Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:255917 original size:27 final size:27
Alignment explanation
Indices: 255879--255930 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
255869 ATAATACCCT
255879 TTTTGAATTAATTCCCAAAATATCATA
1 TTTTGAATTAATTCCCAAAATATCATA
*
255906 TTTTGAATTAATTCCCATAATATCA
1 TTTTGAATTAATTCCCAAAATATCA
255931 CCTTTTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.42
Consensus pattern (27 bp):
TTTTGAATTAATTCCCAAAATATCATA
Found at i:255987 original size:29 final size:29
Alignment explanation
Indices: 255808--255991 Score: 133
Period size: 29 Copynumber: 6.3 Consensus size: 29
255798 CATTTTACAT
* * **
255808 AAATATCACCCCTTTTTAAAATAATAACCA
1 AAATAGCA-CCCTTTTTAAATTAATTCCCA
* *
255838 TAATAGCACCCTTTTTAAATTAATTACCA
1 AAATAGCACCCTTTTTAAATTAATTCCCA
** *
255867 AAATAATACCCTTTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAATTAATTCCCA
* *
255896 AAATATCA---TATTTTGAATTAATTCCCA
1 AAATAGCACCCT-TTTTAAATTAATTCCCA
* * ** *
255923 TAATATCA-CCTTTTTCGAAAAAAATTACCA
1 AAATAGCACCCTTTTT--AAATTAATTCCCA
* *
255953 AAATAGCACCCATTTCAAATTAATTCCCA
1 AAATAGCACCCTTTTTAAATTAATTCCCA
*
255982 GAATAGCACC
1 AAATAGCACC
255992 AAAATCGAAT
Statistics
Matches: 124, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.01
27 24 0.19
28 4 0.03
29 69 0.56
30 21 0.17
31 5 0.04
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (29 bp):
AAATAGCACCCTTTTTAAATTAATTCCCA
Found at i:256015 original size:29 final size:29
Alignment explanation
Indices: 255952--256015 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
255942 AAAAATTACC
* ** *
255952 AAAATAGCACCCATTTCAAATTAATTCCC
1 AAAATAGCACCAAAATCAAATTAATTCCA
* *
255981 AGAATAGCACCAAAATCGAATTAATTCCA
1 AAAATAGCACCAAAATCAAATTAATTCCA
256010 AAAATA
1 AAAATA
256016 TCTCCGGTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.23
Consensus pattern (29 bp):
AAAATAGCACCAAAATCAAATTAATTCCA
Found at i:257921 original size:18 final size:18
Alignment explanation
Indices: 257894--257933 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
257884 TTGAAAATAA
* *
257894 AAATGTCACATCATATAT
1 AAATGCCACATCATAGAT
257912 AAATGCCACATCATAGAT
1 AAATGCCACATCATAGAT
257930 AAAT
1 AAAT
257934 ATTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.28
Consensus pattern (18 bp):
AAATGCCACATCATAGAT
Found at i:257992 original size:31 final size:31
Alignment explanation
Indices: 257954--258024 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
257944 TAAATTATGA
257954 TGATTAAAATATGAATAA-T-TTAAAAGTTGAG
1 TGATTAAAATATGAA-AATTATTAAAA-TTGAG
*
257985 TGATT-AAAT-TGAAAATTATTAAAATTTAG
1 TGATTAAAATATGAAAATTATTAAAATTGAG
258014 TGATTAAAATA
1 TGATTAAAATA
258025 AGAGAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
28 2 0.06
29 14 0.40
30 14 0.40
31 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (31 bp):
TGATTAAAATATGAAAATTATTAAAATTGAG
Found at i:263326 original size:60 final size:61
Alignment explanation
Indices: 263255--263382 Score: 163
Period size: 60 Copynumber: 2.1 Consensus size: 61
263245 AGGATCATTA
* * * * * *
263255 TTTGA-GGATGAATTTAGAATGTTCAAAATTTTATGGA-TAGATTTAAACTGAGAGTGATAG
1 TTTGAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACCA-ATTTAAAATGAGAGTCATAG
*
263315 TTT-AGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAG
1 TTTGAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAG
263375 TTTGAGGG
1 TTTGAGGG
263383 CGTATAATGT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
59 1 0.02
60 52 0.90
61 5 0.09
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.34
Consensus pattern (61 bp):
TTTGAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAG
Found at i:265529 original size:2 final size:2
Alignment explanation
Indices: 265524--265557 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
265514 TTTTTATGTA
265524 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
265558 TAAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268822 original size:25 final size:25
Alignment explanation
Indices: 268788--268859 Score: 144
Period size: 25 Copynumber: 2.9 Consensus size: 25
268778 CATTGTGTTG
268788 AAGTTTGTATCATATAATAATATTT
1 AAGTTTGTATCATATAATAATATTT
268813 AAGTTTGTATCATATAATAATATTT
1 AAGTTTGTATCATATAATAATATTT
268838 AAGTTTGTATCATATAATAATA
1 AAGTTTGTATCATATAATAATA
268860 GAAAAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (25 bp):
AAGTTTGTATCATATAATAATATTT
Found at i:269650 original size:57 final size:57
Alignment explanation
Indices: 269559--269673 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
269549 GACATGGTGG
*
269559 AAGTTCAGTTTCAGTACCTGCAAGTGCATCTACACCATATCAGCACTGATTATGCCA
1 AAGTTCAGTTTCAGTACCTGCAAGTGCATATACACCATATCAGCACTGATTATGCCA
269616 AAGTTCAGTTTCAGTACCTGCAAGTGCATATACACCATATCAGCACTGATTATGCCA
1 AAGTTCAGTTTCAGTACCTGCAAGTGCATATACACCATATCAGCACTGATTATGCCA
269673 A
1 A
269674 GCTTCATTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (57 bp):
AAGTTCAGTTTCAGTACCTGCAAGTGCATATACACCATATCAGCACTGATTATGCCA
Found at i:271498 original size:20 final size:21
Alignment explanation
Indices: 271473--271516 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
271463 CACCTTACAT
* *
271473 ATTTTTAATAATTAAAAA-TA
1 ATTTTTAAAAATAAAAAATTA
271493 ATTTTTAAAAATAAAAAATTA
1 ATTTTTAAAAATAAAAAATTA
271514 ATT
1 ATT
271517 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTTTAAAAATAAAAAATTA
Found at i:279602 original size:36 final size:35
Alignment explanation
Indices: 279554--279692 Score: 190
Period size: 36 Copynumber: 3.9 Consensus size: 35
279544 TGAATAAGAA
*
279554 GAAC-GAAAGAAGCATCAGCACTTTCGATTCAAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTC-AAGT
* *
279589 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGAA
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAG-T
* * *
279625 GAACGAAAGGAAGCACCGGCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
*
279660 GAACGGAAGGAAGCGTCAGCACTTTCGATTCAA
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAA
279693 TTGTTCATCT
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
35 36 0.39
36 56 0.61
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:279633 original size:71 final size:71
Alignment explanation
Indices: 279549--279692 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 71
279539 GAAGGTGAAT
* *
279549 AAGAAGAACGAAA-GAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTT
1 AAGAAGAACGAAAGGAAGCACCAGCACTTTCGATTC-AAGTGAACGGAAGGAAGCATCAGCACTT
279613 TCGATTC
65 TCGATTC
* *
279620 AAGAAGAACGAAAGGAAGCACCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCGTCAGCACTTT
1 AAGAAGAACGAAAGGAAGCACCAGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTT
279685 CGATTC
66 CGATTC
279691 AA
1 AA
279693 TTGTTCATCT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 48 0.71
72 20 0.29
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCACCAGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTT
CGATTC
Found at i:283545 original size:43 final size:43
Alignment explanation
Indices: 283492--283644 Score: 220
Period size: 43 Copynumber: 3.6 Consensus size: 43
283482 TGGTAACAAA
* *
283492 AAACGCCGCAATAGGTGTTGATATTTGGCGGCATTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCAAC
*
283535 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAA-
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTT-CCAAC
*
283578 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC-AC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGC-ATTTTTCCAAC
* *
283621 AAACGTCGCAATAGGTCTTGAGAT
1 AAACGCCGCAATAGGTGTTGAGAT
283645 AATCCATTAT
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
42 1 0.01
43 91 0.90
44 9 0.09
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCAAC
Found at i:285948 original size:135 final size:132
Alignment explanation
Indices: 285693--285960 Score: 509
Period size: 135 Copynumber: 2.0 Consensus size: 132
285683 ATGCACAAAA
285693 AGGCATTAGCCTGTGTGAACTGCAATATGTATGTGTGAGGGTTATATGTGTCTATGTGTGTATAT
1 AGGCATTAGCCTGTGTGAACTGCAATATGTATGTGTGAGGGTTATATGTGTCTATGTGTGTATAT
285758 GGCTATTGTATGGTAGTGTAGTCTATCTACAAAACATACAATCTTTTATATCAGTCAAATAACCA
66 GGCTATTGTATGGTAGTGTAGTCTATCTACAAAACATACAATCTTTTATATCAGTCAAATAACCA
285823 AT
131 AT
285825 AGGCATTAGCCTGTGTGAACTGCAATATGTATGTGTGAGGGTTATATGGTGTCTATGTGTGTATA
1 AGGCATTAGCCTGTGTGAACTGCAATATGTATGTGTGAGGGTTATAT-GTGTCTATGTGTGTATA
285890 TGGCTATTGTATGGTCTAGTGTAGTCTATCTACAAAACATACAATCTTTTATATCAGTCAAATAA
65 TGGCTATTGTATGG--TAGTGTAGTCTATCTACAAAACATACAATCTTTTATATCAGTCAAATAA
285955 CCAAT
128 CCAAT
285960 A
1 A
285961 TCAATATGTG
Statistics
Matches: 133, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
132 47 0.35
133 31 0.23
135 55 0.41
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.36
Consensus pattern (132 bp):
AGGCATTAGCCTGTGTGAACTGCAATATGTATGTGTGAGGGTTATATGTGTCTATGTGTGTATAT
GGCTATTGTATGGTAGTGTAGTCTATCTACAAAACATACAATCTTTTATATCAGTCAAATAACCA
AT
Found at i:288531 original size:19 final size:20
Alignment explanation
Indices: 288488--288531 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
288478 AAACGGCGAA
*
288488 GAGGAGAGGTGGATTGGGAG
1 GAGGAGAGGTGGATCGGGAG
*
288508 G-GGAGAGGT-GATCGGGTG
1 GAGGAGAGGTGGATCGGGAG
288526 GAGGAG
1 GAGGAG
288532 GGAGCAGCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 8 0.38
19 12 0.57
20 1 0.05
ACGTcount: A:0.23, C:0.02, G:0.61, T:0.14
Consensus pattern (20 bp):
GAGGAGAGGTGGATCGGGAG
Found at i:288993 original size:83 final size:83
Alignment explanation
Indices: 288880--289325 Score: 592
Period size: 83 Copynumber: 5.4 Consensus size: 83
288870 TATGACAATT
*
288880 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAGCGC
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGC
288944 CACAAAAGTACATGTCTATA
64 CACAAAAGTACATGTCTATA
* *
288964 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACTAATCTATAGCGGCGTTTGGTATTAAAACGCCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
* *
289029 TAAAAGTACGTGTCTATA
66 CAAAAGTACATGTCTATA
* *
289047 GCGGCGTTTGTGTAAAAAAGCCACTAAAGTACGTGTCTATAGCGGCGTTTGGTATTAAAACGCCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
289112 CAAAAGTACATGTCTATA
66 CAAAAGTACATGTCTATA
* *
289130 GCGGCGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAATGCCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
*
289195 CAAAAGTACGTGTCTATA
66 CAAAAGTACATGTCTATA
*** * * * * * * *
289213 GCATTGTTTGTATAAAAACGCCACTAAAATACTAGTTTATAGCGGCGTTT-ATATAAAAATGCCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
* * * *
289277 CTACATTACGAT-TCTTTA
66 CAAAAGTAC-ATGTCTATA
* * * *
289295 GCGGCGTTTTTATACAAATGCCACTAAAGTA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTA
289326 TAGTATTTTG
Statistics
Matches: 323, Mismatches: 37, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
82 47 0.15
83 263 0.81
84 10 0.03
85 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (83 bp):
GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
CAAAAGTACATGTCTATA
Found at i:289003 original size:41 final size:41
Alignment explanation
Indices: 288880--289356 Score: 431
Period size: 41 Copynumber: 11.5 Consensus size: 41
288870 TATGACAATT
*
288880 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTACTAGTCTATA
* *
288922 GCGGCGTTTG-GTATTAAAGCGCCACAAAAGTAC-ATGTCTATA
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTACTA-GTCTATA
*
288964 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACTAATCTATA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACTAGTCTATA
289005 GCGGCGTTTG-GTATTAAAACGCCA-TAAAAGTACGT-GTCTATA
1 GCGGCGTTTGTGTA--AAAACGCCACT-AAAGTAC-TAGTCTATA
*
289047 GCGGCGTTTGTGTAAAAAAGCCACTAAAGTACGT-GTCTATA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTAC-TAGTCTATA
*
289088 GCGGCGTTTG-GTATTAAAACGCCACAAAAGTAC-ATGTCTATA
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTACTA-GTCTATA
* *
289130 GCGGCGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACTAGTCTATA
* *
289171 GCGGCGTTTG-GTATTAAAATGCCACAAAAGTACGT-GTCTATA
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTAC-TAGTCTATA
*** * * *
289213 GCATTGTTTGTATAAAAACGCCACTAAAATACTAGTTTATA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACTAGTCTATA
* * * * * * * *
289254 GCGGCGTTTATATAAAAATGCCACTACATTACGATTCTTTA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACTAGTCTATA
* * * * * * *
289295 GCGGCGTTTTTATACAAATGCCACTAAAGTA-TAGTATTTT
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACTAGTCTATA
289335 GCGGCGTTTGT-TCAAAAACGCC
1 GCGGCGTTTGTGT-AAAAACGCC
289357 GCTATATTTA
Statistics
Matches: 371, Mismatches: 43, Indels: 44
0.81 0.09 0.10
Matches are distributed among these distances:
39 1 0.00
40 32 0.09
41 179 0.48
42 147 0.40
43 12 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTGTAAAAACGCCACTAAAGTACTAGTCTATA
Found at i:290329 original size:27 final size:27
Alignment explanation
Indices: 290279--290330 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
290269 AGAATGAAAC
* *
290279 GTTAGGCATCAAACTGATACAAAAAAA
1 GTTAGACATCAAACTGATAAAAAAAAA
*
290306 GTTAGACATCAAACT-AGAAAAAAAA
1 GTTAGACATCAAACTGATAAAAAAAA
290331 TATACGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.17
Consensus pattern (27 bp):
GTTAGACATCAAACTGATAAAAAAAAA
Found at i:290566 original size:30 final size:29
Alignment explanation
Indices: 290511--290597 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 29
290501 TTTTTAATTA
* * *
290511 AAGA-CTAAAATGTAAAAATTAAAAGTTT
1 AAGAGCTAAAGTGTAAACATTGAAAGTTT
* *
290539 ACGAGGTTAAAGTGTAAACATTGAAAGTTT
1 AAGA-GCTAAAGTGTAAACATTGAAAGTTT
* *
290569 AAGAGCTAAAGTATGAACATTGAAAGTTT
1 AAGAGCTAAAGTGTAAACATTGAAAGTTT
290598 TGGTACTTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.06
29 22 0.46
30 23 0.48
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (29 bp):
AAGAGCTAAAGTGTAAACATTGAAAGTTT
Found at i:290587 original size:29 final size:30
Alignment explanation
Indices: 290523--290597 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
290513 GACTAAAATG
* * * * *
290523 TAAAAATTAAAAGTTTACGAGGTTAAAGTG
1 TAAACATTGAAAGTTTAAGAGGCTAAAGTA
290553 TAAACATTGAAAGTTTAAGA-GCTAAAGTA
1 TAAACATTGAAAGTTTAAGAGGCTAAAGTA
*
290582 TGAACATTGAAAGTTT
1 TAAACATTGAAAGTTT
290598 TGGTACTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (30 bp):
TAAACATTGAAAGTTTAAGAGGCTAAAGTA
Found at i:291494 original size:14 final size:14
Alignment explanation
Indices: 291472--291540 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
291462 GACCCGCCTG
*
291472 GTCCAAGTCAACTC
1 GTCCGAGTCAACTC
*
291486 GTCCGAGTCAATTC
1 GTCCGAGTCAACTC
* *
291500 GATCTGAGTCAACAC
1 G-TCCGAGTCAACTC
* *
291515 ATCTGAGTCAACTC
1 GTCCGAGTCAACTC
*
291529 ATCCGAGTCAAC
1 GTCCGAGTCAAC
291541 CCGTTGACTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
14 36 0.78
15 10 0.22
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (14 bp):
GTCCGAGTCAACTC
Found at i:291510 original size:29 final size:28
Alignment explanation
Indices: 291477--291540 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
291467 GCCTGGTCCA
* * * *
291477 AGTCAACTCGTCCGAGTCAATTCGATCTG
1 AGTCAACACATCCGAGTCAACTC-ATCCG
*
291506 AGTCAACACATCTGAGTCAACTCATCCG
1 AGTCAACACATCCGAGTCAACTCATCCG
291534 AGTCAAC
1 AGTCAAC
291541 CCGTTGACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
AGTCAACACATCCGAGTCAACTCATCCG
Found at i:300847 original size:21 final size:22
Alignment explanation
Indices: 300823--300877 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
300813 CCCCTTGCTA
300823 TGTATCGATACA-CCTTGAATG
1 TGTATCGATACATCCTTGAATG
*
300844 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACA-TCCTTGAATG
300867 TGTATCGATAC
1 TGTATCGATAC
300878 CTCTTGAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 11 0.37
23 19 0.63
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (22 bp):
TGTATCGATACATCCTTGAATG
Found at i:301183 original size:16 final size:16
Alignment explanation
Indices: 301162--301192 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
301152 TAATATATGA
*
301162 CTAGTTTTAATTAGTT
1 CTAGTTTGAATTAGTT
301178 CTAGTTTGAATTAGT
1 CTAGTTTGAATTAGT
301193 GATCAGGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (16 bp):
CTAGTTTGAATTAGTT
Found at i:303110 original size:13 final size:13
Alignment explanation
Indices: 303081--303115 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
303071 GGGAGTAATT
*
303081 TTTTCAAAATTGA
1 TTTTCAAAAATGA
303094 -TTTCAAAAATGA
1 TTTTCAAAAATGA
303106 TTTTCAAAAA
1 TTTTCAAAAA
303116 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:303248 original size:19 final size:20
Alignment explanation
Indices: 303211--303249 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
303201 AGTGTTAATG
*
303211 AATTTTAAGATTTTATATTC
1 AATTTTAAGATTATATATTC
303231 AATTTTAA-ATTATATATTC
1 AATTTTAAGATTATATATTC
303250 GATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTTTAAGATTATATATTC
Found at i:306541 original size:2 final size:2
Alignment explanation
Indices: 306534--306565 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
306524 GATGAAAATA
306534 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
306566 GCTACTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:307244 original size:3 final size:3
Alignment explanation
Indices: 307236--307338 Score: 181
Period size: 3 Copynumber: 34.7 Consensus size: 3
307226 AAGCCTGTAA
* *
307236 AAT AAT AAT AAT AAT AAT TA- AAT AGT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
307283 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
307331 AAT AAT AA
1 AAT AAT AA
307339 AGAGGGGTCC
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 1 0.01
3 94 0.99
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:307816 original size:134 final size:134
Alignment explanation
Indices: 307535--308035 Score: 634
Period size: 134 Copynumber: 3.8 Consensus size: 134
307525 TCCACTGTTT
*
307535 TTCAAGGAAGATTGAATCAGAA-TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAG
1 TTCAGGGAAGATTGAATC-GAATTCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAG
* * * * *
307599 AAGAA-TATTTGCTCCACTACTCTTTAGGGGAGATTAGACTCGAGGAAACTTTTATCCACTTCAC
65 AAGAAGAATTTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCAC
**
307663 TATTC
130 TGCTC
* *
307668 TTCAGGGAAGATTGAATCGGAA-TCGATTTGCTTTACTGCTCTTCAGGAAGACCAAATCTGAAAA
1 TTCAGGGAAGATTGAATC-GAATTCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAG
**
307732 AAGAAGCGTCTT-CTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCA
65 AAGAAGAAT-TTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCA
307796 CTGCTC
129 CTGCTC
* * * * * *
307802 TTCAGGGAAGATTGAATTGAATTTGATTTGCTTCGCTACTCTTCAGGAAAACCATATCTGAAAGA
1 TTCAGGGAAGATTGAATCGAATTCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGA
* * * * *
307867 AGAAGAATTTGCTCCGCTATTCTTTAGAGGAGATCAGACTCGAGAAAATTTTGATCAACTTCACT
66 AGAAGAATTTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCACT
307932 GCTC
131 GCTC
* * * ** *
307936 TTCAGGGAAGACTGAATCGAATTTGATTCGCTTCGTTGCTCTTCAGGAATACCAAATCTGAAAGA
1 TTCAGGGAAGATTGAATCGAATTCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGA
* * ** *
308001 AGAAAAATATGCTCTGCTACTCTTTA-GAGAGATCA
66 AGAAGAATTTGCTCCACTACTCTTTAGGGGAGATCA
308036 AGAATAAAAA
Statistics
Matches: 324, Mismatches: 40, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
133 77 0.24
134 245 0.76
135 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (134 bp):
TTCAGGGAAGATTGAATCGAATTCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGA
AGAAGAATTTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCACT
GCTC
Found at i:308075 original size:38 final size:38
Alignment explanation
Indices: 308033--308391 Score: 569
Period size: 38 Copynumber: 9.4 Consensus size: 38
308023 TTTAGAGAGA
* * *
308033 TCAAGAATAAAAAAGATTGACTTCTCTTAACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
* * * *
308071 TCAAGAATAAAAAAGCTCAACTTCTCTTCATGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
*
308109 TCAAGAATAACAAAGATCGACTTCGCTTCACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
308147 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
308185 TCAAGAATAA-AAATGATCGACTTCTCTTCACGAGGAAG
1 TCAAGAATAACAAA-GATCGACTTCTCTTCACGAGGAAG
308223 TCAAGAATAACAAAGA-CTGACTTCTCTTCACGAGGAAG
1 TCAAGAATAACAAAGATC-GACTTCTCTTCACGAGGAAG
* * *
308261 TCAAGAATAACGAAGATCAACTTCTCTTCATGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
*
308299 TCAAGAATAACAAAGATCAACTTCTCTTCACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
308337 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
*
308375 TCAAGAATAATAAAGAT
1 TCAAGAATAACAAAGAT
308392 ATTTTTCCTT
Statistics
Matches: 299, Mismatches: 18, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
37 4 0.01
38 291 0.97
39 4 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (38 bp):
TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
Found at i:309978 original size:24 final size:22
Alignment explanation
Indices: 309945--309996 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
309935 AAATCAACAA
* *
309945 TTTTTCAAATAAAATTCATAATTG
1 TTTTTTAAATAAAA-T-AAAATTG
*
309969 TTTTTTAAATAATATAAAATTG
1 TTTTTTAAATAAAATAAAATTG
309991 TTTTTT
1 TTTTTT
309997 TAAAATGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.48
23 1 0.04
24 12 0.48
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTTTTAAATAAAATAAAATTG
Found at i:311207 original size:37 final size:36
Alignment explanation
Indices: 311111--311226 Score: 157
Period size: 35 Copynumber: 3.3 Consensus size: 36
311101 GGCAACCAAC
* * *
311111 TTTG-AAAATGATTTTCAAAATTTGGTAAATGTTTC
1 TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTT
311146 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTT
*
311181 TTTGAAAAATGGTTTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTTT
*
311217 GTTGAAAAAT
1 TTTGAAAAAT
311227 TGTAATGGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 36 0.49
36 19 0.26
37 19 0.26
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (36 bp):
TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTT
Found at i:315716 original size:21 final size:21
Alignment explanation
Indices: 315692--315752 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
315682 CCAACTTTGA
315692 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
315713 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
315727 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
315748 AAATG
1 AAATG
315753 TCTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:315730 original size:35 final size:35
Alignment explanation
Indices: 315686--315800 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
315676 TGGCAACCAA
315686 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
315721 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTCT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
315756 CTTTGAAAAATGGGTTTTCAAAGTTTGGCAGATGTTT
1 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
315793 -GTTGAAAA
1 CTTTGAAAA
315801 ATTGTAATGG
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 43 0.59
36 8 0.11
37 22 0.30
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.42
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:317826 original size:13 final size:13
Alignment explanation
Indices: 317808--317838 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
317798 TTTGTTTCTG
317808 TGGGATCTATCTT
1 TGGGATCTATCTT
317821 TGGGATCTATCTT
1 TGGGATCTATCTT
317834 TGGGA
1 TGGGA
317839 GTATTTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (13 bp):
TGGGATCTATCTT
Found at i:318419 original size:17 final size:17
Alignment explanation
Indices: 318399--318432 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
318389 ATAATTTTTG
*
318399 AAAATAAAAAATTAATT
1 AAAATAAAAAAATAATT
318416 AAAATAAAAAAATAATT
1 AAAATAAAAAAATAATT
318433 TCTTTCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATAAAAAAATAATT
Found at i:320563 original size:3 final size:3
Alignment explanation
Indices: 320555--320611 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
320545 AAATATAAAT
320555 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
320603 TAA TAA TAA
1 TAA TAA TAA
320612 AACTCGAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:321009 original size:138 final size:136
Alignment explanation
Indices: 320793--321088 Score: 394
Period size: 138 Copynumber: 2.2 Consensus size: 136
320783 TAGGTAAATT
* * * * * *
320793 TGGAAATAATACGGTTCCTACATGGTGAGGAAATTTGGTTATCTAAGGGTGACGCGGCTCCTACG
1 TGGAGATAACACGGTTCCTACGTGATGAGGAAATTTGGTTATCCAAGGGTGACGCGGCTCCTACA
* * * * * *
320858 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTGCGTGATGAGGACGTCTTGCCATCTTTA
66 CGATGAGGAGATCTGATCGGTGGATGACACAGTTCCTACATGATGAGGACGTCTGGCCATCTTT-
320923 AGGATAAA
130 AGGAT-AA
* * * * ** *
320931 TGGAGATAACATGGTTCCTACGTGATGAGGAAGTTTGGTTATCCAATGGTGATGTTGTTCCTACA
1 TGGAGATAACACGGTTCCTACGTGATGAGGAAATTTGGTTATCCAAGGGTGACGCGGCTCCTACA
320996 CGATGAGGAGATCTGATCGGTGGATGACACAGTTCCTACATGATGAGGACGTCTGGCCATCTTTA
66 CGATGAGGAGATCTGATCGGTGGATGACACAGTTCCTACATGATGAGGACGTCTGGCCATCTTTA
321061 GGATAA
131 GGATAA
*
321067 TGGAGATAACACAGTTCCTACG
1 TGGAGATAACACGGTTCCTACG
321089 CTAAAAGTCT
Statistics
Matches: 137, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
136 22 0.16
137 5 0.04
138 110 0.80
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (136 bp):
TGGAGATAACACGGTTCCTACGTGATGAGGAAATTTGGTTATCCAAGGGTGACGCGGCTCCTACA
CGATGAGGAGATCTGATCGGTGGATGACACAGTTCCTACATGATGAGGACGTCTGGCCATCTTTA
GGATAA
Found at i:331004 original size:21 final size:21
Alignment explanation
Indices: 330980--331054 Score: 89
Period size: 23 Copynumber: 3.5 Consensus size: 21
330970 CCCCTTGCTA
330980 TGTATCGATACTCCTTGAATG
1 TGTATCGATACTCCTTGAATG
*
331001 TGTACCGATACATTCCTTGAATG
1 TGTATCGATAC--TCCTTGAATG
* *
331024 TGTATCGATACCCCTTG-AGG
1 TGTATCGATACTCCTTGAATG
*
331044 GGTATCGATAC
1 TGTATCGATAC
331055 CCCCTATCGG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.26
21 15 0.32
23 20 0.43
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (21 bp):
TGTATCGATACTCCTTGAATG
Found at i:331341 original size:16 final size:16
Alignment explanation
Indices: 331320--331350 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
331310 TAACATATGA
*
331320 CTAGTTTTAATTAGTT
1 CTAGTTTGAATTAGTT
331336 CTAGTTTGAATTAGT
1 CTAGTTTGAATTAGT
331351 GATCAGGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (16 bp):
CTAGTTTGAATTAGTT
Found at i:336242 original size:7 final size:7
Alignment explanation
Indices: 336226--336274 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
336216 AAATATCACC
336226 TTTTTCA
1 TTTTTCA
*
336233 TTTTTTA
1 TTTTTCA
336240 TTTTTCCA
1 TTTTT-CA
*
336248 TTTTTTA
1 TTTTTCA
336255 TTTTTCCA
1 TTTTT-CA
*
336263 TTTTTTA
1 TTTTTCA
336270 TTTTT
1 TTTTT
336275 AAAGAGAGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 23 0.66
8 12 0.34
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:336249 original size:15 final size:15
Alignment explanation
Indices: 336226--336274 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
336216 AAATATCACC
336226 TTTTT-CATTTTTTA
1 TTTTTCCATTTTTTA
336240 TTTTTCCATTTTTTA
1 TTTTTCCATTTTTTA
336255 TTTTTCCATTTTTTA
1 TTTTTCCATTTTTTA
336270 TTTTT
1 TTTTT
336275 AAAGAGAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 5 0.15
15 29 0.85
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCCATTTTTTA
Found at i:337415 original size:3 final size:3
Alignment explanation
Indices: 337407--337469 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
337397 CCTGTAAGAA
* * *
337407 AAT AAT AAT AAT AAT AAT AAT AAT TA- AAT AGT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
337454 AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AA
337470 AGACGAGTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 3 0.06
3 49 0.94
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:337442 original size:26 final size:26
Alignment explanation
Indices: 337406--337469 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
337396 ACCTGTAAGA
337406 AAATAATAATAATAATAATAATAATT
1 AAATAATAATAATAATAATAATAATT
* *
337432 AAATAGTAATAATAATAATATTAA-T
1 AAATAATAATAATAATAATAATAATT
337457 -AATAATAA-AATAA
1 AAATAATAATAATAA
337470 AGACGAGTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.14
24 7 0.20
25 1 0.03
26 22 0.63
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAATAATAATAATAATAATAATAATT
Found at i:337448 original size:32 final size:32
Alignment explanation
Indices: 337407--337468 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
337397 CCTGTAAGAA
*
337407 AATAATAATAATAATAATAATAATTAAATAGT
1 AATAATAATAATAATAATAATAATAAAATAGT
*
337439 AATAATAATAATATTAATAATAATAAAATA
1 AATAATAATAATAATAATAATAATAAAATA
337469 AAGACGAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (32 bp):
AATAATAATAATAATAATAATAATAAAATAGT
Found at i:338160 original size:134 final size:134
Alignment explanation
Indices: 337671--338167 Score: 624
Period size: 134 Copynumber: 3.7 Consensus size: 134
337661 TGTTTGTCAA
* * * *
337671 GGAATATTGAATCAGAA-TCGATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAA
1 GGAAGATTGAATC-GAATTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAA
* * * * * **
337735 TAATTTGCTCCACTACTCTTTAGGGGAGATTAGACTCGAGGAAACTTTGATCCACTTCACTATTC
65 GAATTTGCTCCACTACTCTTTAGAGGAGATCAGACTCGAGAAAAATTTGATCCACTTCACTGCTC
337800 TTCAG
130 TTCAG
* * ** *
337805 GGAAGATTGAATCGAAATCGATTTGCTTTACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAA-
1 GGAAGATTGAATCGAATTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
* * * *
337869 ACGTCTT-CTCCACTACTCTTTTGGGGAGATTAGACTCGAGAAAAATTTGATCCACTTCACTGCT
66 A-AT-TTGCTCCACTACTCTTTAGAGGAGATCAGACTCGAGAAAAATTTGATCCACTTCACTGCT
*
337933 CTTCAA
129 CTTCAG
* * *
337939 GGAAGATTGAATCGAATTTGATTTACTTCGCTGCTCTTCAGGAAGACCATATCTGAAAGAATAAG
1 GGAAGATTGAATCGAATTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
** * *
338004 AATTTGCTCTGCTATTCTTTAGAGGAGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCT
66 AATTTGCTCCACTACTCTTTAGAGGAGATCAGACTCGAGAAAAATTTGATCCACTTCACTGCTCT
338069 TCAG
131 TCAG
* * * * *
338073 GGAAGACTGAATCGAATTTGATTCGCTTCGTTGCTTTTCAGGAATACCAAATCTGAAAGAAGAAG
1 GGAAGATTGAATCGAATTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
* *
338138 AATTTTCTCCGCTACTCTTTAGA-GAGATCA
66 AATTTGCTCCACTACTCTTTAGAGGAGATCA
338168 AGAATAAAAA
Statistics
Matches: 319, Mismatches: 39, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
133 13 0.04
134 303 0.95
135 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (134 bp):
GGAAGATTGAATCGAATTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
AATTTGCTCCACTACTCTTTAGAGGAGATCAGACTCGAGAAAAATTTGATCCACTTCACTGCTCT
TCAG
Found at i:338227 original size:38 final size:38
Alignment explanation
Indices: 338165--338486 Score: 500
Period size: 38 Copynumber: 8.4 Consensus size: 38
338155 TTTAGAGAGA
* * * *
338165 TCAAGAATAAAAAAAGATTGACTTCTCTTAACGAGAAAG
1 TCAAGAAT-AACAAAGATCGACTTCTCTTCACGAGGAAG
*
338204 TCAAGAATAACAAAGATCAACTTCTCTTCACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
* *
338242 TCAAGAATAACCAAGATCGACTTCGCTTCACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
*
338280 TCAAGAATAACAAAGATCGACTTCTCTTAACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
* *
338318 TCAAAAATAACAAAGATCGACTTCTCTTCATGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
* *
338356 TCAAGAATAAAAAAGATCGACTTCTCTTCACGAGAAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
* *
338394 TTAAGAATAACAAAGACCGACTTCTCTTCACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
338432 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
1 TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
*
338470 TCAAGAATAATAAAGAT
1 TCAAGAATAACAAAGAT
338487 ATTTTTCCTT
Statistics
Matches: 258, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
38 250 0.97
39 8 0.03
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (38 bp):
TCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAG
Found at i:340037 original size:21 final size:21
Alignment explanation
Indices: 340013--340056 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
340003 AATTTAATAC
*
340013 AAAA-TCATCATTTTTTCAAAT
1 AAAATTCATAATTTTTT-AAAT
340034 AAAATTCATAATTTTTTAAAT
1 AAAATTCATAATTTTTTAAAT
340055 AA
1 AA
340057 TATAAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTCATAATTTTTTAAAT
Found at i:340070 original size:22 final size:22
Alignment explanation
Indices: 340045--340100 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
340035 AAATTCATAA
340045 TTTTTTAAATAATATAAAATTG
1 TTTTTTAAATAATATAAAATTG
340067 TTTTTTAAATAATATAAAATTG
1 TTTTTTAAATAATATAAAATTG
*
340089 TTTTTCAAATAA
1 TTTTTTAAATAA
340101 AATTGTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTTTTAAATAATATAAAATTG
Found at i:340078 original size:17 final size:19
Alignment explanation
Indices: 340058--340109 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
340048 TTTAAATAAT
*
340058 ATAAAATTGTTTTTTAAATAA
1 ATAAAATTG-TTTTTCAAT-A
340079 TATAAAATTGTTTTTC-A-A
1 -ATAAAATTGTTTTTCAATA
340097 ATAAAATTGTTTT
1 ATAAAATTGTTTT
340110 AAAATTGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 13 0.45
18 1 0.03
20 1 0.03
21 5 0.17
22 9 0.31
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (19 bp):
ATAAAATTGTTTTTCAATA
Found at i:340114 original size:16 final size:17
Alignment explanation
Indices: 340080--340114 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
340070 TTTAAATAAT
*
340080 ATAAAATTGTTTTTCAA
1 ATAAAATTGTTTTTAAA
340097 ATAAAATTG-TTTTAAA
1 ATAAAATTGTTTTTAAA
340113 AT
1 AT
340115 TGTTGTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (17 bp):
ATAAAATTGTTTTTAAA
Found at i:342858 original size:38 final size:38
Alignment explanation
Indices: 342803--342888 Score: 163
Period size: 38 Copynumber: 2.3 Consensus size: 38
342793 TTGCATTAAT
*
342803 TATGGTGTTGCAGCATTAGAGAAACTCTATATATCTTA
1 TATGGTGTTGCAACATTAGAGAAACTCTATATATCTTA
342841 TATGGTGTTGCAACATTAGAGAAACTCTATATATCTTA
1 TATGGTGTTGCAACATTAGAGAAACTCTATATATCTTA
342879 TATGGTGTTG
1 TATGGTGTTG
342889 TAATGGTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (38 bp):
TATGGTGTTGCAACATTAGAGAAACTCTATATATCTTA
Found at i:345312 original size:11 final size:11
Alignment explanation
Indices: 345283--345316 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
345273 TATTTAGTTA
*
345283 TTTATTTATTT
1 TTTATTTTTTT
*
345294 ATTATTTTTTT
1 TTTATTTTTTT
345305 TTTATTTTTTT
1 TTTATTTTTTT
345316 T
1 T
345317 ATAGGCCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:351348 original size:61 final size:61
Alignment explanation
Indices: 351253--351424 Score: 272
Period size: 61 Copynumber: 2.8 Consensus size: 61
351243 ACATAATCTC
* *
351253 TTGCATCTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAATAACT
1 TTGCAACTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACT
* * *
351314 TTGCAGCTTTCAGAGTCAATTTCAACTTCACAACGAAGAATATTGGACTCAACAAACAACT
1 TTGCAACTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACT
* * *
351375 TTCCAACTTTTAGAGTCAATTTCAACTTCACAACGAAAGATATTGAACTC
1 TTGCAACTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
351425 GAAAGAGATG
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 101 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.30
Consensus pattern (61 bp):
TTGCAACTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACT
Found at i:351748 original size:36 final size:36
Alignment explanation
Indices: 351726--351985 Score: 358
Period size: 36 Copynumber: 7.2 Consensus size: 36
351716 AATTTACTCA
* *
351726 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
*
351762 AAACAAATTTTTTCTCTCTTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
*
351798 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
* * *
351834 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCATTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
* * * **
351870 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
* * * *
351906 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAATTTCCCTTG
*
351943 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
351979 AAACAAA
1 AAACAAA
351986 ATCTTTGAAT
Statistics
Matches: 203, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
36 172 0.85
37 31 0.15
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
Found at i:351782 original size:21 final size:21
Alignment explanation
Indices: 351758--351855 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 21
351748 GACAGTTTCC
351758 CTTGAAACAAATTTTTTCTCT
1 CTTGAAACAAATTTTTTCTCT
*
351779 CTTGAGAC-AA---TTTC-C-
1 CTTGAAACAAATTTTTTCTCT
*
351794 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTTTCTCT
* *
351815 CTTGAGAC--A--GTTTC-C-
1 CTTGAAACAAATTTTTTCTCT
*
351830 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTTTCTCT
351851 CTTGA
1 CTTGA
351856 GATAGTTTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 24
0.63 0.10 0.27
Matches are distributed among these distances:
15 14 0.25
16 4 0.07
17 8 0.14
19 7 0.12
20 4 0.07
21 19 0.34
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (21 bp):
CTTGAAACAAATTTTTTCTCT
Found at i:351810 original size:72 final size:72
Alignment explanation
Indices: 351726--351985 Score: 403
Period size: 72 Copynumber: 3.6 Consensus size: 72
351716 AATTTACTCA
* * *
351726 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAATT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
351791 TCCCTTG
66 TCCCTTG
*
351798 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
*
351863 TCCATTG
66 TCCCTTG
* * ** * *
351870 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGT
*
351935 TTCTCTTG
65 TTCCCTTG
351943 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
351986 ATCTTTGAAT
Statistics
Matches: 167, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
72 104 0.62
73 63 0.38
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
TCCCTTG
Found at i:351959 original size:109 final size:108
Alignment explanation
Indices: 351726--351985 Score: 403
Period size: 109 Copynumber: 2.4 Consensus size: 108
351716 AATTTACTCA
* ** *
351726 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAATT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAATT
351791 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
66 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
351834 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGACAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAATT
** * * *
351899 TCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
66 TCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
351943 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
351986 ATCTTTGAAT
Statistics
Matches: 137, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
108 66 0.48
109 71 0.52
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (108 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAATT
TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:352078 original size:138 final size:140
Alignment explanation
Indices: 351726--352085 Score: 453
Period size: 138 Copynumber: 2.6 Consensus size: 140
351716 AATTTACTCA
* * ** * * *
351726 AAACAAAGTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTTTCTCTCTTGAGACAA
1 AAACAAA-TTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAA
** * *
351789 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTT
65 AGTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-----TATCTCTT
351854 GAGATAGTTTCCATTG
125 GAGATAGTTTCCATTG
* **
351870 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAAA
*
351935 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-ATCT-TTGA-ATA
66 GTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATCTCTTGAGATA
351997 TGTTTTCC-TTG
131 -G-TTTCCATTG
* *
352008 GAACAAATTTCGTTTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAAA
1 AAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAAA
352073 GTCTCTTGAAACA
66 GTCTCTTGAAACA
352086 CCAATGTTTG
Statistics
Matches: 197, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
137 3 0.02
138 80 0.41
139 8 0.04
143 3 0.02
144 32 0.16
145 71 0.36
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (140 bp):
AAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAAA
GTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATCTCTTGAGATA
GTTTCCATTG
Found at i:352224 original size:35 final size:33
Alignment explanation
Indices: 352138--352258 Score: 152
Period size: 33 Copynumber: 3.6 Consensus size: 33
352128 TCTAGAGACA
* * *
352138 GTTTCTCTTGAAACAAAAAAAACTTTTGAACTC
1 GTTTCTCTTGAAACAAAAAAAACCTTTGAAATT
352171 GTTTCTCTTGAAACAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACAAAAAAAACCTTTGAAATT
* * *
352204 GTTTCTCTCGAAACAAAAAAAAAACCTTTAAAAAT
1 GTTTCTCTTGAAAC--AAAAAAAACCTTTGAAATT
* *
352239 GTTTCTCTTGTAACACAAAA
1 GTTTCTCTTGAAACAAAAAA
352259 GCCTTTAAGT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
33 48 0.62
35 29 0.38
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.31
Consensus pattern (33 bp):
GTTTCTCTTGAAACAAAAAAAACCTTTGAAATT
Found at i:352415 original size:84 final size:83
Alignment explanation
Indices: 352256--352415 Score: 257
Period size: 84 Copynumber: 1.9 Consensus size: 83
352246 TTGTAACACA
* **
352256 AAAGCCTTTAAGTTCGACTACGCTCAGCTCCAAGGCATGTCATTTGCAGCATAACTCAAGGCTAG
1 AAAGCCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAG
*
352321 AAGAGTTATCTGCCAACC
66 AAGAGCTATCTGCCAACC
*
352339 AAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTA
1 AAAG-CCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTA
*
352404 GAAGGGCTATCT
65 GAAGAGCTATCT
352416 ATCTATAACA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
83 4 0.06
84 66 0.94
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (83 bp):
AAAGCCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAG
AAGAGCTATCTGCCAACC
Found at i:354421 original size:13 final size:14
Alignment explanation
Indices: 354397--354425 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
354387 TAGGTAATGA
354397 CGGTAGAAAAAATC
1 CGGTAGAAAAAATC
354411 CGGTA-AAAAAATC
1 CGGTAGAAAAAATC
354424 CG
1 CG
354426 AATTCGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (14 bp):
CGGTAGAAAAAATC
Found at i:354592 original size:409 final size:408
Alignment explanation
Indices: 353784--354593 Score: 1442
Period size: 408 Copynumber: 2.0 Consensus size: 408
353774 CCCTTTTTTT
* * *
353784 AAATACCTTCAGTGACCGAAAATACTTTATAATATACGATTTTAACCAATTTTTTTTGGATTTGC
1 AAATAACTTCAGTGACCGAAAATACTTTATAATATACGATTTTAACCAACTTTTTTTAGATTTGC
353849 AAAAATAACCAACAAATTCGCAACGCGAACTCCTATTTCGCAACGCTAATTACCGACATTGGTAA
66 AAAAATAACCAACAAATTCGCAACGCGAACTCCTATTTCGCAACGCTAATTACCGACATTGGTAA
* * *
353914 ACACAACTATCGCAACACGAATTTCGCAAATCGAATTCGTCAATTTTGAAACTTAATTACCGATA
131 ACACAACTATCGCAACACGAATTTCACAAATCGAATTCATCAATTTCGAAACTTAATTACCGATA
*
353979 TAGGTAACGACTGTAGAAAAATCCGATAAAAAAATCCGAATTCGACAATTTGAAAACTGAGTTGC
196 TAGGTAACGACGGTAGAAAAATCCGATAAAAAAATCCGAATTCGACAATTTGAAAACTGAGTTGC
*
354044 GAATTTGGCAAATTCGTGTAATGCACTGGAGTGGTTTTCAACCTGGGACATCCCAGTTGCTAAGT
261 GAATTTGGCAAATTCGTGTAATGCACTGGAGTGGTTTTCAACCTGGAACATCCCAGTTGCTAAGT
*
354109 CCACGTATGAATCACTCAGCTAAACCTACGCCTGTAAATGAATTGAACAAACACGAACGAGAATA
326 CCACGTATGAATCACTCAGCTAAACCTACGCCTGTAAATGAATTAAACAAACACGAACGAGAATA
354174 TGTTCATGTTCATTTTCC
391 TGTTCATGTTCATTTTCC
* *
354192 AAATAACTTTAGTGACCGAAAATGCTTTATAATATACGATTTTAACCAACTTTTTTTAGATTTGC
1 AAATAACTTCAGTGACCGAAAATACTTTATAATATACGATTTTAACCAACTTTTTTTAGATTTGC
354257 AAAAATAACCAACAAATTCGCAACGCGAACTCCTATTTCGCAACGCTAATTACCGACATTGGTAA
66 AAAAATAACCAACAAATTCGCAACGCGAACTCCTATTTCGCAACGCTAATTACCGACATTGGTAA
354322 ACACAACTATCGCAACACGAATTTCACAAATCGAATTCATCAATTTCGAAACTTAATTACCGATA
131 ACACAACTATCGCAACACGAATTTCACAAATCGAATTCATCAATTTCGAAACTTAATTACCGATA
* * *
354387 TAGGTAATGACGGTAGAAAAAATCCGGTAAAAAAATCCGAATTCGACAATTTGAAAATTGAGTTG
196 TAGGTAACGACGGTAG-AAAAATCCGATAAAAAAATCCGAATTCGACAATTTGAAAACTGAGTTG
354452 CGAATTTGGCAAATTCGTGTAATGCACTGGAGTGGTTTT-ATACCTGGAACATCCCAGTTGCTAA
260 CGAATTTGGCAAATTCGTGTAATGCACTGGAGTGGTTTTCA-ACCTGGAACATCCCAGTTGCTAA
* **
354516 GTCCACGTATGAATCACTCAGCTAAACCTATGCCTGTAAATGAATTAAACAAACACGAACGAGCG
324 GTCCACGTATGAATCACTCAGCTAAACCTACGCCTGTAAATGAATTAAACAAACACGAACGAGAA
354581 TATGTTCATGTTC
389 TATGTTCATGTTC
354594 GTTCGTTCGT
Statistics
Matches: 383, Mismatches: 17, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
408 202 0.53
409 181 0.47
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (408 bp):
AAATAACTTCAGTGACCGAAAATACTTTATAATATACGATTTTAACCAACTTTTTTTAGATTTGC
AAAAATAACCAACAAATTCGCAACGCGAACTCCTATTTCGCAACGCTAATTACCGACATTGGTAA
ACACAACTATCGCAACACGAATTTCACAAATCGAATTCATCAATTTCGAAACTTAATTACCGATA
TAGGTAACGACGGTAGAAAAATCCGATAAAAAAATCCGAATTCGACAATTTGAAAACTGAGTTGC
GAATTTGGCAAATTCGTGTAATGCACTGGAGTGGTTTTCAACCTGGAACATCCCAGTTGCTAAGT
CCACGTATGAATCACTCAGCTAAACCTACGCCTGTAAATGAATTAAACAAACACGAACGAGAATA
TGTTCATGTTCATTTTCC
Found at i:354919 original size:21 final size:21
Alignment explanation
Indices: 354866--354919 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
354856 TAATTAGCGT
354866 TGCGAATTTA-AAAATCGCAC
1 TGCGAATTTAGAAAATCGCAC
*
354886 TACGAATTT-GAAAATCGCAC
1 TGCGAATTTAGAAAATCGCAC
354906 TGCGAATTTAGAAA
1 TGCGAATTTAGAAA
354920 CTATGTTGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (21 bp):
TGCGAATTTAGAAAATCGCAC
Found at i:357859 original size:14 final size:14
Alignment explanation
Indices: 357815--357892 Score: 95
Period size: 14 Copynumber: 5.5 Consensus size: 14
357805 GCCTGGTCCA
*
357815 AGTCAACTTGT-TCG
1 AGTCAACTCGTCT-G
*
357829 AGTCAATTCGGTCTG
1 AGTCAACTC-GTCTG
* *
357844 AGTCAACACATCTG
1 AGTCAACTCGTCTG
357858 AGTCAACTCGTCTG
1 AGTCAACTCGTCTG
357872 AGTCAACTCGTCTG
1 AGTCAACTCGTCTG
357886 AGTCAAC
1 AGTCAAC
357893 CCGTTGACTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
14 44 0.80
15 10 0.18
16 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (14 bp):
AGTCAACTCGTCTG
Found at i:357911 original size:13 final size:13
Alignment explanation
Indices: 357893--357919 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
357883 CTGAGTCAAC
357893 CCGTTGACTTTGA
1 CCGTTGACTTTGA
357906 CCGTTGACTTTGA
1 CCGTTGACTTTGA
357919 C
1 C
357920 AGTTAACCGT
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:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (13 bp):
CCGTTGACTTTGA
Found at i:361267 original size:21 final size:21
Alignment explanation
Indices: 361241--361314 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
361231 TAAGTAGGGG
361241 TGTACCGATACACTCTTTGAA
1 TGTACCGATACACTCTTTGAA
361262 TGTACCGATACACTCTTTGAA
1 TGTACCGATACACTCTTTGAA
361283 TGTACCGATACACTCTTTGAA
1 TGTACCGATACACTCTTTGAA
*
361304 TGTATCGATAC
1 TGTACCGATAC
361315 CCCTGAATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (21 bp):
TGTACCGATACACTCTTTGAA
Found at i:367176 original size:23 final size:21
Alignment explanation
Indices: 367123--367184 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
367113 CCCCTTTCTA
367123 TGTATCGATACACCTTGAATG
1 TGTATCGATACACCTTGAATG
367144 TGTA-CTGATACATTCCTTGAATG
1 TGTATC-GATACA--CCTTGAATG
*
367167 TGTATCGATACCCCTTGA
1 TGTATCGATACACCTTGA
367185 GGGGTAACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 1 0.03
21 16 0.44
23 18 0.50
24 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (21 bp):
TGTATCGATACACCTTGAATG
Found at i:367487 original size:16 final size:16
Alignment explanation
Indices: 367466--367496 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
367456 TAACATAGGA
*
367466 CTAGTTTTAATTAGTT
1 CTAGTTTGAATTAGTT
367482 CTAGTTTGAATTAGT
1 CTAGTTTGAATTAGT
367497 GATCAGGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (16 bp):
CTAGTTTGAATTAGTT
Found at i:369387 original size:12 final size:13
Alignment explanation
Indices: 369369--369403 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
369359 GGGGGTAATT
369369 TTTTCAAAATTGA
1 TTTTCAAAATTGA
*
369382 -TTTCAAAAATGA
1 TTTTCAAAATTGA
369394 TTTTCAAAAT
1 TTTTCAAAAT
369404 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (13 bp):
TTTTCAAAATTGA
Found at i:371175 original size:42 final size:42
Alignment explanation
Indices: 371112--371308 Score: 335
Period size: 42 Copynumber: 4.7 Consensus size: 42
371102 ACTATCGCAA
*
371112 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* *
371152 TGCGATTTATTCTAAGTTCGTTGCGATAGTCGAAGTTCACGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* *
371194 TGCGATTTATTCCAAATTCGTTGTGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
371236 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
371278 TGCGATTTATTCCAAGTTCGTTGCGATAGTC
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTC
371309 CAAAATCGCA
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 5 0.03
41 2 0.01
42 139 0.95
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:372204 original size:42 final size:42
Alignment explanation
Indices: 372157--372533 Score: 394
Period size: 42 Copynumber: 9.1 Consensus size: 42
372147 CGATTTTGGC
* *
372157 CTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTGGA
1 CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
*
372199 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* * *
372241 CTATCGCAACGAAATTGGAATAAATCGCAA--CGAATTTGGA
1 CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* * *
372281 ATAAATCGCAACGAACTTGGAATAAATCGCAACACAAACTTCGA
1 CT--ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* * *
372325 CTATCGCAATGAATTTGGAATAAATCACAACGCGAACTTCGA
1 CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* * *
372367 CTATCGCAACGAACTTAGACT--ATCGCAA--CGAACTTAGA
1 CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* *
372405 CTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* *** * *** *
372447 CTATCACAAATCAGTTTCCAT-ATTCGCAACGCGAACTTCGA
1 CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* * *
372488 CTATCGCAACGCGAACTTCGACT--ATCGCAACGCGAACTTGGA
1 CTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGA
372530 CTAT
1 CTAT
372534 ACGCGAACTT
Statistics
Matches: 277, Mismatches: 48, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
38 26 0.09
40 22 0.08
41 27 0.10
42 190 0.69
43 4 0.01
44 8 0.03
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (42 bp):
CTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
Found at i:372496 original size:21 final size:20
Alignment explanation
Indices: 372470--372560 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 20
372460 GTTTCCATAT
*
372470 TCGCAACGCGAACTTCGACTA
1 TCGCAA-GCGAACTTGGACTA
*
372491 TCGCAACGCGAACTTCGACTA
1 TCGCAA-GCGAACTTGGACTA
372512 TCGCAACGCGAACTTGGACTA
1 TCGCAA-GCGAACTTGGACTA
*
372533 T---ACGCGAACTTGGACTA
1 TCGCAAGCGAACTTGGACTA
372550 TCGCAATGCGA
1 TCGCAA-GCGA
372561 TAGTCGAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
17 15 0.24
18 1 0.02
20 1 0.02
21 46 0.73
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGCAAGCGAACTTGGACTA
Found at i:372539 original size:17 final size:17
Alignment explanation
Indices: 372517--372550 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
372507 GACTATCGCA
372517 ACGCGAACTTGGACTAT
1 ACGCGAACTTGGACTAT
372534 ACGCGAACTTGGACTAT
1 ACGCGAACTTGGACTAT
372551 CGCAATGCGA
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:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
ACGCGAACTTGGACTAT
Found at i:372549 original size:38 final size:39
Alignment explanation
Indices: 372352--372560 Score: 135
Period size: 38 Copynumber: 5.2 Consensus size: 39
372342 GAATAAATCA
* * *
372352 CAACGCGAACTTCGACTATCGCAACGAACTTAGACTATCG
1 CAACGCGAACTTCGACTATCAC-GCGAACTTCGACTATCG
* * * * *
372392 CAA--CGAACTTAGACTATCGCAACGAA-TTTGTAATAAATCG
1 CAACGCGAACTTCGACTATCAC-GCGAACTTCG-ACT--ATCG
* *
372432 CAACGCGAACTTCGACTATCA--CAAATCAGTTTCCA-TATTCG
1 CAACGCGAACTTCGACTATCACGCGAA-C---TTCGACTA-TCG
372473 CAACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTAT--C-ACGCGAACTTCGACTATCG
* *
372515 CAACGCGAACTTGGACTAT-ACGCGAACTTGGACTATCG
1 CAACGCGAACTTCGACTATCACGCGAACTTCGACTATCG
*
372553 CAATGCGA
1 CAACGCGA
372561 TAGTCGAAGT
Statistics
Matches: 139, Mismatches: 13, Indels: 36
0.74 0.07 0.19
Matches are distributed among these distances:
37 3 0.02
38 49 0.35
39 3 0.02
40 11 0.08
41 22 0.16
42 40 0.29
43 4 0.03
44 3 0.02
45 1 0.01
46 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (39 bp):
CAACGCGAACTTCGACTATCACGCGAACTTCGACTATCG
Found at i:374125 original size:33 final size:34
Alignment explanation
Indices: 374062--374127 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
374052 AAAATGAATA
**
374062 AAAATAAAAATAAGTGAATAAATTCGAATAATCT
1 AAAATAAAAATAAGTGAATAAATTAAAATAATCT
*
374096 AAAATAATAAA-AA-TGACTAAATTAAAATAATC
1 AAAATAA-AAATAAGTGAATAAATTAAAATAATC
374128 ACAAATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 16 0.57
34 9 0.32
35 3 0.11
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (34 bp):
AAAATAAAAATAAGTGAATAAATTAAAATAATCT
Found at i:374672 original size:2 final size:2
Alignment explanation
Indices: 374665--374708 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
374655 GATAGAAATA
374665 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
374707 AT
1 AT
374709 GCTACTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:375417 original size:3 final size:3
Alignment explanation
Indices: 375409--375471 Score: 94
Period size: 3 Copynumber: 21.7 Consensus size: 3
375399 CCTGCAAGAA
* *
375409 AAT AAT AAT AAT AAT TA- AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
375456 AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AA
375472 AGACGAGTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 3 0.06
3 51 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:375885 original size:134 final size:134
Alignment explanation
Indices: 375630--376354 Score: 874
Period size: 134 Copynumber: 5.4 Consensus size: 134
375620 TCTAAAAGGT
** * * * * *
375630 AGATCAGA-TCGAG-AAACGTTGATTCA-TTCCACTGTTCATCAAGGAAGATTGAATCAGAA-TC
1 AGATCAGACTCGAGAAAATTTTGATCCACTT-CACTGCTCTTCAGGGAAGATTGAATC-GAATTT
* **
375691 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAATAAT-TTGCTCAACTACTCT
64 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTT-CTCCGCTACTCT
*
375755 TTAGGGG
128 TTAGAGG
* * * ** * *
375762 AGATTAGACTCGAGGAAACTTTGATCCACTTCACTATTCTTCAGGGAAAATTGAATCGGAA-TCG
1 AGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATC-GAATTTG
* * * * *
375826 ATTTGCTTTACTGCTCTTGAGGAAGACCAAATCTGAAAGAAGAA-ACGTCTTTTCCACTACTCTT
65 ATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGA-ATCTTCTCCGCTACTCTT
*
375890 TAGGGG
129 TAGAGG
* *
375896 AGATCAGACTCGAGAAAAATTTGATCCACTTCACTGCTCTTCAGGGAAGATTAAATCGAATTTGA
1 AGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAATTTGA
* * *
375961 TTTGCTTCGA-TGCTGTTCAGGAAGACCATATCTGAAAGAAGAAGAAT-TTGCTACGCTACTCTT
66 TTTGCTTC-ACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTT-CTCCGCTACTCTT
376024 TAGAGG
129 TAGAGG
* *
376030 AGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGACTAAATCGAATTTGA
1 AGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAATTTGA
* ** * *
376095 TTCGCTTCGTTGCTCTTCAGGAATACCAAATCTGAAAGAAGAAGAATCTACTCCGCTACTCTTTA
66 TTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTTCTCCGCTACTCTTTA
376160 GAGG
131 GAGG
* * *
376164 AGATCAGACTCGAGAAAATTTTGATTCACTTCACTTCTTTTCAGGGAAGATTGAATCGAATTTGA
1 AGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAATTTGA
* * * * ** * *
376229 TTTGTTTCATTTCTTTTCAGGAAGATAAAATCTGAAAGAAGAAGAATCTGCTCTGCTACTCTTTA
66 TTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTTCTCCGCTACTCTTTA
376294 GAGG
131 GAGG
* *
376298 AGATTAAACTCGAGAAAATTTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAAT
1 AGATCAGACTCGAGAAAA-TTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAAT
376355 ATGAAAATCA
Statistics
Matches: 522, Mismatches: 59, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
132 7 0.01
133 11 0.02
134 462 0.89
135 42 0.08
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (134 bp):
AGATCAGACTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAATTTGA
TTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTTCTCCGCTACTCTTTA
GAGG
Found at i:376993 original size:45 final size:45
Alignment explanation
Indices: 376944--377181 Score: 214
Period size: 45 Copynumber: 5.3 Consensus size: 45
376934 TCCTCTCCGC
* * * **
376944 GAGAAAGTAAAAAAGGACAATACTAAAAGATTGACTTCTCTTCTT
1 GAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTTCTCTTCAA
*
376989 GAGAAAGTCAAGAAGGACAACACTAAAATATTGACTTCTCTTCAA
1 GAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTTCTCTTCAA
** * **
377034 GAGAAAGTCAAGAA-GACAACACCGAAAGATTGACTACTCTTCGC
1 GAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTTCTCTTCAA
* * * * *
377078 GAGAAAATCAAGAAGGATAAAACTAAAAGATTGAC-CCATCTTCAC
1 GAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTTC-TCTTCAA
* * * * * * *
377123 TATAAAGTTAAAGAA-TACAACACTGAAATATTGACTCCTCTTCACA
1 GAGAAAG-TCAAGAAGGACAACACTAAAAGATTGACTTCTCTTCA-A
377169 -AGAAAGTCAAGAA
1 GAGAAAGTCAAGAA
377182 TAATAATAAT
Statistics
Matches: 157, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
44 44 0.28
45 105 0.67
46 8 0.05
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (45 bp):
GAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTTCTCTTCAA
Found at i:377074 original size:89 final size:90
Alignment explanation
Indices: 376969--377181 Score: 241
Period size: 89 Copynumber: 2.4 Consensus size: 90
376959 GACAATACTA
* ** * * *
376969 AAAGATTGACTTCTCTTCTTGAGAAAGTCAAGAAGGACAACACTAAAATATTGACTTC-TCTTCA
1 AAAGATTGACTACTCTTCACGAGAAAGTCAAGAAGGACAAAACTAAAAGATTGAC-CCATCTTCA
*
377033 AGAGAAAG-TCAAGAAGACAACACCG
65 AGAGAAAGTTAAAGAAGACAACACCG
* * * *
377058 AAAGATTGACTACTCTTCGCGAGAAAATCAAGAAGGATAAAACTAAAAGATTGACCCATCTTCAC
1 AAAGATTGACTACTCTTCACGAGAAAGTCAAGAAGGACAAAACTAAAAGATTGACCCATCTTCAA
* * * *
377123 TATAAAGTTAAAGAATACAACACTG
66 GAGAAAGTTAAAGAAGACAACACCG
* * *
377148 AAATATTGACTCCTCTTCACAAGAAAGTCAAGAA
1 AAAGATTGACTACTCTTCACGAGAAAGTCAAGAA
377182 TAATAATAAT
Statistics
Matches: 103, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
88 1 0.01
89 59 0.57
90 43 0.42
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (90 bp):
AAAGATTGACTACTCTTCACGAGAAAGTCAAGAAGGACAAAACTAAAAGATTGACCCATCTTCAA
GAGAAAGTTAAAGAAGACAACACCG
Found at i:377120 original size:134 final size:134
Alignment explanation
Indices: 376936--377181 Score: 311
Period size: 134 Copynumber: 1.8 Consensus size: 134
376926 AAGTTTACTC
* * * * *
376936 CTCTCCGCGAGAAAGTAAAAAAGGACAATACTAAAAGATTGACTTCTCTTC-TTGAGAAAG-TCA
1 CTCTCCGCGAGAAAATAAAAAAGGACAAAACTAAAAGATTGACTCCTCTTCACT-AGAAAGTTAA
*
376999 AGAAGGACAACACTAAAATATTGACTTCTCTTCA-AGAGAAAGTCAAGAAGACAACACCGAAAGA
65 AGAA-GACAACACTAAAATATTGACTCCTCTTCACA-AGAAAGTCAAGAAGACAACACCGAAAGA
377063 TTGACTA
128 TTGACTA
* * * * *
377070 CTCTTCGCGAGAAAATCAAGAAGGATAAAACTAAAAGATTGAC-CCATCTTCACTATAAAGTTAA
1 CTCTCCGCGAGAAAATAAAAAAGGACAAAACTAAAAGATTGACTCC-TCTTCACTAGAAAGTTAA
* *
377134 AGAATACAACACTGAAATATTGACTCCTCTTCACAAGAAAGTCAAGAA
65 AGAAGACAACACTAAAATATTGACTCCTCTTCACAAGAAAGTCAAGAA
377182 TAATAATAAT
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
133 1 0.01
134 86 0.91
135 8 0.08
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (134 bp):
CTCTCCGCGAGAAAATAAAAAAGGACAAAACTAAAAGATTGACTCCTCTTCACTAGAAAGTTAAA
GAAGACAACACTAAAATATTGACTCCTCTTCACAAGAAAGTCAAGAAGACAACACCGAAAGATTG
ACTA
Found at i:377179 original size:90 final size:89
Alignment explanation
Indices: 376944--377181 Score: 235
Period size: 89 Copynumber: 2.7 Consensus size: 89
376934 TCCTCTCCGC
* * ** * ***
376944 GAGAAAGTAAAAAAGGACAATACTAAAAGATTGACTTCTCTTCTTGAGAAAGTCAAGAAGGACAA
1 GAGAAAGTAAAGAA-GACAACACCGAAAGATTGACTACTCTTCACAAGAAAGTCAAGAAGGACAA
* * *
377009 CACTAAAATATTGACTTCTCTTCAA
65 AACTAAAAGATTGACTCCTCTTCAA
* * * * *
377034 GAGAAAGTCAAGAAGACAACACCGAAAGATTGACTACTCTTCGCGAGAAAATCAAGAAGGATAAA
1 GAGAAAGTAAAGAAGACAACACCGAAAGATTGACTACTCTTCACAAGAAAGTCAAGAAGGACAAA
*
377099 ACTAAAAGATTGAC-CCATCTTCAC
66 ACTAAAAGATTGACTCC-TCTTCAA
* * * * * *
377123 TATAAAGTTAAAGAATACAACACTGAAATATTGACTCCTCTTCACAAGAAAGTCAAGAA
1 GAGAAAG-TAAAGAAGACAACACCGAAAGATTGACTACTCTTCACAAGAAAGTCAAGAA
377182 TAATAATAAT
Statistics
Matches: 122, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
88 1 0.01
89 66 0.54
90 55 0.45
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (89 bp):
GAGAAAGTAAAGAAGACAACACCGAAAGATTGACTACTCTTCACAAGAAAGTCAAGAAGGACAAA
ACTAAAAGATTGACTCCTCTTCAA
Found at i:377251 original size:42 final size:42
Alignment explanation
Indices: 376969--377853 Score: 439
Period size: 38 Copynumber: 21.9 Consensus size: 42
376959 GACAATACTA
* ** * * *
376969 AAAGATTGACTTCTCTTCTTGAGAAAGTCAAGAAGGACAACACTA
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAG-A--ATAACATTG
* * * * **
377014 AAATATTGACTTCTCTTCAAGAGAAAGTCAAGAAGACAACACCG
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAG-A-ATAACATTG
* * * * * *
377058 AAAGATTGACTACTCTTCGCGAGAAAATCAAGAAGGATAAAACTA
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAG-A--ATAACATTG
* * * *
377103 AAAGATTGAC-CCATCTTCACTATAAAGTTAAAGAATACAACACTG
1 AAAGATTGACTCC-TCTTCACGAGAAAG-TCAAGAAT--AACATTG
* * *
377148 AAATATTGACTCCTCTTCACAAGAAAGTCAAGAATAATAATAATG
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAA-CAT--TG
* * * * * * *
377193 AGAGACTAAATTCTCTTCACGAGAAAGTTAATAATAACATTG
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * **
377235 AACGATTGACTCCTCTTCAGGAGGTAGTCAAGAATAACATTG
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * ** *
377277 AAAGATTGACTCCCCTTCATGAGGGACTCAAGAATAA-A---
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * * * *
377315 AAAAATTGACTTCTTTTCATGAGGAAGTCAAGAATAACATTG
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * ** *
377357 AAAGATTGACACCTCTTCGCGAGGGAGTCAGGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* *
377395 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA-A---
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * * * * *
377433 AAAGATCGACTTCTCTTTACGAGGACGTC-GGTAATAACATTG
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAG-AATAACATTG
* **
377475 AAAGATTGACTCCTCTTCAAGAGGGAGTCAAGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* *
377513 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
** * *
377551 AAAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * * *
377589 AAAGATCGACTTCGCTTCACGAGGAAGTCAAGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
** * *
377627 AAAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * *
377665 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
** * *
377703 AAAGACCGACTTCTCTTCACGAGGAAGTCAAGAAT-A-A-T-
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * * *
377741 AAAGATCGACTTCTCTTCACGAGGAAGTTAAGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * *
377779 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC----
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
* * *
377817 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAA
377854 TAAAGATGTT
Statistics
Matches: 718, Mismatches: 98, Indels: 55
0.82 0.11 0.06
Matches are distributed among these distances:
37 2 0.00
38 415 0.58
39 3 0.00
41 1 0.00
42 126 0.18
43 4 0.01
44 47 0.07
45 114 0.16
46 6 0.01
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (42 bp):
AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTG
Found at i:377334 original size:38 final size:38
Alignment explanation
Indices: 377277--377860 Score: 774
Period size: 38 Copynumber: 15.2 Consensus size: 38
377267 AATAACATTG
* * * * * * *
377277 AAAGATTGACTCCCCTTCATGAGGGACTCAAGAATAAA
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
377315 AAAAATTGACTTCTTTTCATGAGGAAGTCAAGAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** * * *
377353 ATTGAAAGATTGACACCTCTTCGCGAGGGAGTCAGGAATAAC
1 ----AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
377395 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAA
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
377433 AAAGATCGACTTCTCTTTACGAGGACGTC-GGTAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAG-AATAAC
* * * *
377471 ATTGAAAGATTGACTCCTCTTCAAGAGGGAGTCAAGAATAAC
1 ----AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
377513 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
377551 AAAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
377589 AAAGATCGACTTCGCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
377627 AAAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
377665 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
377703 AAAGACCGACTTCTCTTCACGAGGAAGTCAAGAATAAT
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
377741 AAAGATCGACTTCTCTTCACGAGGAAGTTAAGAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
377779 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
377817 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAT
1 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
377855 AAAGAT
1 AAAGAT
377861 GTTTTTCCTT
Statistics
Matches: 486, Mismatches: 50, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.00
38 425 0.87
42 59 0.12
43 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (38 bp):
AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:377592 original size:76 final size:76
Alignment explanation
Indices: 377203--377860 Score: 787
Period size: 76 Copynumber: 8.4 Consensus size: 76
377193 AGAGACTAAA
* * * * * * *
377203 TTCTCTTCACGAGAAAGTTAATAATAACATTGAACGATTGACTCCTCTTCAGGAGGTAGTCAAGA
1 TTCTCTTCACGAGGAAGTCAAGAATAACA---AA-GATCGACTTCTCTTCACGAGGAAGTCAAGA
*
377268 ATAACATTGAAAGATTGAC
62 ATAAC----AAAGATCGAC
* * * * * * * * * *
377287 TCCCCTTCATGAGGGACTCAAGAATAAAAAAAATTGACTTCTTTTCATGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
*
377352 CATTGAAAGATTGAC
66 C----AAAGATCGAC
** * * * *
377367 ACCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
*
377432 AAAAGATCGAC
66 CAAAGATCGAC
* * * * * * *
377443 TTCTCTTTACGAGGACGTC-GGTAATAACATTGAAAGATTGACTCCTCTTCAAGAGGGAGTCAAG
1 TTCTCTTCACGAGGAAGTCAAG-AATAAC----AAAGATCGACTTCTCTTCACGAGGAAGTCAAG
*
377507 AATAACAAAGATTGAC
61 AATAACAAAGATCGAC
*
377523 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
377588 CAAAGATCGAC
66 CAAAGATCGAC
* *
377599 TTCGCTTCACGAGGAAGTCAAGAATAACAAAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
377664 CAAAGATCGAC
66 CAAAGATCGAC
*
377675 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGACCGACTTCTCTTCACGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
*
377740 TAAAGATCGAC
66 CAAAGATCGAC
*
377751 TTCTCTTCACGAGGAAGTTAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
377816 CAAAGATCGAC
66 CAAAGATCGAC
*
377827 TTCTCTTCACGAGGAAGTCAAGAATAATAAAGAT
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGAT
377861 GTTTTTCCTT
Statistics
Matches: 512, Mismatches: 56, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
75 2 0.00
76 322 0.63
80 165 0.32
81 3 0.01
84 20 0.04
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (76 bp):
TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
CAAAGATCGAC
Found at i:377667 original size:114 final size:114
Alignment explanation
Indices: 377203--377860 Score: 787
Period size: 114 Copynumber: 5.6 Consensus size: 114
377193 AGAGACTAAA
* * * * * * *
377203 TTCTCTTCACGAGAAAGTTAATAATAACATTGAACGATTGACTCCTCTTCAGGAGGTAGTCAAGA
1 TTCTCTTCACGAGGAAGTCAAGAATAACA---AA-GATCGACTTCTCTTCACGAGGAAGTCAAGA
* * * * * * * * *
377268 ATAACATTGAAAGATTGACTCCCCTTCATGAGGGACTCAAGAATAAAAAAAATTGAC
62 ATAAC----AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAC
* * * ** * * *
377325 TTCTTTTCATGAGGAAGTCAAGAATAACATTGAAAGATTGACACCTCTTCGCGAGGGAGTCAGGA
1 TTCTCTTCACGAGGAAGTCAAGAATAAC----AAAGATCGACTTCTCTTCACGAGGAAGTCAAGA
* *
377390 ATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAAAAAGATCGAC
62 ATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAC
* * * * * * *
377443 TTCTCTTTACGAGGACGTC-GGTAATAACATTGAAAGATTGACTCCTCTTCAAGAGGGAGTCAAG
1 TTCTCTTCACGAGGAAGTCAAG-AATAAC----AAAGATCGACTTCTCTTCACGAGGAAGTCAAG
* *
377507 AATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCAAC
61 AATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAC
*
377561 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCGCTTCACGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
*
377626 CAAAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAC
66 CAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAC
*
377675 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGACCGACTTCTCTTCACGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
* *
377740 TAAAGATCGACTTCTCTTCACGAGGAAGTTAAGAATAACAAAGATCGAC
66 CAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAC
377789 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
*
377854 TAAAGAT
66 CAAAGAT
377861 GTTTTTCCTT
Statistics
Matches: 485, Mismatches: 45, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
114 258 0.53
117 1 0.00
118 169 0.35
119 1 0.00
122 53 0.11
123 2 0.00
126 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (114 bp):
TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAA
CAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAC
Found at i:383795 original size:13 final size:13
Alignment explanation
Indices: 383774--383812 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
383764 AAAATAATTT
*
383774 CTTTCTCTTTCTC
1 CTTTCTCTTTCCC
*
383787 CTTTTTCTTTCCC
1 CTTTCTCTTTCCC
383800 CTTTCTC-TTCCC
1 CTTTCTCTTTCCC
383812 C
1 C
383813 ATTACCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (13 bp):
CTTTCTCTTTCCC
Found at i:391610 original size:3 final size:3
Alignment explanation
Indices: 391602--391652 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
391592 AAATATAAAT
391602 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
391650 TAA
1 TAA
391653 AACCCGGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:392049 original size:138 final size:136
Alignment explanation
Indices: 391838--392129 Score: 395
Period size: 138 Copynumber: 2.1 Consensus size: 136
391828 AAATTTGGAA
* * * *
391838 ATAACACGGTTCCTACGTGGTGAGGAAATTTGGTTATCTAAGGGTGAAGCGGCTCTTACGTGATG
1 ATAACACGGTTCCTACGCGATGAGGAAATTTGGTTATCTAAGGGTGAAGCGGCTCCTACGCGATG
* * * *
391903 AGGAGATCTGGTCAGTGAATGGCACAGTTCCTACGTGATGAGGACGTCTGGCCATCTTTAGAGAT
66 AGGAGATCTGATCAGTGAATGACACAATTCCTACGTGATGAAGACGTCTGGCCATCTTTAG-GAT
391968 AAAGGGAG
130 -AAGGGAG
* ** * ** *
391976 ATAACACGGTTCCTACGCGATGAGGAAGTTTGGTTATCTATTGGTGATGTTGTTCCTACGCGATG
1 ATAACACGGTTCCTACGCGATGAGGAAATTTGGTTATCTAAGGGTGAAGCGGCTCCTACGCGATG
* *
392041 AGGAGATCTGATCGGTGGATGACACAATTCCTACGTGATGAAGACGTCTGGCCATCTTTAGGATA
66 AGGAGATCTGATCAGTGAATGACACAATTCCTACGTGATGAAGACGTCTGGCCATCTTTAGGATA
*
392106 ATGGAG
131 AGGGAG
*
392112 ATAACACAGTTCCTACGC
1 ATAACACGGTTCCTACGC
392130 TAAAAGTCTG
Statistics
Matches: 135, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
136 23 0.17
137 3 0.02
138 109 0.81
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (136 bp):
ATAACACGGTTCCTACGCGATGAGGAAATTTGGTTATCTAAGGGTGAAGCGGCTCCTACGCGATG
AGGAGATCTGATCAGTGAATGACACAATTCCTACGTGATGAAGACGTCTGGCCATCTTTAGGATA
AGGGAG
Found at i:395893 original size:59 final size:60
Alignment explanation
Indices: 395806--395955 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 60
395796 GATGTTATTG
* * * **
395806 GAATTTTCAAAAGTTTGGGGACTAATTTAAA-AGAG-GATCATTGTTTGGGGATGAAATTA
1 GAATGTTCAAAAGTTTAGGGACTAATTTAAATAGAGAG-TCATAGTTTAAGGATGAAATTA
* *
395865 GAATGTTCAAAAGTTTAGGGA-TAGATTTAAATTGAGAGTGATAGTTTAAGGATGAAATTA
1 GAATGTTCAAAAGTTTAGGGACTA-ATTTAAATAGAGAGTCATAGTTTAAGGATGAAATTA
* *
395925 GAATGTTCAAAAGTTTAAGGACCAATTTAAA
1 GAATGTTCAAAAGTTTAGGGACTAATTTAAA
395956 ATAAGGGCCA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.03
59 26 0.33
60 48 0.62
61 2 0.03
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (60 bp):
GAATGTTCAAAAGTTTAGGGACTAATTTAAATAGAGAGTCATAGTTTAAGGATGAAATTA
Found at i:395969 original size:60 final size:60
Alignment explanation
Indices: 395854--395971 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
395844 CATTGTTTGG
* * * * **
395854 GGATGAAATTAGAATGTTCAAAAGTTTAGGGATAGATTTAAATTGAGAGTGATAGTTTAA
1 GGATGAAATTAGAATGTTCAAAAGTTTAAGGACAGATTTAAAATAAGAGCCATAGTTTAA
*
395914 GGATGAAATTAGAATGTTCAAAAGTTTAAGGACCA-ATTTAAAATAAGGGCCATAGTTT
1 GGATGAAATTAGAATGTTCAAAAGTTTAAGGA-CAGATTTAAAATAAGAGCCATAGTTT
395972 GAGGGAATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 49 0.98
61 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (60 bp):
GGATGAAATTAGAATGTTCAAAAGTTTAAGGACAGATTTAAAATAAGAGCCATAGTTTAA
Found at i:396126 original size:45 final size:45
Alignment explanation
Indices: 396062--396158 Score: 185
Period size: 45 Copynumber: 2.2 Consensus size: 45
396052 TTGACCGACT
*
396062 AATCCAAATCGAGTTTTGCATAGGCCATTATGGGTCGACCCTCCC
1 AATCCAGATCGAGTTTTGCATAGGCCATTATGGGTCGACCCTCCC
396107 AATCCAGATCGAGTTTTGCATAGGCCATTATGGGTCGACCCTCCC
1 AATCCAGATCGAGTTTTGCATAGGCCATTATGGGTCGACCCTCCC
396152 AATCCAG
1 AATCCAG
396159 TTTACTCCAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.26
Consensus pattern (45 bp):
AATCCAGATCGAGTTTTGCATAGGCCATTATGGGTCGACCCTCCC
Found at i:397650 original size:2 final size:2
Alignment explanation
Indices: 397643--397668 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
397633 AGTCACATGA
397643 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
397669 GAAAGACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:400351 original size:13 final size:13
Alignment explanation
Indices: 400333--400360 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
400323 CTTGGTAAGT
400333 TTCTCAAAATCCC
1 TTCTCAAAATCCC
400346 TTCTCAAAATCCC
1 TTCTCAAAATCCC
400359 TT
1 TT
400361 AAAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (13 bp):
TTCTCAAAATCCC
Found at i:407588 original size:11 final size:11
Alignment explanation
Indices: 407553--407581 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
407543 ATGCTTGAAG
407553 AAAAGAAGAAA
1 AAAAGAAGAAA
407564 AAAAGAAGAAA
1 AAAAGAAGAAA
407575 AAAAGAA
1 AAAAGAA
407582 AATAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:421870 original size:32 final size:32
Alignment explanation
Indices: 421825--421896 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
421815 CAATAGAGGA
* * **
421825 CATCTTTGAAGATTCAACATTAAATGTTGGGG
1 CATCTTTGAAGATTCAACATCAAATATCAGGG
**
421857 CATCTTTTTAGATTCAACATCAAATATCAGGG
1 CATCTTTGAAGATTCAACATCAAATATCAGGG
421889 CATCTTTG
1 CATCTTTG
421897 GGAATTCAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (32 bp):
CATCTTTGAAGATTCAACATCAAATATCAGGG
Found at i:422174 original size:61 final size:61
Alignment explanation
Indices: 422076--422247 Score: 272
Period size: 61 Copynumber: 2.8 Consensus size: 61
422066 ACATAATCTC
*
422076 TTGCATCTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACT
1 TTGCAACTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACT
* * *
422137 TTGCAGCTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACT
1 TTGCAACTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACT
* * * *
422198 TTCCAACTTTTAGAGTCAATTTTAACTTCACAACGAAAGATATTGAACTC
1 TTGCAACTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
422248 GAAAGAGATG
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 101 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (61 bp):
TTGCAACTTTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACT
Found at i:422571 original size:36 final size:36
Alignment explanation
Indices: 422549--422699 Score: 221
Period size: 36 Copynumber: 4.2 Consensus size: 36
422539 AATTTACTCA
* *
422549 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
* *
422585 AAACAAATTTTTTCTCTCTCGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
*
422621 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
* * * *
422657 AGACAAATTTTGTCTCTCTTGAGATAGTTTCCATTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
422693 AAACAAA
1 AAACAAA
422700 ATCTTTGAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 104 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
Found at i:422634 original size:72 final size:72
Alignment explanation
Indices: 422549--422837 Score: 306
Period size: 72 Copynumber: 4.1 Consensus size: 72
422539 AATTTACTCA
*
422549 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCTCTCGAGACAATT
1 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTCGAGACAATT
*
422614 TCCCTTG
66 TCCATTG
* * * * *
422621 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAGACAAATTTTGTCTCTCTTGAGATAGTT
1 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTCGAGACAATT
422686 TCCATTG
66 TCCATTG
* * * * * * *
422693 AAACAAA------ATCT-TTGA-ATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGT
1 AAACAAAGTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTCGAGACAAT
**
422750 TTCTTTTG
65 TTCCATTG
* * * * *
422758 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
1 AAACAAAG-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTCGAGACAAT
*
422823 TTCCCTTG
65 TTCCATTG
422831 AAACAAA
1 AAACAAA
422838 ATCTTTGAAT
Statistics
Matches: 179, Mismatches: 28, Indels: 19
0.79 0.12 0.08
Matches are distributed among these distances:
64 2 0.01
65 48 0.27
66 3 0.02
72 75 0.42
73 49 0.27
74 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (72 bp):
AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTCGAGACAATT
TCCATTG
Found at i:422781 original size:138 final size:138
Alignment explanation
Indices: 422575--422922 Score: 545
Period size: 138 Copynumber: 2.5 Consensus size: 138
422565 TCTTGAGACA
* ** * * ** * *
422575 GTTTCCCTTGAAACAAATTTTTTCTCTCTCGAGACAATTTCCCTTGAAAC-AAATTTTGTCTCTC
1 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTC
* *
422639 TTGAGACAGTTTCCCTTGAGACAAATTTTGTCTCTCTTGAGATAGTTTCCATTGAAACAAAATCT
66 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAACAAAATCT
422704 TTGAATAT
131 TTGAATAT
*
422712 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTC
* *
422777 TTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCT
66 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAACAAAATCT
422842 TTGAATAT
131 TTGAATAT
* *
422850 GTTTTCCTTGGAACAAATTTCGTTTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTC
422915 TTGAGACA
66 TTGAGACA
422923 AAGTCTCTTG
Statistics
Matches: 193, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
137 41 0.21
138 152 0.79
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (138 bp):
GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTC
TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAACAAAATCT
TTGAATAT
Found at i:422813 original size:36 final size:36
Alignment explanation
Indices: 422714--422837 Score: 178
Period size: 36 Copynumber: 3.4 Consensus size: 36
422704 TTGAATATGT
* *
422714 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
422749 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
422786 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
422822 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
422838 ATCTTTGAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 4 0.05
36 43 0.55
37 31 0.40
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:423050 original size:32 final size:32
Alignment explanation
Indices: 422990--423109 Score: 165
Period size: 32 Copynumber: 3.8 Consensus size: 32
422980 TCTGGAGACG
* *
422990 GTTTCTCTTGAAACACAAAAAACTTTTGAACTC
1 GTTTCTCTTGAAACA-AAAAAACCTTTGAAATC
423023 GTTTCTCTTGAAACAAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACAAAAAAACCTTTGAAATC
*
423055 GTTTCTCTCG-AA-AAAAAAACCTTTGAAAAT-
1 GTTTCTCTTGAAACAAAAAAACCTTTG-AAATC
*
423085 GTTTCTCTTGAAACACAAAAACCTT
1 GTTTCTCTTGAAACAAAAAAACCTT
423110 CGAGTTCGAC
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
30 22 0.28
31 8 0.10
32 34 0.43
33 15 0.19
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (32 bp):
GTTTCTCTTGAAACAAAAAAACCTTTGAAATC
Found at i:425558 original size:33 final size:34
Alignment explanation
Indices: 425502--425572 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 34
425492 ATACATCAAC
* *
425502 AGATATTCTTGTGAAAAAACTTGAACTCTATCGA
1 AGATATTCTTGTGAAAAAACTTGAACTCAAACGA
425536 AGATATTCTTGTG-AAAAACTTGAACTCAAACGA
1 AGATATTCTTGTGAAAAAACTTGAACTCAAACGA
425569 AGAT
1 AGAT
425573 GGTCCTCAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 22 0.63
34 13 0.37
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (34 bp):
AGATATTCTTGTGAAAAAACTTGAACTCAAACGA
Found at i:432332 original size:3 final size:3
Alignment explanation
Indices: 432324--432350 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
432314 AAATATAAAT
432324 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
432351 AACCCGGACA
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:432742 original size:138 final size:136
Alignment explanation
Indices: 432494--432775 Score: 393
Period size: 138 Copynumber: 2.1 Consensus size: 136
432484 ACGCTGCTCA
* * * *
432494 TCCTACGTGGTGAGGAAATTTGGTTATCTAAGGGTGACGCGGCTCTTACGTGATGAGGAGATCTG
1 TCCTACGCGATGAGGAAATTTGGTTATCTAAGGGTGACGCGGCTCCTACGCGATGAGGAGATCTG
* * ** *
432559 GTCGGTGGATGGCACGGTTCCTACGTGATGAGGACGTCTGGCCATCTTTAGAGATAAAGGGAGAT
66 ATCGGTGGATGACACAATTCCTACGTGATGAAGACGTCTGGCCATCTTTAG-GAT-AAGGGAGAT
*
432624 AACACGGT
129 AACACAGT
* * * ** *
432632 TCCTACGCGATGAGGAAGTTTGGTTATCTAATGGTGATGTTGTTCCTACGCGATGAGGAGATCTG
1 TCCTACGCGATGAGGAAATTTGGTTATCTAAGGGTGACGCGGCTCCTACGCGATGAGGAGATCTG
*
432697 ATCGGTGGATGACACAATTCCTACGTGATGAAGACGTCTGGCCATCTTTAGGATAATGGAGATAA
66 ATCGGTGGATGACACAATTCCTACGTGATGAAGACGTCTGGCCATCTTTAGGATAAGGGAGATAA
432762 CACAGT
131 CACAGT
432768 TCCTACGC
1 TCCTACGC
432776 TAAAAGTCTG
Statistics
Matches: 127, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
136 23 0.18
137 3 0.02
138 101 0.80
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (136 bp):
TCCTACGCGATGAGGAAATTTGGTTATCTAAGGGTGACGCGGCTCCTACGCGATGAGGAGATCTG
ATCGGTGGATGACACAATTCCTACGTGATGAAGACGTCTGGCCATCTTTAGGATAAGGGAGATAA
CACAGT
Found at i:435467 original size:3 final size:3
Alignment explanation
Indices: 435452--435525 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
435442 ATTTGGTTTT
* * *
435452 TTA TTA -TA TTTA TTA TTT TTA TTT TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
435497 ATA TTA TTT TTA ATA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
435526 CAGATACAAC
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 4 0.07
3 50 0.89
4 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:435470 original size:18 final size:18
Alignment explanation
Indices: 435431--435525 Score: 62
Period size: 15 Copynumber: 5.5 Consensus size: 18
435421 GACACTAGTT
**
435431 TTTTTATATATATTTGGT-
1 TTTTTAT-TATATTTATTA
435449 TTTTTATTATATTTATTA
1 TTTTTATTATATTTATTA
435467 TTTTTA-T-T-TTTATTA
1 TTTTTATTATATTTATTA
* *
435482 CTATTATTATTATTAATATTA
1 TTTTTATTA-TATT--TATTA
435503 TTTTTA--ATA-TTATTA
1 TTTTTATTATATTTATTA
435518 -TTTTATTA
1 TTTTTATTA
435526 CAGATACAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 5 0.08
15 16 0.26
16 3 0.05
17 10 0.16
18 16 0.26
19 3 0.05
21 9 0.15
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTATTATATTTATTA
Found at i:435478 original size:15 final size:15
Alignment explanation
Indices: 435452--435525 Score: 87
Period size: 15 Copynumber: 5.0 Consensus size: 15
435442 ATTTGGTTTT
*
435452 TTATTATATTTATTA
1 TTATTATTTTTATTA
*
435467 TTTTTATTTTTATTA
1 TTATTATTTTTATTA
* *
435482 CTATTATTATTATTA
1 TTATTATTTTTATTA
* *
435497 ATATTATTTTTAATA
1 TTATTATTTTTATTA
435512 TTATTA-TTTTATTA
1 TTATTATTTTTATTA
435526 CAGATACAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
14 7 0.14
15 42 0.86
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTATTTTTATTA
Found at i:436028 original size:7 final size:7
Alignment explanation
Indices: 436027--436079 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
436017 GAGAAAAAAG
436027 AAAGAAA
1 AAAGAAA
436034 AAAGAAA
1 AAAGAAA
*
436041 GGAAA-AAG
1 --AAAGAAA
436049 AAAGAAA
1 AAAGAAA
436056 AAAGAAA
1 AAAGAAA
436063 AAAGAAA
1 AAAGAAA
*
436070 CAAGAAA
1 AAAGAAA
436077 AAA
1 AAA
436080 AAGCAAGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 3 0.08
7 31 0.79
8 2 0.05
9 3 0.08
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:436034 original size:11 final size:11
Alignment explanation
Indices: 436018--436079 Score: 83
Period size: 11 Copynumber: 5.7 Consensus size: 11
436008 GAGGACAGAG
436018 AGAAAAAAGAA
1 AGAAAAAAGAA
436029 AGAAAAAAGAA
1 AGAAAAAAGAA
*
436040 AGGAAAAAGAA
1 AGAAAAAAGAA
436051 AGAAAAAAGAA
1 AGAAAAAAGAA
*
436062 A-AAAGAAA-CA
1 AGAAA-AAAGAA
436072 AGAAAAAA
1 AGAAAAAA
436080 AAGCAAGCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
10 8 0.17
11 38 0.83
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAAAAAGAA
Found at i:436985 original size:15 final size:13
Alignment explanation
Indices: 436954--436981 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
436944 CATTGTTTAG
436954 TTATATGTTAATT
1 TTATATGTTAATT
436967 TTATATGTTAATT
1 TTATATGTTAATT
436980 TT
1 TT
436982 TTATTATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (13 bp):
TTATATGTTAATT
Found at i:436990 original size:3 final size:3
Alignment explanation
Indices: 436982--437013 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
436972 TGTTAATTTT
*
436982 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
437014 TAACCATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:437366 original size:35 final size:35
Alignment explanation
Indices: 437288--437367 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
437278 TGATATTTCT
*
437288 AAATAAATAAATATTTTATTTATAAATATATATATA
1 AAAT-AATATATATTTTATTTATAAATATATATATA
* * *
437324 AATTAATATATATTTT-TTTCATAATTATA-ATCTTA
1 AAATAATATATATTTTATTT-ATAAATATATAT-ATA
437359 AAATAATAT
1 AAATAATAT
437368 GATTATAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
34 5 0.14
35 29 0.78
36 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (35 bp):
AAATAATATATATTTTATTTATAAATATATATATA
Found at i:441187 original size:15 final size:15
Alignment explanation
Indices: 441167--441198 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
441157 GATCAATACC
441167 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
441182 TTTTGCATACATTCA
1 TTTTGCATACATGCA
441197 TT
1 TT
441199 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:444386 original size:10 final size:10
Alignment explanation
Indices: 444371--444406 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
444361 ATGGCAATCA
444371 TTTTTACATT
1 TTTTTACATT
444381 TTTTTACATT
1 TTTTTACATT
444391 TTTTTACATT
1 TTTTTACATT
*
444401 TATTTA
1 TTTTTA
444407 TTTCATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTACATT
Found at i:447944 original size:23 final size:21
Alignment explanation
Indices: 447930--447972 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
447920 GAAAAAATTG
447930 AAAAAAAAAG-AAAGAAAAGAA
1 AAAAAAAAAGAAAAGAAAA-AA
447951 AAAAAAAAAGAAAAAGAAAAAA
1 AAAAAAAAAG-AAAAGAAAAAA
447973 GGGGGTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGAAAAGAAAAAA
Found at i:447954 original size:18 final size:18
Alignment explanation
Indices: 447931--447972 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
447921 AAAAAATTGA
447931 AAAAAAAAGAAAG-AAAAG
1 AAAAAAAA-AAAGAAAAAG
447949 AAAAAAAAAAAGAAAAAG
1 AAAAAAAAAAAGAAAAAG
447967 AAAAAA
1 AAAAAA
447973 GGGGGTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAAAG
Found at i:448367 original size:19 final size:17
Alignment explanation
Indices: 448325--448373 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
448315 TATTTTCTCT
448325 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
448341 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
448359 AAAATTCAACTTATT
1 -AAATTCAATTTATT
448374 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:448872 original size:114 final size:114
Alignment explanation
Indices: 448667--449003 Score: 548
Period size: 114 Copynumber: 3.0 Consensus size: 114
448657 TGCCACGTTA
* *
448667 TCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
448732 TTTGGTATAAACCCTAAAACCAATTATTAGATTTGAAAGATGAATTTTC
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
*
448781 TCATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
448846 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
*
448895 TTATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* ** * * * * *
448960 TTCGGTAGGAACCACAGAACGAATCATTAGAATTGAAAGATGAA
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAA
449004 CTGCATGATT
Statistics
Matches: 208, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 208 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
Done.