Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 57 of 235
Found at i:19284340 original size:9 final size:9
Alignment explanation
Indices: 19284326--19284515 Score: 229
Period size: 9 Copynumber: 20.9 Consensus size: 9
19284316 GTTGATTCAA
*
19284326 ATAACTCAC
1 ATAACTTAC
*
19284335 ATAACTCAC
1 ATAACTTAC
*
19284344 AGAACTTAC
1 ATAACTTAC
19284353 ATAACTTAC
1 ATAACTTAC
*
19284362 ATGACTTA-
1 ATAACTTAC
*
19284370 ATAACTTAT
1 ATAACTTAC
*
19284379 ATATATCATATC
1 ATA-A-CTTA-C
19284391 ATAACTTAC
1 ATAACTTAC
19284400 ATAACTTAC
1 ATAACTTAC
19284409 ATAACTTAC
1 ATAACTTAC
*
19284418 ATACCTTAC
1 ATAACTTAC
19284427 ATAACTTAC
1 ATAACTTAC
*
19284436 ATAACTCAC
1 ATAACTTAC
19284445 ATAACTTAC
1 ATAACTTAC
*
19284454 ACAACTTAC
1 ATAACTTAC
* *
19284463 ATACCTCAC
1 ATAACTTAC
*
19284472 ATAACTCAC
1 ATAACTTAC
*
19284481 ATAACTCAC
1 ATAACTTAC
19284490 ATAACTTAC
1 ATAACTTAC
19284499 ATAACTTAC
1 ATAACTTAC
19284508 ATAACTTA
1 ATAACTTA
19284516 ATTATACTTA
Statistics
Matches: 159, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
8 7 0.04
9 141 0.89
10 4 0.03
11 4 0.03
12 3 0.02
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:19284898 original size:72 final size:72
Alignment explanation
Indices: 19284781--19284929 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
19284771 TATTCGGGGG
19284781 TATAAAAAATGGATTTTCCATGGAGAGTGTACACCTAGTAGAACCTCTTCAATGATTAATCTGGT
1 TATAAAAAATGGATTTTCCATGGAGAGTGTACACCTAGTAGAACCTCTTCAATGATTAATCTGGT
19284846 TTATCCT
66 TTATCCT
*
19284853 TATAAAAAATGGATTTTCCATGGATAGTGTACACCTAGTAGAACCTCTTCAATGATTAATCTGGT
1 TATAAAAAATGGATTTTCCATGGAGAGTGTACACCTAGTAGAACCTCTTCAATGATTAATCTGGT
19284918 TTATCCT
66 TTATCCT
19284925 TATAA
1 TATAA
19284930 TGCTTACCAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (72 bp):
TATAAAAAATGGATTTTCCATGGAGAGTGTACACCTAGTAGAACCTCTTCAATGATTAATCTGGT
TTATCCT
Found at i:19285480 original size:12 final size:12
Alignment explanation
Indices: 19285465--19285506 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
19285455 GAAGATGTGA
19285465 ATGAGGATGAAT
1 ATGAGGATGAAT
* *
19285477 ATGAAGATGTGA-
1 ATGAGGATG-AAT
19285489 ATGAGGATGAAT
1 ATGAGGATGAAT
19285501 ATGAGG
1 ATGAGG
19285507 CACAGTCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (12 bp):
ATGAGGATGAAT
Found at i:19285486 original size:24 final size:24
Alignment explanation
Indices: 19285450--19285504 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 24
19285440 ATGAATAGAC
19285450 ATATAGAAGATGTGAATGAGGATGA
1 ATAT-GAAGATGTGAATGAGGATGA
19285475 ATATGAAGATGTGAATGAGGATGA
1 ATATGAAGATGTGAATGAGGATGA
19285499 ATATGA
1 ATATGA
19285505 GGCACAGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (24 bp):
ATATGAAGATGTGAATGAGGATGA
Found at i:19289610 original size:14 final size:13
Alignment explanation
Indices: 19289568--19289610 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
19289558 TTTTAAATAT
19289568 TTATAATGTTTAA
1 TTATAATGTTTAA
*
19289581 TCATAATAGTTTAA
1 TTATAAT-GTTTAA
19289595 TTATAATGGTTTAA
1 TTATAAT-GTTTAA
19289609 TT
1 TT
19289611 CATTGTTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (13 bp):
TTATAATGTTTAA
Found at i:19290388 original size:43 final size:43
Alignment explanation
Indices: 19290319--19290520 Score: 278
Period size: 43 Copynumber: 4.7 Consensus size: 43
19290309 GTGTTTGTAA
* *
19290319 GAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTTTGA
1 GAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTGT
* * * * * *
19290362 GAGAAGCGCCACTAAAAGTCATGTTCTTTAGCAGTGTTTGTGT
1 GAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTGT
* *
19290405 GAAAAGCGCCGTTAAAGGTCACGTTCTTTAGCGGCATTTGTGT
1 GAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTGT
* * *
19290448 GAAAAGCACCGCTAAAGGTCATGTTCTTTAGCGGCGTTTATGT
1 GAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTGT
*
19290491 GAAAAGCGCTGCTAAAGGTCACGTTCTTTA
1 GAAAAGCGCCGCTAAAGGTCACGTTCTTTA
19290521 ACGCCACTAA
Statistics
Matches: 135, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 135 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
GAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTGT
Found at i:19293381 original size:16 final size:16
Alignment explanation
Indices: 19293360--19293393 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19293350 AAGTCTGTCA
*
19293360 AACCTTAGAGTTCGCC
1 AACCTTAAAGTTCGCC
*
19293376 AACCTTAAAGTTCTCC
1 AACCTTAAAGTTCGCC
19293392 AA
1 AA
19293394 ATGGTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (16 bp):
AACCTTAAAGTTCGCC
Found at i:19296072 original size:20 final size:20
Alignment explanation
Indices: 19296049--19296112 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
19296039 ATTATTGGCA
*
19296049 GCTTGTCTGCATTACTGGTG
1 GCTTATCTGCATTACTGGTG
** ** **
19296069 GCTTATCCACATTTTTGGCA
1 GCTTATCTGCATTACTGGTG
19296089 GCTTATCTGCATTACTGGTG
1 GCTTATCTGCATTACTGGTG
19296109 GCTT
1 GCTT
19296113 GTCCACAAAC
Statistics
Matches: 31, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (20 bp):
GCTTATCTGCATTACTGGTG
Found at i:19296078 original size:40 final size:40
Alignment explanation
Indices: 19295981--19296119 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 40
19295971 TTGTCCATAA
* * * * * * *
19295981 TACTGGTAGCTTTTCTACATTACTGGCAGTTTATTTGCAC
1 TACTGGTGGCTTATCCACATTATTGGCAGCTTATCTGCAT
* ** * *
19296021 TACTAGTCTCTTCTCCACATTATTGGCAGCTTGTCTGCAT
1 TACTGGTGGCTTATCCACATTATTGGCAGCTTATCTGCAT
*
19296061 TACTGGTGGCTTATCCACATTTTTGGCAGCTTATCTGCAT
1 TACTGGTGGCTTATCCACATTATTGGCAGCTTATCTGCAT
*
19296101 TACTGGTGGCTTGTCCACA
1 TACTGGTGGCTTATCCACA
19296120 AACTGGTGTG
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.40
Consensus pattern (40 bp):
TACTGGTGGCTTATCCACATTATTGGCAGCTTATCTGCAT
Found at i:19298676 original size:12 final size:12
Alignment explanation
Indices: 19298659--19298686 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19298649 CACACAACCA
19298659 TGTGCTAGGTCG
1 TGTGCTAGGTCG
19298671 TGTGCTAGGTCG
1 TGTGCTAGGTCG
19298683 TGTG
1 TGTG
19298687 ACAACCTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.43, T:0.36
Consensus pattern (12 bp):
TGTGCTAGGTCG
Found at i:19299832 original size:30 final size:30
Alignment explanation
Indices: 19299798--19299928 Score: 124
Period size: 30 Copynumber: 4.4 Consensus size: 30
19299788 AAGCTATCTT
* * *
19299798 TTTTCATAATTTGATCGTCGTCACCAACCC
1 TTTTCATAATTCGATGGTCGTCACCATCCC
** *
19299828 TTTTCATTGTTCAATGGTCGTCACCATCCC
1 TTTTCATAATTCGATGGTCGTCACCATCCC
* * *
19299858 TTTTCATAATTTC-ATAG-C-TGAAGCCATTCC
1 TTTTCATAA-TTCGATGGTCGT-CA-CCATCCC
*
19299888 TTTTCATAGTTCGATGGTCGTCACCATCCC
1 TTTTCATAATTCGATGGTCGTCACCATCCC
19299918 TTTTCATAATT
1 TTTTCATAATT
19299929 GATAGCCAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
28 1 0.01
29 5 0.06
30 67 0.85
31 5 0.06
32 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.40
Consensus pattern (30 bp):
TTTTCATAATTCGATGGTCGTCACCATCCC
Found at i:19301957 original size:24 final size:23
Alignment explanation
Indices: 19301897--19301958 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
19301887 TCCGAGTTGT
19301897 ATAACGGGAAGCTCATAAGAGCC
1 ATAACGGGAAGCTCATAAGAGCC
* *
19301920 ATAATCAGGAAGCTCATACGAGCC
1 ATAA-CGGGAAGCTCATAAGAGCC
*
19301944 AATAACGGGTAGCTC
1 -ATAACGGGAAGCTC
19301959 CGTAAAGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 4 0.12
24 25 0.76
25 4 0.12
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (23 bp):
ATAACGGGAAGCTCATAAGAGCC
Found at i:19302108 original size:26 final size:26
Alignment explanation
Indices: 19302045--19302109 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
19302035 AGACCCATTA
19302045 ATCAGGAAGCTCACAAAGAGCCAATC
1 ATCAGGAAGCTCACAAAGAGCCAATC
* *
19302071 AAC-GAGAAGCTCACAAAGAGTCATAT-
1 ATCAG-GAAGCTCACAAAGAGCCA-ATC
*
19302097 ATCAGGACGCTCA
1 ATCAGGAAGCTCA
19302110 TAAGAGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 1 0.03
26 28 0.88
27 3 0.09
ACGTcount: A:0.42, C:0.25, G:0.20, T:0.14
Consensus pattern (26 bp):
ATCAGGAAGCTCACAAAGAGCCAATC
Found at i:19302194 original size:24 final size:25
Alignment explanation
Indices: 19302167--19302214 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
19302157 GGATGCTCCG
*
19302167 AAGAGCGAT-TAACGGGAAGCTCGC
1 AAGAACGATATAACGGGAAGCTCGC
**
19302191 AAGAATTATATAACGGGAAGCTCG
1 AAGAACGATATAACGGGAAGCTCG
19302215 AGAGGCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.17
Consensus pattern (25 bp):
AAGAACGATATAACGGGAAGCTCGC
Found at i:19310444 original size:67 final size:67
Alignment explanation
Indices: 19310362--19310494 Score: 257
Period size: 67 Copynumber: 2.0 Consensus size: 67
19310352 TATATTATAA
*
19310362 CACATAAAATAATACTAAAATAATTTTCTCTGGCCTCGAAATAGTGGTCCCGAAACCACTTTTCC
1 CACATAAAATAATACTAAAATAATTTTCTCTGGCCTCGAAATAGTGGTCCCGAAACCACTGTTCC
19310427 GG
66 GG
19310429 CACATAAAATAATACTAAAATAATTTTCTCTGGCCTCGAAATAGTGGTCCCGAAACCACTGTTCC
1 CACATAAAATAATACTAAAATAATTTTCTCTGGCCTCGAAATAGTGGTCCCGAAACCACTGTTCC
19310494 G
66 G
19310495 ACTAGGCCCA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (67 bp):
CACATAAAATAATACTAAAATAATTTTCTCTGGCCTCGAAATAGTGGTCCCGAAACCACTGTTCC
GG
Found at i:19319173 original size:6 final size:6
Alignment explanation
Indices: 19319164--19319188 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19319154 TTTAATTTTC
19319164 TTGAAT TTGAAT TTGAAT TTGAAT T
1 TTGAAT TTGAAT TTGAAT TTGAAT T
19319189 GATGGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TTGAAT
Found at i:19319747 original size:19 final size:18
Alignment explanation
Indices: 19319688--19319741 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
19319678 GTACAGGTTT
*
19319688 ATGCGCTTGTGTGCCAGG
1 ATGCGCTTGTGTGCCAAG
**
19319706 ATGCAATTTGTGTGCCAAG
1 ATGC-GCTTGTGTGCCAAG
19319725 ATGCGCTTCGTGTGCCA
1 ATGCGCTT-GTGTGCCA
19319742 CTATGCACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.30
Consensus pattern (18 bp):
ATGCGCTTGTGTGCCAAG
Found at i:19324098 original size:40 final size:40
Alignment explanation
Indices: 19324021--19324201 Score: 287
Period size: 40 Copynumber: 4.6 Consensus size: 40
19324011 AAACCAAGTA
** * *
19324021 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
19324060 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
19324100 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
19324140 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
19324180 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
19324202 CAATCCGAAT
Statistics
Matches: 134, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
39 26 0.19
40 108 0.81
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:19334695 original size:46 final size:46
Alignment explanation
Indices: 19334642--19334732 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
19334632 ATACTGATGG
19334642 AGAATGGATTTTTGACCCTGAGGTTCTTAAGACGAAAATGGTTAAT
1 AGAATGGATTTTTGACCCTGAGGTTCTTAAGACGAAAATGGTTAAT
19334688 AGAATGGATTTTTGACCCTGAGGTTCTTAAGACGAAAATGGTTAA
1 AGAATGGATTTTTGACCCTGAGGTTCTTAAGACGAAAATGGTTAA
19334733 CTTTTTCCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (46 bp):
AGAATGGATTTTTGACCCTGAGGTTCTTAAGACGAAAATGGTTAAT
Found at i:19343199 original size:34 final size:35
Alignment explanation
Indices: 19343155--19343221 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
19343145 CTGTAAAATG
19343155 TTTTCCGTAAAATGAATT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
* *
19343189 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTT
19343222 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
Found at i:19344596 original size:27 final size:27
Alignment explanation
Indices: 19344566--19344635 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
19344556 AATAATCAAT
*
19344566 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
19344593 TCAATATCTAACCAATTCAAGACATATA
1 TCAATATCCAA-CAATTCAAAACATATA
*
19344621 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
19344636 CTAAAATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:19348966 original size:6 final size:6
Alignment explanation
Indices: 19348955--19348985 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
19348945 AATATTTCCC
*
19348955 ACAGAA ACAGAA ACAGAA ACAAAA ACAGAA A
1 ACAGAA ACAGAA ACAGAA ACAGAA ACAGAA A
19348986 ATACAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.71, C:0.16, G:0.13, T:0.00
Consensus pattern (6 bp):
ACAGAA
Found at i:19356603 original size:281 final size:281
Alignment explanation
Indices: 19356082--19356640 Score: 673
Period size: 281 Copynumber: 2.0 Consensus size: 281
19356072 GAGGCCTCAA
* * * *
19356082 TGTATCCCTTAATATCGAACATGATGCCTTTGTATGCCCTGGATTTCTACAGTACCCTCATAACC
1 TGTATCCCTCAATATCGAACATGATGCCTTCGTATGCCCTGGATTTCTACAGTACCCTAAAAACC
* * *
19356147 TTTGTTGATTGTCTCTCTCTCGAATATCCATATTAGTATGTATCCAAGTGAAAGTCAGACGACCT
66 TCTATTGATTGTCTCTCTCTCGAACATCCATATTAGTATGTATCCAAGTGAAAGTCAGACGACCT
* * * *
19356212 TTCGGGACGCGGCACAAGTTTATGTTCGGGGCCAACTCGAATGGAGCGCTGGACACTAGCAACCA
131 TTCGGGACACGACACAAGTTCATATTCGGGGCCAACTCGAATGGAGCGCTGGACACTAGCAACCA
* * *
19356277 CATACTTTCATCTGGGATGGGTCGGAATTCAGATATTCATACATTGTGCATGCCTTCTAGTTTTT
196 CATACTCTCATCTGGGATAGGTCGGAATTCAGATATTCATACATTGTGCATGCCTTCTAGTTTGT
*
19356342 ACG-CATCGTTAATATAAGACG
261 A-GACATAGTTAATATAAGACG
* * * * *
19356363 TGTATCCCTCAATATGGAACATGTTGCCTTCGTATGCTCTGGGTTTCTACAGTA-CTTGAAAAAC
1 TGTATCCCTCAATATCGAACATGATGCCTTCGTATGCCCTGGATTTCTACAGTACCCT-AAAAAC
* * * * *** ** *
19356427 CTCTATTGATTGTCTCTTTC-CTGAACATCCATTTTGGTGTGTATTTGAGTGAAAGTTGGATGAC
65 CTCTATTGATTGTCTCTCTCTC-GAACATCCATATTAGTATGTATCCAAGTGAAAGTCAGACGAC
** * * *
19356491 CTTTCGGGACACGATGCAAGTTCATATTCGGGGCTAACTTGAACTGGA-CGCTGGACACTAGCAG
129 CTTTCGGGACACGACACAAGTTCATATTCGGGGCCAACTCGAA-TGGAGCGCTGGACACTAGCAA
* *
19356555 CC-CAATACTCTCATCTGGGATAGGT-GAGAATTTAGATA-TCTGTACATTGTGCATGCCTTCTA
193 CCAC-ATACTCTCATCTGGGATAGGTCG-GAATTCAGATATTC-ATACATTGTGCATGCCTTCTA
19356617 GTTTGTAGACATAGTTAATATAAG
255 GTTTGTAGACATAGTTAATATAAG
19356641 GTGTACTCAA
Statistics
Matches: 234, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
280 8 0.03
281 222 0.95
282 4 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (281 bp):
TGTATCCCTCAATATCGAACATGATGCCTTCGTATGCCCTGGATTTCTACAGTACCCTAAAAACC
TCTATTGATTGTCTCTCTCTCGAACATCCATATTAGTATGTATCCAAGTGAAAGTCAGACGACCT
TTCGGGACACGACACAAGTTCATATTCGGGGCCAACTCGAATGGAGCGCTGGACACTAGCAACCA
CATACTCTCATCTGGGATAGGTCGGAATTCAGATATTCATACATTGTGCATGCCTTCTAGTTTGT
AGACATAGTTAATATAAGACG
Found at i:19360034 original size:143 final size:144
Alignment explanation
Indices: 19359732--19360069 Score: 376
Period size: 143 Copynumber: 2.4 Consensus size: 144
19359722 GAAGCTTTGT
* * * ** * *
19359732 TCCTAGTTAATAAACACCAATATAACTCGCAAACCTGCGTTCCCAGCTGATGTTTAAAGGTTATC
1 TCCTAGTTGATAAACTCCAACATAACTCGTGAACCTACGTTCCCAGCTGATGTTTAAAGGTTAGC
* * ** *
19359797 TGAGTTATGTTCACAAATTTTATTTATTCGAGTTAGCTGAGTTAAGCTCGCAACTCTAAGACAGC
66 TGAGTTATGCTCACAAACTCCATTTATTCGAGTTAGCTGAGTTAAGCTCGCAACTCCAAGACAGC
* *
19359862 TCGCAGACGTACAT
131 TCGCAGACCTACAC
*
19359876 TCCCAGTTGATAAACTCCAACATAACTCGTGAACCTACGTTCCCAGCTGATGTTTAAAGGTTAGC
1 TCCTAGTTGATAAACTCCAACATAACTCGTGAACCTACGTTCCCAGCTGATGTTTAAAGGTTAGC
* * * * * *
19359941 TGAG-TATGCTCACAACCTCCATTTACTT-GAGTTAGTTGAGTTAAGCTTGCAATTCCATGATAG
66 TGAGTTATGCTCACAAACTCCATTTA-TTCGAGTTAGCTGAGTTAAGCTCGCAACTCCAAGACAG
*
19360004 CTCGC-GAACCTACGC
130 CTCGCAG-ACCTACAC
* *** * * *
19360019 TCCTAGCTGATAAACTCTGGCATAGCTCGTGGACCTATGTTCCCAGCTGAT
1 TCCTAGTTGATAAACTCCAACATAACTCGTGAACCTACGTTCCCAGCTGAT
19360070 AAACTCCAAC
Statistics
Matches: 162, Mismatches: 30, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
142 1 0.01
143 98 0.60
144 63 0.39
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (144 bp):
TCCTAGTTGATAAACTCCAACATAACTCGTGAACCTACGTTCCCAGCTGATGTTTAAAGGTTAGC
TGAGTTATGCTCACAAACTCCATTTATTCGAGTTAGCTGAGTTAAGCTCGCAACTCCAAGACAGC
TCGCAGACCTACAC
Found at i:19360055 original size:40 final size:40
Alignment explanation
Indices: 19360000--19360103 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 40
19359990 CAATTCCATG
*
19360000 ATAGCTCGCGAACCTACGCTCCTAGCTGATAAACTCTGGC
1 ATAGCTCGCGAACCTACGCTCCCAGCTGATAAACTCTGGC
* * * * ***
19360040 ATAGCTCGTGGACCTATGTTCCCAGCTGATAAACTCCAAC
1 ATAGCTCGCGAACCTACGCTCCCAGCTGATAAACTCTGGC
* * *
19360080 ACAGCTCGCGGACCTACGTTCCCA
1 ATAGCTCGCGAACCTACGCTCCCA
19360104 ACTAATGTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (40 bp):
ATAGCTCGCGAACCTACGCTCCCAGCTGATAAACTCTGGC
Found at i:19360369 original size:103 final size:103
Alignment explanation
Indices: 19360178--19360441 Score: 312
Period size: 103 Copynumber: 2.6 Consensus size: 103
19360168 CTAGCTGATG
* * *
19360178 TTTAAAGGTTAGCTGAGTTAAGCTCTCAACCTAAATATTTTTGAGTTAGCTGAGTCAAGCTTGCA
1 TTTAAAGGTTAGCTGAGTTAAGCTCACAACCTGAAT-TTTTTGAGTTAGCTGAGTTAAGCTTGCA
* *
19360243 AGTCCAAAACAGCTCGCGGACCTACGTTCCCAACTAACA
65 AATCCAAAACAGCTCGCGAACCTACGTTCCCAACTAACA
* * * * * *
19360282 TTTAAAGGTTAGCTAAGTTAAACTCGCAACCTGAATTTTTTTAGTTAGTTGAGTTAAGCTTGGAA
1 TTTAAAGGTTAGCTGAGTTAAGCTCACAACCTGAATTTTTTGAGTTAGCTGAGTTAAGCTTGCAA
** * * * * * **
19360347 ATCTGAAATAGCTCGTGAACCTATGTTCCCAGCTTATG
66 ATCCAAAACAGCTCGCGAACCTACGTTCCCAACTAACA
* * *
19360385 CTTAAAGGTTAGTTGAGTTAAGCTCACAACTTGAATTTTTTGAGTTAGCTGAGTTAA
1 TTTAAAGGTTAGCTGAGTTAAGCTCACAACCTGAATTTTTTGAGTTAGCTGAGTTAA
19360442 ATTAAGACTA
Statistics
Matches: 133, Mismatches: 27, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
103 101 0.76
104 32 0.24
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (103 bp):
TTTAAAGGTTAGCTGAGTTAAGCTCACAACCTGAATTTTTTGAGTTAGCTGAGTTAAGCTTGCAA
ATCCAAAACAGCTCGCGAACCTACGTTCCCAACTAACA
Found at i:19366572 original size:24 final size:23
Alignment explanation
Indices: 19366535--19366583 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
19366525 ATAATTATTT
*
19366535 TAAAATTCTTATAAATAAATAAA
1 TAAAATTATTATAAATAAATAAA
* *
19366558 TAAAATTATTAATAATTGAATAAA
1 TAAAATTATT-ATAAATAAATAAA
19366582 TA
1 TA
19366584 CTAATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
TAAAATTATTATAAATAAATAAA
Found at i:19372862 original size:18 final size:17
Alignment explanation
Indices: 19372825--19372872 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
19372815 CGTTCAGAAC
*
19372825 TCTTCTTCTTTACCTTTTT
1 TCTTCTT-TTTA-TTTTTT
19372844 TCTTTCTTTTTATTTTTT
1 TC-TTCTTTTTATTTTTT
19372862 TCTTCTTTTTA
1 TCTTCTTTTTA
19372873 CTCCTTCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 7 0.26
19 6 0.22
20 5 0.19
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (17 bp):
TCTTCTTTTTATTTTTT
Found at i:19375744 original size:19 final size:19
Alignment explanation
Indices: 19375720--19375762 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19375710 AAAAGCAACG
19375720 CAACATCA-ACCTAAATAAA
1 CAACATCATACC-AAATAAA
* *
19375739 CAACATGATTCCAAATAAA
1 CAACATCATACCAAATAAA
19375758 CAACA
1 CAACA
19375763 AAAATAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.56, C:0.26, G:0.02, T:0.16
Consensus pattern (19 bp):
CAACATCATACCAAATAAA
Found at i:19378525 original size:91 final size:91
Alignment explanation
Indices: 19378411--19378600 Score: 328
Period size: 91 Copynumber: 2.1 Consensus size: 91
19378401 AATAGTACAG
* *
19378411 GTACAACAGCATAAATTAAACAAAAAAAAAGTTTGTTAAGCTACCGTGGAAGATTTAAAGTTAGT
1 GTACAATAGCATAAATTAAACAAAAAAAAAGTTTGTTAAGCTACCGTGGAAAATTTAAAGTTAGT
19378476 TAATTGAAGCCTAAATTAATATAATA
66 TAATTGAAGCCTAAATTAATATAATA
**
19378502 GTACAATAGCATAAATTAAACAAAAAAAAAGTTTGTTAAGCTACCGTTTAAAATTTAAAGTTAGT
1 GTACAATAGCATAAATTAAACAAAAAAAAAGTTTGTTAAGCTACCGTGGAAAATTTAAAGTTAGT
19378567 TAATTGAAGCCTAAATTAATATAATA
66 TAATTGAAGCCTAAATTAATATAATA
*
19378593 -TATAATAG
1 GTACAATAG
19378601 TACAAATACA
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 7 0.07
91 87 0.93
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.31
Consensus pattern (91 bp):
GTACAATAGCATAAATTAAACAAAAAAAAAGTTTGTTAAGCTACCGTGGAAAATTTAAAGTTAGT
TAATTGAAGCCTAAATTAATATAATA
Found at i:19378926 original size:17 final size:17
Alignment explanation
Indices: 19378899--19378941 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
19378889 TATCAATTTT
*
19378899 TTATCTACTAATATTACG
1 TTAT-TACTAATATTACA
19378917 TTATTACTAATATTACA
1 TTATTACTAATATTACA
19378934 TTATTACT
1 TTATTACT
19378942 TTGGAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (17 bp):
TTATTACTAATATTACA
Found at i:19381202 original size:42 final size:42
Alignment explanation
Indices: 19381156--19381276 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
19381146 GACCTAAACA
* * * *
19381156 GAAACCCATAAGGGTTGAACAGAAGTTC-GTAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAAT-AGAGCTGAAAG
19381198 GAAACCCATAAGGGTTAAACAGAAGCTCAATAGAGCTGAAAG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAATAGAGCTGAAAG
* * *
19381240 GAAACTCATATGAGTTAAACAGAAGCTC-ATGAGAGCT
1 GAAACCCATAAGGGTTAAACAGAAGCTCAAT-AGAGCT
19381277 AAACAGAAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.03
42 67 0.96
43 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACAGAAGCTCAATAGAGCTGAAAG
Found at i:19381279 original size:21 final size:21
Alignment explanation
Indices: 19381133--19381284 Score: 92
Period size: 21 Copynumber: 7.2 Consensus size: 21
19381123 GAAAGATGAT
* *
19381133 CAGAAGCTCATGAGACCTAAA
1 CAGAAGCTCATAAGAGCTAAA
* * * * *
19381154 CAGAAACCCATAAGGGTTGAA
1 CAGAAGCTCATAAGAGCTAAA
* * *
19381175 CAGAAGTTCGTAAGAGCTGAA
1 CAGAAGCTCATAAGAGCTAAA
* * * * *
19381196 CGGAAACCCATAAGGGTTAAA
1 CAGAAGCTCATAAGAGCTAAA
19381217 CAGAAGCTCA-ATAGAGCTGAAA
1 CAGAAGCTCATA-AGAGCT-AAA
* * * *
19381239 -GGAAACTCATATGAGTTAAA
1 CAGAAGCTCATAAGAGCTAAA
*
19381259 CAGAAGCTCATGAGAGCTAAA
1 CAGAAGCTCATAAGAGCTAAA
19381280 CAGAA
1 CAGAA
19381285 AGTAAACATG
Statistics
Matches: 92, Mismatches: 35, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
20 4 0.04
21 84 0.91
22 4 0.04
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
CAGAAGCTCATAAGAGCTAAA
Found at i:19384996 original size:21 final size:21
Alignment explanation
Indices: 19384969--19385020 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
19384959 ATAAATAATT
19384969 TAAAAATTAAAATTAAAA-TTCA
1 TAAAAATTAAAA--AAAAGTTCA
19384991 -AAAAATATAAAAAAAAGTTCA
1 TAAAAAT-TAAAAAAAAGTTCA
19385012 TAAAAATTA
1 TAAAAATTA
19385021 GTATGGAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.15
21 12 0.44
22 11 0.41
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAAATTAAAAAAAAGTTCA
Found at i:19385794 original size:16 final size:16
Alignment explanation
Indices: 19385773--19385803 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19385763 CTTTTATTTT
*
19385773 TTTTTAGGTTTTAAGA
1 TTTTTAGGGTTTAAGA
19385789 TTTTTAGGGTTTAAG
1 TTTTTAGGGTTTAAG
19385804 GTATTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (16 bp):
TTTTTAGGGTTTAAGA
Found at i:19388705 original size:40 final size:40
Alignment explanation
Indices: 19388661--19388738 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
19388651 TACTAAAAGG
19388661 GATGCGTCATTTTTCGGTAACATCGGTTGTTAAAGAGATA
1 GATGCGTCATTTTTCGGTAACATCGGTTGTTAAAGAGATA
*
19388701 GATGCGTCATTTTTTGGTAACATCGGTTGTTAAAGAGA
1 GATGCGTCATTTTTCGGTAACATCGGTTGTTAAAGAGA
19388739 CATACTTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.36
Consensus pattern (40 bp):
GATGCGTCATTTTTCGGTAACATCGGTTGTTAAAGAGATA
Found at i:19391085 original size:17 final size:17
Alignment explanation
Indices: 19391054--19391086 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19391044 TGTATAACAC
19391054 TTGTTTTATTGTTAAAT
1 TTGTTTTATTGTTAAAT
19391071 TTGTTATTATT-TTAAA
1 TTGTT-TTATTGTTAAA
19391087 GACATTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (17 bp):
TTGTTTTATTGTTAAAT
Found at i:19392193 original size:16 final size:16
Alignment explanation
Indices: 19392172--19392226 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
19392162 TGATCTGAAC
*
19392172 AATTAAAATACAATAT
1 AATTAAAATAAAATAT
19392188 AATTAAAA-AATAATAT
1 AATTAAAATAA-AATAT
*
19392204 -TTTAAAATGAAAATAT
1 AATTAAAAT-AAAATAT
*
19392220 AAATAAA
1 AATTAAA
19392227 TATTGAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 7 0.23
16 18 0.58
17 6 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
AATTAAAATAAAATAT
Found at i:19396587 original size:6 final size:6
Alignment explanation
Indices: 19396576--19396600 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19396566 CGAAGAAAAG
19396576 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
19396601 TAAAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:19401657 original size:6 final size:6
Alignment explanation
Indices: 19401646--19401673 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19401636 CCAGCAGAGT
19401646 GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGA
19401674 CGGTGGTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:19407088 original size:45 final size:46
Alignment explanation
Indices: 19407021--19407144 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
19407011 CATATGACCT
*
19407021 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
19407064 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
19407110 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
19407145 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:19407127 original size:46 final size:45
Alignment explanation
Indices: 19407021--19407255 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
19407011 CATATGACCT
*
19407021 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
19407064 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
19407110 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
19407147 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
19407184 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
19407221 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
19407256 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:19407148 original size:37 final size:37
Alignment explanation
Indices: 19407106--19407282 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
19407096 AGCTGAAGCT
* **
19407106 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
19407143 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
19407180 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
19407217 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
19407254 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
19407283 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:19414787 original size:45 final size:46
Alignment explanation
Indices: 19414720--19414843 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
19414710 CATATGACCT
*
19414720 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
19414763 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
19414809 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
19414844 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:19414826 original size:46 final size:45
Alignment explanation
Indices: 19414720--19414917 Score: 207
Period size: 37 Copynumber: 4.8 Consensus size: 45
19414710 CATATGACCT
*
19414720 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
19414763 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
19414809 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
19414846 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
19414883 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
19414918 CACTTATCAC
Statistics
Matches: 140, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
37 64 0.46
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.06
44 6 0.04
45 21 0.15
46 34 0.24
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:19414847 original size:37 final size:37
Alignment explanation
Indices: 19414806--19414944 Score: 233
Period size: 37 Copynumber: 3.8 Consensus size: 37
19414796 GCTGAAGCTA
* *
19414806 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
19414843 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
19414880 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
19414917 CCACTTATCACTTTGTTTCTTGATCAGA
1 CCACTTATCACTTTGTCTCTTGATCAGA
19414945 AGTACTCAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:19421044 original size:30 final size:30
Alignment explanation
Indices: 19421010--19421069 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
19421000 ATCTAATACG
*
19421010 AACTTTTGCAAAATTACATTTTTGCCCCTA
1 AACTTTTGCAAAATTACACTTTTGCCCCTA
*
19421040 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTGCAAAATTACACTTTTGCCCCTA
19421070 GGCTTGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTTGCAAAATTACACTTTTGCCCCTA
Found at i:19422035 original size:14 final size:14
Alignment explanation
Indices: 19422018--19422074 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
19422008 AAGGTTAAAA
*
19422018 GTTTAAGGTTCATG
1 GTTTGAGGTTCATG
*
19422032 GTTTGA-GTTCAAG
1 GTTTGAGGTTCATG
19422045 GTTTGAGGTTC-TG
1 GTTTGAGGTTCATG
*
19422058 AGTTTGGGGTTCATG
1 -GTTTGAGGTTCATG
19422073 GT
1 GT
19422075 AAAATAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 13 0.36
14 21 0.58
15 2 0.06
ACGTcount: A:0.16, C:0.07, G:0.35, T:0.42
Consensus pattern (14 bp):
GTTTGAGGTTCATG
Found at i:19424809 original size:18 final size:18
Alignment explanation
Indices: 19424786--19424822 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19424776 TCAGATTGAG
19424786 TTAACCCAAAAAGATCAT
1 TTAACCCAAAAAGATCAT
19424804 TTAACCCAAAAAGATCAT
1 TTAACCCAAAAAGATCAT
19424822 T
1 T
19424823 CTTTTTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.24
Consensus pattern (18 bp):
TTAACCCAAAAAGATCAT
Found at i:19427386 original size:48 final size:48
Alignment explanation
Indices: 19427330--19427425 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
19427320 CAAACACCCT
19427330 TTCCCTCATCGGCCCCGGCGATTCCCTCGGATACCTCTGCAAGAAAAA
1 TTCCCTCATCGGCCCCGGCGATTCCCTCGGATACCTCTGCAAGAAAAA
*
19427378 TTCCCTCATTGGCCCCGGCGATTCCCTCGGATACCTCTGCAAGAAAAA
1 TTCCCTCATCGGCCCCGGCGATTCCCTCGGATACCTCTGCAAGAAAAA
19427426 CTCCGCCAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (48 bp):
TTCCCTCATCGGCCCCGGCGATTCCCTCGGATACCTCTGCAAGAAAAA
Found at i:19429005 original size:21 final size:22
Alignment explanation
Indices: 19428967--19429010 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
19428957 TCTCTTATAC
*
19428967 TTTGTTCTTATTTGTTGT-TTG
1 TTTGTTCTTATTTCTTGTATTG
19428988 TTTGTTCGTTA-TTCTTGTATTG
1 TTTGTTC-TTATTTCTTGTATTG
19429010 T
1 T
19429011 ATTTCTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (22 bp):
TTTGTTCTTATTTCTTGTATTG
Found at i:19431340 original size:100 final size:100
Alignment explanation
Indices: 19431167--19431656 Score: 953
Period size: 100 Copynumber: 4.9 Consensus size: 100
19431157 ACTATTGTGA
19431167 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
1 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
19431232 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
66 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
19431267 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
1 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
19431332 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
66 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
19431367 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
1 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
19431432 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
66 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
19431467 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
1 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
19431532 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
66 CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
19431567 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
1 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
* * *
19431632 CTAAGTGCAGGCTATTATGTGTACC
66 CTAAGTGCAAGCTACTATGCGTACC
19431657 AGATAGCTTC
Statistics
Matches: 387, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 387 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (100 bp):
GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTA
CTAAGTGCAAGCTACTATGCGTACCCGAAAACTGT
Found at i:19434683 original size:15 final size:15
Alignment explanation
Indices: 19434663--19434727 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
19434653 GTATCTTGGG
19434663 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
19434678 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
19434693 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
19434708 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
19434722 TTTCTT
1 TTTCTT
19434728 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.28
15 27 0.63
16 4 0.09
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:19434695 original size:30 final size:31
Alignment explanation
Indices: 19434659--19434727 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
19434649 TATCGTATCT
19434659 TGGGTTTCTT-TAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCT-TGGATTTCTTTATTC
19434689 TGGGTTT-TTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCTTGGATTTCTTTATTC
*
19434719 -GGTTTTCTT
1 TGGGTTTCTT
19434728 GTTATCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.61
Consensus pattern (31 bp):
TGGGTTTCTTCTATCTTGGATTTCTTTATTC
Found at i:19437365 original size:100 final size:100
Alignment explanation
Indices: 19437192--19437581 Score: 726
Period size: 100 Copynumber: 3.9 Consensus size: 100
19437182 ACTATTGTGA
* *
19437192 GATCACGTATGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
1 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
19437257 CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
66 CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
19437292 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
1 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
19437357 CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
66 CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
19437392 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
1 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
19437457 CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
66 CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
** *
19437492 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTA
1 GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
*
19437557 CTAAGTGCAGGCTATTATGCGTACC
66 CTAAGTGCAGGCTACTATGCGTACC
19437582 AGATAGCTTC
Statistics
Matches: 284, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 284 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (100 bp):
GATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTA
CTAAGTGCAGGCTACTATGCGTACCTGAAAACTGT
Found at i:19437581 original size:49 final size:49
Alignment explanation
Indices: 19437201--19437586 Score: 475
Period size: 49 Copynumber: 7.8 Consensus size: 49
19437191 AGATCACGTA
* *
19437201 TGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAATTGGTCGCATG
* * * * *
19437250 TGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAA-T-TGGTCGCATG
* *
19437301 TGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAATTGGTCGCATG
* * * * *
19437350 TGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAA-T-TGGTCGCATG
* *
19437401 TGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAATTGGTCGCATG
* * * * *
19437450 TGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAA-T-TGGTCGCATG
* * *
19437501 TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAATTGGTCGCATG
* * *
19437550 TGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATA
1 TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATA
19437587 GCTTCGGCTA
Statistics
Matches: 285, Mismatches: 46, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
49 156 0.55
50 6 0.02
51 123 0.43
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAATTGGTCGCATG
Found at i:19441480 original size:49 final size:47
Alignment explanation
Indices: 19441421--19441592 Score: 184
Period size: 48 Copynumber: 3.6 Consensus size: 47
19441411 TGTTGTGTGT
*
19441421 CAGTGTAAGACCTGTCTGGGACATGGCATCTACATCGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATC-ACATCAAT-GATGAGAGC
* * * *
19441470 CAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCAATTATGGGAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCA-CATCAATGATGAGAGC
* * * * **
19441518 CAGTGTAAGACCTATCTGGGACATGACGTCAACTTCAATG-TGCTAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATC-ACATCAATGATGAGAGC
*
19441565 TAGTGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
19441593 GTCAGCATTT
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
47 15 0.14
48 53 0.51
49 36 0.35
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (47 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCACATCAATGATGAGAGC
Found at i:19445093 original size:56 final size:56
Alignment explanation
Indices: 19445033--19445168 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
19445023 TCCCAGGTAG
* * *
19445033 GGTCTTACTCACACACATATATCGTAATCACATATCGATGCCAATGTATTAAACGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
* *
19445089 GGTCTTACTCGCACACATATAACGGAATCACATATCGATGCCAACGTATTAAACTT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
19445145 GGTCTTACTCGCACACATATATCG
1 GGTCTTACTCGCACACATATATCG
19445169 ATGCCATGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGT
Found at i:19445748 original size:28 final size:26
Alignment explanation
Indices: 19445705--19445756 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
19445695 TACATTTCAT
**
19445705 TTATTTTACATTTTAGTCCCTCAATTTA
1 TTATTTTACAAATTAG-CCCT-AATTTA
19445733 TTATTTTACAAATTAGCCCTAATT
1 TTATTTTACAAATTAGCCCTAATT
19445757 ACTCAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 4 0.18
28 14 0.64
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (26 bp):
TTATTTTACAAATTAGCCCTAATTTA
Found at i:19446345 original size:14 final size:16
Alignment explanation
Indices: 19446319--19446351 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19446309 TAAAACACAA
19446319 AAATTTCACACAT-AT
1 AAATTTCACACATAAT
19446334 AAATTT-ACACATAAT
1 AAATTTCACACATAAT
19446349 AAA
1 AAA
19446352 CACAGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTTCACACATAAT
Found at i:19451034 original size:31 final size:30
Alignment explanation
Indices: 19450999--19451057 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
19450989 ACCCTTTAAA
*
19450999 ATATTTTCACTATT-AGCCCTTCAAATTTTTC
1 ATATTTACACT-TTAAGCCC-TCAAATTTTTC
*
19451030 ATATTTACACTTTAATCCCTCAAATTTT
1 ATATTTACACTTTAAGCCCTCAAATTTT
19451058 AAGTATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.47
Consensus pattern (30 bp):
ATATTTACACTTTAAGCCCTCAAATTTTTC
Found at i:19462547 original size:23 final size:23
Alignment explanation
Indices: 19462517--19462563 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
19462507 TTGTTTCCAT
19462517 AGATTTCATGCTTACCCATATGC
1 AGATTTCATGCTTACCCATATGC
19462540 AGATTTCATGCTTACCCATATGC
1 AGATTTCATGCTTACCCATATGC
19462563 A
1 A
19462564 TTCATTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (23 bp):
AGATTTCATGCTTACCCATATGC
Found at i:19471441 original size:2 final size:2
Alignment explanation
Indices: 19471434--19471473 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19471424 CTCAATATTT
19471434 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19471474 TATATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:19477200 original size:43 final size:43
Alignment explanation
Indices: 19477152--19477276 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 43
19477142 GCTGGTACTA
*
19477152 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATATG
** *
19477195 TATTCGGGCCTTTATGCCTAGCAGGCTTCGTGCCGGTGATATG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATATG
* *
19477238 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGA
19477277 AATGATATGT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATATG
Found at i:19479540 original size:42 final size:42
Alignment explanation
Indices: 19479494--19479718 Score: 193
Period size: 42 Copynumber: 5.2 Consensus size: 42
19479484 TCCAACTTTA
* * *
19479494 GTCTTACACGAAGTCTCACATCGATGCCATGTCCCAGACATG
1 GTCTTACACGAAATCTCATATCGATGCCATATCCCAGACATG
* * ** * *
19479536 GTCTT-TACGAAATCACATATCGATGCCGCATCCTAGACAAG
1 GTCTTACACGAAATCTCATATCGATGCCATATCCCAGACATG
* * * *
19479577 GTCTTACACGAAATCTCATACCGAAGCCATATCCCAGATATA
1 GTCTTACACGAAATCTCATATCGATGCCATATCCCAGACATG
* * * *
19479619 GTCTTACAAGTAATCTCATATCGATACCGATGCCATATCCCAAATATG
1 GTCTTACACGAAATCTC--AT--AT--CGATGCCATATCCCAGACATG
* *
19479667 GTCTTACAC-AGGATCTCATATCGATGCCATGTCCCAGACATG
1 GTCTTACACGA-AATCTCATATCGATGCCATATCCCAGACATG
*
19479709 GTATTACACG
1 GTCTTACACG
19479719 TATCACAATG
Statistics
Matches: 142, Mismatches: 32, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
41 32 0.23
42 72 0.51
44 4 0.03
46 3 0.02
48 31 0.22
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (42 bp):
GTCTTACACGAAATCTCATATCGATGCCATATCCCAGACATG
Found at i:19479647 original size:48 final size:48
Alignment explanation
Indices: 19479594--19479691 Score: 144
Period size: 48 Copynumber: 2.0 Consensus size: 48
19479584 ACGAAATCTC
*
19479594 ATACCGAAGCCATATCCCAGATATAGTCTTACA-AGTAATCTCATATCG
1 ATACCGAAGCCATATCCCAAATATAGTCTTACACAG-AATCTCATATCG
* * *
19479642 ATACCGATGCCATATCCCAAATATGGTCTTACACAGGATCTCATATCG
1 ATACCGAAGCCATATCCCAAATATAGTCTTACACAGAATCTCATATCG
19479690 AT
1 AT
19479692 GCCATGTCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 43 0.96
49 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (48 bp):
ATACCGAAGCCATATCCCAAATATAGTCTTACACAGAATCTCATATCG
Found at i:19479739 original size:36 final size:37
Alignment explanation
Indices: 19479690--19479762 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
19479680 TCTCATATCG
19479690 ATGCCATGTCCCAGAC-ATGGTATTACACGTA-TCACA
1 ATGCCATGTCCCAG-CTATGGTATTACACGTACTCACA
*
19479726 ATGCCATAG-CCCAGCTATGGTCTTACACGTACTCACA
1 ATGCCAT-GTCCCAGCTATGGTATTACACGTACTCACA
19479763 TGTATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
35 1 0.03
36 26 0.79
37 6 0.18
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (37 bp):
ATGCCATGTCCCAGCTATGGTATTACACGTACTCACA
Found at i:19483996 original size:2 final size:2
Alignment explanation
Indices: 19483991--19484024 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19483981 CATTAAGTGC
19483991 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19484025 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:19484119 original size:40 final size:40
Alignment explanation
Indices: 19484033--19484108 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
19484023 CATATATATA
*
19484033 TAGCCGAAGCTATCACAAATCGCACACCAAGAGCCACATT
1 TAGCCGAAGCTATCACAAACCGCACACCAAGAGCCACATT
** * *
19484073 TAGCCGAAGCTATTTCAAACCGCACACTAAGTGCCA
1 TAGCCGAAGCTATCACAAACCGCACACCAAGAGCCA
19484109 TTCTTAGCCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.17
Consensus pattern (40 bp):
TAGCCGAAGCTATCACAAACCGCACACCAAGAGCCACATT
Found at i:19488468 original size:44 final size:44
Alignment explanation
Indices: 19488420--19488521 Score: 177
Period size: 44 Copynumber: 2.3 Consensus size: 44
19488410 AATTGAGTTT
* *
19488420 GCACTAAGTGTGTGGAAATCATTCTAGCATTAGCTAACTTTTAA
1 GCACTAAGTGTGCGGAAATCATTCTAGCATTAGCTAACCTTTAA
*
19488464 GCACTAAGTGTGCGGAAATCGTTCTAGCATTAGCTAACCTTTAA
1 GCACTAAGTGTGCGGAAATCATTCTAGCATTAGCTAACCTTTAA
19488508 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
19488522 AATGTTTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
GCACTAAGTGTGCGGAAATCATTCTAGCATTAGCTAACCTTTAA
Found at i:19490007 original size:46 final size:46
Alignment explanation
Indices: 19489854--19490076 Score: 195
Period size: 46 Copynumber: 4.8 Consensus size: 46
19489844 CACTCGTGTT
* * * *
19489854 AGCTAGTGTAAGCCATGTCTGGGACATGCATCGGCAAC-ATTATGAG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGA-GACGAG
* * *
19489900 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAG
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAG
* * * *
19489948 TGCTGGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGACGTA-
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACG-AG
* * *
19489994 AGCTAGTGTAAGACATGTCTGGCACATGCATCGGC-TACGAGATGTG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGACGAG
* * *
19490040 -TC-AGTGTAAGACCATGTTTGGGATATGGCATCGGCAT
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAT
19490077 AGATATACTA
Statistics
Matches: 144, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
44 9 0.06
45 13 0.09
46 69 0.48
47 30 0.21
48 22 0.15
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAG
Found at i:19495650 original size:42 final size:42
Alignment explanation
Indices: 19495603--19495687 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
19495593 TCACCATGGG
* *
19495603 GTGCTCCAGTGCTTTTTGTGAAAAAGAAGGATGGGTCGATGA
1 GTGCTCCAGTGCTTTTTGTGAAAAAGAAGGACGGGTCAATGA
*
19495645 GTGCTCCAGTGCTTTTTGTGAAAAAGAAGTACGGGTCAATGA
1 GTGCTCCAGTGCTTTTTGTGAAAAAGAAGGACGGGTCAATGA
19495687 G
1 G
19495688 GTTATGTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (42 bp):
GTGCTCCAGTGCTTTTTGTGAAAAAGAAGGACGGGTCAATGA
Found at i:19502011 original size:43 final size:43
Alignment explanation
Indices: 19501945--19502071 Score: 118
Period size: 43 Copynumber: 3.0 Consensus size: 43
19501935 AGATCGTACA
* *
19501945 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
19501988 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATA--G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAATCAAATATCG
* * * * * * * *
19502029 GTGCCGATGTCCCAAACATGGTCGTACACGAAAACACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
19502072 GATCCTGTGT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
41 31 0.45
42 3 0.04
43 34 0.49
44 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
Found at i:19512109 original size:22 final size:22
Alignment explanation
Indices: 19512080--19512127 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
19512070 CTTGATACAA
19512080 ACTCAAAAATATCTCTTTTCAT
1 ACTCAAAAATATCTCTTTTCAT
19512102 -CTCAAAAATATCTCTTTTCAT
1 ACTCAAAAATATCTCTTTTCAT
19512123 ACTCA
1 ACTCA
19512128 GCCACCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (22 bp):
ACTCAAAAATATCTCTTTTCAT
Found at i:19516242 original size:48 final size:48
Alignment explanation
Indices: 19516007--19516289 Score: 201
Period size: 48 Copynumber: 5.9 Consensus size: 48
19515997 AATTGGGTGA
* * **
19516007 TATGTGTGCCAGTGTAAGACCATGTCTCGGACATGGCATCGGCCAAAT
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGT
* * * * * * *
19516055 TATGAGAGCCAGTGTAGGACCATGTTTGGGACATGGCATC-GACATTGA
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCA-CGT
** * * * * *** *
19516103 TATGTTTGCTAGTATAAGGCCATGTCTAGGACATGACATCGGCGTTGA
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGT
* * * * * * *
19516151 TATGTGTGCTAGTGTAAGATCATGTCT-GAGATATAGCAACGGCCACCT
1 TATGTGAGCCAGTGTAAGACCATGTCTAG-GACATGGCATCGGCCACGT
* * *
19516199 TATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGT
* * * * * *
19516247 CATGTGAGCCAGTGTAAAACAATGCCTTGGACATGACATCGGC
1 TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC
19516290 AATTTACCCT
Statistics
Matches: 179, Mismatches: 52, Indels: 8
0.75 0.22 0.03
Matches are distributed among these distances:
47 4 0.02
48 173 0.97
49 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
TATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGT
Found at i:19516279 original size:144 final size:144
Alignment explanation
Indices: 19516004--19516289 Score: 349
Period size: 144 Copynumber: 2.0 Consensus size: 144
19515994 GACAATTGGG
* *
19516004 TGATATGTGTGCCAGTGTAAGACCATGTCTCGGACATGGCATCGGCCAAATTATGAGAGCCAGTG
1 TGATATGTGTGCCAGTGTAAGACCATGTCTCGGACATAGCAACGGCCAAATTATGAGAGCCAGTG
* * * * * ** * ** * *
19516069 TAGGACCATGTTTGGGACATGGCATCGACATTGATATGTTTGCTAGTATAAGGCCATGTCTAGGA
66 TAAGACCATGTCTAGGACATGGCATCGACATCGACATGTGAGCCAGTATAAAACAATGCCTAGGA
19516134 CATGACATCGGCGT
131 CATGACATCGGCGT
* * * **
19516148 TGATATGTGTGCTAGTGTAAGATCATGTCT-GAGATATAGCAACGGCCACCTTATGAGAGCCAGT
1 TGATATGTGTGCCAGTGTAAGACCATGTCTCG-GACATAGCAACGGCCAAATTATGAGAGCCAGT
* * * *
19516212 GTAAGACCATGTCTAGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAAACAATGCCTTGG
65 GTAAGACCATGTCTAGGACATGGCATCGACATCGACATGTGAGCCAGTATAAAACAATGCCTAGG
19516277 ACATGACATCGGC
130 ACATGACATCGGC
19516290 AATTTACCCT
Statistics
Matches: 118, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
143 1 0.01
144 117 0.99
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (144 bp):
TGATATGTGTGCCAGTGTAAGACCATGTCTCGGACATAGCAACGGCCAAATTATGAGAGCCAGTG
TAAGACCATGTCTAGGACATGGCATCGACATCGACATGTGAGCCAGTATAAAACAATGCCTAGGA
CATGACATCGGCGT
Found at i:19528030 original size:42 final size:43
Alignment explanation
Indices: 19527929--19528033 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 43
19527919 CTGAGATATT
*
19527929 GTGTAAGACCGTGTCTGGGACACAGGCAATGATTGAGATTTAC
1 GTGTAAGACCATGTCTGGGACACAGGCAATGATTGAGATTTAC
* * *
19527972 GTATAAGACCAAGTCTGGGACATC-GGCATTGTATCT-AG-TTT-C
1 GTGTAAGACCATGTCTGGGACA-CAGGCAATG-AT-TGAGATTTAC
*
19528014 GTGTAAGACCCTGTCTGGGA
1 GTGTAAGACCATGTCTGGGA
19528034 TAAGGCATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
42 18 0.35
43 28 0.54
44 5 0.10
45 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACACAGGCAATGATTGAGATTTAC
Found at i:19528441 original size:25 final size:21
Alignment explanation
Indices: 19528391--19528434 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19528381 CTCTTTGTAG
19528391 CTTACTTTGTGTGATTTCTGC
1 CTTACTTTGTGTGATTTCTGC
19528412 CTTACTTTGTGTGATTTCTGC
1 CTTACTTTGTGTGATTTCTGC
19528433 CT
1 CT
19528435 GTTTTACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.20, G:0.18, T:0.52
Consensus pattern (21 bp):
CTTACTTTGTGTGATTTCTGC
Found at i:19528935 original size:26 final size:26
Alignment explanation
Indices: 19528876--19528935 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
19528866 AGAATCACAC
* *
19528876 GGCCGTGGCATACGGGCGTGTCTGTT
1 GGCCGTGGCACACGGGCGTGTCTATT
* **
19528902 AGTTGTGGCACACGGGCGTGTCTATT
1 GGCCGTGGCACACGGGCGTGTCTATT
19528928 GGCCGTGG
1 GGCCGTGG
19528936 GAATAAGTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.10, C:0.22, G:0.42, T:0.27
Consensus pattern (26 bp):
GGCCGTGGCACACGGGCGTGTCTATT
Found at i:19534642 original size:24 final size:25
Alignment explanation
Indices: 19534612--19534669 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
19534602 CGGACCGTAT
19534612 CTTGATGAATTTGTTG-TTGTATTCA
1 CTTGATGAATTTGTTGATT-TATTCA
*
19534637 -TTGATG-ATTTTTTGATTTATTCA
1 CTTGATGAATTTGTTGATTTATTCA
*
19534660 CATGATGAAT
1 CTTGATGAAT
19534670 CTGAGCATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 13 0.46
24 13 0.46
25 2 0.07
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (25 bp):
CTTGATGAATTTGTTGATTTATTCA
Found at i:19538284 original size:43 final size:42
Alignment explanation
Indices: 19538194--19538286 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
19538184 GATTTACGTA
* * *
19538194 TAAGACCATGTTTGGGACATTGGTATCGTATCTGATTTCATG
1 TAAGACCATGTTTGGGACATAGGCATCGTATCTGATTACATG
*
19538236 TAAGACCCTGTTTGGGAC-TGAGGCATCGATAT-TGAATTACATG
1 TAAGACCATGTTTGGGACAT-AGGCATCG-TATCTG-ATTACATG
19538279 TAAGACCA
1 TAAGACCA
19538287 CGTCCGGGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 1 0.02
42 25 0.58
43 17 0.40
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (42 bp):
TAAGACCATGTTTGGGACATAGGCATCGTATCTGATTACATG
Found at i:19549607 original size:39 final size:39
Alignment explanation
Indices: 19549564--19549638 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
19549554 TATTTCTCAA
19549564 GGTTTGAAACCACCTGAACTCCTAACAAATTAGTTACAG
1 GGTTTGAAACCACCTGAACTCCTAACAAATTAGTTACAG
*
19549603 GGTTTGAAACCACCTGAACTCCTAACAAATTGGTTA
1 GGTTTGAAACCACCTGAACTCCTAACAAATTAGTTA
19549639 TGTCCTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (39 bp):
GGTTTGAAACCACCTGAACTCCTAACAAATTAGTTACAG
Found at i:19551356 original size:30 final size:29
Alignment explanation
Indices: 19551322--19551393 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 29
19551312 TTAATAATAG
* *
19551322 TGATAATAATAATAGAAATTAATAAAGGAA
1 TGATAATAGTAATAGAAA-TAAAAAAGGAA
* *
19551352 TGATATTAGTAATAGTAATAAAAAAGGAA
1 TGATAATAGTAATAGAAATAAAAAAGGAA
*
19551381 -AATAATAGTAATA
1 TGATAATAGTAATA
19551394 ATAATGGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 11 0.31
29 10 0.28
30 15 0.42
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (29 bp):
TGATAATAGTAATAGAAATAAAAAAGGAA
Found at i:19551663 original size:23 final size:23
Alignment explanation
Indices: 19551637--19551684 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
19551627 CGGAAATCGC
19551637 CCGTTTTGACTTATATAAGGGTA
1 CCGTTTTGACTTATATAAGGGTA
19551660 CCGTTTTGACTTATATAAGGGTA
1 CCGTTTTGACTTATATAAGGGTA
19551683 CC
1 CC
19551685 AAACGGTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (23 bp):
CCGTTTTGACTTATATAAGGGTA
Found at i:19561754 original size:40 final size:40
Alignment explanation
Indices: 19561699--19561778 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
19561689 TCATAAGAGA
19561699 ATTCGCGAACTCAGTTGGCAAAGCCAATGCCTTATTCACT
1 ATTCGCGAACTCAGTTGGCAAAGCCAATGCCTTATTCACT
19561739 ATTCGCGAACTCAGTTGGCAAAGCCAATGCCTTATTCACT
1 ATTCGCGAACTCAGTTGGCAAAGCCAATGCCTTATTCACT
19561779 CTGAGTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (40 bp):
ATTCGCGAACTCAGTTGGCAAAGCCAATGCCTTATTCACT
Found at i:19564102 original size:99 final size:100
Alignment explanation
Indices: 19563916--19564106 Score: 285
Period size: 100 Copynumber: 1.9 Consensus size: 100
19563906 ATTGTGAATA
* * * *
19563916 CACGTATGTAGTACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATGTGTAGTACT
1 CACGTATGTAGTACAAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
*
19563981 AAGTGCAGGCTACTACGTGTATCAGATGATGAGGT
66 AAGTGCAGGCTACTACGCGTATCAGATGATGAGGT
* * * *
19564016 CACGTGTGTAGTACAAAGTGCAGGCTACTACGTGTACCAGATTGTTGA-TCGCATGTGTGGTACT
1 CACGTATGTAGTACAAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
*
19564080 AAGTGCAGGCTACTATGCGTATCAGAT
66 AAGTGCAGGCTACTACGCGTATCAGAT
19564107 AGCTTCGGCT
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 40 0.49
100 41 0.51
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (100 bp):
CACGTATGTAGTACAAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
AAGTGCAGGCTACTACGCGTATCAGATGATGAGGT
Found at i:19564106 original size:49 final size:50
Alignment explanation
Indices: 19563922--19564106 Score: 239
Period size: 50 Copynumber: 3.7 Consensus size: 50
19563912 AATACACGTA
* * * *
19563922 TGTAGTACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTGAGTCGCATG
* * *
19563972 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGATGAGGTCACGTG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTGA-GTCGCATG
* *
19564022 TGTAGTACAAAGTGCAGGCTACTACGTGTACCAGATTGTTGA-TCGCATG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTGAGTCGCATG
* * *
19564071 TGTGGTACTAAGTGCAGGCTACTATGCGTATCAGAT
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT
19564107 AGCTTCGGCT
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
49 40 0.34
50 72 0.62
51 5 0.04
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (50 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATTGTTGAGTCGCATG
Found at i:19568269 original size:51 final size:52
Alignment explanation
Indices: 19568202--19568300 Score: 182
Period size: 51 Copynumber: 1.9 Consensus size: 52
19568192 AAGTTGAAAG
19568202 AGCGGTTGACCAAAGCACCAATGTTAGTGCAACCCGAGTCG-GGAAAGGAAT
1 AGCGGTTGACCAAAGCACCAATGTTAGTGCAACCCGAGTCGAGGAAAGGAAT
*
19568253 AGCGGTTGACCAAAGCACCAGTGTTAGTGCAACCCGAGTCGAGGAAAG
1 AGCGGTTGACCAAAGCACCAATGTTAGTGCAACCCGAGTCGAGGAAAG
19568301 AATTTGTGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 40 0.87
52 6 0.13
ACGTcount: A:0.32, C:0.22, G:0.30, T:0.15
Consensus pattern (52 bp):
AGCGGTTGACCAAAGCACCAATGTTAGTGCAACCCGAGTCGAGGAAAGGAAT
Found at i:19571504 original size:50 final size:49
Alignment explanation
Indices: 19571429--19571613 Score: 237
Period size: 50 Copynumber: 3.7 Consensus size: 49
19571419 AATACACGTA
*
19571429 TGTAGTACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATG
1 TGTAGTACTAAGTGTAGGCTACTACGTGTATCAGA-TGTTAAGTCGCATG
* * * * *
19571479 TGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGATGAGGTCACGTG
1 TGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATG-TTAAGTCGCATG
* * *
19571529 TGTAGTACAAAGTGTAGGCTACTACGTGTACCAGATTGTTGA-TCGCATG
1 TGTAGTACTAAGTGTAGGCTACTACGTGTATCAGA-TGTTAAGTCGCATG
* *
19571578 TGTAGTACTAAGTGTAGGCTACTATGCGTATCAGAT
1 TGTAGTACTAAGTGTAGGCTACTACGTGTATCAGAT
19571614 AGCTTCGACT
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.01
49 38 0.33
50 74 0.64
51 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (49 bp):
TGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGTTAAGTCGCATG
Found at i:19571609 original size:99 final size:100
Alignment explanation
Indices: 19571423--19571613 Score: 294
Period size: 100 Copynumber: 1.9 Consensus size: 100
19571413 ATTGTGAATA
* * *
19571423 CACGTATGTAGTACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATGTGTAGTACT
1 CACGTATGTAGTACAAAGTGTAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
*
19571488 AAGTGCAGGCTACTACGTGTATCAGATGATGAGGT
66 AAGTGCAGGCTACTACGCGTATCAGATGATGAGGT
* * *
19571523 CACGTGTGTAGTACAAAGTGTAGGCTACTACGTGTACCAGATTGTTGA-TCGCATGTGTAGTACT
1 CACGTATGTAGTACAAAGTGTAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
* *
19571587 AAGTGTAGGCTACTATGCGTATCAGAT
66 AAGTGCAGGCTACTACGCGTATCAGAT
19571614 AGCTTCGACT
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 40 0.49
100 42 0.51
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (100 bp):
CACGTATGTAGTACAAAGTGTAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACT
AAGTGCAGGCTACTACGCGTATCAGATGATGAGGT
Found at i:19573557 original size:28 final size:29
Alignment explanation
Indices: 19573525--19573639 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
19573515 TACCTGTATT
* *
19573525 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
19573553 TGGCCCATTAGGCCCAAATCACCTAT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
* *
19573582 TGGCCCATTAGGCCCAAATCACATTTACA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
19573611 TGGCCCGTTAGGCCC-AATCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
19573639 T
1 T
19573640 TCATGCTCAC
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 27 0.36
29 48 0.63
30 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:19573588 original size:57 final size:57
Alignment explanation
Indices: 19573516--19573631 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 57
19573506 AAATTCTCAT
* * * *
19573516 ACCTGTATTTGGCCCATTAAGCCC-AATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGCCCAAATCACATTCACATGGCCCATTAGGCCC-AATC
* * *
19573573 ACCTATATATGGCCCATTAGGCCCAAATCACATTTACATGGCCCGTTAGGCCCAATC
1 ACCTATATATGGCCCATTAAGCCCAAATCACATTCACATGGCCCATTAGGCCCAATC
19573630 AC
1 AC
19573632 ATTCATATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 27 0.53
58 24 0.47
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (57 bp):
ACCTATATATGGCCCATTAAGCCCAAATCACATTCACATGGCCCATTAGGCCCAATC
Found at i:19576054 original size:16 final size:18
Alignment explanation
Indices: 19576035--19576067 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
19576025 CATACGAATT
19576035 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
19576051 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
19576068 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:19576697 original size:43 final size:43
Alignment explanation
Indices: 19576648--19576837 Score: 317
Period size: 43 Copynumber: 4.4 Consensus size: 43
19576638 GCATTACGCA
*
19576648 TGCTAGGCTCGAAGCCTGATATTAACTCACCGGCATTATAGCC
1 TGCTAGGCTCGAAGCCCGATATTAACTCACCGGCATTATAGCC
*
19576691 TGCTAGGCTCGAAGCCCGATATTAACTCATCGGCATTATAGCC
1 TGCTAGGCTCGAAGCCCGATATTAACTCACCGGCATTATAGCC
* * *
19576734 TGCTAGCCTTGAAGCCCGATATTAACTCACTGGCATTATAGCC
1 TGCTAGGCTCGAAGCCCGATATTAACTCACCGGCATTATAGCC
* *
19576777 TGCTAGGGTCAAAGCCCGATATTAACTCACCGGCATTATAGCC
1 TGCTAGGCTCGAAGCCCGATATTAACTCACCGGCATTATAGCC
19576820 TGCTAGGCTCGAAGCCCG
1 TGCTAGGCTCGAAGCCCG
19576838 TGTAACCTTA
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 134 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (43 bp):
TGCTAGGCTCGAAGCCCGATATTAACTCACCGGCATTATAGCC
Found at i:19580993 original size:16 final size:18
Alignment explanation
Indices: 19580974--19581006 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
19580964 CATACGAATT
19580974 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
19580990 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
19581007 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:19581633 original size:43 final size:43
Alignment explanation
Indices: 19581571--19581822 Score: 380
Period size: 43 Copynumber: 5.9 Consensus size: 43
19581561 CTGAACTCAT
* *
19581571 TCACCGGCATTA-CGCCTGCTAGGCTCGAAGCCTGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
* *
19581613 TCACTGGCATTATAGCCTGCTAGGCTCGAACCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
* *
19581656 TCACCGGTATTATAGCTTGCTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
** * *
19581699 TCACTAGTATTATAGCCTACTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
* *
19581742 TCACCGGCATTATAGCCTGCTAGGCTCGAAGTCTGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
19581785 TCACCGGCATTATAGCCTGCTAGGCTCGAAGTCCCGAT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAG-CCCGAT
19581823 TAGTGCCGTA
Statistics
Matches: 188, Mismatches: 20, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
42 11 0.06
43 173 0.92
44 4 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
Found at i:19585505 original size:29 final size:29
Alignment explanation
Indices: 19585442--19585549 Score: 103
Period size: 29 Copynumber: 3.8 Consensus size: 29
19585432 TTCACATACT
* * * *
19585442 TGTATCTGGCCCATTAAGCCC-AATCATA
1 TGTATATGGCCTATTAGGCCCAAATCACA
* *
19585470 T-TCATATAGCCTATTAGGCCCAAATCACC
1 TGT-ATATGGCCTATTAGGCCCAAATCACA
*
19585499 TGTATATGGCCCATTAGGCCCAAATCACA
1 TGTATATGGCCTATTAGGCCCAAATCACA
* * *
19585528 TTTACATGGCCTGTTAGGCCCA
1 TGTATATGGCCTATTAGGCCCA
19585550 GCCACATTCA
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
27 1 0.02
28 15 0.23
29 47 0.73
30 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (29 bp):
TGTATATGGCCTATTAGGCCCAAATCACA
Found at i:19585822 original size:24 final size:24
Alignment explanation
Indices: 19585773--19585823 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
19585763 GTAGCCAAAC
* *
19585773 TTTTGGCTTTTCGGCATTTCTACT
1 TTTTGGCATTTCGGCATTTCGACT
*
19585797 TTTTGGCATTTCGGCATTTCGGCT
1 TTTTGGCATTTCGGCATTTCGACT
19585821 TTT
1 TTT
19585824 GCCGATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.20, G:0.20, T:0.53
Consensus pattern (24 bp):
TTTTGGCATTTCGGCATTTCGACT
Found at i:19588266 original size:28 final size:28
Alignment explanation
Indices: 19588234--19588288 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
19588224 CATATCGGAC
19588234 AATTTACAATTAATTTGAAATAAATGAG
1 AATTTACAATTAATTTGAAATAAATGAG
19588262 AATTTACAATTAATTTGAAATAAATGA
1 AATTTACAATTAATTTGAAATAAATGA
19588289 CATACATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (28 bp):
AATTTACAATTAATTTGAAATAAATGAG
Found at i:19588760 original size:23 final size:23
Alignment explanation
Indices: 19588678--19588765 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 23
19588668 ACCTGATCAG
*
19588678 TATACGACACA-TAAGTGCCT-A
1 TATACGACACACGAAGTGCCTGA
* * *
19588699 -AAACGACACACGAGGTGCC-CA
1 TATACGACACACGAAGTGCCTGA
*
19588720 -ATACGACACACGAGGTGCCTGA
1 TATACGACACACGAAGTGCCTGA
**
19588742 TATACGACACATAAAGTGCCTGA
1 TATACGACACACGAAGTGCCTGA
19588765 T
1 T
19588766 CGGCAAAGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
20 9 0.16
21 25 0.45
22 1 0.02
23 20 0.36
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (23 bp):
TATACGACACACGAAGTGCCTGA
Found at i:19604461 original size:46 final size:46
Alignment explanation
Indices: 19604411--19604584 Score: 215
Period size: 46 Copynumber: 3.7 Consensus size: 46
19604401 ACATCTTGTA
*
19604411 GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TACGTCACGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CGTCACGAG
* * *
19604457 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCACGAG
* * * * *
19604503 GCTGATGACATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCACGAG
* *
19604551 GCTGATGCATGTGCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
19604585 ACACCAATGA
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
46 59 0.53
47 28 0.25
48 25 0.22
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCACGAG
Found at i:19604530 original size:94 final size:91
Alignment explanation
Indices: 19604323--19604587 Score: 277
Period size: 94 Copynumber: 2.8 Consensus size: 91
19604313 AGGCCAACAC
* * * *
19604323 CATGTCTCAGACATGGTCTTACACTAGCTCTCACATATCTATGCCGATGCCATGTCCCAGACAGG
1 CATGTCCCAGACATGGTCTTACACTAGCTCT-ACATA-CGAGGCCGATG-CATGTCCCAGACA-T
* **
19604388 GTCTTACACTAACACATCTTGTAGCCGATG
62 GTCTTACACTAGCACATCTTCAAGCCGATG
* *
19604418 CATGTCCCAGACAT-GTCTTACACTGGCT-TACGTCACGAGGCCGATGCATGTCCCAGACATGTC
1 CATGTCCCAGACATGGTCTTACACTAGCTCTACAT-ACGAGGCCGATGCATGTCCCAGACATGTC
* *
19604481 TTACACTAGCTC-TCGTCTCAATGCTGATG
65 TTACACTAGCACATC-T-TCAA-GCCGATG
* * * *
19604510 ACATGTCCCAGACATGGTCTTACACTAGCTCT-CATAATGTGGCTGATGCATGTGCCAGACATGT
1 -CATGTCCCAGACATGGTCTTACACTAGCTCTACAT-ACGAGGCCGATGCATGTCCCAGACATGT
19604574 CTTACACTAGCACA
64 CTTACACTAGCACA
19604588 CCAATGACTC
Statistics
Matches: 143, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
89 2 0.01
90 14 0.10
91 15 0.10
92 18 0.13
93 16 0.11
94 64 0.45
95 14 0.10
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (91 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTACATACGAGGCCGATGCATGTCCCAGACATGTCT
TACACTAGCACATCTTCAAGCCGATG
Found at i:19604561 original size:140 final size:143
Alignment explanation
Indices: 19604216--19604581 Score: 394
Period size: 140 Copynumber: 2.6 Consensus size: 143
19604206 CACAGGGTAT
*
19604216 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATTCATCAA-GT-CGATGCCATGT
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCA-TCAT-AATGTGCGATG-CATGT
* * *
19604279 CCTAAACATGGTCTTACACTGACTATCGAAATCGAGGCCAACACCATGTCTCAGACATGGTCTTA
63 CCCAGACAT-GTCTTACACTGACTATCGAAATCGAGGCCAACACCATGTCCCAGACATGGTCTTA
19604344 CACTAGCTCTCACATATC
127 CACTAGCTCT-ACATATC
* * * *
19604362 TATGCCGATGCCATGTCCCAGACAGGGTCTTACACTAACACATC-T--TGTAGCCGATGCATGTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATAATGT-G-CGATGCATGTC
* ** * **
19604424 CCAGACATGTCTTACACTGGCT-TACGTCA-CGAGGCCGA-TGCATGTCCCAGACAT-GTCTTAC
64 CCAGACATGTCTTACACTGACTAT-CGAAATCGAGGCCAACACCATGTCCCAGACATGGTCTTAC
* *
19604485 ACTAGCTCT-CGTCTC
128 ACTAGCTCTACATATC
* * *
19604500 AATGCTGATGACATGTCCCAGACATGGTCTTACACTAGCTC-TCATAATGTGGCTGATGCATGTG
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATAATGT-GC-GATGCATGTC
19604564 CCAGACATGTCTTACACT
64 CCAGACATGTCTTACACT
19604582 AGCACACCAA
Statistics
Matches: 187, Mismatches: 24, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
137 2 0.01
138 40 0.21
139 1 0.01
140 47 0.25
141 13 0.07
142 11 0.06
143 16 0.09
144 13 0.07
145 7 0.04
146 37 0.20
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (143 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATAATGTGCGATGCATGTCCC
AGACATGTCTTACACTGACTATCGAAATCGAGGCCAACACCATGTCCCAGACATGGTCTTACACT
AGCTCTACATATC
Found at i:19607490 original size:42 final size:43
Alignment explanation
Indices: 19607387--19607543 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 43
19607377 TGTGTTCTCA
* * * * *
19607387 TGTAAGACCATGTCTAGAACGTTGGCATCGACT-TATGATTTACG
1 TGTAAGACCATGTCTGGGACATTGGCATC-AATATTTGATTT-CG
* *
19607431 TGTAAGATCATGCCTGGGACATTGGCATC-ATATTTGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCAATATTTGATTTCG
* * * * *
19607473 TGTAAGACCCTGTCTGGGACAGTAGCATCAATATTTGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCAATATTTGATTTCG
* * *
19607516 TGTAAGACCAAGTTTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
19607544 TGTATGAGCT
Statistics
Matches: 91, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
42 27 0.30
43 40 0.44
44 24 0.26
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCAATATTTGATTTCG
Found at i:19607507 original size:43 final size:42
Alignment explanation
Indices: 19607422--19607525 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
19607412 CATCGACTTA
* * *
19607422 TGATTTACGTGTAAGATCATGCCTGGGACATTGGCATCATATT
1 TGATTT-CGTGTAAGACCATGCCTGGGACAGTAGCATCATATT
* *
19607465 TGATTTCGTGTAAGACCCTGTCTGGGACAGTAGCATCAATATT
1 TGATTTCGTGTAAGACCATGCCTGGGACAGTAGCATC-ATATT
* *
19607508 TGATTACATGTAAGACCA
1 TGATTTCGTGTAAGACCA
19607526 AGTTTGGGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 26 0.50
43 26 0.50
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGCCTGGGACAGTAGCATCATATT
Found at i:19608664 original size:50 final size:50
Alignment explanation
Indices: 19608589--19608880 Score: 295
Period size: 50 Copynumber: 5.8 Consensus size: 50
19608579 ACCGAAGCTC
* * * *
19608589 TCTGGTACACATAATAGCCTACACTTAGAACTACACATGCGACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * * *
19608639 TCTGGTACACGTAGTAGCATGCACTTAGTACTACACATGTAACCTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * * * * *
19608689 TTTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGCTA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-CAA
* **
19608740 T-TGGGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTAACAA
1 TCT-GGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
** *
19608790 TCTGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-AA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
*** *
19608839 CCGTCTTAAACACATAGTAGCC-GCACATAGTACTACAC-TGTG
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTG
19608881 TTCTCACAAC
Statistics
Matches: 198, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
49 2 0.01
50 126 0.64
51 56 0.28
52 14 0.07
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
Found at i:19608768 original size:101 final size:101
Alignment explanation
Indices: 19608589--19608831 Score: 283
Period size: 101 Copynumber: 2.4 Consensus size: 101
19608579 ACCGAAGCTC
* * * * * * * * * * *
19608589 TCTGGTACACATAATAGCCTACACTTAGAACTACACATGCGACCTAA-CAATCT-GGTACACGTA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGCTAT-TGGGTACGCATA
** *
19608652 GTAGCATGCACTTAGTACTACACATGTAACCTAACCA
65 GTAGCATGCACTTAGTACTACACATACAACCTAACAA
*
19608689 TTTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGCTATTGGGTACGCATAG
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGCTATTGGGTACGCATAG
* *
19608754 TAGCCTGCACTTAGTACTACACATACGACCTAACAA
66 TAGCATGCACTTAGTACTACACATACAACCTAACAA
* **
19608790 TCTGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGA
19608832 CCTAAAACCG
Statistics
Matches: 120, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
100 39 0.32
101 81 0.68
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (101 bp):
TCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGCTATTGGGTACGCATAG
TAGCATGCACTTAGTACTACACATACAACCTAACAA
Found at i:19608835 original size:151 final size:151
Alignment explanation
Indices: 19608592--19608876 Score: 421
Period size: 151 Copynumber: 1.9 Consensus size: 151
19608582 GAAGCTCTCT
*
19608592 GGTACACATAATAGCCTACACTTAGAACTACACATGCGACCTAACAATCTGGTACACGTAGTAGC
1 GGTACACATAATAGCCTACACTTAGAACTACACATACGACCTAACAATCTGGTACACGTAGTAGC
* * *
19608657 ATGCACTTAGTACTACACATGTAACCT-AACCAT-TTGATACACATAGTAGCCTGCACTTAGTAC
66 ATGCACTTAGTACTACACACGTAACCTAAACCATCTT-AAACACATAGTAGCC-GCACATAGTAC
19608720 TACACACGTGATCAAAGCTATTG
129 TACACACGTGATCAAAGCTATTG
* * * * *
19608743 GGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTAACAATCTGGTACATGTAGTAGC
1 GGTACACATAATAGCCTACACTTAGAACTACACATACGACCTAACAATCTGGTACACGTAGTAGC
* * *
19608808 CTGCACTTAGTACTACACACGTGACCTAAAACCGTCTTAAACACATAGTAGCCGCACATAGTACT
66 ATGCACTTAGTACTACACACGTAACCT-AAACCATCTTAAACACATAGTAGCCGCACATAGTACT
19608873 ACAC
130 ACAC
19608877 TGTGTTCTCA
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
151 83 0.70
152 15 0.13
153 19 0.16
154 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (151 bp):
GGTACACATAATAGCCTACACTTAGAACTACACATACGACCTAACAATCTGGTACACGTAGTAGC
ATGCACTTAGTACTACACACGTAACCTAAACCATCTTAAACACATAGTAGCCGCACATAGTACTA
CACACGTGATCAAAGCTATTG
Found at i:19608870 original size:101 final size:99
Alignment explanation
Indices: 19608645--19608876 Score: 250
Period size: 101 Copynumber: 2.3 Consensus size: 99
19608635 ACAATCTGGT
* * ** * *
19608645 ACACGTAGTAGCATGCACTTAGTACTACACATGTAACCTAACCATTTGATACACATAGTAGCCTG
1 ACACATAGTAGC-CGCACTTAGTACTACACATACAACCTAACAATCTGATACACATAGTAGCCTG
* * **
19608710 CACTTAGTACTACACACGTGATCAAAGCTATTGGGT
65 CACTTAGTACTACACACGTGATAAAACCTATT-GAA
* * * **
19608746 ACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTAACAATCTGGTACATGTAGTAGCCTG
1 ACACATAGTAGCC-GCACTTAGTACTACACATACAACCTAACAATCTGATACACATAGTAGCCTG
*
19608811 CACTTAGTACTACACACGTGACCTAAAACCGTCTT-AA
65 CACTTAGTACTACACACGTGA--TAAAACC-TATTGAA
*
19608848 ACACATAGTAGCCGCACATAGTACTACAC
1 ACACATAGTAGCCGCACTTAGTACTACAC
19608877 TGTGTTCTCA
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
101 89 0.82
102 12 0.11
103 5 0.05
104 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (99 bp):
ACACATAGTAGCCGCACTTAGTACTACACATACAACCTAACAATCTGATACACATAGTAGCCTGC
ACTTAGTACTACACACGTGATAAAACCTATTGAA
Found at i:19609689 original size:30 final size:30
Alignment explanation
Indices: 19609648--19609704 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
19609638 AAAACCATAT
***
19609648 TTTGGCAAAATTATGTTTTTGCCCCTAAAC
1 TTTGGCAAAATTACACTTTTGCCCCTAAAC
*
19609678 TTTGTCAAAATTACACTTTTGCCCCTA
1 TTTGGCAAAATTACACTTTTGCCCCTA
19609705 GGCTCGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (30 bp):
TTTGGCAAAATTACACTTTTGCCCCTAAAC
Found at i:19611009 original size:43 final size:43
Alignment explanation
Indices: 19610961--19611043 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
19610951 TGAATGTAAT
*
19610961 AGTATGGCATGTATAGGCTAGAAGTATTAGGATATGTTTTAAA
1 AGTATGGCATGTATACGCTAGAAGTATTAGGATATGTTTTAAA
19611004 AGTATGGCATGTATACGCTAGAAGTATTAGGATATGTTTT
1 AGTATGGCATGTATACGCTAGAAGTATTAGGATATGTTTT
19611044 GTAATGTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (43 bp):
AGTATGGCATGTATACGCTAGAAGTATTAGGATATGTTTTAAA
Found at i:19612130 original size:23 final size:22
Alignment explanation
Indices: 19612068--19612132 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
19612058 TACTTGACCA
*
19612068 ATATACGACACATAAGTTCCTG
1 ATATACGACACATAAGTGCCTG
* *
19612090 A-A-ACGACACACGAGGTGCCTG
1 ATATACGACACA-TAAGTGCCTG
19612111 ATATACGACACATAAAGTGCCT
1 ATATACGACACAT-AAGTGCCT
19612133 AATCGGCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 8 0.24
21 9 0.26
22 2 0.06
23 15 0.44
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATATACGACACATAAGTGCCTG
Found at i:19613096 original size:27 final size:26
Alignment explanation
Indices: 19613066--19613119 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
19613056 TATTTCATAC
19613066 ATATATTAGTTA-ATAATATTAATAATA
1 ATATATTA-TTATATAATA-TAATAATA
19613093 ATATATTATTATTATAATATAATAATA
1 ATATATTATTA-TATAATATAATAATA
19613120 TTTAATTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.12
27 16 0.64
28 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATATTATTATATAATATAATAATA
Found at i:19613262 original size:15 final size:15
Alignment explanation
Indices: 19613242--19613275 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
19613232 TAATTTATTT
19613242 TAATAATAATAATCA
1 TAATAATAATAATCA
*
19613257 TAATAATCATAATCA
1 TAATAATAATAATCA
19613272 TAAT
1 TAAT
19613276 TTAATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATAATAATAATCA
Found at i:19613584 original size:3 final size:3
Alignment explanation
Indices: 19613571--19613644 Score: 53
Period size: 3 Copynumber: 24.7 Consensus size: 3
19613561 ATTTTATTTC
* * * * *
19613571 ATA AT- ATA ATA ATA TTA ATA ATA ATA TTT A-A ATA GAAA ATC ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* *
19613615 ATA ATA ATTA ATA AGA ATA ATT ATA ATA AT
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA AT
19613645 TGATTAATAA
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
2 3 0.06
3 45 0.85
4 5 0.09
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:19621568 original size:13 final size:13
Alignment explanation
Indices: 19621546--19621578 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19621536 AAGGGTTTGT
19621546 TTAT-TAAACTAA
1 TTATCTAAACTAA
19621558 TTATCTAAACTAA
1 TTATCTAAACTAA
*
19621571 TTAACTAA
1 TTATCTAA
19621579 TTTAAGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:19623112 original size:85 final size:86
Alignment explanation
Indices: 19622956--19623113 Score: 196
Period size: 86 Copynumber: 1.8 Consensus size: 86
19622946 TTGTGATTTC
** * **
19622956 GTGTAAGACCACGTCTGGGATGTTGGCATTGATTTGTGATTTACGTGTAAGACCATGTCTAGGAC
1 GTGTAAGACCACGTCTGGGATGTTGGCACCGATTTGTGATTTACATGTAAGACCACATCTAGGAC
19623021 ATTGGCATCTTATATGAGTTT
66 ATTGGCATCTTATATGAGTTT
* * *
19623042 GTGTAAGACCATGTCTTGGATAG-TGGCACCGATATT-TGA-TTACATGTAAGATCACATCTAGG
1 GTGTAAGACCACGTCTGGGAT-GTTGGCACCGAT-TTGTGATTTACATGTAAGACCACATCTAGG
*
19623104 ACGTTGGCAT
64 ACATTGGCAT
19623114 TGTACTAGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
85 28 0.46
86 30 0.49
87 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (86 bp):
GTGTAAGACCACGTCTGGGATGTTGGCACCGATTTGTGATTTACATGTAAGACCACATCTAGGAC
ATTGGCATCTTATATGAGTTT
Found at i:19626423 original size:28 final size:28
Alignment explanation
Indices: 19626388--19626454 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
19626378 GAAGACACAG
19626388 GCCCGTGTCCTTCACACGGCCATGACAC
1 GCCCGTGTCCTTCACACGGCCATGACAC
19626416 GCCCGTGTCCTTCACACGGCCATGACAC
1 GCCCGTGTCCTTCACACGGCCATGACAC
*
19626444 GCCCGTTTCCT
1 GCCCGTGTCCT
19626455 AGCCCGTGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.15, C:0.43, G:0.21, T:0.21
Consensus pattern (28 bp):
GCCCGTGTCCTTCACACGGCCATGACAC
Found at i:19627597 original size:46 final size:46
Alignment explanation
Indices: 19627531--19627703 Score: 172
Period size: 46 Copynumber: 3.8 Consensus size: 46
19627521 TCGATTGCAC
* * * *
19627531 GGCTGATGTATGTCCTAGACATGTCTTACACTAGCTCTCCTCTCAA
1 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATCAA
* * * * *
19627577 CGCCGATGCATGTCCCAGACAAGTCTT--ACTGGCT-TAAATATCAAGA
1 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATATC-A-A
* * ***
19627623 GGCTGATGCATGTCCCAGACACGTCTTACACTGGCTCTCATATTGT
1 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATCAA
19627669 GGCTGATGCATGTCCCAGACATGTCTTACACTAGC
1 GGCTGATGCATGTCCCAGACATGTCTTACACTAGC
19627704 ATGCATATCA
Statistics
Matches: 103, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
43 1 0.01
44 9 0.09
45 1 0.01
46 80 0.78
48 11 0.11
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (46 bp):
GGCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATCAA
Found at i:19632181 original size:44 final size:46
Alignment explanation
Indices: 19632098--19632213 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 46
19632088 TGTCTTCGAC
** * * * *
19632098 ATGGACTTACATGAATTATTCTTGTCTCCAATGATATAT-A-TAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGACATATAACTAAT
* * *
19632142 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATAACTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGACATATAACTAAT
*
19632188 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
19632214 CTGTCTTGTC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 31 0.53
45 1 0.02
46 27 0.46
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGACATATAACTAAT
Done.