Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011222.1 Kokia drynarioides strain JFW-HI SEQ_126200, 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: 242829
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 140 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:39 original size:26 final size:26
Alignment explanation
Indices: 3--52 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1 TT
*
3 ATATTTTTATTATATTA-AATAATAAA
1 ATATTATTATT-TATTATAATAATAAA
29 ATATTATTATTTATTATAATAATA
1 ATATTATTATTTATTATAATAATA
53 TTATTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATTATTATTTATTATAATAATAAA
Found at i:49 original size:18 final size:18
Alignment explanation
Indices: 28--62 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18 TAAATAATAA
* *
28 AATATTATTATTTATTAT
1 AATAATATTATTAATTAT
46 AATAATATTATTAATTA
1 AATAATATTATTAATTA
63 ATATATCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATATTATTAATTAT
Found at i:52 original size:21 final size:20
Alignment explanation
Indices: 9--67 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
1 TTATATTT
9 TTATTATATTAAATAATAAAATA
1 TTATTA-ATT-AAT-ATAAAATA
* *
32 TTATTATTTATTATAATAATA
1 TTATTAATTAATATAA-AATA
53 TTATTAATTAATATA
1 TTATTAATTAATATA
68 TCTTTTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 19 0.61
22 2 0.06
23 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTAATTAATATAAAATA
Found at i:6296 original size:23 final size:20
Alignment explanation
Indices: 6269--6309 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
6259 TATTTTCTTG
6269 CTCAAGCATTCAAAATCATAATA
1 CTCAAGC-TT-AAAAT-ATAATA
6292 CTCAAGCTTAAAATATAA
1 CTCAAGCTTAAAATATAA
6310 CCATGAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 2 0.11
23 7 0.39
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.27
Consensus pattern (20 bp):
CTCAAGCTTAAAATATAATA
Found at i:6431 original size:16 final size:16
Alignment explanation
Indices: 6410--6440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6400 TTCAAAACTT
6410 ATAAAAATAATATAAA
1 ATAAAAATAATATAAA
*
6426 ATAAAATTAATATAA
1 ATAAAAATAATATAA
6441 TTAATCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAATATAAA
Found at i:22355 original size:23 final size:23
Alignment explanation
Indices: 22325--22369 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
22315 GGTGAGCCCT
22325 GTCCAATGTGTGTCTAAGAAAAC
1 GTCCAATGTGTGTCTAAGAAAAC
22348 GTCCAATGTGTGTCTAAGAAAA
1 GTCCAATGTGTGTCTAAGAAAA
22370 GTGGTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (23 bp):
GTCCAATGTGTGTCTAAGAAAAC
Found at i:28957 original size:18 final size:18
Alignment explanation
Indices: 28934--28970 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28924 TTAGAGATAG
28934 TAAGCTTCGATTGTACTC
1 TAAGCTTCGATTGTACTC
28952 TAAGCTTCGATTGTACTC
1 TAAGCTTCGATTGTACTC
28970 T
1 T
28971 TTAATTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (18 bp):
TAAGCTTCGATTGTACTC
Found at i:32078 original size:24 final size:24
Alignment explanation
Indices: 32046--32101 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
32036 TGTAAATTAG
*
32046 GTTTTAGTTATTTC-TTTTCCTTAA
1 GTTTTAGTT-CTTCATTTTCCTTAA
*
32070 GTTTTAGTTCTTCATTTTCCTTAG
1 GTTTTAGTTCTTCATTTTCCTTAA
*
32094 GCTTTAGT
1 GTTTTAGT
32102 GTTTTGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.59
Consensus pattern (24 bp):
GTTTTAGTTCTTCATTTTCCTTAA
Found at i:33154 original size:24 final size:24
Alignment explanation
Indices: 33122--33167 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
33112 TGTAAATTAG
33122 GTTTTAGTTATTTATTTTCCTTAT
1 GTTTTAGTTATTTATTTTCCTTAT
*
33146 GTTTTAGTTCTTTATTTTCCTT
1 GTTTTAGTTATTTATTTTCCTT
33168 TGGCTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (24 bp):
GTTTTAGTTATTTATTTTCCTTAT
Found at i:33175 original size:24 final size:24
Alignment explanation
Indices: 33124--33177 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
33114 TAAATTAGGT
*
33124 TTTAGTTATTTATTTTCCTTATGT
1 TTTAGTTATTTATTTTCCTTATGC
*
33148 TTTAGTTCTTTATTTTCCTT-TGGC
1 TTTAGTTATTTATTTTCCTTAT-GC
33172 TTTAGT
1 TTTAGT
33178 GTTTTGTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTAGTTATTTATTTTCCTTATGC
Found at i:34999 original size:37 final size:37
Alignment explanation
Indices: 34949--35022 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
34939 GACTAAGGAT
34949 GTGACAACATAGAGACCAAATTCGAAAAATCTTGAAA
1 GTGACAACATAGAGACCAAATTCGAAAAATCTTGAAA
34986 GTGACAACATAGAGACCAAATTCGAAAAATCTTGAAA
1 GTGACAACATAGAGACCAAATTCGAAAAATCTTGAAA
35023 CTACCTTCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (37 bp):
GTGACAACATAGAGACCAAATTCGAAAAATCTTGAAA
Found at i:35360 original size:24 final size:24
Alignment explanation
Indices: 35319--35374 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
35309 TATAAATTAG
*
35319 GTTTTAGTTATTTCTTTTGCTTAA
1 GTTTTAGTTACTTCTTTTGCTTAA
* *
35343 GTTTTAGTT-CTTCATTTTTCTTAG
1 GTTTTAGTTACTTC-TTTTGCTTAA
*
35367 GCTTTAGT
1 GTTTTAGT
35375 GTTTTGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (24 bp):
GTTTTAGTTACTTCTTTTGCTTAA
Found at i:36422 original size:24 final size:24
Alignment explanation
Indices: 36395--36450 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
36385 TGTAAATTAG
**
36395 GTTTTAGTTATTTCTTTTCCTTAA
1 GTTTTAGTTATTAATTTTCCTTAA
* *
36419 GTTTTAGTTCTTAATTTTCCTTAG
1 GTTTTAGTTATTAATTTTCCTTAA
*
36443 GCTTTAGT
1 GTTTTAGT
36451 GTTTTATTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (24 bp):
GTTTTAGTTATTAATTTTCCTTAA
Found at i:37322 original size:24 final size:24
Alignment explanation
Indices: 37292--37355 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
37282 TGTAAATTAG
*
37292 GTTTTAGTTATTTCTTTTCCTTAA
1 GTTTTAGTTATTTATTTTCCTTAA
* *
37316 GTTTTAGTTTTTTATTTTCCTTAG
1 GTTTTAGTTATTTATTTTCCTTAA
*
37340 GCTTTAGTGT-TTTATT
1 GTTTTAGT-TATTTATT
37356 CTTTTTATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 34 0.97
25 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.64
Consensus pattern (24 bp):
GTTTTAGTTATTTATTTTCCTTAA
Found at i:38405 original size:24 final size:24
Alignment explanation
Indices: 38375--38430 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
38365 TGTAAATTAG
*
38375 GTTTTAGTTATTTCTTTTCCTTAA
1 GTTTTAGTTATTTATTTTCCTTAA
* *
38399 GTTTTAGTTCTTTATTTTCCTTAG
1 GTTTTAGTTATTTATTTTCCTTAA
*
38423 GCTTTAGT
1 GTTTTAGT
38431 GTTTTGTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.61
Consensus pattern (24 bp):
GTTTTAGTTATTTATTTTCCTTAA
Found at i:45275 original size:17 final size:18
Alignment explanation
Indices: 45237--45281 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
45227 TAAATTAACA
45237 AAAAATGCAATGACAAAAT
1 AAAAATGCAATGAC-AAAT
45256 AAAAATGCAATGAC-AAT
1 AAAAATGCAATGACAAAT
*
45273 AAATATGCA
1 AAAAATGCA
45282 TGCAAACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.44
19 14 0.56
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.18
Consensus pattern (18 bp):
AAAAATGCAATGACAAAT
Found at i:45734 original size:3 final size:3
Alignment explanation
Indices: 45726--45751 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45716 CAGTGCATTC
45726 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
45752 ATTTTCTTTC
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:62431 original size:33 final size:33
Alignment explanation
Indices: 62393--62459 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
62383 TTTTGATAGT
62393 TTCCAAAAATAGTACACTACTTAGTTTAACATA
1 TTCCAAAAATAGTACACTACTTAGTTTAACATA
62426 TTCCAAAAATAGTACACTACTTAGTTTAACATA
1 TTCCAAAAATAGTACACTACTTAGTTTAACATA
62459 T
1 T
62460 ATAACGGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (33 bp):
TTCCAAAAATAGTACACTACTTAGTTTAACATA
Found at i:63978 original size:17 final size:20
Alignment explanation
Indices: 63951--63990 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
63941 TCCACATCTT
63951 TTTCTAAACTCT-A-AACTC
1 TTTCTAAACTCTCACAACTC
63969 TTTC-AAACTCTCACAACTC
1 TTTCTAAACTCTCACAACTC
63988 TTT
1 TTT
63991 TTATTCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 5 0.25
19 8 0.40
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTCTAAACTCTCACAACTC
Found at i:71858 original size:15 final size:15
Alignment explanation
Indices: 71840--71924 Score: 80
Period size: 15 Copynumber: 5.4 Consensus size: 15
71830 TTCTGTATTA
71840 AATCAATTTAAATAG
1 AATCAATTTAAATAG
* * *
71855 AATCAAATAAAATCTAA
1 AATCAATTTAAA--TAG
71872 AATCAATTTAAATAG
1 AATCAATTTAAATAG
* * *
71887 AATCAAATAAAATCTAA
1 AATCAATTTAAA--TAG
71904 AATCAATTTAAATAG
1 AATCAATTTAAATAG
71919 AATCAA
1 AATCAA
71925 ATAAAATATA
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
15 30 0.56
17 24 0.44
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.28
Consensus pattern (15 bp):
AATCAATTTAAATAG
Found at i:71958 original size:32 final size:32
Alignment explanation
Indices: 71839--71964 Score: 198
Period size: 32 Copynumber: 3.9 Consensus size: 32
71829 ATTCTGTATT
*
71839 AAATCAATTTAAATAGAATCAAATAAAATCTA
1 AAATCAATTTAAATAGAATCAAATAAAATATA
*
71871 AAATCAATTTAAATAGAATCAAATAAAATCTA
1 AAATCAATTTAAATAGAATCAAATAAAATATA
71903 AAATCAATTTAAATAGAATCAAATAAAATATA
1 AAATCAATTTAAATAGAATCAAATAAAATATA
* * * *
71935 AAATCAATTTAATTGGAAACAAATCAAATA
1 AAATCAATTTAAATAGAATCAAATAAAATA
71965 ATATCTGTTG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 89 1.00
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.28
Consensus pattern (32 bp):
AAATCAATTTAAATAGAATCAAATAAAATATA
Found at i:71965 original size:37 final size:32
Alignment explanation
Indices: 71839--71946 Score: 207
Period size: 32 Copynumber: 3.4 Consensus size: 32
71829 ATTCTGTATT
71839 AAATCAATTTAAATAGAATCAAATAAAATCTA
1 AAATCAATTTAAATAGAATCAAATAAAATCTA
71871 AAATCAATTTAAATAGAATCAAATAAAATCTA
1 AAATCAATTTAAATAGAATCAAATAAAATCTA
*
71903 AAATCAATTTAAATAGAATCAAATAAAATATA
1 AAATCAATTTAAATAGAATCAAATAAAATCTA
71935 AAATCAATTTAA
1 AAATCAATTTAA
71947 TTGGAAACAA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 75 1.00
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (32 bp):
AAATCAATTTAAATAGAATCAAATAAAATCTA
Found at i:76026 original size:32 final size:32
Alignment explanation
Indices: 75988--76071 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
75978 ATGTGATTCA
**
75988 ATATGTAAATGATATGTGCAAGCATGGTAATG
1 ATATGTAAATGATATGTAAAAGCATGGTAATG
**
76020 ATATGTAAATGATATACAAAAGCATGGTAATG
1 ATATGTAAATGATATGTAAAAGCATGGTAATG
* *
76052 ATATATAAATGTTATGTAAA
1 ATATGTAAATGATATGTAAA
76072 TGATTTGTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (32 bp):
ATATGTAAATGATATGTAAAAGCATGGTAATG
Found at i:77107 original size:73 final size:73
Alignment explanation
Indices: 76944--77108 Score: 222
Period size: 73 Copynumber: 2.3 Consensus size: 73
76934 CCTTAGCTAA
* * * *
76944 GAATACCCTTCCAGTCTCATCTTCACTAAGGATTACCACCTAAGTCACCCTTTTGGTCTCTTCGT
1 GAATACCCTTCCAATCTCATCTTCACTAAGAATTACCACCTAAGTCACCCTTTTAGTCTATTCGT
*
77009 AGGCATAC
66 AGGCACAC
* ** * *
77017 GAATACCTTTCTGATCTCATCTTCACTAAGAATTACCACCTAAGTCATCCTTTTAGTCTATTTGT
1 GAATACCCTTCCAATCTCATCTTCACTAAGAATTACCACCTAAGTCACCCTTTTAGTCTATTCGT
77082 AGGCACAC
66 AGGCACAC
**
77090 GGGTACCCTTCCAATCTCA
1 GAATACCCTTCCAATCTCA
77109 CAAGTTCGCA
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.33
Consensus pattern (73 bp):
GAATACCCTTCCAATCTCATCTTCACTAAGAATTACCACCTAAGTCACCCTTTTAGTCTATTCGT
AGGCACAC
Found at i:78200 original size:23 final size:19
Alignment explanation
Indices: 78165--78213 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 19
78155 CAATCAAAAC
78165 AAATAAAAATAAAAATAGAA
1 AAATAAAAATAAAAAT-GAA
78185 AACATAACAAACTAAAAATGAA
1 AA-ATAA-AAA-TAAAAATGAA
78207 AAATAAA
1 AAATAAA
78214 CATGCAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.12
21 8 0.31
22 8 0.31
23 7 0.27
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (19 bp):
AAATAAAAATAAAAATGAA
Found at i:78721 original size:64 final size:64
Alignment explanation
Indices: 78620--78748 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 64
78610 TATCCTGGAT
*
78620 ACTCCCCTAATTTCGAACAATCTCACCACCTTATATCCACTTCTCTCACCTTCATTTTCTCTCC
1 ACTCCCCCAATTTCGAACAATCTCACCACCTTATATCCACTTCTCTCACCTTCATTTTCTCTCC
*
78684 ACTCCCCCAATTTCGAACAATCTCACCTCCTTATATCCACTTCTCTCACCTTCATTTTCTCTCC
1 ACTCCCCCAATTTCGAACAATCTCACCACCTTATATCCACTTCTCTCACCTTCATTTTCTCTCC
78748 A
1 A
78749 TTTACAAAGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.22, C:0.41, G:0.02, T:0.36
Consensus pattern (64 bp):
ACTCCCCCAATTTCGAACAATCTCACCACCTTATATCCACTTCTCTCACCTTCATTTTCTCTCC
Found at i:78861 original size:6 final size:6
Alignment explanation
Indices: 78850--78876 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
78840 TTCAACTCAC
78850 TTTGTT TTTGTT TTTGTT TTTGTT TTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTT
78877 ATATTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:80713 original size:15 final size:16
Alignment explanation
Indices: 80693--80723 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
80683 AATGAAAAAT
80693 AAAATTTAAAA-CAAA
1 AAAATTTAAAAGCAAA
80708 AAAATTTAAAAGCAAA
1 AAAATTTAAAAGCAAA
80724 GTCTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATTTAAAAGCAAA
Found at i:92034 original size:2 final size:2
Alignment explanation
Indices: 92027--92060 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
92017 TATTTAATGC
92027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92061 GAAGCATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93218 original size:37 final size:36
Alignment explanation
Indices: 93166--93427 Score: 245
Period size: 37 Copynumber: 7.1 Consensus size: 36
93156 TTGCATCTAA
*
93166 GAATTCGAGCTATGTGCCTAGCAGGCTTTGTGCCAGT
1 GAATTCG-GCTATGTGCCTAGCAGGCTTTGTGCCGGT
* * * *
93203 GTATTCGGTCTATGTGCCTAACAGGCTTAGTGCTGGT
1 GAATTCGG-CTATGTGCCTAGCAGGCTTTGTGCCGGT
* * * * * *
93240 GGATTTAGGCTATGTGCATAGCAAGCTATGTGTCGGT
1 -GAATTCGGCTATGTGCCTAGCAGGCTTTGTGCCGGT
* * * * **
93277 GTATTCGGACTATGTGCCTAACAGGCTTAGTACCAAT
1 GAATTCGG-CTATGTGCCTAGCAGGCTTTGTGCCGGT
* *
93314 GAATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTGGT
1 GAATTC-GGCTATGTGCCTAGCAGGCTTTGTGCCGGT
* *
93351 GAATTCGAGCTATGTGCCTAGCAGGCCTTGTGCTGGT
1 GAATTCG-GCTATGTGCCTAGCAGGCTTTGTGCCGGT
* *
93388 AAATTCGAGCTTTGTGCCTAGCAGGCTTTTGTGCCGGT
1 GAATTCG-GCTATGTGCCTAGCAGGC-TTTGTGCCGGT
93426 GA
1 GA
93428 TTAAAGAATG
Statistics
Matches: 177, Mismatches: 42, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
36 7 0.04
37 153 0.86
38 17 0.10
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (36 bp):
GAATTCGGCTATGTGCCTAGCAGGCTTTGTGCCGGT
Found at i:93394 original size:111 final size:111
Alignment explanation
Indices: 93167--93415 Score: 283
Period size: 111 Copynumber: 2.2 Consensus size: 111
93157 TGCATCTAAG
* * * *
93167 AATTCGAGCTATGTGCCTAGCAGGCTTTGTGCCAGTGTATTCGGTCTATGTGCCTAACAGGCTTA
1 AATTCGAGCTATGTGCCTAGCAGGCTTAGTACCAATGAATTCGGTCTATGTGCCTAACAGGCTTA
* * *
93232 GTGCTGGTGGATTTAGGCTATGTGCATAGCAAGCTATGTGTCGGTG
66 GTGCTGGTGAATTGAGGCTATGTGCATAGCAAGCTATGTGTCGGTA
* * **
93278 TATTCG-GACTATGTGCCTAACAGGCTTAGTACCAATGAATTCAGG-CTATGTGCCTAGTAGGCT
1 AATTCGAG-CTATGTGCCTAGCAGGCTTAGTACCAATGAATTC-GGTCTATGTGCCTAACAGGCT
* * *
93341 TTGTGCTGGTGAATTCGA-GCTATGTGCCTAGCAGGCCT-TGTG-CTGGTA
64 TAGTGCTGGTGAATT-GAGGCTATGTGCATAGCAAG-CTATGTGTC-GGTA
*
93389 AATTCGAGCTTTGTGCCTAGCAGGCTT
1 AATTCGAGCTATGTGCCTAGCAGGCTT
93416 TTGTGCCGGT
Statistics
Matches: 115, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
110 2 0.02
111 107 0.93
112 6 0.05
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (111 bp):
AATTCGAGCTATGTGCCTAGCAGGCTTAGTACCAATGAATTCGGTCTATGTGCCTAACAGGCTTA
GTGCTGGTGAATTGAGGCTATGTGCATAGCAAGCTATGTGTCGGTA
Found at i:105808 original size:31 final size:31
Alignment explanation
Indices: 105767--105825 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
105757 TTGATAATAC
* *
105767 CATTTTTATTAAT-TTAATAAATTAAAAAGTT
1 CATTTATATTAATCTTAA-AAATAAAAAAGTT
*
105798 CATTTATATTAGTCTTAAAAATAAAAAA
1 CATTTATATTAATCTTAAAAATAAAAAA
105826 TTAAAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
CATTTATATTAATCTTAAAAATAAAAAAGTT
Found at i:107144 original size:2 final size:2
Alignment explanation
Indices: 107137--107172 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
107127 TAAGTAAGTG
107137 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
107173 GAGAAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107250 original size:21 final size:22
Alignment explanation
Indices: 107209--107252 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
107199 TTGAATTTGG
*
107209 AAAAAAATTTAACTAATAAATT
1 AAAAAAATTTAACTAACAAATT
107231 AAAAAAA-TTAAGCT-ACAAATT
1 AAAAAAATTTAA-CTAACAAATT
107252 A
1 A
107253 TGAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAAAATTTAACTAACAAATT
Found at i:107988 original size:26 final size:26
Alignment explanation
Indices: 107946--107999 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
107936 TTATTTTTAA
* *
107946 ATTTTTTTGTAAAAATTATTTATTTT
1 ATTTTTTTGTAAAAATTAATAATTTT
*
107972 ATTTTATTT-TAATAATTAATAATTTT
1 ATTTT-TTTGTAAAAATTAATAATTTT
107998 AT
1 AT
108000 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTTTTTGTAAAAATTAATAATTTT
Found at i:110844 original size:2 final size:2
Alignment explanation
Indices: 110839--110871 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
110829 ACACACACAC
110839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
110872 CATACATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111098 original size:19 final size:20
Alignment explanation
Indices: 111074--111113 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
111064 GTTAGCGAAT
111074 AAATATAAATATAAAA-ATA
1 AAATATAAATATAAAATATA
**
111093 AAATATTTATATAAAATATA
1 AAATATAAATATAAAATATA
111113 A
1 A
111114 TATTTGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAAATATAAAATATA
Found at i:111115 original size:18 final size:19
Alignment explanation
Indices: 111082--111118 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
111072 ATAAATATAA
111082 ATATAAAAATAAAATATTT
1 ATATAAAAATAAAATATTT
*
111101 ATAT-AAAATATAATATTT
1 ATATAAAAATAAAATATTT
111119 GAACAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAAAAATAAAATATTT
Found at i:111126 original size:18 final size:18
Alignment explanation
Indices: 111083--111129 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
111073 TAAATATAAA
111083 TATA-AAAATAAAATATT
1 TATACAAAATAAAATATT
* *
111100 TATATAAAATATAATATT
1 TATACAAAATAAAATATT
111118 TGA-ACAAAATAA
1 T-ATACAAAATAA
111130 TATAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 4 0.16
18 20 0.80
19 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
TATACAAAATAAAATATT
Found at i:111149 original size:50 final size:50
Alignment explanation
Indices: 111095--111211 Score: 155
Period size: 50 Copynumber: 2.3 Consensus size: 50
111085 TAAAAATAAA
* * * *
111095 ATATTTATATAAAATATAATATTTGAACAAAAT-AATATAAATAAATATTT
1 ATATTTATATAAAACATAAGATGTAAACAAAATAAAT-TAAATAAATATTT
* *
111145 ATATTTATGTAAAACATCAGATGTAAACAAAATAAATTAAATAAATATTT
1 ATATTTATATAAAACATAAGATGTAAACAAAATAAATTAAATAAATATTT
*
111195 ATATTTATTTAAAACAT
1 ATATTTATATAAAACAT
111212 TTGTTGAGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 56 0.95
51 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (50 bp):
ATATTTATATAAAACATAAGATGTAAACAAAATAAATTAAATAAATATTT
Found at i:112917 original size:61 final size:62
Alignment explanation
Indices: 112801--112920 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 62
112791 TTTAAAAAGT
* * * *
112801 CTTTATTTGAACACTTTTAAAAATGTTCTATCCTTATTTGATCACTTTCGAAAAGATTAAAC
1 CTTTATTTGAACACTTTTAAAAAGGTTCTATCATTATTTGAGCACTTTCAAAAAGATTAAAC
* *
112863 CTTTATTTGAACA-TTTTAAAAAGGTTTTAT-ATTCATTTGAGCA-TTTTAATAAAGATTA
1 CTTTATTTGAACACTTTTAAAAAGGTTCTATCATT-ATTTGAGCACTTTCAA-AAAGATTA
112921 GGCCATTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
60 6 0.12
61 31 0.62
62 13 0.26
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (62 bp):
CTTTATTTGAACACTTTTAAAAAGGTTCTATCATTATTTGAGCACTTTCAAAAAGATTAAAC
Found at i:112930 original size:61 final size:61
Alignment explanation
Indices: 112803--112940 Score: 138
Period size: 61 Copynumber: 2.2 Consensus size: 61
112793 TAAAAAGTCT
* * * * *
112803 TTATTTGAACACTTTTAAAAATGTTCTATCCTTATTTGATCACTTTCGAAAAGATTAAACCT
1 TTATTTGAACA-TTTTAAAAAGGTTCTATCATTATTTGAGCACTTTCAAAAAGATTAAACCA
* * **
112865 TTATTTGAACATTTTAAAAAGGTTTTAT-ATTCATTTGAGCA-TTTTAATAAAGATTAGGCCA
1 TTATTTGAACATTTTAAAAAGGTTCTATCATT-ATTTGAGCACTTTCAA-AAAGATTAAACCA
112926 TTATTT-AACCATTTT
1 TTATTTGAA-CATTTT
112941 GAAATATTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
60 8 0.12
61 45 0.70
62 11 0.17
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (61 bp):
TTATTTGAACATTTTAAAAAGGTTCTATCATTATTTGAGCACTTTCAAAAAGATTAAACCA
Found at i:113463 original size:91 final size:92
Alignment explanation
Indices: 113341--113507 Score: 277
Period size: 91 Copynumber: 1.8 Consensus size: 92
113331 AATAACTTAT
113341 GCAACTTTATTAAATATGAATTATTAGATTTAGTATTTTTATGGTAAATA-TTTTTTAAATGACT
1 GCAACTTTATTAAATATGAATTATTAGATTTAGTATTTTTATGGTAAATATTTTTTTAAATGACT
113405 GATTGAATAAACAAAAAATTAATTTAG
66 GATTGAATAAACAAAAAATTAATTTAG
*
113432 GCAACTTTATTAAATAT-AATTGATT-GAATTTAGTATTTTTATGGTAAATATTTTTTTACATGA
1 GCAACTTTATTAAATATGAATT-ATTAG-ATTTAGTATTTTTATGGTAAATATTTTTTTAAATGA
*
113495 TTGATTGAATAAA
64 CTGATTGAATAAA
113508 ATAGAAGCTT
Statistics
Matches: 71, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
90 5 0.07
91 43 0.61
92 23 0.32
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (92 bp):
GCAACTTTATTAAATATGAATTATTAGATTTAGTATTTTTATGGTAAATATTTTTTTAAATGACT
GATTGAATAAACAAAAAATTAATTTAG
Found at i:114495 original size:12 final size:12
Alignment explanation
Indices: 114480--114553 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
114470 AAATAACATC
*
114480 AAAACAATTAAA
1 AAAACAATCAAA
114492 AAAACAATCAAA
1 AAAACAATCAAA
* *
114504 ATAGCAA-CAAA
1 AAAACAATCAAA
*
114515 AATAATAA--AAA
1 AA-AACAATCAAA
114526 AATAACAA-CAAA
1 AA-AACAATCAAA
114538 AATAACAAT-AAA
1 AA-AACAATCAAA
114550 AAAA
1 AAAA
114554 GCACCAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
11 17 0.33
12 35 0.67
ACGTcount: A:0.76, C:0.11, G:0.01, T:0.12
Consensus pattern (12 bp):
AAAACAATCAAA
Found at i:114515 original size:23 final size:24
Alignment explanation
Indices: 114489--114562 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 24
114479 CAAAACAATT
*
114489 AAAAA-AACAATCAAAATAGCAAC
1 AAAAATAACAATAAAAATAGCAAC
* *
114512 AAAAATAATAA-AAAAATAACAAC
1 AAAAATAACAATAAAAATAGCAAC
* *
114535 AAAAATAACAATAAAAAAAGCACC
1 AAAAATAACAATAAAAATAGCAAC
114559 AAAA
1 AAAA
114563 TAGTAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 25 0.60
24 17 0.40
ACGTcount: A:0.74, C:0.14, G:0.03, T:0.09
Consensus pattern (24 bp):
AAAAATAACAATAAAAATAGCAAC
Found at i:114524 original size:32 final size:33
Alignment explanation
Indices: 114448--114527 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 33
114438 AAAGATAGCT
* *
114448 AAATAATAATAAAAACGCATAAAAATAACATCAA
1 AAATAATAA-AAAAACGAATAAAAATAACAACAA
* * *
114482 AACA-ATTAAAAAAAC-AATCAAAATAGCAACAA
1 AA-ATAATAAAAAAACGAATAAAAATAACAACAA
114514 AAATAATAAAAAAA
1 AAATAATAAAAAAA
114528 TAACAACAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
31 1 0.03
32 24 0.63
33 6 0.16
34 6 0.16
35 1 0.03
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.15
Consensus pattern (33 bp):
AAATAATAAAAAAACGAATAAAAATAACAACAA
Found at i:115142 original size:12 final size:11
Alignment explanation
Indices: 115134--115196 Score: 63
Period size: 12 Copynumber: 5.4 Consensus size: 11
115124 CAAAACAATT
*
115134 AAAATAACAATC
1 AAAATAACAA-A
*
115146 AAAATAGCAACA
1 AAAATAACAA-A
*
115158 AAAATAATAAA
1 AAAATAACAAA
115169 AAAATAACAACA
1 AAAATAACAA-A
115181 AAAATAACAATA
1 AAAATAACAA-A
115193 AAAA
1 AAAA
115197 AAGCACCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 10 0.23
12 33 0.77
ACGTcount: A:0.75, C:0.11, G:0.02, T:0.13
Consensus pattern (11 bp):
AAAATAACAAA
Found at i:115172 original size:23 final size:23
Alignment explanation
Indices: 115146--115222 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
115136 AATAACAATC
115146 AAAATAGCAACAAAAATAATAAA
1 AAAATAGCAACAAAAATAATAAA
* *
115169 AAAATAACAACAAAAATAACAATA
1 AAAATAGCAACAAAAATAATAA-A
* * *
115193 AAAAAAGC-ACCAAAATAGT-AA
1 AAAATAGCAACAAAAATAATAAA
115214 AAAATAGCA
1 AAAATAGCA
115223 CTAAAACAGC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 8 0.18
22 1 0.02
23 28 0.64
24 7 0.16
ACGTcount: A:0.71, C:0.12, G:0.05, T:0.12
Consensus pattern (23 bp):
AAAATAGCAACAAAAATAATAAA
Found at i:115216 original size:645 final size:644
Alignment explanation
Indices: 113986--115275 Score: 2472
Period size: 645 Copynumber: 2.0 Consensus size: 644
113976 TCAAACTTCT
*
113986 CATGCCAACAAATAGTCTGACTTTCTTTTTTTTGAATTATAATTACAATATAAAATCTGAAAAAT
1 CATGCCAACAAATAGTCTGACTTTCTTTTTTTTGAATTAAAATTACAATATAAAATCTGAAAAAT
*
114051 AAGTATATTTAACGTAACTAGTAGAGTTGATCGTGGGTCAGGTCAGGTCGGGCTTCAACAAATTT
66 AAGTACATTTAACGTAACTAGTAGAGTTGATCGTGGGTCAGGTCAGGTCGGGCTTCAACAAATTT
* *
114116 TTAGGTTTAATTGCTAGGTCCAAGTCTGGCCCGGTCTAAAAAATAGGTTTAAAATTTTGTTTAAA
131 TTAGGCTTAATTGCTAGGTCCAAGTCTGGCCCGATCTAAAAAATAGGTTTAAAATTTTGTTTAAA
114181 CCCGACCCGAATCATAGAAGTCAAGCCCGAGCCTGACTCGATCCAACACATATTAATTTTTTTAG
196 CCCGACCCGAATCATAGAAGTCAAGCCCGAGCCTGACTCGATCCAACACATATTAATTTTTTTAG
114246 ATTATTTTATTATGTACAACAAATTTAAAAATATATAATATATCAAATACGCTTAAAAACTTTAA
261 ATTATTTTATTATGTACAACAAATTTAAAAATATATAATATATCAAATACGCTTAAAAACTTTAA
114311 AACAAACATTAAAAAATAAACAAATTAAAAATACATTAAATTTTTTTTATATTAAGATAGTTACA
326 AACAAACATTAAAAAATAAACAAATTAAAAATACATTAAATTTTTTTTATATTAAGATAGTTACA
114376 AATAAAGTAATAGAAAAATTAACAATAAAACATAAGTTCTATAATATTCAAATAATATTAAAAAA
391 AATAAAGTAATAGAAAAATTAACAATAAAACATAAGTTCTATAATATTCAAATAATATTAAAAAA
114441 GATAGCTAAATAATAATAAAAACGCATAAAAATAACATCAAAACAATTAAAAAAACAATCAAAAT
456 GATAGCTAAATAATAATAAAAACGCATAAAAATAACATCAAAACAATTAAAAAAACAATCAAAAT
114506 AGCAACAAAAATAATAAAAAAATAACAACAAAAATAACAATAAAAAAAGCACCAAAATAGTAAAA
521 AGCAACAAAAATAATAAAAAAATAACAACAAAAATAACAATAAAAAAAGCACCAAAATAGTAAAA
* *
114571 ATTAGCACTAAAACAGCAACTAAAACATTAAAAAAACATCAAAACAGTAAAAACACAACA
586 AATAGCACTAAAACAGCAACTAAAACATTAAAAAAA-ACCAAAACAGTAAAAACACAACA
114631 CATGCCAACAAATAGTCTGACTTTCTTTTTTTTGAATTAAAATTACAATATAAAATCTGAAAAAT
1 CATGCCAACAAATAGTCTGACTTTCTTTTTTTTGAATTAAAATTACAATATAAAATCTGAAAAAT
*
114696 AAGTACGTTTAACGTAACTAGTAGAGTTGATCGTGGGTCAGGTCAGGTCGGGCTTCAACAAATTT
66 AAGTACATTTAACGTAACTAGTAGAGTTGATCGTGGGTCAGGTCAGGTCGGGCTTCAACAAATTT
*
114761 TTAGGCTTAATTGCTAGGTCCAAGTCTGGCCCGATCTAAAAAATGGGTTTAAAATTTTGTTTAAA
131 TTAGGCTTAATTGCTAGGTCCAAGTCTGGCCCGATCTAAAAAATAGGTTTAAAATTTTGTTTAAA
*
114826 CCCGACCCGAATCATAGAAGTCAAGCCCGAGCCTGACTCGATCCGACACATATTAATTTTTTTAG
196 CCCGACCCGAATCATAGAAGTCAAGCCCGAGCCTGACTCGATCCAACACATATTAATTTTTTTAG
114891 ATTATTTTATTATGTACAACAAATTTAAAAATATATAATATATCAAATACGCTTAAAAACTTTAA
261 ATTATTTTATTATGTACAACAAATTTAAAAATATATAATATATCAAATACGCTTAAAAACTTTAA
114956 AACAAACATTAAAAAATAAACAAATTAAAAATACATTAAATTTTTTTTATATTAAGATAGTTACA
326 AACAAACATTAAAAAATAAACAAATTAAAAATACATTAAATTTTTTTTATATTAAGATAGTTACA
115021 AATAAAGTAATAGAAAAATTAACAATAAAACATAAGTTCTATAATATTCAAATAATATTAAAAAA
391 AATAAAGTAATAGAAAAATTAACAATAAAACATAAGTTCTATAATATTCAAATAATATTAAAAAA
*
115086 GATAGCTAAATAATAATAAAAACGCATAAAAATAACATCAAAACAATTAAAATAACAATCAAAAT
456 GATAGCTAAATAATAATAAAAACGCATAAAAATAACATCAAAACAATTAAAAAAACAATCAAAAT
115151 AGCAACAAAAATAATAAAAAAATAACAACAAAAATAACAATAAAAAAAGCACCAAAATAGTAAAA
521 AGCAACAAAAATAATAAAAAAATAACAACAAAAATAACAATAAAAAAAGCACCAAAATAGTAAAA
*
115216 AATAGCACTAAAACAGCAATTAAAACATTAAAAAAAACCAAAACAGTAAAAACACAACA
586 AATAGCACTAAAACAGCAACTAAAACATTAAAAAAAACCAAAACAGTAAAAACACAACA
115275 C
1 C
115276 CAAAACAGCA
Statistics
Matches: 634, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
644 23 0.04
645 611 0.96
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (644 bp):
CATGCCAACAAATAGTCTGACTTTCTTTTTTTTGAATTAAAATTACAATATAAAATCTGAAAAAT
AAGTACATTTAACGTAACTAGTAGAGTTGATCGTGGGTCAGGTCAGGTCGGGCTTCAACAAATTT
TTAGGCTTAATTGCTAGGTCCAAGTCTGGCCCGATCTAAAAAATAGGTTTAAAATTTTGTTTAAA
CCCGACCCGAATCATAGAAGTCAAGCCCGAGCCTGACTCGATCCAACACATATTAATTTTTTTAG
ATTATTTTATTATGTACAACAAATTTAAAAATATATAATATATCAAATACGCTTAAAAACTTTAA
AACAAACATTAAAAAATAAACAAATTAAAAATACATTAAATTTTTTTTATATTAAGATAGTTACA
AATAAAGTAATAGAAAAATTAACAATAAAACATAAGTTCTATAATATTCAAATAATATTAAAAAA
GATAGCTAAATAATAATAAAAACGCATAAAAATAACATCAAAACAATTAAAAAAACAATCAAAAT
AGCAACAAAAATAATAAAAAAATAACAACAAAAATAACAATAAAAAAAGCACCAAAATAGTAAAA
AATAGCACTAAAACAGCAACTAAAACATTAAAAAAAACCAAAACAGTAAAAACACAACA
Found at i:115258 original size:51 final size:53
Alignment explanation
Indices: 115186--115286 Score: 134
Period size: 51 Copynumber: 1.9 Consensus size: 53
115176 CAACAAAAAT
* * * *
115186 AACAATAAAAAAAGCACCAAAATAGTAAAAA-ATAGCACTAAAACAGCAATTAA
1 AACAATAAAAAAA-CACCAAAACAGTAAAAACACAACACCAAAACAGCAATTAA
*
115239 AACATTAAAAAAA-ACCAAAACAGTAAAAACACAACACCAAAACAGCAA
1 AACAATAAAAAAACACCAAAACAGTAAAAACACAACACCAAAACAGCAA
115287 AAAAAAAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 15 0.36
52 15 0.36
53 12 0.29
ACGTcount: A:0.65, C:0.19, G:0.06, T:0.10
Consensus pattern (53 bp):
AACAATAAAAAAACACCAAAACAGTAAAAACACAACACCAAAACAGCAATTAA
Found at i:115277 original size:22 final size:21
Alignment explanation
Indices: 115245--115303 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 21
115235 TTAAAACATT
*
115245 AAAAAAAACCAAAACAGTAAA
1 AAAAAAAACCAAAACAGCAAA
* *
115266 AACACAACACCAAAACAGCAAA
1 AA-AAAAAACCAAAACAGCAAA
115288 AAAAAAAACCAAAACA
1 AAAAAAAACCAAAACA
115304 ACAATATAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.73, C:0.22, G:0.03, T:0.02
Consensus pattern (21 bp):
AAAAAAAACCAAAACAGCAAA
Found at i:116608 original size:20 final size:22
Alignment explanation
Indices: 116562--116608 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
116552 ATATTCTGTA
**
116562 TTTAATTTTTATTAATATAATG
1 TTTAATTTTTATTAATATAAAC
*
116584 ATTAA-TTTTA-TAATATAAAC
1 TTTAATTTTTATTAATATAAAC
116604 TTTAA
1 TTTAA
116609 CACTTATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 12 0.57
21 5 0.24
22 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAATTTTTATTAATATAAAC
Found at i:117122 original size:59 final size:56
Alignment explanation
Indices: 117044--117231 Score: 171
Period size: 59 Copynumber: 3.2 Consensus size: 56
117034 CTAATATAAT
* * *
117044 ATTTGGTATTTGAATTTGACATTTTTTTCTTAATTTGATACTTAAA-TTTTTTTTACTCA
1 ATTTGGTACTTGAACTTGACA-TTTTTTC-TAATTTGATACTTAAACTTTTTTAT-C-CA
* * *
117103 ATTTGTTACTTGAACTTGACACTTTTTCCTAAGTTGATACTTAAACTTTTTTATCCA
1 ATTTGGTACTTGAACTTGACA-TTTTTTCTAATTTGATACTTAAACTTTTTTATCCA
* * * * * *
117160 ATTTGGTACATGAACTTGGAAATTTTTTCTAATTTGGTACCTAAGCCTTTTTTTAAATTCA
1 ATTTGGTACTTGAACTT-GACATTTTTTCTAATTTGATACTTAA-AC-TTTTTT--ATCCA
117221 ATTTGGTACTT
1 ATTTGGTACTT
117232 AAATTTATTA
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
57 35 0.33
58 20 0.19
59 37 0.35
61 14 0.13
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.51
Consensus pattern (56 bp):
ATTTGGTACTTGAACTTGACATTTTTTCTAATTTGATACTTAAACTTTTTTATCCA
Found at i:117186 original size:57 final size:58
Alignment explanation
Indices: 117044--117191 Score: 149
Period size: 57 Copynumber: 2.6 Consensus size: 58
117034 CTAATATAAT
** * * * * *
117044 ATTTGGTATTTGAATTTGACATTTTTTTCTTAATTTGATACTTAAATTTTTTTTACTCA
1 ATTTGGTACATGAACTTGACA-ATTTTTCCTAAGTTGATACTTAAATTTTTTATACTCA
* * *
117103 ATTTGTTACTTGAACTTGACACTTTTTCCTAAGTTGATACTTAAACTTTTTTAT-C-CA
1 ATTTGGTACATGAACTTGACAATTTTTCCTAAGTTGATACTTAAA-TTTTTTATACTCA
*
117160 ATTTGGTACATGAACTTGGA-AATTTTTTCTAA
1 ATTTGGTACATGAACTT-GACAATTTTTCCTAA
117192 TTTGGTACCT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
57 27 0.36
58 24 0.32
59 25 0.33
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (58 bp):
ATTTGGTACATGAACTTGACAATTTTTCCTAAGTTGATACTTAAATTTTTTATACTCA
Found at i:117187 original size:58 final size:58
Alignment explanation
Indices: 117066--117188 Score: 151
Period size: 58 Copynumber: 2.1 Consensus size: 58
117056 AATTTGACAT
* * * * * *
117066 TTTTTTCTTAATTTGATACTTAAATTTTTTTTACTCAATTTGTTACTTGAACTTGACA
1 TTTTTTCCTAAGTTGATACTTAAATTTTTTATACTCAATTTGGTACATGAACTTGAAA
*
117124 CTTTTTCCTAAGTTGATACTTAAACTTTTTTAT-C-CAATTTGGTACATGAACTTGGAAA
1 TTTTTTCCTAAGTTGATACTTAAA-TTTTTTATACTCAATTTGGTACATGAACTT-GAAA
117182 TTTTTTC
1 TTTTTTC
117189 TAATTTGGTA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
57 17 0.31
58 31 0.56
59 7 0.13
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (58 bp):
TTTTTTCCTAAGTTGATACTTAAATTTTTTATACTCAATTTGGTACATGAACTTGAAA
Found at i:117211 original size:58 final size:57
Alignment explanation
Indices: 117044--117212 Score: 135
Period size: 57 Copynumber: 2.9 Consensus size: 57
117034 CTAATATAAT
** * * * * * *
117044 ATTTGGTATTTGAATTTGACATTTTTTTCTTAATTTGATACTTAAATTTTTTTTACTCA
1 ATTTGGTACATGAACTTGACA-ATTTTTCCTAAGTTGATACCTAAA-CTTTTTTACTCA
* * * *
117103 ATTTGTTACTTGAACTTGACACTTTTTCCTAAGTTGATACTTAAACTTTTTTA-TCCA
1 ATTTGGTACATGAACTTGACAATTTTTCCTAAGTTGATACCTAAACTTTTTTACT-CA
* * * *
117160 ATTTGGTACATGAACTTGGA-AATTTTTTCTAATTTGGTACCTAAGCCTTTTTT
1 ATTTGGTACATGAACTT-GACAATTTTTCCTAAGTTGATACCTAA-ACTTTTTT
117213 TAAATTCAAT
Statistics
Matches: 92, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
56 1 0.01
57 43 0.47
58 30 0.33
59 18 0.20
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (57 bp):
ATTTGGTACATGAACTTGACAATTTTTCCTAAGTTGATACCTAAACTTTTTTACTCA
Found at i:117487 original size:31 final size:31
Alignment explanation
Indices: 117431--117660 Score: 136
Period size: 31 Copynumber: 7.5 Consensus size: 31
117421 AAACTCCAAA
* * ** *
117431 AAGTTTAAGTGCCAACTTAATAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTATC
* *
117462 AAGTTTAGGTACCAAATTAGGAAAAAGAATC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTATC
* * **
117493 AAGTTCAACTACCAAATT-GGACCTCAA--A--
1 AAGTTTAAGTACCAAATTAGGA--AAAAGTATC
* ** * *
117521 AAGTTTAAGTACCAACTTAATAAAAAATGTC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTATC
* *
117552 AAGTTTAGGTACCAAATTAGGAAAATGTATC
1 AAGTTTAAGTACCAAATTAGGAAAAAGTATC
*
117583 AAGTTTAAGTACCAAATT-GGACAAAA--A-A
1 AAGTTTAAGTACCAAATTAGGA-AAAAGTATC
* *
117611 AAGTTTAAGTATCAAATTAGAAAAAAAAGTATC
1 AAGTTTAAGTACCAAATTAG--GAAAAAGTATC
* * *
117644 AAATTCAAGTACTAAAT
1 AAGTTTAAGTACCAAAT
117661 GTTATATTAA
Statistics
Matches: 148, Mismatches: 37, Indels: 26
0.70 0.18 0.12
Matches are distributed among these distances:
27 2 0.01
28 32 0.22
29 3 0.02
30 11 0.07
31 84 0.57
32 3 0.02
33 13 0.09
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGGAAAAAGTATC
Found at i:117497 original size:90 final size:90
Alignment explanation
Indices: 117393--117598 Score: 297
Period size: 90 Copynumber: 2.3 Consensus size: 90
117383 ATTAAAAAAA
* * *
117393 AAAAAGAGTCAAGTTCAGGTACCAAAATAAA-CTCCAAAAAGTTTAAGTGCCAACTTAATAAAAA
1 AAAAAGAATCAAGTTCAAGTACCAAAATAAACCT-CAAAAAGTTTAAGTACCAACTTAATAAAAA
*
117457 GTGTCAAGTTTAGGTACCAAATTAGG
65 ATGTCAAGTTTAGGTACCAAATTAGG
* * **
117483 AAAAAGAATCAAGTTCAACTACCAAATTGGACCTCAAAAAGTTTAAGTACCAACTTAATAAAAAA
1 AAAAAGAATCAAGTTCAAGTACCAAAATAAACCTCAAAAAGTTTAAGTACCAACTTAATAAAAAA
117548 TGTCAAGTTTAGGTACCAAATTAGG
66 TGTCAAGTTTAGGTACCAAATTAGG
* * *
117573 AAAATGTATCAAGTTTAAGTACCAAA
1 AAAAAGAATCAAGTTCAAGTACCAAA
117599 TTGGACAAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 101 0.98
91 2 0.02
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (90 bp):
AAAAAGAATCAAGTTCAAGTACCAAAATAAACCTCAAAAAGTTTAAGTACCAACTTAATAAAAAA
TGTCAAGTTTAGGTACCAAATTAGG
Found at i:117599 original size:90 final size:90
Alignment explanation
Indices: 117427--117621 Score: 309
Period size: 90 Copynumber: 2.2 Consensus size: 90
117417 AAATAAACTC
* *
117427 CAAAAAGTTTAAGTGCCAACTTAATAAAAAGTGTCAAGTTTAGGTACCAAATTAGGAAAAAGAAT
1 CAAAAAGTTTAAGTACCAACTTAATAAAAAATGTCAAGTTTAGGTACCAAATTAGGAAAAAGAAT
**
117492 CAAGTTCAACTACCAAATTGGACCT
66 CAAGTTCAACTACCAAATTGGACAA
* *
117517 CAAAAAGTTTAAGTACCAACTTAATAAAAAATGTCAAGTTTAGGTACCAAATTAGGAAAATGTAT
1 CAAAAAGTTTAAGTACCAACTTAATAAAAAATGTCAAGTTTAGGTACCAAATTAGGAAAAAGAAT
* *
117582 CAAGTTTAAGTACCAAATTGGACAA
66 CAAGTTCAACTACCAAATTGGACAA
*
117607 AAAAAAGTTTAAGTA
1 CAAAAAGTTTAAGTA
117622 TCAAATTAGA
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 96 1.00
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.26
Consensus pattern (90 bp):
CAAAAAGTTTAAGTACCAACTTAATAAAAAATGTCAAGTTTAGGTACCAAATTAGGAAAAAGAAT
CAAGTTCAACTACCAAATTGGACAA
Found at i:119822 original size:9 final size:8
Alignment explanation
Indices: 119808--119864 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
119798 CGTTGAGTTC
119808 AAAAATTA
1 AAAAATTA
119816 TAAAAATTA
1 -AAAAATTA
*
119825 AAAAGATTC
1 AAAA-ATTA
*
119834 AAATATGTAA
1 AAAAAT-T-A
*
119844 AAAAATTC
1 AAAAATTA
119852 AAAAATTA
1 AAAAATTA
119860 AAAAA
1 AAAAA
119865 CACAAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
8 18 0.46
9 16 0.41
10 5 0.13
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (8 bp):
AAAAATTA
Found at i:119846 original size:18 final size:17
Alignment explanation
Indices: 119817--119864 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
119807 CAAAAATTAT
*
119817 AAAAATTAAAAAGATTC
1 AAAAATTAAAAAAATTC
*
119834 AAATATGTAAAAAAATTC
1 AAAAAT-TAAAAAAATTC
119852 AAAAATTAAAAAA
1 AAAAATTAAAAAA
119865 CACAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAAATTAAAAAAATTC
Found at i:119872 original size:44 final size:45
Alignment explanation
Indices: 119805--119891 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 45
119795 ATTCGTTGAG
** * * *
119805 TTCAAAAATTATAAAAATTAAAAAGATTCA-AATATGTAAAAAAA
1 TTCAAAAATTATAAAAAACAAAAAAATTAATAATATATAAAAAAA
119849 TTCAAAAATTA-AAAAACACAAAAAAATTAATAATATATAAAAA
1 TTCAAAAATTATAAAAA-ACAAAAAAATTAATAATATATAAAAA
119892 TGTAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 5 0.14
44 20 0.56
45 11 0.31
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (45 bp):
TTCAAAAATTATAAAAAACAAAAAAATTAATAATATATAAAAAAA
Found at i:119890 original size:17 final size:17
Alignment explanation
Indices: 119870--119909 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
119860 AAAAACACAA
*
119870 AAAAAT-TAATAATATAT
1 AAAAATGTAAAAATA-AT
119887 AAAAATGTAAAAATAAT
1 AAAAATGTAAAAATAAT
119904 AAAAAT
1 AAAAAT
119910 ATTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAAATGTAAAAATAAT
Found at i:119890 original size:18 final size:17
Alignment explanation
Indices: 119869--119916 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
119859 AAAAAACACA
119869 AAAAAATTAATAAT-AT
1 AAAAAATTAATAATAAT
*
119885 ATAAAAATGTAAAAATAAT
1 A-AAAAAT-TAATAATAAT
119904 AAAAATATTAATA
1 AAAAA-ATTAATA
119917 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.04
17 6 0.23
18 14 0.54
19 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAAAATTAATAATAAT
Found at i:119926 original size:36 final size:35
Alignment explanation
Indices: 119852--119942 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 35
119842 AAAAAAATTC
*
119852 AAAAATTAAAAA-ACACAAAAAAATTAATAATATAT
1 AAAAATTAAAAATA-ATAAAAAAATTAATAATATAT
* * *
119887 AAAAATGTAAAAATAATAAAAATATTAAT-ATTTTT
1 AAAAAT-TAAAAATAATAAAAAAATTAATAATATAT
* *
119922 TAAAATATAAAATTAATAAAA
1 AAAAAT-TAAAAATAATAAAA
119943 TATAAAACAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
35 28 0.60
36 18 0.38
37 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (35 bp):
AAAAATTAAAAATAATAAAAAAATTAATAATATAT
Found at i:121487 original size:28 final size:29
Alignment explanation
Indices: 121455--121511 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
121445 AAATTTAAAT
*
121455 TAATTATAAAATGA-T-TTTTTTAATTTCA
1 TAATTATAAAATAACTATTTTTT-ATTTCA
*
121483 TAATTATTAAATAACTATTTTTTATTTCA
1 TAATTATAAAATAACTATTTTTTATTTCA
121512 AAAATATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.48
29 7 0.28
30 6 0.24
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (29 bp):
TAATTATAAAATAACTATTTTTTATTTCA
Found at i:121526 original size:30 final size:30
Alignment explanation
Indices: 121470--121526 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
121460 ATAAAATGAT
* * *
121470 TTTTTTAATTTCATAATTATTAAATAACTA
1 TTTTTTAATTTCAAAAATATCAAATAACTA
121500 TTTTTT-ATTTCAAAAATATCATAATAA
1 TTTTTTAATTTCAAAAATATCA-AATAA
121527 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTTTTAATTTCAAAAATATCAAATAACTA
Found at i:121532 original size:29 final size:28
Alignment explanation
Indices: 121463--121532 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
121453 ATTAATTATA
* * * *
121463 AAATGATTTTTTTAATTTCATAATTATT
1 AAATAATTTTTTTAATTTCAAAAATATC
121491 AAATAACTATTTTTT-ATTTCAAAAATATC
1 AAATAA-T-TTTTTTAATTTCAAAAATATC
121520 ATAATAATTTTTT
1 A-AATAATTTTTT
121533 AAAAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 10 0.29
29 14 0.40
30 11 0.31
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (28 bp):
AAATAATTTTTTTAATTTCAAAAATATC
Found at i:121759 original size:25 final size:24
Alignment explanation
Indices: 121728--121786 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
121718 TCTACAAACA
121728 TTTAATATATATATTTTT-ATAAAT
1 TTTAATATATATATTTTTGA-AAAT
* * *
121752 TATTAATATTTCTGTTTTTGAAAAT
1 T-TTAATATATATATTTTTGAAAAT
121777 TTTAATATAT
1 TTTAATATAT
121787 TGAATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 9 0.31
25 19 0.66
26 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (24 bp):
TTTAATATATATATTTTTGAAAAT
Found at i:121821 original size:20 final size:19
Alignment explanation
Indices: 121792--121838 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
121782 TATATTGAAT
*
121792 TTTTTTATAACTTTTAGT-AA
1 TTTTTAATAACTTTT--TCAA
*
121812 TTTTTAATAAGTTTTTCAA
1 TTTTTAATAACTTTTTCAA
121831 TTTTTAAT
1 TTTTTAAT
121839 TTTTTAGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 10 0.42
20 13 0.54
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTTAATAACTTTTTCAA
Found at i:121970 original size:19 final size:18
Alignment explanation
Indices: 121941--121980 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
121931 CTAGATGTAT
121941 ATTTTTAATTTTAAAATAAA
1 ATTTTTAA-TTTAAAA-AAA
121961 ATTTTT-ATTTAAAAAAA
1 ATTTTTAATTTAAAAAAA
121978 ATT
1 ATT
121981 AATTTTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 7 0.35
19 1 0.05
20 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTTAATTTAAAAAAA
Found at i:122089 original size:17 final size:17
Alignment explanation
Indices: 122067--122144 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
122057 CCAACAGGAT
122067 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
122084 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
122101 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
122117 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
122135 TTAAAGTTTA
1 TTAAA-TTTA
122145 AAACTATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 4 0.08
17 38 0.76
18 8 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:122109 original size:34 final size:34
Alignment explanation
Indices: 122065--122144 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 34
122055 ACCCAACAGG
* *
122065 ATTTAAATTTATTTTAAAA-TTAAATTTATTTTAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATTATAA
*
122099 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATTATAA
122133 ATTTAAAGTTTA
1 ATTTAAA-TTTA
122145 AAACTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 6 0.15
34 30 0.75
35 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATTATAA
Found at i:122146 original size:7 final size:6
Alignment explanation
Indices: 122065--122146 Score: 57
Period size: 6 Copynumber: 14.2 Consensus size: 6
122055 ACCCAACAGG
* * * *
122065 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
122110 CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA AGTTTAA A
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA A-TTTAA A
122147 ACTATTTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 34 0.59
7 9 0.16
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:122152 original size:24 final size:23
Alignment explanation
Indices: 122111--122157 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
122101 TTAAATTTAC
**
122111 TTAAAATTTAAATTTATTATAAAT
1 TTAAAATTTAAAACTATT-TAAAT
*
122135 TTAAAGTTTAAAACTATTTAAAT
1 TTAAAATTTAAAACTATTTAAAT
122158 CAAATCCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAAATTTAAAACTATTTAAAT
Found at i:123842 original size:29 final size:29
Alignment explanation
Indices: 123801--124086 Score: 210
Period size: 29 Copynumber: 9.7 Consensus size: 29
123791 AAGGTCCCTA
*
123801 AACTGTCCGAAAATTCCATGTTT-ACCCTCG
1 AACT-TCCAAAAATTCCAT-TTTGACCCTCG
* *
123831 AACTTCCAAAAATCCCATTTTTGACCC-CAA
1 AACTTCCAAAAATTCCA-TTTTGACCCTC-G
* *
123861 AACTTTCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTGACCCTCG
*
123890 AACTTCCAAAAATCCCATTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTGACCCTCG
*
123918 AAACTTCCAAAAATTCCATTTTGA-CCTTG
1 -AACTTCCAAAAATTCCATTTTGACCCTCG
* * * *
123947 AAACTTTCAAAATTTCCATTTTTAACCTCG
1 -AACTTCCAAAAATTCCATTTTGACCCTCG
* * **
123977 AAACTTCTAAAATTTCCATTTTCGACCCTAA
1 -AACTTCCAAAAATTCCATTTT-GACCCTCG
* * * *
124008 AACTTTCAAAAACTCCATTTTCAACCTCG
1 AACTTCCAAAAATTCCATTTTGACCCTCG
* *
124037 AAAC-TCTC-AAAATTACCCTTTT-ACCCCCG
1 -AACTTC-CAAAAATT-CCATTTTGACCCTCG
*
124066 AA-TGTCTAAAAATTCCATTTT
1 AACT-TCCAAAAATTCCATTTT
124087 TAACCCTAAA
Statistics
Matches: 206, Mismatches: 37, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
28 13 0.06
29 113 0.55
30 76 0.37
31 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTGACCCTCG
Found at i:123871 original size:30 final size:30
Alignment explanation
Indices: 123810--124048 Score: 204
Period size: 30 Copynumber: 8.1 Consensus size: 30
123800 AAACTGTCCG
* *
123810 AAAATTCCATGTTT-ACCCTCG-AACTTCCA
1 AAAATTCCATTTTTGACCC-CGAAACTTTCA
* *
123839 AAAATCCCATTTTTGACCCCAAAACTTTCA
1 AAAATTCCATTTTTGACCCCGAAACTTTCA
*
123869 AAAATTCCATTTTT-ACCCTCG-AACTTCCA
1 AAAATTCCATTTTTGACCC-CGAAACTTTCA
* * *
123898 AAAATCCCA-TTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTTGACCCCGAAACTTTCA
**
123927 AAAATTCCA-TTTTGACCTTGAAACTTTCA
1 AAAATTCCATTTTTGACCCCGAAACTTTCA
* * *
123956 AAATTTCCATTTTTAACCTCGAAAC-TTCTA
1 AAAATTCCATTTTTGACCCCGAAACTTTC-A
* * **
123986 AAATTTCCATTTTCGACCCTAAAACTTTCA
1 AAAATTCCATTTTTGACCCCGAAACTTTCA
* ** * *
124016 AAAACTCCATTTTCAACCTCGAAACTCTCA
1 AAAATTCCATTTTTGACCCCGAAACTTTCA
124046 AAA
1 AAA
124049 TTACCCTTTT
Statistics
Matches: 175, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.03
29 80 0.46
30 86 0.49
31 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCCCGAAACTTTCA
Found at i:123902 original size:59 final size:59
Alignment explanation
Indices: 123810--124091 Score: 263
Period size: 59 Copynumber: 4.8 Consensus size: 59
123800 AAACTGTCCG
* * * *
123810 AAAATTCCATGTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTTCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTTCA
* *
123869 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTTCA
* * * * *
123927 AAAATTCCATTTTGA-CCTTGAAACTTTCAAAATTTCCATTTTTAACCTCGAAAC-TTCTA
1 AAAATTCCATTTTTACCCTCG-AACTTCCAAAAATCCCATTTTTAACCTCGAAACTTTC-A
* * ** * * *
123986 AAATTTCCATTTTCGACCCTAAAACTTTCAAAAA-CTCCATTTTCAACCTCGAAACTCTC-
1 AAAATTCCATTTT-TACCCTCGAACTTCCAAAAATC-CCATTTTTAACCTCGAAACTTTCA
* * * *
124045 AAAATTACC-CTTTTACCCCCGAA-TGTCTAAAAATTCCATTTTTAACC
1 AAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATCCCATTTTTAACC
124092 CTAAAATTTC
Statistics
Matches: 185, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
57 5 0.03
58 70 0.38
59 72 0.39
60 33 0.18
61 5 0.03
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTTTCA
Found at i:124137 original size:88 final size:88
Alignment explanation
Indices: 123918--124153 Score: 221
Period size: 88 Copynumber: 2.7 Consensus size: 88
123908 TTTGACCTCG
* * ** * * * * *
123918 AAACTTCCAAAAATTCCATTT-TGACCTTGAAACTTTCAAAATTTCCATTTTTAACCTCGAAACT
1 AAACTTTCAAAAACTCCATTTACAACCTCGAAACTCTCAAAATTACCA-TTTTACCCCCG-AA-T
* *
123982 -TCTAAAATTTCCATTTTCGACCCTA
63 GTCTAAAAATTCCATTTTCAACCCTA
* *
124007 AAACTTTCAAAAACTCCATTTTCAACCTCGAAACTCTCAAAATTACCCTTTTACCCCCGAATGTC
1 AAACTTTCAAAAACTCCATTTACAACCTCGAAACTCTCAAAATTACCATTTTACCCCCGAATGTC
*
124072 TAAAAATTCCATTTTTAACCCTA
66 TAAAAATTCCATTTTCAACCCTA
* * **
124095 AAA-TTTCCCAAAATTACCATTTACCCCCTCGAGAA-TCT-AAAATTACCATTTTACCCCCG
1 AAACTTT-CAAAAACT-CCATTTACAACCTCGA-AACTCTCAAAATTACCATTTTACCCCCG
124154 GGTATCCAAA
Statistics
Matches: 123, Mismatches: 19, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
87 4 0.03
88 53 0.43
89 44 0.36
90 22 0.18
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (88 bp):
AAACTTTCAAAAACTCCATTTACAACCTCGAAACTCTCAAAATTACCATTTTACCCCCGAATGTC
TAAAAATTCCATTTTCAACCCTA
Found at i:134960 original size:17 final size:17
Alignment explanation
Indices: 134940--134981 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
134930 CATACATAAA
*
134940 GATTTCCATGGAAAATG
1 GATTCCCATGGAAAATG
134957 GATTCCCATGGAAAATG
1 GATTCCCATGGAAAATG
134974 GATTCCCA
1 GATTCCCA
134982 ATTGGGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (17 bp):
GATTCCCATGGAAAATG
Found at i:136323 original size:205 final size:205
Alignment explanation
Indices: 135971--136831 Score: 1159
Period size: 205 Copynumber: 4.2 Consensus size: 205
135961 AATGACGTGG
* * * *
135971 TCATCTTCCTGATGACATACTGAGAAGAAGTCCAAATCAAACCCACGCTCGATGTGAGTAAATCT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAAATCT
* * * *
136036 TCGAACCCCAGCTTCCTGATGAGACATTGAGAAGTAGGTCGAAGCAATAAAAGGTTAGATTCCTA
66 TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
*
136101 ATGGGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAGCA
131 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAGCA
*
136166 AACGACGCGA
196 AACGACACGA
* * *
136176 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCGCACTCGATGTGAGTAAATTT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAAATCT
* *
136241 TCGAACCCCAGCTTCCTGATGAGACACTGAGATGTAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
66 TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
* *
136306 ATGAGATACTGAGAAGTGGACCGAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA-C
131 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATT-AAAGC
*
136370 AAACGACACGG
195 AAACGACACGA
*
136381 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTTGATGTGAGCAAATCT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAAATCT
* *
136446 TCGAACCCTAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
66 TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
* * *
136511 ATGAGATACTGAGAAGTGGACCAAATTCGTCCTCCTGATGAGGTACAGAGAAGCGAATTGAAGCA
131 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAGCA
* *
136576 AACGACGCGG
196 AACGACACGA
* * * * *
136586 TCATCTTCCTGATGAGATATTGAGAAGAAGAGCAAATCAAACCCACGCTCGATATGAGCAAGTCT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAAATCT
* * * * * *
136651 TCGAACCCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAATAAAACGATTAGCTTCCC
66 TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA-GGTTAGCTTCCT
* * * ** * * * * * * * *
136716 GATAAAATAC-GAGGAAGTGAACCAAAACCATCTTCTTGATGAAACACAGAGAAGTGGATCAAAA
130 GATGAGATACTGA-GAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAG
*** *
136780 CAGGTGATACGA
194 CAAACGACACGA
* * * *
136792 TCGTCTTCTTGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
136832 TGAAACTAGA
Statistics
Matches: 584, Mismatches: 68, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
204 2 0.00
205 484 0.83
206 98 0.17
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (205 bp):
TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAAATCT
TCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTG
ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAGCA
AACGACACGA
Found at i:137171 original size:17 final size:17
Alignment explanation
Indices: 137149--137226 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
137139 CCAACAAGAT
137149 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
137166 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
137183 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
137199 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
137217 TTAAAGTTTA
1 TTAAA-TTTA
137227 AATCTATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 4 0.08
17 38 0.76
18 8 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:137191 original size:34 final size:34
Alignment explanation
Indices: 137147--137226 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 34
137137 GCCCAACAAG
* *
137147 ATTTAAATTTATTTTAAAA-TTAAATTTATTTTAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATTATAA
*
137181 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATTATAA
137215 ATTTAAAGTTTA
1 ATTTAAA-TTTA
137227 AATCTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 6 0.15
34 30 0.75
35 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATTATAA
Found at i:137220 original size:24 final size:23
Alignment explanation
Indices: 137193--137239 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
137183 TTAAATTTAC
*
137193 TTAAAATTTAAATTTATTATAAAT
1 TTAAAATTTAAATCTATT-TAAAT
*
137217 TTAAAGTTTAAATCTATTTAAAT
1 TTAAAATTTAAATCTATTTAAAT
137240 CAAGTCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAAAATTTAAATCTATTTAAAT
Found at i:137228 original size:7 final size:6
Alignment explanation
Indices: 137147--137229 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
137137 GCCCAACAAG
* * * *
137147 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
137192 CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA AGTTTAA AT
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA A-TTTAA AT
137230 CTATTTAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
4 3 0.05
5 12 0.20
6 35 0.59
7 9 0.15
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:138911 original size:29 final size:29
Alignment explanation
Indices: 138879--139065 Score: 146
Period size: 29 Copynumber: 6.4 Consensus size: 29
138869 AACTATCCGT
* *
138879 AAATTCCATTTTTACCCTTAAACTTCTTA
1 AAATTCCATTTTTACCCTAAAACTTCTAA
* *
138908 AAATTCCATTTTTGA-CCTCGAAACTTCTGA
1 AAATTCCATTTTT-ACCCT-AAAACTTCTAA
* ** *
138938 AAATTCCAATTTTACCCTCGAACTTCCAA
1 AAATTCCATTTTTACCCTAAAACTTCTAA
* * * * * *
138967 AAATCCCAATTTGACCCCAAAACATC-CA
1 AAATTCCATTTTTACCCTAAAACTTCTAA
* * *
138995 AAATTTCATTTTTACCCCT-GAACTTCCAA
1 AAATTCCATTTTTA-CCCTAAAACTTCTAA
* *
139024 GAATCCCATTTTTGACCCTAAAACTTCTAA
1 AAATTCCATTTTT-ACCCTAAAACTTCTAA
139054 AAATTCCATTTT
1 AAATTCCATTTT
139066 CGACCCCGAA
Statistics
Matches: 122, Mismatches: 29, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
28 16 0.13
29 62 0.51
30 44 0.36
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAATTCCATTTTTACCCTAAAACTTCTAA
Found at i:139018 original size:57 final size:59
Alignment explanation
Indices: 138879--139065 Score: 191
Period size: 59 Copynumber: 3.2 Consensus size: 59
138869 AACTATCCGT
** ** * * * * * *
138879 AAATTCCATTTTTACCCTTAAACTTCTTAAAATTCCATTTTTGACCTCGAAACTTCTGA
1 AAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATATTTGACCCCAAAACATCTAA
* *
138938 AAATTCCAATTTTACCCTCGAACTTCCAAAAATCCCA-ATTTGACCCCAAAACATC-CA
1 AAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATATTTGACCCCAAAACATCTAA
* * * * *
138995 AAATTTCATTTTTACCC-CTGAACTTCCAAGAATCCCATTTTTGACCCTAAAACTTCTAA
1 AAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCCATATTTGACCCCAAAACATCTAA
139054 AAATTCCATTTT
1 AAATTCCATTTT
139066 CGACCCCGAA
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
56 1 0.01
57 33 0.31
58 29 0.27
59 43 0.41
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATATTTGACCCCAAAACATCTAA
Found at i:139071 original size:30 final size:29
Alignment explanation
Indices: 138879--139134 Score: 150
Period size: 30 Copynumber: 8.7 Consensus size: 29
138869 AACTATCCGT
* * *
138879 AAATTCCATTTTTACCCTTAAACTTCTTA
1 AAATTCCATTTTGACCCTGAAACTTCTAA
*
138908 AAATTCCATTTTTGA-CCTCGAAACTTCTGA
1 AAATTCCA-TTTTGACCCT-GAAACTTCTAA
*
138938 AAATTCCAATTTT-ACCCTCG-AACTTCCAA
1 AAATTCC-ATTTTGACCCT-GAAACTTCTAA
* * ** * *
138967 AAATCCCAATTTGACCCCAAAACATC-CA
1 AAATTCCATTTTGACCCTGAAACTTCTAA
* * *
138995 AAATTTCATTTTTACCCCTG-AACTTCCAA
1 AAATTCCATTTTGA-CCCTGAAACTTCTAA
* * *
139024 GAATCCCATTTTTGACCCTAAAACTTCTAA
1 AAATTCCA-TTTTGACCCTGAAACTTCTAA
* *
139054 AAATTCCATTTTCGACCCCGAAA-TATCCAA
1 AAATTCCATTTT-GACCCTGAAACT-TCTAA
* * *
139084 AAACTCCATTTTCGACCTTGAAAC-TCTTA
1 AAATTCCATTTT-GACCCTGAAACTTCTAA
*
139113 AAATTACCCTTTT-ACCCCTGAA
1 AAATT-CCATTTTGA-CCCTGAA
139135 TGTAAAAATT
Statistics
Matches: 174, Mismatches: 38, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
28 21 0.12
29 65 0.37
30 87 0.50
31 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AAATTCCATTTTGACCCTGAAACTTCTAA
Found at i:139228 original size:27 final size:28
Alignment explanation
Indices: 139167--139227 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
139157 CTGAATTTTC
*
139167 CCAAAATTACCATTTTACCCCCGAGAAT
1 CCAAAATTACCATTTTACCCCCAAGAAT
* *
139195 CCAAAATTACCATTTTGCCCCCAAGTAT
1 CCAAAATTACCATTTTACCCCCAAGAAT
139223 CCAAA
1 CCAAA
139228 TAGTCTCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.25
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCAAGAAT
Found at i:142264 original size:91 final size:90
Alignment explanation
Indices: 142107--142366 Score: 304
Period size: 91 Copynumber: 2.9 Consensus size: 90
142097 TTATATGGTG
* ** * * *
142107 ACTTTTATCTACAAAAATGTTTTGTATTCACAACCATCTGGCAGCGTATTAACCTGTAACTATTG
1 ACTTTTATCTGCAATTATGTTGTGTATTCACAACCATCT-GCAGCGTATTAACCTGCAACTTTTG
*
142172 GTGGTTCACTCACCCATTATCTAACA
65 GTGGTTCACCCACCCATTATCTAACA
* * *
142198 GCTTTTATCTGCAATTATGTTGTGTATTCACAACCATCTAGCAGCATATTAACTTGCAACTTTTG
1 ACTTTTATCTGCAATTATGTTGTGTATTCACAACCATCT-GCAGCGTATTAACCTGCAACTTTTG
** *
142263 GTGGTTTTCCCACTCATTATCTAACA
65 GTGGTTCACCCACCCATTATCTAACA
* * * * * * *
142289 ACTTTTATTTGTAATTATGTTGTGTATTCAAAATCGTCTGACAGTGTATTAACCTGCAACATTTG
1 ACTTTTATCTGCAATTATGTTGTGTATTCACAACCATCTG-CAGCGTATTAACCTGCAACTTTTG
*
142354 GTGGTTCATCCAC
65 GTGGTTCACCCAC
142367 AACCCAGTGT
Statistics
Matches: 141, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
90 1 0.01
91 140 0.99
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (90 bp):
ACTTTTATCTGCAATTATGTTGTGTATTCACAACCATCTGCAGCGTATTAACCTGCAACTTTTGG
TGGTTCACCCACCCATTATCTAACA
Found at i:147882 original size:36 final size:36
Alignment explanation
Indices: 147806--147882 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
147796 TTCAGACAAT
* * **
147806 AATACGTGGGTATGTTATTCATTCCATGAGGTAGTA
1 AATATGTGGGTATGTTATTCATGCCATGAGACAGTA
* *
147842 AATATGTGGGTATGTTATTCATGCCATGTGACAGTG
1 AATATGTGGGTATGTTATTCATGCCATGAGACAGTA
147878 AATAT
1 AATAT
147883 ATTGTGCTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.36
Consensus pattern (36 bp):
AATATGTGGGTATGTTATTCATGCCATGAGACAGTA
Found at i:148399 original size:10 final size:10
Alignment explanation
Indices: 148380--148728 Score: 95
Period size: 10 Copynumber: 33.4 Consensus size: 10
148370 AAAATATTCT
148380 TGTGATTAAA
1 TGTGATTAAA
*
148390 TGTGACTAAA
1 TGTGATTAAA
148400 TGTGATTAATA
1 TGTGATTAA-A
148411 TGTGAATTGATAAA
1 TGTG-A-T--TAAA
**
148425 TGCTGAAATATTCA
1 TG-TG--AT-TAAA
148439 TGTGATTAAA
1 TGTGATTAAA
*
148449 TGTGACTAAA
1 TGTGATTAAA
148459 TGTGATTAATA
1 TGTGATTAA-A
148470 TGTGATGTGATAAA
1 TGTGA--T--TAAA
**
148484 TGCTGAAATATTCA
1 TG-TG--AT-TAAA
*
148498 TGTGATTGAA
1 TGTGATTAAA
148508 TGTGATTAAA
1 TGTGATTAAA
*
148518 TGTGACTAAA
1 TGTGATTAAA
*
148528 TATGATT-AA
1 TGTGATTAAA
*
148537 TTTG--T-AA
1 TGTGATTAAA
148544 TGTGA-TAAA
1 TGTGATTAAA
**
148553 TGTTGAAATATTCA
1 TG-TG--AT-TAAA
148567 TGTGATTAAA
1 TGTGATTAAA
*
148577 TGTGACTAATA
1 TGTGATTAA-A
148588 TGTGATGTGATAA
1 TGTGAT-T-A-AA
148601 -GATG-TTGAAA
1 TG-TGATT-AAA
*
148611 --T-ATT-CA
1 TGTGATTAAA
*
148617 TGTGACT-AA
1 TGTGATTAAA
148626 TGTGATTAAA
1 TGTGATTAAA
*
148636 TGTGACTAAA
1 TGTGATTAAA
148646 TGTGATT-AA
1 TGTGATTAAA
*
148655 TGTG--T-GA
1 TGTGATTAAA
148662 TGTGA-TAAA
1 TGTGATTAAA
**
148671 TGCTGAAATATTCA
1 TG-TG--AT-TAAA
*
148685 TGTGACT-AA
1 TGTGATTAAA
148694 TGTGATTAAA
1 TGTGATTAAA
148704 TGTGATTAAA
1 TGTGATTAAA
148714 TGTGATTAATA
1 TGTGATTAA-A
148725 TGTG
1 TGTG
148729 TTGTGGTAAA
Statistics
Matches: 261, Mismatches: 37, Indels: 81
0.69 0.10 0.21
Matches are distributed among these distances:
6 1 0.00
7 12 0.05
8 6 0.02
9 34 0.13
10 116 0.44
11 32 0.12
12 6 0.02
13 14 0.05
14 25 0.10
15 12 0.05
16 2 0.01
17 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (10 bp):
TGTGATTAAA
Found at i:148434 original size:59 final size:59
Alignment explanation
Indices: 148362--148719 Score: 374
Period size: 59 Copynumber: 5.9 Consensus size: 59
148352 AGTCATGCAT
* *
148362 TAAATGCTAAAATATTCTTGTGATTAAATGTGACTAAATGTGATTAATATGTGAAT-TGA
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTG-ATGTGA
148421 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
* * *
148480 TAAATGCTGAAATATTCATGTGATTGAATGTGATTAAATGTGACTAAATATGATTAATTTGTAAT
1 TAAATGCTGAAATATTC----------ATGTGATTAAATGTGACTAAATGTGATTAATATGTGAT
148545 GTGA
56 GTGA
* * *
148549 TAAATGTTGAAATATTCATGTGATTAAATGTGACTAATATGTGATGTGATA--AGATGTTGA
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAA-ATGTGAT-TAATATGTGATG-TGA
* * * *
148609 -AATATTCATG---TGACTAATGTGATTAAATGTGACTAAATGTGATTAATGTGTGATGTGA
1 TAA-ATGC-TGAAAT-ATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
* *
148667 TAAATGCTGAAATATTCATGTGACT-AATGTGATTAAATGTGATTAA-ATGTGAT
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGAT
148720 TAATATGTGT
Statistics
Matches: 252, Mismatches: 24, Indels: 48
0.78 0.07 0.15
Matches are distributed among these distances:
57 11 0.04
58 36 0.14
59 133 0.53
60 12 0.05
61 5 0.02
69 55 0.22
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (59 bp):
TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGA
Found at i:148511 original size:69 final size:69
Alignment explanation
Indices: 148438--148592 Score: 247
Period size: 69 Copynumber: 2.2 Consensus size: 69
148428 TGAAATATTC
* *
148438 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGA
1 ATGTGATTAAATGTGACTAAATATGATTAATATGTAATGTGATAAATGCTGAAATATTCATGTGA
*
148503 TTGA
66 TTAA
* *
148507 ATGTGATTAAATGTGACTAAATATGATTAATTTGTAATGTGATAAATGTTGAAATATTCATGTGA
1 ATGTGATTAAATGTGACTAAATATGATTAATATGTAATGTGATAAATGCTGAAATATTCATGTGA
148572 TTAA
66 TTAA
*
148576 ATGTGACTAATATGTGA
1 ATGTGATTAA-ATGTGA
148593 TGTGATAAGA
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
69 73 0.92
70 6 0.08
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (69 bp):
ATGTGATTAAATGTGACTAAATATGATTAATATGTAATGTGATAAATGCTGAAATATTCATGTGA
TTAA
Found at i:148512 original size:118 final size:120
Alignment explanation
Indices: 148362--148719 Score: 387
Period size: 128 Copynumber: 3.0 Consensus size: 120
148352 AGTCATGCAT
* *
148362 TAAATGCTAAAATATTCTTGTGATTAAATGTGACTAAATGTGATTAATATGTGAAT-TGATAAAT
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGAATGTGATAAAT
148426 GCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATG-TGA
66 GCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTTGA
* * *
148480 TAAATGCTGAAATATTCATGTGATTGAATGTGATTAAATGTGACTAAATATGATTAATTTGTAAT
1 TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGA-T---TA--A-T-ATGTG-AAT
* * *
148545 GTGATAAATGTTGAAATATTCATGTGATTAAATGTGACTAATATGTGATGTGATA--AGATGTTG
57 GTGATAAATGCTGAAATATTCATGTGATTAAATGTGACTAA-ATGTGAT-TAATATGTGATGTTG
148608 A
120 A
* * * *
148609 -AATATTCATG---TGACTAATGTGATTAAATGTGACTAAATGTGATTAATGTGTG-ATGTGATA
1 TAA-ATGC-TGAAAT-ATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGAATGTGATA
* *
148669 AATGCTGAAATATTCATGTGACT-AATGTGATTAAATGTGATTAA-ATGTGAT
63 AATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGAT
148720 TAATATGTGT
Statistics
Matches: 202, Mismatches: 20, Indels: 38
0.78 0.08 0.15
Matches are distributed among these distances:
114 1 0.00
115 2 0.01
116 10 0.05
117 10 0.05
118 68 0.34
119 1 0.00
120 3 0.01
121 1 0.00
122 3 0.01
124 3 0.01
125 1 0.00
126 4 0.02
127 5 0.02
128 71 0.35
129 13 0.06
130 6 0.03
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (120 bp):
TAAATGCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGAATGTGATAAAT
GCTGAAATATTCATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTTGA
Found at i:148579 original size:24 final size:23
Alignment explanation
Indices: 148543--148689 Score: 101
Period size: 25 Copynumber: 6.3 Consensus size: 23
148533 TTAATTTGTA
148543 ATGTGATAAATGTTGAAATATTC
1 ATGTGATAAATGTTGAAATATTC
*
148566 ATGTGATTAAATG-TGACTAATATGTG
1 ATGTGA-TAAATGTTGA--AATAT-TC
148592 ATGTGATAAGATGTTGAAATATTC
1 ATGTGATAA-ATGTTGAAATATTC
**
148616 ATGTGACT-AATG-TG--AT-TAA
1 ATGTGA-TAAATGTTGAAATATTC
* *
148635 ATGTGACTAAATG-TGATTAATGTGTG
1 ATGTGA-TAAATGTTGA--AATAT-TC
*
148661 ATGTGATAAATGCTGAAATATTC
1 ATGTGATAAATGTTGAAATATTC
148684 ATGTGA
1 ATGTGA
148690 CTAATGTGAT
Statistics
Matches: 101, Mismatches: 8, Indels: 30
0.73 0.06 0.22
Matches are distributed among these distances:
19 9 0.09
20 8 0.08
22 2 0.02
23 19 0.19
24 20 0.20
25 21 0.21
26 19 0.19
27 3 0.03
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (23 bp):
ATGTGATAAATGTTGAAATATTC
Found at i:148620 original size:50 final size:49
Alignment explanation
Indices: 148517--148640 Score: 180
Period size: 49 Copynumber: 2.6 Consensus size: 49
148507 ATGTGATTAA
* * *
148517 ATGTGACTAAATATGATTAATTTGTAATGTGATAAATGTTGAAATATTC
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTC
* *
148566 ATGTGATTAAATGTGACTAATATGTGATGTGATAAGATGTTGAAATATTC
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAA-ATGTTGAAATATTC
148616 ATGTGACT-AATGTGATTAA-ATGTGA
1 ATGTGACTAAATGTGATTAATATGTGA
148641 CTAAATGTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
48 6 0.09
49 40 0.60
50 21 0.31
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (49 bp):
ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTC
Found at i:148701 original size:68 final size:68
Alignment explanation
Indices: 148566--148774 Score: 312
Period size: 68 Copynumber: 3.1 Consensus size: 68
148556 TGAAATATTC
* *
148566 ATGTGATTAAATGTGACTAATATGTGATGTGATAAGATGTTGAAATATTCATGTGACTAATGTGA
1 ATGTGATTAAATGTGATTAATATGTGATGTGATAA-ATGCTGAAATATTCATGTGACTAATGTGA
148631 TTAA
65 TTAA
* *
148635 ATGTGACTAAATGTGATTAATGTGTGATGTGATAAATGCTGAAATATTCATGTGACTAATGTGAT
1 ATGTGATTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGACTAATGTGAT
148700 TAA
66 TAA
* * * * * *
148703 ATGTGATTAAATGTGATTAATATGTGTTGTGGTAAATGCTTAAGTATTCATGTGATTAATGCGAT
1 ATGTGATTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGACTAATGTGAT
148768 T-A
66 TAA
148770 ATGTG
1 ATGTG
148775 TAAAAGGATA
Statistics
Matches: 128, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
67 6 0.05
68 90 0.70
69 32 0.25
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (68 bp):
ATGTGATTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGACTAATGTGAT
TAA
Found at i:152401 original size:49 final size:50
Alignment explanation
Indices: 152329--152452 Score: 209
Period size: 49 Copynumber: 2.5 Consensus size: 50
152319 ATGTGGTTAA
152329 ATGTGACTAAATGTGATTAATATGTGATGTGAT-AAATGTTGAAATATTC
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAAATGTTGAAATATTC
* *
152378 ATGTGATTAAATGTGATTAATATGTGATGTGATAAAATGTTGATATATTC
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAAATGTTGAAATATTC
152428 ATGTGACT-AATGTGATTAA-ATGTGA
1 ATGTGACTAAATGTGATTAATATGTGA
152453 GTAAATTTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
48 6 0.08
49 43 0.61
50 22 0.31
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (50 bp):
ATGTGACTAAATGTGATTAATATGTGATGTGATAAAATGTTGAAATATTC
Found at i:152441 original size:59 final size:61
Alignment explanation
Indices: 152378--152521 Score: 159
Period size: 69 Copynumber: 2.2 Consensus size: 61
152368 TGAAATATTC
* *
152378 ATGTGATTAAATGTG-A-TT-AATATGTGATGTGATAAAATGTTGATATATTCATGTGACTA
1 ATGTGATTAAATGTGAATTTCAATATGTGATGTGAT-AAATGCTGAAATATTCATGTGACTA
152437 ATGTGATTAAATGTGAGTAAATTTTGACCAATATGTGATGTGATAAATGCTGAAATATTCATGTG
1 ATGTGATTAAATGT--G--AA-TTT---CAATATGTGATGTGATAAATGCTGAAATATTCATGTG
152502 ACTA
58 ACTA
152506 ATGTGATTAATATGTG
1 ATGTGATTAA-ATGTG
152522 TTGTGTTAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 15
0.81 0.02 0.17
Matches are distributed among these distances:
59 14 0.20
61 1 0.01
64 1 0.01
66 2 0.03
68 1 0.01
69 33 0.46
70 19 0.27
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (61 bp):
ATGTGATTAAATGTGAATTTCAATATGTGATGTGATAAATGCTGAAATATTCATGTGACTA
Found at i:152519 original size:48 final size:48
Alignment explanation
Indices: 152466--152564 Score: 126
Period size: 48 Copynumber: 2.1 Consensus size: 48
152456 AATTTTGACC
* * *
152466 AATATGTGATGTGATAAATGCTGAAATATTCATGTGACTAATGTGATT
1 AATATGTGATGTGATAAATGATGAAATACTCATGTGACTAATGCGATT
* * * * *
152514 AATATGTGTTGTGTTAAATGATTAAGTACTCATGTGATTAATGCGATT
1 AATATGTGATGTGATAAATGATGAAATACTCATGTGACTAATGCGATT
152562 AAT
1 AAT
152565 GTGTCAGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.39
Consensus pattern (48 bp):
AATATGTGATGTGATAAATGATGAAATACTCATGTGACTAATGCGATT
Found at i:166549 original size:21 final size:21
Alignment explanation
Indices: 166525--166578 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
166515 TTAGTGTTGG
*
166525 TTCTATCGATACAAGTGACAC
1 TTCTACCGATACAAGTGACAC
* **
166546 TTCTACCGAAACAAGTGATGC
1 TTCTACCGATACAAGTGACAC
166567 TTCTACCGATAC
1 TTCTACCGATAC
166579 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTGACAC
Found at i:167334 original size:18 final size:18
Alignment explanation
Indices: 167279--167335 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
167269 TTGTCCAATA
*
167279 ATGCTCAAATGAGCTAGT
1 ATGCTCAAACGAGCTAGT
*
167297 AAGCTCAAACGAGCTAGT
1 ATGCTCAAACGAGCTAGT
*
167315 ATGCTCAAACGAGCCAGT
1 ATGCTCAAACGAGCTAGT
167333 ATG
1 ATG
167336 TTATTCCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (18 bp):
ATGCTCAAACGAGCTAGT
Found at i:183155 original size:16 final size:16
Alignment explanation
Indices: 183134--183164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
183124 TAAATAAAAG
183134 TGTAATTTTTAATTTC
1 TGTAATTTTTAATTTC
*
183150 TGTAATTTTTTATTT
1 TGTAATTTTTAATTT
183165 TTTTATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (16 bp):
TGTAATTTTTAATTTC
Found at i:185871 original size:52 final size:52
Alignment explanation
Indices: 185814--185917 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
185804 TGGGTTATAA
185814 CCATTACTTAGGGGAATGTTCAGTGTTTGAAGTTGAGCTTTGGGGCATTTTG
1 CCATTACTTAGGGGAATGTTCAGTGTTTGAAGTTGAGCTTTGGGGCATTTTG
*
185866 CCATTACTTAGGGGAATGTTTAGTGTTTGAAGTTGAGCTTTGGGGCATTTTG
1 CCATTACTTAGGGGAATGTTCAGTGTTTGAAGTTGAGCTTTGGGGCATTTTG
185918 GATGGCCTGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.19, C:0.11, G:0.31, T:0.39
Consensus pattern (52 bp):
CCATTACTTAGGGGAATGTTCAGTGTTTGAAGTTGAGCTTTGGGGCATTTTG
Found at i:186513 original size:38 final size:39
Alignment explanation
Indices: 186419--186513 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 39
186409 GTGTAGTTAC
*
186419 ACAGTGTTTACAGTGTCACTACTAGTTTAACAATGTATT
1 ACAGTGTTTACAGTGTCACTACCAGTTTAACAATGTATT
* * * *
186458 GCAGCGTTTGCAGTGTCACTACCAG-TTAA-TATAGTATT
1 ACAGTGTTTACAGTGTCACTACCAGTTTAACAAT-GTATT
* *
186496 ACGGTGTTTACAATGTCA
1 ACAGTGTTTACAGTGTCA
186514 TCGTCAGCTC
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
37 2 0.04
38 22 0.49
39 21 0.47
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (39 bp):
ACAGTGTTTACAGTGTCACTACCAGTTTAACAATGTATT
Found at i:193077 original size:39 final size:38
Alignment explanation
Indices: 193034--193136 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
193024 CAGTATAGAG
193034 TTACAGTGTTTACAGTGTCACTGTCAGTTCAACG-ATGTA
1 TTACAGTGTTTACAGTGTCACTGTCAGTT-AACGCA-GTA
* * * * **
193073 TTACAATGTTTACAATGTCGCTGCCAGTTAGTGCAGTA
1 TTACAGTGTTTACAGTGTCACTGTCAGTTAACGCAGTA
*
193111 TTATAGTGTTTACAGTGTCACTGTCA
1 TTACAGTGTTTACAGTGTCACTGTCA
193137 ACTTAATGAA
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
38 26 0.50
39 26 0.50
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (38 bp):
TTACAGTGTTTACAGTGTCACTGTCAGTTAACGCAGTA
Found at i:194666 original size:20 final size:20
Alignment explanation
Indices: 194641--194684 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
194631 ATGATTTGTT
*
194641 TTAAGAGTAAATAG-GCTTAA
1 TTAAGA-TAAATAGAGATTAA
*
194661 TTAAGATTAATAGAGATTAA
1 TTAAGATAAATAGAGATTAA
194681 TTAA
1 TTAA
194685 AGCTTAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (20 bp):
TTAAGATAAATAGAGATTAA
Found at i:195899 original size:21 final size:21
Alignment explanation
Indices: 195887--195937 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
195877 TAGAGATAGG
195887 ACTTGTATCGGTAGAAAAGTC
1 ACTTGTATCGGTAGAAAAGTC
**
195908 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAAAAGTC
195929 ACTTGTATC
1 ACTTGTATC
195938 AGTACAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAAAGTC
Found at i:201292 original size:20 final size:20
Alignment explanation
Indices: 201267--201310 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
201257 ATGATTTGTT
*
201267 TTAAGAGTAAATAG-GCTTAA
1 TTAAGAGTAAA-AGAGATTAA
*
201287 TTAAGATTAAAAGAGATTAA
1 TTAAGAGTAAAAGAGATTAA
201307 TTAA
1 TTAA
201311 AGCTTAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (20 bp):
TTAAGAGTAAAAGAGATTAA
Found at i:203147 original size:21 final size:21
Alignment explanation
Indices: 203123--203173 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
203113 TAGAGGTAAG
203123 ACTTGTATCGGTAGAAAAGAC
1 ACTTGTATCGGTAGAAAAGAC
* ** *
203144 ACTTGTATTGGTAGAACTGTC
1 ACTTGTATCGGTAGAAAAGAC
203165 ACTTGTATC
1 ACTTGTATC
203174 AGTACAGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAAAGAC
Found at i:204035 original size:25 final size:23
Alignment explanation
Indices: 203980--204035 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
203970 AAATTAAAGC
*
203980 TCTTTTGAATTTTGAAAATATTT
1 TCTTTTCAATTTTGAAAATATTT
*
204003 TCAATTTTCAATTTTTGAAAGTAGTTT
1 TC--TTTTCAA-TTTTGAAAATA-TTT
204030 TCTTTT
1 TCTTTT
204036 TTTAATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
25 10 0.37
26 10 0.37
27 5 0.19
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (23 bp):
TCTTTTCAATTTTGAAAATATTT
Found at i:206420 original size:67 final size:67
Alignment explanation
Indices: 206349--206479 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 67
206339 GTTTGAAGAC
* * *
206349 TTAAAAAATATCTGTACAACCTCAAACAAGCTTCAAGACAATGGTATGAGAAATTTCATAAGACT
1 TTAAAAAATATCTATACAACCTCAAACAAGCTCCAAAACAATGGTATGAGAAATTTCATAAGACT
206414 AT
66 AT
* *
206416 TTAAAAAATCTCTATACAACCTCAAACAAGCTCCAAAACAATGGTATGAGAAATTTCTTAAGAC
1 TTAAAAAATATCTATACAACCTCAAACAAGCTCCAAAACAATGGTATGAGAAATTTCATAAGAC
206480 CATTCTCAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (67 bp):
TTAAAAAATATCTATACAACCTCAAACAAGCTCCAAAACAATGGTATGAGAAATTTCATAAGACT
AT
Found at i:214752 original size:52 final size:52
Alignment explanation
Indices: 214644--214754 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 52
214634 GCTGATAAGT
* * ** *
214644 GTAAACACATAAATAAGCTGGCAAGTGTAAACGCATAAATAAGTTGGCAAGT
1 GTAAACGCATAAATAAGCTGGCAAGTGTAAACGCATAAATAAGCTAACAAGC
* * *
214696 GTAAACGCGTAAATAAGCTGGCGAGTGTAAACGCATAAATAAGCTAACGAGC
1 GTAAACGCATAAATAAGCTGGCAAGTGTAAACGCATAAATAAGCTAACAAGC
214748 GTAAACG
1 GTAAACG
214755 TGTGCAAGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (52 bp):
GTAAACGCATAAATAAGCTGGCAAGTGTAAACGCATAAATAAGCTAACAAGC
Found at i:214754 original size:26 final size:26
Alignment explanation
Indices: 214640--214740 Score: 166
Period size: 26 Copynumber: 3.9 Consensus size: 26
214630 GCAAGCTGAT
*
214640 AAGTGTAAACACATAAATAAGCTGGC
1 AAGTGTAAACGCATAAATAAGCTGGC
*
214666 AAGTGTAAACGCATAAATAAGTTGGC
1 AAGTGTAAACGCATAAATAAGCTGGC
*
214692 AAGTGTAAACGCGTAAATAAGCTGGC
1 AAGTGTAAACGCATAAATAAGCTGGC
*
214718 GAGTGTAAACGCATAAATAAGCT
1 AAGTGTAAACGCATAAATAAGCT
214741 AACGAGCGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.21
Consensus pattern (26 bp):
AAGTGTAAACGCATAAATAAGCTGGC
Found at i:221715 original size:18 final size:18
Alignment explanation
Indices: 221678--221721 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
221668 GAGCGTAAAC
* *
221678 GCGTAAATAAGCAAATGA
1 GCGTAAACAAGCAAACGA
*
221696 GCGTAAACAAGCAGACGA
1 GCGTAAACAAGCAAACGA
*
221714 GCGAAAAC
1 GCGTAAAC
221722 GTGTTCAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.18, G:0.25, T:0.09
Consensus pattern (18 bp):
GCGTAAACAAGCAAACGA
Found at i:221771 original size:49 final size:50
Alignment explanation
Indices: 221718--221821 Score: 129
Period size: 49 Copynumber: 2.1 Consensus size: 50
221708 AGACGAGCGA
* ** * * * *
221718 AAACGTGTTCAAGCTGGTGAGCGTAAATGTGTAAATTAGCT-GAGAGCAT
1 AAACGTGTGCAAGCTGGCAAGCGTAAACGCGTAAATAAGCTGGAAAGCAT
*
221767 AAACGTGTGCAAGTTGGCAAGCGTAAACGCGTAAATAAGCTGGAAAGCAT
1 AAACGTGTGCAAGCTGGCAAGCGTAAACGCGTAAATAAGCTGGAAAGCAT
221817 AAACG
1 AAACG
221822 CATGAATAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
49 34 0.74
50 12 0.26
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (50 bp):
AAACGTGTGCAAGCTGGCAAGCGTAAACGCGTAAATAAGCTGGAAAGCAT
Found at i:221821 original size:26 final size:26
Alignment explanation
Indices: 221785--221885 Score: 103
Period size: 26 Copynumber: 3.9 Consensus size: 26
221775 GCAAGTTGGC
*
221785 AAGCGTAAACGCGTAAATAAGCTGGA
1 AAGCGTAAACGCATAAATAAGCTGGA
* * * *
221811 AAGCATAAACGCATGAATAAGTTGGT
1 AAGCGTAAACGCATAAATAAGCTGGA
* * * * *
221837 GAGTGTAAACACGTAAATAAGCTGGC
1 AAGCGTAAACGCATAAATAAGCTGGA
*
221863 AAGCTTAAACGCATAAATAAGCT
1 AAGCGTAAACGCATAAATAAGCT
221886 AATGAGCGTA
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.20
Consensus pattern (26 bp):
AAGCGTAAACGCATAAATAAGCTGGA
Found at i:221897 original size:26 final size:26
Alignment explanation
Indices: 221786--221899 Score: 70
Period size: 26 Copynumber: 4.4 Consensus size: 26
221776 CAAGTTGGCA
*
221786 AGCGTAAACGCGTAAATAAGCTGGAA--
1 AGCGTAAACGCATAAATAAGCT--AATG
* * * **
221812 AGCATAAACGCATGAATAAGTTGGTG
1 AGCGTAAACGCATAAATAAGCTAATG
* * * ****
221838 AGTGTAAACACGTAAATAAGCTGGCA
1 AGCGTAAACGCATAAATAAGCTAATG
*
221864 AGCTTAAACGCATAAATAAGCTAATG
1 AGCGTAAACGCATAAATAAGCTAATG
221890 AGCGTAAACG
1 AGCGTAAACG
221900 TGTGCAAGCT
Statistics
Matches: 63, Mismatches: 23, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (26 bp):
AGCGTAAACGCATAAATAAGCTAATG
Found at i:221897 original size:52 final size:52
Alignment explanation
Indices: 221786--221898 Score: 154
Period size: 52 Copynumber: 2.2 Consensus size: 52
221776 CAAGTTGGCA
* * * **
221786 AGCGTAAACGCGTAAATAAGCTGGAAAGCATAAACGCATGAATAAGTTGGTG
1 AGCGTAAACACGTAAATAAGCTGGAAAGCATAAACGCATAAATAAGCTAATG
* * *
221838 AGTGTAAACACGTAAATAAGCTGGCAAGCTTAAACGCATAAATAAGCTAATG
1 AGCGTAAACACGTAAATAAGCTGGAAAGCATAAACGCATAAATAAGCTAATG
221890 AGCGTAAAC
1 AGCGTAAAC
221899 GTGTGCAAGC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (52 bp):
AGCGTAAACACGTAAATAAGCTGGAAAGCATAAACGCATAAATAAGCTAATG
Done.