Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, 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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 6 of 12
Found at i:3612004 original size:2 final size:2
Alignment explanation
Indices: 3611997--3612026 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3611987 TTCTTGAGTC
3611997 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
3612027 GCTCGAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3624928 original size:25 final size:22
Alignment explanation
Indices: 3624868--3624928 Score: 52
Period size: 25 Copynumber: 2.5 Consensus size: 22
3624858 ATGCACTATG
3624868 ATCCTTCTTCTAAACATGAGAT
1 ATCCTTCTTCTAAACATGAGAT
3624890 AT-CTTGCTGTTTCTAAACATATGTAGAT
1 ATCCTT-C---TTCTAAAC--ATG-AGAT
3624918 ATCCTTCTTCT
1 ATCCTTCTTCT
3624929 CAATCAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
21 3 0.10
22 3 0.10
25 12 0.39
27 3 0.10
28 7 0.23
29 3 0.10
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (22 bp):
ATCCTTCTTCTAAACATGAGAT
Found at i:3648338 original size:24 final size:25
Alignment explanation
Indices: 3648306--3648356 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
3648296 CAATTTCTAT
*
3648306 AATTTTTTTAAAGATAAA-AGTTTA
1 AATTTTTTTAAAAATAAATAGTTTA
*
3648330 AATTTTTTTAAAAATAAATATTTTA
1 AATTTTTTTAAAAATAAATAGTTTA
3648355 AA
1 AA
3648357 ATTATGAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
AATTTTTTTAAAAATAAATAGTTTA
Found at i:3654503 original size:28 final size:28
Alignment explanation
Indices: 3654463--3654518 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3654453 AGATTATAGC
3654463 TGTCATCCATTTGCCTAAAATCTGTTTA
1 TGTCATCCATTTGCCTAAAATCTGTTTA
3654491 TGTCATCCATTTGCCTAAAATCTGTTTA
1 TGTCATCCATTTGCCTAAAATCTGTTTA
3654519 CTCTTTGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (28 bp):
TGTCATCCATTTGCCTAAAATCTGTTTA
Found at i:3660879 original size:14 final size:15
Alignment explanation
Indices: 3660853--3660881 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3660843 AGACGCCGGG
3660853 GTGGGTGTGTGGGGT
1 GTGGGTGTGTGGGGT
3660868 GTGGGT-TGTGGGGT
1 GTGGGTGTGTGGGGT
3660882 TAGCCTACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (15 bp):
GTGGGTGTGTGGGGT
Found at i:3667242 original size:20 final size:19
Alignment explanation
Indices: 3667213--3667252 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3667203 AAAGTCGATC
3667213 TTCCTTTTCTT-TTTTCTAT
1 TTCCTTTTCTTCTTTT-TAT
3667232 TTCCTTTTTCTTCTTTTTAT
1 TTCC-TTTTCTTCTTTTTAT
3667252 T
1 T
3667253 AGAAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (19 bp):
TTCCTTTTCTTCTTTTTAT
Found at i:3672042 original size:24 final size:24
Alignment explanation
Indices: 3671985--3672044 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
3671975 ATAATATTAT
3671985 AATATT-TAATATATATGAAAAGG
1 AATATTGTAATATATATGAAAAGG
3672008 --TATTGATTAATATAT-TGAAAAGAG
1 AATATTG--TAATATATATGAAAAG-G
3672032 AATATTGTAATAT
1 AATATTGTAATAT
3672045 TTATAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
21 4 0.13
23 7 0.23
24 15 0.48
26 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.38
Consensus pattern (24 bp):
AATATTGTAATATATATGAAAAGG
Found at i:3678278 original size:63 final size:63
Alignment explanation
Indices: 3678073--3678391 Score: 570
Period size: 63 Copynumber: 5.1 Consensus size: 63
3678063 CTCTAATGAA
* *
3678073 TCCTGCTCAGCTGACCACTCCATTTCCTTCCAATCCATTCCCTACCAATCTAAATGAGCAAGT
1 TCCTGCTCAGCTGACCACTCCATTTCCTACCAATCCGTTCCCTACCAATCTAAATGAGCAAGT
*
3678136 TCCTGCTCAGCTGACCACTCCATTTCCTA-CAATCCGTT-CCTACCAATCTAAATGAGCTAGT
1 TCCTGCTCAGCTGACCACTCCATTTCCTACCAATCCGTTCCCTACCAATCTAAATGAGCAAGT
* *
3678197 TCCTGCCTCAGCTGACCACTCCATTTCCTAACATTCCGTTCCCTACCAATCTAAATGAGCAAGT
1 TCCTG-CTCAGCTGACCACTCCATTTCCTACCAATCCGTTCCCTACCAATCTAAATGAGCAAGT
3678261 TCCTGCTCAGCTGACCACTCCATTTCCTACCAATCCGTTCCCTACCAATCTAAATGAGCAAGT
1 TCCTGCTCAGCTGACCACTCCATTTCCTACCAATCCGTTCCCTACCAATCTAAATGAGCAAGT
3678324 TCCTGCTCAGCTGACCACTCCATTTCCTACCAATCCGTTCCCTACCAATCTAAATGAGCAAGT
1 TCCTGCTCAGCTGACCACTCCATTTCCTACCAATCCGTTCCCTACCAATCTAAATGAGCAAGT
3678387 TCCTG
1 TCCTG
3678392 GTTTCTTTCC
Statistics
Matches: 246, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
61 27 0.11
62 32 0.13
63 160 0.65
64 27 0.11
ACGTcount: A:0.25, C:0.36, G:0.11, T:0.28
Consensus pattern (63 bp):
TCCTGCTCAGCTGACCACTCCATTTCCTACCAATCCGTTCCCTACCAATCTAAATGAGCAAGT
Found at i:3683576 original size:23 final size:23
Alignment explanation
Indices: 3683546--3683608 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
3683536 AATATAAATA
*
3683546 AATT-AAAATATTTTGAAATT-AT
1 AATTAAAAATA-TTTGAAATTAAC
*
3683568 AATTAAAAATATTTAAAATTAAC
1 AATTAAAAATATTTGAAATTAAC
3683591 AATTAAAAAGTACTTTGA
1 AATTAAAAA-TA-TTTGA
3683609 TATATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 12 0.35
23 16 0.47
24 2 0.06
25 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (23 bp):
AATTAAAAATATTTGAAATTAAC
Found at i:3684170 original size:16 final size:17
Alignment explanation
Indices: 3684149--3684181 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3684139 AGGATACAAA
3684149 AAAG-TTGTTTTGTTAG
1 AAAGTTTGTTTTGTTAG
*
3684165 AAAGTTTTTTTTGTTAG
1 AAAGTTTGTTTTGTTAG
3684182 GTCAAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (17 bp):
AAAGTTTGTTTTGTTAG
Found at i:3684444 original size:32 final size:28
Alignment explanation
Indices: 3684369--3684429 Score: 106
Period size: 27 Copynumber: 2.2 Consensus size: 28
3684359 ATATCACGTG
*
3684369 TAATAATTATATTTTTCAACATAATGTA
1 TAATAATTAAATTTTTCAACATAATGTA
3684397 TAATAATTAAATTTTT-AACATAATGTA
1 TAATAATTAAATTTTTCAACATAATGTA
3684424 TAATAA
1 TAATAA
3684430 CTACATGCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (28 bp):
TAATAATTAAATTTTTCAACATAATGTA
Found at i:3689123 original size:24 final size:24
Alignment explanation
Indices: 3689089--3689136 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3689079 TCTGTCTTTG
* * *
3689089 TTGTTCGTTTTTCTTTTTCTTTCT
1 TTGTTCCTTTTCCTTTTTCCTTCT
3689113 TTGTTCCTTTTCCTTTTTCCTTCT
1 TTGTTCCTTTTCCTTTTTCCTTCT
3689137 GGGTGTAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.71
Consensus pattern (24 bp):
TTGTTCCTTTTCCTTTTTCCTTCT
Found at i:3689306 original size:15 final size:15
Alignment explanation
Indices: 3689286--3689316 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3689276 CGTAGAGAAG
*
3689286 AAAGCTGACTTGGTA
1 AAAGCTAACTTGGTA
3689301 AAAGCTAACTTGGTA
1 AAAGCTAACTTGGTA
3689316 A
1 A
3689317 CTTCTACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (15 bp):
AAAGCTAACTTGGTA
Found at i:3700117 original size:29 final size:29
Alignment explanation
Indices: 3700050--3700129 Score: 67
Period size: 29 Copynumber: 2.8 Consensus size: 29
3700040 TAAAATTTTA
*
3700050 AAATAAATTTTTATTATATTTATTATATTC
1 AAATAAA-TTTTATTATATTTATTATAATC
* * *
3700080 AATTAAAATTTTA-TATTTTTATTTTAAATC
1 AAAT-AAATTTTATTATATTTATTAT-AATC
*
3700110 AAATAAATCTT-TTA-ATTTAT
1 AAATAAATTTTATTATATTTAT
3700130 GATTAACTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
28 5 0.12
29 18 0.45
30 14 0.35
31 3 0.08
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (29 bp):
AAATAAATTTTATTATATTTATTATAATC
Found at i:3700971 original size:31 final size:29
Alignment explanation
Indices: 3700936--3700996 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
3700926 GAGTAGAAAG
*
3700936 ATAATTTTATTATTGATTAATTTTTATAATT
1 ATAATTATATTATTGATT-ATTTTTA-AATT
* *
3700967 ATAATTATATTTTTTATTATTTTTAAATT
1 ATAATTATATTATTGATTATTTTTAAATT
3700996 A
1 A
3700997 ATAAAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 7 0.26
31 15 0.56
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
ATAATTATATTATTGATTATTTTTAAATT
Found at i:3707006 original size:7 final size:7
Alignment explanation
Indices: 3706994--3707041 Score: 69
Period size: 7 Copynumber: 6.6 Consensus size: 7
3706984 CTGAAGCAAT
3706994 AAGAAAA
1 AAGAAAA
3707001 AAGAAAA
1 AAGAAAA
3707008 AAGAAAA
1 AAGAAAA
3707015 AAGAAAA
1 AAGAAAA
*
3707022 AAAAAAA
1 AAGAAAA
3707029 GAAGAAGAA
1 -AAGAA-AA
3707038 AAGA
1 AAGA
3707042 GAGCCTCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
7 27 0.73
8 8 0.22
9 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:3716964 original size:31 final size:31
Alignment explanation
Indices: 3716926--3716992 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
3716916 ACGTGACCAA
* *
3716926 AATGAAAACTTACGCAGTCGTCTCCGTGGAG
1 AATGAAAACTTACACAGTCGTCTACGTGGAG
3716957 AATGAAAACTTACACAGTCGTCTACGTGGAG
1 AATGAAAACTTACACAGTCGTCTACGTGGAG
3716988 AATGA
1 AATGA
3716993 TCACGTGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22
Consensus pattern (31 bp):
AATGAAAACTTACACAGTCGTCTACGTGGAG
Found at i:3724327 original size:6 final size:6
Alignment explanation
Indices: 3724318--3724343 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3724308 ATGGTGATGG
3724318 TGGTCA TGGTCA TGGTCA TGGTCA TG
1 TGGTCA TGGTCA TGGTCA TGGTCA TG
3724344 ATGATCATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (6 bp):
TGGTCA
Found at i:3724332 original size:15 final size:15
Alignment explanation
Indices: 3724308--3724366 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
3724298 CATGATCATG
* *
3724308 ATGGTGATGGTGGTC
1 ATGGTCATGGTGATC
3724323 ATGGTCAT-G-G-TC
1 ATGGTCATGGTGATC
*
3724335 ATGGTCATGATGATC
1 ATGGTCATGGTGATC
*
3724350 ATGGACATGGTGATC
1 ATGGTCATGGTGATC
3724365 AT
1 AT
3724367 TGGAAGCCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 10 0.27
13 1 0.03
14 2 0.05
15 24 0.65
ACGTcount: A:0.22, C:0.12, G:0.34, T:0.32
Consensus pattern (15 bp):
ATGGTCATGGTGATC
Found at i:3724338 original size:21 final size:21
Alignment explanation
Indices: 3724294--3724366 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
3724284 TACTTACTCA
*
3724294 TGATCATGATCATGATGGTGATGG
1 TGATCATGATC---ATGGTCATGG
* *
3724318 TGGTCATGGTCATGGTCATGG
1 TGATCATGATCATGGTCATGG
* * *
3724339 TCATGATGATCATGGACATGG
1 TGATCATGATCATGGTCATGG
3724360 TGATCAT
1 TGATCAT
3724367 TGGAAGCCAT
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
21 30 0.77
24 9 0.23
ACGTcount: A:0.23, C:0.12, G:0.32, T:0.33
Consensus pattern (21 bp):
TGATCATGATCATGGTCATGG
Found at i:3728108 original size:7 final size:7
Alignment explanation
Indices: 3728096--3728122 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3728086 ATTCCTTTCT
3728096 CTTTCCC
1 CTTTCCC
3728103 CTTTCCC
1 CTTTCCC
3728110 CTTTCCC
1 CTTTCCC
3728117 CTTTCC
1 CTTTCC
3728123 TTCTCCAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (7 bp):
CTTTCCC
Found at i:3737599 original size:22 final size:22
Alignment explanation
Indices: 3737571--3737613 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3737561 CCCTCTTTCC
3737571 TGAAATTTTCTTTCAAACGATT
1 TGAAATTTTCTTTCAAACGATT
3737593 TGAAATTTTCTTTCAAACGAT
1 TGAAATTTTCTTTCAAACGAT
3737614 GCCAATATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
TGAAATTTTCTTTCAAACGATT
Found at i:3752506 original size:53 final size:53
Alignment explanation
Indices: 3752398--3752507 Score: 186
Period size: 53 Copynumber: 2.1 Consensus size: 53
3752388 GGGGAATCAT
*
3752398 TGAATTTTAAATTACACAGCAAAAAGTAAAGCTTTTGTTCTCATTCTATGAAA
1 TGAATTTTAAATTACACAGCAAAAAGTAAAGCTTTTGTTCTCATTCCATGAAA
*
3752451 TGAATTTTAAATTACACAGCAAAAAGTGAAGCTTTTGTTCTCATTCCAT-AGAA
1 TGAATTTTAAATTACACAGCAAAAAGTAAAGCTTTTGTTCTCATTCCATGA-AA
3752504 TGAA
1 TGAA
3752508 ACAGTCATCC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
52 1 0.02
53 53 0.98
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (53 bp):
TGAATTTTAAATTACACAGCAAAAAGTAAAGCTTTTGTTCTCATTCCATGAAA
Found at i:3757402 original size:6 final size:6
Alignment explanation
Indices: 3757393--3757444 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
3757383 TGATCTTGAC
* * * *
3757393 CGTGCT CGTGGT CGTGGT CGTGGT CATGGT CGTGAT CGTGAT CGTGGT
1 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
3757441 CGTG
1 CGTG
3757445 ATCCTCTTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.06, C:0.19, G:0.42, T:0.33
Consensus pattern (6 bp):
CGTGGT
Found at i:3758296 original size:29 final size:27
Alignment explanation
Indices: 3758260--3758314 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
3758250 AGTATTACAT
3758260 TAATTATA-ATAAATTAATAAATAAAAAA
1 TAATTATATA-AAATTAA-AAATAAAAAA
*
3758288 TAATATATATAAAATTAAAATTAAAAA
1 TAAT-TATATAAAATTAAAAATAAAAA
3758315 TTATTAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.50
29 11 0.46
30 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
TAATTATATAAAATTAAAAATAAAAAA
Found at i:3770996 original size:23 final size:23
Alignment explanation
Indices: 3770966--3771009 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3770956 CAAGCCGGGC
*
3770966 TTCTACCCAAAAGGAACAGAAAA
1 TTCTACCCAAAAGGAAAAGAAAA
*
3770989 TTCTACCCAAAATGAAAAGAA
1 TTCTACCCAAAAGGAAAAGAA
3771010 CAATCCTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.16
Consensus pattern (23 bp):
TTCTACCCAAAAGGAAAAGAAAA
Found at i:3771818 original size:42 final size:43
Alignment explanation
Indices: 3771769--3771876 Score: 119
Period size: 45 Copynumber: 2.5 Consensus size: 43
3771759 TAAAAATATG
* * *
3771769 TAAATATTATTTAAATATAATAAATATTATAAAGAACATTGTT
1 TAAATATTATTTAAATATAATAAATATAATAAAAAACATTATT
* * *
3771812 TAATATTATTATTTGAATATAATAAATGTAATAAAAAATATTATT
1 TAA-A-TATTATTTAAATATAATAAATATAATAAAAAACATTATT
* *
3771857 T-AGTATTATTTAAATTTAAT
1 TAAATATTATTTAAATATAAT
3771877 GAAGAATATA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
42 15 0.28
43 3 0.06
44 2 0.04
45 34 0.63
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (43 bp):
TAAATATTATTTAAATATAATAAATATAATAAAAAACATTATT
Found at i:3771831 original size:45 final size:45
Alignment explanation
Indices: 3771773--3771866 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
3771763 AATATGTAAA
* * *
3771773 TATTATTTAAATATAATAAATATTATAAAGAACATTGTTTAATAT
1 TATTATTTAAATATAATAAATATAATAAAAAACATTATTTAATAT
* * * *
3771818 TATTATTTGAATATAATAAATGTAATAAAAAATATTATTTAGTAT
1 TATTATTTAAATATAATAAATATAATAAAAAACATTATTTAATAT
3771863 TATT
1 TATT
3771867 TAAATTTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (45 bp):
TATTATTTAAATATAATAAATATAATAAAAAACATTATTTAATAT
Found at i:3772577 original size:21 final size:22
Alignment explanation
Indices: 3772553--3772599 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3772543 GCTGGTGATA
3772553 ATATGCTATGACAACAC-ACGC
1 ATATGCTATGACAACACTACGC
*
3772574 ATATGCTTTGACAACACTACGC
1 ATATGCTATGACAACACTACGC
3772596 ATAT
1 ATAT
3772600 TTTTGTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (22 bp):
ATATGCTATGACAACACTACGC
Found at i:3795949 original size:6 final size:6
Alignment explanation
Indices: 3795938--3795965 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3795928 AATTAGCAGT
3795938 AGAGGC AGAGGC AGAGGC AGAGGC AGAG
1 AGAGGC AGAGGC AGAGGC AGAGGC AGAG
3795966 TTCTCCCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGC
Found at i:3802189 original size:22 final size:22
Alignment explanation
Indices: 3802154--3802273 Score: 118
Period size: 22 Copynumber: 5.5 Consensus size: 22
3802144 ATAACTTAAT
**
3802154 CATTACGTCTCTAATTTTTAGA
1 CATTACGTGACTAATTTTTAGA
* **
3802176 CATTGCGTGACTAACCTTTA-A
1 CATTACGTGACTAATTTTTAGA
*
3802197 GCATTACGTGACTGATTTTTA-A
1 -CATTACGTGACTAATTTTTAGA
**
3802219 GCATTACGTGACTAACCTTTAGA
1 -CATTACGTGACTAATTTTTAGA
*
3802242 CATTACGTGACTGATTTTTAGA
1 CATTACGTGACTAATTTTTAGA
*
3802264 TATTACGTGA
1 CATTACGTGA
3802274 TTAGCCTTTA
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
21 1 0.01
22 78 0.98
23 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (22 bp):
CATTACGTGACTAATTTTTAGA
Found at i:3802217 original size:44 final size:44
Alignment explanation
Indices: 3802149--3802283 Score: 166
Period size: 44 Copynumber: 3.1 Consensus size: 44
3802139 ATTGTATAAC
* ** * *
3802149 TTAATCATTACGTCTCTAATTTTTAGACATTGCGTGACTAACCT
1 TTAAGCATTACGTGACTGATTTTTAGACATTACGTGACTAACCT
3802193 TTAAGCATTACGTGACTGATTTTTA-AGCATTACGTGACTAACCT
1 TTAAGCATTACGTGACTGATTTTTAGA-CATTACGTGACTAACCT
* * *
3802237 TT-AGACATTACGTGACTGATTTTTAGATATTACGTGATTAGCCT
1 TTAAG-CATTACGTGACTGATTTTTAGACATTACGTGACTAACCT
3802281 TTA
1 TTA
3802284 GGCAATACTT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
43 3 0.04
44 75 0.95
45 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (44 bp):
TTAAGCATTACGTGACTGATTTTTAGACATTACGTGACTAACCT
Found at i:3802284 original size:44 final size:45
Alignment explanation
Indices: 3802167--3802284 Score: 170
Period size: 44 Copynumber: 2.7 Consensus size: 45
3802157 TACGTCTCTA
*
3802167 ATTTTTAGACATTGCGTGACTAACCTTTA-AGCATTACGTGACTG
1 ATTTTTAGACATTACGTGACTAACCTTTAGAGCATTACGTGACTG
3802211 ATTTTTA-AGCATTACGTGACTAACCTTTAGA-CATTACGTGACTG
1 ATTTTTAGA-CATTACGTGACTAACCTTTAGAGCATTACGTGACTG
* * *
3802255 ATTTTTAGATATTACGTGATTAGCCTTTAG
1 ATTTTTAGACATTACGTGACTAACCTTTAG
3802285 GCAATACTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
43 1 0.01
44 64 0.96
45 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (45 bp):
ATTTTTAGACATTACGTGACTAACCTTTAGAGCATTACGTGACTG
Found at i:3802382 original size:23 final size:23
Alignment explanation
Indices: 3802336--3802406 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
3802326 ATGCTTTACT
* * *
3802336 AACTAGTCACGCAATGAC-TATC
1 AACTAATCAAGCAATGTCATATC
3802358 AA-TCAATCAAGCAATGTCATATC
1 AACT-AATCAAGCAATGTCATATC
* * *
3802381 AACTAGTCACGTAATGTCATATC
1 AACTAATCAAGCAATGTCATATC
3802404 AAC
1 AAC
3802407 CAGTAATGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 13 0.32
23 25 0.62
24 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.25
Consensus pattern (23 bp):
AACTAATCAAGCAATGTCATATC
Found at i:3802417 original size:23 final size:23
Alignment explanation
Indices: 3802370--3802418 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3802360 TCAATCAAGC
* *
3802370 AATGTCATATCAACTAGTCACGT
1 AATGTCATATCAACCAGTAACGT
*
3802393 AATGTCATATCAACCAGTAATGT
1 AATGTCATATCAACCAGTAACGT
3802416 AAT
1 AAT
3802419 ATCTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
AATGTCATATCAACCAGTAACGT
Found at i:3802477 original size:22 final size:22
Alignment explanation
Indices: 3802452--3802507 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3802442 TTTAAATATA
**
3802452 AGTCATATAATACCTAAAAATT
1 AGTCATATAATACCTAAAAACC
* *
3802474 AGTCACATAATACTTAAAAACC
1 AGTCATATAATACCTAAAAACC
*
3802496 AATCATATAATA
1 AGTCATATAATA
3802508 TATGCTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.29
Consensus pattern (22 bp):
AGTCATATAATACCTAAAAACC
Found at i:3809675 original size:22 final size:23
Alignment explanation
Indices: 3809647--3809693 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
3809637 AAATTAAATT
3809647 TTTTTAAA-TTTTACATAATAAA
1 TTTTTAAATTTTTACATAATAAA
*
3809669 TTTTTAAATTTTTACTTAATAAA
1 TTTTTAAATTTTTACATAATAAA
3809692 TT
1 TT
3809694 AATATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTTAAATTTTTACATAATAAA
Found at i:3827696 original size:15 final size:15
Alignment explanation
Indices: 3827671--3827710 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3827661 CAATGTAATA
* *
3827671 TAATATGATTATAAG
1 TAATTTGATTATAAC
*
3827686 TCATTTGATTATAAC
1 TAATTTGATTATAAC
3827701 TAATTTGATT
1 TAATTTGATT
3827711 GTAAAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (15 bp):
TAATTTGATTATAAC
Found at i:3829722 original size:22 final size:22
Alignment explanation
Indices: 3829697--3829742 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3829687 TATTATTAAA
*
3829697 TTATTAATATGAATTTTTATTT
1 TTATTAATATGAATTTGTATTT
* * *
3829719 TTATTTATTTGTATTTGTATTT
1 TTATTAATATGAATTTGTATTT
3829741 TT
1 TT
3829743 TAATGTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (22 bp):
TTATTAATATGAATTTGTATTT
Found at i:3831247 original size:30 final size:30
Alignment explanation
Indices: 3831189--3831247 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
3831179 CAAATGTTAA
*
3831189 ATTTTTATTTTAAATAAAATAAATTTTTAT
1 ATTTTTATTTTAAATAAAATAAACTTTTAT
* * *
3831219 ATTTTTATTTTGAATCAAATAAGCTTTTA
1 ATTTTTATTTTAAATAAAATAAACTTTTA
3831248 AGACTGATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (30 bp):
ATTTTTATTTTAAATAAAATAAACTTTTAT
Found at i:3840629 original size:28 final size:27
Alignment explanation
Indices: 3840577--3840631 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3840567 TGGTATATAA
* *
3840577 TTTTTTATTTAAAAAGTAAAATTTGAT
1 TTTTTTAATTAAAAAGAAAAATTTGAT
3840604 TTTTTTAATTAAAAA-AAAAGAGTTTGAT
1 TTTTTTAATTAAAAAGAAAA-A-TTTGAT
3840632 AAGTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.12
27 15 0.62
28 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (27 bp):
TTTTTTAATTAAAAAGAAAAATTTGAT
Found at i:3840864 original size:8 final size:9
Alignment explanation
Indices: 3840847--3840875 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
3840837 ATTATTAAAA
3840847 TTTTATTTT
1 TTTTATTTT
3840856 TTTTATTTT
1 TTTTATTTT
3840865 TTTTATTTT
1 TTTTATTTT
3840874 TT
1 TT
3840876 GAGATGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTATTTT
Found at i:3850365 original size:35 final size:35
Alignment explanation
Indices: 3850319--3850393 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
3850309 CTAAAAATGG
**
3850319 ATGAATACTTGTAATCCACCAAAAATAGATAAATA
1 ATGAATACTTGTAATCCAAAAAAAATAGATAAATA
3850354 ATGAATACTTGTAATCCAAAAAAAATAGATAAATA
1 ATGAATACTTGTAATCCAAAAAAAATAGATAAATA
*
3850389 GTGAA
1 ATGAA
3850394 AATAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (35 bp):
ATGAATACTTGTAATCCAAAAAAAATAGATAAATA
Found at i:3872334 original size:2 final size:2
Alignment explanation
Indices: 3872298--3872325 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3872288 AAAAACCAAC
3872298 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3872326 AGATCTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3881058 original size:21 final size:21
Alignment explanation
Indices: 3881022--3881075 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3881012 TCCTAGAAAA
* *
3881022 AAAAAAACAAAGAACCCAAAC
1 AAAAAGACAAAGAAACCAAAC
* *
3881043 -AAAAGCCAAAGAAACCTAAC
1 AAAAAGACAAAGAAACCAAAC
3881063 AAAAAGACAAAGA
1 AAAAAGACAAAGA
3881076 GATGATCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.69, C:0.20, G:0.09, T:0.02
Consensus pattern (21 bp):
AAAAAGACAAAGAAACCAAAC
Found at i:3881662 original size:26 final size:26
Alignment explanation
Indices: 3881596--3881672 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
3881586 AAAAATTAAA
*
3881596 ATAAAATATATAATATAAA-AAAATAT
1 ATAAAAT-TATAATAAAAATAAAATAT
* * *
3881622 AT-TAA-CA-AATGAAAATAAAATAT
1 ATAAAATTATAATAAAAATAAAATAT
3881645 ATAAAATTATAATAAAAATAAAATAT
1 ATAAAATTATAATAAAAATAAAATAT
3881671 AT
1 AT
3881673 GATATTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
22 6 0.15
23 10 0.25
24 2 0.05
25 3 0.08
26 19 0.47
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (26 bp):
ATAAAATTATAATAAAAATAAAATAT
Found at i:3881694 original size:33 final size:33
Alignment explanation
Indices: 3881593--3881694 Score: 120
Period size: 33 Copynumber: 3.1 Consensus size: 33
3881583 TTAAAAAATT
*
3881593 AAAATAAAATATATAATATAAAAAAATATATTA
1 AAAATAAAATATATAATATATAAAAATATATTA
* *
3881626 ACAAATGAAAATA-A-AATATATAAAATTATAATA
1 A-AAAT-AAAATATATAATATATAAAAATATATTA
*
3881659 AAAATAAAATATATGATAT-TAAAAATATATCTA
1 AAAATAAAATATATAATATATAAAAATATAT-TA
3881692 AAA
1 AAA
3881695 GATGATATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
31 6 0.10
32 14 0.24
33 27 0.47
34 5 0.09
35 6 0.10
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (33 bp):
AAAATAAAATATATAATATATAAAAATATATTA
Found at i:3882342 original size:36 final size:35
Alignment explanation
Indices: 3882295--3882380 Score: 113
Period size: 35 Copynumber: 2.4 Consensus size: 35
3882285 AAGTTTGATG
3882295 AATATTAATATTTAA-TTTAAAAT-ATTAAAAAATAAA
1 AATATTAATATTTAACTTTAAAATAATT---AAATAAA
* *
3882331 AATATTAATATTTAACTTTAAAATAATTAATTTAA
1 AATATTAATATTTAACTTTAAAATAATTAAATAAA
3882366 AATATTAATATTTAA
1 AATATTAATATTTAA
3882381 ATTATACAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
35 20 0.43
36 15 0.33
37 8 0.17
38 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (35 bp):
AATATTAATATTTAACTTTAAAATAATTAAATAAA
Found at i:3882382 original size:14 final size:14
Alignment explanation
Indices: 3882337--3882374 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3882327 TAAAAATATT
*
3882337 AATATTTAACTTTAA
1 AATAATTAA-TTTAA
3882352 AATAATTAATTTAA
1 AATAATTAATTTAA
3882366 AAT-ATTAAT
1 AATAATTAAT
3882375 ATTTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATTAATTTAA
Found at i:3882572 original size:74 final size:74
Alignment explanation
Indices: 3882444--3882585 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
3882434 ATAAATGAAA
* * * *
3882444 TAAATCTTATTAATAATTATAATAAAAAATATTTCAATGATCATCATTTGATGAATTCACATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATCATTTAATGAATACACATTTA
3882509 TAATAGGTT
66 TAATAGGTT
** * *
3882518 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATTTTTATTTAATGAATACATATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATCATTTAATGAATACACATTTA
3882583 TAA
66 TAA
3882586 GTATAAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (74 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATCATTTAATGAATACACATTTA
TAATAGGTT
Found at i:3883790 original size:33 final size:33
Alignment explanation
Indices: 3883752--3883828 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
3883742 AATGATGGTG
3883752 GAAAATATTTTCTACAGGACAATCCAAATGATA
1 GAAAATATTTTCTACAGGACAATCCAAATGATA
3883785 GAAAATATTTTCTACAGGACAATCCAAATGATA
1 GAAAATATTTTCTACAGGACAATCCAAATGATA
3883818 GAAAATATTTT
1 GAAAATATTTT
3883829 GATAGTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (33 bp):
GAAAATATTTTCTACAGGACAATCCAAATGATA
Found at i:3884259 original size:23 final size:23
Alignment explanation
Indices: 3884233--3884276 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3884223 ATTACAGTGT
* *
3884233 TTAATATATAAGCAAAATAATGA
1 TTAAAATATAAGAAAAATAATGA
*
3884256 TTAAAATGTAAGAAAAATAAT
1 TTAAAATATAAGAAAAATAAT
3884277 ATTGCAGCGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (23 bp):
TTAAAATATAAGAAAAATAATGA
Found at i:3887980 original size:2 final size:2
Alignment explanation
Indices: 3887973--3888006 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3887963 TTTGCTTATG
3887973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3888007 ACATTATCAT
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):
TA
Found at i:3888861 original size:2 final size:2
Alignment explanation
Indices: 3888854--3888878 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3888844 AAGGTGAATA
3888854 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3888879 CACATAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3898092 original size:2 final size:2
Alignment explanation
Indices: 3898085--3898120 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3898075 CTGCCATTTC
3898085 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3898121 AGTAAAGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3903954 original size:10 final size:10
Alignment explanation
Indices: 3903925--3903954 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3903915 CCTTTTTCCA
3903925 CTTTTTTTTT
1 CTTTTTTTTT
*
3903935 CTCTTTTTTT
1 CTTTTTTTTT
3903945 CTTTTTTTTT
1 CTTTTTTTTT
3903955 ATATCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:3905314 original size:127 final size:127
Alignment explanation
Indices: 3905088--3905337 Score: 387
Period size: 127 Copynumber: 2.0 Consensus size: 127
3905078 TCTTGTTTTT
*
3905088 CCAGTTCCAATTGTTTCTTCTCCCTCATGTCTACATATTTCTATAAAAACCAATCATAAGAACAT
1 CCAGTTCCAATTGTTTCTTCTACCTCATGTCTACATATTTCTATAAAAACCAATCATAAGAACAT
** * *
3905153 AGTTACAAGTTTTCAAATTCAAATCCTTGTTAAGCAAGGAAACGATTAATCAAACTCCTTTA
66 AGTTACAAGTTTTCAAATTCAAATCCTCATTAAGCAAGGAAAAGATAAATCAAACTCCTTTA
* *
3905215 CCAGTTCCAGTTGTTTGC-TCTACCTCATGT-TAACATTTTTCTATAAAAACCAATCATAAGAAC
1 CCAGTTCCAATTGTTT-CTTCTACCTCATGTCT-ACATATTTCTATAAAAACCAATCATAAGAAC
* *
3905278 ATGGTTACAAGTTTTCGAATTCAAATCCTCATTAAGCAAGGAAAAGATAAATCAAACTCC
64 ATAGTTACAAGTTTTCAAATTCAAATCCTCATTAAGCAAGGAAAAGATAAATCAAACTCC
3905338 ACAATCCACA
Statistics
Matches: 112, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
126 1 0.01
127 110 0.98
128 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (127 bp):
CCAGTTCCAATTGTTTCTTCTACCTCATGTCTACATATTTCTATAAAAACCAATCATAAGAACAT
AGTTACAAGTTTTCAAATTCAAATCCTCATTAAGCAAGGAAAAGATAAATCAAACTCCTTTA
Found at i:3909059 original size:26 final size:27
Alignment explanation
Indices: 3909030--3909083 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
3909020 CAAAGAAATA
3909030 AAAAAAAGAGAAAAAAAC-TTCCCAAT
1 AAAAAAAGAGAAAAAAACATTCCCAAT
* * **
3909056 AAAAGAATATCAAAAAACATTCCCAAT
1 AAAAAAAGAGAAAAAAACATTCCCAAT
3909083 A
1 A
3909084 CCCTCATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.63, C:0.17, G:0.06, T:0.15
Consensus pattern (27 bp):
AAAAAAAGAGAAAAAAACATTCCCAAT
Found at i:3911720 original size:44 final size:42
Alignment explanation
Indices: 3911654--3911738 Score: 143
Period size: 44 Copynumber: 2.0 Consensus size: 42
3911644 ATTTAGGACC
*
3911654 TACCCTTTGACGGAAAGTTATATAAATAAATAAATATATATATA
1 TACCCTTTGACGGAAAGCTATATAAAT--ATAAATATATATATA
3911698 TACCCTTTGACGGAAAGCTATATAAATATAAATATATATAT
1 TACCCTTTGACGGAAAGCTATATAAATATAAATATATATAT
3911739 TTATCTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 14 0.35
44 26 0.65
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (42 bp):
TACCCTTTGACGGAAAGCTATATAAATATAAATATATATATA
Found at i:3913227 original size:3 final size:3
Alignment explanation
Indices: 3913219--3913268 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
3913209 AAGATAACAA
3913219 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
3913267 AA
1 AA
3913269 AGGGTGAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3914040 original size:72 final size:74
Alignment explanation
Indices: 3913941--3914091 Score: 234
Period size: 72 Copynumber: 2.1 Consensus size: 74
3913931 GAAAATAAAT
* * * * *
3913941 AATTTAGAGATACTCTACAGTAATCATTATTAATTCATCTGCAAGATGCACTATAGCTAGATATT
1 AATTTAGAAATAC-CTACACTAATCATTATTAATGCATCTGCAAGATGCACTATAGCTAGACATA
3914006 TTTCAATG-A
65 TTTCAATGCA
3914015 AATTTAGAAATA-CTACACTAATCATTATTAATGCATCTGCAAGATGCACTATAGCTAGACATAT
1 AATTTAGAAATACCTACACTAATCATTATTAATGCATCTGCAAGATGCACTATAGCTAGACATAT
3914079 TTCAATGCA
66 TTCAATGCA
3914088 AATT
1 AATT
3914092 ATGCCAGATT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 55 0.77
73 5 0.07
74 11 0.15
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (74 bp):
AATTTAGAAATACCTACACTAATCATTATTAATGCATCTGCAAGATGCACTATAGCTAGACATAT
TTCAATGCA
Found at i:3916578 original size:2 final size:2
Alignment explanation
Indices: 3916565--3916594 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3916555 TTAGGAGCCA
*
3916565 AT AT AC 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
3916595 TCCAACGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3928878 original size:42 final size:42
Alignment explanation
Indices: 3928819--3929262 Score: 261
Period size: 42 Copynumber: 10.0 Consensus size: 42
3928809 GAGAGTTATA
*
3928819 AAACTCAGTCAGTATATAGGTAGAGTTTGCA-ACTATTGTCAT
1 AAACTCAGTCAGCATATAGGTAGAGTTTG-AGACTATTGTCAT
* ** *
3928861 AAACTCAGTCAGCATATAGGTAGAGCTTGAGGTTGTTGTCAAAGGCTAAT
1 AAACTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGT------C--AT
* * *
3928911 AAAACTCAATCAGCATATAGGTAGATTTTGAGACTATTATCA-
1 -AAACTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGTCAT
* * *
3928953 AAAGCTAAGTCAGCATATAAGTAGAGTTTGAGACTGTTGTCAT
1 AAA-CTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGTCAT
*
3928996 AAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAGGCTAAT
1 AAACTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGT------C--AT
* * * * * *
3929046 AAAACTCAATTAACATATAAGTAGAGTTTAAGACT-GT-TCAT
1 -AAACTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGTCAT
* * * * *
3929087 AAACTCAATAAGCATATAGGTAGAGTTTAATAATATTGTCAAAGGCTAAT
1 AAACTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGT------C--AT
* * * * *
3929137 AAAACTCAATCAACATATAAGTAGAGTTTGAGACTGTTAT--T
1 -AAACTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGTCAT
* * *
3929178 AAAGGCTAAGTCAGCATATAAGTAGAATTTGAGACTATTGTCAT
1 AAA--CTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGTCAT
* * *
3929222 AAACTCAGTCAGCATGTAGGTAGAGTTTGAAACTGTTGTCA
1 AAACTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGTCA
3929263 AAGGCTAATA
Statistics
Matches: 313, Mismatches: 53, Indels: 72
0.71 0.12 0.16
Matches are distributed among these distances:
40 32 0.10
41 8 0.03
42 159 0.51
43 5 0.02
44 4 0.01
45 1 0.00
48 3 0.01
49 1 0.00
50 7 0.02
51 93 0.30
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (42 bp):
AAACTCAGTCAGCATATAGGTAGAGTTTGAGACTATTGTCAT
Found at i:3928954 original size:51 final size:50
Alignment explanation
Indices: 3928859--3929321 Score: 281
Period size: 51 Copynumber: 10.0 Consensus size: 50
3928849 AACTATTGTC
* * * ** *
3928859 ATAAACTCAGTCAGCATATAGGTAGAGCTTGAGGTTGTTGTCAAAGGCTA
1 ATAAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
* * * *
3928909 ATAAAACTCAATCAGCATATAGGTAGATTTTGAGACTATTATCAAAAGC--
1 AT-AAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
* *
3928958 -T--A---AGTCAGCATATAAGTAGAGTTTGAGACTGTTGT------C--
1 ATAAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
*
3928994 ATAAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAGGCTA
1 ATAAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
* * * *
3929044 ATAAAACTCAATTAACATATAAGTAGAGTTTAAGAC---TGT-------TC
1 AT-AAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
* * * * *
3929085 ATAAACTCAATAAGCATATAGGTAGAGTTTAATAATATTGTCAAAGGCTA
1 ATAAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
* * * *
3929135 ATAAAACTCAATCAACATATAAGTAGAGTTTGAGACTGTTATTAAAGGC--
1 AT-AAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
* *
3929184 -T--A---AGTCAGCATATAAGTAGAATTTGAGACTATTGT------C--
1 ATAAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
* * * * *
3929220 ATAAACTCAGTCAGCATGTAGGTAGAGTTTGAAACTGTTGTCAAAGGCTA
1 ATAAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
* *
3929270 ATAAAACTTAATCAACATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
1 AT-AAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
3929321 A
1 A
3929322 GAAAAAATAA
Statistics
Matches: 318, Mismatches: 53, Indels: 83
0.70 0.12 0.18
Matches are distributed among these distances:
36 2 0.01
37 2 0.01
39 2 0.01
40 28 0.09
41 3 0.01
42 114 0.36
43 3 0.01
45 2 0.01
48 7 0.02
50 9 0.03
51 146 0.46
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (50 bp):
ATAAACTCAATCAGCATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
Found at i:3928977 original size:93 final size:85
Alignment explanation
Indices: 3928909--3929322 Score: 250
Period size: 93 Copynumber: 4.6 Consensus size: 85
3928899 TCAAAGGCTA
* *
3928909 ATAAAACTCAATCAGCATATAGGTAGATTTTGAGACTATTATCAAAAGCTAAGTCAGCATATAAG
1 ATAAAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAAGCTAAGTCAGCATATAAG
*
3928974 TAGAGTTTGAGACTGTTGTC
66 TAGAGCTTGAGACTGTTGTC
* *
3928994 AT-AAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAGGCTAATAAAACTCAATTA
1 ATAAAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAAGC---T--AAGTC----A
* * *
3929058 ACATATAAGTAGAGTTTAAGACTG-T-TC
57 GCATATAAGTAGAGCTTGAGACTGTTGTC
* * * * * *
3929085 AT-AAACTCAATAAGCATATAGGTAGAGTTTAATAATATTGTCAAAGGCTAATAAAACTCAATCA
1 ATAAAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAAGC---T---A---AGTCA
* * *
3929149 ACATATAAGTAGAGTTTGAGACTGTTAT-
57 GCATATAAGTAGAGCTTGAGACTGTTGTC
* * * * *
3929177 -TAAAGGCT-AAGTCAGCATATAAGTAGAATTTGAGACTATTGTCATAAA-CTCAGTCAGCATGT
1 ATAAA-ACTCAA-TCAGCATATAGGTAGAGTTTGAGACTATTGTCA-AAAGCTAAGTCAGCATAT
* * *
3929239 AGGTAGAGTTTGAAACTGTTGTCAAAGGC
63 AAGTAGAGCTTGAGACTGTTGT------C
* * * *
3929268 TAATAAAACTTAATCAACATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTAAG
1 --ATAAAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAAGCTAAG
3929323 AAAAAATAAA
Statistics
Matches: 266, Mismatches: 32, Indels: 54
0.76 0.09 0.15
Matches are distributed among these distances:
84 70 0.26
85 2 0.01
87 1 0.00
89 4 0.02
90 1 0.00
91 75 0.28
92 11 0.04
93 91 0.34
94 8 0.03
95 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (85 bp):
ATAAAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAAGCTAAGTCAGCATATAAG
TAGAGCTTGAGACTGTTGTC
Found at i:3929070 original size:135 final size:135
Alignment explanation
Indices: 3928825--3929080 Score: 379
Period size: 135 Copynumber: 1.9 Consensus size: 135
3928815 TATAAAACTC
* * *
3928825 AGTCAGTATATAGGTAGAGTTTGCAACTATTGTCATAAACTCAGTCAGCATATAGGTAGAGCTTG
1 AGTCAGCATATAAGTAGAGTTTGCAACTATTGTCATAAACTCAATCAGCATATAGGTAGAGCTTG
** * * * * *
3928890 AGGTTGTTGTCAAAGGCTAATAAAACTCAATCAGCATATAGGTAGATTTTGAGACTATTATCAAA
66 AGACTATTGTCAAAGGCTAATAAAACTCAATCAACATATAAGTAGAGTTTAAGACTATTATCAAA
3928955 AGCTA
131 AGCTA
* *
3928960 AGTCAGCATATAAGTAGAGTTTG-AGACTGTTGTCATAAACTCAATCAGCATATAGGTAGAGTTT
1 AGTCAGCATATAAGTAGAGTTTGCA-ACTATTGTCATAAACTCAATCAGCATATAGGTAGAGCTT
*
3929024 GAGACTATTGTCAAAGGCTAATAAAACTCAATTAACATATAAGTAGAGTTTAAGACT
65 GAGACTATTGTCAAAGGCTAATAAAACTCAATCAACATATAAGTAGAGTTTAAGACT
3929081 GTTCATAAAC
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
134 1 0.01
135 106 0.99
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (135 bp):
AGTCAGCATATAAGTAGAGTTTGCAACTATTGTCATAAACTCAATCAGCATATAGGTAGAGCTTG
AGACTATTGTCAAAGGCTAATAAAACTCAATCAACATATAAGTAGAGTTTAAGACTATTATCAAA
AGCTA
Found at i:3929124 original size:91 final size:91
Alignment explanation
Indices: 3928966--3929174 Score: 346
Period size: 91 Copynumber: 2.3 Consensus size: 91
3928956 GCTAAGTCAG
* * *
3928966 CATATAAGTAGAGTTTGAGACTGTTGTCATAAACTCAATCAGCATATAGGTAGAGTTTGAGACTA
1 CATATAAGTAGAGTTTGAGACTG-T-TCATAAACTCAATAAGCATATAGGTAGAGTTTAAGAATA
*
3929031 TTGTCAAAGGCTAATAAAACTCAATTAA
64 TTGTCAAAGGCTAATAAAACTCAATCAA
* *
3929059 CATATAAGTAGAGTTTAAGACTGTTCATAAACTCAATAAGCATATAGGTAGAGTTTAATAATATT
1 CATATAAGTAGAGTTTGAGACTGTTCATAAACTCAATAAGCATATAGGTAGAGTTTAAGAATATT
3929124 GTCAAAGGCTAATAAAACTCAATCAA
66 GTCAAAGGCTAATAAAACTCAATCAA
3929150 CATATAAGTAGAGTTTGAGACTGTT
1 CATATAAGTAGAGTTTGAGACTGTT
3929175 ATTAAAGGCT
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
91 86 0.79
92 1 0.01
93 22 0.20
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (91 bp):
CATATAAGTAGAGTTTGAGACTGTTCATAAACTCAATAAGCATATAGGTAGAGTTTAAGAATATT
GTCAAAGGCTAATAAAACTCAATCAA
Found at i:3929251 original size:226 final size:226
Alignment explanation
Indices: 3928857--3929306 Score: 693
Period size: 226 Copynumber: 2.0 Consensus size: 226
3928847 GCAACTATTG
* * * ** *
3928857 TCATAAACTCAGTCAGCATATAGGTAGAGCTTGAGGTTGTTGTCAAAGGCTAATAAAACTCAATC
1 TCATAAACTCAATAAGCATATAGGTAGAGCTTAAGAATATTGTCAAAGGCTAATAAAACTCAATC
* * * *
3928922 AGCATATAGGTAGATTTTGAGACTATTATCAAAAGCTAAGTCAGCATATAAGTAGAGTTTGAGAC
66 AACATATAAGTAGAGTTTGAGACTATTATCAAAAGCTAAGTCAGCATATAAGTAGAATTTGAGAC
* *
3928987 TGTTGTCATAAACTCAATCAGCATATAGGTAGAGTTTGAGACTATTGTCAAAGGCTAATAAAACT
131 TATTGTCATAAACTCAATCAGCATATAGGTAGAGTTTGAAACTATTGTCAAAGGCTAATAAAACT
*
3929052 CAATTAACATATAAGTAGAGTTTAAGACTGT
196 CAATCAACATATAAGTAGAGTTTAAGACTGT
* *
3929083 TCATAAACTCAATAAGCATATAGGTAGAGTTTAATAATATTGTCAAAGGCTAATAAAACTCAATC
1 TCATAAACTCAATAAGCATATAGGTAGAGCTTAAGAATATTGTCAAAGGCTAATAAAACTCAATC
* * *
3929148 AACATATAAGTAGAGTTTGAGACTGTTATTAAAGGCTAAGTCAGCATATAAGTAGAATTTGAGAC
66 AACATATAAGTAGAGTTTGAGACTATTATCAAAAGCTAAGTCAGCATATAAGTAGAATTTGAGAC
* * *
3929213 TATTGTCATAAACTCAGTCAGCATGTAGGTAGAGTTTGAAACTGTTGTCAAAGGCTAATAAAACT
131 TATTGTCATAAACTCAATCAGCATATAGGTAGAGTTTGAAACTATTGTCAAAGGCTAATAAAACT
* *
3929278 TAATCAACATATAAGTAGAGTTTGAGACT
196 CAATCAACATATAAGTAGAGTTTAAGACT
3929307 ATTGTCAAAG
Statistics
Matches: 201, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
226 201 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (226 bp):
TCATAAACTCAATAAGCATATAGGTAGAGCTTAAGAATATTGTCAAAGGCTAATAAAACTCAATC
AACATATAAGTAGAGTTTGAGACTATTATCAAAAGCTAAGTCAGCATATAAGTAGAATTTGAGAC
TATTGTCATAAACTCAATCAGCATATAGGTAGAGTTTGAAACTATTGTCAAAGGCTAATAAAACT
CAATCAACATATAAGTAGAGTTTAAGACTGT
Found at i:3929269 original size:135 final size:133
Alignment explanation
Indices: 3929059--3929322 Score: 386
Period size: 135 Copynumber: 2.0 Consensus size: 133
3929049 ACTCAATTAA
*
3929059 CATATAAGTAGAGTTTAAGACTGTTCATAAACTCAATAAGCATATAGGTAGAGTTTAATAATATT
1 CATATAAGTAGAATTTAAGACTGTTCATAAACTCAATAAGCATATAGGTAGAGTTTAATAATATT
* *
3929124 GTCAAAGGCTAATAAAACTCAATCAACATATAAGTAGAGTTTGAGACTGTTATTAAAGGCTAAGT
66 GTCAAAGGCTAATAAAACTCAATCAACATATAAGTAGAGTTTGAGACTATTATCAAAGGCTAAGT
3929189 CAG
131 CAG
* * * * * *
3929192 CATATAAGTAGAATTTGAGACTATTGTCATAAACTCAGTCAGCATGTAGGTAGAGTTTGAA-ACT
1 CATATAAGTAGAATTTAAGACT-GT-TCATAAACTCAATAAGCATATAGGTAGAGTTT-AATAAT
* * *
3929256 GTTGTCAAAGGCTAATAAAACTTAATCAACATATAAGTAGAGTTTGAGACTATTGTCAAAGGCTA
63 ATTGTCAAAGGCTAATAAAACTCAATCAACATATAAGTAGAGTTTGAGACTATTATCAAAGGCTA
3929321 AG
128 AG
3929323 AAAAAATAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
133 20 0.17
134 1 0.01
135 93 0.80
136 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (133 bp):
CATATAAGTAGAATTTAAGACTGTTCATAAACTCAATAAGCATATAGGTAGAGTTTAATAATATT
GTCAAAGGCTAATAAAACTCAATCAACATATAAGTAGAGTTTGAGACTATTATCAAAGGCTAAGT
CAG
Found at i:3935446 original size:2 final size:2
Alignment explanation
Indices: 3935439--3935463 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3935429 TTCAATCATA
3935439 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3935464 AACAAAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3959650 original size:26 final size:26
Alignment explanation
Indices: 3959621--3959687 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
3959611 ACAAAAAGTT
*
3959621 GATAGATAGTTTTGCCACCAGACATG
1 GATAGATAATTTTGCCACCAGACATG
* * * *
3959647 GATAAATAATTTTACCATCAGACGTG
1 GATAGATAATTTTGCCACCAGACATG
3959673 GATAGATAATTTTGC
1 GATAGATAATTTTGC
3959688 TACTAGAAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (26 bp):
GATAGATAATTTTGCCACCAGACATG
Found at i:3969204 original size:18 final size:18
Alignment explanation
Indices: 3969183--3969222 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
3969173 ATTTATGGCA
3969183 ACAAGTTGGAAAAATGAT
1 ACAAGTTGGAAAAATGAT
3969201 ACAAGTTGGAAAAATGAT
1 ACAAGTTGGAAAAATGAT
3969219 ACAA
1 ACAA
3969223 TTGTTGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (18 bp):
ACAAGTTGGAAAAATGAT
Found at i:3983071 original size:21 final size:20
Alignment explanation
Indices: 3983034--3983079 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 20
3983024 CTTATTCAAG
3983034 TTTTAACATATAATAATCTTAT
1 TTTTAACATATAATAA--TTAT
3983056 TTTTAA-ATA-AATTAATTAT
1 TTTTAACATATAA-TAATTAT
3983075 TTTTA
1 TTTTA
3983080 CTCATTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 6 0.26
22 6 0.26
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAACATATAATAATTAT
Found at i:3986546 original size:47 final size:47
Alignment explanation
Indices: 3986494--3986583 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
3986484 ATGAAAAATT
* * * *
3986494 ATAAATCTGTCCATTCCTTGAAGTGAATGCAATATCATTTAATGATC
1 ATAAATCTATCCATTCCTTGAAATAAATGCAACATCATTTAATGATC
*
3986541 ATAAATCTATCCATTCTTTGAAATAAATGCAACATCATTTAAT
1 ATAAATCTATCCATTCCTTGAAATAAATGCAACATCATTTAAT
3986584 AATTATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (47 bp):
ATAAATCTATCCATTCCTTGAAATAAATGCAACATCATTTAATGATC
Found at i:3986998 original size:30 final size:30
Alignment explanation
Indices: 3986962--3987022 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
3986952 TTATCAAGTA
3986962 TCACTGAAGACTAAAACATCTTGTGATGAT
1 TCACTGAAGACTAAAACATCTTGTGATGAT
3986992 TCACTGAAGACTAAAACATCTTGTGATGAT
1 TCACTGAAGACTAAAACATCTTGTGATGAT
3987022 T
1 T
3987023 TTAACCATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (30 bp):
TCACTGAAGACTAAAACATCTTGTGATGAT
Found at i:3993915 original size:2 final size:2
Alignment explanation
Indices: 3993908--3993943 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3993898 TTTTACATTG
3993908 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
3993944 TTACACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4021726 original size:20 final size:21
Alignment explanation
Indices: 4021698--4021741 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
4021688 AGATATGTTT
4021698 AATAAAAAAAACAGTAA-TTA
1 AATAAAAAAAACAGTAATTTA
* * *
4021718 AATACAAAATACATTAATTTA
1 AATAAAAAAAACAGTAATTTA
4021739 AAT
1 AAT
4021742 TTACTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAAAAAAAACAGTAATTTA
Found at i:4021976 original size:36 final size:36
Alignment explanation
Indices: 4021929--4022001 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
4021919 AAGGATATGC
4021929 TGATCCCGAAATGATATATATTTTTATTTCTGTTCT
1 TGATCCCGAAATGATATATATTTTTATTTCTGTTCT
4021965 TGATCCCGAAATGATATATATTTTTATTTCTGTTCT
1 TGATCCCGAAATGATATATATTTTTATTTCTGTTCT
4022001 T
1 T
4022002 CTTAAAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.51
Consensus pattern (36 bp):
TGATCCCGAAATGATATATATTTTTATTTCTGTTCT
Found at i:4035193 original size:6 final size:6
Alignment explanation
Indices: 4035182--4035212 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
4035172 TTCTTTTCTT
4035182 TGGTGA TGGTGA TGGTGA TGGTGA TCGGTGA
1 TGGTGA TGGTGA TGGTGA TGGTGA T-GGTGA
4035213 AGTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.16, C:0.03, G:0.48, T:0.32
Consensus pattern (6 bp):
TGGTGA
Found at i:4042900 original size:2 final size:2
Alignment explanation
Indices: 4042895--4042919 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4042885 TATGTAGCTC
4042895 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4042920 AAACTCTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4055108 original size:2 final size:2
Alignment explanation
Indices: 4055101--4055131 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4055091 AATTTTAGCT
4055101 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4055132 CTATGTCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4061383 original size:22 final size:23
Alignment explanation
Indices: 4061358--4061400 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4061348 TTTGTTTTGT
4061358 TTTAAATATTTAT-AATTTTACC
1 TTTAAATATTTATAAATTTTACC
* *
4061380 TTTAATTTTTTATAAATTTTA
1 TTTAAATATTTATAAATTTTA
4061401 TAGTTTCGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAAATATTTATAAATTTTACC
Found at i:4061396 original size:32 final size:31
Alignment explanation
Indices: 4061334--4061402 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
4061324 ATTTCGAAAG
** * *
4061334 TTTATAATTTTTTCTTTGTTTTGTTTTAAAT
1 TTTATAATTTTACCTTTATTTTGTTATAAAT
4061365 ATTTATAATTTTACCTTTAATTTT-TTATAAAT
1 -TTTATAATTTTACCTTT-ATTTTGTTATAAAT
4061397 TTTATA
1 TTTATA
4061403 GTTTCGTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.19
32 22 0.69
33 4 0.12
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (31 bp):
TTTATAATTTTACCTTTATTTTGTTATAAAT
Found at i:4098922 original size:29 final size:28
Alignment explanation
Indices: 4098881--4098937 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
4098871 TTTTCAGCCT
*
4098881 TTTCATCTCCTTCACCCTTATCATAGTG
1 TTTCATCTCCTTCACCCTTACCATAGTG
*
4098909 TTTCTATCTCCTTCACTCTTACCATAGTG
1 TTTC-ATCTCCTTCACCCTTACCATAGTG
4098938 CTAACTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.18, C:0.32, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTCATCTCCTTCACCCTTACCATAGTG
Found at i:4105340 original size:19 final size:19
Alignment explanation
Indices: 4105304--4105339 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4105294 AAAATCTTTG
4105304 AGCATTTTGAATGTTTTTA
1 AGCATTTTGAATGTTTTTA
4105323 AGCATTTTGAA-GTTTTT
1 AGCATTTTGAATGTTTTT
4105340 TTTTATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.53
Consensus pattern (19 bp):
AGCATTTTGAATGTTTTTA
Found at i:4105608 original size:22 final size:22
Alignment explanation
Indices: 4105552--4105608 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
4105542 GACTAGTTTT
* *
4105552 TAGGTATTGCATGACTGGTTGA
1 TAGGTATTGCGTGAATGGTTGA
*
4105574 TATGGCATTGCGTGAATGGTTGA
1 TA-GGTATTGCGTGAATGGTTGA
4105597 TAGGTATTGCGT
1 TAGGTATTGCGT
4105609 AACTAATTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.21, C:0.09, G:0.33, T:0.37
Consensus pattern (22 bp):
TAGGTATTGCGTGAATGGTTGA
Found at i:4105697 original size:22 final size:22
Alignment explanation
Indices: 4105669--4105718 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
4105659 TAGATATTGT
*
4105669 CTAAAAATCAGTCACATAATGC
1 CTAAAAATCAGTCACACAATGC
* *
4105691 CTAAAAATCAGTTACACAATGT
1 CTAAAAATCAGTCACACAATGC
4105713 CTAAAA
1 CTAAAA
4105719 CCACTCACGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (22 bp):
CTAAAAATCAGTCACACAATGC
Found at i:4111513 original size:78 final size:78
Alignment explanation
Indices: 4111384--4111549 Score: 280
Period size: 78 Copynumber: 2.1 Consensus size: 78
4111374 AAGTTGTAAA
* *
4111384 GAGTTG-GACATTTTCATGAATAAAAACATCAAGTTGATACATTAGCCTCGATACTAGACTTTAT
1 GAGTTGTG-CATTTGCATGAATAAAAACATCAAGTTAATACATTAGCCTCGATACTAGACTTTAT
4111448 CAGCTGGAACCAGT
65 CAGCTGGAACCAGT
*
4111462 GAGTTGTGCATTTGCATGGATAAAAACATCAAGTTAATACATTAGCCTCGATACTAGACTTTATC
1 GAGTTGTGCATTTGCATGAATAAAAACATCAAGTTAATACATTAGCCTCGATACTAGACTTTATC
*
4111527 ATCTGGAACCAGT
66 AGCTGGAACCAGT
4111540 GAGTTGTGCA
1 GAGTTGTGCA
4111550 GATTCAGTTG
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
78 82 0.99
79 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (78 bp):
GAGTTGTGCATTTGCATGAATAAAAACATCAAGTTAATACATTAGCCTCGATACTAGACTTTATC
AGCTGGAACCAGT
Found at i:4121304 original size:11 final size:11
Alignment explanation
Indices: 4121288--4121318 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4121278 TAAAATTTTA
4121288 TAATTAATTAT
1 TAATTAATTAT
4121299 TAATTAATTAT
1 TAATTAATTAT
4121310 T-ATTAATTA
1 TAATTAATTA
4121319 AAATATCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATTAATTAT
Found at i:4137657 original size:42 final size:42
Alignment explanation
Indices: 4137610--4137693 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
4137600 CCCCTCTTTG
4137610 GTGCCACTTGTGCATAAATTTATTCTATTATCCATGGTTTTT
1 GTGCCACTTGTGCATAAATTTATTCTATTATCCATGGTTTTT
4137652 GTGCCACTTGTGCATAAATTTATTCTATTATCCATGGTTTTT
1 GTGCCACTTGTGCATAAATTTATTCTATTATCCATGGTTTTT
4137694 TGGGAGTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (42 bp):
GTGCCACTTGTGCATAAATTTATTCTATTATCCATGGTTTTT
Found at i:4141328 original size:12 final size:12
Alignment explanation
Indices: 4141311--4141343 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
4141301 GTTGTCTTAG
4141311 TTTTTTGATTTT
1 TTTTTTGATTTT
*
4141323 TTTTTT-AATTT
1 TTTTTTGATTTT
4141334 TTTTTTGATT
1 TTTTTTGATT
4141344 CTAGTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTTTTGATTTT
Found at i:4153000 original size:2 final size:2
Alignment explanation
Indices: 4152995--4153029 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4152985 TATATATATA
4152995 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4153030 TTATTTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4156455 original size:6 final size:6
Alignment explanation
Indices: 4156444--4156476 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
4156434 CCACATTGAA
4156444 ATAATT ATAATT ATAATT ATAATT ATAATT ATA
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATA
4156477 TATGTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:4158006 original size:15 final size:15
Alignment explanation
Indices: 4157978--4158020 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
4157968 ATACTAATAT
*
4157978 TTTTATAATGATTAAA
1 TTTTATTAT-ATTAAA
4157994 -TTTATTGATATTAAA
1 TTTTATT-ATATTAAA
4158009 TTTTATTATATT
1 TTTTATTATATT
4158021 TTATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (15 bp):
TTTTATTATATTAAA
Found at i:4159691 original size:14 final size:13
Alignment explanation
Indices: 4159642--4159693 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
4159632 ATAATTTTTA
4159642 AAATTTATTTATAT
1 AAATTT-TTTATAT
*
4159656 -AA-CTTTTATAT
1 AAATTTTTTATAT
*
4159667 AAATTTTTTATCT
1 AAATTTTTTATAT
4159680 AAATTATTTTATAT
1 AAATT-TTTTATAT
4159694 TTTTGTCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
13 14 0.45
14 7 0.23
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (13 bp):
AAATTTTTTATAT
Found at i:4164189 original size:17 final size:18
Alignment explanation
Indices: 4164167--4164204 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
4164157 TCAAATTTCC
4164167 AAAACAAAAGAAAA-AAA
1 AAAACAAAAGAAAAGAAA
*
4164184 AAAACAAAGGAAAAGAAA
1 AAAACAAAAGAAAAGAAA
4164202 AAA
1 AAA
4164205 TGGAGAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAACAAAAGAAAAGAAA
Found at i:4168381 original size:6 final size:6
Alignment explanation
Indices: 4168370--4168397 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4168360 CTATCATACG
4168370 ATTACA ATTACA ATTACA ATTACA ATTA
1 ATTACA ATTACA ATTACA ATTACA ATTA
4168398 AATAATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
ATTACA
Found at i:4169463 original size:19 final size:19
Alignment explanation
Indices: 4169439--4169486 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
4169429 TTTATTCACC
4169439 AAGTTATAATGTACACGTT
1 AAGTTATAATGTACACGTT
4169458 AAGTTATAATGTACACGTT
1 AAGTTATAATGTACACGTT
4169477 AAGTTA-AATG
1 AAGTTATAATG
4169487 GTAGGCAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (19 bp):
AAGTTATAATGTACACGTT
Found at i:4172838 original size:2 final size:2
Alignment explanation
Indices: 4172831--4172860 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4172821 GATGTCCCTT
4172831 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4172861 ACTATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4176434 original size:2 final size:2
Alignment explanation
Indices: 4176427--4176457 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4176417 TGTCATGTTT
*
4176427 TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4176458 GCTTGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4191123 original size:2 final size:2
Alignment explanation
Indices: 4191118--4191154 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4191108 CTACTGGGGG
*
4191118 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4191155 TCTCCTGCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4199448 original size:6 final size:6
Alignment explanation
Indices: 4199439--4199473 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
4199429 AATTTTAATT
*
4199439 AATATA AATATA AATATA AATATA AATATA TATAT
1 AATATA AATATA AATATA AATATA AATATA AATAT
4199474 TTATATAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AATATA
Found at i:4207993 original size:34 final size:34
Alignment explanation
Indices: 4207950--4208018 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
4207940 CAAAATACTG
*
4207950 GTTTGAAAAAGAGGGAACTCGAAAGAGAGAAAGT
1 GTTTGAAAAAGAGAGAACTCGAAAGAGAGAAAGT
4207984 GTTTGAAAAAGAGAGAACTCGAAAGAGAGAAAGT
1 GTTTGAAAAAGAGAGAACTCGAAAGAGAGAAAGT
4208018 G
1 G
4208019 AAAAATTCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.32, T:0.14
Consensus pattern (34 bp):
GTTTGAAAAAGAGAGAACTCGAAAGAGAGAAAGT
Found at i:4211427 original size:87 final size:87
Alignment explanation
Indices: 4211276--4211449 Score: 294
Period size: 87 Copynumber: 2.0 Consensus size: 87
4211266 GTTTCCATTT
* * * *
4211276 CTTTCGCCCTTACACACGTTACAGATTACAGTGTCGCCATCTCTCTTTTTCTCTGCTTTGGTTTT
1 CTTTCACCCTTACACACGTTACAGATTACACTGTAGCCATCTCTCTTTTTCTCTGCTTTAGTTTT
4211341 TGGGTCTTCAAGGTCTTGTTAA
66 TGGGTCTTCAAGGTCTTGTTAA
*
4211363 CTTTCACCGTTACACACGTTACAGATTACACTGTAGCCATCTCTCTTTTTCTCTGCTTTAGTTTT
1 CTTTCACCCTTACACACGTTACAGATTACACTGTAGCCATCTCTCTTTTTCTCTGCTTTAGTTTT
*
4211428 TTGGTCTTCAAGGTCTTGTTAA
66 TGGGTCTTCAAGGTCTTGTTAA
4211450 GAGAGAAACT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.43
Consensus pattern (87 bp):
CTTTCACCCTTACACACGTTACAGATTACACTGTAGCCATCTCTCTTTTTCTCTGCTTTAGTTTT
TGGGTCTTCAAGGTCTTGTTAA
Found at i:4228713 original size:15 final size:16
Alignment explanation
Indices: 4228683--4228721 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
4228673 TAATTTTTTA
4228683 ATTCATATTATTATTT
1 ATTCATATTATTATTT
*
4228699 ATTTATATT-TTATTT
1 ATTCATATTATTATTT
4228714 ATTCATAT
1 ATTCATAT
4228722 GCTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTCATATTATTATTT
Found at i:4229169 original size:20 final size:21
Alignment explanation
Indices: 4229131--4229192 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
4229121 ATTTTACACA
4229131 TTATAGTTTTTTTATTTAATT
1 TTATAGTTTTTTTATTTAATT
4229152 TTATA-TTTTTATTA-TTAATCT
1 TTATAGTTTTT-TTATTTAAT-T
* *
4229173 TT-T-GATTTTTTATTGAATT
1 TTATAGTTTTTTTATTTAATT
4229192 T
1 T
4229193 AACATATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
19 5 0.14
20 19 0.54
21 11 0.31
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (21 bp):
TTATAGTTTTTTTATTTAATT
Found at i:4242478 original size:2 final size:2
Alignment explanation
Indices: 4242471--4242499 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4242461 TTATGGATGA
4242471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4242500 AGTATCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4244630 original size:15 final size:15
Alignment explanation
Indices: 4244606--4244662 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
4244596 ATTTTACATC
*
4244606 GTAATGTGATTATAG
1 GTAATATGATTATAG
4244621 GTAATATGATTATAG
1 GTAATATGATTATAG
* *
4244636 GTAATATGATTGTAA
1 GTAATATGATTATAG
*
4244651 GTAATATTATTA
1 GTAATATGATTA
4244663 CAGAGAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (15 bp):
GTAATATGATTATAG
Found at i:4247454 original size:2 final size:2
Alignment explanation
Indices: 4247447--4247473 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4247437 TCTTCTCTTG
4247447 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4247474 TCTATAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4256549 original size:3 final size:3
Alignment explanation
Indices: 4256537--4256566 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4256527 AAAATAAAAA
4256537 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4256567 TTGATTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:4262408 original size:16 final size:16
Alignment explanation
Indices: 4262379--4262418 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
4262369 TTTTATGCAT
* *
4262379 AGACTCTATGTATCCC
1 AGACTGTATCTATCCC
4262395 AGACTGTATCTATCCC
1 AGACTGTATCTATCCC
4262411 AGACTGTA
1 AGACTGTA
4262419 AGCTGTTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (16 bp):
AGACTGTATCTATCCC
Found at i:4267482 original size:133 final size:133
Alignment explanation
Indices: 4267211--4267474 Score: 476
Period size: 133 Copynumber: 2.0 Consensus size: 133
4267201 AAGGCTTGAC
* * *
4267211 TTTGAGTCCTCCATCCCAGCTCCACCATTGTTTATAGGTAAGTTTTAGCTTAATATATGCTCAAG
1 TTTGAGTCCTCCATCCCAGCACCACCATTGTTTAGAGGTAAGTTTTAGCTTAATATATGCTAAAG
* *
4267276 ATTCTCATAAAGGTCATGTTTTTATCTGGGTTTGCTCCTAAATTGTAGTCCGAATATTTTATCTT
66 ATTCTCATAAAGGTCATATCTTTATCTGGGTTTGCTCCTAAATTGTAGTCCGAATATTTTATCTT
4267341 TTA
131 TTA
4267344 TTTGAGTCCTCCATCCCAGCACCACCATTGTTTAGAGGTAAGTTTTAGCTTAATATATGCTAAAG
1 TTTGAGTCCTCCATCCCAGCACCACCATTGTTTAGAGGTAAGTTTTAGCTTAATATATGCTAAAG
4267409 ATTCTCATAAAGGTCATATCTTTATCTGGGTTTGCTCCTAAATT-TAGTCCGAATATTTTATCTT
66 ATTCTCATAAAGGTCATATCTTTATCTGGGTTTGCTCCTAAATTGTAGTCCGAATATTTTATCTT
4267473 TT
131 TT
4267475 CTTTTGAGCT
Statistics
Matches: 126, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
132 22 0.17
133 104 0.83
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (133 bp):
TTTGAGTCCTCCATCCCAGCACCACCATTGTTTAGAGGTAAGTTTTAGCTTAATATATGCTAAAG
ATTCTCATAAAGGTCATATCTTTATCTGGGTTTGCTCCTAAATTGTAGTCCGAATATTTTATCTT
TTA
Found at i:4271153 original size:1 final size:1
Alignment explanation
Indices: 4271147--4271181 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
4271137 GCCTAGGTGA
4271147 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4271182 TGGTTGGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4276553 original size:2 final size:2
Alignment explanation
Indices: 4276546--4276585 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4276536 AGATTGAAAT
4276546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4276586 CACACATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4282004 original size:3 final size:3
Alignment explanation
Indices: 4281996--4282020 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4281986 GAGCTCCCTA
4281996 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
4282021 ATTTGCAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:4287252 original size:66 final size:66
Alignment explanation
Indices: 4287137--4287281 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
4287127 AGGTAATTAA
** * * *
4287137 GTTGGACTTAATCAAATTAGAGCTTATAATCTTCTCAAGGACTTCATTAAATTGTTTAACTAAGT
1 GTTGGACTTAATTGAATAAGAACTTATAATCTTCTCAAGGACTTAATTAAATTGTTTAACTAAGT
4287202 T
66 T
* * * *
4287203 TTTGGACTTAATTGAATAAGAACTTATAAAT-TTCTTAAGGATTTAATTAAATTGTTTAATTAAG
1 GTTGGACTTAATTGAATAAGAACTTAT-AATCTTCTCAAGGACTTAATTAAATTGTTTAACTAAG
4287267 TT
65 TT
*
4287269 GTTAGA-TTAATTG
1 GTTGGACTTAATTG
4287282 GCAATTACAT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
65 7 0.10
66 57 0.85
67 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (66 bp):
GTTGGACTTAATTGAATAAGAACTTATAATCTTCTCAAGGACTTAATTAAATTGTTTAACTAAGT
T
Found at i:4293301 original size:30 final size:28
Alignment explanation
Indices: 4293233--4293306 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
4293223 ACATAATTTA
* *
4293233 AATAAATTTTTATTTTTTTATTATTTTT
1 AATAAATTTTTATATTTTTATTATTATT
**
4293261 AATATGTTTTTATATTTTTATT-TTAAATT
1 AATAAATTTTTATATTTTTATTATT--ATT
4293290 ATATAAATTTTTATATT
1 A-ATAAATTTTTATATT
4293307 ATAATCAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
27 2 0.05
28 19 0.51
29 3 0.08
30 13 0.35
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (28 bp):
AATAAATTTTTATATTTTTATTATTATT
Found at i:4293447 original size:22 final size:22
Alignment explanation
Indices: 4293422--4293510 Score: 80
Period size: 21 Copynumber: 4.1 Consensus size: 22
4293412 TATAAATATA
4293422 AATAATAAATTATATTTTAATT
1 AATAATAAATTATATTTTAATT
* *
4293444 AATAAT-AATTAAATTATAATT
1 AATAATAAATTATATTTTAATT
*
4293465 CATAATAAAAATT-TA-TTTAATTT
1 AATAAT--AAATTATATTTTAA-TT
4293488 AA-AATAAA-TATATATTTAATT
1 AATAATAAATTATAT-TTTAATT
4293509 AA
1 AA
4293511 ATAAAATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.02
20 5 0.09
21 22 0.41
22 18 0.33
23 4 0.07
24 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATAAATTATATTTTAATT
Found at i:4294458 original size:56 final size:55
Alignment explanation
Indices: 4294361--4294467 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
4294351 TAATCATGAC
* * *
4294361 AAAAAATAAAAATTAAAATACATTATCATCTTTAAGTTTTAA-TCATAATTACTAT
1 AAAAAATAAAAATTAAAATACACTAACATCTTTAAATTTTAACT-ATAATTACTAT
* * *
4294416 AAAAAATAAAAATTAACATATACTAACACTTTTTAAATTTTAACTATAATTA
1 AAAAAATAAAAATTAAAATACACTAACA-TCTTTAAATTTTAACTATAATTA
4294468 TACACAGATT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 24 0.55
56 19 0.43
57 1 0.02
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.37
Consensus pattern (55 bp):
AAAAAATAAAAATTAAAATACACTAACATCTTTAAATTTTAACTATAATTACTAT
Found at i:4294528 original size:18 final size:19
Alignment explanation
Indices: 4294485--4294520 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
4294475 ATTTATTAAT
4294485 TTTTAAAATAAATATTTTA
1 TTTTAAAATAAATATTTTA
4294504 TTTTAAAA-AAATATTTT
1 TTTTAAAATAAATATTTT
4294521 TTATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAAATAAATATTTTA
Done.