Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011364.1 Corchorus capsularis cultivar CVL-1 contig11385, 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: 76895
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5898 original size:24 final size:24
Alignment explanation
Indices: 5853--5898 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
5843 AAGGAAAATC
* *
5853 AGTAAAACCAGGATCATAAATCAT
1 AGTAAAACCAAGATAATAAATCAT
* *
5877 AGTAAAATCAAGATAATCAATC
1 AGTAAAACCAAGATAATAAATC
5899 CAAAACTAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (24 bp):
AGTAAAACCAAGATAATAAATCAT
Found at i:9795 original size:106 final size:106
Alignment explanation
Indices: 9610--9821 Score: 415
Period size: 106 Copynumber: 2.0 Consensus size: 106
9600 GCTTAGATGA
9610 AGATCATCAATTTTACTCATCTAGGAGAGTTGGTGTTTCAAGTCGACTTTGGTGGCTATTCAATG
1 AGATCATCAATTTTACTCATCTAGGAGAGTTGGTGTTTCAAGTCGACTTTGGTGGCTATTCAATG
9675 GATAGATTTGAATCTAACACAACTAGATTCGTATCAATTGG
66 GATAGATTTGAATCTAACACAACTAGATTCGTATCAATTGG
*
9716 AGATCATCGATTTTACTCATCTAGGAGAGTTGGTGTTTCAAGTCGACTTTGGTGGCTATTCAATG
1 AGATCATCAATTTTACTCATCTAGGAGAGTTGGTGTTTCAAGTCGACTTTGGTGGCTATTCAATG
9781 GATAGATTTGAATCTAACACAACTAGATTCGTATCAATTGG
66 GATAGATTTGAATCTAACACAACTAGATTCGTATCAATTGG
9822 TATCAGAGCA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (106 bp):
AGATCATCAATTTTACTCATCTAGGAGAGTTGGTGTTTCAAGTCGACTTTGGTGGCTATTCAATG
GATAGATTTGAATCTAACACAACTAGATTCGTATCAATTGG
Found at i:10051 original size:19 final size:19
Alignment explanation
Indices: 10014--10052 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10004 ACTAGTAGTT
* * *
10014 ATATCAAAAAATATCAAAA
1 ATATAAAAAAAAATAAAAA
10033 ATATAAAAAAAAATAAAAA
1 ATATAAAAAAAAATAAAAA
10052 A
1 A
10053 ATCGACCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (19 bp):
ATATAAAAAAAAATAAAAA
Found at i:11042 original size:30 final size:30
Alignment explanation
Indices: 11006--11068 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
10996 TCTTCAAGGG
*
11006 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGC-ACCAAGGACTTATCAT
11036 GGAGGGAATGATGCACCAAGGACTTATCAT
1 GGAGGGAATGATGCACCAAGGACTTATCAT
11066 GGA
1 GGA
11069 CTTGAAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCACCAAGGACTTATCAT
Found at i:12790 original size:159 final size:159
Alignment explanation
Indices: 11994--13056 Score: 1227
Period size: 158 Copynumber: 6.7 Consensus size: 159
11984 TTCGTATCAA
* *
11994 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTAATCTCACTCCGACATAAGGCTTTTGAGCACTTC
1 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATCTCACTCCGACACAAGGCTTTTGAGCAC-TC
* * * *
12059 -TTGCGCAAAAAACGCTTATGGAATGAGCCTTTCGCTAAGAACGATGTTTTGCACAGAAAAGCAC
65 GTTGCGCAAAAAACGCTTCTAGAATGAGCCTTTCGCTAAGAACGATGTTTTGCACACAAAAGCGC
* *
12123 AAAGTTGAGGCATTGAACTTCGAGGAGAGC
130 AAAGTTGAGGCTTTGGACTTCGAGGAGAGC
* * * * * * * *
12153 TTTGTTTTTCCAAAGGGCTGTCCAACAAGCTCATCTCACTCCGACACACGACTTTTGGGCACTCG
1 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATCTCACTCCGACACAAGGCTTTTGAGCACTCG
* * ** * * * * *
12218 TTGCACAAAAAAACGCATCTCAG-AT-A-AATGTT-GCTAAAAACGATATTTTGCACAGAAATGG
66 TTGCGC-AAAAAACGCTTCT-AGAATGAGCCT-TTCGCTAAGAACGATGTTTTGCACACAAAAGC
*
12279 GCAAAGTTGAGGCTTTGGATTTCGAGGAGAGC
128 GCAAAGTTGAGGCTTTGGACTTCGAGGAGAGC
* * * * * * *
12311 TTTGTTTGTGCACAGGGCTGTCCAACACGCTCATTTCACTCCGACACACGACTTTTGAGAACTCG
1 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATCTCACTCCGACACAAGGCTTTTGAGCACTCG
* * * * * * *
12376 TTGCACAAAAAAACGCATCT-GAGATCAG--TGTT-GCTAAAAACGATATTTTTCACACAAATGC
66 TTGCGC-AAAAAACGCTTCTAGA-ATGAGCCT-TTCGCTAAGAACGATGTTTTGCACACAAAAGC
*
12437 GCAAAGTTGAGGCTTTGGACTTCGAGGAGAGT
128 GCAAAGTTGAGGCTTTGGACTTCGAGGAGAGC
** * * * * *
12469 TTTCCTTGTGCACAAGTCTATCAAATAAGCTCAACTCACTCCGACACAAGGCTTTTGAGCACTCC
1 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATCTCACTCCGACACAAGGCTTTTGAGCACTCG
* * *
12534 TTGCGC-AAAATCGCTTCTAGAATGAGCCTTTCACTAAGAACGATGTTTTGCACACAAAAGTGCA
66 TTGCGCAAAAAACGCTTCTAGAATGAGCCTTTCGCTAAGAACGATGTTTTGCACACAAAAGCGCA
*
12598 AAGTTGAGGCTTTGGACTTCGAGGAGAGT
131 AAGTTGAGGCTTTGGACTTCGAGGAGAGC
* * *
12627 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATTTGACTCCGACACAAGGTTTTTGAGCACTCG
1 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATCTCACTCCGACACAAGGCTTTTGAGCACTCG
* *
12692 TTGTGCAAAAAACGCTTCTAGAATGAGCCTTTCGCTAAGAACGATGTTTTGCACAGAAAAGCGCA
66 TTGCGCAAAAAACGCTTCTAGAATGAGCCTTTCGCTAAGAACGATGTTTTGCACACAAAAGCGCA
* *
12757 AATTTGAGGCTTTGAACTTCGAGGAGAGC
131 AAGTTGAGGCTTTGGACTTCGAGGAGAGC
* * * * * * *
12786 TTTGTTTGTGCACAGGTCTGCCCAACAAGTTCATCTCACTCCGACACATGACTTTTGAGCACTCG
1 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATCTCACTCCGACACAAGGCTTTTGAGCACTCG
* * * * * *
12851 TTGCACAAAAAAACCGCATCTGGAATGAG--TGTT-GCTAAAAACGATATTTTGCACACAAATGC
66 TTGCGC-AAAAAA-CGCTTCTAGAATGAGCCT-TTCGCTAAGAACGATGTTTTGCACACAAAAGC
*
12913 GCAAAGTTGAGGCTTTGGACTTCGAGGAGACC
128 GCAAAGTTGAGGCTTTGGACTTCGAGGAGAGC
* *
12945 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTGATCTCACTCCGACACAAGGCTTTTGAGCCCTTC
1 TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATCTCACTCCGACACAAGGCTTTTGAGCAC-TC
* * *
13010 -TTGTGCAAAAAACGCTTCTGGAATGAGTCTTTCGCTAAGAACGATGT
65 GTTGCGCAAAAAACGCTTCTAGAATGAGCCTTTCGCTAAGAACGATGT
13057 GATACGAATC
Statistics
Matches: 771, Mismatches: 113, Indels: 40
0.83 0.12 0.04
Matches are distributed among these distances:
156 15 0.02
157 18 0.02
158 376 0.49
159 325 0.42
160 23 0.03
161 14 0.02
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (159 bp):
TTTGTTTGTGCACAGGGCTGTCAAATAAGCTCATCTCACTCCGACACAAGGCTTTTGAGCACTCG
TTGCGCAAAAAACGCTTCTAGAATGAGCCTTTCGCTAAGAACGATGTTTTGCACACAAAAGCGCA
AAGTTGAGGCTTTGGACTTCGAGGAGAGC
Found at i:14270 original size:22 final size:23
Alignment explanation
Indices: 14227--14271 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
14217 CGCAAAAAAC
* *
14227 CAAGCTCCGTGCTTATTTTCTCT
1 CAAGCTCCGCGCCTATTTTCTCT
14250 CAAGCTCCGCGCCT-TTTTCTCT
1 CAAGCTCCGCGCCTATTTTCTCT
14272 TATTCATCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.11, C:0.36, G:0.13, T:0.40
Consensus pattern (23 bp):
CAAGCTCCGCGCCTATTTTCTCT
Found at i:15779 original size:13 final size:13
Alignment explanation
Indices: 15734--15780 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
15724 ATCATTTTTA
15734 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
15747 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
15760 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
15774 CTCTTTT
1 CTCTTTT
15781 ATTGATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:15866 original size:21 final size:20
Alignment explanation
Indices: 15842--16043 Score: 136
Period size: 21 Copynumber: 10.1 Consensus size: 20
15832 ACTCTTTGAA
*
15842 TTACTGATCACCTTTTACTC
1 TTACTGATTACCTTTTACTC
15862 TTTACTGA-T---TTTTACTC
1 -TTACTGATTACCTTTTACTC
* * *
15879 TTACTAATTACCACTTTGCTC
1 TTACTGATTACC-TTTTACTC
*
15900 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
*
15921 TTACTGATTACCTTTTACTGA
1 TTACTGATTACCTTTTACT-C
15942 TTACT-A-T--C--TTACTC
1 TTACTGATTACCTTTTACTC
*
15956 TTTACTGATTACCTTCTTACTTT
1 -TTACTGATTACCTT-TTAC-TC
* *
15979 TTACTGATTACTATTTTACTAT
1 TTACTGATTAC-CTTTTACT-C
* *
16001 TTACTGATTACCATCTTGCTC
1 TTACTGATTACC-TTTTACTC
*
16022 TTACTGATTACCCTTTACTC
1 TTACTGATTACCTTTTACTC
16042 TT
1 TT
16044 TATCATTCTT
Statistics
Matches: 142, Mismatches: 20, Indels: 39
0.71 0.10 0.19
Matches are distributed among these distances:
15 10 0.07
16 7 0.05
17 11 0.08
19 2 0.01
20 15 0.11
21 58 0.41
22 36 0.25
23 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.50
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:15943 original size:35 final size:37
Alignment explanation
Indices: 15898--15976 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 37
15888 ACCACTTTGC
*
15898 TCTTACTGATTACTATTTTACTC-TTACTGATTACCT
1 TCTTACTGATTACTATCTTACTCTTTACTGATTACCT
15934 T-TTACTGATTACTATCTTACTCTTTACTGATTACCT
1 TCTTACTGATTACTATCTTACTCTTTACTGATTACCT
15970 TCTTACT
1 TCTTACT
15977 TTTTACTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 20 0.50
36 15 0.38
37 5 0.12
ACGTcount: A:0.22, C:0.23, G:0.05, T:0.51
Consensus pattern (37 bp):
TCTTACTGATTACTATCTTACTCTTTACTGATTACCT
Found at i:15946 original size:79 final size:80
Alignment explanation
Indices: 15842--16012 Score: 206
Period size: 79 Copynumber: 2.1 Consensus size: 80
15832 ACTCTTTGAA
* * * *
15842 TTACTGATCACCTTTTACTCTTTACTGATTTTTACTC-TTACTAATTACCACT-TTGC-TCTTAC
1 TTACTGATTACCTTTTACTCATTACT-A-TCTTACTCTTTACTAATTACC-CTCTTACTTCTTAC
15904 TGATTACTATTTTACT-C
63 TGATTACTATTTTACTAC
* * * *
15921 TTACTGATTACCTTTTACTGATTACTATCTTACTCTTTACTGATTACCTTCTTACTTTTTACTGA
1 TTACTGATTACCTTTTACTCATTACTATCTTACTCTTTACTAATTACCCTCTTACTTCTTACTGA
*
15986 TTACTATTTTACTAT
66 TTACTATTTTACTAC
16001 TTACTGATTACC
1 TTACTGATTACC
16013 ATCTTGCTCT
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
77 8 0.10
78 15 0.19
79 44 0.56
80 12 0.15
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.50
Consensus pattern (80 bp):
TTACTGATTACCTTTTACTCATTACTATCTTACTCTTTACTAATTACCCTCTTACTTCTTACTGA
TTACTATTTTACTAC
Found at i:15959 original size:22 final size:22
Alignment explanation
Indices: 15934--16045 Score: 131
Period size: 22 Copynumber: 5.2 Consensus size: 22
15924 CTGATTACCT
15934 TTTACTGATTACTATCTTACTC
1 TTTACTGATTACTATCTTACTC
*
15956 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATCTTACTC
* *
15978 TTTACTGATTACTATTTTACTA
1 TTTACTGATTACTATCTTACTC
* *
16000 TTTACTGATTACCATCTTGCTC
1 TTTACTGATTACTATCTTACTC
**
16022 -TTACTGATTACCCT-TTACTC
1 TTTACTGATTACTATCTTACTC
16042 TTTA
1 TTTA
16046 TCATTCTTCC
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.06
21 18 0.23
22 53 0.68
23 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTACTGATTACTATCTTACTC
Found at i:15987 original size:44 final size:42
Alignment explanation
Indices: 15932--16045 Score: 147
Period size: 44 Copynumber: 2.6 Consensus size: 42
15922 TACTGATTAC
*
15932 CTTTTACTGATTACTATCTTACTCTTTACTGATTACCTTCTTA
1 CTTTTACTGATTACTAT-TTACTCTTTACTGATTACCATCTTA
* *
15975 CTTTTTACTGATTACTATTTTACTATTTACTGATTACCATCTTG
1 C-TTTTACTGATTACTA-TTTACTCTTTACTGATTACCATCTTA
* **
16019 CTCTTACTGATTACCCTTTACTCTTTA
1 CTTTTACTGATTACTATTTACTCTTTA
16046 TCATTCTTCC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 10 0.16
43 13 0.21
44 38 0.61
45 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (42 bp):
CTTTTACTGATTACTATTTACTCTTTACTGATTACCATCTTA
Found at i:16005 original size:15 final size:14
Alignment explanation
Indices: 15921--15998 Score: 57
Period size: 15 Copynumber: 5.4 Consensus size: 14
15911 TATTTTACTC
*
15921 TTACTGATTACCTT
1 TTACTGATTACTTT
*
15935 TTACTGATTACTATC
1 TTACTGATTACT-TT
** **
15950 TTACTCTTTACTGA
1 TTACTGATTACTTT
**
15964 TTACCTTCTTACTTT
1 TTA-CTGATTACTTT
15979 TTACTGATTACTATT
1 TTACTGATTACT-TT
15994 TTACT
1 TTACT
15999 ATTTACTGAT
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
14 21 0.43
15 28 0.57
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.53
Consensus pattern (14 bp):
TTACTGATTACTTT
Found at i:16039 original size:35 final size:35
Alignment explanation
Indices: 16000--16078 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
15990 TATTTTACTA
*
16000 TTTACTGATTACCA-TCTTGCTCTTACTGATTACCC
1 TTTACTGATTACCATTCTTCCT-TTACTGATTACCC
** * *
16035 TTTACTCTTTATCATTCTTCCTTTACTGATTACTC
1 TTTACTGATTACCATTCTTCCTTTACTGATTACCC
16070 TTTACTGAT
1 TTTACTGAT
16079 CTTTTACCTG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 30 0.83
36 6 0.17
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.49
Consensus pattern (35 bp):
TTTACTGATTACCATTCTTCCTTTACTGATTACCC
Found at i:16072 original size:14 final size:14
Alignment explanation
Indices: 16055--16190 Score: 74
Period size: 14 Copynumber: 10.0 Consensus size: 14
16045 ATCATTCTTC
16055 CTTTACTGATTACT
1 CTTTACTGATTACT
16069 CTTTACTGA-T-CT
1 CTTTACTGATTACT
16081 -TTTACCTGATTACT
1 CTTTA-CTGATTACT
16095 CTTTAC----TACT
1 CTTTACTGATTACT
* **
16105 CTTTGCCATTTTTACT
1 CTTT-AC-TGATTACT
*
16121 TTTTACTGATTACT
1 CTTTACTGATTACT
**
16135 -TTTACCATTTTTACT
1 CTTTA-C-TGATTACT
*
16150 -TTTACTAATTACT
1 CTTTACTGATTACT
** *
16163 CTTTACTTTTTCCT
1 CTTTACTGATTACT
16177 CTTTACTGATTACT
1 CTTTACTGATTACT
16191 ATTTTACTCT
Statistics
Matches: 94, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
10 8 0.09
11 5 0.05
12 6 0.06
13 12 0.13
14 41 0.44
15 15 0.16
16 7 0.07
ACGTcount: A:0.19, C:0.22, G:0.04, T:0.54
Consensus pattern (14 bp):
CTTTACTGATTACT
Found at i:16125 original size:7 final size:7
Alignment explanation
Indices: 16113--16198 Score: 50
Period size: 7 Copynumber: 12.1 Consensus size: 7
16103 CTCTTTGCCA
16113 TTTTTAC
1 TTTTTAC
16120 TTTTTAC
1 TTTTTAC
**
16127 TGATTAC
1 TTTTTAC
16134 -TTTTACC
1 TTTTTA-C
16141 ATTTTTAC
1 -TTTTTAC
16149 -TTTTAC
1 TTTTTAC
**
16155 TAATTAC
1 TTTTTAC
*
16162 TCTTTAC
1 TTTTTAC
*
16169 TTTTTCC
1 TTTTTAC
*
16176 TCTTTAC
1 TTTTTAC
**
16183 TGATTAC
1 TTTTTAC
16190 TATTTTAC
1 T-TTTTAC
16198 T
1 T
16199 CTCTTGAATT
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
6 9 0.16
7 38 0.66
8 6 0.10
9 5 0.09
ACGTcount: A:0.20, C:0.19, G:0.02, T:0.59
Consensus pattern (7 bp):
TTTTTAC
Found at i:16152 original size:28 final size:29
Alignment explanation
Indices: 16101--16190 Score: 114
Period size: 28 Copynumber: 3.1 Consensus size: 29
16091 TACTCTTTAC
*
16101 TACTCTTTGCCATTTTTACTTTTTACTGAT
1 TACTCTTTACCATTTTTAC-TTTTACTGAT
*
16131 TACT-TTTACCATTTTTACTTTTACTAAT
1 TACTCTTTACCATTTTTACTTTTACTGAT
*
16159 TACTCTTTA-C-TTTTTCCTCTTTACTGAT
1 TACTCTTTACCATTTTTACT-TTTACTGAT
16187 TACT
1 TACT
16191 ATTTTACTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.13
28 26 0.48
29 17 0.31
30 4 0.07
ACGTcount: A:0.19, C:0.21, G:0.03, T:0.57
Consensus pattern (29 bp):
TACTCTTTACCATTTTTACTTTTACTGAT
Found at i:16220 original size:26 final size:26
Alignment explanation
Indices: 16185--16279 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
16175 CTCTTTACTG
16185 ATTACTATTTT-ACTCTCTTGAATTTA
1 ATTACTATTTTCACTCT-TTGAATTTA
16211 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTTCACTCTTTGAATTTA
* *
16237 ATCACCATTTGTCATTTTACTCTTTGAATTTA
1 ATTACTATTT-TC-----ACTCTTTGAATTTA
*
16269 ATTACCATTTT
1 ATTACTATTTT
16280 ACCATTTTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 28 0.47
27 7 0.12
31 1 0.02
32 23 0.39
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTACTATTTTCACTCTTTGAATTTA
Found at i:16286 original size:33 final size:33
Alignment explanation
Indices: 16212--16294 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
16202 TTGAATTTAA
*
16212 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACCATTTT-ACTCTTTGAATTTAATCACCATT
*
16246 TGT--CATTTTACTCTTTGAATTTAATTACCATT
1 T-TACCATTTTACTCTTTGAATTTAATCACCATT
16278 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
16295 ACTGATTACT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 1 0.02
32 23 0.52
33 18 0.41
34 1 0.02
35 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.53
Consensus pattern (33 bp):
TTACCATTTTACTCTTTGAATTTAATCACCATT
Found at i:16317 original size:14 final size:14
Alignment explanation
Indices: 16284--16317 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16274 CATTTTACCA
16284 TTTTACTCTTTACT
1 TTTTACTCTTTACT
**
16298 GATTACTCTTTACT
1 TTTTACTCTTTACT
16312 TTTTAC
1 TTTTAC
16318 CATTTTTATT
Statistics
Matches: 16, Mismatches: 4, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (14 bp):
TTTTACTCTTTACT
Found at i:26851 original size:16 final size:16
Alignment explanation
Indices: 26818--26852 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
26808 AAGGTCAAAA
* *
26818 ATTGTTATTATTTTTT
1 ATTGTTATTACTTATT
26834 ATTGTTATTACTTATT
1 ATTGTTATTACTTATT
26850 ATT
1 ATT
26853 ATCATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (16 bp):
ATTGTTATTACTTATT
Found at i:29488 original size:18 final size:18
Alignment explanation
Indices: 29451--29484 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29441 TGCAAAATGC
*
29451 AAAGCGAAAGAACAAAGA
1 AAAGCGAAACAACAAAGA
29469 AAAGC-AAACAACAAAG
1 AAAGCGAAACAACAAAG
29485 GAAATTAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.15, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAGCGAAACAACAAAGA
Found at i:30873 original size:21 final size:21
Alignment explanation
Indices: 30843--31014 Score: 96
Period size: 22 Copynumber: 8.4 Consensus size: 21
30833 TTTACTGATT
*
30843 TTTACTCTTACTAATTACCAC
1 TTTACTCTTACTGATTACCAC
* * * *
30864 TTTGCTCTTACGGATTACTAT
1 TTTACTCTTACTGATTACCAC
30885 TTTACTCTTACTGATTA-C-C
1 TTTACTCTTACTGATTACCAC
*
30904 --T--T-TTACTGATTACTATC
1 TTTACTCTTACTGATTACCA-C
*
30921 -TTACTCTTTACTAATTACCA-
1 TTTACTC-TTACTGATTACCAC
* * *
30941 TCTTACTTTTTACTGATTACTAT
1 T-TTAC-TCTTACTGATTACCAC
*
30964 TTTACTATTTACTGATTACCA-
1 TTTACT-CTTACTGATTACCAC
*
30985 TCTTGCTCTTACTGATTACC-C
1 T-TTACTCTTACTGATTACCAC
*
31006 GTTACTCTT
1 TTTACTCTT
31015 TATCATTCTT
Statistics
Matches: 116, Mismatches: 20, Indels: 31
0.69 0.12 0.19
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
17 2 0.02
18 1 0.01
20 8 0.07
21 45 0.39
22 47 0.41
23 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (21 bp):
TTTACTCTTACTGATTACCAC
Found at i:30915 original size:35 final size:36
Alignment explanation
Indices: 30871--30939 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
30861 CACTTTGCTC
* *
30871 TTACGGATTACTATTTTACTC-TTACTGATTACCTT
1 TTACGGATTACTATCTTACTCTTTACTAATTACCTT
*
30906 TTACTGATTACTATCTTACTCTTTACTAATTACC
1 TTACGGATTACTATCTTACTCTTTACTAATTACC
30940 ATCTTACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.48
Consensus pattern (36 bp):
TTACGGATTACTATCTTACTCTTTACTAATTACCTT
Found at i:30930 original size:22 final size:22
Alignment explanation
Indices: 30905--31016 Score: 131
Period size: 22 Copynumber: 5.2 Consensus size: 22
30895 CTGATTACCT
*
30905 TTTACTGATTACTATCTTACTC
1 TTTACTGATTACCATCTTACTC
* *
30927 TTTACTAATTACCATCTTACTT
1 TTTACTGATTACCATCTTACTC
* * *
30949 TTTACTGATTACTATTTTACTA
1 TTTACTGATTACCATCTTACTC
*
30971 TTTACTGATTACCATCTTGCTC
1 TTTACTGATTACCATCTTACTC
30993 -TTACTGATTACC--CGTTACTC
1 TTTACTGATTACCATC-TTACTC
31013 TTTA
1 TTTA
31017 TCATTCTTCC
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 5 0.07
21 15 0.20
22 55 0.72
ACGTcount: A:0.23, C:0.22, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTACTGATTACCATCTTACTC
Found at i:30957 original size:44 final size:43
Alignment explanation
Indices: 30903--31003 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 43
30893 TACTGATTAC
*
30903 CTTTTACTGATTACTATCTTACTCTTTACTAATTACCATCTTA
1 CTTTTACTGATTACTATCTTACTATTTACTAATTACCATCTTA
* * *
30946 CTTTTTACTGATTACTATTTTACTATTTACTGATTACCATCTTG
1 C-TTTTACTGATTACTATCTTACTATTTACTAATTACCATCTTA
*
30990 CTCTTACTGATTAC
1 CTTTTACTGATTAC
31004 CCGTTACTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
43 13 0.25
44 39 0.75
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.50
Consensus pattern (43 bp):
CTTTTACTGATTACTATCTTACTATTTACTAATTACCATCTTA
Found at i:30975 original size:15 final size:15
Alignment explanation
Indices: 30904--30976 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
30894 ACTGATTACC
30904 TTTTACTGA-TTACTA
1 TTTTACT-ATTTACTA
* *
30919 TCTTACTCTTTACTA
1 TTTTACTATTTACTA
* *
30934 -ATTACCATCTTACT-
1 TTTTACTAT-TTACTA
30948 TTTTACTGA-TTACTA
1 TTTTACT-ATTTACTA
30963 TTTTACTATTTACT
1 TTTTACTATTTACT
30977 GATTACCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 11 0.24
15 33 0.73
16 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTTACTATTTACTA
Found at i:31011 original size:35 final size:35
Alignment explanation
Indices: 30972--31038 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
30962 ATTTTACTAT
* *
30972 TTACTGATTACCA-TCTTGCTCTTACTGATTACCCG
1 TTACTCATTACCATTCTTCCT-TTACTGATTACCCG
* *
31007 TTACTCTTTATCATTCTTCCTTTACTGATTAC
1 TTACTCATTACCATTCTTCCTTTACTGATTAC
31039 TTTTACCTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 21 0.78
36 6 0.22
ACGTcount: A:0.19, C:0.27, G:0.07, T:0.46
Consensus pattern (35 bp):
TTACTCATTACCATTCTTCCTTTACTGATTACCCG
Found at i:31048 original size:14 final size:13
Alignment explanation
Indices: 31027--31149 Score: 54
Period size: 14 Copynumber: 9.0 Consensus size: 13
31017 TCATTCTTCC
31027 TTTACTGATTACT
1 TTTACTGATTACT
*
31040 TTTACCTGATTACCC
1 TTTA-CTGATTA-CT
*
31055 TTTACT-ACT-CT
1 TTTACTGATTACT
** **
31066 TTGCCATTTTTACTT
1 TTTAC-TGATTAC-T
*
31081 TTTATTGATTACT
1 TTTACTGATTACT
**
31094 TTTACCATTTTTACT
1 TTTA-C-TGATTACT
31109 TTTACTGATTACT
1 TTTACTGATTACT
*
31122 CTTTACT-ATTTCCT
1 -TTTACTGA-TTACT
31136 CTTTACTGATTACT
1 -TTTACTGATTACT
31150 ATTTTACTCT
Statistics
Matches: 80, Mismatches: 19, Indels: 21
0.67 0.16 0.17
Matches are distributed among these distances:
11 4 0.05
12 1 0.01
13 19 0.24
14 37 0.46
15 19 0.24
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (13 bp):
TTTACTGATTACT
Found at i:31056 original size:28 final size:29
Alignment explanation
Indices: 31025--31149 Score: 86
Period size: 28 Copynumber: 4.5 Consensus size: 29
31015 TATCATTCTT
*
31025 CCTTTACTGATTACTTTTACC-TGATTAC
1 CCTTTACTGATTACTTTTACCATTATTAC
* * *
31053 CCTTTACT-ACT-C-TTTGCCATTTTTAC
1 CCTTTACTGATTACTTTTACCATTATTAC
** * *
31079 TTTTTATTGATTACTTTTACCATTTTTA-
1 CCTTTACTGATTACTTTTACCATTATTAC
* *
31107 CTTTTACTGATTACTCTTTA-C--TATTTC
1 CCTTTACTGATTACT-TTTACCATTATTAC
31134 CTCTTTACTGATTACT
1 C-CTTTACTGATTACT
31150 ATTTTACTCT
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
25 5 0.07
26 14 0.18
27 5 0.07
28 36 0.47
29 16 0.21
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.54
Consensus pattern (29 bp):
CCTTTACTGATTACTTTTACCATTATTAC
Found at i:31105 original size:29 final size:29
Alignment explanation
Indices: 31060--31149 Score: 105
Period size: 28 Copynumber: 3.1 Consensus size: 29
31050 TACCCTTTAC
* *
31060 TACTCTTTGCCATTTTTACTTTTTATTGAT
1 TACTCTTTACCATTTTTAC-TTTTACTGAT
31090 TACT-TTTACCATTTTTACTTTTACTGAT
1 TACTCTTTACCATTTTTACTTTTACTGAT
* *
31118 TACTCTTTA-C-TATTTCCTCTTTACTGAT
1 TACTCTTTACCATTTTTACT-TTTACTGAT
31146 TACT
1 TACT
31150 ATTTTACTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.11
28 27 0.50
29 17 0.31
30 4 0.07
ACGTcount: A:0.19, C:0.20, G:0.04, T:0.57
Consensus pattern (29 bp):
TACTCTTTACCATTTTTACTTTTACTGAT
Found at i:31179 original size:26 final size:26
Alignment explanation
Indices: 31144--31238 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
31134 CTCTTTACTG
31144 ATTACTATTTT-ACTCTCTTGAATTTA
1 ATTACTATTTTCACTCT-TTGAATTTA
31170 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTTCACTCTTTGAATTTA
* *
31196 ATCACCATTTGTCATTTTACTCTTTGAATTTA
1 ATTACTATTT-TC-----ACTCTTTGAATTTA
*
31228 ATTACCATTTT
1 ATTACTATTTT
31239 ACCATTTTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 28 0.47
27 7 0.12
31 1 0.02
32 23 0.39
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTACTATTTTCACTCTTTGAATTTA
Found at i:31245 original size:33 final size:33
Alignment explanation
Indices: 31171--31253 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
31161 TTGAATTTAA
*
31171 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACCATTTT-ACTCTTTGAATTTAATCACCATT
*
31205 TGT--CATTTTACTCTTTGAATTTAATTACCATT
1 T-TACCATTTTACTCTTTGAATTTAATCACCATT
31237 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
31254 ATTGATTACT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 1 0.02
32 23 0.52
33 18 0.41
34 1 0.02
35 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.53
Consensus pattern (33 bp):
TTACCATTTTACTCTTTGAATTTAATCACCATT
Found at i:41097 original size:10 final size:10
Alignment explanation
Indices: 41082--41106 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41072 AGCAACTGGT
41082 ATGAACCGGC
1 ATGAACCGGC
41092 ATGAACCGGC
1 ATGAACCGGC
41102 ATGAA
1 ATGAA
41107 GAAACAGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.24, G:0.28, T:0.12
Consensus pattern (10 bp):
ATGAACCGGC
Found at i:42951 original size:11 final size:10
Alignment explanation
Indices: 42934--42969 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
42924 TTAATAAAAG
42934 AAAAAAATAA
1 AAAAAAATAA
42944 ATAAAAAATAA
1 A-AAAAAATAA
*
42955 AATAAAATAA
1 AAAAAAATAA
42965 AAAAA
1 AAAAA
42970 GAGAGGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:42958 original size:16 final size:16
Alignment explanation
Indices: 42921--42969 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
42911 ACTCTTCAAT
*
42921 AAATTAATAAAAGAAAA
1 AAATAAATAAAA-AAAA
*
42938 AAATAAATAAAAAATA
1 AAATAAATAAAAAAAA
42954 AAATAAAATAAAAAAA
1 AAAT-AAATAAAAAAA
42970 GAGAGGAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (16 bp):
AAATAAATAAAAAAAA
Found at i:43565 original size:49 final size:48
Alignment explanation
Indices: 43501--43929 Score: 402
Period size: 49 Copynumber: 8.8 Consensus size: 48
43491 TCTCAAATTT
*
43501 TGTTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACC
1 TGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTT-ATTTTACC
*
43550 TGTTATTCCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACC
1 TGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTT-ATTTTACC
* **
43599 TGTTATTTCCCAAAATGCCCTTCCTGGGTGGAAGGCATTTACTTTTACC
1 TGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA-TTTTACC
* * * * *
43648 TGCTACTTTCCAAAAATACCCTTCTCGGATGGAAGGCATTTACTTTTACC
1 TGTTA-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA-TTTTACC
* * * * *
43698 TGTT-TTTCCGAAAATGCCCTTCCCGAACGGAAGACACTAATCTTTACC
1 TGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTAT-TTTACC
*
43746 TGTT-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACTTGC
1 TGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTAC---C
* * *
43796 TATTTTTTCCAAAAATGCCCTTCCCGGACGGAA-G-ATGCTTATTTTTACCC
1 TGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCAT--TTA-TTTTA-CC
** * * * * * *
43846 ACTT-TTTCCCAAAGTGCCTTTCCCAGACGGAAGGCACTAACTTTTACT
1 TGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA-TTTTACC
* * * *
43894 TGCTT-TGTCCTAAAACGCCCTTCCCGGACAGAAGGC
1 TG-TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
43930 GTTAGTTTTG
Statistics
Matches: 319, Mismatches: 47, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
47 6 0.02
48 73 0.23
49 152 0.48
50 51 0.16
51 31 0.10
52 5 0.02
53 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (48 bp):
TGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTACC
Found at i:43964 original size:98 final size:97
Alignment explanation
Indices: 43748--43978 Score: 236
Period size: 97 Copynumber: 2.4 Consensus size: 97
43738 TCTTTACCTG
* * * *
43748 TTTTTCCCAAAATGCCC-TTCCCGGACGGAAGGCACTTATTTTACTTGCTATTTTTTCCAAAAAT
1 TTTTTCCCAAAAT-CCCTTTCCCAGACGGAAGGCACTAATTTTACTTGC--TTTTGTCCAAAAAC
* *
43812 GCCCTTCCCGGACGGAAGATGCTTATTTTTACCCAC
63 GCCCTTCCCGGACAGAAGA-GCTTAGTTTTACCCAC
* * *
43848 TTTTTCCCAAAGTGCCTTTCCCAGACGGAAGGCACTAACTTTTACTTGC-TTTGTCCTAAAACGC
1 TTTTTCCCAAAATCCCTTTCCCAGACGGAAGGCACTAA-TTTTACTTGCTTTTGTCCAAAAACGC
* * *
43912 CCTTCCCGGACAGAAG-GCGTTAGTTTTGCTCGC
65 CCTTCCCGGACAGAAGAGC-TTAGTTTTACCCAC
** *
43945 TTTTTCTTAAAATACCCTTT-CCAGACGAAAGGCA
1 TTTTTCCCAAAAT-CCCTTTCCCAGACGGAAGGCA
43979 AGTTCACTTT
Statistics
Matches: 110, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
96 2 0.02
97 33 0.30
98 32 0.29
99 2 0.02
100 31 0.28
101 10 0.09
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.32
Consensus pattern (97 bp):
TTTTTCCCAAAATCCCTTTCCCAGACGGAAGGCACTAATTTTACTTGCTTTTGTCCAAAAACGCC
CTTCCCGGACAGAAGAGCTTAGTTTTACCCAC
Found at i:46210 original size:21 final size:21
Alignment explanation
Indices: 46186--46238 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
46176 AGCGCTAGGC
* *
46186 GCCCATGTGGTATGCTTGGCG
1 GCCCATGTGGTATGCCTCGCG
*
46207 GCCCATGTGGTTTGCCTCGCG
1 GCCCATGTGGTATGCCTCGCG
*
46228 CCCCATGTGGT
1 GCCCATGTGGT
46239 CCAGTGTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.08, C:0.30, G:0.34, T:0.28
Consensus pattern (21 bp):
GCCCATGTGGTATGCCTCGCG
Found at i:50555 original size:18 final size:18
Alignment explanation
Indices: 50532--50566 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
50522 AAATTCAAAA
50532 AAATGAAAATAAAACAAT
1 AAATGAAAATAAAACAAT
50550 AAATGAAAATAAAACAA
1 AAATGAAAATAAAACAA
50567 CAATCTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (18 bp):
AAATGAAAATAAAACAAT
Found at i:50869 original size:33 final size:33
Alignment explanation
Indices: 50801--50869 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
50791 GGGGTTCAGT
*** **
50801 AGAGAGAAGAAATATGGAGAAGAATTTTAGTAG
1 AGAGAGAAGAAATATGGAGAAGAATGAGAAAAG
50834 AGAGAGAAGAAATATGGAGAAG-ATGAGACAAAG
1 AGAGAGAAGAAATATGGAGAAGAATGAGA-AAAG
50867 AGA
1 AGA
50870 TTTAGGGGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.52, C:0.01, G:0.32, T:0.14
Consensus pattern (33 bp):
AGAGAGAAGAAATATGGAGAAGAATGAGAAAAG
Found at i:52472 original size:42 final size:41
Alignment explanation
Indices: 52402--52487 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 41
52392 CCATGTCATG
*
52402 AAATTCAAACCCTAACAAACAATATAAACCCTAAGTGAGAT
1 AAATTCAAACCCTAAAAAACAATATAAACCCTAAGTGAGAT
*
52443 AAATT-AAACCCTCAAAAAAACACAT-TAAACCCTAGGTGAGAT
1 AAATTCAAACCCT--AAAAAACA-ATATAAACCCTAAGTGAGAT
52485 AAA
1 AAA
52488 AAAGGATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
40 7 0.17
41 5 0.12
42 26 0.65
43 2 0.05
ACGTcount: A:0.52, C:0.21, G:0.08, T:0.19
Consensus pattern (41 bp):
AAATTCAAACCCTAAAAAACAATATAAACCCTAAGTGAGAT
Found at i:53488 original size:20 final size:20
Alignment explanation
Indices: 53435--53490 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
53425 TAATATTAAG
* * *
53435 TTTTTCAATAACATTTTAAA
1 TTTTTTAATAACCTTATAAA
* * *
53455 TTTATTAGTCACCTTATAAA
1 TTTTTTAATAACCTTATAAA
53475 TTTTTTAATAACCTTA
1 TTTTTTAATAACCTTA
53491 AAACCATTCT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTTTAATAACCTTATAAA
Found at i:53659 original size:21 final size:21
Alignment explanation
Indices: 53635--53692 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
53625 TTTACCTAGC
*
53635 CTTATTAAGATTTTTAGTAA-T
1 CTTATTAAGATTTTTAG-AAGG
** *
53656 CTTATTGTGAATTTTAGAAGG
1 CTTATTAAGATTTTTAGAAGG
*
53677 CTTATTAAGCTTTTTA
1 CTTATTAAGATTTTTA
53693 ATAACTTTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (21 bp):
CTTATTAAGATTTTTAGAAGG
Found at i:53748 original size:19 final size:19
Alignment explanation
Indices: 53713--53752 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
53703 AGGTGTTTTC
*
53713 AGTAATCTTAGATATTTGT
1 AGTAACCTTAGATATTTGT
53732 AGTAACCTT-GATAATTTGT
1 AGTAACCTTAGAT-ATTTGT
53751 AG
1 AG
53753 CAATGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (19 bp):
AGTAACCTTAGATATTTGT
Found at i:53781 original size:20 final size:19
Alignment explanation
Indices: 53726--53781 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
53716 AATCTTAGAT
*
53726 ATTTGTAGTAACCTTGA-TA
1 ATTTGTAGTAA-CTTTATTA
*
53745 ATTTGTAGCAA-TGTTATTA
1 ATTTGTAGTAACT-TTATTA
53764 ATATTGTAGTAACTTTAT
1 AT-TTGTAGTAACTTTAT
53782 AAAACTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.03
18 2 0.07
19 14 0.47
20 12 0.40
21 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (19 bp):
ATTTGTAGTAACTTTATTA
Found at i:53861 original size:21 final size:22
Alignment explanation
Indices: 53830--53877 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
53820 TCTTATCAAC
53830 TTTTAACTAACATTATAAAGTT
1 TTTTAACTAACATTATAAAGTT
* * *
53852 TTTTAA-TAACCTTATTATGTT
1 TTTTAACTAACATTATAAAGTT
53873 TTTTA
1 TTTTA
53878 GGAACCGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTTAACTAACATTATAAAGTT
Found at i:53883 original size:21 final size:21
Alignment explanation
Indices: 53847--53899 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
53837 TAACATTATA
* *
53847 AAGTTTTTTAATAACCTTATT
1 AAGTTTTTTAAGAACCGTATT
* *
53868 ATGTTTTTTAGGAACCGTATT
1 AAGTTTTTTAAGAACCGTATT
*
53889 AAGGTTTTTAA
1 AAGTTTTTTAA
53900 TATATAACCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (21 bp):
AAGTTTTTTAAGAACCGTATT
Found at i:62305 original size:2 final size:2
Alignment explanation
Indices: 62298--62324 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
62288 ATTCCACAAC
62298 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
62325 AAACAGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63325 original size:21 final size:21
Alignment explanation
Indices: 63262--63318 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 21
63252 TTTTTCCTAT
* *
63262 TGCTCATTCTTTTTCTTCTGCTGT
1 TGCTCACTCTTTTTCTTCT--T-C
63286 TGCTCACTCTTTTTCTTCTTC
1 TGCTCACTCTTTTTCTTCTTC
63307 TGCT-ACTCTTTT
1 TGCTCACTCTTTT
63319 GTTTTCTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.26
21 4 0.13
22 1 0.03
24 18 0.58
ACGTcount: A:0.05, C:0.28, G:0.09, T:0.58
Consensus pattern (21 bp):
TGCTCACTCTTTTTCTTCTTC
Found at i:64279 original size:12 final size:12
Alignment explanation
Indices: 64262--64287 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64252 TCCCCTTTGT
64262 AGTCATTTCCCA
1 AGTCATTTCCCA
64274 AGTCATTTCCCA
1 AGTCATTTCCCA
64286 AG
1 AG
64288 GATTTGGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (12 bp):
AGTCATTTCCCA
Found at i:67353 original size:49 final size:50
Alignment explanation
Indices: 67296--67392 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
67286 CTTGACAACA
67296 CTAAGCTTTCCCCAAGCTCA-AACAAGTGCTCCCCGCACTAATCACAAAC
1 CTAAGCTTTCCCCAAGCTCAGAACAAGTGCTCCCCGCACTAATCACAAAC
* * *
67345 CTAAGCTTTCCTCAAGCTTAGAACAAGTGCTCCCCGCACTAATTACAA
1 CTAAGCTTTCCCCAAGCTCAGAACAAGTGCTCCCCGCACTAATCACAA
67393 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 18 0.41
50 26 0.59
ACGTcount: A:0.32, C:0.35, G:0.11, T:0.22
Consensus pattern (50 bp):
CTAAGCTTTCCCCAAGCTCAGAACAAGTGCTCCCCGCACTAATCACAAAC
Found at i:68532 original size:19 final size:20
Alignment explanation
Indices: 68483--68532 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
68473 TTATAGGTAA
*
68483 CAGAGC-AAACTATAAGCAT
1 CAGAGCTAAACTAAAAGCAT
* *
68502 TAGAGCTATAAATAAAAGCAT
1 CAGAGCTA-AACTAAAAGCAT
68523 CAGAGCTAAA
1 CAGAGCTAAA
68533 AGATTTTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 3 0.12
21 17 0.68
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (20 bp):
CAGAGCTAAACTAAAAGCAT
Done.