Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1811
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: 30964
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:1419 original size:15 final size:16
Alignment explanation
Indices: 1391--1426 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1381 GGAAGGACTA
*
1391 AAAAAGCAGAAGAGAG
1 AAAAAGAAGAAGAGAG
1407 AAAAAGAAG-AGAGAG
1 AAAAAGAAGAAGAGAG
1422 AAAAA
1 AAAAA
1427 AGTAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAGAGAG
Found at i:1895 original size:14 final size:14
Alignment explanation
Indices: 1876--2051 Score: 79
Period size: 14 Copynumber: 12.1 Consensus size: 14
1866 GAAGGAAGAC
1876 AAAAAAAAAAAACA
1 AAAAAAAAAAAACA
* **
1890 AAAAAAATAAAAGG
1 AAAAAAAAAAAACA
* * * *
1904 ATAAAAAAGAGA-G
1 AAAAAAAAAAAACA
* *
1917 AAAGAGA-AAAACA
1 AAAAAAAAAAAACA
*
1930 ACAAAAAAAAAACA
1 AAAAAAAAAAAACA
1944 AAATAAAAAAAAA-A
1 AAA-AAAAAAAAACA
*
1958 ATATAAAAAAAAAAGA
1 A-A-AAAAAAAAAACA
** *
1974 GGAAAAAAAAAAGA
1 AAAAAAAAAAAACA
* **
1988 AAAAGATTAAAATTCA
1 AAAA-A-AAAAAAACA
*
2004 AATGAAAAAAAAAAAA
1 AA--AAAAAAAAAACA
2020 AAAAATAAAAACAACA
1 AAAAA-AAAAA-AACA
*
2036 AAAAAAAAAAACCA
1 AAAAAAAAAAAACA
2050 AA
1 AA
2052 GATGAAAAAA
Statistics
Matches: 119, Mismatches: 31, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
12 2 0.02
13 9 0.08
14 51 0.43
15 30 0.25
16 24 0.20
17 1 0.01
18 2 0.02
ACGTcount: A:0.81, C:0.05, G:0.07, T:0.06
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:2053 original size:60 final size:59
Alignment explanation
Indices: 1944--2059 Score: 139
Period size: 59 Copynumber: 1.9 Consensus size: 59
1934 AAAAAAAACA
* ** *
1944 AAATAAAAAAAAAAATATAAAAAAAAAAGAGGAAAAAAAAAAGAAAAAGATTAAAATTC
1 AAATAAAAAAAAAAATATAAAAAAAAAACAACAAAAAAAAAAGAAAAAGATGAAAATTC
2003 AAATGAAAAAAAAAAA-A-AAAAATAAAAACAACAAAAAAAAAA-AACCAAAGATGAAAA
1 AAAT-AAAAAAAAAAATATAAAAA-AAAAACAACAAAAAAAAAAGAA--AAAGATGAAAA
2060 AAAAAAAGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
58 7 0.14
59 21 0.43
60 21 0.43
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (59 bp):
AAATAAAAAAAAAAATATAAAAAAAAAACAACAAAAAAAAAAGAAAAAGATGAAAATTC
Found at i:2066 original size:1 final size:1
Alignment explanation
Indices: 1876--2046 Score: 63
Period size: 1 Copynumber: 171.0 Consensus size: 1
1866 GAAGGAAGAC
* * ** * * * * * * * *
1876 AAAAAAAAAAAACAAAAAAAATAAAAGGATAAAAAAGAGAGAAAGAGAAAAACAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * ** * * ** ***
1941 ACAAAATAAAAAAAAAAATATAAAAAAAAAAGAGGAAAAAAAAAAGAAAAAGATTAAAATTCAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * *
2006 TGAAAAAAAAAAAAAAAAATAAAAACAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2047 CCAAAGATGA
Statistics
Matches: 118, Mismatches: 52, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 118 1.00
ACGTcount: A:0.82, C:0.04, G:0.08, T:0.06
Consensus pattern (1 bp):
A
Found at i:2067 original size:15 final size:14
Alignment explanation
Indices: 1877--2086 Score: 88
Period size: 13 Copynumber: 15.3 Consensus size: 14
1867 AAGGAAGACA
*
1877 AAAAAAAAAAACA-
1 AAAAAAAAAAAGAT
1890 AAAAAAATAAAAGGAT
1 AAAAAAA-AAAA-GAT
*
1906 AAAAAAGAGAGAAAGAG
1 AAAAAA-A-A-AAAGAT
* *
1923 AAAAACAACAA-A-
1 AAAAAAAAAAAGAT
*
1935 AAAAAAACAAA-AT
1 AAAAAAAAAAAGAT
*
1948 AAAAAAAAAAATAT
1 AAAAAAAAAAAGAT
*
1962 -AAAAAAAAAAGAG
1 AAAAAAAAAAAGAT
*
1975 GAAAAAAAAAAGA-
1 AAAAAAAAAAAGAT
* **
1988 AAAAGATTAAA-AT
1 AAAAAAAAAAAGAT
** **
2001 TCAAATGAAAA-A-
1 AAAAAAAAAAAGAT
2013 AAAAAAAAAAA-AT
1 AAAAAAAAAAAGAT
2026 AAAAACAACAAAA-A-
1 AAAAA-AA-AAAAGAT
*
2040 AAAAAAACCAAAGAT
1 AAAAAAA-AAAAGAT
2055 GAAAAAAAAAAAG-T
1 -AAAAAAAAAAAGAT
2069 AAACAAAAAAAAGA-
1 AAA-AAAAAAAAGAT
2083 AAAA
1 AAAA
2087 GGATCAAATA
Statistics
Matches: 153, Mismatches: 27, Indels: 34
0.71 0.13 0.16
Matches are distributed among these distances:
12 18 0.12
13 57 0.37
14 41 0.27
15 11 0.07
16 14 0.09
17 9 0.06
18 3 0.02
ACGTcount: A:0.81, C:0.05, G:0.08, T:0.06
Consensus pattern (14 bp):
AAAAAAAAAAAGAT
Found at i:2085 original size:7 final size:7
Alignment explanation
Indices: 2056--2152 Score: 56
Period size: 7 Copynumber: 13.3 Consensus size: 7
2046 ACCAAAGATG
2056 AAAAA-A
1 AAAAAGA
2062 AAAAAGTA
1 AAAAAG-A
*
2070 AACAA-A
1 AAAAAGA
2076 AAAAAGA
1 AAAAAGA
*
2083 AAAAGGA
1 AAAAAGA
** *
2090 TCAAATA
1 AAAAAGA
2097 CAAAAAGAA
1 -AAAAAG-A
2106 AAAAAGA
1 AAAAAGA
2113 AAAAAGA
1 AAAAAGA
2120 AAGAAAGA
1 AA-AAAGA
2128 AGAACAA-A
1 A-AA-AAGA
*
2136 AGAAAAGC
1 A-AAAAGA
2144 AAAAAGA
1 AAAAAGA
2151 AA
1 AA
2153 CAAAAAAGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
6 10 0.14
7 29 0.41
8 27 0.39
9 4 0.06
ACGTcount: A:0.78, C:0.05, G:0.13, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:2986 original size:10 final size:10
Alignment explanation
Indices: 2960--3216 Score: 67
Period size: 10 Copynumber: 25.4 Consensus size: 10
2950 AAAATAAAAC
2960 ATAAATAAAT
1 ATAAATAAAT
*
2970 A-ATAATATAT
1 ATA-AATAAAT
2980 ATAAATAAAT
1 ATAAATAAAT
*
2990 A-AAAAAAAT
1 ATAAATAAAT
2999 ATAAAATAAAT
1 AT-AAATAAAT
*
3010 ATAAATTAAT
1 ATAAATAAAT
*
3020 A-ATA-AAAT
1 ATAAATAAAT
* *
3028 AATAAA-AGAG
1 -ATAAATAAAT
* *
3038 CTAAACAAA-
1 ATAAATAAAT
*
3047 A-AAA-AAAA
1 ATAAATAAAT
3055 AT-AATAAAAT
1 ATAAAT-AAAT
*
3065 ATAAATATAT
1 ATAAATAAAT
3075 ATAAATAAAT
1 ATAAATAAAT
*
3085 -TAAA-AATGT
1 ATAAATAA-AT
*
3094 ATAAA-AACT
1 ATAAATAAAT
*
3103 AATAGATAATAAT
1 -ATAAAT-A-AAT
3116 ATAAATATTATTAT
1 ATAAATA--A--AT
*
3130 ATAAACAAAT
1 ATAAATAAAT
**
3140 AATTTATAATAT
1 -ATAAATAA-AT
*
3152 ATAAAAAAATT
1 ATAAATAAA-T
3163 ATAAA-AAAT
1 ATAAATAAAT
*
3172 AAATAAATATAT
1 --ATAAATAAAT
3184 ATAAA-AAAT
1 ATAAATAAAT
*
3193 A-AAAAAAACT
1 ATAAATAAA-T
*
3203 ATAAAAAAAT
1 ATAAATAAAT
3213 ATAA
1 ATAA
3217 TCATATTTAA
Statistics
Matches: 187, Mismatches: 30, Indels: 60
0.68 0.11 0.22
Matches are distributed among these distances:
7 3 0.02
8 14 0.07
9 30 0.16
10 74 0.40
11 42 0.22
12 14 0.07
13 2 0.01
14 8 0.04
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:3011 original size:11 final size:11
Alignment explanation
Indices: 2951--3029 Score: 69
Period size: 11 Copynumber: 7.2 Consensus size: 11
2941 AAATTTCTAA
2951 AAATA-AAACAT
1 AAATATAAA-AT
2962 AAATA-AATAAT
1 AAATATAA-AAT
2973 AATATATATAAAT
1 AA-ATATA-AAAT
2986 AAATA-AAAA-
1 AAATATAAAAT
2995 AAATATAAAAT
1 AAATATAAAAT
3006 AAATAT-AAAT
1 AAATATAAAAT
*
3016 TAATAATAAAAT
1 AAAT-ATAAAAT
3028 AA
1 AA
3030 TAAAAGAGCT
Statistics
Matches: 58, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
9 5 0.09
10 14 0.24
11 20 0.34
12 12 0.21
13 6 0.10
14 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:3090 original size:37 final size:37
Alignment explanation
Indices: 2994--3213 Score: 92
Period size: 37 Copynumber: 5.7 Consensus size: 37
2984 ATAAATAAAA
**
2994 AAAATATA-AAATAAATATAAATTAATAATAAAATAAT
1 AAAATATATAAATAAAT-TAAAAAAATAATAAAATAAT
* ** * **
3031 AAAAGAGCTAAACAAAAAAAAAAAATAATAAAAT-AT
1 AAAATATATAAATAAATTAAAAAAATAATAAAATAAT
* *
3067 AAATATATATAAATAAATTAAAAATGTATAA-AAACTAAT
1 AAA-ATATATAAATAAATTAAAAA--AATAATAAAATAAT
* * * * * *
3106 AGATAATAATATAAATATTATTATATAAACAA-ATAAT-TT
1 A-A-AAT-ATATAAATA-AATTAAAAAAATAATAAAATAAT
* *
3145 ATAATATATAAAAAAATTATAAAAAATAAATAAATATATAT
1 AAAATATATAAATAAATTA-AAAAAAT-AATAAA-ATA-AT
* *
3186 AAAAAATA-AAAAAAACTATAAAAAAATA
1 AAAATATATAAATAAA-T-TAAAAAAATA
3214 TAATCATATT
Statistics
Matches: 132, Mismatches: 34, Indels: 31
0.67 0.17 0.16
Matches are distributed among these distances:
35 4 0.03
36 17 0.13
37 38 0.29
38 12 0.09
39 11 0.08
40 17 0.13
41 25 0.19
42 8 0.06
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (37 bp):
AAAATATATAAATAAATTAAAAAAATAATAAAATAAT
Found at i:3188 original size:21 final size:21
Alignment explanation
Indices: 3154--3213 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
3144 TATAATATAT
3154 AAAAAAA-T-TATAAAAAATA
1 AAAAAAACTATATAAAAAATA
*
3173 AATAAATA-TATATAAAAAATA
1 AA-AAAAACTATATAAAAAATA
3194 AAAAAAACTATA-AAAAAATA
1 AAAAAAACTATATAAAAAATA
3214 TAATCATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 2 0.06
20 17 0.47
21 17 0.47
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAAACTATATAAAAAATA
Found at i:3231 original size:41 final size:40
Alignment explanation
Indices: 3154--3234 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 40
3144 TATAATATAT
* *
3154 AAAAAAATTATAAAAAATAAATAAATATATATAAAAAATA
1 AAAAAAACTATAAAAAATAAATAAATATATAAAAAAAATA
* *
3194 AAAAAAACTATAAAAAAATATAAT-CATATTTAAAAAAAATA
1 AAAAAAACTAT-AAAAAATA-AATAAATATATAAAAAAAATA
3235 TAAATCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 10 0.29
41 22 0.63
42 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (40 bp):
AAAAAAACTATAAAAAATAAATAAATATATAAAAAAAATA
Found at i:4051 original size:50 final size:50
Alignment explanation
Indices: 3976--4110 Score: 189
Period size: 50 Copynumber: 2.7 Consensus size: 50
3966 TTCCACAACT
* *
3976 TGTATCGATGCATTATTCATTGTATCGATACATTCTGGGTTTTACCCAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGATTTACCCAGA
* * * * *
4026 TGTATCAATTCATTGTTCATTGTATCGATACATTTTGGGATTTACCTAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGATTTACCCAGA
* *
4076 TGTATCGATACATTTTTCAATGTATCGATACATTC
1 TGTATCGATACATTATTCATTGTATCGATACATTC
4111 AAGCATTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (50 bp):
TGTATCGATACATTATTCATTGTATCGATACATTCTGGGATTTACCCAGA
Found at i:6520 original size:31 final size:28
Alignment explanation
Indices: 6451--6523 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
6441 TTCATTCATA
* *
6451 TTTTTATTTCCGATGGGATACTCCAACC
1 TTTTTATTTCCAAGGGGATACTCCAACC
*
6479 TTGTTATTTCCAAGGGGATACTCCAACC
1 TTTTTATTTCCAAGGGGATACTCCAACC
6507 TCAGTTTTATTTCCAAG
1 T---TTTTATTTCCAAG
6524 ACATCAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 26 0.68
31 12 0.32
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (28 bp):
TTTTTATTTCCAAGGGGATACTCCAACC
Found at i:6613 original size:79 final size:79
Alignment explanation
Indices: 6467--6634 Score: 198
Period size: 79 Copynumber: 2.1 Consensus size: 79
6457 TTTCCGATGG
* * *
6467 GATACTCCAACCTTGTTATTTCCAAGGGGATACTCCAACCTCAGTTTTATTTCCAAGACATCAAT
1 GATACTCCAACCTCGTTATTTCCAAGGGGATACTCCAACCCCAGTTATATTTCCAAGACATCAAT
*
6532 TTTTCATAATCGGA
66 TTTTCACAATCGGA
** * *
6546 GATACTCCAACCTCGTTATTTCTGAGGGGATACTCTAACCCC-GATTATATTTTC-AGAACA-CT
1 GATACTCCAACCTCGTTATTTCCAAGGGGATACTCCAACCCCAG-TTATATTTCCAAG-ACATC-
* *
6608 GATTTTTCACAATCGGG
63 AATTTTTCACAATCGGA
6625 GATACTCCAA
1 GATACTCCAA
6635 TCGCGGTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
78 4 0.05
79 72 0.95
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (79 bp):
GATACTCCAACCTCGTTATTTCCAAGGGGATACTCCAACCCCAGTTATATTTCCAAGACATCAAT
TTTTCACAATCGGA
Found at i:6707 original size:79 final size:79
Alignment explanation
Indices: 6624--6846 Score: 286
Period size: 79 Copynumber: 2.8 Consensus size: 79
6614 TCACAATCGG
* * * * * *
6624 GGATACTCCAATCGC-GGTTTTATTTTCAAAACACCAAGTTTCCACAATTGGGGATACTCTAACC
1 GGATACTCCAA-CCCTGGTTTTATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCCAACC
*
6688 CGGTTATTTTTTAGA
65 CGGTTATTTTCTAGA
* * * * * *
6703 GGATACTCTAACCCTGATTTTATTTTCAAAATACTAATTTTTTATAATCGGGGATACTCCAACCT
1 GGATACTCCAACCCTGGTTTTATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCCAACCC
*
6768 TGTTATTTTCTAGA
66 GGTTATTTTCTAGA
* *
6782 GGATACTCCAACCCTGGTTTTATTTTCAAAACACTGATTTTTCACAATCGGGGATACTTCAACCC
1 GGATACTCCAACCCTGGTTTTATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCCAACCC
6847 TGATTTTATT
Statistics
Matches: 121, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
78 2 0.02
79 119 0.98
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (79 bp):
GGATACTCCAACCCTGGTTTTATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCCAACCC
GGTTATTTTCTAGA
Found at i:6727 original size:130 final size:130
Alignment explanation
Indices: 6492--6766 Score: 336
Period size: 130 Copynumber: 2.1 Consensus size: 130
6482 TTATTTCCAA
* * * * * *
6492 GGGGATACTCCAACCTCAGTTTTATTTCCAAGACATCAATTTTTCATAATCGGAGATACTCCAAC
1 GGGGATACTCCAACCGCAGTTTTATTTCCAAAACACCAAGTTTCCACAATCGGAGATACTCCAAC
* * *
6557 CTCGTTATTTCTGAGGGGATACTCTAACCCCGATTATATTTTCAGAACACTGATTTTTCACAATC
66 CTCGTTATTTCTGAGAGGATACTCTAACCCCGATTATATTTTCAAAACACTAATTTTTCACAATC
* * * * * *
6622 GGGGATACTCCAATCGCGGTTTTATTTTCAAAACACCAAGTTTCCACAATTGGGGATACTCTAAC
1 GGGGATACTCCAACCGCAGTTTTATTTCCAAAACACCAAGTTTCCACAATCGGAGATACTCCAAC
* * * * * * *
6687 C-CGGTTATTTTTTAGAGGATACTCTAACCCTGATTTTATTTTCAAAATACTAATTTTTTATAAT
66 CTC-GTTATTTCTGAGAGGATACTCTAACCCCGATTATATTTTCAAAACACTAATTTTTCACAAT
6751 C
130 C
6752 GGGGATACTCCAACC
1 GGGGATACTCCAACC
6767 TTGTTATTTT
Statistics
Matches: 121, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
129 1 0.01
130 120 0.99
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (130 bp):
GGGGATACTCCAACCGCAGTTTTATTTCCAAAACACCAAGTTTCCACAATCGGAGATACTCCAAC
CTCGTTATTTCTGAGAGGATACTCTAACCCCGATTATATTTTCAAAACACTAATTTTTCACAATC
Found at i:6886 original size:130 final size:129
Alignment explanation
Indices: 6703--6974 Score: 286
Period size: 130 Copynumber: 2.1 Consensus size: 129
6693 ATTTTTTAGA
* * ** *
6703 GGATAC-TCTAACCCTGATTTTATTTTCAAAATACTAATTTTTTATAATCGGGGATACTCCAACC
1 GGATACTTC-AACCCTGATTTTATTTCCAAAATACTAATCTTCCACAATCGGGGATACTCCAACC
** *
6767 TTGTTATTTTCTAGA-GGATACTCCAACCCTGGTTTTATTT-TCAAAACA-CTGATTTTTCACAA
65 CCGTTA-TTTCT-GACGGATACTCCAACCCCGGTTTTATTTCT-AAAACATC-GATTTTTCACAA
6829 TCGG
126 TCGG
* * ***
6833 GGATACTTCAACCCTGATTTTATTTCCAAAATA-TCGATCTTCCACAATTGGGGATACTTTGACC
1 GGATACTTCAACCCTGATTTTATTTCCAAAATACT-AATCTTCCACAATCGGGGATACTCCAACC
* * *
6897 CCGTTATTTCTGACGGGATACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTTCACCATTG
65 CCGTTATTTCTGAC-GGATACTCCAACCCCGGTTTTATTTCTAAAACATCGATTTTTCACAATCG
6962 G
129 G
*
6963 GG-TACTCCAACC
1 GGATACTTCAACC
6975 TCATTATTTC
Statistics
Matches: 119, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
128 2 0.02
129 15 0.13
130 98 0.82
131 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (129 bp):
GGATACTTCAACCCTGATTTTATTTCCAAAATACTAATCTTCCACAATCGGGGATACTCCAACCC
CGTTATTTCTGACGGATACTCCAACCCCGGTTTTATTTCTAAAACATCGATTTTTCACAATCGG
Found at i:6891 original size:51 final size:51
Alignment explanation
Indices: 6782--6891 Score: 141
Period size: 51 Copynumber: 2.2 Consensus size: 51
6772 ATTTTCTAGA
* * * * *
6782 GGATACTCCAACCCTGGTTTTATTTTCAAAACACTGATTTTTCACAATCGG
1 GGATACTTCAACCCTGATTTTATTTCCAAAACACTGATCTTCCACAATCGG
* *
6833 GGATACTTCAACCCTGATTTTATTTCCAAAATA-TCGATCTTCCACAATTGG
1 GGATACTTCAACCCTGATTTTATTTCCAAAACACT-GATCTTCCACAATCGG
6884 GGATACTT
1 GGATACTT
6892 TGACCCCGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.02
51 50 0.98
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
GGATACTTCAACCCTGATTTTATTTCCAAAACACTGATCTTCCACAATCGG
Found at i:7005 original size:78 final size:79
Alignment explanation
Indices: 6832--7020 Score: 193
Period size: 79 Copynumber: 2.4 Consensus size: 79
6822 TTCACAATCG
* * * ***
6832 GGGATACTTCAACCCTGATTTTATTTCCAAAATATCGATCTTCCACAATTGGGGATACTTTGACC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATCTTCCACAATTGGGGATACTCCAACC
*
6897 CCGTTATTTCTGAC
66 CCATTATTTCTGAC
* * * * * *
6911 GGGATACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTTCACCATTGGGG-TACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATCTTCCACAATTGGGGATACTCCAACC
*
6975 TCATTATTTCTGA-
66 CCATTATTTCTGAC
* * **
6988 GAGGGTACTCCAACCCCGTTTTTAACTCCAAAA
1 G-GGATACTCCAACCCCGATTTTATTTCCAAAA
7021 TATTAAATTT
Statistics
Matches: 89, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
77 1 0.01
78 43 0.48
79 45 0.51
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (79 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATCTTCCACAATTGGGGATACTCCAACC
CCATTATTTCTGAC
Found at i:7034 original size:209 final size:207
Alignment explanation
Indices: 6465--7011 Score: 593
Period size: 209 Copynumber: 2.6 Consensus size: 207
6455 TATTTCCGAT
* ** ** * * * * *
6465 GGGATACTCCAACCTTGTTATTTCCAAGGGGATACTCCAACCTCAGTTTTATTTCCAAGACATCA
1 GGGATACTCTAACCCCGTTATTTCTGA-GGGATACTCTAACCCCGGTTTTATTTCTAAAACATCA
* * *
6530 ATTTTTCATAATCGGAGATACTCCAACCTCGTTATTTCTGAG-GGGATACTCTAACCCCGATTAT
65 ATTTTTCATAATCGG-GGTACTCCAACCTCGTTATTTCTGAGAGGG-TACTCCAACCCCGATTTT
* * * *
6594 ATTTTCAGAACACTGATTTTTCACAATCGGGGATACTCCAATCGCGGTTTTATTTTCAAAACACC
128 ATTTTCAAAACACTGATTTTTCACAATCGGGGATACTCCAATCCCGATTTTATTTCCAAAACACC
6659 AAGTTTCCACAATTG
193 AAGTTTCCACAATTG
* * * * * *
6674 GGGATACTCTAACCCGGTTATTTTTTAGAGGATACTCTAACCCTGATTTTATTT-TCAAA-ATAC
1 GGGATACTCTAACCCCGTTATTTCTGAG-GGATACTCTAACCCCGGTTTTATTTCTAAAACAT-C
* * * * *
6737 TAATTTTTTATAATCGGGGATACTCCAACCTTGTTATTTTCT-AGAGGATACTCCAACCCTGGTT
64 -AATTTTTCATAATCGGGG-TACTCCAACCTCGTTA-TTTCTGAGAGGGTACTCCAACCCCGATT
* *
6801 TTATTTTCAAAACACTGATTTTTCACAATCGGGGATACTTCAA-CCCTGATTTTATTTCCAAAAT
126 TTATTTTCAAAACACTGATTTTTCACAATCGGGGATACTCCAATCCC-GATTTTATTTCCAAAAC
* *
6865 ATCGA-TCTTCCACAATTG
190 ACCAAGT-TTCCACAATTG
* * *
6883 GGGATACTTTGACCCCGTTATTTCTGACGGGATACTCTAACCCCGGTTTTATTTCTAAAACATCG
1 GGGATACTCTAACCCCGTTATTTCTGA-GGGATACTCTAACCCCGGTTTTATTTCTAAAACATCA
** * * *
6948 ATTTTTCACCATTGGGGTACTCCAACCTCATTATTTCTGAGAGGGTACTCCAACCCCGTTTTTA
65 ATTTTTCATAATCGGGGTACTCCAACCTCGTTATTTCTGAGAGGGTACTCCAACCCCGATTTTA
7012 ACTCCAAAAT
Statistics
Matches: 278, Mismatches: 48, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
207 7 0.03
208 44 0.16
209 212 0.76
210 13 0.05
211 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (207 bp):
GGGATACTCTAACCCCGTTATTTCTGAGGGATACTCTAACCCCGGTTTTATTTCTAAAACATCAA
TTTTTCATAATCGGGGTACTCCAACCTCGTTATTTCTGAGAGGGTACTCCAACCCCGATTTTATT
TTCAAAACACTGATTTTTCACAATCGGGGATACTCCAATCCCGATTTTATTTCCAAAACACCAAG
TTTCCACAATTG
Found at i:8868 original size:28 final size:28
Alignment explanation
Indices: 8824--9063 Score: 265
Period size: 28 Copynumber: 8.6 Consensus size: 28
8814 ATTAGACATT
8824 CCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
8851 CCTTTTCAAAGCCTACAAGTCAATGGCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
8879 TCTTTTCAAAGCCCACAAGTGAGTGGCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
8907 CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
8935 TCTTTTCAAAGACTACAAGTCAGTGGTA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
8963 TCTTTTCAAAGCCTACAAGTCAGTGGCAA
1 CCTTTTCAAAGCCCACAAGTCAGTGGC-A
*
8992 CC--TTCAAAGCCCACAAGACAGTGGCAA
1 CCTTTTCAAAGCCCACAAGTCAGTGGC-A
* * **
9019 CC-TTTAAAAGCACACAAGTTGGT-GCAA
1 CCTTTTCAAAGCCCACAAGTCAGTGGC-A
*
9046 CCCTTTCAAAAGCCCACA
1 CCTTTTC-AAAGCCCACA
9064 CAAGTTGGTG
Statistics
Matches: 184, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
27 38 0.21
28 135 0.73
29 11 0.06
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (28 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:8972 original size:84 final size:85
Alignment explanation
Indices: 8824--9023 Score: 300
Period size: 84 Copynumber: 2.4 Consensus size: 85
8814 ATTAGACATT
*
8824 CCTTTTC-AAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCTACAAGTCAATGGCATCTTTTCAA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGACTACAAGTCAATGGCATCTTTTCAA
*
8888 AGCCCACAAGTGAGTGGC-A
66 AGCCCACAAGTCAGTGGCAA
* * *
8907 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGACTACAAGTCAGTGGTATCTTTTCAA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGACTACAAGTCAATGGCATCTTTTCAA
*
8972 AGCCTACAAGTCAGTGGCAA
66 AGCCCACAAGTCAGTGGCAA
*
8992 CC--TTCAAAGCCCACAAGACAGTGGCAACCTTT
1 CCTTTTCAAAGCCCACAAGTCAGTGGC-ACCTTT
9024 AAAAGCACAC
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
83 29 0.27
84 74 0.70
85 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (85 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGACTACAAGTCAATGGCATCTTTTCAA
AGCCCACAAGTCAGTGGCAA
Found at i:9067 original size:31 final size:27
Alignment explanation
Indices: 9015--9073 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 27
9005 CAAGACAGTG
9015 GCAACCTTTAAAAGCACACAAGTTGGT
1 GCAACCTTTAAAAGCACACAAGTTGGT
9042 GCAACCCTTTCAAAAGCCCACACAAGTTGGT
1 GCAA-CCTTT-AAAAG--CACACAAGTTGGT
9073 G
1 G
9074 GCATCTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 4 0.14
28 5 0.18
29 5 0.18
31 14 0.50
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (27 bp):
GCAACCTTTAAAAGCACACAAGTTGGT
Found at i:9142 original size:49 final size:49
Alignment explanation
Indices: 9085--9417 Score: 389
Period size: 49 Copynumber: 6.8 Consensus size: 49
9075 CATCTTCTTC
*
9085 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* *
9134 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCCTTACCTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* *
9183 TAAGTCCAA-AGTTGCTGGCCTTGAATCAGCACATTGGCACCTTTACCTT
1 TAAGTCCAATA-TTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * * * *
9232 TAAGTCCAATGTTGCTGGCCTTGAATTAACACATTGGCACCTTCATCTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * * * * * *
9281 TAAGTCCTATGTTGCTGGCCTTGAATTAGCATATTGGCGCTCTCATCTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
* * * * * *
9330 TAAGTCCGATATCGCTGGCCTTAAATCAGCATATTGGCACTCTCATCTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
** * * * *
9379 TAAGTCTGATATCGTTGGCCTTGAATCAACATATTGGCA
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCA
9418 TCTTTAACAT
Statistics
Matches: 256, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
49 256 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTT
Found at i:9254 original size:98 final size:98
Alignment explanation
Indices: 9080--9513 Score: 385
Period size: 98 Copynumber: 4.4 Consensus size: 98
9070 GGTGGCATCT
*
9080 TCTTCTAAGTCCAATA-TCGCTGGCCTTGAATCAGCACATTGGCACCCTCACCTTTAAGTCCAAT
1 TCTT-TAAGTCCAA-AGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAAT
*
9144 GTTGCTGGCCTTGAATCAGCACATTGGCACCCTTA
64 GTCGCTGGCCTTGAATCAGCACATTGGCACCCTTA
* * *
9179 CCTTTAAGTCCAAAGTTGCTGGCCTTGAATCAGCACATTGGCACCTTTACCTTTAAGTCCAATGT
1 TCTTTAAGTCCAAAGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATGT
* * *
9244 TGCTGGCCTTGAATTAACACATTGGCA-CCTTCA
66 CGCTGGCCTTGAATCAGCACATTGGCACCCTT-A
* * * * * * * * *
9277 TCTTTAAGTCCTATGTTGCTGGCCTTGAATTAGCATATTGGC-GCTCTCATCTTTAAGTCCGATA
1 TCTTTAAGTCCAAAGTCGCTGGCCTTGAATCAGCACATTGGCACCT-TCACCTTTAAGTCCAATG
* * * *
9341 TCGCTGGCCTTAAATCAGCATATTGGCACTCTCA
65 TCGCTGGCCTTGAATCAGCACATTGGCACCCTTA
* * * * * * * * **
9375 TCTTTAAGTCTGATA-TCGTTGGCCTTGAATCAACATATTGGCATCTTTAACATTCCTAAACCCA
1 TCTTTAAGTC-CAAAGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCACCTT--TAAGTCCA
* ** **
9439 ATGTCGTTGGCCTTGTCTCAGCACATTGGCATTC-T-
62 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTTA
* * * * *
9474 TCTTCAAGTCTAATGTCACTGGCCATGAATCAGCACATTG
1 TCTTTAAGTCCAAAGTCGCTGGCCTTGAATCAGCACATTG
9514 TCATTCTTCG
Statistics
Matches: 269, Mismatches: 56, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
97 7 0.03
98 191 0.71
99 38 0.14
100 1 0.00
101 32 0.12
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (98 bp):
TCTTTAAGTCCAAAGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATGT
CGCTGGCCTTGAATCAGCACATTGGCACCCTTA
Found at i:10182 original size:21 final size:21
Alignment explanation
Indices: 10157--10212 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
10147 TTCTTGTCCA
10157 AATGTATCGATACATTTCTAG
1 AATGTATCGATACATTTCTAG
10178 AATGTATCGATACATTTCTAG
1 AATGTATCGATACATTTCTAG
10199 AATGTATCGATACA
1 AATGTATCGATACA
10213 AGGTCCCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTCTAG
Found at i:10295 original size:19 final size:18
Alignment explanation
Indices: 10248--10333 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 18
10238 ATTTCAACAA
*
10248 TTTGTATCGATACAAACAG
1 TTTGTATCGATACATA-AG
*
10267 TAAATGTATCGATACATAAG
1 T--TTGTATCGATACATAAG
10287 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
10303 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
10319 TTTTGTATCGATACA
1 -TTTGTATCGATACA
10334 ATGTATCGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 24 0.44
20 3 0.05
21 13 0.24
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:10308 original size:13 final size:13
Alignment explanation
Indices: 10290--10314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10280 ACATAAGTGT
10290 TGTATCGATACAA
1 TGTATCGATACAA
10303 TGTATCGATACA
1 TGTATCGATACA
10315 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10310 original size:32 final size:32
Alignment explanation
Indices: 10269--10341 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
10259 ACAAACAGTA
10269 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
10301 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
10333 AATGTATCG
1 AATGTATCG
10342 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:16557 original size:20 final size:20
Alignment explanation
Indices: 16532--16648 Score: 92
Period size: 20 Copynumber: 5.7 Consensus size: 20
16522 TTTTAACTAG
*
16532 ATGTATCGATACATTGTTCA
1 ATGTATCGATACATTGATCA
* *
16552 ATGTATCGATATATCTGGGT-A
1 ATGTATCGATACAT-T-GATCA
* **
16573 GGATGCATCGATACATTGAAGA
1 --ATGTATCGATACATTGATCA
* * *
16595 ATGTATCTATACATTCATCC
1 ATGTATCGATACATTGATCA
**
16615 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGATCA
16635 ATGTATCGATACAT
1 ATGTATCGATACAT
16649 CTGGGTAAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
20 56 0.75
21 3 0.04
22 4 0.05
23 12 0.16
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:17306 original size:19 final size:20
Alignment explanation
Indices: 17261--17318 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
17251 CTGCCAGTTT
*
17261 CATGTATCGATACAATTGTGA
1 CATGTATCGATACAA-TGTAA
17282 -ATGTATCGATACAATG-AA
1 CATGTATCGATACAATGTAA
17300 CATGTATCGATACAATGTA
1 CATGTATCGATACAATGTA
17319 TCGATACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATGTAA
Found at i:17319 original size:13 final size:13
Alignment explanation
Indices: 17301--17327 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17291 TACAATGAAC
17301 ATGTATCGATACA
1 ATGTATCGATACA
17314 ATGTATCGATACA
1 ATGTATCGATACA
17327 A
1 A
17328 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:17322 original size:32 final size:33
Alignment explanation
Indices: 17281--17345 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
17271 TACAATTGTG
*
17281 AATGTATCGATACAATG-A-ACATGTATCGATAC
1 AATGTATCGATACAAAGCATA-ATGTATCGATAC
17313 AATGTATCGATACAAAGCATAATGTATCGATAC
1 AATGTATCGATACAAAGCATAATGTATCGATAC
17346 TTTGGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 16 0.53
33 13 0.43
34 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAAAGCATAATGTATCGATAC
Found at i:19011 original size:16 final size:16
Alignment explanation
Indices: 18992--19024 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18982 TATTTCAAGC
*
18992 ATGTATCGATTCATTT
1 ATGTATCGATACATTT
19008 ATGTATCGATACATTT
1 ATGTATCGATACATTT
19024 A
1 A
19025 CTTATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (16 bp):
ATGTATCGATACATTT
Found at i:19055 original size:21 final size:20
Alignment explanation
Indices: 19000--19070 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
18990 GCATGTATCG
*
19000 ATTCATTTATGTATCGATAC
1 ATTCACTTATGTATCGATAC
*
19020 ATTTACTTATGTATCGATAC
1 ATTCACTTATGTATCGATAC
*
19040 ATTCACTTATTGTATCAATAC
1 ATTCACTTA-TGTATCGATAC
19061 ATTCACTTAT
1 ATTCACTTAT
19071 ATACAAATTG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 27 0.59
21 19 0.41
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (20 bp):
ATTCACTTATGTATCGATAC
Found at i:22478 original size:12 final size:12
Alignment explanation
Indices: 22463--22487 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22453 ATATCAAATA
22463 AAAAATAATAAT
1 AAAAATAATAAT
22475 AAAAATAATAAT
1 AAAAATAATAAT
22487 A
1 A
22488 GCACCCTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:22787 original size:27 final size:28
Alignment explanation
Indices: 22749--22814 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 28
22739 TTTCTTTTTT
22749 TTCTCTTT-TTTTTTTCCTT-CATTCTTC
1 TTCT-TTTCTTTTTTTCCTTCCATTCTTC
* *
22776 TTCTTTTCTTTTTTTTCTTCCTTTCTTC
1 TTCTTTTCTTTTTTTCCTTCCATTCTTC
22804 TCTCTTCTTCT
1 T-TCTT-TTCT
22815 CTCATTCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 3 0.09
27 14 0.42
28 8 0.24
29 4 0.12
30 4 0.12
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (28 bp):
TTCTTTTCTTTTTTTCCTTCCATTCTTC
Found at i:22797 original size:31 final size:31
Alignment explanation
Indices: 22752--22812 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
22742 CTTTTTTTTC
22752 TCTTTTTTTTTTCC-TTCATTCT-TCTTCTTT
1 TCTTTTTTTTTTCCTTTC-TTCTCTCTTCTTT
22782 TCTTTTTTTTCTTCCTTTCTTCTCTCTTCTT
1 TCTTTTTTTT-TTCCTTTCTTCTCTCTTCTT
22813 CTCTCATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 10 0.36
31 8 0.29
32 10 0.36
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (31 bp):
TCTTTTTTTTTTCCTTTCTTCTCTCTTCTTT
Found at i:23461 original size:16 final size:15
Alignment explanation
Indices: 23438--23475 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
23428 TTTTGTCTCT
23438 TTTTTTAT-TATTTTA
1 TTTTTTATGT-TTTTA
23453 TTATTTTATGTTTTTA
1 TT-TTTTATGTTTTTA
23469 TTTTTTA
1 TTTTTTA
23476 ATTAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 13 0.62
17 1 0.05
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTTATGTTTTTA
Found at i:24388 original size:2 final size:2
Alignment explanation
Indices: 24373--24417 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
24363 TTATTAGTAA
* *
24373 AT AT AT GAT TT AT AT AT AT AT AT AT AA AT -T 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 AT AT AT
24415 AT A
1 AT A
24418 CATTAAAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24395 original size:19 final size:19
Alignment explanation
Indices: 24352--24422 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
24342 CAGACTAAAA
*
24352 ATATACATAAATTAT-TAGT
1 ATATATATAAATTATATA-T
* * *
24371 AAATATATGATTTATATAT
1 ATATATATAAATTATATAT
24390 ATATATATAAATTATATAT
1 ATATATATAAATTATATAT
*
24409 ATATATATACATTA
1 ATATATATAAATTA
24423 AAAACACAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 41 0.95
20 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
ATATATATAAATTATATAT
Found at i:25103 original size:19 final size:20
Alignment explanation
Indices: 25057--25108 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
25047 GTGCAATTAT
*
25057 ATTATAAAAT-TTAATGATTA
1 ATTATAAAATATCAATGA-TA
25077 ATTTATAAAATATCAATGA-A
1 A-TTATAAAATATCAATGATA
25097 ATTATAAAATAT
1 ATTATAAAATAT
25109 ATAAAACAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 9 0.31
22 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
ATTATAAAATATCAATGATA
Found at i:25660 original size:20 final size:20
Alignment explanation
Indices: 25631--25672 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
25621 TTTAATCCAT
25631 ACTCGAAATTCCAATATCCC
1 ACTCGAAATTCCAATATCCC
* *
25651 ACTCGGAATTCCAGTATCCC
1 ACTCGAAATTCCAATATCCC
25671 AC
1 AC
25673 GGTTTCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.36, G:0.10, T:0.24
Consensus pattern (20 bp):
ACTCGAAATTCCAATATCCC
Found at i:25718 original size:1 final size:1
Alignment explanation
Indices: 25712--25736 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
25702 CCTTATTCCG
25712 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
25737 GGCCTTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26233 original size:2 final size:2
Alignment explanation
Indices: 26226--26262 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
26216 GAGCTTTGTT
26226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26263 TTTATGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27327 original size:80 final size:80
Alignment explanation
Indices: 27234--27393 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 80
27224 TGCTAAACAC
*
27234 TTAGTTTCTTTTTTCTATATTTTTGTTTATTCGATTATCTGATTTAATAGCCTAGTTTAGTTATG
1 TTAGTTTCTTTTTTCTATATTTTTGTTTATTCAATTATCTGATTTAATAGCCTAGTTTAGTTATG
* *
27299 CTCAATCTGTGGTAT
66 CTCAAACTCTGGTAT
*
27314 TTAGTTTCTTTTTTCTATATTTTTGTTTATTCAATTATCTGATTTAGTAGCCTAGTTTAGTTATG
1 TTAGTTTCTTTTTTCTATATTTTTGTTTATTCAATTATCTGATTTAATAGCCTAGTTTAGTTATG
27379 CTCAAACTCTGGTAT
66 CTCAAACTCTGGTAT
27394 CTATGGCACC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.54
Consensus pattern (80 bp):
TTAGTTTCTTTTTTCTATATTTTTGTTTATTCAATTATCTGATTTAATAGCCTAGTTTAGTTATG
CTCAAACTCTGGTAT
Found at i:29804 original size:1 final size:1
Alignment explanation
Indices: 29798--29870 Score: 146
Period size: 1 Copynumber: 73.0 Consensus size: 1
29788 GGGCTTGCAT
29798 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
29863 CCCCCCCC
1 CCCCCCCC
29871 TGTTGTCATT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Done.