Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1026
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: 86219
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Found at i:1101 original size:11 final size:12
Alignment explanation
Indices: 1085--1116 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1075 ATAAATACTA
1085 ATAATAATAA-C
1 ATAATAATAATC
1096 ATAATAATAATC
1 ATAATAATAATC
1108 ATAA-AATAA
1 ATAATAATAA
1117 ATTAAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATAATAATC
Found at i:1105 original size:17 final size:17
Alignment explanation
Indices: 1077--1116 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1067 AAATTTCTAT
*
1077 AAATACTAATAATAATA
1 AAATAATAATAATAATA
* *
1094 ACATAATAATAATCATA
1 AAATAATAATAATAATA
1111 AAATAA
1 AAATAA
1117 ATTAAAGGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAATAATAATAATA
Found at i:2249 original size:5 final size:5
Alignment explanation
Indices: 2204--2230 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2194 ATATTAAACA
2204 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
2231 CAAATATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:2583 original size:17 final size:18
Alignment explanation
Indices: 2561--2596 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2551 ACAATTAATT
2561 TAAAAA-ATGATATTTAA
1 TAAAAATATGATATTTAA
*
2578 TAAAAATTTGATATTTAA
1 TAAAAATATGATATTTAA
2596 T
1 T
2597 CTTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (18 bp):
TAAAAATATGATATTTAA
Found at i:5200 original size:18 final size:18
Alignment explanation
Indices: 5167--5202 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5157 TCACGAACAT
**
5167 TTCTCTATATGCTATTAA
1 TTCTCTATATAATATTAA
5185 TTCTCTATATAATATTAA
1 TTCTCTATATAATATTAA
5203 CTTAAAGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (18 bp):
TTCTCTATATAATATTAA
Found at i:9396 original size:2 final size:2
Alignment explanation
Indices: 9389--9414 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9379 AAGAGGAATG
9389 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
9415 TAAAGGGCCA
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:9730 original size:2 final size:2
Alignment explanation
Indices: 9723--9754 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9713 GGTAAAATTA
9723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9755 TTGTAACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10937 original size:2 final size:2
Alignment explanation
Indices: 10930--10958 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10920 TTTTCACCCC
10930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10959 TGTCTAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11300 original size:18 final size:18
Alignment explanation
Indices: 11261--11341 Score: 77
Period size: 16 Copynumber: 4.7 Consensus size: 18
11251 AATATTATAA
*
11261 TAATATTTATA-ATATTT
1 TAATATTTATATAAATTT
11278 T-ATATTTATATAAATTT
1 TAATATTTATATAAATTT
11295 TAATATTT-TA-ATAA-TT
1 TAATATTTATATA-AATTT
11311 T-ATA-TTATATAAATTT
1 TAATATTTATATAAATTT
11327 TAAAATATTTATATA
1 T--AATATTTATATA
11342 TTTGTATACA
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
14 2 0.04
15 7 0.13
16 17 0.32
17 11 0.21
18 6 0.11
19 3 0.06
20 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATATTTATATAAATTT
Found at i:11324 original size:32 final size:34
Alignment explanation
Indices: 11261--11339 Score: 117
Period size: 34 Copynumber: 2.3 Consensus size: 34
11251 AATATTATAA
*
11261 TAATATTTATAATATTTTATATTTATATAAATTT
1 TAATATTTATAATAATTTATATTTATATAAATTT
11295 TAATATTT-TAATAATTTATA-TTATATAAATTT
1 TAATATTTATAATAATTTATATTTATATAAATTT
11327 TAAAATATTTATA
1 T--AATATTTATA
11340 TATTTGTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 13 0.32
33 11 0.27
34 15 0.37
35 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TAATATTTATAATAATTTATATTTATATAAATTT
Found at i:11344 original size:18 final size:18
Alignment explanation
Indices: 11235--11344 Score: 57
Period size: 18 Copynumber: 5.7 Consensus size: 18
11225 ATATCCGTAT
* **
11235 TATTTTTATATTTTTTAA
1 TATTTATATATTTTAAAA
*
11253 TA-TTATAATAATATTTATAA
1 TATTTAT-AT-AT-TTTAAAA
11273 TATTT-TATATTTATATAAA
1 TATTTATATATTT-TA-AAA
11292 T-TTTA-ATATTTTAATAA
1 TATTTATATATTTTAA-AA
11309 TTTATATTATATAAATTTTAAAA
1 --TAT-TTATAT--ATTTTAAAA
11332 TATTTATATATTT
1 TATTTATATATTT
11345 GTATACAAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 30
0.69 0.03 0.28
Matches are distributed among these distances:
16 1 0.01
17 9 0.12
18 21 0.28
19 8 0.11
20 16 0.22
21 8 0.11
22 2 0.03
23 2 0.03
24 7 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTATATATTTTAAAA
Found at i:11714 original size:18 final size:18
Alignment explanation
Indices: 11691--11731 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
11681 CCTGGGAGGG
*
11691 ATTGGGGTTGGTTTGGGT
1 ATTGGGGTTGGTTTAGGT
11709 ATTGGGGTTGGTTTAGGT
1 ATTGGGGTTGGTTTAGGT
11727 ATTGG
1 ATTGG
11732 TGGAAGTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.46, T:0.44
Consensus pattern (18 bp):
ATTGGGGTTGGTTTAGGT
Found at i:12956 original size:30 final size:29
Alignment explanation
Indices: 12914--12986 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
12904 TATAAATATT
* * *
12914 AATATAAAA-ATAATTTTTAATTTTATTTTA
1 AATATAAAATA-AAATTTTAA-ATTAATTTA
12944 AATAATAAAATAAAATTTTAAATTAATTTA
1 AAT-ATAAAATAAAATTTTAAATTAATTTA
12974 AATAT-AAATAAAA
1 AATATAAAATAAAA
12987 AATTAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.21
29 2 0.05
30 13 0.34
31 14 0.37
32 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATATAAAATAAAATTTTAAATTAATTTA
Found at i:12989 original size:30 final size:30
Alignment explanation
Indices: 12914--12990 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
12904 TATAAATATT
* * * *
12914 AATATAAAAATAATTTTTAATTTTATTTTA
1 AATATAAAAAAAAATTTTAATATTAATTTA
*
12944 AATAATAAAATAAAATTTTAA-ATTAATTTA
1 AAT-ATAAAAAAAAATTTTAATATTAATTTA
12974 AATATAAATAAAAAATT
1 AATATAAA-AAAAAATT
12991 AAAAAAATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 5 0.13
30 20 0.51
31 14 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AATATAAAAAAAAATTTTAATATTAATTTA
Found at i:12999 original size:28 final size:30
Alignment explanation
Indices: 12940--13004 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
12930 TTAATTTTAT
** **
12940 TTTAAATAATAAAATAAAATTTTAAATTAA
1 TTTAAATAATAAAATAAAAAATTAAAAAAA
12970 TTTAAAT-AT-AAATAAAAAATTAAAAAAA
1 TTTAAATAATAAAATAAAAAATTAAAAAAA
*
12998 TTCAAAT
1 TTTAAAT
13005 TATGGTCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 21 0.70
29 2 0.07
30 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
TTTAAATAATAAAATAAAAAATTAAAAAAA
Found at i:13876 original size:28 final size:28
Alignment explanation
Indices: 13843--13901 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
13833 TTAAAAAAAT
*
13843 TAATATATATT-AAATAA-AAATATTTTAA
1 TAATATAT-TTAAAATAACAAA-ATATTAA
13871 TAATATATTTAAAATAACAAAATATTAA
1 TAATATATTTAAAATAACAAAATATTAA
13899 TAA
1 TAA
13902 AAATATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 23 0.82
29 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
TAATATATTTAAAATAACAAAATATTAA
Found at i:13900 original size:14 final size:14
Alignment explanation
Indices: 13847--13915 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
13837 AAAAATTAAT
13847 ATATATTAAATAAAA
1 ATATATT-AATAAAA
* *
13862 ATATTTTAAT-AAT
1 ATATATTAATAAAA
13875 ATAT-TTAAAATAACAA
1 ATATATT--AATAA-AA
13891 A-ATATTAATAAAA
1 ATATATTAATAAAA
*
13904 ATATTTTAATAA
1 ATATATTAATAA
13916 TAAACATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
12 2 0.05
13 9 0.20
14 20 0.45
15 9 0.20
16 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATATTAATAAAA
Found at i:13926 original size:42 final size:43
Alignment explanation
Indices: 13849--13929 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
13839 AAATTAATAT
* **
13849 ATATTAAATAAAAATATTTTAATAATATATTTAAAATAACAAA
1 ATATTAAATAAAAATATTTTAATAATAAACATAAAATAACAAA
13892 ATATT-AATAAAAATATTTTAATAATAAACATAAAATAA
1 ATATTAAATAAAAATATTTTAATAATAAACATAAAATAA
13930 ATATGTGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (43 bp):
ATATTAAATAAAAATATTTTAATAATAAACATAAAATAACAAA
Found at i:14548 original size:23 final size:24
Alignment explanation
Indices: 14517--14566 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
14507 TACTCATTTA
*
14517 AAAAATTAA-TTTTCTAT-TTTTCT
1 AAAAATTAACTTTTATATATTTT-T
*
14540 AAAATTTAACTTTTATATATTTTT
1 AAAAATTAACTTTTATATATTTTT
14564 AAA
1 AAA
14567 TAAAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 11 0.48
25 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
AAAAATTAACTTTTATATATTTTT
Found at i:14632 original size:2 final size:2
Alignment explanation
Indices: 14625--14650 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14615 ATAAATTCTA
14625 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
14651 GTGTGTGTGT
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:14864 original size:15 final size:16
Alignment explanation
Indices: 14839--14888 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
14829 TTGATTCATA
*
14839 TTATATTTTTTATAAT
1 TTATATTTTTTAAAAT
14855 TTAT-TTTTTTAAAAT
1 TTATATTTTTTAAAAT
*
14870 ATATATTTTTTAAAAT
1 TTATATTTTTTAAAAT
14886 TTA
1 TTA
14889 ATCTTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATTTTTTAAAAT
Found at i:14969 original size:21 final size:21
Alignment explanation
Indices: 14945--14985 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
14935 TAATTTAACT
*
14945 TAATATTTA-ATATTTATATTA
1 TAATA-TTACATATGTATATTA
14966 TAATATTACATATGTATATT
1 TAATATTACATATGTATATT
14986 TTTATATGAT
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:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TAATATTACATATGTATATTA
Found at i:15121 original size:18 final size:18
Alignment explanation
Indices: 15095--15141 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
15085 TGTGGCTCAG
*
15095 TTTATTTTTTAATTT-GA
1 TTTATTTTTTAATTTAAA
15112 TTTAATTTTTT-ATTTAAA
1 TTT-ATTTTTTAATTTAAA
15130 TTTATTTTTTAA
1 TTTATTTTTTAA
15142 ACTTAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTTTTAATTTAAA
Found at i:15201 original size:18 final size:17
Alignment explanation
Indices: 15098--15199 Score: 56
Period size: 17 Copynumber: 6.1 Consensus size: 17
15088 GGCTCAGTTT
**
15098 ATTTTTTAATTTGATTTA
1 ATTTTTTAATTT-AAATA
*
15116 ATTTTTT-ATTTAAATTT
1 ATTTTTTAATTTAAA-TA
*
15133 ATTTTTTAAACTT-AAT-
1 ATTTTTT-AATTTAAATA
15149 A-TTTTT-ATTTAAAT-
1 ATTTTTTAATTTAAATA
*
15163 -TTTTTTAAATATCAAATAA
1 ATTTTTT-AAT-TTAAAT-A
15182 ATTTTTTAATTTAAATA
1 ATTTTTTAATTTAAATA
15199 A
1 A
15200 ATAATTTAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
13 3 0.05
14 8 0.12
15 5 0.08
16 4 0.06
17 20 0.30
18 14 0.21
19 6 0.09
20 6 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (17 bp):
ATTTTTTAATTTAAATA
Found at i:15207 original size:18 final size:18
Alignment explanation
Indices: 15176--15212 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15166 TTTAAATATC
**
15176 AAATAAATTTTTTAATTT
1 AAATAAATAATTTAATTT
15194 AAATAAATAATTTAATTT
1 AAATAAATAATTTAATTT
15212 A
1 A
15213 TGAACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATAAATAATTTAATTT
Found at i:15780 original size:20 final size:21
Alignment explanation
Indices: 15743--15786 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
15733 TTAATTAATT
15743 ATATTAAAATAAAAAATTTTA
1 ATATTAAAATAAAAAATTTTA
* *
15764 ATATT-AAATATATAATTTTA
1 ATATTAAAATAAAAAATTTTA
15784 ATA
1 ATA
15787 ATAGATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATTAAAATAAAAAATTTTA
Found at i:15824 original size:17 final size:17
Alignment explanation
Indices: 15780--15824 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
15770 AATATATAAT
15780 TTTAATAATAGATAAATA
1 TTTAATAATA-ATAAATA
*
15798 TTAAAT-ATAATAAATA
1 TTTAATAATAATAAATA
15814 TTTAATAATAA
1 TTTAATAATAA
15825 CGTATATCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 12 0.50
17 7 0.29
18 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAATAATAATAAATA
Found at i:16013 original size:19 final size:19
Alignment explanation
Indices: 15968--16015 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
15958 ATTTTTTTAT
*
15968 TAATTTTTTATTGAGTAAA
1 TAATTTTTTATTAAGTAAA
*
15987 TAATTTTTTTATTAATTTAAA
1 TAA-TTTTTTATTAA-GTAAA
16008 -AATTTTTT
1 TAATTTTTT
16016 GATTTGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 9 0.36
20 12 0.48
21 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TAATTTTTTATTAAGTAAA
Found at i:16282 original size:23 final size:23
Alignment explanation
Indices: 16255--16314 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
16245 ATTAATTAGT
*
16255 TAAAATATT-ATTTATAATAA-A
1 TAAAAAATTAATTTATAATAATA
*
16276 TAAAAAATTAATTTATATTAATA
1 TAAAAAATTAATTTATAATAATA
16299 TAAAATTAATTAATTT
1 TAAAA--AATTAATTT
16315 TATATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.24
22 10 0.30
23 6 0.18
25 9 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAAATTAATTTATAATAATA
Found at i:16358 original size:16 final size:17
Alignment explanation
Indices: 16328--16361 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16318 ATATTTTATA
*
16328 ATTTTAAATATATTAAT
1 ATTTTAAATAAATTAAT
16345 ATTTT-AATAAATTAAT
1 ATTTTAAATAAATTAAT
16361 A
1 A
16362 ATATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAAATAAATTAAT
Found at i:20530 original size:25 final size:25
Alignment explanation
Indices: 20501--20548 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
20491 AATATTGTTT
*
20501 AAATTTAGAGAGAA-AAAGTATTAGA
1 AAATTTAGA-AGAATAAAATATTAGA
20526 AAATTTAGAAGAATAAAATATTA
1 AAATTTAGAAGAATAAAATATTA
20549 AATATAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (25 bp):
AAATTTAGAAGAATAAAATATTAGA
Found at i:23583 original size:13 final size:13
Alignment explanation
Indices: 23565--23590 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23555 GATAAAGTGT
23565 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
23578 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
23591 AATTCCAAAT
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:23713 original size:19 final size:19
Alignment explanation
Indices: 23689--23756 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
23679 AATTCAACAA
23689 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
23708 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
23723 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
23740 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
23757 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:23728 original size:13 final size:13
Alignment explanation
Indices: 23710--23734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23700 ACATAAGTTT
23710 TGTATCGATACAA
1 TGTATCGATACAA
23723 TGTATCGATACA
1 TGTATCGATACA
23735 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:23732 original size:32 final size:32
Alignment explanation
Indices: 23691--23753 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
23681 TTCAACAATT
*
23691 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
23723 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
23754 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:23814 original size:13 final size:13
Alignment explanation
Indices: 23796--23821 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23786 CATTTTTCTG
23796 TGTATCGATACAT
1 TGTATCGATACAT
23809 TGTATCGATACAT
1 TGTATCGATACAT
23822 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23818 original size:33 final size:33
Alignment explanation
Indices: 23776--23842 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
23766 GCCAAGGAAA
***
23776 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
23809 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
23842 T
1 T
23843 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:26350 original size:51 final size:51
Alignment explanation
Indices: 26288--26458 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
26278 TTATTTCTGA
* * *
26288 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
26339 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
26392 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
26444 GAGGATACTCCAACC
1 GGGGATACTCCAACC
26459 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:26477 original size:28 final size:28
Alignment explanation
Indices: 26441--26522 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
26431 ATTTTTCACA
*
26441 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
26469 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
26497 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
26523 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:28201 original size:25 final size:28
Alignment explanation
Indices: 28149--28202 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 28
28139 TAAAAATAAT
28149 TTTTGATAAAAATATTTAAATTAATTAA
1 TTTTGATAAAAATATTTAAATTAATTAA
*
28177 TTTT-ATAAAAA-A-TTAAATTACTTAA
1 TTTTGATAAAAATATTTAAATTAATTAA
28202 T
1 T
28203 GAGCATCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 13 0.52
26 1 0.04
27 7 0.28
28 4 0.16
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
TTTTGATAAAAATATTTAAATTAATTAA
Found at i:30421 original size:14 final size:14
Alignment explanation
Indices: 30402--30432 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
30392 CCATATCTCT
*
30402 AAATCTAGTTATTC
1 AAATCTAATTATTC
30416 AAATCTAATTATTC
1 AAATCTAATTATTC
30430 AAA
1 AAA
30433 ATGCTCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (14 bp):
AAATCTAATTATTC
Found at i:35549 original size:2 final size:2
Alignment explanation
Indices: 35542--35574 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35532 ATTATTAGTT
35542 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 T
35575 TAGCAATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36321 original size:20 final size:20
Alignment explanation
Indices: 36284--36335 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
36274 TCGATCAATT
36284 ATATTAAAATAAAAAATTTAA
1 ATATT-AAATAAAAAATTTAA
* * *
36305 ATATTAAATATATAATTTTA
1 ATATTAAATAAAAAATTTAA
*
36325 ATAATAAATAA
1 ATATTAAATAA
36336 GTATTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATTAAATAAAAAATTTAA
Found at i:39356 original size:16 final size:17
Alignment explanation
Indices: 39325--39358 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39315 TATTTTTTGT
*
39325 TAAATTATACTTTAATA
1 TAAATAATACTTTAATA
39342 TAAATAATA-TTTAATA
1 TAAATAATACTTTAATA
39358 T
1 T
39359 GACTTTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATAATACTTTAATA
Found at i:39412 original size:25 final size:26
Alignment explanation
Indices: 39381--39434 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
39371 TTTAGTCTTT
39381 AATATATAGTTT-ATTATTTA-ATATA
1 AATATAT-GTTTAATTATTTACATATA
*
39406 AATATATTTTTAATTATTTATCATATA
1 AATATATGTTTAATTATTTA-CATATA
39433 AA
1 AA
39435 CAATCATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 3 0.12
25 15 0.60
27 7 0.28
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
AATATATGTTTAATTATTTACATATA
Found at i:39417 original size:17 final size:19
Alignment explanation
Indices: 39378--39419 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39368 GTTTTTAGTC
* *
39378 TTTAATATATAGTTTATTA
1 TTTAATATATAATATATTA
39397 TTTAATATA-AATATATT-
1 TTTAATATATAATATATTA
39414 TTTAAT
1 TTTAAT
39420 TATTTATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 9 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTAATATATAATATATTA
Found at i:40067 original size:19 final size:18
Alignment explanation
Indices: 40042--40097 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
40032 CAAAATATTG
40042 TTTTAATATTTATTTTAT
1 TTTTAATATTTATTTTAT
** * *
40060 TATTTAATATAAATATAAT
1 T-TTTAATATTTATTTTAT
40079 TTTTAATTATTTATTTTAT
1 TTTTAA-TATTTATTTTAT
40098 ATAAACACAT
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAATATTTATTTTAT
Found at i:40484 original size:18 final size:17
Alignment explanation
Indices: 40463--40588 Score: 60
Period size: 17 Copynumber: 7.8 Consensus size: 17
40453 TTAATAAATA
40463 ATTAAAATTTATATTTAT
1 ATTAAAA-TTATATTTAT
40481 ATT-AAA-TA-A--TA-
1 ATTAAAATTATATTTAT
40492 ATTAAAAATTATATTTAT
1 ATT-AAAATTATATTTAT
*
40510 ATTAAAA--A-A-AT-T
1 ATTAAAATTATATTTAT
*
40522 ATTAAAATTAT-TTTAG
1 ATTAAAATTATATTTAT
* *
40538 ATTAAAAAATATAATATAT
1 ATT-AAAATTAT-ATTTAT
* * *
40557 ATTAAAAATACAGTTAT
1 ATTAAAATTATATTTAT
40574 ATTAAATATTATATT
1 ATTAAA-ATTATATT
40589 AGTTATAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 32
0.65 0.10 0.26
Matches are distributed among these distances:
11 3 0.04
12 10 0.12
13 4 0.05
14 5 0.06
15 5 0.06
16 3 0.04
17 26 0.32
18 18 0.22
19 6 0.08
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTAAAATTATATTTAT
Found at i:40489 original size:30 final size:29
Alignment explanation
Indices: 40435--40548 Score: 128
Period size: 29 Copynumber: 4.0 Consensus size: 29
40425 CATTAAAGAT
* * *
40435 ATTAAAA-TGTATGTATATTTAATAAATA
1 ATTAAAATTATATTTATATTAAATAAATA
40463 ATTAAAATTTATATTTATATTAAAT-AATA
1 ATTAAAA-TTATATTTATATTAAATAAATA
* *
40492 ATTAAAAATTATATTTATATTAAAAAAATT
1 ATT-AAAATTATATTTATATTAAATAAATA
*
40522 ATTAAAATTAT-TTTAGATTAAA-AAATA
1 ATTAAAATTATATTTATATTAAATAAATA
40549 TAATATATAT
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.05
28 17 0.23
29 31 0.41
30 23 0.31
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTAAAATTATATTTATATTAAATAAATA
Found at i:40765 original size:3 final size:3
Alignment explanation
Indices: 40757--40800 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
40747 TATGGTTCAA
40757 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40801 GGTTAATTAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40845 original size:21 final size:22
Alignment explanation
Indices: 40760--40864 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 22
40750 GGTTCAAAAT
* *
40760 AATAATAATAATAATAATAATAA
1 AATAATTATAATAATAA-GATAA
* * *
40783 TAATAATAATAATAATAAGGT-T
1 -AATAATTATAATAATAAGATAA
* * *
40805 AATTATTATAATAGTGAGATAA
1 AATAATTATAATAATAAGATAA
40827 AAT-ATTATAATAATAAGATTAA
1 AATAATTATAATAATAAGA-TAA
40849 AATTAATTATAA-AATA
1 AA-TAATTATAATAATA
40865 TGTATTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
21 28 0.42
22 8 0.12
23 6 0.09
24 24 0.36
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (22 bp):
AATAATTATAATAATAAGATAA
Found at i:41000 original size:40 final size:42
Alignment explanation
Indices: 40910--40998 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 42
40900 GAATATGACC
* * *
40910 ATTAAGATATTAAATTAAAATATGTATATATATTTAATAAATA
1 ATTAAAATA-TAAATTAAAATATATATATATATTAAATAAATA
*
40953 ATTAAAATATAAA-TAAAAT-TATATTTATATTAAAT-AATA
1 ATTAAAATATAAATTAAAATATATATATATATTAAATAAATA
40992 ATTAAAA
1 ATTAAAA
40999 ATTATATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 11 0.26
40 13 0.31
41 6 0.14
42 4 0.10
43 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (42 bp):
ATTAAAATATAAATTAAAATATATATATATATTAAATAAATA
Found at i:41009 original size:29 final size:28
Alignment explanation
Indices: 40957--41049 Score: 109
Period size: 28 Copynumber: 3.3 Consensus size: 28
40947 TAAATAATTA
*
40957 AAAT-ATAAATAAAATTATATTTATATT
1 AAATAATAATTAAAATTATATTTATATT
*
40984 AAATAATAATTAAAAATTATATTTATGTT
1 AAATAATAATT-AAAATTATATTTATATT
* **
41013 AAA-AATTTATTAAAAGCATATTTATATT
1 AAATAA-TAATTAAAATTATATTTATATT
41041 AAATAATAA
1 AAATAATAA
41050 AATATATTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.07
28 26 0.47
29 25 0.45
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (28 bp):
AAATAATAATTAAAATTATATTTATATT
Found at i:45261 original size:16 final size:16
Alignment explanation
Indices: 45229--45268 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
45219 TTTAATGGAT
*
45229 ATTTAAAA-ATTTTAA
1 ATTTAAAATATTTAAA
45244 ATTTAAAATATTTAAA
1 ATTTAAAATATTTAAA
45260 ATTTAAAAT
1 ATTTAAAAT
45269 TTATATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAAAATATTTAAA
Found at i:45653 original size:2 final size:2
Alignment explanation
Indices: 45636--45669 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
45626 CGTGTCTATG
* *
45636 AT AT AT TT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45670 TACATGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49272 original size:2 final size:2
Alignment explanation
Indices: 49265--49295 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49255 AGTTACATAG
49265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49296 GCTATAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53952 original size:17 final size:17
Alignment explanation
Indices: 53930--53983 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
53920 ATATTAAAAT
53930 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
53947 ATTTTATATATTA-AT-A
1 ATTTTATAT-TTATATAA
53963 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
53978 ATTTTA
1 ATTTTA
53984 AAATATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 8 0.24
16 6 0.18
17 11 0.33
18 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:53955 original size:24 final size:24
Alignment explanation
Indices: 53928--54053 Score: 60
Period size: 24 Copynumber: 4.8 Consensus size: 24
53918 TTATATTAAA
53928 ATATTTTATATTTATATAAATTTT
1 ATATTTTATATTTATATAAATTTT
53952 ATATATTAATAATTTATATTATATAAATTTT
1 ATAT-TT--T-A--TAT-TTATATAAATTTT
* *
53983 AAAATATTTATATATTTATGTAATATATT
1 ---ATATTT-TATATTTATATAA-ATTTT
* *
54012 ATTTTTTATA-TTATATTATATTTT
1 ATATTTTATATTTATA-TAAATTTT
*
54036 A-ACTTTTTTA-TTATATAA
1 ATA-TTTTATATTTATATAA
54054 TTATATCGTC
Statistics
Matches: 80, Mismatches: 9, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
23 2 0.03
24 24 0.30
25 8 0.10
26 5 0.06
27 1 0.01
28 8 0.10
29 7 0.09
30 3 0.04
31 14 0.17
32 2 0.03
33 2 0.03
34 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (24 bp):
ATATTTTATATTTATATAAATTTT
Found at i:53968 original size:32 final size:32
Alignment explanation
Indices: 53927--54001 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
53917 ATTATATTAA
* *
53927 AATATTTTATATTTATATAAATTTT-ATATATT
1 AATAATTTATA-TTATATAAATTTTAAAATATT
53959 AATAATTTATATTATATAAATTTTAAAATATT
1 AATAATTTATATTATATAAATTTTAAAATATT
*
53991 TATATATTTAT
1 AATA-ATTTAT
54002 GTAATATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 13 0.34
32 19 0.50
33 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
AATAATTTATATTATATAAATTTTAAAATATT
Found at i:53969 original size:15 final size:14
Alignment explanation
Indices: 53903--53971 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
53893 TATCGCATAT
*
53903 TTTATTATTTTATAA
1 TTTA-TATTTAATAA
* *
53918 -TTATATTAAAATAT
1 TTTATATT-TAATAA
53932 TTTATATTTATATAAA
1 TTTATATTTA-AT-AA
53948 TTTTATATATTAATAA
1 -TTTATAT-TTAATAA
53964 TTTATATT
1 TTTATATT
53972 ATATAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
13 4 0.09
14 8 0.19
15 16 0.37
16 3 0.07
17 9 0.21
18 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATTTAATAA
Found at i:53980 original size:15 final size:15
Alignment explanation
Indices: 53932--53981 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
53922 ATTAAAATAT
53932 TTTATATTTATATAAA
1 TTTATA-TTATATAAA
53948 TTT-TA-TATATTAATAA
1 TTTATATTATA-T-A-AA
53964 TTTATATTATATAAA
1 TTTATATTATATAAA
53979 TTT
1 TTT
53982 TAAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
13 4 0.14
14 1 0.03
15 8 0.28
16 9 0.31
17 3 0.10
18 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:56486 original size:31 final size:31
Alignment explanation
Indices: 56448--56531 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
56438 GATTTAATAT
*
56448 ATTATAAAAATATATAAATATTAATATTAAA
1 ATTATAAAAATATATAAATATAAATATTAAA
* * * ***
56479 ATTATAAAGAT-TATTTATTATAAATATTTTT
1 ATTATAAAAATATA-TAAATATAAATATTAAA
56510 ATTATAAAAATATATAAA-ATAA
1 ATTATAAAAATATATAAATATAA
56532 TAATTTTATA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
30 6 0.15
31 33 0.80
32 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (31 bp):
ATTATAAAAATATATAAATATAAATATTAAA
Found at i:56497 original size:22 final size:22
Alignment explanation
Indices: 56447--56505 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
56437 TGATTTAATA
* *
56447 TATTATAAAAATATATAAATAT
1 TATTATTAAAATATATAAAGAT
*
56469 TAATATTAAAAT-TATAAAGAT
1 TATTATTAAAATATATAAAGAT
56490 TATTTATTATAAATAT
1 TA-TTATTA-AAATAT
56506 TTTTATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 10 0.33
22 15 0.50
23 4 0.13
24 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTATTAAAATATATAAAGAT
Found at i:56510 original size:15 final size:16
Alignment explanation
Indices: 56479--56517 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
56469 TAATATTAAA
56479 ATTATAAAGATTATTT
1 ATTATAAAGATTATTT
*
56495 ATTATAAATATT-TTT
1 ATTATAAAGATTATTT
56510 ATTATAAA
1 ATTATAAA
56518 AATATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTATAAAGATTATTT
Found at i:56553 original size:36 final size:31
Alignment explanation
Indices: 56500--56581 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
56490 TATTTATTAT
*
56500 AAATATT-TTTATTATAA-AAATATATAAAATAA
1 AAATATTATTT-TTATAATAAA-AT-TTAAATAA
* *
56532 TAATTTTATATTTTATAATAAAATTTAAATAA
1 AAATATTAT-TTTTATAATAAAATTTAAATAA
56564 AAATATTATTTTTATAAT
1 AAATATTATTTTTATAAT
56582 TAATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
31 9 0.21
32 19 0.45
33 9 0.21
34 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATATTATTTTTATAATAAAATTTAAATAA
Found at i:56577 original size:38 final size:36
Alignment explanation
Indices: 56525--56597 Score: 92
Period size: 38 Copynumber: 2.0 Consensus size: 36
56515 AAAAATATAT
* *
56525 AAAATAATAATTTTATATTTTATAATAAAATTTAAATA
1 AAAATAATAATTTTATAATTAATAAT--AATTTAAATA
* *
56563 AAAATATTATTTTTATAATTAATAATAATTTAAAT
1 AAAATAATAATTTTATAATTAATAATAATTTAAAT
56598 CAAATCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 9 0.29
38 22 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATAATAATTTTATAATTAATAATAATTTAAATA
Found at i:57480 original size:2 final size:2
Alignment explanation
Indices: 57473--57507 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
57463 TACCAAGATA
57473 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57508 TCCATGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60511 original size:16 final size:16
Alignment explanation
Indices: 60492--60601 Score: 59
Period size: 15 Copynumber: 6.4 Consensus size: 16
60482 AATTAAAATA
60492 AAATATAAAA-TATTAT
1 AAATATAAAATTA-TAT
60508 AAATA-AAAATTATAT
1 AAATATAAAATTATAT
* *
60523 AAATATAATAA-AAAATT
1 AAATATAA-AATTATA-T
60540 AAATTATATTAAGATTTATAT
1 AAA-TATA--AA-A-TTATAT
60561 AAATAT-AAATTAT-T
1 AAATATAAAATTATAT
60575 AATATATAAAAAATTATAAT
1 AA-ATAT--AAAATTAT-AT
60595 AAATATA
1 AAATATA
60602 TAATATTTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 31
0.68 0.04 0.28
Matches are distributed among these distances:
14 3 0.04
15 20 0.27
16 12 0.16
17 9 0.12
18 11 0.15
19 5 0.07
20 8 0.11
21 4 0.05
22 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (16 bp):
AAATATAAAATTATAT
Found at i:60534 original size:20 final size:20
Alignment explanation
Indices: 60509--60568 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
60499 AAATATTATA
60509 AATAAAAATTATATAAATAT
1 AATAAAAATTATATAAATAT
60529 AATAAAAA--AT-TAAATTAT
1 AATAAAAATTATATAAA-TAT
* * *
60547 ATTAAGATTTATATAAATAT
1 AATAAAAATTATATAAATAT
60567 AA
1 AA
60569 ATTATTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 4 0.12
18 10 0.31
20 14 0.44
21 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AATAAAAATTATATAAATAT
Found at i:60969 original size:26 final size:27
Alignment explanation
Indices: 60933--60988 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
60923 TATGATATTT
* *
60933 TTAAT-ATT-TATAAATTTTTAATTAGA
1 TTAATAATTATATAAA-TTTAAATTAAA
60959 TTAATAATTATATAAATTTAAATTAAA
1 TTAATAATTATATAAATTTAAATTAAA
60986 TTA
1 TTA
60989 TATTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
27 15 0.58
28 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TTAATAATTATATAAATTTAAATTAAA
Found at i:61024 original size:19 final size:18
Alignment explanation
Indices: 60985--61037 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
60975 TTTAAATTAA
* *
60985 ATTATATTAAATAATTATT
1 ATTAT-TTAAATATTTTTT
61004 ATTTATTTAAATATTTTTT
1 A-TTATTTAAATATTTTTT
*
61023 ATAATTTAAA-ATTTT
1 ATTATTTAAATATTTT
61038 ATATAAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 5 0.17
18 8 0.27
19 13 0.43
20 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATTTAAATATTTTTT
Found at i:61042 original size:17 final size:18
Alignment explanation
Indices: 61008--61043 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
60998 ATTATTATTT
*
61008 ATTTAAATATTTTTTATA
1 ATTTAAATATTTTATATA
61026 ATTTAAA-ATTTTATATA
1 ATTTAAATATTTTATATA
61043 A
1 A
61044 GTAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTAAATATTTTATATA
Found at i:61105 original size:16 final size:16
Alignment explanation
Indices: 61086--61116 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61076 TAAATTATAA
61086 AAATATAAAATAAAAT
1 AAATATAAAATAAAAT
*
61102 AAATATAATATAAAA
1 AAATATAAAATAAAA
61117 ATAATTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATATAAAATAAAAT
Found at i:61114 original size:11 final size:11
Alignment explanation
Indices: 61087--61174 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 11
61077 AAATTATAAA
61087 AATAT-AAAAT
1 AATATAAAAAT
* *
61097 AAAATAAATAT
1 AATATAAAAAT
61108 AATATAAAAAT
1 AATATAAAAAT
*
61119 AATTTGAAAAAT
1 AATAT-AAAAAT
* *
61131 GAT-TAAAACGT
1 AATATAAAA-AT
61142 AACGTTATAAAAAT
1 AA---TATAAAAAT
*
61156 AATATAAATAT
1 AATATAAAAAT
*
61167 GATATAAA
1 AATATAAA
61175 TATACAAATA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
10 8 0.13
11 35 0.58
12 8 0.13
14 4 0.07
15 5 0.08
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:61956 original size:22 final size:22
Alignment explanation
Indices: 61928--61979 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
61918 TAATCATAGC
61928 ATAAAAATTAATTAAAATAT-AAT
1 ATAAAAA--AATTAAAATATAAAT
**
61951 ATAAAAAAATTATGATATAAAT
1 ATAAAAAAATTAAAATATAAAT
61973 ATAAAAA
1 ATAAAAA
61980 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 9 0.35
22 10 0.38
23 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAAAAAAATTAAAATATAAAT
Found at i:62066 original size:34 final size:34
Alignment explanation
Indices: 62000--62066 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
61990 TTATAATTAT
* * *
62000 TATATAAATTTTTAATATTTTTAGTAATATAAAA
1 TATATAAATATATAATATTTTTAGTAAAATAAAA
*
62034 TATATAAATATATAAT-TTTTTATTAAAAATAAA
1 TATATAAATATATAATATTTTTAGT-AAAATAAA
62067 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (34 bp):
TATATAAATATATAATATTTTTAGTAAAATAAAA
Found at i:62479 original size:22 final size:21
Alignment explanation
Indices: 62452--62557 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 21
62442 AATTAGAGTA
62452 TTAAATTTAATTAATTT-AATT
1 TTAAA-TTAATTAATTTAAATT
*
62473 TTAAAATAATTAAAATTTAAGATAAT
1 TTAAATTAATT--AATTTAA-AT--T
* *
62499 TTAAATATGATTAATTTAAATA
1 TTAAAT-TAATTAATTTAAATT
*
62521 TTAAATTTGATTAATTTAAA-T
1 TTAAA-TTAATTAATTTAAATT
*
62542 TTAAAATAATTAATTT
1 TTAAATTAATTAATTT
62558 GAACTTAAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
20 14 0.20
21 10 0.14
22 23 0.33
23 2 0.03
24 4 0.06
25 7 0.10
26 6 0.09
27 4 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
TTAAATTAATTAATTTAAATT
Found at i:62539 original size:15 final size:16
Alignment explanation
Indices: 62452--62527 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
62442 AATTAGAGTA
62452 TTAAATTT-AATTAAT
1 TTAAATTTAAATTAAT
* *
62467 TTAATTTTAAAATAAT
1 TTAAATTTAAATTAAT
*
62483 TAAAATTTAAGA-TAAT
1 TTAAATTTAA-ATTAAT
* *
62499 TTAAATAT-GATTAAT
1 TTAAATTTAAATTAAT
62514 TTAAATATTAAATT
1 TTAAAT-TTAAATT
62528 TGATTAATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
14 1 0.02
15 17 0.36
16 25 0.53
17 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTAAATTTAAATTAAT
Found at i:62554 original size:15 final size:14
Alignment explanation
Indices: 62451--62554 Score: 58
Period size: 15 Copynumber: 7.4 Consensus size: 14
62441 TAATTAGAGT
*
62451 ATTAAATTTAATTA
1 ATTAAATTTAAATA
*
62465 ATTTAATTTTAAAATA
1 A-TTAAATTT-AAATA
62481 ATTAAAATTTAAGATA
1 ATT-AAATTTAA-ATA
*
62497 ATTTAAA--T--ATG
1 A-TTAAATTTAAATA
62508 ATT-AATTTAAAT-
1 ATTAAATTTAAATA
* *
62520 ATTAAATTTGATTA
1 ATTAAATTTAAATA
62534 ATTTAAATTTAAAATA
1 A-TTAAATTT-AAATA
62550 ATTAA
1 ATTAA
62555 TTTGAACTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 25
0.68 0.08 0.25
Matches are distributed among these distances:
9 2 0.03
10 2 0.03
11 4 0.06
12 3 0.04
13 9 0.13
14 3 0.04
15 23 0.33
16 21 0.30
17 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
ATTAAATTTAAATA
Found at i:62565 original size:20 final size:20
Alignment explanation
Indices: 62530--62571 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
62520 ATTAAATTTG
*
62530 ATTAATTTAAATTTAAAATA
1 ATTAATTTAAACTTAAAATA
* *
62550 ATTAATTTGAACTTAAAGTA
1 ATTAATTTAAACTTAAAATA
62570 AT
1 AT
62572 AAAAATCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (20 bp):
ATTAATTTAAACTTAAAATA
Found at i:62601 original size:17 final size:18
Alignment explanation
Indices: 62579--62617 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
62569 AATAAAAATC
*
62579 AAAATAATTT-ATATTTA
1 AAAATAATTTAAAATTTA
62596 AAAATAATTTAAAATTTA
1 AAAATAATTTAAAATTTA
62614 AAAA
1 AAAA
62618 GTTTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATTTAAAATTTA
Found at i:63083 original size:17 final size:17
Alignment explanation
Indices: 63061--63128 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
63051 ATTTTAAATT
63061 TTTAAAAATTAAATAAA
1 TTTAAAAATTAAATAAA
* **
63078 TTTAAAAAATCGATAAA
1 TTTAAAAATTAAATAAA
* *
63095 ATTAATCAATT-AA-AAA
1 TTTAA-AAATTAAATAAA
*
63111 TTT-AAAATTAAATTAA
1 TTTAAAAATTAAATAAA
63127 TT
1 TT
63129 AAATTTAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 7
0.69 0.18 0.13
Matches are distributed among these distances:
14 4 0.11
15 3 0.08
16 9 0.24
17 19 0.50
18 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (17 bp):
TTTAAAAATTAAATAAA
Found at i:64238 original size:13 final size:13
Alignment explanation
Indices: 64220--64262 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
64210 TAAAATAATT
64220 ATTAAAATATTAA
1 ATTAAAATATTAA
64233 ATTAAAATATGTAA
1 ATTAAAATAT-TAA
*
64247 ATAATAAATAATTAA
1 ATTA-AAAT-ATTAA
64262 A
1 A
64263 ATTTATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 10 0.38
14 6 0.23
15 8 0.31
16 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
ATTAAAATATTAA
Found at i:64252 original size:24 final size:21
Alignment explanation
Indices: 64221--64294 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
64211 AAAATAATTA
64221 TTAA-AATATTAAATTAAAAT
1 TTAATAATATTAAATTAAAAT
*
64241 ATGTAAATAATA-AATAATTAAAAT
1 -T-T-AATAATATTA-AATTAAAAT
* * *
64265 TTATTAATATTAAATTTATAT
1 TTAATAATATTAAATTAAAAT
64286 TTAATAATA
1 TTAATAATA
64295 AAATATATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 22 0.52
22 3 0.07
23 4 0.10
24 13 0.31
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
TTAATAATATTAAATTAAAAT
Found at i:64272 original size:21 final size:21
Alignment explanation
Indices: 64232--64309 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 21
64222 TAAAATATTA
64232 AATTAAAATATGTAAATAATAAAT
1 AATTAAAAT-T-T-AATAATAAAT
* *
64256 AATTAAAATTTATTAAT-ATT
1 AATTAAAATTTAATAATAAAT
* *
64276 AAATTTATATTTAATAATAAAAT
1 -AATTAAAATTTAATAAT-AAAT
64299 ATATTAAAATT
1 A-ATTAAAATT
64310 ATCTTTATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
20 2 0.05
21 19 0.45
22 2 0.05
23 10 0.24
24 9 0.21
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (21 bp):
AATTAAAATTTAATAATAAAT
Found at i:64274 original size:45 final size:43
Alignment explanation
Indices: 64199--64309 Score: 109
Period size: 45 Copynumber: 2.4 Consensus size: 43
64189 GGGGTGAATT
*
64199 ATAATAAA-AAATAAAATAATTATTAAAATATTAAATTAAAATATGTAA
1 ATAATAAATAATTAAAAT--TTATT-AAATATTAAATT--AATAT-TAA
* *
64247 ATAATAAATAATTAAAATTTATT-AATATTAAATTTATATTTA
1 ATAATAAATAATTAAAATTTATTAAATATTAAATTAATATTAA
64289 ATAATAAAATATATTAAAATT
1 ATAAT-AAATA-ATTAAAATT
64310 ATCTTTATAT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
42 7 0.12
43 9 0.16
44 9 0.16
45 11 0.19
47 5 0.09
48 8 0.14
49 8 0.14
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (43 bp):
ATAATAAATAATTAAAATTTATTAAATATTAAATTAATATTAA
Found at i:64297 original size:34 final size:33
Alignment explanation
Indices: 64253--64340 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 33
64243 GTAAATAATA
64253 AATAATTAAAATTTATTAATATTAAATTTATATTT
1 AATAA-TAAAATTTATTAATATTAAATTTATA-TT
* * **
64288 AATAATAAAATATATTAAAATTATCTTTATATT
1 AATAATAAAATTTATTAATATTAAATTTATATT
64321 ACATAATAATAA-TTATTAAT
1 A-ATAATAA-AATTTATTAAT
64341 TAAAAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
33 3 0.07
34 35 0.78
35 7 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
AATAATAAAATTTATTAATATTAAATTTATATT
Found at i:64398 original size:12 final size:12
Alignment explanation
Indices: 64381--64407 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
64371 GTAAATTATG
64381 TTTATATTATTA
1 TTTATATTATTA
64393 TTTATATTATTA
1 TTTATATTATTA
64405 TTT
1 TTT
64408 TTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:66880 original size:19 final size:19
Alignment explanation
Indices: 66834--66871 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
66824 TTTACTGTTT
66834 AAATT-TTTTTAATATTAAA
1 AAATTATTTTT-ATATTAAA
66853 AAATTATTTTTATATTAAA
1 AAATTATTTTTATATTAAA
66872 TTAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATTTTTATATTAAA
Found at i:66933 original size:29 final size:32
Alignment explanation
Indices: 66879--66941 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
66869 AAATTAATAT
*
66879 TTATATATTTTATAATTAAATTTAAATA-AAA
1 TTATATATTTTATAATTAAATATAAATACAAA
66910 TTATATATTTT-T-ATT-AATAATAAATACAAA
1 TTATATATTTTATAATTAAAT-ATAAATACAAA
66940 TT
1 TT
66942 TAAGCTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.10
29 9 0.31
30 6 0.21
31 11 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (32 bp):
TTATATATTTTATAATTAAATATAAATACAAA
Found at i:67777 original size:30 final size:30
Alignment explanation
Indices: 67669--67778 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 30
67659 TGAGTTAATA
* *
67669 TTGAATTTTATC-AT-TATGTATAATTTT-G
1 TTGAATTTTATCAATGTAT-TTTCATTTTCG
* * *
67697 TTGAATTTTATCAGTGTAATTTCAATTTCG
1 TTGAATTTTATCAATGTATTTTCATTTTCG
* * *
67727 TTGAATTTTGTCGATATATTTTCATTTTCG
1 TTGAATTTTATCAATGTATTTTCATTTTCG
**
67757 TTGAATTTTATCCTTGTATTTT
1 TTGAATTTTATCAATGTATTTT
67779 TAGTTTTATG
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
28 12 0.19
29 7 0.11
30 45 0.70
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (30 bp):
TTGAATTTTATCAATGTATTTTCATTTTCG
Found at i:68499 original size:13 final size:13
Alignment explanation
Indices: 68469--68493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68459 AACATATTAT
68469 ATTATATAATACG
1 ATTATATAATACG
68482 ATTATATAATAC
1 ATTATATAATAC
68494 TTTTATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
ATTATATAATACG
Found at i:73422 original size:2 final size:2
Alignment explanation
Indices: 73417--73462 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
73407 TGTGTGTGTC
73417 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73459 TA TA
1 TA TA
73463 GAAAAAAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76343 original size:11 final size:12
Alignment explanation
Indices: 76322--76350 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
76312 TATTTTGTAA
76322 AAAACAAAAAAT
1 AAAACAAAAAAT
76334 AAAA-AAAAAAT
1 AAAACAAAAAAT
76345 AAAACA
1 AAAACA
76351 GGGGAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAACAAAAAAT
Found at i:85225 original size:54 final size:53
Alignment explanation
Indices: 85142--85246 Score: 192
Period size: 54 Copynumber: 2.0 Consensus size: 53
85132 CGACATGACC
*
85142 CGTTGAATGATATGGACCTTTAGATAACCACACCCCAAAAGCTCAGTGTTAGGT
1 CGTTGAATGATATGGACCTTTAGACAACCACA-CCCAAAAGCTCAGTGTTAGGT
85196 CGTTGAATGATATGGACCTTTAGACAACCACACCCAAAAGCTCAGTGTTAG
1 CGTTGAATGATATGGACCTTTAGACAACCACACCCAAAAGCTCAGTGTTAG
85247 CTTGGGAAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 19 0.38
54 31 0.62
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (53 bp):
CGTTGAATGATATGGACCTTTAGACAACCACACCCAAAAGCTCAGTGTTAGGT
Done.