Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008745.1 Hibiscus syriacus cultivar Beakdansim tig00111834_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1915556
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1740623 original size:13 final size:14
Alignment explanation
Indices: 1740595--1740623 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1740585 ATATTTTATA
1740595 ATATTTTTACTATT
1 ATATTTTTACTATT
1740609 ATATTTTTACT-TT
1 ATATTTTTACTATT
1740622 AT
1 AT
1740624 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:1742466 original size:16 final size:18
Alignment explanation
Indices: 1742426--1742463 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1742416 CCAGCAGCCA
*
1742426 CCGCAGCCATATATGATG
1 CCGCAACCATATATGATG
1742444 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
1742462 CC
1 CC
1742464 AACACCGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:1742819 original size:9 final size:9
Alignment explanation
Indices: 1742807--1742859 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
1742797 GGACGACAAC
1742807 GACGACGAT
1 GACGACGAT
1742816 GACGACGAT
1 GACGACGAT
* *
1742825 GACGATGGT
1 GACGACGAT
*
1742834 GACGACGAC
1 GACGACGAT
*
1742843 GATGACGAT
1 GACGACGAT
*
1742852 GACAACGA
1 GACGACGA
1742860 GAAGTTAGAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.34, C:0.21, G:0.34, T:0.11
Consensus pattern (9 bp):
GACGACGAT
Found at i:1742859 original size:21 final size:21
Alignment explanation
Indices: 1742816--1742859 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1742806 CGACGACGAT
***
1742816 GACGACGATGACGATGGTGAC
1 GACGACGATGACGATGACAAC
1742837 GACGACGATGACGATGACAAC
1 GACGACGATGACGATGACAAC
1742858 GA
1 GA
1742860 GAAGTTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.34, T:0.11
Consensus pattern (21 bp):
GACGACGATGACGATGACAAC
Found at i:1743031 original size:49 final size:45
Alignment explanation
Indices: 1742947--1743038 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 45
1742937 GGCATCGATA
* *
1742947 AATTTTTTTTATTATATTTATATTTACTTTATTTTGTTTAATTAT
1 AATTTTTTTTATTATATTTATACTTACTTTATTTTGTTAAATTAT
*
1742992 AATTTTTTATTATTTCTCATTTAATACTTACTTTATTTTGTTAAATT
1 AATTTTTT-TTA-TTAT-ATTT-ATACTTACTTTATTTTGTTAAATT
1743039 TGTTGGACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
45 8 0.20
46 3 0.08
47 3 0.08
48 4 0.10
49 22 0.55
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (45 bp):
AATTTTTTTTATTATATTTATACTTACTTTATTTTGTTAAATTAT
Found at i:1747854 original size:6 final size:6
Alignment explanation
Indices: 1747845--1747877 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1747835 GAAAGAGGCG
*
1747845 GAGGAA GAGGAA GAGGAA GAGGAA GAGCAA GAG
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAG
1747878 TGAGGGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:1750205 original size:103 final size:103
Alignment explanation
Indices: 1750021--1750223 Score: 327
Period size: 103 Copynumber: 2.0 Consensus size: 103
1750011 ACCATATCAG
* * *
1750021 ATACCACTAAACTTTAGATGTATCGTTTACCACTAAACTTTAAATTTTGTCAATTATAGTATTGA
1 ATACCACTAAACTTTAGATGTATCATTTACCACTAAACTTTAAATTTTGTCAATTATAGCACTGA
1750086 ACTTTGATTTTCGTTTTAAGTATACCACTGAATCGCAT
66 ACTTTGATTTTCGTTTTAAGTATACCACTGAATCGCAT
* * *
1750124 ATACTACTAAACTTTAGATGTATCATTTA-CACTGAACTTTTAATTTTGTCAATTATAGCACTGA
1 ATACCACTAAACTTTAGATGTATCATTTACCACTAAACTTTAAATTTTGTCAATTATAGCACTGA
*
1750188 ACTTTGATTTTTCGTTTTAAGTATACCATTGAATCG
66 ACTTTGA-TTTTCGTTTTAAGTATACCACTGAATCG
1750224 TTAAATTGTT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 38 0.41
103 54 0.59
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (103 bp):
ATACCACTAAACTTTAGATGTATCATTTACCACTAAACTTTAAATTTTGTCAATTATAGCACTGA
ACTTTGATTTTCGTTTTAAGTATACCACTGAATCGCAT
Found at i:1761022 original size:6 final size:6
Alignment explanation
Indices: 1761011--1761041 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1761001 TTATGTTTAG
*
1761011 GTGCTT GTGCTT GTACTT GTGCTT GTGCTT G
1 GTGCTT GTGCTT GTGCTT GTGCTT GTGCTT G
1761042 ATAGAGACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.16, G:0.32, T:0.48
Consensus pattern (6 bp):
GTGCTT
Found at i:1765948 original size:20 final size:21
Alignment explanation
Indices: 1765923--1766015 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1765913 TTTTCCCAAT
*
1765923 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1765943 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1765964 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1765984 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1766005 TCGCAATGCGA
1 TCGCAATGCGA
1766016 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1766029 original size:20 final size:20
Alignment explanation
Indices: 1766004--1766057 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1765994 AATTGGGAAA
*
1766004 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
1766024 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1766044 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1766058 ATACATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1766035 original size:41 final size:41
Alignment explanation
Indices: 1765923--1766015 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1765913 TTTTCCCAAT
1765923 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1765964 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1766005 TCGCAATGCGA
1 TCGCAATGCGA
1766016 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1766590 original size:20 final size:20
Alignment explanation
Indices: 1766567--1766609 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1766557 GATAGTCGAA
1766567 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
1766587 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
1766607 TTC
1 TTC
1766610 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:1767950 original size:18 final size:18
Alignment explanation
Indices: 1767929--1767973 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1767919 TCCACTTCGG
*
1767929 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1767947 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1767965 GAGCCATCA
1 GAGCCATCA
1767974 TCTTATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1770056 original size:14 final size:14
Alignment explanation
Indices: 1770037--1770072 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1770027 ATTGTTTACT
1770037 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1770051 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1770065 TGATTTGT
1 TGATTTGT
1770073 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1770196 original size:14 final size:14
Alignment explanation
Indices: 1770179--1770232 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1770169 CAAAATGGCT
1770179 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1770193 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1770212 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1770226 ATCGCAA
1 ATCGCAA
1770233 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1770281 original size:20 final size:20
Alignment explanation
Indices: 1770256--1770293 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1770246 TCGCATTGCG
*
1770256 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1770276 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1770294 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1771366 original size:24 final size:24
Alignment explanation
Indices: 1771339--1771392 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1771329 GTATTCGAAA
* *
1771339 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1771363 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1771387 TTTGAT
1 TTTGAT
1771393 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1771584 original size:12 final size:12
Alignment explanation
Indices: 1771567--1771591 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1771557 ATATAATCCT
1771567 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1771579 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1771591 G
1 G
1771592 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1773897 original size:19 final size:19
Alignment explanation
Indices: 1773872--1774002 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
1773862 GGAAATTACT
1773872 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1773891 ATTGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1773905 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1773924 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
1773938 TTCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1773957 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1773971 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1773990 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1774003 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1773914 original size:33 final size:33
Alignment explanation
Indices: 1773872--1773998 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1773862 GGAAATTACT
*
1773872 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1773905 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1773937 TTTCGCAATACGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1773971 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1773999 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1773979 original size:66 final size:66
Alignment explanation
Indices: 1773873--1774005 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1773863 GAAATTACTA
* * *
1773873 TCGCAATGCGAAATGAAAATTGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1773938 T
66 T
*
1773939 TCGCAATACGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1774004 T
66 T
1774005 T
1 T
1774006 AATTTCGCGA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1774020 original size:19 final size:20
Alignment explanation
Indices: 1773998--1774040 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1773988 AAATCGCAAC
1773998 GCGAATTT-AATTTCGCGAT
1 GCGAATTTCAATTTCGCGAT
* * *
1774017 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGAT
1774037 GCGA
1 GCGA
1774041 TTCTCTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGAT
Found at i:1774200 original size:14 final size:14
Alignment explanation
Indices: 1774181--1774217 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1774171 CATCAATTAA
1774181 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1774195 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1774209 ACAAATCAA
1 ACAAATCAA
1774218 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1775660 original size:42 final size:42
Alignment explanation
Indices: 1775614--1775697 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1775604 CGATGACAGT
* * *
1775614 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1775656 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
1775698 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1777729 original size:20 final size:19
Alignment explanation
Indices: 1777704--1777878 Score: 65
Period size: 20 Copynumber: 9.8 Consensus size: 19
1777694 TTGAAATAAA
*
1777704 AATCGCAACGAGATAATGAG
1 AATCGCAACGAGA-AATGAC
*
1777724 AATCGCAACGCGGAAATGAC
1 AATCGCAACG-AGAAATGAC
*
1777744 TATCGCAACGAG--A-G--
1 AATCGCAACGAGAAATGAC
*
1777758 AATCGCAACGCGAAATGAC
1 AATCGCAACGAGAAATGAC
* **
1777777 TATCG---CGA-CCA-GAC
1 AATCGCAACGAGAAATGAC
*
1777791 AATCGCAACGCGAAATGAC
1 AATCGCAACGAGAAATGAC
* * *
1777810 TATCGCGACCAG---T--C
1 AATCGCAACGAGAAATGAC
* *
1777824 AATCGCAACGCGAAATGAA
1 AATCGCAACGAGAAATGAC
* * *
1777843 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGAGAAATGAC
*
1777863 AATCGCAACGCGAAAT
1 AATCGCAACGAGAAAT
1777879 AAAAATCGTA
Statistics
Matches: 114, Mismatches: 24, Indels: 35
0.66 0.14 0.20
Matches are distributed among these distances:
14 26 0.23
15 1 0.01
16 5 0.04
17 5 0.04
18 1 0.01
19 32 0.28
20 42 0.37
21 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAC
Found at i:1777778 original size:33 final size:33
Alignment explanation
Indices: 1777724--1777852 Score: 186
Period size: 33 Copynumber: 3.9 Consensus size: 33
1777714 AGATAATGAG
* *
1777724 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACCAGAC
*
1777758 AATCGCAACGCGAAATGACTATCGCGACCAGAC
1 AATCGCAACGCGAAATGACTATCGCAACCAGAC
* *
1777791 AATCGCAACGCGAAATGACTATCGCGACCAGTC
1 AATCGCAACGCGAAATGACTATCGCAACCAGAC
**
1777824 AATCGCAACGCGAAATGAAAATCGCAACC
1 AATCGCAACGCGAAATGACTATCGCAACC
1777853 GCGAAATAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 77 0.88
34 11 0.12
ACGTcount: A:0.38, C:0.28, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACCAGAC
Found at i:1777883 original size:20 final size:19
Alignment explanation
Indices: 1777824--1777894 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
1777814 GCGACCAGTC
*
1777824 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
1777843 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
1777863 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
1777882 AATCGTAACGCGA
1 AATCGCAACGCGA
1777895 TTATCTCGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 31 0.63
20 18 0.37
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1778475 original size:20 final size:20
Alignment explanation
Indices: 1778450--1778502 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1778440 GCGCTATGTA
1778450 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1778470 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1778490 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1778503 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1778536 original size:20 final size:20
Alignment explanation
Indices: 1778511--1778564 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1778501 GATTTTGTAT
1778511 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1778531 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1778551 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1778565 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1778549 original size:61 final size:61
Alignment explanation
Indices: 1778451--1778567 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1778441 CGCTATGTAA
* * * * *
1778451 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1778512 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1778568 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1778583 original size:61 final size:61
Alignment explanation
Indices: 1778451--1778585 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1778441 CGCTATGTAA
* * * * * ** *
1778451 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1778512 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1778574 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1778586 TTACTTCTTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1778675 original size:21 final size:21
Alignment explanation
Indices: 1778635--1778675 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1778625 ATTGTATACC
**
1778635 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1778656 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1778676 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1778936 original size:25 final size:25
Alignment explanation
Indices: 1778907--1778979 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 25
1778897 CCAGCTTCAA
1778907 ATTATAAAACACGTTTAATGCATAT
1 ATTATAAAACACGTTTAATGCATAT
** *
1778932 ATTATAAAACACGTAAGACTATACATAT
1 ATTATAAAACACGT-TTA--ATGCATAT
1778960 ATTATAAAACACGTTTAATG
1 ATTATAAAACACGTTTAATG
1778980 GACTTTGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 16 0.41
26 1 0.03
27 1 0.03
28 21 0.54
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (25 bp):
ATTATAAAACACGTTTAATGCATAT
Found at i:1786520 original size:25 final size:25
Alignment explanation
Indices: 1786488--1786537 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1786478 TGCCACATAG
1786488 ATTTGTCCCGAAGGACCGCGTAGAA
1 ATTTGTCCCGAAGGACCGCGTAGAA
1786513 ATTTGTCCCGAAGGACCGCGTAGAA
1 ATTTGTCCCGAAGGACCGCGTAGAA
1786538 CCCTGACTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (25 bp):
ATTTGTCCCGAAGGACCGCGTAGAA
Found at i:1786670 original size:14 final size:15
Alignment explanation
Indices: 1786647--1786680 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1786637 TAGTCACATA
1786647 TTCACATAGG-TATT
1 TTCACATAGGATATT
*
1786661 TTCACGTAGGATATT
1 TTCACATAGGATATT
1786676 TTCAC
1 TTCAC
1786681 TTATAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (15 bp):
TTCACATAGGATATT
Found at i:1788470 original size:4 final size:4
Alignment explanation
Indices: 1788456--1788487 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
1788446 TCTCAATGCT
1788456 ATAC TATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC -ATAC ATAC ATAC ATAC ATAC ATAC ATA
1788488 TACATTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:1800790 original size:21 final size:21
Alignment explanation
Indices: 1800764--1800969 Score: 157
Period size: 21 Copynumber: 9.5 Consensus size: 21
1800754 GTTTCCAGAT
* *
1800764 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
1800785 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1800806 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1800827 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * * *
1800847 TCGCAATGCGATAGTCGAAGT-
1 TCGCAATGCGA-ACTTGGACTA
* * **
1800868 TCGCGTTGCGATAGTCGAATTTGGAAAA
1 T--C---GCAAT-G-CGAACTTGGACTA
* *
1800896 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
1800917 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1800938 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
1800959 TCGCATTGCGA
1 TCGCAATGCGA
1800970 TTTACATATT
Statistics
Matches: 148, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
20 13 0.09
21 115 0.78
22 2 0.01
23 4 0.03
26 5 0.03
27 5 0.03
28 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1800817 original size:42 final size:42
Alignment explanation
Indices: 1800764--1800969 Score: 188
Period size: 42 Copynumber: 4.8 Consensus size: 42
1800754 GTTTCCAGAT
*
1800764 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACAA
* * *
1800806 TCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AA
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACT-TGGACAA
* * * *
1800847 TCGCAATGCGATAGTCGAAGTTCG-CGT-T-GCGATAGTCGAATTTGGAAAA
1 TCGCAA--C----G-CGAACTTCGAC-TATCGCAAT-G-CGAACTTGGACAA
*
1800896 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACAA
*
1800938 TCGCAACGCGAACTTCGACTATCGCATTGCGA
1 TCGCAACGCGAACTTCGACTATCGCAATGCGA
1800970 TTTACATATT
Statistics
Matches: 133, Mismatches: 15, Indels: 32
0.74 0.08 0.18
Matches are distributed among these distances:
41 8 0.06
42 84 0.63
43 4 0.03
44 4 0.03
46 4 0.03
47 5 0.04
48 15 0.11
49 9 0.07
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (42 bp):
TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACAA
Found at i:1801001 original size:132 final size:132
Alignment explanation
Indices: 1800764--1801059 Score: 436
Period size: 132 Copynumber: 2.2 Consensus size: 132
1800754 GTTTCCAGAT
* *
1800764 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATC
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATC
* * *
1800829 GCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAA
66 GCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCGAA
1800894 AA
131 AA
1800896 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATC
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATC
* * **
1800961 GCATTGCG-AT-T-TACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTC
66 GCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTC
**
1801023 GACTA
128 GAAAA
*
1801028 TCGCAACGCGAACTTCGACTATCGCATTGCGA
1 TCGCAACGCGAACTTCGACTATCGCAATGCGA
1801060 TTTACATATT
Statistics
Matches: 149, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
129 2 0.01
130 2 0.01
131 3 0.02
132 142 0.95
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (132 bp):
TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATC
GCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCGAA
AA
Found at i:1801023 original size:21 final size:21
Alignment explanation
Indices: 1800959--1801023 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1800949 ACTTCGACTA
* *
1800959 TCGCATTGCGA-TTTACATAT
1 TCGCATTGCGATTTTCCAAAT
** * *
1800979 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATTTTCCAAAT
*
1801000 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
1801021 TCG
1 TCG
1801024 ACTATCGCAA
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1801086 original size:90 final size:92
Alignment explanation
Indices: 1800933--1801115 Score: 343
Period size: 90 Copynumber: 2.0 Consensus size: 92
1800923 TGCGAACTTG
1800933 GACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAA
1 GACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAA
1800998 GTTCGCGTTGCGA-TT-TTCCAAATTC
66 GTTCGCGTTGCGATTTATTCCAAATTC
1801023 GACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAA
1 GACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAA
*
1801088 GTTCGCGTTGTGATTTATTCCAAATTC
66 GTTCGCGTTGCGATTTATTCCAAATTC
1801115 G
1 G
1801116 TTGCGATAGT
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
90 77 0.86
91 2 0.02
92 11 0.12
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (92 bp):
GACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAA
GTTCGCGTTGCGATTTATTCCAAATTC
Found at i:1801120 original size:132 final size:131
Alignment explanation
Indices: 1800764--1801150 Score: 403
Period size: 132 Copynumber: 2.9 Consensus size: 131
1800754 GTTTCCAGAT
* * *
1800764 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATC
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACGTCGACTATC
* * ** * * * *
1800829 GCAATGCGAATATGTAAA-TCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGA
66 GCATTGCG-ATTTACAAATTCG-ATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCGA
1800893 AAA
129 AAA
*
1800896 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATC
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACGTCGACTATC
* ** *
1800961 GCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGAC
66 GCATTGCGATTTACAAATTCG-ATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCGAA
*
1801026 TA
130 AA
* * ** *
1801028 TCGCAACGCGAACTTCGACTATCGCATTGCG-A-TT-TACATATTCGCATTGCGATA-GTCGAAG
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGAC-TA-TCGCAACGCGA-ACGTCG-AC
* * *
1801089 T-TCGCGTTGTGATTTATTCCAAATTCG-TTGCGATAGTCGAAGTTCGCGTTGC-TTAGTCCAAA
62 TATCGCATTGCGATTTA---CAAATTCGATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAA
1801151 ATCGTAACGA
Statistics
Matches: 220, Mismatches: 27, Indels: 17
0.83 0.10 0.06
Matches are distributed among these distances:
129 2 0.01
130 4 0.02
131 38 0.17
132 169 0.77
134 7 0.03
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (131 bp):
TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACGTCGACTATC
GCATTGCGATTTACAAATTCGATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAATTCGAAA
A
Found at i:1801138 original size:21 final size:21
Alignment explanation
Indices: 1801068--1801140 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
1801058 GATTTACATA
*
1801068 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * * *
1801089 TTCGCGTTGTGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCGAAG
1801112 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
1801131 TTCGCGTTGC
1 TTCGCGTTGC
1801141 TTAGTCCAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 8 0.21
21 23 0.59
23 8 0.21
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:1801713 original size:2 final size:2
Alignment explanation
Indices: 1801706--1801731 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1801696 AAATAAATAA
1801706 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1801732 GCATATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1802803 original size:18 final size:17
Alignment explanation
Indices: 1802780--1802813 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1802770 CTCAATGATA
1802780 AAAATAGTATTATTTTTT
1 AAAATA-TATTATTTTTT
*
1802798 AAAATATCTTATTTTT
1 AAAATATATTATTTTT
1802814 AAGCAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
AAAATATATTATTTTTT
Found at i:1804507 original size:12 final size:12
Alignment explanation
Indices: 1804490--1804527 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
1804480 TTTTTAAAGT
1804490 TTAAAATAATCA
1 TTAAAATAATCA
*
1804502 TTAAAAT-ATAA
1 TTAAAATAATCA
1804513 TTAAAA-AATCA
1 TTAAAATAATCA
1804524 TTAA
1 TTAA
1804528 TTTTATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAAATAATCA
Found at i:1805933 original size:16 final size:17
Alignment explanation
Indices: 1805898--1805938 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1805888 GTAAAATAAT
*
1805898 AATTGTATTAAAAAGTA
1 AATTGTATTAAAAAGAA
*
1805915 AATTGT-TTACAAAGAA
1 AATTGTATTAAAAAGAA
1805931 AATT-TATT
1 AATTGTATT
1805939 TATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 14 0.67
17 6 0.29
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (17 bp):
AATTGTATTAAAAAGAA
Found at i:1807029 original size:17 final size:19
Alignment explanation
Indices: 1807007--1807047 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
1806997 AGTGTCATCT
*
1807007 AAAATATTTAAAA-ATA-A
1 AAAATATTAAAAACATATA
1807024 AAAATATTAAAAACATATA
1 AAAATATTAAAAACATATA
1807043 AAAAT
1 AAAAT
1807048 TAATTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 3 0.14
19 6 0.29
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATATTAAAAACATATA
Found at i:1815939 original size:18 final size:17
Alignment explanation
Indices: 1815908--1815948 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1815898 CCATATATAT
*
1815908 ATATATAATATTATTTC
1 ATATATAATATTATTTA
*
1815925 ATATCATAATGTTATTTA
1 ATAT-ATAATATTATTTA
1815943 ATATAT
1 ATATAT
1815949 CAAATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATATAATATTATTTA
Found at i:1816444 original size:158 final size:158
Alignment explanation
Indices: 1816208--1816577 Score: 453
Period size: 158 Copynumber: 2.3 Consensus size: 158
1816198 AGCATGTGGT
* * * * * *
1816208 TCAAATTTGGTAAAAAAAAGAACTTAAAATAAATCACAAATTGAAGGAATAAGGATATTATGAAA
1 TCAAATTTGGT-AAAAAAAGAACTTAAAATAAATGACGAATTGAAGAAATAATGAGATTATAAAA
* *
1816273 AATTGAAGTACTAAAGTGAAAAAT-AAAAATTT-TCTATCAAAAAAGAGGAATTAAAAGTACATA
65 AATTGAAGTACTAAAGTGAAAAATAAAAAATTTGT-TAT-AAAAAAGAGGAATTAAAAGTAAACA
* * * * *
1816336 TGTATTCTACTATGGTTTAGGAGCACGCGGC
128 CGTATTCTACCAAGGTTTAAGAGCACGAGGC
*
1816367 TCAAATTTGGTAAAAAAAGAACTTAAAATAAATGACGAATTGAAGAAACAATGAGATTATAAAAA
1 TCAAATTTGGTAAAAAAAGAACTTAAAATAAATGACGAATTGAAGAAATAATGAGATTATAAAAA
* *
1816432 ATTGAA-TGACTAAATTGAAAAATAAAAAATTTGTTATAAAAAAGAGGAATTGAAAGTAAACACG
66 ATTGAAGT-ACTAAAGTGAAAAATAAAAAATTTGTTATAAAAAAGAGGAATTAAAAGTAAACACG
* *
1816496 TATTCTACCAAGGTTTAAGAGCATGAGGT
130 TATTCTACCAAGGTTTAAGAGCACGAGGC
* * * * *
1816525 TCAAATTTGGT-AAGAATGGACTTAAAATGAAGGA-GTAATTGAAGAAATAATGA
1 TCAAATTTGGTAAAAAAAGAACTTAAAATAAATGACG-AATTGAAGAAATAATGA
1816578 AATCAGAGAC
Statistics
Matches: 183, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
156 1 0.01
157 35 0.19
158 124 0.68
159 22 0.12
160 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.26
Consensus pattern (158 bp):
TCAAATTTGGTAAAAAAAGAACTTAAAATAAATGACGAATTGAAGAAATAATGAGATTATAAAAA
ATTGAAGTACTAAAGTGAAAAATAAAAAATTTGTTATAAAAAAGAGGAATTAAAAGTAAACACGT
ATTCTACCAAGGTTTAAGAGCACGAGGC
Found at i:1819320 original size:6 final size:6
Alignment explanation
Indices: 1819309--1819859 Score: 1001
Period size: 6 Copynumber: 92.8 Consensus size: 6
1819299 AAGTGAAATG
1819309 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819357 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819405 TATACA TATACA TATACA TATACA TATAC- -ATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * *
1819451 TATACA TACATA CATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819499 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819547 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819595 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819643 TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819689 TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819734 -ATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1819781 TATACA TATACA TATACA TATACA TATACATA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATAC--A TATACA TATACA TATACA
1819831 TATACA TATACA TATACA TATACA TATAC
1 TATACA TATACA TATACA TATACA TATAC
1819860 GTATGCCTTG
Statistics
Matches: 529, Mismatches: 6, Indels: 20
0.95 0.01 0.04
Matches are distributed among these distances:
4 16 0.03
6 507 0.96
8 6 0.01
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:1820089 original size:2 final size:2
Alignment explanation
Indices: 1820082--1820113 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1820072 TTAAATATGC
1820082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1820114 TAGATTGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1821698 original size:29 final size:29
Alignment explanation
Indices: 1821652--1821712 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1821642 CATGAATTTT
** * *
1821652 TTTTAATTACATTGATTTTATCATTGAAC
1 TTTTAATTACATCAATTTCAACATTGAAC
*
1821681 TTTTAATTACATCAATTTCAACTTTGAAC
1 TTTTAATTACATCAATTTCAACATTGAAC
1821710 TTT
1 TTT
1821713 AGTTTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (29 bp):
TTTTAATTACATCAATTTCAACATTGAAC
Found at i:1835991 original size:23 final size:23
Alignment explanation
Indices: 1835930--1836047 Score: 120
Period size: 23 Copynumber: 5.3 Consensus size: 23
1835920 CACCACATCT
1835930 CACATAA-TTTG-CACCGAAGTG-C
1 CACATAATTTTGTC-CCGAAG-GAC
*
1835952 CACAT-A-TTTGTCTCGAAGGAC
1 CACATAATTTTGTCCCGAAGGAC
1835973 CACATAATTTTGTCCCGAAGGAC
1 CACATAATTTTGTCCCGAAGGAC
* * * *
1835996 CACATAGTTTTTTCTCGAATGAC
1 CACATAATTTTGTCCCGAAGGAC
* *
1836019 CACATAGTTTTATCCCGAAGGAC
1 CACATAATTTTGTCCCGAAGGAC
1836042 CACATA
1 CACATA
1836048 GAACCCTCGA
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
20 1 0.01
21 16 0.19
22 7 0.08
23 59 0.71
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (23 bp):
CACATAATTTTGTCCCGAAGGAC
Found at i:1836021 original size:46 final size:45
Alignment explanation
Indices: 1835930--1836048 Score: 147
Period size: 46 Copynumber: 2.7 Consensus size: 45
1835920 CACCACATCT
1835930 CACATAA-TTTG-CACCGAAGTG-CCACATA-TTTGTCTCGAAGGAC
1 CACATAATTTTGTC-CCGAAG-GACCACATAGTTTGTCTCGAAGGAC
* *
1835973 CACATAATTTTGTCCCGAAGGACCACATAGTTTTTTCTCGAATGAC
1 CACATAATTTTGTCCCGAAGGACCACATAG-TTTGTCTCGAAGGAC
* *
1836019 CACATAGTTTTATCCCGAAGGACCACATAG
1 CACATAATTTTGTCCCGAAGGACCACATAG
1836049 AACCCTCGAC
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
43 8 0.12
44 17 0.25
45 1 0.01
46 41 0.61
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
CACATAATTTTGTCCCGAAGGACCACATAGTTTGTCTCGAAGGAC
Found at i:1836048 original size:23 final size:23
Alignment explanation
Indices: 1835965--1836048 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
1835955 ATATTTGTCT
* *
1835965 CGAAGGACCACATAATTTTGTCC
1 CGAAGGACCACATAGTTTTATCC
* *
1835988 CGAAGGACCACATAGTTTTTTCT
1 CGAAGGACCACATAGTTTTATCC
*
1836011 CGAATGACCACATAGTTTTATCC
1 CGAAGGACCACATAGTTTTATCC
1836034 CGAAGGACCACATAG
1 CGAAGGACCACATAG
1836049 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (23 bp):
CGAAGGACCACATAGTTTTATCC
Found at i:1849619 original size:297 final size:298
Alignment explanation
Indices: 1849065--1849663 Score: 1182
Period size: 297 Copynumber: 2.0 Consensus size: 298
1849055 GCCAAACTGA
1849065 CTTTAACTCTTTAAGAGACCTCTAAGTTAGGCAGTGATGCGTTCAAAAATCACAACAAAACAGAA
1 CTTTAACTCTTTAAGAGACCTCTAAGTTAGGCAGTGATGCGTTCAAAAATCACAACAAAACAGAA
1849130 AACAGAACCTTTCATGAACTTGAACACAAATTTCATTAAAAACAGACGAAACAAATCTTTGTATA
66 AACAGAACCTTTCATGAACTTGAACACAAATTTCATTAAAAACAGACGAAACAAATCTTTG-ATA
1849195 TAAAGTACCCTCAGCTGCCTTATTTTATCATCGATGATCTTCAACATTCATTGTTCTTTCTTGTT
130 TAAAGTACCCTCAGCTGCCTTATTTTATCATCGATGATCTTCAACATTCATTGTTCTTTCTTGTT
1849260 CATTGATCTTCATATTATGGGCTACGAGTGTATAGTTGAAGGAATAGTTTCTTTTCTGGGGTTTG
195 CATTGATCTTCATATTATGGGCTACGAGTGTATAGTTGAAGGAATAGTTTCTTTTCTGGGGTTTG
1849325 TTTTCTTGTACAATAGAATAATCAACAAAACAAAAGCTT
260 TTTTCTTGTACAATAGAATAATCAACAAAACAAAAGCTT
1849364 CTTTAACTCTTTAAGAGACCTCTAAGTTAGGCAGTGATGCGTTCAAAAATCACAACAAAACAGAA
1 CTTTAACTCTTTAAGAGACCTCTAAGTTAGGCAGTGATGCGTTCAAAAATCACAACAAAACAGAA
1849429 AACAGAACCTTTCATGAACTTGAACACAAATTTCATTAAAAACAGACGAAACAAATCTTTG-TAT
66 AACAGAACCTTTCATGAACTTGAACACAAATTTCATTAAAAACAGACGAAACAAATCTTTGATAT
1849493 AAAGTACCCTCAGCTGCCTTATTTTATCATCGATGATCTTCAACATTCATTGTTCTTTCTTGTTC
131 AAAGTACCCTCAGCTGCCTTATTTTATCATCGATGATCTTCAACATTCATTGTTCTTTCTTGTTC
1849558 ATTGATCTTCATATTATGGGCTACGAGTGTATAGTTGAAGGAATAGTTTCTTTTCTGGGGTTTGT
196 ATTGATCTTCATATTATGGGCTACGAGTGTATAGTTGAAGGAATAGTTTCTTTTCTGGGGTTTGT
1849623 TTTCTTGTACAATAGAATAATCAACAAAACAAAAGCTT
261 TTTCTTGTACAATAGAATAATCAACAAAACAAAAGCTT
1849661 CTT
1 CTT
1849664 CTTCTGTGTT
Statistics
Matches: 300, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
297 174 0.58
299 126 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (298 bp):
CTTTAACTCTTTAAGAGACCTCTAAGTTAGGCAGTGATGCGTTCAAAAATCACAACAAAACAGAA
AACAGAACCTTTCATGAACTTGAACACAAATTTCATTAAAAACAGACGAAACAAATCTTTGATAT
AAAGTACCCTCAGCTGCCTTATTTTATCATCGATGATCTTCAACATTCATTGTTCTTTCTTGTTC
ATTGATCTTCATATTATGGGCTACGAGTGTATAGTTGAAGGAATAGTTTCTTTTCTGGGGTTTGT
TTTCTTGTACAATAGAATAATCAACAAAACAAAAGCTT
Found at i:1850932 original size:77 final size:77
Alignment explanation
Indices: 1850717--1850966 Score: 484
Period size: 77 Copynumber: 3.3 Consensus size: 77
1850707 CATTACTTAA
1850717 AAACTACAGTGGCTCCTCAGGTACTTGTGTTGGTTTATGTACGAGTTGAATCCTAGTGCTTGATA
1 AAACTACAGTGGCTCCTCAGGTACTTGTGTTGGTTTATGTACGAGTTGAATCCTAGTGCTTGATA
1850782 AACTGAGAATTG
66 AACTGAGAATTG
1850794 AAACTACAGT-GCTCCTCAGGTACTTGTGTTGGTTTATGTACGAGTTGAATCCTAGTGCTTGATA
1 AAACTACAGTGGCTCCTCAGGTACTTGTGTTGGTTTATGTACGAGTTGAATCCTAGTGCTTGATA
1850858 AACTGAGAATTG
66 AACTGAGAATTG
*
1850870 AAACTACAGTGGCTCCTCAGGTACTTGTGTTGGTTTATGTACGAGTTGAATCCTAGTTCTTGATA
1 AAACTACAGTGGCTCCTCAGGTACTTGTGTTGGTTTATGTACGAGTTGAATCCTAGTGCTTGATA
1850935 AACTGAGAATTG
66 AACTGAGAATTG
1850947 AAACTACAGTGGCTCCTCAG
1 AAACTACAGTGGCTCCTCAG
1850967 TGCTTGACAA
Statistics
Matches: 171, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
76 76 0.44
77 95 0.56
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (77 bp):
AAACTACAGTGGCTCCTCAGGTACTTGTGTTGGTTTATGTACGAGTTGAATCCTAGTGCTTGATA
AACTGAGAATTG
Found at i:1851091 original size:44 final size:44
Alignment explanation
Indices: 1851018--1851218 Score: 169
Period size: 43 Copynumber: 4.6 Consensus size: 44
1851008 TCCCGGAGCA
* * * *
1851018 CTTTCTACCTTTATAATTGAGACCTCTAATTTTTTCAATCCCAT
1 CTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAT
* * *
1851062 TTTTTTA-CTTATATAATTTAGGCCCCTAATTTTTTTCAATCTC-G
1 CTTTTTACCTT-TATAATTGAGGCCCCTAA-TTTTTTCAATCTCAT
* * * * * * *
1851106 CTATTTACCTTTAAAATTGATGCCCATATTTTTTTTAATATCA-
1 CTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAT
* *
1851149 CTTTTTACCTTTATAATTGGGGTCCCTAATTTTTTCAATCAT-AT
1 CTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATC-TCAT
* * *
1851193 -TTTTTACTTTTATAATTTAAGCCCCT
1 CTTTTTACCTTTATAATTGAGGCCCCT
1851219 GATTGAATCA
Statistics
Matches: 121, Mismatches: 30, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
43 67 0.55
44 39 0.32
45 15 0.12
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (44 bp):
CTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAT
Found at i:1851347 original size:13 final size:14
Alignment explanation
Indices: 1851317--1851350 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1851307 TATATAAGTA
1851317 AAAAAATGGAATTG
1 AAAAAATGGAATTG
*
1851331 AAAAAATGGGATT-
1 AAAAAATGGAATTG
1851344 AAAAAAT
1 AAAAAAT
1851351 TTAAGATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.21
Consensus pattern (14 bp):
AAAAAATGGAATTG
Found at i:1852194 original size:20 final size:20
Alignment explanation
Indices: 1852169--1852241 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1852159 TAATACAAAA
1852169 TCGCAACGCGATACTGAATT
1 TCGCAACGCGATACTGAATT
1852189 TCGCAACGCGATACTGACA-T
1 TCGCAACGCGATACTGA-ATT
* *
1852209 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGAATT
*
1852229 TCGCAACGAGATA
1 TCGCAACGCGATA
1852242 ATACAGAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 46 0.98
21 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATACTGAATT
Found at i:1852414 original size:12 final size:12
Alignment explanation
Indices: 1852395--1852428 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1852385 CTCTCTGGCG
1852395 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1852407 ATATCCGTTCCT
1 ACATCCGTTCCT
1852419 ACATCC-TTCC
1 ACATCCGTTCC
1852429 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1853010 original size:24 final size:24
Alignment explanation
Indices: 1852983--1853036 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1852973 GTATTCGAAA
* *
1852983 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTAGTCAATACCCGGAC
* *
1853007 TTTGATATTAGTCAATACTCGGAT
1 TTTGATATTAGTCAATACCCGGAC
1853031 TTTGAT
1 TTTGAT
1853037 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTAGTCAATACCCGGAC
Found at i:1855522 original size:20 final size:20
Alignment explanation
Indices: 1855486--1855523 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1855476 ATTCATTTGA
**
1855486 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAAAAAATGG
1855506 CTATCGCAACGAAAAAAT
1 CTATCGCAACGAAAAAAT
1855524 CGCAATGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAAAAAATGG
Found at i:1855583 original size:19 final size:16
Alignment explanation
Indices: 1855542--1855593 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
1855532 GAAATGAAAA
1855542 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1855558 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
*
1855572 ATTTCGCATTGCGATTCTC
1 ---TCGCATTGCGATTTTC
1855591 TCG
1 TCG
1855594 TTGTGATAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 11 0.37
16 6 0.20
17 3 0.10
19 10 0.33
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:1856135 original size:20 final size:20
Alignment explanation
Indices: 1856110--1856147 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1856100 ATTCATTTGA
*
1856110 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
1856130 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
1856148 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:1856207 original size:19 final size:19
Alignment explanation
Indices: 1856166--1856230 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
1856156 GAAATGAAAA
1856166 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1856182 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1856199 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1856218 TCGCATTGCGATT
1 TCGCATTGCGATT
1856231 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1858322 original size:19 final size:19
Alignment explanation
Indices: 1858241--1858360 Score: 88
Period size: 20 Copynumber: 6.4 Consensus size: 19
1858231 TAGTTTACTT
* *
1858241 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1858261 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
* ***
1858281 TCGCAAAGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
1858301 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1858320 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1858334 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1858353 TCGCAACG
1 TCGCAACG
1858361 ACAAAATCAC
Statistics
Matches: 80, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 24 0.30
20 36 0.45
21 4 0.05
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1858335 original size:14 final size:14
Alignment explanation
Indices: 1858316--1858406 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
1858306 ACGCGAAATG
1858316 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1858330 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1858349 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1858363 AAAATCACAATGCGAA
1 AAAATCGCAA--CGAC
1858379 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1858395 AAAATCGCAACG
1 AAAATCGCAACG
1858407 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 9 0.15
19 10 0.16
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1858345 original size:33 final size:33
Alignment explanation
Indices: 1858300--1858411 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
1858290 GGAAATGGCT
1858300 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
1858333 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
* *
1858366 ATCACAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1858398 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1858412 CACAAATCGC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 28 0.37
33 47 0.63
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1858440 original size:19 final size:19
Alignment explanation
Indices: 1858418--1858499 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
1858408 GAAACACAAA
1858418 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1858437 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
1858455 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1858471 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1858488 TCGCATTGCGAT
1 TCGCATTGCGAT
1858500 AACCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1858526 original size:20 final size:19
Alignment explanation
Indices: 1858418--1858527 Score: 63
Period size: 19 Copynumber: 6.1 Consensus size: 19
1858408 GAAACACAAA
* **
1858418 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAATCATT
*
1858437 TCGCGTTGCGAT-TTCATT
1 TCGCGTTGCGATAATCATT
*
1858455 TCGCATTGCG---AT--TT
1 TCGCGTTGCGATAATCATT
**
1858469 T-GTCGTTGCGATTTTCATT
1 TCG-CGTTGCGATAATCATT
* *
1858488 TCGCATTGCGATAACCATT
1 TCGCGTTGCGATAATCATT
*
1858507 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATAATCATT
1858527 T
1 T
1858528 TCGTGTTGTG
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
13 1 0.01
14 9 0.13
16 1 0.01
17 1 0.01
18 15 0.21
19 27 0.38
20 17 0.24
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATAATCATT
Found at i:1858527 original size:39 final size:34
Alignment explanation
Indices: 1858418--1858519 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 34
1858408 GAAACACAAA
1858418 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTCATT
1858455 TCGCATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGA-TTTCATT
1858488 TCGCATTGCGATAACCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
1858520 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
31 1 0.02
32 11 0.20
33 19 0.34
34 1 0.02
37 11 0.20
38 4 0.07
39 8 0.14
40 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTCATT
Found at i:1858535 original size:20 final size:20
Alignment explanation
Indices: 1858484--1858520 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1858474 TTGCGATTTT
*
1858484 CATTT-CGCATTGCGATAAC
1 CATTTCCGCGTTGCGATAAC
1858503 CATTTCCGCGTTGCGATA
1 CATTTCCGCGTTGCGATA
1858521 GTCATTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAAC
Found at i:1859040 original size:18 final size:18
Alignment explanation
Indices: 1859014--1859058 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1859004 GTCGATCAGA
*
1859014 TGATGGCTCTGGGTAAGG
1 TGATGGCTCTGGGCAAGG
* *
1859032 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCAAGG
1859050 TGATGGCTC
1 TGATGGCTC
1859059 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCAAGG
Found at i:1860396 original size:20 final size:20
Alignment explanation
Indices: 1860371--1860444 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1860361 AATAGTTTCT
*
1860371 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
1860391 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
1860411 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
1860431 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1860445 GTTGCGGTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:1860985 original size:61 final size:61
Alignment explanation
Indices: 1860914--1861030 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
1860904 GAAAGTCAGA
* *** *
1860914 ATCGCGTTGCGAAAGTCAGTATCTTGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
* *
1860975 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCGTTGCGATTTT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTCAGTATCGCGTTGCGATTTT
1861031 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
Found at i:1861027 original size:20 final size:20
Alignment explanation
Indices: 1860893--1861027 Score: 146
Period size: 20 Copynumber: 6.7 Consensus size: 20
1860883 GATTATGTAT
*
1860893 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1860913 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
** *
1860933 TATCTTGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
1860953 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
1860974 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1860994 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
1861014 TATCGCGTTGCGAT
1 TATCGCGTTGCGAT
1861028 TTTCCCAATT
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.03
20 82 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1861138 original size:21 final size:21
Alignment explanation
Indices: 1861098--1861138 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1861088 ACTGTAGACA
**
1861098 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1861119 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1861139 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1868763 original size:21 final size:21
Alignment explanation
Indices: 1868734--1868783 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
1868724 AATAATAAGA
*
1868734 AGAATAATG-AGAAGGAAACAAG
1 AGAA-AATGAAGAAAGAAA-AAG
1868756 AGAAAATGAAGAAAGAAAAAG
1 AGAAAATGAAGAAAGAAAAAG
1868777 AGAAAAT
1 AGAAAAT
1868784 ACTTTGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.66, C:0.02, G:0.24, T:0.08
Consensus pattern (21 bp):
AGAAAATGAAGAAAGAAAAAG
Found at i:1872581 original size:2 final size:2
Alignment explanation
Indices: 1872574--1872598 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1872564 AAAGTAAAAC
1872574 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1872599 ATAAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1883855 original size:31 final size:31
Alignment explanation
Indices: 1883777--1883860 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
1883767 ACTCATGTGT
* ** * *
1883777 ATTATTTGAATACAAACCTGACATGCTATGT
1 ATTATCTGAATACAAATTTGACATACTATGC
* * *
1883808 ATTATCTAAATGCAAATTTGACATATTATGC
1 ATTATCTGAATACAAATTTGACATACTATGC
1883839 ATTATCTGAATACAAATTTGAC
1 ATTATCTGAATACAAATTTGAC
1883861 TAGTATCTGG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (31 bp):
ATTATCTGAATACAAATTTGACATACTATGC
Found at i:1899997 original size:108 final size:108
Alignment explanation
Indices: 1899808--1900017 Score: 375
Period size: 108 Copynumber: 1.9 Consensus size: 108
1899798 ACATTCTTGA
*
1899808 GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGAGAGGGTACTTCGGTATGATTAGCAAATGGA
1 GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGAGAGGGTACTCCGGTATGATTAGCAAATGGA
* *
1899873 ATAATAACATTTCCATCTATCCTGTCATGGTCTTTTTTGTTGG
66 ATAAGAACATTTCCATCTATACTGTCATGGTCTTTTTTGTTGG
* *
1899916 GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGTGAGGGTTCTCCGGTATGATTAGCAAATGGA
1 GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGAGAGGGTACTCCGGTATGATTAGCAAATGGA
1899981 ATAAGAACATTTCCATCTATACTGTCATGGTCTTTTT
66 ATAAGAACATTTCCATCTATACTGTCATGGTCTTTTT
1900018 GATGGCCTCA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (108 bp):
GCCTACTAAAATCTTCATTCCCCTCCTTAGTTTGAGAGGGTACTCCGGTATGATTAGCAAATGGA
ATAAGAACATTTCCATCTATACTGTCATGGTCTTTTTTGTTGG
Found at i:1906700 original size:21 final size:21
Alignment explanation
Indices: 1906676--1906739 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1906666 TCGTGCCAAC
1906676 CATATGCACCAAGTGCTTACA
1 CATATGCACCAAGTGCTTACA
* ** *
1906697 CATAAG-GTC--GTGCTCAC-
1 CATATGCACCAAGTGCTTACA
1906714 CATATGCACCGAAGTGCTTACA
1 CATATGCACC-AAGTGCTTACA
1906736 CATA
1 CATA
1906740 AGGTCGTGCC
Statistics
Matches: 30, Mismatches: 8, Indels: 9
0.64 0.17 0.19
Matches are distributed among these distances:
17 5 0.17
18 8 0.27
20 1 0.03
21 12 0.40
22 4 0.13
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (21 bp):
CATATGCACCAAGTGCTTACA
Found at i:1906740 original size:39 final size:38
Alignment explanation
Indices: 1906638--1906772 Score: 202
Period size: 39 Copynumber: 3.5 Consensus size: 38
1906628 CGAGTCAAAT
*
1906638 ATATGCACCGTAA-TACTTACACATAAGGTCGTGCCAACC
1 ATATGCACCG-AAGTGCTTACACATAAGGTCGTGCC-ACC
1906677 ATATGCACC-AAGTGCTTACACATAAGGTCGTGCTCACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCGTGC-CACC
1906715 ATATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCGTG-CCACC
*
1906754 ATGTGCACCGAAGTGCTTA
1 ATATGCACCGAAGTGCTTA
1906773 ATCGATATGC
Statistics
Matches: 90, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
37 2 0.02
38 32 0.36
39 55 0.61
40 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (38 bp):
ATATGCACCGAAGTGCTTACACATAAGGTCGTGCCACC
Found at i:1909712 original size:23 final size:23
Alignment explanation
Indices: 1909663--1909720 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1909653 TAAGCTACCA
*
1909663 AAAGGCAGAGAAAAACTTGTCAC
1 AAAGGCAGAGAAAAACTTGCCAC
* *
1909686 AAAGGCAGAGATAAA-TATGCCAT
1 AAAGGCAGAGAAAAACT-TGCCAC
*
1909709 AAAGCCAGAGAA
1 AAAGGCAGAGAA
1909721 CATGTTACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACTTGCCAC
Found at i:1912148 original size:26 final size:26
Alignment explanation
Indices: 1912096--1912148 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1912086 ATACAATAAG
* *
1912096 TGACATTTATTGAAATGTACCATTAA
1 TGACATGTATTGAAATGTACCAGTAA
* *
1912122 TGACATGTATTTAAATGTACCGGTAA
1 TGACATGTATTGAAATGTACCAGTAA
1912148 T
1 T
1912149 TAAAATAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (26 bp):
TGACATGTATTGAAATGTACCAGTAA
Done.