Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_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: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:1909538 original size:2 final size:2
Alignment explanation
Indices: 1909531--1909562 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1909521 ATTCAGAAGT
1909531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1909563 AGAGAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1911772 original size:21 final size:20
Alignment explanation
Indices: 1911680--1911769 Score: 126
Period size: 21 Copynumber: 4.3 Consensus size: 20
1911670 TATGCCATCT
* *
1911680 CCGCAGGGTTACATTCCGAGC
1 CCGCA-GGTTACATGCCTAGC
*
1911701 CCGCAGGTTACATTCCTAGC
1 CCGCAGGTTACATGCCTAGC
1911721 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
1911742 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
1911763 CCGCAGG
1 CCGCAGG
1911770 GTTTTATACC
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
20 21 0.32
21 45 0.68
ACGTcount: A:0.19, C:0.37, G:0.26, T:0.19
Consensus pattern (20 bp):
CCGCAGGTTACATGCCTAGC
Found at i:1912358 original size:33 final size:34
Alignment explanation
Indices: 1912298--1912383 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 34
1912288 TTAAAATACA
1912298 AATATTATTCGAAATTTAAAATAAAAATAAAAAT
1 AATATTATTCGAAATTTAAAATAAAAATAAAAAT
* * *
1912332 AATATTATTC-AAATTTAAATTTAAAATATAAAT
1 AATATTATTCGAAATTTAAAATAAAAATAAAAAT
* *
1912365 TATAGTATTCGAAATTTAA
1 AATATTATTCGAAATTTAA
1912384 CATTAAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 28 0.61
34 18 0.39
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (34 bp):
AATATTATTCGAAATTTAAAATAAAAATAAAAAT
Found at i:1912390 original size:34 final size:32
Alignment explanation
Indices: 1912288--1912390 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 32
1912278 ATAAATGTTT
*
1912288 TTAAAATACAAA-TAT-TATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATATTCGAAATTT-AAA
* *
1912319 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATA-TATTCGAAATTTAAA
*
1912351 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATA-TATTCGAAATTTAA-A
1912386 TTAAA
1 TTAAA
1912391 TTTCAACTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
31 10 0.17
32 5 0.08
33 25 0.42
34 18 0.31
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (32 bp):
TTAAAATAAAAATTATATATTCGAAATTTAAA
Found at i:1913026 original size:125 final size:126
Alignment explanation
Indices: 1912769--1913486 Score: 1273
Period size: 125 Copynumber: 5.8 Consensus size: 126
1912759 TTTAAGTTAT
*
1912769 TCCCCGA-GGACATGAGTGACATAATAGGGC-ATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1912832 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1912893 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTAACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1912958 GCGCCCCCTGGAACGCGCCTTCACGTGAATAGTGAAATAAT-GGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1913018 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATA-T-TCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1913081 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1913142 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAA-G-
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1913205 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTG-AATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1913265 TCCCCGA-GGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATAGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1913329 GCGCCCCC-GGAACGCACCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1913389 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATAGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1913454 GCGCCCCC-GGAA--CGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
1913487 CCGATTATAG
Statistics
Matches: 575, Mismatches: 10, Indels: 19
0.95 0.02 0.03
Matches are distributed among these distances:
122 52 0.09
123 138 0.24
124 143 0.25
125 152 0.26
126 90 0.16
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:1913207 original size:249 final size:250
Alignment explanation
Indices: 1912769--1913486 Score: 1292
Period size: 247 Copynumber: 2.9 Consensus size: 250
1912759 TTTAAGTTAT
1912769 TCCCCGAGGACATGAGTGACATAATAGGGC-ATGATAATATTCTCTGACGAAATAATGGAAGGCG
1 TCCCCGAGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
1912833 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
*
1912898 GAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTAACGAAATAATGGAAGGCGCGCC
131 GAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCC
1912963 CCCTGGAACGCGCCTTCACGTGAATAGTGAAATAAT-GGTACTGATATATCTAGTG
196 CCC-GGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1913018 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATA-T-TCTGACGAAATAATGGAAGGC
1 TCCCCGA-GGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1913081 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
65 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
*
1913146 CGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGC-C
130 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
*
1913210 CCCGGGAACGCGCCTTCACGTGAATAGTG-AATAATAGGTACTGATATATCTAGTG
195 CCCCGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
* *
1913265 TCCCCGAGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATAGAAGGCG
1 TCCCCGAGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
*
1913330 CGCCCCC-GGAACGCACCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
66 CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
*
1913394 GAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATAGAAGGCGCGCC
131 GAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCC
1913459 CCCGGAA--CGCCTTCACGTGAATAGTGAA
196 CCCGGAACGCGCCTTCACGTGAATAGTGAA
1913487 CCGATTATAG
Statistics
Matches: 453, Mismatches: 9, Indels: 16
0.95 0.02 0.03
Matches are distributed among these distances:
246 57 0.13
247 169 0.37
248 40 0.09
249 154 0.34
250 24 0.05
251 9 0.02
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (250 bp):
TCCCCGAGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG
CGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
GAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCC
CCCGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:1913567 original size:8 final size:8
Alignment explanation
Indices: 1913554--1913594 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1913544 TCACAATCTT
1913554 TCAAATTC
1 TCAAATTC
1913562 TCAAATTC
1 TCAAATTC
* *
1913570 CCAAACTC
1 TCAAATTC
1913578 T-AAATTC
1 TCAAATTC
1913585 TCAAATTC
1 TCAAATTC
1913593 TC
1 TC
1913595 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1916549 original size:11 final size:11
Alignment explanation
Indices: 1916530--1916564 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1916520 AAATACATAA
1916530 ATATATTTAAT
1 ATATATTTAAT
*
1916541 ATATTTTTAAT
1 ATATATTTAAT
1916552 ATAATATTTAAT
1 AT-ATATTTAAT
1916564 A
1 A
1916565 ATGTATACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATATTTAAT
Found at i:1920804 original size:38 final size:38
Alignment explanation
Indices: 1920762--1920848 Score: 147
Period size: 38 Copynumber: 2.3 Consensus size: 38
1920752 TTAACTTTTT
*
1920762 ATTAAAATAATCGAATGATGTTAGTATAAATAAATTTG
1 ATTAAATTAATCGAATGATGTTAGTATAAATAAATTTG
**
1920800 ATTAAATTAATTTAATGATGTTAGTATAAATAAATTTG
1 ATTAAATTAATCGAATGATGTTAGTATAAATAAATTTG
1920838 ATTAAATTAAT
1 ATTAAATTAAT
1920849 ATATTATACT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (38 bp):
ATTAAATTAATCGAATGATGTTAGTATAAATAAATTTG
Found at i:1921505 original size:57 final size:57
Alignment explanation
Indices: 1921426--1921539 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
1921416 ACGCGAATTT
*
1921426 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCACATTGCGA
* *
1921483 TAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGAATTTGAAAATCACCTTGCGA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCACATTGCGA
1921540 ATTTGAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (57 bp):
TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCACATTGCGA
Found at i:1921557 original size:20 final size:20
Alignment explanation
Indices: 1921514--1921559 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1921504 GTAATTAGCG
*
1921514 TTGCGAATTTGAAAATCACC
1 TTGCGAATTTGAAAATCACA
*
1921534 TTGCGAATTTGAAAATCGCA
1 TTGCGAATTTGAAAATCACA
1921554 TTGCGA
1 TTGCGA
1921560 TTGTACTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCACA
Found at i:1921584 original size:77 final size:77
Alignment explanation
Indices: 1921457--1921606 Score: 273
Period size: 77 Copynumber: 1.9 Consensus size: 77
1921447 GTAATTAGCG
* *
1921457 TTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGAAT
1 TTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAAT
1921522 TTGAAAATCACC
66 TTGAAAATCACC
*
1921534 TTGCGAATTTGAAAATCGCATTGCGATTGTACTGTTTACCTATATCGGTAATTAGCATTGCGAAT
1 TTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAAT
1921599 TTGAAAAT
66 TTGAAAAT
1921607 TGAATTGCAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (77 bp):
TTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAAT
TTGAAAATCACC
Found at i:1924277 original size:22 final size:22
Alignment explanation
Indices: 1924252--1924296 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1924242 TAACCAGCAC
1924252 GGAATTATTTTACGACGTTGGT
1 GGAATTATTTTACGACGTTGGT
1924274 GGAATTATTTTACGACGTTGGT
1 GGAATTATTTTACGACGTTGGT
1924296 G
1 G
1924297 AATGATTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.40
Consensus pattern (22 bp):
GGAATTATTTTACGACGTTGGT
Found at i:1925987 original size:21 final size:21
Alignment explanation
Indices: 1925954--1926049 Score: 93
Period size: 21 Copynumber: 4.6 Consensus size: 21
1925944 ACCACTCCTT
* *
1925954 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATCCCA
* * * *
1925975 AAGGACCAAATATGTGTCCCG
1 AAGGACCACATATATATCCCA
* * *
1925996 AAGAACCACATATATGTTCCA
1 AAGGACCACATATATATCCCA
**
1926017 AAGGATTACATATATATCCCA
1 AAGGACCACATATATATCCCA
1926038 AAGGACCACATA
1 AAGGACCACATA
1926050 GAACTCTCGA
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (21 bp):
AAGGACCACATATATATCCCA
Found at i:1926046 original size:42 final size:42
Alignment explanation
Indices: 1925954--1926049 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
1925944 ACCACTCCTT
* * * *
1925954 AAGGATCACATATATATTCCAAAGGACCAAATATGTGTCCCG
1 AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCA
* * ** *
1925996 AAGAACCACATATATGTTCCAAAGGATTACATATATATCCCA
1 AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCA
1926038 AAGGACCACATA
1 AAGGACCACATA
1926050 GAACTCTCGA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (42 bp):
AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCA
Found at i:1934647 original size:31 final size:31
Alignment explanation
Indices: 1934574--1934700 Score: 139
Period size: 31 Copynumber: 4.1 Consensus size: 31
1934564 AGAGTCGAGG
*
1934574 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* ***
1934605 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTAAGGA-ACATATGGACA
1934637 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* * * * *
1934668 GTTTACCTAGGTTCTACGGAACCTATAGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
1934699 GT
1 GT
1934701 TGCCGAGGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
31 54 0.68
32 26 0.32
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTAAGGAACATATGGACA
Found at i:1934739 original size:30 final size:30
Alignment explanation
Indices: 1934698--1934759 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1934688 ACCTATAGAC
*
1934698 AGTTGCCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
1934728 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
1934758 AG
1 AG
1934760 GTCCTTCGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:1939474 original size:31 final size:31
Alignment explanation
Indices: 1939401--1939527 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
1939391 AGAGTCGAGG
1939401 GTATACCTATGTTCT-ACGGAACATATGGACA
1 GTATACCTATGTTCTAAC-GAACATATGGACA
* **
1939432 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTCTAACGA-ACATATGGACA
*
1939464 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAACGAACATATGGACA
* * * *
1939495 GTTTACCTAGGTTCT-ACGGAACCTATAGACA
1 GTATACCTATGTTCTAAC-GAACATATGGACA
1939526 GT
1 GT
1939528 TGCCGAGGAT
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
30 1 0.01
31 52 0.65
32 27 0.34
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (31 bp):
GTATACCTATGTTCTAACGAACATATGGACA
Found at i:1939571 original size:30 final size:30
Alignment explanation
Indices: 1939525--1939586 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1939515 ACCTATAGAC
*
1939525 AGTTGCCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
*
1939555 AGTTACCGATGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
1939585 AG
1 AG
1939587 GTCCTTCGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:1940690 original size:21 final size:21
Alignment explanation
Indices: 1940657--1940752 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
1940647 ACCACTCCTT
*
1940657 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATTCCA
* *
1940678 AAGGACCA-A-ATATGTGTCACG
1 AAGGACCACATATATAT-TC-CA
* * *
1940699 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATATTCCA
** *
1940720 AAGGATTACATATATATCCCA
1 AAGGACCACATATATATTCCA
1940741 AAGGACCACATA
1 AAGGACCACATA
1940753 GAACCCTCGA
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
19 5 0.09
20 3 0.05
21 40 0.70
22 3 0.05
23 6 0.11
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (21 bp):
AAGGACCACATATATATTCCA
Found at i:1941399 original size:19 final size:19
Alignment explanation
Indices: 1941368--1941407 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1941358 CCGATACTTC
*
1941368 CCTACTTGTGGTATCGATA
1 CCTACTTGTGGTATCAATA
1941387 CCTAGCTTG-GGTATCAATA
1 CCTA-CTTGTGGTATCAATA
1941406 CC
1 CC
1941408 CATTTTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (19 bp):
CCTACTTGTGGTATCAATA
Found at i:1942449 original size:8 final size:8
Alignment explanation
Indices: 1942436--1942558 Score: 72
Period size: 8 Copynumber: 14.6 Consensus size: 8
1942426 ATGTATGTTT
1942436 TATATGTA
1 TATATGTA
1942444 TATATGTA
1 TATATGTA
*
1942452 TATCTAAGTA
1 TA--TATGTA
*
1942462 TATATATA
1 TATATGTA
1942470 TATATAG-A
1 TATAT-GTA
*
1942478 TATATATA
1 TATATGTA
*
1942486 TATATATA
1 TATATGTA
*
1942494 TATATATA
1 TATATGTA
*
1942502 TATATATA
1 TATATGTA
1942510 GTATATGTA
1 -TATATGTA
1942519 GT-TATGTA
1 -TATATGTA
1942527 TGATCAATG-A
1 T-AT--ATGTA
* *
1942537 TGTATGTTT
1 TATATG-TA
1942546 TATATGTA
1 TATATGTA
1942554 TATAT
1 TATAT
1942559 ATGTACGTAC
Statistics
Matches: 94, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.04
8 62 0.66
9 16 0.17
10 9 0.10
11 3 0.03
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.48
Consensus pattern (8 bp):
TATATGTA
Found at i:1942465 original size:2 final size:2
Alignment explanation
Indices: 1942436--1942515 Score: 99
Period size: 2 Copynumber: 39.5 Consensus size: 2
1942426 ATGTATGTTT
* * * *
1942436 TA TA TG TA TA TA TG TA TA TC TA -A GTA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
1942478 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
1942516 GTAGTTATGT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
1 1 0.01
2 63 0.94
3 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1942647 original size:15 final size:15
Alignment explanation
Indices: 1942606--1942640 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1942596 ATGTGTGTGT
* *
1942606 TATACATATAATAAG
1 TATATATATAAAAAG
1942621 TATATATATAAAAAG
1 TATATATATAAAAAG
1942636 TATAT
1 TATAT
1942641 CATTAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (15 bp):
TATATATATAAAAAG
Found at i:1944141 original size:13 final size:13
Alignment explanation
Indices: 1944125--1944172 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
1944115 TTAATAAAAT
1944125 TAATTAATGATTA
1 TAATTAATGATTA
1944138 TAATTAA-GATTTA
1 TAATTAATGA-TTA
*
1944151 TAATATAAGGATTA
1 TAAT-TAATGATTA
1944165 TAATTAAT
1 TAATTAAT
1944173 ATAGAAAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 2 0.06
13 17 0.55
14 10 0.32
15 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TAATTAATGATTA
Found at i:1944510 original size:18 final size:18
Alignment explanation
Indices: 1944472--1944512 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1944462 AGAATCATGT
1944472 TTAA-TATAGTTAAGTTA
1 TTAATTATAGTTAAGTTA
*
1944489 --AATTATATTTAAGTTA
1 TTAATTATAGTTAAGTTA
1944505 TTAATTAT
1 TTAATTAT
1944513 TACATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 2 0.10
16 12 0.60
18 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
TTAATTATAGTTAAGTTA
Found at i:1947698 original size:198 final size:201
Alignment explanation
Indices: 1947337--1947862 Score: 542
Period size: 199 Copynumber: 2.6 Consensus size: 201
1947327 TCATGTGTTT
* * *
1947337 ATAGGCATGTTCGA-GGGGTATTTTCGGGTAATTAATCT-AAACTTTTTTGTAATTTATAAGATT
1 ATAGGCATGTTCGAGGGGGTATTTT-GGGTAGTTAATATGAAA-TTTTTCGTAATTTATAAGATT
** * * *
1947400 AGAGGCGTAGTATTAG-AGTTTATCCTTT-AGTTGAGGCCAATATCGGCACATACGAGATATTGT
64 AGAGGCGTAGTATTAGTAACTTAT-CTTTCAATTAAGGCCAATATCGGCACATACGAGACATTGT
* * *
1947463 AAGCGGGTTAAAATCAGATGAAAAAAGAATCCAAAGCTT-GTTTTGTGCATGAAGAA-AAAGCTA
128 AAGCAGGTAAAAATCAGATGAAAAAAGAATACAAAGCTTGGTTTTGTGCATGAAGAAGAAA-CTA
1947526 AAATGG-TTAA
192 AAATGGCTT-A
* *
1947536 ATAGGCATATTCGAGGGGGT-TTTTGGGTAGTTAATGTGAAATTTTTCGTAATTTATAAGATTAG
1 ATAGGCATGTTCGAGGGGGTATTTTGGGTAGTTAATATGAAATTTTTCGTAATTTATAAGATTAG
* * *
1947600 ATGCGTAGTATT-GTAACTT-TCTTTCAATTAAAGG-TAATATCGGCACATATGAGACATTGTAA
66 AGGCGTAGTATTAGTAACTTATCTTTCAATT-AAGGCCAATATCGGCACATACGAGACATTGTAA
** * ** *
1947662 GCAAGGTAAAAATC-GCATTCAAAATGGTTACAAAGCTTGGTTTTGTTCATGAAGAAGAAACTAA
130 GC-AGGTAAAAATCAG-ATGAAAAAAGAATACAAAGCTTGGTTTTGTGCATGAAGAAGAAACTAA
*
1947726 AATGGCTTG
193 AATGGCTTA
* * * *
1947735 ATAGGCATGTTCG-GGGAGTATTTT-CGTGAGTTAATATGAAAATTTTCGTAATCTATAAGATTA
1 ATAGGCATGTTCGAGGGGGTATTTTGGGT-AGTTAATATGAAATTTTTCGTAATTTATAAGATTA
* * * * * * * * *
1947798 AAGGTGTAGTATTAGT-ACTTATGTTTCAATTGAGGCTAGTATCGACACATACAAGACATTTTAA
65 GAGGCGTAGTATTAGTAACTTATCTTTCAATTAAGGCCAATATCGGCACATACGAGACATTGTAA
1947862 G
130 G
1947863 TACTGTAAAA
Statistics
Matches: 274, Mismatches: 38, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
196 4 0.01
197 33 0.12
198 82 0.30
199 110 0.40
200 45 0.16
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (201 bp):
ATAGGCATGTTCGAGGGGGTATTTTGGGTAGTTAATATGAAATTTTTCGTAATTTATAAGATTAG
AGGCGTAGTATTAGTAACTTATCTTTCAATTAAGGCCAATATCGGCACATACGAGACATTGTAAG
CAGGTAAAAATCAGATGAAAAAAGAATACAAAGCTTGGTTTTGTGCATGAAGAAGAAACTAAAAT
GGCTTA
Found at i:1949055 original size:25 final size:25
Alignment explanation
Indices: 1949039--1949106 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
1949029 CACTTAAAAA
*
1949039 TGCCTTGTAGAATTGCACTAGAAAG
1 TGCCTCGTAGAATTGCACTAGAAAG
1949064 TGCCTCGTAGAATTGCACTAGAAAG
1 TGCCTCGTAGAATTGCACTAGAAAG
1949089 TGCCTCGTAGAATTGCAC
1 TGCCTCGTAGAATTGCAC
1949107 CATAAGTGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (25 bp):
TGCCTCGTAGAATTGCACTAGAAAG
Found at i:1954580 original size:22 final size:23
Alignment explanation
Indices: 1954549--1954629 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 23
1954539 AATTGAGACA
*
1954549 AAAAACAAAGATTAAAAAAAT-T
1 AAAAATAAAGATTAAAAAAATAT
*
1954571 AAAAATAAAGATAATAAAAAATAT
1 AAAAATAAAGATTA-AAAAAATAT
* *
1954595 GGATAAAATAAAGA-TAAGAATATAT
1 --A-AAAATAAAGATTAAAAAAATAT
1954620 AAAAATAAAG
1 AAAAATAAAG
1954630 TAGAAATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
22 21 0.43
23 8 0.16
24 1 0.02
25 7 0.14
26 2 0.04
27 10 0.20
ACGTcount: A:0.70, C:0.01, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAAATAAAGATTAAAAAAATAT
Found at i:1954621 original size:21 final size:20
Alignment explanation
Indices: 1954597--1954642 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1954587 AAAAATATGG
1954597 ATAAAATAAAGATA-AGAATAT
1 ATAAAATAAAG-TAGA-AATAT
1954618 ATAAAAATAAAGTAGAAATAT
1 AT-AAAATAAAGTAGAAATAT
1954639 ATAA
1 ATAA
1954643 TGGAAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.09
21 11 0.48
22 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (20 bp):
ATAAAATAAAGTAGAAATAT
Found at i:1963191 original size:81 final size:81
Alignment explanation
Indices: 1963056--1963224 Score: 250
Period size: 81 Copynumber: 2.1 Consensus size: 81
1963046 TGACTTTTCA
** * *
1963056 TCTTTTACTCAGTGGTTTTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATAGC
1 TCTTTTACTCAACGGTCTTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTACCAATAGC
* *
1963121 ATAGTTATGCCATTAT
66 ATAGTCAAGCCATTAT
*
1963137 TCTTTTACTCAACGGTCTTTAA-TCGTTCATCTAACTGGCATAATTGACACATTTCTACCAATTG
1 TCTTTTACTCAACGGTCTTTAACT-GTTCATCTAACTGGCATAATTGACACATTTCTACCAATAG
*
1963201 CATAGTCAAGCCCTTAT
65 CATAGTCAAGCCATTAT
1963218 TCTTTTA
1 TCTTTTA
1963225 TTTTGGACTA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 1 0.01
81 78 0.99
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (81 bp):
TCTTTTACTCAACGGTCTTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTACCAATAGC
ATAGTCAAGCCATTAT
Found at i:1963498 original size:54 final size:54
Alignment explanation
Indices: 1963362--1963911 Score: 742
Period size: 54 Copynumber: 10.2 Consensus size: 54
1963352 ATTTATTAAG
* * * * * * *
1963362 ATGCACACGTAGTGCCTATACAG-TAGTTCATCAACTCATGATAAATTCTGTGGAT
1 ATGCACACTTAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTCCGT-GAA
* * * *
1963417 TTGCACACATAGTGCATGCACGGTTATTCATCAACTCATGATGAATTCCTTGAA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
*
1963471 ATGCACACTTAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCGTGAA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
* * **
1963525 ATGCACACTTAGTGCCTGTACGATTATTCATCAACTCATGATGAATTTTGTGAA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
* * *
1963579 ATGCACACTTAGTACATGTACGGTTATTTATCAACTCATGATGAATTCCATGAA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
* * *
1963633 ATGCACACTTAGTGCTTGTACGGTTATTCATCAACCCATGATGAATTTCGTGAA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
* * *
1963687 ATGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
* * *
1963741 ATGCACACTTAGTGCATGTACGATTATTCATCAACTCATGATGAATTTCGTGGA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
* *
1963795 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATAAATTCCTTGAA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
* * * * ** *
1963849 ATGCACAATTAGTGCCTGCACGTTTATTCATCAACTCATGATGAATTTTGTGGA
1 ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
1963903 ATGCACACT
1 ATGCACACT
1963912 ACAACTCATG
Statistics
Matches: 443, Mismatches: 51, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
54 402 0.91
55 39 0.09
56 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (54 bp):
ATGCACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA
Found at i:1963922 original size:33 final size:33
Alignment explanation
Indices: 1963880--1963944 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1963870 GTTTATTCAT
** *
1963880 CAACTCATGATGAATTTTGTGGAATGCACACTA
1 CAACTCATGATGAATTCCGTGGAATACACACTA
1963913 CAACTCATGATGAATTCCGTGGAATACACACT
1 CAACTCATGATGAATTCCGTGGAATACACACT
1963945 TAGTGCCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (33 bp):
CAACTCATGATGAATTCCGTGGAATACACACTA
Found at i:1967775 original size:81 final size:81
Alignment explanation
Indices: 1967623--1967791 Score: 234
Period size: 81 Copynumber: 2.1 Consensus size: 81
1967613 TGACTTTTTA
* * * *
1967623 TCTTTTACCCAGCGGTCTTTAACCATTCATTTAACTGGCATAATTGACACCTTTTTGCCAGTTGC
1 TCTTTTACCCAACGGTCTTTAACCATTCATCTAACTGGCATAATTGACACATTTTTGCCAATTGC
*
1967688 TCAGTTAGGCCATTGT
66 TCAGTTAGGCCATTAT
* *
1967704 TCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTT-CCAATTG
1 TCTTTTACCCAACGGTCTTTAACCATTCATCTAACTGGCATAATTGACACATTT-TTGCCAATTG
*
1967768 CAT-AGTTAGGCCCTTAT
65 C-TCAGTTAGGCCATTAT
1967785 TCTTTTA
1 TCTTTTA
1967792 TTTTGGACTA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 75 0.96
82 3 0.04
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (81 bp):
TCTTTTACCCAACGGTCTTTAACCATTCATCTAACTGGCATAATTGACACATTTTTGCCAATTGC
TCAGTTAGGCCATTAT
Found at i:1968057 original size:54 final size:54
Alignment explanation
Indices: 1967954--1968696 Score: 1077
Period size: 54 Copynumber: 13.8 Consensus size: 54
1967944 TATACAGTAG
* ** * *
1967954 TTCATCAACTCATGATAAATTCCGTGGATTTGTACACATAGTG-TCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGT-GAAATGCACACTTAGTGCT-TGTACGGTTA
* *
1968009 TTCATCAACTCATGATGAATTTCGTGAAATGTACACTTAGTGCTTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
* * * *
1968063 TTCATCAACTCATGATAAATTTCGTGGAATGTACACTTAGTGGC-TGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGT-GCTTGTACGGTTA
*
1968117 TTCAT---CTCATGATGAATTCCGTGAAATGCACACTTAGTG-TCTGTATGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCT-TGTACGGTTA
* * *
1968168 TTCATTAACTCATTATGAATTCCGTGAAATGCACACTTAGTGCTTGTATGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
* * * *
1968222 TTCATCAACTCATGATGAATTCCTTGGAATGCACACTTAGTGCCTGTACAGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
*
1968276 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
*
1968330 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
* *
1968384 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCCTGTAAGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
*
1968438 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
* *
1968492 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCCTGTAAGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
* *
1968546 TTCATCAACTTATGATGAATTCCGTGAAATGCACACTTAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
* * *
1968600 TTCATCAACTCAT-ATTGAATTCCGTGGAATGCACACTTAGTACATGTACGGTTA
1 TTCATCAACTCATGA-TGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
** * *
1968654 TTCATCAACTCATGATGAATTTTGTGGAATGTACACTTAGTGC
1 TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGC
1968697 CTATTTGGTA
Statistics
Matches: 635, Mismatches: 43, Indels: 21
0.91 0.06 0.03
Matches are distributed among these distances:
50 1 0.00
51 43 0.07
53 1 0.00
54 562 0.89
55 28 0.04
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (54 bp):
TTCATCAACTCATGATGAATTCCGTGAAATGCACACTTAGTGCTTGTACGGTTA
Found at i:1969281 original size:20 final size:20
Alignment explanation
Indices: 1969256--1969298 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1969246 TTACCTTGGG
*
1969256 TATCGATACTACAAGAACAT
1 TATCGATAATACAAGAACAT
**
1969276 TATCGATAATGTAAGAACAT
1 TATCGATAATACAAGAACAT
1969296 TAT
1 TAT
1969299 TGGTACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (20 bp):
TATCGATAATACAAGAACAT
Found at i:1970494 original size:27 final size:30
Alignment explanation
Indices: 1970462--1970527 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 30
1970452 AAGACGATCG
1970462 AAAATAAAGATAATAA-AAAAGA-T-AGAT
1 AAAATAAAGATAATAAGAAAAGATTAAGAT
*
1970489 AAAAT-AA-AT-ATAAGAATAGATTAAGAT
1 AAAATAAAGATAATAAGAAAAGATTAAGAT
1970516 AAAATAAAGATA
1 AAAATAAAGATA
1970528 TGTAAAGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
24 4 0.12
25 7 0.22
26 3 0.09
27 14 0.44
28 2 0.06
29 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (30 bp):
AAAATAAAGATAATAAGAAAAGATTAAGAT
Found at i:1970507 original size:21 final size:21
Alignment explanation
Indices: 1970473--1970522 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1970463 AAATAAAGAT
1970473 AATAAAA-AAG-ATAGA-TAA
1 AATAAAATAAGAATAGATTAA
1970491 AATAAATATAAGAATAGATTAA
1 AATAAA-ATAAGAATAGATTAA
*
1970513 GATAAAATAA
1 AATAAAATAA
1970523 AGATATGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.22
19 1 0.04
20 3 0.11
21 9 0.33
22 8 0.30
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (21 bp):
AATAAAATAAGAATAGATTAA
Found at i:1970525 original size:22 final size:21
Alignment explanation
Indices: 1970468--1970525 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
1970458 ATCGAAAATA
*
1970468 AAGATAATAAAAAAG-ATAGAT
1 AAGATAA-AATAAAGAATAGAT
*
1970489 AAAAT-AAATATAAGAATAGATT
1 AAGATAAAATA-AAGAATAGA-T
1970511 AAGATAAAATAAAGA
1 AAGATAAAATAAAGA
1970526 TATGTAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.10
20 4 0.13
21 9 0.30
22 9 0.30
23 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (21 bp):
AAGATAAAATAAAGAATAGAT
Found at i:1980227 original size:21 final size:23
Alignment explanation
Indices: 1980198--1980239 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1980188 CAATTTTTTT
*
1980198 AAAACTTATGCAATTT-TTGAAC
1 AAAACTTATGAAATTTATTGAAC
1980220 AAAA-TTATGAAATTTATTGA
1 AAAACTTATGAAATTTATTGA
1980240 TTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (23 bp):
AAAACTTATGAAATTTATTGAAC
Found at i:1991983 original size:28 final size:28
Alignment explanation
Indices: 1991952--1992011 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
1991942 TTGAATTTTG
1991952 TTACATTTCACTT-AGATGTTGAAGTACA
1 TTACATTTCACTTGA-ATGTTGAAGTACA
*
1991980 TTACATTTCACTTGAATGTTGAATTACA
1 TTACATTTCACTTGAATGTTGAAGTACA
1992008 TTAC
1 TTAC
1992012 TTGAATGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (28 bp):
TTACATTTCACTTGAATGTTGAAGTACA
Found at i:1992013 original size:21 final size:23
Alignment explanation
Indices: 1991979--1992020 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
1991969 GTTGAAGTAC
1991979 ATTACATTTCACTTGAATGTTGA
1 ATTACATTTCACTTGAATGTTGA
1992002 ATTACA-TT-ACTTGAATGTT
1 ATTACATTTCACTTGAATGTT
1992021 TGTAAACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (23 bp):
ATTACATTTCACTTGAATGTTGA
Found at i:1992539 original size:19 final size:20
Alignment explanation
Indices: 1992501--1992557 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
1992491 CTATAGAGTG
1992501 TATTGTTCTTCCAGTATCGA
1 TATTGTTCTTCCAGTATCGA
* *
1992521 TATTGTTTTTTCA-TATCGA
1 TATTGTTCTTCCAGTATCGA
*
1992540 TATTGTTCTTCCAATATC
1 TATTGTTCTTCCAGTATC
1992558 AATACTTCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.51
Consensus pattern (20 bp):
TATTGTTCTTCCAGTATCGA
Found at i:1998822 original size:17 final size:17
Alignment explanation
Indices: 1998800--1998853 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
1998790 CCGTGTCCCG
1998800 ACCCGGATGTTTCGGGT
1 ACCCGGATGTTTCGGGT
1998817 ACCCGGAT-TTTGCGGGT
1 ACCCGGATGTTT-CGGGT
*
1998834 ACCCGTATG--TCGGGT
1 ACCCGGATGTTTCGGGT
1998849 ACCCG
1 ACCCG
1998854 AATACCTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 10 0.29
16 4 0.12
17 20 0.59
ACGTcount: A:0.13, C:0.28, G:0.33, T:0.26
Consensus pattern (17 bp):
ACCCGGATGTTTCGGGT
Found at i:1998880 original size:12 final size:11
Alignment explanation
Indices: 1998863--1998894 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
1998853 GAATACCTGG
1998863 AATTTTTTTTT
1 AATTTTTTTTT
1998874 CAATTTTTTTTT
1 -AATTTTTTTTT
1998886 AATTTTTTT
1 AATTTTTTT
1998895 GATAGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
AATTTTTTTTT
Found at i:1999577 original size:16 final size:16
Alignment explanation
Indices: 1999556--1999598 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1999546 AAAAAAAGCT
*
1999556 TAACCGGGTACTCGGG
1 TAACCGGGTACTAGGG
1999572 TAACCGGGTACTAGGG
1 TAACCGGGTACTAGGG
1999588 TAACCGGGTAC
1 TAACCGGGTAC
1999599 CCGGAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (16 bp):
TAACCGGGTACTAGGG
Found at i:1999673 original size:15 final size:15
Alignment explanation
Indices: 1999653--1999687 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1999643 GTCATATTCT
1999653 TTTCATTTAGACATA
1 TTTCATTTAGACATA
1999668 TTTCATTTAGACATA
1 TTTCATTTAGACATA
1999683 TTTCA
1 TTTCA
1999688 GAACTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (15 bp):
TTTCATTTAGACATA
Found at i:2002167 original size:3 final size:3
Alignment explanation
Indices: 2002159--2002184 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2002149 TTATTTTACC
2002159 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2002185 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2002240 original size:20 final size:20
Alignment explanation
Indices: 2002215--2002253 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2002205 TTATTTCTTT
2002215 TTTTACCAT-TCAATATTTTA
1 TTTTACCATCT-AATATTTTA
2002235 TTTTACCATCTAATATTTT
1 TTTTACCATCTAATATTTT
2002254 GTTTGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTACCATCTAATATTTTA
Found at i:2002502 original size:16 final size:17
Alignment explanation
Indices: 2002460--2002502 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2002450 AACACATACC
*
2002460 AATTTTTTTTGTCTTAA
1 AATTATTTTTGTCTTAA
* *
2002477 AAATAATTTT-TCTTAA
1 AATTATTTTTGTCTTAA
2002493 AATTATTTTT
1 AATTATTTTT
2002503 AAAAATACAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (17 bp):
AATTATTTTTGTCTTAA
Found at i:2006455 original size:31 final size:31
Alignment explanation
Indices: 2006420--2006481 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2006410 AGGGACAATG
*
2006420 GTGGTATCT-TTGAAGATTCAATATCAAATAT
1 GTGGTAT-TGTTGAAGATTCAACATCAAATAT
* *
2006451 GTGGTATTGTTGGAGATTCAACATCGAATAT
1 GTGGTATTGTTGAAGATTCAACATCAAATAT
2006482 TGGGGCATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (31 bp):
GTGGTATTGTTGAAGATTCAACATCAAATAT
Found at i:2006973 original size:121 final size:121
Alignment explanation
Indices: 2006756--2007204 Score: 527
Period size: 121 Copynumber: 3.8 Consensus size: 121
2006746 TTCAGAGTCA
*
2006756 ATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
* * * *
2006821 GATTTCAATTTCACGACGAAGAATATTGTGCCCACAAACAGCAATGTAACCCTTGG
66 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAACAGCAATGCAACCCTTGG
** * *
2006877 ATTTCAACTTCACGATAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGTCATCCAT
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
* *
2006942 GATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGA-AACAATGCAACCCTTGG
66 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAA-ACAGCAATGCAACCCTTGG
* * *
2006998 ATTTCAACTTCACGACGAAGGATAT-C--GT----G--C--C--CACAAGCAGTAAT-A-CAACC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAA-C-G-AATGAGCCATC
** * * *
2007048 CTTGGATTTCAACTTCACGACGAAGGATATCGTGCCCACGAGCAAG-AATACAACCCTTGG
63 C-ACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAAC-AGCAATGCAACCCTTGG
* *
2007108 ATTTTAACTTTACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
*
2007173 GATTTCAACTTCACGATGAAGGATATCGTGCC
66 GATTTCAACTTCACGACGAAGGATATCGTGCC
2007205 TAATGGATCG
Statistics
Matches: 276, Mismatches: 30, Indels: 44
0.79 0.09 0.13
Matches are distributed among these distances:
108 5 0.02
109 4 0.01
110 74 0.27
111 5 0.02
112 1 0.00
113 1 0.00
114 1 0.00
117 1 0.00
118 1 0.00
119 1 0.00
120 4 0.01
121 167 0.61
122 6 0.02
123 5 0.02
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.24
Consensus pattern (121 bp):
ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAACAGCAATGCAACCCTTGG
Found at i:2007008 original size:55 final size:55
Alignment explanation
Indices: 2006942--2007133 Score: 303
Period size: 55 Copynumber: 3.5 Consensus size: 55
2006932 AGTCATCCAT
* * *
2006942 GATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGAAACAATGCAACCCTTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATACAACCCTTG
**
2006997 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGTAATACAACCCTTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATACAACCCTTG
* *
2007052 GATTTCAACTTCACGACGAAGGATATCGTGCCCACGAGCAAGAATACAACCCTTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATACAACCCTTG
* *
2007107 GATTTTAACTTTACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
2007134 CAATTCAAAG
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 127 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (55 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATACAACCCTTG
Found at i:2008135 original size:45 final size:46
Alignment explanation
Indices: 2008047--2008137 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
2008037 TTGAAAAAGC
* *
2008047 CTGAGTGCATCGATGCATAGTCTTGTGCATCGATACATCAAATGCA
1 CTGAGTGCATCGATGCATAGTCATGTGCATCGATACATAAAATGCA
* *
2008093 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATAGTCATGTGCATCGATACATAAAATGCA
2008138 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATAGTCATGTGCATCGATACATAAAATGCA
Found at i:2008185 original size:20 final size:20
Alignment explanation
Indices: 2008157--2008195 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2008147 CAAGAAATTA
2008157 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
2008177 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2008196 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:2010432 original size:31 final size:31
Alignment explanation
Indices: 2010397--2010463 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
2010387 AAAATCTTAA
2010397 AAAATTGTTTGTTTTTGACGAAATTGGTAGT
1 AAAATTGTTTGTTTTTGACGAAATTGGTAGT
2010428 AAAATTGTTTGTTTTTGACGAAATTGGTAGT
1 AAAATTGTTTGTTTTTGACGAAATTGGTAGT
2010459 AAAAT
1 AAAAT
2010464 CAAGCCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (31 bp):
AAAATTGTTTGTTTTTGACGAAATTGGTAGT
Found at i:2016370 original size:21 final size:21
Alignment explanation
Indices: 2016346--2016385 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2016336 ACCGTCAACC
*
2016346 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
*
2016367 AAATCCAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
2016386 AATCCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:2017652 original size:24 final size:23
Alignment explanation
Indices: 2017602--2017675 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
2017592 GCTTCAACTT
* *
2017602 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
2017625 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
2017649 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
2017672 TTTG
1 TTTG
2017676 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:2027900 original size:24 final size:22
Alignment explanation
Indices: 2027872--2027916 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
2027862 TATGTAGAAT
2027872 TATTTAAATTTAATATAAATATTA
1 TATTTAAATTTAA-A-AAATATTA
**
2027896 TATTTTCATTTAAAAAATATT
1 TATTTAAATTTAAAAAATATT
2027917 TCAGTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTAAATTTAAAAAATATTA
Found at i:2032237 original size:59 final size:62
Alignment explanation
Indices: 2032171--2032295 Score: 148
Period size: 62 Copynumber: 2.1 Consensus size: 62
2032161 ATATGAATAG
* * *
2032171 TCAGGTGAAAATTTTGT-AAC-TTTTAATAGTCGGAGGACT-AACAAAGCAACAACCTATAA
1 TCAGGTGAAAATTTTGTAAACTTTTTAATAATCGGAAGACTCAACAAAGAAACAACCTATAA
** * * * *
2032230 TCAGGTGATCATTTTTTAAACTTTTTAATAATCTGAAGACTCAATAAAGAAACATCCTATAA
1 TCAGGTGAAAATTTTGTAAACTTTTTAATAATCGGAAGACTCAACAAAGAAACAACCTATAA
2032292 TCAG
1 TCAG
2032296 AGGACTCAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
59 14 0.26
60 3 0.06
61 16 0.30
62 21 0.39
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (62 bp):
TCAGGTGAAAATTTTGTAAACTTTTTAATAATCGGAAGACTCAACAAAGAAACAACCTATAA
Found at i:2032784 original size:51 final size:51
Alignment explanation
Indices: 2032729--2032829 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
2032719 ACATTTACTA
*
2032729 TATAATTAATATAATTAGTATATCAAATTTATATTTTTAAATATTTTTAAG
1 TATAATTAATATAATTAGTATATCAAATTTATATTTTTAAATAGTTTTAAG
* *
2032780 TATAATTAATATAATTAGTATATTAATTTTATATTTTTAAATAGTTTTAA
1 TATAATTAATATAATTAGTATATCAAATTTATATTTTTAAATAGTTTTAA
2032830 TAAATATTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (51 bp):
TATAATTAATATAATTAGTATATCAAATTTATATTTTTAAATAGTTTTAAG
Found at i:2034175 original size:13 final size:13
Alignment explanation
Indices: 2034157--2034181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2034147 CGTTTTGATA
2034157 ATTTTAAAATTAT
1 ATTTTAAAATTAT
2034170 ATTTTAAAATTA
1 ATTTTAAAATTA
2034182 CTAAAATGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTAAAATTAT
Found at i:2040438 original size:622 final size:623
Alignment explanation
Indices: 2039639--2040882 Score: 2151
Period size: 622 Copynumber: 2.0 Consensus size: 623
2039629 CATTTCCGAT
*
2039639 TTTACCATACCCTTACATAATCAAGGATTCAACAAACATTTTCAAATCAGGCAATATCAAGCAGA
1 TTTACCATACCCTTACATAATCAAGGATTCAACAAACATTTTCAAATCAGGCAATATCAAGCAAA
*
2039704 ATCAGGACATAATCATTCACAAGAAACAACAAAACATTATGCTTGTTGTAAGGCATCCTACAAAA
66 ATCAGGACATAATCATTCACAAGAAACAACAAAACATTATACTTGTTGTAAGGCATCCTACAAAA
2039769 AATAAAATCATTAATAAACAATTTGAAAAATTAATTAAATAAATATAATAAATATAAAAAAATGA
131 AATAAAATCATTAATAAACAATTTGAAAAATTAATTAAATAAATATAATAAATAT-AAAAAATGA
*
2039834 AGTTACCTTTAAA-GGGAAGAAAAAAGACAGAATCATTCACAAACCAATTCCAATGTATTTACTT
195 AGTTACCTTTAAAGGGGAA-AAAAAAGACAAAATCATTCACAAACCAATTCCAATGTATTTACTT
* *
2039898 ATTGTAAAACACCCAACAAAAATAAAAATAAAATCATTAATAAGAAATTTGAAATACTAATAAAA
259 ACTGTAAAACACCCAACAAAAATAAAAATAAAATCATTAACAAGAAATTTGAAATACTAATAAAA
*
2039963 TTAAAATAAAAAA-TATAGTAAATATTATATTTACCTTTAAATAGAAGAATCATTAACTACAGTA
324 TTAAAATAAAAAACTATAGTAAATATTATATTTACATTTAAATAGAAGAATCATTAACTACAGTA
2040027 AGATAATATTCATCCATTTCCTTTGGTTTAAAACCATACAACCAATTACAAGTTGTTACAAAAAT
389 AGATAATATTCATCCATTTCCTTTGGTTTAAAACCATACAACCAATTACAAGTTGTTACAAAAAT
2040092 CTCAATATTTTTAGGTAAGAGTTTAGCTTTCAACTTGTTCAGAATTTGACCCCCATACTAAAGGA
454 CTCAATATTTTTAGGTAAGAGTTTAGCTTTCAACTTGTTCAGAATTTGACCCCCATACTAAAGGA
**
2040157 CGATTAAGATACAT-TCGCGAC-CATCTTTCGGTTGGGCCCTGAATTAGGCCTCGACTTGAAATA
519 CGATTAAGATAC-TGTCGCGACTC-TCTTTCGGTTGGGCCCAAAATTAGGCCTCGACTTGAAATA
* *
2040220 ATGGGTTAGAGTCATCACCGATCACTTTAAAAATATTTAGGG
582 ATGAGTTAGAGTCATCACCGATCACTTTAAAAACATTTAGGG
*
2040262 TTTACCATACCCTTA-A-AATCAAGGATTCAACAAACATTTTCAAATCCA-GTAATATCAAGCAA
1 TTTACCATACCCTTACATAATCAAGGATTCAACAAACATTTTCAAAT-CAGGCAATATCAAGCAA
*
2040324 AATCAGGACATAATCAATTCACAAGAAACAACAAAACATTATACTTGTTGTAAGGCATTCTACAA
65 AATCAGGACATAATC-ATTCACAAGAAACAACAAAACATTATACTTGTTGTAAGGCATCCTACAA
* *
2040389 AAAATAGAATCATTAATAAACAATTTGAAAAATTAATTAAATAAATATAATAAATATAAAAAGTG
129 AAAATAAAATCATTAATAAACAATTTGAAAAATTAATTAAATAAATATAATAAATATAAAAAATG
*
2040454 AAGTTACCTTTAAAGGGGAAAAACAAGACAAAATCATTCACAAACCAATTCCAATGTATTTACTT
194 AAGTTACCTTTAAAGGGGAAAAAAAAGACAAAATCATTCACAAACCAATTCCAATGTATTTACTT
* *
2040519 ACTGTAAAACACCCTACAAAAATAAAAATAAAATCATTAACAAGAAATTTGAAATACTAATGAAA
259 ACTGTAAAACACCCAACAAAAATAAAAATAAAATCATTAACAAGAAATTTGAAATACTAATAAAA
* * *
2040584 TTAAAATAAAAAACTATAGTAAATATTATATTTATATTTAAATATAGGAATCATTAACTACAGTA
324 TTAAAATAAAAAACTATAGTAAATATTATATTTACATTTAAATAGAAGAATCATTAACTACAGTA
* *
2040649 AGATAATATTCATCCATTTCCTTTGGTTTAAAATCATACAACCAATTACGAGTTGTTACAAAAAT
389 AGATAATATTCATCCATTTCCTTTGGTTTAAAACCATACAACCAATTACAAGTTGTTACAAAAAT
2040714 CTCAATATTTTTAGGTAAGAGTTTAGCTTTCAACTTGTTCAGAATTTGACCCCCATACTAAAGGA
454 CTCAATATTTTTAGGTAAGAGTTTAGCTTTCAACTTGTTCAGAATTTGACCCCCATACTAAAGGA
* * *
2040779 CGATTAAGATACTGTCGCGACTCTCTTTCGGTTGGGCTCAAAATTGGGCTTCGACTTGAAATAAT
519 CGATTAAGATACTGTCGCGACTCTCTTTCGGTTGGGCCCAAAATTAGGCCTCGACTTGAAATAAT
*
2040844 GAGTTAGAGTCGTCACCGATCACTTTAAAAACATTTAGG
584 GAGTTAGAGTCATCACCGATCACTTTAAAAACATTTAGG
2040883 TAGATCAGAC
Statistics
Matches: 589, Mismatches: 26, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
621 195 0.33
622 378 0.64
623 16 0.03
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (623 bp):
TTTACCATACCCTTACATAATCAAGGATTCAACAAACATTTTCAAATCAGGCAATATCAAGCAAA
ATCAGGACATAATCATTCACAAGAAACAACAAAACATTATACTTGTTGTAAGGCATCCTACAAAA
AATAAAATCATTAATAAACAATTTGAAAAATTAATTAAATAAATATAATAAATATAAAAAATGAA
GTTACCTTTAAAGGGGAAAAAAAAGACAAAATCATTCACAAACCAATTCCAATGTATTTACTTAC
TGTAAAACACCCAACAAAAATAAAAATAAAATCATTAACAAGAAATTTGAAATACTAATAAAATT
AAAATAAAAAACTATAGTAAATATTATATTTACATTTAAATAGAAGAATCATTAACTACAGTAAG
ATAATATTCATCCATTTCCTTTGGTTTAAAACCATACAACCAATTACAAGTTGTTACAAAAATCT
CAATATTTTTAGGTAAGAGTTTAGCTTTCAACTTGTTCAGAATTTGACCCCCATACTAAAGGACG
ATTAAGATACTGTCGCGACTCTCTTTCGGTTGGGCCCAAAATTAGGCCTCGACTTGAAATAATGA
GTTAGAGTCATCACCGATCACTTTAAAAACATTTAGGG
Found at i:2041166 original size:11 final size:10
Alignment explanation
Indices: 2041151--2041196 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
2041141 AAAAGCAAAA
*
2041151 AAATAGTAAT
1 AAATAATAAT
2041161 ATAATAATAAT
1 A-AATAATAAT
2041172 AAATAA-AAT
1 AAATAATAAT
2041181 AAATAA-AGAT
1 AAATAATA-AT
2041191 AAATAA
1 AAATAA
2041197 AATTTAGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 10 0.30
10 14 0.42
11 9 0.27
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (10 bp):
AAATAATAAT
Found at i:2041192 original size:10 final size:9
Alignment explanation
Indices: 2041158--2041199 Score: 57
Period size: 10 Copynumber: 4.3 Consensus size: 9
2041148 AAAAAATAGT
2041158 AATATAATAA
1 AATA-AATAA
2041168 TAATAAATAA
1 -AATAAATAA
2041178 AATAAATAA
1 AATAAATAA
2041187 AGATAAATAA
1 A-ATAAATAA
2041197 AAT
1 AAT
2041200 TTAGCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 12 0.40
10 14 0.47
11 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (9 bp):
AATAAATAA
Found at i:2041270 original size:7 final size:7
Alignment explanation
Indices: 2041207--2041274 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
2041197 AATTTAGCAA
*
2041207 AAAAAAA
1 AAAAAAT
*
2041214 AAAAAAG
1 AAAAAAT
*
2041221 AAAACAT
1 AAAAAAT
*
2041228 AAAATA-
1 AAAAAAT
2041234 AAAAAAT
1 AAAAAAT
2041241 AAAAAGGAT
1 AAAAA--AT
2041250 AAAAAAT
1 AAAAAAT
*
2041257 --GAAAT
1 AAAAAAT
2041262 AAAAAAT
1 AAAAAAT
2041269 AAAAAA
1 AAAAAA
2041275 GGTTAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
5 4 0.08
6 5 0.10
7 33 0.67
9 7 0.14
ACGTcount: A:0.82, C:0.01, G:0.06, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:2041282 original size:21 final size:20
Alignment explanation
Indices: 2041237--2041274 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2041227 TAAAATAAAA
2041237 AAATAAAAAGGATAAAAAATG
1 AAATAAAAA-GATAAAAAATG
2041258 AAATAAAAA-ATAAAAAA
1 AAATAAAAAGATAAAAAA
2041275 GGTTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (20 bp):
AAATAAAAAGATAAAAAATG
Found at i:2041294 original size:28 final size:28
Alignment explanation
Indices: 2041205--2041300 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 28
2041195 AAAATTTAGC
** * * *
2041205 AAAAAAAAAAAAAAAGAAAACATAAAAT
1 AAAAAAAAAAAAGGATAAAAAATGAAAT
2041233 AAAAAAATAAAAAGGATAAAAAATGAAAT
1 AAAAAAA-AAAAAGGATAAAAAATGAAAT
* ***
2041262 AAAAAATAAAAAAGGTTAAATTTTGAAAT
1 AAAAAA-AAAAAAGGATAAAAAATGAAAT
*
2041291 AAAAACAAAA
1 AAAAAAAAAA
2041301 TGTTAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
28 11 0.20
29 44 0.79
30 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (28 bp):
AAAAAAAAAAAAGGATAAAAAATGAAAT
Found at i:2043411 original size:85 final size:84
Alignment explanation
Indices: 2043081--2043989 Score: 797
Period size: 85 Copynumber: 10.8 Consensus size: 84
2043071 ATATGTCATC
* * * * * * *
2043081 GAGCTGAATGGAATCGAACTCAACAGTTTTTTGTTGACATATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AG-GTCTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* *
2043146 CTGTAAATTTGATATGCCCTC
64 CTGTAAATTTGATATGCCTTT
* *
2043167 GAGCTGAATGTAAACGAACTCGAAGGT-TTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCT
* *
2043231 GTAAATTTGATGTGCATTT
66 GTAAATTTGATATGCCTTT
* * * *
2043250 GAGCTGAATATAATCGAACTCGATA-GTCTTTTGTTGATAGATAAACCTTCTCGCCTTGAGCTAT
1 GAGCTGAATGTAATCGAACTCGA-AGGTC--TTGTTGACAGATAACCCTTCTCGCCTTGAGTTAT
** *
2043314 GCTACAAA-TTGATATTCCTTT
63 GCTGTAAATTTGATATGCCTTT
* *
2043335 GAGCTGAATGTAATCGAACTGGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGA-TCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTT-GTTGACAGATAACCCTTCTCGCCTTGAGT-TATG
* *
2043399 TTGTAAATTTGATATGTCTTT
64 CTGTAAATTTGATATGCCTTT
* * * * * *
2043420 GA---G--TGTAATTGAACTCGAAGGTCTTTGCTCATAGATAACCCTTCTCCCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
2043480 TGTATATTTGATGTGCCTTT
65 TGTAAATTTGATATGCCTTT
* *
2043500 GAGCTGAATGTAATCGAACTTGAAGGTCACGGTTGTTGGA-AGATAACCCTTCTCACCTTGAGTT
1 GAGCTGAATGTAATCGAACTCGAAGGT--C--TTGTT-GACAGATAACCCTTCTCGCCTTGAGTT
* **
2043564 ATGTTACAAATTTGATATGCCTTT
61 ATGCTGTAAATTTGATATGCCTTT
* * * *
2043588 GAG-TTAAGTGTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTCGCTTTGAG-CAC
1 GAGCTGAA-TGTAATCGAACTCGAAGGTC--TTGTTGACAGATAACCCTTCTCGCCTTGAGTTA-
* *
2043651 TGCTATAAATTTGATGTGCCTTT
62 TGCTGTAAATTTGATATGCCTTT
* * * * * *
2043674 GACCT--A---ACTCGAAGGTC-ACGG--TTGTTG---G-TAGACCCTTCTCACCTTGAGTTATA
1 GAGCTGAATGTAATCGAA-CTCGAAGGTCTTGTTGACAGATA-ACCCTTCTCGCCTTGAGTTATG
*
2043727 CTGTGAATTTGATATGCCTTT
64 CTGTAAATTTGATATGCCTTT
* * * * * *
2043748 GAGCTGAGTTTAATCAAACTCGAAGGTCTTGGTTGATATATAACCCTTCTCGCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTT-GTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
** * *
2043813 TGTACTTTTGATGTGTCTTT
65 TGTAAATTTGATATGCCTTT
* * *
2043833 CAGCAGAATGTAATCGAACTCGAAGGTCACAGTTGTTGGCATG-TAACCCTTCTCGCCTTGAGTT
1 GAGCTGAATGTAATCGAACTCGAAGGT--C--TTGTTGACA-GATAACCCTTCTCGCCTTGAGTT
** *
2043897 ATGCTGCGAATTTGATATGCTTTT
61 ATGCTGTAAATTTGATATGCCTTT
* *
2043921 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACATATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTT-GTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
2043986 TGTA
65 TGTA
2043990 CTTGGCTGGG
Statistics
Matches: 666, Mismatches: 111, Indels: 93
0.77 0.13 0.11
Matches are distributed among these distances:
73 2 0.00
74 38 0.06
75 1 0.00
77 6 0.01
78 2 0.00
79 8 0.01
80 64 0.10
81 14 0.02
82 7 0.01
83 76 0.11
84 37 0.06
85 160 0.24
86 108 0.16
87 6 0.01
88 134 0.20
89 3 0.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (84 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCT
GTAAATTTGATATGCCTTT
Found at i:2043965 original size:173 final size:170
Alignment explanation
Indices: 2043679--2043992 Score: 511
Period size: 173 Copynumber: 1.8 Consensus size: 170
2043669 CCTTTGACCT
* * *
2043679 AACTCGAAGGTCACGGTTGTTGGTAGACCCTTCTCACCTTGAGTTATACTGTGAATTTGATATGC
1 AACTCGAAGGTCACAGTTGTTGGCAGACCCTTCTCACCTTGAGTTATACTGCGAATTTGATATGC
* *
2043744 CTTTGAGCTGAGTTTAATCAAACTCGAAGGTCTTGGTTGATATATAACCCTTCTCGCCTTGAGTT
66 CTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTTGACATATAACCCTTCTCGCCTTGAGTT
*
2043809 ATGTTGTACTTTTGATGTGTCTTTCAGCAGAATGTAATCG
131 ATGCTGTACTTTTGATGTGTCTTTCAGCAGAATGTAATCG
* *
2043849 AACTCGAAGGTCACAGTTGTTGGCATGTAACCCTTCTCGCCTTGAGTTATGCTGCGAATTTGATA
1 AACTCGAAGGTCACAGTTGTTGGCA-G--ACCCTTCTCACCTTGAGTTATACTGCGAATTTGATA
* *
2043914 TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACATATAACCCTTCTCGCCTTGA
63 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTTGACATATAACCCTTCTCGCCTTGA
2043979 GTTATGCTGTACTT
128 GTTATGCTGTACTT
2043993 GGCTGGGGAA
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
170 23 0.18
171 1 0.01
173 107 0.82
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (170 bp):
AACTCGAAGGTCACAGTTGTTGGCAGACCCTTCTCACCTTGAGTTATACTGCGAATTTGATATGC
CTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTTGACATATAACCCTTCTCGCCTTGAGTT
ATGCTGTACTTTTGATGTGTCTTTCAGCAGAATGTAATCG
Found at i:2044427 original size:124 final size:124
Alignment explanation
Indices: 2044060--2044526 Score: 738
Period size: 124 Copynumber: 3.8 Consensus size: 124
2044050 ATCTATTGGA
* * * *
2044060 CACGATATCCTTCGTTGTGAAGTTGAAATCGTTGATGGCTTATTCATTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
*
2044125 ATTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCTAGAGATGGATGCTGCTTGTGGG
66 ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGGG
* * * * *
2044184 CACGATATCCTTTGTCGTGAAGTTGAAATCGT-GATGGTTCTTTCGTTGTGAAATTGGGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
* *
2044248 ATTGGATATCCTTCGTTCTAAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGGG
66 ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGGG
2044307 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
* * * * *
2044372 ATTGGATATCCTTTGTTGTGAATTTGAAATTCAATCTAGATATGGATGCTTCTTGTGGG
66 ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGGG
* * *
2044431 CACGATATCCTTCGCCGTGAAGTTAAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
*
2044496 ATTGGATATCCTTCGTCGTGAAGTTGAAATC
66 ATTGGATATCCTTCGTTGTGAAGTTGAAATC
2044527 GTGGATGGCT
Statistics
Matches: 312, Mismatches: 30, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
123 113 0.36
124 199 0.64
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (124 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGGG
Found at i:2044517 original size:34 final size:33
Alignment explanation
Indices: 2044473--2044588 Score: 119
Period size: 34 Copynumber: 3.5 Consensus size: 33
2044463 GGATGGCTCA
2044473 TTCGTTGTGAAGTTGAGCTTTGAATTGGATATCC
1 TTCGTTGTGAAGTTGAGCTTTGAATTGGATAT-C
* ** * * * *
2044507 TTCGTCGTGAAGTTGAAATCGTGGA-TGGCT-TA
1 TTCGTTGTGAAGTTGAGCT-TTGAATTGGATATC
*
2044539 TTCATTGTGAAGTTGAGCTTTGAATTGGATATTC
1 TTCGTTGTGAAGTTGAGCTTTGAATTGGATA-TC
2044573 TTCGTTGTGAAGTTGA
1 TTCGTTGTGAAGTTGA
2044589 AATCCAAGGG
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
31 3 0.05
32 19 0.31
33 1 0.02
34 36 0.58
35 3 0.05
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.41
Consensus pattern (33 bp):
TTCGTTGTGAAGTTGAGCTTTGAATTGGATATC
Found at i:2044547 original size:66 final size:66
Alignment explanation
Indices: 2044434--2044592 Score: 255
Period size: 66 Copynumber: 2.4 Consensus size: 66
2044424 TTGTGGGCAC
* * *
2044434 GATATCCTTCGCCGTGAAGTTAAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCATTCATTGTGAAGTTGAGCTTTGAATT
2044499 G
66 G
* *
2044500 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTTATTCATTGTGAAGTTGAGCTTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCATTCATTGTGAAGTTGAGCTTTGAATT
2044565 G
66 G
* *
2044566 GATATTCTTCGTTGTGAAGTTGAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
2044593 CAAGGGGTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 86 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (66 bp):
GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCATTCATTGTGAAGTTGAGCTTTGAATT
G
Found at i:2044845 original size:63 final size:64
Alignment explanation
Indices: 2044680--2044845 Score: 246
Period size: 64 Copynumber: 2.6 Consensus size: 64
2044670 GCATTGTTTC
* * *
2044680 GAGTCCAAAATCCTTTGTTGTGAAGTTGAAATTGATTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
2044744 GATTCCAATATCCTTTGAC-GTGAAGTTGAAATTGACTCTGATTGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTTG-CTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
2044808 -AGTCCAATATCCTTCGCTGTGAAGTTGAAATTAACTCT
1 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGACTCT
2044846 AAAAGCTGCA
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
62 1 0.01
63 33 0.36
64 58 0.63
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (64 bp):
GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:2045879 original size:83 final size:86
Alignment explanation
Indices: 2045765--2045975 Score: 196
Period size: 95 Copynumber: 2.4 Consensus size: 86
2045755 AAACTGGGGC
* * * *
2045765 GTTTAACCAGTTG-CTCTAGAGGGGCAGCTCAATAGA-TA-AA-CACCTTTATCAGGTTAGCTGA
1 GTTTAACCAATTGCCT-TAGAGGGACAACTCAATAGATTATAATCACCTTTATCAGGCTAGCTGA
* *
2045826 ATCTTATCCATAAAGCCGGGGA
65 ATCTTATCCATAAAGACAGGGA
* *
2045848 GTTTAACTAATTGCCTTAGAGGGACAACTCAAGCTTTATTATATATTATAATCACCTTTATCAGG
1 GTTTAACCAATTGCCTTAGAGGGACAACT----C---A--ATAGATTATAATCACCTTTATCAGG
* *
2045913 CTAGCTGAATCTTATTCATAAAGACAGGGT
57 CTAGCTGAATCTTATCCATAAAGACAGGGA
* *
2045943 GTTTAACCAATTGCTTTAGAGGGACATCTCAAT
1 GTTTAACCAATTGCCTTAGAGGGACAACTCAAT
2045976 CTTTATTATA
Statistics
Matches: 102, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
83 22 0.22
84 2 0.02
86 2 0.02
87 1 0.01
88 1 0.01
90 1 0.01
91 1 0.01
92 4 0.04
93 2 0.02
94 2 0.02
95 64 0.63
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (86 bp):
GTTTAACCAATTGCCTTAGAGGGACAACTCAATAGATTATAATCACCTTTATCAGGCTAGCTGAA
TCTTATCCATAAAGACAGGGA
Found at i:2045968 original size:95 final size:96
Alignment explanation
Indices: 2045800--2045993 Score: 291
Period size: 95 Copynumber: 2.0 Consensus size: 96
2045790 AGCTCAATAG
* * * *
2045800 ATAAACACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGAGTTTAACTAATTGCCTT
1 ATAAACACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGACAGGGAGTTTAACCAATTGCCTT
2045865 AGAGGGACAACTCAAGCTTTATTATATAT-T
66 AGAGGGACAACTCAAGCTTTATTATATATAT
* * * *
2045895 ATAATCACCTTTATCAGGCTAGCTGAATCTTATTCATAAAGACAGGGTGTTTAACCAATTGCTTT
1 ATAAACACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGACAGGGAGTTTAACCAATTGCCTT
* *
2045960 AGAGGGACATCTCAATCTTTATTATATATAT
66 AGAGGGACAACTCAAGCTTTATTATATATAT
2045991 ATA
1 ATA
2045994 TATAATAATC
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 84 0.95
96 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (96 bp):
ATAAACACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGACAGGGAGTTTAACCAATTGCCTT
AGAGGGACAACTCAAGCTTTATTATATATAT
Found at i:2048597 original size:14 final size:13
Alignment explanation
Indices: 2048574--2048671 Score: 72
Period size: 14 Copynumber: 7.2 Consensus size: 13
2048564 TTAATATAAT
2048574 AATAATAATAAAATA
1 AATAA-AAT-AAATA
*
2048589 AATTAAATAAATA
1 AATAAAATAAATA
2048602 AATAAAGATAAATA
1 AATAAA-ATAAATA
**
2048616 AATAAAATTTATCA
1 AATAAAATAAAT-A
* * *
2048630 AAAAAAAAAAGAAA
1 AATAAAATAA-ATA
*
2048644 ACATAAAATAAAAA
1 A-ATAAAATAAATA
2048658 AATAAAA-AAATA
1 AATAAAATAAATA
2048670 AA
1 AA
2048672 AGGATAAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
12 6 0.09
13 20 0.30
14 29 0.43
15 12 0.18
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:2048603 original size:18 final size:19
Alignment explanation
Indices: 2048580--2048623 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
2048570 TAATAATAAT
*
2048580 AATAAAATAAA-TTAAATA
1 AATAAAATAAAGATAAATA
2048598 AAT-AAATAAAGATAAATA
1 AATAAAATAAAGATAAATA
2048616 AATAAAAT
1 AATAAAAT
2048624 TTATCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AATAAAATAAAGATAAATA
Found at i:2048651 original size:15 final size:14
Alignment explanation
Indices: 2048629--2048687 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 14
2048619 AAAATTTATC
2048629 AAAA-AAAAAAAGA
1 AAAATAAAAAAAGA
*
2048642 AAACATAAAATAA-A
1 AAA-ATAAAAAAAGA
*
2048656 AAAATAAAAAAATA
1 AAAATAAAAAAAGA
*
2048670 AAAGGATAAAAAATGA
1 AAA--ATAAAAAAAGA
2048686 AA
1 AA
2048688 TAAAAAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.30
14 9 0.24
15 6 0.16
16 11 0.30
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAATAAAAAAAGA
Found at i:2048658 original size:21 final size:21
Alignment explanation
Indices: 2048532--2048704 Score: 68
Period size: 21 Copynumber: 7.8 Consensus size: 21
2048522 ATGTTAAATG
*
2048532 ATAAAAAAATAAATATGAAAAA
1 ATAAAAAAATAAA-ATAAAAAA
* * *
2048554 AGAAAAAATATTAATATAATAATA
1 ATAAAAAA-A-TAAAATAA-AAAA
* * *
2048578 ATAATAAAATAAATTAAATAA
1 ATAAAAAAATAAAATAAAAAA
2048599 ATAAATAAAGAT-AAATAAATAAA
1 ATAAA-AAA-ATAAAATAAA-AAA
*
2048622 ATTTATCAAAAAA-AAAA-AGAAAAC
1 A--TA--AAAAAATAAAATA-AAAAA
2048646 ATAAAATAAA-AAAATAAAAAA
1 ATAAAA-AAATAAAATAAAAAA
** **
2048667 ATAAAAGGATAAAA-AATGAA
1 ATAAAAAAATAAAATAAAAAA
2048687 ATAAAAAACAATAAAATA
1 AT-AAAAA-AATAAAATA
2048705 TGTTAAATTT
Statistics
Matches: 112, Mismatches: 21, Indels: 35
0.67 0.12 0.21
Matches are distributed among these distances:
20 10 0.09
21 31 0.28
22 31 0.28
23 11 0.10
24 16 0.14
25 8 0.07
26 3 0.03
27 2 0.02
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
ATAAAAAAATAAAATAAAAAA
Found at i:2048659 original size:8 final size:8
Alignment explanation
Indices: 2048648--2048682 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2048638 AAGAAAACAT
2048648 AAAATAAA
1 AAAATAAA
2048656 AAAATAAA
1 AAAATAAA
2048664 AAAATAAA
1 AAAATAAA
**
2048672 AGGATAAA
1 AAAATAAA
2048680 AAA
1 AAA
2048683 TGAAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:2048672 original size:14 final size:14
Alignment explanation
Indices: 2048532--2048665 Score: 51
Period size: 14 Copynumber: 9.1 Consensus size: 14
2048522 ATGTTAAATG
*
2048532 ATAAAAAAATAAAT
1 ATAAAAAAATAAAA
*
2048546 ATGAAAAAAGAAAAAA
1 AT-AAAAAA-ATAAAA
*
2048562 TATTAATATAATAATAATA
1 -A-TAA-A-AA-AATAAAA
*
2048581 ATAAAATAAAT-TAA
1 ATAAAA-AAATAAAA
* *
2048595 ATAAATAAATAAAG
1 ATAAAAAAATAAAA
*
2048609 ATAAATAAATAAAA
1 ATAAAAAAATAAAA
*
2048623 TTTATCAAAAAA-AAAA
1 ---ATAAAAAAATAAAA
* *
2048639 A-GAAAACAT-AAA
1 ATAAAAAAATAAAA
2048651 ATAAAAAAATAAAA
1 ATAAAAAAATAAAA
2048665 A
1 A
2048666 AATAAAAGGA
Statistics
Matches: 89, Mismatches: 16, Indels: 30
0.66 0.12 0.22
Matches are distributed among these distances:
12 9 0.10
13 11 0.12
14 26 0.29
15 10 0.11
16 10 0.11
17 13 0.15
18 3 0.03
19 6 0.07
20 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (14 bp):
ATAAAAAAATAAAA
Found at i:2048800 original size:26 final size:26
Alignment explanation
Indices: 2048743--2048809 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
2048733 GGAAAAATGT
*
2048743 AAAAAAAT-AAATAAGAATAAATATTA
1 AAAAAAATCAAA-AAGAATAAATAGTA
2048769 ACAAAAAATCAAAAA-AATAAATAAGTA
1 A-AAAAAATCAAAAAGAATAAAT-AGTA
*
2048796 AAAAATGATCAAAA
1 AAAAA-AATCAAAA
2048810 TACAAACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 12 0.34
27 20 0.57
28 3 0.09
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (26 bp):
AAAAAAATCAAAAAGAATAAATAGTA
Found at i:2050268 original size:34 final size:32
Alignment explanation
Indices: 2050207--2050275 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
2050197 ATTTGCATCA
* * *
2050207 AAATTCTAAAAAATAAAGAAAATAAAATAATT
1 AAATTATAAAAAATAAAAAAAATAAAATAAAT
2050239 AAATTATAAAAAATAGAATAAAAATAAAATAAAT
1 AAATTATAAAAAATA-AA-AAAAATAAAATAAAT
2050273 AAA
1 AAA
2050276 ATTAAATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 14 0.44
33 2 0.06
34 16 0.50
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.23
Consensus pattern (32 bp):
AAATTATAAAAAATAAAAAAAATAAAATAAAT
Found at i:2050667 original size:31 final size:31
Alignment explanation
Indices: 2050631--2050689 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2050621 AACTTAAAAG
*
2050631 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
2050662 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2050690 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2050738 original size:22 final size:22
Alignment explanation
Indices: 2050713--2051297 Score: 781
Period size: 22 Copynumber: 26.6 Consensus size: 22
2050703 ATAATAAATT
2050713 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
2050735 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
2050757 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
***
2050779 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
2050801 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
***
2050823 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
2050845 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
2050867 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *
2050889 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
2050911 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
2050933 TTTTAAAATAATTCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
2050955 TTTTAAAATAAAT-ATTTTCATA
1 TTTTAAAATAAATCA-ATTCATA
*
2050977 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
2050999 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
2051021 TTTTAAAATAAATCAATAT-ATA
1 TTTTAAAATAAATCAAT-TCATA
*
2051043 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
*
2051065 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *
2051087 TTTTAAAATGAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
2051109 TTTTAAAATAAATCAATGCATA
1 TTTTAAAATAAATCAATTCATA
*
2051131 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
2051153 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
2051175 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATTCATA
*
2051197 TTTTAAAATAAATGAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
2051219 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
2051241 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
2051263 TTTTAAAATAAATCAATAT-ATA
1 TTTTAAAATAAATCAAT-TCATA
2051285 TTTTAAAATAAAT
1 TTTTAAAATAAAT
2051298 TTTAAAATGG
Statistics
Matches: 506, Mismatches: 42, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
20 2 0.00
21 9 0.02
22 484 0.96
23 10 0.02
24 1 0.00
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:2053391 original size:28 final size:31
Alignment explanation
Indices: 2053330--2053399 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 31
2053320 AAGGAAAGTA
*
2053330 AAAAACTA-ATAATAATAATATGTGTATATT
1 AAAAACTATATAATAATAATATGTATATATT
2053360 AAAAACTATATAAT-AT-ATAT-TATAT-TT
1 AAAAACTATATAATAATAATATGTATATATT
*
2053387 CAAAAACAATATA
1 -AAAAACTATATA
2053400 TAGTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
28 15 0.42
29 4 0.11
30 10 0.28
31 5 0.14
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAACTATATAATAATAATATGTATATATT
Found at i:2054121 original size:72 final size:72
Alignment explanation
Indices: 2054045--2054200 Score: 233
Period size: 72 Copynumber: 2.2 Consensus size: 72
2054035 TCATTCGCCA
* * *
2054045 TGAAGTTGAGTCAATCTATTGGGAATGCTATCCTTCATCTTGAAGTTAAAATCGTAGGTGACTCC
1 TGAAGTTGAGTCAATCTATTGGGAACGATATCCTTCATCGTGAAGTTAAAATCGTAGGTGAC-CC
2054110 -TTCATCG
65 ATTCATCG
* * * *
2054117 TGAAGTTGAGTCAATCTATTGGGCACGATATCCTTCGTCGTGAAGTTAAGATTGTAGGTGACCCA
1 TGAAGTTGAGTCAATCTATTGGGAACGATATCCTTCATCGTGAAGTTAAAATCGTAGGTGACCCA
2054182 TTCATCG
66 TTCATCG
2054189 TGAAGTTGAGTC
1 TGAAGTTGAGTC
2054201 TAAATTCAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
71 2 0.03
72 74 0.97
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (72 bp):
TGAAGTTGAGTCAATCTATTGGGAACGATATCCTTCATCGTGAAGTTAAAATCGTAGGTGACCCA
TTCATCG
Found at i:2056976 original size:21 final size:21
Alignment explanation
Indices: 2056952--2056991 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2056942 TAATTCTCGA
2056952 GAGAAATTATTATATTCTTGG
1 GAGAAATTATTATATTCTTGG
2056973 GAGAAATTATTATATTCTT
1 GAGAAATTATTATATTCTT
2056992 TTTATTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
GAGAAATTATTATATTCTTGG
Found at i:2058294 original size:3 final size:3
Alignment explanation
Indices: 2058282--2058319 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
2058272 TTTTTAAATA
*
2058282 TAT TATT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2058320 TACATTTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2060300 original size:14 final size:15
Alignment explanation
Indices: 2060283--2060315 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2060273 CATATTAGTA
2060283 TTTATTATTTAG-AC
1 TTTATTATTTAGCAC
2060297 TTTATTATTTAGCAC
1 TTTATTATTTAGCAC
2060312 TTTA
1 TTTA
2060316 ATTTTTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTATTATTTAGCAC
Found at i:2068802 original size:24 final size:24
Alignment explanation
Indices: 2068775--2068831 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
2068765 ATGCTTTTGT
2068775 AGTAGATGAAACTTAAGATTTTAC
1 AGTAGATGAAACTTAAGATTTTAC
* * *
2068799 AGTAGACGAAACTTGAGCTTTTAC
1 AGTAGATGAAACTTAAGATTTTAC
*
2068823 AATAGATGA
1 AGTAGATGA
2068832 GTCACCTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (24 bp):
AGTAGATGAAACTTAAGATTTTAC
Found at i:2069148 original size:21 final size:21
Alignment explanation
Indices: 2069122--2069173 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
2069112 GTATTGTGAG
*
2069122 GATGAGGTGTGTTCAGTGCTT
1 GATGAGGTGTGTTCAATGCTT
2069143 GATGAGGTGTGTTCAATGCTT
1 GATGAGGTGTGTTCAATGCTT
*
2069164 AATGAGGTGT
1 GATGAGGTGT
2069174 ATCCAATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.08, G:0.37, T:0.37
Consensus pattern (21 bp):
GATGAGGTGTGTTCAATGCTT
Found at i:2073919 original size:28 final size:29
Alignment explanation
Indices: 2073863--2073925 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
2073853 ATAATAATAA
*
2073863 TATATAATAATATGTGTATATTAAAAAAC
1 TATATAATAATATGTATATATTAAAAAAC
*
2073892 TATATAATATATAT-TATAT-TTCAAAAAC
1 TATATAATA-ATATGTATATATTAAAAAAC
*
2073920 AATATA
1 TATATA
2073926 TTATGTTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 13 0.43
29 13 0.43
30 4 0.13
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (29 bp):
TATATAATAATATGTATATATTAAAAAAC
Found at i:2073946 original size:22 final size:21
Alignment explanation
Indices: 2073899--2073948 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2073889 AACTATATAA
2073899 TATATATTATATTTCAAAAAC
1 TATATATTATATTTCAAAAAC
* * * *
2073920 AATATATTATGTTCTCAAAGAT
1 TATATATTATATT-TCAAAAAC
2073942 TATATAT
1 TATATAT
2073949 ATTATATACA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (21 bp):
TATATATTATATTTCAAAAAC
Found at i:2074002 original size:23 final size:24
Alignment explanation
Indices: 2073971--2074028 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
2073961 TTAAAAACCA
*
2073971 TTTTTAAAAACTATA-TATATATG
1 TTTTCAAAAACTATATTATATATG
2073994 TTTTCAAAAACTATATTATATATG
1 TTTTCAAAAACTATATTATATATG
2074018 TTTTCAAAAAC
1 TTTTCAAAAAC
2074029 CATTTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (24 bp):
TTTTCAAAAACTATATTATATATG
Found at i:2074039 original size:61 final size:59
Alignment explanation
Indices: 2073946--2074063 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 59
2073936 AAAGATTATA
*
2073946 TATATTATATACATTTTAAAAACCATTTTTAAAAACTATATA-TATATGTTTTCAAAAAC
1 TATATTATATACATTTTAAAAACCATTTTT-AAAACTATATATTATATGCTTTCAAAAAC
**
2074005 TATATTATATATGTTTTCAAAAACCATTTTTTAAAACTATATATTATATGCTTTCAAAA
1 TATATTATATACATTTT-AAAAACCA-TTTTTAAAACTATATATTATATGCTTTCAAAA
2074064 CCCATTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 15 0.28
60 19 0.36
61 19 0.36
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (59 bp):
TATATTATATACATTTTAAAAACCATTTTTAAAACTATATATTATATGCTTTCAAAAAC
Found at i:2074053 original size:37 final size:38
Alignment explanation
Indices: 2073994--2074101 Score: 143
Period size: 37 Copynumber: 2.9 Consensus size: 38
2073984 TATATATATG
*
2073994 TTTTCAAAAACTATAT-TATATATGTTTTCAAAAACCAT
1 TTTTTAAAAACTATATAT-TATATGTTTTCAAAAACCAT
* *
2074032 TTTTT-AAAACTATATATTATATGCTTTCAAAACCCAT
1 TTTTTAAAAACTATATATTATATGTTTTCAAAAACCAT
*
2074069 TTTTTAAAAATTATATATTATA--TTTTCAAAAAC
1 TTTTTAAAAACTATATATTATATGTTTTCAAAAAC
2074102 TATATGTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
36 9 0.15
37 33 0.53
38 20 0.32
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (38 bp):
TTTTTAAAAACTATATATTATATGTTTTCAAAAACCAT
Found at i:2074135 original size:2 final size:2
Alignment explanation
Indices: 2074130--2074173 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
2074120 TTGAAATTAT
2074130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
2074172 TA
1 TA
2074174 CTAAATAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2074144 original size:98 final size:97
Alignment explanation
Indices: 2073942--2074153 Score: 232
Period size: 98 Copynumber: 2.2 Consensus size: 97
2073932 TCTCAAAGAT
* *
2073942 TATATATATTATATACATTTTAAAAACCATTTTTAAAAACTATATATATATGTTTTCAAAAACTA
1 TATATATATTATATACATTTCAAAAACCATTTTTAAAAACTATATATATATATTTTCAAAAACTA
* * *
2074007 TATTATATATGTTTTCAAAAACCATTTTTTAA
66 TATTATATATATTTTCAAAAACCATTATATAA
* * * *
2074039 AACTATATATTATATGC-TTTCAAAACCCATTTTTTAAAAATTATATAT-TATATTTTCAAAAAC
1 TA-TATATATTATATACATTTCAAAAACCA-TTTTTAAAAACTATATATATATATTTTCAAAAAC
** **
2074102 TATATGTATTATATATTTT-TGAAATTATTATATATA
64 TATAT-TA-TATATATTTTCAAAAACCATTATATA-A
2074138 TATATATATATATATA
1 TATATATAT-TATATA
2074154 TATATATATA
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
97 30 0.32
98 48 0.51
99 16 0.17
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (97 bp):
TATATATATTATATACATTTCAAAAACCATTTTTAAAAACTATATATATATATTTTCAAAAACTA
TATTATATATATTTTCAAAAACCATTATATAA
Found at i:2075542 original size:12 final size:13
Alignment explanation
Indices: 2075522--2075550 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2075512 TTGAAATAAC
2075522 AAATAAAATTAAA
1 AAATAAAATTAAA
2075535 AAAT-AAATTAAA
1 AAATAAAATTAAA
2075547 AAAT
1 AAAT
2075551 TACATATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAATTAAA
Found at i:2076131 original size:102 final size:102
Alignment explanation
Indices: 2076025--2076251 Score: 230
Period size: 102 Copynumber: 2.2 Consensus size: 102
2076015 GGCTTTGGGG
* *
2076025 TTTTGATCTTAAAAAATAGGTTGAG-AAAT-TTTGTTTTATGTTTGAAAGGATCAAACGAGGGTC
1 TTTTGATC-TAAAAAATAGGTTGAGTAAATATTT-TTGT-TGTTTGAAAGGATCAAACGAGAGTC
** *
2076088 TT-AGGATGAAAAAAAGATGAT-AATTG-TTTGATTTTTGGA
63 TTGAGGATGAAAAAAAGATGATCAA--GCTTAAAGTTTTGGA
* * * * * * *
2076127 TTTTGATATAGAAAAATAAGTTGAGTTAATATTTTTGTTGTTTGTAAGGATCAATCGATAGTTTT
1 TTTTGATCTA-AAAAATAGGTTGAGTAAATATTTTTGTTGTTTGAAAGGATCAAACGAGAGTCTT
* * *
2076192 GGGGATGAAAAAAGGATGATCAAGCTTAAAGTTTTGGG
65 GAGGATGAAAAAAAGATGATCAAGCTTAAAGTTTTGGA
2076230 TTTTGATCTAAAAAATAGGTTG
1 TTTTGATCTAAAAAATAGGTTG
2076252 GGTCAAGGTT
Statistics
Matches: 102, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
101 2 0.02
102 54 0.53
103 41 0.40
104 5 0.05
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (102 bp):
TTTTGATCTAAAAAATAGGTTGAGTAAATATTTTTGTTGTTTGAAAGGATCAAACGAGAGTCTTG
AGGATGAAAAAAAGATGATCAAGCTTAAAGTTTTGGA
Found at i:2077254 original size:32 final size:32
Alignment explanation
Indices: 2077217--2077277 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2077207 CTTAAAATTA
2077217 TATTTTTATTAAAATTAAC-CCATAATTATTTT
1 TATTTTTATTAAAATTAACTCCA-AATTATTTT
* * *
2077249 TATTTTTCTTATAATTTACTCCAAATTAT
1 TATTTTTATTAAAATTAACTCCAAATTAT
2077278 CTACAATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 22 0.88
33 3 0.12
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (32 bp):
TATTTTTATTAAAATTAACTCCAAATTATTTT
Found at i:2081060 original size:18 final size:19
Alignment explanation
Indices: 2081027--2081062 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2081017 TAGAAAATCC
2081027 AATTTGATTAAAAGTAGAA
1 AATTTGATTAAAAGTAGAA
*
2081046 AATTTTATT-AAAGTAGA
1 AATTTGATTAAAAGTAGA
2081063 TTTCTACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (19 bp):
AATTTGATTAAAAGTAGAA
Found at i:2084044 original size:54 final size:54
Alignment explanation
Indices: 2083962--2084074 Score: 219
Period size: 54 Copynumber: 2.1 Consensus size: 54
2083952 GAGTTTTTGT
2083962 TTCTAATATCTCATCCACTATTCAGCCATATTTTTATCATCAAGCTATCAAGTC
1 TTCTAATATCTCATCCACTATTCAGCCATATTTTTATCATCAAGCTATCAAGTC
2084016 TTCTAATATCTCATCCACTATTCAGCCATATTTTTATCATCAAGCTATCAAGTC
1 TTCTAATATCTCATCCACTATTCAGCCATATTTTTATCATCAAGCTATCAAGTC
2084070 -TCTAA
1 TTCTAA
2084075 CTTGGAAAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 5 0.08
54 54 0.92
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (54 bp):
TTCTAATATCTCATCCACTATTCAGCCATATTTTTATCATCAAGCTATCAAGTC
Found at i:2103619 original size:107 final size:109
Alignment explanation
Indices: 2103406--2103624 Score: 388
Period size: 107 Copynumber: 2.0 Consensus size: 109
2103396 GTCGCCTCAG
2103406 ATTTGTTTGATTATATAAAATGCATATCTCTTTAAACTCTTCTGCTTCATTCTTTTTTGTTCATG
1 ATTTGTTTGATTATATAAAATGCATATCTCTTTAAACTCTTCTGCTTCATTCTTTTTTGTTCATG
* *
2103471 GTTTCATTGTAGAGTATGCATGTTTTATTTTTATCTTAATCC-A
66 GTTTCATTGTAGAGTATGCATGTTTTATTTTGATCTCAATCCTA
* *
2103514 ATTTGTTTGATTATATAATATGCATATCTCTTTAAACTCTTCTGTTTC-TTCTTTTTTGTTCATG
1 ATTTGTTTGATTATATAAAATGCATATCTCTTTAAACTCTTCTGCTTCATTCTTTTTTGTTCATG
2103578 GTTTCATTGTAGAGTATGCATGTTTTATTTTGATCTCAATCCTA
66 GTTTCATTGTAGAGTATGCATGTTTTATTTTGATCTCAATCCTA
2103622 ATT
1 ATT
2103625 GAGCACTATG
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
107 56 0.53
108 50 0.47
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.53
Consensus pattern (109 bp):
ATTTGTTTGATTATATAAAATGCATATCTCTTTAAACTCTTCTGCTTCATTCTTTTTTGTTCATG
GTTTCATTGTAGAGTATGCATGTTTTATTTTGATCTCAATCCTA
Found at i:2106592 original size:6 final size:6
Alignment explanation
Indices: 2106583--2106642 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
2106573 CCAGGTTCAG
2106583 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC
1 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC
2106631 GCATTC GCATTC
1 GCATTC GCATTC
2106643 ATACATGCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (6 bp):
GCATTC
Found at i:2107814 original size:32 final size:31
Alignment explanation
Indices: 2107704--2107825 Score: 97
Period size: 32 Copynumber: 3.8 Consensus size: 31
2107694 TGATTATTGG
* * *
2107704 ATCGATTGTTTTTC-GGTTCAGATCAATATCA
1 ATCGGTTGATTTTCGGGTT-AGGTCAATATCA
* * *
2107735 GATCGGTTGATTTTTGGGTT-GGTTTAATACCAA
1 -ATCGGTTGATTTTCGGGTTAGG-TCAATATC-A
2107768 ATCGGTTAGA-TTTCGGGTTAGGTCAATATCGA
1 ATCGGTT-GATTTTCGGGTTAGGTCAATATC-A
* *
2107800 ATTGGTTGATTTTCGGTTTAGGTCAA
1 ATCGGTTGATTTTCGGGTTAGGTCAA
2107826 CCTTTAGATC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
31 3 0.04
32 60 0.83
33 9 0.12
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (31 bp):
ATCGGTTGATTTTCGGGTTAGGTCAATATCA
Found at i:2108449 original size:18 final size:17
Alignment explanation
Indices: 2108401--2108452 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
2108391 ATTTTTATTA
2108401 TTTTATTATAAATATAATAT
1 TTTTATT-TAAAT-T-ATAT
**
2108421 TTTTAAATAAATTATCAT
1 TTTTATTTAAATTAT-AT
2108439 TTTTATTTAAATTA
1 TTTTATTTAAATTA
2108453 ATTAATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 15 0.56
19 5 0.19
20 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATTTAAATTATAT
Found at i:2108583 original size:32 final size:32
Alignment explanation
Indices: 2108545--2108618 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
2108535 ATCCGGTCCA
* ** *
2108545 GGTTAATTTTAGTTTGGGTTGCTTTTGGTTTG
1 GGTTAATTTCAGTTCAGGTTGCTTTTGGTTCG
*
2108577 GGTTAATTTCGGTTCAGGTTGCTTTTGGTTCG
1 GGTTAATTTCAGTTCAGGTTGCTTTTGGTTCG
2108609 GGTTAATTTC
1 GGTTAATTTC
2108619 TATTTCGGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.11, C:0.08, G:0.30, T:0.51
Consensus pattern (32 bp):
GGTTAATTTCAGTTCAGGTTGCTTTTGGTTCG
Found at i:2108590 original size:16 final size:16
Alignment explanation
Indices: 2108545--2108617 Score: 65
Period size: 16 Copynumber: 4.6 Consensus size: 16
2108535 ATCCGGTCCA
* *
2108545 GGTTAATTTTAGTTTG
1 GGTTAATTTTGGTTCG
** *
2108561 GGTTGCTTTTGGTTTG
1 GGTTAATTTTGGTTCG
* *
2108577 GGTTAATTTCGGTTCA
1 GGTTAATTTTGGTTCG
**
2108593 GGTTGCTTTTGGTTCG
1 GGTTAATTTTGGTTCG
2108609 GGTTAATTT
1 GGTTAATTT
2108618 CTATTTCGGT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.11, C:0.07, G:0.30, T:0.52
Consensus pattern (16 bp):
GGTTAATTTTGGTTCG
Found at i:2108641 original size:38 final size:38
Alignment explanation
Indices: 2108582--2108656 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
2108572 GTTTGGGTTA
**
2108582 ATTTCGGTTCAGGTTGCTTTTGGTTCGGGTTAATTTCT
1 ATTTCGGTTCAGGTTAATTTTGGTTCGGGTTAATTTCT
* *
2108620 ATTTCGGTTC-GTGTTAATTTTGGTTCTGGTTGATTTC
1 ATTTCGGTTCAG-GTTAATTTTGGTTCGGGTTAATTTC
2108657 AATTCCCCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.11, C:0.12, G:0.25, T:0.52
Consensus pattern (38 bp):
ATTTCGGTTCAGGTTAATTTTGGTTCGGGTTAATTTCT
Found at i:2108650 original size:22 final size:23
Alignment explanation
Indices: 2108602--2108650 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
2108592 AGGTTGCTTT
*
2108602 TGGTTCGGGTTAATTTCTATTTC
1 TGGTTCGGGTTAATTTCTAGTTC
* *
2108625 -GGTTCGTGTTAATTT-TGGTTC
1 TGGTTCGGGTTAATTTCTAGTTC
2108646 TGGTT
1 TGGTT
2108651 GATTTCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.10, C:0.10, G:0.27, T:0.53
Consensus pattern (23 bp):
TGGTTCGGGTTAATTTCTAGTTC
Found at i:2109514 original size:20 final size:20
Alignment explanation
Indices: 2109483--2109537 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2109473 ACAGGTAATG
2109483 AATTTGACAAAACCGATTGGA
1 AATTTGACAAAACCGATT-GA
* * *
2109504 AA-TTGAAAAAACTGGTTGA
1 AATTTGACAAAACCGATTGA
2109523 AATTTGACAAAACCG
1 AATTTGACAAAACCG
2109538 GTAAAGCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.14
20 22 0.79
21 2 0.07
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (20 bp):
AATTTGACAAAACCGATTGA
Found at i:2109823 original size:177 final size:175
Alignment explanation
Indices: 2109522--2109889 Score: 522
Period size: 177 Copynumber: 2.1 Consensus size: 175
2109512 AAACTGGTTG
* ** *
2109522 AAATTTGACAAAACCGGTAAAGCTATTAGAATTGTTGAAATTTGTATCGATACATTTATAAGTAT
1 AAATTTGACAAAATCGGTAAAGCTACCAAAATTGTTGAAATTTGTATCGATACATTTATAAGTAT
* * *
2109587 ATGTACCAAAGTAGCAGTACTATATGAATTTAAAAGAATTGCAATAATAATAACTATAAAGTATC
66 ATATACCAAAGTAGCAGTACTATAGGAATTTAAAAGAATTGCAATAATAACAACTATAAAGTATC
*
2109652 AATACCTTACACACATGTATCGATACATGATAATATAACCA-GTTT
131 AATACCTTACACACATGTATCGATACATGACAATATAA-CATGTTT
**
2109697 AAATTTGACAAAATCGGTAAAGAGCTACCAAAATTGTTGAAATTTGTATCGATATGTTTATAAGT
1 AAATTTGACAAAATCGGT-AA-AGCTACCAAAATTGTTGAAATTTGTATCGATACATTTATAAGT
* * * * * **
2109762 ATATATATCAAAGTATCAGTACTTTAGGAATTTAAAAGAATTTCAATAATAGCGGCTATAAAGTA
64 ATATATACCAAAGTAGCAGTACTATAGGAATTTAAAAGAATTGCAATAATAACAACTATAAAGTA
* * *
2109827 TCGATACCTTAGACACATGTATTGATACATGACAATATAACATGTTT
129 TCAATACCTTACACACATGTATCGATACATGACAATATAACATGTTT
2109874 AAATTTGACAAAATCG
1 AAATTTGACAAAATCG
2109890 TTTTCAATTT
Statistics
Matches: 170, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
175 17 0.10
176 4 0.02
177 149 0.88
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (175 bp):
AAATTTGACAAAATCGGTAAAGCTACCAAAATTGTTGAAATTTGTATCGATACATTTATAAGTAT
ATATACCAAAGTAGCAGTACTATAGGAATTTAAAAGAATTGCAATAATAACAACTATAAAGTATC
AATACCTTACACACATGTATCGATACATGACAATATAACATGTTT
Found at i:2110033 original size:197 final size:197
Alignment explanation
Indices: 2109698--2110132 Score: 628
Period size: 197 Copynumber: 2.2 Consensus size: 197
2109688 AACCAGTTTA
* * * *
2109698 AATTTGACAAAATCGGTAAAGAGCTACCAAAATTGTTGAAATTTGTATCGATATGTTTATAAGTA
1 AATTTGATAAAACCGGTAAAAAGCTACCAGAATTGTTGAAATTTGTATCGATATGTTTATAAGTA
* * *
2109763 TATATATCAAAGTATCAGTACTTTAGGAATTTAAAAGAATTTCAATAATAGCGGCTATAAAGTAT
66 TATATACCAAAGTATCAATACTTTAGGAATTTAAAAGAATTGCAATAATAGCGGCTATAAAGTAT
* * * * *
2109828 CGATACCTTAGACACATGTATTGATACATGACAATATAACATGTTTAAATTTGACAAAATCGTTT
131 CGATACCTTAGACACATGTATCGATACATGACAATATAACATATTGAAATTTGACAAAACCGATT
2109893 TC
196 TC
* *
2109895 AATTTGATAAAACCAGTAAAAAGCTACCAGAATGGTTGAAATTTGTATC-A-ATGCTTTTATAAG
1 AATTTGATAAAACCGGTAAAAAGCTACCAGAATTGTTGAAATTTGTATCGATATG--TTTATAAG
*
2109958 TATATGTACCAAAGTATCAATACTTTAGGAATTTAAAAGAATTGCAATAATAGC-GCATATAAAG
64 TATATATACCAAAGTATCAATACTTTAGGAATTTAAAAGAATTGCAATAATAGCGGC-TATAAAG
* *
2110022 TATCGATACCTTAGACATATGTATCGATACATGACAATATGACATATTGAAATTTGACAAAACCG
128 TATCGATACCTTAGACACATGTATCGATACATGACAATATAACATATTGAAATTTGACAAAACCG
2110087 ATTTC
193 ATTTC
*
2110092 AATTT-ATCAAAACCGGTAAAGCA-CTACCAGAATTGTTGAAA
1 AATTTGAT-AAAACCGGTAAA-AAGCTACCAGAATTGTTGAAA
2110133 GTATCGATAC
Statistics
Matches: 213, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
195 3 0.01
196 5 0.02
197 204 0.96
198 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (197 bp):
AATTTGATAAAACCGGTAAAAAGCTACCAGAATTGTTGAAATTTGTATCGATATGTTTATAAGTA
TATATACCAAAGTATCAATACTTTAGGAATTTAAAAGAATTGCAATAATAGCGGCTATAAAGTAT
CGATACCTTAGACACATGTATCGATACATGACAATATAACATATTGAAATTTGACAAAACCGATT
TC
Found at i:2112413 original size:18 final size:18
Alignment explanation
Indices: 2112390--2112436 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2112380 TTACAACAAA
*
2112390 TTTGTATGTGAATGGAAT
1 TTTGTATGTGAATGAAAT
2112408 TTTGTATGTGAATGAAAT
1 TTTGTATGTGAATGAAAT
*
2112426 TATGTATGTGA
1 TTTGTATGTGA
2112437 TTACTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.45
Consensus pattern (18 bp):
TTTGTATGTGAATGAAAT
Found at i:2114687 original size:20 final size:22
Alignment explanation
Indices: 2114640--2114693 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
2114630 ATTGAGAGAA
*
2114640 AGGTATCGGTACCATAGTATAG
1 AGGTATCGATACCATAGTATAG
* *
2114662 AAGTATCGATACCAT-G-GTAG
1 AGGTATCGATACCATAGTATAG
*
2114682 AGGTATCCATAC
1 AGGTATCGATAC
2114694 TATTGAGCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 13 0.48
21 1 0.04
22 13 0.48
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (22 bp):
AGGTATCGATACCATAGTATAG
Found at i:2115181 original size:44 final size:46
Alignment explanation
Indices: 2115088--2115190 Score: 138
Period size: 44 Copynumber: 2.3 Consensus size: 46
2115078 TAAAACGAAT
* * *
2115088 CCATAAATGAAATGCATGAAAGGATGCATTAAGTCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGAGG
** *
2115134 CCATAAATGAAATGCAT-ATTGG-TACATTAAGGCTTGAAAGGAGG
1 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGAGG
2115178 CCATAAATGAAAT
1 CCATAAATGAAAT
2115191 TAACGAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
44 31 0.61
45 3 0.06
46 17 0.33
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGAGG
Found at i:2121516 original size:20 final size:22
Alignment explanation
Indices: 2121469--2121522 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
2121459 TCTGAGAGAA
*
2121469 AGGTATCGGTACCATAGTATAG
1 AGGTATCGATACCATAGTATAG
* *
2121491 AAGTATCGATACCAT-G-GTAG
1 AGGTATCGATACCATAGTATAG
*
2121511 AGGTATCCATAC
1 AGGTATCGATAC
2121523 TATTGAGCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 13 0.48
21 1 0.04
22 13 0.48
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (22 bp):
AGGTATCGATACCATAGTATAG
Done.