Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001991.1 Hibiscus syriacus cultivar Beakdansim tig00004072_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2373627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:871871 original size:31 final size:31
Alignment explanation
Indices: 871833--871988 Score: 217
Period size: 31 Copynumber: 5.0 Consensus size: 31
871823 CCCGAAGGAC
* *
871833 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
871864 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
871895 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
871926 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
871957 CAGTCCATATG-TCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
871988 C
1 C
871989 CCTCCACCCT
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
30 2 0.02
31 108 0.97
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:871930 original size:62 final size:62
Alignment explanation
Indices: 871833--871986 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
871823 CCCGAAGGAC
* *
871833 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
871895 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
871957 CAGTCCATATG-TCCAGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
871987 ACCCTCCACC
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 3 0.03
62 82 0.95
63 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:872192 original size:23 final size:24
Alignment explanation
Indices: 872166--872212 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
872156 ATACACTTGT
*
872166 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
872189 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
872213 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:872841 original size:21 final size:21
Alignment explanation
Indices: 872811--872855 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
872801 ATTCTGTCGT
* *
872811 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
872832 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
872853 TTG
1 TTG
872856 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:875845 original size:31 final size:31
Alignment explanation
Indices: 875807--875958 Score: 211
Period size: 31 Copynumber: 5.0 Consensus size: 31
875797 TGTCCCGAAG
* *
875807 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAT
* *
875838 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
* *
875869 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
875900 CAGTCCATATGTCCCGAAGAACATAGGTAA-
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
*
875930 CAGTCCATATGT-CCAAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
875959 ACCCTCCACC
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.15
30 12 0.11
31 80 0.73
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:875904 original size:62 final size:61
Alignment explanation
Indices: 875807--875958 Score: 236
Period size: 62 Copynumber: 2.5 Consensus size: 61
875797 TGTCCCGAAG
* *
875807 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGT-AA
*
875869 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAA
*
875930 CAGTCCATATG-TCCAAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
875959 ACCCTCCACC
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
60 17 0.20
61 12 0.14
62 54 0.64
63 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (61 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:876795 original size:21 final size:21
Alignment explanation
Indices: 876765--876809 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
876755 ATTCTGTCGT
* *
876765 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
876786 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
876807 TTG
1 TTG
876810 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:879192 original size:58 final size:58
Alignment explanation
Indices: 879114--879224 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
879104 CTGTAAACAG
*
879114 TACATACATTTTCTGATCTATCATGTTATACCAATTCCATGCATTCTTCGTATATCAA
1 TACATACATGTTCTGATCTATCATGTTATACCAATTCCATGCATTCTTCGTATATCAA
* *
879172 TACATGCATGTTCTGTTCTATCATGTTATACCAATTCCATGCATTCTTCGTAT
1 TACATACATGTTCTGATCTATCATGTTATACCAATTCCATGCATTCTTCGTAT
879225 CATATAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (58 bp):
TACATACATGTTCTGATCTATCATGTTATACCAATTCCATGCATTCTTCGTATATCAA
Found at i:879614 original size:60 final size:60
Alignment explanation
Indices: 879520--879669 Score: 209
Period size: 60 Copynumber: 2.5 Consensus size: 60
879510 CCCGAAGGAC
* *
879520 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGT-AA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAA-GA-ACAGGTAAA
*
879581 CAGTCCGTATGTTCCG-AGAACATAGGTAATCAGTCCATATGTCCCGAAGAACAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACAGGTAAA
879640 CAGTCCATATG-TCCAGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
879670 AACCCTGACC
Statistics
Matches: 81, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
58 8 0.10
59 15 0.19
60 44 0.54
61 13 0.16
62 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (60 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACAGGTAAA
Found at i:879636 original size:29 final size:29
Alignment explanation
Indices: 879520--879662 Score: 148
Period size: 29 Copynumber: 4.8 Consensus size: 29
879510 CCCGAAGGAC
*
879520 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAA-C-AGGTAAT
*
879551 CAGTCCATATGTCCCGAAGGACATAGGTAA-
1 CAGTCCATATGTCCCGAA-GA-ACAGGTAAT
* *
879581 CAGTCCGTATGTTCCG-AGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAAC--AGGTAAT
*
879611 CAGTCCATATGTCCCGAAGAACAGGTAAA
1 CAGTCCATATGTCCCGAAGAACAGGTAAT
*
879640 CAGTCCATATGTCCAGAAGAACA
1 CAGTCCATATGTCCCGAAGAACA
879663 TAGGTAAAAC
Statistics
Matches: 96, Mismatches: 9, Indels: 16
0.79 0.07 0.13
Matches are distributed among these distances:
27 1 0.01
28 2 0.02
29 35 0.36
30 28 0.29
31 26 0.27
32 3 0.03
33 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (29 bp):
CAGTCCATATGTCCCGAAGAACAGGTAAT
Found at i:880363 original size:35 final size:38
Alignment explanation
Indices: 880311--880381 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
880301 ATCTACATAA
880311 ATGTACATTTTCGAGGT-A-ATTAGATACCTACCCCTT
1 ATGTACATTTTCGAGGTAACATTAGATACCTACCCCTT
880347 ATGTACA-TTTCGAGGTAATCATTAGATACCTACCC
1 ATGTACATTTTCGAGGTAA-CATTAGATACCTACCC
880382 TTGTATGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 9 0.28
36 8 0.25
38 15 0.47
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (38 bp):
ATGTACATTTTCGAGGTAACATTAGATACCTACCCCTT
Found at i:880534 original size:21 final size:21
Alignment explanation
Indices: 880504--880548 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
880494 ATTCTGTCGT
* *
880504 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
880525 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
880546 TTG
1 TTG
880549 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:895834 original size:39 final size:39
Alignment explanation
Indices: 895788--895865 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
895778 GGTGATGAAG
895788 ACTATGATTACTTGTTTAAGTTTGTGTTGATAGGTGACT
1 ACTATGATTACTTGTTTAAGTTTGTGTTGATAGGTGACT
895827 ACTATGATTACTTGTTTAAGTTTGTGTTGATAGGTGACT
1 ACTATGATTACTTGTTTAAGTTTGTGTTGATAGGTGACT
895866 CCGGTGTCGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (39 bp):
ACTATGATTACTTGTTTAAGTTTGTGTTGATAGGTGACT
Found at i:900201 original size:16 final size:16
Alignment explanation
Indices: 900180--900224 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
900170 TCATTTTTGT
*
900180 AGTTTGAGCGTTTCGA
1 AGTTTGAGAGTTTCGA
*
900196 AGTTTGA-AGTTTTGA
1 AGTTTGAGAGTTTCGA
900211 ATGTTTGAGAGTTT
1 A-GTTTGAGAGTTT
900225 AGAGTTACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 13 0.52
17 5 0.20
ACGTcount: A:0.22, C:0.04, G:0.29, T:0.44
Consensus pattern (16 bp):
AGTTTGAGAGTTTCGA
Found at i:900468 original size:82 final size:80
Alignment explanation
Indices: 900305--900663 Score: 326
Period size: 82 Copynumber: 4.3 Consensus size: 80
900295 GAAATGACAG
* * * * *
900305 AGATTCTCTGAATAATAATGAAAAATGTTTTCCCCGAATCACGCCTTTCATTTCGGATGGGATGG
1 AGATTCTCTAAATAATAATGGAAAATG--TT-CCCAAAACATGCCTTTCATTTC-----GGATGG
* * *
900370 GATGAAACATTCTGACATGGCAA
58 GATGAAACACTCTAACATGGAAA
* **
900393 AGATTCTCTGAATAATAATGGAAATATGTTCTCCAAAACATGTTTTTCATTTCGGATGGGATGAA
1 AGATTCTCTAAATAATAATGGAAA-ATGTTC-CCAAAACATGCCTTTCATTTCGGATGGGATGAA
* * *
900458 ACACTTTGACAT-GACAG
64 ACACTCTAACATGGA-AA
* * *
900475 AGATTCTCTAAATAATAATGGAAAATGTTTTCCCCAAAACACGCCTTTCATTT-TGATGAGATGA
1 AGATTCTCTAAATAATAATGGAAAATG--TT-CCCAAAACATGCCTTTCATTTCGGATGGGATGA
900539 AACACTCTAACATGGAAA
63 AACACTCTAACATGGAAA
* * **
900557 AGATTCTCTAAATAATAATGGAAACATTTTACCCGAAATGTGCCTTTCATTTCGGATGGGATGAA
1 AGATTCTCTAAATAATAATGGAAA-ATGTT-CCCAAAACATGCCTTTCATTTCGGATGGGATGAA
*
900622 ACACTCCAACATGGAAA
64 ACACTCTAACATGGAAA
* * * *
900639 AAATTCTCTGAACATTAATGGAAAA
1 AGATTCTCTAAATAATAATGGAAAA
900664 CGCTTCTCTC
Statistics
Matches: 230, Mismatches: 32, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
81 24 0.10
82 137 0.60
83 23 0.10
84 1 0.00
86 1 0.00
87 18 0.08
88 23 0.10
89 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (80 bp):
AGATTCTCTAAATAATAATGGAAAATGTTCCCAAAACATGCCTTTCATTTCGGATGGGATGAAAC
ACTCTAACATGGAAA
Found at i:900620 original size:164 final size:166
Alignment explanation
Indices: 900298--900626 Score: 448
Period size: 164 Copynumber: 2.0 Consensus size: 166
900288 ATTATGTGAA
* * *
900298 ATGACAGAGATTCTCTGAATAATAATGAAAAATGTTTTCCCCGAATCACGCCTTTCATTTCGGAT
1 ATGACAGAGATTCTCTAAATAATAATGAAAAATGTTTTCCCCAAAACACGCCTTTCATTT--G-T
* * * * * *
900363 GGGATGGGATGAAACATTCTGACATGGCAAAGATTCTCTGAATAATAATGGAAATATGTTCTCCA
63 -GGATGAGATGAAACACTCTAACATGGAAAAGATTCTCTAAATAATAATGGAAACATGTTCTCCA
**
900428 AAACATGTTTTTCATTTCGGATGGGATGAAACACTTTGAC
127 AAACATGCCTTTCATTTCGGATGGGATGAAACACTTTGAC
*
900468 ATGACAGAGATTCTCTAAATAATAATGGAAAATGTTTTCCCCAAAACACGCCTTTCATTT-T-GA
1 ATGACAGAGATTCTCTAAATAATAATGAAAAATGTTTTCCCCAAAACACGCCTTTCATTTGTGGA
* *
900531 TGAGATGAAACACTCTAACATGGAAAAGATTCTCTAAATAATAATGGAAACATTTTAC-CCGAAA
66 TGAGATGAAACACTCTAACATGGAAAAGATTCTCTAAATAATAATGGAAACATGTT-CTCCAAAA
**
900595 TGTGCCTTTCATTTCGGATGGGATGAAACACT
130 CATGCCTTTCATTTCGGATGGGATGAAACACT
900627 CCAACATGGA
Statistics
Matches: 142, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
164 84 0.59
165 1 0.01
166 1 0.01
170 56 0.39
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (166 bp):
ATGACAGAGATTCTCTAAATAATAATGAAAAATGTTTTCCCCAAAACACGCCTTTCATTTGTGGA
TGAGATGAAACACTCTAACATGGAAAAGATTCTCTAAATAATAATGGAAACATGTTCTCCAAAAC
ATGCCTTTCATTTCGGATGGGATGAAACACTTTGAC
Found at i:900647 original size:164 final size:166
Alignment explanation
Indices: 900298--900663 Score: 425
Period size: 164 Copynumber: 2.2 Consensus size: 166
900288 ATTATGTGAA
* * * * *
900298 ATGACAGAGATTCTCTGAATAATAATGAAAAATGTTTTCCCCGAATCACGCCTTTCATTTCGGAT
1 ATGACAAAAATTCTCTGAATAATAATGGAAAATGTTTTCCCCAAAACACGCCTTTCATTT--G-T
* * * * * *
900363 GGGATGGGATGAAACATTCTGACATGGCAAAGATTCTCTGAATAATAATGGAAATATGTTCTCCA
63 -GGATGAGATGAAACACTCTAACATGGAAAAGATTCTCTAAATAATAATGGAAACATGTTCTCCA
** ***
900428 AAACATGTTTTTCATTTCGGATGGGATGAAACACTTTGAC
127 AAACATGCCTTTCATTTCGGATGGGATGAAACACTCCAAC
* * *
900468 ATGACAGAGATTCTCTAAATAATAATGGAAAATGTTTTCCCCAAAACACGCCTTTCATTT-T-GA
1 ATGACAAAAATTCTCTGAATAATAATGGAAAATGTTTTCCCCAAAACACGCCTTTCATTTGTGGA
* *
900531 TGAGATGAAACACTCTAACATGGAAAAGATTCTCTAAATAATAATGGAAACATTTTAC-CCGAAA
66 TGAGATGAAACACTCTAACATGGAAAAGATTCTCTAAATAATAATGGAAACATGTT-CTCCAAAA
**
900595 TGTGCCTTTCATTTCGGATGGGATGAAACACTCCAAC
130 CATGCCTTTCATTTCGGATGGGATGAAACACTCCAAC
* *
900632 ATGGA-AAAAATTCTCTGAACATTAATGGAAAA
1 AT-GACAAAAATTCTCTGAATAATAATGGAAAA
900664 CGCTTCTCTC
Statistics
Matches: 170, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
164 110 0.65
165 3 0.02
166 1 0.01
170 56 0.33
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (166 bp):
ATGACAAAAATTCTCTGAATAATAATGGAAAATGTTTTCCCCAAAACACGCCTTTCATTTGTGGA
TGAGATGAAACACTCTAACATGGAAAAGATTCTCTAAATAATAATGGAAACATGTTCTCCAAAAC
ATGCCTTTCATTTCGGATGGGATGAAACACTCCAAC
Found at i:900728 original size:83 final size:83
Alignment explanation
Indices: 900641--900830 Score: 208
Period size: 84 Copynumber: 2.3 Consensus size: 83
900631 CATGGAAAAA
* * * * *
900641 ATTCTCTGAACATTAATGGAAAACGCTTCTC-T-CAAAATGCACATTTTATTTTGGAT-GGTATG
1 ATTCTCTGAATAATAATGGAAAACGCTTCCCTTGCAAAATGC-C-TTTCATTTTGAATAGG-ATG
900703 AAT-ATCTATTATAATCCAGAG
63 AATCA-CTATTATAATCCAGAG
* * ** *
900724 ATTCTTTGAATAATAATGGAAAAACGCTTCCCTTGGAACGTGCCTTTCATTTTGAATAGGATGGA
1 ATTCTCTGAATAATAATGG-AAAACGCTTCCCTTGCAAAATGCCTTTCATTTTGAATAGGATGAA
*
900789 TCACTATTATAATCCAGAT
65 TCACTATTATAATCCAGAG
900808 ATTCTCTGAATAATAATGGAAAA
1 ATTCTCTGAATAATAATGGAAAA
900831 ACACATCCCC
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
83 20 0.22
84 60 0.67
85 5 0.06
86 5 0.06
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (83 bp):
ATTCTCTGAATAATAATGGAAAACGCTTCCCTTGCAAAATGCCTTTCATTTTGAATAGGATGAAT
CACTATTATAATCCAGAG
Found at i:901463 original size:83 final size:80
Alignment explanation
Indices: 901357--901703 Score: 361
Period size: 82 Copynumber: 4.2 Consensus size: 80
901347 GAAAACTCTG
* * * * ***
901357 ACATGACAAAGATTCTCTGAATAATAATGGAAAATATTTTCCCCAAAACATATTTTTCATTTCGG
1 ACATGGCAGAGATTCTCTAAATAATAAT-GAAAACATTTTCCCCAAAACATGCCTTTCATTTC-G
* * *
901422 ATAGGATAAAACAATTTG
64 AT-GGATGAAACAATCTA
* * ** *
901440 ATATGGCAGAGATTCTCTGAATAATAATAGAAAATGTTTTCCCCAAAACACGCCTTTCATTTCGA
1 ACATGGCAGAGATTCTCTAAATAATAAT-GAAAACATTTTCCCCAAAACATGCCTTTCATTTCGA
901505 TGAGATGAAACAATCTA
65 TG-GATGAAACAATCTA
** *
901522 ACATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCTGAAATATGCCTTTCATTTCAGA
1 ACATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCCAAAACATGCCTTTCATTTC-GA
* * *
901587 TGGGATGGAACACTCCA
65 T-GGATGAAACAATCTA
** *
901604 ACATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCTGAAATATGCCTTTCATTTCTGA
1 ACATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCCAAAACATGCCTTTCATTTC-GA
* * *
901669 TGGGATGGAACACTCCA
65 T-GGATGAAACAATCTA
*
901686 ACATGGCAAAGATTCTCT
1 ACATGGCAGAGATTCTCT
901704 GAACATTAAT
Statistics
Matches: 236, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
81 29 0.12
82 152 0.64
83 55 0.23
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (80 bp):
ACATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCCAAAACATGCCTTTCATTTCGAT
GGATGAAACAATCTA
Found at i:901607 original size:82 final size:81
Alignment explanation
Indices: 901442--901703 Score: 389
Period size: 82 Copynumber: 3.2 Consensus size: 81
901432 ACAATTTGAT
* ** ** * *
901442 ATGGCAGAGATTCTCTGAATAATAATAGAAAATGTTTTCCCCAAAACACGCCTTTCATTTCGATG
1 ATGGCAGAGATTCTCTAAATAATAAT-GAAAACATTTTCCCTGAAATATGCCTTTCATTTCGATG
* * * *
901507 AGATGAAACAATCTAAC
65 GGATGGAACACTCCAAC
901524 ATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCTGAAATATGCCTTTCATTTCAGATG
1 ATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCTGAAATATGCCTTTCATTTC-GATG
901589 GGATGGAACACTCCAAC
65 GGATGGAACACTCCAAC
901606 ATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCTGAAATATGCCTTTCATTTCTGATG
1 ATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCTGAAATATGCCTTTCATTTC-GATG
901671 GGATGGAACACTCCAAC
65 GGATGGAACACTCCAAC
*
901688 ATGGCAAAGATTCTCT
1 ATGGCAGAGATTCTCT
901704 GAACATTAAT
Statistics
Matches: 166, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
81 28 0.17
82 138 0.83
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (81 bp):
ATGGCAGAGATTCTCTAAATAATAATGAAAACATTTTCCCTGAAATATGCCTTTCATTTCGATGG
GATGGAACACTCCAAC
Found at i:902847 original size:26 final size:27
Alignment explanation
Indices: 902812--902866 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
902802 TGGACTATAA
*
902812 AAACAACAAACCA-TAAACATTACATT
1 AAACAACAAACCATTAAACATGACATT
* *
902838 AAACAACAAACTATTAATCATGACATT
1 AAACAACAAACCATTAAACATGACATT
902865 AA
1 AA
902867 GAATATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.56, C:0.20, G:0.02, T:0.22
Consensus pattern (27 bp):
AAACAACAAACCATTAAACATGACATT
Found at i:902927 original size:34 final size:32
Alignment explanation
Indices: 902907--902968 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
902897 CATATCTATC
*
902907 ACACACCTTAAACAGTAAATAAAAGCATAGTA
1 ACACACCTTAAACAGTAAATAAAAGCATACTA
* *
902939 ATACACCTTAAACAGTAAATATAAGCATAC
1 ACACACCTTAAACAGTAAATAAAAGCATAC
902969 ACGCGCGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (32 bp):
ACACACCTTAAACAGTAAATAAAAGCATACTA
Found at i:904228 original size:21 final size:21
Alignment explanation
Indices: 904179--904232 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
904169 CCATACATTG
* *
904179 TGGCATATGAACCGATGGATT
1 TGGCATATGAACCGATAGATA
* * *
904200 TGGAATATGAACTGGTAGATA
1 TGGCATATGAACCGATAGATA
904221 TGGCATATGAAC
1 TGGCATATGAAC
904233 AGACAGCAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (21 bp):
TGGCATATGAACCGATAGATA
Found at i:905244 original size:37 final size:38
Alignment explanation
Indices: 905167--905246 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
905157 CCCAACCTGA
*
905167 TCGGGTCAGGTTTTTATAAAAAATTGGGTTCGAGTCGGG
1 TCGGGTCAGGTTTTTAT-AAAAAGTGGGTTCGAGTCGGG
* *
905206 TCGGGTCAGGTTTTT-T-AAAGGTGGTGTTCGAGTTGGG
1 TCGGGTCAGGTTTTTATAAAAAGTGG-GTTCGAGTCGGG
905243 TCGG
1 TCGG
905247 ATTCAAGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 6 0.16
37 15 0.41
38 1 0.03
39 15 0.41
ACGTcount: A:0.17, C:0.10, G:0.38, T:0.35
Consensus pattern (38 bp):
TCGGGTCAGGTTTTTATAAAAAGTGGGTTCGAGTCGGG
Found at i:914533 original size:22 final size:24
Alignment explanation
Indices: 914508--914558 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
914498 TATAATCTCA
914508 AATTTTAATT-AAA-TATATCATT
1 AATTTTAATTAAAACTATATCATT
*
914530 AATTTTGATTCAAAACTATATCATT
1 AATTTTAATT-AAAACTATATCATT
914555 AATT
1 AATT
914559 GAAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 9 0.36
24 3 0.12
25 13 0.52
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (24 bp):
AATTTTAATTAAAACTATATCATT
Found at i:915187 original size:2 final size:2
Alignment explanation
Indices: 915131--915168 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
915121 TATCCCATTG
915131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
915169 CAAATAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:919643 original size:29 final size:28
Alignment explanation
Indices: 919611--919677 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
919601 AATATTTTTC
919611 ATTATTAAAATTTTAAAAG-TTATAAAATA
1 ATTATTAAAATTTTAAAAGATTAT-AAA-A
***
919640 ATTATTACTTTTTTAAAAGATTATAAAA
1 ATTATTAAAATTTTAAAAGATTATAAAA
919668 ATTATTAAAA
1 ATTATTAAAA
919678 CATCAAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 8 0.26
29 19 0.61
30 4 0.13
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTATTAAAATTTTAAAAGATTATAAAA
Found at i:922415 original size:3 final size:3
Alignment explanation
Indices: 922407--922478 Score: 110
Period size: 3 Copynumber: 23.3 Consensus size: 3
922397 CGGGTCTTTT
922407 TTA TTA TTA TT- TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
922453 TTA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA T
922479 GTTTATTAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.02
3 58 0.89
4 5 0.08
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:923908 original size:30 final size:29
Alignment explanation
Indices: 923874--923940 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
923864 CTGTTTTTAT
923874 TATTTTAGTCCTATAA-ATTCATGTTTATGC
1 TATTTTAGTCCTATAACATTC-TGTTT-TGC
* * * *
923904 TATTTCAGTCCTTTAACTTTCTGTTTTGT
1 TATTTTAGTCCTATAACATTCTGTTTTGC
923933 TATTTTAG
1 TATTTTAG
923941 CCATGTAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 9 0.29
30 19 0.61
31 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.55
Consensus pattern (29 bp):
TATTTTAGTCCTATAACATTCTGTTTTGC
Found at i:923966 original size:59 final size:59
Alignment explanation
Indices: 923795--923967 Score: 158
Period size: 59 Copynumber: 2.9 Consensus size: 59
923785 TCTATTTGGC
* ** * * *
923795 CCTTTAAGTTTCTGTTTTT-CCATTTTAGTCCTCTACCTTTCTGTTTTAGCT-TTTCAGT
1 CCTTTAACTTTCTGTTTTTATTATTTTAGTCCTATA-ATTTCTGTTTTATCTATTTCAGT
* ** *
923853 TCTTTATGTTTCTGTTTTTATTATTTTAGTCCTATAAATTCATG-TTTATGCTATTTCAGT
1 CCTTTAACTTTCTGTTTTTATTATTTTAGTCCTATAATTTC-TGTTTTAT-CTATTTCAGT
* *
923913 CCTTTAACTTTCTG-TTTTGTTATTTTAG-CCATGTAAGTTTCTGTTTTATCTATTT
1 CCTTTAACTTTCTGTTTTTATTATTTTAGTCC-TATAA-TTTCTGTTTTATCTATTT
923968 TGATCATTAA
Statistics
Matches: 94, Mismatches: 14, Indels: 13
0.78 0.12 0.11
Matches are distributed among these distances:
58 26 0.28
59 42 0.45
60 26 0.28
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.57
Consensus pattern (59 bp):
CCTTTAACTTTCTGTTTTTATTATTTTAGTCCTATAATTTCTGTTTTATCTATTTCAGT
Found at i:923982 original size:29 final size:28
Alignment explanation
Indices: 923861--923998 Score: 72
Period size: 29 Copynumber: 4.7 Consensus size: 28
923851 GTTCTTTATG
923861 TTTCTGTTTTTATTATTTTAGTCC-TATAAA
1 TTTCTG-TTTTATTATTTTAG-CCAT-TAAA
* * *
923891 -TTCATG-TTTATGCTATTTCAGTCCTTTAAC
1 TTTC-TGTTTTAT--TATTTTAG-CCATTAAA
* *
923921 TTTCTGTTTTGTTATTTTAGCCATGTAAG
1 TTTCTGTTTTATTATTTTAGCCAT-TAAA
*
923950 TTTCTGTTTTATCTATTTT-GATCATTAAA
1 TTTCTGTTTTAT-TATTTTAG-CCATTAAA
923979 TTTCCT-TATTTA-TATTTTAG
1 TTT-CTGT-TTTATTATTTTAG
923999 TCCTATTATT
Statistics
Matches: 87, Mismatches: 9, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
28 14 0.16
29 33 0.38
30 32 0.37
31 8 0.09
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.57
Consensus pattern (28 bp):
TTTCTGTTTTATTATTTTAGCCATTAAA
Found at i:926136 original size:31 final size:32
Alignment explanation
Indices: 926100--926161 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
926090 ATTTTACATG
926100 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
926131 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
926162 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:928636 original size:20 final size:20
Alignment explanation
Indices: 928613--928687 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
928603 ATCTCTTTGA
928613 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
928633 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
928659 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
928678 CACCTTGAAA
1 GACCTTGAAA
928688 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:930469 original size:4 final size:4
Alignment explanation
Indices: 930460--930497 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
930450 AAAAGTATAC
930460 ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
930498 GATACGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 30 0.94
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:931157 original size:105 final size:102
Alignment explanation
Indices: 930970--931208 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 102
930960 TGAGAATTTT
* * *
930970 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
931035 AAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 AAAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
931075 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* * *
931139 ATTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 A-AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
931177 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
931209 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 7 0.06
104 5 0.04
105 78 0.66
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:931199 original size:36 final size:36
Alignment explanation
Indices: 931154--931273 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
931144 ACAAAGTTGA
**
931154 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
931190 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * *
931226 TCTCATTTGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTT-G
*
931260 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
931274 TCATTTTCTC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 8 0.11
36 40 0.57
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:931672 original size:28 final size:29
Alignment explanation
Indices: 931525--931657 Score: 218
Period size: 29 Copynumber: 4.7 Consensus size: 29
931515 ACAGTTTCTC
931525 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
*
931553 TTGAATAAAAATCTTAGAGTTTGTTCCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
*
931582 TTGAATAAAAATCTTAGAGTTTGTTCCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
*
931611 TTGAATAAAAATCTTTGAG-TTGTTTCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
931639 TTGAA-AAAAATCTTTGAGT
1 TTGAATAAAAATCTTTGAGT
931658 CTATTTATTT
Statistics
Matches: 100, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
27 13 0.13
28 18 0.18
29 69 0.69
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (29 bp):
TTGAATAAAAATCTTTGAGTTTGTTCCTT
Found at i:931682 original size:28 final size:27
Alignment explanation
Indices: 931525--931672 Score: 122
Period size: 29 Copynumber: 5.2 Consensus size: 27
931515 ACAGTTTCTC
*
931525 TTGAAAAAAATCTTTGAGTT-TGTTCCTT
1 TTGAAAAAAATCTTTGAGTTAT-TT-ATT
* *
931553 TTGAATAAAAATCTTAGAGTT-TGTTCCTT
1 TTGAA-AAAAATCTTTGAGTTAT-TT-ATT
* *
931582 TTGAATAAAAATCTTAGAGTT-TGTTCCTT
1 TTGAA-AAAAATCTTTGAGTTAT-TT-ATT
* *
931611 TTGAATAAAAATCTTTGAGTTGTTTCTT
1 TTGAA-AAAAATCTTTGAGTTATTTATT
931639 TTGAAAAAAATCTTTGAGTCTATTTATT
1 TTGAAAAAAATCTTTGAGT-TATTTATT
931667 TTGAAA
1 TTGAAA
931673 CAAAGTTTTG
Statistics
Matches: 113, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
27 14 0.12
28 25 0.22
29 73 0.65
30 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.46
Consensus pattern (27 bp):
TTGAAAAAAATCTTTGAGTTATTTATT
Found at i:931746 original size:52 final size:53
Alignment explanation
Indices: 931668--931770 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
931658 CTATTTATTT
* *
931668 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTGTTGTCTCTCTTGAGACAATGTCGTGAAAAAATCTTTGAGTC
931720 TGAAACAAAGTGTTGTCTCTCTTGAGACAATGTCGTGAAAAAATCTTTGAG
1 TGAAACAAAGTGTTGTCTCTCTTGAGACAATGTCGTGAAAAAATCTTTGAG
931771 ATTGTTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 35 0.73
53 13 0.27
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (53 bp):
TGAAACAAAGTGTTGTCTCTCTTGAGACAATGTCGTGAAAAAATCTTTGAGTC
Found at i:931822 original size:29 final size:30
Alignment explanation
Indices: 931758--931821 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
931748 AATGTCGTGA
* *
931758 AAAAATCTTTGAGATTGTTTTTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
*
931788 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
931818 AAAA
1 AAAA
931822 TTTTGTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:932200 original size:50 final size:51
Alignment explanation
Indices: 932099--932204 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 51
932089 GTGATCCATC
* * *
932099 TTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCT
1 TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCGCTTAAAGACAACTTCT
* * **
932150 TTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCGC-TCGAGACAACTTCT
1 TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCGCTTAAAGACAACTTCT
932200 TTTGA
1 TTTGA
932205 AAATACCCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 16 0.33
51 32 0.67
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (51 bp):
TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCGCTTAAAGACAACTTCT
Found at i:932758 original size:36 final size:35
Alignment explanation
Indices: 932705--932818 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 35
932695 GAAACACTGA
*
932705 TCTTTGAGATCA-ATTCCCTTTAAACGAATTTTGTC
1 TCTTTGAGA-CAGTTTCCCTTTAAACGAATTTTGTC
932740 TCATTTGAGACAGTTTCCCTTTAAAC-------GTC
1 TC-TTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
* *
932769 ATCTTTGAGTC-GTTTCCCTTAAAACGAATTTTGTC
1 -TCTTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
932804 TCTTTTGAGACAGTT
1 TC-TTTGAGACAGTT
932819 GCTTTTAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
28 13 0.21
29 10 0.16
30 2 0.03
34 2 0.03
35 14 0.22
36 22 0.35
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (35 bp):
TCTTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
Found at i:933130 original size:129 final size:132
Alignment explanation
Indices: 932916--933240 Score: 442
Period size: 129 Copynumber: 2.5 Consensus size: 132
932906 CCAGCCGTCC
* * *
932916 TCATCATGTAGGAACCGTGTCATCCCCAGACCATATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCATGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
* * *
932981 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA-CCT-T-TAGATGGCCAGAACT
66 ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCCTCTAAAGATGACCAGAACT
933043 CT
131 CT
* *
933045 TCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCATC
1 TCATCATGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
*
933110 C-TAGATAACCAGCCATCCTCATCACGTAGGAATCGTGTTATCACTCCTCCTAAAGATGACCAGA
65 CATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCAC-CCT-CTAAAGATGACCAGA
933174 ACTCT
128 ACTCT
* ** * * * * *
933179 TCATCATGTATGAGCAGTGTCATCCCTTGATCAGATTTCCTCATCATGTAGGAACCTTGTCA
1 TCATCATGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
933241 CTTTTAGACG
Statistics
Matches: 172, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
129 59 0.34
130 41 0.24
131 3 0.02
133 34 0.20
134 35 0.20
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (132 bp):
TCATCATGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCCTCTAAAGATGACCAGAACT
CT
Found at i:933266 original size:134 final size:129
Alignment explanation
Indices: 932932--933281 Score: 373
Period size: 134 Copynumber: 2.7 Consensus size: 129
932922 TGTAGGAACC
* * * * * *
932932 GTGTCA-TCCCCAGACCATATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
1 GTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAACCGTGTCATCC-TAGACAACCAGACA
* * *
932996 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
65 TCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGACCAGAACTCTTCATCACGTATGAGCA
* * *
933061 GTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCATCCTAGATAACCAGCCAT
1 GTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAACCGTGTCATCCTAGACAACCAGACAT
* *
933126 CCTCATCACGTAGGAATCGTGTTATCACTCCTCCTAAAGATGACCAGAACTCTTCATCATGTATG
66 CCTCATCACGTAGGAACCGTGTTATCA--CCT--T-AAGATGACCAGAACTCTTCATCACGTATG
933191 AGCA
126 AGCA
** * * * * ** *
933195 GTGTCA-TCCCTTGATCAGATTTCCTCATCATGTAGGAACCTTGTCACTTTTAGACGACCAGA-A
1 GTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAACCGTGTCA-TCCTAGACAACCAGACA
* * *
933258 CTCTTCATCACGTATGAGCCGTGT
65 -TCCTCATCACGTAGGAACCGTGT
933282 CATTCCCCAG
Statistics
Matches: 189, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
129 46 0.24
130 41 0.22
131 3 0.02
133 35 0.19
134 64 0.34
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (129 bp):
GTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAACCGTGTCATCCTAGACAACCAGACAT
CCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGACCAGAACTCTTCATCACGTATGAGCA
Found at i:933283 original size:217 final size:217
Alignment explanation
Indices: 932996--933499 Score: 909
Period size: 217 Copynumber: 2.3 Consensus size: 217
932986 TAACCAGCCG
* * * * *
932996 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
1 TCCTCATCATGTAGGAACC---TTGTCACTTTTAGACGACCAGAACTCTTCATCACGTATGAGCC
*
933061 GTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCATCCTAGATAACCAGCCAT
63 GTGTCATTCCCCAGACCAGATCTCCACATCACGTAGGAGCCGTGTCATCCTAGATAACCAGCCAT
933126 CCTCATCACGTAGGAATCGTGTTATCACTCCTCCTAAAGATGACCAGAACTCTTCATCATGTATG
128 CCTCATCACGTAGGAATCGTGTTATCACTCCTCCTAAAGATGACCAGAACTCTTCATCATGTATG
933191 AGCAGTGTCATCCCTTGATCAGATT
193 AGCAGTGTCATCCCTTGATCAGATT
933216 TCCTCATCATGTAGGAACCTTGTCACTTTTAGACGACCAGAACTCTTCATCACGTATGAGCCGTG
1 TCCTCATCATGTAGGAACCTTGTCACTTTTAGACGACCAGAACTCTTCATCACGTATGAGCCGTG
933281 TCATTCCCCAGACCAGATCTCCACATCACGTAGGAGCCGTGTCATCCTAGATAACCAGCCATCCT
66 TCATTCCCCAGACCAGATCTCCACATCACGTAGGAGCCGTGTCATCCTAGATAACCAGCCATCCT
933346 CATCACGTAGGAATCGTGTTATCACTCCTCCTAAAGATGACCAGAACTCTTCATCATGTATGAGC
131 CATCACGTAGGAATCGTGTTATCACTCCTCCTAAAGATGACCAGAACTCTTCATCATGTATGAGC
933411 AGTGTCATCCCTTGATCAGATT
196 AGTGTCATCCCTTGATCAGATT
* *
933433 TCCTCATCATGTAGGAACCTTGTCACTTTTAGACGACCAGAACTCTTCATCATGTATGAGCAGTG
1 TCCTCATCATGTAGGAACCTTGTCACTTTTAGACGACCAGAACTCTTCATCACGTATGAGCCGTG
933498 TC
66 TC
933500 GTCCCCAACA
Statistics
Matches: 276, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
217 258 0.93
220 18 0.07
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (217 bp):
TCCTCATCATGTAGGAACCTTGTCACTTTTAGACGACCAGAACTCTTCATCACGTATGAGCCGTG
TCATTCCCCAGACCAGATCTCCACATCACGTAGGAGCCGTGTCATCCTAGATAACCAGCCATCCT
CATCACGTAGGAATCGTGTTATCACTCCTCCTAAAGATGACCAGAACTCTTCATCATGTATGAGC
AGTGTCATCCCTTGATCAGATT
Found at i:933338 original size:83 final size:83
Alignment explanation
Indices: 933163--933338 Score: 210
Period size: 83 Copynumber: 2.1 Consensus size: 83
933153 CTCCTCCTAA
* ** * * * *
933163 AGATGACCAGAACTCTTCATCATGTATGAGCAGTGTCATCCCTTGATCAGATTTCCTCATCATGT
1 AGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCAGACCAGATCTCCACATCACGT
* **
933228 AGGAACCTTGTCACTTTT
66 AGGAACCGTGTCACTCCT
* *
933246 AGACGACCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCCACATCACG
1 AGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCA-TCCCCAGACCAGATCTCCACATCACG
*
933311 TAGGAGCCGTGTCA-TCCT
65 TAGGAACCGTGTCACTCCT
*
933329 AGATAACCAG
1 AGATGACCAG
933339 CCATCCTCAT
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 45 0.58
84 32 0.42
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (83 bp):
AGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCAGACCAGATCTCCACATCACGT
AGGAACCGTGTCACTCCT
Found at i:933660 original size:3 final size:3
Alignment explanation
Indices: 933652--933705 Score: 74
Period size: 3 Copynumber: 17.3 Consensus size: 3
933642 CGGGTCTTTT
933652 TTA TTA TTA TT- TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
933699 TTA TTA T
1 TTA TTA T
933706 GTTTATTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 40 0.85
4 5 0.11
5 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:933686 original size:25 final size:25
Alignment explanation
Indices: 933652--933713 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
933642 CGGGTCTTTT
933652 TTATTATTATT-TATATTTATTATTA
1 TTATTATTATTAT-TATTTATTATTA
933677 TTATTATTATTATTATTTATTATTA
1 TTATTATTATTATTATTTATTATTA
933702 TTATGT-TTATTA
1 TTAT-TATTATTA
933714 ATTACATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (25 bp):
TTATTATTATTATTATTTATTATTA
Found at i:935138 original size:30 final size:29
Alignment explanation
Indices: 935104--935170 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
935094 CTGTTTTTAT
935104 TATTTTAGTCCTATAA-ATTCATGTTTATGC
1 TATTTTAGTCCTATAACATTC-TGTTT-TGC
* * * *
935134 TATTTCAGTCCTTTAACTTTCTGTTTTGT
1 TATTTTAGTCCTATAACATTCTGTTTTGC
935163 TATTTTAG
1 TATTTTAG
935171 CCATGTAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 9 0.29
30 19 0.61
31 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.55
Consensus pattern (29 bp):
TATTTTAGTCCTATAACATTCTGTTTTGC
Found at i:935196 original size:59 final size:59
Alignment explanation
Indices: 935025--935197 Score: 158
Period size: 59 Copynumber: 2.9 Consensus size: 59
935015 TCTATTTGGC
* ** * * *
935025 CCTTTAAGTTTCTGTTTTT-CCATTTTAGTCCTCTACCTTTCTGTTTTAGCT-TTTCAGT
1 CCTTTAACTTTCTGTTTTTATTATTTTAGTCCTATA-ATTTCTGTTTTATCTATTTCAGT
* ** *
935083 TCTTTATGTTTCTGTTTTTATTATTTTAGTCCTATAAATTCATG-TTTATGCTATTTCAGT
1 CCTTTAACTTTCTGTTTTTATTATTTTAGTCCTATAATTTC-TGTTTTAT-CTATTTCAGT
* *
935143 CCTTTAACTTTCTG-TTTTGTTATTTTAG-CCATGTAAGTTTCTGTTTTATCTATTT
1 CCTTTAACTTTCTGTTTTTATTATTTTAGTCC-TATAA-TTTCTGTTTTATCTATTT
935198 TGATCATTAA
Statistics
Matches: 94, Mismatches: 14, Indels: 13
0.78 0.12 0.11
Matches are distributed among these distances:
58 26 0.28
59 42 0.45
60 26 0.28
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.57
Consensus pattern (59 bp):
CCTTTAACTTTCTGTTTTTATTATTTTAGTCCTATAATTTCTGTTTTATCTATTTCAGT
Found at i:935212 original size:29 final size:28
Alignment explanation
Indices: 935091--935228 Score: 72
Period size: 29 Copynumber: 4.7 Consensus size: 28
935081 GTTCTTTATG
935091 TTTCTGTTTTTATTATTTTAGTCC-TATAAA
1 TTTCTG-TTTTATTATTTTAG-CCAT-TAAA
* * *
935121 -TTCATG-TTTATGCTATTTCAGTCCTTTAAC
1 TTTC-TGTTTTAT--TATTTTAG-CCATTAAA
* *
935151 TTTCTGTTTTGTTATTTTAGCCATGTAAG
1 TTTCTGTTTTATTATTTTAGCCAT-TAAA
*
935180 TTTCTGTTTTATCTATTTT-GATCATTAAA
1 TTTCTGTTTTAT-TATTTTAG-CCATTAAA
935209 TTTCCT-TATTTA-TATTTTAG
1 TTT-CTGT-TTTATTATTTTAG
935229 TCCTATTATT
Statistics
Matches: 87, Mismatches: 9, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
28 14 0.16
29 33 0.38
30 32 0.37
31 8 0.09
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.57
Consensus pattern (28 bp):
TTTCTGTTTTATTATTTTAGCCATTAAA
Found at i:945459 original size:20 final size:20
Alignment explanation
Indices: 945430--945500 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
945420 AACGCGATTT
945430 CAAATTCGCAACACGAA-CTC
1 CAAATTCGCAACAC-AATCTC
* *
945450 CAATTTCGCAACACAATTTC
1 CAAATTCGCAACACAATCTC
* * * *
945470 CAAATTCGCAACTCAGTTTT
1 CAAATTCGCAACACAATCTC
945490 CAAATTCGCAA
1 CAAATTCGCAA
945501 GTCGAATTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 2 0.05
20 42 0.95
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACACAATCTC
Found at i:945755 original size:22 final size:22
Alignment explanation
Indices: 945730--945772 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
945720 GGTAATTGAG
*
945730 TTGCAAAATTTGCGAATTCGAT
1 TTGCAAAATTGGCGAATTCGAT
* *
945752 TTGCGAGATTGGCGAATTCGA
1 TTGCAAAATTGGCGAATTCGA
945773 GTGGCGGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (22 bp):
TTGCAAAATTGGCGAATTCGAT
Found at i:945856 original size:22 final size:22
Alignment explanation
Indices: 945830--945871 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
945820 GTGAAATCCG
945830 AATTCGAATTGCGAATTTGGGA
1 AATTCGAATTGCGAATTTGGGA
**
945852 AATTCGTGTTGCGAATTTGG
1 AATTCGAATTGCGAATTTGG
945872 AAACTGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.36
Consensus pattern (22 bp):
AATTCGAATTGCGAATTTGGGA
Found at i:945889 original size:21 final size:21
Alignment explanation
Indices: 945838--945908 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 21
945828 CGAATTCGAA
*
945838 TTGCGAATTTGGGAAATTCGTG
1 TTGCGAATTT-GGAAACTCGTG
945860 TTGCGAATTTGGAAACT-GTG
1 TTGCGAATTTGGAAACTCGTG
*
945880 TTGCGAAATTT-GAAA-TCGCG
1 TTGCG-AATTTGGAAACTCGTG
945900 TTGCGAATT
1 TTGCGAATT
945909 CGTTGGTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.11
20 19 0.42
21 11 0.24
22 10 0.22
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.35
Consensus pattern (21 bp):
TTGCGAATTTGGAAACTCGTG
Found at i:947819 original size:16 final size:15
Alignment explanation
Indices: 947799--947867 Score: 74
Period size: 13 Copynumber: 4.7 Consensus size: 15
947789 TTTAAATATT
947799 AAAATTATGAATGAA
1 AAAATTATGAATGAA
*
947814 ATAAATTA--AATTAA
1 A-AAATTATGAATGAA
947828 AAAATTATGAATGAA
1 AAAATTATGAATGAA
*
947843 ATAAATTA--AATTAA
1 A-AAATTATGAATGAA
947857 AAAATTATGAA
1 AAAATTATGAA
947868 ATATTAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 12 0.27
14 12 0.27
15 9 0.20
16 12 0.27
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAATTATGAATGAA
Found at i:947831 original size:29 final size:29
Alignment explanation
Indices: 947799--947867 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
947789 TTTAAATATT
947799 AAAATTATGAATGAAATAAATTAAATTAA
1 AAAATTATGAATGAAATAAATTAAATTAA
947828 AAAATTATGAATGAAATAAATTAAATTAA
1 AAAATTATGAATGAAATAAATTAAATTAA
947857 AAAATTATGAA
1 AAAATTATGAA
947868 ATATTAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (29 bp):
AAAATTATGAATGAAATAAATTAAATTAA
Found at i:947869 original size:16 final size:16
Alignment explanation
Indices: 947821--947869 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
947811 GAAATAAATT
947821 AAATTAAAAAATTATG
1 AAATTAAAAAATTATG
*
947837 -AATGAAATAAA-T-T-
1 AAATTAAA-AAATTATG
947850 AAATTAAAAAATTATG
1 AAATTAAAAAATTATG
947866 AAAT
1 AAAT
947870 ATTAAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 8 0.31
16 7 0.27
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AAATTAAAAAATTATG
Found at i:949807 original size:20 final size:20
Alignment explanation
Indices: 949784--949835 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
949774 AACGCGATCC
949784 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
949804 CCAGAATCACAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
949824 CCAAAATCGCAA
1 CCAGAATCGCAA
949836 CGCGATTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:949876 original size:21 final size:21
Alignment explanation
Indices: 949826--949883 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
949816 ATCAGTTTCC
*
949826 AAAATCGCAACGCGATTCTTG
1 AAAATCGCGACGCGATTCTTG
949847 AAAATCGCGACGCGATTCTTG
1 AAAATCGCGACGCGATTCTTG
*
949868 AAAATCGCGATGCGAT
1 AAAATCGCGACGCGAT
949884 AGTACAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
AAAATCGCGACGCGATTCTTG
Found at i:949986 original size:20 final size:20
Alignment explanation
Indices: 949912--950144 Score: 272
Period size: 20 Copynumber: 11.6 Consensus size: 20
949902 GATTTTCCAT
* ** *
949912 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
949932 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
949952 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
949972 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
949992 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
950012 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
**
950032 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
950052 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
950072 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
950092 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
950113 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
950133 AATCGCAACGCG
1 AATCGCAACGCG
950145 ATATTTAAAG
Statistics
Matches: 185, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 165 0.89
21 17 0.09
22 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:950566 original size:33 final size:33
Alignment explanation
Indices: 950527--950597 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
950517 TTCACTTAGA
*
950527 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
950560 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
950593 TTTCA
1 TTTCA
950598 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:950737 original size:14 final size:14
Alignment explanation
Indices: 950718--950772 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
950708 AGAATGACTG
950718 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
950732 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
950751 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
950765 TCGCAACG
1 TCGCAACG
950773 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:950755 original size:33 final size:33
Alignment explanation
Indices: 950718--950788 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
950708 AGAATGACTG
**
950718 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
950751 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
950784 TCGCA
1 TCGCA
950789 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:950806 original size:19 final size:19
Alignment explanation
Indices: 950784--950886 Score: 100
Period size: 19 Copynumber: 5.9 Consensus size: 19
950774 GAAACCAAAA
* *
950784 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
950803 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
*
950819 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
*
950836 TCGCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATC
950855 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
950871 T--CGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
950887 TTCAACCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
14 16 0.23
16 11 0.16
17 8 0.11
19 35 0.50
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATC
Found at i:950867 original size:52 final size:52
Alignment explanation
Indices: 950784--950889 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
950774 GAAACCAAAA
* *
950784 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
950836 TCGCGTTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
950888 TC
1 TC
950890 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:952432 original size:14 final size:14
Alignment explanation
Indices: 952413--952469 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
952403 TTTCATTTCG
952413 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
952427 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
952444 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
952460 CGTTGCGATT
1 CGTTGCGATT
952470 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:952442 original size:33 final size:33
Alignment explanation
Indices: 952403--952488 Score: 154
Period size: 33 Copynumber: 2.6 Consensus size: 33
952393 TTCACTTAGA
*
952403 TTTCATTTCGCGTTGCGATTCTTTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTGTCGTTGCGAT
*
952436 TTTCATTTCGCATTGCGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTGTCGTTGCGAT
952469 TTTCATTTCGCGTTGCGATT
1 TTTCATTTCGCGTTGCGATT
952489 TTGGTTTCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATTCTGTCGTTGCGAT
Found at i:952453 original size:19 final size:19
Alignment explanation
Indices: 952403--952525 Score: 113
Period size: 19 Copynumber: 6.9 Consensus size: 19
952393 TTCACTTAGA
952403 TTTCATTTCGCGTTGCGA-
1 TTTCATTTCGCGTTGCGAT
952421 -TTC-TTT--CGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
*
952436 TTTCATTTCGCATTGCGA-
1 TTTCATTTCGCGTTGCGAT
*
952454 -TTC-TGT--CGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
952469 TTTCATTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
**
952488 TTTGGTTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
* *
952507 TTTAAGTTTCGTGTTGCGA
1 TTTCA-TTTCGCGTTGCGA
952526 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 36 0.42
20 12 0.14
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TTTCATTTCGCGTTGCGAT
Found at i:954468 original size:14 final size:14
Alignment explanation
Indices: 954449--954484 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
954439 ATTGTTTAAT
954449 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
954463 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
954477 TGATTTGT
1 TGATTTGT
954485 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:954607 original size:19 final size:19
Alignment explanation
Indices: 954591--954692 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
954581 AAAAATGACT
954591 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
954610 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
954629 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
954643 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
954662 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
954682 ATCGCAATGCG
1 ATCGCAATGCG
954693 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:954741 original size:33 final size:33
Alignment explanation
Indices: 954699--954917 Score: 246
Period size: 33 Copynumber: 6.5 Consensus size: 33
954689 TGCGTTTATA
*
954699 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
954732 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
954765 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
954798 ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TT-CTCTCG--TTGCGATT-T-TC
* * * * *
954838 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
*
954869 ATTTCGCATTGTGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
954902 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
954918 TTCATTTCGC
Statistics
Matches: 159, Mismatches: 16, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
31 8 0.05
32 5 0.03
33 115 0.72
35 4 0.03
36 5 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:954759 original size:14 final size:14
Alignment explanation
Indices: 954707--954794 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
954697 TAATTTCGCA
* *
954707 TTGCGATTATCTCG
1 TTGCGATTCTTTCG
954721 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
954738 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
954754 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
954771 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
954787 TTGCGATT
1 TTGCGATT
954795 TTCATTTCGC
Statistics
Matches: 62, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
14 20 0.32
16 15 0.24
17 15 0.24
19 12 0.19
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:954777 original size:52 final size:50
Alignment explanation
Indices: 954740--954975 Score: 325
Period size: 52 Copynumber: 4.6 Consensus size: 50
954730 TCATTTCGCA
954740 TTGCGA-TTC-TTTCG-TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTCTTTCG
* *
954787 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCG
1 TTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTCTTTCG
* *
954839 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGTGATTCTCTCG
1 TTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTCTTTCG
*
954891 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTCTTTCG
954943 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TTGCGA-TTTCATTT-CG-ATTGCGATTTTCAT
954976 GTTGGGATTT
Statistics
Matches: 177, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
47 6 0.03
49 3 0.02
50 5 0.03
52 146 0.82
53 17 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (50 bp):
TTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTCTTTCG
Found at i:954822 original size:85 final size:85
Alignment explanation
Indices: 954721--954917 Score: 290
Period size: 85 Copynumber: 2.3 Consensus size: 85
954711 GATTATCTCG
*
954721 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTTTC
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGA-T-TTTC
* *
954786 GTTGCG-ATTTTCATT-TCGCA
64 ATTGCGCATTGTCATTCTCGCA
*
954806 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
* * * *
954871 TTCGCATTGTGATTCTCTCG
66 TGCGCATTGTCATTCTCGCA
954891 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
954918 TTCATTTCGC
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
83 8 0.08
84 8 0.08
85 85 0.84
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (85 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
TGCGCATTGTCATTCTCGCA
Found at i:954874 original size:104 final size:105
Alignment explanation
Indices: 954754--954975 Score: 401
Period size: 104 Copynumber: 2.1 Consensus size: 105
954744 GATTCTTTCG
*
954754 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTAAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTAAT
*
954819 TTCGCATTGCGATTCTGTCGTTGCGATTTTCATTT-CGCA
66 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
* *
954858 TTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTAAT
954923 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
66 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
954963 TTGCGATTTTCAT
1 TTGCGATTTTCAT
954976 GTTGGGATTT
Statistics
Matches: 113, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 96 0.85
105 17 0.15
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (105 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTAAT
TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
Found at i:954952 original size:33 final size:33
Alignment explanation
Indices: 954806--955003 Score: 186
Period size: 33 Copynumber: 5.8 Consensus size: 33
954796 TCATTTCGCA
* *
954806 TTGCGATTTTAATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
954839 TTGCGATTTTCATTTCGCATTGCGATT-T-TCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* * * * * *
954870 TTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCG
1 TTGCG-ATTTTCATT-TCGCATTGCGA--TTC-TCTCG
954908 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
954943 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
954977 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
955004 GTATTTTCCG
Statistics
Matches: 137, Mismatches: 17, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
31 6 0.04
32 8 0.06
33 61 0.45
34 29 0.21
35 7 0.05
36 3 0.02
37 1 0.01
38 11 0.08
39 7 0.05
40 4 0.03
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:957304 original size:12 final size:12
Alignment explanation
Indices: 957287--957311 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
957277 TCTTCGGGGA
957287 CTTTTTCTTCTT
1 CTTTTTCTTCTT
957299 CTTTTTCTTCTT
1 CTTTTTCTTCTT
957311 C
1 C
957312 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:957520 original size:24 final size:24
Alignment explanation
Indices: 957486--957532 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
957476 CTGAAACATC
957486 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
957510 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
957533 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:958243 original size:20 final size:20
Alignment explanation
Indices: 958215--958563 Score: 454
Period size: 20 Copynumber: 17.4 Consensus size: 20
958205 AAATTTCAGT
* * * *
958215 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
958235 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
958255 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
958275 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
958295 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
958315 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
958335 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
958355 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
958375 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
958395 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
958415 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
958435 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
958455 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
958475 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
958495 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
958515 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
958535 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
958555 GTTGCGATT
1 GTTGCGATT
958564 ATGTAAAATC
Statistics
Matches: 294, Mismatches: 28, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.02
20 284 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:958912 original size:10 final size:10
Alignment explanation
Indices: 958899--958925 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
958889 AAACTATTAA
958899 TTTTAATTTG
1 TTTTAATTTG
958909 TTTTAATTTG
1 TTTTAATTTG
958919 TTTTAAT
1 TTTTAAT
958926 ATTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (10 bp):
TTTTAATTTG
Found at i:958947 original size:18 final size:18
Alignment explanation
Indices: 958924--958967 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
958914 ATTTGTTTTA
958924 ATATTTAATTTTTTAATT
1 ATATTTAATTTTTTAATT
958942 ATATTTAATTTTTTAATT
1 ATATTTAATTTTTTAATT
958960 ATATTTAA
1 ATATTTAA
958968 AGTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTAATTTTTTAATT
Found at i:958952 original size:23 final size:23
Alignment explanation
Indices: 958926--958988 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 23
958916 TTGTTTTAAT
958926 ATTTAATTTTTTAA-T-TA--T-
1 ATTTAATTTTTTAATTATATTTA
958944 ATTTAATTTTTTAATTATATTTAA
1 ATTTAATTTTTTAATTATATTT-A
958968 AGTTT-ATTTTTT-ATTATATTT
1 A-TTTAATTTTTTAATTATATTT
958989 TAGTACCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
18 14 0.37
19 1 0.03
20 2 0.05
22 1 0.03
23 9 0.24
24 8 0.21
25 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTAATTTTTTAATTATATTTA
Found at i:959910 original size:17 final size:17
Alignment explanation
Indices: 959888--959965 Score: 63
Period size: 17 Copynumber: 4.5 Consensus size: 17
959878 TAGAGAAAAT
959888 AAAATAAATGAAATAAA
1 AAAATAAATGAAATAAA
959905 AAAATAATATGAAGATAAA
1 AAAATAA-ATGAA-ATAAA
* *
959924 AATAT-AATAAAAATAAA
1 AAAATAAAT-GAAATAAA
* *
959941 AAAA-AGAT-AAAGAATA
1 AAAATAAATGAAATAA-A
959957 AAAATAAAT
1 AAAATAAAT
959966 AAAAATAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.10
16 5 0.10
17 22 0.45
18 8 0.16
19 9 0.18
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (17 bp):
AAAATAAATGAAATAAA
Found at i:959927 original size:34 final size:34
Alignment explanation
Indices: 959888--959998 Score: 113
Period size: 34 Copynumber: 3.2 Consensus size: 34
959878 TAGAGAAAAT
*
959888 AAAATAAAT-GAAATAAAAAAATA-ATATGAAG-ATA
1 AAAATAAATAAAAATAAAAAAA-AGATA--AAGAATA
959922 AAAATATAATAAAAATAAAAAAAAGATAAAGAATA
1 AAAATA-AATAAAAATAAAAAAAAGATAAAGAATA
* * *
959957 AAAATAAATAAAAATAAAGATAAGCTAAAGAA-A
1 AAAATAAATAAAAATAAAAAAAAGATAAAGAATA
959990 ATAAATAAA
1 A-AAATAAA
959999 AGGAAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
33 2 0.03
34 39 0.57
35 13 0.19
36 14 0.21
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (34 bp):
AAAATAAATAAAAATAAAAAAAAGATAAAGAATA
Found at i:959940 original size:6 final size:6
Alignment explanation
Indices: 959919--959979 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
959909 TAATATGAAG
* *
959919 ATAAAA AT-ATA ATAAAA ATAAAA A-AAAG ATAAAGA ATAAAA AT--AA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA-A ATAAAA ATAAAA
*
959964 ATAAAA ATAAAG ATAA
1 ATAAAA ATAAAA ATAA
959980 GCTAAAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.09
5 8 0.18
6 28 0.62
7 5 0.11
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:959957 original size:24 final size:23
Alignment explanation
Indices: 959929--959976 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
959919 ATAAAAATAT
959929 AATAAAAATAAAAAAAAGATAAAG
1 AATAAAAATAAAAAAAA-ATAAAG
*
959953 AATAAAAATAAATAAAAATAAAG
1 AATAAAAATAAAAAAAAATAAAG
959976 A
1 A
959977 TAAGCTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (23 bp):
AATAAAAATAAAAAAAAATAAAG
Found at i:959965 original size:28 final size:29
Alignment explanation
Indices: 959883--959979 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 29
959873 TAAGTTAGAG
959883 AAAATAAA-ATAAATGAA-ATAA-AAAAAT-
1 AAAATAAAGATAAA--AATATAATAAAAATA
* *
959910 AATATGAAGATAAAAATATAATAAAAATA
1 AAAATAAAGATAAAAATATAATAAAAATA
959939 AAAA-AAAGATAAAGAATA-AA-AATAAATA
1 AAAATAAAGATAAA-AATATAATAA-AAATA
959967 AAAATAAAGATAA
1 AAAATAAAGATAA
959980 GCTAAAGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
26 2 0.03
27 12 0.20
28 30 0.51
29 15 0.25
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (29 bp):
AAAATAAAGATAAAAATATAATAAAAATA
Found at i:960037 original size:4 final size:4
Alignment explanation
Indices: 960030--960150 Score: 65
Period size: 4 Copynumber: 30.5 Consensus size: 4
960020 ATATATAATC
* * * *
960030 AATA AATA AACA AAAA CAATA ATATA AA-A AA-A CATA AAGGA AAT- AA-A
1 AATA AATA AATA AATA -AATA A-ATA AATA AATA AATA AA-TA AATA AATA
* * *
960077 AATA AATA AATA AATA AATA AACA AACA AAGTA AA-A AATT AATA AA-A
1 AATA AATA AATA AATA AATA AATA AATA AA-TA AATA AATA AATA AATA
* * *
960124 AAGA AATA TATA TATA TAATA AATA AA
1 AATA AATA AATA AATA -AATA AATA AA
960151 ATAATAACAA
Statistics
Matches: 93, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
3 15 0.16
4 62 0.67
5 16 0.17
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:960287 original size:21 final size:20
Alignment explanation
Indices: 960263--960328 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
960253 ATAATATCGT
*
960263 ATAAAAACAATAAGAAATAAA
1 ATAAAAA-AATAATAAATAAA
960284 ATAATAAAAATAATAAATAATA
1 ATAA-AAAAATAATAAATAA-A
*
960306 ATAAATAAATAAATAAATAAA
1 ATAAAAAAAT-AATAAATAAA
960327 AT
1 AT
960329 GATTATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 23 0.57
22 17 0.43
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
ATAAAAAAATAATAAATAAA
Found at i:960306 original size:31 final size:30
Alignment explanation
Indices: 960263--960322 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
960253 ATAATATCGT
960263 ATAAAAACAATAAGAAATAAA-ATAATAAAA
1 ATAAAAACAATAAGAAATAAATA-AATAAAA
* *
960293 ATAATAAATAATAATAAATAAATAAATAAA
1 ATAA-AAACAATAAGAAATAAATAAATAAA
960323 TAAAATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 21 0.81
32 1 0.04
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (30 bp):
ATAAAAACAATAAGAAATAAATAAATAAAA
Found at i:960312 original size:4 final size:4
Alignment explanation
Indices: 960277--960326 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
960267 AAACAATAAG
*
960277 AAAT AAA- ATAAT AAAA ATAAT AAAT -AAT -AAT AAAT AAAT AAAT AAAT
1 AAAT AAAT A-AAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
960324 AAA
1 AAA
960327 ATGATTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 7 0.17
4 29 0.73
5 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:960328 original size:17 final size:16
Alignment explanation
Indices: 960277--960328 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 16
960267 AAACAATAAG
960277 AAATAAAATAATAAAAAT
1 AAAT-AAATAA-AAAAAT
960295 -AATAAATAATAATAAAT
1 AAATAAATAA-AA-AAAT
960312 AAATAAATAAATAAAAT
1 AAATAAATAAA-AAAAT
960329 GATTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.29
17 12 0.39
18 10 0.32
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAATAAAAAAAT
Found at i:963667 original size:50 final size:51
Alignment explanation
Indices: 963550--963673 Score: 173
Period size: 50 Copynumber: 2.5 Consensus size: 51
963540 CACGTAGGGG
*
963550 TATAGCGCGGATCAAGTACCGCGCTATACCTTTACTCCCGACATAATTTTA
1 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCCGACATAATTTTA
** *
963601 TATAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACT-CTGACATAATTTTA
1 TATAGCGCGGATCAGGTACCGCG-CTATACCTTTACTCCCGACATAATTTTA
963651 TATAGCAG-GGATCAGGTACCGCG
1 TATAGC-GCGGATCAGGTACCGCG
963674 TTTTGTATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
50 32 0.49
51 32 0.49
52 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (51 bp):
TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCCGACATAATTTTA
Found at i:966428 original size:25 final size:25
Alignment explanation
Indices: 966391--966443 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
966381 ATTAAATGAG
*
966391 AAATAAAAAAAATA-ACAATTTAATA
1 AAATAAAAAAAATACA-AATATAATA
**
966416 AAATAAAGTAAATACAAATATAATA
1 AAATAAAAAAAATACAAATATAATA
966441 AAA
1 AAA
966444 AACAAAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (25 bp):
AAATAAAAAAAATACAAATATAATA
Found at i:966451 original size:48 final size:48
Alignment explanation
Indices: 966345--966451 Score: 110
Period size: 48 Copynumber: 2.2 Consensus size: 48
966335 GAAATACATT
* * *
966345 AAAAAAATCCAACAAATTTAACAAAATAAAGTAAGTATTAAATGAGAAATA
1 AAAAAAAT--AAC-AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAA
* *
966396 AAAAAAATAACAATTTAATAAAATAAAGTAAATA-CAAAT-ATAATAAA
1 AAAAAAATAACAATTTAACAAAATAAAGTAAATATCAAATGAGAA-AAA
966443 AAACAAAAT
1 AAA-AAAAT
966452 CTATCGATGC
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
46 3 0.06
47 9 0.18
48 26 0.53
49 3 0.06
51 8 0.16
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (48 bp):
AAAAAAATAACAATTTAACAAAATAAAGTAAATATCAAATGAGAAAAA
Found at i:968707 original size:20 final size:19
Alignment explanation
Indices: 968679--968717 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
968669 TCTTAAAAAG
*
968679 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
968699 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
968718 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:969810 original size:31 final size:30
Alignment explanation
Indices: 969742--969812 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
969732 CAATGAGATA
* * *
969742 TTATTTAAAATTTATGATTAAATTAATATT
1 TTATTTAAAATTTAAGATTAAATTAAAAAT
*
969772 TTATTTAAAATTTAAAGTTTAAATTAAAAAAT
1 TTATTTAAAATTT-AAGATTAAATT-AAAAAT
969804 TT-TTTAAAA
1 TTATTTAAAA
969813 ATATGTCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.37
31 16 0.46
32 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTATTTAAAATTTAAGATTAAATTAAAAAT
Found at i:971632 original size:39 final size:39
Alignment explanation
Indices: 971566--971640 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
971556 TACTTGACAT
971566 ATCCATCTATTCAACTTAGTTTCAAATCTAAACCTCTAA
1 ATCCATCTATTCAACTTAGTTTCAAATCTAAACCTCTAA
* * *
971605 ATCCCTCTTTTCAACTTAGTTTGAAATCTAAACCTC
1 ATCCATCTATTCAACTTAGTTTCAAATCTAAACCTC
971641 CAAGTGTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (39 bp):
ATCCATCTATTCAACTTAGTTTCAAATCTAAACCTCTAA
Found at i:974286 original size:2 final size:2
Alignment explanation
Indices: 974281--974307 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
974271 ATTAAAACCC
974281 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
974308 ATACTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:977015 original size:32 final size:31
Alignment explanation
Indices: 976979--977049 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
976969 AACTTTGGAT
*
976979 TTATTACAAAATAATCATTAACTTTGATCAAA
1 TTATTACAAAATAATCATTAAATTT-ATCAAA
* * *
977011 TTATTATAAAATGATTATTAAATTTATCAAA
1 TTATTACAAAATAATCATTAAATTTATCAAA
*
977042 TTTTTACA
1 TTATTACA
977050 TTTATTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 12 0.36
32 21 0.64
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (31 bp):
TTATTACAAAATAATCATTAAATTTATCAAA
Found at i:988029 original size:51 final size:51
Alignment explanation
Indices: 987967--988862 Score: 592
Period size: 51 Copynumber: 17.8 Consensus size: 51
987957 TGAACTCACA
** * * *
987967 ACAAACTTACACTGGTGAAATTTAACACATAATTACAGCATTAATCACATC
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
* * * * * *
988018 ACATACTTACACTAGTC-AATTTAACATATAGTTCTAATATTGAACTCACA--
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATT-AA-TCACATC
* * * * * *
988068 ACAGACTTACACCAGTTAAATTTAACACTTAATTCCAGCATTAATCTCATT
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
** * *
988119 ACATGCTTACACTAGTC-AATTTAACATATAATT--ATGATATTGAACTCACAT-
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCA-G-TATT-AA-TCACATC
* * * * * * *
988170 -CAAACTTACACCAGTCAAATTTAACATATAATTTCGGCATCAATCTCATT
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
* * *
988220 ACAGACTTACACC-GATCAAATTTAACATATAATTCCAATATTGAACTCACA--
1 ACAAACTTACACCAG-TCAAATTTAACACATAATTCCAGTATT-AA-TCACATC
* * * * *
988271 ACAGACTTACACCAGTTAAATTTAACACATAATACCAGCATTAATCTCA-C
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
* * * * * *
988321 ACATACTTACACCAATC-GATTTAACATATGATTCCAATATTGAACTCACA--
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATT-AA-TCACATC
** *
988371 ACAAACTTACACCAGTCAAATTTAACACATAATTTTAGTATTAATCTCATC
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
* * **
988422 ACAAA-TGTACACCAGTCAAATTCAACACATAATTCTAGTATTAATTTCATC
1 ACAAACT-TACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
*
988473 ACAAACTTACACCAGTC-AATTTAACATATAATTCCTA-TATTGAACTCACA--
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCC-AGTATT-AA-TCACATC
* ** *
988523 ACAAACTTACACTAGTCAAATTTAACACATAATTCCAACATTAATCTCATC
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
* * * * * *
988574 ACAAATTTACACC-GACCAAATTTAACATATAATTCTAATATTTAACTTACA--
1 ACAAACTTACACCAG-TCAAATTTAACACATAATTCCAGTA-TTAA-TCACATC
* * * ** **
988625 ACAAACTTGCACCAATCAAATTTAACATAT-A-TCCAACATTAATTTCATC
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
* * * * *
988674 ACATAC-TACACTAGTCAAATTTAACATATAATTACAATATTGAACTCACA--
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATT-AA-TCACATC
* * *** *
988724 A-AAAATTACACCAGTAAAATTTAA-ACATAATTCCAACGTTAATCTCATC
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
* * * * * **
988773 ACAAACTTACACTACTCAAATTTAACATATAGTTCCAATATTAATCTTATC
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
* * ** *
988824 ATAGACTTACACCAGTCAAATTTGTCACATAATTTCAGT
1 ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGT
988863 GGTGGTAATT
Statistics
Matches: 668, Mismatches: 129, Indels: 96
0.75 0.14 0.11
Matches are distributed among these distances:
47 8 0.01
48 27 0.04
49 66 0.10
50 186 0.28
51 349 0.52
52 25 0.04
53 7 0.01
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.31
Consensus pattern (51 bp):
ACAAACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATCACATC
Found at i:988078 original size:101 final size:101
Alignment explanation
Indices: 987946--988607 Score: 675
Period size: 101 Copynumber: 6.5 Consensus size: 101
987936 TTAAAAAAAG
** *
987946 AATTCTAATATTGAACTCACAACAAACTTACACTGGTGAAATTTAACACATAATTACAGCATTAA
1 AATTCTAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTACAGCATTAA
*
988011 TCACATCACATACTTACACTAGTCAATTTAACATAT
66 TCTCATCACATACTTACACTAGTCAATTTAACATAT
* * * * *
988047 AGTTCTAATATTGAACTCACAACAGACTTACACCAGTTAAATTTAACACTTAATTCCAGCATTAA
1 AATTCTAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTACAGCATTAA
* *
988112 TCTCATTACATGCTTACACTAGTCAATTTAACATAT
66 TCTCATCACATACTTACACTAGTCAATTTAACATAT
* * * * * * *
988148 AATTATGATATTGAACTCACATCAAACTTACACCAGTCAAATTTAACATATAATTTCGGCATCAA
1 AATTCTAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTACAGCATTAA
* * *
988213 TCTCATTACAGACTTACAC-CGATCAAATTTAACATAT
66 TCTCATCACATACTTACACTAG-TC-AATTTAACATAT
* * *
988250 AATTCCAATATTGAACTCACAACAGACTTACACCAGTTAAATTTAACACATAA-TACCAGCATTA
1 AATTCTAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTA-CAGCATTA
* * *
988314 ATCTCA-CACATACTTACACCAATCGATTTAACATAT
65 ATCTCATCACATACTTACACTAGTCAATTTAACATAT
* * ** *
988350 GATTCCAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTTTAGTATTAA
1 AATTCTAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTACAGCATTAA
* * * *
988415 TCTCATCACA-AATGTACACCAGTCAAATTCAACACAT
66 TCTCATCACATACT-TACACTAGTC-AATTTAACATAT
* * * * *
988452 AATTCTAGTATT-AATTTCATC-ACAAACTTACACCAGTC-AATTTAACATATAATTCCTA-TAT
1 AATTCTAATATTGAA-CTCA-CAACAAACTTACACCAGTCAAATTTAACACATAATTAC-AGCAT
* *
988513 TGAA-CTCA-CAACAAACTTACACTAGTCAAATTTAACACAT
63 T-AATCTCATC-ACATACTTACACTAGTC-AATTTAACATAT
* * * * *
988553 AATTCCAACATT-AATCTCATC-ACAAATTTACACC-GACCAAATTTAACATATAATT
1 AATTCTAATATTGAA-CTCA-CAACAAACTTACACCAG-TCAAATTTAACACATAATT
988608 CTAATATTTA
Statistics
Matches: 479, Mismatches: 66, Indels: 31
0.83 0.11 0.05
Matches are distributed among these distances:
100 78 0.16
101 271 0.57
102 129 0.27
103 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (101 bp):
AATTCTAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTACAGCATTAA
TCTCATCACATACTTACACTAGTCAATTTAACATAT
Found at i:988224 original size:152 final size:152
Alignment explanation
Indices: 987984--988857 Score: 659
Period size: 152 Copynumber: 5.8 Consensus size: 152
987974 TACACTGGTG
* * * * * * *
987984 AAATTTAACACATAATTACAGCATTAATCACATCACATACTTACACTAGTCAATTTAACATATAG
1 AAATTTAACACATAATTATAGTATTAATCTCA-CACAAACTTACACCAATCAATTTAACATATAA
* * * * *
988049 TTCTAATATTGAACTCACAACAGACTTACACCAGTTAAATTTAACACTTAATTCCAGCATTAATC
65 TTCCAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTCCAACATTAATC
* *
988114 TCATTACATGCTTACACTAG-TC
130 TCATCACATGCTTACACCAGATC
* *
988136 -AATTTAACATATAATTAT-GATATTGAA-CTCACATCAAACTTACACCAGTCAAATTTAACATA
1 AAATTTAACACATAATTATAG-TATT-AATCTCACA-CAAACTTACACCAATC-AATTTAACATA
* *** * ** * * *
988198 TAATTTCGGCA-TCAATCTCATTACAGACTTACACC-GATCAAATTTAACATATAATTCCAATAT
62 TAATTCCAATATTGAA-CTCACAACAAACTTACACCAG-TCAAATTTAACACATAATTCCAACAT
*
988261 TGAA-CTCA-CAACA-GACTTACACCAG-TT
125 T-AATCTCATC-ACATG-CTTACACCAGATC
* * * * *
988288 AAATTTAACACATAA-TACCAGCATTAATCTCACACATACTTACACCAATCGATTTAACATATGA
1 AAATTTAACACATAATTA-TAGTATTAATCTCACACAAACTTACACCAATCAATTTAACATATAA
** **
988352 TTCCAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTTTAGTATTAATC
65 TTCCAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTCCAACATTAATC
988417 TCATCACAAATG--TACACCAG-TC
130 TCATCAC--ATGCTTACACCAGATC
* * * *
988439 AAATTCAACACATAATTCTAGTATTAATTTCATCACAAACTTACACCAGTCAATTTAACATATAA
1 AAATTTAACACATAATTATAGTATTAATCTCA-CACAAACTTACACCAATCAATTTAACATATAA
* *
988504 TTCCTATATTGAACTCACAACAAACTTACACTAGTCAAATTTAACACATAATTCCAACATTAATC
65 TTCCAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTCCAACATTAATC
*** *
988569 TCATCACAAATTTACACC-GACC
130 TCATCACATGCTTACACCAGATC
* * * * *
988591 AAATTTAACATATAATTCTAATATTTAA-CTTACAACAAACTTGCACCAATCAAATTTAACATAT
1 AAATTTAACACATAATTATAGTA-TTAATCTCAC-ACAAACTTACACCAATC-AATTTAACATAT
* * * * * * *
988655 -A-TCCAACATT-AATTTCATC-ACATAC-TACACTAGTCAAATTTAACATATAATTACAATATT
63 AATTCCAATATTGAA-CTCA-CAACAAACTTACACCAGTCAAATTTAACACATAATTCCAACATT
* *** *
988715 GAA-CTCA-CAAAAAATTACACCAG-TA
126 -AATCTCATCACATGCTTACACCAGATC
** *** * *
988740 AAATTTAA-ACATAATTCCAACGTTAATCTCATCACAAACTTACACTACTCAAATTTAACATATA
1 AAATTTAACACATAATTATAGTATTAATCTCA-CACAAACTTACACCAATC-AATTTAACATATA
* * * * **
988804 GTTCCAATATT-AATCTTATC-ATAGACTTACACCAGTCAAATTTGTCACATAATT
64 ATTCCAATATTGAA-CTCA-CAACAAACTTACACCAGTCAAATTTAACACATAATT
988858 TCAGTGGTGG
Statistics
Matches: 588, Mismatches: 97, Indels: 75
0.77 0.13 0.10
Matches are distributed among these distances:
147 4 0.01
148 40 0.07
149 21 0.04
150 64 0.11
151 178 0.30
152 238 0.40
153 41 0.07
154 2 0.00
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.31
Consensus pattern (152 bp):
AAATTTAACACATAATTATAGTATTAATCTCACACAAACTTACACCAATCAATTTAACATATAAT
TCCAATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAATTCCAACATTAATCT
CATCACATGCTTACACCAGATC
Found at i:988645 original size:102 final size:102
Alignment explanation
Indices: 988022--988857 Score: 584
Period size: 101 Copynumber: 8.3 Consensus size: 102
988012 CACATCACAT
* * * * * *
988022 ACTTACACTAGTC-AATTTAACATATAGTTCTAATATTGAA-CTCA-CAACAGACTTACACCAGT
1 ACTTACACCAGTCAAATTTAACACATAATTCCAACATT-AATCTCATC-ACAAACTTACACCAGT
* * ** ** *
988084 TAAATTTAACACT-TAATTCCAGCA-TTAATCTCATTACAT
64 CAAATTTAACA-TATAATTCTAATATTTAA-CTCACAACAA
* * * *** *
988123 GCTTACACTAGTC-AATTTAACATATAATTATGATATTGAA-CTCA-CATCAAACTTACACCAGT
1 ACTTACACCAGTCAAATTTAACACATAATTCCAACATT-AATCTCATCA-CAAACTTACACCAGT
*** * ** *
988185 CAAATTTAACATATAATT-TCGGCA-TCAATCTCATTACAG
64 CAAATTTAACATATAATTCT-AATATTTAA-CTCACAACAA
* * *
988224 ACTTACACC-GATCAAATTTAACATATAATTCCAATATTGAA-CTCA-CAACAGACTTACACCAG
1 ACTTACACCAG-TCAAATTTAACACATAATTCCAACATT-AATCTCATC-ACAAACTTACACCAG
* * * * ** *
988286 TTAAATTTAACACATAATACCAGCA-TTAATCTCAC-ACAT
63 TCAAATTTAACATATAATTCTAATATTTAA-CTCACAACAA
* * * * *
988325 ACTTACACCAATC-GATTTAACATATGATTCCAATATTGAA-CTCA-CAACAAACTTACACCAGT
1 ACTTACACCAGTCAAATTTAACACATAATTCCAACATT-AATCTCATC-ACAAACTTACACCAGT
* * *
988387 CAAATTTAACACATAATTTTAGTA-TTAATCTCATC-ACAA
64 CAAATTTAACATATAATTCTAATATTTAA-CTCA-CAACAA
* * ** *
988426 A-TGTACACCAGTCAAATTCAACACATAATTCTAGTATTAATTTCATCACAAACTTACACCAGTC
1 ACT-TACACCAGTCAAATTTAACACATAATTCCAACATTAATCTCATCACAAACTTACACCAGTC
*
988490 -AATTTAACATATAATTCCT-ATATTGAACTCACAACAA
65 AAATTTAACATATAATT-CTAATATTTAACTCACAACAA
* * *
988527 ACTTACACTAGTCAAATTTAACACATAATTCCAACATTAATCTCATCACAAATTTACACC-GACC
1 ACTTACACCAGTCAAATTTAACACATAATTCCAACATTAATCTCATCACAAACTTACACCAG-TC
*
988591 AAATTTAACATATAATTCTAATATTTAACTTACAACAA
65 AAATTTAACATATAATTCTAATATTTAACTCACAACAA
* * * * * *
988629 ACTTGCACCAATCAAATTTAACATAT-A-TCCAACATTAATTTCATCACATAC-TACACTAGTCA
1 ACTTACACCAGTCAAATTTAACACATAATTCCAACATTAATCTCATCACAAACTTACACCAGTCA
*
988691 AATTTAACATATAATTAC-AATATTGAACTCACAA-AA
66 AATTTAACATATAATT-CTAATATTTAACTCACAACAA
* * * * *
988727 AATTACACCAGTAAAATTTAA-ACATAATTCCAACGTTAATCTCATCACAAACTTACACTACTCA
1 ACTTACACCAGTCAAATTTAACACATAATTCCAACATTAATCTCATCACAAACTTACACCAGTCA
* * * * *
988791 AATTTAACATATAGTTCCAATA-TTAATCTTATC-ATAG
66 AATTTAACATATAATTCTAATATTTAA-CTCA-CAACAA
**
988828 ACTTACACCAGTCAAATTTGTCACATAATT
1 ACTTACACCAGTCAAATTTAACACATAATT
988858 TCAGTGGTGG
Statistics
Matches: 621, Mismatches: 84, Indels: 59
0.81 0.11 0.08
Matches are distributed among these distances:
97 3 0.00
98 20 0.03
99 62 0.10
100 136 0.22
101 224 0.36
102 174 0.28
103 2 0.00
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.31
Consensus pattern (102 bp):
ACTTACACCAGTCAAATTTAACACATAATTCCAACATTAATCTCATCACAAACTTACACCAGTCA
AATTTAACATATAATTCTAATATTTAACTCACAACAA
Found at i:988648 original size:354 final size:351
Alignment explanation
Indices: 988072--988842 Score: 976
Period size: 354 Copynumber: 2.2 Consensus size: 351
988062 CTCACAACAG
* * * * * ** *
988072 ACTTACACCAGTTAAATTTAACACTTAATTCCAGCATTAATCTCATTACATGCTTACACTAGTCA
1 ACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATTTCATCACAAACTTACACCAGTCA
* *
988137 ATTTAACATATAATTATGATATTGAACTCACATCAAACTTACACCAGTCAAATTTAACATATAAT
66 ATTTAACATATAATTATGATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAAT
* ** * * *
988202 TTCGGCATCAATCTCATTACAGACTTACACCGATCAAATTTAACATATAATTCCAATATTGAACT
131 TCCAACATCAATCTCATCACAAACTTACACCGACCAAATTTAACATATAATTCCAATATTGAACT
* * * *
988267 CACAACAGACTTACACCAGTTAAATTTAACACATAATACCAGCATTAATCTCA-CACATACTTAC
196 CACAACAAACTTACACCAATCAAATTTAACACAT-AT-CCAACATTAATCTCATCACATAC-TAC
* * * * *
988331 ACCAATC-GATTTAACATATGATTCCAATATTGAACTCACAACAAACTTACACCAGTCAAATTTA
258 ACCAATCAAATTTAACATATAATTACAATATTGAACTCACAA-AAAATTACACCAGTAAAATTTA
** **
988395 ACACATAATTTTAGTATTAATCTCATCACAA
322 A-ACATAATTCCAACATTAATCTCATCACAA
* *
988426 A-TGTACACCAGTCAAATTCAACACATAATTCTAGTATTAATTTCATCACAAACTTACACCAGTC
1 ACT-TACACCAGTCAAATTTAACACATAATTCCAGTATTAATTTCATCACAAACTTACACCAGTC
* *
988490 AATTTAACATATAATTCCT-ATATTGAACTCACAACAAACTTACACTAGTCAAATTTAACACATA
65 AATTTAACATATAATT-ATGATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATA
* * * *
988554 ATTCCAACATTAATCTCATCACAAATTTACACCGACCAAATTTAACATATAATTCTAATATTTAA
129 ATTCCAACATCAATCTCATCACAAACTTACACCGACCAAATTTAACATATAATTCCAATATTGAA
* * * *
988619 CTTACAACAAACTTGCACCAATCAAATTTAACATATATCCAACATTAATTTCATCACATACTACA
194 CTCACAACAAACTTACACCAATCAAATTTAACACATATCCAACATTAATCTCATCACATACTACA
* *
988684 CTAGTCAAATTTAACATATAATTACAATATTGAACTCACAAAAAATTACACCAGTAAAATTTAAA
259 CCAATCAAATTTAACATATAATTACAATATTGAACTCACAAAAAATTACACCAGTAAAATTTAAA
*
988749 CATAATTCCAACGTTAATCTCATCACAA
324 CATAATTCCAACATTAATCTCATCACAA
* * * * * * *
988777 ACTTACACTACTCAAATTTAACATATAGTTCCAATATTAATCTT-ATCATAGACTTACACCAGTC
1 ACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAAT-TTCATCACAAACTTACACCAGTC
988841 AA
65 AA
988843 ATTTGTCACA
Statistics
Matches: 358, Mismatches: 53, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
351 76 0.21
352 45 0.13
353 41 0.11
354 195 0.54
355 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (351 bp):
ACTTACACCAGTCAAATTTAACACATAATTCCAGTATTAATTTCATCACAAACTTACACCAGTCA
ATTTAACATATAATTATGATATTGAACTCACAACAAACTTACACCAGTCAAATTTAACACATAAT
TCCAACATCAATCTCATCACAAACTTACACCGACCAAATTTAACATATAATTCCAATATTGAACT
CACAACAAACTTACACCAATCAAATTTAACACATATCCAACATTAATCTCATCACATACTACACC
AATCAAATTTAACATATAATTACAATATTGAACTCACAAAAAATTACACCAGTAAAATTTAAACA
TAATTCCAACATTAATCTCATCACAA
Found at i:990867 original size:16 final size:16
Alignment explanation
Indices: 990832--990872 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
990822 GTTTACTTCA
990832 GAATGATT-AAACGCT
1 GAATGATTCAAACGCT
* *
990847 GAATGATTCAAATGTT
1 GAATGATTCAAACGCT
990863 GAATGATTCA
1 GAATGATTCA
990873 GAGGCTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:990885 original size:18 final size:17
Alignment explanation
Indices: 990832--990886 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
990822 GTTTACTTCA
*
990832 GAATGATT-AAACG-CT
1 GAATGATTCAAAGGTCT
*
990847 GAATGATTCAAATGT-T
1 GAATGATTCAAAGGTCT
*
990863 GAATGATTCAGAGGCTCT
1 GAATGATTCAAAGG-TCT
990881 GAATGA
1 GAATGA
990887 ATTAGCTCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 8 0.24
16 17 0.52
17 1 0.03
18 7 0.21
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (17 bp):
GAATGATTCAAAGGTCT
Found at i:991825 original size:20 final size:22
Alignment explanation
Indices: 991800--991843 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
991790 AATTCTATAT
991800 AAAAATCTAA-AGA-TTTTTAA
1 AAAAATCTAATAGATTTTTTAA
*
991820 AAAAATCTAATATATTTTTTAA
1 AAAAATCTAATAGATTTTTTAA
991842 AA
1 AA
991844 GTTCCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAAATCTAATAGATTTTTTAA
Found at i:997407 original size:16 final size:15
Alignment explanation
Indices: 997371--997412 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
997361 TAATGAACTA
997371 TTTAA-TTAAAAAAT
1 TTTAATTTAAAAAAT
*
997385 TCT-ATTTAAAAAAGT
1 TTTAATTTAAAAAA-T
997400 TTTAATTTAAAAA
1 TTTAATTTAAAAA
997413 TCTATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.04
14 10 0.43
15 3 0.13
16 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TTTAATTTAAAAAAT
Found at i:997735 original size:28 final size:28
Alignment explanation
Indices: 997695--997780 Score: 145
Period size: 28 Copynumber: 3.1 Consensus size: 28
997685 TTTTGAGCAC
997695 TGGCTCGACGACATAATATTTCAAGTAT
1 TGGCTCGACGACATAATATTTCAAGTAT
*
997723 TGGCTCGACGACATAATGTTTCAAGTAT
1 TGGCTCGACGACATAATATTTCAAGTAT
* *
997751 TGGCTCGACGACATAATATTTTAAGCAT
1 TGGCTCGACGACATAATATTTCAAGTAT
997779 TG
1 TG
997781 ACTCAAAGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (28 bp):
TGGCTCGACGACATAATATTTCAAGTAT
Found at i:998242 original size:9 final size:8
Alignment explanation
Indices: 998215--998268 Score: 65
Period size: 8 Copynumber: 6.8 Consensus size: 8
998205 TTAATTATTA
998215 AATATTTT
1 AATATTTT
998223 AATATTTT
1 AATATTTT
998231 AATATTTCT
1 AATATTT-T
*
998240 AATATTAT
1 AATATTTT
*
998248 AATATTAT
1 AATATTTT
*
998256 -ATTTTTT
1 AATATTTT
998263 AATATT
1 AATATT
998269 ATAAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
7 5 0.12
8 28 0.70
9 7 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
AATATTTT
Found at i:998242 original size:17 final size:16
Alignment explanation
Indices: 998205--998253 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
998195 TAATCAAATA
998205 TTAATTATTA-AATATT
1 TTAA-TATTATAATATT
*
998221 TTAATATTTTAATATT
1 TTAATATTATAATATT
998237 TCTAATATTATAATATT
1 T-TAATATTATAATATT
998254 ATATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 14 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATATTATAATATT
Found at i:998269 original size:23 final size:23
Alignment explanation
Indices: 998201--998272 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 23
998191 CATTTAATCA
* * *
998201 AATATTA-ATTATTAAATATTTT
1 AATATTATATTTTTTAATATTAT
* *
998223 AATATTTTAATATTTCTAATATTAT
1 AATATTAT-AT-TTTTTAATATTAT
998248 AATATTATATTTTTTAATATTAT
1 AATATTATATTTTTTAATATTAT
998271 AA
1 AA
998273 AAAATATTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
22 6 0.15
23 14 0.35
24 4 0.10
25 16 0.40
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTATATTTTTTAATATTAT
Found at i:1000194 original size:21 final size:21
Alignment explanation
Indices: 1000170--1000211 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1000160 ATATATATGT
1000170 TCAGTGGTCCTTCGGGACATA
1 TCAGTGGTCCTTCGGGACATA
*
1000191 TCAGTGGTCTTTCGGGACATA
1 TCAGTGGTCCTTCGGGACATA
1000212 GTGGTCATTT
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:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (21 bp):
TCAGTGGTCCTTCGGGACATA
Found at i:1000216 original size:18 final size:19
Alignment explanation
Indices: 1000170--1000227 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 19
1000160 ATATATATGT
*
1000170 TCAGTGGTCCTTCGGGACATA
1 TCAGTGGTCTTTCGGGAC--A
1000191 TCAGTGGTCTTTCGGGACA
1 TCAGTGGTCTTTCGGGACA
1000210 T-AGTGGTCATTT-GGGACA
1 TCAGTGGTC-TTTCGGGACA
1000228 AATGTTCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 13 0.37
19 5 0.14
21 17 0.49
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (19 bp):
TCAGTGGTCTTTCGGGACA
Found at i:1006963 original size:21 final size:21
Alignment explanation
Indices: 1006935--1006996 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1006925 AAGAGTCGAT
1006935 GGAT-TATCAGTGGTCCTTCG
1 GGATATATCAGTGGTCCTTCG
1006955 GGATATATCAGTGGTCCTTCG
1 GGATATATCAGTGGTCCTTCG
*
1006976 GG--ACAT-AGTGGTCCTTCG
1 GGATATATCAGTGGTCCTTCG
1006994 GGA
1 GGA
1006997 CAAATGTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 14 0.36
19 3 0.08
20 4 0.10
21 18 0.46
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (21 bp):
GGATATATCAGTGGTCCTTCG
Found at i:1006987 original size:18 final size:19
Alignment explanation
Indices: 1006940--1006998 Score: 84
Period size: 18 Copynumber: 3.1 Consensus size: 19
1006930 TCGATGGATT
*
1006940 ATCAGTGGTCCTTCGGGATAT
1 ATCAGTGGTCCTTCGGG--AC
1006961 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
1006980 AT-AGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
1006998 A
1 A
1006999 AATGTTCAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
18 17 0.46
19 3 0.08
21 17 0.46
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.29
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:1016294 original size:78 final size:78
Alignment explanation
Indices: 1016160--1016307 Score: 208
Period size: 78 Copynumber: 1.9 Consensus size: 78
1016150 TAGAATCTGT
* * *
1016160 GTGCATTTGTGGTAAAACTTTTAGTTTTACATTTTTTTATGATAGTGGATGGTTGAAAACAGATT
1 GTGCATTTATGGTAAAACTTTTAGTTTTACATTTTTTTATAATAGTGGATGATTGAAAACAGATT
1016225 GTTAAGAATCCAC
66 GTTAAGAATCCAC
* * * *
1016238 GTGCATTTATTGTAGAACTTTTAGTTTTACA-TTTTTTATAATTGTGAGATGATTGAAAATAGAT
1 GTGCATTTATGGTAAAACTTTTAGTTTTACATTTTTTTATAATAGTG-GATGATTGAAAACAGAT
*
1016302 TTTTAA
65 TGTTAA
1016308 AATTATCTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 13 0.21
78 48 0.79
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (78 bp):
GTGCATTTATGGTAAAACTTTTAGTTTTACATTTTTTTATAATAGTGGATGATTGAAAACAGATT
GTTAAGAATCCAC
Found at i:1021056 original size:20 final size:20
Alignment explanation
Indices: 1020981--1021056 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
1020971 AAAACATCTT
*
1020981 GCCCGAAGGTCTTATGGATG
1 GCCCGAAGGTCTTATTGATG
* * *
1021001 ACCCGAAGGTCTTATTCATCAC
1 GCCCGAAGGTCTTATTGAT--G
*
1021023 GCTCGAAAGG-CTTATTGATG
1 GCCCG-AAGGTCTTATTGATG
*
1021043 GCCCGAAGGACTTA
1 GCCCGAAGGTCTTA
1021057 CAAATCGTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
19 4 0.09
20 24 0.56
22 11 0.26
23 4 0.09
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (20 bp):
GCCCGAAGGTCTTATTGATG
Done.