Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 76 of 218
Found at i:22711972 original size:18 final size:17
Alignment explanation
Indices: 22711944--22711987 Score: 79
Period size: 18 Copynumber: 2.5 Consensus size: 17
22711934 GAGAAAAAAA
22711944 TAAAAAAATTTATTTGT
1 TAAAAAAATTTATTTGT
22711961 TAAAAAAGATTTATTTGT
1 TAAAAAA-ATTTATTTGT
22711979 TAAAAAAAT
1 TAAAAAAAT
22711988 ATGAATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
TAAAAAAATTTATTTGT
Found at i:22712056 original size:21 final size:21
Alignment explanation
Indices: 22711998--22712056 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
22711988 ATGAATTTAT
22711998 TTAAAATATATATATTAAAAAA
1 TTAAAA-ATATATATTAAAAAA
* * * * *
22712020 GTATAAATTTAAATTAGAAAA
1 TTAAAAATATATATTAAAAAA
22712041 TTAAAAATATATATTA
1 TTAAAAATATATATTA
22712057 TAACTGGTCA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
TTAAAAATATATATTAAAAAA
Found at i:22715934 original size:43 final size:43
Alignment explanation
Indices: 22715779--22715935 Score: 133
Period size: 43 Copynumber: 3.7 Consensus size: 43
22715769 TGAGTTATCT
* * *
22715779 TGTAAGACCACATCTGGGACGTTGGCGTCGAT-TTGAGATTTATG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT-AGA-TTACG
* * * * *
22715823 TGTAGGACCATGTCTGGGACATCGGCATCG-TA-TACGATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTA-GATTACG
** * * *
22715865 TGTAAGACCTTGTCTGAGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCGATATTAGATTACG
22715908 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
22715936 TCTAAGAGCT
Statistics
Matches: 88, Mismatches: 19, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
42 29 0.33
43 34 0.39
44 25 0.28
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTAGATTACG
Found at i:22718433 original size:30 final size:29
Alignment explanation
Indices: 22718324--22718460 Score: 132
Period size: 30 Copynumber: 4.6 Consensus size: 29
22718314 GTCACAGAGA
* *
22718324 AGTTCATATCACTC-GTACATGGGCGGCTTG
1 AGTTCATATCACCCAG-ACATGGGC-GATTG
22718354 AGTTCATATCACCCAGACATGGGCGACTTG
1 AGTTCATATCACCCAGACATGGGCGA-TTG
***
22718384 AGTTCATATCACTTGGACATGGGCGATTCG
1 AGTTCATATCACCCAGACATGGGCGATT-G
* ** *
22718414 AGTTCACATCACCCAGACATAAGCGGTTCG
1 AGTTCATATCACCCAGACATGGGCGATT-G
*
22718444 AGTTCATTTCACCCAGA
1 AGTTCATATCACCCAGA
22718461 GCAACCACCG
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
29 3 0.03
30 86 0.96
31 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (29 bp):
AGTTCATATCACCCAGACATGGGCGATTG
Found at i:22718447 original size:60 final size:60
Alignment explanation
Indices: 22718324--22718455 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
22718314 GTCACAGAGA
* * * **
22718324 AGTTCATATCACTCGTACATGGGCGGCTTGAGTTCATATCACCCAGACATGGGCGACTTG
1 AGTTCATATCACTCGGACATGGGCGGATTGAGTTCACATCACCCAGACATAAGCGACTTG
* *
22718384 AGTTCATATCACTTGGACATGGGC-GATTCGAGTTCACATCACCCAGACATAAGCG-GTTCG
1 AGTTCATATCACTCGGACATGGGCGGATT-GAGTTCACATCACCCAGACATAAGCGACTT-G
*
22718444 AGTTCATTTCAC
1 AGTTCATATCAC
22718456 CCAGAGCAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 5 0.08
60 57 0.92
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (60 bp):
AGTTCATATCACTCGGACATGGGCGGATTGAGTTCACATCACCCAGACATAAGCGACTTG
Found at i:22722088 original size:20 final size:21
Alignment explanation
Indices: 22722063--22722122 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
22722053 TTTTATATTA
22722063 TTAAAAATAT-TTTAAAATTT
1 TTAAAAATATATTTAAAATTT
*
22722083 TTAAAAAAATATTT-AAA-TT
1 TTAAAAATATATTTAAAATTT
*
22722102 TAAAAATATATATTTAAAATT
1 TTAAAA-ATATATTTAAAATT
22722123 AAAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.21
20 19 0.58
21 6 0.18
22 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAAAATATATTTAAAATTT
Found at i:22722124 original size:20 final size:18
Alignment explanation
Indices: 22722083--22722129 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
22722073 TTTAAAATTT
*
22722083 TTAAAAAAATATTTAAAT
1 TTAAAAAAATATTTAAAA
22722101 TTAAAAATATATATTTAAAA
1 TTAAAAA-A-ATATTTAAAA
22722121 TTAAAAAAA
1 TTAAAAAAA
22722130 ATAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 2 0.08
20 16 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAAAAATATTTAAAA
Found at i:22722127 original size:21 final size:22
Alignment explanation
Indices: 22722085--22722143 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
22722075 TAAAATTTTT
*
22722085 AAAAA-AATATTT-AAATTTAA
1 AAAAATAATATTTAAAATTAAA
*
22722105 AAATAT-ATATTTAAAATTAAA
1 AAAAATAATATTTAAAATTAAA
22722126 AAAAATAATATTATAAAA
1 AAAAATAATATT-TAAAA
22722144 CAATTCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 10 0.31
21 12 0.38
22 5 0.16
23 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAATAATATTTAAAATTAAA
Found at i:22724540 original size:27 final size:27
Alignment explanation
Indices: 22724476--22724546 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
22724466 GGTCGAGGGT
*
22724476 CTGCCACAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCGACACCAAAGGTGCCA
* ** *
22724503 GTGGTAAAGGCGACACCAAAGGTGCCA
1 CTGCCACAGGCGACACCAAAGGTGCCA
22724530 CTGCCACAGGCGACACC
1 CTGCCACAGGCGACACC
22724547 TGTGCCATGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.28, C:0.34, G:0.30, T:0.08
Consensus pattern (27 bp):
CTGCCACAGGCGACACCAAAGGTGCCA
Found at i:22724624 original size:3 final size:3
Alignment explanation
Indices: 22724616--22724673 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
22724606 TCAGCTGCAC
* * * *
22724616 GAA GAA GAA GAAA GAA -AA GGA -AA GGA GAA GAA AAA GAA GAA GAT
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
22724660 G-A GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
22724674 TGAGGAGGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:22724668 original size:14 final size:15
Alignment explanation
Indices: 22724649--22724677 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
22724639 GGAGAAGAAA
22724649 AAGAAGAAG-ATGAG
1 AAGAAGAAGAATGAG
22724663 AAGAAGAAGAATGAG
1 AAGAAGAAGAATGAG
22724678 GAGGAGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (15 bp):
AAGAAGAAGAATGAG
Found at i:22724744 original size:20 final size:21
Alignment explanation
Indices: 22724703--22724759 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
22724693 GCGGTGCCAG
* *
22724703 GAAA-AGAAAAGAAAAAGAGA
1 GAAAGAGAATAGAGAAAGAGA
22724723 GAAAGAGAATAGAGAAAG-GA
1 GAAAGAGAATAGAGAAAGAGA
22724743 GAAAGA-AATAGAAGAAA
1 GAAAGAGAATAG-AGAAA
22724760 AAAAATATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.15
20 17 0.52
21 11 0.33
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04
Consensus pattern (21 bp):
GAAAGAGAATAGAGAAAGAGA
Found at i:22724997 original size:42 final size:41
Alignment explanation
Indices: 22724962--22725095 Score: 118
Period size: 42 Copynumber: 3.3 Consensus size: 41
22724952 TTATCGGTAC
* *
22724962 TTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGG
1 TTAGTATTATTGTTAGTAAAAAACTAATATTATTATGATAG
* * *
22725003 TTAGTTATTA-GGATTAGTAAAAACCCT-A-ATTATTATTGTTAG
1 TTAG-TATTATTG-TTAGTAAAAA-ACTAATATTATTA-TGATAG
* *
22725045 TTAGTATTATTTTTAGTAAAAAACTATTATTATTAT--TA-
1 TTAGTATTATTGTTAGTAAAAAACTAATATTATTATGATAG
*
22725083 TTATTATTATTGT
1 TTAGTATTATTGT
22725096 GTTAGTTATT
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
38 11 0.15
39 2 0.03
40 2 0.03
41 28 0.37
42 30 0.40
43 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (41 bp):
TTAGTATTATTGTTAGTAAAAAACTAATATTATTATGATAG
Found at i:22725077 original size:3 final size:3
Alignment explanation
Indices: 22725069--22725093 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
22725059 AGTAAAAAAC
22725069 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
22725094 GTGTTAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22728001 original size:8 final size:8
Alignment explanation
Indices: 22727973--22728014 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
22727963 GAGCTTATGC
*
22727973 TGTAAAGT
1 TGTAATGT
*
22727981 TGTTATG-
1 TGTAATGT
22727988 TGTAATGT
1 TGTAATGT
22727996 TGTAATGT
1 TGTAATGT
22728004 TGTAATGT
1 TGTAATGT
22728012 TGT
1 TGT
22728015 TGTAACACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (8 bp):
TGTAATGT
Found at i:22728802 original size:25 final size:25
Alignment explanation
Indices: 22728752--22728810 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
22728742 TAATTAAATT
**
22728752 TATACAAAAAAGTACAAACTTTGTAA
1 TATA-AAAAAAGTACAAACTGAGTAA
22728778 TATAAAAAAA-TACAAACTAGAGTAA
1 TATAAAAAAAGTACAAACT-GAGTAA
*
22728803 TATCAAAA
1 TATAAAAA
22728811 CCGCAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 8 0.28
25 17 0.59
26 4 0.14
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (25 bp):
TATAAAAAAAGTACAAACTGAGTAA
Found at i:22731219 original size:158 final size:158
Alignment explanation
Indices: 22730815--22731473 Score: 1088
Period size: 158 Copynumber: 4.2 Consensus size: 158
22730805 CCGCGTCAGG
22730815 TTTTATTACTTTCAAAAAATATACTA------T-T-TTATTATTTTATATTATTTTAGTACATAA
1 TTTTATTACTTTCAAAAAATATACTATTTTCGTATGTTATTATTTTATATTATTTTAGTACATAA
22730872 TGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGGCC
66 TGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGGCC
*
22730937 CTTTGTTTGTATTTTTCTTATTTTC-AGA
131 CTTTGTTCGTATTTTTCTTATTTTCGA-A
*
22730965 TTTTATTACTTTCAAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATA
1 TTTTATTACTTTC-AAAAAATATACTATTTTCGTATGTTATTATTTTATATTATTTTAGTACATA
22731030 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGT-AAAAAACCCTTATTTTGGC
65 ATGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGGC
22731094 CCTTTGTTCGTATTTTTCTTATTTTCGAA
130 CCTTTGTTCGTATTTTTCTTATTTTCGAA
22731123 TTTTATTACTTTCAAAAAATATACTATTTTCGTATGTTATTATTTTATATTATTTTAGTACATAA
1 TTTTATTACTTTCAAAAAATATACTATTTTCGTATGTTATTATTTTATATTATTTTAGTACATAA
*
22731188 TGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAATTTTAGT-AAAAAACCCTTATTTTGGC
66 TGTTTGAAATGTATTATTTTAGTGTG-TTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGGC
* **
22731252 CATTTGTTCGTATTTTTCTTATTTTCTTA
130 CCTTTGTTCGTATTTTTCTTATTTTCGAA
*
22731281 TTTTATTACTTTCAAAAAATATACTATTTTCGTATGTTATTATTTTATATTATTTTTGTACATAA
1 TTTTATTACTTTCAAAAAATATACTATTTTCGTATGTTATTATTTTATATTATTTTAGTACATAA
22731346 TGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGG
66 TGTTTGAAATGTATTATTTTAGTGTG--TTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGG
* * *
22731411 CCCTTTGTTCGTATTTTTCTTTTTTTTGGA
129 CCCTTTGTTCGTATTTTTCTTATTTTCGAA
**
22731441 TTTTATTACTTTCAGTAAATATACTATTTTCGT
1 TTTTATTACTTTCAAAAAATATACTATTTTCGT
22731474 TTTTTTAATT
Statistics
Matches: 481, Mismatches: 15, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
150 13 0.03
151 13 0.03
157 78 0.16
158 211 0.44
159 92 0.19
160 74 0.15
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.54
Consensus pattern (158 bp):
TTTTATTACTTTCAAAAAATATACTATTTTCGTATGTTATTATTTTATATTATTTTAGTACATAA
TGTTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGGCC
CTTTGTTCGTATTTTTCTTATTTTCGAA
Found at i:22731679 original size:33 final size:34
Alignment explanation
Indices: 22731639--22731783 Score: 128
Period size: 33 Copynumber: 4.3 Consensus size: 34
22731629 AAATAAAATA
22731639 AAATAATAAAACATAGAAT-GTAGTACATAACAT
1 AAATAATAAAACATAGAATAGTAGTACATAACAT
* *
22731672 AAATAATAAATA-ATA-AATAATAAATA-ATAACAT
1 AAATAATAAA-ACATAGAATAGT-AGTACATAACAT
*
22731705 AAATAATAAAATAATAAGACATAGTATGTACATAACAT
1 AAATAATAAAA-CAT-AGA-ATAGTA-GTACATAACAT
*
22731743 AAATAATAAAACATGGAAT-GT-G--CATAACAT
1 AAATAATAAAACATAGAATAGTAGTACATAACAT
22731773 AAA-AATTAAAA
1 AAATAA-TAAAA
22731784 TTAAATTATG
Statistics
Matches: 95, Mismatches: 6, Indels: 25
0.75 0.05 0.20
Matches are distributed among these distances:
29 2 0.02
30 16 0.17
32 5 0.05
33 31 0.33
34 8 0.08
35 3 0.03
36 4 0.04
37 8 0.08
38 18 0.19
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (34 bp):
AAATAATAAAACATAGAATAGTAGTACATAACAT
Found at i:22731682 original size:7 final size:7
Alignment explanation
Indices: 22731670--22731721 Score: 72
Period size: 7 Copynumber: 7.6 Consensus size: 7
22731660 AGTACATAAC
22731670 ATAAATA
1 ATAAATA
22731677 ATAAATA
1 ATAAATA
22731684 ATAAATA
1 ATAAATA
22731691 ATAAATA
1 ATAAATA
*
22731698 AT-AA-C
1 ATAAATA
22731703 ATAAATA
1 ATAAATA
22731710 ATAAAATA
1 AT-AAATA
22731718 ATAA
1 ATAA
22731722 GACATAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 2 0.05
6 4 0.10
7 27 0.68
8 7 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (7 bp):
ATAAATA
Found at i:22731747 original size:30 final size:30
Alignment explanation
Indices: 22731713--22731783 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
22731703 ATAAATAATA
* *
22731713 AAATAATAAGACATAGTATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
* *
22731743 AAATAATAAAACATGGAATGTGCATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
22731773 AAA-AATTAAAA
1 AAATAA-TAAAA
22731784 TTAAATTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAT
Found at i:22731857 original size:39 final size:39
Alignment explanation
Indices: 22731769--22731849 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
22731759 AATGTGCATA
* * *
22731769 ACATAAAAATTAAAATTAAATTATGAATGAATGAAAATAT
1 ACATAAATA-TAAAATTAAATTATGAATAAATGAAAACAT
*
22731809 AGATAAATATAAAATTAAATTATGAATAAAT-ATAAACAT
1 ACATAAATATAAAATTAAATTATGAATAAATGA-AAACAT
22731848 AC
1 AC
22731850 CTTAATATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.03
39 27 0.77
40 7 0.20
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (39 bp):
ACATAAATATAAAATTAAATTATGAATAAATGAAAACAT
Found at i:22732052 original size:3 final size:3
Alignment explanation
Indices: 22732044--22732152 Score: 55
Period size: 3 Copynumber: 36.3 Consensus size: 3
22732034 CTTCCCTCCC
* * * *
22732044 TCT TCT TCT TCT CCT TC- TCT TTT TCT TTT TCCT TTT TCT TCCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT T-CT TCT
* * * * * * *
22732090 GCG CCT CCT TCC CCT TCT TCA TCT TC- TCT TC- TCT TCT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
22732135 TCT TCT CTCAT TCT TCT T
1 TCT TCT -TC-T TCT TCT T
22732153 TCCTGCAGCT
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
2 8 0.10
3 61 0.77
4 9 0.11
5 1 0.01
ACGTcount: A:0.02, C:0.37, G:0.02, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:22732130 original size:11 final size:11
Alignment explanation
Indices: 22732103--22732152 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
22732093 CCTCCTTCCC
22732103 CTTCTTCATCTT
1 CTTCTTC-TCTT
22732115 C-TCTTCTCTT
1 CTTCTTCTCTT
*
22732125 CTTCTTTTCTT
1 CTTCTTCTCTT
22732136 CTTC-TCTCATT
1 CTTCTTCTC-TT
22732147 CTTCTT
1 CTTCTT
22732153 TCCTGCAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 8 0.24
11 23 0.70
12 2 0.06
ACGTcount: A:0.04, C:0.34, G:0.00, T:0.62
Consensus pattern (11 bp):
CTTCTTCTCTT
Found at i:22732204 original size:27 final size:27
Alignment explanation
Indices: 22732174--22732244 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
22732164 GTGGTGCCGG
22732174 GGTGCCGCTTGTGGCAGTGGCACATTT
1 GGTGCCGCTTGTGGCAGTGGCACATTT
* * *
22732201 GGTGCCGCCTT-TGTCACTGGCACCTTT
1 GGTGCCG-CTTGTGGCAGTGGCACATTT
*
22732228 GGTGCCGCATGTGGCAG
1 GGTGCCGCTTGTGGCAG
22732245 CCCCTAAACC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 2 0.06
27 31 0.86
28 3 0.08
ACGTcount: A:0.10, C:0.27, G:0.35, T:0.28
Consensus pattern (27 bp):
GGTGCCGCTTGTGGCAGTGGCACATTT
Found at i:22732496 original size:30 final size:30
Alignment explanation
Indices: 22732433--22732497 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
22732423 ACTTATTTTA
*
22732433 TTGTTAACTTTGTTATTATTTTAAAGACTT
1 TTGTTAACTTTGTTATTATTTTAAAGACAT
* * * *
22732463 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAACTTTGTTATTATTTTAAAGACAT
22732493 TTGTT
1 TTGTT
22732498 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (30 bp):
TTGTTAACTTTGTTATTATTTTAAAGACAT
Found at i:22732640 original size:12 final size:12
Alignment explanation
Indices: 22732619--22732652 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22732609 TATATATTTT
*
22732619 AAAATTATATAA
1 AAAATAATATAA
22732631 AAAATAATATAA
1 AAAATAATATAA
*
22732643 AAATTAATAT
1 AAAATAATAT
22732653 GGACGGGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:22733430 original size:31 final size:29
Alignment explanation
Indices: 22733355--22733431 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 29
22733345 GGATTGAATC
22733355 AAAATTTCATGTATAAAATTATACAAAACT
1 AAAA-TTCATGTATAAAATTATACAAAACT
* * * *
22733385 AAAATTTATATATAAAATTATACTTTAAATT
1 AAAATTCATGTATAAAATTATAC--AAAACT
22733416 AAAATTCATGTATAAA
1 AAAATTCATGTATAAA
22733432 TTTGAGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 17 0.44
30 4 0.10
31 18 0.46
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTCATGTATAAAATTATACAAAACT
Found at i:22735419 original size:7 final size:7
Alignment explanation
Indices: 22735407--22735443 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
22735397 ACTAAGCTAC
22735407 CACTTAT
1 CACTTAT
22735414 CACTTAT
1 CACTTAT
22735421 CACTTAT
1 CACTTAT
*
22735428 CACTTGT
1 CACTTAT
*
22735435 CACTGAT
1 CACTTAT
22735442 CA
1 CA
22735444 AATAAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (7 bp):
CACTTAT
Found at i:22735443 original size:57 final size:58
Alignment explanation
Indices: 22735355--22735590 Score: 319
Period size: 57 Copynumber: 4.2 Consensus size: 58
22735345 CTTACACGGA
* ** *
22735355 ATCACTTATCATTTATCTTTTGTCACTGATCAGATAAGTGTAACT-AAGCTACCACTT
1 ATCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
22735412 ATCACTTATCACTTATCACTTGTCACTGATCAAATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
22735469 ATCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTATCACTT
1 ATCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
22735527 AT-A---A--A-TTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTACCACTT
1 ATCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
22735578 ATCACTTGTCACT
1 ATCACTTATCACT
22735591 GATTAGAAGT
Statistics
Matches: 160, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
51 46 0.29
52 2 0.01
54 1 0.01
57 97 0.61
58 14 0.09
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (58 bp):
ATCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:22735587 original size:51 final size:51
Alignment explanation
Indices: 22735414--22735590 Score: 230
Period size: 51 Copynumber: 3.4 Consensus size: 51
22735404 TACCACTTAT
* *
22735414 CACTTATCACTTATCACTTGTCACTGATCAAATAAGTGTAGCT-AAGCTACCAC
1 CACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCT---AC
*
22735467 TTATCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAT
1 ----CACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
22735522 CACTTATAAATTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTAC
1 CACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
22735573 CACTTATCACTTGTCACT
1 CACTTATCACTTGTCACT
22735591 GATTAGAAGT
Statistics
Matches: 110, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
51 63 0.57
55 1 0.01
57 41 0.37
58 5 0.05
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
CACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:22736714 original size:30 final size:30
Alignment explanation
Indices: 22736649--22736736 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
22736639 GGTGCAAGGG
*
22736649 TGAGTGCATATTGATAGTAAAACATTTTCTA
1 TGAGTGCATATTGATAGTAAAAC-CTTTCTA
* * *
22736680 TGAGTGTACATTGATAGTAAAACCTTTGTA
1 TGAGTGCATATTGATAGTAAAACCTTTCTA
22736710 TGAGTGCATATTGATAGTAAAACCTTT
1 TGAGTGCATATTGATAGTAAAACCTTT
22736737 TGTGTTGTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 30 0.59
31 21 0.41
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (30 bp):
TGAGTGCATATTGATAGTAAAACCTTTCTA
Found at i:22736898 original size:103 final size:104
Alignment explanation
Indices: 22736710--22736921 Score: 264
Period size: 103 Copynumber: 2.0 Consensus size: 104
22736700 AACCTTTGTA
* * *
22736710 TGAGTGCATATTGATAGTAAAACCTTTTGTGTTGTGGTTTTACTTGCTAAATTCATAAGAGAGAA
1 TGAGTGCATATTGATAGTAAAACC-TTTGTGCTGTGATTTTACTTGCTAAATTCACAAGAGAGAA
* * *
22736775 CTTAGTAGTGAGAGTATTAATGATCTTCAAGGTGCAAGGG
65 CTTAGTAGTGAAAGTATTAATAATCTTCAAGGTACAAGGG
* * * * * * *
22736815 TGAGTGCATATTGATAGTAAAACC-TTGTGCTGTGATTTTACTTGTTGAATTCGCAGGGGTGAAT
1 TGAGTGCATATTGATAGTAAAACCTTTGTGCTGTGATTTTACTTGCTAAATTCACAAGAGAGAAC
* * *
22736879 TTAGTGGTGAAAGTTTTAATAATTTTCAAGGTACAAGGG
66 TTAGTAGTGAAAGTATTAATAATCTTCAAGGTACAAGGG
22736918 TGAG
1 TGAG
22736922 GAAAATTATC
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
103 67 0.74
105 24 0.26
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36
Consensus pattern (104 bp):
TGAGTGCATATTGATAGTAAAACCTTTGTGCTGTGATTTTACTTGCTAAATTCACAAGAGAGAAC
TTAGTAGTGAAAGTATTAATAATCTTCAAGGTACAAGGG
Found at i:22746495 original size:1 final size:1
Alignment explanation
Indices: 22746457--22746481 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22746447 GTATTTAAGG
22746457 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
22746482 GAAGAAGCGA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22751939 original size:24 final size:24
Alignment explanation
Indices: 22751897--22751964 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
22751887 AAGCTCATGT
* *
22751897 GAGCCAGTAACGGGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCGAA
* ** *
22751921 GAGCCATTAACGGAAAGCTTTGGA
1 GAGCCATTAACGGGAAGCTCCGAA
22751945 GAGCCATTAACGGGAAGCTC
1 GAGCCATTAACGGGAAGCTC
22751965 ATAAGAGTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCGAA
Found at i:22751971 original size:24 final size:24
Alignment explanation
Indices: 22751784--22751976 Score: 75
Period size: 24 Copynumber: 7.9 Consensus size: 24
22751774 TTTCATATTT
* *
22751784 GGGAATGCTCATACGAGCACATAAAC
1 GGGAA-GCTCATAAGAGC-CATTAAC
* ** *
22751810 AGGAAGCTCATTTGAGCCATGTAAT
1 GGGAAGCTCATAAGAGCCAT-TAAC
* *** **
22751835 GGGAAGCTTACCCGAGCTGTATAAC
1 GGGAAGCTCATAAGAGCCAT-TAAC
* *
22751860 AGGAAGCTCATAAGAGGCA-TAATC
1 GGGAAGCTCATAAGAGCCATTAA-C
*** ** *
22751884 AAAAAGCTCATGTGAGCCAGTAAC
1 GGGAAGCTCATAAGAGCCATTAAC
* **
22751908 GGGTAGCTCCGAAGAGCCATTAAC
1 GGGAAGCTCATAAGAGCCATTAAC
* * *
22751932 GGAAAGCT-TTGGAGAGCCATTAAC
1 GGGAAGCTCAT-AAGAGCCATTAAC
*
22751956 GGGAAGCTCATAAGAGTCATT
1 GGGAAGCTCATAAGAGCCATT
22751977 TATCGAAAAA
Statistics
Matches: 117, Mismatches: 45, Indels: 12
0.67 0.26 0.07
Matches are distributed among these distances:
23 3 0.03
24 67 0.57
25 43 0.37
26 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (24 bp):
GGGAAGCTCATAAGAGCCATTAAC
Found at i:22766590 original size:25 final size:25
Alignment explanation
Indices: 22766545--22766592 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
22766535 TAATCACGTC
* *
22766545 AATTTTTAATAGTACAAATAAATGA
1 AATTTTTAATAGAAAAAATAAATGA
22766570 AATTTTTAAT-GAAAAAGATAAAT
1 AATTTTTAATAGAAAAA-ATAAAT
22766593 TTACTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (25 bp):
AATTTTTAATAGAAAAAATAAATGA
Found at i:22767373 original size:45 final size:44
Alignment explanation
Indices: 22767308--22767397 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 44
22767298 GAATAGAGGC
* * *
22767308 GTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAAAGGCGTAATAG-AAATCAACTGTTTGGTTGAAT
* ***
22767353 GTAATGGAATAAAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAAAGGCGTAATAGAAATCAACTGTTTGGTTGAAT
22767397 G
1 G
22767398 GAATAGAGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.47
45 20 0.53
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
GTAATGGAATAAAGGCGTAATAGAAATCAACTGTTTGGTTGAAT
Found at i:22767604 original size:51 final size:51
Alignment explanation
Indices: 22767549--22767728 Score: 117
Period size: 51 Copynumber: 3.2 Consensus size: 51
22767539 TATTTAAACA
22767549 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
1 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
** * **
22767600 TAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
1 TAATAAT---TATT-AAATAT--A-TTA-T--AAT-TTAA-ATAT-ATA--ATTTAATA-AAATT
*
22767665 AACA
50 --CT
* * *
22767669 TAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCT
1 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
22767720 TAATAATTA
1 TAATAATTA
22767729 ATATTTTTAT
Statistics
Matches: 95, Mismatches: 16, Indels: 36
0.65 0.11 0.24
Matches are distributed among these distances:
51 16 0.17
53 5 0.05
54 10 0.11
55 4 0.04
56 3 0.03
57 5 0.05
58 5 0.05
59 4 0.04
61 4 0.04
62 5 0.05
63 5 0.05
64 3 0.03
65 4 0.04
66 10 0.11
67 5 0.05
69 7 0.07
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (51 bp):
TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
Found at i:22767688 original size:120 final size:120
Alignment explanation
Indices: 22767545--22767893 Score: 635
Period size: 120 Copynumber: 2.9 Consensus size: 120
22767535 ATCATATTTA
* * * *
22767545 AACATAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
22767610 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
22767665 AACATAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
22767730 TATTTTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
22767785 AACATAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
22767850 TATTCTTATATGAATTTTCTCAAATCATAATAAATGATACTATA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATA
22767894 TGTTGACACC
Statistics
Matches: 221, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 221 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTGTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:22769136 original size:3 final size:3
Alignment explanation
Indices: 22769128--22769185 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
22769118 AAAAACAATT
*
22769128 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22769176 ATA ATA ATA A
1 ATA ATA ATA A
22769186 AATTGCTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:22770875 original size:44 final size:43
Alignment explanation
Indices: 22770814--22771354 Score: 239
Period size: 44 Copynumber: 12.6 Consensus size: 43
22770804 ATCTACTCTG
* * * *
22770814 CTGTAACCTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCATTT-CTTCAATCTGCTCCA
* * * * *
22770858 CTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCA-TTTCTTCAATCTGCTCCA
*
22770901 CTGTAA-CTCAGGGAGATAAGATC-TCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCAT-T-TCTTCAATCTGCTCCA
* * * *
22770944 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCAGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATC---ATTTCTTCAATCTGCTCCA
* * * * * * *
22770990 CTGTAACCTCAGGGAAATAAGA-CCTGAT-GT-GATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCAT-TTCTTCAATCTGCTCCA
* * * **
22771031 CTGTAACTTCAGAGAGATAAGATC----CTTTAATCCACTCCA
1 CTGTAACCTCAGGGAGATAAGATCATTTCTTCAATCTGCTCCA
* * * * * * ** *
22771070 TTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCA-TTTCTTCAATCTGCTCCA
* *
22771114 CTGTAATCTCAGGGAGATAAGATC-TCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCAT-T-TCTTCAATCTGCTCCA
* ** *
22771158 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACT--A
1 CTGTAACCTCAGGGAGATAAGATC---ATTTCTTCAATCTGCTCCA
* * * ** * * * **
22771202 ATGTAACCTCAGGGTGATAAGA-C-CTGATGCGATCTACTCTG
1 CTGTAACCTCAGGGAGATAAGATCATTTCTTCAATCTGCTCCA
* * * * * *
22771243 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCATTT-CTTCAATCTGCTCCA
* * * ** * *
22771287 CTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCG
1 CTGTAACCTCAGGGAGATAAGATCA-TTTCTTCAATCTGCTCCA
* *
22771331 TTGTAATCTCAGGGAGATAAGATC
1 CTGTAACCTCAGGGAGATAAGATC
22771355 TGAAATTCTT
Statistics
Matches: 365, Mismatches: 102, Indels: 60
0.69 0.19 0.11
Matches are distributed among these distances:
38 1 0.00
39 34 0.09
41 45 0.12
42 17 0.05
43 39 0.11
44 183 0.50
45 2 0.01
46 42 0.12
47 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (43 bp):
CTGTAACCTCAGGGAGATAAGATCATTTCTTCAATCTGCTCCA
Found at i:22770943 original size:86 final size:87
Alignment explanation
Indices: 22770802--22770962 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 87
22770792 AGACCTGATG
* * * * *
22770802 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAACTT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCATTGACTTCAATCCGCTCCACTGTAACCT
22770867 CAGGGAGATAGGATAGTGTCTT
66 CAGGGAGATAGGATAGTGTCTT
* * * *
22770889 CGATCTGCTCCGCTGTAA-CTCAGGGAGATAAGATC-TCTGGCTTCAATCTGCTCCACTGTAACC
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCAT-TGACTTCAATCCGCTCCACTGTAACC
22770952 TCAGGGAGATA
65 TCAGGGAGATA
22770963 AGATCTGAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 1 0.02
86 47 0.73
87 16 0.25
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCATTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:22783951 original size:3 final size:3
Alignment explanation
Indices: 22783943--22784000 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
22783933 AAAAACAATT
*
22783943 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22783991 ATA ATA ATA A
1 ATA ATA ATA A
22784001 AATTGCTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:22785401 original size:30 final size:33
Alignment explanation
Indices: 22785372--22785435 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
22785362 ATATAAATTA
*
22785372 ACAT-ATTTATTATTAAATATATTATAATTAAAAT
1 ACATAATTTATTATTAAATATATTACAATT--AAT
*
22785406 ATATAATTTATTATTAAATATATTACAATT
1 ACATAATTTATTATTAAATATATTACAATT
22785436 TAAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
34 3 0.11
35 24 0.89
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (33 bp):
ACATAATTTATTATTAAATATATTACAATTAAT
Found at i:22785405 original size:16 final size:16
Alignment explanation
Indices: 22785367--22785458 Score: 59
Period size: 15 Copynumber: 5.8 Consensus size: 16
22785357 ATAAAATATA
*
22785367 AATTAACATAT-TTAT
1 AATTAAAATATATTAT
*
22785382 TATT-AAATATATTAT
1 AATTAAAATATATTAT
*
22785397 AATTAAAATATATAATT
1 AATTAAAATATATTA-T
* *
22785414 TATTATTAAATATATTAC
1 AATTA--AAATATATTAT
22785432 AATTTAAAAT-TATTA-
1 AA-TTAAAATATATTAT
22785447 ACATT-AAATATA
1 A-ATTAAAATATA
22785459 ATTTAATAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.15
15 15 0.25
16 15 0.25
17 9 0.15
18 1 0.02
19 12 0.20
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:22788690 original size:13 final size:13
Alignment explanation
Indices: 22788672--22788697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22788662 TGCTTTTGAG
22788672 TTCAAAAATAATT
1 TTCAAAAATAATT
22788685 TTCAAAAATAATT
1 TTCAAAAATAATT
22788698 CTGATTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TTCAAAAATAATT
Found at i:22790552 original size:30 final size:30
Alignment explanation
Indices: 22790516--22790578 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
22790506 TAACTCAAAT
*
22790516 AAATAATGCAATACAGGCAATAACCGAAAC
1 AAATAATGCAATACAGGCAAGAACCGAAAC
*
22790546 AAATAATGCAATACAGGCAAGAATCGAAAC
1 AAATAATGCAATACAGGCAAGAACCGAAAC
22790576 AAA
1 AAA
22790579 CTATTTAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.17, G:0.14, T:0.13
Consensus pattern (30 bp):
AAATAATGCAATACAGGCAAGAACCGAAAC
Found at i:22798774 original size:24 final size:23
Alignment explanation
Indices: 22798739--22798785 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
22798729 TTGTAGGTTA
*
22798739 AATTATTCAAATATGTCATTTTTT
1 AATTATTCAAATATAT-ATTTTTT
22798763 AATTGATT-AAATATATATTTTTT
1 AATT-ATTCAAATATATATTTTTT
22798786 TTGAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 11 0.52
25 3 0.14
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
AATTATTCAAATATATATTTTTT
Found at i:22799445 original size:18 final size:18
Alignment explanation
Indices: 22799422--22799456 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22799412 TTACATATAA
22799422 AAATAATAATTATATTTG
1 AAATAATAATTATATTTG
* *
22799440 AAATAATTATTTTATTT
1 AAATAATAATTATATTT
22799457 TATAATATTA
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATAATAATTATATTTG
Found at i:22817586 original size:6 final size:6
Alignment explanation
Indices: 22817577--22817602 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22817567 ATAGAAGCAA
22817577 ATGAAT ATGAAT ATGAAT ATGAAT AT
1 ATGAAT ATGAAT ATGAAT ATGAAT AT
22817603 TGGAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
ATGAAT
Found at i:22823959 original size:22 final size:23
Alignment explanation
Indices: 22823907--22823963 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
22823897 TTTTAATTAA
* * *
22823907 AATTAAAATTAAAATTATTTTTT
1 AATTAAAATTAAAACTAATTGTT
22823930 AATTAAAATTAAAACTAATTGTT
1 AATTAAAATTAAAACTAATTGTT
22823953 -ATTAAAATTAA
1 AATTAAAATTAA
22823964 TTGTTAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTAAAATTAAAACTAATTGTT
Found at i:22823976 original size:16 final size:16
Alignment explanation
Indices: 22823939--22823978 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
22823929 TAATTAAAAT
* *
22823939 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
22823955 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
22823971 TAAAATTA
1 TAAAATTA
22823979 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:22824010 original size:59 final size:64
Alignment explanation
Indices: 22823945--22824168 Score: 247
Period size: 59 Copynumber: 3.6 Consensus size: 64
22823935 AAATTAAAAC
22823945 TAATTGTTATTAAAAT-T-A-A-TTG-TTAGTAAAATTATCAAATTATTAATTATTAATTGTAT
1 TAATTGTTATTAAAATCTAACATTTGATTAGTAAAATTATCAAATTATTAATTATTAATTGTAT
* *
22824004 TAATTGTTGTAATAAAATCTAACATTTGATTAGT-AAATT-T---ATCA--AATTATTAATTGTA
1 TAATTG-T-TATTAAAATCTAACATTTGATTAGTAAAATTATCAAATTATTAATTATTAATTGTA
22824062 T
64 T
*
22824063 TAATTGTTATAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTATATTAATTG
1 TAATTGTTAT--TAAAATCTAACATTTGATTAGTAAAATTATCAAATTATTAA-T-TATTAATTG
22824128 TAT
62 TAT
**
22824131 TAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAA
1 TAATTG-T-TATTAAAATCTAACATTTGATTAGTAAAA
22824169 CAAACTTGAT
Statistics
Matches: 137, Mismatches: 8, Indels: 31
0.78 0.05 0.18
Matches are distributed among these distances:
57 2 0.01
58 1 0.01
59 49 0.36
60 5 0.04
61 12 0.09
62 1 0.01
63 1 0.01
64 5 0.04
65 8 0.06
66 7 0.05
67 1 0.01
68 42 0.31
69 1 0.01
70 2 0.01
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (64 bp):
TAATTGTTATTAAAATCTAACATTTGATTAGTAAAATTATCAAATTATTAATTATTAATTGTAT
Found at i:22824262 original size:23 final size:22
Alignment explanation
Indices: 22824234--22824276 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
22824224 AAATAAAATT
*
22824234 AAAATAAAAACTATTATATTTTA
1 AAAATAAAAAATA-TATATTTTA
22824257 AAAATAAAAAATATATATTT
1 AAAATAAAAAATATATATTT
22824277 AATATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATAAAAAATATATATTTTA
Found at i:22831384 original size:3 final size:3
Alignment explanation
Indices: 22831376--22831452 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
22831366 CGCCTCTCCA
* * **
22831376 CTC CTC CTC CTC CTC CTC CTC CACC CTC CTC CTTC TTC CTC AAAC C-C
1 CTC CTC CTC CTC CTC CTC CTC C-TC CTC CTC C-TC CTC CTC -CTC CTC
* * *
22831423 C-C CTC CTC CTC CAC CTC CAC CTC CAC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
22831453 ACCACAAACA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
2 4 0.07
3 48 0.84
4 5 0.09
ACGTcount: A:0.09, C:0.65, G:0.00, T:0.26
Consensus pattern (3 bp):
CTC
Found at i:22837553 original size:21 final size:21
Alignment explanation
Indices: 22837528--22837583 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
22837518 AACAGCGGTG
* *
22837528 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTATA
*
22837549 GCGGTGAGATTGGATACTATA
1 GCGGTGAGATTAGATACTATA
*
22837570 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
22837584 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:22841185 original size:39 final size:39
Alignment explanation
Indices: 22841131--22841211 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
22841121 ATGCAATCGA
22841131 TTTGTTCAACTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCAACTTTAAAGCTTTACTTGAACTATTGTTTTC
*
22841170 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCAACTTTAAAGCTTTACTTGAACTATTGTTTTC
22841209 TTT
1 TTT
22841212 TCAGTGTAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (39 bp):
TTTGTTCAACTTTAAAGCTTTACTTGAACTATTGTTTTC
Found at i:22841564 original size:32 final size:29
Alignment explanation
Indices: 22841522--22841706 Score: 193
Period size: 32 Copynumber: 6.2 Consensus size: 29
22841512 GAATAAACCG
22841522 AATACACTACATATATTTTTTTGTATTTTTAA
1 AATACACTACATATA--TTTTT-TATTTTTAA
*
22841554 AATACGCTACATATA-TTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
* *
22841582 AATACACAACATATA---TATA-TTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
22841607 AATACACTACATATA-TTTTTATTTTTTAA
1 AATACACTACATATATTTTTTA-TTTTTAA
*
22841636 AATACACGACATATATATTTTTTTATTTTTAA
1 AATACACTAC--ATATA-TTTTTTATTTTTAA
*
22841668 AATCCACTACATATATATTTTTTTATTTTTAA
1 AATACACTAC--ATATA-TTTTTTATTTTTAA
22841700 AATACAC
1 AATACAC
22841707 AAATACAATG
Statistics
Matches: 135, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
25 20 0.15
26 3 0.02
27 3 0.02
28 22 0.16
29 19 0.14
31 5 0.04
32 57 0.42
33 6 0.04
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (29 bp):
AATACACTACATATATTTTTTATTTTTAA
Found at i:22841626 original size:53 final size:55
Alignment explanation
Indices: 22841545--22841708 Score: 197
Period size: 53 Copynumber: 2.8 Consensus size: 55
22841535 TATTTTTTTG
*
22841545 TATTTTTAAAATACGCTACATATATTTTTATTTTTAAAATACACAACATATATA-
1 TATTTTTAAAATACACTACATATATTTTTATTTTTAAAATACACAACATATATAT
*
22841599 TA-TTTTAAAATACACTACATATATTTTTATTTTTTAAAATACACGACATATATATTTTTT
1 TATTTTTAAAATACACTACATATATTTTTA-TTTTTAAAATACACAACATATATA-----T
*
22841659 TATTTTTAAAATCCACTACATATATATTTTTTTATTTTTAAAATACACAA
1 TATTTTTAAAATACACTAC--ATATA--TTTTTATTTTTAAAATACACAA
22841709 ATACAATGTA
Statistics
Matches: 94, Mismatches: 4, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
53 26 0.28
54 25 0.27
60 2 0.02
61 15 0.16
63 5 0.05
64 15 0.16
65 6 0.06
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (55 bp):
TATTTTTAAAATACACTACATATATTTTTATTTTTAAAATACACAACATATATAT
Found at i:22844887 original size:21 final size:22
Alignment explanation
Indices: 22844851--22844935 Score: 93
Period size: 21 Copynumber: 4.0 Consensus size: 22
22844841 CCAAGAACAA
*
22844851 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAACGAGGGGAGAAACC
* *
22844873 AACAAAAACGA-GGGACAAACC
1 AGCAAAAACGAGGGGAGAAACC
* * *
22844894 AGTAAGAAC-AAGGGAGAAACC
1 AGCAAAAACGAGGGGAGAAACC
*
22844915 AGCAAGAACGAGGGGAGAAAC
1 AGCAAAAACGAGGGGAGAAAC
22844936 TGTTGTTTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 1 0.02
21 32 0.62
22 19 0.37
ACGTcount: A:0.53, C:0.16, G:0.29, T:0.01
Consensus pattern (22 bp):
AGCAAAAACGAGGGGAGAAACC
Found at i:22846077 original size:18 final size:17
Alignment explanation
Indices: 22846023--22846260 Score: 201
Period size: 17 Copynumber: 13.2 Consensus size: 17
22846013 CGTGATCCGA
22846023 TTGAAACACGAGAATTTTT
1 TTGAAACACGA-AA-TTTT
* * *
22846042 TTTAAACGCGAAA-ATT
1 TTGAAACACGAAATTTT
*
22846058 TTGAAACACTAAATTTTTT
1 TTGAAACACGAAA--TTTT
*
22846077 TTAAAACACGGAAA-TTT
1 TTGAAACAC-GAAATTTT
22846094 TTGAAACACGAGAATTTT
1 TTGAAACACGA-AATTTT
* *
22846112 TTGCAAAACACGAAAATAT
1 TTG--AAACACGAAATTTT
*
22846131 TTGAAACACGAAAATTT
1 TTGAAACACGAAATTTT
*
22846148 TTGAAAACAAGAAATTTT
1 TTG-AAACACGAAATTTT
22846166 TTGAAACACGGAAATTTT
1 TTGAAACAC-GAAATTTT
*
22846184 TTGAAAACACGAAAATTT
1 TTG-AAACACGAAATTTT
22846202 TTGAAACACTGGAAATTTTT
1 TTGAAACAC--GAAA-TTTT
* **
22846222 TTGAAAACATGAAAAATT
1 TTG-AAACACGAAATTTT
*
22846240 TTGAAACACAAAATTTT
1 TTGAAACACGAAATTTT
22846257 TTGA
1 TTGA
22846261 TAAATTACAT
Statistics
Matches: 179, Mismatches: 25, Indels: 32
0.76 0.11 0.14
Matches are distributed among these distances:
16 14 0.08
17 54 0.30
18 49 0.27
19 40 0.22
20 17 0.09
21 5 0.03
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (17 bp):
TTGAAACACGAAATTTT
Found at i:22846096 original size:36 final size:36
Alignment explanation
Indices: 22846023--22846258 Score: 275
Period size: 36 Copynumber: 6.5 Consensus size: 36
22846013 CGTGATCCGA
* *
22846023 TTGAAACACGAGAATTTTTTT-TAAACGCGAAAA-TT
1 TTGAAACACGA-AATTTTTTTGAAAACACGAAAATTT
* * *
22846058 TTGAAACACTAAATTTTTTTTAAAACACGGAAATTT
1 TTGAAACACGAAATTTTTTTGAAAACACGAAAATTT
*
22846094 TTGAAACACGAGAA-TTTTTTGCAAAACACGAAAATAT
1 TTGAAACACGA-AATTTTTTTG-AAAACACGAAAATTT
* * *
22846131 TTGAAACACGAAA-ATTTTTGAAAACAAGAAATTTT
1 TTGAAACACGAAATTTTTTTGAAAACACGAAAATTT
22846166 TTGAAACACGGAAA-TTTTTTGAAAACACGAAAATTT
1 TTGAAACAC-GAAATTTTTTTGAAAACACGAAAATTT
* *
22846202 TTGAAACACTGGAAATTTTTTTGAAAACATGAAAAATT
1 TTGAAACAC--GAAATTTTTTTGAAAACACGAAAATTT
*
22846240 TTGAAACACAAAATTTTTT
1 TTGAAACACGAAATTTTTT
22846259 GATAAATTAC
Statistics
Matches: 176, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
34 9 0.05
35 40 0.23
36 67 0.38
37 31 0.18
38 29 0.16
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (36 bp):
TTGAAACACGAAATTTTTTTGAAAACACGAAAATTT
Found at i:22846831 original size:13 final size:13
Alignment explanation
Indices: 22846795--22846835 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 13
22846785 TTTGGGCCTG
22846795 TTTT-TTCTTTTT
1 TTTTCTTCTTTTT
22846807 TTTTCCTCTCTTTTT
1 TTTT-CT-TCTTTTT
22846822 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
22846835 T
1 T
22846836 CTGTTAGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.15
13 8 0.31
14 3 0.12
15 11 0.42
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTCTTTTT
Found at i:22847475 original size:60 final size:59
Alignment explanation
Indices: 22847376--22847519 Score: 191
Period size: 60 Copynumber: 2.4 Consensus size: 59
22847366 TAATTTCAAC
* *
22847376 AAAATTTA-GGGTCAAAATGTAATTTAAAGAAAGTTTAGGGGTCAAAACATAATTCTAA
1 AAAATTTAGGGGTTAAAATGTAATTTAAAGAAAGTTTAGGGGTCAAAACACAATTCTAA
* * * ** *
22847434 AAAATTTTAGGGGTTGAAATGTAATTTCAAGGAAGTTTAGGGGTCAAAATGCAATTTTAA
1 AAAA-TTTAGGGGTTAAAATGTAATTTAAAGAAAGTTTAGGGGTCAAAACACAATTCTAA
*
22847494 AAAATTTAGGGGTTAAAATGCAATTT
1 AAAATTTAGGGGTTAAAATGTAATTT
22847520 TTTTACAACA
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
58 4 0.05
59 24 0.32
60 46 0.62
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (59 bp):
AAAATTTAGGGGTTAAAATGTAATTTAAAGAAAGTTTAGGGGTCAAAACACAATTCTAA
Found at i:22847520 original size:29 final size:29
Alignment explanation
Indices: 22847355--22847520 Score: 165
Period size: 30 Copynumber: 5.6 Consensus size: 29
22847345 AAAACTTCTA
*
22847355 GGGTCAAAATGTAATTTCAACAAAATTTA-
1 GGGTCAAAATGTAATTTTAA-AAAATTTAG
22847384 GGGTCAAAATGTAA-TTTAAAGAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAA-AAA-TTTAG
** *
22847414 GGGTCAAAACATAATTCTAAAAAATTTTAG
1 GGGTCAAAATGTAATTTTAAAAAA-TTTAG
** * * *
22847444 GGGTTGAAATGTAATTTCAAGGAAGTTTAG
1 GGGTCAAAATGTAATTTTAA-AAAATTTAG
*
22847474 GGGTCAAAATGCAATTTTAAAAAATTTAG
1 GGGTCAAAATGTAATTTTAAAAAATTTAG
* *
22847503 GGGTTAAAATGCAATTTT
1 GGGTCAAAATGTAATTTT
22847521 TTTACAACAC
Statistics
Matches: 112, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
27 1 0.01
28 7 0.06
29 42 0.38
30 55 0.49
31 7 0.06
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.32
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAAAAAATTTAG
Found at i:22847742 original size:50 final size:50
Alignment explanation
Indices: 22847645--22847742 Score: 119
Period size: 48 Copynumber: 2.0 Consensus size: 50
22847635 CTGTCCAAAA
* * * *
22847645 TTTTCTTTTTATTTGAAAAATAGAAATCGAGAAAAGCTCGGCGTGCGATC
1 TTTTCTTTTTATTTGAAAAACAGAAATCGAAAAAACCTCGGCATGCGATC
*
22847695 TTTT-TTTTT-TTTGAAAAACAGAAATTGAAAAAATACCTCGGCATGCGA
1 TTTTCTTTTTATTTGAAAAACAGAAATCG-AAAAA-ACCTCGGCATGCGA
22847743 CCTAAGGCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 16 0.39
49 9 0.22
50 16 0.39
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (50 bp):
TTTTCTTTTTATTTGAAAAACAGAAATCGAAAAAACCTCGGCATGCGATC
Found at i:22848071 original size:78 final size:77
Alignment explanation
Indices: 22847702--22848675 Score: 1195
Period size: 78 Copynumber: 12.3 Consensus size: 77
22847692 ATCTTTTTTT
* * ** * *
22847702 TTTTTGAAAAACAGAAATTGAAAAAATACCTCGGCATGCGACCTAAGGCTCAACTCACGTCTCGT
1 TTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
22847767 AATATGAGTTGA
66 AATATGAGTTGA
* ** * * * ** *
22847779 TTTTTGAAAAACA-AATTTTTTTTAAAAATACCTCAGCATATAACCCGAACCTCAACTCTCCTCT
1 TTTTTGAAAAACAGAA---ATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCT
22847843 CGCAATATGAGTTGA
63 CGCAATATGAGTTGA
* *
22847858 TTTTTGAAAAACAGAAATTTAAAAGAAATATCTCGGCATGTGACCCAAGGCTCAACTCACCTCTC
1 TTTTTGAAAAACAGAAA-TTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTC
22847923 GCAATATGAGTTGA
64 GCAATATGAGTTGA
* * * *
22847937 TTTTTGAAAAAC--AAATT-GAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCACCTCTCGT
1 TTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
22847999 AATATGAGTTGA
66 AATATGAGTTGA
* *
22848011 TTTTTTGAAAAACATAAATTAAAAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCG
1 -TTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCG
22848076 CAATATGAGTTGA
65 CAATATGAGTTGA
* *** *
22848089 TTTTTTGAAAAAGAACAGAAATTAAAAAAATACATCAATATGTGAGCCGAGGCTCAACTCACCTC
1 -TTTTTG--AAA-AACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTC
22848154 TCGCAATATGAGTTGA
62 TCGCAATATGAGTTGA
* * ** *
22848170 TTTTTTGAAAAAGAACAGAAATTAAAAAAATACATTGATATGTGAGCCGAGGCTCAACTCACCTC
1 -TTTTTG--AAA-AACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTC
22848235 TCGCAATATGAGTTGA
62 TCGCAATATGAGTTGA
* *
22848251 TTTTTGAAAAACAGAAATTTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCT
1 TTTTTGAAAAACAGAAA-TTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCG
22848316 CAATATGAGTTGA
65 CAATATGAGTTGA
* *
22848329 TTTTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCATGTG-TCCGAGGCTCAACTCAC
1 -----TTTTTGAAAAACAGAAA-TTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCAC
*
22848393 CTTTCGCAATATGAGTTGA
59 CTCTCGCAATATGAGTTGA
* * * *
22848412 TTTTTAAAAAACAAAAATTTAAAAGAAATACATCGGCATGTG-TCCGAGGCTCAACTCACCTCTC
1 TTTTTGAAAAACAGAAA-TTAAAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTC
22848476 GCAATATGAGTTGA
64 GCAATATGAGTTGA
* * *
22848490 TTTTTTTGTAAAAAATAGAAATTAAAAAAATACCTCGGTATGTGACTCGAGGCTCAACTCACCTC
1 --TTTTTG--AAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTC
22848555 TCGCAATATGAGTTGA
62 TCGCAATATGAGTTGA
* *
22848571 TTTTTGAAAAACAAGAATTTTAAAAAAATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTC
1 TTTTTGAAAAAC-AGAA-ATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTC
22848636 GCAATATGAGTTGA
64 GCAATATGAGTTGA
*
22848650 TTTTTGAAAAAACAGAAATTGAAAAA
1 TTTTTG-AAAAACAGAAATTAAAAAA
22848676 TATTTCTTGA
Statistics
Matches: 797, Mismatches: 72, Indels: 55
0.86 0.08 0.06
Matches are distributed among these distances:
74 51 0.06
75 14 0.02
76 4 0.01
77 34 0.04
78 203 0.25
79 193 0.24
80 37 0.05
81 180 0.23
82 9 0.01
83 57 0.07
84 15 0.02
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (77 bp):
TTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
AATATGAGTTGA
Found at i:22853380 original size:4 final size:4
Alignment explanation
Indices: 22853366--22853405 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
22853356 ATGTACATGC
*
22853366 AATG CATG AATG AATG AATG AATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
22853406 TTGGTCATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.25, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:22855694 original size:19 final size:19
Alignment explanation
Indices: 22855531--22855711 Score: 148
Period size: 18 Copynumber: 9.9 Consensus size: 19
22855521 GATCCAATTG
* **
22855531 AAACACGAGAATTTTTTTT
1 AAACACGAAAATTTTTTGA
*
22855550 AAACACGGAAA-TTTTTG-
1 AAACACGAAAATTTTTTGA
* *
22855567 AAACATGAGAATTTTTTGCA
1 AAACACGAAAATTTTTTG-A
*
22855587 AAACAC-AAAAATTTTTGA
1 AAACACGAAAATTTTTTGA
* *
22855605 AAACAAG-AATTTTTTTG-
1 AAACACGAAAATTTTTTGA
*
22855622 AAACACGAAATTTTTTTGA
1 AAACACGAAAATTTTTTGA
22855641 AAACACGAAAA-TTTTTG-
1 AAACACGAAAATTTTTTGA
*
22855658 AAACACTGGAAATTTTTTTGA
1 AAACAC--GAAAATTTTTTGA
*
22855679 AAACACGAAAA-ATTTTG-
1 AAACACGAAAATTTTTTGA
*
22855696 AAACAC-AAACTTTTTT
1 AAACACGAAAATTTTTT
22855712 TTATAAATTA
Statistics
Matches: 132, Mismatches: 19, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.02
17 30 0.23
18 46 0.35
19 36 0.27
20 11 0.08
21 6 0.05
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (19 bp):
AAACACGAAAATTTTTTGA
Found at i:22855713 original size:38 final size:36
Alignment explanation
Indices: 22855598--22855712 Score: 160
Period size: 38 Copynumber: 3.1 Consensus size: 36
22855588 AACACAAAAA
* **
22855598 TTTTTGAAAACAAGAATTTTTTTGAAACACGAAATT
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAATT
22855634 TTTTTGAAAACACGAAAATTTTTGAAACACTGGAAATT
1 TTTTTGAAAACACGAAAATTTTTGAAACAC--GAAATT
*
22855672 TTTTTGAAAACACGAAAAATTTTGAAACAC-AAACTT
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAA-TT
22855708 TTTTT
1 TTTTT
22855713 TATAAATTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
35 3 0.04
36 34 0.47
38 35 0.49
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (36 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGAAATT
Found at i:22855915 original size:5 final size:5
Alignment explanation
Indices: 22855905--22855945 Score: 73
Period size: 5 Copynumber: 8.0 Consensus size: 5
22855895 CCTTATTTAT
22855905 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA CTAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA -TAAAA
22855946 ACATAAACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:22856281 original size:11 final size:11
Alignment explanation
Indices: 22856267--22856306 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
22856257 CTTTTGGGCC
22856267 TTTTTTCTCTT
1 TTTTTTCTCTT
22856278 TTTTTTCCTCTCT
1 TTTTTT-CTCT-T
22856291 TTTTTTCTTCTT
1 TTTTTTC-TCTT
22856303 TTTT
1 TTTT
22856307 CTGTTGGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 6 0.23
12 10 0.38
13 10 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:22856288 original size:12 final size:12
Alignment explanation
Indices: 22856267--22856306 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
22856257 CTTTTGGGCC
22856267 TTTTTT-CTCTT
1 TTTTTTCCTCTT
22856278 TTTTTTCCTCTCT
1 TTTTTTCCTCT-T
*
22856291 TTTTTTCTTCTT
1 TTTTTTCCTCTT
22856303 TTTT
1 TTTT
22856307 CTGTTGGGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 9 0.35
13 11 0.42
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTCCTCTT
Found at i:22856307 original size:10 final size:11
Alignment explanation
Indices: 22856266--22856308 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
22856256 ACTTTTGGGC
22856266 CTTTTTTCTCT
1 CTTTTTTCTCT
*
22856277 TTTTTTTCCTCT
1 CTTTTTT-CTCT
22856289 CTTTTTT-TCTT
1 CTTTTTTCTC-T
22856300 CTTTTTTCT
1 CTTTTTTCT
22856309 GTTGGGCCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.07
11 14 0.52
12 11 0.41
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
CTTTTTTCTCT
Found at i:22856839 original size:29 final size:29
Alignment explanation
Indices: 22856794--22856960 Score: 183
Period size: 30 Copynumber: 5.7 Consensus size: 29
22856784 GCAAAACTTC
*
22856794 TAGGGTCAAAATGTAATTTTAAGAAAATT
1 TAGGGTCAAAATGTAATTTCAAGAAAATT
* * *
22856823 TAAGGTCAAAATGTAATTTAAAGAAAGTT
1 TAGGGTCAAAATGTAATTTCAAGAAAATT
* *
22856852 TAGGGATTAAAATGTAATTTCAAGAAATTT
1 TAGGG-TCAAAATGTAATTTCAAGAAAATT
** *
22856882 TAGGGGTTGAAATGTAATTTCAAGAAAGTT
1 TA-GGGTCAAAATGTAATTTCAAGAAAATT
* *
22856912 TAAGGGTTAAAATGTAATTTCAA-AAAAGT
1 T-AGGGTCAAAATGTAATTTCAAGAAAATT
*
22856941 TAGGTGTCAAAATGCAATTT
1 TAGG-GTCAAAATGTAATTT
22856961 GTTTTTTTAA
Statistics
Matches: 120, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
28 3 0.03
29 48 0.40
30 65 0.54
31 4 0.03
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (29 bp):
TAGGGTCAAAATGTAATTTCAAGAAAATT
Found at i:22856909 original size:60 final size:59
Alignment explanation
Indices: 22856795--22856960 Score: 201
Period size: 59 Copynumber: 2.8 Consensus size: 59
22856785 CAAAACTTCT
* *
22856795 AGGGTCAAAATGTAATTTTAAGAAAATTTAAGGTCAAAATGTAATTTAAAGAAAGTTT-
1 AGGGTTAAAATGTAATTTCAAGAAAATTTAAGGTCAAAATGTAATTTAAAGAAAGTTTA
* * ** *
22856853 AGGGATTAAAATGTAATTTCAAGAAATTTTAGGGGTTGAAATGTAATTTCAAGAAAGTTTA
1 AGGG-TTAAAATGTAATTTCAAGAAAATTTA-AGGTCAAAATGTAATTTAAAGAAAGTTTA
* * *
22856914 AGGGTTAAAATGTAATTTCAA-AAAAGTTAGGTGTCAAAATGCAATTT
1 AGGGTTAAAATGTAATTTCAAGAAAATTTAAG-GTCAAAATGTAATTT
22856961 GTTTTTTTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
58 6 0.07
59 41 0.45
60 41 0.45
61 4 0.04
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.33
Consensus pattern (59 bp):
AGGGTTAAAATGTAATTTCAAGAAAATTTAAGGTCAAAATGTAATTTAAAGAAAGTTTA
Found at i:22861541 original size:21 final size:21
Alignment explanation
Indices: 22861517--22861584 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
22861507 CAGTGGTGGT
* * *
22861517 GGTGAGATTAGTTACCGTAGT
1 GGTGAGATTAGATACTGTAGC
22861538 GGTGAGATTAGATACTGTAGC
1 GGTGAGATTAGATACTGTAGC
22861559 GGTGAGATTAGATACTGTAGC
1 GGTGAGATTAGATACTGTAGC
22861580 GGTGA
1 GGTGA
22861585 ATGTGTGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.26, C:0.09, G:0.35, T:0.29
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAGC
Found at i:22861849 original size:33 final size:34
Alignment explanation
Indices: 22861782--22861849 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
22861772 AATAAAATTT
* *
22861782 AAATATTTTTAACTTATATTAATAATAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
* *
22861816 AAATATATTTAAATTAT-TTTATATTAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
22861849 A
1 A
22861850 TTAAACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
AAATATATTTAAATTATATTAATAATAAATAATA
Found at i:22867639 original size:32 final size:33
Alignment explanation
Indices: 22867572--22867643 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
22867562 TCAAAAAGCT
*
22867572 AATATTTTCTGATGTTTGGATGAATTTGTGTAA
1 AATATTTTATGATGTTTGGATGAATTTGTGTAA
*
22867605 AATATTTTATGTTGTTTGGCA-G-ATTTGCTG-AA
1 AATATTTTATGATGTTTGG-ATGAATTTG-TGTAA
22867637 AATATTT
1 AATATTT
22867644 CATAAAAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 14 0.40
33 20 0.57
34 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (33 bp):
AATATTTTATGATGTTTGGATGAATTTGTGTAA
Found at i:22872620 original size:5 final size:5
Alignment explanation
Indices: 22872610--22872702 Score: 186
Period size: 5 Copynumber: 18.6 Consensus size: 5
22872600 TATATTTAGC
22872610 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
22872660 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
22872703 GTATGCATAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 88 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:22873409 original size:23 final size:24
Alignment explanation
Indices: 22873364--22873409 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
22873354 TTATGTAACT
22873364 TTTAATTTGTTTGGAATTATTATG
1 TTTAATTTGTTTGGAATTATTATG
*
22873388 TTTAATTTGTTT-GTATTATTAT
1 TTTAATTTGTTTGGAATTATTAT
22873410 TTAACTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (24 bp):
TTTAATTTGTTTGGAATTATTATG
Found at i:22873898 original size:17 final size:16
Alignment explanation
Indices: 22873872--22873905 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
22873862 ATAACAATTT
*
22873872 TTAATTTGTTATTTAA
1 TTAATTTGTTAATTAA
22873888 TTAATTTTGTTAATTAA
1 TTAA-TTTGTTAATTAA
22873905 T
1 T
22873906 ACTTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAATTTGTTAATTAA
Found at i:22882429 original size:133 final size:134
Alignment explanation
Indices: 22882247--22882540 Score: 288
Period size: 134 Copynumber: 2.2 Consensus size: 134
22882237 TTTTGTCAAT
** * * * ** ** *
22882247 TATCGATAAATTTAAATGAGTATCGATAGATTCACAAATATATCGATACA-TTTTTTGTATTGAT
1 TATCGATAAATTTATTTAAGTATCGATAGATACACAAATATATCAATACACTTTTTAATATCAAA
* * * * * *
22882311 ACGAAAATGACATTTT-ATTTTCCAAAATATTTACCAAGTATCGATTCGGTATTGATACCTTTTG
66 ACGAAAATGACATTTTGA-CTTCCAAAAGATTCACCAAGTATCAATACGGTATCGATACCTTTTG
*
22882375 TTTGG
130 TTTAG
** *
22882380 TATCGATAAATTTATTTAAGTATCGATAG-TAACACACCTTTATCAATACACTTTTTAATATCAA
1 TATCGATAAATTTATTTAAGTATCGATAGAT-ACACAAATATATCAATACACTTTTTAATATCAA
* * * * **
22882444 AACTAAATTGGCATTTTGACTTCCAAAGGATTCATTAAGTATCAATACGGTATCGATACCTTTTG
65 AACGAAAATGACATTTTGACTTCCAAAAGATTCACCAAGTATCAATACGGTATCGATACCTTTTG
22882509 TTTAG
130 TTTAG
* **
22882514 TATCGATAAAATTATTTTGGTATCGAT
1 TATCGATAAATTTATTTAAGTATCGAT
22882541 CAAAATGCTT
Statistics
Matches: 129, Mismatches: 29, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
132 1 0.01
133 40 0.31
134 87 0.67
135 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (134 bp):
TATCGATAAATTTATTTAAGTATCGATAGATACACAAATATATCAATACACTTTTTAATATCAAA
ACGAAAATGACATTTTGACTTCCAAAAGATTCACCAAGTATCAATACGGTATCGATACCTTTTGT
TTAG
Found at i:22889397 original size:30 final size:30
Alignment explanation
Indices: 22889363--22889462 Score: 134
Period size: 30 Copynumber: 3.3 Consensus size: 30
22889353 ACCAAAAATT
22889363 TATTTTAAAAATTTAAAAAAATTAAAAAAG
1 TATTTTAAAAATTTAAAAAAATTAAAAAAG
**
22889393 TATTTTAAAAATATT-TTAAAATTAAAAAAG
1 TATTTTAAAAAT-TTAAAAAAATTAAAAAAG
22889423 TATTTT-AAAA-TTAAAAAAATTAAAAAAAAG
1 TATTTTAAAAATTTAAAAAAATT--AAAAAAG
22889453 TATTTTAAAA
1 TATTTTAAAA
22889463 GTATTTTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
27 2 0.03
28 6 0.10
29 4 0.07
30 44 0.72
31 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
TATTTTAAAAATTTAAAAAAATTAAAAAAG
Found at i:22889402 original size:19 final size:18
Alignment explanation
Indices: 22889399--22889440 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
22889389 AAAGTATTTT
22889399 AAAAATATTTTAAAATTA
1 AAAAATATTTTAAAATTA
22889417 AAAAAGTATTTTAAAATTA
1 AAAAA-TATTTTAAAATTA
22889436 AAAAA
1 AAAAA
22889441 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATATTTTAAAATTA
Found at i:22889429 original size:60 final size:60
Alignment explanation
Indices: 22889363--22889482 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
22889353 ACCAAAAATT
22889363 TATTTTAAAAATTTAAAAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAA-TTAAAAAAG
1 TATTTT-AAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAG
*
22889423 TATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAGTATTTTAAAATTTAAAAAA
1 TATTTTAAAATTAAAAAAATT-AAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAA
22889483 TAAAAAATAA
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
58 11 0.20
59 4 0.07
60 33 0.59
61 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (60 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAG
Found at i:22889462 original size:11 final size:11
Alignment explanation
Indices: 22889448--22889473 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22889438 AAAATTAAAA
22889448 AAAAGTATTTT
1 AAAAGTATTTT
22889459 AAAAGTATTTT
1 AAAAGTATTTT
22889470 AAAA
1 AAAA
22889474 TTTAAAAAAT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:22889481 original size:30 final size:29
Alignment explanation
Indices: 22889363--22889482 Score: 127
Period size: 30 Copynumber: 4.0 Consensus size: 29
22889353 ACCAAAAATT
*
22889363 TATTTTAAAA-ATTTAAAAAAATTAAAAAAG
1 TATTTTAAAATATTT--TAAAATTAAAAAAG
22889393 TATTTTAAAAATATTTTAAAATTAAAAAAG
1 TATTTT-AAAATATTTTAAAATTAAAAAAG
***
22889423 TATTTTAAAAT-TAAAAAAATTAAAAAAAAG
1 TATTTTAAAATATTTTAAAATT--AAAAAAG
22889453 TATTTTAAAAGTATTTTAAAATTTAAAAAA
1 TATTTTAAAA-TATTTTAAAA-TTAAAAAA
22889483 TAAAAAATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
28 7 0.09
29 5 0.07
30 42 0.55
31 11 0.14
32 9 0.12
33 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
TATTTTAAAATATTTTAAAATTAAAAAAG
Found at i:22892363 original size:24 final size:25
Alignment explanation
Indices: 22892322--22892378 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
22892312 TGCTTTTAAA
*
22892322 GGACAAAATAAAAACCATGAAATTGT
1 GGAC-AAATAAAAACCATGAAACTGT
22892348 GGACAAAT-AAAACCATGAAACTGT
1 GGACAAATAAAAACCATGAAACTGT
*
22892372 GAACAAA
1 GGACAAA
22892379 CCATGATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 21 0.72
25 4 0.14
26 4 0.14
ACGTcount: A:0.54, C:0.14, G:0.16, T:0.16
Consensus pattern (25 bp):
GGACAAATAAAAACCATGAAACTGT
Found at i:22894366 original size:13 final size:13
Alignment explanation
Indices: 22894325--22894390 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
22894315 TAGATTTTTC
*
22894325 TTAAATATTATTA
1 TTAAATATTATCA
*
22894338 CTAAATA--ATC-
1 TTAAATATTATCA
22894348 TTAAATATTATCA
1 TTAAATATTATCA
*
22894361 TTAAATAAT-TC-
1 TTAAATATTATCA
22894372 -TAAATATTATCA
1 TTAAATATTATCA
22894384 TTAAATA
1 TTAAATA
22894391 ATTTAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 13 0.31
11 4 0.10
12 5 0.12
13 20 0.48
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATATTATCA
Found at i:22894399 original size:23 final size:22
Alignment explanation
Indices: 22894325--22894397 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 22
22894315 TAGATTTTTC
* *
22894325 TTAAATATTATTACTAAATAAT
1 TTAAATATTATCATTAAATAAT
22894347 CTTAAATATTATCATTAAATAAT
1 -TTAAATATTATCATTAAATAAT
22894370 TCTAAATATTATCATTAAATAAT
1 T-TAAATATTATCATTAAATAAT
22894393 TTAAA
1 TTAAA
22894398 ATTTAAACTA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 5 0.11
23 42 0.89
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAATATTATCATTAAATAAT
Found at i:22903332 original size:15 final size:15
Alignment explanation
Indices: 22903312--22903341 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22903302 GAGTTAGAAC
22903312 TTAATTACAAATTAT
1 TTAATTACAAATTAT
*
22903327 TTAATTACTAATTAT
1 TTAATTACAAATTAT
22903342 ATATGTCTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTACAAATTAT
Found at i:22905769 original size:29 final size:29
Alignment explanation
Indices: 22905727--22905830 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 29
22905717 CACCACTGGT
22905727 ACATAGTACCTGATAAATATAACATCGGC
1 ACATAGTACCTGATAAATATAACATCGGC
* * * *
22905756 ACATAGTGCCTGATAAATAGAACA-CAGT
1 ACATAGTACCTGATAAATATAACATCGGC
* * *
22905784 ACAAAGTACCTAATAAATATAACCATGGGC
1 ACATAGTACCTGATAAATATAA-CATCGGC
* *
22905814 ACTTAGTGCCTGATAAA
1 ACATAGTACCTGATAAA
22905831 CCCTAATGAC
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
28 20 0.34
29 24 0.41
30 14 0.24
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (29 bp):
ACATAGTACCTGATAAATATAACATCGGC
Found at i:22908591 original size:26 final size:25
Alignment explanation
Indices: 22908520--22908590 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
22908510 TTAAATATAT
22908520 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTGATTAAAAATAAAA
22908545 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTGATTAAAAATAAAA
*
22908570 ATATATATATTTAATATAAAA
1 A-ATATATATTTGAT-TAAAA
22908591 TTCATGCTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
25 26 0.60
26 12 0.28
27 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
AATATATATTTGATTAAAAATAAAA
Found at i:22912513 original size:27 final size:27
Alignment explanation
Indices: 22912482--22912536 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
22912472 AAATAGTTTT
22912482 CTTGCATATGGAAAACTAAAATTTTGA
1 CTTGCATATGGAAAACTAAAATTTTGA
*
22912509 CTTGCATATGGAAAATTAAAATTTTGA
1 CTTGCATATGGAAAACTAAAATTTTGA
22912536 C
1 C
22912537 AATCGAGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (27 bp):
CTTGCATATGGAAAACTAAAATTTTGA
Found at i:22913477 original size:78 final size:78
Alignment explanation
Indices: 22913348--22913539 Score: 357
Period size: 78 Copynumber: 2.5 Consensus size: 78
22913338 TTTTTCGTCC
*
22913348 TTTGTGGGTGCGGTGAATGGGTTGTTTTCTCATTTGGGTGAAATCTGGAATATGGAGCAACTTAG
1 TTTGTGGGTGCGATGAATGGGTTGTTTTCTCATTTGGGTGAAATCTGGAATATGGAGCAACTTAG
22913413 GCTTAGGTTTCAG
66 GCTTAGGTTTCAG
22913426 TTTGTGGGTGCGATGAATGGGTTGTTTTCTCATTTGGGTGAAATCTGGAATATGGAGCAACTTAG
1 TTTGTGGGTGCGATGAATGGGTTGTTTTCTCATTTGGGTGAAATCTGGAATATGGAGCAACTTAG
22913491 GCTTAGGTTTCAG
66 GCTTAGGTTTCAG
* *
22913504 TTTGTGGGTGCGATAAATGGGTTGTTTTCTCCTTTG
1 TTTGTGGGTGCGATGAATGGGTTGTTTTCTCATTTG
22913540 TGGGTGCAAT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 111 1.00
ACGTcount: A:0.18, C:0.10, G:0.32, T:0.39
Consensus pattern (78 bp):
TTTGTGGGTGCGATGAATGGGTTGTTTTCTCATTTGGGTGAAATCTGGAATATGGAGCAACTTAG
GCTTAGGTTTCAG
Found at i:22914161 original size:13 final size:13
Alignment explanation
Indices: 22914143--22914169 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22914133 AGTGAGAAAA
22914143 CCACATTCATTTT
1 CCACATTCATTTT
22914156 CCACATTCATTTT
1 CCACATTCATTTT
22914169 C
1 C
22914170 AGATGTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (13 bp):
CCACATTCATTTT
Found at i:22918037 original size:43 final size:43
Alignment explanation
Indices: 22917974--22918210 Score: 252
Period size: 43 Copynumber: 5.6 Consensus size: 43
22917964 ATTTCATGTG
*
22917974 AGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTACGTGTA
1 AGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTA
* *
22918017 AGACCACGTTTGGGACGTTGGCATTGACTTGTGTTTACGTGTA
1 AGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTA
22918060 AGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTA
1 AGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTA
* ** * *
22918103 AGACCATGTCTGAAACATTGGCATCGTA-TT-TGATT-CGTGTA
1 AGACCACGTCTGGGACGTTGGCATCG-ACTTGTGTTTACGTGTA
* * * ** * *
22918144 AGACC-CTGTCTGAGACAG-TGGAATTGA-TATAAGATTACATGTA
1 AGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGTTTACGTGTA
*
22918187 AGACCACGTCTGGGATGTTGGCAT
1 AGACCACGTCTGGGACGTTGGCAT
22918211 TGTATGATAT
Statistics
Matches: 166, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.01
41 26 0.16
42 9 0.05
43 127 0.77
44 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
AGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTA
Found at i:22922997 original size:39 final size:39
Alignment explanation
Indices: 22922916--22922990 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
22922906 TTTTTAAGAA
* *
22922916 TTTACTAATGTTTTTAATGATTTATCAATATATCTAAAT
1 TTTACTAATGATTTTAAAGATTTATCAATATATCTAAAT
*
22922955 TTTACTAAT-ATTTTAAAGATTTATCAATATTTCTAA
1 TTTACTAATGATTTTAAAGATTTATCAATATATCTAA
22922991 GCTTTTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 24 0.73
39 9 0.27
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (39 bp):
TTTACTAATGATTTTAAAGATTTATCAATATATCTAAAT
Found at i:22923043 original size:20 final size:20
Alignment explanation
Indices: 22922928--22923061 Score: 79
Period size: 20 Copynumber: 7.0 Consensus size: 20
22922918 TACTAATGTT
*
22922928 TTTAATGATTTATCAATATA
1 TTTAAAGATTTATCAATATA
* *
22922948 TCTAAA-TTTTA-CTAATAT-
1 TTTAAAGATTTATC-AATATA
22922966 TTTAAAGATTTATCAATAT-
1 TTTAAAGATTTATCAATATA
*
22922985 TTCT-AAGCTTTTATCAA-A-A
1 TT-TAAAG-ATTTATCAATATA
* ** *
22923004 -TTGATCATTTA-CAAAAATA
1 TTTAAAGATTTATC-AATATA
22923023 TTTAAAGATTTATCAATATA
1 TTTAAAGATTTATCAATATA
* *
22923043 TATAAATATTTATCAATAT
1 TTTAAAGATTTATCAATAT
22923062 TTCTAAGACT
Statistics
Matches: 87, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
16 1 0.01
17 7 0.08
18 9 0.10
19 25 0.29
20 44 0.51
21 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
TTTAAAGATTTATCAATATA
Found at i:22923060 original size:10 final size:10
Alignment explanation
Indices: 22923030--22923063 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
22923020 ATATTTAAAG
22923030 ATTTATCAAT
1 ATTTATCAAT
* *
22923040 ATATATAAAT
1 ATTTATCAAT
22923050 ATTTATCAAT
1 ATTTATCAAT
22923060 ATTT
1 ATTT
22923064 CTAAGACTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTTATCAAT
Found at i:22929573 original size:13 final size:13
Alignment explanation
Indices: 22929555--22929583 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22929545 AAAAGGCAAG
22929555 TATTCTTGGGTAA
1 TATTCTTGGGTAA
22929568 TATTCTTGGGTAA
1 TATTCTTGGGTAA
22929581 TAT
1 TAT
22929584 ATTTGTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (13 bp):
TATTCTTGGGTAA
Found at i:22933881 original size:16 final size:16
Alignment explanation
Indices: 22933860--22933898 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
22933850 AGATAATATA
22933860 GCATATAAACTTTAAT
1 GCATATAAACTTTAAT
22933876 GCATATAAACTTTAAT
1 GCATATAAACTTTAAT
22933892 GCATATA
1 GCATATA
22933899 TCCATAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (16 bp):
GCATATAAACTTTAAT
Found at i:22936044 original size:25 final size:25
Alignment explanation
Indices: 22935991--22936038 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
22935981 AAAAAAGGTT
22935991 AAAATTTCAAAAAAAATTAAAAATA
1 AAAATTTCAAAAAAAATTAAAAATA
* *
22936016 AAAATTTCACAAAATA-TAAAAAT
1 AAAATTTCAAAAAAAATTAAAAAT
22936039 TCAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAATTTCAAAAAAAATTAAAAATA
Found at i:22936049 original size:17 final size:17
Alignment explanation
Indices: 22936009--22936049 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
22935999 AAAAAAAATT
*
22936009 AAAAATA-AAAATTTCA
1 AAAAATATAAAAATTCA
*
22936025 CAAAATATAAAAATTCA
1 AAAAATATAAAAATTCA
22936042 AAAAATAT
1 AAAAATAT
22936050 TTAGAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATAAAAATTCA
Found at i:22936266 original size:10 final size:10
Alignment explanation
Indices: 22936226--22936268 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
22936216 TTTTGAAAAC
22936226 TAAATTATTATT
1 TAAATT-TT-TT
*
22936238 TAAATTTTCT
1 TAAATTTTTT
22936248 TAAATTTTTT
1 TAAATTTTTT
*
22936258 TATATTTTTT
1 TAAATTTTTT
22936268 T
1 T
22936269 CCATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 20 0.71
11 2 0.07
12 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TAAATTTTTT
Found at i:22936425 original size:47 final size:46
Alignment explanation
Indices: 22936371--22936464 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 46
22936361 TATATTTTTC
* *
22936371 AATTTTTTATACTTTTTGAAATTTAAACTAAGT-TTTTTTAATTTTTAA
1 AATTTTTT-CACTTTTTGAAATTTAAA-TAA-TCTTTTTAAATTTTTAA
** *
22936419 AATTTTTTCACTTTTTTTAATTTATATAATCTTTTTAAATTTTTAA
1 AATTTTTTCACTTTTTGAAATTTAAATAATCTTTTTAAATTTTTAA
22936465 GGTTTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 1 0.03
46 17 0.43
47 14 0.35
48 8 0.20
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (46 bp):
AATTTTTTCACTTTTTGAAATTTAAATAATCTTTTTAAATTTTTAA
Found at i:22936461 original size:27 final size:27
Alignment explanation
Indices: 22936404--22936462 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
22936394 TAAACTAAGT
* **
22936404 TTTTTTAATTTTTAAAATTTTTTCACT
1 TTTTTTAATTTATAAAATTTTTTCAAA
*
22936431 TTTTTTAATTTATATAATCTTTTT-AAA
1 TTTTTTAATTTATAAAAT-TTTTTCAAA
22936458 TTTTT
1 TTTTT
22936463 AAGGTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTTTAATTTATAAAATTTTTTCAAA
Found at i:22945451 original size:41 final size:41
Alignment explanation
Indices: 22945400--22945493 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
22945390 CTCGGGGATT
* *
22945400 TAGCGACGTTTTCCAAGAAGCACCGATAATGCTCGGGACTA
1 TAGCGGCGTTTTCCAAGAAACACCGATAATGCTCGGGACTA
* * *
22945441 TAGCGGCGTTTTCCAAGAAACGCCGCTAATGCTCGGGACTT
1 TAGCGGCGTTTTCCAAGAAACACCGATAATGCTCGGGACTA
22945482 TAGCGGCGTTTT
1 TAGCGGCGTTTT
22945494 TGAAAAACCG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (41 bp):
TAGCGGCGTTTTCCAAGAAACACCGATAATGCTCGGGACTA
Found at i:22946182 original size:40 final size:40
Alignment explanation
Indices: 22946101--22946182 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
22946091 CGTGTATAAT
* * * *
22946101 AAACGCCGCAAAAGATCATCATTAGTGGCGTTTATATAAA
1 AAACACCGCAAAAGATCAGCATTAGCGGCGTTTATAGAAA
* *
22946141 AAACACCGCAAAA-ATCTAGCATTAGCGGTGTTTCTAGAAA
1 AAACACCGCAAAAGATC-AGCATTAGCGGCGTTTATAGAAA
22946181 AA
1 AA
22946183 TGCCCAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.09
40 32 0.91
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.23
Consensus pattern (40 bp):
AAACACCGCAAAAGATCAGCATTAGCGGCGTTTATAGAAA
Found at i:22946418 original size:113 final size:111
Alignment explanation
Indices: 22946208--22946471 Score: 291
Period size: 113 Copynumber: 2.4 Consensus size: 111
22946198 AAACAAAATG
* * * * * *
22946208 CACCGTTCGTTGTTGAGCTATAATGGCATTAGTGACGCTTAATAAAAAACGCCGCTATAAATCGG
1 CACCGTTCGATCTTGAGCTATAGTGGCATTAGCGGCGC-TAATAAAAAACGCCACTATAAATCGG
* *
22946273 TATTAACGGCGCTTCTAGAAATACGCCACAAAAATGTTAACTAAAACA
65 TATTAACGGCGCTTCTAGAAATACACCACAAAAA-GTTAACCAAAACA
* * *
22946321 CACCGTTCGATCTTGAGCTATAGTGGCGTTAGCGGCGCTAACTTAAAAACGCCACTA-AAGATTG
1 CACCGTTCGATCTTGAGCTATAGTGGCATTAGCGGCGCTAA-TAAAAAACGCCACTATAA-ATCG
* *
22946385 GTATTAACGGCGCTTAATTA-AAA-ACACCGCAAAAAGTTAACCAAAACA
64 GTATTAACGGCGCTT--CTAGAAATACACCACAAAAAGTTAACCAAAACA
* * * * *
22946433 CATCATTTGGTCTTGAGCTATAGTGCCATTAGCGGCGCT
1 CACCGTTCGATCTTGAGCTATAGTGGCATTAGCGGCGCT
22946472 TTTCTAAAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
112 50 0.39
113 73 0.57
114 3 0.02
115 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (111 bp):
CACCGTTCGATCTTGAGCTATAGTGGCATTAGCGGCGCTAATAAAAAACGCCACTATAAATCGGT
ATTAACGGCGCTTCTAGAAATACACCACAAAAAGTTAACCAAAACA
Found at i:22946960 original size:21 final size:20
Alignment explanation
Indices: 22946931--22946981 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
22946921 AGGTTTGGGT
* *
22946931 TTTATGGTTTAGGATTTATAG
1 TTTAAGGTTTAAGATTTAT-G
22946952 TTTAAGGTTTAAGATTTATG
1 TTTAAGGTTTAAGATTTATG
*
22946972 GTTAAGGTTT
1 TTTAAGGTTT
22946982 TTGGTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (20 bp):
TTTAAGGTTTAAGATTTATG
Found at i:22946962 original size:14 final size:14
Alignment explanation
Indices: 22946882--22946955 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
22946872 CAAAGATATG
*
22946882 GTTTAGGA-TTATG
1 GTTTAGGATTTATA
22946895 GTTTAGGATTTATA
1 GTTTAGGATTTATA
*
22946909 GTTTA-GAGTTCA-A
1 GTTTAGGA-TTTATA
* * *
22946922 GGTTTGGGTTTTATG
1 -GTTTAGGATTTATA
22946937 GTTTAGGATTTATA
1 GTTTAGGATTTATA
22946951 GTTTA
1 GTTTA
22946956 AGGTTTAAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
13 11 0.23
14 35 0.74
15 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (14 bp):
GTTTAGGATTTATA
Found at i:22947093 original size:21 final size:21
Alignment explanation
Indices: 22947039--22947094 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
22947029 TGTGGTTGAC
* * *
22947039 GGGTTTATTGTTTATGGTTTA
1 GGGTTTAGTGTTTACGATTTA
*
22947060 GGGTTTAGGGTTTACGATTTA
1 GGGTTTAGTGTTTACGATTTA
22947081 GGGTATT-GTGTTTA
1 GGGT-TTAGTGTTTA
22947095 ATTTGGGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.16, C:0.02, G:0.32, T:0.50
Consensus pattern (21 bp):
GGGTTTAGTGTTTACGATTTA
Found at i:22949420 original size:16 final size:16
Alignment explanation
Indices: 22949399--22949814 Score: 89
Period size: 16 Copynumber: 24.7 Consensus size: 16
22949389 CTTATATATA
22949399 AACTTACATAATACAT
1 AACTTACATAATACAT
* *
22949415 AACTTAAATAAAATTTATATAT
1 AACTTACAT--AA--TACA--T
22949437 AAACTTACATAATACAT
1 AA-CTTACATAATACAT
22949454 AACTTACATAATAACTTACAT
1 AACTTAC---ATAA--TACAT
* *
22949475 AACTTATATATAAACTGGCAT
1 AACTTACATA-ATAC----AT
22949496 AACTTACATAATAACATAAT
1 AACTTACATAAT-AC---AT
22949516 AACTTACATAATACAT
1 AACTTACATAATACAT
* * *
22949532 AGCCTACACAACTTACATAAAT
1 AACTTACATAA--TAC---A-T
22949554 AACTTACATAATACAT
1 AACTTACATAATACAT
*
22949570 AACTTTCATAACTTACATT
1 AACTTACATAA--TACA-T
* *
22949589 ATAC--ACATTATACAC
1 A-ACTTACATAATACAT
22949604 AACTTACAT-A-AC-T
1 AACTTACATAATACAT
* *
22949617 TACTTA-ATATTATACAC
1 AACTTACATA--ATACAT
22949634 AACTTACATAATAC--
1 AACTTACATAATACAT
*
22949648 -A-TTAC-T--TAAAT
1 AACTTACATAATACAT
* *
22949659 AACTTACATTATACAC
1 AACTTACATAATACAT
*
22949675 AACTTACAT-A-ACTT
1 AACTTACATAATACAT
* * * *
22949689 AA-TTATATTATAGAC
1 AACTTACATAATACAT
22949704 AACTTACATAAATTACAT
1 AACTTACAT-AA-TACAT
22949722 AA--TACATAACTTACAT
1 AACTTACATAA--TACAT
* *
22949738 AACTTACATTATACAC
1 AACTTACATAATACAT
22949754 AACTTACATAACTTACAT
1 AACTTACATAA--TACAT
* *
22949772 -TC-TACACAACTTACAT
1 AACTTACATAA--TACAT
*
22949788 AACTTATATAATACAT
1 AACTTACATAATACAT
*
22949804 AACTCACATAA
1 AACTTACATAA
22949815 CCTACATAAT
Statistics
Matches: 296, Mismatches: 49, Indels: 110
0.65 0.11 0.24
Matches are distributed among these distances:
9 2 0.01
11 1 0.00
12 7 0.02
13 15 0.05
14 10 0.03
15 9 0.03
16 119 0.40
17 14 0.05
18 39 0.13
19 12 0.04
20 23 0.08
21 27 0.09
22 12 0.04
23 6 0.02
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:22949433 original size:39 final size:39
Alignment explanation
Indices: 22949390--22949464 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
22949380 ATATCATAAC
22949390 TTATATATAAACTTACATAATACATAACTTAAATAAAAT
1 TTATATATAAACTTACATAATACATAACTTAAATAAAAT
*
22949429 TTATATATAAACTTACATAATACATAACTTACATAA
1 TTATATATAAACTTACATAATACATAACTTAAATAA
22949465 TAACTTACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (39 bp):
TTATATATAAACTTACATAATACATAACTTAAATAAAAT
Found at i:22949463 original size:9 final size:9
Alignment explanation
Indices: 22949438--22949848 Score: 182
Period size: 9 Copynumber: 47.2 Consensus size: 9
22949428 TTTATATATA
22949438 AACTTACAT
1 AACTTACAT
22949447 AA--TACAT
1 AACTTACAT
22949454 AACTTACATAAT
1 AACTTAC---AT
22949466 AACTTACAT
1 AACTTACAT
*
22949475 AACTTATATAT
1 AAC-T-TACAT
**
22949486 AAACTGGCAT
1 -AACTTACAT
22949496 AACTTACAT
1 AACTTACAT
*
22949505 AA-TAACATAAT
1 AACTTAC---AT
22949516 AACTTACAT
1 AACTTACAT
22949525 AA--TACAT
1 AACTTACAT
* * *
22949532 AGCCTACAC
1 AACTTACAT
22949541 AACTTACAT
1 AACTTACAT
22949550 -A---A-AT
1 AACTTACAT
22949554 AACTTACAT
1 AACTTACAT
22949563 AA--TACAT
1 AACTTACAT
*
22949570 AACTTTCAT
1 AACTTACAT
22949579 AACTTACATT
1 AACTTACA-T
22949589 ATAC--ACAT
1 A-ACTTACAT
* *
22949597 TA--TACAC
1 AACTTACAT
22949604 AACTTACAT
1 AACTTACAT
*
22949613 AACTTACTT
1 AACTTACAT
* *
22949622 AATATTATACAC
1 -A-ACT-TACAT
22949634 AACTTACAT
1 AACTTACAT
22949643 AA--TACAT
1 AACTTACAT
* *
22949650 TACTTAAAT
1 AACTTACAT
22949659 AACTTACAT
1 AACTTACAT
* *
22949668 TA--TACAC
1 AACTTACAT
22949675 AACTTACAT
1 AACTTACAT
22949684 AACTTA-ATT
1 AACTTACA-T
* * *
22949693 ATATTATAGAC
1 A-ACT-TACAT
22949704 AACTTACAT
1 AACTTACAT
*
22949713 AAATTACAT
1 AACTTACAT
22949722 AA--TACAT
1 AACTTACAT
22949729 AACTTACAT
1 AACTTACAT
22949738 AACTTACAT
1 AACTTACAT
* *
22949747 TA--TACAC
1 AACTTACAT
22949754 AACTTACAT
1 AACTTACAT
22949763 AACTTACAT
1 AACTTACAT
* *
22949772 -TC-TACAC
1 AACTTACAT
22949779 AACTTACAT
1 AACTTACAT
*
22949788 AACTTATAT
1 AACTTACAT
22949797 AA--TACAT
1 AACTTACAT
*
22949804 AACTCACAT
1 AACTTACAT
*
22949813 AACCTACAT
1 AACTTACAT
*
22949822 AA--TACAC
1 AACTTACAT
22949829 AACTTACAT
1 AACTTACAT
*
22949838 AGCTTACAT
1 AACTTACAT
22949847 AA
1 AA
22949849 GTTGTCTTAT
Statistics
Matches: 299, Mismatches: 56, Indels: 94
0.67 0.12 0.21
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
7 64 0.21
8 9 0.03
9 174 0.58
10 12 0.04
11 17 0.06
12 19 0.06
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:22949469 original size:12 final size:12
Alignment explanation
Indices: 22949452--22949566 Score: 56
Period size: 12 Copynumber: 10.2 Consensus size: 12
22949442 TACATAATAC
22949452 ATAACTTACATA
1 ATAACTTACATA
22949464 ATAACTTAC---
1 ATAACTTACATA
*
22949473 ATAACTTATAT-
1 ATAACTTACATA
**
22949484 ATAAACTGGC--A
1 AT-AACTTACATA
22949495 -TAACTTACATA
1 ATAACTTACATA
22949506 AT-A---ACATA
1 ATAACTTACATA
22949514 ATAACTTACATA
1 ATAACTTACATA
* *
22949526 AT-ACATAGCCTA
1 ATAACTTA-CATA
*
22949538 CACAACTTACATAA
1 -ATAACTTACAT-A
22949552 ATAACTTACATA
1 ATAACTTACATA
22949564 ATA
1 ATA
22949567 CATAACTTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 30
0.64 0.10 0.25
Matches are distributed among these distances:
8 7 0.09
9 14 0.18
10 1 0.01
11 8 0.11
12 28 0.37
13 13 0.17
14 5 0.07
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:22949570 original size:20 final size:20
Alignment explanation
Indices: 22949494--22949571 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
22949484 ATAAACTGGC
22949494 ATAACTTACATAATAACAT-A
1 ATAACTTACATAAT-ACATAA
*
22949514 ATAACTTACATAATACATAGC
1 ATAACTTACATAATACATA-A
* *
22949535 CT-AC--ACA-ACTTACATAA
1 ATAACTTACATA-ATACATAA
22949552 ATAACTTACATAATACATAA
1 ATAACTTACATAATACATAA
22949572 CTTTCATAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
17 2 0.04
18 11 0.24
19 4 0.09
20 26 0.58
21 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.28
Consensus pattern (20 bp):
ATAACTTACATAATACATAA
Found at i:22949580 original size:25 final size:25
Alignment explanation
Indices: 22949552--22949848 Score: 274
Period size: 25 Copynumber: 11.5 Consensus size: 25
22949542 ACTTACATAA
* *
22949552 ATAACTTACATAATACATAACTTTC
1 ATAACTTACATAATACACAACTTAC
* *
22949577 ATAACTTACATTATACAC-ATTATAC
1 ATAACTTACATAATACACAACT-TAC
* *
22949602 ACAACTTACATAACTTACTTA-ATATTATAC
1 ATAACTTACATAA--TAC--ACA-ACT-TAC
* ** *
22949632 ACAACTTACATAATACATTACTTAA
1 ATAACTTACATAATACACAACTTAC
*
22949657 ATAACTTACATTATACACAACTTAC
1 ATAACTTACATAATACACAACTTAC
* *
22949682 ATAACTTAATTATATTATAGACAACTTAC
1 ATAACTT-A-CATA--ATACACAACTTAC
* *
22949711 ATAAATTACATAATACATAACTTAC
1 ATAACTTACATAATACACAACTTAC
*
22949736 ATAACTTACATTATACACAACTTAC
1 ATAACTTACATAATACACAACTTAC
**
22949761 ATAACTTACATTCTACACAACTTAC
1 ATAACTTACATAATACACAACTTAC
* * *
22949786 ATAACTTATATAATACATAACTCAC
1 ATAACTTACATAATACACAACTTAC
*
22949811 ATAACCTACATAATACACAACTTAC
1 ATAACTTACATAATACACAACTTAC
*
22949836 ATAGCTTACATAA
1 ATAACTTACATAA
22949849 GTTGTCTTAT
Statistics
Matches: 224, Mismatches: 36, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
24 2 0.01
25 167 0.75
26 4 0.02
27 8 0.04
28 4 0.02
29 19 0.08
30 20 0.09
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (25 bp):
ATAACTTACATAATACACAACTTAC
Done.