Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold288
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: 358258
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
File 2 of 3
Found at i:133882 original size:19 final size:19
Alignment explanation
Indices: 133858--133983 Score: 61
Period size: 19 Copynumber: 6.9 Consensus size: 19
133848 CCTTTATCCT
133858 TTGCATCATCATTTCATAC
1 TTGCATCATCATTTCATAC
**
133877 TTGCATC--CACGT--TAC
1 TTGCATCATCATTTCATAC
* * *
133892 ATG-ATCATTATTTCATGC
1 TTGCATCATCATTTCATAC
* * * *
133910 TTTCA-CAACCTTT-ATCC
1 TTGCATCATCATTTCATAC
133927 TTTGCATCATCATTTCATAC
1 -TTGCATCATCATTTCATAC
* * *
133947 TTGCGTCCA-CATTACATGC
1 TTGCAT-CATCATTTCATAC
133966 TTTGCATCATCATTTCAT
1 -TTGCATCATCATTTCAT
133984 GTTTTTATGA
Statistics
Matches: 74, Mismatches: 22, Indels: 21
0.63 0.19 0.18
Matches are distributed among these distances:
14 3 0.04
15 5 0.07
16 2 0.03
17 6 0.08
18 12 0.16
19 29 0.39
20 17 0.23
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (19 bp):
TTGCATCATCATTTCATAC
Found at i:133900 original size:70 final size:70
Alignment explanation
Indices: 133795--133964 Score: 322
Period size: 70 Copynumber: 2.4 Consensus size: 70
133785 TGTTTGCCAA
133795 ATCATTTCATACTTGCATCCACGTTACATGATCATTATTTCATGCTTTCACAACCTTTATCCTTT
1 ATCATTTCATACTTGCATCCACGTTACATGATCATTATTTCATGCTTTCACAACCTTTATCCTTT
133860 GCATC
66 GCATC
133865 ATCATTTCATACTTGCATCCACGTTACATGATCATTATTTCATGCTTTCACAACCTTTATCCTTT
1 ATCATTTCATACTTGCATCCACGTTACATGATCATTATTTCATGCTTTCACAACCTTTATCCTTT
133930 GCATC
66 GCATC
* *
133935 ATCATTTCATACTTGCGTCCACATTACATG
1 ATCATTTCATACTTGCATCCACGTTACATG
133965 CTTTGCATCA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 98 1.00
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.41
Consensus pattern (70 bp):
ATCATTTCATACTTGCATCCACGTTACATGATCATTATTTCATGCTTTCACAACCTTTATCCTTT
GCATC
Found at i:133979 original size:20 final size:20
Alignment explanation
Indices: 133895--133984 Score: 73
Period size: 19 Copynumber: 4.7 Consensus size: 20
133885 ACGTTACATG
*
133895 ATCATTATTTCATGCTTT-C
1 ATCATCATTTCATGCTTTGC
* * *
133914 A-CAACCTTT-ATCCTTTGC
1 ATCATCATTTCATGCTTTGC
*
133932 ATCATCATTTCATAC-TTGC
1 ATCATCATTTCATGCTTTGC
* *
133951 GTCCA-CATTACATGCTTTGC
1 AT-CATCATTTCATGCTTTGC
133971 ATCATCATTTCATG
1 ATCATCATTTCATG
133985 TTTTTATGAC
Statistics
Matches: 53, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
17 6 0.11
18 7 0.13
19 22 0.42
20 18 0.34
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (20 bp):
ATCATCATTTCATGCTTTGC
Found at i:134038 original size:16 final size:16
Alignment explanation
Indices: 134017--134049 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
134007 ATCATGTTTT
*
134017 ATTTTTATTTTTATTA
1 ATTTTTATTTATATTA
134033 ATTTTTATTTATATTA
1 ATTTTTATTTATATTA
134049 A
1 A
134050 ATAAATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTATTTATATTA
Found at i:137603 original size:13 final size:12
Alignment explanation
Indices: 137583--137615 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
137573 AATGGACAAT
137583 AGAAAAAAAAAA
1 AGAAAAAAAAAA
137595 AGCAAAAAAAAAA
1 AG-AAAAAAAAAA
137608 AGAAAAAA
1 AGAAAAAA
137616 GTGGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:137616 original size:7 final size:7
Alignment explanation
Indices: 137585--137646 Score: 58
Period size: 7 Copynumber: 9.1 Consensus size: 7
137575 TGGACAATAG
137585 AAAAA-A
1 AAAAAGA
*
137591 AAAAAGC
1 AAAAAGA
137598 AAAAA-A
1 AAAAAGA
137604 AAAAAGA
1 AAAAAGA
*
137611 AAAAAGTG
1 AAAAAG-A
*
137619 GAAAA-A
1 AAAAAGA
137625 AAAAAGA
1 AAAAAGA
137632 AAAAAGA
1 AAAAAGA
*
137639 ACAAAGA
1 AAAAAGA
137646 A
1 A
137647 CTCTTTCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
6 14 0.31
7 27 0.60
8 4 0.09
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:141998 original size:14 final size:13
Alignment explanation
Indices: 141980--142013 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
141970 TTTTCATATC
*
141980 ATATTATTTTTTT
1 ATATTATTATTTT
141993 ATTATTATTATTTT
1 A-TATTATTATTTT
142007 ATATTAT
1 ATATTAT
142014 ATTCATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATATTATTATTTT
Found at i:142163 original size:5 final size:5
Alignment explanation
Indices: 142150--142190 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
142140 TTAACATCGA
*
142150 TATAA TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
142191 CTTGAAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:142217 original size:34 final size:34
Alignment explanation
Indices: 142178--142242 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
142168 ATTATATTAT
*
142178 ATTATATTATATTCTTGAAATTCTTTAAACCTCA
1 ATTATATTATATTATTGAAATTCTTTAAACCTCA
*
142212 ATTATATTATATTATTGGAATTCTTTAAACC
1 ATTATATTATATTATTGAAATTCTTTAAACC
142243 CGCAAGTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (34 bp):
ATTATATTATATTATTGAAATTCTTTAAACCTCA
Found at i:142408 original size:20 final size:19
Alignment explanation
Indices: 142385--142447 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 19
142375 CAAAAAGTTC
142385 AAAATTTTTAAATATATATT
1 AAAATTTTTAAATATAT-TT
* *
142405 AAAAGATATT-AATAT-TTT
1 AAAA-TTTTTAAATATATTT
*
142423 AATATTTTTAAATATATTT
1 AAAATTTTTAAATATATTT
*
142442 TAAATT
1 AAAATT
142448 CAAAATTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
17 3 0.09
18 10 0.30
19 8 0.24
20 9 0.27
21 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AAAATTTTTAAATATATTT
Found at i:143845 original size:1 final size:1
Alignment explanation
Indices: 143835--143868 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
143825 AGCCCCATTC
* *
143835 TTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
143869 ACATTTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:156460 original size:15 final size:15
Alignment explanation
Indices: 156424--156454 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
156414 ATTACGTTGC
*
156424 TCCATTTGTCTTTGT
1 TCCATTTGTCTATGT
156439 TCCATTTGTCTATGT
1 TCCATTTGTCTATGT
156454 T
1 T
156455 GGATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.13, T:0.58
Consensus pattern (15 bp):
TCCATTTGTCTATGT
Found at i:156495 original size:18 final size:19
Alignment explanation
Indices: 156468--156511 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
156458 TTTAAATGCC
* *
156468 ATTTAAATGT-AATATGTT
1 ATTTATATGTGAATATGGT
156486 ATTTATATGTGAATATGGT
1 ATTTATATGTGAATATGGT
156505 ATTTATA
1 ATTTATA
156512 CTATCTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (19 bp):
ATTTATATGTGAATATGGT
Found at i:157136 original size:6 final size:6
Alignment explanation
Indices: 157109--157152 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
157099 ATTTTTATAC
* *
157109 ATAAAT TTAAAT ATATAT -TAAAT ATAAAT ATTAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT A-TAAAT ATAAAT AT
157153 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 4 0.12
6 22 0.69
7 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
ATAAAT
Found at i:157141 original size:13 final size:13
Alignment explanation
Indices: 157109--157153 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
157099 ATTTTTATAC
157109 ATAAAT-TTAAAT
1 ATAAATATTAAAT
157121 AT--ATATTAAAT
1 ATAAATATTAAAT
157132 ATAAATATTAAAT
1 ATAAATATTAAAT
157145 ATAAATATT
1 ATAAATATT
157154 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.07
11 8 0.27
12 2 0.07
13 18 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAAATATTAAAT
Found at i:157981 original size:28 final size:27
Alignment explanation
Indices: 157948--158044 Score: 88
Period size: 29 Copynumber: 3.4 Consensus size: 27
157938 TTTGAGTGTG
157948 TATTATTTTTTATATTTATATCATATTTA
1 TATTATTTTTTATATTT-TAT-ATATTTA
* *
157977 T-TTATTTTTTTTATGTTTATAAATTTA
1 TATTATTTTTTATAT-TTTATATATTTA
* *
158004 TATGATTTTTTTATATTCGTATAATATTTA
1 TATTA-TTTTTTATATT-TTAT-ATATTTA
*
158034 TGTTATTTTTT
1 TATTATTTTTT
158045 GTGTTACTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
27 7 0.13
28 18 0.33
29 21 0.38
30 9 0.16
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTATTTTTTATATTTTATATATTTA
Found at i:157989 original size:30 final size:30
Alignment explanation
Indices: 157948--158044 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
157938 TTTGAGTGTG
157948 TATTATTTTTTATATTTATATCATATTTAT-T
1 TATT-TTTTTTATATTTATAT-ATATTTATAT
*
157979 TATTTTTTTTATGTTTATA-A-ATTTATAT
1 TATTTTTTTTATATTTATATATATTTATAT
* *
158007 GA-TTTTTTTATATTCGTATA-ATATTTATGT
1 TATTTTTTTTATATT--TATATATATTTATAT
158037 TATTTTTT
1 TATTTTTT
158045 GTGTTACTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
27 17 0.30
28 3 0.05
29 5 0.09
30 22 0.39
31 9 0.16
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (30 bp):
TATTTTTTTTATATTTATATATATTTATAT
Found at i:158177 original size:24 final size:22
Alignment explanation
Indices: 158150--158202 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
158140 TCATGACTTA
158150 ATTATTTTTTCATGTCATTTTTAT
1 ATTATTTTTTCAT-TCA-TTTTAT
* * *
158174 ATTATATCTTCATTTATTTTAT
1 ATTATTTTTTCATTCATTTTAT
158196 ATT-TTTT
1 ATTATTTT
158203 ATATATTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 2 0.08
22 9 0.38
23 2 0.08
24 11 0.46
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.68
Consensus pattern (22 bp):
ATTATTTTTTCATTCATTTTAT
Found at i:158226 original size:33 final size:31
Alignment explanation
Indices: 158167--158227 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
158157 TTTCATGTCA
*
158167 TTTTTATATTATATCTTCATTTATTTTATAT
1 TTTTTATATTATATCATCATTTATTTTATAT
* *
158198 TTTTTATATATTTATCATGATTTAATTTTA
1 TTTTTATAT-TATATCATCATTT-ATTTTA
158228 AGTTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
32 10 0.40
33 6 0.24
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTTTATATTATATCATCATTTATTTTATAT
Found at i:158922 original size:21 final size:22
Alignment explanation
Indices: 158882--158923 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
158872 ATATGACTTC
* *
158882 AATTTTTAAATAATATATTTAA
1 AATTATTAAATAACATATTTAA
158904 AATTATTAAA-AACATATTTA
1 AATTATTAAATAACATATTTA
158924 TTTAATTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATTAAATAACATATTTAA
Found at i:160048 original size:22 final size:22
Alignment explanation
Indices: 160023--160066 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
160013 TCTATATTTT
160023 TATTAA-AATTTTATAATTTATA
1 TATTAATAA-TTTATAATTTATA
*
160045 TATTAATAATTTATATTTTATA
1 TATTAATAATTTATAATTTATA
160067 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTAATAATTTATAATTTATA
Found at i:160070 original size:15 final size:15
Alignment explanation
Indices: 160030--160071 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
160020 TTTTATTAAA
160030 ATTTTAT-AATTTAT
1 ATTTTATAAATTTAT
*
160044 ATATTA-ATAATTTAT
1 ATTTTATA-AATTTAT
160059 ATTTTATAAATTT
1 ATTTTATAAATTT
160072 TAAAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 5 0.22
15 17 0.74
16 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATAAATTTAT
Found at i:160869 original size:28 final size:29
Alignment explanation
Indices: 160824--160879 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
160814 TACTTTAATC
*
160824 TTTTTCATTAGTTATATC-TAATTTATAA
1 TTTTTCATTAGTTATATCTTAATATATAA
** *
160852 TTTTTCATTTTTTCTATCTTAATATATA
1 TTTTTCATTAGTTATATCTTAATATATA
160880 TATATATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTCATTAGTTATATCTTAATATATAA
Found at i:161282 original size:12 final size:13
Alignment explanation
Indices: 161267--161306 Score: 59
Period size: 11 Copynumber: 3.3 Consensus size: 13
161257 AATTGGGCTA
161267 AAAAATAT-ATTT
1 AAAAATATGATTT
161279 AAAAATATGA--T
1 AAAAATATGATTT
161290 AAAAATATGATTT
1 AAAAATATGATTT
161303 AAAA
1 AAAA
161307 TTTTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.44
12 8 0.32
13 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (13 bp):
AAAAATATGATTT
Found at i:161842 original size:12 final size:13
Alignment explanation
Indices: 161824--161855 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
161814 TTGAATAATA
161824 AAAATTTAAATTT
1 AAAATTTAAATTT
161837 -AAATTT-AATTT
1 AAAATTTAAATTT
161848 AAAATTTA
1 AAAATTTA
161856 TGTTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:161932 original size:14 final size:14
Alignment explanation
Indices: 161913--161944 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
161903 TAAATTTGAT
161913 TTAAAATTATTTAA
1 TTAAAATTATTTAA
*
161927 TTAAAATTATTTAT
1 TTAAAATTATTTAA
161941 TTAA
1 TTAA
161945 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAAAATTATTTAA
Found at i:168198 original size:12 final size:13
Alignment explanation
Indices: 168181--168211 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
168171 ACTTAAGTCA
168181 TTCTTCCAATT-T
1 TTCTTCCAATTCT
168193 TTCTTCCAATTCT
1 TTCTTCCAATTCT
168206 TTCTTC
1 TTCTTC
168212 GTTTAAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (13 bp):
TTCTTCCAATTCT
Found at i:169793 original size:34 final size:34
Alignment explanation
Indices: 169755--169824 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
169745 TAAATTGTCC
*
169755 GGGTCATTTAACAGTTTCATAATAGACCATTGTA
1 GGGTCATTTAACAGTTACATAATAGACCATTGTA
169789 GGGTCATTTAACAGTTACATAATAGACCATTGTA
1 GGGTCATTTAACAGTTACATAATAGACCATTGTA
169823 GG
1 GG
169825 CTTGCATACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (34 bp):
GGGTCATTTAACAGTTACATAATAGACCATTGTA
Found at i:172732 original size:25 final size:24
Alignment explanation
Indices: 172676--172738 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
172666 TATTTTAAAT
172676 TTATTTTTAATTTAATTATATATA
1 TTATTTTTAATTTAATTATATATA
* * *
172700 TTAATTTTGATGTTAA-TATATTATG
1 TTATTTTTAAT-TTAATTATA-TATA
172725 TTATTTTT-ATTTAA
1 TTATTTTTAATTTAA
172739 AATTTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 4 0.12
24 15 0.45
25 14 0.42
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (24 bp):
TTATTTTTAATTTAATTATATATA
Found at i:173543 original size:27 final size:27
Alignment explanation
Indices: 173483--173554 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 27
173473 ATATCAAAAT
*
173483 ATATAATATAAAT-TATTAATATGTCAA
1 ATATCATATAAATATA-TAATATGTCAA
* *
173510 A-ATTCATATAAATATATAATATTTTAA
1 ATA-TCATATAAATATATAATATGTCAA
*
173537 ATATCATTATAATTATAT
1 ATATCA-TATAAATATAT
173555 CTATTCAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 23 0.62
28 13 0.35
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATCATATAAATATATAATATGTCAA
Found at i:180083 original size:3 final size:3
Alignment explanation
Indices: 180002--180072 Score: 63
Period size: 3 Copynumber: 23.7 Consensus size: 3
179992 TATTATATTT
** * ** **
180002 TAA TAA TAA TAA TAA TAA T-A TTT TAA TAA TAT TATA TTT TGT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
180047 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
180073 TTTTAATAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 53 0.95
4 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:181794 original size:2 final size:2
Alignment explanation
Indices: 181789--181813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
181779 ATGCACTCAA
181789 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
181814 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:182085 original size:22 final size:20
Alignment explanation
Indices: 182048--182087 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
182038 TTAATTTGTT
*
182048 ATATATTTATATAAATTTTA
1 ATATATTTATAAAAATTTTA
182068 ATATATTTATGTAAAAATTT
1 ATATATTTA--TAAAAATTT
182088 AGTTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATATATTTATAAAAATTTTA
Found at i:182542 original size:48 final size:47
Alignment explanation
Indices: 182438--182543 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 47
182428 TTTATGTAAT
*
182438 ATAATATAATATAA-ATAAAATTAAATATATTTATATAATAATTTAAA
1 ATAATATAA-ATAATATAAAATTAAATATATATATATAATAATTTAAA
* *
182485 AT--TGT-AATAATATAATA-TAAATGATATATATTATAAT-ATTTATAA
1 ATAATATAAATAATATAAAATTAAAT-ATATATA-TATAATAATTTA-AA
182530 ATAATATAAATAAT
1 ATAATATAAATAAT
182544 TTATTTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
43 9 0.19
44 17 0.35
45 12 0.25
47 4 0.08
48 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (47 bp):
ATAATATAAATAATATAAAATTAAATATATATATATAATAATTTAAA
Found at i:182943 original size:3 final size:3
Alignment explanation
Indices: 182935--182960 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
182925 ATGGGTGCAT
182935 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
182961 TAGGAGGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:183420 original size:18 final size:19
Alignment explanation
Indices: 183389--183426 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
183379 TTATTTAATA
*
183389 TAATTTTATTATTAAATTT
1 TAATTTTATAATTAAATTT
183408 TAATTTT-TAATTAAATTT
1 TAATTTTATAATTAAATTT
183426 T
1 T
183427 GTTACTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TAATTTTATAATTAAATTT
Found at i:184163 original size:19 final size:20
Alignment explanation
Indices: 184134--184178 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
184124 ATCTAGTTAA
184134 TTATATAAAATTTAATATAT
1 TTATATAAAATTTAATATAT
* *
184154 TTATAT-AAATTTATTATTT
1 TTATATAAAATTTAATATAT
184173 TTATAT
1 TTATAT
184179 TATATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATATAAAATTTAATATAT
Found at i:184181 original size:11 final size:11
Alignment explanation
Indices: 184178--184212 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
184168 TATTTTTATA
184178 TTATATTATTT
1 TTATATTATTT
184189 TTA-ATTATTT
1 TTATATTATTT
*
184199 TTATATTATGT
1 TTATATTATTT
184210 TTA
1 TTA
184213 ATGTTACTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
TTATATTATTT
Found at i:184195 original size:15 final size:15
Alignment explanation
Indices: 184161--184196 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
184151 TATTTATATA
184161 AATT-TATTATTTTT
1 AATTATATTATTTTT
184175 ATATTATATTATTTTT
1 A-ATTATATTATTTTT
184191 AATTAT
1 AATTAT
184197 TTTTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 8 0.40
16 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTATATTATTTTT
Found at i:184202 original size:16 final size:17
Alignment explanation
Indices: 184162--184202 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
184152 ATTTATATAA
184162 ATTTATTATTTTTATATT
1 ATTT-TTATTTTTATATT
*
184180 A-TATTATTTTTA-ATT
1 ATTTTTATTTTTATATT
184195 ATTTTTAT
1 ATTTTTAT
184203 ATTATGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.20
16 14 0.70
17 1 0.05
18 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTATTTTTATATT
Found at i:184256 original size:2 final size:2
Alignment explanation
Indices: 184249--184277 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
184239 TTGGCAGTGC
184249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
184278 ACGTACGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:186177 original size:18 final size:17
Alignment explanation
Indices: 186143--186186 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
186133 TATTAGCCTC
*
186143 ATATTTTTAAATTTTTA
1 ATATTTTAAAATTTTTA
*
186160 TTATTTTAAAATTTTTTA
1 ATATTTTAAAA-TTTTTA
186178 ATATTTTAA
1 ATATTTTAA
186187 TTTCTCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTTAAAATTTTTA
Found at i:187761 original size:16 final size:16
Alignment explanation
Indices: 187738--187770 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
187728 TATGTTAATT
187738 ATTTTAT-ATTTTTAA
1 ATTTTATAATTTTTAA
187753 ATTTATATAATTTTTAA
1 ATTT-TATAATTTTTAA
187770 A
1 A
187771 CTGAATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 3 0.19
17 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATAATTTTTAA
Found at i:188686 original size:16 final size:17
Alignment explanation
Indices: 188665--188701 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
188655 CATGTTTTTG
188665 TTATATTTATA-TTATT
1 TTATATTTATACTTATT
188681 TTATATTTATACCTTATT
1 TTATATTTATA-CTTATT
188699 TTA
1 TTA
188702 ATTCTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTATACTTATT
Found at i:192996 original size:16 final size:16
Alignment explanation
Indices: 192975--193006 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
192965 TAAGACATCA
*
192975 TCTAATGGTGTTTATG
1 TCTAATGGTATTTATG
192991 TCTAATGGTATTTATG
1 TCTAATGGTATTTATG
193007 AGTTGAATTG
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:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (16 bp):
TCTAATGGTATTTATG
Found at i:194007 original size:31 final size:31
Alignment explanation
Indices: 193969--194027 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
193959 AAGAAAAATA
193969 AAAGCTTAAAGTTTAC-TCGCAGTTCTATATG
1 AAAGCTTAAAGTTTACTTC-CAGTTCTATATG
194000 AAAGCTTAAAGTTTACTTCCAGTTCTAT
1 AAAGCTTAAAGTTTACTTCCAGTTCTAT
194028 CTCTTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (31 bp):
AAAGCTTAAAGTTTACTTCCAGTTCTATATG
Found at i:196971 original size:57 final size:57
Alignment explanation
Indices: 196897--197006 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
196887 CTTAAATCCT
* *
196897 CCACCGTCCCCCGAATTTTGCCGCTCACCAGAAAATCTTTTGGATATTTCATCCCCA
1 CCACCGTCCCCCGAATTTTGCCGCTCACCAGAAAAACTTGTGGATATTTCATCCCCA
* * * *
196954 CCACTGTCCCCTGAATTTTGCTGCTCACCAGAAAAACTTGTGGATTTTTCATC
1 CCACCGTCCCCCGAATTTTGCCGCTCACCAGAAAAACTTGTGGATATTTCATC
197007 AGTGGGGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.31
Consensus pattern (57 bp):
CCACCGTCCCCCGAATTTTGCCGCTCACCAGAAAAACTTGTGGATATTTCATCCCCA
Found at i:198934 original size:14 final size:14
Alignment explanation
Indices: 198917--198943 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
198907 GTCATATTCT
198917 CATACTTATATCCC
1 CATACTTATATCCC
198931 CATACTTATATCC
1 CATACTTATATCC
198944 AAATATGGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (14 bp):
CATACTTATATCCC
Found at i:200644 original size:18 final size:19
Alignment explanation
Indices: 200621--200659 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
200611 ATATAGAGTT
200621 ATTTA-TTAAAATTTAAAA
1 ATTTATTTAAAATTTAAAA
* *
200639 ATTTATTTAATATTTTAAA
1 ATTTATTTAAAATTTAAAA
200658 AT
1 AT
200660 ATATAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTATTTAAAATTTAAAA
Found at i:200899 original size:16 final size:17
Alignment explanation
Indices: 200880--200912 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
200870 TTTAGATAAA
200880 AAAT-TACTTTAAAAAT
1 AAATATACTTTAAAAAT
*
200896 AAATATATTTTAAAAAT
1 AAATATACTTTAAAAAT
200913 GAATCAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATACTTTAAAAAT
Found at i:201748 original size:10 final size:10
Alignment explanation
Indices: 201733--201767 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
201723 TTTTATAAAA
201733 TATTTAAATT
1 TATTTAAATT
201743 TATTT-AATT
1 TATTTAAATT
*
201752 TATTTAAATC
1 TATTTAAATT
201762 TATTTA
1 TATTTA
201768 TTATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTTAAATT
Found at i:201891 original size:6 final size:6
Alignment explanation
Indices: 201880--201943 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
201870 ATATTTTTTA
*
201880 AAATAT AAATAT AAA-ATT AAATAA AAAT-T AAATAT ATAA-AT AAATATT
1 AAATAT AAATAT AAATA-T AAATAT AAATAT AAATAT A-AATAT AAATA-T
**
201928 AAATCC AAATAT AAAT
1 AAATAT AAATAT AAAT
201944 GAAAAAGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
5 7 0.15
6 31 0.67
7 8 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:201899 original size:19 final size:19
Alignment explanation
Indices: 201877--201943 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
201867 TAAATATTTT
*
201877 TTAAAATATAAATATAAAA
1 TTAAAATATAAATATTAAA
201896 TT-AAATA-AAA-ATTAAA
1 TTAAAATATAAATATTAAA
*
201912 TATATAA-ATAAATATTAAA
1 T-TAAAATATAAATATTAAA
**
201931 TCCAAATATAAAT
1 TTAAAATATAAAT
201944 GAAAAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.16
17 5 0.13
18 12 0.32
19 15 0.39
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAATATAAATATTAAA
Found at i:201908 original size:11 final size:12
Alignment explanation
Indices: 201878--201942 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 12
201868 AAATATTTTT
201878 TAAAATATAAATA
1 TAAAAT-TAAATA
201891 TAAAATTAAATA
1 TAAAATTAAATA
201903 -AAAATTAAATA
1 TAAAATTAAATA
201914 TATAAA-TAAATA
1 TA-AAATTAAATA
* *
201926 TTAAATCCAAATA
1 TAAAAT-TAAATA
201939 TAAA
1 TAAA
201943 TGAAAAAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
11 14 0.31
12 14 0.31
13 17 0.38
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAAATA
Found at i:201911 original size:23 final size:24
Alignment explanation
Indices: 201879--201925 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
201869 AATATTTTTT
201879 AAAATATAAATATA-AAATTAAATA
1 AAAATATAAATATATAAA-TAAATA
201903 AAAAT-TAAATATATAAATAAATA
1 AAAATATAAATATATAAATAAATA
201926 TTAAATCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAATATAAATATATAAATAAATA
Found at i:202062 original size:25 final size:24
Alignment explanation
Indices: 202039--202088 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
202029 ATATCTAAAT
202039 ATTT-TAAT-TTAAAATTTATTTAA
1 ATTTATAATATTAAAATTTA-TTAA
*
202062 ATTTATAATATTTAAATTTATTAA
1 ATTTATAATATTAAAATTTATTAA
202086 ATT
1 ATT
202089 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 11 0.46
25 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTATAATATTAAAATTTATTAA
Found at i:202082 original size:15 final size:15
Alignment explanation
Indices: 202036--202082 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
202026 TTTATATCTA
* *
202036 AATATTTTAATTTAA
1 AATATTTAAATTTAT
202051 AATTTATTTAAATTTAT
1 AA--TATTTAAATTTAT
202068 AATATTTAAATTTAT
1 AATATTTAAATTTAT
202083 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 15 0.54
17 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATTTAAATTTAT
Found at i:202332 original size:23 final size:25
Alignment explanation
Indices: 202306--202366 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
202296 ATAAAAATAA
*
202306 TATAAATTATAT-ATATTATT-ATT
1 TATAAATTAAATCATATTATTAATT
202329 TATATAATATAAATCATATTATTAATT
1 TATA-AAT-TAAATCATATTATTAATT
*
202356 TATATATTAAA
1 TATAAATTAAA
202367 ATTTTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 4 0.12
24 3 0.09
25 8 0.25
26 10 0.31
27 7 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TATAAATTAAATCATATTATTAATT
Found at i:202333 original size:41 final size:41
Alignment explanation
Indices: 202287--202394 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 41
202277 ATAAAAATAA
202287 TTATATAATATAAA-AATAATATAAATTATATATATTATTAT
1 TTATATAATATAAATAATAATATAAATT-TATATATTATTAT
* * * **
202328 TTATATAATATAAATCATATTATTAATTTATATATTAAAAT
1 TTATATAATATAAATAATAATATAAATTTATATATTATTAT
* *
202369 TTTTATAA-ATATATAAT-ATATTAAAT
1 TTATATAATATAAATAATAATA-TAAAT
202395 ATAATTATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 2 0.04
40 11 0.20
41 32 0.58
42 10 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (41 bp):
TTATATAATATAAATAATAATATAAATTTATATATTATTAT
Found at i:202336 original size:30 final size:27
Alignment explanation
Indices: 202302--202388 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 27
202292 TAATATAAAA
202302 ATAATATAAATTATATATATTATTATTTAT
1 ATAATATAAATTATAT-TATTA--ATTTAT
*
202332 ATAATATAAATCATATTATTAATTTAT
1 ATAATATAAATTATATTATTAATTTAT
* *
202359 ATATTA-AAATT-T-TTA-TAA-ATAT
1 ATAATATAAATTATATTATTAATTTAT
202381 ATAATATA
1 ATAATATA
202389 TTAAATATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 8 0.16
23 4 0.08
24 3 0.06
25 1 0.02
26 4 0.08
27 11 0.22
29 5 0.10
30 15 0.29
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAATATAAATTATATTATTAATTTAT
Found at i:202387 original size:27 final size:27
Alignment explanation
Indices: 202357--202411 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
202347 TTATTAATTT
**
202357 ATATATTAAA-ATTTTTATAAATATATA
1 ATATATTAAATATAATTAT-AATATATA
202384 ATATATTAAATATAATTATAATATATA
1 ATATATTAAATATAATTATAATATATA
202411 A
1 A
202412 AAAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATATTAAATATAATTATAATATATA
Found at i:202589 original size:18 final size:19
Alignment explanation
Indices: 202568--202622 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
202558 CTCTCAATTT
*
202568 TTTTTTATAATTAA-AATA
1 TTTTATATAATTAATAATA
*
202586 TTTTATATATTTAATAATA
1 TTTTATATAATTAATAATA
**
202605 TTAAATATAATTATATAA
1 TTTTATATAATTA-ATAA
202623 ATAAATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 12 0.40
19 14 0.47
20 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTATATAATTAATAATA
Found at i:202591 original size:16 final size:19
Alignment explanation
Indices: 202568--202606 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
202558 CTCTCAATTT
* *
202568 TTTTTTATAATTAA-AATA
1 TTTTATATATTTAATAATA
202586 TTTTATATATTTAATAATA
1 TTTTATATATTTAATAATA
202605 TT
1 TT
202607 AAATATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATATATTTAATAATA
Found at i:202625 original size:14 final size:14
Alignment explanation
Indices: 202606--202653 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
202596 TTAATAATAT
202606 TAAATATAATTATA
1 TAAATATAATTATA
202620 TAAATA-AATATATA
1 TAAATATAAT-TATA
202634 TAAA-ATAA-TA-A
1 TAAATATAATTATA
202645 -AAATATAAT
1 TAAATATAAT
202654 ATAATAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
10 3 0.10
11 5 0.17
12 2 0.07
13 4 0.13
14 16 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:203283 original size:9 final size:9
Alignment explanation
Indices: 203243--203325 Score: 52
Period size: 9 Copynumber: 9.7 Consensus size: 9
203233 TTATAATAAA
*
203243 TATATTAAT
1 TATATTTAT
*
203252 TATATTTAAA
1 TATATTT-AT
*
203262 TATATCATAT
1 TATAT-TTAT
203272 TATATTTA-
1 TATATTTAT
203280 T-TATTT-T
1 TATATTTAT
203287 TATATTTAT
1 TATATTTAT
* *
203296 TAAATATAT
1 TATATTTAT
203305 TATA---AT
1 TATATTTAT
*
203311 TATATTTTT
1 TATATTTAT
203320 TATATT
1 TATATT
203326 ATATCTAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
6 6 0.11
7 6 0.11
8 6 0.11
9 26 0.46
10 12 0.21
11 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (9 bp):
TATATTTAT
Found at i:203296 original size:24 final size:24
Alignment explanation
Indices: 203269--203339 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
203259 AAATATATCA
**
203269 TATTATATTTATTATTTTTATATT
1 TATTATATTTATTATAATTATATT
* *
203293 TATTAAATATATTATAATTATATT
1 TATTATATTTATTATAATTATATT
* *
203317 TTTTATATTATATCTAAAATTAT
1 TATTATATT-TAT-TATAATTAT
203340 CAAATTTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 26 0.70
25 3 0.08
26 8 0.22
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTATATTTATTATAATTATATT
Found at i:203305 original size:33 final size:35
Alignment explanation
Indices: 203268--203334 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 35
203258 TAAATATATC
*
203268 ATATTATATTTAT-TATTTTTATATT-TAT-TAAAT
1 ATATTATAATTATAT-TTTTTATATTATATCTAAAT
203301 ATATTATAATTATATTTTTTATATTATATCTAAA
1 ATATTATAATTATATTTTTTATATTATATCTAAA
203335 ATTATCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 22 0.73
34 4 0.13
35 4 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (35 bp):
ATATTATAATTATATTTTTTATATTATATCTAAAT
Found at i:203312 original size:15 final size:15
Alignment explanation
Indices: 203206--203312 Score: 50
Period size: 15 Copynumber: 7.2 Consensus size: 15
203196 ATATAAATTG
*
203206 TTAAATATATTAAAA
1 TTAAATATATTATAA
203221 TTATAAATATAATTATAA
1 -T-TAAATAT-ATTATAA
203239 -TAAATATATTAATTATA
1 TTAAATATATT-A-TA-A
*
203256 TTTAAATATATCAT-A
1 -TTAAATATATTATAA
*
203271 TT--ATAT-TTATTA
1 TTAAATATATTATAA
**
203283 TT-TTTATATT-T-A
1 TTAAATATATTATAA
203295 TTAAATATATTATAA
1 TTAAATATATTATAA
203310 TTA
1 TTA
203313 TATTTTTTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 27
0.69 0.06 0.26
Matches are distributed among these distances:
11 3 0.04
12 10 0.14
13 10 0.14
14 8 0.11
15 13 0.18
16 3 0.04
17 9 0.12
18 7 0.10
19 9 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAATATATTATAA
Found at i:204829 original size:11 final size:11
Alignment explanation
Indices: 204804--204853 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
204794 TATATATCTT
204804 AATTTTTAATT-
1 AATTTTT-ATTA
*
204815 AATTTTTAGTA
1 AATTTTTATTA
*
204826 AATTTATATTA
1 AATTTTTATTA
204837 TAA-TTTTATTA
1 -AATTTTTATTA
204848 AATTTT
1 AATTTT
204854 AATATTGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 4 0.12
11 26 0.81
12 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
AATTTTTATTA
Found at i:204843 original size:22 final size:25
Alignment explanation
Indices: 204818--204867 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 25
204808 TTTAATTAAT
204818 TTTTAGTAAA-TTT-ATATT-ATAA
1 TTTTAGTAAATTTTAATATTGATAA
*
204840 TTTTATTAAATTTTAATATTGATAA
1 TTTTAGTAAATTTTAATATTGATAA
204865 TTT
1 TTT
204868 AATATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 9 0.38
23 3 0.12
24 5 0.21
25 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TTTTAGTAAATTTTAATATTGATAA
Found at i:205630 original size:97 final size:97
Alignment explanation
Indices: 205522--205704 Score: 278
Period size: 97 Copynumber: 1.9 Consensus size: 97
205512 AAAAAATAAA
205522 AAATTCGATCTTTAAATAAATTTATTTCT-CGTTACTCTTTACTTTTAGCATACTAAATTCAAAA
1 AAATTCGATCTTTAAATAAATTTATTT-TACGTTACTCTTTACTTTTAGCATACTAAATTCAAAA
*
205586 AAATAAAATAAAACTGTTATATGTAATATCTAT
65 AAATAAAATAAAACTGCTATATGTAATATCTAT
* * ****
205619 AAATTCGATCTTTAAATAAATTTATTTTACGTTACTCTTTGCTTTTAGCATACTTAATTGGTTAA
1 AAATTCGATCTTTAAATAAATTTATTTTACGTTACTCTTTACTTTTAGCATACTAAATTCAAAAA
*
205684 AATAAAATAAACCTGCTATAT
66 AATAAAATAAAACTGCTATAT
205705 ACGTAGTAAC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 1 0.01
97 76 0.99
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.42
Consensus pattern (97 bp):
AAATTCGATCTTTAAATAAATTTATTTTACGTTACTCTTTACTTTTAGCATACTAAATTCAAAAA
AATAAAATAAAACTGCTATATGTAATATCTAT
Found at i:206178 original size:26 final size:26
Alignment explanation
Indices: 206144--206207 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
206134 ATTATTTAAA
206144 ATAATATTTAAA-AAATTATTTTTATAAT
1 ATAA-ATTTAAATAAA--ATTTTTATAAT
*
206172 -TAAATTTAAATAAAATTTTTATTAT
1 ATAAATTTAAATAAAATTTTTATAAT
206197 ATAAATATTAA
1 ATAAAT-TTAA
206208 TTTGGACCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 10 0.31
26 12 0.38
27 10 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAAATTTAAATAAAATTTTTATAAT
Found at i:208467 original size:22 final size:20
Alignment explanation
Indices: 208436--208476 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
208426 TATAAGCTAG
208436 AAAATAAATAATTAATATATTT
1 AAAATAAAT-ATTAA-ATATTT
*
208458 AAAATTAATATTAAATATT
1 AAAATAAATATTAAATATT
208477 AAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATAAATATTAAATATTT
Found at i:208493 original size:20 final size:21
Alignment explanation
Indices: 208470--208514 Score: 69
Period size: 18 Copynumber: 2.3 Consensus size: 21
208460 AATTAATATT
208470 AAATATTAAATA-TT-TTTAA
1 AAATATTAAATATTTATTTAA
208489 AAA-ATTAAATATTTATTTAA
1 AAATATTAAATATTTATTTAA
208509 AAATAT
1 AAATAT
208515 ATTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 8 0.35
21 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATATTAAATATTTATTTAA
Found at i:208521 original size:22 final size:21
Alignment explanation
Indices: 208470--208527 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
208460 AATTAATATT
208470 AAATATTAA-ATATT-TTTAAA
1 AAATATTAATAT-TTATTTAAA
*
208490 AAAT-TAAATATTTATTTAAA
1 AAATATTAATATTTATTTAAA
*
208510 AATATATTAATAATTATT
1 AA-ATATTAATATTTATT
208528 ATTTTGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.16
20 14 0.45
21 2 0.06
22 10 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATTAATATTTATTTAAA
Found at i:208625 original size:18 final size:17
Alignment explanation
Indices: 208597--208630 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
208587 TATAATTTTT
*
208597 TAATTTATTAATAAATA
1 TAATTTATTAAAAAATA
208614 TAATTTATTTAAAAAAT
1 TAATTTA-TTAAAAAAT
208631 TTTATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTTATTAAAAAATA
Found at i:209253 original size:27 final size:27
Alignment explanation
Indices: 209215--209269 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
209205 AAAATACTAA
209215 TTCACTCCAAATAAGGACAATTTTGTC
1 TTCACTCCAAATAAGGACAATTTTGTC
209242 TTCACTCCAAATAAGGACAATTTTGTC
1 TTCACTCCAAATAAGGACAATTTTGTC
209269 T
1 T
209270 AAGTAACCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (27 bp):
TTCACTCCAAATAAGGACAATTTTGTC
Found at i:210941 original size:17 final size:18
Alignment explanation
Indices: 210899--210958 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 18
210889 AAATTTTTTT
210899 TATT-AATAATATAAAAA
1 TATTAAATAATATAAAAA
210916 TA--AATATAATA-AAAAA
1 TATTAA-ATAATATAAAAA
*
210932 TATTAAATAA-ATTAAAA
1 TATTAAATAATATAAAAA
*
210949 TTTTAAATAA
1 TATTAAATAA
210959 AAATATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 9 0.25
17 25 0.69
18 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATTAAATAATATAAAAA
Found at i:211289 original size:11 final size:12
Alignment explanation
Indices: 211275--211314 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
211265 ATTTATTTTT
211275 ATATT-ATAAAA
1 ATATTAATAAAA
211286 ATATTAAT-AAA
1 ATATTAATAAAA
*
211297 ATATAAATAAAA
1 ATATTAATAAAA
211309 A-ATTAA
1 ATATTAA
211315 ATTTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATTAATAAAA
Found at i:211329 original size:15 final size:15
Alignment explanation
Indices: 211309--211340 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
211299 ATAAATAAAA
211309 AATTAAATTTAATTT
1 AATTAAATTTAATTT
211324 AATTAAATTTAATTT
1 AATTAAATTTAATTT
211339 AA
1 AA
211341 ATAATCGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTAAATTTAATTT
Found at i:212535 original size:3 final size:3
Alignment explanation
Indices: 212529--212572 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
212519 ATAATAATGA
212529 TAT 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 TAT TA
212573 AGTGGAGGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:212860 original size:2 final size:2
Alignment explanation
Indices: 212853--212884 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
212843 TTTAACATTG
212853 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
212885 GTTTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:213543 original size:2 final size:2
Alignment explanation
Indices: 213536--213561 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
213526 TTGATTCAAC
213536 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
213562 TTAGATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:214724 original size:17 final size:18
Alignment explanation
Indices: 214696--214729 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
214686 TTTTACTGAA
*
214696 AAAGGTAAAAAAGAAAGT
1 AAAGGTAAAAAAAAAAGT
214714 AAAGG-AAAAAAAAAAG
1 AAAGGTAAAAAAAAAAG
214730 GCCTAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (18 bp):
AAAGGTAAAAAAAAAAGT
Found at i:215008 original size:31 final size:28
Alignment explanation
Indices: 214970--215035 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
214960 TAGACTTGAA
214970 TAATAAAAAAAAT-ATTT--ATTTAAGTT
1 TAATAAAAAAAATAATTTAAATTTAA-TT
*
214996 TAATTTAATAAAAATAATTTAAATTTAATT
1 TAA--TAAAAAAAATAATTTAAATTTAATT
215026 TAATAAAAAA
1 TAATAAAAAA
215036 TTTATTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 3 0.09
28 15 0.45
29 4 0.12
30 5 0.15
31 6 0.18
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
TAATAAAAAAAATAATTTAAATTTAATT
Found at i:215022 original size:25 final size:25
Alignment explanation
Indices: 214987--215034 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
214977 AAAAATATTT
*
214987 ATTTAAGTTTAATTTAATAAAAATA
1 ATTTAAATTTAATTTAATAAAAATA
215012 ATTTAAATTTAATTTAATAAAAA
1 ATTTAAATTTAATTTAATAAAAA
215035 ATTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTTAAATTTAATTTAATAAAAATA
Found at i:215074 original size:18 final size:19
Alignment explanation
Indices: 215051--215102 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
215041 TTTATTTTAA
215051 AATATTT-TTAATTATATT
1 AATATTTATTAATTATATT
*
215069 AATATTTATATAATTTTA-T
1 AATATTTAT-TAATTATATT
*
215088 AATTTTTATTAATTA
1 AATATTTATTAATTA
215103 AATAATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 12 0.41
19 10 0.34
20 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATATTTATTAATTATATT
Found at i:215109 original size:37 final size:38
Alignment explanation
Indices: 215019--215114 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 38
215009 ATAATTTAAA
* * *
215019 TTTAATT-TAATAAAAAATTTATTTTATTTTAAAATATT
1 TTTAATTATAAT-AATAATTTATATAATTTTAAAATATT
* * *
215057 TTTAATTATATTAAT-ATTTATATAATTTTATAATTTT
1 TTTAATTATAATAATAATTTATATAATTTTAAAATATT
215094 TATTAATTA-AATAATAATTTA
1 T-TTAATTATAATAATAATTTA
215115 AATTAAATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
37 24 0.50
38 21 0.44
39 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (38 bp):
TTTAATTATAATAATAATTTATATAATTTTAAAATATT
Found at i:215985 original size:24 final size:24
Alignment explanation
Indices: 215957--216002 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
215947 AATAAAAATT
215957 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
*
215981 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
216003 AAATAACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:216043 original size:28 final size:28
Alignment explanation
Indices: 216011--216117 Score: 187
Period size: 28 Copynumber: 3.8 Consensus size: 28
216001 AAAAATAACC
*
216011 ACCATATTTGACAAATATAAAGGAAACT
1 ACCATATTTGACAAATACAAAGGAAACT
*
216039 ACCATATTTGACAAATACAAAAGAAACT
1 ACCATATTTGACAAATACAAAGGAAACT
216067 ACCATATTTGACAAATACAAAGGAAACT
1 ACCATATTTGACAAATACAAAGGAAACT
*
216095 ACCATATTTGACAAATATAAAGG
1 ACCATATTTGACAAATACAAAGG
216118 GTAGCATTTG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.23
Consensus pattern (28 bp):
ACCATATTTGACAAATACAAAGGAAACT
Found at i:216060 original size:56 final size:56
Alignment explanation
Indices: 215999--216111 Score: 192
Period size: 56 Copynumber: 2.0 Consensus size: 56
215989 ATTTTTACAA
*
215999 ACAAAA-ATAACCACCATATTTGACAAATATAAAGGAAACTACCATATTTGACAAAT
1 ACAAAAGA-AACCACCATATTTGACAAATACAAAGGAAACTACCATATTTGACAAAT
*
216055 ACAAAAGAAACTACCATATTTGACAAATACAAAGGAAACTACCATATTTGACAAAT
1 ACAAAAGAAACCACCATATTTGACAAATACAAAGGAAACTACCATATTTGACAAAT
216111 A
1 A
216112 TAAAGGGTAG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 53 0.98
57 1 0.02
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.22
Consensus pattern (56 bp):
ACAAAAGAAACCACCATATTTGACAAATACAAAGGAAACTACCATATTTGACAAAT
Found at i:220640 original size:24 final size:24
Alignment explanation
Indices: 220612--220657 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
220602 AATAAAAATT
220612 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
*
220636 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
220658 AAATAACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:220687 original size:27 final size:27
Alignment explanation
Indices: 220654--220742 Score: 124
Period size: 28 Copynumber: 3.2 Consensus size: 27
220644 ATTTTTACAA
*
220654 ACAAAAATAACCACCATATTTGACAAAT
1 ACAAAAA-AACTACCATATTTGACAAAT
*
220682 ATAAAAGAAACTACCATATTTGACAAAT
1 ACAAAA-AAACTACCATATTTGACAAAT
*
220710 ACAAAGAAAATTACCATATTTGACAAAT
1 ACAAA-AAAACTACCATATTTGACAAAT
220738 ACAAA
1 ACAAA
220743 GAGTGACATT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
28 53 0.96
29 2 0.04
ACGTcount: A:0.55, C:0.17, G:0.06, T:0.22
Consensus pattern (27 bp):
ACAAAAAAACTACCATATTTGACAAAT
Found at i:221468 original size:17 final size:17
Alignment explanation
Indices: 221419--221474 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
221409 TTATTAATTT
*
221419 TAAA-TTATTTAATAAT
1 TAAATTTATTTAATAAA
221435 TAAATTTATTTAATAAA
1 TAAATTTATTTAATAAA
221452 TAAATATT-TTTAATAAA
1 TAAAT-TTATTTAATAAA
*
221469 AAAATT
1 TAAATT
221475 ATGATGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.14
17 29 0.81
18 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTATTTAATAAA
Found at i:221627 original size:23 final size:20
Alignment explanation
Indices: 221570--221636 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 20
221560 AAATTTTGTG
221570 TGTAAAAATTATAATTTATT
1 TGTAAAAATTATAATTTATT
*
221590 TGATAAATATTTTATAATTTTATTT
1 TG-TAAA-A-ATTATAA-TTTA-TT
*
221615 ATGTAAAAATTATAAATTATT
1 -TGTAAAAATTATAATTTATT
221636 T
1 T
221637 TATAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
20 3 0.08
21 6 0.16
22 4 0.11
23 12 0.32
24 5 0.13
25 6 0.16
26 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TGTAAAAATTATAATTTATT
Found at i:221638 original size:23 final size:23
Alignment explanation
Indices: 221570--221639 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 23
221560 AAATTTTGTG
* *
221570 TGTAAAAATTATAATTTATTTGA
1 TGTAAAAATTATAAATTATTTTA
* * *
221593 --TAAATATTTTATAATTTTATTTA
1 TGTAAAAATTATA-AATTAT-TTTA
221616 TGTAAAAATTATAAATTATTTTA
1 TGTAAAAATTATAAATTATTTTA
221639 T
1 T
221640 AAAAAAAGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
21 9 0.26
22 4 0.11
23 8 0.23
24 5 0.14
25 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TGTAAAAATTATAAATTATTTTA
Found at i:221645 original size:23 final size:23
Alignment explanation
Indices: 221573--221646 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
221563 TTTTGTGTGT
* *
221573 AAAAATTATAATTTATTTGATAA
1 AAAAATTATAAATTATTTTATAA
* ** * **
221596 ATATTTTAT-AATTTTATTTATGT
1 AAAAATTATAAATTAT-TTTATAA
221619 AAAAATTATAAATTATTTTATAA
1 AAAAATTATAAATTATTTTATAA
221642 AAAAA
1 AAAAA
221647 GTTTATTATG
Statistics
Matches: 35, Mismatches: 14, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
22 4 0.11
23 26 0.74
24 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (23 bp):
AAAAATTATAAATTATTTTATAA
Found at i:222664 original size:14 final size:15
Alignment explanation
Indices: 222647--222676 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
222637 TTTTAAATAT
222647 AATTTTTTT-ATTTA
1 AATTTTTTTAATTTA
222661 AATTTTTTTAATTTA
1 AATTTTTTTAATTTA
222676 A
1 A
222677 TTTAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTTTTTAATTTA
Found at i:222678 original size:14 final size:13
Alignment explanation
Indices: 222646--222679 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
222636 ATTTTAAATA
222646 TAATTTTTTTATT
1 TAATTTTTTTATT
222659 TAAATTTTTTTAATT
1 T-AATTTTTTT-ATT
222674 TAATTT
1 TAATTT
222680 AAATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 14 0.74
15 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TAATTTTTTTATT
Found at i:222693 original size:17 final size:17
Alignment explanation
Indices: 222671--222718 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
222661 AATTTTTTTA
*
222671 ATTTAATTTAAATTATT
1 ATTTAATTTAAAATATT
*
222688 ATTTAATATAAAATATT
1 ATTTAATTTAAAATATT
222705 -TTT-ATTTATAAATA
1 ATTTAATTTA-AAATA
222719 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 8 0.30
17 15 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTAATTTAAAATATT
Found at i:222735 original size:19 final size:19
Alignment explanation
Indices: 222689--222742 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
222679 TAAATTATTA
**
222689 TTTAATATAAAATATTTTTAT
1 TTTAA-ATAAAAT-TTTAAAT
222710 TTATAAATAAAATTTTAAAT
1 TT-TAAATAAAATTTTAAAT
*
222730 TTTAAATTAAATT
1 TTTAAATAAAATT
222743 AAATTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 10 0.34
20 7 0.24
21 9 0.31
22 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAAATAAAATTTTAAAT
Found at i:222739 original size:5 final size:5
Alignment explanation
Indices: 222731--222778 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
222721 ATTTTAAATT
* *
222731 TTAAA TTAAA TTAAA TTAAA TTAAA TTTAA TTCAAA TTTAAA TAAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT-AAA -TTAAA TTAAA T
222779 ATATTAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 31 0.82
6 5 0.13
7 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:222771 original size:27 final size:27
Alignment explanation
Indices: 222713--222778 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
222703 TTTTTATTTA
222713 TAAATAAAATTTTAAATTTTAAATTAAAT
1 TAAATAAAA--TTAAATTTTAAATTAAAT
*
222742 TAAATTAAATTAAA-TTT-AATTCAAATT
1 TAAATAAAATTAAATTTTAAATT-AAA-T
222769 TAAATAAAAT
1 TAAATAAAAT
222779 ATATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 6 0.18
27 15 0.45
29 8 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATAAAATTAAATTTTAAATTAAAT
Found at i:224210 original size:22 final size:21
Alignment explanation
Indices: 224173--224214 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
224163 GCATGAAAAA
*
224173 TTTTATATCTTGAAAATATTAT
1 TTTTATATATTGAAAA-ATTAT
*
224195 TTTTATATATTTAAAAATTA
1 TTTTATATATTGAAAAATTA
224215 AAATCTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTATATATTGAAAAATTAT
Found at i:227228 original size:2 final size:2
Alignment explanation
Indices: 227221--227261 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
227211 TGAGTGGGAT
227221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
227262 TCAAAAGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:227309 original size:50 final size:50
Alignment explanation
Indices: 227233--227329 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
227223 TATATATATA
227233 TATATATATATATATATATATATATATATTCAAAAGAACATATTGAGAAG
1 TATATATATATATATATATATATATATATTCAAAAGAACATATTGAGAAG
*
227283 TATATATATATATATATATATGTATATATTCAAAAGAACATATTGAG
1 TATATATATATATATATATATATATATATTCAAAAGAACATATTGAG
227330 GAGGAGGATG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.39
Consensus pattern (50 bp):
TATATATATATATATATATATATATATATTCAAAAGAACATATTGAGAAG
Found at i:231682 original size:57 final size:57
Alignment explanation
Indices: 231594--231710 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
231584 GCACCAGGAA
231594 ATAAGCTAGCTTTCACTACTAAGCTATTACAATTTTTTAGTTATTTATGCACTCTTT
1 ATAAGCTAGCTTTCACTACTAAGCTATTACAATTTTTTAGTTATTTATGCACTCTTT
231651 ATAAGCTAGCTTTCACTACTAAGCTATTACAATTTTTTAGTTATTTATGCACTCTTT
1 ATAAGCTAGCTTTCACTACTAAGCTATTACAATTTTTTAGTTATTTATGCACTCTTT
231708 ATA
1 ATA
231711 TCTTCAAACA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (57 bp):
ATAAGCTAGCTTTCACTACTAAGCTATTACAATTTTTTAGTTATTTATGCACTCTTT
Found at i:232519 original size:20 final size:22
Alignment explanation
Indices: 232490--232530 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
232480 TAAAAACCAG
232490 AAAAGCAAG-AAGGAAAAAAGA
1 AAAAGCAAGAAAGGAAAAAAGA
*
232511 AAAAG-AAGAAATGAAAAAAG
1 AAAAGCAAGAAAGGAAAAAAG
232531 GAAATTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (22 bp):
AAAAGCAAGAAAGGAAAAAAGA
Found at i:233755 original size:15 final size:14
Alignment explanation
Indices: 233739--233784 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
233729 GTTTTTGATA
233739 AAATTAAGTTAGAT
1 AAATTAAGTTAGAT
233753 AAAATTAA-TT---T
1 -AAATTAAGTTAGAT
233764 AAATTAAGTTAGAT
1 AAATTAAGTTAGAT
233778 AAATTAA
1 AAATTAA
233785 TTTAAATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
14 10 0.37
15 7 0.26
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (14 bp):
AAATTAAGTTAGAT
Found at i:233767 original size:25 final size:24
Alignment explanation
Indices: 233739--233791 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
233729 GTTTTTGATA
233739 AAATTAAGTTAGATAAAATTAATTT
1 AAATTAAGTTAGAT-AAATTAATTT
233764 AAATTAAGTTAGATAAATTAATTT
1 AAATTAAGTTAGATAAATTAATTT
233788 AAAT
1 AAAT
233792 CAGTTTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
AAATTAAGTTAGATAAATTAATTT
Found at i:242303 original size:2 final size:2
Alignment explanation
Indices: 242296--242320 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
242286 AATTTATTTA
242296 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
242321 CTAAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:243995 original size:11 final size:12
Alignment explanation
Indices: 243981--244010 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
243971 AAATTTGTCA
243981 TTTATTTAA-TT
1 TTTATTTAATTT
243992 TTTATTTAATTT
1 TTTATTTAATTT
244004 TTTATTT
1 TTTATTT
244011 TTATATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTAATTT
Found at i:245009 original size:40 final size:39
Alignment explanation
Indices: 244965--245042 Score: 88
Period size: 40 Copynumber: 2.0 Consensus size: 39
244955 TTTGAAAAGC
*
244965 TATTTATATGATAATATTTGATTAAA-AAATAATA-ATTTTA
1 TATTTATATGAT-ATA-TT-ATTAAATAAAAAATATATTTTA
* *
245005 TATTTTTATTATATATTATTAAATAAAAAATATATTTT
1 TATTTATATGATATATTATTAAATAAAAAATATATTTT
245043 TTTGTTGTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
37 6 0.18
38 9 0.27
39 8 0.24
40 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (39 bp):
TATTTATATGATATATTATTAAATAAAAAATATATTTTA
Found at i:246838 original size:17 final size:17
Alignment explanation
Indices: 246816--246848 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
246806 ATTTTTTAAA
*
246816 ATTTTTATTTGATTATT
1 ATTTTTAATTGATTATT
246833 ATTTTTAATTGATTAT
1 ATTTTTAATTGATTAT
246849 GCAAGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTTTTAATTGATTATT
Found at i:247995 original size:23 final size:25
Alignment explanation
Indices: 247923--247996 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 25
247913 CAAATTAATT
* *
247923 TATAAA-AAAATAAATT-ATACCT-
1 TATAAATAAAATAAATTCAAACTTA
* *
247945 TA-AAATAAAATAAATTTAAACTTC
1 TATAAATAAAATAAATTCAAACTTA
247969 TATAAATAAAA-AAA-TCAAACTTA
1 TATAAATAAAATAAATTCAAACTTA
247992 TATAA
1 TATAA
247997 TCATATCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
21 3 0.07
22 12 0.27
23 16 0.36
24 5 0.11
25 8 0.18
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (25 bp):
TATAAATAAAATAAATTCAAACTTA
Found at i:248268 original size:18 final size:18
Alignment explanation
Indices: 248242--248276 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
248232 TATCTTTTAA
248242 TTTTTTT-AATTTAAAAT
1 TTTTTTTAAATTTAAAAT
248259 TTTTTATTAAATTTAAAA
1 TTTTT-TTAAATTTAAAA
248277 ATCAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 2 0.12
19 9 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTTTAAATTTAAAAT
Found at i:250005 original size:18 final size:18
Alignment explanation
Indices: 249982--250017 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
249972 TGCTGGCTAA
*
249982 GGAAAAGAGAACACGGTT
1 GGAAAAAAGAACACGGTT
250000 GGAAAAAAGAACACGGTT
1 GGAAAAAAGAACACGGTT
250018 TCTGGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.31, T:0.11
Consensus pattern (18 bp):
GGAAAAAAGAACACGGTT
Found at i:251270 original size:26 final size:26
Alignment explanation
Indices: 251236--251286 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
251226 TTTTAAATAT
251236 TTTTTTATTTAAATTTGATTTGGTTA
1 TTTTTTATTTAAATTTGATTTGGTTA
251262 TTTTTTATTTAAATTTGATTTGGTT
1 TTTTTTATTTAAATTTGATTTGGTT
251287 CATAGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.67
Consensus pattern (26 bp):
TTTTTTATTTAAATTTGATTTGGTTA
Found at i:251980 original size:48 final size:53
Alignment explanation
Indices: 251926--252032 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 53
251916 TAGATTACTC
*
251926 ATATTTAT-TA-TCATAATT-AATAAAAATAAAAAAATTTATTT-TTTATT-A
1 ATATTTATATATTCATAATTAAATAAAAATAAAAAAATTTATTTAATTATTAA
* ** *
251974 ATATTTATATATTTTATAATTAAATTTAAATAAAAATATTTATTTAATTATTAA
1 ATATTTATATA-TTCATAATTAAATAAAAATAAAAAAATTTATTTAATTATTAA
252028 ATATT
1 ATATT
252033 AATACGGACC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
48 8 0.17
49 2 0.04
51 7 0.15
52 20 0.42
53 5 0.10
54 6 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (53 bp):
ATATTTATATATTCATAATTAAATAAAAATAAAAAAATTTATTTAATTATTAA
Found at i:251986 original size:21 final size:21
Alignment explanation
Indices: 251962--252001 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
251952 TAAAAAAATT
*
251962 TATTTT-TTATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
251983 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
252002 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Done.