Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 69 of 187
Found at i:20341039 original size:25 final size:25
Alignment explanation
Indices: 20341011--20341064 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
20341001 AGCTCCGAAT
*
20341011 AGCCATATATTGGGAAG-TTCAAGCG
1 AGCCATATATTGGGAAGCTTC-AGAG
20341036 AGCC--ATATTGGGAAGCTTCAGAG
1 AGCCATATATTGGGAAGCTTCAGAG
20341059 AGCCAT
1 AGCCAT
20341065 TAATCAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 18 0.72
24 3 0.12
25 4 0.16
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
AGCCATATATTGGGAAGCTTCAGAG
Found at i:20341047 original size:23 final size:23
Alignment explanation
Indices: 20341017--20341064 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
20341007 GAATAGCCAT
*
20341017 ATATTGGGAAG-TTCAAGCGAGCC
1 ATATTGGGAAGCTTC-AGAGAGCC
20341040 ATATTGGGAAGCTTCAGAGAGCC
1 ATATTGGGAAGCTTCAGAGAGCC
20341063 AT
1 AT
20341065 TAATCAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (23 bp):
ATATTGGGAAGCTTCAGAGAGCC
Found at i:20341100 original size:26 final size:26
Alignment explanation
Indices: 20341057--20341125 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
20341047 GAAGCTTCAG
20341057 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* * *
20341083 AGAGCCTTTGATCGGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
20341109 AGAGCCA-TATATCAGGA
1 AGAGCCATTA-ATCAGGA
20341126 CGCTTATAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 1 0.03
26 35 0.97
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:20341188 original size:26 final size:26
Alignment explanation
Indices: 20341151--20341208 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
20341141 CGTGATATAT
*
20341151 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGATTCCCGATTAAA
* * *
20341177 GGCTCTTTGTGAGATTCCTGATTAAT
1 GGCTCTTCGTGAGATTCCCGATTAAA
20341203 GGCTCT
1 GGCTCT
20341209 CCGAAGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (26 bp):
GGCTCTTCGTGAGATTCCCGATTAAA
Found at i:20343171 original size:18 final size:18
Alignment explanation
Indices: 20343148--20343184 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20343138 GTAACTAGCT
20343148 AATCCCAGAAAGCTTCTA
1 AATCCCAGAAAGCTTCTA
20343166 AATCCCAGAAAGCTTCTA
1 AATCCCAGAAAGCTTCTA
20343184 A
1 A
20343185 CTTATGACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.22
Consensus pattern (18 bp):
AATCCCAGAAAGCTTCTA
Found at i:20348666 original size:27 final size:27
Alignment explanation
Indices: 20348514--20348655 Score: 203
Period size: 27 Copynumber: 5.3 Consensus size: 27
20348504 AGAGGTCAAT
20348514 AAATGACCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
*
20348541 AAATGACCGAATTACCCCCACAGGATA
1 AAATGACCGAATTACCCCCACAGGGTA
*
20348568 AAATGACCGAATTACCCTCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
20348595 AAATAACCGAATTACCCCCATAGGATA
1 AAATGACCGAATTACCCCCACAGGGTA
** * *
20348622 AAATGACTAAAATACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
20348649 AAATGAC
1 AAATGAC
20348656 TATTATACCC
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 103 1.00
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCACAGGGTA
Found at i:20349005 original size:28 final size:28
Alignment explanation
Indices: 20348971--20349050 Score: 142
Period size: 28 Copynumber: 2.9 Consensus size: 28
20348961 ACTGTACCGA
20348971 TACTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
20348999 TGCTGTATTGGGTTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
20349027 TACTGTATTGGGCTAAGGCCCACA
1 TACTGTATTGGGCTAAGGCCCACA
20349051 CTATACTGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:20360019 original size:15 final size:16
Alignment explanation
Indices: 20359999--20360031 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20359989 ATTAACCTTA
*
20359999 TTTATTT-ATTTTTAT
1 TTTATTTGACTTTTAT
20360014 TTTATTTGACTTTTAT
1 TTTATTTGACTTTTAT
20360030 TT
1 TT
20360032 AGTGAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTATTTGACTTTTAT
Found at i:20364126 original size:25 final size:25
Alignment explanation
Indices: 20364096--20364143 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
20364086 AGGTTTGTTT
20364096 GTGAAATTATTAAGGACTTTAATCA
1 GTGAAATTATTAAGGACTTTAATCA
**
20364121 GTGAAATTATTCGGGACTTTAAT
1 GTGAAATTATTAAGGACTTTAAT
20364144 GAGGACTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (25 bp):
GTGAAATTATTAAGGACTTTAATCA
Found at i:20364726 original size:22 final size:22
Alignment explanation
Indices: 20364683--20364726 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20364673 GAAAAATAGT
* *
20364683 TTATTTCTAAATTTTGTTTTTA
1 TTATGTCTAAATTTTGTATTTA
20364705 TTATGTCTAAA-TTTGATATTTA
1 TTATGTCTAAATTTTG-TATTTA
20364727 ATTTCTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (22 bp):
TTATGTCTAAATTTTGTATTTA
Found at i:20366229 original size:25 final size:26
Alignment explanation
Indices: 20366197--20366262 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 26
20366187 GTTAAAATGT
*
20366197 ATAA-ATATTTTTTTATTTAA-AAAA
1 ATAATATATTTTTTTATTAAATAAAA
* *
20366221 ATTATATATTTTTATATTAAATAAAA
1 ATAATATATTTTTTTATTAAATAAAA
*
20366247 ATAAT-TATTTATTTAT
1 ATAATATATTTTTTTAT
20366263 GTAATATGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 3 0.09
25 23 0.68
26 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATAATATATTTTTTTATTAAATAAAA
Found at i:20366232 original size:23 final size:22
Alignment explanation
Indices: 20366199--20366261 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
20366189 TAAAATGTAT
*
20366199 AAATATTTTTTTATTTAAA-AA
1 AAATATATTTTTATTTAAATAA
20366220 AATTATATATTTTTATATTAAATAA
1 AA--ATATATTTTTAT-TTAAATAA
20366245 AAATA-ATTATTTATTTA
1 AAATATATT-TTTATTTA
20366262 TGTAATATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
21 2 0.06
22 6 0.17
23 19 0.53
24 5 0.14
25 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATATATTTTTATTTAAATAA
Found at i:20369622 original size:16 final size:17
Alignment explanation
Indices: 20369591--20369624 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20369581 AACTTTGAAA
20369591 AAAATATTTAAAATATT
1 AAAATATTTAAAATATT
*
20369608 AAAAT-TTTTAAATATT
1 AAAATATTTAAAATATT
20369624 A
1 A
20369625 TGTTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATATTTAAAATATT
Found at i:20371603 original size:41 final size:41
Alignment explanation
Indices: 20371542--20371655 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
20371532 TTAATTTAAA
* * *
20371542 CAGATTCAACGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACATAGCCTGCTAGGCTTATAACCTGATT
* *
20371584 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACATAGCCTGCTAGGCTTATAACCTGATT
*
20371625 CAGATCACCGGCACATAGCCTGCTAGACTTA
1 CAGATCACCGGCACATAGCCTGCTAGGCTTA
20371656 AAGTCTGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 61 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (41 bp):
CAGATCACCGGCACATAGCCTGCTAGGCTTATAACCTGATT
Found at i:20375629 original size:18 final size:18
Alignment explanation
Indices: 20375606--20375650 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
20375596 GATTAGAATG
*
20375606 TAAAAATAAATTTTAAAA
1 TAAAAATAAATATTAAAA
*
20375624 TAAAAA-AAATATTAAGA
1 TAAAAATAAATATTAAAA
*
20375641 TTAAAATAAA
1 TAAAAATAAA
20375651 AAAATGGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATAAATATTAAAA
Found at i:20376825 original size:15 final size:15
Alignment explanation
Indices: 20376805--20376833 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20376795 AAGATTTATT
20376805 CGATCTGATCTGATC
1 CGATCTGATCTGATC
20376820 CGATCTGATCTGAT
1 CGATCTGATCTGAT
20376834 AAAATCCTTA
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:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (15 bp):
CGATCTGATCTGATC
Found at i:20382948 original size:24 final size:24
Alignment explanation
Indices: 20382917--20382981 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
20382907 CCACAGGTTG
20382917 TATGAGCTTACCGATTTCAGCTCA
1 TATGAGCTTACCGATTTCAGCTCA
* * *
20382941 TGA-GAGCTTACTGATTCACAGCTCG
1 T-ATGAGCTTACCGATT-TCAGCTCA
20382966 TATGAGCTTACC-ATTT
1 TATGAGCTTACCGATTT
20382982 TTCAGCTCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 17 0.52
25 16 0.48
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (24 bp):
TATGAGCTTACCGATTTCAGCTCA
Found at i:20382972 original size:25 final size:24
Alignment explanation
Indices: 20382916--20383021 Score: 72
Period size: 25 Copynumber: 4.3 Consensus size: 24
20382906 ACCACAGGTT
*
20382916 GTATGAGCTTACCGATTTCAGCTC
1 GTATGAGCTTACCGATTACAGCTC
* *
20382940 ATGA-GAGCTTACTGATTCACAGCTC
1 GT-ATGAGCTTACCGATT-ACAGCTC
*
20382965 GTATGAGCTTACC-ATTTTTCAGCTC
1 GTATGAGCTTACCGA--TTACAGCTC
* * * * *
20382990 GAAAGATCTTACCGTTTACCGCTC
1 GTATGAGCTTACCGATTACAGCTC
*
20383014 TTATGAGC
1 GTATGAGC
20383022 ATACATGTAC
Statistics
Matches: 60, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
24 26 0.43
25 32 0.53
26 2 0.03
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (24 bp):
GTATGAGCTTACCGATTACAGCTC
Found at i:20385861 original size:16 final size:17
Alignment explanation
Indices: 20385836--20385869 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
20385826 TCAAAAAACA
20385836 AAACACCTAAAAATAGC
1 AAACACCTAAAAATAGC
20385853 AAACA-CTAAAAATAGC
1 AAACACCTAAAAATAGC
20385869 A
1 A
20385870 GTCCTAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.62, C:0.21, G:0.06, T:0.12
Consensus pattern (17 bp):
AAACACCTAAAAATAGC
Found at i:20394262 original size:21 final size:21
Alignment explanation
Indices: 20394221--20394267 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20394211 TAATTTCGCC
*
20394221 ATTTTTTAGTTTAATATTTAT
1 ATTTTTTAATTTAATATTTAT
*
20394242 GTTTTTTAATTTAAT-TATTAT
1 ATTTTTTAATTTAATAT-TTAT
20394263 ATTTT
1 ATTTT
20394268 AATTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
ATTTTTTAATTTAATATTTAT
Found at i:20402152 original size:3 final size:3
Alignment explanation
Indices: 20402146--20402228 Score: 112
Period size: 3 Copynumber: 27.7 Consensus size: 3
20402136 AAACTAATAA
* *
20402146 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
20402194 AGT ATT AAT ATT ATT ATT AAT ATT ATT GTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20402229 CATCATATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:20403938 original size:22 final size:22
Alignment explanation
Indices: 20403913--20403954 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20403903 GAAACATAAG
* *
20403913 ATATCAGATATAGTTACAGAAC
1 ATATCAGATACAGATACAGAAC
*
20403935 ATATTAGATACAGATACAGA
1 ATATCAGATACAGATACAGA
20403955 TGTAGATTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (22 bp):
ATATCAGATACAGATACAGAAC
Found at i:20416791 original size:17 final size:18
Alignment explanation
Indices: 20416760--20416801 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
20416750 ACTCAAAAAA
20416760 TATTTTTTTTAATTT-TC
1 TATTTTTTTTAATTTCTC
*
20416777 TATTTTTTGTT-ATTTCTT
1 TATTTTTT-TTAATTTCTC
20416795 TATTTTT
1 TATTTTT
20416802 ATTTTATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (18 bp):
TATTTTTTTTAATTTCTC
Found at i:20421961 original size:16 final size:16
Alignment explanation
Indices: 20421940--20421989 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 16
20421930 ATATCTAATC
20421940 ATATAATAAATTATTA
1 ATATAATAAATTATTA
20421956 ATATAAT--A-TATTA
1 ATATAATAAATTATTA
*
20421969 ATTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
20421986 ATAT
1 ATAT
20421990 TTCAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 1 0.04
16 9 0.32
17 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:20422947 original size:29 final size:29
Alignment explanation
Indices: 20422898--20422955 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
20422888 AAAATATTAT
* * *
20422898 AAAATAAAATATTATTTGAAACTTTAAAC
1 AAAATAAAATATCACTGGAAACTTTAAAC
20422927 AAAATAAAATATCACTGGAAACTTTAAAC
1 AAAATAAAATATCACTGGAAACTTTAAAC
20422956 GAGAGGGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAATAAAATATCACTGGAAACTTTAAAC
Found at i:20423161 original size:24 final size:25
Alignment explanation
Indices: 20423092--20423168 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 25
20423082 ATTTAAATTT
* *
20423092 ATTTTTATAATATAAAATACATATTCA
1 ATTTTTAT-ATATAAAATA-ATTTTAA
20423119 ATTATTTAATATAATAAAATAATTTTAA
1 ATT-TTT-ATAT-ATAAAATAATTTTAA
*
20423147 ATTTTTATATA-AAAATATTTTT
1 ATTTTTATATATAAAATAATTTT
20423169 CAAAAATACA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
24 10 0.23
25 1 0.02
26 4 0.09
27 6 0.14
28 13 0.30
29 10 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTTTATATATAAAATAATTTTAA
Found at i:20429013 original size:51 final size:51
Alignment explanation
Indices: 20428937--20429033 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
20428927 GGAAGGAATC
20428937 CCACATTGTCTAGGAACAAGTTGCAAACCTATTCATGACTCTATATATACA
1 CCACATTGTCTAGGAACAAGTTGCAAACCTATTCATGACTCTATATATACA
* *
20428988 CCACATTGTGTAGGAACAAGTTGCAAACCTATTCATGACTTTATAT
1 CCACATTGTCTAGGAACAAGTTGCAAACCTATTCATGACTCTATAT
20429034 TTATACATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (51 bp):
CCACATTGTCTAGGAACAAGTTGCAAACCTATTCATGACTCTATATATACA
Found at i:20432472 original size:31 final size:29
Alignment explanation
Indices: 20432437--20432496 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
20432427 TTTAACAGCC
*
20432437 TTTTATAACTTTTTGAATAGTTCAATGACCA
1 TTTTATAACCTTTTG-A-AGTTCAATGACCA
*
20432468 TTTTATAACCTTTTGAAGTTGAATGACCA
1 TTTTATAACCTTTTGAAGTTCAATGACCA
20432497 AAATGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.44
30 1 0.04
31 14 0.52
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (29 bp):
TTTTATAACCTTTTGAAGTTCAATGACCA
Found at i:20432742 original size:16 final size:16
Alignment explanation
Indices: 20432721--20432759 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
20432711 TAAAATTGTT
20432721 TATTTGAGAA-TTAAAA
1 TATTTGA-AATTTAAAA
20432737 TATTTGAAATTTAAAA
1 TATTTGAAATTTAAAA
20432753 T-TTTGAA
1 TATTTGAA
20432760 TTAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (16 bp):
TATTTGAAATTTAAAA
Found at i:20433391 original size:18 final size:17
Alignment explanation
Indices: 20433368--20433407 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
20433358 TTATATTTTC
20433368 AAAAAAAAAAATTTAAA
1 AAAAAAAAAAATTTAAA
**
20433385 TAAAAAAACTAATTTAAA
1 -AAAAAAAAAAATTTAAA
20433403 AAAAA
1 AAAAA
20433408 TTAAATATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAAAAAAAAATTTAAA
Found at i:20443517 original size:2 final size:2
Alignment explanation
Indices: 20443510--20443535 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20443500 AAGTTAAAAG
20443510 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20443536 GTTATGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20447389 original size:23 final size:22
Alignment explanation
Indices: 20447348--20447397 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
20447338 GCTTTATTTG
*
20447348 TTAATATGTTTTGATATAACAAA
1 TTAAAATGTTTTGATATAA-AAA
*
20447371 TTAAAATGTTTTTGA-ATAAAAG
1 TTAAAATG-TTTTGATATAAAAA
20447393 TTAAA
1 TTAAA
20447398 GTTGAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 11 0.46
24 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (22 bp):
TTAAAATGTTTTGATATAAAAA
Found at i:20447480 original size:19 final size:19
Alignment explanation
Indices: 20447424--20447480 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
20447414 AAAATGATAA
*
20447424 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-TTTTC
** *
20447444 AATTGAGTTAGACA-TTTTC
1 AATCAAGTTA-AAATTTTTC
20447463 AATCAAGTTAAAATTTTT
1 AATCAAGTTAAAATTTTT
20447481 TTTAAACAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
18 2 0.07
19 16 0.57
20 8 0.29
21 2 0.07
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (19 bp):
AATCAAGTTAAAATTTTTC
Found at i:20447635 original size:22 final size:21
Alignment explanation
Indices: 20447591--20447632 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20447581 TTCAATTTAC
20447591 ACAAAAAGTATCGACACCTTT
1 ACAAAAAGTATCGACACCTTT
*
20447612 ACAAAAAGTATCGATACCTTT
1 ACAAAAAGTATCGACACCTTT
20447633 TACTAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (21 bp):
ACAAAAAGTATCGACACCTTT
Found at i:20450607 original size:19 final size:19
Alignment explanation
Indices: 20450560--20450617 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
20450550 AAAATGATAA
20450560 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
**
20450580 AATTGAGTTAAACAT-TTTC
1 AATCAAGTTAAA-ATGTTTC
20450599 AATCAAGTTAAAACTGTTT
1 AATCAAGTTAAAA-TGTTT
20450618 TAAAACAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 13 0.42
21 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:20453560 original size:23 final size:23
Alignment explanation
Indices: 20453534--20453580 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
20453524 GTAATTATAA
20453534 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
20453557 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
20453580 A
1 A
20453581 CATACTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:20453716 original size:27 final size:25
Alignment explanation
Indices: 20453681--20453737 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
20453671 ACAGAATAGC
* *
20453681 AAAACGAAAACAGGGGA-GAAAGGAAA
1 AAAAAGAAAA-AGGGAAGGAAA-GAAA
20453707 GAAAAAGAAAAAGGGAAGGAAAGAAA
1 -AAAAAGAAAAAGGGAAGGAAAGAAA
20453733 AAAAA
1 AAAAA
20453738 TTTGGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 5 0.19
26 9 0.33
27 13 0.48
ACGTcount: A:0.68, C:0.04, G:0.28, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAGGGAAGGAAAGAAA
Found at i:20454622 original size:25 final size:25
Alignment explanation
Indices: 20454594--20454675 Score: 119
Period size: 25 Copynumber: 3.3 Consensus size: 25
20454584 ACTTTAGTGC
* *
20454594 GCTCTCTGATTATTAGCACATCAAT
1 GCTCTCTGATTATTAGCACGTCAGT
20454619 GCTCTCTGATTATTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
* * *
20454644 GCTCTCTAAGTACTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTCAGT
20454669 GCTCTCT
1 GCTCTCT
20454676 ATTTAGCACT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAGT
Found at i:20462311 original size:41 final size:41
Alignment explanation
Indices: 20462212--20462303 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
20462202 NNNNNNNNNN
20462212 AGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTT
1 AGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTT
*
20462253 AGCCTGCTAGGCTTATAGCCTGATTCAGTTCATCGGCACTT
1 AGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTT
20462294 AGCCTGCTAG
1 AGCCTGCTAG
20462304 ACATATAGTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTT
Found at i:20463084 original size:2 final size:2
Alignment explanation
Indices: 20463077--20463103 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20463067 CGAATCTAGC
20463077 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20463104 ATTTCATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20464129 original size:13 final size:13
Alignment explanation
Indices: 20464111--20464135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20464101 ACCAACGATA
20464111 AAATTTTCACACG
1 AAATTTTCACACG
20464124 AAATTTTCACAC
1 AAATTTTCACAC
20464136 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:20464534 original size:41 final size:41
Alignment explanation
Indices: 20464456--20464555 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 41
20464446 CTATATGATT
* * * *
20464456 AGCACTAAGTGTGCG-GATTAAATGATGAGGTTTAATAACG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
*
20464496 AGCACTAAGTGTGCGAAACTAAATAATGATGTTAAATAACG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
*
20464537 GGCACTAAGTGTGCGAAAC
1 AGCACTAAGTGTGCGAAAC
20464556 CGAGATCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 15 0.28
41 38 0.72
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAACG
Found at i:20480337 original size:17 final size:18
Alignment explanation
Indices: 20480315--20480359 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
20480305 TTATGAATTA
20480315 AAAAATAATTATA-AAAG
1 AAAAATAATTATACAAAG
*
20480332 AAAAATAGTTATACTAAAG
1 AAAAATAATTATAC-AAAG
*
20480351 ATAAATAAT
1 AAAAATAAT
20480360 ATGAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
AAAAATAATTATACAAAG
Found at i:20482219 original size:25 final size:25
Alignment explanation
Indices: 20482161--20482235 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
20482151 GTCATAAAAG
*
20482161 AAAGAGAAAG-AAAGAAAGCCAAACAA
1 AAAGAGAAAGAAAAGAAAG--AAAGAA
**
20482187 AATTAGAAAGAAAAGAAAGAAAGAA
1 AAAGAGAAAGAAAAGAAAGAAAGAA
20482212 AAAGAGAAAGAAGAA-AAAGAAAGA
1 AAAGAGAAAGAA-AAGAAAGAAAGA
20482236 GAACCCACGG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
25 24 0.57
26 10 0.24
27 8 0.19
ACGTcount: A:0.72, C:0.04, G:0.21, T:0.03
Consensus pattern (25 bp):
AAAGAGAAAGAAAAGAAAGAAAGAA
Found at i:20482225 original size:19 final size:20
Alignment explanation
Indices: 20482191--20482238 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
20482181 AAACAAAATT
20482191 AGAAAGA-AAAGAAAGAAAGA
1 AGAAAGAGAAAGAAAGAAA-A
20482211 A-AAAGAGAAAG-AAGAAAA
1 AGAAAGAGAAAGAAAGAAAA
20482229 AGAAAGAGAA
1 AGAAAGAGAA
20482239 CCCACGGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.08
19 19 0.73
20 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
AGAAAGAGAAAGAAAGAAAA
Found at i:20482227 original size:32 final size:32
Alignment explanation
Indices: 20482158--20482235 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
20482148 AAAGTCATAA
** *
20482158 AAGAAAGAGAAAGAAAGAAAGCCAAACAAAAT
1 AAGAAAGAGAAAGAAAGAAAGAAAAACAAAAG
* *
20482190 TAGAAAGA-AAAGAAAGAAAGAAAAAGAGAAAG
1 AAGAAAGAGAAAGAAAGAAAGAAAAACA-AAAG
*
20482222 AAGAAAAAGAAAGA
1 AAGAAAGAGAAAGA
20482236 GAACCCACGG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 16 0.43
32 16 0.43
33 5 0.14
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.03
Consensus pattern (32 bp):
AAGAAAGAGAAAGAAAGAAAGAAAAACAAAAG
Found at i:20482238 original size:15 final size:15
Alignment explanation
Indices: 20482197--20482238 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
20482187 AATTAGAAAG
20482197 AAAAGAAAGA-AAGA
1 AAAAGAAAGAGAAGA
20482211 AAAAGAGAA-AGAAGA
1 AAAAGA-AAGAGAAGA
20482226 AAAAGAAAGAGAA
1 AAAAGAAAGAGAA
20482239 CCCACGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAGAAGA
Found at i:20482474 original size:12 final size:12
Alignment explanation
Indices: 20482457--20482481 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20482447 GAAAAAGGAT
20482457 TAAATTGTAAAA
1 TAAATTGTAAAA
20482469 TAAATTGTAAAA
1 TAAATTGTAAAA
20482481 T
1 T
20482482 TTGAGTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAATTGTAAAA
Found at i:20483902 original size:2 final size:2
Alignment explanation
Indices: 20483895--20483925 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20483885 TGGTTTGGTG
20483895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20483926 GTAAACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20487400 original size:5 final size:5
Alignment explanation
Indices: 20487390--20487428 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
20487380 TTGGAGATTG
* *
20487390 GGAGA GGAGA GGAAA AGAGA GGAGA GGAGA GGAGA GGAG
1 GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA GGAGA GGAG
20487429 GAGAGATTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (5 bp):
GGAGA
Found at i:20491039 original size:34 final size:34
Alignment explanation
Indices: 20490996--20491065 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
20490986 CTAATACCTA
20490996 AGGCAAAACAAGGAGCAGAATTAGAAGCATATGT
1 AGGCAAAACAAGGAGCAGAATTAGAAGCATATGT
20491030 AGGCAAAACAAGGAGCAGAATTAGAAGCATATGT
1 AGGCAAAACAAGGAGCAGAATTAGAAGCATATGT
20491064 AG
1 AG
20491066 CAGAGAGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.27, T:0.14
Consensus pattern (34 bp):
AGGCAAAACAAGGAGCAGAATTAGAAGCATATGT
Found at i:20505579 original size:17 final size:19
Alignment explanation
Indices: 20505546--20505580 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
20505536 TAATAGAATA
20505546 GAAAATATTGTAAATTGAT
1 GAAAATATTGTAAATTGAT
20505565 GAAAATA-TG-AAATTGA
1 GAAAATATTGTAAATTGA
20505581 CTTTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (19 bp):
GAAAATATTGTAAATTGAT
Found at i:20505734 original size:27 final size:28
Alignment explanation
Indices: 20505672--20505735 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
20505662 GATGAAAATA
20505672 GTGTAAATT-GAAATATGCATACTTAAT
1 GTGTAAATTGGAAATATGCATACTTAAT
*
20505699 GTTGT-AATTGGATATATGCATACTT-AT
1 G-TGTAAATTGGAAATATGCATACTTAAT
20505726 GTGTAAATTG
1 GTGTAAATTG
20505736 ATGAAAATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 13 0.39
28 17 0.52
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (28 bp):
GTGTAAATTGGAAATATGCATACTTAAT
Found at i:20506422 original size:35 final size:35
Alignment explanation
Indices: 20506375--20506465 Score: 121
Period size: 35 Copynumber: 2.6 Consensus size: 35
20506365 TCAAAGGTGA
* * *
20506375 CTTTAAAAAGGTTGGGATAGACCCGTCTAAGGCAAC
1 CTTT-AAAAGGTTGGGATAGACACATCTAAGCCAAC
20506411 CTTTAAAAGGTTGGGATAGACACATCTAAGCCAAC
1 CTTTAAAAGGTTGGGATAGACACATCTAAGCCAAC
*
20506446 C-TTAAATATGTTGGGATAGA
1 CTTTAAA-AGGTTGGGATAGA
20506466 TAAGTCTAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 5 0.10
35 41 0.82
36 4 0.08
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (35 bp):
CTTTAAAAGGTTGGGATAGACACATCTAAGCCAAC
Found at i:20509314 original size:37 final size:37
Alignment explanation
Indices: 20509273--20509368 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 37
20509263 TAATGAAAAA
** *
20509273 AGTGTAAGATAATATTTTTTGTATTAAACAAATAGAT
1 AGTGTAAGATAATATTTTGGGTATTAAACAAATAGAG
20509310 AGTGTAA-ATTTAATGAAATTTTGGGTATTAAACAAATAGAG
1 AGTGTAAGA--TAAT---ATTTTGGGTATTAAACAAATAGAG
20509351 AGTGTAAGATAATATTTT
1 AGTGTAAGATAATATTTT
20509369 ATTTAATTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
36 1 0.02
37 12 0.24
38 4 0.08
40 4 0.08
41 28 0.56
42 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.39
Consensus pattern (37 bp):
AGTGTAAGATAATATTTTGGGTATTAAACAAATAGAG
Found at i:20509954 original size:136 final size:136
Alignment explanation
Indices: 20509736--20509992 Score: 397
Period size: 136 Copynumber: 1.9 Consensus size: 136
20509726 TTGAAAAAAA
* **
20509736 CTGACTCTTATTTAAGTGTTGCCTTAGGCATACATAACCCAACCCTTATACAAAGAGTTGGCCAA
1 CTGAATCTTATTTAAACGTTGCCTTAGGCATACATAACCCAACCCTTATACAAAGAGTTGGCCAA
* * * *
20509801 AGAGTACGTCGGTAAGTCTATCCTAACACTTAGGAAAGTTTCGGCCCAAAAGTGTCGGCATTGTG
66 AGAGTACGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCACAAAAGTGTCGGCATTGTG
20509866 ATAAAT
131 ATAAAT
* * *
20509872 CTGAATCTTATTTAAACGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCTAA
1 CTGAATCTTATTTAAACGTTGCCTTAGGCATACATAACCCAACCCTTATACAAAGAGTTGGCCAA
* * *
20509937 AGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCACAAAAGTGTC
66 AGAGTACGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCACAAAAGTGTC
20509993 ATCTTAAGAC
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
136 108 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (136 bp):
CTGAATCTTATTTAAACGTTGCCTTAGGCATACATAACCCAACCCTTATACAAAGAGTTGGCCAA
AGAGTACGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCACAAAAGTGTCGGCATTGTG
ATAAAT
Found at i:20510802 original size:20 final size:20
Alignment explanation
Indices: 20510773--20510830 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
20510763 GAACAAAGGG
20510773 TAAT-TAAATAATAATATTT
1 TAATATAAATAATAATATTT
20510792 TAATATAAATAATAATATTT
1 TAATATAAATAATAATATTT
20510812 TAATATAAA-AATAA-ATTT
1 TAATATAAATAATAATATTT
20510830 T
1 T
20510831 CCTATTTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 5 0.13
19 9 0.24
20 24 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATAAATAATAATATTT
Found at i:20532781 original size:12 final size:12
Alignment explanation
Indices: 20532764--20532788 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20532754 GGTGTTCATT
20532764 CGGTTAACCGAC
1 CGGTTAACCGAC
20532776 CGGTTAACCGAC
1 CGGTTAACCGAC
20532788 C
1 C
20532789 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:20532962 original size:9 final size:9
Alignment explanation
Indices: 20532948--20533042 Score: 120
Period size: 9 Copynumber: 10.4 Consensus size: 9
20532938 TTTGGTTAAA
20532948 AATTACCCG
1 AATTACCCG
20532957 AATTACCCG
1 AATTACCCG
20532966 AATTACCCG
1 AATTACCCG
*
20532975 AATTAACCG
1 AATTACCCG
20532984 AATTACCCG
1 AATTACCCG
*
20532993 AATTAACCG
1 AATTACCCG
**
20533002 AATTAATCG
1 AATTACCCG
20533011 AATTA-CCG
1 AATTACCCG
*
20533019 AAAAATACCCG
1 --AATTACCCG
20533030 AATTACCCG
1 AATTACCCG
20533039 AATT
1 AATT
20533043 TTTTTTATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
8 2 0.03
9 67 0.88
10 4 0.05
11 3 0.04
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:20536789 original size:14 final size:14
Alignment explanation
Indices: 20536770--20536804 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
20536760 ATTTAAAAGT
20536770 TAACTAAATTTTAA
1 TAACTAAATTTTAA
20536784 TAACTAAATTTTAA
1 TAACTAAATTTTAA
20536798 TAA-TAAA
1 TAACTAAA
20536805 CTAACTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
TAACTAAATTTTAA
Found at i:20544100 original size:7 final size:7
Alignment explanation
Indices: 20544090--20544124 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
20544080 ATTAACAATT
20544090 AATAAAA
1 AATAAAA
20544097 AATAAAA
1 AATAAAA
20544104 AATAAAA
1 AATAAAA
*
20544111 AAAAATAA
1 AATAA-AA
20544119 AATAAA
1 AATAAA
20544125 GTTGATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AATAAAA
Found at i:20547734 original size:33 final size:32
Alignment explanation
Indices: 20547697--20547759 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
20547687 AACAGTCATT
* *
20547697 TTACAATAAAATGGGCCCAAAACCCAAACCCAA
1 TTACAACAAAATAGGCCC-AAACCCAAACCCAA
*
20547730 TTACAACAAAATAGGCCCAAACCCAGACCC
1 TTACAACAAAATAGGCCCAAACCCAAACCC
20547760 GATTTTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.46, C:0.33, G:0.10, T:0.11
Consensus pattern (32 bp):
TTACAACAAAATAGGCCCAAACCCAAACCCAA
Found at i:20548990 original size:34 final size:33
Alignment explanation
Indices: 20548911--20549011 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 33
20548901 ATTATTTCTA
*
20548911 TTTTTATAATTTATATATGTA-AT-TA--T-TT
1 TTTTTATAATATATATATGTATATATATCTATT
*
20548939 TTTTTATAATCTATATATATGTGTATATATCTATT
1 TTTTTATAA--TATATATATGTATATATATCTATT
* *
20548974 TTTTTAT-ATATGTATATGTATATATATTTATAT
1 TTTTTATAATATATATATGTATATATATCTAT-T
20549007 TTTTT
1 TTTTT
20549012 TCTAACGAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
28 9 0.15
30 10 0.17
31 2 0.03
32 22 0.37
33 6 0.10
34 2 0.03
35 9 0.15
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (33 bp):
TTTTTATAATATATATATGTATATATATCTATT
Found at i:20548997 original size:16 final size:16
Alignment explanation
Indices: 20548954--20549006 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
20548944 ATAATCTATA
*
20548954 TATATGTGTATATATC
1 TATATGTATATATATC
* * * *
20548970 TATTTTTTTATATATG
1 TATATGTATATATATC
*
20548986 TATATGTATATATATT
1 TATATGTATATATATC
20549002 TATAT
1 TATAT
20549007 TTTTTTCTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (16 bp):
TATATGTATATATATC
Found at i:20556056 original size:17 final size:17
Alignment explanation
Indices: 20556017--20556075 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
20556007 AAAACAAATA
*
20556017 GAGGCCCAAA-CCTA-T
1 GAGGCCCAAACCCAACT
*
20556032 GTGGCCCAAACCCAACT
1 GAGGCCCAAACCCAACT
* *
20556049 GAGGCCCAAACCAAACA
1 GAGGCCCAAACCCAACT
*
20556066 GAAGCCCAAA
1 GAGGCCCAAA
20556076 GCAGATTCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
15 9 0.25
16 3 0.08
17 24 0.67
ACGTcount: A:0.39, C:0.36, G:0.19, T:0.07
Consensus pattern (17 bp):
GAGGCCCAAACCCAACT
Found at i:20569131 original size:44 final size:44
Alignment explanation
Indices: 20569071--20569665 Score: 317
Period size: 44 Copynumber: 13.8 Consensus size: 44
20569061 TAGTGGCCTG
* * *
20569071 GATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATCTCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * *
20569115 GATCTTATCTCGCTGAAGTTGCAG-AGAGCAGA-TCACATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * *
20569156 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTCA
* * * * * **
20569200 G-TCCTATC-CTCCTGAAGTTGCACT-GAGGCAAACTGAAGATGACA
1 GATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCTCA
*
20569244 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-TGACA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCT--CA
* * * *
20569289 -ATCTTATCTCCTTGAAGTTGCGGTGGAGCGGATTAAAATATCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
** * ***
20569332 GATCTTATCTTTCTGAAGTTGCAG-AGAGCAGA-TCGCATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * *
20569373 G-TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAGTAAGC-AA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTCA
* * * * **
20569417 G-TTTTATCCTCCC-GAAGTTGTAGT-GAGGCAGACTGAAGATGGCA
1 GATCTTAT-CTCCCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCTCA
* * * ** *
20569461 AATCTTATCTCCCCGAAGTTACAGTGGAGCAGATTAAAGCCGACA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TCA
** *
20569506 -AT-TCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATTTCA
1 GATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * ****
20569549 GATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TCGCGTCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * *
20569590 G-TCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTAAGTAA--GCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTCA
** *
20569633 GATCTTATCTCCCT-AAGCAGTAGTGGAGCAGAT
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
20569666 CGAAGATGGC
Statistics
Matches: 419, Mismatches: 93, Indels: 79
0.71 0.16 0.13
Matches are distributed among these distances:
40 64 0.15
41 27 0.06
42 17 0.04
43 46 0.11
44 203 0.48
45 57 0.14
46 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
Found at i:20569217 original size:84 final size:87
Alignment explanation
Indices: 20569076--20569282 Score: 212
Period size: 84 Copynumber: 2.4 Consensus size: 87
20569066 GCCTGGATCC
* * * * * *
20569076 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATCTCAGATCTTATCTCGCTGAAGTTGCA-GA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCTAAGATCCTATCTCGCTGAAGTTGCACGA
* * *
20569140 GAGCAGA-T-CACAT-CTAATCT
66 G-GCAAACTGAACATACAAATCT
20569160 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAG-TCCTATCCTC-CTGAAGTTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AAGCTAAGATCCTAT-CTCGCTGAAGTTGCA
*
20569222 CTGAGGCAAACTGAAGATGACAAATCT
63 C-GAGGCAAACTGAACAT-ACAAATCT
*
20569249 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAA
20569283 TTGACAATCT
Statistics
Matches: 103, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
84 45 0.44
85 9 0.09
86 7 0.07
87 5 0.05
89 37 0.36
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (87 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCTAAGATCCTATCTCGCTGAAGTTGCACGA
GGCAAACTGAACATACAAATCT
Found at i:20569436 original size:217 final size:217
Alignment explanation
Indices: 20569075--20569632 Score: 848
Period size: 217 Copynumber: 2.6 Consensus size: 217
20569065 GGCCTGGATC
* * *
20569075 CTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATCTCAGATCTTATCTCGCTGAAGTTGCAGA
1 CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATATCAGATCTTATCTCTCTGAAGTTGCAGA
* *
20569140 GAGCAGATCACATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCT
66 GAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCT
* * *
20569205 ATCCTCCTGAAGTTGCACTGAGGCAAACTGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTG
131 ATCCTCCCGAAGTTGCACTGAGGCAAACTGAAGATGACAAATCTTATCTCCCCGAAGTTACAGTG
**
20569270 GAGCAGATTAAAATTGACAA-T
196 GAGCAGATTAAAACCGACAATT
* * *
20569291 CTTATCTCCTTGAAGTTGCGGTGGAGCGGATTAAAATATCAGATCTTATCTTTCTGAAGTTGCAG
1 C-TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATATCAGATCTTATCTCTCTGAAGTTGCAG
* * **
20569356 AGAGCAGATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAGTAAGCAAGTTT
65 AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCC
* * * *
20569421 TATCCTCCCGAAGTTGTAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCCGAAGTTACAGT
130 TATCCTCCCGAAGTTGCACTGAGGCAAACTGAAGATGACAAATCTTATCTCCCCGAAGTTACAGT
*
20569486 GGAGCAGATTAAAGCCGACAATT
195 GGAGCAGATTAAAACCGACAATT
* * *
20569509 CTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATTTCAGATCTTATCTCTCTGAAGTTGTAGA
1 CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATATCAGATCTTATCTCTCTGAAGTTGCAGA
* * *
20569574 GAGCAGATCGCGTCTAGTCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTAAGTAAGCA
66 GAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
20569633 GATCTTATCT
Statistics
Matches: 307, Mismatches: 33, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
216 1 0.00
217 304 0.99
218 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATATCAGATCTTATCTCTCTGAAGTTGCAGA
GAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCT
ATCCTCCCGAAGTTGCACTGAGGCAAACTGAAGATGACAAATCTTATCTCCCCGAAGTTACAGTG
GAGCAGATTAAAACCGACAATT
Found at i:20571285 original size:18 final size:18
Alignment explanation
Indices: 20571262--20571304 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20571252 TTTTTCATAT
20571262 TTTTTTTAAAAAT-CAATA
1 TTTTTTTAAAAATGCAA-A
* *
20571280 TTTTTTTGATAATGCAAA
1 TTTTTTTAAAAATGCAAA
20571298 TTTTTTT
1 TTTTTTT
20571305 TATCTTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTTTTTAAAAATGCAAA
Found at i:20575688 original size:21 final size:21
Alignment explanation
Indices: 20575664--20575704 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20575654 TAACGGGACC
20575664 GCTGATGTGGCAAGTTAACTA
1 GCTGATGTGGCAAGTTAACTA
20575685 GCTGATGTGGCAAGTTAACT
1 GCTGATGTGGCAAGTTAACT
20575705 TGCCACGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (21 bp):
GCTGATGTGGCAAGTTAACTA
Found at i:20575945 original size:6 final size:6
Alignment explanation
Indices: 20575796--20575927 Score: 192
Period size: 6 Copynumber: 22.0 Consensus size: 6
20575786 TCCACCATTC
* * * * * * **
20575796 TGATTT TGATTT CGATCT CGATTT CGATTT AGATTT AGATTT CAATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
20575844 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
20575892 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
20575928 AGGGTTATTT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 118 1.00
ACGTcount: A:0.19, C:0.04, G:0.16, T:0.61
Consensus pattern (6 bp):
TGATTT
Found at i:20578358 original size:11 final size:11
Alignment explanation
Indices: 20578342--20578367 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20578332 TAGAAGAGAC
20578342 GAAACAGGGGA
1 GAAACAGGGGA
20578353 GAAACAGGGGA
1 GAAACAGGGGA
20578364 GAAA
1 GAAA
20578368 GAAGAAAAAG
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:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:20579131 original size:39 final size:40
Alignment explanation
Indices: 20579088--20579175 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 40
20579078 CGAATTATGG
*
20579088 AATACTGAATATTGTCT-TG-ATTACTG-AGTGAATTGTGAA
1 AATACTGAATATTGT-TATGCA-TAATGCAGTGAATTGTGAA
*
20579127 AATACTGAATATTGTTATGCATAATGCATTGAATTGTGAA
1 AATACTGAATATTGTTATGCATAATGCAGTGAATTGTGAA
*
20579167 ATTACTGAA
1 AATACTGAA
20579176 GTAAAGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 21 0.49
40 21 0.49
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (40 bp):
AATACTGAATATTGTTATGCATAATGCAGTGAATTGTGAA
Found at i:20579430 original size:39 final size:39
Alignment explanation
Indices: 20579350--20579525 Score: 149
Period size: 45 Copynumber: 4.2 Consensus size: 39
20579340 ATTTGCCGGC
* * *
20579350 TTACTGA-TCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTC-GGCACTTTGTGTGTCGAATACTGTTACTG
20579388 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
* *
20579427 TTACTGTTACCGACTCGGCACTTTGTGTGTCAAATACTGTTACTG
1 TTAC---T---GATTCGGCACTTTGTGTGTCGAATACTGTTACTG
* * *
20579472 TTACTGTTACAGGTTCAGCACTTGGTGTGTTGAATACTGTTACTG
1 TTACTG----A--TTCGGCACTTTGTGTGTCGAATACTGTTACTG
20579517 TTACTGATT
1 TTACTGATT
20579526 ACTGTATACT
Statistics
Matches: 114, Mismatches: 10, Indels: 27
0.75 0.07 0.18
Matches are distributed among these distances:
38 12 0.11
39 29 0.25
41 1 0.01
42 2 0.02
43 1 0.01
45 69 0.61
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:20579445 original size:45 final size:45
Alignment explanation
Indices: 20579377--20579527 Score: 221
Period size: 45 Copynumber: 3.3 Consensus size: 45
20579367 ATGTGCCGAC
*
20579377 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
20579422 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCAAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* * * *
20579467 TACTGTTACTGTTACAGGTTCAGCACTTGGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
20579512 TACTGTTACTGATTAC
1 TACTGTTACTG-TTAC
20579528 TGTATACTGG
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 91 0.96
46 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:20580124 original size:22 final size:22
Alignment explanation
Indices: 20580083--20580124 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20580073 TGAGAATGTG
* *
20580083 AAATGAATTGGTTGTGATTGAA
1 AAATGAAATGGTTGTAATTGAA
*
20580105 AAATGAAATGGTTTTAATTG
1 AAATGAAATGGTTGTAATTG
20580125 CAGGGGGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (22 bp):
AAATGAAATGGTTGTAATTGAA
Found at i:20580857 original size:24 final size:25
Alignment explanation
Indices: 20580830--20580878 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
20580820 GCATGCAATG
20580830 ATTGTTGGTGTGTATGATT-GTTTT
1 ATTGTTGGTGTGTATGATTGGTTTT
20580854 ATTGTTGGTGTGTATGATTGGTTTT
1 ATTGTTGGTGTGTATGATTGGTTTT
20580879 TAATACACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.12, C:0.00, G:0.31, T:0.57
Consensus pattern (25 bp):
ATTGTTGGTGTGTATGATTGGTTTT
Found at i:20580935 original size:68 final size:69
Alignment explanation
Indices: 20580854--20580984 Score: 212
Period size: 69 Copynumber: 1.9 Consensus size: 69
20580844 TGATTGTTTT
20580854 ATTGTTGGTGTGTATGA-T-TGGTTTTTAATACACATGCTGTTGACTATTTTTTTAATATGCATG
1 ATTGTTGGTGTGTATGACTAT-GTTTTTAATACACATGCTGTTGACTATTTTTTTAATATGCATG
20580917 CAGTG
65 CAGTG
* * *
20580922 ATTGTTGGTGTGTATGACTATTTTTTTAATATACATGTTGTTGACTATTTTTTTAATATGCAT
1 ATTGTTGGTGTGTATGACTATGTTTTTAATACACATGCTGTTGACTATTTTTTTAATATGCAT
20580985 ACAATGAGTA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
68 17 0.29
69 40 0.69
70 1 0.02
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (69 bp):
ATTGTTGGTGTGTATGACTATGTTTTTAATACACATGCTGTTGACTATTTTTTTAATATGCATGC
AGTG
Found at i:20581025 original size:29 final size:29
Alignment explanation
Indices: 20580932--20581029 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 29
20580922 ATTGTTGGTG
20580932 TGTA-TGACTATTTTTTTAAT-ATA--CA
1 TGTAGTGACTATTTTTTTAATAATATGCA
*
20580957 TGTTGTTGACTA-TTTTTT--TAATATGCA
1 TGTAG-TGACTATTTTTTTAATAATATGCA
** * *
20580984 TACAATGAGTATTTTTTTAATAATATGCA
1 TGTAGTGACTATTTTTTTAATAATATGCA
20581013 TGTAGTGACTATTTTTT
1 TGTAGTGACTATTTTTT
20581030 ATGTGTGTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
24 1 0.02
25 6 0.11
26 11 0.20
27 15 0.27
29 22 0.40
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (29 bp):
TGTAGTGACTATTTTTTTAATAATATGCA
Found at i:20581027 original size:27 final size:26
Alignment explanation
Indices: 20580932--20581029 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
20580922 ATTGTTGGTG
*
20580932 TGTA-TGACTATTTTTTTAATATACA
1 TGTAGTGACTATTTTTTTAATATGCA
*
20580957 TGTTGTTGACTATTTTTTTAATATGCA
1 TGTAG-TGACTATTTTTTTAATATGCA
** * *
20580984 TACAATGAGTATTTTTTTAATAATATGCA
1 TGTAGTGACTA-TTTTTT--TAATATGCA
20581013 TGTAGTGACTATTTTTT
1 TGTAGTGACTATTTTTT
20581030 ATGTGTGTGT
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.05
26 5 0.09
27 27 0.47
28 6 0.11
29 16 0.28
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (26 bp):
TGTAGTGACTATTTTTTTAATATGCA
Found at i:20583413 original size:8 final size:8
Alignment explanation
Indices: 20583376--20583407 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
20583366 TGTTTTATAT
20583376 ATATAATA
1 ATATAATA
20583384 ATATAATA
1 ATATAATA
20583392 ATATAATA
1 ATATAATA
20583400 ATATAATA
1 ATATAATA
20583408 TAATAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:20583413 original size:16 final size:17
Alignment explanation
Indices: 20583372--20583413 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
20583362 CTTTTGTTTT
20583372 ATATATATAATAATATA
1 ATATATATAATAATATA
20583389 ATA-ATATAATAATATA
1 ATATATATAATAATATA
20583405 ATATA-ATAA
1 ATATATATAA
20583414 CATACTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATATAATAATATA
Found at i:20584131 original size:21 final size:21
Alignment explanation
Indices: 20584105--20584156 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20584095 CAAGTGGTTG
20584105 CCCCAACTCAGCAACAG-GCTA
1 CCCCAACTCAGCAACAGAG-TA
* *
20584126 CCCCAAATCAGCAAGAGAGTA
1 CCCCAACTCAGCAACAGAGTA
20584147 CCCCAACTCA
1 CCCCAACTCA
20584157 ATAGGCTGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.40, G:0.13, T:0.10
Consensus pattern (21 bp):
CCCCAACTCAGCAACAGAGTA
Found at i:20586526 original size:26 final size:25
Alignment explanation
Indices: 20586486--20586564 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 25
20586476 AAATTCAAGC
20586486 GAGCCATAT--TGGGAAGCTCATAAA
1 GAGCCATATAATGGGAAGCTCAT-AA
* *
20586510 GAGCC-TTTAATCGGGAAGCTCACGAA
1 GAGCCATATAAT-GGGAAGCTCA-TAA
*
20586536 GAGCCATATAATGGGATGCTCATAA
1 GAGCCATATAATGGGAAGCTCATAA
20586561 GAGC
1 GAGC
20586565 TGCGGTGTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
23 2 0.04
24 5 0.11
25 7 0.16
26 26 0.58
27 5 0.11
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (25 bp):
GAGCCATATAATGGGAAGCTCATAA
Found at i:20588326 original size:3 final size:3
Alignment explanation
Indices: 20588298--20588360 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
20588288 CCATTTTTCC
* * *
20588298 TCT TCT CCT TCT CCT TC- TCTT TCT TCT TCT TC- TCC TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT
*
20588342 TCTT TCT T-T TCT TTT TCT T
1 TC-T TCT TCT TCT TCT TCT T
20588361 TAACCCTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 6 0.12
3 37 0.77
4 5 0.10
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:20588349 original size:21 final size:21
Alignment explanation
Indices: 20588298--20588345 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
20588288 CCATTTTTCC
*
20588298 TCTTCTCCTTCTCCTTCTCTT
1 TCTTCTTCTTCTCCTTCTCTT
20588319 TCTTCTTCTTCTCC-TCT-TCT
1 TCTTCTTCTTCTCCTTCTCT-T
20588339 TCTTCTT
1 TCTTCTT
20588346 TCTTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 11 0.44
21 13 0.52
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (21 bp):
TCTTCTTCTTCTCCTTCTCTT
Found at i:20589585 original size:27 final size:27
Alignment explanation
Indices: 20589528--20589591 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 27
20589518 ATGAGAATAG
* * * **
20589528 TTTATTAAATAAAAAATTTTATACTTT
1 TTTATTAAATAAAAAAGTATAAACTAA
*
20589555 TTTATTTAATAAAAAAGTATAAACTAA
1 TTTATTAAATAAAAAAGTATAAACTAA
*
20589582 TTTAGTAAAT
1 TTTATTAAAT
20589592 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (27 bp):
TTTATTAAATAAAAAAGTATAAACTAA
Found at i:20589732 original size:25 final size:24
Alignment explanation
Indices: 20589678--20589732 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
20589668 CTTCAGCCCC
20589678 TTTTTTTGGTATATTTTGGTAAATAA
1 TTTTTTTGGTATATTTTGGT-AAT-A
*
20589704 TTTTTTGGGATATATTTTGGT-ATA
1 TTTTTTTGG-TATATTTTGGTAATA
20589728 TTTTT
1 TTTTT
20589733 ATTTCTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 6 0.22
25 2 0.07
26 8 0.30
27 11 0.41
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (24 bp):
TTTTTTTGGTATATTTTGGTAATA
Found at i:20590221 original size:13 final size:13
Alignment explanation
Indices: 20590205--20590267 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
20590195 TTTAAACCAA
*
20590205 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
*
20590218 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
20590231 ACTTTTCTATAGT
1 ACTTTTCAAAAGC
*
20590244 AGTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
20590257 ACTTCTCAAAA
1 ACTTTTCAAAA
20590268 ACAATGAAGA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:20592686 original size:98 final size:98
Alignment explanation
Indices: 20592502--20592692 Score: 292
Period size: 98 Copynumber: 1.9 Consensus size: 98
20592492 AAAAATCATA
* * *
20592502 AAGGAAATTTTCCGAGTTTGGGATTATAAAGGAATTGTGCCTTAACGTATTGGATGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTATAAAGGAATCGTGCCCTAACGTATTGGATGTGATTTCTT
*
20592567 AAATCTTGGATAAGCGAATGTTTTTTTACAATG
66 AAATCTTGGATAAGCGAATGTTCTTTTACAATG
* * *
20592600 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGTTTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTATAAAGGAATCGTGCCCTAACGTATTGGATGTGATTTCTT
* * *
20592665 AAATCTTGGATGAGTGGATGTTCTTTTA
66 AAATCTTGGATAAGCGAATGTTCTTTTA
20592693 AAGTTTTATT
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 83 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGGGATTATAAAGGAATCGTGCCCTAACGTATTGGATGTGATTTCTT
AAATCTTGGATAAGCGAATGTTCTTTTACAATG
Found at i:20604036 original size:26 final size:27
Alignment explanation
Indices: 20603983--20604038 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20603973 TTCTTTATTA
20603983 TTATTTTTTACTTGTTTTTCCTTCTTC
1 TTATTTTTTACTTGTTTTTCCTTCTTC
* *
20604010 TTATTTTTCT-CTTTTTTTTTCTT-TTC
1 TTATTTTT-TACTTGTTTTTCCTTCTTC
20604036 TTA
1 TTA
20604039 AAATATATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 19 0.73
28 1 0.04
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (27 bp):
TTATTTTTTACTTGTTTTTCCTTCTTC
Found at i:20605207 original size:5 final size:5
Alignment explanation
Indices: 20605197--20605257 Score: 88
Period size: 5 Copynumber: 12.0 Consensus size: 5
20605187 TATTAACATA
*
20605197 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -ATAT ATAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT
20605247 AAAAAT AAAAT
1 -AAAAT AAAAT
20605258 TAGGTTGCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
4 3 0.06
5 39 0.76
6 9 0.18
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:20605239 original size:41 final size:41
Alignment explanation
Indices: 20605178--20605257 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
20605168 AAGAAGAGAG
*
20605178 AATAAAATTTATTAACATAAAAATAAAAT-AAAATAAAATAA
1 AATAAAATATATTAACAT-AAAATAAAATAAAAATAAAATAA
20605219 AATAAAATATATATAA-ATAAAATAAAATAAAAATAAAAT
1 AATAAAATATAT-TAACATAAAATAAAATAAAAATAAAAT
20605258 TAGGTTGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
40 10 0.28
41 23 0.64
42 3 0.08
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (41 bp):
AATAAAATATATTAACATAAAATAAAATAAAAATAAAATAA
Found at i:20609818 original size:7 final size:7
Alignment explanation
Indices: 20609806--20609830 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20609796 GAGGGAGAAA
20609806 TTAAATT
1 TTAAATT
20609813 TTAAATT
1 TTAAATT
20609820 TTAAATT
1 TTAAATT
20609827 TTAA
1 TTAA
20609831 TAGCCTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:20618215 original size:9 final size:9
Alignment explanation
Indices: 20618201--20618233 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
20618191 TCGAAAATTT
20618201 TCGAGTTAA
1 TCGAGTTAA
*
20618210 TCGAGTT-T
1 TCGAGTTAA
20618218 TCGAGTTAA
1 TCGAGTTAA
20618227 TCGAGTT
1 TCGAGTT
20618234 TTATCATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
TCGAGTTAA
Found at i:20618220 original size:17 final size:17
Alignment explanation
Indices: 20618198--20618235 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
20618188 GAATCGAAAA
20618198 TTTTCGAGTTAATCGAG
1 TTTTCGAGTTAATCGAG
20618215 TTTTCGAGTTAATCGAG
1 TTTTCGAGTTAATCGAG
20618232 TTTT
1 TTTT
20618236 ATCATCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (17 bp):
TTTTCGAGTTAATCGAG
Found at i:20618979 original size:30 final size:31
Alignment explanation
Indices: 20618940--20618999 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
20618930 GGAGGTGGGA
*
20618940 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
20618971 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
20619000 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:20619517 original size:51 final size:49
Alignment explanation
Indices: 20619461--20619591 Score: 140
Period size: 51 Copynumber: 2.6 Consensus size: 49
20619451 ACTTTAAATG
*
20619461 TAAAAATTAAGAATTAAAATATTTTTATTTATATTAATTAT-TTAAAATATA
1 TAAAAATTAA-AATTAAATTATTTTT-TTTATA-TAATTATATTAAAATATA
* * * *
20619512 TAAAAATT-AAATTAAATTATATTTTGTATATAATTATATTAAATTATT
1 TAAAAATTAAAATTAAATTATTTTTTTTATATAATTATATTAAAATATA
* *
20619560 TAAATATTATATAATTTAATTATTTTTTTTAT
1 TAAAAATTA-A-AATTAAATTATTTTTTTTAT
20619592 TTTCTACTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
47 7 0.10
48 20 0.30
49 13 0.19
50 2 0.03
51 25 0.37
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (49 bp):
TAAAAATTAAAATTAAATTATTTTTTTTATATAATTATATTAAAATATA
Found at i:20621771 original size:4 final size:4
Alignment explanation
Indices: 20621762--20621820 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
20621752 ATGTATGCAA
20621762 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
20621810 ATAC ATAC ATA
1 ATAC ATAC ATA
20621821 GAATCGTTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:20621887 original size:25 final size:26
Alignment explanation
Indices: 20621859--20621921 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
20621849 ATACGTGACT
20621859 GCATGCATAGATCCTA-AATAGTGCG
1 GCATGCATAGATCCTATAATAGTGCG
* *
20621884 GCATGCATAGATCCTATAATGGTGCT
1 GCATGCATAGATCCTATAATAGTGCG
*
20621910 ACATGCATAGAT
1 GCATGCATAGAT
20621922 AGTGTTACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 16 0.47
26 18 0.53
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (26 bp):
GCATGCATAGATCCTATAATAGTGCG
Found at i:20628112 original size:2 final size:2
Alignment explanation
Indices: 20628105--20628131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20628095 TGGTCCAAAT
20628105 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20628132 GCTAAATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20629324 original size:20 final size:20
Alignment explanation
Indices: 20629299--20629341 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
20629289 CTATACGTTT
20629299 TTTAAAAAAT-ATTTTTAAAA
1 TTTAAAAAATGA-TTTTAAAA
*
20629319 TTTAAAATATGATTTTAAAA
1 TTTAAAAAATGATTTTAAAA
20629339 TTT
1 TTT
20629342 CTTAAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAAAAAATGATTTTAAAA
Found at i:20629505 original size:23 final size:22
Alignment explanation
Indices: 20629459--20629509 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
20629449 TGAAACATTA
20629459 TTTTAAAATAATTTTACAAGTT
1 TTTTAAAATAATTTTACAAGTT
* *
20629481 TTATTAAAATATTATTTATAA-TT
1 TT-TTAAAATAAT-TTTACAAGTT
20629504 TTTTAA
1 TTTTAA
20629510 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.24
23 13 0.52
24 6 0.24
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTAAAATAATTTTACAAGTT
Found at i:20630058 original size:112 final size:112
Alignment explanation
Indices: 20629902--20630188 Score: 321
Period size: 112 Copynumber: 2.6 Consensus size: 112
20629892 ATCTGAAGAT
* * *
20629902 CAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGTTTATGGAAAAACGCCGCTA
1 CAAAACGCATCATTTT-GTCTAGATGTATATTAGAATTAGTGGCGTTTATGGAAAAACGCCGCTA
* *
20629967 AAGGAAGTATTAGCGGCACATTGCCGAAAGCGCCGCAA-AAATCTTAAC
65 AAGGAAGTATTAGCGGCAC-TTACCAAAAGCGCCGCAACAAATCTTAAC
* * * * * * * *
20630015 GAAAACGCATCATTTTATCTCGCTGTATATTAGCATTAGTGGCGCTTA-CGAAAACCCGCCGCTA
1 CAAAACGCATCATTTTGTCTAGATGTATATTAGAATTAGTGGCGTTTATGGAAAA-ACGCCGCTA
* * *
20630079 AAGGAAGTATTAGCGGCGCTTACCAAAAGCGCCGCAACATATGTTAAC
65 AAGGAAGTATTAGCGGCACTTACCAAAAGCGCCGCAACAAATCTTAAC
* * * *
20630127 CAAAACGCA-GAGTTTGGTCTAGAGGTATGTTAGAATTTA-TGGCGTTTATGGAAAAACGCCGC
1 CAAAACGCATCA-TTTTGTCTAGATGTATATTAGAA-TTAGTGGCGTTTATGGAAAAACGCCGC
20630189 AAACTATCCT
Statistics
Matches: 142, Mismatches: 27, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
111 22 0.15
112 98 0.69
113 22 0.15
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (112 bp):
CAAAACGCATCATTTTGTCTAGATGTATATTAGAATTAGTGGCGTTTATGGAAAAACGCCGCTAA
AGGAAGTATTAGCGGCACTTACCAAAAGCGCCGCAACAAATCTTAAC
Found at i:20630741 original size:229 final size:227
Alignment explanation
Indices: 20630236--20630793 Score: 550
Period size: 229 Copynumber: 2.4 Consensus size: 227
20630226 TGTATGTTAC
* * * * * * *
20630236 AATTAGTGGCGTTTAAGGGAAAACGCCGCTAAAGCATGATATTAGCGGCGTTTTGAGGAAAGCGC
1 AATTAGTGGCGTCTACGAGAAATCGCCGCTAAAGCATG-TATTAGCGGCGCTTGGAGAAAAGCGC
*
20630301 CACAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCAAAG
65 CACAAAATATCTTAACCAAAACGCAGAGTTTGGTCATGAGGTATACTAGAATTAGTGGCGCAAAG
* * * * * * * *
20630366 GGTACACGCCGCTAAGGCATACTATTAACGGCGTTTTCAGAGAAGAGCCGCAACATTTGGTAACC
130 GGGACACGCCGCTAAAGCATACTATTAACGGCATTTTCAGAGAAGAGCCACAAAATATAGTAACA
* ** *
20630431 AAAACGCAATGTTTTTGTCTTGATGTATACAGT
195 AAAACGCAACGTTTAAGTCTTGATGTATACAGG
* * * * *
20630464 TATTAGTGGCG-CATATCAAAAAAT-GCCGCTAAATCATAGAATTAGCGGCGCTTGGCA-AAAAG
1 AATTAGTGGCGTC-TA-CGAGAAATCGCCGCTAAAGCAT-GTATTAGCGGCGCTTGG-AGAAAAG
* * ** * *
20630526 CGCCGCAAAATATGC-TCACCAAAACGCAGAGTTTTTTCATGAGGTATATTAGACTTAGTGGCGC
62 CGCCACAAAATAT-CTTAACCAAAACGCAGAGTTTGGTCATGAGGTATACTAGAATTAGTGGCGC
** * ** * *
20630590 TTATGGGGGA-ACGCCGCTAAAGCATATTATTTGCGGCATTTTCTGAGAAGCGCCACAAAATATA
126 --AAAGGGGACACGCCGCTAAAGCATACTATTAACGGCATTTTCAGAGAAGAGCCACAAAATATA
* * * *
20630654 TTAACAAAAATGCAGCGTTTAAGTCTTGATGTATACTGG
189 GTAACAAAAACGCAACGTTTAAGTCTTGATGTATACAGG
* * *** *
20630693 AATTAGTGGCGTCCACGAGAAATCGCCGCTAAAGCATCGTATTAGCGGCGTTTTTTGAGAAGCGC
1 AATTAGTGGCGTCTACGAGAAATCGCCGCTAAAGCAT-GTATTAGCGGCGCTTGGAGAAAAGCGC
*
20630758 CAGAAAATATCTTAACCAAAACGCAGAGTTTTGGTC
65 CACAAAATATCTTAACCAAAACGCAGAG-TTTGGTC
20630794 TTAACCATGC
Statistics
Matches: 259, Mismatches: 59, Indels: 22
0.76 0.17 0.06
Matches are distributed among these distances:
228 103 0.40
229 145 0.56
230 11 0.04
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (227 bp):
AATTAGTGGCGTCTACGAGAAATCGCCGCTAAAGCATGTATTAGCGGCGCTTGGAGAAAAGCGCC
ACAAAATATCTTAACCAAAACGCAGAGTTTGGTCATGAGGTATACTAGAATTAGTGGCGCAAAGG
GGACACGCCGCTAAAGCATACTATTAACGGCATTTTCAGAGAAGAGCCACAAAATATAGTAACAA
AAACGCAACGTTTAAGTCTTGATGTATACAGG
Found at i:20630795 original size:115 final size:113
Alignment explanation
Indices: 20630213--20630795 Score: 434
Period size: 115 Copynumber: 5.1 Consensus size: 113
20630203 AAAGTGCACC
* ** * *
20630213 GTTTTGGTCTTGGTGTATGTTACAATTAGTGGCGTTTAAGGGAAAACGCCGCTAAAGCAT-GATA
1 GTTTTGGTCTTGATGTATACTAGAATTAGTGGCG-CTAAGGG-AAACGCCGCTAAAGCATAG-TA
*
20630277 TTAGCGGCG-TTT-TGAGGAAAGCGCCACAAAATATCTTAACCAAAACGCAGA
63 TTAGCGGCGTTTTCTGA-G-AAGCGCCAGAAAATATCTTAACCAAAACGCAGA
* * * * *
20630328 G-TTTGGTCTTGAGGTATACTAGAATTAGTGGCGCAAAGGGTACACGCCGCTAAGGCATACTATT
1 GTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTAAGGG-AAACGCCGCTAAAGCATAGTATT
* * * * * **
20630392 AACGGCGTTTTCAGAGAAGAGCC-GCAACATTTGGTAACCAAAACGCA-A
65 AGCGGCGTTTTCTGAGAAGCGCCAG-AAAATATCTTAACCAAAACGCAGA
* * ** * *
20630440 TGTTTTTGTCTTGATGTATAC-AGTTATTAGTGGCGCATATCA-AAAAATGCCGCTAAATCATAG
1 -GTTTTGGTCTTGATGTATACTAG-AATTAGTGGCGC-TA--AGGGAAACGCCGCTAAAGCATAG
* ** * * *
20630503 AATTAGCGGCGCTTGGC-AAAAAGCGCC-GCAAAATATGC-TCACCAAAACGCAGA
61 TATTAGCGGCG-TTTTCTGAGAAGCGCCAG-AAAATAT-CTTAACCAAAACGCAGA
* * * * * * * *
20630556 GTTTT-TTCATGAGGTATATTAGACTTAGTGGCGCTTATGGGGGAACGCCGCTAAAGCATATTAT
1 GTTTTGGTCTTGATGTATACTAGAATTAGTGGCGC-TA-AGGGAAACGCCGCTAAAGCATAGTAT
* * * * * * *
20630620 TTGCGGCATTTTCTGAGAAGCGCCACAAAATATATTAACAAAAATGCAGC
64 TAGCGGCGTTTTCTGAGAAGCGCCAGAAAATATCTTAACCAAAACGCAGA
** * * * * *
20630670 GTTTAAGTCTTGATGTATACTGGAATTAGTGGCGTCCACGAGAAATCGCCGCTAAAGCATCGTAT
1 GTTTTGGTCTTGATGTATACTAGAATTAGTGGCG-CTAAGGGAAA-CGCCGCTAAAGCATAGTAT
*
20630735 TAGCGGCGTTTTTTGAGAAGCGCCAGAAAATATCTTAACCAAAACGCAGA
64 TAGCGGCGTTTTCTGAGAAGCGCCAGAAAATATCTTAACCAAAACGCAGA
20630785 GTTTTGGTCTT
1 GTTTTGGTCTT
20630796 AACCATGCAT
Statistics
Matches: 355, Mismatches: 92, Indels: 42
0.73 0.19 0.09
Matches are distributed among these distances:
112 1 0.00
113 60 0.17
114 137 0.39
115 151 0.43
116 5 0.01
117 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (113 bp):
GTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTAAGGGAAACGCCGCTAAAGCATAGTATTA
GCGGCGTTTTCTGAGAAGCGCCAGAAAATATCTTAACCAAAACGCAGA
Found at i:20632078 original size:22 final size:21
Alignment explanation
Indices: 20632053--20632149 Score: 97
Period size: 21 Copynumber: 4.4 Consensus size: 21
20632043 CAACAACTTA
* *
20632053 AAGCAGAGGCGGCAGCGAGGGG
1 AAGCAGAGGCAGCAGCGA-GAG
20632075 AAGCAGAGGCTA-CAGCGAGAG
1 AAGCAGAGGC-AGCAGCGAGAG
*
20632096 AAGCAGAGGCAGCAGCAAGAG
1 AAGCAGAGGCAGCAGCGAGAG
* *
20632117 AAGCAGCGAGAGAAGCAGCGATAG
1 AAGCA--GAG-GCAGCAGCGAGAG
20632141 AAGCAGAGG
1 AAGCAGAGG
20632150 TTCAAAAGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.02
21 26 0.41
22 19 0.30
23 3 0.05
24 15 0.23
ACGTcount: A:0.38, C:0.18, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:20632121 original size:12 final size:12
Alignment explanation
Indices: 20632087--20632146 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
20632077 GCAGAGGCTA
20632087 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
20632099 CA--GAG-GCAG
1 CAGCGAGAGAAG
*
20632108 CAGCAAGAGAAG
1 CAGCGAGAGAAG
20632120 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
20632132 CAGCGATAGAAG
1 CAGCGAGAGAAG
20632144 CAG
1 CAG
20632147 AGGTTCAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.12
10 3 0.08
11 2 0.05
12 30 0.75
ACGTcount: A:0.42, C:0.18, G:0.38, T:0.02
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:20632646 original size:42 final size:42
Alignment explanation
Indices: 20632581--20632914 Score: 254
Period size: 42 Copynumber: 7.9 Consensus size: 42
20632571 TTTGTGAAAT
* *
20632581 AAGCGCCGCTA-AGGAACACTACTTTTAGCGGCGTTTTTGACC
1 AAGCGCCGCTATA-GAACATTACTTTTAGCGGCGTTTTTTACC
* * *
20632623 AAGCGCCGCTATAGAATATTACTTTTAGCGGCGTTTTCTTTCA
1 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTT-TTACC
* * * *
20632666 AAGCGCCGCTAAAGATCATGA-TCTTTAGCGGCGTTTTTTCCC
1 AAGCGCCGCTATAGAACATTACT-TTTAGCGGCGTTTTTTACC
* * *
20632708 AAGCGCCGCTATAGAACATTACTTTTAGCGGCATTTTTTTCT
1 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTACC
* * * * *
20632750 AAGCGCCGTTAAAGAACATGA-TCTTTAGCGGTGTTTTTTA-T
1 AAGCGCCGCTATAGAACATTACT-TTTAGCGGCGTTTTTTACC
* * * * *
20632791 AATCGTCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTT-CAT
1 AAGCGCCGCTATAGAACATTACT-TTTAGCGGCGTTTTTTAC-C
* * *
20632833 AAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCATTTATTT-CC
1 AAGCGCCGCTATAGAACATTACT-TTTAGCGGCGTTT-TTTACC
* * * *
20632875 TTAGCGCAGCTAAAGAACATGA-TATTTAGCGGCGTTTTTT
1 -AAGCGCCGCTATAGAACATTACT-TTTAGCGGCGTTTTTT
20632915 TCTGTAAGCG
Statistics
Matches: 248, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
41 37 0.15
42 140 0.56
43 71 0.29
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (42 bp):
AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTACC
Found at i:20632670 original size:85 final size:84
Alignment explanation
Indices: 20632581--20632916 Score: 380
Period size: 85 Copynumber: 4.0 Consensus size: 84
20632571 TTTGTGAAAT
* * *
20632581 AAGCGCCGCTAAGGAACACT-A-CTTTTAGCGGCGTTTTTGACCAAGCGCCGCTATAGAATATTA
1 AAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTACCAAGCGCCGCTATAGAACATTA
20632644 CTTTTAGCGGCGTTTTCTTTCA
64 CTTTTAGCGGCGTTTT-TTTCA
* *
20632666 AAGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTATAGAACATTACT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAGCGCCGCTATAGAACATTACT
* *
20632731 TTTAGCGGCATTTTTTTCT
66 TTTAGCGGCGTTTTTTTCA
* * * * * * *
20632750 AAGCGCCGTTAAAGAACATGATCTTTAGCGGTGTTTTTTA-TAATCGTCGCTAAAGAACATGA-T
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAGCGCCGCTATAGAACATTACT
20632813 CTTTAGCGGCG-TTTTTTCA
66 -TTTAGCGGCGTTTTTTTCA
* * * * *
20632832 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTATTT-CCTTAGCGCAGCTAAAGAACATG
1 -AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTACC-AAGCGCCGCTATAGAACATT
20632896 A-TATTTAGCGGCGTTTTTTTC
63 ACT-TTTAGCGGCGTTTTTTTC
20632917 TGTAAGCGCC
Statistics
Matches: 216, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
82 8 0.04
83 59 0.27
84 44 0.20
85 97 0.45
86 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAGCGCCGCTATAGAACATTACT
TTTAGCGGCGTTTTTTTCA
Found at i:20642100 original size:27 final size:27
Alignment explanation
Indices: 20642058--20642133 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
20642048 ACACATGCAA
* * *
20642058 TCATATAGAGTACGCCACCAAGCCTAT
1 TCATTTAGAGTTCGCCACAAAGCCTAT
*
20642085 TC-TTTCAGAGTTCGCCACAAAGCTTAT
1 TCATTT-AGAGTTCGCCACAAAGCCTAT
*
20642112 TCATTTAGAGTTTGCCACAAAG
1 TCATTTAGAGTTCGCCACAAAG
20642134 GCTGTTCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 37 0.88
28 3 0.07
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (27 bp):
TCATTTAGAGTTCGCCACAAAGCCTAT
Found at i:20645798 original size:15 final size:15
Alignment explanation
Indices: 20645778--20645811 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
20645768 CATGAATTTG
20645778 ACAGTACACCCTGTA
1 ACAGTACACCCTGTA
*
20645793 ACAGTACGCCCTGTA
1 ACAGTACACCCTGTA
20645808 ACAG
1 ACAG
20645812 CCTGCCTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (15 bp):
ACAGTACACCCTGTA
Found at i:20653574 original size:25 final size:25
Alignment explanation
Indices: 20653494--20653574 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
20653484 CTTGCCACCA
*
20653494 AGGCTTCCCAAATAATACGCCACAT
1 AGGCTTCTCAAATAATACGCCACAT
* * *
20653519 AGACCTT-TCAAGTAACTA-GCCACAA
1 AG-GCTTCTCAAATAA-TACGCCACAT
* *
20653544 AAGCTTCTGAAATAATACGCCACAT
1 AGGCTTCTCAAATAATACGCCACAT
20653569 AGGCTT
1 AGGCTT
20653575 TTTAGATAGA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
24 5 0.12
25 32 0.76
26 5 0.12
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (25 bp):
AGGCTTCTCAAATAATACGCCACAT
Found at i:20658355 original size:16 final size:16
Alignment explanation
Indices: 20658331--20658361 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20658321 TGTTTCTGAG
*
20658331 CATGGCATACTGCATA
1 CATGACATACTGCATA
20658347 CATGACATACTGCAT
1 CATGACATACTGCAT
20658362 GGGGTTAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (16 bp):
CATGACATACTGCATA
Found at i:20671088 original size:30 final size:30
Alignment explanation
Indices: 20671033--20671108 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
20671023 CACTAAGCAA
20671033 GTTTCATATATATATATCATCCATTT-CAT
1 GTTTCATATATATATATCATCCATTTCCAT
20671062 GTTTCAATATATCATATAAT-AT-CATTTCCAT
1 GTTTC-ATATAT-ATAT-ATCATCCATTTCCAT
*
20671093 GTATTTCATGTATATA
1 G--TTTCATATATATA
20671109 CCTGTAATAG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
29 5 0.12
30 11 0.28
31 13 0.32
32 7 0.17
33 4 0.10
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.47
Consensus pattern (30 bp):
GTTTCATATATATATATCATCCATTTCCAT
Found at i:20671307 original size:25 final size:25
Alignment explanation
Indices: 20671279--20671352 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
20671269 TATGCTCTCT
20671279 CGAGCTGGAAATCGGTAAGCTCATA
1 CGAGCTGGAAATCGGTAAGCTCATA
** *
20671304 CGAGCT-GAGAATTAGTAAGTTC-TCA
1 CGAGCTGGA-AATCGGTAAGCTCAT-A
*
20671329 CGAGTTGG-AATCGGTAAGCTCATA
1 CGAGCTGGAAATCGGTAAGCTCATA
20671353 TGATCTGTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
24 14 0.37
25 23 0.61
26 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (25 bp):
CGAGCTGGAAATCGGTAAGCTCATA
Found at i:20671338 original size:50 final size:49
Alignment explanation
Indices: 20671247--20671352 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 49
20671237 GTACATGTAT
* *
20671247 GCTCATACGAGCTATGAATCAGTATGCTCTCTCGAGCTGGAAATCGGTAA
1 GCTCATACGAGCTATGAATCAGTAAGCTCTCACGAGCTGG-AATCGGTAA
* * *
20671297 GCTCATACGAGCTGA-GAATTAGTAAGTTCTCACGAGTTGGAATCGGTAA
1 GCTCATACGAGCT-ATGAATCAGTAAGCTCTCACGAGCTGGAATCGGTAA
20671346 GCTCATA
1 GCTCATA
20671353 TGATCTGTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 16 0.32
50 33 0.66
51 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (49 bp):
GCTCATACGAGCTATGAATCAGTAAGCTCTCACGAGCTGGAATCGGTAA
Found at i:20675274 original size:28 final size:29
Alignment explanation
Indices: 20675203--20675280 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
20675193 TGGTATCCAT
** *
20675203 CACCGGTACATAGTACCTATTATATATAA
1 CACCGGTACATAGTACCTGCTATATACAA
** * *
20675232 CACCGACACAAAGTACCTGCTA-CTACAA
1 CACCGGTACATAGTACCTGCTATATACAA
*
20675260 CACCGGTACATAGTACTTGCT
1 CACCGGTACATAGTACCTGCT
20675281 GGATATAATG
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (29 bp):
CACCGGTACATAGTACCTGCTATATACAA
Found at i:20684523 original size:26 final size:26
Alignment explanation
Indices: 20684494--20684566 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
20684484 CCCATTTTAT
*
20684494 GGCTCTTCATGAGCTTCCCGGTTAAA
1 GGCTCTTCATGAGCTTCCCGATTAAA
** ** *
20684520 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTCATGAGCTTCCCGATTAAA
*
20684546 GGCTCTCCA-GAGCTTCCCGAT
1 GGCTCTTCATGAGCTTCCCGAT
20684567 ATGGCTCACT
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
25 10 0.28
26 26 0.72
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCCGATTAAA
Found at i:20684609 original size:25 final size:25
Alignment explanation
Indices: 20684530--20684610 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 25
20684520 GGCTCTTTGT
** * *
20684530 GAGCTTCCTAATTAATGGCTCTCCA
1 GAGCTTCCCGATTTATGGCTATCCA
**
20684555 GAGCTTCCCGA--TATGGCTCA-CTT
1 GAGCTTCCCGATTTATGGCT-ATCCA
* *
20684578 GAACTTCCCGATTTATGGCTATCCG
1 GAGCTTCCCGATTTATGGCTATCCA
20684603 GAGCTTCC
1 GAGCTTCC
20684611 TGTTAGTGGC
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
23 17 0.40
24 1 0.02
25 24 0.57
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGATTTATGGCTATCCA
Done.