Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 35 of 182
Found at i:13409973 original size:2 final size:2
Alignment explanation
Indices: 13409954--13409999 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
13409944 CGAATATGAA
* *
13409954 AT AT AT AA AT AT AA 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
13409996 AT AT
1 AT AT
13410000 TAAACCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:13411396 original size:20 final size:21
Alignment explanation
Indices: 13411360--13411398 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13411350 TGGGGACAAT
13411360 AAAATACAACACATGGTTAGA
1 AAAATACAACACATGGTTAGA
13411381 AAAATACAACAC-TGGTTA
1 AAAATACAACACATGGTTA
13411399 ACGCTGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (21 bp):
AAAATACAACACATGGTTAGA
Found at i:13412175 original size:17 final size:18
Alignment explanation
Indices: 13412139--13412180 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
13412129 TTTATTTTTA
13412139 AAAAATATTAATTACTAT
1 AAAAATATTAATTACTAT
13412157 AAAAATATTAA-TA-TGAT
1 AAAAATATTAATTACT-AT
13412174 AAAAATA
1 AAAAATA
13412181 ATTTTTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 11 0.48
18 11 0.48
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATATTAATTACTAT
Found at i:13418999 original size:24 final size:24
Alignment explanation
Indices: 13418967--13419013 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
13418957 TAATTATTTA
*
13418967 AAATTATAAAAATATATATTATTC
1 AAATAATAAAAATATATATTATTC
* *
13418991 AAATAATAAAATTATATTTTATT
1 AAATAATAAAAATATATATTATT
13419014 ATCTTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATAATAAAAATATATATTATTC
Found at i:13421722 original size:29 final size:30
Alignment explanation
Indices: 13421689--13421750 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
13421679 TTGATTTAAT
13421689 GTGTAATAGTATACA-TG-AATTTTAATT-TG
1 GTGTAAT--TATACAGTGAAATTTTAATTGTG
13421718 GTGTAATTATACATGTGAAATTTTAATTGTG
1 GTGTAATTATACA-GTGAAATTTTAATTGTG
13421749 GT
1 GT
13421751 TCAAATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 6 0.21
29 9 0.31
30 10 0.34
31 4 0.14
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (30 bp):
GTGTAATTATACAGTGAAATTTTAATTGTG
Found at i:13421866 original size:29 final size:30
Alignment explanation
Indices: 13421824--13421882 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
13421814 CAATTGGATC
*
13421824 AAATCAAATTTTTAAGTATAAAATTACACA
1 AAATCAAATATTTAAGTATAAAATTACACA
* * *
13421854 AAATCAAA-ATTTATGTGTACAATTACACA
1 AAATCAAATATTTAAGTATAAAATTACACA
13421883 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAATATTTAAGTATAAAATTACACA
Found at i:13425217 original size:20 final size:20
Alignment explanation
Indices: 13425192--13425229 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13425182 AATTTTAAAG
*
13425192 TTAAGTTAAAATGATTTTAA
1 TTAAGTCAAAATGATTTTAA
13425212 TTAAGTCAAAATGATTTT
1 TTAAGTCAAAATGATTTT
13425230 GTCATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (20 bp):
TTAAGTCAAAATGATTTTAA
Found at i:13426526 original size:24 final size:24
Alignment explanation
Indices: 13426496--13426550 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
13426486 TTGAATGTTA
13426496 AAAATTTATATTTTCA-ATAAAATG
1 AAAATTTATATTTT-ATATAAAATG
*
13426520 AAAATTTATATTTTATGTAAAATG
1 AAAATTTATATTTTATATAAAATG
13426544 AAAATTT
1 AAAATTT
13426551 TCAATGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (24 bp):
AAAATTTATATTTTATATAAAATG
Found at i:13431939 original size:19 final size:20
Alignment explanation
Indices: 13431861--13431937 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 20
13431851 AAAAATCATT
* *
13431861 TTTAAAAAAAATCATTTAAA
1 TTTAAAAAAAATTAATTAAA
* *
13431881 TTATTAAAAAAGTT-A--AAA
1 TT-TAAAAAAAATTAATTAAA
* *
13431899 TATAAAAATAAATT-TTTAAA
1 TTTAAAAA-AAATTAATTAAA
13431919 TTTAAAAAAAATTAATTAA
1 TTTAAAAAAAATTAATTAA
13431938 TTGCTGACAT
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
17 5 0.12
18 8 0.19
19 5 0.12
20 16 0.38
21 8 0.19
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (20 bp):
TTTAAAAAAAATTAATTAAA
Found at i:13433420 original size:28 final size:28
Alignment explanation
Indices: 13433387--13433447 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
13433377 AAATAACTTT
*
13433387 TAAAAA-TACT-TATTTTAGTAAATAATAC
1 TAAAAACTACTATATTTAAGTAAA-AA-AC
*
13433415 TAAAAACTGCTATATTTAAGTAAAAAAC
1 TAAAAACTACTATATTTAAGTAAAAAAC
13433443 TAAAA
1 TAAAA
13433448 TTTTATGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 13 0.45
29 5 0.17
30 11 0.38
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (28 bp):
TAAAAACTACTATATTTAAGTAAAAAAC
Found at i:13434088 original size:21 final size:21
Alignment explanation
Indices: 13434062--13434101 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13434052 CCACATGCTC
13434062 GTAATTAT-AAATTTTGAGAAA
1 GTAATT-TCAAATTTTGAGAAA
*
13434083 GTAATTTCCAATTTTGAGA
1 GTAATTTCAAATTTTGAGA
13434102 GGCACCAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (21 bp):
GTAATTTCAAATTTTGAGAAA
Found at i:13445334 original size:22 final size:23
Alignment explanation
Indices: 13445304--13445355 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
13445294 ATTTTAAAAG
13445304 TTTATAAAATAATTA-TTAAATTA
1 TTTA-AAAATAATTATTTAAATTA
* *
13445327 TTTAAAAATATTTATTTAAGTTA
1 TTTAAAAATAATTATTTAAATTA
13445350 -TTAAAA
1 TTTAAAA
13445356 TGTTATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTAAAAATAATTATTTAAATTA
Found at i:13446008 original size:13 final size:14
Alignment explanation
Indices: 13445984--13446012 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13445974 TTTCAAAGAA
13445984 AAATCGAATTGATT
1 AAATCGAATTGATT
13445998 AAATC-AATTGATT
1 AAATCGAATTGATT
13446011 AA
1 AA
13446013 TTGTTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.34
Consensus pattern (14 bp):
AAATCGAATTGATT
Found at i:13446143 original size:19 final size:20
Alignment explanation
Indices: 13446110--13446153 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
13446100 TTTTAACTAA
**
13446110 AAAAACAATTCAAAAATA-T
1 AAAAACAATAAAAAAATATT
*
13446129 AAAAACAATAAAAAATTATT
1 AAAAACAATAAAAAAATATT
13446149 AAAAA
1 AAAAA
13446154 TTTAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAACAATAAAAAAATATT
Found at i:13448460 original size:24 final size:24
Alignment explanation
Indices: 13448427--13448489 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
13448417 AGAAATAATC
*
13448427 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
13448451 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
13448475 TTTGAATCAAACTCT
1 TTTCAATTAAACTCT
13448490 TATTACTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:13450438 original size:24 final size:24
Alignment explanation
Indices: 13450410--13450472 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
13450400 AGAAATAATC
13450410 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
13450434 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
13450458 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
13450473 TATTACTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:13459202 original size:30 final size:31
Alignment explanation
Indices: 13459166--13459225 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
13459156 TTATTAATCT
* *
13459166 AAACAATGTAA-TTAAATTGCTAGCATTTTG
1 AAACAATGAAATTTAAAATGCTAGCATTTTG
*
13459196 AAACAATGAAATTTAAAATGTTAGCATTTT
1 AAACAATGAAATTTAAAATGCTAGCATTTT
13459226 AAAAATTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (31 bp):
AAACAATGAAATTTAAAATGCTAGCATTTTG
Found at i:13463057 original size:18 final size:19
Alignment explanation
Indices: 13463016--13463059 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
13463006 CCACCTCTGT
* *
13463016 CTCCACCACCGGTATTGAC
1 CTCCACCACCAGTATTCAC
13463035 C-CCACCACCAGT-TTCAC
1 CTCCACCACCAGTATTCAC
13463052 CTCCACCA
1 CTCCACCA
13463060 TCGACCCCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.23, C:0.50, G:0.09, T:0.18
Consensus pattern (19 bp):
CTCCACCACCAGTATTCAC
Found at i:13466753 original size:48 final size:48
Alignment explanation
Indices: 13466681--13466775 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
13466671 TGGAAGAGTC
* * *
13466681 GAGATTATGGGAATCCAAGTGGTGGCTGGAGTCGAGAACAAAGGGATA
1 GAGATTACGGGAATCCAAGCGGTGGCTGGAGCCGAGAACAAAGGGATA
*
13466729 GAGATTACGGGAATCCGAGCGGTGGCTGGAGCCGAGAACAAAGGGAT
1 GAGATTACGGGAATCCAAGCGGTGGCTGGAGCCGAGAACAAAGGGAT
13466776 CGGAACACCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.39, T:0.16
Consensus pattern (48 bp):
GAGATTACGGGAATCCAAGCGGTGGCTGGAGCCGAGAACAAAGGGATA
Found at i:13466884 original size:13 final size:13
Alignment explanation
Indices: 13466846--13466887 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
13466836 ACTCTAAATT
13466846 TTGGATTAGATTCA
1 TTGGATTAGA-TCA
13466860 TT-GATTATGATCA
1 TTGGATTA-GATCA
*
13466873 TTGGATCAGATCA
1 TTGGATTAGATCA
13466886 TT
1 TT
13466888 TTATGTGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (13 bp):
TTGGATTAGATCA
Found at i:13475734 original size:59 final size:57
Alignment explanation
Indices: 13475655--13475867 Score: 169
Period size: 59 Copynumber: 3.6 Consensus size: 57
13475645 AAAATGAAAC
* *
13475655 TTTAGACATCCGGGGGTAAAACAATAATTTTTAGAATAATCGGGATCAAAAACAAAATT
1 TTTAGACATTCGGGGGTAAAACGATAATTTTT-GAATAATCGGGATCAAAAA-AAAATT
* * * ** * ** *
13475714 TTTAGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGG-TCAAAAATGGAGTT
1 TTTAGACATTCGGGGGTAAAACGATAATTTTTG-AA-TAATCGGGATCAAAAA-AAAATT
* * * *
13475773 TTTGGACATTTTGGGGGTAAAACGGTAATTTTTGGAA-AAGTCGAGATCAAAAAAAGAATT
1 TTTAGACA-TTCGGGGGTAAAACGATAATTTTT-GAATAA-TCGGGATCAAAAAAA-AATT
* * *
13475833 TTTGGACATTCGAGGGTAAAATGATAATTTTTGAA
1 TTTAGACATTCGGGGGTAAAACGATAATTTTTGAA
13475868 AGTTTCGAGG
Statistics
Matches: 122, Mismatches: 25, Indels: 15
0.75 0.15 0.09
Matches are distributed among these distances:
58 4 0.03
59 69 0.57
60 48 0.39
61 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (57 bp):
TTTAGACATTCGGGGGTAAAACGATAATTTTTGAATAATCGGGATCAAAAAAAAATT
Found at i:13475805 original size:30 final size:30
Alignment explanation
Indices: 13475710--13476014 Score: 104
Period size: 29 Copynumber: 10.3 Consensus size: 30
13475700 TCAAAAACAA
*
13475710 AATTTTTAGACA-TTTGGGGGTAAAATGGT
1 AATTTTTGGACATTTTGGGGGTAAAATGGT
* *
13475739 AATTTTT-GAAAGTTTT-AGGGTCAAAAATGG-
1 AATTTTTGGACA-TTTTGGGGGT--AAAATGGT
* *
13475769 AGTTTTTGGACATTTTGGGGGTAAAACGGT
1 AATTTTTGGACATTTTGGGGGTAAAATGGT
*** * * * **
13475799 AATTTTTGGA-AAAGTCGAGATCAAAAAAAG-
1 AATTTTTGGACATTTTGGGGGT--AAAATGGT
* * *
13475829 AATTTTTGGACA-TTCGAGGGTAAAATGAT
1 AATTTTTGGACATTTTGGGGGTAAAATGGT
* * ** * *
13475858 AATTTTT-GAAAGTTTCGAGGTCTAGAAT-GA
1 AATTTTTGGACA-TTTTG-GGGGTAAAATGGT
* *
13475888 AATTTTTGGA-AGTTTAGGGGTAAAAAT-GT
1 AATTTTTGGACATTTTGGGGGT-AAAATGGT
* *
13475917 ATTTTTTGGA-AGTTTTGGGGTTAAAATGG-
1 AATTTTTGGACA-TTTTGGGGGTAAAATGGT
*
13475946 AATTTTTGGA-AGTTTTGGGGTTAAAAT-GT
1 AATTTTTGGACA-TTTTGGGGGTAAAATGGT
* * * *
13475975 AA-TTTTGGAGAAATTTAGGGGTCAAAAT-AT
1 AATTTTTGGA-CATTTTGGGGGT-AAAATGGT
13476005 AATTTTTGGA
1 AATTTTTGGA
13476015 TAGTTTAGGA
Statistics
Matches: 205, Mismatches: 48, Indels: 44
0.69 0.16 0.15
Matches are distributed among these distances:
28 21 0.10
29 86 0.42
30 63 0.31
31 35 0.17
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (30 bp):
AATTTTTGGACATTTTGGGGGTAAAATGGT
Found at i:13475876 original size:59 final size:59
Alignment explanation
Indices: 13475698--13475876 Score: 195
Period size: 60 Copynumber: 3.0 Consensus size: 59
13475688 GAATAATCGG
* *
13475698 GATCAAAAACAA-AATTTTTAGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTT-TA
1 GATCAAAAA-AAGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGA
* ** * *
13475756 GGGTCAAAAATGGAGTTTTTGGACATTTTGGGGGTAAAACGGTAATTTTTGGAAAAG--TCGA
1 -GATCAAAAAAAGAATTTTTGGACA-TTTGGGGGTAAAATGGTAATTTTT-G-AAAGTTTCGA
* * *
13475817 GATCAAAAAAAGAATTTTTGGACATTCGAGGGTAAAATGATAATTTTTGAAAGTTTCGA
1 GATCAAAAAAAGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGA
13475876 G
1 G
13475877 GTCTAGAATG
Statistics
Matches: 98, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
57 4 0.04
58 1 0.01
59 43 0.44
60 44 0.45
61 2 0.02
62 4 0.04
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (59 bp):
GATCAAAAAAAGAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGA
Found at i:13475892 original size:59 final size:58
Alignment explanation
Indices: 13475709--13476014 Score: 223
Period size: 59 Copynumber: 5.2 Consensus size: 58
13475699 ATCAAAAACA
* *
13475709 AAATTTTTAGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTT-TAGGGTCAAAAATG
1 AAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGA-GGTC-AAAATG
* * * * **
13475768 GAGTTTTTGGACATTTTGGGGGTAAAACGGTAATTTTTGGAAAAG--TCGAGATCAAAAAA
1 AAATTTTTGGACA-TTTGGGGGTAAAATGGTAATTTTT-G-AAAGTTTCGAGGTCAAAATG
* * * *
13475827 AGAATTTTTGGACATTCGAGGGTAAAATGATAATTTTTGAAAGTTTCGAGGTCTAGAATG
1 A-AATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTC-AAAATG
* * * * * *
13475887 AAATTTTTGGA-AGTTTAGGGGTAAAAAT-GTATTTTTTGGAAGTTTTGGGGTTAAAATG
1 AAATTTTTGGACA-TTTGGGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAATG
* * * * * *
13475945 GAATTTTTGGA-AGTTTTGGGGTTAAAAT-GTAATTTTGGAGAAATTTAGGGGTCAAAAT-
1 AAATTTTTGGACA--TTTGGGGGTAAAATGGTAATTTTTGA-AAGTTTCGAGGTCAAAATG
13476003 ATAATTTTTGGA
1 A-AATTTTTGGA
13476015 TAGTTTAGGA
Statistics
Matches: 195, Mismatches: 39, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
57 4 0.02
58 31 0.16
59 107 0.55
60 47 0.24
61 2 0.01
62 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.37
Consensus pattern (58 bp):
AAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAATG
Found at i:13475894 original size:119 final size:118
Alignment explanation
Indices: 13475666--13475927 Score: 307
Period size: 119 Copynumber: 2.2 Consensus size: 118
13475656 TTAGACATCC
* * * * *
13475666 GGGGGTAAAACAATAATTTTTAGAATAATCGGGATCAAAAACAAAATTTTTAGACATTTGGGGGT
1 GGGGGTAAAACAGTAATTTTTGGAATAATCGAGATCAAAAACAAAATTTTTAGACATTCGAGGGT
* * * * *
13475731 AAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAGTTTTTGGACATTTT
66 AAAATGATAATTTTTGAAAGTTTGAGGGTCAAAAATGAAATTTTTGGA-AGTTT
* *
13475785 GGGGGTAAAACGGTAATTTTTGGAA-AAGTCGAGATCAAAAA-AAGAATTTTTGGACATTCGAGG
1 GGGGGTAAAACAGTAATTTTTGGAATAA-TCGAGATCAAAAACAA-AATTTTTAGACATTCGAGG
* *
13475848 GTAAAATGATAATTTTTGAAAGTTTCGA-GGTCTAGAATGAAATTTTTGGAAGTTT
64 GTAAAATGATAATTTTTGAAAGTTT-GAGGGTCAAAAATGAAATTTTTGGAAGTTT
* *
13475903 AGGGGTAAAA-ATGTATTTTTTGGAA
1 GGGGGTAAAACA-GTAATTTTTGGAA
13475928 GTTTTGGGGT
Statistics
Matches: 122, Mismatches: 17, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
118 29 0.24
119 92 0.75
120 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (118 bp):
GGGGGTAAAACAGTAATTTTTGGAATAATCGAGATCAAAAACAAAATTTTTAGACATTCGAGGGT
AAAATGATAATTTTTGAAAGTTTGAGGGTCAAAAATGAAATTTTTGGAAGTTT
Found at i:13475925 original size:29 final size:29
Alignment explanation
Indices: 13475849--13476023 Score: 188
Period size: 29 Copynumber: 5.9 Consensus size: 29
13475839 CATTCGAGGG
* * *
13475849 TAAAATGATAATTTTTGAAAGTTTCGAGGT
1 TAAAATG-TAATTTTTGGAAGTTTAGGGGT
* *
13475879 CTAGAATGAAATTTTTGGAAGTTTAGGGGT
1 -TAAAATGTAATTTTTGGAAGTTTAGGGGT
* * *
13475909 AAAAATGTATTTTTTGGAAGTTTTGGGGT
1 TAAAATGTAATTTTTGGAAGTTTAGGGGT
* *
13475938 TAAAATGGAATTTTTGGAAGTTTTGGGGT
1 TAAAATGTAATTTTTGGAAGTTTAGGGGT
* *
13475967 TAAAATGTAATTTTGGAGAAATTTAGGGGT
1 TAAAATGTAATTTTTG-GAAGTTTAGGGGT
* *
13475997 CAAAATATAATTTTTGGATAGTTTAGG
1 TAAAATGTAATTTTTGGA-AGTTTAGG
13476024 AACCTCCAGA
Statistics
Matches: 121, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
29 66 0.55
30 49 0.40
31 6 0.05
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.40
Consensus pattern (29 bp):
TAAAATGTAATTTTTGGAAGTTTAGGGGT
Found at i:13477067 original size:3 final size:3
Alignment explanation
Indices: 13477059--13477097 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
13477049 CATTTTCCCT
*
13477059 TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT
13477098 TTTAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13477106 original size:19 final size:19
Alignment explanation
Indices: 13477067--13477106 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13477057 CTTTATTATT
* *
13477067 ATTATTATTATTATTATTA
1 ATTATTAATATTATTAATA
*
13477086 ATTATTAATATTTTTAATA
1 ATTATTAATATTATTAATA
13477105 AT
1 AT
13477107 ATTTATTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATTAATATTATTAATA
Found at i:13477202 original size:78 final size:78
Alignment explanation
Indices: 13477109--13477272 Score: 319
Period size: 78 Copynumber: 2.1 Consensus size: 78
13477099 TTAATAATAT
13477109 TTATTGATGCCATTTATTACCACCATTCATTAATAACATTATTATTTATTAAATAGTTGTTATTA
1 TTATTGATGCCATTTATTACCACCATTCATTAATAACATTATTATTTATTAAATAGTTGTTATTA
13477174 TTAATATTATTCA
66 TTAATATTATTCA
13477187 TTATTGATGCCATTTATTACCACCATTCATTAATAACATTATTATTTATTAAATAGTTGTTATTA
1 TTATTGATGCCATTTATTACCACCATTCATTAATAACATTATTATTTATTAAATAGTTGTTATTA
13477252 TTAATATTATTCA
66 TTAATATTATTCA
*
13477265 TTGTTGAT
1 TTATTGAT
13477273 TCATTTAATA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 85 1.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (78 bp):
TTATTGATGCCATTTATTACCACCATTCATTAATAACATTATTATTTATTAAATAGTTGTTATTA
TTAATATTATTCA
Found at i:13478022 original size:6 final size:6
Alignment explanation
Indices: 13478011--13478091 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
13478001 AATTTAAACC
* * *
13478011 AAATTT AAATTT AAAAATT AATTTT AAATTT AAATTT AAA-AT AAATTT
1 AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * *
13478059 AAA-AT CAATTT AAA-TC AAATAT AAATTT GAAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT -AAAT
13478092 CAAAAGTTAA
Statistics
Matches: 56, Mismatches: 14, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
5 11 0.20
6 36 0.64
7 9 0.16
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:13478055 original size:11 final size:11
Alignment explanation
Indices: 13478016--13478072 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
13478006 AAACCAAATT
13478016 TAAATTTAAAAA
1 TAAATTT-AAAA
* *
13478028 TTAATTTTAAATT
1 -TAAATTTAAA-A
13478041 TAAATTTAAAA
1 TAAATTTAAAA
13478052 TAAATTTAAAA
1 TAAATTTAAAA
*
13478063 TCAATTTAAA
1 TAAATTTAAA
13478073 TCAAATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 20 0.53
12 12 0.32
13 6 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:13478055 original size:17 final size:17
Alignment explanation
Indices: 13478000--13478091 Score: 62
Period size: 17 Copynumber: 5.2 Consensus size: 17
13477990 AAATCATTCC
**
13478000 AAATTTAAACCAAATTT
1 AAATTTAAAATAAATTT
*
13478017 AAATTTAAAAATTAATTTT
1 AAATTT-AAAA-TAAATTT
* *
13478036 AAATTTAAATTTAAA-AT
1 AAATTTAAA-ATAAATTT
*
13478053 AAATTTAAAATCAATTT
1 AAATTTAAAATAAATTT
*
13478070 AAA-TCAAATATAAATTT
1 AAATTTAAA-ATAAATTT
13478087 GAAAT
1 -AAAT
13478092 CAAAAGTTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
16 7 0.12
17 27 0.47
18 12 0.21
19 11 0.19
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (17 bp):
AAATTTAAAATAAATTT
Found at i:13478068 original size:28 final size:28
Alignment explanation
Indices: 13478037--13478094 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
13478027 ATTAATTTTA
*
13478037 AATTTAAATTTAAA-ATAAATTTAAAATC
1 AATTTAAA-TCAAATATAAATTTAAAATC
*
13478065 AATTTAAATCAAATATAAATTTGAAATC
1 AATTTAAATCAAATATAAATTTAAAATC
13478093 AA
1 AA
13478095 AAGTTAACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (28 bp):
AATTTAAATCAAATATAAATTTAAAATC
Found at i:13478075 original size:10 final size:11
Alignment explanation
Indices: 13478043--13478076 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
13478033 TTTAAATTTA
*
13478043 AATTTAAAATA
1 AATTTAAAATC
13478054 AATTTAAAATC
1 AATTTAAAATC
13478065 AATTT-AAATC
1 AATTTAAAATC
13478075 AA
1 AA
13478077 ATATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (11 bp):
AATTTAAAATC
Found at i:13480270 original size:2 final size:2
Alignment explanation
Indices: 13480263--13480310 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
13480253 AAATTAAAGT
13480263 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
13480305 TA TA TA
1 TA TA TA
13480311 ATTACATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13480813 original size:19 final size:18
Alignment explanation
Indices: 13480791--13480865 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
13480781 AAAAATTCAA
13480791 AAAAATATAAAAAATATTT
1 AAAAATATAAAAAATA-TT
*
13480810 AAAAA-ATTAAAAATCATT
1 AAAAATATAAAAAAT-ATT
* * * *
13480828 AAAATTATTAAAGAAGAAT
1 AAAAATA-TAAAAAATATT
13480847 AAAAATTATAAAAAATATT
1 AAAAA-TATAAAAAATATT
13480866 TTTTAATATT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
18 14 0.33
19 21 0.50
20 7 0.17
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAATATAAAAAATATT
Found at i:13481221 original size:17 final size:18
Alignment explanation
Indices: 13481188--13481222 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13481178 CAAAGCATTT
*
13481188 TTTTAATCTTTTTATACA
1 TTTTAATCTTATTATACA
13481206 TTTTAAT-TTATTATACA
1 TTTTAATCTTATTATACA
13481223 CATTTATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATCTTATTATACA
Found at i:13482757 original size:31 final size:30
Alignment explanation
Indices: 13482693--13482757 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
13482683 GTCGAGACTT
* * *
13482693 GATCTTGAAGTTGAGTTTAGAGAAAGTTTG
1 GATCTTGAAGCTGAGTTTAGAAAAAATTTG
*
13482723 GATCTTGAAGCTGAGTTTGGAAAAAAATTTG
1 GATCTTGAAGCTGAGTTTAG-AAAAAATTTG
13482754 GATC
1 GATC
13482758 CAAGGGCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (30 bp):
GATCTTGAAGCTGAGTTTAGAAAAAATTTG
Found at i:13483146 original size:18 final size:19
Alignment explanation
Indices: 13483123--13483160 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
13483113 AGAATTTAGG
*
13483123 ATCTTTTATTTA-TTATTT
1 ATCTTTTATTAATTTATTT
13483141 ATCTTTTATTAATTTATTT
1 ATCTTTTATTAATTTATTT
13483160 A
1 A
13483161 ATTAGAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
ATCTTTTATTAATTTATTT
Found at i:13486298 original size:25 final size:24
Alignment explanation
Indices: 13486270--13486320 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
13486260 TTTAAAAATA
13486270 ATAA-AGTAAATTATTTATTATTTTT
1 ATAATAGTAAA-TATTT-TTATTTTT
* *
13486295 ATAATATTATATATTTTTATTTTT
1 ATAATAGTAAATATTTTTATTTTT
13486319 AT
1 AT
13486321 TAATTCATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 9 0.39
26 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
ATAATAGTAAATATTTTTATTTTT
Found at i:13512463 original size:36 final size:36
Alignment explanation
Indices: 13512423--13512492 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
13512413 ATCATTTAAT
*
13512423 CCAAACTTAATCTCCTA-ACTTCTAACAAGTAATCTG
1 CCAAACTTAATCTCCTATA-TTCTAACAAGAAATCTG
*
13512459 CCAAACTTAATCTCCTATATTCTCACAAGAAATC
1 CCAAACTTAATCTCCTATATTCTAACAAGAAATC
13512493 GACTAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (36 bp):
CCAAACTTAATCTCCTATATTCTAACAAGAAATCTG
Found at i:13514544 original size:78 final size:78
Alignment explanation
Indices: 13514459--13514616 Score: 255
Period size: 78 Copynumber: 2.0 Consensus size: 78
13514449 TTTAACAATC
* * * *
13514459 TAATTTAATTTAAAGTTTTTCGAATTAATTGAAAT-AGAATAAAGAAATTTCAAGACAAATTAAA
1 TAATTTAATTTAAAATTTTTCAAATTAAATGAAATCA-AATAAAAAAATTTCAAGACAAATTAAA
*
13514523 AATATTATTATTTA
65 AATACTATTATTTA
13514537 TAATTTAATTTAAAATTTTTCAAATTAAATGAAATCAAATAAAAAAATTTCAAGACAAATTAAAA
1 TAATTTAATTTAAAATTTTTCAAATTAAATGAAATCAAATAAAAAAATTTCAAGACAAATTAAAA
13514602 ATACTATTATTTA
66 ATACTATTATTTA
13514615 TA
1 TA
13514617 TTCTACTTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
78 73 0.99
79 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (78 bp):
TAATTTAATTTAAAATTTTTCAAATTAAATGAAATCAAATAAAAAAATTTCAAGACAAATTAAAA
ATACTATTATTTA
Found at i:13517621 original size:27 final size:26
Alignment explanation
Indices: 13517565--13517621 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
13517555 ATACCTTAAT
*
13517565 TTAAGTTTTTCTCTCTAATTTAGTAT
1 TTAAGTTTTTCTCTCTAATTTAGTAA
* *
13517591 TTAAGTTGTTTTTTTCTAATTT-GATAA
1 TTAAGTT-TTTCTCTCTAATTTAG-TAA
13517618 TTAA
1 TTAA
13517622 TTTAGATGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.58
Consensus pattern (26 bp):
TTAAGTTTTTCTCTCTAATTTAGTAA
Found at i:13520034 original size:18 final size:18
Alignment explanation
Indices: 13520020--13520054 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13520010 GTAATTAATT
13520020 TAAAATT-TTTAATTAAA
1 TAAAATTATTTAATTAAA
*
13520037 TAAATTTATTTAATTAAA
1 TAAAATTATTTAATTAAA
13520055 AATTTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAAATTATTTAATTAAA
Found at i:13525054 original size:3 final size:3
Alignment explanation
Indices: 13525046--13525101 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
13525036 CAAAAGGCAA
13525046 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
13525094 AAG AAG AA
1 AAG AAG AA
13525102 ATAAGAATAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:13527775 original size:24 final size:24
Alignment explanation
Indices: 13527740--13527790 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
13527730 AAAAAATTCT
* * *
13527740 TATTTCAACAAAAGAATCATTTGA
1 TATTTCAACAAAAAAAACATTTAA
13527764 TATTT-AAGCAAAAAAAACATTTAA
1 TATTTCAA-CAAAAAAAACATTTAA
13527788 TAT
1 TAT
13527791 ATAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
TATTTCAACAAAAAAAACATTTAA
Found at i:13528017 original size:26 final size:28
Alignment explanation
Indices: 13527988--13528042 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
13527978 CGTCATTTCA
13527988 ATAAAT-TATTT-TTAGATCAATT-TTTT
1 ATAAATATATTTGTTAGAT-AATTCTTTT
*
13528014 ATAAATATATTTGTTATATAATTCTTTT
1 ATAAATATATTTGTTAGATAATTCTTTT
13528042 A
1 A
13528043 ACTTAATTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 6 0.24
27 9 0.36
28 10 0.40
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (28 bp):
ATAAATATATTTGTTAGATAATTCTTTT
Found at i:13537332 original size:19 final size:19
Alignment explanation
Indices: 13537310--13537348 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13537300 TTTATATTCT
* *
13537310 TTTAATTTTCCTTTTTTTC
1 TTTAATTTTCATTTTCTTC
*
13537329 TTTATTTTTCATTTTCTTC
1 TTTAATTTTCATTTTCTTC
13537348 T
1 T
13537349 GCTTCCCCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTAATTTTCATTTTCTTC
Found at i:13540713 original size:23 final size:23
Alignment explanation
Indices: 13540668--13540713 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13540658 AATTATATTA
* * *
13540668 ATTATATTTATGATTTATTATAT
1 ATTATATGTATGATTAATAATAT
*
13540691 ATTATATGTATGCTTAATAATAT
1 ATTATATGTATGATTAATAATAT
13540714 TGAAAGTTTT
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:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (23 bp):
ATTATATGTATGATTAATAATAT
Found at i:13543380 original size:9 final size:9
Alignment explanation
Indices: 13543341--13543380 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
13543331 AGGTCAAGAT
13543341 AAAA-TAAA
1 AAAATTAAA
13543349 AAAATTAGAA
1 AAAATTA-AA
*
13543359 AAAATTTAA
1 AAAATTAAA
13543368 AAAATTAAA
1 AAAATTAAA
13543377 AAAA
1 AAAA
13543381 AGTTGGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 4 0.14
9 16 0.57
10 8 0.29
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (9 bp):
AAAATTAAA
Found at i:13555579 original size:15 final size:15
Alignment explanation
Indices: 13555559--13555591 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
13555549 ATCTTACAAA
13555559 TGCGCTGCTGTGTGG
1 TGCGCTGCTGTGTGG
13555574 TGCGCTGCTGTGTGG
1 TGCGCTGCTGTGTGG
13555589 TGC
1 TGC
13555592 CTTCAAAACA
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:0.00, C:0.21, G:0.45, T:0.33
Consensus pattern (15 bp):
TGCGCTGCTGTGTGG
Found at i:13560271 original size:39 final size:39
Alignment explanation
Indices: 13560205--13560302 Score: 92
Period size: 39 Copynumber: 2.5 Consensus size: 39
13560195 TTTTGGAAAA
* *
13560205 TATAAAAATTATAAGAAAACTATAAATACTA-TTAAATAT
1 TATAAAAA-TCTAAGAAAATTATAAATACTATTTAAATAT
* * * *
13560244 TATAAAAATCTAGGAAAATTATAAAATATTATTTATATGT
1 TATAAAAATCTAAGAAAATTAT-AAATACTATTTAAATAT
* *
13560284 TACAAAAA-CTATGAAAATT
1 TATAAAAATCTAAGAAAATT
13560303 TTACATAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 11 0.22
39 25 0.51
40 13 0.27
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (39 bp):
TATAAAAATCTAAGAAAATTATAAATACTATTTAAATAT
Found at i:13560274 original size:29 final size:29
Alignment explanation
Indices: 13560199--13560275 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
13560189 ATATTTTTTT
13560199 GGAAAATATAAAA-ATTATAAGAAAACTA
1 GGAAAATATAAAATATTATAAGAAAACTA
* * *
13560227 -TAAATACTATTAAATATTATAA-AAATCTA
1 GGAAA-A-TATAAAATATTATAAGAAAACTA
13560256 GGAAAATTATAAAATATTAT
1 GGAAAA-TATAAAATATTAT
13560276 TTATATGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
27 3 0.08
28 1 0.03
29 25 0.64
30 10 0.26
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (29 bp):
GGAAAATATAAAATATTATAAGAAAACTA
Found at i:13560834 original size:17 final size:17
Alignment explanation
Indices: 13560814--13560847 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13560804 ATTTCAATTT
*
13560814 TTTTATATATTTTTTAA
1 TTTTATATAATTTTTAA
13560831 TTTTATATAATTTTTAA
1 TTTTATATAATTTTTAA
13560848 AATTTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATATAATTTTTAA
Found at i:13560851 original size:19 final size:17
Alignment explanation
Indices: 13560814--13560853 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
13560804 ATTTCAATTT
*
13560814 TTTTATATATTTTTTAA
1 TTTTATATATTTTTAAA
13560831 TTTTATATAATTTTTAAA
1 TTTTATAT-ATTTTTAAA
*
13560849 ATTTA
1 TTTTA
13560854 GTTAGGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATATATTTTTAAA
Found at i:13561373 original size:23 final size:21
Alignment explanation
Indices: 13561347--13561388 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
13561337 GCACCAACTC
13561347 ATTATAATTTGAATTTGAATGGA
1 ATTATAATTTG-ATTT-AATGGA
*
13561370 ATTATTATTTGATTTAATG
1 ATTATAATTTGATTTAATG
13561389 ATTGAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
ATTATAATTTGATTTAATGGA
Found at i:13563680 original size:18 final size:18
Alignment explanation
Indices: 13563657--13563702 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
13563647 ATAAAAATGC
13563657 ATATATTTATTCAAA-ATT
1 ATATATTT-TTCAAATATT
*
13563675 ATATATATTTCAAATATT
1 ATATATTTTTCAAATATT
*
13563693 TTATATTTTT
1 ATATATTTTT
13563703 TCAACTTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATTTTTCAAATATT
Found at i:13564782 original size:31 final size:32
Alignment explanation
Indices: 13564725--13564786 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
13564715 AGTAAAATGG
*
13564725 TAACAAAATAGTGAAAAATAAGAAGAAAATAA
1 TAACAAAATAATGAAAAATAAGAAGAAAATAA
*
13564757 TAACAAAATAAT-AAAAA-CAGCAAGAAAATA
1 TAACAAAATAATGAAAAATAAG-AAGAAAATA
13564787 GATTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 2 0.07
31 14 0.52
32 11 0.41
ACGTcount: A:0.69, C:0.06, G:0.10, T:0.15
Consensus pattern (32 bp):
TAACAAAATAATGAAAAATAAGAAGAAAATAA
Found at i:13573490 original size:22 final size:22
Alignment explanation
Indices: 13573465--13573526 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
13573455 ATCTCGGAGC
13573465 AAATATTAAATTTTTTATTTTA
1 AAATATTAAATTTTTTATTTTA
* *
13573487 AAATA-TAAAATATTTATTTTA
1 AAATATTAAATTTTTTATTTTA
* *
13573508 ATAATTTTATATATTTTTA
1 A-AATATTAAAT-TTTTTA
13573527 GTATTTACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 15 0.48
22 8 0.26
23 3 0.10
24 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATATTAAATTTTTTATTTTA
Found at i:13581281 original size:19 final size:19
Alignment explanation
Indices: 13581254--13581291 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13581244 AAAATTTAAT
*
13581254 AACAAATTTGATTATGGTG
1 AACAAATTTGATTACGGTG
*
13581273 AACATATTTGATTACGGTG
1 AACAAATTTGATTACGGTG
13581292 GGTGACAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (19 bp):
AACAAATTTGATTACGGTG
Found at i:13585841 original size:24 final size:23
Alignment explanation
Indices: 13585814--13585858 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
13585804 TAAAATAATT
13585814 AATAACTGTTATATAACATTTAAA
1 AATAACTGTTATATAA-ATTTAAA
* *
13585838 AATAATTTTTATATAAATTTA
1 AATAACTGTTATATAAATTTA
13585859 TTAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
AATAACTGTTATATAAATTTAAA
Found at i:13587000 original size:3 final size:3
Alignment explanation
Indices: 13586987--13587024 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
13586977 TCATTCATTT
13586987 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
13587025 GATCTCTGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:13590838 original size:2 final size:2
Alignment explanation
Indices: 13590822--13590859 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
13590812 TACGTTCCAT
*
13590822 TA TA TA T- TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13590860 CTGTGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:13591429 original size:6 final size:6
Alignment explanation
Indices: 13591420--13591445 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
13591410 AATGCAAGCG
13591420 AGAGAC AGAGAC AGAGAC AGAGAC AG
1 AGAGAC AGAGAC AGAGAC AGAGAC AG
13591446 GGTGATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:13601984 original size:69 final size:69
Alignment explanation
Indices: 13601902--13602041 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
13601892 TTGAAAGGCA
13601902 TTATGGCATTAAGATTTCCAAGGTTTAGCCAAGGATTAGCTCAAGACCCCACTACTTGTCGTATT
1 TTATGGCATTAAGATTTCCAAGGTTTAGCCAAGGATTAGCTCAAGACCCCACTACTTGTCGTATT
13601967 TGGT
66 TGGT
*
13601971 TTATGGCATTAAGATTTCCAAGGTTTAGCCAAGGATTAGCTCAAGACCTCACTACTTGTCGTATT
1 TTATGGCATTAAGATTTCCAAGGTTTAGCCAAGGATTAGCTCAAGACCCCACTACTTGTCGTATT
13602036 TGGT
66 TGGT
13602040 TT
1 TT
13602042 GGTATTGCTA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (69 bp):
TTATGGCATTAAGATTTCCAAGGTTTAGCCAAGGATTAGCTCAAGACCCCACTACTTGTCGTATT
TGGT
Found at i:13607626 original size:58 final size:58
Alignment explanation
Indices: 13607492--13607629 Score: 158
Period size: 58 Copynumber: 2.4 Consensus size: 58
13607482 ATGGATACCC
* *
13607492 GGGGG-CAAAATGGTAATTTTGGTGATATCGGGGTTAAAAAGGAATTTTAAAGGTTTT
1 GGGGGTCAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAAGGAATTTTAAAGATTTT
* * *
13607549 GGGGGT-AAAATGGTAAATTTTGGTGAAATCGTGGTTAAAAATGGGA-TTTAGGAGATTTT
1 GGGGGTCAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAA-GGAATTTTA-AAGATTTT
**
13607608 TTGGGTCAAAAT-GTAATTTTGG
1 GGGGGTCAAAATGGTAATTTTGG
13607630 AAAAGTTTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
57 13 0.19
58 36 0.52
59 15 0.22
60 5 0.07
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (58 bp):
GGGGGTCAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAAGGAATTTTAAAGATTTT
Found at i:13607646 original size:30 final size:30
Alignment explanation
Indices: 13607605--13607667 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
13607595 TTTAGGAGAT
*
13607605 TTTTTGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
13607635 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
13607665 TTT
1 TTT
13607668 GGGGACCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.41
Consensus pattern (30 bp):
TTTTAGGGTCAAAATGTAATTTTGGAAAAG
Found at i:13609377 original size:12 final size:14
Alignment explanation
Indices: 13609349--13609392 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
13609339 TTGGGCCTAT
13609349 TTGGGCCATTGTAA
1 TTGGGCCATTGTAA
13609363 TTGGGCC-TT-TAA
1 TTGGGCCATTGTAA
13609375 TTGGGCCATTGTAA
1 TTGGGCCATTGTAA
13609389 TTGG
1 TTGG
13609393 ACCGAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.36
13 4 0.14
14 14 0.50
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.39
Consensus pattern (14 bp):
TTGGGCCATTGTAA
Found at i:13609405 original size:26 final size:26
Alignment explanation
Indices: 13609350--13609405 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
13609340 TGGGCCTATT
* *** *
13609350 TGGGCCATTGTAATTGGGCCTTTAAT
1 TGGGCCATTGTAATTGGACCGAAAAA
13609376 TGGGCCATTGTAATTGGACCGAAAAA
1 TGGGCCATTGTAATTGGACCGAAAAA
13609402 TGGG
1 TGGG
13609406 TCAAAATGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.30
Consensus pattern (26 bp):
TGGGCCATTGTAATTGGACCGAAAAA
Found at i:13609485 original size:6 final size:6
Alignment explanation
Indices: 13609476--13609566 Score: 54
Period size: 6 Copynumber: 15.8 Consensus size: 6
13609466 ACTTTTTCTT
*
13609476 TTTAAA TTTATAA --TAATA TT-AAA TTTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA
* * *
13609523 TTTAAA -TTGAA TTTAAA -GTAAA TTTAAGA -TTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
13609567 TTTTCAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
4 1 0.02
5 23 0.35
6 36 0.55
7 6 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:13609520 original size:17 final size:16
Alignment explanation
Indices: 13609477--13609569 Score: 73
Period size: 17 Copynumber: 5.5 Consensus size: 16
13609467 CTTTTTCTTT
13609477 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
13609494 TTAAATTTTAAATTAAA
1 TTAAA-TTTAAATTAAA
13609511 TTCAAATTTAAATTTAAA
1 TT-AAATTTAAA-TTAAA
* *
13609529 TTGAATTTAAAGTAAA
1 TTAAATTTAAATTAAA
*
13609545 TTTAAGA-TTAAAATAAA
1 -TTAA-ATTTAAATTAAA
*
13609562 TTTAATTT
1 TTAAATTT
13609570 TCAAATGGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.02
16 9 0.14
17 36 0.56
18 18 0.28
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:13609535 original size:11 final size:11
Alignment explanation
Indices: 13609493--13609569 Score: 75
Period size: 11 Copynumber: 6.8 Consensus size: 11
13609483 TTATAATAAT
13609493 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
13609505 ATTAAATTCAA
1 ATTAAATTTAA
13609516 ATTTAAATTTAA
1 A-TTAAATTTAA
*
13609528 ATTGAATTTAA
1 ATTAAATTTAA
*
13609539 AGTAAATTTAA
1 ATTAAATTTAA
*
13609550 GATTAAA-ATAA
1 -ATTAAATTTAA
*
13609561 ATTTAATTT
1 ATTAAATTT
13609570 TCAAATGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.09
11 27 0.51
12 21 0.40
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:13610205 original size:68 final size:68
Alignment explanation
Indices: 13610054--13610655 Score: 999
Period size: 68 Copynumber: 8.9 Consensus size: 68
13610044 CTTATTTCAA
* * * *
13610054 CAATTTCAGAGATAAAGACGTGCTATCCACTCTACTTCAATTCCGA-GGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
13610118 CTT
66 CTT
* * *
13610121 CAATTTCAGAGATAAAGATGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
13610186 CTT
66 CTT
* * *
13610189 CAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
13610254 CTT
66 CTT
* * * *
13610257 CAATTTCAGAGATAAAGATGTGTTATCCACTCCACTTCAATTTCGAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
13610322 CTT
66 CTT
* *
13610325 CAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGCTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
13610390 CTT
66 CTT
* * *
13610393 CAATTTCAGATATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCCCTTG
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
13610458 CTT
66 CTT
13610461 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
13610526 CTT
66 CTT
* *
13610529 CAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGCTGCTCTTA
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
13610594 CTT
66 CTT
*
13610597 CAATTTCAGATATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
13610656 AGACCTGCAG
Statistics
Matches: 507, Mismatches: 27, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
67 43 0.08
68 464 0.92
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (68 bp):
CAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTA
CTT
Found at i:13622590 original size:29 final size:29
Alignment explanation
Indices: 13622558--13622655 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 29
13622548 TATGGATACC
13622558 CGGGGGTAAAATGGTAATTTTGGTGATAT
1 CGGGGGTAAAATGGTAATTTTGGTGATAT
* *** * *
13622587 CGGGGTTAAAATGG-AATTTTAAAGGTTT
1 CGGGGGTAAAATGGTAATTTTGGTGATAT
*
13622615 CGGGGGTAAAATGGTAAATTTTGGTGAAAT
1 CGGGGGTAAAATGGT-AATTTTGGTGATAT
* *
13622645 CGTGGTTAAAA
1 CGGGGGTAAAA
13622656 ATGGGATTTA
Statistics
Matches: 52, Mismatches: 15, Indels: 3
0.74 0.21 0.04
Matches are distributed among these distances:
28 22 0.42
29 13 0.25
30 17 0.33
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.33
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTGGTGATAT
Found at i:13622713 original size:30 final size:30
Alignment explanation
Indices: 13622672--13622734 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
13622662 TTTAGGAGAT
*
13622672 TTTTTGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
13622702 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
13622732 TTT
1 TTT
13622735 GGGGACCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.41
Consensus pattern (30 bp):
TTTTAGGGTCAAAATGTAATTTTGGAAAAG
Found at i:13624454 original size:12 final size:14
Alignment explanation
Indices: 13624430--13624468 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
13624420 GCCTATTTGG
13624430 GCCATTGTAATTGC
1 GCCATTGTAATTGC
*
13624444 GCC-TT-TAATTGG
1 GCCATTGTAATTGC
13624456 GCCATTGTAATTG
1 GCCATTGTAATTG
13624469 GACCGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 9 0.41
13 4 0.18
14 9 0.41
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (14 bp):
GCCATTGTAATTGC
Found at i:13624468 original size:14 final size:14
Alignment explanation
Indices: 13624426--13624469 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
13624416 TTGGGCCTAT
13624426 TTGGGCCATTGTAA
1 TTGGGCCATTGTAA
*
13624440 TTGCGCC-TT-TAA
1 TTGGGCCATTGTAA
13624452 TTGGGCCATTGTAA
1 TTGGGCCATTGTAA
13624466 TTGG
1 TTGG
13624470 ACCGAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.35
13 4 0.15
14 13 0.50
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (14 bp):
TTGGGCCATTGTAA
Found at i:13624482 original size:26 final size:26
Alignment explanation
Indices: 13624427--13624482 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
13624417 TGGGCCTATT
*** *
13624427 TGGGCCATTGTAATTGCGCCTTTAAT
1 TGGGCCATTGTAATTGCGCCGAAAAA
13624453 TGGGCCATTGTAATTG-GACCGAAAAA
1 TGGGCCATTGTAATTGCG-CCGAAAAA
13624479 TGGG
1 TGGG
13624483 TCAAAATGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (26 bp):
TGGGCCATTGTAATTGCGCCGAAAAA
Found at i:13624607 original size:23 final size:22
Alignment explanation
Indices: 13624572--13624633 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
13624562 ATAATAATAT
*
13624572 TAAATTTTAAATTAAATTCAAAT
1 TAAA-TTTAAATTAAATTCAAAG
* *
13624595 TCAAATTTAAATTGAATTTAAAG
1 T-AAATTTAAATTAAATTCAAAG
13624618 TAAATTTAAGATTAAA
1 TAAATTTAA-ATTAAA
13624634 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 8 0.24
23 22 0.67
24 3 0.09
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (22 bp):
TAAATTTAAATTAAATTCAAAG
Found at i:13624612 original size:11 final size:11
Alignment explanation
Indices: 13624570--13624646 Score: 75
Period size: 11 Copynumber: 6.8 Consensus size: 11
13624560 TTATAATAAT
13624570 ATTAAATTTTAA
1 ATTAAA-TTTAA
*
13624582 ATTAAATTCAA
1 ATTAAATTTAA
13624593 ATTCAAATTTAA
1 ATT-AAATTTAA
*
13624605 ATTGAATTTAA
1 ATTAAATTTAA
*
13624616 AGTAAATTTAA
1 ATTAAATTTAA
*
13624627 GATTAAA-ATAA
1 -ATTAAATTTAA
*
13624638 ATTTAATTT
1 ATTAAATTT
13624647 TCAAATGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.09
11 27 0.51
12 21 0.40
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:13627656 original size:22 final size:22
Alignment explanation
Indices: 13627631--13627673 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13627621 TTAACTTTAT
* *
13627631 TTTTATTCTTTTTTATTTTAAA
1 TTTTATTATTTATTATTTTAAA
*
13627653 TTTTCTTATTTATTATTTTAA
1 TTTTATTATTTATTATTTTAA
13627674 CAATGAGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTATTATTTATTATTTTAAA
Found at i:13632510 original size:28 final size:30
Alignment explanation
Indices: 13632444--13632502 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
13632434 TTAAATTAAT
*
13632444 AAAA-ATAAAATTTTATTTTAATTCCTTTA
1 AAAATATAAAATTTTATTTTAATTCATTTA
13632473 AAAATATAAAATTTTA-TTTAATT-ATTTA
1 AAAATATAAAATTTTATTTTAATTCATTTA
13632501 AA
1 AA
13632503 GTTATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.21
29 11 0.39
30 11 0.39
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
AAAATATAAAATTTTATTTTAATTCATTTA
Found at i:13633071 original size:15 final size:15
Alignment explanation
Indices: 13633034--13633075 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
13633024 ATTATAAAAA
13633034 TTATAATTTTATTAT
1 TTATAATTTTATTAT
13633049 TTGAATAATTTATATT-T
1 TT--ATAATTT-TATTAT
13633066 TTATAATTTT
1 TTATAATTTT
13633076 TAAAGAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
17 10 0.42
18 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTATAATTTTATTAT
Found at i:13633149 original size:8 final size:8
Alignment explanation
Indices: 13633138--13633168 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
13633128 TATTTACTAA
13633138 TTTAAAAT
1 TTTAAAAT
13633146 TTTAAAAT
1 TTTAAAAT
13633154 TTTAAAAAT
1 TTT-AAAAT
13633163 TTTAAA
1 TTTAAA
13633169 TAGAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:13634518 original size:26 final size:24
Alignment explanation
Indices: 13634472--13634519 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
13634462 ATTATTTTAT
*
13634472 TATATAAATAATTTTAAAATATGA
1 TATATAAATAATTTAAAAATATGA
13634496 TATATCAAATACATTTAAAAATAT
1 TATAT-AAATA-ATTTAAAAATAT
13634520 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TATATAAATAATTTAAAAATATGA
Found at i:13634529 original size:12 final size:12
Alignment explanation
Indices: 13634514--13634539 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13634504 ATACATTTAA
13634514 AAATATTAAAAC
1 AAATATTAAAAC
13634526 AAATATTAAAAC
1 AAATATTAAAAC
13634538 AA
1 AA
13634540 CAAACAAATT
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:13634546 original size:19 final size:18
Alignment explanation
Indices: 13634522--13634557 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13634512 AAAAATATTA
*
13634522 AAACAAATATTAAAACAAC
1 AAACAAAT-TAAAAACAAC
13634541 AAACAAATTAAAAACAA
1 AAACAAATTAAAAACAA
13634558 TATTAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (18 bp):
AAACAAATTAAAAACAAC
Found at i:13634568 original size:41 final size:43
Alignment explanation
Indices: 13634515--13634602 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 43
13634505 TACATTTAAA
*
13634515 AATATTAAAACAAATATTAAAACAACAAACAAATT-AAAA-AC
1 AATATTAAAACAAATAGTAAAACAACAAACAAATTGAAAATAC
* *
13634556 AATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAATAC
1 AATATTAAAACAAATAGTAAAACAACAAACAAATTGAAAATAC
13634599 AATA
1 AATA
13634603 AGAATCCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
41 32 0.76
42 4 0.10
43 6 0.14
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.20
Consensus pattern (43 bp):
AATATTAAAACAAATAGTAAAACAACAAACAAATTGAAAATAC
Found at i:13634958 original size:24 final size:22
Alignment explanation
Indices: 13634919--13634965 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
13634909 TATTACAAGC
13634919 AAAAAAAAATAGTATTAAAAAT
1 AAAAAAAAATAGTATTAAAAAT
* *
13634941 AAAAATAAAATCATTATTATAAAT
1 AAAAA-AAAAT-AGTATTAAAAAT
13634965 A
1 A
13634966 GGGGCTCGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 5 0.24
24 11 0.52
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAAAAAATAGTATTAAAAAT
Found at i:13635223 original size:5 final size:5
Alignment explanation
Indices: 13635213--13635237 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13635203 ACATTAATAT
13635213 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
13635238 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:13645775 original size:32 final size:32
Alignment explanation
Indices: 13645734--13645800 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
13645724 CATCCGTGTC
13645734 ATGAAATCTGCTGCATAATTGGCCTCGGAACT
1 ATGAAATCTGCTGCATAATTGGCCTCGGAACT
13645766 ATGAAATCTGCTGCATAATTGGCCTCGGAACT
1 ATGAAATCTGCTGCATAATTGGCCTCGGAACT
13645798 ATG
1 ATG
13645801 GGCACATTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (32 bp):
ATGAAATCTGCTGCATAATTGGCCTCGGAACT
Found at i:13649508 original size:44 final size:44
Alignment explanation
Indices: 13649446--13649532 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
13649436 AAAGGAACAT
*
13649446 ATTATTATTCCATGGGACCACTCCATGTGCATAGGTAACATATG
1 ATTATTATTCCATCGGACCACTCCATGTGCATAGGTAACATATG
* *
13649490 ATTATTATTTCATCGGACCACTCCATGTGCATAGGTAATATAT
1 ATTATTATTCCATCGGACCACTCCATGTGCATAGGTAACATAT
13649533 TCACGGGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (44 bp):
ATTATTATTCCATCGGACCACTCCATGTGCATAGGTAACATATG
Found at i:13651034 original size:13 final size:13
Alignment explanation
Indices: 13651016--13651040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13651006 AAGCTTAGGG
13651016 TTAATAATATAAT
1 TTAATAATATAAT
13651029 TTAATAATATAA
1 TTAATAATATAA
13651041 AAATATGAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATAATATAAT
Found at i:13651461 original size:16 final size:15
Alignment explanation
Indices: 13651415--13651462 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
13651405 TGTATGAGCG
13651415 AAAATAATTTATATAA
1 AAAATAATTTATA-AA
* *
13651431 TAAATATACTTATAAA
1 AAAATA-ATTTATAAA
13651447 AAAATAATTTAATAAA
1 AAAATAATTT-ATAAA
13651463 CAAAGGAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 17 0.65
17 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATAATTTATAAA
Found at i:13653201 original size:29 final size:28
Alignment explanation
Indices: 13653169--13653229 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
13653159 AAAATACGAT
*
13653169 TTTTAGATACTCGAGGGGTAAAATGGTAA
1 TTTTAGACACTCG-GGGGTAAAATGGTAA
* *
13653198 TTTTGGACACTCGGGGGTAAAATTGTAA
1 TTTTAGACACTCGGGGGTAAAATGGTAA
13653226 TTTT
1 TTTT
13653230 TGGATGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (28 bp):
TTTTAGACACTCGGGGGTAAAATGGTAA
Found at i:13653230 original size:29 final size:29
Alignment explanation
Indices: 13653167--13653319 Score: 118
Period size: 29 Copynumber: 5.2 Consensus size: 29
13653157 TAAAAATACG
* *
13653167 ATTTTTAGATACTCGAGGGGT-AAAATGGTA
1 ATTTTTGGACACTCGA-GGGTAAAAAT-GTA
* *
13653197 A-TTTTGGACACTCGGGGGTAAAATTGTA
1 ATTTTTGGACACTCGAGGGTAAAAATGTA
*** * *
13653225 ATTTTTGGATGTTTGAGGGTAAAAACGTA
1 ATTTTTGGACACTCGAGGGTAAAAATGTA
* *
13653254 ATTTTTGGAAAGTTC-AGGGTCAAAAATGTA
1 ATTTTTGGACA-CTCGAGGGT-AAAAATGTA
13653284 ATTTTTGGACA-TCCGAGGGT-AAAATGATA
1 ATTTTTGGACACT-CGAGGGTAAAAATG-TA
13653313 ATTTTTG
1 ATTTTTG
13653320 AAAGTTCAAG
Statistics
Matches: 100, Mismatches: 16, Indels: 15
0.76 0.12 0.11
Matches are distributed among these distances:
28 15 0.15
29 59 0.59
30 26 0.26
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.35
Consensus pattern (29 bp):
ATTTTTGGACACTCGAGGGTAAAAATGTA
Found at i:13653336 original size:29 final size:29
Alignment explanation
Indices: 13653212--13653474 Score: 198
Period size: 30 Copynumber: 9.0 Consensus size: 29
13653202 GGACACTCGG
* *
13653212 GGGT-AAAATTGTAATTTTTGG-ATGTTTGA
1 GGGTCAAAA-TGTAATTTTTGGAAAG-TTCA
* *
13653241 GGGTAAAAACGTAATTTTTGGAAAGTTCA
1 GGGTCAAAATGTAATTTTTGGAAAGTTCA
* *
13653270 GGGTCAAAAATGTAATTTTTGGACA-TCCGA
1 GGGTC-AAAATGTAATTTTTGGAAAGTTC-A
13653300 GGGT-AAAATGATAATTTTT-GAAAGTTCA
1 GGGTCAAAATG-TAATTTTTGGAAAGTTCA
* * **
13653328 AGGTCAAAATGGAATTTTT-GAAAGTTTGG
1 GGGTCAAAATGTAATTTTTGGAAAG-TTCA
* * * *
13653357 GGGT-AAAATGGTGATTTTTAGAAAATTCT
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTCA
* * *
13653386 TGGTTAAAATGGTAATTTTTGGAAAGTTTA
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTCA
* *
13653416 GGGTTAAAATGTAATTTTTGAAAAGTTCA
1 GGGTCAAAATGTAATTTTTGGAAAGTTCA
* * *
13653445 GGGGTCAAAATATGATTTTTGGATAGTTCA
1 -GGGTCAAAATGTAATTTTTGGAAAGTTCA
13653475 AGGACATTCT
Statistics
Matches: 189, Mismatches: 33, Indels: 23
0.77 0.13 0.09
Matches are distributed among these distances:
28 30 0.16
29 74 0.39
30 85 0.45
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTCA
Found at i:13653363 original size:116 final size:118
Alignment explanation
Indices: 13653224--13653455 Score: 267
Period size: 116 Copynumber: 2.0 Consensus size: 118
13653214 GTAAAATTGT
* * * *
13653224 AATTTTTGGATGTTTGAGGGTAAAAACGTAATTTTTGGAAAGTTCAGGGTCAAAAAT-GTAATTT
1 AATTTTTGAAAGTTTGAGGGTAAAAACGTAATTTTTAGAAAATTCAGGGT-AAAAATGGTAATTT
*
13653288 TTGGACA-TCCGAGGG-TAAAATGATAATTTTTG-AAAGTTCA-AGGTCAAAATGG
65 TTGGAAAGT-CGAGGGTTAAAATG-TAATTTTTGAAAAGTTCAGAGGTCAAAATGG
* ** * ** *
13653340 AATTTTTGAAAGTTTGGGGGTAAAATGGTGATTTTTAGAAAATTCTTGGTTAAAATGGTAATTTT
1 AATTTTTGAAAGTTTGAGGGTAAAAACGTAATTTTTAGAAAATTCAGGGTAAAAATGGTAATTTT
** *
13653405 TGGAAAGTTTAGGGTTAAAATGTAATTTTTGAAAAGTTCAGGGGTCAAAAT
66 TGGAAAGTCGAGGGTTAAAATGTAATTTTTGAAAAGTTCAGAGGTCAAAAT
13653456 ATGATTTTTG
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
115 5 0.05
116 66 0.69
117 16 0.17
118 9 0.09
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (118 bp):
AATTTTTGAAAGTTTGAGGGTAAAAACGTAATTTTTAGAAAATTCAGGGTAAAAATGGTAATTTT
TGGAAAGTCGAGGGTTAAAATGTAATTTTTGAAAAGTTCAGAGGTCAAAATGG
Found at i:13653463 original size:59 final size:59
Alignment explanation
Indices: 13653212--13653472 Score: 204
Period size: 59 Copynumber: 4.5 Consensus size: 59
13653202 GGACACTCGG
* * * *
13653212 GGGT-AAAAT-TGTAATTTTTGG-ATGTTTGAGGGTAAAAACGTAATTTTTGGAAAGTTCA
1 GGGTCAAAATATG-AATTTTTGGAAAGTTT-AGGGTTAAAATGTAATTTTTGAAAAGTTCA
* **
13653270 GGGTCAAAA-ATGTAATTTTTGGACA-TCCGAGGG-TAAAATGATAATTTTTG-AAAGTTCA
1 GGGTCAAAATATG-AATTTTTGGAAAGT-TTAGGGTTAAAATG-TAATTTTTGAAAAGTTCA
* * * * * *
13653328 AGGTCAAAAT-GGAATTTTT-GAAAGTTTGGGGGTAAAATGGTGATTTTTAGAAAA-TTCT
1 GGGTCAAAATATGAATTTTTGGAAAGTTTAGGGTTAAAAT-GTAATTTTT-GAAAAGTTCA
* * *
13653386 TGGTTAAAAT-GGTAATTTTTGGAAAGTTTAGGGTTAAAATGTAATTTTTGAAAAGTTCA
1 GGGTCAAAATATG-AATTTTTGGAAAGTTTAGGGTTAAAATGTAATTTTTGAAAAGTTCA
*
13653445 GGGGTCAAAATATG-ATTTTTGGATAGTT
1 -GGGTCAAAATATGAATTTTTGGAAAGTT
13653473 CAAGGACATT
Statistics
Matches: 163, Mismatches: 24, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
56 6 0.04
57 21 0.13
58 46 0.28
59 64 0.39
60 25 0.15
61 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (59 bp):
GGGTCAAAATATGAATTTTTGGAAAGTTTAGGGTTAAAATGTAATTTTTGAAAAGTTCA
Found at i:13653847 original size:17 final size:17
Alignment explanation
Indices: 13653806--13653847 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
13653796 TGGAAGGATA
*
13653806 TAAGTTAGAGTGGATTC
1 TAAGTTAGAGCGGATTC
13653823 TAAAGTTAGAGCGGATTC
1 T-AAGTTAGAGCGGATTC
13653841 TAAGTTA
1 TAAGTTA
13653848 AAATAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (17 bp):
TAAGTTAGAGCGGATTC
Found at i:13654988 original size:6 final size:6
Alignment explanation
Indices: 13654977--13655057 Score: 55
Period size: 6 Copynumber: 14.2 Consensus size: 6
13654967 GGCTTTCATC
* * * **
13654977 ATTTAA ATTTAA A-ATAA TTTTAA ATTTAT A-TTAA ATTTAA GCTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
**
13655023 A-ACAA ATTTAA ATTTAA CA--TAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA A
13655058 GTCAACTTAA
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
4 1 0.02
5 13 0.23
6 41 0.73
7 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:13655000 original size:17 final size:17
Alignment explanation
Indices: 13654977--13655085 Score: 103
Period size: 17 Copynumber: 6.4 Consensus size: 17
13654967 GGCTTTCATC
13654977 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* * *
13654994 TTTTAAATTTATATTAA
1 ATTTAAATTTAAAATAA
** *
13655011 ATTTAAGCTTAAAACAA
1 ATTTAAATTTAAAATAA
*
13655028 ATTTAAATTTAACATAA
1 ATTTAAATTTAAAATAA
* *
13655045 ATTTAAATTTAAAGTCA
1 ATTTAAATTTAAAATAA
* *
13655062 ACTT-AATCTTAACATAA
1 ATTTAAAT-TTAAAATAA
13655079 ATTTAAA
1 ATTTAAA
13655086 AAATGAGTTT
Statistics
Matches: 69, Mismatches: 21, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
16 3 0.04
17 64 0.93
18 2 0.03
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:13655073 original size:51 final size:51
Alignment explanation
Indices: 13654977--13655085 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
13654967 GGCTTTCATC
* * * *
13654977 ATTTAAATTTAAAATAATTTTAAATTTATATTAAATTTAAGCTTAAAACAA
1 ATTTAAATTTAAAATAAATTTAAATTTAAAGTAAACTTAAGCTTAAAACAA
* * * * *
13655028 ATTTAAATTTAACATAAATTTAAATTTAAAGTCAACTTAATCTTAACATAA
1 ATTTAAATTTAAAATAAATTTAAATTTAAAGTAAACTTAAGCTTAAAACAA
13655079 ATTTAAA
1 ATTTAAA
13655086 AAATGAGTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (51 bp):
ATTTAAATTTAAAATAAATTTAAATTTAAAGTAAACTTAAGCTTAAAACAA
Found at i:13659127 original size:2 final size:2
Alignment explanation
Indices: 13659120--13659174 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
13659110 AAATAATAAT
13659120 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
13659162 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
13659175 TATCTTAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13659276 original size:22 final size:23
Alignment explanation
Indices: 13659241--13659284 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
13659231 TTCACTGATT
13659241 AAAATAGAACAAATATGAATATA
1 AAAATAGAACAAATATGAATATA
* *
13659264 AAAATATAA-AAATTTGAATAT
1 AAAATAGAACAAATATGAATAT
13659285 CGACAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (23 bp):
AAAATAGAACAAATATGAATATA
Found at i:13660493 original size:24 final size:24
Alignment explanation
Indices: 13660464--13660518 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
13660454 CAGAGCCAGT
13660464 GTGGTGGCTCCACTCCAACCCCTA
1 GTGGTGGCTCCACTCCAACCCCTA
13660488 GTGGTGGCTCCACTCCAACCCCTA
1 GTGGTGGCTCCACTCCAACCCCTA
13660512 GTGGTGG
1 GTGGTGG
13660519 GAATGGTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.15, C:0.36, G:0.27, T:0.22
Consensus pattern (24 bp):
GTGGTGGCTCCACTCCAACCCCTA
Found at i:13664600 original size:10 final size:10
Alignment explanation
Indices: 13664579--13664607 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
13664569 GATATAATTT
13664579 AATTTT-TAA
1 AATTTTATAA
13664588 AATTTTATAA
1 AATTTTATAA
13664598 AATTTTATAA
1 AATTTTATAA
13664608 TATCATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTTTATAA
Found at i:13665532 original size:15 final size:15
Alignment explanation
Indices: 13665495--13665554 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
13665485 TTATGCTATA
*
13665495 TTGAAAAATTAAGTG
1 TTGAAAAAATAAGTG
**
13665510 CTAAAAAAAATAAGTG
1 -TTGAAAAAATAAGTG
* *
13665526 TTGAAAAAATAAATA
1 TTGAAAAAATAAGTG
*
13665541 TTGAAAAATTAAGT
1 TTGAAAAAATAAGT
13665555 ATTCAATTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
15 23 0.66
16 12 0.34
ACGTcount: A:0.57, C:0.02, G:0.13, T:0.28
Consensus pattern (15 bp):
TTGAAAAAATAAGTG
Found at i:13665532 original size:16 final size:16
Alignment explanation
Indices: 13665498--13665548 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
13665488 TGCTATATTG
* * *
13665498 AAAAATTAAGTGCTAA
1 AAAAAATAAGTGTTGA
13665514 AAAAAATAAGTGTTG-
1 AAAAAATAAGTGTTGA
* *
13665529 AAAAAATAAATATTGA
1 AAAAAATAAGTGTTGA
13665545 AAAA
1 AAAA
13665549 TTAAGTATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.24
Consensus pattern (16 bp):
AAAAAATAAGTGTTGA
Found at i:13665557 original size:15 final size:15
Alignment explanation
Indices: 13665514--13665557 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
13665504 TAAGTGCTAA
*
13665514 AAAAAATAAGTGTTG
1 AAAAAATAAGTATTG
*
13665529 AAAAAATAAATATTG
1 AAAAAATAAGTATTG
*
13665544 AAAAATTAAGTATT
1 AAAAAATAAGTATT
13665558 CAATTTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (15 bp):
AAAAAATAAGTATTG
Found at i:13666003 original size:15 final size:15
Alignment explanation
Indices: 13665983--13666013 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13665973 TGAGTGATGA
13665983 TATAAGCTTATATGT
1 TATAAGCTTATATGT
13665998 TATAAGCTTATATGT
1 TATAAGCTTATATGT
13666013 T
1 T
13666014 TTGGCATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (15 bp):
TATAAGCTTATATGT
Found at i:13670897 original size:3 final size:3
Alignment explanation
Indices: 13670889--13670919 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
13670879 CATAAACTAA
13670889 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
13670920 GAAATATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:13672198 original size:3 final size:3
Alignment explanation
Indices: 13672152--13672181 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
13672142 TTTATAAAAC
13672152 TTA TATA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
13672182 TAATAATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13678537 original size:47 final size:47
Alignment explanation
Indices: 13678475--13678572 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
13678465 TTAGATGATT
* *
13678475 TCTGGATCAGGTTGTGTGTGATGAGTTGACGACTGAGTACAGATGCC
1 TCTGGATCAGGTTGTGTGTGATGAGTTGACGACGGAGTACAAATGCC
13678522 TCTGGATCAGGTTGTGTGTGATGAGTTGACGACGGAGTACAAATGCC
1 TCTGGATCAGGTTGTGTGTGATGAGTTGACGACGGAGTACAAATGCC
13678569 TCTG
1 TCTG
13678573 CTACCGCATC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (47 bp):
TCTGGATCAGGTTGTGTGTGATGAGTTGACGACGGAGTACAAATGCC
Found at i:13678666 original size:23 final size:23
Alignment explanation
Indices: 13678636--13678700 Score: 130
Period size: 23 Copynumber: 2.8 Consensus size: 23
13678626 CACCACCATC
13678636 ATTCATTTTGATATAAAGAGCAT
1 ATTCATTTTGATATAAAGAGCAT
13678659 ATTCATTTTGATATAAAGAGCAT
1 ATTCATTTTGATATAAAGAGCAT
13678682 ATTCATTTTGATATAAAGA
1 ATTCATTTTGATATAAAGA
13678701 TCCATTACCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (23 bp):
ATTCATTTTGATATAAAGAGCAT
Found at i:13681040 original size:36 final size:36
Alignment explanation
Indices: 13680995--13681063 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
13680985 AAGTTGGGCA
* *
13680995 ATATTTTCTTTCATTTCATTTGC-CTAGGTTGGAATT
1 ATATCTTCTTTCATATCATTTGCGC-AGGTTGGAATT
13681031 ATATCTTCTTTCATATCATTTGCGCAGGTTGGA
1 ATATCTTCTTTCATATCATTTGCGCAGGTTGGA
13681064 GCTTTTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (36 bp):
ATATCTTCTTTCATATCATTTGCGCAGGTTGGAATT
Found at i:13681553 original size:65 final size:65
Alignment explanation
Indices: 13681483--13681852 Score: 474
Period size: 67 Copynumber: 5.6 Consensus size: 65
13681473 AGTCGTCGAT
** * *
13681483 GCAGCAGCCTCAAAATCCTCTGCTTCTTCATTTTTTTCTCCCCTTTAGTCGGTGAAGAGGTGACA
1 GCAGCAGCCTCAAGGTCCTCTGGTTCTTCATTTTTTTCTCCCCTTTAGTCGGTGAAGAAGTGACA
* * * * *
13681548 GCAGCAGCCTTAAGGTCCTCTGGTTCTTCGTTTTTTTCTCCCCTTTAGTCAGTGAAGAAATGATA
1 GCAGCAGCCTCAAGGTCCTCTGGTTCTTCATTTTTTTCTCCCCTTTAGTCGGTGAAGAAGTGACA
*
13681613 GCAACAGCCTCAAGGTCCTCTGGTTCTTCA-TTTTTTCTCCCCTTTAGTCGGTGAAGAAGTGACA
1 GCAGCAGCCTCAAGGTCCTCTGGTTCTTCATTTTTTTCTCCCCTTTAGTCGGTGAAGAAGTGACA
* * * * *
13681677 GCAGCAACCTCAAGGTCCTCTGGTTCTTCGTTTTTTTTTCTCTCTTTTAATCGGTGAAGAAGTGA
1 GCAGCAGCCTCAAGGTCCTCTGGTTCTTC--ATTTTTTTCTCCCCTTTAGTCGGTGAAGAAGTGA
13681742 CA
64 CA
* * * *
13681744 GCAGTAGCCTCAAGGTCTTTTGGTTCTTCATTTTTTTTTCTCCCCTTT-GATCGGTGAAGAAGAG
1 GCAGCAGCCTCAAGGTCCTCTGGTTCTTCA--TTTTTTTCTCCCCTTTAG-TCGGTGAAGAAGTG
13681808 ACA
63 ACA
* * *
13681811 GCAGCAACCTCAAGGTCTTCTGGTTCTTCCATTTTTTCCTCC
1 GCAGCAGCCTCAAGGTCCTCTGGTTCTT-CATTTTTTTCTCC
13681853 ATTACAAAAT
Statistics
Matches: 264, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
64 58 0.22
65 83 0.31
66 10 0.04
67 111 0.42
68 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (65 bp):
GCAGCAGCCTCAAGGTCCTCTGGTTCTTCATTTTTTTCTCCCCTTTAGTCGGTGAAGAAGTGACA
Found at i:13684352 original size:29 final size:29
Alignment explanation
Indices: 13684306--13684364 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
13684296 TCATTTGGAA
* *
13684306 ACTGCCACATGTGCAACTGCTGATGTGAC
1 ACTGCCACATATGCAACTGCTGACGTGAC
* *
13684335 ACTGCCACGTATGTAACTGCTGACGTGAC
1 ACTGCCACATATGCAACTGCTGACGTGAC
13684364 A
1 A
13684365 TATAAGACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (29 bp):
ACTGCCACATATGCAACTGCTGACGTGAC
Found at i:13684850 original size:18 final size:20
Alignment explanation
Indices: 13684810--13684874 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
13684800 TTTTAATTTT
*
13684810 TTTTAAAGTAATTTATAATAA
1 TTTTAAA-TAATTTTTAATAA
*
13684831 TTTTAAA-ACTTTTT-ATAA
1 TTTTAAATAATTTTTAATAA
*
13684849 TTCTAAATAATTTTTAAATAA
1 TTTTAAATAATTTTT-AATAA
13684870 TTTTA
1 TTTTA
13684875 TCTTTTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 10 0.28
19 11 0.31
21 15 0.42
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTTAAATAATTTTTAATAA
Found at i:13684868 original size:11 final size:11
Alignment explanation
Indices: 13684809--13684873 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
13684799 TTTTTAATTT
13684809 TTTTTAAAGTAA
1 TTTTTAAA-TAA
*
13684821 TTTAT-AATAA
1 TTTTTAAATAA
*
13684831 -TTTTAAA-AC
1 TTTTTAAATAA
13684840 TTTTT--ATAA
1 TTTTTAAATAA
*
13684849 -TTCTAAATAA
1 TTTTTAAATAA
13684859 TTTTTAAATAA
1 TTTTTAAATAA
13684870 TTTT
1 TTTT
13684874 ATCTTTTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
8 4 0.10
9 5 0.12
10 13 0.32
11 15 0.37
12 4 0.10
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTTTAAATAA
Done.