Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008005.1 Hibiscus syriacus cultivar Beakdansim tig00110467_pilon, whole genome shotgun sequence
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: 1778185
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 4 of 7
Found at i:924262 original size:23 final size:23
Alignment explanation
Indices: 924228--924314 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
924218 CATTGTTATA
* * *
924228 TGGCACTACGGTGTAATTCTAAG
1 TGGCACTCCGGTGCAATTCTACG
*
924251 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
*
924274 TGGTACTCCGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
**
924297 TGGCACTTAGGTGCAATT
1 TGGCACTCCGGTGCAATT
924315 ATATGAGATG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTACG
Found at i:930669 original size:14 final size:13
Alignment explanation
Indices: 930635--930700 Score: 61
Period size: 12 Copynumber: 5.3 Consensus size: 13
930625 TACATATATA
930635 TATT-TATTTTAT
1 TATTATATTTTAT
*
930647 TATTATATTTTCT
1 TATTATATTTTAT
*
930660 TATGTATATTTTTT
1 TAT-TATATTTTAT
930674 TA-TAT-TTTTACT
1 TATTATATTTTA-T
930686 TA-T-TATTTTAT
1 TATTATATTTTAT
930697 TATT
1 TATT
930701 CAATATTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
11 8 0.17
12 17 0.37
13 10 0.22
14 11 0.24
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (13 bp):
TATTATATTTTAT
Found at i:930921 original size:27 final size:25
Alignment explanation
Indices: 930875--930936 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
930865 CTTTTTTTTA
*
930875 ATATTATATTTTATTATTACATATT
1 ATATTATATTTAATTATTACATATT
* *
930900 ATATATATATTTAATTTTTTACCTATT
1 ATAT-TATATTTAA-TTATTACATATT
930927 -TATTATATTT
1 ATATTATATTT
930937 CTCTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.34
26 11 0.34
27 10 0.31
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (25 bp):
ATATTATATTTAATTATTACATATT
Found at i:931050 original size:26 final size:26
Alignment explanation
Indices: 931013--931077 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
931003 TATATATATT
931013 TTATTTTATTATTATATCTTT-CTTA
1 TTATTTTATTATTATATCTTTACTTA
*
931038 TGTATATTT-TTATTATATTTTTACTTA
1 T-TAT-TTTATTATTATATCTTTACTTA
931065 TTATTTTATTATT
1 TTATTTTATTATT
931078 CAATATTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
25 4 0.11
26 23 0.66
27 8 0.23
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (26 bp):
TTATTTTATTATTATATCTTTACTTA
Found at i:931053 original size:15 final size:14
Alignment explanation
Indices: 931016--931107 Score: 52
Period size: 15 Copynumber: 6.5 Consensus size: 14
931006 ATATATTTTA
931016 TTTTATTATTATAT
1 TTTTATTATTATAT
* *
931030 CTTTCTTATGTATA-
1 TTTTATTAT-TATAT
931044 -TTT-TTATTATAT
1 TTTTATTATTATAT
931056 TTTTACTTA-T-TA-
1 TTTTA-TTATTATAT
931068 TTTTATTATTCAATAT
1 TTTTATTATT--ATAT
931084 TTGGTTATTATGTATAT
1 TT--TTATTAT-TATAT
*
931101 ATTTATT
1 TTTTATT
931108 CGTTTTTTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 25
0.69 0.03 0.28
Matches are distributed among these distances:
11 7 0.11
12 10 0.16
13 8 0.13
14 8 0.13
15 14 0.23
16 2 0.03
17 5 0.08
18 7 0.11
19 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (14 bp):
TTTTATTATTATAT
Found at i:931166 original size:377 final size:373
Alignment explanation
Indices: 930489--931238 Score: 1437
Period size: 377 Copynumber: 2.0 Consensus size: 373
930479 TTTTTATTTG
*
930489 ATTCTTTTTTTAATATTATATTATATTATTACATATTATATATATATTTAATTTTTTATCTATTT
1 ATTCTTTTTTTAATATTATATTATATTATTACATATTATATATATATTTAATTTTTTACCTATTT
*
930554 ATTATATTTCTCTATTATTGATCTTTTATCTTTTATGTTATATTATATTATATTTTTTGTTATTT
66 ATTATATTTCTCTATTATTGATCTTTTATCTTTTACGTTATATTATATTATATTTTTTGTTATTT
930619 TCTCATTACATATATATATTTATTTTATTATTATATTTTCTTATGTATATTTTTTTATATTTTTA
131 TCTCATTACATATATATATTTATTTTATTATTATATTTTCTTATGTATATTTTTTTATATTTTTA
930684 CTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTTTTTTATCCTTTAT
196 CTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTTTTTTATCCTTTAT
930749 TTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTATTTCCTTATTTTA
261 TTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTATTTCCTTATTTTA
930814 TATTCATTATTATTTCCTTTGTTCGTTTTATTTTATTCATTTTCGTTT
326 TATTCATTATTATTTCCTTTGTTCGTTTTATTTTATTCATTTTCGTTT
*
930862 ATTCTTTTTTTTAATATTATATTTTATTATTACATATTATATATATATTTAATTTTTTACCTATT
1 ATTC-TTTTTTTAATATTATATTATATTATTACATATTATATATATATTTAATTTTTTACCTATT
930927 TATTATATTTCTCTATTATTGATCTTTTATCTTTTACGTTATATTATATTATATTTTTTGTTATT
65 TATTATATTTCTCTATTATTGATCTTTTATCTTTTACGTTATATTATATTATATTTTTTGTTATT
930992 TTCTCATTACATATATATATTTTATTTTATTATTATATCTTTCTTATGTATATTTTTATTATATT
130 TTCTCATTACATATATATA-TTTATTTTATTATTATAT-TTTCTTATGTATATTTTT-TTATATT
931057 TTTACTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTTTTTTATCCT
192 TTTACTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTTTTTTATCCT
931122 TTATTTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTATTTCCTTAT
257 TTATTTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTATTTCCTTAT
931187 TTTATATTCATTATTATTTCCTTTGTTCGTTTTATTTTATTCATTTTCGTTT
322 TTTATATTCATTATTATTTCCTTTGTTCGTTTTATTTTATTCATTTTCGTTT
931239 TTTATGTCTT
Statistics
Matches: 370, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
373 4 0.01
374 141 0.38
375 18 0.05
376 18 0.05
377 189 0.51
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (373 bp):
ATTCTTTTTTTAATATTATATTATATTATTACATATTATATATATATTTAATTTTTTACCTATTT
ATTATATTTCTCTATTATTGATCTTTTATCTTTTACGTTATATTATATTATATTTTTTGTTATTT
TCTCATTACATATATATATTTATTTTATTATTATATTTTCTTATGTATATTTTTTTATATTTTTA
CTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTTTTTTATCCTTTAT
TTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTATTTCCTTATTTTA
TATTCATTATTATTTCCTTTGTTCGTTTTATTTTATTCATTTTCGTTT
Found at i:932948 original size:18 final size:18
Alignment explanation
Indices: 932925--932967 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
932915 TTAGACATTT
932925 TGCATTTCTTATTTTCTG
1 TGCATTTCTTATTTTCTG
* *
932943 TGCATTTTGTTATTTTCTT
1 TGCA-TTTCTTATTTTCTG
932962 TGCATT
1 TGCATT
932968 CACATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.63
Consensus pattern (18 bp):
TGCATTTCTTATTTTCTG
Found at i:941113 original size:105 final size:105
Alignment explanation
Indices: 940931--941948 Score: 1713
Period size: 105 Copynumber: 9.7 Consensus size: 105
940921 GGTTTTACCC
940931 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
940996 CGAATGGACCGCTGGTTGTCACCAAATATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
941036 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
941101 CGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
941141 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
941206 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
941246 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
941311 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
941351 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
941416 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
* *
941456 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
941521 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
941561 AGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
941626 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
*
941666 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
941731 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
* * * ***
941770 CAGAGCCAATTTCAACTTCACAACTAAGGATATTAGACTCAAGACAGTACAAGTTCAACTTCACG
1 -AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
941835 ACGAAGGGACCGCTGACTGTCAACCGACAAC--TTCTC-AATTT
65 ACGAAGGGACCGCTGGTTGTC-ACC-A-AACATTTCTCAAATTT
* * * *
941876 CAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCGGACAACACAAGTTCAACCTCACG
1 -AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
941941 ACG-AGGGA
65 ACGAAGGGA
941949 GTCATTTCGC
Statistics
Matches: 872, Mismatches: 37, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
104 5 0.01
105 791 0.91
106 72 0.08
107 1 0.00
108 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
Found at i:943509 original size:15 final size:14
Alignment explanation
Indices: 943464--943565 Score: 77
Period size: 14 Copynumber: 7.1 Consensus size: 14
943454 CATATATATA
*
943464 TATTTTATTTTTAT
1 TATTATATTTTTAT
* *
943478 TATTATATCTTTCT
1 TATTATATTTTTAT
943492 TATGTATATTTTTAT
1 TAT-TATATTTTTAT
943507 TA-TATATTTTTACT
1 TATTATATTTTTA-T
943521 TA-T-TA-TTTTAT
1 TATTATATTTTTAT
943532 TATTCAATATTTGGTTAT
1 TATT--ATATTT--TTAT
*
943550 TATGTATATATTTAT
1 TAT-TATATTTTTAT
943565 T
1 T
943566 CGTTTTTTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
11 3 0.04
12 6 0.08
13 12 0.17
14 18 0.25
15 18 0.25
16 2 0.03
17 5 0.07
18 7 0.10
19 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (14 bp):
TATTATATTTTTAT
Found at i:943513 original size:28 final size:29
Alignment explanation
Indices: 943464--943535 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
943454 CATATATATA
*
943464 TATTTTATTTTTATTATTATATCTTT-CT
1 TATTATATTTTTATTATTATATCTTTACT
*
943492 TATGTATATTTTTATTA-TATATTTTTACT
1 TAT-TATATTTTTATTATTATATCTTTACT
943521 TATTAT-TTTATTATT
1 TATTATATTT-TTATT
943536 CAATATTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 19 0.49
29 17 0.44
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (29 bp):
TATTATATTTTTATTATTATATCTTTACT
Found at i:943756 original size:27 final size:25
Alignment explanation
Indices: 943710--943771 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
943700 CATTTTTTTA
*
943710 ATATTATATTTTATTATTACATATT
1 ATATTATATTTAATTATTACATATT
* *
943735 ATATATATATTTAATTTTTTACCTATT
1 ATAT-TATATTTAA-TTATTACATATT
943762 -TATTATATTT
1 ATATTATATTT
943772 CTCTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.34
26 11 0.34
27 10 0.31
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (25 bp):
ATATTATATTTAATTATTACATATT
Found at i:943895 original size:15 final size:14
Alignment explanation
Indices: 943855--943951 Score: 76
Period size: 15 Copynumber: 6.7 Consensus size: 14
943845 ATATATATAT
943855 TATTTTTATTATTA
1 TATTTTTATTATTA
* *
943869 TATCTTTCTTATGTA
1 TATTTTTATTAT-TA
943884 TATTTTTATTA-TA
1 TATTTTTATTATTA
943897 TATTTTTACTTA-T-
1 TATTTTTA-TTATTA
943910 TA-TTTTATTATTCAA
1 TATTTTTATTATT--A
943925 TATTTGGTTATTATGTA
1 TATTT--TTATTAT-TA
*
943942 TATGTTTATT
1 TATTTTTATT
943952 CGTTTTTTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
11 3 0.04
12 6 0.09
13 12 0.18
14 14 0.21
15 18 0.26
16 2 0.03
17 5 0.07
18 7 0.10
19 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.65
Consensus pattern (14 bp):
TATTTTTATTATTA
Found at i:943899 original size:28 final size:29
Alignment explanation
Indices: 943855--943921 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 29
943845 ATATATATAT
943855 TATTTTTATTATTATATCTTT-CTTATGTA
1 TATTTTTATTATTATATCTTTACTTAT-TA
*
943884 TATTTTTATTA-TATATTTTTACTTATTA
1 TATTTTTATTATTATATCTTTACTTATTA
943912 T-TTTATTATT
1 TATTT-TTATT
943922 CAATATTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 3 0.09
28 16 0.46
29 16 0.46
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (29 bp):
TATTTTTATTATTATATCTTTACTTATTA
Found at i:943913 original size:26 final size:25
Alignment explanation
Indices: 943852--943920 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 25
943842 TATATATATA
943852 TATTATTTTTATTATTATATCTTTCT
1 TATTATTTTTATTA-TATATCTTTCT
*
943878 TATGTATATTTTTATTATATATTTTTACT
1 TA--T-TATTTTTATTATATATCTTT-CT
943907 TATTA-TTTTATTAT
1 TATTATTTTTATTAT
943921 TCAATATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 9 0.24
26 4 0.11
27 1 0.03
28 9 0.24
29 15 0.39
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (25 bp):
TATTATTTTTATTATATATCTTTCT
Found at i:943927 original size:28 final size:26
Alignment explanation
Indices: 943852--943929 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 26
943842 TATATATATA
*
943852 TATTATTTTTATTATT-ATATCTTTCT
1 TATTA-TTTTATTATTAATATTTTTCT
943878 TATGTATATTT-TTATTATATATTTTTACT
1 TAT-TAT-TTTATTATTA-ATATTTTT-CT
943907 TATTATTTTATTATTCAATATTT
1 TATTATTTTATTATT-AATATTT
943930 GGTTATTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
26 9 0.20
27 8 0.18
28 21 0.48
29 6 0.14
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (26 bp):
TATTATTTTATTATTAATATTTTTCT
Found at i:943956 original size:386 final size:377
Alignment explanation
Indices: 943319--944081 Score: 1409
Period size: 386 Copynumber: 2.0 Consensus size: 377
943309 TTTTTATTTG
* *
943319 ATTCTTTTTTTTAATATATATTTATTATTACATATTATATATATTTAATTTTTTATCTATTTATT
1 ATTCATTTTTTTAATATATATTTATTATTACATATTATATATATTTAATTTTTTACCTATTTATT
*
943384 ATATTTCTCTATTATTGATCTTTTATCTTTTATGTTATATTATATTATATTTTTTGTTATTTTCT
66 ATATTTCTCTATTATTGATCTTTTATCTTTTACGTTATATTATATTATATTTTTTGTTATTTTCT
943449 CATTACATATATATATATTTTATTTTTATTATTATATCTTTCTTATGTATATTTTTATTATATAT
131 CATTACATATATATATATTTTATTTTTATTATTATATCTTTCTTATGTATATTTTTATTATATAT
943514 TTTTACTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTTTTTTATCC
196 TTTTACTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTTTTTTATCC
943579 TTTATTTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTATTTCCTTA
261 TTTATTTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTATTTCCTTA
943644 TTTTATATTCATTATTATTTCCTTTGTTCGTTTTATTTTATTCATTTTCGTTT
326 TTTTATATTCATTATTATTTCCTTTGTTCGTTTTA-TTTATTCATTTTCGTTT
943697 ATTCATTTTTTTAATATTATATTTTATTATTACATATTATATATATATTTAATTTTTTACCTATT
1 ATTCATTTTTTTAATA-TATA-TTTATTATTACATA-T-TATATATATTTAATTTTTTACCTATT
943762 TATTATATTTCTCTATTATTGATCTTTTATCTTTTACGTTATATTATATTATATTTTTTGTTATT
62 TATTATATTTCTCTATTATTGATCTTTTATCTTTTACGTTATATTATATTATATTTTTTGTTATT
943827 TTCTCATTACATATATATATATATATATTATTTTTATTATTATATCTTTCTTATGTATATTTTTA
127 TTCTCATTAC--ATATATATATAT-T-TTATTTTTATTATTATATCTTTCTTATGTATATTTTTA
*
943892 TTATATATTTTTACTTATTATTTTATTATTCAATATTTGGTTATTATGTATATGTTTATTCGTTT
188 TTATATATTTTTACTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTT
943957 TTTTATCCTTTATTTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTA
253 TTTTATCCTTTATTTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTA
944022 TTTCCTTATTTTATATTCATTATTATTTCCTTTGTTCGTTTTATTTATTCATTTTCGTTT
318 TTTCCTTATTTTATATTCATTATTATTTCCTTTGTTCGTTTTATTTATTCATTTTCGTTT
944082 TTTATGTCTT
Statistics
Matches: 373, Mismatches: 4, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
378 15 0.04
379 4 0.01
380 14 0.04
381 1 0.00
382 99 0.27
384 12 0.03
385 18 0.05
386 210 0.56
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.64
Consensus pattern (377 bp):
ATTCATTTTTTTAATATATATTTATTATTACATATTATATATATTTAATTTTTTACCTATTTATT
ATATTTCTCTATTATTGATCTTTTATCTTTTACGTTATATTATATTATATTTTTTGTTATTTTCT
CATTACATATATATATATTTTATTTTTATTATTATATCTTTCTTATGTATATTTTTATTATATAT
TTTTACTTATTATTTTATTATTCAATATTTGGTTATTATGTATATATTTATTCGTTTTTTTATCC
TTTATTTATTGTTACTTTCATCTCATTTATTTATTTCACTTTTAATTTTTTTTATTATTTCCTTA
TTTTATATTCATTATTATTTCCTTTGTTCGTTTTATTTATTCATTTTCGTTT
Found at i:951673 original size:27 final size:27
Alignment explanation
Indices: 951615--951681 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
951605 GATAATGACT
* * *
951615 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATATACTTCTATA
* *
951642 TTGAATCATTGAGAATATACTTCTATA
1 CTGAATCATTCAGAATATACTTCTATA
951669 CTGAATCATTCAG
1 CTGAATCATTCAG
951682 CATTGTTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (27 bp):
CTGAATCATTCAGAATATACTTCTATA
Found at i:957298 original size:72 final size:71
Alignment explanation
Indices: 957216--957475 Score: 268
Period size: 72 Copynumber: 3.8 Consensus size: 71
957206 ATCGTGATTC
* * * * * * *
957216 TCTTCTTGGACCTCATATGAGTTGTCATCATAACTACTCCCATTTTTTGTATTTATCGTACCATC
1 TCTTCTTAGACCCCATGTGAGCTGCCATCACAACTACTCCCATTGTTTGTATTT-TCGTACCATC
957281 ATAATTT
65 ATAATTT
* * * * *
957288 TCTTCTTGGACCCCATGTGAGCTGCCATCACAACAACTCCCA-----TG-ATTGT--TATCATCG
1 TCTTCTTAGACCCCATGTGAGCTGCCATCACAACTACTCCCATTGTTTGTATTTTCGTACCATCA
* *
957345 TGATTC
66 TAATTT
* * * *
957351 TC-TCTTATACCCCATGTGAGTTGCCATCACAACTACTCTCATTGTTTGTATTTTCCGCACCATC
1 TCTTCTTAGACCCCATGTGAGCTGCCATCACAACTACTCCCATTGTTTGTATTTT-CGTACCATC
957415 ATAATTT
65 ATAATTT
*
957422 TCTTCTTAGACCCCATGTGAGCTGCCATCATAACTACTCCCATTGTTTGTATTT
1 TCTTCTTAGACCCCATGTGAGCTGCCATCACAACTACTCCCATTGTTTGTATTT
957476 GCCAAGTGAT
Statistics
Matches: 152, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
62 34 0.22
63 12 0.08
65 1 0.01
66 3 0.02
67 4 0.03
68 4 0.03
71 11 0.07
72 83 0.55
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (71 bp):
TCTTCTTAGACCCCATGTGAGCTGCCATCACAACTACTCCCATTGTTTGTATTTTCGTACCATCA
TAATTT
Found at i:957414 original size:134 final size:135
Alignment explanation
Indices: 957150--957464 Score: 418
Period size: 134 Copynumber: 2.3 Consensus size: 135
957140 TGTATCATTC
* * * * *
957150 TCTTCTTGGACCCCATGTGAGTTACCATCACGATTGCTACCATCATGATTATTATCATCGTGATT
1 TCTTCTTGGACCCCATGTGAGCTGCCATCACAACTACT-CC--CATGATTATTATCATCGTGATT
* * * * * *
957215 CTCTTCTTGGACCTCATATGAGTTGTCATCATAACTACTCCCATTTTTTGTATTTATCGTACCAT
63 CTCTTCTTAGACCCCATATGAGTTGCCATCACAACTACTCCCATTGTTTGTATTTATCGCACCAT
957280 CATAATTT
128 CATAATTT
* *
957288 TCTTCTTGGACCCCATGTGAGCTGCCATCACAACAACTCCCATGATTGTTATCATCGTGATTCTC
1 TCTTCTTGGACCCCATGTGAGCTGCCATCACAACTACTCCCATGATTATTATCATCGTGATTCTC
* * *
957353 -TCTTATACCCCATGTGAGTTGCCATCACAACTACTCTCATTGTTTGTATTT-TCCGCACCATCA
66 TTCTTAGACCCCATATGAGTTGCCATCACAACTACTCCCATTGTTTGTATTTAT-CGCACCATCA
957416 TAATTT
130 TAATTT
* *
957422 TCTTCTTAGACCCCATGTGAGCTGCCATCATAACTACTCCCAT
1 TCTTCTTGGACCCCATGTGAGCTGCCATCACAACTACTCCCAT
957465 TGTTTGTATT
Statistics
Matches: 157, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
133 1 0.01
134 98 0.62
135 24 0.15
137 2 0.01
138 32 0.20
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.37
Consensus pattern (135 bp):
TCTTCTTGGACCCCATGTGAGCTGCCATCACAACTACTCCCATGATTATTATCATCGTGATTCTC
TTCTTAGACCCCATATGAGTTGCCATCACAACTACTCCCATTGTTTGTATTTATCGCACCATCAT
AATTT
Found at i:961157 original size:2 final size:2
Alignment explanation
Indices: 961150--961182 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
961140 GCTTATGATA
*
961150 AT AT AT AT AT AT AT AT AC AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
961183 GTAGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:966414 original size:17 final size:17
Alignment explanation
Indices: 966386--966431 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
966376 ATACAAACGT
* *
966386 TTGTACCATTTAGTAGC
1 TTGTAACATTTAGTAAC
*
966403 TTGTAACGTTTAGTAAC
1 TTGTAACATTTAGTAAC
966420 TTGTAACATTTA
1 TTGTAACATTTA
966432 ATACCTATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (17 bp):
TTGTAACATTTAGTAAC
Found at i:985626 original size:33 final size:33
Alignment explanation
Indices: 985584--985650 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
985574 AGTTTACAAT
* * *
985584 AATTGAAATACTTAAATACTTCTAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
985617 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
985650 A
1 A
985651 TTGAAACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:985670 original size:21 final size:21
Alignment explanation
Indices: 985645--985686 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
985635 CTTCCAAGTT
985645 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
985666 CGATAATTGAAACAAATTTTA
1 CGATAATTGAAACAAAGTTTA
985687 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:994387 original size:28 final size:28
Alignment explanation
Indices: 994356--994413 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
994346 TAAATTGAAA
*
994356 AATAATAAATTAATTTTAAAAATAATTG
1 AATAATAAATTAATTTAAAAAATAATTG
994384 AATAATAAATTAATTTAAAAAATAATTG
1 AATAATAAATTAATTTAAAAAATAATTG
994412 AA
1 AA
994414 GCTACATATG
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:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
AATAATAAATTAATTTAAAAAATAATTG
Found at i:995389 original size:21 final size:21
Alignment explanation
Indices: 995355--995414 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 21
995345 AATTATGTTC
* * *
995355 TTATGATACGTTTTTCTGTCT
1 TTATGACACATTTTTCTGTAT
*
995376 TTATGACACATTTTATTTTGTAT
1 TTATGACACA-TTT-TTCTGTAT
*
995399 TTATGTCACATTTTTC
1 TTATGACACATTTTTC
995415 AGGAATTTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 10 0.32
22 6 0.19
23 15 0.48
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (21 bp):
TTATGACACATTTTTCTGTAT
Found at i:1010724 original size:14 final size:14
Alignment explanation
Indices: 1010705--1010733 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1010695 TATTTAAAAA
1010705 TATATTATAATAAT
1 TATATTATAATAAT
1010719 TATATTATAATAAT
1 TATATTATAATAAT
1010733 T
1 T
1010734 TGAATGAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTATAATAAT
Found at i:1019174 original size:2 final size:2
Alignment explanation
Indices: 1019167--1019194 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1019157 ACAGATGCAA
1019167 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
1019195 CATTGTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1019654 original size:27 final size:28
Alignment explanation
Indices: 1019616--1019669 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
1019606 TTATGGAATT
*
1019616 TTTTTTATAGAATATATATATTTTATAA
1 TTTTTTATAGAATATAGATATTTTATAA
* *
1019644 TTTTTTA-AGAATTTAGATTTTTTATA
1 TTTTTTATAGAATATAGATATTTTATA
1019670 TATGTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (28 bp):
TTTTTTATAGAATATAGATATTTTATAA
Found at i:1020216 original size:72 final size:74
Alignment explanation
Indices: 1020129--1020285 Score: 275
Period size: 72 Copynumber: 2.1 Consensus size: 74
1020119 TCCGTGGTTT
*
1020129 TTTTTCTTCCTTTGATCCATAGTTTTTCTTTTCTCCTTTCGTCTTTAGTGTGGAAAA-AACTTAC
1 TTTTT-TTCCTTTGATCCATAGTTTTCCTTTTCTCCTTTCGTCTTTAGTGTGGAAAACAACTTAC
1020193 CCAAATTCAA
65 CCAAATTCAA
1020203 TTTTTTT-CTTTGATCCATAGTTTTCCTTTTCTCCTTTCGTCTTTAGTGTGGAAAACAACTTACC
1 TTTTTTTCCTTTGATCCATAGTTTTCCTTTTCTCCTTTCGTCTTTAGTGTGGAAAACAACTTACC
1020267 CAAATTCAA
66 CAAATTCAA
1020276 -TTTTTTCCTT
1 TTTTTTTCCTT
1020286 GAAAATAAGT
Statistics
Matches: 80, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
72 53 0.66
73 22 0.28
74 5 0.06
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.49
Consensus pattern (74 bp):
TTTTTTTCCTTTGATCCATAGTTTTCCTTTTCTCCTTTCGTCTTTAGTGTGGAAAACAACTTACC
CAAATTCAA
Found at i:1020889 original size:21 final size:20
Alignment explanation
Indices: 1020845--1020891 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1020835 ATTGAAATAA
* * *
1020845 AATAAAGAAAATAAAGATAT
1 AATAAAGAAAATAAAAAGAC
1020865 AATATAAGAAAATAAAAAGAC
1 AATA-AAGAAAATAAAAAGAC
1020886 AATAAA
1 AATAAA
1020892 AATACGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (20 bp):
AATAAAGAAAATAAAAAGAC
Found at i:1023026 original size:29 final size:29
Alignment explanation
Indices: 1022984--1023040 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1022974 AGTGTTGGCC
1022984 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
1023013 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
1023041 ACCCTTGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.35, G:0.32, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:1023132 original size:29 final size:29
Alignment explanation
Indices: 1023099--1023154 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1023089 TCCCAACACA
*
1023099 TAGGTCGCCATGCTCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
1023128 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
1023155 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:1023277 original size:10 final size:10
Alignment explanation
Indices: 1023262--1023295 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1023252 CATAGCTCGT
1023262 TCGGATGGCC
1 TCGGATGGCC
1023272 TCGGAT-GCTC
1 TCGGATGGC-C
1023282 TCGGATGGCC
1 TCGGATGGCC
1023292 TCGG
1 TCGG
1023296 TCGAATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:1023278 original size:33 final size:33
Alignment explanation
Indices: 1023158--1023315 Score: 181
Period size: 33 Copynumber: 4.8 Consensus size: 33
1023148 GCGACCTACC
* * *
1023158 CTCGCTCGGCTTCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* *
1023191 CTCGCTCGGTTGCCCTCGGATACCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
*
1023224 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* * * * *
1023257 CTCGTTCGGATGGCCTCGGATGCTCTCGGATGG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* * *
1023290 CCTCGGTCGAATGGCCTCGGATGCCC
1 -CTCGCTCGGATGCCCTCGGATGCCC
1023316 AGCGTGTTGG
Statistics
Matches: 111, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 89 0.80
34 22 0.20
ACGTcount: A:0.10, C:0.37, G:0.28, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
Found at i:1032657 original size:21 final size:21
Alignment explanation
Indices: 1032565--1032658 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 21
1032555 AATATGTAAC
*
1032565 ATTATTATAAATTAAGATTAA
1 ATTAATATAAATTAAGATTAA
* * *
1032586 ATTGATATAATTTTAAAATATAA
1 ATTAATATAA-ATTAAGAT-TAA
* * *
1032609 A-T-ATTTAAATT--TATTTA
1 ATTAATATAAATTAAGATTAA
* *
1032626 ATTACTTTAAATTAAGATTAA
1 ATTAATATAAATTAAGATTAA
1032647 ATTAATATAAAT
1 ATTAATATAAAT
1032659 ATATAAATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
17 3 0.06
18 3 0.06
19 8 0.15
20 2 0.04
21 27 0.50
22 7 0.13
23 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTAATATAAATTAAGATTAA
Found at i:1035014 original size:24 final size:24
Alignment explanation
Indices: 1034973--1035036 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
1034963 CACTATGATG
* *
1034973 GTCCTGCTTATGACAGGCACCGGA
1 GTCCTGATTATGACAGGCACAGGA
** *
1034997 GTCCTGATTATGGGAGGCATAGGA
1 GTCCTGATTATGACAGGCACAGGA
* *
1035021 GTCCCGAGTATGACAG
1 GTCCTGATTATGACAG
1035037 ACTCCGCAGG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (24 bp):
GTCCTGATTATGACAGGCACAGGA
Found at i:1042227 original size:19 final size:19
Alignment explanation
Indices: 1042203--1042249 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1042193 TACTCAAAAA
*
1042203 TAATATTATTTTA-TATATT
1 TAATATTATTATACTAT-TT
*
1042222 TAATATTAATATACTATTT
1 TAATATTATTATACTATTT
1042241 TAATATTAT
1 TAATATTAT
1042250 GTTAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATATTATTATACTATTT
Found at i:1042364 original size:23 final size:23
Alignment explanation
Indices: 1042322--1042366 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1042312 TTTTTAGTAT
* *
1042322 TATAATAATATATTAAATTATAC
1 TATAATAATAAATGAAATTATAC
*
1042345 TATAATAATAAATGATATTATA
1 TATAATAATAAATGAAATTATA
1042367 TTTTATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TATAATAATAAATGAAATTATAC
Found at i:1042501 original size:17 final size:17
Alignment explanation
Indices: 1042440--1042502 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
1042430 ATATAATTGA
1042440 TAATATAATATTATTATTT
1 TAATATAAT-TT-TTATTT
**
1042459 TAATAATTAATTAATATTT
1 TAAT-A-TAATTTTTATTT
**
1042478 TTTTATAATTTTTATTT
1 TAATATAATTTTTATTT
1042495 TAATATAA
1 TAATATAA
1042503 CATAATATTC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 16 0.47
18 1 0.03
19 11 0.32
20 2 0.06
21 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATATAATTTTTATTT
Found at i:1042527 original size:33 final size:35
Alignment explanation
Indices: 1042445--1042527 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 35
1042435 ATTGATAATA
* * *
1042445 TAATATTATTATTTTAATAATTAATTAATATTTTT
1 TAATATTTTTATTTTAATAATTAAATAATATTTCT
*
1042480 TTATAATTTTTATTTTAAT-A-TAACATAATA-TTCT
1 TAAT-ATTTTTATTTTAATAATTAA-ATAATATTTCT
1042514 TAATATTTTTATTT
1 TAATATTTTTATTT
1042528 ATAAACTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
33 10 0.24
34 9 0.22
35 9 0.22
36 13 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (35 bp):
TAATATTTTTATTTTAATAATTAAATAATATTTCT
Found at i:1046750 original size:18 final size:18
Alignment explanation
Indices: 1046729--1046765 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1046719 TTTAAATAGG
*
1046729 AAAATATAATTAAAATAAA
1 AAAAT-TAACTAAAATAAA
1046748 AAAATTAACTAAAATAAA
1 AAAATTAACTAAAATAAA
1046766 TATAAGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTAACTAAAATAAA
Found at i:1046852 original size:31 final size:31
Alignment explanation
Indices: 1046811--1046870 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
1046801 AATTCTATTC
* *
1046811 TAAT-ATTTTTTTTAAATTTTATTTATATTGA
1 TAATAATTTTTTTAAAATATTA-TTATATTGA
1046842 TAATAATTTTTTTAAAATATTATTATATT
1 TAATAATTTTTTTAAAATATTATTATATT
1046871 ATTAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (31 bp):
TAATAATTTTTTTAAAATATTATTATATTGA
Found at i:1047009 original size:2 final size:2
Alignment explanation
Indices: 1047002--1047039 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1046992 ATAAAAGATT
1047002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1047040 ATCCACTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1055797 original size:2 final size:2
Alignment explanation
Indices: 1055762--1055955 Score: 64
Period size: 2 Copynumber: 101.0 Consensus size: 2
1055752 TTAATAACAT
* * * *
1055762 TA TA AA TA TA -A TA TA AA TA TA TG T- TA CA TA -A TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1055800 TA TA -A CA CTA TA TA CTA TA TA TA TA TA -A TA CTA TA -A TA CA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
1055840 TA CA TA T- TA TA CGA TA TA T- TA TA TA -A TA TA TA -A TA TA -A
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1055878 TA TA -A CA -A CCA TA TA -A TA TA TA TGA AA TA TA CTA TA TA AA
1 TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA TA TA -TA TA TA TA
1055918 TA CTA TA TA -A TA -A TA TA T- TA TA TA CTA TA TA CTA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
1055956 ATAAATAATA
Statistics
Matches: 145, Mismatches: 19, Indels: 56
0.66 0.09 0.25
Matches are distributed among these distances:
1 18 0.12
2 111 0.77
3 16 0.11
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (2 bp):
TA
Found at i:1055801 original size:7 final size:7
Alignment explanation
Indices: 1055762--1055966 Score: 106
Period size: 7 Copynumber: 29.1 Consensus size: 7
1055752 TTAATAACAT
1055762 TATAA-A
1 TATAATA
1055768 TATAATA
1 TATAATA
1055775 TA-AATA
1 TATAATA
**
1055781 TATGTTA
1 TATAATA
*
1055788 CATAATA
1 TATAATA
1055795 TATAATA
1 TATAATA
1055802 TA-ACACTA
1 TATA-A-TA
*
1055810 TATACTA
1 TATAATA
1055817 TAT-ATA
1 TATAATA
1055823 TATAATA
1 TATAATA
1055830 CTATAATA
1 -TATAATA
*
1055838 CATACATA
1 TATA-ATA
**
1055846 TTATACGA
1 -TATAATA
*
1055854 TATATTA
1 TATAATA
1055861 TATAATA
1 TATAATA
1055868 TAT-A-A
1 TATAATA
1055873 TATAATA
1 TATAATA
* *
1055880 TAACAACCA
1 T-ATAA-TA
1055889 TATAATA
1 TATAATA
*
1055896 TATATGAAA
1 TATA--ATA
*
1055905 TATACTA
1 TATAATA
1055912 TATAA-A
1 TATAATA
1055918 TACT-ATA
1 TA-TAATA
1055925 TAATAATA
1 T-ATAATA
1055933 TAT--TA
1 TATAATA
*
1055938 TATACTA
1 TATAATA
*
1055945 TATACTA
1 TATAATA
1055952 TATAATA
1 TATAATA
*
1055959 AATAATA
1 TATAATA
1055966 T
1 T
1055967 GATACCATAA
Statistics
Matches: 152, Mismatches: 26, Indels: 41
0.69 0.12 0.19
Matches are distributed among these distances:
5 9 0.06
6 23 0.15
7 82 0.54
8 26 0.17
9 12 0.08
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (7 bp):
TATAATA
Found at i:1055966 original size:33 final size:33
Alignment explanation
Indices: 1055862--1055948 Score: 92
Period size: 34 Copynumber: 2.7 Consensus size: 33
1055852 GATATATTAT
* *
1055862 ATAATATATAATATA--ATATAACA-ACCATATA
1 ATAATATATTATATACTATATAA-ATACTATATA
*
1055893 AT-ATATATGAAATATACTATATAAATACTATATA
1 ATAATATAT--TATATACTATATAAATACTATATA
1055927 ATAATATATTATATACTATATA
1 ATAATATATTATATACTATATA
1055949 CTATATAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
30 6 0.12
31 2 0.04
32 6 0.12
33 13 0.27
34 15 0.31
35 6 0.12
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (33 bp):
ATAATATATTATATACTATATAAATACTATATA
Found at i:1056988 original size:3 final size:3
Alignment explanation
Indices: 1056980--1057015 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1056970 TCTCTTGTTT
1056980 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1057016 ATCTGAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1057441 original size:18 final size:19
Alignment explanation
Indices: 1057399--1057442 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1057389 TTTGGTTCAC
* *
1057399 GGAATGTAAGATTACTAGTG
1 GGAATATAAGATTACCAG-G
1057419 GGAATATAAGATTACCA-G
1 GGAATATAAGATTACCAGG
1057437 GGAATA
1 GGAATA
1057443 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.25
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:1060406 original size:2 final size:2
Alignment explanation
Indices: 1060399--1060462 Score: 80
Period size: 2 Copynumber: 33.0 Consensus size: 2
1060389 TGATTATTCC
* *
1060399 AT AT AT AT AT AT AT AT A- AT AT -T ACT -T AT AT AT AA AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
1060439 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
1060463 TATTTTAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.06
2 50 0.93
3 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1071153 original size:2 final size:2
Alignment explanation
Indices: 1071148--1071295 Score: 72
Period size: 2 Copynumber: 78.0 Consensus size: 2
1071138 TAGCACATAG
* *
1071148 TA TA TA TT TA TA T- TA TA T- TA TA TA GTA TA TA TA TA GTA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* * * * *
1071190 TG TA TA -A TA TA TT TT TA GTA T- TT TA TA TT TA TA TA TA GTA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
1071231 TA -A TA TA T- TA TA TA TA -A TA TA TA GTA TA TA TA GT- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
*
1071270 TA T- TA TA TA -A TA T- TA T- TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1071296 ATTATTAATA
Statistics
Matches: 114, Mismatches: 12, Indels: 40
0.69 0.07 0.24
Matches are distributed among these distances:
1 14 0.12
2 89 0.78
3 11 0.10
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1071290 original size:71 final size:72
Alignment explanation
Indices: 1071161--1071312 Score: 179
Period size: 71 Copynumber: 2.1 Consensus size: 72
1071151 ATATTTATAT
* * * *
1071161 TATATTATATAGTATATATATAGTATATTTGTATAATATATTTTTAGTATTTTATATTTATATAT
1 TATATTATATAGTATATATATAGTATATTAGTATAATATATTTATAATATTATATATTTATATA-
1071226 AGTATTAA
65 AGTATTAA
1071234 TATATTATATA-TA-ATATATAGTATATATAGT-T-ATATTATTATATAATATTAT-TATTTATA
1 TATATTATATAGTATATATATAGTATAT-TAGTATAATA-TATT-TATAATATTATATATTTATA
*
1071294 TAATTATTAA
63 TAAGTATTAA
1071304 TATTATTAT
1 TA-TATTAT
1071313 TTTTTGTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
70 12 0.17
71 34 0.49
72 13 0.19
73 11 0.16
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (72 bp):
TATATTATATAGTATATATATAGTATATTAGTATAATATATTTATAATATTATATATTTATATAA
GTATTAA
Found at i:1071294 original size:42 final size:41
Alignment explanation
Indices: 1071158--1071295 Score: 110
Period size: 42 Copynumber: 3.3 Consensus size: 41
1071148 TATATATTTA
*
1071158 TATTATATTATATAGTATATATA-TAGTATATTTGTATAATA-
1 TATTATATTATATAGTATATATATTA-TATA-TTATATAATAT
** *
1071199 TATT-T-TTAGTATTTTATATTTATATATAGTATTA-AT-ATAT
1 TATTATATTA-TATAGTATATATAT-TATA-TATTATATAATAT
*
1071239 TATATATAATATATAGTATATATAGTTATATTATTATATAATAT
1 TAT-TATATTATATAGTATATATA-TTATA-TATTATATAATAT
1071283 TATTAT-TTATATA
1 TATTATATTATATA
1071296 ATTATTAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
39 6 0.08
40 16 0.21
41 9 0.12
42 30 0.39
43 8 0.11
44 7 0.09
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (41 bp):
TATTATATTATATAGTATATATATTATATATTATATAATAT
Found at i:1071299 original size:12 final size:12
Alignment explanation
Indices: 1071264--1071314 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
1071254 GTATATATAG
1071264 TTATATTATTAT
1 TTATATTATTAT
*
1071276 ATAATATTATTAT
1 -TTATATTATTAT
*
1071289 TTATATAATTAT
1 TTATATTATTAT
*
1071301 TAATATTATTAT
1 TTATATTATTAT
1071313 TT
1 TT
1071315 TTTGTTTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:1071299 original size:15 final size:16
Alignment explanation
Indices: 1071231--1071309 Score: 67
Period size: 16 Copynumber: 4.9 Consensus size: 16
1071221 TATATAGTAT
1071231 TAATA-TATTA-TATA
1 TAATATTATTATTATA
*
1071245 TAATATATAGTA-TATA
1 TAATAT-TATTATTATA
*
1071261 TAGT-TATATTATTATA
1 TAATAT-TATTATTATA
1071277 TAATATTATTATTTATA
1 TAATATTATTA-TTATA
*
1071294 TAATTATTAATATTAT
1 TAA-TATTATTATTAT
1071310 TATTTTTTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
14 5 0.09
15 6 0.11
16 23 0.43
17 13 0.24
18 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TAATATTATTATTATA
Found at i:1086794 original size:41 final size:40
Alignment explanation
Indices: 1086723--1086803 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
1086713 CCTGGCCTGG
* *
1086723 CCTATTTAACTAAACTGGCCAGGCCCAGGCCTTTTTAAAAA
1 CCTATTTAACTAAACAGGCCAGGCCCAGGCC-TATTAAAAA
**
1086764 CCTATTTAACTAAACAGGCCAGGCTTAGGCCTATTAAAAA
1 CCTATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAA
1086804 GCCTTATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 8 0.22
41 28 0.78
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (40 bp):
CCTATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAA
Found at i:1089100 original size:38 final size:38
Alignment explanation
Indices: 1089052--1089127 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1089042 TGGTTCACCT
1089052 CTCTCTTCGGTGGTAAACATCCTAAACTTCGCCAACAC
1 CTCTCTTCGGTGGTAAACATCCTAAACTTCGCCAACAC
1089090 CTCTCTTCGGTGGTAAACATCCTAAACTTCGCCAACAC
1 CTCTCTTCGGTGGTAAACATCCTAAACTTCGCCAACAC
1089128 TTGTCTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.26
Consensus pattern (38 bp):
CTCTCTTCGGTGGTAAACATCCTAAACTTCGCCAACAC
Found at i:1095038 original size:24 final size:24
Alignment explanation
Indices: 1095013--1095119 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
1095003 AAACGGAGAT
* *
1095013 ATCAGAAATCAAAACATAATTCAT
1 ATCAGAAATCAAAACAGAATTCAG
* *
1095037 ATCA-AATATCATAACAGAATCCAG
1 ATCAGAA-ATCAAAACAGAATTCAG
* * * *
1095061 GTTAGGAATCAAAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
1095085 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1095109 ATCAGAAATCA
1 ATCAGAAATCA
1095120 GATAAAATAT
Statistics
Matches: 62, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 2 0.03
24 59 0.95
25 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1095119 original size:48 final size:48
Alignment explanation
Indices: 1095013--1095119 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
1095003 AAACGGAGAT
* * * *
1095013 ATCAGAAATCAAAACATAATTCATATCAAATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATCAAATATCAAAACAGAATCCAA
* * * * * * *
1095061 GTTAGGAATCAAAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAGATCAAATATCAAAACAGAATCCAA
1095109 ATCAGAAATCA
1 ATCAGAAATCA
1095120 GATAAAATAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATCAAATATCAAAACAGAATCCAA
Found at i:1099486 original size:22 final size:22
Alignment explanation
Indices: 1099420--1099500 Score: 105
Period size: 23 Copynumber: 3.8 Consensus size: 22
1099410 CCAGAACCCC
*
1099420 AGGGGGTATCGATTCCCC-T--
1 AGGGGGAATCGATTCCCCTTCA
*
1099439 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
1099462 AGGGGGAATCGATTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
1099484 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
1099501 TCTGCCCTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
19 16 0.30
20 1 0.02
22 17 0.31
23 20 0.37
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:1102572 original size:13 final size:13
Alignment explanation
Indices: 1102528--1102574 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1102518 CTTTTCTTTG
*
1102528 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
1102542 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
1102554 TTTATTTAAAATAA
1 -ATATTTAAAATAA
1102568 ATATTTA
1 ATATTTA
1102575 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1104019 original size:3 final size:3
Alignment explanation
Indices: 1104011--1104096 Score: 136
Period size: 3 Copynumber: 28.7 Consensus size: 3
1104001 AAAATATATT
*
1104011 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1104059 TAG TAA TAA TAA TAA TAA TAA TAT TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1104097 TGGATAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1105484 original size:22 final size:21
Alignment explanation
Indices: 1105442--1105481 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1105432 AAGACTATTT
1105442 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
1105463 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
1105482 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1107458 original size:20 final size:21
Alignment explanation
Indices: 1107400--1107453 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1107390 GTTGAATAGT
* **
1107400 GGGGGGAATCGATACCCC-CA
1 GGGGGGAATCGGTACCCCTTG
1107420 GGGGGGAATCGGTACCCCTTG
1 GGGGGGAATCGGTACCCCTTG
1107441 GGGGGGAATCGGT
1 GGGGGGAATCGGT
1107454 TCCCTCTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.19, C:0.22, G:0.44, T:0.15
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCTTG
Found at i:1132015 original size:25 final size:25
Alignment explanation
Indices: 1131987--1132076 Score: 128
Period size: 25 Copynumber: 3.6 Consensus size: 25
1131977 CTATTAAACA
* *
1131987 TAGTGGGATAATCATCATTCAATAC
1 TAGTGGGATAACCATCATCCAATAC
1132012 TAGTGGGATAACCA-CTATCCAATAC
1 TAGTGGGATAACCATC-ATCCAATAC
1132037 TAGTGGGATAACCATCATCCAAATAC
1 TAGTGGGATAACCATCATCC-AATAC
*
1132063 GAGTGGGATAACCA
1 TAGTGGGATAACCA
1132077 CTATGAGCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
24 1 0.02
25 39 0.66
26 19 0.32
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (25 bp):
TAGTGGGATAACCATCATCCAATAC
Found at i:1137287 original size:24 final size:24
Alignment explanation
Indices: 1137254--1137314 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 24
1137244 TTTATTAAAC
1137254 ATGGGATAACCATCAT-CAATACT
1 ATGGGATAACCATCATCCAATACT
1137277 AGTGGGATAACCATCATCCAATACT
1 A-TGGGATAACCATCATCCAATACT
1137302 ATAGGGATAACCA
1 AT-GGGATAACCA
1137315 CTATGAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 1 0.03
24 16 0.46
25 18 0.51
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (24 bp):
ATGGGATAACCATCATCCAATACT
Found at i:1143941 original size:5 final size:5
Alignment explanation
Indices: 1143931--1143968 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
1143921 CGATTACTGA
1143931 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1143969 AAGTCCTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:1152299 original size:20 final size:19
Alignment explanation
Indices: 1152251--1152308 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
1152241 CTCAGTTTCC
1152251 AAATTCGCAACGCGAATATCT
1 AAATTCGCAACGCG-AT-TCT
*
1152272 AAATTCGCAACGCGATTGT
1 AAATTCGCAACGCGATTCT
*
1152291 AAGATTCGCAACACGATT
1 AA-ATTCGCAACGCGATT
1152309 TTGAAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 4 0.12
20 16 0.47
21 14 0.41
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (19 bp):
AAATTCGCAACGCGATTCT
Found at i:1152341 original size:19 final size:19
Alignment explanation
Indices: 1152313--1152417 Score: 111
Period size: 19 Copynumber: 5.2 Consensus size: 19
1152303 ACGATTTTGA
1152313 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
1152332 AAAATATGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
1152351 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
1152371 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
1152395 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
1152414 AAAA
1 AAAA
1152418 ATCCAAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 50 0.68
20 3 0.04
22 8 0.11
24 3 0.04
25 10 0.14
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:1152923 original size:14 final size:15
Alignment explanation
Indices: 1152904--1152936 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1152894 TTTAATTCAA
*
1152904 ATATTATTTA-ATTT
1 ATATTAATTAGATTT
1152918 ATATTAATTAGATTT
1 ATATTAATTAGATTT
1152933 ATAT
1 ATAT
1152937 AGCTTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATATTAATTAGATTT
Found at i:1153067 original size:15 final size:16
Alignment explanation
Indices: 1153039--1153070 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1153029 ATAATAAATG
1153039 AAAATGATTGGATTTA
1 AAAATGATTGGATTTA
1153055 AAAATGATT-GATTTA
1 AAAATGATTGGATTTA
1153070 A
1 A
1153071 TAAAATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (16 bp):
AAAATGATTGGATTTA
Found at i:1162326 original size:23 final size:23
Alignment explanation
Indices: 1162300--1162377 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
1162290 CACCACAGCT
1162300 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
1162323 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * * *
1162346 CGTAGAATTACACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
1162369 TATAATAAT
1 CAT-ATAAT
1162378 GTCCATAAGG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 40 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1162555 original size:103 final size:103
Alignment explanation
Indices: 1162384--1162601 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
1162374 TAATGTCCAT
* *
1162384 AAGGACCACATATCATTCCTTAAGAATCAAATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCAAATACATATACCAAGGATCAAGTATGTGTCTCACCA
1162449 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * * *
1162487 AAGGACTACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCAAATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1162552 GACTTCATACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1162590 AAGGACCACATA
1 AAGGACCACATA
1162602 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCAAATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1167363 original size:163 final size:163
Alignment explanation
Indices: 1167093--1167419 Score: 645
Period size: 163 Copynumber: 2.0 Consensus size: 163
1167083 TAACCACCTA
1167093 GCTAACTGCCTAACTAACTTGCTAACAGCTTCTCAACAATTTTTTTAATGATTTATTAATAGATT
1 GCTAACTGCCTAACTAACTTGCTAACAGCTTCTCAACAATTTTTTTAATGATTTATTAATAGATT
1167158 ACTTTATTAGTTTAATTATCTTTTATGTATTTTATCCTTAAGTTCACGACAAAGTTGATAATGAT
66 ACTTTATTAGTTTAATTATCTTTTATGTATTTTATCCTTAAGTTCACGACAAAGTTGATAATGAT
1167223 GGGTTCTTTTATAATAGCTATCATATATTGAAT
131 GGGTTCTTTTATAATAGCTATCATATATTGAAT
1167256 GCTAACTGCCTAACTAACTTGCTAACAGCTTCTCAACAATTTTTTTAATGATTTATTAATAGATT
1 GCTAACTGCCTAACTAACTTGCTAACAGCTTCTCAACAATTTTTTTAATGATTTATTAATAGATT
*
1167321 ACTTTATTAGTTTAATTATCTTTTATGTATTTTATCCTTAAGTTCACGATAAAGTTGATAATGAT
66 ACTTTATTAGTTTAATTATCTTTTATGTATTTTATCCTTAAGTTCACGACAAAGTTGATAATGAT
1167386 GGGTTCTTTTATAATAGCTATCATATATTGAAT
131 GGGTTCTTTTATAATAGCTATCATATATTGAAT
1167419 G
1 G
1167420 AGTTCTATAA
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 163 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (163 bp):
GCTAACTGCCTAACTAACTTGCTAACAGCTTCTCAACAATTTTTTTAATGATTTATTAATAGATT
ACTTTATTAGTTTAATTATCTTTTATGTATTTTATCCTTAAGTTCACGACAAAGTTGATAATGAT
GGGTTCTTTTATAATAGCTATCATATATTGAAT
Found at i:1176479 original size:243 final size:243
Alignment explanation
Indices: 1176047--1176536 Score: 944
Period size: 243 Copynumber: 2.0 Consensus size: 243
1176037 GTATCAAAAG
1176047 CTTTGCTAAAGTCAGCCTTGATCAACACCGATTCTTTTTTGCTTTTAGACAACCCATCAATAACT
1 CTTTGCTAAAGTCAGCCTTGATCAACACCGATTCTTTTTTGCTTTTAGACAACCCATCAATAACT
*
1176112 TCATTAGCAATCAGACTGCAATCGGCAATTTGTTTCCCTGCAATAAAAGCAAACTGATGCTGCCC
66 TCATTAGCAATCAGACTGCAATCGACAATTTGTTTCCCTGCAATAAAAGCAAACTGATGCTGCCC
*
1176177 AACCACATCAGAAAGACAGCTGGCCAACCTCTTAGACAAAATGAGAGAAACTTTCTTGTATATGC
131 AACCACATCAGAAAGACAGCTGGCCAACCTCTTAGACAAAATGAGAGAAACTATCTTGTATATGC
1176242 TGCCCACTAATGAGATTGGTCTGAAATCCTCCGGGGAAATAGCCTCTA
196 TGCCCACTAATGAGATTGGTCTGAAATCCTCCGGGGAAATAGCCTCTA
*
1176290 CTTTGCTAAAGTCAGCCTTGATCAACACCGCTTCTTTTTTGCTTTTAGACAACCCATCAATAACT
1 CTTTGCTAAAGTCAGCCTTGATCAACACCGATTCTTTTTTGCTTTTAGACAACCCATCAATAACT
1176355 TCATTAGCAATCAGACTGCAATCGACAATTTGTTTCCCTGCAATAAAAGCAAACTGATGCTGCCC
66 TCATTAGCAATCAGACTGCAATCGACAATTTGTTTCCCTGCAATAAAAGCAAACTGATGCTGCCC
*
1176420 AACCACATCAGAAAGACAGCTGGCCAACCTCTTAGACAAAATGCGAGAAACTATCTTGTATATGC
131 AACCACATCAGAAAGACAGCTGGCCAACCTCTTAGACAAAATGAGAGAAACTATCTTGTATATGC
1176485 TGCCCACTAATGAGATTGGTCTGAAATCCTCCGGGGAAATAGCCTCTA
196 TGCCCACTAATGAGATTGGTCTGAAATCCTCCGGGGAAATAGCCTCTA
1176533 CTTT
1 CTTT
1176537 CTTCGGGAAA
Statistics
Matches: 243, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
243 243 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (243 bp):
CTTTGCTAAAGTCAGCCTTGATCAACACCGATTCTTTTTTGCTTTTAGACAACCCATCAATAACT
TCATTAGCAATCAGACTGCAATCGACAATTTGTTTCCCTGCAATAAAAGCAAACTGATGCTGCCC
AACCACATCAGAAAGACAGCTGGCCAACCTCTTAGACAAAATGAGAGAAACTATCTTGTATATGC
TGCCCACTAATGAGATTGGTCTGAAATCCTCCGGGGAAATAGCCTCTA
Found at i:1179322 original size:7 final size:7
Alignment explanation
Indices: 1179303--1179347 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
1179293 ATAAAAATAC
1179303 ATTTATA
1 ATTTATA
*
1179310 ATTTTTA
1 ATTTATA
1179317 TATTT-TA
1 -ATTTATA
1179324 ATTTATA
1 ATTTATA
1179331 ATTTATA
1 ATTTATA
1179338 ATTTATA
1 ATTTATA
1179345 ATT
1 ATT
1179348 GTTCTTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
6 4 0.11
7 27 0.77
8 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTATA
Found at i:1192099 original size:29 final size:28
Alignment explanation
Indices: 1192044--1192099 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1192034 AGCAGACACG
* *
1192044 TATTTTATTATATAATAATAGTTTATTT
1 TATTTTATTATATAATAATAATATATTT
1192072 TATTATTATTATA-AATTAATAATATATT
1 TATT-TTATTATATAA-TAATAATATATT
1192100 ATGTAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TATTTTATTATATAATAATAATATATTT
Found at i:1192511 original size:13 final size:13
Alignment explanation
Indices: 1192482--1192516 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1192472 ATAACTAATA
*
1192482 ATATTAAAT-ATT
1 ATATTAAATAAAT
1192494 ATATTAAATAAAT
1 ATATTAAATAAAT
1192507 ATATTAAATA
1 ATATTAAATA
1192517 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:1195526 original size:8 final size:8
Alignment explanation
Indices: 1195513--1195553 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1195503 CTCATTTTCA
1195513 GAGAATTT
1 GAGAATTT
1195521 GAGAATTT
1 GAGAATTT
*
1195529 -AGAGTTT
1 GAGAATTT
*
1195536 GGGAATTT
1 GAGAATTT
1195544 GAGAATTT
1 GAGAATTT
1195552 GA
1 GA
1195554 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1196477 original size:126 final size:126
Alignment explanation
Indices: 1195621--1196476 Score: 1642
Period size: 126 Copynumber: 6.8 Consensus size: 126
1195611 CTATAATCGG
*
1195621 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
1195686 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATTAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1195747 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1195812 TCATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1195872 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1195937 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
1195998 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1196063 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1196124 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
1196189 TCATTGCCCTATTATGTCACTCATGTCCATCGGGGACACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1196250 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1196315 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGAAACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1196376 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1196441 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
1196477 ATAACTTAAA
Statistics
Matches: 719, Mismatches: 10, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
125 124 0.17
126 595 0.83
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:1196926 original size:33 final size:34
Alignment explanation
Indices: 1196865--1196964 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
1196855 AAATTTAATG
*
1196865 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
1196899 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
1196932 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
1196965 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1197572 original size:21 final size:21
Alignment explanation
Indices: 1197484--1197577 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1197474 TATGGTATAA
*
1197484 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1197505 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1197526 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1197547 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1197568 AACCCTGCGG
1 AACCCTGCGG
1197578 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1197607 original size:21 final size:21
Alignment explanation
Indices: 1197581--1197628 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1197571 CCTGCGGAGA
*
1197581 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1197602 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1197623 GGGCAT
1 TGGCAT
1197629 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1199387 original size:32 final size:32
Alignment explanation
Indices: 1199345--1199422 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
1199335 TTAATAATTC
* *
1199345 TAAATAAATAA-AATTATATAAATATTATT-TTAA
1 TAAA-AAATAATAATTACATAAATA-TATTAAT-A
*
1199378 TAAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTACATAAATATATTAATA
1199410 TAAAAAATAATAA
1 TAAAAAATAATAA
1199423 CTATTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 23 0.59
33 16 0.41
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATATTAATA
Found at i:1216346 original size:21 final size:20
Alignment explanation
Indices: 1216260--1216417 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1216250 AAATGACCAA
**
1216260 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1216279 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1216299 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1216319 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1216340 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1216361 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1216381 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1216402 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1216418 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1216449 original size:20 final size:20
Alignment explanation
Indices: 1216384--1216633 Score: 220
Period size: 20 Copynumber: 12.5 Consensus size: 20
1216374 CGATTTTCCA
* ** *
1216384 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1216404 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
* *
1216424 AAATCGCAATGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1216444 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1216464 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1216484 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1216504 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1216524 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1216544 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1216564 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1216584 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1216604 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1216624 AAATCACAAC
1 AAATCGCAAC
1216634 ACTGAAATTT
Statistics
Matches: 188, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.01
20 184 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1216546 original size:40 final size:40
Alignment explanation
Indices: 1216438--1216633 Score: 279
Period size: 40 Copynumber: 4.9 Consensus size: 40
1216428 CGCAATGTGT
* * * *
1216438 ATCCGTATATCGCAACGCGTATCCGTAAATCGCAATGCG-T-
1 ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA--CGATA
* * * *
1216478 ATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATA
1216518 ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATA
1216558 ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATA
*
1216598 ATCCGTAAATCGCAACGAGAATCTGTAAATCACAAC
1 ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAAC
1216634 ACTGAAATTT
Statistics
Matches: 149, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 146 0.98
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (40 bp):
ATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATA
Found at i:1217355 original size:24 final size:24
Alignment explanation
Indices: 1217316--1217362 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1217306 AAATTTGCTC
1217316 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1217340 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1217363 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1217554 original size:12 final size:12
Alignment explanation
Indices: 1217537--1217561 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1217527 ATATAATCCT
1217537 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1217549 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1217561 G
1 G
1217562 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1219929 original size:19 final size:19
Alignment explanation
Indices: 1219860--1220068 Score: 259
Period size: 19 Copynumber: 11.7 Consensus size: 19
1219850 GCAACGAGAG
1219860 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1219879 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1219893 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1219913 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1219932 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1219951 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1219965 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1219984 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1220003 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1220017 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1220037 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1220056 AATCGCATTGCGA
1 AATCGCAATGCGA
1220069 TTCTCTCGTT
Statistics
Matches: 166, Mismatches: 7, Indels: 34
0.80 0.03 0.16
Matches are distributed among these distances:
14 32 0.19
15 2 0.01
16 4 0.02
17 6 0.04
18 1 0.01
19 92 0.55
20 29 0.17
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1219953 original size:72 final size:71
Alignment explanation
Indices: 1219860--1220068 Score: 289
Period size: 72 Copynumber: 2.9 Consensus size: 71
1219850 GCAACGAGAG
*
1219860 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCG
1219925 AAATGAA
65 AAATGAA
*
1219932 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCG
1219996 AAATGAA
65 AAATGAA
* * * * *
1220003 AATCGCAACGAGAGAATCG-CAATGCGGAA-ATGAAAATCGCAATGCGAAATGAAAATCGCATTG
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACATGAAAATCGCAATGCGAAATGAAAATCGCAATG
1220066 CGA
63 CGA
1220069 TTCTCTCGTT
Statistics
Matches: 124, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
71 39 0.31
72 79 0.64
73 6 0.05
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAA
Found at i:1219974 original size:105 final size:102
Alignment explanation
Indices: 1219846--1220062 Score: 314
Period size: 105 Copynumber: 2.1 Consensus size: 102
1219836 CGGAAATTAC
1219846 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-C-ATGAAAATCGCAATGCGGAAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAGCAATGAAAATCGCAA--C-G--A
1219909 TGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
61 -GAAAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
1219951 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-GC--AATGAAAATCGCAACGAGA
*
1220016 GAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
63 AAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1220056 AATCGCA
1 AATCGCA
1220063 TTGCGATTCT
Statistics
Matches: 104, Mismatches: 2, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
104 13 0.12
105 75 0.72
107 2 0.02
108 1 0.01
110 13 0.12
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (102 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAGCAATGAAAATCGCAACGAGAAAA
TCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1220102 original size:53 final size:52
Alignment explanation
Indices: 1220039--1220154 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
1220029 GAAATGAAAA
*
1220039 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
1220091 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1220144 TCGCATTGCGA
1 TCGCATTGCGA
1220155 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1220171 original size:52 final size:53
Alignment explanation
Indices: 1220058--1220174 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1220048 GAAATGAAAA
1220058 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1220111 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1220163 TCGCATTGCGAT
1 TCGCATTGCGAT
1220175 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1220182 original size:19 final size:19
Alignment explanation
Indices: 1220077--1220174 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1220067 GATTCTCTCG
1220077 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1220097 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1220116 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1220130 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1220149 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1220168 TTGCGAT
1 TTGCGAT
1220175 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1220300 original size:14 final size:14
Alignment explanation
Indices: 1220281--1220317 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1220271 CATCAATTAC
1220281 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1220295 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1220309 ACAAATCAA
1 ACAAATCAA
1220318 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1222315 original size:14 final size:14
Alignment explanation
Indices: 1222296--1222352 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1222286 GCGAAATGAA
*
1222296 AATCGCAACGACAG
1 AATCGCAACGAAAG
1222310 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1222327 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1222343 AATCGCAACG
1 AATCGCAACG
1222353 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1222323 original size:33 final size:33
Alignment explanation
Indices: 1222277--1222369 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1222267 GCGAAACCAA
*
1222277 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1222310 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1222343 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1222370 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1222334 original size:19 final size:19
Alignment explanation
Indices: 1222240--1222374 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1222230 TAGTTTACTT
* *
1222240 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1222260 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1222279 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1222298 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1222312 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1222331 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1222345 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1222364 TCGCAATGCGA
1 TCGCAACGCGA
1222375 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1222392 original size:19 final size:19
Alignment explanation
Indices: 1222370--1222498 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1222360 AAAATCGCAA
1222370 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1222389 TGCGA-TCT--TAT--CGT
1 TGCGATTTTGGTTTCGCGT
1222403 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1222422 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1222436 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1222455 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1222474 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1222494 TGCGA
1 TGCGA
1222499 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 3 0.03
17 3 0.03
18 3 0.03
19 45 0.51
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1222412 original size:33 final size:33
Alignment explanation
Indices: 1222370--1222461 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1222360 AAAATCGCAA
1222370 TGCGATTTTGGTTTCGCGTTGCGA-TCTTATCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TATCGT
*
1222403 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
**
1222436 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1222462 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
Found at i:1222701 original size:93 final size:93
Alignment explanation
Indices: 1222542--1223015 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
1222532 TTGAATGGAT
1222542 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1222607 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1222635 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1222700 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1222728 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1222793 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1222821 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1222886 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1222914 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTTAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1222979 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1223007 AAATTTACT
1 AAATTTACT
1223016 AAGCAATCTA
Statistics
Matches: 377, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 377 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1224732 original size:14 final size:14
Alignment explanation
Indices: 1224713--1224802 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1224703 TTGAAATGAA
1224713 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1224727 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1224744 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1224760 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1224779 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1224793 AATCGCAACG
1 AATCGCAACG
1224803 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1224750 original size:33 final size:33
Alignment explanation
Indices: 1224705--1224819 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1224695 TCTTTTGGTT
1224705 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1224738 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1224771 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1224804 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1224820 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1224751 original size:19 final size:18
Alignment explanation
Indices: 1224712--1224824 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1224702 GTTGAAATGA
1224712 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1224727 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1224744 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1224760 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1224777 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1224793 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1224810 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1224825 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1224842 original size:19 final size:18
Alignment explanation
Indices: 1224820--1224878 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
1224810 AAAATCGCAA
1224820 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1224839 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1224853 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1224872 TGCGATT
1 TGCGATT
1224879 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 11 0.34
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.56
ACGTcount: A:0.08, C:0.19, G:0.27, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1224868 original size:33 final size:33
Alignment explanation
Indices: 1224820--1224890 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1224810 AAAATCGCAA
** *
1224820 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1224853 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1224886 TGCGA
1 TGCGA
1224891 CAGTCATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.08, C:0.21, G:0.27, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1224898 original size:33 final size:33
Alignment explanation
Indices: 1224831--1224912 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
1224821 GCGATTTTGG
* ***
1224831 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1224864 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1224897 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1224913 TTCATTTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 31 0.72
34 12 0.28
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1225058 original size:33 final size:33
Alignment explanation
Indices: 1225011--1225081 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1225001 AATACTAACT
* *
1225011 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1225044 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1225077 TGAAA
1 TGAAA
1225082 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1225315 original size:22 final size:22
Alignment explanation
Indices: 1225263--1225317 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1225253 TGGTTGTGAG
**
1225263 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1225285 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1225307 GGATTTCTTCG
1 GGATTTCTTCG
1225318 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1225488 original size:20 final size:20
Alignment explanation
Indices: 1225463--1225656 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1225453 CTTTAAATAT
1225463 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1225483 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1225505 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1225524 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1225544 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1225564 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1225584 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1225604 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1225624 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1225644 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1225657 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1225650 original size:60 final size:60
Alignment explanation
Indices: 1225463--1225656 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1225453 CTTTAAATAT
**
1225463 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1225524 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1225584 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1225644 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1225657 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1225673 original size:21 final size:21
Alignment explanation
Indices: 1225643--1225725 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1225633 ATTTTCATAT
*
1225643 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1225664 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1225685 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1225706 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1225726 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1225716 original size:42 final size:43
Alignment explanation
Indices: 1225623--1225721 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1225613 ATTTATGTGT
* *
1225623 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1225664 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1225706 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1225722 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1226862 original size:30 final size:31
Alignment explanation
Indices: 1226818--1226889 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
1226808 AGACCCCGAT
* * * *
1226818 AACTATCCAGAGGTCATAAAGAACCTCGG-C
1 AACTGTCCATAGGTCATAAAGAACCTAGGTA
*
1226848 AACTGTCCATAGGTCCTAAAGAACCTAGGTA
1 AACTGTCCATAGGTCATAAAGAACCTAGGTA
1226879 AACTGTCCATA
1 AACTGTCCATA
1226890 TGTTCCGTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 25 0.69
31 11 0.31
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (31 bp):
AACTGTCCATAGGTCATAAAGAACCTAGGTA
Found at i:1239527 original size:11 final size:11
Alignment explanation
Indices: 1239513--1239566 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
1239503 GAGTGTTAAC
1239513 AGTTTGTTATT
1 AGTTTGTTATT
1239524 AGTTTGTTA-T
1 AGTTTGTTATT
*
1239534 GGTTTGTTATT
1 AGTTTGTTATT
*
1239545 AGCTTGTTATT
1 AGTTTGTTATT
*
1239556 AATTTGTTATT
1 AGTTTGTTATT
1239567 GTTGTTGGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 9 0.24
11 28 0.76
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.61
Consensus pattern (11 bp):
AGTTTGTTATT
Found at i:1239540 original size:21 final size:21
Alignment explanation
Indices: 1239514--1239554 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1239504 AGTGTTAACA
*
1239514 GTTTGTTATTAGTTTGTTATG
1 GTTTGTTATTAGCTTGTTATG
1239535 GTTTGTTATTAGCTTGTTAT
1 GTTTGTTATTAGCTTGTTAT
1239555 TAATTTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.02, G:0.22, T:0.61
Consensus pattern (21 bp):
GTTTGTTATTAGCTTGTTATG
Found at i:1241814 original size:21 final size:21
Alignment explanation
Indices: 1241789--1241868 Score: 108
Period size: 21 Copynumber: 3.8 Consensus size: 21
1241779 AATGTTAGAG
* *
1241789 TGTTAATAGTTTGTTA-TGGTT
1 TGTTATTAGTTTGTTATTAG-T
* *
1241810 TGTTATTAGCTTGTTATTAGC
1 TGTTATTAGTTTGTTATTAGT
1241831 TGTTATTAGTTTGTTATTAGT
1 TGTTATTAGTTTGTTATTAGT
1241852 TGTTATTAGTTTGTTAT
1 TGTTATTAGTTTGTTAT
1241869 GGTTGTTGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 50 0.96
22 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.20, T:0.59
Consensus pattern (21 bp):
TGTTATTAGTTTGTTATTAGT
Found at i:1241823 original size:11 final size:11
Alignment explanation
Indices: 1241809--1241868 Score: 88
Period size: 11 Copynumber: 5.6 Consensus size: 11
1241799 TTGTTATGGT
1241809 TTGTTATTAGC
1 TTGTTATTAGC
1241820 TTGTTATTAGC
1 TTGTTATTAGC
*
1241831 -TGTTATTAGT
1 TTGTTATTAGC
1241841 TTGTTATTAG-
1 TTGTTATTAGC
*
1241851 TTGTTATTAGT
1 TTGTTATTAGC
1241862 TTGTTAT
1 TTGTTAT
1241869 GGTTGTTGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
10 19 0.41
11 27 0.59
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.60
Consensus pattern (11 bp):
TTGTTATTAGC
Found at i:1241834 original size:10 final size:10
Alignment explanation
Indices: 1241810--1241860 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
1241800 TGTTATGGTT
1241810 TGTTATTAGC
1 TGTTATTAGC
1241820 TTGTTATTAGC
1 -TGTTATTAGC
*
1241831 TGTTATTAGTT
1 TGTTATTAG-C
*
1241842 TGTTATTAGT
1 TGTTATTAGC
1241852 TGTTATTAG
1 TGTTATTAG
1241861 TTTGTTATGG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
10 19 0.50
11 19 0.50
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.57
Consensus pattern (10 bp):
TGTTATTAGC
Found at i:1256232 original size:70 final size:65
Alignment explanation
Indices: 1256144--1256289 Score: 168
Period size: 65 Copynumber: 2.2 Consensus size: 65
1256134 AGAGAATAAA
* *
1256144 ATTATTATGATATTAAAATTACAAT-GTTCATGAATATATATAAAATTTTATATAGATTCAAAGA
1 ATTATTATAATATAAAAATTACAATGGTTCATG---A-ATATAAAA-TTT-TATAGATTCAAAGA
1256208 TTCCAT
60 TTCCAT
* * * *
1256214 ATTATTATAATATAAAAATTACAATGGTTTATGACTATAAGATTTTATAGATTCAAATATTCCAT
1 ATTATTATAATATAAAAATTACAATGGTTCATGAATATAAAATTTTATAGATTCAAAGATTCCAT
*
1256279 CTTATTATAAT
1 ATTATTATAAT
1256290 TATAGGTTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
65 29 0.43
66 3 0.04
67 6 0.09
68 1 0.01
70 23 0.34
71 6 0.09
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (65 bp):
ATTATTATAATATAAAAATTACAATGGTTCATGAATATAAAATTTTATAGATTCAAAGATTCCAT
Done.