Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 6 of 172
Found at i:1730512 original size:17 final size:18
Alignment explanation
Indices: 1730490--1730523 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1730480 TATCCATGAG
*
1730490 GGGCCCATA-AGCCCATC
1 GGGCCCACACAGCCCATC
1730507 GGGCCCACACAGCCCAT
1 GGGCCCACACAGCCCAT
1730524 TTCAGCCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.44, G:0.24, T:0.09
Consensus pattern (18 bp):
GGGCCCACACAGCCCATC
Found at i:1733925 original size:13 final size:13
Alignment explanation
Indices: 1733907--1733935 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1733897 TGTATGGAAC
1733907 ACGACTTTGGGAT
1 ACGACTTTGGGAT
1733920 ACGACTTTGGGAT
1 ACGACTTTGGGAT
1733933 ACG
1 ACG
1733936 GGCGCGTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (13 bp):
ACGACTTTGGGAT
Found at i:1735910 original size:30 final size:30
Alignment explanation
Indices: 1735876--1735932 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1735866 CGAGCCTAGG
*
1735876 GGCAAAAGTGTAAATATGCAAACGTTTAGA
1 GGCAAAAGTGTAAATATGCAAAAGTTTAGA
* * *
1735906 GGCAAAATTGTAATTTTGCAAAAGTTT
1 GGCAAAAGTGTAAATATGCAAAAGTTT
1735933 GGGTTAAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (30 bp):
GGCAAAAGTGTAAATATGCAAAAGTTTAGA
Found at i:1740335 original size:30 final size:30
Alignment explanation
Indices: 1740301--1740361 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1740291 TTCCCGAGCC
1740301 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
1740331 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1740361 T
1 T
1740362 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:1745615 original size:35 final size:35
Alignment explanation
Indices: 1745566--1745637 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
1745556 CTGCAAGAAT
*
1745566 TGCCCGTTAATGATTTGAGATATCTGTTTTCCTGC
1 TGCCCGTTAATGATTTGAGACATCTGTTTTCCTGC
* *
1745601 TGCCCGTTATTGATTTGAGACATCTTTTTTCCTGC
1 TGCCCGTTAATGATTTGAGACATCTGTTTTCCTGC
1745636 TG
1 TG
1745638 ATCTGATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (35 bp):
TGCCCGTTAATGATTTGAGACATCTGTTTTCCTGC
Found at i:1746572 original size:12 final size:12
Alignment explanation
Indices: 1746555--1746580 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1746545 AGATAAATAG
1746555 TTGTATGCGAAA
1 TTGTATGCGAAA
1746567 TTGTATGCGAAA
1 TTGTATGCGAAA
1746579 TT
1 TT
1746581 CAGTAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (12 bp):
TTGTATGCGAAA
Found at i:1756002 original size:43 final size:42
Alignment explanation
Indices: 1755912--1756075 Score: 154
Period size: 43 Copynumber: 3.9 Consensus size: 42
1755902 ATTGAGATGA
* * * *
1755912 GATTACGTGTAAGACTATGTCTGGGACATTCGCATTGTATTA-T
1 GATTACATGTAAGACCATGTCTGGGACATTGGCA-T-CATTAGT
*
1755955 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCATTAGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCATTAGT
* * *
1755997 CGATTACATGTAAGACCCTGTCTAGGG-CAATGGCATCAATATGT
1 -GATTACATGTAAGACCATGTCT-GGGACATTGGCATCATTA-GT
* * * *
1756041 GATAACATGTAAGACCATATATGGGATA-TGGCATC
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATC
1756076 GTACGAGCTA
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
41 4 0.04
42 12 0.12
43 83 0.80
44 5 0.05
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCATTAGT
Found at i:1759935 original size:54 final size:54
Alignment explanation
Indices: 1759864--1760138 Score: 469
Period size: 54 Copynumber: 5.1 Consensus size: 54
1759854 TAATCGATGG
* * * * * *
1759864 AATGACTGTTTTACCCTTATGAGGTAAAATGACTGTTTTGCCCTTATGGGGTAA
1 AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
* * *
1759918 AATGACTATTCTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
1 AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
1759972 AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
1 AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
1760026 AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
1 AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
1760080 AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
1 AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
1760134 AATGA
1 AATGA
1760139 CTATTTTTCC
Statistics
Matches: 211, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 211 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (54 bp):
AATGATTGTTTTGCCCTTATGGGGTAAAATGACTATTTTTCCCTTATGAGGTAA
Found at i:1760172 original size:27 final size:27
Alignment explanation
Indices: 1759864--1760151 Score: 396
Period size: 27 Copynumber: 10.7 Consensus size: 27
1759854 TAATCGATGG
* *
1759864 AATGACTGTTTTACCCTTATGAGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
* * *
1759891 AATGACTGTTTTGCCCTTATGGGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
* * *
1759918 AATGACTATTCTGCCCTTATGGGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
1759945 AATGACTATTTTTCCCTTATGAGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
* * * *
1759972 AATGATTGTTTTGCCCTTATGGGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
1759999 AATGACTATTTTTCCCTTATGAGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
* * * *
1760026 AATGATTGTTTTGCCCTTATGGGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
1760053 AATGACTATTTTTCCCTTATGAGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
* * * *
1760080 AATGATTGTTTTGCCCTTATGGGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
1760107 AATGACTATTTTTCCCTTATGAGGTAA
1 AATGACTATTTTTCCCTTATGAGGTAA
1760134 AATGACTATTTTTCCCTT
1 AATGACTATTTTTCCCTT
1760152 TTATGGTAAG
Statistics
Matches: 230, Mismatches: 31, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 230 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (27 bp):
AATGACTATTTTTCCCTTATGAGGTAA
Found at i:1760561 original size:18 final size:18
Alignment explanation
Indices: 1760538--1760583 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1760528 TGCATATTGC
1760538 TTACTATTACTGCACTAT
1 TTACTATTACTGCACTAT
* * *
1760556 TTACTATTATTGCATTGT
1 TTACTATTACTGCACTAT
*
1760574 TTACTGTTAC
1 TTACTATTAC
1760584 AGCAATGGGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (18 bp):
TTACTATTACTGCACTAT
Found at i:1762920 original size:48 final size:48
Alignment explanation
Indices: 1762849--1763064 Score: 165
Period size: 48 Copynumber: 4.5 Consensus size: 48
1762839 AGTACCAATT
* * *
1762849 CCATGTCCCCA-ACTTGGTCTTACA-TGAATCCATATATCATCGTTGATG
1 CCATGT-CCCAGACATGGTCTTACACTGAA-CCACATATCATCGTCGATG
* * * * *
1762897 CCATGTCTCAGACATGGTCTTACATTG-GCACACATATCATCATGGATG
1 CCATGTCCCAGACATGGTCTTACACTGAAC-CACATATCATCGTCGATG
* * *
1762945 TCATGTCCCAGACATGGTCTTACACTGGCAA--ACATATCATTGTCGATA
1 CCATGTCCCAGACATGGTCTTACACT-G-AACCACATATCATCGTCGATG
* * * *
1762993 CCATGTCCCAGACATGGTCTTACACAG-GCACATATATCATCGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTGAAC-CACATATCATCGTCGATG
* * * *
1763041 TCATGTCCCAAAAATGTTCTTACA
1 CCATGTCCCAGACATGGTCTTACA
1763065 TAGGCACACA
Statistics
Matches: 134, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
47 5 0.04
48 126 0.94
49 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACACTGAACCACATATCATCGTCGATG
Found at i:1763070 original size:48 final size:48
Alignment explanation
Indices: 1762882--1763075 Score: 228
Period size: 48 Copynumber: 4.0 Consensus size: 48
1762872 ATGAATCCAT
* * *
1762882 ATATCATCGTTGATGCCATGTCTCAGACATGGTCTTACATTGGCACAC
1 ATATCATCGTCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAC
* * * *
1762930 ATATCATCATGGATGTCATGTCCCAGACATGGTCTTACACT-GGCAAAC
1 ATATCATCGTCGATGCCATGTCCCAGACATGGTCTTACA-TAGGCACAC
* * * *
1762978 ATATCATTGTCGATACCATGTCCCAGACATGGTCTTACACAGGCACAT
1 ATATCATCGTCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAC
* * * * *
1763026 ATATCATCGCCGATGTCATGTCCCAAAAATGTTCTTACATAGGCACAC
1 ATATCATCGTCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAC
1763074 AT
1 AT
1763076 TTAGTATGGT
Statistics
Matches: 122, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
48 121 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (48 bp):
ATATCATCGTCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAC
Found at i:1764236 original size:20 final size:20
Alignment explanation
Indices: 1764180--1764294 Score: 104
Period size: 20 Copynumber: 5.8 Consensus size: 20
1764170 TATTATAAGT
* *
1764180 AGCTTGTCTGCATCACTGCC
1 AGCTTGTCTGCATTACTGGC
* * *
1764200 AGTTTATCTACATTACTGGC
1 AGCTTGTCTGCATTACTGGC
* *
1764220 AGCTTGTCTGCACTACTAGC
1 AGCTTGTCTGCATTACTGGC
* * * *
1764240 AGTTTATTTGCATTACTGGT
1 AGCTTGTCTGCATTACTGGC
* **
1764260 AGCTTGACCACATTACTGGC
1 AGCTTGTCTGCATTACTGGC
1764280 AGCTTGTCTGCATTA
1 AGCTTGTCTGCATTA
1764295 TTGGTGACTT
Statistics
Matches: 69, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (20 bp):
AGCTTGTCTGCATTACTGGC
Found at i:1770443 original size:45 final size:45
Alignment explanation
Indices: 1770393--1770478 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1770383 ATTGACGGTT
* *
1770393 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGCAAGGC
1 AAGGATACCATGTAAAACCATGTCAAGACATGGCATCGGCAAGGC
* *
1770438 AAGGATCCCGTGTAAAACCATGTCAAGACATGGCATCGGCA
1 AAGGATACCATGTAAAACCATGTCAAGACATGGCATCGGCA
1770479 TTGATTAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (45 bp):
AAGGATACCATGTAAAACCATGTCAAGACATGGCATCGGCAAGGC
Found at i:1770656 original size:55 final size:53
Alignment explanation
Indices: 1770527--1770723 Score: 243
Period size: 54 Copynumber: 3.7 Consensus size: 53
1770517 GAACTAAGAT
* * *
1770527 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTC-ATAAGGC
* * *
1770581 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACAATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-C-ATAAGGC
* * * *
1770636 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGT
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCATAAGGC
* *
1770689 AAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCA
1770724 ATGGTAAGTT
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 4 0.03
53 32 0.26
54 42 0.34
55 42 0.34
56 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCATAAGGC
Found at i:1770734 original size:108 final size:109
Alignment explanation
Indices: 1770535--1770734 Score: 312
Period size: 108 Copynumber: 1.8 Consensus size: 109
1770525 ATAAGGATAT
* *
1770535 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACC
* *
1770600 ATGTCAAGACATGGCATTGATGAGTTACAATAAGGCAAAGGTCC
66 ATGTCAAGACATGGCAATGATAAGTTACAATAAGGCAAAGGTCC
* * * *
1770644 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGTAAGGATACCACGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACC
*
1770708 ATGTCAAGACATGGCAATGGTAAGTTA
66 ATGTCAAGACATGGCAATGATAAGTTA
1770735 AAAAGGGAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
108 46 0.56
109 36 0.44
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (109 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACC
ATGTCAAGACATGGCAATGATAAGTTACAATAAGGCAAAGGTCC
Found at i:1771559 original size:24 final size:24
Alignment explanation
Indices: 1771532--1771589 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 24
1771522 GGAGAAATGA
*
1771532 AATTAGGTGATGAATGAGACATAG
1 AATTAAGTGATGAATGAGACATAG
1771556 AATTAAATAAGTGATGAATGAGACATAG
1 AA-T---TAAGTGATGAATGAGACATAG
1771584 AATTAA
1 AATTAA
1771590 ATCTTATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 5 0.17
25 1 0.03
27 1 0.03
28 22 0.76
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.26
Consensus pattern (24 bp):
AATTAAGTGATGAATGAGACATAG
Found at i:1771569 original size:28 final size:28
Alignment explanation
Indices: 1771538--1771591 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1771528 ATGAAATTAG
1771538 GTGATGAATGAGACATAGAATTAAATAA
1 GTGATGAATGAGACATAGAATTAAATAA
1771566 GTGATGAATGAGACATAGAATTAAAT
1 GTGATGAATGAGACATAGAATTAAAT
1771592 CTTATTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (28 bp):
GTGATGAATGAGACATAGAATTAAATAA
Found at i:1773298 original size:34 final size:34
Alignment explanation
Indices: 1773256--1773323 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
1773246 TGAATGATCA
1773256 TGGTGGTTTGAGGAGTTTATACTCCTCATTCCTG
1 TGGTGGTTTGAGGAGTTTATACTCCTCATTCCTG
* * *
1773290 TGGTGGTTTGCGGAGTTTATACTTCTTATTCCTG
1 TGGTGGTTTGAGGAGTTTATACTCCTCATTCCTG
1773324 CTATCAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.44
Consensus pattern (34 bp):
TGGTGGTTTGAGGAGTTTATACTCCTCATTCCTG
Found at i:1777496 original size:6 final size:6
Alignment explanation
Indices: 1777485--1777606 Score: 108
Period size: 6 Copynumber: 19.8 Consensus size: 6
1777475 AGTCAAAATG
*
1777485 AGAATC AGAATC AGAATC AG-GTGAC AGAATC AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC
* * *
1777534 AGAATC AGAATT AG-GTGAC AGAATC AGAATC A-ATATC AG-GTGAC AGAATC
1 AGAATC AGAATC AGAAT--C AGAATC AGAATC AGA-ATC AGAAT--C AGAATC
*
1777584 AGAATC AGAATC AGAACC AGAAT
1 AGAATC AGAATC AGAATC AGAAT
1777607 GTGAATGCAA
Statistics
Matches: 95, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
5 4 0.04
6 80 0.84
7 8 0.08
8 3 0.03
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (6 bp):
AGAATC
Found at i:1777516 original size:25 final size:25
Alignment explanation
Indices: 1777485--1777597 Score: 152
Period size: 25 Copynumber: 4.8 Consensus size: 25
1777475 AGTCAAAATG
1777485 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGGTGAC
1777510 AGAATCAGAATCAG-A--A--T--C
1 AGAATCAGAATCAGAATCAGGTGAC
*
1777528 AGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGGTGAC
1777553 AGAATCAGAATCA-ATATCAGGTGAC
1 AGAATCAGAATCAGA-ATCAGGTGAC
1777578 AGAATCAGAATCAGAATCAG
1 AGAATCAGAATCAGAATCAG
1777598 AACCAGAATG
Statistics
Matches: 78, Mismatches: 1, Indels: 18
0.80 0.01 0.19
Matches are distributed among these distances:
18 15 0.19
19 1 0.01
20 1 0.01
21 1 0.01
22 1 0.01
23 1 0.01
24 2 0.03
25 55 0.71
26 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTGAC
Found at i:1777522 original size:31 final size:31
Alignment explanation
Indices: 1777485--1777599 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 31
1777475 AGTCAAAATG
1777485 AGAATCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
*
1777516 AGAATCAGAATCAGAATCA-G-AATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGGTGA-CAG-A--A--T--C
1777553 AGAATCAGAATCA-ATATCAGGTGACAGAATC
1 AGAATCAGAATCAGA-ATCAGGTGACAGAATC
1777584 AGAATCAGAATCAGAA
1 AGAATCAGAATCAGAA
1777600 CCAGAATGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 24
0.73 0.02 0.25
Matches are distributed among these distances:
29 1 0.01
30 4 0.06
31 35 0.50
32 1 0.01
33 2 0.03
35 2 0.03
36 1 0.01
37 19 0.27
38 4 0.06
39 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTGACAGAATC
Found at i:1777612 original size:18 final size:18
Alignment explanation
Indices: 1777464--1777606 Score: 78
Period size: 18 Copynumber: 7.8 Consensus size: 18
1777454 AAGAAACATT
* * *
1777464 ATCAGAACTAGAGTCAAA
1 ATCAGAACCAGAATCAGA
* *
1777482 ATGAGAATCAGAATCAGA
1 ATCAGAACCAGAATCAGA
*
1777500 ATCAGGTGA-CAGAATCAGA
1 ATCA-G-AACCAGAATCAGA
*
1777519 ATCAGAATCAGAATCAGA
1 ATCAGAACCAGAATCAGA
** *
1777537 ATCAGAATTAG-GTGACAGA
1 ATCAGAACCAGAAT--CAGA
*
1777556 ATCAGAATCA-ATATCAG-
1 ATCAGAACCAGA-ATCAGA
* *
1777573 GTGACAGAATCAGAATCAGA
1 AT--CAGAACCAGAATCAGA
1777593 ATCAGAACCAGAAT
1 ATCAGAACCAGAAT
1777607 GTGAATGCAA
Statistics
Matches: 99, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
17 3 0.03
18 51 0.52
19 41 0.41
20 4 0.04
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.17
Consensus pattern (18 bp):
ATCAGAACCAGAATCAGA
Found at i:1777773 original size:27 final size:26
Alignment explanation
Indices: 1777725--1777784 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
1777715 GCGAGGCTGC
*
1777725 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
1777752 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
1777778 TAGATAT
1 CAGATAT
1777785 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:1777871 original size:27 final size:26
Alignment explanation
Indices: 1777823--1777882 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
1777813 GCGAGGCTGC
*
1777823 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
1777850 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
1777876 TAGATAT
1 CAGATAT
1777883 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:1777882 original size:98 final size:98
Alignment explanation
Indices: 1777713--1778103 Score: 782
Period size: 98 Copynumber: 4.0 Consensus size: 98
1777703 ACAGAAAATG
1777713 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
1777778 TAGATATATATATGTGGCGAAGCCACCAGATTA
66 TAGATATATATATGTGGCGAAGCCACCAGATTA
1777811 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
1777876 TAGATATATATATGTGGCGAAGCCACCAGATTA
66 TAGATATATATATGTGGCGAAGCCACCAGATTA
1777909 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
1777974 TAGATATATATATGTGGCGAAGCCACCAGATTA
66 TAGATATATATATGTGGCGAAGCCACCAGATTA
1778007 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
1778072 TAGATATATATATGTGGCGAAGCCACCAGATT
66 TAGATATATATATGTGGCGAAGCCACCAGATT
1778104 NNNNNNNNNN
Statistics
Matches: 293, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 293 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (98 bp):
CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAA
TAGATATATATATGTGGCGAAGCCACCAGATTA
Found at i:1777969 original size:27 final size:26
Alignment explanation
Indices: 1777921--1777980 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
1777911 GCGAGGCTGC
*
1777921 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
1777948 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
1777974 TAGATAT
1 CAGATAT
1777981 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:1778067 original size:27 final size:26
Alignment explanation
Indices: 1778019--1778078 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
1778009 GCGAGGCTGC
*
1778019 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
1778046 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
1778072 TAGATAT
1 CAGATAT
1778079 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:1788308 original size:27 final size:27
Alignment explanation
Indices: 1788278--1789319 Score: 1198
Period size: 27 Copynumber: 38.6 Consensus size: 27
1788268 AACACCCTAG
** * * *
1788278 GGGTAAAATGGTAATTTTATAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1788305 GGGTAAAACGGTAATTCTGTATATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
1788332 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1788359 GGGTAAAACAATAATTTTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1788386 GGGTAAAATAGTAATTCTATCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
**
1788413 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1788440 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1788467 GGGTAAAACAATAATTTTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1788494 GGGTAAAATAGTAATTCTATCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
**
1788521 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1788548 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1788575 GGGTAAAACAATAATTTTATAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1788602 GGGTAAAATAGTAATTCTATCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
**
1788629 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1788656 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
1788683 GGGTAAAAC-GATAATTCTATAAATCGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
* *
1788710 AGGTAAAATAGTAATTCTGTAAA-CTGA
1 GGGTAAAACAGTAATTCTGTAAATC-GA
* * * *
1788737 GGGTACAACTGTAATTCTGTCAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1788764 GGGTAAAAC-GATAACTCTGTAAATTGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
* * * *
1788791 GGGTAAAATAGAAATTTTGTAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
1788818 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1788845 GGGTAAAATAGTAATTCTATAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1788872 GGGTAAAACGGTAACTT-TGTAATTCGA
1 GGGTAAAACAGTAA-TTCTGTAAATCGA
* * *
1788899 GGGTAAAACAGTAATTTTGTAATTTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
1788926 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1788953 GGGTAAAATAGTAATTCTATAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1788980 GGGTAAAACGGTAACTT-TGTAATTCGA
1 GGGTAAAACAGTAA-TTCTGTAAATCGA
* * *
1789007 GGGTAAAACAGTAATTTTGTAATTTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
1789034 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1789061 GGGTAAAATAGTAATTCTATAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1789088 GGGTAAAACGGTAACTT-TGTAATTCGA
1 GGGTAAAACAGTAA-TTCTGTAAATCGA
* * *
1789115 GGGTAAAACAGTAATTTTGTAATTTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
1789142 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
1789169 GGGTAAAATAGTAATTCTATAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
1789196 GGGTAAAACGGTAACTT-TGTAATTCGA
1 GGGTAAAACAGTAA-TTCTGTAAATCGA
* * *
1789223 GGGTAAAACAGTAATTTTGTAATTTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
1789250 GGGTAAAACAGTAATTCTGTAAATCAA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
1789277 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
1789304 GGGTAAAACTGTAATT
1 GGGTAAAACAGTAATT
1789320 TTTTAATTCA
Statistics
Matches: 879, Mismatches: 122, Indels: 28
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.01
27 858 0.98
28 10 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Found at i:1788444 original size:108 final size:108
Alignment explanation
Indices: 1788278--1789335 Score: 1359
Period size: 108 Copynumber: 9.8 Consensus size: 108
1788268 AACACCCTAG
** * * * ** *
1788278 GGGTAAAATGGTAATTTTATAAATTGAGGGTAAAACGGTAATTCTGTATATCGAGGGTAAAACAG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * *
1788343 TAATTTTGTAAATCGAGGGTAAAACAATAATTTTATAAATCGA
66 TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
* * * * *
1788386 GGGTAAAATAGTAATTCTATCAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATAG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * *
1788451 TAATTTTGTAAATCGAGGGTAAAACAATAATTTTATAAATCGA
66 TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
* * * * *
1788494 GGGTAAAATAGTAATTCTATCAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATAG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * *
1788559 TAATTTTGTAAATCGAGGGTAAAACAATAATTTTATAAATCGA
66 TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
* * * * *
1788602 GGGTAAAATAGTAATTCTATCAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATAG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * * * *
1788667 TAATTTTGTAAATCGAGGGTAAAACGATAATTCTATAAATCGA
66 TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
* * * * *
1788710 AGGTAAAATAGTAATTCTGTAAA-CTGAGGGTACAACT-GTAATTCTGTCAATTGAGGGTAAAAC
1 GGGTAAAACAGTAATTCTGTAAATC-GAGGGTA-AAATAGTAATTCTGTAAATCGAGGGTAAAAC
* * *
1788773 -GATAACTCTGTAAATTGAGGGTAAAATAGA-AATTTTGTAAATTGA
64 AG-TAACTTTGTAAATCGAGGGTAAAACA-ATAATTTTGTAAATTGA
* * *
1788818 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATTGAGGGTAAAACGG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * *
1788883 TAACTTTGTAATTCGAGGGTAAAACAGTAATTTTGTAATTTGA
66 TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
* * *
1788926 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATTGAGGGTAAAACGG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * *
1788991 TAACTTTGTAATTCGAGGGTAAAACAGTAATTTTGTAATTTGA
66 TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
* * *
1789034 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATTGAGGGTAAAACGG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * *
1789099 TAACTTTGTAATTCGAGGGTAAAACAGTAATTTTGTAATTTGA
66 TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
* * *
1789142 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATTGAGGGTAAAACGG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * *
1789207 TAACTTTGTAATTCGAGGGTAAAACAGTAATTTTGTAATTTGA
66 TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
* * * *
1789250 GGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAACTG
1 GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
* * * *
1789315 TAATTTTTTAATTCAAGGGTA
66 TAACTTTGTAAATCGAGGGTA
1789336 CTTTGATAAT
Statistics
Matches: 898, Mismatches: 44, Indels: 16
0.94 0.05 0.02
Matches are distributed among these distances:
107 5 0.01
108 887 0.99
109 6 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (108 bp):
GGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACAG
TAACTTTGTAAATCGAGGGTAAAACAATAATTTTGTAAATTGA
Found at i:1789386 original size:27 final size:27
Alignment explanation
Indices: 1789356--1789481 Score: 89
Period size: 27 Copynumber: 4.7 Consensus size: 27
1789346 TTTACATGTC
*
1789356 GAGGGTATTTCAGTAATTTTGCAAACT
1 GAGGGTATTTCAGTAATTTTACAAACT
*
1789383 GAGGGTATTTCGGTAATTTTACAAA-T
1 GAGGGTATTTCAGTAATTTTACAAACT
** ** * *
1789409 CGAGAATATTTGGGTAATTTTATAAACC
1 -GAGGGTATTTCAGTAATTTTACAAACT
* *
1789437 GGGGGTACTTT-GGTAATTTTAC-AACT
1 GAGGGTA-TTTCAGTAATTTTACAAACT
* *
1789463 G-GGAGTTTTTTAGTAATTT
1 GAGG-GTATTTCAGTAATTT
1789482 GGTAAACTAA
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
25 5 0.06
26 14 0.17
27 58 0.73
28 3 0.04
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.40
Consensus pattern (27 bp):
GAGGGTATTTCAGTAATTTTACAAACT
Found at i:1789388 original size:54 final size:54
Alignment explanation
Indices: 1789330--1789460 Score: 147
Period size: 54 Copynumber: 2.4 Consensus size: 54
1789320 TTTTAATTCA
* ** ** * *
1789330 AGGGTACTTTGATAATTTTACATGTCGAGGGTATTTCAGTAATTTTGCAAACTG
1 AGGGTACTTTGGTAATTTTACAAATCGAGAATATTTCAGTAATTTTACAAACCG
** *
1789384 AGGGTA-TTTCGGTAATTTTACAAATCGAGAATATTTGGGTAATTTTATAAACCG
1 AGGGTACTTT-GGTAATTTTACAAATCGAGAATATTTCAGTAATTTTACAAACCG
*
1789438 GGGGTACTTTGGTAATTTTACAA
1 AGGGTACTTTGGTAATTTTACAA
1789461 CTGGGAGTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
53 3 0.05
54 58 0.91
55 3 0.05
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (54 bp):
AGGGTACTTTGGTAATTTTACAAATCGAGAATATTTCAGTAATTTTACAAACCG
Found at i:1793187 original size:27 final size:28
Alignment explanation
Indices: 1793103--1793200 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
1793093 CATGAGATTG
* * * *
1793103 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
1793132 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
1793160 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
1793187 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
1793201 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:1793211 original size:27 final size:27
Alignment explanation
Indices: 1793131--1793213 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
1793121 TAAATTGTAC
* *
1793131 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
1793159 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
1793186 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
1793213 A
1 A
1793214 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:1793214 original size:29 final size:27
Alignment explanation
Indices: 1793103--1793214 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
1793093 CATGAGATTG
** * *
1793103 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
1793132 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
1793160 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
1793187 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
1793215 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:1799966 original size:40 final size:40
Alignment explanation
Indices: 1799876--1800061 Score: 202
Period size: 40 Copynumber: 4.7 Consensus size: 40
1799866 TTGAATGCTG
* * *
1799876 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* * *
1799916 TCAGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
1799956 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
1799996 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTA-AA
* *
1800037 -CCGAGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1800062 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.01
40 111 0.89
41 12 0.10
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:1800079 original size:80 final size:79
Alignment explanation
Indices: 1799929--1800094 Score: 194
Period size: 80 Copynumber: 2.1 Consensus size: 79
1799919 GGACTAAGAT
* * ** *
1799929 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGAGCTAAGTCCCGAAGGCATTTGAACGAGTGACTA
*
1799994 AATCCGGGTTAAGTC
66 AATCC-GGTTAAATC
*
1800009 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGAGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGAGCTAAGTCCCGAAGGCATTTGAACGAGTGA-
* *
1800071 CTATATCCGGTTAAATT
63 CTAAATCCGGTTAAATC
1800088 CCGAAGG
1 CCGAAGG
1800095 TACGTGATGT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
79 18 0.24
80 56 0.76
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGAGCTAAGTCCCGAAGGCATTTGAACGAGTGACTA
AATCCGGTTAAATC
Found at i:1800217 original size:147 final size:148
Alignment explanation
Indices: 1799981--1800274 Score: 475
Period size: 147 Copynumber: 2.0 Consensus size: 148
1799971 GAAGGCATTT
*
1799981 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGAGCTAT
1 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAAACCGAGCTAT
*
1800046 GTCCCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATTCCGAAGGTACGTGATGTGGGAAT
66 GTCCCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATCCCGAAGGTACGTGATGTGGGAAT
*
1800111 GAATGATCTTGCTGTAAC
131 GAATGAGCTTGCTGTAAC
** * * *
1800129 GTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACC-AGGCTA
1 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAAACCGA-GCTA
* *
1800192 TGTCCCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATCCCGAAGGTACGTGATTTGGTAA
65 TGTCCCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATCCCGAAGGTACGTGATGTGGGAA
1800257 TGAATGAGCTTGCTGTAA
130 TGAATGAGCTTGCTGTAA
1800275 AATTCCAGCG
Statistics
Matches: 135, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
146 1 0.01
147 100 0.74
148 34 0.25
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (148 bp):
GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAAACCGAGCTAT
GTCCCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATCCCGAAGGTACGTGATGTGGGAAT
GAATGAGCTTGCTGTAAC
Found at i:1806939 original size:27 final size:27
Alignment explanation
Indices: 1806909--1807962 Score: 1177
Period size: 27 Copynumber: 39.2 Consensus size: 27
1806899 TAACACCCTA
* * *
1806909 AGGGTAAAATGGTAATTTTATAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* *
1806936 AGGGTAAAA-CGATAATTCTGTAAATCA
1 AGGGTAAAATAG-TAATTCTGTAAATCG
* *
1806963 AGGGTAAAACAGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* * *
1806990 AGGGTAAAATAATAATTTTTTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* * *
1807017 AGGGTAAAACAGTAATTCTATTAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* *
1807044 AGGGTAAAATGGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807071 AGGGTAAAATAGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* * *
1807098 AGGGTAAAA-CGATAATTCTGTACATCA
1 AGGGTAAAATAG-TAATTCTGTAAATCG
*
1807125 AGGGTAAAATAGTGATTCTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807152 AGGG-AAAACTA-TAATTCTGTCAATCG
1 AGGGTAAAA-TAGTAATTCTGTAAATCG
* * *
1807178 AGGGTAAAACAGAAATTCTGTAAATTG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807205 AGGGTAAAATAGTAATTCTGTAAATCA
1 AGGGTAAAATAGTAATTCTGTAAATCG
** *
1807232 AGGGTAAAACGGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* * *
1807259 AGGGTAAAA-CGATAATTCTGTACATCA
1 AGGGTAAAATAG-TAATTCTGTAAATCG
*
1807286 AGGGTAAAATAGTGATTCTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807313 AGGG-AAAACTA-TAATTCTGTCAATCG
1 AGGGTAAAA-TAGTAATTCTGTAAATCG
* * *
1807339 AGGGTAAAACAGAAATTCTGTAAATTG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807366 AGGGTAAAATAGTAATTCTGTAAATCA
1 AGGGTAAAATAGTAATTCTGTAAATCG
** *
1807393 AGGGTAAAACGGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* * *
1807420 AGGGTAAAA-CGATAATTCTGTACATCA
1 AGGGTAAAATAG-TAATTCTGTAAATCG
*
1807447 AGGGTAAAATAGTGATTCTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807474 AGGG-AAAACTA-TAATTCTGTCAATCG
1 AGGGTAAAA-TAGTAATTCTGTAAATCG
* * *
1807500 AGGGTAAAACAGAAATTCTGTAAATTG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807527 AGGGTAAAATAGTAATTCTGTAAATCA
1 AGGGTAAAATAGTAATTCTGTAAATCG
** *
1807554 AGGGTAAAACGGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* * *
1807581 AGGGTAAAA-CGATAATTCTGTACATCA
1 AGGGTAAAATAG-TAATTCTGTAAATCG
*
1807608 AGGGTAAAATAGTGATTCTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807635 AGGG-AAAACTA-TAATTCTGTCAATCG
1 AGGGTAAAA-TAGTAATTCTGTAAATCG
* * *
1807661 AGGGTAAAACAGAAATTCTGTAAATTG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807688 AGGGTAAAATAGTAATTCTGTAAATCA
1 AGGGTAAAATAGTAATTCTGTAAATCG
** *
1807715 AGGGTAAAACGGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
* * *
1807742 AGGGTAAAA-CGATAATTCTGTACATCA
1 AGGGTAAAATAG-TAATTCTGTAAATCG
*
1807769 AGGGTAAAATAGTGATTCTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807796 AGGG-AAAACTA-TAATTCTGTCAATCG
1 AGGGTAAAA-TAGTAATTCTGTAAATCG
* * *
1807822 AGGGTAAAACAGAAATTCTGTAAATTG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807849 AGGGTAAAATAGTAATTCTGTAAATCA
1 AGGGTAAAATAGTAATTCTGTAAATCG
** *
1807876 AGGGTAAAACGGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
*
1807903 AGGGTAAAATAGTAATTCTGTAAATCA
1 AGGGTAAAATAGTAATTCTGTAAATCG
* * *
1807930 AGGGTAAAACAGTAATTTTGTAATTCG
1 AGGGTAAAATAGTAATTCTGTAAATCG
1807957 AGGGTA
1 AGGGTA
1807963 CTTTGATAAT
Statistics
Matches: 861, Mismatches: 139, Indels: 54
0.82 0.13 0.05
Matches are distributed among these distances:
26 116 0.13
27 739 0.86
28 6 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (27 bp):
AGGGTAAAATAGTAATTCTGTAAATCG
Found at i:1807252 original size:161 final size:161
Alignment explanation
Indices: 1806908--1807960 Score: 1849
Period size: 161 Copynumber: 6.5 Consensus size: 161
1806898 TTAACACCCT
* * * *
1806908 AAGGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAAC
1 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
* * * * * * *
1806973 AGTAATTTTGTAAATCGAGGGTAAAA-TAATAATTTTTTAAATCGAGGGTAAAACAGTAATTCTA
66 AGTGATTCTGTAAATCGAGGG-AAAACT-ATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTG
* * * *
1807037 TTAATCGAGGGTAAAATGGTAATTTTGTAAATC
129 TAAATTGAGGGTAAAATAGTAATTCTGTAAATC
* **
1807070 GAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1807135 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
66 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
1807200 AATTGAGGGTAAAATAGTAATTCTGTAAATC
131 AATTGAGGGTAAAATAGTAATTCTGTAAATC
1807231 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1807296 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
66 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
1807361 AATTGAGGGTAAAATAGTAATTCTGTAAATC
131 AATTGAGGGTAAAATAGTAATTCTGTAAATC
1807392 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1807457 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
66 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
1807522 AATTGAGGGTAAAATAGTAATTCTGTAAATC
131 AATTGAGGGTAAAATAGTAATTCTGTAAATC
1807553 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1807618 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
66 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
1807683 AATTGAGGGTAAAATAGTAATTCTGTAAATC
131 AATTGAGGGTAAAATAGTAATTCTGTAAATC
1807714 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
1807779 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
66 AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
1807844 AATTGAGGGTAAAATAGTAATTCTGTAAATC
131 AATTGAGGGTAAAATAGTAATTCTGTAAATC
* *
1807875 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAA-TAGTAATTCTGTAAATCAAGGGTAAAA
1 AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGA-TAATTCTGTACATCAAGGGTAAAA
* * * *
1807939 CAGTAATTTTGTAATTCGAGGG
65 TAGTGATTCTGTAAATCGAGGG
1807961 TACTTTGATA
Statistics
Matches: 864, Mismatches: 25, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
160 1 0.00
161 783 0.91
162 80 0.09
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (161 bp):
AAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTACATCAAGGGTAAAAT
AGTGATTCTGTAAATCGAGGGAAAACTATAATTCTGTCAATCGAGGGTAAAACAGAAATTCTGTA
AATTGAGGGTAAAATAGTAATTCTGTAAATC
Found at i:1807984 original size:27 final size:26
Alignment explanation
Indices: 1807954--1808086 Score: 124
Period size: 27 Copynumber: 5.0 Consensus size: 26
1807944 ATTTTGTAAT
* **
1807954 TCGAGGGTACTTTGATAATTTTACATG
1 TCGAGGGTA-TTTGGTAATTTTACAAA
* *
1807981 TCGAGGGTATTTCAGTTATTTTACAAA
1 TCGAGGGTATTT-GGTAATTTTACAAA
1808008 -CTGAGGGTATTTCGGTAATTTTACAAA
1 TC-GAGGGTATTT-GGTAATTTTACAAA
* * *
1808035 TCGAGGATATTTGGTAATTTTATAAG
1 TCGAGGGTATTTGGTAATTTTACAAA
* *
1808061 GCGGGGGTACTTTGGTAATTTTACAA
1 TCGAGGGTA-TTTGGTAATTTTACAA
1808087 CTGGCGGTAT
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
26 22 0.25
27 65 0.74
28 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (26 bp):
TCGAGGGTATTTGGTAATTTTACAAA
Found at i:1808002 original size:54 final size:53
Alignment explanation
Indices: 1807939--1808107 Score: 155
Period size: 53 Copynumber: 3.2 Consensus size: 53
1807929 AAGGGTAAAA
* * * ** *
1807939 CAGTAATTTTGTAATTCGAGGGTACTTTGATAATTTTACATGTCGAGGGTATTT
1 CAGTAATTTTATAA-ACGAGGGTACTTTGGTAATTTTACAAATCGAGGATATTT
* *
1807993 CAGTTATTTTACAAACTGAGGGTA-TTTCGGTAATTTTACAAATCGAGGATATTT
1 CAGTAATTTTATAAAC-GAGGGTACTTT-GGTAATTTTACAAATCGAGGATATTT
* * * * * *
1808047 -GGTAATTTTATAAGGCGGGGGTACTTTGGTAATTTTACAACTGGCGG-TATTT
1 CAGTAATTTTATAA-ACGAGGGTACTTTGGTAATTTTACAAATCGAGGATATTT
1808099 CAGTAATTT
1 CAGTAATTT
1808108 GGTAAACTAA
Statistics
Matches: 93, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
52 5 0.05
53 44 0.47
54 44 0.47
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.40
Consensus pattern (53 bp):
CAGTAATTTTATAAACGAGGGTACTTTGGTAATTTTACAAATCGAGGATATTT
Found at i:1808104 original size:26 final size:25
Alignment explanation
Indices: 1807985--1808107 Score: 97
Period size: 27 Copynumber: 4.7 Consensus size: 25
1807975 TACATGTCGA
* *
1807985 GGGTATTTCAGTTATTTTACAAACTG
1 GGGTATTTCGGTAATTTTAC-AACTG
*
1808011 AGGGTATTTCGGTAATTTTACAAATCG
1 -GGGTATTTCGGTAATTTTACAACT-G
* * *
1808038 AGGATATTT-GGTAATTTTATAAGGCGG
1 -GGGTATTTCGGTAATTTTACAA--CTG
1808065 GGGTACTTT-GGTAATTTTACAACTG
1 GGGTA-TTTCGGTAATTTTACAACTG
*
1808090 GCGGTATTTCAGTAATTT
1 G-GGTATTTCGGTAATTT
1808108 GGTAAACTAA
Statistics
Matches: 79, Mismatches: 11, Indels: 13
0.77 0.11 0.13
Matches are distributed among these distances:
25 6 0.08
26 30 0.38
27 43 0.54
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.40
Consensus pattern (25 bp):
GGGTATTTCGGTAATTTTACAACTG
Found at i:1810120 original size:11 final size:11
Alignment explanation
Indices: 1810106--1810131 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1810096 AATTGACGGA
1810106 AAAGTGACTAT
1 AAAGTGACTAT
1810117 AAAGTGACTAT
1 AAAGTGACTAT
1810128 AAAG
1 AAAG
1810132 AAAAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (11 bp):
AAAGTGACTAT
Found at i:1819414 original size:23 final size:22
Alignment explanation
Indices: 1819363--1819414 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
1819353 CCTCGTCTTT
*
1819363 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
1819385 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
1819408 TTCTTTT
1 TTCTTTT
1819415 TCAATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:1823502 original size:23 final size:23
Alignment explanation
Indices: 1823468--1823514 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1823458 CTAGTATACT
1823468 CAGCCACCGGTAGGACGTACGAG
1 CAGCCACCGGTAGGACGTACGAG
*
1823491 CAGCCACTGGTAGGACGTACGAG
1 CAGCCACCGGTAGGACGTACGAG
1823514 C
1 C
1823515 CTAGCACCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.34, T:0.11
Consensus pattern (23 bp):
CAGCCACCGGTAGGACGTACGAG
Found at i:1831883 original size:48 final size:48
Alignment explanation
Indices: 1831762--1832141 Score: 388
Period size: 48 Copynumber: 7.9 Consensus size: 48
1831752 GGAAAGATGT
* *
1831762 CGATGCCATGT-CCAAGACATGGTCTTACACTGGCTCTCATATATCG-GTGC
1 CGATGCCATGTCCCAA-ACATGGTCTTACACTAGCTCACATATA--GAG-GC
* * * *
1831812 TGATGCCATGTTCCAAACATGGTCTTATACTAGCCCACATATAGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGAGGC
** * *** * *
1831860 TAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTGTATAAATGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGAGGC
* * * *
1831908 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGAGGC
* * * * * *
1831956 CGATGCCATGTCGCAGACATGGTCTTACACTAGCTCTCGTATAAATGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGAGGC
* * * *
1832004 CGATGCCGTGTTCCAAACATGGTCTTACACTAGGTCACATATCGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGAGGC
* * *
1832052 CGATGCCATGT-CCAAGACATGGTCTTACACTAGCTCTCATATAAATGC
1 CGATGCCATGTCCCAA-ACATGGTCTTACACTAGCTCACATATAGAGGC
* * *
1832100 CGATTCCATGTTCCAAACATGGTCTTACACTGGCTCACATAT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATAT
1832142 CCTTAGTATC
Statistics
Matches: 270, Mismatches: 56, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
47 4 0.01
48 224 0.83
49 5 0.02
50 33 0.12
51 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATAGAGGC
Found at i:1831949 original size:96 final size:96
Alignment explanation
Indices: 1831763--1832142 Score: 550
Period size: 96 Copynumber: 3.9 Consensus size: 96
1831753 GAAAGATGTC
* ** *
1831763 GATGCCATGTCCAAGACATGGTCTTACACTGGCTCTCATATATCGGTGCTGATGCCATGTTCCAA
1 GATGCCATGTCCAAGACATGGTCTTACACTAGCTCTCATATA--AATGCCGATGCCATGTTCCAA
* * * *
1831828 ACATGGTCTTATACTAGCCCACATATAGAGGCT
64 ACATGGTCTTACACTGGCTCACATATCGAGGCT
* * **
1831861 AATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTGTATAAATGCCGATGCCATGTTCCAAAC
1 GATGCCATGTCCAAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAAC
1831926 ATGGTCTTACACTGGCTCACATATCGAGG-T
66 ATGGTCTTACACTGGCTCACATATCGAGGCT
* *
1831956 CGATGCCATGTCGC-AGACATGGTCTTACACTAGCTCTCGTATAAATGCCGATGCCGTGTTCCAA
1 -GATGCCATGTC-CAAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAA
*
1832020 ACATGGTCTTACACTAGG-TCACATATCGAGGCC
64 ACATGGTCTTACACT-GGCTCACATATCGAGGCT
*
1832053 GATGCCATGTCCAAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATTCCATGTTCCAAAC
1 GATGCCATGTCCAAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAAC
1832118 ATGGTCTTACACTGGCTCACATATC
66 ATGGTCTTACACTGGCTCACATATC
1832143 CTTAGTATCA
Statistics
Matches: 257, Mismatches: 19, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
95 4 0.02
96 213 0.83
97 3 0.01
98 37 0.14
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (96 bp):
GATGCCATGTCCAAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTCCAAAC
ATGGTCTTACACTGGCTCACATATCGAGGCT
Found at i:1832024 original size:144 final size:144
Alignment explanation
Indices: 1831762--1832141 Score: 449
Period size: 144 Copynumber: 2.6 Consensus size: 144
1831752 GGAAAGATGT
**
1831762 CGATGCCATGTCCAAGACATGGTCTTACACTGGCTCTCATATATCGGTGCTGATGCCATGTTCCA
1 CGATGCCATGTCCAAGACATGGTCTTACACTGGCTCTCATATAAAGGT-C-GATGCCATGTTCCA
* * * * *
1831827 AACATGGTCTTATACTAGCCCACATATAGAGGCTAATGCCATGTCCCAGACATGGTCTTACACTA
64 AACATGGTCTTACACTAGCTCACATATAAAGGCCAATGCCATGTCCCAAACATGGTCTTACACTA
*** *
1831892 GCTCTTGTATAAATGC
129 GCTCACATATAAAGGC
* **
1831908 CGATGCCATGTTCCAA-ACATGGTCTTACACTGGCTCACATATCGAGGTCGATGCCATG-TCGCA
1 CGATGCCATG-TCCAAGACATGGTCTTACACTGGCTCTCATATAAAGGTCGATGCCATGTTC-CA
* * * * * * *
1831971 GACATGGTCTTACACTAGCTCTCGTATAAATGCCGATGCCGTGTTCCAAACATGGTCTTACACTA
64 AACATGGTCTTACACTAGCTCACATATAAAGGCCAATGCCATGTCCCAAACATGGTCTTACACTA
* **
1832036 GGTCACATATCGAGGC
129 GCTCACATATAAAGGC
* * * *
1832052 CGATGCCATGTCCAAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATTCCATGTTCCAAA
1 CGATGCCATGTCCAAGACATGGTCTTACACTGGCTCTCATATAAAGGTCGATGCCATGTTCCAAA
*
1832117 CATGGTCTTACACTGGCTCACATAT
66 CATGGTCTTACACTAGCTCACATAT
1832142 CCTTAGTATC
Statistics
Matches: 196, Mismatches: 34, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
143 7 0.04
144 143 0.73
145 3 0.02
146 38 0.19
147 5 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (144 bp):
CGATGCCATGTCCAAGACATGGTCTTACACTGGCTCTCATATAAAGGTCGATGCCATGTTCCAAA
CATGGTCTTACACTAGCTCACATATAAAGGCCAATGCCATGTCCCAAACATGGTCTTACACTAGC
TCACATATAAAGGC
Found at i:1842438 original size:27 final size:27
Alignment explanation
Indices: 1842408--1842585 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
1842398 ATATTGAGCC
* *
1842408 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
1842435 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
1842462 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
1842490 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
1842517 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
1842544 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
1842571 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1842586 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:1842520 original size:55 final size:54
Alignment explanation
Indices: 1842408--1842585 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
1842398 ATATTGAGCC
* * * * *
1842408 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
1842462 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
1842517 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
1842571 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1842586 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:1856313 original size:32 final size:28
Alignment explanation
Indices: 1856265--1856331 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 28
1856255 AGTGCAATAT
* *
1856265 CTAAAACAATAGTAATAAATAATTAAATTAAA
1 CTAAAATAATAATAAT-AA-AATT-AATT-AA
1856297 CTAAAATAATAATAATAAAATTAATTAA
1 CTAAAATAATAATAATAAAATTAATTAA
1856325 CTAAAAT
1 CTAAAAT
1856332 TAAACCTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 9 0.27
29 4 0.12
30 4 0.12
31 2 0.06
32 14 0.42
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (28 bp):
CTAAAATAATAATAATAAAATTAATTAA
Found at i:1856329 original size:14 final size:14
Alignment explanation
Indices: 1856285--1856334 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1856275 AGTAATAAAT
1856285 AATTAAATTAAACTAA
1 AATT-AATT-AACTAA
1856301 AA-TAATAATAA-TAA
1 AATTAAT--TAACTAA
1856315 AATTAATTAACTAA
1 AATTAATTAACTAA
1856329 AATTAA
1 AATTAA
1856335 ACCTAAGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.10
14 17 0.57
15 7 0.23
16 3 0.10
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTAATTAACTAA
Found at i:1861536 original size:9 final size:9
Alignment explanation
Indices: 1861524--1861569 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
1861514 TAAGAGCTAT
*
1861524 ATGATTTAC
1 ATGAATTAC
1861533 ATGAATT--
1 ATGAATTAC
1861540 AT-AAGTTAC
1 ATGAA-TTAC
1861549 ATGAATTAC
1 ATGAATTAC
1861558 ATGAATTAC
1 ATGAATTAC
1861567 ATG
1 ATG
1861570 GAGTTTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
6 2 0.06
7 4 0.12
9 24 0.75
10 2 0.06
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (9 bp):
ATGAATTAC
Found at i:1863620 original size:33 final size:33
Alignment explanation
Indices: 1863574--1863637 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1863564 AACACAATTC
* *
1863574 TATGAATGTGTATCTCATTA-AAAGATACATCCT
1 TATGAAAGGGTATCTCA-TAGAAAGATACATCCT
1863607 TATGAAAGGGTATCTCATAGAAAGATACATC
1 TATGAAAGGGTATCTCATAGAAAGATACATC
1863638 TTTTGCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (33 bp):
TATGAAAGGGTATCTCATAGAAAGATACATCCT
Found at i:1870231 original size:18 final size:18
Alignment explanation
Indices: 1870196--1870235 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1870186 ATAAATGGTA
*
1870196 CTTTTCATATTATCTCCT
1 CTTTTCATATCATCTCCT
1870214 CTTTTCATATCA-CTTCCT
1 CTTTTCATATCATC-TCCT
1870232 CTTT
1 CTTT
1870236 GGTCTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.55
Consensus pattern (18 bp):
CTTTTCATATCATCTCCT
Found at i:1876611 original size:19 final size:18
Alignment explanation
Indices: 1876568--1876615 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1876558 AAATGAGAGA
1876568 AAAAGAAAAAAGAGAAAAT
1 AAAA-AAAAAAGAGAAAAT
*
1876587 ACAAAAGAAAAGA-AAAAT
1 A-AAAAAAAAAGAGAAAAT
1876605 GAAAAAAAAAA
1 -AAAAAAAAAA
1876616 TTCAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 13 0.52
19 9 0.36
20 3 0.12
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (18 bp):
AAAAAAAAAAGAGAAAAT
Found at i:1880864 original size:21 final size:21
Alignment explanation
Indices: 1880819--1880881 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1880809 TTTGAACCAT
* *
1880819 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
1880841 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
1880862 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
1880882 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:1882589 original size:40 final size:40
Alignment explanation
Indices: 1882532--1882772 Score: 324
Period size: 40 Copynumber: 6.0 Consensus size: 40
1882522 CGAATACACG
* * * *
1882532 TCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * * *
1882572 ACACCAGCACGAATGCTCTTCGGTG-TTTAGCACGGATATA
1 TCACTAGCACGAATGCTCTTCGG-GACTTAGCCCGGATACA
* *
1882612 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
*
1882652 TCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
1882692 TCACTAGCATGAATGCTCTTCGGGACTTAGCCTGGATACA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
*
1882732 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT-CA
1 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
1882771 TC
1 TC
1882773 GTCGAGACCT
Statistics
Matches: 178, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
39 4 0.02
40 173 0.97
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:1882868 original size:38 final size:38
Alignment explanation
Indices: 1882826--1882900 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
1882816 GAATTTTAAT
*
1882826 CCGGACATAATCTCTGT-ACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCT-TCACATAGCCAGCGGGTCTTTAC
* *
1882864 CCGGACATAATCTCTTCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTA
1882901 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTAC
Found at i:1891472 original size:143 final size:141
Alignment explanation
Indices: 1891201--1891495 Score: 394
Period size: 143 Copynumber: 2.1 Consensus size: 141
1891191 TAGAATTAAA
* * * ** *
1891201 CAAGTGCATTGTTTATTCCTCTCTAAGGTTGGGTCTTTTTTGGGTTTAGTATTGTTGTTCCAACT
1 CAAGTACATGGTTTATTCCTATCTAAGGTTGGGTCTTTTTCAGGTTTAGTATTGTTGTTCCAACG
* *
1891266 CTTCATTTTTCTCGAAATCACCATGTCTGAGGCATACTGGGATATATGTATGTCATATTACACTC
66 CTTCATTTTTCTCGAAATCACCATGTCTGAGGCATACCGGGATATATGTATGTCATATGACACTC
**
1891331 CATGAATATTC
131 CACAAATATTC
*
1891342 CAAGTACATGGTTTATTCCTATCTAAGGTTGGGTCTTTTTCAGGTTTAGTATT-TTGATTCTCCG
1 CAAGTACATGGTTTATTCCTATCTAAGGTTGGGTCTTTTTCAGGTTTAGTATTGTTG--T-TCCA
* * ** * *
1891406 AGGCTTCATTTTTCTCGAAGTCACTGTGTTTGATGCATACCGGGATATATGTATGTCATATGACA
63 ACGCTTCATTTTTCTCGAAATCACCATGTCTGAGGCATACCGGGATATATGTATGTCATATGACA
1891471 CTCCACAAATATTC
128 CTCCACAAATATTC
*
1891485 CAAATACATGG
1 CAAGTACATGG
1891496 AAAAACTTAG
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
140 3 0.02
141 48 0.36
142 1 0.01
143 81 0.61
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (141 bp):
CAAGTACATGGTTTATTCCTATCTAAGGTTGGGTCTTTTTCAGGTTTAGTATTGTTGTTCCAACG
CTTCATTTTTCTCGAAATCACCATGTCTGAGGCATACCGGGATATATGTATGTCATATGACACTC
CACAAATATTC
Found at i:1897591 original size:12 final size:12
Alignment explanation
Indices: 1897574--1897604 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1897564 AATTGAAGCT
1897574 AAGAAAGAGAAG
1 AAGAAAGAGAAG
*
1897586 AAGAAAAAGAAG
1 AAGAAAGAGAAG
1897598 AAGAAAG
1 AAGAAAG
1897605 CTGACAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AAGAAAGAGAAG
Found at i:1898613 original size:31 final size:31
Alignment explanation
Indices: 1898551--1898613 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1898541 ATTTGTATAA
* * *
1898551 AAATTAATCTAAATCTAAAATAATTCGATCC
1 AAATTAATCTAAATATAAAATAACTCAATCC
1898582 AAATTAATC-AAATATAAAATCAACTCAATCC
1 AAATTAATCTAAATATAAAAT-AACTCAATCC
1898613 A
1 A
1898614 CTTAAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (31 bp):
AAATTAATCTAAATATAAAATAACTCAATCC
Found at i:1908601 original size:22 final size:22
Alignment explanation
Indices: 1908576--1908622 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1908566 GAGCCGTGGA
*
1908576 GGACCGGAGGTGGATCGGTTCC
1 GGACCGGAGGTGGATCGGTGCC
*
1908598 GGACCGGAGGTGGATTGGTGCC
1 GGACCGGAGGTGGATCGGTGCC
1908620 GGA
1 GGA
1908623 GGTGAAGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (22 bp):
GGACCGGAGGTGGATCGGTGCC
Found at i:1908847 original size:149 final size:145
Alignment explanation
Indices: 1908555--1908853 Score: 411
Period size: 149 Copynumber: 2.0 Consensus size: 145
1908545 CTCTAATTCT
* *
1908555 GGAAATGGGTGGAGCCGTGGAGGACCGGAGGTGGATCGGTTCCGGACCGGAGGTGGATTGGTGCC
1 GGAAATGGGTGGAGCCGTGGAGGACCGGAGGTGGATCGGTTCCGGACCAGAGGTGGATCGGTGCC
* * *
1908620 GGAGGTGAAGGTTGAGAAAAAAAGGAAGGAGGGCAGTCGGGCAAGGGATTAGGGATTTGTGGAAG
66 GGAGGTGAAGGTTGAGAAAAAAAGGAAGGAGGGCAGTCGGGC----GACTAGGAATTTCTGGAAG
1908685 AAGGGAAACGGGAAATGGG
127 AAGGGAAACGGGAAATGGG
* * *
1908704 GGAAATGGGTGGAGCCGTGGAGGACCGGAGGTTGATCGGTGGTGTCGGACTAGAGGTGGATCGGT
1 GGAAATGGGTGGAGCCGTGGAGGACCGGAGGTGGATCGGT--T-CCGGACCAGAGGTGGATCGGT
* *
1908769 GCCGGAGGTGAAGGTTGAGAAAAAAAATGAAGGAGGGTAGTCGGGC-ACTAGGAATTTCTGGAAG
63 GCCGGAGGTGAAGGTTGAG-AAAAAAAGGAAGGAGGGCAGTCGGGCGACTAGGAATTTCTGGAAG
*
1908833 AGGGGAAACGGGGAAATGGG
127 AAGGGAAAC-GGGAAATGGG
1908853 G
1 G
1908854 AAGAAATGTT
Statistics
Matches: 134, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
148 23 0.17
149 50 0.37
151 1 0.01
152 36 0.27
153 24 0.18
ACGTcount: A:0.27, C:0.10, G:0.47, T:0.16
Consensus pattern (145 bp):
GGAAATGGGTGGAGCCGTGGAGGACCGGAGGTGGATCGGTTCCGGACCAGAGGTGGATCGGTGCC
GGAGGTGAAGGTTGAGAAAAAAAGGAAGGAGGGCAGTCGGGCGACTAGGAATTTCTGGAAGAAGG
GAAACGGGAAATGGG
Found at i:1909894 original size:19 final size:21
Alignment explanation
Indices: 1909832--1909888 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1909822 ATTTTCGAGG
1909832 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
1909853 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
1909874 ATATACAATCTTAGA
1 ATATACAATCTTAGA
1909889 AGATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:1910344 original size:5 final size:5
Alignment explanation
Indices: 1910334--1910362 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1910324 GAGCATTTGT
1910334 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1910363 CTTTCTACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1910906 original size:27 final size:24
Alignment explanation
Indices: 1910851--1910938 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 24
1910841 TAGAGTAATC
* *
1910851 ATTATTTTTTATGTATATATGT-A
1 ATTATTTTATATATATATATGTAA
1910874 ATTATTTTATATATATATATGTACA
1 ATTATTTTATATATATATATGTA-A
* *
1910899 GATTTATTATATATATGTATATGTAA
1 -A-TTATTTTATATATATATATGTAA
1910925 ATATATTGTTATAT
1 AT-TATT-TTATAT
1910939 TTTTTAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
23 20 0.37
24 1 0.02
25 6 0.11
26 7 0.13
27 20 0.37
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.55
Consensus pattern (24 bp):
ATTATTTTATATATATATATGTAA
Found at i:1913074 original size:24 final size:25
Alignment explanation
Indices: 1913047--1913093 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1913037 ATTTAGCCTA
1913047 ATTTTCTT-AAATAT-TTTTTTATAT
1 ATTTTCTTGAAA-ATCTTTTTTATAT
1913071 ATTTTCTTGAAAATCTTTTTTAT
1 ATTTTCTTGAAAATCTTTTTTAT
1913094 TTTTGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTTTCTTGAAAATCTTTTTTATAT
Found at i:1914391 original size:21 final size:21
Alignment explanation
Indices: 1914367--1914417 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1914357 GTATGTGGAG
*
1914367 TAGCCACATAGGCGTATAGGA
1 TAGCCACACAGGCGTATAGGA
* * * *
1914388 TAGCCATACGGGCGTGTGGGA
1 TAGCCACACAGGCGTATAGGA
1914409 TAGCCACAC
1 TAGCCACAC
1914418 GACCATGTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (21 bp):
TAGCCACACAGGCGTATAGGA
Found at i:1927023 original size:5 final size:5
Alignment explanation
Indices: 1927013--1927046 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1927003 CATTGCATCA
1927013 ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGG
1 ATGGG ATGGG ATGGG ATGGG ATGGG ATGGG ATGG
1927047 CACAGCTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.59, T:0.21
Consensus pattern (5 bp):
ATGGG
Found at i:1928234 original size:21 final size:20
Alignment explanation
Indices: 1928195--1928234 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1928185 GCTCAAGAAA
* *
1928195 CTAAACTTAAAAGACTTATC
1 CTAAACTTAAAAAAATTATC
1928215 CTAAACATTAAAAAAATTAT
1 CTAAAC-TTAAAAAAATTAT
1928235 TATTTGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.30
Consensus pattern (20 bp):
CTAAACTTAAAAAAATTATC
Found at i:1928696 original size:7 final size:7
Alignment explanation
Indices: 1928684--1928708 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1928674 TATTGTTATG
1928684 TAATTAA
1 TAATTAA
1928691 TAATTAA
1 TAATTAA
1928698 TAATTAA
1 TAATTAA
1928705 TAAT
1 TAAT
1928709 CATAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTAA
Found at i:1928867 original size:19 final size:18
Alignment explanation
Indices: 1928845--1928880 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1928835 ATAATAATTT
*
1928845 ATATTATTATTAATATTAA
1 ATATTAATATTAA-ATTAA
1928864 ATATTAATATTAAATTA
1 ATATTAATATTAAATTA
1928881 TTTTTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTAATATTAAATTAA
Found at i:1928870 original size:13 final size:13
Alignment explanation
Indices: 1928852--1928904 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
1928842 TTTATATTAT
1928852 TATTAATATTAAA
1 TATTAATATTAAA
1928865 TATTAATATTAAA
1 TATTAATATTAAA
* *
1928878 TTATT-TTTTTGAAA
1 -TATTAATATT-AAA
1928892 TA-TAATATTAAA
1 TATTAATATTAAA
1928904 T
1 T
1928905 TATTTTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 5 0.15
13 21 0.64
14 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TATTAATATTAAA
Found at i:1928911 original size:27 final size:27
Alignment explanation
Indices: 1928862--1928913 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
1928852 TATTAATATT
1928862 AAATATTAATATTAAATTATTTTTTTG
1 AAATATTAATATTAAATTATTTTTTTG
1928889 AAATA-TAATATTAAATTATTTTTTT
1 AAATATTAATATTAAATTATTTTTTT
1928914 CATTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
AAATATTAATATTAAATTATTTTTTTG
Found at i:1933973 original size:12 final size:12
Alignment explanation
Indices: 1933956--1933988 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1933946 AGACTCGCCC
1933956 ATATTAATTTTT
1 ATATTAATTTTT
1933968 ATATT-ATTTTT
1 ATATTAATTTTT
1933979 ATA-TAATTTT
1 ATATTAATTTT
1933989 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1934144 original size:30 final size:30
Alignment explanation
Indices: 1934110--1934171 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
1934100 CAACTTAACA
*
1934110 AACAAATGTCTCTAAAATAGTAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
* * *
1934140 AACAAATGTCTTTCAAATAATAACAAATTT
1 AACAAATGTCTCTAAAATAATAACAAAATT
1934170 AA
1 AA
1934172 TAATAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAACAAAATT
Found at i:1935078 original size:18 final size:19
Alignment explanation
Indices: 1935043--1935080 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1935033 AAATATAAAC
*
1935043 ATATAATTATTATTTAATAT
1 ATATAATTACTA-TTAATAT
1935063 ATATAATTACTA-TAATAT
1 ATATAATTACTATTAATAT
1935081 TTTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAATTACTATTAATAT
Found at i:1937081 original size:14 final size:14
Alignment explanation
Indices: 1937058--1937091 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1937048 TACAATATCT
1937058 AAATAATAACAATA
1 AAATAATAACAATA
*
1937072 AAATAGTAACAATA
1 AAATAATAACAATA
*
1937086 TAATAA
1 AAATAA
1937092 CAAAAAGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:1943366 original size:24 final size:25
Alignment explanation
Indices: 1943320--1943367 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1943310 TTAAAATATT
* *
1943320 TTTAAAATACTTTTTTATTTTTATG
1 TTTAAAATACTTTTTGATGTTTATG
*
1943345 TTTAAAATA-TTTTTGGTGTTTAT
1 TTTAAAATACTTTTTGATGTTTAT
1943368 TAAAAAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTAAAATACTTTTTGATGTTTATG
Found at i:1943928 original size:17 final size:17
Alignment explanation
Indices: 1943902--1943942 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1943892 ACCTCTAACA
*
1943902 ACATCTATCAATCTATC
1 ACATCCATCAATCTATC
1943919 ACATCCATCAATCTATC
1 ACATCCATCAATCTATC
1943936 ACATCCA
1 ACATCCA
1943943 ATAGACGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.29
Consensus pattern (17 bp):
ACATCCATCAATCTATC
Found at i:1947564 original size:21 final size:21
Alignment explanation
Indices: 1947538--1947712 Score: 205
Period size: 21 Copynumber: 8.3 Consensus size: 21
1947528 TGAATATGTC
1947538 AACAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTT
1947559 AACAGAAAG-TCATAAGAG-TT
1 AACAG-AAGCTCATAAGAGCTT
* *
1947579 AAACAGAAGCTCGTAAGAGCTA
1 -AACAGAAGCTCATAAGAGCTT
1947601 AACAGAAGCTCATAAGAG-TT
1 AACAGAAGCTCATAAGAGCTT
*
1947621 GAACAGAAGCTCATAAGAGCTG
1 -AACAGAAGCTCATAAGAGCTT
* *
1947643 AACAAAAGCTCGTAAGAGCTT
1 AACAGAAGCTCATAAGAGCTT
* *
1947664 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTT
* *
1947685 AACAGAAGCTCGA-AAAAGCTA
1 AACAGAAGCTC-ATAAGAGCTT
1947706 AACAGAA
1 AACAGAA
1947713 AGTAAAACAC
Statistics
Matches: 134, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
20 6 0.04
21 123 0.92
22 5 0.04
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTT
Found at i:1947618 original size:63 final size:64
Alignment explanation
Indices: 1947538--1947714 Score: 229
Period size: 63 Copynumber: 2.8 Consensus size: 64
1947528 TGAATATGTC
* *
1947538 AACAGAAGCTCATAAGAGCTTAACAGAAAG-TCATAAGAGTTAAACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTTAACAGAAAGCTCATAAGAGCTAAACAAAAGCTCGTAAGAGCTA
* *
1947601 AACAGAAGCTCATAAGAG-TTGAACAG-AAGCTCATAAGAGCTGAACAAAAGCTCGTAAGAGCTT
1 AACAGAAGCTCATAAGAGCTT-AACAGAAAGCTCATAAGAGCTAAACAAAAGCTCGTAAGAGCTA
* * *
1947664 AACAGAAGCTCGTAAGAGCTGAACAG-AAGCTCGA-AAAAGCTAAACAGAAAG
1 AACAGAAGCTCATAAGAGCTTAACAGAAAGCTC-ATAAGAGCTAAACA-AAAG
1947715 TAAAACACAA
Statistics
Matches: 101, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
62 5 0.05
63 90 0.89
64 6 0.06
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (64 bp):
AACAGAAGCTCATAAGAGCTTAACAGAAAGCTCATAAGAGCTAAACAAAAGCTCGTAAGAGCTA
Found at i:1948483 original size:42 final size:42
Alignment explanation
Indices: 1948417--1948539 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
1948407 TTTTGTTTAG
* * * *
1948417 CTCTTTTGAGCTTTAGTTTAGCTCTTACGAGCTTCTATTCAA
1 CTCTTATGAGTTTTTGTTCAGCTCTTACGAGCTTCTATTCAA
* *
1948459 CTCTTATGAGTTTTTGTTCAGCTCTTACGAGCTTCTGTTTAA
1 CTCTTATGAGTTTTTGTTCAGCTCTTACGAGCTTCTATTCAA
* * * * *
1948501 CTCTTGTAAGTTTCTGTTCAGCTCTTATGAACTTCTATT
1 CTCTTATGAGTTTTTGTTCAGCTCTTACGAGCTTCTATT
1948540 GGCATATTCA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (42 bp):
CTCTTATGAGTTTTTGTTCAGCTCTTACGAGCTTCTATTCAA
Found at i:1948536 original size:21 final size:21
Alignment explanation
Indices: 1948410--1948536 Score: 103
Period size: 21 Copynumber: 6.0 Consensus size: 21
1948400 TTTTACTTTT
* *
1948410 TGTTTAGCTCTTTTGAGCTT-
1 TGTTCAGCTCTTATGAGCTTC
* *
1948430 TAGTTTAGCTCTTACGAGCTTC
1 T-GTTCAGCTCTTATGAGCTTC
* * * *
1948452 TATTCAACTCTTATGAGTTTT
1 TGTTCAGCTCTTATGAGCTTC
*
1948473 TGTTCAGCTCTTACGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
* * * * *
1948494 TGTTTAACTCTTGTAAGTTTC
1 TGTTCAGCTCTTATGAGCTTC
*
1948515 TGTTCAGCTCTTATGAACTTC
1 TGTTCAGCTCTTATGAGCTTC
1948536 T
1 T
1948537 ATTGGCATAT
Statistics
Matches: 80, Mismatches: 25, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
20 1 0.01
21 78 0.98
22 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.47
Consensus pattern (21 bp):
TGTTCAGCTCTTATGAGCTTC
Found at i:1953470 original size:17 final size:17
Alignment explanation
Indices: 1953433--1953471 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1953423 GCTTAAAATG
1953433 TTTAAAATAAAAAGTAAA
1 TTTAAAATAAAAAG-AAA
1953451 TTTAAAATATAAAA-AAA
1 TTTAAAATA-AAAAGAAA
1953468 TTTA
1 TTTA
1953472 TATTAACCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TTTAAAATAAAAAGAAA
Found at i:1954159 original size:19 final size:19
Alignment explanation
Indices: 1954137--1954176 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1954127 AAAAATATTT
1954137 AAATTGGAAAAAATTATAA
1 AAATTGGAAAAAATTATAA
*
1954156 AAATTGTAAAAAATTATAA
1 AAATTGGAAAAAATTATAA
1954175 AA
1 AA
1954177 TATATAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (19 bp):
AAATTGGAAAAAATTATAA
Found at i:1954175 original size:10 final size:10
Alignment explanation
Indices: 1954144--1954278 Score: 54
Period size: 10 Copynumber: 14.0 Consensus size: 10
1954134 TTTAAATTGG
1954144 AAAAAATTAT
1 AAAAAATTAT
*
1954154 -AAAAATTGT
1 AAAAAATTAT
1954163 AAAAAATTAT
1 AAAAAATTAT
*
1954173 AAAATA-TAT
1 AAAAAATTAT
* *
1954182 -AGAAATATAGA
1 AAAAAAT-TA-T
1954193 AAAAAATTAT
1 AAAAAATTAT
**
1954203 AAAATTTTAT
1 AAAAAATTAT
****
1954213 -AAGTCGTA-
1 AAAAAATTAT
1954221 AAAAAATTAT
1 AAAAAATTAT
1954231 AAAAAATGTA-
1 AAAAAAT-TAT
*
1954241 AAGAAA-TAT
1 AAAAAATTAT
* *
1954250 -AAAATTTGT
1 AAAAAATTAT
1954259 AAAAAAATTAT
1 -AAAAAATTAT
1954270 -AAAAATTAT
1 AAAAAATTAT
1954279 CGTACCAAAA
Statistics
Matches: 90, Mismatches: 23, Indels: 25
0.65 0.17 0.18
Matches are distributed among these distances:
8 8 0.09
9 31 0.34
10 35 0.39
11 11 0.12
12 5 0.06
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:1954176 original size:28 final size:28
Alignment explanation
Indices: 1954145--1954276 Score: 79
Period size: 30 Copynumber: 4.6 Consensus size: 28
1954135 TTAAATTGGA
1954145 AAAAATTATAAAAATTGTAAAAAATTAT
1 AAAAATTATAAAAATTGTAAAAAATTAT
* *
1954173 -AAAATATATAGAAATATAGAAAAAAATTAT
1 AAAAAT-TATA-AAA-ATTGTAAAAAATTAT
* * * *
1954203 -AAAATTTTATAAGTCGTAAAAAAATTAT
1 AAAAATTATAAAAATTGT-AAAAAATTAT
* * * * ** *
1954231 AAAAAATGTAAAGAAATATAAAATTTGTAA
1 AAAAATTATAAA-AATTGTAAAAAAT-TAT
1954261 AAAAATTATAAAAATT
1 AAAAATTATAAAAATT
1954277 ATCGTACCAA
Statistics
Matches: 77, Mismatches: 20, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
27 7 0.09
28 16 0.21
29 22 0.29
30 32 0.42
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAAATTATAAAAATTGTAAAAAATTAT
Found at i:1954252 original size:19 final size:20
Alignment explanation
Indices: 1954144--1954274 Score: 85
Period size: 19 Copynumber: 6.8 Consensus size: 20
1954134 TTTAAATTGG
*
1954144 AAAAAATTATAAAAATTGT-
1 AAAAAATTATAAAAAATGTA
* *
1954163 AAAAAATTATAAAATATATA
1 AAAAAATTATAAAAAATGTA
* * *
1954183 GAAATA-TAGAAAAAAAT-T-
1 AAAAAATTA-TAAAAAATGTA
* * * *
1954201 ATAAAATT-TTATAAGTCGTA
1 AAAAAATTATAAAAAAT-GTA
1954221 AAAAAATTATAAAAAATGTA
1 AAAAAATTATAAAAAATGTA
* **
1954241 AAGAAA-TATAAAATTTGTA
1 AAAAAATTATAAAAAATGTA
1954260 AAAAAATTATAAAAA
1 AAAAAATTATAAAAA
1954275 TTATCGTACC
Statistics
Matches: 81, Mismatches: 23, Indels: 15
0.68 0.19 0.13
Matches are distributed among these distances:
17 4 0.05
18 3 0.04
19 37 0.46
20 32 0.40
21 5 0.06
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (20 bp):
AAAAAATTATAAAAAATGTA
Found at i:1954473 original size:10 final size:10
Alignment explanation
Indices: 1954458--1954542 Score: 70
Period size: 10 Copynumber: 8.6 Consensus size: 10
1954448 TTTCGTTGTA
1954458 TTTTATAATT
1 TTTTATAATT
*
1954468 TTTTATGA-T
1 TTTTATAATT
*
1954477 TTTTATAAAT
1 TTTTATAATT
*
1954487 TTTTACAATT
1 TTTTATAATT
*
1954497 TTTTATTAAAT
1 TTTTA-TAATT
*
1954508 TTTAATAA-T
1 TTTTATAATT
1954517 TTTTATAACTT
1 TTTTATAA-TT
1954528 TTATT-T-ATT
1 TT-TTATAATT
1954537 TTTTAT
1 TTTTAT
1954543 TTATTATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
8 2 0.03
9 21 0.34
10 25 0.41
11 11 0.18
12 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:1954487 original size:20 final size:19
Alignment explanation
Indices: 1954458--1954529 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
1954448 TTTCGTTGTA
* *
1954458 TTTTATAATTTTTTATGAT
1 TTTTATAAATTTTTATAAT
*
1954477 TTTTATAAATTTTTACAATT
1 TTTTATAAATTTTTATAA-T
*
1954497 TTTTATTAAATTTTAATAAT
1 TTTTA-TAAATTTTTATAAT
*
1954517 TTTTATAACTTTT
1 TTTTATAAATTTT
1954530 ATTTATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 22 0.49
20 12 0.27
21 11 0.24
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTATAAATTTTTATAAT
Found at i:1954500 original size:21 final size:21
Alignment explanation
Indices: 1954476--1954520 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1954466 TTTTTTATGA
*
1954476 TTTTTA-TAAATTTTTACAAT
1 TTTTTATTAAATTTTAACAAT
*
1954496 TTTTTATTAAATTTTAATAAT
1 TTTTTATTAAATTTTAACAAT
1954517 TTTT
1 TTTT
1954521 ATAACTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTATTAAATTTTAACAAT
Found at i:1954545 original size:15 final size:16
Alignment explanation
Indices: 1954527--1954556 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1954517 TTTTATAACT
1954527 TTTATT-TATTTTTTA
1 TTTATTATATTTTTTA
1954542 TTTATTATATTTTTT
1 TTTATTATATTTTTT
1954557 TTGCCACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTATATTTTTTA
Found at i:1963325 original size:69 final size:69
Alignment explanation
Indices: 1963214--1963353 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
1963204 CATTCAAATG
1963214 TTGTTGCTCGGGGTAGTATGGAGAAATCAGGTTAAACTGGTGTTTATTATTATTATTATTATTAT
1 TTGTTGCTCGGGGTAGTATGGAGAAATCAGGTTAAACTGGTGTTTATTATTATTATTATTATTAT
1963279 TTTA
66 TTTA
1963283 TTGTTGCTCGGGGTAGTATGGAGAAATCAGGTTAAACTGGTGTTTATTATTATTATTATTATTAT
1 TTGTTGCTCGGGGTAGTATGGAGAAATCAGGTTAAACTGGTGTTTATTATTATTATTATTATTAT
1963348 TTTA
66 TTTA
1963352 TT
1 TT
1963354 TATGGCCAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (69 bp):
TTGTTGCTCGGGGTAGTATGGAGAAATCAGGTTAAACTGGTGTTTATTATTATTATTATTATTAT
TTTA
Found at i:1968421 original size:19 final size:22
Alignment explanation
Indices: 1968399--1968446 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1968389 AAATTTATAA
1968399 TTATTAATA-T-TA-TAAAAAC
1 TTATTAATATTGTACTAAAAAC
*
1968418 TTATTTATATTGTACTAAAAAC
1 TTATTAATATTGTACTAAAAAC
1968440 TT-TTAAT
1 TTATTAAT
1968447 TGAATTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 1 0.04
21 6 0.25
22 9 0.38
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (22 bp):
TTATTAATATTGTACTAAAAAC
Found at i:1976007 original size:55 final size:55
Alignment explanation
Indices: 1975919--1976033 Score: 214
Period size: 55 Copynumber: 2.1 Consensus size: 55
1975909 GTTTCTATAT
1975919 AAAT-TTTATATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGACGA
1 AAATATTTATATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGACGA
*
1975973 AAATATTTATATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGATGA
1 AAATATTTATATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGACGA
1976028 AAATAT
1 AAATAT
1976034 ACCAGAAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 4 0.07
55 55 0.93
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (55 bp):
AAATATTTATATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGACGA
Found at i:1976044 original size:55 final size:55
Alignment explanation
Indices: 1975928--1976053 Score: 182
Period size: 55 Copynumber: 2.3 Consensus size: 55
1975918 TAAATTTTAT
** *
1975928 ATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGACGAAAATATTTAT
1 ATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGACGAAAATATCCAG
*
1975983 ATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGATGAAAATATACCAG
1 ATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGACGAAAATAT-CCAG
* *
1976039 A-AAAAGGAAAAAAAA
1 ATAAAAGTATAAAAAA
1976054 ACTGTTTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 62 0.97
56 2 0.03
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.25
Consensus pattern (55 bp):
ATAAAAGTATAAAAAATAATAATAGTGCAGTATATTAATGGACGAAAATATCCAG
Found at i:1984112 original size:13 final size:13
Alignment explanation
Indices: 1984094--1984148 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
1984084 TAATATAATT
1984094 TTAATTATTATAA
1 TTAATTATTATAA
1984107 TTAATT-TT-TAA
1 TTAATTATTATAA
**
1984118 TTTTTTATTATAA
1 TTAATTATTATAA
*
1984131 TTTTAATAATTATAA
1 --TTAATTATTATAA
1984146 TTA
1 TTA
1984149 TTCTTAAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
11 7 0.21
12 4 0.12
13 12 0.36
15 10 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTATTATAA
Found at i:1984115 original size:20 final size:19
Alignment explanation
Indices: 1984083--1984148 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
1984073 GTAATTTTAA
1984083 ATAATATAATTTTAATTATT
1 ATAAT-TAATTTTAATTATT
1984103 ATAATTAATTTTTAATT-TT
1 ATAATTAA-TTTTAATTATT
* * *
1984122 TTATTATAATTTTAATAATT
1 ATAAT-TAATTTTAATTATT
1984142 ATAATTA
1 ATAATTA
1984149 TTCTTAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATAATTAATTTTAATTATT
Found at i:1984144 original size:15 final size:15
Alignment explanation
Indices: 1984074--1984147 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
1984064 AATTTTAAAG
1984074 TAATTTTAAATAA-TA
1 TAATTTT-AATAATTA
*
1984089 TAATTTTAATTATTA
1 TAATTTTAATAATTA
*
1984104 TAA--TTAAT--TTT
1 TAATTTTAATAATTA
*
1984115 TAATTTT--TTATTA
1 TAATTTTAATAATTA
1984128 TAATTTTAATAATTA
1 TAATTTTAATAATTA
1984143 TAATT
1 TAATT
1984148 ATTCTTAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 6 0.12
13 16 0.33
14 4 0.08
15 22 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTTTAATAATTA
Found at i:1995673 original size:25 final size:25
Alignment explanation
Indices: 1995625--1995674 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1995615 ATCAATTTAC
* *
1995625 TTTAAATTTAATAATAATATTATTA
1 TTTAAATTTAATAATAAAAATATTA
* *
1995650 TTTAATTTTAATATTAAAAATATTA
1 TTTAAATTTAATAATAAAAATATTA
1995675 AATAATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTAAATTTAATAATAAAAATATTA
Found at i:1998494 original size:7 final size:7
Alignment explanation
Indices: 1998482--1998508 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1998472 TGTTCTTTTT
1998482 AATTTAA
1 AATTTAA
1998489 AATTTAA
1 AATTTAA
1998496 AATTTAA
1 AATTTAA
1998503 AATTTA
1 AATTTA
1998509 TATAAATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:2008708 original size:13 final size:13
Alignment explanation
Indices: 2008692--2008718 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2008682 TTGAGTTTGA
2008692 AAATAATTATTAG
1 AAATAATTATTAG
2008705 AAATAATTATTAG
1 AAATAATTATTAG
2008718 A
1 A
2008719 CTAGTTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATAATTATTAG
Found at i:2010314 original size:39 final size:39
Alignment explanation
Indices: 2010260--2010338 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
2010250 CGAGAAAGAG
2010260 TGTACGAGATAAATTATAAATTGAATTAGTATGTAAATA
1 TGTACGAGATAAATTATAAATTGAATTAGTATGTAAATA
* *
2010299 TGTACGAGTTAAATTATGAATTGAATTAGTATGTAAATA
1 TGTACGAGATAAATTATAAATTGAATTAGTATGTAAATA
2010338 T
1 T
2010339 ATATATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (39 bp):
TGTACGAGATAAATTATAAATTGAATTAGTATGTAAATA
Found at i:2019229 original size:17 final size:17
Alignment explanation
Indices: 2019205--2019248 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2019195 CCTTTTCTAC
2019205 TAAAAAAA-TATTAGTAAA
1 TAAAAAAATTA-TA-TAAA
2019223 TAAAAAAATTATATAAA
1 TAAAAAAATTATATAAA
2019240 TATAAAAAA
1 TA-AAAAAA
2019249 ATATTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 16 0.67
19 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAAAAATTATATAAA
Found at i:2019230 original size:19 final size:19
Alignment explanation
Indices: 2019205--2019280 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 19
2019195 CCTTTTCTAC
2019205 TAAAAAAATATTAGTAAATA
1 TAAAAAAATATTA-TAAATA
*
2019225 -AAAAAATTA-TATAAATA
1 TAAAAAAATATTATAAATA
* ** *
2019242 TAAAAAAATATTTTAGTTT
1 TAAAAAAATATTATAAATA
2019261 TGAAAAAAATA-TATAAATA
1 T-AAAAAAATATTATAAATA
2019280 T
1 T
2019281 TTTAATTTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
17 6 0.14
18 10 0.23
19 18 0.42
20 9 0.21
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
TAAAAAAATATTATAAATA
Found at i:2019718 original size:11 final size:11
Alignment explanation
Indices: 2019696--2019753 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
2019686 AACTAATCCT
2019696 CTCTCAAATTTC
1 CTCTC-AATTTC
2019708 CTCTCAATTTC
1 CTCTCAATTTC
*
2019719 CTCTAAATTTC
1 CTCTCAATTTC
*
2019730 CTCTCAATTTG
1 CTCTCAATTTC
*
2019741 CTCTCAAATTC
1 CTCTCAATTTC
2019752 CT
1 CT
2019754 TCCAAATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 36 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:2019729 original size:22 final size:23
Alignment explanation
Indices: 2019696--2019771 Score: 97
Period size: 22 Copynumber: 3.4 Consensus size: 23
2019686 AACTAATCCT
2019696 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
2019719 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
2019741 CTCTCAAA-TTCCT-TCCAAATTT-
1 CTCTCAAATTTCCTCT-C-AATTTC
2019763 CTCTCAAAT
1 CTCTCAAAT
2019772 CCATATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
21 1 0.02
22 35 0.73
23 12 0.25
ACGTcount: A:0.25, C:0.32, G:0.01, T:0.42
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:2019745 original size:33 final size:33
Alignment explanation
Indices: 2019695--2019769 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
2019685 AAACTAATCC
* *
2019695 TCTCTCAAATTTCCTCTCAATTTCC-TCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCCAAATT
*
2019728 TCCTCTCAATTTGCTCTCAAATTCCTTCCAAATT
1 T-CTCTCAATTTCCTCTCAAATTCCTTCCAAATT
2019762 TCTCTCAA
1 TCTCTCAA
2019770 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.24, C:0.32, G:0.01, T:0.43
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCCAAATT
Found at i:2019770 original size:11 final size:11
Alignment explanation
Indices: 2019695--2019771 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
2019685 AAACTAATCC
2019695 TCTCTCAAATT
1 TCTCTCAAATT
2019706 TCCTCTC-AATT
1 T-CTCTCAAATT
2019717 TC-CTCTAAATT
1 TCTCTC-AAATT
2019728 TCCTCTC-AATT
1 T-CTCTCAAATT
2019739 TGCTCTCAAATT
1 T-CTCTCAAATT
*
2019751 CCT-TCCAAATT
1 TCTCT-CAAATT
2019762 TCTCTCAAAT
1 TCTCTCAAAT
2019772 CCATATTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 3 0.05
10 2 0.04
11 36 0.65
12 11 0.20
13 3 0.05
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:2019789 original size:51 final size:51
Alignment explanation
Indices: 2019731--2019830 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
2019721 CTAAATTTCC
2019731 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * * * *
2019782 TCTCAATTTGCTCTCAAGTTCCTCTTAAATTTCTTTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTT
2019831 TTAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:2022269 original size:21 final size:21
Alignment explanation
Indices: 2022245--2022365 Score: 154
Period size: 21 Copynumber: 5.8 Consensus size: 21
2022235 AACCTAACTC
*
2022245 TAACCCTTAACTTAAAAATCG
1 TAACCCTTAACTTAAAAACCG
* *
2022266 TAACCCTTAAATTAAAAACCT
1 TAACCCTTAACTTAAAAACCG
*
2022287 TAACCCTTAACTTTAAAACCG
1 TAACCCTTAACTTAAAAACCG
* *
2022308 TAACCCTTAAATAAAAAACAC-
1 TAACCCTTAACTTAAAAAC-CG
* *
2022329 TAACACTTAACTTAAAAACCT
1 TAACCCTTAACTTAAAAACCG
2022350 TAACCCTTAACTTAAA
1 TAACCCTTAACTTAAA
2022366 TATAATTTGA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 1 0.01
21 83 0.98
22 1 0.01
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (21 bp):
TAACCCTTAACTTAAAAACCG
Found at i:2025716 original size:124 final size:124
Alignment explanation
Indices: 2025542--2025930 Score: 611
Period size: 124 Copynumber: 3.1 Consensus size: 124
2025532 CCCAAACATG
* * *
2025542 CTACTATAGCAAAAGCGTGTCCACGAGAGCGCGATTTCACAAATTTTTCTCAAATAGCATCCTGC
1 CTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
2025607 TAGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* *
2025666 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * * **
2025731 TTGAAGCGTTTTTTTA-AATTTGCTCAGAAATGTCAACTCGAAATTATTTCTTCCAAAAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
*
2025790 TTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
1 CTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
*
2025854 CTTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
65 CTTGAAGC-GTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
*
2025915 CTACTGTAGCAAAAGC
1 CTACTATAGCAAAAGC
2025931 AGGTACACGT
Statistics
Matches: 239, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
123 31 0.13
124 147 0.62
125 30 0.13
126 31 0.13
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (124 bp):
CTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:2025971 original size:125 final size:124
Alignment explanation
Indices: 2025542--2025981 Score: 568
Period size: 124 Copynumber: 3.5 Consensus size: 124
2025532 CCCAAACATG
* * * ** *
2025542 CTACTATAGCAAAAGCGTGTCCACGAGAGCGCGATTTCACAAATTTTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCAAGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* *
2025606 CTAGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
65 CTTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
*
2025666 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCA-ATTTCACAAATTCTTCTCA-AATAGCATCCT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGC-AAGATTTCACAAATTCTTCTCATAA-AGCATCCT
* * **
2025729 GCTTGAAGCGTTTTTT-TA-AATTTGCTCAGAAATGTCAACTCGAAATTATTTCTTCCAAAAC
64 GCTTGAAGC-TTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* * **
2025790 TTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCAAGATTTCACAAATTCTTCTCATAAAGCATCCTGC
2025855 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
66 TTGAAGC-TTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * *
2025915 CTACTGTAGCAAAAGCAG-GTACACGTGGGCAAGACTTCATAAATCCTTCTGATAAAGCATCCTG
1 CTACTGTAGCAAAAGC-GCGTCCACGAGGGCAAGATTTCACAAATTCTTCTCATAAAGCATCCTG
2025979 CTT
65 CTT
2025982 TGATTTTATT
Statistics
Matches: 277, Mismatches: 31, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
123 31 0.11
124 143 0.52
125 71 0.26
126 32 0.12
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCAAGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:2026132 original size:16 final size:16
Alignment explanation
Indices: 2026110--2026147 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2026100 CCCTAAAAAT
*
2026110 CCTAAAAATCTTAAAC
1 CCTAAAAATCCTAAAC
*
2026126 TCTAAAAATCCTAAAC
1 CCTAAAAATCCTAAAC
2026142 CCTAAA
1 CCTAAA
2026148 CTCTAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
CCTAAAAATCCTAAAC
Found at i:2026164 original size:23 final size:25
Alignment explanation
Indices: 2026097--2026165 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 25
2026087 TTTTTCTCTA
* * *
2026097 AAACCCTAAAAATCCTAAAAATCTT
1 AAACTCTAAAAATCCTAAAAACCCT
2026122 AAACTCTAAAAATCCT--AAACCCT
1 AAACTCTAAAAATCCTAAAAACCCT
2026145 AAACTCT-AAAAT-CTAAAAACC
1 AAACTCTAAAAATCCTAAAAACC
2026166 TAACATGGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.05
22 5 0.13
23 17 0.44
25 15 0.38
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (25 bp):
AAACTCTAAAAATCCTAAAAACCCT
Found at i:2028479 original size:31 final size:31
Alignment explanation
Indices: 2028433--2028494 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2028423 AATAATTGGA
*
2028433 TTTAACTTAATTGAGAA-AAAGATAATAAATT
1 TTTAACTTAAATGAGAACAAA-ATAATAAATT
*
2028464 TTTATCTTAAATGAGAACAAAATAATAAATT
1 TTTAACTTAAATGAGAACAAAATAATAAATT
2028495 CTATCTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (31 bp):
TTTAACTTAAATGAGAACAAAATAATAAATT
Found at i:2043546 original size:12 final size:12
Alignment explanation
Indices: 2043516--2043545 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2043506 AATAATTTTT
2043516 ATATTTTGTTTA
1 ATATTTTGTTTA
2043528 ATATTTTGTTTA
1 ATATTTTGTTTA
2043540 AT-TTTT
1 ATATTTT
2043546 TTAAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
ATATTTTGTTTA
Done.