Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003489.1 Hibiscus syriacus cultivar Beakdansim tig00007383_pilon, 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: 101184
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7027 original size:19 final size:19
Alignment explanation
Indices: 7005--7082 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
6995 TCGGGTCGGG
7005 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
7024 TCAGACCTGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
7043 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
7062 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
7082 T
1 T
7083 GAAAACATGT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.06
19 37 0.76
20 9 0.18
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:7064 original size:29 final size:28
Alignment explanation
Indices: 7004--7082 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
6994 GTCGGGTCGG
* * *
7004 GTCAGACCGGTCAAACCGGTTCAGACCT
1 GTCAAACCGGTCAAACCGGTTAAGACCG
*
7032 GTCAAACCGGTTCGAACCGGTTGAA-ACCG
1 GTCAAACCGG-TCAAACCGGTT-AAGACCG
7061 GTCAAACCGGTCAGAACCGGTT
1 GTCAAACCGGTCA-AACCGGTT
7083 GAAAACATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 11 0.26
29 31 0.72
30 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.18
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTAAGACCG
Found at i:37811 original size:31 final size:31
Alignment explanation
Indices: 37767--37835 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
37757 TGATTATGAG
* * *
37767 AATTCTTAGGAGCAAGTCTTTTATCCAAGCA
1 AATTATTAAGAGCAAGTCTTTTATCCAAACA
* *
37798 AATTATTAAGAGCAAGTGTTTTATTCAAACA
1 AATTATTAAGAGCAAGTCTTTTATCCAAACA
*
37829 AAGTATT
1 AATTATT
37836 TAATCCCTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (31 bp):
AATTATTAAGAGCAAGTCTTTTATCCAAACA
Found at i:43776 original size:20 final size:19
Alignment explanation
Indices: 43753--43799 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
43743 CGATATACCA
43753 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
43773 GGTAAGAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
43793 GGTAAAA
1 GGTAAAA
43800 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.09, G:0.19, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:43876 original size:181 final size:182
Alignment explanation
Indices: 43541--44009 Score: 683
Period size: 181 Copynumber: 2.6 Consensus size: 182
43531 GATCCAAATT
* * * *
43541 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCAGTATTG-AAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-TGAAAATGAT
* * * * *
43605 AAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* *
43670 CGTGAATTTAAAAGAGAAGCAGTTTTAAG-TCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTTT-AGCACCTATAAAGTGTCGATACTTTAA
* *
43723 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAAGAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATGAAAATGATA
* *
43788 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
43852 GTGAATTTAAAAGAGAAGCAGTTTTAGCACCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCACCTATAAAGTGTCGATACTTTAA
* * * * *
43904 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACAGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATGAAAATGATA
* **
43969 AAATCGGTAAAATAATACCGGATATATTGAAAGTGTCGATA
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATA
44010 TTTTCGTAAG
Statistics
Matches: 259, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
180 2 0.01
181 160 0.62
182 97 0.37
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATGAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCACCTATAAAGTGTCGATACTTTAA
Found at i:43953 original size:20 final size:20
Alignment explanation
Indices: 43925--43971 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
43915 GATCCACAAC
* *
43925 GATATAACATGTA-AAAATAT
1 GATAAAACAGGTATAAAA-AT
*
43945 GATAAAACAGGTATCAAAAT
1 GATAAAACAGGTATAAAAAT
43965 GATAAAA
1 GATAAAA
43972 TCGGTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.23
Consensus pattern (20 bp):
GATAAAACAGGTATAAAAAT
Found at i:46173 original size:21 final size:21
Alignment explanation
Indices: 46147--46211 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
46137 AAGACAATCA
*
46147 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
46168 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
46189 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
46210 AG
1 AG
46212 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:46287 original size:33 final size:33
Alignment explanation
Indices: 46245--46310 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
46235 AAATAGATGG
*
46245 AGTGGTGAAAGAAGTAGAG-GTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAG-GTGTGTTAAGGGGTGA
*
46278 AGTGGTGAAAGAAGTTGGTGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGGTGTGTTAAGGGGTGA
46311 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGGTGTGTTAAGGGGTGA
Found at i:48132 original size:19 final size:19
Alignment explanation
Indices: 48108--48156 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
48098 AATGTAGGGT
48108 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
48127 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
48146 TAATTTTGTAT
1 TAATTTTGTAT
48157 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:48617 original size:200 final size:200
Alignment explanation
Indices: 48275--49184 Score: 1286
Period size: 200 Copynumber: 4.7 Consensus size: 200
48265 CAATATGGCC
48275 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
48339 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATGAGA
48404 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
48469 TGGAA
196 TGGAA
*
48474 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATTCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
48539 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATGAGA
*
48604 GAATATGTCTAAATAACGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
**
48669 TGGCC
196 TGGAA
* * *
48674 AACAGGGTGTAACCATAAAGTGTCGATCC-----CAAAAA----C-AT--CGAAAAC--C-AAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
** * * * * * ** * * *
48724 GTATAATGTA-ATATGTAATTTTTCAA--TCT-AACCGGT-ACAAGT---A-TA-CCGGTT-TTA
66 CCA-AAAGTATA-ATGTAATATGT-AATTTTTCAATC--TAACCGGTACAAGTATACCGATTTTA
48778 TGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGA
126 TGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGA
**
48843 ATGAATGGCC
191 ATGAATGGAA
48853 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
* *
48918 CCAAAAGTATAATATAATATGTAATTTTTCAATATAACCGGTACAAGTATACC-AGTTTTATGAG
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGA-TTTTATGAG
* * *
48982 AGAATATGTGTAAATAATATGTCGACAC-TTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTA
130 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
49046 AT-GAA
195 ATGGAA
*
49051 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAGAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
* *
49116 CCAAAAGTACAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATGAGA
49181 GAAT
131 GAAT
49185 TGGTATATAA
Statistics
Matches: 629, Mismatches: 48, Indels: 69
0.84 0.06 0.09
Matches are distributed among these distances:
179 105 0.17
180 3 0.00
181 2 0.00
182 1 0.00
184 8 0.01
185 12 0.02
186 16 0.03
187 2 0.00
188 7 0.01
189 2 0.00
190 2 0.00
191 7 0.01
192 2 0.00
193 15 0.02
194 12 0.02
195 7 0.01
197 1 0.00
198 131 0.21
199 99 0.16
200 195 0.31
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (200 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
TGGAA
Found at i:48742 original size:179 final size:179
Alignment explanation
Indices: 48511--49079 Score: 811
Period size: 179 Copynumber: 3.1 Consensus size: 179
48501 CCATATATAA
*
48511 AAAGTGTCGATTCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
*
48576 CCGGTACAAGTATACCGATTTTATGAGAGAATATGTCTAAATAACGTGTCGACACTTTTTTAGTT
66 CCGGTACAAGTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
*
48641 TGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGTAACCAT
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCAT
48690 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
*
48755 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
66 CCGGTACAAGTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
48820 TGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCAT
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCAT
* *
48869 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATATA
1 AAAGTGTCGATCC------CAAAA------A---C------ATCGAAAACCAAAAGTATAATGTA
* *
48934 ATATGTAATTTTTCAATATAACCGGTACAAGTATACC-AGTTTTATGAGAGAATATGTGTAAATA
45 ATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGA-TTTTATGAGAGAATATGTCTAAATA
* * **
48998 ATATGTCGACAC-TTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAAT-GAAAACAGGGTGC
109 ATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGC
49061 AACCAT
174 AACCAT
49067 AAAGTGTCGATCC
1 AAAGTGTCGATCC
49080 ATATATAGAA
Statistics
Matches: 355, Mismatches: 13, Indels: 25
0.90 0.03 0.06
Matches are distributed among these distances:
179 188 0.53
185 4 0.01
191 1 0.00
194 1 0.00
198 30 0.08
199 37 0.10
200 94 0.26
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (179 bp):
AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
TGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCAT
Found at i:49136 original size:198 final size:199
Alignment explanation
Indices: 48690--49213 Score: 892
Period size: 198 Copynumber: 2.6 Consensus size: 199
48680 GTGTAACCAT
48690 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* *
48755 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTGTAAATAATATGTCGACAC-TTTTTAGTT
**
48820 TGTGTCGATATTTTTGGTCCAGAATGAATGGCCAACAGGGTGCAACCATAAAGTGTCGATCCATA
130 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
48885 TATAA
195 TATAA
* *
48890 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATATAATATGTAATTTTTCAATATAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
*
48955 CCGGTACAAGTATACCAGTTTTATGAGAGAATATGTGTAAATAATATGTCGACACTTTTTAGTTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTGTAAATAATATGTCGACACTTTTTAGTTT
*
49020 GTGTCGATATTTTTGGTCCAGAATTAAT-GAAAACAGGGTGCAACCATAAAGTGTCGATCCATAT
131 GTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATAT
*
49084 ATAG
196 ATAA
*
49088 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTACAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* *
49153 CCGGTACAAGTATACCGGTTTTATGAGAGAAT-TG-GTATATAATATGTATCGACACTGTTTA
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTGTAAATAATATG--TCGACACTTTTTA
49214 ATGTTTTATC
Statistics
Matches: 307, Mismatches: 15, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
196 11 0.04
197 2 0.01
198 142 0.46
199 37 0.12
200 115 0.37
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTGTAAATAATATGTCGACACTTTTTAGTTT
GTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATAT
ATAA
Found at i:50709 original size:6 final size:6
Alignment explanation
Indices: 50698--50791 Score: 80
Period size: 6 Copynumber: 15.7 Consensus size: 6
50688 CAAGCGGTCA
* * * * *
50698 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * * *
50746 CTGACG ATGAAG ATGAAG ATGATG ACGATG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
50792 TCCAAACAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:50719 original size:18 final size:18
Alignment explanation
Indices: 50698--50763 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
50688 CAAGCGGTCA
50698 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGCTGACG
* * *
50716 ATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACG
*
50734 ATGACGATGAAGCTGACG
1 ATGAAGATGAAGCTGACG
50752 ATGAAGATGAAG
1 ATGAAGATGAAG
50764 ATGATGACGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.18
Consensus pattern (18 bp):
ATGAAGATGAAGCTGACG
Found at i:50720 original size:12 final size:12
Alignment explanation
Indices: 50698--50788 Score: 98
Period size: 12 Copynumber: 7.8 Consensus size: 12
50688 CAAGCGGTCA
*
50698 ATGAAGATGAAG
1 ATGACGATGAAG
*
50710 CTGACGATGAAG
1 ATGACGATGAAG
*
50722 ATGACGATGATG
1 ATGACGATGAAG
50734 ATGACGATGAAG
1 ATGACGATGAAG
*
50746 CTGACGATGAAG
1 ATGACGATGAAG
*
50758 ATGA--A-GATG
1 ATGACGATGAAG
*
50767 ATGACGATGATG
1 ATGACGATGAAG
*
50779 ATGATGATGA
1 ATGACGATGA
50789 TGATCCAAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
9 7 0.10
10 1 0.01
11 1 0.01
12 58 0.87
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:50735 original size:3 final size:3
Alignment explanation
Indices: 50715--50792 Score: 75
Period size: 3 Copynumber: 26.0 Consensus size: 3
50705 TGAAGCTGAC
* * * * * * * *
50715 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GAT GAA GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
50763 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
50793 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:50750 original size:36 final size:36
Alignment explanation
Indices: 50698--50779 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
50688 CAAGCGGTCA
*
50698 ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACGATGAAGATGAAGATGATG
*
50734 ATGACGATGAAGCTGACGATGAAGATGAAGATGATG
1 ATGAAGATGAAGCTGACGATGAAGATGAAGATGATG
* *
50770 ACGATGATGA
1 ATGAAGATGA
50780 TGATGATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.20
Consensus pattern (36 bp):
ATGAAGATGAAGCTGACGATGAAGATGAAGATGATG
Found at i:51982 original size:17 final size:17
Alignment explanation
Indices: 51956--51990 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
51946 AATACATGAC
*
51956 TATAGTATTGTTTTCGA
1 TATAGCATTGTTTTCGA
51973 TATAGCATTGTTTTCGA
1 TATAGCATTGTTTTCGA
51990 T
1 T
51991 GATATCCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (17 bp):
TATAGCATTGTTTTCGA
Found at i:52326 original size:183 final size:183
Alignment explanation
Indices: 52011--52612 Score: 979
Period size: 183 Copynumber: 3.2 Consensus size: 183
52001 ACAAAGTTTT
52011 CAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTG
1 CAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTG
*
52076 TCGATACCATTTAAAAAAGTGTCCACATTTACACATCGGAACCCAGATTTATAATGTAATAGATA
66 TCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATA
52141 ATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTA
131 ATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTA
* * *
52194 CAACCTGTATCGACACTTTCTAATAGTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATATG
1 CAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTG
*
52259 TCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATA
66 TCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATA
*
52324 ATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTA
131 ATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTA
* * *
52377 TAACCTGTATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTG
1 CAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTG
* *
52442 TCGATACCATTTAAAAAAGTATCGACATTTACACATCGGAATCCAGATTTATAATGTAATAGATA
66 TCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATA
52507 ATTTTGTAATATAACCGGTATAAATATACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTC
131 ATTTTG-----T-A-----AT--ATA-ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTC
52572 TA
182 TA
52574 CAACCTATATCGACACTTTCTAATATTGTGTCGGTACTT
1 CAACCTATATCGACACTTTCTAATATTGTGTCGGTACTT
52613 GTAAGTAACG
Statistics
Matches: 389, Mismatches: 16, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
183 306 0.79
188 1 0.00
189 1 0.00
194 2 0.01
196 3 0.01
197 76 0.20
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (183 bp):
CAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTG
TCGATACCATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATA
ATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTA
Found at i:52539 original size:14 final size:14
Alignment explanation
Indices: 52514--52553 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
52504 ATAATTTTGT
52514 AATATAACCGGTATA
1 AATAT-ACCGGTATA
52529 AATATACCGGTATA
1 AATATACCGGTATA
52543 AATATACCGGT
1 AATATACCGGT
52554 TTTATGAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (14 bp):
AATATACCGGTATA
Found at i:55091 original size:25 final size:25
Alignment explanation
Indices: 55063--55122 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
55053 TTATCATTAA
55063 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
55088 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
55113 ATTTAGGTAT
1 ATTTAGGTAT
55123 AAGGTTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:55507 original size:23 final size:23
Alignment explanation
Indices: 55476--55548 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
55466 ATAGGTAAAA
*
55476 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
55499 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
55522 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
55545 ATAT
1 ATAT
55549 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:55573 original size:46 final size:45
Alignment explanation
Indices: 55476--55573 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
55466 ATAGGTAAAA
* * *
55476 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATAGCTATCCTTT
* *
55522 ATATAATGTAATAGGTAGTGCTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TAGCTATCCTTT
*
55568 TTATAA
1 ATATAA
55574 AAGTGTTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATAGCTATCCTTT
Found at i:55996 original size:23 final size:23
Alignment explanation
Indices: 55965--56037 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
55955 ATAGGTAAAA
* *
55965 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
55988 ATATAATGTAATAGATATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
56011 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
56034 ATAT
1 ATAT
56038 TGTAAAGTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:56483 original size:23 final size:23
Alignment explanation
Indices: 56452--56524 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
56442 ATAGGTAAAA
*
56452 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
56475 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
56498 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
56521 ATAT
1 ATAT
56525 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:56549 original size:46 final size:45
Alignment explanation
Indices: 56452--56549 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
56442 ATAGGTAAAA
* * *
56452 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATAGCTATCCTTT
* *
56498 ATATAATGTAATAGGTAGTGCTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TAGCTATCCTTT
*
56544 TTATAA
1 ATATAA
56550 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATAGCTATCCTTT
Found at i:56565 original size:487 final size:489
Alignment explanation
Indices: 55122--56926 Score: 3479
Period size: 489 Copynumber: 3.7 Consensus size: 489
55112 TATTTAGGTA
55122 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
1 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
*
55187 TTTTTACTTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTAT
66 TTTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTAT
55252 TATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
131 TATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
*
55317 TCAAATAATTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACT
196 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
55382 ATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAG
261 ATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAG
55447 TATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATA
325 TATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATA
55512 GGTATCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAG
390 GGTATCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAG
55577 TGTTCATACTTTTTTCACTGTGGAAAACATTAATT
455 TGTTCATACTTTTTTCACTGTGGAAAACATTAATT
55612 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
1 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
55677 TTTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTAT
66 TTTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTAT
55742 TATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
131 TATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
*
55807 TCAAATAATTTTTTGTGTAAATGAAATTCTTAAATTAATATTGTAGGTGGAAAACATGAAACACT
196 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
55872 ATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
261 ATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
*
55937 ATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATATAATGTAATAG
326 ATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAG
*
56002 ATATCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGT
391 GTATCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGT
56067 GTTCATACTTTTTTCACTGTGGAAAACATTAATT
456 GTTCATACTTTTTTCACTGTGGAAAACATTAATT
56101 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
1 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
56166 TTTTTACGTTACGATATATATTATTATTAAATT-AAAACAATAAACATATATATTACATATTTAT
66 TTTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTAT
56230 TATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
131 TATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
56295 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
196 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
56360 ATT-AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
261 ATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
56424 ATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAG
326 ATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAG
56489 GTATCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGT
391 GTATCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGT
*
56554 GTCCATACTTTTTTCACTGTGGAAAACATTAATT
456 GTTCATACTTTTTTCACTGTGGAAAACATTAATT
56588 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
1 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
56653 TTTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTAT
66 TTTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTAT
*
56718 TATTATATTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
131 TATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
* * *
56783 TCAAATAATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACT
196 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
*
56848 ATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATTGATCCTTTTTATAAAAAGT
261 ATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
*
56913 ATGAACACTTTCAA
326 ATGGACACTTTCAA
56927 CATATTATAA
Statistics
Matches: 1300, Mismatches: 13, Indels: 5
0.99 0.01 0.00
Matches are distributed among these distances:
487 320 0.25
488 323 0.25
489 395 0.30
490 262 0.20
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (489 bp):
TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
TTTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTAT
TATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAA
TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
ATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
ATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAG
GTATCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGT
GTTCATACTTTTTTCACTGTGGAAAACATTAATT
Found at i:56923 original size:22 final size:22
Alignment explanation
Indices: 56879--56923 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
56869 ATTACATAAC
*
56879 TTTAAAAAAAGTATTGATCCTT
1 TTTAAAAAAAGTATTGAACCTT
*
56901 TTTATAAAAAGTA-TGAACACTT
1 TTTAAAAAAAGTATTGAAC-CTT
56923 T
1 T
56924 CAACATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
TTTAAAAAAAGTATTGAACCTT
Found at i:62997 original size:20 final size:21
Alignment explanation
Indices: 62952--62994 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
62942 TTTATATTTC
* *
62952 AATTTTTTATGCATTGGCTTG
1 AATTTTTTATGCATTCGATTG
62973 AATTTTTTATGCATTCGATTG
1 AATTTTTTATGCATTCGATTG
62994 A
1 A
62995 TTTAAGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.51
Consensus pattern (21 bp):
AATTTTTTATGCATTCGATTG
Found at i:63180 original size:2 final size:2
Alignment explanation
Indices: 63171--63205 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
63161 ATTTTAAAAA
63171 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63206 GTTATATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:66408 original size:84 final size:83
Alignment explanation
Indices: 66218--66409 Score: 201
Period size: 84 Copynumber: 2.3 Consensus size: 83
66208 ATTATAGCAT
* * * * *
66218 GATTGTATGTAGTACATGAAATTTGTAACGGTAGATGATCCATTTAAGACATAATTCACTATTCA
1 GATTTTATGTA-TACATGAAATATATAACGGTAGATGATCCATGTAAGACAAAATTCACTATTCA
*
66283 AAGTAAATTATTATAATAC
65 AAGTAAATTATGATAATAC
* * * * *
66302 GATTTTATGTGTTGCATAAAATATATAAC-GTCAGATGATTCATGTAAGA-AAAGATTCATTATT
1 GATTTTATGT-ATACATGAAATATATAACGGT-AGATGATCCATGTAAGACAAA-ATTCACTATT
*
66365 CAAAGTAAGTTATGATAATATC
63 CAAAGTAAATTATGATAATA-C
66387 G-TTTTATGTATCACATGAAATAT
1 GATTTTATGTAT-ACATGAAATAT
66410 GTAATGATGG
Statistics
Matches: 88, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
83 5 0.06
84 81 0.92
85 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (83 bp):
GATTTTATGTATACATGAAATATATAACGGTAGATGATCCATGTAAGACAAAATTCACTATTCAA
AGTAAATTATGATAATAC
Found at i:71087 original size:27 final size:28
Alignment explanation
Indices: 71039--71099 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
71029 GAATCGAAAC
71039 GATTTTTTCTTAAAATGAAAAAAAGTGA
1 GATTTTTTCTTAAAATGAAAAAAAGTGA
71067 GATTTTTTCTTAAAATG-AAAAAAGTGA
1 GATTTTTTCTTAAAATGAAAAAAAGTGA
71094 GATTTT
1 GATTTT
71100 GAAAACCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.39
Consensus pattern (28 bp):
GATTTTTTCTTAAAATGAAAAAAAGTGA
Found at i:72034 original size:2 final size:2
Alignment explanation
Indices: 72029--72084 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
72019 AAAAAAAATG
*
72029 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
72071 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
72085 CATTAAAGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:72809 original size:45 final size:45
Alignment explanation
Indices: 72745--72836 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
72735 ATACATGTAC
72745 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
*
72790 AAGCAAATTACAAAAACAATTGAGAATGGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
72835 AA
1 AA
72837 CCCTTTTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (45 bp):
AAGCAAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGT
Found at i:73582 original size:53 final size:53
Alignment explanation
Indices: 73500--73807 Score: 386
Period size: 53 Copynumber: 5.8 Consensus size: 53
73490 GACGTATCCA
* * ****
73500 CTCCCTCTTG-TTCAGGGATTAAAGAACTCGAACAATCTTTTAAAAACAGGTTCG
1 CTCCCTCTTGCTTCAGGGAGT--AGAACTCGAACAATCTTCTGCCTACAGGTTCG
* * ** *
73554 CTCCCTGTTGCTTCAGGGAGTAGAACTCGAAAAATCTTCTGTTTAC-GAGTTCA
1 CTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACAG-GTTCG
* *
73607 CTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTCG
1 CTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACAGGTTCG
* * * *
73660 CTCCTTTTTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACAGGTTCT
1 CTCC-CTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACAGGTTCG
* *
73714 CTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCG
1 CTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACAGGTTCG
*
73767 CTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTG
1 CTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
73808 GTGTGATTTT
Statistics
Matches: 223, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
52 1 0.00
53 156 0.70
54 57 0.26
55 9 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (53 bp):
CTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACAGGTTCG
Found at i:73675 original size:107 final size:106
Alignment explanation
Indices: 73498--73807 Score: 408
Period size: 107 Copynumber: 2.9 Consensus size: 106
73488 ATGACGTATC
* * ** * * *
73498 CACTCCCTCTTG-TTCAGGGATTAAAGAACTCGAACAATCTTTTAAAAACAGGTTCGCTCCCTGT
1 CACTCCCTCTTGCTTCAGGGAGT--AGAACTCGAACAATCTTCTGCATACGGGTTCGCTCCCTCT
* **
73562 TGCTTCAGGGAGTAGAACTCGAAAAATCTTCTGTTTAC-GAGTT
64 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACAG-GTT
* * *
73605 CACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTCGCTCCTTTTTT
1 CACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCATACGGGTTCGCTCC-CTCTT
*
73670 GCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACAGGTT
65 GCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACAGGTT
* * *
73712 CTCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTG
1 CACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCATACGGGTTCGCTCCCTCTTG
*
73777 CTTCAAGGAGTAGAACTCGAACAATCTTCTG
66 CTTCAGGGAGTAGAACTCGAACAATCTTCTG
73808 GTGTGATTTT
Statistics
Matches: 180, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
106 63 0.35
107 107 0.59
108 10 0.06
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (106 bp):
CACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCATACGGGTTCGCTCCCTCTTG
CTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACAGGTT
Found at i:74259 original size:42 final size:42
Alignment explanation
Indices: 74202--74416 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 42
74192 CGGAGGACTT
* *
74202 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTC
* * *
74244 ATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGC
1 ATCATCATGCTCGAAAGACTTACTGAT-G-AC---CCGAAGGATTT-C
* * * ** * ** *
74292 TTCA-CTACT-CTTCCGTGAAGGCTTACAAATTACCTTAAGGATTTA
1 ATCATC-A-TGC-T-CG-AAAGACTTACTGATGACCCGAAGGATTTC
* *
74337 ATCATCATGCTCGAAAGACTTACTGATGACACGAAGAATTTC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTC
*
74379 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGA
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGA
74417 CTTGTAAATT
Statistics
Matches: 131, Mismatches: 29, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
42 79 0.60
43 3 0.02
44 4 0.03
45 5 0.04
46 9 0.07
47 9 0.07
48 6 0.05
49 4 0.03
50 2 0.02
51 10 0.08
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTC
Found at i:74279 original size:13 final size:13
Alignment explanation
Indices: 74261--74285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74251 TGCTCGAAAG
74261 ACTTACTGATGGC
1 ACTTACTGATGGC
74274 ACTTACTGATGG
1 ACTTACTGATGG
74286 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:74727 original size:22 final size:21
Alignment explanation
Indices: 74666--74729 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
74656 GAATGATTTA
*
74666 ATCATCATGCTCAAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
74687 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
74707 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
74729 A
1 A
74730 CTGATGACAC
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 3 0.09
22 12 0.38
23 3 0.09
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:74745 original size:42 final size:42
Alignment explanation
Indices: 74666--74748 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
74656 GAATGATTTA
* *
74666 ATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTC
1 ATCATCATGCTCAAAAGACTTACTGATGACACGAAGGACTTC
* *
74708 ATCATCATGCTCGAAAGACTTACTGATGACACTAAGGACTT
1 ATCATCATGCTCAAAAGACTTACTGATGACACGAAGGACTT
74749 AAATTGCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (42 bp):
ATCATCATGCTCAAAAGACTTACTGATGACACGAAGGACTTC
Found at i:83895 original size:22 final size:21
Alignment explanation
Indices: 83821--83901 Score: 126
Period size: 21 Copynumber: 3.8 Consensus size: 21
83811 ATTTCTGGGT
*
83821 AAGGGGAATCGGTACCCATTC
1 AAGGGGAATCGATACCCATTC
*
83842 AAGGGGAATCGGTACCCATTC
1 AAGGGGAATCGATACCCATTC
83863 AAGGGGAATCGATACCCATTC
1 AAGGGGAATCGATACCCATTC
*
83884 AATGAGGAATCGATACCC
1 AA-GGGGAATCGATACCC
83902 CTCAAGTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 43 0.75
22 14 0.25
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (21 bp):
AAGGGGAATCGATACCCATTC
Found at i:83979 original size:23 final size:22
Alignment explanation
Indices: 83936--83980 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
83926 ATCTCATAGG
*
83936 GGAACCGAATCCCCCACAGGAA
1 GGAACCGAATCCCCCAAAGGAA
* *
83958 GGAATCGATTCCCCCTAAAGGAA
1 GGAACCGAATCCCCC-AAAGGAA
83981 AATTGTGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.36, C:0.31, G:0.22, T:0.11
Consensus pattern (22 bp):
GGAACCGAATCCCCCAAAGGAA
Found at i:89909 original size:23 final size:23
Alignment explanation
Indices: 89853--89920 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 23
89843 CATTATTATA
89853 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
89876 -CGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
89898 TGGCACTTCGGTGTAATTATACG
1 TGGCACTACGGTGCAATTCTACG
89921 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 20 0.53
23 18 0.47
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:89968 original size:16 final size:17
Alignment explanation
Indices: 89949--89982 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
89939 GTGCACAACC
89949 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
89965 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
89982 T
1 T
89983 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:92644 original size:16 final size:16
Alignment explanation
Indices: 92623--92665 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
92613 GGTAATTAAA
92623 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
92639 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
92656 GAGTGATAAG
1 GATTGATAAG
92666 AACGGATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:93577 original size:21 final size:21
Alignment explanation
Indices: 93551--93611 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
93541 GATTTCTGGG
93551 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
93572 CAAGGGGAATCAGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
93593 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
93612 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:95157 original size:103 final size:103
Alignment explanation
Indices: 94978--95179 Score: 359
Period size: 103 Copynumber: 2.0 Consensus size: 103
94968 GCGGTCCTTC
* * *
94978 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCA
1 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGATCCCTAGCA
95043 TATGTATATGATTCTTAAGGAATGATATGTGGTCATTT
66 TATGTATATGATTCTTAAGGAATGATATGTGGTCATTT
* *
95081 GGGACATATGTGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGATCCCTAGTA
1 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGATCCCTAGCA
95146 TATGTATATGATTCTTAAGGAATGATATGTGGTC
66 TATGTATATGATTCTTAAGGAATGATATGTGGTC
95180 CTTATGGACA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (103 bp):
GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGATCCCTAGCA
TATGTATATGATTCTTAAGGAATGATATGTGGTCATTT
Found at i:95232 original size:23 final size:23
Alignment explanation
Indices: 95199--95266 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
95189 ATTATTATAT
95199 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
95222 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
95245 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTCTACG
95267 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:100042 original size:22 final size:22
Alignment explanation
Indices: 100014--100065 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
100004 AATAATTGTA
*
100014 ATAATAAATTTAAATTA-ATTAT
1 ATAATAAA-TTAAATTATAATAT
100036 ATAATAAATTAAATTATAATAT
1 ATAATAAATTAAATTATAATAT
*
100058 ATCATAAA
1 ATAATAAA
100066 AAAACAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATAAATTAAATTATAATAT
Done.