Multiple sequence alignment - TraesCS2B01G604600

Loading Multiple Alignment...

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 TraesCS2B01G604600 chr2B 100.000 2393 0 0 1 2393 786104639 786107031 0.000000e+00 4420.0
1 TraesCS2B01G604600 chr2B 79.684 822 154 6 283 1104 559422336 559421528 4.430000e-162 580.0
2 TraesCS2B01G604600 chr2B 100.000 62 0 0 1617 1678 786106195 786106256 5.410000e-22 115.0
3 TraesCS2B01G604600 chr2B 100.000 62 0 0 1557 1618 786106255 786106316 5.410000e-22 115.0
4 TraesCS2B01G604600 chr2D 96.376 1297 44 3 155 1450 650078862 650080156 0.000000e+00 2132.0
5 TraesCS2B01G604600 chr2D 94.625 614 24 5 1785 2393 650190645 650191254 0.000000e+00 942.0
6 TraesCS2B01G604600 chr2D 78.986 947 170 22 166 1104 477425627 477424702 9.400000e-174 619.0
7 TraesCS2B01G604600 chr2D 94.611 167 9 0 1452 1618 650080207 650080373 2.360000e-65 259.0
8 TraesCS2B01G604600 chr2D 94.656 131 6 1 1618 1748 650080313 650080442 4.030000e-48 202.0
9 TraesCS2B01G604600 chr2D 93.069 101 6 1 14 114 650078758 650078857 1.920000e-31 147.0
10 TraesCS2B01G604600 chr2A 95.227 1299 59 3 155 1452 774815533 774814237 0.000000e+00 2052.0
11 TraesCS2B01G604600 chr2A 83.519 1256 175 19 165 1403 619771360 619770120 0.000000e+00 1144.0
12 TraesCS2B01G604600 chr2A 93.359 783 37 7 1618 2393 774814082 774813308 0.000000e+00 1144.0
13 TraesCS2B01G604600 chr2A 94.340 159 9 0 1460 1618 774814180 774814022 6.610000e-61 244.0
14 TraesCS2B01G604600 chr2A 93.069 101 6 1 14 114 774815637 774815538 1.920000e-31 147.0
15 TraesCS2B01G604600 chr3B 83.307 1264 171 21 165 1403 723459797 723461045 0.000000e+00 1129.0
16 TraesCS2B01G604600 chr3B 83.055 1257 181 16 165 1404 723466652 723467893 0.000000e+00 1112.0
17 TraesCS2B01G604600 chr3A 83.280 1256 179 16 165 1403 683214768 683216009 0.000000e+00 1127.0
18 TraesCS2B01G604600 chr3D 83.214 1257 179 15 165 1404 546388405 546389646 0.000000e+00 1123.0
19 TraesCS2B01G604600 chr4A 78.250 1246 248 16 165 1399 18012662 18013895 0.000000e+00 778.0
20 TraesCS2B01G604600 chr1B 84.524 84 10 2 1981 2061 234980810 234980893 1.970000e-11 80.5
21 TraesCS2B01G604600 chr6B 71.805 266 63 7 370 629 73073798 73074057 5.520000e-07 65.8
22 TraesCS2B01G604600 chr5A 80.000 85 8 8 2238 2316 635220379 635220460 1.000000e-03 54.7


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 TraesCS2B01G604600 chr2B 786104639 786107031 2392 False 1550.00 4420 100.00000 1 2393 3 chr2B.!!$F1 2392
1 TraesCS2B01G604600 chr2B 559421528 559422336 808 True 580.00 580 79.68400 283 1104 1 chr2B.!!$R1 821
2 TraesCS2B01G604600 chr2D 650190645 650191254 609 False 942.00 942 94.62500 1785 2393 1 chr2D.!!$F1 608
3 TraesCS2B01G604600 chr2D 650078758 650080442 1684 False 685.00 2132 94.67800 14 1748 4 chr2D.!!$F2 1734
4 TraesCS2B01G604600 chr2D 477424702 477425627 925 True 619.00 619 78.98600 166 1104 1 chr2D.!!$R1 938
5 TraesCS2B01G604600 chr2A 619770120 619771360 1240 True 1144.00 1144 83.51900 165 1403 1 chr2A.!!$R1 1238
6 TraesCS2B01G604600 chr2A 774813308 774815637 2329 True 896.75 2052 93.99875 14 2393 4 chr2A.!!$R2 2379
7 TraesCS2B01G604600 chr3B 723459797 723461045 1248 False 1129.00 1129 83.30700 165 1403 1 chr3B.!!$F1 1238
8 TraesCS2B01G604600 chr3B 723466652 723467893 1241 False 1112.00 1112 83.05500 165 1404 1 chr3B.!!$F2 1239
9 TraesCS2B01G604600 chr3A 683214768 683216009 1241 False 1127.00 1127 83.28000 165 1403 1 chr3A.!!$F1 1238
10 TraesCS2B01G604600 chr3D 546388405 546389646 1241 False 1123.00 1123 83.21400 165 1404 1 chr3D.!!$F1 1239
11 TraesCS2B01G604600 chr4A 18012662 18013895 1233 False 778.00 778 78.25000 165 1399 1 chr4A.!!$F1 1234

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
135 136 0.326238 TGATTCCTAGCTCGGGGGTT 60.326 55.0 4.14 0.0 0.0 4.11 F
136 137 0.837940 GATTCCTAGCTCGGGGGTTT 59.162 55.0 4.14 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 1031 0.035317 TCTTGCCATGCTCGTTCTGT 59.965 50.0 0.0 0.0 0.00 3.41 R
1620 1712 0.971386 AACACCTTATCGACCACCGT 59.029 50.0 0.0 0.0 39.75 4.83 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
49 50 9.829507 TCTAGTATTAGGTAAGCGATCTATACC 57.170 37.037 9.32 9.32 39.51 2.73
63 64 4.336889 TCTATACCGCTTGAAATCCTGG 57.663 45.455 0.00 0.00 0.00 4.45
66 67 0.539438 ACCGCTTGAAATCCTGGCAA 60.539 50.000 0.00 0.00 0.00 4.52
67 68 0.819582 CCGCTTGAAATCCTGGCAAT 59.180 50.000 0.00 0.00 0.00 3.56
68 69 2.023673 CCGCTTGAAATCCTGGCAATA 58.976 47.619 0.00 0.00 0.00 1.90
69 70 2.033801 CCGCTTGAAATCCTGGCAATAG 59.966 50.000 0.00 0.00 0.00 1.73
70 71 2.684881 CGCTTGAAATCCTGGCAATAGT 59.315 45.455 0.00 0.00 0.00 2.12
71 72 3.488047 CGCTTGAAATCCTGGCAATAGTG 60.488 47.826 0.00 0.00 0.00 2.74
72 73 3.445096 GCTTGAAATCCTGGCAATAGTGT 59.555 43.478 0.00 0.00 0.00 3.55
73 74 4.640201 GCTTGAAATCCTGGCAATAGTGTA 59.360 41.667 0.00 0.00 0.00 2.90
114 115 2.611974 ATCGTTCGGTTGCATTGTTC 57.388 45.000 0.00 0.00 0.00 3.18
115 116 0.589223 TCGTTCGGTTGCATTGTTCC 59.411 50.000 0.00 0.00 0.00 3.62
118 119 1.606668 GTTCGGTTGCATTGTTCCTGA 59.393 47.619 0.00 0.00 0.00 3.86
119 120 2.198827 TCGGTTGCATTGTTCCTGAT 57.801 45.000 0.00 0.00 0.00 2.90
120 121 2.513753 TCGGTTGCATTGTTCCTGATT 58.486 42.857 0.00 0.00 0.00 2.57
121 122 2.487762 TCGGTTGCATTGTTCCTGATTC 59.512 45.455 0.00 0.00 0.00 2.52
122 123 2.415893 CGGTTGCATTGTTCCTGATTCC 60.416 50.000 0.00 0.00 0.00 3.01
123 124 2.827921 GGTTGCATTGTTCCTGATTCCT 59.172 45.455 0.00 0.00 0.00 3.36
124 125 4.016444 GGTTGCATTGTTCCTGATTCCTA 58.984 43.478 0.00 0.00 0.00 2.94
125 126 4.096984 GGTTGCATTGTTCCTGATTCCTAG 59.903 45.833 0.00 0.00 0.00 3.02
126 127 3.282021 TGCATTGTTCCTGATTCCTAGC 58.718 45.455 0.00 0.00 0.00 3.42
127 128 3.054139 TGCATTGTTCCTGATTCCTAGCT 60.054 43.478 0.00 0.00 0.00 3.32
128 129 3.563390 GCATTGTTCCTGATTCCTAGCTC 59.437 47.826 0.00 0.00 0.00 4.09
129 130 3.526931 TTGTTCCTGATTCCTAGCTCG 57.473 47.619 0.00 0.00 0.00 5.03
130 131 1.757118 TGTTCCTGATTCCTAGCTCGG 59.243 52.381 0.00 0.00 0.00 4.63
131 132 1.069358 GTTCCTGATTCCTAGCTCGGG 59.931 57.143 4.14 1.70 38.98 5.14
132 133 0.470080 TCCTGATTCCTAGCTCGGGG 60.470 60.000 4.14 0.00 38.30 5.73
133 134 1.476007 CCTGATTCCTAGCTCGGGGG 61.476 65.000 4.14 0.00 34.76 5.40
134 135 0.760945 CTGATTCCTAGCTCGGGGGT 60.761 60.000 4.14 0.00 0.00 4.95
135 136 0.326238 TGATTCCTAGCTCGGGGGTT 60.326 55.000 4.14 0.00 0.00 4.11
136 137 0.837940 GATTCCTAGCTCGGGGGTTT 59.162 55.000 4.14 0.00 0.00 3.27
137 138 2.044758 GATTCCTAGCTCGGGGGTTTA 58.955 52.381 4.14 0.00 0.00 2.01
138 139 1.955451 TTCCTAGCTCGGGGGTTTAA 58.045 50.000 4.14 0.00 0.00 1.52
139 140 1.955451 TCCTAGCTCGGGGGTTTAAA 58.045 50.000 4.14 0.00 0.00 1.52
140 141 2.484602 TCCTAGCTCGGGGGTTTAAAT 58.515 47.619 4.14 0.00 0.00 1.40
141 142 3.656496 TCCTAGCTCGGGGGTTTAAATA 58.344 45.455 4.14 0.00 0.00 1.40
142 143 3.389002 TCCTAGCTCGGGGGTTTAAATAC 59.611 47.826 4.14 0.00 0.00 1.89
143 144 2.723322 AGCTCGGGGGTTTAAATACC 57.277 50.000 0.00 0.00 37.47 2.73
144 145 2.202707 AGCTCGGGGGTTTAAATACCT 58.797 47.619 10.55 0.00 38.30 3.08
145 146 2.579400 AGCTCGGGGGTTTAAATACCTT 59.421 45.455 10.55 0.00 38.30 3.50
146 147 3.010920 AGCTCGGGGGTTTAAATACCTTT 59.989 43.478 10.55 0.00 38.30 3.11
147 148 4.227982 AGCTCGGGGGTTTAAATACCTTTA 59.772 41.667 10.55 0.00 38.30 1.85
148 149 4.949238 GCTCGGGGGTTTAAATACCTTTAA 59.051 41.667 10.55 0.00 38.30 1.52
149 150 5.163622 GCTCGGGGGTTTAAATACCTTTAAC 60.164 44.000 10.55 0.00 36.73 2.01
150 151 6.138391 TCGGGGGTTTAAATACCTTTAACT 57.862 37.500 10.55 0.00 36.73 2.24
151 152 6.179756 TCGGGGGTTTAAATACCTTTAACTC 58.820 40.000 10.55 0.00 36.73 3.01
152 153 5.065090 CGGGGGTTTAAATACCTTTAACTCG 59.935 44.000 10.55 0.00 36.73 4.18
153 154 6.179756 GGGGGTTTAAATACCTTTAACTCGA 58.820 40.000 10.55 0.00 36.73 4.04
277 278 4.836125 TTCAGAAGCGCTTGAGAAAAAT 57.164 36.364 30.47 0.00 0.00 1.82
334 335 8.831550 AGAACAACTTATCTCTTCAGACAAAAC 58.168 33.333 0.00 0.00 0.00 2.43
336 337 9.832445 AACAACTTATCTCTTCAGACAAAACTA 57.168 29.630 0.00 0.00 0.00 2.24
401 405 6.993902 AGAAGGCAACAAACAATTTTGATCAT 59.006 30.769 0.00 0.00 44.38 2.45
815 826 1.278985 TCCATGAACGTGCTCCTGAAT 59.721 47.619 0.00 0.00 0.00 2.57
818 829 2.768253 TGAACGTGCTCCTGAATGAT 57.232 45.000 0.00 0.00 0.00 2.45
909 920 1.223417 CGCCGTTCAGGGTACGTTTT 61.223 55.000 0.00 0.00 41.48 2.43
910 921 1.794512 GCCGTTCAGGGTACGTTTTA 58.205 50.000 0.00 0.00 41.48 1.52
1020 1031 2.494888 TGAGGAGGAAGCCCATCATA 57.505 50.000 0.00 0.00 33.88 2.15
1036 1047 1.206849 TCATACAGAACGAGCATGGCA 59.793 47.619 0.00 0.00 0.00 4.92
1064 1075 5.755861 AGCAGAACTTGTCAAACTACTTCTC 59.244 40.000 0.00 0.00 0.00 2.87
1068 1079 5.007385 ACTTGTCAAACTACTTCTCGTGT 57.993 39.130 0.00 0.00 0.00 4.49
1240 1263 1.675801 CTGCAGCTCCTCACAGGAA 59.324 57.895 0.00 0.00 45.28 3.36
1241 1264 0.252479 CTGCAGCTCCTCACAGGAAT 59.748 55.000 0.00 0.00 45.28 3.01
1280 1323 0.327591 AGGCAAGAAGAAGAGGCAGG 59.672 55.000 0.00 0.00 0.00 4.85
1315 1358 3.771160 GACATGGCGGGGTCGACT 61.771 66.667 16.46 0.00 46.40 4.18
1422 1465 4.380023 GGCACACCTTATTTACATTTCGCA 60.380 41.667 0.00 0.00 0.00 5.10
1442 1485 6.682746 TCGCACTTGCCAGAAAAATAATTTA 58.317 32.000 0.00 0.00 37.91 1.40
1521 1613 8.746530 AGTGTCAATGATTAATGCTTCTCAAAT 58.253 29.630 0.00 0.00 0.00 2.32
1541 1633 8.737168 TCAAATAATAGGACTGGATGAAACTG 57.263 34.615 0.00 0.00 0.00 3.16
1592 1684 8.124199 GTCGATAAGGTGTTTTTGTCTTAAACA 58.876 33.333 0.00 0.00 41.69 2.83
1598 1690 9.744468 AAGGTGTTTTTGTCTTAAACATATCAC 57.256 29.630 0.00 0.00 44.52 3.06
1599 1691 8.908903 AGGTGTTTTTGTCTTAAACATATCACA 58.091 29.630 0.00 0.00 44.52 3.58
1600 1692 9.691362 GGTGTTTTTGTCTTAAACATATCACAT 57.309 29.630 0.00 0.00 44.52 3.21
1626 1718 6.387041 TCTAAAGATGATAGTGTACGGTGG 57.613 41.667 0.00 0.00 0.00 4.61
1627 1719 5.889853 TCTAAAGATGATAGTGTACGGTGGT 59.110 40.000 0.00 0.00 0.00 4.16
1628 1720 4.650754 AAGATGATAGTGTACGGTGGTC 57.349 45.455 0.00 0.00 0.00 4.02
1629 1721 2.617308 AGATGATAGTGTACGGTGGTCG 59.383 50.000 0.00 0.00 45.88 4.79
1630 1722 2.112380 TGATAGTGTACGGTGGTCGA 57.888 50.000 0.00 0.00 42.43 4.20
1631 1723 2.646930 TGATAGTGTACGGTGGTCGAT 58.353 47.619 0.00 0.00 42.43 3.59
1632 1724 3.807553 TGATAGTGTACGGTGGTCGATA 58.192 45.455 0.00 0.00 42.43 2.92
1633 1725 4.198530 TGATAGTGTACGGTGGTCGATAA 58.801 43.478 0.00 0.00 42.43 1.75
1634 1726 4.274214 TGATAGTGTACGGTGGTCGATAAG 59.726 45.833 0.00 0.00 42.43 1.73
1635 1727 1.747355 AGTGTACGGTGGTCGATAAGG 59.253 52.381 0.00 0.00 42.43 2.69
1636 1728 1.474077 GTGTACGGTGGTCGATAAGGT 59.526 52.381 0.00 0.00 42.43 3.50
1637 1729 1.473677 TGTACGGTGGTCGATAAGGTG 59.526 52.381 0.00 0.00 42.43 4.00
1638 1730 1.474077 GTACGGTGGTCGATAAGGTGT 59.526 52.381 0.00 0.00 42.43 4.16
1639 1731 0.971386 ACGGTGGTCGATAAGGTGTT 59.029 50.000 0.00 0.00 42.43 3.32
1640 1732 1.345415 ACGGTGGTCGATAAGGTGTTT 59.655 47.619 0.00 0.00 42.43 2.83
1641 1733 2.224354 ACGGTGGTCGATAAGGTGTTTT 60.224 45.455 0.00 0.00 42.43 2.43
1642 1734 2.809696 CGGTGGTCGATAAGGTGTTTTT 59.190 45.455 0.00 0.00 42.43 1.94
1643 1735 3.364565 CGGTGGTCGATAAGGTGTTTTTG 60.365 47.826 0.00 0.00 42.43 2.44
1644 1736 3.566742 GGTGGTCGATAAGGTGTTTTTGT 59.433 43.478 0.00 0.00 0.00 2.83
1645 1737 4.319984 GGTGGTCGATAAGGTGTTTTTGTC 60.320 45.833 0.00 0.00 0.00 3.18
1646 1738 4.514066 GTGGTCGATAAGGTGTTTTTGTCT 59.486 41.667 0.00 0.00 0.00 3.41
1647 1739 5.008316 GTGGTCGATAAGGTGTTTTTGTCTT 59.992 40.000 0.00 0.00 0.00 3.01
1648 1740 6.203338 GTGGTCGATAAGGTGTTTTTGTCTTA 59.797 38.462 0.00 0.00 0.00 2.10
1649 1741 6.766944 TGGTCGATAAGGTGTTTTTGTCTTAA 59.233 34.615 0.00 0.00 0.00 1.85
1650 1742 7.282675 TGGTCGATAAGGTGTTTTTGTCTTAAA 59.717 33.333 0.00 0.00 0.00 1.52
1651 1743 7.588854 GGTCGATAAGGTGTTTTTGTCTTAAAC 59.411 37.037 0.00 0.00 36.32 2.01
1652 1744 8.124199 GTCGATAAGGTGTTTTTGTCTTAAACA 58.876 33.333 0.00 0.00 41.69 2.83
1653 1745 8.842280 TCGATAAGGTGTTTTTGTCTTAAACAT 58.158 29.630 0.00 0.00 44.52 2.71
1748 1841 5.970692 AGGTATTCCTAGGGGTCTATCTT 57.029 43.478 9.46 0.00 43.12 2.40
1753 1846 1.353091 CTAGGGGTCTATCTTGGGCC 58.647 60.000 0.00 0.00 0.00 5.80
1754 1847 0.104620 TAGGGGTCTATCTTGGGCCC 60.105 60.000 17.59 17.59 38.61 5.80
1758 1851 1.420514 GGGTCTATCTTGGGCCCTAAC 59.579 57.143 25.70 10.02 36.49 2.34
1766 1859 2.310349 TCTTGGGCCCTAACTATTGCAA 59.690 45.455 25.70 0.00 0.00 4.08
1788 1881 8.043113 TGCAAATCTAAGTGACTCAATCATACT 58.957 33.333 0.00 0.00 40.28 2.12
1953 2049 9.167311 GAATTTTGTTGCTAAGAATCCTCTCTA 57.833 33.333 0.00 0.00 0.00 2.43
2041 2138 4.037222 TCCACATGGCACTCCTAAGATAA 58.963 43.478 0.00 0.00 34.44 1.75
2231 2330 6.442244 ACCTCCTAATTAAGAGAAGACAAGCT 59.558 38.462 11.94 0.00 31.43 3.74
2232 2331 7.037945 ACCTCCTAATTAAGAGAAGACAAGCTT 60.038 37.037 11.94 0.00 40.25 3.74
2233 2332 7.826744 CCTCCTAATTAAGAGAAGACAAGCTTT 59.173 37.037 11.94 0.00 36.83 3.51
2234 2333 9.225436 CTCCTAATTAAGAGAAGACAAGCTTTT 57.775 33.333 5.29 0.00 36.83 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.935495 ATGATGCCCCGCGCGATT 62.935 61.111 34.63 10.68 42.08 3.34
9 10 4.662961 TAGATGATGCCCCGCGCG 62.663 66.667 25.67 25.67 42.08 6.86
10 11 2.154798 TACTAGATGATGCCCCGCGC 62.155 60.000 0.00 0.00 38.31 6.86
11 12 0.532573 ATACTAGATGATGCCCCGCG 59.467 55.000 0.00 0.00 0.00 6.46
12 13 2.770164 AATACTAGATGATGCCCCGC 57.230 50.000 0.00 0.00 0.00 6.13
47 48 0.539438 TTGCCAGGATTTCAAGCGGT 60.539 50.000 0.00 0.00 0.00 5.68
49 50 2.684881 ACTATTGCCAGGATTTCAAGCG 59.315 45.455 0.00 0.00 0.00 4.68
63 64 9.793252 ATTTCAAGACATTGATTACACTATTGC 57.207 29.630 0.00 0.00 44.75 3.56
114 115 1.476007 CCCCCGAGCTAGGAATCAGG 61.476 65.000 15.38 6.29 0.00 3.86
115 116 0.760945 ACCCCCGAGCTAGGAATCAG 60.761 60.000 15.38 0.00 0.00 2.90
118 119 2.185663 TAAACCCCCGAGCTAGGAAT 57.814 50.000 15.38 0.00 0.00 3.01
119 120 1.955451 TTAAACCCCCGAGCTAGGAA 58.045 50.000 15.38 0.00 0.00 3.36
120 121 1.955451 TTTAAACCCCCGAGCTAGGA 58.045 50.000 15.38 0.00 0.00 2.94
121 122 3.495629 GGTATTTAAACCCCCGAGCTAGG 60.496 52.174 5.78 5.78 33.02 3.02
122 123 3.390311 AGGTATTTAAACCCCCGAGCTAG 59.610 47.826 0.00 0.00 40.71 3.42
123 124 3.387012 AGGTATTTAAACCCCCGAGCTA 58.613 45.455 0.00 0.00 40.71 3.32
124 125 2.202707 AGGTATTTAAACCCCCGAGCT 58.797 47.619 0.00 0.00 40.71 4.09
125 126 2.723322 AGGTATTTAAACCCCCGAGC 57.277 50.000 0.00 0.00 40.71 5.03
126 127 6.182627 AGTTAAAGGTATTTAAACCCCCGAG 58.817 40.000 0.00 0.00 41.36 4.63
127 128 6.138391 AGTTAAAGGTATTTAAACCCCCGA 57.862 37.500 0.00 0.00 41.36 5.14
128 129 5.065090 CGAGTTAAAGGTATTTAAACCCCCG 59.935 44.000 0.00 0.00 41.36 5.73
129 130 6.094048 GTCGAGTTAAAGGTATTTAAACCCCC 59.906 42.308 0.00 0.00 41.36 5.40
130 131 6.881065 AGTCGAGTTAAAGGTATTTAAACCCC 59.119 38.462 0.00 0.00 41.36 4.95
131 132 7.912056 AGTCGAGTTAAAGGTATTTAAACCC 57.088 36.000 0.00 0.00 41.36 4.11
136 137 9.643693 CCAGTTAAGTCGAGTTAAAGGTATTTA 57.356 33.333 23.50 0.00 0.00 1.40
137 138 7.118825 GCCAGTTAAGTCGAGTTAAAGGTATTT 59.881 37.037 28.49 11.31 0.00 1.40
138 139 6.592994 GCCAGTTAAGTCGAGTTAAAGGTATT 59.407 38.462 28.49 12.47 0.00 1.89
139 140 6.070938 AGCCAGTTAAGTCGAGTTAAAGGTAT 60.071 38.462 28.49 21.02 0.00 2.73
140 141 5.244626 AGCCAGTTAAGTCGAGTTAAAGGTA 59.755 40.000 28.49 10.65 0.00 3.08
141 142 4.040095 AGCCAGTTAAGTCGAGTTAAAGGT 59.960 41.667 28.49 21.54 0.00 3.50
142 143 4.389077 CAGCCAGTTAAGTCGAGTTAAAGG 59.611 45.833 26.32 26.32 0.00 3.11
143 144 4.143094 GCAGCCAGTTAAGTCGAGTTAAAG 60.143 45.833 23.50 18.61 0.00 1.85
144 145 3.744426 GCAGCCAGTTAAGTCGAGTTAAA 59.256 43.478 23.50 8.45 0.00 1.52
145 146 3.243941 TGCAGCCAGTTAAGTCGAGTTAA 60.244 43.478 19.20 19.20 0.00 2.01
146 147 2.297880 TGCAGCCAGTTAAGTCGAGTTA 59.702 45.455 8.66 8.66 0.00 2.24
147 148 1.070134 TGCAGCCAGTTAAGTCGAGTT 59.930 47.619 10.90 10.90 0.00 3.01
148 149 0.679505 TGCAGCCAGTTAAGTCGAGT 59.320 50.000 0.00 0.00 0.00 4.18
149 150 1.354040 CTGCAGCCAGTTAAGTCGAG 58.646 55.000 0.00 0.00 34.31 4.04
150 151 0.037326 CCTGCAGCCAGTTAAGTCGA 60.037 55.000 8.66 0.00 37.38 4.20
151 152 0.320771 ACCTGCAGCCAGTTAAGTCG 60.321 55.000 8.66 0.00 37.38 4.18
152 153 2.762535 TACCTGCAGCCAGTTAAGTC 57.237 50.000 8.66 0.00 37.38 3.01
153 154 2.571653 TGATACCTGCAGCCAGTTAAGT 59.428 45.455 8.66 0.25 37.38 2.24
277 278 4.580995 TGCCTTTGTTCTTCCGAAAATACA 59.419 37.500 0.00 0.00 0.00 2.29
303 304 7.815068 GTCTGAAGAGATAAGTTGTTCTAGCAA 59.185 37.037 0.00 0.00 0.00 3.91
314 315 7.963532 TGGTAGTTTTGTCTGAAGAGATAAGT 58.036 34.615 0.00 0.00 31.62 2.24
334 335 2.422597 TCTTTGTGCCATCGTTGGTAG 58.577 47.619 13.90 4.87 45.57 3.18
336 337 1.909700 ATCTTTGTGCCATCGTTGGT 58.090 45.000 13.90 0.00 45.57 3.67
401 405 4.920112 CGTCCAACCACACGGGCA 62.920 66.667 0.00 0.00 42.05 5.36
815 826 1.553248 ACCTTTGCGGTGTAGCTATCA 59.447 47.619 0.00 0.00 46.80 2.15
909 920 1.229131 ACTCCGGATCCAGGTACCTA 58.771 55.000 15.80 0.00 0.00 3.08
910 921 1.229131 TACTCCGGATCCAGGTACCT 58.771 55.000 9.21 9.21 0.00 3.08
1020 1031 0.035317 TCTTGCCATGCTCGTTCTGT 59.965 50.000 0.00 0.00 0.00 3.41
1036 1047 6.116126 AGTAGTTTGACAAGTTCTGCTTCTT 58.884 36.000 0.00 0.00 34.69 2.52
1299 1342 3.771160 GAGTCGACCCCGCCATGT 61.771 66.667 13.01 0.00 35.37 3.21
1315 1358 1.663379 CCATGCTGACCGACTACCGA 61.663 60.000 0.00 0.00 41.76 4.69
1368 1411 3.713936 CGGTACACGCAGAGATGAA 57.286 52.632 0.00 0.00 34.82 2.57
1419 1462 5.844301 AAATTATTTTTCTGGCAAGTGCG 57.156 34.783 0.00 0.00 43.26 5.34
1453 1545 7.551262 TGTGACTCACATAATAATAACCGCTTT 59.449 33.333 7.84 0.00 39.62 3.51
1464 1556 6.262273 TGCTATCGACTGTGACTCACATAATA 59.738 38.462 12.34 7.31 43.71 0.98
1521 1613 9.396022 GAAAATCAGTTTCATCCAGTCCTATTA 57.604 33.333 0.00 0.00 44.42 0.98
1541 1633 3.001939 CCGTACACGCCCTTATGAAAATC 59.998 47.826 0.00 0.00 38.18 2.17
1556 1648 1.474077 ACCTTATCGACCACCGTACAC 59.526 52.381 0.00 0.00 39.75 2.90
1602 1694 6.550108 ACCACCGTACACTATCATCTTTAGAT 59.450 38.462 0.00 0.00 34.56 1.98
1603 1695 5.889853 ACCACCGTACACTATCATCTTTAGA 59.110 40.000 0.00 0.00 0.00 2.10
1604 1696 6.145338 ACCACCGTACACTATCATCTTTAG 57.855 41.667 0.00 0.00 0.00 1.85
1605 1697 5.220912 CGACCACCGTACACTATCATCTTTA 60.221 44.000 0.00 0.00 0.00 1.85
1606 1698 4.439700 CGACCACCGTACACTATCATCTTT 60.440 45.833 0.00 0.00 0.00 2.52
1607 1699 3.066342 CGACCACCGTACACTATCATCTT 59.934 47.826 0.00 0.00 0.00 2.40
1608 1700 2.617308 CGACCACCGTACACTATCATCT 59.383 50.000 0.00 0.00 0.00 2.90
1609 1701 2.615447 TCGACCACCGTACACTATCATC 59.385 50.000 0.00 0.00 39.75 2.92
1610 1702 2.646930 TCGACCACCGTACACTATCAT 58.353 47.619 0.00 0.00 39.75 2.45
1611 1703 2.112380 TCGACCACCGTACACTATCA 57.888 50.000 0.00 0.00 39.75 2.15
1612 1704 4.320057 CCTTATCGACCACCGTACACTATC 60.320 50.000 0.00 0.00 39.75 2.08
1613 1705 3.567164 CCTTATCGACCACCGTACACTAT 59.433 47.826 0.00 0.00 39.75 2.12
1614 1706 2.945008 CCTTATCGACCACCGTACACTA 59.055 50.000 0.00 0.00 39.75 2.74
1615 1707 1.747355 CCTTATCGACCACCGTACACT 59.253 52.381 0.00 0.00 39.75 3.55
1616 1708 1.474077 ACCTTATCGACCACCGTACAC 59.526 52.381 0.00 0.00 39.75 2.90
1617 1709 1.473677 CACCTTATCGACCACCGTACA 59.526 52.381 0.00 0.00 39.75 2.90
1618 1710 1.474077 ACACCTTATCGACCACCGTAC 59.526 52.381 0.00 0.00 39.75 3.67
1619 1711 1.838112 ACACCTTATCGACCACCGTA 58.162 50.000 0.00 0.00 39.75 4.02
1620 1712 0.971386 AACACCTTATCGACCACCGT 59.029 50.000 0.00 0.00 39.75 4.83
1621 1713 2.088950 AAACACCTTATCGACCACCG 57.911 50.000 0.00 0.00 40.25 4.94
1622 1714 3.566742 ACAAAAACACCTTATCGACCACC 59.433 43.478 0.00 0.00 0.00 4.61
1623 1715 4.514066 AGACAAAAACACCTTATCGACCAC 59.486 41.667 0.00 0.00 0.00 4.16
1624 1716 4.710324 AGACAAAAACACCTTATCGACCA 58.290 39.130 0.00 0.00 0.00 4.02
1625 1717 5.684550 AAGACAAAAACACCTTATCGACC 57.315 39.130 0.00 0.00 0.00 4.79
1626 1718 8.124199 TGTTTAAGACAAAAACACCTTATCGAC 58.876 33.333 0.00 0.00 40.83 4.20
1627 1719 8.211116 TGTTTAAGACAAAAACACCTTATCGA 57.789 30.769 0.00 0.00 40.83 3.59
1632 1724 9.744468 GTGATATGTTTAAGACAAAAACACCTT 57.256 29.630 3.72 0.00 46.40 3.50
1633 1725 8.908903 TGTGATATGTTTAAGACAAAAACACCT 58.091 29.630 3.72 0.00 46.40 4.00
1634 1726 9.691362 ATGTGATATGTTTAAGACAAAAACACC 57.309 29.630 3.72 0.00 46.40 4.16
1724 1816 7.246763 CAAGATAGACCCCTAGGAATACCTAA 58.753 42.308 11.48 0.00 46.59 2.69
1727 1819 4.778427 CCAAGATAGACCCCTAGGAATACC 59.222 50.000 11.48 0.00 36.73 2.73
1748 1841 2.909504 TTTGCAATAGTTAGGGCCCA 57.090 45.000 27.56 7.27 0.00 5.36
1753 1846 8.723942 AGTCACTTAGATTTGCAATAGTTAGG 57.276 34.615 0.00 0.00 0.00 2.69
1754 1847 9.371136 TGAGTCACTTAGATTTGCAATAGTTAG 57.629 33.333 0.00 0.00 0.00 2.34
1758 1851 8.886719 TGATTGAGTCACTTAGATTTGCAATAG 58.113 33.333 0.00 0.00 0.00 1.73
1766 1859 6.989169 GCCAGTATGATTGAGTCACTTAGATT 59.011 38.462 0.00 0.00 40.28 2.40
1788 1881 5.947228 TGTTTGATTGTTTGTTTTTGCCA 57.053 30.435 0.00 0.00 0.00 4.92
2041 2138 3.447229 GCTTTTAGGGCATGTAATGGTGT 59.553 43.478 0.00 0.00 46.86 4.16
2197 2296 8.187913 TCTCTTAATTAGGAGGTGATCATCTG 57.812 38.462 14.71 0.00 31.09 2.90
2207 2306 6.883744 AGCTTGTCTTCTCTTAATTAGGAGG 58.116 40.000 20.83 9.00 31.09 4.30


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

AutoCloner maintained by Alex Coulton.