Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 21 of 22
Found at i:3631625 original size:14 final size:14
Alignment explanation
Indices: 3631589--3631627 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
3631579 ATCATTAATT
* *
3631589 TTTAATTTTATTAG
1 TTTAATCTTATTAA
3631603 TTTAA-CTTATTAA
1 TTTAATCTTATTAA
3631616 TTTAATCTTATT
1 TTTAATCTTATT
3631628 TTTTTAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTAATCTTATTAA
Found at i:3631633 original size:14 final size:14
Alignment explanation
Indices: 3631588--3631634 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3631578 AATCATTAAT
*
3631588 TTTTAATTTTATTA
1 TTTTAATCTTATTA
*
3631602 GTTTAA-CTTATTA
1 TTTTAATCTTATTA
* *
3631615 ATTTAATCTTATTT
1 TTTTAATCTTATTA
3631629 TTTTAA
1 TTTTAA
3631635 CATTAGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (14 bp):
TTTTAATCTTATTA
Found at i:3631889 original size:3 final size:3
Alignment explanation
Indices: 3631883--3631910 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3631873 AGTAGCAATT
3631883 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3631911 TAATAAGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3632632 original size:13 final size:13
Alignment explanation
Indices: 3632614--3632638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3632604 AAGGTCATAT
3632614 TCAACTTTAAAAC
1 TCAACTTTAAAAC
3632627 TCAACTTTAAAA
1 TCAACTTTAAAA
3632639 AGTAACATAA
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
TCAACTTTAAAAC
Found at i:3642554 original size:16 final size:16
Alignment explanation
Indices: 3642535--3642567 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3642525 TACTTTTCCC
3642535 TTTTTT-CTTTTTTTT
1 TTTTTTACTTTTTTTT
3642550 TTTTTTACTTTTTTTT
1 TTTTTTACTTTTTTTT
3642566 TT
1 TT
3642568 GGATGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTTTACTTTTTTTT
Found at i:3644344 original size:16 final size:17
Alignment explanation
Indices: 3644316--3644347 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3644306 AAATATATAT
3644316 AATTTTATTATTTTTAA
1 AATTTTATTATTTTTAA
3644333 AATTTT-TTATTTTTA
1 AATTTTATTATTTTTA
3644348 TATCGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTTATTATTTTTAA
Found at i:3648153 original size:2 final size:2
Alignment explanation
Indices: 3648146--3648170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3648136 TGTATTATAT
3648146 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 T
3648171 TTTCTTTGGG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3650974 original size:2 final size:2
Alignment explanation
Indices: 3650967--3651007 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3650957 TTACAGATCA
*
3650967 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3651008 TTCATTTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3655275 original size:2 final size:2
Alignment explanation
Indices: 3655268--3655321 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3655258 AATTTGGGTG
3655268 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
3655310 TA TA TA TA TA TA
1 TA TA TA TA TA TA
3655322 AATTTTCAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3655363 original size:16 final size:17
Alignment explanation
Indices: 3655342--3655383 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3655332 CATGTGCGAC
3655342 AAAAAATAAAATT-TTT
1 AAAAAATAAAATTATTT
* **
3655358 AAAAAATTATTTTATTT
1 AAAAAATAAAATTATTT
3655375 AAAAAATAA
1 AAAAAATAA
3655384 TAAGTTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAAATAAAATTATTT
Found at i:3663479 original size:30 final size:29
Alignment explanation
Indices: 3663441--3663501 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
3663431 GCTTCTCTGA
*
3663441 TTGTTTGGATCCTGTCTATTCCCTTCAAT
1 TTGTTTGGATCCTGTCTACTCCCTTCAAT
*
3663470 TTGTGTTGGATCCTGTCTACTCCTTTCAAT
1 TTGT-TTGGATCCTGTCTACTCCCTTCAAT
3663500 TT
1 TT
3663502 TGACATGCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (29 bp):
TTGTTTGGATCCTGTCTACTCCCTTCAAT
Found at i:3668603 original size:14 final size:14
Alignment explanation
Indices: 3668586--3668616 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3668576 ATTAACATAA
3668586 AATAATATTATTTT
1 AATAATATTATTTT
*
3668600 AATAATTTTATTTT
1 AATAATATTATTTT
3668614 AAT
1 AAT
3668617 GAAAACATAA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATAATATTATTTT
Found at i:3668677 original size:11 final size:13
Alignment explanation
Indices: 3668661--3668697 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
3668651 AAAACTTAAC
3668661 ATATAA-AAAAT-
1 ATATAATAAAATA
3668672 ATATAATAATAATA
1 ATATAATAA-AATA
3668686 ATATAATAAAAT
1 ATATAATAAAAT
3668698 TTTAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.26
12 2 0.09
13 6 0.26
14 9 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAATAAAATA
Found at i:3669841 original size:19 final size:18
Alignment explanation
Indices: 3669792--3669841 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
3669782 ATATATAAAG
*
3669792 TATTGAATTGAGTTTAATAT
1 TATTGAATTAAG--TAATAT
3669812 TATTGAATTAAGTAATAT
1 TATTGAATTAAGTAATAT
*
3669830 TAATTTAATTAA
1 T-ATTGAATTAA
3669842 AAATATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (18 bp):
TATTGAATTAAGTAATAT
Found at i:3672759 original size:29 final size:29
Alignment explanation
Indices: 3672717--3672776 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3672707 TGCTAAACTA
3672717 TACAATCATGTCTCCATGTCAGTCTTTGT
1 TACAATCATGTCTCCATGTCAGTCTTTGT
3672746 TACAATCATGTCTCCATGTCAGTCTTTGT
1 TACAATCATGTCTCCATGTCAGTCTTTGT
3672775 TA
1 TA
3672777 TTTGCCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (29 bp):
TACAATCATGTCTCCATGTCAGTCTTTGT
Found at i:3675437 original size:19 final size:21
Alignment explanation
Indices: 3675410--3675451 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
3675400 ATAATTTTAA
3675410 TATATTTTAAT-AGTTTAT-AT
1 TATATTTT-ATGAGTTTATGAT
3675430 TATA-TTTATGAGTTTATGAT
1 TATATTTTATGAGTTTATGAT
3675450 TA
1 TA
3675452 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.10
19 10 0.50
20 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TATATTTTATGAGTTTATGAT
Found at i:3678586 original size:3 final size:3
Alignment explanation
Indices: 3678578--3678607 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3678568 AAAGTTTTTC
3678578 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3678608 AAAATTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3678831 original size:2 final size:2
Alignment explanation
Indices: 3678824--3678859 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3678814 TTGTCTCAGA
3678824 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
3678860 CCATACTTTT
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:3680356 original size:17 final size:17
Alignment explanation
Indices: 3680336--3680372 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3680326 AATATGAGTG
3680336 AATTAT-TAATATATAAA
1 AATTATATAA-ATATAAA
3680353 AATTATATAAATATAAA
1 AATTATATAAATATAAA
3680370 AAT
1 AAT
3680373 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTATATAAATATAAA
Found at i:3680372 original size:8 final size:8
Alignment explanation
Indices: 3680346--3680384 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
3680336 AATTATTAAT
3680346 ATATAAAA
1 ATATAAAA
*
3680354 ATTATATAA
1 A-TATAAAA
3680363 ATATAAAA
1 ATATAAAA
3680371 ATATAAAA
1 ATATAAAA
*
3680379 AAATAA
1 ATATAA
3680385 TTTACGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
ATATAAAA
Found at i:3682461 original size:2 final size:2
Alignment explanation
Indices: 3682454--3682498 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3682444 ATAAACCTTT
3682454 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
3682496 TA T
1 TA T
3682499 GAAGTAGCCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3687089 original size:17 final size:17
Alignment explanation
Indices: 3687058--3687152 Score: 50
Period size: 17 Copynumber: 5.3 Consensus size: 17
3687048 ATAGATGAAG
3687058 AATATAATA-ACAATAAA
1 AATATAATATA-AATAAA
*
3687075 AATATAATATAAATATA
1 AATATAATATAAATAAA
* *
3687092 TATAT-ATATGATATAAA
1 AATATAATAT-AAATAAA
* ** *
3687109 TATATTTTATAATCTAAA
1 AATATAATATAA-ATAAA
3687127 TAATATAAATATAAGTATAAA
1 -AATAT-AATATAA--ATAAA
3687148 AATAT
1 AATAT
3687153 TATCGCTGAG
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
16 4 0.07
17 29 0.48
18 8 0.13
19 4 0.07
20 10 0.17
21 5 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AATATAATATAAATAAA
Found at i:3687121 original size:39 final size:39
Alignment explanation
Indices: 3687077--3687153 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
3687067 ACAATAAAAA
* * *
3687077 TATAATATAAAT-ATATATATATATGATATAAATATATTT
1 TATAATATAAATAATATAAATATAAG-TATAAAAATATTT
*
3687116 TATAATCTAAATAATATAAATATAAGTATAAAAATATT
1 TATAATATAAATAATATAAATATAAGTATAAAAATATT
3687154 ATCGCTGAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 22 0.67
40 11 0.33
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (39 bp):
TATAATATAAATAATATAAATATAAGTATAAAAATATTT
Found at i:3687147 original size:12 final size:11
Alignment explanation
Indices: 3687069--3687147 Score: 55
Period size: 11 Copynumber: 7.7 Consensus size: 11
3687059 ATATAATAAC
*
3687069 AATAAAAATAT
1 AATATAAATAT
3687080 AATATAAATAT
1 AATATAAATAT
*
3687091 -ATATATATAT
1 AATATAAATAT
*
3687101 GATATAAATAT
1 AATATAAATAT
*
3687112 -AT-T--TTAT
1 AATATAAATAT
*
3687119 AATCT-AA-AT
1 AATATAAATAT
3687128 AATATAAATAT
1 AATATAAATAT
3687139 AAGTATAAA
1 AA-TATAAA
3687148 AATATTATCG
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
7 3 0.05
8 2 0.04
9 8 0.15
10 13 0.24
11 23 0.42
12 6 0.11
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (11 bp):
AATATAAATAT
Found at i:3687147 original size:21 final size:20
Alignment explanation
Indices: 3687069--3687152 Score: 75
Period size: 21 Copynumber: 4.2 Consensus size: 20
3687059 ATATAATAAC
*
3687069 AATAAAAATATAATATAAAT
1 AATATAAATATAATATAAAT
* *
3687089 ATATATATATATGATATAAAT
1 A-ATATAAATATAATATAAAT
** *
3687110 -ATAT-TTTATAATCTAAAT
1 AATATAAATATAATATAAAT
3687128 AATATAAATATAAGTATAAA-
1 AATATAAATATAA-TATAAAT
3687148 AATAT
1 AATAT
3687153 TATCGCTGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 11 0.22
19 8 0.16
20 11 0.22
21 21 0.41
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (20 bp):
AATATAAATATAATATAAAT
Found at i:3701777 original size:23 final size:22
Alignment explanation
Indices: 3701739--3701795 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 22
3701729 TATCATTAAA
3701739 AATTATTTTTATATT-AATATTT
1 AATTATTTTTATATTAAAT-TTT
3701761 -ATATATTTTTATAATTAAATTTT
1 AAT-TATTTTTAT-ATTAAATTTT
3701784 AATTATTTTTAT
1 AATTATTTTTAT
3701796 CATATGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.06
22 9 0.29
23 15 0.48
24 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
AATTATTTTTATATTAAATTTT
Found at i:3703028 original size:27 final size:27
Alignment explanation
Indices: 3702956--3703028 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
3702946 ATATAATTAT
* *
3702956 TTAAATAATCATAATACTTAATAAATAA
1 TTAAA-AAACATAATTCTTAATAAATAA
* * *
3702984 TTAATAAATATTAA-TCTTAATACATAA
1 TTAAAAAACA-TAATTCTTAATAAATAA
3703011 TTAAAAAACATAATTCTT
1 TTAAAAAACATAATTCTT
3703029 TAATTATTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
26 3 0.08
27 26 0.72
28 7 0.19
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (27 bp):
TTAAAAAACATAATTCTTAATAAATAA
Found at i:3705958 original size:13 final size:13
Alignment explanation
Indices: 3705937--3705976 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3705927 TTATTTTTAA
3705937 AATAATTATATTT
1 AATAATTATATTT
* *
3705950 AATATTTATTTTT
1 AATAATTATATTT
3705963 AA-AATTATATTT
1 AATAATTATATTT
3705975 AA
1 AA
3705977 ATATAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATAATTATATTT
Found at i:3706458 original size:27 final size:27
Alignment explanation
Indices: 3706378--3706444 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
3706368 AATCAAAAGT
* * * **
3706378 TTTAAATATTAAATCTTAAATGTTAAA
1 TTTAAATTTTAAACCCTAAATACTAAA
*
3706405 TTTTAATTTTAAACCCTAAATACTAAA
1 TTTAAATTTTAAACCCTAAATACTAAA
3706432 TTATAAATTTTAA
1 TT-TAAATTTTAA
3706445 TCCCAAAACA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.45
Consensus pattern (27 bp):
TTTAAATTTTAAACCCTAAATACTAAA
Found at i:3710375 original size:19 final size:19
Alignment explanation
Indices: 3710353--3710389 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3710343 TACAGTTATT
3710353 TTTAAAATATAATATTTAA
1 TTTAAAATATAATATTTAA
* *
3710372 TTTAAATTTTAATATTTA
1 TTTAAAATATAATATTTA
3710390 TAAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAAAATATAATATTTAA
Found at i:3710400 original size:19 final size:20
Alignment explanation
Indices: 3710378--3710415 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3710368 TTAATTTAAA
*
3710378 TTTTAATA-TTTATAAATTT
1 TTTTAATAGTTCATAAATTT
*
3710397 TTTTTATAGTTCATAAATT
1 TTTTAATAGTTCATAAATT
3710416 ATGATCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTAATAGTTCATAAATTT
Found at i:3711018 original size:6 final size:6
Alignment explanation
Indices: 3711007--3711043 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3710997 TAGATAATTT
*
3711007 TTTAAA TTTAAA TTT-AA -TTAAA TTTAAT TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
3711044 CACTATCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.07
5 4 0.15
6 21 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:3711029 original size:16 final size:16
Alignment explanation
Indices: 3711008--3711039 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3710998 AGATAATTTT
3711008 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAA
*
3711024 TTAAATTTAATTTTAA
1 TTAAATTTAAATTTAA
3711040 ATTTCACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATTTAAATTTAA
Found at i:3713884 original size:24 final size:23
Alignment explanation
Indices: 3713852--3713979 Score: 55
Period size: 24 Copynumber: 5.2 Consensus size: 23
3713842 TGGTATCTCG
*
3713852 TTATTTTTTTATTTAAATAAATAT
1 TTATATTTTTATTTAAATAAA-AT
3713876 TTATATTTTATTATATTTAAATAAAAT
1 TTATA--TT-TT-TATTTAAATAAAAT
*
3713903 TT-TAATTTTTAATTTACATCAAAAT
1 TTAT-ATTTTT-ATTTAAAT-AAAAT
** * * *
3713928 AAATCTTTAATATTTGACAT-AAAT
1 TTATATTT-TTATTT-AAATAAAAT
*
3713952 TAATA-TTTTATTTAAAATAAAAAT
1 TTATATTTTTATTT-AAAT-AAAAT
3713976 TTAT
1 TTAT
3713980 TTTAATATAA
Statistics
Matches: 80, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
22 8 0.10
23 3 0.04
24 27 0.34
25 14 0.17
26 9 0.11
27 7 0.09
28 12 0.15
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (23 bp):
TTATATTTTTATTTAAATAAAAT
Found at i:3713898 original size:28 final size:25
Alignment explanation
Indices: 3713853--3713927 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 25
3713843 GGTATCTCGT
3713853 TATTTTTTTATTTAAATAAATATTTA
1 TATTTTTTTATTTAAATAAA-ATTTA
3713879 TATTTTATTATATTTAAATAAAATTT-
1 TATTTT-TT-TATTTAAATAAAATTTA
* * *
3713905 TAATTTTTAATTTACATCAAAAT
1 TATTTTTTTATTTAAAT-AAAAT
3713928 AAATCTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 7 0.16
25 7 0.16
26 11 0.26
27 6 0.14
28 12 0.28
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTTTTTATTTAAATAAAATTTA
Found at i:3717704 original size:30 final size:30
Alignment explanation
Indices: 3717661--3717752 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
3717651 TGCGTCTGAA
* * *
3717661 GTCGTTCCCTAATTTGTA-TTTTCTTCGATT
1 GTCGTTTCTTAATTTGTACTTTT-GTCGATT
* *
3717691 GTCGTTTCTTAATTTGTACTCTTGTCGATC
1 GTCGTTTCTTAATTTGTACTTTTGTCGATT
*
3717721 GTCGTTTCTTAGTTTGTACTTTTGTCGATT
1 GTCGTTTCTTAATTTGTACTTTTGTCGATT
3717751 GT
1 GT
3717753 GGACCATCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 50 0.94
31 3 0.06
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.53
Consensus pattern (30 bp):
GTCGTTTCTTAATTTGTACTTTTGTCGATT
Found at i:3718387 original size:2 final size:2
Alignment explanation
Indices: 3718380--3718406 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3718370 AACCCTTCTT
3718380 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
3718407 GTTTTTTTTA
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:3718660 original size:2 final size:2
Alignment explanation
Indices: 3718653--3718678 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3718643 GTACAGCTAC
3718653 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
3718679 GGATGGTTTT
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:3723627 original size:2 final size:2
Alignment explanation
Indices: 3723620--3723647 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3723610 TTTAATTTCT
3723620 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
3723648 ACTTGTAGGA
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:3730833 original size:2 final size:2
Alignment explanation
Indices: 3730826--3730855 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3730816 AATGCTTTTA
3730826 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
3730856 GTTGTTTTTC
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:3736448 original size:2 final size:2
Alignment explanation
Indices: 3736441--3736475 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3736431 TCATAGTAAT
3736441 TA 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 TA T
3736476 CCTTGTATTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3744135 original size:50 final size:48
Alignment explanation
Indices: 3744021--3744136 Score: 114
Period size: 48 Copynumber: 2.4 Consensus size: 48
3744011 TTTTAAAAAA
* *
3744021 ATAATATTTAATAAATATTTATTTTAATATTTATTTTTTATTTTTAAATT
1 ATAATATTTAAT-AA-ATTTATTTTAATATTTATTTATTATTTTTAAAGT
* *
3744071 ATAAAATTT-A-AAATTTATTTTAACTAATTT-TTATAATTATTTTT-ACGT
1 ATAATATTTAATAAATTTATTTTAA-T-ATTTATT-T-ATTATTTTTAAAGT
3744119 ATAATATTTAATAAATTT
1 ATAATATTTAATAAATTT
3744137 CAATTTCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
46 11 0.20
47 5 0.09
48 15 0.27
49 10 0.18
50 14 0.25
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (48 bp):
ATAATATTTAATAAATTTATTTTAATATTTATTTATTATTTTTAAAGT
Found at i:3747069 original size:3 final size:3
Alignment explanation
Indices: 3747061--3747085 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3747051 ACCAAAAAAG
3747061 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3747086 GTAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3751826 original size:2 final size:2
Alignment explanation
Indices: 3751814--3751852 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3751804 TATCAATAAG
*
3751814 TA TA AA 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 TA TA TA T
3751853 TCTTTTTGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 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):
TA
Found at i:3752101 original size:21 final size:21
Alignment explanation
Indices: 3752072--3752136 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
3752062 ATCATGCATG
3752072 AATTGAATTTAAAGTTATATTT
1 AATT-AATTTAAAGTTATATTT
*
3752094 AATTAATTTATAAGAT-TATTT
1 AATTAATTTA-AAGTTATATTT
* * *
3752115 AATAAATTTAAATTTAAATTT
1 AATTAATTTAAAGTTATATTT
3752136 A
1 A
3752137 TTCTTACTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.08
21 25 0.69
22 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AATTAATTTAAAGTTATATTT
Found at i:3754619 original size:3 final size:3
Alignment explanation
Indices: 3754611--3754642 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3754601 ACTTTGACTT
3754611 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3754643 CTTGTTACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3755110 original size:17 final size:17
Alignment explanation
Indices: 3755088--3755124 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3755078 TTTAGAAGCA
3755088 CACGAACATCCATTTAT
1 CACGAACATCCATTTAT
3755105 CACGAACATCCATTTAT
1 CACGAACATCCATTTAT
3755122 CAC
1 CAC
3755125 TTTCTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.27
Consensus pattern (17 bp):
CACGAACATCCATTTAT
Found at i:3759076 original size:2 final size:2
Alignment explanation
Indices: 3759069--3759105 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3759059 GTCAATGATC
3759069 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
3759106 CACACACACA
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:3785535 original size:2 final size:2
Alignment explanation
Indices: 3785528--3785553 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3785518 TCATAAAAAT
3785528 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
3785554 AACCTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3785932 original size:19 final size:19
Alignment explanation
Indices: 3785899--3785940 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3785889 ATTTGATAAA
3785899 TATAGTATTTATATTATGTT
1 TATAGTATTTATATTAT-TT
*
3785919 TATA-TATTTTTATTATTT
1 TATAGTATTTATATTATTT
3785937 TATA
1 TATA
3785941 ATTATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TATAGTATTTATATTATTT
Found at i:3786328 original size:19 final size:18
Alignment explanation
Indices: 3786277--3786330 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 18
3786267 AAATATTTGT
*
3786277 TATATATAT-TAAACATA
1 TATATATATATAAATATA
*
3786294 TATATATACTCTAAATATA
1 TATATATA-TATAAATATA
3786313 TATATATATATAAA-ATA
1 TATATATATATAAATATA
3786330 T
1 T
3786331 TAGAACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 12 0.36
18 6 0.18
19 15 0.45
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATATATATAAATATA
Found at i:3786357 original size:15 final size:13
Alignment explanation
Indices: 3786337--3786369 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3786327 ATATTAGAAC
3786337 ATATATGAT-TTTA
1 ATATAT-ATATTTA
3786350 ATATATATATTTA
1 ATATATATATTTA
3786363 ATATATA
1 ATATATA
3786370 CACTGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
ATATATATATTTA
Found at i:3786865 original size:39 final size:37
Alignment explanation
Indices: 3786780--3786868 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 37
3786770 TGTATATTTT
*
3786780 TTTAAATATTTTTAATTAATTTATAAATTTCTTATAAA
1 TTTAAATA-TTTTAATTAATTTATAAATTTATTATAAA
**
3786818 TACAAAATATTTTAATTAATTTAT-AATTTATAATATAAAA
1 T-TTAAATATTTTAATTAATTTATAAATTTAT--TAT-AAA
3786858 TTTAAATATTT
1 TTTAAATATTT
3786869 CAATCACAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
37 6 0.14
38 16 0.38
39 16 0.38
40 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (37 bp):
TTTAAATATTTTAATTAATTTATAAATTTATTATAAA
Found at i:3787966 original size:18 final size:18
Alignment explanation
Indices: 3787907--3787976 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 18
3787897 GATATTTAAA
*
3787907 AAAATTTAAAT-AATAA-
1 AAAATTTAAATAAAAAAT
* *
3787923 AAAGTTTAAGTAAAAAAT
1 AAAATTTAAATAAAAAAT
**
3787941 AAAATTTATTTAAAAAAT
1 AAAATTTAAATAAAAAAT
* *
3787959 AGATTTTAAATAAAAAAT
1 AAAATTTAAATAAAAAAT
3787977 TTTAAGCTCA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
16 9 0.21
17 4 0.10
18 29 0.69
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAATTTAAATAAAAAAT
Found at i:3788133 original size:30 final size:31
Alignment explanation
Indices: 3788093--3788152 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3788083 TAAAAATAAT
**
3788093 ATTAATAAAATTTTATCA-AAAATATATTTA
1 ATTAATAAAATTAAATCAGAAAATATATTTA
* *
3788123 ATTATTAAAATTAAATTAGAAAATATATTT
1 ATTAATAAAATTAAATCAGAAAATATATTT
3788153 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
ATTAATAAAATTAAATCAGAAAATATATTTA
Found at i:3797442 original size:2 final size:2
Alignment explanation
Indices: 3797437--3797465 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3797427 TATATATATA
3797437 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 T
3797466 ATTATTTTTA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3799107 original size:3 final size:3
Alignment explanation
Indices: 3799099--3799131 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3799089 TTGTTCATTG
*
3799099 TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3799132 ATTGGATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3804027 original size:3 final size:3
Alignment explanation
Indices: 3804019--3804050 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3804009 TAACTCTTAA
3804019 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3804051 AACTAACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3804316 original size:2 final size:2
Alignment explanation
Indices: 3804309--3804348 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3804299 TATTGCAGTC
3804309 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
3804349 GCTGACTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3805702 original size:2 final size:2
Alignment explanation
Indices: 3805693--3805727 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3805683 AAAAATTTGT
*
3805693 TA TA -A TA TA TA CA 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
3805728 ATAAAAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3806246 original size:7 final size:7
Alignment explanation
Indices: 3806197--3806248 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
3806187 AATAGATCTG
3806197 ATATTTGT
1 ATATTT-T
3806205 ATATTTT
1 ATATTTT
*
3806212 ATATATT
1 ATATTTT
*
3806219 ATA-ATT
1 ATATTTT
3806225 ATATTTT
1 ATATTTT
3806232 AAATATTTT
1 --ATATTTT
3806241 ATATTTT
1 ATATTTT
3806248 A
1 A
3806249 AAAAATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
6 6 0.15
7 20 0.51
8 6 0.15
9 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (7 bp):
ATATTTT
Found at i:3806258 original size:17 final size:16
Alignment explanation
Indices: 3806223--3806259 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
3806213 TATATTATAA
*
3806223 TTATATTTTAAATATT
1 TTATATTTTAAAAATT
3806239 TTATATTTTAAAAAATT
1 TTATATTTT-AAAAATT
3806256 TTAT
1 TTAT
3806260 TACTTTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATATTTTAAAAATT
Found at i:3814958 original size:13 final size:13
Alignment explanation
Indices: 3814940--3814964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3814930 GACAGACACA
3814940 CAAGAAAAAGGGG
1 CAAGAAAAAGGGG
3814953 CAAGAAAAAGGG
1 CAAGAAAAAGGG
3814965 ATATAAATTC
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:0.56, C:0.08, G:0.36, T:0.00
Consensus pattern (13 bp):
CAAGAAAAAGGGG
Found at i:3819813 original size:1 final size:1
Alignment explanation
Indices: 3819779--3819804 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3819769 CACGAACATG
3819779 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3819805 GCAAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3824263 original size:14 final size:14
Alignment explanation
Indices: 3824246--3824286 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3824236 GAGATATAAA
3824246 TTTTTATTTTATTT
1 TTTTTATTTTATTT
3824260 TTTTTATTTT-TATT
1 TTTTTATTTTAT-TT
*
3824274 TATTTA-TTTATTT
1 TTTTTATTTTATTT
3824287 CAAAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTATTT
Found at i:3825209 original size:126 final size:126
Alignment explanation
Indices: 3824991--3825235 Score: 418
Period size: 126 Copynumber: 1.9 Consensus size: 126
3824981 GGCATCTTTT
* * *
3824991 TTTTTTTTTTTGTGTGTAATAAAAATCTGTAAATAGTTAATTGTATTTTCTTGAAATTCTGTGTA
1 TTTTTTTTTTGGTGTGTAATAAAAATCTGTAAATAATTAATTGTATTTTCTTGAAATTCTCTGTA
*
3825056 AAATGATTAGAAAGAGACATATTTTTTATTGTGTACTTACGGATATAATGATGTGGGCATC
66 AAATGATTAGAAAGAGACATATTTTTTATTGTGTACTTACGCATATAATGATGTGGGCATC
* *
3825117 TTTTTTTTTTGGTTTGTTATAAAAATCTGTAAATAATTAATTGTATTTTCTTGAAATTCTCTGTA
1 TTTTTTTTTTGGTGTGTAATAAAAATCTGTAAATAATTAATTGTATTTTCTTGAAATTCTCTGTA
* *
3825182 AAATGATTAGAAAGAGACATATTTTTTATTGTGTAGTTATGCATATAATGATGT
66 AAATGATTAGAAAGAGACATATTTTTTATTGTGTACTTACGCATATAATGATGT
3825236 TGTTGAAATC
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 111 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (126 bp):
TTTTTTTTTTGGTGTGTAATAAAAATCTGTAAATAATTAATTGTATTTTCTTGAAATTCTCTGTA
AAATGATTAGAAAGAGACATATTTTTTATTGTGTACTTACGCATATAATGATGTGGGCATC
Found at i:3826550 original size:2 final size:2
Alignment explanation
Indices: 3826545--3826577 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3826535 AAAAAAATGG
3826545 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 A
3826578 ATAGGAAAGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3829493 original size:2 final size:2
Alignment explanation
Indices: 3829486--3829516 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3829476 TCCTTTTGTT
3829486 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 T
3829517 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3829521 original size:2 final size:2
Alignment explanation
Indices: 3829516--3829580 Score: 94
Period size: 2 Copynumber: 32.5 Consensus size: 2
3829506 TCTCTCTCTC
3829516 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
* * * *
3829558 TA TA CA CA TA TA CA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3829581 TAATCAAAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3829906 original size:18 final size:17
Alignment explanation
Indices: 3829862--3829906 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
3829852 GAATAAAAAT
*
3829862 ATTTTATTAAAAATGACA
1 ATTTTA-TAAAAATAACA
*
3829880 ATTTTATAAAAATAATA
1 ATTTTATAAAAATAACA
3829897 ATTTTGATAA
1 ATTTT-ATAA
3829907 TTATCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
ATTTTATAAAAATAACA
Found at i:3830789 original size:16 final size:16
Alignment explanation
Indices: 3830768--3830799 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3830758 ATAATATCAT
3830768 ATTTATTAATAAATTA
1 ATTTATTAATAAATTA
*
3830784 ATTTATTCATAAATTA
1 ATTTATTAATAAATTA
3830800 GTAAATCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTATTAATAAATTA
Found at i:3832821 original size:3 final size:3
Alignment explanation
Indices: 3832815--3832861 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
3832805 GGAGGAGGAG
*
3832815 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3832862 GGAGAAGGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:3840100 original size:43 final size:44
Alignment explanation
Indices: 3840024--3840109 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
3840014 ATTTTTTTTA
* * *
3840024 TTTATATAATTTTATATTAATAAAAATATATTAAGTAATTAATAT
1 TTTATATAATTTTATATAAAAAAAAATATATTAAAT-ATTAATAT
3840069 TTTATA-AATTTTA-ATAAAAACAAAAT-TATTAAATATTAATA
1 TTTATATAATTTTATATAAAAA-AAAATATATTAAATATTAATA
3840110 AAAATAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 7 0.19
43 12 0.32
44 12 0.32
45 6 0.16
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (44 bp):
TTTATATAATTTTATATAAAAAAAAATATATTAAATATTAATAT
Found at i:3840101 original size:25 final size:25
Alignment explanation
Indices: 3840073--3840132 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
3840063 TAATATTTTA
3840073 TAAATTTTAATAAAAACAAAATTAT
1 TAAATTTTAATAAAAACAAAATTAT
* * * *
3840098 TAAATATTAATAAAAATAATATTTT
1 TAAATTTTAATAAAAACAAAATTAT
*
3840123 TTAATTTTAA
1 TAAATTTTAA
3840133 ATTTAAATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAATTTTAATAAAAACAAAATTAT
Found at i:3841451 original size:12 final size:12
Alignment explanation
Indices: 3841422--3841451 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3841412 CTGAATTTGA
*
3841422 ATTTAGATTTAG
1 ATTTATATTTAG
3841434 ATTTATATTTAG
1 ATTTATATTTAG
3841446 ATTTAT
1 ATTTAT
3841452 CTTTTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (12 bp):
ATTTATATTTAG
Found at i:3844995 original size:2 final size:2
Alignment explanation
Indices: 3844990--3845016 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3844980 TCTCTCTCTC
3844990 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
3845017 TAACGTAATA
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:3852648 original size:2 final size:2
Alignment explanation
Indices: 3852641--3852679 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3852631 AAAATCCTCC
3852641 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3852680 CGCCTCCCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3853928 original size:29 final size:28
Alignment explanation
Indices: 3853847--3853929 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
3853837 ATTTACTTTG
3853847 TAATGAAATATAA-TTAAATTAT-TAAAT
1 TAAT-AAATATAATTTAAATTATGTAAAT
*
3853874 TAATAAATAT-ATTTATTAATGA-GTAAATT
1 TAATAAATATAATTTA--AATTATGTAAA-T
**
3853903 TAATATTTATAATTTAAATTATGTAAA
1 TAATAAATATAATTTAAATTATGTAAA
3853930 AAGTTGAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
25 1 0.02
26 9 0.20
27 4 0.09
28 12 0.27
29 14 0.31
30 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (28 bp):
TAATAAATATAATTTAAATTATGTAAAT
Found at i:3854358 original size:25 final size:25
Alignment explanation
Indices: 3854304--3854364 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 25
3854294 TCTTCCTTAT
* *
3854304 TATAATAATTGATGGTTTTTTTGTTCA
1 TATAATAATTGATGGTTTTATAG-T-A
3854331 TATAATAATTGATGGTTTTAATAG-A
1 TATAATAATTGATGGTTTT-ATAGTA
*
3854356 TATAGTAAT
1 TATAATAAT
3854365 CTCACAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.30
27 19 0.63
28 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (25 bp):
TATAATAATTGATGGTTTTATAGTA
Found at i:3854554 original size:2 final size:2
Alignment explanation
Indices: 3854549--3854627 Score: 60
Period size: 2 Copynumber: 40.5 Consensus size: 2
3854539 TTCATGTTCA
*
3854549 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT A- AT AT TT ACT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT A-T AT AT
** *
3854591 -T GC AT -T AT CA- AC 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 AT A
3854628 ACTTAGCCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
1 5 0.08
2 53 0.84
3 5 0.08
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3869792 original size:18 final size:17
Alignment explanation
Indices: 3869743--3869790 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
3869733 AAATGGAGTT
*
3869743 CCAAACCCAAAACAACAAA
1 CCAAA-CCAAAAC-TCAAA
3869762 CCAAACCAAAACTCAAA
1 CCAAACCAAAACTCAAA
3869779 CTCAAACTCAAA
1 C-CAAAC-CAAA
3869791 CTTAGAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 12 0.46
19 9 0.35
ACGTcount: A:0.58, C:0.35, G:0.00, T:0.06
Consensus pattern (17 bp):
CCAAACCAAAACTCAAA
Found at i:3870949 original size:5 final size:5
Alignment explanation
Indices: 3870939--3870974 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
3870929 TTGTATAGAA
3870939 ATTTT ATTTT A-TTT ATTTT ATTTT ATTTT ATCTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT A
3870975 GGTTTTCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:3870958 original size:14 final size:14
Alignment explanation
Indices: 3870939--3870966 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3870929 TTGTATAGAA
3870939 ATTTTATTTTATTT
1 ATTTTATTTTATTT
3870953 ATTTTATTTTATTT
1 ATTTTATTTTATTT
3870967 TATCTTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTTATTTTATTT
Found at i:3876835 original size:3 final size:3
Alignment explanation
Indices: 3876827--3876856 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3876817 CCCCCTCCCC
3876827 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3876857 TACCCGTTTT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3877064 original size:16 final size:16
Alignment explanation
Indices: 3877023--3877053 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3877013 TCAAGCATGC
*
3877023 TCTTTGTTATAAATGA
1 TCTTTGTAATAAATGA
3877039 TCTTTGTAATAAATG
1 TCTTTGTAATAAATG
3877054 GTTTTGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (16 bp):
TCTTTGTAATAAATGA
Found at i:3885036 original size:3 final size:3
Alignment explanation
Indices: 3885028--3885068 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3885018 CATCTCTCTT
3885028 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3885069 TATGCTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3887588 original size:60 final size:60
Alignment explanation
Indices: 3887516--3887636 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
3887506 TTGGTTTGGC
*
3887516 TTCTCTTTTCACAAG-ATCTTTCAAGATTTCTCTCAAATCTCCTATTATCTCTCTTTCAGT
1 TTCTCTTTTCAC-AGTATCTTTCAAGATTTCTCTCAAATCTCCTATTATCTATCTTTCAGT
* * * *
3887576 TTCTGTTTTCACAGTATCTTTCAAGATTTTTCTCATATCTCTTATTATCTATCTTTCAGT
1 TTCTCTTTTCACAGTATCTTTCAAGATTTCTCTCAAATCTCCTATTATCTATCTTTCAGT
3887636 T
1 T
3887637 CAACTCCGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 2 0.04
60 53 0.96
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.50
Consensus pattern (60 bp):
TTCTCTTTTCACAGTATCTTTCAAGATTTCTCTCAAATCTCCTATTATCTATCTTTCAGT
Found at i:3888287 original size:2 final size:2
Alignment explanation
Indices: 3888280--3888312 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3888270 TTAAATAGTT
*
3888280 TA TA TA TA TA TA TA TA TA TA TA TT TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3888313 AATTCATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3892382 original size:2 final size:2
Alignment explanation
Indices: 3892370--3892405 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3892360 ATCTATAAAC
*
3892370 AT AT AT GT 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
3892406 TTGAGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3894090 original size:14 final size:14
Alignment explanation
Indices: 3894071--3894097 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3894061 TTTTTTTTAA
3894071 AAAAAAAAAGAAGG
1 AAAAAAAAAGAAGG
3894085 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
3894098 AAGAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAGG
Found at i:3896404 original size:62 final size:62
Alignment explanation
Indices: 3896325--3896449 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
3896315 AGTTAAAACA
* *
3896325 TATTATATTTTTTAACTCAATTGCACGGAAGTAACATTTTAATTGTTGCCTCATAGCATGTG
1 TATTATATATTTCAACTCAATTGCACGGAAGTAACATTTTAATTGTTGCCTCATAGCATGTG
3896387 TATTATATATTTCAACTCAATTGCACGGAAGTAACATTTTAATTGTTGCCTCATAGCATGTG
1 TATTATATATTTCAACTCAATTGCACGGAAGTAACATTTTAATTGTTGCCTCATAGCATGTG
3896449 T
1 T
3896450 GGCATTAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (62 bp):
TATTATATATTTCAACTCAATTGCACGGAAGTAACATTTTAATTGTTGCCTCATAGCATGTG
Found at i:3899297 original size:17 final size:18
Alignment explanation
Indices: 3899274--3899324 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
3899264 TCATTAAATA
3899274 AAAATATATATTTATATT
1 AAAATATATATTTATATT
* *
3899292 -AAATATTTATTTGTTATT
1 AAAATATATATTT-ATATT
3899310 AAAATCATATATTTA
1 AAAAT-ATATATTTA
3899325 ATGTGTACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 4 0.15
20 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
AAAATATATATTTATATT
Found at i:3901156 original size:58 final size:58
Alignment explanation
Indices: 3901066--3901178 Score: 208
Period size: 58 Copynumber: 1.9 Consensus size: 58
3901056 CCAGTAGAGG
3901066 AAGAAGTTTTACACATTACTAATCCAAAAATATGTATTAAATGATGCATTTAATACAA
1 AAGAAGTTTTACACATTACTAATCCAAAAATATGTATTAAATGATGCATTTAATACAA
* *
3901124 AAGAATTTTTACACATTACTAATCCAAAAATATGTATTAAATGATGCCTTTAATA
1 AAGAAGTTTTACACATTACTAATCCAAAAATATGTATTAAATGATGCATTTAATA
3901179 AAGGATTTCC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (58 bp):
AAGAAGTTTTACACATTACTAATCCAAAAATATGTATTAAATGATGCATTTAATACAA
Found at i:3908499 original size:2 final size:2
Alignment explanation
Indices: 3908492--3908534 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3908482 AAATCCCCTT
3908492 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
3908534 T
1 T
3908535 TATGGTCTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3912060 original size:2 final size:2
Alignment explanation
Indices: 3912053--3912077 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3912043 GGCAATGACC
3912053 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
3912078 GTACATTTTC
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:3913702 original size:2 final size:2
Alignment explanation
Indices: 3913695--3913721 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3913685 TTATACATAC
3913695 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 A
3913722 AGAGTAATTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3917137 original size:2 final size:2
Alignment explanation
Indices: 3917127--3917170 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3917117 TTGTAGTGTG
*
3917127 TA TA GA 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
3917169 TA
1 TA
3917171 ATCTCACTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3918585 original size:54 final size:53
Alignment explanation
Indices: 3918510--3918634 Score: 180
Period size: 54 Copynumber: 2.3 Consensus size: 53
3918500 AATTTAGTTG
3918510 ATATATTTAATAATTTTTAAAAATAATATCTTATAAATTTAAATTTAAAACTTA
1 ATAT-TTTAATAATTTTTAAAAATAATATCTTATAAATTTAAATTTAAAACTTA
* * *
3918564 ATATTTTTATAATTTTTTAAAAATAATATCTTATATATTTAAATTTAAATCTTA
1 ATATTTTAATAA-TTTTTAAAAATAATATCTTATAAATTTAAATTTAAAACTTA
*
3918618 AAATTTATAAT-ATTTTT
1 ATATTT-TAATAATTTTT
3918635 GTGATCTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
53 12 0.19
54 49 0.77
55 3 0.05
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (53 bp):
ATATTTTAATAATTTTTAAAAATAATATCTTATAAATTTAAATTTAAAACTTA
Found at i:3926809 original size:2 final size:2
Alignment explanation
Indices: 3926802--3926846 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3926792 AAGAAGGCAA
3926802 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
3926844 AT A
1 AT A
3926847 ACAATTAATC
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:3935654 original size:6 final size:6
Alignment explanation
Indices: 3935643--3935683 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
3935633 TAATTTGTCA
*
3935643 TGGCAT TGGCAT TGGCCT TGGCAT TGGCAT TGGCA- TGGCAT
1 TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT TGGCAT
3935684 CCTTCAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.15, C:0.20, G:0.34, T:0.32
Consensus pattern (6 bp):
TGGCAT
Found at i:3936693 original size:2 final size:2
Alignment explanation
Indices: 3936649--3936674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3936639 TGACCTCGCA
3936649 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
3936675 GTATGTCGTG
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:3937545 original size:4 final size:4
Alignment explanation
Indices: 3937524--3937570 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
3937514 ATTTTTGTCC
* * * *
3937524 ATAT ACAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT TTAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
3937571 ACATGATAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:3937557 original size:14 final size:14
Alignment explanation
Indices: 3937524--3937570 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3937514 ATTTTTGTCC
* * *
3937524 ATATACATACATAC
1 ATATATATATATAT
3937538 ATATATATATATAT
1 ATATATATATATAT
*
3937552 ATATATATTTATAT
1 ATATATATATATAT
3937566 ATATA
1 ATATA
3937571 ACATGATAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:3940955 original size:30 final size:30
Alignment explanation
Indices: 3940919--3940978 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
3940909 GCAGGTTGGT
3940919 ATCTTTATCAGTTTATGGCAAATATGAGCC
1 ATCTTTATCAGTTTATGGCAAATATGAGCC
3940949 ATCTTTATCAGTTTATGGCAAATATGAGCC
1 ATCTTTATCAGTTTATGGCAAATATGAGCC
3940979 TTTAGGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (30 bp):
ATCTTTATCAGTTTATGGCAAATATGAGCC
Found at i:3942311 original size:3 final size:3
Alignment explanation
Indices: 3942303--3942338 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3942293 AAGACCCATG
3942303 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3942339 CCTGTGTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3945443 original size:21 final size:21
Alignment explanation
Indices: 3945417--3945457 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3945407 AAACAAATTG
*
3945417 ACAAGTTTAAGTTCATCTATA
1 ACAAGTTTAAGCTCATCTATA
3945438 ACAAGTTTAAGCTCATCTAT
1 ACAAGTTTAAGCTCATCTAT
3945458 CACGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
ACAAGTTTAAGCTCATCTATA
Found at i:3949494 original size:2 final size:2
Alignment explanation
Indices: 3949489--3949523 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3949479 ATATATATAT
3949489 AG AG 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 A
3949524 TTAGGGCAGA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3949594 original size:14 final size:15
Alignment explanation
Indices: 3949575--3949612 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3949565 ACGGAAATTA
3949575 TTTTTAATATT-TAT
1 TTTTTAATATTATAT
*
3949589 TTTTTAAAATTATAT
1 TTTTTAATATTATAT
*
3949604 TTTTAAATA
1 TTTTTAATA
3949613 AATTTTCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTAATATTATAT
Found at i:3956946 original size:2 final size:2
Alignment explanation
Indices: 3956941--3956976 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3956931 TTAAAAAACA
3956941 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3956977 GGTTATCCGT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3959453 original size:14 final size:15
Alignment explanation
Indices: 3959434--3959462 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3959424 CAAAAGAAAG
3959434 AAAAA-GATAAAAAA
1 AAAAAGGATAAAAAA
3959448 AAAAAGGATAAAAAA
1 AAAAAGGATAAAAAA
3959463 CAACTAGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAAAGGATAAAAAA
Found at i:3963463 original size:2 final size:2
Alignment explanation
Indices: 3963456--3963486 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3963446 TATAAGGAGC
3963456 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
3963487 TATTGATTTG
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:3972300 original size:5 final size:5
Alignment explanation
Indices: 3972281--3972318 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
3972271 ACCATGTGTA
3972281 AAAAT -AAAT -AAAT AAAAT AAAAT AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
3972319 CTTGGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.26
5 18 0.58
6 5 0.16
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3972502 original size:18 final size:18
Alignment explanation
Indices: 3972466--3972515 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3972456 ATAAAAATAA
* * *
3972466 TATTTAAATATTTATTTT
1 TATTTAAAAAATTACTTT
3972484 TATTTAAAAAATTACTTT
1 TATTTAAAAAATTACTTT
3972502 TAAATTTAAAAAAT
1 T--ATTTAAAAAAT
3972516 ATCAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 16 0.59
20 11 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTTAAAAAATTACTTT
Found at i:3972916 original size:13 final size:14
Alignment explanation
Indices: 3972889--3972922 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3972879 AGTTTATGTG
*
3972889 ATTTGAAAAAAAAA
1 ATTTTAAAAAAAAA
*
3972903 ATTTTAAAACAAAA
1 ATTTTAAAAAAAAA
3972917 ATTTTA
1 ATTTTA
3972923 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (14 bp):
ATTTTAAAAAAAAA
Found at i:3973071 original size:3 final size:3
Alignment explanation
Indices: 3973063--3973098 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3973053 AAGCTAGCAA
3973063 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3973099 TTTGCCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3980116 original size:33 final size:33
Alignment explanation
Indices: 3980076--3980140 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
3980066 AACTACTGAT
3980076 AAAAATGAAATTAGTCTCATTAACAATGCTAAA
1 AAAAATGAAATTAGTCTCATTAACAATGCTAAA
3980109 AAAAATGAAATTAGTCTCATTAACAATGCTAA
1 AAAAATGAAATTAGTCTCATTAACAATGCTAA
3980141 CTTAGTATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (33 bp):
AAAAATGAAATTAGTCTCATTAACAATGCTAAA
Found at i:3982050 original size:2 final size:2
Alignment explanation
Indices: 3982043--3982091 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3982033 TGCATGGTGT
3982043 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3982085 TC TC TC T
1 TC TC TC T
3982092 TTAAGCGGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3982893 original size:6 final size:6
Alignment explanation
Indices: 3982879--3982912 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3982869 ATGAGAACCT
*
3982879 TTCTTC TTCTCC TTCTCC TTCTCC TTCTCC TTCT
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCT
3982913 TCCTCTCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCTCC
Found at i:3982922 original size:2 final size:2
Alignment explanation
Indices: 3982915--3982948 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3982905 CTCCTTCTTC
3982915 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
3982949 TTATTTCTCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3982925 original size:18 final size:18
Alignment explanation
Indices: 3982886--3982947 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 18
3982876 CCTTTCTTCT
3982886 TCTCCTTC-TCCT-TCTCC
1 TCTCCTTCTTCCTCTCT-C
3982903 TTCTCCTTCTTCCTCTCTC
1 -TCTCCTTCTTCCTCTCTC
3982922 TCTCTCTCTCTCTCTCTCTCTC
1 TCTC-CT-TCT-TC-CTCTCTC
3982944 TCTC
1 TCTC
3982948 TTTATTTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
18 12 0.32
19 7 0.18
20 6 0.16
21 2 0.05
22 11 0.29
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (18 bp):
TCTCCTTCTTCCTCTCTC
Done.