Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000417.1 Hibiscus syriacus cultivar Beakdansim tig00000764_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2005044
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1555867 original size:27 final size:27
Alignment explanation
Indices: 1555779--1555873 Score: 91
Period size: 27 Copynumber: 3.5 Consensus size: 27
1555769 CTTCAATTTG
* * * *
1555779 AACAGCATCGGCAATTGGAACTTGAGC
1 AACAGCAGCAGCAGTTGGAACTTCAGC
* * *
1555806 AACAGCATCGGCAGTTGGAACTTGAGC
1 AACAGCAGCAGCAGTTGGAACTTCAGC
*
1555833 AACAGCAGCTGCAGTTGGAACTTCAGC
1 AACAGCAGCAGCAGTTGGAACTTCAGC
** *
1555860 GGCGGCAGCAGCAG
1 AACAGCAGCAGCAG
1555874 CAGCTGGAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.31, T:0.16
Consensus pattern (27 bp):
AACAGCAGCAGCAGTTGGAACTTCAGC
Found at i:1555913 original size:27 final size:27
Alignment explanation
Indices: 1555883--1555963 Score: 135
Period size: 27 Copynumber: 3.0 Consensus size: 27
1555873 GCAGCTGGAA
* * *
1555883 CAGCGGGAACGTATGTGGGAACAGCAG
1 CAGCTGGAACGTATGCGGGAGCAGCAG
1555910 CAGCTGGAACGTATGCGGGAGCAGCAG
1 CAGCTGGAACGTATGCGGGAGCAGCAG
1555937 CAGCTGGAACGTATGCGGGAGCAGCAG
1 CAGCTGGAACGTATGCGGGAGCAGCAG
1555964 ATTCATAACC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.27, C:0.21, G:0.41, T:0.11
Consensus pattern (27 bp):
CAGCTGGAACGTATGCGGGAGCAGCAG
Found at i:1562519 original size:7 final size:7
Alignment explanation
Indices: 1562484--1562518 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
1562474 TCAGGGTATC
1562484 TTAAAAT
1 TTAAAAT
1562491 TTAAAAT
1 TTAAAAT
1562498 TTAAAAT
1 TTAAAAT
1562505 TTAAAAT
1 TTAAAAT
*
1562512 ATAAAAT
1 TTAAAAT
1562519 AGTAACCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TTAAAAT
Found at i:1570214 original size:115 final size:115
Alignment explanation
Indices: 1570012--1570241 Score: 451
Period size: 115 Copynumber: 2.0 Consensus size: 115
1570002 ATGTTGAACG
1570012 GATGTACTAAAATGGAACAAAAACTAAAGTTTTTAATGACGGGTATTAAAATGAAACAAAAATTG
1 GATGTACTAAAATGGAACAAAAACTAAAGTTTTTAATGACGGGTATTAAAATGAAACAAAAATTG
1570077 AACTTTATGTATGATTTTTGAAATTGAAAGTTTAAGTATTCAAACAAATT
66 AACTTTATGTATGATTTTTGAAATTGAAAGTTTAAGTATTCAAACAAATT
1570127 GATGTACTAAAATGGAACAAAAACTAAAGTTTTTAATGACGGGTATTAAAATGAAACAAAAATTG
1 GATGTACTAAAATGGAACAAAAACTAAAGTTTTTAATGACGGGTATTAAAATGAAACAAAAATTG
*
1570192 AATTTTATGTATGATTTTTGAAATTGAAAGTTTAAGTATTCAAACAAATT
66 AACTTTATGTATGATTTTTGAAATTGAAAGTTTAAGTATTCAAACAAATT
1570242 AAAATTAATA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (115 bp):
GATGTACTAAAATGGAACAAAAACTAAAGTTTTTAATGACGGGTATTAAAATGAAACAAAAATTG
AACTTTATGTATGATTTTTGAAATTGAAAGTTTAAGTATTCAAACAAATT
Found at i:1573303 original size:70 final size:71
Alignment explanation
Indices: 1573190--1573333 Score: 263
Period size: 70 Copynumber: 2.0 Consensus size: 71
1573180 TTGATGGGGT
*
1573190 AAATGGCCTCCCTTGTGCTTTCATTCAAGCTCACAACTATTCC-AAAACTGTATAAAAATGGAAC
1 AAATGGCCTCCCTTGTGCTTTCATTCAAGCTCACAACCATTCCAAAAACTGTATAAAAATGGAAC
1573254 AAGGCA
66 AAGGCA
*
1573260 AAATGGCCTCCCTTGTGCTTTCATTCAAGTTCACAACCATTCCAAAAACTGTATAAAAATGGAAC
1 AAATGGCCTCCCTTGTGCTTTCATTCAAGCTCACAACCATTCCAAAAACTGTATAAAAATGGAAC
1573325 AAGGCA
66 AAGGCA
1573331 AAA
1 AAA
1573334 ACTGAATATT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 41 0.58
71 30 0.42
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.25
Consensus pattern (71 bp):
AAATGGCCTCCCTTGTGCTTTCATTCAAGCTCACAACCATTCCAAAAACTGTATAAAAATGGAAC
AAGGCA
Found at i:1574197 original size:42 final size:42
Alignment explanation
Indices: 1574138--1574221 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1574128 ATGAAGAATG
* * *
1574138 AAAGAACTTGCACTTGCTCGTATTATGTACACGGTCATGATT
1 AAAGAACTTACACTTGCTCATATTATGTACACAGTCATGATT
1574180 AAAGAACTTACACTTGCTCATATTATGTACACAGTCATGATT
1 AAAGAACTTACACTTGCTCATATTATGTACACAGTCATGATT
1574222 GTTAATACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (42 bp):
AAAGAACTTACACTTGCTCATATTATGTACACAGTCATGATT
Found at i:1575306 original size:19 final size:19
Alignment explanation
Indices: 1575282--1575324 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1575272 ACAAATTTAA
1575282 ATCCAGCGATTGTTATTTT
1 ATCCAGCGATTGTTATTTT
1575301 ATCCAGCGATTGTTATTTT
1 ATCCAGCGATTGTTATTTT
1575320 ATCCA
1 ATCCA
1575325 AAAATTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (19 bp):
ATCCAGCGATTGTTATTTT
Found at i:1575503 original size:21 final size:21
Alignment explanation
Indices: 1575477--1575517 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1575467 AAATATTAAC
1575477 ATGATGA-CTAAGATACATAAA
1 ATGATGAGCTAAGA-ACATAAA
*
1575498 ATGATGAGCTTAGAACATAA
1 ATGATGAGCTAAGAACATAA
1575518 TAAATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (21 bp):
ATGATGAGCTAAGAACATAAA
Found at i:1575787 original size:61 final size:63
Alignment explanation
Indices: 1575719--1575843 Score: 220
Period size: 61 Copynumber: 2.0 Consensus size: 63
1575709 AAATCAGAAG
1575719 AAAAAAAT-CCACTGGATCTCCCTTACTGTTGATCGTCACTGAGCTTC-TTTGGC-TTGATTTT
1 AAAAAAATCCCACTGGATCTCCCTTACTG-TGATCGTCACTGAGCTTCTTTTGGCTTTGATTTT
1575780 AAAAAAATCCCACTGGATCTCCCTTACTGTGATCGTCACTGAGCTTCTTTTGGCTTTGATTTT
1 AAAAAAATCCCACTGGATCTCCCTTACTGTGATCGTCACTGAGCTTCTTTTGGCTTTGATTTT
1575843 A
1 A
1575844 CATCTTCAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
61 26 0.43
62 26 0.43
63 9 0.15
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (63 bp):
AAAAAAATCCCACTGGATCTCCCTTACTGTGATCGTCACTGAGCTTCTTTTGGCTTTGATTTT
Found at i:1577997 original size:8 final size:8
Alignment explanation
Indices: 1577984--1578008 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1577974 GTATGCTTCC
1577984 CTTCTCTT
1 CTTCTCTT
1577992 CTTCTCTT
1 CTTCTCTT
1578000 CTTCTCTT
1 CTTCTCTT
1578008 C
1 C
1578009 AGTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (8 bp):
CTTCTCTT
Found at i:1580225 original size:3 final size:3
Alignment explanation
Indices: 1580217--1580257 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1580207 GATAATTAAA
1580217 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1580258 GTCATATCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1580784 original size:38 final size:38
Alignment explanation
Indices: 1580734--1580806 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
1580724 AAAAATAATT
1580734 ATTATATATATAATATTAATAAATTTAATTTAAATTAA
1 ATTATATATATAATATTAATAAATTTAATTTAAATTAA
* *
1580772 ATTATATATATAATATTTATATATTTAATTTAAAT
1 ATTATATATATAATATTAATAAATTTAATTTAAAT
1580807 ATATATATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTATATATATAATATTAATAAATTTAATTTAAATTAA
Found at i:1581156 original size:23 final size:23
Alignment explanation
Indices: 1581130--1581177 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1581120 ATAAAGTACA
*
1581130 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1581153 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1581176 AT
1 AT
1581178 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1581628 original size:23 final size:23
Alignment explanation
Indices: 1581602--1581664 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1581592 ATATAACCAC
1581602 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1581625 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1581648 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1581665 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1582127 original size:37 final size:38
Alignment explanation
Indices: 1582077--1582160 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 38
1582067 CAAATTGTAG
*
1582077 ATTTTGATTTCCTTTTACTTGGCATC-ATGAGATTTGA
1 ATTTTGATTTCCTTTTACTTGGCACCAATGAGATTTGA
* * *
1582114 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTACTTGGCACCA-ATGAGATTTGA
1582153 ATTTTGAT
1 ATTTTGAT
1582161 GAGCATCGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 24 0.59
39 17 0.41
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (38 bp):
ATTTTGATTTCCTTTTACTTGGCACCAATGAGATTTGA
Found at i:1582440 original size:18 final size:18
Alignment explanation
Indices: 1582417--1582453 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1582407 CGAAATATAT
1582417 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1582435 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1582453 A
1 A
1582454 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1582911 original size:22 final size:23
Alignment explanation
Indices: 1582885--1582942 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1582875 AACCACTACC
1582885 TATTACATTATATAA-CGATACA
1 TATTACATTATATAAGCGATACA
* *
1582907 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAGCGATACA
*
1582930 TATTACATCATAT
1 TATTACATTATAT
1582943 GTTTACCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (23 bp):
TATTACATTATATAAGCGATACA
Found at i:1582937 original size:23 final size:22
Alignment explanation
Indices: 1582880--1582942 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
1582870 ACAATAACCA
1582880 CTACCTATTACATTATATAACG
1 CTACCTATTACATTATATAACG
* *
1582902 ATACATATTACATTATATAAGCG
1 CTACCTATTACATTATATAA-CG
*
1582925 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
1582943 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (22 bp):
CTACCTATTACATTATATAACG
Found at i:1586266 original size:182 final size:183
Alignment explanation
Indices: 1585799--1586286 Score: 847
Period size: 183 Copynumber: 2.7 Consensus size: 183
1585789 TTAAAATTAC
*
1585799 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
1585864 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
1585929 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
* * *
1585982 CGATATTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1586047 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
1586112 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGT-TAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
1586164 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* *
1586228 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAAAAAACC-GTATATTTATA
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATA
1586287 ATATGTTGAA
Statistics
Matches: 290, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
181 11 0.04
182 109 0.38
183 170 0.59
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:1587745 original size:3 final size:3
Alignment explanation
Indices: 1587737--1587802 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
1587727 ACTTGTTTGG
* * * ** *
1587737 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
1587785 TTC ATC GTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC
1587803 GTCAGCTTTA
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1589621 original size:196 final size:198
Alignment explanation
Indices: 1589276--1590424 Score: 2053
Period size: 196 Copynumber: 5.8 Consensus size: 198
1589266 TTTAAATTAG
* *
1589276 TATCGTCACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
* * *
1589340 CTTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTTGATAATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1589404 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
1589469 AAA
196 AAA
*
1589472 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
1589537 ATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTT-GGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1589600 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
1589665 AAA
196 AAA
*
1589668 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
1589733 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATAATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1589798 CGACACTTTTTATATATGGATCAACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
1589863 AAAA
195 AAAA
*
1589867 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
1589932 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGG-TCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1589995 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
1590060 AAA
196 AAA
1590063 TATCGACACAAACTATATTAGTG-CGACACATTATTTAGACATA-TATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
*
1590126 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTTGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1590191 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
1590256 AAAA
195 AAAA
* *
1590260 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
* * *
1590325 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
* *
1590390 TTGACACTTTTTATATATGGATCAACACTTTATGG
130 TCGACACTTTTTATATATGGATCGACACTTTATGG
1590425 TAAATTTGCC
Statistics
Matches: 922, Mismatches: 20, Indels: 18
0.96 0.02 0.02
Matches are distributed among these distances:
194 61 0.07
195 25 0.03
196 306 0.33
197 205 0.22
198 84 0.09
199 194 0.21
200 47 0.05
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
AAA
Found at i:1590340 original size:393 final size:396
Alignment explanation
Indices: 1589276--1590424 Score: 2071
Period size: 393 Copynumber: 2.9 Consensus size: 396
1589266 TTTAAATTAG
* *
1589276 TATCGTCACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
* *
1589340 CTTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTTGATAATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATAATTTTGGGAT
1589404 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1589468 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGG
1589533 TATAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTT-
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TCGATGATTTTG
1589596 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGA
325 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGA
1589661 AAAAAAA
390 AAAAAAA
*
1589668 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
1589733 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATAATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATAATTTTGGGAT
*
1589798 CGACACTTTTTATATATGGATCAACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1589863 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGG
1589928 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTCGATGATTTTGG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTCGATGATTTTGG
1589992 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAA
1590057 AAAAAA
391 AAAAAA
1590063 TATCGACACAAACTATATTAGTG-CGACACATTATTTAGACATA-TATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
* *
1590126 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTTGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATAATTTTGGGAT
1590191 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
* *
1590256 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGG
* * * *
1590321 TAGACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG--GTCGATGATTTT
* *
1590386 GGGATTGACACTTTTTATATATGGATCAACACTTTATGG
324 GGGATCGACACTTTTTATATATGGATCGACACTTTATGG
1590425 TAAATTTGCC
Statistics
Matches: 731, Mismatches: 18, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
392 33 0.05
393 298 0.41
394 123 0.17
395 220 0.30
396 57 0.08
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (396 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATAATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAA
AAAAAA
Found at i:1592386 original size:33 final size:33
Alignment explanation
Indices: 1592349--1592414 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1592339 CATCTTAATA
*
1592349 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1592382 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1592415 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1592473 original size:21 final size:20
Alignment explanation
Indices: 1592448--1592511 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
1592438 CCCCTTATGC
*
1592448 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGT-TCTCTTCGACT
* *
1592469 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAG-TTCTCTTCGACT
**
1592490 CGATCAAGTTCTCTTCGACT
1 CTCTCAAGTTCTCTTCGACT
1592510 CT
1 CT
1592512 TGATTGTCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 12 0.35
21 21 0.62
22 1 0.03
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (20 bp):
CTCTCAAGTTCTCTTCGACT
Found at i:1594936 original size:20 final size:20
Alignment explanation
Indices: 1594909--1594955 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1594899 TCCGGTAACG
1594909 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1594928 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1594949 TTTTACC
1 TTTTACC
1594956 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1594998 original size:178 final size:179
Alignment explanation
Indices: 1594698--1595166 Score: 658
Period size: 178 Copynumber: 2.6 Consensus size: 179
1594688 CGTACTTACG
* * * *
1594698 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1594763 TATCATATTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTAAAGTATCGACACATTATAG
66 TATCATATTTTACCTGTTATATCGTT-TGGATCGATACATTTTTAAAAGTATCGACACATTATAG
* *
1594828 GCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
1594877 -AAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1594941 TATCATATTTTTACCTGGTATATCGTTTGGATCGATACATTTTTAAAAGTATCGACACTTTATAG
66 TATCATA-TTTTACCTGTTATATCGTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAG
** *
1595006 GATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * *
1595056 AAAGTACCGACACTTTAAATGTATCTGGTAGCGCTTGACCGG-TTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* *
1595119 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAA
65 TTATCATA-TTTTACCTGTTATATCG-TTTGGATCGATACATTTTTAA
1595167 TTTGGATCGA
Statistics
Matches: 259, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
178 144 0.56
179 60 0.23
180 55 0.21
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (179 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTACCTGTTATATCGTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAGG
AGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:1595641 original size:226 final size:223
Alignment explanation
Indices: 1595231--1595703 Score: 824
Period size: 225 Copynumber: 2.1 Consensus size: 223
1595221 ACCTACTTTT
1595231 ATAAGTATGGACACTTTTATAAAAATGATATATACTTCTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTCTTTGAAAGTTATGTAATTTATGTTTCA
1595296 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
66 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
1595361 TATTATTTGATTGTTTTGATTTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCA
131 AATTATTTGATTGTTTTGATTTTTATAAAATATTATTTAGAATTTAAATTTAAC-A-ATTAACCA
*
1595426 AATATAATAATAA-ATATGTTTCAACAGTGAA
194 AAGATAATAATAATATAT-TTTC-ACAGTGAA
*
1595457 ATAAGTATGGACACTTTTATAAAAATGATATATA-TTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTCTTTGAAAGTTATGTAATTTATGTTTCA
* *
1595521 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
* *
1595586 AATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATTAACTAA
131 AATTATTTGATTGTTTTGAT-TTTTATAAAATATTATTTAGAATTTAAATTTAACAATTAACCAA
1595651 AGATAATAATAATATATTTTCACAGTGAA
195 AGATAATAATAATATATTTTCACAGTGAA
1595680 ATAAGTATGGACACTTTTATAAAA
1 ATAAGTATGGACACTTTTATAAAA
1595704 GGATAGATAA
Statistics
Matches: 238, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
223 32 0.13
224 23 0.10
225 116 0.49
226 67 0.28
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (223 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTCTTTGAAAGTTATGTAATTTATGTTTCA
ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
AATTATTTGATTGTTTTGATTTTTATAAAATATTATTTAGAATTTAAATTTAACAATTAACCAAA
GATAATAATAATATATTTTCACAGTGAA
Found at i:1602972 original size:19 final size:20
Alignment explanation
Indices: 1602933--1602972 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1602923 TGGTTCACGG
1602933 AATGTAAGATTACCAGTGGA
1 AATGTAAGATTACCAGTGGA
1602953 AATGTAAGATTACCAG-GGA
1 AATGTAAGATTACCAGTGGA
1602972 A
1 A
1602973 TAAGATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (20 bp):
AATGTAAGATTACCAGTGGA
Found at i:1602978 original size:16 final size:19
Alignment explanation
Indices: 1602931--1602981 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
1602921 TTTGGTTCAC
*
1602931 GGAATGTAAGATTACCAGT
1 GGAAAGTAAGATTACCAGT
1602950 GGAAATGTAAGATTACCAG-
1 GGAAA-GTAAGATTACCAGT
1602969 GG-AA-TAAGATTAC
1 GGAAAGTAAGATTAC
1602982 TGAGAATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.30
18 2 0.07
19 6 0.20
20 13 0.43
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (19 bp):
GGAAAGTAAGATTACCAGT
Found at i:1603201 original size:39 final size:39
Alignment explanation
Indices: 1603121--1603202 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
1603111 AACAAGTTGG
* *
1603121 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTAAAAATCAT
*
1603160 AAAATATTTATATATATATT-TTTTAAAAATTAAAAAT-AT
1 AAAATATTTATATAT-T-TTCTTTAAAAAATTAAAAATCAT
1603199 AAAA
1 AAAA
1603203 AGATTTAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 21 0.55
40 15 0.39
41 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:1609458 original size:32 final size:32
Alignment explanation
Indices: 1609417--1609492 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1609407 CATTATGCTT
*
1609417 GGAGCATTTCTAGTTGAAACAATCAAACCTGG
1 GGAGCATTTCTAGTTGAAACAATCAAACCTGA
1609449 GGAGCATTTCTAGTTGAAACAATCAAACCTGA
1 GGAGCATTTCTAGTTGAAACAATCAAACCTGA
*
1609481 GGAGCATATCTA
1 GGAGCATTTCTA
1609493 CCAATTAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (32 bp):
GGAGCATTTCTAGTTGAAACAATCAAACCTGA
Found at i:1616315 original size:89 final size:93
Alignment explanation
Indices: 1616216--1616387 Score: 280
Period size: 93 Copynumber: 1.9 Consensus size: 93
1616206 TATCCATAAA
1616216 AATTGAAATAATAATAAACATAAT-G-AT-TTTATTTATTTATTTTCTTTATTTTTGAACAATAA
1 AATTGAAATAATAATAAACATAATGGTATATTTATTTATTTATTTTCTTTATTTTTGAACAATAA
*
1616278 TGTGACA-TATTATTATTAGTAGATACC
66 TGTGACATTATCATTATTAGTAGATACC
* *
1616305 AATTGAAATAATAATAAACGTAATGGTTTTATTTATTTATTTATTTTCTTTATTTTTGAACAATA
1 AATTGAAATAATAATAAACATAATGG-TATATTTATTTATTTATTTTCTTTATTTTTGAACAATA
1616370 ATGTGACATTATCATTAT
65 ATGTGACATTATCATTAT
1616388 CAAATTTATT
Statistics
Matches: 75, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
89 23 0.31
90 1 0.01
92 1 0.01
93 42 0.56
94 8 0.11
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (93 bp):
AATTGAAATAATAATAAACATAATGGTATATTTATTTATTTATTTTCTTTATTTTTGAACAATAA
TGTGACATTATCATTATTAGTAGATACC
Found at i:1620559 original size:13 final size:14
Alignment explanation
Indices: 1620529--1620575 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1620519 TAAGTATAAA
1620529 TATAATTTAAATTC
1 TATAATTTAAATTC
*
1620543 TATATTTTAAATT-
1 TATAATTTAAATTC
*
1620556 TATAATAT-AATGTC
1 TATAATTTAAAT-TC
1620570 TATAAT
1 TATAAT
1620576 GAACATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 3 0.11
13 7 0.25
14 18 0.64
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (14 bp):
TATAATTTAAATTC
Found at i:1621860 original size:2 final size:2
Alignment explanation
Indices: 1621855--1621880 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1621845 AATTTTTTTA
1621855 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
1621881 TTTTTGTTGA
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:1630297 original size:270 final size:269
Alignment explanation
Indices: 1629811--1630358 Score: 1015
Period size: 270 Copynumber: 2.0 Consensus size: 269
1629801 TTTGGAAAGA
*
1629811 ACTACGGGTAAAAGAAGAAAAGTCTCATGACACAAATTGATATGGTTTCCTCTACACGTCCCCAA
1 ACTATGGGTAAAAGAAGAAAAGTCTCATGACACAAATTGATATGGTTTCCTCTACACGTCCCCAA
* *
1629876 ACATAGCATGATTACATAGATGTCACTTCTGGATAGACTCCCAACTATGGAGAGGCTCCAAAGAA
66 ACATAACATGATTACATAGATGTCACTTCTGGATAGACTCCCAACTAGGGAGAGGCTCCAAAGAA
1629941 TGGGAATTGTTACCATTGGTTCATGCATAATCTACAATGAAACTACGGAGACTAGGGACCATCTG
131 TGGGAATTGTTACCATTGGTTCATGCATAATCTACAATGAAACTACGGAGACTAGGGACCATCTG
1630006 TTTAGTGAGTGCTATCTAGCAGTTTCCTTATGGAAGGTTATTCCGAATCTCTCTGGCTTAAGCAC
196 TTTAGTGAGTGCTATCTAGCAGTTTCCTTATGGAAGGTTATTCCGAATCTCTCTGGCTTAAGCAC
1630071 TCATATTTT
261 TCATATTTT
* *
1630080 ACTATAGGGTAAAAGAAGAAAAGTCTCATGGCACAATTTGATATGGTTTCCTCTACACGTCCCCA
1 ACTAT-GGGTAAAAGAAGAAAAGTCTCATGACACAAATTGATATGGTTTCCTCTACACGTCCCCA
* *
1630145 AATATAACATGATTACATAGATGTCACTTCTGGATAGACTCCCAATTAGGGAGAGGCTCCAAAGA
65 AACATAACATGATTACATAGATGTCACTTCTGGATAGACTCCCAACTAGGGAGAGGCTCCAAAGA
*
1630210 ATGGGAATTGTTACCATTGGTTCATGCATAATCTACAATGAAACTACGGAGACTAGGGAGCATCT
130 ATGGGAATTGTTACCATTGGTTCATGCATAATCTACAATGAAACTACGGAGACTAGGGACCATCT
1630275 GTTTAGTGAGTGCTATCTAGCAGTTTCCTTATGGAAGGTTATTCCGAATCTCTCTGGCTTAAGCA
195 GTTTAGTGAGTGCTATCTAGCAGTTTCCTTATGGAAGGTTATTCCGAATCTCTCTGGCTTAAGCA
1630340 CTCATATTTT
260 CTCATATTTT
1630350 ACTATGGGT
1 ACTATGGGT
1630359 GAGCATGATA
Statistics
Matches: 270, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
269 8 0.03
270 262 0.97
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (269 bp):
ACTATGGGTAAAAGAAGAAAAGTCTCATGACACAAATTGATATGGTTTCCTCTACACGTCCCCAA
ACATAACATGATTACATAGATGTCACTTCTGGATAGACTCCCAACTAGGGAGAGGCTCCAAAGAA
TGGGAATTGTTACCATTGGTTCATGCATAATCTACAATGAAACTACGGAGACTAGGGACCATCTG
TTTAGTGAGTGCTATCTAGCAGTTTCCTTATGGAAGGTTATTCCGAATCTCTCTGGCTTAAGCAC
TCATATTTT
Found at i:1635275 original size:42 final size:44
Alignment explanation
Indices: 1635213--1635317 Score: 121
Period size: 42 Copynumber: 2.5 Consensus size: 44
1635203 TATTGAAATA
* *
1635213 TAATAAAATATTTTATATTTA-AAAAGTATTGA-TAATATATTTTT
1 TAATAAAATATTTTATATTTATAAAA-TATT-ATTAATAAATTATT
1635257 TAATAAAAT-TTTTA-ATTTATAAAATATTATTAATAAATTATT
1 TAATAAAATATTTTATATTTATAAAATATTATTAATAAATTATT
* *
1635299 TAA-AATATCTTTTATATTT
1 TAATAAAATATTTTATATTT
1635318 TTATTATAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
41 5 0.09
42 27 0.50
43 13 0.24
44 9 0.17
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (44 bp):
TAATAAAATATTTTATATTTATAAAATATTATTAATAAATTATT
Found at i:1635398 original size:13 final size:14
Alignment explanation
Indices: 1635368--1635400 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1635358 TAAGTATAAA
1635368 TATAATTTAAATTC
1 TATAATTTAAATTC
*
1635382 TATATTTTAAATT-
1 TATAATTTAAATTC
1635395 TATAAT
1 TATAAT
1635401 ATAATAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TATAATTTAAATTC
Found at i:1636674 original size:2 final size:2
Alignment explanation
Indices: 1636669--1636706 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1636659 AATTTTTTTA
1636669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1636707 TGTTGATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1637537 original size:32 final size:32
Alignment explanation
Indices: 1637501--1637564 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1637491 AAGGCAAGGA
1637501 ACATCAGTCTCAATAAATTAAGTCATGATTTT
1 ACATCAGTCTCAATAAATTAAGTCATGATTTT
1637533 ACATCAGTCTCAATAAATTAAGTCATGATTTT
1 ACATCAGTCTCAATAAATTAAGTCATGATTTT
1637565 TCCAAGCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (32 bp):
ACATCAGTCTCAATAAATTAAGTCATGATTTT
Found at i:1640376 original size:24 final size:24
Alignment explanation
Indices: 1640349--1640403 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
1640339 ATAAACGAGC
* * *
1640349 TTATAATCGAGTCGATAAATAAAT
1 TTATAAACGAATCAATAAATAAAT
* *
1640373 TTATAAACGAATCAATAAATGAGT
1 TTATAAACGAATCAATAAATAAAT
1640397 TTATAAA
1 TTATAAA
1640404 AAGTTACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (24 bp):
TTATAAACGAATCAATAAATAAAT
Found at i:1647945 original size:161 final size:158
Alignment explanation
Indices: 1647749--1648068 Score: 613
Period size: 161 Copynumber: 2.0 Consensus size: 158
1647739 GTGCTTCTCA
1647749 GTAGAAGAGTTGGTTTCGGTTGGTTCGGAGTGCAAGAACAGCATCAACTTGCATCAAATGTGGAC
1 GTAGAAGAGTTGGTTTCGGTTGGTTCGGAGTGCAAGAACAGCATCAACTTGCATCAAATGTGGAC
1647814 TTGAATTCTCAATTTATAAAGAAAGAAAAAACAGTTGCAACTCTATGGCTGTTGCTATGGTTTTT
66 TTGAATTCTCAATTTATAAAGAAAGAAAAAACAGTTGCAACTCTATGGCTGTTGCTATGGTTTTT
1647879 TCCTTAATTATTATATGCTGTGGTGGGTC
131 TCCTTAATT-TTATATGCTGTGGTGGGTC
1647908 GTAGAAGAGTTGGGTTTCGGTTTGGTTCGGAGTGCAAGAACAGCATCAACTTGCATCAAATGTGG
1 GTAGAAGAGTT-GGTTTCGG-TTGGTTCGGAGTGCAAGAACAGCATCAACTTGCATCAAATGTGG
1647973 ACTTGAATTCTCAATTTATAAAGAAAGAAAAAACAGTTGCAACTCTATGGCTGTTGCTATGGTTT
64 ACTTGAATTCTCAATTTATAAAGAAAGAAAAAACAGTTGCAACTCTATGGCTGTTGCTATGGTTT
1648038 TTTCCTTAATTTTATATGCTGTGGTGGGTC
129 TTTCCTTAATTTTATATGCTGTGGTGGGTC
1648068 G
1 G
1648069 ATACTTTGAG
Statistics
Matches: 159, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
159 11 0.07
160 28 0.18
161 120 0.75
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (158 bp):
GTAGAAGAGTTGGTTTCGGTTGGTTCGGAGTGCAAGAACAGCATCAACTTGCATCAAATGTGGAC
TTGAATTCTCAATTTATAAAGAAAGAAAAAACAGTTGCAACTCTATGGCTGTTGCTATGGTTTTT
TCCTTAATTTTATATGCTGTGGTGGGTC
Found at i:1649019 original size:2 final size:2
Alignment explanation
Indices: 1649007--1649040 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1648997 GCCGGTTGTA
*
1649007 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1649041 AAAATTGAGA
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:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1649980 original size:29 final size:28
Alignment explanation
Indices: 1649933--1649998 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
1649923 GTCAGATGAC
*
1649933 CGGTTCAGCCGGTTCGATCCAAAGGTGA
1 CGGTTCAGCCGATTCGATCCAAAGGTGA
* *
1649961 TCGGTTCAGCCGATTTGATCCAAGGGTGA
1 -CGGTTCAGCCGATTCGATCCAAAGGTGA
1649990 CTGGTTCAG
1 C-GGTTCAG
1649999 TCGGTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.26
Consensus pattern (28 bp):
CGGTTCAGCCGATTCGATCCAAAGGTGA
Found at i:1655720 original size:12 final size:11
Alignment explanation
Indices: 1655703--1655764 Score: 58
Period size: 12 Copynumber: 5.7 Consensus size: 11
1655693 TTCATTTAAA
1655703 TATTATTTATAT
1 TATTA-TTATAT
1655715 TATTATTATAAT
1 TATTATTAT-AT
1655727 TATTATTATA-
1 TATTATTATAT
*
1655737 -ATTATTTTAT
1 TATTATTATAT
* *
1655747 TATTAATA-AA
1 TATTATTATAT
1655757 TATTATTA
1 TATTATTA
1655765 CAGGCCCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 8 0.19
10 8 0.19
11 10 0.24
12 16 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATTATAT
Found at i:1655764 original size:3 final size:3
Alignment explanation
Indices: 1655703--1655751 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
1655693 TTCATTTAAA
* *
1655703 TAT TAT T-T ATAT TAT TAT TAT AAT TAT TAT TAT AAT TAT T-T TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1655747 TAT TA
1 TAT TA
1655752 ATAAATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.08
3 35 0.90
4 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1661236 original size:15 final size:15
Alignment explanation
Indices: 1661216--1661247 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1661206 ATCAATACCT
1661216 TTTTGCATACATACA
1 TTTTGCATACATACA
*
1661231 TTTTGCATACATTCA
1 TTTTGCATACATACA
1661246 TT
1 TT
1661248 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:1669526 original size:92 final size:92
Alignment explanation
Indices: 1669369--1670197 Score: 1417
Period size: 92 Copynumber: 9.0 Consensus size: 92
1669359 ACAAGTGCCG
*
1669369 TGTGCTTATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1669434 AACCAATCATTGAAATTGGAAGATGAA
66 AACCAATCATTGAAATTGGAAGATGAA
1669461 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1669526 AACCAATCATTGAAATTGGAAGATGAA
66 AACCAATCATTGAAATTGGAAGATGAA
1669553 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1669618 AACCAATCATTGAAATTGGAAGATGAA
66 AACCAATCATTGAAATTGGAAGATGAA
1669645 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1669710 AACCAATCATTGAAATTGGAAGATGAA
66 AACCAATCATTGAAATTGGAAGATGAA
1669737 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1669802 AACCAATCATTGAAATTGGAAGATGAA
66 AACCAATCATTGAAATTGGAAGATGAA
1669829 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
* * * *
1669894 AACCAGTTATTGAATTTGGAAGAGGAA
66 AACCAATCATTGAAATTGGAAGATGAA
*
1669921 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
*
1669986 AACCAATCATTGAATTTGGAAGATGAA
66 AACCAATCATTGAAATTGGAAGATGAA
* * * *
1670013 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTTTAAACCACAT
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
* * * * *
1670078 AATCAGTTATTGAATTTGGAAGAGGAA
66 AACCAATCATTGAAATTGGAAGATGAA
* * * * *
1670105 TGTGCTCATAGCATCTTCTGTAAATGTTCTTTTAGTTATCTGATCTGGTTTGATATAAAACC-CA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCACA
* * **
1670169 GAACCAATAATTGGAATTAAAAGATGAA
65 GAACCAATCATTGAAATTGGAAGATGAA
1670197 T
1 T
1670198 TGCATGATCG
Statistics
Matches: 704, Mismatches: 32, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
92 699 0.99
93 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (92 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAG
AACCAATCATTGAAATTGGAAGATGAA
Found at i:1671087 original size:113 final size:113
Alignment explanation
Indices: 1670884--1671782 Score: 970
Period size: 113 Copynumber: 7.8 Consensus size: 113
1670874 GCAAAGATTC
* * * * * *
1670884 AAATACATCAATTGATGGATCAGCATTACCAGA-AAGAGTTCATAATAAGAAGAACTCATCTAAA
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAA
* * * *
1670948 GAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * *
1670997 GAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAAGGAGAAGAACTCATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
1671062 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * *
1671110 GAATTCATCATTTGATGGATTAAAATTTCCATGTAG--AGTTCATAATGAGAAGAACTCATCATC
1 AAATTCATCACTTGATGGATCAACATTTCCA-G-AGAAAGTTCATAATGAGAAGAA--C-TCATC
*
1671173 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTT
61 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * * *
1671226 GAATTCATCATTTGATGGATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCACTT
1 AAATTCATCACTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCAT--C-T
* * *
1671290 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * **** *
1671342 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
1671407 AAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG-TT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * *
1671454 CAAATTCATTACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTTATTTGAA
1 -AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
1671519 G-AGGAAGAAAAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTG-TT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * *
1671566 CAAATTCATTACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTTATTTGAA
1 -AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
1671631 G-AGGAAGAAGAAGTTCACAATGAGAAGAGTTTGTTCAACCTTTTGCAT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * * *
1671679 -AATTCTATCACAGAAGCAGATAGATTAGCATAAACCTTTCCAGAGAAAGTTCATAATAAGAAGA
1 AAATTC-AT--C---A-C---TTGA-T-GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGA
* * * *
1671743 ACTCATATGAAGAAGAAAGAAGAAGTTCAAAATAAGAAGA
54 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1671783 GCTTATTCAA
Statistics
Matches: 691, Mismatches: 67, Indels: 45
0.86 0.08 0.06
Matches are distributed among these distances:
111 5 0.01
112 152 0.22
113 246 0.36
114 5 0.01
115 5 0.01
116 204 0.30
117 1 0.00
118 1 0.00
121 3 0.00
122 1 0.00
123 44 0.06
124 24 0.03
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (113 bp):
AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
Found at i:1671303 original size:229 final size:224
Alignment explanation
Indices: 1670881--1671675 Score: 942
Period size: 229 Copynumber: 3.5 Consensus size: 224
1670871 TTAGCAAAGA
* * * * * * *
1670881 TTCAAATACATCAATTGATGGATCAGCATTACCAGAAAGAGTTCATAATAAGAAGAACTCATCTA
1 TTCAAATTCATCACTTGATGGATCAACATTTCCAG-TAGAGTTCATAATAAGAAGAATTCATCTG
* * * * *
1670946 AAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATCCATCACTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTG
*
1671011 ATGGATCAACATTTCCAGAGAAAGTTCATAAGGAGAAGAACTCAT-C-TGAAGAAGGAAGAAGAA
130 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATACTTGAAGAA-G--GAAGAA
1671074 GTTCATAATGAGAAGAATTTGTTTAACCTTTTG
192 GTTCATAATGAGAAGAATTTGTTTAACCTTTTG
** * * * *
1671107 TTTGAATTCATCATTTGATGGATTAAAATTTCCATGTAGAGTTCATAATGAGAAGAACTCATCAT
1 TTCAAATTCATCACTTGATGGATCAACATTTCCA-GTAGAGTTCATAATAAGAAGAA-T--TCAT
* *
1671172 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTGAATTCATCAT
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
* * *
1671237 TTGATGGATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCACTTGAAGAAGGAAG
127 TTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCAT-ACTTGAAGAAGGAAG
*
1671301 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
190 AAG---TTCATAATGAGAAGAATTTGTTTAACCTTTTG
* * * * * *
1671339 CTCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTG
1 TTCAAATTCATCACTTGATGGATCAACATTTCCAG-TAGAGTTCATAATAAGAAGAATTCATCTG
* * * ** *
1671404 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAAATTCATTACTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTG
* *
1671469 ATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACT--TATTTGAAG-AGGAAGAAAAA
130 ATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATACTTGAAGAAGGAAG---AA
* *
1671531 GTTCATAATAAGAAGAACTTGTTTAACCTTTTG
192 GTTCATAATGAGAAGAATTTGTTTAACCTTTTG
* *
1671564 TTCAAATTCATTACTTGATGGATCAACATTTCCAG-AGAAAGTTCATAATAAGAAGAACTT-ATT
1 TTCAAATTCATCACTTGATGGATCAACATTTCCAGTAG--AGTTCATAATAAGAAGAA-TTCATC
* *
1671627 TGAAG-AGGAAGAAGAAGTTCACAATGAGAAGAGTTTGTTCAACCTTTTG
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
1671676 CATAATTCTA
Statistics
Matches: 489, Mismatches: 61, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
223 1 0.00
224 39 0.08
225 89 0.18
226 54 0.11
227 2 0.00
228 4 0.01
229 212 0.43
230 1 0.00
231 4 0.01
232 83 0.17
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (224 bp):
TTCAAATTCATCACTTGATGGATCAACATTTCCAGTAGAGTTCATAATAAGAAGAATTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGA
TGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATACTTGAAGAAGGAAGAAGTTC
ATAATGAGAAGAATTTGTTTAACCTTTTG
Found at i:1671811 original size:124 final size:123
Alignment explanation
Indices: 1671592--1671818 Score: 355
Period size: 124 Copynumber: 1.8 Consensus size: 123
1671582 TGGATCAACA
* * * * *
1671592 TTTCCAGAGAAAGTTCATAATAAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCACAATGAGAA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAGAAAGAAGAAGTTCAAAATAAGAA
* * * *
1671657 GAGTTTGTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATAAACC
66 GAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAGATAGATTAGCATAAACC
1671715 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAAGAAAGAAGAAGTTCAAAATAAGA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAG-AGAAAGAAGAAGTTCAAAATAAGA
*
1671780 AGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAG
65 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAG
1671819 GAAAGAGGTC
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
123 38 0.41
124 55 0.59
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.26
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAGAAAGAAGAAGTTCAAAATAAGAA
GAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAGATAGATTAGCATAAACC
Found at i:1671887 original size:124 final size:123
Alignment explanation
Indices: 1671594--1671887 Score: 344
Period size: 124 Copynumber: 2.4 Consensus size: 123
1671584 GATCAACATT
* * * *
1671594 TCCAGAGAAAGTTCATAATAAGAAGAACTTATTTGAAG-AG-GAAGAAGAAGTTCACAATGAGAA
1 TCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAAGAGAAGAAGAAGTTCAAAATAAGAA
* * * * * * * *
1671657 GAGTTTGTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATAAACC
66 GAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAAGAGATCAACATAAACC
1671715 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAAGA-AAGAAGAAGTTCAAAATAAG
1 --TCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAAGAGAAGAAGAAGTTCAAAATAAG
* * * * *
1671779 AAGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAAGAGGTCAACATCATCC
64 AAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAAGAGATCAACATAAACC
* * *
1671839 -CCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 TCCAG-AGAAAGTTCATAATAAGAAGAACTCATATGAAG-AAGAGAAGAA
1671888 TTTATTCAAC
Statistics
Matches: 146, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
121 4 0.03
122 30 0.21
123 40 0.27
124 72 0.49
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (123 bp):
TCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAAGAGAAGAAGAAGTTCAAAATAAGAA
GAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAAGAGATCAACATAAACC
Found at i:1672104 original size:3 final size:3
Alignment explanation
Indices: 1672019--1672088 Score: 90
Period size: 3 Copynumber: 23.7 Consensus size: 3
1672009 TTCATTTAAA
* * *
1672019 TAT TAT T-T ATAT CAT TAT TAT AAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1672064 TAT TAT TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1672089 ATAATAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 3 0.05
3 54 0.93
4 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1676564 original size:48 final size:48
Alignment explanation
Indices: 1676508--1676605 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
1676498 TTGTGCGGAG
1676508 AGAATTAGTTGAAACTGACAGATTATCGAAATTCTTGTCTCTCAATTT
1 AGAATTAGTTGAAACTGACAGATTATCGAAATTCTTGTCTCTCAATTT
1676556 AGAATTAGTTGAAACTGACAGATTATCGAAATTCTTGTCTCTCAATTT
1 AGAATTAGTTGAAACTGACAGATTATCGAAATTCTTGTCTCTCAATTT
1676604 AG
1 AG
1676606 TTAATTGGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (48 bp):
AGAATTAGTTGAAACTGACAGATTATCGAAATTCTTGTCTCTCAATTT
Found at i:1680191 original size:2 final size:2
Alignment explanation
Indices: 1680184--1680214 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1680174 GTAAGAGCTT
1680184 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1680215 GCAACAGAAG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1681557 original size:16 final size:15
Alignment explanation
Indices: 1681536--1681579 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
1681526 ATCTAAGTGC
1681536 GACAATGCACCTATAT
1 GACAATGCACC-ATAT
*
1681552 GACAATGGACCATAT
1 GACAATGCACCATAT
1681567 G-CAA-GCACCATAT
1 GACAATGCACCATAT
1681580 TCACATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 8 0.31
14 3 0.12
15 5 0.19
16 10 0.38
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (15 bp):
GACAATGCACCATAT
Found at i:1682980 original size:2 final size:2
Alignment explanation
Indices: 1682975--1683006 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1682965 TTGCTATAAT
1682975 TA TA TA 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 TA TA TA
1683007 ACAAAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1683537 original size:22 final size:22
Alignment explanation
Indices: 1683512--1683556 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1683502 TGATTAAACA
*
1683512 TTAA-TAATTTAATTAATATTAT
1 TTAATTAA-TTAAATAATATTAT
*
1683534 TTAATTAATTAAATAATCTTAT
1 TTAATTAATTAAATAATATTAT
1683556 T
1 T
1683557 AAAATTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTAATTAAATAATATTAT
Found at i:1705742 original size:10 final size:10
Alignment explanation
Indices: 1705727--1705755 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1705717 GCGGCGCCTA
1705727 AAAAACGGCT
1 AAAAACGGCT
1705737 AAAAACGGCT
1 AAAAACGGCT
1705747 AAAAACGGC
1 AAAAACGGC
1705756 GTGACCGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.21, G:0.21, T:0.07
Consensus pattern (10 bp):
AAAAACGGCT
Found at i:1706609 original size:182 final size:182
Alignment explanation
Indices: 1706296--1706743 Score: 702
Period size: 182 Copynumber: 2.5 Consensus size: 182
1706286 ACTTTTTTAC
* * *
1706296 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATATTATATTGTTATGGATCGA
1 TACCCGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTATTATATTGTTATGGATCGA
* *
1706361 TATATTTTTATAAAGTATCGACACTTTATTGACACTATAACTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTGACACTATAACTTCTTCTCTTTTAAATTCCAAAAG
* **
1706426 TGTCGATACTTATAATAAAGTATCGACACTT-TCAACATATCCGGTAGTTCTT
131 TGTCGATACTTATAATAAAATATCGACA-TTATCAACATATCCGGTAGAGCTT
*
1706478 TACCCGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGA
1 TACCCGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTATTATATTGTTATGGATCGA
* * *
1706543 TACATTTTTATAAAGTATCGACACTTTATT-AGCGCTATAATTTCTTCTCTTTTAAATTCTAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTGA-CACTATAACTTCTTCTCTTTTAAATTCCAAAA
1706607 GTGTCGATACTTATAATAAAATATCGACATTATCAACATATCCGGTAGAGCTT
130 GTGTCGATACTTATAATAAAATATCGACATTATCAACATATCCGGTAGAGCTT
* ** * * *
1706660 TACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAA
1 TACCCGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTATTATATTGTTATGGATCGA
1706725 TACATTTTTATAAAGTATC
66 TACATTTTTATAAAGTATC
1706744 TACATTTTCA
Statistics
Matches: 245, Mismatches: 19, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
181 3 0.01
182 242 0.99
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (182 bp):
TACCCGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTATTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTGACACTATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAATATCGACATTATCAACATATCCGGTAGAGCTT
Found at i:1707204 original size:113 final size:112
Alignment explanation
Indices: 1706622--1707868 Score: 1935
Period size: 112 Copynumber: 11.1 Consensus size: 112
1706612 GATACTTATA
* * * *
1706622 ATAAAATATCGACA-TTATCAACATATCCGGTAGAGCTTTACCTGTTTTGTCATTTATAGACCGA
1 ATAAAGTATCGACACTT-TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
*
1706686 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
1706734 ATAAAGTATCTACATTTTCAATATATCCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1706799 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1706845 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1706910 TTTGTCA-TTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1706956 ATAAAGTATCGACACTATCAATATAT-CAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1707020 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
1707067 ATAAAGTATCGACACTTTCGATATATCCAGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * * *
1707132 TTTATCATTTTTTTTACTTGTTATGTTATTATTGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1707180 ATAAAGTATCGACACTTTCAATATATCCGGTAGTGCTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1707245 TTTGTCATTTTTTTTACCTCTTATATTATTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * * *
1707293 ATAAAGTATCGCCACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACTGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1707358 TTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1707405 ATAAAGTATCGACACTTTCAATATATCCGGTAGTGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
1707470 TTTGTCATTTTTTTACCTGTTATGTTATTATTGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
1707517 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1707582 TTTGTCATTTTTTTACCTGTTATACTATTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * ** *
1707629 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGATTGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1707694 TTTGTCATTTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
1707742 ATAAAGTATCGACACTTTCAATATATCTGGTAGCACTTTACCTGTTTTGTCATTTTTAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * ** *
1707807 TTTATCATTTTTTTACCTCTTATATTGTTATGGATTAATACATTTTG
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1707854 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
1707869 AAACCGACAA
Statistics
Matches: 1040, Mismatches: 90, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
110 44 0.04
111 229 0.22
112 462 0.44
113 305 0.29
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:1707532 original size:337 final size:336
Alignment explanation
Indices: 1706622--1707868 Score: 1991
Period size: 337 Copynumber: 3.7 Consensus size: 336
1706612 GATACTTATA
* *
1706622 ATAAAATATCGACATTATCAACATATCCGGTAGA-GCTTTACCTGTTTTGTCATTTATAGACCGA
1 ATAAAGTATCGACACTATCAACATATCCGGTA-ACGCTTTACCTGTTTTGTCATTTATAGACCGA
* * *
1706686 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCA-ATACATTTTTATAAAGTATCTACATT
65 TTTTGTCATTTTTTTACATGTTATATTGTTATGGAT-AGATACATTTTTATAAAGTATCGACACT
* * *
1706750 TTCAATATATCCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCA-TTTTTTAC
129 TTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTAC
* *
1706814 CTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGC
194 CTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGC
*
1706879 GCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCA-TTTTTTACCTGTTATATTATTATGGA
259 GCTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTACCTGTTATATTATTATGGA
1706943 TCGATACATTTTT
324 TCGATACATTTTT
* * * *
1706956 ATAAAGTATCGACACTATCAATATAT-CAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
1707020 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTTT
* * * *
1707085 CGATATATCCAGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTTACT
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTATCA-TTTTTTTACC
* * *
1707150 TGTTATGTTATTATTGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGTG
195 TGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCG
*
1707215 CTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTTACCTCTTATATTATTATGGA
260 CTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCA-TTTTTTTACCTGTTATATTATTATGGA
1707280 TCGATACATTTTT
324 TCGATACATTTTT
* * *
1707293 ATAAAGTATCGCCACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACTGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGAT
1707358 TTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTTT
* * *
1707423 CAATATATCCGGTAGTGTTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCT
* *
1707488 GTTATGTTATTATTGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGC
196 GTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGC
*
1707553 TTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTACCTGTTATACTATTATGGATC
261 TTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTACCTGTTATATTATTATGGATC
1707618 GATACATTTTT
326 GATACATTTTT
* * **
1707629 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGATTGAT
1 ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
1707694 TTTGTCATTTTTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
66 TTTGTCA-TTTTTTTACATGTTATATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTT
* * *
1707759 TCAATATATCTGGTAGCACTTTACCTGTTTTGTCATTTTTAGACCGGTTTTATCATTTTTTTACC
130 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACC
* * ** *
1707824 TCTTATATTGTTATGGATTAATACATTTTGATAAAGTATCGACAC
195 TGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACAC
1707869 AAACCGACAA
Statistics
Matches: 847, Mismatches: 58, Indels: 13
0.92 0.06 0.01
Matches are distributed among these distances:
333 144 0.17
334 23 0.03
335 104 0.12
336 105 0.12
337 325 0.38
338 146 0.17
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (336 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACATGTTATATTGTTATGGATAGATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCT
GTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGC
TTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTACCTGTTATATTATTATGGATC
GATACATTTTT
Found at i:1708350 original size:20 final size:20
Alignment explanation
Indices: 1708325--1708396 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
1708315 TTTTCCCAAT
1708325 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
1708345 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1708365 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1708386 TCGCAATGCGA
1 TCGCAATGCGA
1708397 TACTGACTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1708410 original size:20 final size:20
Alignment explanation
Indices: 1708385--1708438 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1708375 AATTGGGAAA
1708385 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1708405 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
1708425 ATCGCAATGCGATA
1 ATCGCAATGCGATA
1708439 ATACAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1709038 original size:19 final size:19
Alignment explanation
Indices: 1708983--1709069 Score: 120
Period size: 19 Copynumber: 4.5 Consensus size: 19
1708973 TTCGAGAATG
1708983 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1709003 ACTATCGCAACCGCGAAATA
1 AAAATCGCAA-CGCGAAATA
1709023 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1709042 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1709061 AAAATCGCA
1 AAAATCGCA
1709070 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 35 0.58
20 22 0.37
21 3 0.05
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1709092 original size:19 final size:19
Alignment explanation
Indices: 1709065--1709249 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
1709055 GAAACCAAAA
*
1709065 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1709084 TCGAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1709103 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1709122 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1709142 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1709158 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1709175 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1709189 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1709208 TCCGCATTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1709228 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1709248 TC
1 TC
1709250 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 58 0.43
20 47 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1709142 original size:39 final size:38
Alignment explanation
Indices: 1709065--1709249 Score: 147
Period size: 33 Copynumber: 5.1 Consensus size: 38
1709055 GAAACCAAAA
*
1709065 TCGCATTGCGATTTTCATTTCGAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGAGTTGCGATTTTCATT
* *
1709103 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCG-AGTTGCGATTTTCATT
* * **
1709142 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGAGTTGCGATTTTCATT
* **
1709175 TCGCGTTGCGA--TTC-TCTC--GTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGAGTTGCGATTTTCATT
* * **
1709208 TCCGCATTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGAGTTGCGATTTTCATT
1709248 TC
1 TC
1709250 AACCAAAAGA
Statistics
Matches: 121, Mismatches: 15, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
31 2 0.02
33 39 0.32
34 9 0.07
35 1 0.01
36 3 0.02
37 1 0.01
38 22 0.18
39 30 0.25
40 14 0.12
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGAGTTGCGATTTTCATT
Found at i:1709226 original size:20 final size:19
Alignment explanation
Indices: 1709189--1709249 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
1709179 GTTGCGATTC
**
1709189 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATTCTCATT
1709208 TC-CGCATTGCGATTCTCATT
1 TCTCG--TTGCGATTCTCATT
*
1709228 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTCTCATT
1709248 TC
1 TC
1709250 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 25 0.71
21 2 0.06
22 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.16, T:0.44
Consensus pattern (19 bp):
TCTCGTTGCGATTCTCATT
Found at i:1711304 original size:42 final size:42
Alignment explanation
Indices: 1711244--1711366 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1711234 GCCCGACTCG
* * *
1711244 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1711286 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1711328 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1711367 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1711324 original size:21 final size:21
Alignment explanation
Indices: 1711300--1711366 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1711290 TCATTCCTCG
1711300 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1711321 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1711342 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1711363 AGAG
1 AGAG
1711367 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1712734 original size:14 final size:14
Alignment explanation
Indices: 1712715--1712750 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1712705 ATTGTTTAAT
1712715 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1712729 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1712743 TGATTTGT
1 TGATTTGT
1712751 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1712931 original size:19 final size:19
Alignment explanation
Indices: 1712909--1713059 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1712899 CGAAATTAAA
1712909 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1712928 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1712943 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
1712961 TTCACATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1712975 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1712994 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1713009 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1713027 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1713046 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1713060 GGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 45 0.48
20 10 0.11
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1712955 original size:33 final size:32
Alignment explanation
Indices: 1712913--1713039 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1712903 ATTAAATTCG
1712913 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
1712946 CGTTGCGATTTTCATTTCACATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1712979 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1713012 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1713040 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1712991 original size:66 final size:66
Alignment explanation
Indices: 1712906--1713038 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1712896 ACGCGAAATT
*
1712906 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
1712971 G
66 G
* *
1712972 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
1713037 G
66 G
1713038 A
1 A
1713039 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
G
Found at i:1715343 original size:12 final size:12
Alignment explanation
Indices: 1715326--1715350 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1715316 TCTTCGGGGA
1715326 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1715338 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1715350 C
1 C
1715351 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1715556 original size:24 final size:24
Alignment explanation
Indices: 1715522--1715575 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1715512 CTGAAACATC
* *
1715522 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1715546 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1715570 ATCAAA
1 ATCAAA
1715576 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1716659 original size:20 final size:20
Alignment explanation
Indices: 1716634--1716691 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1716624 ATTCATTTGA
1716634 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1716654 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1716674 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1716692 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1716765 original size:19 final size:18
Alignment explanation
Indices: 1716710--1716795 Score: 117
Period size: 19 Copynumber: 4.9 Consensus size: 18
1716700 GAAATGAAAA
1716710 TCGCATTGCGATTTTC--
1 TCGCATTGCGATTTTCAT
*
1716726 TCG--TTGTGATTTTCAT
1 TCGCATTGCGATTTTCAT
1716742 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCA-T
1716761 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCA-T
1716780 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1716796 TCGTTGCGAT
Statistics
Matches: 63, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
14 10 0.16
16 6 0.10
18 11 0.17
19 36 0.57
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (18 bp):
TCGCATTGCGATTTTCAT
Found at i:1716788 original size:38 final size:32
Alignment explanation
Indices: 1716710--1716805 Score: 129
Period size: 38 Copynumber: 2.8 Consensus size: 32
1716700 GAAATGAAAA
*
1716710 TCGCATTGCGATTTTCTCGTTGTGATTTTCAT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCAT
1716742 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCA-T
1716780 TCGCATTGCGATTTTCTCGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
1716806 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
32 16 0.28
33 7 0.12
35 6 0.11
37 11 0.19
38 17 0.30
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (32 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCAT
Found at i:1718842 original size:19 final size:18
Alignment explanation
Indices: 1718818--1718875 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 18
1718808 ATGGCTGGCT
1718818 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
1718837 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
1718851 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
1718869 ATCGCAA
1 ATCGCAA
1718876 CGACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 10 0.31
19 7 0.22
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:1718853 original size:14 final size:14
Alignment explanation
Indices: 1718834--1718891 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1718824 ATGCGAAATG
1718834 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1718848 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1718864 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1718880 AAAATCACAACG
1 AAAATCGCAACG
1718892 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1718876 original size:32 final size:33
Alignment explanation
Indices: 1718818--1718896 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1718808 ATGGCTGGCT
*
1718818 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1718851 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
1718883 ATCACAACGCGAAA
1 ATCGCAACGCGAAA
1718897 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1718925 original size:19 final size:19
Alignment explanation
Indices: 1718903--1718984 Score: 86
Period size: 18 Copynumber: 4.6 Consensus size: 19
1718893 GAAACACAAA
1718903 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1718922 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
1718940 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
1718956 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
1718973 TCGCATTGCGAT
1 TCGCATTGCGAT
1718985 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.05
16 4 0.07
17 4 0.07
18 21 0.38
19 17 0.31
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1718992 original size:19 final size:20
Alignment explanation
Indices: 1718970--1719012 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1718960 TGCGATTTTT
1718970 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
1718989 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
1719009 ATTT
1 ATTT
1719013 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:1719003 original size:20 final size:20
Alignment explanation
Indices: 1718978--1719023 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1718968 TTATTTCGCA
1718978 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
1718998 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
1719018 TTGCGA
1 TTGCGA
1719024 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1719522 original size:18 final size:18
Alignment explanation
Indices: 1719496--1719540 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1719486 GTCGATCAGA
* *
1719496 TGATTGCTCTAGGTGAGG
1 TGATAGCTCTAGGCGAGG
*
1719514 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTAGGCGAGG
*
1719532 TGATGGCTC
1 TGATAGCTC
1719541 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.40, T:0.29
Consensus pattern (18 bp):
TGATAGCTCTAGGCGAGG
Found at i:1720884 original size:20 final size:20
Alignment explanation
Indices: 1720859--1720896 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1720849 AATAGTTTCT
1720859 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1720879 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1720897 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1721185 original size:22 final size:22
Alignment explanation
Indices: 1721160--1721203 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1721150 GATTTAGATA
1721160 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1721182 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1721204 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1721457 original size:41 final size:41
Alignment explanation
Indices: 1721412--1721489 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1721402 CGAAAGTCAG
* * *
1721412 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
1721453 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
1721490 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:1721486 original size:20 final size:20
Alignment explanation
Indices: 1721392--1721486 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1721382 AATTATGTAT
*
1721392 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1721412 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
1721432 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
1721453 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1721473 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
1721487 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1721505 original size:41 final size:41
Alignment explanation
Indices: 1721412--1721507 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
1721402 CGAAAGTCAG
* * * ** *
1721412 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
1721453 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
1721495 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1721508 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:1724911 original size:66 final size:66
Alignment explanation
Indices: 1724733--1724925 Score: 235
Period size: 66 Copynumber: 2.9 Consensus size: 66
1724723 GGAAGAACTC
* * * *
1724733 ATTAAGTGACTTTT-ATAGTAAAAGAGATTGTTGTTCTCTTCAAAAAAACTTAAGTTTAAATAAT
1 ATTAAGTGA-TTTTAATAGTAAAAGAGAATGTTGTTCTCTT-AAAGAAACTTAAGTTTAAACAAC
1724797 TGT
64 TGT
* * * * *
1724800 ATTGAGTGACTTTAATAGTAAAAGAGAATGTTGTTCTCCTCAAGAAACTTAAGTTTAAGCAACTG
1 ATTAAGTGATTTTAATAGTAAAAGAGAATGTTGTTCTCTTAAAGAAACTTAAGTTTAAACAACTG
1724865 T
66 T
* * * * *
1724866 ATTAAGTGATTTTAATAGTAAAAGAGAATGTTATTTTATTTAAGAAATTTAAGTTTAAAC
1 ATTAAGTGATTTTAATAGTAAAAGAGAATGTTGTTCTCTTAAAGAAACTTAAGTTTAAAC
1724926 GATTGCGACT
Statistics
Matches: 107, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
66 75 0.70
67 32 0.30
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.38
Consensus pattern (66 bp):
ATTAAGTGATTTTAATAGTAAAAGAGAATGTTGTTCTCTTAAAGAAACTTAAGTTTAAACAACTG
T
Found at i:1725497 original size:15 final size:15
Alignment explanation
Indices: 1725473--1725524 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
1725463 TGAGACATTA
*
1725473 CCCGCCCCGCATCTG
1 CCCGCCCCGCATCCG
*
1725488 CCCTCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
1725503 CCCGCCCCACATCCG
1 CCCGCCCCGCATCCG
1725518 CCCGCCC
1 CCCGCCC
1725525 AGCTAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.67, G:0.15, T:0.10
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:1726222 original size:2 final size:2
Alignment explanation
Indices: 1726215--1726244 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1726205 CCATCCCTAG
1726215 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
1726245 TTGAGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1730483 original size:39 final size:39
Alignment explanation
Indices: 1730429--1730506 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1730419 ACAAAGAAGA
1730429 GAAACAGATTGACACAAGGTCGATTAAATGATTTAGTCT
1 GAAACAGATTGACACAAGGTCGATTAAATGATTTAGTCT
1730468 GAAACAGATTGACACAAGGTCGATTAAATGATTTAGTCT
1 GAAACAGATTGACACAAGGTCGATTAAATGATTTAGTCT
1730507 TTGTGAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (39 bp):
GAAACAGATTGACACAAGGTCGATTAAATGATTTAGTCT
Found at i:1741851 original size:45 final size:46
Alignment explanation
Indices: 1741767--1741889 Score: 142
Period size: 45 Copynumber: 2.7 Consensus size: 46
1741757 TCGCTAGTTA
* * *
1741767 ATTTATGATAGAAAAAATAATGTTTTAGGTAACATCTAATATTAAC
1 ATTTCTGATAGAAAAAATAATGTTTTAGATAACACCTAATATTAAC
* * *
1741813 ATTTCTGATATAAAAAATAATG-TTTAGATGACACCTAATTTTAAC
1 ATTTCTGATAGAAAAAATAATGTTTTAGATAACACCTAATATTAAC
* * * *
1741858 A-TTCTGGTAGAATAAATAATATTTTAGGTAAC
1 ATTTCTGATAGAAAAAATAATGTTTTAGATAAC
1741890 GTTTTATCGA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 16 0.25
45 28 0.44
46 20 0.31
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37
Consensus pattern (46 bp):
ATTTCTGATAGAAAAAATAATGTTTTAGATAACACCTAATATTAAC
Found at i:1751481 original size:18 final size:18
Alignment explanation
Indices: 1751458--1751509 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
1751448 AGGGTTCTAC
1751458 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1751476 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
1751494 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
1751510 AATTCTACTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1756970 original size:28 final size:28
Alignment explanation
Indices: 1756921--1756979 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1756911 ATTATCTTTA
1756921 TTATGTAAATATTAAAAATTA-TAATATT
1 TTATGTAAATATTAAAAATTATTAA-ATT
* *
1756949 TTATTTAAA-ATTAACAATTTATTAAATT
1 TTATGTAAATATTAA-AAATTATTAAATT
1756977 TTA
1 TTA
1756980 ATTTTAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 19 0.70
29 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TTATGTAAATATTAAAAATTATTAAATT
Found at i:1757859 original size:19 final size:19
Alignment explanation
Indices: 1757835--1757881 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1757825 AATATTGACT
1757835 ATTTTAATTTTGAT-TATTA
1 ATTTTAATTTT-ATCTATTA
* *
1757854 ATTTTAAATTTATCTTTTA
1 ATTTTAATTTTATCTATTA
1757873 ATTTTAATT
1 ATTTTAATT
1757882 AACAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTAATTTTATCTATTA
Found at i:1758104 original size:15 final size:15
Alignment explanation
Indices: 1758065--1758107 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1758055 TTTTAACTTG
*
1758065 ATATTAATTGTGA-A
1 ATATTAATTTTGATA
*
1758079 A-ATTTATTTTGATA
1 ATATTAATTTTGATA
1758093 ATATTAATTTTGATA
1 ATATTAATTTTGATA
1758108 CATAAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.38
14 3 0.12
15 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (15 bp):
ATATTAATTTTGATA
Found at i:1758321 original size:17 final size:17
Alignment explanation
Indices: 1758299--1758334 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1758289 TATACCGAAG
1758299 AAGCACAACTTGAATCT
1 AAGCACAACTTGAATCT
1758316 AAGCACAACTTGAATCT
1 AAGCACAACTTGAATCT
1758333 AA
1 AA
1758335 TGTCGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (17 bp):
AAGCACAACTTGAATCT
Found at i:1765342 original size:20 final size:20
Alignment explanation
Indices: 1765319--1765357 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1765309 TGTTCTTACA
1765319 GTATCGATACCTCATGAACT
1 GTATCGATACCTCATGAACT
1765339 GTATCGATACCTCATGAAC
1 GTATCGATACCTCATGAAC
1765358 AATATTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
GTATCGATACCTCATGAACT
Found at i:1765367 original size:20 final size:20
Alignment explanation
Indices: 1765320--1765368 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1765310 GTTCTTACAG
**
1765320 TATCGATACCTCATGAACTG
1 TATCGATACCTCATGAACAA
1765340 TATCGATACCTCATGAACAA
1 TATCGATACCTCATGAACAA
*
1765360 TATTGATAC
1 TATCGATAC
1765369 TATTCATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (20 bp):
TATCGATACCTCATGAACAA
Found at i:1769486 original size:15 final size:15
Alignment explanation
Indices: 1769466--1769513 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
1769456 TAAATTAAAT
*
1769466 AAAAGAAAAGAGAAA
1 AAAAGAAAAAAGAAA
1769481 AAAAGAAAAAAAGAAA
1 AAAAG-AAAAAAGAAA
*
1769497 AAAAGAAAAAGGAAA
1 AAAAGAAAAAAGAAA
1769512 AA
1 AA
1769514 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAGAAA
Found at i:1769513 original size:16 final size:16
Alignment explanation
Indices: 1769466--1769513 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
1769456 TAAATTAAAT
1769466 AAAAG-AAAAGAGAAA
1 AAAAGAAAAAGAGAAA
*
1769481 AAAAGAAAAAAAGAAA
1 AAAAGAAAAAGAGAAA
1769497 AAAAGAAAAAG-GAAA
1 AAAAGAAAAAGAGAAA
1769512 AA
1 AA
1769514 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAGAAA
Found at i:1769520 original size:8 final size:8
Alignment explanation
Indices: 1769466--1769506 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
1769456 TAAATTAAAT
1769466 AAAAG-AA
1 AAAAGAAA
*
1769473 AAGAGAAA
1 AAAAGAAA
1769481 AAAAGAAA
1 AAAAGAAA
1769489 AAAAGAAA
1 AAAAGAAA
1769497 AAAAGAAA
1 AAAAGAAA
1769505 AA
1 AA
1769507 GGAAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 4 0.13
8 27 0.87
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:1769760 original size:4 final size:4
Alignment explanation
Indices: 1769707--1769773 Score: 52
Period size: 4 Copynumber: 17.2 Consensus size: 4
1769697 TATTTAATAA
* * * *
1769707 AAAT AAAA AAAT -AGT AAAA AAAT AGAAT AAA- AAATT AAA- AAA- AAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAA-T AAAT AAAT AAAT
1769753 AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT A
1769774 TATATATATA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
3 11 0.22
4 33 0.65
5 7 0.14
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:1769761 original size:31 final size:31
Alignment explanation
Indices: 1769705--1769772 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1769695 AGTATTTAAT
*
1769705 AAAAA-TAAAAAAATAGTAAAAAAATAGAATA
1 AAAAATTAAAAAAAAAGTAAAAAAATA-AATA
*
1769736 AAAAATTAAAAAAAAAG-AAATAAATAAATA
1 AAAAATTAAAAAAAAAGTAAAAAAATAAATA
1769766 AATAAAT
1 AA-AAAT
1769773 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 6 0.18
31 17 0.52
32 10 0.30
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (31 bp):
AAAAATTAAAAAAAAAGTAAAAAAATAAATA
Found at i:1769911 original size:2 final size:2
Alignment explanation
Indices: 1769906--1769931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1769896 GTAAAAAACA
1769906 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
1769932 TAATAATATT
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:1778691 original size:21 final size:20
Alignment explanation
Indices: 1778645--1778692 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1778635 GATTCTGACT
1778645 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
1778665 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
1778687 ATCGCA
1 ATCGCA
1778693 ACGAGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:1779719 original size:21 final size:23
Alignment explanation
Indices: 1779671--1779721 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
1779661 AGTATTCGAA
1779671 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATA-CCGGAC
*
1779695 TTTGATCTTGGTC-ATA-CGGAT
1 TTTGATCTTGGTCAATACCGGAC
1779716 TTTGAT
1 TTTGAT
1779722 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.38
23 3 0.12
24 13 0.50
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (23 bp):
TTTGATCTTGGTCAATACCGGAC
Found at i:1782097 original size:20 final size:19
Alignment explanation
Indices: 1782069--1782123 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1782059 CAATCATCTT
*
1782069 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
1782089 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
1782108 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
1782124 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:1782138 original size:33 final size:33
Alignment explanation
Indices: 1782096--1782222 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
1782086 GGAAATGACT
* *
1782096 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGGGA
*
1782129 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGGGA
*
1782162 ATCGCAAAGCAAAATGAAAATCGCAACGAGGGA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGGGA
1782195 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAAAGCGAAATGAAAATCGCAACG
1782223 CGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGAGGGA
Found at i:1782152 original size:19 final size:18
Alignment explanation
Indices: 1782076--1782226 Score: 83
Period size: 19 Copynumber: 8.7 Consensus size: 18
1782066 CTTAATGTCT
**
1782076 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
1782096 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
1782115 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
1782129 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
1782148 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
1782162 ATCGCAAAGCAAAATGAAA
1 ATCGC-AAGCGAAATGAAA
**
1782181 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
1782195 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
1782214 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
1782227 TTTAGTTTCG
Statistics
Matches: 100, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
14 24 0.24
15 7 0.07
16 5 0.05
17 5 0.05
18 7 0.07
19 43 0.43
20 9 0.09
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:1784331 original size:19 final size:17
Alignment explanation
Indices: 1784315--1784376 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 17
1784305 AAAAATGACT
1784315 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
*
1784332 ATCGCAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
*
1784346 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
1784365 ATCGCAACGCGA
1 ATCGCAACGCGA
1784377 TTATAGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
16 4 0.11
17 8 0.22
19 12 0.32
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.11
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:1784653 original size:94 final size:93
Alignment explanation
Indices: 1784507--1784792 Score: 473
Period size: 94 Copynumber: 3.1 Consensus size: 93
1784497 ATGGATTGCA
* *
1784507 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
* * *
1784572 TAGCAGAATTGGCAACAACCGAACAAAT
66 TAGCAGAATTGACAGCAACCGAATAAAT
1784600 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1784665 TTAGCAGAATTGACAGCAACCGAATAAAT
65 TTAGCAGAATTGACAGCAACCGAATAAAT
* *
1784694 TTACTTCAACCAAAAGACAAAATAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAA-CAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
1784759 TTAGCAGTATTAACAGCAACCGAATAAAT
65 TTAGCAGAATTGACAGCAACCGAATAAAT
1784788 TTACT
1 TTACT
1784793 AAGCAATCTA
Statistics
Matches: 182, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
93 22 0.12
94 160 0.88
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGACAGCAACCGAATAAAT
Found at i:1786555 original size:19 final size:19
Alignment explanation
Indices: 1786469--1786569 Score: 95
Period size: 20 Copynumber: 5.5 Consensus size: 19
1786459 TCTTTTGGTT
* *
1786469 GAAATGAAACTCGCAACGA
1 GAAATGAAAATCGCAACGC
1786488 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1786508 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1786526 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1786542 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1786561 GAAACGAAA
1 GAAATGAAA
1786570 TGAAAATCGC
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 23 0.34
20 27 0.40
21 2 0.03
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1786571 original size:24 final size:24
Alignment explanation
Indices: 1786541--1786586 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1786531 AATCGCAACG
1786541 CGAAATGAAAATCGCAACGCGAAA
1 CGAAATGAAAATCGCAACGCGAAA
*
1786565 CGAAATGAAAATCGCAATGCGA
1 CGAAATGAAAATCGCAACGCGA
1786587 TTTTGGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.11
Consensus pattern (24 bp):
CGAAATGAAAATCGCAACGCGAAA
Found at i:1786632 original size:21 final size:21
Alignment explanation
Indices: 1786606--1786664 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1786596 CGCGTTGCGA
1786606 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* **
1786627 TTCTCTCGTTGTGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
1786648 TT-TCGT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
1786665 AAGTTTAGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.53
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1787247 original size:21 final size:21
Alignment explanation
Indices: 1787204--1787261 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1787194 CGATAGTCAG
**
1787204 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTAACTA
*
1787225 ATTCGCATTGCGATTTAAGTA
1 ATTCGCATTGCGATTTAACTA
*
1787246 A-TCGCGTTGCGATTTA
1 ATTCGCATTGCGATTTA
1787262 GGAAAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
ATTCGCATTGCGATTTAACTA
Found at i:1787271 original size:21 final size:20
Alignment explanation
Indices: 1787227--1787300 Score: 58
Period size: 21 Copynumber: 3.6 Consensus size: 20
1787217 TTTTCCTAAT
*
1787227 TCGCATTGCGATTTAAGTAA
1 TCGCATTGCGATTTAAGAAA
* *
1787247 TCGCGTTGCGATTTAGGAAAA
1 TCGCATTGCGATTTAAG-AAA
** **
1787268 TCGCAACGCGAATTTGGGAAA
1 TCGCATTGCG-ATTTAAGAAA
*
1787289 TCGCAATGCGAT
1 TCGCATTGCGAT
1787301 AGTCAGAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.39
21 21 0.48
22 6 0.14
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (20 bp):
TCGCATTGCGATTTAAGAAA
Done.