Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023905.1 Corchorus olitorius cultivar O-4 contig23938, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 54019
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:854 original size:40 final size:40
Alignment explanation
Indices: 763--893 Score: 226
Period size: 41 Copynumber: 3.2 Consensus size: 40
753 ATTCGTATCA
763 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAAATT
1 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTT-AAATT
804 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATT
1 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATT
*
844 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTCGTTTTAAATT
1 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTAAATT
*
885 CTCAGTTTG
1 CCCAGTTTG
894 TCAGCATTCC
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
40 36 0.41
41 51 0.59
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (40 bp):
CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATT
Found at i:949 original size:58 final size:58
Alignment explanation
Indices: 841--953 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
831 TGTTGTTTAA
* * *
841 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTCGTTTTAAATTCTCAGTTTGTCAGC
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATCGTTTTAAATACCCAGTTTGTCAGC
* * * *
899 ATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTG-TTTAAGTACACCAGTTTGTC
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATCGTTTTAAATAC-CCAGTTTGTC
954 CTTCCTCACT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 7 0.15
58 40 0.85
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.38
Consensus pattern (58 bp):
ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATCGTTTTAAATACCCAGTTTGTCAGC
Found at i:991 original size:98 final size:97
Alignment explanation
Indices: 801--993 Score: 237
Period size: 98 Copynumber: 2.0 Consensus size: 97
791 GTTGTTTAAA
* *
801 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCATCG
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAATACCCAGTTTGCCCTTCCTCATCG
* * *
866 GAAGGTGTCGTTTTAAATTCTCAGTTTGTCAGC
66 GAAGGTGTC-TGTCAAATTCCCAGTTTGTCAGC
* * * *
899 ATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTAAGTACACCAGTTTGTCCTTCCTCA-C
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAATAC-CCAGTTTGCCCTTCCTCATC
* *
963 TGGAAGGTGT-TGTCAGCATTCCCCGTTTGTC
65 -GGAAGGTGTCTGTCA-AATTCCCAGTTTGTC
994 CTTCCTCATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
97 3 0.04
98 52 0.64
99 26 0.32
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (97 bp):
ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAATACCCAGTTTGCCCTTCCTCATCG
GAAGGTGTCTGTCAAATTCCCAGTTTGTCAGC
Found at i:1008 original size:40 final size:40
Alignment explanation
Indices: 899--1099 Score: 212
Period size: 40 Copynumber: 5.0 Consensus size: 40
889 GTTTGTCAGC
* *
899 ATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTA-
1 ATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAG
* *
938 AGTACACCAGTTTGTCCTTCCTCA-CTGGAAGGTGTTG-TCAG
1 A-TTC-CCAGTTTGTCCTTCCTCATC-GGAAGGTGTTGTTTAG
* *
979 CATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTA-
1 -ATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAG
* *
1019 AGTTCTCTAGTTTGTCCTTCCTCACCGGAAGGTGTTGTTTAG
1 A-TTC-CCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAG
** * *
1061 ATTTTCAGTTTGCCCTTCCTTATCGGAAGGTGTTGTTTA
1 ATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTA
1100 AAGCCCATTC
Statistics
Matches: 134, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
39 2 0.01
40 65 0.49
41 65 0.49
42 2 0.01
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (40 bp):
ATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAG
Found at i:1031 original size:81 final size:81
Alignment explanation
Indices: 891--1100 Score: 305
Period size: 81 Copynumber: 2.6 Consensus size: 81
881 AATTCTCAGT
891 TTGTCAGCATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTAAGTACACCAGTTTGTCCT
1 TTGTCAGCATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTAAGTACACCAGTTTGTCCT
*
956 TCCTCACTGGAAGGTG
66 TCCTCACCGGAAGGTG
* * *
972 TTGTCAGCATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTAAGTTCTCTAGTTTGTCCT
1 TTGTCAGCATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTAAGTACACCAGTTTGTCCT
1037 TCCTCACCGGAAGGTG
66 TCCTCACCGGAAGGTG
* ** * * * *
1053 TTGTTTAG-ATTTTCAGTTTGCCCTTCCTTATCGGAAGGTGTTGTTTAA
1 TTG-TCAGCATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTAA
1101 AGCCCATTCT
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 114 0.97
82 3 0.03
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (81 bp):
TTGTCAGCATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTAAGTACACCAGTTTGTCCT
TCCTCACCGGAAGGTG
Found at i:1031 original size:139 final size:139
Alignment explanation
Indices: 767--1034 Score: 364
Period size: 139 Copynumber: 1.9 Consensus size: 139
757 GTATCACCCA
* *
767 GTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGT
1 GTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAAATACCCAGTTTGCCCTTCCTCATCGGAAGGT
* *
832 GTTGTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTCGTTTTAAATTCTCAGTTTGTCA
66 GTTGTTCAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATCGTTTTAAATTCTCAGTTTGTCA
897 GCATTCCCC
131 GCATTCCCC
* * *
906 GTTTGTCCTTCCTCATCGGAAGGTATTGTTT-AAGTACACCAGTTTGTCCTTCCTCA-CTGGAAG
1 GTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAAATAC-CCAGTTTGCCCTTCCTCATC-GGAAG
* * * * *
969 GTGTTG-TCAGCATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTG-TTTAAGTTCTCTAGTTT
64 GTGTTGTTCA-AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATCGTTTTAAATTCTC-AGTTT
1032 GTC
127 GTC
1035 CTTCCTCACC
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
138 17 0.15
139 96 0.85
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (139 bp):
GTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAAATACCCAGTTTGCCCTTCCTCATCGGAAGGT
GTTGTTCAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTATCGTTTTAAATTCTCAGTTTGTCA
GCATTCCCC
Found at i:1205 original size:40 final size:40
Alignment explanation
Indices: 1123--1223 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
1113 CCAGTTTGCG
* *
1123 CTTCCCCACCAGAAGGTGTTGATTTCATTCCCGCTATGCC
1 CTTCCCCACCGGAAGGTGTTGATTTCATTCCCGCTATCCC
* * * *
1163 CTTCCCCACCGGAAGGTGTTGATTTTATTCCTGTTTTCCC
1 CTTCCCCACCGGAAGGTGTTGATTTCATTCCCGCTATCCC
***
1203 CTTCCCGGTCGGAAGGTGTTG
1 CTTCCCCACCGGAAGGTGTTG
1224 TCTTCAATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.34
Consensus pattern (40 bp):
CTTCCCCACCGGAAGGTGTTGATTTCATTCCCGCTATCCC
Found at i:1238 original size:48 final size:47
Alignment explanation
Indices: 1186--1886 Score: 668
Period size: 48 Copynumber: 14.2 Consensus size: 47
1176 AGGTGTTGAT
*
1186 TTTATTCCTGTTTTCCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
1 TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-A
*
1234 TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA
1 TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
* *
1281 TTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGT
1 -TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-A
* * *
1330 TTTATT-CTCGTTTTGCCCTTCCTGGTCGGAAGGTGTTTTTTTCAATA
1 TTTATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
*
1377 TTTTATTCCTGTTTTGCCCTTCCCGTTCGGAAGGTGTTGTCTTCAATGA
1 -TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-A
* * * *
1426 TTTATTACAGTTTAGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA
1 TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
** * *
1473 TATTATTCCAATTTCGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGT
1 T-TTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-A
* ** *
1522 TTTATACCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA
1 TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
*
1569 TTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGT
1 -TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-A
* * *
1618 TTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA
1 TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
* ** * ** * ***
1665 TTTCATTCCTGTCTTCAATGTTTTATTCCCGTTTTTCCC-TTCCCGGTCGGAAGGTATTGTTTTC
1 TTT-ATTCCTGT-TT---TG-------CCC----TTCCCGGT--CGGAAGG--TGTTGTCTTCAA
*
1729 AA
46 TA
* * * * * *
1731 TATTTTATTTCAGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATA
1 TTTATT---CCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
1781 TTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
1 -TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
* * *
1829 TTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTCAATA
1 -TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
1877 TTTCATTCCT
1 TTT-ATTCCT
1887 TTCTTCAATG
Statistics
Matches: 540, Mismatches: 77, Indels: 72
0.78 0.11 0.10
Matches are distributed among these distances:
47 10 0.02
48 468 0.87
49 6 0.01
50 6 0.01
51 4 0.01
52 7 0.01
53 4 0.01
54 1 0.00
57 3 0.01
59 3 0.01
62 1 0.00
63 5 0.01
64 7 0.01
65 2 0.00
66 8 0.01
67 2 0.00
68 3 0.01
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (47 bp):
TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
Found at i:1348 original size:96 final size:96
Alignment explanation
Indices: 1184--1886 Score: 965
Period size: 96 Copynumber: 7.1 Consensus size: 96
1174 GAAGGTGTTG
* * *
1184 ATTTTATTCCTGTTTTCCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGATTTATTCCTGTTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
1249 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* *
1280 ATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCTCGTTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
* *
1345 CCCTTCCTGGTCGGAAGGTGTTTTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* * * * *
1376 ATTTTATTCCTGTTTTGCCCTTCCCGTTCGGAAGGTGTTGTCTTCAATGATTTATTACAGTTTAG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
1441 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* ** * * *
1472 ATATTATTCCAATTTCGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATACCCATTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
1537 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
*
1568 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTAATCCCGTTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
1633 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* * *
1664 ATTTCATTCCTGTCTTCAATGTTTTATTCCCGTTTTTCCCTTCCCGGTCGGAAGGTATTGTTTTC
1 ATTTTATTCCTGT-TT---TG----------------CCCTTCCCGGTCGGAAGGTGTTGTCTTC
* * * *
1729 AATATTTTATTTCAGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAAT
46 AATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
*
1780 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGTTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
*
1845 CCCTTCCCGGTCGGAAGGCGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
*
1876 ATTTCATTCCT
1 ATTTTATTCCT
1887 TTCTTCAATG
Statistics
Matches: 537, Mismatches: 50, Indels: 40
0.86 0.08 0.06
Matches are distributed among these distances:
96 445 0.83
97 2 0.00
100 2 0.00
112 2 0.00
115 2 0.00
116 84 0.16
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (96 bp):
ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
Found at i:1401 original size:144 final size:144
Alignment explanation
Indices: 1184--1885 Score: 897
Period size: 144 Copynumber: 4.7 Consensus size: 144
1174 GAAGGTGTTG
*
1184 ATTTTATTCCTGTTTTCCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA-TTTATTCCTGTTTT
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-ATTTTATTCCTGTTTT
1248 GCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAA
65 GCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAA
1313 GGTGTTGTCTTCAAT
130 GGTGTTGTCTTCAAT
* * * *
1328 GTTTTATT-CTCGTTTTGCCCTTCCTGGTCGGAAGGTGTTTTTTTCAATATTTTATTCCTGTTTT
1 ATTTTATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCTGTTTT
* * * *
1392 GCCCTTCCCGTTCGGAAGGTGTTGTCTTCAATGA-TTTATTACAGTTTAGCCCTTCCCGGTCGGA
65 GCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-ATTTTATTCCAGTTTTGCCCTTCCCGGTCGGA
*
1456 AGGTGTTGTTTTCAAT
129 AGGTGTTGTCTTCAAT
* ** * * * **
1472 ATATTATTCCAATTTCGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATACCCATTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCTGTTTTG
*
1537 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAG
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAG
1602 GTGTTGTCTTCAAT
131 GTGTTGTCTTCAAT
* * * * *
1616 GTTTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTCTTC
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA-TT--TT-AT-TC--C
* *
1681 AATGTTTTATTCCCGTTTTTCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTTATTTCAGTT
59 --TG--TT-TT---G-----CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCAGTT
* *
1746 TTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAAT
111 TTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT
*
1780 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGTTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCTGTTTTG
* *
1845 CCCTTCCCGGTCGGAAGGCGTTGTTTTCAATATTTCATTCC
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCC
1886 TTTCTTCAAT
Statistics
Matches: 478, Mismatches: 55, Indels: 50
0.82 0.09 0.09
Matches are distributed among these distances:
143 4 0.01
144 327 0.68
145 4 0.01
147 2 0.00
148 1 0.00
149 2 0.00
151 1 0.00
152 2 0.00
153 2 0.00
155 3 0.01
156 2 0.00
157 1 0.00
159 3 0.01
160 1 0.00
161 2 0.00
163 2 0.00
164 119 0.25
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (144 bp):
ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCTGTTTTG
CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAG
GTGTTGTCTTCAAT
Found at i:1695 original size:68 final size:68
Alignment explanation
Indices: 1606--1735 Score: 233
Period size: 68 Copynumber: 1.9 Consensus size: 68
1596 CGGAAGGTGT
*
1606 TGTCTTCAATGTTTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCAT
1 TGTCTTCAATGTTTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTCAT
1671 TCC
66 TCC
* *
1674 TGTCTTCAATGTTTTATTCCCGTTTTTCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTT
1 TGTCTTCAATGTTTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTT
1736 TATTTCAGTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (68 bp):
TGTCTTCAATGTTTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTCAT
TCC
Found at i:1766 original size:116 final size:116
Alignment explanation
Indices: 1562--1792 Score: 363
Period size: 116 Copynumber: 2.0 Consensus size: 116
1552 AGGTGTTGTT
* * * *
1562 TTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTAATCCC
1 TTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTATTGTCTTCAATATTTTAATCCA
1627 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
66 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
* * * * *
1678 TTCAATGTTTTATTCCCGTTTTTCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTTATTTCA
1 TTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTATTGTCTTCAATATTTTAATCCA
* *
1743 GTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
66 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGT
1793 TTTGCCCTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
116 104 1.00
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (116 bp):
TTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTATTGTCTTCAATATTTTAATCCA
GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
Found at i:1797 original size:164 final size:164
Alignment explanation
Indices: 1510--1837 Score: 539
Period size: 164 Copynumber: 2.0 Consensus size: 164
1500 CGGAAGGTGT
*
1510 TGTCTTCAATGTTTTATACCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTCTTCAATGTTTTATACCCATTTTGCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTTAT
* *
1575 TCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTAATCCCGTTTTGCCCTTCC
66 TCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTAATCCCGTTTTGCCCTTCC
*
1640 CGGTCGGAAGGTGTTGTTTTCAATATTTCATTCC
131 CGGTCGGAAGGTGTTGTCTTCAATATTTCATTCC
* * *
1674 TGTCTTCAATGTTTTATTCCCGTTTTTCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTTAT
1 TGTCTTCAATGTTTTATACCCATTTTGCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTTAT
* * * * *
1739 TTCAGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCC
66 TCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTAATCCCGTTTTGCCCTTCC
*
1804 CGGTCGGAAGGTGTTGTCTTCAATATTTTATTCC
131 CGGTCGGAAGGTGTTGTCTTCAATATTTCATTCC
1838 CGTTTTGCCC
Statistics
Matches: 151, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
164 151 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (164 bp):
TGTCTTCAATGTTTTATACCCATTTTGCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTTAT
TCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTAATCCCGTTTTGCCCTTCC
CGGTCGGAAGGTGTTGTCTTCAATATTTCATTCC
Found at i:1842 original size:212 final size:212
Alignment explanation
Indices: 1488--1920 Score: 751
Period size: 212 Copynumber: 2.0 Consensus size: 212
1478 TTCCAATTTC
* *
1488 GCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATACCCATTTTGCCCTTCCCGGTCGGAA
1 GCCCTTCCCGGTCGGAAGGTATTGTCTTCAATATTTTATACCCATTTTGCCCTTCCCGGTCGGAA
*
1553 GGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGT
66 GGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATAT
*
1618 TTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTCTTCAA
131 TTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTCAATATTTCATTCCTGTCTTCAA
1683 TGTTTTATTCCCGTTTT
196 TGTTTTATTCCCGTTTT
* * ** *
1700 TCCCTTCCCGGTCGGAAGGTATTGTTTTCAATATTTTAT-TTCAGTTTTGCCCTTCCTGGTCGGA
1 GCCCTTCCCGGTCGGAAGGTATTGTCTTCAATATTTTATACCCA-TTTTGCCCTTCCCGGTCGGA
1764 AGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
65 AGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
* *
1829 TTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTCAATATTTCATTCCTTTCTTCA
130 TTTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTCAATATTTCATTCCTGTCTTCA
1894 ATGTTTTATTCCCGTTTT
195 ATGTTTTATTCCCGTTTT
1912 GCCCTTCCC
1 GCCCTTCCC
1921 CATCGGAAAG
Statistics
Matches: 208, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
211 2 0.01
212 206 0.99
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (212 bp):
GCCCTTCCCGGTCGGAAGGTATTGTCTTCAATATTTTATACCCATTTTGCCCTTCCCGGTCGGAA
GGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATAT
TTTAATCCCGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTCAATATTTCATTCCTGTCTTCAA
TGTTTTATTCCCGTTTT
Found at i:3001 original size:27 final size:29
Alignment explanation
Indices: 2944--3004 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 29
2934 ATTCAACAAT
*
2944 TAAAAGTAAATAAGAAAAATAAACAAGAA
1 TAAAAGTAAATAAGAAAAATAAACAAAAA
**
2973 TAAAAG-AAA-AAGAAAAATAATGAAAAA
1 TAAAAGTAAATAAGAAAAATAAACAAAAA
3000 TAAAA
1 TAAAA
3005 AGATAAGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 20 0.69
28 3 0.10
29 6 0.21
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.13
Consensus pattern (29 bp):
TAAAAGTAAATAAGAAAAATAAACAAAAA
Found at i:3306 original size:26 final size:26
Alignment explanation
Indices: 3257--3308 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3247 CAAAATAGCT
*
3257 AAATTAAACTAGAAAACAATAAAATA
1 AAATTAAACTAGAAAACAAGAAAATA
*
3283 AAATTAAACTA-AAAATTAAGAAAATA
1 AAATTAAACTAGAAAA-CAAGAAAATA
3309 GTTTAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (26 bp):
AAATTAAACTAGAAAACAAGAAAATA
Found at i:8338 original size:19 final size:18
Alignment explanation
Indices: 8314--8349 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8304 TGAAGATTTA
8314 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
8333 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
8350 ATTATCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:13884 original size:17 final size:17
Alignment explanation
Indices: 13862--13894 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13852 AGGGTAATTA
*
13862 AAAAAAAGTGTTTTCAC
1 AAAAAAAGCGTTTTCAC
13879 AAAAAAAGCGTTTTCA
1 AAAAAAAGCGTTTTCA
13895 TGATAGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (17 bp):
AAAAAAAGCGTTTTCAC
Found at i:14759 original size:19 final size:18
Alignment explanation
Indices: 14735--14770 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14725 TGAAGATTTA
14735 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
14754 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
14771 ATTATCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:19222 original size:39 final size:40
Alignment explanation
Indices: 19179--19331 Score: 161
Period size: 39 Copynumber: 3.9 Consensus size: 40
19169 GATAGTGAAC
*
19179 TGAAAAATGCATATGGCTAGGTTTTGAGATGCTA-TGGAT
1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCTAGTGGAT
* **
19218 TGAAAAATGCATATGGCTAAGTTTTGTG-TTTTAGTGGAT
1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCTAGTGGAT
* * * * *
19257 TGCATAATACATATGGCTAAGTTTTGTGTTG-TAGTGGAT
1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCTAGTGGAT
* * * *
19296 CGAAAAATGCATATGGCTAGGTCTTGAAATGC-AGTG
1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCTAGTG
19332 AACTTTCATT
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
38 3 0.03
39 90 0.96
40 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (40 bp):
TGAAAAATGCATATGGCTAAGTTTTGAGATGCTAGTGGAT
Found at i:20931 original size:28 final size:28
Alignment explanation
Indices: 20899--20997 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
20889 GCACTTGAAG
* * *
20899 TGACCAAAATGCCCCTAGATGTGTAAAA
1 TGACCAAAATGCCCCTGGATATGCAAAA
*
20927 TGACCAAAATGCCCCTGGACATGCAAAA
1 TGACCAAAATGCCCCTGGATATGCAAAA
* * *
20955 TGACAAAAATACCCCTGGATATGCAATA
1 TGACCAAAATGCCCCTGGATATGCAAAA
20983 TGACCAAAATGCCCC
1 TGACCAAAATGCCCC
20998 CTTAAGTGAC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.18
Consensus pattern (28 bp):
TGACCAAAATGCCCCTGGATATGCAAAA
Found at i:21295 original size:35 final size:35
Alignment explanation
Indices: 21254--21528 Score: 478
Period size: 35 Copynumber: 7.9 Consensus size: 35
21244 CGAGTTTATA
* **
21254 TTGAAGATGCTACACCGAGTCATCTAAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
*
21289 TTGAAGATGCTACACCGAGTCATCTGAATTTTTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
*
21324 CTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
21359 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
21394 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
* *
21429 CTGAAGATGCTACACCGAATCATCTGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
*
21464 TTGTAGATGCTACACCGAGTCATCTGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
21499 TTGAAGATGCTACACCGAGTCATCTGAATT
1 TTGAAGATGCTACACCGAGTCATCTGAATT
21529 CCTGAGAATT
Statistics
Matches: 228, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 228 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
Found at i:24305 original size:41 final size:41
Alignment explanation
Indices: 24260--24354 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
24250 TCTCTAAAAC
* * *
24260 CAGGGACCAAATTGAATTAAACAGTAACTAAAATCCTAAAT
1 CAGGGACTAAATTGAATCAAACAGTAAATAAAATCCTAAAT
* * * *
24301 CAGGGACTAAATTGCATCAAATAGTAAATAGAATCTTAAAT
1 CAGGGACTAAATTGAATCAAACAGTAAATAAAATCCTAAAT
*
24342 TAGGGACTAAATT
1 CAGGGACTAAATT
24355 AAAGAAATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (41 bp):
CAGGGACTAAATTGAATCAAACAGTAAATAAAATCCTAAAT
Found at i:25424 original size:26 final size:26
Alignment explanation
Indices: 25395--25445 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
25385 TGGAGATTTG
25395 AGTGAGAGAGAGAGCCGAGAGGCGTC
1 AGTGAGAGAGAGAGCCGAGAGGCGTC
25421 AGTGAGAGAGAGAGCCGAGAGGCGT
1 AGTGAGAGAGAGAGCCGAGAGGCGT
25446 AAATCGATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.14, G:0.47, T:0.08
Consensus pattern (26 bp):
AGTGAGAGAGAGAGCCGAGAGGCGTC
Found at i:28335 original size:16 final size:16
Alignment explanation
Indices: 28314--28370 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
28304 TTAGCAATTT
28314 CCCTAAAATGACTTCA
1 CCCTAAAATGACTTCA
* ****
28330 CCCTAAAATAAAAGGA
1 CCCTAAAATGACTTCA
*
28346 CTCTAAAATGACTTCA
1 CCCTAAAATGACTTCA
28362 CCCTAAAAT
1 CCCTAAAAT
28371 AAAAGGACTC
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (16 bp):
CCCTAAAATGACTTCA
Found at i:28357 original size:32 final size:32
Alignment explanation
Indices: 28316--28393 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
28306 AGCAATTTCC
28316 CTAAAATGACTTCACCCTAAAATAAAAGGACT
1 CTAAAATGACTTCACCCTAAAATAAAAGGACT
28348 CTAAAATGACTTCACCCTAAAATAAAAGGACT
1 CTAAAATGACTTCACCCTAAAATAAAAGGACT
28380 CTAAAATGACTTCA
1 CTAAAATGACTTCA
28394 TATTGTAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (32 bp):
CTAAAATGACTTCACCCTAAAATAAAAGGACT
Found at i:28383 original size:16 final size:16
Alignment explanation
Indices: 28332--28386 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
28322 TGACTTCACC
28332 CTAAAATAAAAGGACT
1 CTAAAATAAAAGGACT
* **** *
28348 CTAAAATGACTTCACC
1 CTAAAATAAAAGGACT
28364 CTAAAATAAAAGGACT
1 CTAAAATAAAAGGACT
28380 CTAAAAT
1 CTAAAAT
28387 GACTTCATAT
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (16 bp):
CTAAAATAAAAGGACT
Found at i:32536 original size:2 final size:2
Alignment explanation
Indices: 32529--32553 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32519 AGTGGCATTA
32529 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
32554 GTTAAGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35688 original size:25 final size:25
Alignment explanation
Indices: 35660--35713 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
35650 TTTTATATAA
35660 TTTATGACGCAGAAAA-TCT-TTTTCT
1 TTTATGACGCA-AAAACTCTCTTTT-T
35685 TTTATGACGCAAAAACTCTCTTTTT
1 TTTATGACGCAAAAACTCTCTTTTT
35710 TTTA
1 TTTA
35714 AATTAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 4 0.15
25 19 0.70
26 4 0.15
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (25 bp):
TTTATGACGCAAAAACTCTCTTTTT
Found at i:35792 original size:60 final size:59
Alignment explanation
Indices: 35679--35803 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 59
35669 CAGAAAATCT
* * *
35679 TTTTCTTTTATGACGCAAAAACTCTCTTTTTTTTAAATTAAAAACGCAAAACTCTTCTCTC
1 TTTT-TTTTATGACGCAAAAACACACTTTTTTTTAAATCAAAAACGCAAAACTCTT-TCTC
* * *
35740 TTTTTTTTATGACGCAAAAACACAACTTTTTTTTATCA-CAAAAACG-ATAACTCTTTTTC
1 TTTTTTTTATGACGCAAAAACAC-ACTTTTTTTTA-AATCAAAAACGCAAAACTCTTTCTC
35799 TTTTT
1 TTTTT
35804 CAAAGACGCA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
59 8 0.14
60 26 0.46
61 21 0.38
62 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (59 bp):
TTTTTTTTATGACGCAAAAACACACTTTTTTTTAAATCAAAAACGCAAAACTCTTTCTC
Found at i:40166 original size:15 final size:16
Alignment explanation
Indices: 40139--40184 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
40129 GCAGAGGTTA
40139 AGAATAACAATTATAA-
1 AGAA-AACAATTATAAC
*
40155 AGAAAGCAATTA-AAC
1 AGAAAACAATTATAAC
40170 TAGAAAACAATTATA
1 -AGAAAACAATTATA
40185 CTAGAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.08
15 7 0.28
16 15 0.60
17 1 0.04
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.22
Consensus pattern (16 bp):
AGAAAACAATTATAAC
Found at i:40174 original size:16 final size:16
Alignment explanation
Indices: 40155--40191 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40145 ACAATTATAA
*
40155 AGAAAGCAATTAAACT
1 AGAAAACAATTAAACT
*
40171 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
40187 AGAAA
1 AGAAA
40192 CAAAGCAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:40194 original size:15 final size:15
Alignment explanation
Indices: 40144--40194 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
40134 GGTTAAGAAT
*
40144 AACAATTATA-AAGA
1 AACAATTATACTAGA
*
40158 AAGCAATTAAACTAGAA
1 AA-CAATTATACTAG-A
40175 AACAATTATACTAGA
1 AACAATTATACTAGA
40190 AACAA
1 AACAA
40195 AGCAAAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.06
15 13 0.42
16 13 0.42
17 3 0.10
ACGTcount: A:0.61, C:0.12, G:0.08, T:0.20
Consensus pattern (15 bp):
AACAATTATACTAGA
Done.