Multiple sequence alignment - TraesCS2B01G341500

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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 TraesCS2B01G341500 chr2B 100.000 2659 0 0 1695 4353 486975793 486978451 0.000000e+00 4911.0
1 TraesCS2B01G341500 chr2B 100.000 1495 0 0 1 1495 486974099 486975593 0.000000e+00 2761.0
2 TraesCS2B01G341500 chr2B 90.154 975 87 6 2380 3352 486952164 486953131 0.000000e+00 1260.0
3 TraesCS2B01G341500 chr2B 89.968 628 60 1 2725 3352 486966057 486966681 0.000000e+00 808.0
4 TraesCS2B01G341500 chr2B 78.481 316 53 13 2331 2639 486965660 486965967 4.440000e-45 193.0
5 TraesCS2B01G341500 chr2A 93.121 1788 71 22 1695 3463 580848128 580849882 0.000000e+00 2573.0
6 TraesCS2B01G341500 chr2A 88.823 1521 109 25 3 1495 580846604 580848091 0.000000e+00 1810.0
7 TraesCS2B01G341500 chr2A 90.705 979 82 5 2380 3356 580721154 580722125 0.000000e+00 1295.0
8 TraesCS2B01G341500 chr2A 85.343 846 104 15 2520 3352 580760273 580761111 0.000000e+00 857.0
9 TraesCS2B01G341500 chr2A 97.500 80 2 0 3458 3537 580849911 580849990 2.110000e-28 137.0
10 TraesCS2B01G341500 chr2D 95.007 1382 47 12 2100 3463 413773807 413775184 0.000000e+00 2150.0
11 TraesCS2B01G341500 chr2D 90.501 979 84 7 2380 3356 413690972 413691943 0.000000e+00 1284.0
12 TraesCS2B01G341500 chr2D 87.761 1103 104 16 409 1494 413771135 413772223 0.000000e+00 1260.0
13 TraesCS2B01G341500 chr2D 91.561 628 50 1 2725 3352 413724931 413725555 0.000000e+00 863.0
14 TraesCS2B01G341500 chr2D 79.848 660 99 19 2720 3352 413353532 413354184 6.640000e-123 451.0
15 TraesCS2B01G341500 chr2D 81.595 326 32 14 1750 2072 413773521 413773821 1.210000e-60 244.0
16 TraesCS2B01G341500 chr2D 79.430 316 50 12 2331 2639 413724557 413724864 4.410000e-50 209.0
17 TraesCS2B01G341500 chr2D 93.750 80 5 0 3458 3537 413775210 413775289 2.130000e-23 121.0
18 TraesCS2B01G341500 chr2D 93.103 58 4 0 1695 1752 413772261 413772318 7.760000e-13 86.1
19 TraesCS2B01G341500 chr6A 99.023 819 8 0 3535 4353 180192946 180192128 0.000000e+00 1469.0
20 TraesCS2B01G341500 chr4B 99.142 816 7 0 3538 4353 603045877 603045062 0.000000e+00 1469.0
21 TraesCS2B01G341500 chr5B 98.786 824 9 1 3531 4353 695761916 695762739 0.000000e+00 1465.0
22 TraesCS2B01G341500 chr5B 98.667 825 10 1 3530 4353 653233444 653234268 0.000000e+00 1461.0
23 TraesCS2B01G341500 chr3B 99.020 816 8 0 3538 4353 104978460 104977645 0.000000e+00 1463.0
24 TraesCS2B01G341500 chr3B 98.662 822 10 1 3532 4353 242668157 242667337 0.000000e+00 1456.0
25 TraesCS2B01G341500 chr3B 98.084 835 14 2 3519 4353 459097906 459097074 0.000000e+00 1452.0
26 TraesCS2B01G341500 chr1B 99.020 816 8 0 3538 4353 131502408 131501593 0.000000e+00 1463.0
27 TraesCS2B01G341500 chr6B 98.897 816 9 0 3538 4353 82549573 82548758 0.000000e+00 1458.0


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 TraesCS2B01G341500 chr2B 486974099 486978451 4352 False 3836.000000 4911 100.0000 1 4353 2 chr2B.!!$F3 4352
1 TraesCS2B01G341500 chr2B 486952164 486953131 967 False 1260.000000 1260 90.1540 2380 3352 1 chr2B.!!$F1 972
2 TraesCS2B01G341500 chr2B 486965660 486966681 1021 False 500.500000 808 84.2245 2331 3352 2 chr2B.!!$F2 1021
3 TraesCS2B01G341500 chr2A 580846604 580849990 3386 False 1506.666667 2573 93.1480 3 3537 3 chr2A.!!$F3 3534
4 TraesCS2B01G341500 chr2A 580721154 580722125 971 False 1295.000000 1295 90.7050 2380 3356 1 chr2A.!!$F1 976
5 TraesCS2B01G341500 chr2A 580760273 580761111 838 False 857.000000 857 85.3430 2520 3352 1 chr2A.!!$F2 832
6 TraesCS2B01G341500 chr2D 413690972 413691943 971 False 1284.000000 1284 90.5010 2380 3356 1 chr2D.!!$F2 976
7 TraesCS2B01G341500 chr2D 413771135 413775289 4154 False 772.220000 2150 90.2432 409 3537 5 chr2D.!!$F4 3128
8 TraesCS2B01G341500 chr2D 413724557 413725555 998 False 536.000000 863 85.4955 2331 3352 2 chr2D.!!$F3 1021
9 TraesCS2B01G341500 chr2D 413353532 413354184 652 False 451.000000 451 79.8480 2720 3352 1 chr2D.!!$F1 632
10 TraesCS2B01G341500 chr6A 180192128 180192946 818 True 1469.000000 1469 99.0230 3535 4353 1 chr6A.!!$R1 818
11 TraesCS2B01G341500 chr4B 603045062 603045877 815 True 1469.000000 1469 99.1420 3538 4353 1 chr4B.!!$R1 815
12 TraesCS2B01G341500 chr5B 695761916 695762739 823 False 1465.000000 1465 98.7860 3531 4353 1 chr5B.!!$F2 822
13 TraesCS2B01G341500 chr5B 653233444 653234268 824 False 1461.000000 1461 98.6670 3530 4353 1 chr5B.!!$F1 823
14 TraesCS2B01G341500 chr3B 104977645 104978460 815 True 1463.000000 1463 99.0200 3538 4353 1 chr3B.!!$R1 815
15 TraesCS2B01G341500 chr3B 242667337 242668157 820 True 1456.000000 1456 98.6620 3532 4353 1 chr3B.!!$R2 821
16 TraesCS2B01G341500 chr3B 459097074 459097906 832 True 1452.000000 1452 98.0840 3519 4353 1 chr3B.!!$R3 834
17 TraesCS2B01G341500 chr1B 131501593 131502408 815 True 1463.000000 1463 99.0200 3538 4353 1 chr1B.!!$R1 815
18 TraesCS2B01G341500 chr6B 82548758 82549573 815 True 1458.000000 1458 98.8970 3538 4353 1 chr6B.!!$R1 815

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
184 185 0.178858 TAGGGGGTCAACCATGTCCA 60.179 55.000 0.89 0.0 42.91 4.02 F
215 216 0.615331 TGAGAGGCCAATGTCCTGAC 59.385 55.000 5.01 0.0 33.24 3.51 F
999 1018 1.745489 CTTCCTGCGTGCTAACCCC 60.745 63.158 0.00 0.0 0.00 4.95 F
1980 3221 2.024176 AAAGCACCGCACCTATACAG 57.976 50.000 0.00 0.0 0.00 2.74 F
2776 4032 1.982395 CTACCAGGTGTCGAGCCCA 60.982 63.158 0.76 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 3333 0.398696 TGAAGGAAGCTACCCGCAAA 59.601 50.0 0.0 0.0 42.61 3.68 R
2092 3334 0.618458 ATGAAGGAAGCTACCCGCAA 59.382 50.0 0.0 0.0 42.61 4.85 R
2093 3335 0.618458 AATGAAGGAAGCTACCCGCA 59.382 50.0 0.0 0.0 42.61 5.69 R
3226 4500 0.392998 CAAGGCAGAACCCAGCGTAT 60.393 55.0 0.0 0.0 40.58 3.06 R
4201 5531 6.546395 GCATTCTTCGTTATGTTCAGTTCAT 58.454 36.0 0.0 0.0 0.00 2.57 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
46 47 3.070159 GCTTCATAGGAGTGGTAGCATGA 59.930 47.826 0.00 0.00 31.73 3.07
60 61 1.144503 AGCATGATCCCCAACATCCTC 59.855 52.381 0.00 0.00 0.00 3.71
70 71 2.224305 CCCAACATCCTCGAATACCTCC 60.224 54.545 0.00 0.00 0.00 4.30
87 88 3.246387 ACCTCCACCCCTCTTAATAGTGT 60.246 47.826 0.00 0.00 0.00 3.55
97 98 5.420409 CCTCTTAATAGTGTGGTTGTCCTC 58.580 45.833 0.00 0.00 34.23 3.71
101 102 6.440647 TCTTAATAGTGTGGTTGTCCTCTGAT 59.559 38.462 0.00 0.00 34.23 2.90
145 146 6.884832 TCTTTGAGTCTTCAGAAAACTGGTA 58.115 36.000 0.00 0.00 34.15 3.25
147 148 5.607939 TGAGTCTTCAGAAAACTGGTACA 57.392 39.130 0.00 0.00 0.00 2.90
148 149 6.174720 TGAGTCTTCAGAAAACTGGTACAT 57.825 37.500 0.00 0.00 38.20 2.29
175 176 3.331294 TCCTTTTCGAATTAGGGGGTCAA 59.669 43.478 20.58 4.16 0.00 3.18
184 185 0.178858 TAGGGGGTCAACCATGTCCA 60.179 55.000 0.89 0.00 42.91 4.02
202 203 4.942852 GTCCATAGACAACTCATGAGAGG 58.057 47.826 29.27 20.60 43.36 3.69
203 204 3.386078 TCCATAGACAACTCATGAGAGGC 59.614 47.826 29.27 21.37 46.44 4.70
204 205 3.494048 CCATAGACAACTCATGAGAGGCC 60.494 52.174 29.27 12.45 46.44 5.19
205 206 1.649321 AGACAACTCATGAGAGGCCA 58.351 50.000 29.27 0.00 46.44 5.36
206 207 1.980765 AGACAACTCATGAGAGGCCAA 59.019 47.619 29.27 0.00 46.44 4.52
207 208 2.575279 AGACAACTCATGAGAGGCCAAT 59.425 45.455 29.27 1.44 46.44 3.16
208 209 2.681848 GACAACTCATGAGAGGCCAATG 59.318 50.000 29.27 15.88 46.44 2.82
209 210 2.040813 ACAACTCATGAGAGGCCAATGT 59.959 45.455 29.27 16.42 46.44 2.71
210 211 2.681848 CAACTCATGAGAGGCCAATGTC 59.318 50.000 29.27 0.00 46.44 3.06
211 212 1.211457 ACTCATGAGAGGCCAATGTCC 59.789 52.381 29.27 0.00 46.44 4.02
212 213 1.489649 CTCATGAGAGGCCAATGTCCT 59.510 52.381 18.34 0.00 38.26 3.85
213 214 1.211212 TCATGAGAGGCCAATGTCCTG 59.789 52.381 5.01 0.00 33.24 3.86
214 215 1.211212 CATGAGAGGCCAATGTCCTGA 59.789 52.381 5.01 0.00 33.24 3.86
215 216 0.615331 TGAGAGGCCAATGTCCTGAC 59.385 55.000 5.01 0.00 33.24 3.51
216 217 0.615331 GAGAGGCCAATGTCCTGACA 59.385 55.000 5.01 1.93 46.44 3.58
266 267 3.903090 ACAAACCCCATTGTCATCAACAT 59.097 39.130 0.00 0.00 39.23 2.71
267 268 5.047448 CACAAACCCCATTGTCATCAACATA 60.047 40.000 0.00 0.00 41.44 2.29
275 276 8.477256 CCCCATTGTCATCAACATAAAAATACT 58.523 33.333 0.00 0.00 37.82 2.12
392 393 2.355132 TCTCGACAAGAGCTTCGATACC 59.645 50.000 8.57 0.00 46.44 2.73
505 506 3.360867 TGTTCAACAACCTGACAACCAT 58.639 40.909 0.00 0.00 0.00 3.55
510 513 7.040755 TGTTCAACAACCTGACAACCATATTAG 60.041 37.037 0.00 0.00 0.00 1.73
544 547 6.251471 AGTTAGAGTAACCTAGCAAGTACCA 58.749 40.000 0.00 0.00 39.47 3.25
576 579 3.134458 AGTAGTTGAAGCAAGCTCACAC 58.866 45.455 0.00 0.00 0.00 3.82
646 650 4.588951 AGCAGACCGTCAATCAGGATAATA 59.411 41.667 0.40 0.00 0.00 0.98
706 710 5.155161 AGAGTAATGTCATGCCTATGGGTA 58.845 41.667 0.00 0.00 34.97 3.69
833 851 5.416952 CAGGTTCTTGAAGCCATTAGTCATT 59.583 40.000 8.68 0.00 0.00 2.57
835 853 6.825721 AGGTTCTTGAAGCCATTAGTCATTAG 59.174 38.462 8.68 0.00 0.00 1.73
884 902 3.644966 AGACGAGATCTCCTCACTTCT 57.355 47.619 17.13 6.50 42.06 2.85
911 929 6.804295 CGATAATGAGTGCTCCTAGTTGATAC 59.196 42.308 0.00 0.00 0.00 2.24
999 1018 1.745489 CTTCCTGCGTGCTAACCCC 60.745 63.158 0.00 0.00 0.00 4.95
1186 1205 3.242091 CGACAACAAAGGTATGATGAGCG 60.242 47.826 0.00 0.00 0.00 5.03
1393 1424 5.125356 TCGATGAGTATTCATGCCAATTGT 58.875 37.500 5.32 0.00 44.01 2.71
1403 1434 4.172505 TCATGCCAATTGTGTTTTATCGC 58.827 39.130 4.43 0.00 0.00 4.58
1409 1440 4.791163 CCAATTGTGTTTTATCGCCGTAAG 59.209 41.667 4.43 0.00 0.00 2.34
1412 1443 4.914312 TGTGTTTTATCGCCGTAAGAAG 57.086 40.909 0.00 0.00 43.02 2.85
1424 1455 6.684686 TCGCCGTAAGAAGTTATAGCATTAT 58.315 36.000 0.00 0.00 43.02 1.28
1427 1458 8.371053 CGCCGTAAGAAGTTATAGCATTATAAC 58.629 37.037 7.47 7.47 44.47 1.89
1480 1513 5.970640 AGGACATAGGGGAGTTAGATTTCAA 59.029 40.000 0.00 0.00 0.00 2.69
1483 1516 7.614192 GGACATAGGGGAGTTAGATTTCAAAAA 59.386 37.037 0.00 0.00 0.00 1.94
1841 3081 7.507616 ACAAAAGGAAGGGTTGTGTGATAAATA 59.492 33.333 0.00 0.00 34.28 1.40
1847 3087 8.527810 GGAAGGGTTGTGTGATAAATATTTGAA 58.472 33.333 11.05 0.00 0.00 2.69
1879 3119 8.803235 ACATAACAGAAAGGTTTTAATTCCCTC 58.197 33.333 0.00 0.00 32.29 4.30
1886 3126 9.601810 AGAAAGGTTTTAATTCCCTCTGTAAAT 57.398 29.630 0.00 0.00 0.00 1.40
1909 3149 9.860650 AAATACTAGTAATTGTATTCCATGCCA 57.139 29.630 6.70 0.00 38.10 4.92
1964 3205 6.934083 AGTTTTGCCCCATACACAAATTAAAG 59.066 34.615 0.00 0.00 33.62 1.85
1980 3221 2.024176 AAAGCACCGCACCTATACAG 57.976 50.000 0.00 0.00 0.00 2.74
2068 3310 8.814038 ATTGTCATGTTTAATAGCTTCCTTCT 57.186 30.769 0.00 0.00 0.00 2.85
2149 3391 6.488344 TGTTTTTGTGTGTGAGGCTTGATATA 59.512 34.615 0.00 0.00 0.00 0.86
2174 3416 8.356000 ACCGAAATGATTTTGTAGGGAATTTA 57.644 30.769 4.57 0.00 0.00 1.40
2177 3419 8.190784 CGAAATGATTTTGTAGGGAATTTAGCT 58.809 33.333 0.00 0.00 0.00 3.32
2642 3887 2.687566 ACGGGGAGCAAGGTAGGG 60.688 66.667 0.00 0.00 0.00 3.53
2650 3895 2.074576 GAGCAAGGTAGGGAAAACGAC 58.925 52.381 0.00 0.00 0.00 4.34
2714 3968 3.029320 TCAATCATGCTTGCAACCAAC 57.971 42.857 4.37 0.00 0.00 3.77
2720 3974 4.496360 TCATGCTTGCAACCAACATTATG 58.504 39.130 0.00 0.00 0.00 1.90
2758 4014 2.503375 CTGGACGTGTACGCGACC 60.503 66.667 33.37 33.37 44.48 4.79
2776 4032 1.982395 CTACCAGGTGTCGAGCCCA 60.982 63.158 0.76 0.00 0.00 5.36
2818 4074 2.025441 GCAACGGCGCTGAACAAA 59.975 55.556 25.98 0.00 0.00 2.83
3226 4500 2.435234 GGCATCGTGTACCGGCAA 60.435 61.111 0.00 0.00 37.11 4.52
3326 4603 1.073199 GGCCAGGTGTACAAGCACT 59.927 57.895 0.00 0.00 39.21 4.40
3356 4633 6.071278 GCTCCTCAAGTTCTCCTTCTAACTTA 60.071 42.308 0.00 0.00 42.52 2.24
3357 4634 7.525692 GCTCCTCAAGTTCTCCTTCTAACTTAA 60.526 40.741 0.00 0.00 42.52 1.85
3358 4635 7.668492 TCCTCAAGTTCTCCTTCTAACTTAAC 58.332 38.462 0.00 0.00 42.52 2.01
3359 4636 7.509659 TCCTCAAGTTCTCCTTCTAACTTAACT 59.490 37.037 0.00 0.00 42.52 2.24
3360 4637 8.151596 CCTCAAGTTCTCCTTCTAACTTAACTT 58.848 37.037 0.00 0.00 42.52 2.66
3378 4655 9.716531 ACTTAACTTTGTAGTAGTATGGTTTCC 57.283 33.333 0.00 0.00 33.17 3.13
3379 4656 9.159364 CTTAACTTTGTAGTAGTATGGTTTCCC 57.841 37.037 0.00 0.00 33.17 3.97
3380 4657 6.691255 ACTTTGTAGTAGTATGGTTTCCCA 57.309 37.500 0.00 0.00 37.81 4.37
3381 4658 7.266905 ACTTTGTAGTAGTATGGTTTCCCAT 57.733 36.000 0.00 0.00 42.90 4.00
3383 4660 7.846914 ACTTTGTAGTAGTATGGTTTCCCATCG 60.847 40.741 0.00 0.00 40.94 3.84
3454 4750 4.372656 CAGGACATCGGGTATCTTCTTTC 58.627 47.826 0.00 0.00 0.00 2.62
3467 4797 0.825840 TTCTTTCCAAACGGGCCCAG 60.826 55.000 24.92 17.36 36.21 4.45
4201 5531 6.040729 CCAAATATGCATACCAAATGTCAGGA 59.959 38.462 8.99 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.422597 CTATGAAGCAACCCAACACGA 58.577 47.619 0.00 0.00 0.00 4.35
23 24 2.466846 TGCTACCACTCCTATGAAGCA 58.533 47.619 0.00 0.00 36.59 3.91
46 47 2.372172 GGTATTCGAGGATGTTGGGGAT 59.628 50.000 0.00 0.00 0.00 3.85
60 61 1.497161 AAGAGGGGTGGAGGTATTCG 58.503 55.000 0.00 0.00 0.00 3.34
87 88 7.831691 TTTTATTTGAATCAGAGGACAACCA 57.168 32.000 0.00 0.00 38.94 3.67
153 154 2.914278 TGACCCCCTAATTCGAAAAGGA 59.086 45.455 24.37 7.53 31.64 3.36
160 161 2.297701 CATGGTTGACCCCCTAATTCG 58.702 52.381 0.00 0.00 34.29 3.34
184 185 3.378512 TGGCCTCTCATGAGTTGTCTAT 58.621 45.455 21.92 0.00 38.61 1.98
194 195 1.211212 TCAGGACATTGGCCTCTCATG 59.789 52.381 8.54 0.00 32.12 3.07
195 196 1.211457 GTCAGGACATTGGCCTCTCAT 59.789 52.381 8.54 0.00 32.12 2.90
207 208 7.117236 GTCGTTTATCAAGTTTATGTCAGGACA 59.883 37.037 4.37 4.37 46.44 4.02
208 209 7.117236 TGTCGTTTATCAAGTTTATGTCAGGAC 59.883 37.037 0.00 0.00 0.00 3.85
209 210 7.156000 TGTCGTTTATCAAGTTTATGTCAGGA 58.844 34.615 0.00 0.00 0.00 3.86
210 211 7.359262 TGTCGTTTATCAAGTTTATGTCAGG 57.641 36.000 0.00 0.00 0.00 3.86
215 216 9.916397 GGTCTAATGTCGTTTATCAAGTTTATG 57.084 33.333 0.00 0.00 0.00 1.90
216 217 9.886132 AGGTCTAATGTCGTTTATCAAGTTTAT 57.114 29.630 0.00 0.00 0.00 1.40
217 218 9.362539 GAGGTCTAATGTCGTTTATCAAGTTTA 57.637 33.333 0.00 0.00 0.00 2.01
218 219 7.876068 TGAGGTCTAATGTCGTTTATCAAGTTT 59.124 33.333 0.00 0.00 0.00 2.66
219 220 7.331193 GTGAGGTCTAATGTCGTTTATCAAGTT 59.669 37.037 0.00 0.00 0.00 2.66
220 221 6.812160 GTGAGGTCTAATGTCGTTTATCAAGT 59.188 38.462 0.00 0.00 0.00 3.16
221 222 6.811665 TGTGAGGTCTAATGTCGTTTATCAAG 59.188 38.462 0.00 0.00 0.00 3.02
222 223 6.693466 TGTGAGGTCTAATGTCGTTTATCAA 58.307 36.000 0.00 0.00 0.00 2.57
223 224 6.275494 TGTGAGGTCTAATGTCGTTTATCA 57.725 37.500 0.00 0.00 0.00 2.15
224 225 7.412672 GGTTTGTGAGGTCTAATGTCGTTTATC 60.413 40.741 0.00 0.00 0.00 1.75
225 226 6.370718 GGTTTGTGAGGTCTAATGTCGTTTAT 59.629 38.462 0.00 0.00 0.00 1.40
226 227 5.697633 GGTTTGTGAGGTCTAATGTCGTTTA 59.302 40.000 0.00 0.00 0.00 2.01
349 350 9.265901 CGAGACAAATATACTTGAAGATGGATT 57.734 33.333 0.04 0.00 0.00 3.01
405 406 9.620660 AGGTGAATTTTATTGTCAAAACGTATC 57.379 29.630 0.00 0.00 30.57 2.24
439 440 6.318144 GCCAACTTCATATATCATGGGATGAG 59.682 42.308 0.00 0.00 43.53 2.90
510 513 7.488792 GCTAGGTTACTCTAACTTGCTAGAAAC 59.511 40.741 1.04 0.00 38.68 2.78
591 595 8.103305 TGCTGGATTTTACATAGGGATATCTTC 58.897 37.037 2.05 0.00 0.00 2.87
615 619 3.552604 TTGACGGTCTGCTTTTATTGC 57.447 42.857 9.88 0.00 0.00 3.56
678 682 7.173907 CCCATAGGCATGACATTACTCTTTAAG 59.826 40.741 0.00 0.00 33.67 1.85
686 690 6.490040 ACAATTACCCATAGGCATGACATTAC 59.510 38.462 0.00 0.00 36.11 1.89
698 702 4.652421 TGCATGCAACAATTACCCATAG 57.348 40.909 20.30 0.00 0.00 2.23
731 735 3.851128 GGACTAGGGAGCGGTGCC 61.851 72.222 18.43 18.43 0.00 5.01
737 741 1.574263 AAAGGAGTGGACTAGGGAGC 58.426 55.000 0.00 0.00 0.00 4.70
833 851 5.876651 TTTTCTAGAGATCTGCATGCCTA 57.123 39.130 16.68 7.07 0.00 3.93
835 853 4.880696 ACTTTTTCTAGAGATCTGCATGCC 59.119 41.667 16.68 0.00 0.00 4.40
884 902 5.359860 TCAACTAGGAGCACTCATTATCGAA 59.640 40.000 0.00 0.00 0.00 3.71
911 929 1.066143 AGTAGAACGGATGGGCAGTTG 60.066 52.381 0.00 0.00 34.99 3.16
1186 1205 3.652057 TGAAAGGGAGGAACATCATCC 57.348 47.619 2.53 2.53 45.96 3.51
1311 1330 9.334947 CTATGGATATATTCATGGACATCAACC 57.665 37.037 15.74 0.00 0.00 3.77
1348 1379 2.077413 TTGCGCATGGAAATGGTTTC 57.923 45.000 12.75 0.00 38.94 2.78
1393 1424 7.043192 GCTATAACTTCTTACGGCGATAAAACA 60.043 37.037 16.62 0.00 0.00 2.83
1453 1484 5.952161 ATCTAACTCCCCTATGTCCTAGT 57.048 43.478 0.00 0.00 0.00 2.57
1454 1485 6.782988 TGAAATCTAACTCCCCTATGTCCTAG 59.217 42.308 0.00 0.00 0.00 3.02
1455 1486 6.689561 TGAAATCTAACTCCCCTATGTCCTA 58.310 40.000 0.00 0.00 0.00 2.94
1458 1491 8.575649 TTTTTGAAATCTAACTCCCCTATGTC 57.424 34.615 0.00 0.00 0.00 3.06
1841 3081 4.046286 TCTGTTATGTGGGCCTTCAAAT 57.954 40.909 4.53 0.00 0.00 2.32
1847 3087 1.710809 ACCTTTCTGTTATGTGGGCCT 59.289 47.619 4.53 0.00 0.00 5.19
1886 3126 7.717875 GGTTGGCATGGAATACAATTACTAGTA 59.282 37.037 0.00 0.00 0.00 1.82
1887 3127 6.546034 GGTTGGCATGGAATACAATTACTAGT 59.454 38.462 0.00 0.00 0.00 2.57
1888 3128 6.016276 GGGTTGGCATGGAATACAATTACTAG 60.016 42.308 0.00 0.00 0.00 2.57
1889 3129 5.830991 GGGTTGGCATGGAATACAATTACTA 59.169 40.000 0.00 0.00 0.00 1.82
1890 3130 4.649218 GGGTTGGCATGGAATACAATTACT 59.351 41.667 0.00 0.00 0.00 2.24
1891 3131 4.404073 TGGGTTGGCATGGAATACAATTAC 59.596 41.667 0.00 0.00 0.00 1.89
1892 3132 4.614475 TGGGTTGGCATGGAATACAATTA 58.386 39.130 0.00 0.00 0.00 1.40
1898 3138 7.093988 CGATTATTTATGGGTTGGCATGGAATA 60.094 37.037 0.00 0.00 0.00 1.75
1909 3149 7.231925 GGTTGGTAATCCGATTATTTATGGGTT 59.768 37.037 4.15 0.00 34.02 4.11
1964 3205 1.202533 ACATCTGTATAGGTGCGGTGC 60.203 52.381 0.00 0.00 38.67 5.01
1980 3221 2.818751 TGGATACCCAAACCCACATC 57.181 50.000 0.00 0.00 40.09 3.06
2028 3270 7.259290 ACATGACAATTTTACTCGAGTGTTT 57.741 32.000 28.12 12.44 0.00 2.83
2034 3276 9.982291 GCTATTAAACATGACAATTTTACTCGA 57.018 29.630 0.00 0.00 0.00 4.04
2035 3277 9.988350 AGCTATTAAACATGACAATTTTACTCG 57.012 29.630 0.00 0.00 0.00 4.18
2044 3286 8.635765 AAGAAGGAAGCTATTAAACATGACAA 57.364 30.769 0.00 0.00 0.00 3.18
2089 3331 1.883926 GAAGGAAGCTACCCGCAAAAA 59.116 47.619 0.00 0.00 42.61 1.94
2090 3332 1.202830 TGAAGGAAGCTACCCGCAAAA 60.203 47.619 0.00 0.00 42.61 2.44
2091 3333 0.398696 TGAAGGAAGCTACCCGCAAA 59.601 50.000 0.00 0.00 42.61 3.68
2092 3334 0.618458 ATGAAGGAAGCTACCCGCAA 59.382 50.000 0.00 0.00 42.61 4.85
2093 3335 0.618458 AATGAAGGAAGCTACCCGCA 59.382 50.000 0.00 0.00 42.61 5.69
2149 3391 6.850752 AATTCCCTACAAAATCATTTCGGT 57.149 33.333 0.00 0.00 0.00 4.69
2174 3416 0.692476 TACCCAGCACAACATCAGCT 59.308 50.000 0.00 0.00 39.63 4.24
2177 3419 3.146066 GTCTTTACCCAGCACAACATCA 58.854 45.455 0.00 0.00 0.00 3.07
2299 3543 6.998968 AGAGCAAATATTCAGAGGAAACAG 57.001 37.500 0.00 0.00 36.43 3.16
2500 3745 7.435068 AACAGTAGAAAATGAAGTAACGCAT 57.565 32.000 0.00 0.00 0.00 4.73
2501 3746 6.854496 AACAGTAGAAAATGAAGTAACGCA 57.146 33.333 0.00 0.00 0.00 5.24
2530 3775 2.124570 CTGAATCCCCTGTGGCCG 60.125 66.667 0.00 0.00 0.00 6.13
2642 3887 2.546789 AGAATTGGGTCGTGTCGTTTTC 59.453 45.455 0.00 0.00 0.00 2.29
2650 3895 4.938832 TGTATGGTAAAGAATTGGGTCGTG 59.061 41.667 0.00 0.00 0.00 4.35
2714 3968 4.012374 CCGGGGAATCCTGATTCATAATG 58.988 47.826 18.71 6.19 46.77 1.90
2720 3974 1.070914 GTCTCCGGGGAATCCTGATTC 59.929 57.143 5.00 10.72 44.82 2.52
2758 4014 1.330655 ATGGGCTCGACACCTGGTAG 61.331 60.000 0.00 0.00 0.00 3.18
2776 4032 1.592669 GCGGATGCTCAGCACGTAT 60.593 57.895 0.00 0.00 43.04 3.06
2803 4059 2.331451 GCTTTGTTCAGCGCCGTT 59.669 55.556 2.29 0.00 0.00 4.44
2818 4074 4.295119 AAGTTCACCGGCGTCGCT 62.295 61.111 18.11 0.00 34.56 4.93
3226 4500 0.392998 CAAGGCAGAACCCAGCGTAT 60.393 55.000 0.00 0.00 40.58 3.06
3326 4603 3.445008 AGGAGAACTTGAGGAGCATGTA 58.555 45.455 0.00 0.00 34.14 2.29
3454 4750 3.683937 CAAGCTGGGCCCGTTTGG 61.684 66.667 24.93 10.72 37.09 3.28
3570 4900 1.866943 AGATAAGCCACCCCTAGAGGA 59.133 52.381 0.00 0.00 38.24 3.71
4178 5508 7.506599 TCATCCTGACATTTGGTATGCATATTT 59.493 33.333 10.16 0.00 0.00 1.40
4201 5531 6.546395 GCATTCTTCGTTATGTTCAGTTCAT 58.454 36.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.