Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 41 of 206
Found at i:11652644 original size:116 final size:116
Alignment explanation
Indices: 11652440--11652657 Score: 400
Period size: 116 Copynumber: 1.9 Consensus size: 116
11652430 TGATAAATTG
*
11652440 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATACAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
11652505 TAGTACCAATCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAATCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
* *
11652556 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
*
11652621 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
66 TAGTACCAATCAAAACATTTTTCCAAATCTAACATTA
11652658 CGTTAAGGTT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 98 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.39
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAATCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
Found at i:11652769 original size:22 final size:22
Alignment explanation
Indices: 11652744--11652799 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
11652734 AAATATAGAT
11652744 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
11652766 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
11652788 TTGAGAGGAATT
1 TTGAGA-GAATT
11652800 GAGAGGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:11652816 original size:12 final size:11
Alignment explanation
Indices: 11652760--11652816 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
11652750 GAATTTTGGA
11652760 AGGAAATTGAG
1 AGGAAATTGAG
*
11652771 A-GAATTTTG-G
1 AGGAA-ATTGAG
11652781 AAGGAAATTGAG
1 -AGGAAATTGAG
11652793 AGG-AATTGAG
1 AGGAAATTGAG
11652803 AGGAAATATGAG
1 AGGAAAT-TGAG
11652815 AG
1 AG
11652817 AGGATTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 14 0.37
11 14 0.37
12 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:11654820 original size:3 final size:3
Alignment explanation
Indices: 11654812--11654848 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
11654802 TTTAGTTTAA
* *
11654812 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAG TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11654849 TTTTTATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:11654952 original size:21 final size:24
Alignment explanation
Indices: 11654898--11654952 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 24
11654888 TTATTATGTA
11654898 GTATTATTTTAAGTTTTCCATATAT
1 GTATTATTTTAAG-TTTCCATATAT
11654923 -TATTA-TTTAA-TTT-CATA-AT
1 GTATTATTTTAAGTTTCCATATAT
11654942 GTATTATTTTA
1 GTATTATTTTA
11654953 TATATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.07
20 9 0.32
21 7 0.25
23 5 0.18
24 5 0.18
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.58
Consensus pattern (24 bp):
GTATTATTTTAAGTTTCCATATAT
Found at i:11657563 original size:152 final size:153
Alignment explanation
Indices: 11656985--11657547 Score: 787
Period size: 153 Copynumber: 3.7 Consensus size: 153
11656975 TTTAGTGTGT
* * * * *
11656985 TTTTTATTGAAAGTAATAAAATCCGGGGAAAAAATAAGAGCAAAGGGCCGAAATAAGGGTTTTTT
1 TTTTTATTAAAAGTAATAAAAT-CTGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGTTTTTT
*
11657050 TTTAAATTTATTTAAAAAACACAGTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTA
64 TTT-AATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTA
*
11657115 AAATAATAAAA-TATGAAAATAATATA
128 AAATAATAAAATTA-GAAAATAGTATA
* *
11657141 TTTTTATTAAAAGTAATAAAATCCGGAAAAAAAATACGAACAAATGGCCGAAATAAGAG--TTTT
1 TTTTTATTAAAAGTAATAAAATCTGG-AAAAAAATACGAACAAAGGGCCGAAATAAG-GTTTTTT
* **
11657204 TTTAATTTATTTAAAAAACACACTAAATGAATACTTTTCAAATGTAATGTACTAAAATAATGTAA
64 TTTAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
*
11657269 AATAATAAAATTATAAAATAGTATA
129 AATAATAAAATTAGAAAATAGTATA
* * **
11657294 TTTTTATTGAAAGTGATAAAATCTGGAAAAAAATACGAACAAAGGGTTGAAATAAAGGTTTTTTT
1 TTTTTATTAAAAGTAATAAAATCTGGAAAAAAATACGAACAAAGGGCCGAAAT-AAGGTTTTTTT
* * *
11657359 TAAATTTATTTAAAAAACACATTAAATGAATACATTTCAAACATAATGTACTAAAATAATTTAAA
65 TTAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
11657424 ATAATAAAATTAGAAAATAGTATA
130 ATAATAAAATTAGAAAATAGTATA
* * *
11657448 -TTTT-TTAAAAGTAATAAAATCTAGGGAAAAAATAC-AACAAATGGCTGAAATAATGGTTTTTT
1 TTTTTATTAAAAGTAATAAAATCT-GGAAAAAAATACGAACAAAGGGCCGAAATAA-GGTTTTTT
*
11657510 TTTAATTTATTTAAAAAACACTCTAAATGAATACATTT
64 TTTAATTTATTTAAAAAACACACTAAATGAATACATTT
11657548 TTAAAAAAAT
Statistics
Matches: 366, Mismatches: 33, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
151 2 0.01
152 98 0.27
153 119 0.33
154 96 0.26
155 4 0.01
156 47 0.13
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (153 bp):
TTTTTATTAAAAGTAATAAAATCTGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTT
TAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
TAATAAAATTAGAAAATAGTATA
Found at i:11657803 original size:118 final size:119
Alignment explanation
Indices: 11657571--11657805 Score: 400
Period size: 119 Copynumber: 2.0 Consensus size: 119
11657561 CTATTTTCTA
* *
11657571 ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTA
1 ATTTTATTATTTTACATTATTTTAGTACAGTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTA
**
11657636 AATAAATTTTAAAAAAAATTCTTATTTCGGCCCTTTGTTCGTATGTTTTTCCGG
66 AATAAATTTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATGTTTTTCCGG
*
11657690 ATTTTATTATTTTACATTATTTTAGTACAGTATGTTTGAAATGTATTAATTTATTGTGTTTTTTA
1 ATTTTATTATTTTACATTATTTTAGTACAGTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTA
* *
11657755 AATAAA-TTTAAAAAACACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCC
66 AATAAATTTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATGTTTTTCC
11657806 CCGAATTTTA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
118 41 0.38
119 68 0.62
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (119 bp):
ATTTTATTATTTTACATTATTTTAGTACAGTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTA
AATAAATTTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATGTTTTTCCGG
Found at i:11662914 original size:27 final size:27
Alignment explanation
Indices: 11662876--11662929 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
11662866 ACACAGTGTG
11662876 TAGTTGATACTCCCAAGAAGCCAATCT
1 TAGTTGATACTCCCAAGAAGCCAATCT
11662903 TAGTTGATACTCCCAAGAAGCCAATCT
1 TAGTTGATACTCCCAAGAAGCCAATCT
11662930 ATCCTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (27 bp):
TAGTTGATACTCCCAAGAAGCCAATCT
Found at i:11681038 original size:7 final size:7
Alignment explanation
Indices: 11681026--11681052 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
11681016 TAACATATTT
11681026 TTTTTTA
1 TTTTTTA
11681033 TTTTTTA
1 TTTTTTA
11681040 TTTTTTA
1 TTTTTTA
11681047 TTTTTT
1 TTTTTT
11681053 CAATTTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:11685779 original size:5 final size:5
Alignment explanation
Indices: 11685769--11685794 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11685759 GAGATGGAAT
11685769 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
11685795 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:11690368 original size:5 final size:5
Alignment explanation
Indices: 11690358--11690387 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
11690348 TGCCTTATCA
11690358 AATCT AATCT AATCT AATCT AATCT AATCT
1 AATCT AATCT AATCT AATCT AATCT AATCT
11690388 TTACAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
AATCT
Found at i:11693419 original size:21 final size:21
Alignment explanation
Indices: 11693378--11693420 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
11693368 ACCCCAAACT
* *
11693378 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
11693399 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
11693420 C
1 C
11693421 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:11693574 original size:30 final size:31
Alignment explanation
Indices: 11693526--11693585 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
11693516 AAACCTTTTA
**
11693526 TTTTCCCCCAAAGTTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
11693556 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
11693586 TTCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.40, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:11694344 original size:5 final size:5
Alignment explanation
Indices: 11694334--11694364 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
11694324 CTCAAAAATT
11694334 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
11694365 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:11699479 original size:35 final size:35
Alignment explanation
Indices: 11699433--11699502 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
11699423 AAAAAAAATG
11699433 TAAGTACCATAATTGATATCTATGGATTATGATAT
1 TAAGTACCATAATTGATATCTATGGATTATGATAT
11699468 TAAGTACCATAATTGATATCTATGGATTATGATAT
1 TAAGTACCATAATTGATATCTATGGATTATGATAT
11699503 CATGTGGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (35 bp):
TAAGTACCATAATTGATATCTATGGATTATGATAT
Found at i:11700723 original size:24 final size:25
Alignment explanation
Indices: 11700671--11700742 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
11700661 AAATTTAAAA
11700671 TTATATATTATTATGAC-TTTTTAACAT
1 TTATATATTA-TAT--CTTTTTTAACAT
*
11700698 TTATAT-TTATAT-TTTTTTAATTAT
1 TTATATATTATATCTTTTTTAA-CAT
*
11700722 TTATATATTATTTCTTTTTTA
1 TTATATATTATATCTTTTTTA
11700743 CTTTTTAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 7 0.18
24 8 0.21
25 8 0.21
26 10 0.26
27 6 0.15
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (25 bp):
TTATATATTATATCTTTTTTAACAT
Found at i:11705222 original size:21 final size:23
Alignment explanation
Indices: 11705191--11705232 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
11705181 AGCTTTATTT
11705191 TTCACCCATTTGATC-TTTTAAC
1 TTCACCCATTTGATCATTTTAAC
*
11705213 TTCA-CCATTTGTTCATTTTA
1 TTCACCCATTTGATCATTTTA
11705233 TAGCTATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.21, C:0.24, G:0.05, T:0.50
Consensus pattern (23 bp):
TTCACCCATTTGATCATTTTAAC
Found at i:11706742 original size:46 final size:46
Alignment explanation
Indices: 11706594--11706802 Score: 361
Period size: 46 Copynumber: 4.6 Consensus size: 46
11706584 TACGTATGAT
* *
11706594 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
11706637 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC-TAAAGCTAC
*
11706684 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCCAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
11706730 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
11706776 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
11706803 AGTACTCAAA
Statistics
Matches: 158, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
43 10 0.06
44 5 0.03
45 19 0.12
46 81 0.51
47 43 0.27
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:11708634 original size:21 final size:21
Alignment explanation
Indices: 11708610--11708651 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
11708600 CTTTTTGTTC
11708610 AATTAATT-ATCGAAACTTTAA
1 AATTAATTAAT-GAAACTTTAA
**
11708631 AATTTCTTAATGAAACTTTAA
1 AATTAATTAATGAAACTTTAA
11708652 TACTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
AATTAATTAATGAAACTTTAA
Found at i:11711468 original size:21 final size:23
Alignment explanation
Indices: 11711447--11711490 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11711437 AAAATTGTTT
11711447 AATTAA-AAA-AATAATTTATTTA
1 AATTAATAAATAAT-ATTTATTTA
11711469 AATTAATAAATAATATTTATTT
1 AATTAATAAATAATATTTATTT
11711491 TGGGAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 11 0.55
24 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTAATAAATAATATTTATTTA
Found at i:11718166 original size:2 final size:2
Alignment explanation
Indices: 11718159--11718183 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11718149 TTGAATAGAT
11718159 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
11718184 TTTGTAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11721493 original size:17 final size:17
Alignment explanation
Indices: 11721469--11721506 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
11721459 TTAAATTTTG
*
11721469 AAAAAAAATAAATTGTAA
1 AAAAAAAAGAAATT-TAA
11721487 AAAAAAAAGAAATTTAA
1 AAAAAAAAGAAATTTAA
11721504 AAA
1 AAA
11721507 TAATTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAAAAAAGAAATTTAA
Found at i:11721687 original size:2 final size:2
Alignment explanation
Indices: 11721675--11721714 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
11721665 TTTTTAGTCA
11721675 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11721715 ACATTAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11732278 original size:42 final size:42
Alignment explanation
Indices: 11732232--11732318 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
11732222 TAGCTCTCAC
* * * *
11732232 GAGCTTCTGTTTAA-CTTATATGAGTTTCCGTTCAGCTCTTTT
1 GAGCTTCTATTTAACCCT-TATGAGTTTCCGTTCAACTCTTAT
*
11732274 GAGCTTCTATTTAACCCTTATGGGTTTCCGTTCAACTCTTAT
1 GAGCTTCTATTTAACCCTTATGAGTTTCCGTTCAACTCTTAT
11732316 GAG
1 GAG
11732319 GTTCCGTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 37 0.95
43 2 0.05
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
GAGCTTCTATTTAACCCTTATGAGTTTCCGTTCAACTCTTAT
Found at i:11732316 original size:21 final size:20
Alignment explanation
Indices: 11732289--11732343 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 20
11732279 TCTATTTAAC
11732289 CCTTATGGGTTTCCGTTCAA
1 CCTTATGGGTTTCCGTTCAA
11732309 CTCTTATGAGG-TTCCGTTCAA
1 C-CTTATG-GGTTTCCGTTCAA
11732330 CCTTTATGGGTTTC
1 CC-TTATGGGTTTC
11732344 TGTTTAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.13
21 25 0.81
22 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.42
Consensus pattern (20 bp):
CCTTATGGGTTTCCGTTCAA
Found at i:11732337 original size:42 final size:42
Alignment explanation
Indices: 11732250--11732343 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
11732240 GTTTAACTTA
* * * * *
11732250 TATGAGTTTCCGTTCAGCTCTTTTGAGCTTCTATTTAACCCT
1 TATGGGTTTCCGTTCAACTCTTATGAGCTTCCATTCAACCCT
* * *
11732292 TATGGGTTTCCGTTCAACTCTTATGAGGTTCCGTTCAACCTT
1 TATGGGTTTCCGTTCAACTCTTATGAGCTTCCATTCAACCCT
11732334 TATGGGTTTC
1 TATGGGTTTC
11732344 TGTTTAGCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (42 bp):
TATGGGTTTCCGTTCAACTCTTATGAGCTTCCATTCAACCCT
Found at i:11732356 original size:21 final size:21
Alignment explanation
Indices: 11732332--11732372 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11732322 CCGTTCAACC
*
11732332 TTTATG-GGTTTCTGTTTAGCA
1 TTTATGTGCTTTC-GTTTAGCA
11732353 TTTATGTGCTTTCGTTTAGC
1 TTTATGTGCTTTCGTTTAGC
11732373 CTTCGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.54
Consensus pattern (21 bp):
TTTATGTGCTTTCGTTTAGCA
Found at i:11736312 original size:24 final size:24
Alignment explanation
Indices: 11736280--11736364 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
11736270 ACAGCCTCGT
*
11736280 CCATTCCCTCCTCGCCCACCACGA
1 CCATTCCCTCCTCACCCACCACGA
* *
11736304 CCATTCCCTCCTCACCCGCCGCGA
1 CCATTCCCTCCTCACCCACCACGA
** *
11736328 CCGGTCCCTCCTCATCCACCACGA
1 CCATTCCCTCCTCACCCACCACGA
11736352 CCATTCCCTCCTC
1 CCATTCCCTCCTC
11736365 CTCATCCTCA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.14, C:0.58, G:0.09, T:0.19
Consensus pattern (24 bp):
CCATTCCCTCCTCACCCACCACGA
Found at i:11743056 original size:40 final size:40
Alignment explanation
Indices: 11743009--11743144 Score: 166
Period size: 40 Copynumber: 3.3 Consensus size: 40
11742999 CTACAACGTC
11743009 AGGGAGATAAGACTTGCTGTGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGACTTGCTGTGATCTGCTCCACTACTGCTT
* * *
11743049 AGGGAGATAAGACTTGATGCGATTTGCTCCACTACTGCTT
1 AGGGAGATAAGACTTGCTGTGATCTGCTCCACTACTGCTT
* * *
11743089 AGGGAGATAAGATCTGGTTTCTTTCG-TCTGCTTCACTACTGCTT
1 AGGGAGATAAGA-C---TTGCTGT-GATCTGCTCCACTACTGCTT
11743133 AGGGAGATAAGA
1 AGGGAGATAAGA
11743145 TCTGTGGTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
40 49 0.60
41 1 0.01
44 31 0.38
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (40 bp):
AGGGAGATAAGACTTGCTGTGATCTGCTCCACTACTGCTT
Found at i:11743260 original size:46 final size:44
Alignment explanation
Indices: 11743167--11743493 Score: 239
Period size: 46 Copynumber: 7.5 Consensus size: 44
11743157 ATCCGTTCCG
* * * *
11743167 CTGTAACTTCAGGGAGATAGGAT-AG-TGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTGAT-TCTTCGATCTGCTCCA
* * *
11743210 CTGTAACCTCAGGGGGATAAGATCTGAAATTCTTCGATCTACTCTA
1 CTGTAACCTCAGGGAGATAAGATCTG--ATTCTTCGATCTGCTCCA
* * *
11743256 CTGTAACCTCAGGGAGATAAGACCTG----TGCGATCTGCTCTA
1 CTGTAACCTCAGGGAGATAAGATCTGATTCTTCGATCTGCTCCA
* * * * *
11743296 CTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-AATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGAT-C-TGATTCTTCGATCTGCTCCA
* * * *
11743340 CTGTAACTTCAGGGAGATAGGAT-T-ATGTCTTCAATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTGAT-TCTTCGATCTGCTCCA
* * *
11743383 CTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCTG--ATTCTTCGATCTGCTCCA
* * * *
11743429 CTGTAACCTCAGGGAGATAAGACCTG---GTGCGATCTGCTCTA
1 CTGTAACCTCAGGGAGATAAGATCTGATTCTTCGATCTGCTCCA
* *
11743470 CTGTAACTTCAGAGAGATAAGATC
1 CTGTAACCTCAGGGAGATAAGATC
11743494 GGTTTTTCGT
Statistics
Matches: 229, Mismatches: 39, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
40 34 0.15
41 34 0.15
42 3 0.01
43 50 0.22
44 31 0.14
45 1 0.00
46 74 0.32
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (44 bp):
CTGTAACCTCAGGGAGATAAGATCTGATTCTTCGATCTGCTCCA
Found at i:11743268 original size:89 final size:88
Alignment explanation
Indices: 11743167--11743493 Score: 324
Period size: 87 Copynumber: 3.8 Consensus size: 88
11743157 ATCCGTTCCG
* *
11743167 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGGGATAAGA
1 CTGTAACCTCAGGGAGATAGGATA-TGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
*
11743232 TCTGAAATTCTTCGATCTACTCTA
65 TCTGAAATTCTTCGATCTACTCCA
* ** * ** * *
11743256 CTGTAACCTCAGGGAGATAAGACCTG--TGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGAT
1 CTGTAACCTCAGGGAGATAGGATATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGAT
** * **
11743319 CCT-TTATT-TT-AATCCGCTCCA
66 -CTGAAATTCTTCGATCTACTCCA
* *
11743340 CTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
1 CTGTAACCTCAGGGAGATAGGA-TATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
* *
11743405 TCTGAAAGTCTTCGGTCTACTCCA
65 TCTGAAATTCTTCGATCTACTCCA
* ** * * ** * *
11743429 CTGTAACCTCAGGGAGATAAGACCTG-GTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGAT
1 CTGTAACCTCAGGGAGATAGGATATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGAT
11743493 C
66 C
11743494 GGTTTTTCGT
Statistics
Matches: 187, Mismatches: 44, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
84 27 0.14
85 4 0.02
86 36 0.19
87 67 0.36
88 6 0.03
89 47 0.25
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (88 bp):
CTGTAACCTCAGGGAGATAGGATATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGAT
CTGAAATTCTTCGATCTACTCCA
Found at i:11743331 original size:173 final size:174
Alignment explanation
Indices: 11743152--11743493 Score: 598
Period size: 173 Copynumber: 2.0 Consensus size: 174
11743142 AGATCTGTGG
* * *
11743152 TTTTAATCCGTTCCGCTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAA
1 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTA-TGTCTTCAATCTGCTCCGCTGTAA
* * *
11743216 CCTCAGGGGGATAAGATCTGAAATTCTTCGATCTACTCTACTGTAACCTCAGGGAGATAAGACCT
65 CCTCAGGGAGATAAGATCTGAAAGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCT
11743281 -GTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTTTA
130 GGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTTTA
11743325 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAAC
1 TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAAC
*
11743390 CTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG
66 CTCAGGGAGATAAGATCTGAAAGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTG
11743455 GTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATC
131 GTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATC
11743494 GGTTTTTCGT
Statistics
Matches: 160, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
173 119 0.74
174 41 0.26
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (174 bp):
TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAAC
CTCAGGGAGATAAGATCTGAAAGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACCTG
GTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTTTA
Found at i:11743779 original size:88 final size:88
Alignment explanation
Indices: 11743630--11744213 Score: 979
Period size: 88 Copynumber: 6.6 Consensus size: 88
11743620 NNNNNNNNNN
* *
11743630 AGGTTTGTGTCTTCGACCTGTTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAG
**
11743695 CTCCATCACAATTGAGAGAGGCA
66 CTCCATCACAACCGAGAGAGGCA
11743718 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAG
11743783 CTCCATCACAACCGAGAGAGGCA
66 CTCCATCACAACCGAGAGAGGCA
* *
11743806 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTATCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAG
*
11743871 CTCCATCACAACCGAGAAAGGCA
66 CTCCATCACAACCGAGAGAGGCA
* * *
11743894 AGGTTTGTGTCTTAGACCTGCTTCGTTGTCAATACAGGAAGGCAAGATCTTTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAG
11743959 CTCCATCACAACCGAGAGAGGCA
66 CTCCATCACAACCGAGAGAGGCA
* * * * *
11743982 AGGTTTGTGTCTTCGACCTACTTCGCTGTCAATGTAGGAAGGCAAGATATATTATCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAG
11744047 CTCCATCACAACCGAGAGAGGCA
66 CTCCATCACAACCGAGAGAGGCA
*
11744070 AGGTTTGTGTCTTCGACCTGCTTCACTGTCAATCAATGCAGGAAGGCAAGATCTTTTGTCTTCAA
1 AGGTTTGTGTCTTCGACCTGCTTCGCTG----TCAATGCAGGAAGGCAAGATCTTTTGTCTTCAA
*
11744135 CCAGCTCCATCACAACCGAGAGAGGTA
62 CCAGCTCCATCACAACCGAGAGAGGCA
11744162 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
11744214 AACTTCGTTG
Statistics
Matches: 463, Mismatches: 29, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
88 381 0.82
92 82 0.18
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (88 bp):
AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAG
CTCCATCACAACCGAGAGAGGCA
Found at i:11747193 original size:44 final size:44
Alignment explanation
Indices: 11747130--11747567 Score: 290
Period size: 44 Copynumber: 9.7 Consensus size: 44
11747120 TCGGATTGAG
* *
11747130 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA
* * * ** *
11747174 CAAATCTTATCTCGCTGAAGCTGCAATAAAGTAGATTGAAGCAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA
* * *
11747218 CAAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA
* * ** *
11747262 CAAATCTTATCTCCCTAAAGTTACAGTGGAACAAATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA
* *
11747306 CAAATCTTATCTCGCTGAAGTTGCAGTGGAATAGATTGAAG-TGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCT-A
* * * * *
11747350 CAAATCCTATAC-CTCTGAAGTTGCAGTGG-GTCGAATTAAATCTA
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGGAGTAG-ATTGAAGCTA
* * ** *
11747394 CCATAACGAGTCTTATTTCCCTGAAGTTACAGTGGAACAAATTAAAGGTACAAGCTA
1 -C--AA--A-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT----G---AAGCTA
* * * * * * * *
11747451 CAAGTCATATCTCGCTGAAGTAGTAGTGGGGCAGATTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA
* * * * * * *
11747495 CGAATCTCATTTCCCTGAAGTTACAGTAGAGTAAATTGAAACTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA
* *
11747539 CAATTCCTATAC-CCCTGAAGTTGCAGTGG
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGG
11747568 GTTAGAATGA
Statistics
Matches: 297, Mismatches: 77, Indels: 40
0.72 0.19 0.10
Matches are distributed among these distances:
43 3 0.01
44 232 0.78
45 3 0.01
47 3 0.01
49 1 0.00
50 23 0.08
51 24 0.08
54 2 0.01
56 1 0.00
57 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA
Found at i:11747368 original size:132 final size:133
Alignment explanation
Indices: 11747130--11747446 Score: 374
Period size: 132 Copynumber: 2.4 Consensus size: 133
11747120 TCGGATTGAG
* * *
11747130 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCTACAAATCTTATCTCGCTGAAGC
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAACAAATTGAAGCTACAAATCTTATCTCGCTGAAGC
*
11747195 TGCAATAAAGTAGATTGAAGCAACAAATCTTATCTCCCTGAAGTTACAGTGGAGTAG-ATTAAAG
66 TGCAATAAAGTAGATTGAAGCAACAAATCCTATCTCCCTGAAGTTACAGTGG-GTAGAATTAAA-
11747259 T-TA-
129 TCTAC
* *
11747262 CAAATCTTATCTCCCTAAAGTTACAGTGGAACAAATTGAAGCTACAAATCTTATCTCGCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAACAAATTGAAGCTACAAATCTTATCTCGCTGAAGC
* * ** * * *
11747327 TGCAGTGGAA-TAGATTGAAGTGACAAATCCTATAC-CTCTGAAGTTGCAGTGGGTCGAATTAAA
66 TGCAAT-AAAGTAGATTGAAGCAACAAATCCTAT-CTCCCTGAAGTTACAGTGGGTAGAATTAAA
11747390 TCTAC
129 TCTAC
* * *
11747395 CATAACGAGTCTTATTTCCCTGAAGTTACAGTGGAACAAATTAAAGGTACAA
1 C--AA--A-TCTTATCTCCCTGAAGTTACAGTGGAACAAATTGAAGCTACAA
11747447 GCTACAAGTC
Statistics
Matches: 158, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
131 4 0.03
132 108 0.68
133 4 0.03
135 2 0.01
137 1 0.01
138 39 0.25
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (133 bp):
CAAATCTTATCTCCCTGAAGTTACAGTGGAACAAATTGAAGCTACAAATCTTATCTCGCTGAAGC
TGCAATAAAGTAGATTGAAGCAACAAATCCTATCTCCCTGAAGTTACAGTGGGTAGAATTAAATC
TAC
Found at i:11750755 original size:25 final size:24
Alignment explanation
Indices: 11750727--11750788 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
11750717 TCGGTGCATG
*
11750727 AATATTTTATATTTGAAATTTATTTA
1 AATATTTTATATTTGAAA-TT-TGTA
* *
11750753 ATATAATTTAT-TTTGATATTTGTA
1 A-ATATTTTATATTTGAAATTTGTA
11750777 AATATTTTATAT
1 AATATTTTATAT
11750789 ACATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
23 8 0.27
24 5 0.17
25 2 0.07
26 7 0.23
27 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (24 bp):
AATATTTTATATTTGAAATTTGTA
Found at i:11750783 original size:32 final size:31
Alignment explanation
Indices: 11750729--11750789 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
11750719 GGTGCATGAA
11750729 TATTTTATATTTGAAATTTATTTAATATAATT
1 TATTTTATATTTGAAA-TTATTTAATATAATT
*
11750761 TATTTTGATATTTGTAAA-TATTTTATATA
1 TATTTT-ATATTTG-AAATTATTTAATATA
11750790 CATATATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 16 0.62
33 7 0.27
34 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (31 bp):
TATTTTATATTTGAAATTATTTAATATAATT
Found at i:11751237 original size:25 final size:25
Alignment explanation
Indices: 11751204--11751253 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
11751194 TTTAAGTTCA
*
11751204 ATTTTATTTCTGAAAA-TATTTTTT
1 ATTTTATTTCTAAAAATTATTTTTT
*
11751228 ATTTTCATTTTTAAAAATTATTTTTT
1 ATTTT-ATTTCTAAAAATTATTTTTT
11751254 TAAAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTTTATTTCTAAAAATTATTTTTT
Found at i:11754879 original size:20 final size:19
Alignment explanation
Indices: 11754844--11754884 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
11754834 ATTGAAATAA
11754844 TAAAAATGAATAAAAATTT
1 TAAAAATGAATAAAAATTT
11754863 TAAAACATGAA-ATAAAATTT
1 TAAAA-ATGAATA-AAAATTT
11754883 TA
1 TA
11754885 TGAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAAAATGAATAAAAATTT
Found at i:11756431 original size:13 final size:13
Alignment explanation
Indices: 11756406--11756439 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
11756396 AACATTAGAC
11756406 TATTATTTTTATT
1 TATTATTTTTATT
11756419 TATT-TTTTGTATT
1 TATTATTTT-TATT
11756432 TATTATTT
1 TATTATTT
11756440 AGTTTGGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 12 0.63
14 3 0.16
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TATTATTTTTATT
Found at i:11757903 original size:42 final size:42
Alignment explanation
Indices: 11757805--11757907 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
11757795 ATGCTAAATG
* * * *
11757805 AAAACCCACAAGGGTTAAACTGAACCTCAAAAGAGCTTAACA
1 AAAACCCATAAGGGTTAAACTGAACCTCAAAAAAACTGAACA
* *
11757847 AAAACCCATAAGGGTTAAACTGAAGCTCAAAAAAACTGAACT
1 AAAACCCATAAGGGTTAAACTGAACCTCAAAAAAACTGAACA
* * *
11757889 GAAACTCATTAGGGTTAAA
1 AAAACCCATAAGGGTTAAA
11757908 TGGAAACTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (42 bp):
AAAACCCATAAGGGTTAAACTGAACCTCAAAAAAACTGAACA
Found at i:11761206 original size:3 final size:3
Alignment explanation
Indices: 11761198--11761250 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
11761188 ACATGGTTGG
11761198 TTA TTA TTA TTA 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 TTA TTA TTA TTA
11761246 TTA TT
1 TTA TT
11761251 GGGAATGAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11771319 original size:11 final size:11
Alignment explanation
Indices: 11771268--11771320 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
11771258 AATTTTATGA
11771268 TTTTTAATTAAT
1 TTTTTAA-TAAT
* *
11771280 TTCTTAACAAT
1 TTTTTAATAAT
*
11771291 TTTTATACATGAT
1 TTTT-TA-ATAAT
11771304 TTTTTAATAAT
1 TTTTTAATAAT
11771315 TTTTTA
1 TTTTTA
11771321 TGGTTTTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
11 16 0.48
12 10 0.30
13 7 0.21
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:11772273 original size:200 final size:200
Alignment explanation
Indices: 11771930--11772325 Score: 729
Period size: 200 Copynumber: 2.0 Consensus size: 200
11771920 TTGATTGCAG
11771930 GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAAGGTATTTA
1 GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAAGGTATTTA
*
11771995 TAGAAGAAGTCCTCTTGTCTAGTAGTGGTGATATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
66 TAGAAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
*
11772060 GAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTATGAGATTAT
131 GAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTAT
11772125 TTATA
196 TTATA
*
11772130 GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAATGTATTTA
1 GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAAGGTATTTA
* *
11772195 TAGGAGAAGTCCTCTTGTCTGGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
66 TAGAAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
* *
11772260 GAGTAGGTGAGGACGTATAAGGTAGGGCCCATTCTATTATTCCTTTTGAGAGAGTACGAGATTAT
131 GAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTAT
11772325 T
196 T
11772326 ATGTTCATTT
Statistics
Matches: 189, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 189 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (200 bp):
GGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCGTCTTAAAAGGTATTTA
TAGAAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCATT
GAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTAT
TTATA
Found at i:11778785 original size:19 final size:19
Alignment explanation
Indices: 11778763--11778823 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
11778753 TTTTTATACA
*
11778763 TTTTATATTTTTTTATAAT
1 TTTTATATTTTTTTACAAT
**
11778782 TTTTATA-AATTTTACAAT
1 TTTTATATTTTTTTACAAT
*
11778800 TTTT-TATATGTTTTACAAT
1 TTTTATAT-TTTTTTACAAT
11778819 TTTTA
1 TTTTA
11778824 CAATTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.06
18 12 0.35
19 20 0.59
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATATTTTTTTACAAT
Found at i:11778793 original size:28 final size:28
Alignment explanation
Indices: 11778753--11778839 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 28
11778743 TTAAAGGGTT
* * *
11778753 TTTTTATACATTTTATATTTTTTTATAA
1 TTTTTATAAATTTTACAATTTTTTATAA
11778781 TTTTTATAAATTTTACAATTTTTTAT-A
1 TTTTTATAAATTTTACAATTTTTTATAA
* * *
11778808 TGTTTTACAATTTTTACAA-TTTTTCTAA
1 T-TTTTATAAATTTTACAATTTTTTATAA
11778836 TTTT
1 TTTT
11778840 AACAAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 11 0.22
28 40 0.78
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTTTATAAATTTTACAATTTTTTATAA
Found at i:11778822 original size:9 final size:9
Alignment explanation
Indices: 11778772--11778844 Score: 60
Period size: 9 Copynumber: 8.0 Consensus size: 9
11778762 ATTTTATATT
*
11778772 TTTTTATAA
1 TTTTTACAA
*
11778781 TTTTTATAA
1 TTTTTACAA
*
11778790 ATTTTACAA
1 TTTTTACAA
*
11778799 TTTTTTA-TA
1 -TTTTTACAA
11778808 TGTTTTACAA
1 T-TTTTACAA
11778818 TTTTTACAA
1 TTTTTACAA
11778827 TTTTT-CTAA
1 TTTTTAC-AA
*
11778836 TTTTAACAA
1 TTTTTACAA
11778845 AATTTTAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
8 2 0.04
9 43 0.81
10 8 0.15
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTTACAA
Found at i:11778850 original size:28 final size:28
Alignment explanation
Indices: 11778762--11778851 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
11778752 TTTTTTATAC
* * * *
11778762 ATTTTATATTTTTTTATAAT-TTTTATAA
1 ATTTTACAATTTTTTAT-ATGTTTAACAA
*
11778790 ATTTTACAATTTTTTATATGTTTTACAA
1 ATTTTACAATTTTTTATATGTTTAACAA
*
11778818 TTTTTACAATTTTTCTA-AT-TTTAACAAA
1 ATTTTACAATTTTT-TATATGTTTAAC-AA
11778846 ATTTTA
1 ATTTTA
11778852 ATATACTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.13
28 44 0.83
29 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (28 bp):
ATTTTACAATTTTTTATATGTTTAACAA
Found at i:11778868 original size:29 final size:28
Alignment explanation
Indices: 11778836--11778896 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
11778826 ATTTTTCTAA
*
11778836 TTTTAACAAAATTTTAATATACTTTATAT
1 TTTTAACAAAA-TTTAATAAACTTTATAT
** * *
11778865 TTTTATTAAAATTTAATAAATTTTATTT
1 TTTTAACAAAATTTAATAAACTTTATAT
11778893 TTTT
1 TTTT
11778897 TATTTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTAACAAAATTTAATAAACTTTATAT
Found at i:11779405 original size:3 final size:3
Alignment explanation
Indices: 11779397--11779452 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
11779387 ACAATCACTC
11779397 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11779445 ATT ATT AT
1 ATT ATT AT
11779453 CTCGCAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11782043 original size:28 final size:28
Alignment explanation
Indices: 11782003--11782056 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
11781993 AAGTTCCCAT
11782003 TTTCTTTGTCTTTATTCTCTT-TTTTTCC
1 TTTCTTTGTCTTTATTCT-TTATTTTTCC
*
11782031 TTTCTTTTTCTTTATTCTTTATTTTT
1 TTTCTTTGTCTTTATTCTTTATTTTT
11782057 ATTTTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.76
Consensus pattern (28 bp):
TTTCTTTGTCTTTATTCTTTATTTTTCC
Found at i:11782055 original size:17 final size:17
Alignment explanation
Indices: 11782030--11782073 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
11782020 TCTTTTTTTC
*
11782030 CTTTCTTTTTCTTTATT
1 CTTTCTTTTTATTTATT
* *
11782047 CTTTATTTTTATTTTTT
1 CTTTCTTTTTATTTATT
11782064 CTTTCTTTTT
1 CTTTCTTTTT
11782074 GCTGTTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTCTTTTTATTTATT
Found at i:11782062 original size:34 final size:34
Alignment explanation
Indices: 11782002--11782073 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
11781992 CAAGTTCCCA
11782002 TTTTCTTTGTCTTTATTCTCTTTTTTTCCTTTCT
1 TTTTCTTTGTCTTTATTCTCTTTTTTTCCTTTCT
* *
11782036 TTTTCTTTATTCTTTATT-T-TTATTTTTTCTTTCT
1 TTTTCTTT-GTCTTTATTCTCTT-TTTTTCCTTTCT
11782070 TTTT
1 TTTT
11782074 GCTGTTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 2 0.06
34 24 0.71
35 8 0.24
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.78
Consensus pattern (34 bp):
TTTTCTTTGTCTTTATTCTCTTTTTTTCCTTTCT
Found at i:11782068 original size:28 final size:29
Alignment explanation
Indices: 11782002--11782071 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
11781992 CAAGTTCCCA
*
11782002 TTTTCTTTGTCTTTATTCTCTTTTTTTCCTT
1 TTTTC-TT-TCTTTATTCTCTTTTTTTCATT
*
11782033 TCTT-TTTCTTTATTCT-TTATTTTT-ATT
1 TTTTCTTTCTTTATTCTCTT-TTTTTCATT
11782060 TTTTCTTTCTTT
1 TTTTCTTTCTTT
11782072 TTGCTGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 7 0.21
28 22 0.65
29 2 0.06
31 3 0.09
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (29 bp):
TTTTCTTTCTTTATTCTCTTTTTTTCATT
Found at i:11782726 original size:41 final size:41
Alignment explanation
Indices: 11782636--11782713 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
11782626 TAATCTACAT
* * *
11782636 CACACGGACGTGTGGTTGGCCGTGTGTCAGGCCGTGTATGC
1 CACACGGACGTGTGGTCGACCGTGTGCCAGGCCGTGTATGC
* *
11782677 CACACGGACGTGTGGTCGACTGTGTGCCAGGTCGTGT
1 CACACGGACGTGTGGTCGACCGTGTGCCAGGCCGTGT
11782714 GGAGCACACG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.13, C:0.24, G:0.38, T:0.24
Consensus pattern (41 bp):
CACACGGACGTGTGGTCGACCGTGTGCCAGGCCGTGTATGC
Found at i:11784357 original size:53 final size:52
Alignment explanation
Indices: 11784277--11784435 Score: 203
Period size: 53 Copynumber: 3.0 Consensus size: 52
11784267 CCATGGCACT
* * *
11784277 GAAGACTATATTCTGTAAGACCGTAACTGGTTGGTTATGGAATCATATGGAAA
1 GAAGACAATA-TCTGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
*
11784330 GAAGACAATATCGTGTAAGACCATAACTGGTGGGTTATGAAATCATATGGAAA
1 GAAGACAATATC-TGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
* * * *
11784383 GAATACCATATCATGTAAGACCATAATTGATGGGTTAT-GACATCATATGGAAA
1 GAAGACAATATC-TGTAAGACCATAACTGGTGGGTTATGGA-ATCATATGGAAA
11784436 ATTTAAGAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 3 0.03
53 91 0.97
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (52 bp):
GAAGACAATATCTGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
Found at i:11784628 original size:27 final size:29
Alignment explanation
Indices: 11784585--11784651 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
11784575 AAGGATACAT
* *
11784585 CTTTGTGGCGA-ACCTCTTA-AAGG-ATGC
1 CTTTGTAGCGAGACCTC-TAGAAGGAAAGC
*
11784612 CTTTGTTGCGAGA-CTCTAGAAGGAAAGC
1 CTTTGTAGCGAGACCTCTAGAAGGAAAGC
11784640 CTTTGTAGCGAG
1 CTTTGTAGCGAG
11784652 TACTTAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 17 0.50
28 15 0.44
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (29 bp):
CTTTGTAGCGAGACCTCTAGAAGGAAAGC
Found at i:11787849 original size:15 final size:15
Alignment explanation
Indices: 11787829--11787857 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11787819 TTCAGATAAT
11787829 TTCACTTCGATTCAA
1 TTCACTTCGATTCAA
11787844 TTCACTTCGATTCA
1 TTCACTTCGATTCA
11787858 CTTTTCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (15 bp):
TTCACTTCGATTCAA
Found at i:11788700 original size:16 final size:17
Alignment explanation
Indices: 11788670--11788702 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11788660 TTGTTTATTA
*
11788670 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
11788687 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
11788703 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:11788848 original size:15 final size:15
Alignment explanation
Indices: 11788828--11788865 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
11788818 ATTTCACAAT
11788828 ATAATAATAATATTA
1 ATAATAATAATATTA
* *
11788843 ATAATATTATTATTA
1 ATAATAATAATATTA
11788858 ATAATAAT
1 ATAATAAT
11788866 TTAATAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATAATAATATTA
Found at i:11788879 original size:12 final size:12
Alignment explanation
Indices: 11788825--11788878 Score: 60
Period size: 11 Copynumber: 4.5 Consensus size: 12
11788815 TTTATTTCAC
11788825 AATA-TAATAAT
1 AATATTAATAAT
11788836 AATATTAATAAT
1 AATATTAATAAT
11788848 ATTATTATTAATAAT
1 A--A-TATTAATAAT
11788863 AAT-TTAATAAT
1 AATATTAATAAT
11788874 -ATATT
1 AATATT
11788879 TTTACACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
10 2 0.05
11 14 0.37
12 9 0.24
13 1 0.03
14 1 0.03
15 11 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:11796127 original size:21 final size:22
Alignment explanation
Indices: 11796089--11796131 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
11796079 AGTATGTTAT
11796089 GTCGTGACGAGAAACCCCCAAC
1 GTCGTGACGAGAAACCCCCAAC
*
11796111 GTCGTGATGAG-AACCCCCAAC
1 GTCGTGACGAGAAACCCCCAAC
11796132 ATCCTGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (22 bp):
GTCGTGACGAGAAACCCCCAAC
Found at i:11798227 original size:2 final size:2
Alignment explanation
Indices: 11798220--11798258 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
11798210 CATCATAAAT
11798220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
11798259 AAAGAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11804499 original size:37 final size:37
Alignment explanation
Indices: 11804449--11804524 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
11804439 TCACGAGTTC
11804449 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
1 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
*
11804486 CTTTAGCTGATTCTATGGAAGAGGTGGTGAAGCTTAA
1 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
11804523 CT
1 CT
11804525 CTTCTAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (37 bp):
CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
Found at i:11806313 original size:228 final size:228
Alignment explanation
Indices: 11805910--11806365 Score: 716
Period size: 228 Copynumber: 2.0 Consensus size: 228
11805900 TTTAGAAAGA
*
11805910 GTGGTCACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGCTCCGGGTAG
1 GTGGTCACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGCTCCGGGCAG
* * * * * *
11805975 TGATGACTTTTATGCCCTCTTTTTCCAGGAGCAGTGGGGTACAATAGGCCCAGCTATTTGTTATT
66 TGATAACTTTCATGCCCTCTTCTTCCAGAAACAGTGGGGTACAATAGGCCCAGCTATTTGTGATT
* *
11806040 GGGTGAAAATGGTATTTAATGGAGGCATTATTGATACTAAGCTTAATAACACATTGATTATTCTT
131 GGGTGAAAATGGTATTTAATGGAGGCATTATTAATAATAAGCTTAATAACACATTGATTATTCTT
*
11806105 ATTCCCAAGTTTTAGAGTCTTGAA-GGGTTTTCT
196 ATTCCCAAGTTTTAGAGTCCT-AAGGGGTTTTCT
* * * *
11806138 GTGGTTACTGATGAATAAATTAAAAAGGTTTTGTTTGACATGGCTCCTCTAAAAGCTCTGGGCAG
1 GTGGTCACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGCTCCGGGCAG
* * *
11806203 TGGTAACTTTCATGCCCTCTTCTTCCAGAAACAGTGGGGTACAGTGGGCCCAGCTATTTGTGATT
66 TGATAACTTTCATGCCCTCTTCTTCCAGAAACAGTGGGGTACAATAGGCCCAGCTATTTGTGATT
* * *
11806268 GGGTGAAAATGGTATTTAATGGAGGCGTTATTAATAATGAGCTTAATAACACATTGATTGTTCTT
131 GGGTGAAAATGGTATTTAATGGAGGCATTATTAATAATAAGCTTAATAACACATTGATTATTCTT
11806333 ATTCCCAAGTTTTAGAGTCCTAAGGGGTTTTCT
196 ATTCCCAAGTTTTAGAGTCCTAAGGGGTTTTCT
11806366 TAGTTTTTTC
Statistics
Matches: 207, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
227 2 0.01
228 205 0.99
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (228 bp):
GTGGTCACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGCTCCGGGCAG
TGATAACTTTCATGCCCTCTTCTTCCAGAAACAGTGGGGTACAATAGGCCCAGCTATTTGTGATT
GGGTGAAAATGGTATTTAATGGAGGCATTATTAATAATAAGCTTAATAACACATTGATTATTCTT
ATTCCCAAGTTTTAGAGTCCTAAGGGGTTTTCT
Found at i:11808308 original size:17 final size:17
Alignment explanation
Indices: 11808286--11808318 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11808276 ATATTTAATA
11808286 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
11808303 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
11808319 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:11810050 original size:17 final size:18
Alignment explanation
Indices: 11810030--11810071 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
11810020 CATAATTTTT
11810030 AAATATAAAATATTTA-A
1 AAATATAAAATATTTATA
*
11810047 AAAT-TGAAAATGTTTATA
1 AAATAT-AAAATATTTATA
11810065 AAATATA
1 AAATATA
11810072 TTTATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 6 0.29
19 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
AAATATAAAATATTTATA
Found at i:11816848 original size:11 final size:11
Alignment explanation
Indices: 11816834--11816859 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11816824 TTTTTTAAAA
11816834 TTTTAAAATAC
1 TTTTAAAATAC
11816845 TTTTAAAATAC
1 TTTTAAAATAC
11816856 TTTT
1 TTTT
11816860 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:11816870 original size:41 final size:41
Alignment explanation
Indices: 11816816--11816928 Score: 144
Period size: 39 Copynumber: 2.8 Consensus size: 41
11816806 AATATTTTTA
*
11816816 TTTTTT-ATTTTTTTAAAATTTTAAAATACTTTT-AAAATAC
1 TTTTTTAAATTTTTT-AAATTTTAAAATACTTTTAAAAATAC
**
11816856 TTTTTTTAAATTTTTTAAATTTT-AAATTTTTTTAAAAATAC
1 -TTTTTTAAATTTTTTAAATTTTAAAATACTTTTAAAAATAC
*
11816897 -TTTTTAAATTTTTTTAATTTTAAAATACTTTT
1 TTTTTTAAATTTTTTAAATTTTAAAATACTTTT
11816929 TTTATTTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
39 20 0.32
40 16 0.25
41 20 0.32
42 7 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (41 bp):
TTTTTTAAATTTTTTAAATTTTAAAATACTTTTAAAAATAC
Found at i:11816871 original size:9 final size:9
Alignment explanation
Indices: 11816857--11816917 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
11816847 TTAAAATACT
11816857 TTTTTTAAA
1 TTTTTTAAA
11816866 TTTTTTAAA
1 TTTTTTAAA
11816875 --TTTTAAA
1 TTTTTTAAA
11816882 TTTTTTTAAAAA
1 -TTTTTT--AAA
11816894 TACTTTTTAAA
1 T--TTTTTAAA
*
11816905 TTTTTTTAA
1 TTTTTTAAA
11816914 TTTT
1 TTTT
11816918 AAAATACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
7 7 0.16
9 20 0.45
10 4 0.09
11 5 0.11
12 3 0.07
13 5 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:11825233 original size:108 final size:108
Alignment explanation
Indices: 11825044--11825261 Score: 409
Period size: 108 Copynumber: 2.0 Consensus size: 108
11825034 CAATACCATG
**
11825044 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATCATTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
*
11825109 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAA
66 GTTTATATAGTATACATATATCACTACTCTCTCTCTTAGACAA
11825152 CATGTAGTTGTATCATTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATCATTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
11825217 GTTTATATAGTATACATATATCACTACTCTCTCTCTTAGACAA
66 GTTTATATAGTATACATATATCACTACTCTCTCTCTTAGACAA
11825260 CA
1 CA
11825262 ATACTTCATC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (108 bp):
CATGTAGTTGTATCATTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
GTTTATATAGTATACATATATCACTACTCTCTCTCTTAGACAA
Found at i:11825803 original size:14 final size:15
Alignment explanation
Indices: 11825781--11825856 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 15
11825771 CAATCAAACA
11825781 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
11825795 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
11825810 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
11825830 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
11825844 ACGGAAAA-CATTT
1 CCAGAAAATCATTT
11825857 ACTGGCAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.43
15 14 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:11825822 original size:20 final size:20
Alignment explanation
Indices: 11825797--11825836 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11825787 AATATTTTCC
*
11825797 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
11825817 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
11825837 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:11825842 original size:34 final size:35
Alignment explanation
Indices: 11825785--11825851 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
11825775 CAAACACCAG
*
11825785 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
11825820 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11825852 CATTTACTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11836808 original size:26 final size:26
Alignment explanation
Indices: 11836772--11836823 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
11836762 CGTTGATTTT
11836772 ATAGAATGCTTAAATAATTAGAATCA
1 ATAGAATGCTTAAATAATTAGAATCA
*
11836798 ATAGAATGCTTAAATAGTTAGAATCA
1 ATAGAATGCTTAAATAATTAGAATCA
11836824 TGTGCGTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (26 bp):
ATAGAATGCTTAAATAATTAGAATCA
Found at i:11849549 original size:41 final size:41
Alignment explanation
Indices: 11849492--11849572 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
11849482 ACCTAATTGT
*
11849492 GAAAATAATTCCCTTATTCTGATAAACTACTAAAAGATAAG
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
11849533 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
11849573 AATAAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (41 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
Found at i:11852695 original size:17 final size:18
Alignment explanation
Indices: 11852662--11852695 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11852652 CAGATTGTTA
11852662 AGATAATCAAGGAAATGG
1 AGATAATCAAGGAAATGG
*
11852680 AGATAA-CAAGGGAATG
1 AGATAATCAAGGAAATG
11852696 CAGGTTACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.29, T:0.15
Consensus pattern (18 bp):
AGATAATCAAGGAAATGG
Found at i:11853492 original size:35 final size:35
Alignment explanation
Indices: 11853443--11853514 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
11853433 GAGAAAACAG
*
11853443 AAAGAAAAATGGATCTTAGCACTTAAAAAAGCACA
1 AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
11853478 AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
1 AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
11853513 AA
1 AA
11853515 TGGCACAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.56, C:0.14, G:0.15, T:0.15
Consensus pattern (35 bp):
AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
Found at i:11854887 original size:2 final size:2
Alignment explanation
Indices: 11854880--11854922 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11854870 CCTTTTTGCT
11854880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11854922 T
1 T
11854923 GAATATGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11859728 original size:27 final size:23
Alignment explanation
Indices: 11859698--11859750 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
11859688 TTTTTTAAGT
11859698 TAAAAAAGTAGAATTATAATATAAT-
1 TAAAAAA-TAGAATTA-AAT-TAATA
*
11859723 TATAAAATAGAATTAAATTAATA
1 TAAAAAATAGAATTAAATTAATA
11859746 TAAAA
1 TAAAA
11859751 TAGACCGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.16
23 7 0.28
24 8 0.32
25 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (23 bp):
TAAAAAATAGAATTAAATTAATA
Found at i:11859749 original size:21 final size:24
Alignment explanation
Indices: 11859701--11859754 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 24
11859691 TTTAAGTTAA
11859701 AAAAGTAGAATTATAATATAATTAT
1 AAAA-TAGAATTATAATATAATTAT
11859726 AAAATAGAATTA-AAT-TAA-TAT
1 AAAATAGAATTATAATATAATTAT
11859747 AAAATAGA
1 AAAATAGA
11859755 CCGATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.38
22 3 0.10
23 3 0.10
24 8 0.28
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAATAGAATTATAATATAATTAT
Found at i:11867657 original size:23 final size:23
Alignment explanation
Indices: 11867631--11867679 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
11867621 GACTTTTAGA
11867631 ACAATGGTTAGAGCTCTTCTTTG
1 ACAATGGTTAGAGCTCTTCTTTG
11867654 ACAATGGTTAGAGCTCTTCTTTG
1 ACAATGGTTAGAGCTCTTCTTTG
11867677 ACA
1 ACA
11867680 CTTAGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (23 bp):
ACAATGGTTAGAGCTCTTCTTTG
Found at i:11868504 original size:2 final size:2
Alignment explanation
Indices: 11868493--11868523 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
11868483 AAAAGGTCTG
11868493 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11868524 TTAATGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:11878163 original size:2 final size:2
Alignment explanation
Indices: 11878156--11878192 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11878146 AAGTAAAACT
11878156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11878193 TTGCTTTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11892462 original size:3 final size:3
Alignment explanation
Indices: 11892430--11892489 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
11892420 TATTTTAATG
* * * *
11892430 TTA TTA TCA TTA TCA -TA TTA -TA TCA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
11892476 TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TT
11892490 TGTTTATTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:11893291 original size:110 final size:107
Alignment explanation
Indices: 11893005--11893445 Score: 661
Period size: 108 Copynumber: 4.1 Consensus size: 107
11892995 TACGCATATT
** * *
11893005 AATATCCTTTTAAAAAAATTTAAAATAAGGCAATGTTTTGTGTTTGAAAATTCGAGGAAACGTGC
1 AATATCCTTTT--AAAAATTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGC
11893070 CCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
64 CCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
* * *
11893114 AATATCCTTTTAAAAATTCAAAATAAGGTAATGTTTTGCATTTGGAAATTCGAGAAAATGTGCCC
1 AATATCCTTTTAAAAATTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCC
11893179 TAATGTG-TCGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 TAATGTGCT-GGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCA
* *
11893222 AATATCCTTTTAAAAATTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGT
1 AATATCCTTTTAAAAATTT--AAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGC
* *
11893287 CCTAATGTGCTGGGTTTTGATTTTTCTCGTTCGACCAAATAGCCG
64 CCTAATGTGCTGGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCA
* * *
11893332 AATATCCTTTTAAAATTTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGGAAACATGCCC
1 AATATCCTTTTAAAAATTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCC
* *
11893397 TAATGTGCTGGGTTTC-AATTTCTCGTTGGACCAAATAGCCA
66 TAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
11893438 AATATCCT
1 AATATCCT
11893446 CTTATATCTT
Statistics
Matches: 304, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
106 30 0.10
107 64 0.21
108 99 0.33
109 11 0.04
110 99 0.33
111 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (107 bp):
AATATCCTTTTAAAAATTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCC
TAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
Found at i:11893382 original size:218 final size:214
Alignment explanation
Indices: 11893005--11893445 Score: 679
Period size: 218 Copynumber: 2.0 Consensus size: 214
11892995 TACGCATATT
* *
11893005 AATATCCTTTTAAAAAAATTTAAAATAAGGCAATGTTTTGTGTTTGAAAATTCGAGGAAACGTGC
1 AATATCCTTTT-AAAAAATTTAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGC
11893070 CCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTCAA
65 CCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTCAA
* ** *
11893135 AATAAGGTAATGTTTTGCATTTGGAAATTCGAGAAAATGTGCCCTAATGTG-TCGGGTTTCGATT
130 AATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCT-GGGTTTC-A-A
11893199 TTTCTCGTTCGACCAAATAGCCA
192 TTTCTCGTTCGACCAAATAGCCA
*
11893222 AATATCCTTTT-AAAAATTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTG
1 AATATCCTTTTAAAAAATTT--AAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTG
* * * * *
11893286 TCCTAATGTGCTGGGTTTTGATTTTTCTCGTTCGACCAAATAGCCGAATATCCTTTTAAAATTTT
64 CCCTAATGTGCTGGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTC
*
11893351 AAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGGAAACATGCCCTAATGTGCTGGGTTTCAAT
128 AAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGGGTTTCAAT
*
11893416 TTCTCGTTGGACCAAATAGCCA
193 TTCTCGTTCGACCAAATAGCCA
11893438 AATATCCT
1 AATATCCT
11893446 CTTATATCTT
Statistics
Matches: 206, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
215 8 0.04
216 30 0.15
217 71 0.34
218 96 0.47
219 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (214 bp):
AATATCCTTTTAAAAAATTTAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCC
CTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTCAAA
ATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGGGTTTCAATTTC
TCGTTCGACCAAATAGCCA
Found at i:11894386 original size:16 final size:16
Alignment explanation
Indices: 11894365--11894399 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
11894355 TGTTGTTTTG
*
11894365 TTTTGACTGCATGGCA
1 TTTTGACTACATGGCA
11894381 TTTTGACTACATGGCA
1 TTTTGACTACATGGCA
11894397 TTT
1 TTT
11894400 CATTAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (16 bp):
TTTTGACTACATGGCA
Found at i:11904081 original size:107 final size:108
Alignment explanation
Indices: 11903890--11904086 Score: 245
Period size: 107 Copynumber: 1.8 Consensus size: 108
11903880 TTCATCTTTG
* * * * * * *
11903890 TATCTTAGCGAAATTTGCTATCTTGATTAATTTGTTCATTTAGAGTTTTGCTCTCAATAAATTCT
1 TATCTCAGCAAAATTTGCTATCTTGATTAATATATTCATTTAGAGATCTGCTCTCAAAAAATTCT
*
11903955 CATCTTATCCATTGCGATAA-CCTTGTATATCTTATTCATTTC
66 CATCGTATCCATTGCGATAATCCTTGTATATCTTATTCATTTC
* **
11903997 TATCTCAGCAAAATTTGCTATCTTGATTGATATATTTGTTTAGAGATCTGCTCTCAACAAAATT-
1 TATCTCAGCAAAATTTGCTATCTTGATTAATATATTCATTTAGAGATCTGCTCTCAA-AAAATTC
* **
11904061 TCATCGTGTCCATTTTGATAATCCTT
65 TCATCGTATCCATTGCGATAATCCTT
11904087 TTCAAGCATC
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
107 65 0.88
108 9 0.12
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (108 bp):
TATCTCAGCAAAATTTGCTATCTTGATTAATATATTCATTTAGAGATCTGCTCTCAAAAAATTCT
CATCGTATCCATTGCGATAATCCTTGTATATCTTATTCATTTC
Found at i:11905197 original size:44 final size:43
Alignment explanation
Indices: 11905129--11905328 Score: 104
Period size: 44 Copynumber: 4.6 Consensus size: 43
11905119 GAGCAGACTG
* *
11905129 AAATCACAA-ATTAT-TCCCCTGAAGTTACAGCGGGGCAGGTCA
1 AAATCACAATCTTATCT-CCCTGAAGTTACAGCGGAGCAGGTCA
* * * * * **
11905171 AAATCATGAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGGTTG
1 AAATCA-CAATCTTATCTCCCTGAAGTTACAGCGGAGCAGGTCA
* * ** * * * * *
11905215 AAGTTACAAGTCTTATCTCCCCAAAGTTGCGGTGGAGCA-GACTG
1 AAATCACAA-TCTTATCTCCCTGAAGTTACAGCGGAGCAGGTC-A
* * *
11905259 AAATCACAA-ATTAT-TCCCCTGAAGTTACAGCGGGGTAGGTCA
1 AAATCACAATCTTATCT-CCCTGAAGTTACAGCGGAGCAGGTCA
* *
11905301 AAATCATGAATCTTATCTCCTTGAAGTT
1 AAATCA-CAATCTTATCTCCCTGAAGTT
11905329 GCAGTGGAAC
Statistics
Matches: 114, Mismatches: 34, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.26
43 9 0.08
44 72 0.63
45 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (43 bp):
AAATCACAATCTTATCTCCCTGAAGTTACAGCGGAGCAGGTCA
Found at i:11905208 original size:130 final size:130
Alignment explanation
Indices: 11905055--11905336 Score: 528
Period size: 130 Copynumber: 2.2 Consensus size: 130
11905045 GACAAACCTG
* *
11905055 ATCTCCATGAAGTTGTAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGCTGCGGTGG
1 ATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGCTGCGGTGG
11905120 AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGCAGGTCAAAATCATGAATCTT
66 AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGCAGGTCAAAATCATGAATCTT
*
11905185 ATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGTTGCGGTGG
1 ATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGCTGCGGTGG
*
11905250 AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGTAGGTCAAAATCATGAATCTT
66 AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGCAGGTCAAAATCATGAATCTT
11905315 ATCTCCTTGAAGTTGCAGTGGA
1 ATCTCCTTGAAGTTGCAGTGGA
11905337 ACATACTAAA
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 148 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (130 bp):
ATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCCAAAGCTGCGGTGG
AGCAGACTGAAATCACAAATTATTCCCCTGAAGTTACAGCGGGGCAGGTCAAAATCATGAATCTT
Found at i:11905979 original size:18 final size:20
Alignment explanation
Indices: 11905956--11905993 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
11905946 TAATGTTTAC
11905956 AGAGAA-AAAAAATA-CAAT
1 AGAGAACAAAAAATATCAAT
*
11905974 AGAGAACCAAAAATATCAAT
1 AGAGAACAAAAAATATCAAT
11905994 TAGAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.13
Consensus pattern (20 bp):
AGAGAACAAAAAATATCAAT
Found at i:11906960 original size:29 final size:31
Alignment explanation
Indices: 11906901--11906964 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
11906891 TAGATTTGAT
*
11906901 TATATATATATACATACATATCTTTGATTTA
1 TATATATATATACATACATATCTATGATTTA
*
11906932 TATATATATATGCATAC-T-TCTAT-ACTTTA
1 TATATATATATACATACATATCTATGA-TTTA
11906961 TATA
1 TATA
11906965 CTTTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 12 0.40
30 1 0.03
31 16 0.53
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (31 bp):
TATATATATATACATACATATCTATGATTTA
Found at i:11907838 original size:34 final size:35
Alignment explanation
Indices: 11907795--11907873 Score: 128
Period size: 34 Copynumber: 2.3 Consensus size: 35
11907785 TTTATTTATA
*
11907795 ATTT-TAATTTTTTCTAAATA-TTTTTATTAATTT
1 ATTTGTAATTTTTTATAAATATTTTTTATTAATTT
11907828 ATTTGTAA-TTTTTATAAATATTTTTTATTAATTT
1 ATTTGTAATTTTTTATAAATATTTTTTATTAATTT
11907862 ATTTGTAATTTT
1 ATTTGTAATTTT
11907874 ACTTATTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 15 0.36
34 24 0.57
35 3 0.07
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (35 bp):
ATTTGTAATTTTTTATAAATATTTTTTATTAATTT
Found at i:11922545 original size:10 final size:11
Alignment explanation
Indices: 11922519--11922544 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11922509 AAAAATAAAA
11922519 AAAAATATTTT
1 AAAAATATTTT
11922530 AAAAATATTTT
1 AAAAATATTTT
11922541 AAAA
1 AAAA
11922545 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:11922550 original size:17 final size:17
Alignment explanation
Indices: 11922528--11922562 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11922518 AAAAAATATT
* *
11922528 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
11922545 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
11922562 T
1 T
11922563 ATATGTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:11934803 original size:34 final size:34
Alignment explanation
Indices: 11934759--11934849 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
11934749 ATATTTTTTA
*
11934759 AAAATTAATTAAATTAGATTTTAAG-GGTTTTAA-
1 AAAATTAATTAAATTAGAGTTT-AGCGGTTTTAAG
* *
11934792 ATAAATTAATTAAATTAGGGTTTAGCGTTTTTAAG
1 A-AAATTAATTAAATTAGAGTTTAGCGGTTTTAAG
*
11934827 AAAATTAATTAAATTAGGGTTTA
1 AAAATTAATTAAATTAGAGTTTA
11934850 ATTTTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
33 3 0.06
34 48 0.92
35 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.42
Consensus pattern (34 bp):
AAAATTAATTAAATTAGAGTTTAGCGGTTTTAAG
Found at i:11934862 original size:34 final size:33
Alignment explanation
Indices: 11934759--11934863 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 33
11934749 ATATTTTTTA
** *
11934759 AAAATTAATTAAATTAGATTTTAAGGGTTTTAAA-
1 AAAATTAATTAAATTAGGGTTTAA--TTTTTAAAG
* *
11934793 TAAATTAATTAAATTAGGGTTTAGCGTTTTT-AAG
1 AAAATTAATTAAATTAGGGTTTA--ATTTTTAAAG
11934827 AAAATTAATTAAATTAGGGTTTAATTTTTAAAAG
1 AAAATTAATTAAATTAGGGTTTAATTTTT-AAAG
11934861 AAA
1 AAA
11934864 TAATTTTGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
32 5 0.08
33 2 0.03
34 52 0.88
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (33 bp):
AAAATTAATTAAATTAGGGTTTAATTTTTAAAG
Found at i:11935123 original size:126 final size:126
Alignment explanation
Indices: 11934989--11935326 Score: 493
Period size: 126 Copynumber: 2.7 Consensus size: 126
11934979 GAAAAGATAA
* * *
11934989 TGTCAAAAACGCTTCAAGCAGAATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCTACGTGGA
1 TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCTACATGGA
* * * *
11935053 CGCTAGTTTTT-TATAGTAGTT-TCTGAAAAAATAATTTTGAAAAGACGGTTCTAAATAAATAG
65 CGCT-CTTTTTCTACAATAGTTCT-TGAAAAAATAATTTTGAAAAGACGGTTCTAAACAAATAG
* *
11935115 TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAGAGCTCCTACTTGGAC
1 TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGAC
* *
11935180 GCTCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAG
66 GCTCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAAAAGACGGTTCTAAACAAATAG
* *
11935241 TGTCAAAAATGCTTCAAGCAGGATTCACTGTCAGCGAAATTGATGAAAAAAGCTCCTACATGGAC
1 TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGAC
* *
11935306 ACTCTTTTTCTACAGTAGTTC
66 GCTCTTTTTCTACAATAGTTC
11935327 ATGTTTGGCT
Statistics
Matches: 193, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
125 5 0.03
126 186 0.96
127 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (126 bp):
TGTCAAAAATGCTTCAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGAC
GCTCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAAAAGACGGTTCTAAACAAATAG
Found at i:11938815 original size:18 final size:18
Alignment explanation
Indices: 11938789--11938832 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
11938779 GACTGAGAAA
* *
11938789 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
11938807 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
11938825 AGGATACA
1 AGGATACA
11938833 CACCTGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:11940363 original size:15 final size:16
Alignment explanation
Indices: 11940335--11940367 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
11940325 CAGACTGCTA
11940335 TAAAAAAATATAAAAT
1 TAAAAAAATATAAAAT
*
11940351 TAAAATAAT-TAAAAT
1 TAAAAAAATATAAAAT
11940366 TA
1 TA
11940368 CATAAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAAAATATAAAAT
Found at i:11943351 original size:26 final size:26
Alignment explanation
Indices: 11943317--11943367 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
11943307 GGATAAAAAA
11943317 GGGTCGCTAAGTGCAGATTCCCCGAG
1 GGGTCGCTAAGTGCAGATTCCCCGAG
* *
11943343 GGGTTGCTAAGTGCTGATTCCCCGA
1 GGGTCGCTAAGTGCAGATTCCCCGA
11943368 ATTATTGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24
Consensus pattern (26 bp):
GGGTCGCTAAGTGCAGATTCCCCGAG
Found at i:11943561 original size:42 final size:40
Alignment explanation
Indices: 11943510--11943656 Score: 134
Period size: 43 Copynumber: 3.5 Consensus size: 40
11943500 TTTGATTGTG
*
11943510 AAAGGGGTTGC-AATGTGCTGATTCCCCGTATCACTGAATAT
1 AAAGTGGTTGCTAA-GTGCTGATTCCCCGTATCACTGAAT-T
* * ** *
11943551 AAATGTGGTTGCTAAGTGCTGATTTCACTGTATCTTTGATTGT
1 AAA-GTGGTTGCTAAGTGCTGA-TTCCCCGTATCACTGAAT-T
* * *
11943594 GAAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTGAATTT
1 -AAAGTGGTTGCTAAGTGCTGATTCCCCGTATCACTGAA-TT
*
11943636 AAGGTGGTTGCTAAGTGCTGA
1 AAAGTGGTTGCTAAGTGCTGA
11943657 ATCCACCGAG
Statistics
Matches: 82, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
41 20 0.24
42 27 0.33
43 32 0.39
44 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (40 bp):
AAAGTGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATT
Found at i:11943604 original size:43 final size:43
Alignment explanation
Indices: 11943485--11943656 Score: 133
Period size: 42 Copynumber: 4.1 Consensus size: 43
11943475 NNNNNNNTGT
* *
11943485 TGATTCCACGGTATCTTTGATTGTGAAAGGGGTTGC-AATGTGC
1 TGATTTCACCGTATCTTTGATTGTGAAAGGGGTTGCTAA-GTGC
* ** * * *
11943528 TGA-TTCCCCGTATCACTGAATAT-AAATGTGGTTGCTAAGTGC
1 TGATTTCACCGTATCTTTGATTGTGAAA-GGGGTTGCTAAGTGC
* * *
11943570 TGATTTCACTGTATCTTTGATTGTGAAAGGGGTTGCTATGTGT
1 TGATTTCACCGTATCTTTGATTGTGAAAGGGGTTGCTAAGTGC
* **
11943613 TGA-TTCCCCGTATCACTGAATT-T--AAGGTGGTTGCTAAGTGC
1 TGATTTCACCGTATCTTTG-ATTGTGAAAGG-GGTTGCTAAGTGC
11943654 TGA
1 TGA
11943657 ATCCACCGAG
Statistics
Matches: 100, Mismatches: 23, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
40 4 0.04
41 17 0.17
42 39 0.39
43 37 0.37
44 3 0.03
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (43 bp):
TGATTTCACCGTATCTTTGATTGTGAAAGGGGTTGCTAAGTGC
Found at i:11943628 original size:85 final size:84
Alignment explanation
Indices: 11943485--11943662 Score: 284
Period size: 85 Copynumber: 2.1 Consensus size: 84
11943475 NNNNNNNTGT
11943485 TGATTCCACGGTATCTTTGATTGTGAAAGGGGTTGCAATGTGCTGATTCCCCGTATCACTGAATA
1 TGATTCCACGGTATCTTTGATTGTGAAAGGGGTTGCAATGTGCTGATTCCCCGTATCACTGAAT-
*
11943550 TAAATGTGGTTGCTAAGTGC
65 TAAAGGTGGTTGCTAAGTGC
* * * *
11943570 TGATTTCACTGTATCTTTGATTGTGAAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTGAATT
1 TGATTCCACGGTATCTTTGATTGTGAAAGGGGTTGCAATGTGCTGATTCCCCGTATCACTGAATT
*
11943635 TAAGGTGGTTGCTAAGTGC
66 AAAGGTGGTTGCTAAGTGC
*
11943654 TGAATCCAC
1 TGATTCCAC
11943663 CGAGTAACGG
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 25 0.29
85 60 0.71
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.36
Consensus pattern (84 bp):
TGATTCCACGGTATCTTTGATTGTGAAAGGGGTTGCAATGTGCTGATTCCCCGTATCACTGAATT
AAAGGTGGTTGCTAAGTGC
Found at i:11946077 original size:104 final size:103
Alignment explanation
Indices: 11945886--11946256 Score: 609
Period size: 104 Copynumber: 3.6 Consensus size: 103
11945876 TGTATATAAA
** * *
11945886 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
*
11945950 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
11945990 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
**
11946055 TTGAAATGAAAAGGGGGTTGCTATGTTTTGATTCCCCCG
65 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
11946094 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
11946159 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
11946198 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
11946257 ATAACGGTTA
Statistics
Matches: 253, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
103 29 0.11
104 182 0.72
105 41 0.16
106 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:11949575 original size:397 final size:396
Alignment explanation
Indices: 11948834--11949599 Score: 920
Period size: 397 Copynumber: 1.9 Consensus size: 396
11948824 TCTAGTGTCT
* * *
11948834 TAAGTGTAGTATTTTCGTCTATATACAATTGTATTTTTTCAAACATATTAGCTAATAAAATTATT
1 TAAGTGTAGTATTTTCGTCAATATACAATTGTATTTTTTCAAACAGATTAGATAATAAAATTATT
* **
11948899 CATGAATTACATTAATATCCTTTGTATATTATCCTCAATGGTTTTTGTATGCAAAGCAAAATGAA
66 CATGAATTACATTAATA-CCTTTGTATAATATCCTCAATGGTTTTTGTACACAAAGCAAAATGAA
* * **
11948964 AGCAAATATTAGCTCATTGGTTGTCTAATGTTTAACTAATACTAAACAGTATTATGTGATTAGAT
130 AGCAAATATTAGCTCACTGGTTGTCTAATGTTTAACTAATACTAAACAGTATTATATGACCAGAT
* * * * *
11949029 CGTAATACAGAAAGATAGTTTATATTAGTAGATGAACCTAAAGATATCCTTAATCTGATATAAAA
195 CGTAATACAGAAAGATAATTTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAATAGAAAA
** * *
11949094 TGAGCAAACTGATTAAAAGAGTAATATGTCATCTATCAAGTTCAATTGGAGAGATGCTTTGTCTT
260 TGAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATTGGAGAGATGCTTTGTCTT
* * * * *
11949159 GGCCATCGGAGCAGATGACTCCTAGAATATAGAGACATAGATGTCATTGACCGGCTATTGGATTA
325 AGACATCGAAGCAGATGACTCCTAAAAGATAGAGACATAGATGTCATTGACCGGCTATTGGATTA
11949224 GGTGCCC
390 GGTGCCC
* * ** *
11949231 TAAGTGTAGTATTTTCGTCAATGTACACTTGTAATTTTTTTGAACAGGTT-GATAAATAAAATTA
1 TAAGTGTAGTATTTTCGTCAATATACAATTGT-ATTTTTTCAAACAGATTAGAT-AATAAAATTA
* *
11949295 TTCATGAATTACATTAATA-CTTTGTATAATGTCCTCATGTGGTTTTTGTACACAAAGCAAAAT-
64 TTCATGAATTACATTAATACCTTTGTATAATATCCTCA-ATGGTTTTTGTACACAAAGCAAAATG
* * * ** *
11949358 AGGAGCAAATGTT-GCTCACTGGTTGTTTAATGTTTAAACTAATACT-AAGTGATATTATATGGC
128 A-AAGCAAATATTAGCTCACTGGTTGTCTAATGTTT-AACTAATACTAAACAG-TATTATATGAC
* * * * *
11949421 CGGATTGTAATAC-GAAA-ATACATCTTATATTAGTAGACGAACCTAAATATGTCCCTAGTCTAA
190 CAGATCGTAATACAGAAAGATA-AT-TTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAA
* * * **
11949484 TCGAAAATGAGTAAACCAATTGAAAGACTAATATGTTGTCTATCAAGTCCAATTAGG-GAGATG-
253 TAGAAAATGAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATT-GGAGAGATGC
** *
11949547 TTTCGTCTTAGACATCGAAGTGGATGACTCCTAAAAGATAGAGACATGGATGT
317 TTT-GTCTTAGACATCGAAGCAGATGACTCCTAAAAGATAGAGACATAGATGT
11949600 GACTGACTAG
Statistics
Matches: 309, Mismatches: 50, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
395 3 0.01
396 48 0.16
397 214 0.69
398 44 0.14
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (396 bp):
TAAGTGTAGTATTTTCGTCAATATACAATTGTATTTTTTCAAACAGATTAGATAATAAAATTATT
CATGAATTACATTAATACCTTTGTATAATATCCTCAATGGTTTTTGTACACAAAGCAAAATGAAA
GCAAATATTAGCTCACTGGTTGTCTAATGTTTAACTAATACTAAACAGTATTATATGACCAGATC
GTAATACAGAAAGATAATTTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAATAGAAAAT
GAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATTGGAGAGATGCTTTGTCTTA
GACATCGAAGCAGATGACTCCTAAAAGATAGAGACATAGATGTCATTGACCGGCTATTGGATTAG
GTGCCC
Found at i:11950439 original size:63 final size:66
Alignment explanation
Indices: 11950338--11950471 Score: 213
Period size: 63 Copynumber: 2.1 Consensus size: 66
11950328 ATAGAAATTG
*
11950338 TGAAAATGGAGAAATTGAAATCATTTGGAAATTATTATGGTTTTCTCCAAAATGAAAAT-GA-AA
1 TGAAAATGGAGAAATGGAAATCATTTGGAAATTATTATGGTTTTCTCCAAAATGAAAATGGAGAA
11950401 A
66 A
*
11950402 TGAAAATGGAGAAATGGAAA-CATTTGG-AATTGATTATGGTTTTTTCCAAAATGAAAATGGAGA
1 TGAAAATGGAGAAATGGAAATCATTTGGAAATT-ATTATGGTTTTCTCCAAAATGAAAATGGAGA
11950465 AA
65 AA
11950467 TGAAA
1 TGAAA
11950472 TCATTTGGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
62 4 0.06
63 32 0.49
64 21 0.32
65 8 0.12
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (66 bp):
TGAAAATGGAGAAATGGAAATCATTTGGAAATTATTATGGTTTTCTCCAAAATGAAAATGGAGAA
A
Found at i:11950454 original size:51 final size:51
Alignment explanation
Indices: 11950398--11950511 Score: 176
Period size: 51 Copynumber: 2.2 Consensus size: 51
11950388 AATGAAAATG
* * *
11950398 AAAATGAAAATGGAGAAATGGAAA-CATTTGGAATTGATTATGGTTTTTTCC
1 AAAATGAAAATGGAGAAAT-GAAATCATTTGGAAATGAATATGGTTTTCTCC
*
11950449 AAAATGAAAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCC
1 AAAATGAAAATGGAGAAATGAAATCATTTGGAAATGAATATGGTTTTCTCC
11950500 AAAATGAAAATG
1 AAAATGAAAATG
11950512 ACCTGAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 4 0.07
51 54 0.93
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (51 bp):
AAAATGAAAATGGAGAAATGAAATCATTTGGAAATGAATATGGTTTTCTCC
Found at i:11952914 original size:19 final size:20
Alignment explanation
Indices: 11952873--11952915 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
11952863 ATGTTTCCTT
11952873 CTTTCTCTATTTTTTTTCTA
1 CTTTCTCTATTTTTTTTCTA
11952893 CTTTCTCT-TTTCTTTTTC-A
1 CTTTCTCTATTT-TTTTTCTA
11952912 CTTT
1 CTTT
11952916 TGATACTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (20 bp):
CTTTCTCTATTTTTTTTCTA
Found at i:11958757 original size:2 final size:2
Alignment explanation
Indices: 11958750--11958774 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11958740 CGGTTGCCAT
11958750 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
11958775 TTCTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11971909 original size:150 final size:148
Alignment explanation
Indices: 11971553--11972138 Score: 840
Period size: 150 Copynumber: 4.0 Consensus size: 148
11971543 TAGGCGATCT
* * *
11971553 GGAGGCACATTCCACTGAGGATCTACTACTAGCCATCACATTGGATGGAGAAGAGTGCGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATTC
** * * *
11971618 CACTGTATGTCTCACTTCTAGTAGTCC-T--TCCACTCTTCTTATTAGTTTTCCTTCCAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTT-TTATCAGTTTTCCTTCCAAGATTT
11971680 TCTTCACTGTGCAATTT--
130 TCTTCACTGTGCAATTTGG
* * *
11971697 GGAGGCACCTTCCACTGAGGATCTACTACTGCCCATCACGTTGGATGGAGAAGAGTGGGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATTC
*
11971762 CACCGTGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCATTTTATCAGTTTTCCTTCCAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATTT
11971827 TCTTCACTGTGCAATTTGGG
130 TCTTCACTGTGCAATTT-GG
* * * *
11971847 GGAGGCACCTTTCACTGAGGATCTACTACTACCGATCACATTGGACGGAGAAGGGTGAGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATTC
* ** * * * *
11971912 CACTATGCATCTCACTCCTAGGAATCCTTCCTCCACCCTTTATATCAGTTTTCCTTACAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTT-TATCAGTTTTCCTTCCAAGATTT
11971977 TCTTCACTGTGCAATTTGG
130 TCTTCACTGTGCAATTTGG
11971996 AGGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATT
1 -GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATT
* * **
11972061 CCATCATGTGTCTCACTTCTAGGAGTCCGTCCTCCACTCTTTTTATCAGTTTTCCTTCCATTATT
65 CCACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATT
11972126 TTCTTCACTGTGC
129 TTCTTCACTGTGC
11972139 TTTCTCTTCT
Statistics
Matches: 393, Mismatches: 39, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
144 84 0.21
145 1 0.00
147 47 0.12
148 2 0.01
149 5 0.01
150 251 0.64
151 3 0.01
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (148 bp):
GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATTC
CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTTTATCAGTTTTCCTTCCAAGATTTT
CTTCACTGTGCAATTTGG
Found at i:11973848 original size:30 final size:29
Alignment explanation
Indices: 11973807--11973863 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 29
11973797 ATATAAAAGC
11973807 AAAAGAAGAAAACATAAGAGGG-GAGAGAGGT
1 AAAAGAAG-AAA-A-AAGAGGGAGAGAGAGGT
11973838 AAAA-AAGAAAAAAGAGGGAGAGAGAG
1 AAAAGAAGAAAAAAGAGGGAGAGAGAG
11973864 AGAAGAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 7 0.28
28 8 0.32
29 3 0.12
30 3 0.12
31 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.35, T:0.04
Consensus pattern (29 bp):
AAAAGAAGAAAAAAGAGGGAGAGAGAGGT
Found at i:11991264 original size:27 final size:27
Alignment explanation
Indices: 11991234--11991290 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
11991224 TAAATATTCA
*
11991234 TGGGACATTTCGCAATATAGGTGTCCG
1 TGGGACATTCCGCAATATAGGTGTCCG
* * *
11991261 TGGGACATTCCGTAATATATGTGTTCG
1 TGGGACATTCCGCAATATAGGTGTCCG
11991288 TGG
1 TGG
11991291 AAAAGTCCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (27 bp):
TGGGACATTCCGCAATATAGGTGTCCG
Found at i:11998704 original size:18 final size:18
Alignment explanation
Indices: 11998679--11998724 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
11998669 TATCTTGTAG
11998679 ATAA-ATATTATATTAAT
1 ATAATATATTATATTAAT
* *
11998696 TTAATATATTAAATTAAT
1 ATAATATATTATATTAAT
11998714 ATAATAT-TTAT
1 ATAATATATTAT
11998725 CTTGATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAATATATTATATTAAT
Found at i:11998705 original size:13 final size:13
Alignment explanation
Indices: 11998687--11998716 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11998677 AGATAAATAT
*
11998687 TATATTAATTTAA
1 TATATTAAATTAA
11998700 TATATTAAATTAA
1 TATATTAAATTAA
11998713 TATA
1 TATA
11998717 ATATTTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATTAAATTAA
Found at i:12000294 original size:10 final size:9
Alignment explanation
Indices: 12000270--12000320 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
12000260 ATGCCAATTT
12000270 AATTTTTAA
1 AATTTTTAA
12000279 AATTTTTAA
1 AATTTTTAA
12000288 AATTTTTAA
1 AATTTTTAA
* *
12000297 TTATTATTTTA
1 -AATT-TTTAA
*
12000308 AATTTTTAT
1 AATTTTTAA
12000317 AATT
1 AATT
12000321 AGGATTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 25 0.71
10 6 0.17
11 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
AATTTTTAA
Found at i:12001942 original size:19 final size:19
Alignment explanation
Indices: 12001896--12001943 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
12001886 GTATACATTT
12001896 TAAA-TTTATTTAAGTAGA
1 TAAATTTTATTTAAGTAGA
* *
12001914 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAAGTAGA
12001933 TAAATTTTATT
1 TAAATTTTATT
12001944 CATATTCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAAGTAGA
Found at i:12007185 original size:21 final size:21
Alignment explanation
Indices: 12007137--12007185 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
12007127 TTGTTAAATA
* *
12007137 TAAATTATTAAAAATTATATT
1 TAAATTTTTAAAAAATATATT
*
12007158 TATATTTTTAATAAAATATA-T
1 TAAATTTTTAA-AAAATATATT
12007179 TAAATTT
1 TAAATTT
12007186 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATTTTTAAAAAATATATT
Found at i:12007643 original size:41 final size:41
Alignment explanation
Indices: 12007590--12007672 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
12007580 TATCTAAAAT
*
12007590 AATATAAAATATTATATTAATAAGATTCAAATTAGAAATAA
1 AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAA
* *
12007631 AATATAAAATATTATATTATTAAGATCCTAATTAGAAATAA
1 AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAA
12007672 A
1 A
12007673 TAATCTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.35
Consensus pattern (41 bp):
AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAA
Done.