Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 81 of 85
Found at i:28247126 original size:35 final size:35
Alignment explanation
Indices: 28247059--28247185 Score: 175
Period size: 35 Copynumber: 3.6 Consensus size: 35
28247049 ACTCTCTATT
** *
28247059 TTGGTGTGTTTTGGATGGA-TAGCTCTTTTGAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
28247093 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
* *
28247128 TTGGTGTGTTTCAGATGGATTAACTCTTATAAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
* *
28247163 TCTGGTGTGTTTCGGTTGGATTA
1 T-TGGTGTGTTTCAGATGGATTA
28247186 ATCAATGTAC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
34 17 0.20
35 48 0.57
36 19 0.23
ACGTcount: A:0.18, C:0.10, G:0.29, T:0.43
Consensus pattern (35 bp):
TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
Found at i:28250952 original size:29 final size:29
Alignment explanation
Indices: 28250915--28251202 Score: 265
Period size: 29 Copynumber: 9.9 Consensus size: 29
28250905 AGTGTGCTAA
*
28250915 TGATGGTCGAAACCATCCCTTTTCATATT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* **
28250944 TGACGGTCGTCACCATCCCTTTTCATA-T
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* * *
28250972 TCGATGGCCGAAACCATCCATTTTCATTAAT
1 T-GATGGTCGAAACCATCCCTTTTCA-TAGT
* * * *
28251003 CGGTGGTCGTAACCATCCTTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* **
28251032 TGATGGTTGTCACCATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* * *
28251061 TGATAGTCGAAACTATCCCTTTTCATAAT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* ** * *
28251090 CGATAATTGAAACTATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* **
28251119 CGATGGTCGTCACCATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
** *
28251148 TGATGGTCGTCACGATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
**
28251177 TGATGGTC-ATCGCCATCCCTTTTCAT
1 TGATGGTCGA-AACCATCCCTTTTCAT
28251203 TGATCGATGA
Statistics
Matches: 215, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
28 2 0.01
29 190 0.88
30 22 0.10
31 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (29 bp):
TGATGGTCGAAACCATCCCTTTTCATAGT
Found at i:28251072 original size:88 final size:87
Alignment explanation
Indices: 28250912--28251202 Score: 327
Period size: 87 Copynumber: 3.3 Consensus size: 87
28250902 CGAAGTGTGC
* *
28250912 TAAT-GATGGTCGAAACCATCCCTTTTCATATTTGACGGTCGTCACCATCCCTTTTCATA-TTCG
1 TAATCGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTT-G
*
28250975 ATGGCCGAAACCATCCATTTTCA
65 ATGGTCGAAACCATCCATTTTCA
* * * *
28250998 TTAATCGGTGGTCGTAACCATCCTTTTTCATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTG
1 -TAATCGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTTG
* * *
28251063 ATAGTCGAAACTATCCCTTTTCA
65 ATGGTCGAAACCATCCATTTTCA
** * * *
28251086 TAATCGATAATTGAAACTATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGTTGA
1 TAATCGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTTGA
** * *
28251151 TGGTCGTCACGATCCCTTTTCA
66 TGGTCGAAACCATCCATTTTCA
* * **
28251173 TAGTTGATGGTC-ATCGCCATCCCTTTTCAT
1 TAATCGATGGTCGA-AACCATCCCTTTTCAT
28251203 TGATCGATGA
Statistics
Matches: 170, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
86 1 0.01
87 98 0.58
88 69 0.41
89 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (87 bp):
TAATCGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTTGA
TGGTCGAAACCATCCATTTTCA
Found at i:28251166 original size:58 final size:58
Alignment explanation
Indices: 28250915--28251202 Score: 299
Period size: 58 Copynumber: 4.9 Consensus size: 58
28250905 AGTGTGCTAA
* *
28250915 TGATGGTCGAAACCATCCCTTTTCATATTTGACGGTCGTCACCATCCCTTTTCATA-T
1 TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
* * * * * * *
28250972 TCGATGGCCGAAACCATCCATTTTCATTAATCGGTGGTCGTAACCATCCTTTTTCATAGT
1 T-GATGGTCGAAACCATCCCTTTTCA-TAGTTGATGGTCGTCACCATCCCTTTTCATAGT
* ** * ** * *
28251032 TGATGGTTGTCACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAAT
1 TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
* ** * * *
28251090 CGATAATTGAAACTATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
** * * *
28251148 TGATGGTCGTCACGATCCCTTTTCATAGTTGATGGTCATCGCCATCCCTTTTCAT
1 TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCAT
28251203 TGATCGATGA
Statistics
Matches: 185, Mismatches: 43, Indels: 5
0.79 0.18 0.02
Matches are distributed among these distances:
57 1 0.01
58 138 0.75
59 44 0.24
60 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (58 bp):
TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
Found at i:28254373 original size:19 final size:19
Alignment explanation
Indices: 28254349--28254394 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28254339 TCCCTCAACA
28254349 CTCATTTCTCATTCAT-TCT
1 CTCATTTCTCATTC-TCTCT
*
28254368 CTCATTTGTCATTCTCTCT
1 CTCATTTCTCATTCTCTCT
*
28254387 TTCATTTC
1 CTCATTTC
28254395 CCTTTTCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.13, C:0.30, G:0.02, T:0.54
Consensus pattern (19 bp):
CTCATTTCTCATTCTCTCT
Found at i:28263868 original size:18 final size:16
Alignment explanation
Indices: 28263845--28263880 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
28263835 TGATTTAAAA
28263845 AATAAAAAGTAAATAAGT
1 AATAAAAA-TAAA-AAGT
28263863 AATAAAAATAAAAAGT
1 AATAAAAATAAAAAGT
28263879 AA
1 AA
28263881 AAATTCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (16 bp):
AATAAAAATAAAAAGT
Found at i:28266047 original size:3 final size:3
Alignment explanation
Indices: 28266039--28266070 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28266029 ACATATGCTT
28266039 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
28266071 TTTTGAGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:28269725 original size:14 final size:14
Alignment explanation
Indices: 28269708--28269735 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28269698 AATTGAATAA
28269708 AGTAAAATATTGGG
1 AGTAAAATATTGGG
28269722 AGTAAAATATTGGG
1 AGTAAAATATTGGG
28269736 GGCAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (14 bp):
AGTAAAATATTGGG
Found at i:28270955 original size:20 final size:20
Alignment explanation
Indices: 28270930--28270978 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
28270920 AAGTTTATAT
28270930 TAAGTAAATGGAATCA-AAAG
1 TAAGTAAATGGAAT-AGAAAG
28270950 TAAGTAAATGGAATAGAAAG
1 TAAGTAAATGGAATAGAAAG
28270970 TAAGTAAAT
1 TAAGTAAAT
28270979 AGAGTGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGGAATAGAAAG
Found at i:28275256 original size:12 final size:12
Alignment explanation
Indices: 28275230--28275268 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28275220 CGCTGCTTCT
* *
28275230 TTACTTACTTTC
1 TTACTTGCTTAC
*
28275242 TTACTTGGTTAC
1 TTACTTGCTTAC
28275254 TTACTTGCTTAC
1 TTACTTGCTTAC
28275266 TTA
1 TTA
28275269 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.54
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:28275580 original size:50 final size:49
Alignment explanation
Indices: 28275460--28275631 Score: 145
Period size: 50 Copynumber: 3.5 Consensus size: 49
28275450 CATGCCAAAA
* * * *
28275460 CCATGTCCCAGACATGGTCTTACATGGGATGTTTTCGGTA--CTGCCAATG
1 CCATGTCCTAGACATGGTCTTACATGGGA-GTTCTC-ATATGGTGCCAATG
* * *
28275509 CCATAT-CTCAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATG
1 CCATGTCCT-AGACATGGTCTTACATGGGAGTTCTCATA-TGGTGCCAATG
** * *
28275559 CCATGTCCTAGACATGGTCTTACGA-GGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCTAGACATGGTCTTAC-ATGGGAGTTCTCATAT-GGTGCCAATG
* *
28275609 CCATGTCCAAGACAAGGTCTTAC
1 CCATGTCCTAGACATGGTCTTAC
28275632 GTGTGACCTC
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
47 2 0.02
48 6 0.06
49 25 0.25
50 64 0.64
51 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (49 bp):
CCATGTCCTAGACATGGTCTTACATGGGAGTTCTCATATGGTGCCAATG
Found at i:28275632 original size:50 final size:50
Alignment explanation
Indices: 28275540--28275646 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
28275530 ACATGGGAGT
* * * * *
28275540 TCTCATATTGGTGCCCATGCCATGTCCTAGACATGGTCTTACGAGGGACC
1 TCTCATATCGGTGCCAACGCCATGTCCAAGACAAGGTCTTACGAGGGACC
* * *
28275590 TCTCATCTCGGTGCCAACGCCATGTCCAAGACAAGGTCTTACGTGTGACC
1 TCTCATATCGGTGCCAACGCCATGTCCAAGACAAGGTCTTACGAGGGACC
28275640 TCTCATA
1 TCTCATA
28275647 ACCTCAATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TCTCATATCGGTGCCAACGCCATGTCCAAGACAAGGTCTTACGAGGGACC
Found at i:28284169 original size:16 final size:18
Alignment explanation
Indices: 28284136--28284169 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28284126 GTTTAAAAAC
28284136 TAAAAATAGAATAAGTAA
1 TAAAAATAGAATAAGTAA
28284154 TAAAAATA-AA-AAGTAA
1 TAAAAATAGAATAAGTAA
28284170 AAATTCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
TAAAAATAGAATAAGTAA
Found at i:28287147 original size:14 final size:15
Alignment explanation
Indices: 28287123--28287151 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28287113 AAAGAGGCAA
28287123 GAAGAAGGAAAAGAG
1 GAAGAAGGAAAAGAG
28287138 GAAG-AGGAAAAGAG
1 GAAGAAGGAAAAGAG
28287152 AACAAAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAAAAGAG
Found at i:28293663 original size:12 final size:12
Alignment explanation
Indices: 28293646--28293671 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28293636 CTCTGTGGGA
28293646 TCTTTTTCTTCT
1 TCTTTTTCTTCT
28293658 TCTTTTTCTTCT
1 TCTTTTTCTTCT
28293670 TC
1 TC
28293672 GGGATCCTTC
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:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTTTTCTTCT
Found at i:28318732 original size:23 final size:23
Alignment explanation
Indices: 28318703--28318752 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
28318693 CTATTCTCAT
28318703 TTCTTCATACGTTTATAGTTTCC
1 TTCTTCATACGTTTATAGTTTCC
**
28318726 TTCTTCATATTTTTATAGTTTCC
1 TTCTTCATACGTTTATAGTTTCC
28318749 TTCT
1 TTCT
28318753 ATTTCAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.06, T:0.58
Consensus pattern (23 bp):
TTCTTCATACGTTTATAGTTTCC
Found at i:28319355 original size:13 final size:13
Alignment explanation
Indices: 28319337--28319361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28319327 ATTATTAATA
28319337 TTATTTTGTGTGT
1 TTATTTTGTGTGT
28319350 TTATTTTGTGTG
1 TTATTTTGTGTG
28319362 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:28320118 original size:17 final size:17
Alignment explanation
Indices: 28320085--28320118 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28320075 TTGTGTTTTG
*
28320085 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
28320102 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
28320119 GTGAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:28320362 original size:21 final size:21
Alignment explanation
Indices: 28320336--28320377 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28320326 AGAATATATA
*
28320336 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTAAATTT
28320357 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCTAAATTT
28320378 GATTTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (21 bp):
TATGTTCTATAAGCTAAATTT
Found at i:28335986 original size:28 final size:28
Alignment explanation
Indices: 28335946--28336003 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
28335936 GAGTTTAAAT
*
28335946 GATAGAAAGACTACTGAATCAATACCGA
1 GATAGAAAGACTACTGAATCAACACCGA
*
28335974 GATAGAAAGACTACTGAATCCACACCGA
1 GATAGAAAGACTACTGAATCAACACCGA
28336002 GA
1 GA
28336004 AAATGTGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.16
Consensus pattern (28 bp):
GATAGAAAGACTACTGAATCAACACCGA
Found at i:28337884 original size:23 final size:23
Alignment explanation
Indices: 28337854--28337965 Score: 121
Period size: 23 Copynumber: 5.1 Consensus size: 23
28337844 AGTGCCACAT
*
28337854 TGAAATGTAGCTGAAGCTACCAC
1 TGAAATGTAGCCGAAGCTACCAC
* *
28337877 TGATATGTAGTC---G-TA--AC
1 TGAAATGTAGCCGAAGCTACCAC
28337894 TGAAATGTAGCC-ATAGCTACCAC
1 TGAAATGTAGCCGA-AGCTACCAC
* *
28337917 TAAAATGTAGCCGAAGCTACCGC
1 TGAAATGTAGCCGAAGCTACCAC
28337940 TGAAATGTAGCCGAAGCTACCAC
1 TGAAATGTAGCCGAAGCTACCAC
28337963 TGA
1 TGA
28337966 TCAATAACAC
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
17 12 0.16
19 2 0.03
20 2 0.03
21 2 0.03
23 54 0.74
24 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (23 bp):
TGAAATGTAGCCGAAGCTACCAC
Found at i:28347487 original size:22 final size:22
Alignment explanation
Indices: 28347459--28347505 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
28347449 ACAAATCCTA
28347459 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
*
28347481 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
28347503 TCT
1 TCT
28347506 TAAACTCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:28349377 original size:21 final size:21
Alignment explanation
Indices: 28349351--28349392 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28349341 CAGACGCCGA
*
28349351 ACCGGAAGAACAACAATCACC
1 ACCGGAAGAACAACAACCACC
*
28349372 ACCGGAAGAAGAACAACCACC
1 ACCGGAAGAACAACAACCACC
28349393 GCCAGAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.33, G:0.17, T:0.02
Consensus pattern (21 bp):
ACCGGAAGAACAACAACCACC
Found at i:28349400 original size:21 final size:21
Alignment explanation
Indices: 28349355--28349400 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
28349345 CGCCGAACCG
* *
28349355 GAAGAACAACAATCACCACCG
1 GAAGAACAACAACCACCACCA
* *
28349376 GAAGAAGAACAACCACCGCCA
1 GAAGAACAACAACCACCACCA
28349397 GAAG
1 GAAG
28349401 CTAGAGGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.30, G:0.20, T:0.02
Consensus pattern (21 bp):
GAAGAACAACAACCACCACCA
Found at i:28349663 original size:29 final size:29
Alignment explanation
Indices: 28349628--28349949 Score: 566
Period size: 29 Copynumber: 11.3 Consensus size: 29
28349618 TTTATTTCAT
28349628 ACCCTAACCCTAACCTAATTTAATT--AA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349655 A----AACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349680 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349709 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349738 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349767 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349796 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349825 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349854 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
28349883 ACCCTAACCTTAACCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
28349912 ACCCTAACACTAACCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
28349941 ACCCTAACC
1 ACCCTAACC
28349950 TAATTTATTT
Statistics
Matches: 284, Mismatches: 5, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
23 20 0.07
25 3 0.01
27 1 0.00
29 260 0.92
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.28
Consensus pattern (29 bp):
ACCCTAACCCTAACCTAATTTAATTAAAA
Found at i:28349686 original size:18 final size:20
Alignment explanation
Indices: 28349640--28349682 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
28349630 CCTAACCCTA
28349640 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
28349661 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
28349683 CTAACCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:28350032 original size:56 final size:56
Alignment explanation
Indices: 28349972--28350096 Score: 180
Period size: 56 Copynumber: 2.2 Consensus size: 56
28349962 AAACCATAAC
* * * * *
28349972 ATAATTTTACCTAATTTGGT-AATCTTACTAACCATTAACACACCTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAAAT-TTACTAACCATTAACAAAACTTATTGGGCTTA
*
28350028 ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTA
1 ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAACTTATTGGGCTTA
28350084 ATAATTTTACATA
1 ATAATTTTACATA
28350097 GTTTTACATA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
56 59 0.95
57 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAACTTATTGGGCTTA
Found at i:28355718 original size:26 final size:28
Alignment explanation
Indices: 28355689--28355752 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 28
28355679 TATTATTATT
28355689 ATATATAATATTTTT-TAT-ATATGTAC
1 ATATATAATATTTTTATATAATATGTAC
*
28355715 --ATATAATATTTTTAGTATACATATGTAT
1 ATATATAATATTTTTA-TATA-ATATGTAC
28355743 ATATATAATA
1 ATATATAATA
28355753 ATATATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 13 0.42
26 3 0.10
28 7 0.23
30 8 0.26
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (28 bp):
ATATATAATATTTTTATATAATATGTAC
Found at i:28362950 original size:45 final size:45
Alignment explanation
Indices: 28362877--28363040 Score: 122
Period size: 45 Copynumber: 3.7 Consensus size: 45
28362867 AGACACCAAC
* * *
28362877 CTTGCCTTCTTATACTGACAGCGGAGCAGATTGAAGATAGTAGAT
1 CTTGCCTTCCTATACTGACGGCGAAGCAGATTGAAGATAGTAGAT
* * * * *
28362922 CTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACA-TA-AGC
1 CTTGCCTTCCTATACTGACGGCGAAGCAGATTGAAGATAGTAGA-T
* * * ** * **
28362966 CATGCCTCCCTCTGTTGTA-GTG-G-AGTAGGCTGAAGATAGTAGAT
1 CTTGCCTTCCTATACTG-ACG-GCGAAGCAGATTGAAGATAGTAGAT
28363010 CTTGCCTTCCTATACTGACGGCGAAGCAGAT
1 CTTGCCTTCCTATACTGACGGCGAAGCAGAT
28363041 CAAAGACACA
Statistics
Matches: 84, Mismatches: 27, Indels: 16
0.66 0.21 0.13
Matches are distributed among these distances:
43 13 0.15
44 32 0.38
45 39 0.46
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (45 bp):
CTTGCCTTCCTATACTGACGGCGAAGCAGATTGAAGATAGTAGAT
Found at i:28363027 original size:88 final size:87
Alignment explanation
Indices: 28362899--28363309 Score: 534
Period size: 88 Copynumber: 4.7 Consensus size: 87
28362889 TACTGACAGC
* * * *
28362899 GGAGCAGATTGAAGATAGTAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACATAA
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTA-TGACAGTGAAGCAGATCGAAGACACAA
* *
28362964 GCCATGCCTCCCTCTGTTGTAGT
65 GCCTTGCCTCCCTCGGTTGTAGT
* * * * * * *
28362987 GGAGTAGGCTGAAGATAGTAGATCTTGCCTTCCTATACTGACGGCGAAGCAGATCAAAGACACAA
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTA-TGACAGTGAAGCAGATCGAAGACACAA
*
28363052 GCCTTGCCTCCCTCGATTGTAGT
65 GCCTTGCCTCCCTCGGTTGTAGT
* ** *
28363075 GGAGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTACATCGACAGTGAAGCAAATCGAAGACACAA
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTAT-GACAGTGAAGCAGATCGAAGACACAA
* * *
28363140 GTCTTGCCTCCTTCGGTTGTAAT
65 GCCTTGCCTCCCTCGGTTGTAGT
*
28363163 GGAGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTGTATCGACAGTGAAGCAGATCGAAGACACAA
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTAT-GACAGTGAAGCAGATCGAAGACACAA
*
28363228 ACCTTGCCTCCCTCGGTTGTAGT
65 GCCTTGCCTCCCTCGGTTGTAGT
* * * *
28363251 GGAGTAGGTTAAAGATAGTAGGTCTTGCCTTCCTGCATTGACAGTGAAACAGATCGAAG
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTA-TGACAGTGAAGCAGATCGAAG
28363310 CGAATGGTCC
Statistics
Matches: 286, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
87 1 0.00
88 284 0.99
89 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (87 bp):
GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTATGACAGTGAAGCAGATCGAAGACACAAG
CCTTGCCTCCCTCGGTTGTAGT
Found at i:28363102 original size:44 final size:44
Alignment explanation
Indices: 28363054--28363280 Score: 156
Period size: 44 Copynumber: 5.2 Consensus size: 44
28363044 AGACACAAGC
28363054 CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
1 CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
* * * * ** * * *
28363098 CTTGCCTTCCTAC-ATCGACAGTGAAGCAAATCGAAGACA-CAAGT
1 CTTGCCTCCCT-CGATTG-TAGTGGAGCAGGTTGAAGATAGCAGGT
* * *
28363142 CTTGCCTCCTTCGGTTGTAATGGAGCAGGTTGAAGATAGCAGGT
1 CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
* * * * * * * ***
28363186 CTTGCCTTCCT-GTATCGACAGTGAAGCAGATCGAAGACA-CAAAC
1 CTTGCCTCCCTCG-ATTG-TAGTGGAGCAGGTTGAAGATAGCAGGT
* * * *
28363230 CTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTAAAGATAGTAGGT
1 CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
28363274 CTTGCCT
1 CTTGCCT
28363281 TCCTGCATTG
Statistics
Matches: 127, Mismatches: 48, Indels: 16
0.66 0.25 0.08
Matches are distributed among these distances:
43 30 0.24
44 65 0.51
45 32 0.25
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (44 bp):
CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
Found at i:28363150 original size:176 final size:175
Alignment explanation
Indices: 28362849--28363309 Score: 539
Period size: 176 Copynumber: 2.6 Consensus size: 175
28362839 TTCCTGTACT
* * * * * ** * * * *
28362849 GACAGCGAAACAGATCGAAGACACCAACCTTGCCTTCTTATACTGACAGCGGAGCAGATTGAAGA
1 GACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCCCTCGATTG-TAGTGGAGCAGGTTGAAGA
* * *
28362914 TAGTAGATCTTGCCTTCCTGTAC-TGACGGTGAAGCAGATCGAAGACATAAGCCATGCCTCCCTC
65 TAGTAGGTCTTGCCTTCC--TACATGACAGTGAAGCAGATCGAAGACACAAGCCATGCCTCCCTC
* * * *
28362978 TGTTGTAGTGGAGTAGGCTGAAGATAGTAGATCTTGCCTTCCTATA-C
128 GGTTGTAATGGAGCAGGCTGAAGATAGCAGATCTTGCCTTCCTATATC
* *
28363025 TGACGGCGAAGCAGATCAAAGACACAAGCCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGA
1 -GACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGA
* * * * *
28363090 TAGCAGGTCTTGCCTTCCTACATCGACAGTGAAGCAAATCGAAGACACAAGTCTTGCCTCCTTCG
65 TAGTAGGTCTTGCCTTCCTACAT-GACAGTGAAGCAGATCGAAGACACAAGCCATGCCTCCCTCG
* * *
28363155 GTTGTAATGGAGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTGTATC
129 GTTGTAATGGAGCAGGCTGAAGATAGCAGATCTTGCCTTCCTATATC
* * * * *
28363202 GACAGTGAAGCAGATCGAAGACACAAACCTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTAAAGAT
1 GACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGAT
* *
28363267 AGTAGGTCTTGCCTTCCTGCATTGACAGTGAAACAGATCGAAG
66 AGTAGGTCTTGCCTTCCTACA-TGACAGTGAAGCAGATCGAAG
28363310 CGAATGGTCC
Statistics
Matches: 241, Mismatches: 39, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
174 3 0.01
175 1 0.00
176 200 0.83
177 37 0.15
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (175 bp):
GACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGAT
AGTAGGTCTTGCCTTCCTACATGACAGTGAAGCAGATCGAAGACACAAGCCATGCCTCCCTCGGT
TGTAATGGAGCAGGCTGAAGATAGCAGATCTTGCCTTCCTATATC
Found at i:28364832 original size:23 final size:24
Alignment explanation
Indices: 28364806--28364861 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
28364796 ATATAGATCC
28364806 TTTTATTTTATTATAAG-A-TATTA
1 TTTTATTTTATT-TAAGTATTATTA
* *
28364829 TTTTATGTT-TTTAGGTATTATTA
1 TTTTATTTTATTTAAGTATTATTA
28364852 TTTTATTTTA
1 TTTTATTTTA
28364862 CAAGGATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 3 0.11
23 21 0.78
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (24 bp):
TTTTATTTTATTTAAGTATTATTA
Found at i:28367995 original size:2 final size:2
Alignment explanation
Indices: 28367988--28368016 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28367978 GCTCACCGCC
28367988 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
28368017 CATGTAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:28372740 original size:16 final size:16
Alignment explanation
Indices: 28372719--28372749 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28372709 CACCCAAGAC
28372719 ACACCTCAACCTTATA
1 ACACCTCAACCTTATA
*
28372735 ACACCTCAATCTTAT
1 ACACCTCAACCTTAT
28372750 CTGATTAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
ACACCTCAACCTTATA
Found at i:28386400 original size:23 final size:23
Alignment explanation
Indices: 28386352--28386400 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28386342 TTGTTCTTAT
* *
28386352 TTTGTTGATTTGTGTATAATTTA
1 TTTGTTGATTTGTATATAATTGA
**
28386375 TTTGTTGATTTGTATATTGTTGA
1 TTTGTTGATTTGTATATAATTGA
28386398 TTT
1 TTT
28386401 CAAATCTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63
Consensus pattern (23 bp):
TTTGTTGATTTGTATATAATTGA
Found at i:28386660 original size:9 final size:9
Alignment explanation
Indices: 28386640--28386677 Score: 67
Period size: 9 Copynumber: 4.1 Consensus size: 9
28386630 AATATGTATA
28386640 TTTATATTTT
1 TTTAT-TTTT
28386650 TTTATTTTT
1 TTTATTTTT
28386659 TTTATTTTT
1 TTTATTTTT
28386668 TTTATTTTT
1 TTTATTTTT
28386677 T
1 T
28386678 ATAATTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 23 0.82
10 5 0.18
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTATTTTT
Found at i:28386718 original size:23 final size:22
Alignment explanation
Indices: 28386688--28386731 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
28386678 ATAATTCATA
*
28386688 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
28386711 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
28386732 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:28396245 original size:2 final size:2
Alignment explanation
Indices: 28396238--28396271 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28396228 AACTAGGATT
28396238 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28396272 AGTGTACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:28398662 original size:24 final size:24
Alignment explanation
Indices: 28398626--28398672 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28398616 AGTTGAATCA
*
28398626 TCTTTTTATTTTTGTATTTTTCTC
1 TCTTTTTATTTTTATATTTTTCTC
28398650 TCTTGTTTA-TTTTATATTTTTCT
1 TCTT-TTTATTTTTATATTTTTCT
28398673 TTGTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (24 bp):
TCTTTTTATTTTTATATTTTTCTC
Found at i:28403585 original size:37 final size:37
Alignment explanation
Indices: 28403544--28403619 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
28403534 CTCCAAAACC
*
28403544 ATCTCCACTCCAATTCCCCATAACACGCCAAATTACA
1 ATCTCCACTCCAATTCCACATAACACGCCAAATTACA
28403581 ATCTCCACTCCAATTCCACATAACACGCCAAATTACA
1 ATCTCCACTCCAATTCCACATAACACGCCAAATTACA
28403618 AT
1 AT
28403620 TGTACTCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.38, G:0.03, T:0.22
Consensus pattern (37 bp):
ATCTCCACTCCAATTCCACATAACACGCCAAATTACA
Found at i:28406445 original size:2 final size:2
Alignment explanation
Indices: 28406438--28406472 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28406428 ATAAATTGTA
*
28406438 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28406473 AAGNNNNNNN
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:28407390 original size:79 final size:80
Alignment explanation
Indices: 28407299--28407458 Score: 279
Period size: 79 Copynumber: 2.0 Consensus size: 80
28407289 ATTGTATCTC
* *
28407299 TCTTATTTTATTATTAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGC-CTCTGTTT
1 TCTTATTTTATTATTAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGCAC-CTATGT
28407363 TACTG-TATTTAAGTG
65 TACTGTTATTTAAGTG
28407378 TCTTATTTTATTATTAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGCACCTATGTT
1 TCTTATTTTATTATTAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGCACCTATGTT
28407443 ACTGTTATTTAAGTG
66 ACTGTTATTTAAGTG
28407458 T
1 T
28407459 AAAGATTTTT
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
79 65 0.84
80 12 0.16
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (80 bp):
TCTTATTTTATTATTAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGCACCTATGTT
ACTGTTATTTAAGTG
Found at i:28407476 original size:79 final size:79
Alignment explanation
Indices: 28407303--28407476 Score: 237
Period size: 79 Copynumber: 2.2 Consensus size: 79
28407293 TATCTCTCTT
* * *
28407303 ATTTTATTATTAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGCCTCTGTTTTACTG
1 ATTTTATTATAAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGCCTCTATGTTACTG
***
28407368 TATTTAAGTGTCTT
66 TATTTAAGTGTAAG
*
28407382 ATTTTATTATTAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGCAC-CTATGTTACT
1 ATTTTATTATAAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGC-CTCTATGTTACT
28407446 GTTATTTAAGTGTAAAG
65 G-TATTTAAGTGT-AAG
28407463 ATTTT-TT-TAAATTT
1 ATTTTATTATAAATTT
28407477 ATTTTCAATT
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
79 67 0.78
80 14 0.16
81 5 0.06
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (79 bp):
ATTTTATTATAAATTTTGCTACTATTTTAGAAATATTTATTTGTTAAGTTGCCTCTATGTTACTG
TATTTAAGTGTAAG
Found at i:28409203 original size:20 final size:21
Alignment explanation
Indices: 28409178--28409224 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
28409168 AAATCTGCCA
* *
28409178 TCAAATCT-CCTTCCAGCTTC
1 TCAAATCTGCCATCCAACTTC
28409198 TCAAATCTGCCATCCAACTTC
1 TCAAATCTGCCATCCAACTTC
28409219 TCAAAT
1 TCAAAT
28409225 AGCTACTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (21 bp):
TCAAATCTGCCATCCAACTTC
Found at i:28409209 original size:32 final size:34
Alignment explanation
Indices: 28409144--28409211 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 34
28409134 ATCTATTTCC
28409144 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
1 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
* *
28409178 TCAAATCT-CCTTCCAGC-TTCTCAAATCTGCCA
1 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
28409210 TC
1 TC
28409212 CAACTTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 16 0.50
33 8 0.25
34 8 0.25
ACGTcount: A:0.26, C:0.37, G:0.04, T:0.32
Consensus pattern (34 bp):
TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
Found at i:28409873 original size:83 final size:83
Alignment explanation
Indices: 28409783--28410046 Score: 257
Period size: 83 Copynumber: 3.1 Consensus size: 83
28409773 GTGGTGATAG
28409783 TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
1 TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
28409848 TAATGTTGTGAATTTTCC
66 TAATGTTGTGAATTTTCC
* ** * * * * * * * *
28409866 TGGCGTTTT-TATGTATGTGCCGTACACCGCTAGTGTTAAGGTA-TTTGCAGCGTTTTTCTCTTA
1 TGGCGTTTTCT-GGTAAAT--CG----CCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTA
* * ** **
28409929 GCGCTGCT-ATCGGTTGGTG-GTGATAG
59 GCGCCGCTAAT--GTT-GTGAATTTTCC
28409955 TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
1 TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
28410020 TAATGTTGTGAATTTTCC
66 TAATGTTGTGAATTTTCC
28410038 TGGCGTTTT
1 TGGCGTTTT
28410047 TATGTATGTG
Statistics
Matches: 133, Mismatches: 34, Indels: 28
0.68 0.17 0.14
Matches are distributed among these distances:
82 4 0.03
83 41 0.31
84 22 0.17
85 4 0.03
87 4 0.03
88 22 0.17
89 32 0.24
90 4 0.03
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (83 bp):
TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
TAATGTTGTGAATTTTCC
Found at i:28409919 original size:172 final size:172
Alignment explanation
Indices: 28409718--28410060 Score: 686
Period size: 172 Copynumber: 2.0 Consensus size: 172
28409708 TTTGGTCAAT
28409718 CACCGCTAGTGTTAAGGTATTTGCAGCGTTTTTCTCTTAGCGCTGCTATCGGTTGGTGGTGATAG
1 CACCGCTAGTGTTAAGGTATTTGCAGCGTTTTTCTCTTAGCGCTGCTATCGGTTGGTGGTGATAG
28409783 TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
66 TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
28409848 TAATGTTGTGAATTTTCCTGGCGTTTTTATGTATGTGCCGTA
131 TAATGTTGTGAATTTTCCTGGCGTTTTTATGTATGTGCCGTA
28409890 CACCGCTAGTGTTAAGGTATTTGCAGCGTTTTTCTCTTAGCGCTGCTATCGGTTGGTGGTGATAG
1 CACCGCTAGTGTTAAGGTATTTGCAGCGTTTTTCTCTTAGCGCTGCTATCGGTTGGTGGTGATAG
28409955 TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
66 TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
28410020 TAATGTTGTGAATTTTCCTGGCGTTTTTATGTATGTGCCGT
131 TAATGTTGTGAATTTTCCTGGCGTTTTTATGTATGTGCCGT
28410061 TATTGGTTGG
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 171 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (172 bp):
CACCGCTAGTGTTAAGGTATTTGCAGCGTTTTTCTCTTAGCGCTGCTATCGGTTGGTGGTGATAG
TGGCGTTTTCTGGTAAATCGCCACTAATATTAAGGTACTTAGCGGCGTTTCTATCCTAGCGCCGC
TAATGTTGTGAATTTTCCTGGCGTTTTTATGTATGTGCCGTA
Found at i:28410162 original size:84 final size:84
Alignment explanation
Indices: 28410056--28410213 Score: 266
Period size: 84 Copynumber: 1.9 Consensus size: 84
28410046 TTATGTATGT
*
28410056 GCCGTTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATG-T-AGGTATTTA
1 GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTT-
28410119 GAGCGGCGTTTCTATCCTAGC
65 -AGCGGCGTTTCTATCCTAGC
*
28410140 GCCGCTATTGGTTGGGGTTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
28410205 GCGGCGTTT
66 GCGGCGTTT
28410214 GGTTTTAAAG
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
84 61 0.87
85 1 0.01
86 8 0.11
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (84 bp):
GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
GCGGCGTTTCTATCCTAGC
Found at i:28410237 original size:84 final size:83
Alignment explanation
Indices: 28410056--28410239 Score: 237
Period size: 84 Copynumber: 2.2 Consensus size: 83
28410046 TTATGTATGT
* *
28410056 GCCGTTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTAGGTATTTAGA
1 GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTAGGTATTTA-A
**
28410121 GCGGCGTTTCTATCCTAGC
65 GCGGCGTTTCTATCAAAGC
* *
28410140 GCCGCTATTGGTTGGGGTTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTT-
1 GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATG-T-AGGTATTTA
* * *
28410204 AGCGGCGTTTGGTTTTAAAGC
64 AGCGGCGTTT-CTATCAAAGC
28410225 GCCGCTA-AGGTTGGG
1 GCCGCTATAGGTTGGG
28410240 TTTTTTGCGG
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
84 68 0.76
85 13 0.15
86 8 0.09
ACGTcount: A:0.17, C:0.16, G:0.33, T:0.34
Consensus pattern (83 bp):
GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTAGGTATTTAAG
CGGCGTTTCTATCAAAGC
Found at i:28413132 original size:20 final size:21
Alignment explanation
Indices: 28413107--28413153 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
28413097 AAATCTGCCA
* *
28413107 TCAAATCT-CCTTCCAGCTTC
1 TCAAATCTGCCATCCAACTTC
28413127 TCAAATCTGCCATCCAACTTC
1 TCAAATCTGCCATCCAACTTC
28413148 TCAAAT
1 TCAAAT
28413154 AGCTACTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (21 bp):
TCAAATCTGCCATCCAACTTC
Found at i:28413138 original size:32 final size:34
Alignment explanation
Indices: 28413073--28413140 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 34
28413063 ATCTATTTCC
28413073 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
1 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
* *
28413107 TCAAATCT-CCTTCCAGC-TTCTCAAATCTGCCA
1 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
28413139 TC
1 TC
28413141 CAACTTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 16 0.50
33 8 0.25
34 8 0.25
ACGTcount: A:0.26, C:0.37, G:0.04, T:0.32
Consensus pattern (34 bp):
TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
Found at i:28413918 original size:84 final size:84
Alignment explanation
Indices: 28413812--28413969 Score: 289
Period size: 84 Copynumber: 1.9 Consensus size: 84
28413802 TTATGTATGT
*
28413812 GCCGTTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
*
28413877 GCGGCGTTTCTATCCTAGC
66 GCAGCGTTTCTATCCTAGC
*
28413896 GCCGCTATTGGTTGGGGTTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
28413961 GCAGCGTTT
66 GCAGCGTTT
28413970 GGTTTTAAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.17, C:0.16, G:0.31, T:0.36
Consensus pattern (84 bp):
GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
GCAGCGTTTCTATCCTAGC
Found at i:28413993 original size:84 final size:84
Alignment explanation
Indices: 28413812--28413995 Score: 262
Period size: 84 Copynumber: 2.2 Consensus size: 84
28413802 TTATGTATGT
* *
28413812 GCCGTTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
* **
28413877 GCGGCGTTTCTATCCTAGC
66 GCAGCGTTTCTATCAAAGC
* *
28413896 GCCGCTATTGGTTGGGGTTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
* * *
28413961 GCAGCGTTTGGTTTTAAAGC
66 GCAGCGTTT-CTATCAAAGC
28413981 GCCGCTA-AGGTTGGG
1 GCCGCTATAGGTTGGG
28413996 TTTTTTGCGG
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 78 0.87
85 12 0.13
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (84 bp):
GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
GCAGCGTTTCTATCAAAGC
Found at i:28414823 original size:21 final size:21
Alignment explanation
Indices: 28414781--28414824 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28414771 GTATGGATTA
* *
28414781 GGGTTTGGGATTAAGGTTTAG
1 GGGTTGGGGATTAAGGTCTAG
* *
28414802 GGGTTGGGGGTTAGGGTCTAG
1 GGGTTGGGGATTAAGGTCTAG
28414823 GG
1 GG
28414825 TTACGGTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.52, T:0.32
Consensus pattern (21 bp):
GGGTTGGGGATTAAGGTCTAG
Found at i:28414825 original size:13 final size:13
Alignment explanation
Indices: 28414809--28414843 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
28414799 TAGGGGTTGG
28414809 GGGTTAGGGTCTA
1 GGGTTAGGGTCTA
*
28414822 GGGTTACGGTCTA
1 GGGTTAGGGTCTA
28414835 GGGTTAGGG
1 GGGTTAGGG
28414844 GTTAGGGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.09, G:0.49, T:0.29
Consensus pattern (13 bp):
GGGTTAGGGTCTA
Found at i:28414849 original size:13 final size:13
Alignment explanation
Indices: 28414778--28414850 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
28414768 CAGGTATGGA
* *
28414778 TTAGGGTTTGGGA
1 TTAGGGTTAGGGG
*
28414791 TTAAGGTTTAGGGG
1 TT-AGGGTTAGGGG
*
28414805 TTGGGGGTTA-GGG
1 TT-AGGGTTAGGGG
*
28414818 TCTAGGGTTA-CGG
1 T-TAGGGTTAGGGG
28414831 TCTAGGGTTAGGGG
1 T-TAGGGTTAGGGG
28414845 TTAGGG
1 TTAGGG
28414851 GTCAAGGATT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
13 29 0.60
14 19 0.40
ACGTcount: A:0.15, C:0.04, G:0.48, T:0.33
Consensus pattern (13 bp):
TTAGGGTTAGGGG
Found at i:28414896 original size:14 final size:14
Alignment explanation
Indices: 28414795--28414924 Score: 54
Period size: 14 Copynumber: 9.4 Consensus size: 14
28414785 TTGGGATTAA
*
28414795 GGTTTAGGGGTTGG
1 GGTTTAGGGTTTGG
* * *
28414809 GGGTTAGGGTCTAG
1 GGTTTAGGGTTTGG
* * *
28414823 GG-TTACGGTCTAG
1 GGTTTAGGGTTTGG
*
28414836 GG-TTAGGGGTTAGG
1 GGTTTA-GGGTTTGG
** *
28414850 GGTCAAGGATTTGG
1 GGTTTAGGGTTTGG
* *
28414864 GATTT-GGGGTTGG
1 GGTTTAGGGTTTGG
*
28414877 TAGTTTAGGGTTTGG
1 -GGTTTAGGGTTTGG
28414892 GGTTT-GTGAG-TTGG
1 GGTTTAG-G-GTTTGG
*
28414906 GGTTTGGGGTTTGG
1 GGTTTAGGGTTTGG
28414920 GGTTT
1 GGTTT
28414925 GGGATTAAGG
Statistics
Matches: 86, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
13 23 0.27
14 53 0.62
15 10 0.12
ACGTcount: A:0.11, C:0.03, G:0.49, T:0.37
Consensus pattern (14 bp):
GGTTTAGGGTTTGG
Found at i:28414917 original size:21 final size:21
Alignment explanation
Indices: 28414859--28414927 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
28414849 GGGTCAAGGA
* *
28414859 TTTGGGATTTGGGGTTGGTAG
1 TTTGGGGTTTGGGGTTTGTAG
*
28414880 TTTAGGGTTTGGGGTTTGTGAG
1 TTTGGGGTTTGGGGTTTGT-AG
**
28414902 -TTGGGGTTTGGGGTTTGGGG
1 TTTGGGGTTTGGGGTTTGTAG
28414922 TTTGGG
1 TTTGGG
28414928 ATTAAGGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.93
22 2 0.05
ACGTcount: A:0.06, C:0.00, G:0.51, T:0.43
Consensus pattern (21 bp):
TTTGGGGTTTGGGGTTTGTAG
Found at i:28414925 original size:14 final size:14
Alignment explanation
Indices: 28414859--28414927 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
28414849 GGGTCAAGGA
*
28414859 TTTGGGATTTGGGG
1 TTTGGGGTTTGGGG
* *
28414873 -TTGGTAGTTTAGGG
1 TTTGG-GGTTTGGGG
*
28414887 TTTGGGGTTTGTGAG
1 TTTGGGGTTTG-GGG
28414902 -TTGGGGTTTGGGG
1 TTTGGGGTTTGGGG
28414915 TTTGGGGTTTGGG
1 TTTGGGGTTTGGG
28414928 ATTAAGGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 6 0.14
14 32 0.73
15 6 0.14
ACGTcount: A:0.06, C:0.00, G:0.51, T:0.43
Consensus pattern (14 bp):
TTTGGGGTTTGGGG
Found at i:28415161 original size:16 final size:16
Alignment explanation
Indices: 28415140--28415195 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
28415130 CAAAAGTAAT
28415140 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
28415156 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
* * *
28415172 GAAATAAATA-AATAAA
1 TAAA-AGATACAATTAA
28415188 TAAAAGAT
1 TAAAAGAT
28415196 GTGAGATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.23
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:28415509 original size:23 final size:24
Alignment explanation
Indices: 28415483--28415539 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
28415473 CACTTAGCCG
28415483 AAATTCCCCCCAAATTAT-CCCAA
1 AAATTCCCCCCAAATTATCCCCAA
* *
28415506 AAATTCCCCCCGAATTTTCCCCCAA
1 AAATTCCCCCCAAATTAT-CCCCAA
28415531 AAA-TCCCCC
1 AAATTCCCCC
28415540 AATTCTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 16 0.53
24 6 0.20
25 8 0.27
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATTCCCCCCAAATTATCCCCAA
Found at i:28416020 original size:12 final size:12
Alignment explanation
Indices: 28416005--28416044 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
28415995 TGTAATGCTA
28416005 TTTGTTCATAAT
1 TTTGTTCATAAT
28416017 TTTGTT-ACTAAT
1 TTTGTTCA-TAAT
*
28416029 TTTGTTCATAAG
1 TTTGTTCATAAT
28416041 TTTG
1 TTTG
28416045 AAACTGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (12 bp):
TTTGTTCATAAT
Found at i:28416252 original size:14 final size:14
Alignment explanation
Indices: 28416220--28416246 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28416210 TTGAAACTTT
28416220 AAATTTAAATTTTA
1 AAATTTAAATTTTA
28416234 AAATTTAAATTTT
1 AAATTTAAATTTT
28416247 GTAATTATAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTTAAATTTTA
Found at i:28417533 original size:69 final size:69
Alignment explanation
Indices: 28417375--28418099 Score: 1364
Period size: 69 Copynumber: 10.5 Consensus size: 69
28417365 CTATATTTAA
* *
28417375 ATATTGTT-AATAATAAATTTTATATTTTTA-AAACTAATTGTACATGTTATTTTTCTAAATATT
1 ATATT-TTCAATAATAAATTTTATAATTTTAGAAA-TAATTGTAAATGTTA-TTTTCTAAATATT
*
28417438 AACATAT
63 AACATCT
28417445 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
28417510 ATCT
66 ATCT
28417514 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
*
28417579 ATAT
66 ATCT
28417583 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
28417648 ATCT
66 ATCT
28417652 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
*
28417717 ATAT
66 ATCT
28417721 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
28417786 ATCT
66 ATCT
28417790 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
28417855 ATCT
66 ATCT
28417859 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
28417924 ATCT
66 ATCT
28417928 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
28417993 ATCT
66 ATCT
28417997 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
28418062 ATCT
66 ATCT
28418066 ATATTTTCAATAATAAATTTTATAATTTTAGAAA
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAA
28418100 NNNNNNNNNN
Statistics
Matches: 646, Mismatches: 7, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
69 603 0.93
70 40 0.06
71 3 0.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (69 bp):
ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
ATCT
Found at i:28420078 original size:43 final size:42
Alignment explanation
Indices: 28419965--28420172 Score: 161
Period size: 43 Copynumber: 4.9 Consensus size: 42
28419955 TTTTTATGAA
* * * *
28419965 AAGCGTCGCTAAAAGTCAAGGTCTTTTTGCGGCGTTTGCA-AG
1 AAGCGCCGCTAAAAGTCAAGGTC-TTTAGCGGCGTTTGTATTG
* * *
28420007 AAATCGCCGCTAAAAGT-TAGGGCATTTAGCGGCGTTTGTGATTG
1 -AAGCGCCGCTAAAAGTCAAGGTC-TTTAGCGGCGTTTGT-ATTG
* * * * *
28420051 AAGCGTCGCTAAAGGTCAAGGTCTTTAGTGGCGTTTGTAAATC
1 AAGCGCCGCTAAAAGTCAAGGTCTTTAGCGGCGTTTGT-ATTG
* * * * * *
28420094 AAGCGCCGCT-ATAGGCTAATGTATTTTGCGGCGTTTGTAGTGG
1 AAGCGCCGCTAAAAGTC-AAGGTCTTTAGCGGCGTTTGTA-TTG
*
28420137 AAGCGCCGCTAAAAGTCAAGCTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAAGTCAAGGTCTTTAGCGGCGTTT
28420173 TATGGTAAAG
Statistics
Matches: 125, Mismatches: 34, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
42 21 0.17
43 95 0.76
44 9 0.07
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (42 bp):
AAGCGCCGCTAAAAGTCAAGGTCTTTAGCGGCGTTTGTATTG
Found at i:28420101 original size:86 final size:85
Alignment explanation
Indices: 28419902--28420172 Score: 242
Period size: 86 Copynumber: 3.2 Consensus size: 85
28419892 AGTTGCTCAA
*** * * * * * * *
28419902 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGGTAATGCATTTAGTGGCGTTTTTA-TGAAA
1 TTTAGCGGCGTTTGCAAG-AAAGCGCCGCTAAAAGCTAAGGCATTTAGCGGCGTTTGTAGTG-GA
28419966 AGCGTCGCTAAAAGTCAAGGTC
64 AGCGTCGCTAAAAGTCAAGGTC
* * * * *
28419988 TTTTTGCGGCGTTTGCAAGAAATCGCCGCTAAAAGTTAGGGCATTTAGCGGCGTTTGT-GATTGA
1 -TTTAGCGGCGTTTGCAAGAAAGCGCCGCTAAAAGCTAAGGCATTTAGCGGCGTTTGTAG-TGGA
*
28420052 AGCGTCGCTAAAGGTCAAGGTC
64 AGCGTCGCTAAAAGTCAAGGTC
* * * * * * *
28420074 TTTAGTGGCGTTTGTAA-ATCAAGCGCCGCTATAGGCTAATGTATTTTGCGGCGTTTGTAGTGGA
1 TTTAGCGGCGTTTGCAAGA--AAGCGCCGCTAAAAGCTAAGGCATTTAGCGGCGTTTGTAGTGGA
* *
28420138 AGCGCCGCTAAAAGTCAAGCTC
64 AGCGTCGCTAAAAGTCAAGGTC
28420160 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
28420173 TATGGTAAAG
Statistics
Matches: 148, Mismatches: 31, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
84 1 0.01
85 14 0.09
86 117 0.79
87 16 0.11
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (85 bp):
TTTAGCGGCGTTTGCAAGAAAGCGCCGCTAAAAGCTAAGGCATTTAGCGGCGTTTGTAGTGGAAG
CGTCGCTAAAAGTCAAGGTC
Found at i:28420207 original size:43 final size:43
Alignment explanation
Indices: 28420184--28420279 Score: 183
Period size: 43 Copynumber: 2.2 Consensus size: 43
28420174 ATGGTAAAGT
28420184 GCCGCTAAAGAGCTTGACTTTTAGCGGCGCTTAAGTCACAAAC
1 GCCGCTAAAGAGCTTGACTTTTAGCGGCGCTTAAGTCACAAAC
*
28420227 GCCGCTAAAGAGCTTGACTTTTAGCGGCGCTCAAGTCACAAAC
1 GCCGCTAAAGAGCTTGACTTTTAGCGGCGCTTAAGTCACAAAC
28420270 GCCGCTAAAG
1 GCCGCTAAAG
28420280 TTAACGACGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (43 bp):
GCCGCTAAAGAGCTTGACTTTTAGCGGCGCTTAAGTCACAAAC
Found at i:28420211 original size:86 final size:86
Alignment explanation
Indices: 28419902--28420212 Score: 210
Period size: 86 Copynumber: 3.6 Consensus size: 86
28419892 AGTTGCTCAA
** * * * * *
28419902 TTTAGCGGCGTTTGTGGGA-AAAGTGCCGCTAAAGGGTAATGCA-TTTAGTGGCGTTT-TTATGA
1 TTTAGCGGCGTTTGT-AAATAAAGCGCCGCTAAAGGCT-ATGTATTTTAGCGGCGTTTGTGATG-
* * *
28419964 AAAGCGTCGCTAAAAGTCAAGGTC
63 GAAGCGCCGCTAAAAGTCAAGCTC
* * * * * * * * *
28419988 TTTTTGCGGCGTTTG-CAAGAAATCGCCGCTAAAAGTTAGGGCA-TTTAGCGGCGTTTGTGATTG
1 -TTTAGCGGCGTTTGTAAATAAAGCGCCGCTAAAGGCTA-TGTATTTTAGCGGCGTTTGTGATGG
* * *
28420051 AAGCGTCGCTAAAGGTCAAGGTC
64 AAGCGCCGCTAAAAGTCAAGCTC
* * *
28420074 TTTAGTGGCGTTTGTAAATCAAGCGCCGCTATAGGCTAATGTATTTT-GCGGCGTTTGT-AGTGG
1 TTTAGCGGCGTTTGTAAATAAAGCGCCGCTAAAGGCT-ATGTATTTTAGCGGCGTTTGTGA-TGG
28420137 AAGCGCCGCTAAAAGTCAAGCTC
64 AAGCGCCGCTAAAAGTCAAGCTC
** *
28420160 TTTAGCGGCGTTT-TATGGTAAAGTGCCGCTAAAGAGCT-TG-ACTTTTAGCGGCG
1 TTTAGCGGCGTTTGTA-AATAAAGCGCCGCTAAAG-GCTATGTA-TTTTAGCGGCG
28420213 CTTAAGTCAC
Statistics
Matches: 179, Mismatches: 34, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
84 1 0.01
85 23 0.13
86 132 0.74
87 23 0.13
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTAAATAAAGCGCCGCTAAAGGCTATGTATTTTAGCGGCGTTTGTGATGGAA
GCGCCGCTAAAAGTCAAGCTC
Found at i:28420394 original size:22 final size:22
Alignment explanation
Indices: 28420351--28420394 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28420341 TTGCGACGCT
*
28420351 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAGCCCTA
*
28420373 AAAAAGCGCCGCTAAATCCCTA
1 AAAAAGCGCCGCTAAAGCCCTA
28420395 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.30, G:0.18, T:0.11
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAGCCCTA
Found at i:28425585 original size:3 final size:3
Alignment explanation
Indices: 28425577--28426132 Score: 1112
Period size: 3 Copynumber: 185.3 Consensus size: 3
28425567 ATATGATACT
28425577 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28425625 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28425673 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28425721 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28425769 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28425817 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28425865 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28425913 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28425961 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28426009 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28426057 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28426105 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28426133 NNNNNNNNNN
Statistics
Matches: 553, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 553 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28430987 original size:3 final size:3
Alignment explanation
Indices: 28430979--28431024 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
28430969 ATATGATACT
28430979 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28431025 AACAGAGGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28431136 original size:3 final size:3
Alignment explanation
Indices: 28431130--28431166 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28431120 ATTTTAGCCT
28431130 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28431167 AACAGAGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28431244 original size:142 final size:143
Alignment explanation
Indices: 28430988--28431276 Score: 553
Period size: 142 Copynumber: 2.0 Consensus size: 143
28430978 TTTATTATTA
* *
28430988 TTATTATTATTATTATTATTATTATTATTATTATTATAACAGAGGAGAGAGGGGATATTAGATTT
1 TTATTATTATTATTATTATTATTATTATTATTATTATAACAGAGGAGAGAAGAGATATTAGATTT
28431053 GAACTAGTGCTATCTAGATGCTAAAAAGGAGCTCTAATAATTTGATATTTTACTTTAGCATAATA
66 GAACTAGTGCTATCTAGATGCTAAAAAGGAGCTCTAATAATTTGATATTTTACTTTAGCATAATA
28431118 AT-ATTTTAGCCT
131 ATAATTTTAGCCT
28431130 TTATTATTATTATTATTATTATTATTATTATTATTATAACAGAGGAGAGAAGAGATATTAGATTT
1 TTATTATTATTATTATTATTATTATTATTATTATTATAACAGAGGAGAGAAGAGATATTAGATTT
28431195 GAACTAGTGCTATCTAGATGCTAAAAAGGAGCTCTAATAATTTGATATTTTACTTTAGCATAATA
66 GAACTAGTGCTATCTAGATGCTAAAAAGGAGCTCTAATAATTTGATATTTTACTTTAGCATAATA
28431260 ATAATTTTAGCCT
131 ATAATTTTAGCCT
28431273 TTAT
1 TTAT
28431277 GGTTTATTTC
Statistics
Matches: 144, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
142 130 0.90
143 14 0.10
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.43
Consensus pattern (143 bp):
TTATTATTATTATTATTATTATTATTATTATTATTATAACAGAGGAGAGAAGAGATATTAGATTT
GAACTAGTGCTATCTAGATGCTAAAAAGGAGCTCTAATAATTTGATATTTTACTTTAGCATAATA
ATAATTTTAGCCT
Found at i:28432912 original size:247 final size:248
Alignment explanation
Indices: 28432476--28432970 Score: 983
Period size: 247 Copynumber: 2.0 Consensus size: 248
28432466 TATTCAGGAT
28432476 GCAATTAAGGAAAGTCTTATTTCTCTTATATGTCTCCAATACAGATCAACTAGCAAATATATTTA
1 GCAATTAAGGAAAGTCTTATTTCTCTTATATGTCTCCAATACAGATCAACTAGCAAATATATTTA
28432541 CAAAGGCTTTGGAAAAGAAACGATTTGATTATTGTCTTAACAAATTGGGCATTTACGATTTACAT
66 CAAAGGCTTTGGAAAAGAAACGATTTGATTATTGTCTTAACAAATTGGGCATTTACGATTTACAT
28432606 GCTCCAACTTGAGGTAAGTATTATGGAAAGATATAAATATTATGAAATAATTTATTTTAGGAGTA
131 GCTCCAACTTGAGGTAAGTATTATGGAAAGATATAAATATTATGAAATAATTTATTTTAGGAGTA
28432671 GTTTCCTATATTATAGGAAGTAGAGGACGAATAGGAATAA-TTTACTATTTCG
196 GTTTCCTATATTATAGGAAGTAGAGGACGAATAGGAATAATTTTACTATTTCG
28432723 GCAATTAAGGAAAGTCTTATTTCTCTTATATGTCTCCAATACAGATCAACTAGCAAATATATTTA
1 GCAATTAAGGAAAGTCTTATTTCTCTTATATGTCTCCAATACAGATCAACTAGCAAATATATTTA
28432788 CAAAGGCTTTGGAAAAGAAACGATTTGATTATTGTCTTAACAAATTGGGCATTTACGATTTACAT
66 CAAAGGCTTTGGAAAAGAAACGATTTGATTATTGTCTTAACAAATTGGGCATTTACGATTTACAT
28432853 GCTCCAACTTGAGGTAAGTATTATGGAAAGATATAAATATTATGAAATAATTTATTTTAGGAGTA
131 GCTCCAACTTGAGGTAAGTATTATGGAAAGATATAAATATTATGAAATAATTTATTTTAGGAGTA
28432918 GTTTCCTATATTATAGGAAGTAGAGGACGAATAGGAATAATTTTACTATTTCG
196 GTTTCCTATATTATAGGAAGTAGAGGACGAATAGGAATAATTTTACTATTTCG
28432971 ATTCTAAGTG
Statistics
Matches: 247, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
247 235 0.95
248 12 0.05
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (248 bp):
GCAATTAAGGAAAGTCTTATTTCTCTTATATGTCTCCAATACAGATCAACTAGCAAATATATTTA
CAAAGGCTTTGGAAAAGAAACGATTTGATTATTGTCTTAACAAATTGGGCATTTACGATTTACAT
GCTCCAACTTGAGGTAAGTATTATGGAAAGATATAAATATTATGAAATAATTTATTTTAGGAGTA
GTTTCCTATATTATAGGAAGTAGAGGACGAATAGGAATAATTTTACTATTTCG
Found at i:28432997 original size:2 final size:2
Alignment explanation
Indices: 28432990--28433015 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28432980 GCAATATGGC
28432990 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
28433016 TCTTTTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28434457 original size:48 final size:49
Alignment explanation
Indices: 28434386--28434482 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 49
28434376 ATGATGACAT
28434386 TCTCTAAATATTATTTACAAATTATAAAAGAATCT-AAAATATATTTAA
1 TCTCTAAATATTATTTACAAATTATAAAAGAATCTAAAAATATATTTAA
28434434 TCTCTAAATATTATTTACAAATTATAAAAGAATCTAAAAATATATTTAA
1 TCTCTAAATATTATTTACAAATTATAAAAGAATCTAAAAATATATTTAA
28434483 AATTAATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 35 0.73
49 13 0.27
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (49 bp):
TCTCTAAATATTATTTACAAATTATAAAAGAATCTAAAAATATATTTAA
Found at i:28438505 original size:37 final size:37
Alignment explanation
Indices: 28438452--28438526 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
28438442 GAGACTCAAA
*
28438452 TGATTTATAATAAATTTTCGACTTTTCACCTATTAAT
1 TGATTTATAATAAATTTTCGAATTTTCACCTATTAAT
* * **
28438489 TGATTTATAATTAATTTTTGAATTTTCGTCTATTAAT
1 TGATTTATAATAAATTTTCGAATTTTCACCTATTAAT
28438526 T
1 T
28438527 ATAAACCTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (37 bp):
TGATTTATAATAAATTTTCGAATTTTCACCTATTAAT
Found at i:28447334 original size:36 final size:36
Alignment explanation
Indices: 28447287--28447436 Score: 138
Period size: 36 Copynumber: 3.9 Consensus size: 36
28447277 GCTAAGCTAC
*
28447287 CACTTATCACTTTTTCACTTGATCAGATAAGTATAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
*
28447323 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--A--T
* * * *
28447367 ACCACTTATCACTTTGCCTCTTGATCAGATAAGTGTAG
1 --CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
* *
28447405 CTCTTATTACTTTGTCACTTGATCAGATAAGT
1 CACTTATCACTTTGTCACTTGATCAGATAAGT
28447437 GTAGCTAAAG
Statistics
Matches: 95, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
36 58 0.61
38 3 0.03
40 2 0.02
42 2 0.02
44 3 0.03
46 27 0.28
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
Found at i:28447374 original size:46 final size:46
Alignment explanation
Indices: 28447323--28447463 Score: 167
Period size: 46 Copynumber: 3.3 Consensus size: 46
28447313 ATAAGTATAT
*
28447323 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
28447369 CACTTATCACTTTGCCTCTTGATCAGATAA--GT-G-T--AGCT--
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
28447407 --CTTATTACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
28447451 TACTTATCACTTT
1 CACTTATCACTTT
28447464 ATTTGTTGAT
Statistics
Matches: 78, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
36 25 0.32
38 2 0.03
39 1 0.01
40 5 0.06
42 5 0.06
43 1 0.01
44 2 0.03
46 37 0.47
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:28447390 original size:82 final size:82
Alignment explanation
Indices: 28447248--28447463 Score: 319
Period size: 82 Copynumber: 2.7 Consensus size: 82
28447238 CTTATGTATG
* **
28447248 ATCAC-TTATCACTTTATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTTTCACTTGATC
1 ATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGCCACTTGATC
*
28447311 AGATAAGTATATCACTT
66 AGATAAGTATAGCACTT
* *
28447328 ATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGCCTCTTGATC
1 ATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGCCACTTGATC
* *
28447393 AGATAAGTGTAGCTCTT
66 AGATAAGTATAGCACTT
* * *
28447410 ATTACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTT
1 ATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
28447464 ATTTGTTGAT
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
80 5 0.04
81 25 0.20
82 93 0.76
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (82 bp):
ATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGCCACTTGATC
AGATAAGTATAGCACTT
Found at i:28453046 original size:45 final size:44
Alignment explanation
Indices: 28452965--28453055 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
28452955 ATCTCTATTC
*
28452965 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
28453009 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
28453054 CA
1 CA
28453056 CCTCTATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:28453055 original size:16 final size:16
Alignment explanation
Indices: 28453034--28453103 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
28453024 TTGATTTGCT
*
28453034 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
* *
28453050 ATTACACCTCTATTCT
1 ATTACACCTCTAATCC
28453066 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
28453082 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
28453098 AATACA
1 ATTACA
28453104 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:28453068 original size:32 final size:32
Alignment explanation
Indices: 28453032--28453093 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
28453022 AGTTGATTTG
* *
28453032 CTATTACACCTCTATTCCATTACACCTCTATT
1 CTATTACACCTCTAATCCAATACACCTCTATT
28453064 CTATTACACCTCTAATCCAATACACCTCTA
1 CTATTACACCTCTAATCCAATACACCTCTA
28453094 ATCCAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (32 bp):
CTATTACACCTCTAATCCAATACACCTCTATT
Found at i:28453743 original size:133 final size:134
Alignment explanation
Indices: 28453571--28453840 Score: 524
Period size: 133 Copynumber: 2.0 Consensus size: 134
28453561 CCCCTGCAGT
*
28453571 TTGTAAATTTTCATCTTTTCCCTAAAATTTCTATATGTTTTTAATTTAGTCCCGATTTGTTTCTA
1 TTGTAAATTTTCATCTTTTCCCTAAAATTTCTATATGTTTCTAATTTAGTCCCGATTTGTTTCTA
28453636 ATGTGGTTCTAGGGCCTTGAGGGCTCGTATAAGGGACAATATGTATTATATTGATTGG-TTTGAT
66 ATGTGGTTCTAGGGCCTTGAGGGCTCGTATAAGGGACAATATGTATTATATTGATTGGTTTTGAT
28453700 GTGA
131 GTGA
28453704 TTGTAAATTTTCATCTTTTCCCTAAAATTTCTATATGTTTCTAATTTAGTCCCGATTTGTTTCTA
1 TTGTAAATTTTCATCTTTTCCCTAAAATTTCTATATGTTTCTAATTTAGTCCCGATTTGTTTCTA
28453769 ATGTGGTTCTAGGGCCTTGAGGGCTCGTATAAGGGACAATATGTATTATATTGATTGGTTTTGAT
66 ATGTGGTTCTAGGGCCTTGAGGGCTCGTATAAGGGACAATATGTATTATATTGATTGGTTTTGAT
28453834 GTGA
131 GTGA
28453838 TTG
1 TTG
28453841 ATGATATGAA
Statistics
Matches: 135, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
133 122 0.90
134 13 0.10
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (134 bp):
TTGTAAATTTTCATCTTTTCCCTAAAATTTCTATATGTTTCTAATTTAGTCCCGATTTGTTTCTA
ATGTGGTTCTAGGGCCTTGAGGGCTCGTATAAGGGACAATATGTATTATATTGATTGGTTTTGAT
GTGA
Found at i:28455702 original size:33 final size:33
Alignment explanation
Indices: 28455629--28455703 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
28455619 TGGACGTACC
*
28455629 TCGTGTTTATTATCCTAACAGATTATCTCTGTT
1 TCGTGTTTATTATCCTAACAGACTATCTCTGTT
** * *
28455662 TTATGTTTATTATCCTAGCAGACTATCTTTGTT
1 TCGTGTTTATTATCCTAACAGACTATCTCTGTT
28455695 TCGTGTTTA
1 TCGTGTTTA
28455704 CTGTCTCGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (33 bp):
TCGTGTTTATTATCCTAACAGACTATCTCTGTT
Found at i:28458884 original size:43 final size:43
Alignment explanation
Indices: 28458835--28458921 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
28458825 GTGTGTCCGC
* * * *
28458835 CCATGTGGGTATTTGAAATAGTGCCAGATGACCGTGTGCCAAA
1 CCATGTGGGTATTCGAAATAGGGCCACACGACCGTGTGCCAAA
* * *
28458878 CCATGTGTGTATTCGAAGTAGGGTCACACGACCGTGTGCCAAA
1 CCATGTGGGTATTCGAAATAGGGCCACACGACCGTGTGCCAAA
28458921 C
1 C
28458922 TGTGCCACAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (43 bp):
CCATGTGGGTATTCGAAATAGGGCCACACGACCGTGTGCCAAA
Found at i:28459828 original size:2 final size:2
Alignment explanation
Indices: 28459821--28459855 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28459811 TATAACCGTC
28459821 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
28459856 TCATATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28460096 original size:22 final size:21
Alignment explanation
Indices: 28460062--28460127 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
28460052 GAGGTACGAT
28460062 TGTACAATCAGAGGCATCGTAAAG
1 TGTA-AAT-AGAGGCATC-TAAAG
28460086 TGTAAATAGAGGCA-CTAAAG
1 TGTAAATAGAGGCATCTAAAG
** *
28460106 TGCGAACAGAGGCATC-AAAG
1 TGTAAATAGAGGCATCTAAAG
28460126 TG
1 TG
28460128 CGATCCTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 22 0.58
21 2 0.05
22 7 0.18
23 3 0.08
24 4 0.11
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.18
Consensus pattern (21 bp):
TGTAAATAGAGGCATCTAAAG
Found at i:28480981 original size:25 final size:25
Alignment explanation
Indices: 28480953--28481033 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
28480943 GTTTTGTGAT
*
28480953 TTAAATTGGTCTTGGTTTAGACAAA
1 TTAAATTGGTCTTAGTTTAGACAAA
*
28480978 TTAAATTGGTCTTAGTTTAGAC-AC
1 TTAAATTGGTCTTAGTTTAGACAAA
* * *
28481002 TTTAATTGTGTCTATTGTTTGGACAAA
1 TTAAATTG-GTCT-TAGTTTAGACAAA
28481029 TTAAA
1 TTAAA
28481034 GTGTGTCTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 8 0.17
25 25 0.54
26 8 0.17
27 5 0.11
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:28489180 original size:128 final size:128
Alignment explanation
Indices: 28489042--28489393 Score: 481
Period size: 128 Copynumber: 2.7 Consensus size: 128
28489032 TAGGATTATC
*
28489042 GGCTTCAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTGCTCCGCTAATGC
1 GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTGCTCCGCTAATGC
* *
28489107 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGAC-CAGGGACATAGAACTTGT
66 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCT-ACTCAGAGAAATAGAACTTGT
*
28489170 GGCTTGAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTGCTCCGCTAATGC
1 GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTGCTCCGCTAATGC
* *
28489235 TTAGGGAGACAAGATCTGTAATTTCCTACCTATTCCACTGCTACTCAGAGAAATAGGACTTGT
66 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTACTCAGAGAAATAGAACTTGT
* * * * * * * * * ** *
28489298 GGCTTAAATCAGTTTCCCTACTCCTGGGGAAGCTAAGATTCGTCGTCTTCGATCTACTCCATTAT
1 GGCTTAAATCTGCTTCCTTAC-ACT--TGAAGATAAGATTTGCCGTCTTCGATCTGCTCCGCTAA
* *
28489363 TTCTTAGGGAGATAAGATCTGTAATTTCCAA
63 TGCTTAGGGAGACAAGATCTGTAATTTCCAA
28489394 TCTTCAACCT
Statistics
Matches: 199, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
127 2 0.01
128 137 0.69
129 2 0.01
131 58 0.29
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (128 bp):
GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTGCTCCGCTAATGC
TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTACTCAGAGAAATAGAACTTGT
Found at i:28489515 original size:44 final size:44
Alignment explanation
Indices: 28489467--28489604 Score: 143
Period size: 44 Copynumber: 3.2 Consensus size: 44
28489457 CGACGCAGGA
**
28489467 AGGCAAGATCTGCTATCTTCAACCTGCAACACTGCAACCGAGGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGG
* * * * **** **
28489511 AGGCAAG-GCTGGTATCTTCGATCTGCTCCACTATTGCTTAGGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGG
* *
28489554 AGGCAAGATCCGCTATCTTTAACCTGCTCCACTGCAACCGAGGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGG
28489598 AGGCAAG
1 AGGCAAG
28489605 GCTTTGTTTT
Statistics
Matches: 69, Mismatches: 24, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
43 31 0.45
44 38 0.55
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (44 bp):
AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGG
Found at i:28489587 original size:87 final size:88
Alignment explanation
Indices: 28489393--28489607 Score: 263
Period size: 87 Copynumber: 2.5 Consensus size: 88
28489383 GTAATTTCCA
* * * * * *
28489393 ATCTTCAACCTGTTCTACTACAATCGAGGGAGGCAAGGCTTGTGCCTTCGATCTGCTTCCCCATC
1 ATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTACCTTCGATCTGCTTCCCCATC
*
28489458 GACGCAGGAAGGCAAGATCTGCT
66 GACGCAGGAAGGCAAGATCCGCT
** * *
28489481 ATCTTCAACCTGCAACACTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGC-TCCACTAT
1 ATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTACCTTCGATCTGCTTCC-CCAT
* ** *
28489545 TG-CTTAGGGAGGCAAGATCCGCT
65 CGACGCAGGAAGGCAAGATCCGCT
*
28489568 ATCTTTAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCT
1 ATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCT
28489608 TTGTTTTCGA
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
87 57 0.53
88 51 0.47
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (88 bp):
ATCTTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTACCTTCGATCTGCTTCCCCATC
GACGCAGGAAGGCAAGATCCGCT
Found at i:28490875 original size:6 final size:6
Alignment explanation
Indices: 28490866--28490911 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
28490856 CATTTTTACT
28490866 TTTTCA TTTTTCA TTTTTCA TTTTCA TTTTCA TTTT-- TTTTCA TTTT
1 TTTTCA -TTTTCA -TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
28490912 TTATTTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.11
6 20 0.54
7 13 0.35
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTCA
Found at i:28490911 original size:9 final size:10
Alignment explanation
Indices: 28490879--28490926 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 10
28490869 TCATTTTTCA
28490879 TTTTTCATTT
1 TTTTTCATTT
28490889 TCATTTTCATTT
1 T--TTTTCATTT
28490901 TTTTTCATTTT
1 TTTTTCA-TTT
28490912 TTATTTC-TTT
1 TT-TTTCATTT
28490922 TTTTT
1 TTTTT
28490927 ACTCAAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.09
10 12 0.35
11 5 0.15
12 14 0.41
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:28490912 original size:7 final size:7
Alignment explanation
Indices: 28490854--28490902 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
28490844 ACTTAGCCTC
28490854 TTCATTT
1 TTCATTT
28490861 TT-ACTTT
1 TTCA-TTT
28490868 TTCATTT
1 TTCATTT
28490875 TTCATTT
1 TTCATTT
28490882 TTCA-TT
1 TTCATTT
28490888 TTCA-TT
1 TTCATTT
28490894 TTCATTT
1 TTCATTT
28490901 TT
1 TT
28490903 TTTCATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 13 0.33
7 25 0.64
8 1 0.03
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
TTCATTT
Found at i:28500844 original size:21 final size:21
Alignment explanation
Indices: 28500819--28500880 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
28500809 TAGAGTGTAA
28500819 ACAGGGGCATGTAAGTGCAAT
1 ACAGGGGCATGTAAGTGCAAT
* * *
28500840 GCAGGGGTA-GTGAAGTACAA-
1 ACAGGGGCATGT-AAGTGCAAT
*
28500860 ACAGGGGCATGTATGTGCAAT
1 ACAGGGGCATGTAAGTGCAAT
28500881 TCATGGATAC
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.19
Consensus pattern (21 bp):
ACAGGGGCATGTAAGTGCAAT
Found at i:28500878 original size:41 final size:41
Alignment explanation
Indices: 28500817--28500928 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
28500807 ACTAGAGTGT
* * * ***
28500817 AAACAGGGGCATGTAAGTGCAATGCAGGGGTAGTGAAGTAC
1 AAACAGGGGCATGTATGTGCAATTCAGGGATACCAAAGTAC
*
28500858 AAACAGGGGCATGTATGTGCAATTCATGGATACCAAAGTAC
1 AAACAGGGGCATGTATGTGCAATTCAGGGATACCAAAGTAC
* * *
28500899 AAATAGGAGCATATATGTGCAATTCAGGGA
1 AAACAGGGGCATGTATGTGCAATTCAGGGA
28500929 AATAATTCAG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (41 bp):
AAACAGGGGCATGTATGTGCAATTCAGGGATACCAAAGTAC
Found at i:28502882 original size:25 final size:25
Alignment explanation
Indices: 28502820--28502883 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
28502810 CTACAGATCA
* * *
28502820 TGAGAGCATACCAATTTATAGCTTG
1 TGAGATCATACCGATTTATAGCTCG
28502845 TGAGATCATACCGATTTATAGCTCG
1 TGAGATCATACCGATTTATAGCTCG
28502870 TGAGATCATACCGA
1 TGAGATCATACCGA
28502884 CCTAGAGCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (25 bp):
TGAGATCATACCGATTTATAGCTCG
Found at i:28502892 original size:25 final size:25
Alignment explanation
Indices: 28502839--28502893 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
28502829 ACCAATTTAT
* ** *
28502839 AGCTTGTGAGATCATACCGATTTAT
1 AGCTCGTGAGATCATACCGACCTAG
28502864 AGCTCGTGAGATCATACCGACCTAG
1 AGCTCGTGAGATCATACCGACCTAG
28502889 AGCTC
1 AGCTC
28502894 AAGTGAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (25 bp):
AGCTCGTGAGATCATACCGACCTAG
Found at i:28504566 original size:121 final size:122
Alignment explanation
Indices: 28504352--28504592 Score: 475
Period size: 121 Copynumber: 2.0 Consensus size: 122
28504342 CACAACCGTG
28504352 TGACCCCTGCAGTGTTGAAAATTTTTGCTATTTTCAGAAAAATTCTCTAAGTTTCCTATTTAGTC
1 TGACCCCTGCAGTGTTGAAAATTTTTGCTATTTTCAGAAAAATTCTCTAAGTTTCCTATTTAGTC
28504417 CCAACTTGTTTTTAGCACATATTTAGGGCCTTGAAGGCTCGTAGAA-GGACAATAAT
66 CCAACTTGTTTTTAGCACATATTTAGGGCCTTGAAGGCTCGTAGAAGGGACAATAAT
28504473 TGACCCCTGCAGTGTTGAAAATTTTTGCTATTTTCAGAAAAATTCTCTAAGTTTCCTATTTAGTC
1 TGACCCCTGCAGTGTTGAAAATTTTTGCTATTTTCAGAAAAATTCTCTAAGTTTCCTATTTAGTC
28504538 CCAACTTGTTTTTAGCACATATTTAGGGCCTTGAAGGCTCGTAGAAGGGACAATA
66 CCAACTTGTTTTTAGCACATATTTAGGGCCTTGAAGGCTCGTAGAAGGGACAATA
28504593 TGTATGATTT
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
121 111 0.93
122 8 0.07
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (122 bp):
TGACCCCTGCAGTGTTGAAAATTTTTGCTATTTTCAGAAAAATTCTCTAAGTTTCCTATTTAGTC
CCAACTTGTTTTTAGCACATATTTAGGGCCTTGAAGGCTCGTAGAAGGGACAATAAT
Found at i:28516524 original size:25 final size:25
Alignment explanation
Indices: 28516473--28516612 Score: 119
Period size: 25 Copynumber: 5.7 Consensus size: 25
28516463 TCGATATATT
* * *
28516473 GCTCTCTTGGGCTTCCCG-TTATTTG
1 GCTCTCATGAGCTTCCCGATTA-ATG
*
28516498 GCTCTCATGAGCTTCCTGATTAATG
1 GCTCTCATGAGCTTCCCGATTAATG
* *
28516523 GCTCTC-CGAAGCTTCCCGA-TATTG
1 GCTCTCATG-AGCTTCCCGATTAATG
* * *
28516547 GCTCGCATGAGTTTCCCGATT-ACG
1 GCTCTCATGAGCTTCCCGATTAATG
*
28516571 GCTCTTATGAGCTTCCCG-TTACATG
1 GCTCTCATGAGCTTCCCGATTA-ATG
*
28516596 GCTCACATGAGCTTCCC
1 GCTCTCATGAGCTTCCC
28516613 ATTTACATAC
Statistics
Matches: 91, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
23 2 0.02
24 35 0.38
25 51 0.56
26 3 0.03
ACGTcount: A:0.15, C:0.30, G:0.21, T:0.34
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATTAATG
Found at i:28516573 original size:24 final size:24
Alignment explanation
Indices: 28516532--28516612 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
28516522 GGCTCTCCGA
* ** *
28516532 AGCTTCCCGATATTGGCTCGCATG
1 AGCTTCCCGTTACAGGCTCACATG
* **
28516556 AGTTTCCCGATTAC-GGCTCTTATG
1 AGCTTCCCG-TTACAGGCTCACATG
28516580 AGCTTCCCGTTACATGGCTCACATG
1 AGCTTCCCGTTACA-GGCTCACATG
28516605 AGCTTCCC
1 AGCTTCCC
28516613 ATTTACATAC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 4 0.09
24 24 0.52
25 18 0.39
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (24 bp):
AGCTTCCCGTTACAGGCTCACATG
Found at i:28516598 original size:49 final size:49
Alignment explanation
Indices: 28516483--28516612 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 49
28516473 GCTCTCTTGG
* * * *
28516483 GCTTCCCGTTATTTGGCTCTCATGAGCTTCCTGATTAATGGCTCTCCGAA
1 GCTTCCCGTTA-TTGGCTCACATGAGCTTCCCGATTAACGGCTCTACGAA
* * * *
28516533 GCTTCCCGATATTGGCTCGCATGAGTTTCCCGATT-ACGGCTCTTATG-A
1 GCTTCCCGTTATTGGCTCACATGAGCTTCCCGATTAACGGCTC-TACGAA
*
28516581 GCTTCCCGTTACATGGCTCACATGAGCTTCCC
1 GCTTCCCGTTA-TTGGCTCACATGAGCTTCCC
28516613 ATTTACATAC
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
48 17 0.25
49 40 0.60
50 10 0.15
ACGTcount: A:0.16, C:0.30, G:0.21, T:0.33
Consensus pattern (49 bp):
GCTTCCCGTTATTGGCTCACATGAGCTTCCCGATTAACGGCTCTACGAA
Found at i:28516630 original size:25 final size:25
Alignment explanation
Indices: 28516576--28516632 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
28516566 TTACGGCTCT
*
28516576 TATGAGCTTCCCGTTACATGGCTCA
1 TATGAGCTTCCCGTTACATGACTCA
* * *
28516601 CATGAGCTTCCCATTTACAT-ACTCG
1 TATGAGCTTCCC-GTTACATGACTCA
28516626 TATGAGC
1 TATGAGC
28516633 ATACATGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32
Consensus pattern (25 bp):
TATGAGCTTCCCGTTACATGACTCA
Found at i:28522680 original size:3 final size:3
Alignment explanation
Indices: 28522672--28522707 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
28522662 AAATTGAACA
28522672 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28522708 TGACTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28522808 original size:3 final size:3
Alignment explanation
Indices: 28522800--28522835 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
28522790 AAATTGAACA
28522800 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28522836 TGACTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28522835 original size:128 final size:130
Alignment explanation
Indices: 28522607--28522864 Score: 502
Period size: 128 Copynumber: 2.0 Consensus size: 130
28522597 TCAAATCCTC
28522607 CAGCCACATGTTGAATTTTTAATTATCCCTTGCAATCCCAAAATATATATTCAGGAAATTGAACA
1 CAGCCACATGTTGAATTTTTAATTATCCCTTGCAATCCCAAAATATATATTCAGGAAATTGAACA
28522672 AATAATAATAATAATAATAATAATAATAATAATAATTGACTTTTTAATTT-AA-AAATAAGAAAA
66 AATAATAATAATAATAATAATAATAATAATAATAATTGACTTTTTAATTTAAAGAAATAAGAAAA
28522735 CAGCCACATGTTGAATTTTTAATTATCCCTTGCAATCCCAAAATATATATTCAGGAAATTGAACA
1 CAGCCACATGTTGAATTTTTAATTATCCCTTGCAATCCCAAAATATATATTCAGGAAATTGAACA
28522800 AATAATAATAATAATAATAATAATAATAATAATAATTGACTTTTTAATTTAAAGAAATAAGAAAA
66 AATAATAATAATAATAATAATAATAATAATAATAATTGACTTTTTAATTTAAAGAAATAAGAAAA
28522865 TCTCCAGAAT
Statistics
Matches: 128, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
128 115 0.90
129 2 0.02
130 11 0.09
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (130 bp):
CAGCCACATGTTGAATTTTTAATTATCCCTTGCAATCCCAAAATATATATTCAGGAAATTGAACA
AATAATAATAATAATAATAATAATAATAATAATAATTGACTTTTTAATTTAAAGAAATAAGAAAA
Found at i:28527669 original size:21 final size:21
Alignment explanation
Indices: 28527637--28527677 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28527627 TCCTGCAGCA
28527637 TAAAAAATCTGAACCGGACAC
1 TAAAAAATCTGAACCGGACAC
28527658 TAAAAGAA-CTGAACCGGACA
1 TAAAA-AATCTGAACCGGACA
28527678 GGGGAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (21 bp):
TAAAAAATCTGAACCGGACAC
Found at i:28537751 original size:31 final size:30
Alignment explanation
Indices: 28537705--28537766 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
28537695 GCAGATTATA
* *
28537705 TTTTACCTAAGTCATTCGATTTTGAGGTATT
1 TTTTACCTAAATCATTCGATTTTAAGG-ATT
*
28537736 TTTTATCTAAATCATTCGATTTTAAGGATT
1 TTTTACCTAAATCATTCGATTTTAAGGATT
28537766 T
1 T
28537767 AGCTTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (30 bp):
TTTTACCTAAATCATTCGATTTTAAGGATT
Found at i:28538331 original size:13 final size:13
Alignment explanation
Indices: 28538313--28538373 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
28538303 CTCAAATTTT
*
28538313 TCAAAAGTACTTC
1 TCAAAAGCACTTC
*
28538326 TCAAAAGCATTTC
1 TCAAAAGCACTTC
28538339 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
28538352 TTAAAAGCATTTC
1 TCAAAAGCACTTC
28538365 TCAAAAGCA
1 TCAAAAGCA
28538374 ATGAAGAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:28538344 original size:26 final size:26
Alignment explanation
Indices: 28538308--28538373 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
28538298 AAACACTCAA
* *
28538308 ATTTTTCAAAAGTACTTCTCAAAAGC
1 ATTTCTCAAAAGCACTTCTCAAAAGC
*
28538334 ATTTCTCAAAAGCACTTCTTAAAAGC
1 ATTTCTCAAAAGCACTTCTCAAAAGC
28538360 ATTTCTCAAAAGCA
1 ATTTCTCAAAAGCA
28538374 ATGAAGAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (26 bp):
ATTTCTCAAAAGCACTTCTCAAAAGC
Found at i:28541372 original size:16 final size:18
Alignment explanation
Indices: 28541335--28541372 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
28541325 TTTCGGAATT
*
28541335 TTCAAGATTTTTTTATAC
1 TTCAAGATTTTTTAATAC
28541353 TTCAA-ATTTTTTAATA-
1 TTCAAGATTTTTTAATAC
28541369 TTCA
1 TTCA
28541373 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 10 0.53
18 5 0.26
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (18 bp):
TTCAAGATTTTTTAATAC
Found at i:28548757 original size:6 final size:6
Alignment explanation
Indices: 28548746--28548775 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28548736 ATGAGATTGC
28548746 CATAGT CATAGT CATAGT CATAGT CATAGT
1 CATAGT CATAGT CATAGT CATAGT CATAGT
28548776 AATACTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (6 bp):
CATAGT
Found at i:28562477 original size:33 final size:34
Alignment explanation
Indices: 28562402--28562466 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
28562392 TTGAGAAGTT
* **
28562402 GAAGTATGCCTTGAAGGCTAAGTGTCTTGGAAGAC
1 GAAGCATGCCTTGAAGGCT-AGTGTCTAAGAAGAC
28562437 GAAGCATGCCTTGAAGGCT-GTGTCTAAGAA
1 GAAGCATGCCTTGAAGGCTAGTGTCTAAGAA
28562467 TAGCAAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 9 0.33
35 18 0.67
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (34 bp):
GAAGCATGCCTTGAAGGCTAGTGTCTAAGAAGAC
Found at i:28565531 original size:25 final size:27
Alignment explanation
Indices: 28565477--28565531 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 27
28565467 TCTTTGATGA
*
28565477 AATTTATTTATTAATATTATTATATTG
1 AATTTATTTATTAATATTATTATATAG
*
28565504 AATTT-TTTA-TAATTTTAATTA-ATAG
1 AATTTATTTATTAATATT-ATTATATAG
28565529 AAT
1 AAT
28565532 AAATTTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 12 0.48
26 8 0.32
27 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (27 bp):
AATTTATTTATTAATATTATTATATAG
Found at i:28590976 original size:18 final size:19
Alignment explanation
Indices: 28590953--28590988 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28590943 TATTTATTAT
28590953 TCTC-TTTCCTTTCCCATC
1 TCTCTTTTCCTTTCCCATC
*
28590971 TCTCTTTTTCTTTCCCAT
1 TCTCTTTTCCTTTCCCAT
28590989 TCGAATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTCTTTTCCTTTCCCATC
Found at i:28595315 original size:107 final size:108
Alignment explanation
Indices: 28595129--28595343 Score: 414
Period size: 107 Copynumber: 2.0 Consensus size: 108
28595119 GGTTTGGATG
*
28595129 GGCGATTGGGTGCGGTGCGATGCGTTTAGTTTACTTTTTATCTCACGCTATAGTATCGCTACAGT
1 GGCGATTGGGTGCGGTGCGATGCGTTTAGTTTACTTTTTATCTCACGCTATAGTATCGCTAAAGT
28595194 ATCTAATCTCACCGCCACCGCTGTTTTTACAC-AACCGCAGGT
66 ATCTAATCTCACCGCCACCGCTGTTTTTACACTAACCGCAGGT
28595236 GGCGATTGGGTGCGGTGCGATGCGTTTAGTTTACTTTTTATCTCACGCTATAGTATCGCTAAAGT
1 GGCGATTGGGTGCGGTGCGATGCGTTTAGTTTACTTTTTATCTCACGCTATAGTATCGCTAAAGT
28595301 ATCTAATCTCACCGCCACCGCTGTTTTTACACTAACCGCAGGT
66 ATCTAATCTCACCGCCACCGCTGTTTTTACACTAACCGCAGGT
28595344 AAACGCACCG
Statistics
Matches: 106, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
107 96 0.91
108 10 0.09
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (108 bp):
GGCGATTGGGTGCGGTGCGATGCGTTTAGTTTACTTTTTATCTCACGCTATAGTATCGCTAAAGT
ATCTAATCTCACCGCCACCGCTGTTTTTACACTAACCGCAGGT
Found at i:28597203 original size:12 final size:12
Alignment explanation
Indices: 28597186--28597212 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28597176 TTTTTATTAT
28597186 TAAAAATTTGTG
1 TAAAAATTTGTG
28597198 TAAAAATTTGTG
1 TAAAAATTTGTG
28597210 TAA
1 TAA
28597213 TTGACTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (12 bp):
TAAAAATTTGTG
Found at i:28605158 original size:18 final size:18
Alignment explanation
Indices: 28605135--28605199 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
28605125 AATTTTATCT
28605135 ATTTATTTATAAAGACTA
1 ATTTATTTATAAAGACTA
*** *
28605153 ATTTATTTATTTATTTA-AA
1 ATTTATTTA--TAAAGACTA
*
28605172 ATTTTTTTATAAAGACTA
1 ATTTATTTATAAAGACTA
28605190 ATTTATTTAT
1 ATTTATTTAT
28605200 TTTTTGAGTA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
17 3 0.09
18 19 0.56
19 9 0.26
20 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
ATTTATTTATAAAGACTA
Done.