Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 55 of 171
Found at i:22103962 original size:13 final size:13
Alignment explanation
Indices: 22103946--22103988 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
22103936 TTTTTTACAT
22103946 AAATAATACAAAA
1 AAATAATACAAAA
*
22103959 AAATTATACACCAAA
1 AAATAATACA--AAA
*
22103974 ATATAATACAAAA
1 AAATAATACAAAA
22103987 AA
1 AA
22103989 TAAAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 13 0.54
15 11 0.46
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAATACAAAA
Found at i:22107285 original size:26 final size:25
Alignment explanation
Indices: 22107256--22107304 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
22107246 ATTAATTCTA
22107256 TTTAAATTTGAATTTATTTAATAATT
1 TTTAAATTTGAA-TTATTTAATAATT
**
22107282 TTTATGTTTGAATTATTTAATAA
1 TTTAAATTTGAATTATTTAATAA
22107305 GGTCTAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (25 bp):
TTTAAATTTGAATTATTTAATAATT
Found at i:22109838 original size:18 final size:17
Alignment explanation
Indices: 22109826--22109880 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
22109816 AATTTGTCTT
22109826 TTTTAAAATATTTTTTA
1 TTTTAAAATATTTTTTA
**
22109843 TTTTAAAAT-TTTAATA
1 TTTTAAAATATTTTTTA
22109859 -TTTAAAA-A--TTTTA
1 TTTTAAAATATTTTTTA
22109872 TTTTAAAAT
1 TTTTAAAAT
22109881 TTTAATACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 7 0.23
16 5 0.16
17 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAAATATTTTTTA
Found at i:22109854 original size:13 final size:13
Alignment explanation
Indices: 22109838--22109884 Score: 67
Period size: 13 Copynumber: 3.4 Consensus size: 13
22109828 TTAAAATATT
22109838 TTTTATTTTAAAA
1 TTTTATTTTAAAA
22109851 TTTTAATATTTAAAAA
1 TTTT-AT-TTT-AAAA
22109867 TTTTATTTTAAAA
1 TTTTATTTTAAAA
22109880 TTTTA
1 TTTTA
22109885 ATACAGTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 13 0.42
14 5 0.16
15 5 0.16
16 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTATTTTAAAA
Found at i:22109866 original size:16 final size:15
Alignment explanation
Indices: 22109827--22109884 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
22109817 ATTTGTCTTT
*
22109827 TTTAAAATATTTTTTA
1 TTTAAAA-ATTTTATA
*
22109843 TTTTAAAATTTTAATA
1 TTTAAAAATTTT-ATA
22109859 TTTAAAAATTTTAT-
1 TTTAAAAATTTTATA
22109873 TTT-AAAATTTTA
1 TTTAAAAATTTTA
22109885 ATACAGTAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
13 9 0.24
14 3 0.08
15 7 0.18
16 19 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAAAAATTTTATA
Found at i:22110454 original size:15 final size:15
Alignment explanation
Indices: 22110407--22110457 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
22110397 TTCTCTCATA
*
22110407 TTATATTTTAATTAT
1 TTATGTTTTAATTAT
* * * *
22110422 CTAGGTTTAAAATA-
1 TTATGTTTTAATTAT
22110436 TTATGTTTTAATTAT
1 TTATGTTTTAATTAT
22110451 TTATGTT
1 TTATGTT
22110458 ATCTTTTTAT
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (15 bp):
TTATGTTTTAATTAT
Found at i:22110616 original size:11 final size:10
Alignment explanation
Indices: 22110592--22110624 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
22110582 AATTTTTTAA
22110592 TTAAATAAAT
1 TTAAATAAAT
22110602 TTAAATAACAT
1 TTAAATAA-AT
22110613 TTAAATAAAT
1 TTAAATAAAT
22110623 TT
1 TT
22110625 TTTTAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (10 bp):
TTAAATAAAT
Found at i:22117791 original size:28 final size:28
Alignment explanation
Indices: 22117751--22118219 Score: 461
Period size: 28 Copynumber: 16.9 Consensus size: 28
22117741 CAATTAGGGG
*
22117751 AATAGGCCGATTTTAAAAATAATTACAA
1 AATAGGCCGATTTTAAAAATAATTACGA
* ** *
22117779 AATAAGCTAATTTTAAAAATAATTACGG
1 AATAGGCCGATTTTAAAAATAATTACGA
* *
22117807 AATAGGCCGATTTT-AAAATAAATTATGG
1 AATAGGCCGATTTTAAAAAT-AATTACGA
* * *
22117835 AATAGGCCTATTTTAAAAATAATTAGGG
1 AATAGGCCGATTTTAAAAATAATTACGA
* * *
22117863 ACTAGGCCAATTTTAAAAATAATTACGG
1 AATAGGCCGATTTTAAAAATAATTACGA
* *
22117891 ATTAGGCCGATTTTAAAAATAATTACAA
1 AATAGGCCGATTTTAAAAATAATTACGA
* * * *
22117919 AATATGCTGATTTTGAAAATAATTACAA
1 AATAGGCCGATTTTAAAAATAATTACGA
22117947 AATAGGCCGATTTTAAAAA-AATT---A
1 AATAGGCCGATTTTAAAAATAATTACGA
* *
22117971 AATAGGCCAATTTTAAAAATAAATAC-A
1 AATAGGCCGATTTTAAAAATAATTACGA
* **
22117998 AATTATGCCGATTTT-AAAATAATTAAAAA
1 AA-TAGGCCGATTTTAAAAATAATT-ACGA
* *
22118027 AATAGACCGATTTTAAAAATAATTACAA
1 AATAGGCCGATTTTAAAAATAATTACGA
* *
22118055 AATAGGCTGATTTTAAAAATAATTACGG
1 AATAGGCCGATTTTAAAAATAATTACGA
* * * *
22118083 AATAGGTCGATTTTAAAAATAATCATGG
1 AATAGGCCGATTTTAAAAATAATTACGA
* * *
22118111 AATAGGTCGATTTT-AAAATAATTATGG
1 AATAGGCCGATTTTAAAAATAATTACGA
* *
22118138 AATAGGCTGATTTTAAAAATAATTA-TA
1 AATAGGCCGATTTTAAAAATAATTACGA
* * * *
22118165 GAGTAAGCCAATTTTAAAAATAATTAGGGA
1 -AATAGGCCGATTTTAAAAATAATTA-CGA
22118195 AATAGGCCGATTTTAAAAATAATTA
1 AATAGGCCGATTTTAAAAATAATTA
22118220 GGCAAATATG
Statistics
Matches: 373, Mismatches: 55, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
24 19 0.05
25 3 0.01
27 44 0.12
28 267 0.72
29 39 0.10
30 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (28 bp):
AATAGGCCGATTTTAAAAATAATTACGA
Found at i:22120463 original size:33 final size:31
Alignment explanation
Indices: 22120414--22120483 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 31
22120404 AATTTTTAAA
22120414 ATTTTTAAAAAATTAAAAATTATATAAAAAAACT
1 ATTTTTAAAAAATTAAAAA-TAT-TAAAAAAA-T
*
22120448 ATTTTT-AAAAATTAAAAATATTAAAAATAT
1 ATTTTTAAAAAATTAAAAATATTAAAAAAAT
22120478 ATTTTT
1 ATTTTT
22120484 TAGTATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
30 7 0.20
31 7 0.20
32 3 0.09
33 12 0.34
34 6 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (31 bp):
ATTTTTAAAAAATTAAAAATATTAAAAAAAT
Found at i:22124179 original size:53 final size:53
Alignment explanation
Indices: 22124025--22124185 Score: 191
Period size: 54 Copynumber: 3.0 Consensus size: 53
22124015 AAAATTAGTA
* *
22124025 GTGTTGGCCATGCATTGACCGACACCAATATTTTTTATTAGATAAAAAAAA-TTG
1 GTGTTGGCCATGCATTGACCGACACC-AT-CTTTTTATCAGATAAAAAAAATTTG
* * *
22124079 GTATTGGTCATGCATTGACCGACACCACCTTTTTTATCAGATAAAAAAAAATTTG
1 GTGTTGGCCATGCATTGACCGACACCATC-TTTTTATCAGAT-AAAAAAAATTTG
* * *
22124134 GTGTTAGCCATACATT-AGCCGACACCATCTTTTTATCAGATAAAAAATATTT
1 GTGTTGGCCATGCATTGA-CCGACACCATCTTTTTATCAGATAAAAAAAATTT
22124186 TTTTTGTATT
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
53 22 0.24
54 45 0.49
55 25 0.27
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (53 bp):
GTGTTGGCCATGCATTGACCGACACCATCTTTTTATCAGATAAAAAAAATTTG
Found at i:22124349 original size:92 final size:93
Alignment explanation
Indices: 22124229--22124436 Score: 355
Period size: 94 Copynumber: 2.2 Consensus size: 93
22124219 CTTTTTTATC
*
22124229 TGACAAAATATTATTTATCAAATTCAAATTTTAAATTTATTTAAAT-AAAAATTATTATAATATT
1 TGACAATATATTATTTATCAAATTCAAATTTTAAATTTATTTAAATAAAAAATTATTATAATATT
*
22124293 TCAATTTTTATCAAATAATTTGTTGATT
66 TCAATTTTTATCAAATAATGTGTTGATT
* *
22124321 TGACAATACATTATTTACCAAATTCAAATTTTAAATTTATTTAAATAAAAAAATTATTATAATAT
1 TGACAATATATTATTTATCAAATTCAAATTTTAAATTTATTTAAAT-AAAAAATTATTATAATAT
22124386 TTCAATTTTTATCAAATAATGTGTTGATT
65 TTCAATTTTTATCAAATAATGTGTTGATT
*
22124415 TGATAATATATTATTTATCAAA
1 TGACAATATATTATTTATCAAA
22124437 ATACCCTTAA
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 43 0.40
94 64 0.60
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (93 bp):
TGACAATATATTATTTATCAAATTCAAATTTTAAATTTATTTAAATAAAAAATTATTATAATATT
TCAATTTTTATCAAATAATGTGTTGATT
Found at i:22125716 original size:19 final size:19
Alignment explanation
Indices: 22125672--22125717 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
22125662 TTTTTAAAAT
* *
22125672 ATTTTTTTCTATTTTTGAA
1 ATTTTTTTATATTTTCGAA
*
22125691 ATATTTTTATATTTTCG-A
1 ATTTTTTTATATTTTCGAA
22125709 ATTTTTTTA
1 ATTTTTTTA
22125718 AAACAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTTTATATTTTCGAA
Found at i:22125775 original size:19 final size:18
Alignment explanation
Indices: 22125751--22125794 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
22125741 TTTACATATA
*
22125751 TTTTTTATATTTTCGAAAT
1 TTTTTTAGATTTTCG-AAT
*
22125770 TTTTTTAGCTTTTCGAAT
1 TTTTTTAGATTTTCGAAT
22125788 TTTTTTA
1 TTTTTTA
22125795 AAAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTTTTAGATTTTCGAAT
Found at i:22125788 original size:77 final size:76
Alignment explanation
Indices: 22125661--22125805 Score: 202
Period size: 77 Copynumber: 1.9 Consensus size: 76
22125651 TAATATATAA
* * *
22125661 TTTTTTAAAATATTTTTTTCTATTTTTGAAATATTTTTATATTTTCGAATTTTTTTAAAACAATA
1 TTTTTTAAAATATTTTTTTATATTTTCGAAATATTTTTAGATTTTCGAATTTTTTTAAAA-AATA
22125726 TTTTCGAAACAC
65 TTTTCGAAACAC
* * * *
22125738 TTTTTT-ACATATATTTTTTATATTTTCGAAATTTTTTTAGCTTTTCGAATTTTTTTAAAAATTA
1 TTTTTTAAAATAT-TTTTTTATATTTTCGAAATATTTTTAGATTTTCGAATTTTTTTAAAAAATA
22125802 TTTT
65 TTTT
22125806 TTATGTCTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
76 12 0.20
77 48 0.80
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (76 bp):
TTTTTTAAAATATTTTTTTATATTTTCGAAATATTTTTAGATTTTCGAATTTTTTTAAAAAATAT
TTTCGAAACAC
Found at i:22127029 original size:29 final size:29
Alignment explanation
Indices: 22126885--22127029 Score: 179
Period size: 29 Copynumber: 5.0 Consensus size: 29
22126875 TTTTTTTAGT
*
22126885 TTATTTTTTAAATTTAATTT-TAATTTTGA
1 TTATATTTTAAATTTAATTTCTAATTTT-A
*
22126914 TACATATTTTAAATTTAATTT-TAATTTCGT-
1 T-TATATTTTAAATTTAATTTCTAATTT--TA
* *
22126944 TTATATTTTGAATTTTATTTCTAATTTTA
1 TTATATTTTAAATTTAATTTCTAATTTTA
*
22126973 TTATATTTTAAATTTCATTTCTAATTTTA
1 TTATATTTTAAATTTAATTTCTAATTTTA
*
22127002 TTATATTTTAAATTTCATTTCTAATTTT
1 TTATATTTTAAATTTAATTTCTAATTTT
22127030 TTTTTCAATA
Statistics
Matches: 104, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.01
29 72 0.69
30 30 0.29
32 1 0.01
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (29 bp):
TTATATTTTAAATTTAATTTCTAATTTTA
Found at i:22128029 original size:52 final size:52
Alignment explanation
Indices: 22127893--22128215 Score: 318
Period size: 53 Copynumber: 6.2 Consensus size: 52
22127883 AAAAAAATTT
* * * ** ** *
22127893 ATTTTTTTATCAGATAAAAAAAGTGATGTCGATTAAGCATTGGTTAACACAAAAAA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACAC----CA
*
22127949 ATATTTTTTATCTGAT-AAAAAGGTGGTGTCGGCCAATGCA-TGGCCAACACCA
1 AT-TTTTTTATCTGATAAAAAAGGTGGTGTCGACCAA-GCATTGGCCAACACCA
* * * *
22128001 ATTTTTTTATTTGATAAAAAAGATGGTGTTGACCAATGCA-TGACCAACA-CA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGACCAA-GCATTGGCCAACACCA
* ** *
22128052 ATTTTTTTCATC---TAAAAAAGTTGGTGTCGACCAAGCATTGATCAACATCAA
1 ATTTTTTT-ATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACA-CCA
* * *
22128103 ATTTTTTTATTTGATTAAAAAGGTGGTGTCGACCAAACATTGGCCAACACCA
1 ATTTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCA
*
22128155 ATTTTTTTTATCTGATAAAAAAGGTAGTGTCGACCAAGCATTGGCCAACACCA
1 A-TTTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCA
22128208 ATTTTTTT
1 ATTTTTTT
22128216 TCAAAATCTC
Statistics
Matches: 226, Mismatches: 30, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
48 3 0.01
49 28 0.12
50 2 0.01
51 31 0.14
52 44 0.19
53 78 0.35
56 25 0.11
57 15 0.07
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (52 bp):
ATTTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCA
Found at i:22128130 original size:102 final size:101
Alignment explanation
Indices: 22127952--22128215 Score: 309
Period size: 102 Copynumber: 2.5 Consensus size: 101
22127942 CAAAAAAATA
* *
22127952 TTTTTTATCTGATAAAAAGGTGGTGTCGGCCAATGCA-TGGCCAACACCAATTTTTTTATTTGAT
1 TTTTTTATCT-A-AAAAAGGTGGTGTCGACCAA-GCATTGGCCAACACAAATTTTTTTATTTGAT
* *
22128016 AAAAAAGATGGTGTTGACCAATGCA-TGACCAACA-CAAT
63 AAAAAAGATGGTGTCGACCAA-ACATTGACCAACACCAAT
* ** *
22128054 TTTTTTCATCTAAAAAAGTTGGTGTCGACCAAGCATTGATCAACATCAAATTTTTTTATTTGATT
1 TTTTTT-ATCTAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACA-CAAATTTTTTTATTTGATA
* *
22128119 AAAAAGGTGGTGTCGACCAAACATTGGCCAACACCAATT
64 AAAAAGATGGTGTCGACCAAACATTGACCAACACCAA-T
* *
22128158 TTTTTTATCTGATAAAAAAGGTAGTGTCGACCAAGCATTGGCCAACACCAATTTTTTT
1 TTTTTTATC---TAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACAAATTTTTTT
22128216 TCAAAATCTC
Statistics
Matches: 138, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
100 3 0.02
101 27 0.20
102 50 0.36
103 10 0.07
104 7 0.05
105 10 0.07
106 31 0.22
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (101 bp):
TTTTTTATCTAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACAAATTTTTTTATTTGATAAA
AAAGATGGTGTCGACCAAACATTGACCAACACCAAT
Found at i:22128216 original size:53 final size:53
Alignment explanation
Indices: 22127952--22128216 Score: 321
Period size: 53 Copynumber: 5.1 Consensus size: 53
22127942 CAAAAAAATA
*
22127952 TTTTTTATCTGAT-AAAAAGGTGGTGTCGGCCAATGCA-TGGCCAACACCAA-T
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGACCAA-GCATTGGCCAACACCAATT
* * * *
22128003 TTTTTTATTTGATAAAAAAGATGGTGTTGACCAATGCA-TGACCAACA-CAATT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGACCAA-GCATTGGCCAACACCAATT
* * ** * *
22128055 TTTTTCATC---TAAAAAAGTTGGTGTCGACCAAGCATTGATCAACATCAAAT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAATT
* * *
22128105 TTTTTTATTTGATTAAAAAGGTGGTGTCGACCAAACATTGGCCAACACCAATT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAATT
*
22128158 TTTTTTATCTGATAAAAAAGGTAGTGTCGACCAAGCATTGGCCAACACCAATT
1 TTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAATT
22128211 TTTTTT
1 TTTTTT
22128217 CAAAATCTCG
Statistics
Matches: 183, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
48 3 0.02
49 28 0.15
50 11 0.06
51 15 0.08
52 37 0.20
53 89 0.49
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (53 bp):
TTTTTTATCTGATAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACCAATT
Found at i:22134901 original size:6 final size:6
Alignment explanation
Indices: 22134892--22134921 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
22134882 ACATGTACAA
*
22134892 TTGTGT TTGTAT TTGTAT TTGTAT TTGTAT
1 TTGTAT TTGTAT TTGTAT TTGTAT TTGTAT
22134922 GGCGAATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.20, T:0.67
Consensus pattern (6 bp):
TTGTAT
Found at i:22141205 original size:12 final size:11
Alignment explanation
Indices: 22141182--22141234 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
22141172 ATATATTATG
*
22141182 TTTTTCTATTT
1 TTTTTCTCTTT
22141193 TTCTTTCTCTTT
1 TT-TTTCTCTTT
*
22141205 TTTTTCTCACTGT
1 TTTTTCT--CTTT
22141218 TTTTTCTCTTT
1 TTTTTCTCTTT
22141229 ATTTTT
1 -TTTTT
22141235 TGCAGGTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 10 0.29
12 15 0.43
13 10 0.29
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:22142086 original size:14 final size:14
Alignment explanation
Indices: 22142067--22142094 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22142057 GAATAAAATT
22142067 ATATTTGGGTTTAA
1 ATATTTGGGTTTAA
22142081 ATATTTGGGTTTAA
1 ATATTTGGGTTTAA
22142095 TTTATGAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
ATATTTGGGTTTAA
Found at i:22142128 original size:55 final size:56
Alignment explanation
Indices: 22142038--22142267 Score: 297
Period size: 55 Copynumber: 4.1 Consensus size: 56
22142028 AAAAGGAGTT
* **
22142038 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTT-AAATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGA-AAATAAAATTATATTTGGGTTTAAAATATTTAAGTTTA
* * *
22142094 ATTTATGAGTGTTTTTGAAAATGAAATTATATTTGGGTTTAAAAATATTTAGGTTTA
1 GTTTATGAGTGTTTTTGAAAATAAAATTATATTTGGGTTT-AAAATATTTAAGTTTA
*
22142151 GTTTATGA--GTTTTTGAAAATGAAATTATATTTGGGTTTAAAAATATTTAAGTTTA
1 GTTTATGAGTGTTTTTGAAAATAAAATTATATTTGGGTTT-AAAATATTTAAGTTTA
* *
22142206 GTTTATGAGTGTTTTTGAAGAATAAAATTATATGTGGGTTTAAAAATATTTGAGTTTA
1 GTTTATGAGTGTTTTTGAA-AATAAAATTATATTTGGGTTT-AAAATATTTAAGTTTA
22142264 GTTT
1 GTTT
22142268 GTTGATGGGT
Statistics
Matches: 159, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
55 77 0.48
56 13 0.08
57 30 0.19
58 39 0.25
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (56 bp):
GTTTATGAGTGTTTTTGAAAATAAAATTATATTTGGGTTTAAAATATTTAAGTTTA
Found at i:22142251 original size:113 final size:110
Alignment explanation
Indices: 22142062--22142267 Score: 324
Period size: 113 Copynumber: 1.8 Consensus size: 110
22142052 TTTAGGAATA
** * *
22142062 AAATTATATTTGGGTTTAAATATTTGGGTTTAATTTATGAGTGTTTTTGAAAATGAAATTATATT
1 AAATTATATTTGGGTTTAAATATTTAAGTTTAATTTATGAGTGTTTTTGAAAATAAAATTATATG
22142127 TGGGTTTAAAAATATTT-AGGTTTAGTTTATGAGTTTTTGAAAATG
66 TGGGTTTAAAAATATTTGA-GTTTAGTTTATGAGTTTTTGAAAATG
*
22142172 AAATTATATTTGGGTTTAAAAATATTTAAGTTTAGTTTATGAGTGTTTTTGAAGAATAAAATTAT
1 AAATTATATTTGGGTTT--AAATATTTAAGTTTAATTTATGAGTGTTTTTGAA-AATAAAATTAT
22142237 ATGTGGGTTTAAAAATATTTGAGTTTAGTTT
63 ATGTGGGTTTAAAAATATTTGAGTTTAGTTT
22142268 GTTGATGGGT
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
110 17 0.20
112 31 0.36
113 38 0.44
114 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (110 bp):
AAATTATATTTGGGTTTAAATATTTAAGTTTAATTTATGAGTGTTTTTGAAAATAAAATTATATG
TGGGTTTAAAAATATTTGAGTTTAGTTTATGAGTTTTTGAAAATG
Found at i:22142526 original size:9 final size:9
Alignment explanation
Indices: 22142489--22142514 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
22142479 TCGATTTGTT
22142489 TAACTCGAA
1 TAACTCGAA
22142498 TAACTCGAA
1 TAACTCGAA
22142507 TAACTCGA
1 TAACTCGA
22142515 TTCGAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (9 bp):
TAACTCGAA
Found at i:22145882 original size:28 final size:29
Alignment explanation
Indices: 22145851--22145921 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
22145841 CTAATCTGTT
* *
22145851 ATTATATTTAAAATTTG-CTTAATCCGA-A
1 ATTATTTTTAAAATTTGTC-TAATCCAATA
*
22145879 ATTATTTTTAAAATTTGTCTGATCCAATA
1 ATTATTTTTAAAATTTGTCTAATCCAATA
22145908 ATTATTTTTAAAAT
1 ATTATTTTTAAAAT
22145922 CTTCCTTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (29 bp):
ATTATTTTTAAAATTTGTCTAATCCAATA
Found at i:22145938 original size:28 final size:28
Alignment explanation
Indices: 22145878--22145966 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 28
22145868 CTTAATCCGA
* **
22145878 AATTATTTTTAAAAT-TTGTCTGATCCAAT
1 AATTATTTTTAAAATCTT-CCTGAT-CTGT
*
22145907 AATTATTTTTAAAATCTTCCTTATCTGT
1 AATTATTTTTAAAATCTTCCTGATCTGT
* * *
22145935 AATTATTATT-GAATCTGCCTGATCTGT
1 AATTATTTTTAAAATCTTCCTGATCTGT
22145962 AATTA
1 AATTA
22145967 CAAATTAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 19 0.37
28 11 0.22
29 19 0.37
30 2 0.04
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (28 bp):
AATTATTTTTAAAATCTTCCTGATCTGT
Found at i:22146001 original size:28 final size:28
Alignment explanation
Indices: 22145961--22146374 Score: 437
Period size: 28 Copynumber: 14.9 Consensus size: 28
22145951 GCCTGATCTG
* * *
22145961 TAATTACAAATTAGAAAAATATTAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* *
22145989 TAATTACTAATTAGGGAAATTTTAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
** *
22146017 TAATTACG-CGTAGGAAAATTTGAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* *
22146044 T-ATTACGACTTAGGAAAATTTGAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* * *
22146071 TAATTAAGGATTAGGAAAATTTGAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* *
22146099 TAATTACGATTTAGGAAACTTTTAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* *
22146127 TAATTACTG-CTTAGGGAAATTTTAAAAA
1 TAATTAC-GAATTAGGAAAATTTTAAAAA
* *
22146155 TAATTACTAATTAGGAAAATTTGAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
*
22146183 T-ATTACGAATTAGGGAAATTTTAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* *
22146210 TAATTACAAATGAGGAAAATTTTAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* * *
22146238 TAATTATGGATTA-AAAAATTTTAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* * *
22146265 TAATTTCGATTTATGAAAATTTTAAAAA
1 TAATTACGAATTAGGAAAATTTTAAAAA
* *
22146293 TAATTA-AAGATTAGGAAACTTTTAAAAA
1 TAATTACGA-ATTAGGAAAATTTTAAAAA
* * *
22146321 TAATTA-AAATTTTGGAAAATTTGAAAAA
1 TAATTACGAA-TTAGGAAAATTTTAAAAA
* *
22146349 TAATTACGATTTAGTAAAATTTTAAA
1 TAATTACGAATTAGGAAAATTTTAAA
22146375 TCTGTAATTA
Statistics
Matches: 323, Mismatches: 54, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
26 6 0.02
27 83 0.26
28 232 0.72
29 2 0.01
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (28 bp):
TAATTACGAATTAGGAAAATTTTAAAAA
Found at i:22146154 original size:166 final size:166
Alignment explanation
Indices: 22145977--22146357 Score: 500
Period size: 166 Copynumber: 2.3 Consensus size: 166
22145967 CAAATTAGAA
* * * *
22145977 AAATATTAAAAATAATTACTAATTAGGGAAATTTTAAAAATAATTACG-CGTAGGAAAATTTGAA
1 AAATTTTAAAAATAATTACTAATTAGGAAAATTTGAAAAATAATTACGAAGTAGGAAAATTTGAA
* * * *
22146041 AAAT-ATTACGACTTAGGAAAATTTGAAAAATAATTAAGGATTAGGAAAATTTGAAAAATAATTA
66 AAATAATTACAAATGAGGAAAATTTGAAAAATAATTAAGGATTA-AAAAATTTGAAAAATAATTA
* ** *
22146105 CGATTTAGGAAACTTTTAAAAATAATTACTGCTTAGGG
130 CGATTTAGGAAAATTTTAAAAATAATTAAAGATTA-GG
* * *
22146143 AAATTTTAAAAATAATTACTAATTAGGAAAATTTGAAAAAT-ATTACGAATTAGGGAAATTTTAA
1 AAATTTTAAAAATAATTACTAATTAGGAAAATTTGAAAAATAATTACGAAGTAGGAAAATTTGAA
* * * *
22146207 AAATAATTACAAATGAGGAAAATTTTAAAAATAATTATGGATTAAAAAATTTTAAAAATAATTTC
66 AAATAATTACAAATGAGGAAAATTTGAAAAATAATTAAGGATTAAAAAATTTGAAAAATAATTAC
*
22146272 GATTTATGAAAATTTTAAAAATAATTAAAGATTAGG
131 GATTTAGGAAAATTTTAAAAATAATTAAAGATTAGG
* *
22146308 AAACTTTTAAAAATAATTA-AAATTTTGGAAAATTTGAAAAATAATTACGA
1 AAA-TTTTAAAAATAATTACTAA-TTAGGAAAATTTGAAAAATAATTACGA
22146358 TTTAGTAAAA
Statistics
Matches: 188, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
165 13 0.07
166 134 0.71
167 41 0.22
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (166 bp):
AAATTTTAAAAATAATTACTAATTAGGAAAATTTGAAAAATAATTACGAAGTAGGAAAATTTGAA
AAATAATTACAAATGAGGAAAATTTGAAAAATAATTAAGGATTAAAAAATTTGAAAAATAATTAC
GATTTAGGAAAATTTTAAAAATAATTAAAGATTAGG
Found at i:22146407 original size:28 final size:26
Alignment explanation
Indices: 22146374--22146465 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 26
22146364 AAAATTTTAA
22146374 ATCTGTAATTATTTTTGAAATCTGTCTG
1 ATCTGTAATT-TTTTTGAAATCTG-CTG
*
22146402 ATCTGTAATTTTCCTTGAAATCTGCTGG
1 ATCTGTAATTTT-TTTGAAATCTGCT-G
* * *
22146430 ATCTGTAATTGCTTCTAAAATCTGCCTG
1 ATCTGTAATT-TTTTTGAAATCTG-CTG
22146458 ATCTGTAA
1 ATCTGTAA
22146466 AATCGACCTA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.07
28 48 0.87
29 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.43
Consensus pattern (26 bp):
ATCTGTAATTTTTTTGAAATCTGCTG
Found at i:22146621 original size:28 final size:28
Alignment explanation
Indices: 22146463--22146628 Score: 156
Period size: 28 Copynumber: 5.9 Consensus size: 28
22146453 GCCTGATCTG
* * *
22146463 TAAAATCGACCTAATTCTTAATTATTTT
1 TAAAATCGATCTAATCCGTAATTATTTT
* *
22146491 TAAAATCGATCTATTTCCATAATTATTTT
1 TAAAATCGATCTA-ATCCGTAATTATTTT
* *
22146520 TAAAATC-ATCTTAATCTGTAATGATTTT
1 TAAAATCGATC-TAATCCGTAATTATTTT
* *
22146548 TAAAATC-ATCGTAATCCATAATGATTTT
1 TAAAATCGATC-TAATCCGTAATTATTTT
* ** *
22146576 TAAAATTGGCCTACTCCGTAATTATTTT
1 TAAAATCGATCTAATCCGTAATTATTTT
* *
22146604 TAAAATCGATTTATTCCGTAATTAT
1 TAAAATCGATCTAATCCGTAATTAT
22146629 ATAACATGTA
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
28 91 0.81
29 22 0.19
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.45
Consensus pattern (28 bp):
TAAAATCGATCTAATCCGTAATTATTTT
Found at i:22151610 original size:18 final size:18
Alignment explanation
Indices: 22151586--22151634 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
22151576 CAGTTCAAGT
22151586 TTTTATATTTTATAT-AA
1 TTTTATATTTTATATCAA
*
22151603 TATTTATAAGTTTATATCAA
1 T-TTTAT-ATTTTATATCAA
22151623 TTTTAATATTTT
1 TTTT-ATATTTT
22151635 TTTTATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 15 0.58
20 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTATATTTTATATCAA
Found at i:22151718 original size:9 final size:9
Alignment explanation
Indices: 22151701--22151775 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
22151691 GTTTATTAAG
22151701 TTTAT-ATT
1 TTTATAATT
22151709 TTTATAATT
1 TTTATAATT
*
22151718 TCTTA-AAAT
1 T-TTATAATT
*
22151727 TTCAT-A-T
1 TTTATAATT
22151734 TTTATAATAT
1 TTTATAAT-T
22151744 TTATATAATT
1 TT-TATAATT
*
22151754 TTAATAATT
1 TTTATAATT
22151763 TTATATTAATT
1 TT-TA-TAATT
22151774 TT
1 TT
22151776 AATATTTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
7 5 0.09
8 9 0.17
9 16 0.30
10 10 0.19
11 13 0.25
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTATAATT
Found at i:22151752 original size:11 final size:10
Alignment explanation
Indices: 22151736--22151792 Score: 61
Period size: 8 Copynumber: 6.0 Consensus size: 10
22151726 TTTCATATTT
22151736 TATAATATTTA
1 TATAAT-TTTA
22151747 TATAATTTTA
1 TATAATTTTA
22151757 -ATAATTTTA
1 TATAATTTTA
22151766 TATTAATTTTA
1 TA-TAATTTTA
22151777 -AT-ATTTTA
1 TATAATTTTA
22151785 -AT-ATTTTA
1 TATAATTTTA
22151793 ATATTTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
8 14 0.32
9 10 0.23
10 6 0.14
11 14 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATAATTTTA
Found at i:22151766 original size:28 final size:27
Alignment explanation
Indices: 22151730--22151800 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
22151720 TTAAAATTTC
22151730 ATATTTTATAATATTTAT-ATAATTTTA
1 ATATTTTATAATATTTATAAT-ATTTTA
*
22151757 ATAATTTTATATTAATTT-TAATATTTTA
1 AT-ATTTTATAAT-ATTTATAATATTTTA
22151785 ATA-TTT-TAATATTTAT
1 ATATTTTATAATATTTAT
22151801 TTTCAAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
24 4 0.11
25 4 0.11
26 3 0.08
27 3 0.08
28 18 0.47
29 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
ATATTTTATAATATTTATAATATTTTA
Found at i:22151803 original size:20 final size:20
Alignment explanation
Indices: 22151732--22151789 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
22151722 AAAATTTCAT
22151732 ATTTT-ATAATATTTATA-TA
1 ATTTTAATAAT-TTTATATTA
22151751 ATTTTAATAATTTTATATTA
1 ATTTTAATAATTTTATATTA
22151771 ATTTTAAT-ATTTTAATATT
1 ATTTTAATAATTTT-ATATT
22151790 TTAATATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTAATAATTTTATATTA
Found at i:22163140 original size:19 final size:21
Alignment explanation
Indices: 22163096--22163147 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 21
22163086 ATCTAATTAC
22163096 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
22163117 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
22163137 -AATATTCTAAT
1 AAATATT-TAAT
22163148 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 10 0.36
20 8 0.29
21 10 0.36
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:22163162 original size:32 final size:33
Alignment explanation
Indices: 22163101--22163194 Score: 83
Period size: 32 Copynumber: 2.9 Consensus size: 33
22163091 ATTACAAATA
*
22163101 TTTAATAATTATATTTAAATATTTAAAATATAG
1 TTTAATAATTATAATTAAATATTTAAAATATAG
*
22163134 TTTAAT-ATTCTAATTAAAT-TTTATAAATA-A-
1 TTTAATAATTATAATTAAATATTTA-AAATATAG
22163164 -TTAAT-ATTAATAACTTAGAAATATTTAAAAT
1 TTTAATAATT-ATAA-TT--AAATATTTAAAAT
22163195 TAATATTTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
29 8 0.15
30 3 0.06
31 7 0.13
32 16 0.31
33 14 0.27
34 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (33 bp):
TTTAATAATTATAATTAAATATTTAAAATATAG
Found at i:22164649 original size:29 final size:29
Alignment explanation
Indices: 22164616--22164675 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
22164606 TGTTTATATT
* *
22164616 AAGTCCAAGTTTTTACAATTTAGGAGGCA
1 AAGTCCAAATTTATACAATTTAGGAGGCA
* *
22164645 AAGTCCAAATTTATATAGTTTAGGAGGCA
1 AAGTCCAAATTTATACAATTTAGGAGGCA
22164674 AA
1 AA
22164676 ATGAAAGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (29 bp):
AAGTCCAAATTTATACAATTTAGGAGGCA
Found at i:22167187 original size:17 final size:17
Alignment explanation
Indices: 22167165--22167199 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22167155 CATGAATTAC
*
22167165 TATATTATCATAAAAAA
1 TATATTATAATAAAAAA
*
22167182 TATATTATAATAAGAAA
1 TATATTATAATAAAAAA
22167199 T
1 T
22167200 TATAAATTGT
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:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
TATATTATAATAAAAAA
Found at i:22184609 original size:30 final size:30
Alignment explanation
Indices: 22184495--22184611 Score: 126
Period size: 30 Copynumber: 3.9 Consensus size: 30
22184485 ATTAAAACCA
* ** * *
22184495 GGTCAAATTTGAATTTTTGGAAGCTTCAAG
1 GGTCAAATTTAAATTTTTGGAAAATTTAGG
** *
22184525 GGTCAAATCAAAATTTTTGGAAAATCTAGG
1 GGTCAAATTTAAATTTTTGGAAAATTTAGG
* *
22184555 GGTCAAATTCAAATTTTTGAAAAATTTAGG
1 GGTCAAATTTAAATTTTTGGAAAATTTAGG
* *
22184585 GGTTAAATTTGAATTTTTGGAAAATTT
1 GGTCAAATTTAAATTTTTGGAAAATTT
22184612 GGTGGTTAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (30 bp):
GGTCAAATTTAAATTTTTGGAAAATTTAGG
Found at i:22184619 original size:30 final size:29
Alignment explanation
Indices: 22184535--22184623 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
22184525 GGTCAAATCA
* *
22184535 AAATTTTTGGAAAATCTAGGGGTCAAATTC
1 AAATTTTTGGAAAAT-TTGGGGTTAAATTC
* *
22184565 AAATTTTTGAAAAATTTAGGGGTTAAATTT
1 AAATTTTTGGAAAATTT-GGGGTTAAATTC
*
22184595 GAATTTTTGGAAAATTTGGTGGTTAAATT
1 AAATTTTTGGAAAATTTGG-GGTTAAATT
22184624 AAAACCTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 3 0.06
30 48 0.94
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.40
Consensus pattern (29 bp):
AAATTTTTGGAAAATTTGGGGTTAAATTC
Found at i:22188211 original size:30 final size:29
Alignment explanation
Indices: 22188175--22188236 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
22188165 ATACATAATA
* *
22188175 AAAAAATATATACATAACATATAATAAAAT
1 AAAAAATATACACATAACATAAAAT-AAAT
* *
22188205 AAAAAATATACATATAAGATAAAATAAAT
1 AAAAAATATACACATAACATAAAATAAAT
22188234 AAA
1 AAA
22188237 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (29 bp):
AAAAAATATACACATAACATAAAATAAAT
Found at i:22188226 original size:25 final size:24
Alignment explanation
Indices: 22188164--22188238 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 24
22188154 GATTTACAAG
* * *
22188164 TATACATAATAAAAAAATATATACA
1 TATACAT-ATAATAAAATAAATAAA
22188189 TA-ACATATAATAAAATAAA-AAA
1 TATACATATAATAAAATAAATAAA
22188211 TATACATATAAGATAAAATAAATAAA
1 TATACATAT-A-ATAAAATAAATAAA
22188237 TA
1 TA
22188239 AAAAATTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.09
23 17 0.40
24 5 0.12
25 12 0.28
26 5 0.12
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (24 bp):
TATACATATAATAAAATAAATAAA
Found at i:22188226 original size:28 final size:28
Alignment explanation
Indices: 22188169--22188236 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
22188159 ACAAGTATAC
* *
22188169 ATAAT-AAA-AAAATATATACATAACAT
1 ATAATAAAATAAAAAATATACATAACAG
22188195 ATAATAAAATAAAAAATATACATATA-AG
1 ATAATAAAATAAAAAATATACATA-ACAG
*
22188223 ATAAAATAAATAAA
1 ATAATA-AAATAAA
22188237 TAAAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 5 0.14
27 3 0.09
28 19 0.54
29 8 0.23
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.25
Consensus pattern (28 bp):
ATAATAAAATAAAAAATATACATAACAG
Found at i:22188289 original size:30 final size:30
Alignment explanation
Indices: 22188253--22188452 Score: 192
Period size: 30 Copynumber: 6.7 Consensus size: 30
22188243 ATTAAAACCA
** * *
22188253 GGTCAAATTTGAATTTTTGGAAGCTTCAAG
1 GGTCAAATTTGAATTTTTGGAAAATTTAGG
*
22188283 GGTCAAATTAGAATTTTTGGAAAATTTAGG
1 GGTCAAATTTGAATTTTTGGAAAATTTAGG
*
22188313 GGTCAAATTTAAATTTTTGGAAAATTTAGG
1 GGTCAAATTTGAATTTTTGGAAAATTTAGG
*
22188343 GGTGAAATTTGAATTTTT-GAAAATTT-GAG
1 GGTCAAATTTGAATTTTTGGAAAATTTAG-G
* ** * *
22188372 GGTAAAATTCAAATTTTTAG-AAATTTTGAG
1 GGTCAAATTTGAATTTTTGGAAAATTTAG-G
** *
22188402 GGTCAAATTCAAATTTTTGGAAAATTT-GAT
1 GGTCAAATTTGAATTTTTGGAAAATTTAG-G
* *
22188432 GGTTAAATTCGAATTTTTGGA
1 GGTCAAATTTGAATTTTTGGA
22188453 TAGTTTGGGG
Statistics
Matches: 149, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
28 1 0.01
29 30 0.20
30 112 0.75
31 6 0.04
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (30 bp):
GGTCAAATTTGAATTTTTGGAAAATTTAGG
Found at i:22188387 original size:89 final size:89
Alignment explanation
Indices: 22188257--22188450 Score: 232
Period size: 89 Copynumber: 2.2 Consensus size: 89
22188247 AAACCAGGTC
** * *
22188257 AAATTTGAATTTTTGGAAGCTTCAAGGGTCAAATTAGAATTTTTGGAAAATTTAG-GGGTCAAAT
1 AAATTTGAATTTTT-GAAAATTCAAGGGTAAAATTAGAATTTTTAG-AAATTTAGAGGGTCAAAT
*
22188321 TTAAATTTTTGGAAAATTT-AGGGGTG
64 TCAAATTTTTGGAAAATTTGA-GGGTG
** *
22188347 AAATTTGAATTTTTGAAAATTTGAGGGTAAAATTCA-AATTTTTAGAAATTTTGAGGGTCAAATT
1 AAATTTGAATTTTTGAAAATTCAAGGGTAAAATT-AGAATTTTTAGAAATTTAGAGGGTCAAATT
* *
22188411 CAAATTTTTGGAAAATTTGATGGTT
65 CAAATTTTTGGAAAATTTGAGGGTG
*
22188436 AAATTCGAATTTTTG
1 AAATTTGAATTTTTG
22188451 GATAGTTTGG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
88 7 0.08
89 67 0.74
90 16 0.18
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (89 bp):
AAATTTGAATTTTTGAAAATTCAAGGGTAAAATTAGAATTTTTAGAAATTTAGAGGGTCAAATTC
AAATTTTTGGAAAATTTGAGGGTG
Found at i:22188477 original size:60 final size:61
Alignment explanation
Indices: 22188287--22188478 Score: 189
Period size: 60 Copynumber: 3.2 Consensus size: 61
22188277 TTCAAGGGTC
* * *
22188287 AAATTAGAATTTTTGGAAAATTT-AGGGGTCAAATTTAAATTTTTGGAAAATTTAGGGGT-GA
1 AAATTA-AATTTTTGGAAAATTTGA-GGGTAAAATTCAAATTTTTGGAAAATTTGGGGGTCGA
* * * * *
22188348 AATTTGAATTTTT-GAAAATTTGAGGGTAAAATTCAAATTTTTAGAAATTTTGAGGGTC--
1 AAATTAAATTTTTGGAAAATTTGAGGGTAAAATTCAAATTTTTGGAAAATTTGGGGGTCGA
* * * * *
22188406 AAATTCAAATTTTTGGAAAATTTGATGGTTAAATTCGAATTTTTGGATAGTTTGGGGGTCGA
1 AAATT-AAATTTTTGGAAAATTTGAGGGTAAAATTCAAATTTTTGGAAAATTTGGGGGTCGA
*
22188468 AAAAT-AATTTT
1 AAATTAAATTTT
22188479 AAAATAAAGC
Statistics
Matches: 107, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
58 4 0.04
59 43 0.40
60 52 0.49
61 4 0.04
62 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (61 bp):
AAATTAAATTTTTGGAAAATTTGAGGGTAAAATTCAAATTTTTGGAAAATTTGGGGGTCGA
Found at i:22197105 original size:4 final size:4
Alignment explanation
Indices: 22197096--22197133 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
22197086 CACTACCTTG
22197096 TACA TACA TACA TACA TACA TACA TACAA TACAA TACA
1 TACA TACA TACA TACA TACA TACA TAC-A TAC-A TACA
22197134 AAGAGTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 24 0.73
5 9 0.27
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:22199259 original size:32 final size:33
Alignment explanation
Indices: 22199215--22199277 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
22199205 TATGGTTTTA
*
22199215 TTAAAATATTAAAATA-TCATTTATTTTTATGT
1 TTAAAATATTAAAATATTCATGTATTTTTATGT
*
22199247 TTAAAATTTTAAAATATTTCATGTATTTTTA
1 TTAAAATATTAAAATA-TTCATGTATTTTTA
22199278 ATTTTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 15 0.56
34 12 0.44
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (33 bp):
TTAAAATATTAAAATATTCATGTATTTTTATGT
Found at i:22203338 original size:31 final size:28
Alignment explanation
Indices: 22203283--22203339 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
22203273 TTAGATATCA
*
22203283 TATTGAATATTTTAAAGTACAAATAATG
1 TATTGAATATTTTAAAATACAAATAATG
22203311 TATTGAATATTTTATGAAAATACAAATAA
1 TATTGAATA-TTT-T-AAAATACAAATAA
22203340 AAGCACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 3 0.12
30 1 0.04
31 12 0.48
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.39
Consensus pattern (28 bp):
TATTGAATATTTTAAAATACAAATAATG
Found at i:22217932 original size:21 final size:21
Alignment explanation
Indices: 22217891--22217934 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22217881 AATTTAACAA
*
22217891 TTAAATAATTTAAATAAAATT
1 TTAAATAATTCAAATAAAATT
* *
22217912 TTAAATAATTCAATTATAATT
1 TTAAATAATTCAAATAAAATT
22217933 TT
1 TT
22217935 TTAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATAATTCAAATAAAATT
Found at i:22217959 original size:29 final size:31
Alignment explanation
Indices: 22217912--22217973 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
22217902 AAATAAAATT
* ** *
22217912 TTAAATAATTCAATTAT-AATTTTTTAA-AA
1 TTAAATAATTAAAACATAAATTTATTAATAA
22217941 TTAAATAATTAAAACATAAATTTATTAATAA
1 TTAAATAATTAAAACATAAATTTATTAATAA
22217972 TT
1 TT
22217974 TATTTACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.52
30 9 0.33
31 4 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
TTAAATAATTAAAACATAAATTTATTAATAA
Found at i:22220580 original size:45 final size:45
Alignment explanation
Indices: 22220510--22220597 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
22220500 AAACCAAGCA
* * *
22220510 ATGACTACAAAGTACAAACAAAAGACTAGTTCTAATAGTGAAGAG
1 ATGACTACAAAGTACAAACAAAAGACAAATTCTAATAGGGAAGAG
***
22220555 ATGACTACAAAGTACAAATGGAAGACAAATTCTAATAGGGAAG
1 ATGACTACAAAGTACAAACAAAAGACAAATTCTAATAGGGAAG
22220598 CTACCTCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.19
Consensus pattern (45 bp):
ATGACTACAAAGTACAAACAAAAGACAAATTCTAATAGGGAAGAG
Found at i:22225528 original size:11 final size:11
Alignment explanation
Indices: 22225507--22225578 Score: 69
Period size: 11 Copynumber: 6.4 Consensus size: 11
22225497 AGTCTCTCAT
22225507 TTTTCCTTTCTC
1 TTTT-CTTTCTC
22225519 TTTTCTTTCTC
1 TTTTCTTTCTC
*
22225530 TCATTCCTTTCT-
1 T--TTTCTTTCTC
22225542 TATTTCTTTCTC
1 T-TTTCTTTCTC
22225554 -TTTCTTT-TC
1 TTTTCTTTCTC
22225563 TATTTCTTTCTC
1 T-TTTCTTTCTC
22225575 TTTT
1 TTTT
22225579 AATCACTCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
9 2 0.04
10 7 0.13
11 27 0.52
12 8 0.15
13 8 0.15
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:22225541 original size:24 final size:23
Alignment explanation
Indices: 22225508--22225577 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 23
22225498 GTCTCTCATT
22225508 TTTCCTTTCTCT-TTTCTTTCTC
1 TTTCCTTTCTCTATTTCTTTCTC
22225530 TCATTCCTTTCT-TATTTCTTTCTC
1 T--TTCCTTTCTCTATTTCTTTCTC
22225554 TTT-CTTT-TCTATTTCTTTCTC
1 TTTCCTTTCTCTATTTCTTTCTC
22225575 TTT
1 TTT
22225578 TAATCACTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.02
21 19 0.43
22 3 0.07
23 1 0.02
24 20 0.45
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTCCTTTCTCTATTTCTTTCTC
Found at i:22225566 original size:21 final size:21
Alignment explanation
Indices: 22225512--22225577 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 21
22225502 CTCATTTTTC
22225512 CTTTCTCT-TTTCTTTCTCTCATT
1 CTTT-TCTATTTCTTTCTCT--TT
*
22225535 CCTTTCTTATTTCTTTCTCTTT
1 CTTTTC-TATTTCTTTCTCTTT
22225557 CTTTTCTATTTCTTTCTCTTT
1 CTTTTCTATTTCTTTCTCTTT
22225578 TAATCACTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 15 0.38
22 9 0.23
23 4 0.10
24 11 0.28
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (21 bp):
CTTTTCTATTTCTTTCTCTTT
Found at i:22225568 original size:17 final size:17
Alignment explanation
Indices: 22225513--22225578 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 17
22225503 TCATTTTTCC
22225513 TTTCTCTTTTCTTTCTCTCA
1 TTTCTC-TTTCTTT-TCT-A
*
22225533 -TTC-CTTTCTTATT-TC
1 TTTCTCTTTCTT-TTCTA
22225548 TTTCTCTTTCTTTTCTA
1 TTTCTCTTTCTTTTCTA
22225565 TTTCT-TTCTCTTTT
1 TTTCTCTT-TCTTTT
22225579 AATCACTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
16 8 0.21
17 26 0.67
18 2 0.05
19 3 0.08
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTCTCTTTCTTTTCTA
Found at i:22226921 original size:6 final size:6
Alignment explanation
Indices: 22226907--22226996 Score: 69
Period size: 6 Copynumber: 14.8 Consensus size: 6
22226897 TTTAAATTTG
* * *
22226907 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAAA TTAAATA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A TTTAAA TTTAAA
* * *
22226955 TTTGAA TTTAAA TTTAAA -TAAAGA TTAAAA TATTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA T-TTAAA TTTAA
22226997 CCATTAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
5 11 0.16
6 38 0.56
7 19 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:22226953 original size:31 final size:31
Alignment explanation
Indices: 22226912--22226974 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
22226902 ATTTGTTTAA
* *
22226912 ATTTAGATTTATTTTAAATTTAAAATTAAAT
1 ATTTAAATTTAATTTAAATTTAAAATTAAAT
* *
22226943 ATTTAAATTTAATTTGAATTTAAATTTAAAT
1 ATTTAAATTTAATTTAAATTTAAAATTAAAT
22226974 A
1 A
22226975 AAGATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTAAATTTAATTTAAATTTAAAATTAAAT
Found at i:22226962 original size:11 final size:11
Alignment explanation
Indices: 22226911--22226973 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
22226901 AATTTGTTTA
*
22226911 AATTTAGATTT
1 AATTTAAATTT
*
22226922 ATTTTAAATTT
1 AATTTAAATTT
*
22226933 AAAATTAAA--T
1 -AATTTAAATTT
22226943 -ATTTAAATTT
1 AATTTAAATTT
*
22226953 AATTTGAATTT
1 AATTTAAATTT
22226964 AAATTTAAAT
1 -AATTTAAAT
22226974 AAAGATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
8 6 0.15
10 2 0.05
11 18 0.45
12 14 0.35
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:22226994 original size:37 final size:37
Alignment explanation
Indices: 22226910--22226990 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
22226900 AAATTTGTTT
* * *
22226910 AAATTTAGATTT-ATTTTAAATTTAAAATTAAATATTT
1 AAATTTA-ATTTGAATTTAAATTTAAAATTAAAGATTA
22226947 AAATTTAATTTGAATTTAAATTT-AAA-TAAAGATTA
1 AAATTTAATTTGAATTTAAATTTAAAATTAAAGATTA
22226982 AAATATTAA
1 AAAT-TTAA
22226991 ATTTAACCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 11 0.28
36 11 0.28
37 17 0.44
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (37 bp):
AAATTTAATTTGAATTTAAATTTAAAATTAAAGATTA
Found at i:22227191 original size:20 final size:20
Alignment explanation
Indices: 22227166--22227221 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
22227156 GTGCCTACTG
*
22227166 CTGCTGGCCACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
22227186 CTGCTGACCACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
*
22227206 CTGCTGCTCCACCAGC
1 CTGCTG-ACCACCAGC
22227222 CGCCTGCTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.16, C:0.46, G:0.18, T:0.20
Consensus pattern (20 bp):
CTGCTGACCACCAGCTCCAT
Found at i:22228054 original size:24 final size:25
Alignment explanation
Indices: 22228027--22228088 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
22228017 GGAAATATTA
*
22228027 ATGG-AAAAAGAAAGAATAAAA-AAG
1 ATGGAAAAAAG-AAGAAGAAAAGAAG
22228051 ATGGAAAAAAGAAGAAGAAAAGAAG
1 ATGGAAAAAAGAAGAAGAAAAGAAG
*
22228076 A--GAAGAAAGAAGA
1 ATGGAAAAAAGAAGA
22228089 CGGCTTACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 11 0.32
24 13 0.38
25 10 0.29
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (25 bp):
ATGGAAAAAAGAAGAAGAAAAGAAG
Found at i:22228826 original size:30 final size:30
Alignment explanation
Indices: 22228795--22229159 Score: 437
Period size: 29 Copynumber: 12.4 Consensus size: 30
22228785 AAACAATCCA
*
22228795 AAAATTATATTTTGACCCCAAAAC-TTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
22228824 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
22228854 AAAATTATA-TTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
22228883 AAAATTACATTTTGACCCCAAAACTTTTCCC
1 AAAATTACATTTTGACCCCAAAACTTTT-CC
* *
22228914 AAAATTACATTTT-AACCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
22228943 AAAATTACATTTTTAACCCTAAAACTTTTCC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCC
**
22228974 AAAATTACATTTTGACCTTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
** * *
22229004 AAAATTTTATTTTGA-CCCTAAAC-TTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
22229032 AAAATTAC-TTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
22229061 AAAA-TATATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
22229090 AAAATTACATTTCGACCCCAAAA-TTTTCA
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
22229119 AAAATTACCATTTT-ACCCCGAATCTTTT--
1 AAAATTA-CATTTTGACCCCAAAACTTTTCC
*
22229147 AAAATTCCATTTT
1 AAAATTACATTTT
22229160 TAACCTCGGT
Statistics
Matches: 291, Mismatches: 34, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.04
28 24 0.08
29 115 0.40
30 103 0.35
31 37 0.13
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:22228884 original size:59 final size:59
Alignment explanation
Indices: 22228795--22229136 Score: 426
Period size: 60 Copynumber: 5.8 Consensus size: 59
22228785 AAACAATCCA
*
22228795 AAAATTATATTTTGACCCCAAAAC-TTTCCAAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACA-TTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCC
* *
22228854 AAAATTATATTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCC
1 AAAATTACATTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTT-CC
* * * *
22228914 AAAATTACATTTTAACCCTAAACTTTTCCAAAATTACATTTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTGACCCCAAAACTTTTCCAAAATTACA-TTTTGACCCTAAAACTTTTCC
** ** *
22228974 AAAATTACATTTTGACCTTAAAACTTTTCCAAAATTTTATTTTGACCCT-AAAC-TTTCT
1 AAAATTACA-TTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCC
* * * * *
22229032 AAAATTACTTTTGACCCTAAAACTTTTCCAAAA-TATATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCC
*
22229090 AAAATTACATTTCGACCCCAAAA-TTTTCAAAAATTACCATTTT-ACCC
1 AAAATTACATTT-GACCCCAAAACTTTTCCAAAATTA-CATTTTGACCC
22229137 CGAATCTTTT
Statistics
Matches: 248, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
56 11 0.04
57 27 0.11
58 50 0.20
59 60 0.24
60 61 0.25
61 39 0.16
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (59 bp):
AAAATTACATTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCC
Found at i:22236788 original size:69 final size:69
Alignment explanation
Indices: 22236715--22236860 Score: 170
Period size: 69 Copynumber: 2.1 Consensus size: 69
22236705 TTGTCGTGTA
* * **
22236715 GATTTTTACTGTATT-TTGAACTTTTGCTTATGTTTTTTTATAATTTTATTGTGTTATTGTTGT-
1 GATTTTTACTGT-TTATTGAACTTTTGCTTAT-TTTTATTATAATCTTATTGTGTTATCATTGTA
22236778 TACTTG
64 TACTTG
* ** * *
22236784 GATTTATGTTGTTTACTTGAACTTTTGCTTATTTTTATTATAATCTTGTTGTGTTGTCATTGTAT
1 GATTTTTACTGTTTA-TTGAACTTTTGCTTATTTTTATTATAATCTTATTGTGTTATCATTGTAT
22236849 ACTTG
65 ACTTG
22236854 GATTTTT
1 GATTTTT
22236861 TCACTTATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
68 2 0.03
69 34 0.53
70 28 0.44
ACGTcount: A:0.18, C:0.07, G:0.15, T:0.60
Consensus pattern (69 bp):
GATTTTTACTGTTTATTGAACTTTTGCTTATTTTTATTATAATCTTATTGTGTTATCATTGTATA
CTTG
Found at i:22237230 original size:21 final size:22
Alignment explanation
Indices: 22237205--22237255 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
22237195 ATGTGTCACA
22237205 AAATGAAA-TTAAAATG-AAACC
1 AAATGAAAGTT-AAATGAAAACC
22237226 AAATGAAAGTTAAATGAAAACC
1 AAATGAAAGTTAAATGAAAACC
*
22237248 TAATGAAA
1 AAATGAAA
22237256 AAAGCAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.20
Consensus pattern (22 bp):
AAATGAAAGTTAAATGAAAACC
Found at i:22238647 original size:1 final size:1
Alignment explanation
Indices: 22238641--22238665 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22238631 ATGGGTCCCT
22238641 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
22238666 TTCACAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:22261391 original size:8 final size:8
Alignment explanation
Indices: 22261374--22261415 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
22261364 TTAATTTTTT
22261374 TAAAATTA
1 TAAAATTA
*
22261382 TAAAAATA
1 TAAAATTA
22261390 T-AAATTA
1 TAAAATTA
*
22261397 TTAAAATAA
1 -TAAAATTA
22261406 TAAAATTA
1 TAAAATTA
22261414 TA
1 TA
22261416 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:22261396 original size:15 final size:17
Alignment explanation
Indices: 22261374--22261415 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
22261364 TTAATTTTTT
22261374 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATAA
*
22261390 T-AAATTATTAAAATAA
1 TAAAATTATAAAAATAA
22261406 TAAAATTATA
1 TAAAATTATA
22261416 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 3 0.14
17 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:22262665 original size:83 final size:82
Alignment explanation
Indices: 22262525--22262838 Score: 438
Period size: 83 Copynumber: 4.0 Consensus size: 82
22262515 TTGTTTCGAA
*
22262525 AATTTTTATCCCAACGCTTTTTTTTTTATTGACACCGGTTAGACTTTCTTGAATAATATTAAATA
1 AATTTTTATCCCAACGC--TTTTTTTTATTGACACCGATTAGACTTTCTTGAATAATATTAAATA
22262590 TTATATCATATTTAACTTG
64 TTATATCATATTTAACTTG
*
22262609 AATTTTTATCTCAACGCTTTTTTTTTATTGACACCGATTAGACTTTCTTGAATAATATTAAATAT
1 AATTTTTATCCCAACGC-TTTTTTTTATTGACACCGATTAGACTTTCTTGAATAATATTAAATAT
22262674 TATATCATATTTAACTTG
65 TATATCATATTTAACTTG
* *
22262692 AATTTTTATCCCAACGC-TTTTTTTATTGACACCGATTAGACTTTCTTGAATAAT-TGAAATATA
1 AATTTTTATCCCAACGCTTTTTTTTATTGACACCGATTAGACTTTCTTGAATAATATTAAATATT
*
22262755 ATATTATATTT---TTG
66 ATATCATATTTAACTTG
* * *
22262769 AAATTTTATCCCAACGCTTTTTTTTA--CACACCGATTAGACTTT-TT-TA-AATATT--AT-TT
1 AATTTTTATCCCAACGCTTTTTTTTATTGACACCGATTAGACTTTCTTGAATAATATTAAATATT
22262826 ATATCATATTTAA
66 ATATCATATTTAA
22262839 TTTAAACTTG
Statistics
Matches: 214, Mismatches: 12, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
71 11 0.05
72 2 0.01
73 3 0.01
74 2 0.01
75 2 0.01
76 16 0.07
77 19 0.09
78 8 0.04
80 17 0.08
81 37 0.17
83 81 0.38
84 16 0.07
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.47
Consensus pattern (82 bp):
AATTTTTATCCCAACGCTTTTTTTTATTGACACCGATTAGACTTTCTTGAATAATATTAAATATT
ATATCATATTTAACTTG
Found at i:22262972 original size:18 final size:18
Alignment explanation
Indices: 22262949--22262984 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
22262939 TTTTTATATA
22262949 TATTTT-ATATTGATTTAT
1 TATTTTCAT-TTGATTTAT
22262967 TATTTTCATTTGATTTAT
1 TATTTTCATTTGATTTAT
22262985 GAGTGATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.67
Consensus pattern (18 bp):
TATTTTCATTTGATTTAT
Found at i:22266751 original size:11 final size:11
Alignment explanation
Indices: 22266735--22266759 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22266725 CTATTCATGT
22266735 AAAAAAAAGAA
1 AAAAAAAAGAA
22266746 AAAAAAAAGAA
1 AAAAAAAAGAA
22266757 AAA
1 AAA
22266760 GGAGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:22274304 original size:12 final size:13
Alignment explanation
Indices: 22274287--22274316 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
22274277 TAAAACCCCA
22274287 AAATATTT-AATT
1 AAATATTTCAATT
22274299 AAATATTTCAATT
1 AAATATTTCAATT
22274312 AAATA
1 AAATA
22274317 ATTATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATATTTCAATT
Found at i:22274348 original size:18 final size:17
Alignment explanation
Indices: 22274325--22274358 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22274315 TAATTATAAT
22274325 TTTTATATGTAAATATGA
1 TTTTAT-TGTAAATATGA
*
22274343 TTTTATTTTAAATATG
1 TTTTATTGTAAATATG
22274359 CTAATAATCA
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:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTATTGTAAATATGA
Found at i:22274827 original size:26 final size:26
Alignment explanation
Indices: 22274798--22274852 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
22274788 AAAAATTTTC
22274798 ATTATT-ATTTGATAAGTTTAATTATT
1 ATTATTAATTTGAT-AGTTTAATTATT
* *
22274824 ATTATTAATTTGATAGTTTTATTGTT
1 ATTATTAATTTGATAGTTTAATTATT
22274850 ATT
1 ATT
22274853 TGATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (26 bp):
ATTATTAATTTGATAGTTTAATTATT
Found at i:22275060 original size:22 final size:20
Alignment explanation
Indices: 22275033--22275092 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
22275023 TCAAAATTAT
22275033 TATATTTTTATTATAAATTAAA
1 TATA-TTTTATTA-AAATTAAA
*
22275055 TATATTTTATTAAATTATAAA
1 TATATTTTATTAAAAT-TAAA
22275076 T-TAGTTTTATTAAAATT
1 TATA-TTTTATTAAAATT
22275093 CCTATGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.18
21 24 0.71
22 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATATTTTATTAAAATTAAA
Found at i:22279133 original size:18 final size:18
Alignment explanation
Indices: 22279110--22279144 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22279100 ATTGTATAGT
*
22279110 GCAAATAAATTTTTCTTA
1 GCAAATAAATTATTCTTA
*
22279128 GCAAATACATTATTCTT
1 GCAAATAAATTATTCTT
22279145 TATCATTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (18 bp):
GCAAATAAATTATTCTTA
Found at i:22287281 original size:91 final size:93
Alignment explanation
Indices: 22287052--22287321 Score: 517
Period size: 91 Copynumber: 2.9 Consensus size: 93
22287042 TGTTTTTTGT
22287052 TTTGTAGGTTTTAGCTGAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACCAATC
1 TTTGTAGGTTTTAGCTGAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACCAATC
22287117 CTCCAATTATGCCCAAATCAGATGTAAA
66 CTCCAATTATGCCCAAATCAGATGTAAA
22287145 TTTGTAGGTTTTAGCTGAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACC-ATC
1 TTTGTAGGTTTTAGCTGAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACCAATC
22287209 CTCCAATTATG-CCAAATCAGATGTAAA
66 CTCCAATTATGCCCAAATCAGATGTAAA
*
22287236 TTTGTAGGTTTTAGCTGAACAAGATATTGCAACATTCACCAAACACTAGGGTTTCACTACCAATC
1 TTTGTAGGTTTTAGCTGAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACCAATC
22287301 CTCCAATTATGCCCAAATCAG
66 CTCCAATTATGCCCAAATCAG
22287322 CTATAAAATC
Statistics
Matches: 174, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
91 76 0.44
92 28 0.16
93 70 0.40
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (93 bp):
TTTGTAGGTTTTAGCTGAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACCAATC
CTCCAATTATGCCCAAATCAGATGTAAA
Found at i:22288263 original size:17 final size:18
Alignment explanation
Indices: 22288234--22288268 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
22288224 GAATAAATAT
22288234 TTAATTAAAAAATTTTAA
1 TTAATTAAAAAATTTTAA
22288252 TTAATT-AAAAATTTTAA
1 TTAATTAAAAAATTTTAA
22288269 ACCCTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATTAAAAAATTTTAA
Found at i:22289629 original size:50 final size:50
Alignment explanation
Indices: 22289571--22289687 Score: 195
Period size: 50 Copynumber: 2.4 Consensus size: 50
22289561 AATATTTGTG
*
22289571 TTAA-ATCGAAAAACTTAATTTTTTATTCGAATTGATCCGAATAACTTGA
1 TTAACATCGAAAAACTTAATTTTTTATTCAAATTGATCCGAATAACTTGA
22289620 TTAACATCGAAAAACTTAATTTTTTATTCAAATTGATCCGAATAACTTGA
1 TTAACATCGAAAAACTTAATTTTTTATTCAAATTGATCCGAATAACTTGA
22289670 TTAAC-TC-AAATAACTTAA
1 TTAACATCGAAA-AACTTAA
22289688 ACTATTTAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
48 3 0.05
49 13 0.20
50 49 0.75
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (50 bp):
TTAACATCGAAAAACTTAATTTTTTATTCAAATTGATCCGAATAACTTGA
Found at i:22295926 original size:76 final size:75
Alignment explanation
Indices: 22295791--22295944 Score: 181
Period size: 76 Copynumber: 2.0 Consensus size: 75
22295781 GCTAAGAGGG
* * * *
22295791 CTAAGGAGCTGACTCAAGCCACAAGAGACCACAACAACGATTTAGAAGTCAATCTTCTAAGTTGA
1 CTAAGGAGCTGACTCAAGCCACAAGAGACCACAAAAACGAGTTAGAAGTCAATCCTCTAAGTTCA
22295856 TTCTAGTTTGC
66 TTCTAGTTT-C
*
22295867 CTAAGGAGCTGACTCCAA-CCACACA-AGACCA-AAAAAGCTAGTTAGAAG-CAGATCCTCTAAG
1 CTAAGGAGCTGACT-CAAGCCACA-AGAGACCACAAAAA-CGAGTTAGAAGTCA-ATCCTCTAAG
*
22295928 TTCATTTTAGTTTC
62 TTCATTCTAGTTTC
22295942 CTA
1 CTA
22295945 CTATGCACAA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
75 10 0.15
76 54 0.79
77 4 0.06
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (75 bp):
CTAAGGAGCTGACTCAAGCCACAAGAGACCACAAAAACGAGTTAGAAGTCAATCCTCTAAGTTCA
TTCTAGTTTC
Found at i:22298514 original size:406 final size:406
Alignment explanation
Indices: 22297762--22298574 Score: 1626
Period size: 406 Copynumber: 2.0 Consensus size: 406
22297752 AGATTTTGGG
22297762 TGTAGGGGTAGAGGATGTAATTGGAGTGTTCTTTGTAAATCTCTTGTTTTAGTTAAATGTTCCAT
1 TGTAGGGGTAGAGGATGTAATTGGAGTGTTCTTTGTAAATCTCTTGTTTTAGTTAAATGTTCCAT
22297827 AATCATCATGTCTTGTGGACGTAAGCTGAACCACAGGCAAAATTCAATCAATGGAAATTCACTCC
66 AATCATCATGTCTTGTGGACGTAAGCTGAACCACAGGCAAAATTCAATCAATGGAAATTCACTCC
22297892 ATGGAATATCCCTTCCCCACCTTTTCTTGAAGGACGTTCATGGAGTTTCTTGGGGGAGAAGAAAC
131 ATGGAATATCCCTTCCCCACCTTTTCTTGAAGGACGTTCATGGAGTTTCTTGGGGGAGAAGAAAC
22297957 AATATTGATGATTTTATTTAGTTTTCCCCTGGTGGGATACTATCGAACTTTCCATTTTACCTGTG
196 AATATTGATGATTTTATTTAGTTTTCCCCTGGTGGGATACTATCGAACTTTCCATTTTACCTGTG
22298022 CTCACTAATGTATTCGTGCTCTTAGAGGTGAAAGTTTTGATTTTTAACAATTCTCCGCCAACATT
261 CTCACTAATGTATTCGTGCTCTTAGAGGTGAAAGTTTTGATTTTTAACAATTCTCCGCCAACATT
22298087 CTTCTTTTAGAATAATCTCTAACTAGTATCATGTTGGGAAAATCTTATTCTGCAATATGTTATTG
326 CTTCTTTTAGAATAATCTCTAACTAGTATCATGTTGGGAAAATCTTATTCTGCAATATGTTATTG
22298152 TTGCTCTGGCTCATTA
391 TTGCTCTGGCTCATTA
22298168 TGTAGGGGTAGAGGATGTAATTGGAGTGTTCTTTGTAAATCTCTTGTTTTAGTTAAATGTTCCAT
1 TGTAGGGGTAGAGGATGTAATTGGAGTGTTCTTTGTAAATCTCTTGTTTTAGTTAAATGTTCCAT
22298233 AATCATCATGTCTTGTGGACGTAAGCTGAACCACAGGCAAAATTCAATCAATGGAAATTCACTCC
66 AATCATCATGTCTTGTGGACGTAAGCTGAACCACAGGCAAAATTCAATCAATGGAAATTCACTCC
22298298 ATGGAATATCCCTTCCCCACCTTTTCTTGAAGGACGTTCATGGAGTTTCTTGGGGGAGAAGAAAC
131 ATGGAATATCCCTTCCCCACCTTTTCTTGAAGGACGTTCATGGAGTTTCTTGGGGGAGAAGAAAC
22298363 AATATTGATGATTTTATTTAGTTTTCCCCTGGTGGGATACTATCGAACTTTCCATTTTACCTGTG
196 AATATTGATGATTTTATTTAGTTTTCCCCTGGTGGGATACTATCGAACTTTCCATTTTACCTGTG
22298428 CTCACTAATGTATTCGTGCTCTTAGAGGTGAAAGTTTTGATTTTTAACAATTCTCCGCCAACATT
261 CTCACTAATGTATTCGTGCTCTTAGAGGTGAAAGTTTTGATTTTTAACAATTCTCCGCCAACATT
22298493 CTTCTTTTAGAATAATCTCTAACTAGTATCATGTTGGGAAAATCTTATTCTGCAATATGTTATTG
326 CTTCTTTTAGAATAATCTCTAACTAGTATCATGTTGGGAAAATCTTATTCTGCAATATGTTATTG
22298558 TTGCTCTGGCTCATTA
391 TTGCTCTGGCTCATTA
22298574 T
1 T
22298575 ATTATCACCC
Statistics
Matches: 407, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
406 407 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (406 bp):
TGTAGGGGTAGAGGATGTAATTGGAGTGTTCTTTGTAAATCTCTTGTTTTAGTTAAATGTTCCAT
AATCATCATGTCTTGTGGACGTAAGCTGAACCACAGGCAAAATTCAATCAATGGAAATTCACTCC
ATGGAATATCCCTTCCCCACCTTTTCTTGAAGGACGTTCATGGAGTTTCTTGGGGGAGAAGAAAC
AATATTGATGATTTTATTTAGTTTTCCCCTGGTGGGATACTATCGAACTTTCCATTTTACCTGTG
CTCACTAATGTATTCGTGCTCTTAGAGGTGAAAGTTTTGATTTTTAACAATTCTCCGCCAACATT
CTTCTTTTAGAATAATCTCTAACTAGTATCATGTTGGGAAAATCTTATTCTGCAATATGTTATTG
TTGCTCTGGCTCATTA
Found at i:22301602 original size:38 final size:39
Alignment explanation
Indices: 22301550--22301633 Score: 161
Period size: 38 Copynumber: 2.2 Consensus size: 39
22301540 CAACATACAA
22301550 AACCTTTCATCCCATTATGATGTTCAAGTACACAATTCT
1 AACCTTTCATCCCATTATGATGTTCAAGTACACAATTCT
22301589 -ACCTTTCATCCCATTATGATGTTCAAGTACACAATTCT
1 AACCTTTCATCCCATTATGATGTTCAAGTACACAATTCT
22301627 AACCTTT
1 AACCTTT
22301634 TAAAACTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 38 0.86
39 6 0.14
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (39 bp):
AACCTTTCATCCCATTATGATGTTCAAGTACACAATTCT
Found at i:22303374 original size:37 final size:37
Alignment explanation
Indices: 22303333--22303408 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
22303323 TTCATCTCAT
*
22303333 ATGAACAATGAACATTCATTCCTTTTCTAATACATAC
1 ATGAACAATGAACATTCATTCCTTTTCTAATACACAC
22303370 ATGAACAATGAACATTCATTCCTTTTCTAATACACAC
1 ATGAACAATGAACATTCATTCCTTTTCTAATACACAC
22303407 AT
1 AT
22303409 CATAATTCAT
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:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (37 bp):
ATGAACAATGAACATTCATTCCTTTTCTAATACACAC
Found at i:22311757 original size:6 final size:6
Alignment explanation
Indices: 22311740--22311771 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
22311730 ATGCTAAATA
22311740 ATATTAT ATATTT ATATTT ATATTT ATATTT A
1 ATATT-T ATATTT ATATTT ATATTT ATATTT A
22311772 ATAACTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
ATATTT
Found at i:22311911 original size:39 final size:41
Alignment explanation
Indices: 22311867--22311959 Score: 136
Period size: 39 Copynumber: 2.3 Consensus size: 41
22311857 AAAAATTATA
*
22311867 TTTAATACAATAAAATATTTATTATATTTAT-TTGTG-TTT
1 TTTAATATAATAAAATATTTATTATATTTATGTTGTGTTTT
* *
22311906 TTTAATATAATTAAATATTTATTATGTTTATGGTTGTGTTTT
1 TTTAATATAATAAAATATTTATTATATTTAT-GTTGTGTTTT
22311948 TTTAATATAATA
1 TTTAATATAATA
22311960 TTTTAATGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
39 28 0.60
41 5 0.11
42 14 0.30
ACGTcount: A:0.34, C:0.01, G:0.08, T:0.57
Consensus pattern (41 bp):
TTTAATATAATAAAATATTTATTATATTTATGTTGTGTTTT
Found at i:22319563 original size:17 final size:17
Alignment explanation
Indices: 22319543--22319594 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
22319533 ATTAAATTTT
*
22319543 AATAAAAATTATTAATA
1 AATATAAATTATTAATA
* *
22319560 AATATAATTTAATAGA-A
1 AATATAAATTATTA-ATA
*
22319577 AATATAAATAATTAATA
1 AATATAAATTATTAATA
22319594 A
1 A
22319595 CATTTTTAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 1 0.04
17 25 0.93
18 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATATAAATTATTAATA
Found at i:22321714 original size:21 final size:20
Alignment explanation
Indices: 22321684--22321723 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
22321674 TATTAGAATT
*
22321684 TTTAAATTTTTTATATATTC
1 TTTAAATTTTTAATATATTC
22321704 TTTAGAATTTTTAATATATT
1 TTTA-AATTTTTAATATATT
22321724 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTAAATTTTTAATATATTC
Found at i:22326478 original size:84 final size:84
Alignment explanation
Indices: 22326328--22326481 Score: 190
Period size: 84 Copynumber: 1.8 Consensus size: 84
22326318 TTCTTGAGAG
* ** *
22326328 ATAAATTTATCATATATTAATTTGTAATTTCATTATTTTTGAAAAGATTAAATAAAATTTTATTT
1 ATAAATTTATCATAGATTAATTCATAATTTCATTATTTATGAAAAGATTAAATAAAATTTTATTT
22326393 ATTTTTATAGGATCAAAAT
66 ATTTTTATAGGATCAAAAT
* *
22326412 ATAAATTTATTATAGATTAATTCATAATTT-ATTTATTTAT-AAAAGGATTGAATTGAAAA-TTT
1 ATAAATTTATCATAGATTAATTCATAATTTCA-TTATTTATGAAAA-GATT-AAAT-AAAATTTT
22326474 -TTTATTTT
62 ATTTATTTT
22326482 GAGGTGCTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
83 5 0.08
84 45 0.75
85 6 0.10
86 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (84 bp):
ATAAATTTATCATAGATTAATTCATAATTTCATTATTTATGAAAAGATTAAATAAAATTTTATTT
ATTTTTATAGGATCAAAAT
Found at i:22329333 original size:16 final size:15
Alignment explanation
Indices: 22329312--22329361 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
22329302 TGCTTTGGAA
*
22329312 AGAAAATTGGAATGAT
1 AGAAAATT-AAATGAT
*
22329328 AGAAAATTAAAGGAT
1 AGAAAATTAAATGAT
22329343 AGAAAATTAAAATGAT
1 AGAAAATT-AAATGAT
22329359 AGA
1 AGA
22329362 GAAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (15 bp):
AGAAAATTAAATGAT
Found at i:22329345 original size:15 final size:15
Alignment explanation
Indices: 22329325--22329353 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22329315 AAATTGGAAT
22329325 GATAGAAAATTAAAG
1 GATAGAAAATTAAAG
22329340 GATAGAAAATTAAA
1 GATAGAAAATTAAA
22329354 ATGATAGAGA
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:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (15 bp):
GATAGAAAATTAAAG
Found at i:22330430 original size:19 final size:19
Alignment explanation
Indices: 22330394--22330435 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
22330384 TTATAAAATG
22330394 ATTA-TTAAGAAATGATAA
1 ATTAGTTAAGAAATGATAA
*
22330412 TTTAGTTAACGAAAT-ATAA
1 ATTAGTTAA-GAAATGATAA
22330431 ATTAG
1 ATTAG
22330436 ATATAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.15
19 12 0.60
20 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (19 bp):
ATTAGTTAAGAAATGATAA
Found at i:22337442 original size:21 final size:21
Alignment explanation
Indices: 22337418--22337457 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
22337408 AAGTGTGCAT
22337418 TTAAAAATAACATATAATATA
1 TTAAAAATAACATATAATATA
22337439 TTAAAAATAACATATAATA
1 TTAAAAATAACATATAATA
22337458 AATAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAAATAACATATAATATA
Found at i:22340129 original size:19 final size:19
Alignment explanation
Indices: 22340089--22340133 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
22340079 TTTTATTAGG
22340089 ATTTAATATTTAAGATATT
1 ATTTAATATTTAAGATATT
* *
22340108 ATTTATTATTTAA-ATTTGT
1 ATTTAATATTTAAGATAT-T
22340127 ATTTAAT
1 ATTTAAT
22340134 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAGATATT
Found at i:22346583 original size:21 final size:20
Alignment explanation
Indices: 22346545--22346583 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22346535 ATGCTTCTTA
* *
22346545 TTTGCTGAGTTAATTTTGAT
1 TTTGCTAAGTTAAATTTGAT
22346565 TTTGCTAAGATTAAATTTG
1 TTTGCTAAG-TTAAATTTG
22346584 TCCCACTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTGCTAAGTTAAATTTGAT
Found at i:22347883 original size:23 final size:23
Alignment explanation
Indices: 22347857--22347925 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
22347847 CAATTAGGAA
22347857 AATTAAATGTTAGATATAATGCT
1 AATTAAATGTTAGATATAATGCT
** *
22347880 AATTATCTTTTAGAGT-T--T--T
1 AATTAAATGTTAGA-TATAATGCT
22347899 AATTAAATGTTAGATATAATGCT
1 AATTAAATGTTAGATATAATGCT
22347922 AATT
1 AATT
22347926 TATGTACTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 1 0.03
19 13 0.38
21 2 0.06
23 17 0.50
24 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (23 bp):
AATTAAATGTTAGATATAATGCT
Found at i:22348753 original size:12 final size:12
Alignment explanation
Indices: 22348736--22348761 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22348726 TAGACCTTAC
22348736 TTCTCTTTACTG
1 TTCTCTTTACTG
22348748 TTCTCTTTACTG
1 TTCTCTTTACTG
22348760 TT
1 TT
22348762 TTTATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.08, T:0.62
Consensus pattern (12 bp):
TTCTCTTTACTG
Found at i:22349514 original size:29 final size:29
Alignment explanation
Indices: 22349466--22349541 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
22349456 AGTTATCACT
*
22349466 TACCACACGACCGTGTGACCCACACGATC
1 TACCACACGACCGTGTGACCCACACGACC
* *
22349495 TAGCATACGACCGTGTGACCCACACGACC
1 TACCACACGACCGTGTGACCCACACGACC
*
22349524 TACCACACGGCCGTGTGA
1 TACCACACGACCGTGTGA
22349542 TGTAGAGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.38, G:0.21, T:0.14
Consensus pattern (29 bp):
TACCACACGACCGTGTGACCCACACGACC
Found at i:22354557 original size:25 final size:26
Alignment explanation
Indices: 22354501--22354565 Score: 96
Period size: 25 Copynumber: 2.5 Consensus size: 26
22354491 TAAGTGTAAT
22354501 ATTATATCTATTATTTTTTTTAATAAA
1 ATTATATCTATTA-TTTTTTTAATAAA
*
22354528 ATTATATCTATTA-TTTTTTAATGAA
1 ATTATATCTATTATTTTTTTAATAAA
*
22354553 GTTATATCTATTA
1 ATTATATCTATTA
22354566 AATACATGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 23 0.64
27 13 0.36
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (26 bp):
ATTATATCTATTATTTTTTTAATAAA
Found at i:22357240 original size:29 final size:29
Alignment explanation
Indices: 22357208--22357547 Score: 190
Period size: 29 Copynumber: 11.3 Consensus size: 29
22357198 TGGATACCCG
22357208 GAGGGTAAAATGGTAATTTTGGTGAAATC
1 GAGGGTAAAATGGTAATTTTGGTGAAATC
* *
22357237 GAGGTTAAAATGG-AATTTTGG-GAAGTTC
1 GAGGGTAAAATGGTAATTTTGGTGAA-ATC
* *
22357265 GGGGGTAAAATGGCAATTTTGGTGAAATC
1 GAGGGTAAAATGGTAATTTTGGTGAAATC
22357294 GGGAAATAAGGGTTAAAAATGG-AATTTT-G-GAAAGTTC
1 --G-----AGGG-T-AAAATGGTAATTTTGGTGAAA--TC
* *
22357331 AAGGGTAAAATGGTAATTATTGATGAAAT-
1 GAGGGTAAAATGGTAATT-TTGGTGAAATC
* *
22357360 TAGGGTTAAAAATGG-AATTTT-G-GAAAGTT
1 GAGGG-T-AAAATGGTAATTTTGGTGAAA-TC
*
22357389 TAGGGGTAAAATGGTAATTTTTGGTGAAATC
1 GA-GGGTAAAATGGTAA-TTTTGGTGAAATC
* *
22357420 GAGGTTAAAAAT-GAAATTTT-G-GAAAGTTC
1 GAGGGT-AAAATGGTAATTTTGGTGAAA--TC
*
22357449 GGGGGTAAAATGGTAATTTTTTGGTGAAATC
1 GAGGGTAAAATGGTAA--TTTTGGTGAAATC
* *
22357480 GAGGTTAAAAATGG-AATTTTGG-GAAATT
1 GAGGGT-AAAATGGTAATTTTGGTGAAATC
*
22357508 TAGGGGT-AAATGGTAATTTTTGGTGAAATC
1 GA-GGGTAAAATGGTAA-TTTTGGTGAAATC
22357538 G-GGGTTAAAA
1 GAGGG-TAAAA
22357548 ATGAAATTTT
Statistics
Matches: 245, Mismatches: 24, Indels: 83
0.70 0.07 0.24
Matches are distributed among these distances:
27 17 0.07
28 53 0.22
29 67 0.27
30 36 0.15
31 28 0.11
32 16 0.07
33 4 0.02
35 4 0.02
36 4 0.02
37 9 0.04
38 7 0.03
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.32
Consensus pattern (29 bp):
GAGGGTAAAATGGTAATTTTGGTGAAATC
Found at i:22357388 original size:59 final size:59
Alignment explanation
Indices: 22357296--22357590 Score: 375
Period size: 59 Copynumber: 5.0 Consensus size: 59
22357286 GTGAAATCGG
* * * *
22357296 GAAATAAGGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTATTGAT
1 GAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGT
*
22357355 GAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
1 GAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGT
* * *
22357414 GAAA-TCGAGGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTTGGT
1 GAAATTAG-GGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAA-TTTTTGGT
* *
22357474 GAAA-TCGAGGTTAAAAATGGAATTTTGGGAAA-TTTAGGGGT-AAATGGTAATTTTTGGT
1 GAAATTAG-GGTTAAAAATGGAATTTT-GGAAAGTTCAGGGGTAAAATGGTAATTTTTGGT
** * *
22357532 GAAATCGGGGTTAAAAATGAAATTTTGGAAAGTT-TGGGGATAAAATAGGTAATTTTTGG
1 GAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGG-TAAAAT-GGTAATTTTTGG
22357591 ACTGTTTGGG
Statistics
Matches: 212, Mismatches: 16, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
57 9 0.04
58 34 0.16
59 112 0.53
60 52 0.25
61 5 0.02
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (59 bp):
GAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGT
Found at i:22357457 original size:118 final size:117
Alignment explanation
Indices: 22357304--22357585 Score: 424
Period size: 118 Copynumber: 2.4 Consensus size: 117
22357294 GGGAAATAAG
* **
22357304 GGTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATTATTGATGAAATTAG-GGTTA
1 GGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTATTGATGAAA-TAGAGGTTA
22357368 AAAATGGAATTTT-GGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGA
65 AAAATGGAATTTTGGGAAA-TTTAGGGGT-AAATGGTAATTTTTGGTGAAATCGA
* * *
22357422 GGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTTGGTGAAATCGAGGTTA
1 GGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAAAATGGTAA-TTATTGATGAAATAGAGGTTA
*
22357487 AAAATGGAATTTTGGGAAATTTAGGGGTAAATGGTAATTTTTGGTGAAATCGG
65 AAAATGGAATTTTGGGAAATTTAGGGGTAAATGGTAATTTTTGGTGAAATCGA
* *
22357540 GGTTAAAAATGAAATTTTGGAAAGTTTGGGGATAAAATAGGTAATT
1 GGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAAAAT-GGTAATT
22357586 TTTGGACTGT
Statistics
Matches: 151, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
118 104 0.69
119 42 0.28
120 5 0.03
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (117 bp):
GGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTATTGATGAAATAGAGGTTAA
AAATGGAATTTTGGGAAATTTAGGGGTAAATGGTAATTTTTGGTGAAATCGA
Found at i:22357570 original size:29 final size:28
Alignment explanation
Indices: 22357303--22357576 Score: 95
Period size: 29 Copynumber: 9.3 Consensus size: 28
22357293 CGGGAAATAA
* *
22357303 GGGTTAAAAATGGAATTTTGGAAAGTTCAA
1 GGGTTAAAAATGAAATTTTGGAAA-TTC-G
* *
22357333 GGG-T-AAAATGGTAATTATTGATGAAATT-A
1 GGGTTAAAAAT-GAAATT-TTG--GAAATTCG
* *
22357362 GGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTTAAAAATGAAATTTTGGAAA--TTCG
*
22357392 GGG-T-AAAATGGTAATTTTTGGTGAAA-TCG
1 GGGTTAAAAAT-G-AAATTTT-G-GAAATTCG
*
22357421 AGGTTAAAAATGAAATTTTGGAAAGTTCG
1 GGGTTAAAAATGAAATTTTGGAAA-TTCG
* *
22357450 GGGGT-AAAATGGTAATTTTTTGGTGAAA-TCG
1 GGGTTAAAAAT-G-AA-ATTTT-G-GAAATTCG
* * *
22357481 AGGTTAAAAATGGAATTTTGGGAAATTTAG
1 GGGTTAAAAATGAAATTTT-GGAAA-TTCG
*
22357511 GGG-T--AAATGGTAATTTTTGGTGAAA-TCG
1 GGGTTAAAAAT-G-AAATTTT-G-GAAATTCG
*
22357539 GGGTTAAAAATGAAATTTTGGAAAGTTTG
1 GGGTTAAAAATGAAATTTTGGAAA-TTCG
*
22357568 GGGATAAAA
1 GGGTTAAAA
22357577 TAGGTAATTT
Statistics
Matches: 188, Mismatches: 23, Indels: 67
0.68 0.08 0.24
Matches are distributed among these distances:
27 16 0.09
28 27 0.14
29 65 0.35
30 34 0.18
31 28 0.15
32 14 0.07
33 4 0.02
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (28 bp):
GGGTTAAAAATGAAATTTTGGAAATTCG
Found at i:22358579 original size:19 final size:22
Alignment explanation
Indices: 22358531--22358585 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
22358521 TCCTTTGTTC
22358531 TTCTTTTTTTCTTTTAAAAACA
1 TTCTTTTTTTCTTTTAAAAACA
*
22358553 TTTCTTTTTTTCTTTT-GAAA-A
1 -TTCTTTTTTTCTTTTAAAAACA
22358574 -TCTTTTTTTCTT
1 TTCTTTTTTTCTT
22358586 CATTTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.39
21 1 0.03
22 3 0.10
23 15 0.48
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.67
Consensus pattern (22 bp):
TTCTTTTTTTCTTTTAAAAACA
Found at i:22359050 original size:22 final size:23
Alignment explanation
Indices: 22359022--22359075 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
22359012 AATATTTAAT
*
22359022 ATTAATTACTGCTATTATTA-TC
1 ATTAATTACTACTATTATTATTC
* *
22359044 ATTAATTATTATTATTATTATTC
1 ATTAATTACTACTATTATTATTC
22359067 ATATAATTA
1 AT-TAATTA
22359076 ATATTCACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 17 0.63
23 4 0.15
24 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTAATTACTACTATTATTATTC
Found at i:22359728 original size:6 final size:6
Alignment explanation
Indices: 22359719--22359807 Score: 71
Period size: 6 Copynumber: 15.0 Consensus size: 6
22359709 ATTTTTAATG
* * **
22359719 TTTAAA TTTAGTA TTTAAA TTTAAC TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
22359769 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
22359808 ATCAATTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
4 5 0.08
5 5 0.08
6 44 0.67
7 6 0.09
8 6 0.09
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:22359771 original size:31 final size:32
Alignment explanation
Indices: 22359733--22359807 Score: 107
Period size: 31 Copynumber: 2.3 Consensus size: 32
22359723 AATTTAGTAT
* *
22359733 TTAAATTTAACTTTAAGGTAAATTTAAA-TAA
1 TTAAATTTAAATTTAAGATAAATTTAAATTAA
22359764 TTAAATTTAAATTTAAGATAAATTTAAATTTAA
1 TTAAATTTAAATTTAAGATAAATTTAAA-TTAA
*
22359797 ATAAATTTAAA
1 TTAAATTTAAA
22359808 ATCAATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 26 0.67
33 13 0.33
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (32 bp):
TTAAATTTAAATTTAAGATAAATTTAAATTAA
Found at i:22359776 original size:11 final size:11
Alignment explanation
Indices: 22359762--22359817 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
22359752 AAATTTAAAT
22359762 AATTAAATTTA
1 AATTAAATTTA
* **
22359773 AATTTAAGATA
1 AATTAAATTTA
22359784 AATTTAAATTTA
1 AA-TTAAATTTA
22359796 AA-TAAATTTA
1 AATTAAATTTA
* *
22359806 AAATCAATTTA
1 AATTAAATTTA
22359817 A
1 A
22359818 CTCTAAATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
10 10 0.28
11 18 0.50
12 8 0.22
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:22359809 original size:17 final size:17
Alignment explanation
Indices: 22359734--22359807 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
22359724 ATTTAGTATT
* *
22359734 TAAATTTAACTTTAAGG
1 TAAATTTAAATTTAAGA
*
22359751 TAAATTTAAA--TAA-T
1 TAAATTTAAATTTAAGA
22359765 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAGA
22359782 TAAATTTAAATTTAA-A
1 TAAATTTAAATTTAAGA
22359798 TAAATTTAAA
1 TAAATTTAAA
22359808 ATCAATTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 14 0.27
17 24 0.47
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAGA
Found at i:22359824 original size:27 final size:27
Alignment explanation
Indices: 22359771--22359825 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
22359761 TAATTAAATT
* *
22359771 TAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
* *
22359798 TAAATTTAAAATCAATTTAACTCTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
22359825 T
1 T
22359826 TAAAACAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCTAAA
Found at i:22368402 original size:28 final size:27
Alignment explanation
Indices: 22368370--22368428 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
22368360 CCATTTGTTC
*
22368370 GTTTCCATCTCTGCAATTA-TTGTTACAT
1 GTTTCCA-ATCTG-AATTAGTTGTTACAT
*
22368398 GTTTCCAATGTGAATTAGTTGTTACAT
1 GTTTCCAATCTGAATTAGTTGTTACAT
22368425 GTTT
1 GTTT
22368429 AACTAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.18
27 16 0.57
28 7 0.25
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.47
Consensus pattern (27 bp):
GTTTCCAATCTGAATTAGTTGTTACAT
Found at i:22372799 original size:23 final size:23
Alignment explanation
Indices: 22372773--22372897 Score: 117
Period size: 23 Copynumber: 5.4 Consensus size: 23
22372763 GAACATTAGC
*
22372773 GTGCTTACTG-TTCAACACTGTGT
1 GTGCTTACTGATTC-ACACTATGT
*
22372796 GTGCTTACTGATTCACGCTATGT
1 GTGCTTACTGATTCACACTATGT
**
22372819 GTGCTTACTGATTTGCACTATGT
1 GTGCTTACTGATTCACACTATGT
* ** *
22372842 GTGCTTACTGTTTTGCATTATGT
1 GTGCTTACTGATTCACACTATGT
* * ** *
22372865 GTGCCTACTAATTTGCACTGTGT
1 GTGCTTACTGATTCACACTATGT
22372888 GTGCTTACTG
1 GTGCTTACTG
22372898 TTTCCCTAGC
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 84 0.97
24 3 0.03
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.42
Consensus pattern (23 bp):
GTGCTTACTGATTCACACTATGT
Found at i:22372898 original size:46 final size:46
Alignment explanation
Indices: 22372788--22372901 Score: 156
Period size: 46 Copynumber: 2.5 Consensus size: 46
22372778 TACTGTTCAA
* * * *
22372788 CACTGTGTGTGCTTACTGATTCACGCTATGTGTGCTTACTGATTTG
1 CACTGTGTGTGCTTACTGTTTCACACTATGTGTGCCTACTAATTTG
* ** *
22372834 CACTATGTGTGCTTACTGTTTTGCATTATGTGTGCCTACTAATTTG
1 CACTGTGTGTGCTTACTGTTTCACACTATGTGTGCCTACTAATTTG
22372880 CACTGTGTGTGCTTACTGTTTC
1 CACTGTGTGTGCTTACTGTTTC
22372902 CCTAGCACTT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (46 bp):
CACTGTGTGTGCTTACTGTTTCACACTATGTGTGCCTACTAATTTG
Found at i:22380082 original size:23 final size:23
Alignment explanation
Indices: 22380064--22380154 Score: 139
Period size: 23 Copynumber: 4.0 Consensus size: 23
22380054 TTACTGTTCA
22380064 GCACTGTGTGTGCTTACTGATTT
1 GCACTGTGTGTGCTTACTGATTT
* *
22380087 GTACTGTGTGTGCTTACTGTTTT
1 GCACTGTGTGTGCTTACTGATTT
*
22380110 GCACTGTGTGTGCCTACTGATTT
1 GCACTGTGTGTGCTTACTGATTT
*
22380133 GCACTATGTGTGCTTACT-ATTT
1 GCACTGTGTGTGCTTACTGATTT
22380155 CTCCAGCACT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
22 4 0.07
23 57 0.93
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (23 bp):
GCACTGTGTGTGCTTACTGATTT
Found at i:22380119 original size:46 final size:46
Alignment explanation
Indices: 22380052--22380150 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
22380042 ACATTAGCGC
* * *
22380052 GCTTACTGTTCAGCACTGTGTGTGCTTACTGATTTGTACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGTGCCTACTGATTTGCACTATGTGT
**
22380098 GCTTACTGTTTTGCACTGTGTGTGCCTACTGATTTGCACTATGTGT
1 GCTTACTGTTCAGCACTGTGTGTGCCTACTGATTTGCACTATGTGT
22380144 GCTTACT
1 GCTTACT
22380151 ATTTCTCCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.43
Consensus pattern (46 bp):
GCTTACTGTTCAGCACTGTGTGTGCCTACTGATTTGCACTATGTGT
Found at i:22381470 original size:6 final size:6
Alignment explanation
Indices: 22381445--22381483 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
22381435 ACAATTCATA
* * *
22381445 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
22381484 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:22383906 original size:32 final size:32
Alignment explanation
Indices: 22383854--22383922 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
22383844 TGGTAAATGA
*
22383854 AGACAGTGTAGGCACACTAACCATGGGTGTAG
1 AGACAGTGTAGGCACACTAACCAAGGGTGTAG
* **
22383886 AGACTGTGTAGGCATGCTAACCAAGGGTGTAG
1 AGACAGTGTAGGCACACTAACCAAGGGTGTAG
*
22383918 TGACA
1 AGACA
22383923 ATCTATCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.20
Consensus pattern (32 bp):
AGACAGTGTAGGCACACTAACCAAGGGTGTAG
Found at i:22386924 original size:26 final size:26
Alignment explanation
Indices: 22386895--22386976 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
22386885 TGTGTCATCG
22386895 TGAGTATATGAATCCTTTACGGATTA
1 TGAGTATATGAATCCTTTACGGATTA
** * * * *
22386921 TGAGGTCCGATGACT-ATGTT--GCATTG
1 TGA-GT-ATATGAATCCT-TTACGGATTA
22386947 TGAGTATATGAATCCTTTACGGATTA
1 TGAGTATATGAATCCTTTACGGATTA
22386973 TGAG
1 TGAG
22386977 GTCCAATGAT
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
24 7 0.18
25 3 0.08
26 18 0.47
27 3 0.08
28 7 0.18
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (26 bp):
TGAGTATATGAATCCTTTACGGATTA
Found at i:22386955 original size:52 final size:52
Alignment explanation
Indices: 22386872--22387057 Score: 293
Period size: 52 Copynumber: 3.6 Consensus size: 52
22386862 AAATGAAAAG
*
22386872 GGTCGGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
22386924 GGTCCGATGACTATGT-TGCATTGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGT-CATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
22386976 GGTCCAATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
22387028 GATCCGATAACTATGTGTCATCGTGAGTAT
1 GGTCCGATGACTATGTGTCATCGTGAGTAT
22387058 TAAATGAAAT
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
51 1 0.01
52 120 0.98
53 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.35
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Done.