Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007910.1 Hibiscus syriacus cultivar Beakdansim tig00110306_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 704475
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:5978 original size:2 final size:2
Alignment explanation
Indices: 5971--6000 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5961 TTTTAAATAA
5971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6001 GTTGATACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11744 original size:22 final size:22
Alignment explanation
Indices: 11719--11773 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
11709 AGATCTCCAT
11719 TTTGTGAAGTGGCCTTCATGCC
1 TTTGTGAAGTGGCCTTCATGCC
11741 TTTGTGAA-TGGGCCTTCATGCC
1 TTTGTGAAGT-GGCCTTCATGCC
11763 TTTGTGAAGTG
1 TTTGTGAAGTG
11774 TCTTCTTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.15, C:0.18, G:0.29, T:0.38
Consensus pattern (22 bp):
TTTGTGAAGTGGCCTTCATGCC
Found at i:13741 original size:131 final size:131
Alignment explanation
Indices: 13506--13743 Score: 361
Period size: 131 Copynumber: 1.8 Consensus size: 131
13496 ATAATTTTAA
* * *
13506 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCGAATCATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
* *
13571 ATCATTTATTACTCCAATCAAAATGAATAGATATCACTATTCCGTCTTAAAAATCAATATTGATT
66 ACCATTTATTACTCCAACCAAAATGAATAGATATCACTATTCCGTCTTAAAAATCAATATTGATT
13636 C
131 C
* * *
13637 GAGAGAAAACGGTAATATCGAATCATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCGAATCATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
* * *
13702 GCCATTTATTACTCCAACCGAAATGAA-AGGATATTACTATTC
66 ACCATTTATTACTCCAACCAAAATGAATA-GATATCACTATTC
13744 TCAATATCGA
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
130 1 0.01
131 94 0.99
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCGAATCATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
ACCATTTATTACTCCAACCAAAATGAATAGATATCACTATTCCGTCTTAAAAATCAATATTGATT
C
Found at i:16075 original size:21 final size:20
Alignment explanation
Indices: 16012--16078 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
16002 TAATGATATC
16012 ATTTTAATAA-AT-ATATTA-
1 ATTTTAA-AATATAATATTAT
*
16030 ATTATTAAAATATATTTATTAAT
1 ATT-TTAAAATATA-ATATT-AT
16053 ATTTTAACAATATAATATTAT
1 ATTTTAA-AATATAATATTAT
16074 ATTTT
1 ATTTT
16079 TAGTATTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 5 0.12
19 6 0.15
21 11 0.28
22 9 0.22
23 9 0.22
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTTAAAATATAATATTAT
Found at i:16094 original size:55 final size:50
Alignment explanation
Indices: 16035--16175 Score: 128
Period size: 47 Copynumber: 2.8 Consensus size: 50
16025 TATTAATTAT
16035 TAAAATATATTTATTAATATTTTAACAATATAATATTATATTTTTAGTATTATAA
1 TAAAATA-ATTTATTAATATTTTAA-AATATAATATTATATTTTTA-T-TT-TAA
** * *
16090 TAAAATAATAAATT-ATATTGTAAAA-AT-ATATAATATTTTTATTTTAA
1 TAAAATAATTTATTAATATTTTAAAATATAATATTATATTTTTATTTTAA
** *
16137 TATTATAATTT-TTAATATTATTAAAATAATATTATTATA
1 TAAAATAATTTATTAATATT-TTAAAAT-ATAATATTATA
16176 AATAATTATA
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
46 2 0.03
47 15 0.21
48 7 0.10
49 1 0.01
50 15 0.21
51 8 0.11
52 2 0.03
53 8 0.11
54 5 0.07
55 7 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (50 bp):
TAAAATAATTTATTAATATTTTAAAATATAATATTATATTTTTATTTTAA
Found at i:16166 original size:14 final size:15
Alignment explanation
Indices: 16149--16181 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
16139 TTATAATTTT
16149 TAATATTATTA-AAA
1 TAATATTATTATAAA
16163 TAATATTATTATAAA
1 TAATATTATTATAAA
16178 TAAT
1 TAAT
16182 TATAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATTATTATAAA
Found at i:16295 original size:14 final size:15
Alignment explanation
Indices: 16268--16296 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16258 TTTCAATAAT
16268 AATATTGATATAAAC
1 AATATTGATATAAAC
16283 AATATTGA-ATAAAC
1 AATATTGATATAAAC
16297 TATTATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (15 bp):
AATATTGATATAAAC
Found at i:18584 original size:57 final size:57
Alignment explanation
Indices: 18494--18620 Score: 209
Period size: 57 Copynumber: 2.2 Consensus size: 57
18484 TATGTAAAGG
*
18494 ATCCTAAATACCCCATTTGGTTCAATTGGACTTAAAATCCTGATAATTAAATTCATA
1 ATCCTGAATACCCCATTTGGTTCAATTGGACTTAAAATCCTGATAATTAAATTCATA
* *
18551 ATCCTGAATACCCCATTTGGTTCAATTGTACTTAAAATCCTTATAATTAAATTCATA
1 ATCCTGAATACCCCATTTGGTTCAATTGGACTTAAAATCCTGATAATTAAATTCATA
* *
18608 AGCATGAATACCC
1 ATCCTGAATACCC
18621 TTGATTGTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (57 bp):
ATCCTGAATACCCCATTTGGTTCAATTGGACTTAAAATCCTGATAATTAAATTCATA
Found at i:20561 original size:9 final size:9
Alignment explanation
Indices: 20547--20584 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
20537 CCAGGTCAAA
*
20547 AATATTAAT
1 AATATTATT
20556 AATATTATT
1 AATATTATT
20565 AA-ATTATT
1 AATATTATT
*
20573 ATTATTATT
1 AATATTATT
20582 AAT
1 AAT
20585 TTACATGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AATATTATT
Found at i:21891 original size:13 final size:13
Alignment explanation
Indices: 21873--21902 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21863 ATATTTTGTT
21873 GCATTATGTGTAA
1 GCATTATGTGTAA
*
21886 GCATTATGTGTAG
1 GCATTATGTGTAA
21899 GCAT
1 GCAT
21903 ATAGAACACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (13 bp):
GCATTATGTGTAA
Found at i:28121 original size:19 final size:18
Alignment explanation
Indices: 28106--28158 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
28096 GGAAAAAAAG
28106 GAAAAATGAAAGAAAATAA
1 GAAAAAT-AAAGAAAATAA
*
28125 AACAAAATAAAGAAAATAAA
1 GA-AAAATAAAGAAAAT-AA
28145 GAAAAATAAAGAAA
1 GAAAAATAAAGAAA
28159 GAATAAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.09
Consensus pattern (18 bp):
GAAAAATAAAGAAAATAA
Found at i:28142 original size:9 final size:9
Alignment explanation
Indices: 28108--28158 Score: 66
Period size: 10 Copynumber: 5.3 Consensus size: 9
28098 AAAAAAAGGA
28108 AAAATGAAAG
1 AAAAT-AAAG
*
28118 AAAATAAAAC
1 AAAAT-AAAG
28128 AAAATAAAG
1 AAAATAAAG
28137 AAAATAAAG
1 AAAATAAAG
28146 AAAAATAAAG
1 -AAAATAAAG
28156 AAA
1 AAA
28159 GAATAAGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
9 15 0.41
10 22 0.59
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAATAAAG
Found at i:29499 original size:51 final size:51
Alignment explanation
Indices: 29328--29519 Score: 215
Period size: 52 Copynumber: 3.7 Consensus size: 51
29318 CCATATTATC
* * *
29328 CATGT-GGGTATCTTGAAGGCTCACATCAGCATGAAAATATAGAAGTAATC
1 CATGTGGGGAATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATT
* ** * *
29378 CAAGTGGGGGAATCTTGAAGGCTCACATCAATATGAAAAAGACATAAGTAATT
1 CATGT-GGGGAATCTTGAAGGCTCACATCAGCATG-AAAAGATAGAAGTAATT
* * *
29431 CATATGGGGAATCTTGAAGGGTCACATCAGCATGAAGAGATAGAAGTAATT
1 CATGTGGGGAATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATT
* * * * *
29482 TATGTGGGGCATCTTGAAGGCTTACACCAGCATAAAAA
1 CATGTGGGGAATCTTGAAGGCTCACATCAGCATGAAAA
29520 TGTTAGGACA
Statistics
Matches: 115, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
50 4 0.03
51 44 0.38
52 51 0.44
53 16 0.14
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (51 bp):
CATGTGGGGAATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATT
Found at i:31056 original size:43 final size:43
Alignment explanation
Indices: 30992--31248 Score: 362
Period size: 43 Copynumber: 6.0 Consensus size: 43
30982 ATAAGAAACT
**
30992 AAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAAAGTGATATGTAGGGGTTCCTTGATGAC
*
31035 AAGCTTGAGGGACCAAAGTGATATATAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAAAGTGATATGTAGGGGTTCCTTGATGAC
* *
31078 AAGCTTGAGGGACCATAGTGATATGTAAGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAAAGTGATATGTAGGGGTTCCTTGATGAC
* **
31121 AAGCTTAAGGGACCATCGTGATATGTA--GGTTCCTTGATGAC
1 AAGCTTGAGGGACCAAAGTGATATGTAGGGGTTCCTTGATGAC
*
31162 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGA-
1 AAGCTTGAGGGACCAAAGTGATATGTAGGGGTTCCTTGATGAC
* *
31204 ACA-CTTGAGGGACTAACA-TGATATGTAGGGGTTCCTTGGTGAC
1 A-AGCTTGAGGGACCAA-AGTGATATGTAGGGGTTCCTTGATGAC
31247 AA
1 AA
31249 CTAAAAAACT
Statistics
Matches: 196, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
41 39 0.20
42 37 0.19
43 120 0.61
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (43 bp):
AAGCTTGAGGGACCAAAGTGATATGTAGGGGTTCCTTGATGAC
Found at i:31287 original size:127 final size:127
Alignment explanation
Indices: 31003--31257 Score: 322
Period size: 127 Copynumber: 2.0 Consensus size: 127
30993 AGCTTGAGGG
* *
31003 ACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAGGGACCAAAGTGATATATAGGGGTT
1 ACCAGCGTCATATGTA--GGTTCCTTGATGACAAGCTTGAGGGACCAAAGTGATATATAGGGGTT
* ***
31068 CCTTGATGACAAGCTTGAGGGACCATAGTGATATGTAAGGGTTCCTTGATGACAAGCTTAAGGG
64 CCTTGATGACAAGCTTGAGGGACCATAATGATATGTAAGGGTTCCTTGATGACAAGCTTAAAAA
* * * *
31132 ACCATCGTGATATGTAGGTTCCTTGATGACAAGCTTGAGGGACCAACGTGATATGTAGGGGTTCC
1 ACCAGCGTCATATGTAGGTTCCTTGATGACAAGCTTGAGGGACCAAAGTGATATATAGGGGTTCC
* * *
31197 TTGATGA-ACA-CTTGAGGGACTA-ACATGATATGTAGGGGTTCCTTGGTGACAA-C-TAAAAA
66 TTGATGACA-AGCTTGAGGGACCATA-ATGATATGTAAGGGTTCCTTGATGACAAGCTTAAAAA
31256 AC
1 AC
31258 TGAGCTTCAT
Statistics
Matches: 115, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
124 5 0.04
125 2 0.02
126 37 0.32
127 55 0.48
129 16 0.14
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (127 bp):
ACCAGCGTCATATGTAGGTTCCTTGATGACAAGCTTGAGGGACCAAAGTGATATATAGGGGTTCC
TTGATGACAAGCTTGAGGGACCATAATGATATGTAAGGGTTCCTTGATGACAAGCTTAAAAA
Found at i:31341 original size:22 final size:22
Alignment explanation
Indices: 31304--31383 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
31294 CCTTCAGGCC
* *
31304 ATGAGTAAGTCTTTCGAGCATG
1 ATGAGTAAATCCTTCGAGCATG
* *
31326 ATGTGTAAATCCTTCGGGTCAT-
1 ATGAGTAAATCCTTCGAG-CATG
* *
31348 -T-AGTAAGTCTTTCGAGCATG
1 ATGAGTAAATCCTTCGAGCATG
*
31368 ATGCGTAAATCCTTCG
1 ATGAGTAAATCCTTCG
31384 GGTCATCTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
19 3 0.07
20 11 0.26
21 2 0.05
22 24 0.56
23 3 0.07
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (22 bp):
ATGAGTAAATCCTTCGAGCATG
Found at i:31353 original size:42 final size:41
Alignment explanation
Indices: 31293--31426 Score: 171
Period size: 42 Copynumber: 3.2 Consensus size: 41
31283 GATGAGTATG
* * *
31293 TCCTTCAGGCCATGAGTAAGTCTTTCGAGCATGATGTGTAAA
1 TCCTTCGGGTCATTAGTAAGTCTTTCGAGCATGATG-GTAAA
31335 TCCTTCGGGTCATTAGTAAGTCTTTCGAGCATGATGCGTAAA
1 TCCTTCGGGTCATTAGTAAGTCTTTCGAGCATGATG-GTAAA
* * * *
31377 TCCTTCGGGTCATCTA-TAAGTCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGTCAT-TAGTAAGTCTTTCGAGCATGATGGTAAA
31418 TCCTTCGGG
1 TCCTTCGGG
31427 CCATCTATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
41 12 0.14
42 69 0.83
43 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGTCATTAGTAAGTCTTTCGAGCATGATGGTAAA
Found at i:31567 original size:90 final size:90
Alignment explanation
Indices: 31414--31872 Score: 670
Period size: 90 Copynumber: 5.1 Consensus size: 90
31404 AGCAAGATGA
* * * *
31414 TAAGTCCTTCGGGCCATCTATAAGACCTTCAGTG-TAGAACGTTTTCAAATGTGATTTAAGAAAC
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAG-ATGTTTTCAAATGAGATTTAAGAAAC
* *
31478 TAAGCCTTCGAGGGTTTCATGATTTG
65 TAAGCCTTCGGGGGTTTCTTGATTTG
* * *
31504 TAAGTCCTTCAGGCCATCCATAAGACCTTCAGTGCAAGTTGTTTTCAAATGAGATTTTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTAAGAAACT
*
31569 AAGCCTTTGGGGGTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTG
* * *
31594 TAAGTACTTCGGGCCATCCATAAGACCTTCAGTGTAGGATGTTTTCAAATGAGATTTAAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTAAGAAACT
*
31659 AAGACTTCGGGGGTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTG
* *
31684 TAAGTCCTTCGGGACATCCATAAGACCTTCAGTAC-AGAATGTTTTCAAATGAGATTTAAGAAAC
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAG-ATGTTTTCAAATGAGATTTAAGAAAC
*
31748 TAAGCCTTCGGGGGTTTCTTGATTTT
65 TAAGCCTTCGGGGGTTTCTTGATTTG
* * * *
31774 TAAGTCATTCGGGCAATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTAAGAAACT
* *
31839 AAGCCTTCAGGGGTTTCTTGATTTT
66 AAGCCTTCGGGGGTTTCTTGATTTG
*
31864 TAAATCCTT
1 TAAGTCCTT
31873 TAGCCATCTA
Statistics
Matches: 332, Mismatches: 34, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
89 1 0.00
90 328 0.99
91 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (90 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTAAGAAACT
AAGCCTTCGGGGGTTTCTTGATTTG
Found at i:33719 original size:65 final size:64
Alignment explanation
Indices: 33606--33727 Score: 156
Period size: 65 Copynumber: 1.9 Consensus size: 64
33596 ACTAAGAATA
* * * *
33606 CATCAATGCATGAAGTGCATTCGATATTTCAAAATAGCCTGAGAGCATCTATGCATGTCTTGTG
1 CATCAATGCATCAAATGCATTCGATATTTCAAAATAACCTGAGAGCATCGATGCATGTCTTGTG
* * *
33670 CATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AACCTGAGTGCATCGATGCATG
1 CATCAATGCATCAAATGCATTCGAT-ATTTCA-AAATAACCTGAGAGCATCGATGCATG
33728 GTATGTTCGA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
64 22 0.45
65 24 0.49
66 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (64 bp):
CATCAATGCATCAAATGCATTCGATATTTCAAAATAACCTGAGAGCATCGATGCATGTCTTGTG
Found at i:34174 original size:21 final size:20
Alignment explanation
Indices: 34128--34176 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
34118 AAAAATATTA
34128 CTCCCCCTTACTTTAACACT
1 CTCCCCCTTACTTTAACACT
34148 -TCCCCCTTACTTTAACACTT
1 CTCCCCCTTACTTTAACAC-T
34168 CTCCCCCTT
1 CTCCCCCTT
34177 TTTGTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.67
20 1 0.04
21 8 0.30
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (20 bp):
CTCCCCCTTACTTTAACACT
Found at i:45242 original size:35 final size:35
Alignment explanation
Indices: 45203--45319 Score: 119
Period size: 35 Copynumber: 3.3 Consensus size: 35
45193 GATCAAACTA
* *
45203 GTAATTTCTTATATAGGTTCAGACCAATCGAATTG
1 GTAATTCCTTATATAGGTTCAGACCGATCGAATTG
** * * *
45238 GTAATTCCTTACTGCAAGTTCAG-CTCGGTCAAATTG
1 GTAATTCCTTA-TATAGGTTCAGAC-CGATCGAATTG
* **
45274 GTAATTCTTTATATAGGTTCAGACCGATCGAGCTG
1 GTAATTCCTTATATAGGTTCAGACCGATCGAATTG
45309 GTAATTCCTTA
1 GTAATTCCTTA
45320 CGGATCTAAG
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
35 36 0.57
36 27 0.43
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (35 bp):
GTAATTCCTTATATAGGTTCAGACCGATCGAATTG
Found at i:45262 original size:71 final size:71
Alignment explanation
Indices: 45178--45320 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 71
45168 TATGAAGTCT
* *
45178 CTGCAGGTTCAGCTCGATCAAACTAGTAATT-TCTTATATAGGTTCAGACCAATCGAATTGGTAA
1 CTGCAAGTTCAGCTCGATCAAACTAGTAATTCT-TTATATAGGTTCAGACCAATCGAACTGGTAA
45242 TTCCTTA
65 TTCCTTA
* * * * *
45249 CTGCAAGTTCAGCTCGGTCAAATTGGTAATTCTTTATATAGGTTCAGACCGATCGAGCTGGTAAT
1 CTGCAAGTTCAGCTCGATCAAACTAGTAATTCTTTATATAGGTTCAGACCAATCGAACTGGTAAT
45314 TCCTTA
66 TCCTTA
45320 C
1 C
45321 GGATCTAAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
71 63 0.98
72 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (71 bp):
CTGCAAGTTCAGCTCGATCAAACTAGTAATTCTTTATATAGGTTCAGACCAATCGAACTGGTAAT
TCCTTA
Found at i:46729 original size:2 final size:2
Alignment explanation
Indices: 46722--46767 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
46712 TAGCTCCAAA
*
46722 CT CT CT CT CT CG CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46764 CT CT
1 CT CT
46768 ATTTGAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:47046 original size:2 final size:2
Alignment explanation
Indices: 47041--47067 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47031 CAATACTCTC
47041 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
47068 TATGAATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49969 original size:14 final size:15
Alignment explanation
Indices: 49942--49983 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
49932 TTTTTTATAA
* *
49942 ATAAATTAAGTTTTT
1 ATAAATAAAATTTTT
49957 A-AAATAAAATTTTT
1 ATAAATAAAATTTTT
*
49971 ATTAATAAAATTT
1 ATAAATAAAATTT
49984 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
ATAAATAAAATTTTT
Found at i:60019 original size:17 final size:17
Alignment explanation
Indices: 59997--60049 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
59987 AGAATAAAGT
59997 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
60014 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
60031 TAGTTCATTTATTAGAC
1 TAGTTCATTAATTAAAC
60048 TA
1 TA
60050 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:62449 original size:20 final size:21
Alignment explanation
Indices: 62426--62464 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
62416 TAAACGAGAG
*
62426 TTGAAAAGA-CATTGAGAGCA
1 TTGAAAAGAGAATTGAGAGCA
62446 TTGAAAAGAGAATTGAGAG
1 TTGAAAAGAGAATTGAGAG
62465 TGAAAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.05, G:0.28, T:0.21
Consensus pattern (21 bp):
TTGAAAAGAGAATTGAGAGCA
Found at i:64068 original size:17 final size:17
Alignment explanation
Indices: 64027--64098 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
64017 ATTCATGCAT
64027 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
64044 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
64062 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
64079 CTAGTTCATTTATTAGA
1 CTAGTTCATTAATTAAA
64096 CTA
1 CTA
64099 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:68773 original size:19 final size:19
Alignment explanation
Indices: 68749--68792 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
68739 GATCAGACTG
*
68749 GTCAACGGGTC-AGGTTAAA
1 GTCAACGGGTCGA-GTCAAA
68768 GTCAACGGGTCGAGTCAAA
1 GTCAACGGGTCGAGTCAAA
68787 GTCAAC
1 GTCAAC
68793 AGGCCCAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (19 bp):
GTCAACGGGTCGAGTCAAA
Found at i:69923 original size:10 final size:10
Alignment explanation
Indices: 69908--69947 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
69898 CAAGATTTTG
69908 CGTTCGTTTA
1 CGTTCGTTTA
69918 CGTTCGATTATA
1 CGTTCG-TT-TA
*
69930 TGTTCGTTTA
1 CGTTCGTTTA
69940 CGTTCGTT
1 CGTTCGTT
69948 CATTTATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.58
11 4 0.15
12 7 0.27
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.50
Consensus pattern (10 bp):
CGTTCGTTTA
Found at i:69976 original size:10 final size:10
Alignment explanation
Indices: 69945--69978 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
69935 GTTTACGTTC
69945 GTTCATTTAT
1 GTTCATTTAT
*
69955 GCTCATTTAT
1 GTTCATTTAT
69965 GTTCATTTAT
1 GTTCATTTAT
69975 GTTC
1 GTTC
69979 GTTCTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.56
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:70275 original size:13 final size:13
Alignment explanation
Indices: 70259--70314 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 13
70249 GTGTTTGTGT
70259 TGTTCGTTTATTG
1 TGTTCGTTTATTG
70272 TGTTCGTTTA---
1 TGTTCGTTTATTG
* *
70282 TGTTCATTTATTA
1 TGTTCGTTTATTG
70295 TGTTCG--T-TTG
1 TGTTCGTTTATTG
70305 TGTTCGTTTA
1 TGTTCGTTTA
70315 CGTTCGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
10 17 0.50
11 1 0.03
12 1 0.03
13 15 0.44
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.61
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:70291 original size:10 final size:10
Alignment explanation
Indices: 70272--70335 Score: 74
Period size: 10 Copynumber: 6.1 Consensus size: 10
70262 TCGTTTATTG
70272 TGTTCGTTTA
1 TGTTCGTTTA
*
70282 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
70295 TGTTCGTTTG
1 TGTTCGTTTA
70305 TGTTCGTTTA
1 TGTTCGTTTA
*
70315 CGTTCGTTTA
1 TGTTCGTTTA
70325 TGTTCGTTTA
1 TGTTCGTTTA
70335 T
1 T
70336 CATTTAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
10 35 0.78
11 1 0.02
12 1 0.02
13 8 0.18
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:70291 original size:23 final size:22
Alignment explanation
Indices: 70259--70335 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
70249 GTGTTTGTGT
70259 TGTTCGTTTATTGTGTTCGTTTA
1 TGTTCGTTTATT-TGTTCGTTTA
* *
70282 TGTTCATTTATTATGTTCGTTTG
1 TGTTCGTTTATT-TGTTCGTTTA
*
70305 TGTTCGTTTA--CGTTCGTTTA
1 TGTTCGTTTATTTGTTCGTTTA
70325 TGTTCGTTTAT
1 TGTTCGTTTAT
70336 CATTTAAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 18 0.38
23 29 0.62
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (22 bp):
TGTTCGTTTATTTGTTCGTTTA
Found at i:73024 original size:18 final size:18
Alignment explanation
Indices: 72984--73027 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
72974 ATCTATTAAG
72984 TAAAATAATAAAATATCA
1 TAAAATAATAAAATATCA
*
73002 T-AAATACTAAAAATAT-A
1 TAAAATAAT-AAAATATCA
73019 TAAAATAAT
1 TAAAATAAT
73028 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAATAATAAAATATCA
Found at i:75618 original size:26 final size:26
Alignment explanation
Indices: 75589--75641 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
75579 TTCGATAATC
*
75589 TTAGAGTTTA-AGGTATTCTGGTTATT
1 TTAGAGTTTAGA-GTATTCTGGTCATT
* *
75615 TTAGGGTTTAGAGTATTTTGGTCATT
1 TTAGAGTTTAGAGTATTCTGGTCATT
75641 T
1 T
75642 GAATATTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.51
Consensus pattern (26 bp):
TTAGAGTTTAGAGTATTCTGGTCATT
Found at i:80750 original size:21 final size:22
Alignment explanation
Indices: 80708--80750 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
80698 TATCTCATGT
*
80708 AATTGTTTTATTATTTTTATTA
1 AATTGTTTTATTATTTTAATTA
80730 AATT-TTTTATT-TTTATAATTA
1 AATTGTTTTATTATTT-TAATTA
80751 TAAATCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 12 0.63
22 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
AATTGTTTTATTATTTTAATTA
Found at i:82232 original size:396 final size:396
Alignment explanation
Indices: 81500--82295 Score: 1556
Period size: 396 Copynumber: 2.0 Consensus size: 396
81490 TAATTTTATA
81500 GAATTATTAATTTATAATATTGAAGGGACCAAAAATTTATAAAAGTCTTTAGGAAAATTATCGTT
1 GAATTATTAATTTATAATATTGAAGGGACCAAAAATTTATAAAAGTCTTTAGGAAAATTATCGTT
81565 TTATTAATTTATCAAAATTATTAATTTAAACATTGTGCCTAAATCGGGACAGAGAAACATCATTA
66 TTATTAATTTATCAAAATTATTAATTTAAACATTGTGCCTAAATCGGGACAGAGAAACATCATTA
81630 TTTTAAAGAAATTATTAATTTATCTAGTATTAATTTATAAATATTGTATAGTATAAAGCAAGACA
131 TTTTAAAGAAATTATTAATTTATCTAGTATTAATTTATAAATATTGTATAGTATAAAGCAAGACA
*
81695 AAGTAAAATTAACATCATGTTAGTATTTACTGTCATTTTGATATTTAGGACATATCATTCTTCTA
196 AAGTAAAATTAACATCATGTTAGTATTTACTGTCATTTTGATATTCAGGACATATCATTCTTCTA
81760 GTTAGTTACTTAATTTTTTTTATCAAAGTAAATATTTAAATTATATTATTTATCTTATAATATTT
261 GTTAGTTACTTAATTTTTTTTATCAAAGTAAATATTTAAATTATATTATTTATCTTATAATATTT
81825 TCTAATCAAAGCCAATGAGTGTTAACACAAGTTGTTGCGATTCAAGAATTTAAGCTTGTAAGCCC
326 TCTAATCAAAGCCAATGAGTGTTAACACAAGTTGTTGCGATTCAAGAATTTAAGCTTGTAAGCCC
81890 AAATTC
391 AAATTC
* *
81896 GAATTATTAATTTATAATATTGAATGGACCATAAATTTATAAAAGTCTTTAGGAAAATTATCGTT
1 GAATTATTAATTTATAATATTGAAGGGACCAAAAATTTATAAAAGTCTTTAGGAAAATTATCGTT
81961 TTATTAATTTATCAAAATTATTAATTTAAACATTGTGCCTAAATCGGGACAGAGAAACATCATTA
66 TTATTAATTTATCAAAATTATTAATTTAAACATTGTGCCTAAATCGGGACAGAGAAACATCATTA
82026 TTTTAAAGAAATTATTAATTTATCTAGTATTAATTTATAAATATTGTATAGTATAAAGCAAGACA
131 TTTTAAAGAAATTATTAATTTATCTAGTATTAATTTATAAATATTGTATAGTATAAAGCAAGACA
82091 AAGTAAAATTAACATCATGTTAGTATTTACTGTCATTTTGATATTCAGGACATATCATTCTTCTA
196 AAGTAAAATTAACATCATGTTAGTATTTACTGTCATTTTGATATTCAGGACATATCATTCTTCTA
82156 GTTAGTTACTTAATTTTTTTTATCAAAGTAAATATTTAAATTATATTATTTATCTTATAATATTT
261 GTTAGTTACTTAATTTTTTTTATCAAAGTAAATATTTAAATTATATTATTTATCTTATAATATTT
82221 TCTAATCAAAGCCAATGAGTGTTAACACAAGTTGTTGCGATTCAAGAATTTAAGCTTGTAAGCCC
326 TCTAATCAAAGCCAATGAGTGTTAACACAAGTTGTTGCGATTCAAGAATTTAAGCTTGTAAGCCC
*
82286 AAGTTC
391 AAATTC
82292 GAAT
1 GAAT
82296 CCTATCACCA
Statistics
Matches: 396, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
396 396 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (396 bp):
GAATTATTAATTTATAATATTGAAGGGACCAAAAATTTATAAAAGTCTTTAGGAAAATTATCGTT
TTATTAATTTATCAAAATTATTAATTTAAACATTGTGCCTAAATCGGGACAGAGAAACATCATTA
TTTTAAAGAAATTATTAATTTATCTAGTATTAATTTATAAATATTGTATAGTATAAAGCAAGACA
AAGTAAAATTAACATCATGTTAGTATTTACTGTCATTTTGATATTCAGGACATATCATTCTTCTA
GTTAGTTACTTAATTTTTTTTATCAAAGTAAATATTTAAATTATATTATTTATCTTATAATATTT
TCTAATCAAAGCCAATGAGTGTTAACACAAGTTGTTGCGATTCAAGAATTTAAGCTTGTAAGCCC
AAATTC
Found at i:88575 original size:29 final size:29
Alignment explanation
Indices: 88513--88669 Score: 185
Period size: 29 Copynumber: 5.4 Consensus size: 29
88503 CACATTCGAA
* *
88513 AATTACAAAAATATCACCTTTTTTAAAAAT
1 AATTACCAAAATATCA-CTGTTTTAAAAAT
88543 AATTACCAAAATATCACTGTTTTAAAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
*
88572 AATTACCAAAATATCA-TCGTTTTACAAAT
1 AATTACCAAAATATCACT-GTTTTAAAAAT
* *
88601 AATTCCCAAAATGTCA-TAGTTTTAAAAAT
1 AATTACCAAAATATCACT-GTTTTAAAAAT
* *
88630 AATTACCAGAATGTCACTGTTTTTAAAAA-
1 AATTACCAAAATATCACTG-TTTTAAAAAT
*
88659 AATTCCCAAAA
1 AATTACCAAAA
88670 ATGTCATTGG
Statistics
Matches: 113, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
28 1 0.01
29 87 0.77
30 25 0.22
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.34
Consensus pattern (29 bp):
AATTACCAAAATATCACTGTTTTAAAAAT
Found at i:94735 original size:33 final size:32
Alignment explanation
Indices: 94696--94773 Score: 124
Period size: 31 Copynumber: 2.4 Consensus size: 32
94686 TCGAAAATAT
94696 TATATATATATATATTAATAT-AAAATATAAAA
1 TATATATATATA-ATTAATATAAAAATATAAAA
94728 TA-ATATATATAATTAATATAAAAATATAAAA
1 TATATATATATAATTAATATAAAAATATAAAA
94759 TATTATATATATAAT
1 TA-TATATATATAAT
94774 CGGGGCGGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
30 8 0.19
31 22 0.51
32 2 0.05
33 11 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TATATATATATAATTAATATAAAAATATAAAA
Found at i:95040 original size:4 final size:4
Alignment explanation
Indices: 95031--95063 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
95021 TCATTTTCTC
95031 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
95064 CTTTAGGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:95654 original size:46 final size:46
Alignment explanation
Indices: 95579--95667 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
95569 ACAACCTTGG
* * *
95579 GAAGATGGAGAACAATCAAGTAGCTGGAGAAAAATCCATGAGAGAT
1 GAAGATGGAGAACAATCAAGCAACCGGAGAAAAATCCATGAGAGAT
* *
95625 GAAGATGGAGAATAATCAAGCAACCGGAGAAGAATCCATGAGA
1 GAAGATGGAGAACAATCAAGCAACCGGAGAAAAATCCATGAGA
95668 AAGGAGGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.46, C:0.12, G:0.28, T:0.13
Consensus pattern (46 bp):
GAAGATGGAGAACAATCAAGCAACCGGAGAAAAATCCATGAGAGAT
Found at i:98403 original size:12 final size:12
Alignment explanation
Indices: 98386--98413 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
98376 TCTTCTTCTC
98386 CTCCCCGTTCAT
1 CTCCCCGTTCAT
98398 CTCCCCGTTCAT
1 CTCCCCGTTCAT
98410 CTCC
1 CTCC
98414 TCCGACTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.54, G:0.07, T:0.32
Consensus pattern (12 bp):
CTCCCCGTTCAT
Found at i:103597 original size:12 final size:12
Alignment explanation
Indices: 103577--103606 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
103567 TCTTCTTCTC
*
103577 CTCCCCGTTCAT
1 CTCCTCGTTCAT
103589 CTCCTCGTTCAT
1 CTCCTCGTTCAT
103601 CTCCTC
1 CTCCTC
103607 CGACTGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.50, G:0.07, T:0.37
Consensus pattern (12 bp):
CTCCTCGTTCAT
Found at i:109842 original size:23 final size:23
Alignment explanation
Indices: 109808--109868 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
109798 CCGTCTGACT
*
109808 GTTGATCGATCTGACTGTTAACC
1 GTTGATCAATCTGACTGTTAACC
109831 GTTGATCAATCTGACTGTTAACC
1 GTTGATCAATCTGACTGTTAACC
* *
109854 GTTGATTAGTCTGAC
1 GTTGATCAATCTGAC
109869 CGTTGATCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (23 bp):
GTTGATCAATCTGACTGTTAACC
Found at i:113678 original size:23 final size:24
Alignment explanation
Indices: 113650--113697 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
113640 ACCATTTAAT
* *
113650 TAAAAAAAAATAAATA-TCAAATAA
1 TAAAAATAAA-AAATAGTAAAATAA
113674 TAAAAATAAAAAATAGTAAAATAA
1 TAAAAATAAAAAATAGTAAAATAA
113698 AAACAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (24 bp):
TAAAAATAAAAAATAGTAAAATAA
Found at i:113687 original size:16 final size:16
Alignment explanation
Indices: 113676--113732 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
113666 TCAAATAATA
*
113676 AAAATAAAAAATA-GT
1 AAAATAAAAAATACAT
113691 AAAATAAAAACA-ACAT
1 AAAATAAAAA-ATACAT
* *
113707 AAAATAAAAATTAGAT
1 AAAATAAAAAATACAT
113723 AAACATAAAA
1 AAA-ATAAAA
113733 TATGACTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 11 0.31
16 18 0.51
17 6 0.17
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.18
Consensus pattern (16 bp):
AAAATAAAAAATACAT
Found at i:113716 original size:22 final size:22
Alignment explanation
Indices: 113647--113734 Score: 58
Period size: 22 Copynumber: 3.9 Consensus size: 22
113637 TAAACCATTT
*
113647 AATTAAAAAAAAATAAATATCAAA
1 AATTAAAAAAACATAAA-AT-AAA
*
113671 TAA-TAAAAATA-A-AAAATAGTAA
1 -AATTAAAAAAACATAAAATA--AA
113693 AA-TAAAAACAACATAAAATAAA
1 AATTAAAAA-AACATAAAATAAA
* *
113715 AATTAGATAAACATAAAATA
1 AATTAAAAAAACATAAAATA
113735 TGACTACAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
20 1 0.02
21 10 0.19
22 21 0.40
23 6 0.11
24 13 0.25
25 2 0.04
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (22 bp):
AATTAAAAAAACATAAAATAAA
Found at i:114643 original size:2 final size:2
Alignment explanation
Indices: 114636--114667 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
114626 AAAGAAAGAA
114636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
114668 TACAGAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115484 original size:92 final size:93
Alignment explanation
Indices: 115279--115527 Score: 277
Period size: 92 Copynumber: 2.7 Consensus size: 93
115269 TGGTCTTTCC
* * * * * * * * *
115279 ACTGGAAATATTGATCCCTCGAGTGATGCATTGCTGATTCAAAATGTCGTGAATCAAGAAAAGGT
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATCGTTGATTCGAAATGTTGTGAATCGAGCAAAGGT
* *
115344 TGAACAAACTCTTCATTATGAATTCTAT
66 TGAACAAACTATTCATCATGAATTCTAT
* * *
115372 ACTGGAAATATTGGTCCCTCAAGTGAGGCGTCGTTGATTCGAAGTGTTGTGAATCGAGCCAAGGT
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATCGTTGATTCGAAATGTTGTGAATCGAGCAAAGGT
* ** *
115437 TGAATAAGTTATTC-TCATGAATTCTTT
66 TGAACAAACTATTCATCATGAATTCTAT
* * * *
115464 ACTGGAAATATTGGTCCCTCATGTGAGGCATCACTT-ATTTGAAATATTGTGAATCGAGCAAAGG
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATC-GTTGATTCGAAATGTTGTGAATCGAGCAAAGG
115528 AAATGTTGAT
Statistics
Matches: 130, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
92 65 0.50
93 65 0.50
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (93 bp):
ACTGGAAATATTGGTCCCTCAAGTGAGGCATCGTTGATTCGAAATGTTGTGAATCGAGCAAAGGT
TGAACAAACTATTCATCATGAATTCTAT
Found at i:115551 original size:59 final size:58
Alignment explanation
Indices: 115488--115598 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 58
115478 TCCCTCATGT
* *
115488 GAGGCATCACTT-ATTTGAAATATTGTGAATCGAGCAAAGGAAATGTTGATCCCTCAAAC
1 GAGGCATCA-TTGATTCGAAATATTGTGAATCGAACAAAGGAAATGTT-ATCCCTCAAAC
* * * *
115547 GAGGCATTATTGATTCGAAGTGTTGTGAATCTAACAAAGGAAATGTTATCCC
1 GAGGCATCATTGATTCGAAATATTGTGAATCGAACAAAGGAAATGTTATCCC
115599 CTATGGTGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
58 7 0.16
59 38 0.84
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (58 bp):
GAGGCATCATTGATTCGAAATATTGTGAATCGAACAAAGGAAATGTTATCCCTCAAAC
Found at i:115747 original size:39 final size:39
Alignment explanation
Indices: 115628--115922 Score: 324
Period size: 39 Copynumber: 7.5 Consensus size: 39
115618 GTTTTAAGAA
* * * * *
115628 AAACAATCTCAAGTGTGAT-AAATCTTATTTTTCAAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* *
115666 AAACTATCTCAAGCGAGAT-AAATCTTCTGTTTTGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* *
115704 AAACTATCTCAAGTGAGATAAAATATTATGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* * * *
115743 AAACTATATCAATCGAGAGGAAGATAAATCTTCTATTTCGAGTG
1 AAACTATCTCAA--GTGA-G-ATA-AAATCTTCTGTTTCGAGTG
* *
115787 AAACTATCTCAAGCGAGATAAATTCTTCTGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* * *
115826 AAACTATCTCAAGCGAGATAAAATTTTCCGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* * *
115865 AAACTATCTCAAGTGAGATAAAATCTTCTATTTCAAGAG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* *
115904 AAGCTATCTAAAGTGAGAT
1 AAACTATCTCAAGTGAGAT
115923 TTTGATCCCT
Statistics
Matches: 218, Mismatches: 33, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
38 49 0.22
39 130 0.60
40 2 0.01
41 4 0.02
42 4 0.02
43 2 0.01
44 27 0.12
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
Found at i:115795 original size:83 final size:79
Alignment explanation
Indices: 115628--115888 Score: 296
Period size: 83 Copynumber: 3.3 Consensus size: 79
115618 GTTTTAAGAA
* * * * * * *
115628 AAACAATCTCAAGTGTGAT-AAATCTTATTTTTCAAGTGAAACTATCTC-A-AGCGAGATAAATC
1 AAACTATCTCAAGTGAGATAAAATATTATGTTTCGAGTGAAACTATATCAAGAGAGAGATAAATC
*
115690 TTCTGTTTTGAGTG
66 TTCTGTTTCGAGTG
115704 AAACTATCTCAAGTGAGATAAAATATTATGTTTCGAGTGAAACTATATCAATCGAGAGGAAGATA
1 AAACTATCTCAAGTGAGATAAAATATTATGTTTCGAGTGAAACTATATCAA--GAGA-G-AGATA
*
115769 AATCTTCTATTTCGAGTG
62 AATCTTCTGTTTCGAGTG
* * * * * * * *
115787 AAACTATCTCAAGCGAGATAAATTCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA-AAATT
1 AAACTATCTCAAGTGAGATAAAATATTATGTTTCGAGTGAAACTATATCAAGAGAGAGATAAATC
*
115851 TTCCGTTTCGAGTG
66 TTCTGTTTCGAGTG
115865 AAACTATCTCAAGTGAGATAAAAT
1 AAACTATCTCAAGTGAGATAAAAT
115889 CTTCTATTTC
Statistics
Matches: 157, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
76 17 0.11
77 25 0.16
78 39 0.25
79 2 0.01
80 1 0.01
81 5 0.03
82 1 0.01
83 67 0.43
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (79 bp):
AAACTATCTCAAGTGAGATAAAATATTATGTTTCGAGTGAAACTATATCAAGAGAGAGATAAATC
TTCTGTTTCGAGTG
Found at i:115859 original size:122 final size:121
Alignment explanation
Indices: 115644--115876 Score: 376
Period size: 122 Copynumber: 1.9 Consensus size: 121
115634 TCTCAAGTGT
* *
115644 GATAAATCTTATTTTTCAAGTGAAACTATCTCAAGCGAGATAAATCTTCTGTTTTGAGTGAAACT
1 GATAAATCTTATATTTCAAGTGAAACTATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACT
* *
115709 ATCTCAAGTGAGATAAAATATTATGTTTCGAGTGAAACTATATCAATCGAGAGGAA
66 ATCTCAAGCGAGATAAAATATTACGTTTCGAGTGAAACTATATCAATCGAGAGGAA
* *
115765 GATAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAATTCTTCTGTTTCGAGTGAAAC
1 GATAAATCTTATATTTCAAGTGAAACTATCTCAAGCGAGATAAA-TCTTCTGTTTCGAGTGAAAC
* * *
115830 TATCTCAAGCGAGATAAAATTTTCCGTTTCGAGTGAAACTATCTCAA
65 TATCTCAAGCGAGATAAAATATTACGTTTCGAGTGAAACTATATCAA
115877 GTGAGATAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
121 41 0.40
122 61 0.60
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (121 bp):
GATAAATCTTATATTTCAAGTGAAACTATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACT
ATCTCAAGCGAGATAAAATATTACGTTTCGAGTGAAACTATATCAATCGAGAGGAA
Found at i:116198 original size:136 final size:136
Alignment explanation
Indices: 115947--116214 Score: 421
Period size: 136 Copynumber: 2.0 Consensus size: 136
115937 TGAGCCATCA
* *
115947 CTGATTCGAAATGTCATGAATCGAGCAATAGGTTGAACAAGCTCTTCTCATTAGGAACTTCTTAT
1 CTGATTCGAAATGTCATGAATCGAGCAATAGGTCGAACAAACTCTTCTCATTAGGAACTTCTTAT
* * *
116012 CCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCAATTTAAAGTGTTAATCCTTTAAGCAAG
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCAATTTAAAATGTTAATCCCTTAAGCAAG
116077 GCTTCG
131 GCTTCG
** * *
116083 CTGATTCGAAATGTCATGAATCGAGTGATAGGTCGAACAAACTCTTCTCATTATGAACTT-TTCT
1 CTGATTCGAAATGTCATGAATCGAGCAATAGGTCGAACAAACTCTTCTCATTAGGAACTTCTTAT
* *
116147 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTTGAAAATGTTAATCCCTTAAGCGA
66 CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCAATTT-AAAATGTTAATCCCTTAAGCAA
116212 GGC
130 GGC
116215 GTAGTTGGTT
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
135 43 0.36
136 77 0.64
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (136 bp):
CTGATTCGAAATGTCATGAATCGAGCAATAGGTCGAACAAACTCTTCTCATTAGGAACTTCTTAT
CCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCAATTTAAAATGTTAATCCCTTAAGCAAG
GCTTCG
Found at i:116509 original size:41 final size:42
Alignment explanation
Indices: 116450--116536 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
116440 ACCCGAAGGT
* * *
116450 CTTATGGATGACCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
* *
116491 CTTATAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
116533 CTTA
1 CTTA
116537 CTGATAGCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 20 0.50
42 20 0.50
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:116808 original size:55 final size:56
Alignment explanation
Indices: 116614--117047 Score: 362
Period size: 52 Copynumber: 7.8 Consensus size: 56
116604 GTTTTCAGTT
** * * *
116614 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTAAAAAAATTCTTTGGAAATA
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTT-TTAAAATTCATTGAAAATC
* * * * * *
116672 ATCATCAAGAAACCCCTGAAAATCAAGTTTAGTTTC--TAAAAACTCATTTG--AGT-
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTTAAAATTCA-TTGAAAATC
*
116725 A-CATCAAGAAACCCCTAAAAATTAGGCTTATTTTCTTTTAAAATTCATTGAAAATC
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTTAAAATTCATTGAAAATC
* * * * * *
116781 ATCATAAAGAAACCCCT-GAATCAGGCTTAGTTTCTTTAAAAATTCTTTTAAAA--
1 ATCATCAAGAAACCCCTAAAATTAGGCTTAGTTTCTTTTAAAATTCATTGAAAATC
* * * *
116834 AT-ATCCAGAAACCCCTAAAAATTAGGCTTAGGTTCTTTTAAAAAATTCTTTGGAAATC
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTT--AAAATTCATTGAAAATC
* *
116892 ATCATCAAGAAACCCCTGAAAAGTAGGCTTTGTTTC---TAAAATCTCATTTG-AAA--
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTTAAAAT-TCA-TTGAAAATC
* *
116945 A-CATCAAGAAACCCCTAAAAATTAGGCATAGCTTCTTTTAAGAAATTCATTGAAAATC
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTT-A-AAATTCATTGAAAATC
* *
117003 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTTTTTTAAAAT
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTTAAAAT
117048 CTTTCTTTTG
Statistics
Matches: 304, Mismatches: 47, Indels: 51
0.76 0.12 0.13
Matches are distributed among these distances:
52 70 0.23
53 7 0.02
54 32 0.11
55 48 0.16
56 28 0.09
57 22 0.07
58 36 0.12
59 61 0.20
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (56 bp):
ATCATCAAGAAACCCCTAAAATTAGGCTTAGTTTCTTTTAAAATTCATTGAAAATC
Found at i:116932 original size:111 final size:111
Alignment explanation
Indices: 116616--117037 Score: 561
Period size: 111 Copynumber: 3.8 Consensus size: 111
116606 TTTCAGTTAT
* * * *
116616 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTC-TTAAAAAAATTCTTTGGAAATAATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
* * * **
116680 GAAACCCCTGAAAATCAAGTTTAGTTTCTAAAAACTCATTTGAGTA
66 GAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAATTCATTTGAAAA
* *
116726 CATCAAGAAACCCCTAAAAATTAGGCTTATTTTCTTTT--AAAATTCATTGAAAATCATCATAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
* *
116789 GAAACCCCTG--AATCAGGCTTAGTTTCTTTAAAAATTCTTTTAAAAA
66 GAAACCCCTGAAAATCAGGCTTAGTTTC--TAAAAATTCATTTGAAAA
* * * * *
116835 TATCCAGAAACCCCTAAAAATTAGGCTTAGGTTCTTTTAAAAAATTCTTTGGAAATCATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
*
116900 GAAACCCCTGAAAAGT-AGGCTTTGTTTCT-AAAATCTCATTTGAAAA
66 GAAACCCCTGAAAA-TCAGGCTTAGTTTCTAAAAAT-TCATTTGAAAA
* * *
116946 CATCAAGAAACCCCTAAAAATTAGGCATAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
117011 GAAACCCCTGAAAATCAGGCTTAGTTT
66 GAAACCCCTGAAAATCAGGCTTAGTTT
117038 TTTTTAAAAT
Statistics
Matches: 271, Mismatches: 31, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
107 14 0.05
109 78 0.29
110 39 0.14
111 126 0.46
113 13 0.05
114 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (111 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
GAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAATTCATTTGAAAA
Found at i:121744 original size:16 final size:16
Alignment explanation
Indices: 121725--121767 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
121715 TAAAAAGTAG
121725 TAAAATAAAAACAACA
1 TAAAATAAAAACAACA
* *
121741 TAAAATAAAAATAAGA
1 TAAAATAAAAACAACA
121757 TAAACATAAAA
1 TAAA-ATAAAA
121768 TATGAAGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
TAAAATAAAAACAACA
Found at i:121751 original size:22 final size:22
Alignment explanation
Indices: 121726--121769 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
121716 AAAAAGTAGT
121726 AAAATAA-AAACAACATAAAATA
1 AAAATAAGAAA-AACATAAAATA
*
121748 AAAATAAGATAAACATAAAATA
1 AAAATAAGAAAAACATAAAATA
121770 TGAAGACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAAGAAAAACATAAAATA
Found at i:122618 original size:18 final size:20
Alignment explanation
Indices: 122588--122624 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
122578 CAAAGATGAT
122588 TCGAAACAGAAAA-AAATAC
1 TCGAAACAGAAAATAAATAC
122607 TCGAAA-AGAAAATAAATA
1 TCGAAACAGAAAATAAATA
122625 AACCTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.14
Consensus pattern (20 bp):
TCGAAACAGAAAATAAATAC
Found at i:122914 original size:20 final size:20
Alignment explanation
Indices: 122889--122930 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
122879 ATGGGTGTCT
122889 GGTTAGACAAATCCGGGTCA
1 GGTTAGACAAATCCGGGTCA
*
122909 GGTTAGACAAATCTGGGTCA
1 GGTTAGACAAATCCGGGTCA
122929 GG
1 GG
122931 GTTGGTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (20 bp):
GGTTAGACAAATCCGGGTCA
Found at i:124603 original size:87 final size:87
Alignment explanation
Indices: 124457--124619 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
124447 TATGTTATAT
* *
124457 TATTTAACCGGAAATATTATCAAGTACAGTAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
124522 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
124544 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTCTATAATGTAATAGGT
1 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
124609 AGCGCTTATAT
66 AGCGCTTATAT
124620 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:125062 original size:182 final size:182
Alignment explanation
Indices: 124755--125955 Score: 2042
Period size: 182 Copynumber: 6.6 Consensus size: 182
124745 TGCGTTCACC
** * *
124755 TTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
124820 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTTAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* *
124885 TACTTAAAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * *
124937 TTTTGTCATTTCGAGACCGATTTTGCCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
125002 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
125067 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTA
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
125119 TTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
125184 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
125249 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
125301 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * *
125366 TTTATAAATTATCGACACGTTATTGGCGCTATAACTTATTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
125428 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
125481 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * *
125546 TTTATAAATTATCGACACGTTATTGGCGCTATAACTTATTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
* *
125608 ATATTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTATCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
125661 TTTTGTCATTTCGAGACTGGTTTTGTCATATTTTTACATGTTAT-TTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
125725 TTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
125789 TA-TGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTA
131 TACT-TATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
125841 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* ** *
125906 TTTATAAAGTATTGACACTTTATTGAAGATATAACTTCTTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
125956 AAAGGTAAAA
Statistics
Matches: 975, Mismatches: 37, Indels: 14
0.95 0.04 0.01
Matches are distributed among these distances:
177 2 0.00
178 18 0.02
179 54 0.06
180 372 0.38
181 51 0.05
182 476 0.49
183 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:130211 original size:181 final size:180
Alignment explanation
Indices: 129825--130297 Score: 662
Period size: 181 Copynumber: 2.6 Consensus size: 180
129815 CGTACTTAAG
* *
129825 AAAGTATCGACACTTTTAATATATCTGGTATCATTTTACCGGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCTGGTACCATTTTACCGGTTTTATCATTTT-ATACTGGTTT
* *
129890 TATCATATTTTTACCTGTTATATCGTTGTTTGATCGATACATTTTTTTAAAGTATCGACACTTTA
65 TATCATATTTTTACCTATTATATCGTTG-TTGATCGATACATTTTTTGAAAGTATCGACACTTTA
* *
129955 TAGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTTTCGATCCTTATAT
129 TAGACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATAT
* * * * * ***
130007 AAAGTTTCGACACTTTAAATATATCTGGTAGCGTTTTACCTGTTTCATCATTTGTATACCAATTT
1 AAAGTATCGACACTTTAAATATATCTGGTACCATTTTACCGGTTTTATCATTT-TATACTGGTTT
*
130072 TATCATATTTTTACCTATTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTATTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTAT
* *
130137 AGGCGCTAAAA-TGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATT
130 AGACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATA-T
* * * *
130188 AAAGTACCGGCACTTTAAATATAT-TCGGTACCACTTTACCGGTTTTATCATTTCAATACTGGTT
1 AAAGTATCGACACTTTAAATATATCT-GGTACCATTTTACCGGTTTTATCATTT-TATACTGGTT
* * *
130252 TTGTCATAGTTTTACCTATTATATCGTTGTGGATCGATACATTTTT
64 TTATCATATTTTTACCTATTATATCGTTGTTGATCGATACATTTTT
130298 AATTTGGATC
Statistics
Matches: 255, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
180 36 0.14
181 137 0.54
182 81 0.32
183 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCTGGTACCATTTTACCGGTTTTATCATTTTATACTGGTTTT
ATCATATTTTTACCTATTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTATA
GACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATAT
Found at i:131582 original size:24 final size:24
Alignment explanation
Indices: 131530--131579 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
131520 TTTCATATTT
* * *
131530 TTATTTTTATTTTTTAAAAAATGA
1 TTATTATTATTTTTAAAAAAATCA
131554 TTATTATTATTATTTAAAAAAATCA
1 TTATTATTATT-TTTAAAAAAATCA
131579 T
1 T
131580 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATTATTATTTTTAAAAAAATCA
Found at i:132707 original size:2 final size:2
Alignment explanation
Indices: 132700--132724 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
132690 TTACAAATGT
132700 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
132725 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:132729 original size:2 final size:2
Alignment explanation
Indices: 132724--132748 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
132714 TATATATATA
132724 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
132749 TGGGACCGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:137260 original size:15 final size:15
Alignment explanation
Indices: 137240--137325 Score: 109
Period size: 15 Copynumber: 5.7 Consensus size: 15
137230 ATTTTATTGG
*
137240 TATGTGAAAATGTTA
1 TATGTGAAAATGTTC
* *
137255 TATGTGAATATGTTT
1 TATGTGAAAATGTTC
*
137270 TATATGAAAATGTTC
1 TATGTGAAAATGTTC
*
137285 TATGTGAAAATGTGC
1 TATGTGAAAATGTTC
*
137300 TAAGTGAAAATGTTC
1 TATGTGAAAATGTTC
*
137315 TACGTGAAAAT
1 TATGTGAAAAT
137326 ACCCTATGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (15 bp):
TATGTGAAAATGTTC
Found at i:137337 original size:30 final size:30
Alignment explanation
Indices: 137274--137337 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
137264 ATGTTTTATA
* ***
137274 TGAAAATGTTCTATGTGAAAATGTGCTAAG
1 TGAAAATGTTCTACGTGAAAATACCCTAAG
*
137304 TGAAAATGTTCTACGTGAAAATACCCTATG
1 TGAAAATGTTCTACGTGAAAATACCCTAAG
137334 TGAA
1 TGAA
137338 TGTACTCTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (30 bp):
TGAAAATGTTCTACGTGAAAATACCCTAAG
Found at i:137494 original size:25 final size:24
Alignment explanation
Indices: 137466--137530 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
137456 TTCTATGTGG
*
137466 TCCTTCAGGATAAATTTCTACGCGA
1 TCCTTC-GGAAAAATTTCTACGCGA
137491 TCCTTTCGGAAAAATTTCTACGCGA
1 TCC-TTCGGAAAAATTTCTACGCGA
*
137516 TCCTTCCGGACAAAT
1 TCCTT-CGGAAAAAT
137531 CTATGTGGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 2 0.06
25 31 0.86
26 3 0.08
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (24 bp):
TCCTTCGGAAAAATTTCTACGCGA
Found at i:140066 original size:21 final size:21
Alignment explanation
Indices: 140036--140075 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
140026 AAAAGAGTTG
*
140036 TAATTGTCAAATAAATAAACA
1 TAATTATCAAATAAATAAACA
*
140057 TAATTATCAAATAAGTAAA
1 TAATTATCAAATAAATAAA
140076 TAAATAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TAATTATCAAATAAATAAACA
Found at i:151091 original size:59 final size:59
Alignment explanation
Indices: 151015--151128 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 59
151005 ATTACCCTAA
* *
151015 CTCCCCTTACCTCATTGCATAT-GGAAATA-AGGTTTTATTATTGTTGTTGTAAAATATAC
1 CTCCCCTTACCTCATTGCATATAAG-AATAGA-ATTTTATTATTGTTGTTGTAAAATATAC
* * *
151074 CTCCTCTTACCTTATTGCATATAAGAATAGAATTTTATTGTTGTTGTTGTAAAAT
1 CTCCCCTTACCTCATTGCATATAAGAATAGAATTTTATTATTGTTGTTGTAAAAT
151129 GGAGAACAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 46 0.96
60 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (59 bp):
CTCCCCTTACCTCATTGCATATAAGAATAGAATTTTATTATTGTTGTTGTAAAATATAC
Found at i:154906 original size:23 final size:23
Alignment explanation
Indices: 154872--154932 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
154862 CCGTCTGACT
*
154872 GTTGATCGATCTGACTGTTAACC
1 GTTGATCAATCTGACTGTTAACC
154895 GTTGATCAATCTGACTGTTAACC
1 GTTGATCAATCTGACTGTTAACC
*
154918 GTTGATCAGTCTGAC
1 GTTGATCAATCTGAC
154933 CGTTGATCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (23 bp):
GTTGATCAATCTGACTGTTAACC
Found at i:158741 original size:23 final size:24
Alignment explanation
Indices: 158713--158760 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
158703 ACCATTTAAT
* *
158713 TAAAAAAAAATAAATA-TCAAATAA
1 TAAAAATAAA-AAATAGTAAAATAA
158737 TAAAAATAAAAAATAGTAAAATAA
1 TAAAAATAAAAAATAGTAAAATAA
158761 AAACAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (24 bp):
TAAAAATAAAAAATAGTAAAATAA
Found at i:158750 original size:16 final size:16
Alignment explanation
Indices: 158739--158795 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
158729 TCAAATAATA
*
158739 AAAATAAAAAATA-GT
1 AAAATAAAAAATACAT
158754 AAAATAAAAACA-ACAT
1 AAAATAAAAA-ATACAT
* *
158770 AAAATAAAAATTAGAT
1 AAAATAAAAAATACAT
158786 AAACATAAAA
1 AAA-ATAAAA
158796 TATGACTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 11 0.31
16 18 0.51
17 6 0.17
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.18
Consensus pattern (16 bp):
AAAATAAAAAATACAT
Found at i:158779 original size:22 final size:22
Alignment explanation
Indices: 158710--158797 Score: 58
Period size: 22 Copynumber: 3.9 Consensus size: 22
158700 TAAACCATTT
*
158710 AATTAAAAAAAAATAAATATCAAA
1 AATTAAAAAAACATAAA-AT-AAA
*
158734 TAA-TAAAAATA-A-AAAATAGTAA
1 -AATTAAAAAAACATAAAATA--AA
158756 AA-TAAAAACAACATAAAATAAA
1 AATTAAAAA-AACATAAAATAAA
* *
158778 AATTAGATAAACATAAAATA
1 AATTAAAAAAACATAAAATA
158798 TGACTACAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
20 1 0.02
21 10 0.19
22 21 0.40
23 6 0.11
24 13 0.25
25 2 0.04
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (22 bp):
AATTAAAAAAACATAAAATAAA
Found at i:160541 original size:92 final size:93
Alignment explanation
Indices: 160336--160555 Score: 262
Period size: 93 Copynumber: 2.4 Consensus size: 93
160326 TGGTCTTTCC
* * * *
160336 ACTGGAAATATTGATCCCTCGAGTGATGCATTACTGATTCAAAATGTCGTGAATCAAGAAAAGGT
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATCACTGATTCAAAATGTCGTGAATCAAGAAAAGGT
* *
160401 TGAACAAACTCTTCATTATGAATTCTAT
66 TGAACAAACTATTCATCATGAATTCTAT
* ** * * * **
160429 ACTGGAAATATTGGTCCCTCAAGTGAGGCGTCGTTGATTCAAAGTGTTGTGAATCGAGCCAAGGT
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATCACTGATTCAAAATGTCGTGAATCAAGAAAAGGT
* ** *
160494 TGAATAAGTTATTC-TCATGAATTCTTT
66 TGAACAAACTATTCATCATGAATTCTAT
*
160521 ACTGGAAATATTGGTCCCTCATGTGAGGCATCACT
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATCACT
160556 TATTTGAAAT
Statistics
Matches: 105, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
92 42 0.40
93 63 0.60
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (93 bp):
ACTGGAAATATTGGTCCCTCAAGTGAGGCATCACTGATTCAAAATGTCGTGAATCAAGAAAAGGT
TGAACAAACTATTCATCATGAATTCTAT
Found at i:160608 original size:59 final size:58
Alignment explanation
Indices: 160545--160655 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 58
160535 TCCCTCATGT
* *
160545 GAGGCATCACTT-ATTTGAAATATTGTGAATCGAGCAAAGGAAATGTTGATCCCTCAAAC
1 GAGGCATCA-TTGATTCGAAATATTGTGAATCGAACAAAGGAAATGTT-ATCCCTCAAAC
* * * *
160604 GAGGCATTATTGATTCGAAGTGTTGTGAATCTAACAAAGGAAATGTTATCCC
1 GAGGCATCATTGATTCGAAATATTGTGAATCGAACAAAGGAAATGTTATCCC
160656 CTATGGTGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
58 7 0.16
59 38 0.84
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (58 bp):
GAGGCATCATTGATTCGAAATATTGTGAATCGAACAAAGGAAATGTTATCCCTCAAAC
Found at i:160804 original size:39 final size:39
Alignment explanation
Indices: 160685--160979 Score: 324
Period size: 39 Copynumber: 7.5 Consensus size: 39
160675 GTTTTAAGAA
* * * * *
160685 AAACAATCTCAAGTGTGAT-AAATCTTATTTTTCAAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* *
160723 AAACTATCTCAAGCGAGAT-AAATCTTCTGTTTTGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* *
160761 AAACTATCTCAAGTGAGATAAAATATTATGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* * * *
160800 AAACTATATCAATCGAGAGGAAGATAAATCTTCTATTTCGAGTG
1 AAACTATCTCAA--GTGA-G-ATA-AAATCTTCTGTTTCGAGTG
* * *
160844 AAACTATCTCAAGCGAGATAAATTCTTCTGTATCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* * *
160883 AAACTATCTCAAGCGAGATAAAATTTTCCGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
* * *
160922 AAACTATCTCAAGTGAGATAAAATCTTCTATTTCAAGAG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
*
160961 AAGCTATCTCAAGTGAGAT
1 AAACTATCTCAAGTGAGAT
160980 TTTGATCCCT
Statistics
Matches: 217, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
38 49 0.23
39 129 0.59
40 2 0.01
41 4 0.02
42 4 0.02
43 2 0.01
44 27 0.12
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
Found at i:160852 original size:83 final size:79
Alignment explanation
Indices: 160685--160945 Score: 278
Period size: 83 Copynumber: 3.3 Consensus size: 79
160675 GTTTTAAGAA
* * * * * * * *
160685 AAACAATCTCAAGTGTGAT-AAATCTTATTTTTCAAGTGAAACTATCTC-A-AGCGAGATAAATC
1 AAACTATCTCAAGTGAGATAAAATATTATGTATCGAGTGAAACTATATCAAGAGAGAGATAAATC
*
160747 TTCTGTTTTGAGTG
66 TTCTGTTTCGAGTG
*
160761 AAACTATCTCAAGTGAGATAAAATATTATGTTTCGAGTGAAACTATATCAATCGAGAGGAAGATA
1 AAACTATCTCAAGTGAGATAAAATATTATGTATCGAGTGAAACTATATCAA--GAGA-G-AGATA
*
160826 AATCTTCTATTTCGAGTG
62 AATCTTCTGTTTCGAGTG
* * * * * * * *
160844 AAACTATCTCAAGCGAGATAAATTCTTCTGTATCGAGTGAAACTATCTCAAGCGAGATA-AAATT
1 AAACTATCTCAAGTGAGATAAAATATTATGTATCGAGTGAAACTATATCAAGAGAGAGATAAATC
*
160908 TTCCGTTTCGAGTG
66 TTCTGTTTCGAGTG
160922 AAACTATCTCAAGTGAGATAAAAT
1 AAACTATCTCAAGTGAGATAAAAT
160946 CTTCTATTTC
Statistics
Matches: 156, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
76 17 0.11
77 25 0.16
78 39 0.25
79 2 0.01
80 1 0.01
81 5 0.03
82 1 0.01
83 66 0.42
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (79 bp):
AAACTATCTCAAGTGAGATAAAATATTATGTATCGAGTGAAACTATATCAAGAGAGAGATAAATC
TTCTGTTTCGAGTG
Found at i:160917 original size:122 final size:117
Alignment explanation
Indices: 160701--160979 Score: 371
Period size: 122 Copynumber: 2.4 Consensus size: 117
160691 TCTCAAGTGT
* * * *
160701 GATAAATCTTATTTTTCAAGTGAAACTATCTCAAGCGAGATAAATCTTCTGTTTTGAGTGAAACT
1 GATAAATCTTCTATTTCAAGTGAAACTATCTCAAGCGAGATAAATCTTCTGTATCGAGTGAAACT
* *
160766 ATCTCAAGTGAGATAAAATATTATGTTTCGAGTGAAACTATATCAATCGAGAGGAA
66 ATCTCAAGCGAGATAAAATATTACGTTTCGAGTGAAACTATATCAA--GAGA-G-A
*
160822 GATAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAATTCTTCTGTATCGAGTGAAAC
1 GATAAATCTTCTATTTCAAGTGAAACTATCTCAAGCGAGATAAA-TCTTCTGTATCGAGTGAAAC
* * * *
160887 TATCTCAAGCGAGATAAAATTTTCCGTTTCGAGTGAAACTATCTCAAGTGAGA
65 TATCTCAAGCGAGATAAAATATTACGTTTCGAGTGAAACTATATCAAGAGAGA
* * * *
160940 TA-AAATCTTCTATTTCAAGAGAAGCTATCTCAAGTGAGAT
1 GATAAATCTTCTATTTCAAGTGAAACTATCTCAAGCGAGAT
160980 TTTGATCCCT
Statistics
Matches: 141, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
117 34 0.24
118 2 0.01
119 1 0.01
120 3 0.02
121 41 0.29
122 60 0.43
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (117 bp):
GATAAATCTTCTATTTCAAGTGAAACTATCTCAAGCGAGATAAATCTTCTGTATCGAGTGAAACT
ATCTCAAGCGAGATAAAATATTACGTTTCGAGTGAAACTATATCAAGAGAGA
Found at i:161567 original size:41 final size:42
Alignment explanation
Indices: 161508--161594 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
161498 ACCCGAAGGT
* * *
161508 CTTATGGATGACCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
* *
161549 CTTATAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
161591 CTTA
1 CTTA
161595 CTGATAGCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 20 0.50
42 20 0.50
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:161818 original size:110 final size:111
Alignment explanation
Indices: 161674--162096 Score: 577
Period size: 111 Copynumber: 3.8 Consensus size: 111
161664 TTTCAGTTAT
* * * *
161674 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTC-TTAAAAAAATTCTTTGGAAATAATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
* * **
161738 GAAACCCCTGAAAATCAAGTTTAGTTTCTAAAAACTCATTTGAGTA
66 GAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
* *
161784 CATCAAGAAACCCCTAAAAATTAGGCTTATTTTCTTTT-AAAAATTCATTGAAAATCATCATAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
* * * *
161848 GAAACCCCTG--AATCAGGCTTATTTTCTTTAAAAATTCTTTTAAAAA
66 GAAACCCCTGAAAATCAGGCTTAGTTTC--TAAAAACTCATTTGAAAA
* * * * *
161894 TATCCAGAAACCCCTAAAAATTAGGCTTAGGTTCTTTTAAAAAATTCTTTGGAAATCATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
*
161959 GAAACCCCTGAAAAGT-AGGCTTTGTTTCTAAAAACTCATTTGAAAA
66 GAAACCCCTGAAAA-TCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
* * *
162005 CATCAAGAAACCCCTAAAAATTAGGCATAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
162070 GAAACCCCTGAAAATCAGGCTTAGTTT
66 GAAACCCCTGAAAATCAGGCTTAGTTT
162097 TTTTTAAAAT
Statistics
Matches: 271, Mismatches: 34, Indels: 15
0.85 0.11 0.05
Matches are distributed among these distances:
108 13 0.05
110 113 0.42
111 132 0.49
113 12 0.04
114 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (111 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
GAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
Found at i:161894 original size:56 final size:56
Alignment explanation
Indices: 161672--162105 Score: 321
Period size: 55 Copynumber: 7.8 Consensus size: 56
161662 GTTTTCAGTT
* ** * *
161672 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTAAAAAAATTCTTTGGAAATA
1 ATCAT-AAGAAACCCCT-AAAATTAGGCTTATTTTCTTTTAAAAATTCTTTGAAAATC
* * * * * **
161730 ATCATCAAGAAACCCCTGAAAATCAAGTTTAGTTTC---TAAAAACTCATTTGAGTA-C
1 ATCAT-AAGAAACCCCT-AAAATTAGGCTTATTTTCTTTTAAAAATTC-TTTGAAAATC
*
161785 ATC--AAGAAACCCCTAAAAATTAGGCTTATTTTCTTTTAAAAATTCATTGAAAATC
1 ATCATAAGAAACCCCT-AAAATTAGGCTTATTTTCTTTTAAAAATTCTTTGAAAATC
* * *
161840 ATCATAAAGAAACCCCT-GAATCAGGCTTATTTTC-TTTAAAAATTCTTTTAAAA--
1 ATCAT-AAGAAACCCCTAAAATTAGGCTTATTTTCTTTTAAAAATTCTTTGAAAATC
* ** *
161893 AT-ATCCAGAAACCCCTAAAAATTAGGCTTAGGTTCTTTTAAAAAATTCTTTGGAAATC
1 ATCAT-AAGAAACCCCT-AAAATTAGGCTTATTTTCTTTT-AAAAATTCTTTGAAAATC
* *
161951 ATCATCAAGAAACCCCTGAAAAGTAGGCTT-TGTTTC---TAAAAACTCATTTGAAAA-C
1 ATCAT-AAGAAACCCCT-AAAATTAGGCTTAT-TTTCTTTTAAAAATTC-TTTGAAAATC
* ** *
162006 ATC--AAGAAACCCCTAAAAATTAGGCATAGCTTCTTTTAAGAAATTCATTGAAAATC
1 ATCATAAGAAACCCCT-AAAATTAGGCTTATTTTCTTTTAA-AAATTCTTTGAAAATC
*
162062 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTT-TTTTAAAA
1 ATCAT-AAGAAACCCCT-AAAATTAGGCTTA-TTTTCTTTTAAAA
162106 TCTTTCTTTT
Statistics
Matches: 299, Mismatches: 50, Indels: 54
0.74 0.12 0.13
Matches are distributed among these distances:
52 61 0.20
53 2 0.01
54 18 0.06
55 63 0.21
56 51 0.17
58 47 0.16
59 55 0.18
60 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (56 bp):
ATCATAAGAAACCCCTAAAATTAGGCTTATTTTCTTTTAAAAATTCTTTGAAAATC
Found at i:166804 original size:16 final size:16
Alignment explanation
Indices: 166785--166827 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
166775 TAAAAAGTAG
166785 TAAAATAAAAACAACA
1 TAAAATAAAAACAACA
* *
166801 TAAAATAAAAATAAGA
1 TAAAATAAAAACAACA
166817 TAAACATAAAA
1 TAAA-ATAAAA
166828 TATGAAGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
TAAAATAAAAACAACA
Found at i:166811 original size:22 final size:22
Alignment explanation
Indices: 166786--166829 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
166776 AAAAAGTAGT
166786 AAAATAA-AAACAACATAAAATA
1 AAAATAAGAAA-AACATAAAATA
*
166808 AAAATAAGATAAACATAAAATA
1 AAAATAAGAAAAACATAAAATA
166830 TGAAGACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAAGAAAAACATAAAATA
Found at i:167671 original size:18 final size:20
Alignment explanation
Indices: 167641--167677 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
167631 CAAAGATGAT
167641 TCGAAACAGAAAA-AAATAC
1 TCGAAACAGAAAATAAATAC
167660 TCGAAA-AGAAAATAAATA
1 TCGAAACAGAAAATAAATA
167678 AACCTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.14
Consensus pattern (20 bp):
TCGAAACAGAAAATAAATAC
Found at i:167971 original size:20 final size:20
Alignment explanation
Indices: 167946--167987 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
167936 ATGGGTGTCT
167946 GGTTAGACAAATCCGGGTCA
1 GGTTAGACAAATCCGGGTCA
*
167966 GGTTAGACAAATCTGGGTCA
1 GGTTAGACAAATCCGGGTCA
167986 GG
1 GG
167988 GTTGGTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (20 bp):
GGTTAGACAAATCCGGGTCA
Found at i:169655 original size:87 final size:87
Alignment explanation
Indices: 169509--169671 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
169499 TATGTTATAT
* *
169509 TATTTAACCGGAAATATTATCAAGTACAGTAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
169574 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
169596 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTCTATAATGTAATAGGT
1 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
169661 AGCGCTTATAT
66 AGCGCTTATAT
169672 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:170143 original size:182 final size:182
Alignment explanation
Indices: 169804--171005 Score: 2027
Period size: 182 Copynumber: 6.7 Consensus size: 182
169794 ATATGCGTTC
** * *
169804 ACCT-TTTT-TCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGAT
1 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
169867 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAG
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAG
* *
169931 TGTCGATACTTATAATAAATTATTGACACTTTCAACATATCCGGTAGCGCTTT
130 TGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
* *
169984 ACCTGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
1 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
170049 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
170114 GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
131 GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
* * *
170166 ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACCTGTTATATTGTTATGGATCGAT
1 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* *
170231 ACATTTTTATAAAGTATTGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGT
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
170296 GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
131 GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
170348 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATG-T-TATTGTTATGGATCGAT
1 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* * *
170411 ACATTTTTATAAATTATCGACACGTTATTGGCGCTATAACTTATTCTCTTATT-AATTCCAAAA-
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAG
170474 -GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
130 TGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
170526 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
1 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* * *
170591 ACATTTTTATAAATTATCGACACGTTATTGGCGCTATAACTTATTCTCTTATT-AATTCCAAAA-
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAG
170654 -GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
130 TGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
* *
170706 ATCTGTTTTGTCATTTCGAGACTGGTTTTGTCATATTTTTACATGTTAT-TTGTTATGGATCGAT
1 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
170770 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGT
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
170834 GTCGATA-TGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
131 GTCGATACT-TATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
* *
170886 ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
1 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* ** *
170951 ACATTTTTATAAAGTATTGACACTTTATTGAAGATATAACTTCTTCTCTTTTAAA
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
171006 AAAGGTAAAA
Statistics
Matches: 976, Mismatches: 34, Indels: 22
0.95 0.03 0.02
Matches are distributed among these distances:
177 2 0.00
178 115 0.12
179 55 0.06
180 350 0.36
181 60 0.06
182 394 0.40
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
Found at i:170621 original size:360 final size:361
Alignment explanation
Indices: 169804--171004 Score: 2026
Period size: 360 Copynumber: 3.3 Consensus size: 361
169794 ATATGCGTTC
** * *
169804 ACCT-TTTT-TCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGAT
1 ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
169867 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGT
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGT
* *
169932 GTCGATACTTATAATAAATTATTGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCA
131 GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCA
* *
169997 TTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAA
196 TTTCGAGACCGGTTTTGTCATATTTTTACATG-T-TATTGTTATGGATCGATACATTTTTATAAA
170062 GTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATA
259 GTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG-GTCGATACTTATA
170127 ATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
323 ATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
* *
170166 ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACCTGTTATATTGTTATGGATCGAT
1 ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* *
170231 ACATTTTTATAAAGTATTGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTTCAAAAG
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAG
170295 TGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTC
130 TGTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTC
*
170360 ATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATTGTTATGGATCGATACATTTTTATAAAT
195 ATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATTGTTATGGATCGATACATTTTTATAAAG
* *
170425 TATCGACACGTTATTGGCGCTATAACTTATTCTCTTATT-AATTCCAAAA-GTCGATACTTATAA
260 TATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGGTCGATACTTATAA
170488 TAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
324 TAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
*
170526 ACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
1 ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* * *
170591 ACATTTTTATAAATTATCGACACGTTATTGGCGCTATAACTTATTCTCTTATTAATTCCAAAA--
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGT
*
170654 GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTATCTGTTTTGTCA
131 GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCA
*
170719 TTTCGAGACTGGTTTTGTCATATTTTTACATGTTATTTGTTATGGATCGATACATTTTTATAAAG
196 TTTCGAGACCGGTTTTGTCATATTTTTACATGTTA-TTGTTATGGATCGATACATTTTTATAAAG
170784 TATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGATA-TGTATA
260 TATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG-GTCGATACT-TATA
170847 ATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
323 ATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTT
*
170886 ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
1 ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
* ** *
170951 ACATTTTTATAAAGTATTGACACTTTATTGAAGATATAACTTCTTCTCTT-TTAA
66 ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAA
171005 AAAAGGTAAA
Statistics
Matches: 792, Mismatches: 37, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
357 2 0.00
358 116 0.15
359 58 0.07
360 325 0.41
361 2 0.00
362 78 0.10
363 9 0.01
364 202 0.26
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (361 bp):
ACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGT
GTCGATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCA
TTTCGAGACCGGTTTTGTCATATTTTTACATGTTATTGTTATGGATCGATACATTTTTATAAAGT
ATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGGTCGATACTTATAATA
AATTATCGACACTTTCAACATAACCGGTAGCGCTTT
Found at i:175183 original size:25 final size:25
Alignment explanation
Indices: 175149--175198 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
175139 ATAACATCAA
175149 CAAAATTAATGGTTGCAACTCTATC
1 CAAAATTAATGGTTGCAACTCTATC
175174 CAAAATTAATGGTTGCAACTCTATC
1 CAAAATTAATGGTTGCAACTCTATC
175199 GGTATATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (25 bp):
CAAAATTAATGGTTGCAACTCTATC
Found at i:176984 original size:15 final size:15
Alignment explanation
Indices: 176964--177049 Score: 109
Period size: 15 Copynumber: 5.7 Consensus size: 15
176954 ATTTTATTGG
*
176964 TATGTGAAAATGTTA
1 TATGTGAAAATGTTC
* *
176979 TATGTGAATATGTTT
1 TATGTGAAAATGTTC
*
176994 TATATGAAAATGTTC
1 TATGTGAAAATGTTC
*
177009 TATGTGAAAATGTGC
1 TATGTGAAAATGTTC
*
177024 TAAGTGAAAATGTTC
1 TATGTGAAAATGTTC
*
177039 TACGTGAAAAT
1 TATGTGAAAAT
177050 ACCCTATGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (15 bp):
TATGTGAAAATGTTC
Found at i:177061 original size:30 final size:30
Alignment explanation
Indices: 176998--177061 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
176988 ATGTTTTATA
* ***
176998 TGAAAATGTTCTATGTGAAAATGTGCTAAG
1 TGAAAATGTTCTACGTGAAAATACCCTAAG
*
177028 TGAAAATGTTCTACGTGAAAATACCCTATG
1 TGAAAATGTTCTACGTGAAAATACCCTAAG
177058 TGAA
1 TGAA
177062 TGTACTCTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (30 bp):
TGAAAATGTTCTACGTGAAAATACCCTAAG
Found at i:177218 original size:25 final size:24
Alignment explanation
Indices: 177190--177254 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 24
177180 TTCTATGTGG
177190 TCCTTCGGGACAAATTTCTACGCGA
1 TCCTTC-GGACAAATTTCTACGCGA
177215 TCCTTTCGGACAAATTTCTACGCGA
1 TCC-TTCGGACAAATTTCTACGCGA
177240 TCCTTCCGGACAAAT
1 TCCTT-CGGACAAAT
177255 CTATGTGGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 2 0.05
25 33 0.87
26 3 0.08
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (24 bp):
TCCTTCGGACAAATTTCTACGCGA
Found at i:179791 original size:21 final size:21
Alignment explanation
Indices: 179761--179800 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
179751 AAAAGAGTTG
*
179761 TAATTGTCAAATAAATAAACA
1 TAATTATCAAATAAATAAACA
179782 TAATTATCAAATAAATAAA
1 TAATTATCAAATAAATAAA
179801 TAAATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (21 bp):
TAATTATCAAATAAATAAACA
Found at i:179812 original size:9 final size:9
Alignment explanation
Indices: 179790--179838 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 9
179780 CATAATTATC
179790 AAAT-AAAT
1 AAATAAAAT
179798 AAAT-AAAT
1 AAATAAAAT
179806 AAAATAAAAT
1 -AAATAAAAT
*
179816 GAATAAAAT
1 AAATAAAAT
179825 -AATAAAGAT
1 AAATAAA-AT
179834 AAATA
1 AAATA
179839 GGGTCGATCT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
8 14 0.39
9 14 0.39
10 8 0.22
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (9 bp):
AAATAAAAT
Found at i:179820 original size:14 final size:14
Alignment explanation
Indices: 179769--179826 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
179759 TGTAATTGTC
179769 AAATAAATAAACATA
1 AAATAAATAAA-ATA
*
179784 ATTATCAAAT-AAAT-
1 A-AAT-AAATAAAATA
179798 AAATAAATAAAATA
1 AAATAAATAAAATA
*
179812 AAATGAATAAAATA
1 AAATAAATAAAATA
179826 A
1 A
179827 TAAAGATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
12 4 0.11
13 6 0.17
14 15 0.42
15 3 0.08
16 4 0.11
17 4 0.11
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:179820 original size:22 final size:23
Alignment explanation
Indices: 179790--179836 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
179780 CATAATTATC
179790 AAATAAAT-AAATAAATAAA-ATA
1 AAATAAATAAAAT-AATAAAGATA
*
179812 AAATGAATAAAATAATAAAGATA
1 AAATAAATAAAATAATAAAGATA
179835 AA
1 AA
179837 TAGGGTCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (23 bp):
AAATAAATAAAATAATAAAGATA
Found at i:192661 original size:2 final size:2
Alignment explanation
Indices: 192654--192705 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
192644 TTGCAGTGAA
192654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
192696 AT AT AT AT AT
1 AT AT AT AT AT
192706 CAAACCATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193950 original size:2 final size:2
Alignment explanation
Indices: 193943--193968 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
193933 AATTGCTTAA
193943 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
193969 TCGGGTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194263 original size:27 final size:27
Alignment explanation
Indices: 194187--194264 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
194177 AGTACCCATG
* *
194187 AACTTTAAAATGACCAAAATACCCCTA
1 AACTCTAAAATGACCAAAATATCCCTA
* * * *
194214 AAATC-CAATTTACCAAAATATCCCTA
1 AACTCTAAAATGACCAAAATATCCCTA
*
194240 AACTCTAAAATGACCAAAACATCCC
1 AACTCTAAAATGACCAAAATATCCC
194265 AAGCTCCAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.22
Consensus pattern (27 bp):
AACTCTAAAATGACCAAAATATCCCTA
Found at i:195334 original size:2 final size:2
Alignment explanation
Indices: 195329--195376 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
195319 TATATATATA
195329 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
195371 TG TG TG
1 TG TG TG
195377 AGTAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:200463 original size:35 final size:35
Alignment explanation
Indices: 200404--200500 Score: 131
Period size: 35 Copynumber: 2.8 Consensus size: 35
200394 ACCCCAGGTT
* * *
200404 CTTAAGCTATATGTAGAAGGTTCTTACCATAGGCC
1 CTTATGCTAAATGCAGAAGGTTCTTACCATAGGCC
* * *
200439 CTTATGCTAAATGCATAAGTTTCTTACCGTAGGCC
1 CTTATGCTAAATGCAGAAGGTTCTTACCATAGGCC
*
200474 CTTATGCTAATTGCAGAAGGTTCTTAC
1 CTTATGCTAAATGCAGAAGGTTCTTAC
200501 GTGGCGTATA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (35 bp):
CTTATGCTAAATGCAGAAGGTTCTTACCATAGGCC
Found at i:205018 original size:14 final size:14
Alignment explanation
Indices: 204995--205032 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
204985 TCTGTCTATA
*
204995 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
205008 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
205023 TGCAGGGATT
1 TGCAGGGATT
205033 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:212169 original size:15 final size:15
Alignment explanation
Indices: 212151--212207 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
212141 AATAAAACAA
212151 AATAAAAAATAAAAT
1 AATAAAAAATAAAAT
* *
212166 AATAATAAATAAAAG
1 AATAAAAAATAAAAT
*
212181 AGA-AATATAATAAAAT
1 A-ATAA-AAAATAAAAT
212197 AATAAAAAATA
1 AATAAAAAATA
212208 GTAGTAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 22 0.67
16 11 0.33
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (15 bp):
AATAAAAAATAAAAT
Found at i:212172 original size:11 final size:11
Alignment explanation
Indices: 212139--212207 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 11
212129 TGGGAAAATA
*
212139 AAAATAA-AAC
1 AAAATAATAAT
*
212149 AAAATAAAAAAT
1 AAAAT-AATAAT
212161 AAAATAATAAT
1 AAAATAATAAT
*
212172 -AAATAA-AAG
1 AAAATAATAAT
212181 AGAAAT-ATAAT
1 A-AAATAATAAT
212192 AAAATAATAA-
1 AAAATAATAAT
212202 AAAATA
1 AAAATA
212208 GTAGTAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
9 2 0.04
10 22 0.45
11 18 0.37
12 7 0.14
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:212223 original size:28 final size:26
Alignment explanation
Indices: 212157--212223 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 26
212147 ACAAAATAAA
212157 AAATA-AAATAATAATAAATAAAAGAG
1 AAATATAAA-AATAATAAATAAAAGAG
212183 AAATATAATAAAATAATAAA-AAATAGTAG
1 AAATAT-A-AAAATAATAAATAAA-AG-AG
212212 TAAATATAAAAA
1 -AAATATAAAAA
212224 GGGGTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
26 5 0.14
27 3 0.09
28 16 0.46
29 5 0.14
30 6 0.17
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (26 bp):
AAATATAAAAATAATAAATAAAAGAG
Found at i:214485 original size:24 final size:22
Alignment explanation
Indices: 214451--214513 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
214441 AAAATGTTTC
*
214451 AAAGTTCTGAAAATATCAATTAA
1 AAAGTTTTGAAAATATCAA-TAA
* * *
214474 AAGAGTTTTGAAAATGTTTAATCA
1 AA-AGTTTTGAAAAT-ATCAATAA
214498 AAAGTTTTGAAAATAT
1 AAAGTTTTGAAAATAT
214514 TTCCCCTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 14 0.42
24 15 0.45
25 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.35
Consensus pattern (22 bp):
AAAGTTTTGAAAATATCAATAA
Found at i:218612 original size:31 final size:31
Alignment explanation
Indices: 218575--218636 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
218565 ATAAATGAAG
* *
218575 AAAATAT-TAAATTTTAGAAAAAGAAAATAAT
1 AAAATATAAAAATGTTA-AAAAAGAAAATAAT
218606 AAAATATAAAAAATGTTAAAAAAGAAAATAA
1 AAAATAT-AAAAATGTTAAAAAAGAAAATAA
218637 AAATACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 7 0.26
32 13 0.48
33 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (31 bp):
AAAATATAAAAATGTTAAAAAAGAAAATAAT
Found at i:218639 original size:6 final size:5
Alignment explanation
Indices: 218625--218728 Score: 50
Period size: 5 Copynumber: 19.4 Consensus size: 5
218615 AAAATGTTAA
* *
218625 AAAAG AAAAT AAAAAT ACAAT AAAAT AAAA- AAGAAGT GGGAAAAT AAAAAT
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AA-AA-T ---AAAAT -AAAAT
** * * *
218676 AAAGC AAAAT AAAAT AATAA- AAAAA AAAAT AAAAG AGAAAT ATAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT
218727 AA
1 AA
218729 TAAATAATAG
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
4 4 0.05
5 51 0.67
6 16 0.21
8 1 0.01
9 2 0.03
10 2 0.03
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:218798 original size:18 final size:18
Alignment explanation
Indices: 218777--218816 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
218767 GTTGTTTTTA
*
218777 AAATAAAAGATAATAATT
1 AAATAAAAGAAAATAATT
218795 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
218813 AAAT
1 AAAT
218817 TAATAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:237129 original size:15 final size:16
Alignment explanation
Indices: 237109--237148 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
237099 TTTACTTCAA
*
237109 AATGATT-AAGCGCTG
1 AATGATTCAAACGCTG
*
237124 AATGATTCAAATGCTG
1 AATGATTCAAACGCTG
237140 AATGATTCA
1 AATGATTCA
237149 GAGGCTCCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (16 bp):
AATGATTCAAACGCTG
Found at i:239050 original size:5 final size:5
Alignment explanation
Indices: 239040--239070 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
239030 ATGGATTTAA
*
239040 TAAAT TAAAT TAAAA TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
239071 CATATCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAAAT
Found at i:239058 original size:15 final size:15
Alignment explanation
Indices: 239038--239068 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
239028 TGATGGATTT
239038 AATAAATTAAATTAA
1 AATAAATTAAATTAA
239053 AATAAATTAAATTAA
1 AATAAATTAAATTAA
239068 A
1 A
239069 TTCATATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAATTAAATTAA
Found at i:239154 original size:30 final size:32
Alignment explanation
Indices: 239120--239184 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
239110 ATCTTTTTAA
*
239120 TTTTGAATATTACAAA-TATATA-AATATCTT
1 TTTTGAATATTACAAATTAAATATAATATCTT
* *
239150 TTTTGAATATTTCAAATTAAATATATTATCTT
1 TTTTGAATATTACAAATTAAATATAATATCTT
239182 TTT
1 TTT
239185 AGAGTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 15 0.50
31 5 0.17
32 10 0.33
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTTGAATATTACAAATTAAATATAATATCTT
Found at i:242299 original size:84 final size:84
Alignment explanation
Indices: 242150--242334 Score: 230
Period size: 84 Copynumber: 2.2 Consensus size: 84
242140 CCAGACCCGG
* * *
242150 GTGTTATTTTCGTAAATATTTTAAAAATGTACTTTTTTTGTAAATATTTTTAAAAGGGAGATATT
1 GTGTTATTTTCGTAAATATTTTAAAAAGGTACTTTTTTCGTAAATATTTTAAAAAGGGAGATATT
*
242215 TTCGTAAATATTTTTAAAA
66 TTCATAAATATTTTTAAAA
* * * * *
242234 GTGTTATTTTTGTAAATATTTTTAAAAGGT-GTTATTTTCGTAAATATTTATAAAAAGGTA-TTA
1 GTGTTATTTTCGTAAATATTTTAAAAAGGTACTT-TTTTCGTAAATATTT-TAAAAAGGGAGATA
242297 TTTTCATAAATATTTTTAAAA
64 TTTTCATAAATATTTTTAAAA
*
242318 GGGTGTTAGTTTCGTAA
1 --GTGTTATTTTCGTAA
242335 TTAATTTATG
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 2 0.02
84 63 0.73
85 8 0.09
86 13 0.15
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.49
Consensus pattern (84 bp):
GTGTTATTTTCGTAAATATTTTAAAAAGGTACTTTTTTCGTAAATATTTTAAAAAGGGAGATATT
TTCATAAATATTTTTAAAA
Found at i:242330 original size:29 final size:28
Alignment explanation
Indices: 242149--242334 Score: 223
Period size: 29 Copynumber: 6.6 Consensus size: 28
242139 ACCAGACCCG
*
242149 GGTGTTATTTTCGTAAATATTTTAAAAA
1 GGTGTTATTTTCGTAAATATTTTTAAAA
* * *
242177 TGTACTT-TTTTTGTAAATATTTTTAAAA
1 GGT-GTTATTTTCGTAAATATTTTTAAAA
* *
242205 GGGAGATATTTTCGTAAATATTTTTAAAA
1 -GGTGTTATTTTCGTAAATATTTTTAAAA
*
242234 -GTGTTATTTTTGTAAATATTTTTAAAA
1 GGTGTTATTTTCGTAAATATTTTTAAAA
*
242261 GGTGTTATTTTCGTAAATATTTATAAAAA
1 GGTGTTATTTTCGTAAATATTT-TTAAAA
* *
242290 GGTATTATTTTCATAAATATTTTTAAAA
1 GGTGTTATTTTCGTAAATATTTTTAAAA
*
242318 GGGTGTTAGTTTCGTAA
1 -GGTGTTATTTTCGTAA
242335 TTAATTTATG
Statistics
Matches: 132, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
27 24 0.18
28 47 0.36
29 61 0.46
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (28 bp):
GGTGTTATTTTCGTAAATATTTTTAAAA
Found at i:242965 original size:2 final size:2
Alignment explanation
Indices: 242958--243001 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
242948 GATTTGATAA
* * * *
242958 AT AT AT AT GT TT AC AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
243000 AT
1 AT
243002 TTCACTGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Done.