Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 29
Found at i:135075 original size:150 final size:149
Alignment explanation
Indices: 134892--135173 Score: 410
Period size: 150 Copynumber: 1.9 Consensus size: 149
134882 TTTAAATTTA
*
134892 ATTTATAAATTAGTTAAAATTTAAAAATATATATATTTAAAAA-TATAAAA-TATAAATTTTAAA
1 ATTTATAAATTAGTTAAAATTTAAAAATATATATATTTAAAAATTAAAAAACTATAAATTTT---
** * * *
134955 AAAATTAT-AACCTATATAAAATTCACCATTTCATAAATATGTAACAAATTTATAAATTTTTAAA
63 AAAATTATAAAAATATATAAAATACACCA-TTAATAAATATGCAACAAATTTATAAATTTTTAAA
135019 AATAATTAAAATTTTAAAAAATT
127 AATAATTAAAATTTTAAAAAATT
135042 ATTTATAAATTAGTTAAAATTTTAAAAAT-TATATATTTAAAAATTAAAAAACTATAAATTTTAA
1 ATTTATAAATTAGTTAAAA-TTTAAAAATATATATATTTAAAAATTAAAAAACTATAAATTTTAA
* * *
135106 ATTTATAAAAATTTATAAAATACACCATTAATAAATATGCAACAAGTTTATAAATTTTTAAAAAT
65 AATTATAAAAATATATAAAATACACCATTAATAAATATGCAACAAATTTATAAATTTTTAAAAAT
135171 AAT
130 AAT
135174 AAACTTCATT
Statistics
Matches: 119, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
149 45 0.38
150 49 0.41
151 15 0.13
152 10 0.08
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (149 bp):
ATTTATAAATTAGTTAAAATTTAAAAATATATATATTTAAAAATTAAAAAACTATAAATTTTAAA
ATTATAAAAATATATAAAATACACCATTAATAAATATGCAACAAATTTATAAATTTTTAAAAATA
ATTAAAATTTTAAAAAATT
Found at i:135081 original size:23 final size:23
Alignment explanation
Indices: 135055--135122 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
135045 TATAAATTAG
135055 TTAAAATTTTAAAAATTATATAT
1 TTAAAATTTTAAAAATTATATAT
* * * *
135078 TTAAAAATTAAAAAACTATAAAT
1 TTAAAATTTTAAAAATTATATAT
*
135101 TTTAAATTTATAAAAATT-TATA
1 TTAAAATTT-TAAAAATTATATA
135123 AAATACACCA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 29 0.83
24 6 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAAATTTTAAAAATTATATAT
Found at i:135089 original size:30 final size:28
Alignment explanation
Indices: 135022--135090 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 28
135012 TTTTAAAAAT
135022 AATTAAAATTTTAAAAAATTATTTATAA
1 AATTAAAATTTTAAAAAATTATTTATAA
135050 ATTAGTTAAAATTTTAAAAATTATATATTTA-AA
1 A--A-TTAAAATTTTAAAAA--AT-TATTTATAA
135083 AATTAAAA
1 AATTAAAA
135091 AACTATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
28 1 0.03
30 7 0.20
31 16 0.46
33 5 0.14
34 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
AATTAAAATTTTAAAAAATTATTTATAA
Found at i:135618 original size:2 final size:2
Alignment explanation
Indices: 135601--135635 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
135591 CAATTTCCCA
* *
135601 CT CT GT CT CA CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
135636 GAAATCTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.49, G:0.03, T:0.46
Consensus pattern (2 bp):
CT
Found at i:139582 original size:23 final size:23
Alignment explanation
Indices: 139543--139587 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
139533 AAAATTAAAA
139543 TTTTAATATTTATATTTTTTTAG
1 TTTTAATATTTATATTTTTTTAG
*
139566 TTTTAA-ATTTTTAATTTTTTTA
1 TTTTAATATTTAT-ATTTTTTTA
139588 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTAATATTTATATTTTTTTAG
Found at i:139594 original size:22 final size:24
Alignment explanation
Indices: 139551--139594 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
139541 AATTTTAATA
* *
139551 TTTATATTTTTTTAGTTTTAAATT
1 TTTATATTTTTTTAGATATAAATT
139575 TTTA-ATTTTTTTA-ATATAAA
1 TTTATATTTTTTTAGATATAAA
139595 AAAAAGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 9 0.50
24 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTATATTTTTTTAGATATAAATT
Found at i:139984 original size:2 final size:2
Alignment explanation
Indices: 139977--140007 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
139967 TCCTAATAGT
*
139977 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
140008 TACATGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:140204 original size:31 final size:31
Alignment explanation
Indices: 140168--140262 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 31
140158 TTTTGAAAAA
140168 TATTTTATTATATATTTAATATAAATATATT
1 TATTTTATTATATATTTAATATAAATATATT
** *
140199 TA-TTT-TTATATATTTTTTAAAAATTATATT
1 TATTTTATTATATATTTAATATAAA-TATATT
* * * *
140229 TATATTTAATAATAAATTAAAAATAAATAT-TT
1 TAT-TTT-ATTATATATTTAATATAAATATATT
140261 TA
1 TA
140263 AAAATTAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
29 15 0.31
30 11 0.22
31 2 0.04
32 7 0.14
33 3 0.06
34 11 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TATTTTATTATATATTTAATATAAATATATT
Found at i:140207 original size:32 final size:32
Alignment explanation
Indices: 140167--140262 Score: 83
Period size: 32 Copynumber: 3.0 Consensus size: 32
140157 GTTTTGAAAA
140167 ATATTTTATTATATATTTAATATAAATATATTT
1 ATATTTTATTATATATTTAA-ATAAATATATTT
* *
140200 AT-TTTTA-TATATTTTTTAAA-AATTATATTT
1 ATATTTTATTATA-TATTTAAATAAATATATTT
* * * *
140230 ATATTTAATAATAAATTAAAAATAAATAT-TTT
1 ATATTTTATTATATATT-TAAATAAATATATTT
140262 A
1 A
140263 AAAATTAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
30 11 0.22
31 11 0.22
32 21 0.42
33 7 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATTTTATTATATATTTAAATAAATATATTT
Found at i:140222 original size:29 final size:30
Alignment explanation
Indices: 140167--140236 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
140157 GTTTTGAAAA
*
140167 ATATTT-TA-TTATATATTTAATATAAA-T
1 ATATTTATATTTATATATTTAATAAAAATT
* **
140194 ATATTTATTTTTATATATTTTTTAAAAATT
1 ATATTTATATTTATATATTTAATAAAAATT
140224 ATATTTATATTTA
1 ATATTTATATTTA
140237 ATAATAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 6 0.17
28 1 0.03
29 15 0.43
30 13 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
ATATTTATATTTATATATTTAATAAAAATT
Found at i:140731 original size:23 final size:23
Alignment explanation
Indices: 140705--140748 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
140695 GTGTTAAAAT
*
140705 TATAAATAAAATATGATATAATA
1 TATAAATAAAATATAATATAATA
* *
140728 TATATATTAAATATAATATAA
1 TATAAATAAAATATAATATAA
140749 ATCATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TATAAATAAAATATAATATAATA
Found at i:140762 original size:23 final size:24
Alignment explanation
Indices: 140711--140763 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
140701 AAATTATAAA
*
140711 TAAAATATGATATAATATATATAT
1 TAAAATATAATATAATATATATAT
140735 T-AAATATAATATAA-ATCATAT-T
1 TAAAATATAATATAATAT-ATATAT
140757 TAAAATA
1 TAAAATA
140764 CTGTATTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 4 0.15
23 21 0.81
24 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAAATATAATATAATATATATAT
Found at i:147788 original size:21 final size:22
Alignment explanation
Indices: 147764--147815 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
147754 TTAATGTAAT
147764 AATTTTAA-AAA-TTAATATTTA
1 AATTTTAATAAATTTAA-ATTTA
147785 AA-TTTAATAAATTTAAATTTA
1 AATTTTAATAAATTTAAATTTA
*
147806 AATATTAATA
1 AATTTTAATA
147816 TTTATAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.19
21 12 0.44
22 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTTAATAAATTTAAATTTA
Found at i:147809 original size:29 final size:29
Alignment explanation
Indices: 147760--147827 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
147750 TTAATTAATG
*
147760 TAATAATTTTAAAAATTAATATTTAA-ATT
1 TAATAAATTTAAAAATTAATA-TTAATATT
*
147789 TAATAAATTT-AAATTTAAATATTAATATT
1 TAATAAATTTAAAAATT-AATATTAATATT
147818 T-ATAATATTT
1 TAATAA-ATTT
147828 TTTATCTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TAATAAATTTAAAAATTAATATTAATATT
Found at i:147824 original size:15 final size:15
Alignment explanation
Indices: 147776--147827 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
147766 TTTTAAAAAT
147776 TAATATTTAAATTTAA
1 TAATATTTAAATTT-A
147792 TAA-ATTTAAATTTA
1 TAATATTTAAATTTA
147806 -AATA-TTAATATTTA
1 TAATATTTAA-ATTTA
147820 TAATATTT
1 TAATATTT
147828 TTTATCTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.19
14 7 0.22
15 14 0.44
16 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATATTTAAATTTA
Found at i:148433 original size:31 final size:32
Alignment explanation
Indices: 148391--148455 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
148381 TAATTAGAAC
*
148391 ATAATATATATAGTAATATAGTAACGTAAAAT
1 ATAATATATATAATAATATAGTAACGTAAAAT
* *
148423 ATAAT-TATATAATAATATCGTATCGTAAAAT
1 ATAATATATATAATAATATAGTAACGTAAAAT
148454 AT
1 AT
148456 TTAATAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.37
Consensus pattern (32 bp):
ATAATATATATAATAATATAGTAACGTAAAAT
Found at i:150450 original size:5 final size:5
Alignment explanation
Indices: 150440--150464 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
150430 CAACAGCAAC
150440 AGGCA AGGCA AGGCA AGGCA AGGCA
1 AGGCA AGGCA AGGCA AGGCA AGGCA
150465 TGCATGCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
AGGCA
Found at i:150718 original size:13 final size:12
Alignment explanation
Indices: 150688--150721 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
150678 TTGTATTTTC
*
150688 ATATTAAAATAT
1 ATATTAAAATAA
150700 ATATTAAATATAA
1 ATATTAAA-ATAA
150713 ATATTAAAA
1 ATATTAAAA
150722 AAAGTTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATTAAAATAA
Found at i:150974 original size:15 final size:14
Alignment explanation
Indices: 150942--150991 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
150932 ATTGAGATAG
150942 ATATTAAT-TTTAT
1 ATATTAATATTTAT
150955 CATATATAATATTTAT
1 -ATAT-TAATATTTAT
*
150971 ATATGTAATATCTAT
1 ATAT-TAATATTTAT
150986 AT-TTAA
1 ATATTAA
150992 AATTACTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 3 0.09
14 5 0.16
15 19 0.59
16 5 0.16
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (14 bp):
ATATTAATATTTAT
Found at i:152756 original size:14 final size:14
Alignment explanation
Indices: 152739--152787 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
152729 CGTATTTAAA
152739 ATATATTAATATTT
1 ATATATTAATATTT
*
152753 ATATA--AATATTA
1 ATATATTAATATTT
152765 ATATATTAATAATTT
1 ATATATTAAT-ATTT
152780 A-ATATTAA
1 ATATATTAA
152788 ATAAATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 11 0.37
14 15 0.50
15 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTAATATTT
Found at i:152764 original size:18 final size:17
Alignment explanation
Indices: 152731--152798 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
152721 TAAAAAATCG
152731 TATTTAA-AATATATTAA
1 TATTTAATAA-ATATTAA
152748 TATTTATATAAATATTAA
1 TATTTA-ATAAATATTAA
152766 TATATTAAT-AAT-TTAA
1 TAT-TTAATAAATATTAA
* *
152782 TATTAAATAAATTTTAA
1 TATTTAATAAATATTAA
152799 AATATTTATG
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
15 4 0.09
16 10 0.22
17 13 0.29
18 13 0.29
19 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTTAATAAATATTAA
Found at i:152771 original size:26 final size:29
Alignment explanation
Indices: 152738--152790 Score: 85
Period size: 26 Copynumber: 1.9 Consensus size: 29
152728 TCGTATTTAA
152738 AATATATTAAT-ATTT-ATA-TAAATATT
1 AATATATTAATAATTTAATATTAAATATT
152764 AATATATTAATAATTTAATATTAAATA
1 AATATATTAATAATTTAATATTAAATA
152791 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 11 0.46
27 4 0.17
28 3 0.12
29 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATATTAATAATTTAATATTAAATATT
Found at i:154266 original size:18 final size:18
Alignment explanation
Indices: 154229--154278 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
154219 ATGTTAAATA
*
154229 TAAATATATTTAATATTT
1 TAAATATTTTTAATATTT
154247 TAAATATTTTT-ATATATT
1 TAAATATTTTTAATAT-TT
*
154265 TAAAAATTTATTAA
1 TAAATATTT-TTAA
154279 AAAACTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 20 0.74
19 2 0.07
20 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAATATTTTTAATATTT
Found at i:155897 original size:14 final size:13
Alignment explanation
Indices: 155869--155919 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
155859 TAAATAAAAG
*
155869 AATTATAAATATT
1 AATTTTAAATATT
*
155882 AATATTTAAATTTT
1 AAT-TTTAAATATT
155896 AATTATTAAATATT
1 AATT-TTAAATATT
155910 ACATTTTAAA
1 A-ATTTTAAA
155920 AGTAATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 4 0.12
14 25 0.78
15 3 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTTTAAATATT
Found at i:155915 original size:21 final size:21
Alignment explanation
Indices: 155869--155918 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
155859 TAAATAAAAG
* *
155869 AATTATAAATATTAATATTTA
1 AATTTTAATTATTAATATTTA
155890 AATTTTAATTATTAA-ATATTA
1 AATTTTAATTATTAATAT-TTA
*
155911 CATTTTAA
1 AATTTTAA
155919 AAGTAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTTAATTATTAATATTTA
Found at i:157112 original size:2 final size:2
Alignment explanation
Indices: 157105--157133 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
157095 ATTCCTCATA
157105 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
157134 ACCTTATTTA
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:157364 original size:10 final size:11
Alignment explanation
Indices: 157351--157393 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
157341 AAAATATTAA
157351 AATAT-AATAT
1 AATATGAATAT
157361 AATATGAA-AT
1 AATATGAATAT
*
157371 AATATAAATAT
1 AATATGAATAT
*
157382 TATATGAATAT
1 AATATGAATAT
157393 A
1 A
157394 TGAAGATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (11 bp):
AATATGAATAT
Found at i:157391 original size:20 final size:20
Alignment explanation
Indices: 157351--157389 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
157341 AAAATATTAA
157351 AATATAATATAATATGAAAT
1 AATATAATATAATATGAAAT
*
157371 AATATAAATATTATATGAA
1 AATAT-AATATAATATGAA
157390 TATATGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
AATATAATATAATATGAAAT
Found at i:157438 original size:17 final size:18
Alignment explanation
Indices: 157407--157456 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
157397 AGATTTTAAA
157407 ATTTATATAATAAAAA-TT
1 ATTTATAT-ATAAAAATTT
157425 ATTTATATATAAAAATTT
1 ATTTATATATAAAAATTT
* *
157443 ATGTAAATATAAAA
1 ATTTATATATAAAA
157457 TATATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTTATATATAAAAATTT
Found at i:158538 original size:19 final size:20
Alignment explanation
Indices: 158509--158562 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
158499 TACTTTCGAA
*
158509 AATTT-AATTTTTTTTTA-T
1 AATTTAAATTTTATTTTATT
158527 AATTTAAATTTTATTTTATT
1 AATTTAAATTTTATTTTATT
*
158547 AAATTAAATTATTATT
1 AATTTAAATT-TTATT
158563 AAAATTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 10 0.32
21 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATTTAAATTTTATTTTATT
Found at i:158568 original size:32 final size:31
Alignment explanation
Indices: 158523--158611 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 31
158513 TAATTTTTTT
* *
158523 TTATAATTTAAATTTTATTTTATTAA-ATTAAA
1 TTATTATTAAAATTTTATTTTATTAACA-T-AA
158555 TTATTATTAAAATTATT-TTTTA-TAACATAA
1 TTATTATTAAAATT-TTATTTTATTAACATAA
*
158585 TTATTTTATTACAATTTTATTTTATTA
1 TTA--TTATTAAAATTTTATTTTATTA
158612 CAGTGAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
30 5 0.10
31 6 0.12
32 33 0.69
33 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (31 bp):
TTATTATTAAAATTTTATTTTATTAACATAA
Found at i:158577 original size:16 final size:17
Alignment explanation
Indices: 158532--158611 Score: 73
Period size: 16 Copynumber: 5.0 Consensus size: 17
158522 TTTATAATTT
158532 AAATT-TTATTTTATT-
1 AAATTATTATTTTATTA
*
158547 AAATTA-AATTATTATTA
1 AAATTATTATT-TTATTA
158564 AAATTATT-TTTTA-TA
1 AAATTATTATTTTATTA
* *
158579 ACATAATTATTTTATTA
1 AAATTATTATTTTATTA
*
158596 CAATT-TTATTTTATTA
1 AAATTATTATTTTATTA
158612 CAGTGAATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
15 16 0.31
16 24 0.46
17 12 0.23
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATTATTATTTTATTA
Found at i:159804 original size:26 final size:26
Alignment explanation
Indices: 159758--159807 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
159748 AATTATTATG
**
159758 TAATTAATAAAATTTTTTATTAAATT
1 TAATTAATAAAATTTAATATTAAATT
159784 TAATT-ATAAAATATTAATATTAAA
1 TAATTAATAAAAT-TTAATATTAAA
159808 ATAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATTAATAAAATTTAATATTAAATT
Found at i:159842 original size:14 final size:14
Alignment explanation
Indices: 159790--159843 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
159780 AATTTAATTA
*
159790 TAAAATATTAATAT
1 TAAAATAATAATAT
*
159804 TAAAATAAAATTATATT
1 TAAAAT--AATAATA-T
*
159821 TTAAATAATAATAT
1 TAAAATAATAATAT
159835 TAAAATAAT
1 TAAAATAAT
159844 TTTTAAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 15 0.47
15 6 0.19
16 5 0.16
17 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATAATAATAT
Found at i:161242 original size:55 final size:57
Alignment explanation
Indices: 161140--161250 Score: 192
Period size: 56 Copynumber: 2.0 Consensus size: 57
161130 AACTTTTATC
161140 AAATTTCTCAAAAAAATTTTGATCAGAAAAAGTTTGAATTTGAAAATAAAAAGGTTT
1 AAATTTCTCAAAAAAATTTTGATCAGAAAAAGTTTGAATTTGAAAATAAAAAGGTTT
161197 AAATTTCTC-AAAAAATTTTGAT-AGAAAAAGGTTTGAATTTG-AAATAAAAAGGTT
1 AAATTTCTCAAAAAAATTTTGATCAGAAAAA-GTTTGAATTTGAAAATAAAAAGGTT
161251 AAAGTCCCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
55 20 0.38
56 24 0.45
57 9 0.17
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.33
Consensus pattern (57 bp):
AAATTTCTCAAAAAAATTTTGATCAGAAAAAGTTTGAATTTGAAAATAAAAAGGTTT
Found at i:161577 original size:3 final size:3
Alignment explanation
Indices: 161569--161597 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
161559 CAAGTTTGTT
161569 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
161598 TCACAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:163019 original size:18 final size:18
Alignment explanation
Indices: 162996--163030 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
162986 AAAATTTATT
162996 TAAATA-TAATTATAAAAA
1 TAAATATTAA-TATAAAAA
163014 TAAATATTAATATAAAA
1 TAAATATTAATATAAAA
163031 TAATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAATATTAATATAAAAA
Found at i:164095 original size:3 final size:3
Alignment explanation
Indices: 164089--164118 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
164079 GAGATATTGG
*
164089 TGA TGA TGA TGA TGA TGA TGA TGA TAA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
164119 AATGGCCGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:167334 original size:28 final size:28
Alignment explanation
Indices: 167267--167328 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
167257 TACTGTGATA
* * *
167267 AAAATAA-AA-TATTTAAATGATTTGTT
1 AAAATAATAATTATATAAATAATCTGTT
167293 AAAATAATAATTATATAAATAATCTGTT
1 AAAATAATAATTATATAAATAATCTGTT
167321 AAATATAA
1 AAA-ATAA
167329 ATTTATTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 7 0.23
27 2 0.07
28 17 0.57
29 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (28 bp):
AAAATAATAATTATATAAATAATCTGTT
Found at i:167375 original size:15 final size:15
Alignment explanation
Indices: 167346--167374 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
167336 TTGAAAACTT
167346 TAAATAAACAAAAAA
1 TAAATAAACAAAAAA
167361 TAAAT-AACAAAAAA
1 TAAATAAACAAAAAA
167375 AAAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAATAAACAAAAAA
Found at i:170800 original size:3 final size:3
Alignment explanation
Indices: 170792--170832 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
170782 AACCAAGGGG
170792 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 AA
170833 ATTGAATGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:171241 original size:16 final size:16
Alignment explanation
Indices: 171213--171245 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
171203 AAATAGATAG
171213 TTTAAAATAATAAAAA
1 TTTAAAATAATAAAAA
171229 TTTATAAAT-ATAAAAA
1 TTTA-AAATAATAAAAA
171245 T
1 T
171246 AATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TTTAAAATAATAAAAA
Found at i:171894 original size:14 final size:15
Alignment explanation
Indices: 171875--171905 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
171865 GAATAGATGC
171875 AAATATTTATT-TTT
1 AAATATTTATTATTT
171889 AAATATTTATTATTT
1 AAATATTTATTATTT
171904 AA
1 AA
171906 GTTCGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AAATATTTATTATTT
Found at i:173144 original size:28 final size:30
Alignment explanation
Indices: 173083--173146 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
173073 ATAAAAATGC
*
173083 AATAAATTTTATTTATTATATAATGAATAT
1 AATAAATTTTATTTATCATATAATGAATAT
*
173113 -ATAAATTTTATTT-TCATATAAT-AATTT
1 AATAAATTTTATTTATCATATAATGAATAT
173140 AATAAAT
1 AATAAAT
173147 AAATTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 4 0.13
28 14 0.45
29 13 0.42
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
AATAAATTTTATTTATCATATAATGAATAT
Found at i:173169 original size:28 final size:28
Alignment explanation
Indices: 173083--173171 Score: 88
Period size: 32 Copynumber: 3.0 Consensus size: 28
173073 ATAAAAATGC
* *
173083 AATAAATTTTATTTATTATATAATGAATA
1 AATAAATTTTA-TTATTATAAAATTAATA
* *
173112 TATAAATTTTATTTTCATATAATAATTTAATA
1 AATAAATTTTATTAT--TATAA-AA-TTAATA
*
173144 AATAAATTTTATAATTATAAAATTAATA
1 AATAAATTTTATTATTATAAAATTAATA
173172 TTAACTAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 9 0.18
29 12 0.24
30 9 0.18
31 2 0.04
32 17 0.35
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATAAATTTTATTATTATAAAATTAATA
Found at i:179809 original size:26 final size:25
Alignment explanation
Indices: 179780--179840 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 25
179770 TTTATTTAAA
**
179780 TAAAATTATAATTAATAAAATTTATT
1 TAAAATTATAATTAAT-AAATAAATT
179806 TAAAA-TAT--TTAATAAATAAATT
1 TAAAATTATAATTAATAAATAAATT
*
179828 TAAAATTAAAATT
1 TAAAATTATAATT
179841 TAATCACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 12 0.41
23 7 0.24
25 5 0.17
26 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAAATTATAATTAATAAATAAATT
Found at i:179828 original size:13 final size:14
Alignment explanation
Indices: 179776--179844 Score: 63
Period size: 13 Copynumber: 5.1 Consensus size: 14
179766 AATTTTTATT
179776 TAAATAAAATTATAA
1 TAAATAAAATT-TAA
* *
179791 TTAATAAAATTTAT
1 TAAATAAAATTTAA
* *
179805 TTAA-AATATTTAA
1 TAAATAAAATTTAA
179818 TAAAT-AAATTTAA
1 TAAATAAAATTTAA
*
179831 -AATTAAAATTTAA
1 TAAATAAAATTTAA
179844 T
1 T
179845 CACATAGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
12 3 0.07
13 25 0.57
14 6 0.14
15 10 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATAAAATTTAA
Found at i:180035 original size:32 final size:31
Alignment explanation
Indices: 179964--180036 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
179954 AAATATACGA
*
179964 ATATATAAATATTTATATAAAATAAATTATT
1 ATATATAAATATTTATATAAAATAAATAATT
* * *
179995 AATGTATAACTATTTATATAAATTTATAATAATT
1 -ATATATAAATATTTATATAAA-ATA-AATAATT
180029 -TATATAAA
1 ATATATAAA
180037 CAAAACTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
32 25 0.76
33 2 0.06
34 6 0.18
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (31 bp):
ATATATAAATATTTATATAAAATAAATAATT
Found at i:180172 original size:59 final size:59
Alignment explanation
Indices: 180073--180184 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
180063 ATACAAAATT
* *
180073 TTTTTAATTAAATTACTATAACAAATTATGAGAAAAATGTCATGAATTGAGATGTAATA
1 TTTTAAATTAAATTACTATAACAAATTATGAGAAAAATGTCATGAATGGAGATGTAATA
* * * *
180132 TTTTAAATTAAATTATTATGATAAATTATGCA-AAATATGTCATGAATGGAGAT
1 TTTTAAATTAAATTACTATAACAAATTATG-AGAAAAATGTCATGAATGGAGAT
180185 ACGACATGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.38
Consensus pattern (59 bp):
TTTTAAATTAAATTACTATAACAAATTATGAGAAAAATGTCATGAATGGAGATGTAATA
Found at i:181898 original size:19 final size:19
Alignment explanation
Indices: 181857--181899 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
181847 CTCTTTTTTT
* *
181857 TCTCTTTCATTTCTTTATT
1 TCTCTTTCATTTCCTTATC
*
181876 TCTCTTTCATTTCCTTCTC
1 TCTCTTTCATTTCCTTATC
181895 TCTCT
1 TCTCT
181900 CAATTCACGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (19 bp):
TCTCTTTCATTTCCTTATC
Found at i:182847 original size:56 final size:56
Alignment explanation
Indices: 182761--182870 Score: 184
Period size: 56 Copynumber: 2.0 Consensus size: 56
182751 AACAGATATT
* *
182761 CAAAAGAAATTTGGACATGTGTCAATTATATATTCTTTTATGTAGTTCAAATTATC
1 CAAAAGAAATTTGGACAGGTATCAATTATATATTCTTTTATGTAGTTCAAATTATC
* *
182817 CAAAAGAAATTTGGACAGGTATCAATTATATATTTTTTTATGTAGTTTAAATTA
1 CAAAAGAAATTTGGACAGGTATCAATTATATATTCTTTTATGTAGTTCAAATTA
182871 GTTATATAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (56 bp):
CAAAAGAAATTTGGACAGGTATCAATTATATATTCTTTTATGTAGTTCAAATTATC
Found at i:182925 original size:69 final size:69
Alignment explanation
Indices: 182814--182950 Score: 238
Period size: 69 Copynumber: 2.0 Consensus size: 69
182804 AGTTCAAATT
* *
182814 ATCCAAAAGAAATTTGGACAGGTATCAATTATATATTTTTTTATGTAGTTTAAATTAGTTATATA
1 ATCCAAAAGAAATTTAGACAGGTATCAATTATATATTTTTTTATGTAGTTCAAATTAGTTATATA
182879 GTAG
66 GTAG
* *
182883 ATCCAAAAGAAATTTAGATAGGTGTCAATTATATATTTTTTTATGTAGTTCAAATTAGTTATATA
1 ATCCAAAAGAAATTTAGACAGGTATCAATTATATATTTTTTTATGTAGTTCAAATTAGTTATATA
182948 GTA
66 GTA
182951 TCTATAGATA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (69 bp):
ATCCAAAAGAAATTTAGACAGGTATCAATTATATATTTTTTTATGTAGTTCAAATTAGTTATATA
GTAG
Found at i:183019 original size:22 final size:23
Alignment explanation
Indices: 182994--183036 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
182984 TAAATAACAA
182994 TATTT-ATAAATTA-TTTAAAATT
1 TATTTAATAAA-TAGTTTAAAATT
183016 TATTTAATAAATAGTTTAAAA
1 TATTTAATAAATAGTTTAAAA
183037 CTCTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTTAATAAATAGTTTAAAATT
Found at i:183163 original size:38 final size:37
Alignment explanation
Indices: 183053--183164 Score: 113
Period size: 38 Copynumber: 3.0 Consensus size: 37
183043 TATTGTTTTA
* * * *
183053 TATAATATAATTAATAATATGTTTGTTTGTGTTTTATT
1 TATAATAAAATTAATAATATGTTTATTTGTATTAT-TT
*
183091 TATAATATAATTAATAATAT-TTATATTT-TATTATTT
1 TATAATAAAATTAATAATATGTT-TATTTGTATTATTT
*
183127 TATATTTAAAATTAATAAATATGTTTATTTGT-TTATTT
1 TATA-ATAAAATTAAT-AATATGTTTATTTGTATTATTT
183165 AAATTTATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
36 6 0.09
37 15 0.23
38 40 0.62
39 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (37 bp):
TATAATAAAATTAATAATATGTTTATTTGTATTATTT
Found at i:184599 original size:17 final size:17
Alignment explanation
Indices: 184579--184632 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
184569 TTTAATATTT
184579 ATAAAATTTTTAATTAA
1 ATAAAATTTTTAATTAA
*
184596 ATAAAA-TTATAATT-A
1 ATAAAATTTTTAATTAA
*
184611 ATAAATTTATTTAA-TAA
1 ATAAAATT-TTTAATTAA
184628 ATAAA
1 ATAAA
184633 TTTAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.19
16 9 0.29
17 16 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAAATTTTTAATTAA
Found at i:184629 original size:32 final size:33
Alignment explanation
Indices: 184570--184651 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 33
184560 GTCGAGAGTT
* * *
184570 TTAATATTTATAAAATT-TTTAATTAAATAAAA
1 TTAAAATTAATAAATTTATTTAATTAAATAAAA
* *
184602 TTATAATTAATAAATTTATTTAA-TAAATAAAT
1 TTAAAATTAATAAATTTATTTAATTAAATAAAA
*
184634 TTAAAATTAA-AATTTTAT
1 TTAAAATTAATAAATTTAT
184652 CATATAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 7 0.17
32 30 0.71
33 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TTAAAATTAATAAATTTATTTAATTAAATAAAA
Found at i:184659 original size:31 final size:30
Alignment explanation
Indices: 184580--184666 Score: 81
Period size: 32 Copynumber: 2.9 Consensus size: 30
184570 TTAATATTTA
* *
184580 TAAAATTTT-TA-ATTAAATAAAATTATAAT
1 TAAAATTTTATATA-TAAATAAATTTAAAAT
* *
184609 TAATAAATTTATTTAATAAATAAATTTAAAAT
1 TAA-AATTTTATAT-ATAAATAAATTTAAAAT
184641 TAAAATTTTATCATATAAA-AAATTTA
1 TAAAATTTTAT-ATATAAATAAATTTA
184667 TATAAAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
29 3 0.06
30 12 0.26
31 13 0.28
32 18 0.38
33 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
TAAAATTTTATATATAAATAAATTTAAAAT
Found at i:184694 original size:24 final size:24
Alignment explanation
Indices: 184666--184712 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
184656 TAAAAAATTT
*
184666 ATATAAAATATAAGATAA-ATTAAG
1 ATATAAAATA-AACATAATATTAAG
*
184690 ATATAACATAAACATAATATTAA
1 ATATAAAATAAACATAATATTAA
184713 AAAATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (24 bp):
ATATAAAATAAACATAATATTAAG
Found at i:184747 original size:20 final size:20
Alignment explanation
Indices: 184722--184762 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
184712 AAAAATAATT
184722 AAAATAT-AATATGATATAAA
1 AAAATATAAATATGATA-AAA
184742 AAAATATAAATATGATAAAA
1 AAAATATAAATATGATAAAA
184762 A
1 A
184763 TACACAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAATATAAATATGATAAAA
Found at i:185408 original size:32 final size:32
Alignment explanation
Indices: 185360--185421 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
185350 ATTATATTTA
*
185360 TAATATTATATGTTATATAAATTTTGATATAT
1 TAATATTATATATTATATAAATTTTGATATAT
*
185392 TAATATTTTATATTATATAAATTTTGATAT
1 TAATATTATATATTATATAAATTTTGATAT
185422 TTTTGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (32 bp):
TAATATTATATATTATATAAATTTTGATATAT
Found at i:186961 original size:28 final size:28
Alignment explanation
Indices: 186929--186986 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
186919 TTTTATTGTC
*
186929 AAATGCAATATTTTATACTCATAAAAAG
1 AAATGCAACATTTTATACTCATAAAAAG
186957 AAATGCAACATTTTATACTCATAAAAAG
1 AAATGCAACATTTTATACTCATAAAAAG
186985 AA
1 AA
186987 TTGAACTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (28 bp):
AAATGCAACATTTTATACTCATAAAAAG
Found at i:187451 original size:21 final size:22
Alignment explanation
Indices: 187426--187472 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
187416 AATTTAAAAA
187426 ATAATTTTA-ATTATATAATAT
1 ATAATTTTATATTATATAATAT
* *
187447 ATAA-TTTATTTTATGTAATAT
1 ATAATTTTATATTATATAATAT
187468 ATAAT
1 ATAAT
187473 ATCAACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATAATTTTATATTATATAATAT
Found at i:187539 original size:24 final size:23
Alignment explanation
Indices: 187511--187572 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
187501 TCTTAATTAT
*
187511 TCAATCAAATTAATTTTACTTAAA
1 TCAATC-AATTAATTTAACTTAAA
* *
187535 TCAATTTCGATTAA-TTAATTTAAA
1 TCAA--TCAATTAATTTAACTTAAA
187559 TCAATCAATTAATT
1 TCAATCAATTAATT
187573 CAATTTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
22 7 0.23
23 1 0.03
24 16 0.52
25 5 0.16
26 2 0.06
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (23 bp):
TCAATCAATTAATTTAACTTAAA
Found at i:188396 original size:2 final size:2
Alignment explanation
Indices: 188391--188417 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
188381 TCTGTGTGTG
188391 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
188418 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:189448 original size:2 final size:2
Alignment explanation
Indices: 189441--189479 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
189431 AGCAAACAGC
189441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
189480 GTACTAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:190800 original size:18 final size:18
Alignment explanation
Indices: 190758--190793 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
190748 CATTTTTTTA
*
190758 AATATATGTATTAAATAT
1 AATATATGTATTAAACAT
190776 AATATATGTATTAAACAT
1 AATATATGTATTAAACAT
190794 GTTATATTAA
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:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (18 bp):
AATATATGTATTAAACAT
Found at i:190822 original size:24 final size:24
Alignment explanation
Indices: 190786--190855 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
190776 AATATATGTA
* *
190786 TTAAACATGTTATATTAATTATAT
1 TTAAATATATTATATTAATTATAT
*
190810 TTAAATATATTATATCATATT-TAT
1 TTAAATATATTATATTA-ATTATAT
* * *
190834 TTTATTATTTTCATATTAATTA
1 TTAAATATATT-ATATTAATTA
190856 AATATATTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 28 0.78
25 8 0.22
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (24 bp):
TTAAATATATTATATTAATTATAT
Found at i:191130 original size:57 final size:58
Alignment explanation
Indices: 191021--191133 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
191011 AAAAAAATAA
*
191021 TTAAAATTTAATATGATATAATTAAAAAAGAATACGAATTTGATATAGATAAAATATT
1 TTAAAATTTAATATGATATAATTAAAAAAGAATACAAATTTGATATAGATAAAATATT
* * *
191079 TTAAAATTT-ATATGATATAAATTAATAAA-TATATCAAATTTTATATA-ATAAAATA
1 TTAAAATTTAATATGATAT-AATTAAAAAAGAATA-CAAATTTGATATAGATAAAATA
191134 CTCTAAACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 20 0.41
58 29 0.59
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (58 bp):
TTAAAATTTAATATGATATAATTAAAAAAGAATACAAATTTGATATAGATAAAATATT
Found at i:191940 original size:26 final size:26
Alignment explanation
Indices: 191902--191951 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
191892 TAAAAAGTTC
*
191902 TTTTTTATGAAAAAAAG-AAGAAATA
1 TTTTTTATAAAAAAAAGAAAGAAATA
191927 TTTTTTATAAAAAAAAAGAAAGAAA
1 TTTTTTAT-AAAAAAAAGAAAGAAA
191952 AATAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.36
26 8 0.36
27 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (26 bp):
TTTTTTATAAAAAAAAGAAAGAAATA
Found at i:192625 original size:15 final size:15
Alignment explanation
Indices: 192607--192636 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
192597 ATGAATTTTT
192607 AATATTAAATTTATA
1 AATATTAAATTTATA
*
192622 AATATTGAATTTATA
1 AATATTAAATTTATA
192637 TTGTCAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATATTAAATTTATA
Found at i:194436 original size:8 final size:8
Alignment explanation
Indices: 194354--194507 Score: 51
Period size: 8 Copynumber: 19.0 Consensus size: 8
194344 CCTCTCTCTA
*
194354 TATATATA
1 TATATATT
194362 TATATATT
1 TATATATT
194370 TGATA-ATT
1 T-ATATATT
*
194378 AATATATT
1 TATATATT
194386 TATAT-TAT
1 TATATAT-T
*
194394 TAT-TTTT
1 TATATATT
*
194401 TATTATAAT
1 TA-TATATT
194410 TA-A-ATT
1 TATATATT
*
194416 TAAAGTA-T
1 TATA-TATT
194424 TATATATT
1 TATATATT
194432 TATATAAATT
1 TATAT--ATT
194442 T-TAATATGT
1 TAT-ATAT-T
*
194451 TA-ATAAT
1 TATATATT
194458 T-TATA-T
1 TATATATT
194464 TATAATAATT
1 TAT-AT-ATT
194474 TAATATATT
1 T-ATATATT
194483 TATATTATTT
1 TATA-TA-TT
*
194493 TTTATATT
1 TATATATT
194501 T-TATATT
1 TATATATT
194508 AATTTTTAAC
Statistics
Matches: 114, Mismatches: 9, Indels: 47
0.67 0.05 0.28
Matches are distributed among these distances:
6 6 0.05
7 24 0.21
8 47 0.41
9 20 0.18
10 15 0.13
11 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TATATATT
Found at i:194513 original size:18 final size:18
Alignment explanation
Indices: 194423--194513 Score: 66
Period size: 19 Copynumber: 5.1 Consensus size: 18
194413 ATTTAAAGTA
*
194423 TTATATATTTATATAAATT
1 TTATAT-TTTATATTAATT
*
194442 TTAATATGTTA-A-TAA-T
1 TT-ATATTTTATATTAATT
*
194458 TTATA--TTATAATAATT
1 TTATATTTTATATTAATT
* *
194474 TAATATATTTATATTATTTT
1 TTATAT-TTTATATTA-ATT
194494 TTATATTTTATATTAATT
1 TTATATTTTATATTAATT
194512 TT
1 TT
194514 TAACGTGTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
13 3 0.05
14 1 0.02
15 6 0.11
16 8 0.14
17 2 0.04
18 5 0.09
19 21 0.37
20 11 0.19
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
TTATATTTTATATTAATT
Found at i:195139 original size:19 final size:20
Alignment explanation
Indices: 195115--195158 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
195105 CTTATTTTAA
* *
195115 TATATTTTTAT-TCTATATC
1 TATATTTTAATATCAATATC
195134 TATA-TTTAATATCAATATC
1 TATATTTTAATATCAATATC
195153 TATATT
1 TATATT
195159 CAATAGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 5 0.24
19 15 0.71
20 1 0.05
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATTTTAATATCAATATC
Found at i:195495 original size:2 final size:2
Alignment explanation
Indices: 195488--195524 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
195478 AAATTGGTGT
195488 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 T
195525 TTAAAAGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:195554 original size:5 final size:5
Alignment explanation
Indices: 195544--195568 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
195534 GGTGGAATAC
195544 CCCCA CCCCA CCCCA CCCCA CCCCA
1 CCCCA CCCCA CCCCA CCCCA CCCCA
195569 AAGGCCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCCA
Found at i:198336 original size:16 final size:16
Alignment explanation
Indices: 198271--198343 Score: 62
Period size: 16 Copynumber: 4.4 Consensus size: 16
198261 AAATTATTAC
198271 TATAAT-TT-TTTTAT
1 TATAATATTATTTTAT
*
198285 TAT-ATCTTTATTTTAT
1 TATAAT-ATTATTTTAT
*
198301 TATTGGAATATAATTTTTAT
1 TA-T--AATATTA-TTTTAT
198321 TATAATATTATTTTAT
1 TATAATATTATTTTAT
198337 TATAATA
1 TATAATA
198344 AATTAAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
13 2 0.04
14 3 0.06
15 2 0.04
16 21 0.44
17 7 0.15
19 3 0.06
20 10 0.21
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (16 bp):
TATAATATTATTTTAT
Found at i:198376 original size:27 final size:28
Alignment explanation
Indices: 198339--198404 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
198329 TATTTTATTA
* *
198339 TAATAAATTAAA-TAAATTATTATAATAT
1 TAATAATTTAAATTAAATTATAAT-ATAT
* *
198367 TAA-AATTTAAATTTATTTATAATATAT
1 TAATAATTTAAATTAAATTATAATATAT
198394 TAATAATTTAA
1 TAATAATTTAA
198405 TTATTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATAATTTAAATTAAATTATAATATAT
Found at i:198406 original size:27 final size:27
Alignment explanation
Indices: 198363--198416 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
198353 AATTATTATA
198363 ATATTAAAATTTAAATT-TATTTATAAT
1 ATATTAAAATTTAAATTAT-TTTATAAT
198390 ATATTAATAATTT-AATTATTTTATAAT
1 ATATTAA-AATTTAAATTATTTTATAAT
198417 TCATGTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATTAAAATTTAAATTATTTTATAAT
Found at i:198822 original size:13 final size:13
Alignment explanation
Indices: 198804--198828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
198794 AACAATGACC
198804 TGTCCTTTTATTG
1 TGTCCTTTTATTG
198817 TGTCCTTTTATT
1 TGTCCTTTTATT
198829 TTATTTTGGA
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:0.08, C:0.16, G:0.12, T:0.64
Consensus pattern (13 bp):
TGTCCTTTTATTG
Found at i:198996 original size:26 final size:27
Alignment explanation
Indices: 198945--198999 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
198935 TTCATATAAA
* *
198945 ATTTTATTAATAAATATTTTTAAAATT
1 ATTTTATTAATAAATAATTATAAAATT
198972 ATTTTATTAAT-AATACATTAT-AAATT
1 ATTTTATTAATAAATA-ATTATAAAATT
198998 AT
1 AT
199000 CAAATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTTATTAATAAATAATTATAAAATT
Found at i:201687 original size:2 final size:2
Alignment explanation
Indices: 201680--201711 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
201670 AAGAACTTTC
201680 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
201712 GAATTCCACA
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:203246 original size:17 final size:17
Alignment explanation
Indices: 203226--203324 Score: 74
Period size: 17 Copynumber: 5.5 Consensus size: 17
203216 CATATCATAT
203226 AATTAATTTTTTATTAA
1 AATTAATTTTTTATTAA
*
203243 AATTAATTATTAATTATTATT
1 AATTAATT-TT--TTATTA-A
* * *
203264 AATAAAATGTTTATTAA
1 AATTAATTTTTTATTAA
* *
203281 AATT-ATTAATAATTATTAT
1 AATTAATT--T-TTTATTAA
203300 AATTAATTTTTTATTAA
1 AATTAATTTTTTATTAA
203317 AATTAATT
1 AATTAATT
203325 GTTGAAACCC
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
16 2 0.03
17 25 0.40
18 9 0.15
19 10 0.16
20 10 0.16
21 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
AATTAATTTTTTATTAA
Found at i:203246 original size:37 final size:36
Alignment explanation
Indices: 203199--203321 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 36
203189 TCGATAATAA
* * *
203199 TTATTGAAATTTTTAATCATATCATATAATTAATTTT
1 TTATTAAAATTATTAAT-ATATTATATAATTAATTTT
* * * *
203236 TTATTAAAATTAATTATTA-ATTATTATTAATAAAATGT
1 TTATTAAAATT-ATTAATATATTA-TA-TAATTAATTTT
203274 TTATTAAAATTATTAATA-ATTATTATAATTAATTTT
1 TTATTAAAATTATTAATATATTA-TATAATTAATTTT
203310 TTATTAAAATTA
1 TTATTAAAATTA
203322 ATTGTTGAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
36 23 0.32
37 26 0.36
38 23 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (36 bp):
TTATTAAAATTATTAATATATTATATAATTAATTTT
Found at i:203370 original size:11 final size:11
Alignment explanation
Indices: 203352--203393 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
203342 TTAAAAAATG
203352 AATTATTAATT
1 AATTATTAATT
*
203363 ATTTATT-ATT
1 AATTATTAATT
*
203373 AAATTATTAATA
1 -AATTATTAATT
203385 AATTATTAA
1 AATTATTAA
203394 AATAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 3 0.12
11 21 0.81
12 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTATTAATT
Found at i:203404 original size:38 final size:39
Alignment explanation
Indices: 203370--203444 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
203360 ATTATTTATT
203370 ATTAAATTATTA-ATA-AATTAT-TAAAATAAATATTTACC
1 ATTAAATTATTACATATAA-TATGT-AAATAAATATTTACC
*
203408 ATTTAATTATTACATATAATATGTAAATAAATATTTA
1 ATTAAATTATTACATATAATATGTAAATAAATATTTA
203445 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
38 11 0.33
39 19 0.58
40 3 0.09
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (39 bp):
ATTAAATTATTACATATAATATGTAAATAAATATTTACC
Found at i:205459 original size:30 final size:29
Alignment explanation
Indices: 205424--205486 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
205414 TCTATGAGTA
*
205424 CTCTCAATCTCCTTTATAACATTTTTCAAT
1 CTCTCAATCTCCTTTATAACA-CTTTCAAT
*
205454 CTCTCAATCTCCTTTTTAACACTTTCAAT
1 CTCTCAATCTCCTTTATAACACTTTCAAT
205483 CTCT
1 CTCT
205487 TTTAGTCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (29 bp):
CTCTCAATCTCCTTTATAACACTTTCAAT
Found at i:210231 original size:29 final size:28
Alignment explanation
Indices: 210121--210260 Score: 122
Period size: 29 Copynumber: 4.7 Consensus size: 28
210111 TTAAGTATGC
*
210121 ATAAAAAGTTAAAAATTTATTTAAATAAAA
1 ATAAAAA-TTAAAAATATATTTAAAT-AAA
*
210151 ATTAAAAA-TAAAAAGTTTATTTAAATGTAAAA
1 A-TAAAAATTAAAAA-TATATTTAAA--T-AAA
* * *
210183 ATAAAGATTAAAAACT-TATTTTAATATA
1 ATAAAAATTAAAAA-TATATTTAAATAAA
210211 ATAAAAATATAAAAATATATTTAAATAAA
1 ATAAAAAT-TAAAAATATATTTAAATAAA
*
210240 ATTAAAAATTAAAAAAATATT
1 A-TAAAAATTAAAAATATATT
210261 AATATTTTAA
Statistics
Matches: 94, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
28 10 0.11
29 35 0.37
30 18 0.19
31 18 0.19
32 13 0.14
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (28 bp):
ATAAAAATTAAAAATATATTTAAATAAA
Found at i:210259 original size:31 final size:29
Alignment explanation
Indices: 210122--210260 Score: 113
Period size: 30 Copynumber: 4.7 Consensus size: 29
210112 TAAGTATGCA
* *
210122 TAAAAAGTTAAAAATTTATTTAAATAAAAAT
1 TAAAAA-TAAAAAATATATTTAAAT-AAAAT
* * *
210153 TAAAAATAAAAAGTTTATTTAAATGTAAAAA
1 TAAAAATAAAAAATATATTTAAA--TAAAAT
* * * *
210184 TAAAGATTAAAAACT-TATTTTAATATAA-
1 TAAA-AATAAAAAATATATTTAAATAAAAT
210212 TAAAAATATAAAAATATATTTAAATAAAAT
1 TAAAAATA-AAAAATATATTTAAATAAAAT
210242 TAAAAATTAAAAAA-ATATT
1 TAAAAA-TAAAAAATATATT
210261 AATATTTTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.03
28 9 0.10
29 20 0.22
30 26 0.29
31 23 0.26
32 9 0.10
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (29 bp):
TAAAAATAAAAAATATATTTAAATAAAAT
Found at i:210718 original size:30 final size:30
Alignment explanation
Indices: 210682--210752 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
210672 TAAAAATAAT
210682 TTTAAATTTTTATTAATTTATGAATAGTAA
1 TTTAAATTTTTATTAATTTATGAATAGTAA
210712 TTTAAATTTTTATTAATTTATGAATAGTAA
1 TTTAAATTTTTATTAATTTATGAATAGTAA
210742 TTTAAATTTTT
1 TTTAAATTTTT
210753 TAATTTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (30 bp):
TTTAAATTTTTATTAATTTATGAATAGTAA
Found at i:210767 original size:2 final size:2
Alignment explanation
Indices: 210762--210806 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
210752 TTAATTTGAA
210762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
210804 AT A
1 AT A
210807 AAGCACTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:214086 original size:2 final size:2
Alignment explanation
Indices: 214079--214108 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
214069 GTCTTCTGGT
214079 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
214109 GAGTGTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:217183 original size:20 final size:20
Alignment explanation
Indices: 217150--217189 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
217140 TTAATTTTTT
*
217150 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
217170 ATATTAT-ATATATATATAAA
1 ATATTATAAT-TATATATAAA
217190 TTTTGACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:218916 original size:20 final size:21
Alignment explanation
Indices: 218880--218920 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
218870 ATTCATATCA
*
218880 TATTATTTTATTTTTTAAAAT
1 TATTATCTTATTTTTTAAAAT
218901 TATTATCTTA-TTTTTAAAAT
1 TATTATCTTATTTTTTAAAAT
218921 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTATCTTATTTTTTAAAAT
Found at i:219098 original size:22 final size:22
Alignment explanation
Indices: 219068--219122 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
219058 CTTTTATTAA
219068 AATATTTTAAATATTTT-TATATT
1 AATA-TTTAAATATTTTATA-ATT
*
219091 AATATTTATATATTTTATAATT
1 AATATTTAAATATTTTATAATT
219113 -A-ATTTAAATA
1 AATATTTAAATA
219123 AAAATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 8 0.28
21 1 0.03
22 14 0.48
23 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATTTAAATATTTTATAATT
Found at i:219212 original size:15 final size:17
Alignment explanation
Indices: 219178--219214 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
219168 ACTAATTTTA
*
219178 TATATATATTGAAGAGT
1 TATATATATTGAAGAAT
219195 TATATATATT-AA-AAT
1 TATATATATTGAAGAAT
219210 TATAT
1 TATAT
219215 TAATGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 2 0.11
17 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (17 bp):
TATATATATTGAAGAAT
Found at i:220111 original size:7 final size:7
Alignment explanation
Indices: 220077--220122 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
220067 TATCGATAAA
*
220077 TTAATTT
1 TTAATAT
220084 TTATATATT
1 TTA-ATA-T
220093 TTAATA-
1 TTAATAT
220099 -TAATAT
1 TTAATAT
220105 TTAATAT
1 TTAATAT
220112 TTAATAT
1 TTAATAT
220119 TTAA
1 TTAA
220123 ATGCATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
5 5 0.15
7 20 0.59
8 5 0.15
9 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTAATAT
Found at i:220116 original size:19 final size:21
Alignment explanation
Indices: 220078--220118 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
220068 ATCGATAAAT
*
220078 TAATTTTTATATATTTTAATA
1 TAATATTTATATATTTTAATA
220099 TAATATTTA-ATA-TTTAATA
1 TAATATTTATATATTTTAATA
220118 T
1 T
220119 TTAAATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATTTATATATTTTAATA
Found at i:220277 original size:18 final size:18
Alignment explanation
Indices: 220240--220274 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
220230 TTAAAATAAA
*
220240 AATAAAGATAAGATAATT
1 AATAAAAATAAGATAATT
220258 AATAAAAATAA-ATAATT
1 AATAAAAATAAGATAATT
220275 TAACTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AATAAAAATAAGATAATT
Found at i:220771 original size:22 final size:21
Alignment explanation
Indices: 220746--220797 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
220736 TTTACATGTG
220746 TTAATATTTTTTAAAAATATAT
1 TTAATATTTTTT-AAAATATAT
* *
220768 TTAAT-TTATTTATAATATAT
1 TTAATATTTTTTAAAATATAT
*
220788 TT-TTATTTTT
1 TTAATATTTTT
220798 ATTTAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 14 0.56
21 5 0.20
22 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAATATTTTTTAAAATATAT
Found at i:220830 original size:32 final size:32
Alignment explanation
Indices: 220765--220830 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
220755 TTTAAAAATA
* * * *
220765 TATTTAATTTATTTATAATATATTTTTATTTT
1 TATTTAATTAATTTATAATAAAATATTATTTT
220797 TATTTAATTAATTTAT-ATAAAATATTATATTT
1 TATTTAATTAATTTATAATAAAATATTAT-TTT
220829 TA
1 TA
220831 AAATTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
TATTTAATTAATTTATAATAAAATATTATTTT
Found at i:220861 original size:26 final size:24
Alignment explanation
Indices: 220806--220886 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 24
220796 TTATTTAATT
220806 AATTTATATAAAATATTATATTTTAA
1 AATTTAT-T-AAATATTATATTTTAA
*
220832 AATTTTTTAAAT-TTATACTTTTCAA
1 AATTTATTAAATATTATA-TTTT-AA
220857 TAATTTATTAATAATGATTATAATTTTAA
1 -AATTTATT-A-AAT-ATTAT-ATTTTAA
220886 A
1 A
220887 GCGTCTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
23 5 0.11
24 8 0.18
25 3 0.07
26 13 0.29
27 1 0.02
28 4 0.09
29 2 0.04
30 8 0.18
31 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (24 bp):
AATTTATTAAATATTATATTTTAA
Found at i:224949 original size:59 final size:58
Alignment explanation
Indices: 224878--225071 Score: 255
Period size: 58 Copynumber: 3.3 Consensus size: 58
224868 AATTTTGGGG
* * * * * * * *
224878 GACTTGGTGTCACTTAGTATG-GTAATCTGGGTCACCTTGGTGGTGATCTATGTTTGGGT
1 GACTTGGCGTCACCTAGTGTGTG-AATC-GGGTCACCCTGGTGGCGATCTAAGTTCGAGT
* **
224937 GACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCTGACGGCGATCTAAGTTCGAGT
1 GACTTGGCGTCACCTAGTGTGTGAATCGGGTCACCCTGGTGGCGATCTAAGTTCGAGT
*
224995 GACTTGGCGTCACTTAGTGTGTGAATCGGGTCACCCTGGTGGCGATCTAAGTTCGAGT
1 GACTTGGCGTCACCTAGTGTGTGAATCGGGTCACCCTGGTGGCGATCTAAGTTCGAGT
225053 GACTTGGCGTCACCTAGTG
1 GACTTGGCGTCACCTAGTG
225072 CATGGATCTG
Statistics
Matches: 118, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
58 95 0.81
59 22 0.19
60 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.31
Consensus pattern (58 bp):
GACTTGGCGTCACCTAGTGTGTGAATCGGGTCACCCTGGTGGCGATCTAAGTTCGAGT
Found at i:225095 original size:58 final size:58
Alignment explanation
Indices: 224917--225103 Score: 187
Period size: 58 Copynumber: 3.2 Consensus size: 58
224907 GGTCACCTTG
* * * * ** * *
224917 GTGGTGATCTATGTTTGGGTGACTTGGCGTCACCTAGTGTGTGAATCGGGTCGCCCT-
1 GTGGCGATCTAAGTTCGAGTGACTTGGCGTCACCTAGTGCATGAATCGGGTCACACTA
* * ** * *
224974 GACGGCGATCTAAGTTCGAGTGACTTGGCGTCACTTAGTGTGTGAATCGGGTCACCCTG
1 G-TGGCGATCTAAGTTCGAGTGACTTGGCGTCACCTAGTGCATGAATCGGGTCACACTA
* * ** *
225033 GTGGCGATCTAAGTTCGAGTGACTTGGCGTCACCTAGTGCATGGATCTGGTCGTATTA
1 GTGGCGATCTAAGTTCGAGTGACTTGGCGTCACCTAGTGCATGAATCGGGTCACACTA
225091 GTGGCGATCTAAG
1 GTGGCGATCTAAG
225104 GACGTAGTGT
Statistics
Matches: 110, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
57 1 0.01
58 108 0.98
59 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (58 bp):
GTGGCGATCTAAGTTCGAGTGACTTGGCGTCACCTAGTGCATGAATCGGGTCACACTA
Found at i:235935 original size:32 final size:32
Alignment explanation
Indices: 235899--235963 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
235889 ATAATAAAGA
* * *
235899 TAATTTATATTTTGAATTATTAA-ATTTAATTT
1 TAATTTATA-TGTAAATTATAAATATTTAATTT
*
235931 TAATTTTTATGTAAATTATAAATATTTAATTT
1 TAATTTATATGTAAATTATAAATATTTAATTT
235963 T
1 T
235964 TATTAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (32 bp):
TAATTTATATGTAAATTATAAATATTTAATTT
Found at i:235958 original size:26 final size:24
Alignment explanation
Indices: 235915--235978 Score: 89
Period size: 26 Copynumber: 2.7 Consensus size: 24
235905 ATATTTTGAA
235915 TTATTAAATT-T-AATTTTAATTT
1 TTATTAAATTATAAATTTTAATTT
235937 TTATGTAAATTATAAATATTTAATTT
1 TTAT-TAAATTATAAAT-TTTAATTT
235963 TTATT-AATTATAAATT
1 TTATTAAATTATAAATT
235979 AAGTTATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.11
23 7 0.18
24 11 0.29
25 4 0.11
26 12 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATTAAATTATAAATTTTAATTT
Found at i:235987 original size:25 final size:24
Alignment explanation
Indices: 235930--235996 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
235920 AAATTTAATT
*
235930 TTAATTTTTATGTAAATTATAAATAT
1 TTAATTTTTAT-T-AATTATAAATAG
235956 TTAATTTTTATTAATTATAAATTAAG
1 TTAATTTTTATTAATTATAAA-T-AG
*
235982 TT-ATTTATATTAATT
1 TTAATTTTTATTAATT
235997 TTGTTAAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.24
25 14 0.38
26 14 0.38
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (24 bp):
TTAATTTTTATTAATTATAAATAG
Found at i:236164 original size:16 final size:17
Alignment explanation
Indices: 236131--236168 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
236121 TAAAATTACT
236131 TAATTTAATTAGTATAAA
1 TAATTTAATTA-TATAAA
236149 TAATTTAATT-TATAAA
1 TAATTTAATTATATAAA
236165 TAAT
1 TAAT
236169 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATTTAATTATATAAA
Found at i:236181 original size:30 final size:29
Alignment explanation
Indices: 236147--236213 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
236137 AATTAGTATA
236147 AATAATTTAATTT-ATAAATAATAAAAATTT
1 AATAATTTAATTTAAT-AA-AATAAAAATTT
* * *
236177 AATAATATGATTTAATAAAATAAATATTT
1 AATAATTTAATTTAATAAAATAAAAATTT
236206 -ATAATTTA
1 AATAATTTA
236214 CATAAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 6 0.19
29 10 0.32
30 13 0.42
31 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
AATAATTTAATTTAATAAAATAAAAATTT
Found at i:238578 original size:16 final size:18
Alignment explanation
Indices: 238557--238595 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
238547 TTTTTAATAA
238557 TATAAT-CAAAAAAT-TT
1 TATAATACAAAAAATGTT
238573 TATAATACAAAAAATGTT
1 TATAATACAAAAAATGTT
238591 TATAA
1 TATAA
238596 ATTCAATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (18 bp):
TATAATACAAAAAATGTT
Found at i:238769 original size:3 final size:3
Alignment explanation
Indices: 238763--238803 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
238753 TAATATAATA
238763 ATT ATT ATT ATT ATT AATT ATT ATT ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT AT
238804 GTGAAAGGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:238782 original size:16 final size:16
Alignment explanation
Indices: 238761--238803 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
238751 AATAATATAA
238761 TAATTATTATTATTAT
1 TAATTATTATTATTAT
238777 TAATTATTATTATTAT
1 TAATTATTATTATTAT
238793 T-ATTA-TATTAT
1 TAATTATTATTAT
238804 GTGAAAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 17 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTATTATTATTAT
Found at i:238785 original size:19 final size:19
Alignment explanation
Indices: 238758--238803 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
238748 TATAATAATA
*
238758 TAATAATTATTATTATTAT
1 TAATTATTATTATTATTAT
238777 TAATTATTATTATTATTAT
1 TAATTATTATTATTATTAT
238796 TATATTAT
1 TA-ATTAT
238804 GTGAAAGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATTATTATTATTATTAT
Found at i:238958 original size:14 final size:13
Alignment explanation
Indices: 238939--238968 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
238929 TGAATAGTAA
238939 TTTTTTAAATATAT
1 TTTTTTAAATA-AT
238953 TTTTTTAAATAAT
1 TTTTTTAAATAAT
238966 TTT
1 TTT
238969 AAAATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTTAAATAAT
Found at i:239155 original size:25 final size:24
Alignment explanation
Indices: 239086--239157 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
239076 TGAAAAATTA
239086 ATTAA-ATTTAAAAAATTTATGA--
1 ATTAATATTTAAAAAATTTAT-ATT
* * *
239108 A-TAATTTTTAATAAAAATAATATTT
1 ATTAATATTTAA-AAAATTTATA-TT
239133 ATTAATATTTAAAAAATTTATATT
1 ATTAATATTTAAAAAATTTATATT
239157 A
1 A
239158 AGAATTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
21 3 0.08
22 7 0.18
23 7 0.18
24 3 0.08
25 9 0.24
26 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
ATTAATATTTAAAAAATTTATATT
Found at i:239158 original size:21 final size:21
Alignment explanation
Indices: 239078--239167 Score: 60
Period size: 21 Copynumber: 4.1 Consensus size: 21
239068 TGTTATTTTG
239078 AAAAA-TTA-ATTAA-ATTTA
1 AAAAATTTATATTAATATTTA
* *
239096 AAAAATTTATGAATAATTTTTAA
1 AAAAATTTAT-ATTAATATTT-A
*
239119 TAAAAATAATATTTATTAATATTTA
1 -AAAAAT--T-TATATTAATATTTA
* *
239144 AAAAATTTATATTAAGAATTA
1 AAAAATTTATATTAATATTTA
239165 AAA
1 AAA
239168 TATTAATTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
18 5 0.09
19 3 0.05
21 18 0.33
22 4 0.07
23 1 0.02
24 12 0.22
25 1 0.02
26 9 0.16
27 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAATTTATATTAATATTTA
Found at i:239514 original size:21 final size:21
Alignment explanation
Indices: 239490--239534 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
239480 TTATTTTTTA
239490 TTTTATTAATACTA-TTAAAAT
1 TTTTATT-ATACTATTTAAAAT
* *
239511 TTTTATTTTTCTATTTAAAAT
1 TTTTATTATACTATTTAAAAT
239532 TTT
1 TTT
239535 AAACTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATTATACTATTTAAAAT
Found at i:239891 original size:24 final size:24
Alignment explanation
Indices: 239859--239919 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
239849 AGTTAATTTA
* *
239859 AAATATTATTTTA-TTTTAAAGAT
1 AAATTTTATTTTATTTTTAAAAAT
*
239882 AGGATTTTATTTTATTTTTAAAAAT
1 A-AATTTTATTTTATTTTTAAAAAT
239907 AAATTTTATTTTA
1 AAATTTTATTTTA
239920 ATTCTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.03
24 21 0.66
25 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (24 bp):
AAATTTTATTTTATTTTTAAAAAT
Found at i:240997 original size:11 final size:12
Alignment explanation
Indices: 240976--241013 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
240966 AGATTTTACT
240976 TTTTTTAATTAA
1 TTTTTTAATTAA
240988 TTTTTT-ATTAA
1 TTTTTTAATTAA
*
240999 TTTTTATAACTAA
1 TTTTT-TAATTAA
241012 TT
1 TT
241014 GCTATTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 7 0.30
13 6 0.26
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTTAATTAA
Found at i:244866 original size:23 final size:24
Alignment explanation
Indices: 244826--244871 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
244816 TATTATTTTT
** *
244826 TTAATGTTTTAATCAAATTGATTA
1 TTAATGTTTTAAAAAAATAGATTA
244850 TTAAT-TTTTAAAAAAATAGATT
1 TTAATGTTTTAAAAAAATAGATT
244872 TATATTGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (24 bp):
TTAATGTTTTAAAAAAATAGATTA
Found at i:246429 original size:14 final size:14
Alignment explanation
Indices: 246410--246437 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
246400 AAATATTAAA
246410 AATATTTTTATATT
1 AATATTTTTATATT
246424 AATATTTTTATATT
1 AATATTTTTATATT
246438 TTTAAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Done.