Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold163
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: 1788591
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.32
Warning! 179834 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:982638 original size:26 final size:26
Alignment explanation
Indices: 982579--982629 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
982569 TTTAATATTT
**
982579 TTAAAAATTTTATTTATTTAGTTTAA
1 TTAAAAAAATTATTTATTTAGTTTAA
982605 TTAAAAAAATTATTTATTTAGTTTA
1 TTAAAAAAATTATTTATTTAGTTTA
982630 CTTTCAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TTAAAAAAATTATTTATTTAGTTTAA
Found at i:984190 original size:23 final size:23
Alignment explanation
Indices: 984139--984190 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
984129 CATCTTTGTG
*
984139 TATTTAATTATGTTTTTATCTCA
1 TATTTAATTATGTTTTTATATCA
* * *
984162 TTTTTAATTATTTTTTTATATTA
1 TATTTAATTATGTTTTTATATCA
984185 TATTTA
1 TATTTA
984191 TGTTGTATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTTAATTATGTTTTTATATCA
Found at i:986358 original size:13 final size:13
Alignment explanation
Indices: 986340--986364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
986330 ATTACTCAAA
986340 TGTATCGATACAT
1 TGTATCGATACAT
986353 TGTATCGATACA
1 TGTATCGATACA
986365 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:986429 original size:52 final size:52
Alignment explanation
Indices: 986373--986493 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
986363 CACTGATCTT
*
986373 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
986425 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
986477 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
986494 ATTTTGAGAC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:992900 original size:12 final size:12
Alignment explanation
Indices: 992866--992900 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
992856 ATTAGGGGGA
992866 AGAAGAGAG-AG
1 AGAAGAGAGAAG
992877 AGAGAGAGAGAAG
1 AGA-AGAGAGAAG
992890 AGAAGAGAGAA
1 AGAAGAGAGAA
992901 AGGAGGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 14 0.64
13 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
AGAAGAGAGAAG
Found at i:993209 original size:12 final size:12
Alignment explanation
Indices: 993187--993217 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
993177 AATTATTATT
993187 TTAATTA-AAAA
1 TTAATTACAAAA
993198 TTAATTACAAAA
1 TTAATTACAAAA
993210 TTAATTAC
1 TTAATTAC
993218 TCAACTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (12 bp):
TTAATTACAAAA
Found at i:993285 original size:21 final size:22
Alignment explanation
Indices: 993250--993290 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
993240 TTGACTATCT
*
993250 AACACTCAAAATTATTAAAATG
1 AACACTCAAAATTATAAAAATG
*
993272 AACAC-CAATATTATAAAAA
1 AACACTCAAAATTATAAAAA
993291 ATAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (22 bp):
AACACTCAAAATTATAAAAATG
Found at i:993372 original size:12 final size:12
Alignment explanation
Indices: 993340--993372 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
993330 ATAATTAGAT
993340 TATTATTTAAAA
1 TATTATTTAAAA
*
993352 TAATA-TTAAAA
1 TATTATTTAAAA
993363 TATTATTTAA
1 TATTATTTAA
993373 CTTTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TATTATTTAAAA
Found at i:994566 original size:20 final size:22
Alignment explanation
Indices: 994527--994567 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
994517 ATTTATAAAA
*
994527 ATTATTTTATATTAATATTTAT
1 ATTATTATATATTAATATTTAT
994549 ATTATTATA-ATTAA-ATTTA
1 ATTATTATATATTAATATTTA
994568 AATAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATTATATATTAATATTTAT
Found at i:996612 original size:21 final size:21
Alignment explanation
Indices: 996588--996659 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 21
996578 AAAATAGTGT
* *
996588 TAGTAATTAAATTAATTATTA
1 TAGTAATGAAATTAAGTATTA
* *
996609 TAGTGATGAGATTAAGTATTA
1 TAGTAATGAAATTAAGTATTA
* *
996630 T-GATGATGAAATTAA-AATTA
1 TAG-TAATGAAATTAAGTATTA
996650 -A-TAATGAAAT
1 TAGTAATGAAAT
996660 ATAGATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 8 0.19
20 5 0.12
21 29 0.69
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (21 bp):
TAGTAATGAAATTAAGTATTA
Found at i:996859 original size:25 final size:24
Alignment explanation
Indices: 996798--996891 Score: 93
Period size: 25 Copynumber: 3.7 Consensus size: 24
996788 AAATATAAAT
*
996798 AAATTATATTTA-ATTTGCATAATA
1 AAATTATATTTATA-TTGAATAATA
996822 ACTAA-TATATTTATATTGAATAATA
1 A--AATTATATTTATATTGAATAATA
996847 AAATTATATTTTATATTGAATAACAATTA
1 AAATTATA-TTTATATTGAAT---AA-TA
996876 AAATTATATTTATATT
1 AAATTATATTTATATT
996892 AAAAATTATT
Statistics
Matches: 60, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
23 2 0.03
24 5 0.08
25 30 0.50
26 3 0.05
28 10 0.17
29 10 0.17
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
AAATTATATTTATATTGAATAATA
Found at i:997203 original size:14 final size:15
Alignment explanation
Indices: 997176--997211 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
997166 TTATTTGGTT
997176 AAGAGAATATAAAGAA
1 AAGA-AATATAAAGAA
997192 AAGAAATA-AAAGAA
1 AAGAAATATAAAGAA
997206 AAGAAA
1 AAGAAA
997212 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.60
15 4 0.20
16 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (15 bp):
AAGAAATATAAAGAA
Found at i:998785 original size:15 final size:17
Alignment explanation
Indices: 998761--998798 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
998751 ACAATTCATA
998761 ATTTTT-AAAAAT-ATT
1 ATTTTTAAAAAATAATT
998776 -TTTTTAAAAAATAATT
1 ATTTTTAAAAAATAATT
998792 ATTTTTA
1 ATTTTTA
998799 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 3 0.15
17 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTAAAAAATAATT
Found at i:1000779 original size:19 final size:19
Alignment explanation
Indices: 1000735--1000781 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
1000725 AATGTATTAA
*
1000735 TAAATTATTTTTTATATATT
1 TAAATT-TTATTTATATATT
*
1000755 TTAATTTTATTTATCATA-T
1 TAAATTTTATTTAT-ATATT
1000774 TAAATTTT
1 TAAATTTT
1000782 GAAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TAAATTTTATTTATATATT
Found at i:1001334 original size:22 final size:20
Alignment explanation
Indices: 1001304--1001345 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1001294 TTTTATTAAA
1001304 TATTAAATATCATATTAATATT
1 TATTAAATA--ATATTAATATT
*
1001326 TATTTAATAATATTAATATT
1 TATTAAATAATATTAATATT
1001346 AAATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAATAATATTAATATT
Found at i:1003738 original size:17 final size:18
Alignment explanation
Indices: 1003706--1003739 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1003696 TTTTTAAAAA
*
1003706 TATTTATATTAAATTAAT
1 TATTTATATGAAATTAAT
1003724 TATTT-TATGAAATTAA
1 TATTTATATGAAATTAA
1003740 AAAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTTATATGAAATTAAT
Found at i:1003975 original size:3 final size:3
Alignment explanation
Indices: 1003969--1003996 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1003959 CAACAACAGG
1003969 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1003997 GGAAAGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1004242 original size:3 final size:3
Alignment explanation
Indices: 1004236--1004276 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1004226 TCTTTAAATT
1004236 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1004277 TCTTGCAAGA
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1004411 original size:24 final size:24
Alignment explanation
Indices: 1004379--1004425 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1004369 CTGATGCCAG
*
1004379 TTGTGTCTAAATTTATGGAACTCC
1 TTGTGTCTAAATTTACGGAACTCC
1004403 TTGTGTCTAAATTTACGGAACTC
1 TTGTGTCTAAATTTACGGAACTC
1004426 GGTTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (24 bp):
TTGTGTCTAAATTTACGGAACTCC
Found at i:1005315 original size:14 final size:13
Alignment explanation
Indices: 1005290--1005314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1005280 TAGAGGAAAA
1005290 TCTTTATTTTTTC
1 TCTTTATTTTTTC
1005303 TCTTTATTTTTT
1 TCTTTATTTTTT
1005315 TAATTTTTTA
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:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTTATTTTTTC
Found at i:1005804 original size:15 final size:14
Alignment explanation
Indices: 1005754--1005804 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
1005744 TGATAATATT
1005754 TTTAAA-TATAATA
1 TTTAAATTATAATA
* * *
1005767 TTTAACTGTTTAAAA
1 TTTAAAT-TATAATA
1005782 TTTAAATTATAATA
1 TTTAAATTATAATA
1005796 TTTATAATT
1 TTTA-AATT
1005805 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 5 0.17
14 9 0.31
15 15 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
TTTAAATTATAATA
Found at i:1005908 original size:24 final size:26
Alignment explanation
Indices: 1005876--1005924 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
1005866 TTATAATTAT
*
1005876 AATTATAATAT-TTTAT-ATTTTTAA
1 AATTATAATATATTAATAATTTTTAA
*
1005900 AATTTTAATATATTAATAATTTTTA
1 AATTATAATATATTAATAATTTTTA
1005925 TATAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 4 0.19
26 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTATAATATATTAATAATTTTTAA
Found at i:1005920 original size:17 final size:17
Alignment explanation
Indices: 1005863--1005942 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 17
1005853 AAATTTTCTC
*
1005863 ATATT-ATAATTATAAT
1 ATATTAATAATTTTAAT
1005879 -TA-TAAT-ATTTT-AT
1 ATATTAATAATTTTAAT
*
1005892 ATTTTTAA-AATTTTAAT
1 A-TATTAATAATTTTAAT
1005909 ATATTAATAATTTT--T
1 ATATTAATAATTTTAAT
1005924 ATA-TAATATATTTTAAT
1 ATATTAATA-ATTTTAAT
1005941 AT
1 AT
1005943 TTATATTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 19
0.70 0.04 0.26
Matches are distributed among these distances:
13 2 0.04
14 10 0.20
15 14 0.27
16 13 0.25
17 12 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTAATAATTTTAAT
Found at i:1005921 original size:26 final size:24
Alignment explanation
Indices: 1005876--1005944 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 24
1005866 TTATAATTAT
*
1005876 AATTATAATATTTTATATTTTTAA
1 AATTATAATATTTAATATTTTTAA
*
1005900 AATTTTAATATATTAATAATTTTTATA
1 AATTATAATAT-TTAAT-ATTTTTA-A
1005927 TAA-TAT-AT-TTTAATATTT
1 -AATTATAATATTTAATATTT
1005945 ATATTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 4 0.11
24 15 0.39
25 5 0.13
26 9 0.24
27 3 0.08
28 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTATAATATTTAATATTTTTAA
Found at i:1005932 original size:22 final size:21
Alignment explanation
Indices: 1005905--1005965 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
1005895 TTTAAAATTT
*
1005905 TAATATATTAATAATTTTTATA
1 TAATATATT-ATAATATTTATA
*
1005927 TAATATATTTTAATATTTATA
1 TAATATATTATAATATTTATA
* * *
1005948 T-TTATATAATTATATTTA
1 TAATATATTATAATATTTA
1005966 AAATTATCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 13 0.39
21 11 0.33
22 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATATTATAATATTTATA
Found at i:1005936 original size:15 final size:15
Alignment explanation
Indices: 1005908--1005964 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 15
1005898 AAAATTTTAA
1005908 TATATTAATA-ATTTT
1 TATA-TAATATATTTT
1005923 TATATAATATA-TTT
1 TATATAATATATTTT
* *
1005937 TA-AT-ATTTATATT
1 TATATAATATATTTT
1005950 TATATAATTATATTT
1 TATATAA-TATATTT
1005965 AAAATTATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
12 4 0.12
13 6 0.18
14 12 0.36
15 6 0.18
16 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATAATATATTTT
Found at i:1005944 original size:8 final size:8
Alignment explanation
Indices: 1005881--1005944 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
1005871 ATTATAATTA
1005881 TAATATTT
1 TAATATTT
1005889 T-ATATTTT
1 TAATA-TTT
*
1005897 TAAAATTT
1 TAATATTT
*
1005905 TAATATAT
1 TAATATTT
1005913 TAATAATTT
1 TAAT-ATTT
* **
1005922 TTATATAA
1 TAATATTT
1005930 T-ATATTT
1 TAATATTT
1005937 TAATATTT
1 TAATATTT
1005945 ATATTTATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
7 8 0.19
8 27 0.63
9 8 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TAATATTT
Found at i:1011774 original size:2 final size:2
Alignment explanation
Indices: 1011769--1011820 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
1011759 AAATTTGTAT
* *
1011769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1011811 TA -A T- TA TA TA
1 TA TA TA TA TA TA
1011821 ATTTTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1011857 original size:13 final size:13
Alignment explanation
Indices: 1011839--1011866 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1011829 AATATAAAAA
1011839 AAATATTTATATT
1 AAATATTTATATT
1011852 AAATATTTATATT
1 AAATATTTATATT
1011865 AA
1 AA
1011867 TATAGCACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTATATT
Found at i:1012260 original size:2 final size:2
Alignment explanation
Indices: 1012253--1012282 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1012243 GAATCAGATC
1012253 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1012283 GTCCCTTTCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1013504 original size:16 final size:18
Alignment explanation
Indices: 1013469--1013506 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1013459 AAAAATTATT
1013469 ATATATGTTATGAATATA
1 ATATATGTTATGAATATA
*
1013487 ATATATG-TATTAAT-TA
1 ATATATGTTATGAATATA
1013503 ATAT
1 ATAT
1013507 TATTTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 6 0.32
18 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
ATATATGTTATGAATATA
Found at i:1013538 original size:14 final size:14
Alignment explanation
Indices: 1013514--1013550 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1013504 TATTATTTTG
*
1013514 ATTATATTTAAATAT
1 ATTATA-TTAAAAAT
1013529 ATTATATTAAAAAT
1 ATTATATTAAAAAT
1013543 ATTATATT
1 ATTATATT
1013551 GTTGTCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATATTAAAAAT
Found at i:1014613 original size:19 final size:18
Alignment explanation
Indices: 1014576--1014626 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
1014566 TTTAAAATAA
*
1014576 AATTTTAA--TAATTTTT
1 AATTTTAATTTAATTTAT
*
1014592 AATTTTATTTTATATTTAT
1 AATTTTAATTTA-ATTTAT
1014611 AATTTTAATTTAATTT
1 AATTTTAATTTAATTT
1014627 TTTAGTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 7 0.24
18 6 0.21
19 16 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AATTTTAATTTAATTTAT
Found at i:1016293 original size:19 final size:19
Alignment explanation
Indices: 1016269--1016307 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1016259 TTTTCATATA
1016269 AAATTATATTCATTAAAAT
1 AAATTATATTCATTAAAAT
1016288 AAATTATATTCATTAAAAT
1 AAATTATATTCATTAAAAT
1016307 A
1 A
1016308 TTAAACAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTATATTCATTAAAAT
Found at i:1016599 original size:25 final size:24
Alignment explanation
Indices: 1016550--1016599 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
1016540 TTTCATTAAA
*
1016550 TATTTTTGTTAAATAATTTTATTT
1 TATTTTTGTTAAATAAATTTATTT
*
1016574 TATTTTATTTTAAA-AAATTTAGTTT
1 TATTTT-TGTTAAATAAATTTA-TTT
1016599 T
1 T
1016600 TTATTAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (24 bp):
TATTTTTGTTAAATAAATTTATTT
Found at i:1016845 original size:21 final size:20
Alignment explanation
Indices: 1016783--1016841 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
1016773 AATTGATTTA
*
1016783 AATGAGATTAATTATTGTAGT
1 AATGAGATTAA-TATTATAGT
* *
1016804 AATTAGATTGGATATTATAGT
1 AATGAGATT-AATATTATAGT
1016825 AATGAGATTAATATTAT
1 AATGAGATTAATATTAT
1016842 TAGTTGGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 7 0.22
21 24 0.75
22 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.42
Consensus pattern (20 bp):
AATGAGATTAATATTATAGT
Found at i:1019407 original size:125 final size:124
Alignment explanation
Indices: 1019205--1019430 Score: 364
Period size: 125 Copynumber: 1.8 Consensus size: 124
1019195 CTCAAATATA
* *
1019205 TTTTTGAATCAGTAATTTCCACTTAAAAATTTATCTTCTTTTTTGATGTCTTATCTAACACATTC
1 TTTTTGAATCAATAATTTCCACTTAAAAATTTATCTTCTTTTTTGATATCTTATCTAACACATTC
* *
1019270 AAGTATGGAATATATCATGAAAATAGCCACAATAAACCGTTCAAACATGCTCAAACTTG
66 AAGTATGAAATATATCATGAAAATAGCCAAAATAAACCGTTCAAACATGCTCAAACTTG
* *
1019329 TTTTTGAATCAATAATATTCCACTTAAAATTTTATCTTC-TTTTTGAATATCTTATGTAACACAT
1 TTTTTGAATCAATAAT-TTCCACTTAAAAATTTATCTTCTTTTTTG-ATATCTTATCTAACACAT
*
1019393 TCAAGTATGAAATATATCATGAAAATAGTCAAAATAAA
64 TCAAGTATGAAATATATCATGAAAATAGCCAAAATAAA
1019431 TCGTATAATA
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
124 21 0.23
125 72 0.77
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (124 bp):
TTTTTGAATCAATAATTTCCACTTAAAAATTTATCTTCTTTTTTGATATCTTATCTAACACATTC
AAGTATGAAATATATCATGAAAATAGCCAAAATAAACCGTTCAAACATGCTCAAACTTG
Found at i:1020210 original size:2 final size:2
Alignment explanation
Indices: 1020203--1020237 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1020193 AGGTGTAAAT
1020203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1020238 AACAGGGCTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1021119 original size:2 final size:2
Alignment explanation
Indices: 1021112--1021136 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1021102 CCAATATGAA
1021112 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1021137 AAATATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1023774 original size:31 final size:34
Alignment explanation
Indices: 1023728--1023801 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
1023718 TTATTTGATG
1023728 TTTAAA-AA-AAA-TTAAAT-AAAAAT-ATTTTA
1 TTTAAATAATAAATTTAAATAAAAAATAATTTTA
1023757 TTT-AATAATAAATTTAAATAAAAAATAAATTTTA
1 TTTAAATAATAAATTTAAATAAAAAAT-AATTTTA
1023791 TTTAAATAATA
1 TTTAAATAATA
1023802 GTTAAGTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
28 2 0.05
29 5 0.13
30 3 0.08
31 6 0.16
32 6 0.16
34 9 0.24
35 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
TTTAAATAATAAATTTAAATAAAAAATAATTTTA
Found at i:1023910 original size:23 final size:24
Alignment explanation
Indices: 1023866--1023912 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1023856 ATTATATAAT
*
1023866 ATATTATTTATATATATATAAAAA
1 ATATCATTTATATATATATAAAAA
1023890 ATATCATTTATAT-TATATAAAAA
1 ATATCATTTATATATATATAAAAA
1023913 TAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATCATTTATATATATATAAAAA
Found at i:1023911 original size:22 final size:22
Alignment explanation
Indices: 1023852--1023914 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 22
1023842 TATTTTATTT
* *
1023852 TTTA-ATTATAT-AATATATTA
1 TTTATATTATATAAAAATATCA
1023872 TTTATATATATATAAAAAATATCA
1 TTTATAT-TATAT-AAAAATATCA
1023896 TTTATATTATATAAAAATA
1 TTTATATTATATAAAAATA
1023915 AAAATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 4 0.11
21 2 0.05
22 12 0.32
23 5 0.14
24 14 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTATATTATATAAAAATATCA
Found at i:1024183 original size:26 final size:24
Alignment explanation
Indices: 1024147--1024217 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 24
1024137 AAATATATAT
1024147 TAAATTATTAAAAATTAAATAAAAAA
1 TAAATT-TTAAAAATTAAAT-AAAAA
* *
1024173 TAAATATTTAAATA-TATAATATAAA
1 TAAAT-TTTAAAAATTA-AATAAAAA
*
1024198 TAAATTTAAAAAATTTAAAT
1 TAAATTTTAAAAA-TTAAAT
1024218 GTCATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
24 6 0.16
25 14 0.38
26 16 0.43
27 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAATTTTAAAAATTAAATAAAAA
Found at i:1025184 original size:2 final size:2
Alignment explanation
Indices: 1025177--1025203 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1025167 TAAGAAAAAC
1025177 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 A
1025204 ATTTAAAGGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1026037 original size:23 final size:24
Alignment explanation
Indices: 1026011--1026073 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 24
1026001 ATTAATGTAT
1026011 TTATATATTTTATAAAATTATA-A
1 TTATATATTTTATAAAATTATATA
*
1026034 -T-TATA-TTTAAAATAATTATATA
1 TTATATATTTTATAA-AATTATATA
*
1026056 TTA-ATATTTTATTAAATT
1 TTATATATTTTATAAAATT
1026074 TCTTTTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
20 6 0.19
21 11 0.34
22 2 0.06
23 8 0.25
24 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATATATTTTATAAAATTATATA
Found at i:1026048 original size:15 final size:16
Alignment explanation
Indices: 1026030--1026059 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1026020 TTATAAAATT
1026030 ATAATTATAT-TTAAA
1 ATAATTATATATTAAA
1026045 ATAATTATATATTAA
1 ATAATTATATATTAA
1026060 TATTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTATATATTAAA
Found at i:1026618 original size:18 final size:17
Alignment explanation
Indices: 1026581--1026616 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1026571 CATTAAGGCA
*
1026581 TTATTCTTACATGGTTT
1 TTATTCTTAAATGGTTT
*
1026598 TTATTCTTAAATTGTTT
1 TTATTCTTAAATGGTTT
1026615 TT
1 TT
1026617 TACTCAATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.64
Consensus pattern (17 bp):
TTATTCTTAAATGGTTT
Found at i:1027926 original size:18 final size:20
Alignment explanation
Indices: 1027891--1027952 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
1027881 TATTTTTATA
1027891 TAAATATTTATAATTAAATT
1 TAAATATTTATAATTAAATT
*
1027911 TAAATATTT-T-ATTAAATA
1 TAAATATTTATAATTAAATT
*
1027929 AAAATAATTTA-AATTAAA-T
1 TAAAT-ATTTATAATTAAATT
1027948 TAAAT
1 TAAAT
1027953 CTATAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
18 11 0.31
19 9 0.26
20 15 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATATTTATAATTAAATT
Found at i:1029260 original size:23 final size:25
Alignment explanation
Indices: 1029234--1029301 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 25
1029224 ATGACCTAAA
*
1029234 TAAAATTAAG-T-TAATTTTAAAAT
1 TAAAATTAAGATAAAATTTTAAAAT
1029257 T-AAATT-AGATAAAATTTTAAAAT
1 TAAAATTAAGATAAAATTTTAAAAT
* *
1029280 TAAATTTAA-A-AAAATTATAAAA
1 TAAAATTAAGATAAAATTTTAAAA
1029302 CAAAGTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.05
22 6 0.16
23 24 0.63
24 5 0.13
25 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
TAAAATTAAGATAAAATTTTAAAAT
Found at i:1029498 original size:21 final size:21
Alignment explanation
Indices: 1029474--1029513 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1029464 TATAAAAAAT
1029474 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAAT-TTTATA
1029495 TATTTTATAATTAATTTTA
1 TATTTTATAATTAATTTTA
1029514 ATAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATAATTAATTTTATA
Found at i:1029564 original size:49 final size:49
Alignment explanation
Indices: 1029465--1029556 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 49
1029455 ATTTAAAAAT
* * *
1029465 ATAAAAAATTATTTTATATTAATATTTATATATTTTATAATTAATTTTA
1 ATAAAAAATTATTTTATATTAATATATATATATATTAAAATTAATTTTA
1029514 ATAAAAAA-TATTTT-TATTAA-ATATATA-ATAATTAAAATTAATT
1 ATAAAAAATTATTTTATATTAATATATATATAT-ATTAAAATTAATT
1029557 AAATTAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
45 2 0.05
46 17 0.44
47 6 0.15
48 6 0.15
49 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (49 bp):
ATAAAAAATTATTTTATATTAATATATATATATATTAAAATTAATTTTA
Found at i:1029765 original size:8 final size:8
Alignment explanation
Indices: 1029719--1029822 Score: 51
Period size: 8 Copynumber: 12.9 Consensus size: 8
1029709 CATAACATAA
1029719 ATAT-AAT
1 ATATAAAT
*
1029726 ATA-AAAA
1 ATATAAAT
1029733 AT-TAAAT
1 ATATAAAT
1029740 -TATAATAT
1 ATATAA-AT
*
1029748 AATATTAAT
1 -ATATAAAT
1029757 ATATAAAT
1 ATATAAAT
1029765 ATATTAAA-
1 ATA-TAAAT
*
1029773 ATTTATAA-
1 ATATA-AAT
1029781 ATATAAAT
1 ATATAAAT
1029789 A-ATTAATAT
1 ATA-TAA-AT
*
1029798 ATTTAAATTT
1 ATATAAA--T
1029808 ATATAAAT
1 ATATAAAT
1029816 ATATAAA
1 ATATAAA
1029823 ATAATATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 27
0.68 0.07 0.25
Matches are distributed among these distances:
6 1 0.01
7 18 0.24
8 33 0.44
9 12 0.16
10 11 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:1029780 original size:31 final size:30
Alignment explanation
Indices: 1029745--1029822 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
1029735 TAAATTATAA
1029745 TATAATATTAATATATAAATATATTAAAATT
1 TATAATA-TAATATATAAATATATTAAAATT
* *
1029776 TATAAATATAA-ATAATTAATATATTTAAATT
1 TAT-AATATAATAT-ATAAATATATTAAAATT
1029807 TAT-ATA-AATATATAAA
1 TATAATATAATATATAAA
1029823 ATAATATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 6 0.15
29 5 0.12
30 2 0.05
31 24 0.59
32 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TATAATATAATATATAAATATATTAAAATT
Found at i:1029834 original size:31 final size:31
Alignment explanation
Indices: 1029734--1029836 Score: 93
Period size: 32 Copynumber: 3.2 Consensus size: 31
1029724 ATATAAAAAA
* * * *
1029734 TTAAATTATAATATAATATTAATATATAAATATA
1 TTAAATT-TTATA-AATATAAATA-ATTAATATT
*
1029768 TTAAAATTTATAAATATAAATAATTAATATAT
1 TTAAATTTTATAAATATAAATAATTAATAT-T
1029800 TTAAATTTATATAAATATATAA-AA-TAATATT
1 TTAAATTT-TATAAATATA-AATAATTAATATT
1029831 TTAAAT
1 TTAAAT
1029837 AAATAAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
31 14 0.23
32 22 0.37
33 16 0.27
34 8 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TTAAATTTTATAAATATAAATAATTAATATT
Found at i:1030248 original size:15 final size:16
Alignment explanation
Indices: 1030228--1030257 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1030218 TATTCTGTTA
1030228 TTTTTTTAT-TTTTAT
1 TTTTTTTATCTTTTAT
1030243 TTTTTTTATCTTTTA
1 TTTTTTTATCTTTTA
1030258 CTTATCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTATCTTTTAT
Found at i:1030350 original size:22 final size:22
Alignment explanation
Indices: 1030314--1030379 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1030304 GATACTCATT
1030314 TAATT-TAAATTATTATTATAAA
1 TAATTATAAA-TATTATTATAAA
*
1030336 -AATATATAAATATTAATATAAA
1 TAAT-TATAAATATTATTATAAA
* *
1030358 TAATTTTTAATATTATT-TAAA
1 TAATTATAAATATTATTATAAA
1030379 T
1 T
1030380 TATAAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
21 8 0.22
22 22 0.59
23 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATTATAAATATTATTATAAA
Found at i:1030432 original size:31 final size:32
Alignment explanation
Indices: 1030363--1030439 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 32
1030353 ATAAATAATT
* *
1030363 TTTAATATT-ATTTAAATTATAAAATATGTTAA
1 TTTAAT-TTAATTTAAATTAAAAAATATGTAAA
1030395 TTTAATTTAATTTAAA-TAAAAAATAT-TAAA
1 TTTAATTTAATTTAAATTAAAAAATATGTAAA
1030425 TTATAATTTAATTTA
1 TT-TAATTTAATTTA
1030440 TAAATAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
30 5 0.12
31 23 0.56
32 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
TTTAATTTAATTTAAATTAAAAAATATGTAAA
Found at i:1030442 original size:29 final size:28
Alignment explanation
Indices: 1030372--1030470 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 28
1030362 TTTTAATATT
* *
1030372 ATTTAAATTATAAAATATGTT-AATT-TA
1 ATTTAATTTATAAAAAAT-TTAAATTATA
1030399 ATTTAATTTAAATAAAAAATATTAAATTATA
1 ATTTAATTT--ATAAAAAAT-TTAAATTATA
*
1030430 ATTTAATTTATAAATAATTTATAATTA-A
1 ATTTAATTTATAAAAAATTTA-AATTATA
*
1030458 TATTTATTTTATA
1 -ATTTAATTTATA
1030471 TATAACCATG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
27 8 0.13
28 4 0.07
29 34 0.56
30 4 0.07
31 11 0.18
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATTTAATTTATAAAAAATTTAAATTATA
Found at i:1030618 original size:2 final size:2
Alignment explanation
Indices: 1030606--1030641 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1030596 CATGAAATAA
*
1030606 AT AT GT 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
1030642 TTAAAGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1031207 original size:24 final size:25
Alignment explanation
Indices: 1031149--1031213 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
1031139 TTTAAAACTC
*
1031149 ATTTTATTGA-ATAAAAATATTAAAA
1 ATTTTATT-ATATAAATATATTAAAA
*
1031174 ATTATT-TTATATAAATAT-TTATAA
1 ATT-TTATTATATAAATATATTAAAA
*
1031198 ATTTTATTATTTAAAT
1 ATTTTATTATATAAAT
1031214 TTAGATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 12 0.35
26 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
ATTTTATTATATAAATATATTAAAA
Found at i:1032066 original size:17 final size:18
Alignment explanation
Indices: 1032044--1032100 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1032034 ATTAAGTATT
1032044 TATTTAATAAAAATAT-A
1 TATTTAATAAAAATATAA
1032061 TATTTAATTAAATAATATAA
1 TATTTAA-TAAA-AATATAA
* * *
1032081 TTTTTAATATAAATCTAA
1 TATTTAATAAAAATATAA
1032099 TA
1 TA
1032101 GATTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 7 0.21
18 11 0.33
19 8 0.24
20 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTTAATAAAAATATAA
Found at i:1032949 original size:20 final size:21
Alignment explanation
Indices: 1032905--1032951 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1032895 TAATAAAAAC
*
1032905 TAAAATTATTTTATTAATATCT
1 TAAAATTATATTA-TAATATCT
*
1032927 TAAAATTATATTA-AATATGT
1 TAAAATTATATTATAATATCT
1032947 TAAAA
1 TAAAA
1032952 AAGTTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAAATTATATTATAATATCT
Found at i:1033137 original size:16 final size:16
Alignment explanation
Indices: 1033116--1033156 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1033106 AATTATGAAT
1033116 AATAATATAATAATTA
1 AATAATATAATAATTA
* *
1033132 AATAATAT-GTATTTA
1 AATAATATAATAATTA
1033147 AAT-ATATAAT
1 AATAATATAAT
1033157 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AATAATATAATAATTA
Found at i:1034492 original size:17 final size:18
Alignment explanation
Indices: 1034456--1034493 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1034446 TCCACCAAAG
* *
1034456 TTAAACCCTTAAATCACC
1 TTAAACCCTAAAACCACC
1034474 TTAAA-CCTAAAACCACC
1 TTAAACCCTAAAACCACC
1034491 TTA
1 TTA
1034494 TGTTTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (18 bp):
TTAAACCCTAAAACCACC
Found at i:1038464 original size:32 final size:33
Alignment explanation
Indices: 1038400--1038464 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1038390 TTTCAACGAT
*
1038400 TTGTATCGATACATAAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTATATCGATACA
* *
1038433 TTGTATTGATACAT-AAGTTTTATATCGATACA
1 TTGTATCGATACATAAAGTGTTATATCGATACA
1038465 ATTTAAGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (33 bp):
TTGTATCGATACATAAAGTGTTATATCGATACA
Found at i:1038525 original size:13 final size:13
Alignment explanation
Indices: 1038507--1038534 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1038497 ATTACTCAAA
1038507 TGTATCGATACAT
1 TGTATCGATACAT
1038520 TGTATCGATACAT
1 TGTATCGATACAT
1038533 TG
1 TG
1038535 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1049063 original size:83 final size:80
Alignment explanation
Indices: 1048969--1049185 Score: 220
Period size: 83 Copynumber: 2.6 Consensus size: 80
1048959 AAAAAATATG
* * **
1048969 AACTGAATTTGGTGTCAGTAATCATCTACAAATAAAATGAATGGTTATGTTTTAGTGTCAGTTAC
1 AACTGAATTTGGTATCA-TAATCATCTACAAATAAAAAGAATGACTATGTTTTA-TGTCAGTTAC
***
1049034 ATTAATTATAAAAGTTTA
64 ATTAATTAT-AAAGCACA
* * *
1049052 AACTGAATTTGGTATTACA-AATCATCTACAAATAAAAAAAAATGACTGTGTTTTATGTCATTTA
1 AACTGAATTTGGTA-T-CATAATCATCTACAAAT-AAAAAGAATGACTATGTTTTATGTCAGTTA
* *
1049116 TATTAATTATAAAGCACG
63 CATTAATTATAAAGCACA
* * * *
1049134 AACTAAATTTGGTATCATAAATCATCTACAAATAAAAGGAATAACTAAGTTT
1 AACTGAATTTGGTATCAT-AATCATCTACAAATAAAAAGAATGACTATGTTT
1049186 AGTATCGCAA
Statistics
Matches: 111, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
80 2 0.02
81 15 0.14
82 31 0.28
83 44 0.40
84 17 0.15
85 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (80 bp):
AACTGAATTTGGTATCATAATCATCTACAAATAAAAAGAATGACTATGTTTTATGTCAGTTACAT
TAATTATAAAGCACA
Found at i:1049353 original size:21 final size:21
Alignment explanation
Indices: 1049329--1049404 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
1049319 TAACTTCTCA
*
1049329 AAAAACTAACCACTTATTTTT
1 AAAAACTAACCATTTATTTTT
*
1049350 AAAAA-TGACCAATTTATTTTT
1 AAAAACTAACC-ATTTATTTTT
* * * *
1049371 CAAAACTATCTATTTATTCTTA
1 AAAAACTAACCATTTATT-TTT
1049393 AAAAACT-ACCAT
1 AAAAACTAACCAT
1049405 ATAAAATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
20 4 0.10
21 28 0.67
22 10 0.24
ACGTcount: A:0.43, C:0.17, G:0.01, T:0.38
Consensus pattern (21 bp):
AAAAACTAACCATTTATTTTT
Found at i:1052178 original size:246 final size:250
Alignment explanation
Indices: 1051730--1052234 Score: 892
Period size: 246 Copynumber: 2.0 Consensus size: 250
1051720 CCAATACATA
* *
1051730 AATAGGTCTAACAAAATTGAGTTCTTAACTTGAATACAAGGGTTAAGATTCAAATCTTATTATTT
1 AATAGGTCTAACAAAATTGAGTTCTTAACCTGAATACAAAGGTTAAGATTCAAATCTTATTATTT
1051795 GCTAAAAAATAAAGAAAAAATTGGTTCAATATCAAACTGATTCAATTTAATTTGATTTAATTAAA
66 GCT----AATAAAGAAAAAATTGGTTCAATATCAAACTGATTCAATTTAATTTGATTTAATTAAA
*
1051860 TGTTTGATAGATTCGAAATTAACTTAACTATTTTTTCAATGATTTAGTATATATTTATAAAAAAT
127 TGTTTGATAGATTCGAAATTAACTTAACTATTTATTCAATGATTTAGTATATATTTATAAAAAAT
*
1051925 ATGAGATAAAAAGAAACAAAACTCTAAGTTATATACTTGAACATTCTATTATCCTTATT
192 ATGAGATAAAAAGAAACAAAACTCTAAGTTATATACTTGAACATTCTATCATCCTTATT
*
1051984 AATAGGTCTACCAAAATTGAGTTCTTAACCTGAATACAAAGGTTAAGATTCAAATCTTATTATTT
1 AATAGGTCTAACAAAATTGAGTTCTTAACCTGAATACAAAGGTTAAGATTCAAATCTTATTATTT
*
1052049 GCT-A-AAA-AAAAAATTTGTTCAATATCAAACTGATTCAATTTAATTTGATTTAATTAAA-GTT
66 GCTAATAAAGAAAAAATTGGTTCAATATCAAACTGATTCAATTTAATTTGATTTAATTAAATGTT
1052110 TGATAGATTCGAAATTAACTTAACTATTTATTCAATGATTTAGTATATATTTATAAAAAATATGA
131 TGATAGATTCGAAATTAACTTAACTATTTATTCAATGATTTAGTATATATTTATAAAAAATATGA
1052175 GATAAAAAGAAACAAAACTCTAAGTTATATACTTGAACATTCTATCATCCTTATT
196 GATAAAAAGAAACAAAACTCTAAGTTATATACTTGAACATTCTATCATCCTTATT
1052230 AATAG
1 AATAG
1052235 CCTCATTATT
Statistics
Matches: 245, Mismatches: 6, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
246 126 0.51
247 50 0.20
248 3 0.01
249 1 0.00
254 65 0.27
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (250 bp):
AATAGGTCTAACAAAATTGAGTTCTTAACCTGAATACAAAGGTTAAGATTCAAATCTTATTATTT
GCTAATAAAGAAAAAATTGGTTCAATATCAAACTGATTCAATTTAATTTGATTTAATTAAATGTT
TGATAGATTCGAAATTAACTTAACTATTTATTCAATGATTTAGTATATATTTATAAAAAATATGA
GATAAAAAGAAACAAAACTCTAAGTTATATACTTGAACATTCTATCATCCTTATT
Found at i:1053022 original size:26 final size:26
Alignment explanation
Indices: 1052986--1053044 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
1052976 CAAAATCTAG
* * *
1052986 AATCTTAAATAAAGTTGAATTTTATT
1 AATCCTAAATAAAGTTGAACTTTATC
1053012 AATCCTAAATAAAGTTGAACTTTATC
1 AATCCTAAATAAAGTTGAACTTTATC
1053038 AATCCTA
1 AATCCTA
1053045 TTTCTATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (26 bp):
AATCCTAAATAAAGTTGAACTTTATC
Found at i:1058715 original size:19 final size:19
Alignment explanation
Indices: 1058647--1058707 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1058637 GATTCGAAAT
* *
1058647 TATTTAAAAATTTATTTTA
1 TATTAAAAAATATATTTTA
*
1058666 TTATT-TAAAATA-A-TTTA
1 -TATTAAAAAATATATTTTA
1058683 TATTAAAAAATATATTTTA
1 TATTAAAAAATATATTTTA
1058702 TATTAA
1 TATTAA
1058708 TATTTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 4 0.11
17 10 0.29
18 2 0.06
19 15 0.43
20 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTAAAAAATATATTTTA
Found at i:1058719 original size:41 final size:41
Alignment explanation
Indices: 1058657--1058740 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
1058647 TATTTAAAAA
* * *
1058657 TTTATTTTATTATTTAAAATAATTTATATTAAAAAATA-TAT
1 TTTATATTAATATTTAAAATAACTTA-ATTAAAAAATATTAT
* *
1058698 TTTATATTAATATTTATAATAACTTAATTAAAAATTATTAT
1 TTTATATTAATATTTAAAATAACTTAATTAAAAAATATTAT
1058739 TT
1 TT
1058741 AAATAATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 10 0.27
41 27 0.73
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (41 bp):
TTTATATTAATATTTAAAATAACTTAATTAAAAAATATTAT
Found at i:1059353 original size:2 final size:2
Alignment explanation
Indices: 1059348--1059372 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1059338 TTTTTAATTT
1059348 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 T
1059373 CAGCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1060039 original size:14 final size:14
Alignment explanation
Indices: 1060020--1060077 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
1060010 TGAATAATTC
1060020 TTTTAAATACATT-A
1 TTTTAAATA-ATTAA
*
1060034 TTTTAATTAATTAA
1 TTTTAAATAATTAA
*
1060048 TTTTAAATTAATT-T
1 TTTTAAA-TAATTAA
1060062 TTATTAAATAA-TAA
1 TT-TTAAATAATTAA
1060076 TT
1 TT
1060078 ATTGATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 4 0.11
14 22 0.61
15 10 0.28
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAATAATTAA
Found at i:1060076 original size:28 final size:28
Alignment explanation
Indices: 1060012--1060077 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
1060002 TGAACGTATG
*
1060012 AATAATT-CTTTTAAATACATTATTTTA
1 AATAATTAATTTTAAATACATTATTTTA
* *
1060039 ATTAATTAATTTTAAATTA-ATTTTTATTA
1 AATAATTAATTTTAAA-TACATTATT-TTA
1060068 AATAA-TAATT
1 AATAATTAATT
1060078 ATTGATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 6 0.19
28 17 0.53
29 9 0.28
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (28 bp):
AATAATTAATTTTAAATACATTATTTTA
Found at i:1060618 original size:13 final size:12
Alignment explanation
Indices: 1060585--1060625 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
1060575 TAAAAATTTT
1060585 AAATACATAAAAA
1 AAATACA-AAAAA
*
1060598 AAACACAAAAATA
1 AAATACAAAAA-A
1060611 AAATACAAAAAA
1 AAATACAAAAAA
1060623 AAA
1 AAA
1060626 CTTAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (12 bp):
AAATACAAAAAA
Found at i:1061039 original size:12 final size:13
Alignment explanation
Indices: 1061014--1061043 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1061004 ATAAAATAAA
1061014 TAAAATTATTTTT
1 TAAAATTATTTTT
1061027 TAAAATT-TTTTT
1 TAAAATTATTTTT
1061039 TAAAA
1 TAAAA
1061044 GGGTTGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TAAAATTATTTTT
Found at i:1061381 original size:23 final size:24
Alignment explanation
Indices: 1061334--1061382 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 24
1061324 ATATATTATT
1061334 TAAAAATAAAATAAATTAAAAAATA
1 TAAAAAT-AAATAAATTAAAAAATA
1061359 TAAAAAT-AATAAA-TAAAATAATA
1 TAAAAATAAATAAATTAAAA-AATA
1061382 T
1 T
1061383 TTTTCTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.22
23 11 0.48
25 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAAATAAATAAATTAAAAAATA
Found at i:1062086 original size:14 final size:14
Alignment explanation
Indices: 1062067--1062093 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1062057 AATTAATAAA
1062067 ATTATTATTTTTAC
1 ATTATTATTTTTAC
1062081 ATTATTATTTTTA
1 ATTATTATTTTTA
1062094 TATATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTATTTTTAC
Found at i:1065021 original size:2 final size:2
Alignment explanation
Indices: 1064965--1065010 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1064955 ACCATTTTTC
*
1064965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1065007 AT AT
1 AT AT
1065011 TACGTATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1067978 original size:22 final size:22
Alignment explanation
Indices: 1067913--1067979 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
1067903 GTATTTGATG
* *
1067913 AATTTTTTTTGAAAATAT-TTA
1 AATTTTATTTGAAAATATATTT
* ** *
1067934 AATATTTGATATGTGAATTTATTT
1 AAT-TTT-ATTTGAAAATATATTT
1067958 AATTTTATTTGAAAATATATTT
1 AATTTTATTTGAAAATATATTT
1067980 TATATATTAA
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
21 3 0.09
22 15 0.45
23 10 0.30
24 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
AATTTTATTTGAAAATATATTT
Found at i:1068745 original size:28 final size:29
Alignment explanation
Indices: 1068682--1068745 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
1068672 CAACAAATAA
1068682 TTAAATTTAATCTTAAAAAAAAAATTAAT
1 TTAAATTTAATCTTAAAAAAAAAATTAAT
* *
1068711 TTCAAATTT-A-CTTAAAAGAAAACTTAAT
1 TT-AAATTTAATCTTAAAAAAAAAATTAAT
1068739 CTTAAAT
1 -TTAAAT
1068746 AAAATGGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 20 0.65
29 5 0.16
30 6 0.19
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (29 bp):
TTAAATTTAATCTTAAAAAAAAAATTAAT
Found at i:1069097 original size:21 final size:21
Alignment explanation
Indices: 1069047--1069098 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1069037 GTCAATAACA
* *
1069047 AATTAA-TTTCTTGGAATTTT
1 AATTAATTTTTTTGAAATTTT
*
1069067 AATCT-TTTTTTTTGAAATTTT
1 AAT-TAATTTTTTTGAAATTTT
1069088 AATTAATTTTT
1 AATTAATTTTT
1069099 CTCTTTCTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (21 bp):
AATTAATTTTTTTGAAATTTT
Found at i:1069226 original size:22 final size:22
Alignment explanation
Indices: 1069161--1069226 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
1069151 ATTTTTTTCA
* *
1069161 TAAATATAACTTTAATAGTTTT
1 TAAATATAATTTTAATAATTTT
* * * *
1069183 TAATTATTATATT--TAA-CTT
1 TAAATATAATTTTAATAATTTT
1069202 TAAATATAATTTTAATAATTTT
1 TAAATATAATTTTAATAATTTT
1069224 TAA
1 TAA
1069227 TAAATAAATA
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
19 12 0.39
20 2 0.06
21 3 0.10
22 14 0.45
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAATATAATTTTAATAATTTT
Found at i:1069793 original size:21 final size:21
Alignment explanation
Indices: 1069769--1069808 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1069759 ATTTTTTATT
1069769 TAAAT-TTAATAATAAAATATA
1 TAAATATTAAT-ATAAAATATA
1069790 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
1069809 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:1072580 original size:15 final size:15
Alignment explanation
Indices: 1072560--1072674 Score: 112
Period size: 15 Copynumber: 7.9 Consensus size: 15
1072550 CTTGCGTCTC
1072560 TTTGGGCATGCTGCT
1 TTTGGGCATGCTGCT
*
1072575 TTTGGGCATG-T-CAC
1 TTTGGGCATGCTGC-T
*
1072589 TTTGGGCATGCCGCT
1 TTTGGGCATGCTGCT
* *
1072604 TTTAGGCATGCCGC-
1 TTTGGGCATGCTGCT
*
1072618 TTTGGGCATGTTGCT
1 TTTGGGCATGCTGCT
* *
1072633 TTTAGGCATGCCGC-
1 TTTGGGCATGCTGCT
*
1072647 TTTGGGCATGTTGCT
1 TTTGGGCATGCTGCT
*
1072662 TTTAGGCATGCTG
1 TTTGGGCATGCTG
1072675 GTATTGTCTT
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
13 1 0.01
14 33 0.41
15 45 0.56
16 1 0.01
ACGTcount: A:0.10, C:0.21, G:0.31, T:0.37
Consensus pattern (15 bp):
TTTGGGCATGCTGCT
Found at i:1072591 original size:29 final size:29
Alignment explanation
Indices: 1072559--1072672 Score: 174
Period size: 29 Copynumber: 3.9 Consensus size: 29
1072549 TCTTGCGTCT
* * *
1072559 CTTTGGGCATGCTGCTTTTGGGCATGTCA
1 CTTTGGGCATGCTGCTTTTAGGCATGCCG
*
1072588 CTTTGGGCATGCCGCTTTTAGGCATGCCG
1 CTTTGGGCATGCTGCTTTTAGGCATGCCG
*
1072617 CTTTGGGCATGTTGCTTTTAGGCATGCCG
1 CTTTGGGCATGCTGCTTTTAGGCATGCCG
*
1072646 CTTTGGGCATGTTGCTTTTAGGCATGC
1 CTTTGGGCATGCTGCTTTTAGGCATGC
1072673 TGGTATTGTC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 79 1.00
ACGTcount: A:0.11, C:0.22, G:0.31, T:0.37
Consensus pattern (29 bp):
CTTTGGGCATGCTGCTTTTAGGCATGCCG
Found at i:1072900 original size:16 final size:16
Alignment explanation
Indices: 1072879--1072924 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
1072869 CCTTAGCAAA
*
1072879 AGCGCTACCTGGCAGT
1 AGCGCTACCTAGCAGT
1072895 AGCGCTACCTAGCAGT
1 AGCGCTACCTAGCAGT
1072911 AGCGCTACCTAGCA
1 AGCGCTACCTAGCA
1072925 TGATGCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (16 bp):
AGCGCTACCTAGCAGT
Found at i:1072956 original size:34 final size:34
Alignment explanation
Indices: 1072913--1072977 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
1072903 CTAGCAGTAG
1072913 CGCTACCTAGCATGATGCTATTTAGCTCACCCAA
1 CGCTACCTAGCATGATGCTATTTAGCTCACCCAA
1072947 CGCTACCTAGCATGATGCTATTTAGCTCACC
1 CGCTACCTAGCATGATGCTATTTAGCTCACC
1072978 ACTTTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (34 bp):
CGCTACCTAGCATGATGCTATTTAGCTCACCCAA
Found at i:1080361 original size:38 final size:38
Alignment explanation
Indices: 1080319--1080398 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
1080309 TAATCTCTTG
*
1080319 ATTTGAGGGATTTCAAATAATTTACAGATTCTAACTAC
1 ATTTGAGGGATTTCAAATAATCTACAGATTCTAACTAC
1080357 ATTTGAGGGATTTCAAATAATCTACAGATTCTAACTAC
1 ATTTGAGGGATTTCAAATAATCTACAGATTCTAACTAC
1080395 ATTT
1 ATTT
1080399 TAGGATCAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (38 bp):
ATTTGAGGGATTTCAAATAATCTACAGATTCTAACTAC
Found at i:1083330 original size:193 final size:193
Alignment explanation
Indices: 1083001--1083383 Score: 730
Period size: 193 Copynumber: 2.0 Consensus size: 193
1082991 ATTCACATCA
1083001 GATTTGTGTTTTAACAGAAAAATCCAAGTGACCTTAGTACAATCATCAATAAATGACACAAACCA
1 GATTTGTGTTTTAACAGAAAAATCCAAGTGACCTTAGTACAATCATCAATAAATGACACAAACCA
1083066 TCTAGAACCGGTCACATTAGGCACTGTAGAAGGTCCCTAAATATCACTATAAATCAGCTGAAAAG
66 TCTAGAACCGGTCACATTAGGCACTGTAGAAGGTCCCTAAATATCACTATAAATCAGCTGAAAAG
*
1083131 GTTTTGATGTTTCTTTTATTGCTAATAGGGAAAGACATTCGTTTATGTTTAGCAAACTCAGCT
131 GTTTTGATGTTTCTTTTATTGCTAATAGAGAAAGACATTCGTTTATGTTTAGCAAACTCAGCT
*
1083194 GATTTGTGTTTTAACAGAAAAATCCAAGTGACCTTAGTACGATCATCAATAAATGACACAAACCA
1 GATTTGTGTTTTAACAGAAAAATCCAAGTGACCTTAGTACAATCATCAATAAATGACACAAACCA
1083259 TCTAGAACCGGTCACATTAGGCACTGTAGAAGGTCCCTAAATATCACTATAAATCAGCTGAAAAG
66 TCTAGAACCGGTCACATTAGGCACTGTAGAAGGTCCCTAAATATCACTATAAATCAGCTGAAAAG
* *
1083324 GTTTTGATTTTTTTTTTATTGCTAATAGAGAAAGACATTCGTTTATGTTTAGCAAACTCA
131 GTTTTGATGTTTCTTTTATTGCTAATAGAGAAAGACATTCGTTTATGTTTAGCAAACTCA
1083384 CACACATCAC
Statistics
Matches: 186, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 186 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (193 bp):
GATTTGTGTTTTAACAGAAAAATCCAAGTGACCTTAGTACAATCATCAATAAATGACACAAACCA
TCTAGAACCGGTCACATTAGGCACTGTAGAAGGTCCCTAAATATCACTATAAATCAGCTGAAAAG
GTTTTGATGTTTCTTTTATTGCTAATAGAGAAAGACATTCGTTTATGTTTAGCAAACTCAGCT
Found at i:1084203 original size:14 final size:15
Alignment explanation
Indices: 1084170--1084208 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1084160 TTTCCAACAT
*
1084170 TTTTCTCTGGTATGCC
1 TTTT-TCTGTTATGCC
1084186 TTTTTCTGTTAT-CC
1 TTTTTCTGTTATGCC
1084200 TTTTTCTGT
1 TTTTTCTGT
1084209 AAATCTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 7 0.32
16 4 0.18
ACGTcount: A:0.05, C:0.21, G:0.13, T:0.62
Consensus pattern (15 bp):
TTTTTCTGTTATGCC
Found at i:1089852 original size:33 final size:33
Alignment explanation
Indices: 1089810--1089876 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
1089800 AATAGGTGGG
1089810 TAGGACTTAGGAGTGTAT-TTATTTGGTTAAGTT
1 TAGGACTTAGGAGTGTATGTT-TTTGGTTAAGTT
1089843 TAGGACTTAGGAGTGTATGTTTTTGGTTAAGTT
1 TAGGACTTAGGAGTGTATGTTTTTGGTTAAGTT
1089876 T
1 T
1089877 GAGCTTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.46
Consensus pattern (33 bp):
TAGGACTTAGGAGTGTATGTTTTTGGTTAAGTT
Found at i:1092227 original size:19 final size:19
Alignment explanation
Indices: 1092203--1092241 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1092193 TTACCAAAAG
1092203 ACATGATCTAACTACTAAC
1 ACATGATCTAACTACTAAC
1092222 ACATGATCTAACTACTAAC
1 ACATGATCTAACTACTAAC
1092241 A
1 A
1092242 AATAGTACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (19 bp):
ACATGATCTAACTACTAAC
Found at i:1094514 original size:22 final size:22
Alignment explanation
Indices: 1094467--1094514 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1094457 AAATAAATCT
* *
1094467 TTAACATAAACTAATCTTTTAT
1 TTAACATAAACTAATCATTTAA
*
1094489 TTAACATAAACT-ATGATTTAGA
1 TTAACATAAACTAATCATTTA-A
1094511 TTAA
1 TTAA
1094515 AGTTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (22 bp):
TTAACATAAACTAATCATTTAA
Found at i:1097560 original size:2 final size:2
Alignment explanation
Indices: 1097553--1097583 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1097543 AATAAAAAGA
1097553 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1097584 AAGGAAAGTA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1099723 original size:24 final size:24
Alignment explanation
Indices: 1099696--1099741 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1099686 AAATTAATAT
*
1099696 AATAAATATGATATGATATATTTA
1 AATAAATATAATATGATATATTTA
* *
1099720 AATATATTTAATATGATATATT
1 AATAAATATAATATGATATATT
1099742 ATATTTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (24 bp):
AATAAATATAATATGATATATTTA
Found at i:1099751 original size:6 final size:6
Alignment explanation
Indices: 1099722--1099766 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
1099712 TATATTTAAA
*
1099722 TATATT TA-ATAT GATATAT TATATT TATATT TATATT TATATT TA
1 TATATT TATAT-T TATAT-T TATATT TATATT TATATT TATATT TA
1099767 AAATTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 2 0.06
6 25 0.71
7 8 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:1099757 original size:24 final size:24
Alignment explanation
Indices: 1099706--1099768 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1099696 AATAAATATG
1099706 ATATGATATATTTAAATATATTTA
1 ATATGATATATTTAAATATATTTA
**
1099730 ATATGATATATTATATTTATATTT-
1 ATATGATATATT-TAAATATATTTA
*
1099754 ATAT-TTATATTTAAA
1 ATATGATATATTTAAA
1099769 ATTAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 2 0.06
23 6 0.18
24 16 0.48
25 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
ATATGATATATTTAAATATATTTA
Found at i:1099760 original size:31 final size:29
Alignment explanation
Indices: 1099691--1099748 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1099681 ATATAAAATT
* *
1099691 AATATAATAAATATGATATGATATATTTA
1 AATATATTTAATATGATATGATATATTTA
1099720 AATATATTTAATATGATAT-ATTATATTTA
1 AATATATTTAATATGATATGA-TATATTTA
1099749 TATTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (29 bp):
AATATATTTAATATGATATGATATATTTA
Found at i:1100125 original size:3 final size:3
Alignment explanation
Indices: 1100119--1100153 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1100109 TTACACTATA
1100119 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1100154 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1102202 original size:13 final size:13
Alignment explanation
Indices: 1102184--1102208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1102174 CATAAAGTGT
1102184 TGTATCGATACAA
1 TGTATCGATACAA
1102197 TGTATCGATACA
1 TGTATCGATACA
1102209 TATTTTTTTG
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:1102206 original size:33 final size:33
Alignment explanation
Indices: 1102164--1102230 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1102154 TTCAACGATT
1102164 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1102197 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1102230 T
1 T
1102231 TCAAGCTACT
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:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1102360 original size:52 final size:52
Alignment explanation
Indices: 1102304--1102432 Score: 188
Period size: 52 Copynumber: 2.5 Consensus size: 52
1102294 CACTGATCTT
* *
1102304 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCACATGTATCGATACACTATAAAA
* **
1102356 TGTATCGATACATGCAGG-AAACTTTTCCCACATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAA-TTTGCCCACATGTATCGATACACTATAAAA
*
1102408 TGTATCGATACATGCAAGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1102433 TCATATTTCG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
51 3 0.04
52 63 0.91
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCACATGTATCGATACACTATAAAA
Found at i:1107449 original size:21 final size:21
Alignment explanation
Indices: 1107425--1107475 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1107415 TTCCAAGCAA
1107425 GAAATCAAGAACAAGAAATGC
1 GAAATCAAGAACAAGAAATGC
1107446 GAAATCAAGAACAAGAAATGC
1 GAAATCAAGAACAAGAAATGC
*
1107467 AAAATCAAG
1 GAAATCAAG
1107476 CTTATTTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.59, C:0.14, G:0.18, T:0.10
Consensus pattern (21 bp):
GAAATCAAGAACAAGAAATGC
Found at i:1112015 original size:16 final size:15
Alignment explanation
Indices: 1111994--1112027 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1111984 AACATAGATT
1111994 AAATAAATAAAATAAA
1 AAAT-AATAAAATAAA
*
1112010 AAATAATCAAATAAA
1 AAATAATAAAATAAA
1112025 AAA
1 AAA
1112028 AAGACAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAATAAAATAAA
Found at i:1112036 original size:19 final size:20
Alignment explanation
Indices: 1111998--1112039 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1111988 TAGATTAAAT
*
1111998 AAATAAAATAAAAAATAATC
1 AAATAAAATAAAAAACAATC
*
1112018 AAATAAAA-AAAAGACAATC
1 AAATAAAATAAAAAACAATC
1112037 AAA
1 AAA
1112040 CTTACTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (20 bp):
AAATAAAATAAAAAACAATC
Found at i:1112215 original size:15 final size:15
Alignment explanation
Indices: 1112195--1112238 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1112185 AATATAATTC
*
1112195 TAATATTATAATATA
1 TAATATTATAATAAA
*
1112210 TAATATGATAATAAA
1 TAATATTATAATAAA
*
1112225 TAATTATTCTAATA
1 TAA-TATTATAATA
1112239 GCTATTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TAATATTATAATAAA
Found at i:1113939 original size:112 final size:114
Alignment explanation
Indices: 1113771--1113993 Score: 315
Period size: 112 Copynumber: 2.0 Consensus size: 114
1113761 ACATTTAATT
* *
1113771 TTTTAATTTATTAAATAAAGTAGTTTTTCCTTGCGTAAATAATGAATTAATTGATAATAATTTAA
1 TTTTAATTTATTAAATAAAGTAGTTTTT-CTTACGTAAATAATAAATTAATTGATAATAATTTAA
*
1113836 ATAATAACTTAATTTCAAAAACCTCTATAATGAATTCTGTTTTAAATTTA
65 ATAATAACTTAATTTCAAAAACCTCTATAATAAATTCTGTTTTAAATTTA
* * * *
1113886 TTTTACTTTGTTAAATAAAGTA-TTTTT-TTATGTAAATAATAAATTAATTGATAATAATTTAAG
1 TTTTAATTTATTAAATAAAGTAGTTTTTCTTACGTAAATAATAAATTAATTGATAATAATTTAAA
* * * * *
1113949 TAATAACTTAGTTTCAAAAACTTTTATAATAAATTTTTTTTTAAA
66 TAATAACTTAATTTCAAAAACCTCTATAATAAATTCTGTTTTAAA
1113994 ATCTATTAGA
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
112 71 0.74
114 5 0.05
115 20 0.21
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (114 bp):
TTTTAATTTATTAAATAAAGTAGTTTTTCTTACGTAAATAATAAATTAATTGATAATAATTTAAA
TAATAACTTAATTTCAAAAACCTCTATAATAAATTCTGTTTTAAATTTA
Found at i:1116426 original size:6 final size:6
Alignment explanation
Indices: 1116411--1116439 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1116401 GATATCAAAT
1116411 AATA-A AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA
1116440 TTTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:1122936 original size:2 final size:2
Alignment explanation
Indices: 1122931--1123008 Score: 111
Period size: 2 Copynumber: 39.0 Consensus size: 2
1122921 TCACACATGA
* * * *
1122931 AT AT AT AT AT AT AT AT AT TT AC AT AT AT AT AT AT AT AT TT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1122973 AT AT AT AT AT AT AT AT AT AT TT 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
1123009 TTAAAGTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1122956 original size:20 final size:20
Alignment explanation
Indices: 1122933--1123011 Score: 131
Period size: 20 Copynumber: 4.0 Consensus size: 20
1122923 ACACATGAAT
1122933 ATATATATATATATATTTAC
1 ATATATATATATATATTTAC
1122953 ATATATATATATATATTTAC
1 ATATATATATATATATTTAC
* *
1122973 ATATATATATATATATATAT
1 ATATATATATATATATTTAC
*
1122993 TTATATATATATATATTTA
1 ATATATATATATATATTTA
1123012 AAGTTTTGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATATATATATATATTTAC
Found at i:1125984 original size:18 final size:18
Alignment explanation
Indices: 1125958--1125992 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1125948 CAAAGAATAA
*
1125958 AAAGCAAAAGGAAAAAAG
1 AAAGAAAAAGGAAAAAAG
1125976 AAAGAAAAAGGAAAAAA
1 AAAGAAAAAGGAAAAAA
1125993 AAGGAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGGAAAAAAG
Found at i:1125994 original size:20 final size:20
Alignment explanation
Indices: 1125969--1126013 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1125959 AAGCAAAAGG
1125969 AAAAAAGAAAGAAAAAG-GAA
1 AAAAAAGAAA-AAAAAGAGAA
* *
1125989 AAAAAAGGAAAACAAGAGAA
1 AAAAAAGAAAAAAAAGAGAA
1126009 AAAAA
1 AAAAA
1126014 TCATCCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAGAGAA
Found at i:1130423 original size:25 final size:25
Alignment explanation
Indices: 1130386--1130433 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1130376 CATTTTAAGA
*
1130386 TCATTTTAATAATTTGTCATGATAG
1 TCATTTTAATAATTTATCATGATAG
*
1130411 TCATTTTAGTAATTTATCATGAT
1 TCATTTTAATAATTTATCATGAT
1130434 TTAGGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (25 bp):
TCATTTTAATAATTTATCATGATAG
Found at i:1130648 original size:54 final size:54
Alignment explanation
Indices: 1130547--1130649 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
1130537 CATTTCATGC
** ** *
1130547 ATTTTAATATTATTTAGGTCATTTTTCATGATCTGGAGACTTAGATGCAATTAA
1 ATTTTAATACCATTTAGGTCATTTACCATGATCTAGAGACTTAGATGCAATTAA
* *
1130601 ATTTTAATACCATTTAGGTCATTTACCATGATTTA-AGAACTTGGATGCA
1 ATTTTAATACCATTTAGGTCATTTACCATGATCTAGAG-ACTTAGATGCA
1130650 TTTTGTGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 2 0.05
54 39 0.95
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (54 bp):
ATTTTAATACCATTTAGGTCATTTACCATGATCTAGAGACTTAGATGCAATTAA
Found at i:1132648 original size:2 final size:2
Alignment explanation
Indices: 1132641--1132671 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1132631 TATCAAAATT
1132641 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
1132672 GTGTGTGTGT
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:1133205 original size:16 final size:16
Alignment explanation
Indices: 1133163--1133268 Score: 88
Period size: 16 Copynumber: 6.4 Consensus size: 16
1133153 TTGAAATTAA
* *
1133163 ATTTTGAATTTCAATT
1 ATTTTAAATTTAAATT
1133179 ATTTTTTAAATTTAAATT
1 A--TTTTAAATTTAAATT
* *
1133197 ATATTAAATTTAAATA
1 ATTTTAAATTTAAATT
* *
1133213 ATTTTTTATTTTAAATT
1 A-TTTTAAATTTAAATT
*
1133230 ATTTTAAATTTAATTT
1 ATTTTAAATTTAAATT
* *
1133246 ATTTTCAA-TTCAATT
1 ATTTTAAATTTAAATT
1133261 ATTCTTAA
1 ATT-TTAA
1133269 GTTAATCAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
15 8 0.11
16 37 0.52
17 12 0.17
18 14 0.20
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:1133240 original size:33 final size:34
Alignment explanation
Indices: 1133163--1133242 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
1133153 TTGAAATTAA
* * *
1133163 ATTTTGAATTTCAATTATTTTTTAAATTTAAATT
1 ATTTTAAATTTAAATAATTTTTTAAATTTAAATT
* *
1133197 ATATTAAATTTAAATAATTTTTT-ATTTTAAATT
1 ATTTTAAATTTAAATAATTTTTTAAATTTAAATT
1133230 ATTTTAAATTTAA
1 ATTTTAAATTTAA
1133243 TTTATTTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 21 0.52
34 19 0.47
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (34 bp):
ATTTTAAATTTAAATAATTTTTTAAATTTAAATT
Found at i:1133321 original size:15 final size:15
Alignment explanation
Indices: 1133301--1133356 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
1133291 AAATTAAAAT
1133301 TTTTAAATTGATTAA
1 TTTTAAATTGATTAA
* **
1133316 TTTTAAATTAAATCGA
1 TTTTAAATT-GATTAA
*
1133332 TCTTATAATTGATTAA
1 TTTTA-AATTGATTAA
1133348 TTTTAAATT
1 TTTTAAATT
1133357 AAATCGATCT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 13 0.42
16 14 0.45
17 4 0.13
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (15 bp):
TTTTAAATTGATTAA
Done.