Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold21
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: 2821038
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 98422 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:1821323 original size:2 final size:2
Alignment explanation
Indices: 1821310--1821349 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1821300 TTATCTATCA
*
1821310 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1821350 GTGCGCGCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1822586 original size:25 final size:26
Alignment explanation
Indices: 1822553--1822616 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
1822543 TATAAAAAAT
* *
1822553 AATATAAATATATTAAATTTTATATA
1 AATATAAATATATTAAATATAATATA
1822579 AATA-AAATACT-TTAAATATAATATA
1 AATATAAATA-TATTAAATATAATATA
*
1822604 AATATTAATATAT
1 AATATAAATATAT
1822617 ATGATCAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATAAATATATTAAATATAATATA
Found at i:1822614 original size:12 final size:11
Alignment explanation
Indices: 1822551--1822615 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
1822541 GATATAAAAA
1822551 ATAATATAAAT
1 ATAATATAAAT
1822562 AT-AT-TAAAT
1 ATAATATAAAT
* *
1822571 TTTATATAAAT
1 ATAATATAAAT
*
1822582 AAAATACTTTAAAT
1 ATAATA---TAAAT
1822596 ATAATATAAAT
1 ATAATATAAAT
1822607 ATTAATATA
1 A-TAATATA
1822616 TATGATCAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
9 6 0.14
10 4 0.09
11 16 0.37
12 7 0.16
14 10 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1823606 original size:28 final size:25
Alignment explanation
Indices: 1823551--1823609 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 25
1823541 TTATTTTATT
1823551 AAAAATAATTTAATTATTATTCTTA
1 AAAAATAATTTAATTATTATTCTTA
1823576 AAAATATATATTTAATATATTATT-TTGA
1 AAAA-ATA-ATTTAAT-TATTATTCTT-A
1823604 AAAAAT
1 AAAAAT
1823610 TTATAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.13
26 3 0.10
27 11 0.37
28 12 0.40
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
AAAAATAATTTAATTATTATTCTTA
Found at i:1825300 original size:20 final size:20
Alignment explanation
Indices: 1825275--1825318 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1825265 AATAATTTAG
1825275 ATTTAT-TAATTTATATATAT
1 ATTTATATAATTTATATA-AT
* *
1825295 ATTTATATATTTTATCTAAT
1 ATTTATATAATTTATATAAT
1825315 ATTT
1 ATTT
1825319 TTACATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTATATAATTTATATAAT
Found at i:1825343 original size:6 final size:6
Alignment explanation
Indices: 1825332--1825377 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
1825322 CATATTAATT
* *
1825332 ATATAA ATATAA A-ATAA ATAAAA ATTTTAA ATATAA ATA-AA ATATA
1 ATATAA ATATAA ATATAA ATATAA A-TATAA ATATAA ATATAA ATATA
1825378 TGTTAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 10 0.30
6 19 0.58
7 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:1825435 original size:19 final size:19
Alignment explanation
Indices: 1825390--1825425 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1825380 TTAAAATATG
*
1825390 TCATA-ATAATTATATTAA
1 TCATATATAAATATATTAA
1825408 TCATATATAAATATATTA
1 TCATATATAAATATATTA
1825426 TTATATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TCATATATAAATATATTAA
Found at i:1825447 original size:15 final size:15
Alignment explanation
Indices: 1825415--1825459 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1825405 TAATCATATA
1825415 TAAATATATTATTATAT
1 TAAATATA-TATT-TAT
* *
1825432 TATATTTATATTTAT
1 TAAATATATATTTAT
1825447 TAAATATATATTT
1 TAAATATATATTT
1825460 CCGTATTCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 14 0.58
16 4 0.17
17 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAAATATATATTTAT
Found at i:1825815 original size:2 final size:2
Alignment explanation
Indices: 1825808--1825833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1825798 TCCCCTCCTA
1825808 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1825834 TAATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1826570 original size:8 final size:8
Alignment explanation
Indices: 1826557--1826616 Score: 54
Period size: 8 Copynumber: 7.2 Consensus size: 8
1826547 ATATTAAAAA
1826557 TATATATT
1 TATATATT
1826565 TATATAAATT
1 TATAT--ATT
1826575 T-TAATATT
1 TAT-ATATT
1826583 TATATATT
1 TATATATT
1826591 TATATTATT
1 TATA-TATT
1826600 T-TATTATT
1 TATA-TATT
1826608 TATAT-TT
1 TATATATT
1826615 TA
1 TA
1826617 ACTGCAGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
7 4 0.09
8 27 0.59
9 9 0.20
10 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATATATT
Found at i:1826707 original size:20 final size:21
Alignment explanation
Indices: 1826679--1826720 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1826669 GAATCATGAC
* *
1826679 TTCATTTAAATT-TATTAATA
1 TTCAATTAAATTATATAAATA
1826699 TTCAATTAAATTATATAAATA
1 TTCAATTAAATTATATAAATA
1826720 T
1 T
1826721 AATGTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TTCAATTAAATTATATAAATA
Found at i:1826771 original size:27 final size:27
Alignment explanation
Indices: 1826740--1826819 Score: 81
Period size: 32 Copynumber: 2.8 Consensus size: 27
1826730 AAAATATTTA
1826740 AAATATAATAGTTATTTTAAATTTATAT
1 AAATATAATA-TTATTTTAAATTTATAT
*
1826768 AATATAAATAATTAATATATTTAAATTTATAT
1 AA-AT--ATAA-TATTAT-TTTAAATTTATAT
*
1826800 AAATATAA-ATTATTTAAAAT
1 AAATATAATATTATTTTAAAT
1826820 CTAATTATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
26 6 0.14
27 4 0.09
28 2 0.05
29 6 0.14
31 9 0.20
32 17 0.39
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
AAATATAATATTATTTTAAATTTATAT
Found at i:1829671 original size:3 final size:3
Alignment explanation
Indices: 1829663--1829695 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1829653 ATTCTGTTTT
1829663 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1829696 TGTATCAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1833098 original size:18 final size:19
Alignment explanation
Indices: 1833064--1833099 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1833054 TTTAATATTT
*
1833064 ATATTTTTATTACATTTAA
1 ATATTTTTATTAAATTTAA
1833083 ATATTTTT-TTAAATTTA
1 ATATTTTTATTAAATTTA
1833100 TATTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTTATTAAATTTAA
Found at i:1833129 original size:17 final size:17
Alignment explanation
Indices: 1833109--1833153 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
1833099 ATATTTAATT
1833109 AAAATTTTATTTTTTAA
1 AAAATTTTATTTTTTAA
1833126 AAAATTTTATTTTTTAA
1 AAAATTTTATTTTTTAA
1833143 AAAATTTTATT
1 AAAATTTTATT
1833154 AACTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAAATTTTATTTTTTAA
Found at i:1833233 original size:17 final size:18
Alignment explanation
Indices: 1833189--1833223 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1833179 TTCTTAATAT
*
1833189 AAATTAAAATTTCATTTA
1 AAATAAAAATTTCATTTA
1833207 AAATAAAAATTT-ATTTA
1 AAATAAAAATTTCATTTA
1833224 GATACAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAAAAATTTCATTTA
Found at i:1846299 original size:2 final size:2
Alignment explanation
Indices: 1846292--1846326 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1846282 GCTTCAATCC
1846292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1846327 ATGTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1846494 original size:14 final size:14
Alignment explanation
Indices: 1846475--1846505 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1846465 AAAATATATA
*
1846475 ATATATATATGTAT
1 ATATATAAATGTAT
1846489 ATATATAAATGTAT
1 ATATATAAATGTAT
1846503 ATA
1 ATA
1846506 ACAAGCCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (14 bp):
ATATATAAATGTAT
Found at i:1852847 original size:19 final size:19
Alignment explanation
Indices: 1852816--1852856 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
1852806 AATTATATTT
1852816 AAAATATTATTTAATTAATA
1 AAAATATTATTTAA-TAATA
1852836 AAAATATT-TTTAATAATA
1 AAAATATTATTTAATAATA
1852854 AAA
1 AAA
1852857 TAAATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATATTATTTAATAATA
Found at i:1852854 original size:18 final size:20
Alignment explanation
Indices: 1852802--1852856 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1852792 TATTTTGATA
*
1852802 ATTTAATTATATTTAAAATATT
1 ATTTAATTA-A-TAAAAATATT
1852824 ATTTAATTAATAAAAATATT
1 ATTTAATTAATAAAAATATT
1852844 -TTTAA-TAATAAAA
1 ATTTAATTAATAAAA
1852857 TAAATTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 8 0.25
19 5 0.16
20 9 0.28
21 1 0.03
22 9 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAATTAATAAAAATATT
Found at i:1852863 original size:19 final size:19
Alignment explanation
Indices: 1852825--1852863 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1852815 TAAAATATTA
*
1852825 TTTAATTAATAAAAATATT
1 TTTAATTAATAAAAAAATT
1852844 TTTAA-TAATAAAATAAATT
1 TTTAATTAATAAAA-AAATT
1852863 T
1 T
1852864 ATAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTAATTAATAAAAAAATT
Found at i:1852864 original size:17 final size:19
Alignment explanation
Indices: 1852801--1852864 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
1852791 TTATTTTGAT
*
1852801 AATTTAATTATATTTAAAATA
1 AATTTAATTA-A-TAAAAATA
*
1852822 TTATTTAATTAATAAAAATA
1 -AATTTAATTAATAAAAATA
**
1852842 TTTTTAA-TAAT-AAAATA
1 AATTTAATTAATAAAAATA
1852859 AATTTA
1 AATTTA
1852865 TAAAATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 10 0.27
18 4 0.11
19 6 0.16
20 7 0.19
21 1 0.03
22 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTAATTAATAAAAATA
Found at i:1853605 original size:16 final size:16
Alignment explanation
Indices: 1853576--1853618 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1853566 GTTTAATTAA
1853576 TATTTTTATAATTTAAAT
1 TATTTTT-T-ATTTAAAT
*
1853594 TATTTTTTATTTAACT
1 TATTTTTTATTTAAAT
*
1853610 TATTATTTA
1 TATTTTTTA
1853619 AATAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
17 1 0.04
18 7 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTTATTTAAAT
Found at i:1864958 original size:6 final size:6
Alignment explanation
Indices: 1864949--1864980 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1864939 GATTAACCTC
1864949 AACCAG AACCAG AACCAG AACCAG AACCAG AA
1 AACCAG AACCAG AACCAG AACCAG AACCAG AA
1864981 ATCTCGAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (6 bp):
AACCAG
Found at i:1868523 original size:11 final size:12
Alignment explanation
Indices: 1868481--1868531 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
1868471 TTTACGTATA
1868481 TTTAAATATAAAT
1 TTTAAATAT-AAT
* *
1868494 ATAAAATATAATTT
1 TTTAAATATAA--T
1868508 TTTAAA-ATAAT
1 TTTAAATATAAT
1868519 TTTAAATATAAT
1 TTTAAATATAAT
1868531 T
1 T
1868532 ATATTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 7 0.23
12 8 0.26
13 11 0.35
14 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTAAATATAAT
Found at i:1873411 original size:22 final size:22
Alignment explanation
Indices: 1873383--1873428 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1873373 CCCCCCTTTT
1873383 TTTTTTTTGAAGAATTGTATGA
1 TTTTTTTTGAAGAATTGTATGA
1873405 TTTTTTTTGAAGAATTGTATGA
1 TTTTTTTTGAAGAATTGTATGA
1873427 TT
1 TT
1873429 CATCTTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (22 bp):
TTTTTTTTGAAGAATTGTATGA
Found at i:1873776 original size:16 final size:16
Alignment explanation
Indices: 1873744--1873797 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1873734 TCGAAATCCG
*
1873744 AAATAATTCAAACTCA
1 AAATGATTCAAACTCA
*
1873760 AAATGA-TCATAATTCA
1 AAATGATTCA-AACTCA
1873776 AAATGATTCAAACTCA
1 AAATGATTCAAACTCA
1873792 AAATGA
1 AAATGA
1873798 CCTGGATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 3 0.09
16 27 0.82
17 3 0.09
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.26
Consensus pattern (16 bp):
AAATGATTCAAACTCA
Found at i:1874619 original size:53 final size:53
Alignment explanation
Indices: 1874518--1874638 Score: 154
Period size: 53 Copynumber: 2.3 Consensus size: 53
1874508 TTTAAACCTA
*
1874518 AATCTAAAATGACTTGAACCTGACTTAACTCGAATGTTAAATCAATTGACCCG
1 AATCTAAAATGACTTGAACCTCACTTAACTCGAATGTTAAATCAATTGACCCG
* * ** *
1874571 AATCTAGAATGACTTGAACC-CAGTTAACTCGAATGTTAAACTTGATTGATCCG
1 AATCTAAAATGACTTGAACCTCACTTAACTCGAATGTTAAA-TCAATTGACCCG
* *
1874624 AATCCAAAATTACTT
1 AATCTAAAATGACTT
1874639 AAACTTAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 18 0.31
53 40 0.69
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (53 bp):
AATCTAAAATGACTTGAACCTCACTTAACTCGAATGTTAAATCAATTGACCCG
Found at i:1876003 original size:2 final size:2
Alignment explanation
Indices: 1875985--1876026 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1875975 AATCCAGGTG
* *
1875985 TA TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1876027 GTATCATACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1888703 original size:16 final size:16
Alignment explanation
Indices: 1888684--1888730 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1888674 GTTAATTTAA
1888684 AATTTTTTTAAAAAAT
1 AATTTTTTTAAAAAAT
*
1888700 AATTTTATTT-AAATAT
1 AATTTT-TTTAAAAAAT
*
1888716 TATTTTTTTAAAAAA
1 AATTTTTTTAAAAAA
1888731 ATTAAGGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTTTTTAAAAAAT
Found at i:1893595 original size:84 final size:83
Alignment explanation
Indices: 1893445--1893605 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 83
1893435 TGAACTTATG
* * * * * *
1893445 ATTTTATCTACAAAAAGTGTTTTAAATTAAAATGATTTGAATATTAATATACTCATTCAAATTTT
1 ATTTTATCCACAAAAAATATTTTAAATTAAAATAATTTGAACATTAATATACTCATTCAAACTTT
*
1893510 AATATATAATTTTTTGTA
66 AATATACAATTTTTTGTA
* * *
1893528 ATTTTATCCACAAAAAATATTTTAAATTGAAAATAATTTGAACATTAATATATTTATTCGAACTT
1 ATTTTATCCACAAAAAATATTTTAAATT-AAAATAATTTGAACATTAATATACTCATTCAAACTT
1893593 TAATATACAATTT
65 TAATATACAATTT
1893606 ATGTGAAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
83 25 0.37
84 42 0.63
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (83 bp):
ATTTTATCCACAAAAAATATTTTAAATTAAAATAATTTGAACATTAATATACTCATTCAAACTTT
AATATACAATTTTTTGTA
Found at i:1895191 original size:2 final size:2
Alignment explanation
Indices: 1895184--1895217 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1895174 TCTTTTATGA
1895184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1895218 TGGTAATTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1895776 original size:15 final size:15
Alignment explanation
Indices: 1895747--1895779 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1895737 AATAAATATG
1895747 TATAAATATTATTAA
1 TATAAATATTATTAA
1895762 TATAATATATT-TTAA
1 TATAA-ATATTATTAA
1895777 TAT
1 TAT
1895780 TTATTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATAAATATTATTAA
Found at i:1895868 original size:91 final size:91
Alignment explanation
Indices: 1895713--1895896 Score: 323
Period size: 91 Copynumber: 2.0 Consensus size: 91
1895703 AATTATGATA
* * **
1895713 TATTTAATAATATGTAAATATTACAATAAATATGTATAAATATTATTAATATAATATATTTTAAT
1 TATTTAATAACATGTAAATATTACAAGAAATATGTATAAATACCATTAATATAATATATTTTAAT
*
1895778 ATTTATTATATTTAAATTTAAAATTT
66 ACTTATTATATTTAAATTTAAAATTT
1895804 TATTTAATAACATGTAAATATTACAAGAAATATGTATAAATACCATTAATATAATATATTTTAAT
1 TATTTAATAACATGTAAATATTACAAGAAATATGTATAAATACCATTAATATAATATATTTTAAT
1895869 ACTTATTATATTTAAATTTAAAATTT
66 ACTTATTATATTTAAATTTAAAATTT
1895895 TA
1 TA
1895897 ACGTATTTGA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TATTTAATAACATGTAAATATTACAAGAAATATGTATAAATACCATTAATATAATATATTTTAAT
ACTTATTATATTTAAATTTAAAATTT
Found at i:1897352 original size:25 final size:25
Alignment explanation
Indices: 1897298--1897365 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
1897288 ATTTCTTTTG
1897298 TTAAATTATGTAAATA-TAATAAAAT
1 TTAAATTAT-TAAATATTAATAAAAT
* ** *
1897323 ATAAATTATTAAATATTTTTAAATT
1 TTAAATTATTAAATATTAATAAAAT
1897348 TTAAA-TA-TAAATA-TAATA
1 TTAAATTATTAAATATTAATA
1897366 CGTATATTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 3 0.09
23 6 0.17
24 8 0.23
25 18 0.51
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
TTAAATTATTAAATATTAATAAAAT
Found at i:1897391 original size:20 final size:20
Alignment explanation
Indices: 1897368--1897405 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1897358 ATATAATACG
*
1897368 TATATTAATTATATTATTTT
1 TATATTAATTAAATTATTTT
*
1897388 TATATTTATTAAATTATT
1 TATATTAATTAAATTATT
1897406 ATTTTTCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTAATTAAATTATTTT
Found at i:1897732 original size:2 final size:2
Alignment explanation
Indices: 1897725--1897769 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1897715 AATCTAACCA
1897725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1897767 AT A
1 AT A
1897770 CCTAATGCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1897847 original size:8 final size:8
Alignment explanation
Indices: 1897834--1897934 Score: 51
Period size: 8 Copynumber: 11.1 Consensus size: 8
1897824 ATATAAATAT
1897834 TATATAAA
1 TATATAAA
1897842 TATATAAA
1 TATATAAA
1897850 TATATTAAAA
1 TATA-T-AAA
1897860 TTTATATAAA
1 --TATATAAA
*
1897870 TAT-TTAA
1 TATATAAA
*
1897877 TAATTTAAA
1 T-ATATAAA
1897886 TATAATTATAA
1 TAT-A-TA-AA
*
1897897 TACATAAAAA
1 T--ATATAAA
1897907 TATATAAA
1 TATATAAA
1897915 TTTAATATAAA
1 --T-ATATAAA
1897926 TATATAAA
1 TATATAAA
1897934 T
1 T
1897935 TATCATATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 28
0.69 0.05 0.26
Matches are distributed among these distances:
7 4 0.05
8 33 0.45
9 6 0.08
10 12 0.16
11 12 0.16
12 5 0.07
13 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATAAA
Found at i:1897880 original size:55 final size:56
Alignment explanation
Indices: 1897821--1897928 Score: 141
Period size: 55 Copynumber: 1.9 Consensus size: 56
1897811 ACACACAAGC
* * *
1897821 ATAATATAAATATTA-TATAA-ATATATAAATATATTAAAATTT-ATATAAATATTTA
1 ATAATATAAATATAATTATAATACATAAAAATATA-T-AAATTTAATATAAATATTTA
*
1897876 ATAATTTAAATATAATTATAATACATAAAAATATATAAATTTAATATAAATAT
1 ATAATATAAATATAATTATAATACATAAAAATATATAAATTTAATATAAATAT
1897929 ATAAATTATC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
55 19 0.41
56 16 0.35
57 11 0.24
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (56 bp):
ATAATATAAATATAATTATAATACATAAAAATATATAAATTTAATATAAATATTTA
Found at i:1897935 original size:19 final size:19
Alignment explanation
Indices: 1897822--1897935 Score: 73
Period size: 19 Copynumber: 6.0 Consensus size: 19
1897812 CACACAAGCA
*
1897822 TAATATAAATATTATATAA-A
1 TAATATAAATA-TATA-AATT
1897842 T-ATATAAATATATTAAAATT
1 TAATATAAATATA-T-AAATT
*
1897862 T-ATATAAATATTTAATAATT
1 TAATATAAATATAT-A-AATT
1897882 TAA-ATATAAT-TAT-AA--
1 TAATATA-AATATATAAATT
*
1897897 TACATAAAAATATATAAATT
1 TA-ATATAAATATATAAATT
1897917 TAATATAAATATATAAATT
1 TAATATAAATATATAAATT
1897936 ATCATATTTA
Statistics
Matches: 77, Mismatches: 5, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
15 2 0.03
16 4 0.05
17 7 0.09
18 4 0.05
19 31 0.40
20 25 0.32
21 4 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATATAAATATATAAATT
Found at i:1901612 original size:39 final size:39
Alignment explanation
Indices: 1901441--1901601 Score: 223
Period size: 39 Copynumber: 4.1 Consensus size: 39
1901431 TGTTGAGCAG
* * **
1901441 GAAGAGAAAGAGAAGAGATTGAAGGAAGCTCGTGAACGA
1 GAAGAGAACGAGAAGAAAGAGAAGGAAGCTCGTGAACGA
* *
1901480 GAAGAGAATGAGGAGAAAGAGAAGGAAGCTCGTGAACGA
1 GAAGAGAACGAGAAGAAAGAGAAGGAAGCTCGTGAACGA
*
1901519 GAAGAGAACAAGAAGAAAGAGAAGGAAGCTCGTGAACGA
1 GAAGAGAACGAGAAGAAAGAGAAGGAAGCTCGTGAACGA
* ** *
1901558 GAAGAGAACGAGAAGAAAGAGAAGGAGGCAAGTGAACTA
1 GAAGAGAACGAGAAGAAAGAGAAGGAAGCTCGTGAACGA
1901597 GAAGA
1 GAAGA
1901602 AAGTGAGAAG
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 109 1.00
ACGTcount: A:0.49, C:0.08, G:0.36, T:0.07
Consensus pattern (39 bp):
GAAGAGAACGAGAAGAAAGAGAAGGAAGCTCGTGAACGA
Found at i:1905673 original size:19 final size:18
Alignment explanation
Indices: 1905651--1905690 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1905641 TATAATATGA
1905651 ATATGAAAAAAATTAAAAT
1 ATATGAAAAAAA-TAAAAT
*
1905670 ATATTAAAAAAATAAAAT
1 ATATGAAAAAAATAAAAT
1905688 ATA
1 ATA
1905691 AACATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
ATATGAAAAAAATAAAAT
Found at i:1906297 original size:26 final size:26
Alignment explanation
Indices: 1906268--1906318 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1906258 TACGATAAAT
1906268 ATAATATATAAAATTATGAAATTTAA
1 ATAATATATAAAATTATGAAATTTAA
1906294 ATAATATATAAAATTATGAAATTTA
1 ATAATATATAAAATTATGAAATTTA
1906319 CTTGGAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
ATAATATATAAAATTATGAAATTTAA
Found at i:1912081 original size:30 final size:31
Alignment explanation
Indices: 1912040--1912105 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
1912030 CTTGAGCTTG
1912040 TAAATCATACAATATTA-GGACATGATATGA
1 TAAATCATACAATATTAGGGACATGATATGA
*
1912070 TAAATCGTACAATATTAGGGACATGATATGA
1 TAAATCATACAATATTAGGGACATGATATGA
1912101 TAAAT
1 TAAAT
1912106 TTTGAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (31 bp):
TAAATCATACAATATTAGGGACATGATATGA
Found at i:1914198 original size:15 final size:15
Alignment explanation
Indices: 1914178--1914210 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1914168 ATAGGATGGA
1914178 TTAAATTATTATAGG
1 TTAAATTATTATAGG
*
1914193 TTAAATTATTTTAGG
1 TTAAATTATTATAGG
1914208 TTA
1 TTA
1914211 TAAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
TTAAATTATTATAGG
Found at i:1914252 original size:16 final size:16
Alignment explanation
Indices: 1914218--1914351 Score: 74
Period size: 16 Copynumber: 8.3 Consensus size: 16
1914208 TTATAAAATT
*
1914218 TTTAAATTATTTTTAAA
1 TTTAAATTA-TTTTGAA
1914235 TTTAAATTATTTTGAA
1 TTTAAATTATTTTGAA
* * *
1914251 TTTGAATTATTTCGAG
1 TTTAAATTATTTTGAA
** *
1914267 TTTGGATTACTTTGAA
1 TTTAAATTATTTTGAA
** *
1914283 TTTGGATCATTTT-AGA
1 TTTAAATTATTTTGA-A
*
1914299 TTTGAATTATTTT-AA
1 TTTAAATTATTTTGAA
* * *
1914314 GTTAGAATTGTTTCGAA
1 TTTA-AATTATTTTGAA
* * *
1914331 TTTAGATCATTTTGAG
1 TTTAAATTATTTTGAA
1914347 TTTAA
1 TTTAA
1914352 GTCAATCGAG
Statistics
Matches: 91, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
15 4 0.04
16 73 0.80
17 14 0.15
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (16 bp):
TTTAAATTATTTTGAA
Found at i:1915410 original size:16 final size:16
Alignment explanation
Indices: 1915389--1915474 Score: 100
Period size: 16 Copynumber: 5.4 Consensus size: 16
1915379 ATTATTTGGG
*
1915389 TCATTTCAGATTCGGA
1 TCATTTCGGATTCGGA
*
1915405 TCATTTCGGGTTCGGA
1 TCATTTCGGATTCGGA
*
1915421 TCATTTCGGATTCAGA
1 TCATTTCGGATTCGGA
* * *
1915437 TTATTTCAGATTCAGA
1 TCATTTCGGATTCGGA
* *
1915453 TTATTTCGGGTTCGGA
1 TCATTTCGGATTCGGA
1915469 TCATTT
1 TCATTT
1915475 TGAATTTGGG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 60 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (16 bp):
TCATTTCGGATTCGGA
Found at i:1920249 original size:27 final size:28
Alignment explanation
Indices: 1920219--1920283 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
1920209 ATTCGTATTT
1920219 AATATTTATATTTAAA-AT-TAAATATAA
1 AATATTTATATTTAAATATATAAATA-AA
*
1920246 AATA-TAATTATTTAAATATATAAATAAA
1 AATATTTA-TATTTAAATATATAAATAAA
*
1920274 AAAATTTATA
1 AATATTTATA
1920284 AAATTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 2 0.06
27 12 0.39
28 9 0.29
29 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AATATTTATATTTAAATATATAAATAAA
Found at i:1920356 original size:15 final size:15
Alignment explanation
Indices: 1920336--1920366 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1920326 ACCCACTCGT
1920336 ACTTGAACAAACTAA
1 ACTTGAACAAACTAA
1920351 ACTTGAACAAACTAA
1 ACTTGAACAAACTAA
1920366 A
1 A
1920367 TGTTCAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
ACTTGAACAAACTAA
Found at i:1922963 original size:90 final size:90
Alignment explanation
Indices: 1922810--1922993 Score: 323
Period size: 90 Copynumber: 2.0 Consensus size: 90
1922800 AACTTTGATT
*
1922810 TGTCCTGCTGGTGTGGCTTACACTACATAAACCAACTAGGCAATTGCCATGTTTTTCTAAGTTCA
1 TGTCCTGCTGGTGTGGCTTACACTAAATAAACCAACTAGGCAATTGCCATGTTTTTCTAAGTTCA
*
1922875 GTGGGGGCAAATTGATTGACCAACA
66 ATGGGGGCAAATTGATTGACCAACA
* *
1922900 TGTCCTGCTGGTGTGGGTTACACTAAATAAACCAACTTGGCAATTGCCATGTTTTTCTAAGTTCA
1 TGTCCTGCTGGTGTGGCTTACACTAAATAAACCAACTAGGCAATTGCCATGTTTTTCTAAGTTCA
*
1922965 ATGGGGGCCAATTGATTGACCAACA
66 ATGGGGGCAAATTGATTGACCAACA
1922990 TGTC
1 TGTC
1922994 AATATAGGTC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (90 bp):
TGTCCTGCTGGTGTGGCTTACACTAAATAAACCAACTAGGCAATTGCCATGTTTTTCTAAGTTCA
ATGGGGGCAAATTGATTGACCAACA
Found at i:1930621 original size:30 final size:29
Alignment explanation
Indices: 1930562--1930623 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
1930552 TATTGTATCT
* *
1930562 AATAAAAAATAAATTTTTACATTATTTTA
1 AATAAAAAATAAATTTTTACATAAATTTA
* *
1930591 AATAATAATATAAATTTTTAGATAAATTTA
1 AATAA-AAAATAAATTTTTACATAAATTTA
1930621 AAT
1 AAT
1930624 CGATCTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
AATAAAAAATAAATTTTTACATAAATTTA
Found at i:1938236 original size:17 final size:17
Alignment explanation
Indices: 1938216--1938251 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1938206 AAGGAAGATG
* *
1938216 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
1938233 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
1938250 AA
1 AA
1938252 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1945028 original size:13 final size:13
Alignment explanation
Indices: 1945010--1945035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1945000 AATCCTAAAA
1945010 AAAAAAAAAAACC
1 AAAAAAAAAAACC
1945023 AAAAAAAAAAACC
1 AAAAAAAAAAACC
1945036 TTTTCACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACC
Found at i:1946130 original size:27 final size:27
Alignment explanation
Indices: 1946087--1946933 Score: 1220
Period size: 27 Copynumber: 31.0 Consensus size: 27
1946077 GTGGCATTTT
* *
1946087 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1946115 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1946142 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1946170 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1946197 CTTTTAAAATCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1946225 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1946252 CTTTTAAGTCCACAACTCTGTGG-ACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946278 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946305 CTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
*** *
1946331 C-TTTAAGTCCACAACTATATGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1946358 CTTTTAAGTCCACAAACTCCGT-GCACC
1 CTTTTAAGTCCAC-AACTCCGTGGCACC
* *
1946385 CTTTTAAGTCCACAACTCTGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1946413 CTTTTAA-TACCAACAACTCTGTGGCACC
1 CTTTTAAGT-CC-ACAACTCCGTGGCACC
*
1946441 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1946468 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946495 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946522 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946549 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1946576 C-TTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1946603 CTGTTTAAAGACCACAACTCCGTGGCACC
1 CT-TTT-AAGTCCACAACTCCGTGGCACC
* * **
1946632 CTTTTAAGTCCATAACTTCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946659 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1946686 TTTTTAAGTCCACAACGCCGTGGAACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946713 CTCTTTAAGTCCACAACTCCGTGGCACC
1 CT-TTTAAGTCCACAACTCCGTGGCACC
1946741 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946768 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946795 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1946823 CGTTTAAGTCCACAACTCCGTGGCAATCC
1 CTTTTAAGTCCACAACTCCGTGGC-A-CC
*
1946852 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1946879 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1946906 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1946933 C
1 C
1946934 ATTTCAAAGC
Statistics
Matches: 749, Mismatches: 51, Indels: 39
0.89 0.06 0.05
Matches are distributed among these distances:
25 20 0.03
26 56 0.07
27 460 0.61
28 142 0.19
29 53 0.07
30 18 0.02
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1946971 original size:32 final size:32
Alignment explanation
Indices: 1946916--1947356 Score: 701
Period size: 32 Copynumber: 13.8 Consensus size: 32
1946906 CTTTTAAATC
* *
1946916 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1946947 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1946979 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1947011 CACAAGTCGGTGGCAACCCA-TTCCAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1947042 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1947074 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1947106 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1947138 CACAAGTCGGTGGCAACCCATTTCAAAG-CCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1947169 CACAAGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
1947201 CCACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 -CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
1947234 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
1947266 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1947298 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
1947330 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
1947357 TCACCATTTT
Statistics
Matches: 383, Mismatches: 21, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
30 3 0.01
31 69 0.18
32 281 0.73
33 27 0.07
34 3 0.01
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.17
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:1948615 original size:17 final size:17
Alignment explanation
Indices: 1948595--1948630 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1948585 AAGGAAGATG
* *
1948595 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
1948612 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
1948629 AA
1 AA
1948631 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1955358 original size:2 final size:2
Alignment explanation
Indices: 1955351--1955387 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1955341 TTCTCCATAC
1955351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1955388 ATTCTTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1956456 original size:19 final size:19
Alignment explanation
Indices: 1956420--1956467 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1956410 AAAATTAAAA
1956420 AAATT-ATTTTTTGATATT
1 AAATTAATTTTTTGATATT
**
1956438 ATTTTAATTTTTT-ATTATT
1 AAATTAATTTTTTGA-TATT
1956457 AAATTAATTTT
1 AAATTAATTTT
1956468 AAATTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
AAATTAATTTTTTGATATT
Found at i:1956467 original size:25 final size:24
Alignment explanation
Indices: 1956438--1956520 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 24
1956428 TTTTGATATT
1956438 ATTTTAATTTTTTATTATTAAATTA
1 ATTTTAATTTTTTATTATT-AATTA
* *
1956463 ATTTTAAATTTTTTAATA-TAATTC
1 ATTTT-AATTTTTTATTATTAATTA
* *
1956487 ATTTAAATTTTTATATTTTTAATTA
1 ATTTTAATTTTT-TATTATTAATTA
*
1956512 A-ATTAATTT
1 ATTTTAATTT
1956521 AATAAATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
23 7 0.15
24 17 0.36
25 12 0.26
26 11 0.23
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTTAATTTTTTATTATTAATTA
Found at i:1956474 original size:24 final size:24
Alignment explanation
Indices: 1956438--1956498 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
1956428 TTTTGATATT
*
1956438 ATTTT-AATTTTTTATTATTAAATTA
1 ATTTTAAATTTTTTAATA-T-AATTA
*
1956463 ATTTTAAATTTTTTAATATAATTC
1 ATTTTAAATTTTTTAATATAATTA
1956487 A-TTTAAATTTTT
1 ATTTTAAATTTTT
1956499 ATATTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 11 0.33
24 5 0.15
25 6 0.18
26 11 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTAAATTTTTTAATATAATTA
Found at i:1956495 original size:23 final size:25
Alignment explanation
Indices: 1956438--1956498 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 25
1956428 TTTTGATATT
* *
1956438 ATTTTAATTTTTTATTATTAAATTA
1 ATTTAAATTTTTTAATATTAAATTA
*
1956463 ATTTTAAATTTTTTAATA-T-AATTC
1 A-TTTAAATTTTTTAATATTAAATTA
1956487 ATTTAAATTTTT
1 ATTTAAATTTTT
1956499 ATATTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 11 0.34
24 5 0.16
25 2 0.06
26 14 0.44
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTAAATTTTTTAATATTAAATTA
Found at i:1956496 original size:30 final size:30
Alignment explanation
Indices: 1956438--1956522 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 30
1956428 TTTTGATATT
*
1956438 ATTTTAAT-TTTTT-ATT--ATTAAATT-A
1 ATTTTAATATTTTTAATTAAATTAATTTAA
*
1956463 ATTTTAA-ATTTTTTAA-TATAATTCATTTAA
1 ATTTTAATA-TTTTTAATTA-AATTAATTTAA
*
1956493 ATTTTTATATTTTTAATTAAATTAATTTAA
1 ATTTTAATATTTTTAATTAAATTAATTTAA
1956523 TAAATAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
25 7 0.15
26 6 0.13
27 1 0.02
29 6 0.13
30 24 0.51
31 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
ATTTTAATATTTTTAATTAAATTAATTTAA
Found at i:1961060 original size:14 final size:13
Alignment explanation
Indices: 1961037--1961075 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1961027 GAGAATAAAA
1961037 AAATTATAAATTTT
1 AAATTATAAA-TTT
*
1961051 AAATTTTAAATTT
1 AAATTATAAATTT
1961064 AAATTATCAAAT
1 AAATTAT-AAAT
1961076 ATCTTGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATAAATTT
Found at i:1970975 original size:20 final size:18
Alignment explanation
Indices: 1970947--1970996 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
1970937 ATATGATTAG
*
1970947 TTTAGATTTATTAATTTT
1 TTTAAATTTATTAATTTT
*
1970965 AATTTAAATTTA-AAATTTT
1 --TTTAAATTTATTAATTTT
1970984 TTT-AATTTATTAA
1 TTTAAATTTATTAA
1970997 AATTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.23
17 5 0.19
19 6 0.23
20 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTAAATTTATTAATTTT
Found at i:1971114 original size:24 final size:24
Alignment explanation
Indices: 1971046--1971114 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
1971036 AAAAAATAAT
1971046 ATAAATTTAAA-ATTATCAAATTTA
1 ATAAATTTAAATATT-TCAAATTTA
* *
1971070 ATAAATTTAATTGATTT-AAATTTG
1 ATAAATTTAAAT-ATTTCAAATTTA
*
1971094 ATCAATTTAAATATTTCAAAT
1 ATAAATTTAAATATTTCAAAT
1971115 ATAAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 4 0.11
24 30 0.79
25 1 0.03
26 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (24 bp):
ATAAATTTAAATATTTCAAATTTA
Found at i:1971183 original size:8 final size:8
Alignment explanation
Indices: 1971157--1971200 Score: 61
Period size: 8 Copynumber: 5.1 Consensus size: 8
1971147 GAAATAATTT
1971157 AAATTTAA
1 AAATTTAA
1971165 AAATTACTTAA
1 AAA-T--TTAA
1971176 AAATTTAA
1 AAATTTAA
1971184 AAATTTAA
1 AAATTTAA
1971192 AAATTTAA
1 AAATTTAA
1971200 A
1 A
1971201 TTAATTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 24 0.73
9 1 0.03
10 1 0.03
11 7 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATTTAA
Found at i:1971801 original size:17 final size:18
Alignment explanation
Indices: 1971762--1971809 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1971752 ATACATACAT
*
1971762 ATATTTATATATTATTAG
1 ATATTTATATATTAATAG
1971780 ATA-TTATATATTAATATG
1 ATATTTATATATTAATA-G
1971798 -TATTTATATATT
1 ATATTTATATATT
1971810 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
ATATTTATATATTAATAG
Found at i:1977533 original size:116 final size:116
Alignment explanation
Indices: 1977389--1977607 Score: 325
Period size: 116 Copynumber: 1.9 Consensus size: 116
1977379 AGAAAACAGG
* *
1977389 AAAAAATTGAATTATCAAAGATACAGATATATCATGAATAAAATAATTAAAATATGATACAATAT
1 AAAAAATTAAATTATCAAAGATACAGATATATCATGAATAAAATAATTAAAATATGAAACAATAT
*
1977454 AAATACAT-GTTTTAAAATTTATATAAGATGAATTATTACGTATATAAATAA
66 AAATACATAG-TTTAAAATTTATATAAGACGAATTATTACGTATATAAATAA
* * *
1977505 AAAAAATTAAATTATTAACA-ATATAGATATATCATGAATAAAATAATTAAAATATGAAATAATA
1 AAAAAATTAAATTATCAA-AGATACAGATATATCATGAATAAAATAATTAAAATATGAAACAATA
** *
1977569 TAAATATTTAGTTTAAAATTTATATATGACGAATTATTA
65 TAAATACATAGTTTAAAATTTATATAAGACGAATTATTA
1977608 TTATATATAA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
116 90 0.98
117 2 0.02
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (116 bp):
AAAAAATTAAATTATCAAAGATACAGATATATCATGAATAAAATAATTAAAATATGAAACAATAT
AAATACATAGTTTAAAATTTATATAAGACGAATTATTACGTATATAAATAA
Found at i:1977569 original size:41 final size:41
Alignment explanation
Indices: 1977413--1977575 Score: 98
Period size: 39 Copynumber: 4.1 Consensus size: 41
1977403 TCAAAGATAC
*
1977413 AGATATATCATGAATAAAATAATTAAAATATGATACAATAT
1 AGATATATCATGAATAAAATAATTAAAATATGAAACAATAT
** * **
1977454 A-A-ATA-CATGTTTTAAAAT--TTATATAAGATG-AATTAT-T
1 AGATATATCATG-AATAAAATAATTA-A-AATATGAAACAATAT
* * *
1977491 ACG-TATAT-A--AATAAAAAAAATTAAATTAT-TAACAATAT
1 A-GATATATCATGAAT-AAAATAATTAAAATATGAAACAATAT
*
1977529 AGATATATCATGAATAAAATAATTAAAATATGAAATAATAT
1 AGATATATCATGAATAAAATAATTAAAATATGAAACAATAT
*
1977570 AAATAT
1 AGATAT
1977576 TTAGTTTAAA
Statistics
Matches: 87, Mismatches: 18, Indels: 34
0.63 0.13 0.24
Matches are distributed among these distances:
36 1 0.01
37 17 0.20
38 16 0.18
39 22 0.25
40 15 0.17
41 16 0.18
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (41 bp):
AGATATATCATGAATAAAATAATTAAAATATGAAACAATAT
Found at i:1982354 original size:36 final size:36
Alignment explanation
Indices: 1982308--1982380 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1982298 GTTTCCCTGT
1982308 AAGTATTCTCTTACAAGTTACACCGTTTGGTTTCAG
1 AAGTATTCTCTTACAAGTTACACCGTTTGGTTTCAG
1982344 AAGTATTCTCTTACAAGTTACACCGTTTGGTTTCAG
1 AAGTATTCTCTTACAAGTTACACCGTTTGGTTTCAG
1982380 A
1 A
1982381 GCCCAGGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (36 bp):
AAGTATTCTCTTACAAGTTACACCGTTTGGTTTCAG
Found at i:1985376 original size:25 final size:27
Alignment explanation
Indices: 1985351--1985402 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1985341 TATTTAATTA
*
1985351 TTTATATAATTTTAA-TTA-ATTTTTAT
1 TTTATA-AATTATAATTTATATTTTTAT
1985377 TTTATAAATTATAATTTATATTTTTA
1 TTTATAAATTATAATTTATATTTTTA
1985403 ATTAATCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 9 0.39
27 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTATAAATTATAATTTATATTTTTAT
Found at i:1985386 original size:19 final size:17
Alignment explanation
Indices: 1985331--1985408 Score: 68
Period size: 21 Copynumber: 4.3 Consensus size: 17
1985321 ATAATTAATT
* *
1985331 TTAATTTGTATATTTAA
1 TTAATTTATATTTTTAA
1985348 TT-ATTTATATAATTTTAA
1 TTAATTTATAT--TTTTAA
*
1985366 TTAATTTTTATTTTATAAA
1 TTAATTTATATTTT-T-AA
1985385 TTATAATTTATATTTTTAA
1 -T-TAATTTATATTTTTAA
1985404 TTAAT
1 TTAAT
1985409 CAATATCATA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
16 7 0.14
17 9 0.18
18 9 0.18
19 11 0.22
20 2 0.04
21 12 0.24
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (17 bp):
TTAATTTATATTTTTAA
Found at i:1986098 original size:2 final size:2
Alignment explanation
Indices: 1986091--1986120 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1986081 ATAATAAAGA
*
1986091 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1986121 TCAAAAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1990819 original size:2 final size:2
Alignment explanation
Indices: 1990814--1990844 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1990804 TGTGTGCGTG
1990814 TA TA TA 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 TA TA TA T
1990845 TGTTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1990905 original size:55 final size:55
Alignment explanation
Indices: 1990826--1990937 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
1990816 TATATATATA
1990826 TATATATATATATATATATTGTTTTTTAATTAATTGTTCTTAAACAATTGAAAAT
1 TATATATATATATATATATTGTTTTTTAATTAATTGTTCTTAAACAATTGAAAAT
1990881 TATATATATATATATATATTGTTTTTTAATTAATTGTTCTTAAACAATTGAAAAT
1 TATATATATATATATATATTGTTTTTTAATTAATTGTTCTTAAACAATTGAAAAT
1990936 TA
1 TA
1990938 AATTCCAGAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (55 bp):
TATATATATATATATATATTGTTTTTTAATTAATTGTTCTTAAACAATTGAAAAT
Found at i:1991935 original size:2 final size:2
Alignment explanation
Indices: 1991930--1991967 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1991920 TAGGACCCTT
* *
1991930 TA TA TA TA TA TT TA TG 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 TA TA
1991968 GAAGTATGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1992577 original size:26 final size:26
Alignment explanation
Indices: 1992538--1992588 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1992528 TTTTGAACGT
*
1992538 ATTTAGTTAAAAAAATTATTTTTTAC
1 ATTTAGTTAAAAAAATAATTTTTTAC
1992564 ATTTA-TTAATAAAAATAATTTTTTA
1 ATTTAGTTAA-AAAAATAATTTTTTA
1992589 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTTAGTTAAAAAAATAATTTTTTAC
Found at i:1992585 original size:25 final size:26
Alignment explanation
Indices: 1992538--1992586 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1992528 TTTTGAACGT
*
1992538 ATTTAGTTAAAAAAATTATTTTTTAC
1 ATTTAGTTAAAAAAATTAATTTTTAC
1992564 ATTTA-TTAATAAAAA-TAATTTTT
1 ATTTAGTTAA-AAAAATTAATTTTT
1992587 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTTAGTTAAAAAAATTAATTTTTAC
Found at i:1992599 original size:25 final size:26
Alignment explanation
Indices: 1992548--1992602 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
1992538 ATTTAGTTAA
* * * *
1992548 AAAAATTATTTTTTACATTTATTAAT
1 AAAAATAATTTTTTAAAATTATAAAT
1992574 AAAAATAATTTTTTAAAATTA-AAAT
1 AAAAATAATTTTTTAAAATTATAAAT
1992599 AAAA
1 AAAA
1992603 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAAATAATTTTTTAAAATTATAAAT
Found at i:2002130 original size:30 final size:31
Alignment explanation
Indices: 2002088--2002152 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
2002078 AGATATTAGC
*
2002088 ATTTATATAATTT-TTTTAATTTAAAA-TTTA
1 ATTTATATAATTTATATT-ATTTAAAATTTTA
2002118 ATTTA-ATGAATTTATATTATTTAAAATTTTA
1 ATTTATAT-AATTTATATTATTTAAAATTTTA
2002149 ATTT
1 ATTT
2002153 TAATATCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 2 0.06
30 18 0.58
31 11 0.35
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
ATTTATATAATTTATATTATTTAAAATTTTA
Found at i:2002621 original size:2 final size:2
Alignment explanation
Indices: 2002616--2002657 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2002606 TGTGTGTGTG
2002616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2002658 GGGAACTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2006642 original size:2 final size:2
Alignment explanation
Indices: 2006635--2006671 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2006625 CTTAAATATT
2006635 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2006672 TGTATATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2016077 original size:19 final size:19
Alignment explanation
Indices: 2016036--2016078 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2016026 TTACTATCTA
2016036 AAAAATAATAATATTAATT
1 AAAAATAATAATATTAATT
*
2016055 -AAAATAATAA-ATATATTT
1 AAAAATAATAATAT-TAATT
2016073 AAAAAT
1 AAAAAT
2016079 TTTCACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.10
18 14 0.67
19 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATAATAATATTAATT
Found at i:2017023 original size:15 final size:15
Alignment explanation
Indices: 2017003--2017033 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2016993 ATTAACATCC
*
2017003 AACATGTATATATAT
1 AACATGCATATATAT
2017018 AACATGCATATATAT
1 AACATGCATATATAT
2017033 A
1 A
2017034 TTCTAATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (15 bp):
AACATGCATATATAT
Found at i:2018130 original size:21 final size:19
Alignment explanation
Indices: 2018089--2018132 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2018079 TGAATAAAAT
* *
2018089 TATAAATTTTTATATTTAA
1 TATAAATTATTATATATAA
2018108 TATAATATTATTACTATATAA
1 TATAA-ATTATTA-TATATAA
2018129 TATA
1 TATA
2018133 TTAATTAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 6 0.29
21 10 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TATAAATTATTATATATAA
Found at i:2018374 original size:31 final size:32
Alignment explanation
Indices: 2018329--2018389 Score: 115
Period size: 31 Copynumber: 1.9 Consensus size: 32
2018319 AATATAATAA
2018329 AATAATAAAAAATAATATAAATATAAAAATTT
1 AATAATAAAAAATAATATAAATATAAAAATTT
2018361 AATAAT-AAAAATAATATAAATATAAAAAT
1 AATAATAAAAAATAATATAAATATAAAAAT
2018390 ATATTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (32 bp):
AATAATAAAAAATAATATAAATATAAAAATTT
Found at i:2018398 original size:17 final size:17
Alignment explanation
Indices: 2018322--2018390 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
2018312 TGAATACAAT
2018322 ATAATA-AAATAATAAAAA
1 ATAATATAAAT-AT-AAAA
2018340 ATAATATAAATATAAAA
1 ATAATATAAATATAAAA
2018357 AT--T-T-AATAATAAAA
1 ATAATATAAAT-ATAAAA
2018371 ATAATATAAATATAAAA
1 ATAATATAAATATAAAA
2018388 ATA
1 ATA
2018391 TATTAAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.07
14 9 0.20
15 1 0.02
16 1 0.02
17 16 0.36
18 11 0.24
19 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAATATAAATATAAAA
Found at i:2019220 original size:2 final size:2
Alignment explanation
Indices: 2019213--2019237 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2019203 AGAGAAAACC
2019213 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
2019238 CAGAGATTGA
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:2019423 original size:2 final size:2
Alignment explanation
Indices: 2019416--2019448 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2019406 TAAACATGTT
2019416 TA TA TA TA 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 TA TA TA TA T
2019449 CCCTTGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2021398 original size:4 final size:4
Alignment explanation
Indices: 2021389--2021415 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2021379 TTTAACGCGT
2021389 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
2021416 TTACATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:2021537 original size:3 final size:3
Alignment explanation
Indices: 2021529--2021555 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2021519 TGTTTGTATC
2021529 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2021556 GAATGACTGA
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):
ATA
Found at i:2021843 original size:19 final size:19
Alignment explanation
Indices: 2021819--2021861 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2021809 ACCTCCTCCC
*
2021819 AAAAAATAA-AAATTAAAAT
1 AAAAAATAAGAAA-GAAAAT
2021838 AAAAAATAAGAAAGAAAAT
1 AAAAAATAAGAAAGAAAAT
2021857 AAAAA
1 AAAAA
2021862 CCATATTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAAAATAAGAAAGAAAAT
Found at i:2022130 original size:21 final size:23
Alignment explanation
Indices: 2022106--2022162 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 23
2022096 ATATTATATT
2022106 AATTTAATTTATTTA-AAT-AAA
1 AATTTAATTTATTTATAATAAAA
*
2022127 AA-TTATTTATATTTATTAATAAAA
1 AATTTAATT-TATTTA-TAATAAAA
2022151 AATTTTAATTTA
1 AA-TTTAATTTA
2022163 ATGATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 5 0.18
21 8 0.29
23 3 0.11
24 5 0.18
25 2 0.07
26 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTAATTTATTTATAATAAAA
Found at i:2022134 original size:24 final size:22
Alignment explanation
Indices: 2022107--2022162 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
2022097 TATTATATTA
*
2022107 ATTTAATTTATTTAAATAAAAATT
1 ATTTAATTTA-TT-AATAAAAAAT
2022131 ATTTATATTTATTAATAAAAAAT
1 ATTTA-ATTTATTAATAAAAAAT
2022154 -TTTAATTTA
1 ATTTAATTTA
2022163 ATGATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.17
22 4 0.13
23 9 0.30
24 7 0.23
25 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTAATTTATTAATAAAAAAT
Found at i:2022177 original size:18 final size:18
Alignment explanation
Indices: 2022156--2022198 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2022146 TAAAAAATTT
*
2022156 TAATTTAATGATATAATA
1 TAATTTAATAATATAATA
* * *
2022174 TAATATATTAATATTATA
1 TAATTTAATAATATAATA
2022192 TAATTTA
1 TAATTTA
2022199 TATTCTATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAATTTAATAATATAATA
Found at i:2024674 original size:22 final size:22
Alignment explanation
Indices: 2024646--2024711 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
2024636 TAATTTGATT
2024646 TAATTTAATTTATAAATATTTA
1 TAATTTAATTTATAAATATTTA
*
2024668 TAATTTAAATTT-TAAAAATTT-
1 TAATTT-AATTTATAAATATTTA
*
2024689 TAATTTTAA-TTAAAAAT-TTTA
1 TAA-TTTAATTTATAAATATTTA
2024710 TA
1 TA
2024712 CCAATAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.14
21 10 0.27
22 17 0.46
23 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATTTAATTTATAAATATTTA
Found at i:2025072 original size:23 final size:24
Alignment explanation
Indices: 2025041--2025093 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2025031 ATTTAAAATG
2025041 ATTAATAAATATTAA-ATTTTAAA
1 ATTAATAAATATTAATATTTTAAA
* *
2025064 ATTATTAAATATTAATTTTTTAAA
1 ATTAATAAATATTAATATTTTAAA
*
2025088 AATAAT
1 ATTAAT
2025094 TATATAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTAATAAATATTAATATTTTAAA
Found at i:2025383 original size:2 final size:2
Alignment explanation
Indices: 2025378--2025402 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2025368 AAAAAGACAA
2025378 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2025403 AAATTAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2027471 original size:3 final size:3
Alignment explanation
Indices: 2027463--2027492 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2027453 AAATTTCTAC
2027463 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2027493 AAGGAGGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2028146 original size:24 final size:24
Alignment explanation
Indices: 2028082--2028183 Score: 66
Period size: 25 Copynumber: 4.1 Consensus size: 24
2028072 TAATAAATTT
* *
2028082 TTTTTTATAAATTTATATTTA-ATA
1 TTTTTAATAAA-TTAAATTTATATA
*
2028106 -TATTAATAATATATAAATTTATATA
1 TTTTTAATAA-AT-TAAATTTATATA
*
2028131 TTTTTAATAAATTAAA-TAATATTA
1 TTTTTAATAAATTAAATTTATA-TA
* * *
2028155 TTTTTTAAAAAATAAAATTATTTATA
1 -TTTTTAATAAATTAAATT-TATATA
2028181 TTT
1 TTT
2028184 ATTTTTTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
23 12 0.20
24 14 0.23
25 22 0.36
26 11 0.18
27 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTTAATAAATTAAATTTATATA
Found at i:2028176 original size:23 final size:25
Alignment explanation
Indices: 2028108--2028183 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
2028098 ATTTAATATA
*
2028108 TTAATAATATATAAATT-TATATATTT
1 TTAATAAAATA-AAATTAT-TATATTT
* *
2028134 TTAATAAATTAAATAATATTAT-TTT
1 TTAATAAAATAAA-ATTATTATATTT
2028159 TTAA-AAAATAAAATTATTTATATTT
1 TTAATAAAATAAAATTA-TTATATTT
2028184 ATTTTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
23 3 0.07
24 11 0.27
25 12 0.29
26 14 0.34
27 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAATAAAATAAAATTATTATATTT
Found at i:2031300 original size:23 final size:23
Alignment explanation
Indices: 2031266--2031319 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
2031256 CCACTTGAAT
*
2031266 GAAATCTAAAGCTGTTTCTTCAC
1 GAAATCTCAAGCTGTTTCTTCAC
2031289 GAAATCTCAAGCTGTTTCTTCAC
1 GAAATCTCAAGCTGTTTCTTCAC
2031312 GAAATCTC
1 GAAATCTC
2031320 CACAGCATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (23 bp):
GAAATCTCAAGCTGTTTCTTCAC
Found at i:2040188 original size:18 final size:18
Alignment explanation
Indices: 2040158--2040197 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2040148 CAATTTTTTT
*
2040158 TTAATGTTTTATATTATA
1 TTAATGTTTTATATTAAA
2040176 TTAAT-TTTATATATTAAA
1 TTAATGTTT-TATATTAAA
2040194 TTAA
1 TTAA
2040198 ATATATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTAATGTTTTATATTAAA
Found at i:2041984 original size:2 final size:2
Alignment explanation
Indices: 2041946--2041972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2041936 ACCTTAAATT
2041946 TA 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 TA T
2041973 TGATGAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2045762 original size:21 final size:22
Alignment explanation
Indices: 2045737--2045777 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2045727 TGAATTTAAT
*
2045737 ATATAAAATAATAA-AAATATG
1 ATATAAAATAAAAATAAATATG
*
2045758 ATATAATATAAAAATAAATA
1 ATATAAAATAAAAATAAATA
2045778 AAATAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
ATATAAAATAAAAATAAATATG
Found at i:2045768 original size:18 final size:18
Alignment explanation
Indices: 2045734--2045783 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2045724 TTTTGAATTT
2045734 AATATATAAAATAATAAA
1 AATATATAAAATAATAAA
*
2045752 AATATGATATAAT-ATAAA
1 AATAT-ATAAAATAATAAA
*
2045770 AATAAATAAAATAA
1 AATATATAAAATAA
2045784 ACATGATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 15 0.56
19 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AATATATAAAATAATAAA
Found at i:2047052 original size:15 final size:17
Alignment explanation
Indices: 2047028--2047068 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2047018 TAAGAGAATA
2047028 ATTAATAAATACTT-AT
1 ATTAATAAATACTTAAT
*
2047044 ATTAA-AAATAGTTAAT
1 ATTAATAAATACTTAAT
2047060 ATTAATAAA
1 ATTAATAAA
2047069 AAAATCAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 12 0.55
17 3 0.14
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTAATAAATACTTAAT
Found at i:2049661 original size:2 final size:2
Alignment explanation
Indices: 2049654--2049708 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2049644 GTTACAATTA
2049654 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
2049696 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
2049709 ATGCTTAAGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2058259 original size:17 final size:17
Alignment explanation
Indices: 2058239--2058272 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2058229 GCAACGAATA
2058239 GAAACAAAAAAATTAAT
1 GAAACAAAAAAATTAAT
*
2058256 GAAACAAACAAATTAAT
1 GAAACAAAAAAATTAAT
2058273 CATTGAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.09, G:0.06, T:0.18
Consensus pattern (17 bp):
GAAACAAAAAAATTAAT
Found at i:2060495 original size:18 final size:16
Alignment explanation
Indices: 2060472--2060506 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
2060462 GATATTAAAA
2060472 TTTTTTATATATATATAT
1 TTTTTTAT-TATAT-TAT
2060490 TTTTTTATTATATTAT
1 TTTTTTATTATATTAT
2060506 T
1 T
2060507 AGTATCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTATTATATTAT
Found at i:2060979 original size:324 final size:329
Alignment explanation
Indices: 2060621--2061230 Score: 869
Period size: 324 Copynumber: 1.9 Consensus size: 329
2060611 TCTTATGTTA
*
2060621 TATTTATTATATTATTTTTATATTAATTAAATATATCATATTCATATTATATTTAAAATTTACAA
1 TATTTATTATATTATTTTTATATTAATAAAATATATCATATTCATATTATATTTAAAATTTACAA
* * *
2060686 TACAACCG-ATTAAATACATTAAAATTTTAAACGTAAATATAATACATATATTAAAC-ATATAAT
66 CAC-A-CGAATAAAATACATTAAAATTTTAAACATAAATATAATACATATA-TAAACTATATAAT
* *
2060749 TTTAATCATTTTAAAC-GT-GTTATA-TT-A-TATTTATTATATTATTTTTATATTAATTAAACA
128 TTTAATCATTTTAAACACTAATTATATTTAATTATTTATTATATTATTTTTATATTAATTAAACA
* *
2060809 TATCAAATTTATATTATATTTAAAATTTATAATA-CACGTGATTAAATATATTAAAATTTTAAGC
193 TATCAAATTTATATTATATTTAAAATTTATAATATCA-GTAATTAAATATATTAAAATTTTAAAC
*
2060873 ACAAATATAATATATA-TATATATATTAAATATGTAATTTTAACCATTTTAAACAAGCTATATTA
257 ACAAATATAATATATATTAAATATATTAAATATGTAATTTTAACCATTTTAAACAAGCTATATTA
2060937 TATGTAAT
322 TATGTAAT
*
2060945 TATTTATTATATTATTTTTATATTAATAAAATATATCATATTCATATTATATTTAAAATTTATAA
1 TATTTATTATATTATTTTTATATTAATAAAATATATCATATTCATATTATATTTAAAATTTACAA
* * *
2061010 CACACGTAATAAAATATATTAAAATTTTAAATATAAATATAATACATATATCAACTATATAATTT
66 CACACG-AATAAAATACATTAAAATTTTAAACATAAATATAATACATATATAAACTATATAATTT
* * * *
2061075 TAATTATTTTAAACATACTACATTGTATTTAATTATTTGTTATATTATTTTTATATTAATTAAAT
130 TAATCATTTTAAAC--ACTA-ATTATATTTAATTATTTATTATATTATTTTTATATTAATTAAAC
* * * * *
2061140 ATATTATATTTATATTATATTTAAAATTTATAGTATTAGTAATTAAATATATTAAAATTTTAAAT
192 ATATCAAATTTATATTATATTTAAAATTTATAATATCAGTAATTAAATATATTAAAATTTTAAAC
**
2061205 TTAAATATAATATATATTAAATATAT
257 ACAAATATAATATATATTAAATATAT
2061231 AATTTTTTAT
Statistics
Matches: 249, Mismatches: 24, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
322 2 0.01
323 5 0.02
324 125 0.50
327 1 0.00
329 4 0.02
330 2 0.01
331 1 0.00
332 100 0.40
333 9 0.04
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (329 bp):
TATTTATTATATTATTTTTATATTAATAAAATATATCATATTCATATTATATTTAAAATTTACAA
CACACGAATAAAATACATTAAAATTTTAAACATAAATATAATACATATATAAACTATATAATTTT
AATCATTTTAAACACTAATTATATTTAATTATTTATTATATTATTTTTATATTAATTAAACATAT
CAAATTTATATTATATTTAAAATTTATAATATCAGTAATTAAATATATTAAAATTTTAAACACAA
ATATAATATATATTAAATATATTAAATATGTAATTTTAACCATTTTAAACAAGCTATATTATATG
TAAT
Found at i:2061130 original size:11 final size:11
Alignment explanation
Indices: 2061102--2061162 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
2061092 CTACATTGTA
2061102 TTTA-ATTATT
1 TTTATATTATT
2061112 TGTTATATTATT
1 T-TTATATTATT
2061124 TTTATATTAATT
1 TTTATATT-ATT
** *
2061136 AAATATATTATA
1 -TTTATATTATT
*
2061148 TTTATATTATA
1 TTTATATTATT
2061159 TTTA
1 TTTA
2061163 AAATTTATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
10 1 0.02
11 23 0.55
12 12 0.29
13 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2061142 original size:163 final size:161
Alignment explanation
Indices: 2060621--2061247 Score: 781
Period size: 163 Copynumber: 3.9 Consensus size: 161
2060611 TCTTATGTTA
*
2060621 TATTTATTATATTATTTTTATATTAATTAAATATATCATATTCATATTATATTTAAAATTTACAA
1 TATTTATTATATTATTTTTATATTAATTAAATATATCATATTCATATTATATTTAAAATTTATAA
* ** *
2060686 TACAACCG--ATTAAATACATTAAAATTTTAAACGTAAATATAATACATATATTAAACATATAAT
66 TAC-A-CGTAATTAAATATATTAAAATTTTAAATATAAATATAATACATATATTAAATATATAAT
* *
2060749 TTTAATCATTTTAAAC--GT-GTTATA-TT-A-
129 TTTAATCATTTTAAACAACTAATTATATTTAAT
* * *
2060776 TATTTATTATATTATTTTTATATTAATTAAACATATCAAATTTATATTATATTTAAAATTTATAA
1 TATTTATTATATTATTTTTATATTAATTAAATATATCATATTCATATTATATTTAAAATTTATAA
* * * *
2060841 TACACGTGATTAAATATATTAAAATTTTAAGCACAAATATAATATATATATATATATTAAATATG
66 TACACGTAATTAAATATATTAAAATTTT-A--A-ATATA-AATATA-ATACATATATTAAATATA
* *
2060906 TAATTTTAACCATTTTAAACAAGCTATATTATATGTAAT
125 TAATTTTAATCATTTTAAACAA-CTA-ATTATATTTAAT
*
2060945 TATTTATTATATTATTTTTATATTAATAAAATATATCATATTCATATTATATTTAAAATTTATAA
1 TATTTATTATATTATTTTTATATTAATTAAATATATCATATTCATATTATATTTAAAATTTATAA
* * * *
2061010 CACACGTAATAAAATATATTAAAATTTTAAATATAAATATAATACATATATCAACTATATAATTT
66 TACACGTAATTAAATATATTAAAATTTTAAATATAAATATAATACATATATTAAATATATAATTT
* *
2061075 TAATTATTTTAAACATACTACATTGTATTTAAT
131 TAATCATTTTAAACA-ACTA-ATTATATTTAAT
* * * *
2061108 TATTTGTTATATTATTTTTATATTAATTAAATATATTATATTTATATTATATTTAAAATTTATAG
1 TATTTATTATATTATTTTTATATTAATTAAATATATCATATTCATATTATATTTAAAATTTATAA
* *
2061173 TATTA-GTAATTAAATATATTAAAATTTTAAATTTAAATATAAT--ATATATTAAATATATAATT
66 TA-CACGTAATTAAATATATTAAAATTTTAAATATAAATATAATACATATATTAAATATATAA-T
*
2061235 TTTTATCATTTTA
129 TTTAATCATTTTA
2061248 GATGTATTAT
Statistics
Matches: 409, Mismatches: 44, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
153 2 0.00
154 1 0.00
155 83 0.20
156 1 0.00
158 1 0.00
159 3 0.01
160 6 0.01
161 49 0.12
162 12 0.03
163 143 0.35
164 9 0.02
165 4 0.01
166 6 0.01
167 1 0.00
168 2 0.00
169 86 0.21
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (161 bp):
TATTTATTATATTATTTTTATATTAATTAAATATATCATATTCATATTATATTTAAAATTTATAA
TACACGTAATTAAATATATTAAAATTTTAAATATAAATATAATACATATATTAAATATATAATTT
TAATCATTTTAAACAACTAATTATATTTAAT
Found at i:2061170 original size:24 final size:24
Alignment explanation
Indices: 2061115--2061193 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
2061105 AATTATTTGT
*
2061115 TATATTATTTTTATATTAATTAAA
1 TATATTATATTTATATTAATTAAA
2061139 TATATTATATTTATATTATATTTAAA
1 TATATTATATTTATATTA-A-TTAAA
* *
2061165 -AT-TTATA-GTATTAGTAATTAAA
1 TATATTATATTTA-TATTAATTAAA
2061187 TATATTA
1 TATATTA
2061194 AAATTTTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 5 0.11
23 5 0.11
24 29 0.62
25 3 0.06
26 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
TATATTATATTTATATTAATTAAA
Found at i:2061691 original size:21 final size:21
Alignment explanation
Indices: 2061658--2061701 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2061648 TAAAAATAAT
2061658 AATAAATTAATATGA-TGAATA
1 AATAAATTAATAT-ATTGAATA
* *
2061679 AATATATTTATATATTGAATA
1 AATAAATTAATATATTGAATA
2061700 AA
1 AA
2061702 GTAATATTGC
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:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AATAAATTAATATATTGAATA
Found at i:2062332 original size:21 final size:23
Alignment explanation
Indices: 2062308--2062349 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
2062298 TTTTCATTAA
2062308 CATAATATAAAA-A-AATTAAAT
1 CATAATATAAAATATAATTAAAT
2062329 CATAATATAAAATATAATTAA
1 CATAATATAAAATATAATTAA
2062350 CTTATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (23 bp):
CATAATATAAAATATAATTAAAT
Found at i:2063759 original size:2 final size:2
Alignment explanation
Indices: 2063752--2063779 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2063742 TTTTCAATCC
2063752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2063780 TCCATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2067451 original size:16 final size:16
Alignment explanation
Indices: 2067430--2067474 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2067420 GATTCGAAAC
2067430 TCAAAATAATTTAAAT
1 TCAAAATAATTTAAAT
* *
2067446 TTAAAATAATTCAAAT
1 TCAAAATAATTTAAAT
*
2067462 TCAAAATGATTTA
1 TCAAAATAATTTA
2067475 GATAATTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (16 bp):
TCAAAATAATTTAAAT
Found at i:2072854 original size:2 final size:2
Alignment explanation
Indices: 2072849--2072882 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2072839 GAAAAGTGTG
2072849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2072883 AAACTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2077138 original size:2 final size:2
Alignment explanation
Indices: 2077133--2077172 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2077123 TTTTTTCAAA
2077133 AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2077173 CAGCATAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.