Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007909.1 Hibiscus syriacus cultivar Beakdansim tig00110303_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: 3382237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 17
Found at i:1932756 original size:36 final size:36
Alignment explanation
Indices: 1932708--1932812 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
1932698 TTGGTTGGTA
*
1932708 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
1932744 TTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
1932780 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
1932813 CTTTAGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:1933337 original size:64 final size:63
Alignment explanation
Indices: 1933191--1933339 Score: 208
Period size: 65 Copynumber: 2.3 Consensus size: 63
1933181 TGTGTACGAT
* * * *
1933191 TCCCTTCGTCGTGGAGTTGAAATTGGTTCTGGAACTGGAAAATTGTTTGTTGACAACCAGCCG
1 TCCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTATTGACAACCAGCCG
* * * *
1933254 TCCCTTCGTTTGTGAAGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
1 TCCCTTCG-TCGTGAAGTTGAAATTGGCTC-TGAAACTGGAAAATTGTTTATTGACAACCAGCCG
1933319 TCCCTTCGTCGTGAAGTTGAA
1 TCCCTTCGTCGTGAAGTTGAA
1933340 CTTGCGTTGT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
63 8 0.11
64 30 0.40
65 37 0.49
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (63 bp):
TCCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTATTGACAACCAGCCG
Found at i:1933449 original size:106 final size:106
Alignment explanation
Indices: 1933256--1934983 Score: 2974
Period size: 106 Copynumber: 16.3 Consensus size: 106
1933246 ACCAGCCGTC
*
1933256 CCTTCGTTTGTGAAGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
1 CCTTCG-TTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTC
1933321 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
64 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
1933364 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
* *
1933429 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATGT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
1933470 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATT-AGGAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTATTGACAACCAGCGGTCC
*
1933534 CTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1933576 CCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCC
1933641 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1933683 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
* *
1933748 TTCATCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1933789 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
1933854 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1933895 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
1933960 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1934001 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
* *
1934066 TTCATCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1934107 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
1934172 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1934213 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
1934278 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * *
1934319 CCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
* *
1934384 TTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1934425 CCTTCGCTGTGAAGTTGAAATTGACTCTCAAATTCG-GAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATTGTTTATTGACAACCAGCGGTCC
1934489 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1934531 CCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCC
1934596 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1934638 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
* * *
1934703 TTCGTCGTGAAGTTGAACTTGCATTGTCTTGATTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1934744 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
1934809 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1934850 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
*
1934915 TTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1934956 CCTTCGTTGTGAAGTTGAAATTGGCTCT
1 CCTTCGTTGTGAAGTTGAAATTGGCTCT
1934984 CGAGCAAATT
Statistics
Matches: 1530, Mismatches: 84, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
105 1 0.00
106 1295 0.85
107 228 0.15
108 6 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:1940035 original size:13 final size:13
Alignment explanation
Indices: 1939997--1940026 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1939987 ATATATAAAA
*
1939997 TAATAATAGTAAT
1 TAATAATAATAAT
1940010 TAATAATAATAAT
1 TAATAATAATAAT
1940023 TAAT
1 TAAT
1940027 TATTATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:1940036 original size:16 final size:18
Alignment explanation
Indices: 1939982--1940028 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1939972 TAACTAACCC
1939982 AATATATATATAA-AATAAT
1 AATATA-AT-TAATAATAAT
1940001 AATAGTAATTAATAATAAT
1 AATA-TAATTAATAATAAT
1940020 AAT-TAATTA
1 AATATAATTA
1940029 TTATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.23
18 3 0.12
19 15 0.58
20 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AATATAATTAATAATAAT
Found at i:1941113 original size:43 final size:43
Alignment explanation
Indices: 1941043--1941394 Score: 397
Period size: 43 Copynumber: 8.2 Consensus size: 43
1941033 TGAAAACAAA
* * ** *
1941043 AAACGCCGCTATAGGTCAAGATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAAC
* * *
1941086 AAACGCCGCAAAAGGTTGAGATTTATAGCAGCGTTTTTAGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAAC
* *
1941129 AAACGCCGCAAAAGGTTGAGATTTATAGCGGCGTTTTTAGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAAC
* *
1941172 AAACGCCGCAAAAAGTTGAGGTCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
1941215 AAACGCCGCAAAAGGATGATATATATAGCGGGGTTTTTGGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAAC
* * *
1941258 AAACGCCGCAAAAGG-TCATATCTATAACGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
1941300 AAACGCCGCAAAAAG-TCAGATCTATAACGGCGTTTTTTTGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCG-TTTTTGGAAC
* * * * *
1941343 -AACACCGTAAAA-GATCAGATATATAGCGGCGTTTTTTGGATAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCG-TTTTTGGA-AC
1941386 AAACGCCGC
1 AAACGCCGC
1941395 TAATTTCCTT
Statistics
Matches: 272, Mismatches: 33, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
41 1 0.00
42 86 0.32
43 179 0.66
44 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAAC
Found at i:1945118 original size:41 final size:41
Alignment explanation
Indices: 1945073--1945181 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 41
1945063 AATTTTTTGT
**
1945073 GGCGTTTATTTAAAAACGCCACTATAAGTGAAC-CCTA-TTGC
1 GGCGTTTATTTAAAAACGCCACTATAAGT--ACTAATAGTTGC
* * *
1945114 GGCGTTTGTATAAAAACGCCGCTA-AAGTACTAATATGTTGC
1 GGCGTTTATTTAAAAACGCCACTATAAGTACTAATA-GTTGC
*
1945155 GGCGTTTATTGAAAAAACGCCACTATA
1 GGCGTTTATT-TAAAAACGCCACTATA
1945182 TATAGACCTG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
38 2 0.04
39 2 0.04
40 4 0.07
41 33 0.61
42 12 0.22
43 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
GGCGTTTATTTAAAAACGCCACTATAAGTACTAATAGTTGC
Found at i:1945159 original size:82 final size:80
Alignment explanation
Indices: 1945044--1945223 Score: 213
Period size: 82 Copynumber: 2.2 Consensus size: 80
1945034 ATTTGCTACC
* * * * *
1945044 AAAACTCCGCTAAAGTTATAATTTTTTGTGGCGTTTATT-TAAAAACGCCACTATA-AGT-GAAC
1 AAAACGCCGCTAAAG-TATAATATGTTGCGGCGTTTATTGAAAAAACGCCACTATATA-TAG-A-
*
1945106 CCTATTGCGGCGTTTGTATA
62 CCTATGGCGGCGTTTGTA-A
1945126 AAAACGCCGCTAAAGTACTAATATGTTGCGGCGTTTATTGAAAAAACGCCACTATATATAGACCT
1 AAAACGCCGCTAAAGTA-TAATATGTTGCGGCGTTTATTGAAAAAACGCCACTATATATAGACCT
*
1945191 GTGGCGGCGTTTGTAA
65 ATGGCGGCGTTTGTAA
*
1945207 AAAACGCCGCCAAAGTA
1 AAAACGCCGCTAAAGTA
1945224 ACCATTTTGT
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
81 19 0.22
82 48 0.56
83 17 0.20
84 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (80 bp):
AAAACGCCGCTAAAGTATAATATGTTGCGGCGTTTATTGAAAAAACGCCACTATATATAGACCTA
TGGCGGCGTTTGTAA
Found at i:1945213 original size:39 final size:40
Alignment explanation
Indices: 1945112--1945223 Score: 102
Period size: 41 Copynumber: 2.8 Consensus size: 40
1945102 GAACCCTATT
* * *
1945112 GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTAATATGTT
1 GCGGCGTTTGTA-AAAAACGCCACTAAAGTACTAACATGTG
* * *
1945153 GCGGCGTTTATTGAAAAAACGCCACTATA-TA-TAGACCTGTG
1 GCGGCGTTT-GT-AAAAAACGCCACTAAAGTACTA-ACATGTG
* *
1945194 GCGGCGTTTGTAAAAAACGCCGCCAAAGTA
1 GCGGCGTTTGTAAAAAACGCCACTAAAGTA
1945224 ACCATTTTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
39 13 0.23
40 5 0.09
41 24 0.42
42 14 0.25
43 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (40 bp):
GCGGCGTTTGTAAAAAACGCCACTAAAGTACTAACATGTG
Found at i:1946338 original size:9 final size:9
Alignment explanation
Indices: 1946324--1946364 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
1946314 GGGATGGAAT
1946324 TTGAGAGAG
1 TTGAGAGAG
1946333 TTGAGAGAG
1 TTGAGAGAG
1946342 TT--GAGAG
1 TTGAGAGAG
1946349 TTGAGAGAG
1 TTGAGAGAG
*
1946358 ATGAGAG
1 TTGAGAG
1946365 TTGAGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.24
9 22 0.76
ACGTcount: A:0.34, C:0.00, G:0.44, T:0.22
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:1946349 original size:16 final size:16
Alignment explanation
Indices: 1946328--1946370 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1946318 TGGAATTTGA
*
1946328 GAGAGTTGAGAGAGTT
1 GAGAGTTGAGAGAGAT
1946344 GAGAGTTGAGAGAGAT
1 GAGAGTTGAGAGAGAT
1946360 GAGAGTTGAGA
1 GAGAGTTGAGA
1946371 AAATAAAAGA
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:0.35, C:0.00, G:0.44, T:0.21
Consensus pattern (16 bp):
GAGAGTTGAGAGAGAT
Found at i:1947396 original size:27 final size:26
Alignment explanation
Indices: 1947332--1947399 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
1947322 ACTCAGGCTA
1947332 TCTTAAGAATCTTTTTTTTTTAACAT
1 TCTTAAGAATCTTTTTTTTTTAACAT
* * * ** *
1947358 GC-TAGGATTCTTTTTTTTTCTTTCTT
1 TCTTAAGAATCTTTTTTTTT-TAACAT
1947384 TCTTAAGAATCTTTTT
1 TCTTAAGAATCTTTTT
1947400 AATCTGTTTC
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
25 15 0.48
26 5 0.16
27 11 0.35
ACGTcount: A:0.19, C:0.13, G:0.07, T:0.60
Consensus pattern (26 bp):
TCTTAAGAATCTTTTTTTTTTAACAT
Found at i:1948727 original size:9 final size:9
Alignment explanation
Indices: 1948713--1948740 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1948703 GGCAATAAAT
1948713 AACAAATAA
1 AACAAATAA
1948722 AACAAATAA
1 AACAAATAA
1948731 AACAAATAA
1 AACAAATAA
1948740 A
1 A
1948741 GAAATAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (9 bp):
AACAAATAA
Found at i:1952531 original size:26 final size:25
Alignment explanation
Indices: 1952501--1952549 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
1952491 TTTCTAATAC
*
1952501 TGCAATTAGGTATTTAATATTTTGGG
1 TGCAATTAGATATTTAAT-TTTTGGG
1952527 TGCAATTAGATATTTAATTTTTG
1 TGCAATTAGATATTTAATTTTTG
1952550 TTTTCTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (25 bp):
TGCAATTAGATATTTAATTTTTGGG
Found at i:1953581 original size:12 final size:13
Alignment explanation
Indices: 1953536--1953580 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
1953526 CGCCCCGATT
*
1953536 ACCCGATTACTCG
1 ACCCGATTACCCG
1953549 ACCCGATTACCCG
1 ACCCGATTACCCG
1953562 ACCCGA-TACCCG
1 ACCCGATTACCCG
1953574 ACCCGAT
1 ACCCGAT
1953581 AAATATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.24, C:0.44, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:1953603 original size:2 final size:2
Alignment explanation
Indices: 1953592--1953629 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1953582 AATATTAAAA
1953592 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1953630 TAATAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1954712 original size:21 final size:21
Alignment explanation
Indices: 1954670--1954712 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1954660 TTTCTGAGTT
* * *
1954670 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1954691 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1954712 A
1 A
1954713 CGGATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1954773 original size:67 final size:68
Alignment explanation
Indices: 1954692--1954843 Score: 225
Period size: 67 Copynumber: 2.2 Consensus size: 68
1954682 ACCCATTCAA
* *
1954692 GGGGAACCGATACCCCCTCAACGGATATGAATTTCCAGATTACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
1954757 -GG
66 GGG
* * * * *
1954759 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
1954824 GGG
66 GGG
*
1954827 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1954844 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
67 58 0.76
68 18 0.24
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
GGG
Found at i:1955591 original size:149 final size:149
Alignment explanation
Indices: 1955321--1955624 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
1955311 GGGTAGAGGG
1955321 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1955386 AATTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 AATTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1955451 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1955470 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
*
1955535 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 AATTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
1955600 TATGGCACTCCGGTGCAAT
131 TATGGCACTACGGTGCAAT
1955619 TCTACG
1 TCTACG
1955625 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
AATTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1955647 original size:23 final size:23
Alignment explanation
Indices: 1955603--1955647 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1955593 ATCATTATAT
*
1955603 GGCACTCCGGTGCAATTCTACGG
1 GGCACTCCGGTGCAATTATACGG
*
1955626 GGCACTTCGGTGC-ATTGATACG
1 GGCACTCCGGTGCAATT-ATACG
1955648 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATACGG
Found at i:1961721 original size:21 final size:21
Alignment explanation
Indices: 1961679--1961721 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1961669 TTTCTGAGTT
* * *
1961679 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1961700 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1961721 A
1 A
1961722 CGGATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1961782 original size:67 final size:66
Alignment explanation
Indices: 1961701--1961849 Score: 217
Period size: 67 Copynumber: 2.2 Consensus size: 66
1961691 ACCCATTCAA
* *
1961701 GGGGAACCGATACCCCCTCAACGGATATGAATTTCCAGATTACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATA-CCCCA
1961766 GG
65 GG
* * * * *
1961768 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCAG
1961833 G
66 G
*
1961834 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
1961850 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
66 22 0.30
67 52 0.70
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCAG
G
Found at i:1962596 original size:149 final size:149
Alignment explanation
Indices: 1962326--1962629 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1962316 GGGTAGAGGG
1962326 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1962391 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1962456 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1962475 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1962540 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
1962605 TATGGCACTCCGGTGCAAT
131 TATGGCACTACGGTGCAAT
1962624 TCTACG
1 TCTACG
1962630 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1962652 original size:23 final size:23
Alignment explanation
Indices: 1962608--1962652 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1962598 ATCATTATAT
*
1962608 GGCACTCCGGTGCAATTCTACGG
1 GGCACTCCGGTGCAATTATACGG
*
1962631 GGCACTTCGGTGC-ATTGATACG
1 GGCACTCCGGTGCAATT-ATACG
1962653 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATACGG
Found at i:1963727 original size:42 final size:41
Alignment explanation
Indices: 1963625--1963736 Score: 197
Period size: 41 Copynumber: 2.7 Consensus size: 41
1963615 CCTCGAATTC
1963625 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
*
1963666 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAATTGTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
*
1963707 CCAGTGTTTGTTTCACGTAATTGGTTTTCC
1 CC-GTGTTTGTTTCACGTAATTCGTTTTCC
1963737 TGAACGTAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 42 0.62
42 26 0.38
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.47
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
Found at i:1964065 original size:21 final size:21
Alignment explanation
Indices: 1964036--1964088 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1964026 ATTCTGACTA
1964036 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1964057 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1964078 TCGCAATGCGA
1 TCGCATTGCGA
1964089 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1964103 original size:20 final size:20
Alignment explanation
Indices: 1964078--1964190 Score: 190
Period size: 20 Copynumber: 5.7 Consensus size: 20
1964068 TTTTCCTAAT
1964078 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1964098 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1964118 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1964138 TCACAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1964158 TCGTAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
1964178 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1964191 CTGACTATCG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1964415 original size:22 final size:21
Alignment explanation
Indices: 1964390--1964452 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 21
1964380 GACATCCGTC
1964390 CCCATCTCCGACGAAATCAGT
1 CCCATCTCCGACGAAATCAGT
*
1964411 ACCCATCTCCGACGATATCAGT
1 -CCCATCTCCGACGAAATCAGT
*
1964433 CTCCATCTCCGGCGAAATCA
1 C-CCATCTCCGACGAAATCA
1964453 TTCACGATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.27, C:0.38, G:0.14, T:0.21
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCAGT
Found at i:1964857 original size:20 final size:20
Alignment explanation
Indices: 1964790--1964859 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
1964780 CGATTCTGTC
*
1964790 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
* **
1964809 ATTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
1964829 GTTGCGATTTTCATTTTTGT
1 GTTGCGATTTTCATTTTCGT
1964849 GTTGCGATTTT
1 GTTGCGATTTT
1964860 AAGTTTCAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 10 0.24
20 32 0.76
ACGTcount: A:0.13, C:0.14, G:0.21, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1966784 original size:20 final size:20
Alignment explanation
Indices: 1966755--1966899 Score: 155
Period size: 20 Copynumber: 7.6 Consensus size: 20
1966745 AGAATAGTTT
1966755 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1966775 ACTATTGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1966795 ACTATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
1966814 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* *
1966830 A--ATCGCAACGTGAAAATG
1 ACTATCGCAATGCGAAAATG
1966848 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1966868 ACTATCGCAATGC-AAATTTG
1 ACTATCGCAATGCGAAA-ATG
1966888 ACTATCGCAATG
1 ACTATCGCAATG
1966900 AAAGAATCGC
Statistics
Matches: 107, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.07
16 3 0.03
17 4 0.04
18 3 0.03
19 16 0.15
20 74 0.69
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1966973 original size:20 final size:20
Alignment explanation
Indices: 1966944--1967015 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
1966934 GATTCTCTCG
1966944 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCAAATTCGTA
* *
1966964 TTGTGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGTA
** *
1966984 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGTA
1967004 TTGCGATAGTCA
1 TTGCGATAGTCA
1967016 TTTTCGCGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGTA
Found at i:1967002 original size:40 final size:40
Alignment explanation
Indices: 1966944--1967030 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
1966934 GATTCTCTCG
*
1966944 TTGCGATAGTCAAATTCGTATTGTGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGTATTGCGATAGTCAAATTCGCA
** * ** *
1966984 TTGCGATAGTCATTTTCGTGTTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGTATTGCGATAGTCAAATTCGCA
1967024 TTGCGAT
1 TTGCGAT
1967031 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCGTATTGCGATAGTCAAATTCGCA
Found at i:1967016 original size:20 final size:20
Alignment explanation
Indices: 1966942--1967030 Score: 97
Period size: 20 Copynumber: 4.5 Consensus size: 20
1966932 GTGATTCTCT
1966942 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** *
1966962 TATTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
1966982 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* **
1967002 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
1967022 CGTTGCGAT
1 CGTTGCGAT
1967031 TTTAAGTTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1967605 original size:21 final size:21
Alignment explanation
Indices: 1967514--1967618 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1967504 GACTCACCTG
*
1967514 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1967536 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1967556 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1967577 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1967598 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1967619 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1967611 original size:42 final size:42
Alignment explanation
Indices: 1967511--1967621 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1967501 CCCGACTCAC
* * * *
1967511 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1967553 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1967595 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1967622 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1969023 original size:14 final size:14
Alignment explanation
Indices: 1969004--1969039 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1968994 ATTGTTTAAT
1969004 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1969018 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1969032 TGATTTGT
1 TGATTTGT
1969040 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1969203 original size:20 final size:20
Alignment explanation
Indices: 1969178--1969252 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
1969168 GCAACGAGAG
1969178 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
1969198 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
* *
1969218 AATCGCAATGTGAAAATAAA
1 AATCGCAATGCGAAAATGAA
*
1969238 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
1969253 CTAAATTTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.51, C:0.16, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:1969319 original size:33 final size:33
Alignment explanation
Indices: 1969262--1969357 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
1969252 ACTAAATTTG
*
1969262 CGTTGCGATTTTTATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
1969296 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
1969329 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
1969358 AGTCAATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 33 0.60
34 22 0.40
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1969354 original size:20 final size:19
Alignment explanation
Indices: 1969329--1969417 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 19
1969319 GTGATTCTCT
1969329 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1969349 CGTTGCGATAGTCAATTTCG
1 CGTTGCGATAGTC-ATTTCG
1969369 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTC-G
* *
1969389 TGTTGCGAAAGTCATATTCG
1 CGTTGCGATAGTCAT-TTCG
1969409 CGTTGCGAT
1 CGTTGCGAT
1969418 TTCCGCGTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
19 5 0.08
20 50 0.81
21 7 0.11
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1971884 original size:24 final size:24
Alignment explanation
Indices: 1971857--1971903 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1971847 ATCATTAAAA
*
1971857 TCCGAGTATTGACTAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
1971881 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
1971904 TTTCGAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:1972767 original size:20 final size:20
Alignment explanation
Indices: 1972742--1972813 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
1972732 AAATTCAGTA
1972742 TTGCGATAGTCAGAATCGT-G
1 TTGCGATAGTCAGAATC-TCG
1972762 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
1972782 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
1972802 TTGCGATAGTCA
1 TTGCGATAGTCA
1972814 AATTCGCGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 1 0.02
20 50 0.98
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:1972823 original size:20 final size:20
Alignment explanation
Indices: 1972742--1972823 Score: 121
Period size: 20 Copynumber: 4.1 Consensus size: 20
1972732 AAATTCAGTA
*
1972742 TTGCGATAGTCAGAATCGTG
1 TTGCGATAGTCAGAATCGCG
*
1972762 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1972782 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
1972802 TTGCGATAGTCA-AATTCGCG
1 TTGCGATAGTCAGAA-TCGCG
1972822 TT
1 TT
1972824 TCAATTTACG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 2 0.03
20 56 0.97
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1972840 original size:20 final size:20
Alignment explanation
Indices: 1972827--1972907 Score: 153
Period size: 20 Copynumber: 4.0 Consensus size: 20
1972817 TCGCGTTTCA
*
1972827 ATTTACGTAGTCGCATTGCG
1 ATTTACGTATTCGCATTGCG
1972847 ATTTACGTATTCGCATTGCG
1 ATTTACGTATTCGCATTGCG
1972867 ATTTACGTATTCGCATTGCG
1 ATTTACGTATTCGCATTGCG
1972887 ATTTACGTATTCGCATTGCG
1 ATTTACGTATTCGCATTGCG
1972907 A
1 A
1972908 ATTAGGAAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTACGTATTCGCATTGCG
Found at i:1972846 original size:40 final size:40
Alignment explanation
Indices: 1972802--1972910 Score: 103
Period size: 40 Copynumber: 2.7 Consensus size: 40
1972792 CAGAATCTCG
* *
1972802 TTGCGATAGT-CAAATTCGCGTTTCAATTTACGTAGTCGCA
1 TTGCGAT-GTACAAATTCGCATTGCAATTTACGTAGTCGCA
* ** * *
1972842 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATGTACAAATTCGCATTGCAATTTACGTAGTCGCA
* **
1972882 TTGCGATTTACGTATTCGCATTGCGAATT
1 TTGCGATGTACAAATTCGCATTGC-AATT
1972911 AGGAAAATCA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
39 1 0.02
40 55 0.93
41 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (40 bp):
TTGCGATGTACAAATTCGCATTGCAATTTACGTAGTCGCA
Found at i:1973211 original size:31 final size:31
Alignment explanation
Indices: 1973176--1973309 Score: 99
Period size: 28 Copynumber: 4.5 Consensus size: 31
1973166 AAATATTATT
1973176 TATTA-ATTTATTAATATT-TATAATAATATAA
1 TATTATATTT-TTAATATTATATAA-AATATAA
*
1973207 TATTATATTTTTAATATTATATAAAATAATCA
1 TATTATATTTTTAATATTATATAAAAT-ATAA
* * *
1973239 -ATTATA-TTATAATA--ATATAAGATATTA
1 TATTATATTTTTAATATTATATAAAATATAA
* *
1973266 TATTTTA-TTTTAATAATATATAATAA-A-AA
1 TATTATATTTTTAATATTATATAA-AATATAA
*
1973295 -ATTATATATTTAATA
1 TATTATATTTTTAATA
1973310 ATGAATAATA
Statistics
Matches: 85, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.04
28 25 0.29
29 8 0.09
30 14 0.16
31 23 0.27
32 12 0.14
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
TATTATATTTTTAATATTATATAAAATATAA
Found at i:1973214 original size:22 final size:23
Alignment explanation
Indices: 1973184--1973227 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1973174 TTTATTAATT
1973184 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
1973207 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
1973228 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:1973303 original size:58 final size:59
Alignment explanation
Indices: 1973197--1973351 Score: 153
Period size: 58 Copynumber: 2.7 Consensus size: 59
1973187 TAATATTTAT
* * * ** *
1973197 AATAATATAATATTATAT-TTTTAATATTATATAAAATAATCAATTATAT-TATAATAAT-
1 AATAATATTAT-TTATATATTTTAATAATAT-TATAATAAAAAATTATATATTTAATAATG
1973255 -ATAAGATATTATATT-T-TATTTTAATAATA-TATAATAAAAAATTATATATTTAATAATG
1 AAT-A-ATATTAT-TTATATATTTTAATAATATTATAATAAAAAATTATATATTTAATAATG
*
1973313 AATAATATTATTTATATATTTTAATAATATTTTAATAAA
1 AATAATATTATTTATATATTTTAATAATATTATAATAAA
1973352 GATATTTAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
56 17 0.21
57 19 0.23
58 26 0.32
59 19 0.23
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (59 bp):
AATAATATTATTTATATATTTTAATAATATTATAATAAAAAATTATATATTTAATAATG
Found at i:1973320 original size:19 final size:19
Alignment explanation
Indices: 1973277--1973350 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
1973267 ATTTTATTTT
*
1973277 AATAATATA--TAATAAAA
1 AATAATATATTTAATAATA
* *
1973294 AATTATATATTTAATAATG
1 AATAATATATTTAATAATA
* *
1973313 AATAATATTATTTATATATTTT
1 AATAATA-TATTTA-ATA-ATA
1973335 AATAATAT-TTTAATAA
1 AATAATATATTTAATAA
1973351 AGATATTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
17 8 0.18
19 15 0.33
20 10 0.22
21 4 0.09
22 8 0.18
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (19 bp):
AATAATATATTTAATAATA
Found at i:1973358 original size:14 final size:11
Alignment explanation
Indices: 1973313--1973350 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1973303 TTTAATAATG
1973313 AATAATATTATT
1 AATAATATT-TT
*
1973325 TAT-ATATTTT
1 AATAATATTTT
1973335 AATAATATTTT
1 AATAATATTTT
1973346 AATAA
1 AATAA
1973351 AGATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATATTTT
Found at i:1973371 original size:23 final size:23
Alignment explanation
Indices: 1973345--1973389 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1973335 AATAATATTT
1973345 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1973368 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1973390 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1973694 original size:14 final size:14
Alignment explanation
Indices: 1973672--1973710 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1973662 ATGTAATTCA
*
1973672 TTTTACGGAAAACC
1 TTTTCCGGAAAACC
*
1973686 TTTTCCGGAAAACG
1 TTTTCCGGAAAACC
*
1973700 TTTTCCAGAAA
1 TTTTCCGGAAA
1973711 TGTAATTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (14 bp):
TTTTCCGGAAAACC
Found at i:1973737 original size:20 final size:20
Alignment explanation
Indices: 1973700--1973738 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1973690 CCGGAAAACG
**
1973700 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
1973720 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
1973739 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:1973764 original size:30 final size:30
Alignment explanation
Indices: 1973712--1973793 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
1973702 TTCCAGAAAT
1973712 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
1973741 GTAATTCATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1973771 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1973794 TTTTCCGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1973799 original size:15 final size:15
Alignment explanation
Indices: 1973712--1973793 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
1973702 TTCCAGAAAT
**
1973712 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1973727 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
1973741 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
1973756 GTAATTCAAATTCTA
1 GTAATTCAAATTCCA
1973771 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1973786 GTAATTCA
1 GTAATTCA
1973794 TTTTCCGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1974556 original size:16 final size:16
Alignment explanation
Indices: 1974535--1974584 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
1974525 TGCACTGTTA
1974535 TACATGAACTATGTGT
1 TACATGAACTATGTGT
*
1974551 TACATGTCATCCTATGTGT
1 TACATG--A-ACTATGTGT
*
1974570 TACATGATCTATGTG
1 TACATGAACTATGTG
1974585 GATACATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 1 0.03
19 14 0.48
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (16 bp):
TACATGAACTATGTGT
Found at i:1974663 original size:23 final size:23
Alignment explanation
Indices: 1974637--1974730 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
1974627 GGTTCTACAC
*
1974637 GGTCCTTTGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
* **
1974660 GGTCCTTCGGGACATTTCTACAC
1 GGTCCTTCGGGACAATTCTACGT
* *
1974683 GGTCCTTCGAGAC-ATATCTATGT
1 GGTCCTTCGGGACAAT-TCTACGT
* *
1974706 GGTCCTCCGGGACATTTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
1974729 GG
1 GG
1974731 AACTTCGGTG
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
22 1 0.02
23 54 0.96
24 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACGT
Found at i:1974708 original size:46 final size:46
Alignment explanation
Indices: 1974629--1974726 Score: 144
Period size: 46 Copynumber: 2.1 Consensus size: 46
1974619 GAGTCGAGGG
* * *
1974629 TTCTACACGGTCCTTTGGGACAATTCTACGTGGTCCTTCGGGACAT
1 TTCTACACGGTCCTTCGAGACAATTCTACGTGGTCCTCCGGGACAT
*
1974675 TTCTACACGGTCCTTCGAGAC-ATATCTATGTGGTCCTCCGGGACAT
1 TTCTACACGGTCCTTCGAGACAAT-TCTACGTGGTCCTCCGGGACAT
1974721 TTCTAC
1 TTCTAC
1974727 GTGGAACTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
45 2 0.04
46 45 0.96
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (46 bp):
TTCTACACGGTCCTTCGAGACAATTCTACGTGGTCCTCCGGGACAT
Found at i:1977405 original size:28 final size:26
Alignment explanation
Indices: 1977355--1977419 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 26
1977345 TATGTTTAAG
** *
1977355 TTATTTTATCGTATTTTCATATCACTT
1 TTATTTTATTTTATCTTCATATCA-TT
*
1977382 TATATTTTATTTTATCTTCGTATCATT
1 T-TATTTTATTTTATCTTCATATCATT
1977409 TTA-TTTATTTT
1 TTATTTTATTTT
1977420 TATATTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 8 0.24
26 2 0.06
27 4 0.12
28 19 0.58
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.65
Consensus pattern (26 bp):
TTATTTTATTTTATCTTCATATCATT
Found at i:1978020 original size:83 final size:82
Alignment explanation
Indices: 1977872--1978204 Score: 335
Period size: 87 Copynumber: 4.0 Consensus size: 82
1977862 TGGGAATAGC
* * * * * * * **
1977872 AGAAATAGTGTTTTTTTCATATTA-ACAAATAAGGATGGAGCACTCAATTGGTTAGAAGGCAAAA
1 AGAAATGGTGCTTTTTTCCTATTAGA-AAATAAGGATGGAGCACCCAAATGGTTAAAATGTGAAA
*
1977936 CTCCGATTTTGAATAACA
65 CTCCGATTTTGAATGACA
* **
1977954 TGGAAATGGTGCTTTTTTCCTATTAGAAAATAAGGATGGAATACCCAAATGGTTAAAATGTGAAA
1 -AGAAATGGTGCTTTTTTCCTATTAGAAAATAAGGATGGAGCACCCAAATGGTTAAAATGTGAAA
*
1978019 CTCCAATTTTGAATGACA
65 CTCCGATTTTGAATGACA
* * * * ** *
1978037 AGAAACGGTACCTTTTTTTTTTCTTATGAGCGAATAAGGATGGAGCATCCAAATGGTTAAAATGT
1 AGAAATGGT-GC----TTTTTTCCTATTAGAAAATAAGGATGGAGCACCCAAATGGTTAAAATGT
1978102 GAAACTCCGATTTTGAATGACA
61 GAAACTCCGATTTTGAATGACA
* * * * *
1978124 AGAACTGGTACTTTTTTCTTCTTATTAGCAAATAAGGATGGACCACCCAAATGGTTAGAATGTGA
1 AGAAATGGTGCTTTTTTC--C-TATTAGAAAATAAGGATGGAGCACCCAAATGGTTAAAATGTGA
1978189 AACTCCGATTTTGAAT
63 AACTCCGATTTTGAAT
1978205 CACAGGTTTG
Statistics
Matches: 207, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
82 14 0.07
83 67 0.32
84 1 0.00
85 54 0.26
86 1 0.00
87 70 0.34
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (82 bp):
AGAAATGGTGCTTTTTTCCTATTAGAAAATAAGGATGGAGCACCCAAATGGTTAAAATGTGAAAC
TCCGATTTTGAATGACA
Found at i:1978193 original size:85 final size:85
Alignment explanation
Indices: 1977882--1978204 Score: 377
Period size: 85 Copynumber: 3.8 Consensus size: 85
1977872 AGAAATAGTG
* * * * * * **
1977882 TTTTT-TTCATATTAACAAATAAGGATGGAGCACTCAATTGGTTAGAAGGCAAAACTCCGATTTT
1 TTTTTCTTCTTATTAGCAAATAAGGATGGAGCACCCAAATGGTTAAAATGTGAAACTCCGATTTT
* * * *
1977946 GAATAACATGGAAATGGTGCT
66 GAATGACA-AGAACTGGTACT
* ** *
1977967 TTTTTC--C-TATTAGAAAATAAGGATGGAATACCCAAATGGTTAAAATGTGAAACTCCAATTTT
1 TTTTTCTTCTTATTAGCAAATAAGGATGGAGCACCCAAATGGTTAAAATGTGAAACTCCGATTTT
1978029 GAATGACAAGAAAC-GGTACCTT
66 GAATGACAAG-AACTGGTA-C-T
* * * *
1978051 TTTTTTTTCTTATGAGCGAATAAGGATGGAGCATCCAAATGGTTAAAATGTGAAACTCCGATTTT
1 TTTTTCTTCTTATTAGCAAATAAGGATGGAGCACCCAAATGGTTAAAATGTGAAACTCCGATTTT
1978116 GAATGACAAGAACTGGTACT
66 GAATGACAAGAACTGGTACT
* *
1978136 TTTTTCTTCTTATTAGCAAATAAGGATGGACCACCCAAATGGTTAGAATGTGAAACTCCGATTTT
1 TTTTTCTTCTTATTAGCAAATAAGGATGGAGCACCCAAATGGTTAAAATGTGAAACTCCGATTTT
1978201 GAAT
66 GAAT
1978205 CACAGGTTTG
Statistics
Matches: 201, Mismatches: 29, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
82 4 0.02
83 54 0.27
84 7 0.03
85 69 0.34
86 5 0.02
87 62 0.31
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (85 bp):
TTTTTCTTCTTATTAGCAAATAAGGATGGAGCACCCAAATGGTTAAAATGTGAAACTCCGATTTT
GAATGACAAGAACTGGTACT
Found at i:1979878 original size:204 final size:204
Alignment explanation
Indices: 1979527--1979910 Score: 644
Period size: 204 Copynumber: 1.9 Consensus size: 204
1979517 GGATTTATGC
* * *
1979527 TTTCTCACTGGCTTTCAAGCAGGTTATGAAACCTTTTAAGGTCTGGAAAGCACAACCTTGAATAT
1 TTTCTCACTGGCTTTCAAGCAGGATATGAAACCTTTTAACGTCTGGAAAGCACAACCTTGAAGAT
* * *
1979592 TAATCTATTCCTAGCAGCTTTGAAGGTGTCAATTTCTAAAATACATGCATCACCTCAGTGTTGCT
66 TAATCTATTCCTAGCAGCTTTGAAGGCGTAAATTTCTAAAATACATGCAACACCTCAGTGTTGCT
*
1979657 AACTTTGGATAACAGTTGACCCTAATGT-TTTTTTATCAAGAAACTAAGTTGTGGACAACTAATG
131 AACTTTGGAGAACAGTTG-CCCTAATGTCTTTTTTATCAAGAAACTAAGTTGTGGACAACTAATG
1979721 TTGGCCAACA
195 TTGGCCAACA
1979731 TTTCTCACTGGCTTTCAAGCAGGATATGAAACCTTTTAACGTCTGGAAAGCACAACCTTGAAGAT
1 TTTCTCACTGGCTTTCAAGCAGGATATGAAACCTTTTAACGTCTGGAAAGCACAACCTTGAAGAT
* * *
1979796 TCATCTATTCCTAGCAGCTTTGAAGGCGTAAATTTCTGAAGTACATGCAACACCTCAGTGTTGCT
66 TAATCTATTCCTAGCAGCTTTGAAGGCGTAAATTTCTAAAATACATGCAACACCTCAGTGTTGCT
* *
1979861 AACTTTGGAGGACAGTTGGCCTAATGTCTTTTTTATCAAGAAACTAAGTT
131 AACTTTGGAGAACAGTTGCCCTAATGTCTTTTTTATCAAGAAACTAAGTT
1979911 TTGGTAATGG
Statistics
Matches: 167, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
203 8 0.05
204 159 0.95
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (204 bp):
TTTCTCACTGGCTTTCAAGCAGGATATGAAACCTTTTAACGTCTGGAAAGCACAACCTTGAAGAT
TAATCTATTCCTAGCAGCTTTGAAGGCGTAAATTTCTAAAATACATGCAACACCTCAGTGTTGCT
AACTTTGGAGAACAGTTGCCCTAATGTCTTTTTTATCAAGAAACTAAGTTGTGGACAACTAATGT
TGGCCAACA
Found at i:1982616 original size:20 final size:18
Alignment explanation
Indices: 1982571--1982639 Score: 93
Period size: 18 Copynumber: 3.7 Consensus size: 18
1982561 TGAATATTTA
1982571 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
1982589 TCCCGAAGGACCACTAATTG
1 TCCCGAAGGACCACT-A-TG
* *
1982609 TTCCGAAGAACCACTATG
1 TCCCGAAGGACCACTATG
*
1982627 TGCCGAAGGACCA
1 TCCCGAAGGACCA
1982640 TTGATAATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
18 28 0.62
19 2 0.04
20 15 0.33
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:1989350 original size:22 final size:22
Alignment explanation
Indices: 1989309--1989376 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 22
1989299 CTCATATAAA
*
1989309 TGCATCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
1989332 TGCACTGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1989354 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1989376 T
1 T
1989377 ATGTCCATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 32 0.76
23 10 0.24
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.22
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1989624 original size:30 final size:30
Alignment explanation
Indices: 1989579--1989648 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1989569 CCGTAGTTCA
* * * *
1989579 TATCGCATAGTCATATTATTTCCATACCTT
1 TATCACATAGACATATCATTTACATACCTT
1989609 TATCACATAGACATATCATTTACATACCTT
1 TATCACATAGACATATCATTTACATACCTT
1989639 TATCACATAG
1 TATCACATAG
1989649 CTCATATAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (30 bp):
TATCACATAGACATATCATTTACATACCTT
Found at i:1990162 original size:66 final size:67
Alignment explanation
Indices: 1990014--1990187 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 67
1990004 TTTTTCTCAT
* * *
1990014 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
1990079 ATGA
64 ATGA
* * * *
1990083 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
1990147 GA
66 GA
* *
1990149 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
1990188 AACCCAGAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 6 0.06
66 19 0.20
67 57 0.61
69 12 0.13
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:1996261 original size:22 final size:22
Alignment explanation
Indices: 1996220--1996287 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
1996210 CTCGTATAAA
1996220 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
1996243 TGCACTGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1996265 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1996287 T
1 T
1996288 ATGTCCATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 32 0.74
23 11 0.26
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1996535 original size:30 final size:30
Alignment explanation
Indices: 1996490--1996559 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1996480 CCGTAGTTCA
* * * *
1996490 TATCGCATAGTCATATTATTTCCATACCTT
1 TATCACATAGACATATCATTTACATACCTT
1996520 TATCACATAGACATATCATTTACATACCTT
1 TATCACATAGACATATCATTTACATACCTT
1996550 TATCACATAG
1 TATCACATAG
1996560 CTCATATAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (30 bp):
TATCACATAGACATATCATTTACATACCTT
Found at i:1997075 original size:66 final size:67
Alignment explanation
Indices: 1996942--1997100 Score: 207
Period size: 67 Copynumber: 2.4 Consensus size: 67
1996932 TCGGTTCCCC
* *
1996942 CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGGTATCGG
1 CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
1997007 TT
66 TT
* * *
1997009 CCCCCCTGGGGGTACCGATTCCCCT-ATAGCATTCTGGAAATTCAT-TTCGTTGAGGGGGTATCG
1 CCCCCCTGGGGGTACCGATTCCCCTCA-AGCAATCTGGAAATTCATATACGATGAGGGGGTATCG
1997072 GTT
65 GTT
* *
1997075 -CCCCTTGAATGGGTACCGATTCCCCT
1 CCCCCCTG--GGGGTACCGATTCCCCT
1997101 TGAATGGGTA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
65 6 0.07
66 20 0.24
67 56 0.68
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (67 bp):
CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
TT
Found at i:1997088 original size:21 final size:21
Alignment explanation
Indices: 1997064--1997121 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1997054 TTCGTTGAGG
* *
1997064 GGGTATCGGTTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
1997085 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
1997106 GGGTACCGATTCCCCT
1 GGGTACCGATTCCCCT
1997122 AACCCAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:1998292 original size:13 final size:15
Alignment explanation
Indices: 1998258--1998296 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1998248 TCGATTACAC
1998258 GATAACATATATGAT
1 GATAACATATATGAT
*
1998273 GATAACATGTAT-AT
1 GATAACATATATGAT
1998287 -ATAACATATA
1 GATAACATATA
1998297 CATTCTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (15 bp):
GATAACATATATGAT
Found at i:1998461 original size:18 final size:18
Alignment explanation
Indices: 1998438--1998510 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
1998428 ACTGAATATT
*
1998438 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
1998456 TGTCCCGAAGGACCACTAA
1 TGTCCCGAAGGACCACT-A
* * **
1998475 TTATTCCGAAAAACCACTA
1 -TGTCCCGAAGGACCACTA
1998494 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1998511 GATAATCCCT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 29 0.66
19 2 0.05
20 13 0.30
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2013917 original size:2 final size:2
Alignment explanation
Indices: 2013910--2013936 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2013900 TATTTTTACT
2013910 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2013937 CGAGCATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2014155 original size:22 final size:22
Alignment explanation
Indices: 2014129--2014181 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
2014119 TTCCATTTCG
2014129 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
2014151 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
2014173 CGTTGCGAT
1 CGTTGCGAT
2014182 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:2014919 original size:19 final size:19
Alignment explanation
Indices: 2014895--2014960 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
2014885 TTAACTATCA
2014895 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
2014914 CAACGACAACTATAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
2014936 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
2014955 CAACGA
1 CAACGA
2014961 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:2014937 original size:22 final size:22
Alignment explanation
Indices: 2014910--2014981 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
2014900 AATTTGGAAA
2014910 ATCGCAACGACAACTATAGACT
1 ATCGCAACGACAACTATAGACT
* * **
2014932 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTATAGACT
*
2014951 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTATAGACT
2014973 ATCGCAACG
1 ATCGCAACG
2014982 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTATAGACT
Found at i:2014945 original size:41 final size:41
Alignment explanation
Indices: 2014888--2014981 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2014878 TTTTTTTTTA
*
2014888 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTATAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTATAG
*
2014929 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTATAG
2014970 ACTATCGCAACG
1 ACTATCGCAACG
2014982 CGAAATGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTATAG
Found at i:2014992 original size:41 final size:41
Alignment explanation
Indices: 2014888--2015001 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 41
2014878 TTTTTTTTTA
* *
2014888 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTATAG
1 ACTATCGCAACGAATATGGAAAATCGCAACGACAACTATAG
* *
2014929 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATATGGAAAATCGCAACGACAACTATAG
*
2014970 ACTATCGCAACGCGAA-ATGAAAAATCGCAACG
1 ACTATCGCAA--CGAATATGGAAAATCGCAACG
2015002 CGAAATGAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
41 49 0.73
42 14 0.21
43 4 0.06
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGAATATGGAAAATCGCAACGACAACTATAG
Found at i:2014998 original size:20 final size:20
Alignment explanation
Indices: 2014973--2015185 Score: 123
Period size: 20 Copynumber: 10.8 Consensus size: 20
2014963 ACTGTAGACT
2014973 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
2014993 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* * ** * **
2015013 ATCGCTACGTGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
* *
2015034 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGAAAA
*
2015054 ATCGCAACGCG--AT----T
1 ATCGCAACGCGAAATGAAAA
*
2015068 ATCACAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* ** * **
2015088 ATCGCAACGTGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
* ** * **
2015109 ATCACAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
2015130 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
* *
2015150 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGAAAA
2015170 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
2015186 CAACGCGAAT
Statistics
Matches: 148, Mismatches: 37, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
14 10 0.07
16 2 0.01
18 1 0.01
20 89 0.60
21 46 0.31
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:2015012 original size:61 final size:61
Alignment explanation
Indices: 2014948--2015065 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
2014938 ACGAATTTGG
2014948 AAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAATGAAAAATCGCAACGCGAAATGA
1 AAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAATGAAAAATCGCAACGCGAAATGA
* ** * * * *
2015010 AAAATCGCTACGTGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGA
1 AAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAATGAAAAATCGCAACGCGA
2015066 TTATCACAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
61 36 0.75
62 12 0.25
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (61 bp):
AAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAATGAAAAATCGCAACGCGAAATGA
Found at i:2015043 original size:41 final size:41
Alignment explanation
Indices: 2014997--2015120 Score: 154
Period size: 41 Copynumber: 3.2 Consensus size: 41
2014987 TGAAAAATCG
* *
2014997 CAACGCGAAATGAAAAATCGCTACGTGATTTTCAACTATCG
1 CAACGCGAAATGAAAAATCGCAACGTGATTTTCAACTATCA
* * *
2015038 CAACGCGAACTGGAAAATCGCAACGCGA---T----TATCA
1 CAACGCGAAATGAAAAATCGCAACGTGATTTTCAACTATCA
2015072 CAACGCGAAATGAAAAATCGCAACGTGATTTTCAACTATCA
1 CAACGCGAAATGAAAAATCGCAACGTGATTTTCAACTATCA
2015113 CAACGCGA
1 CAACGCGA
2015121 TTTTCAACTA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
34 29 0.43
37 1 0.01
38 1 0.01
41 37 0.54
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
CAACGCGAAATGAAAAATCGCAACGTGATTTTCAACTATCA
Found at i:2015089 original size:34 final size:34
Alignment explanation
Indices: 2015033--2015101 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
2015023 GATTTTCAAC
* * *
2015033 TATCGCAACGCGAACTGGAAAATCGCAACGCGAT
1 TATCACAACGCGAAATGAAAAATCGCAACGCGAT
*
2015067 TATCACAACGCGAAATGAAAAATCGCAACGTGAT
1 TATCACAACGCGAAATGAAAAATCGCAACGCGAT
2015101 T
1 T
2015102 TTCAACTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (34 bp):
TATCACAACGCGAAATGAAAAATCGCAACGCGAT
Found at i:2015122 original size:21 final size:21
Alignment explanation
Indices: 2015092--2015141 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2015082 TGAAAAATCG
*
2015092 CAACGTGATTTTCAACTATCA
1 CAACGCGATTTTCAACTATCA
*
2015113 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCA
2015134 CAACGCGA
1 CAACGCGA
2015142 AATGGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
CAACGCGATTTTCAACTATCA
Found at i:2015148 original size:96 final size:95
Alignment explanation
Indices: 2014972--2015161 Score: 272
Period size: 96 Copynumber: 2.0 Consensus size: 95
2014962 AACTGTAGAC
* * * * *
2014972 TATCGCAACGCGAAATGAAAAATCGCAACGCGAAATGAAAAATCGCTACGTGATTTTCAACTATC
1 TATCACAACGCGAAATGAAAAATCGCAACGCGAAATCAAAAATCACAACGCGATTTTCAACTATC
*
2015037 GCAACGCGAACTGGAAAATCGCAACGCGAT
66 GCAACGCGAAATGGAAAATCGCAACGCGAT
* ** **
2015067 TATCACAACGCGAAATGAAAAATCGCAACGTGATTTTCAACTATCACAACGCGATTTTCAACTAT
1 TATCACAACGCGAAATGAAAAATCGCAACGCGA-AATCAAAAATCACAACGCGATTTTCAACTAT
2015132 CGCAACGCGAAATGGAAAATCGCAACGCGA
65 CGCAACGCGAAATGGAAAATCGCAACGCGA
2015162 ACTGGAAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 31 0.37
96 52 0.63
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (95 bp):
TATCACAACGCGAAATGAAAAATCGCAACGCGAAATCAAAAATCACAACGCGATTTTCAACTATC
GCAACGCGAAATGGAAAATCGCAACGCGAT
Found at i:2015720 original size:17 final size:17
Alignment explanation
Indices: 2015687--2015724 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2015677 ACATTTTCAA
2015687 ATTTTATATAAAGAAATT
1 ATTTTATATAAAGAAA-T
*
2015705 ATTTTA-ATAAATAAAT
1 ATTTTATATAAAGAAAT
2015721 ATTT
1 ATTT
2015725 ATTACGTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTTTATATAAAGAAAT
Found at i:2016273 original size:21 final size:21
Alignment explanation
Indices: 2016222--2016274 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2016212 ATTCTGACTA
2016222 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
2016243 TTGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
2016264 TCGCAATGCGA
1 TCGCATTGCGA
2016275 ATACATAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2019766 original size:33 final size:33
Alignment explanation
Indices: 2019716--2019895 Score: 166
Period size: 33 Copynumber: 5.3 Consensus size: 33
2019706 GAAAATTACT
2019716 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
* * *
2019749 ATCGCAAC-ATGAAAATCGCAACGCG-AATATGAA
1 ATCGCAACGA-GAGAATCGCAATGCGAAATA-AAA
* * * * *
2019782 ATTGTAACGCGGAAATGACTATCGCAATGCAAAATGAAA
1 ATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATAAAA
2019821 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
* * * *
2019854 ATTGCAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
2019887 ATCGCAACG
1 ATCGCAACG
2019896 TGAATTTAGT
Statistics
Matches: 116, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
32 5 0.04
33 82 0.71
35 3 0.03
36 4 0.03
37 3 0.03
39 16 0.14
40 3 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
Found at i:2019840 original size:105 final size:105
Alignment explanation
Indices: 2019689--2019886 Score: 283
Period size: 105 Copynumber: 1.9 Consensus size: 105
2019679 CAATAATCTT
* * **
2019689 AATGTCTATCGCAACGCGAAAATTACTATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGC
1 AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGC
*
2019754 AAC-ATGAAAATCGCAACGCGAATATGAAATTGTAACGCGGA
66 AACGA-GAAAATCGCAAAGCGAA-ATGAAATTGTAACGCGGA
* *
2019795 AATGACTATCGCAATGC-AAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATTGC
1 AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGC
**
2019859 AACGAGGGAATCGCAAAGCGAAATGAAA
66 AACGAGAAAATCGCAAAGCGAAATGAAA
2019887 ATCGCAACGT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
104 6 0.07
105 60 0.73
106 16 0.20
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (105 bp):
AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGC
AACGAGAAAATCGCAAAGCGAAATGAAATTGTAACGCGGA
Found at i:2019922 original size:19 final size:19
Alignment explanation
Indices: 2019900--2019940 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2019890 GCAACGTGAA
2019900 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
2019919 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
2019938 TTT
1 TTT
2019941 GTCGTTGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:2020096 original size:14 final size:14
Alignment explanation
Indices: 2020077--2020110 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2020067 CATCAATTAA
2020077 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2020091 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2020105 ACAAAT
1 ACAAAT
2020111 AAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2021546 original size:42 final size:42
Alignment explanation
Indices: 2021500--2021579 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
2021490 CGATGACAGT
* * *
2021500 GGCCTCTTGAACGGTTGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
2021542 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
2021580 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:2022061 original size:19 final size:19
Alignment explanation
Indices: 2022034--2022095 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
2022024 ACAACGAGAG
*
2022034 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2022053 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2022067 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2022086 AATCGCAACG
1 AATCGCAACG
2022096 ATAGAATCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2022119 original size:33 final size:33
Alignment explanation
Indices: 2022004--2022107 Score: 167
Period size: 33 Copynumber: 3.2 Consensus size: 33
2021994 AAAAATGACT
*
2022004 ATCGCAACGCGAAATG--AATCACAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
2022035 ATCACAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
2022068 ATCGCAACGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2022101 ATCGCAA
1 ATCGCAA
2022108 TGTAAATTGA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 15 0.22
33 52 0.78
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2022293 original size:78 final size:78
Alignment explanation
Indices: 2022193--2022357 Score: 305
Period size: 78 Copynumber: 2.1 Consensus size: 78
2022183 TTAAAGAATA
2022193 CACAGT-TTAGCAAAATTAGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGA
1 CACAGTGTTAGCAAAATTAGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGA
2022257 CAAATACTAACTT
66 CAAATACTAACTT
* *
2022270 CACAGTGTTAGCAAAATTGGCAGCAACCGAACAAATTTATTTTCAACCAAAAGACAAAACAAAGA
1 CACAGTGTTAGCAAAATTAGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGA
2022335 CAAATACTAACTT
66 CAAATACTAACTT
2022348 CACAGTGTTA
1 CACAGTGTTA
2022358 AAGAATACAC
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
77 6 0.07
78 79 0.93
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (78 bp):
CACAGTGTTAGCAAAATTAGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGA
CAAATACTAACTT
Found at i:2022409 original size:19 final size:19
Alignment explanation
Indices: 2022387--2022429 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2022377 GAATTGACAG
2022387 CAACCGAATAAATTTACTT
1 CAACCGAATAAATTTACTT
2022406 CAACCGAATAAATTTACTT
1 CAACCGAATAAATTTACTT
*
2022425 TAACC
1 CAACC
2022430 AAAAGGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (19 bp):
CAACCGAATAAATTTACTT
Found at i:2022447 original size:113 final size:113
Alignment explanation
Indices: 2022293--2022517 Score: 362
Period size: 113 Copynumber: 2.0 Consensus size: 113
2022283 AAATTGGCAG
*
2022293 CAACCGAACAAATTTATTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTA
1 CAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTA
* *
2022358 AAGAATACACAGTTTAGCAGAATTGACAGCAACCGAATAAATTTACTT
66 AAGAATAAACAGTTTAACAGAATTGACAGCAACCGAATAAATTTACTT
* **
2022406 CAACCGAATAAATTTACTTT-AACCAAAAGGTAAAACAAAAGACAAATACTAACTTCACAGTGTT
1 CAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTT
* *
2022470 AAAGAATAAACAGTTTAACAGTATTGGCAGCAACCGAATAAATTTACT
65 AAAGAATAAACAGTTTAACAGAATTGACAGCAACCGAATAAATTTACT
2022518 AAGCAATCTA
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 14 0.14
113 89 0.86
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (113 bp):
CAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTA
AAGAATAAACAGTTTAACAGAATTGACAGCAACCGAATAAATTTACTT
Found at i:2024269 original size:20 final size:19
Alignment explanation
Indices: 2024220--2024274 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
2024210 TAAAATGAAA
*
2024220 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
2024240 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
2024260 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
2024275 AAAAATCGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 5 0.15
20 26 0.79
21 2 0.06
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2024382 original size:20 final size:20
Alignment explanation
Indices: 2024317--2024407 Score: 114
Period size: 20 Copynumber: 4.5 Consensus size: 20
2024307 CGATTATCTC
*
2024317 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
2024336 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
2024356 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
2024377 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
2024397 GTTGCGATTTT
1 GTTGCGATTTT
2024408 AAGTTTAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
19 13 0.21
20 32 0.52
21 17 0.27
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:2024979 original size:20 final size:20
Alignment explanation
Indices: 2024954--2025167 Score: 243
Period size: 20 Copynumber: 10.6 Consensus size: 20
2024944 CTTTAAAAAT
2024954 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2024974 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2024994 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
2025015 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
2025035 CTCGTTGCGATTTACAAATA
1 CGCGTTGCGATTTACGGATA
* *
2025055 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
2025075 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2025095 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2025115 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
2025136 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
2025157 CTCGTTGCGAT
1 CGCGTTGCGAT
2025168 AGTCAGAATC
Statistics
Matches: 162, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
20 109 0.67
21 53 0.33
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2025184 original size:41 final size:41
Alignment explanation
Indices: 2024956--2025167 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
2024946 TTAAAAATCG
*
2024956 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2024997 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
2025037 CGTTGCGATTTACAAATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2025077 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2025118 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
2025159 CGTTGCGAT
1 CGTTGCGAT
2025168 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 74 0.47
41 85 0.53
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2025199 original size:20 final size:20
Alignment explanation
Indices: 2025176--2025228 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2025166 ATAGTCAGAA
*
2025176 TCGCGTTGCTATTTATATGT
1 TCGCGTTGCGATTTATATGT
2025196 TCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTATATGT
2025216 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2025229 CTTCTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATGT
Found at i:2031404 original size:21 final size:22
Alignment explanation
Indices: 2031371--2031415 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2031361 TAGGGATTTT
2031371 TATTTTTATATTATT-AAAATA
1 TATTTTTATATTATTAAAAATA
2031392 TATTCTTTA-ATTATTAAAAATA
1 TATT-TTTATATTATTAAAAATA
2031414 TA
1 TA
2031416 AAAATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTATATTATTAAAAATA
Found at i:2031484 original size:17 final size:15
Alignment explanation
Indices: 2031465--2031500 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2031455 TAATTATTAT
2031465 TATTATTAT-AAATA
1 TATTATTATAAAATA
2031479 TATTATTATAAAATA
1 TATTATTATAAAATA
2031494 TATTATT
1 TATTATT
2031501 TTGATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATTATAAAATA
Found at i:2031508 original size:38 final size:36
Alignment explanation
Indices: 2031412--2031520 Score: 109
Period size: 38 Copynumber: 3.0 Consensus size: 36
2031402 TTATTAAAAA
* *
2031412 TATAAAA-ATATTATTTTAATAGTTTAAA-ATATAAT
1 TATAAAATATATTATTTTATTA-TTTAAATATATTAT
*
2031447 AATAATAATA-ATTATTATTATTATTATAAATATATTAT
1 TATAA-AATATATTATT-TTATTATT-TAAATATATTAT
2031485 TATAAAATATATTATTTTGATTATTTTAAAT-TATTA
1 TATAAAATATATTATTTT-ATTA-TTTAAATATATTA
2031521 ATTTATTTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
35 4 0.06
36 10 0.16
37 21 0.34
38 25 0.40
39 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (36 bp):
TATAAAATATATTATTTTATTATTTAAATATATTAT
Found at i:2036095 original size:35 final size:35
Alignment explanation
Indices: 2036056--2036201 Score: 122
Period size: 35 Copynumber: 4.2 Consensus size: 35
2036046 TTTAAAGTAA
*
2036056 ATAAAATATATTATATTTAAAATATATTATAAATT
1 ATAAAATATATTATAATTAAAATATATTATAAATT
* * *
2036091 ATAAAGTATATTATAAATAAAATATAGTAT--ATT
1 ATAAAATATATTATAATTAAAATATATTATAAATT
**
2036124 -TAAAATATATTATAAATTATAAA-ATATTATAAGTAAC
1 ATAAAATATATTAT-AATTA-AAATATATTATAA--ATT
* * * *
2036161 ATTAAATTTA-AAGTAAATAAAATATATTATAAATT
1 ATAAAATATATTA-TAATTAAAATATATTATAAATT
2036196 ATAAAA
1 ATAAAA
2036202 GGATATAATT
Statistics
Matches: 86, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
32 12 0.14
33 13 0.15
34 3 0.03
35 32 0.37
36 3 0.03
37 15 0.17
38 8 0.09
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (35 bp):
ATAAAATATATTATAATTAAAATATATTATAAATT
Found at i:2036108 original size:51 final size:49
Alignment explanation
Indices: 2036053--2036201 Score: 181
Period size: 51 Copynumber: 2.9 Consensus size: 49
2036043 AAATTTAAAG
2036053 TAAATAAAATATATTATATTTAAAATATATTATAAATTATAAAGTATATTA
1 TAAATAAAATATATTATATTTAAAATATATTATAAATTATAAA--ATATTA
*
2036104 TAAATAAAATATAGTATATTTAAAATATATTATAAATTATAAAATATTA
1 TAAATAAAATATATTATATTTAAAATATATTATAAATTATAAAATATTA
* * * **
2036153 TAAGTAACATTAAATTTAAAGTAAATAAAATATATTATAAATTATAAAA
1 TAAATAA-AATATA-TT--A-TATTTAAAATATATTATAAATTATAAAA
2036202 GGATATAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
49 12 0.14
50 4 0.05
51 43 0.50
53 1 0.01
54 26 0.30
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (49 bp):
TAAATAAAATATATTATATTTAAAATATATTATAAATTATAAAATATTA
Found at i:2036137 original size:21 final size:21
Alignment explanation
Indices: 2036078--2036127 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
2036068 ATATTTAAAA
* *
2036078 TATATTATAAAT--TATAAAG
1 TATATTATAAATAAAATATAG
2036097 TATATTATAAATAAAATATAG
1 TATATTATAAATAAAATATAG
2036118 TATATT-TAAA
1 TATATTATAAA
2036128 ATATATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 12 0.44
20 4 0.15
21 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
TATATTATAAATAAAATATAG
Found at i:2036193 original size:16 final size:16
Alignment explanation
Indices: 2036053--2036194 Score: 115
Period size: 16 Copynumber: 8.3 Consensus size: 16
2036043 AAATTTAAAG
2036053 TAAATAAAATATATTA
1 TAAATAAAATATATTA
**
2036069 TATTTAAAATATATTA
1 TAAATAAAATATATTA
2036085 TAAATTATAAAGTATATTA
1 TAAA-TA-AAA-TATATTA
*
2036104 TAAATAAAATATAGTA
1 TAAATAAAATATATTA
**
2036120 TATTTAAAATATATTA
1 TAAATAAAATATATTA
2036136 TAAATTATAAA-ATATTA
1 TAAA-TA-AAATATATTA
* * *
2036153 TAAGTAACATTAAATTTAAA
1 TAAATAA-AATATA-TT--A
2036173 GTAAATAAAATATATTA
1 -TAAATAAAATATATTA
2036190 TAAAT
1 TAAAT
2036195 TATAAAAGGA
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
15 1 0.01
16 45 0.45
17 19 0.19
18 10 0.10
19 13 0.13
20 5 0.05
21 6 0.06
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (16 bp):
TAAATAAAATATATTA
Found at i:2038202 original size:21 final size:20
Alignment explanation
Indices: 2038178--2038216 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2038168 AAAGACTGAA
2038178 ATAACTAACAAAATCGATCCT
1 ATAACTAA-AAAATCGATCCT
* *
2038199 ATAATTGAAAAATCGATC
1 ATAACTAAAAAATCGATC
2038217 AAATCATCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (20 bp):
ATAACTAAAAAATCGATCCT
Found at i:2043011 original size:18 final size:19
Alignment explanation
Indices: 2042988--2043030 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2042978 CAGTAATCCT
2042988 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATCTTAC
*
2043006 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGATAATCTTAC
2043026 ATTCC
1 ATTCC
2043031 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:2048288 original size:18 final size:18
Alignment explanation
Indices: 2048265--2048306 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2048255 AGAGGTACCG
2048265 ATACCCCTATAAGTATCA
1 ATACCCCTATAAGTATCA
*
2048283 ATACCCCTATGAGTATCA
1 ATACCCCTATAAGTATCA
2048301 ATACCC
1 ATACCC
2048307 TGGGTACCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.31, G:0.07, T:0.26
Consensus pattern (18 bp):
ATACCCCTATAAGTATCA
Found at i:2048341 original size:22 final size:22
Alignment explanation
Indices: 2048307--2048350 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2048297 ATCAATACCC
*
2048307 TGGGTACCGATACCCCTATGAA
1 TGGGTACCAATACCCCTATGAA
*
2048329 TGGGTATCAATACCCCTATGAA
1 TGGGTACCAATACCCCTATGAA
2048351 GGCTCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (22 bp):
TGGGTACCAATACCCCTATGAA
Found at i:2048403 original size:18 final size:18
Alignment explanation
Indices: 2048382--2048439 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
2048372 AAGGGTACCG
*
2048382 ATACCCCTATGGGTATTA
1 ATACCCCTATGGGTATCA
*
2048400 ATA-CCC--TGGGTACCA
1 ATACCCCTATGGGTATCA
2048415 ATACCCCTATGGGTATCA
1 ATACCCCTATGGGTATCA
2048433 ATACCCC
1 ATACCCC
2048440 CTGGCTCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.29
16 3 0.09
17 3 0.09
18 18 0.53
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.26
Consensus pattern (18 bp):
ATACCCCTATGGGTATCA
Found at i:2048419 original size:33 final size:33
Alignment explanation
Indices: 2048374--2048438 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2048364 AATGCAAAAA
* *
2048374 GGGTACCGATACCCCTATGGGTATTAATACCCT
1 GGGTACCAATACCCCTATGGGTATCAATACCCT
2048407 GGGTACCAATACCCCTATGGGTATCAATACCC
1 GGGTACCAATACCCCTATGGGTATCAATACCC
2048439 CCTGGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (33 bp):
GGGTACCAATACCCCTATGGGTATCAATACCCT
Found at i:2048505 original size:21 final size:21
Alignment explanation
Indices: 2048481--2048536 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2048471 AACAAAGGTA
2048481 GTACCGATACCCCTTGAAGGG
1 GTACCGATACCCCTTGAAGGG
2048502 GTACCGATACCCCTTGAAGGG
1 GTACCGATACCCCTTGAAGGG
*
2048523 GTATCGATACCCCT
1 GTACCGATACCCCT
2048537 ATTCTGAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.21
Consensus pattern (21 bp):
GTACCGATACCCCTTGAAGGG
Found at i:2051795 original size:22 final size:22
Alignment explanation
Indices: 2051761--2051808 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2051751 ATCAATACCC
*
2051761 TGGGTACCGATACCCCTATGAA
1 TGGGTACCAATACCCCTATGAA
*
2051783 TGGGTATCAATACCCCTATGAA
1 TGGGTACCAATACCCCTATGAA
2051805 -GGGT
1 TGGGT
2051809 CAAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
TGGGTACCAATACCCCTATGAA
Found at i:2052253 original size:33 final size:33
Alignment explanation
Indices: 2052216--2052285 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2052206 TTTTGTAAAG
* * *
2052216 GGGAAAGGTTCTAGCTGATCCCGTGAAAAGCTA
1 GGGAAAGGTTCTAGCTGAGCCCATGAAAAACTA
* * *
2052249 GGGAAATGTTCTAGTTTAGCCCATGAAAAACTA
1 GGGAAAGGTTCTAGCTGAGCCCATGAAAAACTA
2052282 GGGA
1 GGGA
2052286 GTTTGTAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTGAGCCCATGAAAAACTA
Found at i:2057051 original size:15 final size:15
Alignment explanation
Indices: 2057031--2057071 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
2057021 GACTGGGTCT
2057031 AAGAAGAAAATGTCA
1 AAGAAGAAAATGTCA
2057046 AAGAAGAAAATGTCA
1 AAGAAGAAAATGTCA
2057061 AAGAAGGAAAA
1 AAGAA-GAAAA
2057072 AGAAAGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.63, C:0.05, G:0.22, T:0.10
Consensus pattern (15 bp):
AAGAAGAAAATGTCA
Found at i:2060947 original size:51 final size:49
Alignment explanation
Indices: 2060889--2060987 Score: 144
Period size: 51 Copynumber: 2.0 Consensus size: 49
2060879 AGAACTTGTT
* *
2060889 GAAAAGGAAGAGGAGAAAGGAGAAGGGACACCGAAGAAGGAAAAAGAGAAA
1 GAAAAGGAAAAGGAGAAAGAAGAAGGGACACCGAA-AAGGAAAAA-AGAAA
* *
2060940 GAAAAGGAAAAGGGGAAAGAAGAAGGGACACCGCAAAGGAAAAAAGAA
1 GAAAAGGAAAAGGAGAAAGAAGAAGGGACACCGAAAAGGAAAAAAGAA
2060988 GAGGAGAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 4 0.09
50 9 0.20
51 31 0.70
ACGTcount: A:0.58, C:0.07, G:0.35, T:0.00
Consensus pattern (49 bp):
GAAAAGGAAAAGGAGAAAGAAGAAGGGACACCGAAAAGGAAAAAAGAAA
Found at i:2060948 original size:18 final size:19
Alignment explanation
Indices: 2060921--2060965 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
2060911 AAGGGACACC
2060921 GAAGAAGGAAAAAGAGAAA
1 GAAGAAGGAAAAAGAGAAA
* *
2060940 GAA-AAGGAAAAGGGGAAA
1 GAAGAAGGAAAAAGAGAAA
2060958 GAAGAAGG
1 GAAGAAGG
2060966 GACACCGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (19 bp):
GAAGAAGGAAAAAGAGAAA
Found at i:2060986 original size:45 final size:49
Alignment explanation
Indices: 2060889--2061002 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 49
2060879 AGAACTTGTT
* *
2060889 GAAAAGGAAGAGGAGAAAGGAGAAGGGACACCGAAGAAGGAAAAAGAGAAA
1 GAAAAGGAAAAGGAGAAAGAAGAAGGGACACCGAAGAAGG--AAAGAGAAA
* *
2060940 GAAAAGGAAAAGGGGAAAGAAGAAGGGACACCGCA-AAGG-AA-A-AAA
1 GAAAAGGAAAAGGAGAAAGAAGAAGGGACACCGAAGAAGGAAAGAGAAA
*
2060985 GAAGAGGAGAAAGGAGAA
1 GAAAAGGA-AAAGGAGAA
2061003 GGGACACCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
45 10 0.18
46 9 0.16
47 2 0.04
50 4 0.07
51 31 0.55
ACGTcount: A:0.57, C:0.06, G:0.37, T:0.00
Consensus pattern (49 bp):
GAAAAGGAAAAGGAGAAAGAAGAAGGGACACCGAAGAAGGAAAGAGAAA
Done.