Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 25
Found at i:2550318 original size:11 final size:11
Alignment explanation
Indices: 2550298--2550349 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
2550288 TATACATACA
2550298 TTTT-TATATT
1 TTTTATATATT
2550308 TTTTATATATT
1 TTTTATATATT
2550319 TTTTAT-TATTT
1 TTTTATATA-TT
2550330 TATTTATACTATT
1 T-TTTATA-TATT
2550343 TATTTAT
1 T-TTTAT
2550350 TTTCATTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.16
11 15 0.41
12 5 0.14
13 9 0.24
14 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTATATATT
Found at i:2550328 original size:21 final size:24
Alignment explanation
Indices: 2550277--2550350 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 24
2550267 CTATTTAGTA
* **
2550277 TTTTATTATATTATACATAC-A-T
1 TTTTATTATTTTATTTATACTATT
2550299 TTTTA-TA-TTT-TTTATA-TATT
1 TTTTATTATTTTATTTATACTATT
2550319 TTTTATTATTTTATTTATACTATT
1 TTTTATTATTTTATTTATACTATT
2550343 TATTTATT
1 T-TTTATT
2550351 TTCATTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
19 5 0.12
20 8 0.19
21 4 0.10
22 8 0.19
23 6 0.14
24 5 0.12
25 6 0.14
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTATTATTTTATTTATACTATT
Found at i:2550490 original size:21 final size:19
Alignment explanation
Indices: 2550449--2550504 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
2550439 TTTTATATTC
*
2550449 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATCCA
*
2550468 ATTTCATTTTTTTTTCATCCA
1 ATTT-ATTTTATTTT-ATCCA
2550489 A-TTATTTTATGTTTAT
1 ATTTATTTTAT-TTTAT
2550505 TATTATTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATCCA
Found at i:2554775 original size:8 final size:8
Alignment explanation
Indices: 2554770--2554831 Score: 63
Period size: 8 Copynumber: 7.5 Consensus size: 8
2554760 GGGCAAAAAC
2554770 AAAAAAGA
1 AAAAAAGA
2554778 AAAAAAGA
1 AAAAAAGA
2554786 AAAAAAGA
1 AAAAAAGA
*
2554794 AGAAAACAAA
1 A-AAAA-AGA
2554804 AAAAAAGA
1 AAAAAAGA
*
2554812 ACAAAAA-T
1 A-AAAAAGA
*
2554820 CAAAAAGA
1 AAAAAAGA
2554828 AAAA
1 AAAA
2554832 GGGACAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 5 0.11
8 23 0.52
9 13 0.30
10 3 0.07
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2554782 original size:15 final size:15
Alignment explanation
Indices: 2554764--2554818 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
2554754 CAAAAAGGGC
2554764 AAAAACAAAAAAGAA
1 AAAAACAAAAAAGAA
*
2554779 AAAAAGAAAAAAAGAA
1 AAAAA-CAAAAAAGAA
*
2554795 GAAAAC-AAAAA-AA
1 AAAAACAAAAAAGAA
*
2554808 AAGAACAAAAA
1 AAAAACAAAAA
2554819 TCAAAAAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 6 0.18
14 9 0.27
15 5 0.15
16 13 0.39
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAAAGAA
Found at i:2554783 original size:16 final size:17
Alignment explanation
Indices: 2554764--2554825 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
2554754 CAAAAAGGGC
2554764 AAAAACAAAAAAGAA-A
1 AAAAACAAAAAAGAACA
*
2554780 AAAAGA-AAAAAAGAAGA
1 AAAA-ACAAAAAAGAACA
*
2554797 AAACAAAAAAAAAGAACA
1 AAA-AACAAAAAAGAACA
*
2554815 AAAATCAAAAA
1 AAAAACAAAAA
2554826 GAAAAAGGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 13 0.33
17 12 0.31
18 14 0.36
ACGTcount: A:0.84, C:0.06, G:0.08, T:0.02
Consensus pattern (17 bp):
AAAAACAAAAAAGAACA
Found at i:2556558 original size:106 final size:106
Alignment explanation
Indices: 2556428--2557444 Score: 1611
Period size: 106 Copynumber: 9.6 Consensus size: 106
2556418 ATATCGTGCC
* * * * **
2556428 ACTCAAGACAACACAAGTTTAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2556493 AAATTAAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
2556534 ACTCCAGACAACGCAAGTTCAACTTCATGAGGAAGGGACCGCTAGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
2556599 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2556640 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2556705 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2556746 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
2556811 AATTTCAGAGCCAATTTTAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2556852 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2556917 AATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
2556958 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2557023 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
2557064 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCTCTGGGTGTCAACATACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
2557129 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
2557170 ACTCCAGACAACTCAAGTTAAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2557235 AATTTCGGAGCCAATTTCAACTTCACAACGAAGTATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2557276 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
2557341 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
2557382 ACTCCAAACAACGCAAGTTCAATTTCACAACGAAGGGACCGATGGTTGTCAACAAACAACTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
2557445 ACAGCTAAGG
Statistics
Matches: 841, Mismatches: 70, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 841 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2557494 original size:186 final size:186
Alignment explanation
Indices: 2557252--2557623 Score: 609
Period size: 186 Copynumber: 2.0 Consensus size: 186
2557242 GAGCCAATTT
* *
2557252 CAACTTCACAACGAAGTATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
2557317 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
* *
2557382 ACTCCAAACAACGCAAGTTCAATTTCACAACGAAGGGACCGATGGTTGTCAACAAA
131 ACTCCAAACAACACAAGTTCAACTTCACAACGAAGGGACCGATGGTTGTCAACAAA
* * *
2557438 CAACTTCACAGCTAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
2557503 CTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
* * * *
2557568 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA
131 ACTCCAAACAACACAAGTTCAACTTCACAACGAAGGGACCGATGGTTGTCAACAAA
2557624 TAATTTCCTG
Statistics
Matches: 171, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
186 171 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (186 bp):
CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
ACTCCAAACAACACAAGTTCAACTTCACAACGAAGGGACCGATGGTTGTCAACAAA
Found at i:2557495 original size:80 final size:80
Alignment explanation
Indices: 2557358--2557520 Score: 263
Period size: 80 Copynumber: 2.0 Consensus size: 80
2557348 GAGCCAATTT
*
2557358 CAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAATTTCACAACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCG
2557423 ATGGTTGTCAACAAA
66 ATGGTTGTCAACAAA
* * * * *
2557438 CAACTTCACAGCTAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCG
*
2557503 CTGGTTGTCAACAAA
66 ATGGTTGTCAACAAA
2557518 CAA
1 CAA
2557521 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (80 bp):
CAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCG
ATGGTTGTCAACAAA
Found at i:2557567 original size:292 final size:292
Alignment explanation
Indices: 2557146--2557677 Score: 877
Period size: 292 Copynumber: 1.8 Consensus size: 292
2557136 GAGCCAATTT
* *
2557146 CAACTTCACAGCGAAAGATATTGGACTCCAGACAACTCAAGTTAAACTTCACGATGAAGGGACCG
1 CAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTAAACTTCACGACGAAGGGACCG
* *
2557211 CTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGTATATTGG
66 CTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
* * *
2557276 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT-CT
131 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCT
*
2557340 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAAT
196 -AATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAAT
2557405 TTCACAACGAAGGGACCGATGGTTGTCAACAAA
260 TTCACAACGAAGGGACCGATGGTTGTCAACAAA
* * * *
2557438 CAACTTCACAGCTAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTAAACTTCACGACGAAGGGACCG
2557503 CTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 CTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
* * * *
2557568 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCT
131 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCT
* * *
2557633 GATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
196 AATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
2557678 GGAACAATGC
Statistics
Matches: 220, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
292 218 0.99
293 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (292 bp):
CAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTAAACTTCACGACGAAGGGACCG
CTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCT
AATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAATT
TCACAACGAAGGGACCGATGGTTGTCAACAAA
Found at i:2557623 original size:106 final size:106
Alignment explanation
Indices: 2557438--2557678 Score: 365
Period size: 106 Copynumber: 2.3 Consensus size: 106
2557428 TGTCAACAAA
* * * *
2557438 CAACTTCACAGCTAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCG
* *
2557503 CTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCAATTT
*
2557544 CAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGG
1 CAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCG
* **
2557609 CTGGTTGTCAACAAATAATTTCCTGATTCCAGAGCCAATTT
66 CTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCAATTT
* **
2557650 CAACTTCACGACGGAGGATATTGGACTCG
1 CAACTTCACAACAAAGGATATTGGACTCG
2557679 GAACAATGCT
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 122 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (106 bp):
CAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCG
CTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCAATTT
Found at i:2558483 original size:37 final size:37
Alignment explanation
Indices: 2558426--2558530 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
2558416 CATTTTCGTC
*
2558426 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2558463 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
2558500 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2558531 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:2558973 original size:23 final size:24
Alignment explanation
Indices: 2558926--2558973 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2558916 TAACCCTTAT
2558926 TATTTATATGTATATATTTAATTA
1 TATTTATATGTATATATTTAATTA
* * *
2558950 TATTT-TATTTATTTATTTATTTA
1 TATTTATATGTATATATTTAATTA
2558973 T
1 T
2558974 TATAATTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATTTATATGTATATATTTAATTA
Found at i:2559008 original size:5 final size:5
Alignment explanation
Indices: 2559000--2559050 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
2558990 TTTCTTTGCG
* *
2559000 TTATA TTATA TTATT TTCTTA TTATA -TATA TGTATA TTATA TTATTA
1 TTATA TTATA TTATA TT-ATA TTATA TTATA T-TATA TTATA TTA-TA
2559047 TTAT
1 TTAT
2559051 TTTTATCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.11
5 21 0.55
6 13 0.34
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:2559047 original size:26 final size:25
Alignment explanation
Indices: 2559001--2559050 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
2558991 TTCTTTGCGT
* *
2559001 TATATTATATTATTTTCTTATTATA
1 TATATTATATTATATTATTATTATA
2559026 TATATGTATATTATATTATTATTAT
1 TATAT-TATATTATATTATTATTAT
2559051 TTTTATCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TATATTATATTATATTATTATTATA
Found at i:2559196 original size:30 final size:28
Alignment explanation
Indices: 2559162--2559289 Score: 73
Period size: 33 Copynumber: 4.2 Consensus size: 28
2559152 CTATGATTAC
2559162 TATTTTTTTAGTTAATATTATATGTATATT
1 TATTTTTTTA-TTAATATTATAT-TATATT
*
2559192 TATTTTTCATTTATTTATTATTATTATTACTATT
1 TA-TTTT--TTTA-TTAATATTA-TATTA-TATT
* *
2559226 TATTATTTTATT-ATATTATACATATATT
1 TATTTTTTTATTAATATTATA-TTATATT
*
2559254 T-TTATATTTTATATATATATTTTTATTAT-TT
1 TATT-T-TTTTAT-TA-ATA-TTATATTATATT
2559285 TATTT
1 TATTT
2559290 ATACTATTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
27 2 0.03
28 7 0.09
29 13 0.17
30 5 0.06
31 12 0.16
32 8 0.10
33 21 0.27
34 9 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (28 bp):
TATTTTTTTATTAATATTATATTATATT
Found at i:2559209 original size:27 final size:25
Alignment explanation
Indices: 2559179--2559317 Score: 77
Period size: 27 Copynumber: 5.1 Consensus size: 25
2559169 TTAGTTAATA
2559179 TTATATGTATATTTATTTTTCATTTAT
1 TTATAT-TATATTTATTTTT-ATTTAT
2559206 TTATTATTATTATTACTATTTATTATTT-T
1 TTA-TATTA-TATT--TATTT-TTATTTAT
* *
2559235 ATTATATTATACATATATTTTTATAT-T
1 -TTATATTAT--ATTTATTTTTATTTAT
*
2559262 TTATATATATATTT-TTATTATTTTAT
1 TTATAT-TATATTTATTTTTA-TTTAT
* *
2559288 TTATACTATTTATTTATTTTCATTATAT
1 TTATA-T-TATATTTATTTTTATT-TAT
2559316 TT
1 TT
2559318 TTAGTTTCTT
Statistics
Matches: 90, Mismatches: 8, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
24 5 0.06
25 5 0.06
26 12 0.13
27 24 0.27
28 22 0.24
29 6 0.07
30 14 0.16
31 2 0.02
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (25 bp):
TTATATTATATTTATTTTTATTTAT
Found at i:2559216 original size:21 final size:20
Alignment explanation
Indices: 2559191--2559320 Score: 79
Period size: 21 Copynumber: 6.0 Consensus size: 20
2559181 ATATGTATAT
*
2559191 TTATTTTTCATTTATTTATTA
1 TTATTTTACATTTATTT-TTA
2559212 TTATTATTACTATTTATTATTTTA
1 TTATT-TTAC-ATTTA-T-TTTTA
*
2559236 TTATATTATACATATATTTTTA
1 TTAT-TT-TACATTTATTTTTA
*
2559258 -TATTTTATATATATATTTTTA
1 TTATTTTACAT-T-TATTTTTA
2559279 TTATTTT--ATTTATACTATTTA
1 TTATTTTACATTTAT--T-TTTA
2559300 TTTATTTT-CATTATATTTTTA
1 -TTATTTTACATT-TATTTTTA
2559321 GTTTCTTTGC
Statistics
Matches: 90, Mismatches: 4, Indels: 30
0.73 0.03 0.24
Matches are distributed among these distances:
18 3 0.03
19 5 0.06
20 5 0.06
21 24 0.27
22 22 0.24
23 9 0.10
24 16 0.18
25 6 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTACATTTATTTTTA
Found at i:2559225 original size:19 final size:17
Alignment explanation
Indices: 2559186--2559317 Score: 78
Period size: 19 Copynumber: 7.4 Consensus size: 17
2559176 ATATTATATG
*
2559186 TATATTTATT-TTTCAT
1 TATATTTATTATTTTAT
2559202 T-TATTTATTATTATTAT
1 TATATTTATTATT-TTAT
2559219 TACTATTTATTATTTTAT
1 TA-TATTTATTATTTTAT
*
2559237 TATATTATACATATATTT-T
1 TATATT-TA-TTAT-TTTAT
*
2559256 TATA-TT-TTA-TATAT
1 TATATTTATTATTTTAT
*
2559270 ATATTTTTATTATTTTATTT
1 -TATATTTATTATTTTA--T
2559290 ATACTATTTATTTATTTTCAT
1 -TA-TATTTA-TTATTTT-AT
2559311 TATATTT
1 TATATTT
2559318 TTAGTTTCTT
Statistics
Matches: 92, Mismatches: 7, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
13 2 0.02
14 1 0.01
15 13 0.14
16 5 0.05
17 12 0.13
18 12 0.13
19 24 0.26
20 9 0.10
21 6 0.07
22 7 0.08
23 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTATTATTTTAT
Found at i:2559228 original size:13 final size:12
Alignment explanation
Indices: 2559212--2559305 Score: 57
Period size: 13 Copynumber: 7.4 Consensus size: 12
2559202 TTATTTATTA
2559212 TTATTATTACTAT
1 TTATTATTA-TAT
*
2559225 TTATTATTTTAT
1 TTATTATTATAT
*
2559237 TATATTA-TACAT
1 T-TATTATTATAT
* *
2559249 ATATTTTTATATT
1 TTATTATTATA-T
*
2559262 TTATATATATATTT
1 TTAT-TAT-TATAT
*
2559276 TTATTATTTTAT
1 TTATTATTATAT
2559288 TTATACTATT-TAT
1 TTAT--TATTATAT
2559301 TTATT
1 TTATT
2559306 TTCATTATAT
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
11 5 0.08
12 17 0.27
13 27 0.43
14 11 0.17
15 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:2559279 original size:43 final size:42
Alignment explanation
Indices: 2559231--2559320 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
2559221 CTATTTATTA
*
2559231 TTTTATTATATTATACATA-TATTT-TTATATTTTATATATATAT
1 TTTTATTATATTATACATACTATTTATT-TATTTT-CAT-TATAT
* **
2559274 TTTTATTATTTTATTTATACTATTTATTTATTTTCATTATAT
1 TTTTATTATATTATACATACTATTTATTTATTTTCATTATAT
2559316 TTTTA
1 TTTTA
2559321 GTTTCTTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 10 0.24
43 18 0.44
44 11 0.27
45 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (42 bp):
TTTTATTATATTATACATACTATTTATTTATTTTCATTATAT
Found at i:2559430 original size:20 final size:19
Alignment explanation
Indices: 2559403--2559459 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2559393 TTTTATCTTC
2559403 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
2559422 ATTTCATTTTTTTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
2559443 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
2559460 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:2565393 original size:17 final size:18
Alignment explanation
Indices: 2565373--2565418 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2565363 CTTTATGTTA
2565373 TAATTTTATAAATA-TAT
1 TAATTTTATAAATATTAT
*
2565390 TAATTTGATAAATATTAT
1 TAATTTTATAAATATTAT
* *
2565408 TTATATTATAA
1 TAATTTTATAA
2565419 TAATAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTTTATAAATATTAT
Found at i:2565453 original size:25 final size:25
Alignment explanation
Indices: 2565384--2565455 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
2565374 AATTTTATAA
* * *
2565384 ATATATTAATTTGATAAATATTATTT
1 ATATAATAATTTTAT-AATATTACTT
* ** *
2565410 ATATTATAATAATAAAATATTACTT
1 ATATAATAATTTTATAATATTACTT
2565435 ATATAATAATTTTATAATATT
1 ATATAATAATTTTATAATATT
2565456 TATAAATATG
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
25 26 0.74
26 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
ATATAATAATTTTATAATATTACTT
Found at i:2570660 original size:2 final size:2
Alignment explanation
Indices: 2570653--2570724 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
2570643 GATGGTTGTT
2570653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2570695 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2570725 AGAATTTGTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2573810 original size:24 final size:23
Alignment explanation
Indices: 2573761--2573815 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
2573751 AGGTTCAAAT
*
2573761 TCGAGTTCGAGTTCGAGCTTGAA
1 TCGAGCTCGAGTTCGAGCTTGAA
2573784 TCGAGCTCGAGTCTCGAGCTTCG-A
1 TCGAGCTCGAGT-TCGAGCTT-GAA
2573808 TCGAGCTC
1 TCGAGCTC
2573816 CTGAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 11 0.38
24 17 0.59
25 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.27
Consensus pattern (23 bp):
TCGAGCTCGAGTTCGAGCTTGAA
Found at i:2576467 original size:23 final size:23
Alignment explanation
Indices: 2576416--2576469 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2576406 TGCCTTTATA
*
2576416 GCATGTTTATCTCTGTATTTGTG
1 GCATGTTTATCTCTGTATCTGTG
** *
2576439 ATATGTTTATCTCTGTGTCTGTG
1 GCATGTTTATCTCTGTATCTGTG
2576462 GCATGTTT
1 GCATGTTT
2576470 TTCATTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.22, T:0.52
Consensus pattern (23 bp):
GCATGTTTATCTCTGTATCTGTG
Found at i:2577534 original size:138 final size:138
Alignment explanation
Indices: 2577301--2577556 Score: 350
Period size: 138 Copynumber: 1.9 Consensus size: 138
2577291 TACCGATACA
* * * * * *
2577301 CTTTACTAGAGTATTAGTACACATATTTGAAATAAATAATAGTGTACAATTATTGTACCAGTACA
1 CTTTACTAAAGTATCAGTACACATATATGAAATAAATAACAATGTACAATTATTATACCAGTACA
* * * * *
2577366 CAACCAATACTGATACTCGAATATCTGCGTACCGATACACATGAGCCAAGGTATCGGTGGGACAT
66 CAACCAATACCGATACTCGAATACCCGCGTACCAATACACATAAGCCAAGGTATCGGTGGGACAT
2577431 GTGGGATT
131 GTGGGATT
* *
2577439 CTTTACTAAATTATCAGTACACATATATGAAATAAATAACAATGTACAATTATTATACCGGTACA
1 CTTTACTAAAGTATCAGTACACATATATGAAATAAATAACAATGTACAATTATTATACCAGTACA
* * * * *
2577504 CAACCAGTACCGATACTCGTATGCCCGCGTACCAATACATATAAGCCATGGTA
66 CAACCAATACCGATACTCGAATACCCGCGTACCAATACACATAAGCCAAGGTA
2577557 CCGATACGAC
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
138 100 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (138 bp):
CTTTACTAAAGTATCAGTACACATATATGAAATAAATAACAATGTACAATTATTATACCAGTACA
CAACCAATACCGATACTCGAATACCCGCGTACCAATACACATAAGCCAAGGTATCGGTGGGACAT
GTGGGATT
Found at i:2585295 original size:21 final size:21
Alignment explanation
Indices: 2585271--2585327 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
2585261 TATTTCAATT
*
2585271 AATTAATATATATCGAACATA
1 AATTAATATATATCAAACATA
* *
2585292 AATTTATAAATATCAAACATA
1 AATTAATATATATCAAACATA
2585313 ATATTATATATATAT
1 A-ATTA-ATATATAT
2585328 ATATATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 19 0.66
22 3 0.10
23 7 0.24
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTAATATATATCAAACATA
Found at i:2585324 original size:2 final size:2
Alignment explanation
Indices: 2585313--2585349 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2585303 ATCAAACATA
2585313 AT AT -T 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
2585350 TAAATCAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2591968 original size:270 final size:270
Alignment explanation
Indices: 2591504--2592043 Score: 1080
Period size: 270 Copynumber: 2.0 Consensus size: 270
2591494 GATTATGGAA
2591504 TCTTAGCTTCTGACCACAACGTACATAAAACTACTAAAATATTCAGCATCAATGTAGTTTTATTT
1 TCTTAGCTTCTGACCACAACGTACATAAAACTACTAAAATATTCAGCATCAATGTAGTTTTATTT
2591569 GGTTAAAAAGATTACGAAAATATATTTTTATATTATAATGACCCATTCTATTTATAATTAAACAA
66 GGTTAAAAAGATTACGAAAATATATTTTTATATTATAATGACCCATTCTATTTATAATTAAACAA
2591634 ATGTATTTGTATTTATAATTTTTACATATCGTATTCAACTATTGATCCATTATAATTTAGTGATT
131 ATGTATTTGTATTTATAATTTTTACATATCGTATTCAACTATTGATCCATTATAATTTAGTGATT
2591699 TCTAAAATAACTTATCAACTCTATTTGAAAAGAATAAAAATAATCTAGTAATGAACATGGTAATT
196 TCTAAAATAACTTATCAACTCTATTTGAAAAGAATAAAAATAATCTAGTAATGAACATGGTAATT
2591764 CATTATACAT
261 CATTATACAT
2591774 TCTTAGCTTCTGACCACAACGTACATAAAACTACTAAAATATTCAGCATCAATGTAGTTTTATTT
1 TCTTAGCTTCTGACCACAACGTACATAAAACTACTAAAATATTCAGCATCAATGTAGTTTTATTT
2591839 GGTTAAAAAGATTACGAAAATATATTTTTATATTATAATGACCCATTCTATTTATAATTAAACAA
66 GGTTAAAAAGATTACGAAAATATATTTTTATATTATAATGACCCATTCTATTTATAATTAAACAA
2591904 ATGTATTTGTATTTATAATTTTTACATATCGTATTCAACTATTGATCCATTATAATTTAGTGATT
131 ATGTATTTGTATTTATAATTTTTACATATCGTATTCAACTATTGATCCATTATAATTTAGTGATT
2591969 TCTAAAATAACTTATCAACTCTATTTGAAAAGAATAAAAATAATCTAGTAATGAACATGGTAATT
196 TCTAAAATAACTTATCAACTCTATTTGAAAAGAATAAAAATAATCTAGTAATGAACATGGTAATT
2592034 CATTATACAT
261 CATTATACAT
2592044 GTACTGCTTT
Statistics
Matches: 270, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
270 270 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (270 bp):
TCTTAGCTTCTGACCACAACGTACATAAAACTACTAAAATATTCAGCATCAATGTAGTTTTATTT
GGTTAAAAAGATTACGAAAATATATTTTTATATTATAATGACCCATTCTATTTATAATTAAACAA
ATGTATTTGTATTTATAATTTTTACATATCGTATTCAACTATTGATCCATTATAATTTAGTGATT
TCTAAAATAACTTATCAACTCTATTTGAAAAGAATAAAAATAATCTAGTAATGAACATGGTAATT
CATTATACAT
Found at i:2593402 original size:17 final size:18
Alignment explanation
Indices: 2593363--2593408 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2593353 ATTTTATGAG
2593363 GTAAAAAATAAAATTATT
1 GTAAAAAATAAAATTATT
*
2593381 GTAAAAAGTAAAATTATT
1 GTAAAAAATAAAATTATT
2593399 -TAAAATAATA
1 GTAAAA-AATA
2593409 TCTAAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
GTAAAAAATAAAATTATT
Found at i:2593747 original size:19 final size:20
Alignment explanation
Indices: 2593706--2593755 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2593696 CAACATTCTA
*
2593706 ATAATCTTAT-TTCTAGATG
1 ATAATCTTATATTCTAGAAG
2593725 -TAATCTTATATTCTA-AAG
1 ATAATCTTATATTCTAGAAG
*
2593743 ATAATATTATATT
1 ATAATCTTATATT
2593756 ATGTGAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (20 bp):
ATAATCTTATATTCTAGAAG
Found at i:2595332 original size:34 final size:35
Alignment explanation
Indices: 2595278--2595384 Score: 128
Period size: 34 Copynumber: 3.1 Consensus size: 35
2595268 ACTTTACTTC
* *
2595278 AAAAAAATTTCAATGGTATATCACTTCATTTCAAA
1 AAAAAAATTTCAGTGATATATCACTTCATTTCAAA
*
2595313 AAAAAAATTT-AGTGATATATCACTTTATTTC-AA
1 AAAAAAATTTCAGTGATATATCACTTCATTTCAAA
** * * *
2595346 AAAAACTTTTCAGTGATATACCACTACATTTCAGA
1 AAAAAAATTTCAGTGATATATCACTTCATTTCAAA
2595381 AAAA
1 AAAA
2595385 CATCCTTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
33 10 0.16
34 36 0.59
35 15 0.25
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAAAAATTTCAGTGATATATCACTTCATTTCAAA
Found at i:2596335 original size:50 final size:50
Alignment explanation
Indices: 2596260--2596358 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
2596250 TATGTTAAGT
*
2596260 TTGTTGTTTTTATCTTCTGAATGTAATGTTTATGGTTCATTGTTTTTATC
1 TTGTTATTTTTATCTTCTGAATGTAATGTTTATGGTTCATTGTTTTTATC
*
2596310 TTGTTATTTTTATCTTCTTAATGTAATGTTTATGGTTCATTGTTTTTAT
1 TTGTTATTTTTATCTTCTGAATGTAATGTTTATGGTTCATTGTTTTTAT
2596359 ATCCTAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (50 bp):
TTGTTATTTTTATCTTCTGAATGTAATGTTTATGGTTCATTGTTTTTATC
Found at i:2597461 original size:5 final size:5
Alignment explanation
Indices: 2597451--2597477 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2597441 AAATTATATA
2597451 TCGGG TCGGG TCGGG TCGGG TCGGG TC
1 TCGGG TCGGG TCGGG TCGGG TCGGG TC
2597478 AGATTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.56, T:0.22
Consensus pattern (5 bp):
TCGGG
Found at i:2603177 original size:15 final size:15
Alignment explanation
Indices: 2603157--2603192 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2603147 ATATTTAGCT
*
2603157 GGGCGGGTGGATGCG
1 GGGCGGGCGGATGCG
2603172 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
2603187 AGGCGG
1 GGGCGG
2603193 ATAATGTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.17, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:2617275 original size:33 final size:31
Alignment explanation
Indices: 2617201--2617277 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
2617191 AAAGCATTAT
** * *
2617201 TAAAAATATTATTATTATTTTAATATTTTTG
1 TAAAAATATTATTAAAATATTAATATTTTTA
*
2617232 TAAAAA-ATTATTAGAAATATTATTATTTTTA
1 TAAAAATATTATTA-AAATATTAATATTTTTA
2617263 TCAAAAATATTATTA
1 T-AAAAATATTATTA
2617278 TTGGGTGCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 7 0.18
31 19 0.50
32 5 0.13
33 7 0.18
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (31 bp):
TAAAAATATTATTAAAATATTAATATTTTTA
Found at i:2617345 original size:12 final size:11
Alignment explanation
Indices: 2617321--2617345 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2617311 TAAAGCGTTA
2617321 TTTAAAATATT
1 TTTAAAATATT
2617332 TTTAAAATATT
1 TTTAAAATATT
2617343 TTT
1 TTT
2617346 TTATCGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTAAAATATT
Found at i:2617433 original size:41 final size:41
Alignment explanation
Indices: 2617378--2617458 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
2617368 ATACTTTATT
* * *
2617378 AAAAATGTTAAAAAATATTAATATTTTAGATAAT-TTTTTTA
1 AAAAATATTAAAAAATAATAACATTTT-GATAATATTTTTTA
*
2617419 AAAAATATTAAAAAATAATAACATTTTTATAATATTTTTT
1 AAAAATATTAAAAAATAATAACATTTTGATAATATTTTTT
2617459 CTTAATCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.14
41 30 0.86
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (41 bp):
AAAAATATTAAAAAATAATAACATTTTGATAATATTTTTTA
Found at i:2618587 original size:17 final size:17
Alignment explanation
Indices: 2618565--2618604 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
2618555 ATGTCTTTCG
2618565 ACCCATCCATAACTCCA
1 ACCCATCCATAACTCCA
2618582 ACCCATCCATAACTCCA
1 ACCCATCCATAACTCCA
2618599 ACCCAT
1 ACCCAT
2618605 GGTTTACACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.17
Consensus pattern (17 bp):
ACCCATCCATAACTCCA
Found at i:2618935 original size:23 final size:23
Alignment explanation
Indices: 2618909--2618978 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 23
2618899 GGTAACATTA
*
2618909 TTAAATTATGTTATTTTAATTTT
1 TTAAATTATTTTATTTTAATTTT
*
2618932 TT-AA-TATTTTATTATTATTTTT
1 TTAAATTATTTTATT-TTAATTTT
2618954 TTCAATATTATTTTAAATTTTAATT
1 TT-AA-ATTATTTT--ATTTTAATT
2618979 CATAGAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
21 8 0.22
22 11 0.30
23 2 0.05
24 1 0.03
25 1 0.03
26 6 0.16
27 5 0.14
28 3 0.08
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (23 bp):
TTAAATTATTTTATTTTAATTTT
Found at i:2618943 original size:21 final size:20
Alignment explanation
Indices: 2618919--2618974 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
2618909 TTAAATTATG
2618919 TTATTTTAATTTTTT-AATA
1 TTATTTTAATTTTTTCAATA
*
2618938 TTTTATTATTATTTTTTTCAATA
1 --TTATT-TTAATTTTTTCAATA
2618961 TTATTTTAAATTTT
1 TTATTTT-AATTTT
2618975 AATTCATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 15 0.50
22 9 0.30
23 4 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTAATTTTTTCAATA
Found at i:2626095 original size:21 final size:21
Alignment explanation
Indices: 2626071--2626110 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2626061 ATTTTTTACA
2626071 ATTTAATGTTTAGGATTTATT
1 ATTTAATGTTTAGGATTTATT
** *
2626092 ATTTTTTGTTTAGGGTTTA
1 ATTTAATGTTTAGGATTTA
2626111 GTTCTTGTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (21 bp):
ATTTAATGTTTAGGATTTATT
Found at i:2627328 original size:20 final size:20
Alignment explanation
Indices: 2627277--2627406 Score: 91
Period size: 20 Copynumber: 6.3 Consensus size: 20
2627267 ACTTCGACTA
*
2627277 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* *
2627298 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACAAAT
* * * *
2627318 TTGCATTGCGATAGTCCAAGT
1 TCGCATTGCGAT-TTACAAAT
* * *
2627339 TCGCGTTGCGATAGT-CGAAGT
1 TCGCATTGCGAT-TTAC-AAAT
* * *
2627360 TCACGTTGCGATTTACATAT
1 TCGCATTGCGATTTACAAAT
*
2627380 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACAAAT
2627400 TCGCATT
1 TCGCATT
2627407 TACCCAAAAT
Statistics
Matches: 89, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
20 46 0.52
21 43 0.48
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:2628463 original size:81 final size:81
Alignment explanation
Indices: 2628365--2628616 Score: 375
Period size: 81 Copynumber: 3.1 Consensus size: 81
2628355 AAATATGTAA
* *
2628365 ATCGCAACGAATTTGGAAAATCGTAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGC
2628430 AACGTGAACTTGGACT
66 AACGTGAACTTGGACT
*
2628446 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCAC
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGC
*
2628511 AACGTGAACTTGGATT
66 AACGTGAACTTGGACT
* * * * *
2628527 ATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCGTAA--CGAATTTGGAAAATCG
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATAT-GTAAATCG
*
2628590 CAACGCGAACTCT-GACT
65 CAACGTGAACT-TGGACT
2628607 ATCGCAACGA
1 ATCGCAACGA
2628617 GAACTTGGAC
Statistics
Matches: 157, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
79 6 0.04
80 29 0.18
81 122 0.78
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (81 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGC
AACGTGAACTTGGACT
Found at i:2628479 original size:40 final size:40
Alignment explanation
Indices: 2628365--2628616 Score: 312
Period size: 40 Copynumber: 6.2 Consensus size: 40
2628355 AAATATGTAA
* *
2628365 ATCGCAACGAATTTGGAAAATCGTAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACT
* * * *
2628405 ATCGCAATGCGAATAT-GTAAATCGTAACGTGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTGGACT
*
2628446 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACT
* * * * *
2628486 ATCGCAATGCGAATAT-GTAAATCACAACGTGAACTTGGATT
1 ATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTGGACT
*
2628527 ATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACT
*
2628567 ATCGTAACGAATTTGGAAAATCGCAACGCGAACTCT-GACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACT-TGGACT
2628607 ATCGCAACGA
1 ATCGCAACGA
2628617 GAACTTGGAC
Statistics
Matches: 183, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
39 12 0.07
40 102 0.56
41 57 0.31
42 12 0.07
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (40 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACT
Found at i:2628652 original size:121 final size:122
Alignment explanation
Indices: 2628423--2628675 Score: 336
Period size: 121 Copynumber: 2.1 Consensus size: 122
2628413 GCGAATATGT
*
2628423 AAATCGTAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTAT
1 AAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTAT
* * * *
2628488 CGCAATGCGAATATGTAAATCACAACGTGAACTTGGATTATCGCAA-CGAATTTGGA
66 CGCAACGAGAATATGGAAATCACAACGTGAACTTGGATAATCGCAACCGAATTTGGA
*
2628544 AAATCGCAACGTGAACTTGGACTATCGTAACGAATTTGGAAAATCGCAACGCGAAC-TCTGACTA
1 AAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC-GACTA
* * * *
2628608 TCGCAACGAGAACT-TGGACTATCGCAATGTGAA-TATGTA-AATCGCAACGCGAATTTGGA
65 TCGCAACGAGAA-TATGGA-AATCACAACGTGAACT-TGGATAATCGCAAC-CGAATTTGGA
2628667 AAATCGCAA
1 AAATCGCAA
2628676 TGCGATAGTC
Statistics
Matches: 116, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
120 2 0.02
121 80 0.69
122 15 0.13
123 19 0.16
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (122 bp):
AAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTAT
CGCAACGAGAATATGGAAATCACAACGTGAACTTGGATAATCGCAACCGAATTTGGA
Found at i:2628672 original size:21 final size:21
Alignment explanation
Indices: 2628363--2628680 Score: 165
Period size: 21 Copynumber: 15.7 Consensus size: 21
2628353 GCAAATATGT
2628363 AAATCGCAA--CGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
* * *
2628382 AAATCGTAACGCGAACTTCGA
1 AAATCGCAACGCGAATTTGGA
** * * *
2628403 CTATCGCAATGCGAATAT-GT
1 AAATCGCAACGCGAATTTGGA
* * *
2628423 AAATCGTAACGTGAACTTGGA
1 AAATCGCAACGCGAATTTGGA
**
2628444 CTATCGCAA--CGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
* *
2628463 AAATCGCAACGCGAACTTCGA
1 AAATCGCAACGCGAATTTGGA
** * * *
2628484 CTATCGCAATGCGAATAT-GT
1 AAATCGCAACGCGAATTTGGA
* * *
2628504 AAATCACAACGTGAACTTGGA
1 AAATCGCAACGCGAATTTGGA
**
2628525 TTATCGCAA--CGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
* *
2628544 AAATCGCAACGTGAACTTGGA
1 AAATCGCAACGCGAATTTGGA
** *
2628565 CTATCGTAA--CGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
*
2628584 AAATCGCAACGCGAACTCT-GA
1 AAATCGCAACGCGAA-TTTGGA
** * *
2628605 CTATCGCAACGAGAACTTGGA
1 AAATCGCAACGCGAATTTGGA
** * * * *
2628626 CTATCGCAATGTGAATAT-GT
1 AAATCGCAACGCGAATTTGGA
2628646 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
*
2628667 AAATCGCAATGCGA
1 AAATCGCAACGCGA
2628681 TAGTCGAAGT
Statistics
Matches: 210, Mismatches: 76, Indels: 24
0.68 0.25 0.08
Matches are distributed among these distances:
19 52 0.25
20 39 0.19
21 117 0.56
22 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (21 bp):
AAATCGCAACGCGAATTTGGA
Found at i:2630872 original size:29 final size:29
Alignment explanation
Indices: 2630833--2630903 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
2630823 TAAAATGTCC
2630833 AACTGTTTGAAAAGCTTCTGATAGAACCA
1 AACTGTTTGAAAAGCTTCTGATAGAACCA
2630862 AACTGTTTGAAAAGCTTCTGATAGAACCA
1 AACTGTTTGAAAAGCTTCTGATAGAACCA
*
2630891 AACTATTTGAAAA
1 AACTGTTTGAAAA
2630904 CCTCACTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (29 bp):
AACTGTTTGAAAAGCTTCTGATAGAACCA
Found at i:2631004 original size:24 final size:23
Alignment explanation
Indices: 2630977--2631064 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 23
2630967 CGTGCGCGGG
*
2630977 ATTCGTTCATTTATGTTCATGAAC
1 ATTCGTTCATTTATGTTCAT-TAC
* *
2631001 ATTCG---ATTATATGTTCGTTTAT
1 ATTCGTTCATT-TATGTTC-ATTAC
* *
2631023 GTTCGTTCATTTATGTTCATTTC
1 ATTCGTTCATTTATGTTCATTAC
2631046 TATTCGTTCATTTATGTTC
1 -ATTCGTTCATTTATGTTC
2631065 GAACAGAGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
21 3 0.06
22 12 0.24
23 3 0.06
24 29 0.58
25 3 0.06
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.53
Consensus pattern (23 bp):
ATTCGTTCATTTATGTTCATTAC
Found at i:2631035 original size:14 final size:14
Alignment explanation
Indices: 2631013--2631065 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
2631003 TCGATTATAT
*
2631013 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
2631027 GTTCATTTA---T-
1 GTTCATTTATGTTC
* *
2631037 GTTCATTTCTATTC
1 GTTCATTTATGTTC
2631051 GTTCATTTATGTTC
1 GTTCATTTATGTTC
2631065 G
1 G
2631066 AACAGAGGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
13 1 0.03
14 21 0.68
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:2631348 original size:23 final size:23
Alignment explanation
Indices: 2631322--2631395 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
2631312 TTTTTGTTGT
*
2631322 GTTTG-TGTTGTTCGTTTATGTTC
1 GTTTGTTG-TGTTCGTTTATATTC
*
2631345 GTTTATTGTGTTCGTTTATATTC
1 GTTTGTTGTGTTCGTTTATATTC
*
2631368 GTTCGTTCGTGTTCGTTTATATTC
1 GTTTGTT-GTGTTCGTTTATATTC
2631392 GTTT
1 GTTT
2631396 ATTATTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
23 23 0.52
24 21 0.48
ACGTcount: A:0.08, C:0.11, G:0.22, T:0.59
Consensus pattern (23 bp):
GTTTGTTGTGTTCGTTTATATTC
Found at i:2637732 original size:24 final size:26
Alignment explanation
Indices: 2637705--2637759 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
2637695 GAAATTTATT
2637705 TTTATGTTATTATTTT-T-TTAA-ATA
1 TTTATGTTATT-TTTTATATTAATATA
2637729 TTTA--TTATTTTTTATATTAATATA
1 TTTATGTTATTTTTTATATTAATATA
2637753 TTTATGT
1 TTTATGT
2637760 AAATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 4 0.15
22 6 0.23
23 4 0.15
24 11 0.42
26 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (26 bp):
TTTATGTTATTTTTTATATTAATATA
Found at i:2637741 original size:18 final size:18
Alignment explanation
Indices: 2637711--2637779 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 18
2637701 TATTTTTATG
2637711 TTATTATTTTTTTAAATAT
1 TTATTA-TTTTTTAAATAT
2637730 TTATTATTTTTT--ATAT
1 TTATTATTTTTTAAATAT
* *
2637746 TAATATATTTATGTAAATA-
1 TTAT-TATTT-TTTAAATAT
2637765 TTA-TATTTTATTAAA
1 TTATTATTTT-TTAAA
2637780 ATAATATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
16 8 0.20
17 14 0.34
18 8 0.20
19 8 0.20
20 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (18 bp):
TTATTATTTTTTAAATAT
Found at i:2637782 original size:18 final size:20
Alignment explanation
Indices: 2637742--2637779 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
2637732 ATTATTTTTT
2637742 ATATTAATATATTTATGTAA
1 ATATTAATATATTTATGTAA
2637762 ATATT-ATAT-TTTAT-TAA
1 ATATTAATATATTTATGTAA
2637779 A
1 A
2637780 ATAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 4 0.22
20 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATATTAATATATTTATGTAA
Found at i:2637788 original size:16 final size:18
Alignment explanation
Indices: 2637746--2637788 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
2637736 TTTTTTATAT
2637746 TAATATATTTATGTAAATA
1 TAATAT-TTTATGTAAATA
*
2637765 TTATATTTTAT-TAAA-A
1 TAATATTTTATGTAAATA
2637781 TAATATTT
1 TAATATTT
2637789 ATAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 4 0.18
18 5 0.23
19 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATATTTTATGTAAATA
Found at i:2639553 original size:21 final size:21
Alignment explanation
Indices: 2639523--2639570 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2639513 GCAGGGGTAC
* *
2639523 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
2639544 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
2639565 ATGCCA
1 ATGCCA
2639571 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:2639597 original size:42 final size:42
Alignment explanation
Indices: 2639550--2639667 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
2639540 TCATATGCCA
* * *
2639550 AGCCCACCAGTTTATATGCC-ATCTCCGCAGGGTTACATTCCG
1 AGCCCACCAGGTTACATGCCGAGC-CCGCAGGGTTACATTCCG
* *
2639592 AGCCCA-CATGGTTACATTCCGAGCCCGCAGGGTTACATTCCT
1 AGCCCACCA-GGTTACATGCCGAGCCCGCAGGGTTACATTCCG
* *
2639634 AGCCCGCCAGGTTACATGCCTAGCCCGCAGGGTT
1 AGCCCACCAGGTTACATGCCGAGCCCGCAGGGTT
2639668 TTATACCATA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.03
42 59 0.91
43 4 0.06
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (42 bp):
AGCCCACCAGGTTACATGCCGAGCCCGCAGGGTTACATTCCG
Found at i:2639606 original size:21 final size:21
Alignment explanation
Indices: 2639577--2639667 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
2639567 GCCATCTCCG
2639577 CAGGGTTACATTCCGAGCCCA
1 CAGGGTTACATTCCGAGCCCA
* *
2639598 CATGGTTACATTCCGAGCCCG
1 CAGGGTTACATTCCGAGCCCA
* *
2639619 CAGGGTTACATTCCTAGCCCGC
1 CAGGGTTACATTCCGAGCCC-A
* * *
2639641 CA-GGTTACATGCCTAGCCCG
1 CAGGGTTACATTCCGAGCCCA
2639661 CAGGGTT
1 CAGGGTT
2639668 TTATACCATA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.22
Consensus pattern (21 bp):
CAGGGTTACATTCCGAGCCCA
Found at i:2640472 original size:128 final size:128
Alignment explanation
Indices: 2640244--2641243 Score: 1721
Period size: 128 Copynumber: 7.9 Consensus size: 128
2640234 TTACCTGATT
*
2640244 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
** *
2640309 TGACAAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
2640372 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2640437 TGATGAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
2640500 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2640565 TGATGAAATAACGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
2640628 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2640693 TGATGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
2640756 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
2640821 TGATGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
2640884 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
** *
2640949 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATG---AATAGTGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
2641010 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
2641075 TGATG----AATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
2641134 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2641199 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT
2641244 GAATAATACT
Statistics
Matches: 848, Mismatches: 17, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
122 34 0.04
124 86 0.10
126 87 0.10
127 1 0.00
128 640 0.75
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
Found at i:2641334 original size:8 final size:8
Alignment explanation
Indices: 2641321--2641361 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2641311 TCACAATCTT
2641321 TCAAATTC
1 TCAAATTC
2641329 TCAAATTC
1 TCAAATTC
* *
2641337 CCAAACTC
1 TCAAATTC
2641345 T-AAATTC
1 TCAAATTC
2641352 TCAAATTC
1 TCAAATTC
2641360 TC
1 TC
2641362 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:2645673 original size:33 final size:33
Alignment explanation
Indices: 2645631--2645697 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2645621 TAGGGTAAAT
2645631 ATGCATTTGTGTCTTGATTGGGGGATCTTTTAG
1 ATGCATTTGTGTCTTGATTGGGGGATCTTTTAG
* *
2645664 ATGCATTTGTGTGTTTATTGGGGGATCTTTTAG
1 ATGCATTTGTGTCTTGATTGGGGGATCTTTTAG
2645697 A
1 A
2645698 CTTAGAGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.16, C:0.07, G:0.30, T:0.46
Consensus pattern (33 bp):
ATGCATTTGTGTCTTGATTGGGGGATCTTTTAG
Found at i:2646240 original size:42 final size:42
Alignment explanation
Indices: 2646181--2646262 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
2646171 ACCTGTAGCA
*
2646181 TTATCCAATAAACTTAACATCCATAACAACGAACTTGAAAAC
1 TTATCCAATAAACTTAACATCCATAACAACAAACTTGAAAAC
2646223 TTATCCAATAAACTTAACATCCATAACAACAAACTTGAAA
1 TTATCCAATAAACTTAACATCCATAACAACAAACTTGAAA
2646263 TCCATAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.49, C:0.23, G:0.04, T:0.24
Consensus pattern (42 bp):
TTATCCAATAAACTTAACATCCATAACAACAAACTTGAAAAC
Found at i:2646256 original size:21 final size:21
Alignment explanation
Indices: 2646190--2646269 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
2646180 ATTATCCAAT
2646190 AAACTT-AACATCCATAACAAC
1 AAACTTGAA-ATCCATAACAAC
* * * * *
2646211 GAACTTGAAA-ACTTATCCAAT
1 AAACTTGAAATCCATA-ACAAC
2646232 AAACTT-AACATCCATAACAAC
1 AAACTTGAA-ATCCATAACAAC
2646253 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
2646270 TAATAAATCG
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
20 5 0.11
21 32 0.73
22 7 0.16
ACGTcount: A:0.50, C:0.24, G:0.04, T:0.23
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:2650195 original size:72 final size:72
Alignment explanation
Indices: 2650117--2650260 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
2650107 ATAATTCTCT
2650117 CATATTAACATAAAGGTTAAGACATAATCTCTATTTATAGAGCCAAATACATGGTCACCAAGAAT
1 CATATTAACATAAAGGTTAAGACATAATCTCTATTTATAGAGCCAAATACATGGTCACCAAGAAT
2650182 TCTTATG
66 TCTTATG
2650189 CATATTAACATAAAGGTTAAGACATAATCTCTATTTATAGAGCCAAATACATGGTCACCAAGAAT
1 CATATTAACATAAAGGTTAAGACATAATCTCTATTTATAGAGCCAAATACATGGTCACCAAGAAT
2650254 TCTTATG
66 TCTTATG
2650261 GATCAAGCCT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (72 bp):
CATATTAACATAAAGGTTAAGACATAATCTCTATTTATAGAGCCAAATACATGGTCACCAAGAAT
TCTTATG
Found at i:2653815 original size:12 final size:12
Alignment explanation
Indices: 2653798--2653841 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2653788 ATAAACAATA
2653798 ATGAACAGTGCC
1 ATGAACAGTGCC
2653810 ATGAACAGTG--
1 ATGAACAGTGCC
*
2653820 ATGAACAGTACC
1 ATGAACAGTGCC
*
2653832 GTGAACAGTG
1 ATGAACAGTG
2653842 AAAATTTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (12 bp):
ATGAACAGTGCC
Found at i:2653823 original size:22 final size:22
Alignment explanation
Indices: 2653798--2653842 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2653788 ATAAACAATA
*
2653798 ATGAACAGTGCCATGAACAGTG
1 ATGAACAGTACCATGAACAGTG
*
2653820 ATGAACAGTACCGTGAACAGTG
1 ATGAACAGTACCATGAACAGTG
2653842 A
1 A
2653843 AAATTTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
ATGAACAGTACCATGAACAGTG
Found at i:2654569 original size:18 final size:18
Alignment explanation
Indices: 2654542--2654576 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2654532 CCGCGTAGAA
*
2654542 ATGTCTCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
2654560 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
2654577 ATATCACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:2654726 original size:23 final size:23
Alignment explanation
Indices: 2654685--2654728 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2654675 ATTACATATA
*
2654685 TGTCCCGAAGGATCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
* *
2654708 TGTCCCGAATGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
2654729 CCCTCGACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:2660095 original size:9 final size:8
Alignment explanation
Indices: 2660081--2660166 Score: 52
Period size: 9 Copynumber: 10.2 Consensus size: 8
2660071 AATAGTTTAT
2660081 ATATAATTA
1 ATATAA-TA
*
2660090 ATATAAAA
1 ATATAATA
2660098 ATATAA-A
1 ATATAATA
*
2660105 ATATTATA
1 ATATAATA
2660113 TATATAATTA
1 -ATATAA-TA
2660123 ATATAA-A
1 ATATAATA
2660130 ATAT-ATA
1 ATATAATA
* *
2660137 AAATATTA
1 ATATAATA
2660145 TATATATATA
1 -ATATA-ATA
2660155 TATATATATA
1 -ATATA-ATA
2660165 AT
1 AT
2660167 CGGGGCGGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
6 1 0.02
7 15 0.24
8 10 0.16
9 23 0.37
10 14 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAATA
Found at i:2660116 original size:2 final size:2
Alignment explanation
Indices: 2660105--2660164 Score: 53
Period size: 2 Copynumber: 33.5 Consensus size: 2
2660095 AAAATATAAA
* *
2660105 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2660141 AT -T 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
2660165 ATCGGGGCGG
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
1 7 0.14
2 42 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2660119 original size:16 final size:16
Alignment explanation
Indices: 2660098--2660164 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 16
2660088 TAATATAAAA
2660098 ATATAAAATATTATAT
1 ATATAAAATATTATAT
* *
2660114 ATATAATTAATATAAAAT
1 ATATAA--AATATTATAT
2660132 ATATAAAATATTATAT
1 ATATAAAATATTATAT
*
2660148 ATAT-ATATA-TATAT
1 ATATAAAATATTATAT
2660162 ATA
1 ATA
2660165 ATCGGGGCGG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
14 8 0.18
15 4 0.09
16 18 0.41
18 14 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAAAATATTATAT
Found at i:2660141 original size:34 final size:33
Alignment explanation
Indices: 2660078--2660152 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 33
2660068 GATAATAGTT
2660078 TATATATAATTAATATAAAAATATAAAATATTA
1 TATATATAATTAATATAAAAATATAAAATATTA
2660111 TATATATAATTAATATAAAATATATAAAATATTA
1 TATATATAATTAATATAAAA-ATATAAAATATTA
2660145 TATATATA
1 TATATATA
2660153 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 20 0.49
34 21 0.51
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TATATATAATTAATATAAAAATATAAAATATTA
Found at i:2660160 original size:33 final size:33
Alignment explanation
Indices: 2660077--2660162 Score: 124
Period size: 34 Copynumber: 2.6 Consensus size: 33
2660067 TGATAATAGT
2660077 TTATATATA-AT-TAATATAAAAATATAAAATA
1 TTATATATATATATAATATAAAAATATAAAATA
2660108 TTATATATATA-ATTAATATAAAATATATAAAATA
1 TTATATATATATA-TAATATAAAA-ATATAAAATA
2660142 TTATATATATATATATATATA
1 TTATATATATATATA-ATATA
2660163 TAATCGGGGC
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
31 9 0.18
32 1 0.02
33 10 0.20
34 23 0.47
35 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TTATATATATATATAATATAAAAATATAAAATA
Found at i:2671677 original size:15 final size:15
Alignment explanation
Indices: 2671657--2671691 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2671647 GATAAGACTC
2671657 AAGAATAAGGAAGAG
1 AAGAATAAGGAAGAG
**
2671672 AAGAATAAGGTGGAG
1 AAGAATAAGGAAGAG
2671687 AAGAA
1 AAGAA
2671692 GAAAATTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.34, T:0.09
Consensus pattern (15 bp):
AAGAATAAGGAAGAG
Found at i:2680988 original size:64 final size:64
Alignment explanation
Indices: 2680919--2681074 Score: 183
Period size: 64 Copynumber: 2.4 Consensus size: 64
2680909 TTGAAGGTGT
**
2680919 ATCGATGCACAGGTAGTGCATCGATGCACTCTTTTAA-AATATAAACATCGAATGCA-ATTAGTG
1 ATCGATGCACAGGTAGTGCATCGATGCACTCCATTAATAATA-AAACATCGAATGCATATTA-TG
2680982 C
64 C
* * * * *
2680983 ATCGATGCATAAGGCA-TGCATCGATGCATTCCATTAATAATAAAACATTGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCACTCCATTAATAATAAAACATCGAATGCATATTATGC
* *
2681047 ACCGATGCACAAGTAGTGCATCGATGCA
1 ATCGATGCACAGGTAGTGCATCGATGCA
2681075 TACCTTCATT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
63 3 0.04
64 63 0.82
65 11 0.14
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCACTCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:2681491 original size:29 final size:29
Alignment explanation
Indices: 2681452--2681532 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2681442 TATGTGATAT
2681452 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
2681482 GAGAAATGACATGAGCTACATGATCATAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
2681511 GAGAATTGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
2681533 ACATATGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 37 0.76
30 5 0.10
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:2689228 original size:37 final size:37
Alignment explanation
Indices: 2689175--2689252 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
2689165 CACGTTTAAT
*
2689175 ACTTAAACCATTAGTTTTAGTCTGATTTAGCACATAA
1 ACTTAAACCATCAGTTTTAGTCTGATTTAGCACATAA
* * * *
2689212 ACTTAAATCATCAGTTTTAGTCTGTTTTAGTACTTAA
1 ACTTAAACCATCAGTTTTAGTCTGATTTAGCACATAA
2689249 ACTT
1 ACTT
2689253 TCAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (37 bp):
ACTTAAACCATCAGTTTTAGTCTGATTTAGCACATAA
Found at i:2693792 original size:175 final size:175
Alignment explanation
Indices: 2693501--2693850 Score: 700
Period size: 175 Copynumber: 2.0 Consensus size: 175
2693491 CCTTGATTTC
2693501 CTAATTGACAAGCTTGAACCCAATCCATGGAAGCTTATTCCATAAAATCATCCCCAAACCATCCT
1 CTAATTGACAAGCTTGAACCCAATCCATGGAAGCTTATTCCATAAAATCATCCCCAAACCATCCT
2693566 TCTTTTCCACCGAAATAATTCCCCAAAACTCCACACAAACATTCCTTATTTCCTTCATTTCATTC
66 TCTTTTCCACCGAAATAATTCCCCAAAACTCCACACAAACATTCCTTATTTCCTTCATTTCATTC
2693631 AAAACTCACTGATTTCCCCTCAAGCAAACATACCCATATCTTCAA
131 AAAACTCACTGATTTCCCCTCAAGCAAACATACCCATATCTTCAA
2693676 CTAATTGACAAGCTTGAACCCAATCCATGGAAGCTTATTCCATAAAATCATCCCCAAACCATCCT
1 CTAATTGACAAGCTTGAACCCAATCCATGGAAGCTTATTCCATAAAATCATCCCCAAACCATCCT
2693741 TCTTTTCCACCGAAATAATTCCCCAAAACTCCACACAAACATTCCTTATTTCCTTCATTTCATTC
66 TCTTTTCCACCGAAATAATTCCCCAAAACTCCACACAAACATTCCTTATTTCCTTCATTTCATTC
2693806 AAAACTCACTGATTTCCCCTCAAGCAAACATACCCATATCTTCAA
131 AAAACTCACTGATTTCCCCTCAAGCAAACATACCCATATCTTCAA
2693851 ATCCCCAGCC
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.29
Consensus pattern (175 bp):
CTAATTGACAAGCTTGAACCCAATCCATGGAAGCTTATTCCATAAAATCATCCCCAAACCATCCT
TCTTTTCCACCGAAATAATTCCCCAAAACTCCACACAAACATTCCTTATTTCCTTCATTTCATTC
AAAACTCACTGATTTCCCCTCAAGCAAACATACCCATATCTTCAA
Found at i:2698133 original size:17 final size:19
Alignment explanation
Indices: 2698111--2698145 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2698101 ATAAAAAAGT
2698111 ATTAAAAT-TT-TAAATAA
1 ATTAAAATATTATAAATAA
2698128 ATTAAAATATTATAAATA
1 ATTAAAATATTATAAATA
2698146 TTTACAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAAATATTATAAATAA
Found at i:2698198 original size:27 final size:27
Alignment explanation
Indices: 2698113--2698199 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
2698103 AAAAAAGTAT
*
2698113 TAAAA-TTTTAAAT--AAATTAAAATA
1 TAAAATTTTTAAATAAAAATTAAATTA
* *
2698137 TTATAAATATTTACAATGAAAAA-TCAATTA
1 -TA-AAATTTTTA-AAT-AAAAATTAAATTA
*
2698167 AAAAATTTTTAAATAAAAATTAAATTA
1 TAAAATTTTTAAATAAAAATTAAATTA
2698194 TAAAAT
1 TAAAAT
2698200 AGAGCTCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
25 2 0.04
26 8 0.17
27 18 0.38
28 11 0.23
29 1 0.02
30 5 0.10
31 3 0.06
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (27 bp):
TAAAATTTTTAAATAAAAATTAAATTA
Found at i:2698691 original size:15 final size:15
Alignment explanation
Indices: 2698671--2698708 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2698661 CACCGCAGCG
*
2698671 GCAGCAGCAGGAGCA
1 GCAGCAACAGGAGCA
*
2698686 GCAGCAACAGGGGCA
1 GCAGCAACAGGAGCA
2698701 GCAGCAAC
1 GCAGCAAC
2698709 TGCAAACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.34, C:0.29, G:0.37, T:0.00
Consensus pattern (15 bp):
GCAGCAACAGGAGCA
Found at i:2700470 original size:16 final size:16
Alignment explanation
Indices: 2700449--2700497 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
2700439 TAATAAATAA
2700449 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2700465 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
* *
2700481 ACTATCATAAACGAAC
1 ACGAACATAAACGAAC
2700497 A
1 A
2700498 TAAACGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.55, C:0.22, G:0.10, T:0.12
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2701451 original size:24 final size:24
Alignment explanation
Indices: 2701424--2701470 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2701414 TAAATGAATG
2701424 AACATAAAAGAACATAACCGAACA
1 AACATAAAAGAACATAACCGAACA
* *
2701448 AACATAAACGAACATGACCGAAC
1 AACATAAAAGAACATAACCGAAC
2701471 GTTCACGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (24 bp):
AACATAAAAGAACATAACCGAACA
Found at i:2716499 original size:118 final size:120
Alignment explanation
Indices: 2716291--2716528 Score: 453
Period size: 118 Copynumber: 2.0 Consensus size: 120
2716281 CGGATATAAA
*
2716291 TAGCCTTCTCCCCGTAAACTCTCTCACAATTCCCTCTCAACCGAGAAATTAATTCAACAATCCTT
1 TAGCCTTCTCCCCGTAAACTCTCTCACAATTCCCTCTCAACCGAGAAATTAATACAACAATCCTT
2716356 TCAACCAGTAAATAACACCCGACAATGCTC-T-TATTTAATTCAGAAGTTCGTTC
66 TCAACCAGTAAATAACACCCGACAATGCTCTTATATTTAATTCAGAAGTTCGTTC
2716409 TAGCCTTCTCCCCGTAAACTCTCTCACAATTCCCTCTCAACCGAGAAATTAATACAACAATCCTT
1 TAGCCTTCTCCCCGTAAACTCTCTCACAATTCCCTCTCAACCGAGAAATTAATACAACAATCCTT
2716474 TCAACCAGTAAATAACACCCGACAATGCTCTTATATTTAATTCAGAAGTTCGTTC
66 TCAACCAGTAAATAACACCCGACAATGCTCTTATATTTAATTCAGAAGTTCGTTC
2716529 GATCTTTCGT
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
118 94 0.80
119 1 0.01
120 22 0.19
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.29
Consensus pattern (120 bp):
TAGCCTTCTCCCCGTAAACTCTCTCACAATTCCCTCTCAACCGAGAAATTAATACAACAATCCTT
TCAACCAGTAAATAACACCCGACAATGCTCTTATATTTAATTCAGAAGTTCGTTC
Found at i:2722744 original size:5 final size:5
Alignment explanation
Indices: 2722734--2722771 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
2722724 AGGTATTGTA
2722734 GGGAG GGGAG GGGAG GGGAG GGGAG GGGAG GGGAG GGG
1 GGGAG GGGAG GGGAG GGGAG GGGAG GGGAG GGGAG GGG
2722772 GTGGGGTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.82, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:2734152 original size:133 final size:133
Alignment explanation
Indices: 2733972--2734237 Score: 532
Period size: 133 Copynumber: 2.0 Consensus size: 133
2733962 ATAATTCAAT
2733972 TTAATCCTTCTTAACACAAAAACGTTTTAGCTTTGCCCCCCCTCAAAATTTGATAATTTATCTAG
1 TTAATCCTTCTTAACACAAAAACGTTTTAGCTTTGCCCCCCCTCAAAATTTGATAATTTATCTAG
2734037 GCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAAGGGGGACAGAAGAATGCACACCTCTA
66 GCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAAGGGGGACAGAAGAATGCACACCTCTA
2734102 TCA
131 TCA
2734105 TTAATCCTTCTTAACACAAAAACGTTTTAGCTTTGCCCCCCCTCAAAATTTGATAATTTATCTAG
1 TTAATCCTTCTTAACACAAAAACGTTTTAGCTTTGCCCCCCCTCAAAATTTGATAATTTATCTAG
2734170 GCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAAGGGGGACAGAAGAATGCACACCTCTA
66 GCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAAGGGGGACAGAAGAATGCACACCTCTA
2734235 TCA
131 TCA
2734238 ACTGTTTGCC
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (133 bp):
TTAATCCTTCTTAACACAAAAACGTTTTAGCTTTGCCCCCCCTCAAAATTTGATAATTTATCTAG
GCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAAGGGGGACAGAAGAATGCACACCTCTA
TCA
Found at i:2734320 original size:102 final size:102
Alignment explanation
Indices: 2734144--2734347 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
2734134 GCTTTGCCCC
2734144 CCCTCAAAATTTGATAATTTATCTAGGCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAA
1 CCCTCAAAATTTGATAATTTATCTAGGCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAA
2734209 GGGGGACAGAAGAATGCACACCTCTATCAACTGTTTG
66 GGGGGACAGAAGAATGCACACCTCTATCAACTGTTTG
2734246 CCCTCAAAATTTGATAATTTATCTAGGCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAA
1 CCCTCAAAATTTGATAATTTATCTAGGCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAA
2734311 GGGGGACAGAAGAATGCACACCTCTATCAACTGTTTG
66 GGGGGACAGAAGAATGCACACCTCTATCAACTGTTTG
2734348 GTAAATTGTG
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (102 bp):
CCCTCAAAATTTGATAATTTATCTAGGCCACCAAAACAAATTTGCTGGCTTACCCCCTGCTTGAA
GGGGGACAGAAGAATGCACACCTCTATCAACTGTTTG
Found at i:2738279 original size:146 final size:145
Alignment explanation
Indices: 2738012--2738273 Score: 361
Period size: 146 Copynumber: 1.8 Consensus size: 145
2738002 AATAAAAATG
* *
2738012 TTTATTTATTTTTCAATATTAAGAAGGGGCAGTCTTAAAGCAACTGAATGTCCATTTTCTGATAT
1 TTTATTTATTTTTCAATATTAAGAAAGAGCAGTCTTAAAGCAACTGAATGTCCATTTTCTGATAT
* * * **
2738077 TTTTAAATAAATAAATATTTTACTTTTATAAATTATATTAATCTATTTTTTAATTATTTTTAAAT
66 TTCTAAATAAATAAATATCTTAC-TTTATAAATTATATAAATAGATTTTTTAATTATTTTTAAAT
2738142 AAATGTTTTATTAATA
130 AAATGTTTTATTAATA
* * *
2738158 TTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAA-GT-CATTTTCTGAT
1 TTTATTTATTTTTCAATATTAAG-AAAGAGCAGTCTTAAAGCAACT-GAATGTCCATTTTCTGAT
*
2738221 ATTTCTAAATAAATAAATATCTTA-TTTATATA-TATATAAATAGATTTTCTTAA
64 ATTTCTAAATAAATAAATATCTTACTTTATAAATTATATAAATAGATTTT-TTAA
2738274 AATTATAATA
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
143 13 0.13
144 11 0.11
146 55 0.54
147 20 0.20
148 3 0.03
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (145 bp):
TTTATTTATTTTTCAATATTAAGAAAGAGCAGTCTTAAAGCAACTGAATGTCCATTTTCTGATAT
TTCTAAATAAATAAATATCTTACTTTATAAATTATATAAATAGATTTTTTAATTATTTTTAAATA
AATGTTTTATTAATA
Found at i:2740499 original size:7 final size:6
Alignment explanation
Indices: 2740464--2740498 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2740454 ACATTCACAT
*
2740464 ATTTAC ATTTGC ATTTGC ATTTGC ATTTTGC ATTT
1 ATTTGC ATTTGC ATTTGC ATTTGC A-TTTGC ATTT
2740499 TTACATTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.54
Consensus pattern (6 bp):
ATTTGC
Found at i:2740506 original size:33 final size:34
Alignment explanation
Indices: 2740465--2740532 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
2740455 CATTCACATA
* *
2740465 TTTACATTTGCATTTGCATTTGCA-TTTTGCATT
1 TTTACATTTGCATTTACATTTCCATTTTTGCATT
* *
2740498 TTTACATTTGTATTTATATTTCCATTTTTGCATT
1 TTTACATTTGCATTTACATTTCCATTTTTGCATT
2740532 T
1 T
2740533 GCATCTTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 20 0.67
34 10 0.33
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.59
Consensus pattern (34 bp):
TTTACATTTGCATTTACATTTCCATTTTTGCATT
Found at i:2740541 original size:14 final size:13
Alignment explanation
Indices: 2740471--2740544 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 13
2740461 CATATTTACA
2740471 TTTGCATTTGCA-
1 TTTGCATTTGCAT
2740483 TTTGCATTTTGCATT
1 TTTGCA-TTTGCA-T
* *
2740498 TTTACATTTGTAT
1 TTTGCATTTGCAT
*
2740511 TTAT--ATTTCCATT
1 TT-TGCATTTGCA-T
2740524 TTTGCATTTGCAT
1 TTTGCATTTGCAT
2740537 CTTTGCAT
1 -TTTGCAT
2740545 AATTACATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
12 12 0.24
13 13 0.27
14 19 0.39
15 5 0.10
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.57
Consensus pattern (13 bp):
TTTGCATTTGCAT
Found at i:2743303 original size:7 final size:8
Alignment explanation
Indices: 2743284--2743313 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
2743274 ATACTTGAAA
2743284 AAAAAAGG
1 AAAAAAGG
2743292 AAAAAAGG
1 AAAAAAGG
2743300 AAAAAAGG
1 AAAAAAGG
2743308 AAAAAA
1 AAAAAA
2743314 AATTGAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:2750907 original size:13 final size:13
Alignment explanation
Indices: 2750889--2750913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2750879 CAATGGTCAA
2750889 CGGTCGGGTCGGC
1 CGGTCGGGTCGGC
2750902 CGGTCGGGTCGG
1 CGGTCGGGTCGG
2750914 TTGGGTCGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.56, T:0.16
Consensus pattern (13 bp):
CGGTCGGGTCGGC
Found at i:2750913 original size:18 final size:18
Alignment explanation
Indices: 2750890--2750931 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2750880 AATGGTCAAC
2750890 GGTCGGGTCGGCCGGTCG
1 GGTCGGGTCGGCCGGTCG
* * *
2750908 GGTCGGTTGGGTCGGTCG
1 GGTCGGGTCGGCCGGTCG
2750926 GGTCGG
1 GGTCGG
2750932 TCAAACCGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.57, T:0.21
Consensus pattern (18 bp):
GGTCGGGTCGGCCGGTCG
Found at i:2750919 original size:9 final size:9
Alignment explanation
Indices: 2750902--2750933 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2750892 TCGGGTCGGC
2750902 CGGTCGGGT
1 CGGTCGGGT
*
2750911 CGGTTGGGT
1 CGGTCGGGT
2750920 CGGTCGGGT
1 CGGTCGGGT
2750929 CGGTC
1 CGGTC
2750934 AAACCGGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.22, G:0.53, T:0.25
Consensus pattern (9 bp):
CGGTCGGGT
Found at i:2750947 original size:10 final size:9
Alignment explanation
Indices: 2750929--2750966 Score: 58
Period size: 10 Copynumber: 4.0 Consensus size: 9
2750919 TCGGTCGGGT
2750929 CGGTCAAAC
1 CGGTCAAAC
2750938 CGGTTCAAAC
1 CGG-TCAAAC
2750948 CGGTCGAAAC
1 CGGTC-AAAC
2750958 CGGTCAAAC
1 CGGTCAAAC
2750967 TGGTTTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.13
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:2750964 original size:19 final size:19
Alignment explanation
Indices: 2750929--2750966 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2750919 TCGGTCGGGT
2750929 CGGTCAAACCGGTTCAAAC
1 CGGTCAAACCGGTTCAAAC
2750948 CGGTCGAAACCGG-TCAAAC
1 CGGTC-AAACCGGTTCAAAC
2750967 TGGTTTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.13
Consensus pattern (19 bp):
CGGTCAAACCGGTTCAAAC
Found at i:2756597 original size:28 final size:28
Alignment explanation
Indices: 2756557--2756610 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
2756547 GTAGTAGAAA
* *
2756557 CGGTTCCGCGTGGTTTCCCTAGGGTAAG
1 CGGTTCCACGTGGTTGCCCTAGGGTAAG
*
2756585 CGGTTCCATGTGGTTGCCCTAGGGTA
1 CGGTTCCACGTGGTTGCCCTAGGGTA
2756611 TCATACCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.24, G:0.35, T:0.30
Consensus pattern (28 bp):
CGGTTCCACGTGGTTGCCCTAGGGTAAG
Found at i:2756750 original size:3 final size:3
Alignment explanation
Indices: 2756744--2756799 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
2756734 ATTTATTATT
*
2756744 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA -AA T-A TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
2756788 TAA TAA AAA TAA
1 TAA TAA TAA TAA
2756800 ATTTGAGACA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2757804 original size:225 final size:225
Alignment explanation
Indices: 2757394--2757844 Score: 658
Period size: 225 Copynumber: 2.0 Consensus size: 225
2757384 GATAGAGTCA
* * * *
2757394 AGAAAAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGGGTTCTTCTC
1 AGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCATCTTCAGACGAGTTCTTCTC
* *
2757459 ATTATGAACTTCCTCTGGAAAAGTTGATCAATCGAGTGATGAATTCGAGCGAAAGGTTGAAAAAA
66 ATTATGAACTTACTCTGGAAAAGTTGATCAATCAAGTGATGAATTCGAGCGAAAGGTTGAAAAAA
*
2757524 TTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
131 TTCTTCTCATTATGAACTTCTTCATCACTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* * *
2757589 GCAATGTTAATCCATTAAGTGGCGGATTTG
196 GAAATGTTAATCCATCAAGTGACGGATTTG
*
2757619 AGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGACGAGTTCTTCT
1 AGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATT-CATCTTCAGACGAGTTCTTCT
* * * * *
2757684 CATTATGAACTCTAC-CT-GACAATGTTGATCCATCAAGTGATGGATTTGAGCGAAAGGTTGAAC
65 CATTATGAACT-TACTCTGGA-AAAGTTGATCAATCAAGTGATGAATTCGAGCGAAAGGTTGAAA
* *
2757747 AAGTTCTTCTCATTATGAACTT-TCTCTTC-CTCTTCAGATGAGTTCTTCTCATTATGAACTCTA
128 AAATTCTTCTCATTATGAACTTCT-TCATCACTCTTCAGATGAGTTCTTCTCATTATGAACTCTA
* *
2757810 CCTGGAAATGTTGATCCATCAAGTGATGGATTTG
192 CCTGGAAATGTTAATCCATCAAGTGACGGATTTG
2757844 A
1 A
2757845 ATCATTGCTA
Statistics
Matches: 202, Mismatches: 20, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
225 107 0.53
226 93 0.46
227 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (225 bp):
AGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCATCTTCAGACGAGTTCTTCTC
ATTATGAACTTACTCTGGAAAAGTTGATCAATCAAGTGATGAATTCGAGCGAAAGGTTGAAAAAA
TTCTTCTCATTATGAACTTCTTCATCACTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
GAAATGTTAATCCATCAAGTGACGGATTTG
Found at i:2757838 original size:112 final size:112
Alignment explanation
Indices: 2757398--2757844 Score: 630
Period size: 113 Copynumber: 4.0 Consensus size: 112
2757388 GAGTCAAGAA
* * *
2757398 AAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGGGTTCTTCTCATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* * * * * *
2757463 TGAACT-TCCTCTGGAAAAGTTGATCAATCGAGTGATGAATTCGAGCG
66 TGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCG
* * * *
2757510 AAAGGTTGAAAAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATT
* * * ** **
2757575 ATGAACTCTACCTGGCAATGTTAATCCATTAAGTGGCGGATTTGAGAA
65 ATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCG
* *
2757623 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGACGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
2757688 ATGAACTCTACCT-GACAATGTTGATCCATCAAGTGATGGATTTGAGCG
65 ATGAACTCTACCTGGA-AATGTTGATCCATCAAGTGATGGATTTGAGCG
2757736 AAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TCTCTTCCTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT-TCTTCCTCTTCAGATGAGTTCTTCTCATT
2757800 ATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGA
65 ATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGA
2757845 ATCATTGCTA
Statistics
Matches: 296, Mismatches: 33, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
112 103 0.35
113 191 0.65
114 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCG
Found at i:2758689 original size:54 final size:54
Alignment explanation
Indices: 2758606--2758709 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
2758596 TACTGGTTCT
* * *
2758606 TAAAACACTTGACATCACATTCATTATTTCTTGTGGCTTCTACTCAGATGCTTG
1 TAAAACACTTGACAACACATTCATCATTTCATGTGGCTTCTACTCAGATGCTTG
* *
2758660 TAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTTCTCAGATG
1 TAAAACACTTGACAACACATTCATCATTTCATGTGGCTTCTACTCAGATG
2758710 TTTGGTCAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (54 bp):
TAAAACACTTGACAACACATTCATCATTTCATGTGGCTTCTACTCAGATGCTTG
Found at i:2767230 original size:26 final size:26
Alignment explanation
Indices: 2767201--2767290 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 26
2767191 TCTTAAATTT
2767201 TTAACTTTTTCTTTTCTCTTTCTTTA
1 TTAACTTTTTCTTTTCTCTTTCTTTA
2767227 TTAA----TT-TTTTCTCTTT-TATT-
1 TTAACTTTTTCTTTTCTCTTTCT-TTA
*
2767247 TTAACTTTTACTTTTTCTCTTTCCTTTA
1 TTAACTTTTTC-TTTTCTCTTT-CTTTA
* *
2767275 TTCATCTTCTTCTTTT
1 TT-AACTTTTTCTTTT
2767291 GTTATTCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 20
0.67 0.05 0.27
Matches are distributed among these distances:
20 5 0.10
21 12 0.24
22 2 0.04
24 1 0.02
26 14 0.29
27 2 0.04
28 7 0.14
29 6 0.12
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (26 bp):
TTAACTTTTTCTTTTCTCTTTCTTTA
Found at i:2767250 original size:20 final size:22
Alignment explanation
Indices: 2767212--2767255 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2767202 TAACTTTTTC
2767212 TTTTCTCTTTCTTTATTAA-TT
1 TTTTCTCTTTCTTTATTAACTT
2767233 TTTTCTCTTT-TATT-TTAACTT
1 TTTTCTCTTTCT-TTATTAACTT
2767254 TT
1 TT
2767256 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTCTCTTTCTTTATTAACTT
Found at i:2767289 original size:47 final size:46
Alignment explanation
Indices: 2767199--2767290 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 46
2767189 CCTCTTAAAT
* * *
2767199 TTTTAACTTTTTCTTTTCTCTTTCTTTATTAATTTTTTCTCTTTTA
1 TTTTAACTTTTACTTTTCTCTTTCTTTATTAATCTTCTCTCTTTTA
*
2767245 TTTTAACTTTTACTTTTTCTCTTTCCTTTATTCATCTTCT-TCTTTT
1 TTTTAACTTTTAC-TTTTCTCTTT-CTTTATTAATCTTCTCTCTTTT
2767291 GTTATTCTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 12 0.30
47 16 0.40
48 12 0.30
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (46 bp):
TTTTAACTTTTACTTTTCTCTTTCTTTATTAATCTTCTCTCTTTTA
Found at i:2770515 original size:24 final size:24
Alignment explanation
Indices: 2770488--2770537 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2770478 TGGTGGTTGA
*
2770488 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
2770512 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
2770536 TT
1 TT
2770538 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:2774805 original size:114 final size:114
Alignment explanation
Indices: 2774593--2774817 Score: 360
Period size: 114 Copynumber: 2.0 Consensus size: 114
2774583 AAAACTACAT
* *
2774593 ACGAAAACAAGCATTCTATACAGATAACTCGAAATCTCATTTTCTCCAAAGGTCATGCAAGTGGG
1 ACGAAAACAAGCATTCTATACAGATAACTCGAAATCTCATTTTCTCAAAAGATCATGCAAGTGGG
* * * * *
2774658 ATGTTCACAAAGTCCATCCTTGGAATATGTATCCTTCAAAATGCAACAC
66 ATATCCACAAAGTCCATCCTCGGAACATCTATCCTTCAAAATGCAACAC
* *
2774707 ACGAAAACAAGCATTCTATACTGATAACTCGAAATCTCATTTTCTCAAAAGATTATGCAAGTGGG
1 ACGAAAACAAGCATTCTATACAGATAACTCGAAATCTCATTTTCTCAAAAGATCATGCAAGTGGG
*
2774772 ATATCCACAAAGTCCATCCTCGGAACATCTATCCTTGAAAATGCAA
66 ATATCCACAAAGTCCATCCTCGGAACATCTATCCTTCAAAATGCAA
2774818 TGCTATTGAC
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (114 bp):
ACGAAAACAAGCATTCTATACAGATAACTCGAAATCTCATTTTCTCAAAAGATCATGCAAGTGGG
ATATCCACAAAGTCCATCCTCGGAACATCTATCCTTCAAAATGCAACAC
Found at i:2778219 original size:18 final size:19
Alignment explanation
Indices: 2778183--2778219 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2778173 CACAGAATGC
2778183 AAGATTATCAGTAGGAATAA
1 AAGATTATCAG-AGGAATAA
2778203 AAGATTATCAG-GGAATA
1 AAGATTATCAGAGGAATA
2778220 GGATTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGAGGAATAA
Found at i:2778273 original size:178 final size:171
Alignment explanation
Indices: 2777976--2778328 Score: 548
Period size: 178 Copynumber: 2.0 Consensus size: 171
2777966 TCCAAGGCAA
*
2777976 AAATACACTTAAGGGTGCGTTTGGTTCACGGAATATAATATTAGAATAAAAGATTACCAGGGAAT
1 AAATACACTTAAGGGTGCGTTTGGTTCACAGAATATAATATTAGAATAAAAGATTACCAGGGAAT
2778041 AAGATTACTGAAAATGTTGTATTTTGTGTTTGGTTGGTTTAACAGGGATGTAAGATTACAATGTT
66 AAGATTACTGAAAATGTTGTATTTTGTGTTTGGTTGGTTTAACAGGGATGTAAGATTACAATGTT
2778106 TGGTTAAAGGAATAAAAGATTATTGAAATATGTATTTTACC
131 TGGTTAAAGGAATAAAAGATTATTGAAATATGTATTTTACC
* *
2778147 AAATGCACTTAAGGGTGCGTTTGGTTCACAGAATGCA-AGATTATCAGTAGGAATAAAAGATTAT
1 AAATACACTTAAGGGTGCGTTTGGTTCACAGAAT--ATA-A-TAT---TA-GAATAAAAGATTAC
* * *
2778211 CAGGGAATAGGATTATTGAAAATGTTGTATTTTGTGTTTGGTTGGTTTAGA-TGGGATGTAAGAT
58 CAGGGAATAAGATTACTGAAAATGTTGTATTTTGTGTTTGGTTGGTTTA-ACAGGGATGTAAGAT
*
2778275 TACAGTGTTTGGTTAAAGGAATAAAAGATTATTGAAATATGTATTTTACC
122 TACAATGTTTGGTTAAAGGAATAAAAGATTATTGAAATATGTATTTTACC
2778325 AAAT
1 AAAT
2778329 TGTTCTTATT
Statistics
Matches: 166, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
171 32 0.19
172 1 0.01
173 2 0.01
174 3 0.02
177 2 0.01
178 125 0.75
179 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (171 bp):
AAATACACTTAAGGGTGCGTTTGGTTCACAGAATATAATATTAGAATAAAAGATTACCAGGGAAT
AAGATTACTGAAAATGTTGTATTTTGTGTTTGGTTGGTTTAACAGGGATGTAAGATTACAATGTT
TGGTTAAAGGAATAAAAGATTATTGAAATATGTATTTTACC
Found at i:2778463 original size:37 final size:37
Alignment explanation
Indices: 2778389--2778463 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
2778379 TACTATAATT
**
2778389 AATTTATATATTTTCTTTAAAAAATTTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAATTTAAAAACATAA
* * *
2778426 AATTTATATAATTTTTTTTACAAAA-TTAAAAAGATAA
1 AATTTATAT-ATTTTCTTTAAAAAATTTAAAAACATAA
2778463 A
1 A
2778464 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.59
38 13 0.41
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAAATTTAAAAACATAA
Found at i:2788905 original size:43 final size:44
Alignment explanation
Indices: 2788814--2788919 Score: 153
Period size: 43 Copynumber: 2.4 Consensus size: 44
2788804 GATATGTATG
* **
2788814 TTTGGAGTATTTGTGAATTATTTTTCCTGGTTGTAAGATATTAA
1 TTTGGTGTATTTGTGAATTATTTTTCCTAATTGTAAGATATTAA
*
2788858 TTTGGTGTATTTATGAATTATTTTT-CTAATTGTAAGATATTAA
1 TTTGGTGTATTTGTGAATTATTTTTCCTAATTGTAAGATATTAA
2788901 TTTGGTAG-ATTTGTGAATT
1 TTTGGT-GTATTTGTGAATT
2788920 TTAATTTGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
43 32 0.57
44 24 0.43
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (44 bp):
TTTGGTGTATTTGTGAATTATTTTTCCTAATTGTAAGATATTAA
Found at i:2794571 original size:21 final size:21
Alignment explanation
Indices: 2794542--2794594 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2794532 ATTCTGACTA
2794542 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2794563 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
2794584 TCGCAATGCGA
1 TCGCATTGCGA
2794595 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2795495 original size:24 final size:24
Alignment explanation
Indices: 2795468--2795521 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2795458 GTATTCGAAA
2795468 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2795492 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2795516 TTTGAT
1 TTTGAT
2795522 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2798093 original size:33 final size:33
Alignment explanation
Indices: 2798056--2798203 Score: 161
Period size: 33 Copynumber: 4.3 Consensus size: 33
2798046 GGAAATTACT
2798056 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * * * *
2798089 ATCGCAACGTGAAAATCACAACGCGAATATGAAT
1 ATCGCAACGAGAGAATCGCAATGCGAA-ATGAAA
*
2798123 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAAA
* *
2798162 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
2798195 ATCGCAACG
1 ATCGCAACG
2798204 CGAATTTAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
33 50 0.53
34 12 0.13
35 2 0.02
36 3 0.03
37 3 0.03
38 1 0.01
39 12 0.13
40 11 0.12
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:2798121 original size:20 final size:19
Alignment explanation
Indices: 2798069--2798207 Score: 109
Period size: 19 Copynumber: 7.7 Consensus size: 19
2798059 GCAACGAGAG
*
2798069 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2798088 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
*
2798102 AATCACAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
2798122 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
2798142 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
**
2798161 AATCGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
2798175 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2798194 AATCGCAACGCGAA
1 AATCGCAACGCGAA
2798208 TTTAATTTCG
Statistics
Matches: 96, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
14 20 0.21
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 36 0.38
20 27 0.28
21 3 0.03
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2798159 original size:73 final size:72
Alignment explanation
Indices: 2798070--2798205 Score: 209
Period size: 73 Copynumber: 1.9 Consensus size: 72
2798060 CAACGAGAGA
* * *
2798070 ATCGCAATGCGAAATGAAAATCGCAACGTGAAAATCACAACGCGAATATGAATATCGCAACGCGG
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAAAGCGAA-ATGAAAATCGCAACGCGG
2798135 AAATGACT
65 AAATGACT
** *
2798143 ATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCG
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAAAGCGAAATGAAAATCGCAACGCG
2798206 AATTTAATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
72 16 0.28
73 41 0.72
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.14
Consensus pattern (72 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAAAGCGAAATGAAAATCGCAACGCGGA
AATGACT
Found at i:2798225 original size:19 final size:19
Alignment explanation
Indices: 2798203--2798244 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2798193 AAATCGCAAC
*
2798203 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
2798222 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCATT
2798241 GCGA
1 GCGA
2798245 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:2798286 original size:19 final size:19
Alignment explanation
Indices: 2798212--2798278 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
2798202 CGCGAATTTA
*
2798212 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2798231 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
2798248 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
2798264 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
2798279 AGTCATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 7 0.17
19 20 0.50
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Done.