Multiple sequence alignment - TraesCS6B01G373900

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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 TraesCS6B01G373900 chr6B 100.000 4145 0 0 1 4145 646720883 646725027 0.000000e+00 7655.0
1 TraesCS6B01G373900 chr6B 95.563 2862 109 4 1290 4145 114230011 114232860 0.000000e+00 4566.0
2 TraesCS6B01G373900 chr6B 94.640 2220 90 5 1289 3491 476708871 476711078 0.000000e+00 3413.0
3 TraesCS6B01G373900 chr6B 96.356 1921 58 11 2230 4145 707590467 707592380 0.000000e+00 3149.0
4 TraesCS6B01G373900 chr2B 96.541 2862 78 5 1290 4145 451484992 451487838 0.000000e+00 4717.0
5 TraesCS6B01G373900 chr2B 97.312 2083 54 2 2062 4144 178741719 178743799 0.000000e+00 3535.0
6 TraesCS6B01G373900 chr2B 92.946 2013 100 10 1290 3282 36422145 36420155 0.000000e+00 2892.0
7 TraesCS6B01G373900 chr2B 93.147 788 41 3 1290 2067 178732204 178732988 0.000000e+00 1144.0
8 TraesCS6B01G373900 chr2B 93.485 307 20 0 1290 1596 451517173 451516867 1.360000e-124 457.0
9 TraesCS6B01G373900 chr2B 92.508 307 23 0 1290 1596 178758752 178758446 1.370000e-119 440.0
10 TraesCS6B01G373900 chr2B 72.995 611 107 32 116 704 41407636 41407062 1.190000e-35 161.0
11 TraesCS6B01G373900 chr2B 77.612 268 44 14 445 703 245000489 245000229 9.280000e-32 148.0
12 TraesCS6B01G373900 chr2B 78.629 248 33 16 494 728 245106200 245105960 3.340000e-31 147.0
13 TraesCS6B01G373900 chr5B 95.881 2865 93 6 1287 4145 434055866 434053021 0.000000e+00 4614.0
14 TraesCS6B01G373900 chr6A 95.089 2871 100 7 1290 4145 35946509 35949353 0.000000e+00 4482.0
15 TraesCS6B01G373900 chr6A 89.655 1276 62 23 2 1268 574523089 574524303 0.000000e+00 1561.0
16 TraesCS6B01G373900 chr6A 71.351 555 99 46 201 733 457097552 457097036 5.710000e-14 89.8
17 TraesCS6B01G373900 chr4A 96.196 2103 53 3 1585 3677 706721827 706719742 0.000000e+00 3415.0
18 TraesCS6B01G373900 chr4A 97.149 1999 45 4 2150 4145 621804894 621802905 0.000000e+00 3365.0
19 TraesCS6B01G373900 chr4A 94.265 558 31 1 1289 1845 706719187 706719744 0.000000e+00 852.0
20 TraesCS6B01G373900 chr2A 97.044 1996 58 1 2150 4145 772403893 772405887 0.000000e+00 3358.0
21 TraesCS6B01G373900 chr2A 77.143 210 35 12 207 410 59578185 59578387 4.380000e-20 110.0
22 TraesCS6B01G373900 chr5A 96.648 1969 61 3 2177 4145 13344011 13342048 0.000000e+00 3265.0
23 TraesCS6B01G373900 chr5A 91.374 313 18 2 1289 1592 13331593 13331905 1.780000e-113 420.0
24 TraesCS6B01G373900 chr5A 73.620 326 54 22 115 433 480298853 480299153 3.410000e-16 97.1
25 TraesCS6B01G373900 chr5A 92.593 54 4 0 689 742 648860337 648860390 1.240000e-10 78.7
26 TraesCS6B01G373900 chr7A 96.416 1925 53 13 2230 4145 299416182 299418099 0.000000e+00 3158.0
27 TraesCS6B01G373900 chr7A 93.486 875 40 7 1292 2150 299415306 299416179 0.000000e+00 1284.0
28 TraesCS6B01G373900 chr7A 90.667 300 21 2 1303 1596 299423026 299422728 3.880000e-105 392.0
29 TraesCS6B01G373900 chr7B 93.014 2004 112 16 1289 3279 27945203 27947191 0.000000e+00 2900.0
30 TraesCS6B01G373900 chr7B 91.379 58 5 0 686 743 14980172 14980115 3.430000e-11 80.5
31 TraesCS6B01G373900 chr3A 93.707 1017 49 3 1290 2292 171625547 171626562 0.000000e+00 1509.0
32 TraesCS6B01G373900 chr3A 74.086 629 121 29 117 732 574251250 574251849 1.940000e-53 220.0
33 TraesCS6B01G373900 chr3B 92.202 872 46 7 1290 2150 344147567 344146707 0.000000e+00 1214.0
34 TraesCS6B01G373900 chr3B 75.298 336 52 19 44 367 151588576 151588892 9.350000e-27 132.0
35 TraesCS6B01G373900 chr6D 90.054 925 52 14 1290 2194 4320193 4319289 0.000000e+00 1162.0
36 TraesCS6B01G373900 chr6D 77.524 307 50 17 445 743 79892059 79892354 2.560000e-37 167.0
37 TraesCS6B01G373900 chrUn 86.168 882 72 17 1290 2158 30900493 30901337 0.000000e+00 907.0
38 TraesCS6B01G373900 chr1A 87.306 772 68 9 1290 2054 556662915 556663663 0.000000e+00 856.0
39 TraesCS6B01G373900 chr1A 77.407 270 46 12 478 736 497491557 497491292 3.340000e-31 147.0
40 TraesCS6B01G373900 chr1A 80.000 160 26 6 200 355 18946743 18946586 3.390000e-21 113.0
41 TraesCS6B01G373900 chr1A 80.000 160 27 5 200 355 19044392 19044234 3.390000e-21 113.0
42 TraesCS6B01G373900 chr1A 77.841 176 29 8 187 355 18782395 18782223 2.640000e-17 100.0
43 TraesCS6B01G373900 chr1A 77.714 175 30 8 187 355 18864338 18864167 9.480000e-17 99.0
44 TraesCS6B01G373900 chr2D 87.955 714 64 7 1290 1996 625378060 625377362 0.000000e+00 822.0
45 TraesCS6B01G373900 chr2D 73.663 729 131 46 117 822 372595373 372594683 4.170000e-55 226.0
46 TraesCS6B01G373900 chr2D 77.647 255 44 11 445 692 188880616 188880368 4.320000e-30 143.0
47 TraesCS6B01G373900 chr2D 84.211 152 15 9 187 333 59656435 59656582 5.590000e-29 139.0
48 TraesCS6B01G373900 chr2D 85.507 69 6 4 678 743 28912472 28912405 7.440000e-08 69.4
49 TraesCS6B01G373900 chr7D 73.684 475 93 23 196 648 565298316 565297852 5.550000e-34 156.0
50 TraesCS6B01G373900 chr1D 71.901 605 110 40 162 743 214831539 214830972 2.020000e-23 121.0
51 TraesCS6B01G373900 chr5D 80.537 149 21 8 289 433 379802867 379803011 1.580000e-19 108.0
52 TraesCS6B01G373900 chr4D 81.481 108 10 6 2 99 38589820 38589713 3.430000e-11 80.5
53 TraesCS6B01G373900 chr4B 79.630 108 12 7 2 99 56270552 56270445 7.440000e-08 69.4


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 TraesCS6B01G373900 chr6B 646720883 646725027 4144 False 7655 7655 100.000 1 4145 1 chr6B.!!$F3 4144
1 TraesCS6B01G373900 chr6B 114230011 114232860 2849 False 4566 4566 95.563 1290 4145 1 chr6B.!!$F1 2855
2 TraesCS6B01G373900 chr6B 476708871 476711078 2207 False 3413 3413 94.640 1289 3491 1 chr6B.!!$F2 2202
3 TraesCS6B01G373900 chr6B 707590467 707592380 1913 False 3149 3149 96.356 2230 4145 1 chr6B.!!$F4 1915
4 TraesCS6B01G373900 chr2B 451484992 451487838 2846 False 4717 4717 96.541 1290 4145 1 chr2B.!!$F3 2855
5 TraesCS6B01G373900 chr2B 178741719 178743799 2080 False 3535 3535 97.312 2062 4144 1 chr2B.!!$F2 2082
6 TraesCS6B01G373900 chr2B 36420155 36422145 1990 True 2892 2892 92.946 1290 3282 1 chr2B.!!$R1 1992
7 TraesCS6B01G373900 chr2B 178732204 178732988 784 False 1144 1144 93.147 1290 2067 1 chr2B.!!$F1 777
8 TraesCS6B01G373900 chr5B 434053021 434055866 2845 True 4614 4614 95.881 1287 4145 1 chr5B.!!$R1 2858
9 TraesCS6B01G373900 chr6A 35946509 35949353 2844 False 4482 4482 95.089 1290 4145 1 chr6A.!!$F1 2855
10 TraesCS6B01G373900 chr6A 574523089 574524303 1214 False 1561 1561 89.655 2 1268 1 chr6A.!!$F2 1266
11 TraesCS6B01G373900 chr4A 706719742 706721827 2085 True 3415 3415 96.196 1585 3677 1 chr4A.!!$R2 2092
12 TraesCS6B01G373900 chr4A 621802905 621804894 1989 True 3365 3365 97.149 2150 4145 1 chr4A.!!$R1 1995
13 TraesCS6B01G373900 chr4A 706719187 706719744 557 False 852 852 94.265 1289 1845 1 chr4A.!!$F1 556
14 TraesCS6B01G373900 chr2A 772403893 772405887 1994 False 3358 3358 97.044 2150 4145 1 chr2A.!!$F2 1995
15 TraesCS6B01G373900 chr5A 13342048 13344011 1963 True 3265 3265 96.648 2177 4145 1 chr5A.!!$R1 1968
16 TraesCS6B01G373900 chr7A 299415306 299418099 2793 False 2221 3158 94.951 1292 4145 2 chr7A.!!$F1 2853
17 TraesCS6B01G373900 chr7B 27945203 27947191 1988 False 2900 2900 93.014 1289 3279 1 chr7B.!!$F1 1990
18 TraesCS6B01G373900 chr3A 171625547 171626562 1015 False 1509 1509 93.707 1290 2292 1 chr3A.!!$F1 1002
19 TraesCS6B01G373900 chr3A 574251250 574251849 599 False 220 220 74.086 117 732 1 chr3A.!!$F2 615
20 TraesCS6B01G373900 chr3B 344146707 344147567 860 True 1214 1214 92.202 1290 2150 1 chr3B.!!$R1 860
21 TraesCS6B01G373900 chr6D 4319289 4320193 904 True 1162 1162 90.054 1290 2194 1 chr6D.!!$R1 904
22 TraesCS6B01G373900 chrUn 30900493 30901337 844 False 907 907 86.168 1290 2158 1 chrUn.!!$F1 868
23 TraesCS6B01G373900 chr1A 556662915 556663663 748 False 856 856 87.306 1290 2054 1 chr1A.!!$F1 764
24 TraesCS6B01G373900 chr2D 625377362 625378060 698 True 822 822 87.955 1290 1996 1 chr2D.!!$R4 706
25 TraesCS6B01G373900 chr2D 372594683 372595373 690 True 226 226 73.663 117 822 1 chr2D.!!$R3 705

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
873 911 3.267031 AGCTAACTATTTGGTGGGCTTCT 59.733 43.478 0.0 0.0 0.00 2.85 F
1283 1324 1.689984 TGTGCTTTGATGTTGCCTCA 58.310 45.000 0.0 0.0 0.00 3.86 F
1679 1772 1.679153 GGTTTTGGAGGACGAAAGCAA 59.321 47.619 0.0 0.0 45.84 3.91 F
2467 2605 1.766494 TGAAGCTATGGGCAATGGTG 58.234 50.000 0.0 0.0 44.79 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1772 0.739561 GAGGCTAGAATGGTCGTCGT 59.260 55.000 0.00 0.0 0.00 4.34 R
2467 2605 2.424956 CCTAGCACTTTTGGCATCTTCC 59.575 50.000 0.00 0.0 0.00 3.46 R
2922 3060 3.329300 TCAGCAACCTGAAGCTTCC 57.671 52.632 23.42 7.0 44.79 3.46 R
3961 4125 0.832135 TGCTCAACTCCGAGGAAGGT 60.832 55.000 0.00 0.0 33.36 3.50 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
91 92 7.867921 AGGGTAATACCAATAACACTCATTCA 58.132 34.615 12.03 0.00 41.02 2.57
101 102 7.756722 CCAATAACACTCATTCATTCCTTCAAC 59.243 37.037 0.00 0.00 0.00 3.18
113 114 3.915437 TCCTTCAACCATTTTCTTCGC 57.085 42.857 0.00 0.00 0.00 4.70
185 186 7.488792 TGCAATTTCTATGTAAATCATGTGCAC 59.511 33.333 10.75 10.75 37.91 4.57
680 718 7.378995 ACTTTTGTGTAAATTACGCGCAAATTA 59.621 29.630 17.29 7.80 41.91 1.40
823 861 5.885912 GGGCCAGTTTCTATTATGTTTCAGA 59.114 40.000 4.39 0.00 0.00 3.27
824 862 6.183360 GGGCCAGTTTCTATTATGTTTCAGAC 60.183 42.308 4.39 0.00 0.00 3.51
825 863 6.183360 GGCCAGTTTCTATTATGTTTCAGACC 60.183 42.308 0.00 0.00 0.00 3.85
826 864 6.374333 GCCAGTTTCTATTATGTTTCAGACCA 59.626 38.462 0.00 0.00 0.00 4.02
827 865 7.067494 GCCAGTTTCTATTATGTTTCAGACCAT 59.933 37.037 0.00 0.00 0.00 3.55
828 866 8.960591 CCAGTTTCTATTATGTTTCAGACCATT 58.039 33.333 0.00 0.00 0.00 3.16
829 867 9.778993 CAGTTTCTATTATGTTTCAGACCATTG 57.221 33.333 0.00 0.00 0.00 2.82
830 868 9.739276 AGTTTCTATTATGTTTCAGACCATTGA 57.261 29.630 0.00 0.00 0.00 2.57
845 883 4.224991 CCATTGATTGGGCCATTTTTCT 57.775 40.909 7.26 0.00 42.33 2.52
846 884 4.591929 CCATTGATTGGGCCATTTTTCTT 58.408 39.130 7.26 0.00 42.33 2.52
873 911 3.267031 AGCTAACTATTTGGTGGGCTTCT 59.733 43.478 0.00 0.00 0.00 2.85
964 1002 9.423427 CTTAAGTATATACGCAAGAGCTATACG 57.577 37.037 17.79 2.49 43.62 3.06
1007 1045 7.101054 ACTAGAGTGCGAAAATTACACCATTA 58.899 34.615 0.00 0.00 34.83 1.90
1049 1088 6.863126 GTGAAATTTAGTGCAAAGCTATGTGT 59.137 34.615 0.00 0.00 0.00 3.72
1161 1202 8.445275 AGTTTTTATTGGAATTTGGTTGTTCC 57.555 30.769 0.00 0.00 43.33 3.62
1177 1218 6.272792 TGGTTGTTCCTTAAGGGTACTATCAA 59.727 38.462 21.53 9.99 36.50 2.57
1180 1221 6.895782 TGTTCCTTAAGGGTACTATCAATGG 58.104 40.000 21.53 0.00 36.50 3.16
1242 1283 8.915871 TTTCAATTGTCTATGCTTATTCTTGC 57.084 30.769 5.13 0.00 0.00 4.01
1258 1299 9.970395 CTTATTCTTGCATAATATGAAAAGCCA 57.030 29.630 4.14 0.00 0.00 4.75
1272 1313 6.542574 TGAAAAGCCAATAATTGTGCTTTG 57.457 33.333 18.57 2.28 46.54 2.77
1273 1314 6.286758 TGAAAAGCCAATAATTGTGCTTTGA 58.713 32.000 18.57 10.05 46.54 2.69
1274 1315 6.935771 TGAAAAGCCAATAATTGTGCTTTGAT 59.064 30.769 18.57 8.93 46.54 2.57
1275 1316 6.730960 AAAGCCAATAATTGTGCTTTGATG 57.269 33.333 17.68 0.00 46.03 3.07
1276 1317 5.410355 AGCCAATAATTGTGCTTTGATGT 57.590 34.783 0.00 0.00 34.84 3.06
1277 1318 5.797051 AGCCAATAATTGTGCTTTGATGTT 58.203 33.333 0.00 0.00 34.84 2.71
1278 1319 5.640357 AGCCAATAATTGTGCTTTGATGTTG 59.360 36.000 0.00 0.00 34.84 3.33
1279 1320 5.671825 GCCAATAATTGTGCTTTGATGTTGC 60.672 40.000 0.00 0.00 0.00 4.17
1280 1321 5.163834 CCAATAATTGTGCTTTGATGTTGCC 60.164 40.000 0.00 0.00 0.00 4.52
1281 1322 3.756933 AATTGTGCTTTGATGTTGCCT 57.243 38.095 0.00 0.00 0.00 4.75
1282 1323 2.798976 TTGTGCTTTGATGTTGCCTC 57.201 45.000 0.00 0.00 0.00 4.70
1283 1324 1.689984 TGTGCTTTGATGTTGCCTCA 58.310 45.000 0.00 0.00 0.00 3.86
1284 1325 2.030371 TGTGCTTTGATGTTGCCTCAA 58.970 42.857 0.00 0.00 0.00 3.02
1285 1326 2.223782 TGTGCTTTGATGTTGCCTCAAC 60.224 45.455 2.96 2.96 43.78 3.18
1296 1337 2.552743 GTTGCCTCAACCCAGAGTTAAC 59.447 50.000 0.00 0.00 38.30 2.01
1415 1456 7.085746 ACAAATTAGGCTAAAACGCGTATTTT 58.914 30.769 14.46 13.54 35.76 1.82
1479 1520 3.578456 CCACACTGGCCAATCGAC 58.422 61.111 7.01 0.00 0.00 4.20
1480 1521 2.390599 CCACACTGGCCAATCGACG 61.391 63.158 7.01 0.00 0.00 5.12
1481 1522 2.742372 ACACTGGCCAATCGACGC 60.742 61.111 7.01 0.00 0.00 5.19
1482 1523 3.853330 CACTGGCCAATCGACGCG 61.853 66.667 7.01 3.53 0.00 6.01
1483 1524 4.373116 ACTGGCCAATCGACGCGT 62.373 61.111 13.85 13.85 0.00 6.01
1484 1525 3.853330 CTGGCCAATCGACGCGTG 61.853 66.667 20.70 9.70 0.00 5.34
1514 1586 4.476410 CGCGCGCTGACTAGGACA 62.476 66.667 30.48 0.00 0.00 4.02
1583 1667 2.778717 CCATTCCCCTCCCCTCCC 60.779 72.222 0.00 0.00 0.00 4.30
1679 1772 1.679153 GGTTTTGGAGGACGAAAGCAA 59.321 47.619 0.00 0.00 45.84 3.91
1778 1892 7.457535 AGGGTTTCATATTTGGGATTTCTTGAA 59.542 33.333 0.00 0.00 0.00 2.69
1978 2098 3.243704 GGAGGTTTTTAGCATGTGCACAA 60.244 43.478 25.72 3.79 45.16 3.33
2199 2334 7.097834 AGTAGAGTAGCTTACAAATGGTTGAC 58.902 38.462 0.00 0.00 38.20 3.18
2375 2513 7.305474 TGTTTTGTTGTTGTTGTTGTTTTTGT 58.695 26.923 0.00 0.00 0.00 2.83
2467 2605 1.766494 TGAAGCTATGGGCAATGGTG 58.234 50.000 0.00 0.00 44.79 4.17
2501 2639 4.307032 AGTGCTAGGGTGAATGACAATT 57.693 40.909 0.00 0.00 0.00 2.32
2591 2729 3.431346 GCTAGTCCAAGATGTGCATGAGA 60.431 47.826 0.00 0.00 0.00 3.27
2638 2776 3.084039 GGTGGATTTCAGACATCTGCAA 58.916 45.455 3.88 0.03 43.46 4.08
2735 2873 2.159599 GCAAAGAAAGATGCAGAGACCG 60.160 50.000 0.00 0.00 42.12 4.79
2790 2928 2.224719 ACCTGACAAGAGCTCAAGCAAT 60.225 45.455 17.77 0.00 45.16 3.56
2922 3060 2.828520 TCACCCAAGAGAAGCTAGAGTG 59.171 50.000 0.00 0.00 0.00 3.51
3096 3234 1.631405 TGCTGACCTTTTGGGAATGG 58.369 50.000 0.00 0.00 46.08 3.16
3209 3348 8.159344 AGTAGTTATGCTATTCATCCTTTTGC 57.841 34.615 0.00 0.00 36.63 3.68
3279 3418 5.960113 TGTGAACAATGGTTATGTATTGCC 58.040 37.500 0.00 0.00 37.36 4.52
3415 3574 8.974060 AAAAGAGGAACAACACTCACTAAATA 57.026 30.769 0.00 0.00 36.20 1.40
3577 3741 2.434336 GTGAAATTTGGCCCTAATCCCC 59.566 50.000 0.00 0.00 0.00 4.81
3819 3983 6.040247 CACCGTGCTATTAAGATACACAAGA 58.960 40.000 4.81 0.00 0.00 3.02
3961 4125 0.841961 CCAGGAGATCCATCTTGGCA 59.158 55.000 0.92 0.00 37.47 4.92
4070 4234 1.681666 CCTTCCTTCCTGCAGCTCA 59.318 57.895 8.66 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 6.947733 TGAAGGAATGAATGAGTGTTATTGGT 59.052 34.615 0.00 0.00 0.00 3.67
91 92 4.615912 CGCGAAGAAAATGGTTGAAGGAAT 60.616 41.667 0.00 0.00 0.00 3.01
120 121 8.491134 ACGCAATAATAAGCATATAATAGGGGA 58.509 33.333 0.00 0.00 0.00 4.81
366 380 5.305036 CGCAAAAATAGTGAAATTTTCCGC 58.695 37.500 6.68 0.53 37.93 5.54
376 390 3.673052 GCAGGAATGCGCAAAAATAGTGA 60.673 43.478 17.11 0.00 0.00 3.41
470 501 7.008021 AGGAACAAATGAATTAGTGGCATTT 57.992 32.000 0.00 0.00 41.44 2.32
559 595 6.515272 AGGAATAAATTAGTGGCACTTGTG 57.485 37.500 27.24 0.00 0.00 3.33
768 806 5.538053 TGATAAGACACAAGGCAAAAATGGA 59.462 36.000 0.00 0.00 0.00 3.41
769 807 5.782047 TGATAAGACACAAGGCAAAAATGG 58.218 37.500 0.00 0.00 0.00 3.16
770 808 5.865552 CCTGATAAGACACAAGGCAAAAATG 59.134 40.000 0.00 0.00 0.00 2.32
778 816 5.126067 CCCAATACCTGATAAGACACAAGG 58.874 45.833 0.00 0.00 0.00 3.61
825 863 5.585844 GGTAAGAAAAATGGCCCAATCAATG 59.414 40.000 0.00 0.00 0.00 2.82
826 864 5.250313 TGGTAAGAAAAATGGCCCAATCAAT 59.750 36.000 0.00 0.00 0.00 2.57
827 865 4.594920 TGGTAAGAAAAATGGCCCAATCAA 59.405 37.500 0.00 0.00 0.00 2.57
828 866 4.163427 TGGTAAGAAAAATGGCCCAATCA 58.837 39.130 0.00 0.00 0.00 2.57
829 867 4.817318 TGGTAAGAAAAATGGCCCAATC 57.183 40.909 0.00 0.00 0.00 2.67
830 868 4.565444 GCTTGGTAAGAAAAATGGCCCAAT 60.565 41.667 0.00 0.00 30.73 3.16
831 869 3.244387 GCTTGGTAAGAAAAATGGCCCAA 60.244 43.478 0.00 0.00 0.00 4.12
832 870 2.301583 GCTTGGTAAGAAAAATGGCCCA 59.698 45.455 0.00 0.00 0.00 5.36
833 871 2.567169 AGCTTGGTAAGAAAAATGGCCC 59.433 45.455 0.00 0.00 0.00 5.80
834 872 3.961480 AGCTTGGTAAGAAAAATGGCC 57.039 42.857 0.00 0.00 0.00 5.36
835 873 6.025749 AGTTAGCTTGGTAAGAAAAATGGC 57.974 37.500 0.00 0.00 0.00 4.40
873 911 1.406614 CCCTTTTGCAACCACAAAGCA 60.407 47.619 0.00 0.00 40.43 3.91
935 973 5.921408 AGCTCTTGCGTATATACTTAAGCAC 59.079 40.000 11.05 9.38 45.42 4.40
948 986 7.606858 ACTTATATCGTATAGCTCTTGCGTA 57.393 36.000 0.00 0.00 45.42 4.42
970 1008 8.997621 TTTCGCACTCTAGTTCAATTTATACT 57.002 30.769 0.00 0.00 0.00 2.12
981 1019 5.302360 TGGTGTAATTTTCGCACTCTAGTT 58.698 37.500 0.00 0.00 33.96 2.24
987 1025 7.647715 GCAATATAATGGTGTAATTTTCGCACT 59.352 33.333 0.00 0.00 33.96 4.40
1023 1061 6.308766 CACATAGCTTTGCACTAAATTTCACC 59.691 38.462 3.86 0.00 0.00 4.02
1024 1062 6.863126 ACACATAGCTTTGCACTAAATTTCAC 59.137 34.615 3.86 0.00 0.00 3.18
1025 1063 6.980593 ACACATAGCTTTGCACTAAATTTCA 58.019 32.000 3.86 0.00 0.00 2.69
1026 1064 9.013490 CATACACATAGCTTTGCACTAAATTTC 57.987 33.333 3.86 0.00 0.00 2.17
1147 1188 5.801531 ACCCTTAAGGAACAACCAAATTC 57.198 39.130 23.74 0.00 42.04 2.17
1154 1195 7.282450 CCATTGATAGTACCCTTAAGGAACAAC 59.718 40.741 23.74 13.87 39.89 3.32
1161 1202 5.930135 AGTGCCATTGATAGTACCCTTAAG 58.070 41.667 0.00 0.00 0.00 1.85
1217 1258 8.522003 TGCAAGAATAAGCATAGACAATTGAAA 58.478 29.630 13.59 0.00 35.51 2.69
1258 1299 5.797051 AGGCAACATCAAAGCACAATTATT 58.203 33.333 0.00 0.00 41.41 1.40
1268 1309 1.962807 TGGGTTGAGGCAACATCAAAG 59.037 47.619 11.83 0.00 45.11 2.77
1269 1310 1.962807 CTGGGTTGAGGCAACATCAAA 59.037 47.619 11.83 0.00 45.11 2.69
1270 1311 1.144708 TCTGGGTTGAGGCAACATCAA 59.855 47.619 11.83 0.00 45.11 2.57
1271 1312 0.770499 TCTGGGTTGAGGCAACATCA 59.230 50.000 11.83 8.43 45.11 3.07
1272 1313 1.271597 ACTCTGGGTTGAGGCAACATC 60.272 52.381 11.83 4.75 45.11 3.06
1273 1314 0.773644 ACTCTGGGTTGAGGCAACAT 59.226 50.000 11.83 0.00 45.11 2.71
1274 1315 0.550914 AACTCTGGGTTGAGGCAACA 59.449 50.000 11.83 0.00 45.11 3.33
1275 1316 2.552743 GTTAACTCTGGGTTGAGGCAAC 59.447 50.000 2.47 1.82 42.89 4.17
1276 1317 2.441750 AGTTAACTCTGGGTTGAGGCAA 59.558 45.455 1.12 0.00 38.75 4.52
1277 1318 2.054799 AGTTAACTCTGGGTTGAGGCA 58.945 47.619 1.12 0.00 38.75 4.75
1278 1319 2.427506 CAGTTAACTCTGGGTTGAGGC 58.572 52.381 4.77 0.00 38.75 4.70
1279 1320 2.224523 TGCAGTTAACTCTGGGTTGAGG 60.225 50.000 4.77 0.00 38.75 3.86
1280 1321 2.808543 GTGCAGTTAACTCTGGGTTGAG 59.191 50.000 4.77 0.00 38.75 3.02
1281 1322 2.171659 TGTGCAGTTAACTCTGGGTTGA 59.828 45.455 4.77 0.00 38.75 3.18
1282 1323 2.549754 CTGTGCAGTTAACTCTGGGTTG 59.450 50.000 4.77 0.00 38.75 3.77
1283 1324 2.438021 TCTGTGCAGTTAACTCTGGGTT 59.562 45.455 4.77 0.00 41.54 4.11
1284 1325 2.047061 TCTGTGCAGTTAACTCTGGGT 58.953 47.619 4.77 0.00 36.12 4.51
1285 1326 2.839486 TCTGTGCAGTTAACTCTGGG 57.161 50.000 4.77 0.00 36.12 4.45
1296 1337 3.120546 CGAATTGTGGTACTTCTGTGCAG 60.121 47.826 0.00 0.00 0.00 4.41
1583 1667 2.184579 GGAAACGAGCGAGGAGGG 59.815 66.667 0.00 0.00 0.00 4.30
1679 1772 0.739561 GAGGCTAGAATGGTCGTCGT 59.260 55.000 0.00 0.00 0.00 4.34
1778 1892 5.242838 TCAAAACCTAGCGAAATCAACCAAT 59.757 36.000 0.00 0.00 0.00 3.16
1908 2028 0.917533 AAGCCTCTCAGATGCCATGT 59.082 50.000 0.00 0.00 0.00 3.21
1978 2098 3.714798 ACAATCCTACAATCCATACCGGT 59.285 43.478 13.98 13.98 35.57 5.28
2019 2148 2.496899 ATGGCACTGACCAAGTAAGG 57.503 50.000 0.00 0.00 44.65 2.69
2199 2334 6.097554 ACTCTACTGTTCATATCAAGGAGTGG 59.902 42.308 0.00 0.00 0.00 4.00
2348 2483 4.723879 ACAACAACAACAACAAAACAGC 57.276 36.364 0.00 0.00 0.00 4.40
2375 2513 2.576191 AGCCACAATTGCTACCTTCCTA 59.424 45.455 5.05 0.00 37.28 2.94
2467 2605 2.424956 CCTAGCACTTTTGGCATCTTCC 59.575 50.000 0.00 0.00 0.00 3.46
2591 2729 6.159398 ACCTTATCTTCCTGGAAGTTCATCAT 59.841 38.462 30.15 19.57 40.24 2.45
2638 2776 4.287845 TCCTGCTGATATGTAATGGCAGAT 59.712 41.667 13.27 0.00 46.65 2.90
2735 2873 5.518487 GCTCATACTTCTGAGTAAGTTGCTC 59.482 44.000 13.52 13.52 43.75 4.26
2790 2928 7.768582 TGTTCAACTTCAAGTTCTGAATGACTA 59.231 33.333 7.73 0.00 43.20 2.59
2922 3060 3.329300 TCAGCAACCTGAAGCTTCC 57.671 52.632 23.42 7.00 44.79 3.46
3096 3234 3.670625 TGCTAGGTCATTACACAACCAC 58.329 45.455 0.00 0.00 35.43 4.16
3209 3348 5.998454 ATGCATAGTTCATCCTTTTCTCG 57.002 39.130 0.00 0.00 0.00 4.04
3819 3983 2.104451 TGTGGCAGCATGGTGAAATTTT 59.896 40.909 28.34 0.00 35.86 1.82
3961 4125 0.832135 TGCTCAACTCCGAGGAAGGT 60.832 55.000 0.00 0.00 33.36 3.50


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

AutoCloner maintained by Alex Coulton.