Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 81 of 93
Found at i:12451213 original size:24 final size:24
Alignment explanation
Indices: 12451145--12451201 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 24
12451135 ATTTTTTTGT
12451145 TTTTTTTAGAATATCTCAAAA-T-TTA
1 TTTTTTT--AATATCT-AAAATTCTTA
12451170 TTTTTTTAATATCTAAAATTCTTA
1 TTTTTTTAATATCTAAAATTCTTA
12451194 TTTTTTTA
1 TTTTTTTA
12451202 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.13
23 8 0.27
24 11 0.37
25 7 0.23
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTTTAATATCTAAAATTCTTA
Found at i:12451629 original size:25 final size:26
Alignment explanation
Indices: 12451595--12451643 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
12451585 ATAAAATAAA
* *
12451595 ATAAATAATTTTATATTAAAAAATAT
1 ATAAATAATTATAAATTAAAAAATAT
*
12451621 ATAAA-AATTATAAATTAATAAAT
1 ATAAATAATTATAAATTAAAAAAT
12451644 TGAATCGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATAAATAATTATAAATTAAAAAATAT
Found at i:12452534 original size:19 final size:20
Alignment explanation
Indices: 12452510--12452554 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
12452500 TAATTTTATA
12452510 TTTATA-TTAAAAATAATAT
1 TTTATATTTAAAAATAATAT
12452529 TTTATATTTTAAAAATAATAT
1 TTTATA-TTTAAAAATAATAT
12452550 TTTAT
1 TTTAT
12452555 TAATTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
21 18 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATATTTAAAAATAATAT
Found at i:12452922 original size:10 final size:9
Alignment explanation
Indices: 12452881--12452954 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 9
12452871 AATATTATAT
12452881 AATTATTAA
1 AATTATTAA
12452890 AA-TATTAAA
1 AATTATT-AA
12452899 AATTATT--
1 AATTATTAA
*
12452906 TATTATTAA
1 AATTATTAA
12452915 AATATATTAA
1 AAT-TATTAA
12452925 AATTATT--
1 AATTATTAA
*
12452932 TATTATTAA
1 AATTATTAA
12452941 AATTATTAA
1 AATTATTAA
*
12452950 TATTA
1 AATTA
12452955 AAAAATAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
7 12 0.23
8 4 0.08
9 24 0.45
10 13 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:12452926 original size:26 final size:26
Alignment explanation
Indices: 12452882--12452954 Score: 114
Period size: 25 Copynumber: 2.9 Consensus size: 26
12452872 ATATTATATA
*
12452882 ATTATTAAAATAT-TAAAAATTATTT
1 ATTATTAAAATATATTAAAATTATTT
12452907 ATTATTAAAATATATTAAAATTATTT
1 ATTATTAAAATATATTAAAATTATTT
*
12452933 ATTATTAAAAT-TATTAATATTA
1 ATTATTAAAATATATTAAAATTA
12452955 AAAAATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 23 0.51
26 22 0.49
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTATTAAAATATATTAAAATTATTT
Found at i:12452938 original size:16 final size:15
Alignment explanation
Indices: 12452892--12452957 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
12452882 ATTATTAAAA
12452892 TATTAAAAATTATTTAT
1 TATT-AAAATTA-TTAT
12452909 TATT-AAA--A-TA-
1 TATTAAAATTATTAT
12452919 TATTAAAATTATTTAT
1 TATTAAAATTA-TTAT
*
12452935 TATTAAAATTATTAA
1 TATTAAAATTATTAT
12452950 TATTAAAA
1 TATTAAAA
12452958 AATAATTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
10 4 0.10
11 5 0.12
13 2 0.05
15 16 0.38
16 11 0.26
17 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAAAATTATTAT
Found at i:12452954 original size:25 final size:25
Alignment explanation
Indices: 12452882--12452954 Score: 112
Period size: 26 Copynumber: 2.9 Consensus size: 25
12452872 ATATTATATA
12452882 ATTATTAAAA-TATTAAAAATTATTT
1 ATTATTAAAATTATT-AAAATTATTT
12452907 ATTATTAAAATATATTAAAATTATTT
1 ATTATTAAAAT-TATTAAAATTATTT
*
12452933 ATTATTAAAATTATTAATATTA
1 ATTATTAAAATTATTAAAATTA
12452955 AAAAATAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 20 0.44
26 21 0.47
27 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTATTAAAATTATTAAAATTATTT
Found at i:12452958 original size:16 final size:16
Alignment explanation
Indices: 12452918--12452957 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
12452908 TTATTAAAAT
12452918 ATATTAAAATTATTTA
1 ATATTAAAATTATTTA
*
12452934 TTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
12452949 ATATTAAAA
1 ATATTAAAA
12452958 AATAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:12453106 original size:6 final size:6
Alignment explanation
Indices: 12453086--12453126 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
12453076 ACTATTCTTA
* *
12453086 AAATAT TAA-AT AAATAT AAATAT AAATAT AATTAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
12453127 TTATTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AAATAT
Found at i:12453141 original size:15 final size:16
Alignment explanation
Indices: 12453116--12453145 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12453106 TATAAATATA
12453116 ATTATAAATATTTATT
1 ATTATAAATATTTATT
12453132 ATTA-AAATATTTAT
1 ATTATAAATATTTAT
12453146 ACTATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATAAATATTTATT
Found at i:12453370 original size:39 final size:42
Alignment explanation
Indices: 12453324--12453404 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
12453314 TTAATAATAT
*
12453324 TATTATTATATTAT-TTAACATTAATTATTAAAATAATAAAAA
1 TATTATTATA-TATGTTAACATTAATTATTAAAAAAATAAAAA
** *
12453366 TATTATTATATATGTTATTATTTATTATTAAAAAAATAA
1 TATTATTATATATGTTAACATTAATTATTAAAAAAATAA
12453405 TATAATAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.09
42 31 0.91
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (42 bp):
TATTATTATATATGTTAACATTAATTATTAAAAAAATAAAAA
Found at i:12453574 original size:31 final size:29
Alignment explanation
Indices: 12453509--12453567 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
12453499 CGTTAATTTT
*
12453509 TAATTTTTTAATTAAAATTAAATAAAATA
1 TAATTTTTTAATAAAAATTAAATAAAATA
*
12453538 TAATTTTTATAATAAAAATTTAAATCAAAT
1 TAATTTTT-TAATAAAAA-TTAAATAAAAT
12453568 CAAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 8 0.31
31 10 0.38
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATTTTTTAATAAAAATTAAATAAAATA
Found at i:12453703 original size:21 final size:20
Alignment explanation
Indices: 12453665--12453705 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12453655 TAATTTTTTA
*
12453665 ATTTTTTAAATAAAAATATT
1 ATTTATTAAATAAAAATATT
*
12453685 ATTTATTAATATAATAATATT
1 ATTTATTAA-ATAAAAATATT
12453706 TTGATAAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATTAAATAAAAATATT
Found at i:12453802 original size:16 final size:16
Alignment explanation
Indices: 12453781--12453813 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12453771 ATATTCAAAA
12453781 TATTGATA-ACTAATTT
1 TATTGATAGA-TAATTT
12453797 TATTGATAGATAATTT
1 TATTGATAGATAATTT
12453813 T
1 T
12453814 TTTTCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (16 bp):
TATTGATAGATAATTT
Found at i:12463421 original size:16 final size:16
Alignment explanation
Indices: 12463400--12463430 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12463390 TTTTTTTGGT
12463400 ATTTTATTTATTTATG
1 ATTTTATTTATTTATG
*
12463416 ATTTTATTTGTTTAT
1 ATTTTATTTATTTAT
12463431 TTGTTTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
ATTTTATTTATTTATG
Found at i:12463655 original size:23 final size:23
Alignment explanation
Indices: 12463627--12463691 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
12463617 AAATAAAGTG
12463627 AAAATTTAGATAAATTTTC-AATA
1 AAAATTTA-ATAAATTTTCAAATA
* *
12463650 AGAA-TTAATATTTATTTTCAAAATA
1 AAAATTTAATA--AATTTTC-AAATA
12463675 AAAATTTAATAAATTTT
1 AAAATTTAATAAATTTT
12463692 GGGAATGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
21 3 0.09
22 3 0.09
23 9 0.27
24 5 0.15
25 7 0.21
26 6 0.18
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (23 bp):
AAAATTTAATAAATTTTCAAATA
Found at i:12468047 original size:16 final size:16
Alignment explanation
Indices: 12468026--12468058 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12468016 GAAGAGAAAT
12468026 AAAATG-AAAAATAAAA
1 AAAATGTAAAAA-AAAA
12468042 AAAATGTAAAAAAAAA
1 AAAATGTAAAAAAAAA
12468058 A
1 A
12468059 GAAGACTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAATGTAAAAAAAAA
Found at i:12469769 original size:16 final size:16
Alignment explanation
Indices: 12469582--12469775 Score: 67
Period size: 16 Copynumber: 12.0 Consensus size: 16
12469572 GCGAATTTGA
**
12469582 AAATTTTTGTGAATCT
1 AAATTTTTGCAAATCT
12469598 CAAATTTTTGCAAATC-
1 -AAATTTTTGCAAATCT
* * *
12469614 AAATTCTTGCGAATTT
1 AAATTTTTGCAAATCT
* * * *
12469630 GAGTTTTTACAAACCT
1 AAATTTTTGCAAATCT
* ** *
12469646 GAAATTCTTGTGATTC-
1 -AAATTTTTGCAAATCT
*
12469662 AATTTTTTGCAAATCT
1 AAATTTTTGCAAATCT
* *
12469678 AAAAATTTTTACAAATAT
1 --AAATTTTTGCAAATCT
* *
12469696 AAGTTTTTGTGAAA-CT
1 AAATTTTTG-CAAATCT
* * *
12469712 CAAATTCTTACAAACCT
1 -AAATTTTTGCAAATCT
12469729 GAAA-TTTTG-ATAATC-
1 -AAATTTTTGCA-AATCT
* *
12469744 AAATTCTTGCGAATCT
1 AAATTTTTGCAAATCT
12469760 AAATTTTTGCAAATCT
1 AAATTTTTGCAAATCT
12469776 TTGAATTGTG
Statistics
Matches: 121, Mismatches: 44, Indels: 25
0.64 0.23 0.13
Matches are distributed among these distances:
14 3 0.02
15 31 0.26
16 40 0.33
17 34 0.28
18 13 0.11
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (16 bp):
AAATTTTTGCAAATCT
Found at i:12470119 original size:22 final size:21
Alignment explanation
Indices: 12470088--12470145 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
12470078 CCCAACTATC
12470088 AAAAATTTTATTTTATTT-AA
1 AAAAATTTTATTTTATTTAAA
12470108 AAAAA---TATTTTATTTAAA
1 AAAAATTTTATTTTATTTAAA
12470126 AAAATATTTTATTTTATTTA
1 AAAA-ATTTTATTTTATTTA
12470146 TTCATTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 10 0.30
18 6 0.18
19 1 0.03
20 5 0.15
22 11 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAAATTTTATTTTATTTAAA
Found at i:12470141 original size:18 final size:17
Alignment explanation
Indices: 12470096--12470139 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
12470086 TCAAAAATTT
12470096 TATTTTATTTAAAAAAA
1 TATTTTATTTAAAAAAA
12470113 TATTTTATTTAAAAAAA
1 TATTTTATTTAAAAAAA
12470130 TATTTTATTT
1 TATTTTATTT
12470140 TATTTATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTTATTTAAAAAAA
Found at i:12470739 original size:15 final size:16
Alignment explanation
Indices: 12470711--12470742 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12470701 ATTTTTTTGC
12470711 CAAATTTAAAAATTTT
1 CAAATTTAAAAATTTT
12470727 CAAATTT-AAAATTTT
1 CAAATTTAAAAATTTT
12470742 C
1 C
12470743 GACAAACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
CAAATTTAAAAATTTT
Found at i:12478748 original size:23 final size:23
Alignment explanation
Indices: 12478701--12478748 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
12478691 TTTATGAGAT
*
12478701 ATTTTTTATGAAATAAAATCGTA
1 ATTTTTTATGAAATAAAACCGTA
12478724 ATTTTTT-T-AAATTAAAACCGATA
1 ATTTTTTATGAAA-TAAAACCG-TA
12478747 AT
1 AT
12478749 ACTTTGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 3 0.14
22 8 0.36
23 11 0.50
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (23 bp):
ATTTTTTATGAAATAAAACCGTA
Found at i:12480011 original size:12 final size:12
Alignment explanation
Indices: 12479994--12480019 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12479984 TACCCTTTGA
12479994 TTTTTTTTCTTT
1 TTTTTTTTCTTT
12480006 TTTTTTTTCTTT
1 TTTTTTTTCTTT
12480018 TT
1 TT
12480020 CCCAAGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:12481315 original size:23 final size:23
Alignment explanation
Indices: 12481289--12481336 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
12481279 CTCACTTCAT
*
12481289 TAAAATTAAAATATAATATTTAA
1 TAAAATTAAAATATAAAATTTAA
* *
12481312 TAAATTTAAAATTTAAAATTTAA
1 TAAAATTAAAATATAAAATTTAA
12481335 TA
1 TA
12481337 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAATTAAAATATAAAATTTAA
Found at i:12481323 original size:7 final size:7
Alignment explanation
Indices: 12481288--12481339 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
12481278 TCTCACTTCA
12481288 TTAAAA-
1 TTAAAAT
12481294 TTAAAAT
1 TTAAAAT
* *
12481301 ATAATAT
1 TTAAAAT
12481308 TTAATAAAT
1 TT-A-AAAT
12481317 TTAAAAT
1 TTAAAAT
12481324 TTAAAAT
1 TTAAAAT
*
12481331 TTAATAT
1 TTAAAAT
12481338 TT
1 TT
12481340 GTAATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
6 6 0.16
7 25 0.66
8 2 0.05
9 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTAAAAT
Found at i:12481649 original size:12 final size:12
Alignment explanation
Indices: 12481615--12481651 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
12481605 TAATGTGAAA
*
12481615 ATTAATAATA-T
1 ATTAAAAATATT
12481626 ATTAAAAA-ATT
1 ATTAAAAATATT
12481637 ATTAAAAATATT
1 ATTAAAAATATT
12481649 ATT
1 ATT
12481652 TATAATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 16 0.70
12 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTAAAAATATT
Found at i:12493447 original size:2 final size:2
Alignment explanation
Indices: 12493435--12493483 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
12493425 TTGCTTGAAT
*
12493435 TA TA CTA TA TA TA TA TA TA CA TA TA TA TA -A TA TA -A 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
12493476 T- TA TA TA T
1 TA TA TA TA T
12493484 TTTTCATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.07
2 36 0.88
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12495582 original size:23 final size:23
Alignment explanation
Indices: 12495556--12495599 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12495546 AATTTACGAA
12495556 TATTAAA-ATTTATATTTTAAATT
1 TATTAAACA-TTATATTTTAAATT
*
12495579 TATTAAACATTATTTTTTAAA
1 TATTAAACATTATATTTTAAA
12495600 ATAACGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAAACATTATATTTTAAATT
Found at i:12510254 original size:24 final size:24
Alignment explanation
Indices: 12510227--12510274 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12510217 TAGTAATATG
* *
12510227 ATATGAAAATAATACGAATAAAAA
1 ATATAAAAATAATACAAATAAAAA
*
12510251 ATATAAAAATAATACAAATTAAAA
1 ATATAAAAATAATACAAATAAAAA
12510275 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (24 bp):
ATATAAAAATAATACAAATAAAAA
Found at i:12515323 original size:20 final size:20
Alignment explanation
Indices: 12515298--12515337 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12515288 ATATATATAT
12515298 AAACCTCCAATTTTATGATG
1 AAACCTCCAATTTTATGATG
12515318 AAACCTCCAATTTTATGATG
1 AAACCTCCAATTTTATGATG
12515338 GAATACATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
AAACCTCCAATTTTATGATG
Found at i:12516609 original size:21 final size:22
Alignment explanation
Indices: 12516568--12516611 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
12516558 TTTTTTATTT
12516568 TTTTACTATTTTATATATAATA
1 TTTTACTATTTTATATATAATA
*
12516590 TTTTA-TATTATTA-ATTTAATA
1 TTTTACTATT-TTATATATAATA
12516611 T
1 T
12516612 ATAGATTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTACTATTTTATATATAATA
Found at i:12521802 original size:3 final size:3
Alignment explanation
Indices: 12521794--12521857 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
12521784 CATTTCAATT
** *
12521794 TAA TAA TAA TAA TTT TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA CTTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA
*
12521844 AAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA
12521858 AAAAAAAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
5 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:12523313 original size:17 final size:17
Alignment explanation
Indices: 12523291--12523346 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
12523281 TACGAAACCT
12523291 TTAAAATCCAAAATCCC
1 TTAAAATCCAAAATCCC
* * *
12523308 TTAAAATTCGAAACCCC
1 TTAAAATCCAAAATCCC
* *
12523325 TAAAAATCTAAAATCCC
1 TTAAAATCCAAAATCCC
12523342 TTAAA
1 TTAAA
12523347 TCTAAACCCA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (17 bp):
TTAAAATCCAAAATCCC
Found at i:12523386 original size:16 final size:16
Alignment explanation
Indices: 12523358--12523418 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
12523348 CTAAACCCAA
12523358 TAAAATCTC-AAACCTC
1 TAAAA-CTCAAAACCTC
*
12523374 TAAAACTCAAAACCCC
1 TAAAACTCAAAACCTC
* * *
12523390 AAAAATTCAAAACTTC
1 TAAAACTCAAAACCTC
*
12523406 TTAAA-TCAAAACC
1 TAAAACTCAAAACC
12523419 ACATACCTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
15 10 0.28
16 26 0.72
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAACTCAAAACCTC
Found at i:12523395 original size:32 final size:31
Alignment explanation
Indices: 12523309--12523418 Score: 89
Period size: 32 Copynumber: 3.4 Consensus size: 31
12523299 CAAAATCCCT
* *
12523309 TAAAATTCGAAACCCCTAAAAATCTAAAATCC-C
1 TAAAA-TCAAAACCCC-AAAAATCTCAAA-CCTC
* * *
12523342 TTAAATCTAAACCCAATAAAATCTCAAACCTC
1 TAAAATCAAAACCCCA-AAAATCTCAAACCTC
*
12523374 TAAAACTCAAAACCCCAAAAAT-TCAAAACTTC
1 TAAAA-TCAAAACCCCAAAAATCTC-AAACCTC
*
12523406 TTAAATCAAAACC
1 TAAAATCAAAACC
12523419 ACATACCTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
31 13 0.20
32 38 0.59
33 13 0.20
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (31 bp):
TAAAATCAAAACCCCAAAAATCTCAAACCTC
Found at i:12523415 original size:31 final size:32
Alignment explanation
Indices: 12523327--12523418 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
12523317 GAAACCCCTA
* *
12523327 AAAATCTAAAATCC-CTTAAATCTAAACCCAAT
1 AAAATCTCAAA-CCTCTTAAATCAAAACCCAAT
* *
12523359 AAAATCTCAAACCTCTAAAACTCAAAACCCCA-
1 AAAATCTCAAACCTCTTAAA-TCAAAACCCAAT
*
12523391 AAAAT-TCAAAACTTCTTAAATCAAAACC
1 AAAATCTC-AAACCTCTTAAATCAAAACC
12523419 ACATACCTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
31 12 0.24
32 30 0.59
33 9 0.18
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (32 bp):
AAAATCTCAAACCTCTTAAATCAAAACCCAAT
Found at i:12523457 original size:14 final size:14
Alignment explanation
Indices: 12523438--12523514 Score: 64
Period size: 14 Copynumber: 5.2 Consensus size: 14
12523428 ATTTTTTAAA
12523438 AAAATCAAAACCCT
1 AAAATCAAAACCCT
* **
12523452 AAAATCTCTAAACTTT
1 AAAA--TCAAAACCCT
12523468 AAAATCAAAACCCT
1 AAAATCAAAACCCT
* **
12523482 AAAATCTCTAAACTTT
1 AAAA--TCAAAACCCT
12523498 AAAATCAAAACCCT
1 AAAATCAAAACCCT
12523512 AAA
1 AAA
12523515 CCTTCAATAC
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 25 0.53
16 22 0.47
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATCAAAACCCT
Found at i:12523464 original size:16 final size:16
Alignment explanation
Indices: 12523445--12523494 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
12523435 AAAAAAATCA
12523445 AAACCCTAAAATCTCT
1 AAACCCTAAAATCTCT
** *
12523461 AAACTTTAAAA--TCA
1 AAACCCTAAAATCTCT
12523475 AAACCCTAAAATCTCT
1 AAACCCTAAAATCTCT
12523491 AAAC
1 AAAC
12523495 TTTAAAATCA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 11 0.42
16 15 0.58
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACCCTAAAATCTCT
Found at i:12523474 original size:30 final size:30
Alignment explanation
Indices: 12523438--12523514 Score: 154
Period size: 30 Copynumber: 2.6 Consensus size: 30
12523428 ATTTTTTAAA
12523438 AAAATCAAAACCCTAAAATCTCTAAACTTT
1 AAAATCAAAACCCTAAAATCTCTAAACTTT
12523468 AAAATCAAAACCCTAAAATCTCTAAACTTT
1 AAAATCAAAACCCTAAAATCTCTAAACTTT
12523498 AAAATCAAAACCCTAAA
1 AAAATCAAAACCCTAAA
12523515 CCTTCAATAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (30 bp):
AAAATCAAAACCCTAAAATCTCTAAACTTT
Found at i:12523500 original size:16 final size:16
Alignment explanation
Indices: 12523451--12523503 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
12523441 ATCAAAACCC
12523451 TAAAATCTCTAAACTT
1 TAAAATCTCTAAACTT
* **
12523467 TAAAA--TCAAAACCC
1 TAAAATCTCTAAACTT
12523481 TAAAATCTCTAAACTT
1 TAAAATCTCTAAACTT
12523497 TAAAATC
1 TAAAATC
12523504 AAAACCCTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 11 0.38
16 18 0.62
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAATCTCTAAACTT
Found at i:12523578 original size:30 final size:31
Alignment explanation
Indices: 12523438--12523603 Score: 109
Period size: 30 Copynumber: 5.6 Consensus size: 31
12523428 ATTTTTTAAA
* *
12523438 AAAATCAAAACCCTAAAA-TCTCTAAACTTT
1 AAAATCAAAACCCTAAAACCCTCTAAACCTT
* *
12523468 AAAATCAAAACCCTAAAA-TCTCTAAACTTT
1 AAAATCAAAACCCTAAAACCCTCTAAACCTT
* *
12523498 AAAATCAAAACCCT-AAACCTTC-AATACCCT
1 AAAATCAAAACCCTAAAACCCTCTAA-ACCTT
*** *
12523528 AAAATTC--AAGTTTAAGACCCTCTAAACCTT
1 AAAA-TCAAAACCCTAAAACCCTCTAAACCTT
* *
12523558 AAAATC-GAACTCTAAAACCCTC-AAGA-C-T
1 AAAATCAAAACCCTAAAACCCTCTAA-ACCTT
* *
12523586 CAAATCAAAACCTTAAAA
1 AAAATCAAAACCCTAAAA
12523604 TCCGAATCTT
Statistics
Matches: 111, Mismatches: 17, Indels: 17
0.77 0.12 0.12
Matches are distributed among these distances:
28 6 0.05
29 21 0.19
30 80 0.72
31 4 0.04
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.23
Consensus pattern (31 bp):
AAAATCAAAACCCTAAAACCCTCTAAACCTT
Found at i:12525645 original size:15 final size:14
Alignment explanation
Indices: 12525620--12525663 Score: 65
Period size: 12 Copynumber: 3.2 Consensus size: 14
12525610 TTTTCATTTC
12525620 AATTTAATAATAAT
1 AATTTAATAATAAT
12525634 AATTTCAATAATAAT
1 AATTT-AATAATAAT
12525649 -A-TTAATAATAAT
1 AATTTAATAATAAT
12525661 AAT
1 AAT
12525664 AATAACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 9 0.33
13 3 0.11
14 6 0.22
15 9 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTAATAATAAT
Found at i:12525687 original size:3 final size:3
Alignment explanation
Indices: 12525624--12525668 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
12525614 CATTTCAATT
* *
12525624 TAA TAA TAA TAA T-T TCAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12525669 CTTTAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:12526815 original size:3 final size:3
Alignment explanation
Indices: 12526807--12526835 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12526797 AATGCTTTAA
12526807 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12526836 TTTTATTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12527127 original size:17 final size:17
Alignment explanation
Indices: 12527105--12527160 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
12527095 TACGAAACCT
12527105 TTAAAATCCAAAATCCC
1 TTAAAATCCAAAATCCC
* * *
12527122 TTAAAATTCGAAACCCC
1 TTAAAATCCAAAATCCC
* *
12527139 TAAAAATCTAAAATCCC
1 TTAAAATCCAAAATCCC
12527156 TTAAA
1 TTAAA
12527161 TCTAAACCCA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (17 bp):
TTAAAATCCAAAATCCC
Found at i:12527200 original size:16 final size:16
Alignment explanation
Indices: 12527172--12527232 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
12527162 CTAAACCCAA
12527172 TAAAATCTC-AAACCTC
1 TAAAA-CTCAAAACCTC
*
12527188 TAAAACTCAAAACCCC
1 TAAAACTCAAAACCTC
* * *
12527204 AAAAATTCAAAACTTC
1 TAAAACTCAAAACCTC
*
12527220 TTAAA-TCAAAACC
1 TAAAACTCAAAACC
12527233 ACATACCTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
15 10 0.28
16 26 0.72
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAACTCAAAACCTC
Found at i:12527209 original size:32 final size:31
Alignment explanation
Indices: 12527123--12527232 Score: 89
Period size: 32 Copynumber: 3.4 Consensus size: 31
12527113 CAAAATCCCT
* *
12527123 TAAAATTCGAAACCCCTAAAAATCTAAAATCC-C
1 TAAAA-TCAAAACCCC-AAAAATCTCAAA-CCTC
* * *
12527156 TTAAATCTAAACCCAATAAAATCTCAAACCTC
1 TAAAATCAAAACCCCA-AAAATCTCAAACCTC
*
12527188 TAAAACTCAAAACCCCAAAAAT-TCAAAACTTC
1 TAAAA-TCAAAACCCCAAAAATCTC-AAACCTC
*
12527220 TTAAATCAAAACC
1 TAAAATCAAAACC
12527233 ACATACCTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
31 13 0.20
32 38 0.59
33 13 0.20
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (31 bp):
TAAAATCAAAACCCCAAAAATCTCAAACCTC
Found at i:12527229 original size:31 final size:32
Alignment explanation
Indices: 12527141--12527232 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
12527131 GAAACCCCTA
* *
12527141 AAAATCTAAAATCC-CTTAAATCTAAACCCAAT
1 AAAATCTCAAA-CCTCTTAAATCAAAACCCAAT
* *
12527173 AAAATCTCAAACCTCTAAAACTCAAAACCCCA-
1 AAAATCTCAAACCTCTTAAA-TCAAAACCCAAT
*
12527205 AAAAT-TCAAAACTTCTTAAATCAAAACC
1 AAAATCTC-AAACCTCTTAAATCAAAACC
12527233 ACATACCTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
31 12 0.24
32 30 0.59
33 9 0.18
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (32 bp):
AAAATCTCAAACCTCTTAAATCAAAACCCAAT
Found at i:12529437 original size:13 final size:13
Alignment explanation
Indices: 12529419--12529443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12529409 GAAAGGCAAC
12529419 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
12529432 AAAAAAGAAAAA
1 AAAAAAGAAAAA
12529444 GAGAGAGAGA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:12529985 original size:17 final size:16
Alignment explanation
Indices: 12529940--12530018 Score: 67
Period size: 17 Copynumber: 4.9 Consensus size: 16
12529930 AACATAAGAT
*
12529940 AATATTAATATTACTT-
1 AATATTAATTTTA-TTC
12529956 AATA-TAATTTTATTC
1 AATATTAATTTTATTC
* *
12529971 ATATATTAATATTATTT
1 A-ATATTAATTTTATTC
12529988 AATA-TAATTTTATTC
1 AATATTAATTTTATTC
12530003 -ATAATATAATTTTATT
1 AAT-AT-TAATTTTATT
12530019 TTATCTCATT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
14 4 0.08
15 18 0.35
16 10 0.19
17 20 0.38
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTAATTTTATTC
Found at i:12530018 original size:32 final size:33
Alignment explanation
Indices: 12529938--12530019 Score: 132
Period size: 32 Copynumber: 2.5 Consensus size: 33
12529928 CAAACATAAG
*
12529938 ATAATATTAATATTACTTAATATAATTTTATTC
1 ATAATATTAATATTATTTAATATAATTTTATTC
12529971 AT-ATATTAATATTATTTAATATAATTTTATTC
1 ATAATATTAATATTATTTAATATAATTTTATTC
*
12530003 ATAATA-TAATTTTATTT
1 ATAATATTAATATTATTT
12530020 TATCTCATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 41 0.89
33 5 0.11
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (33 bp):
ATAATATTAATATTATTTAATATAATTTTATTC
Found at i:12532351 original size:28 final size:27
Alignment explanation
Indices: 12532318--12532372 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
12532308 ATTCAATTCA
*
12532318 TTTTTTGTTTTTTAAATTTTTTATTTGAC
1 TTTTTTG-ATTTTAAA-TTTTTATTTGAC
*
12532347 TTTTTTGATTTTATATTTTTATTTGA
1 TTTTTTGATTTTAAATTTTTATTTGA
12532373 TAAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.46
28 6 0.25
29 7 0.29
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (27 bp):
TTTTTTGATTTTAAATTTTTATTTGAC
Found at i:12532509 original size:32 final size:31
Alignment explanation
Indices: 12532468--12532528 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 31
12532458 ATAAGTGCCT
12532468 TTTTTTTTTTTTTAAATTGAGATTGGATTGAG
1 TTTTTTTTTTTTTAAA-TGAGATTGGATTGAG
*
12532500 TTTTTTTTTTTTTAAATGAGGTTGGATTG
1 TTTTTTTTTTTTTAAATGAGATTGGATTG
12532529 GAGACGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.61
Consensus pattern (31 bp):
TTTTTTTTTTTTTAAATGAGATTGGATTGAG
Found at i:12545685 original size:32 final size:34
Alignment explanation
Indices: 12545603--12545686 Score: 106
Period size: 32 Copynumber: 2.6 Consensus size: 34
12545593 ATTTATATTA
12545603 TATTTTATATAAAATT-TA-AATATTATAATTTT
1 TATTTTATATAAAATTATATAATATTATAATTTT
* *
12545635 TA-TTAATATAAAAATATATAATA-TATAATTTT
1 TATTTTATATAAAATTATATAATATTATAATTTT
*
12545667 TATTTTAT-TAAATTTATATA
1 TATTTTATATAAAATTATATA
12545687 TAATTATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 11 0.25
32 25 0.57
33 8 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TATTTTATATAAAATTATATAATATTATAATTTT
Found at i:12545711 original size:22 final size:22
Alignment explanation
Indices: 12545671--12545712 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12545661 AATTTTTATT
*
12545671 TTATTAAATTTATATATAATTA
1 TTATTAAATTTATAAATAATTA
12545693 TTATTAAAATTT-TAAATAAT
1 TTATT-AAATTTATAAATAAT
12545713 GTTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTAAATTTATAAATAATTA
Found at i:12545732 original size:13 final size:13
Alignment explanation
Indices: 12545714--12545738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12545704 TTAAATAATG
12545714 TTATTTTTATATT
1 TTATTTTTATATT
12545727 TTATTTTTATAT
1 TTATTTTTATAT
12545739 AATTTTACAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTATATT
Found at i:12546207 original size:11 final size:11
Alignment explanation
Indices: 12546191--12546223 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12546181 TTGTTATTCA
12546191 AAATTTAATTT
1 AAATTTAATTT
12546202 AAATTTAA-TT
1 AAATTTAATTT
12546212 AAATTTTAATTT
1 AAA-TTTAATTT
12546224 TTAAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 13 0.65
12 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:12546432 original size:20 final size:20
Alignment explanation
Indices: 12546386--12546434 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
12546376 ATAATAGTTT
12546386 TTTAATTAAAATAATAAAAA
1 TTTAATTAAAATAATAAAAA
* *
12546406 TAT-ATTAAATTTAA-AAAAA
1 TTTAATTAAA-ATAATAAAAA
12546425 TTTAATTAAA
1 TTTAATTAAA
12546435 CTCACGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTAATTAAAATAATAAAAA
Found at i:12550115 original size:2 final size:2
Alignment explanation
Indices: 12550110--12550155 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
12550100 TTCTCTTTTT
*
12550110 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC -C T- TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12550149 TC TC TC T
1 TC TC TC T
12550156 TTTTCTCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:12557091 original size:2 final size:2
Alignment explanation
Indices: 12557084--12557123 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12557074 TGATTCTGTA
12557084 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
12557124 AGTTGCTTGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12562281 original size:2 final size:2
Alignment explanation
Indices: 12562274--12562303 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12562264 CATTTATGAA
12562274 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
12562304 GTATGAAAGG
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:12568787 original size:2 final size:2
Alignment explanation
Indices: 12568780--12568821 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
12568770 AAGCTTCATT
12568780 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
12568822 ATATCATAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12580625 original size:249 final size:250
Alignment explanation
Indices: 12580187--12580927 Score: 1109
Period size: 249 Copynumber: 3.0 Consensus size: 250
12580177 CCCTCCCAGG
**
12580187 TGACTCATTCTCACAGAAGTCTGGCCTAATCAATTTTCTCTTTTTACAATGTGCAGCTGATGCAC
1 TGACTCAAACTCACAGAAGTCTGGCCTAATCAATTTTCTCTTTTTACAATGTGCAGCTGATGCAC
*
12580252 TCTTGTCATTCAGACTTTCACAATGGTTTCCAGTCTTATCATCTTCAAAGTTCTTTCTCACTGCA
66 TCTTGTTATTCAGACTTTCACAAT-GTTTCCAGTCTTATCATCTTCAAAGTTCTTTCTCACTGCA
*
12580317 -CTTAGACGTTTGAAATTCACAAAAGT-TGTCTCTTCAGCTTTTTGGCTGCTATTCTCCTTGCTT
130 CCAT-GACGTTTGAAATTCACAAAAGTCTGTCTCTTCAGCTTTTTGGCTGCTATTCTCCTTGCTT
*
12580380 AATGAGATAGGCTTATCATTCATCTCCTTTGAGATCATAGCCATGCCCT-TGTCAGA
194 AATGAGATAGGCTTATCATTCATCTCCTTTGAGATCATAGCCAAGCCCTCTGTCAGA
* * *
12580436 TGACTCAAACTCGCAGAAATCAGGCCTAATCAATTTTCTCTTTTTACAATGTGCAGCTGATGCAC
1 TGACTCAAACTCACAGAAGTCTGGCCTAATCAATTTTCTCTTTTTACAATGTGCAGCTGATGCAC
* * *
12580501 TCTTGTTATTCAGACTTTCACAAGTGTTCCCAGTTTTATCATCTTCAAAATTCTTTCTCACTGCA
66 TCTTGTTATTCAGACTTTCACAA-TGTTTCCAGTCTTATCATCTTCAAAGTTCTTTCTCACTGCA
* * * *
12580566 CCATGATGTTTGAAATTCTCAAAAGTCT-TCTCTTCACCTTTTTGGCTACTATTCTCCTTGCTTA
130 CCATGACGTTTGAAATTCACAAAAGTCTGTCTCTTCAGCTTTTTGGCTGCTATTCTCCTTGCTTA
* **
12580630 ATGGGATAGGCTTATCATTCATCTCCTTTGAGATTGTAGCCAAG-CCTCTGTCAGA
195 ATGAGATAGGCTTATCATTCATCTCCTTTGAGATCATAGCCAAGCCCTCTGTCAGA
* *
12580685 TGACTGAAACTCACAGAAGTCTGCCCTAATCAATTTTCTCTTTTTACAATGTGCAGCTGATGCAC
1 TGACTCAAACTCACAGAAGTCTGGCCTAATCAATTTTCTCTTTTTACAATGTGCAGCTGATGCAC
* * ** * *
12580750 TCTTGTTATTCAGACTTCCACAACAGTTTCCAGTCTTGCCATCTTCAAGGTTCTTTCTCACTGAA
66 TCTTGTTATTCAGACTTTCACAA-TGTTTCCAGTCTTATCATCTTCAAAGTTCTTTCTCACTGCA
* * *
12580815 CTACGACGTTTGAAATTCACAAAAG-CTGTCTCTTCAGTTTTTTGGCTGCTATTCTCCTTGCTTA
130 CCATGACGTTTGAAATTCACAAAAGTCTGTCTCTTCAGCTTTTTGGCTGCTATTCTCCTTGCTTA
* *
12580879 ATGAGATAGGCTTCA-CATTCATCTCCTTTGAAATCATAGTCAAGCCCTC
195 ATGAGATAGGCTT-ATCATTCATCTCCTTTGAGATCATAGCCAAGCCCTC
12580928 CTTCCTGGTC
Statistics
Matches: 440, Mismatches: 45, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
248 5 0.01
249 426 0.97
250 9 0.02
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (250 bp):
TGACTCAAACTCACAGAAGTCTGGCCTAATCAATTTTCTCTTTTTACAATGTGCAGCTGATGCAC
TCTTGTTATTCAGACTTTCACAATGTTTCCAGTCTTATCATCTTCAAAGTTCTTTCTCACTGCAC
CATGACGTTTGAAATTCACAAAAGTCTGTCTCTTCAGCTTTTTGGCTGCTATTCTCCTTGCTTAA
TGAGATAGGCTTATCATTCATCTCCTTTGAGATCATAGCCAAGCCCTCTGTCAGA
Found at i:12593318 original size:24 final size:24
Alignment explanation
Indices: 12593291--12593339 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
12593281 TTGCCTTGTC
12593291 AAACAGTAAACGATTGTTATGCAA
1 AAACAGTAAACGATTGTTATGCAA
*
12593315 AAACAGTAAATGATTGTTATGCAA
1 AAACAGTAAACGATTGTTATGCAA
12593339 A
1 A
12593340 TTACCTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (24 bp):
AAACAGTAAACGATTGTTATGCAA
Found at i:12596315 original size:42 final size:43
Alignment explanation
Indices: 12596268--12596355 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
12596258 TATTAATAAG
* * *
12596268 TGAAGCAATAAAAA-GCTGATAAATGAGTAAGTTTTTTATGGC
1 TGAAGCAATAAAAAGGCTGAAAAATGAATAAGTTTTTGATGGC
12596310 TGAAGCAATAAAAAGGCTGAAAAATGAATAAGTTTTTGATGGC
1 TGAAGCAATAAAAAGGCTGAAAAATGAATAAGTTTTTGATGGC
12596353 TGA
1 TGA
12596356 TTATATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 14 0.33
43 28 0.67
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (43 bp):
TGAAGCAATAAAAAGGCTGAAAAATGAATAAGTTTTTGATGGC
Found at i:12600071 original size:15 final size:15
Alignment explanation
Indices: 12600051--12600081 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12600041 TTTTAAATTC
12600051 TTAAGGGAGTTAAAA
1 TTAAGGGAGTTAAAA
12600066 TTAAGGGAGTTAAAA
1 TTAAGGGAGTTAAAA
12600081 T
1 T
12600082 GAGAGACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (15 bp):
TTAAGGGAGTTAAAA
Found at i:12603027 original size:15 final size:15
Alignment explanation
Indices: 12602991--12603036 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12602981 CGTGAATTTA
*
12602991 ATAATT-ATTGTAAT
1 ATAATTAATTTTAAT
12603005 AT--TTAATTTTAAT
1 ATAATTAATTTTAAT
12603018 ATAATTAATTTTAA-
1 ATAATTAATTTTAAT
12603032 ATAAT
1 ATAAT
12603037 AAAAAATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 9 0.32
14 7 0.25
15 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATAATTAATTTTAAT
Found at i:12605459 original size:16 final size:15
Alignment explanation
Indices: 12605438--12605472 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12605428 ATCATTTTCA
*
12605438 TATTTTTTATTTATAT
1 TATTTTGTA-TTATAT
12605454 TATTTTGTATTATAT
1 TATTTTGTATTATAT
12605469 TATT
1 TATT
12605473 ATATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTTGTATTATAT
Found at i:12605464 original size:23 final size:24
Alignment explanation
Indices: 12605423--12605479 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
12605413 AAAATTTTAA
* *
12605423 ATTATATCATTTTCATATT-TTTT
1 ATTATATTATTTTCATATTATATT
*
12605446 ATTTATATTATTTT-GTATTATATT
1 A-TTATATTATTTTCATATTATATT
12605470 ATTATATTAT
1 ATTATATTAT
12605480 ATTTTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (24 bp):
ATTATATTATTTTCATATTATATT
Found at i:12605479 original size:13 final size:12
Alignment explanation
Indices: 12605454--12605497 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
12605444 TTATTTATAT
*
12605454 TATTTTGTATTA
1 TATTTTATATTA
12605466 TATTATTATATTA
1 TATT-TTATATTA
*
12605479 TATTTTAAATTA
1 TATTTTATATTA
12605491 TCATTTT
1 T-ATTTT
12605498 TAATTATGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 12 0.43
13 16 0.57
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:12605502 original size:13 final size:12
Alignment explanation
Indices: 12605462--12605504 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
12605452 ATTATTTTGT
*
12605462 ATTATATTATTA
1 ATTATATTTTTA
*
12605474 TATTATATTTTAA
1 -ATTATATTTTTA
12605487 ATTATCATTTTTA
1 ATTAT-ATTTTTA
12605500 ATTAT
1 ATTAT
12605505 GAGTATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTATATTTTTA
Found at i:12609394 original size:11 final size:11
Alignment explanation
Indices: 12609353--12609394 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
12609343 ATTTTTTTTA
12609353 TAAAATTTAAT
1 TAAAATTTAAT
*
12609364 T-TAATTTAAT
1 TAAAATTTAAT
12609374 TATAAA-TTAAT
1 TA-AAATTTAAT
12609385 TAAAATTTAA
1 TAAAATTTAA
12609395 AGTGATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 12 0.46
11 12 0.46
12 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAAAATTTAAT
Found at i:12610005 original size:22 final size:22
Alignment explanation
Indices: 12609980--12610021 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12609970 ATAATGTTCG
*
12609980 ATTTAATTTGAATTAATTTTTT
1 ATTTAATTTAAATTAATTTTTT
12610002 ATTTAATTTAAATTAATTTT
1 ATTTAATTTAAATTAATTTT
12610022 AAATATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTAATTTAAATTAATTTTTT
Found at i:12610030 original size:18 final size:17
Alignment explanation
Indices: 12610006--12610062 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
12609996 TTTTTTATTT
12610006 AATTTAAATTAATTTTA
1 AATTTAAATTAATTTTA
*
12610023 AATATTAAA-TATATATTA
1 AAT-TTAAATTA-ATTTTA
*
12610041 AATTTAAATCAAATTTTA
1 AATTTAAAT-TAATTTTA
12610059 AATT
1 AATT
12610063 AAGATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 10 0.30
18 22 0.67
19 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTAAATTAATTTTA
Found at i:12610109 original size:16 final size:16
Alignment explanation
Indices: 12610085--12610123 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12610075 ATAAATTGAA
* *
12610085 TTAAATTATATATTTT
1 TTAATTTATATATATT
12610101 TTAATTTATATATATT
1 TTAATTTATATATATT
12610117 TTAATTT
1 TTAATTT
12610124 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATTTATATATATT
Found at i:12611646 original size:20 final size:21
Alignment explanation
Indices: 12611611--12611651 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
12611601 AGTTAAAATA
*
12611611 ATAATAATACAATTTATTTAT
1 ATAATAACACAATTTATTTAT
12611632 ATAATAACA-AATTTATTTAT
1 ATAATAACACAATTTATTTAT
12611652 TTATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAATAACACAATTTATTTAT
Found at i:12611744 original size:21 final size:21
Alignment explanation
Indices: 12611701--12611756 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
12611691 ATAGTTTTTA
* * *
12611701 AATAAAATTGA-TAATAAACT
1 AATAAAATTTATTTATAAAAT
12611721 AATAAAATTTATTTATAAAAT
1 AATAAAATTTATTTATAAAAT
*
12611742 AATAAATTATTATTT
1 AATAAAAT-TTATTT
12611757 GCAAAATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 10 0.33
21 14 0.47
22 6 0.20
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAAAATTTATTTATAAAAT
Found at i:12611762 original size:22 final size:21
Alignment explanation
Indices: 12611720--12611763 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
12611710 GATAATAAAC
*
12611720 TAATAAAATTTATTTATAAAA
1 TAATAAAATTTATTTACAAAA
* *
12611741 TAATAAATTATTATTTGCAAAA
1 TAATAAAAT-TTATTTACAAAA
12611763 T
1 T
12611764 CTTTAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TAATAAAATTTATTTACAAAA
Found at i:12613406 original size:18 final size:17
Alignment explanation
Indices: 12613383--12613425 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
12613373 ATTTATTTTA
12613383 TTTTATTTTAAATAATTT
1 TTTTATTTTAAAT-ATTT
* *
12613401 TTTTATATTATATATTT
1 TTTTATTTTAAATATTT
*
12613418 TTTAATTT
1 TTTTATTT
12613426 GTATCTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATTTTAAATATTT
Found at i:12616371 original size:19 final size:19
Alignment explanation
Indices: 12616347--12616383 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12616337 ATTAAAAGGT
*
12616347 ATAAATAAATTTTAAATTG
1 ATAAATAAATTTCAAATTG
*
12616366 ATAAATATATTTCAAATT
1 ATAAATAAATTTCAAATT
12616384 TAAAAAAATG
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:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
ATAAATAAATTTCAAATTG
Found at i:12616462 original size:14 final size:14
Alignment explanation
Indices: 12616425--12616467 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
12616415 AAGAATTTTA
*
12616425 AAAATAAAAAGATT
1 AAAATAAAAATATT
* *
12616439 ATAAAGAAAATTATT
1 A-AAATAAAAATATT
12616454 AAAATAAAAATATT
1 AAAATAAAAATATT
12616468 TTTTTGAGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (14 bp):
AAAATAAAAATATT
Found at i:12616859 original size:13 final size:14
Alignment explanation
Indices: 12616824--12616862 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
12616814 ATTTATTAAA
12616824 ATAATTTTAAATAT
1 ATAATTTTAAATAT
12616838 ATAATTTTAAATAT
1 ATAATTTTAAATAT
*
12616852 -TTATTTTAAAT
1 ATAATTTTAAAT
12616863 TATTAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAATTTTAAATAT
Found at i:12616866 original size:14 final size:13
Alignment explanation
Indices: 12616825--12616868 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
12616815 TTTATTAAAA
12616825 TAATTTTAAATAT
1 TAATTTTAAATAT
12616838 ATAATTTTAAATAT
1 -TAATTTTAAATAT
*
12616852 TTATTTTAAATTAT
1 TAATTTTAAA-TAT
12616866 TAA
1 TAA
12616869 ATATAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTTTAAATAT
Found at i:12617769 original size:14 final size:15
Alignment explanation
Indices: 12617745--12617775 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12617735 TAGAATTACA
12617745 ATTTAATATTTTTAT
1 ATTTAATATTTTTAT
12617760 ATTT-ATATTTTTAT
1 ATTTAATATTTTTAT
12617774 AT
1 AT
12617776 CATCATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTAATATTTTTAT
Found at i:12627922 original size:2 final size:2
Alignment explanation
Indices: 12627915--12627948 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12627905 TTGAAGTTTC
12627915 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
12627949 AGCTAAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12635785 original size:23 final size:24
Alignment explanation
Indices: 12635759--12635804 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
12635749 TTTATGTCAA
*
12635759 ATAAT-ATATCATTTTTA-AAATTG
1 ATAATAATAT-ATTTATATAAATTG
12635782 ATAATAATATATTTATATAAATT
1 ATAATAATATATTTATATAAATT
12635805 AAAACTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
ATAATAATATATTTATATAAATTG
Found at i:12641209 original size:29 final size:30
Alignment explanation
Indices: 12641154--12641223 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
12641144 TCGATTAATT
***
12641154 TTTAAAATTAAAAAATTTTATTCAA-TTAA
1 TTTAAAATTAAAAAATTTTAAAAAATTTAA
*
12641183 TTTAAATTTAAAAAATTTTAAAAAATTTAA
1 TTTAAAATTAAAAAATTTTAAAAAATTTAA
*
12641213 TTCAAAATTAA
1 TTTAAAATTAA
12641224 TCAAATGGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAAAATTAAAAAATTTTAAAAAATTTAA
Found at i:12643534 original size:52 final size:52
Alignment explanation
Indices: 12643378--12643534 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
12643368 TATAACCATA
* * *
12643378 CAAACTTGCCCATTAAGAA-TATCTTTTCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATTATC-TTTCTCTTAGAATTTTTCTCTTGTAAGT
* * *
12643430 CAAATTTGCCTATTAAGAATT-TCTTTCATTTTAAAATTTTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATTATCTTTC-TCTTAGAATTTTTCTCTTGTAAGT
* * *
12643482 CAAACTTACCTATTAAGAATTATCTTTCTCTTAGAATTTTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATTATCTTTCTCTTAGAATTTTTCTCTTGTAAGT
12643534 C
1 C
12643535 TTCTTGTCCA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
51 4 0.04
52 79 0.88
53 7 0.08
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.45
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATTATCTTTCTCTTAGAATTTTTCTCTTGTAAGT
Found at i:12643864 original size:24 final size:25
Alignment explanation
Indices: 12643835--12643936 Score: 91
Period size: 25 Copynumber: 4.1 Consensus size: 25
12643825 AAACTATACA
*
12643835 CTTTTCATATCTTAAACCTTTAGCT
1 CTTTCCATATCTTAAACCTTTAGCT
**
12643860 CTTTCCATATCTCGAA-CTTTCAGCT
1 CTTTCCATATCTTAAACCTTT-AGCT
** * **
12643885 CTTT-CACGTCTTGAACCTTCGGCT
1 CTTTCCATATCTTAAACCTTTAGCT
* *
12643909 CTTTCCATATCTTAAATCTTTAACT
1 CTTTCCATATCTTAAACCTTTAGCT
12643934 CTT
1 CTT
12643937 ATCACGTTTC
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
24 19 0.32
25 40 0.68
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.44
Consensus pattern (25 bp):
CTTTCCATATCTTAAACCTTTAGCT
Found at i:12643936 original size:49 final size:50
Alignment explanation
Indices: 12643856--12643960 Score: 126
Period size: 49 Copynumber: 2.1 Consensus size: 50
12643846 TTAAACCTTT
* * *
12643856 AGCTCTTTCCATATCTCGAACTTTCAGCTCTT-TCACGTCTT-GAACCTTC
1 AGCTCTTTCCATATCTCAAACTTTCAACTCTTATCACGT-TTCGAACATTC
* *
12643905 GGCTCTTTCCATATCTTAAATCTTT-AACTCTTATCACGTTTCGAACATTC
1 AGCTCTTTCCATATCTCAAA-CTTTCAACTCTTATCACGTTTCGAACATTC
12643955 AGCTCT
1 AGCTCT
12643961 GATACCACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
49 25 0.53
50 22 0.47
ACGTcount: A:0.21, C:0.30, G:0.10, T:0.40
Consensus pattern (50 bp):
AGCTCTTTCCATATCTCAAACTTTCAACTCTTATCACGTTTCGAACATTC
Found at i:12644033 original size:31 final size:31
Alignment explanation
Indices: 12643954--12644035 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
12643944 TTCGAACATT
*
12643954 CAGCTCTGATACCACTTGTTGGTGAATACCA
1 CAGCTCTGATACCATTTGTTGGTGAATACCA
*
12643985 CAGCTCTGATACTATTTGTTGAG-G-ATCACCA
1 CAGCTCTGATACCATTTGTTG-GTGAAT-ACCA
* *
12644016 TAGCTCTGATACGATTTGTT
1 CAGCTCTGATACCATTTGTT
12644036 AAGCTAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 2 0.04
31 42 0.93
32 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (31 bp):
CAGCTCTGATACCATTTGTTGGTGAATACCA
Found at i:12644634 original size:52 final size:52
Alignment explanation
Indices: 12644530--12644674 Score: 182
Period size: 52 Copynumber: 2.8 Consensus size: 52
12644520 ATAACTATAT
* * **
12644530 AAACTTGCCCATTAAGAATCTTTTTTTTTTTTAGAATTCTTCTCCTGTAAGTC
1 AAACTTGCCTATTAAGAATC-TTTTTTCTTTTAGAATTCTTCTCCTACAAGTC
**
12644583 AAACTTGCCTATTAAGAATCTTTTTTCTTTTAGAATTCTTCTTTTACAAGTC
1 AAACTTGCCTATTAAGAATCTTTTTTCTTTTAGAATTCTTCTCCTACAAGTC
* * ** *
12644635 AAACTTACCTATTAAGAATCATCATTCTCTTAGAATTCTT
1 AAACTTGCCTATTAAGAATCTTTTTTCTTTTAGAATTCTT
12644675 TTCTTGTAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 62 0.77
53 19 0.23
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.46
Consensus pattern (52 bp):
AAACTTGCCTATTAAGAATCTTTTTTCTTTTAGAATTCTTCTCCTACAAGTC
Found at i:12645057 original size:25 final size:24
Alignment explanation
Indices: 12644979--12645069 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 24
12644969 CACTTCTCAT
* * * *
12644979 ATCTTAAACCTTTAGCTCTTTTCGC
1 ATCTTGAACCTTCAACT-TTTTCAC
* *
12645004 ATCTCGAACTTTCAACTTTTTCATC
1 ATCTTGAACCTTCAACTTTTTCA-C
*
12645029 -TCTTGAACCTTCGACTTTTTTCAC
1 ATCTTGAACCTTCAAC-TTTTTCAC
*
12645053 ATCTTGAATCTTCAACT
1 ATCTTGAACCTTCAACT
12645070 CTTCTCACGT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
24 19 0.37
25 33 0.63
ACGTcount: A:0.22, C:0.27, G:0.07, T:0.44
Consensus pattern (24 bp):
ATCTTGAACCTTCAACTTTTTCAC
Found at i:12645077 original size:25 final size:25
Alignment explanation
Indices: 12644971--12645077 Score: 74
Period size: 25 Copynumber: 4.3 Consensus size: 25
12644961 AAACTATGCA
* * * *
12644971 CTTCTCATATCTTAAACCTTTAGCT
1 CTTCTCACATCTTGAACCTTCAACT
* * * *
12644996 CTTTTCGCATCTCGAACTTTCAACT
1 CTTCTCACATCTTGAACCTTCAACT
* *
12645021 -TTTTCATC-TCTTGAACCTTCGACT
1 CTTCTCA-CATCTTGAACCTTCAACT
* * *
12645045 TTTTTCACATCTTGAATCTTCAACT
1 CTTCTCACATCTTGAACCTTCAACT
12645070 CTTCTCAC
1 CTTCTCAC
12645078 GTTCCGAACC
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
24 19 0.30
25 44 0.70
ACGTcount: A:0.21, C:0.30, G:0.06, T:0.44
Consensus pattern (25 bp):
CTTCTCACATCTTGAACCTTCAACT
Found at i:12645140 original size:31 final size:30
Alignment explanation
Indices: 12645092--12645168 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
12645082 CGAACCTTTA
* *
12645092 GCTCTGATACCACTTA-TTGAGAAAT-ACCAC
1 GCTCTGATACTATTTATTTGAG--ATCACCAC
12645122 TGCTCTGATACTATTTATTTGAGATCACCAC
1 -GCTCTGATACTATTTATTTGAGATCACCAC
12645153 GTCTCTGATACTATTT
1 G-CTCTGATACTATTT
12645169 GTTAGGCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 3 0.07
31 33 0.80
32 5 0.12
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (30 bp):
GCTCTGATACTATTTATTTGAGATCACCAC
Found at i:12645814 original size:11 final size:11
Alignment explanation
Indices: 12645779--12645814 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
12645769 ACAAGCAATA
*
12645779 TCTAATAAATC
1 TCTAACAAATC
*
12645790 TCAAACAAATC
1 TCTAACAAATC
12645801 TCTAACAAATC
1 TCTAACAAATC
12645812 TCT
1 TCT
12645815 TATGAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:12646148 original size:25 final size:25
Alignment explanation
Indices: 12646055--12646155 Score: 105
Period size: 25 Copynumber: 4.1 Consensus size: 25
12646045 AACCATACAT
* * *
12646055 TTTTTACATCTTAAACCTTTAGCTC
1 TTTTCACATCTTGAACCTTCAGCTC
* ** *
12646080 TTCTCACATCTCAAACTTTCAGCTC
1 TTTTCACATCTTGAACCTTCAGCTC
*
12646105 -TTTCACATCTCGAACCTTCAGCTC
1 TTTTCACATCTTGAACCTTCAGCTC
* *
12646129 TTTTCACATCTTGAATCTTCAACTC
1 TTTTCACATCTTGAACCTTCAGCTC
12646154 TT
1 TT
12646156 CTTACGTTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 21 0.33
25 43 0.67
ACGTcount: A:0.23, C:0.31, G:0.05, T:0.42
Consensus pattern (25 bp):
TTTTCACATCTTGAACCTTCAGCTC
Found at i:12646155 original size:49 final size:50
Alignment explanation
Indices: 12646060--12646179 Score: 127
Period size: 49 Copynumber: 2.4 Consensus size: 50
12646050 TACATTTTTT
* * *
12646060 ACATCTTAAACCTTTAGCTCTTCTCACATCTCAAACTTTCAGCTCTT-TC
1 ACATCTCAAACCTTCAGCTCTTCTCACATCTCAAACTTTCAACTCTTCTC
* * ** *
12646109 ACATCTCGAACCTTCAGCTCTTTTCACATCTTGAA-TCTTCAACTCTTCTT
1 ACATCTCAAACCTTCAGCTCTTCTCACATCTCAAACT-TTCAACTCTTCTC
* *
12646159 ACGTTTCAAACCTTCAGCTCT
1 ACATCTCAAACCTTCAGCTCT
12646180 GATACCACTT
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.02
49 38 0.66
50 19 0.33
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (50 bp):
ACATCTCAAACCTTCAGCTCTTCTCACATCTCAAACTTTCAACTCTTCTC
Found at i:12646832 original size:52 final size:54
Alignment explanation
Indices: 12646742--12646874 Score: 166
Period size: 52 Copynumber: 2.5 Consensus size: 54
12646732 TATAACCATA
*
12646742 CAAACTTACCCATTAAGAATCT-TTT-TTCTCTTAAAATTCTTCTCCTGTAAGT
1 CAAACTTACCCATTAAGAATCTCTTTCTTCTCTTAAAATTCTTCTCCTGCAAGT
* * *
12646794 CAAACTTGCCCATTAAGAATCTCTTTCTT-T-TTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCCATTAAGAATCTCTTTCTTCTCTTAAAATTCTTCTCCTGCAAGT
* * *
12646846 TAAACTTATCTATTAAGAATCATCTTTCT
1 CAAACTTACCCATTAAGAATC-TCTTTCT
12646875 CTTAAAATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
52 57 0.81
53 11 0.16
54 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.43
Consensus pattern (54 bp):
CAAACTTACCCATTAAGAATCTCTTTCTTCTCTTAAAATTCTTCTCCTGCAAGT
Found at i:12647944 original size:52 final size:52
Alignment explanation
Indices: 12647843--12647999 Score: 197
Period size: 52 Copynumber: 3.0 Consensus size: 52
12647833 TATAACCATA
* * * * **
12647843 CAAATTTACCCATTAAGAATATTTTTTCTCTTAAAATTTTTCTCGTGTAAGT
1 CAAACTTACCTATTAAGAATCTTTTTTCTCTTAGAATTTTTCTATTGTAAGT
* * *
12647895 CAAACTTACCTATTAAGAATCTTTTTTCTTTTAGAATTCTTCTATTGTAAAT
1 CAAACTTACCTATTAAGAATCTTTTTTCTCTTAGAATTTTTCTATTGTAAGT
* * * *
12647947 CAAACTTACGTATTAAGAATCATCTTTCTCTTAGAATTTTTCTTTTGTAAGT
1 CAAACTTACCTATTAAGAATCTTTTTTCTCTTAGAATTTTTCTATTGTAAGT
12647999 C
1 C
12648000 TTATTGTCCA
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCTTTTTTCTCTTAGAATTTTTCTATTGTAAGT
Found at i:12656866 original size:128 final size:128
Alignment explanation
Indices: 12656605--12656852 Score: 349
Period size: 126 Copynumber: 1.9 Consensus size: 128
12656595 ACCCGAAAAG
* *
12656605 ATTGAATTATTTCTAGCACAGAAGACAAAAATCTTTATCATCCTGAGAATAGCTAATTTTTTCTG
1 ATTGAATTATTTCTAGCACAGAAGACAAAAATCTTTATCATCATGAGAATAGCTAATTTTTACTG
* * *
12656670 CTTCAGCAGGCTGAATGAAAGCAATTTACCAAACTACAAGGTTTACCGTTGAAACCCAGATAA
66 CTTCAGCAGGCTGAATGAAAGCAATTTAACAAACTACAAGGGTTACCATTGAAACCCAGATAA
* * *
12656733 ATTGAATTAATTTC-AGCACAGAAGAC-ACAATTTTTATGATCATGAGAATAGCTAA-TTTTACT
1 ATTGAATT-ATTTCTAGCACAGAAGACAAAAATCTTTATCATCATGAGAATAGCTAATTTTTACT
* *
12656795 GTTTCAGCAGGCTGAATGAAAGCAATTTCAAACAAACCTACAGGGGTTACCATTGAAA
65 GCTTCAGCAGGCTGAATGAAAGCAATTT--AACAAA-CTACAAGGGTTACCATTGAAA
12656853 GCTAATGATT
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
126 33 0.31
127 25 0.24
128 25 0.24
129 23 0.22
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (128 bp):
ATTGAATTATTTCTAGCACAGAAGACAAAAATCTTTATCATCATGAGAATAGCTAATTTTTACTG
CTTCAGCAGGCTGAATGAAAGCAATTTAACAAACTACAAGGGTTACCATTGAAACCCAGATAA
Found at i:12660885 original size:103 final size:105
Alignment explanation
Indices: 12660680--12660894 Score: 310
Period size: 103 Copynumber: 2.1 Consensus size: 105
12660670 GCCTTAACAT
* * * *
12660680 CATTTAAGTATATTCCATAAATAAGAGGAAAGTGAATCTTTTTAAGTACTAGATTTGATGCAATC
1 CATTTAAGCATATTCCATAAATAAAAGGAAAATGAATCTTTTTAAATACTAGATTTGATGCAATC
*
12660745 ACTTTAACTCCAAGGGCAAACTTCATAGTTTGAAACTTTG
66 ACTTTAACTCCAAGGGCAAACTTCAAAGTTTGAAACTTTG
* * *
12660785 CATTTAAGCAT-TTCTATAACTAAAAGGAAAATGAATC-TTTTAAATACTAGATTTGATGCTATC
1 CATTTAAGCATATTCCATAAATAAAAGGAAAATGAATCTTTTTAAATACTAGATTTGATGCAATC
* *
12660848 ACTTTAACTCCAAGGGTAAACTT-AGAAGTTTGTAACTTTG
66 ACTTTAACTCCAAGGGCAAACTTCA-AAGTTTGAAACTTTG
12660888 CATTTAA
1 CATTTAA
12660895 AAGAGTATTC
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
102 1 0.01
103 66 0.67
104 22 0.22
105 10 0.10
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (105 bp):
CATTTAAGCATATTCCATAAATAAAAGGAAAATGAATCTTTTTAAATACTAGATTTGATGCAATC
ACTTTAACTCCAAGGGCAAACTTCAAAGTTTGAAACTTTG
Found at i:12662796 original size:27 final size:27
Alignment explanation
Indices: 12662754--12662805 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
12662744 TATTTATTCG
* *
12662754 TTAAATATTATTATTTAAAATTAGTCA
1 TTAAATATCATCATTTAAAATTAGTCA
12662781 TTAAATATCATCATTTAAAATTAGT
1 TTAAATATCATCATTTAAAATTAGT
12662806 TAGTCGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (27 bp):
TTAAATATCATCATTTAAAATTAGTCA
Found at i:12662882 original size:28 final size:31
Alignment explanation
Indices: 12662841--12662914 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 31
12662831 TTACAAAATC
12662841 ATAATTCAAATATTACATTAAA-A-ATTTTT
1 ATAATTCAAATATTACATTAAATATATTTTT
*
12662870 A-AATTCAAATATTATATTAAATATATTTTT
1 ATAATTCAAATATTACATTAAATATATTTTT
* *
12662900 ATAATTTAAAAATTA
1 ATAATTCAAATATTA
12662915 TTCATGTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 19 0.49
29 2 0.05
30 7 0.18
31 11 0.28
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
ATAATTCAAATATTACATTAAATATATTTTT
Found at i:12674601 original size:16 final size:18
Alignment explanation
Indices: 12674574--12674606 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12674564 TCAACCCTTT
12674574 TCTTTCATA-TTTAATTC
1 TCTTTCATATTTTAATTC
12674591 TCTTT-ATATTTTAATT
1 TCTTTCATATTTTAATT
12674607 TTGGGTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (18 bp):
TCTTTCATATTTTAATTC
Found at i:12678171 original size:100 final size:99
Alignment explanation
Indices: 12677991--12678172 Score: 285
Period size: 100 Copynumber: 1.8 Consensus size: 99
12677981 ATTCAGCCAT
* *
12677991 AACAGACAAAAGTGTTTGAAGATGGAGGTTAACCCACGTGAGCAACGATCTAAGGTTTCTGACCT
1 AACAGACAAAAGTGTTTAAAGATGGAGGTTAACCCACATGAGCAACGATCTAAGGTTTCTGACCT
*
12678056 TGTCTTTTCTATTTTTTATTCCATTTTTGGTTAG
66 TGTCTTTCCTATTTTTTATTCCATTTTTGGTTAG
* * *
12678090 AACAGACAAAA-TGATTTTAAAGATGGAGGTTAACCCACATGCGCAATGATCTCAGGTTTCTGAC
1 AACAGACAAAAGTG--TTTAAAGATGGAGGTTAACCCACATGAGCAACGATCTAAGGTTTCTGAC
12678154 CTTGTCTTTCCTATTTTTT
64 CTTGTCTTTCCTATTTTTT
12678173 TATCGACATC
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
98 2 0.03
99 11 0.15
100 62 0.83
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (99 bp):
AACAGACAAAAGTGTTTAAAGATGGAGGTTAACCCACATGAGCAACGATCTAAGGTTTCTGACCT
TGTCTTTCCTATTTTTTATTCCATTTTTGGTTAG
Found at i:12681532 original size:236 final size:237
Alignment explanation
Indices: 12681119--12681572 Score: 766
Period size: 236 Copynumber: 1.9 Consensus size: 237
12681109 TTATTTCATA
* * *
12681119 TTCATAGTAAATTTCCAACCCTTGTTAGAGGAATTTGTACTTCTCCAGAAAGAAAGAGACACTCA
1 TTCATAGTAAATTTCAAACCCTTGTGACAGGAATTTGTACTTCTCCAGAAAGAAAGAGACACTCA
* *
12681184 GCTGCTGACGGTCTCTACTGCAGTCTAATGCATTGTAATGACTGAAAAAGAAACGGTTGAAGATA
66 ACTGCTGACAGTCTCTACTGCAGTCTAATGCATTGTAATGACTGAAAAAGAAACGGTTGAAGATA
*
12681249 GAGCTTGGCATATATTGAAATGCAACACTTTCCCATAGCAACTCCAATGGTCA-GGAATACATGT
131 GAGCTTGGCATAGATTGAAATGCAACACTTTCCCATAGCAACTCCAATGGTCAGGGAATACATGT
12681313 GAAAAGGAAACAAAAATTTTCATAGATAACAAGAGGTTTTAT
196 GAAAAGGAAACAAAAATTTTCATAGATAACAAGAGGTTTTAT
* *
12681355 TTCATAGTAAATTTGAAACCCTTGTGACAGGAATTTTTACTTCTCCAGAAAGAAAGAGACACTCA
1 TTCATAGTAAATTTCAAACCCTTGTGACAGGAATTTGTACTTCTCCAGAAAGAAAGAGACACTCA
* * * *
12681420 ATTGCTGACAGTCTTTACTGCAGTGTAATGCATTGTAATGACTGAAAAAGAAGCGGTTGAAGATA
66 ACTGCTGACAGTCTCTACTGCAGTCTAATGCATTGTAATGACTGAAAAAGAAACGGTTGAAGATA
*
12681485 TAGCTTGGCATAGATTGAAATGCAACACTTTCCCATAGCAACTCCAATGGTCAGGGGAATACATG
131 GAGCTTGGCATAGATTGAAATGCAACACTTTCCCATAGCAACTCCAATGGTCA-GGGAATACATG
*
12681550 TGAAAAGGAAGCAAAAATTTTCA
195 TGAAAAGGAAACAAAAATTTTCA
12681573 CACTGAAGAT
Statistics
Matches: 202, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
236 170 0.84
238 32 0.16
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (237 bp):
TTCATAGTAAATTTCAAACCCTTGTGACAGGAATTTGTACTTCTCCAGAAAGAAAGAGACACTCA
ACTGCTGACAGTCTCTACTGCAGTCTAATGCATTGTAATGACTGAAAAAGAAACGGTTGAAGATA
GAGCTTGGCATAGATTGAAATGCAACACTTTCCCATAGCAACTCCAATGGTCAGGGAATACATGT
GAAAAGGAAACAAAAATTTTCATAGATAACAAGAGGTTTTAT
Found at i:12683993 original size:4 final size:4
Alignment explanation
Indices: 12683984--12684008 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12683974 AGCAATGGAA
12683984 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
12684009 GAGGTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:12684340 original size:16 final size:15
Alignment explanation
Indices: 12684315--12684344 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12684305 GTAAATAAAT
12684315 TTAAAAAATTTATTA
1 TTAAAAAATTTATTA
12684330 TTAACAAAATTTATT
1 TTAA-AAAATTTATT
12684345 GTTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAAAAATTTATTA
Found at i:12687299 original size:21 final size:20
Alignment explanation
Indices: 12687275--12687324 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
12687265 AATAAAAAAA
12687275 TTAAAATATT-AATATTATCTT
1 TTAAAATATTAAATA-TAT-TT
12687296 TTAATAAT-TTAAATATATTT
1 TTAA-AATATTAAATATATTT
12687316 TATAAAATA
1 T-TAAAATA
12687325 ATTTATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 7 0.28
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAATATTAAATATATTT
Found at i:12688626 original size:111 final size:111
Alignment explanation
Indices: 12688286--12688614 Score: 579
Period size: 111 Copynumber: 3.0 Consensus size: 111
12688276 TAGTTAGTTG
12688286 CTTTCTGTGCTGATATGTTGGCAAAGTTCAAAATTTTGGTTTCGGAATGCTAAGTAATCAATTGT
1 CTTTCTGTGCTGATATGTTGGCAAAGTTCAAAATTTTGGTTTCGGAATGCTAAGTAATCAATTGT
12688351 GAAGTATGTTAATGGTACTTGAAATAGTTCTGATTATTTGTTGAAA
66 GAAGTATGTTAATGGTACTTGAAATAGTTCTGATTATTTGTTGAAA
12688397 CTTTCTGTGCTGATATGTTGGCAAAGTTCAAAATTTTGGTTTCGGAATGCTAAGTAATCAATTGT
1 CTTTCTGTGCTGATATGTTGGCAAAGTTCAAAATTTTGGTTTCGGAATGCTAAGTAATCAATTGT
12688462 GAAGTATGTTAATGGTACTTGAAATAGTTCTGATTATTTGTTGAAA
66 GAAGTATGTTAATGGTACTTGAAATAGTTCTGATTATTTGTTGAAA
* * **
12688508 CTTTCTGTGCTGATATGTTGGCAAAGTTCTAAATTTTGATTTCAGG-ATGCCGAGTAATCAATTG
1 CTTTCTGTGCTGATATGTTGGCAAAGTTCAAAATTTTGGTTTC-GGAATGCTAAGTAATCAATTG
* * *
12688572 TGAAGTATGTTTATAGTACTTGAAATAGTTCTGATTGTTTGTT
65 TGAAGTATGTTAATGGTACTTGAAATAGTTCTGATTATTTGTT
12688615 AAAATTATCT
Statistics
Matches: 210, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
111 208 0.99
112 2 0.01
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (111 bp):
CTTTCTGTGCTGATATGTTGGCAAAGTTCAAAATTTTGGTTTCGGAATGCTAAGTAATCAATTGT
GAAGTATGTTAATGGTACTTGAAATAGTTCTGATTATTTGTTGAAA
Found at i:12692205 original size:454 final size:454
Alignment explanation
Indices: 12691358--12692262 Score: 1801
Period size: 454 Copynumber: 2.0 Consensus size: 454
12691348 TGTAGGGGTC
12691358 GAAACCATTTCCCATGTCAAACAATGGCATTTAGATAGGCCATTTTATTGGAAATAAAGAAATAA
1 GAAACCATTTCCCATGTCAAACAATGGCATTTAGATAGGCCATTTTATTGGAAATAAAGAAATAA
12691423 ATAAATTGTGCACAAGATGGAAACCATATCAACCACAATGGTGAACCCAAAATAGCATTCAGCCC
66 ATAAATTGTGCACAAGATGGAAACCATATCAACCACAATGGTGAACCCAAAATAGCATTCAGCCC
12691488 TGTGACGATTTCGACAATTTCCAATTGAACTGGTAGATCGAAGTGGCCATGTCTATGCCAACTTT
131 TGTGACGATTTCGACAATTTCCAATTGAACTGGTAGATCGAAGTGGCCATGTCTATGCCAACTTT
12691553 GAGAAACTTGTAGCTACTCCTCTCATTAAATTTCCTTACTGTTATTTTTGCTTATTATGGGCTAG
196 GAGAAACTTGTAGCTACTCCTCTCATTAAATTTCCTTACTGTTATTTTTGCTTATTATGGGCTAG
12691618 CAGTTAGCTAGGAGTTACTTGTTGGTGTCAGCCCATGAAAGGCAGAATAGACATTCAAGAGTCTG
261 CAGTTAGCTAGGAGTTACTTGTTGGTGTCAGCCCATGAAAGGCAGAATAGACATTCAAGAGTCTG
12691683 TTAACTGTTATGATCAGTACAAATGATAATCTTGGAATGTTATATGGAAGTCAGTGAATGAATCA
326 TTAACTGTTATGATCAGTACAAATGATAATCTTGGAATGTTATATGGAAGTCAGTGAATGAATCA
12691748 GTATTGCCGTTATTCCTTTCATCATTGGATTTTCTCTCTCTTTTTCCTCTCTCACGATTCTCAT
391 GTATTGCCGTTATTCCTTTCATCATTGGATTTTCTCTCTCTTTTTCCTCTCTCACGATTCTCAT
12691812 GAAACCATTTCCCATGTCAAACAATGGCATTTAGATAGGCCATTTTATTGGAAATAAAGAAATAA
1 GAAACCATTTCCCATGTCAAACAATGGCATTTAGATAGGCCATTTTATTGGAAATAAAGAAATAA
*
12691877 ATAAATTGTGCACAAGATGGAAACCATATCAACCACAATGGTGAACCCAAAATAGCATTCAGTCC
66 ATAAATTGTGCACAAGATGGAAACCATATCAACCACAATGGTGAACCCAAAATAGCATTCAGCCC
12691942 TGTGACGATTTCGACAATTTCCAATTGAACTGGTAGATCGAAGTGGCCATGTCTATGCCAACTTT
131 TGTGACGATTTCGACAATTTCCAATTGAACTGGTAGATCGAAGTGGCCATGTCTATGCCAACTTT
12692007 GAGAAACTTGTAGCTACTCCTCTCATTAAATTTCCTTACTGTTATTTTTGCTTATTATGGGCTAG
196 GAGAAACTTGTAGCTACTCCTCTCATTAAATTTCCTTACTGTTATTTTTGCTTATTATGGGCTAG
12692072 CAGTTAGCTAGGAGTTACTTGTTGGTGTCAGCCCATGAAAGGCAGAATAGACATTCAAGAGTCTG
261 CAGTTAGCTAGGAGTTACTTGTTGGTGTCAGCCCATGAAAGGCAGAATAGACATTCAAGAGTCTG
12692137 TTAACTGTTATGATCAGTACAAATGATAATCTTGGAATGTTATATGGAAGTCAGTGAATGAATCA
326 TTAACTGTTATGATCAGTACAAATGATAATCTTGGAATGTTATATGGAAGTCAGTGAATGAATCA
12692202 GTATTGCCGTTATTCCTTTCATCATTGGATTTTCTCTCTCTTTTTCCTCTCTCACGATTCT
391 GTATTGCCGTTATTCCTTTCATCATTGGATTTTCTCTCTCTTTTTCCTCTCTCACGATTCT
12692263 TTCTTCTTTC
Statistics
Matches: 450, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
454 450 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (454 bp):
GAAACCATTTCCCATGTCAAACAATGGCATTTAGATAGGCCATTTTATTGGAAATAAAGAAATAA
ATAAATTGTGCACAAGATGGAAACCATATCAACCACAATGGTGAACCCAAAATAGCATTCAGCCC
TGTGACGATTTCGACAATTTCCAATTGAACTGGTAGATCGAAGTGGCCATGTCTATGCCAACTTT
GAGAAACTTGTAGCTACTCCTCTCATTAAATTTCCTTACTGTTATTTTTGCTTATTATGGGCTAG
CAGTTAGCTAGGAGTTACTTGTTGGTGTCAGCCCATGAAAGGCAGAATAGACATTCAAGAGTCTG
TTAACTGTTATGATCAGTACAAATGATAATCTTGGAATGTTATATGGAAGTCAGTGAATGAATCA
GTATTGCCGTTATTCCTTTCATCATTGGATTTTCTCTCTCTTTTTCCTCTCTCACGATTCTCAT
Found at i:12695830 original size:2 final size:2
Alignment explanation
Indices: 12695825--12695858 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12695815 AAAAAAAAAT
*
12695825 TA TA TA TA TG 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
12695859 GTTCTTCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12696601 original size:26 final size:28
Alignment explanation
Indices: 12696566--12696623 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
12696556 AAATAATAAT
*
12696566 AATTATTATTATAATTATGA-TTAAAAA
1 AATTATTATTATAATTATGAGTGAAAAA
*
12696593 AATT-TTATTATAATTGTGAGTGAAAAA
1 AATTATTATTATAATTATGAGTGAAAAA
12696620 AATT
1 AATT
12696624 CAATGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (28 bp):
AATTATTATTATAATTATGAGTGAAAAA
Found at i:12697860 original size:4 final size:4
Alignment explanation
Indices: 12697851--12697875 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12697841 CAGTGTGCCA
12697851 CTGG CTGG CTGG CTGG CTGG CTGG C
1 CTGG CTGG CTGG CTGG CTGG CTGG C
12697876 AATGGCCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.48, T:0.24
Consensus pattern (4 bp):
CTGG
Found at i:12698746 original size:11 final size:11
Alignment explanation
Indices: 12698730--12698755 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12698720 TTAATAAAAT
12698730 ATATGAATATA
1 ATATGAATATA
12698741 ATATGAATATA
1 ATATGAATATA
12698752 ATAT
1 ATAT
12698756 AAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
ATATGAATATA
Found at i:12704633 original size:23 final size:21
Alignment explanation
Indices: 12704592--12704633 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
12704582 AGCTGTGAGC
*
12704592 TTTTTTTTTTGTTGTAAATAT
1 TTTTTTTTTTGTTGAAAATAT
12704613 TTTTGTTTTTTGTATGAAAAT
1 TTTT-TTTTTTGT-TGAAAAT
12704634 TCAAGTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (21 bp):
TTTTTTTTTTGTTGAAAATAT
Found at i:12705623 original size:4 final size:4
Alignment explanation
Indices: 12705614--12705639 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12705604 GCAAAGAGAG
12705614 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
12705640 AGAGGGTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:12709327 original size:25 final size:25
Alignment explanation
Indices: 12709281--12709328 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12709271 TTTAGATGAA
**
12709281 ATTTATAAAATTCTTTTTTAAAATG
1 ATTTATAAAATTCTTTAATAAAATG
12709306 ATTTAATAAAA-TCTTTAATAAAA
1 ATTT-ATAAAATTCTTTAATAAAA
12709329 AATTCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTATAAAATTCTTTAATAAAATG
Found at i:12709587 original size:21 final size:19
Alignment explanation
Indices: 12709541--12709588 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
12709531 GTAACGAGAT
*
12709541 TTTTTAATTTTTATTTTCG
1 TTTTTAGTTTTTATTTTCG
*
12709560 ATTTTAGTTTTTATTTAATCG
1 TTTTTAGTTTTTATTT--TCG
12709581 TTTTTAGT
1 TTTTTAGT
12709589 AGAAAACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.58
21 10 0.42
ACGTcount: A:0.19, C:0.04, G:0.08, T:0.69
Consensus pattern (19 bp):
TTTTTAGTTTTTATTTTCG
Done.