Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000572.1 Hibiscus syriacus cultivar Beakdansim tig00001120_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: 2399138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:2096979 original size:44 final size:43
Alignment explanation
Indices: 2096859--2096979 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 43
2096849 AATGTTTTGT
* *
2096859 AGTTTGAGAGCACACTAAGAGGTCGTGGATATCAAATGCAATA
1 AGTTTGAGAGCACACTAAGAGGTTGTGAATATCAAATGCAATA
* * * * *
2096902 AGTTTGAGAGAACAGTATGAGATTGTGATTATCAAATGCAATA
1 AGTTTGAGAGCACACTAAGAGGTTGTGAATATCAAATGCAATA
* *
2096945 AGTTTTGATAGCACACTAAGTGGTTGTGAATATCA
1 AG-TTTGAGAGCACACTAAGAGGTTGTGAATATCA
2096980 TGGAATTTCC
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 38 0.60
44 25 0.40
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (43 bp):
AGTTTGAGAGCACACTAAGAGGTTGTGAATATCAAATGCAATA
Found at i:2103361 original size:25 final size:25
Alignment explanation
Indices: 2103333--2103382 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2103323 ATTGGTTATT
* *
2103333 TAATTTTGTATGTTCTAAAATTTTA
1 TAATTTCGTATCTTCTAAAATTTTA
*
2103358 TAATTTCGTATCTTTTAAAATTTTA
1 TAATTTCGTATCTTCTAAAATTTTA
2103383 AAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (25 bp):
TAATTTCGTATCTTCTAAAATTTTA
Found at i:2107986 original size:15 final size:17
Alignment explanation
Indices: 2107955--2107987 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2107945 ACGGAAATGT
2107955 TCTACAATCTGCTGAGC
1 TCTACAATCTGCTGAGC
2107972 TCTACAAT-T-CTGAGC
1 TCTACAATCTGCTGAGC
2107987 T
1 T
2107988 TGGTACTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (17 bp):
TCTACAATCTGCTGAGC
Found at i:2117801 original size:27 final size:27
Alignment explanation
Indices: 2117771--2117832 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2117761 TTTAGAATAA
*
2117771 ATTACTTATTTTAATCAT-TTAATTATT
1 ATTA-TTATTTAAATCATCTTAATTATT
*
2117798 ATTATTATTTAAATTATCTTAATTATCT
1 ATTATTATTTAAATCATCTTAATTAT-T
*
2117826 ATCATTA
1 ATTATTA
2117833 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 11 0.37
27 12 0.40
28 7 0.23
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTATTATTTAAATCATCTTAATTATT
Found at i:2122490 original size:2 final size:2
Alignment explanation
Indices: 2122483--2122512 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2122473 TGCCATTTCT
*
2122483 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2122513 GGAGTGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2130967 original size:17 final size:17
Alignment explanation
Indices: 2130940--2130978 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2130930 AATTTACAAT
2130940 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
2130956 TAATTATAAATAATATC
1 TAATTATAAATAATATC
2130973 TAATTA
1 TAATTA
2130979 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:2137032 original size:16 final size:16
Alignment explanation
Indices: 2137011--2137045 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2137001 AACGATGTTT
2137011 GCACTAGCTTGTGTGA
1 GCACTAGCTTGTGTGA
2137027 GCACTAGCTTGTGTGA
1 GCACTAGCTTGTGTGA
2137043 GCA
1 GCA
2137046 AAAGCATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (16 bp):
GCACTAGCTTGTGTGA
Found at i:2138034 original size:43 final size:43
Alignment explanation
Indices: 2137986--2138107 Score: 165
Period size: 43 Copynumber: 2.8 Consensus size: 43
2137976 TTTAGCGGTG
2137986 AAACGCCGCAATAGGTGTTGATATTTAGCGGTGTTTGTCAGAA
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGTGTTTGTCAGAA
* * * * * *
2138029 AAACGCCACAATAGGTATT-TTAATTTTGCGGCGTTTGTCATAA
1 AAACGCCGCAATAGGTGTTGAT-ATTTAGCGGTGTTTGTCAGAA
*
2138072 AAACGTCGCAATAGGTGTTGATATTTAGCGGTGTTT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGTGTTT
2138108 TTTTAGACAA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 63 0.97
44 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGTGTTTGTCAGAA
Found at i:2138642 original size:24 final size:23
Alignment explanation
Indices: 2138615--2138663 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
2138605 TCTGCTGATA
*
2138615 TACTGCTTCTCTCTGTGCTGCCGT
1 TACT-CTTCTCTCTGTGCTGCCGC
2138639 TA--CTTCTCTCTGTGCTGCCGC
1 TACTCTTCTCTCTGTGCTGCCGC
2138660 TACT
1 TACT
2138664 ACTCTGGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 20 0.91
24 2 0.09
ACGTcount: A:0.06, C:0.35, G:0.18, T:0.41
Consensus pattern (23 bp):
TACTCTTCTCTCTGTGCTGCCGC
Found at i:2138644 original size:21 final size:21
Alignment explanation
Indices: 2138620--2138668 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2138610 TGATATACTG
*
2138620 CTTCTCTCTGTGCTGCCGTTA
1 CTTCTCTCTGTGCTGCCGCTA
2138641 CTTCTCTCTGTGCTGCCGCTA
1 CTTCTCTCTGTGCTGCCGCTA
*
2138662 CTACTCT
1 CTTCTCT
2138669 GGCTGCTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.06, C:0.37, G:0.16, T:0.41
Consensus pattern (21 bp):
CTTCTCTCTGTGCTGCCGCTA
Found at i:2139840 original size:36 final size:36
Alignment explanation
Indices: 2139800--2139870 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2139790 AAAATATCGA
* *
2139800 CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
1 CATTGGTATAGATAATTATTCTAGGTAAACTATATT
2139836 CATTGGTATAGATAATTATTCTAGGTAAACTATAT
1 CATTGGTATAGATAATTATTCTAGGTAAACTATAT
2139871 ATAATAATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (36 bp):
CATTGGTATAGATAATTATTCTAGGTAAACTATATT
Found at i:2141004 original size:18 final size:16
Alignment explanation
Indices: 2140961--2140996 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2140951 ACTTTTTTTT
* *
2140961 AAAGCAAAGGTATTCC
1 AAAGAAAAGATATTCC
2140977 AAAGAAAAGATATTCC
1 AAAGAAAAGATATTCC
2140993 AAAG
1 AAAG
2140997 CTAAAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.17
Consensus pattern (16 bp):
AAAGAAAAGATATTCC
Found at i:2143980 original size:82 final size:82
Alignment explanation
Indices: 2143874--2144070 Score: 245
Period size: 82 Copynumber: 2.4 Consensus size: 82
2143864 TCATATTTTT
* * * * *
2143874 GCGGCGTTTTTTGCACAAACGCCACTATAAACAATACTATTGCGGCATTT-TTTATTAAACGCCG
1 GCGGCGTTTGTTGAACAAACGCCACTATAAACAACACTATAGCGGCATTTGTTTA-AAAACGCCG
*
2143938 CGAAATTACTTA-TCTATA
65 CGAAATTAC-CACTCTATA
* * * *
2143956 GCGTCGTTTGTTGAACAAATGCCACTATAAACAACACTATAGCGGCTTTTGTTTAAAAACGTCGC
1 GCGGCGTTTGTTGAACAAACGCCACTATAAACAACACTATAGCGGCATTTGTTTAAAAACGCCGC
* *
2144021 TAAATTACCACTCTATT
66 GAAATTACCACTCTATA
*
2144038 GCGGCGTTTGTTGAAAAAACGCCACTATAAACA
1 GCGGCGTTTGTTGAACAAACGCCACTATAAACA
2144071 TCTCTATTAC
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
81 1 0.01
82 93 0.95
83 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (82 bp):
GCGGCGTTTGTTGAACAAACGCCACTATAAACAACACTATAGCGGCATTTGTTTAAAAACGCCGC
GAAATTACCACTCTATA
Found at i:2144008 original size:41 final size:40
Alignment explanation
Indices: 2143951--2144070 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 40
2143941 AATTACTTAT
* *
2143951 CTATAGCGTCGTTTGTTGAACAAATGCCACTATAAACAACA
1 CTATAGCGGCGTTTGTTGAA-AAACGCCACTATAAACAACA
* * * * * *
2143992 CTATAGCGGCTTTTGTTTAAAAACGTCGCTA-AATTACCACT
1 CTATAGCGGCGTTTGTTGAAAAACGCCACTATAA--ACAACA
*
2144033 CTATTGCGGCGTTTGTTGAAAAAACGCCACTATAAACA
1 CTATAGCGGCGTTTGTTG-AAAAACGCCACTATAAACA
2144071 TCTCTATTAC
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
39 2 0.03
40 8 0.13
41 38 0.62
42 11 0.18
43 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (40 bp):
CTATAGCGGCGTTTGTTGAAAAACGCCACTATAAACAACA
Found at i:2144076 original size:41 final size:41
Alignment explanation
Indices: 2143872--2144078 Score: 111
Period size: 41 Copynumber: 5.0 Consensus size: 41
2143862 GTTCATATTT
* * * *
2143872 TTGCGGCGTTTTTTGCACAAACGCCACTATAAACAAT-ACTA
1 TTGCGGCGTTTGTTGAAAAAACGCCACTATAAAC-ATCTCTA
* * ** * * * *
2143913 TTGCGGCATTT-TTTATTAAACGCCGCGA-AATTACTTATCTA
1 TTGCGGCGTTTGTTGAAAAAACGCCACTATAA--ACATCTCTA
* * * * * *
2143954 TAGCGTCGTTTGTTGAACAAATGCCACTATAAACAACACTA
1 TTGCGGCGTTTGTTGAAAAAACGCCACTATAAACATCTCTA
* * * * *
2143995 TAGCGGCTTTTGTT-TAAAAACGTCGCTA-AATTACCA-CTCTA
1 TTGCGGCGTTTGTTGAAAAAACGCCACTATAA--A-CATCTCTA
2144036 TTGCGGCGTTTGTTGAAAAAACGCCACTATAAACATCTCTA
1 TTGCGGCGTTTGTTGAAAAAACGCCACTATAAACATCTCTA
2144077 TT
1 TT
2144079 ACGCTTTTGA
Statistics
Matches: 120, Mismatches: 35, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
39 4 0.03
40 23 0.19
41 65 0.54
42 24 0.20
43 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (41 bp):
TTGCGGCGTTTGTTGAAAAAACGCCACTATAAACATCTCTA
Found at i:2144107 original size:82 final size:81
Alignment explanation
Indices: 2143872--2144137 Score: 207
Period size: 82 Copynumber: 3.3 Consensus size: 81
2143862 GTTCATATTT
* * * * * * * *
2143872 TTGCGGCGTTTTTTGCACAAACGCCACTATAAACAATACTATTGCGGCATTTT--TTATTAAACG
1 TTGCGACGTTTGTTGAAAAAACGCCACTATAAACAACACTATAGCGGC-TTTTGGCTA-AAAACG
* **
2143935 CCGCGAAATTACTTATCTA
64 CCGCTAAATTAC-CCTCTA
* * * * ** *
2143954 TAGCGTCGTTTGTTGAACAAATGCCACTATAAACAACACTATAGCGGCTTTTGTTTAAAAACGTC
1 TTGCGACGTTTGTTGAAAAAACGCCACTATAAACAACACTATAGCGGCTTTTGGCTAAAAACGCC
2144019 GCTAAATTACCACTCTA
66 GCTAAATTACC-CTCTA
* * * **
2144036 TTGCGGCGTTTGTTGAAAAAACGCCACTATAAACATCTCTATTA-C-GCTTTTGAGCTATTAACG
1 TTGCGACGTTTGTTGAAAAAACGCCACTATAAACAACACTA-TAGCGGCTTTTG-GCTAAAAACG
*
2144099 CCGTTAAATTACCCTCTA
64 CCGCTAAATTACCCTCTA
* * *
2144117 TTACGATGTTTGTTTAAAAAA
1 TTGCGACGTTTGTTGAAAAAA
2144138 TGCAGCTAAA
Statistics
Matches: 151, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
81 33 0.22
82 113 0.75
83 5 0.03
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (81 bp):
TTGCGACGTTTGTTGAAAAAACGCCACTATAAACAACACTATAGCGGCTTTTGGCTAAAAACGCC
GCTAAATTACCCTCTA
Found at i:2144248 original size:12 final size:12
Alignment explanation
Indices: 2144214--2144249 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2144204 GTTTTCCCTT
2144214 AAAACGCCGCTA
1 AAAACGCCGCTA
*
2144226 AAAACACCGCTA
1 AAAACGCCGCTA
*
2144238 AAAACGTCGCTA
1 AAAACGCCGCTA
2144250 CAGAACACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.14, T:0.11
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:2171255 original size:21 final size:20
Alignment explanation
Indices: 2171209--2171257 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
2171199 CTGAACTGAA
* *
2171209 AAACAGAAGCATAACAGTTT
1 AAACAGAAGCATAACACTTG
2171229 AAACAGAAGCATAACAACTTG
1 AAACAGAAGCATAAC-ACTTG
2171250 AAACAGAA
1 AAACAGAA
2171258 AACTCAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.14
Consensus pattern (20 bp):
AAACAGAAGCATAACACTTG
Found at i:2172963 original size:54 final size:54
Alignment explanation
Indices: 2172882--2172994 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
2172872 AGTACTCTTG
* *
2172882 TATTATTTGATAGAGTAACAACTTGCTGACTGTGACCAGTATCGGGGGCAGAGT
1 TATTATTTGATAGAGCAACAACTTGCTGACTGTGACCAGTATCGGGGGCAAAGT
* ** *
2172936 TATTATTTGATGGAGCAACTGCTTGCTGACTGTGACCAGTATCGGGTGCAAAGT
1 TATTATTTGATAGAGCAACAACTTGCTGACTGTGACCAGTATCGGGGGCAAAGT
2172990 TATTA
1 TATTA
2172995 GCAATACTGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (54 bp):
TATTATTTGATAGAGCAACAACTTGCTGACTGTGACCAGTATCGGGGGCAAAGT
Found at i:2175880 original size:21 final size:20
Alignment explanation
Indices: 2175834--2175882 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
2175824 CTGAACTGAA
* *
2175834 AAACAGAAGCATAACAGTTT
1 AAACAGAAGCATAACACTTG
2175854 AAACAGAAGCATAACAACTTG
1 AAACAGAAGCATAAC-ACTTG
2175875 AAACAGAA
1 AAACAGAA
2175883 AACTCAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.14
Consensus pattern (20 bp):
AAACAGAAGCATAACACTTG
Found at i:2183481 original size:139 final size:138
Alignment explanation
Indices: 2183290--2183683 Score: 619
Period size: 139 Copynumber: 2.8 Consensus size: 138
2183280 AGTGATGTTC
* * * * *
2183290 CAACTCCTTATGTGATGGAAACAAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTC
1 CAACTCCATATGTGA-CGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* *
2183355 TCTTATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAAGGTTGATCCCTCGAGTGAGGT
65 -CTTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAGGTTGATCCCTCGAGTGAGGT
2183420 GTTGCTGATT
129 GTTGCTGATT
2183430 CAACTCCATATGTGACGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
1 CAACTCCATATGTGACGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
** *
2183495 TTCATCGGCCGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGTGAGGTG
66 TT-ATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAGGTTGATCCCTCGAGTGAGGTG
2183560 TTGCTGATT
130 TTGCTGATT
*
2183569 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
1 CAACTCCATATGTGACGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-C
* *
2183634 CTCATCGGATGAGCTCTTCTCATTATGAACTCTCCATTGG-AAGTGTTGAT
65 CTTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAG-GTTGAT
2183684 TGGTTTCCCT
Statistics
Matches: 235, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
138 5 0.02
139 213 0.91
140 17 0.07
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (138 bp):
CAACTCCATATGTGACGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
TTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAGGTTGATCCCTCGAGTGAGGTGT
TGCTGATT
Found at i:2186233 original size:28 final size:28
Alignment explanation
Indices: 2186193--2186252 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
2186183 GAGAAGGTAA
* *
2186193 TGTTTTAGGTTAATTAAGGGAAGTAATG
1 TGTTTTAGATTAATTAAGGGAAATAATG
* *
2186221 TGTTTTCGATTAATTTAGGGAAATAATG
1 TGTTTTAGATTAATTAAGGGAAATAATG
2186249 TGTT
1 TGTT
2186253 CCAGGTTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (28 bp):
TGTTTTAGATTAATTAAGGGAAATAATG
Found at i:2186925 original size:15 final size:14
Alignment explanation
Indices: 2186904--2186938 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2186894 ATTTTCTCTC
2186904 TTTTTTTCTCTTTT
1 TTTTTTTCTCTTTT
*
2186918 TCTTTTTTCTGTTTT
1 T-TTTTTTCTCTTTT
2186933 TTTTTT
1 TTTTTT
2186939 GCATGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (14 bp):
TTTTTTTCTCTTTT
Found at i:2189196 original size:30 final size:30
Alignment explanation
Indices: 2189160--2189221 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2189150 ACTGGTAAAT
2189160 GAACCATAAAATACAGTGATAAAACACACA
1 GAACCATAAAATACAGTGATAAAACACACA
2189190 GAACCATAAAATACAGTGATAAAACACACA
1 GAACCATAAAATACAGTGATAAAACACACA
2189220 GA
1 GA
2189222 GGAAATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.56, C:0.19, G:0.11, T:0.13
Consensus pattern (30 bp):
GAACCATAAAATACAGTGATAAAACACACA
Found at i:2196044 original size:92 final size:92
Alignment explanation
Indices: 2195938--2196119 Score: 247
Period size: 92 Copynumber: 2.0 Consensus size: 92
2195928 AAAGTAATAA
*
2195938 ATTATACATAATTTAAAAATATATTATCTTAAAAACAATATTTAATAATTAATATAATTAATTTG
1 ATTATACATAATTTAAAAATATATTATCTCAAAAACAATATTTAATAATTAATATAATTAATTTG
* **
2196003 AGCATAAATTTTTTCATGTTCCATATG
66 AACATAAAACTTTTCATGTTCCATATG
* ** * * * * *
2196030 ATTATACATGATTTAAATGTATATTATCTCAAAACCAATATTTTATTATTAATATAGTTAATTTT
1 ATTATACATAATTTAAAAATATATTATCTCAAAAACAATATTTAATAATTAATATAATTAATTTG
*
2196095 AACTTAAAACTTTTCATGTTCCATA
66 AACATAAAACTTTTCATGTTCCATA
2196120 CATACCTAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (92 bp):
ATTATACATAATTTAAAAATATATTATCTCAAAAACAATATTTAATAATTAATATAATTAATTTG
AACATAAAACTTTTCATGTTCCATATG
Found at i:2197491 original size:38 final size:40
Alignment explanation
Indices: 2197430--2197510 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 40
2197420 GTTTTTTTAT
* * *
2197430 ATTAATTATTAGTTTATTTTTTTTACT-TTAATTTGATAAA
1 ATTAATTATTAGTTTAATATTTTTA-TATTAATTCGATAAA
*
2197470 ATTAATT-TT-GTTTAATATTTTTATATTCATTCGATAAA
1 ATTAATTATTAGTTTAATATTTTTATATTAATTCGATAAA
2197508 ATT
1 ATT
2197511 TTAAGGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 1 0.03
38 26 0.72
39 2 0.06
40 7 0.19
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (40 bp):
ATTAATTATTAGTTTAATATTTTTATATTAATTCGATAAA
Found at i:2201055 original size:21 final size:22
Alignment explanation
Indices: 2201008--2201056 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
2200998 TTAATAATAA
2201008 TGTTTTATGATATGTTTTCGGT
1 TGTTTTATGATATGTTTTCGGT
* * * *
2201030 CGTTTTATTAT-TGTTTTTGTT
1 TGTTTTATGATATGTTTTCGGT
2201051 TGTTTT
1 TGTTTT
2201057 TTTTTCTCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.67
Consensus pattern (22 bp):
TGTTTTATGATATGTTTTCGGT
Found at i:2204467 original size:16 final size:18
Alignment explanation
Indices: 2204445--2204483 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2204435 GAAAAATAAT
*
2204445 TAATTTAT-TATTTTTAA
1 TAATTTATAAATTTTTAA
2204462 -AATTTATAAATTTTTAA
1 TAATTTATAAATTTTTAA
2204479 TAATT
1 TAATT
2204484 AAACATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATTTATAAATTTTTAA
Found at i:2204995 original size:11 final size:12
Alignment explanation
Indices: 2204979--2205008 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2204969 TATGTGTATG
2204979 ATATATGAAGAA
1 ATATATGAAGAA
2204991 A-ATATGAAGAA
1 ATATATGAAGAA
2205002 ATATATG
1 ATATATG
2205009 TACCGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.27
Consensus pattern (12 bp):
ATATATGAAGAA
Found at i:2211455 original size:21 final size:23
Alignment explanation
Indices: 2211430--2211489 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
2211420 TATTTTTAAT
2211430 TATATTTTTTTATTTA-TT-TAC
1 TATATTTTTTTATTTATTTATAC
* *
2211451 TATATTTCTTTTTTTTATTTATAT
1 TATATTT-TTTTATTTATTTATAC
2211475 TATATTATTTTTATT
1 TATATT-TTTTTATT
2211490 ATATATATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 7 0.22
22 8 0.25
23 2 0.06
24 14 0.44
25 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (23 bp):
TATATTTTTTTATTTATTTATAC
Found at i:2211484 original size:14 final size:14
Alignment explanation
Indices: 2211465--2211504 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2211455 TTTCTTTTTT
2211465 TTATTTATATTATA
1 TTATTTATATTATA
*
2211479 TTATTTTTATTATA
1 TTATTTATATTATA
2211493 TATATCTTATAT
1 T-TAT-TTATAT
2211505 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:2211495 original size:40 final size:40
Alignment explanation
Indices: 2211422--2211500 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
2211412 TATACATATA
* * *
2211422 TTTTTAATTATATTTTTTTATTTATTTACTATATTTCTTT
1 TTTTTAATTATATTATATTATTTATTTACTATATATCTTT
* *
2211462 TTTTTATTTATATTATATTATTTTTATTA-TATATATCTT
1 TTTTTAATTATATTATATTATTTAT-TTACTATATATCTT
2211501 ATATCATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 30 0.91
41 3 0.09
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (40 bp):
TTTTTAATTATATTATATTATTTATTTACTATATATCTTT
Found at i:2211496 original size:2 final size:2
Alignment explanation
Indices: 2211489--2211535 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
2211479 TTATTTTTAT
*
2211489 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
2211530 TA TA TA
1 TA TA TA
2211536 GATGTATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2211691 original size:13 final size:13
Alignment explanation
Indices: 2211673--2211697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2211663 TTACTTTATT
2211673 TTATTTTTTTCTA
1 TTATTTTTTTCTA
2211686 TTATTTTTTTCT
1 TTATTTTTTTCT
2211698 TAATATCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:2211835 original size:18 final size:18
Alignment explanation
Indices: 2211808--2211842 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2211798 TTTTTATTCA
2211808 TTTTTAATTTCTTTTACC
1 TTTTTAATTTCTTTTACC
* *
2211826 TTTTTTATTTTTTTTAC
1 TTTTTAATTTCTTTTAC
2211843 TCCATTAATA
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:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTAATTTCTTTTACC
Found at i:2211925 original size:27 final size:25
Alignment explanation
Indices: 2211895--2211950 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
2211885 ATTTTATTCA
* *
2211895 TTTTGTTTTTTTATTATTTTTTACGTG
1 TTTTGTTATTTT-TCATTTTTT-CGTG
*
2211922 TTTTGTTATTTTTCATTTTTTCTTG
1 TTTTGTTATTTTTCATTTTTTCGTG
2211947 TTTT
1 TTTT
2211951 ATTTATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 8 0.31
27 11 0.42
ACGTcount: A:0.09, C:0.05, G:0.09, T:0.77
Consensus pattern (25 bp):
TTTTGTTATTTTTCATTTTTTCGTG
Found at i:2215002 original size:10 final size:10
Alignment explanation
Indices: 2214982--2215012 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
2214972 AGATTCAATC
2214982 AGAACAAAAAG
1 AGAA-AAAAAG
2214993 AGAAAAAAAG
1 AGAAAAAAAG
2215003 AGAAAAAAAG
1 AGAAAAAAAG
2215013 CAAAGAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:2215023 original size:13 final size:13
Alignment explanation
Indices: 2214989--2215037 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
2214979 ATCAGAACAA
2214989 AAAGAGAAAAA--
1 AAAGAGAAAAAGC
*
2215000 AAGAGAAAAAAAGC
1 AA-AGAGAAAAAGC
2215014 AAAGAGAAAAAGC
1 AAAGAGAAAAAGC
2215027 AAAGAGAAAAA
1 AAAGAGAAAAA
2215038 ATAAAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 2 0.06
12 8 0.24
13 21 0.64
14 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAGAAAAAGC
Found at i:2215043 original size:13 final size:13
Alignment explanation
Indices: 2214989--2215048 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
2214979 ATCAGAACAA
2214989 AAAGAGAAAAAA-
1 AAAGAGAAAAAAC
*
2215001 AGAGA-AAAAAAGC
1 AAAGAGAAAAAA-C
*
2215014 AAAGAGAAAAAGC
1 AAAGAGAAAAAAC
*
2215027 AAAGAGAAAAAAT
1 AAAGAGAAAAAAC
2215040 AAAG-GAAAA
1 AAAGAGAAAA
2215049 TTGAAGTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 6 0.15
12 9 0.22
13 20 0.50
14 5 0.12
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:2216840 original size:36 final size:36
Alignment explanation
Indices: 2216793--2216882 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
2216783 ATTGAAAACA
*
2216793 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
2216829 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
2216865 TTTCCCTTGAAACAAATT
1 TTTCCCTTGAAACAAATT
2216883 ATTTGAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:2216904 original size:101 final size:102
Alignment explanation
Indices: 2216717--2216961 Score: 260
Period size: 101 Copynumber: 2.4 Consensus size: 102
2216707 TTTTACTTCG
* *
2216717 CTTGAGATAATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACATAAA
* * * * *
2216782 CATTGAAAACATTTCCCTTGAAATAAATTTCGTCTCT
66 CATTGAAAACATTTCACTTGAAACAAATTCCATCTCC
* * *
2216819 CTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAT
1 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACATAAA
* **** * *
2216882 TATTTGAATTTGTTTTATTTGAAACAAATTCCATCTCC
66 CA-TTGAAAACATTTCACTTGAAACAAATTCCATCTCC
* ** * * *
2216920 CTTGATATAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGA
1 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGA
2216962 AACAAATTTC
Statistics
Matches: 118, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
100 3 0.03
101 77 0.65
102 38 0.32
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (102 bp):
CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACATAAA
CATTGAAAACATTTCACTTGAAACAAATTCCATCTCC
Found at i:2217055 original size:123 final size:123
Alignment explanation
Indices: 2216834--2217057 Score: 295
Period size: 123 Copynumber: 1.8 Consensus size: 123
2216824 GACAGTTTCC
* * * * *
2216834 CTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTATTTGAATTTGTTTTA
1 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATTTATTTCA
** * * * *
2216899 TTTGAAACAAATTCCATCTCCCTTGATATAGTTTCTTTTGGAACTAAGTTTTGTCTCT
66 CCTAAAACAAATTCCATCTCACTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
* * *
2216957 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCTTTGAAACAAAATCTTTGAATTTATTTCC
1 CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATTTATTTCA
***
2217022 CCTAAAACAAATTTTGTCTCACTTGAGACAGTTTCT
66 CCTAAAACAAATTCCATCTCACTTGAGACAGTTTCT
2217058 CTTGAAACAC
Statistics
Matches: 84, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
123 84 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (123 bp):
CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATTTATTTCA
CCTAAAACAAATTCCATCTCACTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
Found at i:2217065 original size:65 final size:67
Alignment explanation
Indices: 2216961--2217106 Score: 208
Period size: 65 Copynumber: 2.2 Consensus size: 67
2216951 GTCTCTCTTG
* * **
2216961 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCTTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCACTTGAGACAGTTTCCTTTGAAACACAAAATCTTCAAATTTATTTCCCC
2217024 TA
66 TA
2217026 AAACAAATTTTGTCTCACTTGAGACAGTTT-CTCTTGAAACACAAAATCTTCAAATTTATTTCCC
1 AAACAAATTTTGTCTCACTTGAGACAGTTTCCT-TTGAAACACAAAATCTTCAAATTTATTTCCC
*
2217090 TTA
65 CTA
2217093 AAACAAAATTTTGT
1 AAAC-AAATTTTGT
2217107 TTACCGTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
64 2 0.03
65 31 0.43
66 2 0.03
67 28 0.39
68 9 0.12
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (67 bp):
AAACAAATTTTGTCTCACTTGAGACAGTTTCCTTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:2218041 original size:110 final size:110
Alignment explanation
Indices: 2217843--2218049 Score: 292
Period size: 110 Copynumber: 1.9 Consensus size: 110
2217833 GCTTCCCAGT
* * * *
2217843 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTCCACAGCAAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
*
2217908 CAACGAAGGGATGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAACGAAGGGATGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * *
2217953 TTCAGAGTCAATTTCAACTCCACAGTAAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTCCACAGCAAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
2218018 CAGCGAAGGG--GCAGTTGACTGTCAACAAACAA
66 CAACGAAGGGATG-A-CTGACTGTCAACAAACAA
2218050 TTTCCAGAGC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
108 1 0.01
109 1 0.01
110 83 0.98
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTCCACAGCAAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGATGACTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:2219436 original size:14 final size:14
Alignment explanation
Indices: 2219417--2219447 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2219407 CCCCTATATA
2219417 TATATATTTTTAAT
1 TATATATTTTTAAT
*
2219431 TATATATTTTTATT
1 TATATATTTTTAAT
2219445 TAT
1 TAT
2219448 TTACTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATATATTTTTAAT
Found at i:2219450 original size:22 final size:22
Alignment explanation
Indices: 2219425--2219490 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
2219415 TATATATATT
2219425 TTTAATTATATATTTTTATTTA
1 TTTAATTATATATTTTTATTTA
* *
2219447 TTT-ACTATAT-TCCTTTTTTTTA
1 TTTAATTATATAT--TTTTATTTA
2219469 TTTATATTATATTATTTTTATT
1 TTTA-ATTATA-TATTTTTATT
2219491 ATATATATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
20 1 0.03
21 6 0.18
22 14 0.41
24 11 0.32
25 1 0.03
26 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTAATTATATATTTTTATTTA
Found at i:2219485 original size:14 final size:14
Alignment explanation
Indices: 2219466--2219505 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2219456 TTCCTTTTTT
2219466 TTATTTATATTATA
1 TTATTTATATTATA
*
2219480 TTATTTTTATTATA
1 TTATTTATATTATA
2219494 TATATCTTATAT
1 T-TAT-TTATAT
2219506 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:2219575 original size:17 final size:17
Alignment explanation
Indices: 2219555--2219605 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 17
2219545 TTTACTATGT
2219555 ATATATATTTTTTCTTA
1 ATATATATTTTTTCTTA
*
2219572 ATAT-TA-TGTTT-TT-
1 ATATATATTTTTTCTTA
2219585 ATATATATTTTTTCTTA
1 ATATATATTTTTTCTTA
2219602 ATAT
1 ATAT
2219606 TCTATTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 8 0.29
16 4 0.14
17 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (17 bp):
ATATATATTTTTTCTTA
Found at i:2219590 original size:15 final size:14
Alignment explanation
Indices: 2219556--2219606 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
2219546 TTACTATGTA
2219556 TATATATTTTTTCT
1 TATATATTTTTTCT
*
2219570 TAATATTATGTTTTT-A
1 T-ATA-TAT-TTTTTCT
2219586 TATATATTTTTTCT
1 TATATATTTTTTCT
2219600 TA-ATATT
1 TATATATT
2219607 CTATTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 10 0.32
14 6 0.19
15 6 0.19
16 4 0.13
17 5 0.16
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (14 bp):
TATATATTTTTTCT
Found at i:2219624 original size:30 final size:30
Alignment explanation
Indices: 2219554--2219614 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2219544 ATTTACTATG
*
2219554 TATATATATTTTTTCTTAATATTATGTTTT
1 TATATATATTTTTTCTTAATATTATATTTT
*
2219584 TATATATATTTTTTCTTAATATTCTATTTT
1 TATATATATTTTTTCTTAATATTATATTTT
2219614 T
1 T
2219615 GTTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (30 bp):
TATATATATTTTTTCTTAATATTATATTTT
Found at i:2219666 original size:18 final size:18
Alignment explanation
Indices: 2219640--2219677 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2219630 TATATATATA
2219640 TTATATTTTTACT-TTATT
1 TTATATTTTT-CTATTATT
*
2219658 TTATTTTTTTCTATTATT
1 TTATATTTTTCTATTATT
2219676 TT
1 TT
2219678 TTTCTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATATTTTTCTATTATT
Found at i:2219674 original size:13 final size:13
Alignment explanation
Indices: 2219658--2219682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2219648 TTACTTTATT
2219658 TTATTTTTTTCTA
1 TTATTTTTTTCTA
2219671 TTATTTTTTTCT
1 TTATTTTTTTCT
2219683 TAATATCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:2219815 original size:18 final size:17
Alignment explanation
Indices: 2219783--2219827 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2219773 TGTACACATT
2219783 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
2219800 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
2219818 ATTTTTTTAC
1 ATTTTTTTAC
2219828 TCTATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:2219825 original size:17 final size:17
Alignment explanation
Indices: 2219781--2219827 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
2219771 TATGTACACA
2219781 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
2219798 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
2219816 TTATTTTTTTAC
1 TTATTTTTTTAC
2219828 TCTATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:2219892 original size:19 final size:19
Alignment explanation
Indices: 2219870--2219911 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2219860 TTTTTTAACA
2219870 TTTTATTCATTTTGT-TTAT
1 TTTTATTCATTTT-TATTAT
*
2219889 TTTTATTTATTTTTATTAT
1 TTTTATTCATTTTTATTAT
2219908 TTTT
1 TTTT
2219912 TACGTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTATTCATTTTTATTAT
Found at i:2219930 original size:9 final size:9
Alignment explanation
Indices: 2219870--2219911 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
2219860 TTTTTTAACA
2219870 TTTTATTCAT
1 TTTTATT-AT
2219880 TTTGT-TTAT
1 TTT-TATTAT
2219889 TTTTATTTAT
1 TTTTA-TTAT
2219899 TTTTATTAT
1 TTTTATTAT
2219908 TTTT
1 TTTT
2219912 TACGTGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 13 0.45
10 14 0.48
11 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTATTAT
Found at i:2221555 original size:3 final size:3
Alignment explanation
Indices: 2221549--2221573 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2221539 TAACAAGGAG
2221549 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
2221574 CTTATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2222614 original size:14 final size:14
Alignment explanation
Indices: 2222595--2222624 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2222585 CCGGCATCAA
2222595 CACTAACACCATTG
1 CACTAACACCATTG
2222609 CACTAACACCATTG
1 CACTAACACCATTG
2222623 CA
1 CA
2222625 ACTTCCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.20
Consensus pattern (14 bp):
CACTAACACCATTG
Found at i:2223316 original size:33 final size:33
Alignment explanation
Indices: 2223257--2223393 Score: 130
Period size: 33 Copynumber: 4.0 Consensus size: 33
2223247 CTCATAAGCA
* * *
2223257 AAGTTGGCCACCTACCAAAGATGAATTTTTCAAT
1 AAGTTGGACACCAACC-AAGATGAATTTTCCAAT
* *
2223291 AAGTTTGTCACCAACCAAGATGAATTTTCCAAT
1 AAGTTGGACACCAACCAAGATGAATTTTCCAAT
* * *
2223324 AAGTTGGACACCAACCAAGATGAAATTCCCATGT
1 AAGTTGGACACCAACCAAGATGAATTTTCCA-AT
* *
2223358 GCAAAGTTGGCCACCTACCAAAGATGAATTTTCCAA
1 ---AAGTTGGACACCAACC-AAGATGAATTTTCCAA
2223394 CTTGCCAAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
33 43 0.51
34 14 0.17
37 14 0.17
38 13 0.15
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (33 bp):
AAGTTGGACACCAACCAAGATGAATTTTCCAAT
Found at i:2227960 original size:34 final size:33
Alignment explanation
Indices: 2227917--2228053 Score: 139
Period size: 33 Copynumber: 4.0 Consensus size: 33
2227907 CTCATATGCA
* *
2227917 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGACCACCAACC-AAGATGAATTTTCCAAT
* *
2227951 AAGTTGGCCACCAACCAAGATGAATTTTTCAAT
1 AAGTTGACCACCAACCAAGATGAATTTTCCAAT
* * *
2227984 AAGTTGACCACCAACCAAGATGAAATTCCCATGT
1 AAGTTGACCACCAACCAAGATGAATTTTCCA-AT
* *
2228018 GCAAAGTTGACCACCTACCAAAGATGAGTTTTCCAA
1 ---AAGTTGACCACCAACC-AAGATGAATTTTCCAA
2228054 CCTGTCAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
33 43 0.50
34 16 0.19
37 15 0.17
38 12 0.14
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (33 bp):
AAGTTGACCACCAACCAAGATGAATTTTCCAAT
Found at i:2227976 original size:33 final size:33
Alignment explanation
Indices: 2227917--2228007 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
2227907 CTCATATGCA
*
2227917 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
*
2227951 AAGTTGGCCACCAACCAAGATGAATTTTTCAAT
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
*
2227984 AAGTTGACCACCAACCAAGATGAA
1 AAGTTGGCCACCAACCAAGATGAA
2228008 ATTCCCATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 39 0.72
34 15 0.28
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
Found at i:2228025 original size:37 final size:34
Alignment explanation
Indices: 2227891--2228044 Score: 123
Period size: 33 Copynumber: 4.4 Consensus size: 34
2227881 ATATTTTAGG
* *
2227891 AACCAAAGATGAAATTCTCATATGCAAAGTTGGCCACC
1 AACCAAAGATGAAATTCCCA-AT---AAGTTGACCACC
* * * *
2227929 TACCAAAGATGAATTTTCCAATAAGTTGGCCACC
1 AACCAAAGATGAAATTCCCAATAAGTTGACCACC
* **
2227963 AACC-AAGATGAATTTTTCAATAAGTTGACCACC
1 AACCAAAGATGAAATTCCCAATAAGTTGACCACC
*
2227996 AACC-AAGATGAAATTCCCATGTGCAAAGTTGACCACC
1 AACCAAAGATGAAATTCCCA-AT---AAGTTGACCACC
*
2228033 TACCAAAGATGA
1 AACCAAAGATGA
2228045 GTTTTCCAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
33 43 0.43
34 16 0.16
37 17 0.17
38 23 0.23
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (34 bp):
AACCAAAGATGAAATTCCCAATAAGTTGACCACC
Found at i:2229340 original size:17 final size:17
Alignment explanation
Indices: 2229318--2229365 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
2229308 ATCGAATGGA
2229318 CTCGACTCGAGTTCGAG
1 CTCGACTCGAGTTCGAG
2229335 CTCGACTCGAGTTCGAG
1 CTCGACTCGAGTTCGAG
*
2229352 CTCAACTCGAGTTC
1 CTCGACTCGAGTTC
2229366 TTAACGATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (17 bp):
CTCGACTCGAGTTCGAG
Found at i:2230347 original size:2 final size:2
Alignment explanation
Indices: 2230340--2230364 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2230330 CTAGCTTTTA
2230340 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 A
2230365 GAGTGACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2230524 original size:2 final size:2
Alignment explanation
Indices: 2230517--2230553 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2230507 ATCTACCACC
2230517 AT AT 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 AT AT A
2230554 ATAAATCACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2235196 original size:20 final size:20
Alignment explanation
Indices: 2235171--2235209 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2235161 GCACATGTTA
*
2235171 AAGAATACATCGATGCACTG
1 AAGAATACACCGATGCACTG
*
2235191 AAGAATGCACCGATGCACT
1 AAGAATACACCGATGCACT
2235210 TCAATGGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
AAGAATACACCGATGCACTG
Found at i:2235907 original size:15 final size:15
Alignment explanation
Indices: 2235889--2235924 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
2235879 ATCATATGAA
2235889 ATGTGATAAAGAGCT
1 ATGTGATAAAGAGCT
2235904 ATGTG--AAAGAGCT
1 ATGTGATAAAGAGCT
2235917 ATGTGATA
1 ATGTGATA
2235925 TGAATATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.68
15 6 0.32
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (15 bp):
ATGTGATAAAGAGCT
Found at i:2236042 original size:21 final size:21
Alignment explanation
Indices: 2236016--2236059 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2236006 AGAGTCGAGG
* *
2236016 ATCTATGTGGTCCTTCGGGAC
1 ATCTATGTAGTCCTTCGAGAC
2236037 ATCTATGTAGTCCTTCGAGAC
1 ATCTATGTAGTCCTTCGAGAC
2236058 AT
1 AT
2236060 TCTACGCGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (21 bp):
ATCTATGTAGTCCTTCGAGAC
Found at i:2240160 original size:21 final size:21
Alignment explanation
Indices: 2240134--2240176 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2240124 AGAGTCGAGG
2240134 ATCTATGTGGTCATTCGGGAC
1 ATCTATGTGGTCATTCGGGAC
*
2240155 ATCTATGTGGTCCTTCGGGAC
1 ATCTATGTGGTCATTCGGGAC
2240176 A
1 A
2240177 AATTCTACGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (21 bp):
ATCTATGTGGTCATTCGGGAC
Found at i:2242355 original size:16 final size:16
Alignment explanation
Indices: 2242304--2242372 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
2242294 GGGTCTCCAA
2242304 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
2242320 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
**
2242336 CGTTTATGTTCGTGCG
1 CGTTTATGTTCGTGTT
*
2242352 CGTTTATATTCGT-TT
1 CGTTTATGTTCGTGTT
2242367 -GTTTAT
1 CGTTTAT
2242373 TAAATGAACG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
14 6 0.13
16 40 0.87
ACGTcount: A:0.10, C:0.13, G:0.22, T:0.55
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:2244276 original size:81 final size:80
Alignment explanation
Indices: 2244131--2244284 Score: 258
Period size: 81 Copynumber: 1.9 Consensus size: 80
2244121 TTCTCTCATG
*
2244131 TTTTCTTTGAGTTAATTGCATATGAGGTCCGAAAATCATGATTCATTTTAAATTAGTCTATAAAC
1 TTTTCTTTGAATTAATTGCATATGAGGTCCGAAAATCATGATTCATTTTAAATTAGTCTATAAAC
2244196 TTTATAAACTTTAATA
66 TTTA-AAACTTTAATA
2244212 TTTTCTTTGAATTAATTGCATATGAGGTCCGAAAATCATGATTCATTTTAAATT-GTTTCT-TAA
1 TTTTCTTTGAATTAATTGCATATGAGGTCCGAAAATCATGATTCATTTTAAATTAG--TCTATAA
2244275 ACTTTAAAAC
64 ACTTTAAAAC
2244285 ATTATTTATG
Statistics
Matches: 70, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
80 5 0.07
81 62 0.89
82 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (80 bp):
TTTTCTTTGAATTAATTGCATATGAGGTCCGAAAATCATGATTCATTTTAAATTAGTCTATAAAC
TTTAAAACTTTAATA
Found at i:2246929 original size:3 final size:3
Alignment explanation
Indices: 2246869--2246912 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2246859 GTTTTTAATA
**
2246869 TAT TAT TAT CGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2246913 ATTAAATGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2249652 original size:19 final size:19
Alignment explanation
Indices: 2249628--2249665 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2249618 CATAAATATA
2249628 TATAGGCTTGCAATTGCAT
1 TATAGGCTTGCAATTGCAT
2249647 TATAGGCTTGCAATTGCAT
1 TATAGGCTTGCAATTGCAT
2249666 GCATGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (19 bp):
TATAGGCTTGCAATTGCAT
Found at i:2253232 original size:18 final size:19
Alignment explanation
Indices: 2253197--2253236 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2253187 TGATAAAAAT
*
2253197 ATAAAAATATATTATTATA
1 ATAAAAATATAATATTATA
2253216 ATAAAAATATAAT-TTATA
1 ATAAAAATATAATATTATA
2253234 ATA
1 ATA
2253237 GCTCATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATATAATATTATA
Found at i:2254822 original size:2 final size:2
Alignment explanation
Indices: 2254815--2254911 Score: 55
Period size: 2 Copynumber: 52.0 Consensus size: 2
2254805 TATCGGGCCG
* * * *
2254815 TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
2254855 TA TT TT TA -A TT TA -A TT TA AA TT TA T- TA -A TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2254892 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
2254912 ATAATTATTT
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
1 7 0.10
2 63 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2255022 original size:35 final size:36
Alignment explanation
Indices: 2254974--2255041 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
2254964 GATTACTAAA
*
2254974 CCCGTCCCTGTTTAACATAAAC-GATTTTCCCCATC
1 CCCGTCCCCGTTTAACATAAACGGATTTTCCCCATC
* *
2255009 CCCGTCCCCGTTTAGCATAAACGGTTTTTCCCC
1 CCCGTCCCCGTTTAACATAAACGGATTTTCCCC
2255042 GTCTCTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 20 0.69
36 9 0.31
ACGTcount: A:0.19, C:0.38, G:0.12, T:0.31
Consensus pattern (36 bp):
CCCGTCCCCGTTTAACATAAACGGATTTTCCCCATC
Found at i:2285587 original size:21 final size:20
Alignment explanation
Indices: 2285548--2285591 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2285538 AATCTTTCTG
2285548 ATTTTTATTCAATTCTAAAAT
1 ATTTTTATTCAATTCT-AAAT
*
2285569 ATTTTTATTTTAATT-TAAAT
1 ATTTTTA-TTCAATTCTAAAT
2285589 ATT
1 ATT
2285592 AATATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 8 0.38
22 6 0.29
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTATTCAATTCTAAAT
Found at i:2286194 original size:7 final size:7
Alignment explanation
Indices: 2286182--2286210 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2286172 AGACCCTAAC
2286182 TGTGCAG
1 TGTGCAG
2286189 TGTGCAG
1 TGTGCAG
2286196 TGTGCAG
1 TGTGCAG
2286203 TGTGCAG
1 TGTGCAG
2286210 T
1 T
2286211 AGTAGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.41, T:0.31
Consensus pattern (7 bp):
TGTGCAG
Found at i:2292081 original size:141 final size:141
Alignment explanation
Indices: 2291827--2292111 Score: 507
Period size: 141 Copynumber: 2.0 Consensus size: 141
2291817 TTCATCTGGA
* *
2291827 GCAGATCATGGTGTGGTTCCTATTAAAGAGATTGATGGTGGTAATGCCGTCTCTGGTATTCAAGG
1 GCAGATCATGGCGTGGTTCCTATTAAAGAGATTGATGGTAGTAATGCCGTCTCTGGTATTCAAGG
* *
2291892 AACATGCGAACATGCTGCTGGTGAACCAAAAAATGAATACGAGGATATGGAAGAAATAGAGACGG
66 AACAAGCGAACATGCTGCTGGTGAACCAAAAAATGAATACAAGGATATGGAAGAAATAGAGACGG
2291957 AGACCAAGGTG
131 AGACCAAGGTG
*
2291968 GCAGATCATGGCGTGGTTCCTATTAAAGAGATTGATTGTAGTAATGCCGTCTCTGGTATTCAAGG
1 GCAGATCATGGCGTGGTTCCTATTAAAGAGATTGATGGTAGTAATGCCGTCTCTGGTATTCAAGG
*
2292033 AACAAGTGAACATGCTGCTGGTGAACCAAAAAATGAATACAAGGATATGGAAGAAATAGAGACGG
66 AACAAGCGAACATGCTGCTGGTGAACCAAAAAATGAATACAAGGATATGGAAGAAATAGAGACGG
*
2292098 AGACTAAGGTG
131 AGACCAAGGTG
2292109 GCA
1 GCA
2292112 CTACCTGTTC
Statistics
Matches: 137, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
141 137 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (141 bp):
GCAGATCATGGCGTGGTTCCTATTAAAGAGATTGATGGTAGTAATGCCGTCTCTGGTATTCAAGG
AACAAGCGAACATGCTGCTGGTGAACCAAAAAATGAATACAAGGATATGGAAGAAATAGAGACGG
AGACCAAGGTG
Found at i:2305266 original size:192 final size:194
Alignment explanation
Indices: 2304938--2305324 Score: 760
Period size: 192 Copynumber: 2.0 Consensus size: 194
2304928 AAGGAACCAC
2304938 ATCGAATTCAGGCGACAAAATATACTGTACTTTCAGCAAAAGTGCAGTAGGCTCGAGAAATCGAT
1 ATCGAATTCAGGCGACAAAATATACTGTACTTTCAGCAAAAGTGCAGTAGGCTCGAGAAATCGAT
2305003 CATCATCTCGGTGTTGGTGGCGAGTGTGGGAGAGACAACTGAGGGTCTGAAATGAGAAAGAGCCA
66 CATCATCTCGGTGTTGGTGGCGAGTGTGGGAGAGACAACTGAGGGTCTGAAATGAGAAAGAGCCA
2305068 TTGTTTGGAGACACACTTGAACTTGAGGAGGGATTTGCT-GGTAACCTGAGGAGGAGTTGGGTT
131 TTGTTTGGAGACACACTTGAACTTGAGGAGGGATTTGCTGGGTAACCTGAGGAGGAGTTGGGTT
2305131 ATCGAATTCAGGCGAC-AAATATACTGTACTTTCAGCAAAAGTGCAGTAGGCTCGAGAAATCGAT
1 ATCGAATTCAGGCGACAAAATATACTGTACTTTCAGCAAAAGTGCAGTAGGCTCGAGAAATCGAT
2305195 CATCATCTCGGTGTTGGTGGCGAGTGTGGGAGAGACAACTGAGGGTCTGAAATGAGAAAGAGCCA
66 CATCATCTCGGTGTTGGTGGCGAGTGTGGGAGAGACAACTGAGGGTCTGAAATGAGAAAGAGCCA
2305260 TTGTTTGGAGACACACTTGAACTTGAGGAGGGATTTGCTGGGTAACCTGAGGAGGAGTTGGGTT
131 TTGTTTGGAGACACACTTGAACTTGAGGAGGGATTTGCTGGGTAACCTGAGGAGGAGTTGGGTT
2305324 A
1 A
2305325 ACAAATCATG
Statistics
Matches: 193, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
192 152 0.79
193 41 0.21
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (194 bp):
ATCGAATTCAGGCGACAAAATATACTGTACTTTCAGCAAAAGTGCAGTAGGCTCGAGAAATCGAT
CATCATCTCGGTGTTGGTGGCGAGTGTGGGAGAGACAACTGAGGGTCTGAAATGAGAAAGAGCCA
TTGTTTGGAGACACACTTGAACTTGAGGAGGGATTTGCTGGGTAACCTGAGGAGGAGTTGGGTT
Found at i:2306058 original size:30 final size:30
Alignment explanation
Indices: 2306022--2306095 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
2306012 CCCGAAGGAC
2306022 CTATCCAGAGGTCCTAAAGATCCTCGGTAA
1 CTATCCAGAGGTCCTAAAGATCCTCGGTAA
*
2306052 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCCTAAAGATCCTCGGTAA
* *
2306082 CTGTCCATAGGTCC
1 CTATCCAGAGGTCC
2306096 CGAAGAACCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCCTAAAGATCCTCGGTAA
Found at i:2306118 original size:31 final size:31
Alignment explanation
Indices: 2306080--2306144 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2306070 GATCCTCGGT
*
2306080 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
2306111 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
2306142 AAC
1 AAC
2306145 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:2306307 original size:17 final size:19
Alignment explanation
Indices: 2306275--2306310 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2306265 CATATATCTC
2306275 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
2306294 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
2306311 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:2310098 original size:30 final size:30
Alignment explanation
Indices: 2310062--2310135 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
2310052 CCCAAAGGAC
2310062 CTATCCAGAGGTCCTAAAGATCCTCGGTAA
1 CTATCCAGAGGTCCTAAAGATCCTCGGTAA
*
2310092 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCCTAAAGATCCTCGGTAA
* *
2310122 CTGTCCATAGGTCC
1 CTATCCAGAGGTCC
2310136 CGAAGAACCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCCTAAAGATCCTCGGTAA
Found at i:2310158 original size:31 final size:31
Alignment explanation
Indices: 2310120--2310184 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2310110 GATCCTCGGT
*
2310120 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
2310151 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
2310182 AAC
1 AAC
2310185 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:2310348 original size:17 final size:19
Alignment explanation
Indices: 2310314--2310362 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
2310304 ACCATATATC
2310314 TCATATCATATCACATGTAT
1 TCATAT-ATATCACATGTAT
2310334 T-ATATATAT-ACATGTAT
1 TCATATATATCACATGTAT
*
2310351 TCATATAAATCA
1 TCATATATATCA
2310363 TTTTATGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.35
18 11 0.42
19 5 0.19
20 1 0.04
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (19 bp):
TCATATATATCACATGTAT
Found at i:2314241 original size:21 final size:21
Alignment explanation
Indices: 2314212--2314264 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2314202 ATTCTGACTA
*
2314212 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGACTTTCCAAAT
* *
2314233 TCGCGTTGCGACTTTCCTAAT
1 TCGCATTGCGACTTTCCAAAT
*
2314254 TCGCAATGCGA
1 TCGCATTGCGA
2314265 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGACTTTCCAAAT
Found at i:2314279 original size:20 final size:20
Alignment explanation
Indices: 2314254--2314306 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2314244 CTTTCCTAAT
2314254 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2314274 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
2314294 TCGCAACGCGAAT
1 TCGCAATGCGAAT
2314307 CTGACTATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2314530 original size:22 final size:22
Alignment explanation
Indices: 2314505--2314568 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
2314495 CGACATCCGA
2314505 CCCCATCTCCGACGAAATCAGT
1 CCCCATCTCCGACGAAATCAGT
*
2314527 CCCCATCTCCGACGATATCAGT
1 CCCCATCTCCGACGAAATCAGT
* * *
2314549 CTCAATCTCCGGCGAAATCA
1 CCCCATCTCCGACGAAATCA
2314569 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.27, C:0.39, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCCATCTCCGACGAAATCAGT
Found at i:2314992 original size:20 final size:20
Alignment explanation
Indices: 2314904--2314994 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
2314894 GCGATTCTGT
2314904 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** ** *
2314923 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATTTTCATTTTCG
**
2314943 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2314963 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2314983 TGTTGCGATTTT
1 CGTTGCGATTTT
2314995 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 49 0.80
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:2315001 original size:20 final size:20
Alignment explanation
Indices: 2314958--2315001 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2314948 CGATAGTCAT
* *
2314958 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
2314978 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
2314998 TTTC
1 TTTC
2315002 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:2316915 original size:20 final size:20
Alignment explanation
Indices: 2316890--2316941 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2316880 AGAATAGTTT
*
2316890 ACTATCGCAATGCAAAAATG
1 ACTATCGCAACGCAAAAATG
* *
2316910 ACTATCACAACGCGAAAATG
1 ACTATCGCAACGCAAAAATG
2316930 ACTATCGCAACG
1 ACTATCGCAACG
2316942 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (20 bp):
ACTATCGCAACGCAAAAATG
Found at i:2317005 original size:20 final size:20
Alignment explanation
Indices: 2316980--2317028 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2316970 CAACAACAAA
2316980 ATCGCAACGCGAAAATT-ACT
1 ATCGCAACGC-AAAATTGACT
* *
2317000 ATCGCAATGCAAATTTGACT
1 ATCGCAACGCAAAATTGACT
*
2317020 ATTGCAACG
1 ATCGCAACG
2317029 AAAGAATCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCAAAATTGACT
Found at i:2317039 original size:87 final size:87
Alignment explanation
Indices: 2316893--2317058 Score: 244
Period size: 87 Copynumber: 1.9 Consensus size: 87
2316883 ATAGTTTACT
* *
2316893 ATCGCAATGCAAAAATGACTATCACAACGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAACGCAAAAATGACTATCACAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
2316958 AAATGAAAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
* * * * * *
2316980 ATCGCAACGCGAAAATTACTATCGCAATGC-AAATTTGACTATTGCAACGAAAGAATCGCAATGC
1 ATCGCAACGCAAAAATGACTATCACAACGCGAAA-ATGACTATCGCAACGAAAGAATCGCAATGC
2317044 GAAATGAAAATCGCA
65 GAAATGAAAATCGCA
2317059 TTGCGATTCT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
86 3 0.04
87 67 0.96
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (87 bp):
ATCGCAACGCAAAAATGACTATCACAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
AAATGAAAATCGCAACAACAAA
Found at i:2317098 original size:20 final size:20
Alignment explanation
Indices: 2317073--2317139 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
2317063 GATTCTCTCG
*
2317073 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
*
2317093 TTGCGATTGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
2317113 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
2317133 TTGCGAT
1 TTGCGAT
2317140 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:2317714 original size:21 final size:21
Alignment explanation
Indices: 2317623--2317721 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 21
2317613 GACTCACATG
*
2317623 TCATCGTTCAAGAGGCCTCCC
1 TCATCGTTCAAGAGGCCTCTC
* *
2317644 TTATCGTTCAAGAGGCCTCTA
1 TCATCGTTCAAGAGGCCTCTC
** * *
2317665 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCTCTC
* * * *
2317686 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCTCTC
*
2317707 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
2317722 TCCCTCCCAA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCTCTC
Found at i:2317720 original size:42 final size:42
Alignment explanation
Indices: 2317648--2317730 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
2317638 CCTCCCTTAT
*
2317648 CGTTCAAGAGGCCTCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
2317690 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
2317731 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:2319315 original size:34 final size:33
Alignment explanation
Indices: 2319227--2319322 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
2319217 AAAACAGACT
** *
2319227 ATCGCAATGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
2319261 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2319294 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
2319323 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 31 0.53
34 27 0.47
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2319318 original size:20 final size:19
Alignment explanation
Indices: 2319260--2319327 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
2319250 ACAACGAGAG
2319260 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2319279 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2319293 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2319313 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
2319328 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2319399 original size:33 final size:34
Alignment explanation
Indices: 2319337--2319412 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
2319327 ACTAAATTCG
*
2319337 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTACGATTCTCT
2319371 CGTTGCGATTTTCA-TTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTACGATTCTCT
2319404 CGTTGCGAT
1 CGTTGCGAT
2319413 AGTCAATTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 27 0.66
34 14 0.34
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTACGATTCTCT
Found at i:2319469 original size:20 final size:21
Alignment explanation
Indices: 2319404--2319462 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
2319394 ACGATTCTCT
2319404 CGTTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTCATATTCCG
2319424 CGTTGCGATAGTCAT-TTCCG
1 CGTTGCGATAGTCATATTCCG
*
2319444 TGTTGCGATAGTCATATTC
1 CGTTGCGATAGTCATATTC
2319463 GCATTGCAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 33 0.92
21 3 0.08
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCATATTCCG
Found at i:2320106 original size:20 final size:20
Alignment explanation
Indices: 2320081--2320147 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
2320071 AAATTCAGTA
2320081 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
2320101 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
* *
2320121 TTGCGATAGTCAGATTCGTG
1 TTGCGATAGTCAGAATCGCG
2320141 TTGCGAT
1 TTGCGAT
2320148 TTACGTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:2320187 original size:21 final size:21
Alignment explanation
Indices: 2320163--2320208 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2320153 TATTCGCATT
*
2320163 GCGAATTAGGAAAGTCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
2320184 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2320205 GCGA
1 GCGA
2320209 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2320590 original size:23 final size:25
Alignment explanation
Indices: 2320546--2320592 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
2320536 CTATTTATTT
2320546 TCTTATGAATATAGTAAAGTTTTTA
1 TCTTATGAATATAGTAAAGTTTTTA
* *
2320571 TCTTAT-ATTATA-TAAGGTTTTT
1 TCTTATGAATATAGTAAAGTTTTT
2320593 CGTTACAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 5 0.25
25 6 0.30
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (25 bp):
TCTTATGAATATAGTAAAGTTTTTA
Found at i:2324878 original size:13 final size:13
Alignment explanation
Indices: 2324860--2324885 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2324850 ACAAGTCATG
2324860 CGGTCCCTTTCTA
1 CGGTCCCTTTCTA
2324873 CGGTCCCTTTCTA
1 CGGTCCCTTTCTA
2324886 ATGCTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.38, G:0.15, T:0.38
Consensus pattern (13 bp):
CGGTCCCTTTCTA
Found at i:2357708 original size:18 final size:18
Alignment explanation
Indices: 2357674--2357708 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2357664 AACTTTCCCA
*
2357674 AGAAATCAGCCTCCCCTG
1 AGAAATCAACCTCCCCTG
*
2357692 AGAAATCAACCTTCCCT
1 AGAAATCAACCTCCCCT
2357709 AATTACCTCC
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:0.31, C:0.37, G:0.11, T:0.20
Consensus pattern (18 bp):
AGAAATCAACCTCCCCTG
Found at i:2363452 original size:27 final size:27
Alignment explanation
Indices: 2363414--2363475 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
2363404 ACATCTACTG
2363414 AATTGCAAGCCCTACTCATAAATTTAA
1 AATTGCAAGCCCTACTCATAAATTTAA
2363441 AATTGCAAGCCCTACTCATAAATTTAA
1 AATTGCAAGCCCTACTCATAAATTTAA
2363468 AATTGCAA
1 AATTGCAA
2363476 AGTTCGTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTGCAAGCCCTACTCATAAATTTAA
Found at i:2368007 original size:45 final size:46
Alignment explanation
Indices: 2367930--2368017 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
2367920 GAAAAACCTT
* * *
2367930 AGTGTATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTG
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTG
2367976 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
2368018 TTTGATGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTG
Found at i:2371951 original size:15 final size:13
Alignment explanation
Indices: 2371932--2371967 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
2371922 TTTGAATGCC
2371932 TAATTTTTAGTTTT
1 TAATTTTT-GTTTT
2371946 TCAATTTTTGTTTT
1 T-AATTTTTGTTTT
2371960 TAATTTTT
1 TAATTTTT
2371968 TCCGTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.33
14 7 0.33
15 7 0.33
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (13 bp):
TAATTTTTGTTTT
Found at i:2377723 original size:83 final size:84
Alignment explanation
Indices: 2377576--2377738 Score: 267
Period size: 83 Copynumber: 2.0 Consensus size: 84
2377566 AAAACAGTAC
* *
2377576 TGCTGAACTTAACGCTAGCTCGATTTTTTTTCTGCACTGATAATTTGGTCTTTCAATTTCTTTTT
1 TGCTGAACTTAACGCTAGCTCGATTTTTTTTCTGCACTAATAATTTGGTCTGTCAATTTCTTTTT
2377641 ATTTAACAGGAGCATGTAT
66 ATTTAACAGGAGCATGTAT
* *
2377660 TGCTGAACTTAACGCTTGCTCGA-TTTTTTTCTGTACTAATAATTCT-GTCTGTCAATTTCTTTT
1 TGCTGAACTTAACGCTAGCTCGATTTTTTTTCTGCACTAATAATT-TGGTCTGTCAATTTCTTTT
2377723 TATTTAACAGGAGCAT
65 TATTTAACAGGAGCAT
2377739 AGGATGCGTC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
83 51 0.69
84 23 0.31
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (84 bp):
TGCTGAACTTAACGCTAGCTCGATTTTTTTTCTGCACTAATAATTTGGTCTGTCAATTTCTTTTT
ATTTAACAGGAGCATGTAT
Found at i:2381557 original size:15 final size:15
Alignment explanation
Indices: 2381539--2381571 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2381529 ATCAACAAAT
2381539 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
2381554 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
2381569 ATA
1 ATA
2381572 TTTAGAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:2387561 original size:101 final size:100
Alignment explanation
Indices: 2387354--2387549 Score: 342
Period size: 101 Copynumber: 2.0 Consensus size: 100
2387344 TTTTTCAATG
* * *
2387354 AAAAAAAAACTTGGGGATTTTCACAAACAAGTTCCTTACTCTTTCAATAAACCTTTTCTTTTTTT
1 AAAAAAAAACTTGGGAACTTTCACAAACAAGTTCCATACTCTTTCAATAAACC-TTTCTTTTTTT
2387419 TACCTCAAAGGGTCTAAAGAGAAGCCATAGCTGAAC
65 TACCTCAAAGGGTCTAAAGAGAAGCCATAGCTGAAC
2387455 AAAAAAAAACTTGGGAACTTTCACAAACAAGTTCCATACTCTTTCAATAAACC-TT-TTTTTTTT
1 AAAAAAAAACTTGGGAACTTTCACAAACAAGTTCCATACTCTTTCAATAAACCTTTCTTTTTTTT
2387518 ACCTCAAAGGGTCTAAAGAGAAGCCATAGCTG
66 ACCTCAAAGGGTCTAAAGAGAAGCCATAGCTG
2387550 CACTCATAAA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
98 40 0.43
99 2 0.02
101 50 0.54
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (100 bp):
AAAAAAAAACTTGGGAACTTTCACAAACAAGTTCCATACTCTTTCAATAAACCTTTCTTTTTTTT
ACCTCAAAGGGTCTAAAGAGAAGCCATAGCTGAAC
Found at i:2387715 original size:100 final size:97
Alignment explanation
Indices: 2387530--2387726 Score: 367
Period size: 100 Copynumber: 2.0 Consensus size: 97
2387520 CTCAAAGGGT
2387530 CTAAAGAGAAGCCATAGCTGCACTCATAAAAAGCAAAGGGAGGGGGGGCAATCCTCTGTACCCTT
1 CTAAAGAGAAGCCATAGCTGCACTCATAAAAAGCAAAGGGAGGGGGGGCAATCCTCTGTACCCTT
2387595 TATTCCCCATTACTCAGAATTGCCATACAAAC
66 TATTCCCCATTACTCAGAATTGCCATACAAAC
2387627 CTAAAGAGAAGCCATAGCTGCACTCATAAAAAGCTAAAGGGAGGGGGGAGGCAATCCTCTGTACC
1 CTAAAGAGAAGCCATAGCTGCACTCATAAAAAGC-AAAGGGA-GGGGG-GGCAATCCTCTGTACC
2387692 CTTTATTCCCCATTACTCAGAATTGCCATACAAAC
63 CTTTATTCCCCATTACTCAGAATTGCCATACAAAC
2387727 AAGTTCTAGA
Statistics
Matches: 97, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
97 34 0.35
98 7 0.07
99 5 0.05
100 51 0.53
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (97 bp):
CTAAAGAGAAGCCATAGCTGCACTCATAAAAAGCAAAGGGAGGGGGGGCAATCCTCTGTACCCTT
TATTCCCCATTACTCAGAATTGCCATACAAAC
Found at i:2392688 original size:109 final size:111
Alignment explanation
Indices: 2392559--2392779 Score: 410
Period size: 112 Copynumber: 2.0 Consensus size: 111
2392549 TACCACCAAA
*
2392559 GAGAAGTGATAGTGTAAAGAAGAAGAAGAAGATCAAAC-AA-TAAAAGAAAACCTACTCTTTGTT
1 GAGAAGTGATAGTGTAAAGAAGAAGAAGAAGATCAAACAAACTAAAAGAAAACATACTCTTTGTT
2392622 GGCAGTAACTCCACAATAGTGTTGCAGAAGATGCTCTAAACTATTT
66 GGCAGTAACTCCACAATAGTGTTGCAGAAGATGCTCTAAACTATTT
2392668 GAGAAGTGATAGTGTAAAGAAGAAGAAGAAGATCAAACAAATCTAAAAGAAAACATACTCTTTGT
1 GAGAAGTGATAGTGTAAAGAAGAAGAAGAAGATCAAACAAA-CTAAAAGAAAACATACTCTTTGT
2392733 TGGCAGTAACTCCACAATAGTGTTGCAGAAGATGCTCTAAACTATTT
65 TGGCAGTAACTCCACAATAGTGTTGCAGAAGATGCTCTAAACTATTT
2392780 CTTTCCATTT
Statistics
Matches: 108, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
109 38 0.35
110 2 0.02
112 68 0.63
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.24
Consensus pattern (111 bp):
GAGAAGTGATAGTGTAAAGAAGAAGAAGAAGATCAAACAAACTAAAAGAAAACATACTCTTTGTT
GGCAGTAACTCCACAATAGTGTTGCAGAAGATGCTCTAAACTATTT
Found at i:2396034 original size:24 final size:24
Alignment explanation
Indices: 2396003--2396058 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
2395993 TAGAAGTTCG
* *
2396003 ATTGAAGCCTAAAATTTTAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTAA
2396027 ATTGAAGCCTAAAATTTGAGCTAA
1 ATTGAAGCCTAAAATTTGAGCTAA
2396051 ATTGAAGC
1 ATTGAAGC
2396059 GAAAGAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTAA
Found at i:2397859 original size:21 final size:21
Alignment explanation
Indices: 2397833--2397878 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2397823 GGGGAAATGT
*
2397833 AGTATCGATACTGA-TATAATA
1 AGTATCAATACT-ACTATAATA
2397854 AGTATCAATACTACTATAATA
1 AGTATCAATACTACTATAATA
2397875 AGTA
1 AGTA
2397879 ATATCGATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (21 bp):
AGTATCAATACTACTATAATA
Done.