Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:1940449 original size:43 final size:42
Alignment explanation
Indices: 1940378--1940498 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 42
1940368 GCTAAAGTTC
1940378 GCGGCGTTTGTTAACGAAAAACGCCGCAATAGGTGACGATATATA
1 GCGGCGTTTGTT-A--AAAAACGCCGCAATAGGTGACGATATATA
* ** * *
1940423 GCGGCGTTTGTTGAAAAAATGCCGCAATAGGTGTTGCTATTTA
1 GCGGCGTTTGTT-AAAAAACGCCGCAATAGGTGACGATATATA
*
1940466 GCGGCGTTTGTCTTAAAAACGCCGCAATAGGTG
1 GCGGCGTTTGT-TAAAAAACGCCGCAATAGGTG
1940499 TTGTCGTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 53 0.79
44 1 0.01
45 13 0.19
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (42 bp):
GCGGCGTTTGTTAAAAAACGCCGCAATAGGTGACGATATATA
Found at i:1940604 original size:43 final size:43
Alignment explanation
Indices: 1940394--1940606 Score: 203
Period size: 43 Copynumber: 5.0 Consensus size: 43
1940384 TTTGTTAACG
** * * * **
1940394 AAAAACGCCGCAATAGGTGACGATATATAGCGGCGTTTGTT-GA
1 AAAAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTT-TTCCC
* * * * **
1940437 AAAAATGCCGCAATAGGTGTTGCTATTTAGCGGCGTTTGTCTT
1 AAAAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTTCCC
*
1940480 AAAAACGCCGCAATAGGTGTTGTCGTTTAGCGGCGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTTCCC
** * * * *
1940523 CCAAACACCGCAGTAGGTATCGTTGTTTAGCGGCGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTTCCC
* * *
1940566 AAAAATGCCGCAATATGTGTTGTTGTTTAGCGGTGTTTTTC
1 AAAAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTTC
1940607 AAACAAGCGC
Statistics
Matches: 138, Mismatches: 31, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
42 1 0.01
43 137 0.99
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTTCCC
Found at i:1942449 original size:22 final size:22
Alignment explanation
Indices: 1942421--1942467 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1942411 GCTTTACAAA
1942421 AAGTAAACATTCAAGGATCAAG
1 AAGTAAACATTCAAGGATCAAG
*
1942443 AAGTAAACATTTAAGGATCAAG
1 AAGTAAACATTCAAGGATCAAG
1942465 AAG
1 AAG
1942468 GCTTTACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (22 bp):
AAGTAAACATTCAAGGATCAAG
Found at i:1945662 original size:41 final size:40
Alignment explanation
Indices: 1945617--1945768 Score: 128
Period size: 41 Copynumber: 3.7 Consensus size: 40
1945607 CACTAACTTA
* *
1945617 TTGCGGCGTTTGTTTAAAAACGCCGCTAATGGACCGATTT
1 TTGCGGCATTTGTTTAAAAACGCCGCTAATGCACCGATTT
* * *
1945657 CTTGCGGCATTTTTTTAAAAACGCCGCTAATGTTA-CTA-TT
1 -TTGCGGCATTTGTTTAAAAACGCCGCTAATG-CACCGATTT
* * * * *
1945697 TTGTGGCGTTTGTATTTAAAAACGCTGCTAATTCACTGATTT
1 TTGCGGCATTTG--TTTAAAAACGCCGCTAATGCACCGATTT
* **
1945739 ATAGCGGCATTTGTAGAAAAACGCCGCTAA
1 -TTGCGGCATTTGTTTAAAAACGCCGCTAA
1945769 AGTACTACGT
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
39 9 0.10
40 3 0.03
41 63 0.72
42 3 0.03
43 9 0.10
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (40 bp):
TTGCGGCATTTGTTTAAAAACGCCGCTAATGCACCGATTT
Found at i:1945920 original size:82 final size:84
Alignment explanation
Indices: 1945807--1946039 Score: 278
Period size: 83 Copynumber: 2.8 Consensus size: 84
1945797 ATAAACGCCG
* * * * * * *
1945807 ATAAA-GA-ACCCTATTGCGGCATTTATATAAAAACGCTACTAAAGTACT-CTTTATTGCGACGT
1 ATAAACGATACCCTATTGCGGCGTTTGTATAAAAACACTGCTAAAGTACTAATCTATCGCGACGT
* *
1945869 TTGTTGGAAAAATGCCACT
66 TTGTTAGAAAAACGCCACT
* * *
1945888 ATGAAC-ATACCCTATTGCGACGTTTGTATAAAAACACTGCTAAAGTACTAATCTATCGCGGCGT
1 ATAAACGATACCCTATTGCGGCGTTTGTATAAAAACACTGCTAAAGTACTAATCTATCGCGACGT
1945952 TTGTTAGAAAAACGCCACT
66 TTGTTAGAAAAACGCCACT
* * * * *
1945971 ATAAACGAT-CCCTTTTACGGCGTTTGTATAAAAACACCGCTAAAGTACTAATCTATAGCGGCGT
1 ATAAACGATACCCTATTGCGGCGTTTGTATAAAAACACTGCTAAAGTACTAATCTATCGCGACGT
1946035 TTGTT
66 TTGTT
1946040 TAAGAAACGC
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
81 5 0.04
82 36 0.28
83 87 0.67
84 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (84 bp):
ATAAACGATACCCTATTGCGGCGTTTGTATAAAAACACTGCTAAAGTACTAATCTATCGCGACGT
TTGTTAGAAAAACGCCACT
Found at i:1945953 original size:41 final size:41
Alignment explanation
Indices: 1945899--1946059 Score: 148
Period size: 41 Copynumber: 3.9 Consensus size: 41
1945889 TGAACATACC
* *
1945899 CTATTGCGACGTTTGTATAAAAACACTGCTAAAGTACTAAT
1 CTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTAAT
* * * * *
1945940 CTATCGCGGCGTTTGTTAGAAAAACGCCACTATAA--AC-GAT
1 CTATTGCGGCGTTTG-TATAAAAACACCGCTA-AAGTACTAAT
* *
1945980 CCCTTTTACGGCGTTTGTATAAAAACACCGCTAAAGTACTAAT
1 --CTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTAAT
* * *
1946023 CTATAGCGGCGTTTGTTTAAGAAACGCCGCTAAAGTA
1 CTATTGCGGCGTTTGTATAA-AAACACCGCTAAAGTA
1946060 TCGTTTTGTG
Statistics
Matches: 93, Mismatches: 19, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
40 4 0.04
41 44 0.47
42 41 0.44
43 4 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (41 bp):
CTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTAAT
Found at i:1950324 original size:3 final size:3
Alignment explanation
Indices: 1950316--1950342 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1950306 AGCATATTGT
1950316 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1950343 AAGTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1950835 original size:83 final size:83
Alignment explanation
Indices: 1950691--1950880 Score: 238
Period size: 83 Copynumber: 2.3 Consensus size: 83
1950681 GATGATGATA
* *
1950691 ACACGGTTCCTACGCGATGAGGATGGATGGTTATCTAAGGGTGACGCTACTCCTACATGATGAGG
1 ACACGGTTCCTACGTGATGAGGATCGATGGTTATCTAAGGGTGACGCTACTCCTACATGATGAGG
*
1950756 AGATATGGTCAGTGGATG
66 AGATATGCTCAGTGGATG
* * * * * *
1950774 ACACGGTTCCTACGTGATAAGGA-CGACTGGTTATCTAAGGTTGGCGTTCCTCCTACGTGATGAG
1 ACACGGTTCCTACGTGATGAGGATCGA-TGGTTATCTAAGGGTGACGCTACTCCTACATGATGAG
* *
1950838 GAGATCTGCTCAGTTGATG
65 GAGATATGCTCAGTGGATG
* * *
1950857 ACATGGTTCTTATGTGATGAGGAT
1 ACACGGTTCCTACGTGATGAGGAT
1950881 TGTTGACCAT
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
82 2 0.02
83 88 0.98
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (83 bp):
ACACGGTTCCTACGTGATGAGGATCGATGGTTATCTAAGGGTGACGCTACTCCTACATGATGAGG
AGATATGCTCAGTGGATG
Found at i:1951128 original size:68 final size:69
Alignment explanation
Indices: 1950903--1951256 Score: 427
Period size: 69 Copynumber: 5.2 Consensus size: 69
1950893 TTAGGGATAA
* * * * *
1950903 TATGTTTCAAGGGAAACTGTCTCAATAGAGAACAAAA---ATTTCAAGGGTAACAATCTC-AA-T
1 TATGTTTCAAGAGAAACTATCTCAAGAGAG-ACAAAATTTGTTTCAAGGGAAACAATCTCAAAGT
*
1950963 ATTTT
65 TTTTT
* *
1950968 TATTTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGTT
1 TATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTT
*
1951033 GTTT
66 TTTT
* * * *
1951037 TATGTTTCAAGAGAAATTCTCTCAAGAGAGACAAAACTTGTTTCAA-GAAAACAATCTCAAAGTT
1 TATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTT
1951101 TTTT
66 TTTT
* ** *
1951105 TATGTTTCAAGAGAAACTTTCTCAAGAGAGACAAAATTTAATTCAAGGGAAACAATCTCAAAGGT
1 TATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTT
1951170 TTTT
66 TTTT
* * * * *
1951174 TCTATTTCAAGAGAAACTATCTCAAGAGAGATAAAATTTGTATCAAGAGAAACAATCTCAAAG--
1 TATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTT
*
1951237 GTTT
66 TTTT
*
1951241 TATGTTTCACGAGAAA
1 TATGTTTCAAGAGAAA
1951257 ATCACAAGGA
Statistics
Matches: 248, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
64 6 0.02
65 26 0.10
67 33 0.13
68 62 0.25
69 121 0.49
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (69 bp):
TATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTT
TTTT
Found at i:1951150 original size:137 final size:137
Alignment explanation
Indices: 1950907--1951256 Score: 428
Period size: 137 Copynumber: 2.6 Consensus size: 137
1950897 GGATAATATG
* * * * * *
1950907 TTTCAAGGGAAACTGTCTCAATAGAGAACAAAA-AT-T-TCAAGGGTAACAATCTC-AA-TATTT
1 TTTCAAGAGAAACTATCTCAAGAGAG-ACAAAACTTGTATCAAGAGAAACAATCTCAAAGT-TTT
* ** *
1950967 TTATTTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAA-G
64 TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTAATTCAAGGGAAACAATCTCAAAGG
*
1951031 TTGTTTTATG
129 TT-TTTTATA
* * *
1951041 TTTCAAGAGAAATTCTCTCAAGAGAGACAAAACTTGTTTCAAGA-AAACAATCTCAAAGTTTTTT
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTATCAAGAGAAACAATCTCAAAG-TTTTT
*
1951105 TATGTTTCAAGAGAAACTTTCTCAAGAGAGACAAAATTTAATTCAAGGGAAACAATCTCAAAGGT
65 TATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTAATTCAAGGGAAACAATCTCAAAGGT
*
1951170 TTTTTCTA
130 TTTTTATA
* * *
1951178 TTTCAAGAGAAACTATCTCAAGAGAGATAAAATTTGTATCAAGAGAAACAATCTCAAAG-GTTTT
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTATCAAGAGAAACAATCTCAAAGTTTTTT
*
1951242 ATGTTTCACGAGAAA
66 ATGTTTCAAGAGAAA
1951257 ATCACAAGGA
Statistics
Matches: 187, Mismatches: 21, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
133 6 0.03
134 23 0.12
135 10 0.05
136 25 0.13
137 105 0.56
138 18 0.10
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (137 bp):
TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTATCAAGAGAAACAATCTCAAAGTTTTTT
ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTAATTCAAGGGAAACAATCTCAAAGGTT
TTTTATA
Found at i:1951190 original size:33 final size:32
Alignment explanation
Indices: 1951145--1951241 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 32
1951135 ACAAAATTTA
*
1951145 ATTCAAGGGAAACAATCTCAAAGGTTTTTTCT
1 ATTCAAGAGAAACAATCTCAAAGGTTTTTTCT
* ** *
1951177 ATTTCAAGAGAAACTATCTCAAGAGAGATAAAATTTGT
1 A-TTCAAGAGAAACAATCTCAA-AG-G-T--TTTTTCT
1951215 A-TCAAGAGAAACAATCTCAAAGGTTTT
1 ATTCAAGAGAAACAATCTCAAAGGTTTT
1951242 ATGTTTCACG
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
31 1 0.02
32 1 0.02
33 19 0.37
34 3 0.06
35 3 0.06
36 19 0.37
38 5 0.10
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (32 bp):
ATTCAAGAGAAACAATCTCAAAGGTTTTTTCT
Found at i:1952169 original size:20 final size:20
Alignment explanation
Indices: 1952144--1952188 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1952134 GGAAATCAAA
*
1952144 GACCACTGCCTGGAGTTAAC
1 GACCACTGCCTAGAGTTAAC
1952164 GACCACTGCCTAGAGTTAAC
1 GACCACTGCCTAGAGTTAAC
1952184 GACCA
1 GACCA
1952189 TAGTAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (20 bp):
GACCACTGCCTAGAGTTAAC
Found at i:1953035 original size:25 final size:25
Alignment explanation
Indices: 1952971--1953038 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 25
1952961 TTTTATTTTC
1952971 AAAATTTTGAAAAAATATCAATTAA
1 AAAATTTTGAAAAAATATCAATTAA
** *
1952996 AAGAATTTTTGAAAATGT-TTAA-TAA
1 AA-AA-TTTTGAAAAAATATCAATTAA
1953021 AAAATTTTGAAAAAATAT
1 AAAATTTTGAAAAAATAT
1953039 TGCTCATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 10 0.29
24 3 0.09
25 7 0.20
26 5 0.14
27 10 0.29
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.35
Consensus pattern (25 bp):
AAAATTTTGAAAAAATATCAATTAA
Found at i:1953942 original size:20 final size:21
Alignment explanation
Indices: 1953898--1953942 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1953888 CTTCTTGTAT
1953898 TCTTTTTTTCTTTTCTTTTTC
1 TCTTTTTTTCTTTTCTTTTTC
*
1953919 -CTTTTTTTC-TTTGTTTTTC
1 TCTTTTTTTCTTTTCTTTTTC
1953938 TCTTT
1 TCTTT
1953943 GCTTCTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (21 bp):
TCTTTTTTTCTTTTCTTTTTC
Found at i:1963330 original size:38 final size:40
Alignment explanation
Indices: 1963283--1963384 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 40
1963273 TTTGTGACAC
* * *
1963283 TGTAACAAAAACGCCGCTAAGGACCT-TT-TTGTGGTGTT
1 TGTAACAAAAACGCCGCTAAAGACCTATTGTTGCGGCGTT
* *
1963321 TGTAACAAAAACGTCGTTAAAGACCTAACTTGTTGCGGCGTT
1 TGTAACAAAAACGCCGCTAAAGACCT-A-TTGTTGCGGCGTT
1963363 TGTTAACATAAAACGCCGCTAA
1 TG-TAACA-AAAACGCCGCTAA
1963385 CCGTTGTGGC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
38 23 0.45
41 2 0.04
42 10 0.20
43 5 0.10
44 11 0.22
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (40 bp):
TGTAACAAAAACGCCGCTAAAGACCTATTGTTGCGGCGTT
Found at i:1965191 original size:2 final size:2
Alignment explanation
Indices: 1965184--1965210 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1965174 ATGCAGTATC
1965184 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1965211 CACTATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1965750 original size:14 final size:14
Alignment explanation
Indices: 1965731--1965762 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1965721 TTTGTTAGGG
1965731 TTTAGGATTTAAGC
1 TTTAGGATTTAAGC
*
1965745 TTTAGGCTTTAAGC
1 TTTAGGATTTAAGC
1965759 TTTA
1 TTTA
1965763 TGTTTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (14 bp):
TTTAGGATTTAAGC
Found at i:1966648 original size:3 final size:3
Alignment explanation
Indices: 1966598--1966640 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
1966588 TCCAAGCATA
*
1966598 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1966641 AATTATTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1973358 original size:21 final size:20
Alignment explanation
Indices: 1973300--1973364 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
1973290 CCTAAAATTA
1973300 TAAACCCTAAATCC-AAACCC
1 TAAA-CCTAAATCCTAAACCC
* * * *
1973320 CAAACCTCAAAACATAAACCT
1 TAAACCT-AAATCCTAAACCC
1973341 TAAATCCTAAATCCTAAACCC
1 TAAA-CCTAAATCCTAAACCC
1973362 TAA
1 TAA
1973365 CAAAAAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.09
20 7 0.21
21 21 0.62
22 3 0.09
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAACCTAAATCCTAAACCC
Found at i:1974078 original size:18 final size:19
Alignment explanation
Indices: 1974055--1974090 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1974045 CTGGCGAAAT
1974055 TCATGC-CGCCTACTCCCC
1 TCATGCTCGCCTACTCCCC
*
1974073 TCATGCTCGCCTGCTCCC
1 TCATGCTCGCCTACTCCC
1974091 ATGCAGCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.08, C:0.53, G:0.14, T:0.25
Consensus pattern (19 bp):
TCATGCTCGCCTACTCCCC
Found at i:1974148 original size:23 final size:24
Alignment explanation
Indices: 1974118--1974163 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1974108 GCATTATTGC
1974118 AGCATCATTTTT-CTGCTTCATGT
1 AGCATCATTTTTGCTGCTTCATGT
*
1974141 AGCATCATTTTTGTTGCTTCATG
1 AGCATCATTTTTGCTGCTTCATG
1974164 CAACAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.48
Consensus pattern (24 bp):
AGCATCATTTTTGCTGCTTCATGT
Found at i:1974534 original size:43 final size:41
Alignment explanation
Indices: 1974491--1974595 Score: 112
Period size: 36 Copynumber: 2.6 Consensus size: 41
1974481 TCATACATTA
*
1974491 ATAAAAAAAATATTTAATTAGTTTGTTTGATAGTTA-TA-T
1 ATAAAAAAAATATTTAATTAGTTTGTTTGATAGTCATTATT
* * *
1974530 AT-TAAAAAA-A-TTAATTAGTTTGTTTGTTAGTCGTTAGTT
1 ATAAAAAAAATATTTAATTAGTTTGTTTGATAGTCATTA-TT
*
1974569 ATATATAAAAATATTTAATTAGTTTGT
1 ATA-AAAAAAATATTTAATTAGTTTGT
1974596 AGTTAGTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
36 20 0.38
37 3 0.06
38 6 0.11
39 5 0.09
41 5 0.09
42 1 0.02
43 13 0.25
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (41 bp):
ATAAAAAAAATATTTAATTAGTTTGTTTGATAGTCATTATT
Found at i:1974611 original size:43 final size:43
Alignment explanation
Indices: 1974520--1974612 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
1974510 AGTTTGTTTG
* **
1974520 ATAGTTATATATTAAAAAAATTAATTAGTTTGTTTGTTAGTCG
1 ATAGTTATATATTAAAAAAATTAATTAGTTTGTTAGTTAGTAA
* *
1974563 TTAGTTATATA-TAAAAATATTTAATTAGTTTG-TAGTTAGTTAA
1 ATAGTTATATATTAAAAA-AATTAATTAGTTTGTTAGTTAG-TAA
1974606 ATAGTTA
1 ATAGTTA
1974613 AGTTATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 12 0.29
43 30 0.71
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (43 bp):
ATAGTTATATATTAAAAAAATTAATTAGTTTGTTAGTTAGTAA
Found at i:1975389 original size:38 final size:38
Alignment explanation
Indices: 1975329--1975429 Score: 112
Period size: 38 Copynumber: 2.7 Consensus size: 38
1975319 ACGACAAAGT
* *
1975329 CTCCAAGATTACGCGGCTTCTTCAGGCAAAAATGAAGA
1 CTCCAAGATTACGCGGCGTCTTCAGGCAAAAAGGAAGA
***
1975367 CTCCAAGATTATTTGGCGTCTTCAGGCAAAAAGGAAGA
1 CTCCAAGATTACGCGGCGTCTTCAGGCAAAAAGGAAGA
*** * *
1975405 CTTTGAGAATACGCGGCATCTTCAG
1 CTCCAAGATTACGCGGCGTCTTCAG
1975430 TCCATGCAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (38 bp):
CTCCAAGATTACGCGGCGTCTTCAGGCAAAAAGGAAGA
Found at i:1976498 original size:104 final size:101
Alignment explanation
Indices: 1976248--1976498 Score: 242
Period size: 104 Copynumber: 2.4 Consensus size: 101
1976238 TTTAGTATAA
* * *
1976248 TTTTTGTTTTTAATT-TAAAT-TATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTTG
1 TTTTTGTTTTT-ATTGTAAATATA-AATTATTAGAC---TTATTTTGATTTTACAGATTAAATCG
*
1976311 TATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTGTTTTTTT
61 TATTTGAGTAGTTTGGTAAGTTTAGTCTAAATTGTTTTTTT
** * *
1976352 TAATT-TTTTTATTG-AGTAATATAAATGATTGGACTATTTATTTTGATTTTACAGATTAAATCG
1 TTTTTGTTTTTATTGTA--AATATAAATTATTAGAC---TTATTTTGATTTTACAGATTAAATCG
* * *
1976415 TATTTGAGTGGTTTGGTAAGTTTAGTCTAATTTTTTTGTTTTGT
61 TATTTGAGTAGTTTGGTAAGTTTAGTCTAA-ATTGTT-TTTT-T
1976459 TTTTTGTTTTTATTGTAAATATAAATTAATTAGAC-TATTT
1 TTTTTGTTTTTATTGTAAATATAAATT-ATTAGACTTATTT
1976499 CTTTTTATTT
Statistics
Matches: 122, Mismatches: 15, Indels: 20
0.78 0.10 0.13
Matches are distributed among these distances:
102 4 0.03
103 5 0.04
104 74 0.61
105 6 0.05
106 4 0.03
107 13 0.11
108 15 0.12
109 1 0.01
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (101 bp):
TTTTTGTTTTTATTGTAAATATAAATTATTAGACTTATTTTGATTTTACAGATTAAATCGTATTT
GAGTAGTTTGGTAAGTTTAGTCTAAATTGTTTTTTT
Found at i:1979150 original size:17 final size:17
Alignment explanation
Indices: 1979128--1979179 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1979118 AAAGTTTGTA
1979128 AAAAATGTAAATATATT
1 AAAAATGTAAATATATT
* ** *
1979145 AAAAATAT-TTTTTATT
1 AAAAATGTAAATATATT
1979161 AAAAATGTAAATATATT
1 AAAAATGTAAATATATT
1979178 AA
1 AA
1979180 CAATATTTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
AAAAATGTAAATATATT
Found at i:1979658 original size:25 final size:25
Alignment explanation
Indices: 1979630--1979689 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1979620 TAATGGTGTC
1979630 ATTATTTTTCGTCATTATAATAAAT
1 ATTATTTTTCGTCATTATAATAAAT
** *
1979655 ATTATTTTTATTTATTATAATAAAT
1 ATTATTTTTCGTCATTATAATAAAT
1979680 ATTATTTTTC
1 ATTATTTTTC
1979690 TACTACAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTATTTTTCGTCATTATAATAAAT
Found at i:1979686 original size:19 final size:20
Alignment explanation
Indices: 1979662--1979706 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1979652 AATATTATTT
1979662 TTATTTATTATAATA-AATA
1 TTATTTATTATAATACAATA
* *
1979681 TTATTT-TTCTACTACAATA
1 TTATTTATTATAATACAATA
1979700 TTATTTA
1 TTATTTA
1979707 ACCTTGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTTATTATAATACAATA
Found at i:1980229 original size:302 final size:302
Alignment explanation
Indices: 1979668--1980306 Score: 1079
Period size: 302 Copynumber: 2.1 Consensus size: 302
1979658 ATTTTTATTT
1979668 ATTATAATAAATATTATTTTTCTACTACAATATTATTTAACCTTGCAAAAAAATGTAAATATATT
1 ATTATAATAAATATTATTTTTCTACTACAATATTATTTAACCTTGCAAAAAAATGTAAATATATT
1979733 AACAATATTTTTTATAAAAATAATGATTAAATACTATGATTACATTATAATAATGATTAAATTTA
66 AACAATATTTTTTATAAAAATAATGATTAAATACTATGATTACATTATAATAATGATTAAATTTA
* * * *
1979798 TTATTTCGGATTTTTTATAACTACTTATTATTACTTCGAATTTATTACTCCCTAATTTTCAACTA
131 TTACTTCGGATTTTTTATAACTACTTATTATTACTTCGAATTTATTACACCCTAATTCTCAACCA
1979863 AGAAACCCCATTTTATAACATCCCGGGGTATTCATTATATTTTCCCGTTCAACCACCAACCTACC
196 AGAAACCCCATTTTATAACATCCCGGGGTATTCATTATATTTTCCCGTTCAACCACCAACCTACC
* * *
1979928 TGAGTAATTAATGGATAATTAATGGTTCCATTATTTTTCGTC
261 CGAGTAATTAATGGATAATTAATGGTGCCATTATTTTTCGTA
1979970 ATTATAATAAATATTATTTTTCTACTACAATATTATTTAACCTTGC-AAAAAATGTAAATATATT
1 ATTATAATAAATATTATTTTTCTACTACAATATTATTTAACCTTGCAAAAAAATGTAAATATATT
*
1980034 AACAATGTTTTTTATATAAAAATAATGATTAAATACTATGATTACATTATAATAATGATTAAATT
66 AACAAT-ATTTTT-TATAAAAATAATGATTAAATACTATGATTACATTATAATAATGATTAAATT
1980099 TATTACTTCGGATTTTTTATAACTACTTATTATTACTTCGAATTTATTACACCCTAATTCTCAAC
129 TATTACTTCGGATTTTTTATAACTACTTATTATTACTTCGAATTTATTACACCCTAATTCTCAAC
* ** * *
1980164 CAA-AACACTCCATTTTATAGTAT-CCGGGTTATTCATTATATTTTCCCTTTCAACCACCAACCT
194 CAAGAA-ACCCCATTTTATAACATCCCGGGGTATTCATTATATTTTCCCGTTCAACCACCAACCT
* *
1980227 ACCCGGGTTATTAATGGATAATTAATGGTGCCATTATTTTTCGTA
258 ACCCGAGTAATTAATGGATAATTAATGGTGCCATTATTTTTCGTA
1980272 ATTATAATAAATATT-TTTTTCTACTACAAATATTA
1 ATTATAATAAATATTATTTTTCTACTAC-AATATTA
1980307 AGTCAAATAT
Statistics
Matches: 318, Mismatches: 15, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
301 36 0.11
302 153 0.48
303 129 0.41
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (302 bp):
ATTATAATAAATATTATTTTTCTACTACAATATTATTTAACCTTGCAAAAAAATGTAAATATATT
AACAATATTTTTTATAAAAATAATGATTAAATACTATGATTACATTATAATAATGATTAAATTTA
TTACTTCGGATTTTTTATAACTACTTATTATTACTTCGAATTTATTACACCCTAATTCTCAACCA
AGAAACCCCATTTTATAACATCCCGGGGTATTCATTATATTTTCCCGTTCAACCACCAACCTACC
CGAGTAATTAATGGATAATTAATGGTGCCATTATTTTTCGTA
Found at i:1981020 original size:39 final size:39
Alignment explanation
Indices: 1980916--1981022 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
1980906 TCACCCTAGA
* * **
1980916 CTGAAGATGCCAGGTAAACTTGGAGTCTTCCTATTTTTC
1 CTGAAGACGCCAGGTAATCTTGGAGTCTTCCTATTTGGC
* ***
1980955 CTGAAGACGCCAGGTAGTCCCAGAGTCTTCCTGA-TTGGC
1 CTGAAGACGCCAGGTAATCTTGGAGTCTTCCT-ATTTGGC
**
1980994 CTGAAGACGTTAGGTAATCTTGGAGTCTT
1 CTGAAGACGCCAGGTAATCTTGGAGTCTT
1981023 TGGCTCGGTA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
39 52 0.98
40 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (39 bp):
CTGAAGACGCCAGGTAATCTTGGAGTCTTCCTATTTGGC
Found at i:1984387 original size:43 final size:43
Alignment explanation
Indices: 1984271--1984588 Score: 287
Period size: 43 Copynumber: 7.6 Consensus size: 43
1984261 TCTCGACATA
* *
1984271 TAGCTGCGTTTGTATTTACAAACGCCGCTATTGACTGTGTATT
1 TAGCGGCGTTTGTATTTACAAACGCCGATATTGACTGTGTATT
* * * * * *
1984314 TAGCAGC--ATGTCTTTACAAATGCCGCTATTGGCTGTGTATT
1 TAGCGGCGTTTGTATTTACAAACGCCGATATTGACTGTGTATT
* * *
1984355 TAGCGGCGTTTGTCTTTACAAACGCCGATATTGATTTTGTATT
1 TAGCGGCGTTTGTATTTACAAACGCCGATATTGACTGTGTATT
* *
1984398 TAGCGGCGTTTGTATTTACAAACGCC-ACTATTGATTGTATATT
1 TAGCGGCGTTTGTATTTACAAACGCCGA-TATTGACTGTGTATT
* * * *
1984441 TAGCGACGTTAGTATTTACAAACG-C--TATTGACTATATATT
1 TAGCGGCGTTTGTATTTACAAACGCCGATATTGACTGTGTATT
* *
1984481 TAGCGGCGCTTT-TATTTACAAATGCC-ACTATTGATTGTGTATT
1 TAGCGGCG-TTTGTATTTACAAACGCCGA-TATTGACTGTGTATT
* * *** * *
1984524 AAGCGGGGTTTGTAAAGACAAACACCGCTATTGAC--TGTATT
1 TAGCGGCGTTTGTATTTACAAACGCCGATATTGACTGTGTATT
* *
1984565 TAGCGGCATTTGTATTTAAAAACG
1 TAGCGGCGTTTGTATTTACAAACG
1984589 TCACAAATAA
Statistics
Matches: 224, Mismatches: 42, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
40 31 0.14
41 61 0.27
42 5 0.02
43 127 0.57
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (43 bp):
TAGCGGCGTTTGTATTTACAAACGCCGATATTGACTGTGTATT
Found at i:1984516 original size:126 final size:125
Alignment explanation
Indices: 1984271--1984563 Score: 324
Period size: 126 Copynumber: 2.3 Consensus size: 125
1984261 TCTCGACATA
* * * *
1984271 TAGCTGCGTTTGTATTTACAAACGCCGCTATTGACTGTGTATTTAGCAGCATGTCTTTACAAATG
1 TAGCGGCGTTTGTATTTACAAACGCCACTATTGACTGTATATTTAGCAGCATGTATTTACAAA--
* * * * *
1984336 CCGCTATTGGCTGTGTATTTAGCGGCGTTTGTCTTTACAAACGCCGATATTGATTTTGTATT
64 CCGCTATTGACTATATATTTAGCGGCGTTTGTATTTACAAACGCCGATATTGATTGTGTATT
* *
1984398 TAGCGGCGTTTGTATTTACAAACGCCACTATTGATTGTATATTTAGC-GACGTTAGTATTTACAA
1 TAGCGGCGTTTGTATTTACAAACGCCACTATTGACTGTATATTTAGCAG-C-AT-GTATTTACAA
*
1984462 A-CGCTATTGACTATATATTTAGCGGCGCTTT-TATTTACAAATGCC-ACTATTGATTGTGTATT
63 ACCGCTATTGACTATATATTTAGCGGCG-TTTGTATTTACAAACGCCGA-TATTGATTGTGTATT
* * *** * *
1984524 AAGCGGGGTTTGTAAAGACAAACACCGCTATTGACTGTAT
1 TAGCGGCGTTTGTATTTACAAACGCCACTATTGACTGTAT
1984564 TTAGCGGCAT
Statistics
Matches: 141, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
125 1 0.01
126 82 0.58
127 47 0.33
128 1 0.01
129 10 0.07
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (125 bp):
TAGCGGCGTTTGTATTTACAAACGCCACTATTGACTGTATATTTAGCAGCATGTATTTACAAACC
GCTATTGACTATATATTTAGCGGCGTTTGTATTTACAAACGCCGATATTGATTGTGTATT
Found at i:1984545 original size:83 final size:82
Alignment explanation
Indices: 1984271--1984582 Score: 299
Period size: 83 Copynumber: 3.7 Consensus size: 82
1984261 TCTCGACATA
* * * *
1984271 TAGCTGCGTTTGTATTTACAAACGCCGCTATTGACTGTGTATTTAGCAGC--ATGTCTTTACAAA
1 TAGCGGCGTTTGTATTTACAAA---CGCTATTGACT-TGTATTTAGCGGCGTTTGTATTTACAAA
* **
1984334 TGCCGCTATTGGCTGTGTATT
62 TGCCACTATTGATTGTGTATT
* *
1984355 TAGCGGCGTTTGTCTTTACAAACGCCGATATTGATTTTGTATTTAGCGGCGTTTGTATTTACAAA
1 TAGCGGCGTTTGTATTTACAAACG-C--TATTGA-CTTGTATTTAGCGGCGTTTGTATTTACAAA
* *
1984420 CGCCACTATTGATTGTATATT
62 TGCCACTATTGATTGTGTATT
* * *
1984441 TAGCGACGTTAGTATTTACAAACGCTATTGACTATATATTTAGCGGCGCTTT-TATTTACAAATG
1 TAGCGGCGTTTGTATTTACAAACGCTATTGACT-TGTATTTAGCGGCG-TTTGTATTTACAAATG
1984505 CCACTATTGATTGTGTATT
64 CCACTATTGATTGTGTATT
* * *** *
1984524 AAGCGGGGTTTGTAAAGACAAACACCGCTATTGAC-TGTATTTAGCGGCATTTGTATTTA
1 TAGCGGCGTTTGTATTTAC-AA-A-CGCTATTGACTTGTATTTAGCGGCGTTTGTATTTA
1984583 AAAACGTCAC
Statistics
Matches: 189, Mismatches: 27, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
81 2 0.01
82 2 0.01
83 63 0.33
84 61 0.32
85 3 0.02
86 58 0.31
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (82 bp):
TAGCGGCGTTTGTATTTACAAACGCTATTGACTTGTATTTAGCGGCGTTTGTATTTACAAATGCC
ACTATTGATTGTGTATT
Found at i:1990450 original size:36 final size:36
Alignment explanation
Indices: 1990392--1990460 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
1990382 TAGCATCCTG
1990392 TTTGAACTTGTTTTTTTGAACTTTCTCATATTTCTT
1 TTTGAACTTGTTTTTTTGAACTTTCTCATATTTCTT
1990428 TTTGTAACTTG-TTTTTTGAACTTTCTCATATTT
1 TTTG-AACTTGTTTTTTTGAACTTTCTCATATTT
1990461 TTATAAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 26 0.81
37 6 0.19
ACGTcount: A:0.17, C:0.13, G:0.09, T:0.61
Consensus pattern (36 bp):
TTTGAACTTGTTTTTTTGAACTTTCTCATATTTCTT
Found at i:1992783 original size:85 final size:85
Alignment explanation
Indices: 1992638--1992878 Score: 367
Period size: 85 Copynumber: 2.8 Consensus size: 85
1992628 GCAATGTAGT
* ** * * *
1992638 TCAAGGCGAGAAGGGCTATATGTCAACAAAAATATTCGAGTTTGATTACATTCAGCTCAAGAGTA
1 TCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGAA
*
1992703 TATCAAATTTACAGCATAGC
66 TATCAAATTTACAACATAGC
* *
1992723 TCAAGGCAAGAAGGGCTATCTGTCAACAAAAACC-TCTGAGTTCGATTACATTCAGATCAAGGGA
1 TCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTC-GAGTTCGATTACATTCAGCTCAAGGGA
1992787 ATATCAAATTTACAACATAGC
65 ATATCAAATTTACAACATAGC
* *
1992808 TCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCA
1 TCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGAA
1992873 TATCAA
66 TATCAA
1992879 CCGCATGGTA
Statistics
Matches: 141, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
84 2 0.01
85 137 0.97
86 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (85 bp):
TCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGAA
TATCAAATTTACAACATAGC
Found at i:1994116 original size:34 final size:33
Alignment explanation
Indices: 1994062--1994132 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
1994052 CCTTACAAAC
* *
1994062 TCCCTAGTTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACCGGGCTAAACTAGAACCTT
*
1994095 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTAC-CGGGCTAAACTAGAACCTT
1994129 TCCC
1 TCCC
1994133 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 12 0.35
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.32
Consensus pattern (33 bp):
TCCCTAGCTTTTACCGGGCTAAACTAGAACCTT
Found at i:1994441 original size:21 final size:21
Alignment explanation
Indices: 1994415--1994456 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1994405 CCAGAATGGG
*
1994415 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1994436 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1994457 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1994587 original size:19 final size:19
Alignment explanation
Indices: 1994563--1994609 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1994553 GAGTCTCGGG
* *
1994563 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAAAT
* *
1994582 TACTGTTCCAATAGTAAAT
1 TACTGTTCAAACAGTAAAT
1994601 TACTGTTCA
1 TACTGTTCA
1994610 TAAAAACATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (19 bp):
TACTGTTCAAACAGTAAAT
Found at i:1994701 original size:31 final size:32
Alignment explanation
Indices: 1994666--1994733 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
1994656 ATTTTTGTAA
*
1994666 ATTTTGAATAAATTCAATT-AAGTCCAAATA-C
1 ATTTTGAA-AAATTCAATTCAAGTCCAAAAATC
*
1994697 ATTTT-TAAAATTCAATTCAAGTCCAAAAATC
1 ATTTTGAAAAATTCAATTCAAGTCCAAAAATC
1994728 ATTTTG
1 ATTTTG
1994734 CCTTAAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 10 0.31
30 11 0.34
31 11 0.34
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (32 bp):
ATTTTGAAAAATTCAATTCAAGTCCAAAAATC
Found at i:1994707 original size:29 final size:31
Alignment explanation
Indices: 1994675--1994732 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
1994665 AATTTTGAAT
*
1994675 AAATTCAATT-AAGTCCAAATA-CATTTTTA
1 AAATTCAATTCAAGTCCAAAAATCATTTTTA
1994704 AAATTCAATTCAAGTCCAAAAATCATTTT
1 AAATTCAATTCAAGTCCAAAAATCATTTT
1994733 GCCTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.38
30 10 0.38
31 6 0.23
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (31 bp):
AAATTCAATTCAAGTCCAAAAATCATTTTTA
Found at i:1995933 original size:16 final size:17
Alignment explanation
Indices: 1995912--1995951 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1995902 TAAAAAATCA
1995912 TATTTTT-AT-TGCTTT
1 TATTTTTAATATGCTTT
*
1995927 TATTTTTAATATGTTTT
1 TATTTTTAATATGCTTT
1995944 TATTTTTA
1 TATTTTTA
1995952 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 2 0.09
17 13 0.59
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (17 bp):
TATTTTTAATATGCTTT
Found at i:1998086 original size:17 final size:17
Alignment explanation
Indices: 1998064--1998097 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1998054 CATGCTTTCA
1998064 TTTCATTTCATTTTAGT
1 TTTCATTTCATTTTAGT
1998081 TTTCATTTCATTTTAGT
1 TTTCATTTCATTTTAGT
1998098 ACACTGTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTCATTTCATTTTAGT
Found at i:1998405 original size:20 final size:21
Alignment explanation
Indices: 1998366--1998409 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1998356 TAAACTCTCA
1998366 TGTATTTTTTAGTATGTTATT
1 TGTATTTTTTAGTATGTTATT
1998387 TGTATTTTTTA-T-TGATTATT
1 TGTATTTTTTAGTATG-TTATT
1998407 TGT
1 TGT
1998410 TTATGTACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 11 0.50
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (21 bp):
TGTATTTTTTAGTATGTTATT
Found at i:2001433 original size:3 final size:3
Alignment explanation
Indices: 2001427--2001455 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2001417 TTTTTAATTT
2001427 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2001456 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2001462 original size:3 final size:3
Alignment explanation
Indices: 2001456--2001530 Score: 141
Period size: 3 Copynumber: 24.7 Consensus size: 3
2001446 AATAATAATA
2001456 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2001504 TAT TAT TAT TAT TAT TATT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TA
2001531 CAAACTTTTG
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2002267 original size:17 final size:17
Alignment explanation
Indices: 2002247--2002280 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2002237 TAGGTCACCG
2002247 AAGTTCAAAGGTAACCT
1 AAGTTCAAAGGTAACCT
2002264 AAGTTCAAAGGTAACCT
1 AAGTTCAAAGGTAACCT
2002281 CTGGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (17 bp):
AAGTTCAAAGGTAACCT
Found at i:2003550 original size:22 final size:23
Alignment explanation
Indices: 2003524--2003586 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
2003514 TCCACGTTTA
*
2003524 TTTATTCTG-ATTATTTTTCTCT
1 TTTATTCTGTATTATTTTTCACT
* *
2003546 TTTATTTTGTTTTATTTTTCACT
1 TTTATTCTGTATTATTTTTCACT
* *
2003569 TTTATTTTGTTTTATTTT
1 TTTATTCTGTATTATTTT
2003587 ATGATATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 8 0.22
23 29 0.78
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.75
Consensus pattern (23 bp):
TTTATTCTGTATTATTTTTCACT
Found at i:2003558 original size:5 final size:5
Alignment explanation
Indices: 2003545--2003601 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
2003535 TATTTTTCTC
* * **
2003545 TTTTA TTTTG TTTTA TTTTTCA CTTTTA TTTTG TTTTA TTTTA TGATA
1 TTTTA TTTTA TTTTA -TTTT-A -TTTTA TTTTA TTTTA TTTTA TTTTA
2003593 TTTTA TTTT
1 TTTTA TTTT
2003602 TACAAAAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
5 31 0.76
6 5 0.12
7 5 0.12
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:2003564 original size:23 final size:23
Alignment explanation
Indices: 2003534--2003586 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
2003524 TTTATTCTGA
*
2003534 TTATTTTTCTCTTTTATTTTGTT
1 TTATTTTTCACTTTTATTTTGTT
2003557 TTATTTTTCACTTTTATTTTGTT
1 TTATTTTTCACTTTTATTTTGTT
2003580 TTATTTT
1 TTATTTT
2003587 ATGATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.08, G:0.04, T:0.77
Consensus pattern (23 bp):
TTATTTTTCACTTTTATTTTGTT
Found at i:2008284 original size:4 final size:4
Alignment explanation
Indices: 2008275--2010806 Score: 4987
Period size: 4 Copynumber: 635.8 Consensus size: 4
2008265 ATTGAGAAAA
2008275 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008323 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008371 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008419 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008467 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008515 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008563 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC--
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008609 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008657 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008705 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008753 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008801 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008849 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008897 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008945 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2008993 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009041 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009089 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009137 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009185 ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009231 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009279 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009327 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009375 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009421 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009469 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009517 ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009563 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009611 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009659 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009707 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009755 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009803 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009851 ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009897 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009945 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2009993 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010041 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010089 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010137 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010185 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010233 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010281 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010329 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010377 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010425 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010473 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010521 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010569 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010617 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010664 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010712 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2010760 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
2010807 CATATATACA
Statistics
Matches: 2517, Mismatches: 0, Indels: 22
0.99 0.00 0.01
Matches are distributed among these distances:
2 10 0.00
3 3 0.00
4 2504 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:2012187 original size:3 final size:3
Alignment explanation
Indices: 2012175--2012219 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
2012165 TTATTTAATT
2012175 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
2012220 CAAACTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2013990 original size:30 final size:30
Alignment explanation
Indices: 2013926--2014003 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
2013916 GTCTTTTAAC
* * * *
2013926 TTTCTGTTTTTATTATTTTTGTCATTTAAG
1 TTTCTATTTTTATTATTTTAGTCATGTAAA
* *
2013956 TTTCTATTTTTGTTATTTTAGTCCTGTAAA
1 TTTCTATTTTTATTATTTTAGTCATGTAAA
* *
2013986 TTTCTATTATTACTATTT
1 TTTCTATTTTTATTATTT
2014004 AATCCTTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.19, C:0.09, G:0.08, T:0.64
Consensus pattern (30 bp):
TTTCTATTTTTATTATTTTAGTCATGTAAA
Found at i:2027246 original size:19 final size:19
Alignment explanation
Indices: 2027224--2027286 Score: 83
Period size: 19 Copynumber: 3.2 Consensus size: 19
2027214 AATTTTAAAA
2027224 GAAATATTGTTTTTTTAG-G
1 GAAAT-TTGTTTTTTTAGAG
2027243 GAAATTTGATTTTTTTTAGAG
1 GAAATTTG--TTTTTTTAGAG
*
2027264 GAAATTTGATTTTTTAGAG
1 GAAATTTGTTTTTTTAGAG
2027283 GAAA
1 GAAA
2027287 ATCTATTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
18 3 0.08
19 19 0.47
20 9 0.22
21 9 0.22
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.48
Consensus pattern (19 bp):
GAAATTTGTTTTTTTAGAG
Found at i:2027259 original size:21 final size:21
Alignment explanation
Indices: 2027233--2027286 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
2027223 AGAAATATTG
2027233 TTTTTTTAG-GGAAATTTGAT
1 TTTTTTTAGAGGAAATTTGAT
2027253 TTTTTTTAGAGGAAATTTGA-
1 TTTTTTTAGAGGAAATTTGAT
2027273 -TTTTTTAGAGGAAA
1 TTTTTTTAGAGGAAA
2027287 ATCTATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 14 0.42
20 9 0.27
21 10 0.30
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (21 bp):
TTTTTTTAGAGGAAATTTGAT
Found at i:2027611 original size:2 final size:2
Alignment explanation
Indices: 2027604--2027728 Score: 71
Period size: 2 Copynumber: 61.5 Consensus size: 2
2027594 ATGTTTAATG
* *
2027604 AT AT AT AT AT AT AT AT AT AT ACT AT AT AGT TT AT AT AT -T TT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* * * *
2027647 AGT TT AT AGT TT AT AT AT TT AT ACT AT AT AGT TT AT AT A- AT -T
1 A-T AT AT A-T AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* * *
2027689 AT ACT -T AT -T CT TT AT AT AT AT GT AT AT AT AT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2027729 CTTAATTGTA
Statistics
Matches: 96, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
1 5 0.05
2 82 0.85
3 9 0.09
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2027748 original size:45 final size:44
Alignment explanation
Indices: 2027611--2027749 Score: 140
Period size: 45 Copynumber: 3.1 Consensus size: 44
2027601 ATGATATATA
* *
2027611 TATATATATATATACTATATAGTTTATATATTTTATAGTTTATAGTT
1 TATATATAT-TATACTATATAGTTTATATA-ATTATAG-TTATTGTT
* *
2027658 TATATAT-TTATACTATATAGTTTATATAATTATACTTATTCTT
1 TATATATATTATACTATATAGTTTATATAATTATAGTTATTGTT
* * *
2027701 TATATATATGTATA-TATATA-TATATATACTTAATTGTATATTGTT
1 TATATATAT-TATACTATATAGTTTATATAATT-ATAGT-TATTGTT
2027746 TATA
1 TATA
2027750 AGTATTGGGC
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
43 22 0.28
44 15 0.19
45 34 0.43
46 1 0.01
47 7 0.09
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.55
Consensus pattern (44 bp):
TATATATATTATACTATATAGTTTATATAATTATAGTTATTGTT
Found at i:2028014 original size:6 final size:6
Alignment explanation
Indices: 2028003--2028035 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2027993 TTGATCAATG
2028003 ATAACT ATAACT ATAACT ATAACT ATAACT ATA
1 ATAACT ATAACT ATAACT ATAACT ATAACT ATA
2028036 TATATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAACT
Found at i:2028261 original size:2 final size:2
Alignment explanation
Indices: 2028256--2028429 Score: 91
Period size: 2 Copynumber: 88.0 Consensus size: 2
2028246 ATACATTGCT
*
2028256 TA TA TA T- TA TA TA CTT TA TA CT- TA TA TA TA TA TA TA TA CT-
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * * * * * *
2028296 TA TA TG CA CT- TT TA TA TA TA -A T- TA TG TA CA TA CA TCA TA CA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
2028337 TA TA TA CT- TA TG TA TA TA CT- TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
2028379 TA CT- TA TA TA TA TA T- TG TA TA TA TA CT- TA TA TA TA 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
2028420 TA TA TA TA TA
1 TA TA TA TA TA
2028430 CTTAATTGTA
Statistics
Matches: 132, Mismatches: 20, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
1 11 0.08
2 112 0.85
3 9 0.07
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2028608 original size:104 final size:104
Alignment explanation
Indices: 2028418--2028611 Score: 293
Period size: 104 Copynumber: 1.9 Consensus size: 104
2028408 TATATATATA
* * *
2028418 TATATATATATACTTAATTGTATATTAGGCTTATAAATGAGTTTATAAGTATTGGGTTACGTATT
1 TATATATATATACTTAATTGTATATTAGGCTTACAAATGAGTGTATAAGTATTGGGTTACGTAAT
* *
2028483 TTGTAATTCAAATGGGCTTATATTATTAATATGGACTTT
66 TTGTAATACAAATGAGCTTATATTATTAATATGGACTTT
* *
2028522 TATATATATATACTTAATTGTATATTAGGCTTACAAATGGGTGTAT-AGATATTGGGTTATGTAA
1 TATATATATATACTTAATTGTATATTAGGCTTACAAATGAGTGTATAAG-TATTGGGTTACGTAA
2028586 TTTGTAATACAAATGAAG-TTATATTA
65 TTTGTAATACAAATG-AGCTTATATTA
2028612 ATAAAACAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
103 2 0.02
104 78 0.96
105 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (104 bp):
TATATATATATACTTAATTGTATATTAGGCTTACAAATGAGTGTATAAGTATTGGGTTACGTAAT
TTGTAATACAAATGAGCTTATATTATTAATATGGACTTT
Found at i:2042023 original size:21 final size:23
Alignment explanation
Indices: 2041988--2042045 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2041978 TTAGTGCAGA
*
2041988 GGGAATCAA-TCCCCCCTTG-A-
1 GGGAACCAATTCCCCCCTTGAAG
* *
2042008 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCAATTCCCCCCTTGAAG
2042031 GGGAACCAATTCCCC
1 GGGAACCAATTCCCC
2042046 TCACAGGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 7 0.23
21 9 0.29
22 1 0.03
23 14 0.45
ACGTcount: A:0.24, C:0.34, G:0.22, T:0.19
Consensus pattern (23 bp):
GGGAACCAATTCCCCCCTTGAAG
Found at i:2046490 original size:60 final size:60
Alignment explanation
Indices: 2046417--2046537 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
2046407 GGTGCAATAA
*
2046417 CTTGCAAACCAAGAATGGTTACGATAGGATTCCGGTCAAGCACCGACACATTCGGGGCAT
1 CTTGCAAACCAAGAATGGTTACGATAGGATTCCGGTCAAGCACCGACACATTCAGGGCAT
* *
2046477 CTTGCAAACCAAGAATGGTTACGATAGGATTCCGGTGAAGCATCGACACATTCAGGGCAT
1 CTTGCAAACCAAGAATGGTTACGATAGGATTCCGGTCAAGCACCGACACATTCAGGGCAT
2046537 C
1 C
2046538 GAAGCAACTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.21
Consensus pattern (60 bp):
CTTGCAAACCAAGAATGGTTACGATAGGATTCCGGTCAAGCACCGACACATTCAGGGCAT
Found at i:2049418 original size:4 final size:4
Alignment explanation
Indices: 2049391--2049443 Score: 65
Period size: 4 Copynumber: 13.5 Consensus size: 4
2049381 CTAAAAATGG
*
2049391 AATA AA-A AATA AA-A AACAA AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AA-TA AATA AATA AATA AATA AATA AATA AATA
*
2049438 CATA AA
1 AATA AA
2049444 ATAATCAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
3 6 0.14
4 34 0.79
5 3 0.07
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:2049616 original size:36 final size:36
Alignment explanation
Indices: 2049498--2049695 Score: 122
Period size: 36 Copynumber: 5.4 Consensus size: 36
2049488 ATATATTTAT
* * * *
2049498 TATACGTTTTCAAAATTTGTTTTTCAAAAATATAATATA
1 TATATGTTTTCAAAAATTGATTTT-AAAACTAT-ATA-A
* * * * *
2049537 TATATATATATACAAAAATTGTTTTTGAAATTATATAA
1 TATATGT-T-TTCAAAAATTGATTTTAAAACTATATAA
2049575 TATATGTTTTCAAAAATTGATTTTAAAACTATATAA
1 TATATGTTTTCAAAAATTGATTTTAAAACTATATAA
*
2049611 TATATGTTTTTAAAACA-T-ATTTTCAAAATCGTAT-T-A
1 TATATGTTTTCAAAA-ATTGATTTT-AAAA-C-TATATAA
** * *
2049647 TATA--TTTTCAAAACCTGATTTTTAAAATTATATAT
1 TATATGTTTTCAAAAATTGA-TTTTAAAACTATATAA
*
2049682 TATATGATTT-AAAA
1 TATATGTTTTCAAAA
2049696 CGTTTAAATT
Statistics
Matches: 129, Mismatches: 17, Indels: 29
0.74 0.10 0.17
Matches are distributed among these distances:
33 3 0.02
34 10 0.08
35 14 0.11
36 56 0.43
37 7 0.05
38 10 0.08
39 8 0.06
40 7 0.05
41 14 0.11
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATGTTTTCAAAAATTGATTTTAAAACTATATAA
Found at i:2053451 original size:36 final size:36
Alignment explanation
Indices: 2053411--2053741 Score: 419
Period size: 36 Copynumber: 8.9 Consensus size: 36
2053401 TTTGTGATTT
* *
2053411 CATCGGCACTTCTGATTCAAGTCGAACCGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* *
2053447 CATCGGCACTTTCGATTCAAGTCGAACGGAAGAAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* *
2053483 CAACGACACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
*
2053519 CAACGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* * *
2053555 CAACGACACTTCTGATTCAAGTCGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* * *
2053591 CACCGGCATTTTCGATTCAAGTCGAACGGAAGGAAGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAAC--------GGAAGGAAG
* *
2053635 AATCGACACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* *
2053671 CATCGGCACTTTCCGATTCAAGACTAACGGAAGGAAG
1 CATCGGCAC-TTCCGATTCAAGTCGAACGGAAGGAAG
*
2053708 CATCGACACTTCCGATTCAAGTCGAACGGAAGGA
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGA
2053742 GGTGATGCAC
Statistics
Matches: 258, Mismatches: 28, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
36 194 0.75
37 33 0.13
44 31 0.12
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (36 bp):
CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
Found at i:2053643 original size:80 final size:81
Alignment explanation
Indices: 2053546--2053741 Score: 259
Period size: 80 Copynumber: 2.5 Consensus size: 81
2053536 CAAGTCGAAC
* *
2053546 GGAAGGAAGCAACGACACTTCTGATTCAAGTCGAACGGAAGGAAGCACCGGCA-TTTTCGATTCA
1 GGAAGGAAGCAACGACACTTCCGATTCAAGTCGAACGGAAGGAAGCACCGGCACTTTCCGATTCA
*
2053610 AGTCGAACGGAAGGAA
66 AGACGAACGGAAGGAA
*
2053626 GGAAGGAAG-AATCGACACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTTCCGATTC
1 GGAAGGAAGCAA-CGACACTTCCGATTCAAGTCGAACGGAAGGAAGCACCGGCACTTTCCGATTC
*
2053690 AAGACTAAC--------
65 AAGACGAACGGAAGGAA
*
2053699 GGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
1 GGAAGGAAGCAACGACACTTCCGATTCAAGTCGAACGGAAGGA
2053742 GGTGATGCAC
Statistics
Matches: 107, Mismatches: 6, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
73 40 0.37
74 1 0.01
79 2 0.02
80 48 0.45
81 16 0.15
ACGTcount: A:0.35, C:0.21, G:0.28, T:0.16
Consensus pattern (81 bp):
GGAAGGAAGCAACGACACTTCCGATTCAAGTCGAACGGAAGGAAGCACCGGCACTTTCCGATTCA
AGACGAACGGAAGGAA
Found at i:2053681 original size:116 final size:117
Alignment explanation
Indices: 2053510--2053741 Score: 351
Period size: 117 Copynumber: 2.0 Consensus size: 117
2053500 CAAGTCGAAC
* *
2053510 GGAAGGAAGCAACGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGACAC-TTCTGATTCA
1 GGAAGGAAGCAACGACACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGACACTTTCCGATTCA
* * * *
2053574 AGTCGAACGGAAGGAAGCACCGGCATTTTCGATTCAAGTCGAACGGAAGGAA
66 AGACGAACGGAAGGAAGCACCGACACTTCCGATTCAAGTCGAACGGAAGGAA
* *
2053626 GGAAGGAAG-AATCGACACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTTCCGATTC
1 GGAAGGAAGCAA-CGACACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGACACTTTCCGATTC
* *
2053690 AAGACTAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
65 AAGACGAACGGAAGGAAGCACCGACACTTCCGATTCAAGTCGAACGGAAGGA
2053742 GGTGATGCAC
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
115 2 0.02
116 48 0.46
117 54 0.52
ACGTcount: A:0.34, C:0.22, G:0.28, T:0.16
Consensus pattern (117 bp):
GGAAGGAAGCAACGACACTTCCGATTCAAGTCGAACGGAAGGAAGCAACGACACTTTCCGATTCA
AGACGAACGGAAGGAAGCACCGACACTTCCGATTCAAGTCGAACGGAAGGAA
Found at i:2053875 original size:18 final size:17
Alignment explanation
Indices: 2053852--2053897 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
2053842 TGTTTATGAG
2053852 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCT-TGAA
* *
2053870 GGAATTGAAAT-TTGTA
1 GGAATTGGAATCTTGAA
2053886 GGAATTGGAATC
1 GGAATTGGAATC
2053898 CAATTCCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 13 0.54
17 1 0.04
18 10 0.42
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTTGAA
Found at i:2058150 original size:21 final size:20
Alignment explanation
Indices: 2058126--2058191 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
2058116 TTCAAAGAAA
2058126 CATTTACTAAACTTTGAAAAC
1 CATTTAC-AAACTTTGAAAAC
*
2058147 CATTTTCAAA----G-AAA-
1 CATTTACAAACTTTGAAAAC
2058161 CATTTACCAAACTTTGAAAAC
1 CATTTA-CAAACTTTGAAAAC
*
2058182 CATTTTCAAA
1 CATTTACAAA
2058192 GTTGGTTGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 15
0.66 0.06 0.28
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 1 0.03
19 1 0.03
20 10 0.29
21 11 0.31
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (20 bp):
CATTTACAAACTTTGAAAAC
Found at i:2058151 original size:36 final size:35
Alignment explanation
Indices: 2058077--2058192 Score: 171
Period size: 35 Copynumber: 3.3 Consensus size: 35
2058067 ACCTATTCCT
* * *
2058077 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAAC
1 ATTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
*
2058112 ATTTTTCAAAGAAACATTTACTAAACTTTGAAAACC
1 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACC
2058148 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
2058183 ATTTTCAAAG
1 ATTTTCAAAG
2058193 TTGGTTGCCA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 44 0.59
36 11 0.15
37 19 0.26
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:2060911 original size:21 final size:21
Alignment explanation
Indices: 2060887--2060931 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2060877 TGTTGTTCGT
* *
2060887 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2060908 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2060929 TTG
1 TTG
2060932 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2065866 original size:21 final size:21
Alignment explanation
Indices: 2065842--2065886 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2065832 TGTTGTTCGT
* *
2065842 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2065863 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2065884 TTG
1 TTG
2065887 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2070767 original size:35 final size:35
Alignment explanation
Indices: 2070698--2070812 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
2070688 ACCTATTCCT
* *
2070698 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAAC
1 ATTTTCAAACAAACATTTACCAAACTTTG-AAAACC
*
2070733 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 A-TTTTCAAACAAACATTTACCAAACTTTGAAAACC
*
2070769 ATTTTCAAACAAACATTTATCAAACTTTGAAAACC
1 ATTTTCAAACAAACATTTACCAAACTTTGAAAACC
2070804 ATTTTCAAA
1 ATTTTCAAA
2070813 GTTGGTTGCC
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 42 0.58
36 11 0.15
37 20 0.27
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.30
Consensus pattern (35 bp):
ATTTTCAAACAAACATTTACCAAACTTTGAAAACC
Found at i:2072353 original size:44 final size:44
Alignment explanation
Indices: 2072290--2072377 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
2072280 AGCCATACCA
2072290 CTTCAGATACAACATCATCTATCCCTTGATACTCAACCTCAGTG
1 CTTCAGATACAACATCATCTATCCCTTGATACTCAACCTCAGTG
2072334 CTTCAGATACAACATCATCTATCCCTTGATACTCAACCTCAGTG
1 CTTCAGATACAACATCATCTATCCCTTGATACTCAACCTCAGTG
2072378 ATAGACTGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.30
Consensus pattern (44 bp):
CTTCAGATACAACATCATCTATCCCTTGATACTCAACCTCAGTG
Found at i:2072364 original size:22 final size:22
Alignment explanation
Indices: 2072295--2072365 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
2072285 TACCACTTCA
2072295 GATACAACATCATCTATCCCTT
1 GATACAACATCATCTATCCCTT
* *
2072317 GATACTCAACCTCAGTGCT-T--C-A
1 GATA--CAACATCA-T-CTATCCCTT
2072339 GATACAACATCATCTATCCCTT
1 GATACAACATCATCTATCCCTT
2072361 GATAC
1 GATAC
2072366 TCAACCTCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 7 0.19
21 1 0.03
22 13 0.35
23 1 0.03
24 7 0.19
25 2 0.05
26 2 0.05
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.30
Consensus pattern (22 bp):
GATACAACATCATCTATCCCTT
Found at i:2077834 original size:30 final size:30
Alignment explanation
Indices: 2077798--2077855 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2077788 TAGTAACCCC
* * *
2077798 GGTGTTATTAGTATGGTTGGTGTGACGAGT
1 GGTGTTATGAATATGGTTGGTATGACGAGT
2077828 GGTGTTATGAATATGGTTGGTATGACGA
1 GGTGTTATGAATATGGTTGGTATGACGA
2077856 CTGACAGAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.03, G:0.38, T:0.38
Consensus pattern (30 bp):
GGTGTTATGAATATGGTTGGTATGACGAGT
Found at i:2078105 original size:20 final size:20
Alignment explanation
Indices: 2078076--2078122 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2078066 TAAATTTGTG
*
2078076 TATTTTTTTAAGTGAACACT
1 TATTTCTTTAAGTGAACACT
*
2078096 TATTTCTTTAATTGAACACT
1 TATTTCTTTAAGTGAACACT
2078116 TATTTCT
1 TATTTCT
2078123 ATATGAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.53
Consensus pattern (20 bp):
TATTTCTTTAAGTGAACACT
Found at i:2080333 original size:3 final size:3
Alignment explanation
Indices: 2080327--2080352 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2080317 AAACATCATC
2080327 CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CC
2080353 ATGGATGATG
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:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:2082799 original size:39 final size:39
Alignment explanation
Indices: 2082745--2082827 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
2082735 CTCATGATTT
*
2082745 TATCAAAACCATGATAAACAATATTAGACATAATGGTCA
1 TATCAAAACCATGATAAACAATATTAGACATAATAGTCA
* *
2082784 TATCAAAGCCATGATAAACAATATTATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATTAGACATAATAGTCA
2082823 TATCA
1 TATCA
2082828 TAATCTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATTAGACATAATAGTCA
Found at i:2083010 original size:19 final size:19
Alignment explanation
Indices: 2082940--2083039 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 19
2082930 ACTTTCACAT
*
2082940 TTCATAAC-TCATTGTCAAA
1 TTCATAACTTAATT-TCAAA
* * **
2082959 TTCAGAACTTATTTTCGGA
1 TTCATAACTTAATTTCAAA
* *
2082978 CTCAAAACTT-ATTTCAAA
1 TTCATAACTTAATTTCAAA
* *
2082996 TTCATAAGTTAATTTCATA
1 TTCATAACTTAATTTCAAA
* *
2083015 TTCATAACTTATTTTCAAG
1 TTCATAACTTAATTTCAAA
2083034 TTCATA
1 TTCATA
2083040 GCCCAATGCA
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
18 12 0.20
19 46 0.75
20 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (19 bp):
TTCATAACTTAATTTCAAA
Found at i:2083024 original size:37 final size:37
Alignment explanation
Indices: 2082940--2083039 Score: 101
Period size: 37 Copynumber: 2.6 Consensus size: 37
2082930 ACTTTCACAT
* * * *
2082940 TTCATAACTCATTGTCAAATTCAGAACTTATTTTCGGA
1 TTCATAACTTATT-TCAAATTCATAACTTAATTTCAGA
* * * *
2082978 CTCAAAACTTATTTCAAATTCATAAGTTAATTTCATA
1 TTCATAACTTATTTCAAATTCATAACTTAATTTCAGA
*
2083015 TTCATAACTTATTTTCAAGTTCATA
1 TTCATAACTTA-TTTCAAATTCATA
2083040 GCCCAATGCA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
37 28 0.56
38 22 0.44
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (37 bp):
TTCATAACTTATTTCAAATTCATAACTTAATTTCAGA
Found at i:2087198 original size:18 final size:18
Alignment explanation
Indices: 2087175--2087228 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2087165 GTATTTTATA
*
2087175 TTACATCTTAAGTTAAAT
1 TTACATCTTAAATTAAAT
*
2087193 TTACATATTAAATTAAAT
1 TTACATCTTAAATTAAAT
* *
2087211 TAAAATCTTAACATTAAA
1 TTACATCTTAA-ATTAAA
2087229 AAAATATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (18 bp):
TTACATCTTAAATTAAAT
Found at i:2087301 original size:43 final size:41
Alignment explanation
Indices: 2087218--2087322 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 41
2087208 AATTAAAATC
2087218 TTAACATTAAAAAAATATATTTTAATTTATCTTAATTTTAAT
1 TTAAC-TTAAAAAAATATATTTTAATTTATCTTAATTTTAAT
* ** *
2087260 TTCACTTAAATAAAATATATTTTGTTCTTTTCTTAATTTTAAT
1 TTAACTTAAA-AAAATATATTTTAAT-TTATCTTAATTTTAAT
*
2087303 TTAACTTAAAAATATA-ATTT
1 TTAACTTAAAAAAATATATTT
2087323 ATTCTTACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 9 0.16
42 22 0.40
43 24 0.44
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (41 bp):
TTAACTTAAAAAAATATATTTTAATTTATCTTAATTTTAAT
Found at i:2087404 original size:29 final size:27
Alignment explanation
Indices: 2087364--2087467 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 27
2087354 TATTCTTATA
2087364 ATATTTTAAAATTAAGATAAAAATATAAT
1 ATATTTTAAAATTAA-ATAAAAATA-AAT
*
2087393 ATATTTTTAAATTAAATAAAGAATAAAAT
1 ATATTTTAAAATTAAATAAA-AAT-AAAT
* *
2087422 ATACATTTGT-AAATAAAAATAAATATAAAT
1 AT--ATTT-TAAAAT-TAAATAAAAATAAAT
*
2087452 ATATATTAAAATTAAA
1 ATATTTTAAAATTAAA
2087468 AGATATATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
27 4 0.06
28 12 0.19
29 22 0.35
30 7 0.11
31 10 0.16
32 8 0.13
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.37
Consensus pattern (27 bp):
ATATTTTAAAATTAAATAAAAATAAAT
Found at i:2087521 original size:30 final size:29
Alignment explanation
Indices: 2087464--2087598 Score: 127
Period size: 29 Copynumber: 4.7 Consensus size: 29
2087454 ATATTAAAAT
* * * *
2087464 TAAAAGATATATTTATGTTAAAGTAAGAA
1 TAAAATATATTTTTAAGTTAAAATAAGAA
* *
2087493 TAAATTATATTTTTTAAGTTAAAATAAGAC
1 TAAAATATA-TTTTTAAGTTAAAATAAGAA
2087523 TAAAATATATTTTTAAGTTAAAATAAGAA
1 TAAAATATATTTTTAAGTTAAAATAAGAA
* * *
2087552 TAAAA-ATGTATTTAAGATAAAAATAA-AA
1 TAAAATATATTTTTAAG-TTAAAATAAGAA
2087580 T---ATATATTTTTAATGTTAA
1 TAAAATATATTTTTAA-GTTAA
2087599 GATGTTAATT
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
25 1 0.01
26 11 0.12
27 1 0.01
28 12 0.14
29 39 0.44
30 24 0.27
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (29 bp):
TAAAATATATTTTTAAGTTAAAATAAGAA
Found at i:2087566 original size:23 final size:24
Alignment explanation
Indices: 2087540--2087588 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
2087530 TATTTTTAAG
* *
2087540 TTAAAATAAGAATAAAA-ATGTAT
1 TTAAAATAAAAATAAAATATATAT
*
2087563 TTAAGATAAAAATAAAATATATAT
1 TTAAAATAAAAATAAAATATATAT
2087587 TT
1 TT
2087589 TTAATGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (24 bp):
TTAAAATAAAAATAAAATATATAT
Found at i:2087621 original size:18 final size:18
Alignment explanation
Indices: 2087588--2087639 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
2087578 AATATATATT
*
2087588 TTTAATGTTAAGATGTTAA
1 TTTAAT-TTAAGATGTGAA
*
2087607 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGTGAA
*
2087625 TTTAAGTTAAGATGT
1 TTTAATTTAAGATGT
2087640 AGTATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (18 bp):
TTTAATTTAAGATGTGAA
Found at i:2088482 original size:2 final size:2
Alignment explanation
Indices: 2088475--2088522 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2088465 TAATTTTGTC
2088475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2088517 AT AT AT
1 AT AT AT
2088523 GGATGGATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2093425 original size:13 final size:13
Alignment explanation
Indices: 2093407--2093433 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2093397 GCTGTGAAGT
2093407 TGAAATTGGGAAA
1 TGAAATTGGGAAA
2093420 TGAAATTGGGAAA
1 TGAAATTGGGAAA
2093433 T
1 T
2093434 TGTTTATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (13 bp):
TGAAATTGGGAAA
Found at i:2093585 original size:106 final size:106
Alignment explanation
Indices: 2093276--2094241 Score: 1280
Period size: 94 Copynumber: 9.6 Consensus size: 106
2093266 TATTGTTCCA
* * * * *
2093276 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
2093341 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
***
2093382 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGGAAATGAAATTGGGAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATT-GGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
2093447 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2093489 AGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAGATTGAGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
2093554 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
2093595 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCAGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
2093660 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
2093701 AGTCCAATATCCTTCG-T-TG-A---G-AA---G-T-TGAAATTGGAAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
2093754 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2093795 AGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * *
2093848 CAGCGGTCCCTTCGTCGTAAAGTTGAACTTGTGTTGTCCGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2093889 AGTCCAATATCCTTCGC--T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
2093942 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2093983 AGTCCAATATCCTTCGC--T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
2094036 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2094077 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG----GAAATTGAGAAGTTGGTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
2094138 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
2094179 AATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTGTTTGTTGACA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
2094242 GACAACTTTT
Statistics
Matches: 797, Mismatches: 45, Indels: 36
0.91 0.05 0.04
Matches are distributed among these distances:
94 356 0.45
95 1 0.00
96 2 0.00
99 3 0.00
100 3 0.00
101 2 0.00
102 95 0.12
103 1 0.00
104 3 0.00
105 1 0.00
106 234 0.29
107 96 0.12
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:2093729 original size:43 final size:43
Alignment explanation
Indices: 2093668--2094105 Score: 146
Period size: 43 Copynumber: 9.4 Consensus size: 43
2093658 ACCAGCGGTC
2093668 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
2093711 CCTTCGTTGAGAAGTTGAAATTG-GAAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG----TTG--TCTGGA-GTCCA-ATAT
2093761 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
2093805 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
* * *
2093855 CCCTTCGTCGTAAAGTTGAACTTGTGTTGTCCGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** ***
2093899 CCTTCG-CTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTC-GTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
*
2093949 CCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** **
2093993 CCTTCG-CTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCAGT
1 CCTTCGTC-GTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCAATA-T
*
2094043 CCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
2094087 CCTTCG-CTGTGAAGTTGAA
1 CCTTCGTC-GTGAAGTTGAA
2094106 ATTGGGAAAT
Statistics
Matches: 278, Mismatches: 78, Indels: 78
0.64 0.18 0.18
Matches are distributed among these distances:
42 4 0.01
43 100 0.36
44 4 0.01
45 13 0.05
46 27 0.10
48 27 0.10
49 13 0.05
50 4 0.01
51 83 0.30
52 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:2094185 original size:102 final size:102
Alignment explanation
Indices: 2094009--2094212 Score: 345
Period size: 102 Copynumber: 2.0 Consensus size: 102
2093999 CTGTGAAGTT
* * **
2094009 GAAATTGGGAAATTGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTC
1 GAAATTGAGAAATTGGTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
*
2094074 TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
66 TGGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGG
* *
2094111 GAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 GAAATTGAGAAATTGGTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
2094176 TGGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGG
66 TGGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGG
2094213 CTCCGAAATT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (102 bp):
GAAATTGAGAAATTGGTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
TGGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGG
Found at i:2096921 original size:2 final size:2
Alignment explanation
Indices: 2096914--2096938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2096904 TTTAAACAAA
2096914 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
2096939 AATACATAAA
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:2101915 original size:21 final size:21
Alignment explanation
Indices: 2101889--2101928 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2101879 CAGAACCCCA
*
2101889 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2101910 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2101929 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2101963 original size:20 final size:21
Alignment explanation
Indices: 2101909--2101971 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
2101899 GATTCCCCTG
2101909 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
2101933 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
2101953 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
2101972 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:2105821 original size:22 final size:21
Alignment explanation
Indices: 2105779--2105818 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2105769 GAGTTTGTTT
*
2105779 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2105800 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2105819 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2109300 original size:23 final size:23
Alignment explanation
Indices: 2109265--2109312 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2109255 ATCAAGTACA
*
2109265 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
2109288 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
2109311 AT
1 AT
2109313 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:2110323 original size:182 final size:183
Alignment explanation
Indices: 2109933--2110386 Score: 768
Period size: 183 Copynumber: 2.5 Consensus size: 183
2109923 ACTTTTTTAC
* * *
2109933 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTTCCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
** *
2109998 TACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTTCTTTTAAATTCCAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTTCTCTTTTAAATTCCAAAA
* *
2110063 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCTCTT
131 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
*
2110116 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
2110181 TACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTC-TTCTCTTTTAAATTCCAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTTCTCTTTTAAATTCCAAAA
2110245 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
131 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
* ** * *
2110298 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCAT-TTTTTACATGTTTTATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
2110362 TACATTTTTATAAAGTATCGACACT
66 TACATTTTTATAAAGTATCGACACT
2110387 ATCAACATAT
Statistics
Matches: 256, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
181 51 0.20
182 102 0.40
183 103 0.40
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (183 bp):
TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTTCTCTTTTAAATTCCAAAA
GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
Found at i:2110529 original size:112 final size:111
Alignment explanation
Indices: 2110260--2110718 Score: 765
Period size: 111 Copynumber: 4.1 Consensus size: 111
2110250 GATACTTATA
2110260 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2110325 TTTGTCATTTTTTACATGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
2110371 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
2110436 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
66 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
2110483 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
2110548 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATAGATACATTTTT
66 TTTGTCA--TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * **
2110596 ATAAAGTATCGACACTTTTAATATATCTAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
2110661 TTTGTCATTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
2110707 ATAAAGTATCGA
1 ATAAAGTATCGA
2110719 TACAAACCGA
Statistics
Matches: 332, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
111 119 0.36
112 106 0.32
113 107 0.32
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (111 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:2110954 original size:16 final size:16
Alignment explanation
Indices: 2110915--2110956 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
2110905 CGACCAAATG
*
2110915 AAGTTTGATTCTTAAA
1 AAGTTTGTTTCTTAAA
2110931 AAGTTTGTTTCTTAAA
1 AAGTTTGTTTCTTAAA
2110947 AAGTTTGTTT
1 AAGTTTGTTT
2110957 TATCTCCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (16 bp):
AAGTTTGTTTCTTAAA
Found at i:2111518 original size:32 final size:32
Alignment explanation
Indices: 2111476--2111540 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2111466 TATATATATA
* *
2111476 TTACTTTATGGTATGTTAATGTCATTTGTGAT
1 TTACTCTATGGTATGTTAACGTCATTTGTGAT
*
2111508 TTACTCTATGGTATGTTAGCGTCATTTGTGAT
1 TTACTCTATGGTATGTTAACGTCATTTGTGAT
2111540 T
1 T
2111541 CTATGCTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (32 bp):
TTACTCTATGGTATGTTAACGTCATTTGTGAT
Found at i:2112519 original size:19 final size:20
Alignment explanation
Indices: 2112495--2112533 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2112485 TTTTAATAAA
2112495 ATTAAAAT-TAATTTTTTTT
1 ATTAAAATATAATTTTTTTT
2112514 ATTAAAATGATAATTTTTTT
1 ATTAAAAT-ATAATTTTTTT
2112534 GTGCTCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTAAAATATAATTTTTTTT
Found at i:2116713 original size:140 final size:140
Alignment explanation
Indices: 2116526--2116929 Score: 478
Period size: 137 Copynumber: 2.9 Consensus size: 140
2116516 AACAACATGG
* * * * * * *
2116526 TTCCTATGTGATGAGGAAATCTGGT-TATCTAAGGGTGATATTGCTCCTACATGATGAGGAGATC
1 TTCCTACGTGATGAGGAAGT-TCGTCTATCTAAGGATGATGTTACTCCTACGTGATGAGGAGATC
* * **
2116590 TGGTCGATGAATGATATTGTTCCTACGTGATGAGGACGTCTTGGCCATCTTTAGGGATAATTTGG
65 TGGTCGATGGATGACACAGTTCCTACGTGATGAGGACGTCTTGGCCATCTTTAGGGATAATTTGG
*
2116655 AGATAACACGA
130 AGATAACACAA
* * **
2116666 TTCTTACGTGATGAGGAAGTTCGTCTATCTAAGGATGATGTTACTCCTACGTGATAAGGAGAAAT
1 TTCCTACGTGATGAGGAAGTTCGTCTATCTAAGGATGATGTTACTCCTACGTGATGAGGAGATCT
* * * * *
2116731 AGTCGCTGGATGACACAGTTCCTATGTGATGAGGACGTC-TGACCATCTTTAGGGATAA--TAGA
66 GGTCGATGGATGACACAGTTCCTACGTGATGAGGACGTCTTGGCCATCTTTAGGGATAATTTGGA
2116793 GATAACACAA
131 GATAACACAA
* * * * * *
2116803 TTCCTACGTGATGAGGAGGTTTGACTATCTAAGGATGACG-TAGCTCCTATGTGATGGGGAGATC
1 TTCCTACGTGATGAGGAAGTTCGTCTATCTAAGGATGATGTTA-CTCCTACGTGATGAGGAGATC
* * *
2116867 TGGTCGGTGGATGACACGGTTCCTACGTGATGAGGATGT-TTGGCCATCTTTAGGGATAATTTG
65 TGGTCGATGGATGACACAGTTCCTACGTGATGAGGACGTCTTGGCCATCTTTAGGGATAATTTG
2116930 TTTCAAGAGA
Statistics
Matches: 221, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
136 2 0.01
137 115 0.52
139 22 0.10
140 82 0.37
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (140 bp):
TTCCTACGTGATGAGGAAGTTCGTCTATCTAAGGATGATGTTACTCCTACGTGATGAGGAGATCT
GGTCGATGGATGACACAGTTCCTACGTGATGAGGACGTCTTGGCCATCTTTAGGGATAATTTGGA
GATAACACAA
Found at i:2116971 original size:36 final size:36
Alignment explanation
Indices: 2116924--2117022 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
2116914 CTTTAGGGAT
*
2116924 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAA
*
2116960 AATTTGTTTCAAGAGAAACTATCTCAAGCGAGACAA
1 AATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAA
* *
2116996 AATTTGTTTCAAGGGAAACAATCTCAA
1 AATTTGTTTCAAGAGAAACTATCTCAA
2117023 AGGTTTTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
AATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAA
Found at i:2126664 original size:17 final size:18
Alignment explanation
Indices: 2126632--2126665 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2126622 AAATTAAATA
2126632 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
2126650 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
2126666 ACCTAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:2128953 original size:17 final size:18
Alignment explanation
Indices: 2128930--2128979 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
2128920 TCAGCTCAAG
2128930 TAATATTTTGAATTTAAA
1 TAATATTTTGAATTTAAA
*
2128948 -AATATTAT-AATATTAAA
1 TAATATTTTGAAT-TTAAA
*
2128965 TAATTTTTTGAATTT
1 TAATATTTTGAATTT
2128980 TTTTATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
16 3 0.12
17 12 0.46
18 8 0.31
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
TAATATTTTGAATTTAAA
Found at i:2129279 original size:7 final size:7
Alignment explanation
Indices: 2129267--2129313 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
2129257 TTTCAAACTC
2129267 AAATCTT
1 AAATCTT
2129274 AAATCTT
1 AAATCTT
2129281 AAAT-TCT
1 AAATCT-T
2129288 AAATCTT
1 AAATCTT
*
2129295 TAATCTT
1 AAATCTT
2129302 AAATCTT
1 AAATCTT
2129309 AAATC
1 AAATC
2129314 ACAAACTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 1 0.03
7 34 0.94
8 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATCTT
Found at i:2129400 original size:16 final size:16
Alignment explanation
Indices: 2129375--2129416 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
2129365 TAAACCCATA
*
2129375 ATCCTTAGACCATAAG
1 ATCCTGAGACCATAAG
2129391 ATCCTGAGACCATAAG
1 ATCCTGAGACCATAAG
2129407 ATCCTGAGAC
1 ATCCTGAGAC
2129417 TCTAAAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (16 bp):
ATCCTGAGACCATAAG
Found at i:2129480 original size:14 final size:14
Alignment explanation
Indices: 2129463--2129500 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2129453 CTAAAGTCTA
2129463 AAATTCTAAACTTC
1 AAATTCTAAACTTC
2129477 AAA-TCATAAACTTC
1 AAATTC-TAAACTTC
*
2129491 AAATTTTAAA
1 AAATTCTAAA
2129501 AGTCAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATTCTAAACTTC
Found at i:2129535 original size:14 final size:14
Alignment explanation
Indices: 2129505--2129590 Score: 54
Period size: 14 Copynumber: 6.2 Consensus size: 14
2129495 TTTAAAAGTC
*
2129505 AAACCCTAAATCTT
1 AAACCATAAATCTT
2129519 AAACCATAAA-CTCT
1 AAACCATAAATCT-T
*
2129533 AAATC-TAAAT-TAT
1 AAACCATAAATCT-T
* *
2129546 GAACCATAAATCCT
1 AAACCATAAATCTT
* *
2129560 AAGCCTTAAATCATT
1 AAACCATAAATC-TT
*
2129575 -AACCATAAACCTT
1 AAACCATAAATCTT
2129588 AAA
1 AAA
2129591 TTATATACCA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
13 13 0.25
14 39 0.74
15 1 0.02
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (14 bp):
AAACCATAAATCTT
Found at i:2129600 original size:21 final size:21
Alignment explanation
Indices: 2129563--2129615 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2129553 AAATCCTAAG
*
2129563 CCTTAAATCATTAACCATAAA
1 CCTTAAATTATTAACCATAAA
*
2129584 CCTTAAATTA-TATACCATCAA
1 CCTTAAATTATTA-ACCATAAA
*
2129605 CATTAAATTAT
1 CCTTAAATTAT
2129616 GAAATGTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (21 bp):
CCTTAAATTATTAACCATAAA
Found at i:2129855 original size:25 final size:25
Alignment explanation
Indices: 2129825--2129873 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2129815 TAACCCTAAA
*
2129825 TTCATAAATATTAAATCTATAAATT
1 TTCATAAATACTAAATCTATAAATT
*
2129850 TTCATAAATCCTAAATCTATAAAT
1 TTCATAAATACTAAATCTATAAAT
2129874 ACATTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (25 bp):
TTCATAAATACTAAATCTATAAATT
Found at i:2151272 original size:3 final size:3
Alignment explanation
Indices: 2151264--2151304 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2151254 GGTACAGTAG
2151264 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
2151305 CTCACCAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2157139 original size:2 final size:2
Alignment explanation
Indices: 2157134--2157164 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2157124 TTTTTAGTGT
2157134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2157165 TTCTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2157230 original size:18 final size:19
Alignment explanation
Indices: 2157209--2157264 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
2157199 TTTGATTTTT
2157209 TTATTATTAT-TATTTTAC
1 TTATTATTATATATTTTAC
*
2157227 TTA-TATATATATGTTTTTAC
1 TTATTAT-TATAT-ATTTTAC
2157247 TT-TT-TTATATATTTTAC
1 TTATTATTATATATTTTAC
2157264 T
1 T
2157265 CATTTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.31
18 11 0.34
19 2 0.06
20 9 0.28
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (19 bp):
TTATTATTATATATTTTAC
Found at i:2157246 original size:20 final size:20
Alignment explanation
Indices: 2157221--2157258 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2157211 ATTATTATTA
2157221 TTTTACTTATATATATATGT
1 TTTTACTTATATATATATGT
* *
2157241 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
2157259 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTACTTATATATATATGT
Found at i:2158782 original size:19 final size:19
Alignment explanation
Indices: 2158758--2158798 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2158748 AAGACGTGGT
2158758 GCTTCCCAAACACTTCTGG
1 GCTTCCCAAACACTTCTGG
2158777 GCTTCCCAAACACTTCTGG
1 GCTTCCCAAACACTTCTGG
2158796 GCT
1 GCT
2158799 GAGGCTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.27
Consensus pattern (19 bp):
GCTTCCCAAACACTTCTGG
Found at i:2162221 original size:21 final size:22
Alignment explanation
Indices: 2162195--2162257 Score: 92
Period size: 23 Copynumber: 2.9 Consensus size: 22
2162185 ATATATGTTA
*
2162195 TATGTGGTCCTTCGGGACA-TC
1 TATGTGGTCATTCGGGACATTC
2162216 TATGTGGTCATTCGGGACATTTC
1 TATGTGGTCATTCGGGACA-TTC
*
2162239 TACGTGGTCATTCGGGACA
1 TATGTGGTCATTCGGGACA
2162258 AATTCTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 18 0.47
23 20 0.53
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (22 bp):
TATGTGGTCATTCGGGACATTC
Found at i:2168392 original size:24 final size:24
Alignment explanation
Indices: 2168360--2168407 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2168350 GTGATCATGG
*
2168360 TACTGAATTTGAAAATCTTGGATT
1 TACTAAATTTGAAAATCTTGGATT
2168384 TACTAAATTTGAAAATCTTGGATT
1 TACTAAATTTGAAAATCTTGGATT
2168408 GATTGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (24 bp):
TACTAAATTTGAAAATCTTGGATT
Found at i:2170980 original size:21 final size:21
Alignment explanation
Indices: 2170913--2171077 Score: 131
Period size: 23 Copynumber: 7.7 Consensus size: 21
2170903 TTGTGCACTA
*
2170913 TGCATCGATACACTA-GACA-G
1 TGCATCGATACACCATGA-ATG
* * *
2170933 TGCATCGATGCATCCCTTGAATA
1 TGCATCGATACA--CCATGAATG
2170956 TGCATCGATACACCATGAATG
1 TGCATCGATACACCATGAATG
2170977 TGCATCGATACACTCCATGAATG
1 TGCATCGATACA--CCATGAATG
*
2171000 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCATGAATG
*
2171021 TGCA-CTGATACAGTCCTTGAATG
1 TGCATC-GATACA--CCATGAATG
* * * * *
2171044 TGCATCAATGCACAATG-CTA
1 TGCATCGATACACCATGAATG
2171064 TGCATCGATACACC
1 TGCATCGATACACC
2171078 CATCGGGTTT
Statistics
Matches: 116, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
20 24 0.21
21 40 0.34
22 2 0.02
23 49 0.42
24 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCATGAATG
Found at i:2170998 original size:44 final size:44
Alignment explanation
Indices: 2170911--2171080 Score: 154
Period size: 44 Copynumber: 3.9 Consensus size: 44
2170901 TTTTGTGCAC
* * *
2170911 TATGCATCGATACACTA-GACA-GTGCATCGATGCA-TCCCTTGAA
1 TATGCATCGATACACCATGA-ATGTGCATCGATACACT-CCATGAA
2170954 TATGCATCGATACACCATGAATGTGCATCGATACACTCCATGAA
1 TATGCATCGATACACCATGAATGTGCATCGATACACTCCATGAA
* * * *
2170998 TGTGCATCGATACACCATGAAGGTGCA-CTGATACAGTCCTTGAA
1 TATGCATCGATACACCATGAATGTGCATC-GATACACTCCATGAA
* * * * * *
2171042 TGTGCATCAATGCACAATG-CTATGCATCGATACAC-CCAT
1 TATGCATCGATACACCATGAATGTGCATCGATACACTCCAT
2171081 CGGGTTTTTG
Statistics
Matches: 107, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
42 3 0.03
43 28 0.26
44 75 0.70
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
TATGCATCGATACACCATGAATGTGCATCGATACACTCCATGAA
Done.