Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 5 of 33
Found at i:537565 original size:6 final size:6
Alignment explanation
Indices: 537554--537580 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
537544 GTTCCGGAGT
537554 ACCATA ACCATA ACCATA ACCATA ACC
1 ACCATA ACCATA ACCATA ACCATA ACC
537581 TGAGTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCATA
Found at i:539479 original size:17 final size:17
Alignment explanation
Indices: 539459--539512 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
539449 ATTTTTTAAT
539459 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
539476 ATTTTA-ATATA-ATTAA
1 ATTTTATATTTATA-TAA
*
539492 A-ATT-TATTTATATAA
1 ATTTTATATTTATATAA
539507 ATTTTA
1 ATTTTA
539513 AAATATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
15 11 0.39
16 11 0.39
17 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:539571 original size:28 final size:31
Alignment explanation
Indices: 539516--539582 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
539506 AATTTTAAAA
*
539516 TATTAATATATTCATATTACTTTTTTAT-CT
1 TATTAATATATTCATATTACTTTATTATACT
539546 TATTAATAT-TT-ATATTA-TTTAATTATACT
1 TATTAATATATTCATATTACTTT-ATTATACT
539575 TATCTAAT
1 TAT-TAAT
539583 GTTATCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 10 0.30
29 7 0.21
30 13 0.39
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.58
Consensus pattern (31 bp):
TATTAATATATTCATATTACTTTATTATACT
Found at i:539976 original size:16 final size:17
Alignment explanation
Indices: 539950--539992 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
539940 ATAAATTTAT
539950 ATAATTATTTTTAA-AAA
1 ATAA-TATTTTTAATAAA
539967 ATAATA-TTTTAATAAA
1 ATAATATTTTTAATAAA
*
539983 ATAAAATTTT
1 ATAATATTTT
539993 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 10 0.43
17 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATATTTTTAATAAA
Found at i:539993 original size:16 final size:16
Alignment explanation
Indices: 539958--539995 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
539948 ATATAATTAT
*
539958 TTTTAA-AAAATAATA
1 TTTTAATAAAATAAAA
539973 TTTTAATAAAATAAAA
1 TTTTAATAAAATAAAA
539989 TTTTAAT
1 TTTTAAT
539996 TTTTTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTAATAAAATAAAA
Found at i:540825 original size:2 final size:2
Alignment explanation
Indices: 540818--540847 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
540808 GGTATCATAC
540818 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
540848 CAGCAACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:541556 original size:57 final size:55
Alignment explanation
Indices: 541468--541581 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 55
541458 ATTCTTTTCT
* ** *
541468 TTCTTTTTCAATTCTCATTTCTACACTATTTTTATTTTATGTTTTTTTCCCACATCA
1 TTCTTTTTCAATTCACATTTCTACACTA-TTTTATTCAATG-TTTCTTCCCACATCA
541525 TTCTTTTTCAATTCACATTTCTACACTATTTTATTCAATGTTTCTTCCCACATCA
1 TTCTTTTTCAATTCACATTTCTACACTATTTTATTCAATGTTTCTTCCCACATCA
541580 TT
1 TT
541582 GGGTGACGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 16 0.30
56 10 0.19
57 27 0.51
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.54
Consensus pattern (55 bp):
TTCTTTTTCAATTCACATTTCTACACTATTTTATTCAATGTTTCTTCCCACATCA
Found at i:542624 original size:33 final size:33
Alignment explanation
Indices: 542582--542648 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
542572 AGATAATTTT
542582 TTACATTATACTTTATAACTTAAGCATTTGAAA
1 TTACATTATACTTTATAACTTAAGCATTTGAAA
542615 TTACATTATACTTTATAACTTAAGCATTTGAAA
1 TTACATTATACTTTATAACTTAAGCATTTGAAA
542648 T
1 T
542649 CAGAAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (33 bp):
TTACATTATACTTTATAACTTAAGCATTTGAAA
Found at i:549065 original size:2 final size:2
Alignment explanation
Indices: 549058--549082 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
549048 TCAAATATTT
549058 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
549083 TCATGGTTAT
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:549689 original size:15 final size:15
Alignment explanation
Indices: 549665--549699 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
549655 ATAATAATTT
549665 AATT-TTAATTTTAA
1 AATTATTAATTTTAA
*
549679 ATTTATTAATTTTAA
1 AATTATTAATTTTAA
549694 AATTAT
1 AATTAT
549700 ATTATCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTATTAATTTTAA
Found at i:552175 original size:30 final size:27
Alignment explanation
Indices: 552137--552211 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 27
552127 ATATAACATG
552137 AAAATTATATAAAATATAATAATATATAA
1 AAAATTATATAAAATATAA-AATATAT-A
** *
552166 AATAATTATATGTAATAT-AAATATATT
1 AA-AATTATATAAAATATAAAATATATA
552193 AAAATT-TATAAAATATAAA
1 AAAATTATATAAAATATAAA
552212 TTTATTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
25 8 0.21
26 6 0.15
27 2 0.05
28 7 0.18
29 3 0.08
30 13 0.33
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
AAAATTATATAAAATATAAAATATATA
Found at i:552223 original size:14 final size:15
Alignment explanation
Indices: 552194--552261 Score: 55
Period size: 18 Copynumber: 4.1 Consensus size: 15
552184 AAATATATTA
552194 AAATTTATAAAATAT
1 AAATTTATAAAATAT
*
552209 AAATTTATTAATATATT
1 AAATTTA-TAAAATA-T
*
552226 AAATTTTATATAAATAA
1 AAA-TTTATA-AAATAT
552243 AAATCATTATAAACATAT
1 AAAT--TTATAAA-ATAT
552261 A
1 A
552262 CATAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
15 7 0.17
16 7 0.17
17 11 0.26
18 17 0.40
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTATAAAATAT
Found at i:552224 original size:16 final size:16
Alignment explanation
Indices: 552138--552241 Score: 66
Period size: 17 Copynumber: 5.9 Consensus size: 16
552128 TATAACATGA
*
552138 AAATTATATAAAATATA
1 AAATT-TATAAAATATT
*
552155 ATAATATATAAAATAATT
1 A-AATTTATAAAAT-ATT
*
552173 ATATGTAATATAAATATATT
1 AAAT-T--TATAAA-ATATT
552193 AAAATTTATAAAATA-T
1 -AAATTTATAAAATATT
*
552209 AAATTTATTAATATATT
1 AAATTTA-TAAAATATT
552226 AAATTTTATATAAATA
1 AAA-TTTATA-AAATA
552242 AAAATCATTA
Statistics
Matches: 69, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
15 7 0.10
16 7 0.10
17 20 0.29
18 20 0.29
20 10 0.14
21 5 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
AAATTTATAAAATATT
Found at i:556551 original size:17 final size:17
Alignment explanation
Indices: 556529--556562 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
556519 AAAACAAAAA
556529 AAAATAATTTTAATTTT
1 AAAATAATTTTAATTTT
*
556546 AAAATAATTTTAGTTTT
1 AAAATAATTTTAATTTT
556563 TTATTTAATT
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AAAATAATTTTAATTTT
Found at i:561525 original size:2 final size:2
Alignment explanation
Indices: 561518--561549 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
561508 GACGTAAATA
561518 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
561550 GCTTGCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:563075 original size:2 final size:2
Alignment explanation
Indices: 563068--563095 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
563058 CATATGTATG
563068 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
563096 AAATTAAATT
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):
TA
Found at i:563278 original size:23 final size:22
Alignment explanation
Indices: 563252--563324 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
563242 TATAAATTTG
563252 ATATAAATATATTAATTTATATA
1 ATATAAATATATTAATTTAT-TA
* *
563275 ATATAAAT-TATAAACTTATTA
1 ATATAAATATATTAATTTATTA
*
563296 A-A-AAATATATGTAATAT-TTA
1 ATATAAATATAT-TAATTTATTA
*
563316 AAATAAATA
1 ATATAAATA
563325 ATGATATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.10
20 8 0.20
21 7 0.17
22 14 0.34
23 8 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
ATATAAATATATTAATTTATTA
Found at i:563284 original size:19 final size:19
Alignment explanation
Indices: 563236--563284 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
563226 ACAAAATAAA
*
563236 AAATAATATAAATTTGATAT
1 AAATAA-ATTAATTTGATAT
*
563256 AAATATATTAATTT-ATAT
1 AAATAAATTAATTTGATAT
563274 AATATAAATTA
1 AA-ATAAATTA
563285 TAAACTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATAAATTAATTTGATAT
Found at i:564477 original size:13 final size:12
Alignment explanation
Indices: 564450--564586 Score: 58
Period size: 13 Copynumber: 11.7 Consensus size: 12
564440 GTTAAATTTA
*
564450 ATAATTTTAAAT
1 ATAATTATAAAT
564462 ATAATTATATAAT
1 ATAATTATA-AAT
564475 ATAA-TATAAAT
1 ATAATTATAAAT
* *
564486 AAAAATATTAAAT
1 ATAATTA-TAAAT
** *
564499 ATATAGCACAAAT
1 ATA-ATTATAAAT
564512 ATATATTA-AAAT
1 ATA-ATTATAAAT
*
564524 ATATATAATAAATT
1 ATA-ATTATAAA-T
* *
564538 ATTATTAT-ATT
1 ATAATTATAAAT
*
564549 AAAATTAT--AT
1 ATAATTATAAAT
564559 A-AATTATAAAT
1 ATAATTATAAAT
*
564570 -T--TTTTAAAT
1 ATAATTATAAAT
564579 ATAATTAT
1 ATAATTAT
564587 GATATGATAA
Statistics
Matches: 96, Mismatches: 17, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
9 13 0.14
10 3 0.03
11 15 0.16
12 29 0.30
13 31 0.32
14 5 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (12 bp):
ATAATTATAAAT
Found at i:564529 original size:14 final size:14
Alignment explanation
Indices: 564510--564559 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
564500 TATAGCACAA
564510 ATATATATTAAAAT
1 ATATATATTAAAAT
* *
564524 ATATATAATAAATT
1 ATATATATTAAAAT
564538 ATTATTATATTAAAAT
1 A-TA-TATATTAAAAT
564554 -TATATA
1 ATATATA
564560 AATTATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.13
14 15 0.50
15 2 0.07
16 9 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATATATTAAAAT
Found at i:565480 original size:2 final size:2
Alignment explanation
Indices: 565473--565507 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
565463 GTTTTAATGA
565473 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 A
565508 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:565512 original size:2 final size:2
Alignment explanation
Indices: 565507--565533 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
565497 ATATATATAT
565507 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 A
565534 TTGATGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:565916 original size:11 final size:11
Alignment explanation
Indices: 565902--565987 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
565892 TAATAATTTA
565902 TTTTTTATATT
1 TTTTTTATATT
**
565913 TTTTGACATATT
1 TTTT-TTATATT
565925 TTTTATT-TATT
1 TTTT-TTATATT
565936 TTATATTTATATT
1 TT-T-TTTATATT
*
565949 ATTTTTATA-T
1 TTTTTTATATT
*
565959 TTTTTTAAATT
1 TTTTTTATATT
*
565970 TTATATTTAAATT
1 TT-T-TTTATATT
565983 TTTTT
1 TTTTT
565988 ATTTGATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
10 8 0.13
11 21 0.35
12 15 0.25
13 16 0.27
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (11 bp):
TTTTTTATATT
Found at i:565954 original size:17 final size:17
Alignment explanation
Indices: 565926--565989 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
565916 TGACATATTT
565926 TTTAT-TTA-TTTTATA
1 TTTATATTATTTTTATA
565941 TTTATATTATTTTTATA
1 TTTATATTATTTTTATA
* *
565958 TTT-TTTTAAATTTTATA
1 TTTATATT-ATTTTTATA
*
565975 TTTAAATT-TTTTTAT
1 TTTATATTATTTTTAT
565990 TTGATTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
15 5 0.12
16 12 0.30
17 21 0.52
18 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATATTATTTTTATA
Found at i:565971 original size:34 final size:33
Alignment explanation
Indices: 565933--566002 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
565923 TTTTTTATTT
*
565933 ATTTTATATTTATATTATTTTTATATT-TTTTTAA
1 ATTTTATATTTAAATT-TTTTTAT-TTATTTTTAA
565967 ATTTTATATTTAAATTTTTTTATTTGATTTTTAA
1 ATTTTATATTTAAATTTTTTTATTT-ATTTTTAA
566001 AT
1 AT
566003 AATGTATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 2 0.06
33 7 0.21
34 24 0.73
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (33 bp):
ATTTTATATTTAAATTTTTTTATTTATTTTTAA
Found at i:565991 original size:21 final size:21
Alignment explanation
Indices: 565941--566002 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
565931 TTATTTTATA
* *
565941 TTTATATTATTTTTATATTTT
1 TTTATTTTATTTTTAAATTTT
*
565962 TTTAAATTTTATATTTAAATTTT
1 TTT--ATTTTATTTTTAAATTTT
*
565985 TTTATTTGATTTTTAAAT
1 TTTATTTTATTTTTAAAT
566003 AATGTATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 16 0.47
23 18 0.53
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTATTTTATTTTTAAATTTT
Found at i:566011 original size:34 final size:34
Alignment explanation
Indices: 565937--566014 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
565927 TTATTTATTT
* **
565937 TATATTTATATTATTTTTATATTTTTTTAAATTT
1 TATATTTAAATTATTTTTATATTTTTTTAAATAA
565971 TATATTTAAATT-TTTTTAT-TTGATTTTTAAATAA
1 TATATTTAAATTATTTTTATATT--TTTTTAAATAA
*
566005 TGTATTTAAA
1 TATATTTAAA
566015 AAAATTAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 2 0.05
33 7 0.18
34 29 0.76
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (34 bp):
TATATTTAAATTATTTTTATATTTTTTTAAATAA
Found at i:566485 original size:19 final size:20
Alignment explanation
Indices: 566461--566511 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
566451 CGATACATTT
*
566461 TATCGATACATGCT-TATTA
1 TATCGATACATGCTCAATTA
* *
566480 TATCGATACATACTCAATTG
1 TATCGATACATGCTCAATTA
566500 TATCGATACATG
1 TATCGATACATG
566512 AAACTGACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (20 bp):
TATCGATACATGCTCAATTA
Found at i:566566 original size:19 final size:20
Alignment explanation
Indices: 566536--566591 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
566526 TACCCTAAGT
*
566536 GAAATTTATCGATACAT-AG
1 GAAATGTATCGATACATGAG
* * *
566555 GCATTGTATCGATACATGAT
1 GAAATGTATCGATACATGAG
566575 GAAATGTATCGATACAT
1 GAAATGTATCGATACAT
566592 TATGCCTAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (20 bp):
GAAATGTATCGATACATGAG
Found at i:568145 original size:32 final size:33
Alignment explanation
Indices: 568109--568173 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
568099 AAAATATAAA
*
568109 AATATATTAAAATTTATAT-AATATAAATTATT
1 AATATATTAAAATTTATATAAATATAAAATATT
* *
568141 AATATATTAAATTTTTTATAAATATAAAATATT
1 AATATATTAAAATTTATATAAATATAAAATATT
568174 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AATATATTAAAATTTATATAAATATAAAATATT
Found at i:568168 original size:6 final size:6
Alignment explanation
Indices: 568157--568209 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
568147 TTAAATTTTT
* * *
568157 TATAAA TATAAA -AT-AT TTTAAA TAAAAA TA-AAA TA-AAA TATAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
568201 TATAAA TAT
1 TATAAA TAT
568210 CATCCGTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
4 1 0.03
5 13 0.33
6 25 0.64
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TATAAA
Found at i:568171 original size:27 final size:30
Alignment explanation
Indices: 568069--568179 Score: 79
Period size: 27 Copynumber: 3.7 Consensus size: 30
568059 AAAACAAAGA
* * * *
568069 AAATAAAAAATTTAATAAATATA-ATATGAT
1 AAATATAAAATATATTAAATTTATATAT-AT
568099 AAAATATAAAAATATATTAAAATTTATATAATAT
1 -AAATAT-AAAATATATT-AAATTTATAT-ATAT
*
568133 AAAT-TATTAATATATTAAATTT-T-T-TAT
1 AAATATA-AAATATATTAAATTTATATATAT
*
568160 AAATATAAAATATTTTAAAT
1 AAATATAAAATATATTAAAT
568180 AAAAATAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
27 18 0.27
28 2 0.03
29 1 0.01
30 1 0.01
31 12 0.18
32 17 0.25
33 10 0.15
34 4 0.06
35 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
AAATATAAAATATATTAAATTTATATATAT
Found at i:568712 original size:25 final size:24
Alignment explanation
Indices: 568676--568765 Score: 80
Period size: 25 Copynumber: 3.8 Consensus size: 24
568666 TAAAATTGAT
568676 TTAAT-TATTATTTTAATTTTTTA
1 TTAATATATTATTTTAATTTTTTA
* **
568699 TTTAATATATTATTTTTATTAAATTA
1 -TTAATATATTATTTTAATT-TTTTA
**
568725 AAAATATATTAATTTT-ATTTTTTA
1 TTAATATATT-ATTTTAATTTTTTA
568749 -TAA-ATATTATTTTAATT
1 TTAATATATTATTTTAATT
568766 AATATTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
21 5 0.09
22 8 0.15
23 2 0.04
24 8 0.15
25 23 0.43
26 8 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTAATATATTATTTTAATTTTTTA
Found at i:570729 original size:19 final size:20
Alignment explanation
Indices: 570691--570737 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
570681 TTAAAAATAA
*
570691 ATTAATTATTAAATAAATATT
1 ATTAA-TATCAAATAAATATT
570712 ATTAATATCAAA-AAATATT
1 ATTAATATCAAATAAATATT
*
570731 TTTAATA
1 ATTAATA
570738 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.54
20 6 0.25
21 5 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAATATCAAATAAATATT
Found at i:580125 original size:9 final size:9
Alignment explanation
Indices: 580100--580141 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
580090 TCATTCAATC
*
580100 ATTAAAATT
1 ATTAAAAAT
580109 ATTTAAAAAT
1 A-TTAAAAAT
580119 ATTAAAAAT
1 ATTAAAAAT
*
580128 AATAAAAAT
1 ATTAAAAAT
580137 -TTAAA
1 ATTAAA
580142 GATAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 4 0.14
9 17 0.59
10 8 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:580140 original size:17 final size:18
Alignment explanation
Indices: 580112--580147 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
580102 TAAAATTATT
580112 TAAAAATATTAAAAATAA
1 TAAAAATATTAAAAATAA
*
580130 TAAAAAT-TTAAAGATAA
1 TAAAAATATTAAAAATAA
580147 T
1 T
580148 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAAATATTAAAAATAA
Found at i:580645 original size:13 final size:14
Alignment explanation
Indices: 580621--580649 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
580611 TGATATATAA
580621 ATAAATTTTTTTAT
1 ATAAATTTTTTTAT
580635 ATAAA-TTTTTTAT
1 ATAAATTTTTTTAT
580648 AT
1 AT
580650 TTATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATAAATTTTTTTAT
Found at i:581103 original size:15 final size:15
Alignment explanation
Indices: 581080--581113 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
581070 ATAAAATATC
581080 AAAACAACTAATAAAT
1 AAAACAACTAA-AAAT
581096 AAAA-AACTAAAAAT
1 AAAACAACTAAAAAT
581110 AAAA
1 AAAA
581114 GCTTACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 6 0.33
16 4 0.22
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAACAACTAAAAAT
Found at i:581650 original size:11 final size:11
Alignment explanation
Indices: 581630--581662 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
581620 ATTTTTAATT
581630 TTTAATTTAAA
1 TTTAATTTAAA
*
581641 TTTAAATTAAA
1 TTTAATTTAAA
581652 TTTAATTTAAA
1 TTTAATTTAAA
581663 AACTCGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:587533 original size:24 final size:24
Alignment explanation
Indices: 587501--587549 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
587491 GATCTTATTC
587501 TGTTTTCGCCCACCTTTTAGTCTT
1 TGTTTTCGCCCACCTTTTAGTCTT
587525 TGTTTTCGCCCACCTTTTAGTCTT
1 TGTTTTCGCCCACCTTTTAGTCTT
587549 T
1 T
587550 CTTCTGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.29, G:0.12, T:0.51
Consensus pattern (24 bp):
TGTTTTCGCCCACCTTTTAGTCTT
Found at i:587984 original size:16 final size:17
Alignment explanation
Indices: 587954--587989 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
587944 ATATTTTTAT
587954 TTATTTTATAATTTAAAA
1 TTATTTTAT-ATTTAAAA
587972 TTATTTTAT-TTTAAAA
1 TTATTTTATATTTAAAA
587988 TT
1 TT
587990 TATAATCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTTTATATTTAAAA
Found at i:588286 original size:2 final size:2
Alignment explanation
Indices: 588279--588307 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
588269 GATTATTCTT
588279 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 T
588308 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:597350 original size:13 final size:13
Alignment explanation
Indices: 597332--597359 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
597322 TCTCCACAAA
597332 CTTCATCATCTGT
1 CTTCATCATCTGT
597345 CTTCATCATCTGT
1 CTTCATCATCTGT
597358 CT
1 CT
597360 ACATTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.32, G:0.07, T:0.46
Consensus pattern (13 bp):
CTTCATCATCTGT
Found at i:598925 original size:39 final size:37
Alignment explanation
Indices: 598873--598966 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 37
598863 TTATTATAAA
*
598873 AATATT-TTAATAAATTAATAATTAGTAAAATAAAATTAT
1 AATATTATT-ATAAATTAA-AATTA-TAAAATAAAAATAT
**
598912 AATATTATTATAAATATAAAATTATATTATAAAAATAT
1 AATATTATTATAAAT-TAAAATTATAAAATAAAAATAT
598950 AA-A-TATTAT-AATTAAAA
1 AATATTATTATAAATTAAAA
598967 ATTTTATCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
34 5 0.10
35 3 0.06
36 6 0.12
37 1 0.02
38 13 0.26
39 17 0.34
40 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (37 bp):
AATATTATTATAAATTAAAATTATAAAATAAAAATAT
Found at i:598930 original size:25 final size:25
Alignment explanation
Indices: 598893--598961 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
598883 TAAATTAATA
598893 ATTAGTAAA-ATAAAATTATAATATT
1 ATTA-TAAATATAAAATTATAATATT
598918 ATTATAAATATAAAA-T-T-ATATT
1 ATTATAAATATAAAATTATAATATT
*
598940 A-TAAAAATATAAATATTATAAT
1 ATTATAAATATAAA-ATTATAAT
598962 TAAAAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
21 11 0.29
22 7 0.18
23 2 0.05
24 6 0.16
25 12 0.32
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (25 bp):
ATTATAAATATAAAATTATAATATT
Found at i:598938 original size:22 final size:22
Alignment explanation
Indices: 598899--598968 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 22
598889 AATAATTAGT
*
598899 AAAATA-AAATTATAATATTATTA
1 AAAATATAAA-TATTATATTA-TA
*
598922 TAAATATAAA-ATTATATTATA
1 AAAATATAAATATTATATTATA
*
598943 AAAATATAAATATTATAAT-TA
1 AAAATATAAATATTATATTATA
598964 AAAAT
1 AAAAT
598969 TTTATCCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 18 0.44
22 15 0.37
23 5 0.12
24 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATAAATATTATATTATA
Found at i:598939 original size:19 final size:21
Alignment explanation
Indices: 598893--598968 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 21
598883 TAAATTAATA
*
598893 ATTAGTAAAATA-AAATTATAAT
1 ATTA-TAAAATATAAA-TATTAT
598915 ATTATTATAAATATAAA-ATTAT
1 ATTA-TA-AAATATAAATATTAT
598937 ATTATAAAAATATAAATATTAT
1 ATTAT-AAAATATAAATATTAT
598959 AATTA-AAAAT
1 -ATTATAAAAT
598969 TTTATCCAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
21 15 0.32
22 20 0.43
23 9 0.19
24 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
ATTATAAAATATAAATATTAT
Found at i:599084 original size:54 final size:55
Alignment explanation
Indices: 599020--599123 Score: 183
Period size: 55 Copynumber: 1.9 Consensus size: 55
599010 TCAAAACTTG
*
599020 ATCTA-TTTTTTAAACGAATTTTATTATTTTGTTTAAACTTATTTTTCAATCGTA
1 ATCTATTTTTTTAAACGAATTTTATTATTTTATTTAAACTTATTTTTCAATCGTA
*
599074 ATCTATTTTTTTAAACGAATTTTATTATTTTATTTAAATTTATTTTTCAA
1 ATCTATTTTTTTAAACGAATTTTATTATTTTATTTAAACTTATTTTTCAA
599124 CTATAATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 5 0.11
55 42 0.89
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.58
Consensus pattern (55 bp):
ATCTATTTTTTTAAACGAATTTTATTATTTTATTTAAACTTATTTTTCAATCGTA
Found at i:599220 original size:16 final size:16
Alignment explanation
Indices: 599201--599235 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
599191 ACGAGGGAGC
*
599201 ACTACTGTTAAGGATT
1 ACTACTGATAAGGATT
599217 ACTACTGATAAGGATT
1 ACTACTGATAAGGATT
599233 ACT
1 ACT
599236 GCTAGAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (16 bp):
ACTACTGATAAGGATT
Found at i:601497 original size:16 final size:16
Alignment explanation
Indices: 601478--601534 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
601468 TAATTTATAT
601478 TAATAATAAAAATTTA
1 TAATAATAAAAATTTA
* *
601494 TAATTATAAATAATAATA
1 TAATAATAAA-AAT-TTA
*
601512 TAATAA-AAAAA-TAA
1 TAATAATAAAAATTTA
601526 TAATAATAA
1 TAATAATAA
601535 TTTATTATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 7 0.21
15 2 0.06
16 11 0.33
17 6 0.18
18 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATAATAAAAATTTA
Found at i:601613 original size:24 final size:26
Alignment explanation
Indices: 601586--601647 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
601576 TTTAATTTTA
*
601586 TTTATAAATTAAAA-A-TTTAAAAAT
1 TTTATAAATAAAAATATTTTAAAAAT
601610 TTTAT-AATAAAAATATTTTAAAAAT
1 TTTATAAATAAAAATATTTTAAAAAT
*
601635 TATTAAAAATAAA
1 T-TTATAAATAAA
601648 TTTTTTATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 7 0.22
24 6 0.19
25 10 0.31
26 3 0.09
27 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTATAAATAAAAATATTTTAAAAAT
Found at i:602680 original size:80 final size:80
Alignment explanation
Indices: 602547--602706 Score: 230
Period size: 80 Copynumber: 2.0 Consensus size: 80
602537 AGATATTTTT
* *
602547 ATTAGTCACCATCCTACTGCAATGGATACTTATTAACGGATGTAATCATTGTTTCTAAGTTTGCG
1 ATTAGTCACCATCCTACTGCAATCGATACTTATTAACGGATGTAATCATTGTTTCTAAGTTTGCA
602612 TAGGGGATCTGTGGA
66 TAGGGGATCTGTGGA
* * * * * * * *
602627 ATTAGTTACCATCTTACTGCAGTCGATATTTATTAACTGATTTGATCATTGTTTTTAAGTTTGCA
1 ATTAGTCACCATCCTACTGCAATCGATACTTATTAACGGATGTAATCATTGTTTCTAAGTTTGCA
602692 TAGGGGATCTGTGGA
66 TAGGGGATCTGTGGA
602707 CTGGATAGTC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (80 bp):
ATTAGTCACCATCCTACTGCAATCGATACTTATTAACGGATGTAATCATTGTTTCTAAGTTTGCA
TAGGGGATCTGTGGA
Found at i:603662 original size:19 final size:19
Alignment explanation
Indices: 603638--603692 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
603628 TGATAAATTA
603638 ATATTATTTTTATATTATT
1 ATATTATTTTTATATTATT
** *
603657 ATATTATAATTATTTTATT
1 ATATTATTTTTATATTATT
*
603676 ATTTTATATTTT-TATTA
1 ATATTAT-TTTTATATTA
603693 ATTTAATATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATTATTTTTATATTATT
Found at i:603682 original size:24 final size:24
Alignment explanation
Indices: 603640--603705 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
603630 ATAAATTAAT
603640 ATTATTTT-TATATTATTATATTATA
1 ATTATTTTAT-TATT-TTATATTATA
* *
603665 ATTATTTTATTATTTTATATTTTT
1 ATTATTTTATTATTTTATATTATA
* *
603689 ATTAATTTAATATTTTA
1 ATTATTTTATTATTTTA
603706 CATAATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 23 0.64
25 12 0.33
26 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTATTTTATTATTTTATATTATA
Found at i:603696 original size:17 final size:16
Alignment explanation
Indices: 603639--603704 Score: 55
Period size: 16 Copynumber: 4.0 Consensus size: 16
603629 GATAAATTAA
* *
603639 TATTATTTTTATATTAT
1 TATTA-TTTAATATTTT
603656 TA-TATTATAAT-TATTT
1 TATTATT-TAATAT-TTT
*
603672 TATTATTTTATATTTT
1 TATTATTTAATATTTT
603688 TATTAATTTAATATTTT
1 TATT-ATTTAATATTTT
603705 ACATAATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
15 3 0.08
16 19 0.47
17 18 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATTTAATATTTT
Found at i:603705 original size:16 final size:16
Alignment explanation
Indices: 603652--603705 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
603642 TATTTTTATA
603652 TTATTATATTATAATTATT
1 TTATTA-ATT-TAA-TATT
*
603671 TTATT-ATTTTATATTT
1 TTATTAATTTAATA-TT
603687 TTATTAATTTAATATT
1 TTATTAATTTAATATT
603703 TTA
1 TTA
603706 CATAATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 2 0.06
16 14 0.45
17 10 0.32
19 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTAATTTAATATT
Found at i:605233 original size:18 final size:18
Alignment explanation
Indices: 605159--605252 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
605149 TTATAATTAA
*
605159 ATTTA-AAA-TTTGATAT
1 ATTTATAAATTTTAATAT
605175 ATTTATATAAATTTTAATAT
1 A-TT-TATAAATTTTAATAT
**
605195 ATCAAT-AA-TTT-AT-T
1 ATTTATAAATTTTAATAT
*
605209 TTTTATAAATTTTAATAT
1 ATTTATAAATTTTAATAT
* *
605227 ATTTATAAATTCATATTAT
1 ATTTATAAATT-TTAATAT
605246 ATTTATA
1 ATTTATA
605253 TTTTTTATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
14 4 0.07
15 4 0.07
16 7 0.12
17 6 0.10
18 15 0.25
19 16 0.27
20 8 0.13
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (18 bp):
ATTTATAAATTTTAATAT
Found at i:605248 original size:19 final size:18
Alignment explanation
Indices: 605148--605252 Score: 60
Period size: 18 Copynumber: 5.9 Consensus size: 18
605138 TATTATTTTT
*
605148 ATTATAATTAAATTTA-AA
1 ATTATAA-TATATTTATAA
*
605166 ATT-TGATATATTTATATAA
1 ATTATAATATA-TT-TATAA
* **
605185 ATTTTAATATATCAAT-A
1 ATTATAATATATTTATAA
*
605202 ATT-T-AT-TTTTTATAA
1 ATTATAATATATTTATAA
*
605217 ATTTTAATATATTTATAA
1 ATTATAATATATTTATAA
*
605235 ATTCATATTATATTTATA
1 ATT-ATAATATATTTATA
605253 TTTTTTATAT
Statistics
Matches: 67, Mismatches: 11, Indels: 17
0.71 0.12 0.18
Matches are distributed among these distances:
14 4 0.06
15 6 0.09
16 5 0.07
17 10 0.15
18 18 0.27
19 18 0.27
20 6 0.09
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (18 bp):
ATTATAATATATTTATAA
Found at i:605739 original size:24 final size:24
Alignment explanation
Indices: 605694--605739 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
605684 TTGTCTATCC
* *
605694 ATATTATATTATATAATTATATTT
1 ATATTATAATATATAATGATATTT
605718 ATATTATAATATATTAA-GATAT
1 ATATTATAATATA-TAATGATAT
605740 AAAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATATTATAATATATAATGATATTT
Found at i:606065 original size:13 final size:13
Alignment explanation
Indices: 606047--606071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
606037 AGAGCTTATG
606047 TGTTTATATTTTA
1 TGTTTATATTTTA
606060 TGTTTATATTTT
1 TGTTTATATTTT
606072 TTTAATTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TGTTTATATTTTA
Found at i:606330 original size:36 final size:37
Alignment explanation
Indices: 606290--606365 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 37
606280 AATCATGTCA
* *
606290 TATTTATATTATTTTTATATTATGTTTTAATTC-TTT
1 TATTTATATTATTTTGATATTATATTTTAATTCATTT
* * *
606326 TATTTATGTTATTTTGGTATTGTATTTTAATTCATTT
1 TATTTATATTATTTTGATATTATATTTTAATTCATTT
606363 TAT
1 TAT
606366 ATTTTGTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 28 0.82
37 6 0.18
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.67
Consensus pattern (37 bp):
TATTTATATTATTTTGATATTATATTTTAATTCATTT
Found at i:611427 original size:18 final size:18
Alignment explanation
Indices: 611404--611441 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
611394 TTAGATTATA
611404 ATTTAAAAAAATTATTTT
1 ATTTAAAAAAATTATTTT
**
611422 ATTTAAAAACTTTATTTT
1 ATTTAAAAAAATTATTTT
611440 AT
1 AT
611442 ATTGAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAAAAAATTATTTT
Found at i:612102 original size:32 final size:34
Alignment explanation
Indices: 612057--612120 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
612047 ATATTCAATA
*
612057 AATTATATATTTATTTAAATTTTGATATGTTAAT
1 AATTATATATTTATATAAATTTTGATATGTTAAT
* *
612091 AATT-TAT-TTTATATAGATTTTGATGTGTTA
1 AATTATATATTTATATAAATTTTGATATGTTA
612121 GTCTATTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 20 0.74
33 3 0.11
34 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (34 bp):
AATTATATATTTATATAAATTTTGATATGTTAAT
Found at i:615168 original size:9 final size:9
Alignment explanation
Indices: 615145--615191 Score: 53
Period size: 8 Copynumber: 5.1 Consensus size: 9
615135 AAATTATAAA
615145 TTTATATAAT
1 TTTATAT-AT
615155 ATTTATATAT
1 -TTTATATAT
615165 TTTATATA-
1 TTTATATAT
615173 TTTATAT-T
1 TTTATATAT
615181 TTTATCATAT
1 TTTAT-ATAT
615191 T
1 T
615192 CATTTTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 12 0.36
9 10 0.30
10 4 0.12
11 7 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTATATAT
Found at i:615175 original size:17 final size:18
Alignment explanation
Indices: 615138--615191 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
615128 ATTTAAAAAA
*
615138 TTATAAATTTATATAATAT
1 TTATATATTT-TATAATAT
615157 TTATATATTTTAT-ATAT
1 TTATATATTTTATAATAT
*
615174 TTATAT-TTTTATCATAT
1 TTATATATTTTATAATAT
615191 T
1 T
615192 CATTTTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 6 0.18
17 15 0.45
18 3 0.09
19 9 0.27
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATATTTTATAATAT
Found at i:615178 original size:15 final size:16
Alignment explanation
Indices: 615160--615200 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
615150 ATAATATTTA
615160 TATATTTTAT-ATATT
1 TATATTTTATCATATT
615175 TATATTTTTATCATATT
1 TATA-TTTTATCATATT
*
615192 CAT-TTTTAT
1 TATATTTTAT
615201 GTTATGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 6 0.26
17 7 0.30
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (16 bp):
TATATTTTATCATATT
Found at i:616966 original size:29 final size:27
Alignment explanation
Indices: 616924--616978 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
616914 TTCATTATTT
*
616924 AATTTTTAAATAATATGTTTAAAATAATA
1 AATTTTTAAATAAT-T-TATAAAATAATA
* *
616953 AATTTTTTATTAATTTATAAAATAAT
1 AATTTTTAAATAATTTATAAAATAAT
616979 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 1 0.04
29 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
AATTTTTAAATAATTTATAAAATAATA
Found at i:616984 original size:29 final size:28
Alignment explanation
Indices: 616941--617010 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
616931 AAATAATATG
*
616941 TTTAAAATAA-T-AAATTT-TTTATTAAT
1 TTTAAAATAATTAAAATTTAATT-TTAAT
616967 TTATAAAATAATTAAAATTTAATTTTAAT
1 TT-TAAAATAATTAAAATTTAATTTTAAT
616996 TTTAAATATAATTAA
1 TTTAAA-ATAATTAA
617011 TTATTATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 2 0.05
27 8 0.21
28 5 0.13
29 21 0.55
30 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTAAAATAATTAAAATTTAATTTTAAT
Found at i:616990 original size:5 final size:5
Alignment explanation
Indices: 616982--617048 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
616972 AAATAATTAA
* * **
616982 AATTT AATTTT AATTTT AAATAT AA-TT AATTAT TATTT AATAA AATTT
1 AATTT AA-TTT AA-TTT -AATTT AATTT AATT-T AATTT AATTT AATTT
617030 AATTT AATTT AATTT AATT
1 AATTT AATTT AATTT AATT
617049 ACAAATTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.06
5 30 0.60
6 15 0.30
7 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:617012 original size:27 final size:26
Alignment explanation
Indices: 616941--617018 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 26
616931 AAATAATATG
* *
616941 TTTAAAATAATAAATTTTTTATTAAT
1 TTTAAAATAATTAATTTATTATTAAT
616967 TTATAAAATAATTAAAATTTAATT-TTAAT
1 TT-TAAAATAATT--AATTT-ATTATTAAT
616996 TTTAAATATAATTAA-TTATTATT
1 TTTAAA-ATAATTAATTTATTATT
617019 TAATAAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
25 3 0.07
26 6 0.14
27 11 0.25
28 4 0.09
29 18 0.41
30 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTAAAATAATTAATTTATTATTAAT
Found at i:617024 original size:47 final size:48
Alignment explanation
Indices: 616973--617084 Score: 115
Period size: 48 Copynumber: 2.3 Consensus size: 48
616963 TAATTTATAA
*
616973 AATAATTAAAATTTAATTTTAATTTTAAATA-TAATT-AATTATTATT-T
1 AATAATTAAAATTTAA-TTTAA-TTTAAATACAAATTAAATTATTATTAT
* * *
617020 AATAAAATT-TAATTTAATTTAATTTAATTACAAATTAAATTTTTATTAAT
1 AAT--AATTAAAATTTAATTTAATTTAAATACAAATTAAATTATTATT-AT
617070 AATAATTAAAATTTA
1 AATAATTAAAATTTA
617085 TAAAATAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
46 7 0.13
47 12 0.23
48 20 0.38
49 10 0.19
50 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (48 bp):
AATAATTAAAATTTAATTTAATTTAAATACAAATTAAATTATTATTAT
Found at i:617028 original size:20 final size:20
Alignment explanation
Indices: 616979--617042 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
616969 ATAAAATAAT
616979 TAAAATTTAATTTTAATTTTAAA
1 TAAAATTTAA-TTTAA-TTT-AA
* *
617002 TATAA-TTAATTATTATTTAA
1 TAAAATTTAATT-TAATTTAA
617022 TAAAATTTAATTTAATTTAA
1 TAAAATTTAATTTAATTTAA
617042 T
1 T
617043 TTAATTACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 14 0.40
21 11 0.31
22 6 0.17
23 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAATTTAATTTAATTTAA
Found at i:617368 original size:17 final size:17
Alignment explanation
Indices: 617346--617378 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
617336 GGAGTCACTT
617346 TCTCTCATTTA-ATTTTC
1 TCTCTC-TTTACATTTTC
617363 TCTCTCTTTACATTTT
1 TCTCTCTTTACATTTT
617379 TGCAATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (17 bp):
TCTCTCTTTACATTTTC
Found at i:626128 original size:15 final size:15
Alignment explanation
Indices: 626108--626169 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 15
626098 CGAAGATAAA
626108 AAAAAATTATAAATT
1 AAAAAATTATAAATT
626123 AAAAAATT-TAAATT
1 AAAAAATTATAAATT
*
626137 TAAAAA--AT-AATT
1 AAAAAATTATAAATT
626149 AAATAAATTAATTAAATT
1 AAA-AAATT-A-TAAATT
626167 AAA
1 AAA
626170 TCTTAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
12 6 0.16
13 4 0.11
14 11 0.29
15 8 0.21
16 1 0.03
17 1 0.03
18 7 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAATTATAAATT
Found at i:626134 original size:14 final size:16
Alignment explanation
Indices: 626108--626144 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
626098 CGAAGATAAA
626108 AAAAAATTATAAA-TT
1 AAAAAATTATAAATTT
626123 AAAAAATT-TAAATTT
1 AAAAAATTATAAATTT
626138 AAAAAAT
1 AAAAAAT
626145 AATTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAAATTATAAATTT
Found at i:626169 original size:35 final size:34
Alignment explanation
Indices: 626104--626175 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
626094 GATTCGAAGA
626104 TAAAAAAAAATTATAAATTAAAAAATTTAAAT-T
1 TAAAAAAAAATTATAAATTAAAAAATTTAAATCT
* *
626137 TAAAAAATAATTAAATAAATTAATTAAA-TTAAATCT
1 TAAAAAAAAATT--ATAAATTAA-AAAATTTAAATCT
626173 TAA
1 TAA
626176 TTTTTTTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 11 0.33
35 15 0.45
36 7 0.21
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (34 bp):
TAAAAAAAAATTATAAATTAAAAAATTTAAATCT
Found at i:626803 original size:23 final size:23
Alignment explanation
Indices: 626751--626811 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
626741 CTTATATTTT
* *
626751 AATTTTTAATTATTTACATTATTA
1 AATTTTTAATT-TTTACATAAATA
626775 AA-TTTTAATTTTTATC-TAAATA
1 AATTTTTAATTTTTA-CATAAATA
*
626797 AATTTTTAACTTTTA
1 AATTTTTAATTTTTA
626812 ACTTATACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 10 0.31
23 20 0.62
24 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTTTTAATTTTTACATAAATA
Found at i:632112 original size:18 final size:20
Alignment explanation
Indices: 632074--632110 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
632064 ATAATTAGAG
*
632074 TCGATAAAATTGATCTAAAT
1 TCGATAAAATTCATCTAAAT
632094 TCGA-AAAATTCATCTAA
1 TCGATAAAATTCATCTAA
632111 TTTATCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (20 bp):
TCGATAAAATTCATCTAAAT
Found at i:633774 original size:24 final size:25
Alignment explanation
Indices: 633743--633800 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
633733 GTAACCACCA
*
633743 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
633767 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
633793 TTGTTGAC
1 TTGTTGAC
633801 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:638343 original size:24 final size:25
Alignment explanation
Indices: 638312--638369 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
638302 GTAACCACCA
*
638312 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
638336 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
638362 TTGTTGAC
1 TTGTTGAC
638370 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:639218 original size:21 final size:20
Alignment explanation
Indices: 639166--639220 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
639156 ATAATTTGAG
* *
639166 TATTTATATTTTATTTTATA
1 TATTTATATTTTATTTAAAA
*
639186 TTTTTATAATTTTATTTAAAA
1 TATTTAT-ATTTTATTTAAAA
639207 TATTATATATTTTA
1 TATT-TATATTTTA
639221 ATATATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 20 0.69
22 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTATATTTTATTTAAAA
Found at i:639823 original size:21 final size:22
Alignment explanation
Indices: 639793--639837 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
639783 TAATTATATA
639793 ATAATAAATATAACTTTA-TAAT
1 ATAATAAATATAA-TTTATTAAT
639815 ATAAT-AATATAATTTATTAAT
1 ATAATAAATATAATTTATTAAT
639836 AT
1 AT
639838 TATATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATAAATATAATTTATTAAT
Found at i:639825 original size:13 final size:13
Alignment explanation
Indices: 639788--639842 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
639778 CATATTAATT
639788 ATATAATAATA-A
1 ATATAATAATATA
*
639800 ATATAACT-TTATA
1 ATATAA-TAATATA
639813 ATATAATAATATA
1 ATATAATAATATA
* * *
639826 ATTTATTAATATT
1 ATATAATAATATA
639839 ATAT
1 ATAT
639843 TAAATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
12 9 0.26
13 25 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATAATAATATA
Found at i:641203 original size:2 final size:2
Alignment explanation
Indices: 641196--641231 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
641186 CTCATGAATA
641196 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
641232 GGATACTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:643369 original size:18 final size:18
Alignment explanation
Indices: 643346--643380 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
643336 TGTATACATG
643346 AACTTATTCTCTTGTATA
1 AACTTATTCTCTTGTATA
643364 AACTTATTCTCTTGTAT
1 AACTTATTCTCTTGTAT
643381 TTATACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (18 bp):
AACTTATTCTCTTGTATA
Found at i:644988 original size:28 final size:27
Alignment explanation
Indices: 644933--644998 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
644923 GTCACCCATT
644933 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
* *
644960 TGTTTGTTAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
644988 TATTTGTCAAA
1 TATTTGTCAAA
644999 TATGAAGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.58
28 13 0.39
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:645144 original size:11 final size:13
Alignment explanation
Indices: 645113--645142 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
645103 TCTTAAGCAT
645113 CTCTCTTGTATCC
1 CTCTCTTGTATCC
645126 CTCTCTTGTATCC
1 CTCTCTTGTATCC
645139 CTCT
1 CTCT
645143 TGAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.40, G:0.07, T:0.47
Consensus pattern (13 bp):
CTCTCTTGTATCC
Found at i:646889 original size:27 final size:27
Alignment explanation
Indices: 646832--646920 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 27
646822 CACCCATTTG
*
646832 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTGTA
* *
646859 TTTGTTAAAAATGGTGGTTCCTTTT-TA
1 TTTGTCAAAAATGGTGGTT-ATTTTGTA
* * * *
646886 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTGTA
646911 TTTGTCAAAA
1 TTTGTCAAAA
646921 TTTATGGCTA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 14 0.27
27 34 0.65
28 4 0.08
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTGTA
Found at i:648782 original size:27 final size:27
Alignment explanation
Indices: 648712--648785 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 27
648702 ATAAGCCATA
* * *
648712 ATTTTTTACAAACAAAAAAGGATCCACC
1 ATTTTTGACAAAC-ACAAAGGAACCACC
* *
648740 ATTTTTGAC-AATACAAAGTAACCACC
1 ATTTTTGACAAACACAAAGGAACCACC
648766 ATTTTTGACAAACACAAAGG
1 ATTTTTGACAAACACAAAGG
648786 GTGGCTTTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 20 0.53
27 10 0.26
28 8 0.21
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (27 bp):
ATTTTTGACAAACACAAAGGAACCACC
Found at i:651869 original size:27 final size:27
Alignment explanation
Indices: 651811--651874 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
651801 CAAAAGCCAC
* * *
651811 CCTTTGTGTTTGTCAAAAATGGTGGTT
1 CCTTTGTATTTGTCAAAAATGGTAGAT
*
651838 ACTTTGTATTTGTCAAAAATGGTAGAT
1 CCTTTGTATTTGTCAAAAATGGTAGAT
*
651865 CCTTTTTATT
1 CCTTTGTATT
651875 GCAAAATAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (27 bp):
CCTTTGTATTTGTCAAAAATGGTAGAT
Found at i:653630 original size:14 final size:15
Alignment explanation
Indices: 653611--653644 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
653601 GTGGACTTAG
653611 GTTTA-GCGTAATTA
1 GTTTAGGCGTAATTA
*
653625 GTTTAGGGGTAATTA
1 GTTTAGGCGTAATTA
653640 GTTTA
1 GTTTA
653645 AAGTCCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.44
Consensus pattern (15 bp):
GTTTAGGCGTAATTA
Found at i:658543 original size:15 final size:15
Alignment explanation
Indices: 658525--658565 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
658515 TGATCCTGTC
658525 CATCCACCACCAGTG
1 CATCCACCACCAGTG
* *
658540 CATCCACAACCCGTG
1 CATCCACCACCAGTG
*
658555 CATCCATCACC
1 CATCCACCACC
658566 TGTTTACCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.49, G:0.10, T:0.15
Consensus pattern (15 bp):
CATCCACCACCAGTG
Found at i:658685 original size:30 final size:28
Alignment explanation
Indices: 658651--658719 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
658641 ATTTTATGCT
*
658651 TACCCATCATATTTCCCTACTCAATCTCCA
1 TACCCATCATA-TT-CCTACTCAACCTCCA
* *
658681 TACCCGTCATA-TCCTACTCAACCTCTA
1 TACCCATCATATTCCTACTCAACCTCCA
*
658708 TACCCAACATAT
1 TACCCATCATAT
658720 CCTGCCACGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 22 0.67
28 1 0.03
30 10 0.30
ACGTcount: A:0.29, C:0.39, G:0.01, T:0.30
Consensus pattern (28 bp):
TACCCATCATATTCCTACTCAACCTCCA
Found at i:658710 original size:27 final size:27
Alignment explanation
Indices: 658666--658722 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
658656 ATCATATTTC
* **
658666 CCTACTCAATCTCCATACCCGTCATAT
1 CCTACTCAACCTCCATACCCAACATAT
*
658693 CCTACTCAACCTCTATACCCAACATAT
1 CCTACTCAACCTCCATACCCAACATAT
658720 CCT
1 CCT
658723 GCCACGACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.42, G:0.02, T:0.28
Consensus pattern (27 bp):
CCTACTCAACCTCCATACCCAACATAT
Found at i:662802 original size:20 final size:21
Alignment explanation
Indices: 662739--662802 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
662729 TTTCAATAAG
* *
662739 ATAACTAGTATAATAAAAT-T
1 ATAACTATTATTATAAAATAT
662759 ATAACTATTATTATAAAATTTAT
1 ATAACTATTATTATAAAA--TAT
*
662782 ATAATTA-TATTATAAAATAT
1 ATAACTATTATTATAAAATAT
662802 A
1 A
662803 ATTTTTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 20 0.53
22 11 0.29
23 7 0.18
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (21 bp):
ATAACTATTATTATAAAATAT
Found at i:666025 original size:50 final size:50
Alignment explanation
Indices: 665955--666264 Score: 449
Period size: 50 Copynumber: 6.2 Consensus size: 50
665945 AGTTGCTTAG
* * *
665955 AGTCAATAATTACGGCCACCTCTCTCTATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * * *
666005 AATCAACAATTATGGTCACCTCTCTCAATTGTTAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
**
666055 AGTCAACAATTATAGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
666105 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
666155 AGTCAACAATTACGGCCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* ** * * *
666205 AGTCAATAATTACGATCATCTCTCTCGATTTTCAAAGGTCGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
666255 AATCAACAAT
1 AGTCAACAAT
666265 AATAATACCT
Statistics
Matches: 234, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 234 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:670706 original size:50 final size:50
Alignment explanation
Indices: 670645--670854 Score: 251
Period size: 50 Copynumber: 4.2 Consensus size: 50
670635 AGTTGCTTAG
* * * *
670645 AGTCAACAATTACGGCCACGTCTCTCTATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
* * * * *
670695 AGTCAATAATTATGGTCACCTCTCTCAATTCTTAAAGGTTGGTGAAAAAT
1 AGTCAACAATTACGGTCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
* ** * *
670745 CA-TCAACAATTATGGTCACCTCTCTTTATTGTTAAAGGTTGGTGAAGTAT
1 -AGTCAACAATTACGGTCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
* *
670795 AGTCAACAATTACGGTCACCTCTCTCAATTGTCAAAGGTTAGTGAACAAT
1 AGTCAACAATTACGGTCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
*
670845 AATCAACAAT
1 AGTCAACAAT
670855 AGCAACACCT
Statistics
Matches: 136, Mismatches: 22, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
49 1 0.01
50 134 0.99
51 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
Found at i:670820 original size:100 final size:100
Alignment explanation
Indices: 670647--670854 Score: 290
Period size: 100 Copynumber: 2.1 Consensus size: 100
670637 TTGCTTAGAG
* * *
670647 TCAACAATTACGGCCACGTCTCTCTATTATCAAAGGTTGGTGAAGAATAGTCAATAATTATGGTC
1 TCAACAATTACGGCCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATAGTCAACAATTACGGTC
* * *
670712 ACCTCTCTCAATTCTTAAAGGTTGGTGAAAAATCA
66 ACCTCTCTCAATTCTCAAAGGTTAGTGAAAAATAA
* * * * * *
670747 TCAACAATTATGGTCACCTCTCTTTATTGTTAAAGGTTGGTGAAGTATAGTCAACAATTACGGTC
1 TCAACAATTACGGCCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATAGTCAACAATTACGGTC
* *
670812 ACCTCTCTCAATTGTCAAAGGTTAGTGAACAATAA
66 ACCTCTCTCAATTCTCAAAGGTTAGTGAAAAATAA
670847 TCAACAAT
1 TCAACAAT
670855 AGCAACACCT
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 94 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (100 bp):
TCAACAATTACGGCCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATAGTCAACAATTACGGTC
ACCTCTCTCAATTCTCAAAGGTTAGTGAAAAATAA
Found at i:672262 original size:20 final size:22
Alignment explanation
Indices: 672223--672263 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
672213 ATTACTTTAT
672223 TTCTAAAATGTAATTAAAAATA
1 TTCTAAAATGTAATTAAAAATA
* *
672245 TTCTAATATG-AATAAAAAA
1 TTCTAAAATGTAATTAAAAA
672264 AATTTCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (22 bp):
TTCTAAAATGTAATTAAAAATA
Found at i:681922 original size:23 final size:23
Alignment explanation
Indices: 681886--681929 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
681876 AGCCTTTGAC
* *
681886 AAAGCGTTTGTAATAATTCACTA
1 AAAGCCTTTATAATAATTCACTA
681909 AAAGCCTTTATAATAATTCAC
1 AAAGCCTTTATAATAATTCAC
681930 CAACCCAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (23 bp):
AAAGCCTTTATAATAATTCACTA
Found at i:692871 original size:13 final size:13
Alignment explanation
Indices: 692853--692877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
692843 ATACAAAGAT
692853 CAATGTATCGATG
1 CAATGTATCGATG
692866 CAATGTATCGAT
1 CAATGTATCGAT
692878 ACAACACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATG
Found at i:694853 original size:33 final size:33
Alignment explanation
Indices: 694811--694878 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
694801 TAGATTGTGT
*
694811 AAGTTGAATTCGATTTTGGACAAACTGTCGTAA
1 AAGTTGAATTCGATGTTGGACAAACTGTCGTAA
694844 AAGTTGAATTCGATGTTGGACAAACTGTCGTAA
1 AAGTTGAATTCGATGTTGGACAAACTGTCGTAA
694877 AA
1 AA
694879 ACTAGGAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (33 bp):
AAGTTGAATTCGATGTTGGACAAACTGTCGTAA
Found at i:697046 original size:20 final size:19
Alignment explanation
Indices: 697018--697061 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
697008 ACTAAATTAA
* *
697018 TTTTGTATATTTTCATATTT
1 TTTTATATAATTT-ATATTT
697038 TTTTATATAATTTATATTT
1 TTTTATATAATTTATATTT
697057 TTTTA
1 TTTTA
697062 ATTCGATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTATATAATTTATATTT
Found at i:698363 original size:20 final size:21
Alignment explanation
Indices: 698313--698363 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
698303 ACTAACATAG
698313 TAAAAT-TATAACTATTATTA
1 TAAAATATATAACTATTATTA
*
698333 TAAAATTTATATAATTA-TATTA
1 TAAAA--TATATAACTATTATTA
698355 TAAAATATA
1 TAAAATATA
698364 ATTTTTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 9 0.33
22 11 0.41
23 7 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATATATAACTATTATTA
Found at i:698711 original size:14 final size:15
Alignment explanation
Indices: 698692--698733 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 15
698682 GATGTTTTAA
698692 AATTTTAAAAAA-AT
1 AATTTTAAAAAATAT
698706 AATTTTAAAAAATAT
1 AATTTTAAAAAATAT
698721 AATATATTAAAAA
1 AAT-T-TTAAAAA
698734 TTTATTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.48
15 5 0.20
16 1 0.04
17 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTTTAAAAAATAT
Found at i:699886 original size:27 final size:27
Alignment explanation
Indices: 699845--699916 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
699835 TTGATTCGTA
*
699845 TTTATA-TTATAATTATATTTAAAATA-T
1 TTTATATTTAT-ATTATATTT-AAATACG
*
699872 TTTATATTTATATTA-ATTTTAATACG
1 TTTATATTTATATTATATTTAAATACG
*
699898 TTAATAATTTATATTATAT
1 TTTAT-ATTTATATTATAT
699917 ATAATTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.11
26 8 0.21
27 20 0.53
28 6 0.16
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTATATTTATATTATATTTAAATACG
Found at i:704747 original size:14 final size:14
Alignment explanation
Indices: 704728--704756 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
704718 ATTTATTATT
704728 TTTAAAATTTTTTC
1 TTTAAAATTTTTTC
704742 TTTAAAATTTTTTC
1 TTTAAAATTTTTTC
704756 T
1 T
704757 CTTTCTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTAAAATTTTTTC
Found at i:708417 original size:73 final size:72
Alignment explanation
Indices: 708277--708422 Score: 211
Period size: 73 Copynumber: 2.0 Consensus size: 72
708267 TGAACATTAT
* * *
708277 TATATTATATAGTAATTTCTTTATCTTGTTAAAACCCGTATTACTGGAAATGCAATGCAATGACT
1 TATATTATATAGTAATTTCTTTATCATGTTAAAACCCGTATTACTAGAAATGAAATGCAATGACT
708342 TTGAATA
66 TTGAATA
* * * * *
708349 TATATTATATAGTAATTTCTTGTATCATGTTAAAACCCGTATTCCTAGAACTGAAATGTAGTGGC
1 TATATTATATAGTAATTTCTT-TATCATGTTAAAACCCGTATTACTAGAAATGAAATGCAATGAC
708414 TTTGAATA
65 TTTGAATA
708422 T
1 T
708423 TAGAAAAACA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 21 0.32
73 44 0.68
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (72 bp):
TATATTATATAGTAATTTCTTTATCATGTTAAAACCCGTATTACTAGAAATGAAATGCAATGACT
TTGAATA
Found at i:710321 original size:2 final size:2
Alignment explanation
Indices: 710314--710338 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
710304 ACAATTTCAC
710314 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
710339 GAGAGAGAGA
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:711187 original size:12 final size:11
Alignment explanation
Indices: 711166--711236 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 11
711156 TAATGTTTAG
*
711166 ATTTAATATAT
1 ATTTAAAATAT
711177 ATTT-AAATAT
1 ATTTAAAATAT
* *
711187 AAATAAAAATAT
1 -ATTTAAAATAT
711199 AATTTTTAAAATAT
1 -A--TTTAAAATAT
711213 A--TAAAATA-
1 ATTTAAAATAT
711221 ATTTAAAATAT
1 ATTTAAAATAT
711232 ATTTA
1 ATTTA
711237 TTTATATTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
8 1 0.02
9 7 0.15
10 12 0.25
11 11 0.23
12 8 0.17
13 1 0.02
14 8 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAAAATAT
Found at i:711197 original size:24 final size:24
Alignment explanation
Indices: 711170--711218 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
711160 GTTTAGATTT
711170 AATAT-ATATTTAAATATAAATAAA
1 AATATAATATTTAAA-ATAAATAAA
* *
711194 AATATAATTTTTAAAATATATAAA
1 AATATAATATTTAAAATAAATAAA
711218 A
1 A
711219 TAATTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATATAATATTTAAAATAAATAAA
Found at i:714797 original size:2 final size:2
Alignment explanation
Indices: 714787--714824 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
714777 TATATATATA
714787 TG TG T- TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
714825 TTGTTCTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:715257 original size:15 final size:15
Alignment explanation
Indices: 715237--715266 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
715227 TCATATAGAT
715237 ATTTATTTTTAATTA
1 ATTTATTTTTAATTA
*
715252 ATTTATTTTTTATTA
1 ATTTATTTTTAATTA
715267 TACTTTAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTATTTTTAATTA
Found at i:716824 original size:14 final size:12
Alignment explanation
Indices: 716801--716853 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
716791 AACTTAACAC
716801 ATTT-TATA-AT
1 ATTTATATATAT
716811 ATTTATACTATA-
1 ATTTATA-TATAT
716823 ATATTATATATAT
1 AT-TTATATATAT
*
716836 ATATATATATAT
1 ATTTATATATAT
716848 ATTTAT
1 ATTTAT
716854 TCATCGTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 4 0.11
11 2 0.06
12 22 0.61
13 8 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:716834 original size:2 final size:2
Alignment explanation
Indices: 716805--716849 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
716795 TAACACATTT
*
716805 TA TA -A TA TT TA TA CTA TA -A TA T- 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
716845 TA TA T
1 TA TA T
716850 TTATTCATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 32 0.86
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:717586 original size:25 final size:26
Alignment explanation
Indices: 717522--717586 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 26
717512 TAATACATAA
*
717522 ATTTATATATTATTAATAAATCAAATG
1 ATTTATAT-TTATTAATAAATAAAATG
** *
717549 ATATTAT-CGTATTAA-AAATAAAATT
1 AT-TTATATTTATTAATAAATAAAATG
717574 ATTTATATTTATT
1 ATTTATATTTATT
717587 TTTAAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
24 4 0.13
25 14 0.47
26 6 0.20
27 2 0.07
28 4 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (26 bp):
ATTTATATTTATTAATAAATAAAATG
Found at i:717653 original size:39 final size:42
Alignment explanation
Indices: 717610--717691 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 42
717600 AAAGAGAAAG
*
717610 TATTATCTAATTTC-CTAATAATATA-AAA-ATATATT-TTAA
1 TATTATCCAA-TTCACTAATAATATATAAATATATATTATTAA
*
717649 TATTATCCGATTCACTAATAATATATAAATATATATTATTAA
1 TATTATCCAATTCACTAATAATATATAAATATATATTATTAA
717691 T
1 T
717692 GCATTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
38 3 0.08
39 19 0.51
40 3 0.08
41 7 0.19
42 5 0.14
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (42 bp):
TATTATCCAATTCACTAATAATATATAAATATATATTATTAA
Found at i:718267 original size:3 final size:3
Alignment explanation
Indices: 718261--718289 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
718251 TTTTTCTTTT
718261 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
718290 TCATTTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:720407 original size:44 final size:45
Alignment explanation
Indices: 720336--720424 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 45
720326 AACTAATCCG
* *
720336 AAATACTATATATTTAATTAAATAATATTATTTATTTTTTATTAT
1 AAATACTATATAATTAATTAAATAATATTATTTATATTTTATTAT
*
720381 AAATA-TATATAATTAATATAAA-AATATTTTTTATATTTTATTAT
1 AAATACTATATAATTAAT-TAAATAATATTATTTATATTTTATTAT
720425 TTTTAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 31 0.77
45 9 0.22
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (45 bp):
AAATACTATATAATTAATTAAATAATATTATTTATATTTTATTAT
Found at i:720872 original size:10 final size:10
Alignment explanation
Indices: 720836--720865 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
720826 AAATTTATTC
720836 ATAAATTAAA
1 ATAAATTAAA
720846 ATAAATTAAA
1 ATAAATTAAA
720856 ATAAATTAAA
1 ATAAATTAAA
720866 TTCAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAAATTAAA
Done.