Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 169 of 310
Found at i:55386918 original size:91 final size:93
Alignment explanation
Indices: 55386804--55386978 Score: 239
Period size: 91 Copynumber: 1.9 Consensus size: 93
55386794 TTACACATCT
* * *
55386804 TCACATAATGATGTCATAGCCCAGCTATGGTCTTACACATATTCACATA-T-C-GATGCCATAGC
1 TCACATAATGATGCCATAGCCCAGCTATAGTCTTACACAGA-TCACATACTACTGATGCCATAGC
*
55386866 CCAGCTATGGTCTTACACGTAATCACATA
65 CCAGATATGGTCTTACACGTAATCACATA
* * *
55386895 TCACATATTGATGCCATAGCCCAGCTATAGTCTTACACGGATCACATATCTCACTGATGCCATAT
1 TCACATAATGATGCCATAGCCCAGCTATAGTCTTACACAGATCACATA-CT-ACTGATGCCATAG
55386960 CCCAGATATGGTCTTACAC
64 CCCAGATATGGTCTTACAC
55386979 AGAAGCATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
90 7 0.10
91 36 0.50
92 1 0.01
94 1 0.01
95 27 0.38
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (93 bp):
TCACATAATGATGCCATAGCCCAGCTATAGTCTTACACAGATCACATACTACTGATGCCATAGCC
CAGATATGGTCTTACACGTAATCACATA
Found at i:55397662 original size:3 final size:3
Alignment explanation
Indices: 55397654--55397692 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
55397644 ATAACAAGAC
55397654 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55397693 GCAATGTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55403182 original size:46 final size:46
Alignment explanation
Indices: 55403039--55403182 Score: 143
Period size: 46 Copynumber: 3.1 Consensus size: 46
55403029 CCCGCCCATA
* *
55403039 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CT
* * * * *
55403088 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCCT
*
55403132 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
55403178 AGTGA
1 AGTGA
55403183 CATGTCACTT
Statistics
Matches: 76, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
44 8 0.11
46 33 0.43
47 31 0.41
49 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
Found at i:55406674 original size:37 final size:37
Alignment explanation
Indices: 55406624--55406698 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
55406614 ATAAGTAAGT
* * *
55406624 ACACAATAGTAACATTTTATCAATGATCTGCATGCTC
1 ACACAACAATAACATTTTATCAATGATCTACATGCTC
*
55406661 ACACAACAATAACATTTTATCAATGATCTATATGCTC
1 ACACAACAATAACATTTTATCAATGATCTACATGCTC
55406698 A
1 A
55406699 TGATACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (37 bp):
ACACAACAATAACATTTTATCAATGATCTACATGCTC
Found at i:55406986 original size:47 final size:46
Alignment explanation
Indices: 55406912--55407177 Score: 166
Period size: 47 Copynumber: 5.7 Consensus size: 46
55406902 TGGGTAAAGT
55406912 GTCGATGCCATGTCCCAGACATAGTCTTACACTGGCTCA-CATCT-TAA
1 GTCGATGCCATGTCCCAGACAT-GTCTTACACTGGCT-ATCATCTCT-A
*
55406959 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTA
1 GTCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTATCATCTC-TA
* * * * *
55407007 GCCGATG-CATGTTCCAGACATGTCCTACACTGGCT-TACGTCTCGA
1 GTCGATGCCATGTCCCAGACATGTCTTACACTGGCTAT-CATCTCTA
* * * * * * ***
55407052 GGCCGATG-CATGTCCCAAACATATCTTACACTAGCTCTCGTCAAAA
1 -GTCGATGCCATGTCCCAGACATGTCTTACACTGGCTATCATCTCTA
* * * * * * * * *
55407098 TGCCGATGCCATGACCCAGGCATAATCTTTCACTGGCTCTCATAATGTG
1 -GTCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTATCAT-CTCTA
**
55407147 GTCGATG-CATGTTTCAGACATGTCTTACACT
1 GTCGATGCCATGTCCCAGACATGTCTTACACT
55407178 AGCCAAATAA
Statistics
Matches: 175, Mismatches: 35, Indels: 19
0.76 0.15 0.08
Matches are distributed among these distances:
45 2 0.01
46 68 0.39
47 75 0.43
48 29 0.17
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
GTCGATGCCATGTCCCAGACATGTCTTACACTGGCTATCATCTCTA
Found at i:55407057 original size:46 final size:47
Alignment explanation
Indices: 55406914--55407083 Score: 188
Period size: 47 Copynumber: 3.7 Consensus size: 47
55406904 GGTAAAGTGT
* ** *
55406914 CGATGCCATGTCCCAGACATAGTCTTACACTGGCTCACATCTTAAGT
1 CGATGCCATGTCCCAGACATAGTCTTACACTGGCTTACATCTCGAGC
* *
55406961 CGATGCCATGTCCCAGACATGGTCTTACACTGAC-TATCATCTCGTAGC
1 CGATGCCATGTCCCAGACATAGTCTTACACTGGCTTA-CATCTCG-AGC
* * *
55407009 CGATG-CATGTTCCAGACAT-GTCCTACACTGGCTTACGTCTCGAGGC
1 CGATGCCATGTCCCAGACATAGTCTTACACTGGCTTACATCTCGA-GC
*
55407055 CGATG-CATGTCCCAAACATA-TCTTACACT
1 CGATGCCATGTCCCAGACATAGTCTTACACT
55407084 AGCTCTCGTC
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
45 1 0.01
46 45 0.43
47 52 0.50
48 7 0.07
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATAGTCTTACACTGGCTTACATCTCGAGC
Found at i:55409544 original size:31 final size:31
Alignment explanation
Indices: 55409506--55409574 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
55409496 CCTTAACCAT
*
55409506 ATTAAATTACCACAATAGTTAATACATCCCA
1 ATTAAATTACCACAATAGTTAATACATCACA
* * *
55409537 ATTAAATTACCATATTAGTTAATATATCACA
1 ATTAAATTACCACAATAGTTAATACATCACA
55409568 ATTAAAT
1 ATTAAAT
55409575 AAAAAAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (31 bp):
ATTAAATTACCACAATAGTTAATACATCACA
Found at i:55419858 original size:10 final size:10
Alignment explanation
Indices: 55419843--55419881 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
55419833 ATAACTTTAT
55419843 TTAAATATAA
1 TTAAATATAA
55419853 TTAAATAATAA
1 TTAAAT-ATAA
*
55419864 TTAATTATAA
1 TTAAATATAA
*
55419874 ATAAATAT
1 TTAAATAT
55419882 TAAACCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAAATATAA
Found at i:55427482 original size:20 final size:20
Alignment explanation
Indices: 55427457--55427501 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
55427447 TCCTATATTG
*
55427457 ATACAAGTTCACTTT-TATCC
1 ATACAAGTCCA-TTTCTATCC
55427477 ATACAAGTCCATTTCTATCC
1 ATACAAGTCCATTTCTATCC
55427497 ATACA
1 ATACA
55427502 TCTTGTGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (20 bp):
ATACAAGTCCATTTCTATCC
Found at i:55428907 original size:25 final size:25
Alignment explanation
Indices: 55428864--55428931 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
55428854 AAAATTAGGA
*
55428864 TTAGAACTTAGAACTTAAGTTTAAAAC
1 TTAGAA-TTAG-ATTTAAGTTTAAAAC
* *
55428891 TTCGAATTAGATTTAAGTTTAGAAC
1 TTAGAATTAGATTTAAGTTTAAAAC
*
55428916 TTAGGATTAGATTTAA
1 TTAGAATTAGATTTAA
55428932 TAAGGATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 27 0.75
26 4 0.11
27 5 0.14
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (25 bp):
TTAGAATTAGATTTAAGTTTAAAAC
Found at i:55436571 original size:18 final size:18
Alignment explanation
Indices: 55436550--55436648 Score: 94
Period size: 18 Copynumber: 5.5 Consensus size: 18
55436540 ATTAACTGCC
55436550 ACTGAATAATCGACTGTT
1 ACTGAATAATCGACTGTT
55436568 ACTGAATCAAT-GACTGTT
1 ACTGAAT-AATCGACTGTT
* **
55436586 ACTGAATAA-CTAACTACT
1 ACTGAATAATC-GACTGTT
* *
55436604 ACTGAATAATTGACTGAT
1 ACTGAATAATCGACTGTT
* * *
55436622 AATGAATAAACGACCGTT
1 ACTGAATAATCGACTGTT
55436640 ACTGAATAA
1 ACTGAATAA
55436649 CTGATTATTA
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
17 2 0.03
18 59 0.92
19 3 0.05
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (18 bp):
ACTGAATAATCGACTGTT
Found at i:55436592 original size:36 final size:35
Alignment explanation
Indices: 55436532--55436648 Score: 103
Period size: 36 Copynumber: 3.3 Consensus size: 35
55436522 TAAATAAAGA
* **
55436532 TACTGAA-AATTAACTGCCACTGAATAATCGACTGT
1 TACTGAATAATTGACTGATACTGAATAA-CGACTGT
* * **
55436567 TACTGAATCAA-TGACTGTTACTGAATAACTAACTAC
1 TACTGAAT-AATTGACTGATACTGAATAAC-GACTGT
* *
55436603 TACTGAATAATTGACTGATAATGAATAAACGACCGT
1 TACTGAATAATTGACTGATACTGAAT-AACGACTGT
55436639 TACTGAATAA
1 TACTGAATAA
55436649 CTGATTATTA
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
35 10 0.15
36 50 0.77
37 5 0.08
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (35 bp):
TACTGAATAATTGACTGATACTGAATAACGACTGT
Found at i:55436600 original size:54 final size:54
Alignment explanation
Indices: 55436532--55436650 Score: 150
Period size: 54 Copynumber: 2.2 Consensus size: 54
55436522 TAAATAAAGA
* * * * * * *
55436532 TACTGAA-AATTAACTGCCACTGAATAATCGACTGTTACTGAATCAATGACTGT
1 TACTGAATAACTAACTACCACTGAATAATCGACTGATAATGAATAAACGACCGT
* *
55436585 TACTGAATAACTAACTACTACTGAATAATTGACTGATAATGAATAAACGACCGT
1 TACTGAATAACTAACTACCACTGAATAATCGACTGATAATGAATAAACGACCGT
55436639 TACTGAATAACT
1 TACTGAATAACT
55436651 GATTATTACT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
53 7 0.12
54 49 0.88
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (54 bp):
TACTGAATAACTAACTACCACTGAATAATCGACTGATAATGAATAAACGACCGT
Found at i:55438862 original size:29 final size:29
Alignment explanation
Indices: 55438795--55438864 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
55438785 TCTTTTTTGG
* **
55438795 TCACCCAACTATTAAAAGTTAAAAAATGG
1 TCACCCAACTATGAAAAGTTAAAAAATAA
* * *
55438824 TTACCTAACTATGAGAAA-TTACAAAATAA
1 TCACCCAACTATGA-AAAGTTAAAAAATAA
55438853 TCACCCAACTAT
1 TCACCCAACTAT
55438865 TTAATATTCT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (29 bp):
TCACCCAACTATGAAAAGTTAAAAAATAA
Found at i:55441948 original size:56 final size:56
Alignment explanation
Indices: 55441866--55441978 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
55441856 CACAGTTTAT
*
55441866 ACATGAAATCAAGGAATCACAGTTATATTTGGATTCAGAAGCTCAAAGAATAATAC
1 ACATGAAATCAAGGAATCACAGTTATATTTGAATTCAGAAGCTCAAAGAATAATAC
* *
55441922 ACATGTAATCAAGGAATCACAGTTATATTTGAATTCAGGAGCTCAAAGAATAATAC
1 ACATGAAATCAAGGAATCACAGTTATATTTGAATTCAGAAGCTCAAAGAATAATAC
55441978 A
1 A
55441979 TACCAAACGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (56 bp):
ACATGAAATCAAGGAATCACAGTTATATTTGAATTCAGAAGCTCAAAGAATAATAC
Found at i:55460688 original size:20 final size:20
Alignment explanation
Indices: 55460663--55460700 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55460653 CTTGTATTTA
55460663 ATTTTAA-TGTTTATTTTAGT
1 ATTTTAAGT-TTTATTTTAGT
55460683 ATTTTAAGTTTTATTTTA
1 ATTTTAAGTTTTATTTTA
55460701 TCCCAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (20 bp):
ATTTTAAGTTTTATTTTAGT
Found at i:55464021 original size:20 final size:20
Alignment explanation
Indices: 55463983--55464050 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
55463973 AAAAAATTAT
* *
55463983 ATTTT-AAAAATATTTAATA
1 ATTTTAAAAAAAATTAAATA
55464002 ATTTTAAAAAAAATTAAATA
1 ATTTTAAAAAAAATTAAATA
* * *
55464022 ATATATAAAGAAAGTTAAA-A
1 AT-TTTAAAAAAAATTAAATA
55464042 A-TTTAAAAA
1 ATTTTAAAAA
55464051 TATTCTAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
18 6 0.15
19 5 0.12
20 16 0.40
21 13 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
ATTTTAAAAAAAATTAAATA
Found at i:55464887 original size:4 final size:4
Alignment explanation
Indices: 55464878--55464916 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
55464868 TTGAAATATG
55464878 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
55464917 TAGTTGTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:55468448 original size:20 final size:20
Alignment explanation
Indices: 55468425--55468467 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
55468415 CTACAAATCG
55468425 ATAGCGTTAATGACAATTTC
1 ATAGCGTTAATGACAATTTC
*
55468445 ATAGTGTTAATGACAATTTC
1 ATAGCGTTAATGACAATTTC
55468465 ATA
1 ATA
55468468 ACAAACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (20 bp):
ATAGCGTTAATGACAATTTC
Found at i:55469839 original size:43 final size:43
Alignment explanation
Indices: 55469691--55469837 Score: 140
Period size: 43 Copynumber: 3.4 Consensus size: 43
55469681 CACTTTTCCC
** * *
55469691 ACAAACGCCGCTATAGAACATGATTTTTAGCGGAGCTTT--TT
1 ACAAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTCCAT
* * *
55469732 GAAAAACGCCGCTATAGAACATGACCTTTGGTGGCGCTTATCTCAT
1 -ACAAACGCCGCTATAGAACATGACCTTTAGCGGCGCTT-TC-CAT
* * *
55469778 --AATCGCCGTTATAGAACGTGACCTTTAGCGGCGCTTTCCAT
1 ACAAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTCCAT
*
55469819 ACAAACGCTGCTATAGAAC
1 ACAAACGCCGCTATAGAAC
55469838 GTAAACTTTA
Statistics
Matches: 84, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.04
42 34 0.40
43 46 0.55
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (43 bp):
ACAAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTCCAT
Found at i:55469996 original size:25 final size:25
Alignment explanation
Indices: 55469968--55470016 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
55469958 CTTCTTGTAA
*
55469968 CAACCAAAAACAATAAATACAAATC
1 CAACCAAAAACAACAAATACAAATC
*
55469993 CAACCAAAAATAACAAATACAAAT
1 CAACCAAAAACAACAAATACAAAT
55470017 TATACTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.65, C:0.22, G:0.00, T:0.12
Consensus pattern (25 bp):
CAACCAAAAACAACAAATACAAATC
Found at i:55474342 original size:41 final size:41
Alignment explanation
Indices: 55474215--55474342 Score: 166
Period size: 41 Copynumber: 3.1 Consensus size: 41
55474205 ATAAAATGTT
*
55474215 TTTTGCAGCGTTTTTAGCATAAACGCCGCTAATGCTGGACC
1 TTTTGCAGCGTTTTTATCATAAACGCCGCTAATGCTGGACC
* * * * * *
55474256 TTTTACTGCATTTTTCTCATAAACGTCGCTAATGCTGGACT
1 TTTTGCAGCGTTTTTATCATAAACGCCGCTAATGCTGGACC
* * *
55474297 TTTTGCAGCGTTTTTATCATAAATGCCGCTAATGTTAGACC
1 TTTTGCAGCGTTTTTATCATAAACGCCGCTAATGCTGGACC
55474338 TTTTG
1 TTTTG
55474343 TGGCGTTTCC
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (41 bp):
TTTTGCAGCGTTTTTATCATAAACGCCGCTAATGCTGGACC
Found at i:55474383 original size:82 final size:82
Alignment explanation
Indices: 55474215--55474392 Score: 191
Period size: 82 Copynumber: 2.2 Consensus size: 82
55474205 ATAAAATGTT
* **
55474215 TTTTGCAGCGTTTTTAGCATAAACGCCGCTAATGCTGGACCTTTTACTGCATTTTTCTCATAAAC
1 TTTTGCAGCGTTTTTAGCATAAACGCCGCTAATGCTAGACCTTTTACTGCATTTCCCTCATAAAC
* * *
55474280 GTCGCTAATGCTGGACT
66 CTCGCTAATGCTCGACC
* * * * *
55474297 TTTTGCAGCGTTTTTATCATAAATGCCGCTAATGTTAGACCTTTT-GTGGCGTTTCCCTCATAAA
1 TTTTGCAGCGTTTTTAGCATAAACGCCGCTAATGCTAGACCTTTTACT-GCATTTCCCTCATAAA
*
55474361 CACT-GCT-ATAGCTCTACC
65 C-CTCGCTAAT-GCTCGACC
*
55474379 TTTTGCTGCGTTTT
1 TTTTGCAGCGTTTT
55474393 CTGTTTAGCG
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
81 3 0.04
82 76 0.95
83 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.39
Consensus pattern (82 bp):
TTTTGCAGCGTTTTTAGCATAAACGCCGCTAATGCTAGACCTTTTACTGCATTTCCCTCATAAAC
CTCGCTAATGCTCGACC
Found at i:55485059 original size:12 final size:12
Alignment explanation
Indices: 55485023--55485061 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
55485013 TTTCACCCCT
55485023 TTTACCTTTTTA
1 TTTACCTTTTTA
* *
55485035 TTT-TCTATTTA
1 TTTACCTTTTTA
55485046 TTTACCTTTTTA
1 TTTACCTTTTTA
55485058 TTTA
1 TTTA
55485062 TTTTGTTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTACCTTTTTA
Found at i:55486626 original size:14 final size:14
Alignment explanation
Indices: 55486607--55486646 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55486597 TTGATTGGCA
55486607 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
55486621 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
55486635 GGAAAATGTTTT
1 GTAAAATGTTTT
55486647 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:55486659 original size:34 final size:35
Alignment explanation
Indices: 55486615--55486681 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
55486605 CAGTAAAATG
* *
55486615 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
55486649 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
55486682 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:55486668 original size:20 final size:20
Alignment explanation
Indices: 55486630--55486669 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55486620 CGTAAAATGA
**
55486630 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
55486650 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
55486670 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:55493948 original size:23 final size:22
Alignment explanation
Indices: 55493882--55493948 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
55493872 TAAAAAAATT
* *
55493882 TAAATTTTAATACGTTA-AAAA
1 TAAATTTAAATACTTTATAAAA
* * *
55493903 TAGATTTAAATAATTTTTGAAAA
1 TAAATTTAAATACTTTAT-AAAA
55493926 TAAATTTAAATACTTCTATAAAA
1 TAAATTTAAATACTT-TATAAAA
55493949 ACAAAATCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 12 0.34
23 21 0.60
24 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAATTTAAATACTTTATAAAA
Found at i:55499247 original size:21 final size:21
Alignment explanation
Indices: 55499203--55499253 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
55499193 TTTTATTTTG
*
55499203 TATATTATGTCTATACTTTAA
1 TATATTATGTATATACTTTAA
*
55499224 TATATTATGTATAT--TTTTA
1 TATATTATGTATATACTTTAA
*
55499243 TATATCATGTA
1 TATATTATGTA
55499254 CATATTATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 14 0.52
21 13 0.48
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (21 bp):
TATATTATGTATATACTTTAA
Found at i:55499627 original size:3 final size:3
Alignment explanation
Indices: 55499608--55499725 Score: 55
Period size: 3 Copynumber: 40.3 Consensus size: 3
55499598 GCATTATTTG
* * * * * * * *
55499608 TAT TAT CAT TCT TAT TAT TAC TAA TAT TAA TAT TCT TA- TAT GAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
55499655 TAT TAT TAT TAT CAT TAG TAT TAT CA- TAT T-T TAC CAC TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
55499701 TAT T-T ATAT TAC TAT TAT TAT TAT T
1 TAT TAT -TAT TAT TAT TAT TAT TAT T
55499726 GTTTTCGTTA
Statistics
Matches: 81, Mismatches: 29, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
2 6 0.07
3 74 0.91
4 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:55503233 original size:31 final size:31
Alignment explanation
Indices: 55503186--55503244 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
55503176 TTTACCATAA
* *
55503186 GTACTAATTTGGACCAAAAAACCAAGTTCAG
1 GTACCAATTTGAACCAAAAAACCAAGTTCAG
* *
55503217 GTACCAATTTGAACCAAGAAGCCAAGTT
1 GTACCAATTTGAACCAAAAAACCAAGTT
55503245 TAGATACCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (31 bp):
GTACCAATTTGAACCAAAAAACCAAGTTCAG
Found at i:55503364 original size:59 final size:60
Alignment explanation
Indices: 55503249--55503371 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 60
55503239 CAAGTTTAGA
* * *
55503249 TACCTAATTGGATCAAAATAAACTTTAGGTACCAAATTGGATCTTAAAGTCAAGTTCAAG
1 TACCTAATTGGATCAAAATAAACCTTAGGTACCAAATTGAATCTTAAAGGCAAGTTCAAG
** * * * *
55503309 TACCTAATTGGATTGAAA-AAACCTTAGGTGCCAATTTGAA-CTTTGAAGGCAAGTTCAGG
1 TACCTAATTGGATCAAAATAAACCTTAGGTACCAAATTGAATC-TTAAAGGCAAGTTCAAG
55503368 TACC
1 TACC
55503372 AAAATGTATA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
58 1 0.02
59 36 0.68
60 16 0.30
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (60 bp):
TACCTAATTGGATCAAAATAAACCTTAGGTACCAAATTGAATCTTAAAGGCAAGTTCAAG
Found at i:55509126 original size:41 final size:44
Alignment explanation
Indices: 55509051--55509263 Score: 215
Period size: 45 Copynumber: 4.9 Consensus size: 44
55509041 TTTTATCAAA
* * ** *
55509051 TCACTGGCATT-TAGCCTGCTAGGTTTTAA-ACCCGAAT-TCATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAT-ATC
* * *
55509093 -CACCGGCATT-TCGCCTGCTAGGTTCGAA-GCCCG-ATATCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAT-ATC
* * *
55509134 TCACTGGCATTATAGCTTGCTAGGCTCGAAGGCCTGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TATC
*
55509179 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TATC
* *
55509224 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
55509264 GTACCGTACA
Statistics
Matches: 148, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.01
41 32 0.22
42 9 0.06
43 15 0.10
44 4 0.03
45 85 0.57
46 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (44 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATATC
Found at i:55509200 original size:45 final size:45
Alignment explanation
Indices: 55509093--55509266 Score: 230
Period size: 45 Copynumber: 3.9 Consensus size: 45
55509083 CGAATTCATC
* * * *
55509093 CACCGGCATT-TCGCCTGCTAGGTTCGAA-GCCCG-ATA-TCATTT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCT
* * * *
55509135 CACTGGCATTATAGCTTGCTAGGCTCGAAGGCCTGAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
55509180 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
*
55509225 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTA
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
55509267 CCGTACAATA
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
42 9 0.08
43 15 0.13
44 4 0.03
45 88 0.75
46 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (45 bp):
CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
Found at i:55512976 original size:15 final size:14
Alignment explanation
Indices: 55512947--55512996 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
55512937 TATACTTCAG
*
55512947 TTAACATTTAATTAA
1 TTAAAATTT-ATTAA
*
55512962 TTATAATTTATTTAA
1 TTAAAATTTA-TTAA
55512977 TTAAAATTTGATTAA
1 TTAAAATTT-ATTAA
55512992 TTAAA
1 TTAAA
55512997 CATAAATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (14 bp):
TTAAAATTTATTAA
Found at i:55515763 original size:41 final size:43
Alignment explanation
Indices: 55515704--55515818 Score: 148
Period size: 43 Copynumber: 2.7 Consensus size: 43
55515694 ATATGTGGTA
*
55515704 TCGTGTAAGACCACGTCT-GGATGTTGGCATCG-TATTTGATT
1 TCGTGTAAGACCACGTCTGGGAAGTTGGCATCGATATTTGATT
*
55515745 TCGTGTAAGACC-CTGTCTGGGACAG-TGACATCGATATTTGATT
1 TCGTGTAAGACCAC-GTCTGGGA-AGTTGGCATCGATATTTGATT
* *
55515788 ACATGTAAGACCACGTCTGGGAAGTTGGCAT
1 TCGTGTAAGACCACGTCTGGGAAGTTGGCAT
55515819 TATACGAGCT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
40 1 0.02
41 16 0.25
42 12 0.19
43 33 0.52
44 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TCGTGTAAGACCACGTCTGGGAAGTTGGCATCGATATTTGATT
Found at i:55520963 original size:12 final size:12
Alignment explanation
Indices: 55520946--55520970 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55520936 GGTTTGGCCA
55520946 AGTTTTGCCTTT
1 AGTTTTGCCTTT
55520958 AGTTTTGCCTTT
1 AGTTTTGCCTTT
55520970 A
1 A
55520971 AAGTAAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.56
Consensus pattern (12 bp):
AGTTTTGCCTTT
Found at i:55525027 original size:20 final size:20
Alignment explanation
Indices: 55524994--55525032 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55524984 ATAGTTGAGG
55524994 ATCCAAAAACCAAT-GATGA
1 ATCCAAAAACCAATAGATGA
*
55525013 ATCCATAAAATCAATAGATG
1 ATCCA-AAAACCAATAGATG
55525033 CTAGTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (20 bp):
ATCCAAAAACCAATAGATGA
Found at i:55531239 original size:14 final size:14
Alignment explanation
Indices: 55531217--55531246 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55531207 TACTGTTTAA
*
55531217 GACTTCTTAAGAGG
1 GACTGCTTAAGAGG
55531231 GACTGCTTAAGAGG
1 GACTGCTTAAGAGG
55531245 GA
1 GA
55531247 GCTAATCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.23
Consensus pattern (14 bp):
GACTGCTTAAGAGG
Found at i:55537118 original size:20 final size:20
Alignment explanation
Indices: 55537093--55537131 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55537083 CCTCTCCAAT
*
55537093 TTGCAACCTTTAACTATTGA
1 TTGCAACCGTTAACTATTGA
55537113 TTGCAACCGTTAACTATTG
1 TTGCAACCGTTAACTATTG
55537132 GGGGTTACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (20 bp):
TTGCAACCGTTAACTATTGA
Found at i:55539641 original size:60 final size:58
Alignment explanation
Indices: 55539568--55539705 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 58
55539558 TAGTTAATTG
* * * * **
55539568 GTGACCGATAAAGACAAAATTGAATAGTTTGGTGA-CTGTTTTGTAACTTTTCATAGTTGG
1 GTGACCAAAAAAGA-AAAATT-AATAGTTAGGTGATC-ATTTTGTAACTTTTCATAGTTAA
* * * *
55539628 GTGATCAAAAAAGAAATTTATTTATAGTTAGGTGATCATTTTGTAATTTTTCATAGTTAA
1 GTGACCAAAAAAGAAA--AATTAATAGTTAGGTGATCATTTTGTAACTTTTCATAGTTAA
55539688 GTGACCAAAAAAGAAAAA
1 GTGACCAAAAAAGAAAAA
55539706 ACTATAATTG
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
58 1 0.02
59 2 0.03
60 56 0.89
61 4 0.06
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (58 bp):
GTGACCAAAAAAGAAAAATTAATAGTTAGGTGATCATTTTGTAACTTTTCATAGTTAA
Found at i:55544015 original size:21 final size:21
Alignment explanation
Indices: 55543989--55544029 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55543979 AGACGAGCAA
* *
55543989 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
55544010 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
55544030 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:55545968 original size:16 final size:16
Alignment explanation
Indices: 55545935--55545968 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55545925 GGAGATTGTT
* *
55545935 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
55545951 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
55545967 AA
1 AA
55545969 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:55550293 original size:36 final size:37
Alignment explanation
Indices: 55550223--55550293 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
55550213 TATTTGATTT
* *
55550223 TTTGTTTTAATCGGAAGAACTAAACAAAAGATGATAG
1 TTTGTTTTAATCGGAACAACTAAACAAAAAATGATAG
* * *
55550260 TTTGTTTTGAT-GGAACAATTAAGCAAAAAATGAT
1 TTTGTTTTAATCGGAACAACTAAACAAAAAATGAT
55550294 TATTTTGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 19 0.66
37 10 0.34
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.32
Consensus pattern (37 bp):
TTTGTTTTAATCGGAACAACTAAACAAAAAATGATAG
Found at i:55560586 original size:51 final size:51
Alignment explanation
Indices: 55560510--55560613 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
55560500 CATATATAAT
*
55560510 AAGGATAATTACATGTTATTATTTACTATCATGATAGGTTAAGTTAAATTA
1 AAGGATAATTACATGTTATTATTTACTATCATGATAGGTTAACTTAAATTA
*
55560561 AAGGATAATTATATGTTATTATTTACTATCATGATAGGTTAACTTAAATTA
1 AAGGATAATTACATGTTATTATTTACTATCATGATAGGTTAACTTAAATTA
55560612 AA
1 AA
55560614 AGTGATCTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.41
Consensus pattern (51 bp):
AAGGATAATTACATGTTATTATTTACTATCATGATAGGTTAACTTAAATTA
Found at i:55560601 original size:23 final size:23
Alignment explanation
Indices: 55560524--55560601 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
55560514 ATAATTACAT
55560524 GTTATTATTTACTATCATGATAG
1 GTTATTATTTACTATCATGATAG
* ** * * *
55560547 GTTAAGTTAAATTAAAGGATAATTATAT
1 GTT-A-TT--ATT-TACTATCATGATAG
55560575 GTTATTATTTACTATCATGATAG
1 GTTATTATTTACTATCATGATAG
55560598 GTTA
1 GTTA
55560602 ACTTAAATTA
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
23 15 0.39
24 4 0.11
25 2 0.05
26 2 0.05
27 4 0.11
28 11 0.29
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (23 bp):
GTTATTATTTACTATCATGATAG
Found at i:55562307 original size:14 final size:14
Alignment explanation
Indices: 55562288--55562314 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55562278 CGAAAAGATC
55562288 ATCTCAATTTACTT
1 ATCTCAATTTACTT
55562302 ATCTCAATTTACT
1 ATCTCAATTTACT
55562315 CCTTCATACT
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:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (14 bp):
ATCTCAATTTACTT
Found at i:55568454 original size:38 final size:38
Alignment explanation
Indices: 55568411--55568664 Score: 238
Period size: 38 Copynumber: 6.2 Consensus size: 38
55568401 TTTCAAATTA
* *
55568411 ACATGTATAACCGTGACATATCCACTTCGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * *
55568449 ACATGTTTAACCATGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
*
55568490 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
* *
55568534 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * *
55568572 ACATGTTTAACCGTGGTATATTCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
*
55568613 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
55568657 ACATGTAT
1 ACATGTAT
55568665 CAATATGTGT
Statistics
Matches: 180, Mismatches: 18, Indels: 36
0.77 0.08 0.15
Matches are distributed among these distances:
38 97 0.54
39 2 0.01
40 7 0.04
41 4 0.02
42 2 0.01
43 2 0.01
44 4 0.02
45 6 0.03
46 2 0.01
47 54 0.30
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:55568558 original size:123 final size:123
Alignment explanation
Indices: 55568411--55568664 Score: 454
Period size: 123 Copynumber: 2.1 Consensus size: 123
55568401 TTTCAAATTA
*
55568411 ACATGTATAACCGTGACATATCCACTTCGCACCACGTTACATGTTTAACCATGGTATATCCACTT
1 ACATGTATAACCGTGACATATCCACTTAGCACCACGTTACATGTTTAACCATGGTATATCCACTT
55568476 AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
66 AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
* ** * *
55568534 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATTCACTT
1 ACATGTATAACCGTGACATATCCACTTAGCACCACGTTACATGTTTAACCATGGTATATCCACTT
55568599 AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
66 AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
55568657 ACATGTAT
1 ACATGTAT
55568665 CAATATGTGT
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (123 bp):
ACATGTATAACCGTGACATATCCACTTAGCACCACGTTACATGTTTAACCATGGTATATCCACTT
AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:55568682 original size:48 final size:47
Alignment explanation
Indices: 55568574--55568704 Score: 190
Period size: 48 Copynumber: 2.8 Consensus size: 47
55568564 ACCACGTTAC
* *
55568574 ATGTTTAACCGTGGTATATTCACTTAGCACCACGTTAATGAATCAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAAT
* * *
55568621 ATATGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAAT
* *
55568669 ATGTGTAATCGTGGTATATCTACTTAGCACCACGTT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTT
55568705 TTTTATTCCG
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 33 0.45
48 41 0.55
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (47 bp):
ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAAT
Found at i:55573150 original size:38 final size:38
Alignment explanation
Indices: 55573098--55573304 Score: 162
Period size: 47 Copynumber: 5.0 Consensus size: 38
55573088 TCAATATATG
*
55573098 TAACCGTGGCATATCCACTTAGCGCCACATTACATGTT
1 TAACCGTGGCATATCCACTTAGCACCACATTACATGTT
* * * *
55573136 TAACCGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATAT
1 TAACCGTGGCATATCCACTTAGCACCAC----AT-TA-C-ATGT-T
*
55573182 GTAACCGTGGCATATCCACTTAGCGCCACATTACATGTT
1 -TAACCGTGGCATATCCACTTAGCACCACATTACATGTT
* * *
55573221 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATAT
1 TAACCGTGGCATATCCACTTAGCACCAC----AT-TA-C-ATGT-T
*
55573267 GTAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 -TAACCGTGGCATATCCACTTAGCACCACATTACATGT
55573305 ATCAATATGT
Statistics
Matches: 133, Mismatches: 18, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
38 51 0.38
39 1 0.01
40 6 0.05
41 2 0.02
42 6 0.05
43 5 0.04
44 2 0.02
45 6 0.05
46 2 0.02
47 52 0.39
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (38 bp):
TAACCGTGGCATATCCACTTAGCACCACATTACATGTT
Found at i:55573185 original size:85 final size:85
Alignment explanation
Indices: 55573042--55573304 Score: 490
Period size: 85 Copynumber: 3.1 Consensus size: 85
55573032 NNNNNNCACG
*
55573042 TTACATGTTTAACTGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGG
1 TTACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGG
55573107 CATATCCACTTAGCGCCACA
66 CATATCCACTTAGCGCCACA
*
55573127 TTACATGTTTAACCGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAACCGTGG
1 TTACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGG
55573192 CATATCCACTTAGCGCCACA
66 CATATCCACTTAGCGCCACA
55573212 TTACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGG
1 TTACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGG
* *
55573277 CATATCCACTTAGCACCACG
66 CATATCCACTTAGCGCCACA
55573297 TTACATGT
1 TTACATGT
55573305 ATCAATATGT
Statistics
Matches: 173, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 173 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (85 bp):
TTACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGG
CATATCCACTTAGCGCCACA
Found at i:55573205 original size:47 final size:47
Alignment explanation
Indices: 55573136--55573346 Score: 260
Period size: 47 Copynumber: 4.7 Consensus size: 47
55573126 ATTACATGTT
*
55573136 TAACCGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * * *
55573183 TAACCGTGGCATATCCACTTAGCGCCAC----AT-TA-C-ATGT-T-
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
55573221 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * *
55573268 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
* *
55573316 TAATCGTGGTATATCTACTTAGCACCACGTT
1 TAACCGTGGTATATCCACTTAGCACCACGTT
55573347 TTTTATTCCG
Statistics
Matches: 139, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
38 26 0.19
39 1 0.01
40 3 0.02
41 1 0.01
42 3 0.02
43 3 0.02
44 1 0.01
45 3 0.02
46 1 0.01
47 56 0.40
48 41 0.29
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (47 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
Found at i:55573330 original size:48 final size:47
Alignment explanation
Indices: 55573216--55573346 Score: 199
Period size: 48 Copynumber: 2.8 Consensus size: 47
55573206 GCCACATTAC
*
55573216 ATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAAT
* * *
55573263 ATATGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAAT
* *
55573311 ATGTGTAATCGTGGTATATCTACTTAGCACCACGTT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTT
55573347 TTTTATTCCG
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
47 34 0.45
48 41 0.55
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (47 bp):
ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAAT
Found at i:55581601 original size:16 final size:16
Alignment explanation
Indices: 55581582--55581615 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55581572 ATAAATAAAT
55581582 AAATAAGAATAATAAG
1 AAATAAGAATAATAAG
* *
55581598 AAATAATACTAATAAG
1 AAATAAGAATAATAAG
55581614 AA
1 AA
55581616 TGAAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (16 bp):
AAATAAGAATAATAAG
Found at i:55590083 original size:28 final size:28
Alignment explanation
Indices: 55590039--55590133 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 28
55590029 GTTTTAACCA
*
55590039 TTATAATATCATCATTGGAATATGACCG
1 TTATAATATGATCATTGGAATATGACCG
* * * * *
55590067 TTATAATATGATTATTGAAATTTAACTG
1 TTATAATATGATCATTGGAATATGACCG
* * * * *
55590095 TTATAACATGGTCGTTGGAATCTGACCA
1 TTATAATATGATCATTGGAATATGACCG
55590123 TTATAATATGA
1 TTATAATATGA
55590134 CTGATGCAAT
Statistics
Matches: 50, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (28 bp):
TTATAATATGATCATTGGAATATGACCG
Found at i:55590557 original size:17 final size:19
Alignment explanation
Indices: 55590535--55590573 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
55590525 AGCGAATTTA
55590535 CTTCTA-AG-ACAGTGATT
1 CTTCTATAGCACAGTGATT
*
55590552 CTTCTATTGCACAGTGATT
1 CTTCTATAGCACAGTGATT
55590571 CTT
1 CTT
55590574 TCTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 1 0.05
19 12 0.63
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (19 bp):
CTTCTATAGCACAGTGATT
Found at i:55592115 original size:10 final size:10
Alignment explanation
Indices: 55592093--55592129 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
55592083 TGATAATCAA
*
55592093 TAAAAAATA-
1 TAAAAATTAT
55592102 TAAAAATTAT
1 TAAAAATTAT
55592112 TAAAAATTAT
1 TAAAAATTAT
55592122 TAAAAATT
1 TAAAAATT
55592130 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:55592467 original size:20 final size:20
Alignment explanation
Indices: 55592442--55592481 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55592432 GTTAAATGAT
55592442 TTTTTTGATGCAT-TTTATAA
1 TTTTTTGATG-ATCTTTATAA
*
55592462 TTTTTTTATGATCTTTATAA
1 TTTTTTGATGATCTTTATAA
55592482 AATTTCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTTTTGATGATCTTTATAA
Found at i:55593440 original size:14 final size:15
Alignment explanation
Indices: 55593414--55593442 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55593404 TTTTCCCATA
55593414 AATATTATATATTAT
1 AATATTATATATTAT
55593429 AATATT-TATATTAT
1 AATATTATATATTAT
55593443 TTTTAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATTATATATTAT
Found at i:55603154 original size:12 final size:12
Alignment explanation
Indices: 55603137--55603170 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
55603127 CTGGCCCGCC
55603137 TATATTAATTTT
1 TATATTAATTTT
55603149 TATATT-ATTTT
1 TATATTAATTTT
55603160 TATA-TAATTTT
1 TATATTAATTTT
55603171 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:55603328 original size:30 final size:31
Alignment explanation
Indices: 55603292--55603355 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
55603282 ACTTAACAAG
55603292 CAAATGT-TTCTAAAATAATAACAAAA-TTAA
1 CAAATGTCTT-TAAAATAATAACAAAACTTAA
*
55603322 CAAATGTCTTTAAAATAATAATAAAACTTAA
1 CAAATGTCTTTAAAATAATAACAAAACTTAA
55603353 CAA
1 CAA
55603356 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (31 bp):
CAAATGTCTTTAAAATAATAACAAAACTTAA
Found at i:55610566 original size:11 final size:11
Alignment explanation
Indices: 55610552--55610582 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
55610542 AAATAAAAAA
55610552 TAAAAAATATT
1 TAAAAAATATT
55610563 T-AAAAATATT
1 TAAAAAATATT
55610573 TAAAAAATAT
1 TAAAAAATAT
55610583 AAAAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAAATATT
Found at i:55628643 original size:31 final size:31
Alignment explanation
Indices: 55628608--55628669 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
55628598 GTTTATTGTC
55628608 AATGTTTGATTGCTATAACAAGAGTACCGCT
1 AATGTTTGATTGCTATAACAAGAGTACCGCT
55628639 AATGTTTGATTGCTATAACAAGAGTACCGCT
1 AATGTTTGATTGCTATAACAAGAGTACCGCT
55628670 TACTGTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (31 bp):
AATGTTTGATTGCTATAACAAGAGTACCGCT
Found at i:55636651 original size:44 final size:44
Alignment explanation
Indices: 55636582--55636670 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
55636572 AAGTAACAGA
* *
55636582 AACAGTACGACACATAAAGTGCCTCATCGACACAAAGTTGAAGT
1 AACAGTACGACACATAAAGTACCTCATCGACACAAAGTCGAAGT
* * * *
55636626 AACAGTACGACAC-TATTAGTACCTCATTGACTCAAGGTCGAAGT
1 AACAGTACGACACATA-AAGTACCTCATCGACACAAAGTCGAAGT
55636670 A
1 A
55636671 TCCCTGTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (44 bp):
AACAGTACGACACATAAAGTACCTCATCGACACAAAGTCGAAGT
Found at i:55637039 original size:24 final size:25
Alignment explanation
Indices: 55637010--55637057 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
55637000 TAGGAGAAAG
55637010 GACTAGATTGCATAAAGAG-AAAAT
1 GACTAGATTGCATAAAGAGTAAAAT
55637034 GACTAGATTGCATAAAGAGTAAAA
1 GACTAGATTGCATAAAGAGTAAAA
55637058 GTCTAGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (25 bp):
GACTAGATTGCATAAAGAGTAAAAT
Found at i:55638264 original size:51 final size:53
Alignment explanation
Indices: 55638182--55638293 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 53
55638172 TCGACCACTA
* *
55638182 TTACTGTTCCGGATTTATTCTGAAGAAGTACT-T-TGTAC-CTGACTATTACTG
1 TTACTGTTCCAGATTTATTCCGAAGAAGTACTCTGTGTACACT-ACTATTACTG
* * * *
55638233 TTACTGTTCCAGATTTGTTCCGATGAGGTACTCTGTGTACACTACTGTTACTG
1 TTACTGTTCCAGATTTATTCCGAAGAAGTACTCTGTGTACACTACTATTACTG
55638286 TTACTGTT
1 TTACTGTT
55638294 ACTGTTACCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 27 0.52
52 1 0.02
53 22 0.42
54 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (53 bp):
TTACTGTTCCAGATTTATTCCGAAGAAGTACTCTGTGTACACTACTATTACTG
Found at i:55638286 original size:6 final size:6
Alignment explanation
Indices: 55638275--55638301 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
55638265 CTGTGTACAC
55638275 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
55638302 CTCTACGGTG
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:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:55640343 original size:18 final size:19
Alignment explanation
Indices: 55640303--55640344 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
55640293 ATTTTATGCT
* *
55640303 TTATTTTATTATTATATTA
1 TTATTTTAGTAATATATTA
55640322 -TATTTTAGTAATA-ATTA
1 TTATTTTAGTAATATATTA
55640339 TTATTT
1 TTATTT
55640345 ACTTAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTTAGTAATATATTA
Found at i:55644536 original size:26 final size:26
Alignment explanation
Indices: 55644500--55644550 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
55644490 TCCTTTCAGT
55644500 CTCACTATTCGGCACAATTATATCGC
1 CTCACTATTCGGCACAATTATATCGC
55644526 CTCACTATTCGGCACAATTATATCG
1 CTCACTATTCGGCACAATTATATCG
55644551 TACTATCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.31
Consensus pattern (26 bp):
CTCACTATTCGGCACAATTATATCGC
Found at i:55644923 original size:25 final size:24
Alignment explanation
Indices: 55644889--55644936 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
55644879 ATAAAACAAC
*
55644889 AAAAAGAAAATCTATTCTAAAAAG
1 AAAAAGAAAATCTAATCTAAAAAG
55644913 AAAAGAGAAAATCTAATCTAAAAA
1 AAAA-AGAAAATCTAATCTAAAAA
55644937 AAGTGAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (24 bp):
AAAAAGAAAATCTAATCTAAAAAG
Found at i:55646162 original size:49 final size:50
Alignment explanation
Indices: 55646056--55646164 Score: 118
Period size: 49 Copynumber: 2.2 Consensus size: 50
55646046 TTAATTCAAT
* * * * * *
55646056 ATTCTACCATCTTGGATAGCCTGAAAACGATGGCTTTCACTATTCTTACA
1 ATTCTACCATCTCGAATAGCCTCAAAACGATGGCTCTCACTATACATACA
55646106 ATT-TACCATCTCGAATAG-CTCAACAACGATGGCTCTCA-T-TACATACA
1 ATTCTACCATCTCGAATAGCCTCAA-AACGATGGCTCTCACTATACATACA
55646153 CATTCTACCATC
1 -ATTCTACCATC
55646165 CTTAATAGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
47 6 0.12
48 8 0.16
49 33 0.66
50 3 0.06
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (50 bp):
ATTCTACCATCTCGAATAGCCTCAAAACGATGGCTCTCACTATACATACA
Found at i:55648175 original size:48 final size:48
Alignment explanation
Indices: 55648109--55648217 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 48
55648099 AGTGTCGCCA
* * **
55648109 GACTGTGACTGTTTCGGATTTATTCCGATAAGGTACTTAGTGTACTGT
1 GACTGTGACTGTTCCGGATTCATTCCGATAAGGTACTTAGTGTACCAT
* * * *
55648157 GACTGTGACTGTTCCGGATTCGTTCTGATGAGGTACTTTGTGTACCAT
1 GACTGTGACTGTTCCGGATTCATTCCGATAAGGTACTTAGTGTACCAT
*
55648205 GACTGAGACTGTT
1 GACTGTGACTGTT
55648218 ACAGTTACGG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.38
Consensus pattern (48 bp):
GACTGTGACTGTTCCGGATTCATTCCGATAAGGTACTTAGTGTACCAT
Found at i:55648375 original size:18 final size:18
Alignment explanation
Indices: 55648354--55648406 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
55648344 GACTGCTACG
*
55648354 GAATAATTGACTGTTATT
1 GAATAAATGACTGTTATT
* *
55648372 GAATAAATGATTGTTACT
1 GAATAAATGACTGTTATT
* *
55648390 GCATAACTGACTGTTAT
1 GAATAAATGACTGTTAT
55648407 AGAGTGCCGG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (18 bp):
GAATAAATGACTGTTATT
Found at i:55652725 original size:16 final size:18
Alignment explanation
Indices: 55652699--55652731 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55652689 TCAAATTAAA
55652699 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
55652716 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
55652732 CTCAACTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:55656006 original size:13 final size:13
Alignment explanation
Indices: 55655988--55656013 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55655978 TATATAGACT
55655988 AAATAAAAAAATA
1 AAATAAAAAAATA
55656001 AAATAAAAAAATA
1 AAATAAAAAAATA
55656014 TCTTATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:55656063 original size:27 final size:27
Alignment explanation
Indices: 55655995--55656063 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
55655985 ACTAAATAAA
* *
55655995 AAAATAAAATAAAA-AAATATCTTATT
1 AAAATAATATAAAATAAATATCTAATT
*
55656021 AAAATAATA-AATAATAATTATCTAATT
1 AAAATAATATAA-AATAAATATCTAATT
55656048 -AAATAACTATAAAATA
1 AAAATAA-TATAAAATA
55656064 TCACCAACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 2 0.06
26 16 0.44
27 16 0.44
28 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAATAATATAAAATAAATATCTAATT
Found at i:55656065 original size:23 final size:24
Alignment explanation
Indices: 55656002--55656065 Score: 60
Period size: 27 Copynumber: 2.6 Consensus size: 24
55655992 AAAAAAATAA
* *
55656002 AATAAAAAAATATCTTATTAAAAT
1 AATAATAAAATATCTAATTAAAAT
55656026 AATAAATAATAATTATCTAATT-AAAT
1 AAT-AATAA-AA-TATCTAATTAAAAT
55656052 AACT-ATAAAATATC
1 AA-TAATAAAATATC
55656066 ACCAACATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
23 4 0.12
24 5 0.15
25 8 0.24
26 8 0.24
27 9 0.26
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (24 bp):
AATAATAAAATATCTAATTAAAAT
Found at i:55658277 original size:20 final size:20
Alignment explanation
Indices: 55658254--55658293 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55658244 AAATTTTAGG
55658254 ATTTAATTT-CATTTATCTTT
1 ATTT-ATTTGCATTTATCTTT
*
55658274 ATTTATTTGTATTTATCTTT
1 ATTTATTTGCATTTATCTTT
55658294 TAGAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTATTTGCATTTATCTTT
Found at i:55658443 original size:37 final size:37
Alignment explanation
Indices: 55658396--55658468 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
55658386 CCCTCTCCCA
55658396 AAAACTCTGTCTTTTGT-TT-TCTCCATATCTTTCTTCG
1 AAAACTCTGTCTTTT-TATTCTCTCCATAT-TTTCTTCG
55658433 AAAACTCTGTCTTTTTATTCTCTCCATATTTTCTTC
1 AAAACTCTGTCTTTTTATTCTCTCCATATTTTCTTC
55658469 CATAAAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 1 0.03
37 24 0.71
38 9 0.26
ACGTcount: A:0.18, C:0.25, G:0.05, T:0.52
Consensus pattern (37 bp):
AAAACTCTGTCTTTTTATTCTCTCCATATTTTCTTCG
Found at i:55659091 original size:17 final size:18
Alignment explanation
Indices: 55659059--55659092 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55659049 CTCTTTTTTT
55659059 TTTAATTTCTGCAATTTA
1 TTTAATTTCTGCAATTTA
55659077 TTTAATTTC-GCAATTT
1 TTTAATTTCTGCAATTT
55659093 CAATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTCTGCAATTTA
Found at i:55659268 original size:12 final size:12
Alignment explanation
Indices: 55659248--55659280 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
55659238 CTACTTCCCC
*
55659248 TTTATTATTATT
1 TTTACTATTATT
55659260 TTTACTATTATT
1 TTTACTATTATT
55659272 TTTACTATT
1 TTTACTATT
55659281 TTACAGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTACTATTATT
Found at i:55662049 original size:5 final size:5
Alignment explanation
Indices: 55662035--55662085 Score: 57
Period size: 5 Copynumber: 9.4 Consensus size: 5
55662025 GCAACCCAAT
*
55662035 TTTTA TTTTTA TTTTA TTTTA GTTTA TTTTA TTTTTTA TTATTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA --TTTTA TT-TTA TTTTA
55662084 TT
1 TT
55662086 ATTTATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 25 0.62
6 10 0.25
7 5 0.12
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:55662051 original size:11 final size:11
Alignment explanation
Indices: 55662035--55662092 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
55662025 GCAACCCAAT
55662035 TTTTATTTTTA
1 TTTTATTTTTA
55662046 TTTTA-TTTTA
1 TTTTATTTTTA
* *
55662056 GTTTATTTTATT
1 TTTTATTTT-TA
*
55662068 TTTTATTATTA
1 TTTTATTTTTA
55662079 TTTTATTATTTA
1 TTTTATT-TTTA
55662091 TT
1 TT
55662093 ATTTTTAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 9 0.24
11 16 0.42
12 13 0.34
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:55662076 original size:15 final size:15
Alignment explanation
Indices: 55662042--55662097 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
55662032 AATTTTTATT
55662042 TTTATT-TTATTTTA
1 TTTATTATTATTTTA
55662056 GTTTATT-TTA-TTT-
1 -TTTATTATTATTTTA
55662069 TTTATTATTATTTTA
1 TTTATTATTATTTTA
55662084 -TTATTTATTATTTT
1 TTTA-TTATTATTTT
55662098 TAGATATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.16
13 3 0.08
14 9 0.24
15 19 0.51
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTATTATTATTTTA
Found at i:55662081 original size:18 final size:18
Alignment explanation
Indices: 55662034--55662095 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
55662024 GGCAACCCAA
*
55662034 TTTTTATTTTTATTTTA-
1 TTTTTATTATTATTTTAT
*
55662051 -TTTTAGT-TTATTTTAT
1 TTTTTATTATTATTTTAT
55662067 TTTTTATTATTATTTTAT
1 TTTTTATTATTATTTTAT
*
55662085 TATTTATTATT
1 TTTTTATTATT
55662096 TTTAGATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
15 8 0.21
16 6 0.15
17 6 0.15
18 19 0.49
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTATTATTATTTTAT
Found at i:55663668 original size:20 final size:20
Alignment explanation
Indices: 55663645--55663684 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55663635 AAATTTTAGG
55663645 ATTTAATTT-AATTTATCTTT
1 ATTT-ATTTGAATTTATCTTT
*
55663665 ATTTATTTGTATTTATCTTT
1 ATTTATTTGAATTTATCTTT
55663685 TAGAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTATTTGAATTTATCTTT
Found at i:55665488 original size:58 final size:59
Alignment explanation
Indices: 55665411--55665529 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
55665401 CATGTGAACA
55665411 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
55665470 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
55665528 TG
1 TG
55665530 ATTTCGTGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 55 0.92
59 5 0.08
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (59 bp):
TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:55665520 original size:28 final size:28
Alignment explanation
Indices: 55665430--55665520 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
55665420 GTGATTCCGT
55665430 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
55665458 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
55665487 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
55665516 GTAAG
1 GTAAG
55665521 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:55665543 original size:49 final size:49
Alignment explanation
Indices: 55665471--55665611 Score: 219
Period size: 49 Copynumber: 2.9 Consensus size: 49
55665461 AGTGATATGT
* *
55665471 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* * *
55665520 GTGATATGTGATTTCGTGTAAGACCGTAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
55665569 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCAT
55665612 TGAGAAAACG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 84 1.00
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.33
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:55668792 original size:52 final size:48
Alignment explanation
Indices: 55668773--55668975 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
55668763 TGACAAGTGG
* *
55668773 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
55668819 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
55668871 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
55668917 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
55668963 AAAGTGATAAGTG
1 AAAGTGATAAGTG
55668976 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:55668827 original size:98 final size:98
Alignment explanation
Indices: 55668707--55668975 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
55668697 TTTGAGTACT
*
55668707 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
55668772 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
55668805 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
55668870 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
55668903 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
55668968 GATAAGTG
65 GAAAAGTG
55668976 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:55668983 original size:37 final size:37
Alignment explanation
Indices: 55668939--55669084 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
55668929 GATAGCTTTA
*
55668939 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
55668976 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
55669013 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
55669050 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
55669085 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:55669609 original size:17 final size:18
Alignment explanation
Indices: 55669577--55669610 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55669567 TCCTCTTTTT
55669577 TTTAATTTCTGCAATTTA
1 TTTAATTTCTGCAATTTA
55669595 TTTAATTTC-GCAATTT
1 TTTAATTTCTGCAATTT
55669611 CAATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTCTGCAATTTA
Found at i:55671795 original size:68 final size:70
Alignment explanation
Indices: 55671682--55671839 Score: 212
Period size: 68 Copynumber: 2.2 Consensus size: 70
55671672 CAACTTTACC
*
55671682 CTTCTCCCTCTTTTTCGTTCTCACGTCTGAAGCAACTTCTTTTTTTCATTCTTC-CC-ATTTCCT
1 CTTCT-CCTCTTTTTCATTCTCACGTCTGAAGCAACTTCTTTTTTTCATTCTTCTCCTATTTCCT
*
55671745 TCGAAA
65 TCCAAA
* * *
55671751 CTTCTCCTCTTTTTCATTGTCACGTCTGAATCATCTTCTTTTTTTCATTCTTCTTCCTATTTCCT
1 CTTCTCCTCTTTTTCATTCTCACGTCTGAAGCAACTTCTTTTTTTCATTCTTC-TCCTATTTCCT
*
55671816 TCCAAC
65 TCCAAA
*
55671822 CATCTCTCTCTTTTTCAT
1 CTTCTC-CTCTTTTTCAT
55671840 GCTTCTATCC
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
68 44 0.56
69 5 0.06
70 2 0.03
71 16 0.21
72 11 0.14
ACGTcount: A:0.13, C:0.32, G:0.05, T:0.50
Consensus pattern (70 bp):
CTTCTCCTCTTTTTCATTCTCACGTCTGAAGCAACTTCTTTTTTTCATTCTTCTCCTATTTCCTT
CCAAA
Found at i:55681728 original size:17 final size:19
Alignment explanation
Indices: 55681626--55681720 Score: 146
Period size: 17 Copynumber: 5.3 Consensus size: 19
55681616 CAAAATCATA
55681626 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
*
55681643 ATGATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
55681662 ATCATATCTAAGATTGCA-
1 ATCATATCTAAGATTGCAT
55681680 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
55681697 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
55681716 ATCAT
1 ATCAT
55681721 TAAAGATTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
17 31 0.44
18 16 0.23
19 24 0.34
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:55681740 original size:54 final size:54
Alignment explanation
Indices: 55681625--55681729 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
55681615 ACAAAATCAT
* * *
55681625 AATCATATCTAAGATTGTATGATATCTAAGATTGCATATCATATCTAAGATTGC
1 AATCATATCTAAGATTGTATCATATCTAAGATTGCATATCATATCAAAGATTAC
55681679 AATCATATCTAAGATTGTATCATATCTAAGATTGCATATCAT-T-AAAGATTA
1 AATCATATCTAAGATTGTATCATATCTAAGATTGCATATCATATCAAAGATTA
55681730 TATTTCCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 6 0.12
53 1 0.02
54 41 0.85
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.37
Consensus pattern (54 bp):
AATCATATCTAAGATTGTATCATATCTAAGATTGCATATCATATCAAAGATTAC
Found at i:55682102 original size:45 final size:45
Alignment explanation
Indices: 55682032--55682231 Score: 258
Period size: 45 Copynumber: 4.5 Consensus size: 45
55682022 GGAAGGCGAT
* * *
55682032 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGACAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
*
55682077 ATCTATTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * ** * *
55682122 ATCTGCT-TCTTCAATCTGCTTTCCGTCTAATACAAAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * *
55682166 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
55682211 ATCTGTCATCTTGGATCTGCT
1 ATCTGTTATCTTCGATCTGCT
55682232 TCGATGTAAA
Statistics
Matches: 132, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 38 0.29
45 94 0.71
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:55682197 original size:89 final size:90
Alignment explanation
Indices: 55682032--55682215 Score: 262
Period size: 89 Copynumber: 2.1 Consensus size: 90
55682022 GGAAGGCGAT
** * *
55682032 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGACAAATCTATTATCTTCGATCTGC
1 ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAGACGACAAATCTATTATCTCCGATCTGC
55682097 TCCCCGTCTAATACAGAGACGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
** * * * *
55682122 ATCTGCT-TCTTCAATCTGCTTTCCGTCTAATACAAAGATGCCAAATCTGTTATCTCCGATTTGC
1 ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAGACGACAAATCTATTATCTCCGATCTGC
*
55682186 TCCCCGTCTAATACAGAGATGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
55682211 ATCTG
1 ATCTG
55682216 TCATCTTGGA
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 76 0.92
90 7 0.08
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (90 bp):
ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAGACGACAAATCTATTATCTCCGATCTGC
TCCCCGTCTAATACAGAGACGCCAA
Found at i:55682374 original size:78 final size:78
Alignment explanation
Indices: 55682245--55682626 Score: 516
Period size: 78 Copynumber: 4.8 Consensus size: 78
55682235 ATGTAAACAC
* * *
55682245 ATGAAGGTTAGATCTGCTATGTCTTTGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
55682310 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* *
55682323 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGTTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
55682387 TTGGATCTGCTTCAATGTAAACA
65 TTGGATCTG---C--T-T---CA
*
55682410 CATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATC
1 -ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
55682475 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* *
55682489 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
*
55682553 TTGGATCTGCCTCA
65 TTGGATCTGCTTCA
* ** * *
55682567 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAAT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAAT
55682627 ATGTTTCTTC
Statistics
Matches: 273, Mismatches: 17, Indels: 28
0.86 0.05 0.09
Matches are distributed among these distances:
77 2 0.01
78 189 0.69
79 5 0.02
81 1 0.00
82 1 0.00
83 2 0.01
84 1 0.00
85 1 0.00
87 4 0.01
88 67 0.25
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:55682464 original size:166 final size:165
Alignment explanation
Indices: 55682165--55682626 Score: 671
Period size: 166 Copynumber: 2.8 Consensus size: 165
55682155 AAAGATGCCA
* *
55682165 AATCTGTTA--TCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGGATC
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGATC
* *
55682228 TGCTTCGATGTAAACACATGAAGGTTAGATCTGCTATGTCTTTGATCTGCTTCCC-GTCTAATAC
62 TGCTTC-ATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGC-TCCCTGTCTAATAC
55682292 AGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
125 AGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
*
55682333 AATCTGTTATGTCTTCGATCTGTTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
55682398 TCAATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGA
66 TC-ATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGA
55682463 TGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
130 TGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
*
55682499 AATCTGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGC-
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
* * * *
55682563 -C---T---CA-ATGAAGGTCAGATCTGCTATGTCTTCGATCTACT-CTTCGTCGAATATAGAGA
66 TCATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCT-GTCTAATACAGAGA
55682619 TGCCAAAT
130 TGCCAAAT
55682627 ATGTTTCTTC
Statistics
Matches: 278, Mismatches: 12, Indels: 20
0.90 0.04 0.06
Matches are distributed among these distances:
155 2 0.01
156 53 0.19
157 2 0.01
160 1 0.00
164 1 0.00
165 4 0.01
166 171 0.62
168 9 0.03
170 35 0.13
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (165 bp):
AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
TCATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGAT
GCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
Found at i:55682851 original size:376 final size:374
Alignment explanation
Indices: 55682373--55683108 Score: 1222
Period size: 376 Copynumber: 2.0 Consensus size: 374
55682363 CTAATACAGA
* *
55682373 GATGCCAAATCATCTTGGATCTGCTTCAATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCG
1 GATGCCAAATCATATTGGATCTACTTCAATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCG
* *
55682438 ATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCAATC
66 ATCTGCTCCCCGTCTAATACAAAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCAATC
55682503 TGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCCTCAA
131 TGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCCTCAA
*
55682568 TGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAATATGTTT
196 TGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAATATGTTC
* **
55682633 CTTCGATTTGTTCTCTAACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACAC
261 CTTCGATTTGTTCTCTAACAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACAC
***
55682698 GTGAAATCCAAATCTGCTATGTCTTCGATCTGCTCATTGTCAACGTAAG
326 GTGAAAGAAAAATCTGCTATGTCTTCGATCTGCTCATTGTCAACGTAAG
* * *
55682747 GATGCCAAATCATATTGGATCTACTTCGATGTGAAA-ACATCCTAAGGTTAGATCTGCTATGTCT
1 GATGCCAAATCATATTGGATCTACTTCAATGT-AAACACAT--GAAGGTCAGATCTGCTATGTCT
*
55682811 TCGATCTGCTCCCCGTTTAATACAAAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCA
63 TCGATCTGCTCCCCGTCTAATACAAAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCA
* * *
55682876 ATCTGTTATGTCTTCGATCTACTCCCCGTTTAATACAGAGATGCCAAATCATCTTGGATTTGCTT
128 ATCTGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCCT
* * *
55682941 CAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTTCGTCGAATATGGAGATGCCAAATCTG
193 CAATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAATATG
* * *
55683006 TTCCTTCGATTTGTTCTCTGACAGTACAGATATGTCAAATCATCGTAGATCTGCAACAGCGTAAA
258 TTCCTTCGATTTGTTCTCTAACAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAA
55683071 CACGTGAAAGAAAAATCTGCTATGTCTTCGATCTGCTC
323 CACGTGAAAGAAAAATCTGCTATGTCTTCGATCTGCTC
55683109 TCCGTCGAAT
Statistics
Matches: 335, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
374 33 0.10
375 3 0.01
376 299 0.89
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (374 bp):
GATGCCAAATCATATTGGATCTACTTCAATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCG
ATCTGCTCCCCGTCTAATACAAAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCAATC
TGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCCTCAA
TGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAATATGTTC
CTTCGATTTGTTCTCTAACAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACAC
GTGAAAGAAAAATCTGCTATGTCTTCGATCTGCTCATTGTCAACGTAAG
Found at i:55682892 original size:298 final size:287
Alignment explanation
Indices: 55682367--55682924 Score: 721
Period size: 298 Copynumber: 1.9 Consensus size: 287
55682357 CCCCGTCTAA
* * * *
55682367 TACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGTAAACACATGAAGGTCAGATCTGCTATG
1 TACAGAGATGCCAAATCATCTTAGATCTGCTTCAACGTAAACACATGAAGATCAAATCTGCTATG
* * * **
55682432 TCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
66 TCTTCGATCTGCTCACTGTCTAATACAGAGATGCCAAATCATATTGGATCTACTTCAATGAACAT
* *
55682497 CCAATCTGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTG
131 CCAATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAAAGATGCCAAATCATCTTGGATCTG
** *
55682562 CCTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAAT
196 CCTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAAT
55682627 ATGTTTCTTCGATTTGTTCTCTAACAG
261 ATGTTTCTTCGATTTGTTCTCTAACAG
* *
55682654 TACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAA-ATCCAAATCTGCTAT
1 TACAGAGATGCCAAATCATCTTAGATCTGCTTCAACGTAAACACATGAAGAT-CAAATCTGCTAT
* *
55682718 GTCTTCGATCTGCTCATTGTC-AACGTA-AG-GATGCCAAATCATATTGGATCTACTTCGATGTG
65 GTCTTCGATCTGCTCACTGTCTAA--TACAGAGATGCCAAATCATATTGGATCTACTTC-A-ATG
* *
55682780 AAAACATCCTAAGGTTAGATCTGCTATGTCTTCGATCTGCTCCCCGTTTAATACAAAGATGCCAA
126 --AACATCC-------A-ATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAAAGATGCCAA
* * **
55682845 ATCATCTTGGATCTGCTTCAATGAAGGTCCA-ATCTGTTATGTCTTCGATCTACTCCCCGTTTAA
181 ATCATCTTGGATCTGCCTCAATGAAGGT-CAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAA
55682909 TACAGAGATGCCAAAT
245 TACAGAGATGCCAAAT
55682925 CATCTTGGAT
Statistics
Matches: 231, Mismatches: 24, Indels: 21
0.84 0.09 0.08
Matches are distributed among these distances:
286 28 0.12
287 78 0.34
288 4 0.02
290 5 0.02
297 1 0.00
298 113 0.49
299 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (287 bp):
TACAGAGATGCCAAATCATCTTAGATCTGCTTCAACGTAAACACATGAAGATCAAATCTGCTATG
TCTTCGATCTGCTCACTGTCTAATACAGAGATGCCAAATCATATTGGATCTACTTCAATGAACAT
CCAATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAAAGATGCCAAATCATCTTGGATCTG
CCTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAAT
ATGTTTCTTCGATTTGTTCTCTAACAG
Found at i:55683003 original size:78 final size:78
Alignment explanation
Indices: 55682790--55682977 Score: 315
Period size: 78 Copynumber: 2.4 Consensus size: 78
55682780 AAAACATCCT
* *
55682790 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCCCCGTTTAATACAAAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTTTAATACAGAGATGCCAAATCATCTTGG
55682855 ATCTGCTTCAATG
66 ATCTGCTTCAATG
* *
55682868 AAGGTCCA-ATCTGTTATGTCTTCGATCTACTCCCCGTTTAATACAGAGATGCCAAATCATCTTG
1 AAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTTTAATACAGAGATGCCAAATCATCTTG
*
55682932 GATTTGCTTCAATG
65 GATCTGCTTCAATG
55682946 AAGGTCAGATCTGCTATGTCTTCGATCTGCTC
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTC
55682978 TTCGTCGAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
77 2 0.02
78 98 0.97
79 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (78 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTTTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATG
Found at i:55683188 original size:131 final size:131
Alignment explanation
Indices: 55682954--55683239 Score: 464
Period size: 131 Copynumber: 2.2 Consensus size: 131
55682944 TGAAGGTCAG
* * *
55682954 ATCTGCTATGTCTTCGATCTGCTCTTCGTCGAATATGGAGATGCCAAATCTGTTCCTTCGATTTG
1 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTCATTCGATTTG
* * *
55683019 TTCTCTGACAGTACAGATATGTCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGAAA
66 TTCTCTGAAAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGAAA
55683084 A
131 A
*
55683085 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTATTCGATTTG
1 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTCATTCGATTTG
* ** **
55683150 TTCTCTGAAAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
66 TTCTCTGAAAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGAAA
55683215 A
131 A
55683216 ATCTGCTATGTCTTCGATCTGCTC
1 ATCTGCTATGTCTTCGATCTGCTC
55683240 CTTAACAACG
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 143 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (131 bp):
ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTCATTCGATTTG
TTCTCTGAAAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGAAA
A
Found at i:55687670 original size:25 final size:25
Alignment explanation
Indices: 55687636--55687685 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
55687626 TTTTCACCTA
*
55687636 TTTCCCTTCCTCCAGGACTACATTC
1 TTTCCCTTCCACCAGGACTACATTC
* *
55687661 TTTCCCTTCCACTAGGGCTACATTC
1 TTTCCCTTCCACCAGGACTACATTC
55687686 CCTACTGCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.16, C:0.38, G:0.10, T:0.36
Consensus pattern (25 bp):
TTTCCCTTCCACCAGGACTACATTC
Found at i:55688983 original size:5 final size:5
Alignment explanation
Indices: 55688975--55689000 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55688965 CTTTTCTTTG
55688975 ATGTA ATGTA ATGTA ATGTA ATGTA A
1 ATGTA ATGTA ATGTA ATGTA ATGTA A
55689001 ATGCATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (5 bp):
ATGTA
Found at i:55691821 original size:14 final size:15
Alignment explanation
Indices: 55691784--55691821 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
55691774 AAAATCATAA
55691784 TCATATCTAAGATTG
1 TCATATCTAAGATTG
55691799 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
55691816 -CATATC
1 TCATATC
55691822 ATTGAAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
17 15 0.71
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:55691823 original size:19 final size:17
Alignment explanation
Indices: 55691783--55691815 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
55691773 CAAAATCATA
55691783 ATCATATCTAAGATTGT
1 ATCATATCTAAGATTGT
55691800 ATCATATCTAAGATTG
1 ATCATATCTAAGATTG
55691816 CATATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (17 bp):
ATCATATCTAAGATTGT
Found at i:55691980 original size:21 final size:20
Alignment explanation
Indices: 55691942--55691981 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55691932 TTGGACTTCG
**
55691942 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
55691962 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
55691982 TCTGGGCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:55692497 original size:38 final size:38
Alignment explanation
Indices: 55692425--55692497 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
55692415 AAAATACGAT
* * * *
55692425 TTTTAGGGACTGAATCATAAAATTTTGTAAATTTGTGA
1 TTTTAGAGACTAAATCATAAAATATTGCAAATTTGTGA
55692463 TTTTAGAGACTAAATCATAAAA-ATTGCAATATTTG
1 TTTTAGAGACTAAATCATAAAATATTGCAA-ATTTG
55692498 AATTCCACGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 5 0.17
38 25 0.83
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (38 bp):
TTTTAGAGACTAAATCATAAAATATTGCAAATTTGTGA
Found at i:55694015 original size:32 final size:32
Alignment explanation
Indices: 55693978--55694074 Score: 194
Period size: 32 Copynumber: 3.0 Consensus size: 32
55693968 ATTTGTGATG
55693978 AATTAGTAAGAATGATTTTAAATTAAATTTTA
1 AATTAGTAAGAATGATTTTAAATTAAATTTTA
55694010 AATTAGTAAGAATGATTTTAAATTAAATTTTA
1 AATTAGTAAGAATGATTTTAAATTAAATTTTA
55694042 AATTAGTAAGAATGATTTTAAATTAAATTTTA
1 AATTAGTAAGAATGATTTTAAATTAAATTTTA
55694074 A
1 A
55694075 GGATATGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.43
Consensus pattern (32 bp):
AATTAGTAAGAATGATTTTAAATTAAATTTTA
Found at i:55694029 original size:20 final size:20
Alignment explanation
Indices: 55694004--55694066 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
55693994 TTTAAATTAA
55694004 ATTTTAAATTAGTAAGAATG
1 ATTTTAAATTAGTAAGAATG
55694024 ATTTTAAA-T--T---AA--
1 ATTTTAAATTAGTAAGAATG
55694036 ATTTTAAATTAGTAAGAATG
1 ATTTTAAATTAGTAAGAATG
55694056 ATTTTAAATTA
1 ATTTTAAATTA
55694067 AATTTTAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
12 8 0.23
13 1 0.03
14 2 0.06
15 1 0.03
17 1 0.03
18 2 0.06
19 1 0.03
20 19 0.54
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (20 bp):
ATTTTAAATTAGTAAGAATG
Found at i:55699180 original size:25 final size:23
Alignment explanation
Indices: 55699105--55699221 Score: 78
Period size: 25 Copynumber: 4.9 Consensus size: 23
55699095 ATGTGATAAA
*
55699105 AATATAATA-AATAAATAATAAGT
1 AATATAATATAAAAAAT-ATAAGT
** *
55699128 AATGAT-ATATGTTAAAATATATATT
1 AAT-ATAATAT-AAAAAATATA-AGT
*
55699153 AATATGATAATAAAAAATATGAAGT
1 AATATAAT-ATAAAAAATAT-AAGT
*
55699178 AATATAATATAATAAGATATAAGT
1 AATATAATATAA-AAAATATAAGT
*
55699202 AA-ATAATTATAAAATATATA
1 AATATAA-TATAAAAAATATA
55699222 TAATATGTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
23 17 0.23
24 22 0.29
25 33 0.44
26 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (23 bp):
AATATAATATAAAAAATATAAGT
Found at i:55701354 original size:206 final size:205
Alignment explanation
Indices: 55700857--55701508 Score: 909
Period size: 206 Copynumber: 3.2 Consensus size: 205
55700847 GGTCAAATTT
* * *
55700857 GCTACGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGT-GTCAGT
1 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCT-TCTTCAGT
* * * *
55700921 GA-AATCATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCGTCGAATATGGAGACGCCAAACT
65 -ATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACT
* *
55700985 TCGATTTTTTCTCTGACAATACAGAAATGTCAAATCATCTT--A--G----A-CGTAAGCACGTG
129 TCGATTTTTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTGCTTCAGCGTAAGCACGTG
55701041 AAAGCCAAATCA
194 AAAGCCAAATCA
* ** *
55701053 ACTATGTCTTCGATTTGTTCCTTGTGAA-CACAAGAATATCAAATCATCTTGGATCTACTTCAGT
1 GCTATGTCTTCGATTTGTTCCTTGT-AAGCACAAGAATGCCAAATCATCTTGGATCTTCTTCAGT
* *
55701117 ATAAACATTTAAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTT
65 ATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTT
55701182 CGATTTTTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGTG
130 CGATTTTTTCTCTGACAATACAGAGATGCCAAATCATCTTAGA-TTGCTTCAGCGTAAGCACGTG
*
55701247 AAAGCCAAATTA
194 AAAGCCAAATCA
* * * *
55701259 GCTATGTCTTTGATTCGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTCTTCAGTA
1 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTTCTTCAGTA
* ***
55701324 TAAACATCTGAAGGTGGGATCCATTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTTC
66 TAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTTC
* * * *
55701389 AATTTGTTCTCTGACAATACAGAGATACCAAATTATCTTAGATTCGCTTCAGCGTAAGCACGTGA
131 GATTTTTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATT-GCTTCAGCGTAAGCACGTGA
55701454 AAGCCAAATCA
195 AAGCCAAATCA
55701465 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT--CAAATCA
1 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCA
55701509 GCTATGTCTT
Statistics
Matches: 403, Mismatches: 38, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
195 1 0.00
196 149 0.37
197 2 0.00
198 1 0.00
201 1 0.00
204 7 0.02
205 5 0.01
206 237 0.59
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (205 bp):
GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTTCTTCAGTA
TAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTTC
GATTTTTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTGCTTCAGCGTAAGCACGTGAA
AGCCAAATCA
Found at i:55701509 original size:44 final size:44
Alignment explanation
Indices: 55701458--55701545 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
55701448 ACGTGAAAGC
55701458 CAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT
1 CAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT
55701502 CAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT
1 CAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT
55701546 GTCAAACCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (44 bp):
CAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT
Found at i:55701703 original size:250 final size:250
Alignment explanation
Indices: 55701252--55701748 Score: 805
Period size: 250 Copynumber: 2.0 Consensus size: 250
55701242 ACGTGAAAGC
* * * * *
55701252 CAAATTAGCTATGTCTTTGATTCGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTC
1 CAAATCAGCTATGTCTTCGATTCGCTCCTTGTAAGCACAAGAATGCCAAACCATCTTGGATCTGC
* * * *
55701317 TTCAGTATAAACATCTGAAGGTGGGATCCATTATGTATCTGCTCTCCATCGAATATGGAGATGCC
66 TTCAGTATAAACATCTAAAGGTGAGATCCACTATGTATCTGCTCTCCATCGAATATGGAGATACC
* *
55701382 AGACTTCAATTTGTTCTCTGACAATACAGAGATACCAAATTATCTTAGATTCGCTTCAGCGTAAG
131 AGACTTCAATTTGTTCTCTGACAATACAGAGATACCAAATCATCTTAGATTCGCTTCAGCGTAAA
55701447 CACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT
196 CACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT
* * *
55701502 CAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGTCAAACCATCTTGGATCTGC
1 CAAATCAGCTATGTCTTCGATTCGCTCCTTGTAAGCACAAGAATGCCAAACCATCTTGGATCTGC
* ** * *
55701567 TTCAGTATAATCATCTAAAGGTGAGATCTGCTATGTATCTGCTCTTCGTCGAATATGGAGATACC
66 TTCAGTATAAACATCTAAAGGTGAGATCCACTATGTATCTGCTCTCCATCGAATATGGAGATACC
* *
55701632 AGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTCGCTTCAGCGTAAA
131 AGACTTCAATTTGTTCTCTGACAATACAGAGATACCAAATCATCTTAGATTCGCTTCAGCGTAAA
55701697 CACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAG
196 CACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAG
55701749 GATACCAAAC
Statistics
Matches: 226, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
250 226 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (250 bp):
CAAATCAGCTATGTCTTCGATTCGCTCCTTGTAAGCACAAGAATGCCAAACCATCTTGGATCTGC
TTCAGTATAAACATCTAAAGGTGAGATCCACTATGTATCTGCTCTCCATCGAATATGGAGATACC
AGACTTCAATTTGTTCTCTGACAATACAGAGATACCAAATCATCTTAGATTCGCTTCAGCGTAAA
CACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAAT
Found at i:55713501 original size:25 final size:23
Alignment explanation
Indices: 55713426--55713542 Score: 78
Period size: 25 Copynumber: 4.9 Consensus size: 23
55713416 ATGTGATAAA
*
55713426 AATATAATA-AATAAATAATAAGT
1 AATATAATATAAAAAAT-ATAAGT
** *
55713449 AATGAT-ATATGTTAAAATATATATT
1 AAT-ATAATAT-AAAAAATATA-AGT
*
55713474 AATATGATAATAAAAAATATGAAGT
1 AATATAAT-ATAAAAAATAT-AAGT
*
55713499 AATATAATATAATAAGATATAAGT
1 AATATAATATAA-AAAATATAAGT
*
55713523 AA-ATAATTATAAAATATATA
1 AATATAA-TATAAAAAATATA
55713543 TAATATGTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
23 17 0.23
24 22 0.29
25 33 0.44
26 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (23 bp):
AATATAATATAAAAAATATAAGT
Found at i:55721030 original size:25 final size:25
Alignment explanation
Indices: 55720998--55721047 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
55720988 TGGTTTTTTT
55720998 TCTTGCCTTTATATTTTATATACTA
1 TCTTGCCTTTATATTTTATATACTA
55721023 TCTTGCCTTTATATTTTATATACTA
1 TCTTGCCTTTATATTTTATATACTA
55721048 AGCCTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (25 bp):
TCTTGCCTTTATATTTTATATACTA
Found at i:55722579 original size:42 final size:42
Alignment explanation
Indices: 55722481--55722616 Score: 141
Period size: 42 Copynumber: 3.2 Consensus size: 42
55722471 TGATTTTGAA
** *
55722481 TAAGACCACATCTGGGACGTTGGCATTG-ATTTGAGATTTACGTG
1 TAAGACCATGTCTGGGACGTTGGCATCGTATTT--GATTT-CGTG
*
55722525 TAAGACCATGTCTGGGACGTTGGCATCGTATATGATTTCGTG
1 TAAGACCATGTCTGGGACGTTGGCATCGTATTTGATTTCGTG
* * * *
55722567 TAAGACCCTGTCTGGGACAG-TGACATCGATATTTGATTACATG
1 TAAGACCATGTCTGGGAC-GTTGGCATCG-TATTTGATTTCGTG
55722610 TAAGACC
1 TAAGACC
55722617 TCATTTGGGA
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
42 28 0.35
43 24 0.30
44 25 0.31
45 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACGTTGGCATCGTATTTGATTTCGTG
Done.