Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 5 of 19
Found at i:1409016 original size:2 final size:2
Alignment explanation
Indices: 1409009--1409042 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1408999 AATAATACTG
*
1409009 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1409043 ATTTTATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1413125 original size:16 final size:16
Alignment explanation
Indices: 1413104--1413146 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1413094 AACTATTATT
*
1413104 AAAATAAATTAAAATA
1 AAAATAAAATAAAATA
1413120 AAAATAAAATAAAAT-
1 AAAATAAAATAAAATA
*
1413135 AAACTAAAATAA
1 AAAATAAAATAA
1413147 CTTAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:1413156 original size:5 final size:5
Alignment explanation
Indices: 1413103--1413146 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
1413093 AAACTATTAT
* *
1413103 TAAAA TAAAT TAAAA TAAAAA TAAAA TAAAA TAAAC TAAAA TAA
1 TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAA
1413147 CTTAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:1414173 original size:18 final size:18
Alignment explanation
Indices: 1414150--1414186 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1414140 ATGGAAAAAA
*
1414150 AATTAAATTGATAATTTT
1 AATTAAATTAATAATTTT
*
1414168 AATTAATTTAATAATTTT
1 AATTAAATTAATAATTTT
1414186 A
1 A
1414187 TATATTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTAAATTAATAATTTT
Found at i:1414184 original size:8 final size:8
Alignment explanation
Indices: 1414160--1414218 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
1414150 AATTAAATTG
1414160 ATAATTTTA
1 ATAA-TTTA
1414169 ATTAATTTA
1 A-TAATTTA
*
1414178 ATAATTTT
1 ATAATTTA
1414186 ATATATTTA
1 ATA-ATTTA
* *
1414195 ATTATATA
1 ATAATTTA
1414203 A-AA-TTA
1 ATAATTTA
1414209 ATAATTTA
1 ATAATTTA
1414217 AT
1 AT
1414219 TATCAATAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 19 0.47
9 12 0.30
10 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATAATTTA
Found at i:1414563 original size:28 final size:28
Alignment explanation
Indices: 1414503--1414557 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1414493 AGATTGAAAT
1414503 TTTATTTATGTTTGATATAATTTGTTTA
1 TTTATTTATGTTTGATATAATTTGTTTA
* *
1414531 TTTATTTATGTTTGGTGTAATTTGTTT
1 TTTATTTATGTTTGATATAATTTGTTT
1414558 TATTATAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.65
Consensus pattern (28 bp):
TTTATTTATGTTTGATATAATTTGTTTA
Found at i:1416314 original size:2 final size:2
Alignment explanation
Indices: 1416307--1416334 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1416297 ATTGGGCCAA
1416307 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
1416335 CTTTGATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1424506 original size:22 final size:23
Alignment explanation
Indices: 1424463--1424508 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1424453 ATTCGTGGGT
*
1424463 AAGTATCTTTGATATAAATTAAA
1 AAGTATCTTTGATAAAAATTAAA
*
1424486 AAGTATCTTTTA-AAAAATTAAA
1 AAGTATCTTTGATAAAAATTAAA
1424508 A
1 A
1424509 TTTTTCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (23 bp):
AAGTATCTTTGATAAAAATTAAA
Found at i:1429921 original size:76 final size:76
Alignment explanation
Indices: 1429823--1430303 Score: 455
Period size: 76 Copynumber: 6.3 Consensus size: 76
1429813 CACGTCACAT
* ** * * *
1429823 TTGTTAGATGTCGTTTACATCTTGTCATGACATGCTATGTCGTTGATGTATTATAGGGTCACACA
1 TTGTTAGATGTCATTTACATCTTGTGGTGACATGCCATGTCGTTGATGTATTATAGGGTTACACG
*
1429888 CCACGCTCCAA
66 CCACACTCCAA
* * * * * * *
1429899 TTGTAAGATGTCGTTTATATCTTGTTGTGACATGCCAGGTTGTTG-TAGTATTATAGGGTTACAT
1 TTGTTAGATGTCATTTACATCTTGTGGTGACATGCCATGTCGTTGAT-GTATTATAGGGTTACAC
*
1429963 GCCACACTCGAA
65 GCCACACTCCAA
* * * * * * * **
1429975 TTGTTAGGTATCGTTTACATCTTATGGTGACATGCCATGCCATTGACGTATTATATTGTTACACG
1 TTGTTAGATGTCATTTACATCTTGTGGTGACATGCCATGTCGTTGATGTATTATAGGGTTACACG
* *
1430040 CCACATTCGAA
66 CCACACTCCAA
* * * ** * *
1430051 TTGTTATATGTCATTTACATCTTATAGTGACATATCATGTCGTTGCA-ATATTATAGGGTTATAC
1 TTGTTAGATGTCATTTACATCTTGTGGTGACATGCCATGTCGTTG-ATGTATTATAGGGTTACAC
* ** *
1430115 GTCATGCTGCAA
65 GCCACACTCCAA
* * * * *
1430127 TTGCTAGATGTCTTTTACATCTTGTGGTGACATGCCATGTTGTTGAAGTATTATAGTGTTACACG
1 TTGTTAGATGTCATTTACATCTTGTGGTGACATGCCATGTCGTTGATGTATTATAGGGTTACACG
**
1430192 CCATGCTCCAA
66 CCACACTCCAA
* * *
1430203 TTGTTAGATATCATTTACATCTTGTGGTGACATGCCATGTCG-TCATAATATTATAGGGTTACAC
1 TTGTTAGATGTCATTTACATCTTGTGGTGACATGCCATGTCGTTGAT-GTATTATAGGGTTACAC
**
1430267 GCCACACTTGAA
65 GCCACACTCCAA
* *
1430279 TTGTTAAATGTCATTAACATCTTGT
1 TTGTTAGATGTCATTTACATCTTGT
1430304 CATGACACGC
Statistics
Matches: 326, Mismatches: 74, Indels: 10
0.80 0.18 0.02
Matches are distributed among these distances:
75 4 0.01
76 321 0.98
77 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (76 bp):
TTGTTAGATGTCATTTACATCTTGTGGTGACATGCCATGTCGTTGATGTATTATAGGGTTACACG
CCACACTCCAA
Found at i:1430028 original size:152 final size:151
Alignment explanation
Indices: 1429800--1430303 Score: 530
Period size: 152 Copynumber: 3.3 Consensus size: 151
1429790 GTTATTGAAG
* * ** *
1429800 TATTATAGGGTTGCACGTCACA-T---TTGTTAGATGTCGTTTACATCTTGTCATGACATGCTAT
1 TATTATAGGGTTACACGCCACACTGAATTGTTAGATGTCGTTTACATCTTGTGGTGACATGCCAT
* * * * * * * *
1429861 GTCGTTGATGTATTATAGGGTCACACACCACGCTCCAATTGTAAGATGTCGTTTATATCTTGTTG
66 GTCGTTGAAGTATTATAGTGTTACACGCCACGCTCCAATTGTTAGATGTCATTTACATCTTGTAG
* * *
1429926 TGACATGCCAGGTTGTTGTAG
131 TGACATGCCATGTCGTTGTAA
* * * *
1429947 TATTATAGGGTTACATGCCACACTCGAATTGTTAGGTATCGTTTACATCTTATGGTGACATGCCA
1 TATTATAGGGTTACACGCCACACT-GAATTGTTAGATGTCGTTTACATCTTGTGGTGACATGCCA
* * * * ** * * *
1430012 TGCCATTGACGTATTATATTGTTACACGCCACATTCGAATTGTTATATGTCATTTACATCTTATA
65 TGTCGTTGAAGTATTATAGTGTTACACGCCACGCTCCAATTGTTAGATGTCATTTACATCTTGTA
** *
1430077 GTGACATATCATGTCGTTGCAA
130 GTGACATGCCATGTCGTTGTAA
* * ** * *
1430099 TATTATAGGGTTATACGTCATGCTGCAATTGCTAGATGTCTTTTACATCTTGTGGTGACATGCCA
1 TATTATAGGGTTACACGCCACACTG-AATTGTTAGATGTCGTTTACATCTTGTGGTGACATGCCA
* * * *
1430164 TGTTGTTGAAGTATTATAGTGTTACACGCCATGCTCCAATTGTTAGATATCATTTACATCTTGTG
65 TGTCGTTGAAGTATTATAGTGTTACACGCCACGCTCCAATTGTTAGATGTCATTTACATCTTGTA
**
1430229 GTGACATGCCATGTCGTCATAA
130 GTGACATGCCATGTCGTTGTAA
* * *
1430251 TATTATAGGGTTACACGCCACACTTGAATTGTTAAATGTCATTAACATCTTGT
1 TATTATAGGGTTACACGCCACAC-TGAATTGTTAGATGTCGTTTACATCTTGT
1430304 CATGACACGC
Statistics
Matches: 283, Mismatches: 67, Indels: 9
0.79 0.19 0.03
Matches are distributed among these distances:
147 19 0.07
148 1 0.00
151 1 0.00
152 260 0.92
153 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (151 bp):
TATTATAGGGTTACACGCCACACTGAATTGTTAGATGTCGTTTACATCTTGTGGTGACATGCCAT
GTCGTTGAAGTATTATAGTGTTACACGCCACGCTCCAATTGTTAGATGTCATTTACATCTTGTAG
TGACATGCCATGTCGTTGTAA
Found at i:1433345 original size:81 final size:81
Alignment explanation
Indices: 1433203--1433380 Score: 223
Period size: 81 Copynumber: 2.2 Consensus size: 81
1433193 GCTGTTGAAA
* * ** * *
1433203 GAGACAATGTAACTCATGTCGATGACGTTGTCGATGAAGCTATGGGAGGAGATATGCACCTTCAA
1 GAGACCATGTACCTCATACCGATGACGTTGTCGATGAAGCTATGGGAGGAGATAAGAACCTTCAA
*
1433268 TCAGTTGATGCTAAAG
66 TCAGTTGAGGCTAAAG
* * *
1433284 GAGACCATGTACCTCATACCGATGTA-GTTGTCGATGTAGCTATGGGAGGGGATAAGAACCTTGA
1 GAGACCATGTACCTCATACCGATG-ACGTTGTCGATGAAGCTATGGGAGGAGATAAGAACCTTCA
* *
1433348 ATCAGTTGAGGTTGAAG
65 ATCAGTTGAGGCTAAAG
*
1433365 GAGATCATGTACCTCA
1 GAGACCATGTACCTCA
1433381 GAACACTCTT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 82 0.99
82 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (81 bp):
GAGACCATGTACCTCATACCGATGACGTTGTCGATGAAGCTATGGGAGGAGATAAGAACCTTCAA
TCAGTTGAGGCTAAAG
Found at i:1434848 original size:76 final size:76
Alignment explanation
Indices: 1434767--1435090 Score: 270
Period size: 76 Copynumber: 4.3 Consensus size: 76
1434757 AACGTGTTAT
** *
1434767 GACAAGATGTAAATAACATTTAACAATTCGAGTGTGGCATGTAACCCTATAATATTGCAACGACA
1 GACAAGATGTAAACGACATTTAACAATTCGAGTGTGGCGTGTAACCCTATAATATTGCAACGACA
1434832 TGACATGTCAC
66 TGACATGTCAC
* * * * * * * * *
1434843 CACAAGATGTAAACAAGATCTAACAATTTGAGTGTGGTGTATAACCCTATAATACTACAACGACA
1 GACAAGATGTAAACGACATTTAACAATTCGAGTGTGGCGTGTAACCCTATAATATTGCAACGACA
*** *
1434908 TGGTGTATCAC
66 TGACATGTCAC
* * *
1434919 GACAAGATGTAAGCGAC-TTCTAACAATTGGAGTGTGGCGTGTAACCCTATAATA-TGTCAATGA
1 GACAAGATGTAAACGACATT-TAACAATTCGAGTGTGGCGTGTAACCCTATAATATTG-CAACGA
**
1434982 CATGATGTGTCAC
64 CATGACATGTCAC
* * * * * *
1434995 AACAAAATGTAAACGACATCTAACAA-GC-AG-GT---GTGTTACCCTATAATACTT-TAACGAC
1 GACAAGATGTAAACGACATTTAACAATTCGAGTGTGGCGTGTAACCCTATAATA-TTGCAACGAC
* *
1435053 AGGGCATGTCAC
65 ATGACATGTCAC
* * *
1435065 GACAAAATGTCAATGACATTTAACAA
1 GACAAGATGTAAACGACATTTAACAA
1435091 GCGGAATGTG
Statistics
Matches: 200, Mismatches: 43, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
70 50 0.25
72 1 0.00
73 2 0.01
74 2 0.01
75 2 0.01
76 142 0.71
77 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (76 bp):
GACAAGATGTAAACGACATTTAACAATTCGAGTGTGGCGTGTAACCCTATAATATTGCAACGACA
TGACATGTCAC
Found at i:1435800 original size:25 final size:24
Alignment explanation
Indices: 1435772--1435831 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
1435762 TGAAAAATTT
1435772 TTGTTACATGCCATATTC-AAAAAAA
1 TTGTTACA--CCATATTCAAAAAAAA
1435797 TTGTTAGGCACCATATTCAAAAAAAA
1 TTGTTA--CACCATATTCAAAAAAAA
*
1435823 ATGTTACAC
1 TTGTTACAC
1435832 GTCATGTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 3 0.10
25 14 0.45
26 12 0.39
27 2 0.06
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (24 bp):
TTGTTACACCATATTCAAAAAAAA
Found at i:1441088 original size:21 final size:20
Alignment explanation
Indices: 1441063--1441109 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1441053 AGAGAAATAT
1441063 AAGAAAAGATATTTAAAGAGA
1 AAGAAAAG-TATTTAAAGAGA
*
1441084 AAG-AAAGTATTTAAAGGGA
1 AAGAAAAGTATTTAAAGAGA
*
1441103 GAGAAAA
1 AAGAAAA
1441110 AATTTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 13 0.57
20 7 0.30
21 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (20 bp):
AAGAAAAGTATTTAAAGAGA
Found at i:1444339 original size:53 final size:53
Alignment explanation
Indices: 1444279--1444397 Score: 139
Period size: 53 Copynumber: 2.2 Consensus size: 53
1444269 ATTTTTAATT
** * * *
1444279 TTTTTATTAATATTTCATTTGTCATATTCACCTCAGGAAATGAGCATTCATAA
1 TTTTTATTAATAACTCATTTGTCACATTCACCTCAGAAAATGAACATTCATAA
* * * **
1444332 TTTTTATTAGTAACTCGTTTGTCACATTCACTTCAGAAAATGAACATTCATGG
1 TTTTTATTAATAACTCATTTGTCACATTCACCTCAGAAAATGAACATTCATAA
1444385 TTTTTCATTAATA
1 TTTTT-ATTAATA
1444398 GCTATATACT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
53 48 0.89
54 6 0.11
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (53 bp):
TTTTTATTAATAACTCATTTGTCACATTCACCTCAGAAAATGAACATTCATAA
Found at i:1444728 original size:19 final size:19
Alignment explanation
Indices: 1444685--1444728 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1444675 GAGAAATATA
1444685 AGAGAAAGTATTTAGAGGG
1 AGAGAAAGTATTTAGAGGG
*
1444704 AAAGAAAGTATTTA-AGGGG
1 AGAGAAAGTATTTAGA-GGG
1444723 AGAGAA
1 AGAGAA
1444729 GAAATCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.18
Consensus pattern (19 bp):
AGAGAAAGTATTTAGAGGG
Found at i:1449613 original size:16 final size:17
Alignment explanation
Indices: 1449585--1449616 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1449575 CGGTTTGAAG
1449585 AATAAAAATAATTATTA
1 AATAAAAATAATTATTA
1449602 AATAAAAA-AATTATT
1 AATAAAAATAATTATT
1449617 TTGAGAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAAAATAATTATTA
Found at i:1450721 original size:22 final size:22
Alignment explanation
Indices: 1450696--1450762 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
1450686 ACTTAATCGA
* *
1450696 TTTTTGGGTATTGTGTGACTAG
1 TTTTTAGGTATTATGTGACTAG
* *
1450718 -TTTTAAGTATTATGTGATTAG
1 TTTTTAGGTATTATGTGACTAG
* *
1450739 TTTTTAGGCATTACGTGACTAG
1 TTTTTAGGTATTATGTGACTAG
1450761 TT
1 TT
1450763 GATATAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.49
Consensus pattern (22 bp):
TTTTTAGGTATTATGTGACTAG
Found at i:1450923 original size:22 final size:22
Alignment explanation
Indices: 1450874--1450934 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1450864 AATCAGTTAC
* *
1450874 GCAATGCCTAAAACCTAGTCAA
1 GCAATGTCTAAAAACTAGTCAA
*
1450896 GGAATGTCTAAAAACTAGTCACA
1 GCAATGTCTAAAAACTAGTCA-A
1450919 -CAATGTCTAAAAACTA
1 GCAATGTCTAAAAACTA
1450935 AAAACGTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.21
Consensus pattern (22 bp):
GCAATGTCTAAAAACTAGTCAA
Found at i:1457722 original size:19 final size:20
Alignment explanation
Indices: 1457695--1457735 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1457685 AAAATGAAAA
1457695 TAAAGAAAA-AGAAATTAAAT
1 TAAAGAAAATAGAAA-TAAAT
*
1457715 TAAA-AAAATAGTAATAAAT
1 TAAAGAAAATAGAAATAAAT
1457734 TA
1 TA
1457736 TTAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
TAAAGAAAATAGAAATAAAT
Found at i:1457835 original size:14 final size:13
Alignment explanation
Indices: 1457758--1457835 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
1457748 AATTTTGATG
1457758 AAAATAAAAATAA
1 AAAATAAAAATAA
**
1457771 AAATATTAAAAATTC
1 AAA-A-TAAAAATAA
1457786 AAAATAAAAA-ATA
1 AAAATAAAAATA-A
* *
1457799 GAGA-AAAAATAAA
1 AAAATAAAAAT-AA
*
1457812 AAAATTAAAATAA
1 AAAATAAAAATAA
1457825 AGAAATAAAAA
1 A-AAATAAAAA
1457836 CATCAAATTA
Statistics
Matches: 48, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
12 5 0.10
13 17 0.35
14 16 0.33
15 10 0.21
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:1458665 original size:31 final size:29
Alignment explanation
Indices: 1458630--1458737 Score: 103
Period size: 30 Copynumber: 3.7 Consensus size: 29
1458620 AATTATTAAT
* *
1458630 TATAAACACTTATTTAACTCAAAAATAAAAA
1 TATAAAAACTTATTTAAAT--AAAATAAAAA
** *
1458661 TATAAAAACTTATTTAGTTTAAAAGAAAAA
1 TATAAAAACTTATTTA-AATAAAATAAAAA
*
1458691 TATAAAAACTTGA-TTAAATATAATAAAAA
1 TATAAAAACTT-ATTTAAATAAAATAAAAA
*
1458720 TATAAATA-TTATTTAAAT
1 TATAAAAACTTATTTAAAT
1458738 TTTTTTAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.02
28 8 0.12
29 16 0.25
30 23 0.35
31 16 0.25
32 1 0.02
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (29 bp):
TATAAAAACTTATTTAAATAAAATAAAAA
Found at i:1459409 original size:25 final size:28
Alignment explanation
Indices: 1459353--1459413 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1459343 AAAAAATTTA
*
1459353 AATTAATTTTTATTCTTTTATTATGTTC
1 AATTAAATTTTATTCTTTTATTATGTTC
1459381 AATTAAATTTTATAT-TTTTATT-T-TT-
1 AATTAAATTTTAT-TCTTTTATTATGTTC
1459406 AATTAAAT
1 AATTAAAT
1459414 AAATTTTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 8 0.26
26 2 0.06
27 1 0.03
28 19 0.61
29 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (28 bp):
AATTAAATTTTATTCTTTTATTATGTTC
Found at i:1459428 original size:30 final size:30
Alignment explanation
Indices: 1459384--1459452 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1459374 TATGTTCAAT
* * *
1459384 TAAA-TTTTATATTTTTATTTTTAATTAAA
1 TAAATTTTTAGATTTTTATTTTAAACTAAA
1459413 TAAATTTTTAGATTTTTATTTTAAACTAAA
1 TAAATTTTTAGATTTTTATTTTAAACTAAA
1459443 TAAATTTTTA
1 TAAATTTTTA
1459453 TAATTAATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 4 0.11
30 32 0.89
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
TAAATTTTTAGATTTTTATTTTAAACTAAA
Found at i:1459647 original size:11 final size:11
Alignment explanation
Indices: 1459626--1459654 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1459616 TAATATTTTA
1459626 ATTAA-TAATT
1 ATTAATTAATT
1459636 ATTAATTAATT
1 ATTAATTAATT
1459647 ATTAATTA
1 ATTAATTA
1459655 TAAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTAATTAATT
Found at i:1459720 original size:28 final size:28
Alignment explanation
Indices: 1459654--1459720 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
1459644 ATTATTAATT
* * *
1459654 ATAAAAATTTATTTAATTTAAAATAAAA
1 ATAAAAATTTACTGAATATAAAATAAAA
** *
1459682 A-AAGATTTTTACTGAATATAATATAAAA
1 ATAA-AAATTTACTGAATATAAAATAAAA
1459710 ATAAAAATTTA
1 ATAAAAATTTA
1459721 TATAAAATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
27 2 0.07
28 25 0.86
29 2 0.07
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (28 bp):
ATAAAAATTTACTGAATATAAAATAAAA
Found at i:1465307 original size:14 final size:15
Alignment explanation
Indices: 1465288--1465594 Score: 60
Period size: 16 Copynumber: 20.2 Consensus size: 15
1465278 TATTGTTATA
1465288 ATTAAAATAAAA-AT
1 ATTAAAATAAAATAT
1465302 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
* *
1465317 A-TAATATAAGAATCAAAA
1 ATTAAAATAA-AAT---AT
1465335 ATTAAAATAAAATA-
1 ATTAAAATAAAATAT
*
1465349 A--AATATAAAA-A-
1 ATTAAAATAAAATAT
**
1465360 ATTAAAAT-TTATAT
1 ATTAAAATAAAATAT
* ** * *
1465374 AATATAGGTAAAACAA
1 ATTA-AAATAAAATAT
1465390 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
*
1465405 A-TAATATAAAAAATAT
1 ATTAA-A-ATAAAATAT
*
1465421 ATT--AA-AGAA-AT
1 ATTAAAATAAAATAT
1465432 A--AAAATAAAATAT
1 ATTAAAATAAAATAT
*
1465445 A-TAAGATTATAATAATAA
1 ATTAA-A--ATAA-AATAT
*
1465463 ATAAAAATAAAATAT
1 ATTAAAATAAAATAT
* * *
1465478 ATGACATTAAAAATAT
1 ATTAAAAT-AAAATAT
* *
1465494 ATTTAAGAGATGATATTAT
1 A-TTAA-A-AT-AAAATAT
*
1465513 ATAAAAATTAATAATA-
1 ATTAAAA-TAA-AATAT
1465529 A--AAAATATAAATAT
1 ATTAAAATA-AAATAT
1465543 ATTAAAAATAAAATAT
1 ATT-AAAATAAAATAT
*
1465559 A-TAAGATTATAATAATAA
1 ATTAA-A--ATAA-AATAT
*
1465577 ATGAAAATAAAATAT
1 ATTAAAATAAAATAT
1465592 ATT
1 ATT
1465595 TAAGAGATGG
Statistics
Matches: 211, Mismatches: 41, Indels: 81
0.63 0.12 0.24
Matches are distributed among these distances:
11 7 0.03
12 15 0.07
13 15 0.07
14 37 0.18
15 36 0.17
16 40 0.19
17 22 0.10
18 21 0.10
19 18 0.09
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:1465377 original size:24 final size:25
Alignment explanation
Indices: 1465349--1465418 Score: 50
Period size: 30 Copynumber: 2.5 Consensus size: 25
1465339 AAATAAAATA
* *
1465349 AAATATAAAAAATTAAAATTTATATA
1 AAATATAAAAAATTAAAA-TAAAATA
*
1465375 ATATAGGTAAAACAAATTAAAATAAAATA
1 AAATA--T-AAA-AAATTAAAATAAAATA
1465404 TATAATATAAAAAAT
1 -A-AATATAAAAAAT
1465419 ATATTAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
26 4 0.12
27 4 0.12
28 4 0.12
29 9 0.26
30 10 0.29
31 3 0.09
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (25 bp):
AAATATAAAAAATTAAAATAAAATA
Found at i:1465444 original size:33 final size:33
Alignment explanation
Indices: 1465394--1465478 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
1465384 AAACAAATTA
* *
1465394 AAATAAAATATATAATATAAAAAA-TATATTAAAG
1 AAATAAAA-ATAAAATATAAAAAATTATAAT-AAG
* * *
1465428 AAATAAAAATAAAATATATAAGATTATAATAAT
1 AAATAAAAATAAAATATAAAAAATTATAATAAG
1465461 AAATAAAAATAAAATATA
1 AAATAAAAATAAAATATA
1465479 TGACATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAAAATATAAAAAATTATAATAAG
Found at i:1465644 original size:24 final size:24
Alignment explanation
Indices: 1465511--1465645 Score: 95
Period size: 24 Copynumber: 5.6 Consensus size: 24
1465501 AGATGATATT
1465511 ATATAAA-A-ATTAATAATAAAAA
1 ATATAAATATATTAATAATAAAAA
* *
1465533 ATATAAATATATTAAAAATAAAAT
1 ATATAAATATATTAATAATAAAAA
1465557 ATATAAGAT-TA-TAATAATAAATGAA
1 ATATAA-ATATATTAATAATAAA--AA
* ** **
1465582 A-ATAAAATATATTTAAGAGATGGTATT
1 ATAT-AAATATA-TTAATA-AT-AAAAA
1465609 ATATAAA-A-ATTAATAATAAAAA
1 ATATAAATATATTAATAATAAAAA
1465631 ATATAAATATATTAA
1 ATATAAATATATTAA
1465646 ACTTGTATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
22 15 0.18
23 13 0.15
24 34 0.40
25 9 0.11
26 1 0.01
27 8 0.09
28 4 0.05
29 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
ATATAAATATATTAATAATAAAAA
Found at i:1471139 original size:2 final size:2
Alignment explanation
Indices: 1471128--1471170 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1471118 GTATATACAC
*
1471128 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1471170 A
1 A
1471171 AAGACACGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1472768 original size:80 final size:80
Alignment explanation
Indices: 1472538--1472769 Score: 338
Period size: 80 Copynumber: 2.9 Consensus size: 80
1472528 GCATTTCCGT
* **
1472538 CGGAGTTGTTCGATTCGGAAACTTCCAACTTACAGATCGGAGGCTTCACACTCGAGGAGGCTGGG
1 CGGAGTTGTTCGATTCGGAAACTTCCAGCCGACAGATCGGAGGCTTCACACTCGAGGAGGCTGGG
* * *
1472603 CTTCGACGTTTTTGC
66 CTTCGGCGTGTCTGC
* * *
1472618 CGGAGTTGTTCGATTCGAAAACTTTCAGCCGACAGATCGGAGGCTTCACAGTCGAGGAGGCTGGG
1 CGGAGTTGTTCGATTCGGAAACTTCCAGCCGACAGATCGGAGGCTTCACACTCGAGGAGGCTGGG
1472683 CTTCGGCGTGTCTGC
66 CTTCGGCGTGTCTGC
* * * *
1472698 CGGAGCTGTTCGATTCGGAAGCTTCCAGCCGACAGATCGGAGGCTTCACATTCGATGAGGCTGGG
1 CGGAGTTGTTCGATTCGGAAACTTCCAGCCGACAGATCGGAGGCTTCACACTCGAGGAGGCTGGG
*
1472763 GTTCGGC
66 CTTCGGC
1472770 TTTTGATCTG
Statistics
Matches: 136, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 136 1.00
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.25
Consensus pattern (80 bp):
CGGAGTTGTTCGATTCGGAAACTTCCAGCCGACAGATCGGAGGCTTCACACTCGAGGAGGCTGGG
CTTCGGCGTGTCTGC
Found at i:1474522 original size:15 final size:14
Alignment explanation
Indices: 1474491--1474520 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1474481 TTTCCAACGG
*
1474491 AATTTTTTCGTTGA
1 AATTTTTTCGATGA
1474505 AATTTTTTCGATGA
1 AATTTTTTCGATGA
1474519 AA
1 AA
1474521 ATCCGTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (14 bp):
AATTTTTTCGATGA
Found at i:1475229 original size:18 final size:18
Alignment explanation
Indices: 1475208--1475243 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1475198 ATATATTTTG
1475208 TTTAGATGTTAGATGTTA
1 TTTAGATGTTAGATGTTA
*
1475226 TTTATATGTTAGATGTTA
1 TTTAGATGTTAGATGTTA
1475244 GATGGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (18 bp):
TTTAGATGTTAGATGTTA
Found at i:1475256 original size:25 final size:25
Alignment explanation
Indices: 1475209--1475259 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1475199 TATATTTTGT
*
1475209 TTAGATGTTAGATGTTATTTATATG
1 TTAGATGTTAGATGTTATATATATG
1475234 TTAGATGTTAGATGGTTTATATATAT
1 TTAGATGTTAGAT-G-TTATATATAT
1475260 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 1 0.04
27 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (25 bp):
TTAGATGTTAGATGTTATATATATG
Found at i:1475258 original size:2 final size:2
Alignment explanation
Indices: 1475251--1475276 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1475241 TTAGATGGTT
1475251 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1475277 GTGTTAGATG
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):
TA
Found at i:1480072 original size:30 final size:29
Alignment explanation
Indices: 1480010--1480072 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1480000 AAGGCCCAAG
*
1480010 ATGATATTGTGCATATATTTGGCACCTAA
1 ATGATATTGTGCATATATTTGGCACATAA
* *
1480039 ATGATGTTGTGCATAGT-TGTTGGCACATGA
1 ATGATATTGTGCATA-TAT-TTGGCACATAA
1480069 ATGA
1 ATGA
1480073 ATGATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (29 bp):
ATGATATTGTGCATATATTTGGCACATAA
Found at i:1482169 original size:17 final size:17
Alignment explanation
Indices: 1482143--1482175 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1482133 AAAAATTTGA
1482143 TGAAAACTTTT-AAGGT
1 TGAAAACTTTTGAAGGT
1482159 TGAAGAACTTTTGAAGG
1 TGAA-AACTTTTGAAGG
1482176 CCTTTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (17 bp):
TGAAAACTTTTGAAGGT
Found at i:1482949 original size:20 final size:20
Alignment explanation
Indices: 1482911--1482949 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1482901 ACAGCCTTCC
* *
1482911 TTTAATTGGTTAACTCTCCT
1 TTTAACTGGTTAACGCTCCT
*
1482931 TTTAACTGGTTAAGGCTCC
1 TTTAACTGGTTAACGCTCC
1482950 ACTTTCTTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (20 bp):
TTTAACTGGTTAACGCTCCT
Found at i:1483663 original size:29 final size:29
Alignment explanation
Indices: 1483622--1483678 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1483612 AAATATTTAT
*
1483622 AATATCCACAATAGCTAAACAGGATATAC
1 AATATCCACAATAGCTAAACAAGATATAC
*
1483651 AATATCC-CTAATAGCTAAGCAAGATATA
1 AATATCCAC-AATAGCTAAACAAGATATA
1483679 TAGAATATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (29 bp):
AATATCCACAATAGCTAAACAAGATATAC
Found at i:1499067 original size:17 final size:16
Alignment explanation
Indices: 1499045--1499078 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1499035 TTTTTCTTCT
*
1499045 ATTTAATTATTCCATTC
1 ATTTAATCATT-CATTC
1499062 ATTTAATCATTCATTC
1 ATTTAATCATTCATTC
1499078 A
1 A
1499079 ATTCATTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAATCATTCATTC
Found at i:1504405 original size:14 final size:15
Alignment explanation
Indices: 1504382--1504411 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1504372 TTTATATTCC
1504382 TTTTATTCTTTTCAT
1 TTTTATTCTTTTCAT
1504397 TTTTA-TCTTTTCAT
1 TTTTATTCTTTTCAT
1504411 T
1 T
1504412 ATTCATCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATTCTTTTCAT
Found at i:1504576 original size:25 final size:25
Alignment explanation
Indices: 1504543--1504627 Score: 143
Period size: 25 Copynumber: 3.4 Consensus size: 25
1504533 TTTTTGTGAT
1504543 AAAATTATTCTTAGATTCTGATGGC
1 AAAATTATTCTTAGATTCTGATGGC
1504568 AAAATTATTCTTAGATTCTGATGGC
1 AAAATTATTCTTAGATTCTGATGGC
* * *
1504593 AAAATTATTCTTAGACTCTGATAGT
1 AAAATTATTCTTAGATTCTGATGGC
1504618 AAAATTATTC
1 AAAATTATTC
1504628 ATTCAATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (25 bp):
AAAATTATTCTTAGATTCTGATGGC
Found at i:1504885 original size:59 final size:59
Alignment explanation
Indices: 1504706--1504885 Score: 191
Period size: 59 Copynumber: 3.1 Consensus size: 59
1504696 CTTCCATATC
* * * * * * *
1504706 TATGATCATAATTATTAAATGATGTGACATTTACTTCAGGGAATAGATAAATTTATAAC
1 TATGACCATAATTATTAAATGATGTCACATTCACTTTAGAGAATGGATAAATTTATAAT
* * * ** * *
1504765 CATGACCATAATTATTAAATGATGTCTCATTCACTTTA-AGGAATGAATGGATTCATGAT
1 TATGACCATAATTATTAAATGATGTCACATTCACTTTAGA-GAATGGATAAATTTATAAT
* * *
1504824 TATGACCATAATTATTAAATAATATCACATTCACTTTAGAAAATGGATAAATTTATAAT
1 TATGACCATAATTATTAAATGATGTCACATTCACTTTAGAGAATGGATAAATTTATAAT
1504883 TAT
1 TAT
1504886 TTTATTAGTA
Statistics
Matches: 95, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
59 94 0.99
60 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (59 bp):
TATGACCATAATTATTAAATGATGTCACATTCACTTTAGAGAATGGATAAATTTATAAT
Found at i:1508707 original size:27 final size:28
Alignment explanation
Indices: 1508658--1508722 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
1508648 AATGTTATTA
* * *
1508658 TGATTATTTATTTTTAAATATTAATAA-
1 TGATAATTTATTTTAAAATATTAAAAAT
1508685 TGTATAATTTA-TTTAAAATATTAAAAAT
1 TG-ATAATTTATTTTAAAATATTAAAAAT
1508713 TGATAATTTA
1 TGATAATTTA
1508723 AATATTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (28 bp):
TGATAATTTATTTTAAAATATTAAAAAT
Found at i:1508845 original size:22 final size:22
Alignment explanation
Indices: 1508820--1508898 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 22
1508810 TTTTTATTTT
1508820 ATTTTATTTTTAAATATTAATA
1 ATTTTATTTTTAAATATTAATA
1508842 ATTTATATTTTATTTATAATATTAATA
1 ATTT-TA--TT-TTTA-AATATTAATA
*
1508869 A-TTTATCATTTAAATATTAAT-
1 ATTTTAT-TTTTAAATATTAATA
*
1508890 ACTTTATTT
1 ATTTTATTT
1508899 ATAATTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
21 2 0.04
22 18 0.38
23 7 0.15
25 4 0.08
26 6 0.12
27 11 0.23
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTATTTTTAAATATTAATA
Found at i:1508861 original size:142 final size:144
Alignment explanation
Indices: 1508558--1509087 Score: 359
Period size: 142 Copynumber: 3.8 Consensus size: 144
1508548 ATATATGATT
* *
1508558 ATTT-TATTTTATTTGAT-TTTTAAATATTAATATTTTATTTATAATCTAATCATTAACATTATA
1 ATTTATATTTTATTT-ATAATTTAAATATTAATATTTTATTTATAATCTAATCATTAACAGTATA
* *
1508621 AAATACTAATATTTTATTTATAATTTAAATGTTATTATGATTATTTATTTTTAAATATTAATAAT
65 AAATAATAATATTTAATTTATAATTTAAATGTTATTATGATTATTTATTTTT-AATATTAATAAT
*
1508686 GTATAATTTATTTAAA
129 GTATAATATATTTAAA
** * * * *
1508702 ATATTA-A--AAATTGATAATTTAAATATTAATATTTTATTTATACTTTAATCATTAATAGTA-A
1 AT-TTATATTTTATTTATAATTTAAATATTAATATTTTATTTATAATCTAATCATTAACAGTATA
* * *
1508763 AAATAATAATATTTAATTTATAATTTAAATGTTATTATGATTATTTATTTTT-ATTTTATTTTAT
65 AAATAATAATATTTAATTTATAATTTAAATGTTATTATGATTATTTATTTTTAATATTA-ATAAT
* *
1508827 TTTTAA-ATA-TTAATA
129 GTATAATATATTTAA-A
* * *
1508842 ATTTATATTTTATTTATAATATT--A-A-TAAT-TTATCATTTA-AATATTAAT-ACTT--TA-T
1 ATTTATATTTTATTTATAAT-TTAAATATTAATATT-TTATTTATAAT-CTAATCA-TTAACAGT
* * * * * * * *
1508897 TTATAAT-TTAA-ATTTTATTATGATTATTT-ATTTTTATT-T-A-AATTTATCTTTTAAATATT
62 ATAAAATAATAATATTTAATT-T-ATAATTTAAATGTTATTATGATTATTTAT-TTTT-AATATT
*
1508956 AATAAT-T-T-ATAT-TTTTAA
123 AATAATGTATAATATATTTAAA
* * * * * * *
1508974 ATATTA-A--TAATTAATTATTTAAGTATTAATATTTTATTTATAATTTAATCATTAATATTATA
1 AT-TTATATTTTATTTATAATTTAAATATTAATATTTTATTTATAATCTAATCATTAACAGTATA
* * * *
1509036 AAATAGTACTATTTTATTTATAATTTAAATGTTATTATGATTATTTGTTTTT
65 AAATAATAATATTTAATTTATAATTTAAATGTTATTATGATTATTTATTTTT
1509088 GTTTTATTTT
Statistics
Matches: 302, Mismatches: 47, Indels: 79
0.71 0.11 0.18
Matches are distributed among these distances:
129 2 0.01
130 8 0.03
132 6 0.02
133 32 0.11
134 12 0.04
135 13 0.04
136 29 0.10
137 22 0.07
138 14 0.05
139 29 0.10
140 17 0.06
141 8 0.03
142 61 0.20
143 44 0.15
144 2 0.01
145 3 0.01
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (144 bp):
ATTTATATTTTATTTATAATTTAAATATTAATATTTTATTTATAATCTAATCATTAACAGTATAA
AATAATAATATTTAATTTATAATTTAAATGTTATTATGATTATTTATTTTTAATATTAATAATGT
ATAATATATTTAAA
Found at i:1508880 original size:27 final size:28
Alignment explanation
Indices: 1508815--1508879 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
1508805 ATTTATTTTT
*
1508815 ATTT-TATTTTATTTTTAAATATTAATA
1 ATTTATATTTTATTTATAAATATTAATA
1508842 ATTTATATTTTATTTAT-AATATTAATA
1 ATTTATATTTTATTTATAAATATTAATA
1508869 ATTTATCATTT
1 ATTTAT-ATTT
1508880 AAATATTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 20 0.57
28 15 0.43
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTATATTTTATTTATAAATATTAATA
Found at i:1508903 original size:117 final size:113
Alignment explanation
Indices: 1508763--1509021 Score: 385
Period size: 117 Copynumber: 2.2 Consensus size: 113
1508753 TTAATAGTAA
* * *
1508763 AAATAATAATATTTAATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTAT-
1 AAATATTAATATTT-ATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTAAATTTATC
*
1508827 TTTTAAATATTAATAATTTATATTTTATTTATAATATTAATAATTTATCATTT
65 TTTTAAATATTAATAATTTATA--TT-TTTA-AATATTAATAATTAATCATTT
*
1508880 AAATATTAATACTTTATTTATAATTTAAATTTTATTATGATTATTTATTTTTATTTAAATTTATC
1 AAATATTAATA-TTTATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTAAATTTATC
*
1508945 TTTTAAATATTAATAATTTATATTTTTAAATATTAATAATTAATTATTT
65 TTTTAAATATTAATAATTTATATTTTTAAATATTAATAATTAATCATTT
*
1508994 AAGTATTAATATTTTATTTATAATTTAA
1 AAATATTAATA-TTTATTTATAATTTAA
1509022 TCATTAATAT
Statistics
Matches: 132, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
114 45 0.34
115 4 0.03
116 2 0.02
117 56 0.42
118 25 0.19
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (113 bp):
AAATATTAATATTTATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTAAATTTATCT
TTTAAATATTAATAATTTATATTTTTAAATATTAATAATTAATCATTT
Found at i:1508963 original size:22 final size:21
Alignment explanation
Indices: 1508937--1509012 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 21
1508927 TTTTTATTTA
1508937 AATTTATCTTTTAAATATTAAT
1 AATTTAT-TTTTAAATATTAAT
1508959 AATTTATATTTTTAAATATTAAT
1 AA-TT-TATTTTTAAATATTAAT
* *
1508982 AATTAATTATTTAAGTATTAAT
1 AATTTATT-TTTAAATATTAAT
*
1509004 ATTTTATTT
1 AATTTATTT
1509013 ATAATTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 4 0.09
22 22 0.47
23 18 0.38
24 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (21 bp):
AATTTATTTTTAAATATTAAT
Found at i:1509001 original size:45 final size:41
Alignment explanation
Indices: 1508946--1509063 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 41
1508936 AAATTTATCT
*
1508946 TTTAAATATTAATAATTTATATTTTTAAATATTAATAATTAATTA
1 TTTAAATATTAAT-ATTT-TATTTAT-AAT-TTAATAATTAATTA
* *
1508991 TTTAAGTATTAATATTTTATTTATAATTTAATCATTAA-TA
1 TTTAAATATTAATATTTTATTTATAATTTAATAATTAATTA
* *
1509031 TTATAAAATAGTACTATTTTATTTATAATTTAA
1 TT-T-AAATATTAATATTTTATTTATAATTTAA
1509064 ATGTTATTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
40 4 0.06
41 11 0.17
42 28 0.43
43 6 0.09
44 4 0.06
45 12 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (41 bp):
TTTAAATATTAATATTTTATTTATAATTTAATAATTAATTA
Found at i:1509049 original size:114 final size:116
Alignment explanation
Indices: 1508763--1509049 Score: 287
Period size: 114 Copynumber: 2.5 Consensus size: 116
1508753 TTAATAGTAA
* * * * ** * ** * *
1508763 AAATAATAATA-TTTAATTTATAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTAT
1 AAATATTAATACTTT-ATTTATAATTTAAATATTAATATGATAAAATAGTACTATTTAAATTTAT
*
1508827 TTTTAAATATTAATAATTTATATTTTATTTATAATATTAATAATTTATCATTT
65 TTTTAAATATTAATAATTTATA-TTTATTTATAATATTAATAATTAATCATTT
* * * ** * **
1508880 AAATATTAATACTTTATTTATAATTTAAATTTTATTATGATTATTTATTTTTATTTAAATTTATC
1 AAATATTAATACTTTATTTATAATTTAAATATTAATATGATAAAATAGTACTATTTAAATTTAT-
*
1508945 TTTTAAATATTAATAATTTATA-TT-TTTA-AATATTAATAATTAATTATTT
65 TTTTAAATATTAATAATTTATATTTATTTATAATATTAATAATTAATCATTT
* * *
1508994 AAGTATTAATATTTTATTTATAATTT-AATCATTAATATTATAAAATAGTACTATTT
1 AAATATTAATACTTTATTTATAATTTAAAT-ATTAATATGATAAAATAGTACTATTT
1509050 TATTTATAAT
Statistics
Matches: 150, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
113 3 0.02
114 60 0.40
115 4 0.03
116 2 0.01
117 56 0.37
118 25 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (116 bp):
AAATATTAATACTTTATTTATAATTTAAATATTAATATGATAAAATAGTACTATTTAAATTTATT
TTTAAATATTAATAATTTATATTTATTTATAATATTAATAATTAATCATTT
Found at i:1509052 original size:156 final size:153
Alignment explanation
Indices: 1508846--1509139 Score: 391
Period size: 156 Copynumber: 1.9 Consensus size: 153
1508836 TTAATAATTT
* * *
1508846 ATATTTTATTTATAATATTAATAATTTATCATTTAAATATTAATACTTTATTTATAATTTAAATT
1 ATATTTTATTTATAATATTAATAATTAATCATTTAAATAGTAATACTTTATTTATAATTTAAATG
* *
1508911 TTATTATGATTATTTATTTTTATTTAAATTTATCTTTTAAATATTAATAATTTAT-ATT-TTT-A
66 TTATTATGATTATTT-GTTTT-TGT---TTTAT-TTTTAAATATTAATAATTTATAATTATTTAA
1508973 AATATTAATAATTAATTATTTAAGTATTA
125 AATATTAATAATTAATTATTTAAGTATTA
* * *
1509002 ATATTTTATTTATAAT-TTAATCATTAAT-ATTATAAAATAGTACTATTTTATTTATAATTTAAA
1 ATATTTTATTTATAATATTAATAATTAATCATT-T-AAATAGTAATACTTTATTTATAATTTAAA
*
1509065 TGTTATTATGATTATTTGTTTTTGTTTTATTTTTAAATATTACTAATTTATAATTGATTTAAAAT
64 TGTTATTATGATTATTTGTTTTTGTTTTATTTTTAAATATTAATAATTTATAATT-ATTTAAAAT
1509130 ATTAATAATT
128 ATTAATAATT
1509140 GGTAANNNNN
Statistics
Matches: 123, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
150 20 0.16
151 8 0.07
153 3 0.02
154 19 0.15
155 15 0.12
156 58 0.47
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (153 bp):
ATATTTTATTTATAATATTAATAATTAATCATTTAAATAGTAATACTTTATTTATAATTTAAATG
TTATTATGATTATTTGTTTTTGTTTTATTTTTAAATATTAATAATTTATAATTATTTAAAATATT
AATAATTAATTATTTAAGTATTA
Found at i:1509382 original size:22 final size:23
Alignment explanation
Indices: 1509352--1509398 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1509342 TAATTTTTAT
*
1509352 TTAATATTT-AAATATATT-ATAA
1 TTAAAATTTGAAA-ATATTAATAA
1509374 TTAAAATTTGAAAATATTAATAA
1 TTAAAATTTGAAAATATTAATAA
1509397 TT
1 TT
1509399 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAAATTTGAAAATATTAATAA
Found at i:1509413 original size:14 final size:14
Alignment explanation
Indices: 1509394--1509451 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
1509384 AAAATATTAA
*
1509394 TAATTTTTTAATTT
1 TAATTTTATAATTT
* *
1509408 TAA-TTTAAAATAT
1 TAATTTTATAATTT
*
1509421 TAATTTTATAAGTT
1 TAATTTTATAATTT
* *
1509435 TAAGTTTGTAATTT
1 TAATTTTATAATTT
1509449 TAA
1 TAA
1509452 AAAATAAATA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 10 0.29
14 24 0.71
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
TAATTTTATAATTT
Found at i:1510863 original size:2 final size:2
Alignment explanation
Indices: 1510851--1510897 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1510841 TGGAGACCTT
* *
1510851 TA TA CA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1510893 TA TA T
1 TA TA T
1510898 TTCAATTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1518516 original size:16 final size:16
Alignment explanation
Indices: 1518495--1518527 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1518485 AAATTGAGTT
*
1518495 GGTGCAATTGTGTTTA
1 GGTGCAATTATGTTTA
1518511 GGTGCAATTATGTTTA
1 GGTGCAATTATGTTTA
1518527 G
1 G
1518528 TCGTGAAGTA
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:0.21, C:0.06, G:0.30, T:0.42
Consensus pattern (16 bp):
GGTGCAATTATGTTTA
Found at i:1528125 original size:18 final size:17
Alignment explanation
Indices: 1528084--1528133 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
1528074 ACTTCACTCA
* *
1528084 ATTTTAATTTTTTTTAT
1 ATTTTAATTTATATTAT
*
1528101 TTTTTAATTTATATTACT
1 ATTTTAATTTATATTA-T
1528119 ATTTTAATTTATATT
1 ATTTTAATTTATATT
1528134 TTTTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTAATTTATATTAT
Found at i:1528596 original size:20 final size:22
Alignment explanation
Indices: 1528550--1528596 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
1528540 ATATTTAACT
*
1528550 ATTTATATTTTATGCATTATAG
1 ATTTATATTTTATGCATTATAA
* *
1528572 TTTTATA-TTTA-GTATTATAA
1 ATTTATATTTTATGCATTATAA
1528592 ATTTA
1 ATTTA
1528597 GATAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (22 bp):
ATTTATATTTTATGCATTATAA
Found at i:1540499 original size:18 final size:19
Alignment explanation
Indices: 1540476--1540511 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1540466 TATAATAATC
1540476 AAAAATTAAAA-TAAAATA
1 AAAAATTAAAATTAAAATA
1540494 AAAAATTAAAATTAAAAT
1 AAAAATTAAAATTAAAAT
1540512 TTATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAATTAAAATTAAAATA
Found at i:1540584 original size:20 final size:19
Alignment explanation
Indices: 1540539--1540617 Score: 83
Period size: 20 Copynumber: 4.2 Consensus size: 19
1540529 NNNNNNNNNN
*
1540539 AATAAAATATATAATAT-A
1 AATAAAATATATAAAATAA
*
1540557 AA-AAAATATTTAAAATGAA
1 AATAAAATATATAAAAT-AA
*
1540576 AATAAAATATATAAAATTAT
1 AATAAAATATATAAAA-TAA
*
1540596 AATAAAAAATA-AAAATAA
1 AATAAAATATATAAAATAA
1540614 AATA
1 AATA
1540618 TATGACATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
17 12 0.24
18 8 0.16
19 7 0.14
20 23 0.45
21 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (19 bp):
AATAAAATATATAAAATAA
Found at i:1540611 original size:33 final size:33
Alignment explanation
Indices: 1540568--1540733 Score: 102
Period size: 33 Copynumber: 4.6 Consensus size: 33
1540558 AAAAATATTT
*
1540568 AAAATGAAAATAAAATATATAAAATTATAATAA
1 AAAATAAAAATAAAATATATAAAATTATAATAA
* *
1540601 AAAATAAAAATAAAATATATGACATTA-AA-AA
1 AAAATAAAAATAAAATATATAAAATTATAATAA
** * *
1540632 TATATTTAAGAAATGATATTATATAAAAATTAATAATAA
1 -A-AAATAA-AAAT-AAAATATAT-AAAATT-ATAATAA
1540671 AAATATAAAATATATAAAAATAAAATATATAAATTTATAATAA
1 AAA-AT-AAA-A-AT-AAAAT---ATATA-AAA-TTATAATAA
*
1540714 TAAATAAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
1540734 GATATTAAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
31 2 0.02
32 3 0.03
33 28 0.28
34 4 0.04
35 11 0.11
36 4 0.04
37 2 0.02
38 10 0.10
39 7 0.07
40 6 0.06
41 3 0.03
42 3 0.03
43 16 0.16
44 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAATTATAATAA
Found at i:1540687 original size:30 final size:33
Alignment explanation
Indices: 1540651--1540733 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
1540641 GAAATGATAT
*
1540651 TATATAAAAAT-TAATA-ATAAAAATATAA-AA
1 TATATAAAAATAAAATATATAAAAATATAATAA
**
1540681 TATATAAAAATAAAATATATAAATTTATAATAA
1 TATATAAAAATAAAATATATAAAAATATAATAA
*
1540714 TAAATAAAAATAAAATATAT
1 TATATAAAAATAAAATATAT
1540734 GATATTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
30 11 0.24
31 4 0.09
32 10 0.22
33 21 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (33 bp):
TATATAAAAATAAAATATATAAAAATATAATAA
Found at i:1540692 original size:23 final size:23
Alignment explanation
Indices: 1540652--1540748 Score: 85
Period size: 23 Copynumber: 4.2 Consensus size: 23
1540642 AAATGATATT
*
1540652 ATATAAAA-AT-TAATAATAAAA
1 ATATAAAATATATAAAAATAAAA
1540673 ATATAAAATATATAAAAATAAAA
1 ATATAAAATATATAAAAATAAAA
*
1540696 TATATAAATTTATAATAATAAAT-AAA
1 -ATATAAA-ATAT-ATAA-AAATAAAA
* * *
1540722 A-ATAAAATATATGATATTAAAA
1 ATATAAAATATATAAAAATAAAA
1540744 ATATA
1 ATATA
1540749 TTTAAGAGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
21 10 0.16
22 9 0.15
23 16 0.26
24 12 0.19
25 4 0.06
26 7 0.11
27 4 0.06
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (23 bp):
ATATAAAATATATAAAAATAAAA
Found at i:1540697 original size:113 final size:113
Alignment explanation
Indices: 1540574--1540798 Score: 398
Period size: 113 Copynumber: 2.0 Consensus size: 113
1540564 ATTTAAAATG
1540574 AAAATAAAATATATAAAATTATAATAAAAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATATAAAATTATAATAAAAAATAAAAATAAAATATATGACATTAAAAATATATTT
1540639 AAGAAATGATATTATATAAAAATTAATAAT-AAAAATATAAAATATATA
66 AAGAAATGATATTATATAAAAATTAATAATAAAAAATAT-AAATATATA
* * *
1540687 AAAATAAAATATATAAATTTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
1 AAAATAAAATATATAAAATTATAATAAAAAATAAAAATAAAATATATGACATTAAAAATATATTT
*
1540752 AAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
66 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
1540799 TAAACTTGTA
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
113 99 0.93
114 8 0.07
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (113 bp):
AAAATAAAATATATAAAATTATAATAAAAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATA
Found at i:1540709 original size:8 final size:8
Alignment explanation
Indices: 1540671--1540719 Score: 52
Period size: 7 Copynumber: 6.6 Consensus size: 8
1540661 TTAATAATAA
1540671 AAATATA-
1 AAATATAT
1540678 AAATATAT
1 AAATATAT
*
1540686 AAAAATA-
1 AAATATAT
1540693 AAATATAT
1 AAATATAT
*
1540701 AAATTTAT
1 AAATATAT
1540709 -AATA-AT
1 AAATATAT
1540715 AAATA
1 AAATA
1540720 AAAATAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 2 0.06
7 20 0.57
8 13 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATATAT
Found at i:1556804 original size:15 final size:14
Alignment explanation
Indices: 1556773--1556832 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
1556763 TAGAAGTTAA
*
1556773 GAGGGAAAAGGTGT
1 GAGGGAAAAGGTAT
*
1556787 GAGGGAAAAATGTAT
1 GAGGG-AAAAGGTAT
* *
1556802 GAGTGAACAAGGTAA
1 GAGGGAA-AAGGTAT
*
1556817 GAAGGAAAAGGTAT
1 GAGGGAAAAGGTAT
1556831 GA
1 GA
1556833 TAGAAGAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 15 0.42
15 21 0.58
ACGTcount: A:0.45, C:0.02, G:0.38, T:0.15
Consensus pattern (14 bp):
GAGGGAAAAGGTAT
Found at i:1556922 original size:34 final size:34
Alignment explanation
Indices: 1556849--1556936 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 34
1556839 AAGATAAGTT
* * **
1556849 AGAAAAGGTAAAAGGGAGAAACACTTATATTTCA
1 AGAAAAGGTAAGAGGAAGAAACACTTATACATCA
* *
1556883 GGAAAAGGTAAGAGGAAGAAACACTTGTACATCA
1 AGAAAAGGTAAGAGGAAGAAACACTTATACATCA
*
1556917 AGAAAAGATTAAGAGGAAGA
1 AGAAAAG-GTAAGAGGAAGA
1556937 CTTTCTAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 34 0.76
35 11 0.24
ACGTcount: A:0.51, C:0.08, G:0.25, T:0.16
Consensus pattern (34 bp):
AGAAAAGGTAAGAGGAAGAAACACTTATACATCA
Found at i:1558527 original size:3 final size:3
Alignment explanation
Indices: 1558521--1558561 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
1558511 ATTATTATTG
*
1558521 TTC TTC TTC TTC TTC TTT TTC TTC TTC TT- TGTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TT
1558562 ATTGTTAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:1558542 original size:12 final size:12
Alignment explanation
Indices: 1558521--1558561 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1558511 ATTATTATTG
*
1558521 TTCTTCTTCTTC
1 TTCTTTTTCTTC
1558533 TTCTTTTTCTTC
1 TTCTTTTTCTTC
*
1558545 TTCTTTGTCTTC
1 TTCTTTTTCTTC
1558557 TTCTT
1 TTCTT
1558562 ATTGTTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:1566336 original size:1 final size:1
Alignment explanation
Indices: 1566330--1566374 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
1566320 CTCTGATTTC
1566330 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1566375 GAGTCTTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1573545 original size:30 final size:30
Alignment explanation
Indices: 1573509--1573583 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
1573499 CGACGGTTGG
*
1573509 ATTTGATCATGAAATGTTGGATCTGGTTTT
1 ATTTGATCGTGAAATGTTGGATCTGGTTTT
*
1573539 ATTTGATCGTAAAATGTTGGATCTGGTTTT
1 ATTTGATCGTGAAATGTTGGATCTGGTTTT
1573569 ATTTGATCGTGAAAT
1 ATTTGATCGTGAAAT
1573584 ATTAAATTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (30 bp):
ATTTGATCGTGAAATGTTGGATCTGGTTTT
Found at i:1574758 original size:19 final size:21
Alignment explanation
Indices: 1574734--1574775 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1574724 GGTTTTTTGG
1574734 TTAAG-AA-GATGATAATCAA
1 TTAAGAAAGGATGATAATCAA
*
1574753 TTAAGAAAGGATGGTAATCAA
1 TTAAGAAAGGATGATAATCAA
1574774 TT
1 TT
1574776 TAAAGCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.29
Consensus pattern (21 bp):
TTAAGAAAGGATGATAATCAA
Found at i:1580257 original size:41 final size:42
Alignment explanation
Indices: 1580203--1580338 Score: 179
Period size: 41 Copynumber: 3.3 Consensus size: 42
1580193 TCCATTTATG
* *
1580203 TACATAAACCTTAAAACAATTGAG-TCTTACTCATCGTAACA
1 TACATAAACCTTAAAACAATTGAGATCTTACCCATCATAACA
1580244 TACATAAACCTTAAAACAATT-AGATCTTACCCATCATAACA
1 TACATAAACCTTAAAACAATTGAGATCTTACCCATCATAACA
* * * * *
1580285 TATATAAACTTTAAAACAATTGA-ATTTTGCCCATCATAATA
1 TACATAAACCTTAAAACAATTGAGATCTTACCCATCATAACA
*
1580326 TTCATAAACCTTA
1 TACATAAACCTTA
1580339 TATACATCAT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.02
41 80 0.96
42 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (42 bp):
TACATAAACCTTAAAACAATTGAGATCTTACCCATCATAACA
Found at i:1592137 original size:3 final size:3
Alignment explanation
Indices: 1592129--1592162 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1592119 AACATGTGTA
*
1592129 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1592163 GCAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1594926 original size:35 final size:35
Alignment explanation
Indices: 1594877--1594999 Score: 156
Period size: 35 Copynumber: 3.5 Consensus size: 35
1594867 AACATTCATT
* * *
1594877 ACAAGTGAAACACTATTTTACACAAAACAACTAAA
1 ACAAGTGAAGCACTACTTTACACAAAATAACTAAA
*
1594912 ACAAGTGAAGCACTACTTTATACAAAATAACTAAA
1 ACAAGTGAAGCACTACTTTACACAAAATAACTAAA
* ** *
1594947 ACAAGTTAAGTGCTACTTTACACAAAATAACTAGA
1 ACAAGTGAAGCACTACTTTACACAAAATAACTAAA
* *
1594982 ATAAGTGGAGCACTACTT
1 ACAAGTGAAGCACTACTT
1595000 CACGTGAAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 74 1.00
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.24
Consensus pattern (35 bp):
ACAAGTGAAGCACTACTTTACACAAAATAACTAAA
Found at i:1603733 original size:29 final size:29
Alignment explanation
Indices: 1603701--1603769 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1603691 GAAAAAGTAC
**
1603701 AAGAGAAGAAACTATACATGGATAGGTAT
1 AAGAGAAGAAACTATACATAAATAGGTAT
***
1603730 AAGA-AAGGATGTTATACATAAATAGGTAT
1 AAGAGAA-GAAACTATACATAAATAGGTAT
1603759 AAGAGAAGAAA
1 AAGAGAAGAAA
1603770 GTGTATGTGA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
28 2 0.06
29 27 0.87
30 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.20
Consensus pattern (29 bp):
AAGAGAAGAAACTATACATAAATAGGTAT
Found at i:1617548 original size:9 final size:9
Alignment explanation
Indices: 1617536--1617567 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1617526 GTAAAGTAGG
1617536 AGGAGGAGC
1 AGGAGGAGC
1617545 AGGAGGAGC
1 AGGAGGAGC
*
1617554 TGGAGGAGC
1 AGGAGGAGC
1617563 AGGAG
1 AGGAG
1617568 AGGGGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.31, C:0.09, G:0.56, T:0.03
Consensus pattern (9 bp):
AGGAGGAGC
Found at i:1623366 original size:19 final size:19
Alignment explanation
Indices: 1623342--1623380 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1623332 TTACATTTGC
1623342 GCTGATGTTGCCAGTGTCT
1 GCTGATGTTGCCAGTGTCT
1623361 GCTGATGTTGCCAGTGTCT
1 GCTGATGTTGCCAGTGTCT
1623380 G
1 G
1623381 TTGAAAGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.33, T:0.36
Consensus pattern (19 bp):
GCTGATGTTGCCAGTGTCT
Found at i:1628565 original size:31 final size:31
Alignment explanation
Indices: 1628520--1628598 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
1628510 ATATTTTTAA
* * *
1628520 AATTTTTTTTAATTTAGTCCCTA-AATATTTT
1 AATTTTGTTCAATTTAGTCCCTATAATA-TAT
* * *
1628551 AATTTTGTTCAATTTAATTCCTATACTATAT
1 AATTTTGTTCAATTTAGTCCCTATAATATAT
*
1628582 ATTTTTGTTCAATTTAG
1 AATTTTGTTCAATTTAG
1628599 ATCTTATGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 36 0.92
32 3 0.08
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (31 bp):
AATTTTGTTCAATTTAGTCCCTATAATATAT
Found at i:1638546 original size:6 final size:6
Alignment explanation
Indices: 1638535--1638562 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1638525 TTTTCTCCAC
1638535 TCTCAA TCTCAA TCTCAA TCTCAA TCTC
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTC
1638563 TCCCGTCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (6 bp):
TCTCAA
Found at i:1657761 original size:14 final size:13
Alignment explanation
Indices: 1657732--1657769 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1657722 ATTTAAAATC
1657732 AATAATTAT-AAA
1 AATAATTATAAAA
1657744 AATAATTATAACAA
1 AATAATTATAA-AA
*
1657758 AATAATAATAAA
1 AATAATTATAAA
1657770 TATCAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 12 0.52
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATTATAAAA
Found at i:1658486 original size:2 final size:2
Alignment explanation
Indices: 1658479--1658509 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1658469 TTTTAATCAC
1658479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1658510 GTCAATAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1658937 original size:2 final size:2
Alignment explanation
Indices: 1658930--1658955 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1658920 AATAATAATA
1658930 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
1658956 TTTACATATT
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:1659851 original size:29 final size:30
Alignment explanation
Indices: 1659819--1659877 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1659809 ATTTATTCTA
1659819 TTATTGTAT-TC-AATCAAATTTTTATAATT
1 TTATTGTATATCAAAT-AAATTTTTATAATT
* *
1659848 TTATTTTATATCAAATAATTTTTTATAATT
1 TTATTGTATATCAAATAAATTTTTATAATT
1659878 AATCATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 8 0.31
30 15 0.58
31 3 0.12
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (30 bp):
TTATTGTATATCAAATAAATTTTTATAATT
Found at i:1663939 original size:2 final size:2
Alignment explanation
Indices: 1663932--1663956 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1663922 ACCAAATAAG
1663932 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
1663957 ATAATGCCAT
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:1681226 original size:20 final size:20
Alignment explanation
Indices: 1681202--1681242 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1681192 TAAAATATTA
*
1681202 AAAAAACTCTTAAATTATTTT
1 AAAAAA-TCTTAAATAATTTT
*
1681223 AAAAAATTTTAAATAATTTT
1 AAAAAATCTTAAATAATTTT
1681243 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAAATCTTAAATAATTTT
Found at i:1687813 original size:2 final size:2
Alignment explanation
Indices: 1687808--1687835 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1687798 ATATATTTGC
1687808 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1687836 TGACATACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1699156 original size:15 final size:16
Alignment explanation
Indices: 1699113--1699159 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1699103 ATTTTTTTTA
* * *
1699113 AAATAATTTTAAATTC
1 AAATCATTTCAAATTT
1699129 AAATCATTTCAAATTT
1 AAATCATTTCAAATTT
1699145 AAATCA-TTCAAATTT
1 AAATCATTTCAAATTT
1699160 GATATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATCATTTCAAATTT
Found at i:1699186 original size:15 final size:16
Alignment explanation
Indices: 1699156--1699201 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1699146 AATCATTCAA
1699156 ATTTGATATTTAAATT
1 ATTTGATATTTAAATT
*
1699172 ATTTGA-ATTTGAATT
1 ATTTGATATTTAAATT
* *
1699187 ATTTTAGATTTAAAT
1 ATTTGATATTTAAAT
1699202 GATTAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (16 bp):
ATTTGATATTTAAATT
Found at i:1702486 original size:37 final size:37
Alignment explanation
Indices: 1702445--1702515 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1702435 AAATAACAAA
*
1702445 CTTTAATATACATAAT-GAGTAACAGTTATTGAAAAAG
1 CTTTAATATACATAATAG-GTAACAGTTACTGAAAAAG
* *
1702482 CTTTAATGTACATAATAGGTAATAGTTACTGAAA
1 CTTTAATATACATAATAGGTAACAGTTACTGAAA
1702516 CCCCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 29 0.97
38 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (37 bp):
CTTTAATATACATAATAGGTAACAGTTACTGAAAAAG
Found at i:1720671 original size:125 final size:126
Alignment explanation
Indices: 1720522--1720798 Score: 299
Period size: 125 Copynumber: 2.2 Consensus size: 126
1720512 ATTCTAAATT
* * * * *
1720522 ATGTTGAAAAAATAAAATTCTTACACG-CTATGTTTAAGGCATTTAACTCTAAAAATTTATATTT
1 ATGTTG-AAAAA-AAAATTATTACACGTC-ATATTTAAAGCATTTAACTCCAAAAATTTATATTC
** * *
1720586 TAGTGAAATATAAAAATA-AAGACTCAGTTACATGTCATGTT-AAAAAAAAAGTTGTTACACACC
63 TAGTGAAATATAAAAATAGAA-ACTCAGTTACACATCATATTGAAAAAAAAAATTGTTACACACC
* * * * * * * *
1720649 TTGTTGAAAAGAAAATTATTACATGTCATATTTAAAGTATTTAACTCCAAGAGTTTGTGTTCTAG
1 ATGTTGAAAAAAAAATTATTACACGTCATATTTAAAGCATTTAACTCCAAAAATTTATATTCTAG
* * * **
1720714 TGAAATATAAAAATAGAAACTGAGTTTCACATCATATTGAAAAAAAAAATTGTTATATGCC
66 TGAAATATAAAAATAGAAACTCAGTTACACATCATATTGAAAAAAAAAATTGTTACACACC
1720775 ATGTTGAAAAAAAAATTATTACAC
1 ATGTTGAAAAAAAAATTATTACAC
1720799 ACCATTAATT
Statistics
Matches: 122, Mismatches: 25, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
125 71 0.58
126 46 0.38
127 5 0.04
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (126 bp):
ATGTTGAAAAAAAAATTATTACACGTCATATTTAAAGCATTTAACTCCAAAAATTTATATTCTAG
TGAAATATAAAAATAGAAACTCAGTTACACATCATATTGAAAAAAAAAATTGTTACACACC
Found at i:1721006 original size:29 final size:28
Alignment explanation
Indices: 1720974--1721035 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 28
1720964 TATAAATTAA
1720974 GTTACACATCATATATATTAAAAAAAA-TT
1 GTTACACA-CAT-TATATTAAAAAAAAGTT
1721003 GTT--ACACATTATATTAAAAAAAAGTT
1 GTTACACACATTATATTAAAAAAAAGTT
*
1721029 ATTACAC
1 GTTACAC
1721036 GCTATGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 14 0.48
26 7 0.24
27 3 0.10
28 2 0.07
29 3 0.10
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (28 bp):
GTTACACACATTATATTAAAAAAAAGTT
Found at i:1721015 original size:25 final size:26
Alignment explanation
Indices: 1720987--1721035 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1720977 ACACATCATA
*
1720987 TATATTAAAAAAAA-TTGTTACACAT
1 TATATTAAAAAAAAGTTATTACACAT
1721012 TATATTAAAAAAAAGTTATTACAC
1 TATATTAAAAAAAAGTTATTACAC
1721036 GCTATGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (26 bp):
TATATTAAAAAAAAGTTATTACACAT
Found at i:1721051 original size:22 final size:22
Alignment explanation
Indices: 1721023--1721090 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
1721013 ATATTAAAAA
*
1721023 AAAGTTATTACACGCTATGTTT
1 AAAGTTATTACACACTATGTTT
* *
1721045 AAGGTTATTACATACTATGTTT
1 AAAGTTATTACACACTATGTTT
*
1721067 AAAGTGTA-TA-ACTCTATGTTT
1 AAAGT-TATTACACACTATGTTT
1721088 AAA
1 AAA
1721091 TCATACCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
21 12 0.31
22 25 0.64
23 2 0.05
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.41
Consensus pattern (22 bp):
AAAGTTATTACACACTATGTTT
Found at i:1735985 original size:2 final size:2
Alignment explanation
Indices: 1735978--1736004 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1735968 ACTAAAATGC
1735978 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1736005 ACTATTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1744923 original size:78 final size:77
Alignment explanation
Indices: 1744778--1744985 Score: 233
Period size: 78 Copynumber: 2.7 Consensus size: 77
1744768 CAAGGCATGA
* * * * * * **
1744778 GCATGTGGCATTCCTATTATACATTAAGATATAATGATGTCAATATGTAAGTATCACCAAAGTCC
1 GCATATGGCATTCATATTATACA-TAAGGTATAATGATGTCAATATGTAAATACCACAAAAAACC
1744843 ATGTGATC-AGTGG
65 ATGTGA-CAAGTGG
* *
1744856 GCATATGGCATTCTTATTATACAGTAAGGTATAATGATGTCAATATGTAAATACCATAAAAAACC
1 GCATATGGCATTCATATTATACA-TAAGGTATAATGATGTCAATATGTAAATACCACAAAAAACC
1744921 ATGTGACAAGTGG
65 ATGTGACAAGTGG
* *
1744934 ACATTTGGCATTCATATTATACATAAAGGTATAAT-A-GTACTAATATGTAAAT
1 GCATATGGCATTCATATTATACAT-AAGGTATAATGATGT-C-AATATGTAAAT
1744986 TTAATATCTT
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
76 2 0.02
77 4 0.04
78 107 0.95
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (77 bp):
GCATATGGCATTCATATTATACATAAGGTATAATGATGTCAATATGTAAATACCACAAAAAACCA
TGTGACAAGTGG
Found at i:1753756 original size:17 final size:17
Alignment explanation
Indices: 1753736--1753772 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1753726 TAATAAATTA
1753736 ATATATTAAATGTATAC
1 ATATATTAAATGTATAC
* *
1753753 ATATATTTAATTTATAC
1 ATATATTAAATGTATAC
1753770 ATA
1 ATA
1753773 ATTTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (17 bp):
ATATATTAAATGTATAC
Found at i:1760459 original size:74 final size:69
Alignment explanation
Indices: 1760372--1760539 Score: 189
Period size: 74 Copynumber: 2.3 Consensus size: 69
1760362 NNNNNNNNTA
* *
1760372 ATGTCATATATTTTATTTTCATTTCTTATTA-TAATC-TTAGATATTTTATTTT-TATTTATTTA
1 ATGTTATATATTTTATTTTAATTTCTT-TTACT-ATCATTA-A-ATTTTATTTTAT-TTTATTT-
1760434 ATATAATTTTTT
60 -T-TAATTTTTT
*
1760446 ATGTTATATATTTTATTTTAATTTCTTTTACCTATCATTTAAATTTTATTTTATTTTATTTTTTA
1 ATGTTATATATTTTATTTTAATTTCTTTTA-CTATCA-TTAAATTTTATTTTATTTTATTTTTAA
1760511 TTTTTT
64 TTTTTT
*
1760517 ATATTATATATTTTATTTTAATT
1 ATGTTATATATTTTATTTTAATT
1760540 ATAACATTAC
Statistics
Matches: 85, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
71 30 0.35
72 1 0.01
73 3 0.04
74 45 0.53
75 3 0.04
76 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (69 bp):
ATGTTATATATTTTATTTTAATTTCTTTTACTATCATTAAATTTTATTTTATTTTATTTTTAATT
TTTT
Found at i:1760498 original size:5 final size:5
Alignment explanation
Indices: 1760488--1760536 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
1760478 TATCATTTAA
* *
1760488 ATTTT ATTTT ATTTT ATTTT -TTATT -TTTT ATATT A-TAT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT ATTTT ATTTT ATTTT ATTTT
1760536 A
1 A
1760537 ATTATAACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
4 6 0.16
5 31 0.84
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:1760518 original size:14 final size:14
Alignment explanation
Indices: 1760497--1760536 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1760487 AATTTTATTT
*
1760497 TATTTTATTTTTTA
1 TATTTTATTTTATA
* *
1760511 TTTTTTATATTATA
1 TATTTTATTTTATA
1760525 TATTTTATTTTA
1 TATTTTATTTTA
1760537 ATTATAACAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TATTTTATTTTATA
Found at i:1760529 original size:33 final size:35
Alignment explanation
Indices: 1760377--1760536 Score: 98
Period size: 38 Copynumber: 4.4 Consensus size: 35
1760367 NNNTAATGTC
**
1760377 ATATATTTTATTTTCATTTCTTATTATAATCTTAGATATT
1 ATATATTTTATTTT-ATTTCTT-TTAT--T-TTTTATATT
* * * * *
1760417 TTAT-TTTTA-TTTATTTAATATAATTTTTTATGTT
1 ATATATTTTATTTTATTT-CTTTTATTTTTTATATT
* *
1760451 ATATATTTTATTTTAATTTCTTTTACCTATCATTTAAATT
1 ATATATTTTATTTT-ATTTCTTTTA--T-T-TTTTATATT
1760491 -T-TATTTTATTTTA-TT-TTTTATTTTTTATATT
1 ATATATTTTATTTTATTTCTTTTATTTTTTATATT
1760522 ATATATTTTATTTTA
1 ATATATTTTATTTTA
1760537 ATTATAACAT
Statistics
Matches: 94, Mismatches: 16, Indels: 27
0.69 0.12 0.20
Matches are distributed among these distances:
31 7 0.07
32 2 0.02
33 13 0.14
34 9 0.10
35 11 0.12
36 8 0.09
37 12 0.13
38 16 0.17
39 7 0.07
40 9 0.10
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (35 bp):
ATATATTTTATTTTATTTCTTTTATTTTTTATATT
Found at i:1762450 original size:21 final size:20
Alignment explanation
Indices: 1762426--1762482 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
1762416 AAAATATAAA
*
1762426 AATTAAAATATTATTTTTATT
1 AATTAAAA-ATTATTATTATT
1762447 AATTTTAAAAATTATTATTATT
1 AA--TTAAAAATTATTATTATT
*
1762469 ATTTAAAAAATTAT
1 AATT-AAAAATTAT
1762483 ATAATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 11 0.35
22 12 0.39
23 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTAAAAATTATTATTATT
Found at i:1762462 original size:22 final size:21
Alignment explanation
Indices: 1762428--1762499 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 21
1762418 AATATAAAAA
*
1762428 TTAAAATATTATTTTTATTAATT
1 TTAAAA-ATTATTATTATT-ATT
1762451 TTAAAAATTATTATTATTATT
1 TTAAAAATTATTATTATTATT
* * *
1762472 TAAAAAATTA-TATAATAATT
1 TTAAAAATTATTATTATTATT
*
1762492 TTTAAAAT
1 TTAAAAAT
1762500 GAATAAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
20 14 0.33
21 12 0.28
22 11 0.26
23 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAAATTATTATTATTATT
Found at i:1762492 original size:20 final size:21
Alignment explanation
Indices: 1762420--1762492 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
1762410 TAATAAAAAA
* *
1762420 TATAA-AAATTAAAATATTATT
1 TATAATAATTTAAAAAATTA-T
* * *
1762441 TTTATTAATTTTAAAAATTAT
1 TATAATAATTTAAAAAATTAT
* *
1762462 TATTATTATTTAAAAAATTA-
1 TATAATAATTTAAAAAATTAT
1762482 TATAATAATTT
1 TATAATAATTT
1762493 TTAAAATGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
20 9 0.23
21 19 0.49
22 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATAATAATTTAAAAAATTAT
Found at i:1762498 original size:20 final size:21
Alignment explanation
Indices: 1762428--1762499 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
1762418 AATATAAAAA
* *
1762428 TTAAAATATTATTTTTATTAATT
1 TTAAAA-ATTA-TTATAATAATT
* *
1762451 TTAAAAATTATTATTATTATT
1 TTAAAAATTATTATAATAATT
*
1762472 TAAAAAATTA-TATAATAATT
1 TTAAAAATTATTATAATAATT
*
1762492 TTTAAAAT
1 TTAAAAAT
1762500 GAATAAAAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 14 0.35
21 16 0.40
22 4 0.10
23 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAAATTATTATAATAATT
Found at i:1766276 original size:50 final size:50
Alignment explanation
Indices: 1766201--1766304 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
1766191 TAGAGGTTGA
1766201 TTAAATTGGTTAGGCCTCCCTCATATGTAATTGTAAGTTCTGGTGTGCAT
1 TTAAATTGGTTAGGCCTCCCTCATATGTAATTGTAAGTTCTGGTGTGCAT
1766251 TTAAATTGGTTAGGCCTCCCTCATATGTAATTGTAAGTTCTGGTGTGCAT
1 TTAAATTGGTTAGGCCTCCCTCATATGTAATTGTAAGTTCTGGTGTGCAT
1766301 TTAA
1 TTAA
1766305 TCTTTTTCGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (50 bp):
TTAAATTGGTTAGGCCTCCCTCATATGTAATTGTAAGTTCTGGTGTGCAT
Found at i:1768841 original size:21 final size:21
Alignment explanation
Indices: 1768815--1768856 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1768805 AAGCACAATA
1768815 TGCAAAGAGAACGCATAACTT
1 TGCAAAGAGAACGCATAACTT
1768836 TGCAAAGAGAACGCATAACTT
1 TGCAAAGAGAACGCATAACTT
1768857 GTAATGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (21 bp):
TGCAAAGAGAACGCATAACTT
Found at i:1771799 original size:10 final size:9
Alignment explanation
Indices: 1771774--1771811 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
1771764 TCATTTAATG
1771774 ATAAAA-AT
1 ATAAAATAT
1771782 ATAAAATAT
1 ATAAAATAT
1771791 ATAAAAATAT
1 AT-AAAATAT
1771801 GATAAAATAT
1 -ATAAAATAT
1771811 A
1 A
1771812 ACTTAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 6 0.22
9 5 0.19
10 14 0.52
11 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (9 bp):
ATAAAATAT
Found at i:1778494 original size:18 final size:16
Alignment explanation
Indices: 1778458--1778492 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1778448 AATATTTTTT
*
1778458 AAGATATTAATAAAAA
1 AAGATATTAAAAAAAA
1778474 AAGATATTAAAAATAAA
1 AAGATATTAAAAA-AAA
1778491 AA
1 AA
1778493 AGCATAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
AAGATATTAAAAAAAA
Found at i:1778530 original size:7 final size:8
Alignment explanation
Indices: 1778482--1778550 Score: 75
Period size: 8 Copynumber: 8.0 Consensus size: 8
1778472 AAAAGATATT
1778482 AAAAATAA
1 AAAAATAA
1778490 AAAAGCATAGA
1 AAAA--ATA-A
*
1778501 ATAGAAATGA
1 A-A-AAATAA
*
1778511 AATAATAA
1 AAAAATAA
1778519 AAAAATAA
1 AAAAATAA
1778527 AAAAATAA
1 AAAAATAA
1778535 AAAAATAA
1 AAAAATAA
1778543 AAAAATAA
1 AAAAATAA
1778551 TACTAATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
8 39 0.75
9 1 0.02
10 5 0.10
11 4 0.08
12 1 0.02
13 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (8 bp):
AAAAATAA
Found at i:1779117 original size:20 final size:19
Alignment explanation
Indices: 1779092--1779133 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1779082 GTTGCTAATA
*
1779092 AAATAATGAATAACGTAAAT
1 AAATAATGAATAA-GGAAAT
*
1779112 AAATAATGATTAAGGAAAT
1 AAATAATGAATAAGGAAAT
1779131 AAA
1 AAA
1779134 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (19 bp):
AAATAATGAATAAGGAAAT
Found at i:1779536 original size:18 final size:19
Alignment explanation
Indices: 1779513--1779551 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1779503 ATGGATATTC
1779513 ATAAAAT-ATTTATAATAA
1 ATAAAATAATTTATAATAA
1779531 ATAAAATAATTTATAATAA
1 ATAAAATAATTTATAATAA
1779550 AT
1 AT
1779552 TATATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAATAATTTATAATAA
Found at i:1781294 original size:1 final size:1
Alignment explanation
Indices: 1781288--1781315 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1781278 TTATTCCCAA
1781288 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1781316 AAAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1784337 original size:25 final size:25
Alignment explanation
Indices: 1784299--1784355 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1784289 AATGAAGATG
1784299 TAAAATAATTTAATTTAAA-ATAAAAA
1 TAAAAT-ATTTAA-TTAAATATAAAAA
*
1784325 TAAAATATTTAATTAAATATAATAA
1 TAAAATATTTAATTAAATATAAAAA
1784350 -AAAATA
1 TAAAATA
1784356 AAAATTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 11 0.38
25 12 0.41
26 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAAATATTTAATTAAATATAAAAA
Found at i:1788944 original size:58 final size:58
Alignment explanation
Indices: 1788849--1788964 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
1788839 AGAGAAGAGC
* **
1788849 CTTAACAACTTCTCCACCACAATTTCTGAAGTTAATGAATGAAAGCTTTGTATCATTG
1 CTTAACAACTTCTCCACCACAATTTCCGAAGAGAATGAATGAAAGCTTTGTATCATTG
1788907 CTTAACAACTTCTCCACCACAATTTCCGAAGAGAATGAATGAAAGCTTTGTATCATTG
1 CTTAACAACTTCTCCACCACAATTTCCGAAGAGAATGAATGAAAGCTTTGTATCATTG
1788965 TATGTAACGT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (58 bp):
CTTAACAACTTCTCCACCACAATTTCCGAAGAGAATGAATGAAAGCTTTGTATCATTG
Found at i:1789039 original size:2 final size:2
Alignment explanation
Indices: 1789032--1789072 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
1789022 CTTTAATAGG
1789032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1789073 TTTGAGAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1792848 original size:88 final size:88
Alignment explanation
Indices: 1792689--1792859 Score: 213
Period size: 88 Copynumber: 2.0 Consensus size: 88
1792679 TATCTTGATC
* ** * * ** * * *
1792689 TCTATCTTTGTATTTCACTAGGATATAAACTCTTGGAGTTAAAATCCTTAAACATGGTGTGTGAT
1 TCTATATTTGTATTTCACTAAAATATAAACTATTAGAGTTAAAATCCTTAAACAAAGCGTGTAAC
1792754 AATTTTTTTTTTCAACATGGCGT
66 AATTTTTTTTTTCAACATGGCGT
1792777 TCTATATTTGTATTTCACTAAAATATAAACTATTAGAGTTAAACA-CCTTAAACAAAGCGTGTAA
1 TCTATATTTGTATTTCACTAAAATATAAACTATTAGAGTTAAA-ATCCTTAAACAAAGCGTGTAA
*
1792841 C-A-TTTTTTTTTCAATATGG
65 CAATTTTTTTTTTCAACATGG
1792860 TGTGCAACAA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
86 16 0.23
87 1 0.01
88 53 0.75
89 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (88 bp):
TCTATATTTGTATTTCACTAAAATATAAACTATTAGAGTTAAAATCCTTAAACAAAGCGTGTAAC
AATTTTTTTTTTCAACATGGCGT
Found at i:1795446 original size:62 final size:64
Alignment explanation
Indices: 1795373--1795560 Score: 179
Period size: 62 Copynumber: 3.0 Consensus size: 64
1795363 ATATTATATG
* *
1795373 CTAGAGAAATTGGGCTTAAAAATCTTTTCG-GCCAACATTATTAGATTTAAACATCTTAGATGT
1 CTAGATAAATTGGGCTTAAAAATCTTTTCGAGCCAACATTACTAGATTTAAACATCTTAGATGT
* * * * * * * * *
1795436 C-AGATCAATTGGGC-TCAAACTCTTTTCGTGCCAA-TTTAACTAAATGTACACATCTTGGATG-
1 CTAGATAAATTGGGCTTAAAAATCTTTTCGAGCCAACATT-ACTAGATTTAAACATCTTAGATGT
* * * * * *
1795497 CTAGATAAATTGGGCTTAAACATCTTTTCGAACCAGCATAACTAGAATTAAATATCTTAGATGT
1 CTAGATAAATTGGGCTTAAAAATCTTTTCGAGCCAACATTACTAGATTTAAACATCTTAGATGT
1795561 TAGCTTTTTT
Statistics
Matches: 94, Mismatches: 25, Indels: 11
0.72 0.19 0.08
Matches are distributed among these distances:
61 15 0.16
62 46 0.49
63 32 0.34
64 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (64 bp):
CTAGATAAATTGGGCTTAAAAATCTTTTCGAGCCAACATTACTAGATTTAAACATCTTAGATGT
Found at i:1796173 original size:20 final size:20
Alignment explanation
Indices: 1796148--1796192 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1796138 ATTCATTCAG
1796148 ATAAATATCTTTAAAACTTA
1 ATAAATATCTTTAAAACTTA
* * *
1796168 ATAAATTTCTTTGAGACTTA
1 ATAAATATCTTTAAAACTTA
1796188 ATAAA
1 ATAAA
1796193 AAATAATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (20 bp):
ATAAATATCTTTAAAACTTA
Done.