935 TTCAAGATGATCCAAACACATGAAT 57.529 32.000 0.00 0.00 0.00 2.57
3941 4042 6.897706 TTCAAGATGATCCAAACACATGAA 57.102 33.333 0.00 0.00 0.00 2.57
3942 4043 7.177041 TCAATTCAAGATGATCCAAACACATGA 59.823 33.333 0.00 0.00 0.00 3.07
3943 4044 7.317390 TCAATTCAAGATGATCCAAACACATG 58.683 34.615 0.00 0.00 0.00 3.21
3944 4045 7.395206 TCTCAATTCAAGATGATCCAAACACAT 59.605 33.333 0.00 0.00 0.00 3.21
3945 4046 6.716173 TCTCAATTCAAGATGATCCAAACACA 59.284 34.615 0.00 0.00 0.00 3.72
3946 4047 7.094463 ACTCTCAATTCAAGATGATCCAAACAC 60.094 37.037 0.00 0.00 0.00 3.32
3947 4048 6.944290 ACTCTCAATTCAAGATGATCCAAACA 59.056 34.615 0.00 0.00 0.00 2.83
3948 4049 7.388460 ACTCTCAATTCAAGATGATCCAAAC 57.612 36.000 0.00 0.00 0.00 2.93
3949 4050 9.690913 AATACTCTCAATTCAAGATGATCCAAA 57.309 29.630 0.00 0.00 0.00 3.28
4051 4152 3.577649 TGAACTACTCTGCCTTCTTCG 57.422 47.619 0.00 0.00 0.00 3.79
4090 4191 1.879380 GCATGCAGGACAGTGTTAACA 59.121 47.619 14.21 3.59 0.00 2.41
4096 4221 1.645704 GCTGAGCATGCAGGACAGTG 61.646 60.000 21.98 5.04 36.41 3.66
4097 4222 1.376942 GCTGAGCATGCAGGACAGT 60.377 57.895 21.98 0.00 36.41 3.55
4098 4223 2.113433 GGCTGAGCATGCAGGACAG 61.113 63.158 21.98 21.45 36.41 3.51
4099 4224 1.266867 TAGGCTGAGCATGCAGGACA 61.267 55.000 21.98 12.82 36.41 4.02
4100 4225 0.532417 CTAGGCTGAGCATGCAGGAC 60.532 60.000 21.98 11.33 36.41 3.85
4101 4226 0.979709 ACTAGGCTGAGCATGCAGGA 60.980 55.000 21.98 1.46 36.41 3.86
4102 4227 0.814410 CACTAGGCTGAGCATGCAGG 60.814 60.000 21.98 10.21 36.41 4.85
4103 4228 0.177373 TCACTAGGCTGAGCATGCAG 59.823 55.000 21.98 10.76 38.91 4.41
4104 4229 0.177373 CTCACTAGGCTGAGCATGCA 59.823 55.000 21.98 0.00 31.57 3.96
4105 4230 0.463204 TCTCACTAGGCTGAGCATGC 59.537 55.000 10.51 10.51 38.07 4.06
4106 4231 2.975732 TTCTCACTAGGCTGAGCATG 57.024 50.000 6.82 0.00 38.07 4.06
4107 4232 3.453717 TCATTTCTCACTAGGCTGAGCAT 59.546 43.478 6.82 0.11 38.07 3.79
4108 4233 2.833943 TCATTTCTCACTAGGCTGAGCA 59.166 45.455 6.82 0.00 38.07 4.26
4109 4234 3.533606 TCATTTCTCACTAGGCTGAGC 57.466 47.619 0.00 0.00 38.07 4.26
4110 4235 5.240891 TGTTTCATTTCTCACTAGGCTGAG 58.759 41.667 0.00 4.36 39.35 3.35
4127 4269 2.178769 CGCATGCCGCATGTTTCA 59.821 55.556 29.36 0.00 43.10 2.69
4143 4860 4.039245 AGTTGGGGACTCATGTATATCACG 59.961 45.833 0.00 0.00 31.20 4.35
4194 4915 8.299570 GCTTCAGGTTCATTCATCTCTTTAAAA 58.700 33.333 0.00 0.00 0.00 1.52
4241 4962 3.795688 AAATCCCTCTGCAGAAACTGA 57.204 42.857 18.85 11.67 32.44 3.41
4269 4990 0.035439 GATCCGAAACAGCTCCCCAA 60.035 55.000 0.00 0.00 0.00 4.12
4273 4994 2.275318 CTCTTGATCCGAAACAGCTCC 58.725 52.381 0.00 0.00 0.00 4.70
4276 4997 1.734465 CACCTCTTGATCCGAAACAGC 59.266 52.381 0.00 0.00 0.00 4.40
4292 5013 1.566298 GCATTGTCTCCCTCCCACCT 61.566 60.000 0.00 0.00 0.00 4.00
4293 5014 1.077429 GCATTGTCTCCCTCCCACC 60.077 63.158 0.00 0.00 0.00 4.61
4311 5032 9.891535 GTTATTAACAAGTTACGTATCCTTTCG 57.108 33.333 0.00 0.00 0.00 3.46
4316 5037 8.325997 CAGCAGTTATTAACAAGTTACGTATCC 58.674 37.037 9.15 0.00 0.00 2.59
4400 5121 0.171231 GGTACGTCCTACACCCGTTC 59.829 60.000 0.00 0.00 36.12 3.95
4423 5145 0.601311 GCTTCGTGTCTCCAGTGCTT 60.601 55.000 0.00 0.00 0.00 3.91
4437 5159 0.318275 GATCCTACCGCAGAGCTTCG 60.318 60.000 0.00 0.00 0.00 3.79
4479 5202 0.988832 TTCGGTTCCAGCCATAACCT 59.011 50.000 9.31 0.00 42.51 3.50


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

AutoCloner maintained by Alex Coulton.