Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1338
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: 96590
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4135 original size:1 final size:1
Alignment explanation
Indices: 4115--4192 Score: 57
Period size: 1 Copynumber: 78.0 Consensus size: 1
4105 GGCGTCCTCC
* * * * ** * * * *
4115 AAAAAACAAACAAAACAAAAAAAAACAAAAAAAAAAACCAAAAACAAAAACAAAAAAAACAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
4180 AAAACAAAAAAAA
1 AAAAAAAAAAAAA
4193 GGGGGTCCGG
Statistics
Matches: 57, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4139 original size:19 final size:18
Alignment explanation
Indices: 4115--4192 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 18
4105 GGCGTCCTCC
4115 AAAAAACAAACAAAACAAA
1 AAAAAACAAA-AAAACAAA
4134 AAAAAACAAAAAAA-AAA
1 AAAAAACAAAAAAACAAA
4151 ACCAAAAAC--AAAAAC-AA
1 A--AAAAACAAAAAAACAAA
4168 AAAAAACAAACAAAAACAAA
1 AAAAAAC-AA-AAAAACAAA
4188 AAAAA
1 AAAAA
4193 GGGGGTCCGG
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
15 6 0.12
17 12 0.24
18 4 0.08
19 22 0.43
20 7 0.14
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAACAAA
Found at i:4163 original size:25 final size:25
Alignment explanation
Indices: 4116--4189 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 25
4106 GCGTCCTCCA
4116 AAAAACAAACAAA-ACAAAA-AAAAAC
1 AAAAA-AAACAAACA-AAAACAAAAAC
4141 AAAAAAAA-AAACCAAAAACAAAAAC
1 AAAAAAAACAAA-CAAAAACAAAAAC
4166 AAAAAAAACAAACAAAAACAAAAA
1 AAAAAAAACAAACAAAAACAAAAA
4190 AAAGGGGGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.07
24 7 0.16
25 32 0.71
26 3 0.07
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAAAAAACAAACAAAAACAAAAAC
Found at i:5699 original size:30 final size:30
Alignment explanation
Indices: 5630--5948 Score: 314
Period size: 30 Copynumber: 10.7 Consensus size: 30
5620 TTTATCACCC
* ***
5630 TTCAAAAGTCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
***
5660 TTC-AAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
5689 TTCAAAAGCCCACAAGTCAGTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
5717 TTC-AAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCC-TT
* * *
5747 TTC-GAAGCCCACAAGTCGGTGGCA-TCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
* * * * *
5775 TTCCAAAGCTCACAACTCTA-TAGCACTCTTT
1 TTCAAAAGCCCACAAGTC-AGTGGCAC-CCTT
** *
5806 TTCTTTTTAAGCCCACAAGTTAGTGGCACCCTT
1 TTC---AAAAGCCCACAAGTCAGTGGCACCCTT
*
5839 TTCAAAAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
5869 TTCAAAAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
5899 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
5928 TT-AAAAGCCCACAAGTCAGTG
1 TTCAAAAGCCCACAAGTCAGTG
5949 ATGCAAACCT
Statistics
Matches: 248, Mismatches: 29, Indels: 26
0.82 0.10 0.09
Matches are distributed among these distances:
27 22 0.09
28 27 0.11
29 46 0.19
30 126 0.51
31 5 0.02
33 7 0.03
34 15 0.06
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCACCCTT
Found at i:5867 original size:123 final size:121
Alignment explanation
Indices: 5694--5913 Score: 300
Period size: 123 Copynumber: 1.8 Consensus size: 121
5684 TTTTTTTCAA
*
5694 AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTTC-GAAGCCCA
1 AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCC-TTTTCAAAAGCCCA
* * * *
5758 CAAGTCGGTGGCA-TCTTTTCCAAAGCTCACAACTCTATAGCACTCTTTTTCTTTTT
65 CAAGTCAGTGGCACCCTTTTCAAAAGCCCACAACTCTATAGCACTCTTTTTCTTTTT
* * * *
5814 AAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCC
1 AAGCCCACAAGTCAGTGGCAACC--TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCAAAAGCC
*
5879 CACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAA
63 CACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAA
5914 GTCAGTGGCA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
120 21 0.25
122 8 0.09
123 40 0.47
124 16 0.19
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (121 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCAAAAGCCCAC
AAGTCAGTGGCACCCTTTTCAAAAGCCCACAACTCTATAGCACTCTTTTTCTTTTT
Found at i:6061 original size:48 final size:48
Alignment explanation
Indices: 5992--6282 Score: 254
Period size: 48 Copynumber: 6.0 Consensus size: 48
5982 GGCGTCTCCT
* *
5992 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCC
* * **
6040 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTATA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT-CC
* * *
6089 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA-----CC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCC
6132 -TTAAGTCCAATATAGCTGGCCTTGAATCAGCAT-TTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT-C--C
* * * *
6182 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-TC--C
* * * * * *
6237 TTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
6283 ATCACTTTTC
Statistics
Matches: 196, Mismatches: 31, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
41 6 0.03
42 30 0.15
48 43 0.22
49 36 0.18
50 2 0.01
51 32 0.16
52 5 0.03
53 2 0.01
54 1 0.01
55 38 0.19
56 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (48 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCC
Found at i:6149 original size:42 final size:41
Alignment explanation
Indices: 6090--6174 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 41
6080 ACCTTTATAT
*
6090 TTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACC
1 TTAAGTCCAATATAGCTGACCTTGAATCAGCA-ATTGGCACC
* *
6132 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATTTGGCACC
1 TTAAGTCCAATATAGCTGACCTTGAATCAGCAATTGGCACC
6173 TT
1 TT
6175 TTCCATCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.25
42 30 0.75
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (41 bp):
TTAAGTCCAATATAGCTGACCTTGAATCAGCAATTGGCACC
Found at i:6214 original size:93 final size:91
Alignment explanation
Indices: 6041--6219 Score: 279
Period size: 93 Copynumber: 1.9 Consensus size: 91
6031 CACCTTGCCT
*
6041 TTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTATATTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACCTTTATATTTAAGTCCAATGTAGC
6106 TGACCTTGAATCAGCACATTGGCACC
66 TGACCTTGAATCAGCACATTGGCACC
* * *
6132 TTAAGTCCAATATAGCTGGCCTTGAATCAGCAT-TTGGCACCTTTTCCATCTTTAAGTTCAATGT
1 TTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACC-TTT--ATATTTAAGTCCAATGT
*
6196 AGCTGGCCTTGAATCAGCACATTG
63 AGCTGACCTTGAATCAGCACATTG
6220 ACATCCTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
90 8 0.10
91 34 0.43
93 38 0.47
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (91 bp):
TTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCACCTTTATATTTAAGTCCAATGTAGC
TGACCTTGAATCAGCACATTGGCACC
Found at i:11180 original size:20 final size:20
Alignment explanation
Indices: 11157--11230 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
11147 ACAATTCAAA
11157 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
11177 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
11198 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
11218 GTATCGATACATG
1 GTATCGATACATG
11231 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:11201 original size:21 final size:21
Alignment explanation
Indices: 11175--11250 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
11165 ACATGTTGCA
11175 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
11196 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
11216 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
11237 ATGTATCGATACAT
1 ATGTATCGATACAT
11251 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:11208 original size:41 final size:41
Alignment explanation
Indices: 11157--11250 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
11147 ACAATTCAAA
11157 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
11198 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
11239 GTATCGATACAT
1 GTATCGATACAT
11251 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:11307 original size:13 final size:13
Alignment explanation
Indices: 11289--11314 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11279 TACAGCAAGT
11289 ATGTATCGATACA
1 ATGTATCGATACA
11302 ATGTATCGATACA
1 ATGTATCGATACA
11315 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11834 original size:34 final size:35
Alignment explanation
Indices: 11771--11837 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
11761 CTAAGTGATT
11771 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
11807 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
11838 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:15015 original size:13 final size:13
Alignment explanation
Indices: 14997--15021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14987 ATTTCCAGAT
14997 TGTATCGATACAA
1 TGTATCGATACAA
15010 TGTATCGATACA
1 TGTATCGATACA
15022 TTGCTTCAGT
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:16848 original size:20 final size:20
Alignment explanation
Indices: 16825--16898 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
16815 ACAATTCAAA
16825 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
16845 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
16866 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
16886 GTATCGATACATG
1 GTATCGATACATG
16899 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:16869 original size:21 final size:21
Alignment explanation
Indices: 16843--16918 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
16833 ACATGTTGCA
16843 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
16864 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
16884 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
16905 ATGTATCGATACAT
1 ATGTATCGATACAT
16919 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:16876 original size:41 final size:41
Alignment explanation
Indices: 16825--16918 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
16815 ACAATTCAAA
16825 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
16866 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
16907 GTATCGATACAT
1 GTATCGATACAT
16919 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:16975 original size:13 final size:13
Alignment explanation
Indices: 16957--16982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16947 TACAGCAAGT
16957 ATGTATCGATACA
1 ATGTATCGATACA
16970 ATGTATCGATACA
1 ATGTATCGATACA
16983 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:17503 original size:34 final size:35
Alignment explanation
Indices: 17440--17506 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
17430 CTAAGTGATT
17440 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
17476 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
17507 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:18220 original size:34 final size:35
Alignment explanation
Indices: 18182--18248 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
18172 CCTTACAACA
18182 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
18216 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
18249 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:18739 original size:13 final size:13
Alignment explanation
Indices: 18721--18756 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
18711 ATTTATGATG
*
18721 TATCGATACACTA
1 TATCGATACAATA
*
18734 TATCGATACAATG
1 TATCGATACAATA
18747 TATCGATACA
1 TATCGATACA
18757 TGAATAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:18846 original size:21 final size:21
Alignment explanation
Indices: 18821--18860 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
18811 CTATGAACAA
18821 TGATGTATCGATACATGAAAG
1 TGATGTATCGATACATGAAAG
18842 TGATGTATCGATACATGAA
1 TGATGTATCGATACATGAA
18861 CACTGATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (21 bp):
TGATGTATCGATACATGAAAG
Found at i:19026 original size:20 final size:20
Alignment explanation
Indices: 18963--19033 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
18953 GCCAATGTCC
**
18963 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
18983 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
19003 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
19023 TGTATCGATAC
1 TGTATCGATAC
19034 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:22372 original size:84 final size:84
Alignment explanation
Indices: 22217--22381 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
22207 CATTTTCCAC
* * * *
22217 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
22282 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
22301 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
22363 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
22382 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:23936 original size:34 final size:35
Alignment explanation
Indices: 23898--23964 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
23888 CCTTACAACA
23898 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
23932 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
23965 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:24454 original size:13 final size:13
Alignment explanation
Indices: 24436--24471 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
24426 ATTTATGATG
*
24436 TATCGATACACTA
1 TATCGATACAATA
*
24449 TATCGATACAATG
1 TATCGATACAATA
24462 TATCGATACA
1 TATCGATACA
24472 TGAATAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:24561 original size:21 final size:21
Alignment explanation
Indices: 24536--24575 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
24526 CTATGAACAA
24536 TGATGTATCGATACATGAAAG
1 TGATGTATCGATACATGAAAG
24557 TGATGTATCGATACATGAA
1 TGATGTATCGATACATGAA
24576 CACTGATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (21 bp):
TGATGTATCGATACATGAAAG
Found at i:24741 original size:20 final size:20
Alignment explanation
Indices: 24678--24748 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
24668 GCCAATGTCC
**
24678 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
24698 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
24718 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
24738 TGTATCGATAC
1 TGTATCGATAC
24749 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:25588 original size:11 final size:11
Alignment explanation
Indices: 25572--25596 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25562 TATAAATATA
25572 ATTAAATAATT
1 ATTAAATAATT
25583 ATTAAATAATT
1 ATTAAATAATT
25594 ATT
1 ATT
25597 TAATTTGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTAAATAATT
Found at i:29968 original size:13 final size:14
Alignment explanation
Indices: 29937--29967 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29927 TTAAAATTTG
*
29937 AAAATTATTTTTTA
1 AAAATTATTTATTA
29951 AAAATTATTTATTA
1 AAAATTATTTATTA
29965 AAA
1 AAA
29968 TAAGTTACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATTATTTATTA
Found at i:30852 original size:32 final size:33
Alignment explanation
Indices: 30793--30854 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
30783 CACCCAGATG
* *
30793 TATCGATACATATTGCTTAGTATCGATACATTA
1 TATCGATACATATTGCATAGTAGCGATACATTA
*
30826 TATCGATACATGTT-CATAGTAGCGATACA
1 TATCGATACATATTGCATAGTAGCGATACA
30855 CCTTAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (33 bp):
TATCGATACATATTGCATAGTAGCGATACATTA
Found at i:32805 original size:56 final size:54
Alignment explanation
Indices: 32743--33262 Score: 304
Period size: 56 Copynumber: 9.3 Consensus size: 54
32733 TAGTTGAAAT
*
32743 GTTGAAATGGGCACCAAAATAAGCAAACCAAAAAGTAGCTAAG-AGGTATAGCTCTA
1 GTTGAAATTGGCACCAAAATAAG-AAACC-AAAAGTAGCT-AGTAGGTATAGCTCTA
* *
32799 GTTGAAATTGGCACCCAAATGAA-AAAGCCAAAAGTATCTAGTAGGTATAGCTCTA
1 GTTGAAATTGGCACCAAAAT-AAGAAA-CCAAAAGTAGCTAGTAGGTATAGCTCTA
* * * *
32854 GTTAAAATTGGCACCAAAATAAGAAAACCTAAAATTAGTTGGTAGGTATAGCTCTA
1 GTTGAAATTGGCACCAAAATAAG-AAACC-AAAAGTAGCTAGTAGGTATAGCTCTA
* * * * *
32910 GTTGAAATTGACATCAAATTGAA-AAGCTTCAAAAGTAGCTTGTAGGTATAGCTCTA
1 GTTGAAATTGGCACCAAAAT-AAGAAAC--CAAAAGTAGCTAGTAGGTATAGCTCTA
* * * * * * * *
32966 GTCGAAACTAGCACCAAATTAAAAAAGCCTAAAAGTATCTAGTGGGTATA-CTCCCA
1 GTTGAAATTGGCACCAAAATAAGAAA-CC-AAAAGTAGCTAGTAGGTATAGCT-CTA
* * * * * * * *
33022 GTTAAAATTAGCACCCAAATTATAAAGCCTAAAAGTAGTTAG-CGAGAATAGCTCTA
1 GTTGAAATTGGCACCAAAATAAGAAA-CC-AAAAGTAGCTAGTAG-GTATAGCTCTA
* * * * *
33078 TTTAAAATTGGCACCAAAATGAA-AAGGCTTAAAAATAG-TAAGTAAGG-ATAGCTCTA
1 GTTGAAATTGGCACCAAAAT-AAGAA-AC-CAAAAGTAGCT-AGT-AGGTATAGCTCTA
* * * * *
33134 ATTAAAATTGGCA-TATAAATGAA-AAAGCCCAAAAGTGGCTAGTAGGGATAGCTCTA
1 GTTGAAATTGGCACCA-AAAT-AAGAAA--CCAAAAGTAGCTAGTAGGTATAGCTCTA
* * * * * * * * *
33190 ATTGAAATTAGAACCCAACTGAGAAAACCCAAAAGTAGCTAGTGGGGATAGCTCCA
1 GTTGAAATTGGCACCAAAATAAG-AAA-CCAAAAGTAGCTAGTAGGTATAGCTCTA
33246 GTTGAAATTGGCACCAA
1 GTTGAAATTGGCACCAA
33263 GATGAAAAAG
Statistics
Matches: 368, Mismatches: 67, Indels: 58
0.75 0.14 0.12
Matches are distributed among these distances:
54 4 0.01
55 60 0.16
56 288 0.78
57 15 0.04
58 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (54 bp):
GTTGAAATTGGCACCAAAATAAGAAACCAAAAGTAGCTAGTAGGTATAGCTCTA
Found at i:33131 original size:168 final size:167
Alignment explanation
Indices: 32771--33270 Score: 413
Period size: 168 Copynumber: 3.0 Consensus size: 167
32761 ATAAGCAAAC
* * * *
32771 CAAAAAGTAGCTAAG-AGGTATAGCTCTAGTTGAAATTGGCACCCAAATGAAAAAGCCAAAAGTA
1 CAAAAA-TAGCT-AGTAGGTATAGCTCTAGTCGAAACTAGCACCCAAATAAAAAAGCCAAAAGTA
* * *
32835 TCTAGTAGGTATAGCTCTAGTTAAAATTGGCACCAAAATAAGAAAACCTAAAATTAGTTGGTAGG
64 TCTAGTAGGTATAGCTCCAGTTAAAATTAGCACCAAAATAAGAAAACCTAAAAGTAGTTGGTAGG
* * * *
32900 TATAGCTCTAGTTGAAATTGACATCAAATTGAAAAGCTT
129 AATAGCTCTAGTTAAAATTGACACCAAAATGAAAAGCTT
* *
32939 CAAAAGTAGCTTGTAGGTATAGCTCTAGTCGAAACTAGCA-CCAAATTAAAAAAGCCTAAAAGTA
1 CAAAAATAGCTAGTAGGTATAGCTCTAGTCGAAACTAGCACCCAAA-TAAAAAAGCC-AAAAGTA
* * * * *
33003 TCTAGTGGGTATA-CTCCCAGTTAAAATTAGCACCCAAATTATAAAGCCTAAAAGTAGTTAGCG-
64 TCTAGTAGGTATAGCT-CCAGTTAAAATTAGCACCAAAATAAGAAAACCTAAAAGTAGTT-G-GT
* *
33066 A-GAATAGCTCTATTTAAAATTGGCACCAAAATGAAAAGGCTT
126 AGGAATAGCTCTAGTTAAAATTGACACCAAAATGAAAA-GCTT
* ** * * *** *
33108 -AAAAATAG-TAAGTAAGG-ATAGCTCTAATTAAAATTGGCATATAAATGAAAAAGCCCAAAAGT
1 CAAAAATAGCT-AGT-AGGTATAGCTCTAGTCGAAACTAGCACCCAAATAAAAAAG-CCAAAAGT
** * * * * * * * * * * * *
33170 GGCTAGTAGGGATAGCTCTAATTGAAATTAGAACCCAACTGAGAAAACCCAAAAGTAGCTAGTGG
63 ATCTAGTAGGTATAGCTCCAGTTAAAATTAGCACCAAAATAAGAAAACCTAAAAGTAGTTGGTAG
* * * * *
33235 GGATAGCTCCAGTTGAAATTGGCACCAAGATGAAAA
128 GAATAGCTCTAGTTAAAATTGACACCAAAATGAAAA
33271 AGCCTAATGT
Statistics
Matches: 267, Mismatches: 51, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
166 7 0.03
167 40 0.15
168 203 0.76
169 16 0.06
170 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (167 bp):
CAAAAATAGCTAGTAGGTATAGCTCTAGTCGAAACTAGCACCCAAATAAAAAAGCCAAAAGTATC
TAGTAGGTATAGCTCCAGTTAAAATTAGCACCAAAATAAGAAAACCTAAAAGTAGTTGGTAGGAA
TAGCTCTAGTTAAAATTGACACCAAAATGAAAAGCTT
Found at i:33984 original size:21 final size:21
Alignment explanation
Indices: 33960--34000 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33950 AAAATAGTAG
*
33960 GATTTT-TAATTAAATTTTTAA
1 GATTTTCT-ATTAAACTTTTAA
33981 GATTTTCTATTAAACTTTTA
1 GATTTTCTATTAAACTTTTA
34001 CTTAAGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
GATTTTCTATTAAACTTTTAA
Found at i:35570 original size:20 final size:18
Alignment explanation
Indices: 35543--35598 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
35533 ACTGCTAGTT
*
35543 TCATGTATCGATACAATT
1 TCATGTATCGATACAATA
*
35561 TGCTATGTATCGATACCAAGA
1 T-C-ATGTATCGATA-CAATA
35582 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
35599 GTATCGATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 12 0.38
21 4 0.12
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATA
Found at i:35602 original size:13 final size:13
Alignment explanation
Indices: 35584--35610 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35574 TACCAAGATC
35584 ATGTATCGATACA
1 ATGTATCGATACA
35597 ATGTATCGATACA
1 ATGTATCGATACA
35610 A
1 A
35611 AGCAATATGT
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:35606 original size:32 final size:32
Alignment explanation
Indices: 35565--35628 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
35555 ACAATTTGCT
*
35565 ATGTATCGATACCAAG-ATCATGTATCGATACA
1 ATGTATCGATACAAAGAAT-ATGTATCGATACA
35597 ATGTATCGATACAAAGCAATATGTATCGATAC
1 ATGTATCGATACAAAG-AATATGTATCGATAC
35629 TTATGGGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 12 0.41
34 2 0.07
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAATATGTATCGATACA
Found at i:36268 original size:21 final size:20
Alignment explanation
Indices: 36238--36280 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
36228 TAATTTATAA
36238 CTCCCCCTTAATAAAATTTTT
1 CTCCCCCTTAAT-AAATTTTT
*
36259 CTCCCTCTTAATAAATTTTT
1 CTCCCCCTTAATAAATTTTT
36279 CT
1 CT
36281 TTCCCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.47
Consensus pattern (20 bp):
CTCCCCCTTAATAAATTTTT
Found at i:36276 original size:20 final size:21
Alignment explanation
Indices: 36238--36295 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
36228 TAATTTATAA
36238 CTCCCCCTTAATAAAATTTTT
1 CTCCCCCTTAATAAAATTTTT
*
36259 CTCCCTCTTAAT-AAATTTTT
1 CTCCCCCTTAATAAAATTTTT
** *
36279 CTTTCCCTTAAAAAAAT
1 CTCCCCCTTAATAAAAT
36296 AATTTTTCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (21 bp):
CTCCCCCTTAATAAAATTTTT
Found at i:36295 original size:21 final size:19
Alignment explanation
Indices: 36242--36309 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 19
36232 TTATAACTCC
*
36242 CCCTTAATAAAATTTTTCT
1 CCCTTAAAAAAATTTTTCT
* *
36261 CCCTCTTAATAAATTTTTCTTT
1 CCCT-TAAAAAAATTTTTC--T
36283 CCCTTAAAAAAATAATTTTTCT
1 CCCTT--AAAAA-AATTTTTCT
36305 CCCTT
1 CCCTT
36310 TTTCAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.11
20 11 0.29
21 1 0.03
22 11 0.29
23 3 0.08
24 8 0.21
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (19 bp):
CCCTTAAAAAAATTTTTCT
Found at i:37966 original size:13 final size:13
Alignment explanation
Indices: 37948--37973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37938 TACAGCAAGT
37948 ATGTATCGATACA
1 ATGTATCGATACA
37961 ATGTATCGATACA
1 ATGTATCGATACA
37974 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:40221 original size:21 final size:21
Alignment explanation
Indices: 40188--40232 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
40178 TTGCAAGTTG
*
40188 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
40210 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
40230 AAA
1 AAA
40233 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:44154 original size:20 final size:20
Alignment explanation
Indices: 44075--44154 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
44065 AATGTCCAAA
*
44075 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
44095 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
44120 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
44140 TTGTATCGATACATT
1 ATGTATCGATACATT
44155 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:44158 original size:13 final size:13
Alignment explanation
Indices: 44140--44178 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
44130 ACATTTTTCT
44140 TTGTATCGATACA
1 TTGTATCGATACA
44153 TTGTATCGATACA
1 TTGTATCGATACA
*
44166 CTGTATCGATACA
1 TTGTATCGATACA
44179 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:46373 original size:13 final size:13
Alignment explanation
Indices: 46355--46380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46345 TACAGCAAGT
46355 ATGTATCGATACA
1 ATGTATCGATACA
46368 ATGTATCGATACA
1 ATGTATCGATACA
46381 CAAAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:47753 original size:13 final size:13
Alignment explanation
Indices: 47732--47766 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
47722 AATGCCTTTA
*
47732 TATCGATACAGTG
1 TATCGATACAATG
*
47745 TATCAATACAATG
1 TATCGATACAATG
47758 TATCGATAC
1 TATCGATAC
47767 TACAAACACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:54100 original size:20 final size:20
Alignment explanation
Indices: 54077--54114 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
54067 CAAAGCAATA
54077 TGTATTGATACTTTTAGGTC
1 TGTATTGATACTTTTAGGTC
54097 TGTATTGATACTTTTAGG
1 TGTATTGATACTTTTAGG
54115 ATTTTAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (20 bp):
TGTATTGATACTTTTAGGTC
Found at i:54563 original size:19 final size:19
Alignment explanation
Indices: 54538--54579 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54528 TAAACAAAAC
*
54538 AAAAAAAGAGGAAAAAAGAG
1 AAAAAAA-AAGAAAAAAGAG
*
54558 AAAAAAAAAGAGAAAAGAG
1 AAAAAAAAAGAAAAAAGAG
54577 AAA
1 AAA
54580 TTCTAAGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAGAG
Found at i:54564 original size:12 final size:12
Alignment explanation
Indices: 54549--54573 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54539 AAAAAAGAGG
54549 AAAAAAGAGAAA
1 AAAAAAGAGAAA
54561 AAAAAAGAGAAA
1 AAAAAAGAGAAA
54573 A
1 A
54574 GAGAAATTCT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:55980 original size:136 final size:135
Alignment explanation
Indices: 55728--55984 Score: 378
Period size: 136 Copynumber: 1.9 Consensus size: 135
55718 AAGGTTATAT
55728 GGGAACTTTCATGTTCAAACATGTCCATTAGGGGTATTTAGGTAATAGTAGCTTAAAACCAAGTC
1 GGGAACTTTCATGTTCAAACATGTCCATTAGGGGTATTTAGGTAATAGTAGCTTAAAACCAAGTC
* *
55793 TAGGGTCATGTTGGAATCTTCATGTCAAAACATGTCTATTAAGGGTATTTAAGTAATAGCAAGGG
66 TAGGGTCATATAGGAATCTTCATGTCAAAACATGTCTATTAAGGGTATTTAA-TAATAGCAAGGG
55858 TCATGA
130 TCATGA
* * * * *
55864 GGGAATTTTCATG-TCAAAGCATGTCTATTAGGGTTATTTAGGTCATAGTAGCTTAAAACCGAGT
1 GGGAACTTTCATGTTCAAA-CATGTCCATTAGGGGTATTTAGGTAATAGTAGCTTAAAACCAAGT
55928 CTAGGGTCATATAGGAA-CTTTCATGTCAAAACATGT-TCATT-AGGGTATTTTAATAAT
65 CTAGGGTCATATAGGAATC-TTCATGTCAAAACATGTCT-ATTAAGGGTA-TTTAATAAT
55985 GGTACCTTGA
Statistics
Matches: 110, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
135 17 0.15
136 93 0.85
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (135 bp):
GGGAACTTTCATGTTCAAACATGTCCATTAGGGGTATTTAGGTAATAGTAGCTTAAAACCAAGTC
TAGGGTCATATAGGAATCTTCATGTCAAAACATGTCTATTAAGGGTATTTAATAATAGCAAGGGT
CATGA
Found at i:56638 original size:13 final size:15
Alignment explanation
Indices: 56617--56648 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
56607 TCAACTATTT
56617 TTTTCTCTTTTTT-C
1 TTTTCTCTTTTTTGC
56631 TTTT-TCTTTTTTGC
1 TTTTCTCTTTTTTGC
56645 TTTT
1 TTTT
56649 ACTATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (15 bp):
TTTTCTCTTTTTTGC
Found at i:59969 original size:18 final size:18
Alignment explanation
Indices: 59927--59962 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
59917 TTAAACATGA
*
59927 CCTGTATGAGAACTCTAT
1 CCTGTATGAAAACTCTAT
59945 CCTGTATGAAAACTCTAT
1 CCTGTATGAAAACTCTAT
59963 TTGGTATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (18 bp):
CCTGTATGAAAACTCTAT
Found at i:61220 original size:52 final size:51
Alignment explanation
Indices: 61111--61228 Score: 141
Period size: 52 Copynumber: 2.3 Consensus size: 51
61101 GAAAATAACA
* *
61111 AGGTTGGAGTATCCCTGATTATAGAAAATCGGTATTTTGAAAATAAAATCG
1 AGGTTGGAGTATCCCCGATTATAGAAAATCGGTATTTTGAAAATAAAATAG
* * *
61162 AAGTTGGAGTATCCCCGATT-TGTGAAAATTTGGTATTTT-AGAAATAAAATAG
1 AGGTTGGAGTATCCCCGATTAT-AGAAAA-TCGGTATTTTGA-AAATAAAATAG
*
61214 GGGTTGGAGTATCCC
1 AGGTTGGAGTATCCC
61229 ATCGGAAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 1 0.02
51 24 0.42
52 32 0.56
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (51 bp):
AGGTTGGAGTATCCCCGATTATAGAAAATCGGTATTTTGAAAATAAAATAG
Found at i:61264 original size:28 final size:28
Alignment explanation
Indices: 61233--61288 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
61223 TATCCCATCG
*
61233 GAAATAACAGGATTAGAGTATCCCCGAT
1 GAAATAACAGGATTAGAGTACCCCCGAT
* * *
61261 GAAATAACGGGGTTGGAGTACCCCCGAT
1 GAAATAACAGGATTAGAGTACCCCCGAT
61289 TATGAAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (28 bp):
GAAATAACAGGATTAGAGTACCCCCGAT
Found at i:61361 original size:28 final size:27
Alignment explanation
Indices: 61321--61392 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 27
61311 TATAAAGCCG
61321 GGGTTGGAGTATCCTCTCGA-AAATAACA
1 GGGTTGGAGTATCC-C-CGAGAAATAACA
61349 GGGTTGGAGTATCCCCGATGAAATAACA
1 GGGTTGGAGTATCCCCGA-GAAATAACA
61377 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
61393 AATTGTGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
26 3 0.07
27 1 0.02
28 38 0.90
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGAAATAACA
Found at i:61457 original size:109 final size:106
Alignment explanation
Indices: 61215--61476 Score: 373
Period size: 107 Copynumber: 2.4 Consensus size: 106
61205 ATAAAATAGG
* * * *
61215 GGTTGGAGTATCCCATCGGAAATAACAGGATTAGAGTATCCCCGATGAAATAACGGGGTTGGAGT
1 GGTTGGAGTATCCCTTC-GAAATAACAGGGTTGGAGTATCCCCGATGAAATAACAGGGTTGGAGT
* *
61280 ACCCCCGATTATGAAAAACAATATTTTTAGATATAAAGCCGG
65 ACCCCCAATTATGAAAAACAATATTTTTAGATATAAAGCCGA
61322 GGTTGGAGTAT-CCTCTCGAAAATAACAGGGTTGGAGTATCCCCGATGAAATAACAGGGTTGGAG
1 GGTTGGAGTATCCCT-TCG-AAATAACAGGGTTGGAGTATCCCCGATGAAATAACAGGGTTGGAG
* * *
61386 TATCCCCAATTGTGAAAAACACAATATTTTTAGATATAAAGCTGA
64 TACCCCCAATTATG-AAAA-ACAATATTTTTAGATATAAAGCCGA
*
61431 GGTTGGAGTATCCCTTCAGAAATAACAGGGTTGGAGTACCCCCGAT
1 GGTTGGAGTATCCCTTC-GAAATAACAGGGTTGGAGTATCCCCGAT
61477 TGTGAAAAAT
Statistics
Matches: 139, Mismatches: 10, Indels: 10
0.87 0.06 0.06
Matches are distributed among these distances:
106 3 0.02
107 66 0.47
108 4 0.03
109 62 0.45
110 4 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (106 bp):
GGTTGGAGTATCCCTTCGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACAGGGTTGGAGTA
CCCCCAATTATGAAAAACAATATTTTTAGATATAAAGCCGA
Found at i:61603 original size:51 final size:51
Alignment explanation
Indices: 61460--61603 Score: 146
Period size: 51 Copynumber: 2.8 Consensus size: 51
61450 AAATAACAGG
* ** * * *
61460 GTTGGAGTACCCCCGATTGTGAAAAATTGGTGTTTTGGCAATAAAATCGAA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATAGAA
* * ** * * *
61511 GTTGGAATATCCCCGATTACGGTAAATCGATGCTTTAGAAATAAAATTAG-A
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAA-TAGAA
*
61562 GTTGGAGTATCCCCGATTAAGAAAAATTGACGTTTTGGAAAT
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAAT
61604 GGAACTGGGA
Statistics
Matches: 72, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
51 70 0.97
52 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATAGAA
Found at i:63979 original size:21 final size:21
Alignment explanation
Indices: 63933--63994 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
63923 ACTGCCTGAA
*
63933 TGTATCGATACATTGTAA-AA-
1 TGTATCGATACAATG-AACAAT
*
63953 TGTATCGATACAATGAGCAAT
1 TGTATCGATACAATGAACAAT
63974 TGTATCGATACAATGAACAAT
1 TGTATCGATACAATGAACAAT
63995 GCATCAATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.03
20 16 0.43
21 20 0.54
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAATGAACAAT
Found at i:64006 original size:20 final size:21
Alignment explanation
Indices: 63960--64006 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
63950 AAATGTATCG
* * *
63960 ATACAATGAGCAATTGTATCG
1 ATACAATGAACAATTGCATCA
63981 ATACAATGAACAA-TGCATCA
1 ATACAATGAACAATTGCATCA
64001 ATACAA
1 ATACAA
64007 ATTGTGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (21 bp):
ATACAATGAACAATTGCATCA
Found at i:64524 original size:28 final size:28
Alignment explanation
Indices: 64493--64548 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
64483 AGCCAATGTA
*
64493 AGACAACATAGATGATGTTCTAAAAGGC
1 AGACAACATAGATGATGTTCGAAAAGGC
64521 AGACAACATAGATGATGTTCGAAAAGGC
1 AGACAACATAGATGATGTTCGAAAAGGC
64549 TTTTAAGTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (28 bp):
AGACAACATAGATGATGTTCGAAAAGGC
Found at i:66969 original size:20 final size:20
Alignment explanation
Indices: 66946--67049 Score: 75
Period size: 20 Copynumber: 5.7 Consensus size: 20
66936 CACATCTAGA
*
66946 TGTATCGATACATTGTGCTT
1 TGTATCGATACATTGTGCAT
*
66966 TGTATCGATACA-TGTTCAT
1 TGTATCGATACATTGTGCAT
*
66985 TGTAT---TA-A---TACAT
1 TGTATCGATACATTGTGCAT
*
66998 TGTATCGATACA-TGTTCAT
1 TGTATCGATACATTGTGCAT
**
67017 TGTATCGATACATACT-CAAT
1 TGTATCGATACATTGTGC-AT
67037 TGTATCGATACAT
1 TGTATCGATACAT
67050 GAAACTGGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
13 9 0.13
15 1 0.01
16 4 0.06
17 1 0.01
19 27 0.39
20 28 0.40
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTGTGCAT
Found at i:67028 original size:32 final size:32
Alignment explanation
Indices: 66965--67029 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
66955 ACATTGTGCT
*
66965 TTGTATCGATACATGTTCATTGTATTAATACA
1 TTGTATCGATACATGTTCATTGTATCAATACA
*
66997 TTGTATCGATACATGTTCATTGTATCGATACA
1 TTGTATCGATACATGTTCATTGTATCAATACA
67029 T
1 T
67030 ACTCAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (32 bp):
TTGTATCGATACATGTTCATTGTATCAATACA
Found at i:68171 original size:51 final size:51
Alignment explanation
Indices: 68096--68213 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 51
68086 AAAAATAACG
* * *
68096 GGGTTAGAGTATCCCCAATGGTGAAAAATAGATATTTTGGAAATAAAATCA
1 GGGTTGGAGTATCCCCAATGGTGAAAAATAGATATTTTAGAAATAAAACCA
* * * * * **
68147 GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTAGAAATAAGGCCA
1 GGGTTGGAGTATCCCCAATGGTGAAAAATAGATATTTTAGAAATAAAACCA
*
68198 GGGTTGGAGTGTCCCC
1 GGGTTGGAGTATCCCC
68214 TTAGAAATAA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCAATGGTGAAAAATAGATATTTTAGAAATAAAACCA
Found at i:68230 original size:79 final size:79
Alignment explanation
Indices: 68147--68587 Score: 467
Period size: 79 Copynumber: 5.6 Consensus size: 79
68137 AATAAAATCA
* * * *
68147 GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTAGAAATAAGGCCAGGGTTGGAGTGTCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAGCCAGGGTTGGAGTATCC
*
68212 CCTTAGAAATAACG
66 CCTCAGAAATAACG
* * * * * * *
68226 GGGTTAGGGTATCCTCAATTGTGAAAATTTGATGTTTTAGAAATAAGGTC-GAGATTGGAGTATC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAGCCAG-GGTTGGAGTATC
* *
68290 CCCTCAAAAATAATG
65 CCCTCAGAAATAACG
* * * * ** *
68305 GGGTAAGAGTATCCCCGATTGTGAAAAGTTAATGTTTTGGAAATAAAATC-GAGGTTGAAGTATC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAGCCAG-GGTTGGAGTATC
**
68369 CCCTTGGAAATAACG
65 CCCTCAGAAATAACG
* * * *
68384 GGGTT-GAAATATCCCCGATTATGGAAAATTGATGTTTTAAAAATAAAGCCAGGGTTGGAGTATC
1 GGGTTAG-AGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAGCCAGGGTTGGAGTATC
*
68448 CCCTCAGAAATAA-T
65 CCCTCAGAAATAACG
* * * * * *
68462 GGGTTAGAGTATCCTCAATTATGGAAAATCGATGTTTTAGAAATAAAGCCAAGGTTGGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAGCCAGGGTTGGAGTATCC
* *
68527 CCTCGGAAATAACA
66 CCTCAGAAATAACG
* * * *
68541 GGGTTAAAGTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAA
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAA
68588 AAACATCAAT
Statistics
Matches: 303, Mismatches: 54, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
78 70 0.23
79 232 0.77
80 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (79 bp):
GGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAGCCAGGGTTGGAGTATCC
CCTCAGAAATAACG
Found at i:68527 original size:236 final size:237
Alignment explanation
Indices: 68147--68588 Score: 620
Period size: 236 Copynumber: 1.9 Consensus size: 237
68137 AATAAAATCA
* * * * * * *
68147 GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTAGAAATAAGGCCAGGGTTGGAGTGTCC
1 GGGTTGAAATATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAGCCAGGGTTGGAGTATCC
* * * * * * *
68212 CCTTAGAAATAACGGGGTTAGGGTATCCTCAATTGTGAAAATTTGATGTTTTAGAAATAAGGTCG
66 CCTCAGAAATAACGGGGTTAGAGTATCCTCAATTATGAAAATTCGATGTTTTAGAAATAAAGCCA
* * * *
68277 AGATTGGAGTATCCCCTCAAAAATAA-TGGGGTAAGAGTATCCCCGATTGTGAAAAGTTAATGTT
131 AGATTGGAGTATCCCCTCAAAAATAACAGGGGTAA-AGTATCCCCGATGGTGAAAAATCAATGTT
68341 TTGGAAATAAAATCGAGGTTGAAGTATCCCCTTGGAAATAACG
195 TTGGAAATAAAATCGAGGTTGAAGTATCCCCTTGGAAATAACG
*
68384 GGGTTGAAATATCCCCGATTATGGAAAATTGATGTTTTAAAAATAAAGCCAGGGTTGGAGTATCC
1 GGGTTGAAATATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAGCCAGGGTTGGAGTATCC
*
68449 CCTCAGAAATAA-TGGGTTAGAGTATCCTCAATTATGGAAAA-TCGATGTTTTAGAAATAAAGCC
66 CCTCAGAAATAACGGGGTTAGAGTATCCTCAATTAT-GAAAATTCGATGTTTTAGAAATAAAGCC
* ** * *
68512 AAGGTTGGAGTATCCCCTCGGAAATAACAGGGTTAAAGTATCCCCGATGGTGAAAAATCGATGTT
130 AAGATTGGAGTATCCCCTCAAAAATAACAGGGGTAAAGTATCCCCGATGGTGAAAAATCAATGTT
68577 TTGGAAATAAAA
195 TTGGAAATAAAA
68589 AACATCAATG
Statistics
Matches: 178, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
236 99 0.56
237 79 0.44
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (237 bp):
GGGTTGAAATATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAGCCAGGGTTGGAGTATCC
CCTCAGAAATAACGGGGTTAGAGTATCCTCAATTATGAAAATTCGATGTTTTAGAAATAAAGCCA
AGATTGGAGTATCCCCTCAAAAATAACAGGGGTAAAGTATCCCCGATGGTGAAAAATCAATGTTT
TGGAAATAAAATCGAGGTTGAAGTATCCCCTTGGAAATAACG
Found at i:70928 original size:20 final size:20
Alignment explanation
Indices: 70903--70940 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
70893 GGGTAAAACC
70903 AAGAATGTATCGAAACAATG
1 AAGAATGTATCGAAACAATG
*
70923 AAGAATGTATCGATACAA
1 AAGAATGTATCGAAACAA
70941 ATTGTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (20 bp):
AAGAATGTATCGAAACAATG
Found at i:71703 original size:41 final size:42
Alignment explanation
Indices: 71622--71703 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
71612 AAAAGAGTAT
*
71622 ATCCTGCTCTTTGAGGACAAAAAAGAAAAGGAAATAAAGTGC
1 ATCCTACTCTTTGAGGACAAAAAAGAAAAGGAAATAAAGTGC
**
71664 ATCCTACTCTTTGAGGAC-AAAGGGAAAAGGAAATAAAGTG
1 ATCCTACTCTTTGAGGACAAAAAAGAAAAGGAAATAAAGTG
71704 GGCTTTGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 20 0.54
42 17 0.46
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (42 bp):
ATCCTACTCTTTGAGGACAAAAAAGAAAAGGAAATAAAGTGC
Found at i:71782 original size:61 final size:60
Alignment explanation
Indices: 71701--72207 Score: 510
Period size: 61 Copynumber: 8.4 Consensus size: 60
71691 AGGAAATAAA
** * * *
71701 GTGGGCTTTGCAAGAAGAAAGCATCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGT
1 GTGGGCTTTAAAAGAA-AAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
* * *
71762 GTGGGCTTTGCAATAAG-AAA-GTGTCCTACTCTTTGAGGACTAGAAGGTGCCATCAACTTGT
1 GTGGGCTTT--AA-AAGAAAAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
* * * * *
71823 GTGGGCTTTGAAAGGAAAA--TGTCC-AGCTCTTTGAGAACTGAAAGGTGCCACCAACTTAT
1 GTGGGCTTT-AAAAGAAAAGGCGTCCTA-CTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
* * *
71882 GTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGATTGGAAAGTGCCACCAACTTGT
1 GTGGGCTTTAAAA-GAAAAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
* * * * * * *
71943 ATGGGCTTTAAAAGGAAAATGTGTCATGCTCTTTGAGGACTGGAAAGTGCCACCAATTTGT
1 GTGGGCTTTAAAA-GAAAAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
*
72004 GTGGGCTTTATAAAGAAAAGGCGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAAC-T-T
1 GTGGGCTTTA-AAAGAAAAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
* *
72063 GTGAGCTTTAAAAGGAAAAGGCGTCC-AGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGT
1 GTGGGCTTTAAAA-GAAAAGGCGTCCTA-CTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
* * * * * * * *
72124 GTGGACTTGAAAAGGAAAAGGCGTCCTGCTTTTTGAGGATTGAAAGATGCCACCAACTTAT
1 GTGGGCTTTAAAA-GAAAAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
* *
72185 GTGGG-TTTGAAAGGAGAAGGCGT
1 GTGGGCTTT-AAAAGAAAAGGCGT
72208 ATTGCTTTTT
Statistics
Matches: 383, Mismatches: 47, Indels: 33
0.83 0.10 0.07
Matches are distributed among these distances:
58 8 0.02
59 98 0.26
60 18 0.05
61 250 0.65
62 5 0.01
63 1 0.00
64 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.26
Consensus pattern (60 bp):
GTGGGCTTTAAAAGAAAAGGCGTCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
Found at i:71872 original size:120 final size:120
Alignment explanation
Indices: 71729--72199 Score: 584
Period size: 120 Copynumber: 3.9 Consensus size: 120
71719 AAGCATCCTA
*
71729 CTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTGCAATAA-G-AAA-GTGTCCTA
1 CTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT--AA-AAGGAAAAGGCGTCCTA
* * * *
71790 CTCTTTGAGGACTAGAAGGTGCCATCAACTTGTGTGGGCTTTGAAAGGAAAATGTCCAG
62 CTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGTCCAG
* * *
71849 CTCTTTGAGAACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCT
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCT
* * *
71914 TTGAGGATTGGAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAATGTGTCATG
66 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGT-CCA-G
*
71971 CTCTTTGAGGACTGGAAA-GTGCCACCAATTTGTGTGGGCTTTATAAA-GAAAAGGCGTCCTACT
1 CTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTA-AAAGGAAAAGGCGTCCTACT
* *
72034 CTTTGAGGACTGGAAAGTGCCACCAAC-T-TGTGAGCTTTAAAAGGAAAAGGCGTCCAG
64 CTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA--TGTCCAG
* * * *
72091 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGACTTGAAAAGGAAAAGGCGTCCTGCTTT
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCT
* * *
72156 TTGAGGA-TTGAAAGATGCCACCAACTTATGTGGG-TTTGAAAGGA
66 TTGAGGACTGGAAAG-TGCCACCAACTTGTGTGGGCTTTAAAAGGA
72200 GAAGGCGTAT
Statistics
Matches: 308, Mismatches: 28, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
117 2 0.01
118 3 0.01
119 16 0.05
120 180 0.58
121 16 0.05
122 84 0.27
123 7 0.02
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (120 bp):
CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCT
TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGTCCAG
Found at i:72006 original size:181 final size:178
Alignment explanation
Indices: 71724--72199 Score: 572
Period size: 181 Copynumber: 2.6 Consensus size: 178
71714 GAAGAAAGCA
* *
71724 TCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAATAA-G-AAAGTGTC
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT--AA-AAGGAAAAGTGTC
* * * *
71787 CTACTCTTTGAGGACTAGAAGGTGCCATCAACTTGTGTGGGCTTTGAAAGGAAAA-TGTCC-AGC
62 CTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCGTCCTA-C
*
71850 TCTTTGAGAACT-GAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCG
126 TCTTTGAGAACTGGAAA-GTGCCACCAAC-T-TGTGAGCTTTAAAAGGAAAAGGCG
* * *
71905 TCCTGCTCTTTGAGGATTGGAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAATGTGTCAT
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GTGTCCT
* * *
71970 GCTCTTTGAGGACTGGAAAGTGCCACCAATTTGTGTGGGCTTT-ATAAAGAAAAGGCGTCCTACT
64 GCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGA-AAGGAAAA-GCGTCCTACT
*
72034 CTTTGAGGACTGGAAAGTGCCACCAACTTGTGAGCTTTAAAAGGAAAAGGCG
127 CTTTGAGAACTGGAAAGTGCCACCAACTTGTGAGCTTTAAAAGGAAAAGGCG
* * * *
72086 TCCAGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGACTTGAAAAGGAAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GTGTCCT
* * *
72151 GCTTTTTGAGGA-TTGAAAGATGCCACCAACTTATGTGGG-TTTGAAAGGA
64 GCTCTTTGAGGACTAGAAAG-TGCCACCAACTTGTGTGGGCTTTGAAAGGA
72200 GAAGGCGTAT
Statistics
Matches: 256, Mismatches: 28, Indels: 23
0.83 0.09 0.07
Matches are distributed among these distances:
178 2 0.01
179 3 0.01
180 21 0.08
181 197 0.77
182 1 0.00
183 27 0.11
184 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (178 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGTGTCCTGC
TCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCGTCCTACTCTTT
GAGAACTGGAAAGTGCCACCAACTTGTGAGCTTTAAAAGGAAAAGGCG
Found at i:73230 original size:15 final size:16
Alignment explanation
Indices: 73203--73240 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
73193 AGGCAGGTTC
73203 TTTTTTTTCTCTTT-T
1 TTTTTTTTCTCTTTCT
73218 TTATTTTTT-TCTTTCT
1 TT-TTTTTTCTCTTTCT
73234 TTTTTTT
1 TTTTTTT
73241 GTGTTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTTCTCTTTCT
Found at i:73236 original size:17 final size:16
Alignment explanation
Indices: 73203--73240 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
73193 AGGCAGGTTC
73203 TTTTTTTTCTCTTTTT
1 TTTTTTTTCTCTTTTT
73219 TATTTTTTTCT-TTCTTT
1 T-TTTTTTTCTCTT-TTT
73236 TTTTT
1 TTTTT
73241 GTGTTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTTCTCTTTTT
Found at i:85699 original size:79 final size:79
Alignment explanation
Indices: 85541--85716 Score: 194
Period size: 79 Copynumber: 2.2 Consensus size: 79
85531 GATAAAAAGT
* * * * *
85541 TTAATATTTTGGAGATAAAACCAAGGTTAGAGTATCCCCTCGAAAATAACGAGGTTGGAGTCTCC
1 TTAATGTTTTGGAAATAAAACCAAGGTTAGAGTATCCACTCGAAAATAACGAGATTGGAGTATCC
85606 CCAATGGTGAAAAA
66 CCAATGGTGAAAAA
* ** *
85620 TTAATGTTTTGGAAATAAAATCGGGGTTAGAGTATCCACTC-AGAAATAACGAGATTTGAGTATC
1 TTAATGTTTTGGAAATAAAACCAAGGTTAGAGTATCCACTCGA-AAATAACGAGATTGGAGTATC
* *
85684 CTCGAAT-GTGGAAAA
65 C-CCAATGGTGAAAAA
** *
85699 TCGATGTTTTAGAAATAA
1 TTAATGTTTTGGAAATAA
85717 GGCTGGGGTT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 1 0.01
79 76 0.94
80 4 0.05
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (79 bp):
TTAATGTTTTGGAAATAAAACCAAGGTTAGAGTATCCACTCGAAAATAACGAGATTGGAGTATCC
CCAATGGTGAAAAA
Found at i:85735 original size:51 final size:51
Alignment explanation
Indices: 85677--85788 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
85667 AACGAGATTT
* * * * * * *
85677 GAGTATCCTCGAATGTGGAAAATCGATGTTTTAGAAATAAGGCTGGGGTTG
1 GAGTATCCCCGAATATGAAAAATAGATGTTTTAAAAATAAGGCTGCGGTTA
* *
85728 GAGTATCCCCGATTATGAAAAATAGATGTTTTAAAAATAAGGTTGCGGTTA
1 GAGTATCCCCGAATATGAAAAATAGATGTTTTAAAAATAAGGCTGCGGTTA
85779 GAGTATCCCC
1 GAGTATCCCC
85789 TCGGAAATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GAGTATCCCCGAATATGAAAAATAGATGTTTTAAAAATAAGGCTGCGGTTA
Found at i:85861 original size:78 final size:79
Alignment explanation
Indices: 85722--85876 Score: 188
Period size: 78 Copynumber: 2.0 Consensus size: 79
85712 AATAAGGCTG
* * *
85722 GGGTTGGAGTATCCCCGATTATGAAAAATAGATGTTTTAAAAATAAGGTTGCGGTTAGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATAGATATTTTAAAAATAAAGCTGCGGTTAGAGTATCC
*
85787 CCTCGGAAATAATA
66 CCTCGAAAATAATA
* * * * * *
85801 GGGTTGGAGTATCCCTGATTGTGAAAATTA-ATATTTTAGAAATAAAGCTG-GTGTTGGAGTATT
1 GGGTTGGAGTATCCCCGATTATGAAAAATAGATATTTTAAAAATAAAGCTGCG-GTTAGAGTATC
*
85864 CCTTCGAAAATAA
65 CCCTCGAAAATAA
85877 CGGGGTTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
77 1 0.02
78 36 0.56
79 27 0.42
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATAGATATTTTAAAAATAAAGCTGCGGTTAGAGTATCC
CCTCGAAAATAATA
Found at i:86533 original size:20 final size:20
Alignment explanation
Indices: 86502--86556 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
86492 TTACCCAGAT
* *
86502 GTATCGATACATTTTTCAAA
1 GTATCAATACATTCTTCAAA
* *
86522 GTTTCAATACATTCTTCAAT
1 GTATCAATACATTCTTCAAA
*
86542 GTATCGATACATTCT
1 GTATCAATACATTCT
86557 ATCTTTTTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (20 bp):
GTATCAATACATTCTTCAAA
Done.