Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 188 of 199
Found at i:54832863 original size:6 final size:6
Alignment explanation
Indices: 54832852--54832878 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
54832842 ATCGATTTAT
54832852 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
54832879 GTTCGATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:54832942 original size:12 final size:11
Alignment explanation
Indices: 54832921--54832950 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
54832911 ATTAAATAAT
54832921 AAAAAAGGAAA
1 AAAAAAGGAAA
*
54832932 AAAAAAGGGAA
1 AAAAAAGGAAA
54832943 AAAAAAGG
1 AAAAAAGG
54832951 CCGACAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAAGGAAA
Found at i:54842815 original size:6 final size:6
Alignment explanation
Indices: 54842804--54842835 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
54842794 CTTCTTCTCA
*
54842804 GCTTTG GCTTTG GCTTTG GCTGTG GCTTTG GC
1 GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG GC
54842836 AGGAGGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.44
Consensus pattern (6 bp):
GCTTTG
Found at i:54847722 original size:20 final size:24
Alignment explanation
Indices: 54847676--54847724 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
54847666 TTTGTCTGTC
54847676 AATTTTTAATTATATAAATAGATT
1 AATTTTTAATTATATAAATAGATT
54847700 AATTTTTAA-TA-A-AAATA-ATT
1 AATTTTTAATTATATAAATAGATT
54847720 AATTT
1 AATTT
54847725 ATTATTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.32
21 5 0.20
22 1 0.04
23 2 0.08
24 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTTTTAATTATATAAATAGATT
Found at i:54847765 original size:26 final size:27
Alignment explanation
Indices: 54847701--54847766 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 27
54847691 AAATAGATTA
54847701 ATTTTTAATAAAAATAATTAATTTATT
1 ATTTTTAATAAAAATAATTAATTTATT
*
54847728 ATTTAAGATAATATAAAA-AATTAATTTATT
1 ATTT---TTAATA-AAAATAATTAATTTATT
54847758 -TTTTTAATA
1 ATTTTTAATA
54847767 GAGTAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
26 5 0.15
27 4 0.12
29 3 0.09
30 17 0.52
31 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTTTTAATAAAAATAATTAATTTATT
Found at i:54849168 original size:3 final size:3
Alignment explanation
Indices: 54849160--54849205 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
54849150 TTATCCAAAA
54849160 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
54849206 GGTAATAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:54854482 original size:2 final size:2
Alignment explanation
Indices: 54854475--54854524 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
54854465 AGTAACTTTG
54854475 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
54854517 AT AT AT AT
1 AT AT AT AT
54854525 TTGTATTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54864967 original size:2 final size:2
Alignment explanation
Indices: 54864960--54864990 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54864950 TTTATCTTCA
54864960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54864991 ACCAACTTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54870657 original size:15 final size:16
Alignment explanation
Indices: 54870626--54870658 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54870616 GGAATTCACA
*
54870626 TATTTTTCAATATTAT
1 TATTTTTAAATATTAT
54870642 TATTTTTAAATA-TAT
1 TATTTTTAAATATTAT
54870657 TA
1 TA
54870659 CATTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAAATATTAT
Found at i:54871102 original size:22 final size:25
Alignment explanation
Indices: 54871077--54871124 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
54871067 GTAGATATGA
*
54871077 TCAAA-ATCTATA-ATGAG-ATTAT
1 TCAAATATATATATATGAGAATTAT
54871099 TCAAATATATATATATGAGAATTAT
1 TCAAATATATATATATGAGAATTAT
54871124 T
1 T
54871125 TGATATACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 6 0.27
24 5 0.23
25 6 0.27
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (25 bp):
TCAAATATATATATATGAGAATTAT
Found at i:54874317 original size:17 final size:19
Alignment explanation
Indices: 54874285--54874322 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
54874275 GACTAAGAGG
*
54874285 TTGAGACTTATATATTTTC
1 TTGAGACTTATATATTCTC
54874304 TTGAG-CTT-TATATTCTC
1 TTGAGACTTATATATTCTC
54874321 TT
1 TT
54874323 AGCCTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (19 bp):
TTGAGACTTATATATTCTC
Found at i:54888082 original size:15 final size:15
Alignment explanation
Indices: 54888062--54888094 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
54888052 TTTTTTAAGT
54888062 AATTATATTTACTAA
1 AATTATATTTACTAA
54888077 AATTATATTTACTAA
1 AATTATATTTACTAA
54888092 AAT
1 AAT
54888095 AATGATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATATTTACTAA
Found at i:54889550 original size:19 final size:18
Alignment explanation
Indices: 54889515--54889557 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
54889505 AAAATTATGC
54889515 TTTTTAAAATTAATTTATA
1 TTTTTAAAATTAATTTA-A
*
54889534 TTTTTAAAA-TATTTTTAA
1 TTTTTAAAATTA-ATTTAA
54889552 TTTTTA
1 TTTTTA
54889558 TTTTAGGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAAATTAATTTAA
Found at i:54890440 original size:7 final size:7
Alignment explanation
Indices: 54890428--54890462 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
54890418 AAAAATCATA
54890428 TTTATAT
1 TTTATAT
54890435 TTTATAT
1 TTTATAT
54890442 TTTATAT
1 TTTATAT
54890449 TTTATAT
1 TTTATAT
54890456 TTTATAT
1 TTTATAT
54890463 GAATGACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTATAT
Found at i:54895040 original size:15 final size:15
Alignment explanation
Indices: 54895020--54895059 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
54895010 CACCAACGCC
54895020 GCCGCGGCACACACG
1 GCCGCGGCACACACG
54895035 GCCGCGGCACACACG
1 GCCGCGGCACACACG
*
54895050 GCCGCCGCAC
1 GCCGCGGCAC
54895060 CCACCGCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.33, T:0.00
Consensus pattern (15 bp):
GCCGCGGCACACACG
Found at i:54895056 original size:18 final size:17
Alignment explanation
Indices: 54895015--54895057 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
54895005 TGTACCACCA
54895015 ACGCCGCCGCGGCACAC
1 ACGCCGCCGCGGCACAC
54895032 ACG--GCCGCGGCACAC
1 ACGCCGCCGCGGCACAC
54895047 ACGGCCGCCGC
1 AC-GCCGCCGC
54895058 ACCCACCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 14 0.61
16 1 0.04
17 3 0.13
18 5 0.22
ACGTcount: A:0.16, C:0.51, G:0.33, T:0.00
Consensus pattern (17 bp):
ACGCCGCCGCGGCACAC
Found at i:54898716 original size:6 final size:6
Alignment explanation
Indices: 54898705--54898730 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54898695 AAATTATATA
54898705 AACAAT AACAAT AACAAT AACAAT AA
1 AACAAT AACAAT AACAAT AACAAT AA
54898731 TAGCAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AACAAT
Found at i:54900237 original size:33 final size:33
Alignment explanation
Indices: 54900200--54900266 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
54900190 AGAGTTAGCG
54900200 TATTAATTAGGTTTTTAGTTAGGTTTAAGGGCT
1 TATTAATTAGGTTTTTAGTTAGGTTTAAGGGCT
54900233 TATTAATTAGGTTTTTAGTTAGGTTTAAGGGCT
1 TATTAATTAGGTTTTTAGTTAGGTTTAAGGGCT
54900266 T
1 T
54900267 CATCGTCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.49
Consensus pattern (33 bp):
TATTAATTAGGTTTTTAGTTAGGTTTAAGGGCT
Found at i:54909108 original size:20 final size:19
Alignment explanation
Indices: 54909105--54909170 Score: 80
Period size: 18 Copynumber: 3.3 Consensus size: 19
54909095 AAAGTATTTT
54909105 AAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAATTAA
*
54909124 AAAAAGTATTTTAAAAAAATTTA
1 AAAAA-TATTTT---AAAATTAA
54909147 AAAAA-ATTTTAAAATTAA
1 AAAAATATTTTAAAATTAA
54909165 AAAAAT
1 AAAAAT
54909171 TTAAAAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 12 0.30
19 5 0.12
20 6 0.15
21 5 0.12
23 12 0.30
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATATTTTAAAATTAA
Found at i:54909113 original size:11 final size:11
Alignment explanation
Indices: 54909093--54909160 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
54909083 TAAAAATTAA
54909093 AAAAAGTATTTT
1 AAAAA-TATTTT
54909105 AAAAATATTTT
1 AAAAATATTTT
**
54909116 --AAA-ATTAA
1 AAAAATATTTT
54909124 AAAAAGTATTTT
1 AAAAA-TATTTT
*
54909136 AAAAA-AATTT
1 AAAAATATTTT
*
54909146 AAAAAAATTTT
1 AAAAATATTTT
54909157 AAAA
1 AAAA
54909161 TTAAAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 12 0.27
11 14 0.31
12 13 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54909123 original size:31 final size:31
Alignment explanation
Indices: 54909083--54909150 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
54909073 AAAATTAAAA
*
54909083 TAAAAATTAAAAAAAGTATTTTAAAAATATT
1 TAAAAATTAAAAAAAGTATTTTAAAAAAATT
*
54909114 TTAAAATTAAAAAAAGTATTTTAAAAAAATT
1 TAAAAATTAAAAAAAGTATTTTAAAAAAATT
54909145 TAAAAA
1 TAAAAA
54909151 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (31 bp):
TAAAAATTAAAAAAAGTATTTTAAAAAAATT
Found at i:54909148 original size:10 final size:10
Alignment explanation
Indices: 54909133--54909179 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
54909123 AAAAAAGTAT
54909133 TTTAAAAAAA
1 TTTAAAAAAA
54909143 TTTAAAAAAA
1 TTTAAAAAAA
*
54909153 TTT--TAAAA
1 TTTAAAAAAA
54909161 -TTAAAAAAA
1 TTTAAAAAAA
54909170 TTTAAAAAAA
1 TTTAAAAAAA
54909180 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 2 0.06
8 4 0.12
9 4 0.12
10 22 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:54909191 original size:30 final size:27
Alignment explanation
Indices: 54909134--54909200 Score: 107
Period size: 30 Copynumber: 2.4 Consensus size: 27
54909124 AAAAAGTATT
54909134 TTAAAAAAATTTAAAAAAATTTTAAAA
1 TTAAAAAAATTTAAAAAAATTTTAAAA
54909161 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TTAAAAAAATTT-AAAAAA--ATTTTAAAA
54909191 TTAAAAAAAT
1 TTAAAAAAAT
54909201 AAAAATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
27 12 0.32
28 6 0.16
30 19 0.51
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (27 bp):
TTAAAAAAATTTAAAAAAATTTTAAAA
Found at i:54909204 original size:27 final size:26
Alignment explanation
Indices: 54909134--54909210 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 26
54909124 AAAAAGTATT
54909134 TTAAAAAAATTTAAAAAAATTTTAAAA
1 TTAAAAAAA-TTAAAAAAATTTTAAAA
54909161 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TTAAAAAAA-TT-AAAAAA--ATTTTAAAA
*
54909191 TTAAAAAAA-TAAAAATATTT
1 TTAAAAAAATTAAAAAAATTT
54909211 ATTATTCGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
25 4 0.09
27 17 0.37
28 7 0.15
30 18 0.39
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAAAAAAATTAAAAAAATTTTAAAA
Found at i:54909565 original size:3 final size:3
Alignment explanation
Indices: 54909557--54909598 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
54909547 AATAGTGAAT
54909557 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
54909599 TGTTTATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:54913685 original size:17 final size:16
Alignment explanation
Indices: 54913662--54913701 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
54913652 TTTATATTTT
54913662 TTAAAAATTCTAAAAAA
1 TTAAAAATT-TAAAAAA
*
54913679 TATAAAAAGTTAAAAAA
1 T-TAAAAATTTAAAAAA
54913696 TTAAAA
1 TTAAAA
54913702 TTTTTCTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (16 bp):
TTAAAAATTTAAAAAA
Found at i:54915148 original size:5 final size:5
Alignment explanation
Indices: 54915138--54915178 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
54915128 TATGCTGGAT
54915138 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
54915179 GTATTATGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:54917063 original size:19 final size:20
Alignment explanation
Indices: 54917026--54917065 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
54917016 TCAAATACAT
54917026 ACACCAAATTAATCATAAAA
1 ACACCAAATTAATCATAAAA
54917046 ACACCAATATT-A-CATAAAA
1 ACACCAA-ATTAATCATAAAA
54917065 A
1 A
54917066 AAATCCAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 8 0.42
21 3 0.16
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (20 bp):
ACACCAAATTAATCATAAAA
Found at i:54917066 original size:21 final size:20
Alignment explanation
Indices: 54917026--54917067 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
54917016 TCAAATACAT
*
54917026 ACACCAAATTAATCATAAAA
1 ACACCAAATTAATCAAAAAA
54917046 ACACCAATATTACAT-AAAAAA
1 ACACCAA-ATTA-ATCAAAAAA
54917067 A
1 A
54917068 ATCCAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 10 0.53
22 2 0.11
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (20 bp):
ACACCAAATTAATCAAAAAA
Found at i:54917700 original size:2 final size:2
Alignment explanation
Indices: 54917682--54917759 Score: 126
Period size: 2 Copynumber: 40.0 Consensus size: 2
54917672 NNNNNNNNNN
54917682 TA TA T- TA T- TA T- TA TA TA TA TA TA TA TA TA TA CTA 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
54917722 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
54917760 AATGCATAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.04
2 67 0.93
3 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54923264 original size:39 final size:39
Alignment explanation
Indices: 54923208--54923286 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
54923198 TCAGACAATG
54923208 ATTAAAGCTAAAAAAGCTAAAATATTCGATCGAAAAACA
1 ATTAAAGCTAAAAAAGCTAAAATATTCGATCGAAAAACA
* *
54923247 ATTAAAGCTGAACAAGCTAAAATATTCGATCGAAAAACA
1 ATTAAAGCTAAAAAAGCTAAAATATTCGATCGAAAAACA
54923286 A
1 A
54923287 AGTTCAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.20
Consensus pattern (39 bp):
ATTAAAGCTAAAAAAGCTAAAATATTCGATCGAAAAACA
Found at i:54925355 original size:16 final size:17
Alignment explanation
Indices: 54925334--54925368 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
54925324 AAACAGCAAA
54925334 ATTTT-ATTTTAAAAAT
1 ATTTTAATTTTAAAAAT
54925350 ATTTTAAATTTTAAAAAT
1 ATTTT-AATTTTAAAAAT
54925368 A
1 A
54925369 AAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
18 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTAATTTTAAAAAT
Found at i:54926401 original size:28 final size:27
Alignment explanation
Indices: 54926347--54926442 Score: 70
Period size: 29 Copynumber: 3.5 Consensus size: 27
54926337 CAAAAAAATT
** *
54926347 TATTTTAAAAAT-TTAAAAAATAAAAAA
1 TATTTTAAAAATATTTTAAAAT-TAAAA
54926374 CTATTTTAAAAATATTTTAAAATTAAAAA
1 -TATTTTAAAAATATTTTAAAATT-AAAA
* ***
54926403 AATACAAAAAAATATTTTAAAATTAAAA
1 TAT-TTTAAAAATATTTTAAAATTAAAA
*
54926431 -AATTTAAAAATA
1 TATTTTAAAAATA
54926443 AATATATTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
26 7 0.13
27 1 0.02
28 18 0.33
29 28 0.52
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
TATTTTAAAAATATTTTAAAATTAAAA
Found at i:54926425 original size:39 final size:39
Alignment explanation
Indices: 54926347--54926424 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
54926337 CAAAAAAATT
* *
54926347 TATTTTAAAAATTTAAAAAATAAAAAACTATTTTAAAAA
1 TATTTTAAAAATTAAAAAAATAAAAAAATATTTTAAAAA
54926386 TATTTT-AAAATTAAAAAAATACAAAAAAATATTTTAAAA
1 TATTTTAAAAATTAAAAAAAT--AAAAAAATATTTTAAAA
54926425 TTAAAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 13 0.37
39 6 0.17
40 16 0.46
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.35
Consensus pattern (39 bp):
TATTTTAAAAATTAAAAAAATAAAAAAATATTTTAAAAA
Found at i:54926438 original size:38 final size:38
Alignment explanation
Indices: 54926353--54926440 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 38
54926343 AATTTATTTT
* *
54926353 AAAAATTT-AAAAAATAAAAAACTATTTTAAAAATATTT
1 AAAAATTTAAAAAAATAAAAAAATATTTT-AAAATATTA
*
54926391 TAAAA-TTAAAAAAATACAAAAAAATATTTT-AAA-ATTA
1 AAAAATTTAAAAAAAT--AAAAAAATATTTTAAAATATTA
54926428 AAAAATTTAAAAA
1 AAAAATTTAAAAA
54926441 TAAATATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
37 9 0.21
38 21 0.50
40 12 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (38 bp):
AAAAATTTAAAAAAATAAAAAAATATTTTAAAATATTA
Found at i:54926452 original size:16 final size:16
Alignment explanation
Indices: 54926408--54926452 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
54926398 AAAAAAATAC
54926408 AAAA-AAATAT-TTTA
1 AAAATAAATATATTTA
* *
54926422 AAATTAAA-AAATTTA
1 AAAATAAATATATTTA
54926437 AAAATAAATATATTTA
1 AAAATAAATATATTTA
54926453 TTATATAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATAAATATATTTA
Found at i:54927721 original size:18 final size:18
Alignment explanation
Indices: 54927680--54927747 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
54927670 TTGAATTCTA
*
54927680 TTAACATTTTATATAA-TT
1 TTAATATTTT-TATAATTT
54927698 TT--TATTTTT-TAATTT
1 TTAATATTTTTATAATTT
54927713 TTGAATATTTTTATAATTT
1 TT-AATATTTTTATAATTT
*
54927732 TTAAAATTTTTATAAT
1 TTAATATTTTTATAAT
54927748 ATGACATACA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.07
15 5 0.12
16 5 0.12
18 22 0.51
19 8 0.19
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (18 bp):
TTAATATTTTTATAATTT
Found at i:54927731 original size:9 final size:9
Alignment explanation
Indices: 54927685--54927747 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
54927675 TTCTATTAAC
54927685 ATTTTATATA
1 ATTTT-TATA
54927695 A-TTTT-T-
1 ATTTTTATA
54927701 ATTTTT-TA
1 ATTTTTATA
54927709 ATTTTTGA-A
1 ATTTTT-ATA
54927718 TATTTTTATA
1 -ATTTTTATA
*
54927728 ATTTTTAAA
1 ATTTTTATA
54927737 ATTTTTATA
1 ATTTTTATA
54927746 AT
1 AT
54927748 ATGACATACA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
6 1 0.02
7 6 0.13
8 7 0.16
9 23 0.51
10 8 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:54927742 original size:35 final size:37
Alignment explanation
Indices: 54927663--54927743 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 37
54927653 ATGTATTTCA
54927663 AAAATTTTTGAATTCTATTAACATTTTATATAATTTTT
1 AAAATTTTT-AATTCTATTAACATTTTATATAATTTTT
* *
54927701 --ATTTTTTAATT-T-TTGAATATTTT-TATAATTTTT
1 AAAATTTTTAATTCTATT-AACATTTTATATAATTTTT
54927734 AAAATTTTTA
1 AAAATTTTTA
54927744 TAATATGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
33 12 0.32
34 8 0.22
35 11 0.30
36 6 0.16
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (37 bp):
AAAATTTTTAATTCTATTAACATTTTATATAATTTTT
Found at i:54935020 original size:25 final size:26
Alignment explanation
Indices: 54934968--54935030 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
54934958 AATAAAAATA
54934968 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAA--TTTTTTTATTT
*
54934996 ACCAATATATTATAA-TTTTTTATTT
1 ACCAAAATATTATAATTTTTTTATTT
*
54935021 ATCAAAATAT
1 ACCAAAATAT
54935031 ACCAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.56
28 14 0.44
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.51
Consensus pattern (26 bp):
ACCAAAATATTATAATTTTTTTATTT
Found at i:54938544 original size:23 final size:24
Alignment explanation
Indices: 54938498--54938565 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 24
54938488 ATAATGAAAA
*
54938498 TATAATTTTATTATTTTAATAGTT
1 TATAATTTTATTATTTTAAGAGTT
* *
54938522 TATATTTTTA-TATTTTGAGAGTT
1 TATAATTTTATTATTTTAAGAGTT
54938545 AAAATATAATTTTATTATTTT
1 ----TATAATTTTATTATTTT
54938566 TAAATTGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 11 0.31
24 9 0.26
27 9 0.26
28 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
TATAATTTTATTATTTTAAGAGTT
Found at i:54951401 original size:32 final size:31
Alignment explanation
Indices: 54951356--54951451 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
54951346 CTTAGATAAT
54951356 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
54951387 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
54951419 TTAAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
54951450 TT
1 TT
54951452 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:54952064 original size:24 final size:23
Alignment explanation
Indices: 54952000--54952065 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
54951990 CTTATTCTTT
*
54952000 AAAAAAAAA-AAGAAAAAAGTGC
1 AAAAAAAAAGAAGAAAAAAGCGC
* *
54952022 AAAAAAAAAGTGAGTAAAAAGCGC
1 AAAAAAAAAG-AAGAAAAAAGCGC
*
54952046 AAAAAAAAAAGAAAAAAAAA
1 -AAAAAAAAAGAAGAAAAAA
54952066 CAAAAAGCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 9 0.26
24 16 0.46
25 10 0.29
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (23 bp):
AAAAAAAAAGAAGAAAAAAGCGC
Found at i:54952070 original size:16 final size:16
Alignment explanation
Indices: 54952046--54952079 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
54952036 TAAAAAGCGC
54952046 AAAAAAAAAAG-AAAA
1 AAAAAAAAAAGCAAAA
54952061 AAAAACAAAAAGCAAAA
1 AAAAA-AAAAAGCAAAA
54952078 AA
1 AA
54952080 GTGCAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGCAAAA
Found at i:54952295 original size:10 final size:10
Alignment explanation
Indices: 54952280--54952308 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54952270 AATTGGGTAG
54952280 AGTTTTCTTA
1 AGTTTTCTTA
54952290 AGTTTTCTTA
1 AGTTTTCTTA
54952300 AGTTTTCTT
1 AGTTTTCTT
54952309 CTTATTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (10 bp):
AGTTTTCTTA
Found at i:54957712 original size:31 final size:30
Alignment explanation
Indices: 54957669--54957762 Score: 170
Period size: 31 Copynumber: 3.1 Consensus size: 30
54957659 TTAGATAATT
54957669 TTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTAAAGAGTTTTATTAGGATTCAATTACTC
54957699 TTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTAAAGAG-TTTTATTAGGATTCAATTACTC
54957730 TTAAAAGAGTTTTATTAGGATTCAATTACTC
1 TT-AAAGAGTTTTATTAGGATTCAATTACTC
54957761 TT
1 TT
54957763 GTAATTTGCC
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
30 8 0.13
31 48 0.77
32 6 0.10
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.45
Consensus pattern (30 bp):
TTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:54958384 original size:2 final size:2
Alignment explanation
Indices: 54958377--54958404 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54958367 GCACCAGCTT
54958377 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
54958405 NNNNNNNNNN
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:54963171 original size:15 final size:15
Alignment explanation
Indices: 54963151--54963191 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
54963141 AATTCTCCAC
54963151 TTTAAATATTATAGA
1 TTTAAATATTATAGA
54963166 TTTAAATATTATAGA
1 TTTAAATATTATAGA
**
54963181 TAGAAATATTA
1 TTTAAATATTA
54963192 ATAAAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (15 bp):
TTTAAATATTATAGA
Found at i:54968332 original size:16 final size:16
Alignment explanation
Indices: 54968308--54968338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54968298 TTAAAATTTT
54968308 AATAAATATTTTTAAA
1 AATAAATATTTTTAAA
*
54968324 AATATATATTTTTAA
1 AATAAATATTTTTAA
54968339 TCATGTGGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATATTTTTAAA
Found at i:54977744 original size:27 final size:26
Alignment explanation
Indices: 54977713--54977763 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
54977703 TAAATTATGC
*
54977713 TATATTCATTAAAAATTATATAATAAA
1 TATATTCATTAAAAACTATA-AATAAA
*
54977740 TATATTTATTAAAAACTATAAATA
1 TATATTCATTAAAAACTATAAATA
54977764 TATTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
TATATTCATTAAAAACTATAAATAAA
Found at i:54977763 original size:22 final size:25
Alignment explanation
Indices: 54977735--54977782 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 25
54977725 AAATTATATA
54977735 ATAAATATA-TTT-ATTAAAA-ACT
1 ATAAATATATTTTAATTAAAATACT
54977757 ATAAATATATTTTAATTAAAATACT
1 ATAAATATATTTTAATTAAAATACT
54977782 A
1 A
54977783 AGATTAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 3 0.13
24 7 0.30
25 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAAATATATTTTAATTAAAATACT
Found at i:54978535 original size:22 final size:21
Alignment explanation
Indices: 54978509--54978551 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
54978499 AGCATTTAAT
54978509 TTATTTTTAAAAATTATAAAAA
1 TTATTTTTAAAAATT-TAAAAA
54978531 TTATTTTTAAAAATTTAAAAA
1 TTATTTTTAAAAATTTAAAAA
54978552 GTGTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATTTTTAAAAATTTAAAAA
Found at i:54982760 original size:45 final size:46
Alignment explanation
Indices: 54982690--54982776 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 46
54982680 ACAAGCAGTC
* *
54982690 GCTTCGTATCTGTGATTCGACTCCT-AAGCTTATAGCCCCTCGACT
1 GCTTCGTATCCGTGATTCGAATCCTAAAGCTTATAGCCCCTCGACT
* *
54982735 GCTTTGTATCCGTGATTTGAATCCTAAAGCTTATAGCCCCTC
1 GCTTCGTATCCGTGATTCGAATCCTAAAGCTTATAGCCCCTC
54982777 TTCAAGCTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 21 0.57
46 16 0.43
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (46 bp):
GCTTCGTATCCGTGATTCGAATCCTAAAGCTTATAGCCCCTCGACT
Found at i:54983287 original size:24 final size:24
Alignment explanation
Indices: 54983243--54983288 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
54983233 ATATAATTGG
*
54983243 AAAAAAAGTAAGAAATCATCATAA
1 AAAAAAAGTAAGAAATAATCATAA
54983267 AAAAAAAGTAAGAAGA-AATCAT
1 AAAAAAAGTAAGAA-ATAATCAT
54983289 CATACACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (24 bp):
AAAAAAAGTAAGAAATAATCATAA
Found at i:54990041 original size:11 final size:11
Alignment explanation
Indices: 54990021--54990072 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
54990011 ATCCCTATCA
*
54990021 AATTTTCTCTC
1 AATTTCCTCTC
*
54990032 AATTTCCTCTA
1 AATTTCCTCTC
54990043 AATTTCCTCTC
1 AATTTCCTCTC
* *
54990054 AATTTGCTATC
1 AATTTCCTCTC
*
54990065 AAATTCCT
1 AATTTCCT
54990073 TCCAAATTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46
Consensus pattern (11 bp):
AATTTCCTCTC
Found at i:54990072 original size:22 final size:23
Alignment explanation
Indices: 54990014--54990069 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
54990004 CAAACTAATC
*
54990014 CCTATCAAATTTTCTCTCAATTT
1 CCTATCAAATTTCCTCTCAATTT
*
54990037 CCTCT-AAATTTCCTCTCAATTT
1 CCTATCAAATTTCCTCTCAATTT
*
54990059 GCTATCAAATT
1 CCTATCAAATT
54990070 CCTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.45
Consensus pattern (23 bp):
CCTATCAAATTTCCTCTCAATTT
Found at i:54990895 original size:29 final size:29
Alignment explanation
Indices: 54990851--54990925 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
54990841 GCCGGAAAAT
*
54990851 GGCCCATTCCGGTAAATAATAAAATACCG
1 GGCCCATTTCGGTAAATAATAAAATACCG
*
54990880 GGCCCATTTCGATAAATAATAAAATACCG
1 GGCCCATTTCGGTAAATAATAAAATACCG
*
54990909 GACCCATTTCGGTAAAT
1 GGCCCATTTCGGTAAAT
54990926 TGATAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (29 bp):
GGCCCATTTCGGTAAATAATAAAATACCG
Found at i:54991613 original size:25 final size:26
Alignment explanation
Indices: 54991585--54991637 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
54991575 TACAGCCCAG
54991585 CAAA-CTAAACCCTATTAA-CCTAGCC
1 CAAACCTAAACCC-ATTAAGCCTAGCC
54991610 CAAACCTAAACCCATTAAGCCTAGCC
1 CAAACCTAAACCCATTAAGCCTAGCC
54991636 CA
1 CA
54991638 GCAAACCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.40, C:0.38, G:0.06, T:0.17
Consensus pattern (26 bp):
CAAACCTAAACCCATTAAGCCTAGCC
Found at i:54992794 original size:18 final size:18
Alignment explanation
Indices: 54992773--54992810 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54992763 GAAATTATTG
*
54992773 TTATTTTTATTTTTATAC
1 TTATTTTTATTATTATAC
54992791 TTATTTTTATTATTATAC
1 TTATTTTTATTATTATAC
54992809 TT
1 TT
54992811 TCTCTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTTATTATTATAC
Found at i:55007422 original size:16 final size:17
Alignment explanation
Indices: 55007401--55007433 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
55007391 GGGGTTTGAT
55007401 TGAAACAAT-AATAAGG
1 TGAAACAATGAATAAGG
*
55007417 TGAAACACTGAATAAGG
1 TGAAACAATGAATAAGG
55007434 GAAGGTGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.09, G:0.21, T:0.18
Consensus pattern (17 bp):
TGAAACAATGAATAAGG
Found at i:55014799 original size:50 final size:50
Alignment explanation
Indices: 55014684--55014932 Score: 300
Period size: 50 Copynumber: 4.8 Consensus size: 50
55014674 GATAATAACA
* ** * *
55014684 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
55014735 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
55014785 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
55014835 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
* *
55014890 ATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
55014933 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
50 94 0.55
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:55014870 original size:100 final size:104
Alignment explanation
Indices: 55014683--55014932 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
55014673 TGATAATAAC
** * *
55014683 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
55014748 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
55014785 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
55014849 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* * *
55014890 ATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
55014933 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:55015048 original size:13 final size:13
Alignment explanation
Indices: 55015027--55015058 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
55015017 GCTTGGATCA
*
55015027 TCATCAAATAAAT
1 TCATAAAATAAAT
55015040 TCATAAAATAAAT
1 TCATAAAATAAAT
55015053 TCATAA
1 TCATAA
55015059 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:55026592 original size:25 final size:25
Alignment explanation
Indices: 55026564--55026613 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
55026554 TTTATATATA
55026564 AAATCTAT-AAAAAATAACTTAAAAT
1 AAATCTATAAAAAAAT-ACTTAAAAT
*
55026589 AAATTTATAAAAAAATACTTAAAAT
1 AAATCTATAAAAAAATACTTAAAAT
55026614 TAAGACACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (25 bp):
AAATCTATAAAAAAATACTTAAAAT
Found at i:55030430 original size:16 final size:16
Alignment explanation
Indices: 55030409--55030439 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55030399 ATATTATATT
*
55030409 TATTCTTATTTAAGTA
1 TATTCTAATTTAAGTA
55030425 TATTCTAATTTAAGT
1 TATTCTAATTTAAGT
55030440 TTAGTTGTAT
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:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TATTCTAATTTAAGTA
Found at i:55044735 original size:24 final size:24
Alignment explanation
Indices: 55044704--55044775 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 24
55044694 GACAAACTAA
55044704 AAATAATTTAAATTAAATATTATT
1 AAATAATTTAAATTAAATATTATT
*
55044728 AAATAATTT-TA-TAAA-ATTATT
1 AAATAATTTAAATTAAATATTATT
* * *
55044749 ATATTATATTAAATATAAATATAATT
1 AAATAAT-TTAAAT-TAAATATTATT
55044775 A
1 A
55044776 GTAAATAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
21 11 0.29
22 6 0.16
23 2 0.05
24 9 0.24
25 4 0.11
26 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATAATTTAAATTAAATATTATT
Found at i:55045066 original size:20 final size:19
Alignment explanation
Indices: 55045041--55045080 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55045031 ATATTTGTAT
*
55045041 TTATAAAATATTTACATATA
1 TTATAAAATA-GTACATATA
*
55045061 TTATAAATTAGTACATATA
1 TTATAAAATAGTACATATA
55045080 T
1 T
55045081 AAAGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (19 bp):
TTATAAAATAGTACATATA
Found at i:55045894 original size:8 final size:9
Alignment explanation
Indices: 55045876--55045914 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
55045866 ATATGAGTGT
*
55045876 AAAACTATA
1 AAAATTATA
55045885 AAAATT-TA
1 AAAATTATA
55045893 AAAATTATA
1 AAAATTATA
*
55045902 AAGATTATA
1 AAAATTATA
55045911 AAAA
1 AAAA
55045915 AGTTTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAATTATA
Found at i:55045901 original size:17 final size:18
Alignment explanation
Indices: 55045876--55045914 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
55045866 ATATGAGTGT
55045876 AAAACTATAAAAATT-TA
1 AAAACTATAAAAATTATA
* *
55045893 AAAATTATAAAGATTATA
1 AAAACTATAAAAATTATA
55045911 AAAA
1 AAAA
55045915 AGTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAACTATAAAAATTATA
Found at i:55046428 original size:28 final size:25
Alignment explanation
Indices: 55046397--55046453 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
55046387 AAAAGATTCA
55046397 AATATGTAAAAGATTCAAAAAAAATATT
1 AATAT-TAAAA-ATTCAAAAAAAAT-TT
* * *
55046425 AATATTAATAATTTATAAAAAATTT
1 AATATTAAAAATTCAAAAAAAATTT
55046450 AATA
1 AATA
55046454 AAAAACACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 6 0.23
26 11 0.42
27 4 0.15
28 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
AATATTAAAAATTCAAAAAAAATTT
Found at i:55048389 original size:3 final size:3
Alignment explanation
Indices: 55048381--55048481 Score: 134
Period size: 3 Copynumber: 32.7 Consensus size: 3
55048371 TTAGTAATTC
55048381 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
55048429 TAT TAT TACT TACT TAT TATT TAG T-T TAGT TAT TAT TACT TA- TAT
1 TAT TAT TA-T TA-T TAT TA-T TAT TAT TA-T TAT TAT TA-T TAT TAT
55048474 TAT TAT TA
1 TAT TAT TA
55048482 NNNNNNNNNN
Statistics
Matches: 90, Mismatches: 2, Indels: 12
0.87 0.02 0.12
Matches are distributed among these distances:
2 3 0.03
3 71 0.79
4 16 0.18
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:55049094 original size:61 final size:64
Alignment explanation
Indices: 55049029--55049155 Score: 188
Period size: 67 Copynumber: 2.0 Consensus size: 64
55049019 TTTGTTAGTC
*
55049029 TTGTTCGTTTATTTATGTACA-TG-T-TTGTTTTTCTTGCTTTAGTTTTTATCTGTTTATCATT
1 TTGTTCGTTTATTTATGTACATTGTTATTGTTTTTCTTGCTTTAGTTTTTACCTGTTTATCATT
*
55049090 TTGTTCGTTTATTTATGTACATGTTTGTTATTGTTTTTCTTGCTTTAGTTTTTGCCTGTTTATCA
1 TTGTTCGTTTATTTATGTACA---TTGTTATTGTTTTTCTTGCTTTAGTTTTTACCTGTTTATCA
55049155 T
63 T
55049156 CTGTCATGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
61 21 0.36
65 2 0.03
66 1 0.02
67 34 0.59
ACGTcount: A:0.13, C:0.10, G:0.14, T:0.63
Consensus pattern (64 bp):
TTGTTCGTTTATTTATGTACATTGTTATTGTTTTTCTTGCTTTAGTTTTTACCTGTTTATCATT
Found at i:55049622 original size:110 final size:110
Alignment explanation
Indices: 55049502--55049809 Score: 469
Period size: 110 Copynumber: 2.8 Consensus size: 110
55049492 TTTTCTAAAA
* * * **
55049502 AAAAAATTCAAAATAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACATGTCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
* *
55049567 GGTATCGATTTTTTTCGTTCAACCAAATGGCTTAATATCTTTTTT
66 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* *
55049612 AAAAATTTCAAAATATGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
55049677 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
66 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* * *
55049722 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTACCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
* *
55049786 GGTTTCGA--TTTCTCGTTTAACCAA
66 GGTATCGATTTTTCTCGTTCAACCAA
55049810 GTTGCCAAAT
Statistics
Matches: 182, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
107 15 0.08
109 25 0.14
110 142 0.78
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (110 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
Found at i:55059585 original size:36 final size:36
Alignment explanation
Indices: 55059534--55059610 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
55059524 GATTGTGCCA
55059534 ATAG-GCGTTTGTAGTCCAACGGTTAGGATACTTTG
1 ATAGTGCGTTTGTAGTCCAACGGTTAGGATACTTTG
55059569 ATAGTGCGTTTGTAGTCCAACGGTTAGGATACTTTG
1 ATAGTGCGTTTGTAGTCCAACGGTTAGGATACTTTG
55059605 ATAGTG
1 ATAGTG
55059611 GATAAATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 4 0.10
36 37 0.90
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.35
Consensus pattern (36 bp):
ATAGTGCGTTTGTAGTCCAACGGTTAGGATACTTTG
Found at i:55063001 original size:9 final size:9
Alignment explanation
Indices: 55062987--55063082 Score: 129
Period size: 9 Copynumber: 10.7 Consensus size: 9
55062977 AAATGGAGAT
*
55062987 ATAACAATA
1 ATAATAATA
*
55062996 ATAACAATA
1 ATAATAATA
* *
55063005 ATATTGATA
1 ATAATAATA
*
55063014 ATAATACTA
1 ATAATAATA
*
55063023 ATACTAATA
1 ATAATAATA
*
55063032 CTAATAATA
1 ATAATAATA
55063041 ATAATAATA
1 ATAATAATA
55063050 ATAATAATA
1 ATAATAATA
55063059 ATAATAATA
1 ATAATAATA
55063068 ATAATAATA
1 ATAATAATA
55063077 ATAATA
1 ATAATA
55063083 TATTAGTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAATAATA
Found at i:55063024 original size:6 final size:6
Alignment explanation
Indices: 55062987--55063082 Score: 129
Period size: 6 Copynumber: 16.0 Consensus size: 6
55062977 AAATGGAGAT
* * * * * * *
55062987 ATAACA ATAATA ACAATA ATATTG ATAATA ATACTA ATACTA ATACTA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
55063035 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
55063083 TATTAGTTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (6 bp):
ATAATA
Found at i:55065909 original size:2 final size:2
Alignment explanation
Indices: 55065902--55065945 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
55065892 GTATATGTGA
55065902 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
55065944 AT
1 AT
55065946 TTGGCCTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55066417 original size:2 final size:2
Alignment explanation
Indices: 55066410--55066439 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55066400 GGTCTAATGA
*
55066410 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55066440 GATGCTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55073183 original size:3 final size:3
Alignment explanation
Indices: 55073175--55073234 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
55073165 TTTATTTTTG
*
55073175 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
55073223 TGT TAT TAT TAT
1 TAT TAT TAT TAT
55073235 CATCATCATC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:55073239 original size:3 final size:3
Alignment explanation
Indices: 55073233--55073363 Score: 208
Period size: 3 Copynumber: 43.7 Consensus size: 3
55073223 TGTTATTATT
* * * * *
55073233 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC GTC GTC GTC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
55073281 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
55073329 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
55073364 GTATATCTTT
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 122 1.00
ACGTcount: A:0.29, C:0.33, G:0.05, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:55087048 original size:14 final size:14
Alignment explanation
Indices: 55087029--55087055 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55087019 TATATTTATA
55087029 AAATTACAAAATAC
1 AAATTACAAAATAC
55087043 AAATTACAAAATA
1 AAATTACAAAATA
55087056 AATAAAAAAT
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:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATTACAAAATAC
Found at i:55097135 original size:2 final size:2
Alignment explanation
Indices: 55097128--55097184 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
55097118 TCCATACATA
55097128 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
55097170 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
55097185 AAAACTCCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:55105299 original size:16 final size:16
Alignment explanation
Indices: 55105278--55105312 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
55105268 AATCTAAGAA
55105278 AAACGGAACCAAGTTT
1 AAACGGAACCAAGTTT
55105294 AAACGGAACCAAGTTT
1 AAACGGAACCAAGTTT
55105310 AAA
1 AAA
55105313 TGGATCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (16 bp):
AAACGGAACCAAGTTT
Found at i:55109339 original size:13 final size:13
Alignment explanation
Indices: 55109321--55109345 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55109311 TTTCGTCCTG
55109321 TTTTTATTGTTTA
1 TTTTTATTGTTTA
55109334 TTTTTATTGTTT
1 TTTTTATTGTTT
55109346 CCATACAAAA
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:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTTATTGTTTA
Found at i:55113601 original size:30 final size:30
Alignment explanation
Indices: 55113565--55113625 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
55113555 TTGGTTGGAC
55113565 CCGATTTGGCCCATATTGAAACCCATTAAT
1 CCGATTTGGCCCATATTGAAACCCATTAAT
55113595 CCGATTTGGCCCATATTGAAACCCATTAAT
1 CCGATTTGGCCCATATTGAAACCCATTAAT
55113625 C
1 C
55113626 TATCTTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (30 bp):
CCGATTTGGCCCATATTGAAACCCATTAAT
Found at i:55117172 original size:49 final size:48
Alignment explanation
Indices: 55117096--55117193 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 48
55117086 GTTTAAAAAG
*
55117096 TGCAAAATAGAGGGATCAAATTTTAAAAGATGTATGGACATCAAAATCA
1 TGCAAAATAGAGGGATCAAATTCTAAAAGATGTAT-GACATCAAAATCA
*
55117145 TGCAAAATAGAGGGATTAAATTCTAAAAGATGTATGACATCAAAATCA
1 TGCAAAATAGAGGGATCAAATTCTAAAAGATGTATGACATCAAAATCA
55117193 T
1 T
55117194 TAGTTCATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 14 0.30
49 33 0.70
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (48 bp):
TGCAAAATAGAGGGATCAAATTCTAAAAGATGTATGACATCAAAATCA
Found at i:55122872 original size:13 final size:14
Alignment explanation
Indices: 55122847--55122876 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
55122837 ATTTACGTTT
55122847 TTTTTTAATTTAAA
1 TTTTTTAATTTAAA
55122861 TTTTTTAA-TTAAA
1 TTTTTTAATTTAAA
55122874 TTT
1 TTT
55122877 GAAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTAATTTAAA
Found at i:55123402 original size:59 final size:60
Alignment explanation
Indices: 55123315--55123443 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 60
55123305 ATTAATAGAA
55123315 TCATATAAGTAATTTATTTTTTAAAATAAAAGAAAATTACACTAAGCATTTAATAGTATATT
1 TCAT-TAA-TAATTTATTTTTTAAAATAAAAGAAAATTACACTAAGCATTTAATAGTATATT
*
55123377 TCATTAATAATTTA-TTTTTAAAATAAAAGAAAATTACCCTAAGCATTTAATAGTATATT
1 TCATTAATAATTTATTTTTTAAAATAAAAGAAAATTACACTAAGCATTTAATAGTATATT
*
55123436 GCATTAAT
1 TCATTAAT
55123444 TAGTATCTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
59 51 0.78
60 7 0.11
61 3 0.05
62 4 0.06
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (60 bp):
TCATTAATAATTTATTTTTTAAAATAAAAGAAAATTACACTAAGCATTTAATAGTATATT
Found at i:55124368 original size:27 final size:25
Alignment explanation
Indices: 55124337--55124393 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
55124327 TTATATCAAT
* *
55124337 AATTATATTAATAATTTATAAAAATTA
1 AATTAAATT-ATAATTT-TAAAAATCA
*
55124364 AATTAAATTATAATTTTATAAATCA
1 AATTAAATTATAATTTTAAAAATCA
55124389 AATTA
1 AATTA
55124394 CACAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 12 0.44
26 7 0.26
27 8 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTAAATTATAATTTTAAAAATCA
Found at i:55126185 original size:30 final size:30
Alignment explanation
Indices: 55126144--55126259 Score: 102
Period size: 30 Copynumber: 4.0 Consensus size: 30
55126134 ATATTTTATT
*
55126144 ATTTT-ATTTTAAT-TTAAAATACTTTATTAA
1 ATTTTAATTTAAATATTAAAATACTTT-TT-A
* *
55126174 ATTTTAATTTAAAATATTTAAATAC-TTTAA
1 ATTTTAATTT-AAATATTAAAATACTTTTTA
*
55126204 ATTTTAATTTAAAATATTTAAATAC-TTTTA
1 ATTTTAATTT-AAATATTAAAATACTTTTTA
*
55126234 A-TTT-ATTTAAGT-TTAAAATACTTTTT
1 ATTTTAATTTAAATATTAAAATACTTTTT
55126260 TTAATTTATT
Statistics
Matches: 76, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.11
27 7 0.09
28 4 0.05
29 3 0.04
30 36 0.47
31 5 0.07
32 5 0.07
33 8 0.11
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (30 bp):
ATTTTAATTTAAATATTAAAATACTTTTTA
Found at i:55126206 original size:24 final size:24
Alignment explanation
Indices: 55126149--55126207 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
55126139 TTATTATTTT
*
55126149 ATTTTAATTTAAAATACTTTATTAA
1 ATTTAAATTTAAAATACTTTA-TAA
*
55126174 ATTTTAATTTAAAATA-TTTA-AA
1 ATTTAAATTTAAAATACTTTATAA
55126196 TACTTTAAATTT
1 -A-TTTAAATTT
55126208 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 12 0.39
25 16 0.52
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTAAATTTAAAATACTTTATAA
Found at i:55127985 original size:21 final size:20
Alignment explanation
Indices: 55127961--55128001 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
55127951 TTAATGTTAA
*
55127961 AATTTTAAATTGTAATTAAAT
1 AATTTTAAATT-CAATTAAAT
*
55127982 AATTTTATATTCAATTAAAT
1 AATTTTAAATTCAATTAAAT
55128002 GATTACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AATTTTAAATTCAATTAAAT
Found at i:55131265 original size:2 final size:2
Alignment explanation
Indices: 55131260--55131287 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55131250 CTTCTCTCAC
55131260 AT 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 AT
55131288 TCGATAAAAA
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):
AT
Found at i:55140414 original size:28 final size:29
Alignment explanation
Indices: 55140381--55140441 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
55140371 TTTATATATA
* *
55140381 TATTATTTTTAAAATTAT-GTTTTTATGG
1 TATTATTATTAAAATTATCATTTTTATGG
*
55140409 TATTATTATTAAAATTATCATTTTTTTGG
1 TATTATTATTAAAATTATCATTTTTATGG
55140438 TATT
1 TATT
55140442 TTCCATATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.61
Consensus pattern (29 bp):
TATTATTATTAAAATTATCATTTTTATGG
Found at i:55141428 original size:2 final size:2
Alignment explanation
Indices: 55141421--55141446 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55141411 ATAAAATGCA
55141421 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
55141447 TGAACTCAAA
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:55152718 original size:4 final size:4
Alignment explanation
Indices: 55152709--55152734 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
55152699 TTAATAAACT
55152709 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
55152735 CTAAAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:55153189 original size:23 final size:23
Alignment explanation
Indices: 55153158--55153208 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
55153148 ACTTACTTTC
* * *
55153158 TTACTGTAGAAATTTTTGGGGTA
1 TTACAGTAGAAATTTTCGGGATA
*
55153181 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGAAATTTTCGGGATA
55153204 TTACA
1 TTACA
55153209 CTTATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGAAATTTTCGGGATA
Found at i:55157267 original size:53 final size:53
Alignment explanation
Indices: 55157187--55157294 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
55157177 CTTTGTGTCC
*
55157187 TCAATAGACTAATAAACCTGACTGAAGTGAACATCTCTTTTGCTGTTTACATA
1 TCAATAGACTAATAAACCCGACTGAAGTGAACATCTCTTTTGCTGTTTACATA
55157240 TCAATAGACTAATAAACCCGACTGAAGTGAACATCTCTTTTGCTGTTTACATA
1 TCAATAGACTAATAAACCCGACTGAAGTGAACATCTCTTTTGCTGTTTACATA
55157293 TC
1 TC
55157295 TGGGCATGAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (53 bp):
TCAATAGACTAATAAACCCGACTGAAGTGAACATCTCTTTTGCTGTTTACATA
Found at i:55165446 original size:45 final size:45
Alignment explanation
Indices: 55165346--55165447 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 45
55165336 AACGGTAGCA
55165346 GTAACAGTAACAATAACAATATTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACAATAACAATATTCAACACACAAAGTGCTGAATCT
* ** * * *
55165391 GTAACTGTAACGGTAATAGTATTCAACACACAAAGTGTTGAATC-
1 GTAACAGTAACAATAACAATATTCAACACACAAAGTGCTGAATCT
55165435 GATAACAGTAACA
1 G-TAACAGTAACA
55165448 GTAGTTGGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 1 0.02
45 47 0.98
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACAATAACAATATTCAACACACAAAGTGCTGAATCT
Found at i:55165693 original size:40 final size:41
Alignment explanation
Indices: 55165649--55165736 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 41
55165639 AATTCATTAC
* * *
55165649 TTCAGTAATTTCACAGTTCAATGCAGTACAC-ATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAAACAATA
* *
55165689 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAAACAATA
55165730 TTCAGTA
1 TTCAGTA
55165737 TTCCATAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 27 0.64
41 15 0.36
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (41 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAAACAATA
Found at i:55165714 original size:21 final size:21
Alignment explanation
Indices: 55165649--55165716 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
55165639 AATTCATTAC
* *
55165649 TTCAGTAATTTCACAGTTCAA
1 TTCAGTAACTTCACAATTCAA
* * *
55165670 TGCAGTACACATAACAA-T--A
1 TTCAGTA-ACTTCACAATTCAA
55165689 TTCAGTAACTTCACAATTCAA
1 TTCAGTAACTTCACAATTCAA
55165710 TTCAGTA
1 TTCAGTA
55165717 CTCAAAAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 7 0.20
19 8 0.23
21 15 0.43
22 5 0.14
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
TTCAGTAACTTCACAATTCAA
Found at i:55166573 original size:25 final size:25
Alignment explanation
Indices: 55166543--55166601 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
55166533 TATAATTAAG
55166543 TTAATTAATAATTATAAAATATCTA
1 TTAATTAATAATTATAAAATATCTA
55166568 TTAATTAATAATTATAAAATATCTA
1 TTAATTAATAATTATAAAATATCTA
55166593 TT--TTAATAA
1 TTAATTAATAA
55166602 CAAATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 7 0.21
25 27 0.79
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATTAATAATTATAAAATATCTA
Found at i:55166707 original size:30 final size:28
Alignment explanation
Indices: 55166673--55166728 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
55166663 TTATCAAATA
55166673 AATAAAATCTTTTAATATAATAATTTAATT
1 AATAAAATCTTTTAAT-TAA-AATTTAATT
* *
55166703 AATAATATCTTTTACTTAAAATTTAA
1 AATAAAATCTTTTAATTAAAATTTAA
55166729 GAAAATATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 3 0.12
30 14 0.58
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (28 bp):
AATAAAATCTTTTAATTAAAATTTAATT
Found at i:55168953 original size:250 final size:245
Alignment explanation
Indices: 55168517--55168972 Score: 617
Period size: 250 Copynumber: 1.8 Consensus size: 245
55168507 TTATTATTGT
* * * * *
55168517 TTATTATTATACCTGTTGAAATATGCTCCAACTCTCTATACTTTTCGTATATTTGAAAGGTAACC
1 TTATTATTATACCTGTTAAAATATGCTCCAACTCCCTATACTTTTCATACATTTAAAAGGTAACC
* * **
55168582 TTCTTACTATATTAAATAATGTTATATCATATCATATCATATACTAATAGTTTATATATAGGCAT
66 CTCCTACTATATTAAATAATACTATATCATATCATATCATATACTAATAGTTTATATATAGGCAT
* * *
55168647 TAATTATTAAACATCATAATATAATGTAATATTATATCTTTGATTATAATCTATATTACAATAAC
131 CAATGATTAAACATCATAATATAATGTAATACTATATCTTTGATTATAATCTATATTACAATAAC
55168712 AGTTATATATAATAGTAGTACATTATATATTACTTATTGTATATTATATA
196 AGTTATATATAATAGTAGTACATTATATATTACTTATTGTATATTATATA
* * * *
55168762 TTATTATTATA-CTAGTTAAAATATGCTCTAAGTCCCTATACTTTTCATACATTTAAAAGTTAGC
1 TTATTATTATACCT-GTTAAAATATGCTCCAACTCCCTATACTTTTCATACATTTAAAAGGTAAC
* * *
55168826 CCTCCTACTATATTATATAATACTATATCATATCATATAATATAATACACTTATAGTTTATATAT
65 CCTCCTACTATATTAAATAATACTATATCATATCATAT--CAT-AT--ACTAATAGTTTATATAT
* * * * * *
55168891 ATGCATCGATGATTAAACATTATAATATCATGTAATACTATATCTTTTATTATAATCTATATTAT
125 AGGCATCAATGATTAAACATCATAATATAATGTAATACTATATCTTTGATTATAATCTATATTAC
*
55168956 AATAATAGTTATATATA
190 AATAACAGTTATATATA
55168973 TATATTAATA
Statistics
Matches: 179, Mismatches: 26, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
244 2 0.01
245 85 0.47
247 2 0.01
248 2 0.01
250 88 0.49
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (245 bp):
TTATTATTATACCTGTTAAAATATGCTCCAACTCCCTATACTTTTCATACATTTAAAAGGTAACC
CTCCTACTATATTAAATAATACTATATCATATCATATCATATACTAATAGTTTATATATAGGCAT
CAATGATTAAACATCATAATATAATGTAATACTATATCTTTGATTATAATCTATATTACAATAAC
AGTTATATATAATAGTAGTACATTATATATTACTTATTGTATATTATATA
Found at i:55169162 original size:17 final size:19
Alignment explanation
Indices: 55169120--55169163 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
55169110 TCGTTAAAGT
55169120 TTAAT-TTTATATGTATAA
1 TTAATATTTATATGTATAA
*
55169138 TAAATATTTATAT-TA-AA
1 TTAATATTTATATGTATAA
55169155 TTAATATTT
1 TTAATATTT
55169164 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTAATATTTATATGTATAA
Found at i:55173437 original size:2 final size:2
Alignment explanation
Indices: 55173430--55173463 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55173420 AATTGAAATC
55173430 AT AT AT AT 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 AT AT AT AT
55173464 TTATTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55174676 original size:3 final size:3
Alignment explanation
Indices: 55174668--55174716 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
55174658 TAACAGTAAC
55174668 AAT AAT AAT AAGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55174714 AAT
1 AAT
55174717 GGTATGAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55175423 original size:3 final size:3
Alignment explanation
Indices: 55175415--55175580 Score: 287
Period size: 3 Copynumber: 54.3 Consensus size: 3
55175405 GAATATGAAA
*
55175415 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55175463 AAT AAT AAT AAT AAT AAT AAT AAGT AAGT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT -AAT AAT AAT AAT AAT
*
55175511 AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55175559 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
55175581 TGAAATTTGT
Statistics
Matches: 157, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
3 147 0.94
4 10 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55181292 original size:13 final size:13
Alignment explanation
Indices: 55181260--55181325 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
55181250 TAAATGGAAA
* *
55181260 TGGTTATATTAAG
1 TGGTTATATGAAT
*
55181273 TGTTTATATGAAT
1 TGGTTATATGAAT
*
55181286 TGGTTATATGGAAA
1 TGGTTATAT-GAAT
* *
55181300 TAGATATATGAAT
1 TGGTTATATGAAT
*
55181313 TGGTGATATGAAT
1 TGGTTATATGAAT
55181326 CGATTTTATG
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 31 0.76
14 10 0.24
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (13 bp):
TGGTTATATGAAT
Found at i:55181297 original size:40 final size:40
Alignment explanation
Indices: 55181253--55181351 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 40
55181243 AAAAGAGTAA
* * * * * *
55181253 ATGGAAATGGTTATATTAAGTGTTTATATGAATTGGTTAT
1 ATGGAAATAGATATATTAAGTGGTGATATGAATCGATTAT
* * *
55181293 ATGGAAATAGATATATGAATTGGTGATATGAATCGATTTT
1 ATGGAAATAGATATATTAAGTGGTGATATGAATCGATTAT
55181333 ATGGAAATAGATATATTAA
1 ATGGAAATAGATATATTAA
55181352 ATGAAACATT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.39
Consensus pattern (40 bp):
ATGGAAATAGATATATTAAGTGGTGATATGAATCGATTAT
Found at i:55185596 original size:23 final size:22
Alignment explanation
Indices: 55185553--55185596 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
55185543 TTCTAAGTCG
55185553 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
55185576 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
55185597 TTAGTCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:55185690 original size:23 final size:23
Alignment explanation
Indices: 55185664--55185831 Score: 282
Period size: 23 Copynumber: 7.3 Consensus size: 23
55185654 ATAAGTGCCA
55185664 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55185687 CACTGATACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
55185710 CACTAATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55185733 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55185756 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
55185779 CACTAATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55185802 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55185825 CACTGAT
1 CACTGAT
55185832 CAATAACATT
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 133 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:55185775 original size:69 final size:69
Alignment explanation
Indices: 55185664--55185830 Score: 316
Period size: 69 Copynumber: 2.4 Consensus size: 69
55185654 ATAAGTGCCA
*
55185664 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGCCGAAGCTACCACTAATATGTAGCCGTAG
1 CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTAATATGTAGCCGTAG
55185729 CTAC
66 CTAC
*
55185733 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTAATATGTAGCCGTAG
1 CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTAATATGTAGCCGTAG
55185798 CTAC
66 CTAC
55185802 CACTGATATGTAGCCGAAGCTACCACTGA
1 CACTGATATGTAGCCGAAGCTACCACTGA
55185831 TCAATAACAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 96 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (69 bp):
CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTAATATGTAGCCGTAG
CTAC
Found at i:55187260 original size:18 final size:18
Alignment explanation
Indices: 55187226--55187260 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55187216 TTTCAAATTG
* *
55187226 TTTTATTCGTTTTCAAAA
1 TTTTATTCATTTACAAAA
55187244 TTTTATTCATTTACAAA
1 TTTTATTCATTTACAAA
55187261 TCGTTATTCA
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:0.31, C:0.11, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTATTCATTTACAAAA
Found at i:55188964 original size:43 final size:43
Alignment explanation
Indices: 55188899--55189026 Score: 161
Period size: 43 Copynumber: 3.0 Consensus size: 43
55188889 TAGTATTTTT
* *
55188899 GATATGTGTTTTCATGTAAGACCACGTCAGGGACGTTGGCATC
1 GATATGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCATC
* * *
55188942 GATTTGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGACATC
1 GATATGTGTTTACATGTAAGACCAC-GTCTGGGAC-GTTGGCATC
* *
55188985 GATATGTGATTACATGTAAGACCACGTCTGGGACTTTGGCAT
1 GATATGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCAT
55189027 TGTACGAGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.01
43 68 0.96
44 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
GATATGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:55193822 original size:11 final size:12
Alignment explanation
Indices: 55193798--55193823 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55193788 TTGTCCGGTA
55193798 TTTCAAATTTTT
1 TTTCAAATTTTT
55193810 TTTCAAATTTTT
1 TTTCAAATTTTT
55193822 TT
1 TT
55193824 AAAAACACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCAAATTTTT
Found at i:55195027 original size:5 final size:5
Alignment explanation
Indices: 55195017--55195044 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
55195007 TGTTAAACCT
55195017 TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TAT
55195045 GTTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:55197946 original size:25 final size:24
Alignment explanation
Indices: 55197901--55198036 Score: 110
Period size: 25 Copynumber: 5.5 Consensus size: 24
55197891 AGCTATAAAC
* * *
55197901 AGGAAGCTCCTCCGAGATGAATAAT
1 AGGAAGCTCATGCGAGCTGAAT-AT
* *
55197926 AGGAAGCTCATGTGAGCTGAATAAC
1 AGGAAGCTCATGCGAGCTGAAT-AT
**
55197951 AAAAAGCTCATGCGAGCTGAATAT
1 AGGAAGCTCATGCGAGCTGAATAT
* *
55197975 CGAGAAGCTCATGCGAGTTGAATAT
1 AG-GAAGCTCATGCGAGCTGAATAT
* * * *
55198000 CGAGAAGCTCATGCGAGTTGTATTAC
1 AG-GAAGCTCATGCGAGCTG-AATAT
55198026 AGGAAGCTCAT
1 AGGAAGCTCAT
55198037 ATGAGCTGTG
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
24 1 0.01
25 88 0.95
26 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (24 bp):
AGGAAGCTCATGCGAGCTGAATAT
Found at i:55197972 original size:50 final size:49
Alignment explanation
Indices: 55197904--55198044 Score: 138
Period size: 50 Copynumber: 2.8 Consensus size: 49
55197894 TATAAACAGG
* *
55197904 AAGCTCCTCCGAGATGAATAATAGGAAGCTCATGTGAGCTGAATAACAAA
1 AAGCTCATGCGAGATGAAT-ATAGGAAGCTCATGTGAGCTGAATAACAAA
* * * * * * *
55197954 AAGCTCATGCGAGCTGAATATCGAGAAGCTCATGCGAGTTGAATATCGAG
1 AAGCTCATGCGAGATGAATATAG-GAAGCTCATGTGAGCTGAATAACAAA
* * * *
55198004 AAGCTCATGCGAGTTGTATTACAGGAAGCTCATATGAGCTG
1 AAGCTCATGCGAGATG-AATATAGGAAGCTCATGTGAGCTG
55198045 TGGTGTATCC
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
49 3 0.04
50 66 0.90
51 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (49 bp):
AAGCTCATGCGAGATGAATATAGGAAGCTCATGTGAGCTGAATAACAAA
Found at i:55200110 original size:28 final size:27
Alignment explanation
Indices: 55200077--55200153 Score: 127
Period size: 28 Copynumber: 2.8 Consensus size: 27
55200067 TAATGTTGGC
55200077 CTTAGCCCAATACAGTAACAGTGTGAG
1 CTTAGCCCAATACAGTAACAGTGTGAG
*
55200104 CTTTAGCCCAATACAGTAACAGTGTGGG
1 C-TTAGCCCAATACAGTAACAGTGTGAG
*
55200132 CCTAGCCCAATACAGTAACAGT
1 CTTAGCCCAATACAGTAACAGT
55200154 ACAGTGCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 21 0.45
28 26 0.55
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (27 bp):
CTTAGCCCAATACAGTAACAGTGTGAG
Done.