Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 4 of 91
Found at i:360137 original size:25 final size:24
Alignment explanation
Indices: 360059--360127 Score: 104
Period size: 24 Copynumber: 2.8 Consensus size: 24
360049 TATCTTAAAC
360059 CTTT-AGCTCTTCTCACATCTCGAA
1 CTTTCAGCTCTTC-CACATCTCGAA
360083 CTTTCAGCTCTTCCACATCTCGAA
1 CTTTCAGCTCTTCCACATCTCGAA
*
360107 CTTTCAGCTCTTTCCATATCT
1 CTTTCAGCTC-TTCCACATCT
360128 TGAATCTTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 25 0.60
25 17 0.40
ACGTcount: A:0.19, C:0.35, G:0.07, T:0.39
Consensus pattern (24 bp):
CTTTCAGCTCTTCCACATCTCGAA
Found at i:360862 original size:52 final size:51
Alignment explanation
Indices: 360710--360863 Score: 177
Period size: 52 Copynumber: 3.0 Consensus size: 51
360700 TATAACCATA
* * * *
360710 CAAACTTGCCTATTAAGAAT-TACTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCT-CT-TTCTCTTAGAATTCTTCTCTTGCAAAT
* *
360762 CAAACTTGCCTATTAATAATCTCTTTCTTTTTAGAATTCTTCTCTTGCAAAT
1 CAAACTTGCCTATTAAGAATCTCTTTC-TCTTAGAATTCTTCTCTTGCAAAT
* *
360814 CAAACTTACCTATTAAGAATCCTCTTTCTCTT-GAAATTCTTCTTTTGCAA
1 CAAACTTGCCTATTAAGAAT-CTCTTTCTCTTAG-AATTCTTCTCTTGCAA
360864 GTCTTCTTGT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
51 3 0.03
52 77 0.88
53 8 0.09
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.42
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCTCTTTCTCTTAGAATTCTTCTCTTGCAAAT
Found at i:360901 original size:11 final size:11
Alignment explanation
Indices: 360885--360916 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
360875 CATCAAGCAA
360885 TAACAAATCTC
1 TAACAAATCTC
360896 TAACAAATCTC
1 TAACAAATCTC
*
360907 AAACAAATCT
1 TAACAAATCT
360917 TTTATGGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (11 bp):
TAACAAATCTC
Found at i:363850 original size:10 final size:10
Alignment explanation
Indices: 363831--363868 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
363821 TACATATATT
363831 CACACACATG
1 CACACACATG
*
363841 CACGCACATG
1 CACACACATG
363851 CACACACATG
1 CACACACATG
*
363861 CGCACACA
1 CACACACA
363869 CACATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.37, C:0.42, G:0.13, T:0.08
Consensus pattern (10 bp):
CACACACATG
Found at i:364041 original size:2 final size:2
Alignment explanation
Indices: 364034--364059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
364024 CACATGCATT
364034 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
364060 ACAAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:366420 original size:371 final size:370
Alignment explanation
Indices: 365643--366595 Score: 1588
Period size: 371 Copynumber: 2.6 Consensus size: 370
365633 GAAAAAATTA
* *
365643 ACCCGGGCATTCACCCTTCTGGCGTCCCAGATCAGCC-TCCGCCACGGTTCACACCCTTGTGAGG
1 ACCCGGGCATTCACCCTTCCGGCGTCCCAGATCAGCCTTCTGCCACGGTTCACACCCTTGTGAGG
* * * **
365707 TATTGTCCGCTCTGGCCCTCCT-AGCCTCATGATTTTGTCTTACAAAAGGCATCTCACAAGGCGG
66 TATTGTCCGCTCTGGCCCCCCTGA-CCTCACGATTTTGTCCTACAAAAGGCGCCTCACAAGGCGG
* *
365771 AGATGGTGTGAATCCTTTTATACCCCAGGGACCCTCCTATTATGTTCGATGTGGGATTCAGGACT
130 AGATGGTGTGAACCCTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACT
** * * * * *
365836 CTTCCTTAGGTCCGTGACATTCTCCCGCACCCAACCTCGTGACGCCTTCGTCACGGAGGTCGGCC
195 CCCCCTTAGGTCCGTGACATTCTCCCGCACCCAACCTCGTGACGCCCTCGTCACGAAAGCCGACC
**
365901 ACCCTGCCTACCTCCCTCGAGGTGCTCGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGATACCA
260 ACCCTGCCTACCTCCCTCGAGGCACTCGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGATACCA
*
365966 CTTGTCACGGGTCGAGACTCAAGCTCCGAACCCGCGCGGCTCCGGG
325 CTTGTCACGGGTCGAGACTCAAGCTCCGAACCCGCGCGGCTCCGAG
*
366012 ACCCGGGCATTCACCCTTCCGACGTCCCAGATCAGCCTTCTGCCACGGTTCACACCCTTGTGAGG
1 ACCCGGGCATTCACCCTTCCGGCGTCCCAGATCAGCCTTCTGCCACGGTTCACACCCTTGTGAGG
*
366077 TATTGTCCGCTCTGGCCCCCCCTGACCTCACGATTTTGTCCTACAAAAGGTGCCTCACAAGGCGG
66 TATTGTCCGCTCTGG-CCCCCCTGACCTCACGATTTTGTCCTACAAAAGGCGCCTCACAAGGCGG
*
366142 AGATGGTGTGAACCCTTTTATACCTCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACT
130 AGATGGTGTGAACCCTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACT
366207 CCCCCTTAGGTCCGTGACATTCTCCCGCACCCAACCTCGTGACGCCCTCGTCACGAAAGCCGACC
195 CCCCCTTAGGTCCGTGACATTCTCCCGCACCCAACCTCGTGACGCCCTCGTCACGAAAGCCGACC
366272 ACCCTGCCTACCTCCCTCGAGGCACTCGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGATACCA
260 ACCCTGCCTACCTCCCTCGAGGCACTCGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGATACCA
*
366337 CTTGTCACGGGTCGAGACTCAAGCTCCGAACCCGTGCGGCTCCGAG
325 CTTGTCACGGGTCGAGACTCAAGCTCCGAACCCGCGCGGCTCCGAG
* * *
366383 ACCCAGGCATTCACCCTTCCGGCATCCCAGATCAGCCTT-TCGCCACGGTTCACACCCTTATGAG
1 ACCCGGGCATTCACCCTTCCGGCGTCCCAGATCAGCCTTCT-GCCACGGTTCACACCCTTGTGAG
* *
366447 GTATTGTCCGCTCTGGCCCCCCTGAGCTCACGGTTTTGTCCTACAAAAGGCGCCTCACAAGGCGG
65 GTATTGTCCGCTCTGGCCCCCCTGACCTCACGATTTTGTCCTACAAAAGGCGCCTCACAAGGCGG
*
366512 AGATGGTGTGAACCCTTTTATACCCCAAGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACT
130 AGATGGTGTGAACCCTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACT
*
366577 CCCCTTTAGGTCCGTGACA
195 CCCCCTTAGGTCCGTGACA
366596 CATGCACATA
Statistics
Matches: 547, Mismatches: 33, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
369 35 0.06
370 169 0.31
371 342 0.63
372 1 0.00
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.24
Consensus pattern (370 bp):
ACCCGGGCATTCACCCTTCCGGCGTCCCAGATCAGCCTTCTGCCACGGTTCACACCCTTGTGAGG
TATTGTCCGCTCTGGCCCCCCTGACCTCACGATTTTGTCCTACAAAAGGCGCCTCACAAGGCGGA
GATGGTGTGAACCCTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACTC
CCCCTTAGGTCCGTGACATTCTCCCGCACCCAACCTCGTGACGCCCTCGTCACGAAAGCCGACCA
CCCTGCCTACCTCCCTCGAGGCACTCGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGATACCAC
TTGTCACGGGTCGAGACTCAAGCTCCGAACCCGCGCGGCTCCGAG
Found at i:367441 original size:2 final size:2
Alignment explanation
Indices: 367434--367467 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
367424 CACATGCATT
*
367434 TA TA TA TA CA 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 TA
367468 ACAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:368171 original size:1 final size:1
Alignment explanation
Indices: 368160--368189 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
368150 GTATAATCGC
*
368160 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
368190 AAATAAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:375356 original size:17 final size:18
Alignment explanation
Indices: 375322--375357 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
375312 GTTATGTTTA
*
375322 CATTTAAGTTATTTGTAT
1 CATTTAAGTTACTTGTAT
375340 CATTTAAG-TACTTGTAT
1 CATTTAAGTTACTTGTAT
375357 C
1 C
375358 GTGTTCGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
CATTTAAGTTACTTGTAT
Found at i:379806 original size:23 final size:23
Alignment explanation
Indices: 379776--379823 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
379766 TTGCAGGATT
379776 TACACTAAGCTTTTTGATTGGGG
1 TACACTAAGCTTTTTGATTGGGG
379799 TACACTAAGCTTTTTGATTGGGG
1 TACACTAAGCTTTTTGATTGGGG
379822 TA
1 TA
379824 AATTGCCAGA
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:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (23 bp):
TACACTAAGCTTTTTGATTGGGG
Found at i:380109 original size:2 final size:2
Alignment explanation
Indices: 380104--380128 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
380094 TCTCTCTCTC
380104 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
380129 TTATGGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:387344 original size:50 final size:48
Alignment explanation
Indices: 387242--387389 Score: 179
Period size: 48 Copynumber: 3.0 Consensus size: 48
387232 TCCTTTTCCT
* * * * * *
387242 AGGTTTGCTTCTGTTGCTTGTGCTTCTATGTTTACCTGTATGGATTGG
1 AGGTTTGTTTCTGTTGCTTGTTCATCTATATTTACCTATATGCATTGG
* *
387290 AGGTTTGTTTCTGTTTCTTGTTTATCTACGTATTTACCTATATGCATTGG
1 AGGTTTGTTTCTGTTGCTTGTTCATCTA--TATTTACCTATATGCATTGG
* * *
387340 AGGTTTGTTTCTGTTGCTTGTTCGTCTATGTTTACCTATATGCACTGG
1 AGGTTTGTTTCTGTTGCTTGTTCATCTATATTTACCTATATGCATTGG
387388 AG
1 AG
387390 AATGGAGGGA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
48 43 0.51
50 42 0.49
ACGTcount: A:0.14, C:0.15, G:0.23, T:0.49
Consensus pattern (48 bp):
AGGTTTGTTTCTGTTGCTTGTTCATCTATATTTACCTATATGCATTGG
Found at i:387407 original size:8 final size:8
Alignment explanation
Indices: 387394--387418 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
387384 CTGGAGAATG
387394 GAGGGAGA
1 GAGGGAGA
387402 GAGGGAGA
1 GAGGGAGA
387410 GAGGGAGA
1 GAGGGAGA
387418 G
1 G
387419 TTTTGCGATA
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:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (8 bp):
GAGGGAGA
Found at i:394561 original size:30 final size:30
Alignment explanation
Indices: 394521--394588 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
394511 ATTAATTTTT
* * *
394521 TAAT-TTTTTAATTATATATATTTATATAA
1 TAATATTTTTAAATATATATATTTAAAAAA
* *
394550 TGATATTTTTAAATATTTATATTTAAAAAA
1 TAATATTTTTAAATATATATATTTAAAAAA
394580 TAATATTTT
1 TAATATTTT
394589 ATTAATTTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (30 bp):
TAATATTTTTAAATATATATATTTAAAAAA
Found at i:396906 original size:88 final size:88
Alignment explanation
Indices: 396757--396932 Score: 289
Period size: 88 Copynumber: 2.0 Consensus size: 88
396747 TACACCATAA
*
396757 TCAATCTAATCCATGATATTGACCAAAATGAGGAAGCTATAACGACAGAATCTCAACATAGAGCT
1 TCAATCTAATCCATGATATTGACCAAAATGAGGAAGCTATAACAACAGAATCTCAACATAGAGCT
* * *
396822 TATCTGTGCTTTTTGATCAAATT
66 TATCTGTACTTTTGGATAAAATT
** *
396845 TCAATCTAATCCATGATATTGACGGAAATGATGAAGCTATAACAACAGAATCTCAACATAGAGCT
1 TCAATCTAATCCATGATATTGACCAAAATGAGGAAGCTATAACAACAGAATCTCAACATAGAGCT
396910 TATCTGTACTTTTGGATAAAATT
66 TATCTGTACTTTTGGATAAAATT
396933 ATCTTAGTAC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (88 bp):
TCAATCTAATCCATGATATTGACCAAAATGAGGAAGCTATAACAACAGAATCTCAACATAGAGCT
TATCTGTACTTTTGGATAAAATT
Found at i:397872 original size:28 final size:29
Alignment explanation
Indices: 397840--397896 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
397830 ACAAAAAGAG
397840 TAGATTCACATGCATTC-TAACAATGCTT
1 TAGATTCACATGCATTCTTAACAATGCTT
* *
397868 TAGATTTACATGCATTCTTAGCAATGCTT
1 TAGATTCACATGCATTCTTAACAATGCTT
397897 GTCATAGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (29 bp):
TAGATTCACATGCATTCTTAACAATGCTT
Found at i:398589 original size:3 final size:3
Alignment explanation
Indices: 398581--398607 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
398571 TTCGTGAACG
398581 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
398608 CACTGCCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:403324 original size:2 final size:2
Alignment explanation
Indices: 403317--403349 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
403307 ATTTCTATCT
*
403317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
403350 CCCAGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:420781 original size:26 final size:26
Alignment explanation
Indices: 420751--420802 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
420741 AACATTAGAA
420751 TTCTATTTATTTATTCTTACTTGGAC
1 TTCTATTTATTTATTCTTACTTGGAC
420777 TTCTATTTATTTATTCTTACTTGGAC
1 TTCTATTTATTTATTCTTACTTGGAC
420803 AAAGATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (26 bp):
TTCTATTTATTTATTCTTACTTGGAC
Found at i:434970 original size:26 final size:25
Alignment explanation
Indices: 434941--434991 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
434931 TTCTGCTTTG
*
434941 AGAGTTTTGAGTTTTTATTATATCAT
1 AGAGTTTTGAGGTTTTATTAT-TCAT
434967 AGAGTTTTGAGGTTTTATTATTCAT
1 AGAGTTTTGAGGTTTTATTATTCAT
434992 GCTTCAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (25 bp):
AGAGTTTTGAGGTTTTATTATTCAT
Found at i:438383 original size:7 final size:7
Alignment explanation
Indices: 438367--438404 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
438357 ATCATGTTCG
438367 TATATGA
1 TATATGA
*
438374 TATCTGA
1 TATATGA
438381 TATATGA
1 TATATGA
438388 TATATGA
1 TATATGA
438395 TATATGA
1 TATATGA
438402 TAT
1 TAT
438405 GATATGAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (7 bp):
TATATGA
Found at i:438869 original size:15 final size:15
Alignment explanation
Indices: 438849--438904 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
438839 GTTAAAAAAT
438849 TATTTTATTTATTTA
1 TATTTTATTTATTTA
*
438864 TATTTTATTCATTTA
1 TATTTTATTTATTTA
* * * *
438879 AATAATAAATTATTTA
1 TAT-TTTATTTATTTA
438895 TATTTTATTT
1 TATTTTATTT
438905 GTATTTATTT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
15 20 0.67
16 10 0.33
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTATTTATTTA
Found at i:438978 original size:26 final size:27
Alignment explanation
Indices: 438948--439003 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
438938 ATAAAAATTT
* * *
438948 AATAAACATATTTATGAAC-ATATATA
1 AATAAACACATTCATGAACAATAAATA
*
438974 AATAAATACATTCATGAACAATAAATA
1 AATAAACACATTCATGAACAATAAATA
439001 AAT
1 AAT
439004 TATAATCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (27 bp):
AATAAACACATTCATGAACAATAAATA
Found at i:439032 original size:14 final size:14
Alignment explanation
Indices: 438996--439034 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
438986 CATGAACAAT
*
438996 AAATAAATTATAATC
1 AAATAAATT-TAAAC
*
439011 AGATAAATTTAAAC
1 AAATAAATTTAAAC
439025 AAATAAATTT
1 AAATAAATTT
439035 TAAATGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (14 bp):
AAATAAATTTAAAC
Found at i:439036 original size:15 final size:15
Alignment explanation
Indices: 438996--439038 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
438986 CATGAACAAT
* *
438996 AAATAAATTATAATC
1 AAATAAATTTTAAAC
*
439011 AGATAAA-TTTAAAC
1 AAATAAATTTTAAAC
439025 AAATAAATTTTAAA
1 AAATAAATTTTAAA
439039 TGAACATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (15 bp):
AAATAAATTTTAAAC
Found at i:439165 original size:22 final size:22
Alignment explanation
Indices: 439133--439192 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
439123 TTATAAACAA
439133 ATAAT-AA-ATAAATAAAATTT
1 ATAATAAATATAAATAAAATTT
*
439153 A-AATAAATTATAAAT-GAATTT
1 ATAATAAA-TATAAATAAAATTT
439174 ATTAATAAATATAAATAAA
1 A-TAATAAATATAAATAAA
439193 TAAACAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 6 0.19
22 13 0.41
23 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAATAAATATAAATAAAATTT
Found at i:441053 original size:30 final size:30
Alignment explanation
Indices: 440961--441090 Score: 131
Period size: 30 Copynumber: 4.4 Consensus size: 30
440951 TTTTAAAAAA
*
440961 TTATTTAAATATAAATTAAATATTAAGAAC
1 TTATTTAAATATAAATTAAATATTAAGAAT
* *
440991 TTCTTAAAATATAAATTAAA-ACTTAAGAAT
1 TTATTTAAATATAAATTAAATA-TTAAGAAT
***
441021 TTATTTAAATATAAATTAAATATTATTTAT
1 TTATTTAAATATAAATTAAATATTAAGAAT
** *
441051 TTATTTATGTAT-AATTAAA-ATATAAAAAT
1 TTATTTAAATATAAATTAAATAT-TAAGAAT
*
441080 TTATCTAAATA
1 TTATTTAAATA
441091 AGATTATAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
28 2 0.02
29 20 0.25
30 58 0.72
31 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
TTATTTAAATATAAATTAAATATTAAGAAT
Found at i:441064 original size:60 final size:59
Alignment explanation
Indices: 440954--441090 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 59
440944 TAATTTATTT
* *
440954 TAAAAAATTATTTAAATATAAATTAAATATTAAGAACTTCTTAAAATATAAATTAAAACT-
1 TAAAAATTTATTTAAATATAAATTAAATATTAAGAACTTATTAAAATAT-AATTAAAA-TA
* *** * * **
441014 TAAGAATTTATTTAAATATAAATTAAATATTATTTATTTATTTATGTATAATTAAAATA
1 TAAAAATTTATTTAAATATAAATTAAATATTAAGAACTTATTAAAATATAATTAAAATA
*
441073 TAAAAATTTATCTAAATA
1 TAAAAATTTATTTAAATA
441091 AGATTATAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 1 0.02
59 24 0.38
60 39 0.61
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (59 bp):
TAAAAATTTATTTAAATATAAATTAAATATTAAGAACTTATTAAAATATAATTAAAATA
Found at i:441653 original size:7 final size:7
Alignment explanation
Indices: 441641--441675 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
441631 CCAAGTCAAT
441641 CAGCCAC
1 CAGCCAC
441648 CAGCCAC
1 CAGCCAC
441655 CAGCCAC
1 CAGCCAC
441662 CAGCCAC
1 CAGCCAC
441669 CAGCCAC
1 CAGCCAC
441676 GTCAGGGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.57, G:0.14, T:0.00
Consensus pattern (7 bp):
CAGCCAC
Found at i:444139 original size:74 final size:74
Alignment explanation
Indices: 444005--444154 Score: 185
Period size: 74 Copynumber: 2.0 Consensus size: 74
443995 ATATTTTGAT
* * * *
444005 AAATTAAATTGTAAAAATGAAAACTTTGAGGTAGTAATAGTAAATTTGAAAAGTTAGGACTGAAT
1 AAATGAAATTGTAAAAATGAAAACTTTGAGGTAGTAATAGTAAATATGAAAACTGAGGACTGAAT
* *
444070 ATGATTTCC
66 ATAAATTCC
* * * * *
444079 AAATGAAATTGTGAAAATGAAATCTTAT-AGGTAGTAATGGTAAATATGAAAACTGGGGACTGGA
1 AAATGAAATTGTAAAAATGAAAACTT-TGAGGTAGTAATAGTAAATATGAAAACTGAGGACTGAA
444143 TATAAATTCC
65 TATAAATTCC
444153 AA
1 AA
444155 GTAGCAGAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 63 0.98
75 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (74 bp):
AAATGAAATTGTAAAAATGAAAACTTTGAGGTAGTAATAGTAAATATGAAAACTGAGGACTGAAT
ATAAATTCC
Found at i:446724 original size:2 final size:2
Alignment explanation
Indices: 446717--446770 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
446707 AATGGTTCTG
446717 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
446759 CT CT CT CT CT CT
1 CT CT CT CT CT CT
446771 GTGTGCTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:451458 original size:25 final size:25
Alignment explanation
Indices: 451423--451471 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
451413 AATACCACAT
451423 AAGTTGATGTACTAGAGCTGATCAC
1 AAGTTGATGTACTAGAGCTGATCAC
* * *
451448 AAGTTGGTGTATTAGAGTTGATCA
1 AAGTTGATGTACTAGAGCTGATCA
451472 TGGGATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.33
Consensus pattern (25 bp):
AAGTTGATGTACTAGAGCTGATCAC
Found at i:457711 original size:19 final size:16
Alignment explanation
Indices: 457672--457708 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
457662 TGATAAACCA
*
457672 ATGATAATGATGATTT
1 ATGATAATAATGATTT
457688 ATGATAATAATGATTT
1 ATGATAATAATGATTT
457704 ATGAT
1 ATGAT
457709 GATTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (16 bp):
ATGATAATAATGATTT
Found at i:464063 original size:2 final size:2
Alignment explanation
Indices: 464056--464089 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
464046 TAAGACATGA
*
464056 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
464090 TTCTTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:473612 original size:16 final size:17
Alignment explanation
Indices: 473566--473623 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
473556 TTTAATTATC
473566 ATATAAATAATTTTTTAA
1 ATATAAAT-ATTTTTTAA
*
473584 ATATGAATA--TTTT-A
1 ATATAAATATTTTTTAA
*
473598 CTATAAATATTTTTTTAA
1 ATATAAATA-TTTTTTAA
473616 A-ATAAATA
1 ATATAAATA
473624 AAACACATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 8 0.25
15 4 0.12
17 12 0.38
18 8 0.25
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
ATATAAATATTTTTTAA
Found at i:482091 original size:59 final size:59
Alignment explanation
Indices: 481778--482351 Score: 550
Period size: 58 Copynumber: 9.7 Consensus size: 59
481768 TTTGTGCAGG
* * * * *
481778 GAAAAATTGATACTCTCAAC-TTTTCCCCAAAATA-TTTTTTAAAAATTTTAATCTCGA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
* * * **
481835 GGAAAATTGATACTTTCAACTTTTTCCCAAAAAT-TCATTTTTGAAAAC-TTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATAT-TTTTTTGAAAACTTTAATTTCGA
*
481893 GAAAAATTGATACTTTCAA-TTTTTCCCCCAAAAATATTTTTGTTTTTAAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTT--CCCAAAAATA---TT-TTTTTGAAAACTTTAATTTCGA
* *** **
481957 GGAAAATTGATACTTTCAAC-TTTTCCTC-AAAA-ATCCCTTTGAAAA-TTT-ATCTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGAAAACTTTAAT-TTCGA
*
482013 GAAAAATTGATACTTTCAACTTTGTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
* *
482072 GAAAAATTAATACTTTCAACTTTTTCCTAAAAATATTTTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
* * *
482131 GGAAAATTGATACTTTCAACTTTTTTCCAAAAATA-TTTTTTGGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
* * * **
482189 -AGAAAATTGATACTTTCAAC-TTTTCCTCAAAAAAAAAAACTTTTTTTTAAAA-TTTATTTTTA
1 GA-AAAATTGATACTTTCAACTTTTTCC-C----AAAAATA-TTTTTTTGAAAACTTTAATTTCG
482251 A
59 A
* ** * * * **
482252 GAAAAATTAATACTTTCAACTTTTTTTCAAAAATATTTTTTGGAAAGC-TTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
*
482310 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTT
1 GAAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTT
482352 TGAATTTTAT
Statistics
Matches: 428, Mismatches: 58, Indels: 61
0.78 0.11 0.11
Matches are distributed among these distances:
55 2 0.00
56 26 0.06
57 48 0.11
58 139 0.32
59 117 0.27
60 2 0.00
61 1 0.00
62 12 0.03
63 38 0.09
64 43 0.10
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
Found at i:482152 original size:31 final size:30
Alignment explanation
Indices: 482117--482211 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
482107 TTTTTTTGAA
482117 AACTTTAATTTCGAGGAAAATTGATACTTTC
1 AACTTTAATTTCGA-GAAAATTGATACTTTC
* ** *
482148 AACTTT--TTTCCA-AAAA-T-ATTTTTTGGA
1 AACTTTAATTTCGAGAAAATTGATACTTT--C
482175 AACTTTAATTTCGAAGAAAATTGATACTTTC
1 AACTTTAATTTCG-AGAAAATTGATACTTTC
482206 AACTTT
1 AACTTT
482212 TCCTCAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
25 5 0.10
26 1 0.02
27 10 0.21
29 9 0.19
30 1 0.02
31 16 0.33
32 1 0.02
33 5 0.10
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTCGAGAAAATTGATACTTTC
Found at i:482379 original size:121 final size:115
Alignment explanation
Indices: 481779--482365 Score: 464
Period size: 121 Copynumber: 5.0 Consensus size: 115
481769 TTGTGCAGGG
* * * ** * * * *
481779 AAAAATTGATACTCTCAAC-TTTTCCCCAAAATATTTTTTAAAAATTTTAATCTCGAGGAAAATT
1 AAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGGAAACTTTATTTTCAAGGAAAATT
**
481843 GATACTTTCAACTTTTTCC-CAAAAAT-TCATTTTTGAAAACTTATT-TTTAAG-
66 GATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTTG--AA-TT-TTATTTAAGA
* ** * *
481894 AAAAATTGATACTTTCAA-TTTTTCCCCCAAAAATATTTTTGTTTTTAAAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTT--TCCAAAAATA----T-TTTTTGGAAACTTTATTTTCAAG
*** *** *
481958 GAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CCCTTTGAAAATTTATCTTTAAG-
59 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAATTT-TATTTAAGA
* * * * * *
482014 AAAAATTGATACTTTCAACTTTGTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGAGAAAAAT
1 AAAAATTGATACTTTCAACTTTTTTCCAAAAATA-TTTTTTGGAAACTTTATTTTCAAGGAAAAT
* * *
482079 TAATACTTTCAACTTTTTCCT-AAAAATA-TTTTTTTGAAAACTTTAATTT-CGA
65 TGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTTG--AA-TTTTATTTAAGA
* *
482131 GGAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGGAAACTTTAATTTCGAA-GAAAA
1 -AAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGGAAACTTTATTTTC-AAGGAAAA
* * *
482195 TTGATACTTTCAACTTTTCCTCAAAAAAAAAAACTTTTTTTTAAAATTTATTTTTAAG-
64 TTGATACTTTCAACTTTTCCTC----AAAAATA-TTTTTTTT-GAATTT-TATTTAAGA
* * *
482253 AAAAATTAATACTTTCAACTTTTTTTCAAAAATATTTTTTGGAAAGC-TTATTTTTAAGGAAAAT
1 AAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGGAAA-CTTTATTTTCAAGGAAAAT
482317 TGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAATTTTATTTAA
65 TGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAATTTTATTTAA
482366 AAGAAATAAA
Statistics
Matches: 399, Mismatches: 41, Indels: 65
0.79 0.08 0.13
Matches are distributed among these distances:
114 6 0.02
115 74 0.19
116 25 0.06
117 57 0.14
118 36 0.09
119 13 0.03
120 28 0.07
121 95 0.24
122 57 0.14
123 8 0.02
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.43
Consensus pattern (115 bp):
AAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGGAAACTTTATTTTCAAGGAAAATT
GATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAATTTTATTTAAGA
Found at i:482400 original size:15 final size:15
Alignment explanation
Indices: 482363--482404 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
482353 GAATTTTATT
*
482363 TAAAAGAAAT-AAAA
1 TAAAAAAAATGAAAA
*
482377 -AATAAAAATGAAAA
1 TAAAAAAAATGAAAA
482391 TAAAAAAAATGAAA
1 TAAAAAAAATGAAA
482405 TTTAAACCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 7 0.30
14 4 0.17
15 12 0.52
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
TAAAAAAAATGAAAA
Found at i:483432 original size:24 final size:24
Alignment explanation
Indices: 483374--483432 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
483364 AGGTAATGGT
*
483374 ACCAAAGGCAGGGATGCTTGTGGA
1 ACCAAAGGCAGGGATGCTCGTGGA
* *
483398 ACTAAAGGCA-GGAGTGCTCGTGGC
1 ACCAAAGGCAGGGA-TGCTCGTGGA
*
483422 ACCAAAAGCAG
1 ACCAAAGGCAG
483433 AAGTACTGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.32, C:0.20, G:0.34, T:0.14
Consensus pattern (24 bp):
ACCAAAGGCAGGGATGCTCGTGGA
Found at i:484170 original size:20 final size:20
Alignment explanation
Indices: 484142--484184 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
484132 AAAAGAAAAT
484142 AAATCATAAA-ATAAAAATAA
1 AAATCATAAATAT-AAAATAA
* *
484162 AAATGATAAATATGAAATAA
1 AAATCATAAATATAAAATAA
484182 AAA
1 AAA
484185 AACCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATCATAAATATAAAATAA
Found at i:484386 original size:14 final size:14
Alignment explanation
Indices: 484351--484385 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
484341 CTCAACTGAA
484351 TTTTTTTTGCCTAT
1 TTTTTTTTGCCTAT
*
484365 TTTGTTTTG-CTAT
1 TTTTTTTTGCCTAT
484378 TTTTTTTT
1 TTTTTTTT
484386 TTTTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.77
Consensus pattern (14 bp):
TTTTTTTTGCCTAT
Found at i:484713 original size:41 final size:41
Alignment explanation
Indices: 484506--484916 Score: 565
Period size: 41 Copynumber: 10.0 Consensus size: 41
484496 TTTGATCAAA
* * * ** *
484506 GCTCCTCTAAGCAGAGGCTCAACGA-TTTCAAAAAGTAAATA
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GGAAAGTAAATT
* * * *
484547 GCTCATCCAAACAGAGGCACCACGACTTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATT
* *
484589 GCTCATCTAAACAGAGTCACCACGACTTT-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
*
484629 GCTCATCTAAACAGAGGCACCACGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATT
484671 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* * *
484712 GCTCCTTTAAACAGAGGCACCATGACTTTGTAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* * * * *
484753 GCTCTTCTAAATAGAGGCATCATGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
*
484794 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
484835 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* *
484876 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
484917 ACTCATTGAC
Statistics
Matches: 336, Mismatches: 30, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
40 34 0.10
41 230 0.68
42 69 0.21
43 3 0.01
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
Found at i:486550 original size:11 final size:11
Alignment explanation
Indices: 486534--486588 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 11
486524 TCAATTTGAA
486534 TCTTTTTTTTT
1 TCTTTTTTTTT
*
486545 TCTTTTTTCTT
1 TCTTTTTTTTT
486556 TCTTTTTTATCATCT
1 TCTTTTTT-T--T-T
486571 T-TTTTTTTTT
1 TCTTTTTTTTT
486581 TCTTTTTT
1 TCTTTTTT
486589 CATCCATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 2 0.05
11 25 0.68
13 1 0.03
14 7 0.19
15 2 0.05
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.84
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:486571 original size:23 final size:23
Alignment explanation
Indices: 486545--486592 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
486535 CTTTTTTTTT
486545 TCTTTTTTCTTTCTT-TTTTATCA
1 TCTTTTTT-TTTCTTCTTTTATCA
* *
486568 TCTTTTTTTTTTTTCTTTTTTCA
1 TCTTTTTTTTTCTTCTTTTATCA
486591 TC
1 TC
486593 CATTGTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (23 bp):
TCTTTTTTTTTCTTCTTTTATCA
Found at i:486607 original size:36 final size:36
Alignment explanation
Indices: 486536--486608 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
486526 AATTTGAATC
* * * *
486536 TTTTTTTTTTCTTTTTTCTTTCTTTTTTATCATCTT
1 TTTTTTTTTTCTTTTTTCATCCTTGTTGATCATCTT
486572 TTTTTTTTTTCTTTTTTCATCCATTGTTGAT-ATCTT
1 TTTTTTTTTTCTTTTTTCATCC-TTGTTGATCATCTT
486608 T
1 T
486609 CATACATCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 26 0.81
37 6 0.19
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.75
Consensus pattern (36 bp):
TTTTTTTTTTCTTTTTTCATCCTTGTTGATCATCTT
Found at i:490975 original size:58 final size:59
Alignment explanation
Indices: 490397--490984 Score: 512
Period size: 58 Copynumber: 10.1 Consensus size: 59
490387 TTGTGCAGAA
* * ** * * **
490397 AAAATTGATACTCTCAACTTTTCC-CCAAAATA--TTTTTAAAAAATTTTAATCTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAA-TTTATTTTTAAGG
* * ** *
490454 AAAATTGATACTTTTAACTTTTTCTCAAAAAT-TCATTTTTGAAAACTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
* * * * **
490512 AAAATTGATACTTACAACTTTTCCCCCAAAAATATTTTTGTTTTTAAAAACTTTAATTTCGA-G
1 AAAATTGATACTTTCAACTTTT-CCTCAAAAATA--TTT-TTTTTGAAAA-TTTATTTTTAAGG
*** *
490575 AGAAATTGATACTTTCAACTTTTCCTC-AAAA-A-TCCCTTTGAAAATTTATCTTTAAGG
1 A-AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
* * **
490632 AAAATTGATACTTTCAACTTTT-TTCCAAAAATA-TTTTTTTGAAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTTGAAAA-TTTATTTTTAAGG
*
490691 AAAATTGATACTTTCAACTTTTTCTCAAAAAT-TTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
* * * * **
490749 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAACTTTAAATTCGAA-G
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTT-ATTTTTAAGG
* * ** * *
490807 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAACGTTTTTTAAAAATTTATTTTTAA-A
1 AAAATTGATACTTTCAACTTTTCCT--CAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
* * *
490867 AAAATTAATACTTACAACTTTT-CTCCAAAAATA--TTTTTTGAAAAGCTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTTGAAAA-TTTATTTTTAAGG
* *
490925 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTG-AATTTTA-TTTAAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
490982 AAA
1 AAA
490985 TAAAAAATAA
Statistics
Matches: 428, Mismatches: 76, Indels: 54
0.77 0.14 0.10
Matches are distributed among these distances:
55 1 0.00
56 39 0.09
57 54 0.13
58 160 0.37
59 77 0.18
60 39 0.09
61 12 0.03
62 5 0.01
63 14 0.03
64 27 0.06
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
Found at i:492768 original size:19 final size:19
Alignment explanation
Indices: 492740--492803 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
492730 AAGAAAGAAA
492740 AAAAAT-AAATCATAAAAT
1 AAAAATAAAATCATAAAAT
*
492758 AAAAATAAAATGATAAATAT
1 AAAAATAAAATCATAAA-AT
*
492778 GAAATAAAAAAATC-TAAAAT
1 -AAA-AATAAAATCATAAAAT
492798 AAAAAT
1 AAAAAT
492804 GAATAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 8 0.21
19 12 0.32
20 4 0.11
21 7 0.18
22 7 0.18
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAAATAAAATCATAAAAT
Found at i:502347 original size:16 final size:16
Alignment explanation
Indices: 502326--502359 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
502316 TAATTCGTCT
502326 AGAAGTATCCATGCGG
1 AGAAGTATCCATGCGG
502342 AGAAGTATCCATGCGG
1 AGAAGTATCCATGCGG
502358 AG
1 AG
502360 GTCTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (16 bp):
AGAAGTATCCATGCGG
Found at i:503080 original size:23 final size:23
Alignment explanation
Indices: 503050--503094 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
503040 ACATATACTC
*
503050 TCTTTCTACCCCAAGTTTAGAAA
1 TCTTTCTACCCCAAGCTTAGAAA
*
503073 TCTTTCTACCCCATGCTTAGAA
1 TCTTTCTACCCCAAGCTTAGAA
503095 CTCGCCTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.29, G:0.09, T:0.36
Consensus pattern (23 bp):
TCTTTCTACCCCAAGCTTAGAAA
Found at i:507104 original size:236 final size:233
Alignment explanation
Indices: 506657--509325 Score: 916
Period size: 236 Copynumber: 11.5 Consensus size: 233
506647 TAATTAAATA
* * * * * * * * **
506657 TAAGAACAATCATAAAAATAAATTACTGTAATGTAAATAATTA-AGTTGCCAACATAAAATTTTA
1 TAAGAACAACCATAATAATATATTATTATAATATAAATAATTATA-TAGACAATGTAAAATTTTA
* * * ** * * *
506721 GTTAATTATT-TTTT-TAAAACATATTAGAAAAATACCTAAAAATTAAAAAACATATTGGTAACA
65 ATTAATTATTATTTTGT-AAATATATAAG-AAAATAAATAAAAATTAAAAAATAAATTGATAA-A
* * * * * *
506784 -TAAACAAGTGAGAAGAAATGTAAAATTAGTATCATTTAGTATAAAATGGGTATGAATTGTCAT-
127 GTAAACAAGTGAGAA-AAA-ATAAAATTAGTATAATTTAG-GTAAAAT-GGTAAGAAGTGTCGTA
* ** *
506847 A-ATA-T-ACTAAAAAATGTTATAACAATTCTAAATGTATAATGGAAAG
188 ACACATTAAGAAAAAAAAGTTATAACAATTCTAAA--TATAAT-GAAAG
* ** * * *
506893 TAAGAACAACCATATTAATATATTATTATAAGGTAAATAATTATATTGACAACGT-AAAGTTTAA
1 TAAGAACAACCATAATAATATATTATTATAATATAAATAATTATATAGACAATGTAAAATTTTAA
* * *
506957 TTAATTATTATTTTGTAAATATTTAA-AAAATAAATAGAAATTAAAAAAGAAATTGATAAAGTAA
66 TTAATTATTATTTTGTAAATATATAAGAAAATAAATAAAAATTAAAAAATAAATTGATAAAGTAA
* * *
507021 ACAAGTAAGAAAAACATAAAATTAGTATAATTTAGTGTCAAATAAGTAAGAAGTGTCG-AACACA
131 ACAAGTGAGAAAAA-ATAAAATTAGTATAATTTAG-GTAAAAT-GGTAAGAAGTGTCGTAACACA
*
507085 TTAAGAAAAAAAAGTTATAACAATTCTAAATGTAAT-AAA-
193 TTAAGAAAAAAAAGTTATAACAATTCTAAATATAATGAAAG
* * * * * *
507124 AAAAAACAA-TACTAATAAAATATTATTATAA-AGTAAATAATTATGTAGATAATGTAAAATTTT
1 TAAGAACAACCA-TAATAATATATTATTATAATA-TAAATAATTATATAGACAATGTAAAATTTT
* * * ** *
507187 AATTAATTATTGTTGCTATAAATATATAAGAAAAATAGCTAAAAATAAAAAAAATAAATTGATAA
64 AATTAATTATTATT-TTGTAAATATATAAG-AAAATAAATAAAAAT-TAAAAAATAAATTGATAA
* * ** * ** *
507252 TGTAAAC-A-TGCGATAAATGTAAAATTAGTATCATTTTAGGTAAAATGGGTAAGTGGTGACGTA
126 AGTAAACAAGTGAGA-AAAAATAAAATTAGTAT-AATTTAGGTAAAAT-GGTAAGAAGTGTCGTA
* * * * *
507315 A-ACTATT---AAAAAAGAGTTATGATAATTCTAAACATAATTCAAAG
188 ACAC-ATTAAGAAAAAAAAGTTATAACAATTCTAAATATAA-TGAAAG
* ** * *
507359 TAAGAATAATTATAAAAATATATTATTATAATATAAATAATTATGATAG-TAATGTAAAATTTTA
1 TAAGAACAACCATAATAATATATTATTATAATATAAATAATTAT-ATAGACAATGTAAAATTTTA
* * * *
507423 ATTAATTATTATTTTTGTATATATATAAGAAAA-ATAGTCAAAAACTAAAAAATAAATTGGTAAT
65 ATTAATTATTA-TTTTGTAAATATATAAGAAAATA-AAT-AAAAATTAAAAAATAAATTGATAA-
** * * * *
507487 A-TAAACAAGTGAGAGGAAATGAAAAATTAGTATTATTT-GGCTAAAATGGTTATGAAATATCGT
126 AGTAAACAAGTGAGAAAAAAT--AAAATTAGTATAATTTAGG-TAAAATGG-TAAGAAGTGTCGT
* *
507550 AACACATTAAG---AAAGAGTTATAATAATTCTAAATATAATGAAAGG
187 AACACATTAAGAAAAAAAAGTTATAACAATTCTAAATATAATGAAA-G
* * * * * * *
507595 TAAAAACAACCATAAGAATATATTATTGTAATATAAATAATTATGTTGGCAATTTAAAA-TTTAA
1 TAAGAACAACCATAATAATATATTATTATAATATAAATAATTATATAGACAATGTAAAATTTTAA
* *** * *
507659 TTAATTATTATTTTTTAAATATATAAGAAAAATAGCCAAAAATT-TAAAATCAAA-T-A-AGTAG
66 TTAATTATTATTTTGTAAATATATAAG-AAAATAAATAAAAATTAAAAAAT-AAATTGATA-AAG
* * * * * **
507720 TACAAAAAG-GTAAAAAAAATGTAAAATTAGTATAATTTGACGTAAAATAAGTAAAAAGTGTCCC
128 TA-AACAAGTG-AGAAAAAA--TAAAATTAGTATAATTT-AGGTAAAAT-GGTAAGAAGTGTCGT
* * * * ** * *
507784 AATACACTAAG---AAAAAGTAATGACAATTCTAAACGTTATTAAAG
187 AACACATTAAGAAAAAAAAGTTATAACAATTCTAAATATAATGAAAG
* *
507828 ATAAGAACAATCACA-AATATATATATATATATATATTATAACGTAAATAATTA-AGTTGCCAAT
1 -TAAGAACAA-C-CATAATA-ATATAT-TAT-TATA--AT-A--TAAATAATTATA-TAGACAAT
* * * *
507891 GTAAAATTTTAATT-A-T-TTATTTTTTATACATATAAGAAAAGTAGCA-AAAAATTAAAAAATA
54 GTAAAATTTTAATTAATTATTATTTTGTAAATATATAAGAAAA-TA-AATAAAAATTAAAAAATA
* * * *
507952 AATTGATAACA-TAAACTAGTGAGAAAAAAAACATAAAATTTA-TATCATTTGACGAAAAATGGG
117 AATTGATAA-AGTAAACAAGTGAG---AAAAA-ATAAAA-TTAGTATAATTT-AGGTAAAAT-GG
* * * * * ** * * * * * *
508015 TATGAATTATTGTAATACGCT----AAAAAAAGTTATGATAATTATAAACATAATAAAAAT
174 TAAGAAGTGTCGTAACACATTAAGAAAAAAAAGTTATAACAATTCTAAATATAAT-GAAAG
* * * *
508072 TAAG-A-AA--A-ACT-GTA-A-TA--AT-ATAT---T-A-T-TGTA-AC---GTAAAACTTTAA
1 TAAGAACAACCATAATAATATATTATTATAATATAAATAATTATATAGACAATGTAAAATTTTAA
* * * * * *
508116 TTAATTATTATTTTATAAATATCTAAGGCAAATAACT-AAAATTAAAAAAATAAATTGGTAATGT
66 TTAATTATTATTTTGTAAATATATAA-GAAAATAAATAAAAATT-AAAAAATAAATTGATAAAGT
* ** * * ** * * *
508180 AAATAAGTGAGACCAAATGTAAATTACTACCATTTAGCGTAAAATGGATAAAAAGTATTGTAACA
129 AAACAAGTGAGAAAAAAT-AAAATTAGTATAATTTAG-GTAAAATGG-TAAGAAGTGTCGTAACA
* * * * *
508245 CATTAAG---AAAGAGTTATGATAATTATAAACATAATGAAAAG
191 CATTAAGAAAAAAAAGTTATAACAATTCTAAATATAATG-AAAG
* * * ** * * * ** *
508286 TAAAAATAGTCGTTAA-AAGATATTATTGTAA-AGGT-AATAACTACGTTGACAATGTAAAATTT
1 TAAGAACA-ACCATAATAATATATTATTATAATA--TAAATAATTATATAGACAATGTAAAATTT
* **
508348 TAAATT-TTTATTATTCTTGTAAATATATAAGAAAAATAGCT-AAAATTAAAAAATAAATTGATA
63 T-AATTAATTATTATT-TTGTAAATATATAAG-AAAATAAATAAAAATTAAAAAATAAATTGATA
* * ** * *
508411 ACA-TAAACAAGTGAGAAATAACGTAAAATTAGTATCATTTGAAATAAAATGGTTTAGAAATGTC
125 A-AGTAAACAAGTGAGAAA-AA-ATAAAATTAGTATAATTT-AGGTAAAATGG-TAAGAAGTGTC
* * * * * * *
508475 GTAATATATTAAG---AAAAAGGTACAATAATTCTAAACATGATGAAAAG
185 GTAACACATTAAGAAAAAAAAGTTATAACAATTCTAAATATAATG-AAAG
* * * * * * * ** *
508522 CAAAAATAA-TAGTAAAAATATATCAGTATAACGTAAATAATTATA-ATGGCAATGTAAAATTTT
1 TAAGAACAACCA-TAATAATATATTATTATAATATAAATAATTATATA-GACAATGTAAAATTTT
** *
508585 AATTAATTATTATTTTTGTATATATATATAAGGAAAAT--AGCAAAATTAAAAAAT--TTTGATA
64 AATTAATTATTA-TTTTGTA-A-ATATATAA-GAAAATAAATAAAAATTAAAAAATAAATTGATA
* * *
508646 AAATAAACAAGTGA-AAAGAAACGTAAAATTAGTATAATTT-GGCATAAAATGAGAAAAAAGTGT
125 AAGTAAACAAGTGAGAAA-AAA--TAAAATTAGTATAATTTAGG--TAAAATG-GTAAGAAGTGT
* * * * * * * * * *
508709 TGTAATATACT-A-AAAAAAGA-TTATGATAATTCTAAACATATTAAAAG
184 CGTAACACATTAAGAAAAAAAAGTTATAACAATTCTAAATATAATGAAAG
*** * * * *
508756 ATAAGAACAATTGTAAAAAGATATTATTGTAATGA-AAATATTTA-AGTAGACAATGTAAAATTT
1 -TAAGAACAACCATAATAATATATTATTATAAT-ATAAATAATTATA-TAGACAATGTAAAATTT
* * * *
508819 TAATTAATTATTATTTTATAAATATATAAGAAAAATAACTAATAATTAAAAAGTAAATATG-T-A
63 TAATTAATTATTATTTTGTAAATATATAAG-AAAATAAATAAAAATTAAAAAATAAAT-TGATAA
* * * * * *
508882 ACTAGACAAATAAGAAAAAACATAAAATTTGTATGATTTA-G-----T-GTAA-AA------T--
126 AGTAAACAAGTGAG-AAAAA-ATAAAATTAGTATAATTTAGGTAAAATGGTAAGAAGTGTCGTAA
* * *
508931 -ACA-T---AAAAAATAGTTATCACAATTCTACATATAATGGAAAG
189 CACATTAAGAAAAAAAAGTTATAACAATTCTAAATATAAT-GAAAG
* * * * * * * * *
508972 TAAGAACAATCTTAAGAAAATATAATTGTAACATAAATAATTA-AGTAGATAATGTAAACTTTTA
1 TAAGAACAACCATAATAATATATTATTATAATATAAATAATTATA-TAGACAATGTAAAATTTTA
* * * * * * * *
509036 ATTGATTATGGATTTTATAAATGTATAAGAAAAATAACT--AAATT-AAAAA-AAATAGGTAATG
65 ATTAATTAT-TATTTTGTAAATATATAAG-AAAATAAATAAAAATTAAAAAATAAATTGATAAAG
* * * **
509097 TAAACAAGTGAGAAAAACATAAAATTTGTATCATTT-GCTGTAAAATGGGTAAAAAGTGTTATAA
128 TAAACAAGTGAGAAAAA-ATAAAATTAGTATAATTTAG--GTAAAAT-GGTAAGAAGTGTCGTAA
* * * *
509161 TACACT--G-TAAAAAAGTTATAACAATTCTAAACGTAATGAAATTGAAAAA
189 CACATTAAGAAAAAAAAGTTATAACAATTCTAAA--T-AT--AA-TG-AAAG
* ** * * * *
509210 TAAGAATAACTGTAAGAAAATATTATTATAACATAAATAATTA-AGTAGATAATGTAAAATTTTA
1 TAAGAACAACCATAATAATATATTATTATAATATAAATAATTATA-TAGACAATGTAAAATTTTA
* * * **
509274 ATTAATTATTGTTTTATAAATATACAAGCAAAATAGCTAAAAATTTAAAAAA
65 ATTAATTATTATTTTGTAAATATATAAG-AAAATAAATAAAAA-TTAAAAAA
509326 AACAAATAGG
Statistics
Matches: 1868, Mismatches: 363, Indels: 399
0.71 0.14 0.15
Matches are distributed among these distances:
211 1 0.00
212 36 0.02
213 61 0.03
214 47 0.03
215 87 0.05
216 78 0.04
217 5 0.00
218 1 0.00
219 3 0.00
220 3 0.00
221 5 0.00
222 4 0.00
223 1 0.00
224 2 0.00
225 4 0.00
226 6 0.00
228 3 0.00
229 3 0.00
230 2 0.00
231 50 0.03
232 88 0.05
233 85 0.05
234 218 0.12
235 372 0.20
236 374 0.20
237 71 0.04
238 85 0.05
239 4 0.00
240 8 0.00
241 38 0.02
242 13 0.01
243 54 0.03
244 47 0.03
245 8 0.00
246 1 0.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (233 bp):
TAAGAACAACCATAATAATATATTATTATAATATAAATAATTATATAGACAATGTAAAATTTTAA
TTAATTATTATTTTGTAAATATATAAGAAAATAAATAAAAATTAAAAAATAAATTGATAAAGTAA
ACAAGTGAGAAAAAATAAAATTAGTATAATTTAGGTAAAATGGTAAGAAGTGTCGTAACACATTA
AGAAAAAAAAGTTATAACAATTCTAAATATAATGAAAG
Found at i:507398 original size:235 final size:233
Alignment explanation
Indices: 506614--509442 Score: 947
Period size: 235 Copynumber: 12.2 Consensus size: 233
506604 AAAAAAACAT
* * * * * * ** * * *
506614 CACATTAAGAAAGAGTTATTACAATTTTCAACATAATTAAATATAAGAACAATCATAAAAATAAA
1 CACATTAAAAAAGAGTTATAATAATTCTAAACATAATCAAAGGTAAAAACAACCATAAAAATATA
* * * * * * ** * * *
506679 TTACTGTAATGTAAATAATTAAGTTGCCAACATAAAATTTTAGTTAATTATTTTTTTA-AAACAT
66 TTATTATAATATAAATAATTATGTAG-TAATGTAAAATTTTAATTAATTATTATTTTATAAATAT
* * * * * * * *
506743 ATTAGAAAAATACCTAAAAATTAAAAAACATATTGGTAACATAAACAAGTGAGAAGAAATGTAAA
130 ATAAGAAAAATAGCTAAAAA-TAAAAAATAAATTGATAATATAAACAAGTGAGAGGAAATGAAAA
** * * * *
506808 ATTAGTATCATTTAGTATAAAATGGGTATGAATTGTCATAA
194 ATTAGTATCATTT-GGCTAAAATGGGTAAGAAATATCGTAA
* * * * * * * * **
506849 TATACTAAAAAA-TGTTATAACAATTCTAAATGTATAATGGAAA-GTAAGAACAACCATATTAAT
1 CACATTAAAAAAGAGTTATAATAATTCTAAA--CATAAT-CAAAGGTAAAAACAACCATAAAAAT
** * * * * * *
506912 ATATTATTATAAGGTAAATAATTATATTGACAACGT-AAAGTTTAATTAATTATTATTTTGTAAA
63 ATATTATTATAATATAAATAATTATGTAG-TAATGTAAAATTTTAATTAATTATTATTTTATAAA
* ** * * * **
506976 TAT-TTA-AAAAATAAATAGAAATTAAAAAAGAAATTGATAA-AGTAAACAAGT-A-AGAAAAAC
127 TATATAAGAAAAATAGCTA-AAAATAAAAAATAAATTGATAATA-TAAACAAGTGAGAGGAAATG
* * ** * *
507036 ATAAAATTAGTATAATTTAGTG-TCAAATAAGTAAGAAGTGTCG-AA
190 A-AAAATTAGTATCATTT-G-GCTAAAATGGGTAAGAAATATCGTAA
* * ** * *
507081 CACATTAAGAAAAAAAAGTTATAACAATTCTAAATGTAAT-AAA--AAAAAACAA-TACTAATAA
1 CACATT---AAAAAAGAGTTATAATAATTCTAAACATAATCAAAGGTAAAAACAACCA-TAA-AA
* *
507142 A-ATATTATTATAA-AGTAAATAATTATGTAGATAATGTAAAATTTTAATTAATTATTGTTGCTA
61 ATATATTATTATAATA-TAAATAATTATGTAG-TAATGTAAAATTTTAATTAATTATTATT-TTA
* * *
507205 TAAATATATAAGAAAAATAGCTAAAAATAAAAAAAATAAATTGATAATGTAAAC-A-TGCGA-TA
123 TAAATATATAAGAAAAATAGCTAAAAAT--AAAAAATAAATTGATAATATAAACAAGTGAGAGGA
* ***
507267 AATGTAAAATTAGTATCATTTTAGG-TAAAATGGGTAAGTGGTGA-CGTAA
186 AATGAAAAATTAGTATCA-TTT-GGCTAAAATGGGTAAGAAAT-ATCGTAA
* * * **
507316 -ACTATTAAAAAAGAGTTATGATAATTCTAAACATAATTCAAA-GTAAGAATAATTATAAAAATA
1 CAC-ATTAAAAAAGAGTTATAATAATTCTAAACATAA-TCAAAGGTAAAAACAACCATAAAAATA
* *
507379 TATTATTATAATATAAATAATTATGATAGTAATGTAAAATTTTAATTAATTATTATTTTTGTATA
64 TATTATTATAATATAAATAATTATG-TAGTAATGTAAAATTTTAATTAATTATTA-TTTTATAAA
*
507444 TATATAAGAAAAATAG-TCAAAAACTAAAAAATAAATTGGTAATATAAACAAGTGAGAGGAAATG
127 TATATAAGAAAAATAGCT-AAAAA-TAAAAAATAAATTGATAATATAAACAAGTGAGAGGAAATG
* * *
507508 AAAAATTAGTATTATTTGGCTAAAATGGTTATGAAATATCGTAA
190 AAAAATTAGTATCATTTGGCTAAAATGGGTAAGAAATATCGTAA
* * * *
507552 CACATTAAGAAAGAGTTATAATAATTCTAAATATAATGAAAGGTAAAAACAACCATAAGAATATA
1 CACATTAAAAAAGAGTTATAATAATTCTAAACATAATCAAAGGTAAAAACAACCATAAAAATATA
* * * * *
507617 TTATTGTAATATAAATAATTATGTTGGCAATTTAAAA-TTTAATTAATTATTATTTTTTAAATAT
66 TTATTATAATATAAATAATTATG-TAGTAATGTAAAATTTTAATTAATTATTATTTTATAAATAT
* ** * * * * ** *
507681 ATAAGAAAAATAGCCAAAAATTTAAAATCAAA-TAAGTAGTACAAA-AAG-GTAAAAAAAATGTA
130 ATAAGAAAAATAGCTAAAAATAAAAAAT-AAATTGA-TAATATAAACAAGTG-AGAGGAAATGAA
* * ** * **
507743 AAATTAGTATAATTTGACGTAAAATAAGTAA-AAAGTGTCCCAA
192 AAATTAGTATCATTTGGC-TAAAATGGGTAAGAAA-TATCGTAA
* * * * * * * * * *
507786 TACACTAAGAAAA-AGTAATGACAATTCTAAACGTTATTAAAGATAAGAACAATCACAAATATAT
1 CACATTAA-AAAAGAGTTATAATAATTCTAAACATAATCAAAGGTAAAAACAA-C-C--ATA-A-
** * * * *
507850 ATATATATATATATTATAACGTAAATAATTAAGTTGCCAATGTAAAATTTTAATTATTTATT-TT
59 A-A-ATATAT-TATTATAATATAAATAATTATGTAG-TAATGTAAAATTTTAATTAATTATTATT
* * * * *
507914 TTAT--ACATATAAGAAAAGTAGCAAAAAATTAAAAAATAAATTGATAACATAAACTAGTGAGAA
120 TTATAAATATATAAGAAAAATAGCTAAAAA-TAAAAAATAAATTGATAATATAAACAAGTGAG-A
** ** * * * * *
507977 AAAAAACATAAAATTTA-TATCATTTGACGAAAAATGGGTATGAATTATTGTAA
183 GGAAATGA-AAAA-TTAGTATCATTTGGC-TAAAATGGGTAAGAAATATCGTAA
* ** * * * ** ** *
508030 TACGCTAAAAAA-AGTTATGATAATTATAAACATAATAAAAATTAAGAAA-AACTGTAATAATAT
1 CACATTAAAAAAGAGTTATAATAATTCTAAACATAATCAAAGGTAA-AAACAACCATAAAAATAT
* ** * * * ** * *** *
508093 ATTATTGTAACGTAAA-ACTT-T-AATTAAT-TATTATTTT-A-TAA--A-TA-TCTA-AGGCAA
65 ATTATTATAATATAAATAATTATGTAGTAATGTAAAATTTTAATTAATTATTATTTTATAAATAT
** * *** * * * ** *
508147 ATAACTAAAAT---TAAAAA-AATAAAT-TGGTAAT-GTA-AAT-AAGTGAGACCAAATG-TAAA
130 ATAAGAAAAATAGCTAAAAATAAAAAATAAATTGATAATATAAACAAGTGAGAGGAAATGAAAAA
* * * * *
508203 TTACTACCATTTAGCGTAAAATGGATAA-AAAGTATTGTAA
195 TTAGTATCATTTGGC-TAAAATGGGTAAGAAA-TATCGTAA
* * * * * * ** * * *
508243 CACATTAAGAAAGAGTTATGATAATTATAAACATAATGAAAAGTAAAAATAGTCGTTAAAAGATA
1 CACATTAAAAAAGAGTTATAATAATTCTAAACATAATCAAAGGTAAAAACAACCATAAAAATATA
* * * * * * *
508308 TTATTGTAA-AGGT-AATAACTACGTTGACAATGTAAAATTTTAAATT-TTTATTATTCTTGTAA
66 TTATTATAATA--TAAATAATTATGTAG-TAATGTAAAATTTT-AATTAATTATTATT-TTATAA
* * * *
508370 ATATATAAGAAAAATAGCTAAAATTAAAAAATAAATTGATAACATAAACAAGTGAGA-AATAACG
126 ATATATAAGAAAAATAGCTAAAAATAAAAAATAAATTGATAATATAAACAAGTGAGAGGA-AATG
* ** * * *
508434 TAAAATTAGTATCATTTGAAATAAAATGGTTTAGAAATGTCGTAA
190 AAAAATTAGTATCATTTG-GCTAAAATGGGTAAGAAATATCGTAA
* * * * * * * * * *
508479 TATATTAAGAAAA-AGGTACAATAATTCTAAACATGATGAAAAGCAAAAATAA-TAGTAAAAATA
1 CACATTAA-AAAAGAGTTATAATAATTCTAAACATAATCAAAGGTAAAAACAACCA-TAAAAATA
* * ** * * *
508542 TATCAGTATAACGTAAATAATTATAATGGCAATGTAAAATTTTAATTAATTATTATTTTTGTATA
64 TATTATTATAATATAAATAATTAT-GTAGTAATGTAAAATTTTAATTAATTATTA--TTT-TATA
* * * * * * * *
508607 TATATATAAGGAAAATAGC-AAAATTAAAAAAT--TTTGATAAAATAAACAAGTGAAAAGAAACG
125 AATATATAAGAAAAATAGCTAAAAATAAAAAATAAATTGATAATATAAACAAGTGAGAGGAAATG
* * * * * *
508669 TAAAATTAGTATAATTTGGCATAAAATGAG-AAAAAAGTGTTGTAA
190 AAAAATTAGTATCATTTGGC-TAAAATGGGTAAGAAA-TATCGTAA
* * * * * * * * *** *
508714 TATACTAAAAAA-AGATTATGATAATTCTAAACATATTAAAAGATAAGAACAATTGTAAAAAGAT
1 CACATTAAAAAAGAG-TTATAATAATTCTAAACATAATCAAAGGTAAAAACAACCATAAAAATAT
* * * *
508778 ATTATTGTAATGA-AAATATTTAAGTAGACAATGTAAAATTTTAATTAATTATTATTTTATAAAT
65 ATTATTATAAT-ATAAATAATTATGTAG-TAATGTAAAATTTTAATTAATTATTATTTTATAAAT
* * * * * * * * **
508842 ATATAAGAAAAATAACTAATAATTAAAAAGTAAATATG-TAA-CTAGACAAATAAGA-AAAAACA
128 ATATAAGAAAAATAGCTAA-AAATAAAAAATAAAT-TGATAATATAAACAAGTGAGAGGAAATGA
* * *
508904 TAAAATTTGTATGA-TT---T---A-GTGT---AAA-A---T--
191 -AAAATTAGTATCATTTGGCTAAAATGGGTAAGAAATATCGTAA
* * * * * * * * *
508931 -ACA-TAAAAAATAGTTATCACAATTCTACATATAATGGAAA-GTAAGAACAATCTTAAGAAA-A
1 CACATTAAAAAAGAGTTATAATAATTCTAAACATAAT-CAAAGGTAAAAACAACCATAA-AAATA
* * * * * * *
508992 TATAATTGTAACATAAATAATTAAGTAGATAATGTAAACTTTTAATTGATTATGGATTTTATAAA
64 TATTATTATAATATAAATAATTATGTAG-TAATGTAAAATTTTAATTAATTAT-TATTTTATAAA
* * * * * * **
509057 TGTATAAGAAAAATAACT--AAATTAAAAA-AAATAGGTAATGTAAACAAGTGAGA--AAAACAT
127 TATATAAGAAAAATAGCTAAAAATAAAAAATAAATTGATAATATAAACAAGTGAGAGGAAATGA-
* * **
509117 AAAATTTGTATCATTT-GCTGTAAAATGGGTAA-AAAGTGTTATAA
191 AAAATTAGTATCATTTGGC--TAAAATGGGTAAGAAA-TATCGTAA
* * * * * * **
509161 TACACTGT-AAAAA-AGTTATAACAATTCTAAACGTAATGAAA-TTGAAAAATAAGAATAACTGT
1 CACA-T-TAAAAAAGAGTTATAATAATTCTAAACATAATCAAAGGT-AAAAACAACCAT-A----
* * * *
509223 AAGAAAATATTATTATAACATAAATAATTAAGTAGATAATGTAAAATTTTAATTAATTATTGTTT
58 AA-AATATATTATTATAATATAAATAATTATGTAG-TAATGTAAAATTTTAATTAATTATTATTT
* * * * * * *
509288 TATAAATATACAAGCAAAATAGCTAAAAATTTAAAAAAAACAAATAGGTAACATAAACAAGTGAA
121 TATAAATATATAAGAAAAATAGCTAAAAA--T--AAAAAATAAATTGATAATATAAACAAGTGAG
* * * ** *** * * *
509353 AAG-AATCGTAAAATTCA-TATCAATTAACATAAAATAAATAAGAAGTATCATAG
182 AGGAAAT-GAAAAATT-AGTATCATTTGGC-TAAAATGGGTAAGAAATATCGTAA
* *
509406 CACATTAAAAAAGAGTTATAACAATTCTAAACGTAAT
1 CACATTAAAAAAGAGTTATAATAATTCTAAACATAAT
509443 GAAATATAAG
Statistics
Matches: 1975, Mismatches: 437, Indels: 354
0.71 0.16 0.13
Matches are distributed among these distances:
211 1 0.00
212 31 0.02
213 59 0.03
214 52 0.03
215 90 0.05
216 43 0.02
217 3 0.00
218 4 0.00
219 11 0.01
220 7 0.00
221 4 0.00
222 6 0.00
223 4 0.00
224 9 0.00
225 12 0.01
226 3 0.00
227 14 0.01
228 2 0.00
229 7 0.00
230 10 0.01
231 53 0.03
232 109 0.06
233 95 0.05
234 248 0.13
235 352 0.18
236 323 0.16
237 72 0.04
238 76 0.04
239 6 0.00
241 32 0.02
242 20 0.01
243 76 0.04
244 77 0.04
245 61 0.03
246 3 0.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (233 bp):
CACATTAAAAAAGAGTTATAATAATTCTAAACATAATCAAAGGTAAAAACAACCATAAAAATATA
TTATTATAATATAAATAATTATGTAGTAATGTAAAATTTTAATTAATTATTATTTTATAAATATA
TAAGAAAAATAGCTAAAAATAAAAAATAAATTGATAATATAAACAAGTGAGAGGAAATGAAAAAT
TAGTATCATTTGGCTAAAATGGGTAAGAAATATCGTAA
Found at i:512719 original size:59 final size:57
Alignment explanation
Indices: 512626--512903 Score: 285
Period size: 59 Copynumber: 4.7 Consensus size: 57
512616 AAAAGATTAA
** * *
512626 AAAAATATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCTTCGAAAATCAAAGTTTCC
1 AAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTCAAAAAT-AAA-TTTTC
* *
512686 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT-TCTCGAAAATCAAAGTTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCT-TCAAAAAT-AAA-TTTTC
**
512745 AAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTT-AAAAATAAATTTAAAA
1 AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTT-CTTCAAAAATAAATTT--TC
* * *
512804 AAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTC-CCTAAAAATAAATTTTT
1 AAAAAATA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTC-AAAAATAAATTTTC
*
512863 AAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAA--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
512904 TCCTGCACAA
Statistics
Matches: 192, Mismatches: 13, Indels: 27
0.83 0.06 0.12
Matches are distributed among these distances:
57 3 0.02
58 6 0.03
59 133 0.69
60 7 0.04
61 41 0.21
62 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTCAAAAATAAATTTTC
Found at i:512838 original size:120 final size:116
Alignment explanation
Indices: 512626--512903 Score: 314
Period size: 120 Copynumber: 2.3 Consensus size: 116
512616 AAAAGATTAA
** * **
512626 AAAAATATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCTTCGAAAATCAAAGTTTCCAAAAA
1 AAAAA-ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCTTCAAAAATCAAAGTTTAAAAAAA
* * * *
512691 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT-TCTCGAAAATCAAAGTTTTC
65 AAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCCT-AAAAAT-AAA-TTTTC
512745 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTT-AAAAAT-AAA-TTTAAAAAAA
1 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTT-CTTCAAAAATCAAAGTTT--AAAAA
*
512807 AAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAATAAATTTTT
63 AAAAA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAATAAATTTTC
*
512863 AAAAAAGGTTTTTTTGAGG-AAAAGTTGAAAGTATCAATTTT
1 AAAAAA--TATTTTTG-GGAAAAAGTTGAAAGTATCAATTTT
512904 TCCTGCACAA
Statistics
Matches: 139, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
116 3 0.02
117 3 0.02
118 54 0.39
119 11 0.08
120 64 0.46
121 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (116 bp):
AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCTTCAAAAATCAAAGTTTAAAAAAAA
AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAATAAATTTTC
Found at i:517488 original size:19 final size:20
Alignment explanation
Indices: 517464--517506 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
517454 CAATGGATAA
517464 AAAATGA-GAAAAAAAAAAG
1 AAAATGATGAAAAAAAAAAG
*
517483 AAAATGATGAAACAAAAAAG
1 AAAATGATGAAAAAAAAAAG
517503 AAAA
1 AAAA
517507 AAAATATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAATGATGAAAAAAAAAAG
Found at i:518869 original size:43 final size:42
Alignment explanation
Indices: 518820--518901 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 42
518810 ACCTTTGAAC
*
518820 TCAAATGAAAAGCTTTAAATTTTTGGATGTGAATTTCCAAAAT
1 TCAAATGAAAAGCTTTAAATTTTTGGATATGAA-TTCCAAAAT
*
518863 TCAAATGAAAAGCTTTAGATTTTTGGATATGAATTCCAA
1 TCAAATGAAAAGCTTTAAATTTTTGGATATGAATTCCAA
518902 GTTTGCCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 6 0.16
43 31 0.84
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (42 bp):
TCAAATGAAAAGCTTTAAATTTTTGGATATGAATTCCAAAAT
Found at i:519276 original size:42 final size:41
Alignment explanation
Indices: 519186--519490 Score: 457
Period size: 42 Copynumber: 7.3 Consensus size: 41
519176 TTGAACATGA
* *
519186 CTGTTTAGAGGAGTAATTTACTTTTCAAAGTCATGGTGCCT
1 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCT
*
519227 CTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCATGGTGCCT
1 CTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCT
* *
519269 CTATTTAGAGGAGCAATTTACTTTCTTAAAGTCGTGGTGCCT
1 CTGTTTAGAGGAGCAATTTACTTT-TCAAAGTCGTGGTGCCT
** *
519311 CTGTTTAGAGGAGCAATTTACTTACCAAAAGTCGTAGTGCCT
1 CTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCT
* *
519353 CTGTTTAGAGGAACAATTTACTTTTCAAAGTCATGGTGCCT
1 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCT
*
519394 CTATTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCT
1 CTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCT
* *
519436 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGAGCCT
1 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCT
519477 CTGTTTAGAGGAGC
1 CTGTTTAGAGGAGC
519491 TTTAAAAAAA
Statistics
Matches: 240, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
41 89 0.37
42 150 0.62
43 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (41 bp):
CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCT
Found at i:519408 original size:125 final size:125
Alignment explanation
Indices: 519186--519488 Score: 493
Period size: 125 Copynumber: 2.4 Consensus size: 125
519176 TTGAACATGA
* * * *
519186 CTGTTTAGAGGAGTAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTT
1 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTAGTGCCTCTGTTTAGAGGAACAATTTACTTT
*
519251 TCAAAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTAC-TTTCTTAAAGTCGTGGTGCCT
66 TCAAAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTC-AAAAGTCGTGGTGCCT
**
519311 CTGTTTAGAGGAGCAATTTACTTACCAAAAGTCGTAGTGCCTCTGTTTAGAGGAACAATTTACTT
1 CTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTAGTGCCTCTGTTTAGAGGAACAATTTACTT
519376 TTC-AAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCT
65 TTCAAAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCT
* *
519436 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGA
1 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTAGTGCCTCTGTTTAGAGGA
519489 GCTTTAAAAA
Statistics
Matches: 165, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
124 25 0.15
125 98 0.59
126 42 0.25
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (125 bp):
CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTAGTGCCTCTGTTTAGAGGAACAATTTACTTT
TCAAAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCT
Found at i:519423 original size:83 final size:83
Alignment explanation
Indices: 519186--519490 Score: 484
Period size: 83 Copynumber: 3.7 Consensus size: 83
519176 TTGAACATGA
*
519186 CTGTTTAGAGGAGTAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTT
1 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTT
*
519251 TCAAAAGTCATGGTGCCT
66 TCAAAAGTCGTGGTGCCT
* * *
519269 CTATTTAGAGGAGCAATTTACTTTCTTAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTT
1 CTGTTTAGAGGAGCAATTTACTTT-TCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTT
** *
519334 ACCAAAAGTCGTAGTGCCT
65 TTCAAAAGTCGTGGTGCCT
* *
519353 CTGTTTAGAGGAACAATTTACTTTTCAAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTACTTT
1 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTT
519418 TCAAAAGTCGTGGTGCCT
66 TCAAAAGTCGTGGTGCCT
* * *
519436 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
1 CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGC
519491 TTTAAAAAAA
Statistics
Matches: 200, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
83 125 0.62
84 75 0.38
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (83 bp):
CTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTT
TCAAAAGTCGTGGTGCCT
Found at i:519500 original size:1 final size:1
Alignment explanation
Indices: 519494--519585 Score: 76
Period size: 1 Copynumber: 92.0 Consensus size: 1
519484 GAGGAGCTTT
* * * * * * * *
519494 AAAAAAAAAACAAAACAAAAAAAAAAAACAAGAAACAAAAAAAAACAAAAAAAATAAAAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * *
519559 AAAAAAAAGTAAGAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
519586 TTGAGCTTCT
Statistics
Matches: 68, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:519517 original size:18 final size:17
Alignment explanation
Indices: 519494--519585 Score: 112
Period size: 18 Copynumber: 5.2 Consensus size: 17
519484 GAGGAGCTTT
519494 AAAAAAAAAACAAAACAA
1 AAAAAAAAAACAAAA-AA
*
519512 AAAAAAAAAACAAGAAA
1 AAAAAAAAAACAAAAAA
*
519529 CAAAAAAAAACAAAAAA
1 AAAAAAAAAACAAAAAA
*
519546 AATAAAAAAAATAAAAAA
1 AA-AAAAAAAACAAAAAA
*
519564 AAAGTAAGAAAACAAAAAA
1 AAA--AAAAAAACAAAAAA
519583 AAA
1 AAA
519586 TTGAGCTTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
17 19 0.30
18 30 0.47
19 15 0.23
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAA
Found at i:519564 original size:20 final size:19
Alignment explanation
Indices: 519494--519585 Score: 94
Period size: 20 Copynumber: 4.7 Consensus size: 19
519484 GAGGAGCTTT
*
519494 AAAAAAAAAACAAAACAAA
1 AAAAAAAAAAAAAAACAAA
*
519513 AAAAAAAAACAAGAAACAAA
1 AAAAAAAAA-AAAAAACAAA
* *
519533 AAAAAACAAAAAAAATAAA
1 AAAAAAAAAAAAAAACAAA
**
519552 AAAAATAAAAAAAAAGTAAGA
1 AAAAA-AAAAAAAAAACAA-A
*
519573 AAACAAAAAAAAA
1 AAAAAAAAAAAAA
519586 TTGAGCTTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
19 22 0.35
20 35 0.56
21 5 0.08
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAAAAAACAAA
Found at i:519575 original size:19 final size:19
Alignment explanation
Indices: 519496--519586 Score: 93
Period size: 19 Copynumber: 5.0 Consensus size: 19
519486 GGAGCTTTAA
*
519496 AAAAAAAACAAAACAAAA-
1 AAAAAAAACAAAAAAAAAT
* *
519514 AAAAAAAAC-AAGAAACA-
1 AAAAAAAACAAAAAAAAAT
519531 AAAAAAAAC-AAAAAAAAT
1 AAAAAAAACAAAAAAAAAT
*
519549 AAAAAAAATAAAAAAAAAGT
1 AAAAAAAACAAAAAAAAA-T
*
519569 -AAGAAAACAAAAAAAAAT
1 AAAAAAAACAAAAAAAAAT
519587 TGAGCTTCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
17 20 0.32
18 18 0.29
19 23 0.37
20 1 0.02
ACGTcount: A:0.86, C:0.07, G:0.03, T:0.04
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAAAT
Found at i:519719 original size:115 final size:113
Alignment explanation
Indices: 519558--519811 Score: 352
Period size: 115 Copynumber: 2.2 Consensus size: 113
519548 TAAAAAAAAT
* * * *
519558 AAAAAAAAAGTAAGAAAAC---AAAAAAAAATTGAGCTTCTGTTTAGAGGAGCTTTGTTTATGTT
1 AAAAAAAAAGAAAGAAAACAAAAAAAAAAAACTGAGCCTATGTTTAGAGGAGCTTTGTTTATGTT
* * * **
519620 TCTCAAAGTCGTTGATCCTCTGCTTAGAGGAGCTTTGATCAATTTTTTTA
66 TCTCAAAGTCGTTAAGCCTCTGCTTAGAGGAGCTTCGATCAA--AATTTA
*
519670 AAAAAAAAAGCAAGAAAACAAAAAAAAAAAACTGAGCCTATGTTTAGAGGAGCTTTGTTTATGTT
1 AAAAAAAAAGAAAGAAAACAAAAAAAAAAAACTGAGCCTATGTTTAGAGGAGCTTTGTTTATGTT
519735 TCTCAAAGTCGTTAAGCCTCTGCTTAGAGGAGCTTCGATCAAAATTTA
66 TCTCAAAGTCGTTAAGCCTCTGCTTAGAGGAGCTTCGATCAAAATTTA
* *
519783 AAAAAAAAAAAAAGAAAAGCAAAACAAAA
1 AAAAAAAAAGAAAGAAAA-CAAAAAAAAA
519812 TAGGCAAAAA
Statistics
Matches: 126, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
112 18 0.14
113 20 0.16
114 9 0.07
115 79 0.63
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (113 bp):
AAAAAAAAAGAAAGAAAACAAAAAAAAAAAACTGAGCCTATGTTTAGAGGAGCTTTGTTTATGTT
TCTCAAAGTCGTTAAGCCTCTGCTTAGAGGAGCTTCGATCAAAATTTA
Found at i:522183 original size:29 final size:29
Alignment explanation
Indices: 522151--522241 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
522141 AAAAAAAATA
522151 TTTTTGAGGAAAAGTTGAAAGTATCAATT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATT
* * * * *
522180 TTTTTAAGAAATAAATTTTCAAA--A-AAAGGTT
1 TTTTTGAG-GA-AAA-GTTGAAAGTATCAA--TT
522211 TTTTTGAGGAAAAGTTGAAAGTATCAATT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATT
522240 TT
1 TT
522242 CCTTAAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 16
0.63 0.14 0.23
Matches are distributed among these distances:
28 5 0.11
29 16 0.36
30 4 0.09
31 14 0.32
32 5 0.11
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.40
Consensus pattern (29 bp):
TTTTTGAGGAAAAGTTGAAAGTATCAATT
Found at i:522293 original size:59 final size:58
Alignment explanation
Indices: 522136--522591 Score: 482
Period size: 59 Copynumber: 7.8 Consensus size: 58
522126 CGATAAAAAG
* *
522136 ATTTT-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-TTTAAGAAATAA
1 ATTTTCAAAAAAAGT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA-AAATAA
522194 ATTTTCAAAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA
1 ATTTTCAAAAAAA-G-TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA
**
522254 ATTTTCAAAAAAAGTTTTTCTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAA
1 ATTTTCAAAAAAAGTTTTT-TGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AA
* * *
522314 AGTTTCCAAAAAA-TATTTTTG-GAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA
1 ATTTTCAAAAAAAGT-TTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA
* * *
522372 ATTTTAAAAAAAAAG-TTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCC-TAAAAATAA
1 ATTTT-CAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAA
* * *
522430 ATTTTCAAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCC-TGAAATTAA
1 ATTTTCAAAAAAAG-TTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAA
* * * * ** * *
522489 AGTTTCAAAAGATA-TTTTGTGA--AAAAGTTGAAAGTATCAATTTTACTCGAGATTAAA
1 ATTTTCAAAA-AAAGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AA
** * * *
522546 ATTTAAAAAAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 ATTTTCAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
522592 TCCTGCACAA
Statistics
Matches: 345, Mismatches: 33, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
55 5 0.01
56 25 0.07
57 21 0.06
58 62 0.18
59 159 0.46
60 68 0.20
61 5 0.01
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (58 bp):
ATTTTCAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA
Found at i:522456 original size:176 final size:173
Alignment explanation
Indices: 522143--522595 Score: 610
Period size: 176 Copynumber: 2.6 Consensus size: 173
522133 AAGATTTTAA
* * *
522143 AAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTTTTAAGAAATAAATTTTCAAAAAAA
1 AAAAAATATTTTTGGA-AAAAAGTTGAAAGTATCAATTTTCTTAA-AAATAAATTTTAAAAAAAA
*
522207 GGTTTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAAATTTTCAAAAAAAGTTT
64 AG--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCC-TAAAAATAAATTTTCAAAAAAAGTTT
522271 TTCTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTCGAAAATCAAAGTTTCC
126 TTCTGAGGAAAAGTTGAAAGTATCAATTTTTCCT-G-AAATCAAAGTTT-C
522321 AAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTAAAAAAAAA
1 AAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTT-CTTAAAAATAAATTTTAAAAAAAAA
* * * *
522386 GTTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCCTAAAAATAAATTTTCAAAAAAGGTTTTTTT
65 GTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTAAAAATAAATTTTCAAAAAAAGTTTTTCT
*
522451 GAGGAAAAGTTGAAAGTATCAATTTTTCCTGAAATTAAAGTTTC
130 GAGGAAAAGTTGAAAGTATCAATTTTTCCTGAAATCAAAGTTTC
* ** * * *
522495 AAAAGATA-TTTTGTG-AAAAAGTTGAAAGTATCAATTTTACTCGAGATTAAAATTTAAAAAAAA
1 AAAAAATATTTTTG-GAAAAAAGTTGAAAGTATCAATTTT-CTTAAAAATAAATTTTAAAAAAAA
* *
522558 AATATTTTGGGGAAAAGTTGAAAGTATCAATTTTTCCT
64 AGT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCT
522596 GCACAAGAAC
Statistics
Matches: 249, Mismatches: 20, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
173 49 0.20
174 40 0.16
175 11 0.04
176 76 0.31
177 13 0.05
178 54 0.22
179 6 0.02
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (173 bp):
AAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCTTAAAAATAAATTTTAAAAAAAAAG
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTAAAAATAAATTTTCAAAAAAAGTTTTTCTG
AGGAAAAGTTGAAAGTATCAATTTTTCCTGAAATCAAAGTTTC
Found at i:523703 original size:21 final size:21
Alignment explanation
Indices: 523670--523717 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
523660 CATGTCATCA
523670 TTAAAAAAATTTTAAATAA-TT
1 TTAAAAAAATTTTAAA-AACTT
* *
523691 TTAAACAATTTTTAAAAACTT
1 TTAAAAAAATTTTAAAAACTT
523712 TTAAAA
1 TTAAAA
523718 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAAAATTTTAAAAACTT
Found at i:523738 original size:11 final size:11
Alignment explanation
Indices: 523673--523766 Score: 58
Period size: 10 Copynumber: 9.0 Consensus size: 11
523663 GTCATCATTA
523673 AAAAAATTT-T
1 AAAAAATTTAT
*
523683 AAATAATTT-T
1 AAAAAATTTAT
* *
523693 AAACAATTTTT
1 AAAAAATTTAT
*
523704 AAAAACTTT-T
1 AAAAAATTTAT
523714 --AAAATTTAT
1 AAAAAATTTAT
*
523723 AAAAAATTATAA
1 AAAAAATT-TAT
*
523735 AAAAAATTCTTT
1 AAAAAATT-TAT
*
523747 AAAAAA--TCT
1 AAAAAATTTAT
523756 AAAAAATTTAT
1 AAAAAATTTAT
523767 GTAAAATTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
8 6 0.09
9 9 0.14
10 18 0.27
11 16 0.24
12 17 0.26
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAAATTTAT
Found at i:539838 original size:20 final size:20
Alignment explanation
Indices: 539813--539851 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
539803 GCATATTTAT
539813 TGGATACTAGGAAATATTAG
1 TGGATACTAGGAAATATTAG
*
539833 TGGATACTAGGAGATATTA
1 TGGATACTAGGAAATATTA
539852 TAAGTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (20 bp):
TGGATACTAGGAAATATTAG
Found at i:541083 original size:21 final size:22
Alignment explanation
Indices: 541049--541089 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
541039 GATTATTTAT
*
541049 TTTTTATATATTTATTTATCTC
1 TTTTTATATATTTAATTATCTC
*
541071 TTTTTA-ATTTTTAATTATC
1 TTTTTATATATTTAATTATC
541090 ATATAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATATATTTAATTATCTC
Found at i:541774 original size:22 final size:23
Alignment explanation
Indices: 541733--541778 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
541723 CACATTTAAG
541733 TTCAAAGGAAACTTAAAAAAAAA
1 TTCAAAGGAAACTTAAAAAAAAA
*
541756 TTCAAAGGAAACTAAAAAAAAAA
1 TTCAAAGGAAACTTAAAAAAAAA
541779 AAAGTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (23 bp):
TTCAAAGGAAACTTAAAAAAAAA
Found at i:542403 original size:21 final size:21
Alignment explanation
Indices: 542363--542521 Score: 64
Period size: 21 Copynumber: 7.3 Consensus size: 21
542353 GATGCTTACT
*
542363 AAAATTATATA-AAAATTTATC
1 AAAATTATATATAAGA-TTATC
542384 AAAATTATATATAAGATTAT-
1 AAAATTATATATAAGATTATC
* * *
542404 TAAATTATGTCA-AACATTATCC
1 AAAATTATAT-ATAAGATTAT-C
** * *
542426 AAATAAGAACTGTATTAAAGTTTATC
1 -AA-AATTA-TATA-T-AAGATTATC
*
542452 AAAATTATAT-TAATAATTA-C
1 AAAATTATATATAA-GATTATC
542472 TAAGAA-TATATAATAA-ATTATC
1 -AA-AATTATAT-ATAAGATTATC
542494 AAAATTATATGA-AAGATTATC
1 AAAATTATAT-ATAAGATTATC
542515 AAAATTA
1 AAAATTA
542522 CGTTGGTAAG
Statistics
Matches: 105, Mismatches: 15, Indels: 36
0.67 0.10 0.23
Matches are distributed among these distances:
20 22 0.21
21 52 0.50
22 6 0.06
23 6 0.06
24 7 0.07
25 5 0.05
26 1 0.01
27 6 0.06
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAATTATATATAAGATTATC
Found at i:542565 original size:21 final size:21
Alignment explanation
Indices: 542541--542584 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
542531 GTTATCAATG
542541 TTTTATAAAAAGT-TACTAAAA
1 TTTTATAAAAA-TATACTAAAA
* *
542562 TTTTATTAATATATACTAAAA
1 TTTTATAAAAATATACTAAAA
542583 TT
1 TT
542585 ATATCATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTATAAAAATATACTAAAA
Found at i:542707 original size:21 final size:21
Alignment explanation
Indices: 542674--542731 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
542664 AAAACATATA
* *
542674 AAAAGTTGCCAAAATTGTACCT
1 AAAAGTTACCAAAATTGCA-CT
*
542696 AAAA-TTACCAAAATTGCATT
1 AAAAGTTACCAAAATTGCACT
542716 AAAAGTTACCAAAATT
1 AAAAGTTACCAAAATT
542732 ATTTCACACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.16
21 23 0.72
22 4 0.12
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAAGTTACCAAAATTGCACT
Found at i:547728 original size:18 final size:18
Alignment explanation
Indices: 547686--547730 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
547676 AAGATAATTT
547686 ACAATAAAAAATATTATG
1 ACAATAAAAAATATTATG
*
547704 A-AGTAAAAAATTATTA-G
1 ACAATAAAAAA-TATTATG
547721 ACAATAAAAA
1 ACAATAAAAA
547731 TAATGTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.24
Consensus pattern (18 bp):
ACAATAAAAAATATTATG
Found at i:548312 original size:9 final size:10
Alignment explanation
Indices: 548282--548430 Score: 53
Period size: 10 Copynumber: 14.8 Consensus size: 10
548272 TTATTGATGC
548282 TTAT-AAAATT
1 TTATCAAAA-T
548292 TTATCAAAAT
1 TTATCAAAAT
*
548302 TTATCAAATT
1 TTATCAAAAT
*
548312 TCTAAT-AAAAA
1 T-T-ATCAAAAT
*
548323 TTACCAAAAT
1 TTATCAAAAT
*
548333 ATAT-AAAAGT
1 TTATCAAAA-T
*
548343 TTA-CCAAA-
1 TTATCAAAAT
*
548351 --ACCAAAAT
1 TTATCAAAAT
*
548359 TGTATCAAAAG
1 T-TATCAAAAT
548370 TTATCAAAAT
1 TTATCAAAAT
* *
548380 TATATAAAAAC
1 T-TATCAAAAT
*
548391 TTATTAAAAT
1 TTATCAAAAT
*
548401 TGTATCTAAGA-
1 T-TATC-AAAAT
*
548412 TTACCAAAAT
1 TTATCAAAAT
548422 TATATCAAA
1 T-TATCAAA
548431 CTTACAAAAA
Statistics
Matches: 101, Mismatches: 22, Indels: 31
0.66 0.14 0.20
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
9 8 0.08
10 49 0.49
11 34 0.34
12 5 0.05
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (10 bp):
TTATCAAAAT
Found at i:548379 original size:21 final size:21
Alignment explanation
Indices: 548353--548503 Score: 87
Period size: 21 Copynumber: 7.3 Consensus size: 21
548343 TTACCAAAAC
*
548353 CAAAATTGTATCAAAAGTTAT
1 CAAAATTATATCAAAAGTTAT
* *
548374 CAAAATTATATAAAAACTTAT
1 CAAAATTATATCAAAAGTTAT
* * * *
548395 TAAAATTGTATC-TAAGATTAC
1 CAAAATTATATCAAAAG-TTAT
*
548416 CAAAATTATATC-AAACTTA-
1 CAAAATTATATCAAAAGTTAT
* * * *
548435 CAAAAATTTTATTAAATGTTAC
1 C-AAAATTATATCAAAAGTTAT
* *
548457 CAAAATTATAT-AAATAATTAC
1 CAAAATTATATCAAA-AGTTAT
* * *
548478 CCAAATTATATTATAAGTTAT
1 CAAAATTATATCAAAAGTTAT
548499 -AAAAT
1 CAAAAT
548504 AGAAAAAAAG
Statistics
Matches: 99, Mismatches: 25, Indels: 13
0.72 0.18 0.09
Matches are distributed among these distances:
19 1 0.01
20 21 0.21
21 74 0.75
22 3 0.03
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.36
Consensus pattern (21 bp):
CAAAATTATATCAAAAGTTAT
Found at i:548457 original size:41 final size:41
Alignment explanation
Indices: 548354--548534 Score: 138
Period size: 41 Copynumber: 4.4 Consensus size: 41
548344 TACCAAAACC
* * **
548354 AAAATTGTATCAAAAGTTATCAAAATTATATAAAAACTTATT
1 AAAATTGTAT-TAAAGTTACCAAAATTATATAAAAACTTACA
*
548396 AAAATTGTATCT-AAGATTACCAAAATTATAT-CAAACTTACA
1 AAAATTGTAT-TAAAG-TTACCAAAATTATATAAAAACTTACA
* *
548437 AAAATTTTATTAAATGTTACCAAAATTATATAAATAA-TTACC
1 AAAATTGTATTAAA-GTTACCAAAATTATATAAA-AACTTACA
* * * * * * *
548479 CAAATTATATTATAAGTTA-TAAAA-TAGAAAAAAAGATTACC
1 AAAATTGTATTA-AAGTTACCAAAATTATATAAAAA-CTTACA
548520 AAAATTGTATTAAAG
1 AAAATTGTATTAAAG
548535 GTCACTACAA
Statistics
Matches: 116, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
39 2 0.02
40 10 0.09
41 55 0.47
42 45 0.39
43 4 0.03
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.34
Consensus pattern (41 bp):
AAAATTGTATTAAAGTTACCAAAATTATATAAAAACTTACA
Found at i:548534 original size:21 final size:21
Alignment explanation
Indices: 548351--548534 Score: 80
Period size: 21 Copynumber: 8.9 Consensus size: 21
548341 GTTTACCAAA
* *
548351 ACCAAAATTGTATCAAA-AGTT
1 ACCAAAATTATATTAAAGA-TT
* *
548372 ATCAAAATTATA-TAAAAACTT
1 ACCAAAATTATATTAAAGA-TT
** *
548393 ATTAAAATTGTATCT-AAGATT
1 ACCAAAATTATAT-TAAAGATT
* *
548414 ACCAAAATTATATCAAA-CTT
1 ACCAAAATTATATTAAAGATT
* *
548434 ACAAAAATTTTATTAAATG-TT
1 ACCAAAATTATATTAAA-GATT
*
548455 ACCAAAATTATA-TAAATAATT
1 ACCAAAATTATATTAAA-GATT
*
548476 ACCCAAATTATATTATAAG-TT
1 ACCAAAATTATATTA-AAGATT
* * **
548497 A-TAAAA-TAGAAAAAAAGATT
1 ACCAAAATTA-TATTAAAGATT
*
548517 ACCAAAATTGTATTAAAG
1 ACCAAAATTATATTAAAG
548535 GTCACTACAA
Statistics
Matches: 120, Mismatches: 30, Indels: 26
0.68 0.17 0.15
Matches are distributed among these distances:
19 5 0.04
20 32 0.27
21 74 0.62
22 6 0.05
23 3 0.03
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (21 bp):
ACCAAAATTATATTAAAGATT
Found at i:548757 original size:21 final size:21
Alignment explanation
Indices: 548733--548880 Score: 76
Period size: 21 Copynumber: 7.1 Consensus size: 21
548723 AAGGTTATCT
*
548733 ATTATAT-CAAAATTTACTAAA
1 ATTATATCCAAAA-TTACCAAA
*
548754 ATTATATCCAAGATTACCAAA
1 ATTATATCCAAAATTACCAAA
* ** *
548775 ATTATAT-TAATGGTTATCAAA
1 ATTATATCCAA-AATTACCAAA
*
548796 ATTATAT-CATAAA-CACCAAA
1 ATTATATCCA-AAATTACCAAA
* * *
548816 ATTGTAT-TAAAGTCTACCAAA
1 ATTATATCCAAAAT-TACCAAA
*
548837 ATTATAT-CAAACTTA-CAAA
1 ATTATATCCAAAATTACCAAA
* **
548856 TATTTTATTAAAAATTACCAAA
1 -ATTATATCCAAAATTACCAAA
548878 ATT
1 ATT
548881 GTCTTAATGA
Statistics
Matches: 99, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
19 6 0.06
20 22 0.22
21 62 0.63
22 9 0.09
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (21 bp):
ATTATATCCAAAATTACCAAA
Found at i:548964 original size:21 final size:20
Alignment explanation
Indices: 548810--548964 Score: 71
Period size: 21 Copynumber: 7.5 Consensus size: 20
548800 TATCATAAAC
*
548810 ACCAAAATTGTATTAAAGTCT
1 ACCAAAATTGTATTAAAAT-T
* * *
548831 ACCAAAATTATATCAAACTT
1 ACCAAAATTGTATTAAAATT
*
548851 A-CAAATATTTTATTAAAAATT
1 ACCAAA-ATTGTATT-AAAATT
* * **
548872 ACCAAAATTGTCTTAATGAGC
1 ACCAAAATTGTATTAA-AATT
* * **
548893 ACCTAAGTCATA-TAATAAGTT
1 ACCAAAATTGTATTAA-AA-TT
* * *
548914 ACCAAAATAGAATTAAAGGTT
1 ACCAAAATTGTATTAAA-ATT
*
548935 ACGAAAATTGTATTAAACATT
1 ACCAAAATTGTATTAAA-ATT
548956 ACCAAAATT
1 ACCAAAATT
548965 TTATCAAATG
Statistics
Matches: 96, Mismatches: 31, Indels: 14
0.68 0.22 0.10
Matches are distributed among these distances:
19 4 0.04
20 15 0.16
21 70 0.73
22 7 0.07
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (20 bp):
ACCAAAATTGTATTAAAATT
Found at i:550429 original size:48 final size:48
Alignment explanation
Indices: 550294--550410 Score: 155
Period size: 48 Copynumber: 2.4 Consensus size: 48
550284 GGCTAAATAC
* * * *** *
550294 GGTACTGCTAATTTGGTAGAAAACAATGGTGCTAATGAGGTTGATGAT
1 GGTACTTCTAATTTGGCAAAAAACAATGAAACAAATGAGGTTGATGAT
550342 GGTACTTCTAATTTGGCAAAAAACAATGAAACAAATGAGGTTGATGAT
1 GGTACTTCTAATTTGGCAAAAAACAATGAAACAAATGAGGTTGATGAT
550390 GGTAC-TCGTAATTTGGCAAAA
1 GGTACTTC-TAATTTGGCAAAA
550411 GATAATAGGG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 2 0.03
48 59 0.97
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (48 bp):
GGTACTTCTAATTTGGCAAAAAACAATGAAACAAATGAGGTTGATGAT
Found at i:555001 original size:5 final size:5
Alignment explanation
Indices: 554993--555024 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
554983 TCAAAAATAA
554993 AAAAT AAAAT -AAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
555025 TGAATGCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:555008 original size:9 final size:9
Alignment explanation
Indices: 554994--555025 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
554984 CAAAAATAAA
554994 AAATAAAAT
1 AAATAAAAT
555003 AAATAAAAT
1 AAATAAAAT
555012 AAAATAAAAT
1 -AAATAAAAT
555022 AAAT
1 AAAT
555026 GAATGCCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAATAAAAT
Found at i:555025 original size:14 final size:15
Alignment explanation
Indices: 554993--555024 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
554983 TCAAAAATAA
554993 AAAATAAAAT-AAAT
1 AAAATAAAATAAAAT
555007 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
555022 AAA
1 AAA
555025 TGAATGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:555417 original size:9 final size:9
Alignment explanation
Indices: 555403--555460 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
555393 TGAAAGAAAG
555403 AAAAAAATA
1 AAAAAAATA
*
555412 AAAAAAGT-
1 AAAAAAATA
*
555420 GAAAAAATA
1 AAAAAAATA
555429 AAAAAAATA
1 AAAAAAATA
555438 AAAAAAATAA
1 AAAAAAAT-A
555448 AAAGAAAATA
1 AAA-AAAATA
555458 AAA
1 AAA
555461 GGAATACTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
8 6 0.14
9 23 0.55
10 8 0.19
11 5 0.12
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:555426 original size:17 final size:18
Alignment explanation
Indices: 555403--555460 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 18
555393 TGAAAGAAAG
*
555403 AAAAAAATAAAAAAAGT-
1 AAAAAAATAAAAAAAATA
*
555420 GAAAAAATAAAAAAAATA
1 AAAAAAATAAAAAAAATA
555438 AAAAAAATAAAAAGAAAATA
1 AAAAAAAT-AAAA-AAAATA
555458 AAA
1 AAA
555461 GGAATACTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.43
18 7 0.20
19 4 0.11
20 9 0.26
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.10
Consensus pattern (18 bp):
AAAAAAATAAAAAAAATA
Found at i:556092 original size:46 final size:45
Alignment explanation
Indices: 556036--556354 Score: 268
Period size: 46 Copynumber: 7.0 Consensus size: 45
556026 CATATAGTTT
* *
556036 TTTGAGTCTTAAATGACAATCTTTAAGAAATCCTCAAATAAGAATC
1 TTTGAGTCTTAAATGAAAATCTTTAA-AAATCCTCAAATGAGAATC
* * * * *
556082 TTTGAATCTTAAATAAAAATATTTAAAGAATCCACAAATGAGAATT
1 TTTGAGTCTTAAATGAAAATCTTTAAA-AATCCTCAAATGAGAATC
* *
556128 TTTTAGTCTTAAATGAAAATCTTTAAAGAATCCACAAATGAGAATC
1 TTTGAGTCTTAAATGAAAATCTTTAAA-AATCCTCAAATGAGAATC
* * ** *
556174 TTTGAGTCTTAAATGAGAATCCTTAAAACATTTTCAAATGAGAAGC
1 TTTGAGTCTTAAATGAAAATCTTTAAAA-ATCCTCAAATGAGAATC
* * ** **
556220 --TGAGTCTCAAATGAGAATCTTTAAGATGTTTTCAAATGAGAATC
1 TTTGAGTCTTAAATGAAAATCTTTAA-AAATCCTCAAATGAGAATC
* * * ** *
556264 TTTGAGTTTTAAATAAAAAT-TTTAAATGCATTTTCAAATGAGAAGC
1 TTTGAGTCTTAAATGAAAATCTTTAAA--AATCCTCAAATGAGAATC
* * *
556310 TTTGAGTCTTAAATGAGAATGTTT-AAAATGCTTTCAAATGAGAAT
1 TTTGAGTCTTAAATGAAAATCTTTAAAAAT-C-CTCAAATGAGAAT
556355 TTTTAAGATG
Statistics
Matches: 226, Mismatches: 37, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
44 40 0.18
45 8 0.04
46 175 0.77
47 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.34
Consensus pattern (45 bp):
TTTGAGTCTTAAATGAAAATCTTTAAAAATCCTCAAATGAGAATC
Found at i:556141 original size:21 final size:21
Alignment explanation
Indices: 556117--556193 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
556107 AAGAATCCAC
*
556117 AAATGAGAATTTTTTAGTCTT
1 AAATGAGAATTTTTAAGTCTT
* * **
556138 AAATGAAAATCTTTAAAGAATCCAC
1 AAATGAGAAT-TTTTAAG--T-CTT
* *
556163 AAATGAGAATCTTTGAGTCTT
1 AAATGAGAATTTTTAAGTCTT
556184 AAATGAGAAT
1 AAATGAGAAT
556194 CCTTAAAACA
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
21 20 0.49
22 6 0.15
24 5 0.12
25 10 0.24
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (21 bp):
AAATGAGAATTTTTAAGTCTT
Found at i:556166 original size:25 final size:25
Alignment explanation
Indices: 556092--556176 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 25
556082 TTTGAATCTT
* *
556092 AAATAAAAATATTTAAAGAATCCAC
1 AAATGAAAATCTTTAAAGAATCCAC
* ** **
556117 AAATGAGAAT-TTTTTAG--T-CTT
1 AAATGAAAATCTTTAAAGAATCCAC
556138 AAATGAAAATCTTTAAAGAATCCAC
1 AAATGAAAATCTTTAAAGAATCCAC
*
556163 AAATGAGAATCTTT
1 AAATGAAAATCTTT
556177 GAGTCTTAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
21 10 0.23
22 6 0.14
24 6 0.14
25 22 0.50
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (25 bp):
AAATGAAAATCTTTAAAGAATCCAC
Found at i:556212 original size:92 final size:91
Alignment explanation
Indices: 556034--556354 Score: 321
Period size: 92 Copynumber: 3.5 Consensus size: 91
556024 TACATATAGT
* * *
556034 TTTTTGAGTCTTAAATGACAATCTTTAAGAAATCCTCAAATAAGAATCTTTGAATCTTAAATAAA
1 TTTTTGAGTCTTAAATGAGAATCTTTAAG-AATCCTCAAATGAGAATCTTTGAGTCTTAAATAAA
***
556099 AATATTTAAAGA-ATCCACAAATGAGAA
65 AAT-TTTAAAGACATTTTCAAATGAGAA
* * * * *
556126 TTTTTTAGTCTTAAATGAAAATCTTTAAAGAATCCACAAATGAGAATCTTTGAGTCTTAAATGAG
1 TTTTTGAGTCTTAAATGAGAATCTTT-AAGAATCCTCAAATGAGAATCTTTGAGTCTTAAATAAA
*
556191 AATCCTTAAA-ACATTTTCAAATGAGAA
65 AAT-TTTAAAGACATTTTCAAATGAGAA
** * * ** *
556218 --GCTGAGTCTCAAATGAGAATCTTTAAGATGTTTTCAAATGAGAATCTTTGAGTTTTAAATAAA
1 TTTTTGAGTCTTAAATGAGAATCTTTAAGA-ATCCTCAAATGAGAATCTTTGAGTCTTAAATAAA
556281 AATTTTAAATG-CATTTTCAAATGAGAA
65 AATTTTAAA-GACATTTTCAAATGAGAA
** * *
556308 GCTTTGAGTCTTAAATGAGAATGTTTAA-AATGCTTTCAAATGAGAAT
1 TTTTTGAGTCTTAAATGAGAATCTTTAAGAAT-C-CTCAAATGAGAAT
556355 TTTTAAGATG
Statistics
Matches: 189, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
89 9 0.05
90 66 0.35
91 2 0.01
92 109 0.58
93 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (91 bp):
TTTTTGAGTCTTAAATGAGAATCTTTAAGAATCCTCAAATGAGAATCTTTGAGTCTTAAATAAAA
ATTTTAAAGACATTTTCAAATGAGAA
Found at i:556260 original size:25 final size:25
Alignment explanation
Indices: 556226--556532 Score: 200
Period size: 25 Copynumber: 12.9 Consensus size: 25
556216 AAGCTGAGTC
556226 TCAAATGAGAATCTTTAAGATGTTT
1 TCAAATGAGAATCTTTAAGATGTTT
556251 TCAAATGAGAATCTTT--GA-GTTT
1 TCAAATGAGAATCTTTAAGATGTTT
* *
556273 T-AAATAAAAAT-TTTAA-ATGCATTT
1 TCAAATGAGAATCTTTAAGATG--TTT
* *
556297 TCAAATGAGAAGCTTT--GA-GTCT
1 TCAAATGAGAATCTTTAAGATGTTT
* * *
556319 T-AAATGAGAATGTTTAAAATGCTT
1 TCAAATGAGAATCTTTAAGATGTTT
*
556343 TCAAATGAGAATTTTTAAGATGTTT
1 TCAAATGAGAATCTTTAAGATGTTT
* * *
556368 TCAAATAAGAAT-TTT-TGA-GTCT
1 TCAAATGAGAATCTTTAAGATGTTT
* *
556390 T-AAATGAAAATCTTTAAGACGTTT
1 TCAAATGAGAATCTTTAAGATGTTT
* * * *
556414 TCAAATGAAAAGCTTT--TA-GTCT
1 TCAAATGAGAATCTTTAAGATGTTT
*
556436 T-AAATGAGAATCTTTAAGATATTT
1 TCAAATGAGAATCTTTAAGATGTTT
* * ** **
556460 TCAAATGAGAATCATTAAAAAATCC
1 TCAAATGAGAATCTTTAAGATGTTT
* ** **
556485 TCAAATGAGAATCTTTAAAAAATCC
1 TCAAATGAGAATCTTTAAGATGTTT
*
556510 TCAAATGAGAATCTTTGAGATGT
1 TCAAATGAGAATCTTTAAGATGT
556533 AAAAATTTGT
Statistics
Matches: 223, Mismatches: 39, Indels: 40
0.74 0.13 0.13
Matches are distributed among these distances:
20 3 0.01
21 41 0.18
22 20 0.09
23 9 0.04
24 18 0.08
25 129 0.58
26 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (25 bp):
TCAAATGAGAATCTTTAAGATGTTT
Found at i:556365 original size:117 final size:117
Alignment explanation
Indices: 556226--556477 Score: 355
Period size: 117 Copynumber: 2.2 Consensus size: 117
556216 AAGCTGAGTC
* *
556226 TCAAATGAGAATCTTTAAGATGTTTTCAAATGAGAATCTTTGAGTTTTAAATAAAAAT-TTTAA-
1 TCAAATGAGAATCTTTAAGATGTTTTCAAATAAGAATCTTTGAGTCTTAAATAAAAATCTTTAAG
* * *
556289 ATGCATTTTCAAATGAGAAGCTTTGAGTCTTAAATGAGAATGTTTAAAATGCTT
66 A--CATTTTCAAATGAAAAGCTTTGAGTCTTAAATGAGAATCTTTAAAATACTT
* * *
556343 TCAAATGAGAATTTTTAAGATGTTTTCAAATAAGAATTTTTGAGTCTTAAATGAAAATCTTTAAG
1 TCAAATGAGAATCTTTAAGATGTTTTCAAATAAGAATCTTTGAGTCTTAAATAAAAATCTTTAAG
* * * *
556408 ACGTTTTCAAATGAAAAGCTTTTAGTCTTAAATGAGAATCTTTAAGATATTT
66 ACATTTTCAAATGAAAAGCTTTGAGTCTTAAATGAGAATCTTTAAAATACTT
*
556460 TCAAATGAGAATCATTAA
1 TCAAATGAGAATCTTTAA
556478 AAAATCCTCA
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
117 113 0.95
118 5 0.04
119 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.38
Consensus pattern (117 bp):
TCAAATGAGAATCTTTAAGATGTTTTCAAATAAGAATCTTTGAGTCTTAAATAAAAATCTTTAAG
ACATTTTCAAATGAAAAGCTTTGAGTCTTAAATGAGAATCTTTAAAATACTT
Found at i:556395 original size:46 final size:45
Alignment explanation
Indices: 556345--556471 Score: 166
Period size: 46 Copynumber: 2.8 Consensus size: 45
556335 AAATGCTTTC
*
556345 AAATGAGAATTTTTAAGATGTTTTCAAATAAGAATTTTTGAGTCTT
1 AAATGAGAATCTTTAAGATGTTTTCAAATAAGAATTTTT-AGTCTT
* * *
556391 AAATGAAAATCTTTAAGACGTTTTCAAATGAA-AAGCTTTTAGTCTT
1 AAATGAGAATCTTTAAGATGTTTTCAAAT-AAGAA-TTTTTAGTCTT
* *
556437 AAATGAGAATCTTTAAGATATTTTCAAATGAGAAT
1 AAATGAGAATCTTTAAGATGTTTTCAAATAAGAAT
556472 CATTAAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
45 1 0.01
46 62 0.90
47 6 0.09
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (45 bp):
AAATGAGAATCTTTAAGATGTTTTCAAATAAGAATTTTTAGTCTT
Found at i:561040 original size:17 final size:18
Alignment explanation
Indices: 561015--561049 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
561005 GTGGAATTTT
561015 TATAC-AAAAAATAAAAA
1 TATACAAAAAAATAAAAA
*
561032 TATATAAAAAAATAAAAA
1 TATACAAAAAAATAAAAA
561050 ATGTTGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (18 bp):
TATACAAAAAAATAAAAA
Found at i:573572 original size:20 final size:20
Alignment explanation
Indices: 573547--573585 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
573537 AATCGATGTG
* *
573547 ATGTATAGGCCTTTTATTTA
1 ATGTATAAGCCTTTCATTTA
573567 ATGTATAAGCCTTTCATTT
1 ATGTATAAGCCTTTCATTT
573586 TCTATTTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (20 bp):
ATGTATAAGCCTTTCATTTA
Found at i:576823 original size:21 final size:20
Alignment explanation
Indices: 576797--576886 Score: 56
Period size: 21 Copynumber: 4.3 Consensus size: 20
576787 ATAAACATTA
576797 TATCAAAGTTTATCAAAATTC
1 TATCAAAG-TTATCAAAATTC
* * * *
576818 TATCAAGGGTTCTCAAAACTA
1 TATCAA-AGTTATCAAAATTC
* * *
576839 TACTCAATGTTACCAAAATGC
1 TA-TCAAAGTTATCAAAATTC
*
576860 TATCAAAGATTA-CTAAAATTG
1 TATCAAAG-TTATC-AAAATTC
576881 TATCAA
1 TATCAA
576887 TGATTACTAA
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
20 6 0.12
21 41 0.79
22 5 0.10
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (20 bp):
TATCAAAGTTATCAAAATTC
Found at i:576891 original size:21 final size:21
Alignment explanation
Indices: 576842--576898 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
576832 AAAACTATAC
*
576842 TCAATG-TTACCAAAATGCTA
1 TCAATGATTACTAAAATGCTA
*
576862 TCAAAGATTACTAAAATTG-TA
1 TCAATGATTACTAAAA-TGCTA
576883 TCAATGATTACTAAAA
1 TCAATGATTACTAAAA
576899 ATATATCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.16
21 25 0.78
22 2 0.06
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.32
Consensus pattern (21 bp):
TCAATGATTACTAAAATGCTA
Found at i:576905 original size:21 final size:21
Alignment explanation
Indices: 576860--576906 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
576850 ACCAAAATGC
* *
576860 TATCAAAGATTACTAAAATTG
1 TATCAAAGATTACTAAAAATA
*
576881 TATCAATGATTACTAAAAATA
1 TATCAAAGATTACTAAAAATA
576902 TATCA
1 TATCA
576907 TCAACTACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (21 bp):
TATCAAAGATTACTAAAAATA
Found at i:577178 original size:20 final size:20
Alignment explanation
Indices: 577103--577768 Score: 151
Period size: 21 Copynumber: 31.8 Consensus size: 20
577093 AAAATGTATA
* *
577103 AAAGATTACCATAATTGTATC
1 AAAG-TTACCAAAATTATATC
* * *
577124 TAAGATTACCAAAATTGTATTA
1 AAAG-TTACCAAAATTATA-TC
577146 AAAGTTACCAAAATTATATC
1 AAAGTTACCAAAATTATATC
* * *
577166 AAACTTACTAAAATTTTATC
1 AAAGTTACCAAAATTATATC
*
577186 AAATGTTACCAAAATTATATA
1 AAA-GTTACCAAAATTATATC
*
577207 AATAGTTACTAAAATTATATC
1 AA-AGTTACCAAAATTATATC
* * *
577228 ATAA-TTATCAAAATAGAAAT-
1 A-AAGTTACCAAAAT-TATATC
* * * *
577248 AAAGGTCATCAAAATTGTATT
1 AAA-GTTACCAAAATTATATC
* * *
577269 AAAGGTTACTAAAATTTTATG
1 AAA-GTTACCAAAATTATATC
* ** *
577290 AATTGTTACCAAAATGCTATT
1 AA-AGTTACCAAAATTATATC
* *
577311 AAAGATTACCAAAAATATATA
1 AAAG-TTACCAAAATTATATC
* ** *
577332 ATAAGTTATCAAAATTGCATA
1 A-AAGTTACCAAAATTATATC
*
577353 AAAGGTTACCAAAATTACATC
1 AAA-GTTACCAAAATTATATC
* ** ** *
577374 AGTAAATTGTCAATGTTTTATC
1 A--AAGTTACCAAAATTATATC
* *
577396 AAATGTTACCAAAA-CATATT
1 AAA-GTTACCAAAATTATATC
* *
577416 AATAGTTAACAAAATTACATC
1 AA-AGTTACCAAAATTATATC
* * * *
577437 -ATGTTACCAAACTAATACC
1 AAAGTTACCAAAATTATATC
* * * *
577456 TAATGTTACCAATATTTTATTG
1 -AAAGTTACCAAAATTATA-TC
**
577478 ATGGTTA-CAAAATTATATC
1 AAAGTTACCAAAATTATATC
* * * *
577497 GAAGTTAATCAAATTTATAAC
1 AAAGTT-ACCAAAATTATATC
* * * *
577518 AAAAATGAGCAAAA-TATATGG
1 -AAAGTTACCAAAATTATAT-C
* * *
577539 AAACTTACTAGAATCAAAATTGTATAA
1 AAAGTTAC------CAAAATTATAT-C
* *
577566 AAAATTATCAAAATTATATC
1 AAAGTTACCAAAATTATATC
* * *
577586 AAAACTTATCAAAATTGTATC
1 -AAAGTTACCAAAATTATATC
* * * *
577607 TAAGGCTACCAAAATTGTATTA
1 -AAAGTTACCAAAATTATA-TC
*
577629 AAAGTTATCAAAATTATATC
1 AAAGTTACCAAAATTATATC
* * *
577649 AAACTTACTAAAAGTT-TATT
1 AAAGTTACCAAAA-TTATATC
* *
577669 AAATGTTGCCAAAATTATATA
1 AAA-GTTACCAAAATTATATC
* *
577690 AATAGTTACCCAAATTATGTC
1 AA-AGTTACCAAAATTATATC
* * * *
577711 ATAACTTATCAAAA-TAGAAAC
1 A-AAGTTACCAAAATTA-TATC
* *
577732 AAAGGTTATCAAAATTATATT
1 AAA-GTTACCAAAATTATATC
*
577753 AAAGGTTACTAAAATT
1 AAA-GTTACCAAAATT
577769 TTACAAATTG
Statistics
Matches: 464, Mismatches: 140, Indels: 82
0.68 0.20 0.12
Matches are distributed among these distances:
19 18 0.04
20 93 0.20
21 308 0.66
22 28 0.06
23 2 0.00
26 5 0.01
27 10 0.02
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAGTTACCAAAATTATATC
Found at i:577194 original size:41 final size:42
Alignment explanation
Indices: 577129--577241 Score: 131
Period size: 41 Copynumber: 2.7 Consensus size: 42
577119 GTATCTAAGA
* * * *
577129 TTACCAAAATTGTATTAAAAGTTACCAAAATTATATCAA-AC
1 TTACTAAAATTATATCAAAAGTTACCAAAATTATATAAATAC
* * *
577170 TTACTAAAATTTTATCAAATGTTACCAAAATTATATAAATAG
1 TTACTAAAATTATATCAAAAGTTACCAAAATTATATAAATAC
* *
577212 TTACTAAAATTATATCATAA-TTATCAAAAT
1 TTACTAAAATTATATCAAAAGTTACCAAAAT
577242 AGAAATAAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 43 0.70
42 18 0.30
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (42 bp):
TTACTAAAATTATATCAAAAGTTACCAAAATTATATAAATAC
Found at i:577303 original size:42 final size:42
Alignment explanation
Indices: 577092--577369 Score: 180
Period size: 42 Copynumber: 6.7 Consensus size: 42
577082 CAAAAATTAT
* * * * *
577092 CAAAA-TGTATAAAAGATTACCATAATTGTAT-CTAAGATTAC
1 CAAAATTGTATTAAAGGTTACCAAAATTATATAATAAG-TTAC
* * *
577133 CAAAATTGTATTAAAAGTTACCAAAATTATATCA-AACTTAC
1 CAAAATTGTATTAAAGGTTACCAAAATTATATAATAAGTTAC
* * * *
577174 TAAAATTTTATCAAATGTTACCAAAATTATATAA-ATAGTTAC
1 CAAAATTGTATTAAAGGTTACCAAAATTATATAATA-AGTTAC
* * * * * * *
577216 TAAAATTATATCATAA--TTATCAAAA-TAGA-AATAAAGGTCAT
1 CAAAATTGTATTA-AAGGTTACCAAAATTATATAAT-AA-GTTAC
* * *
577257 CAAAATTGTATTAAAGGTTACTAAAATTTTATGAAT-TGTTAC
1 CAAAATTGTATTAAAGGTTACCAAAATTATAT-AATAAGTTAC
* * *
577299 CAAAA-TGCTATTAAAGATTACCAAAAATATATAATAAGTTAT
1 CAAAATTG-TATTAAAGGTTACCAAAATTATATAATAAGTTAC
* *
577341 CAAAATTGCATAAAAGGTTACCAAAATTA
1 CAAAATTGTATTAAAGGTTACCAAAATTA
577370 CATCAGTAAA
Statistics
Matches: 184, Mismatches: 38, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
39 2 0.01
40 6 0.03
41 66 0.36
42 101 0.55
43 6 0.03
45 3 0.02
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (42 bp):
CAAAATTGTATTAAAGGTTACCAAAATTATATAATAAGTTAC
Found at i:577578 original size:10 final size:11
Alignment explanation
Indices: 577551--577651 Score: 57
Period size: 11 Copynumber: 9.5 Consensus size: 11
577541 ACTTACTAGA
*
577551 ATCAAAATTGT
1 ATCAAAATTAT
* *
577562 ATAAAAAAT-T
1 ATCAAAATTAT
577572 ATCAAAATTAT
1 ATCAAAATTAT
*
577583 ATCAAAACT-T
1 ATCAAAATTAT
*
577593 ATCAAAATTGT
1 ATCAAAATTAT
* ***
577604 ATC-TAAGGCT
1 ATCAAAATTAT
* *
577614 ACCAAAATTGT
1 ATCAAAATTAT
* *
577625 ATTAAAAGT-T
1 ATCAAAATTAT
577635 ATCAAAATTAT
1 ATCAAAATTAT
577646 ATCAAA
1 ATCAAA
577652 CTTACTAAAA
Statistics
Matches: 66, Mismatches: 20, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
10 30 0.45
11 36 0.55
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (11 bp):
ATCAAAATTAT
Found at i:577643 original size:63 final size:62
Alignment explanation
Indices: 577553--577725 Score: 183
Period size: 62 Copynumber: 2.8 Consensus size: 62
577543 TTACTAGAAT
* *
577553 CAAAATTGTATAAAAAATTATCAAAATTATATCAAAACTTATCAAAATTGTATCT-AAGGCTAC
1 CAAAATTGTATTAAAAGTTATCAAAATTATATCAAAACTTATCAAAATT-TAT-TAAAGGCTAC
* * *
577616 CAAAATTGTATTAAAAGTTATCAAAATTATATC-AAACTTA-CTAAAAGTTTATTAAATGTTGC
1 CAAAATTGTATTAAAAGTTATCAAAATTATATCAAAACTTATC-AAAA-TTTATTAAAGGCTAC
* * * * *
577678 CAAAATTATA-TAAATAGTTACCCAAATTATGTCATAACTTATCAAAAT
1 CAAAATTGTATTAAA-AGTTATCAAAATTATATCAAAACTTATCAAAAT
577726 AGAAACAAAG
Statistics
Matches: 94, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
61 6 0.06
62 44 0.47
63 43 0.46
64 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (62 bp):
CAAAATTGTATTAAAAGTTATCAAAATTATATCAAAACTTATCAAAATTTATTAAAGGCTAC
Found at i:578011 original size:128 final size:127
Alignment explanation
Indices: 577744--578044 Score: 313
Period size: 128 Copynumber: 2.3 Consensus size: 127
577734 AGGTTATCAA
* *
577744 AATTATATTAAAGGTTACTAAAATTTTACAAATTGTTATAAAACTTCTAATAAAGTTTATTACAA
1 AATTATATTAAAGGTTAC-AAAATTTTACAAATTGTTATAAAACTTCTAATAAAGATCATTACAA
* * * * *
577809 TATATCAAAATTTATCAAAATCAAAATTATATAAATGGTTATCAAGTTGCATCAAAAGTTACC
65 TATATCAAAAGTTATCAAAATCAAAATTATATAAAAGGTTATCAAGTTACATCAAAACTTAAC
* * * ** * * *
577872 AAATAGGATTAAATGTTAGC-AAATTTTATTAATTGTTATTAAATTTCTAATAAAGATCA-TCCT
1 AATTA-TATTAAAGGTTA-CAAAATTTTACAAATTGTTATAAAACTTCTAATAAAGATCATTAC-
*
577935 AATATAT-AAAAGGTTATCAAAATCAAAATTATATAAAAGGTTATCAA-TTATATCAAAACTTAG
63 AATATATCAAAA-GTTATCAAAATCAAAATTATATAAAAGGTTATCAAGTTACATCAAAACTTA-
577998 TAC
126 -AC
* * * *
578001 AATTATATTAAAGATTACCAAAATTCTACTAATGGTTATCAAAA
1 AATTATATTAAAGGTTA-CAAAATTTTACAAATTGTTAT-AAAA
578045 TTATATAATA
Statistics
Matches: 140, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
127 18 0.13
128 87 0.62
129 31 0.22
130 4 0.03
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.36
Consensus pattern (127 bp):
AATTATATTAAAGGTTACAAAATTTTACAAATTGTTATAAAACTTCTAATAAAGATCATTACAAT
ATATCAAAAGTTATCAAAATCAAAATTATATAAAAGGTTATCAAGTTACATCAAAACTTAAC
Found at i:578025 original size:21 final size:21
Alignment explanation
Indices: 578001--578204 Score: 87
Period size: 21 Copynumber: 9.8 Consensus size: 21
577991 AACTTAGTAC
578001 AATTATATTAAAGATTACCAA
1 AATTATATTAAAGATTACCAA
* * * * *
578022 AATTCTACTAATGGTTATCAA
1 AATTATATTAAAGATTACCAA
* *
578043 AATTATATAATAAG-CTACCAA
1 AATTATATTA-AAGATTACCAA
*
578064 AATTATATTAAA-ACCTACC-A
1 AATTATATTAAAGA-TTACCAA
* * *
578084 AATTATATCAAA-CTTACTAA
1 AATTATATTAAAGATTACCAA
* * *
578104 AATTTTATTAAAAATTATCAA
1 AATTATATTAAAGATTACCAA
* * ** * *
578125 AATTGTCTTAATCAGTACCTA
1 AATTATATTAAAGATTACCAA
* * *
578146 AGTCATATAATAAG-TTACCAA
1 AATTATATTA-AAGATTACCAA
* * *
578167 AA-TAGAATTAAAGGTTACGAA
1 AATTA-TATTAAAGATTACCAA
*
578188 AATTGTATTAAAGATTA
1 AATTATATTAAAGATTA
578205 TTAAAATTTT
Statistics
Matches: 129, Mismatches: 45, Indels: 18
0.67 0.23 0.09
Matches are distributed among these distances:
19 3 0.02
20 29 0.22
21 93 0.72
22 4 0.03
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.34
Consensus pattern (21 bp):
AATTATATTAAAGATTACCAA
Found at i:582156 original size:21 final size:21
Alignment explanation
Indices: 582132--582199 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
582122 ACCAAACTGC
582132 TATCAA-ATATTACCAAAATTA
1 TATCAATA-ATTACCAAAATTA
*
582153 TATCAATAATTACCAAAAATA
1 TATCAATAATTACCAAAATTA
*
582174 TATC-ATCAGTTACCAAAATTA
1 TATCAAT-AATTACCAAAATTA
582195 CTATC
1 -TATC
582200 TATAGGTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.05
21 34 0.83
22 5 0.12
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (21 bp):
TATCAATAATTACCAAAATTA
Found at i:582430 original size:20 final size:20
Alignment explanation
Indices: 582355--582626 Score: 111
Period size: 21 Copynumber: 13.1 Consensus size: 20
582345 AAAATGTATA
*
582355 AAAGATTACCAAAATTGTATC
1 AAAG-TTACCAAAATTATATC
* *
582376 TAAGATTACCAAAATTGCAT-TA
1 AAAG-TTACCAAAATT--ATATC
582398 AAAGTTACCAAAATTATATC
1 AAAGTTACCAAAATTATATC
* * *
582418 AAACTTACTAAAATTTTATC
1 AAAGTTACCAAAATTATATC
* * *
582438 AAATGTTACCAAAAGTATTTA
1 AAA-GTTACCAAAATTATATC
*
582459 AATAGTTACTAAAATTATATC
1 AA-AGTTACCAAAATTATATC
* * *
582480 ATAA-TTATCAAAATAGAAAT-
1 A-AAGTTACCAAAAT-TATATC
* * * *
582500 AAAGGTCATCAAAATTGTATT
1 AAA-GTTACCAAAATTATATC
* * *
582521 AAAGGTTACTAAAATTTTATG
1 AAA-GTTACCAAAATTATATC
* ** *
582542 AATTGTTACCAAAATGCTATT
1 AA-AGTTACCAAAATTATATC
* *
582563 AAAGATTACTAAAAGTATA-C
1 AAAG-TTACCAAAATTATATC
* * *
582583 AATAAGTTATCAAAATTGTATA
1 -A-AAGTTACCAAAATTATATC
*
582605 AAAGGTTACCAAAATTACATC
1 AAA-GTTACCAAAATTATATC
582626 A
1 A
582627 GTAGATTGTC
Statistics
Matches: 184, Mismatches: 51, Indels: 32
0.69 0.19 0.12
Matches are distributed among these distances:
19 4 0.02
20 35 0.19
21 135 0.73
22 9 0.05
23 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAGTTACCAAAATTATATC
Found at i:582431 original size:62 final size:62
Alignment explanation
Indices: 582360--582493 Score: 150
Period size: 62 Copynumber: 2.2 Consensus size: 62
582350 GTATAAAAGA
*
582360 TTACCAAAATTGTATCTAA-GATTACCAAAATTGCA-TTAAA-AGTTACCAAAATTATATCAAAC
1 TTACCAAAATTGTATCAAATG-TTACCAAAA--GCATTTAAATAGTTACCAAAATTATATCAAAC
* * * *
582422 TTACTAAAATTTTATCAAATGTTACCAAAAGTATTTAAATAGTTACTAAAATTATATCATAA-
1 TTACCAAAATTGTATCAAATGTTACCAAAAGCATTTAAATAGTTACCAAAATTATATCA-AAC
*
582484 TTATCAAAAT
1 TTACCAAAAT
582494 AGAAATAAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
60 2 0.03
61 5 0.08
62 51 0.84
63 3 0.05
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (62 bp):
TTACCAAAATTGTATCAAATGTTACCAAAAGCATTTAAATAGTTACCAAAATTATATCAAAC
Found at i:582606 original size:104 final size:105
Alignment explanation
Indices: 582396--582620 Score: 257
Period size: 104 Copynumber: 2.2 Consensus size: 105
582386 AAAATTGCAT
* * * *
582396 TAAAA-GTTACCAAAATTATATCAAA-CTTACTAAAATTTTATCAAATGTTACCAAAAGTATTTA
1 TAAAAGGTCACCAAAATTGTATTAAAGGTTACTAAAATTTTATCAAATGTTACCAAAAGTATTTA
* *
582459 AATAGTTACTAAAATTATATCATAATTATCAAAATAGAAA
66 AAGAGTTACTAAAAGTATATCATAATTATCAAAATAGAAA
* * *
582499 T-AAAGGTCATCAAAATTGTATTAAAGGTTACTAAAATTTTATGAATTGTTACCAAAATGCTA-T
1 TAAAAGGTCACCAAAATTGTATTAAAGGTTACTAAAATTTTATCAAATGTTACCAAAA-G-TATT
* *
582562 TAAAGA-TTACTAAAAGTATA-CAATAAGTTATCAAAATTG-TA
64 TAAAGAGTTACTAAAAGTATATC-ATAA-TTATCAAAATAGAAA
*
582603 TAAAAGGTTACCAAAATT
1 TAAAAGGTCACCAAAATT
582621 ACATCAGTAG
Statistics
Matches: 102, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
102 3 0.03
103 18 0.18
104 47 0.46
105 32 0.31
106 2 0.02
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (105 bp):
TAAAAGGTCACCAAAATTGTATTAAAGGTTACTAAAATTTTATCAAATGTTACCAAAAGTATTTA
AAGAGTTACTAAAAGTATATCATAATTATCAAAATAGAAA
Found at i:582829 original size:22 final size:21
Alignment explanation
Indices: 582803--582858 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
582793 GCTTTCCAAA
*
582803 ATCAAAATTGTATAAAAAAATT
1 ATCAAAATTGTAT-AAAAAATC
* * *
582825 ATCAAAATTTTATCAAAACTC
1 ATCAAAATTGTATAAAAAATC
582846 ATCAAAATTGTAT
1 ATCAAAATTGTAT
582859 CTAACATTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.34
Consensus pattern (21 bp):
ATCAAAATTGTATAAAAAATC
Found at i:582914 original size:20 final size:20
Alignment explanation
Indices: 582827--582916 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 20
582817 AAAAAATTAT
* * *
582827 CAAAATTTTATCAAAACTCAT
1 CAAAATTGTATC-AAACTTAC
*
582848 CAAAATTGTATCTAACATTAC
1 CAAAATTGTATCAAAC-TTAC
* *
582869 CAAAATTGTATTACAAGTTAC
1 CAAAATTGTATCA-AACTTAC
*
582890 CAAAATTATATCAAACTTAC
1 CAAAATTGTATCAAACTTAC
*
582910 TAAAATT
1 CAAAATT
582917 TTATTAAATG
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
20 15 0.27
21 39 0.70
22 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (20 bp):
CAAAATTGTATCAAACTTAC
Found at i:582922 original size:41 final size:42
Alignment explanation
Indices: 582848--582958 Score: 120
Period size: 41 Copynumber: 2.7 Consensus size: 42
582838 CAAAACTCAT
* *
582848 CAAAATTGTATCTAACATTACCAAAATTGTATTACAA-GTTAC
1 CAAAATTATATCAAACATTACCAAAATTGTATTA-AATGTTAC
* * *
582890 CAAAATTATATCAAAC-TTACTAAAATTTTATTAAATGTTGC
1 CAAAATTATATCAAACATTACCAAAATTGTATTAAATGTTAC
* *
582931 CAAAATTATAT-AAATAGTTACCTAAATT
1 CAAAATTATATCAAACA-TTACCAAAATT
582959 ATGTCACAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 5 0.09
41 30 0.52
42 23 0.40
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (42 bp):
CAAAATTATATCAAACATTACCAAAATTGTATTAAATGTTAC
Found at i:582936 original size:21 final size:20
Alignment explanation
Indices: 582865--583014 Score: 95
Period size: 21 Copynumber: 7.2 Consensus size: 20
582855 GTATCTAACA
*
582865 TTACCAAAATTGTATTACAAG
1 TTACCAAAATTATATTA-AAG
* *
582886 TTACCAAAATTATATCAAAC
1 TTACCAAAATTATATTAAAG
* *
582906 TTACTAAAATTTTATTAAATG
1 TTACCAAAATTATATTAAA-G
* *
582927 TTGCCAAAATTATATAAATAG
1 TTACCAAAATTATATTAA-AG
* * *
582948 TTACCTAAATTATGTCACAAG
1 TTACCAAAATTATATTA-AAG
* * *
582969 TTATCAAAA-TAGAAGTAAAGG
1 TTACCAAAATTA-TATTAAA-G
* *
582990 TTATCAAATTTATATTAAAGG
1 TTACCAAAATTATATTAAA-G
583011 TTAC
1 TTAC
583015 TAATATTTTA
Statistics
Matches: 98, Mismatches: 25, Indels: 12
0.73 0.19 0.09
Matches are distributed among these distances:
20 22 0.22
21 72 0.73
22 4 0.04
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (20 bp):
TTACCAAAATTATATTAAAG
Found at i:583129 original size:21 final size:21
Alignment explanation
Indices: 583094--583134 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
583084 GAAATTAAAT
*
583094 AAATGGTTATCAAATTGTATC
1 AAATGGTTATCAAATAGTATC
583115 AAAT-GTTATCAAAATAGTAT
1 AAATGGTTATC-AAATAGTAT
583135 TAAACGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATGGTTATCAAATAGTATC
Found at i:583259 original size:21 final size:21
Alignment explanation
Indices: 583233--583379 Score: 88
Period size: 21 Copynumber: 7.1 Consensus size: 21
583223 AAAAGTTATT
*
583233 AATTATATCAAAACTTACTAA
1 AATTATATCAAAACTTACCAA
* *
583254 AATTATATTCAAGA-TTAACAA
1 AATTATA-TCAAAACTTACCAA
* * *
583275 AATTCTATTAACTA-TTACCAA
1 AATTATATCAA-AACTTACCAA
* *
583296 AATTATATGATAAGC-TACCAA
1 AATTATATCA-AAACTTACCAA
* *
583317 AATTATATTAAAACCTACC-A
1 AATTATATCAAAACTTACCAA
* **
583337 AATTATATC-AAACTAATTAA
1 AATTATATCAAAACTTACCAA
* * *
583357 AATTTTATTAAAAATTACCAA
1 AATTATATCAAAACTTACCAA
583378 AA
1 AA
583380 ATGTCTTAAT
Statistics
Matches: 95, Mismatches: 24, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
19 5 0.05
20 23 0.24
21 61 0.64
22 6 0.06
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (21 bp):
AATTATATCAAAACTTACCAA
Found at i:583457 original size:21 final size:21
Alignment explanation
Indices: 583431--583475 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
583421 ATAGGTTACG
*
583431 AAAATTGTATGAAA-GATTATC
1 AAAATTGTATCAAATG-TTATC
*
583452 AAAATTTTATCAAATGTTATC
1 AAAATTGTATCAAATGTTATC
583473 AAA
1 AAA
583476 CTTCTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36
Consensus pattern (21 bp):
AAAATTGTATCAAATGTTATC
Found at i:587323 original size:21 final size:21
Alignment explanation
Indices: 587299--587415 Score: 74
Period size: 21 Copynumber: 5.6 Consensus size: 21
587289 CATCAAAATA
*
587299 AAAACTATATCAAAGTTTATC
1 AAAACTATATCAAAGATTATC
* * * * *
587320 AAAATTGTATCAAGGGTTCTC
1 AAAACTATATCAAAGATTATC
* * * *
587341 AAAACTATAACCAATATTACC
1 AAAACTATATCAAAGATTATC
*
587362 AAAA-TGCTATCAAAGATTATC
1 AAAACT-ATATCAAAGATTATC
* * * *
587383 AAAATTGTATCAATGATTACC
1 AAAACTATATCAAAGATTATC
*
587404 AAAAATATATCA
1 AAAACTATATCA
587416 TCAGTTACCA
Statistics
Matches: 70, Mismatches: 24, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
20 1 0.01
21 68 0.97
22 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (21 bp):
AAAACTATATCAAAGATTATC
Found at i:587415 original size:42 final size:41
Alignment explanation
Indices: 587352--587433 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 41
587342 AAACTATAAC
* *
587352 CAATATTACCAAAATGCTATCA-AAGATTATCAAAATTGTAT
1 CAATATTACCAAAATGATATCATAAG-TTACCAAAATTGTAT
*
587393 CAATGATTACCAAAAAT-ATATCATCAGTTACCAAAATTGTA
1 CAAT-ATTACC-AAAATGATATCATAAGTTACCAAAATTGTA
587434 CAAAAGGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 4 0.11
42 24 0.69
43 7 0.20
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.30
Consensus pattern (41 bp):
CAATATTACCAAAATGATATCATAAGTTACCAAAATTGTAT
Done.