Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007985.1 Hibiscus syriacus cultivar Beakdansim tig00110430_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2235968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1647661 original size:21 final size:21
Alignment explanation
Indices: 1647613--1647667 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1647603 GTTATTTTTT
*
1647613 TCTACTGGAAATATTAATTTA
1 TCTACTTGAAATATTAATTTA
*
1647634 TCTACTTGAAATATTAATTTC
1 TCTACTTGAAATATTAATTTA
*
1647655 TCTACTTAAAATA
1 TCTACTTGAAATA
1647668 AATATTTCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (21 bp):
TCTACTTGAAATATTAATTTA
Found at i:1650140 original size:25 final size:24
Alignment explanation
Indices: 1650107--1650153 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1650097 TTTAAATGAT
*
1650107 TTAATATTTTATTA-ATTATTTTTA
1 TTAATATTTAATTACA-TATTTTTA
1650131 TTAATAATTTAATTACATATTTT
1 TTAAT-ATTTAATTACATATTTT
1650154 AAATATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 14 0.70
26 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTAATATTTAATTACATATTTTTA
Found at i:1650154 original size:13 final size:12
Alignment explanation
Indices: 1650107--1650155 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
1650097 TTTAAATGAT
1650107 TTAATATTTT-A
1 TTAATATTTTAA
*
1650118 TTAATTATTTTTA
1 TTAA-TATTTTAA
*
1650131 TTAATAATTTAA
1 TTAATATTTTAA
1650143 TTACATATTTTAA
1 TTA-ATATTTTAA
1650156 ATATTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 4 0.12
12 15 0.47
13 13 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAATATTTTAA
Found at i:1654808 original size:16 final size:17
Alignment explanation
Indices: 1654786--1654835 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
1654776 TGACTCACAG
1654786 TTTCCATGTTGAAACAA
1 TTTCCATGTTGAAACAA
*
1654803 -TTCCATG-TGACTCACAA
1 TTTCCATGTTGA--AACAA
1654820 TTTCCATGTTGAAACA
1 TTTCCATGTTGAAACA
1654836 TTAACCCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 3 0.11
16 7 0.26
17 7 0.26
18 7 0.26
19 3 0.11
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (17 bp):
TTTCCATGTTGAAACAA
Found at i:1654826 original size:18 final size:18
Alignment explanation
Indices: 1654776--1654828 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1654766 TCCATGCTTC
*
1654776 TGACTCACAGTTTCCATG
1 TGACTCACAATTTCCATG
*
1654794 TTGA--AACAA-TTCCATG
1 -TGACTCACAATTTCCATG
1654810 TGACTCACAATTTCCATG
1 TGACTCACAATTTCCATG
1654828 T
1 T
1654829 TGAAACATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.11
16 7 0.25
17 7 0.25
18 8 0.29
19 3 0.11
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (18 bp):
TGACTCACAATTTCCATG
Found at i:1655766 original size:31 final size:31
Alignment explanation
Indices: 1655708--1655766 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
1655698 ATTTTAGTTT
* * **
1655708 TTTAGAGTTTTTTTTATAATTTCATTAAAAG
1 TTTAGAGTTTTTTTAATAAATAAATTAAAAG
*
1655739 TTTAGGGTTTTTTTAATAAATAAATTAA
1 TTTAGAGTTTTTTTAATAAATAAATTAA
1655767 GTTTTTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.53
Consensus pattern (31 bp):
TTTAGAGTTTTTTTAATAAATAAATTAAAAG
Found at i:1660051 original size:16 final size:17
Alignment explanation
Indices: 1660017--1660049 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1660007 TTTCGGTTTG
*
1660017 AAAAAAATCGGTTTTTT
1 AAAAAAACCGGTTTTTT
1660034 AAAAAAACCGGTTTTT
1 AAAAAAACCGGTTTTT
1660050 AATCCGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (17 bp):
AAAAAAACCGGTTTTTT
Found at i:1660102 original size:19 final size:20
Alignment explanation
Indices: 1660078--1660141 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
1660068 ATCATCCAAT
*
1660078 TTTTTAAA-CCCATACCGGA
1 TTTTTAAACCCCAGACCGGA
* *
1660097 TTTTTAAACCCCAGACTGAA
1 TTTTTAAACCCCAGACCGGA
1660117 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
1660137 TTTTT
1 TTTTT
1660142 TTCCGGATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:1660234 original size:16 final size:16
Alignment explanation
Indices: 1660215--1660249 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1660205 CGATTTTAAA
*
1660215 AAAACCGATTTTTCCC
1 AAAACAGATTTTTCCC
1660231 AAAACAGATTTTTCCC
1 AAAACAGATTTTTCCC
1660247 AAA
1 AAA
1660250 TTCGATTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAACAGATTTTTCCC
Found at i:1668078 original size:2 final size:2
Alignment explanation
Indices: 1668067--1668098 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1668057 ACATTCATGC
1668067 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1668099 AGCAGGTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1671157 original size:14 final size:14
Alignment explanation
Indices: 1671138--1671164 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1671128 GGTAAAACAT
1671138 CCTTACTTTTCAGA
1 CCTTACTTTTCAGA
1671152 CCTTACTTTTCAG
1 CCTTACTTTTCAG
1671165 TGTATAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.30, G:0.07, T:0.44
Consensus pattern (14 bp):
CCTTACTTTTCAGA
Found at i:1671415 original size:12 final size:12
Alignment explanation
Indices: 1671386--1671423 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1671376 AATTATTAAC
1671386 ATATTTAA-AAT
1 ATATTTAATAAT
*
1671397 ATATTTATTAAT
1 ATATTTAATAAT
*
1671409 ATTTTTAATAAT
1 ATATTTAATAAT
1671421 ATA
1 ATA
1671424 ATATAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:1671415 original size:23 final size:23
Alignment explanation
Indices: 1671368--1671425 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
1671358 TTTTAATAAA
1671368 AAAATATTAATTATTAACATATTT
1 AAAATA-TAATTATTAACATATTT
* * *
1671392 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAACATATTT
1671415 AATAATATAAT
1 AA-AATATAAT
1671426 ATAATATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAACATATTT
Found at i:1671480 original size:23 final size:20
Alignment explanation
Indices: 1671421--1671468 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1671411 TTTTAATAAT
1671421 ATAATATA-ATATTATTACA
1 ATAATATACATATTATTACA
1671440 ATAATATACATATTATTACA
1 ATAATATACATATTATTACA
1671460 ATAATATAC
1 ATAATATAC
1671469 TCAATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATATACATATTATTACA
Found at i:1671814 original size:15 final size:15
Alignment explanation
Indices: 1671767--1671817 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
1671757 ATACTAGAGT
* *
1671767 TAATATTTTTATTTA
1 TAATATTTTTAATAA
* * *
1671782 TAA-AATTATAAAAA
1 TAATATTTTTAATAA
1671796 TAATATTTTTAATAA
1 TAATATTTTTAATAA
1671811 TAATATT
1 TAATATT
1671818 GGCATAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAATATTTTTAATAA
Found at i:1671901 original size:22 final size:20
Alignment explanation
Indices: 1671849--1671902 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
1671839 ATTATTATAA
*
1671849 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
1671869 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
1671892 TATTTATTATA
1 TATTT-TTATA
1671903 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 15 0.52
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:1673775 original size:37 final size:34
Alignment explanation
Indices: 1673694--1673775 Score: 85
Period size: 37 Copynumber: 2.3 Consensus size: 34
1673684 AATTTTGTAA
* *
1673694 AAAAAT-TATATAAATATTATAATTTAATTTTTT
1 AAAAATATATATAAATATTATAATTTAATATTAT
*
1673727 AAAGAAAATATATAAATATTTTATAATTGTAATATTAT
1 AAA-AATATATATAAATA--TTATAATT-TAATATTAT
*
1673765 ACAAATATATA
1 AAAAATATATA
1673776 ATTTAGACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 3 0.08
34 2 0.05
35 10 0.26
37 15 0.38
38 9 0.23
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (34 bp):
AAAAATATATATAAATATTATAATTTAATATTAT
Found at i:1685291 original size:37 final size:39
Alignment explanation
Indices: 1685250--1685335 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 39
1685240 TAAAAAAAAA
* *
1685250 TTGGGTTTGGGTC-GATC-AGTTTTTTTAAGTTTGATAT
1 TTGGGTTCGGGTCAGATCGAGTTTTTTTAAGTGTGATAT
* * *
1685287 TTGGG-TCGTGTCAGGTCGGGTTTTTTTAAGTGTGATAT
1 TTGGGTTCGGGTCAGATCGAGTTTTTTTAAGTGTGATAT
1685325 TTGGG-TCGGGT
1 TTGGGTTCGGGT
1685336 TCAGGTTTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 5 0.12
37 8 0.20
38 28 0.68
ACGTcount: A:0.13, C:0.07, G:0.34, T:0.47
Consensus pattern (39 bp):
TTGGGTTCGGGTCAGATCGAGTTTTTTTAAGTGTGATAT
Found at i:1685317 original size:38 final size:39
Alignment explanation
Indices: 1685268--1685341 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 39
1685258 GGGTCGATCA
* *
1685268 GTTTTTTTAAGTTTGATATTTGGGTCGTG-TCAGGTCGG
1 GTTTTTTTAAGTGTGATATTTGGGTCGGGTTCAGGTCGG
1685306 GTTTTTTTAAGTGTGATATTTGGGTCGGGTTCAGGT
1 GTTTTTTTAAGTGTGATATTTGGGTCGGGTTCAGGT
1685342 TTAGGGTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 27 0.82
39 6 0.18
ACGTcount: A:0.14, C:0.07, G:0.32, T:0.47
Consensus pattern (39 bp):
GTTTTTTTAAGTGTGATATTTGGGTCGGGTTCAGGTCGG
Found at i:1686366 original size:31 final size:31
Alignment explanation
Indices: 1686328--1686455 Score: 168
Period size: 31 Copynumber: 4.0 Consensus size: 31
1686318 CCCGAAGGAC
*
1686328 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1686359 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1686390 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * * *
1686421 CCCTCGACCCTTTGTCCCGAAGAACATAGGTAAA
1 --C-AGTCCATATGTCCCGAAGAACATAGGTAAA
1686455 C
1 C
1686456 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
31 59 0.67
32 2 0.02
33 1 0.01
34 26 0.30
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1686442 original size:34 final size:34
Alignment explanation
Indices: 1686368--1686466 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
1686358 ACAGTCCATA
* * * *
1686368 TGTCCCGAAGAACATAGGTAAA--C-AGTCCATA
1 TGTCCCGAAGAACATAGGTAAACCCTCGACCCTT
1686399 TGTCCCGAAGAACATAGGTAAACCCTCGACCCTT
1 TGTCCCGAAGAACATAGGTAAACCCTCGACCCTT
1686433 TGTCCCGAAGAACATAGGTAAACCCTCGACCCTT
1 TGTCCCGAAGAACATAGGTAAACCCTCGACCCTT
1686467 GGCATGCCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 22 0.36
33 1 0.02
34 38 0.62
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.20
Consensus pattern (34 bp):
TGTCCCGAAGAACATAGGTAAACCCTCGACCCTT
Found at i:1704614 original size:2 final size:2
Alignment explanation
Indices: 1704607--1704636 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1704597 TGTTTGACTT
1704607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1704637 ACAAGACCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1711787 original size:2 final size:2
Alignment explanation
Indices: 1711780--1711807 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1711770 CTATCAATCC
1711780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1711808 ACAAGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1718885 original size:4 final size:4
Alignment explanation
Indices: 1718878--1719069 Score: 325
Period size: 4 Copynumber: 48.5 Consensus size: 4
1718868 AAATAAATCT
1718878 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1718926 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
1718974 TGTA TGTA TG-- TGTG TGTG TGTG TGTG TGTG TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1719020 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1719068 TG
1 TG
1719070 AATGAATGAA
Statistics
Matches: 185, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
2 2 0.01
4 183 0.99
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:1718989 original size:2 final size:2
Alignment explanation
Indices: 1718982--1719006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1718972 TATGTATGTA
1718982 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1719007 ATGTATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1734777 original size:18 final size:18
Alignment explanation
Indices: 1734750--1734784 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1734740 GTGACATGGG
*
1734750 AATTAAATATTTTATCTT
1 AATTAAATATTTAATCTT
*
1734768 AATTACATATTTAATCT
1 AATTAAATATTTAATCT
1734785 CTGTTATTTA
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:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTAAATATTTAATCTT
Found at i:1740429 original size:41 final size:41
Alignment explanation
Indices: 1740384--1740475 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
1740374 GACCTCTAGG
* *
1740384 CCATCAGTAAAACTTCTGAATTAGATAAAAAGATCTTTCAA
1 CCATCAGTAAAACTTCTGAACTAGATAAAAAGATCTCTCAA
* * *
1740425 CCATCAGTAAATCTTCTGAACTAGATGAAAAGATCTCTCAG
1 CCATCAGTAAAACTTCTGAACTAGATAAAAAGATCTCTCAA
1740466 CCATCAGTAA
1 CCATCAGTAA
1740476 GACCTTTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (41 bp):
CCATCAGTAAAACTTCTGAACTAGATAAAAAGATCTCTCAA
Found at i:1746506 original size:19 final size:17
Alignment explanation
Indices: 1746482--1746520 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
1746472 TTTGATAAAT
1746482 ATAAAAGAATGAATATATA
1 ATAAAAGAAT-AATAT-TA
1746501 ATAAAAGAATAATATTA
1 ATAAAAGAATAATATTA
1746518 ATA
1 ATA
1746521 TTGTTATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 5 0.25
19 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (17 bp):
ATAAAAGAATAATATTA
Found at i:1751724 original size:16 final size:18
Alignment explanation
Indices: 1751684--1751726 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1751674 TGTTTATGAG
1751684 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGTGAA
1751702 GGAATTGAAATCTGT-AA
1 GGAATTGAAATCTGTGAA
1751719 -GAATTGAA
1 GGAATTGAA
1751727 TCCAATTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 8 0.32
17 2 0.08
18 15 0.60
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:1752388 original size:36 final size:37
Alignment explanation
Indices: 1752305--1752389 Score: 136
Period size: 38 Copynumber: 2.3 Consensus size: 37
1752295 TTCACCCTAA
*
1752305 ACCCGACCTGACCCGAATATCACACTTAAAAAATCCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAT-CCG
*
1752343 ACCTGACCCGACCCGAATATCACACTTAAAAAAT-CG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAATCCG
1752379 ACCCGACCCGA
1 ACCCGACCCGA
1752390 ACAAAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 12 0.27
38 32 0.73
ACGTcount: A:0.36, C:0.38, G:0.12, T:0.14
Consensus pattern (37 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAATCCG
Found at i:1752652 original size:31 final size:31
Alignment explanation
Indices: 1752617--1752726 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 31
1752607 ACACTTAAAA
1752617 ATCCGACCCGACCCGAACAAAATAAAGTTTC
1 ATCCGACCCGACCCGAACAAAATAAAGTTTC
** ** *
1752648 ATCCGATTCGACCCGAATATCACACTTAAA----A
1 ATCCGACCCGACCCG-A-A-CA-AAATAAAGTTTC
*
1752679 ACCCGACCCGACCCGAACAAAATAAAGTTTC
1 ATCCGACCCGACCCGAACAAAATAAAGTTTC
**
1752710 ATCCGATTCGACCCGAA
1 ATCCGACCCGACCCGAA
1752727 TATATGAATT
Statistics
Matches: 57, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
27 5 0.09
28 2 0.04
29 1 0.02
30 1 0.02
31 39 0.68
32 1 0.02
33 1 0.02
34 2 0.04
35 5 0.09
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (31 bp):
ATCCGACCCGACCCGAACAAAATAAAGTTTC
Found at i:1752668 original size:62 final size:62
Alignment explanation
Indices: 1752588--1752756 Score: 259
Period size: 62 Copynumber: 2.7 Consensus size: 62
1752578 AAAAACCCAA
* *
1752588 CCGACTCGACCCGGATATCACACTTAAAAATCCGACCCGACCCGAACAAAATAAAGTTTCAT
1 CCGATTCGACCCGAATATCACACTTAAAAATCCGACCCGACCCGAACAAAATAAAGTTTCAT
*
1752650 CCGATTCGACCCGAATATCACACTTAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCAT
1 CCGATTCGACCCGAATATCACACTTAAAAATCCGACCCGACCCGAACAAAATAAAGTTTCAT
* * * *
1752712 CCGATTCGACCCGAATAT-ATGAATTAGAAATCCAACCCGACCCGA
1 CCGATTCGACCCGAATATCA-CACTTAAAAATCCGACCCGACCCGA
1752757 CCCGAAATAA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
61 1 0.01
62 97 0.99
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (62 bp):
CCGATTCGACCCGAATATCACACTTAAAAATCCGACCCGACCCGAACAAAATAAAGTTTCAT
Found at i:1753626 original size:30 final size:30
Alignment explanation
Indices: 1753583--1753647 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
1753573 AGTGCTCCAT
* *
1753583 AGGTCGCCGTGTGCTATTGGAGACCTATGG
1 AGGTCGCCATGTGCTACTGGAGACCTATGG
* * *
1753613 AGGTCGTCATGTGCTCCTGGAGACTTATGG
1 AGGTCGCCATGTGCTACTGGAGACCTATGG
*
1753643 TGGTC
1 AGGTC
1753648 ATTGTAGCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.15, C:0.20, G:0.35, T:0.29
Consensus pattern (30 bp):
AGGTCGCCATGTGCTACTGGAGACCTATGG
Found at i:1759821 original size:28 final size:30
Alignment explanation
Indices: 1759743--1759822 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 30
1759733 TTTTATACAT
1759743 TTTAAAATATAATA-ATA-ATTATTATTAA
1 TTTAAAATATAATATATATATTATTATTAA
* *
1759771 TTTAAAATATAATAACTCGTATATT-TTTTTAA
1 TTTAAAATATAAT-A-T-ATATATTATTATTAA
1759803 TTTAAAA-ATAATATATATAT
1 TTTAAAATATAATATATATAT
1759823 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
28 18 0.41
29 2 0.05
30 1 0.02
31 5 0.11
32 15 0.34
33 3 0.07
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (30 bp):
TTTAAAATATAATATATATATTATTATTAA
Found at i:1767966 original size:65 final size:65
Alignment explanation
Indices: 1767882--1768012 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
1767872 TCAAAATGAG
* *
1767882 TAACCTACAATGCGTCAAAGACATCGACTGCATAATCTCTAGCGTAAATCATGAAAAATAAAACA
1 TAACCTACAATGCATCAAAGACATCGACTGAATAATCTCTAGCGTAAATCATGAAAAATAAAACA
*
1767947 TAACCTACAATGCATCAAAGACATCGACTGAATAATCTCTAGCGTAAATCATGAAAACTAAAACA
1 TAACCTACAATGCATCAAAGACATCGACTGAATAATCTCTAGCGTAAATCATGAAAAATAAAACA
1768012 T
1 T
1768013 TATGTTGTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.22
Consensus pattern (65 bp):
TAACCTACAATGCATCAAAGACATCGACTGAATAATCTCTAGCGTAAATCATGAAAAATAAAACA
Found at i:1780354 original size:20 final size:20
Alignment explanation
Indices: 1780329--1780367 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1780319 TAAATTAAAT
*
1780329 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
1780349 ATTAGATAGAATTAGTTTT
1 ATTAGATAGAATCAGTTTT
1780368 TTTTTCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.44
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1780408 original size:53 final size:53
Alignment explanation
Indices: 1780328--1780478 Score: 234
Period size: 53 Copynumber: 2.9 Consensus size: 53
1780318 CTAAATTAAA
* * * *
1780328 TATTAGATAGGATCAGTTTTAATTAGATAGAATTAGTTTTTTTTTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTCTTTTATTCTATTAGT
*
1780381 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTCTTTTATTGTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTCTTTTATTCTATTAGT
*
1780434 TATTAGATATGATCATTTTTAATTAGATAGAATCA-T-TTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTCTTTTATTCT
1780479 GTTGCTAATT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 8 0.09
52 1 0.01
53 82 0.90
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTCTTTTATTCTATTAGT
Found at i:1780460 original size:20 final size:20
Alignment explanation
Indices: 1780435--1780474 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1780425 TGTATTAGTT
1780435 ATTAGATATG-ATCATTTTTA
1 ATTAGATA-GAATCATTTTTA
1780455 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1780475 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:1785004 original size:20 final size:20
Alignment explanation
Indices: 1784979--1785017 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1784969 TAAATTAAAT
*
1784979 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1784999 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
1785018 TTTTTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1785058 original size:53 final size:53
Alignment explanation
Indices: 1784978--1785128 Score: 252
Period size: 53 Copynumber: 2.9 Consensus size: 53
1784968 CTAAATTAAA
* *
1784978 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTTTTTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
* *
1785031 TATTAGATAAGATCATTTTTAATTAGATAGAATCAGTCTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1785084 TATTAGATAGGATCATTTTTAATTAGATAGAATCA--TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCT
1785129 GTTGTTAATT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 9 0.10
53 83 0.90
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
Found at i:1785110 original size:20 final size:20
Alignment explanation
Indices: 1785085--1785124 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1785075 TCTATTAGTT
*
1785085 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1785105 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1785125 TTCTGTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:1786202 original size:3 final size:3
Alignment explanation
Indices: 1786194--1786222 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1786184 CCATTAAATT
1786194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1786223 TTGATAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1795941 original size:21 final size:21
Alignment explanation
Indices: 1795915--1796024 Score: 86
Period size: 21 Copynumber: 5.2 Consensus size: 21
1795905 AGAAATTGAT
1795915 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
* *
1795936 TTGCGATTTATTAC-AAATT--CG
1 TTGCGA--TAGT-CGAAGTTCGCG
*
1795957 TTGCGATAGTCGAAGTTCGTG
1 TTGCGATAGTCGAAGTTCGCG
* * *
1795978 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCGAAGTTCGCG
1795999 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
1796020 TTGCG
1 TTGCG
1796025 GTTTATTCCA
Statistics
Matches: 67, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
18 1 0.01
19 15 0.22
21 35 0.52
23 15 0.22
24 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:1796032 original size:42 final size:42
Alignment explanation
Indices: 1795915--1796034 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
1795905 AGAAATTGAT
*
1795915 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1795957 TTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1795999 TTGCGATAGTCGAAGTTCGCGTTGCGGTTTATTCCA
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCA
1796035 TGTTCGCGTT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1796807 original size:2 final size:2
Alignment explanation
Indices: 1796802--1796854 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1796792 GTCGCTCCAT
1796802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1796844 TA TA TA TA TA T
1 TA TA TA TA TA T
1796855 GTCGCGGCCG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1797218 original size:25 final size:24
Alignment explanation
Indices: 1797185--1797265 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
1797175 GAAAGGTGTT
1797185 AGAAAAAATGTGATGAAAATAAATA
1 AGAAAAAAT-TGATGAAAATAAATA
*
1797210 AGAATAAATAAT-AT-AAAATAAATA
1 AGAA-AAA-ATTGATGAAAATAAATA
*
1797234 AGGAAAAAATAGATG-AAATAAATA
1 A-GAAAAAATTGATGAAAATAAATA
*
1797258 ATAAAAAA
1 AGAAAAAA
1797266 GTAAATAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 7 0.15
24 26 0.55
25 9 0.19
26 4 0.09
27 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (24 bp):
AGAAAAAATTGATGAAAATAAATA
Found at i:1797220 original size:14 final size:14
Alignment explanation
Indices: 1797201--1797234 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1797191 AATGTGATGA
1797201 AAATAA-ATAAGAAT
1 AAATAATATAA-AAT
1797215 AAATAATATAAAAT
1 AAATAATATAAAAT
1797229 AAATAA
1 AAATAA
1797235 GGAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATATAAAAT
Found at i:1797228 original size:10 final size:9
Alignment explanation
Indices: 1797200--1797288 Score: 51
Period size: 9 Copynumber: 9.9 Consensus size: 9
1797190 AAATGTGATG
1797200 AAAATAAAT
1 AAAATAAAT
1797209 AAGAATAAAT
1 AA-AATAAAT
*
1797219 AATATAAA-
1 AAAATAAAT
*
1797227 ATAAATAAGGAA
1 A-AAATAA--AT
*
1797239 AAAATAGAT
1 AAAATAAAT
*
1797248 GAAATAAAT
1 AAAATAAAT
1797257 --AATAAA-
1 AAAATAAAT
*
1797263 AAAGTAAAT
1 AAAATAAAT
* *
1797272 AACATAATT
1 AAAATAAAT
1797281 AAAATAAA
1 AAAATAAA
1797289 GATGGAGAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.10
8 6 0.10
9 32 0.53
10 9 0.15
11 6 0.10
12 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1797231 original size:24 final size:23
Alignment explanation
Indices: 1797200--1797278 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
1797190 AAATGTGATG
*
1797200 AAAATAAATAAGAATAAATAATAT
1 AAAATAAATAAGAAAAAATAA-AT
*
1797224 AAAATAAATAAGGAAAAAATAGAT
1 AAAATAAATAA-GAAAAAATAAAT
* *
1797248 GAAATAAATAATAAAAAAGTAAAT
1 AAAATAAATAAGAAAAAA-TAAAT
*
1797272 AACATAA
1 AAAATAA
1797279 TTAAAATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
23 6 0.13
24 32 0.70
25 8 0.17
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.20
Consensus pattern (23 bp):
AAAATAAATAAGAAAAAATAAAT
Found at i:1797378 original size:26 final size:26
Alignment explanation
Indices: 1797338--1797400 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
1797328 AAAAATATAC
1797338 ATAAATAAAACAAAATAAA-AAAAAGAG
1 ATAAATAAAACAAAA-AAAGAAAAA-AG
*
1797365 ATAAATAAAGA-AAAAAATGAAAAAAG
1 ATAAATAAA-ACAAAAAAAGAAAAAAG
*
1797391 ATAAACAAAA
1 ATAAATAAAA
1797401 AATAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
26 12 0.38
27 18 0.56
28 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (26 bp):
ATAAATAAAACAAAAAAAGAAAAAAG
Found at i:1797544 original size:17 final size:17
Alignment explanation
Indices: 1797508--1797561 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1797498 AAAATATTAG
* *
1797508 AAAAAATATAGTAAGGAT
1 AAAAAATA-AATAAGAAT
1797526 AAAAAATAAGATAA-AAT
1 AAAAAATAA-ATAAGAAT
*
1797543 AAATAATAAATAAGAAT
1 AAAAAATAAATAAGAAT
1797560 AA
1 AA
1797562 TGATAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 16 0.52
18 11 0.35
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (17 bp):
AAAAAATAAATAAGAAT
Found at i:1797553 original size:21 final size:20
Alignment explanation
Indices: 1797527--1797611 Score: 70
Period size: 18 Copynumber: 4.2 Consensus size: 20
1797517 AGTAAGGATA
1797527 AAAAATAAGATAAAATAAAT
1 AAAAATAAGATAAAATAAAT
*
1797547 AATAAATAAGAATAATGATAATAT
1 AA-AAATAAG-ATAA-AATAA-AT
*
1797571 AAAAATTAA-AGAAAAT-AAT
1 AAAAA-TAAGATAAAATAAAT
*
1797590 AAAAATAATA-AAAAT-AAT
1 AAAAATAAGATAAAATAAAT
1797608 AAAA
1 AAAA
1797612 GAAACAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
18 15 0.27
19 8 0.14
20 3 0.05
21 9 0.16
22 7 0.12
23 7 0.12
24 7 0.12
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAAATAAGATAAAATAAAT
Found at i:1797596 original size:9 final size:9
Alignment explanation
Indices: 1797540--1797611 Score: 67
Period size: 9 Copynumber: 7.8 Consensus size: 9
1797530 AATAAGATAA
1797540 AATAAATAAT
1 AATAAA-AAT
*
1797550 AAATAAGAAT
1 -AATAAAAAT
* *
1797560 AATGATAAT
1 AATAAAAAT
1797569 -ATAAAAATT
1 AATAAAAA-T
1797578 AA-AGAAAAT
1 AATA-AAAAT
1797587 AATAAAAAT
1 AATAAAAAT
1797596 AATAAAAAT
1 AATAAAAAT
1797605 AATAAAA
1 AATAAAA
1797612 GAAACAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
8 5 0.10
9 33 0.63
10 9 0.17
11 5 0.10
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (9 bp):
AATAAAAAT
Found at i:1798139 original size:14 final size:14
Alignment explanation
Indices: 1798118--1798156 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1798108 CTTTTTGGTA
1798118 ATTTTAAAAAAAAT
1 ATTTTAAAAAAAAT
1798132 -TATTTAAAAAAAAT
1 AT-TTTAAAAAAAAT
1798146 ATTTTAAAAAA
1 ATTTTAAAAAA
1798157 CTTAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTTTAAAAAAAAT
Found at i:1798142 original size:13 final size:13
Alignment explanation
Indices: 1798120--1798156 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1798110 TTTTGGTAAT
1798120 TTTAAAAAAAATTA
1 TTTAAAAAAAA-TA
1798134 TTTAAAAAAAATA
1 TTTAAAAAAAATA
*
1798147 TTTTAAAAAA
1 TTTAAAAAAA
1798157 CTTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TTTAAAAAAAATA
Found at i:1801938 original size:15 final size:15
Alignment explanation
Indices: 1801914--1801955 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1801904 ACAACATTAA
*
1801914 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
1801929 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
*
1801944 ATTAAAGTATAA
1 ATTAAATTATAA
1801956 TTATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:1802432 original size:23 final size:22
Alignment explanation
Indices: 1802406--1802452 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1802396 TAAATTACAT
*
1802406 TTATATTTTTAACTAATTAATAA
1 TTATATGTTT-ACTAATTAATAA
* *
1802429 TTATATGTTTAGTAATTTATAA
1 TTATATGTTTACTAATTAATAA
1802451 TT
1 TT
1802453 TAACGTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
TTATATGTTTACTAATTAATAA
Found at i:1806467 original size:36 final size:35
Alignment explanation
Indices: 1806417--1806494 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 35
1806407 CCCCTTACGG
* *
1806417 AACTTATCACCTCATCCCGCTAAACCAAACTTAAGA
1 AACTTATCACCTCATCCCACTAAACC-AACTTAACA
*
1806453 AATTTATCACCTCATCCCACTAAACCAACTTAACA
1 AACTTATCACCTCATCCCACTAAACCAACTTAACA
1806488 AACTTAT
1 AACTTAT
1806495 TGTTGATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
35 14 0.37
36 24 0.63
ACGTcount: A:0.40, C:0.32, G:0.03, T:0.26
Consensus pattern (35 bp):
AACTTATCACCTCATCCCACTAAACCAACTTAACA
Found at i:1826439 original size:77 final size:77
Alignment explanation
Indices: 1826371--1826513 Score: 216
Period size: 77 Copynumber: 1.9 Consensus size: 77
1826361 TTATCGGTCG
* * *
1826371 ATTTTGTTTAATGCATATGTTGCATTT-TCGTATAAGTACCTTTGTGTACTTTCGGCATTATGTG
1 ATTTTGTTTAATACATATGTTGCATTTCT-GTATAAGTACCCTTGTGTACTTTCGGCACTATGTG
1826435 TGGTTATCGATAA
65 TGGTTATCGATAA
* * *
1826448 ATTTTGTTTAATACATATGTTGCATTTCTGTATCAGTACCCTTGTGTACTTTTGGCACTATTTGT
1 ATTTTGTTTAATACATATGTTGCATTTCTGTATAAGTACCCTTGTGTACTTTCGGCACTATGTGT
1826513 G
66 G
1826514 CATGTATGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
77 58 0.98
78 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (77 bp):
ATTTTGTTTAATACATATGTTGCATTTCTGTATAAGTACCCTTGTGTACTTTCGGCACTATGTGT
GGTTATCGATAA
Found at i:1828145 original size:31 final size:30
Alignment explanation
Indices: 1828044--1828147 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
1828034 ATGAATTTAG
* * *
1828044 AGATCAATTTGATATTTTATCTAAAGTTCA
1 AGATCAAATTAATATTTTATCTAAAATTCA
* * * *
1828074 ATGGTCAAATTAGTATTTTAACTAAAGTGT-A
1 A-GATCAAATTAATATTTTATCTAAAAT-TCA
* *
1828105 AGTTCAAATTAATATTCTATCTAAAATTCA
1 AGATCAAATTAATATTTTATCTAAAATTCA
1828135 GAGATCAAATTAA
1 -AGATCAAATTAA
1828148 AATTAAAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 1 0.02
30 23 0.39
31 34 0.58
32 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (30 bp):
AGATCAAATTAATATTTTATCTAAAATTCA
Found at i:1828569 original size:29 final size:29
Alignment explanation
Indices: 1828445--1828562 Score: 209
Period size: 29 Copynumber: 4.1 Consensus size: 29
1828435 CTACAGTGAA
1828445 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1828474 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
*
1828503 CTTGGAGGTCGCCATGACATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
* *
1828532 CTTGGAGGTCGTCATGGCATCCGAGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1828561 CT
1 CT
1828563 GTGAGGTGTT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 85 1.00
ACGTcount: A:0.15, C:0.31, G:0.36, T:0.19
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:1828896 original size:10 final size:10
Alignment explanation
Indices: 1828883--1828936 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
1828873 GGCCATCCGA
1828883 CCGAGGCCAT
1 CCGAGGCCAT
*
1828893 CCGAAAG-CAT
1 CCG-AGGCCAT
*
1828903 CCGATGCCAT
1 CCGAGGCCAT
1828913 CCGAGAG-CAT
1 CCGAG-GCCAT
1828923 CCGAGGCCAT
1 CCGAGGCCAT
1828933 CCGA
1 CCGA
1828937 ACGAGCTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 3 0.08
10 31 0.84
11 3 0.08
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:1828911 original size:20 final size:20
Alignment explanation
Indices: 1828883--1828937 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1828873 GGCCATCCGA
1828883 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
* *
1828903 CCGATGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
1828923 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
1828938 CGAGCTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.36, G:0.25, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:1828956 original size:23 final size:23
Alignment explanation
Indices: 1828924--1828982 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1828914 CGAGAGCATC
*
1828924 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
*
1828947 TGAGGGCATCCGAACGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
1828970 CGAGGGCATCCGA
1 CGAGGGCATCCGA
1828983 GGACAACCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (23 bp):
CGAGGGCATCCGAACGAGCTATG
Found at i:1828999 original size:33 final size:31
Alignment explanation
Indices: 1828956--1829028 Score: 110
Period size: 33 Copynumber: 2.3 Consensus size: 31
1828946 GTGAGGGCAT
* *
1828956 CCGAACGAGCTATGCGAGGGCATCCGAGGACAA
1 CCGAGCGAGCTATGCGAGGGAATCCGA-G-CAA
1828989 CCGAGCGAGCTATGCGAGGGAATCCGAGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGCAA
1829020 CCGAGCGAG
1 CCGAGCGAG
1829029 GGTAGGTCGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 12 0.32
32 1 0.03
33 25 0.66
ACGTcount: A:0.29, C:0.27, G:0.36, T:0.08
Consensus pattern (31 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGCAA
Found at i:1829119 original size:33 final size:33
Alignment explanation
Indices: 1829078--1829162 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
1829068 GCGACCTACC
1829078 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
*
1829111 CTCGCTCGGTTGCCCTCGGATTCTCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
* * *
1829144 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
1829163 TCGGATGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.08, C:0.36, G:0.27, T:0.28
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
Found at i:1829166 original size:14 final size:14
Alignment explanation
Indices: 1829144--1829176 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1829134 TCTCGCATAG
*
1829144 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1829158 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1829172 CTCGG
1 CTCGG
1829177 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1832077 original size:2 final size:2
Alignment explanation
Indices: 1832065--1832099 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1832055 TACACAACAG
1832065 TA TA T- TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1832100 CATACCTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1851061 original size:23 final size:23
Alignment explanation
Indices: 1851031--1851095 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1851021 ACAACCTTAT
1851031 ATGGCACTTCGGTGCATTTCTAC
1 ATGGCACTTCGGTGCATTTCTAC
* * *
1851054 ATGGCACTACGGTGAAATTCTAC
1 ATGGCACTTCGGTGCATTTCTAC
*
1851077 GTGGCACTTCGGTGCATTT
1 ATGGCACTTCGGTGCATTT
1851096 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (23 bp):
ATGGCACTTCGGTGCATTTCTAC
Found at i:1854606 original size:14 final size:15
Alignment explanation
Indices: 1854577--1854608 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1854567 AGGTGAAGGA
1854577 AAATATTTTATATAG
1 AAATATTTTATATAG
1854592 AAATATTTT-TATAG
1 AAATATTTTATATAG
1854606 AAA
1 AAA
1854609 GTAATTCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (15 bp):
AAATATTTTATATAG
Found at i:1855112 original size:21 final size:19
Alignment explanation
Indices: 1855083--1855121 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1855073 TATATATTAT
1855083 ATTAATTTTTCAAATGAAATA
1 ATTAATTTTT-AAAT-AAATA
*
1855104 ATTATTTTTTAAATAAAT
1 ATTAATTTTTAAATAAAT
1855122 CATAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTAATTTTTAAATAAATA
Found at i:1860851 original size:17 final size:16
Alignment explanation
Indices: 1860826--1860859 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1860816 TGTGTCGTGT
1860826 TTATATTTTTTGAAATA
1 TTATATTTTTT-AAATA
*
1860843 TTATTTTTTTTAAATA
1 TTATATTTTTTAAATA
1860859 T
1 T
1860860 AAAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATATTTTTTAAATA
Found at i:1860852 original size:16 final size:17
Alignment explanation
Indices: 1860826--1860859 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1860816 TGTGTCGTGT
1860826 TTATATTTTTTGAAATA
1 TTATATTTTTTGAAATA
*
1860843 TTAT-TTTTTTTAAATA
1 TTATATTTTTTGAAATA
1860859 T
1 T
1860860 AAAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTATATTTTTTGAAATA
Found at i:1861124 original size:23 final size:23
Alignment explanation
Indices: 1861097--1861142 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1861087 ATTTGAGATT
1861097 TTAATAAAGATATTTAAAATATA
1 TTAATAAAGATATTTAAAATATA
** * *
1861120 TTAATTTATATTTTTAAAATATA
1 TTAATAAAGATATTTAAAATATA
1861143 ATATAACACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATAAAGATATTTAAAATATA
Found at i:1862272 original size:226 final size:228
Alignment explanation
Indices: 1861799--1862545 Score: 931
Period size: 226 Copynumber: 3.3 Consensus size: 228
1861789 TAACTTATTT
* * * * * *
1861799 AACAGTCATAAATCTATGTAACAGTAAAATAGTTTTACATTGTGTAACAGAATCTTATCTCTATT
1 AACAGTCATAAATATGTGTAAAACTAAAATAGTTTTACATTGTGTAATAG-ATCTTATCCCTATT
* * * * * *
1861864 AGGGTTAGG-TTCACTTACACAATTTAAAATTCTTTTAGCTTTATACAGATTTAGCATCC-TTGG
65 AGGGTTAGGATCCACTTACACAATGTAAAACTCTTTTAGTTTTACACAGATTTAG-AGCCTTTGG
* *
1861927 ATAAGTGAAAACAAATGGTTGGGATTGACTCATTGTTTTGTTTTTTTCCAGTGAATATCTTCTCA
129 ATAAGTGAAAACAAATGGTTGGGATTGACTC-----CTTATTTTTTTCCAGTGAATATCTTCTCA
**
1861992 TTTCCTACTGTTAATCTCAGTCATCTACTTT-CACTCATCC
189 TTTCCTACTGTTAATCTCAACCATCTA-TTTCCACTCATCC
* *
1862032 AACAGTCTTAAATATCTGTAAAACTAAAATAGTTTTACATTGTGTAATACGATCTTATCCCTATT
1 AACAGTCATAAATATGTGTAAAACTAAAATAGTTTTACATTGTGTAATA-GATCTTATCCCTATT
* * *
1862097 AGGGTTAGGATCCACTTACATAGTGTAAAACTCTTTTAGTTTTACATAGATTTAGAGCCTTTGGA
65 AGGGTTAGGATCCACTTACACAATGTAAAACTCTTTTAGTTTTACACAGATTTAGAGCCTTTGGA
* *
1862162 TAAGTGAAAACAAAT-GTT-GGATCGACTCCTTATTTTTTT-CAGTGAATATCTTCTCATTTCTT
130 TAAGTGAAAACAAATGGTTGGGATTGACTCCTTATTTTTTTCCAGTGAATATCTTCTCATTTCCT
*
1862224 ACTGTTAATCTCAACCATCTATTTCCACTCATCT
195 ACTGTTAATCTCAACCATCTATTTCCACTCATCC
* * *
1862258 AATAGTCATAAATATGTGTAAAACTAAAATAGTTTTACATTGTGTAATAGGATTTTATCCATATT
1 AACAGTCATAAATATGTGTAAAACTAAAATAGTTTTACATTGTGTAATA-GATCTTATCCCTATT
* * *
1862323 AGGGTTAGGATCCACTTACACAATGTAAAACT-TTTTAGTTTTACACAGGTTTA-AGACTGCTGG
65 AGGGTTAGGATCCACTTACACAATGTAAAACTCTTTTAGTTTTACACAGATTTAGAGCCT-TTGG
* * *
1862386 ATAAGTGAAAACAAATGGTTGGGATTGACTCCTTGCTTTTTTTCCCATTGAATATCTTCTTA-TT
129 ATAAGTGAAAACAAATGGTTGGGATTGACTCCTT-ATTTTTTT-CCAGTGAATATCTTCTCATTT
* *
1862450 CCTATTGTTAATCTCAACCATTTATTTCCACTCATCC
192 CCTACTGTTAATCTCAACCATCTATTTCCACTCATCC
* * * * * *
1862487 AACAGTCTTGAATCTGTGTAAAACTAAAATAGTTTTATA-T-TGTAACATATCTTATCCCT
1 AACAGTCATAAATATGTGTAAAACTAAAATAGTTTTACATTGTGTAATAGATCTTATCCCT
1862546 TCATATTATA
Statistics
Matches: 452, Mismatches: 52, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
224 4 0.01
225 41 0.09
226 150 0.33
227 27 0.06
228 8 0.02
229 69 0.15
230 15 0.03
232 9 0.02
233 71 0.16
234 58 0.13
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (228 bp):
AACAGTCATAAATATGTGTAAAACTAAAATAGTTTTACATTGTGTAATAGATCTTATCCCTATTA
GGGTTAGGATCCACTTACACAATGTAAAACTCTTTTAGTTTTACACAGATTTAGAGCCTTTGGAT
AAGTGAAAACAAATGGTTGGGATTGACTCCTTATTTTTTTCCAGTGAATATCTTCTCATTTCCTA
CTGTTAATCTCAACCATCTATTTCCACTCATCC
Found at i:1864727 original size:59 final size:60
Alignment explanation
Indices: 1864582--1864729 Score: 158
Period size: 59 Copynumber: 2.5 Consensus size: 60
1864572 AGTTTATATG
* * * * * * *
1864582 TCTCCAAACTATAACCTTCATTTTAAATTGGTCTTTAAACTTTTGAATATTTCAATTTCA
1 TCTCTAAACTATGACCCTCATTTTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCA
* **
1864642 TC-CTTAAATTATGAATCTCATTTTAAATTAGTCCTTAAAC-TTTAAACATTAT-AATTTCA
1 TCTC-TAAACTATGACCCTCATTTTAAATTAGTCCTTAAACTTTTAAACATT-TCAATTTCA
*
1864701 TCTCTAAACTATGACCCTCTTTTTAAATT
1 TCTCTAAACTATGACCCTCATTTTAAATT
1864730 GGTCACCAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
59 39 0.55
60 32 0.45
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (60 bp):
TCTCTAAACTATGACCCTCATTTTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCA
Found at i:1869653 original size:232 final size:232
Alignment explanation
Indices: 1869247--1869712 Score: 916
Period size: 232 Copynumber: 2.0 Consensus size: 232
1869237 TTGGAGGGGG
1869247 AAAAGGTGCCACTTTATGGAGCTGGATCAAGCTTGACGTTTACACAGAATGGTGCTGCTGAAGTT
1 AAAAGGTGCCACTTTATGGAGCTGGATCAAGCTTGACGTTTACACAGAATGGTGCTGCTGAAGTT
1869312 CCATTGATACTGAAGTTCGAAGTCCGGTCACGAGGGAACGTGGTTGGAAAACTCGTGAGAACGAA
66 CCATTGATACTGAAGTTCGAAGTCCGGTCACGAGGGAACGTGGTTGGAAAACTCGTGAGAACGAA
1869377 GCACCGGAAACAAATTTCTTGCCCTCTGGTAATCGATTCTATGAAAACCAAGCTCATTAAGTTCA
131 GCACCGGAAACAAATTTCTTGCCCTCTGGTAATCGATTCTATGAAAACCAAGCTCATTAAGTTCA
1869442 AGAAAAACGCATGCACATAATGA-TGAAAGTCATGGTC
196 AGAAAAACGCATGCACAT-ATGACTGAAAGTCATGGTC
1869479 AAAAGGTGCCACTTTATGGAGCTGGATCAAGCTTGACGTTTACACAGAATGGTGCTGCTGAAGTT
1 AAAAGGTGCCACTTTATGGAGCTGGATCAAGCTTGACGTTTACACAGAATGGTGCTGCTGAAGTT
1869544 CCATTGATACTGAAGTTCGAAGTCCGGTCACGAGGGAACGTGGTTGGAAAACTCGTGAGAACGAA
66 CCATTGATACTGAAGTTCGAAGTCCGGTCACGAGGGAACGTGGTTGGAAAACTCGTGAGAACGAA
1869609 GCACCGGAAACAAATTTCTTGCCCTCTGGTAATCGATTCTATGAAAACCAAGCTCATTAAGTTCA
131 GCACCGGAAACAAATTTCTTGCCCTCTGGTAATCGATTCTATGAAAACCAAGCTCATTAAGTTCA
1869674 AGAAAAACGCATGCACATATGACTGAAAGTCATGGTC
196 AGAAAAACGCATGCACATATGACTGAAAGTCATGGTC
1869711 AA
1 AA
1869713 GATGTTGATT
Statistics
Matches: 233, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
231 4 0.02
232 229 0.98
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (232 bp):
AAAAGGTGCCACTTTATGGAGCTGGATCAAGCTTGACGTTTACACAGAATGGTGCTGCTGAAGTT
CCATTGATACTGAAGTTCGAAGTCCGGTCACGAGGGAACGTGGTTGGAAAACTCGTGAGAACGAA
GCACCGGAAACAAATTTCTTGCCCTCTGGTAATCGATTCTATGAAAACCAAGCTCATTAAGTTCA
AGAAAAACGCATGCACATATGACTGAAAGTCATGGTC
Found at i:1883084 original size:24 final size:24
Alignment explanation
Indices: 1883047--1883112 Score: 114
Period size: 24 Copynumber: 2.7 Consensus size: 24
1883037 GAAGTACTGT
1883047 GTAGAAATTTGTCCCGAAGGACCGC
1 GTAG-AATTTGTCCCGAAGGACCGC
1883072 GTAGAATTTGTCCCGAAGGACCGC
1 GTAGAATTTGTCCCGAAGGACCGC
*
1883096 GTAGAATTTATCCCGAA
1 GTAGAATTTGTCCCGAA
1883113 TGACTACATA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 36 0.90
25 4 0.10
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (24 bp):
GTAGAATTTGTCCCGAAGGACCGC
Found at i:1885875 original size:124 final size:125
Alignment explanation
Indices: 1885643--1885916 Score: 408
Period size: 124 Copynumber: 2.2 Consensus size: 125
1885633 TACGGTTAAA
* * * * *
1885643 AAAAGGCGGTACCGGTTTTGTTATTGTTGTGCATAACAAAGTCGGTAAAAATTATCGAAAACGTC
1 AAAA-GCGCTACCGGTTTTGTTATTGTTGTGCATAACAAAGACGGTAAAAAATACCGAAAACATC
*
1885708 ATTATTTCTACCGGTTTTATTATTATTTTGGCATTTAACCGGGTTTCTTAACAAAATCGGT
65 ATTATTTCTACCGGTTTTATTATTATTTTGGCATTTAACCGGGTTTCTTAACAAAACCGGT
*
1885769 AAAAGCGCTACCGGTTTTGTTATTGTTGTGCATAA-AAA-ACAGGTAAAAAATACCGAAAATATC
1 AAAAGCGCTACCGGTTTTGTTATTGTTGTGCATAACAAAGAC-GGTAAAAAATACCGAAAACATC
* * * *
1885832 ATTATTTCTACCGGTTTTGTTATTATTTTGGCATTTTATCGGGTTTCTTAATAAAACCGGT
65 ATTATTTCTACCGGTTTTATTATTATTTTGGCATTTAACCGGGTTTCTTAACAAAACCGGT
*
1885893 AAAAGTGCTACCGGTTTTGTTATT
1 AAAAGCGCTACCGGTTTTGTTATT
1885917 TATTTTCCGG
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
123 1 0.01
124 100 0.74
125 30 0.22
126 4 0.03
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (125 bp):
AAAAGCGCTACCGGTTTTGTTATTGTTGTGCATAACAAAGACGGTAAAAAATACCGAAAACATCA
TTATTTCTACCGGTTTTATTATTATTTTGGCATTTAACCGGGTTTCTTAACAAAACCGGT
Found at i:1886712 original size:198 final size:198
Alignment explanation
Indices: 1886249--1886719 Score: 639
Period size: 199 Copynumber: 2.4 Consensus size: 198
1886239 GTAAACATAT
* * *
1886249 GTGTCGATACATTTTCTAAAAGTATCGACCCCAAAAATATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACA-TTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
1886314 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGATAGAATAGGTCAACATAATGT
65 GGTAAATTTACAATGTAACCGGCAGAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGT
1886379 ATCGACACAAATTTAAAAATTGTTGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACAC
130 ATCGACAC-AATTTAAAAATTGTTGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACAC
1886444 ATAAA
194 ATAAA
* *
1886449 GTGTCGATACATTTATTAAAAGTATCGATCTCAAAAACATCG-AACCGATAATTACAATGTAATA
1 GTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* *
1886513 GGTAAATTTACAATGTACCCGGCAGGAATATACCGATTTTATGAGAAAATAGGT-ATACATAATG
65 GGTAAATTTACAATGTAACCGGCAGAAATATACCGATTTTATGAGAAAATAGGTCA-ACATAATG
* * * * * *
1886577 TATCGACAC-GTTTTAAATTTGTGTCGATA-TTTTTTTTCAGAATGAATGTCC-AACGAGGTGCA
129 TATCGACACAATTTAAAAATTGT-T-GATACATTTTGTCCAGAATGAATG-CCAAACGAGGTGCA
1886639 CACATAAA
191 CACATAAA
* * *
1886647 GTGTTGATACATTTA-AAACTGTATTGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1886711 GGTAAATTT
65 GGTAAATTT
1886720 GTAATATTAA
Statistics
Matches: 241, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
196 3 0.01
197 29 0.12
198 81 0.34
199 94 0.39
200 34 0.14
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGCAGAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGTA
TCGACACAATTTAAAAATTGTTGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACACAT
AAA
Found at i:1886743 original size:198 final size:197
Alignment explanation
Indices: 1886249--1886772 Score: 630
Period size: 198 Copynumber: 2.6 Consensus size: 197
1886239 GTAAACATAT
* * *
1886249 GTGTCGATACATTTTCTAAAAGTATCGACCCCAAAAATATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACA-TTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * *
1886314 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGATAGAATAGGTCAACATAATGT
65 GGTAAATTTACAATGTAA-CGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGT
1886379 ATCGACACAAATTTAAAAATTGTTGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACAC
129 ATCGACAC-AATTTAAAAATTGTTGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACAC
1886444 ATAAA
193 ATAAA
* *
1886449 GTGTCGATACATTTATTAAAAGTATCGATCTCAAAAACATCG-AACCGATAATTACAATGTAATA
1 GTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * **
1886513 GGTAAATTTACAATGTACCCGGCAGGAATATACCGATTTTATGAGAAAATAGGT-ATACATAATG
65 GGTAAATTTACAATGTA-ACGGTATAAATATACCGATTTTATGAGAAAATAGGTCA-ACATAATG
* * * * * *
1886577 TATCGACAC-GTTTTAAATTTGTGTCGATA-TTTTTTTTCAGAATGAATGTCC-AACGAGGTGCA
128 TATCGACACAATTTAAAAATTGT-T-GATACATTTTGTCCAGAATGAATG-CCAAACGAGGTGCA
1886639 CACATAAA
190 CACATAAA
* * *
1886647 GTGTTGATACATTTA-AAACTGTATTGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
** * * * * * *
1886711 GGTAAATTTGTAATATTAACAGTATAAATATACC-AGTTTAGTTAGAAATTAGGTCAATATAA
65 GGTAAATTTACAAT-GTAACGGTATAAATATACCGATTTTA-TGAGAAAATAGGTCAACATAA
1886773 GCGCTACCTA
Statistics
Matches: 278, Mismatches: 35, Indels: 24
0.82 0.10 0.07
Matches are distributed among these distances:
196 3 0.01
197 34 0.12
198 111 0.40
199 96 0.35
200 34 0.12
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (197 bp):
GTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGTAT
CGACACAATTTAAAAATTGTTGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACACATA
AA
Found at i:1886786 original size:11 final size:11
Alignment explanation
Indices: 1886770--1886794 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1886760 TAGGTCAATA
1886770 TAAGCGCTACC
1 TAAGCGCTACC
1886781 TAAGCGCTACC
1 TAAGCGCTACC
1886792 TAA
1 TAA
1886795 TATGTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (11 bp):
TAAGCGCTACC
Found at i:1886889 original size:23 final size:23
Alignment explanation
Indices: 1886839--1886883 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1886829 TACGTATTTT
*
1886839 ATTATATAAGCTCTACCTATTAC
1 ATTATATAAGCTCTACCTAATAC
1886862 ATTATATAAGCGT-TACCTAATA
1 ATTATATAAGC-TCTACCTAATA
1886884 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCTCTACCTAATAC
Found at i:1886976 original size:23 final size:23
Alignment explanation
Indices: 1886926--1886970 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1886916 TGCTTATTTT
*
1886926 ATTATATAAGCGATACCTATTAC
1 ATTATATAAGCGATACCTAATAC
* *
1886949 ATTATATAAGTGCTACCTAATA
1 ATTATATAAGCGATACCTAATA
1886971 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGATACCTAATAC
Found at i:1887004 original size:87 final size:87
Alignment explanation
Indices: 1886781--1887004 Score: 385
Period size: 87 Copynumber: 2.6 Consensus size: 87
1886771 AAGCGCTACC
* *
1886781 TAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTACGGTTAAATACGTATTTTATTATAT
1 TAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCGTATTTTATTATAT
**
1886846 AAGCTCTACCTATTACATTATA
66 AAGCGATACCTATTACATTATA
* *
1886868 TAAGCGTTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCTTATTTTATTATAT
1 TAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCGTATTTTATTATAT
1886933 AAGCGATACCTATTACATTATA
66 AAGCGATACCTATTACATTATA
*
1886955 TAAGTGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATG
1 TAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATG
1887005 ATATAACATA
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 129 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (87 bp):
TAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCGTATTTTATTATAT
AAGCGATACCTATTACATTATA
Found at i:1887078 original size:17 final size:16
Alignment explanation
Indices: 1887027--1887078 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
1887017 CGATGTAAAT
1887027 TTTAACCGATCACTTA
1 TTTAACCGATCACTTA
1887043 TTTAACCGATCACTTA
1 TTTAACCGATCACTTA
1887059 TTTAACC-AGTCACGTTA
1 TTTAACCGA-TCAC-TTA
1887076 TTT
1 TTT
1887079 TTTAGCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 1 0.03
16 27 0.79
17 6 0.18
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (16 bp):
TTTAACCGATCACTTA
Found at i:1888209 original size:20 final size:18
Alignment explanation
Indices: 1888167--1888209 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1888157 TATTAATAAA
1888167 TTATTTTTTATTATTTCC
1 TTATTTTTTATTATTTCC
* *
1888185 ATATTTTGTTAATTTTTTCC
1 TTATTTT-TT-ATTATTTCC
1888205 TTATT
1 TTATT
1888210 ATATGTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 6 0.30
19 2 0.10
20 12 0.60
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (18 bp):
TTATTTTTTATTATTTCC
Found at i:1901091 original size:16 final size:16
Alignment explanation
Indices: 1901067--1901097 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1901057 CTAAACTATC
1901067 TTCTCTCTTTTTTTCT
1 TTCTCTCTTTTTTTCT
*
1901083 TTCTTTCTTTTTTTC
1 TTCTCTCTTTTTTTC
1901098 ATTTTTTGTT
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:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTCTCTTTTTTTCT
Found at i:1905107 original size:74 final size:74
Alignment explanation
Indices: 1904986--1905134 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
1904976 GCCTTGATAG
1904986 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
1 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
1905051 TAATTCCTA
66 TAATTCCTA
1905060 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
1 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
1905125 TAATTCCTA
66 TAATTCCTA
1905134 A
1 A
1905135 ATTATAGCCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (74 bp):
ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
TAATTCCTA
Found at i:1905133 original size:19 final size:19
Alignment explanation
Indices: 1905111--1905147 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1905101 TATTTAGTTG
*
1905111 CCTAAGTTATAGCCTAATT
1 CCTAAATTATAGCCTAATT
1905130 CCTAAATTATAGCCTAAT
1 CCTAAATTATAGCCTAAT
1905148 GATTAGGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (19 bp):
CCTAAATTATAGCCTAATT
Found at i:1909610 original size:73 final size:74
Alignment explanation
Indices: 1909490--1909637 Score: 280
Period size: 73 Copynumber: 2.0 Consensus size: 74
1909480 AGAGTGATAG
*
1909490 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
1 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAATTATAGCC
1909555 TAATTCCTA
66 TAATTCCTA
1909564 ATTACAAAATATTCT-CAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAATTATAGCC
1 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAATTATAGCC
1909628 TAATTCCTA
66 TAATTCCTA
1909637 A
1 A
1909638 ATTATAACTA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 58 0.79
74 15 0.21
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (74 bp):
ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAATTATAGCC
TAATTCCTA
Found at i:1933727 original size:6 final size:6
Alignment explanation
Indices: 1933716--1933757 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
1933706 GTCACCACCT
1933716 TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC
1 TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC
1933758 ATCAAGTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TCATCC
Found at i:1944150 original size:25 final size:25
Alignment explanation
Indices: 1944116--1944171 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
1944106 GATGATATTG
1944116 GATTTCTGAACCGAGTTCTTGCTTA
1 GATTTCTGAACCGAGTTCTTGCTTA
1944141 GATTTCTGAACCGAGTTCTTGCTTA
1 GATTTCTGAACCGAGTTCTTGCTTA
*
1944166 GTTTTC
1 GATTTC
1944172 ATGCCAAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.43
Consensus pattern (25 bp):
GATTTCTGAACCGAGTTCTTGCTTA
Found at i:1948470 original size:142 final size:142
Alignment explanation
Indices: 1948209--1948485 Score: 464
Period size: 142 Copynumber: 2.0 Consensus size: 142
1948199 TTTTTTCCAT
* *
1948209 ACACCGAAGCATTTTAGAATCTTTGTATTTCCATTCTAAGTGCAATGATATATAATTTCTTTGTA
1 ACACCGAAGCATTTTAGAATCTTTGTATTTCCATTCGAAGTGCAATGATATATAATTTCTTTGCA
**
1948274 CTCACGTGACATGAATCAGTTGGGCTTGCATGTTTTAATTTCTTTGTACTCATGCTTCATCAATC
66 CTCACGTGACATGAATCAGTTGGGCTTGCATGTTTTAATTTCTTTGTACTCATGCAACATCAATC
1948339 AGTTGTTTTCAA
131 AGTTGTTTTCAA
* * * *
1948351 ACACTGAAGCATTTTAGTATCTTTGTATTTCTATTCGAAGTGCAATGATATTTAATTTCTTTGCA
1 ACACCGAAGCATTTTAGAATCTTTGTATTTCCATTCGAAGTGCAATGATATATAATTTCTTTGCA
* *
1948416 CTCATGTGACATGAATCAGTTGGGCTTGCATGTTTTAATTTCTTTGTACTCATGCAACATGAATC
66 CTCACGTGACATGAATCAGTTGGGCTTGCATGTTTTAATTTCTTTGTACTCATGCAACATCAATC
1948481 AGTTG
131 AGTTG
1948486 GGCTTGCATG
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 125 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (142 bp):
ACACCGAAGCATTTTAGAATCTTTGTATTTCCATTCGAAGTGCAATGATATATAATTTCTTTGCA
CTCACGTGACATGAATCAGTTGGGCTTGCATGTTTTAATTTCTTTGTACTCATGCAACATCAATC
AGTTGTTTTCAA
Found at i:1948540 original size:51 final size:50
Alignment explanation
Indices: 1948401--1948549 Score: 225
Period size: 48 Copynumber: 3.0 Consensus size: 50
1948391 TGCAATGATA
* *
1948401 TTTAATTTCTTTGCA-CTCATGTGACATGAATCAGTTGGGCTTGCATG-T
1 TTTAATTTCTTTGTACCTCATGAGACATGAATCAGTTGGGCTTGCATGTT
1948449 TTTAATTTCTTTGTA-CTCATGCA-ACATGAATCAGTTGGGCTTGCATGTT
1 TTTAATTTCTTTGTACCTCATG-AGACATGAATCAGTTGGGCTTGCATGTT
*
1948498 TTTAATTTCTTTGTACTCTCATGAGAGATGAATCAGTTGGGCTTGCATGTT
1 TTTAATTTCTTTGTAC-CTCATGAGACATGAATCAGTTGGGCTTGCATGTT
1948549 T
1 T
1948550 CTGTTATGAT
Statistics
Matches: 93, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
48 44 0.47
49 16 0.17
50 1 0.01
51 32 0.34
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.43
Consensus pattern (50 bp):
TTTAATTTCTTTGTACCTCATGAGACATGAATCAGTTGGGCTTGCATGTT
Found at i:1950773 original size:31 final size:31
Alignment explanation
Indices: 1950737--1950834 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
1950727 TTTATTTTTT
* * *
1950737 AATTTGACCACTCAACTTTAAATAAAATATT
1 AATTTGACCACTAAAATTTAAATAAAATATC
* *
1950768 AATTTGACTCA-TAAAATTTATATCAAATATC
1 AATTTGAC-CACTAAAATTTAAATAAAATATC
*
1950799 AATTTGACC-CTGAAATTTTAAATAAAATATC
1 AATTTGACCACT-AAAATTTAAATAAAATATC
1950830 AATTT
1 AATTT
1950835 AAGTCTTGGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.04
31 52 0.93
32 2 0.04
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (31 bp):
AATTTGACCACTAAAATTTAAATAAAATATC
Found at i:1952512 original size:53 final size:54
Alignment explanation
Indices: 1952436--1952541 Score: 126
Period size: 53 Copynumber: 2.0 Consensus size: 54
1952426 TCACATCAAA
** * * **
1952436 ATGTTATAAATAGATAATTTAAATAATCAACATGTTAA-TTTTTTAAAATTAAC
1 ATGTTATAAATAGATAACGTAAATAATCAAAATATTAACACTTTTAAAATTAAC
*
1952489 ATGTTATAAATTA-ATAACGTAAATGATCAAAATATTAACACTTTTAAAATTAA
1 ATGTTATAAA-TAGATAACGTAAATAATCAAAATATTAACACTTTTAAAATTAA
1952542 TTTATGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
53 30 0.68
54 14 0.32
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.39
Consensus pattern (54 bp):
ATGTTATAAATAGATAACGTAAATAATCAAAATATTAACACTTTTAAAATTAAC
Found at i:1959840 original size:24 final size:23
Alignment explanation
Indices: 1959787--1959843 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1959777 TGAAAGGGGC
1959787 AATATTTTCAAAATCTTTGATTA
1 AATATTTTCAAAATCTTTGATTA
* *
1959810 AACATTTTTAAAACTCTTTTGA-TA
1 AATATTTTCAAAA-TC-TTTGATTA
*
1959834 GATATTTTCA
1 AATATTTTCA
1959844 GACTTTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 11 0.41
24 11 0.41
25 5 0.19
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (23 bp):
AATATTTTCAAAATCTTTGATTA
Found at i:1960141 original size:12 final size:12
Alignment explanation
Indices: 1960126--1960171 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
1960116 ATACATCAAC
1960126 ACATGCATACAT
1 ACATGCATACAT
*
1960138 ACATACATACAT
1 ACATGCATACAT
1960150 AC--GCATACAT
1 ACATGCATACAT
*
1960160 GCATG-ATACAT
1 ACATGCATACAT
1960171 A
1 A
1960172 AATTTTGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
10 8 0.29
11 6 0.21
12 14 0.50
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (12 bp):
ACATGCATACAT
Found at i:1960554 original size:35 final size:35
Alignment explanation
Indices: 1960464--1960603 Score: 140
Period size: 36 Copynumber: 3.9 Consensus size: 35
1960454 GTTTCTCTCG
* * *
1960464 AAACAAAATGTTGTCTCGCTAGAGACAACTTCTTTTGAA
1 AAAC-AAATTTTGTCTCGCTTGAGAC-A-TT-TTCTGAA
1960503 AAACAAATCTTT-TCTCGCTTGAGACAGTTTTCT-AA
1 AAACAAAT-TTTGTCTCGCTTGAGACA-TTTTCTGAA
* * *
1960538 AATCAAATTTTGTCTCGTTTGAGACAATTTCTTGAA
1 AAACAAATTTTGTCTCGCTTGAGACATTTTC-TGAA
*
1960574 AAACAAATTTCGTCTCGCTTGAGACATTTT
1 AAACAAATTTTGTCTCGCTTGAGACATTTT
1960604 TCCTTTGAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
34 7 0.08
35 23 0.27
36 31 0.36
37 3 0.03
38 16 0.19
39 6 0.07
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (35 bp):
AAACAAATTTTGTCTCGCTTGAGACATTTTCTGAA
Found at i:1960589 original size:36 final size:36
Alignment explanation
Indices: 1960476--1960624 Score: 133
Period size: 36 Copynumber: 4.0 Consensus size: 36
1960466 ACAAAATGTT
* *
1960476 GTCTCGCTAGAGACAACTTCTTTTGAAAAACAAATCTT-
1 GTCTCGCTTGAGACAA-TT-TCTTGAAAAACAAAT-TTC
* * * *
1960514 TTCTCGCTTGAGACAGTTT-TCT-AAAATCAAATTTT
1 GTCTCGCTTGAGACAATTTCT-TGAAAAACAAATTTC
*
1960549 GTCTCGTTTGAGACAATTTCTTGAAAAACAAATTTC
1 GTCTCGCTTGAGACAATTTCTTGAAAAACAAATTTC
* *
1960585 GTCTCGCTTGAGACATTTTTCCTTTGAAATACAAATTTC
1 GTCTCGCTTGAGACA-ATTT-C-TTGAAAAACAAATTTC
1960624 G
1 G
1960625 AATTTGTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
34 2 0.02
35 27 0.29
36 28 0.30
37 5 0.05
38 14 0.15
39 16 0.17
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (36 bp):
GTCTCGCTTGAGACAATTTCTTGAAAAACAAATTTC
Found at i:1960592 original size:71 final size:73
Alignment explanation
Indices: 1960469--1960605 Score: 190
Period size: 71 Copynumber: 1.9 Consensus size: 73
1960459 TCTCGAAACA
* *
1960469 AAATGTTGTCTCGCTAGAGACAACTTCTTTTGAAAAACAAATCTTTTCTCGCTTGAGACAGTTTT
1 AAATGTTGTCTCGCTAGAGACAACTTCTCTTGAAAAACAAATCTTGTCTCGCTTGAGACAGTTTT
1960534 CTAAAATC
66 CTAAAATC
* * * *
1960542 AAATTTTGTCTCGTTTGAGACAA-TT-TCTTGAAAAACAAAT-TTCGTCTCGCTTGAGACATTTT
1 AAATGTTGTCTCGCTAGAGACAACTTCTCTTGAAAAACAAATCTT-GTCTCGCTTGAGACAGTTT
1960604 TC
65 TC
1960606 CTTTGAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
70 2 0.04
71 33 0.58
72 2 0.04
73 20 0.35
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (73 bp):
AAATGTTGTCTCGCTAGAGACAACTTCTCTTGAAAAACAAATCTTGTCTCGCTTGAGACAGTTTT
CTAAAATC
Found at i:1960715 original size:36 final size:35
Alignment explanation
Indices: 1960641--1960776 Score: 132
Period size: 36 Copynumber: 3.8 Consensus size: 35
1960631 TTTTCATATT
** *
1960641 AAACAAAGTTGATCTCACTTGAGATCGTTTTC-TCAA
1 AAACAAAGTTG-TCTCACTTGAGA-CAATTTCTTTAA
*
1960677 AAACAAACGTTGTCTCGCTTGAGACAATTTCTTTAA
1 AAACAAA-GTTGTCTCACTTGAGACAATTTCTTTAA
* * * ** *
1960713 AAAC-AATTTTTGTCGTTTGAGACAATTTCTCTAA
1 AAACAAAGTTGTCTCACTTGAGACAATTTCTTTAA
1960747 AAACAAATGTTGTCTCACTTGAGACAATTT
1 AAACAAA-GTTGTCTCACTTGAGACAATTT
1960777 TCCAAATTAT
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
34 27 0.33
35 9 0.11
36 42 0.51
37 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (35 bp):
AAACAAAGTTGTCTCACTTGAGACAATTTCTTTAA
Found at i:1960760 original size:34 final size:34
Alignment explanation
Indices: 1960669--1960776 Score: 119
Period size: 34 Copynumber: 3.1 Consensus size: 34
1960659 TTGAGATCGT
*
1960669 TTTCTC-AAAAACAAACGTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATGTTG--TCGCTTGAGACAA
* * * *
1960704 TTTCTTTAAAAACAATTTTTGTCGTTTGAGACAA
1 TTTCTCTAAAAACAAATGTTGTCGCTTGAGACAA
*
1960738 TTTCTCTAAAAACAAATGTTGTCTCACTTGAGACAA
1 TTTCTCTAAAAACAAATGTTG--TCGCTTGAGACAA
1960774 TTT
1 TTT
1960777 TCCAAATTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
34 30 0.50
35 5 0.08
36 25 0.42
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (34 bp):
TTTCTCTAAAAACAAATGTTGTCGCTTGAGACAA
Found at i:1960982 original size:22 final size:22
Alignment explanation
Indices: 1960954--1961001 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1960944 GAGTATGTTT
1960954 CTTTGATAACAAAATTTTGTCA
1 CTTTGATAACAAAATTTTGTCA
1960976 CTTTGATAACAAAATTTTGTCA
1 CTTTGATAACAAAATTTTGTCA
1960998 CTTT
1 CTTT
1961002 TGAGAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (22 bp):
CTTTGATAACAAAATTTTGTCA
Found at i:1961182 original size:30 final size:32
Alignment explanation
Indices: 1961139--1961217 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
1961129 TTTGAGACAA
*
1961139 TTTCTCTTAAAACAAA-C-ATCTTTAAGATTG
1 TTTCTCTTGAAACAAACCTATCTTTAAGATTG
* ** *
1961169 TTTCCCTTGAAACAAAACCTATCTTTGTGTTTG
1 TTTCTCTTGAAAC-AAACCTATCTTTAAGATTG
1961202 TTTCTCTTGAAACAAA
1 TTTCTCTTGAAACAAA
1961218 AGTCTGTGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 11 0.28
31 3 0.08
32 4 0.10
33 22 0.55
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.41
Consensus pattern (32 bp):
TTTCTCTTGAAACAAACCTATCTTTAAGATTG
Found at i:1961298 original size:28 final size:28
Alignment explanation
Indices: 1961189--1961298 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 28
1961179 AACAAAACCT
* * *
1961189 ATCTTTGTGTTTGTTTCTCTTGAAACAAA
1 ATCTTTGAG-TTGTTTCTTTTGAAATAAA
*
1961218 AGTCTGTGAGTTGTTTCTTTTGAAATAAAA
1 A-TCTTTGAGTTGTTTCTTTTGAAAT-AAA
1961248 ATCTTTGAGTTGTTTCTTTTGAAAT-AA
1 ATCTTTGAGTTGTTTCTTTTGAAATAAA
*
1961275 TTCTTTGAGTCTGTTTCTTTTGAA
1 ATCTTTGAGT-TGTTTCTTTTGAA
1961299 CCAAAGTTCT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
27 11 0.15
28 13 0.18
29 38 0.53
30 10 0.14
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (28 bp):
ATCTTTGAGTTGTTTCTTTTGAAATAAA
Found at i:1961644 original size:38 final size:38
Alignment explanation
Indices: 1961553--1961658 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 38
1961543 TCTTTGAGAA
* * ***
1961553 AAATCTTTGAGTCTG-TTTCTTTGGAAACAAAATTTACC
1 AAATCTTTGAGTATGTTTTCCTT-GAAACAAAACAAACC
*
1961591 --ATCTTTGAGTTTGTTTTCCTTGAAACAAAACAAACC
1 AAATCTTTGAGTATGTTTTCCTTGAAACAAAACAAACC
*
1961627 AAATCTTTGAGTATGTTTTTCTTGAAACAAAA
1 AAATCTTTGAGTATGTTTTCCTTGAAACAAAA
1961659 ACATCTTTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
36 24 0.41
37 6 0.10
38 28 0.48
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (38 bp):
AAATCTTTGAGTATGTTTTCCTTGAAACAAAACAAACC
Found at i:1961667 original size:32 final size:33
Alignment explanation
Indices: 1961555--1961687 Score: 108
Period size: 36 Copynumber: 3.8 Consensus size: 33
1961545 TTTGAGAAAA
* *
1961555 ATCTTTGAGTCTGTTTCTT-TGGAAACAAAATTTACC
1 ATCTTTGAGTTTGTTT-TTCTTGAAACAAAA---ACC
*
1961591 ATCTTTGAGTTTGTTTTCCTTGAAACAAAACAAACC
1 ATCTTTGAGTTTGTTTTTCTTGAAAC--AA-AAACC
*
1961627 AAATCTTTGAGTATGTTTTTCTTGAAACAAAAA-C
1 --ATCTTTGAGTTTGTTTTTCTTGAAACAAAAACC
* * *
1961661 ATCTTTGAATTTGTTTCTCTCGAAACA
1 ATCTTTGAGTTTGTTTTTCTTGAAACA
1961688 CCGATCTTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
32 23 0.28
34 1 0.01
35 4 0.05
36 26 0.32
38 26 0.32
39 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.40
Consensus pattern (33 bp):
ATCTTTGAGTTTGTTTTTCTTGAAACAAAAACC
Found at i:1962119 original size:18 final size:18
Alignment explanation
Indices: 1962096--1962135 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1962086 TAGGAGCATT
1962096 GTCACCCCTAGATAACCA
1 GTCACCCCTAGATAACCA
*
1962114 GTCACCCCTAGATAACTA
1 GTCACCCCTAGATAACCA
1962132 GTCA
1 GTCA
1962136 TCCTCATCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (18 bp):
GTCACCCCTAGATAACCA
Found at i:1962462 original size:3 final size:3
Alignment explanation
Indices: 1962454--1962479 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1962444 TATTTTAATT
1962454 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1962480 GTTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1963317 original size:10 final size:10
Alignment explanation
Indices: 1963302--1963339 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1963292 TGGAGAGAAT
1963302 TTTCTCTCTC
1 TTTCTCTCTC
1963312 TTTCTC-C-C
1 TTTCTCTCTC
*
1963320 CTTCTCTCTC
1 TTTCTCTCTC
1963330 TTTCTCTCTC
1 TTTCTCTCTC
1963340 GCAGGCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTCTCTCTC
Found at i:1964162 original size:74 final size:65
Alignment explanation
Indices: 1964106--1964236 Score: 230
Period size: 64 Copynumber: 2.0 Consensus size: 65
1964096 TTGTATATTC
*
1964106 GTATATATATGTACATATATTACCAATGTTTGTTCCACGTTATTTAATATGATTTA-TTTAACTT
1 GTATATATATGTACATATATTACCAATGTTTGTTCCACGTTATTTAATATGATTTATTTTAAATT
*
1964170 GTATATATATGTACATATATTACCAATGTTTGTTCCACGTTATTTAATATGATTTA-TTTAACTT
1 GTATATATATGTACATATATTACCAATGTTTGTTCCACGTTATTTAATATGATTTATTTTAAATT
1964234 GTA
1 GTA
1964237 AAAATATATA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (65 bp):
GTATATATATGTACATATATTACCAATGTTTGTTCCACGTTATTTAATATGATTTATTTTAAATT
Found at i:1969314 original size:21 final size:21
Alignment explanation
Indices: 1969290--1969340 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1969280 AGTTCAAATT
1969290 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCA
* *
1969311 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCA
1969332 CGTTGCGAT
1 CGTTGCGAT
1969341 TAACGACTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCA
Found at i:1976160 original size:2 final size:2
Alignment explanation
Indices: 1976153--1976200 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1976143 TACGGTACGA
* * * *
1976153 AT AT AT AT AC CT AT AT AC CT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1976195 AT AT AT
1 AT AT AT
1976201 TAGAGAAACT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1977600 original size:22 final size:22
Alignment explanation
Indices: 1977575--1977621 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1977565 ACAATTAGAG
* *
1977575 AAAAAGCGTATCACAAGAGCAT
1 AAAAAACGTATCACAAGAACAT
* *
1977597 AAAAAATGTATTACAAGAACAT
1 AAAAAACGTATCACAAGAACAT
1977619 AAA
1 AAA
1977622 TTCTTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (22 bp):
AAAAAACGTATCACAAGAACAT
Found at i:1984728 original size:14 final size:14
Alignment explanation
Indices: 1984709--1984740 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1984699 ATATTTTTGA
1984709 AATAAAGTTATGAT
1 AATAAAGTTATGAT
*
1984723 AATAAATTTATGAT
1 AATAAAGTTATGAT
1984737 AATA
1 AATA
1984741 TACTATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
AATAAAGTTATGAT
Found at i:1995271 original size:20 final size:20
Alignment explanation
Indices: 1995233--1995274 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1995223 CATTTAATAA
**
1995233 TTATCTTTATGGTAAATTTT
1 TTATCTTTATGACAAATTTT
*
1995253 TTATCTTTATGACACATTTT
1 TTATCTTTATGACAAATTTT
1995273 TT
1 TT
1995275 CTACATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.60
Consensus pattern (20 bp):
TTATCTTTATGACAAATTTT
Found at i:2008169 original size:23 final size:23
Alignment explanation
Indices: 2008090--2008162 Score: 137
Period size: 23 Copynumber: 3.2 Consensus size: 23
2008080 AATCATTTTC
2008090 TTCTTCTTCTTCCATAAACTCGT
1 TTCTTCTTCTTCCATAAACTCGT
*
2008113 TTCTTCTTCTTCCATAAACCCGT
1 TTCTTCTTCTTCCATAAACTCGT
2008136 TTCTTCTTCTTCCATAAACTCGT
1 TTCTTCTTCTTCCATAAACTCGT
2008159 TTCT
1 TTCT
2008163 CTTTCTTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.16, C:0.32, G:0.04, T:0.48
Consensus pattern (23 bp):
TTCTTCTTCTTCCATAAACTCGT
Found at i:2009657 original size:40 final size:40
Alignment explanation
Indices: 2009575--2009659 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
2009565 AGAAAGCCAG
*
2009575 AACCATTTTTGTTTCAGACAATGATGGGGGAAGGGGACAA
1 AACCATTTTTGTTTCAGACAATGATGGGGGAAGGAGACAA
**
2009615 AACCATTTTTGTTTCAGA-AGATGATGGGGGAAGGAGTTAA
1 AACCATTTTTGTTTCAGACA-ATGATGGGGGAAGGAGACAA
2009655 AACCA
1 AACCA
2009660 GAAAGGTGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (40 bp):
AACCATTTTTGTTTCAGACAATGATGGGGGAAGGAGACAA
Done.