Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 11 of 240
Found at i:4072908 original size:50 final size:50
Alignment explanation
Indices: 4072833--4073075 Score: 351
Period size: 50 Copynumber: 4.8 Consensus size: 50
4072823 ATTTGGGTAA
4072833 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
4072883 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGTATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
4072933 AGAGGTCCCATATAAGACCATGTCTGGGACATGTCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
4072983 AGAGGTCCCCTATAAGACCATGTTTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
4073033 AGAACATCCCATGTAAGACCATGTCTGGAACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
4073076 TGTTATTATC
Statistics
Matches: 172, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 140 0.81
51 32 0.19
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:4074220 original size:29 final size:30
Alignment explanation
Indices: 4074183--4074239 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
4074173 TCCGAGCCTT
* *
4074183 GGGGAAAAAT-GTAATTATGTAAAAGTTTA
1 GGGGAAAAATCATAATTATGAAAAAGTTTA
* *
4074212 GGGGCAAAATCATAATTTTGAAAAAGTT
1 GGGGAAAAATCATAATTATGAAAAAGTT
4074240 AGAGTCGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 9 0.39
30 14 0.61
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.30
Consensus pattern (30 bp):
GGGGAAAAATCATAATTATGAAAAAGTTTA
Found at i:4074652 original size:50 final size:50
Alignment explanation
Indices: 4074577--4074836 Score: 171
Period size: 50 Copynumber: 4.8 Consensus size: 50
4074567 ATTTGGGTAA
4074577 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
4074627 AGAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTTGCATCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * ** * * *
4074677 -GCGTTGGCATCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAG
1 AGAGGTCCCAT---G-T-A-A-G----A--C-----CATGTCTGGGACATGGCATTGGCACCGAG
4074741 ATG
48 ATG
* * *
4074744 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
4074794 AGAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
4074837 TGTTATTATC
Statistics
Matches: 158, Mismatches: 32, Indels: 39
0.69 0.14 0.17
Matches are distributed among these distances:
49 6 0.04
50 76 0.48
51 33 0.21
52 1 0.01
53 1 0.01
54 1 0.01
55 1 0.01
56 1 0.01
57 1 0.01
60 1 0.01
61 1 0.01
62 1 0.01
63 1 0.01
64 1 0.01
67 27 0.17
68 5 0.03
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:4074677 original size:17 final size:17
Alignment explanation
Indices: 4074655--4074689 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4074645 CATGTCTGGA
*
4074655 ACATGGCGTTTGCATCG
1 ACATGGCGTTGGCATCG
4074672 ACATGGCGTTGGCATCG
1 ACATGGCGTTGGCATCG
4074689 A
1 A
4074690 GATGAGAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (17 bp):
ACATGGCGTTGGCATCG
Found at i:4074712 original size:67 final size:67
Alignment explanation
Indices: 4074604--4074731 Score: 220
Period size: 67 Copynumber: 1.9 Consensus size: 67
4074594 CCATGTCTGG
4074604 GACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTTGCA
1 GACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTTGCA
4074669 TC
66 TC
* * * *
4074671 GACATGGCGTTGGCATCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTT
1 GACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTT
4074732 GGCACCGAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.23
Consensus pattern (67 bp):
GACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTTGCA
TC
Found at i:4074827 original size:51 final size:50
Alignment explanation
Indices: 4074671--4074836 Score: 233
Period size: 50 Copynumber: 3.3 Consensus size: 50
4074661 CGTTTGCATC
*
4074671 GACATGGCGTTGGCATCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
1 GACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
* * *
4074721 GATATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACCATGTCTGG
1 GACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
* * ** *
4074771 GACATGGCATGGGCACCGAGATGAGAACATCCCATGTAAGACCATGTTTGG
1 GACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTCTGG
*
4074822 GACATGGCTTTGGCA
1 GACATGGCGTTGGCA
4074837 TGTTATTATC
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 68 0.67
51 33 0.33
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (50 bp):
GACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
Found at i:4078404 original size:60 final size:60
Alignment explanation
Indices: 4078331--4078452 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 60
4078321 ATACTAAACT
* * *
4078331 AAACACAACAATTTATAA-ATTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACA-TAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
*
4078391 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAGATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
4078451 AA
1 AA
4078453 TATTCATACA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
60 56 0.98
61 1 0.02
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:4078469 original size:21 final size:21
Alignment explanation
Indices: 4078445--4078486 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4078435 ATTATAAGAT
4078445 AATTACAATATTCATACAAAA
1 AATTACAATATTCATACAAAA
4078466 AATTACAATATTCATACAAAA
1 AATTACAATATTCATACAAAA
4078487 TACTAATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTACAATATTCATACAAAA
Found at i:4078629 original size:4 final size:4
Alignment explanation
Indices: 4078620--4078649 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
4078610 CATTACATTT
4078620 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
4078650 CTTCTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:4079428 original size:21 final size:21
Alignment explanation
Indices: 4079378--4079456 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
4079368 ATAGGGAGAG
* *
4079378 TTAAATTATTATTAAACT-TAA
1 TTAAATTAATATTAAA-TATTA
**
4079399 TTACTTTAATATTAAATATTA
1 TTAAATTAATATTAAATATTA
*
4079420 TTAAATTAATA--AAATACTA
1 TTAAATTAATATTAAATATTA
4079439 TTAACA-TAGATATTAAAT
1 TTAA-ATTA-ATATTAAAT
4079457 TAAATTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
19 13 0.28
20 5 0.11
21 24 0.52
22 4 0.09
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (21 bp):
TTAAATTAATATTAAATATTA
Found at i:4080715 original size:10 final size:9
Alignment explanation
Indices: 4080684--4080712 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
4080674 TACTGCTCAT
4080684 CCACTTCCC
1 CCACTTCCC
4080693 CCACTTCCC
1 CCACTTCCC
4080702 CCACTTCCC
1 CCACTTCCC
4080711 CC
1 CC
4080713 CACATATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.69, G:0.00, T:0.21
Consensus pattern (9 bp):
CCACTTCCC
Found at i:4084628 original size:13 final size:13
Alignment explanation
Indices: 4084610--4084635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4084600 ACTTAAAAAG
4084610 GTACCAAATTCAA
1 GTACCAAATTCAA
4084623 GTACCAAATTCAA
1 GTACCAAATTCAA
4084636 AATCTTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTACCAAATTCAA
Found at i:4107424 original size:21 final size:21
Alignment explanation
Indices: 4107400--4107441 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4107390 ATCGTGAAAG
*
4107400 AAGGATTGGAGACGGCGGAGA
1 AAGGACTGGAGACGGCGGAGA
*
4107421 AAGGGCTGGAGACGGCGGAGA
1 AAGGACTGGAGACGGCGGAGA
4107442 GAGGGATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.50, T:0.07
Consensus pattern (21 bp):
AAGGACTGGAGACGGCGGAGA
Found at i:4107446 original size:21 final size:21
Alignment explanation
Indices: 4107406--4107446 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4107396 AAAGAAGGAT
4107406 TGGAGACGGCGGAGAAAGGGC
1 TGGAGACGGCGGAGAAAGGGC
*
4107427 TGGAGACGGCGGAGAGAGGG
1 TGGAGACGGCGGAGAAAGGG
4107447 ATCTTTACAG
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:0.27, C:0.12, G:0.56, T:0.05
Consensus pattern (21 bp):
TGGAGACGGCGGAGAAAGGGC
Found at i:4124367 original size:13 final size:13
Alignment explanation
Indices: 4124349--4124402 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
4124339 GTATCATCAG
4124349 AAGAGAGAAAGAA
1 AAGAGAGAAAGAA
*
4124362 AAGAGAGAAAGGAG
1 AAGAGAGAAA-GAA
4124376 AAGAAGAAGAAA-AA
1 AAG-AG-AGAAAGAA
4124390 AA-A-AGAAAGAA
1 AAGAGAGAAAGAA
4124401 AA
1 AA
4124403 AGATAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
12 1 0.03
13 10 0.29
14 8 0.23
15 2 0.06
16 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAGAGAGAAAGAA
Found at i:4124518 original size:61 final size:59
Alignment explanation
Indices: 4124452--4124609 Score: 165
Period size: 60 Copynumber: 2.6 Consensus size: 59
4124442 TTAAAGATTG
* * * * *
4124452 ATTAGTATTTTGTATGAATATTGTAATTTTTTTGTTTTTATAATTATTTTAAAATTAATTT
1 ATTAGTATTTAGGAT-AATATTATAA-ATTTTTGTGTTTATAATTATTTTAAAATTAATTT
* * * *
4124513 GTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTTAAAATTAATTT
1 ATTAGT-ATTTAGGATAATATTATAAATTTTTGTGTTTATAATTATTTTAAAATTAATTT
* *
4124573 ATTAGTAATTTAGGATTAA-GTTATAAATTGTTGTGTT
1 ATTAGT-ATTTAGGA-TAATATTATAAATTTTTGTGTT
4124610 GTGTTTAGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
60 62 0.75
61 14 0.17
62 7 0.08
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (59 bp):
ATTAGTATTTAGGATAATATTATAAATTTTTGTGTTTATAATTATTTTAAAATTAATTT
Found at i:4124556 original size:60 final size:60
Alignment explanation
Indices: 4124480--4124609 Score: 215
Period size: 60 Copynumber: 2.2 Consensus size: 60
4124470 TATTGTAATT
* * *
4124480 TTTTTGTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAA
1 TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
4124540 TTTTTGTGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
1 TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
4124600 TTGTTGTGTT
1 TTTTTGTGTT
4124610 GTGTTTAGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (60 bp):
TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
Found at i:4125003 original size:55 final size:54
Alignment explanation
Indices: 4124920--4125032 Score: 172
Period size: 55 Copynumber: 2.1 Consensus size: 54
4124910 TTAAAAAAAA
* * *
4124920 TTTTAATTGCGCCTATTTGACAGACGCGAATCAATTTTTTATATTAAAAAATATT
1 TTTTAATCGCGCCTATCTAACAGACGCGAATCAATTTTTTATATT-AAAAATATT
* *
4124975 TTTTAATCGCGCCTATCTAATAGGCGCGAATCAATTTTTTATATTAAAAATATT
1 TTTTAATCGCGCCTATCTAACAGACGCGAATCAATTTTTTATATTAAAAATATT
4125029 TTTT
1 TTTT
4125033 GTTTAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 13 0.25
55 40 0.75
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (54 bp):
TTTTAATCGCGCCTATCTAACAGACGCGAATCAATTTTTTATATTAAAAATATT
Found at i:4125057 original size:20 final size:22
Alignment explanation
Indices: 4125007--4125058 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
4124997 GGCGCGAATC
*
4125007 AATTTTTTATATTAAAAATATT
1 AATTTTTTATAATAAAAATATT
*
4125029 -TTTTGTTTA-AAT-AAAATATT
1 AATTT-TTTATAATAAAAATATT
4125049 AATTTTTTAT
1 AATTTTTTAT
4125059 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 7
0.71 0.09 0.21
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTTTTATAATAAAAATATT
Found at i:4133109 original size:18 final size:17
Alignment explanation
Indices: 4133072--4133110 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
4133062 TTTTTTATTT
4133072 TAAAATTTTTATTAAAA
1 TAAAATTTTTATTAAAA
4133089 TAAAATTTTAATATT-AAA
1 TAAAATTTT--TATTAAAA
4133107 TAAA
1 TAAA
4133111 TATTAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 7 0.35
19 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTTTATTAAAA
Found at i:4133111 original size:17 final size:19
Alignment explanation
Indices: 4133081--4133117 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
4133071 TTAAAATTTT
*
4133081 TATTAAAATAAAATTTTAA
1 TATTAAAATAAAATATTAA
4133100 TATT-AAAT-AAATATTAA
1 TATTAAAATAAAATATTAA
4133117 T
1 T
4133118 GTAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTAAAATAAAATATTAA
Found at i:4133536 original size:25 final size:25
Alignment explanation
Indices: 4133508--4133556 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
4133498 TTGTTACAAA
*
4133508 ATATTTGCATTATGGTTCACAATTT
1 ATATTTGCATTATGGTCCACAATTT
4133533 ATATTTGCATTATGGTCCACAATT
1 ATATTTGCATTATGGTCCACAATT
4133557 GCATTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (25 bp):
ATATTTGCATTATGGTCCACAATTT
Found at i:4136530 original size:24 final size:24
Alignment explanation
Indices: 4136503--4136554 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4136493 TTAGTAAGTC
*
4136503 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4136527 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4136551 AAAT
1 AAAT
4136555 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4148908 original size:11 final size:11
Alignment explanation
Indices: 4148894--4148939 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
4148884 TTTATTGTTG
*
4148894 TTTTTTTATTA
1 TTTTGTTATTA
* *
4148905 TTTTGTTGTAA
1 TTTTGTTATTA
4148916 TTTTGTTATTA
1 TTTTGTTATTA
*
4148927 TATTGTTATTA
1 TTTTGTTATTA
4148938 TT
1 TT
4148940 CTATTGTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:4148912 original size:19 final size:21
Alignment explanation
Indices: 4148886--4148933 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
4148876 AAATATTTTT
4148886 TATTGTTGT-TTTT-TTATTA
1 TATTGTTGTATTTTGTTATTA
*
4148905 TTTTGTTGTAATTTTGTTATTA
1 TATTGTTGT-ATTTTGTTATTA
4148927 TATTGTT
1 TATTGTT
4148934 ATTATTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
21 4 0.17
22 12 0.50
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (21 bp):
TATTGTTGTATTTTGTTATTA
Found at i:4148944 original size:14 final size:14
Alignment explanation
Indices: 4148921--4148950 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4148911 TGTAATTTTG
4148921 TTATTATATTGTTA
1 TTATTATATTGTTA
*
4148935 TTATTCTATTGTTA
1 TTATTATATTGTTA
4148949 TT
1 TT
4148951 GTTTAGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (14 bp):
TTATTATATTGTTA
Found at i:4156939 original size:45 final size:45
Alignment explanation
Indices: 4156868--4156956 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
4156858 TATCGTTTAA
4156868 TTAATTGTTTATTATTATATTATTATATA-ATCAA-TAATATTATTG
1 TTAATTGTTTATTATTATATTATTATA-ACAT-AATTAATATTATTG
*
4156913 TTAATGTGTTTATT-TTGT-TTATTTATAACATAATTAATATTATT
1 TTAAT-TGTTTATTATTATATTA-TTATAACATAATTAATATTATT
4156957 TATGTTTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
44 6 0.15
45 25 0.64
46 8 0.21
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (45 bp):
TTAATTGTTTATTATTATATTATTATAACATAATTAATATTATTG
Found at i:4157631 original size:26 final size:25
Alignment explanation
Indices: 4157579--4157633 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
4157569 AATTTTAAAA
*
4157579 TATTTTTAAAATAATTTTTTATTTT
1 TATTTTTAAAATAATTTTTTATGTT
* *
4157604 TATTTTTAAAATATTTTTTTGGTGTT
1 TATTTTTAAAATAATTTTTT-ATGTT
4157630 TATT
1 TATT
4157634 AAAAATGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.67
Consensus pattern (25 bp):
TATTTTTAAAATAATTTTTTATGTT
Found at i:4164045 original size:18 final size:19
Alignment explanation
Indices: 4164022--4164066 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
4164012 AAATGTACTA
4164022 ATTAATTT-TTTGGACCAC
1 ATTAATTTCTTTGGACCAC
*
4164040 ATTAATTTCTTTGGACGAC
1 ATTAATTTCTTTGGACCAC
4164059 ATTAATTT
1 ATTAATTT
4164067 AAGATCTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTAATTTCTTTGGACCAC
Found at i:4167628 original size:22 final size:20
Alignment explanation
Indices: 4167587--4167628 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4167577 ACAAACATAT
4167587 TAAATAAGAACAAGATTGAA
1 TAAATAAGAACAAGATTGAA
*
4167607 TAAATAATTAACAATGATTGAA
1 TAAATAA-GAACAA-GATTGAA
4167629 ACAATTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (20 bp):
TAAATAAGAACAAGATTGAA
Found at i:4175605 original size:11 final size:12
Alignment explanation
Indices: 4175589--4175617 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4175579 TTTAATTCTC
4175589 TTTTTTCT-GCT
1 TTTTTTCTGGCT
4175600 TTTTTTCTGGCT
1 TTTTTTCTGGCT
4175612 TTTTTT
1 TTTTTT
4175618 TTTTGCAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (12 bp):
TTTTTTCTGGCT
Found at i:4177874 original size:18 final size:17
Alignment explanation
Indices: 4177835--4177877 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
4177825 ATGTTTATAT
4177835 GTATATATATATTACAA
1 GTATATATATATTACAA
*
4177852 -AATATATATATGTACAA
1 GTATATATATAT-TACAA
4177869 GTATATATA
1 GTATATATA
4177878 AAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (17 bp):
GTATATATATATTACAA
Found at i:4177885 original size:12 final size:12
Alignment explanation
Indices: 4177870--4177898 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4177860 TATGTACAAG
4177870 TATATATAAAAA
1 TATATATAAAAA
4177882 TATATATAAAAA
1 TATATATAAAAA
4177894 TATAT
1 TATAT
4177899 GTATATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATATATAAAAA
Found at i:4183615 original size:15 final size:16
Alignment explanation
Indices: 4183595--4183635 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
4183585 GCAAGCAATC
4183595 ACAGCAACCCGGGTA-
1 ACAGCAACCCGGGTAG
*
4183610 ACAGC-ACCAGGGTAG
1 ACAGCAACCCGGGTAG
4183625 AGCAGCAACCC
1 A-CAGCAACCC
4183636 TTCCACATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 8 0.38
15 6 0.29
16 4 0.19
17 3 0.14
ACGTcount: A:0.34, C:0.34, G:0.27, T:0.05
Consensus pattern (16 bp):
ACAGCAACCCGGGTAG
Found at i:4188274 original size:21 final size:19
Alignment explanation
Indices: 4188248--4188286 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
4188238 ATTTCAGTTA
4188248 TAAGAACTAATAAAAGAATAT
1 TAAGAA-TAATAAAA-AATAT
*
4188269 TAAGAATTATAAAAAATA
1 TAAGAATAATAAAAAATA
4188287 ATAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (19 bp):
TAAGAATAATAAAAAATAT
Found at i:4188473 original size:9 final size:9
Alignment explanation
Indices: 4188410--4188474 Score: 53
Period size: 10 Copynumber: 7.0 Consensus size: 9
4188400 ATAATCATTA
4188410 TTTATAATT
1 TTTATAATT
4188419 TCTTATAATT
1 T-TTATAATT
*
4188429 CTTAATAATT
1 -TTTATAATT
4188439 TTTA-AATAT
1 TTTATAAT-T
* *
4188448 TTTTTTATAT
1 TTTATAAT-T
4188458 TTT-TAATT
1 TTTATAATT
4188466 TTTATAATT
1 TTTATAATT
4188475 ATGCAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
8 7 0.15
9 16 0.35
10 22 0.48
11 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:4189685 original size:22 final size:22
Alignment explanation
Indices: 4189660--4189711 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
4189650 TAAACAAGAA
*
4189660 AAAAATATCTTATACATCAAAC
1 AAAAATATCTAATACATCAAAC
* *
4189682 AAAATTATCTAATACATTAAAC
1 AAAAATATCTAATACATCAAAC
*
4189704 AACAATAT
1 AAAAATAT
4189712 TACTTCATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATATCTAATACATCAAAC
Found at i:4194416 original size:19 final size:19
Alignment explanation
Indices: 4194389--4194449 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
4194379 CAAATTTTTT
*
4194389 TTTAAATTTTTTATCTTAC
1 TTTATATTTTTTATCTTAC
4194408 TTTATA---TTT-T-TT--
1 TTTATATTTTTTATCTTAC
4194420 TTTA-ATTTTTTATCTTAC
1 TTTATATTTTTTATCTTAC
4194438 TTTATATTTTTT
1 TTTATATTTTTT
4194450 TAGATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 16
0.66 0.02 0.32
Matches are distributed among these distances:
11 1 0.03
12 4 0.12
14 5 0.15
15 2 0.06
16 5 0.15
18 4 0.12
19 12 0.36
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATATTTTTTATCTTAC
Found at i:4194417 original size:31 final size:30
Alignment explanation
Indices: 4194382--4194450 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
4194372 TAGAGCACAA
4194382 ATTTTTTTTTAAATTTTTTATCTTACTTTAT
1 ATTTTTTTTT-AATTTTTTATCTTACTTTAT
4194413 ATTTTTTTTTAATTTTTTATCTTACTTTAT
1 ATTTTTTTTTAATTTTTTATCTTACTTTAT
4194443 ATTTTTTT
1 ATTTTTTT
4194451 AGATTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 28 0.74
31 10 0.26
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (30 bp):
ATTTTTTTTTAATTTTTTATCTTACTTTAT
Found at i:4194420 original size:30 final size:30
Alignment explanation
Indices: 4194384--4194459 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
4194374 GAGCACAAAT
4194384 TTTTTTTTAAATTTTTTATCTTACTTTATA
1 TTTTTTTTAAATTTTTTATCTTACTTTATA
*
4194414 TTTTTTTTTAATTTTTTATCTTACTTTATA
1 TTTTTTTTAAATTTTTTATCTTACTTTATA
*
4194444 -TTTTTTTAGATTTTTT
1 TTTTTTTTAAATTTTTT
4194460 TTTTAAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
29 14 0.33
30 29 0.67
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (30 bp):
TTTTTTTTAAATTTTTTATCTTACTTTATA
Found at i:4194431 original size:20 final size:20
Alignment explanation
Indices: 4194408--4194480 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
4194398 TTTATCTTAC
4194408 TTTATATTTTTTTTTAATTT
1 TTTATATTTTTTTTTAATTT
* ** * *
4194428 TTTATCTTACTTTATATTTT
1 TTTATATTTTTTTTTAATTT
* *
4194448 TTTAGATTTTTTTTTTAA-AT
1 TTTATA-TTTTTTTTTAATTT
4194468 TTTATAATTTTTT
1 TTTAT-ATTTTTT
4194481 AGAAAATATA
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
20 30 0.79
21 8 0.21
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (20 bp):
TTTATATTTTTTTTTAATTT
Found at i:4194447 original size:18 final size:18
Alignment explanation
Indices: 4194396--4194448 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 18
4194386 TTTTTTAAAT
4194396 TTTTTATCTTACTTTATA
1 TTTTTATCTTACTTTATA
*
4194414 -TTTT-T-TT--TTAAT-
1 TTTTTATCTTACTTTATA
4194426 TTTTTATCTTACTTTATA
1 TTTTTATCTTACTTTATA
4194444 TTTTT
1 TTTTT
4194449 TTAGATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
13 8 0.30
14 1 0.04
15 4 0.15
16 1 0.04
17 8 0.30
18 5 0.19
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATCTTACTTTATA
Found at i:4194451 original size:10 final size:10
Alignment explanation
Indices: 4194385--4194460 Score: 55
Period size: 10 Copynumber: 7.7 Consensus size: 10
4194375 AGCACAAATT
4194385 TTTTTTTA-A
1 TTTTTTTATA
* *
4194394 ATTTTTTATC
1 TTTTTTTATA
**
4194404 TTACTTTATA
1 TTTTTTTATA
*
4194414 TTTTTTTTTA
1 TTTTTTTATA
* *
4194424 ATTTTTTATC
1 TTTTTTTATA
**
4194434 TTACTTTATA
1 TTTTTTTATA
*
4194444 TTTTTTTAGA
1 TTTTTTTATA
4194454 TTTTTTT
1 TTTTTTT
4194461 TTTAAATTTT
Statistics
Matches: 47, Mismatches: 19, Indels: 1
0.70 0.28 0.01
Matches are distributed among these distances:
9 7 0.15
10 40 0.85
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:4196900 original size:29 final size:29
Alignment explanation
Indices: 4196867--4196924 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
4196857 GGCCACTACA
*
4196867 CCCTCAGGAAGATAAAAAAATAATACTAG
1 CCCTCAAGAAGATAAAAAAATAATACTAG
*
4196896 CCCTCAAGAAGATTAAAAAATAATACTAG
1 CCCTCAAGAAGATAAAAAAATAATACTAG
4196925 TTTAATAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (29 bp):
CCCTCAAGAAGATAAAAAAATAATACTAG
Found at i:4251231 original size:23 final size:23
Alignment explanation
Indices: 4251193--4251371 Score: 171
Period size: 23 Copynumber: 7.7 Consensus size: 23
4251183 CTACCCTGTT
* *
4251193 TTGGACAGCTTTTATACATCAAA
1 TTGGACAGCATATATACATCAAA
* *
4251216 TCGGACAGCATATATATATACCAAA
1 TTGGACAGCATATATACAT--CAAA
*
4251241 TTGGACAGCATATATACACCAAA
1 TTGGACAGCATATATACATCAAA
*
4251264 TTGGACAGCATATATAAATCAAA
1 TTGGACAGCATATATACATCAAA
* * *
4251287 TTGGACAACATTTATACA-CCAA
1 TTGGACAGCATATATACATCAAA
* *
4251309 TTGGACAACATATATACACCAAA
1 TTGGACAGCATATATACATCAAA
* * * *
4251332 TTGAACAACATTTTATACACCAAA
1 TTGGACAGCA-TATATACATCAAA
* *
4251356 TTGAACAGAATATATA
1 TTGGACAGCATATATA
4251372 TATACCGAAT
Statistics
Matches: 132, Mismatches: 20, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
22 20 0.15
23 72 0.55
24 20 0.15
25 20 0.15
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (23 bp):
TTGGACAGCATATATACATCAAA
Found at i:4251303 original size:46 final size:46
Alignment explanation
Indices: 4251193--4251371 Score: 216
Period size: 48 Copynumber: 3.8 Consensus size: 46
4251183 CTACCCTGTT
* * * *
4251193 TTGGACAGCTTTTATACATCAAATCGGACAGCATATATATATACCAAA
1 TTGGACAACATTTATACACCAAATTGGACAGCATATATA-A-ACCAAA
* * *
4251241 TTGGACAGCATATATACACCAAATTGGACAGCATATATAAATCAAA
1 TTGGACAACATTTATACACCAAATTGGACAGCATATATAAACCAAA
* *
4251287 TTGGACAACATTTATACACC-AATTGGACAACATATATACACCAAA
1 TTGGACAACATTTATACACCAAATTGGACAGCATATATAAACCAAA
* * *
4251332 TTGAACAACATTTTATACACCAAATTGAACAGAATATATA
1 TTGGACAACA-TTTATACACCAAATTGGACAGCATATATA
4251372 TATACCGAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
45 31 0.27
46 33 0.29
47 16 0.14
48 35 0.30
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (46 bp):
TTGGACAACATTTATACACCAAATTGGACAGCATATATAAACCAAA
Found at i:4252415 original size:42 final size:42
Alignment explanation
Indices: 4252312--4252433 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
4252302 ATAAAGCTCG
* * *
4252312 TACAATGCCAACGTCCCAAAC-GTGGTATTACATGTAATTAAA
1 TACAATGCCAATGTCCCAGACAG-GGTCTTACATGTAATTAAA
* * * *
4252354 TATCGATGCCACTGTCCCAGACAGGGTCTTACACGTAATTATA
1 TA-CAATGCCAATGTCCCAGACAGGGTCTTACATGTAATTAAA
*
4252397 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAA
1 TACAATGCCAATGTCCCAGACAGGGTCTTACATGTAA
4252434 ATCTCAAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 33 0.49
43 33 0.49
44 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGACAGGGTCTTACATGTAATTAAA
Found at i:4256386 original size:51 final size:51
Alignment explanation
Indices: 4256310--4256570 Score: 421
Period size: 51 Copynumber: 5.3 Consensus size: 51
4256300 CGGATCACAT
*
4256310 TTATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
4256361 TTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
4256412 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
4256463 TTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
4256514 TTATCACTTGTCA----T---TGATCA-ATTAAGTGTAGTTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGA-TAAGTGTAGCTAAAGCTACCAC
4256558 TTATCACTTGTCA
1 TTATCACTTGTCA
4256571 TGTAACACCC
Statistics
Matches: 203, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
43 1 0.00
44 39 0.19
47 1 0.00
51 162 0.80
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:4256571 original size:44 final size:44
Alignment explanation
Indices: 4256467--4256571 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 44
4256457 TACCACTTAT
* *
4256467 CACTTGTCACTTGTCACTGATAAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCATTGATAAGATAAGTGTAGCTAAAGCTAC
* *
4256511 CACTTATCACTTGTCATTGATCAA-TTAAGTGTAGTTAAAGCTAC
1 CACTTATCACTTGTCATTGAT-AAGATAAGTGTAGCTAAAGCTAC
4256555 CACTTATCACTTGTCAT
1 CACTTATCACTTGTCAT
4256572 GTAACACCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
44 54 0.96
45 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (44 bp):
CACTTATCACTTGTCATTGATAAGATAAGTGTAGCTAAAGCTAC
Found at i:4257663 original size:11 final size:12
Alignment explanation
Indices: 4257635--4257668 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
4257625 GCCCAAACGT
4257635 CGAAATTTTTGAA
1 CGAAATTTTT-AA
4257648 CGAAATTTTT-A
1 CGAAATTTTTAA
4257659 CGAAATTTTT
1 CGAAATTTTT
4257669 CCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:4260072 original size:41 final size:41
Alignment explanation
Indices: 4259913--4260064 Score: 286
Period size: 41 Copynumber: 3.7 Consensus size: 41
4259903 TTAAAGTCTA
*
4259913 ATTCAGTTCACCGGCACTTAGCCTTCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
4259954 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
4259995 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
4260036 ATTCAATTCACCGGCACTTAGCCTGCTAG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAG
4260065 ACATATAGTC
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (41 bp):
ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:4260087 original size:41 final size:41
Alignment explanation
Indices: 4259917--4260092 Score: 255
Period size: 41 Copynumber: 4.3 Consensus size: 41
4259907 AGTCTAATTC
* *
4259917 AGTTCACCGGCACTTAGCCTTCTAGGCTTATAGCCTGATTC
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
*
4259958 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
4259999 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCA
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT-A
* * * *
4260041 A-TTCACCGGCACTTAGCCTGCTAGACATATAGTCTGAATA
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
* *
4260081 ATTTCACTGGCA
1 AGTTCACCGGCA
4260093 ATAAATCCGA
Statistics
Matches: 126, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
40 2 0.02
41 123 0.98
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (41 bp):
AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
Found at i:4261870 original size:13 final size:13
Alignment explanation
Indices: 4261852--4261876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4261842 ACCAACGATA
4261852 AAATTTTCACACG
1 AAATTTTCACACG
4261865 AAATTTTCACAC
1 AAATTTTCACAC
4261877 ATATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:4265273 original size:19 final size:19
Alignment explanation
Indices: 4265261--4265298 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4265251 TACCAGAATA
4265261 CCAGCTAACTACCACAACT
1 CCAGCTAACTACCACAACT
*
4265280 GCAGCTAACTACCACAACT
1 CCAGCTAACTACCACAACT
4265299 ACTTTCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.39, G:0.08, T:0.16
Consensus pattern (19 bp):
CCAGCTAACTACCACAACT
Found at i:4267518 original size:17 final size:17
Alignment explanation
Indices: 4267496--4267529 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4267486 ATCCACTAAT
*
4267496 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4267513 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4267530 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4272157 original size:17 final size:17
Alignment explanation
Indices: 4272135--4272168 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4272125 ATCCACTAAT
*
4272135 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4272152 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4272169 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4278605 original size:31 final size:31
Alignment explanation
Indices: 4278553--4278613 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
4278543 ATGTGATGCG
*
4278553 TGTTTATTTATATATAAATAAAAAGTAATTAT
1 TGTTTATTTAAATATAAATAAAAA-TAATTAT
*
4278585 TGTTTA-TTAAATATATATAAAAATAATTA
1 TGTTTATTTAAATATAAATAAAAATAATTA
4278614 AATACATTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 6 0.22
31 15 0.56
32 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (31 bp):
TGTTTATTTAAATATAAATAAAAATAATTAT
Found at i:4287458 original size:11 final size:11
Alignment explanation
Indices: 4287442--4287472 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4287432 AAGTATGGGT
4287442 AGGTATGGGAA
1 AGGTATGGGAA
*
4287453 AGGTATGGGCA
1 AGGTATGGGAA
4287464 AGGTATGGG
1 AGGTATGGG
4287473 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:4291549 original size:18 final size:18
Alignment explanation
Indices: 4291526--4291618 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
4291516 CCCAACTACT
*
4291526 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
**
4291544 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
**
4291562 GTATACGTGAATAGTATT
1 GTATACGTGAATAGTACC
*
4291580 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
4291598 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
4291616 GTA
1 GTA
4291619 AACGGTCGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:4291584 original size:36 final size:36
Alignment explanation
Indices: 4291526--4291618 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
4291516 CCCAACTACT
* *
4291526 GTATACGTGAACAGTACCGTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
**
4291562 GTATACGTGAATAGTATTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
4291598 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
4291619 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:4295772 original size:8 final size:8
Alignment explanation
Indices: 4295761--4295795 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
4295751 CCAATATCTA
*
4295761 ATTATCAT
1 ATTATCAC
*
4295769 ATTAGCAC
1 ATTATCAC
4295777 ATTATCAC
1 ATTATCAC
4295785 ATTATCAC
1 ATTATCAC
4295793 ATT
1 ATT
4295796 TATACATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (8 bp):
ATTATCAC
Found at i:4296596 original size:9 final size:8
Alignment explanation
Indices: 4296579--4296621 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
4296569 GTCGTGCGTC
4296579 TCTTTCTT
1 TCTTTCTT
*
4296587 TTTCTTCTT
1 TCT-TTCTT
4296596 TCTATTCTT
1 TCT-TTCTT
4296605 TCTTTCTTT
1 TCTTTC-TT
4296614 TCTTTCTT
1 TCTTTCTT
4296622 ATTTCGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (8 bp):
TCTTTCTT
Found at i:4296597 original size:13 final size:14
Alignment explanation
Indices: 4296579--4296621 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
4296569 GTCGTGCGTC
4296579 TCTTTCTTTTTC-T
1 TCTTTCTTTTTCTT
*
4296592 TCTTTC-TATTCTT
1 TCTTTCTTTTTCTT
4296605 TCTTTC-TTTTCTT
1 TCTTTCTTTTTCTT
4296618 TCTT
1 TCTT
4296622 ATTTCGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 4 0.15
13 23 0.85
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTTTCTTTTTCTT
Found at i:4296598 original size:4 final size:4
Alignment explanation
Indices: 4296579--4296621 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
4296569 GTCGTGCGTC
*
4296579 TCTT TCTT TTTCT TCTT TCTAT TCTT TCTT TCTTT TCTT TCTT
1 TCTT TCTT TCT-T TCTT TCT-T TCTT TCTT TC-TT TCTT TCTT
4296622 ATTTCGTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 23 0.68
5 11 0.32
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:4299683 original size:11 final size:10
Alignment explanation
Indices: 4299662--4299692 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
4299652 TCGGCAAAAA
4299662 TAAAAAAATT
1 TAAAAAAATT
4299672 TAAAAGAAATT
1 TAAAA-AAATT
4299683 TAAAAAAATT
1 TAAAAAAATT
4299693 AAATTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:4303148 original size:16 final size:17
Alignment explanation
Indices: 4303112--4303148 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
4303102 AATTTTATTT
4303112 TAATAATAATTTTTAAA
1 TAATAATAATTTTTAAA
4303129 -AATAATAA-TTTTAAA
1 TAATAATAATTTTTAAA
4303144 TAATA
1 TAATA
4303149 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAATAATTTTTAAA
Found at i:4304676 original size:85 final size:85
Alignment explanation
Indices: 4304504--4304716 Score: 227
Period size: 85 Copynumber: 2.5 Consensus size: 85
4304494 CTAAGGGTGT
* * * * *
4304504 AAAAATCCCTCAAACTTTTTCAAAAAAAAGTAATTAAGCTCCTTTTTTTTGCACTTAATTGAGCA
1 AAAAAACCCTCAAACTTTTT-ATAAAAAAGCAATTAAGCCCCTTTTTTTTGCACTCAATTGAGCA
*
4304569 CTTAAACTTTCAAAGTGCATC
65 CTTAAACTTTCAAAATGCATC
*
4304590 AAAAAACCCTCAAACTTCTTATAAAAAAGCAATTAAGCCCCTACTTTTTTT-CACTCAATT-AGG
1 AAAAAACCCTCAAACTTTTTATAAAAAAGCAATTAAGCCCCT--TTTTTTTGCACTCAATTGA-G
* * * *
4304653 TATTTGAA-TTTTAAAATGCATC
63 CACTTAAACTTTCAAAATGCATC
* * *
4304675 AAAAAGACCCTTAAAATTTTTCT-AAAAAGCAATTAAGCCCCT
1 AAAAA-ACCCTCAAACTTTTTATAAAAAAGCAATTAAGCCCCT
4304717 GCTCTTATTA
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
85 56 0.52
86 45 0.42
87 7 0.06
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (85 bp):
AAAAAACCCTCAAACTTTTTATAAAAAAGCAATTAAGCCCCTTTTTTTTGCACTCAATTGAGCAC
TTAAACTTTCAAAATGCATC
Found at i:4304794 original size:19 final size:18
Alignment explanation
Indices: 4304747--4304807 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
4304737 AACAAAAAAA
* *
4304747 TAAAACAATAATAAATTT
1 TAAAAAAATATTAAATTT
*
4304765 TAGAAATAATATTAAATTT
1 TA-AAAAAATATTAAATTT
*
4304784 TAATAAAAATATAAAAATTT
1 TAA-AAAAATAT-TAAATTT
4304804 TAAA
1 TAAA
4304808 TTTTATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.08
19 24 0.67
20 9 0.25
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAAAAATATTAAATTT
Found at i:4305137 original size:19 final size:18
Alignment explanation
Indices: 4305115--4305197 Score: 76
Period size: 19 Copynumber: 4.4 Consensus size: 18
4305105 ATTTCTATAT
* *
4305115 ATTTTATATATTTTTTACG
1 ATTTT-TATATATTTTACA
*
4305134 ATTTTTATAAAATTTTACA
1 ATTTTTAT-ATATTTTACA
*
4305153 ATTTCATATATATTTTACA
1 ATTT-TTATATATTTTACA
* *
4305172 ATTTTTATATTTTTTTCTA
1 ATTTTTATATATTTTAC-A
4305191 ATTTTTA
1 ATTTTTA
4305198 ATAAATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
18 13 0.25
19 37 0.70
20 3 0.06
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.61
Consensus pattern (18 bp):
ATTTTTATATATTTTACA
Found at i:4305137 original size:29 final size:27
Alignment explanation
Indices: 4305088--4305156 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
4305078 ACTTTATAAA
*
4305088 ATTTTATAATTTTTTGCATTTCTATAT
1 ATTTTATAATTTTTTACATTTCTATAT
* *
4305115 ATTTTATATATTTTTTACGATTTTTATAAA
1 ATTTTATA-ATTTTTTAC-ATTTCTAT-AT
*
4305145 ATTTTACAATTT
1 ATTTTATAATTT
4305157 CATATATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.23
28 8 0.23
29 11 0.31
30 8 0.23
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (27 bp):
ATTTTATAATTTTTTACATTTCTATAT
Found at i:4307791 original size:26 final size:26
Alignment explanation
Indices: 4307745--4307798 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
4307735 TGTTATCAAT
*
4307745 TTAAATTTTTTTTTCTAATTTGGTAC
1 TTAAATTTTTTTTTCTAATTTGATAC
* *
4307771 TTAATTTTTTTTGTTC-GATTTGATAC
1 TTAAATTTTTTT-TTCTAATTTGATAC
4307797 TT
1 TT
4307799 GAACTTGTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.63
Consensus pattern (26 bp):
TTAAATTTTTTTTTCTAATTTGATAC
Found at i:4311845 original size:4 final size:5
Alignment explanation
Indices: 4311818--4311846 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
4311808 GTGAAACAAT
4311818 ATAAA ATAAA ATAAA ATAAA AT-AA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
4311847 GCACTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:4312283 original size:26 final size:25
Alignment explanation
Indices: 4312254--4312318 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
4312244 AAAAATAAGT
4312254 GTATATGTATATATATAGTACAAAAA
1 GTATATGTATATATATA-TACAAAAA
*
4312280 GTATGCATGTA-A-ATATATAGAAAAA
1 GTAT--ATGTATATATATATACAAAAA
*
4312305 -TATATTTATATATA
1 GTATATGTATATATA
4312319 AAAGAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 6 0.18
25 7 0.21
26 9 0.27
27 1 0.03
28 5 0.15
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (25 bp):
GTATATGTATATATATATACAAAAA
Found at i:4313366 original size:20 final size:20
Alignment explanation
Indices: 4313330--4313369 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4313320 TCCTATTGTT
4313330 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
4313350 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
4313370 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:4314151 original size:44 final size:43
Alignment explanation
Indices: 4313847--4314135 Score: 193
Period size: 44 Copynumber: 6.7 Consensus size: 43
4313837 TTTAAGTCTA
* * * *
4313847 CTCCACTGTAATCTTAGGGAGATAAGATCTCTTATTTTAATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTT-CTTTGATCTG
* * * * *
4313891 CCCCACTGTAA-CTTCAGGGAGATAGGATAGT-GTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTTCTTTGATCTG
* * * *
4313934 TTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT---CTTCTTTGATCTG
* ** * *
4313980 TTCCACTGTAATCTCAGGGAGATAAGA-C-CTGATGTGATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTTCTTTGATCTG
* * * *
4314021 CTCTACTGTAA-CTTCAGAGAGATAAGA--TC--CTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTCTTCTTTGATCTG
* * *
4314060 CTCCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT-CT-TCTTTGATCTG
*
4314104 CTCCGCTGTAATCTCAGGGAGATAAGATCTCT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCT
4314136 GGCTTCAATC
Statistics
Matches: 186, Mismatches: 43, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
39 25 0.13
40 3 0.02
41 31 0.17
42 1 0.01
43 29 0.16
44 59 0.32
45 3 0.02
46 35 0.19
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (43 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTCTTCTTTGATCTG
Found at i:4314197 original size:86 final size:87
Alignment explanation
Indices: 4314093--4314667 Score: 660
Period size: 88 Copynumber: 6.6 Consensus size: 87
4314083 AGGATTACTA
* * * ** * * * *
4314093 TCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC-TCTGGCTTCAATCTGCTCCAAT-G
1 TCTTTGATCTGCTTCGCTGTAATGT-AGGAAGGCAAGATCTTCTGTCTTCAACCAGCT-CAATCA
**
4314156 CAACCGATGGAGGCAAGGCTT-TG
64 CAACCGAAAGAGGCAAGGCTTGTG
* * * * * *
4314179 TCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACTAGCTCCA-CTG
1 TCTTTGATCTGCTTCGCTG-TAATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATC-A
* ** *
4314242 CAATCGATGGATGCAAGGCTT-TG
64 CAACCGAAAGAGGCAAGGCTTGTG
* *
4314265 T-TTTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCA
1 TCTTT-GATCTGCTTCGCTG-TAATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATCA
*
4314329 CAACCGAAAGAGGCAAGGTTTGTG
64 CAACCGAAAGAGGCAAGGCTTGTG
* * *
4314353 TCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCAC
1 TCTTTGATCTGCTTCGCTGT-AATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATCAC
*
4314418 AACCGAAAGAGGCAAGGTTTGTG
65 AACCGAAAGAGGCAAGGCTTGTG
* * *
4314441 TCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCAC
1 TCTTTGATCTGCTTCGCTGT-AATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATCAC
* *
4314506 AACCGAAAGAAGCAAGGTTTGTG
65 AACCGAAAGAGGCAAGGCTTGTG
* * *
4314529 TCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCAC
1 TCTTTGATCTGCTTCGCTGT-AATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATCAC
*
4314594 AACCGAAAGAGGCAAGGTTTGTG
65 AACCGAAAGAGGCAAGGCTTGTG
* *
4314617 TCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCA
1 TCTTTGATCTGCTTCGCTGT-AATGTAGGAAGGCAAGATCTTCTGTCTTCA
4314668 TTGATCTGTC
Statistics
Matches: 449, Mismatches: 30, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
85 5 0.01
86 96 0.21
87 36 0.08
88 310 0.69
89 2 0.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (87 bp):
TCTTTGATCTGCTTCGCTGTAATGTAGGAAGGCAAGATCTTCTGTCTTCAACCAGCTCAATCACA
ACCGAAAGAGGCAAGGCTTGTG
Found at i:4314215 original size:43 final size:43
Alignment explanation
Indices: 4314166--4314301 Score: 104
Period size: 43 Copynumber: 3.2 Consensus size: 43
4314156 CAACCGATGG
4314166 AGGCAAGGCTTTGTCTTTGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTTGTCTTTGATCTGCTTCGCTGTTAATGCAGGA
* * * * * *
4314209 AGGCAA-GATCTGCTTCTTT-AACTAGCTCCACTG-CAAT-CGATGG-
1 AGGCAAGGCTTTG--TCTTTGATCT-GCTTCGCTGTTAATGC-A-GGA
* *
4314252 ATGCAAGGCTTTGT-TTTCGATCTGCTTCGCTGTTAATGTAGGA
1 AGGCAAGGCTTTGTCTTT-GATCTGCTTCGCTGTTAATGCAGGA
4314295 AGGCAAG
1 AGGCAAG
4314302 ATCTTTTGTC
Statistics
Matches: 67, Mismatches: 15, Indels: 22
0.64 0.14 0.21
Matches are distributed among these distances:
41 3 0.04
42 15 0.22
43 31 0.46
44 18 0.27
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (43 bp):
AGGCAAGGCTTTGTCTTTGATCTGCTTCGCTGTTAATGCAGGA
Found at i:4314378 original size:88 final size:88
Alignment explanation
Indices: 4314156--4314667 Score: 809
Period size: 88 Copynumber: 5.9 Consensus size: 88
4314146 TGCTCCAATG
** * * * *
4314156 CAACCGATGGAGGCAAGGCTT-TGTCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
** * * * *
4314220 GCT-TCTTTAACTAGCTCCA-CTG
66 TTTGTCTTCAACCAGCTCTATC-A
* ** * *
4314242 CAATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATC
4314305 TTTTGTCTTCAACCAGCTCTATCA
65 TTTTGTCTTCAACCAGCTCTATCA
4314329 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
4314394 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
4314417 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
4314482 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
4314505 CAACCGAAAGAAGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
4314570 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
4314593 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
4314658 TTTGTCTTCA
66 TTTGTCTTCA
4314668 TTGATCTGTC
Statistics
Matches: 402, Mismatches: 18, Indels: 10
0.93 0.04 0.02
Matches are distributed among these distances:
86 59 0.15
87 31 0.08
88 312 0.78
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (88 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCTATCA
Found at i:4314878 original size:15 final size:15
Alignment explanation
Indices: 4314858--4314887 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4314848 GTAAAAACTT
4314858 ATTAAGGTTTTATCA
1 ATTAAGGTTTTATCA
4314873 ATTAAGGTTTTATCA
1 ATTAAGGTTTTATCA
4314888 CTGACGTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
ATTAAGGTTTTATCA
Found at i:4316856 original size:7 final size:8
Alignment explanation
Indices: 4316832--4316860 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4316822 CTATTTTGAC
4316832 TTTGATTT
1 TTTGATTT
4316840 TTTGATTT
1 TTTGATTT
4316848 TTTGATTT
1 TTTGATTT
4316856 TTTGA
1 TTTGA
4316861 ATTCATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (8 bp):
TTTGATTT
Found at i:4321257 original size:4 final size:5
Alignment explanation
Indices: 4321230--4321258 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
4321220 GTGAAACAAT
4321230 ATAAA ATAAA ATAAA ATAAA AT-AA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
4321259 GCACTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:4321698 original size:26 final size:25
Alignment explanation
Indices: 4321669--4321733 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
4321659 AAAAATAAGT
4321669 GTATATGTATATATATAGTACAAAAA
1 GTATATGTATATATATA-TACAAAAA
*
4321695 GTATGCATGTA-A-ATATATAGAAAAA
1 GTAT--ATGTATATATATATACAAAAA
*
4321720 -TATATTTATATATA
1 GTATATGTATATATA
4321734 AAAGAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 6 0.18
25 7 0.21
26 9 0.27
27 1 0.03
28 5 0.15
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (25 bp):
GTATATGTATATATATATACAAAAA
Found at i:4322781 original size:20 final size:20
Alignment explanation
Indices: 4322745--4322784 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4322735 TCCTATTGTT
4322745 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
4322765 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
4322785 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:4332189 original size:19 final size:18
Alignment explanation
Indices: 4332165--4332226 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
4332155 TAGGATTTAG
4332165 ATTTTTTAAATTTCATATA
1 ATTTTTTAAATTT-ATATA
* *
4332184 ATTTTTT-TATTTTTAATA
1 ATTTTTTAAATTTAT-ATA
4332202 ATGTTTTTAAATATTAT-TA
1 AT-TTTTTAAAT-TTATATA
4332221 ATTTTT
1 ATTTTT
4332227 ATTTTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.03
18 13 0.37
19 16 0.46
20 2 0.06
21 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTTAAATTTATATA
Found at i:4332191 original size:20 final size:19
Alignment explanation
Indices: 4332166--4332226 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
4332156 AGGATTTAGA
4332166 TTTTTTAAATTTCATATAAT
1 TTTTTTAAATTT-ATATAAT
**
4332186 TTTTTTATTTTTA-ATAAT
1 TTTTTTAAATTTATATAAT
*
4332204 GTTTTTAAATATTAT-TAAT
1 TTTTTTAAAT-TTATATAAT
4332223 TTTT
1 TTTT
4332227 ATTTTTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 12 0.36
19 11 0.33
20 10 0.30
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTTAAATTTATATAAT
Found at i:4332805 original size:22 final size:23
Alignment explanation
Indices: 4332780--4332822 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4332770 AAATATTTAA
4332780 TAAAAAATTT-ATAATATAAATG
1 TAAAAAATTTAATAATATAAATG
* *
4332802 TAAATATTTTAATAATATAAA
1 TAAAAAATTTAATAATATAAA
4332823 CAGATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAAAATTTAATAATATAAATG
Found at i:4333953 original size:13 final size:13
Alignment explanation
Indices: 4333932--4333995 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
4333922 AATTTTTCAT
4333932 TACTTTTGAAAAG
1 TACTTTTGAAAAG
*
4333945 TATTTTTGAAAAG
1 TACTTTTGAAAAG
* * *
4333958 TGCTGTGGAAAAG
1 TACTTTTGAAAAG
*
4333971 TACTTTTGAGAAG
1 TACTTTTGAAAAG
*
4333984 TGCTTTTGAAAA
1 TACTTTTGAAAA
4333996 ATTTGAGTGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:4333994 original size:26 final size:26
Alignment explanation
Indices: 4333934--4333995 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
4333924 TTTTTCATTA
*
4333934 CTTTTGAAAAGTATTTTTGAAAAGTG
1 CTTTTGAAAAGTACTTTTGAAAAGTG
* * *
4333960 CTGTGGAAAAGTACTTTTGAGAAGTG
1 CTTTTGAAAAGTACTTTTGAAAAGTG
4333986 CTTTTGAAAA
1 CTTTTGAAAA
4333996 ATTTGAGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
CTTTTGAAAAGTACTTTTGAAAAGTG
Found at i:4337048 original size:17 final size:18
Alignment explanation
Indices: 4337026--4337059 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4337016 TTCTTCATTG
4337026 CTTTTCAAAG-AAAAGCA
1 CTTTTCAAAGTAAAAGCA
*
4337043 CTTTTCCAAGTAAAAGC
1 CTTTTCAAAGTAAAAGC
4337060 TCGTTTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (18 bp):
CTTTTCAAAGTAAAAGCA
Found at i:4351393 original size:2 final size:2
Alignment explanation
Indices: 4351386--4351431 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
4351376 CGATGAATGT
*
4351386 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4351428 GA GA
1 GA GA
4351432 ACCAGTTTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4354609 original size:25 final size:25
Alignment explanation
Indices: 4354556--4354609 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
4354546 CGGCCCATTT
* * *
4354556 TTAATTAAAATTAAAATTAGTTTTT
1 TTAATTAAAATTAAAACTAATTTTA
4354581 TTAA-TAAAATTAAAACTAATTGTTA
1 TTAATTAAAATTAAAACTAATT-TTA
4354606 TTAA
1 TTAA
4354610 AATTAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAATTAAAATTAAAACTAATTTTA
Found at i:4354628 original size:16 final size:16
Alignment explanation
Indices: 4354591--4354630 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
4354581 TTAATAAAAT
* *
4354591 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
4354607 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
4354623 TAAAATTA
1 TAAAATTA
4354631 TCAATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:4354658 original size:16 final size:15
Alignment explanation
Indices: 4354633--4354663 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4354623 TAAAATTATC
4354633 AATTTATTAATTGTT
1 AATTTATTAATTGTT
4354648 AATTGTATTAATTGTT
1 AATT-TATTAATTGTT
4354664 GTAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (15 bp):
AATTTATTAATTGTT
Found at i:4354709 original size:59 final size:59
Alignment explanation
Indices: 4354633--4354780 Score: 271
Period size: 59 Copynumber: 2.5 Consensus size: 59
4354623 TAAAATTATC
* *
4354633 AATTTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
4354691 AATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
4354750 AATTTATCAAATTATTAATTGTATTAATTGT
1 AATTTATCAAATTATTAATTGTATTAATTGT
4354781 ATTAATTGTT
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
58 7 0.08
59 80 0.92
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (59 bp):
AATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
Found at i:4354774 original size:9 final size:9
Alignment explanation
Indices: 4354762--4354789 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4354752 TTTATCAAAT
4354762 TATTAATTG
1 TATTAATTG
4354771 TATTAATTG
1 TATTAATTG
4354780 TATTAATTG
1 TATTAATTG
4354789 T
1 T
4354790 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:4354922 original size:24 final size:26
Alignment explanation
Indices: 4354883--4354931 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
4354873 AAATAAACTT
4354883 AAAATAAAAAACTA-TT-ATATTTTA
1 AAAATAAAAAACTATTTAATATTTTA
4354907 AAAATAAAAATA-TATTTAATATTTT
1 AAAATAAAAA-ACTATTTAATATTTT
4354932 TCGGACCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 12 0.55
25 3 0.14
26 7 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAATAAAAAACTATTTAATATTTTA
Found at i:4371228 original size:26 final size:26
Alignment explanation
Indices: 4371180--4371230 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4371170 CACCATGTAT
*
4371180 CAATTTTTTTTATCAAATCTAATAAA
1 CAATTTTTTTTATAAAATCTAATAAA
*
4371206 CAATTTGTTTTTGTAAAAT-TAATAA
1 CAATTT-TTTTTATAAAATCTAATAA
4371231 TTTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (26 bp):
CAATTTTTTTTATAAAATCTAATAAA
Found at i:4371279 original size:26 final size:27
Alignment explanation
Indices: 4371233--4371291 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
4371223 ATTAATAATT
*
4371233 TATTTTTAGTTAAAAATAGAATATATA
1 TATTTTTAGTTAAAAATAGAATATACA
*
4371260 TATTTTTA-TTATTAAA-AGAATATACA
1 TATTTTTAGTTA-AAAATAGAATATACA
4371286 TATTTT
1 TATTTT
4371292 AACATTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (27 bp):
TATTTTTAGTTAAAAATAGAATATACA
Found at i:4371712 original size:23 final size:23
Alignment explanation
Indices: 4371686--4371732 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4371676 CCTTTTCATG
4371686 GCCTCTTCGTTGGGCAAGTTTTA
1 GCCTCTTCGTTGGGCAAGTTTTA
4371709 GCCTCTTCGTTGGGCAAGTTTTA
1 GCCTCTTCGTTGGGCAAGTTTTA
4371732 G
1 G
4371733 GCCATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.38
Consensus pattern (23 bp):
GCCTCTTCGTTGGGCAAGTTTTA
Found at i:4376487 original size:16 final size:16
Alignment explanation
Indices: 4376444--4376479 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4376434 TGATTAAGAA
*
4376444 ATTATTATTATATTAC
1 ATTATTATAATATTAC
*
4376460 ATTATTATAATATTAT
1 ATTATTATAATATTAC
4376476 ATTA
1 ATTA
4376480 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTATAATATTAC
Found at i:4376517 original size:16 final size:15
Alignment explanation
Indices: 4376487--4376529 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
4376477 TTAATTAAAT
*
4376487 AATAAAAAAACGTAA
1 AATAAAAAAAAGTAA
4376502 AATAAAAATAAAGTAA
1 AATAAAAA-AAAGTAA
*
4376518 AAGAAAGAAAAA
1 AATAAA-AAAAA
4376530 AAGCAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 14 0.58
17 2 0.08
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (15 bp):
AATAAAAAAAAGTAA
Found at i:4377237 original size:3 final size:3
Alignment explanation
Indices: 4377229--4377269 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4377219 GTGAGGTAAG
4377229 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4377270 GTGGGAATTA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4377435 original size:23 final size:21
Alignment explanation
Indices: 4377416--4377475 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
4377406 TTTGTGGATT
4377416 AATTATTGATTGAAAGGTGGAAA
1 AATTATTGATTGAAAGGTGG--A
*
4377439 AATGATTGAATTGAAAAGGTGAGA
1 AATTATTG-ATTG-AAAGGTG-GA
4377463 AATTA-TGATTGAA
1 AATTATTGATTGAA
4377476 TTGAGATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 2 0.06
22 4 0.12
23 9 0.28
24 9 0.28
25 7 0.22
26 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (21 bp):
AATTATTGATTGAAAGGTGGA
Found at i:4377451 original size:24 final size:26
Alignment explanation
Indices: 4377415--4377479 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 26
4377405 ATTTGTGGAT
*
4377415 TAATTATTG-ATTGAAAGGTG-GAAA
1 TAATGATTGAATTGAAAGGTGAGAAA
4377439 -AATGATTGAATTGAAAAGGTGAGAAA
1 TAATGATTGAATTG-AAAGGTGAGAAA
*
4377465 TTATGATTGAATTGA
1 TAATGATTGAATTGA
4377480 GATTATATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 7 0.20
24 4 0.11
25 7 0.20
26 5 0.14
27 12 0.34
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.32
Consensus pattern (26 bp):
TAATGATTGAATTGAAAGGTGAGAAA
Found at i:4380267 original size:13 final size:13
Alignment explanation
Indices: 4380243--4380276 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4380233 CCCTCATTGG
4380243 TATCACAATTATAT
1 TATCA-AATTATAT
4380257 TATCAAATTATAT
1 TATCAAATTATAT
*
4380270 CATCAAA
1 TATCAAA
4380277 ATATCATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TATCAAATTATAT
Found at i:4387445 original size:16 final size:16
Alignment explanation
Indices: 4387424--4387455 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4387414 CCCTTAGTCA
*
4387424 TGATTATTTAATTAAT
1 TGATTAGTTAATTAAT
4387440 TGATTAGTTAATTAAT
1 TGATTAGTTAATTAAT
4387456 CACCTCTTAA
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:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (16 bp):
TGATTAGTTAATTAAT
Found at i:4395889 original size:19 final size:18
Alignment explanation
Indices: 4395847--4395904 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
4395837 TATAAAAAAT
*
4395847 AAAAAATAATAAATTTTA
1 AAAAAATATTAAATTTTA
*
4395865 GAAAAATTATTAAATTTTA
1 -AAAAAATATTAAATTTTA
* *
4395884 ATAAAAATATAAAAATTTA
1 A-AAAAATATTAAATTTTA
4395903 AA
1 AA
4395905 TTTTATTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 2 0.06
19 31 0.94
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAAAATATTAAATTTTA
Found at i:4395916 original size:19 final size:20
Alignment explanation
Indices: 4395891--4395938 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
4395881 TTAATAAAAA
**
4395891 TATAAAAATTTAAATTTTAT
1 TATAAAAATAGAAATTTTAT
*
4395911 TA-AAAAATAGAAATTTTTT
1 TATAAAAATAGAAATTTTAT
4395930 TATAAAAAT
1 TATAAAAAT
4395939 CATAAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TATAAAAATAGAAATTTTAT
Found at i:4395924 original size:25 final size:26
Alignment explanation
Indices: 4395874--4395926 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
4395864 AGAAAAATTA
4395874 TTAAATTTTAATAAAAATATAAAAAT
1 TTAAATTTTAATAAAAATATAAAAAT
* *
4395900 TTAAATTTTATTAAAAA-ATAGAAAT
1 TTAAATTTTAATAAAAATATAAAAAT
4395925 TT
1 TT
4395927 TTTTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAAATTTTAATAAAAATATAAAAAT
Found at i:4395925 original size:45 final size:45
Alignment explanation
Indices: 4395841--4395927 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
4395831 TAGAATTATA
* *
4395841 AAAAATAAAAAATAATAAATTTTAGAAAAATTATTAAATTTTAAT
1 AAAAATAAAAAATAATAAATTTTAGAAAAAATATGAAATTTTAAT
* *
4395886 AAAAATATAAAAAT-TTAAATTTTATTAAAAAATA-GAAATTTT
1 AAAAATA-AAAAATAATAAATTTTA-GAAAAAATATGAAATTTT
4395928 TTTATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 23 0.64
46 13 0.36
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (45 bp):
AAAAATAAAAAATAATAAATTTTAGAAAAAATATGAAATTTTAAT
Found at i:4396241 original size:45 final size:44
Alignment explanation
Indices: 4396183--4396268 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
4396173 TTTCTTACAA
* * *
4396183 TTTTATAAAATTTTATATTTCTATATACTTTATAATTTTTAAGAT
1 TTTTATAAAATTTTACAATTATATATA-TTTATAATTTTTAAGAT
* *
4396228 TTTTATAAGATTTTACAATTATATATATTTTTAATTTTTAA
1 TTTTATAAAATTTTACAATTATATATATTTATAATTTTTAA
4396269 TAAATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 13 0.36
45 23 0.64
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.58
Consensus pattern (44 bp):
TTTTATAAAATTTTACAATTATATATATTTATAATTTTTAAGAT
Found at i:4396282 original size:27 final size:29
Alignment explanation
Indices: 4396246--4396313 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
4396236 GATTTTACAA
*
4396246 TTATATATATTTTTAA-TTTTTAATAAATT
1 TTATA-ATATTTTGAATTTTTTAATAAATT
*
4396275 TT-TAATA-TTTGAATTTTTTATTAAATT
1 TTATAATATTTTGAATTTTTTAATAAATT
4396302 TTAATAATATTT
1 TT-ATAATATTT
4396314 ATAGCTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 5 0.15
27 17 0.52
28 2 0.06
29 7 0.21
30 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (29 bp):
TTATAATATTTTGAATTTTTTAATAAATT
Found at i:4399003 original size:18 final size:18
Alignment explanation
Indices: 4398976--4399018 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4398966 CCAAAAGGAT
*
4398976 AAAGACAAAGACAAAAAC
1 AAAGATAAAGACAAAAAC
* *
4398994 AAAGATAAAGATAAAAAT
1 AAAGATAAAGACAAAAAC
4399012 AAAGATA
1 AAAGATA
4399019 GAGAGGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.07, G:0.12, T:0.09
Consensus pattern (18 bp):
AAAGATAAAGACAAAAAC
Found at i:4403938 original size:13 final size:13
Alignment explanation
Indices: 4403897--4403951 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4403887 CTAGTTTAGC
4403897 AGTGCTTTTGAAA
1 AGTGCTTTTGAAA
* * *
4403910 AAT-ATTGTGTAAA
1 AGTGCTTTTG-AAA
*
4403923 AGTGCTTTTGAGA
1 AGTGCTTTTGAAA
4403936 AGTGCTTTTGAAA
1 AGTGCTTTTGAAA
4403949 AGT
1 AGT
4403952 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
12 4 0.12
13 24 0.75
14 4 0.12
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (13 bp):
AGTGCTTTTGAAA
Found at i:4404226 original size:33 final size:35
Alignment explanation
Indices: 4404130--4404227 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
4404120 GTTAATATTT
*
4404130 TAATATATGAAATATAAATTTTAAATATTT--TTAAG
1 TAATATAT-AAAT-TATATTTTAAATATTTAATTAAG
* *
4404165 TAATAAATATTAATTAT-TTATAAA-ATTTAATT-AG
1 TAAT--ATATAAATTATATTTTAAATATTTAATTAAG
4404199 -AATATATAAATTATATTTTAAATATTTAA
1 TAATATATAAATTATATTTTAAATATTTAA
4404228 ATATAACCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.19
32 6 0.12
33 13 0.25
34 8 0.15
35 8 0.15
36 3 0.06
37 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (35 bp):
TAATATATAAATTATATTTTAAATATTTAATTAAG
Found at i:4406872 original size:11 final size:11
Alignment explanation
Indices: 4406816--4406881 Score: 55
Period size: 11 Copynumber: 6.1 Consensus size: 11
4406806 AATAAATAAA
*
4406816 TATTAGTTTAT
1 TATTATTTTAT
*
4406827 TAATATTTTA-
1 TATTATTTTAT
* *
4406837 AATTAATTTTTT
1 TATT-ATTTTAT
* *
4406849 TATGATATT-T
1 TATTATTTTAT
4406859 TATTATTTTAT
1 TATTATTTTAT
4406870 TATTATTTTAT
1 TATTATTTTAT
4406881 T
1 T
4406882 TAGTGTATAT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
10 10 0.24
11 30 0.71
12 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:4413371 original size:30 final size:31
Alignment explanation
Indices: 4413327--4413389 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
4413317 TAGTAAAAAT
4413327 AAAATTATACTTTAACCCCTTAAAAATGATA
1 AAAATTATACTTTAACCCCTTAAAAATGATA
* * * *
4413358 AAAATT-TATTTTAATCCTTTAAAAATTATA
1 AAAATTATACTTTAACCCCTTAAAAATGATA
4413388 AA
1 AA
4413390 TATATAGACT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (31 bp):
AAAATTATACTTTAACCCCTTAAAAATGATA
Found at i:4413656 original size:17 final size:16
Alignment explanation
Indices: 4413620--4413658 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
4413610 TTATTTTATG
*
4413620 TTAATTTAAATATATT
1 TTAATTTAAATATATC
*
4413636 TTAATTGTAAGTATATC
1 TTAATT-TAAATATATC
4413653 TTAATT
1 TTAATT
4413659 ATTAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (16 bp):
TTAATTTAAATATATC
Found at i:4421759 original size:23 final size:24
Alignment explanation
Indices: 4421733--4421796 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
4421723 TGGATACAGA
4421733 GTTA-TATCAACAAAAATACTAGG
1 GTTAGTATCAACAAAAATACTAGG
**
4421756 GTTAGTATTGACAAAAATACTAGG
1 GTTAGTATCAACAAAAATACTAGG
**
4421780 GTTAGTATTGACAAAAA
1 GTTAGTATCAACAAAAA
4421797 GAAGAGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 4 0.11
24 34 0.89
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.28
Consensus pattern (24 bp):
GTTAGTATCAACAAAAATACTAGG
Found at i:4421796 original size:25 final size:24
Alignment explanation
Indices: 4421742--4421796 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
4421732 AGTTATATCA
4421742 ACAAAAATACTAGGGTTAGTATTG
1 ACAAAAATACTAGGGTTAGTATTG
4421766 ACAAAAATACTAGGGTTAGTATTG
1 ACAAAAATACTAGGGTTAGTATTG
4421790 ACAAAAA
1 ACAAAAA
4421797 GAAGAGTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.25
Consensus pattern (24 bp):
ACAAAAATACTAGGGTTAGTATTG
Done.