Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 136 of 185
Found at i:42143745 original size:16 final size:16
Alignment explanation
Indices: 42143724--42143778 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
42143714 CTCTGGTTCA
*
42143724 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
42143740 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
42143756 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
42143772 CTATAAT
1 CTGTAAT
42143779 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:42143938 original size:6 final size:6
Alignment explanation
Indices: 42143927--42143955 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42143917 AGGTAGATGA
42143927 TTATTG TTATTG TTATTG TTATTG TTATT
1 TTATTG TTATTG TTATTG TTATTG TTATT
42143956 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
TTATTG
Found at i:42144092 original size:58 final size:58
Alignment explanation
Indices: 42143969--42144094 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 58
42143959 TTTTAATAAG
* * *
42143969 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTGACCATATTTAAAAATA
1 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATTTAAAAATA
* * * * * * *
42144027 ATAATTATTAAATATATTTTAAT-AAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATT-TAAAAATA
*
42144085 TTTATTATTA
1 ATTATTATTA
42144095 TATGAATTAA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 21 0.38
58 34 0.62
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATTTAAAAATA
Found at i:42146664 original size:126 final size:126
Alignment explanation
Indices: 42146441--42146675 Score: 321
Period size: 126 Copynumber: 1.9 Consensus size: 126
42146431 TTTTCTCTAC
* *
42146441 AGTAGTTTTAGAAAAAATAATTTTGAGAAGATGGTTCTGAAAAGATAATATAAAAAACGCTTCAA
1 AGTAGTTTTAGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAAAACGCTTCAA
* * *
42146506 ACAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCTCACGTAGACACTTTTTTTATAT
66 ACAAGATGCACTGTCAGCAAAATTACTAAAAAAAACTCCCACGTAGACACTTTTTTTATAT
* * * * *
42146567 AGTAGTTCTT-GAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGTCAAAAATGCTTCA
1 AGTAGTT-TTAGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAAAACGCTTCA
* * *
42146631 AGCAAGATGCACTGTTAGCAAAATTGA-TGAAAAAAACTCCCACGT
65 AACAAGATGCACTGTCAGCAAAATT-ACTAAAAAAAACTCCCACGT
42146676 GGATGCTCTT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
126 91 0.97
127 3 0.03
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (126 bp):
AGTAGTTTTAGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAAAACGCTTCAA
ACAAGATGCACTGTCAGCAAAATTACTAAAAAAAACTCCCACGTAGACACTTTTTTTATAT
Found at i:42149789 original size:24 final size:23
Alignment explanation
Indices: 42149733--42149789 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
42149723 AAGAACTTCT
*
42149733 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAACA
42149756 ATTTACTATT-AAAATATTAAAAACA
1 ATTT--TATTAAAAATA-TAAAAACA
42149781 ACTTTTATT
1 A-TTTTATT
42149790 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAACA
Found at i:42150048 original size:24 final size:24
Alignment explanation
Indices: 42150016--42150070 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
42150006 GAATGCGGAA
42150016 GTGTTTGCAACACCCACGGTGGAG
1 GTGTTTGCAACACCCACGGTGGAG
*
42150040 GTGTTTGCATCACCCACGGTGGAG
1 GTGTTTGCAACACCCACGGTGGAG
42150064 GTGTTTG
1 GTGTTTG
42150071 AATCTCATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27
Consensus pattern (24 bp):
GTGTTTGCAACACCCACGGTGGAG
Found at i:42150261 original size:18 final size:18
Alignment explanation
Indices: 42150238--42150275 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42150228 AGAAAATGAA
* *
42150238 ACATATAAGGGTTAGGAT
1 ACATATAAAGGCTAGGAT
42150256 ACATATAAAGGCTAGGAT
1 ACATATAAAGGCTAGGAT
42150274 AC
1 AC
42150276 GCAGTTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
ACATATAAAGGCTAGGAT
Found at i:42152062 original size:32 final size:32
Alignment explanation
Indices: 42152026--42152086 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
42152016 ATTTAATTAA
*
42152026 AGAGA-GCTTTGAGAAATTTAGGGAGAAATTTG
1 AGAGATGCTTTGAGAAATTT-GGAAGAAATTTG
**
42152058 AGAGATTTTTTGAGAAATTTGGAAGAAAT
1 AGAGATGCTTTGAGAAATTTGGAAGAAAT
42152087 GTTGTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 13 0.52
33 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.28, T:0.31
Consensus pattern (32 bp):
AGAGATGCTTTGAGAAATTTGGAAGAAATTTG
Found at i:42160790 original size:18 final size:19
Alignment explanation
Indices: 42160762--42160797 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42160752 GATTCAAACA
*
42160762 AAAAAATCAAAATCAAAAT
1 AAAAAATCAAAAACAAAAT
42160781 AAAAAA-CAAAAACAAAA
1 AAAAAATCAAAAACAAAA
42160798 AAAGAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAAAATCAAAAACAAAAT
Found at i:42160867 original size:20 final size:20
Alignment explanation
Indices: 42160842--42160891 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
42160832 AATGAAAATG
* *
42160842 AAAAAGAGAGAAGAGAAAA-A
1 AAAAAGA-AAAAGAAAAAAGA
42160862 AAAAAGAAAAAGAAAAAAGA
1 AAAAAGAAAAAGAAAAAAGA
42160882 AAAAAGAAAA
1 AAAAAGAAAA
42160892 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAGAAAAAAGA
Found at i:42160870 original size:26 final size:24
Alignment explanation
Indices: 42160836--42160892 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
42160826 TGTCAAAATG
* *
42160836 AAAATGAAAAAGAGAGAAGAGAAAAA
1 AAAAAGAAAAAGA-A-AAAAGAAAAA
42160862 AAAAAGAAAAAGAAAAAAGAAAAA
1 AAAAAGAAAAAGAAAAAAGAAAAA
42160886 AGAAAAG
1 A-AAAAG
42160893 GAGAGGCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.36
25 6 0.21
26 12 0.43
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAAAAGAAAAA
Found at i:42160871 original size:6 final size:6
Alignment explanation
Indices: 42160830--42160891 Score: 54
Period size: 6 Copynumber: 9.7 Consensus size: 6
42160820 AATCAATGTC
* *
42160830 AAAATG AAAATG AAAAAG AGAGAAGAG AAAAA- AAAAAG AAAAAG AAAAAAG
1 AAAAAG AAAAAG AAAAAG A-A-AA-AG AAAAAG AAAAAG AAAAAG -AAAAAG
42160881 AAAAAAG AAAA
1 -AAAAAG AAAA
42160892 GGAGAGGCCA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
5 5 0.10
6 23 0.46
7 16 0.32
8 3 0.06
9 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:42160871 original size:7 final size:7
Alignment explanation
Indices: 42160842--42160891 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
42160832 AATGAAAATG
42160842 AAAAAGA
1 AAAAAGA
* *
42160849 GAGAAGA
1 AAAAAGA
*
42160856 GAAAA-A
1 AAAAAGA
42160862 AAAAAG-
1 AAAAAGA
42160868 AAAAAGA
1 AAAAAGA
42160875 AAAAAGA
1 AAAAAGA
42160882 AAAAAGA
1 AAAAAGA
42160889 AAA
1 AAA
42160892 GGAGAGGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 11 0.30
7 26 0.70
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:42160877 original size:14 final size:15
Alignment explanation
Indices: 42160860--42160891 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
42160850 AGAAGAGAAA
42160860 AAAAAAAG-AAAAAG
1 AAAAAAAGAAAAAAG
42160874 -AAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
42160888 AAAA
1 AAAA
42160892 GGAGAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.44
14 6 0.38
15 3 0.19
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:42161231 original size:15 final size:15
Alignment explanation
Indices: 42161211--42161240 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42161201 TTGTCACTGT
*
42161211 ATTGCAAAACAATGA
1 ATTGCAAAAAAATGA
42161226 ATTGCAAAAAAATGA
1 ATTGCAAAAAAATGA
42161241 CTGAGACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (15 bp):
ATTGCAAAAAAATGA
Found at i:42161761 original size:7 final size:7
Alignment explanation
Indices: 42161749--42161789 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
42161739 AAAAAGGGGG
42161749 ATGAAAA
1 ATGAAAA
42161756 ATGAAAA
1 ATGAAAA
*
42161763 ATGAAAC
1 ATGAAAA
42161770 ATG-AAA
1 ATGAAAA
42161776 ATGAAAA
1 ATGAAAA
42161783 ATGAAAA
1 ATGAAAA
42161790 GTAATGACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:42162858 original size:21 final size:21
Alignment explanation
Indices: 42162832--42162881 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
42162822 CTACAACTTA
* * *
42162832 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAACGAGAG
42162853 AAGCAGAGGCGGCAACGAGAG
1 AAGCAGAGGCGGCAACGAGAG
42162874 AAGCAGAG
1 AAGCAGAG
42162882 TAGAGCAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACGAGAG
Found at i:42163297 original size:43 final size:43
Alignment explanation
Indices: 42163201--42163428 Score: 278
Period size: 43 Copynumber: 5.3 Consensus size: 43
42163191 CGTTTATAGA
* ** * * *
42163201 AAAAACACCGCTAAAAGTCACCAAACAATAGTGGCGTTTGTGGG
1 AAAAACGCCGCTAAAAGTCA-TGATCTATAGCGGCGTTTGTGGG
* *
42163245 AAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCATTTGTGGG
1 AAAAACGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
* * *
42163288 AAAAACGCCGCTAAAGGTCATGATCTATAGCGGCATTTGTGAG
1 AAAAACGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
* * * *
42163331 ATAAGCGTCGCTAAAAGTCATGATCTATAGCGGCGTTTG-AGG
1 AAAAACGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
*
42163373 AAAAATCGCCGCTAAAAGTCATGATCTATAGCCGCGTTTGTGGG
1 AAAAA-CGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
*
42163417 AAAAGCGCCGCT
1 AAAAACGCCGCT
42163429 TATTTCTAGA
Statistics
Matches: 158, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
42 4 0.03
43 130 0.82
44 24 0.15
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
Found at i:42172630 original size:21 final size:21
Alignment explanation
Indices: 42172601--42172641 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42172591 CCTTTGTCAG
* *
42172601 TCAATTCTTGCAACTGCGCTT
1 TCAACTCTTGCAACTCCGCTT
*
42172622 TCAACTCTTGTAACTCCGCT
1 TCAACTCTTGCAACTCCGCT
42172642 AAGGCCATTC
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:0.20, C:0.32, G:0.12, T:0.37
Consensus pattern (21 bp):
TCAACTCTTGCAACTCCGCTT
Found at i:42177604 original size:18 final size:17
Alignment explanation
Indices: 42177583--42177618 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42177573 AAATAGATTG
42177583 ATGAGATAAAAATAAATA
1 ATGAGA-AAAAATAAATA
*
42177601 ATGAGAATAAATAAATA
1 ATGAGAAAAAATAAATA
42177618 A
1 A
42177619 GTAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (17 bp):
ATGAGAAAAAATAAATA
Found at i:42180338 original size:19 final size:18
Alignment explanation
Indices: 42180309--42180360 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
42180299 GAATGACACA
*
42180309 TTAACAAATATTAATATTTT
1 TTAA-AAATATTAA-ATTAT
42180329 TTAAAAATATTCAAATTAT
1 TTAAAAATATT-AAATTAT
42180348 TTAAAAA-ATTAAA
1 TTAAAAATATTAAA
42180361 AAGTTATTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 18 0.60
20 6 0.20
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAAAATATTAAATTAT
Found at i:42185722 original size:41 final size:41
Alignment explanation
Indices: 42185677--42185793 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
42185667 GTCAGGCTCG
* *
42185677 AAGCCTGATGTAACACACCAGCATAAAGCCTACTAGGCACA
1 AAGCCTGATATAACACACCAGCACAAAGCCTACTAGGCACA
* *
42185718 AAGCCTGATATAATACACCAGCACAAAGCCTGCTAGGCACA
1 AAGCCTGATATAACACACCAGCACAAAGCCTACTAGGCACA
* * * *
42185759 TAGCCTGA-AT-A-TCACCGGCACAAAGCCTGCTAGGC
1 AAGCCTGATATAACACACCAGCACAAAGCCTACTAGGC
42185794 GTAGAGCCCG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 22 0.32
39 1 0.01
40 2 0.03
41 44 0.64
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (41 bp):
AAGCCTGATATAACACACCAGCACAAAGCCTACTAGGCACA
Found at i:42185789 original size:38 final size:38
Alignment explanation
Indices: 42185692--42185823 Score: 149
Period size: 38 Copynumber: 3.4 Consensus size: 38
42185682 TGATGTAACA
* *
42185692 CACCAGCATAAAGCCTACTAGGCACAAAGCCTGATATAAT
1 CACCAGCACAAAGCCTGCTAGGCACAAAGCCTGA-AT-AT
*
42185732 ACACCAGCACAAAGCCTGCTAGGCACATAGCCTGAATAT
1 -CACCAGCACAAAGCCTGCTAGGCACAAAGCCTGAATAT
* ** * *
42185771 CACCGGCACAAAGCCTGCTAGGCGTAGAGCCCGAATAT
1 CACCAGCACAAAGCCTGCTAGGCACAAAGCCTGAATAT
42185809 CACC-GACACAAAGCC
1 CACCAG-CACAAAGCC
42185824 CAAATAACAA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
37 1 0.01
38 46 0.56
39 2 0.02
40 2 0.02
41 31 0.38
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.14
Consensus pattern (38 bp):
CACCAGCACAAAGCCTGCTAGGCACAAAGCCTGAATAT
Found at i:42187251 original size:3 final size:3
Alignment explanation
Indices: 42187245--42187278 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42187235 CCTCTTATTA
42187245 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
42187279 GATTTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:42200631 original size:16 final size:16
Alignment explanation
Indices: 42200610--42200640 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42200600 TGTATTGAAA
42200610 TAGAGGCGTAATGGAT
1 TAGAGGCGTAATGGAT
42200626 TAGAGGCGTAATGGA
1 TAGAGGCGTAATGGA
42200641 AAGGAGACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.39, T:0.23
Consensus pattern (16 bp):
TAGAGGCGTAATGGAT
Found at i:42200904 original size:16 final size:16
Alignment explanation
Indices: 42200867--42200908 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42200857 TTAATCATAT
*
42200867 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
42200883 TT-AAATATATTATAA
1 TTAAAATATATTATAA
42200898 TTAAAATATAT
1 TTAAAATATAT
42200909 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:42200915 original size:14 final size:15
Alignment explanation
Indices: 42200876--42200917 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42200866 TTTAAACATA
*
42200876 ATTATTATTAAATAT
1 ATTATAATTAAATAT
42200891 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
42200905 A-TATAATTTAATA
1 ATTATAATTAAATA
42200918 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:42201083 original size:120 final size:120
Alignment explanation
Indices: 42200865--42201401 Score: 925
Period size: 120 Copynumber: 4.5 Consensus size: 120
42200855 ATTTAATCAT
*
42200865 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
42200930 GTCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * *
42200986 AATTAACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
42201051 TTAATAATCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
42201106 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
42201171 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
42201226 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
42201290 TCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
42201345 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
42201402 TAAAATAATT
Statistics
Matches: 400, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
119 110 0.28
120 287 0.72
121 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:42201148 original size:18 final size:17
Alignment explanation
Indices: 42201127--42201161 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42201117 TTATTATTAA
*
42201127 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42201145 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42201162 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42201268 original size:18 final size:17
Alignment explanation
Indices: 42201247--42201281 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42201237 TTATTATTAA
*
42201247 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42201265 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42201282 TCTAATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42205411 original size:28 final size:28
Alignment explanation
Indices: 42205380--42205449 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
42205370 CATACACAGC
* *
42205380 ATAAATAAATAAAATCACAATATAAAAT
1 ATAAATAAATAAAATAACAATAAAAAAT
** *
42205408 ATAAATGAAATTCAATAATAATAAAAAAT
1 ATAAAT-AAATAAAATAACAATAAAAAAT
42205437 -TAAATTAAATAAA
1 ATAAA-TAAATAAA
42205450 TTAAAACCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.27
Consensus pattern (28 bp):
ATAAATAAATAAAATAACAATAAAAAAT
Found at i:42215178 original size:19 final size:19
Alignment explanation
Indices: 42215154--42215198 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
42215144 GAGATCTGAA
42215154 TTGTGGAAGCATTCAAACT
1 TTGTGGAAGCATTCAAACT
**
42215173 TTGTGGATTCATTCAAACT
1 TTGTGGAAGCATTCAAACT
*
42215192 TTTTGGA
1 TTGTGGA
42215199 TTCGTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGTGGAAGCATTCAAACT
Found at i:42215199 original size:19 final size:19
Alignment explanation
Indices: 42215163--42215201 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
42215153 ATTGTGGAAG
42215163 CATTCAAACTTTGTGGATT
1 CATTCAAACTTTGTGGATT
*
42215182 CATTCAAACTTTTTGGATT
1 CATTCAAACTTTGTGGATT
42215201 C
1 C
42215202 GTAATTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (19 bp):
CATTCAAACTTTGTGGATT
Found at i:42237053 original size:18 final size:18
Alignment explanation
Indices: 42237030--42237064 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42237020 CTTGGATTTT
42237030 TAAACCCCCATATTACCC
1 TAAACCCCCATATTACCC
**
42237048 TAAACCTTCATATTACC
1 TAAACCCCCATATTACC
42237065 TAGTCATTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAACCCCCATATTACCC
Found at i:42241641 original size:88 final size:88
Alignment explanation
Indices: 42241492--42241668 Score: 302
Period size: 88 Copynumber: 2.0 Consensus size: 88
42241482 TCCTCGGACT
* *
42241492 ACTCACGTACTCCGTTGTAATTATATTACAACTAGGCCTGTATACTTGCTGATACCACCTCATTC
1 ACTCACCTACTCCGTTGTAACTATATTACAACTAGGCCTGTATACTTGCTGATACCACCTCATTC
42241557 ATATATCTTTTACTACAGTATTC
66 ATATATCTTTTACTACAGTATTC
*
42241580 ACTCACCTACTCCGTTGTAACTATATTACAACTCGG-CTCGTATACTTGCTGATACCACCTCATT
1 ACTCACCTACTCCGTTGTAACTATATTACAACTAGGCCT-GTATACTTGCTGATACCACCTCATT
*
42241644 GATATATCTTTTACTACAGTATTC
65 CATATATCTTTTACTACAGTATTC
42241668 A
1 A
42241669 TATTCTGGAC
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
87 2 0.02
88 82 0.98
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (88 bp):
ACTCACCTACTCCGTTGTAACTATATTACAACTAGGCCTGTATACTTGCTGATACCACCTCATTC
ATATATCTTTTACTACAGTATTC
Found at i:42245896 original size:10 final size:10
Alignment explanation
Indices: 42245881--42245962 Score: 74
Period size: 10 Copynumber: 7.6 Consensus size: 10
42245871 AGCAACATAC
*
42245881 AAATTATAAT
1 AAATTACAAT
42245891 AAATTACAAT
1 AAATTACAAT
42245901 AAATTAGCCCTTAAAT
1 AAATTA---C---AAT
*
42245917 TAATTACAAT
1 AAATTACAAT
*
42245927 TAATTACAAT
1 AAATTACAAT
*
42245937 TAATTACAAT
1 AAATTACAAT
42245947 AAATTACAAT
1 AAATTACAAT
42245957 AAATTA
1 AAATTA
42245963 GCCCTCAAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
10 53 0.84
13 2 0.03
16 8 0.13
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (10 bp):
AAATTACAAT
Found at i:42249376 original size:23 final size:22
Alignment explanation
Indices: 42249333--42249376 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
42249323 TTCTAAGTCA
42249333 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
42249356 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
42249377 TTAGTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:42249535 original size:51 final size:50
Alignment explanation
Indices: 42249475--42249660 Score: 221
Period size: 51 Copynumber: 3.7 Consensus size: 50
42249465 TCGGTTCACA
42249475 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGATACACG
* * * * * *
42249526 TTGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCCGATACACA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATCCGATACACG
* * * *
42249577 TGGTAGCCTGCACATAGTATTACACATGCGACC-TATCATTCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGATACACG
* * *
42249627 TAGTAGTCTGTACATAATACTACACATGTGACCA
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA
42249661 CCACTTTCAC
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.34
51 69 0.62
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGATACACG
Found at i:42249595 original size:102 final size:101
Alignment explanation
Indices: 42249471--42249657 Score: 268
Period size: 101 Copynumber: 1.8 Consensus size: 101
42249461 ATGTTCGGTT
* *
42249471 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA-TCCGATACACGTTGTAGCCT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACC--TACCATTCCGATACACGTAGTAGCCT
*
42249535 GCACATAGTACTACACACGTGATCAAAACTATCCGATA
64 GCACATAATACTACACACGTGATCAAAACTATCCGATA
* * * * *
42249573 CACATGGTAGCCTGCACATAGTATTACACATGCGACCTATCATTCCGATACACGTAGTAGTCTGT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCTACCATTCCGATACACGTAGTAGCCTGC
*
42249638 ACATAATACTACACATGTGA
66 ACATAATACTACACACGTGA
42249658 CCACCACTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
100 4 0.05
101 37 0.49
102 34 0.45
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (101 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCTACCATTCCGATACACGTAGTAGCCTGC
ACATAATACTACACACGTGATCAAAACTATCCGATA
Found at i:42252094 original size:12 final size:13
Alignment explanation
Indices: 42252077--42252105 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42252067 GTTTTATCTA
42252077 CTTCCAC-TTTCC
1 CTTCCACATTTCC
42252089 CTTCCACATTTCC
1 CTTCCACATTTCC
42252102 CTTC
1 CTTC
42252106 TTCTTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.10, C:0.48, G:0.00, T:0.41
Consensus pattern (13 bp):
CTTCCACATTTCC
Found at i:42255380 original size:26 final size:26
Alignment explanation
Indices: 42255341--42255399 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
42255331 TCTTTTCTCG
*
42255341 AAATTTTACTAGGGGCAAAATCATCA
1 AAATTTTACCAGGGGCAAAATCATCA
*
42255367 AAATTTTACCAGGGGTAAAATCATCA
1 AAATTTTACCAGGGGCAAAATCATCA
42255393 AAATTTT
1 AAATTTT
42255400 GTTAAGGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (26 bp):
AAATTTTACCAGGGGCAAAATCATCA
Found at i:42255408 original size:26 final size:26
Alignment explanation
Indices: 42255341--42255413 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
42255331 TCTTTTCTCG
* * *
42255341 AAATTTTACTAGGGGCAAAATCATCA
1 AAATTTTACCAAGGGTAAAATCATCA
*
42255367 AAATTTTACCAGGGGTAAAATCATCA
1 AAATTTTACCAAGGGTAAAATCATCA
***
42255393 AAATTTTGTTAAGGGTAAAAT
1 AAATTTTACCAAGGGTAAAAT
42255414 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (26 bp):
AAATTTTACCAAGGGTAAAATCATCA
Found at i:42263212 original size:40 final size:39
Alignment explanation
Indices: 42263168--42263302 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
42263158 ACTAGTTTGG
42263168 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAA-TTGA
* * * * * *
42263208 CACCCAGTGTCTCATTGGCTAAATAGAAGT-A-AATTGG
1 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTGA
* * * *
42263245 CACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAAT-AATTGA
* *
42263286 CACCTAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
42263303 ACTCGAAGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
37 18 0.25
38 9 0.12
39 1 0.01
40 25 0.34
41 20 0.27
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTGA
Found at i:42264185 original size:17 final size:18
Alignment explanation
Indices: 42264163--42264198 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42264153 TCTCCTTTTG
*
42264163 TTTCCTTTTTGTTT-ATT
1 TTTCCTTTCTGTTTCATT
42264180 TTTCCTTTCTGTTTCATT
1 TTTCCTTTCTGTTTCATT
42264198 T
1 T
42264199 CTATCTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTCCTTTCTGTTTCATT
Found at i:42264208 original size:16 final size:18
Alignment explanation
Indices: 42264189--42264233 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
42264179 TTTTCCTTTC
42264189 TGTTTCATTT-CTA-TCT
1 TGTTTCATTTACTATTCT
*
42264205 TGTTTCTTTTACTATTTCT
1 TGTTTCATTTACTA-TTCT
42264224 T-TTTCATTTA
1 TGTTTCATTTA
42264234 TTTAATTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 9 0.38
17 3 0.12
18 8 0.33
19 4 0.17
ACGTcount: A:0.13, C:0.16, G:0.04, T:0.67
Consensus pattern (18 bp):
TGTTTCATTTACTATTCT
Found at i:42265761 original size:26 final size:26
Alignment explanation
Indices: 42265689--42265764 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
42265679 ACATATTTTC
* * *
42265689 TCAAAATTTTACCAGGGGCAAAATCA
1 TCAAAATTTTTCTAGGGGTAAAATCA
** *
42265715 TCAAAATTTTTCTAGATGTAAAATCG
1 TCAAAATTTTTCTAGGGGTAAAATCA
42265741 TCAAAATTTTGT-TAGGGGTAAAAT
1 TCAAAATTTT-TCTAGGGGTAAAAT
42265765 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 40 0.98
27 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTTCTAGGGGTAAAATCA
Found at i:42270569 original size:22 final size:22
Alignment explanation
Indices: 42270539--42270580 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42270529 ACACCAAAAC
*
42270539 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
*
42270561 AGGCCTTTAGCGGTGCTTTT
1 AGGCCTTTAGCGGCGCTTTT
42270581 ACCACTAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.43
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:42270633 original size:42 final size:41
Alignment explanation
Indices: 42270565--42270725 Score: 139
Period size: 42 Copynumber: 3.8 Consensus size: 41
42270555 TTTTTTAGGC
* * * *
42270565 CTTTAGCGGTGCTTTTACCACTAACGCCACTAAAGACCTATT
1 CTTTAGCGGCGC-TTTATCACAAACGCCGCTAAAGACCTATT
* *
42270607 CTTTAGCGGCGCTTTCCTCTCAAACGCCGC-AATAGACTCTGA-T
1 CTTTAGCGGCGCTTT-ATCACAAACGCCGCTAA-AGAC-CT-ATT
*
42270650 CTGTAGCGGCGCTTTATCACAAACGCCGCTAAAGACCCT-TAT
1 CTTTAGCGGCGCTTTATCACAAACGCCGCTAAAGA-CCTAT-T
* * *
42270692 CTTTAGCGGCGCTTTGACCAAAAACGCCACTAAA
1 CTTTAGCGGCGCTTT-ATCACAAACGCCGCTAAA
42270726 AAGGCCAACA
Statistics
Matches: 97, Mismatches: 13, Indels: 17
0.76 0.10 0.13
Matches are distributed among these distances:
41 5 0.05
42 56 0.58
43 35 0.36
44 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (41 bp):
CTTTAGCGGCGCTTTATCACAAACGCCGCTAAAGACCTATT
Found at i:42271072 original size:21 final size:21
Alignment explanation
Indices: 42271046--42271137 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
42271036 TTTGACGCTG
*
42271046 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTTCAGC
42271067 CTCTGCTTCCCTCGCTTCAGC
1 CTCTGCTTCCCTCGCTTCAGC
*
42271088 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTTCAGC
* * * *
42271109 CTGTACTTCTCTCGCTGCTA-C
1 CTCTGCTTCCCTCGCTTC-AGC
42271130 CTCTGCTT
1 CTCTGCTT
42271138 GTCTTGTTGC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
21 62 0.98
22 1 0.02
ACGTcount: A:0.05, C:0.43, G:0.15, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTTCAGC
Found at i:42271221 original size:66 final size:66
Alignment explanation
Indices: 42271149--42271294 Score: 179
Period size: 66 Copynumber: 2.2 Consensus size: 66
42271139 TCTTGTTGCC
* * *
42271149 GCATCTACTTTAAGCTGCT-GCTGGAGTTGTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGCT
1 GCATCTACTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTTGAACCTCAACTTCTCTCGAT
42271212 GCT
64 GCT
* * * *
42271215 GCATCTACTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAACTTCTCTCGATGT
1 GCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCAACTTCTCTCGATGC
42271280 T
66 T
**
42271281 GCATCCGCTTTAAG
1 GCATCTACTTTAAG
42271295 TTGTGTAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.93
67 4 0.06
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (66 bp):
GCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCAACTTCTCTCGATGC
T
Found at i:42276750 original size:16 final size:16
Alignment explanation
Indices: 42276729--42276772 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
42276719 ATTAAGCTAC
42276729 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
42276745 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
* *
42276761 GAAAATTATGTA
1 GTAAGTTATGTA
42276773 AGTTGTGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:42276768 original size:25 final size:25
Alignment explanation
Indices: 42276740--42276879 Score: 99
Period size: 25 Copynumber: 5.7 Consensus size: 25
42276730 TAAGTTATGT
*
42276740 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
*
42276765 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
* * * *
42276790 AGTATGCTATG-TAAG--TTATGTAA
1 ATTATG-TAAGTTATGTATTATGAAA
* ** * * *
42276813 GTCGTATAAGTTATGTAAGT-TGTAA
1 ATTATGTAAGTTATGT-ATTATGAAA
* *
42276838 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
*
42276863 ATTAAGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
42276880 ATTTACGAAT
Statistics
Matches: 85, Mismatches: 24, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
22 3 0.04
23 11 0.13
24 2 0.02
25 65 0.76
26 4 0.05
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTATGAAA
Found at i:42276809 original size:9 final size:9
Alignment explanation
Indices: 42276797--42276945 Score: 104
Period size: 9 Copynumber: 17.7 Consensus size: 9
42276787 AAAAGTATGC
42276797 TATGTAAGT
1 TATGTAAGT
42276806 TATGTAAGT
1 TATGTAAGT
** *
42276815 CGTATAAGT
1 TATGTAAGT
42276824 TATGTAAG-
1 TATGTAAGT
42276832 T-TGTAAGT
1 TATGTAAGT
42276840 TATGTAAGT
1 TATGTAAGT
*
42276849 TAT-TTA-T
1 TATGTAAGT
* *
42276856 TATGAAAAT
1 TATGTAAGT
*
42276865 TAAGTAAGT
1 TATGTAAGT
*
42276874 TATGTAATT
1 TATGTAAGT
*
42276883 TACG-AA-T
1 TATGTAAGT
* **
42276890 AAT-TAAAAA
1 TATGT-AAGT
42276899 TATGTAAGT
1 TATGTAAGT
42276908 TATGTAAG-
1 TATGTAAGT
42276916 T-TGTAAGT
1 TATGTAAGT
42276924 TATGTAAG-
1 TATGTAAGT
42276932 T-TGTAAGT
1 TATGTAAGT
42276940 TATGTA
1 TATGTA
42276946 TAATATTAAA
Statistics
Matches: 107, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
7 24 0.22
8 13 0.12
9 69 0.64
10 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (9 bp):
TATGTAAGT
Found at i:42276840 original size:16 final size:16
Alignment explanation
Indices: 42276799--42276945 Score: 104
Period size: 16 Copynumber: 8.8 Consensus size: 16
42276789 AAGTATGCTA
42276799 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
*
42276815 CGTATAAGTTATGTAAGT
1 --TGTAAGTTATGTAAGT
42276833 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
* * * *
42276849 TATTTA-TTATGAAAAT
1 T-GTAAGTTATGTAAGT
*
42276865 TAAGTAAGTTATGTAATT
1 T--GTAAGTTATGTAAGT
* *
42276883 TACGAATAA-TTA--AAAAT
1 T--G--TAAGTTATGTAAGT
42276900 ATGTAAGTTATGTAAGT
1 -TGTAAGTTATGTAAGT
42276917 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
42276933 TGTAAGTTATGTA
1 TGTAAGTTATGTA
42276946 TAATATTAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.03
15 3 0.03
16 55 0.52
17 11 0.10
18 27 0.26
19 3 0.03
20 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.42
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:42276842 original size:34 final size:31
Alignment explanation
Indices: 42276799--42276945 Score: 114
Period size: 34 Copynumber: 4.4 Consensus size: 31
42276789 AAGTATGCTA
* *
42276799 TGTAAGTTATGTAAGTCGTATAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT--TATAA-TTATGAAAAT
*
42276833 TGTAAGTTATGTAAGTTATTTATTATGAAAAT
1 TGTAAGTTATGTAAGTTA-TAATTATGAAAAT
* * * *
42276865 TAAGTAAGTTATGTAATTTACGAATAATTAAAAAT
1 T--GTAAGTTATGTAAGTTA-TAATTA-TGAAAAT
* * *
42276900 ATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
1 -TGTAAGTTATGTAAGTTATAA-TTATGAAAAT
42276933 TGTAAGTTATGTA
1 TGTAAGTTATGTA
42276946 TAATATTAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
32 24 0.26
33 8 0.09
34 52 0.57
35 6 0.07
36 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.42
Consensus pattern (31 bp):
TGTAAGTTATGTAAGTTATAATTATGAAAAT
Found at i:42277010 original size:56 final size:56
Alignment explanation
Indices: 42276933--42277456 Score: 859
Period size: 56 Copynumber: 9.2 Consensus size: 56
42276923 TTATGTAAGT
42276933 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
*
42276989 TGTATGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
*
42277045 TGTAAGTTATGTATAATATTAAATAACTAAGTTATTTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
42277101 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
42277157 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
* *
42277213 TGTATGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
* *
42277269 TGTATGTTATGTATAATATTAAATAACTAAGTTATGCAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
* * *
42277325 TGTATGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATCAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
* * * * *
42277381 TGTATGTTATGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATGTATATTAACTAA
1 TGTAAGTTATGT-A--TA---ATATTAAATAACTAAGTTATGTAATTTATGTATAAT-ATTAA
42277444 TGTAAGTTATGTA
1 TGTAAGTTATGTA
42277457 ATATCTTATA
Statistics
Matches: 444, Mismatches: 17, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
56 393 0.89
57 1 0.00
59 2 0.00
62 34 0.08
63 14 0.03
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (56 bp):
TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
Found at i:42277047 original size:22 final size:22
Alignment explanation
Indices: 42277022--42277066 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
42277012 TAACTAAGTT
*
42277022 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
42277044 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
42277066 A
1 A
42277067 ATAACTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:42277159 original size:22 final size:22
Alignment explanation
Indices: 42277134--42277178 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
42277124 TAACTAAGTT
*
42277134 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
42277156 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
42277178 A
1 A
42277179 ATAACTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:42277413 original size:18 final size:18
Alignment explanation
Indices: 42277392--42277444 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
42277382 GTATGTTATG
42277392 TAATTTATGTATATTAAC
1 TAATTTATGTATATTAAC
* *
42277410 TAA-TTAAGT-TA-T--G
1 TAATTTATGTATATTAAC
42277423 TAATTTATGTATATTAAC
1 TAATTTATGTATATTAAC
42277441 TAAT
1 TAAT
42277445 GTAAGTTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
13 3 0.12
14 5 0.19
15 3 0.12
16 3 0.12
17 5 0.19
18 7 0.27
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (18 bp):
TAATTTATGTATATTAAC
Found at i:42277468 original size:31 final size:32
Alignment explanation
Indices: 42277184--42277458 Score: 197
Period size: 31 Copynumber: 9.4 Consensus size: 32
42277174 ATTAAATAAC
* *
42277184 TAAGTTATGTAATTTATGTATAAT-ATTAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* * *
42277215 TATGTTATGT-A--TA---ATATTAATTAA-C
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* *
42277240 TAAGTTATGTAATTTATGTATAAT-ATTAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* * *
42277271 TATGTTATGT-A--TA---ATATTAAATAA-C
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* * *
42277296 TAAGTTATGCAATTTATGTATAAT-ATTAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* * *
42277327 TATGTTATGT-A--TA---ATATTAATTAA-C
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* *
42277352 TAAGTTATGTAATTTATGTATAATATC-AATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
*
42277383 TATGTTATGTAATTTATGTATATTAACTAAT-
1 TAAGTTATGTAATTTATGTATATTAACTAATG
42277414 TAAGTTATGTAATTTATGTATATTAACTAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
42277446 TAAGTTATGTAAT
1 TAAGTTATGTAAT
42277459 ATCTTATATT
Statistics
Matches: 190, Mismatches: 28, Indels: 51
0.71 0.10 0.19
Matches are distributed among these distances:
25 38 0.20
26 17 0.09
28 12 0.06
30 14 0.07
31 93 0.49
32 16 0.08
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (32 bp):
TAAGTTATGTAATTTATGTATATTAACTAATG
Found at i:42280354 original size:35 final size:36
Alignment explanation
Indices: 42280306--42280375 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
42280296 CAACTTTTAA
*
42280306 TTTGTAATATTATAATATTT-ATTTTTTTGTATAAAG
1 TTTGTAATATTATAATATTTAATTTTATTG-ATAAAG
*
42280342 TTTG-AATTTTATAATATTTAATTTTATTGATAAA
1 TTTGTAATATTATAATATTTAATTTTATTGATAAA
42280376 TAAATAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 19 0.61
36 12 0.39
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (36 bp):
TTTGTAATATTATAATATTTAATTTTATTGATAAAG
Found at i:42280560 original size:7 final size:7
Alignment explanation
Indices: 42280538--42280577 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
42280528 CCCAAATCCA
42280538 TAACCCC
1 TAACCCC
42280545 TTAACCCC
1 -TAACCCC
*
42280553 TTACCCC
1 TAACCCC
42280560 TAATCCCC
1 TAA-CCCC
42280568 TAACCCC
1 TAACCCC
42280575 TAA
1 TAA
42280578 AGCATAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.28, C:0.50, G:0.00, T:0.23
Consensus pattern (7 bp):
TAACCCC
Found at i:42280576 original size:15 final size:15
Alignment explanation
Indices: 42280520--42280577 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
42280510 ACCGTTGAAA
*
42280520 CCCTAAACCCCAAAT-
1 CCCT-AACCCCTAATC
*
42280535 CCATAACCCCTTAA-C
1 CCCTAACCCC-TAATC
*
42280550 CCCTTACCCCTAATC
1 CCCTAACCCCTAATC
42280565 CCCTAACCCCTAA
1 CCCTAACCCCTAA
42280578 AGCATAACCC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 9 0.26
15 26 0.74
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (15 bp):
CCCTAACCCCTAATC
Found at i:42280754 original size:37 final size:38
Alignment explanation
Indices: 42280713--42280784 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 38
42280703 CATAACCCCC
* * *
42280713 TAACCCTTTACCCCTAAATCCC-TTAACCCCTAAAGCA
1 TAACCCTTAAACCCTAAATCCCACTAACCCCTAAAGCA
42280750 TAACCCTTAAACCCTAAATCCCACTAACCCCTAAA
1 TAACCCTTAAACCCTAAATCCCACTAACCCCTAAA
42280785 CATCAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 20 0.65
38 11 0.35
ACGTcount: A:0.36, C:0.40, G:0.01, T:0.22
Consensus pattern (38 bp):
TAACCCTTAAACCCTAAATCCCACTAACCCCTAAAGCA
Found at i:42282109 original size:15 final size:15
Alignment explanation
Indices: 42282089--42282126 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42282079 TTGAAATTAA
42282089 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
42282104 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
42282119 CCCTAAAT
1 CCCTAAAT
42282127 TAATCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:42282664 original size:41 final size:42
Alignment explanation
Indices: 42282600--42282920 Score: 151
Period size: 41 Copynumber: 7.8 Consensus size: 42
42282590 TTTTGTTACT
* ** *
42282600 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTA-AATA-C
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-ACAATAGA
* *
42282641 ATTAGCGGCGCTTAGATACAAACGCCGCTGAA-GACAATAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGACAATAGA
* * * * *** *
42282682 ATTAGTGGCGCTCAGTTAGAAACGCCGCTAAA-GACCCGAGT
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGACAATAGA
* * * * *** *
42282723 ATTAGCGGCTCATAGACAAAAACGTCGCTAAA-GACCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGACAATAGA
* * *** *
42282764 ATTAGCGGCGCATAGACAAAAACGCCGCTAAA-GACTCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGACAATAGA
** * *** *
42282805 ATTAGCGGCGCTTAGACGAAATCGCCGCTAAA-GATC-GGGGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGA-CAATAGA
* * * * *
42282846 ATTAGCGGCGTTTTTG-TGAAAGCGCCGCTAAA-GATCAA-AGC
1 ATTAGCGGCG-CTTAGATAAAAACGCCGCTAAAGGA-CAATAGA
* *
42282887 ATTAGCGGCGCTTACACAAAAACGCCGCTAAAGG
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
42282921 TTTAAAAAAT
Statistics
Matches: 229, Mismatches: 44, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.00
40 7 0.03
41 216 0.94
42 5 0.02
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (42 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGACAATAGA
Found at i:42282746 original size:82 final size:82
Alignment explanation
Indices: 42282640--42282919 Score: 233
Period size: 82 Copynumber: 3.4 Consensus size: 82
42282630 AAGGTAAATA
* * * * * ** *
42282640 CATTAGCGGCGCTTAGATACAAACGCCGCTGAAGACAATAGAATTAGTGGCGC-TCAGTTAGAAA
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAAGAGAATTAGCGGCGCAT-AGACAAAAA
42282704 CGCCGCTAAAGACCCGAG
65 CGCCGCTAAAGACCCGAG
* * * * ** *
42282722 TATTAGCGGCTCATAGACAAAAACGTCGCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAAC
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAAGAGAATTAGCGGCGCATAGACAAAAAC
*
42282787 GCCGCTAAAGACTCGAG
66 GCCGCTAAAGACCCGAG
* * * * * ** * **
42282804 CATTAGCGGCGCTTAGACGAAATCGCCGCTAAAGATC-GGGGCATTAGCGGCGTTTTTG-TGAAA
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGA-CAAGAGAATTAGCGGCG-CATAGACAAAA
* * **
42282867 GCGCCGCTAAAGATCAAAG
64 ACGCCGCTAAAGACCCGAG
*
42282886 CATTAGCGGCGCTTACACAAAAACGCCGCTAAAG
1 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
42282920 GTTTAAAAAA
Statistics
Matches: 158, Mismatches: 37, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
82 154 0.97
83 4 0.03
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (82 bp):
CATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAAGAGAATTAGCGGCGCATAGACAAAAAC
GCCGCTAAAGACCCGAG
Found at i:42282831 original size:123 final size:122
Alignment explanation
Indices: 42282615--42282919 Score: 292
Period size: 123 Copynumber: 2.5 Consensus size: 122
42282605 CGGCGCTTCG
** * * * * *
42282615 GCAAAAACGCCGCTAAAG-GTAAATACATTAGCGGCGCTTAGATACAAACGCCGCTGAAGACAAT
1 GCAAAAACGCCGCTAAAGACCAAA-GCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAAG
* *
42282679 AGAATTAGTGGCGCTCAGTTAGAAACGCCGCTAAAGACCCGAGTATTAGCGGC-TCATA
65 AGAATTAGCGGCGCTCAG-TAGAAACGCCGCTAAAGACCCGAGCATTAGCGGCGTCATA
* ** * **
42282737 GACAAAAACGTCGCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAACGCCGCTAAAGACTCG
1 G-CAAAAACGCCGCTAAAGACCAAAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAAG
* * * * * ** *
42282802 AGCATTAGCGGCGCTTAG-ACGAAATCGCCGCTAAAGATCGGGGCATTAGCGGCGTTTTT
65 AGAATTAGCGGCGCTCAGTA-GAAA-CGCCGCTAAAGACCCGAGCATTAGCGGCGTCATA
** * * *
42282861 GTGAAAGCGCCGCTAAAGATCAAAGCATTAGCGGCGCTTACACAAAAACGCCGCTAAAG
1 GCAAAAACGCCGCTAAAGACCAAAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
42282920 GTTTAAAAAA
Statistics
Matches: 146, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
121 1 0.01
122 5 0.03
123 136 0.93
124 4 0.03
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (122 bp):
GCAAAAACGCCGCTAAAGACCAAAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAAGA
GAATTAGCGGCGCTCAGTAGAAACGCCGCTAAAGACCCGAGCATTAGCGGCGTCATA
Found at i:42283050 original size:40 final size:40
Alignment explanation
Indices: 42282999--42283074 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
42282989 AATTCCTAGT
*
42282999 TTTAGCGGCGCTTCCGGAT-AATCGCCGCTGATGCTCTTCC
1 TTTAGCGGCGCTT-CGGATAAATCGCCGCTAATGCTCTTCC
* *
42283039 TTTAGCGGCGCTTTGGCTAAATCGCCGCTAATGCTC
1 TTTAGCGGCGCTTCGGATAAATCGCCGCTAATGCTC
42283075 GATTTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 3 0.09
40 29 0.91
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.30
Consensus pattern (40 bp):
TTTAGCGGCGCTTCGGATAAATCGCCGCTAATGCTCTTCC
Found at i:42295138 original size:22 final size:23
Alignment explanation
Indices: 42295088--42295132 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
42295078 ATAAAGATAT
* *
42295088 AATTTATAATATATAAAATTTTA
1 AATTAATAATATATAAAATTGTA
42295111 AATTAATAATA-ATAAAATTGTA
1 AATTAATAATATATAAAATTGTA
42295133 CTTTAAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AATTAATAATATATAAAATTGTA
Found at i:42295205 original size:17 final size:18
Alignment explanation
Indices: 42295180--42295216 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
42295170 TATTTTAAAA
42295180 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
42295198 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
42295215 AT
1 AT
42295217 ATTTGTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:42296455 original size:21 final size:18
Alignment explanation
Indices: 42296396--42296460 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
42296386 ATTATTTTTT
*
42296396 AAAATTAAAAAATATAAAA
1 AAAATT-AAAATTATAAAA
*
42296415 AAAATTAAAATTATTTAAA
1 AAAATTAAAATTA-TAAAA
*
42296434 AAAGTATACAAATTAT-AAA
1 AAAAT-TA-AAATTATAAAA
42296453 AAAATTAA
1 AAAATTAA
42296461 TATTTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.03
18 8 0.21
19 21 0.54
20 3 0.08
21 6 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAATTAAAATTATAAAA
Found at i:42304900 original size:13 final size:14
Alignment explanation
Indices: 42304877--42304918 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
42304867 TTAAATTTTA
42304877 TTTTAATAATAA-AT
1 TTTTAA-AATAATAT
42304891 TTTTAAAATAATAT
1 TTTTAAAATAATAT
*
42304905 ATTT-AAATAATAT
1 TTTTAAAATAATAT
42304918 T
1 T
42304919 CTTCACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAAAATAATAT
Found at i:42304916 original size:16 final size:15
Alignment explanation
Indices: 42304875--42304916 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
42304865 ATTTAAATTT
42304875 TATTTTAATAATAAA
1 TATTTTAATAATAAA
42304890 T-TTTTAA-AATAATA
1 TATTTTAATAATAA-A
*
42304904 TATTTAAATAATA
1 TATTTTAATAATA
42304917 TTCTTCACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 5 0.22
14 8 0.35
15 6 0.26
16 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTTAATAATAAA
Found at i:42311882 original size:21 final size:21
Alignment explanation
Indices: 42311858--42311899 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
42311848 AGCCATCGGG
*
42311858 CCTAGCCGGGTAGCCCAACGA
1 CCTAGCCGGGTAACCCAACGA
42311879 CCTAGCCGGGTAACCCAACGA
1 CCTAGCCGGGTAACCCAACGA
42311900 ATAATCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.38, G:0.26, T:0.10
Consensus pattern (21 bp):
CCTAGCCGGGTAACCCAACGA
Found at i:42312511 original size:26 final size:26
Alignment explanation
Indices: 42312475--42312525 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
42312465 TACTAAGTTG
42312475 ACTTAAACTTATAAGCTTCCTGCTCT
1 ACTTAAACTTATAAGCTTCCTGCTCT
42312501 ACTTAAACTTATAAGCTTCCTGCTC
1 ACTTAAACTTATAAGCTTCCTGCTC
42312526 AAATTGCAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.37
Consensus pattern (26 bp):
ACTTAAACTTATAAGCTTCCTGCTCT
Found at i:42317136 original size:24 final size:26
Alignment explanation
Indices: 42317112--42317161 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
42317102 ACAGCGCATT
42317112 AATTAAAAATATT-TTTAAATAATTAA
1 AATTAAAAATATTATTTAAATAATT-A
* *
42317138 AATTAAAAATTTTATTTTAATAAT
1 AATTAAAAATATTATTTAAATAAT
42317162 ATTACATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTAAAAATATTATTTAAATAATTA
Found at i:42317309 original size:16 final size:16
Alignment explanation
Indices: 42317285--42317315 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42317275 GTTATTATGA
*
42317285 TTGATTAAAAAACAAC
1 TTGAGTAAAAAACAAC
42317301 TTGAGTAAAAAACAA
1 TTGAGTAAAAAACAA
42317316 GTATTTGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (16 bp):
TTGAGTAAAAAACAAC
Found at i:42320629 original size:90 final size:91
Alignment explanation
Indices: 42320504--42320709 Score: 272
Period size: 90 Copynumber: 2.3 Consensus size: 91
42320494 TGATTTTAGT
* *
42320504 AAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTATA
1 AAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
* *
42320569 TTTAAT-ATTAATTATTTTAAATTGTA-
65 TGTAATAATT-ATTATTTTAAATTATAC
* * * *
42320595 TAATTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATAT
*
42320660 GTAATAATTATTTTTTTAAATTATAC
66 GTAATAATTATTATTTTAAATTATAC
* * *
42320686 AAATTCATAAAATATAATTTATTA
1 AAATTCATATAAGAAAATTTATTA
42320710 GTTATAATTA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
90 63 0.63
91 37 0.37
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (91 bp):
AAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATAT
GTAATAATTATTATTTTAAATTATAC
Found at i:42320681 original size:44 final size:43
Alignment explanation
Indices: 42320543--42320684 Score: 110
Period size: 44 Copynumber: 3.2 Consensus size: 43
42320533 GAATTTTATG
* * *
42320543 AAATTATATATCACTATTAAATTATATTTAAT-ATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATT-ATTTTTTT
* ** * * *
42320587 AAATTGTATAATTCATATAAGAAAATT-TATT-ATCAATAATTTTATG
1 AAATTATAT-ATT-AT-T-ATTAAATTATATTAAT-AATTATTTTTTT
42320633 AAATTATATATTATTATTAAATTATATGTAATAATTATTTTTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATTATTTTTTT
42320677 AAATTATA
1 AAATTATA
42320685 CAAATTCATA
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 28 0.38
45 9 0.12
46 16 0.22
47 5 0.07
48 6 0.08
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATTATTTTTTT
Found at i:42320838 original size:66 final size:64
Alignment explanation
Indices: 42320763--42321095 Score: 226
Period size: 66 Copynumber: 5.4 Consensus size: 64
42320753 AAATATATTT
* *
42320763 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTACAGTATCATATATTATGAATTGAGTAAATTCATATAA
42320828 G
64 G
* ** * * * *
42320829 AATATTAATTATTAAGAATTTT-GCTCCA-TAATTATATATT-TTAATT-A-T-AA-T-ATAT-T
1 AATATTAATTATTTA-AATTTTATTTACAGT-ATCATATATTATGAATTGAGTAAATTCATATAA
*
42320885 T
64 G
*
42320886 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATG-ATTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTACAGTATCATATATTATGAATTGAGTAAATTCATATA
42320949 AG
63 AG
* * * **
42320951 AATATTAATTATTAAGAATTTTA-TTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTACAGTATCATATATTATGAATTGAGTAAATTCATATAAG
* *
42321005 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTACAGTATCATATATTATGAATTGAGTAAATTCATATA
42321069 AG
63 AG
*
42321071 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
42321096 AAATTATATA
Statistics
Matches: 200, Mismatches: 34, Indels: 67
0.66 0.11 0.22
Matches are distributed among these distances:
53 5 0.03
54 13 0.06
55 5 0.03
56 9 0.05
57 15 0.08
58 6 0.03
59 27 0.14
60 21 0.10
61 3 0.01
62 5 0.03
63 11 0.05
64 17 0.09
65 21 0.10
66 37 0.19
67 5 0.03
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.48
Consensus pattern (64 bp):
AATATTAATTATTTAAATTTTATTTACAGTATCATATATTATGAATTGAGTAAATTCATATAAG
Found at i:42320888 original size:15 final size:15
Alignment explanation
Indices: 42320857--42320904 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
42320847 TTTTGCTCCA
42320857 TAATTAT-ATAT-TT
1 TAATTATAATATATT
42320870 TAATTATAATATATT
1 TAATTATAATATATT
*
42320885 TAATAATAAT-TATGT
1 TAATTATAATATAT-T
42320900 TAATT
1 TAATT
42320905 TATATTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 7 0.23
14 7 0.23
15 16 0.53
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TAATTATAATATATT
Found at i:42321007 original size:15 final size:15
Alignment explanation
Indices: 42320972--42321023 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
42320962 TTAAGAATTT
*
42320972 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42320986 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42321000 TATTTAATAATAAT-
1 TATTTAATTATAATA
42321014 TATGTTAATT
1 TAT-TTAATT
42321024 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42321027 original size:119 final size:120
Alignment explanation
Indices: 42320725--42321139 Score: 694
Period size: 120 Copynumber: 3.4 Consensus size: 120
42320715 AATTATTTTA
* * *
42320725 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
42320787 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
42320845 AATTTTGCTCCATAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAT
1 AATTTT-AT-TA-AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAT
42320910 TTTACAGTATCATATATTATGA-TTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
42320967 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
42321032 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
42321087 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
42321140 TAAATATGAT
Statistics
Matches: 280, Mismatches: 8, Indels: 14
0.93 0.03 0.05
Matches are distributed among these distances:
119 74 0.26
120 95 0.34
121 2 0.01
122 48 0.17
123 59 0.21
124 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:42321122 original size:16 final size:16
Alignment explanation
Indices: 42321101--42321142 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42321091 TTATTAAATT
*
42321101 ATATATTTTAATTATA
1 ATATATTTTAATAATA
42321117 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
42321132 AT-TATGTTTAA
1 ATATAT-TTTAA
42321143 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:42321127 original size:15 final size:15
Alignment explanation
Indices: 42321092--42321133 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42321082 TTAAGAATTT
*
42321092 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42321106 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42321120 TATTTAATAATAAT
1 TATTTAATTATAAT
42321134 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42321254 original size:157 final size:157
Alignment explanation
Indices: 42321076--42321392 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
42321066 ATAAGAATAT
*
42321076 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
42321141 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
42321206 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
42321233 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
42321298 AAATATGATTAAATTATTTATTATTGATAATAATAATTTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
42321363 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
42321390 TAA
1 TAA
42321393 GGGTATTTTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:42321273 original size:18 final size:17
Alignment explanation
Indices: 42321245--42321279 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42321235 ATTATTAAGA
*
42321245 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42321262 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42321280 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42321313 original size:75 final size:75
Alignment explanation
Indices: 42321077--42321315 Score: 191
Period size: 75 Copynumber: 3.1 Consensus size: 75
42321067 TAAGAATATT
*
42321077 AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
42321142 AATATGATTA
66 AATATGATTA
* ** * * * * *
42321152 AATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATA-A--CAATAATAATT
1 AATTATTAAGAATT-TTATT-A-AA--TTA-TATATTTTAATTAA-AATATATTTAATAATAATT
**** * * *
42321214 -TACCAAAACAAAT-TTCTGCT
59 AT-GTTTAA-ATATGAT-T--A
42321234 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
42321299 AATATGATTA
66 AATATGATTA
42321309 AATTATT
1 AATTATT
42321316 TATTATTGAT
Statistics
Matches: 116, Mismatches: 31, Indels: 34
0.64 0.17 0.19
Matches are distributed among these distances:
75 22 0.19
76 16 0.14
77 8 0.07
78 16 0.14
79 16 0.14
80 8 0.07
81 15 0.13
82 15 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:42321537 original size:16 final size:16
Alignment explanation
Indices: 42321516--42321551 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
42321506 AATTTACTAT
*
42321516 TACACCTCTAATTTAA
1 TACACCTCTAATCTAA
42321532 TACACCTCTAATCTAA
1 TACACCTCTAATCTAA
42321548 TACA
1 TACA
42321552 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (16 bp):
TACACCTCTAATCTAA
Found at i:42323232 original size:16 final size:16
Alignment explanation
Indices: 42323233--42323265 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42323223 TGTATTGGAT
*
42323233 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
42323249 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
42323265 T
1 T
42323266 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:42323238 original size:21 final size:21
Alignment explanation
Indices: 42323212--42323252 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42323202 TTCGCTGTAC
*
42323212 TGGATTAGAGGTGTATTGGAT
1 TGGATTAGAGGTGTAATGGAT
42323233 TGGATTAGAGGTGTAATGGA
1 TGGATTAGAGGTGTAATGGA
42323253 ATAGAGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.39, T:0.34
Consensus pattern (21 bp):
TGGATTAGAGGTGTAATGGAT
Found at i:42323310 original size:45 final size:44
Alignment explanation
Indices: 42323244--42323338 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
42323234 GGATTAGAGG
* *
42323244 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
42323289 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
42323333 TGTAAT
1 TGTAAT
42323339 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:42323521 original size:18 final size:17
Alignment explanation
Indices: 42323500--42323534 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42323490 TTATTATTTA
*
42323500 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42323518 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42323535 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42323528 original size:28 final size:27
Alignment explanation
Indices: 42323458--42323530 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
42323448 TTTATTATCA
*
42323458 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
42323486 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
42323513 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
42323531 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:42323647 original size:144 final size:147
Alignment explanation
Indices: 42323419--42323690 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
42323409 ATGATTATTG
42323419 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
42323484 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
42323549 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
42323568 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
42323630 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
42323691 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:42323665 original size:18 final size:17
Alignment explanation
Indices: 42323644--42323678 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42323634 TTATTATTAA
*
42323644 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42323662 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42323679 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42323722 original size:54 final size:54
Alignment explanation
Indices: 42323664--42323842 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
42323654 ATTAAAATAT
*
42323664 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
42323718 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
42323781 TAT
53 -AC
*
42323784 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
42323838 ATAAT
1 ATAAT
42323843 ATATGATTAT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:42323724 original size:61 final size:61
Alignment explanation
Indices: 42323659--42323846 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
42323649 TTTTAATTAA
*
42323659 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
42323720 AATATATGATACT-GTAAAA-T-ATAA-AATAACATAATTATTAT-TAAATATAAT-ATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAATTA-AT-ATTCTTATATGAATTTACTCA-AATCAT
42323779 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
42323840 AATATAT
1 AATATAT
42323847 GATTATAACT
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 29 0.31
60 16 0.17
61 37 0.39
62 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:42323757 original size:120 final size:120
Alignment explanation
Indices: 42323627--42323849 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
42323617 ATCATATTTA
* *
42323627 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
42323692 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
42323747 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
42323812 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGAT
42323850 TATAACTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
Found at i:42323785 original size:18 final size:17
Alignment explanation
Indices: 42323764--42323798 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42323754 TTATTATTAA
42323764 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
42323782 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
42323799 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:42323861 original size:17 final size:16
Alignment explanation
Indices: 42323839--42323885 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
42323829 ACTCAAATCA
42323839 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
42323856 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
42323870 TAAATATATGATTTAA
1 T-AATATATGATTTAA
42323886 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:42323886 original size:17 final size:17
Alignment explanation
Indices: 42323858--42323891 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42323848 ATTATAACTA
*
42323858 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
42323875 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
42323892 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:42324034 original size:93 final size:92
Alignment explanation
Indices: 42323924--42324118 Score: 277
Period size: 93 Copynumber: 2.1 Consensus size: 92
42323914 GATTATAGTT
* * *
42323924 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* * *
42323987 ATAAAATTCTTGATAGTAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
42324017 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
42324082 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
42324109 TATGAATTTA
1 TATGAATTTA
42324119 CTAAAATCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
92 21 0.23
93 67 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:42335427 original size:43 final size:43
Alignment explanation
Indices: 42335373--42335457 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
42335363 AAATAAAAAA
* * * *
42335373 AAGTCGTGGTTTTTTT-TTATTCTTTTTCTTTATTTTGTTTTTG
1 AAGTAGTGGTTTTTTTATT-TTATTTTTCTCTATGTTGTTTTTG
42335416 AAGTAGTGGTTTTTTTATTTTATTTTTCTCTATGTTGTTTTT
1 AAGTAGTGGTTTTTTTATTTTATTTTTCTCTATGTTGTTTTT
42335458 ATTATTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.12, C:0.06, G:0.14, T:0.68
Consensus pattern (43 bp):
AAGTAGTGGTTTTTTTATTTTATTTTTCTCTATGTTGTTTTTG
Found at i:42336623 original size:5 final size:5
Alignment explanation
Indices: 42336608--42336641 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
42336598 AAAATATGAA
42336608 GCCCGG GCCCG GCCCG GCCCG GCCCG GCCCG GCC
1 GCCC-G GCCCG GCCCG GCCCG GCCCG GCCCG GCC
42336642 TTTTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.00, C:0.59, G:0.41, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:42340321 original size:21 final size:21
Alignment explanation
Indices: 42340279--42340324 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42340269 CTTGTACAAA
*
42340279 GTATTGATATCTTTGTAATAG
1 GTATTGATATCTGTGTAATAG
*
42340300 GTATTGATAT-TGTGTTATTAG
1 GTATTGATATCTGTG-TAATAG
42340321 GTAT
1 GTAT
42340325 CGATGCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (21 bp):
GTATTGATATCTGTGTAATAG
Found at i:42342630 original size:40 final size:40
Alignment explanation
Indices: 42342575--42342712 Score: 249
Period size: 40 Copynumber: 3.5 Consensus size: 40
42342565 AGGCTTGTGC
*
42342575 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
42342615 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
*
42342655 CTAGCAGGCTTAATGCCAGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
*
42342695 CTAGCAGGCTTCATGCCG
1 CTAGCAGGCTTAATGCCG
42342713 ATGTACGGAA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
Found at i:42374093 original size:16 final size:16
Alignment explanation
Indices: 42374072--42374120 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
42374062 AAATAACACG
42374072 TTTAAATTTAAAAATA
1 TTTAAATTTAAAAATA
* *
42374088 TTTAAAATTAAAAAAA
1 TTTAAATTTAAAAATA
*
42374104 ATTAAATCTTATAAAAT
1 TTTAAAT-TTA-AAAAT
42374121 CAAACATGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 19 0.73
17 3 0.12
18 4 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTAAATTTAAAAATA
Found at i:42376652 original size:14 final size:14
Alignment explanation
Indices: 42376633--42376670 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
42376623 AATAATACTA
*
42376633 TTTAAAATTATTAT
1 TTTAAAATAATTAT
42376647 TTTAAAA-AATTAT
1 TTTAAAATAATTAT
42376660 TATTAAAATAA
1 T-TTAAAATAA
42376671 AATTGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 13 0.62
15 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAAAATAATTAT
Found at i:42376725 original size:16 final size:16
Alignment explanation
Indices: 42376679--42376728 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
42376669 AAAATTGAAA
42376679 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
42376696 A-A--AATAATAAATT
1 ATATTAATAATTTATT
42376709 ATATTAATAATTTATT
1 ATATTAATAATTTATT
42376725 ATAT
1 ATAT
42376729 GACTTAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:42377878 original size:41 final size:41
Alignment explanation
Indices: 42377821--42377914 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
42377811 ACCATCAACA
*
42377821 ATTCAAAATCAAGCATTAATCAAGGATCAAATCAAAACTATC
1 ATTCAAAGT-AAGCATTAATCAAGGATCAAATCAAAACTATC
42377863 ATTCAAAGTAAGCATTAATCAAGGATCAAATCAAAACTATC
1 ATTCAAAGTAAGCATTAATCAAGGATCAAATCAAAACTATC
42377904 ATTCAAAGTAA
1 ATTCAAAGTAA
42377915 ACACATATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 43 0.84
42 8 0.16
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (41 bp):
ATTCAAAGTAAGCATTAATCAAGGATCAAATCAAAACTATC
Found at i:42381126 original size:34 final size:34
Alignment explanation
Indices: 42381077--42381144 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
42381067 GATTCAAGAT
* *
42381077 TTTCATGACCTGTAAAGAAGGAAAGATGAGCTAG
1 TTTCATGACCGGTAAAGAAGGAAAGAGGAGCTAG
*
42381111 TTTCATGATCGGTAAAGAAGGAAAGAGGAGCTAG
1 TTTCATGACCGGTAAAGAAGGAAAGAGGAGCTAG
42381145 AGAGTGAGAC
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:0.38, C:0.10, G:0.29, T:0.22
Consensus pattern (34 bp):
TTTCATGACCGGTAAAGAAGGAAAGAGGAGCTAG
Found at i:42382190 original size:34 final size:34
Alignment explanation
Indices: 42382141--42382208 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
42382131 GATTCAAGAT
*
42382141 TTTCATGACCTGTAAAGAAGGAAAGAGGAGCTAG
1 TTTCATGACCGGTAAAGAAGGAAAGAGGAGCTAG
*
42382175 TTTCATGATCGGTAAAGAAGGAAAGAGGAGCTAG
1 TTTCATGACCGGTAAAGAAGGAAAGAGGAGCTAG
42382209 AGAGTGAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (34 bp):
TTTCATGACCGGTAAAGAAGGAAAGAGGAGCTAG
Found at i:42383258 original size:34 final size:34
Alignment explanation
Indices: 42383205--42383272 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
42383195 GATTCAAGAT
42383205 TTTCATGACCCGTAAAGAAGGAAAGAGGAGCTAG
1 TTTCATGACCCGTAAAGAAGGAAAGAGGAGCTAG
* * *
42383239 TTTCATGATCGGTAGAGAAGGAAAGAGGAGCTAG
1 TTTCATGACCCGTAAAGAAGGAAAGAGGAGCTAG
42383273 AGAGTGAGAC
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:0.37, C:0.12, G:0.32, T:0.19
Consensus pattern (34 bp):
TTTCATGACCCGTAAAGAAGGAAAGAGGAGCTAG
Found at i:42384318 original size:34 final size:34
Alignment explanation
Indices: 42384269--42384336 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
42384259 GATTCAAGAT
42384269 TTTCATGACCCGTAAAGAAGGAAAGAGGAGCTAG
1 TTTCATGACCCGTAAAGAAGGAAAGAGGAGCTAG
* *
42384303 TTTCATGATCGGTAAAGAAGGAAAGAGGAGCTAG
1 TTTCATGACCCGTAAAGAAGGAAAGAGGAGCTAG
42384337 AGAGTGAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.19
Consensus pattern (34 bp):
TTTCATGACCCGTAAAGAAGGAAAGAGGAGCTAG
Found at i:42386436 original size:34 final size:34
Alignment explanation
Indices: 42386398--42386465 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
42386388 GATTCAAGAT
*
42386398 TTTCATGACCT-GTAAAGAAGGAAAGATGAGCTAG
1 TTTCATGA-CTGGTAAAGAAGGAAAGAGGAGCTAG
*
42386432 TTTCATGATTGGTAAAGAAGGAAAGAGGAGCTAG
1 TTTCATGACTGGTAAAGAAGGAAAGAGGAGCTAG
42386466 AGAGTGAGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 30 0.97
ACGTcount: A:0.38, C:0.09, G:0.29, T:0.24
Consensus pattern (34 bp):
TTTCATGACTGGTAAAGAAGGAAAGAGGAGCTAG
Found at i:42387508 original size:34 final size:34
Alignment explanation
Indices: 42387459--42387526 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
42387449 GATTCAAGAT
*
42387459 TTTCATGACCTGTAAAGAAGGAAAGAGAAGCTAG
1 TTTCATGACCGGTAAAGAAGGAAAGAGAAGCTAG
* * *
42387493 TTTCATGATCGGTAAAGAAGGAAAGTGGAGCTAG
1 TTTCATGACCGGTAAAGAAGGAAAGAGAAGCTAG
42387527 AGAGTGAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.22
Consensus pattern (34 bp):
TTTCATGACCGGTAAAGAAGGAAAGAGAAGCTAG
Found at i:42389030 original size:21 final size:22
Alignment explanation
Indices: 42388999--42389039 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
42388989 AGTGTTTAAG
42388999 AAGGAAATAATCATCACAAAAT
1 AAGGAAATAATCATCACAAAAT
42389021 AAGG-AATAATCATCACAAA
1 AAGGAAATAATCATCACAAA
42389040 TATTAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.17
Consensus pattern (22 bp):
AAGGAAATAATCATCACAAAAT
Found at i:42389186 original size:17 final size:17
Alignment explanation
Indices: 42389164--42389198 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42389154 AAATATAATG
42389164 AATGCTCAAAAGTGTTT
1 AATGCTCAAAAGTGTTT
42389181 AATGCTCAAAAGTGTTT
1 AATGCTCAAAAGTGTTT
42389198 A
1 A
42389199 CAAGAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (17 bp):
AATGCTCAAAAGTGTTT
Done.